#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
MUC5B	727897	hgsc.bcm.edu	37	11	1271219	1271221	+	In_Frame_Del	DEL	CCA	CCA	-	rs61430934|rs199629887	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1271219_1271221delCCA	ENST00000529681.1	+	31	13167_13169	c.13109_13111delCCA	c.(13108-13113)gccacc>gcc	p.T4373del	MUC5B_ENST00000447027.1_In_Frame_Del_p.T4376del|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4373	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.			Missing (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)		ACCACGAAGGCCACCACGACAAG	0.635														328	0.0654952	0.0242	0.1095	5008	,	,		19711	0.0496		0.0805	False		,,,				2504	0.091				p.4370_4370del		Pindel,Atlas-Indel	.											.	MUC5B	473	.	0			c.13108_13110del						PASS	.			85,4011		5,75,1968						-0.1	0.0		dbSNP_129	110	576,7474		25,526,3474	no	coding	MUC5B	NM_002458.2		30,601,5442	A1A1,A1R,RR		7.1553,2.0752,5.4421				661,11485				SO:0001651	inframe_deletion	727897	exon31			.	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.13109_13111delCCA	11.37:g.1271222_1271224delCCA	ENSP00000436812:p.Thr4373del	Somatic	223	.	.		WXS	Illumina HiSeq	Phase_I	254	66	0.260	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	In_Frame_Del	DEL	ENST00000529681.1	37	CCDS44515.2																																																																																			CCA|0.926;-|0.074	0.074	strong		0.635	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ADM2	79924	hgsc.bcm.edu	37	22	50921149	50921166	+	In_Frame_Del	DEL	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG	-	rs559809485|rs72438078|rs3840963|rs199649182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	ACACTCGGGCCCCCGAAG	ACACTCGGGCCCCCGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50921149_50921166delACACTCGGGCCCCCGAAG	ENST00000395738.2	+	2	556_573	c.264_281delACACTCGGGCCCCCGAAG	c.(262-282)caacactcgggcccccgaaga>caa	p.HSGPRR95del	ADM2_ENST00000362068.2_In_Frame_Del_p.TRAPED6del|ADM2_ENST00000395737.1_In_Frame_Del_p.HSGPRR95del	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	95					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|digestion (GO:0007586)|feeding behavior (GO:0007631)|negative regulation of blood pressure (GO:0045776)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)	extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.H95_R100delHSGPRR(1)		breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GTGGCCGCCAACACTCGGGCCCCCGAAGACACTCGGGC	0.693														589	0.117612	0.0968	0.1686	5008	,	,		17047	0.1915		0.1213	False		,,,				2504	0.0297				p.88_94del		Pindel,Atlas-Indel	.											.	ADM2	15	.	1	Deletion - In frame(1)	breast(1)	c.263_280del						PASS	.			288,3296		54,180,1558						2.4	0.0		dbSNP_130	10	572,6758		74,424,3167	no	coding	ADM2	NM_024866.4		128,604,4725	A1A1,A1R,RR		7.8035,8.0357,7.8798				860,10054				SO:0001651	inframe_deletion	79924	exon3			.	AF529213	CCDS33682.1	22q13.33	2013-02-25			ENSG00000128165	ENSG00000128165		"""Endogenous ligands"""	28898	protein-coding gene	gene with protein product		608682				14706825	Standard	NM_024866		Approved	AM2, FLJ21135	uc003blj.3	Q7Z4H4	OTTHUMG00000150202	ENST00000395738.2:c.264_281delACACTCGGGCCCCCGAAG	22.37:g.50921149_50921166delACACTCGGGCCCCCGAAG	ENSP00000379087:p.His95_Arg100del	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_001253845	Q3LFQ0	In_Frame_Del	DEL	ENST00000395738.2	37	CCDS33682.1																																																																																			ACACTCGGGCCCCCGAAG|0.874;-|0.126	0.126	strong		0.693	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866	
TTLL9	164395	hgsc.bcm.edu	37	20	30510797	30510798	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:30510797_30510798delAT	ENST00000375938.4	+	8	858_859	c.605_606delAT	c.(604-606)gatfs	p.D202fs	TTLL9_ENST00000375934.4_Frame_Shift_Del_p.D184fs|TTLL9_ENST00000375922.4_Frame_Shift_Del_p.D129fs|TTLL9_ENST00000310998.4_Frame_Shift_Del_p.D152fs|TTLL9_ENST00000375921.2_Frame_Shift_Del_p.D129fs|TTLL9_ENST00000535842.1_Frame_Shift_Del_p.D202fs			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	202	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CAGAAAGATGATATTCCCGTGG	0.401																																					p.202_202del		Pindel,Atlas-Indel	.											.	TTLL9	95	.	0			c.604_605del						PASS	.																																			SO:0001589	frameshift_variant	164395	exon8			.	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.605_606delAT	20.37:g.30510799_30510800delAT	ENSP00000365105:p.Asp202fs	Somatic	80	.	.		WXS	Illumina HiSeq	Phase_I	101	34	0.337	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Frame_Shift_Del	DEL	ENST00000375938.4	37	CCDS42863.1																																																																																			.	.	none		0.401	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	
AAK1	22848	hgsc.bcm.edu	37	2	69741754	69741756	+	In_Frame_Del	DEL	TGT	TGT	-	rs66931661|rs3832159|rs55712143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:69741754_69741756delTGT	ENST00000409085.4	-	13	1999_2001	c.1623_1625delACA	c.(1621-1626)caacag>cag	p.541_542QQ>Q	AAK1_ENST00000406297.3_In_Frame_Del_p.541_542QQ>Q|AAK1_ENST00000409068.1_In_Frame_Del_p.541_542QQ>Q|RN7SL604P_ENST00000492589.2_RNA	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	541	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						ttgctgttgctgttgttgttgct	0.547														1782	0.355831	0.1755	0.4755	5008	,	,		19080	0.5129		0.3897	False		,,,				2504	0.318				p.542_542del		Pindel,Atlas-Indel	.											.	AAK1	121	.	0			c.1624_1626del						PASS	.			952,3280		126,700,1290						3.2	1.0		dbSNP_107	34	3317,4915		696,1925,1495	no	coding	AAK1	NM_014911.3		822,2625,2785	A1A1,A1R,RR		40.294,22.4953,34.2506				4269,8195				SO:0001651	inframe_deletion	22848	exon13			.	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1623_1625delACA	2.37:g.69741760_69741762delTGT	ENSP00000386456:p.Gln546del	Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	94	48	0.511	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	In_Frame_Del	DEL	ENST00000409085.4	37	CCDS1893.2																																																																																			TGT|0.607;-|0.393	0.393	strong		0.547	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
OR8J1	219477	hgsc.bcm.edu	37	11	56128673	56128674	+	Stop_Codon_Ins	INS	-	-	T	rs56266017|rs372964103|rs34649252	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56128673_56128674insT	ENST00000303039.3	+	0	983_984					NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					AAACAATGTAATTTTAAACAGT	0.361													TTTT|TTTT|TTTTT|insertion	345	0.0688898	0.0431	0.0317	5008	,	,		18925	0.0933		0.0934	False		,,,				2504	0.0798				p.X317delinsX		Pindel,Atlas-Indel	.											.	OR8J1	87	.	0			c.951_952insT						PASS	.			204,4056		4,196,1930						1.4	0.0		dbSNP_126	35	720,7518		32,656,3431	no	frameshift	OR8J1	NM_001005205.2		36,852,5361	A1A1,A1R,RR		8.74,4.7887,7.3932				924,11574				SO:0001567	stop_retained_variant	219477	exon1			.	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.952dupT	11.37:g.56128677_56128677dupT		Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	44	16	0.364	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Frame_Shift_Ins	INS	ENST00000303039.3	37	CCDS31529.1																																																																																			-|0.931;T|0.069	0.069	strong		0.361	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
ATXN1	6310	hgsc.bcm.edu	37	6	16327907	16327909	+	In_Frame_Del	DEL	TGA	TGA	-	rs59310777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:16327907_16327909delTGA	ENST00000244769.4	-	8	1569_1571	c.633_635delTCA	c.(631-636)catcag>cag	p.H211del	ATXN1_ENST00000436367.1_In_Frame_Del_p.H211del	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)				ctgctgctgctgatgctgatgct	0.67																																					p.212_212del		Atlas-Indel	.											ATXN1,colon,carcinoma,0,3	ATXN1	117	3	1	Deletion - In frame(1)	prostate(1)	c.634_636del						PASS	.																																			SO:0001651	inframe_deletion	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.633_635delTCA	6.37:g.16327907_16327909delTGA	ENSP00000244769:p.His211del	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	14	0.225806	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	In_Frame_Del	DEL	ENST00000244769.4	37	CCDS34342.1																																																																																			.	.	none		0.670	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
DHDH	27294	hgsc.bcm.edu	37	19	49447749	49447750	+	Frame_Shift_Del	DEL	GA	GA	-	rs3835153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49447749_49447750delGA	ENST00000221403.2	+	6	920_921	c.880_881delGA	c.(880-882)gagfs	p.E294fs	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Frame_Shift_Del_p.E155fs	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	294					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)		GCACGTCTGGGAGTGCCTACGC	0.609														265	0.0529153	0.0008	0.1052	5008	,	,		19887	0.0437		0.0944	False		,,,				2504	0.0532				p.293_294del		Pindel,Atlas-Indel	.											.	DHDH	35	.	0			c.879_880del						PASS	.			52,4212		0,52,2080						-10.1	0.1		dbSNP_107	67	617,7637		22,573,3532	yes	frameshift	DHDH	NM_014475.3		22,625,5612	A1A1,A1R,RR		7.4752,1.2195,5.3443				669,11849				SO:0001589	frameshift_variant	27294	exon6			.	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.880_881delGA	19.37:g.49447749_49447750delGA	ENSP00000221403:p.Glu294fs	Somatic	146	.	.		WXS	Illumina HiSeq	Phase_I	166	54	0.325	NM_014475		Frame_Shift_Del	DEL	ENST00000221403.2	37	CCDS12741.1																																																																																			GA|0.941;-|0.059	0.059	strong		0.609	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
ZNF701	55762	hgsc.bcm.edu	37	19	53086620	53086624	+	Frame_Shift_Del	DEL	ACCTT	ACCTT	-	rs142390931		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	ACCTT	ACCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53086620_53086624delACCTT	ENST00000540331.1	+	5	1731_1735	c.1506_1510delACCTT	c.(1504-1512)aaaccttacfs	p.PY503fs	ZNF701_ENST00000391785.3_Frame_Shift_Del_p.PY437fs|ZNF701_ENST00000301093.2_Frame_Shift_Del_p.PY503fs|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		CTGGAGAGAAACCTTACAAGTGTAA	0.351																																					p.502_503del	NSCLC(89;451 1475 9611 20673 52284)	Pindel,Atlas-Indel	.											.	ZNF701	44	.	0			c.1505_1509del						PASS	.																																			SO:0001589	frameshift_variant	55762	exon5			.	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"""Zinc fingers, C2H2-type"", ""-"""	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.1506_1510delACCTT	19.37:g.53086620_53086624delACCTT	ENSP00000444339:p.Pro503fs	Somatic	154	.	.		WXS	Illumina HiSeq	Phase_I	156	36	0.231	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Frame_Shift_Del	DEL	ENST00000540331.1	37	CCDS54311.1																																																																																			.	.	none		0.351	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376882	168376883	+	lincRNA	INS	-	-	T	rs71305248		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168376882_168376883insT	ENST00000538528.1	-	0	736_737																											CTGCAGTGTTGGGGGAGGAGAA	0.609																																					p.Q151fs		Atlas-Indel	.											.	.	.	.	0			c.451_452insA						PASS	.																																					0	exon1			.																													6.37:g.168376882_168376883insT		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	194	34	0.175258	NM_001129895		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																				.	.	none		0.609	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
VEZF1	7716	hgsc.bcm.edu	37	17	56056586	56056587	+	In_Frame_Ins	INS	-	-	TGT	rs199628152	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56056586_56056587insTGT	ENST00000581208.1	-	5	1104_1105	c.1064_1065insACA	c.(1063-1065)cat>caACAt	p.354_355insQ	VEZF1_ENST00000584396.1_In_Frame_Ins_p.345_346insQ	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	354	Poly-Gln.			Missing (in Ref. 1; BAA05663). {ECO:0000305}.	angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|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)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						AGCTTGTCACAtgttgttgttg	0.475														309	0.0617013	0.1483	0.0245	5008	,	,		20971	0.005		0.0169	False		,,,				2504	0.0757				p.H355delinsQH		Atlas-Indel	.											.	VEZF1	50	.	0			c.1065_1066insACA						PASS	.																																			SO:0001652	inframe_insertion	7716	exon5			.	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1062_1064dupACA	17.37:g.56056593_56056595dupTGT	ENSP00000462337:p.Gln354_Gln354dup	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	229	88	0.384279	NM_007146		In_Frame_Ins	INS	ENST00000581208.1	37	CCDS32687.1																																																																																			-|0.946;TGT|0.054	0.054	strong		0.475	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
COBL	23242	hgsc.bcm.edu	37	7	51098568	51098570	+	In_Frame_Del	DEL	TCT	TCT	-	rs201819395|rs398095077|rs58682836|rs142060269|rs75207469	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:51098568_51098570delTCT	ENST00000265136.7	-	9	1608_1610	c.1443_1445delAGA	c.(1441-1446)gaagac>gac	p.E481del	COBL_ENST00000395542.2_In_Frame_Del_p.E563del	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	481				Missing (in Ref. 5; AAH29275). {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)					AATTAATAGGTCTTCTTCATCAT	0.409																																					p.482_482del	NSCLC(189;2119 2138 12223 30818 34679)	Pindel,Atlas-Indel	.											.	COBL	167	.	0			c.1444_1446del						PASS	.			1826,2438		396,1034,702						-2.4	0.0		dbSNP_131	158	2452,5802		364,1724,2039	no	coding	COBL	NM_015198.3		760,2758,2741	A1A1,A1R,RR		29.7068,42.8236,34.1748				4278,8240				SO:0001651	inframe_deletion	23242	exon9			.	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.1443_1445delAGA	7.37:g.51098571_51098573delTCT	ENSP00000265136:p.Glu481del	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	155	49	0.316	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	In_Frame_Del	DEL	ENST00000265136.7	37	CCDS34637.1																																																																																			TCT|0.609;-|0.391	0.391	strong		0.409	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
ACOT4	122970	hgsc.bcm.edu	37	14	74060511	74060512	+	Frame_Shift_Ins	INS	-	-	TCAA	rs79684878|rs373880503	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74060511_74060512insTCAA	ENST00000326303.4	+	2	817_818	c.563_564insTCAA	c.(562-567)ctagctfs	p.A189fs		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		ACGTTGGCTCTAGCTTATTATA	0.495														6	0.00119808	0.0	0.0	5008	,	,		16663	0.0		0.006	False		,,,				2504	0.0				p.L188fs		Atlas-Indel	.											.	ACOT4	25	.	0			c.563_564insTCAA						PASS	.																																			SO:0001589	frameshift_variant	122970	exon2			.	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	Exception_encountered	14.37:g.74060511_74060512insTCAA	ENSP00000323071:p.Ala189fs	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	60	13	0.216667	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Frame_Shift_Ins	INS	ENST00000326303.4	37	CCDS9817.1																																																																																			.	.	weak		0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
GTF3C3	9330	hgsc.bcm.edu	37	2	197657762	197657767	+	In_Frame_Del	DEL	TCCTCC	TCCTCC	-	rs372304935|rs555178972		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCCTCC	TCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:197657762_197657767delTCCTCC	ENST00000263956.3	-	3	413_418	c.324_329delGGAGGA	c.(322-330)gaggaggaa>gaa	p.108_110EEE>E	GTF3C3_ENST00000409364.3_In_Frame_Del_p.108_110EEE>E|GTF3C3_ENST00000470386.1_5'Flank	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	108	Glu-rich.				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.E109E(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						AGGTGTTtcttcctcctcctcctcct	0.437																																					p.109_110del		Pindel,Atlas-Indel	.											.	GTF3C3	96	.	1	Substitution - coding silent(1)	large_intestine(1)	c.325_330del						PASS	.																																			SO:0001651	inframe_deletion	9330	exon3			.	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.324_329delGGAGGA	2.37:g.197657768_197657773delTCCTCC	ENSP00000263956:p.Glu110_Glu111del	Somatic	314	.	.		WXS	Illumina HiSeq	Phase_I	276	66	0.239	NM_012086	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	In_Frame_Del	DEL	ENST00000263956.3	37	CCDS2316.1																																																																																			.	.	alt		0.437	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1		
TRPC4AP	26133	hgsc.bcm.edu	37	20	33588699	33588720	+	IGR	DEL	GAGGCTGGGCAAGGGCTGTGGG	GAGGCTGGGCAAGGGCTGTGGG	-	rs13040287|rs367622744|rs201461555|rs529023323|rs67885143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAGGCTGGGCAAGGGCTGTGGG	GAGGCTGGGCAAGGGCTGTGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:33588699_33588720delGAGGCTGGGCAAGGGCTGTGGG	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Intron			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)			TCACTGATGTGAGGCTGGGCAAGGGCTGTGGGGAGCCTGGGA	0.644														856	0.170927	0.1619	0.134	5008	,	,		20384	0.1081		0.1918	False		,,,				2504	0.2526				.		Pindel,Atlas-Indel	.											.	MYH7B	145	.	0			.						PASS	.			701,3457		63,575,1441						4.7	0.9		dbSNP_130	75	1521,6637		152,1217,2710	no	intron	MYH7B	NM_020884.3		215,1792,4151	A1A1,A1R,RR		18.6443,16.8591,18.0416				2222,10094				SO:0001628	intergenic_variant	57644	.			.	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.33588699_33588720delGAGGCTGGGCAAGGGCTGTGGG		Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	79	29	0.367	.	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Splice_Site	DEL	ENST00000252015.2	37	CCDS13246.1																																																																																			GAGGCTGGGCAAGGGCTGTGGG|0.835;-|0.165	0.165	strong		0.644	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
FAM171B	165215	hgsc.bcm.edu	37	2	187559047	187559048	+	In_Frame_Ins	INS	-	-	CAA	rs73979342|rs144403657|rs71017336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:187559047_187559048insCAA	ENST00000304698.5	+	1	350_351	c.147_148insCAA	c.(148-150)caa>CAAcaa	p.50_50Q>QQ	AC017101.10_ENST00000453665.1_RNA	NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	50	Gln-rich.					integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						agcagcagcagcaacaacaaca	0.634														2602	0.519569	0.5106	0.5216	5008	,	,		14904	0.7183		0.4404	False		,,,				2504	0.407				p.Q49delinsQQ		Pindel,Atlas-Indel	.											FAM171B,NS,carcinoma,0,1	FAM171B	146	1	0			c.147_148insCAA						PASS	.																																			SO:0001652	inframe_insertion	165215	exon1			.	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.160_162dupCAA	2.37:g.187559054_187559056dupCAA	ENSP00000304108:p.Gln56dup	Somatic	47	.	.		WXS	Illumina HiSeq	Phase_I	62	10	0.161	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	In_Frame_Ins	INS	ENST00000304698.5	37	CCDS33347.1																																																																																			-|0.371;CAA|0.629	0.629	strong		0.634	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
GRP	2922	hgsc.bcm.edu	37	18	56897668	56897671	+	Frame_Shift_Del	DEL	GAAG	GAAG	-	rs185933795|rs149962068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAAG	GAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:56897668_56897671delGAAG	ENST00000256857.2	+	3	513_516	c.415_418delGAAG	c.(415-420)gaaggafs	p.EG139fs	GRP_ENST00000529320.2_Frame_Shift_Del_p.VK132fs|GRP_ENST00000420468.2_Frame_Shift_Del_p.EG132fs	NM_001012512.1|NM_002091.3	NP_001012530.1|NP_002082.2	P07492	GRP_HUMAN	gastrin-releasing peptide	139					neuropeptide signaling pathway (GO:0007218)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			large_intestine(1)|lung(3)	4		Colorectal(73;0.0946)				TTCTCAACGTGAAGGAAGGAACCC	0.426														78	0.0155751	0.0	0.0245	5008	,	,		19519	0.0		0.0507	False		,,,				2504	0.0102				p.138_139del		Atlas-Indel	.											.	GRP	17	.	0			c.414_417del						PASS	.		,,	37,4227		0,37,2095					,,	-3.2	0.0		dbSNP_134	83	354,7900		5,344,3778	yes	frameshift,frameshift,frameshift	GRP	NM_002091.3,NM_001012513.1,NM_001012512.1	,,	5,381,5873	A1A1,A1R,RR		4.2888,0.8677,3.1235	,,	,,		391,12127				SO:0001589	frameshift_variant	2922	exon3			.		CCDS11971.1, CCDS45877.1, CCDS45878.1	18q21.1-q21.32	2013-02-26			ENSG00000134443	ENSG00000134443		"""Endogenous ligands"""	4605	protein-coding gene	gene with protein product	"""bombesin"", ""neuromedin C"", ""prepro-GRP"""	137260					Standard	NM_002091		Approved		uc002lhv.3	P07492	OTTHUMG00000132760	ENST00000256857.2:c.415_418delGAAG	18.37:g.56897672_56897675delGAAG	ENSP00000256857:p.Glu139fs	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	31	10	0.322581	NM_002091	P07491|P81553|Q14454|Q53YA0|Q9BSY7	Frame_Shift_Del	DEL	ENST00000256857.2	37	CCDS11971.1																																																																																			.	.	strong		0.426	GRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256131.2	NM_002091	
WT1-AS	51352	hgsc.bcm.edu	37	11	32461025	32461026	+	RNA	INS	-	-	AG	rs373529925|rs386373507|rs57991818|rs113953318|rs199598071|rs144116821|rs59966210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:32461025_32461026insAG	ENST00000395900.1	+	0	1903_1904				WT1-AS_ENST00000426618.2_RNA|WT1-AS_ENST00000442957.1_RNA|WT1-AS_ENST00000459866.1_RNA|WT1-AS_ENST00000478367.1_RNA|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000525436.1_RNA	NR_023920.1		Q06250	WIT1_HUMAN	WT1 antisense RNA											endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6						AATTAAAAAAAGGGGGGGGCAA	0.485														2251	0.449481	0.2799	0.4063	5008	,	,		12882	0.7391		0.2694	False		,,,				2504	0.5961				.		Pindel,Atlas-Indel	.											.	WT1-AS	7	.	0			.						PASS	.																																					51352	.			.	BC002734		11p13	2012-10-19	2012-08-15	2012-01-25	ENSG00000183242	ENSG00000183242		"""Long non-coding RNAs"", ""-"""	18135	non-coding RNA	RNA, long non-coding	"""Wilms tumor associated protein"""	607899	"""Wilms tumor upstream neighbor 1"", ""WT1 antisense RNA (non-protein coding)"""	WIT1		2173145, 8406502, 17210670	Standard	NR_120546		Approved	WIT-1, WT1AS, WT1-AS1	uc010red.2	Q06250	OTTHUMG00000039557		11.37:g.32461025_32461026insAG		Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	50	12	0.240	.	Q4KMY0|Q96A27	RNA	INS	ENST00000395900.1	37																																																																																				.	.	strong		0.485	WT1-AS-001	KNOWN	basic	antisense	antisense	OTTHUMT00000095437.1	NR_023920	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254335	39254336	+	Start_Codon_Ins	INS	-	-	T	rs201764113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254335_39254336insT	ENST00000333822.4	-	0	57_58					NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8						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						GGAGTTGACCATGGTGTCAGAG	0.55													T|T|TT|insertion	2826	0.564297	0.6543	0.6124	5008	,	,		18816	0.4147		0.6183	False		,,,				2504	0.5072				p.M1fs		Pindel,Atlas-Indel	.											.	KRTAP4-8	57	.	0			c.2_3insA						PASS	.			2669,1587		858,953,317						3.6	1.0			26	5156,3084		1626,1904,590	no	frameshift	KRTAP4-8	NM_031960.2		2484,2857,907	A1A1,A1R,RR		37.4272,37.2885,37.38				7825,4671				SO:0001582	initiator_codon_variant	728224	exon1			.	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.2dupA	17.37:g.39254336_39254336dupT		Somatic	230	.	.		WXS	Illumina HiSeq	Phase_I	246	64	0.260	NM_031960	A8MSH3	Frame_Shift_Ins	INS	ENST00000333822.4	37	CCDS45674.1																																																																																			-|0.420;T|0.580	0.580	strong		0.550	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324346	39324347	+	In_Frame_Ins	INS	-	-	TTT			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39324346_39324347insTTT	ENST00000391356.2	-	1	77_78	c.78_79insAAA	c.(76-81)cgcccc>cgcAAAccc	p.26_27RP>RKP		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	26					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)			CAGCAGCTGGGGCGGCAGCAGC	0.639																																					p.P27delinsKP		Atlas-Indel	.											KRTAP4-3,NS,carcinoma,+2,1	KRTAP4-3	40	1	0			c.79_80insAAA						PASS	.																																			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.78_79insAAA	17.37:g.39324346_39324347insTTT	ENSP00000375151:p.Arg26_Pro27insLys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	196	18	0.0918367	NM_033187		In_Frame_Ins	INS	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.639	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
OR51B5	282763	hgsc.bcm.edu	37	11	5364542	5364558	+	Frame_Shift_Del	DEL	CAGCCCCAGGTCTGTGG	CAGCCCCAGGTCTGTGG	-	rs546965603|rs372207902|rs147062602	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CAGCCCCAGGTCTGTGG	CAGCCCCAGGTCTGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364542_5364558delCAGCCCCAGGTCTGTGG	ENST00000300773.2	-	1	251_267	c.197_213delCCACAGACCTGGGGCTG	c.(196-213)gccacagacctggggctgfs	p.ATDLGL66fs	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	66					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A66fs*48(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGTCAGGGCCAGCCCCAGGTCTGTGGCAGCCAGCAT	0.525														252	0.0503195	0.1377	0.0274	5008	,	,		22155	0.0		0.0457	False		,,,				2504	0.0051				p.66_72del		Pindel,Atlas-Indel	.											.	OR51B5	60	.	1	Deletion - Frameshift(1)	upper_aerodigestive_tract(1)	c.198_214del						PASS	.			487,3771		28,431,1670						3.6	0.1		dbSNP_134	48	401,7853		15,371,3741	no	frameshift	OR51B5	NM_001005567.2		43,802,5411	A1A1,A1R,RR		4.8583,11.4373,7.0972				888,11624				SO:0001589	frameshift_variant	282763	exon5			.	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.197_213delCCACAGACCTGGGGCTG	11.37:g.5364542_5364558delCAGCCCCAGGTCTGTGG	ENSP00000300773:p.Ala66fs	Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	74	23	0.311	NM_001005567	B2RN59	Frame_Shift_Del	DEL	ENST00000300773.2	37	CCDS31378.1																																																																																			.	.	strong		0.525	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
HLA-B	3106	hgsc.bcm.edu	37	6	31324604	31324604	+	Frame_Shift_Del	DEL	T	T	-	rs9266179|rs200186034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31324604delT	ENST00000412585.2	-	2	232	c.204delA	c.(202-204)agafs	p.R68fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	68	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.E69fs*8(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GCGGCTCCTCTCTCGGACTCG	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.E69fs		Atlas-Indel	.											.	HLA-B	54	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.205delG						PASS	.			1993,2105		740,513,796	33.0	33.0	33.0			-6.4	0.0	6	dbSNP_118	34	3347,4625		1272,803,1911	no	frameshift	HLA-B	NM_005514.6		2012,1316,2707	A1A1,A1R,RR		41.9844,48.6335,44.2419			31324604	5340,6730	2015	3950	5965	SO:0001589	frameshift_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	.	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.204delA	6.37:g.31324604delT	ENSP00000399168:p.Arg68fs	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	20	19	0.95	NM_005514	Q29764	Frame_Shift_Del	DEL	ENST00000412585.2	37	CCDS34394.1																																																																																			T|0.467;-|0.533	0.533	strong		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SLC41A3	54946	hgsc.bcm.edu	37	3	125725269	125725272	+	Frame_Shift_Del	DEL	AACA	AACA	-	rs200886927|rs111477552|rs377657493	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AACA	AACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:125725269_125725272delAACA	ENST00000315891.6	-	12	1740_1743	c.1502_1505delTGTT	c.(1501-1506)ttgttafs	p.LL501fs	SLC41A3_ENST00000346785.5_Frame_Shift_Del_p.LL465fs|SLC41A3_ENST00000383598.2_3'UTR|SLC41A3_ENST00000360370.4_3'UTR	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	501						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		GGTTTTTGCTAACAAACAAAAAGG	0.348														859	0.171526	0.1241	0.1326	5008	,	,		22766	0.1458		0.2187	False		,,,				2504	0.2413				p.501_502del		Pindel,Atlas-Indel	.											.	SLC41A3	80	.	0			c.1503_1506del						PASS	.		,,,,	531,3735		36,459,1638					,,,,	2.4	0.0		dbSNP_132	33	1780,6474		206,1368,2553	no	utr-3,utr-3,utr-3,frameshift,frameshift	SLC41A3	NM_017836.3,NM_001164475.1,NM_001008487.1,NM_001008486.1,NM_001008485.1	,,,,	242,1827,4191	A1A1,A1R,RR		21.5653,12.4473,18.4585	,,,,	,,,,		2311,10209				SO:0001589	frameshift_variant	54946	exon12			.		CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"""Solute carriers"""	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.1502_1505delTGTT	3.37:g.125725273_125725276delAACA	ENSP00000326070:p.Leu501fs	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	108	66	0.611	NM_001008485	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Frame_Shift_Del	DEL	ENST00000315891.6	37	CCDS33843.1																																																																																			AACA|0.841;-|0.159	0.159	strong		0.348	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836	
CTAGE5	4253	hgsc.bcm.edu	37	14	39784005	39784006	+	Splice_Site	DEL	TA	TA	-	rs577313725|rs548723883|rs75318507|rs201697727	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:39784005_39784006delTA	ENST00000280083.3	+	15	1670		c.e15+2		CTAGE5_ENST00000557038.1_Splice_Site|CTAGE5_ENST00000341749.3_Splice_Site|RP11-407N17.3_ENST00000603904.1_Splice_Site|RP11-407N17.3_ENST00000553728.1_Splice_Site|CTAGE5_ENST00000556148.1_Splice_Site|CTAGE5_ENST00000553352.1_Splice_Site|CTAGE5_ENST00000348007.3_Splice_Site|CTAGE5_ENST00000396165.4_Splice_Site|CTAGE5_ENST00000341502.5_Splice_Site|CTAGE5_ENST00000396158.2_Splice_Site			O15320	CTGE5_HUMAN	CTAGE family, member 5						positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)	p.?(1)	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)		CAAGGGCAGGTATATATATAtg	0.297																																					.		Atlas-Indel	.											.	CTAGE5	75	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	.						PASS	.																																			SO:0001630	splice_region_variant	4253	.			.	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.1356+2TA>-	14.37:g.39784013_39784014delTA		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	160	92	0.575	.	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Splice_Site	DEL	ENST00000280083.3	37	CCDS9674.1																																																																																			.	.	strong		0.297	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	Intron
CLDN16	10686	hgsc.bcm.edu	37	3	190106072	190106072	+	Frame_Shift_Del	DEL	G	G	-	rs386669518|rs201380153|rs56086318|rs368234054	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:190106072delG	ENST00000264734.2	+	1	412	c.164delG	c.(163-165)aggfs	p.R55fs	CLDN16_ENST00000456423.1_Frame_Shift_Del_p.R55fs|CLDN16_ENST00000468220.1_Intron	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	205	0	0		WXS	Illumina HiSeq	Phase_I	215	209	0.972093	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	
LENG9	94059	hgsc.bcm.edu	37	19	54973989	54973991	+	In_Frame_Del	DEL	CCT	CCT	-	rs140013148|rs36031488|rs201201812|rs115301361	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54973989_54973991delCCT	ENST00000333834.4	-	1	903_905	c.785_787delAGG	c.(784-789)gaggca>gca	p.E262del		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	262							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		GGCTTCAGTGCCTCCTCAGTCAC	0.67														2078	0.414936	0.4138	0.4193	5008	,	,		15817	0.2321		0.5716	False		,,,				2504	0.4407				p.262_263del		Pindel,Atlas-Indel	.											.	LENG9	46	.	0			c.786_788del						PASS	.			1758,2474		401,956,759						-8.3	0.0		dbSNP_126	46	4543,3643		1316,1911,866	no	coding	LENG9	NM_198988.1		1717,2867,1625	A1A1,A1R,RR		44.5028,41.5406,49.2591				6301,6117				SO:0001651	inframe_deletion	94059	exon1			.	AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.785_787delAGG	19.37:g.54973992_54973994delCCT	ENSP00000331647:p.Glu262del	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	87	26	0.299	NM_198988	B2VAM3	In_Frame_Del	DEL	ENST00000333834.4	37	CCDS12895.2																																																																																			CCT|0.607;-|0.393	0.393	strong		0.670	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988	
AKR7L	246181	hgsc.bcm.edu	37	1	19597275	19597275	+	RNA	DEL	C	C	-	rs140586925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19597275delC	ENST00000429712.1	-	0	488				AKR7L_ENST00000420396.2_RNA			Q8NHP1	ARK74_HUMAN	aldo-keto reductase family 7-like							extracellular vesicular exosome (GO:0070062)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|ovary(1)|prostate(1)|urinary_tract(1)	6						CACGCAGTGTCTCTTCCACCG	0.607													|||unknown(NO_COVERAGE)	155	0.0309505	0.0	0.0202	5008	,	,		18026	0.0476		0.0288	False		,,,				2504	0.0654				.		Pindel,Atlas-Indel	.											.	AKR7L	11	.	0			.						PASS	.			44,4222		0,44,2089	41.0	37.0	39.0			4.2	1.0	1	dbSNP_134	39	323,7931		9,305,3813	no	intergenic				9,349,5902	A1A1,A1R,RR		3.9133,1.0314,2.9313			19597275	367,12153	2203	4293	6496			246181	.			.			1p36.1-p35	2008-12-09			ENSG00000211454	ENSG00000211454			24056	protein-coding gene	gene with protein product		608478				12879023	Standard	NR_040288		Approved	AFAR3	uc021ohn.1	Q8NHP1	OTTHUMG00000002520		1.37:g.19597275delC		Somatic	269	.	.		WXS	Illumina HiSeq	Phase_I	291	73	0.251	.	Q5U614	RNA	DEL	ENST00000429712.1	37																																																																																				C|0.973;-|0.027	0.027	strong		0.607	AKR7L-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000007163.3	NM_201252	
CCDC9	26093	hgsc.bcm.edu	37	19	47774666	47774668	+	In_Frame_Del	DEL	GAG	GAG	-	rs138370983|rs79550409|rs373093080	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47774666_47774668delGAG	ENST00000221922.6	+	12	1549_1551	c.1327_1329delGAG	c.(1327-1329)gagdel	p.E445del		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	445	Glu-rich.						poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		agaaggtgatgaggaggaACCAG	0.606														552	0.110224	0.034	0.1844	5008	,	,		16057	0.0903		0.0895	False		,,,				2504	0.2025				p.442_443del		Pindel,Atlas-Indel	.											.	CCDC9	37	.	0			c.1326_1328del						PASS	.			208,4056		4,200,1928						-8.6	0.0		dbSNP_134	113	947,7301		59,829,3236	no	coding	CCDC9	NM_015603.2		63,1029,5164	A1A1,A1R,RR		11.4816,4.878,9.2311				1155,11357				SO:0001651	inframe_deletion	26093	exon12			.	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1327_1329delGAG	19.37:g.47774669_47774671delGAG	ENSP00000221922:p.Glu445del	Somatic	57	.	.		WXS	Illumina HiSeq	Phase_I	47	17	0.362	NM_015603		In_Frame_Del	DEL	ENST00000221922.6	37	CCDS12698.1																																																																																			GAG|0.916;-|0.084	0.084	strong		0.606	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
POLI	11201	hgsc.bcm.edu	37	18	51795958	51795960	+	In_Frame_Del	DEL	CGA	CGA	-	rs78943519|rs10584411|rs3729509	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:51795958_51795960delCGA	ENST00000579534.1	+	1	185_187	c.42_44delCGA	c.(40-45)ggcgac>ggc	p.D17del	POLI_ENST00000217800.5_5'Flank|POLI_ENST00000406285.3_In_Frame_Del_p.D17del|POLI_ENST00000579434.1_5'UTR	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	17					DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.D17delD(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		AAGGCGGCGGCGACGACGACGAG	0.729								DNA polymerases (catalytic subunits)						3926	0.783946	0.9705	0.6427	5008	,	,		12312	0.7054		0.7078	False		,,,				2504	0.7914				p.14_15del		Pindel,Atlas-Indel	.											.	POLI	132	.	1	Deletion - In frame(1)	large_intestine(1)	c.41_43del						PASS	.			3523,343		1644,235,54						1.5	0.0		dbSNP_119	14	5235,2405		1985,1265,570	no	coding	POLI	NM_007195.2		3629,1500,624	A1A1,A1R,RR		31.4791,8.8722,23.8832				8758,2748				SO:0001651	inframe_deletion	11201	exon1			.		CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"""DNA polymerases"""	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.42_44delCGA	18.37:g.51795967_51795969delCGA	ENSP00000462664:p.Asp17del	Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	62	37	0.597	NM_007195	Q8N590|Q9H0S1|Q9NYH6	In_Frame_Del	DEL	ENST00000579534.1	37	CCDS11954.2																																																																																			CGA|0.254;-|0.746	0.746	strong		0.729	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195	
TNP2	7142	hgsc.bcm.edu	37	16	11362797	11362797	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:11362797delT	ENST00000312693.3	-	1	392	c.323delA	c.(322-324)aacfs	p.N108fs	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	108					acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.0?(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						GCCTTCCAAGTTCTTTCTGTT	0.522																																					p.N108fs		Pindel,Atlas-Indel	.											.	TNP2	15	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.324delC						PASS	.						77.0	77.0	77.0					16																	11362797		1957	4150	6107	SO:0001589	frameshift_variant	7142	exon1			.		CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.323delA	16.37:g.11362797delT	ENSP00000325738:p.Asn108fs	Somatic	232	.	.		WXS	Illumina HiSeq	Phase_I	266	47	0.177	NM_005425	Q9NZB0	Frame_Shift_Del	DEL	ENST00000312693.3	37	CCDS45410.1																																																																																			.	.	none		0.522	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417806.1	NM_005425	
EFCAB6	64800	hgsc.bcm.edu	37	22	43933285	43933286	+	Frame_Shift_Del	DEL	CT	CT	-	rs3833393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:43933285_43933286delCT	ENST00000262726.7	-	29	4272_4273	c.4019_4020delAG	c.(4018-4020)cagfs	p.Q1340fs	EFCAB6_ENST00000461800.1_5'UTR|EFCAB6_ENST00000396231.2_Frame_Shift_Del_p.Q1188fs|EFCAB6-AS1_ENST00000431327.3_RNA	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1340	Interaction with PARK7.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TGATGTCCCCCTGTCTGGCCAC	0.554														28	0.00559105	0.0008	0.0058	5008	,	,		17247	0.0159		0.007	False		,,,				2504	0.0				p.1340_1341del		Pindel,Atlas-Indel	.											.	EFCAB6	177	.	0			c.4020_4021del						PASS	.		,	3,4261		0,3,2129					,	4.7	0.1		dbSNP_107	140	71,8183		1,69,4057	yes	frameshift,frameshift	EFCAB6	NM_198856.2,NM_022785.3	,	1,72,6186	A1A1,A1R,RR		0.8602,0.0704,0.5911	,	,		74,12444				SO:0001589	frameshift_variant	64800	exon29			.	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.4019_4020delAG	22.37:g.43933285_43933286delCT	ENSP00000262726:p.Gln1340fs	Somatic	115	.	.		WXS	Illumina HiSeq	Phase_I	119	40	0.336	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Frame_Shift_Del	DEL	ENST00000262726.7	37	CCDS14049.1																																																																																			CT|0.993;-|0.007	0.007	strong		0.554	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
SCN3A	6328	hgsc.bcm.edu	37	2	166032776	166032778	+	In_Frame_Del	DEL	ATT	ATT	-	rs34236036|rs72471101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:166032776_166032778delATT	ENST00000360093.3	-	3	618_620	c.127_129delAAT	c.(127-129)aatdel	p.N43del	SCN3A_ENST00000283254.7_In_Frame_Del_p.N43del|SCN3A_ENST00000409101.3_In_Frame_Del_p.N43del	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	43			Missing. {ECO:0000269|PubMed:12610651}.		membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTCATCATCATTATCTTGTTCC	0.433														257	0.0513179	0.0424	0.0245	5008	,	,		17721	0.002		0.0934	False		,,,				2504	0.09				p.43_44del		Pindel,Atlas-Indel	.											.	SCN3A	544	.	0			c.128_130del						PASS	.		,,	238,4028		8,222,1903					,,	5.3	1.0		dbSNP_130	217	824,7430		45,734,3348	no	coding,coding,coding	SCN3A	NM_006922.3,NM_001081677.1,NM_001081676.1	,,	53,956,5251	A1A1,A1R,RR		9.983,5.579,8.4824	,,	,,		1062,11458				SO:0001651	inframe_deletion	6328	exon3			.	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.127_129delAAT	2.37:g.166032776_166032778delATT	ENSP00000353206:p.Asn43del	Somatic	292	.	.		WXS	Illumina HiSeq	Phase_I	246	78	0.317	NM_001081677	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	In_Frame_Del	DEL	ENST00000360093.3	37																																																																																				ATT|0.949;-|0.051	0.051	strong		0.433	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
EXO5	64789	hgsc.bcm.edu	37	1	40981245	40981246	+	Frame_Shift_Ins	INS	-	-	G	rs150018949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40981245_40981246insG	ENST00000372703.1	+	2	2103_2104	c.1029_1030insG	c.(1030-1032)cggfs	p.R344fs	EXO5_ENST00000296380.4_Frame_Shift_Ins_p.R344fs|RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000358527.2_Frame_Shift_Ins_p.R344fs|RP11-656D10.5_ENST00000453437.1_RNA			Q9H790	EXO5_HUMAN	exonuclease 5	344					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)										CTTGGAAGTGCCGGACGTGTAC	0.54													-|-|G|insertion	42	0.00838658	0.0015	0.0144	5008	,	,		19343	0.0		0.0209	False		,,,				2504	0.0092				p.C343fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1029_1030insG						PASS	.			17,4249		0,17,2116						0.4	0.4		dbSNP_134	52	186,8064		3,180,3942	no	frameshift	DEM1	NM_022774.1		3,197,6058	A1A1,A1R,RR		2.2545,0.3985,1.6219				203,12313				SO:0001589	frameshift_variant	64789	exon3			.	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	Exception_encountered	1.37:g.40981245_40981246insG	ENSP00000361788:p.Arg344fs	Somatic	114	.	.		WXS	Illumina HiSeq	Phase_I	89	29	0.326	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Frame_Shift_Ins	INS	ENST00000372703.1	37	CCDS453.1																																																																																			-|0.989;G|0.011	0.011	strong		0.540	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
SCN9A	6335	hgsc.bcm.edu	37	2	167138320	167138321	+	Splice_Site	INS	-	-	A	rs35888674|rs202239471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:167138320_167138321insA	ENST00000409435.1	-	12	1974		c.e12-2		SCN9A_ENST00000409672.1_Splice_Site|SCN9A_ENST00000375387.4_Splice_Site|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Splice_Site			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit						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)	GGTCGTGCCCTAAAAAAAAAAT	0.337													|||unknown(HR)	286	0.0571086	0.0772	0.0375	5008	,	,		20055	0.0308		0.0835	False		,,,				2504	0.044				.		Pindel,Atlas-Indel	.											.	SCN9A	296	.	0			c.1942-2->T						PASS	.																																			SO:0001630	splice_region_variant	6335	exon14			.	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.1975-2->T	2.37:g.167138330_167138330dupA		Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	47	13	0.277	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Splice_Site	INS	ENST00000409435.1	37	CCDS46441.1																																																																																			A|1.000;|0.000	1.000	weak		0.337	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	Intron
DENND4B	9909	hgsc.bcm.edu	37	1	153907279	153907287	+	In_Frame_Del	DEL	CTGCTGCTG	CTGCTGCTG	-	rs3835302|rs368800700|rs375006474|rs199597671		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTGCTGCTG	CTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153907279_153907287delCTGCTGCTG	ENST00000361217.4	-	18	3140_3148	c.2722_2730delCAGCAGCAG	c.(2722-2730)cagcagcagdel	p.QQQ908del	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ACACctgctcctgctgctgctgctgctgc	0.636																																					p.908_911del		Pindel,Atlas-Indel	.											.	DENND4B	210	.	0			c.2723_2731del						PASS	.																																			SO:0001651	inframe_deletion	9909	exon18			.	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722_2730delCAGCAGCAG	1.37:g.153907288_153907296delCTGCTGCTG	ENSP00000354597:p.Gln908_Gln910del	Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	71	17	0.239	NM_014856	Q5T4K0	In_Frame_Del	DEL	ENST00000361217.4	37	CCDS44228.1																																																																																			.	.	strong		0.636	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
SMARCA2	6595	hgsc.bcm.edu	37	9	2039777	2039779	+	In_Frame_Del	DEL	CAG	CAG	-	rs376509101|rs62639301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:2039777_2039779delCAG	ENST00000382203.1	+	4	876_878	c.667_669delCAG	c.(667-669)cagdel	p.Q238del	RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_In_Frame_Del_p.Q238del|SMARCA2_ENST00000357248.2_In_Frame_Del_p.Q238del|SMARCA2_ENST00000349721.2_In_Frame_Del_p.Q238del|SMARCA2_ENST00000491574.1_3'UTR			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	238	Poly-Gln.			Missing (in Ref. 1; CAA51407). {ECO:0000305}.	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)		gcagcagcaacagcagcagcagc	0.635																																					p.222_223del		Atlas-Indel	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.666_668del						PASS	.																																			SO:0001651	inframe_deletion	6595	exon4			.	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.667_669delCAG	9.37:g.2039786_2039788delCAG	ENSP00000371638:p.Gln238del	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	91	20	0.21978	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	In_Frame_Del	DEL	ENST00000382203.1	37	CCDS34977.1																																																																																			.	.	weak		0.635	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
ITPKB	3707	hgsc.bcm.edu	37	1	226924876	226924884	+	In_Frame_Del	DEL	CTGCCGCTG	CTGCCGCTG	-	rs147889095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTGCCGCTG	CTGCCGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226924876_226924884delCTGCCGCTG	ENST00000272117.3	-	1	275_283	c.276_284delCAGCGGCAG	c.(274-285)agcagcggcagt>agt	p.92_95SSGS>S	ITPKB_ENST00000366784.1_In_Frame_Del_p.92_95SSGS>S|ITPKB_ENST00000429204.1_In_Frame_Del_p.92_95SSGS>S			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	92					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				GCTCACgctactgccgctgctgccgctgc	0.746														1412	0.281949	0.2428	0.317	5008	,	,		9854	0.2659		0.3141	False		,,,				2504	0.2935				p.93_95del	Colon(84;110 1851 5306 33547)	Atlas-Indel	.											.	ITPKB	158	.	0			c.277_285del						PASS	.			530,2426		156,218,1104						0.6	1.0		dbSNP_120	7	1381,4925		379,623,2151	no	coding	ITPKB	NM_002221.3		535,841,3255	A1A1,A1R,RR		21.8998,17.9296,20.6327				1911,7351				SO:0001651	inframe_deletion	3707	exon2			.	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.276_284delCAGCGGCAG	1.37:g.226924885_226924893delCTGCCGCTG	ENSP00000272117:p.Ser92_Gly94del	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	14	0.823529	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	In_Frame_Del	DEL	ENST00000272117.3	37	CCDS1555.1																																																																																			CTGCCGCTG|0.711;-|0.289	0.289	strong		0.746	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
DLGAP2	9228	hgsc.bcm.edu	37	8	1626460	1626461	+	In_Frame_Ins	INS	-	-	CAC	rs200151488	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:1626460_1626461insCAC	ENST00000421627.2	+	9	2263_2264	c.2129_2130insCAC	c.(2128-2133)atcacc>atCACcacc	p.712_713insT		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	791					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		CCAGGCCACATCACCACGGAGG	0.609														107	0.0213658	0.0053	0.0331	5008	,	,		18378	0.001		0.0497	False		,,,				2504	0.0266				p.I710delinsIT		Pindel,Atlas-Indel	.											.	DLGAP2	292	.	0			c.2129_2130insCAC						PASS	.			36,4032		1,34,1999						3.9	0.0			63	413,7659		18,377,3641	no	coding	DLGAP2	NM_004745.3		19,411,5640	A1A1,A1R,RR		5.1165,0.885,3.6985				449,11691				SO:0001652	inframe_insertion	9228	exon9			.	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.2133_2135dupCAC	8.37:g.1626464_1626466dupCAC	ENSP00000400258:p.Thr712_Thr712dup	Somatic	90	.	.		WXS	Illumina HiSeq	Phase_I	90	29	0.322	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	In_Frame_Ins	INS	ENST00000421627.2	37	CCDS47760.1																																																																																			-|0.982;CAC|0.018	0.018	strong		0.609	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144923729	144923729	+	Frame_Shift_Del	DEL	T	T	-	rs3215779|rs369106087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:144923729delT	ENST00000369354.3	-	6	918	c.729delA	c.(727-729)gaafs	p.E243fs	PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.E406fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.E309fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.E30fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.E380fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.E380fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.E406fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	243					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTTCCTGGAGTTCTGCCAAGT	0.448			T	PDGFRB	MPD								TT|TT|T|deletion	928	0.185304	0.0113	0.2205	5008	,	,		39069	0.3988		0.1799	False		,,,				2504	0.181				p.L407fs		Atlas-Indel	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.1219delC						PASS	.						364.0	305.0	325.0					1																	144923729		2203	4300	6503	SO:0001589	frameshift_variant	9659	exon2			.	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.729delA	1.37:g.144923729delT	ENSP00000358360:p.Glu243fs	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	398	89	0.223618	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	37	CCDS30824.1																																																																																			.	.	weak		0.448	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
AGAP1	116987	hgsc.bcm.edu	37	2	236761414	236761415	+	Intron	INS	-	-	CAGG	rs142341634|rs370965020	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:236761414_236761415insCAGG	ENST00000304032.8	+	10	1630				AGAP1_ENST00000336665.5_Intron|AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000409457.1_Frame_Shift_Ins_p.-380fs|AGAP1_ENST00000428334.2_Intron	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1						protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						CTCCCCCTGGCCAGGGCCGAGG	0.619														719	0.14357	0.0257	0.1268	5008	,	,		15083	0.1677		0.1978	False		,,,				2504	0.2342				p.P379fs		Pindel,Atlas-Indel	.											.	AGAP1	95	.	0			c.1135_1136insCAGG						PASS	.																																			SO:0001627	intron_variant	116987	exon10			.	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1051-30574->CAGG	2.37:g.236761415_236761418dupCAGG		Somatic	343	.	.		WXS	Illumina HiSeq	Phase_I	364	78	0.214	NM_001244888	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Frame_Shift_Ins	INS	ENST00000304032.8	37	CCDS33408.1																																																																																			-|0.857;CAGG|0.143	0.143	strong		0.619	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
EMCN	51705	hgsc.bcm.edu	37	4	101401162	101401164	+	In_Frame_Del	DEL	AAC	AAC	-	rs199955415|rs367883693|rs80331904|rs201510590	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:101401162_101401164delAAC	ENST00000296420.4	-	2	275_277	c.97_99delGTT	c.(97-99)gttdel	p.V33del	EMCN_ENST00000511970.1_In_Frame_Del_p.V33del|EMCN_ENST00000305864.3_In_Frame_Del_p.V33del|EMCN_ENST00000502327.1_5'UTR	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	33						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		TTGTTGTAGTAACAACAAGTGAA	0.31														1741	0.347644	0.2458	0.4092	5008	,	,		16968	0.7202		0.0944	False		,,,				2504	0.318				p.33_34del		Pindel,Atlas-Indel	.											.	EMCN	37	.	0			c.98_100del						PASS	.		,	958,3302		118,722,1290					,	-3.3	0.0		dbSNP_54	133	803,7437		45,713,3362	no	coding,coding	EMCN	NM_016242.3,NM_001159694.1	,	163,1435,4652	A1A1,A1R,RR		9.7451,22.4883,14.088	,	,		1761,10739				SO:0001651	inframe_deletion	51705	exon2			.	AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"""Mucins"""	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.97_99delGTT	4.37:g.101401165_101401167delAAC	ENSP00000296420:p.Val33del	Somatic	177	.	.		WXS	Illumina HiSeq	Phase_I	173	53	0.306	NM_016242	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	In_Frame_Del	DEL	ENST00000296420.4	37	CCDS3655.1																																																																																			AAC|0.680;-|0.320	0.320	strong		0.310	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242	
SLC5A10	125206	hgsc.bcm.edu	37	17	18918510	18918511	+	In_Frame_Ins	INS	-	-	CGGTACGGGGGTGGGGGC	rs62066653|rs56122861		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:18918510_18918511insCGGTACGGGGGTGGGGGC	ENST00000395645.3	+	11	1257_1258	c.1239_1240insCGGTACGGGGGTGGGGGC	c.(1240-1242)cgg>CGGTACGGGGGTGGGGGCcgg	p.414_414R>RYGGGGR	SLC5A10_ENST00000317977.6_In_Frame_Ins_p.347_347R>RYGGGGR|SLC5A10_ENST00000395642.1_In_Frame_Ins_p.347_347R>RYGGGGR|SLC5A10_ENST00000395643.2_In_Frame_Ins_p.387_387R>RYGGGGR|SLC5A10_ENST00000417251.2_In_Frame_Ins_p.378_378R>RYGGGGR|SLC5A10_ENST00000395647.2_In_Frame_Ins_p.430_430R>RYGGGGR	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	414					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						TGCTGGTGGGACGGTACGGGGG	0.644																																					p.G429delinsGRYGGGG		Atlas-Indel	.											SLC5A10,right_lower_lobe,carcinoma,+1,1	SLC5A10	55	1	0			c.1287_1288insCGGTACGGGGGTGGGGGC						PASS	.		,	879,3059		216,447,1306					,	-6.3	0.9		dbSNP_130	13	5584,1796		2403,778,509	no	coding-near-splice,coding-near-splice	SLC5A10	NM_152351.3,NM_001042450.1	,	2619,1225,1815	A1A1,A1R,RR		24.336,22.321,42.8963	,	,		6463,4855				SO:0001652	inframe_insertion	125206	exon11			.		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	Exception_encountered	17.37:g.18918510_18918511insCGGTACGGGGGTGGGGGC	Exception_encountered	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	61	18	0.295082	NM_152351	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	In_Frame_Ins	INS	ENST00000395645.3	37	CCDS42275.1																																																																																			.	.	none		0.644	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
DHDH	27294	hgsc.bcm.edu	37	19	49442849	49442850	+	Frame_Shift_Ins	INS	-	-	G	rs3830420|rs397960489|rs78637763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49442849_49442850insG	ENST00000221403.2	+	4	550_551	c.510_511insG	c.(511-513)gggfs	p.G171fs	DHDH_ENST00000522614.1_Frame_Shift_Ins_p.G171fs|DHDH_ENST00000523250.1_Intron	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	171					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)		GGGCCCAGGCTGGGGGGGCCCT	0.604													GGGGGGG|GGGGGGG|GGGGGGGG|insertion	1276	0.254792	0.0575	0.232	5008	,	,		18577	0.5417		0.1759	False		,,,				2504	0.3231				p.A170fs		Pindel,Atlas-Indel	.											.	DHDH	35	.	0			c.510_511insG						PASS	.																																			SO:0001589	frameshift_variant	27294	exon4			.	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.517dupG	19.37:g.49442856_49442856dupG	ENSP00000221403:p.Gly171fs	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	61	36	0.590	NM_014475		Frame_Shift_Ins	INS	ENST00000221403.2	37	CCDS12741.1																																																																																			-|0.754;G|0.246	0.246	strong		0.604	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18435399	18435401	+	In_Frame_Del	DEL	CCC	CCC	-	rs398055356|rs35277916	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:18435399_18435401delCCC	ENST00000266497.5	+	1	422_424	c.384_386delCCC	c.(382-387)agcccc>agc	p.P129del	PIK3C2G_ENST00000538779.1_In_Frame_Del_p.P129del|PIK3C2G_ENST00000535651.1_In_Frame_Del_p.P129del|RERGL_ENST00000541632.1_Intron|PIK3C2G_ENST00000433979.1_In_Frame_Del_p.P129del			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	129				Missing (in Ref. 3; EAW96387 and 4; AAI30278). {ECO:0000305}.	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)				CCTGGGGAAGCCCCATAGGAAAA	0.374														1544	0.308307	0.1989	0.3934	5008	,	,		18294	0.3046		0.3917	False		,,,				2504	0.3139				p.128_129del		Pindel,Atlas-Indel	.											.	PIK3C2G	315	.	0			c.383_385del						PASS	.			763,2763		88,587,1088						0.4	0.1		dbSNP_126	65	3123,4701		610,1903,1399	no	coding	PIK3C2G	NM_004570.4		698,2490,2487	A1A1,A1R,RR		39.9156,21.6393,34.2379				3886,7464				SO:0001651	inframe_deletion	5288	exon2			.	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.384_386delCCC	12.37:g.18435399_18435401delCCC	ENSP00000266497:p.Pro129del	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	88	29	0.330	NM_004570	A1L3U0	In_Frame_Del	DEL	ENST00000266497.5	37	CCDS44839.1																																																																																			CCC|0.695;-|0.305	0.305	strong		0.374	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
SAAL1	113174	hgsc.bcm.edu	37	11	18127558	18127559	+	In_Frame_Ins	INS	-	-	CGG	rs74589784|rs72431213|rs148650821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:18127558_18127559insCGG	ENST00000524803.1	-	1	79_80	c.30_31insCCG	c.(28-33)ccgggt>ccgCCGggt	p.10_11insP	SAAL1_ENST00000529318.1_In_Frame_Ins_p.10_11insP|SAAL1_ENST00000300013.4_In_Frame_Ins_p.10_11insP|SAAL1_ENST00000533851.1_5'UTR			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	10				P -> PP (in Ref. 3; AAH12010). {ECO:0000305}.						breast(2)|large_intestine(5)|lung(8)	15						TTGTCGCGACCCGGCGGCGGCG	0.673											OREG0020819	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		734	0.146565	0.0174	0.1556	5008	,	,		17393	0.1349		0.2604	False		,,,				2504	0.2096				p.G11delinsPG		Atlas-Indel	.											.	SAAL1	34	.	0			c.31_32insCCG						PASS	.																																			SO:0001652	inframe_insertion	113174	exon1			.	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.28_30dupCCG	11.37:g.18127565_18127567dupCGG	ENSP00000432487:p.Pro10_Pro10dup	Somatic	21	0	0	723	WXS	Illumina HiSeq	Phase_I	13	10	0.769231	NM_138421	A6NH05	In_Frame_Ins	INS	ENST00000524803.1	37	CCDS31439.1																																																																																			.	.	strong		0.673	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
C19orf33	64073	hgsc.bcm.edu	37	19	38795547	38795549	+	In_Frame_Del	DEL	GAA	GAA	-	rs139805446	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38795547_38795549delGAA	ENST00000301246.5	+	4	365_367	c.264_266delGAA	c.(262-267)gtgaag>gtg	p.K91del	CTB-102L5.4_ENST00000591889.1_3'UTR|C19orf33_ENST00000588605.1_3'UTR	NM_033520.1	NP_277055.1	Q9GZP8	IMUP_HUMAN	chromosome 19 open reading frame 33	91						nucleus (GO:0005634)						all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGCCCAAAGTgaagaagaaggag	0.596														771	0.153954	0.0386	0.2349	5008	,	,		18940	0.1478		0.1839	False		,,,				2504	0.228				p.88_89del		Pindel,Atlas-Indel	.											.	C19orf33	9	.	0			c.263_265del						PASS	.		,,,,,,,	367,3897		16,335,1781					,,,,,,,	0.9	0.4		dbSNP_130	84	1288,6966		99,1090,2938	no	utr-3,coding,utr-3,utr-3,utr-3,utr-3,utr-3,utr-3	C19orf33,YIF1B	NM_033557.3,NM_033520.1,NM_001145463.1,NM_001145462.1,NM_001145461.1,NM_001039673.2,NM_001039672.2,NM_001039671.2	,,,,,,,	115,1425,4719	A1A1,A1R,RR		15.6046,8.6069,13.221	,,,,,,,	,,,,,,,		1655,10863				SO:0001651	inframe_deletion	64073	exon4			.	AF213678	CCDS12511.1	19q13.2	2012-10-26			ENSG00000167644	ENSG00000167644			16668	protein-coding gene	gene with protein product	"""immortalization-upregulated protein"", ""HAI-2 related small protein"", ""hepatocyte growth factor activator inhibitor type 2-related small protein"""					11080599	Standard	NM_033520		Approved	IMUP-1, IMUP-2, H2RSP, IMUP	uc002ohu.1	Q9GZP8	OTTHUMG00000181894	ENST00000301246.5:c.264_266delGAA	19.37:g.38795553_38795555delGAA	ENSP00000301246:p.Lys91del	Somatic	237	.	.		WXS	Illumina HiSeq	Phase_I	274	63	0.230	NM_033520	Q0P6G2|Q96H58|Q9HCR4	In_Frame_Del	DEL	ENST00000301246.5	37	CCDS12511.1																																																																																			GAA|0.847;-|0.153	0.153	strong		0.596	C19orf33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458168.1	NM_033520	
POLD3	10714	hgsc.bcm.edu	37	11	74336609	74336609	+	Frame_Shift_Del	DEL	A	A	-	rs375954131		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:74336609delA	ENST00000263681.2	+	8	1019	c.890delA	c.(889-891)gaafs	p.E297fs	POLD3_ENST00000527458.1_Frame_Shift_Del_p.E258fs|POLD3_ENST00000532497.1_Frame_Shift_Del_p.E191fs	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	297					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					CTGCAGAAGGAAAAAAAAAGG	0.458																																					p.E297fs		Atlas-Indel	.											POLD3_ENST00000263681,NS,carcinoma,-1,4	POLD3	87	4	0			c.889delG						PASS	.						27.0	29.0	29.0					11																	74336609		2198	4291	6489	SO:0001589	frameshift_variant	10714	exon8			.	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.890delA	11.37:g.74336609delA	ENSP00000263681:p.Glu297fs	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	95	11	0.115789	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Frame_Shift_Del	DEL	ENST00000263681.2	37	CCDS8233.1																																																																																			.	.	none		0.458	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591	
TRIM52	84851	hgsc.bcm.edu	37	5	180687429	180687431	+	In_Frame_Del	DEL	TCT	TCT	-	rs200454506|rs78075294|rs3073543|rs33972170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180687429_180687431delTCT	ENST00000327767.4	-	1	688_690	c.384_386delAGA	c.(382-387)gaagag>gag	p.128_129EE>E	TRIM52-AS1_ENST00000509252.1_RNA|TRIM52_ENST00000514805.1_5'UTR|CTC-338M12.4_ENST00000511331.1_RNA|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|TRIM52-AS1_ENST00000507434.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	128	Glu-rich.				positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	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;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CTGATCTTCCTCTTCTTCTTCTT	0.453														2462	0.491613	0.916	0.304	5008	,	,		21160	0.3393		0.2773	False		,,,				2504	0.4284				p.129_129del		Pindel,Atlas-Indel	.											.	TRIM52	20	.	0			c.385_387del						PASS	.																																			SO:0001651	inframe_deletion	84851	exon1			.		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19024	protein-coding gene	gene with protein product			"""tripartite motif-containing 52"""				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.384_386delAGA	5.37:g.180687438_180687440delTCT	ENSP00000332152:p.Glu130del	Somatic	126	.	.		WXS	Illumina HiSeq	Phase_I	123	37	0.301	NM_032765		In_Frame_Del	DEL	ENST00000327767.4	37	CCDS4467.1																																																																																			TCT|0.580;-|0.420	0.420	strong		0.453	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765	
ITGA7	3679	hgsc.bcm.edu	37	12	56091333	56091333	+	Intron	DEL	G	G	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56091333delG	ENST00000555728.1	-	11	1570				ITGA7_ENST00000257879.6_Intron|ITGA7_ENST00000553804.1_Intron|ITGA7_ENST00000394230.2_Intron|ITGA7_ENST00000347027.6_Intron|ITGA7_ENST00000257880.7_Intron|ITGA7_ENST00000452168.2_Intron|ITGA7_ENST00000394229.2_Intron			Q13683	ITA7_HUMAN	integrin, alpha 7						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						GTCTGGCCCTGGGATTGGGGA	0.562																																					.		Pindel,Atlas-Indel	.											.	ITGA7	194	.	0			c.1422-2C>-						PASS	.		,,	0,4264		0,0,2132	57.0	56.0	57.0		,,	4.6	1.0	12		57	36,8218		1,34,4092	no	intron,intron,intron	ITGA7	NM_002206.2,NM_001144997.1,NM_001144996.1	,,	1,34,6224	A1A1,A1R,RR		0.4362,0.0,0.2876	,,	,,	56091333	36,12482	2203	4300	6503	SO:0001627	intron_variant	3679	exon11			.		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.1542-3C>-	12.37:g.56091333delG		Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	68	26	0.382	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Splice_Site	DEL	ENST00000555728.1	37																																																																																				.	.	none		0.562	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
RYR3	6263	hgsc.bcm.edu	37	15	34137080	34137082	+	In_Frame_Del	DEL	AGA	AGA	-	rs3217346|rs397840365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:34137080_34137082delAGA	ENST00000389232.4	+	93	13384_13386	c.13314_13316delAGA	c.(13312-13317)ttagaa>tta	p.E4441del	RYR3_ENST00000415757.3_In_Frame_Del_p.E4436del	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4441					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)	p.E4440delE(1)		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)		AAGAACCTTTAGAAGAAGAGACA	0.419														372	0.0742812	0.0424	0.1124	5008	,	,		20594	0.0069		0.1491	False		,,,				2504	0.0828				p.4438_4439del		Pindel,Atlas-Indel	.											.	RYR3	760	.	1	Deletion - In frame(1)	ovary(1)	c.13313_13315del						PASS	.			177,3473		13,151,1661						3.8	1.0		dbSNP_134	95	1380,6492		115,1150,2671	no	coding	RYR3	NM_001036.3		128,1301,4332	A1A1,A1R,RR		17.5305,4.8493,13.5133				1557,9965				SO:0001651	inframe_deletion	6263	exon93			.		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.13314_13316delAGA	15.37:g.34137086_34137088delAGA	ENSP00000373884:p.Glu4441del	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	90	36	0.400	NM_001036	O15175|Q15412	In_Frame_Del	DEL	ENST00000389232.4	37	CCDS45210.1																																																																																			AGA|0.918;-|0.082	0.082	strong		0.419	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs367746100|rs111905975	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	.	.		WXS	Illumina HiSeq	Phase_I	86	26	0.302	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	
BDNF	627	hgsc.bcm.edu	37	11	27681176	27681177	+	5'UTR	INS	-	-	TG	rs149254890|rs397725548|rs28722151	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:27681176_27681177insTG	ENST00000525528.1	-	0	28_29				BDNF_ENST00000418212.1_Intron|BDNF-AS_ENST00000530686.1_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395986.2_Intron|BDNF_ENST00000530861.1_Intron|BDNF_ENST00000395978.3_Intron|BDNF_ENST00000525950.1_Intron|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000584049.1_Intron|BDNF_ENST00000314915.6_Intron|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000439476.2_5'UTR|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000532997.1_Intron|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000356660.4_Intron|BDNF_ENST00000420794.1_Intron|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000438929.1_Intron|BDNF_ENST00000395983.3_Intron|BDNF_ENST00000533131.1_Intron|BDNF_ENST00000395981.3_Intron|BDNF_ENST00000395980.2_Intron|BDNF_ENST00000533246.1_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						GATGTTCTCTCtgtgtgtgtgt	0.446																																					.		Atlas-Indel	.											.	BDNF	63	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	627	.			.	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.-1066->CA	11.37:g.27681185_27681186dupTG		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	171	70	0.409357	.	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	RNA	INS	ENST00000525528.1	37	CCDS7866.1																																																																																			.	.	strong		0.446	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
NUP155	9631	hgsc.bcm.edu	37	5	37309372	37309374	+	Intron	DEL	AGA	AGA	-	rs552603277|rs201100022|rs3835198	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:37309372_37309374delAGA	ENST00000231498.3	-	24	2832				NUP155_ENST00000502533.1_Intron|NUP155_ENST00000513532.1_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	41	.	.		WXS	Illumina HiSeq	Phase_I	43	18	0.419	.	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	
TRDN	10345	hgsc.bcm.edu	37	6	123594510	123594511	+	Splice_Site	INS	-	-	A	rs147062785|rs386359375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:123594510_123594511insA	ENST00000398178.3	-	28	1619		c.e28-2		TRDN_ENST00000334268.4_Splice_Site	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin						cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CAGATATAGCTAAAATAAATAA	0.238													AAAAA|AAAA|AAAAA|deletion	1317	0.262979	0.0946	0.2104	5008	,	,		12974	0.5069		0.1859	False		,,,				2504	0.3558				.		Pindel,Atlas-Indel	.											.	TRDN	88	.	0			c.1598-2->T						PASS	.			198,1964		33,132,916						4.2	0.0		dbSNP_130	5	764,4058		183,398,1830	no	splice-3	TRDN	NM_006073.2		216,530,2746	A1A1,A1R,RR		15.844,9.1582,13.7743				962,6022				SO:0001630	splice_region_variant	10345	exon29			.	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1598-2->T	6.37:g.123594514_123594514dupA		Somatic	62	.	.		WXS	Illumina HiSeq	Phase_I	52	14	0.269	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Splice_Site	INS	ENST00000398178.3	37	CCDS55053.1																																																																																			-|0.740;A|0.260	0.260	strong		0.238	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Intron
SGK223	157285	hgsc.bcm.edu	37	8	8234868	8234869	+	In_Frame_Ins	INS	-	-	GCCGCT	rs59372311|rs150979349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:8234868_8234869insGCCGCT	ENST00000520004.1	-	3	1314_1315	c.1050_1051insAGCGGC	c.(1048-1053)ggcgcc>ggcAGCGGCgcc	p.349_350insGS	SGK223_ENST00000330777.4_In_Frame_Ins_p.349_350insGS			Q86YV5	SG223_HUMAN		349							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.G350_A351insSG(1)|p.G350_S351insSG(1)									GGGCTACTGGCGCCGCTGCCGC	0.653														2980	0.595048	0.7254	0.4942	5008	,	,		15838	0.629		0.3827	False		,,,				2504	0.6738				p.A351delinsSGA	GBM(34;731 755 10259 33573 33867)	Pindel,Atlas-Indel	.											.	.	.	.	2	Insertion - In frame(2)	breast(2)	c.1051_1052insAGCGGC						PASS	.																																			SO:0001652	inframe_insertion	0	exon2			.																												ENST00000520004.1:c.1045_1050dupAGCGGC	8.37:g.8234869_8234874dupGCCGCT	ENSP00000428054:p.Gly348_Ser349dup	Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	87	41	0.471	NM_001080826	Q8N3N5	In_Frame_Ins	INS	ENST00000520004.1	37	CCDS43706.1																																																																																			.	.	strong		0.653	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
PRKCSH	5589	hgsc.bcm.edu	37	19	11558340	11558341	+	In_Frame_Ins	INS	-	-	GAG	rs71166603|rs3217229	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11558340_11558341insGAG	ENST00000589838.1	+	10	936_937	c.936_937insGAG	c.(937-939)gag>GAGgag	p.313_313E>EE	PRKCSH_ENST00000591462.1_In_Frame_Ins_p.313_313E>EE|PRKCSH_ENST00000412601.1_In_Frame_Ins_p.313_313E>EE|PRKCSH_ENST00000592741.1_In_Frame_Ins_p.313_313E>EE|PRKCSH_ENST00000252455.2_In_Frame_Ins_p.313_313E>EE|PRKCSH_ENST00000587327.1_In_Frame_Ins_p.313_313E>EE			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	313	Glu-rich (acidic).				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						CGTCGCCCACAgaggaggagga	0.653																																					p.T312delinsTE		Pindel,Atlas-Indel	.											.	PRKCSH	55	.	0			c.936_937insGAG						PASS	.																																			SO:0001652	inframe_insertion	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.964_966dupGAG	19.37:g.11558347_11558349dupGAG	ENSP00000465461:p.Glu325dup	Somatic	128	.	.		WXS	Illumina HiSeq	Phase_I	144	24	0.167	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	In_Frame_Ins	INS	ENST00000589838.1	37	CCDS32911.1																																																																																			-|0.500;GAG|0.500	0.500	strong		0.653	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
THAP2	83591	hgsc.bcm.edu	37	12	72070506	72070508	+	In_Frame_Del	DEL	GTT	GTT	-	rs140783391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	94	.	.		WXS	Illumina HiSeq	Phase_I	106	34	0.321	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	
ZNF772	400720	hgsc.bcm.edu	37	19	57988666	57988667	+	In_Frame_Ins	INS	-	-	GCC	rs77164240|rs528587884|rs34678661|rs193920834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57988666_57988667insGCC	ENST00000343280.4	-	1	271_272	c.11_12insGGC	c.(10-12)gct>gcGGCt	p.4_4A>AA	ZNF772_ENST00000600175.1_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000356584.3_In_Frame_Ins_p.4_4A>AA|AC004076.9_ENST00000415705.3_5'UTR|ZNF772_ENST00000425074.3_In_Frame_Ins_p.4_4A>AA|AC003005.2_ENST00000595422.1_lincRNA|ZNF772_ENST00000427512.2_5'UTR|ZNF772_ENST00000601768.1_In_Frame_Ins_p.4_4A>AA|AC004076.9_ENST00000596831.1_In_Frame_Ins_p.4_4A>AA	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	4					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		CCATCGGCTCAGCCGCCGCCAT	0.644											OREG0025695	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		2037	0.406749	0.3124	0.4481	5008	,	,		16965	0.5823		0.2753	False		,,,				2504	0.4591				p.A4delinsAA	Melanoma(5;289 436 14293 15924 30817)	Pindel,Atlas-Indel	.											ZNF772,colon,carcinoma,0,1	ZNF772	42	1	0			c.12_13insGGC						PASS	.		,	1273,2975		195,883,1046					,	-4.0	0.0		dbSNP_126	62	2294,5946		320,1654,2146	no	coding,coding	ZNF772	NM_001144068.1,NM_001024596.2	,	515,2537,3192	A1A1,A1R,RR		27.8398,29.967,28.5634	,	,		3567,8921				SO:0001652	inframe_insertion	400720	exon1			.	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"""Zinc fingers, C2H2-type"", ""-"""	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.9_11dupGGC	19.37:g.57988673_57988675dupGCC	ENSP00000341165:p.Ala4dup	Somatic	199	.	.	1027	WXS	Illumina HiSeq	Phase_I	239	109	0.456	NM_001024596	A6NJK9|B4DH56|B4DYS0	In_Frame_Ins	INS	ENST00000343280.4	37	CCDS33133.1																																																																																			GCC|1.000;|0.000	1.000	strong		0.644	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144915624	144915624	+	Frame_Shift_Del	DEL	G	G	-	rs66512216|rs1778112	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:144915624delG	ENST00000369354.3	-	14	1990	c.1801delC	c.(1801-1803)ctgfs	p.L602fs	PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.L765fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.L668fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.L389fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.L739fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.L739fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.L765fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	602					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTGCAGAGCAGTGTTGCACTA	0.463			T	PDGFRB	MPD																																p.L764fs		Pindel,Atlas-Indel	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.2291delT						PASS	.		,,,,	205,4061		0,205,1928	117.0	102.0	107.0		,,,,	5.2	0.9	1	dbSNP_130	115	1400,6846		0,1400,2723	no	frameshift,frameshift,frameshift,frameshift,frameshift	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1,NM_001002812.1,NM_001002811.1	,,,,	0,1605,4651	A1A1,A1R,RR		16.9779,4.8054,12.8277	,,,,	,,,,	144915624	1605,10907	2203	4296	6499	SO:0001589	frameshift_variant	9659	exon10			.	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1801delC	1.37:g.144915624delG	ENSP00000358360:p.Leu602fs	Somatic	147	.	.		WXS	Illumina HiSeq	Phase_I	178	33	0.185	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	37	CCDS30824.1																																																																																			G|0.808;-|0.192	0.192	strong		0.463	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
ACOT4	122970	hgsc.bcm.edu	37	14	74060514	74060517	+	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs74553611|rs562751690|rs77261428|rs77814755|rs375801976|rs77408762	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTTA	CTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74060514_74060517delCTTA	ENST00000326303.4	+	2	820_823	c.566_569delCTTA	c.(565-570)gcttatfs	p.AY189fs		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)	p.A189fs*32(2)		endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		TTGGCTCTAGCTTATTATAACTTT	0.495																																					p.189_190del		Atlas-Indel	.											.	ACOT4	25	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.565_568del						PASS	.			103,4159		3,97,2031						4.3	1.0			126	861,7311		130,601,3355	no	frameshift	ACOT4	NM_152331.3		133,698,5386	A1A1,A1R,RR		10.536,2.4167,7.7529				964,11470				SO:0001589	frameshift_variant	122970	exon2			.	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.566_569delCTTA	14.37:g.74060514_74060517delCTTA	ENSP00000323071:p.Ala189fs	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	56	14	0.25	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Frame_Shift_Del	DEL	ENST00000326303.4	37	CCDS9817.1																																																																																			.	.	weak		0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
REXO1	57455	hgsc.bcm.edu	37	19	1825928	1825930	+	In_Frame_Del	DEL	CTC	CTC	-	rs149465929|rs75443592|rs199696044	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1825928_1825930delCTC	ENST00000170168.4	-	3	2018_2020	c.1924_1926delGAG	c.(1924-1926)gagdel	p.E642del	CTB-31O20.4_ENST00000590531.1_RNA|CTB-31O20.4_ENST00000593201.1_RNA|CTB-31O20.4_ENST00000587741.1_RNA|REXO1_ENST00000587524.1_5'Flank	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	168	.	.		WXS	Illumina HiSeq	Phase_I	162	44	0.272	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	
TBP	6908	hgsc.bcm.edu	37	6	170871038	170871040	+	In_Frame_Del	DEL	CAA	CAA	-	rs71815788|rs55736770	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170871038_170871040delCAA	ENST00000392092.2	+	3	493_495	c.214_216delCAA	c.(214-216)caadel	p.Q95del	TBP_ENST00000230354.6_In_Frame_Del_p.Q95del|TBP_ENST00000540980.1_In_Frame_Del_p.Q75del	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	95	Poly-Gln.		Missing. {ECO:0000269|PubMed:2374612}.	Missing (in Ref. 4; BAG65425). {ECO:0000305}.	cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q72del(3)		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)		gcagcagcagcaacagcaacagc	0.567																																					p.71_72del		Atlas-Indel	.											TBP,caecum,carcinoma,0,1	TBP	58	1	3	Deletion - In frame(3)	ovary(1)|prostate(1)|breast(1)	c.213_215del						PASS	.																																			SO:0001651	inframe_deletion	6908	exon3			.	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.214_216delCAA	6.37:g.170871038_170871040delCAA	ENSP00000375942:p.Gln95del	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	60	0.789474	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	In_Frame_Del	DEL	ENST00000392092.2	37	CCDS5315.1																																																																																			.	.	strong		0.567	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350728	50350729	+	In_Frame_Ins	INS	-	-	TCC	rs6614552|rs375199494|rs143151534		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:50350728_50350729insTCC	ENST00000289292.7	-	6	3696_3697	c.3413_3414insGGA	c.(3412-3414)gaa>gaGGAa	p.1138_1138E>EE	SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1138_1138E>EE|SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1022_1022E>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	45	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	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	
ACIN1	22985	hgsc.bcm.edu	37	14	23528502	23528503	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23528502_23528503delTC	ENST00000262710.1	-	19	4207_4208	c.3880_3881delGA	c.(3880-3882)gaafs	p.E1294fs	ACIN1_ENST00000555053.1_Frame_Shift_Del_p.E1281fs|ACIN1_ENST00000605057.1_Frame_Shift_Del_p.E1236fs|ACIN1_ENST00000457657.1_Frame_Shift_Del_p.E1254fs|CDH24_ENST00000487137.2_5'Flank|CDH24_ENST00000397359.3_5'Flank|ACIN1_ENST00000338631.6_Frame_Shift_Del_p.E567fs|ACIN1_ENST00000357481.2_Frame_Shift_Del_p.E536fs|ACIN1_ENST00000397341.3_Frame_Shift_Del_p.E536fs|ACIN1_ENST00000557515.1_Frame_Shift_Del_p.E535fs	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	1294	Arg/Asp/Glu/Lys-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		ccgctccctttctctctctctc	0.629											OREG0022595	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.1294_1294del		Atlas-Indel	.											.	ACIN1	147	.	0			c.3881_3882del						PASS	.																																			SO:0001589	frameshift_variant	22985	exon19			.	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.3880_3881delGA	14.37:g.23528512_23528513delTC	ENSP00000262710:p.Glu1294fs	Somatic	151	0	0	764	WXS	Illumina HiSeq	Phase_I	166	10	0.060241	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Frame_Shift_Del	DEL	ENST00000262710.1	37	CCDS9587.1																																																																																			.	.	none		0.629	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
RIMBP3	85376	hgsc.bcm.edu	37	22	20457872	20457873	+	Frame_Shift_Ins	INS	-	-	A	rs201588919	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:20457872_20457873insA	ENST00000426804.1	-	1	3913_3914	c.3429_3430insT	c.(3427-3432)gctgggfs	p.G1144fs	SCARNA18_ENST00000516215.1_RNA|SCARNA17_ENST00000516762.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1144	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			AGGGTGCTCCCAGCAGTGGCAT	0.55													a|A|AA|insertion	21	0.00419329	0.0008	0.0101	5008	,	,		39034	0.0		0.0129	False		,,,				2504	0.0				p.G1144fs		Atlas-Indel	.											.	RIMBP3	42	.	0			c.3430_3431insT						PASS	.			4,3998		0,4,1997						3.4	1.0			110	115,7949		1,113,3918	no	frameshift	RIMBP3	NM_015672.1		1,117,5915	A1A1,A1R,RR		1.4261,0.1,0.9862				119,11947				SO:0001589	frameshift_variant	85376	exon1			.	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3430dupT	22.37:g.20457873_20457873dupA	ENSP00000391564:p.Gly1144fs	Somatic	1680	0	0		WXS	Illumina HiSeq	Phase_I	1699	343	0.201883	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Frame_Shift_Ins	INS	ENST00000426804.1	37	CCDS46665.1																																																																																			-|0.994;A|0.006	0.006	strong		0.550	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
OR51F1	256892	hgsc.bcm.edu	37	11	4790874	4790874	+	Frame_Shift_Del	DEL	G	G	-	rs563980182|rs34672924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790874delG	ENST00000380383.1	-	1	294	c.295delC	c.(295-297)cgtfs	p.R99fs	OR51F1_ENST00000343430.3_Frame_Shift_Del_p.R92fs|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	99						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)		CTGATTTCACGTGCCTCAAAC	0.423													G|G|-|deletion	1081	0.215855	0.4569	0.2017	5008	,	,		22520	0.0		0.2714	False		,,,				2504	0.0654				p.R92fs		Pindel,Atlas-Indel	.											OR51F1,NS,carcinoma,-1,1	OR51F1	60	1	0			c.275delG	GRCh37	CD035870	OR51F1	D	rs34672924	PASS	.			1902,2362		424,1054,654	57.0	62.0	60.0			-0.4	0.0	11	dbSNP_126	75	2098,6156		281,1536,2310	no	frameshift	OR51F1	NM_001004752.1		705,2590,2964	A1A1,A1R,RR		25.418,44.606,31.954			4790874	4000,8518	1817	4059	5876	SO:0001589	frameshift_variant	256892	exon1			.	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.295delC	11.37:g.4790874delG	ENSP00000369744:p.Arg99fs	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	104	27	0.260	NM_001004752		Frame_Shift_Del	DEL	ENST00000380383.1	37																																																																																				G|0.772;-|0.228	0.228	strong		0.423	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
TTBK1	84630	hgsc.bcm.edu	37	6	43250726	43250728	+	In_Frame_Del	DEL	GAA	GAA	-	rs373093693|rs113160341	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43250726_43250728delGAA	ENST00000259750.4	+	14	2331_2333	c.2248_2250delGAA	c.(2248-2250)gaadel	p.E771del		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	771	Glu-rich.				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)			agaggatgaggaagaagaagagg	0.596														1066	0.212859	0.3041	0.1988	5008	,	,		16464	0.1131		0.172	False		,,,				2504	0.2444				p.749_750del		Pindel,Atlas-Indel	.											TTBK1,NS,carcinoma,0,1	TTBK1	124	1	0			c.2247_2249del						PASS	.			1250,3010		180,890,1060						2.3	0.3		dbSNP_132	18	1640,6596		164,1312,2642	no	coding	TTBK1	NM_032538.1		344,2202,3702	A1A1,A1R,RR		19.9126,29.3427,23.1274				2890,9606				SO:0001651	inframe_deletion	84630	exon14			.	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.2248_2250delGAA	6.37:g.43250732_43250734delGAA	ENSP00000259750:p.Glu771del	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	68	12	0.176	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	In_Frame_Del	DEL	ENST00000259750.4	37	CCDS34455.1																																																																																			GAA|0.806;-|0.194	0.194	strong		0.596	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
C11orf40	143501	hgsc.bcm.edu	37	11	4592708	4592709	+	Frame_Shift_Ins	INS	-	-	AG	rs67037861|rs71280817|rs3064108|rs79804156	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4592708_4592709insAG	ENST00000307616.1	-	4	597_598	c.598_599insCT	c.(598-600)tgtfs	p.C200fs		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	200										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)		acgatccatacagtttttccCT	0.431																																					p.C200fs		Atlas-Indel	.											.	C11orf40	37	.	0			c.599_600insCT						PASS	.			1965,709,1460		611,170,573,143,253,317						-1.1	0.0		dbSNP_102	79	1984,2343,3691		483,304,714,544,951,1013	no	codingComplex	C11orf40	NM_144663.1		1094,474,1287,687,1204,1330	A1A1,A1A2,A1R,A2A2,A2R,RR		53.9661,52.4673,57.6119				3949,3052,5151				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.597_598dupCT	11.37:g.4592709_4592710dupAG	ENSP00000302918:p.Cys200fs	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	154	55	0.357143	NM_144663		Frame_Shift_Ins	INS	ENST00000307616.1	37	CCDS31354.1																																																																																			-|0.378;AC|0.622	.	strong		0.431	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
CYP3A43	64816	hgsc.bcm.edu	37	7	99434078	99434078	+	Frame_Shift_Del	DEL	A	A	-	rs61469810	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99434078delA	ENST00000354829.2	+	2	177	c.74delA	c.(73-75)tatfs	p.Y25fs	CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000421837.2_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000312017.5_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000417625.1_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000222382.5_Frame_Shift_Del_p.Y25fs|CYP3A43_ENST00000415413.1_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	84	.	.		WXS	Illumina HiSeq	Phase_I	92	49	0.533	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		
TMPRSS6	164656	hgsc.bcm.edu	37	22	37465386	37465390	+	Splice_Site	DEL	TGGGG	TGGGG	-	rs188283136|rs200434923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGGGG	TGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37465386_37465390delTGGGG	ENST00000346753.3	-	16	1985		c.e16-2		TMPRSS6_ENST00000381792.2_Splice_Site|TMPRSS6_ENST00000406856.1_Splice_Site|TMPRSS6_ENST00000406725.1_Splice_Site	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6						angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GAGGCCATGCtggggtggggtgggg	0.668														2248	0.448882	0.7504	0.2435	5008	,	,		11865	0.4266		0.4036	False		,,,				2504	0.2566				.		Pindel,Atlas-Indel	.											.	TMPRSS6	99	.	0			.						PASS	.			1238,890		571,96,397						5.1	1.0			10	2211,3145		918,375,1385	no	splice-3	TMPRSS6	NM_153609.2		1489,471,1782	A1A1,A1R,RR		41.2808,41.8233,46.085				3449,4035				SO:0001630	splice_region_variant	164656	.			.	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.1869-2CCCCA>-	22.37:g.37465396_37465400delTGGGG		Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	67	17	0.254	.	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
NEIL3	55247	hgsc.bcm.edu	37	4	178256864	178256864	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:178256864delT	ENST00000264596.3	+	3	419	c.301delT	c.(301-303)ttcfs	p.F101fs		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	101					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)		AATGAAAGGCTTCATCATGAT	0.323								Base excision repair (BER), DNA glycosylases																													p.G100fs		Pindel,Atlas-Indel	.											.	NEIL3	89	.	0			c.300delC						PASS	.						61.0	69.0	66.0					4																	178256864		2200	4300	6500	SO:0001589	frameshift_variant	55247	exon3			.	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.301delT	4.37:g.178256864delT	ENSP00000264596:p.Phe101fs	Somatic	157	.	.		WXS	Illumina HiSeq	Phase_I	178	53	0.298	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Frame_Shift_Del	DEL	ENST00000264596.3	37	CCDS3828.1																																																																																			.	.	none		0.323	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376880	168376881	+	lincRNA	INS	-	-	G	rs200170849|rs71305248|rs368066294		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168376880_168376881insG	ENST00000538528.1	-	0	738_739																											CCCTGCAGTGTTGGGGGAGGAG	0.609																																					p.Q151fs		Atlas-Indel	.											.	.	.	.	0			c.453_454insC						PASS	.																																					0	exon1			.																													6.37:g.168376880_168376881insG		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	193	38	0.196891	NM_001129895		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																				.	.	alt		0.609	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458574	39458586	+	Frame_Shift_Del	DEL	GTACAGATGGTTG	GTACAGATGGTTG	-	rs540900200|rs2874235|rs144150438|rs368037290	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GTACAGATGGTTG	GTACAGATGGTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39458574_39458586delGTACAGATGGTTG	ENST00000391353.1	-	1	517_529	c.518_530delCAACCATCTGTAC	c.(517-531)ccaaccatctgtacafs	p.PTICT173fs		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	173	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											TGGACTAGCTGTACAGATGGTTGGTAGGCAAGA	0.516														793	0.158347	0.0189	0.1282	5008	,	,		26627	0.3194		0.1869	False		,,,				2504	0.1728				p.173_177del		Pindel,Atlas-Indel	.											.	KRTAP29-1	2	.	0			c.519_531del						PASS	.																																			SO:0001589	frameshift_variant	100533177	exon1			.		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.518_530delCAACCATCTGTAC	17.37:g.39458574_39458586delGTACAGATGGTTG	ENSP00000375148:p.Pro173fs	Somatic	54	.	.		WXS	Illumina HiSeq	Phase_I	57	23	0.404	NM_001257309		Frame_Shift_Del	DEL	ENST00000391353.1	37																																																																																				.	.	strong		0.516	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
TPRX1	284355	hgsc.bcm.edu	37	19	48305639	48305650	+	In_Frame_Del	DEL	GGGCCTGGGATC	GGGCCTGGGATC	-	rs112397458|rs112842028		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GGGCCTGGGATC	GGGCCTGGGATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48305639_48305650delGGGCCTGGGATC	ENST00000322175.3	-	2	773_784	c.618_629delGATCCCAGGCCC	c.(616-630)ccgatcccaggccca>cca	p.206_210PIPGP>P	TPRX1_ENST00000543508.1_In_Frame_Del_p.196_200PIPGP>P|TPRX1_ENST00000535759.1_In_Frame_Del_p.303_307PIPGP>P	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)		gcctgagattgggcctgggatcgggcctggga	0.675																																					p.207_210del	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-Indel	.											TPRX1,NS,carcinoma,0,1	TPRX1	46	1	0			c.619_630del						PASS	.			195,3079		53,89,1495						-0.7	0.0			11	984,5118		202,580,2269	no	coding	TPRX1	NM_198479.2		255,669,3764	A1A1,A1R,RR		16.1259,5.956,12.5747				1179,8197				SO:0001651	inframe_deletion	284355	exon2			.		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.618_629delGATCCCAGGCCC	19.37:g.48305639_48305650delGGGCCTGGGATC	ENSP00000323455:p.Pro206_Gly209del	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_198479	A5D8Y3|B2RPL5	In_Frame_Del	DEL	ENST00000322175.3	37	CCDS33066.1																																																																																			.	.	none		0.675	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
ZSCAN18	65982	hgsc.bcm.edu	37	19	58598358	58598369	+	In_Frame_Del	DEL	TGGAAAGGACTT	TGGAAAGGACTT	-	rs368736992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGGAAAGGACTT	TGGAAAGGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58598358_58598369delTGGAAAGGACTT	ENST00000240727.6	-	5	1048_1059	c.649_660delAAGTCCTTTCCA	c.(649-660)aagtcctttccadel	p.KSFP217del	ZSCAN18_ENST00000601144.1_In_Frame_Del_p.KSFP217del|ZSCAN18_ENST00000421612.2_In_Frame_Del_p.KSFP82del|ZSCAN18_ENST00000600404.1_In_Frame_Del_p.KSFP273del	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	217					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)		GAGGGTCCTCTGGAAAGGACTTCAGCTTCTGA	0.637														7	0.00139776	0.0	0.0	5008	,	,		18211	0.0		0.0	False		,,,				2504	0.0072				p.273_277del		Pindel,Atlas-Indel	.											.	ZSCAN18	104	.	0			c.818_829del						PASS	.																																			SO:0001651	inframe_deletion	65982	exon5			.	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.649_660delAAGTCCTTTCCA	19.37:g.58598358_58598369delTGGAAAGGACTT	ENSP00000240727:p.Lys217_Pro220del	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	44	11	0.250	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	In_Frame_Del	DEL	ENST00000240727.6	37	CCDS12971.1																																																																																			.	.	weak		0.637	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926	
KTI12	112970	hgsc.bcm.edu	37	1	52499071	52499097	+	In_Frame_Del	DEL	GCCCGCCACCTGAGGTCCCGCGATCGG	GCCCGCCACCTGAGGTCCCGCGATCGG	-	rs375799302|rs144538502|rs377187997|rs563103084|rs372478725|rs116535272|rs147206420	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GCCCGCCACCTGAGGTCCCGCGATCGG	GCCCGCCACCTGAGGTCCCGCGATCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:52499071_52499097delGCCCGCCACCTGAGGTCCCGCGATCGG	ENST00000371614.1	-	1	391_417	c.337_363delCCGATCGCGGGACCTCAGGTGGCGGGC	c.(337-363)ccgatcgcgggacctcaggtggcgggcdel	p.PIAGPQVAG113del	TXNDC12_ENST00000371626.4_Intron|RP11-91A18.4_ENST00000425802.1_RNA	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	113							ATP binding (GO:0005524)	p.A115A(1)|p.G116E(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						TCTCGTTCGCGCCCGCCACCTGAGGTCCCGCGATCGGGCCGCCGGGC	0.687														223	0.0445288	0.0575	0.0331	5008	,	,		19222	0.004		0.0507	False		,,,				2504	0.0706				p.113_122del		Pindel,Atlas-Indel	.											.	KTI12	30	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	urinary_tract(1)|central_nervous_system(1)	c.338_364del						PASS	.		,	206,4044		10,186,1929					,	0.2	0.0			34	394,7838		13,368,3735	no	coding,intron	TXNDC12,KTI12	NM_138417.2,NM_015913.2	,	23,554,5664	A1A1,A1R,RR		4.7862,4.8471,4.8069	,	,		600,11882				SO:0001651	inframe_deletion	112970	exon1			.		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.337_363delCCGATCGCGGGACCTCAGGTGGCGGGC	1.37:g.52499071_52499097delGCCCGCCACCTGAGGTCCCGCGATCGG	ENSP00000360676:p.Pro113_Gly121del	Somatic	18	.	.		WXS	Illumina HiSeq	Phase_I	23	15	0.652	NM_138417		In_Frame_Del	DEL	ENST00000371614.1	37	CCDS562.1																																																																																			.	.	none		0.687	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417	
C16orf96	342346	hgsc.bcm.edu	37	16	4644390	4644392	+	In_Frame_Del	DEL	AGG	AGG	-	rs139232890|rs59955859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4644390_4644392delAGG	ENST00000444310.4	+	13	2906_2908	c.2906_2908delAGG	c.(2905-2910)caggag>cag	p.E970del		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						CTCGGTATCCAGGAGGATTGTCA	0.631														371	0.0740815	0.2247	0.0331	5008	,	,		17641	0.003		0.0457	False		,,,				2504	0.002				p.969_969del		Pindel,Atlas-Indel	.											.	C16orf96	28	.	0			c.2905_2907del						PASS	.			407,2191		81,245,973						1.8	0.0		dbSNP_129	48	160,4518		20,120,2199	no	coding	C16orf96	NM_001145011.1		101,365,3172	A1A1,A1R,RR		3.4203,15.6659,7.7927				567,6709				SO:0001651	inframe_deletion	342346	exon13			.		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.2906_2908delAGG	16.37:g.4644393_4644395delAGG	ENSP00000415027:p.Glu970del	Somatic	103	.	.		WXS	Illumina HiSeq	Phase_I	112	36	0.321	NM_001145011		In_Frame_Del	DEL	ENST00000444310.4	37	CCDS53986.1																																																																																			AGG|0.931;-|0.069	0.069	strong		0.631	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
MN1	4330	hgsc.bcm.edu	37	22	28194962	28194963	+	In_Frame_Ins	INS	-	-	CTGCTG			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:28194962_28194963insCTGCTG	ENST00000302326.4	-	1	2523_2524	c.1569_1570insCAGCAG	c.(1567-1572)caacag>caaCAGCAGcag	p.523_524QQ>QQQQ		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	523	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						tgctgctgctgttgcAGGGACT	0.668			T	ETV6	"""AML, meningioma"""																																p.Q524delinsQQQ		Atlas-Indel	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	MN1,NS,carcinoma,+2,1	MN1	122	1	0			c.1570_1571insCAGCAG						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.1564_1569dupCAGCAG	22.37:g.28194957_28194962dupCTGCTG	ENSP00000304956:p.Gln549_Gln550dup	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	10	0.123457	NM_002430	A9Z1V9	In_Frame_Ins	INS	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	none		0.668	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
AK9	221264	hgsc.bcm.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197|rs73519211|rs568921203|rs141134529	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:109906330_109906332delCTT	ENST00000424296.2	-	19	2184_2186	c.2108_2110delAAG	c.(2107-2112)gaagca>gca	p.E703del	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000368948.2_In_Frame_Del_p.E703del	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	703					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTTTACCTTGCTTCTTCTTCTTC	0.227														1863	0.372005	0.2542	0.4092	5008	,	,		14640	0.377		0.4095	False		,,,				2504	0.4611				p.703_704del		Pindel,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	61	.	.		WXS	Illumina HiSeq	Phase_I	57	11	0.193	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	
IFNE	338376	hgsc.bcm.edu	37	9	21482239	21482241	+	5'UTR	DEL	AAT	AAT	-	rs3028326|rs397894161|rs34533918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	59	.	.		WXS	Illumina HiSeq	Phase_I	39	14	0.359	.		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	
ALLC	55821	hgsc.bcm.edu	37	2	3749152	3749154	+	In_Frame_Del	DEL	GAA	GAA	-	rs34308920|rs66473381|rs201406139|rs397869421|rs200664184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:3749152_3749154delGAA	ENST00000252505.3	+	11	1063_1065	c.901_903delGAA	c.(901-903)gaadel	p.E303del	AC010907.5_ENST00000441632.1_RNA|ALLC_ENST00000471711.1_3'UTR	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	322					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)	p.E301delE(2)		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)		GACAACTCAGGAAGAAGAAGCCG	0.512										HNSCC(21;0.051)				2063	0.411941	0.621	0.2997	5008	,	,		17803	0.3284		0.4404	False		,,,				2504	0.2658				p.300_301del		Pindel,Atlas-Indel	.											.	ALLC	61	.	2	Deletion - In frame(2)	upper_aerodigestive_tract(1)|breast(1)	c.900_902del						PASS	.			2273,1463		704,865,299						0.4	0.2		dbSNP_130	58	3628,4278		863,1902,1188	no	coding	ALLC	NM_018436.3		1567,2767,1487	A1A1,A1R,RR		45.8892,39.1595,49.3128				5901,5741				SO:0001651	inframe_deletion	55821	exon11			.	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.901_903delGAA	2.37:g.3749158_3749160delGAA	ENSP00000252505:p.Glu303del	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	65	41	0.631	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	In_Frame_Del	DEL	ENST00000252505.3	37	CCDS46223.1																																																																																			GAA|0.578;-|0.422	0.422	strong		0.512	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1		
PRDM2	7799	hgsc.bcm.edu	37	1	14106394	14106395	+	In_Frame_Ins	INS	-	-	CTC	rs2308040|rs148293494|rs59028030		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:14106394_14106395insCTC	ENST00000235372.7	+	8	2960_2961	c.2104_2105insCTC	c.(2104-2106)act>aCTCct	p.703_704insP	PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000343137.4_In_Frame_Ins_p.502_503insP|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000413440.1_In_Frame_Ins_p.502_503insP|PRDM2_ENST00000311066.5_In_Frame_Ins_p.703_704insP	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	97	.	.		WXS	Illumina HiSeq	Phase_I	107	38	0.355	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	
EFCAB13	124989	hgsc.bcm.edu	37	17	45438887	45438890	+	Splice_Site	DEL	AGTG	AGTG	-	rs10538163|rs201433080|rs55920564	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AGTG	AGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45438887_45438890delAGTG	ENST00000331493.2	+	10	1216	c.805delAGTG	c.(805-807)agt>gt	p.S269fs	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	269						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										CTATATTGACAGTGAGTTATTTGC	0.328														2236	0.446486	0.5772	0.4135	5008	,	,		17784	0.254		0.5249	False		,,,				2504	0.411				p.268_269del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.804_805del						PASS	.		,	2341,1923		660,1021,451					,	1.8	1.0		dbSNP_119	128	4468,3784		1232,2004,890	no	frameshift-near-splice,intron	C17orf57	NM_152347.4,NM_001195192.1	,	1892,3025,1341	A1A1,A1R,RR		45.8556,45.0985,45.5976	,	,		6809,5707				SO:0001630	splice_region_variant	124989	exon10			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.805+1AGTG>-	17.37:g.45438887_45438890delAGTG		Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	102	33	0.324	NM_152347	G3V128|Q49AG9	Frame_Shift_Del	DEL	ENST00000331493.2	37	CCDS11512.1																																																																																			AGTG|0.561;-|0.439	0.439	strong		0.328	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	Frame_Shift_Del
LFNG	3955	hgsc.bcm.edu	37	7	2552881	2552882	+	Frame_Shift_Ins	INS	-	-	GATG	rs34637446|rs61564232|rs397694506|rs373004749		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2552881_2552882insGATG	ENST00000402506.1	+	2	264_265	c.138_139insGATG	c.(139-141)gatfs	p.-48fs		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase						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)		acagatggacagatggatggat	0.564																																					p.T46fs		Pindel,Atlas-Indel	.											LFNG_ENST00000402506,caecum,carcinoma,0,2	LFNG	57	2	0			c.138_139insGATG						PASS	.																																			SO:0001589	frameshift_variant	3955	exon2			.	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	ENST00000402506.1:c.163_166dupGATG	7.37:g.2552886_2552889dupGATG	ENSP00000385764:p.Gly48fs	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	111	25	0.225	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Frame_Shift_Ins	INS	ENST00000402506.1	37	CCDS55081.1																																																																																			.	.	strong		0.564	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304	
PCDHB2	56133	hgsc.bcm.edu	37	5	140475633	140475634	+	In_Frame_Ins	INS	-	-	CATCAC	rs372005802		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140475633_140475634insCATCAC	ENST00000194155.4	+	1	1407_1408	c.1259_1260insCATCAC	c.(1258-1263)aacatc>aaCATCACcatc	p.423_424insTI		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	423	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)			TCCGAATACAACATCACCATCA	0.515																																					p.N420delinsNIT		Pindel,Atlas-Indel	.											.	PCDHB2	163	.	0			c.1259_1260insCATCAC						PASS	.			24,4240		0,24,2108						2.5	0.9			132	264,7990		2,260,3865	no	coding	PCDHB2	NM_018936.2		2,284,5973	A1A1,A1R,RR		3.1984,0.5629,2.3007				288,12230				SO:0001652	inframe_insertion	56133	exon1			.	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.1266_1271dupCATCAC	5.37:g.140475634_140475639dupCATCAC	ENSP00000194155:p.Thr422_Ile423dup	Somatic	195	.	.		WXS	Illumina HiSeq	Phase_I	229	48	0.210	NM_018936	Q4KMU1	In_Frame_Ins	INS	ENST00000194155.4	37	CCDS4244.1																																																																																			.	.	weak		0.515	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316851	39316865	+	In_Frame_Del	DEL	GCAGCAGGTGGTCTG	GCAGCAGGTGGTCTG	-	rs199889274|rs201042607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GCAGCAGGTGGTCTG	GCAGCAGGTGGTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39316851_39316865delGCAGCAGGTGGTCTG	ENST00000390661.3	-	1	118_132	c.79_93delCAGACCACCTGCTGC	c.(79-93)cagaccacctgctgcdel	p.QTTCC27del		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	27	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			AGGTGGTCCTGCAGCAGGTGGTCTGGCAGTAGCTG	0.637																																					p.27_32del		Pindel,Atlas-Indel	.											.	KRTAP4-4	21	.	0			c.80_94del						PASS	.			19,4221		3,13,2104						-0.9	0.6			51	51,8203		5,41,4081	no	coding	KRTAP4-4	NM_032524.1		8,54,6185	A1A1,A1R,RR		0.6179,0.4481,0.5603				70,12424				SO:0001651	inframe_deletion	84616	exon1			.	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.79_93delCAGACCACCTGCTGC	17.37:g.39316851_39316865delGCAGCAGGTGGTCTG	ENSP00000375076:p.Gln27_Cys31del	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	130	24	0.185	NM_032524	Q9BYU7	In_Frame_Del	DEL	ENST00000390661.3	37	CCDS11383.1																																																																																			.	.	none		0.637	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
IRF5	3663	hgsc.bcm.edu	37	7	128587352	128587381	+	In_Frame_Del	DEL	ACTCTGCAGCCGCCCACTCTGCGGCCGCCT	ACTCTGCAGCCGCCCACTCTGCGGCCGCCT	-	rs199508964|rs113806178|rs60344245|rs566635242|rs202130620|rs375983447|rs534043449|rs79724471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	ACTCTGCAGCCGCCCACTCTGCGGCCGCCT	ACTCTGCAGCCGCCCACTCTGCGGCCGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128587352_128587381delACTCTGCAGCCGCCCACTCTGCGGCCGCCT	ENST00000402030.2	+	6	574_603	c.502_531delACTCTGCAGCCGCCCACTCTGCGGCCGCCT	c.(502-531)actctgcagccgcccactctgcggccgcctdel	p.TLQPPTLRPP168del	IRF5_ENST00000477535.1_Intron|IRF5_ENST00000357234.5_In_Frame_Del_p.TLQPPTLRPP184del|IRF5_ENST00000473745.1_In_Frame_Del_p.TLQPPTLRPP168del|IRF5_ENST00000249375.4_In_Frame_Del_p.TLQPPTLRPP168del	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	168					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						GTGGCCGCCCACTCTGCAGCCGCCCACTCTGCGGCCGCCTACTCTGCAGC	0.652														2428	0.484824	0.534	0.366	5008	,	,		17245	0.4425		0.5338	False		,,,				2504	0.4959				p.183_193del		Pindel,Atlas-Indel	.											.	IRF5	40	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.549_578del						PASS	.		,,,,	1942,1932		603,736,598					,,,,	0.1	0.9		dbSNP_129	14	3856,4082		1083,1690,1196	no	coding,intron,coding,coding,coding	IRF5	NM_032643.3,NM_001242452.1,NM_001098630.1,NM_001098629.1,NM_001098627.2	,,,,	1686,2426,1794	A1A1,A1R,RR		48.5765,49.8709,49.0857	,,,,	,,,,		5798,6014				SO:0001651	inframe_deletion	3663	exon6			.		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.502_531delACTCTGCAGCCGCCCACTCTGCGGCCGCCT	7.37:g.128587352_128587381delACTCTGCAGCCGCCCACTCTGCGGCCGCCT	ENSP00000385352:p.Thr168_Pro177del	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	98	39	0.398	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	In_Frame_Del	DEL	ENST00000402030.2	37	CCDS5808.1																																																																																			.	.	none		0.652	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
OR2T4	127074	hgsc.bcm.edu	37	1	248525639	248525639	+	Frame_Shift_Del	DEL	A	A	-	rs34079073|rs76878172	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248525639delA	ENST00000366475.1	+	1	757	c.757delA	c.(757-759)atcfs	p.I253fs		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	253						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)			CTATTTACTCATCCTCCTCAC	0.522													a|A|-|deletion	2010	0.401358	0.3389	0.4452	5008	,	,		21944	0.3393		0.4811	False		,,,				2504	0.4366				p.L252fs		Pindel,Atlas-Indel	.											.	OR2T4	126	.	0			c.756delC						PASS	.			1560,2706		284,992,857	94.0	74.0	81.0			-2.8	0.0	1	dbSNP_126	132	4448,3806		1199,2050,878	no	frameshift	OR2T4	NM_001004696.1		1483,3042,1735	A1A1,A1R,RR		46.111,36.5682,47.9872			248525639	6008,6512	2024	3426	5450	SO:0001589	frameshift_variant	127074	exon1			.	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.757delA	1.37:g.248525639delA	ENSP00000355431:p.Ile253fs	Somatic	755	.	.		WXS	Illumina HiSeq	Phase_I	801	157	0.196	NM_001004696	Q6IEZ8	Frame_Shift_Del	DEL	ENST00000366475.1	37	CCDS31113.1																																																																																			A|0.602;-|0.398	0.398	strong		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
SH3BGR	6450	hgsc.bcm.edu	37	21	40883671	40883672	+	In_Frame_Ins	INS	-	-	AGA	rs111921581|rs397694871|rs3831201|rs77389080	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:40883671_40883672insAGA	ENST00000333634.4	+	6	767_768	c.689_690insAGA	c.(688-693)ggagaa>ggAGAagaa	p.232_233insE	SH3BGR_ENST00000380637.3_In_Frame_Ins_p.121_122insE|SH3BGR_ENST00000380631.1_In_Frame_Ins_p.121_122insE|SH3BGR_ENST00000458295.1_In_Frame_Ins_p.90_91insE|SH3BGR_ENST00000380634.1_In_Frame_Ins_p.121_122insE	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	232	Glu-rich (acidic).			E -> EE (in Ref. 4; BM474020). {ECO:0000305}.	positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		ACTGCAGAAGGAGAAGAGCCTG	0.46																																					p.G230delinsGE		Pindel,Atlas-Indel	.											SH3BGR,colon,carcinoma,0,1	SH3BGR	29	1	0			c.689_690insAGA						PASS	.		,	2200,2064		562,1076,494					,	-5.7	0.0		dbSNP_131	112	4701,3553		1343,2015,769	no	coding,coding	SH3BGR	NM_007341.2,NM_001001713.1	,	1905,3091,1263	A1A1,A1R,RR		43.0458,48.4053,44.8714	,	,		6901,5617				SO:0001652	inframe_insertion	6450	exon6			.		CCDS13666.1, CCDS33560.1	21q22.3	2014-02-19	2014-02-19		ENSG00000185437	ENSG00000185437			10822	protein-coding gene	gene with protein product	"""21-glutamic acid-rich protein"""	602230	"""SH3 domain binding glutamic acid-rich protein"""			9050928	Standard	NM_007341		Approved	21-GARP	uc002yya.3	P55822	OTTHUMG00000074113	ENST00000333634.4:c.693_695dupAGA	21.37:g.40883675_40883677dupAGA	ENSP00000332513:p.Glu232_Glu232dup	Somatic	83	.	.		WXS	Illumina HiSeq	Phase_I	85	57	0.671	NM_007341	A6ND59|D3DSI2|Q9BRB8	In_Frame_Ins	INS	ENST00000333634.4	37	CCDS13666.1																																																																																			.	.	strong		0.460	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341	
UGDH	7358	hgsc.bcm.edu	37	4	39515807	39515813	+	Intron	DEL	AAAAAGA	AAAAAGA	-	rs201039591|rs372782074|rs151116497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AAAAAGA	AAAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:39515807_39515813delAAAAAGA	ENST00000316423.6	-	3	505				UGDH_ENST00000515398.1_Intron|UGDH_ENST00000501493.2_Intron|UGDH_ENST00000507089.1_Intron|UGDH_ENST00000506179.1_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	105	.	.		WXS	Illumina HiSeq	Phase_I	112	26	0.232	.	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	
SHKBP1	92799	hgsc.bcm.edu	37	19	41095087	41095112	+	Intron	DEL	GAGGACAGTCCTGTCCAACAGGGAGG	GAGGACAGTCCTGTCCAACAGGGAGG	-	rs528660073|rs547185289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAGGACAGTCCTGTCCAACAGGGAGG	GAGGACAGTCCTGTCCAACAGGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41095087_41095112delGAGGACAGTCCTGTCCAACAGGGAGG	ENST00000291842.5	+	15	1638				SHKBP1_ENST00000600733.1_Intron|SHKBP1_ENST00000597649.1_Intron	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1						protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGGCAGCGGTGAGGACAGTCCTGTCCAACAGGGAGGGAGGACAGTC	0.606														1576	0.314696	0.3275	0.3242	5008	,	,		11236	0.3155		0.3231	False		,,,				2504	0.2812				.		Pindel,Atlas-Indel	.											.	SHKBP1	68	.	0			.						PASS	.																																			SO:0001627	intron_variant	92799	.			.	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"""WD repeat domain containing"""	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1589+3GAGGACAGTCCTGTCCAACAGGGAGG>-	19.37:g.41095087_41095112delGAGGACAGTCCTGTCCAACAGGGAGG		Somatic	73	.	.		WXS	Illumina HiSeq	Phase_I	69	12	0.174	.	Q8N2I6|Q8WY93|Q96IB8	Splice_Site	DEL	ENST00000291842.5	37	CCDS12560.1																																																																																			.	.	none		0.606	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376925	168376926	+	lincRNA	INS	-	-	T	rs2516606|rs71305247|rs35001101|rs66632147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168376925_168376926insT	ENST00000538528.1	-	0	693_694																											TGCAGTGTGTGGGGAAGGAGGA	0.634													?|-|T|unsure	1595	0.31849	0.2579	0.3199	5008	,	,		19949	0.3998		0.2535	False		,,,				2504	0.3824				p.P136fs		Atlas-Indel	.											.	.	.	.	0			c.408_409insA						PASS	.			559,21,2008		29,0,501,4,13,747							0.0		dbSNP_130	23	1115,56,3729		66,2,981,3,48,1350	no	codingComplex	HGC6.3	NM_001129895.2		95,2,1482,7,61,2097	A1A1,A1A2,A1R,A2A2,A2R,RR		23.898,22.4111,23.3841				1674,77,5737						0	exon1			.																													6.37:g.168376925_168376926insT		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	226	42	0.185841	NM_001129895		Frame_Shift_Ins	INS	ENST00000538528.1	37																																																																																				.	.	strong		0.634	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
IST1	9798	hgsc.bcm.edu	37	16	71956512	71956517	+	In_Frame_Del	DEL	ATGCCC	ATGCCC	-	rs549750934|rs372825060	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	ATGCCC	ATGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71956512_71956517delATGCCC	ENST00000378799.6	+	7	1044_1049	c.688_693delATGCCC	c.(688-693)atgcccdel	p.MP238del	IST1_ENST00000535424.1_In_Frame_Del_p.MP251del|IST1_ENST00000329908.8_In_Frame_Del_p.MP238del|IST1_ENST00000538565.1_3'UTR|IST1_ENST00000606369.1_In_Frame_Del_p.MP90del|IST1_ENST00000378798.5_In_Frame_Del_p.MP238del|IST1_ENST00000538850.1_In_Frame_Del_p.MP90del|IST1_ENST00000541571.2_In_Frame_Del_p.MP238del|RP11-498D10.5_ENST00000567146.1_RNA|IST1_ENST00000544564.1_In_Frame_Del_p.MP238del			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	236	Interaction with VPS37B.|Interaction with VTA1.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										AACGGtgccaatgcccatgcccatgc	0.495														1400	0.279553	0.1725	0.2507	5008	,	,		22310	0.2649		0.341	False		,,,				2504	0.3967				p.242_244del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.726_731del						PASS	.																																			SO:0001651	inframe_deletion	9798	exon8			.	BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"""KIAA0174"""	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.688_693delATGCCC	16.37:g.71956518_71956523delATGCCC	ENSP00000368076:p.Met238_Pro239del	Somatic	115	.	.		WXS	Illumina HiSeq	Phase_I	96	19	0.198	NM_001270976	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	In_Frame_Del	DEL	ENST00000378799.6	37	CCDS59272.1																																																																																			.	.	strong		0.495	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761	
MIR205HG	642587	hgsc.bcm.edu	37	1	209605637	209605648	+	lincRNA	DEL	AGCAGCAGCAGC	AGCAGCAGCAGC	-	rs71788170|rs74820836|rs150848171|rs3842530		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AGCAGCAGCAGC	AGCAGCAGCAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:209605637_209605648delAGCAGCAGCAGC	ENST00000384891.1	+	0	220					NR_029622.1				MIR205 host gene (non-protein coding)																		ccaccaccgTagcagcagcagcagcagcagca	0.561																																					p.84_88del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.251_262del						PASS	.																																					642587	exon4			.			1q32.2	2014-02-12	2011-11-07		ENSG00000230937	ENSG00000230937		"""Long non-coding RNAs"""	43562	non-coding RNA	RNA, long non-coding	"""long intergenic non-protein coding RNA 510"""						Standard	NM_001104548		Approved	LINC00510	uc009xcn.3		OTTHUMG00000036267		1.37:g.209605637_209605648delAGCAGCAGCAGC		Somatic	51	.	.		WXS	Illumina HiSeq	Phase_I	61	24	0.393	NM_001104548		In_Frame_Del	DEL	ENST00000384891.1	37																																																																																				.	.	strong		0.561	MIR205HG-202	KNOWN	basic	miRNA	lincRNA			
C5orf60	285679	hgsc.bcm.edu	37	5	179071810	179071812	+	In_Frame_Del	DEL	TCC	TCC	-	rs3987734|rs151013485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:179071810_179071812delTCC	ENST00000448248.2	-	1	235_237	c.210_212delGGA	c.(208-213)gaggac>gac	p.E70del	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	70			Missing. {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						ATTCTCGCTGTCCTCCTCTCTGG	0.522														348	0.0694888	0.0522	0.0461	5008	,	,		23659	0.0417		0.0994	False		,,,				2504	0.1074				p.71_71del		Pindel,Atlas-Indel	.											.	C5orf60	24	.	0			c.211_213del						PASS	.			148,2586		16,116,1235						-0.9	0.0		dbSNP_119	55	363,4813		36,291,2261	no	coding	C5orf60	NM_001142306.1		52,407,3496	A1A1,A1R,RR		7.0131,5.4133,6.4602				511,7399				SO:0001651	inframe_deletion	285679	exon1			.	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.210_212delGGA	5.37:g.179071813_179071815delTCC	ENSP00000404583:p.Glu70del	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	140	31	0.221	NM_001142306	A1L488|B7ZM52|B7ZM53	In_Frame_Del	DEL	ENST00000448248.2	37	CCDS47353.1																																																																																			TCC|0.934;-|0.066	0.066	strong		0.522	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
LOR	4014	hgsc.bcm.edu	37	1	153233488	153233489	+	In_Frame_Ins	INS	-	-	GGCGGT	rs150026164	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153233488_153233489insGGCGGT	ENST00000368742.3	+	2	120_121	c.63_64insGGCGGT	c.(64-66)ggc>GGCGGTggc	p.22_22G>GGG		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	22					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.G22S(1)		lung(2)	2	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)			AGACCTCTggcggcggtggcgg	0.673														971	0.19389	0.3812	0.1542	5008	,	,		8118	0.0685		0.2326	False		,,,				2504	0.0583				p.G21delinsGGG		Pindel,Atlas-Indel	.											.	LOR	19	.	1	Substitution - Missense(1)	lung(1)	c.63_64insGGCGGT						PASS	.			1372,2418		364,644,887						1.9	0.9		dbSNP_130	14	1619,5813		315,989,2412	no	coding	LOR	NM_000427.2		679,1633,3299	A1A1,A1R,RR		21.7842,36.2005,26.653				2991,8231				SO:0001652	inframe_insertion	4014	exon2			.	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.70_75dupGGCGGT	1.37:g.153233489_153233494dupGGCGGT	ENSP00000357731:p.GlyGly28dup	Somatic	69	.	.		WXS	Illumina HiSeq	Phase_I	51	11	0.216	NM_000427	Q5T869|Q5XKF8	In_Frame_Ins	INS	ENST00000368742.3	37	CCDS30870.1																																																																																			-|0.771;GGCGGT|0.229	0.229	strong		0.673	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427	
HLA-G	3135	hgsc.bcm.edu	37	6	29796435	29796435	+	Frame_Shift_Del	DEL	C	C	-	rs41557518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29796435delC	ENST00000360323.6	+	3	483	c.459delC	c.(457-459)gacfs	p.D153fs	HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376828.2_Frame_Shift_Del_p.D158fs|HLA-G_ENST00000428701.1_Frame_Shift_Del_p.D153fs			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	153	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.L154fs*60(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TGAACGAGGACCTGCGCTCCT	0.617													cc|CC|C|deletion	142	0.0283546	0.0741	0.013	5008	,	,		16865	0.0149		0.0119	False		,,,				2504	0.0082				p.D153fs		Pindel,Atlas-Indel	.											.	HLA-G	90	.	1	Deletion - Frameshift(1)	pancreas(1)	c.458delA						PASS	.			272,3948		19,234,1857	107.0	99.0	102.0			1.7	0.8	6	dbSNP_134	105	112,8078		11,90,3994	no	frameshift	HLA-G	NM_002127.5		30,324,5851	A1A1,A1R,RR		1.3675,6.4455,3.0943			29796435	384,12026	1510	2709	4219	SO:0001589	frameshift_variant	3135	exon4			.		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.459delC	6.37:g.29796435delC	ENSP00000353472:p.Asp153fs	Somatic	177	.	.		WXS	Illumina HiSeq	Phase_I	226	74	0.327	NM_002127		Frame_Shift_Del	DEL	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.967;-|0.033	0.033	strong		0.617	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
TPM2	7169	hgsc.bcm.edu	37	9	35683240	35683241	+	Splice_Site	INS	-	-	G	rs35401252|rs199476157|rs368128547|rs149115565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35683240_35683241insG	ENST00000360958.2	-	9	877		c.e9-2		TPM2_ENST00000329305.2_Intron|TPM2_ENST00000378292.3_Intron|TPM2_ENST00000378300.5_Intron	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)						muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			AGACTTCATCTGGGGGGGGTCC	0.55													GGGGGGG|GGGGGGGG|GGGGGGGGG|cryptic_indel	1313	0.262181	0.1505	0.2896	5008	,	,		19764	0.2917		0.3608	False		,,,				2504	0.2618				.		Pindel,Atlas-Indel	.											.	TPM2	64	.	0			c.773-2->C						PASS	.																																			SO:0001630	splice_region_variant	7169	exon10			.		CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"""Tropomyosins"""	12011	protein-coding gene	gene with protein product	"""nemaline myopathy type 4"""	190990	"""arthrogryposis multiplex congenital, distal, type 1"""	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.773-2->C	9.37:g.35683248_35683248dupG		Somatic	184	.	.		WXS	Illumina HiSeq	Phase_I	216	60	0.278	NM_003289	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Splice_Site	INS	ENST00000360958.2	37	CCDS6587.1																																																																																			.	.	strong		0.550	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289	Intron
BBX	56987	hgsc.bcm.edu	37	3	107491759	107491761	+	In_Frame_Del	DEL	AGA	AGA	-	rs397757043|rs34531902	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:107491759_107491761delAGA	ENST00000325805.8	+	11	1478_1480	c.1191_1193delAGA	c.(1189-1194)ttagaa>tta	p.E399del	BBX_ENST00000402543.1_In_Frame_Del_p.E399del|BBX_ENST00000416476.2_Intron|BBX_ENST00000415149.2_In_Frame_Del_p.E399del|BBX_ENST00000406780.1_In_Frame_Del_p.E399del			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	399					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			AGGAAGAGTTAGAAGAAGATCAC	0.325														187	0.0373403	0.0076	0.0706	5008	,	,		18681	0.0		0.1074	False		,,,				2504	0.0204				p.397_398del		Pindel,Atlas-Indel	.											.	BBX	156	.	0			c.1190_1192del						PASS	.		,	130,4136		1,128,2004					,	2.6	1.0		dbSNP_126	71	978,7272		62,854,3209	no	coding,coding	BBX	NM_020235.5,NM_001142568.1	,	63,982,5213	A1A1,A1R,RR		11.8545,3.0474,8.8527	,	,		1108,11408				SO:0001651	inframe_deletion	56987	exon11			.	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1191_1193delAGA	3.37:g.107491765_107491767delAGA	ENSP00000319974:p.Glu399del	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	143	47	0.329	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	In_Frame_Del	DEL	ENST00000325805.8	37	CCDS46881.1																																																																																			AGA|0.951;-|0.049	0.049	strong		0.325	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
MDP1	145553	hgsc.bcm.edu	37	14	24683267	24683267	+	Frame_Shift_Del	DEL	A	A	-	rs3215610|rs398102305	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24683267delA	ENST00000288087.7	-	6	605	c.494delT	c.(493-495)ttgfs	p.L165fs	NEDD8-MDP1_ENST00000604306.1_5'Flank|MDP1_ENST00000396833.2_Frame_Shift_Del_p.F118fs|TM9SF1_ENST00000556387.1_5'Flank|CHMP4A_ENST00000347519.6_5'Flank|TM9SF1_ENST00000530611.1_5'Flank|MDP1_ENST00000532557.1_5'UTR|CHMP4A_ENST00000530996.1_5'Flank|AL136419.6_ENST00000565988.1_RNA|CHMP4A_ENST00000542700.2_5'Flank|CHMP4A_ENST00000609024.1_5'Flank	NM_001199822.1|NM_138476.3	NP_001186751.1|NP_612485.2	Q86V88	MGDP1_HUMAN	magnesium-dependent phosphatase 1	165						extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|large_intestine(2)|lung(3)	7						GCTGGACCTCAAAGGCCCAGT	0.418													AA|AAA|AA|insertion	1020	0.203674	0.4342	0.0807	5008	,	,		23163	0.2123		0.0686	False		,,,				2504	0.1094				p.L182fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.546delG						PASS	.		,,,	1728,2536		344,1040,748	42.0	63.0	56.0		,,,	2.4	0.9	14	dbSNP_134	68	579,7675		25,529,3573	no	frameshift,frameshift,utr-3,frameshift	MDP1,NEDD8-MDP1	NM_138476.3,NM_001199823.1,NM_001199822.1,NM_001199821.1	,,,	369,1569,4321	A1A1,A1R,RR		7.0148,40.5253,18.4295	,,,	,,,	24683267	2307,10211	2162	4299	6461	SO:0001589	frameshift_variant	100528064	exon7			.	BC046912	CCDS9620.1, CCDS55908.1	14q12	2009-07-09			ENSG00000213920	ENSG00000213920			28781	protein-coding gene	gene with protein product	"""fructosamine-6-phosphatase"""					10889041, 16670083	Standard	NM_138476		Approved	MGC5987, FN6Pase		Q86V88	OTTHUMG00000133477	ENST00000288087.7:c.494delT	14.37:g.24683267delA	ENSP00000288087:p.Leu165fs	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	110	64	0.582	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	
ATN1	1822	hgsc.bcm.edu	37	12	7045891	7045892	+	In_Frame_Ins	INS	-	-	CAG	rs199920334|rs377147612|rs150855426|rs60216939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:7045891_7045892insCAG	ENST00000356654.4	+	5	1698_1699	c.1461_1462insCAG	c.(1462-1464)cag>CAGcag	p.488_488Q>QQ	ATN1_ENST00000396684.2_In_Frame_Ins_p.488_488Q>QQ	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	488	Poly-Gln.		Missing. {ECO:0000269|PubMed:7485154, ECO:0000269|PubMed:7842016, ECO:0000269|PubMed:8965642}.		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)	p.Q487_Q488insQ(1)|p.Q488delQ(1)		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						agcaacagcaacagcagcagca	0.634																																					p.Q487delinsQQ		Atlas-Indel	.											ATN1,NS,carcinoma,0,3	ATN1	95	3	2	Insertion - In frame(1)|Deletion - In frame(1)	breast(2)	c.1461_1462insCAG						PASS	.																																			SO:0001652	inframe_insertion	1822	exon5			.	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.1504_1506dupCAG	12.37:g.7045898_7045900dupCAG	ENSP00000349076:p.Gln502dup	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	127	23	0.181102	NM_001007026	Q99495|Q99621|Q9UEK7	In_Frame_Ins	INS	ENST00000356654.4	37	CCDS31734.1																																																																																			.	.	alt		0.634	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
RTL1	388015	hgsc.bcm.edu	37	14	101350670	101350671	+	In_Frame_Ins	INS	-	-	TCT	rs55755518|rs397823434|rs35401447	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:101350670_101350671insTCT	ENST00000534062.1	-	1	513_514	c.455_456insAGA	c.(454-456)gag>gaAGAg	p.152_152E>EE	MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	152					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						TCTGGTTTTGCTCTTGAGGAGT	0.52														784	0.15655	0.0847	0.1902	5008	,	,		20517	0.0575		0.2684	False		,,,				2504	0.2168				p.E152delinsEE		Pindel,Atlas-Indel	.											.	RTL1	120	.	0			c.456_457insAGA						PASS	.			459,3511		59,341,1585						2.5	0.0		dbSNP_126	223	2155,5335		412,1331,2002	no	coding	RTL1	NM_001134888.2		471,1672,3587	A1A1,A1R,RR		28.7717,11.5617,22.8098				2614,8846				SO:0001652	inframe_insertion	388015	exon1			.		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.453_455dupAGA	14.37:g.101350671_101350673dupTCT	ENSP00000435342:p.Glu152dup	Somatic	201	.	.		WXS	Illumina HiSeq	Phase_I	193	101	0.523	NM_001134888	E9PKS8	In_Frame_Ins	INS	ENST00000534062.1	37	CCDS53910.1																																																																																			.	.	strong		0.520	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
KRT1	3848	hgsc.bcm.edu	37	12	53069223	53069243	+	In_Frame_Del	DEL	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	-	rs77846840|rs540699806|rs11170232|rs370799361|rs267607656	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53069223_53069243delACCTCCGGAGCCGTAGCTGCT	ENST00000252244.3	-	9	1727_1747	c.1669_1689delAGCAGCTACGGCTCCGGAGGT	c.(1669-1689)agcagctacggctccggaggtdel	p.SSYGSGG557del		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	557	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.S557_G563delSSYGSGG(3)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						catagctgccacctccggagccgtagctgctacctccggag	0.697														1779	0.355232	0.4372	0.3905	5008	,	,		11351	0.1349		0.3459	False		,,,				2504	0.456				p.557_564del		Atlas-Indel	.											.	KRT1	110	.	3	Deletion - In frame(3)	prostate(2)|central_nervous_system(1)	c.1670_1690del						PASS	.			1255,1949		405,445,752						0.8	0.1		dbSNP_130	5	2781,3759		866,1049,1355	no	coding	KRT1	NM_006121.3		1271,1494,2107	A1A1,A1R,RR		42.5229,39.1698,41.4204				4036,5708				SO:0001651	inframe_deletion	3848	exon9			.	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1669_1689delAGCAGCTACGGCTCCGGAGGT	12.37:g.53069223_53069243delACCTCCGGAGCCGTAGCTGCT	ENSP00000252244:p.Ser557_Gly563del	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	In_Frame_Del	DEL	ENST00000252244.3	37	CCDS8836.1																																																																																			.	.	none		0.697	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
MYO5B	4645	hgsc.bcm.edu	37	18	47405425	47405426	+	In_Frame_Ins	INS	-	-	GAG	rs33910398|rs3841750|rs200219597|rs397841722	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	134	.	.		WXS	Illumina HiSeq	Phase_I	194	56	0.289	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		
KREMEN2	79412	hgsc.bcm.edu	37	16	3017836	3017836	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:3017836delG	ENST00000303746.5	+	9	1781	c.1204delG	c.(1204-1206)gggfs	p.G402fs	PKMYT1_ENST00000571102.1_5'Flank|KREMEN2_ENST00000571007.1_Frame_Shift_Del_p.G363fs|PAQR4_ENST00000318782.8_5'Flank|PAQR4_ENST00000572687.1_5'Flank|PAQR4_ENST00000293978.8_5'Flank|KREMEN2_ENST00000575769.1_3'UTR|KREMEN2_ENST00000572045.1_3'UTR|KREMEN2_ENST00000319500.6_Frame_Shift_Del_p.K375fs|PAQR4_ENST00000576565.1_5'Flank|KREMEN2_ENST00000575885.1_Frame_Shift_Del_p.K336fs			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	402					Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						TCCGGGAAAAGGGCCCCCGGC	0.706																																					p.K401fs		Pindel,Atlas-Indel	.											.	KREMEN2	13	.	0			c.1203delA						PASS	.						8.0	8.0	8.0					16																	3017836		2028	4033	6061	SO:0001589	frameshift_variant	79412	exon9			.	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.1204delG	16.37:g.3017836delG	ENSP00000304422:p.Gly402fs	Somatic	136	.	.		WXS	Illumina HiSeq	Phase_I	130	41	0.315	NM_172229	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Frame_Shift_Del	DEL	ENST00000303746.5	37	CCDS10483.1																																																																																			.	.	none		0.706	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347	
TNRC6A	27327	hgsc.bcm.edu	37	16	24788423	24788434	+	In_Frame_Del	DEL	GCAGCCACAGCC	GCAGCCACAGCC	-	rs10593507|rs60829899|rs71156436|rs11644562|rs71383714	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GCAGCCACAGCC	GCAGCCACAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:24788423_24788434delGCAGCCACAGCC	ENST00000395799.3	+	5	462_473	c.333_344delGCAGCCACAGCC	c.(331-345)cagcagccacagccg>cag	p.QPQP112del	TNRC6A_ENST00000315183.7_In_Frame_Del_p.QPQP112del	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	112	Gln-rich.|Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		agccacagcagcagccacagccgcagccgcag	0.59														660	0.131789	0.0908	0.1455	5008	,	,		12550	0.126		0.162	False		,,,				2504	0.1524				p.111_115del		Atlas-Indel	.											.	TNRC6A	171	.	0			c.332_343del						PASS	.			502,3262		90,322,1470						1.3	0.2		dbSNP_130	23	1410,6010		189,1032,2489	no	coding	TNRC6A	NM_014494.2		279,1354,3959	A1A1,A1R,RR		19.0027,13.3369,17.0959				1912,9272				SO:0001651	inframe_deletion	27327	exon5			.	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.333_344delGCAGCCACAGCC	16.37:g.24788423_24788434delGCAGCCACAGCC	ENSP00000379144:p.Gln112_Pro115del	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	In_Frame_Del	DEL	ENST00000395799.3	37	CCDS10624.2																																																																																			GCAGCCACAGCC|0.906;-|0.094	0.094	strong		0.590	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
CPLX3	594855	hgsc.bcm.edu	37	15	75122558	75122560	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:75122558_75122560delGAG	ENST00000395018.4	+	3	497_499	c.340_342delGAG	c.(340-342)gagdel	p.E118del	RP11-414J4.2_ENST00000564823.1_RNA	NM_001030005.2	NP_001025176.1	Q8WVH0	CPLX3_HUMAN	complexin 3	118					insulin secretion (GO:0030073)|regulation of neurotransmitter secretion (GO:0046928)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)	neurotransmitter transporter activity (GO:0005326)			large_intestine(2)|lung(2)	4						GGAGGACACAGAGGAGGAGGAGG	0.616																																					p.113_114del		Pindel,Atlas-Indel	.											.	CPLX3	12	.	0			c.339_341del						PASS	.			22,4242		10,2,2120						-5.3	1.0			72	52,8202		23,6,4098	no	coding	CPLX3	NM_001030005.2		33,8,6218	A1A1,A1R,RR		0.63,0.5159,0.5911				74,12444				SO:0001651	inframe_deletion	594855	exon3			.	BC018026	CCDS32294.1	15q24.1	2005-08-09			ENSG00000213578	ENSG00000213578			27652	protein-coding gene	gene with protein product		609585				15911881	Standard	NM_001030005		Approved	CPX-III	uc002ayu.1	Q8WVH0	OTTHUMG00000142816	ENST00000395018.4:c.340_342delGAG	15.37:g.75122567_75122569delGAG	ENSP00000378464:p.Glu118del	Somatic	198	.	.		WXS	Illumina HiSeq	Phase_I	169	48	0.284	NM_001030005	D3DW66|Q8TEM6|Q9H818	In_Frame_Del	DEL	ENST00000395018.4	37	CCDS32294.1																																																																																			.	.	none		0.616	CPLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286402.2	NM_001030005	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744827	23744829	+	In_Frame_Del	DEL	TCC	TCC	-	rs79723196|rs35076736|rs67447855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23744827_23744829delTCC	ENST00000357460.5	-	2	1772_1774	c.1608_1610delGGA	c.(1606-1611)gaggaa>gaa	p.536_537EE>E	HOMEZ_ENST00000431326.2_In_Frame_Del_p.538_539EE>E|HOMEZ_ENST00000561013.1_In_Frame_Del_p.538_539EE>E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	536	Glu-rich.|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)		atcatcatcttcctcctcctcct	0.483														1763	0.352037	0.3949	0.3386	5008	,	,		20301	0.1974		0.3738	False		,,,				2504	0.4407				p.537_537del		Atlas-Indel	.											.	HOMEZ	80	.	0			c.1609_1611del						PASS	.																																			SO:0001651	inframe_deletion	57594	exon2			.	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1608_1610delGGA	14.37:g.23744836_23744838delTCC	ENSP00000350049:p.Glu537del	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	23	0.169118	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	In_Frame_Del	DEL	ENST00000357460.5	37	CCDS45085.1																																																																																			TCC|0.500;-|0.500	0.500	weak		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
TIGD6	81789	hgsc.bcm.edu	37	5	149374880	149374880	+	Frame_Shift_Del	DEL	T	T	-	rs397756704|rs3832324|rs201139146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	237	.	.		WXS	Illumina HiSeq	Phase_I	232	98	0.422	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	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	rs201922875|rs553160982		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ|SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>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	65	.	.		WXS	Illumina HiSeq	Phase_I	59	18	0.305	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	
HOXA1	3198	hgsc.bcm.edu	37	7	27135314	27135316	+	In_Frame_Del	DEL	CGA	CGA	-	rs368428758|rs10951154|rs544314279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:27135314_27135316delCGA	ENST00000343060.4	-	1	277_279	c.216_218delTCG	c.(214-219)catcgc>cac	p.R73del	HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOXA1_ENST00000355633.5_In_Frame_Del_p.R73del|HOTAIRM1_ENST00000425358.2_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	73	Poly-His.		H -> R (frequent polymorphism in individuals of European or African origin; dbSNP:rs10951154). {ECO:0000269|PubMed:11091361, ECO:0000269|PubMed:14702039}.		abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						Ctgggggtggcgatggtggtggt	0.65											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		37	0.00738818	0.0	0.0144	5008	,	,		11776	0.001		0.0209	False		,,,				2504	0.0051				p.73_73del		Atlas-Indel	.											.	HOXA1	64	.	0			c.217_219del						PASS	.																																			SO:0001651	inframe_deletion	3198	exon1			.		CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.216_218delTCG	7.37:g.27135314_27135316delCGA	ENSP00000343246:p.Arg73del	Somatic	43	0	0	792	WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_005522	A4D184|B2R8U7|O43363	In_Frame_Del	DEL	ENST00000343060.4	37	CCDS5401.1																																																																																			.	.	weak		0.650	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
HLA-B	3106	hgsc.bcm.edu	37	6	31324601	31324602	+	Frame_Shift_Ins	INS	-	-	A	rs41562914|rs41541416|rs9281379	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31324601_31324602insA	ENST00000412585.2	-	2	234_235	c.206_207insT	c.(205-207)gagfs	p.E69fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	69	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.E69fs*30(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCCGCGGCTCCTCTCTCGGACT	0.673									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				|||unknown(NO_COVERAGE)	34	0.00678914	0.0	0.0014	5008	,	,		7961	0.0188		0.0	False		,,,				2504	0.0143				p.E69fs		Atlas-Indel	.											.	HLA-B	54	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.207_208insT						PASS	.			1399,160,2559		395,63,546,25,47,983						0.1	0.1		dbSNP_130	35	1793,477,5714		469,110,745,86,195,2387	no	codingComplex	HLA-B	NM_005514.6		864,173,1291,111,242,3370	A1A1,A1A2,A1R,A2A2,A2R,RR		28.4319,37.8582,31.6394				3192,637,8273				SO:0001589	frameshift_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	.	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.206_207insT	6.37:g.31324601_31324602insA	ENSP00000399168:p.Glu69fs	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	25	19	0.76	NM_005514	Q29764	Frame_Shift_Ins	INS	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	weak		0.673	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
DNAJC28	54943	hgsc.bcm.edu	37	21	34860750	34860754	+	Frame_Shift_Del	DEL	AATTA	AATTA	-	rs139852262|rs3834674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AATTA	AATTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:34860750_34860754delAATTA	ENST00000314399.3	-	2	1385_1389	c.947_951delTAATT	c.(946-951)ttaattfs	p.LI316fs	DNAJC28_ENST00000381947.3_Frame_Shift_Del_p.LI316fs|DNAJC28_ENST00000402202.1_Frame_Shift_Del_p.LI316fs	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	316				LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185). {ECO:0000305}.				p.L316*(2)|p.L316fs*12(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						GGATGGGAACAATTAAATTAAAATC	0.341														760	0.151757	0.0151	0.2262	5008	,	,		20822	0.1667		0.2664	False		,,,				2504	0.1503				p.316_318del		Pindel,Atlas-Indel	.											.	DNAJC28	47	.	3	Substitution - Nonsense(2)|Deletion - Frameshift(1)	lung(3)	c.948_952del						PASS	.		,	229,4035		5,219,1908					,	5.1	1.0		dbSNP_130	84	1814,6438		207,1400,2519	no	frameshift,frameshift	DNAJC28	NM_017833.3,NM_001040192.1	,	212,1619,4427	A1A1,A1R,RR		21.9825,5.3705,16.3231	,	,		2043,10473				SO:0001589	frameshift_variant	54943	exon2			.	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"""Heat shock proteins / DNAJ (HSP40)"""	1297	protein-coding gene	gene with protein product	"""Orf28"""		"""chromosome 21 open reading frame 55"""	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.947_951delTAATT	21.37:g.34860755_34860759delAATTA	ENSP00000320303:p.Leu316fs	Somatic	157	.	.		WXS	Illumina HiSeq	Phase_I	166	54	0.325	NM_001040192	D3DSF2	Frame_Shift_Del	DEL	ENST00000314399.3	37	CCDS13626.1																																																																																			AATTA|0.826;-|0.174	0.174	strong		0.341	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3		
RRP15	51018	hgsc.bcm.edu	37	1	218504400	218504400	+	Frame_Shift_Del	DEL	C	C	-	rs541335404	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:218504400delC	ENST00000366932.3	+	5	846	c.816delC	c.(814-816)agcfs	p.S272fs		NM_016052.3	NP_057136.2	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog (S. cerevisiae)	272						mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)			ACBD6/RRP15(2)	NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		CAGATGACAGCAGACCAGAAT	0.408													C|C|-|deletion	13	0.00259585	0.0	0.0014	5008	,	,		14545	0.0		0.007	False		,,,				2504	0.0051				p.S272fs		Pindel,Atlas-Indel	.											.	RRP15	33	.	0			c.815delG						PASS	.			3,4263		0,3,2130	76.0	70.0	72.0			1.5	0.0	1		73	29,8225		0,29,4098	no	frameshift	RRP15	NM_016052.3		0,32,6228	A1A1,A1R,RR		0.3513,0.0703,0.2556			218504400	32,12488	2203	4300	6503	SO:0001589	frameshift_variant	51018	exon5			.		CCDS1520.2	1q41	2008-02-05			ENSG00000067533	ENSG00000067533			24255	protein-coding gene	gene with protein product		611193	"""KIAA0507"""	KIAA0507		15769876	Standard	NM_016052		Approved	CGI-115	uc001hlj.3	Q9Y3B9	OTTHUMG00000039494	ENST00000366932.3:c.816delC	1.37:g.218504400delC	ENSP00000355899:p.Ser272fs	Somatic	143	.	.		WXS	Illumina HiSeq	Phase_I	154	54	0.351	NM_016052		Frame_Shift_Del	DEL	ENST00000366932.3	37	CCDS1520.2																																																																																			.	.	none		0.408	RRP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095284.1	NM_016052	
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471753	39471767	+	In_Frame_Del	DEL	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	-	rs373758570|rs74252500|rs572148015|rs386797077|rs577925182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39471753_39471767delGCCCCCGCAGCCAGA	ENST00000334202.3	-	1	180_194	c.136_150delTCTGGCTGCGGGGGC	c.(136-150)tctggctgcgggggcdel	p.SGCGG46del		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	46						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			cgcagcagctgcccccgcagccagagcccccgcag	0.679														1164	0.232428	0.2935	0.1499	5008	,	,		12020	0.3185		0.1829	False		,,,				2504	0.1708				p.46_51del		Pindel,Atlas-Indel	.											.	KRTAP17-1	14	.	0			c.137_151del						PASS	.			1060,2972		251,558,1207						-1.9	0.1		dbSNP_130	17	1435,6399		241,953,2723	no	coding	KRTAP17-1	NM_031964.1		492,1511,3930	A1A1,A1R,RR		18.3176,26.2897,21.0265				2495,9371				SO:0001651	inframe_deletion	83902	exon1			.	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"""Keratin associated proteins"""	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.136_150delTCTGGCTGCGGGGGC	17.37:g.39471753_39471767delGCCCCCGCAGCCAGA	ENSP00000333993:p.Ser46_Gly50del	Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	39	17	0.436	NM_031964		In_Frame_Del	DEL	ENST00000334202.3	37	CCDS11387.1																																																																																			.	.	none		0.679	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1		
ATF7IP2	80063	hgsc.bcm.edu	37	16	10565979	10565981	+	In_Frame_Del	DEL	TGT	TGT	-	rs566280429|rs199605421	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10565979_10565981delTGT	ENST00000396560.2	+	8	1592_1594	c.1365_1367delTGT	c.(1363-1368)gatgtt>gat	p.V456del	ATF7IP2_ENST00000543967.1_5'UTR|ATF7IP2_ENST00000396559.1_In_Frame_Del_p.V456del|ATF7IP2_ENST00000324570.5_In_Frame_Del_p.V456del|ATF7IP2_ENST00000356427.2_In_Frame_Del_p.V456del	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						ACAATGATGATGTTATGTTGATT	0.296														25	0.00499201	0.0008	0.0086	5008	,	,		16695	0.001		0.0099	False		,,,				2504	0.0072				p.455_456del		Pindel,Atlas-Indel	.											.	ATF7IP2	40	.	0			c.1364_1366del						PASS	.			6,4252		0,6,2123						2.3	1.0			67	99,8125		1,97,4014	no	coding	ATF7IP2	NM_024997.2		1,103,6137	A1A1,A1R,RR		1.2038,0.1409,0.8412				105,12377				SO:0001651	inframe_deletion	80063	exon9			.	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.1365_1367delTGT	16.37:g.10565979_10565981delTGT	ENSP00000379808:p.Val456del	Somatic	21	.	.		WXS	Illumina HiSeq	Phase_I	26	10	0.385	NM_001256160	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	In_Frame_Del	DEL	ENST00000396560.2	37	CCDS10540.1																																																																																			.	.	none		0.296	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
NCOA3	8202	hgsc.bcm.edu	37	20	46279837	46279839	+	In_Frame_Del	DEL	CAG	CAG	-	rs147879509|rs2664555|rs397778717|rs3830809		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:46279837_46279839delCAG	ENST00000371998.3	+	20	3954_3956	c.3763_3765delCAG	c.(3763-3765)cagdel	p.Q1276del	NCOA3_ENST00000341724.6_In_Frame_Del_p.Q1202del|NCOA3_ENST00000371997.3_In_Frame_Del_p.Q1267del|NCOA3_ENST00000372004.3_In_Frame_Del_p.Q1272del			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1276	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1255delQ(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						gcagcagcaacagcagcagcagc	0.552																																					p.1254_1255del		Atlas-Indel	.											NCOA3,NS,carcinoma,0,1	NCOA3	156	1	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.3762_3764del						PASS	.		,,,	586,1098,2378		46,154,340,141,662,688					,,,	0.5	0.0		dbSNP_107	50	208,3200,4626		14,44,136,605,1946,1272	no	codingComplex,codingComplex,codingComplex,codingComplex	NCOA3	NM_181659.2,NM_006534.3,NM_001174088.1,NM_001174087.1	,,,	60,198,476,746,2608,1960	A1A1,A1A2,A1R,A2A2,A2R,RR		42.4197,41.4574,42.0966	,,,	,,,		794,4298,7004				SO:0001651	inframe_deletion	8202	exon20			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3763_3765delCAG	20.37:g.46279846_46279848delCAG	ENSP00000361066:p.Gln1276del	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	23	0.270588	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	37	CCDS13407.1																																																																																			CAG|0.669;-|0.331	0.331	strong		0.552	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
PIEZO1	9780	hgsc.bcm.edu	37	16	88787608	88787610	+	In_Frame_Del	DEL	CTT	CTT	-	rs3217718|rs150376294|rs113773794	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88787608_88787610delCTT	ENST00000301015.9	-	39	5878_5880	c.5632_5634delAAG	c.(5632-5634)aagdel	p.K1878del	RP5-1142A6.9_ENST00000564984.1_RNA|PIEZO1_ENST00000327397.7_5'Flank	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1878					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)	p.K1878delK(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CTGGGCCCTCCTTCTTCCTTCTT	0.616														1081	0.215855	0.1452	0.2003	5008	,	,		19820	0.0774		0.334	False		,,,				2504	0.3436				p.1878_1879del		Pindel,Atlas-Indel	.											.	PIEZO1	79	.	1	Deletion - In frame(1)	breast(1)	c.5633_5635del						PASS	.			433,2117		88,257,930						3.8	0.1		dbSNP_131	32	1667,3279		392,883,1198	no	coding	PIEZO1	NM_001142864.2		480,1140,2128	A1A1,A1R,RR		33.704,16.9804,28.0149				2100,5396				SO:0001651	inframe_deletion	9780	exon39			.	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.5632_5634delAAG	16.37:g.88787611_88787613delCTT	ENSP00000301015:p.Lys1878del	Somatic	34	.	.		WXS	Illumina HiSeq	Phase_I	32	12	0.375	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	In_Frame_Del	DEL	ENST00000301015.9	37	CCDS54058.1																																																																																			CTT|0.800;-|0.200	0.200	strong		0.616	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140767492	140767497	+	In_Frame_Del	DEL	TGCCAG	TGCCAG	-	rs145222727|rs370380135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGCCAG	TGCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140767492_140767497delTGCCAG	ENST00000519479.1	+	1	41_46	c.41_46delTGCCAG	c.(40-48)ctgccagtg>ctg	p.PV15del	PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	15					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P15_V16delPV(1)		endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGAGAGGCTGCCAGTGCTCTTTCT	0.617											OREG0016859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		166	0.033147	0.0045	0.0476	5008	,	,		16199	0.0		0.0944	False		,,,				2504	0.0327				p.14_15del		Atlas-Indel	.											.	PCDHGB4	125	.	1	Deletion - In frame(1)	prostate(1)	c.40_45del						PASS	.		,,,,,,,,,,,	50,3074		6,38,1518					,,,,,,,,,,,	3.7	0.9		dbSNP_134	6	518,6570		64,390,3090	no	coding,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_032098.1,NM_018924.2,NM_018923.2,NM_018922.2,NM_018920.2,NM_018919.2,NM_018918.2,NM_018917.2,NM_018916.3,NM_018915.2,NM_018912.2,NM_003736.2	,,,,,,,,,,,	70,428,4608	A1A1,A1R,RR		7.3081,1.6005,5.5621	,,,,,,,,,,,	,,,,,,,,,,,		568,9644				SO:0001651	inframe_deletion	8641	exon1			.	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.41_46delTGCCAG	5.37:g.140767492_140767497delTGCCAG	ENSP00000428288:p.Pro15_Val16del	Somatic	603	0	0	1658	WXS	Illumina HiSeq	Phase_I	482	60	0.124481	NM_003736	O15099|Q2M267|Q9UN64	In_Frame_Del	DEL	ENST00000519479.1	37	CCDS54928.1																																																																																			.	.	weak		0.617	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
ZNF570	148268	hgsc.bcm.edu	37	19	37976121	37976123	+	In_Frame_Del	DEL	CAC	CAC	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:37976121_37976123delCAC	ENST00000330173.1	+	5	2126_2128	c.1597_1599delCAC	c.(1597-1599)cacdel	p.H533del	CTD-2086O20.3_ENST00000591976.1_lincRNA|ZNF570_ENST00000586475.1_In_Frame_Del_p.H589del|ZNF570_ENST00000388801.3_In_Frame_Del_p.H330del	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	533					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)			cccagtcaatcaccaagtcctat	0.404																																					p.532_533del		Pindel,Atlas-Indel	.											ZNF570,NS,carcinoma,+2,1	ZNF570	58	1	0			c.1596_1598del						PASS	.																																			SO:0001651	inframe_deletion	148268	exon5			.	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.1597_1599delCAC	19.37:g.37976121_37976123delCAC	ENSP00000331540:p.His533del	Somatic	80	.	.		WXS	Illumina HiSeq	Phase_I	81	25	0.309	NM_144694	A1L472|B4DMP1	In_Frame_Del	DEL	ENST00000330173.1	37	CCDS12504.1																																																																																			.	.	none		0.404	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694	
PI4KAP2	375133	hgsc.bcm.edu	37	22	21841122	21841126	+	RNA	DEL	TCTTA	TCTTA	-	rs200598591		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCTTA	TCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21841122_21841126delTCTTA	ENST00000450651.1	-	0	866_870							A4QPH2	PI4P2_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha pseudogene 2						phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(3)|urinary_tract(1)	4						GTCAGGTACTTCTTATCTGAGAACA	0.537																																					.		Atlas-Indel	.											.	PI4KAP2	11	.	0			.						PASS	.																																					375133	.			.			22q11.21	2014-03-20	2007-08-14		ENSG00000183506	ENSG00000183506			33577	pseudogene	pseudogene							Standard	NR_003700		Approved		uc011aie.1	A4QPH2	OTTHUMG00000150827		22.37:g.21841122_21841126delTCTTA		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	177	29	0.163842	.	Q6ICJ0|Q6ZT68|Q8WUK7	RNA	DEL	ENST00000450651.1	37																																																																																				TCTTA|0.738;-|0.262	0.262	strong		0.537	PI4KAP2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334908.1		
GDPD4	220032	hgsc.bcm.edu	37	11	76954788	76954789	+	Frame_Shift_Ins	INS	-	-	A	rs34784710|rs76229203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76954788_76954789insA	ENST00000376217.2	-	12	1441_1442	c.1191_1192insT	c.(1189-1194)aatatcfs	p.I398fs	GDPD4_ENST00000315938.4_Frame_Shift_Ins_p.I398fs			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	398	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						ATTATACTGATATTGTTTTTAG	0.416													A|A|AA|insertion	1272	0.253994	0.0514	0.1916	5008	,	,		16545	0.256		0.3718	False		,,,				2504	0.4489				p.I398fs		Pindel,Atlas-Indel	.											.	GDPD4	49	.	0			c.1192_1193insT						PASS	.			442,3822		29,384,1719						1.2	0.7		dbSNP_126	119	2948,5306		503,1942,1682	no	frameshift	GDPD4	NM_182833.1		532,2326,3401	A1A1,A1R,RR		35.716,10.3659,27.081				3390,9128				SO:0001589	frameshift_variant	220032	exon12			.	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1192dupT	11.37:g.76954789_76954789dupA	ENSP00000365390:p.Ile398fs	Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	92	25	0.272	NM_182833	Q7Z5B0	Frame_Shift_Ins	INS	ENST00000376217.2	37																																																																																				-|0.773;A|0.227	0.227	strong		0.416	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496323	39496325	+	In_Frame_Del	DEL	AAC	AAC	-	rs140936762|rs139292|rs201177427	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39496323_39496325delAAC	ENST00000401756.1	+	2	116_118	c.40_42delAAC	c.(40-42)aacdel	p.N15del	APOBEC3H_ENST00000348946.4_In_Frame_Del_p.N15del|APOBEC3H_ENST00000421988.2_In_Frame_Del_p.N15del|APOBEC3H_ENST00000442487.3_In_Frame_Del_p.N15del	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	15			Missing (decreases protein stability). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					CTTACAGTTTAACAACAAGCGCC	0.532														1590	0.317492	0.3071	0.2795	5008	,	,		17995	0.2579		0.339	False		,,,				2504	0.3978				p.13_14del		Pindel,Atlas-Indel	.											.	APOBEC3H	28	.	0			c.39_41del						PASS	.		,,,	1382,2882		240,902,990					,,,	-1.8	0.2		dbSNP_129	82	2684,5570		426,1832,1869	no	coding,coding,coding,coding	APOBEC3H	NM_181773.3,NM_001166004.1,NM_001166003.1,NM_001166002.1	,,,	666,2734,2859	A1A1,A1R,RR		32.5176,32.4109,32.4812	,,,	,,,		4066,8452				SO:0001651	inframe_deletion	164668	exon2			.	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.40_42delAAC	22.37:g.39496326_39496328delAAC	ENSP00000385741:p.Asn15del	Somatic	172	.	.		WXS	Illumina HiSeq	Phase_I	167	51	0.305	NM_181773	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	In_Frame_Del	DEL	ENST00000401756.1	37	CCDS54530.1																																																																																			AAC|0.696;-|0.304	0.304	strong		0.532	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38482353	38482394	+	In_Frame_Del	DEL	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	-	rs371997714|rs66500630|rs113792005|rs376182024|rs541462698|rs369923129|rs553799224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	TGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38482353_38482394delTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	ENST00000381669.3	-	12	1466_1507	c.1322_1363delTAGCACCCTCGGAGTACTGGGATGGCCAGTCCCGCTCCCGCA	c.(1321-1365)atagcaccctcggagtactgggatggccagtcccgctcccgcacc>acc	p.IAPSEYWDGQSRSR441del	SLC16A8_ENST00000469516.1_5'Flank	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	441					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					CGGCTTGGGGTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTATGGAGTTGCC	0.674														708	0.141374	0.0272	0.2291	5008	,	,		20774	0.0565		0.1918	False		,,,				2504	0.2689				p.441_455del		Pindel	.											.	BAIAP2L2	39	.	0			c.1323_1364del						PASS	.			138,3818		23,92,1863						2.2	0.8		dbSNP_130	20	1131,6525		291,549,2988	no	coding	BAIAP2L2	NM_025045.4		314,641,4851	A1A1,A1R,RR		14.7727,3.4884,10.9283				1269,10343				SO:0001651	inframe_deletion	80115	exon12			.	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1322_1363delTAGCACCCTCGGAGTACTGGGATGGCCAGTCCCGCTCCCGCA	22.37:g.38482353_38482394delTGCGGGAGCGGGACTGGCCATCCCAGTACTCCGAGGGTGCTA	ENSP00000371085:p.Ile441_Arg454del	Somatic	146	.	.		WXS	Illumina HiSeq	Phase_I	64	16	0.250	NM_025045	B0QYE2|Q96BG7	In_Frame_Del	DEL	ENST00000381669.3	37	CCDS43018.1																																																																																			.	.	none		0.674	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
RIMBP3C	150221	hgsc.bcm.edu	37	22	21904075	21904077	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21904075_21904077delCTC	ENST00000433039.1	-	1	1673_1675	c.1189_1191delGAG	c.(1189-1191)gagdel	p.E397del	UBE2L3_ENST00000458578.2_Intron|RIMBP3C_ENST00000331505.5_In_Frame_Del_p.E303del	NM_001128633.1	NP_001122105.1	A6NJZ7	RIM3C_HUMAN	RIMS binding protein 3C	397										large_intestine(1)	1						GCTGCTTGTTCTCCTCTTGCAGG	0.67																																					p.397_398del		Pindel	.											.	RIMBP3C	6	.	0			c.1190_1192del						PASS	.																																			SO:0001651	inframe_deletion	150221	exon1			.		CCDS46669.1	22q11.21	2008-10-21			ENSG00000183246	ENSG00000183246			33892	protein-coding gene	gene with protein product		612701				17855024	Standard	NM_001128633		Approved		uc002zuq.4	A6NJZ7	OTTHUMG00000150825	ENST00000433039.1:c.1189_1191delGAG	22.37:g.21904078_21904080delCTC	ENSP00000390630:p.Glu397del	Somatic	217	.	.		WXS	Illumina HiSeq	Phase_I	214	33	0.154	NM_001128633		In_Frame_Del	DEL	ENST00000433039.1	37	CCDS46669.1																																																																																			.	.	none		0.670	RIMBP3C-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		XM_036942	
CLDN16	10686	hgsc.bcm.edu	37	3	190106073	190106074	+	Frame_Shift_Del	DEL	GG	GG	-	rs386669518|rs3214506	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:190106073_190106074delGG	ENST00000264734.2	+	1	413_414	c.165_166delGG	c.(163-168)agggctfs	p.RA55fs	CLDN16_ENST00000456423.1_Frame_Shift_Del_p.RA55fs|CLDN16_ENST00000468220.1_Intron	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	211	.	.		WXS	Illumina HiSeq	Phase_I	220	58	0.264	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	
DARS	1615	hgsc.bcm.edu	37	2	136690415	136690415	+	Intron	DEL	A	A	-	rs34744196|rs397872816	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:136690415delA	ENST00000264161.4	-	7	720				DARS_ENST00000537273.1_Intron	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	CTTCCTTCCTaaaaaaaaaaa	0.279													|||unknown(HR)	3311	0.661142	0.8411	0.6297	5008	,	,		16104	0.6042		0.4682	False		,,,				2504	0.6973				.		Pindel	.											.	DARS	44	.	0			c.505-2T>-						PASS	.						39.0	46.0	43.0					2																	136690415		2203	4300	6503	SO:0001627	intron_variant	1615	exon8			.	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"""Aminoacyl tRNA synthetases / Class II"""	2678	protein-coding gene	gene with protein product	"""aspartate tRNA ligase 1, cytoplasmic"""	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.505-3T>-	2.37:g.136690415delA		Somatic	34	.	.		WXS	Illumina HiSeq	Phase_I	54	16	0.296	NM_001349	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Splice_Site	DEL	ENST00000264161.4	37	CCDS2180.1																																																																																			A|1.000;|0.000	.	weak		0.279	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349	
ZNF83	55769	hgsc.bcm.edu	37	19	53116934	53117017	+	In_Frame_Del	DEL	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	-	rs78562523|rs573424533|rs561268356|rs575275768|rs542853549|rs7248435|rs201794892|rs557033862|rs144905073|rs560464978|rs199821089|rs201460258|rs542573550|rs201157018|rs199590691|rs556550175|rs367946778|rs146207784|rs200250390|rs7247691|rs7247690|rs113015820|rs75857698|rs78207921|rs140513277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53116934_53117017delCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	ENST00000597597.1	-	2	3054_3137	c.801_884delAAAGGTCTTCCATCATATTTCACACCTTGCACAACATCAGAGAATCCACACTGGAGAGAAACCTTACAAATGTAATGAGTGTGG	c.(799-885)ggaaaggtcttccatcatatttcacaccttgcacaacatcagagaatccacactggagagaaaccttacaaatgtaatgagtgtggc>ggc	p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G	ZNF83_ENST00000391789.4_Splice_Site_p.KV268del|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000301096.3_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000544146.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000545872.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G			P51522	ZNF83_HUMAN	zinc finger protein 83	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		GAAGACCTTGCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTTCCACATACAT	0.405																																					p.268_295del		Pindel	.											.	ZNF83	73	.	0			c.802_885del						PASS	.		,,,,,,,,	1161,3099		263,635,1232					,,,,,,,,	-2.2	0.0			87	1473,6779		168,1137,2821	no	coding,coding-near-splice,coding-near-splice,coding-near-splice,coding-near-splice,coding,coding,coding,coding	ZNF83	NM_018300.3,NM_001242538.1,NM_001242531.1,NM_001105554.1,NM_001105553.1,NM_001105552.1,NM_001105551.1,NM_001105550.1,NM_001105549.1	,,,,,,,,	431,1772,4053	A1A1,A1R,RR		17.8502,27.2535,21.0518	,,,,,,,,	,,,,,,,,		2634,9878				SO:0001651	inframe_deletion	55769	exon5			.	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.801_884delAAAGGTCTTCCATCATATTTCACACCTTGCACAACATCAGAGAATCCACACTGGAGAGAAACCTTACAAATGTAATGAGTGTGG	19.37:g.53116934_53117017delCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	ENSP00000472619:p.Gly267_Cys294del	Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	56	10	0.179	NM_001105551	A8MT75|Q3ZCX0|Q6PI08	In_Frame_Del	DEL	ENST00000597597.1	37	CCDS12854.1																																																																																			.	.	none		0.405	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
ACOT4	122970	hgsc.bcm.edu	37	14	74060512	74060517	+	In_Frame_Del	DEL	AGCTTA	AGCTTA	-	rs74553611|rs80196271|rs562751690|rs79684878|rs77261428|rs77814755|rs375801976|rs77408762	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AGCTTA	AGCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74060512_74060517delAGCTTA	ENST00000326303.4	+	2	818_823	c.564_569delAGCTTA	c.(562-570)ctagcttat>ctt	p.AY189del		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)	p.A189fs*32(2)		endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		CGTTGGCTCTAGCTTATTATAACTTT	0.495																																					p.188_190del		Pindel	.											.	ACOT4	25	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.563_568del						PASS	.																																			SO:0001651	inframe_deletion	122970	exon2			.	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.564_569delAGCTTA	14.37:g.74060512_74060517delAGCTTA	ENSP00000323071:p.Ala189_Tyr190del	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	65	21	0.323	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	In_Frame_Del	DEL	ENST00000326303.4	37	CCDS9817.1																																																																																			.	.	alt		0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376110	113376111	+	In_Frame_Ins	INS	-	-	TGC	rs59601191|rs112313093|rs10606566|rs59990801|rs397990842		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:113376110_113376111insTGC	ENST00000478658.1	-	5	4435_4436	c.4418_4419insGCA	c.(4417-4419)caa>caGCAa	p.1473_1473Q>QQ	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_In_Frame_Ins_p.1473_1473Q>QQ			Q68DE3	K2018_HUMAN	KIAA2018	1473	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgttgctgttgctgctgctg	0.51																																					p.Q1473delinsQQ		Pindel	.											.	KIAA2018	180	.	0			c.4419_4420insGCA						PASS	.																																			SO:0001652	inframe_insertion	205717	exon7			.	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.4416_4418dupGCA	3.37:g.113376117_113376119dupTGC	ENSP00000420721:p.Gln1478dup	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	143	27	0.189	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	In_Frame_Ins	INS	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	alt		0.510	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
DCAF8	50717	hgsc.bcm.edu	37	1	160209874	160209885	+	In_Frame_Del	DEL	CTCTTCTTCCTC	CTCTTCTTCCTC	-	rs570543933|rs144631187|rs199748027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTCTTCTTCCTC	CTCTTCTTCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160209874_160209885delCTCTTCTTCCTC	ENST00000368073.3	-	4	759_770	c.325_336delGAGGAAGAAGAG	c.(325-336)gaggaagaagagdel	p.EEEE109del	DCAF8_ENST00000326837.2_In_Frame_Del_p.EEEE109del|DCAF8_ENST00000368074.1_In_Frame_Del_p.EEEE109del|DCAF8_ENST00000475733.1_In_Frame_Del_p.EEEE109del|DCAF8_ENST00000610139.1_In_Frame_Del_p.EEEE109del|DCAF8_ENST00000608310.1_In_Frame_Del_p.EEEE263del|DCAF8_ENST00000556710.1_In_Frame_Del_p.EEEE263del			Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	109					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(16)|skin(3)|upper_aerodigestive_tract(1)	33						GCCGAGGCTGctcttcttcctcctcttcttcc	0.538														37	0.00738818	0.0015	0.0101	5008	,	,		24370	0.0		0.0278	False		,,,				2504	0.0				p.109_113del		Pindel	.											.	DCAF8	64	.	0			c.326_337del						PASS	.			20,4246		0,20,2113						4.9	1.0			60	205,8049		4,197,3926	no	coding	DCAF8	NM_015726.3		4,217,6039	A1A1,A1R,RR		2.4836,0.4688,1.7971				225,12295				SO:0001651	inframe_deletion	50717	exon4			.	AK093176	CCDS1200.1	1q22-q23	2013-01-09	2009-07-17	2009-07-17	ENSG00000132716	ENSG00000132716		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	24891	protein-coding gene	gene with protein product		615820	"""WD repeat domain 42A"""	WDR42A		11401431	Standard	NM_015726		Approved	H326, FLJ35857	uc010pjb.1	Q5TAQ9	OTTHUMG00000031604	ENST00000368073.3:c.325_336delGAGGAAGAAGAG	1.37:g.160209874_160209885delCTCTTCTTCCTC	ENSP00000357052:p.Glu109_Glu112del	Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	83	24	0.289	NM_015726	D3DVE6|Q12839|Q4QQI6|Q53F14|Q66K50|Q68CS7|Q96E00	In_Frame_Del	DEL	ENST00000368073.3	37	CCDS1200.1																																																																																			CTCTTCTTCCTC|0.992;-|0.008	0.008	strong		0.538	DCAF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077402.2	NM_015726	
AUTS2	26053	hgsc.bcm.edu	37	7	70255576	70255577	+	In_Frame_Ins	INS	-	-	CCA	rs538005366|rs35604576|rs375018695		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:70255576_70255577insCCA	ENST00000342771.4	+	19	3695_3696	c.3374_3375insCCA	c.(3373-3378)agccac>agCCAccac	p.1133_1134insH	AUTS2_ENST00000406775.2_In_Frame_Ins_p.1109_1110insH	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1133	His-rich.									breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CACGACTACAGccaccaccacc	0.678																																					p.S1125delinsSH		Pindel	.											.	AUTS2	173	.	0			c.3374_3375insCCA						PASS	.																																			SO:0001652	inframe_insertion	26053	exon19			.	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3396_3398dupCCA	7.37:g.70255583_70255585dupCCA	ENSP00000344087:p.His1133_His1133dup	Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	63	21	0.333	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	In_Frame_Ins	INS	ENST00000342771.4	37	CCDS5539.1																																																																																			.	.	none		0.678	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
SLC7A7	9056	hgsc.bcm.edu	37	14	23240713	23240714	+	IGR	INS	-	-	AGC	rs397761468|rs57267429|rs148216086|rs200470407|rs36078271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23240713_23240714insAGC	ENST00000397532.3	-	0	2447				OXA1L_ENST00000358043.5_In_Frame_Ins_p.403_403S>SS|OXA1L_ENST00000604262.1_In_Frame_Ins_p.419_419S>SS|OXA1L_ENST00000412791.1_In_Frame_Ins_p.392_392S>SS|SLC7A7_ENST00000554061.1_5'Flank|OXA1L_ENST00000285848.5_In_Frame_Ins_p.479_479S>SS			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7						amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		CCAATATCCCTAGCAGCAGCAG	0.48														1057	0.211062	0.1596	0.2133	5008	,	,		22040	0.1458		0.2396	False		,,,				2504	0.317				p.P478delinsPS		Pindel	.											.	OXA1L	49	.	0			c.1434_1435insAGC						PASS	.			857,3407		86,685,1361						-4.3	0.0		dbSNP_130	182	2307,5947		310,1687,2130	no	coding	OXA1L	NM_005015.3		396,2372,3491	A1A1,A1R,RR		27.9501,20.0985,25.2756				3164,9354				SO:0001628	intergenic_variant	5018	exon10			.	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"""Solute carriers"""	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692		14.37:g.23240720_23240722dupAGC		Somatic	118	.	.		WXS	Illumina HiSeq	Phase_I	131	37	0.282	NM_005015	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	In_Frame_Ins	INS	ENST00000397532.3	37	CCDS9574.1																																																																																			-|0.809;AGC|0.191	0.191	strong		0.480	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3		
ZNF516	9658	hgsc.bcm.edu	37	18	74090958	74090958	+	Frame_Shift_Del	DEL	G	G	-	rs398079646|rs398033573|rs56087742		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:74090958delG	ENST00000443185.2	-	5	3428	c.3111delC	c.(3109-3111)cccfs	p.P1037fs	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1037					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		AGTGTAGGACGGGGGGGCGCC	0.652													GGGGGG|GGGGGGG|GGGGGG|insertion	5008	1.0	1.0	1.0	5008	,	,		13278	1.0		1.0	False		,,,				2504	1.0				p.V1038fs		Pindel	.											.	ZNF516	102	.	0			c.3112delG						PASS	.			3517,17		1755,7,5	7.0	7.0	7.0			-0.6	0.0	18	dbSNP_131	33	7701,27		3846,9,9	no	frameshift	ZNF516	NM_014643.3		5601,16,14	A1A1,A1R,RR		0.3494,0.481,0.3907			74090958	11218,44	1730	3829	5559	SO:0001589	frameshift_variant	9658	exon5			.	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.3111delC	18.37:g.74090958delG	ENSP00000394757:p.Pro1037fs	Somatic	28	.	.		WXS	Illumina HiSeq	Phase_I	29	13	0.448	NM_014643		Frame_Shift_Del	DEL	ENST00000443185.2	37																																																																																				G|0.016;-|0.984	0.984	strong		0.652	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
ZNF233	353355	hgsc.bcm.edu	37	19	44778796	44778799	+	Frame_Shift_Del	DEL	GTTG	GTTG	-	rs59660444|rs76295615|rs2884016|rs386809644|rs386809645|rs2884015|rs75921463	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GTTG	GTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44778796_44778799delGTTG	ENST00000391958.2	+	5	2110_2113	c.1983_1986delGTTG	c.(1981-1986)tcgttgfs	p.SL661fs	ZNF233_ENST00000592581.1_3'UTR|ZNF233_ENST00000334152.1_Frame_Shift_Del_p.SL643fs|ZNF235_ENST00000589799.1_Intron	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	33	.	.		WXS	Illumina HiSeq	Phase_I	28	19	0.679	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	
CNDP1	84735	hgsc.bcm.edu	37	18	72223591	72223592	+	In_Frame_Ins	INS	-	-	TGC	rs10663835|rs60017744|rs67791561	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:72223591_72223592insTGC	ENST00000358821.3	+	2	271_272	c.43_44insTGC	c.(43-45)gtg>gTGCtg	p.20_21insL	CNDP1_ENST00000585136.1_3'UTR|CNDP1_ENST00000582365.1_Intron	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	20			L -> LL. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16046297}.			extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.L20_E21insL(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		CCTGCTGGCTGTGCTGCTGCTG	0.559																																					p.V15delinsVL	Melanoma(32;1029 1042 25286 38395 44237)	Pindel	.											.	CNDP1	98	.	1	Insertion - In frame(1)	kidney(1)	c.43_44insTGC						PASS	.																																			SO:0001652	inframe_insertion	84735	exon2			.		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.56_58dupTGC	18.37:g.72223598_72223600dupTGC	ENSP00000351682:p.Leu20_Leu20dup	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	102	30	0.294	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	In_Frame_Ins	INS	ENST00000358821.3	37	CCDS12007.1																																																																																			-|0.500;TGC|0.500	0.500	strong		0.559	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
OR5P2	120065	hgsc.bcm.edu	37	11	7818383	7818384	+	In_Frame_Ins	INS	-	-	ATATGGTTACCAGGTAGATGC	rs138967151	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7818383_7818384insATATGGTTACCAGGTAGATGC	ENST00000329434.2	-	1	136_137	c.106_107insGCATCTACCTGGTAACCATAT	c.(106-108)tct>tGCATCTACCTGGTAACCATATct	p.35_36insCIYLVTI	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAGATTACCAGATAGGATGATC	0.436														1170	0.233626	0.3404	0.2896	5008	,	,		17899	0.128		0.2763	False		,,,				2504	0.1145				p.S36delinsCIYLVTIS		Pindel	.											.	OR5P2	68	.	0			c.107_108insGCATCTACCTGGTAACCATAT						PASS	.																																			SO:0001652	inframe_insertion	120065	exon1			.	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.106_107insGCATCTACCTGGTAACCATAT	11.37:g.7818383_7818384insATATGGTTACCAGGTAGATGC	ENSP00000331823:p.Leu35_Ser36insCysIleTyrLeuValThrIle	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	40	27	0.675	NM_153444	Q3MIS8	In_Frame_Ins	INS	ENST00000329434.2	37	CCDS7782.1																																																																																			.	.	strong		0.436	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
VILL	50853	hgsc.bcm.edu	37	3	38040434	38040435	+	In_Frame_Ins	INS	-	-	CAC	rs368878844|rs143137431	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:38040434_38040435insCAC	ENST00000283713.6	+	10	1240_1241	c.974_975insCAC	c.(973-978)tacacc>taCACcacc	p.326_327insT	VILL_ENST00000383759.2_In_Frame_Ins_p.326_327insT|VILL_ENST00000465644.1_In_Frame_Ins_p.44_45insT			O15195	VILL_HUMAN	villin-like	326					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.Y325>*(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)		TACCCGACCTACACCAACGTGG	0.663														202	0.0403355	0.0439	0.0231	5008	,	,		10091	0.1032		0.0169	False		,,,				2504	0.0072				p.Y325delinsYT		Pindel	.											.	VILL	61	.	1	Unknown(1)	liver(1)	c.974_975insCAC						PASS	.			175,4075		5,165,1955						2.9	0.9		dbSNP_134	28	108,8124		4,100,4012	no	coding	VILL	NM_015873.3		9,265,5967	A1A1,A1R,RR		1.312,4.1176,2.2673				283,12199				SO:0001652	inframe_insertion	50853	exon9			.		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.975_977dupCAC	3.37:g.38040435_38040437dupCAC	ENSP00000283713:p.Thr326_Thr326dup	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	67	20	0.299	NM_015873	A8MZP1|Q9BT80|Q9BWH7	In_Frame_Ins	INS	ENST00000283713.6	37	CCDS2670.2																																																																																			.	.	strong		0.663	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
DCHS2	54798	hgsc.bcm.edu	37	4	155244402	155244405	+	Intron	DEL	TTTG	TTTG	-	rs199840326|rs140019361		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TTTG	TTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155244402_155244405delTTTG	ENST00000357232.4	-	13	2653				DCHS2_ENST00000339452.1_Frame_Shift_Del_p.NK1365fs	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2						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)		aggtCAGGATtttgtttgtttgtt	0.377																																					p.1366_1367del		Pindel	.											DCHS2_ENST00000339452,caecum,carcinoma,+2,2	DCHS2	594	2	0			c.4096_4099del						PASS	.																																			SO:0001627	intron_variant	54798	exon8			.	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.2654-762CAAA>-	4.37:g.155244410_155244413delTTTG		Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	48	14	0.292	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	37	CCDS3785.1																																																																																			TTTG|0.214;-|0.786	0.786	strong		0.377	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
BEST3	144453	hgsc.bcm.edu	37	12	70088220	70088220	+	Frame_Shift_Del	DEL	T	T	-	rs566733141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:70088220delT	ENST00000330891.5	-	3	403	c.177delA	c.(175-177)aaafs	p.K59fs	BEST3_ENST00000266661.4_Intron|BEST3_ENST00000476098.1_Intron|BEST3_ENST00000533674.1_5'UTR|BEST3_ENST00000393365.1_5'UTR|BEST3_ENST00000331471.4_Frame_Shift_Del_p.K59fs|BEST3_ENST00000553096.1_Intron|BEST3_ENST00000551160.1_5'UTR	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	59					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			CAAAGTAACGTTTTTGGACTC	0.373													TTTTT|TTTTT|TTTT|deletion	53	0.0105831	0.0008	0.0187	5008	,	,		17586	0.0		0.0288	False		,,,				2504	0.0102				p.R60fs		Pindel	.											.	BEST3	129	.	0			c.178delC						PASS	.			3,28,3577		1,0,1,2,24,1776	101.0	94.0	96.0			5.1	1.0	12		98	0,284,7584		0,0,0,8,268,3658	no	codingComplex	BEST3	NM_032735.2		1,0,1,10,292,5434	A1A1,A1A2,A1R,A2A2,A2R,RR		3.6096,0.8592,2.7449			70088220	3,312,11161	1872	4113	5985	SO:0001589	frameshift_variant	144453	exon3			.	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17105	protein-coding gene	gene with protein product		607337	"""vitelliform macular dystrophy 2-like 3"""	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.177delA	12.37:g.70088220delT	ENSP00000332413:p.Lys59fs	Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	80	27	0.338	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Frame_Shift_Del	DEL	ENST00000330891.5	37	CCDS8992.2																																																																																			.	.	none		0.373	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439	
HOXA1	3198	hgsc.bcm.edu	37	7	27135317	27135319	+	In_Frame_Del	DEL	TGG	TGG	-	rs2074398|rs587777901|rs544314279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:27135317_27135319delTGG	ENST00000343060.4	-	1	274_276	c.213_215delCCA	c.(211-216)caccat>cat	p.71_72HH>H	HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOXA1_ENST00000355633.5_In_Frame_Del_p.71_72HH>H|HOTAIRM1_ENST00000425358.2_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	71	Poly-His.				abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ggggtggcgatggtggtggtggt	0.64											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.72_72del		Pindel	.											.	HOXA1	64	.	0			c.214_216del						PASS	.																																			SO:0001651	inframe_deletion	3198	exon1			.		CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.213_215delCCA	7.37:g.27135326_27135328delTGG	ENSP00000343246:p.His72del	Somatic	42	.	.	792	WXS	Illumina HiSeq	Phase_I	61	26	0.426	NM_005522	A4D184|B2R8U7|O43363	In_Frame_Del	DEL	ENST00000343060.4	37	CCDS5401.1																																																																																			.	.	none		0.640	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
RHBG	57127	hgsc.bcm.edu	37	1	156354348	156354348	+	Frame_Shift_Del	DEL	C	C	-	rs11303415	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156354348delC	ENST00000368249.1	+	9	1303	c.1265delC	c.(1264-1266)tccfs	p.S422fs	RHBG_ENST00000255013.3_Frame_Shift_Del_p.S353fs|RHBG_ENST00000400992.2_Frame_Shift_Del_p.S390fs|RHBG_ENST00000368246.2_Splice_Site|RHBG_ENST00000494874.1_Intron	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	422	Interaction with ANK3.				ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)	p.R425fs*>17(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TTTCTGGACTCCCCCCCCAGA	0.632											OREG0013871	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		2118	0.422923	0.6059	0.2925	5008	,	,		18146	0.5446		0.2396	False		,,,				2504	0.3313				p.S422fs		Pindel	.											.	RHBG	133	.	1	Deletion - Frameshift(1)	ovary(1)	c.1264delT						PASS	.						38.0	63.0	55.0					1																	156354348		1930	4140	6070	SO:0001589	frameshift_variant	57127	exon9			.	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.1265delC	1.37:g.156354348delC	ENSP00000357232:p.Ser422fs	Somatic	117	.	.	1777	WXS	Illumina HiSeq	Phase_I	140	43	0.307	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Frame_Shift_Del	DEL	ENST00000368249.1	37																																																																																				-|1.000;|0.000	1.000	strong		0.632	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
TP53BP1	7158	hgsc.bcm.edu	37	15	43739687	43739687	+	Intron	DEL	A	A	-	rs546609337	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43739687delA	ENST00000263801.3	-	13	2954				TP53BP1_ENST00000382044.4_Intron|TP53BP1_ENST00000382039.3_Intron|TP53BP1_ENST00000450115.2_Intron|TP53BP1_ENST00000605155.1_Intron	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1						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)		GGGGTTTCTGaaaaaaaaaaa	0.308								Other conserved DNA damage response genes																													.		Pindel	.											.	.	.	.	0			.						PASS	.						32.0	34.0	34.0					15																	43739687		2199	4297	6496	SO:0001627	intron_variant	100873756	.			.	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.2702-4T>-	15.37:g.43739687delA		Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	61	10	0.164	.	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	RNA	DEL	ENST00000263801.3	37	CCDS10096.1																																																																																			.	.	none		0.308	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
HMGN2P46	283651	hgsc.bcm.edu	37	15	45848231	45848231	+	lincRNA	DEL	T	T	-	rs372861121|rs368577527		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:45848231delT	ENST00000557965.1	+	0	0				HMGN2P46_ENST00000409454.1_RNA																							TTTGTTTAGCTTTTTTTTTTT	0.323																																					.		Pindel	.											.	.	.	.	0			.						PASS	.																																					283651	.			.																													15.37:g.45848231delT		Somatic	36	.	.		WXS	Illumina HiSeq	Phase_I	41	10	0.244	.		RNA	DEL	ENST00000557965.1	37																																																																																				.	.	weak		0.323	RP11-96O20.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000416553.1		
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38483155	38483156	+	In_Frame_Ins	INS	-	-	TCATGGGTG	rs132924|rs142739979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38483155_38483156insTCATGGGTG	ENST00000381669.3	-	11	1378_1379	c.1234_1235insCACCCATGA	c.(1234-1236)aac>aCACCCATGAac	p.411_412insTPM	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	411				M -> MTPM (in Ref. 3; AAH15619). {ECO:0000305}.	filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					GTTCCCggggttcatgggtgtc	0.653														1505	0.300519	0.2814	0.3602	5008	,	,		13633	0.1796		0.3529	False		,,,				2504	0.3548				p.N412delinsTPMN		Pindel	.											BAIAP2L2,NS,carcinoma,0,4	BAIAP2L2	39	4	0			c.1235_1236insCACCCATGA						PASS	.			1032,2628		159,714,957						-3.7	0.0		dbSNP_130	29	2800,5058		480,1840,1609	no	coding	BAIAP2L2	NM_025045.4		639,2554,2566	A1A1,A1R,RR		35.6325,28.1967,33.2697				3832,7686				SO:0001652	inframe_insertion	80115	exon11			.	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1226_1234dupCACCCATGA	22.37:g.38483156_38483164dupTCATGGGTG	ENSP00000371085:p.Thr409_Met411dup	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	68	21	0.309	NM_025045	B0QYE2|Q96BG7	In_Frame_Ins	INS	ENST00000381669.3	37	CCDS43018.1																																																																																			.	.	strong		0.653	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
LIMK2	3985	hgsc.bcm.edu	37	22	31672776	31672777	+	Intron	INS	-	-	C	rs540206607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31672776_31672777insC	ENST00000331728.4	+	15	1886				LIMK2_ENST00000406516.1_Splice_Site_p.A514fs|LIMK2_ENST00000444929.2_Intron|LIMK2_ENST00000340552.4_Splice_Site_p.A571fs|LIMK2_ENST00000333611.4_Intron|LIMK2_ENST00000467301.1_Intron	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2						phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						TACTTTCAGAGCCCCCCCCGGG	0.733													?|CCCCCCCC|CCCCCCCCC|unsure	14	0.00279553	0.0023	0.0	5008	,	,		7875	0.006		0.002	False		,,,				2504	0.0031				p.A571fs		Pindel	.											.	LIMK2	101	.	0			c.1711_1712insC						PASS	.																																			SO:0001627	intron_variant	3985	exon15			.	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1772+1482->C	22.37:g.31672784_31672784dupC		Somatic	71	.	.		WXS	Illumina HiSeq	Phase_I	70	23	0.329	NM_001031801	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Frame_Shift_Ins	INS	ENST00000331728.4	37	CCDS13891.1																																																																																			.	.	none		0.733	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133954074	133954151	+	Splice_Site	DEL	CTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG	CTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG	-	rs111390655|rs376494575|rs186558312|rs377397710|rs9733324|rs373132662|rs375807579|rs531085140|rs370170942|rs565380893	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG	CTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:133954074_133954151delCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG	ENST00000298622.4	+	9	1602_1611	c.1464_1473delCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG	c.(1462-1473)gacttggaggag>ga	p.DLEE488del		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	488						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)		CGGACGATGACTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAG	0.644														1120	0.223642	0.2284	0.2363	5008	,	,		23752	0.3056		0.1899	False		,,,				2504	0.1585				p.488_491del		Pindel	.											.	JAKMIP3	69	.	0			c.1463_1473del						PASS	.																																			SO:0001630	splice_region_variant	282973	exon9			.	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.1473+1CTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG>-	10.37:g.133954074_133954151delCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGGCTTGGAGGAGGTAACGAGGGTCTCCTGCCGGGTCCTGGG		Somatic	53	.	.		WXS	Illumina HiSeq	Phase_I	56	17	0.304	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Frame_Shift_Del	DEL	ENST00000298622.4	37	CCDS44494.1																																																																																			.	.	none		0.644	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	In_Frame_Del
DNAH2	146754	hgsc.bcm.edu	37	17	7722365	7722365	+	Missense_Mutation	SNP	C	C	T	rs7213894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7722365C>T	ENST00000572933.1	+	71	12259	c.10799C>T	c.(10798-10800)aCt>aTt	p.T3600I	DNAH2_ENST00000389173.2_Missense_Mutation_p.T3600I			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3600			T -> I (in dbSNP:rs7213894).		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)				GAGATCAACACTGACTTGGCG	0.592													T|||	3060	0.611022	0.7905	0.5418	5008	,	,		19035	0.3522		0.6064	False		,,,				2504	0.6892				p.T3600I		Atlas-SNP	.											.	DNAH2	498	.	0			c.C10799T						PASS	.	T	ILE/THR	3311,1095	386.5+/-326.1	1259,793,151	55.0	48.0	51.0		10799	4.1	0.8	17	dbSNP_116	51	5141,3459	500.4+/-375.2	1552,2037,711	yes	missense	DNAH2	NM_020877.2	89	2811,2830,862	TT,TC,CC		40.2209,24.8525,35.0146	benign	3600/4428	7722365	8452,4554	2203	4300	6503	SO:0001583	missense	146754	exon70			TCAACACTGACTT	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.10799C>T	17.37:g.7722365C>T	ENSP00000458355:p.Thr3600Ile	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	1285	0.5883699633699634	384	0.7804878048780488	212	0.585635359116022	220	0.38461538461538464	469	0.6187335092348285	T	0.019	-1.459140	0.01062	0.751475	0.597791	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.24151	1.87	4.07	4.07	0.47477	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00001	-3.685	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42172	-0.9467	9	0.02654	T	1	.	7.3461	0.26664	0.0:0.1034:0.0:0.8966	rs7213894;rs17733464;rs60464786;rs7213894	3561;3600	Q9P225-2;Q9P225	.;DYH2_HUMAN	I	3561;3600	ENSP00000373825:T3600I	ENSP00000353818:T3561I	T	+	2	0	DNAH2	7663090	1.000000	0.71417	0.753000	0.31225	0.162000	0.22319	5.350000	0.66016	0.616000	0.30141	-0.521000	0.04368	ACT	C|0.377;N|0.000	.	strong		0.592	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
TJP3	27134	hgsc.bcm.edu	37	19	3750622	3750622	+	Silent	SNP	A	A	C	rs1046271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3750622A>C	ENST00000541714.2	+	21	3162	c.2700A>C	c.(2698-2700)gtA>gtC	p.V900V	TJP3_ENST00000587641.1_3'UTR|TJP3_ENST00000262968.9_Silent_p.V933V|TJP3_ENST00000589378.1_Silent_p.V909V|TJP3_ENST00000587686.1_Silent_p.V919V|TJP3_ENST00000382008.3_Silent_p.V914V|TJP3_ENST00000539908.2_Silent_p.V864V	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	900					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)		TTATGCGAGTACATGATGCGG	0.547													C|||	2986	0.596246	0.5212	0.7075	5008	,	,		17006	0.6409		0.5636	False		,,,				2504	0.6063				p.V909V		Atlas-SNP	.											.	TJP3	79	.	0			c.A2727C						PASS	.	C		2374,2032	551.2+/-378.2	627,1120,456	75.0	67.0	70.0		2799	-0.9	0.0	19	dbSNP_86	70	4772,3824	523.4+/-380.3	1303,2166,829	no	coding-synonymous	TJP3	NM_014428.1		1930,3286,1285	CC,CA,AA		44.4858,46.1189,45.0392		933/953	3750622	7146,5856	2203	4298	6501	SO:0001819	synonymous_variant	27134	exon21			GCGAGTACATGAT	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.2700A>C	19.37:g.3750622A>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			A|0.434;C|0.566	0.566	strong		0.547	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
DNAJC30	84277	hgsc.bcm.edu	37	7	73097238	73097238	+	Silent	SNP	G	G	A	rs1569062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:73097238G>A	ENST00000395176.2	-	1	545	c.516C>T	c.(514-516)taC>taT	p.Y172Y	WBSCR22_ENST00000423497.1_5'Flank|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000265758.2_5'Flank	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	172						mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						GTTGTTCCCCGTAGTGGGCCT	0.672													G|||	1163	0.232228	0.0325	0.3473	5008	,	,		12916	0.1746		0.337	False		,,,				2504	0.3722				p.Y172Y		Atlas-SNP	.											.	DNAJC30	12	.	0			c.C516T						PASS	.	G		361,4045	174.4+/-204.0	19,323,1861	32.0	33.0	33.0		516	2.1	1.0	7	dbSNP_88	33	2907,5693	430.2+/-356.4	509,1889,1902	no	coding-synonymous	DNAJC30	NM_032317.2		528,2212,3763	AA,AG,GG		33.8023,8.1934,25.1269		172/227	73097238	3268,9738	2203	4300	6503	SO:0001819	synonymous_variant	84277	exon1			TTCCCCGTAGTGG	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.516C>T	7.37:g.73097238G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_032317	Q9BSG8	Silent	SNP	ENST00000395176.2	37	CCDS5556.1																																																																																			G|0.763;A|0.237	0.237	strong		0.672	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2		
POLQ	10721	hgsc.bcm.edu	37	3	121208833	121208833	+	Missense_Mutation	SNP	G	G	C	rs3218649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:121208833G>C	ENST00000264233.5	-	16	3073	c.2945C>G	c.(2944-2946)aCa>aGa	p.T982R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	982				T -> R (in Ref. 2; AAR08421). {ECO:0000305}.	ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		AATGGAACATGTCTGATGTTC	0.353								DNA polymerases (catalytic subunits)					C|||	3488	0.696486	0.5424	0.634	5008	,	,		395	0.876		0.6143	False		,,,				2504	0.8487				p.T982R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C2945G						PASS	.	C	ARG/THR	2431,1971	528.9+/-372.5	683,1065,453	51.0	53.0	53.0		2945	-3.9	0.0	3	dbSNP_106	53	5405,3193	476.3+/-369.4	1707,1991,601	yes	missense	POLQ	NM_199420.3	71	2390,3056,1054	CC,CG,GG		37.1365,44.7751,39.7231	benign	982/2591	121208833	7836,5164	2201	4299	6500	SO:0001583	missense	10721	exon16			GAACATGTCTGAT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.2945C>G	3.37:g.121208833G>C	ENSP00000264233:p.Thr982Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	1454	0.6657509157509157	257	0.5223577235772358	226	0.6243093922651933	510	0.8916083916083916	461	0.6081794195250659	C	0.020	-1.438016	0.01098	0.552249	0.628635	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.48201	0.82	4.99	-3.86	0.04230	.	1.969910	0.02087	N	0.052835	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26916	-1.0089	9	0.15499	T	0.54	.	8.791	0.34850	0.1538:0.139:0.6117:0.0955	rs3218649;rs3772125;rs52789693;rs59762555;rs3218649	982;154	O75417;O75417-2	DPOLQ_HUMAN;.	R	605;982;1118	ENSP00000264233:T982R	ENSP00000264233:T982R	T	-	2	0	POLQ	122691523	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-2.240000	0.01197	-1.432000	0.01979	-0.986000	0.02555	ACA	G|0.377;C|0.623	0.623	strong		0.353	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
ZNF644	84146	hgsc.bcm.edu	37	1	91404352	91404352	+	Silent	SNP	A	A	G	rs149082287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:91404352A>G	ENST00000370440.1	-	3	2776	c.2559T>C	c.(2557-2559)taT>taC	p.Y853Y	ZNF644_ENST00000337393.5_Silent_p.Y853Y|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	853					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(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		CTTCTGTTTCATAACTATCTT	0.363																																					p.Y853Y		Atlas-SNP	.											.	ZNF644	120	.	0			c.T2559C						PASS	.	A	,,	0,4406		0,0,2203	77.0	80.0	79.0		,,2559	2.0	1.0	1	dbSNP_134	79	4,8594	3.7+/-12.6	0,4,4295	no	intron,intron,coding-synonymous	ZNF644	NM_016620.3,NM_032186.4,NM_201269.2	,,	0,4,6498	GG,GA,AA		0.0465,0.0,0.0308	,,	,,853/1328	91404352	4,13000	2203	4299	6502	SO:0001819	synonymous_variant	84146	exon3			TGTTTCATAACTA	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.2559T>C	1.37:g.91404352A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	37	CCDS731.1																																																																																			A|0.999;G|0.001	0.001	strong		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186	
ZNF18	7566	hgsc.bcm.edu	37	17	11881356	11881356	+	Missense_Mutation	SNP	G	G	A	rs117755721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:11881356G>A	ENST00000322748.3	-	9	2172	c.1568C>T	c.(1567-1569)tCg>tTg	p.S523L	ZNF18_ENST00000454073.3_Missense_Mutation_p.S522L|ZNF18_ENST00000580306.2_Missense_Mutation_p.S523L|RP11-1096G20.5_ENST00000580270.1_RNA	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	523					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(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		CCCACAGTGCGAACATTTATA	0.403													G|||	34	0.00678914	0.0015	0.0101	5008	,	,		16423	0.0		0.0229	False		,,,				2504	0.002				p.S523L		Atlas-SNP	.											.	ZNF18	42	.	0			c.C1568T						PASS	.	G	LEU/SER	28,4378	33.5+/-64.1	0,28,2175	115.0	115.0	115.0		1568	4.9	0.0	17	dbSNP_132	115	221,8379	91.9+/-153.9	6,209,4085	yes	missense	ZNF18	NM_144680.2	145	6,237,6260	AA,AG,GG		2.5698,0.6355,1.9145	benign	523/550	11881356	249,12757	2203	4300	6503	SO:0001583	missense	7566	exon9			CAGTGCGAACATT	X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12969	protein-coding gene	gene with protein product		194524	"""zinc finger protein 18 (KOX 11)"""			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.1568C>T	17.37:g.11881356G>A	ENSP00000315664:p.Ser523Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Missense_Mutation	SNP	ENST00000322748.3	37	CCDS32568.1	25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	20	0.026385224274406333	G	9.459	1.092567	0.20471	0.006355	0.025698	ENSG00000154957	ENST00000454073;ENST00000322748	T	0.07567	3.18	5.89	4.91	0.64330	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.647764	0.14479	N	0.317053	T	0.03136	0.0092	L	0.48986	1.54	0.09310	N	1	P;P	0.49090	0.901;0.919	B;B	0.38655	0.182;0.278	T	0.10405	-1.0631	10	0.66056	D	0.02	-2.5706	14.1445	0.65341	0.0:0.0:0.849:0.151	.	522;523	P17022-2;P17022	.;ZNF18_HUMAN	L	523	ENSP00000315664:S523L	ENSP00000315664:S523L	S	-	2	0	ZNF18	11822081	0.000000	0.05858	0.005000	0.12908	0.667000	0.39255	0.211000	0.17474	1.468000	0.48064	0.551000	0.68910	TCG	G|0.982;A|0.018	0.018	strong		0.403	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596	
EIF4G1	1981	hgsc.bcm.edu	37	3	184049807	184049807	+	Silent	SNP	C	C	T	rs11559218	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184049807C>T	ENST00000346169.2	+	32	4822	c.4551C>T	c.(4549-4551)gaC>gaT	p.D1517D	EIF4G1_ENST00000427845.1_Silent_p.D1431D|EIF4G1_ENST00000424196.1_Silent_p.D1524D|EIF4G1_ENST00000414031.1_Silent_p.D1477D|EIF4G1_ENST00000435046.2_Silent_p.D1321D|EIF4G1_ENST00000350481.5_Silent_p.D1353D|EIF4G1_ENST00000382330.3_Silent_p.D1524D|EIF4G1_ENST00000411531.1_Silent_p.D1478D|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Silent_p.D1354D|EIF4G1_ENST00000434061.2_Silent_p.D1322D|EIF4G1_ENST00000352767.3_Silent_p.D1524D|EIF4G1_ENST00000342981.4_Silent_p.D1518D|EIF4G1_ENST00000392537.2_Silent_p.D1430D|EIF4G1_ENST00000319274.6_Silent_p.D1517D	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1517	EIF4A-binding.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				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)			ACCTGTGTGACGAGCAGAAGG	0.587													C|||	12	0.00239617	0.0	0.0072	5008	,	,		20060	0.0		0.006	False		,,,				2504	0.001				p.D1524D		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C4572T						PASS	.	C	,,,,,,	9,4397	15.5+/-35.6	0,9,2194	64.0	61.0	62.0		4572,4572,3966,4554,4551,4059,4290	-9.6	0.7	3	dbSNP_120	62	69,8531	42.2+/-99.7	0,69,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	,,,,,,	0,78,6425	TT,TC,CC		0.8023,0.2043,0.5997	,,,,,,	1524/1607,1524/1607,1322/1405,1518/1601,1517/1600,1353/1436,1430/1513	184049807	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1981	exon33			GTGTGACGAGCAG	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.4551C>T	3.37:g.184049807C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			C|0.995;T|0.005	0.005	strong		0.587	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
SPTBN2	6712	hgsc.bcm.edu	37	11	66460527	66460527	+	Silent	SNP	C	C	T	rs639938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66460527C>T	ENST00000533211.1	-	25	5230	c.4899G>A	c.(4897-4899)ctG>ctA	p.L1633L	SPTBN2_ENST00000529997.1_Silent_p.L1633L|SPTBN2_ENST00000309996.2_Silent_p.L1633L			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1633					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GGGCTTGCTCCAGCACCTGGT	0.642													C|||	389	0.0776757	0.056	0.0562	5008	,	,		19218	0.1329		0.0567	False		,,,				2504	0.0869				p.L1633L		Atlas-SNP	.											.	SPTBN2	188	.	0			c.G4899A						PASS	.	C		224,4176	132.1+/-168.6	4,216,1980	91.0	84.0	86.0		4899	1.6	0.8	11	dbSNP_83	86	429,8161	132.0+/-189.7	13,403,3879	no	coding-synonymous	SPTBN2	NM_006946.2		17,619,5859	TT,TC,CC		4.9942,5.0909,5.0269		1633/2391	66460527	653,12337	2200	4295	6495	SO:0001819	synonymous_variant	6712	exon24			TTGCTCCAGCACC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4899G>A	11.37:g.66460527C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			C|0.938;T|0.062	0.062	strong		0.642	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
CHMP6	79643	hgsc.bcm.edu	37	17	78968837	78968837	+	Silent	SNP	C	C	A	rs146625286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78968837C>A	ENST00000325167.5	+	3	270	c.192C>A	c.(190-192)ctC>ctA	p.L64L		NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	64					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)			AGCTGCTGCTCAAGAAGAAGC	0.687													C|||	7	0.00139776	0.0	0.0058	5008	,	,		10104	0.0		0.003	False		,,,				2504	0.0				p.L64L		Atlas-SNP	.											.	CHMP6	16	.	0			c.C192A						PASS	.	C		1,4383		0,1,2191	34.0	33.0	34.0		192	-0.4	1.0	17	dbSNP_134	34	10,8570		0,10,4280	no	coding-synonymous	CHMP6	NM_024591.4		0,11,6471	AA,AC,CC		0.1166,0.0228,0.0849		64/202	78968837	11,12953	2192	4290	6482	SO:0001819	synonymous_variant	79643	exon3			GCTGCTCAAGAAG	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.192C>A	17.37:g.78968837C>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.999;A|0.001	0.001	strong		0.687	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591	
PSPH	5723	hgsc.bcm.edu	37	7	56088811	56088811	+	Missense_Mutation	SNP	T	T	C	rs78599516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	189	0	0		WXS	Illumina HiSeq	Phase_I	195	31	0.158974	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	
SHISA3	152573	hgsc.bcm.edu	37	4	42400112	42400112	+	Missense_Mutation	SNP	G	G	T	rs11733156	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:42400112G>T	ENST00000319234.4	+	1	257	c.39G>T	c.(37-39)tgG>tgT	p.W13C		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	13			W -> C (in dbSNP:rs11733156). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						TCCTTGGCTGGCTGCGCTGGG	0.706													G|||	1027	0.205072	0.2231	0.281	5008	,	,		14398	0.1339		0.2306	False		,,,				2504	0.1738				p.W13C		Atlas-SNP	.											.	SHISA3	27	.	0			c.G39T						PASS	.	G	CYS/TRP	1029,3285		140,749,1268	8.0	9.0	9.0		39	4.4	1.0	4	dbSNP_120	9	2011,6359		280,1451,2454	no	missense	SHISA3	NM_001080505.1	215	420,2200,3722	TT,TG,GG		24.0263,23.8526,23.9672	benign	13/239	42400112	3040,9644	2157	4185	6342	SO:0001583	missense	152573	exon1			TGGCTGGCTGCGC	BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"""Shisa homologs"""	25159	protein-coding gene	gene with protein product			"""shisa homolog 3 (Xenopus laevis)"""				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.39G>T	4.37:g.42400112G>T	ENSP00000326445:p.Trp13Cys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_001080505	A0PJX3|Q96EQ5	Missense_Mutation	SNP	ENST00000319234.4	37	CCDS33979.1	430	0.19688644688644688	91	0.18495934959349594	95	0.26243093922651933	67	0.11713286713286714	177	0.23350923482849603	G	12.01	1.809960	0.31961	0.238526	0.240263	ENSG00000178343	ENST00000319234	T	0.42900	0.96	4.38	4.38	0.52667	.	0.492839	0.19949	N	0.102464	T	0.00012	0.0000	N	0.14661	0.345	0.25425	P	0.9882369	B	0.27732	0.187	B	0.26614	0.071	T	0.16660	-1.0395	9	0.51188	T	0.08	-2.9601	11.1392	0.48392	0.0:0.0:0.8152:0.1848	rs11733156;rs59183676	13	A0PJX4	SHSA3_HUMAN	C	13	ENSP00000326445:W13C	ENSP00000326445:W13C	W	+	3	0	SHISA3	42094869	1.000000	0.71417	0.996000	0.52242	0.684000	0.39900	1.787000	0.38704	2.247000	0.74100	0.467000	0.42956	TGG	G|0.801;T|0.199	0.199	strong		0.706	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505	
OR6C70	390327	hgsc.bcm.edu	37	12	55863398	55863398	+	Silent	SNP	G	G	A	rs12313730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:55863398G>A	ENST00000327335.4	-	1	524	c.525C>T	c.(523-525)ttC>ttT	p.F175F	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	175						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)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						TGTCACAAATGAAATGATCAA	0.348													G|||	806	0.160942	0.0189	0.2291	5008	,	,		21963	0.0665		0.3131	False		,,,				2504	0.2454				p.F175F		Atlas-SNP	.											.	OR6C70	35	.	0			c.C525T						PASS	.	G		263,4143	146.1+/-180.8	4,255,1944	94.0	97.0	96.0		525	-1.0	0.1	12	dbSNP_120	96	2551,6049	412.8+/-350.9	384,1783,2133	no	coding-synonymous	OR6C70	NM_001005499.1		388,2038,4077	AA,AG,GG		29.6628,5.9691,21.6362		175/313	55863398	2814,10192	2203	4300	6503	SO:0001819	synonymous_variant	390327	exon1			ACAAATGAAATGA		CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"""GPCR / Class A : Olfactory receptors"""	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.525C>T	12.37:g.55863398G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_001005499		Silent	SNP	ENST00000327335.4	37	CCDS31825.1																																																																																			G|0.814;A|0.186	0.186	strong		0.348	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1		
PCDHB14	56122	hgsc.bcm.edu	37	5	140605445	140605445	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140605445C>T	ENST00000239449.4	+	1	2368	c.2368C>T	c.(2368-2370)Cga>Tga	p.R790*	PCDHB14_ENST00000515856.2_Nonsense_Mutation_p.R637*	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	790					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.R790*(2)		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)			CGAGAACTTTCGAAATAGCTT	0.343																																					p.R790X	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											PCDHB14,NS,carcinoma,0,5	PCDHB14	132	5	2	Substitution - Nonsense(2)	large_intestine(1)|prostate(1)	c.C2368T						scavenged	.						66.0	73.0	71.0					5																	140605445		2203	4300	6503	SO:0001587	stop_gained	56122	exon1			AACTTTCGAAATA	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.2368C>T	5.37:g.140605445C>T	ENSP00000239449:p.Arg790*	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Nonsense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	-	19.03	3.748491	0.69533	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	.	.	.	4.07	-0.837	0.10766	.	.	.	.	.	.	.	.	.	.	.	0.31292	N	0.689291	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.2849	0.37751	0.2957:0.5843:0.12:0.0	.	.	.	.	X	637;790	.	ENSP00000239449:R790X	R	+	1	2	PCDHB14	140585629	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-1.168000	0.03123	-0.071000	0.12886	0.585000	0.79938	CGA	.	.	none		0.343	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
NASP	4678	hgsc.bcm.edu	37	1	46073489	46073489	+	Silent	SNP	G	G	A	rs2230657	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46073489G>A	ENST00000350030.3	+	6	993	c.906G>A	c.(904-906)ccG>ccA	p.P302P	NASP_ENST00000402363.3_Silent_p.P304P|NASP_ENST00000351223.3_Intron|NASP_ENST00000537798.1_Silent_p.P238P|NASP_ENST00000372052.4_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	302	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					CTTTAGACCCGACAGTCAAGC	0.522													G|||	2872	0.573482	0.6831	0.5346	5008	,	,		17281	0.6329		0.4861	False		,,,				2504	0.4816				p.P302P		Atlas-SNP	.											NASP,colon,carcinoma,0,1	NASP	77	1	0			c.G906A						PASS	.	G	,,	2933,1473	672.8+/-402.7	988,957,258	46.0	47.0	47.0		714,906,	-8.8	0.0	1	dbSNP_98	47	4098,4502	556.7+/-386.9	986,2126,1188	no	coding-synonymous,coding-synonymous,intron	NASP	NM_001195193.1,NM_002482.3,NM_152298.3	,,	1974,3083,1446	AA,AG,GG		47.6512,33.4317,45.9403	,,	238/725,302/789,	46073489	7031,5975	2203	4300	6503	SO:0001819	synonymous_variant	4678	exon6			AGACCCGACAGTC	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.906G>A	1.37:g.46073489G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Silent	SNP	ENST00000350030.3	37	CCDS524.1																																																																																			G|0.444;A|0.556	0.556	strong		0.522	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
BTNL8	79908	hgsc.bcm.edu	37	5	180374534	180374534	+	Silent	SNP	G	G	A	rs3733756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180374534G>A	ENST00000340184.4	+	4	902	c.696G>A	c.(694-696)tcG>tcA	p.S232S	BTNL8_ENST00000400707.3_Silent_p.S107S|BTNL8_ENST00000511704.1_Silent_p.S116S|BTNL8_ENST00000533815.2_Silent_p.S48S|BTNL8_ENST00000508408.1_Silent_p.S232S|BTNL8_ENST00000231229.4_Silent_p.S232S|BTNL8_ENST00000505126.1_Silent_p.S25S	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	232					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.S232S(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCCTATATCGTGGCACCTGG	0.398													A|||	2208	0.440895	0.6641	0.4496	5008	,	,		19003	0.3462		0.4036	False		,,,				2504	0.2689				p.S232S		Atlas-SNP	.											BTNL8_ENST00000340184,NS,carcinoma,0,2	BTNL8	114	2	2	Substitution - coding silent(2)	prostate(2)	c.G696A						PASS	.	A	,,,,,	2840,1566	490.4+/-361.8	924,992,287	216.0	230.0	225.0		696,348,696,321,144,696	-1.3	0.0	5	dbSNP_107	225	3469,5123	636.0+/-399.0	705,2059,1532	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	,,,,,	1629,3051,1819	AA,AG,GG		40.3748,35.5424,48.5382	,,,,,	232/501,116/385,232/341,107/376,48/317,232/348	180374534	6309,6689	2203	4296	6499	SO:0001819	synonymous_variant	79908	exon4			TATATCGTGGCAC	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.696G>A	5.37:g.180374534G>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	242	99	0.409091	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Silent	SNP	ENST00000340184.4	37	CCDS43413.1																																																																																			G|0.508;A|0.492	0.492	strong		0.398	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
POM121	9883	hgsc.bcm.edu	37	7	72413243	72413243	+	Missense_Mutation	SNP	A	A	C	rs437678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:72413243A>C	ENST00000434423.2	+	11	2711	c.2711A>C	c.(2710-2712)cAc>cCc	p.H904P	POM121_ENST00000446813.1_Missense_Mutation_p.H639P|POM121_ENST00000358357.3_Missense_Mutation_p.H639P|POM121_ENST00000257622.4_Missense_Mutation_p.H639P|POM121_ENST00000395270.1_Missense_Mutation_p.H639P			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	904	Pore side. {ECO:0000255}.|Thr-rich.			H -> P (in Ref. 3; BAB14097). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.H639P(6)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CAGTCCCTGCACACTGCCGTG	0.647																																					p.H639P		Atlas-SNP	.											POM121_ENST00000395270,NS,carcinoma,0,6	POM121	131	6	6	Substitution - Missense(6)	prostate(6)	c.A1916C						scavenged	.						88.0	107.0	101.0					7																	72413243		2117	4262	6379	SO:0001583	missense	9883	exon11			CCCTGCACACTGC	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.2711A>C	7.37:g.72413243A>C	ENSP00000405562:p.His904Pro	Somatic	456	0	0		WXS	Illumina HiSeq	Phase_I	370	5	0.0135135	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	C	0.003	-2.495477	0.00159	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.04454	3.62;3.62;3.62;3.62;3.87	1.77	1.77	0.24775	.	0.328471	0.18142	N	0.150374	T	0.00815	0.0027	N	0.00063	-2.32	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41124	-0.9526	9	0.02654	T	1	.	7.4894	0.27452	0.2589:0.7411:0.0:0.0	.	639;904	A8MXF9;Q96HA1	.;P121A_HUMAN	P	639;639;639;639;904	ENSP00000393020:H639P;ENSP00000257622:H639P;ENSP00000378687:H639P;ENSP00000351124:H639P;ENSP00000405562:H904P	ENSP00000257622:H639P	H	+	2	0	POM121	72051179	0.000000	0.05858	0.008000	0.14137	0.223000	0.24884	0.580000	0.23803	0.325000	0.23359	-1.203000	0.01651	CAC	A|0.500;C|0.500	0.500	strong		0.647	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
CYP2C9	1559	hgsc.bcm.edu	37	10	96701987	96701987	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:96701987C>T	ENST00000260682.6	+	3	382	c.370C>T	c.(370-372)Cgg>Tgg	p.R124W	CYP2C9_ENST00000461906.1_3'UTR	NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	124					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	GAAGGAGATCCGGCGTTTCTC	0.507																																					p.R124W	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											CYP2C9,right_upper_lobe,carcinoma,-1,1	CYP2C9	82	1	0			c.C370T						scavenged	.						121.0	113.0	116.0					10																	96701987		2203	4300	6503	SO:0001583	missense	1559	exon3			GAGATCCGGCGTT	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.370C>T	10.37:g.96701987C>T	ENSP00000260682:p.Arg124Trp	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	239	4	0.0167364	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	.	17.20	3.329585	0.60743	.	.	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.42513	0.97	3.34	-1.71	0.08133	.	0.000000	0.64402	U	0.000010	T	0.68384	0.2995	H	0.98068	4.14	0.19775	N	0.999957	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.973;0.973;0.995	T	0.59332	-0.7474	10	0.87932	D	0	.	3.6412	0.08168	0.5014:0.2764:0.0:0.2222	.	124;124;124	Q5VX92;P11712;Q8WW80	.;CP2C9_HUMAN;.	W	124	ENSP00000260682:R124W	ENSP00000260682:R124W	R	+	1	2	CYP2C9	96691977	0.000000	0.05858	0.001000	0.08648	0.678000	0.39670	-0.347000	0.07750	-0.514000	0.06488	0.484000	0.47621	CGG	.	.	none		0.507	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
SIM2	6493	hgsc.bcm.edu	37	21	38081480	38081480	+	Missense_Mutation	SNP	C	C	T	rs116988298	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:38081480C>T	ENST00000290399.6	+	2	801	c.188C>T	c.(187-189)gCg>gTg	p.A63V	SIM2_ENST00000460783.1_3'UTR|SIM2_ENST00000430056.3_Missense_Mutation_p.A63V	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	63					cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						TTAGGAGACGCGTGGGGACAG	0.701													C|||	78	0.0155751	0.0023	0.0202	5008	,	,		11078	0.0		0.0567	False		,,,				2504	0.0041				p.A63V		Atlas-SNP	.											.	SIM2	55	.	0			c.C188T						PASS	.	C	VAL/ALA,VAL/ALA	49,4343		1,47,2148	21.0	23.0	22.0		188,188	5.3	1.0	21	dbSNP_132	22	497,8091		18,461,3815	yes	missense,missense	SIM2	NM_005069.3,NM_009586.2	64,64	19,508,5963	TT,TC,CC		5.7871,1.1157,4.2065	benign,benign	63/668,63/571	38081480	546,12434	2196	4294	6490	SO:0001583	missense	6493	exon2			GAGACGCGTGGGG		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.188C>T	21.37:g.38081480C>T	ENSP00000290399:p.Ala63Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	37	CCDS13646.1	57	0.0260989010989011	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	48	0.0633245382585752	C	16.02	3.004750	0.54254	0.011157	0.057871	ENSG00000159263	ENST00000290399;ENST00000430056	T;T	0.07216	3.21;3.21	5.28	5.28	0.74379	.	0.050146	0.85682	D	0.000000	T	0.00875	0.0029	L	0.35593	1.075	0.22787	P	0.99873726	P;P	0.51933	0.949;0.526	B;B	0.39876	0.312;0.15	T	0.17837	-1.0356	9	0.59425	D	0.04	.	18.5104	0.90914	0.0:1.0:0.0:0.0	.	63;63	Q14190;Q14190-2	SIM2_HUMAN;.	V	63	ENSP00000290399:A63V;ENSP00000404176:A63V	ENSP00000290399:A63V	A	+	2	0	SIM2	37003350	0.992000	0.36948	0.981000	0.43875	0.370000	0.29829	2.778000	0.47726	2.488000	0.83962	0.462000	0.41574	GCG	C|0.967;T|0.033	0.033	strong		0.701	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
TTBK1	84630	hgsc.bcm.edu	37	6	43252029	43252029	+	Missense_Mutation	SNP	T	T	C	rs3800298	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	26	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	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		
DCLK1	9201	hgsc.bcm.edu	37	13	36385031	36385031	+	Silent	SNP	G	G	T	rs2322807	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:36385031G>T	ENST00000360631.3	-	12	1840	c.1629C>A	c.(1627-1629)ccC>ccA	p.P543P	DCLK1_ENST00000379893.1_Silent_p.P236P|DCLK1_ENST00000255448.4_Silent_p.P543P			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	135	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	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	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34831856	34831856	+	Missense_Mutation	SNP	T	T	C	rs13205210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:34831856T>C	ENST00000192788.5	+	15	3464	c.3293T>C	c.(3292-3294)aTg>aCg	p.M1098T	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.M1098T	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	1098			M -> T (in dbSNP:rs13205210).				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						TTTTTCTCCATGAAGAGGACG	0.488													T|||	720	0.14377	0.2133	0.1081	5008	,	,		19013	0.1339		0.1352	False		,,,				2504	0.0941				p.M1098T		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.T3293C						PASS	.	T	THR/MET	778,3248		73,632,1308	114.0	123.0	120.0		3293	6.0	1.0	6	dbSNP_121	120	924,7386		66,792,3297	yes	missense	UHRF1BP1	NM_017754.3	81	139,1424,4605	CC,CT,TT		11.1191,19.3244,13.797	possibly-damaging	1098/1441	34831856	1702,10634	2013	4155	6168	SO:0001583	missense	54887	exon15			TCTCCATGAAGAG	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.3293T>C	6.37:g.34831856T>C	ENSP00000192788:p.Met1098Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	311	0.1423992673992674	102	0.2073170731707317	42	0.11602209944751381	73	0.12762237762237763	94	0.12401055408970976	T	21.5	4.165605	0.78339	0.193244	0.111191	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.18016	2.24;2.24	6.04	6.04	0.98038	.	0.039451	0.85682	D	0.000000	T	0.08403	0.0209	N	0.19112	0.55	0.20196	P	0.9999201035	P	0.44429	0.835	B	0.43445	0.42	T	0.04991	-1.0913	9	0.87932	D	0	-25.5457	15.1474	0.72667	0.0:0.0:0.0:1.0	rs13205210;rs52805012;rs59502513;rs13205210	1098	Q6BDS2	URFB1_HUMAN	T	1098	ENSP00000192788:M1098T;ENSP00000400628:M1098T	ENSP00000192788:M1098T	M	+	2	0	UHRF1BP1	34939834	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.833000	0.75334	2.317000	0.78254	0.459000	0.35465	ATG	T|0.851;C|0.149	0.149	strong		0.488	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
HOMEZ	57594	hgsc.bcm.edu	37	14	23746269	23746269	+	Silent	SNP	C	C	G	rs1057119	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23746269C>G	ENST00000357460.5	-	2	332	c.168G>C	c.(166-168)acG>acC	p.T56T	HOMEZ_ENST00000431326.2_Silent_p.T58T|HOMEZ_ENST00000561013.1_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	155	0	0		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	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	
RNASET2	8635	hgsc.bcm.edu	37	6	167343141	167343141	+	Missense_Mutation	SNP	G	G	A	rs11159	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:167343141G>A	ENST00000508775.1	-	9	1225	c.706C>T	c.(706-708)Cgg>Tgg	p.R236W	RNASET2_ENST00000366855.6_Missense_Mutation_p.R198W|RP11-514O12.4_ENST00000507747.1_Intron|RNASET2_ENST00000476238.2_Missense_Mutation_p.R236W	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	236			R -> W (in dbSNP:rs11159).		RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)			large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		CTCAGACCCCGGCTCTCGGCG	0.547													G|||	378	0.0754792	0.1044	0.0634	5008	,	,		15334	0.0585		0.0795	False		,,,				2504	0.0583				p.R236W		Atlas-SNP	.											RNASET2,colon,carcinoma,0,2	RNASET2	18	2	0			c.C706T						PASS	.	G	TRP/ARG	482,3924	224.9+/-240.9	34,414,1755	136.0	160.0	152.0		706	0.0	0.0	6	dbSNP_52	152	660,7940	165.4+/-217.5	33,594,3673	yes	missense	RNASET2	NM_003730.4	101	67,1008,5428	AA,AG,GG		7.6744,10.9396,8.7806	probably-damaging	236/257	167343141	1142,11864	2203	4300	6503	SO:0001583	missense	8635	exon9			GACCCCGGCTCTC	AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.706C>T	6.37:g.167343141G>A	ENSP00000426455:p.Arg236Trp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Missense_Mutation	SNP	ENST00000508775.1	37	CCDS5295.1	156	0.07142857142857142	50	0.1016260162601626	25	0.06906077348066299	33	0.057692307692307696	48	0.0633245382585752	G	11.41	1.631848	0.29068	0.109396	0.076744	ENSG00000026297	ENST00000366855;ENST00000508775;ENST00000428859;ENST00000476238;ENST00000478180	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.09	4.2	0.0208	0.14126	.	1.496370	0.03949	N	0.288231	T	0.40595	0.1123	N	0.14661	0.345	0.80722	P	0.0	D;D	0.69078	0.997;0.99	P;B	0.52672	0.706;0.076	T	0.27571	-1.0070	9	0.66056	D	0.02	-18.8687	11.1693	0.48563	0.0:0.0:0.3603:0.6397	rs11159;rs1044143;rs3183816;rs11159	286;236	C9JIU8;O00584	.;RNT2_HUMAN	W	198;236;286;236;236	ENSP00000424947:R198W;ENSP00000426455:R236W;ENSP00000422846:R236W;ENSP00000426059:R236W	ENSP00000424947:R198W	R	-	1	2	RNASET2	167263131	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.618000	0.05578	-0.397000	0.07691	-0.219000	0.12488	CGG	G|0.914;A|0.086	0.086	strong		0.547	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730	
CPSF4	10898	hgsc.bcm.edu	37	7	99047978	99047978	+	Silent	SNP	T	T	C	rs883403	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99047978T>C	ENST00000292476.5	+	4	397	c.387T>C	c.(385-387)cgT>cgC	p.R129R	PTCD1_ENST00000555673.1_Intron|CPSF4_ENST00000471455.1_3'UTR|CPSF4_ENST00000451876.1_Intron|CPSF4_ENST00000436336.2_Silent_p.R129R|ATP5J2-PTCD1_ENST00000413834.1_Intron|CPSF4_ENST00000441580.1_Silent_p.R76R|ATP5J2-PTCD1_ENST00000437572.1_Intron|ATP5J2_ENST00000466753.1_Intron			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	129					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GGTATGACCGTGGCTTCTGCA	0.617													C|||	2277	0.454673	0.9054	0.2824	5008	,	,		19251	0.3403		0.165	False		,,,				2504	0.3834				p.R129R		Atlas-SNP	.											.	CPSF4	24	.	0			c.T387C						PASS	.	C	,,	3396,1010	375.1+/-321.5	1304,788,111	69.0	59.0	62.0		387,,387	-11.7	0.3	7	dbSNP_86	62	1238,7362	761.7+/-407.6	102,1034,3164	no	coding-synonymous,intron,coding-synonymous	CPSF4,ATP5J2-PTCD1	NM_001081559.1,NM_001198879.1,NM_006693.2	,,	1406,1822,3275	CC,CT,TT		14.3953,22.9233,35.6297	,,	129/245,,129/270	99047978	4634,8372	2203	4300	6503	SO:0001819	synonymous_variant	10898	exon4			TGACCGTGGCTTC		CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"""cleavage and polyadenylation specific factor 4, 30kD subunit"""			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.387T>C	7.37:g.99047978T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	93	36	0.387097	NM_001081559	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Silent	SNP	ENST00000292476.5	37	CCDS5664.1	858	0.39285714285714285	428	0.8699186991869918	112	0.30939226519337015	192	0.3356643356643357	126	0.1662269129287599	C	9.966	1.224022	0.22457	0.770767	0.143953	ENSG00000160917	ENST00000440514	.	.	.	5.93	-11.7	0.00046	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999811	.	.	.	.	.	.	T	0.23190	-1.0195	3	.	.	.	-8.6058	5.2076	0.15299	0.1613:0.3878:0.0609:0.39	rs883403;rs11539768;rs17854666;rs57853370;rs883403	.	.	.	R	11	.	.	W	+	1	0	CPSF4	98885914	0.000000	0.05858	0.280000	0.24747	0.974000	0.67602	-1.672000	0.01952	-2.308000	0.00652	-0.733000	0.03571	TGG	T|0.639;C|0.361	0.361	strong		0.617	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336254.1		
ECE2	9718	hgsc.bcm.edu	37	3	183995839	183995839	+	Splice_Site	SNP	T	T	C	rs56080981		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:183995839T>C	ENST00000402825.3	+	5	957		c.e5+2		ECE2_ENST00000359140.4_Splice_Site|ECE2_ENST00000404464.3_Splice_Site|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000357474.5_Splice_Site	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)			ATTGAGAAGGTAGGGCCACTG	0.577																																					.		Atlas-SNP	.											.	ECE2	303	.	0			c.957+2T>C						PASS	.						56.0	53.0	54.0					3																	183995839		2203	4300	6503	SO:0001630	splice_region_variant	9718	exon5			AGAAGGTAGGGCC	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.957+2T>C	3.37:g.183995839T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Splice_Site	SNP	ENST00000402825.3	37	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	T	6.303	0.424006	0.11928	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	.	.	.	4.96	1.22	0.21188	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.2333	0.10613	0.0:0.2167:0.1723:0.6111	rs56080981;rs62619887	.	.	.	.	-1	.	.	.	+	.	.	ECE2	185478533	0.998000	0.40836	0.167000	0.22817	0.190000	0.23558	2.513000	0.45494	0.060000	0.16281	0.459000	0.35465	.	.	.	weak		0.577	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	Intron
TNKS	8658	hgsc.bcm.edu	37	8	9564437	9564437	+	Silent	SNP	A	A	G	rs7006985	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:9564437A>G	ENST00000310430.6	+	8	1412	c.1386A>G	c.(1384-1386)acA>acG	p.T462T	TNKS_ENST00000518281.1_Silent_p.T225T|TNKS_ENST00000520408.1_Silent_p.T462T|TNKS_ENST00000518027.1_3'UTR	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	462					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)	p.T462T(1)		NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		CTGATCCTACATTAGTCAACT	0.473													A|||	2738	0.546725	0.5605	0.5331	5008	,	,		16415	0.3829		0.663	False		,,,				2504	0.5869				p.T462T		Atlas-SNP	.											TNKS_ENST00000310430,NS,carcinoma,0,1	TNKS	198	1	1	Substitution - coding silent(1)	stomach(1)	c.A1386G						PASS	.	A		2399,2007	614.9+/-392.5	643,1113,447	98.0	84.0	89.0		1386	-11.3	0.0	8	dbSNP_116	89	5455,3145	656.3+/-401.3	1743,1969,588	no	coding-synonymous	TNKS	NM_003747.2		2386,3082,1035	GG,GA,AA		36.5698,45.5515,39.6125		462/1328	9564437	7854,5152	2203	4300	6503	SO:0001819	synonymous_variant	8658	exon8			TCCTACATTAGTC	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.1386A>G	8.37:g.9564437A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	37	CCDS5974.1																																																																																			A|0.409;G|0.590	0.590	strong		0.473	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
PLEKHM2	23207	hgsc.bcm.edu	37	1	16042766	16042766	+	Missense_Mutation	SNP	T	T	C	rs12091750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16042766T>C	ENST00000375799.3	+	2	322	c.95T>C	c.(94-96)aTc>aCc	p.I32T	PLEKHM2_ENST00000375793.2_Missense_Mutation_p.I32T	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	32	Interaction with KIF5B.		I -> T (in dbSNP:rs12091750).		Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GAGGATGAGATCCCTGCCATC	0.473													C|||	1618	0.323083	0.7466	0.2176	5008	,	,		19438	0.0367		0.2445	False		,,,				2504	0.2014				p.I32T		Atlas-SNP	.											PLEKHM2_ENST00000375799,NS,carcinoma,0,2	PLEKHM2	94	2	0			c.T95C						PASS	.	C	THR/ILE	2599,1401		866,867,267	40.0	41.0	41.0		95	5.2	1.0	1	dbSNP_120	41	2127,6243		264,1599,2322	yes	missense	PLEKHM2	NM_015164.2	89	1130,2466,2589	CC,CT,TT		25.4122,35.025,38.2053	benign	32/1020	16042766	4726,7644	2000	4185	6185	SO:0001583	missense	23207	exon2			ATGAGATCCCTGC	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.95T>C	1.37:g.16042766T>C	ENSP00000364956:p.Ile32Thr	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	37	CCDS44063.1	672	0.3076923076923077	365	0.741869918699187	100	0.27624309392265195	24	0.04195804195804196	183	0.24142480211081793	C	8.527	0.870134	0.17322	0.64975	0.254122	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.10005	2.92;2.92	6.07	5.15	0.70609	.	0.052226	0.85682	N	0.000000	T	0.00012	0.0000	N	0.02539	-0.55	0.47994	P	4.3999999999999595E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.32851	-0.9891	9	0.02654	T	1	-17.0574	12.3717	0.55258	0.0:0.8172:0.1191:0.0636	rs12091750;rs52816379;rs57392857;rs12091750	32	Q8IWE5	PKHM2_HUMAN	T	32	ENSP00000364956:I32T;ENSP00000364950:I32T	ENSP00000364950:I32T	I	+	2	0	PLEKHM2	15915353	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.750000	0.62162	0.900000	0.36469	-0.128000	0.14901	ATC	T|0.665;C|0.335	0.335	strong		0.473	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144921924	144921924	+	Silent	SNP	G	G	A	rs71664015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:144921924G>A	ENST00000369354.3	-	9	1294	c.1105C>T	c.(1105-1107)Ctg>Ttg	p.L369L	PDE4DIP_ENST00000369351.3_Silent_p.L369L|PDE4DIP_ENST00000369349.3_Silent_p.L369L|PDE4DIP_ENST00000529945.1_Silent_p.L532L|PDE4DIP_ENST00000369356.4_Silent_p.L369L|PDE4DIP_ENST00000313382.9_Silent_p.L435L|PDE4DIP_ENST00000479408.2_Silent_p.L156L|PDE4DIP_ENST00000369359.4_Silent_p.L506L|PDE4DIP_ENST00000530740.1_Silent_p.L506L|PDE4DIP_ENST00000313431.9_Silent_p.L532L			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	369					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCATCAGCCAGTTGGCGCTCT	0.463			T	PDGFRB	MPD																																p.L532L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C1594T						PASS	.	G	,,,,	203,4203		0,203,2000	375.0	388.0	384.0		1594,1105,1303,1105,1105	5.8	1.0	1	dbSNP_130	384	1431,7161		0,1431,2865	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	,,,,	0,1634,4865	AA,AG,GG		16.655,4.6074,12.5712	,,,,	532/1133,369/970,435/2241,369/2363,369/2347	144921924	1634,11364	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon5			CAGCCAGTTGGCG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.1105C>T	1.37:g.144921924G>A		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	358	95	0.265363	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			A|0.001;C|0.795	0.001	strong		0.463	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
FCRL5	83416	hgsc.bcm.edu	37	1	157504433	157504433	+	Missense_Mutation	SNP	C	C	G	rs73011568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:157504433C>G	ENST00000361835.3	-	8	1809	c.1652G>C	c.(1651-1653)cGc>cCc	p.R551P	FCRL5_ENST00000356953.4_Missense_Mutation_p.R551P|FCRL5_ENST00000368190.3_Missense_Mutation_p.R551P|FCRL5_ENST00000368189.3_Missense_Mutation_p.R551P|FCRL5_ENST00000368191.3_Missense_Mutation_p.R466P	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	551	Ig-like C2-type 5.				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)				CACTTCACTGCGCTGGGGACC	0.507													c|||	628	0.125399	0.3268	0.0231	5008	,	,		20321	0.0893		0.0109	False		,,,				2504	0.0808				p.R551P		Atlas-SNP	.											FCRL5,colon,carcinoma,-1,1	FCRL5	177	1	0			c.G1652C						PASS	.	C	PRO/ARG,PRO/ARG	1164,3242	406.2+/-333.8	160,844,1199	49.0	51.0	50.0		1652,1652	-6.2	0.0	1	dbSNP_130	50	72,8528	40.8+/-97.7	1,70,4229	no	missense,missense	FCRL5	NM_001195388.1,NM_031281.2	103,103	161,914,5428	GG,GC,CC		0.8372,26.4185,9.5033	probably-damaging,probably-damaging	551/999,551/978	157504433	1236,11770	2203	4300	6503	SO:0001583	missense	83416	exon8			TCACTGCGCTGGG	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.1652G>C	1.37:g.157504433C>G	ENSP00000354691:p.Arg551Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	225	0.10302197802197802	151	0.30691056910569103	7	0.019337016574585635	60	0.1048951048951049	7	0.009234828496042216	C	11.16	1.558377	0.27827	0.264185	0.008372	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	3.39	-6.16	0.02098	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.13970	0.0338	M	0.91561	3.22	0.46131	P	0.0011160000000000059	D;P;P;B;D;B	0.89917	0.999;0.508;0.95;0.312;1.0;0.135	D;B;P;B;D;B	0.81914	0.983;0.13;0.649;0.199;0.995;0.074	T	0.02214	-1.1194	8	0.30078	T	0.28	.	2.1778	0.03866	0.1406:0.2057:0.139:0.5146	.	582;466;551;551;551;551	B4DW39;F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;.;FCRL5_HUMAN	P	551;551;551;466;551	ENSP00000354691:R551P;ENSP00000349434:R551P;ENSP00000357173:R551P;ENSP00000357174:R466P;ENSP00000357172:R551P	ENSP00000349434:R551P	R	-	2	0	FCRL5	155771057	0.000000	0.05858	0.002000	0.10522	0.049000	0.14656	-3.591000	0.00421	-1.200000	0.02662	0.313000	0.20887	CGC	C|0.903;G|0.097	0.097	strong		0.507	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
ASPM	259266	hgsc.bcm.edu	37	1	197073932	197073932	+	Silent	SNP	T	T	C	rs2878749	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:197073932T>C	ENST00000367409.4	-	18	4705	c.4449A>G	c.(4447-4449)aaA>aaG	p.K1483K	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1483					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						TATAAATATATTTCCGTAATT	0.289													T|||	1074	0.214457	0.0431	0.2262	5008	,	,		17830	0.1647		0.4115	False		,,,				2504	0.2863				p.K1483K		Atlas-SNP	.											.	ASPM	444	.	0			c.A4449G						PASS	.	T	,	463,3941	194.7+/-219.5	32,399,1771	51.0	52.0	52.0		,4449	-2.4	0.0	1	dbSNP_101	52	3724,4860	518.5+/-379.3	813,2098,1381	no	intron,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	845,2497,3152	CC,CT,TT		43.383,10.5132,32.2374	,	,1483/3478	197073932	4187,8801	2202	4292	6494	SO:0001819	synonymous_variant	259266	exon18			AATATATTTCCGT	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.4449A>G	1.37:g.197073932T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			T|0.719;C|0.281	0.281	strong		0.289	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394239	103394239	+	RNA	SNP	C	C	T	rs16960471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103394239C>T	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		TAATCCTTAACGGTCCAATAT	0.358													C|||	348	0.0694888	0.1399	0.0159	5008	,	,		21957	0.1052		0.0268	False		,,,				2504	0.0194				p.P2936P		Atlas-SNP	.											.	.	.	.	0			c.G8808A						PASS	.	C		158,1226		10,138,544	91.0	76.0	81.0		8808	-7.1	0.0	13	dbSNP_123	81	66,3116		2,62,1527	no	coding-synonymous	CCDC168	NM_001146197.1		12,200,2071	TT,TC,CC		2.0742,11.4162,4.9058		2936/7082	103394239	224,4342	692	1591	2283			643677	exon4			CCTTAACGGTCCA			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.103394239C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	75	0.517241	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				C|0.924;T|0.076	0.076	strong		0.358	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
NIT1	4817	hgsc.bcm.edu	37	1	161088583	161088583	+	Missense_Mutation	SNP	T	T	G	rs41270017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161088583T>G	ENST00000368009.2	+	2	86	c.10T>G	c.(10-12)Ttc>Gtc	p.F4V	NIT1_ENST00000496861.1_3'UTR|NIT1_ENST00000368007.4_Intron|NIT1_ENST00000368008.1_Missense_Mutation_p.F4V|DEDD_ENST00000489249.1_5'Flank|PFDN2_ENST00000468311.1_5'Flank|PFDN2_ENST00000368010.3_5'Flank|NIT1_ENST00000392190.5_5'UTR	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	4					nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)			NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			CAGGCTGGGCTTCATCACCAG	0.483													T|||	465	0.0928514	0.1067	0.0663	5008	,	,		20822	0.0675		0.0736	False		,,,				2504	0.1391				p.F4V		Atlas-SNP	.											.	NIT1	41	.	0			c.T10G						PASS	.	T	VAL/PHE,,,VAL/PHE	510,3896	236.8+/-248.8	35,440,1728	156.0	130.0	139.0		10,,,10	2.5	1.0	1	dbSNP_127	139	681,7919	170.7+/-221.8	32,617,3651	yes	missense,intron,utr-5,missense	NIT1	NM_001185092.1,NM_001185093.1,NM_001185094.1,NM_005600.2	50,,,50	67,1057,5379	GG,GT,TT		7.9186,11.5751,9.1573	benign,,,benign	4/244,,,4/328	161088583	1191,11815	2203	4300	6503	SO:0001583	missense	4817	exon2			CTGGGCTTCATCA	AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.10T>G	1.37:g.161088583T>G	ENSP00000356988:p.Phe4Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_001185092	B1AQP3|D3DVF4|O76091	Missense_Mutation	SNP	ENST00000368009.2	37	CCDS1218.1	160	0.07326007326007326	48	0.0975609756097561	21	0.058011049723756904	36	0.06293706293706294	55	0.07255936675461741	T	11.11	1.542148	0.27563	0.115751	0.079186	ENSG00000158793	ENST00000368009;ENST00000368008	T;D	0.81739	-0.94;-1.53	5.0	2.52	0.30459	.	0.719779	0.12631	N	0.452160	T	0.46073	0.1374	N	0.14661	0.345	0.09310	P	0.99999999791456	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10847	-1.0612	9	0.31617	T	0.26	-1.1472	9.2106	0.37316	0.0:0.0:0.3544:0.6456	rs41270017	4;4	B1AQP4;Q86X76	.;NIT1_HUMAN	V	4	ENSP00000356988:F4V;ENSP00000356987:F4V	ENSP00000356987:F4V	F	+	1	0	NIT1	159355207	0.995000	0.38212	1.000000	0.80357	0.969000	0.65631	0.594000	0.24014	0.903000	0.36546	0.533000	0.62120	TTC	T|0.917;G|0.083	0.083	strong		0.483	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1		
ARHGEF10	9639	hgsc.bcm.edu	37	8	1806229	1806229	+	Silent	SNP	A	A	C	rs4875950	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:1806229A>C	ENST00000398564.1	+	3	213	c.213A>C	c.(211-213)ccA>ccC	p.P71P	ARHGEF10_ENST00000520359.1_Silent_p.P47P|ARHGEF10_ENST00000518288.1_Silent_p.P71P|ARHGEF10_ENST00000349830.3_Silent_p.P47P|ARHGEF10_ENST00000398560.1_Silent_p.P71P|ARHGEF10_ENST00000262112.6_Silent_p.P71P			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	71					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)		GACAGGCCCCATCCGCCCCTG	0.542													C|||	1531	0.305711	0.3079	0.2853	5008	,	,		12838	0.2421		0.2714	False		,,,				2504	0.4182				p.P47P		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.A141C						PASS	.	C		1453,2953	676.7+/-403.3	232,989,982	49.0	50.0	49.0		141	-9.9	0.0	8	dbSNP_111	49	2417,6183	697.6+/-405.0	312,1793,2195	no	coding-synonymous	ARHGEF10	NM_014629.2		544,2782,3177	CC,CA,AA		28.1047,32.9778,29.7555		47/1345	1806229	3870,9136	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon3			GGCCCCATCCGCC	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.213A>C	8.37:g.1806229A>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	204	105	0.514706	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				A|0.720;C|0.280	0.280	strong		0.542	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
CENPF	1063	hgsc.bcm.edu	37	1	214818846	214818846	+	Missense_Mutation	SNP	A	A	G	rs3790646	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214818846A>G	ENST00000366955.3	+	13	6101	c.5933A>G	c.(5932-5934)gAt>gGt	p.D1978G		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2074					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)		ACGGCACTGGATCAGTTGTCT	0.433													A|||	543	0.108427	0.1089	0.1066	5008	,	,		19311	0.126		0.0507	False		,,,				2504	0.1503				p.D1978G	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A5933G						PASS	.	A	GLY/ASP	428,3978	191.6+/-217.2	21,386,1796	60.0	65.0	63.0		5933	-1.2	0.0	1	dbSNP_107	63	461,8139	132.5+/-190.1	12,437,3851	yes	missense	CENPF	NM_016343.3	94	33,823,5647	GG,GA,AA		5.3605,9.714,6.8353	benign	1978/3115	214818846	889,12117	2203	4300	6503	SO:0001583	missense	1063	exon13			CACTGGATCAGTT	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.5933A>G	1.37:g.214818846A>G	ENSP00000355922:p.Asp1978Gly	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	159	87	0.54717	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	230	0.10531135531135531	64	0.13008130081300814	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	A	1.047	-0.677078	0.03378	0.09714	0.053605	ENSG00000117724	ENST00000366955	T	0.44482	0.92	5.46	-1.21	0.09524	.	0.609367	0.13596	N	0.376240	T	0.00144	0.0004	L	0.43923	1.385	0.80722	P	0.0	B	0.12630	0.006	B	0.08055	0.003	T	0.13282	-1.0515	9	0.31617	T	0.26	.	0.6781	0.00870	0.4337:0.1198:0.2141:0.2325	rs3790646;rs52807378;rs3790646	2074	P49454	CENPF_HUMAN	G	1978	ENSP00000355922:D1978G	ENSP00000355922:D1978G	D	+	2	0	CENPF	212885469	0.018000	0.18449	0.001000	0.08648	0.016000	0.09150	0.256000	0.18351	-0.220000	0.09988	-0.412000	0.06146	GAT	A|0.920;G|0.080	0.080	strong		0.433	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
RP1	6101	hgsc.bcm.edu	37	8	55541450	55541450	+	Missense_Mutation	SNP	G	G	A	rs446227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:55541450G>A	ENST00000220676.1	+	4	5156	c.5008G>A	c.(5008-5010)Gca>Aca	p.A1670T		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1670			A -> T (in dbSNP:rs446227). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11095597, ECO:0000269|PubMed:11527933, ECO:0000269|PubMed:20664799}.		axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TTCCAGGAAAGCAAGTCTTTA	0.398													G|||	1243	0.248203	0.0772	0.2824	5008	,	,		21103	0.4415		0.2614	False		,,,				2504	0.2423				p.A1670T	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G5008A						PASS	.	G	THR/ALA	474,3932	213.1+/-232.8	27,420,1756	142.0	146.0	145.0		5008	-0.3	0.0	8	dbSNP_80	145	2199,6401	372.4+/-336.6	274,1651,2375	yes	missense	RP1	NM_006269.1	58	301,2071,4131	AA,AG,GG		25.5698,10.7581,20.5521	benign	1670/2157	55541450	2673,10333	2203	4300	6503	SO:0001583	missense	6101	exon4			AGGAAAGCAAGTC	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.5008G>A	8.37:g.55541450G>A	ENSP00000220676:p.Ala1670Thr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	601	0.2751831501831502	66	0.13414634146341464	94	0.2596685082872928	250	0.4370629370629371	191	0.2519788918205805	G	3.593	-0.083196	0.07141	0.107581	0.255698	ENSG00000104237	ENST00000220676	T	0.19394	2.15	5.86	-0.331	0.12679	.	1.243950	0.05754	N	0.603645	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.14805	0.011	B	0.08055	0.003	T	0.48175	-0.9058	9	0.18276	T	0.48	4.0012	1.8554	0.03177	0.4247:0.1285:0.3156:0.1312	rs446227;rs16920623;rs59806829;rs446227	1670	P56715	RP1_HUMAN	T	1670	ENSP00000220676:A1670T	ENSP00000220676:A1670T	A	+	1	0	RP1	55704003	0.007000	0.16637	0.003000	0.11579	0.722000	0.41435	0.010000	0.13242	-0.379000	0.07906	-0.182000	0.12963	GCA	G|0.766;A|0.233	0.233	strong		0.398	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
SFTPB	6439	hgsc.bcm.edu	37	2	85895338	85895338	+	5'UTR	SNP	T	T	G	rs2077079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:85895338T>G	ENST00000342375.3	-	0	104				SFTPB_ENST00000409383.1_Missense_Mutation_p.H2P|SFTPB_ENST00000393822.3_Missense_Mutation_p.H2P|SFTPB_ENST00000519937.2_5'Flank	NM_000542.3|NM_198843.2	NP_000533.3|NP_942140.2	P07988	PSPB_HUMAN	surfactant protein B						organ morphogenesis (GO:0009887)|respiratory gaseous exchange (GO:0007585)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						CCCTGCTTGGTGCATGGCCCC	0.632													G|||	2096	0.41853	0.3533	0.4438	5008	,	,		17894	0.505		0.3757	False		,,,				2504	0.4438				p.H2P		Atlas-SNP	.											.	SFTPB	49	.	0			c.A5C	GRCh37	CR077669	SFTPB	R	rs2077079	PASS	.	G	PRO/HIS,PRO/HIS	1343,2545		252,839,853	34.0	21.0	26.0		5,5	2.5	0.0	2	dbSNP_96	26	2642,4820		505,1632,1594	yes	missense,missense	SFTPB	NM_000542.3,NM_198843.2	77,77	757,2471,2447	GG,GT,TT		35.4061,34.5422,35.1101	,	2/394,2/394	85895338	3985,7365	1944	3731	5675	SO:0001623	5_prime_UTR_variant	6439	exon2			GCTTGGTGCATGG	J02761	CCDS1983.1, CCDS1983.2	2p12-p11.2	2008-08-26	2008-08-26		ENSG00000168878	ENSG00000168878			10801	protein-coding gene	gene with protein product		178640	"""surfactant, pulmonary-associated protein B"""	SFTP3		2924687, 1346779	Standard	NM_198843		Approved	SP-B	uc002sqh.3	P07988	OTTHUMG00000130181	ENST00000342375.3:c.-32A>C	2.37:g.85895338T>G		Somatic	338	1	0.00295858		WXS	Illumina HiSeq	Phase_I	316	135	0.427215	NM_198843	Q96R04	Missense_Mutation	SNP	ENST00000342375.3	37		929	0.42536630036630035	186	0.3780487804878049	165	0.4558011049723757	281	0.49125874125874125	297	0.391820580474934	G	0.706	-0.789066	0.02884	0.345422	0.354061	ENSG00000168878	ENST00000393822;ENST00000409383	T;T	0.66995	-0.24;-0.24	4.39	2.47	0.30058	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46541	-0.9184	7	.	.	.	.	5.5933	0.17313	0.0999:0.0:0.553:0.3471	rs2077079;rs59193627	2	D6W5L6	.	P	2	ENSP00000377409:H2P;ENSP00000386346:H2P	.	H	-	2	0	SFTPB	85748849	0.441000	0.25626	0.008000	0.14137	0.010000	0.07245	0.821000	0.27338	0.387000	0.25024	-0.217000	0.12591	CAC	T|0.576;G|0.424	0.424	strong		0.632	SFTPB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198843	
GSTP1	2950	hgsc.bcm.edu	37	11	67352640	67352640	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:67352640C>T	ENST00000398606.3	+	5	513	c.264C>T	c.(262-264)gcC>gcT	p.A88A	GSTP1_ENST00000398603.1_Silent_p.A88A|GSTP1_ENST00000498765.1_3'UTR	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1	88	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)	AGGAGGCAGCCCTGGTGGACA	0.607																																					p.A88A		Atlas-SNP	.											GSTP1,NS,carcinoma,0,1	GSTP1	21	1	0			c.C264T						scavenged	.						73.0	82.0	79.0					11																	67352640		2093	4222	6315	SO:0001819	synonymous_variant	2950	exon5			GGCAGCCCTGGTG	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.264C>T	11.37:g.67352640C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	115	3	0.026087	NM_000852	O00460|Q15690|Q5TZY3	Silent	SNP	ENST00000398606.3	37	CCDS41679.1																																																																																			.	.	none		0.607	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852	
TNFSF4	7292	hgsc.bcm.edu	37	1	173155860	173155860	+	Missense_Mutation	SNP	C	C	T	rs146261831		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:173155860C>T	ENST00000281834.3	-	3	483	c.347G>A	c.(346-348)aGc>aAc	p.S116N	TNFSF4_ENST00000488053.1_5'Flank|TNFSF4_ENST00000367718.1_Missense_Mutation_p.S66N	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	116					acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|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-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						GTAATGAAGGCTAATGTTGAC	0.463																																					p.S116N		Atlas-SNP	.											.	TNFSF4	29	.	0			c.G347A						PASS	.	C	ASN/SER	0,4406		0,0,2203	98.0	101.0	100.0		347	-0.7	0.0	1	dbSNP_134	100	5,8595	4.3+/-15.6	0,5,4295	yes	missense	TNFSF4	NM_003326.3	46	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	benign	116/184	173155860	5,13001	2203	4300	6503	SO:0001583	missense	7292	exon3			TGAAGGCTAATGT	D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11934	protein-coding gene	gene with protein product		603594	"""tax-transcriptionally activated glycoprotein 1, 34kD"""	TXGP1		1996093, 8076595	Standard	XM_005245475		Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.347G>A	1.37:g.173155860C>T	ENSP00000281834:p.Ser116Asn	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	178	79	0.44382	NM_003326	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	ENST00000281834.3	37	CCDS1306.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581728	0.28180	0.0	5.81E-4	ENSG00000117586	ENST00000367718;ENST00000281834;ENST00000545292	D;D	0.94613	-3.47;-3.47	5.91	-0.7	0.11273	Tumour necrosis factor (2);Tumour necrosis factor-like (1);	1.170620	0.05958	N	0.640076	T	0.81503	0.4836	L	0.41236	1.265	0.09310	N	1	B;B	0.12630	0.001;0.006	B;B	0.13407	0.009;0.009	T	0.69639	-0.5091	10	0.30078	T	0.28	-0.9441	4.6924	0.12786	0.0:0.2516:0.3912:0.3572	.	116;66	P23510;Q8IV74	TNFL4_HUMAN;.	N	66;116;66	ENSP00000356691:S66N;ENSP00000281834:S116N	ENSP00000281834:S116N	S	-	2	0	TNFSF4	171422483	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	-1.057000	0.03486	0.221000	0.20879	0.655000	0.94253	AGC	C|1.000;T|0.000	0.000	weak		0.463	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084271.1		
NFASC	23114	hgsc.bcm.edu	37	1	204966428	204966428	+	Missense_Mutation	SNP	C	C	G	rs2802808	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204966428C>G	ENST00000401399.1	+	24	3112	c.2913C>G	c.(2911-2913)atC>atG	p.I971M	NFASC_ENST00000367172.4_Missense_Mutation_p.I1078M|NFASC_ENST00000367170.4_Intron|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000360049.4_Intron|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000539706.1_Intron|NFASC_ENST00000513543.1_Intron|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000367171.4_Missense_Mutation_p.I1063M|NFASC_ENST00000495396.1_Intron|NFASC_ENST00000339876.6_Missense_Mutation_p.I971M|NFASC_ENST00000338586.6_Intron|NFASC_ENST00000338515.6_Missense_Mutation_p.I1078M			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	216	0	0		WXS	Illumina HiSeq	Phase_I	206	111	0.538835	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	
PYROXD2	84795	hgsc.bcm.edu	37	10	100144782	100144782	+	Missense_Mutation	SNP	C	C	T	rs2296441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	56	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	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	
ZNF71	58491	hgsc.bcm.edu	37	19	57133633	57133633	+	Silent	SNP	C	C	T	rs35011777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57133633C>T	ENST00000328070.6	+	3	1212	c.978C>T	c.(976-978)taC>taT	p.Y326Y		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	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)|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)		AGAAGCCCTACGTGTGCGGCG	0.647													.|||	82	0.0163738	0.003	0.036	5008	,	,		22163	0.0		0.0507	False		,,,				2504	0.002				p.Y326Y		Atlas-SNP	.											.	ZNF71	69	.	0			c.C978T						PASS	.	C		49,4357	48.2+/-83.0	0,49,2154	83.0	76.0	78.0		978	0.3	1.0	19	dbSNP_126	78	508,8092	144.5+/-200.4	11,486,3803	no	coding-synonymous	ZNF71	NM_021216.4		11,535,5957	TT,TC,CC		5.907,1.1121,4.2826		326/490	57133633	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	58491	exon3			GCCCTACGTGTGC	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.978C>T	19.37:g.57133633C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	179	83	0.463687	NM_021216	Q15919|Q9UC09|Q9UQD3	Silent	SNP	ENST00000328070.6	37	CCDS12947.1																																																																																			C|0.960;T|0.040	0.040	strong		0.647	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216	
RNF213	57674	hgsc.bcm.edu	37	17	78263486	78263486	+	Missense_Mutation	SNP	T	T	C	rs17853989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78263486T>C	ENST00000582970.1	+	6	1105	c.962T>C	c.(961-963)aTg>aCg	p.M321T	RNF213_ENST00000456466.1_Missense_Mutation_p.M321T|RNF213_ENST00000319921.4_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						scavenged	.	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	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	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	
NFATC4	4776	hgsc.bcm.edu	37	14	24843620	24843620	+	Silent	SNP	T	T	C	rs2295298	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24843620T>C	ENST00000250373.4	+	6	1962	c.1821T>C	c.(1819-1821)acT>acC	p.T607T	NFATC4_ENST00000553708.1_Silent_p.T607T|NFATC4_ENST00000555802.1_5'UTR|NFATC4_ENST00000557451.1_Silent_p.T537T|NFATC4_ENST00000554966.1_Silent_p.T620T|NFATC4_ENST00000555590.1_Silent_p.T620T|NFATC4_ENST00000554591.1_Silent_p.T670T|NFATC4_ENST00000554473.1_Silent_p.T142T|NFATC4_ENST00000556169.1_Silent_p.T595T|NFATC4_ENST00000413692.2_Silent_p.T670T|NFATC4_ENST00000553469.1_Silent_p.T639T|NFATC4_ENST00000553879.1_Silent_p.T537T|NFATC4_ENST00000555167.1_Silent_p.T142T|NFATC4_ENST00000556759.1_Silent_p.T142T|NFATC4_ENST00000539237.2_Silent_p.T639T|NFATC4_ENST00000422617.3_Silent_p.T595T|NFATC4_ENST00000554344.1_Silent_p.T537T|NFATC4_ENST00000555393.1_5'UTR|NFATC4_ENST00000556279.1_Silent_p.T639T|NFATC4_ENST00000554661.1_Silent_p.T537T|NFATC4_ENST00000555453.1_Silent_p.T595T|NFATC4_ENST00000557767.1_5'UTR|NFATC4_ENST00000424781.2_Silent_p.T620T|NFATC4_ENST00000554050.1_Silent_p.T607T	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	607	IPT/TIG.				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)		TGGTACTGACTGGCTCCAACT	0.637													T|||	1425	0.284545	0.0741	0.3876	5008	,	,		17306	0.1528		0.5885	False		,,,				2504	0.319				p.T670T		Atlas-SNP	.											.	NFATC4	115	.	0			c.T2010C						PASS	.	T	,,,,	692,3714	290.7+/-281.1	61,570,1572	79.0	61.0	67.0		2010,1821,1611,2010,1821	-1.8	1.0	14	dbSNP_100	67	5202,3398	637.7+/-399.3	1559,2084,657	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	,,,,	1620,2654,2229	CC,CT,TT		39.5116,15.7059,45.3175	,,,,	670/965,607/795,537/833,670/858,607/903	24843620	5894,7112	2203	4300	6503	SO:0001819	synonymous_variant	4776	exon7			ACTGACTGGCTCC	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.1821T>C	14.37:g.24843620T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	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																																																																																			T|0.629;C|0.371	0.371	strong		0.637	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
ZNF347	84671	hgsc.bcm.edu	37	19	53644386	53644386	+	Silent	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53644386T>A	ENST00000334197.7	-	5	1763	c.1695A>T	c.(1693-1695)ggA>ggT	p.G565G	ZNF347_ENST00000601469.2_Silent_p.G566G|ZNF347_ENST00000452676.2_Silent_p.G566G|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	565					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(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		AAGGTTTTTCTCCAGTATGGA	0.408																																					p.G566G	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											ZNF347,NS,carcinoma,0,1	ZNF347	87	1	0			c.A1698T						scavenged	.						156.0	149.0	152.0					19																	53644386		2203	4300	6503	SO:0001819	synonymous_variant	84671	exon5			TTTTTCTCCAGTA	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"""Zinc fingers, C2H2-type"", ""-"""	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1695A>T	19.37:g.53644386T>A		Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	77	3	0.038961	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	37	CCDS33097.1																																																																																			.	.	none		0.408	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584	
SCAF11	9169	hgsc.bcm.edu	37	12	46321158	46321158	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:46321158T>G	ENST00000369367.3	-	11	2559	c.2326A>C	c.(2326-2328)Agc>Cgc	p.S776R	SCAF11_ENST00000465950.1_Missense_Mutation_p.S461R|SCAF11_ENST00000549162.1_Missense_Mutation_p.S584R|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000419565.2_Missense_Mutation_p.S776R	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	776					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)	p.S776G(1)		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						TCTTTTGGGCTTTCAGATGGT	0.383																																					p.S776R		Atlas-SNP	.											SCAF11,NS,carcinoma,0,1	SCAF11	145	1	1	Substitution - Missense(1)	kidney(1)	c.A2326C						PASS	.						177.0	174.0	175.0					12																	46321158		2203	4300	6503	SO:0001583	missense	9169	exon11			TTGGGCTTTCAGA	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.2326A>C	12.37:g.46321158T>G	ENSP00000358374:p.Ser776Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	9.433	1.085940	0.20390	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.49139	1.45;2.18;1.45;2.18;0.79	5.93	2.17	0.27698	.	0.432900	0.26146	N	0.026061	T	0.35653	0.0939	L	0.59436	1.845	0.09310	N	1	P;P	0.45078	0.85;0.498	B;B	0.37304	0.246;0.125	T	0.21415	-1.0246	10	0.34782	T	0.22	0.8665	5.4177	0.16384	0.1281:0.1381:0.0:0.7337	.	584;776	F8VXG7;Q99590	.;SCAFB_HUMAN	R	461;776;584;776;716	ENSP00000449812:S461R;ENSP00000358374:S776R;ENSP00000448864:S584R;ENSP00000413036:S776R;ENSP00000446746:S716R	ENSP00000358374:S776R	S	-	1	0	SCAF11	44607425	0.169000	0.23002	0.127000	0.21898	0.023000	0.10783	0.397000	0.20883	0.121000	0.18284	0.533000	0.62120	AGC	.	.	none		0.383	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
ANKRD12	23253	hgsc.bcm.edu	37	18	9255982	9255982	+	Missense_Mutation	SNP	A	A	G	rs4798791	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:9255982A>G	ENST00000262126.4	+	9	2957	c.2717A>G	c.(2716-2718)aAg>aGg	p.K906R	ANKRD12_ENST00000400020.3_Missense_Mutation_p.K883R|ANKRD12_ENST00000383440.2_Missense_Mutation_p.K883R	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	906			K -> R (in dbSNP:rs4798791). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						AGTAGAGAAAAGATGGATAGG	0.348													A|||	3072	0.613419	0.3835	0.7104	5008	,	,		17420	0.6607		0.6581	False		,,,				2504	0.7607				p.K906R		Atlas-SNP	.											.	ANKRD12	167	.	0			c.A2717G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	1798,2602		370,1058,772	44.0	45.0	45.0		2648,2648,2717	5.6	1.0	18	dbSNP_111	45	5283,3303		1660,1963,670	yes	missense,missense,missense	ANKRD12	NM_001083625.2,NM_001204056.1,NM_015208.4	26,26,26	2030,3021,1442	GG,GA,AA		38.4696,40.8636,45.472	probably-damaging,probably-damaging,probably-damaging	883/2040,883/2040,906/2063	9255982	7081,5905	2200	4293	6493	SO:0001583	missense	23253	exon9			GAGAAAAGATGGA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2717A>G	18.37:g.9255982A>G	ENSP00000262126:p.Lys906Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	1276	0.5842490842490843	186	0.3780487804878049	238	0.6574585635359116	358	0.6258741258741258	494	0.6517150395778364	A	15.28	2.787958	0.49997	0.408636	0.615304	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.37058	1.22;1.22	5.55	5.55	0.83447	.	0.047619	0.85682	D	0.000000	T	0.00012	0.0000	L	0.34521	1.04	0.18873	P	0.9999845786	P;P	0.45474	0.859;0.779	B;B	0.42555	0.391;0.219	T	0.30031	-0.9992	9	0.51188	T	0.08	-16.5632	15.691	0.77453	1.0:0.0:0.0:0.0	rs4798791;rs17498857;rs59415891;rs4798791	883;906	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	R	883;906	ENSP00000372932:K883R;ENSP00000262126:K906R	ENSP00000262126:K906R	K	+	2	0	ANKRD12	9245982	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	5.872000	0.69636	2.106000	0.64143	0.455000	0.32223	AAG	A|0.446;G|0.554	0.554	strong		0.348	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
HCN2	610	hgsc.bcm.edu	37	19	613307	613307	+	Silent	SNP	C	C	T	rs2301778	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:613307C>T	ENST00000251287.2	+	6	1697	c.1644C>T	c.(1642-1644)gcC>gcT	p.A548A	AC005559.2_ENST00000591847.1_RNA	NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	548					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			endometrium(5)|lung(4)	9		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGCCAACGCCGACCCCAACT	0.627													c|||	1428	0.285144	0.2837	0.1859	5008	,	,		11918	0.2659		0.3241	False		,,,				2504	0.3374				p.A548A	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.C1644T						PASS	.	T		1182,3224		148,886,1169	60.0	50.0	53.0		1644	-7.9	0.0	19	dbSNP_100	53	2551,6047		378,1795,2126	no	coding-synonymous	HCN2	NM_001194.3		526,2681,3295	TT,TC,CC		29.6697,26.8271,28.7066		548/890	613307	3733,9271	2203	4299	6502	SO:0001819	synonymous_variant	610	exon6			CAACGCCGACCCC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.1644C>T	19.37:g.613307C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	123	67	0.544715	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			C|0.712;T|0.288	0.288	strong		0.627	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
SMTN	6525	hgsc.bcm.edu	37	22	31491295	31491295	+	Missense_Mutation	SNP	G	G	C	rs3205187	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31491295G>C	ENST00000347557.2	+	12	1857	c.1639G>C	c.(1639-1641)Gca>Cca	p.A547P	SMTN_ENST00000404574.1_Missense_Mutation_p.A146P|SMTN_ENST00000358743.1_Missense_Mutation_p.A547P|SMTN_ENST00000333137.7_Missense_Mutation_p.A547P	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	547			A -> P (in dbSNP:rs3205187). {ECO:0000269|PubMed:10023782, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.8}.		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						GCAGATGGAAGCAGAGCCAGC	0.587													C|||	2462	0.491613	0.5159	0.5159	5008	,	,		19525	0.123		0.672	False		,,,				2504	0.636				p.A632P		Atlas-SNP	.											.	SMTN	219	.	0			c.G1894C						PASS	.	C	PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	2190,2216	586.8+/-386.5	547,1096,560	40.0	40.0	40.0		1894,1807,1639,1639,1639	3.9	1.0	22	dbSNP_105	40	5707,2893	451.8+/-362.8	1892,1923,485	yes	missense,missense,missense,missense,missense	SMTN	NM_001207017.1,NM_001207018.1,NM_006932.4,NM_134269.2,NM_134270.2	27,27,27,27,27	2439,3019,1045	CC,CG,GG		33.6395,49.7049,39.2819	benign,benign,benign,benign,benign	632/1003,603/972,547/918,547/916,547/941	31491295	7897,5109	2203	4300	6503	SO:0001583	missense	6525	exon13			ATGGAAGCAGAGC	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.1639G>C	22.37:g.31491295G>C	ENSP00000328635:p.Ala547Pro	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_001207017	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	37	CCDS13886.1	1039	0.4757326007326007	268	0.5447154471544715	201	0.5552486187845304	59	0.10314685314685315	511	0.6741424802110818	C	1.831	-0.469884	0.04445	0.497049	0.663605	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496;ENST00000455608;ENST00000404574;ENST00000403419	T;T;T;T;D	0.92595	0.2;-0.26;-0.26;1.94;-3.07	4.98	3.9	0.45041	.	0.000000	0.37530	N	0.002053	T	0.00012	0.0000	N	0.01352	-0.895	0.09310	P	0.999999849924	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	0.06405	0.001;0.0;0.0;0.0;0.0;0.0;0.002	T	0.36359	-0.9751	9	0.02654	T	1	-10.793	11.3436	0.49548	0.1208:0.5398:0.3393:0.0	rs3205187;rs4820935;rs11547959;rs17401035;rs17857009;rs56520094;rs61217606;rs4820935	603;3;146;570;547;547;547	E7ETT8;B5MBZ4;B5MCI0;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;.;SMTN_HUMAN;.	P	547;547;547;545;570;24;146;3	ENSP00000351593:A547P;ENSP00000328635:A547P;ENSP00000329532:A547P;ENSP00000392329:A24P;ENSP00000383919:A146P	ENSP00000329393:A545P	A	+	1	0	SMTN	29821295	0.161000	0.22892	0.995000	0.50966	0.495000	0.33615	1.084000	0.30828	1.495000	0.48549	-0.216000	0.12614	GCA	G|0.465;C|0.535	0.535	strong		0.587	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
CCDC13	152206	hgsc.bcm.edu	37	3	42787469	42787469	+	Silent	SNP	A	A	G	rs2240859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42787469A>G	ENST00000310232.6	-	7	854	c.771T>C	c.(769-771)tcT>tcC	p.S257S	CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	257										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TCCCTGGCGAAGATAGGAGCT	0.512													G|||	2511	0.501398	0.5439	0.402	5008	,	,		18576	0.4534		0.4592	False		,,,				2504	0.6074				p.S257S		Atlas-SNP	.											.	CCDC13	71	.	0			c.T771C						PASS	.	G		2397,2009	561.2+/-380.7	650,1097,456	93.0	90.0	91.0		771	2.1	0.9	3	dbSNP_98	91	3943,4657	602.8+/-394.6	898,2147,1255	yes	coding-synonymous	CCDC13	NM_144719.3		1548,3244,1711	GG,GA,AA		45.8488,45.5969,48.7467		257/716	42787469	6340,6666	2203	4300	6503	SO:0001819	synonymous_variant	152206	exon7			TGGCGAAGATAGG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.771T>C	3.37:g.42787469A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_144719		Silent	SNP	ENST00000310232.6	37	CCDS2705.1																																																																																			A|0.512;G|0.488	0.488	strong		0.512	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
TAF1L	138474	hgsc.bcm.edu	37	9	32631966	32631966	+	Silent	SNP	G	G	A	rs45559233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:32631966G>A	ENST00000242310.4	-	1	3701	c.3612C>T	c.(3610-3612)gtC>gtT	p.V1204V	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1204					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTGGTTTTCGGACTGTCTCAC	0.428													G|||	474	0.0946486	0.1868	0.0749	5008	,	,		25205	0.0446		0.0686	False		,,,				2504	0.0624				p.V1204V		Atlas-SNP	.											.	TAF1L	382	.	0			c.C3612T						PASS	.	G		865,3541	339.4+/-305.8	83,699,1421	210.0	179.0	190.0		3612	0.5	1.0	9	dbSNP_127	190	547,8049	150.6+/-205.5	23,501,3774	no	coding-synonymous	TAF1L	NM_153809.2		106,1200,5195	AA,AG,GG		6.3634,19.6323,10.8599		1204/1827	32631966	1412,11590	2203	4298	6501	SO:0001819	synonymous_variant	138474	exon1			TTTTCGGACTGTC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3612C>T	9.37:g.32631966G>A		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	346	173	0.5	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			G|0.906;A|0.094	0.094	strong		0.428	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
CIITA	4261	hgsc.bcm.edu	37	16	11001821	11001821	+	Silent	SNP	C	C	T	rs45621432	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:11001821C>T	ENST00000324288.8	+	11	2605	c.2472C>T	c.(2470-2472)caC>caT	p.H824H	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	824					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						TTTGGCAGCACGTGGTACAGG	0.687			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								C|||	39	0.00778754	0.0	0.0058	5008	,	,		13150	0.0		0.0328	False		,,,				2504	0.002				p.H824H		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.C2472T						PASS	.	C		21,4371		0,21,2175	29.0	34.0	32.0		2472	-3.6	0.8	16	dbSNP_127	32	204,8394		2,200,4097	no	coding-synonymous	CIITA	NM_000246.3		2,221,6272	TT,TC,CC		2.3726,0.4781,1.7321		824/1131	11001821	225,12765	2196	4299	6495	SO:0001819	synonymous_variant	4261	exon11			GCAGCACGTGGTA	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.2472C>T	16.37:g.11001821C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			C|0.983;T|0.017	0.017	strong		0.687	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
RRP36	88745	hgsc.bcm.edu	37	6	42992808	42992808	+	Silent	SNP	T	T	C	rs3749904	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42992808T>C	ENST00000244496.5	+	2	226	c.216T>C	c.(214-216)aaT>aaC	p.N72N		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	72					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						TAGCTGGAAATAGTCCTAAGA	0.453													C|||	1724	0.344249	0.7133	0.2421	5008	,	,		22411	0.2123		0.1223	False		,,,				2504	0.2822				p.N72N		Atlas-SNP	.											.	RRP36	20	.	0			c.T216C						PASS	.	C		2782,1624	499.5+/-364.4	882,1018,303	135.0	118.0	124.0		216	2.0	0.0	6	dbSNP_107	124	1118,7482	767.9+/-407.6	65,988,3247	no	coding-synonymous	RRP36	NM_033112.2		947,2006,3550	CC,CT,TT		13.0,36.8588,29.9862		72/260	42992808	3900,9106	2203	4300	6503	SO:0001819	synonymous_variant	88745	exon2			TGGAAATAGTCCT	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.216T>C	6.37:g.42992808T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_033112	Q9BRF6|Q9P0C8	Silent	SNP	ENST00000244496.5	37	CCDS34453.1																																																																																			T|0.691;C|0.309	0.309	strong		0.453	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
MPHOSPH9	10198	hgsc.bcm.edu	37	12	123664514	123664514	+	Silent	SNP	G	G	A	rs1727301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:123664514G>A	ENST00000606320.1	-	15	2519	c.2313C>T	c.(2311-2313)aaC>aaT	p.N771N	MPHOSPH9_ENST00000541076.2_Silent_p.N741N|MPHOSPH9_ENST00000302349.5_Silent_p.N619N|MPHOSPH9_ENST00000392425.3_Silent_p.N619N			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	771						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		CAAGCAATTTGTTCTCAGTTG	0.269													G|||	1970	0.393371	0.0234	0.4179	5008	,	,		19244	0.6855		0.3956	False		,,,				2504	0.5726				p.N619N		Atlas-SNP	.											.	MPHOSPH9	75	.	0			c.C1857T						PASS	.	G		353,4041	177.6+/-206.5	17,319,1861	72.0	66.0	68.0		1857	2.7	1.0	12	dbSNP_89	68	3226,5366	474.7+/-368.9	587,2052,1657	no	coding-synonymous	MPHOSPH9	NM_022782.2		604,2371,3518	AA,AG,GG		37.5466,8.0337,27.5604		619/1032	123664514	3579,9407	2197	4296	6493	SO:0001819	synonymous_variant	10198	exon11			CAATTTGTTCTCA	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.2313C>T	12.37:g.123664514G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	212	79	0.372642	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Silent	SNP	ENST00000606320.1	37																																																																																				G|0.666;A|0.334	0.334	strong		0.269	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2		
NAV1	89796	hgsc.bcm.edu	37	1	201780773	201780773	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201780773C>T	ENST00000367296.4	+	25	5260	c.4840C>T	c.(4840-4842)Cgg>Tgg	p.R1614W	NAV1_ENST00000367300.3_Missense_Mutation_p.R1554W|NAV1_ENST00000367297.4_Missense_Mutation_p.R1606W|NAV1_ENST00000367295.1_Missense_Mutation_p.R1220W|NAV1_ENST00000295624.6_Missense_Mutation_p.R1611W|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367302.1_Missense_Mutation_p.R1567W|MIR1231_ENST00000408101.1_RNA	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1614					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						CCAGATAGACCGGGAAACAGG	0.517																																					p.R1614W		Atlas-SNP	.											NAV1,colon,carcinoma,0,1	NAV1	143	1	0			c.C4840T						scavenged	.						187.0	188.0	188.0					1																	201780773		2203	4300	6503	SO:0001583	missense	89796	exon25			ATAGACCGGGAAA	AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.4840C>T	1.37:g.201780773C>T	ENSP00000356265:p.Arg1614Trp	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	189	3	0.015873	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342657	0.82022	.	.	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295;ENST00000367301	T;T;T;T;T;T	0.07908	3.18;3.15;3.15;3.15;3.18;3.16	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.28830	0.0715	M	0.62723	1.935	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00533	-1.1685	10	0.72032	D	0.01	-28.1678	18.893	0.92412	0.0:1.0:0.0:0.0	.	1220;1611	Q8NEY1-5;Q8NEY1-3	.;.	W	1567;1614;1611;1606;1554;1220;22	ENSP00000356271:R1567W;ENSP00000356265:R1614W;ENSP00000295624:R1611W;ENSP00000356266:R1606W;ENSP00000356269:R1554W;ENSP00000356264:R1220W	ENSP00000295624:R1611W	R	+	1	2	NAV1	200047396	0.848000	0.29623	1.000000	0.80357	0.996000	0.88848	1.172000	0.31908	2.634000	0.89283	0.555000	0.69702	CGG	.	.	none		0.517	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
SLC35G5	83650	hgsc.bcm.edu	37	8	11188806	11188806	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11188806G>C	ENST00000382435.4	+	1	410	c.191G>C	c.(190-192)gGt>gCt	p.G64A		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	64	EamA 1.					integral component of membrane (GO:0016021)		p.G64A(1)									GCTTACCAGGGTTCCAACCTG	0.637																																					p.G64A		Atlas-SNP	.											AMAC1L2,trunk,malignant_melanoma,0,1	.	.	1	1	Substitution - Missense(1)	skin(1)	c.G191C						scavenged	.						151.0	146.0	148.0					8																	11188806		2203	4300	6503	SO:0001583	missense	83650	exon1			ACCAGGGTTCCAA	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.191G>C	8.37:g.11188806G>C	ENSP00000371872:p.Gly64Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	174	17	0.0977011	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.054055	0.00390	.	.	ENSG00000177710	ENST00000382435	T	0.50277	0.75	0.34	0.34	0.15985	.	0.536315	0.15627	N	0.252577	T	0.16471	0.0396	N	0.02539	-0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.25847	-1.0120	10	0.07644	T	0.81	-3.0E-4	6.0882	0.19978	0.0:0.3644:0.6356:0.0	.	64	Q96KT7	S35G5_HUMAN	A	64	ENSP00000371872:G64A	ENSP00000371872:G64A	G	+	2	0	SLC35G5	11226216	0.005000	0.15991	0.845000	0.33349	0.156000	0.22039	0.073000	0.14640	-1.304000	0.02329	-1.954000	0.00483	GGT	.	.	none		0.637	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
STK33	65975	hgsc.bcm.edu	37	11	8435077	8435077	+	Missense_Mutation	SNP	C	C	T	rs3751095|rs386750506	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8435077C>T	ENST00000447869.1	-	11	2227	c.1309G>A	c.(1309-1311)Gcc>Acc	p.A437T	STK33_ENST00000473980.1_5'UTR|STK33_ENST00000534493.1_Missense_Mutation_p.A396T|STK33_ENST00000396672.1_Missense_Mutation_p.A437T|STK33_ENST00000358872.3_Missense_Mutation_p.A250T|STK33_ENST00000315204.1_Missense_Mutation_p.A437T|STK33_ENST00000396673.1_Intron			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	437			A -> T (in dbSNP:rs3751095). {ECO:0000269|PubMed:17344846}.	DA -> ET (in Ref. 3; AAH31231). {ECO:0000305}.	protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		GTGTAATTGGCATCAGGGACA	0.418													C|||	1250	0.249601	0.1142	0.2565	5008	,	,		19625	0.2877		0.2545	False		,,,				2504	0.3834				p.A437T		Atlas-SNP	.											.	STK33	147	.	0			c.G1309A						PASS	.	C	THR/ALA	50,4352		16,18,2167	281.0	257.0	265.0		1309	-1.1	0.0	11	dbSNP_107	265	293,8299		104,85,4107	yes	missense	STK33	NM_030906.2	58	120,103,6274	TT,TC,CC		3.4101,1.1358,2.6397	benign	437/515	8435077	343,12651	2201	4296	6497	SO:0001583	missense	65975	exon13			AATTGGCATCAGG	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.1309G>A	11.37:g.8435077C>T	ENSP00000416750:p.Ala437Thr	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	403	188	0.466501	NM_030906	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	37	CCDS7789.1	407	0.18635531135531136	41	0.08333333333333333	101	0.27900552486187846	128	0.22377622377622378	137	0.18073878627968337	C	10.64	1.407242	0.25378	0.011358	0.034101	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000358872;ENST00000534493	T;T;T;T;T	0.71103	-0.48;-0.48;-0.48;-0.54;-0.47	4.67	-1.09	0.09904	Protein kinase-like domain (1);	3.221300	0.00669	N	0.000621	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.04991	-1.0913	9	0.12766	T	0.61	.	3.0517	0.06172	0.3164:0.3907:0.0:0.2929	rs3751095;rs33944616;rs3751095	437	Q9BYT3	STK33_HUMAN	T	437;437;437;250;396	ENSP00000416750:A437T;ENSP00000320754:A437T;ENSP00000379905:A437T;ENSP00000351743:A250T;ENSP00000436418:A396T	ENSP00000320754:A437T	A	-	1	0	STK33	8391653	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.871000	0.04223	-0.280000	0.09154	0.563000	0.77884	GCC	C|0.785;T|0.215	0.215	strong		0.418	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906	
PTPN5	84867	hgsc.bcm.edu	37	11	18764026	18764026	+	Missense_Mutation	SNP	G	G	C	rs4757707	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:18764026G>C	ENST00000358540.2	-	7	938	c.508C>G	c.(508-510)Cca>Gca	p.P170A	PTPN5_ENST00000477854.1_5'UTR|PTPN5_ENST00000396171.4_Missense_Mutation_p.P170A|PTPN5_ENST00000396170.1_Missense_Mutation_p.P138A|PTPN5_ENST00000496201.2_5'UTR|PTPN5_ENST00000396167.2_Missense_Mutation_p.P138A|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000396168.1_Missense_Mutation_p.P146A	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	170			P -> A (in dbSNP:rs4757707). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)	p.P170A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GGTGGCTCTGGGGGTGTCCTC	0.632													G|||	1489	0.297324	0.0242	0.4899	5008	,	,		16566	0.3194		0.3857	False		,,,				2504	0.4162				p.P170A		Atlas-SNP	.											PTPN5_ENST00000358540,caecum,carcinoma,0,3	PTPN5	163	3	1	Substitution - Missense(1)	skin(1)	c.C508G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO	419,3979	203.5+/-225.9	22,375,1802	41.0	45.0	43.0		412,508,508	1.4	0.8	11	dbSNP_111	43	3372,5214	497.7+/-374.6	674,2024,1595	yes	missense,missense,missense	PTPN5	NM_001039970.1,NM_006906.1,NM_032781.3	27,27,27	696,2399,3397	CC,CG,GG		39.2732,9.5271,29.1975	benign,benign,benign	138/534,170/566,170/566	18764026	3791,9193	2199	4293	6492	SO:0001583	missense	84867	exon7			GCTCTGGGGGTGT	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.508C>G	11.37:g.18764026G>C	ENSP00000351342:p.Pro170Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	37	CCDS7845.1	679	0.3108974358974359	20	0.04065040650406504	191	0.5276243093922652	173	0.30244755244755245	295	0.3891820580474934	G	11.26	1.587311	0.28268	0.095271	0.392732	ENSG00000110786	ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	T;T;T;T;T	0.03831	3.79;3.92;3.79;3.92;3.81	4.41	1.4	0.22301	.	0.320871	0.27039	N	0.021226	T	0.00012	0.0000	N	0.24115	0.695	0.40928	P	0.015637000000000012	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31668	-0.9935	9	0.13108	T	0.6	.	9.4819	0.38906	0.0:0.3185:0.5364:0.1451	rs4757707;rs4757707	170;138	P54829;B3KXG7	PTN5_HUMAN;.	A	170;138;170;138;146	ENSP00000351342:P170A;ENSP00000379473:P138A;ENSP00000379474:P170A;ENSP00000379470:P138A;ENSP00000379471:P146A	ENSP00000351342:P170A	P	-	1	0	PTPN5	18720602	0.979000	0.34478	0.803000	0.32268	0.930000	0.56654	1.786000	0.38694	0.111000	0.17947	0.561000	0.74099	CCA	G|0.702;C|0.298	0.298	strong		0.632	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
TENM4	26011	hgsc.bcm.edu	37	11	78482155	78482155	+	Silent	SNP	G	G	A	rs116862565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:78482155G>A	ENST00000278550.7	-	18	2883	c.2421C>T	c.(2419-2421)aaC>aaT	p.N807N		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	807	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)										TACATCTGCCGTTGCCATTGC	0.552													G|||	28	0.00559105	0.0008	0.0086	5008	,	,		20730	0.0		0.0159	False		,,,				2504	0.0051				p.N807N		Atlas-SNP	.											ODZ4_ENST00000278550,NS,carcinoma,0,2	.	.	2	0			c.C2421T						PASS	.	G		15,4275		0,15,2130	55.0	56.0	56.0		2421	-8.1	0.0	11	dbSNP_132	56	129,8347		0,129,4109	no	coding-synonymous	ODZ4	NM_001098816.2		0,144,6239	AA,AG,GG		1.5219,0.3497,1.128		807/2770	78482155	144,12622	2145	4238	6383	SO:0001819	synonymous_variant	26011	exon18			TCTGCCGTTGCCA	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.2421C>T	11.37:g.78482155G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	9.215	1.031812	0.19590	0.003497	0.015219	ENSG00000149256	ENST00000533525	.	.	.	5.24	-8.12	0.01078	.	.	.	.	.	T	0.49457	0.1558	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70019	-0.4987	4	.	.	.	.	18.6176	0.91308	0.781:0.0:0.219:0.0	.	.	.	.	M	112	.	.	T	-	2	0	ODZ4	78159803	0.027000	0.19231	0.033000	0.17914	0.940000	0.58332	-0.469000	0.06648	-1.967000	0.01008	-1.069000	0.02264	ACG	G|0.993;A|0.007	0.007	strong		0.552	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
TBX2	6909	hgsc.bcm.edu	37	17	59485555	59485555	+	Silent	SNP	C	C	T	rs1057987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:59485555C>T	ENST00000240328.3	+	7	2108	c.1827C>T	c.(1825-1827)agC>agT	p.S609S	RP11-332H18.4_ENST00000592009.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	609					aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						TCTCCCGGAGCCCCTTCCTGG	0.706													C|||	2125	0.424321	0.1997	0.4236	5008	,	,		14506	0.369		0.7276	False		,,,				2504	0.4734				p.S609S	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C1827T						PASS	.	C		1267,3129		192,883,1123	20.0	21.0	21.0		1827	3.1	1.0	17	dbSNP_86	21	6225,2367		2262,1701,333	no	coding-synonymous	TBX2	NM_005994.3		2454,2584,1456	TT,TC,CC		27.5489,28.8217,42.316		609/713	59485555	7492,5496	2198	4296	6494	SO:0001819	synonymous_variant	6909	exon7			CCGGAGCCCCTTC	AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068		"""T-boxes"""	11597	protein-coding gene	gene with protein product		600747				8530034	Standard	NM_005994		Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.1827C>T	17.37:g.59485555C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_005994	Q16424|Q7Z647	Silent	SNP	ENST00000240328.3	37	CCDS11627.2																																																																																			C|0.456;G|0.000;T|0.544	0.544	strong		0.706	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994	
SWT1	54823	hgsc.bcm.edu	37	1	185143721	185143721	+	Missense_Mutation	SNP	A	A	G	rs10489579	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	159	0	0		WXS	Illumina HiSeq	Phase_I	191	91	0.47644	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	
BSN	8927	hgsc.bcm.edu	37	3	49701298	49701298	+	Missense_Mutation	SNP	G	G	A	rs2005557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49701298G>A	ENST00000296452.4	+	8	11701	c.11587G>A	c.(11587-11589)Gca>Aca	p.A3863T		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3863			A -> T (in dbSNP:rs2005557). {ECO:0000269|PubMed:10329005, ECO:0000269|PubMed:9455477, ECO:0000269|PubMed:9806829}.		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)		GGCCCAGCCAGCACCAGGACC	0.592													A|||	3207	0.640375	0.4032	0.683	5008	,	,		19609	0.9325		0.5099	False		,,,				2504	0.7638				p.A3863T		Atlas-SNP	.											BSN,NS,adenoma,0,1	BSN	272	1	0			c.G11587A						PASS	.	A	THR/ALA	1903,2503	626.4+/-394.7	413,1077,713	108.0	94.0	99.0		11587	1.3	0.6	3	dbSNP_92	99	4443,4157	566.4+/-388.7	1166,2111,1023	yes	missense	BSN	NM_003458.3	58	1579,3188,1736	AA,AG,GG		48.3372,43.1911,48.7929	possibly-damaging	3863/3927	49701298	6346,6660	2203	4300	6503	SO:0001583	missense	8927	exon8			CAGCCAGCACCAG	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.11587G>A	3.37:g.49701298G>A	ENSP00000296452:p.Ala3863Thr	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	200	199	0.995	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	1341	0.614010989010989	188	0.3821138211382114	229	0.6325966850828729	536	0.9370629370629371	388	0.5118733509234829	A	5.748	0.322360	0.10900	0.431911	0.516628	ENSG00000164061	ENST00000296452	T	0.17854	2.25	3.43	1.26	0.21427	.	0.977424	0.08377	N	0.955199	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	0.41431	-0.9509	9	0.02654	T	1	-0.4728	1.03	0.01536	0.3322:0.2632:0.2701:0.1345	rs2005557;rs59206941;rs2005557	3863	Q9UPA5	BSN_HUMAN	T	3863	ENSP00000296452:A3863T	ENSP00000296452:A3863T	A	+	1	0	BSN	49676302	0.019000	0.18553	0.580000	0.28601	0.385000	0.30292	0.707000	0.25704	0.010000	0.14839	-0.521000	0.04368	GCA	G|0.472;A|0.528	0.528	strong		0.592	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
RP1L1	94137	hgsc.bcm.edu	37	8	10466482	10466482	+	Missense_Mutation	SNP	G	G	A	rs13267180	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10466482G>A	ENST00000382483.3	-	4	5349	c.5126C>T	c.(5125-5127)gCc>gTc	p.A1709V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1789					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTTGCCAGGGGCCACCTCTGC	0.647													G|||	1556	0.310703	0.4009	0.33	5008	,	,		14848	0.0208		0.499	False		,,,				2504	0.2802				p.A1709V		Atlas-SNP	.											RP1L1,colon,carcinoma,-1,1	RP1L1	453	1	0			c.C5126T						PASS	.	G	VAL/ALA	1604,2440		316,972,734	79.0	88.0	85.0		5126	0.7	0.0	8	dbSNP_121	85	3972,4380		959,2054,1163	yes	missense	RP1L1	NM_178857.5	64	1275,3026,1897	AA,AG,GG		47.5575,39.6637,44.9823	benign	1709/2401	10466482	5576,6820	2022	4176	6198	SO:0001583	missense	94137	exon4			CCAGGGGCCACCT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5126C>T	8.37:g.10466482G>A	ENSP00000371923:p.Ala1709Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	727	0.33287545787545786	210	0.4268292682926829	128	0.35359116022099446	13	0.022727272727272728	376	0.49604221635883905	G	13.50	2.255844	0.39896	0.396637	0.475575	ENSG00000183638	ENST00000382483	T	0.05855	3.38	4.54	0.695	0.18070	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.29862	0.259	B	0.22386	0.039	T	0.38001	-0.9681	8	0.33940	T	0.23	0.0686	8.0577	0.30614	0.4262:0.0:0.5738:0.0	rs13267180;rs58866563;rs13267180	1709	A6NKC6	.	V	1709	ENSP00000371923:A1709V	ENSP00000371923:A1709V	A	-	2	0	RP1L1	10503892	0.000000	0.05858	0.000000	0.03702	0.101000	0.19017	-0.304000	0.08199	-0.059000	0.13154	0.462000	0.41574	GCC	G|0.614;A|0.386	0.386	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
UBQLNL	143630	hgsc.bcm.edu	37	11	5537161	5537161	+	Missense_Mutation	SNP	A	A	G	rs2047456	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5537161A>G	ENST00000380184.1	-	1	774	c.511T>C	c.(511-513)Tgc>Cgc	p.C171R	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	171			C -> R (in dbSNP:rs2047456). {ECO:0000269|PubMed:15489334}.							endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		TGTGCTTTGCACTCTGGGTGG	0.493													a|||	1581	0.315695	0.3328	0.3487	5008	,	,		21650	0.376		0.2555	False		,,,				2504	0.2689				p.C171R		Atlas-SNP	.											.	UBQLNL	74	.	0			c.T511C						PASS	.	A	ARG/CYS	1410,2992	462.3+/-353.2	234,942,1025	127.0	124.0	125.0		511	-3.1	0.0	11	dbSNP_94	125	2339,6255	391.8+/-343.8	330,1679,2288	yes	missense	UBQLNL	NM_145053.4	180	564,2621,3313	GG,GA,AA		27.2167,32.0309,28.8473	benign	171/476	5537161	3749,9247	2201	4297	6498	SO:0001583	missense	143630	exon1			CTTTGCACTCTGG	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.511T>C	11.37:g.5537161A>G	ENSP00000369531:p.Cys171Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	37	CCDS31385.1	722	0.3305860805860806	170	0.34552845528455284	112	0.30939226519337015	237	0.4143356643356643	203	0.2678100263852243	a	0.006	-2.103227	0.00356	0.320309	0.272167	ENSG00000175518	ENST00000380184	T	0.45276	0.9	4.87	-3.1	0.05315	.	1.830600	0.02860	N	0.130137	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	0.39921	-0.9590	9	0.34782	T	0.22	.	3.4562	0.07516	0.4121:0.0:0.2801:0.3078	rs2047456;rs3802977;rs17846117;rs17859121;rs58916449;rs2047456	171	Q8IYU4	UBQLN_HUMAN	R	171	ENSP00000369531:C171R	ENSP00000369531:C171R	C	-	1	0	UBQLNL	5493737	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	-0.203000	0.09438	-0.345000	0.08325	-0.140000	0.14226	TGC	A|0.694;G|0.306	0.306	strong		0.493	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
TNRC6A	27327	hgsc.bcm.edu	37	16	24801737	24801737	+	Missense_Mutation	SNP	G	G	A	rs6497759	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:24801737G>A	ENST00000395799.3	+	6	1903	c.1774G>A	c.(1774-1776)Gca>Aca	p.A592T	TNRC6A_ENST00000315183.7_Missense_Mutation_p.A592T	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	592	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.|Sufficient for interaction with AGO2.		A -> T (in dbSNP:rs6497759).		cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		TGGAAATGGCGCAAATTCTGG	0.483													G|||	800	0.159744	0.1974	0.1455	5008	,	,		21893	0.126		0.162	False		,,,				2504	0.1513				p.A592T		Atlas-SNP	.											.	TNRC6A	171	.	0			c.G1774A						PASS	.	G	THR/ALA	819,3575	325.9+/-299.3	73,673,1451	95.0	94.0	94.0		1774	1.2	0.6	16	dbSNP_116	94	1643,6957	302.5+/-306.0	156,1331,2813	yes	missense	TNRC6A	NM_014494.2	58	229,2004,4264	AA,AG,GG		19.1047,18.6391,18.9472	benign	592/1963	24801737	2462,10532	2197	4300	6497	SO:0001583	missense	27327	exon6			AATGGCGCAAATT	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.1774G>A	16.37:g.24801737G>A	ENSP00000379144:p.Ala592Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	146	62	0.424658	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	304	0.1391941391941392	80	0.16260162601626016	55	0.15193370165745856	59	0.10314685314685315	110	0.14511873350923482	G	0.006	-2.114307	0.00349	0.186391	0.191047	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11169	2.8;2.8	5.66	1.22	0.21188	.	0.346332	0.32134	N	0.006527	T	0.00012	0.0000	N	0.11427	0.14	0.41321	P	0.012826000000000004	P;P;P	0.42871	0.709;0.792;0.688	B;B;B	0.24974	0.057;0.043;0.028	T	0.48614	-0.9020	9	0.12103	T	0.63	-2.3485	6.1035	0.20061	0.0692:0.2501:0.5514:0.1293	rs6497759;rs52832662;rs59562937;rs6497759	339;592;592	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	T	592	ENSP00000326900:A592T;ENSP00000379144:A592T	ENSP00000326900:A592T	A	+	1	0	TNRC6A	24709238	0.997000	0.39634	0.630000	0.29268	0.014000	0.08584	3.886000	0.56190	0.314000	0.23086	-0.499000	0.04595	GCA	G|0.839;A|0.161	0.161	strong		0.483	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
MYO5B	4645	hgsc.bcm.edu	37	18	47363963	47363963	+	Missense_Mutation	SNP	T	T	C	rs112417235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:47363963T>C	ENST00000285039.7	-	37	5361	c.5062A>G	c.(5062-5064)Atg>Gtg	p.M1688V	MYO5B_ENST00000592688.1_Missense_Mutation_p.M258V|SCARNA17_ENST00000589499.1_RNA|RP11-886H22.1_ENST00000590532.2_Missense_Mutation_p.M11V|MYO5B_ENST00000324581.6_Missense_Mutation_p.M803V	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1688	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.		M -> V. {ECO:0000269|PubMed:21206382}.		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)		GCGTTGATCATGTAGAAGAGC	0.517													T|||	82	0.0163738	0.0015	0.0288	5008	,	,		23453	0.0		0.0358	False		,,,				2504	0.0245				p.M1688V		Atlas-SNP	.											.	MYO5B	178	.	0			c.A5062G						PASS	.	T	VAL/MET	24,4024		0,24,2000	65.0	62.0	63.0		5062	2.4	1.0	18	dbSNP_132	63	256,8102		2,252,3925	no	missense	MYO5B	NM_001080467.2	21	2,276,5925	CC,CT,TT		3.0629,0.5929,2.257	benign	1688/1849	47363963	280,12126	2024	4179	6203	SO:0001583	missense	4645	exon37			TGATCATGTAGAA	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.5062A>G	18.37:g.47363963T>C	ENSP00000285039:p.Met1688Val	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	311	115	0.369775	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	34	0.015567765567765568	0	0.0	11	0.03038674033149171	0	0.0	23	0.030343007915567283	T	11.24	1.579427	0.28180	0.005929	0.030629	ENSG00000167306	ENST00000285039;ENST00000324581	D;T	0.85629	-2.01;2.61	4.77	2.37	0.29283	Dilute (1);Dil domain (1);	0.264499	0.42172	N	0.000759	T	0.48484	0.1502	N	0.05230	-0.09	0.29582	N	0.849093	B;P	0.45283	0.001;0.855	B;P	0.44647	0.004;0.456	T	0.63292	-0.6670	10	0.54805	T	0.06	.	8.8779	0.35356	0.0:0.156:0.0:0.844	.	1688;803	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	V	1688;803	ENSP00000285039:M1688V;ENSP00000315531:M803V	ENSP00000285039:M1688V	M	-	1	0	MYO5B	45617961	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.620000	0.36976	0.412000	0.25729	-0.353000	0.07706	ATG	T|0.979;C|0.021	0.021	strong		0.517	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
SLC13A3	64849	hgsc.bcm.edu	37	20	45242269	45242269	+	Silent	SNP	G	G	C	rs2273024	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:45242269G>C	ENST00000279027.4	-	2	225	c.207C>G	c.(205-207)ctC>ctG	p.L69L	SLC13A3_ENST00000290317.5_Silent_p.L22L|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000339636.3_Silent_p.L69L|SLC13A3_ENST00000472148.1_Silent_p.L22L|SLC13A3_ENST00000495082.1_Silent_p.L22L|SLC13A3_ENST00000417157.2_Silent_p.L22L|SLC13A3_ENST00000372121.1_Silent_p.L69L|SLC13A3_ENST00000413164.2_Silent_p.L69L|SLC13A3_ENST00000396360.1_Silent_p.L22L	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	69					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)	TGAAGGGGAAGAGGACGATGG	0.612													G|||	1548	0.309105	0.2088	0.3617	5008	,	,		14974	0.2798		0.3539	False		,,,				2504	0.3916				p.L69L		Atlas-SNP	.											.	SLC13A3	88	.	0			c.C207G						PASS	.	G	,,,,	1028,3378	373.4+/-320.8	116,796,1291	74.0	55.0	61.0		66,207,66,,207	-0.3	1.0	20	dbSNP_100	61	2852,5748	440.6+/-359.6	451,1950,1899	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	SLC13A3	NM_001011554.2,NM_001193339.1,NM_001193340.1,NM_001193342.1,NM_022829.5	,,,,	567,2746,3190	CC,CG,GG		33.1628,23.3318,29.8324	,,,,	22/556,69/553,22/521,,69/603	45242269	3880,9126	2203	4300	6503	SO:0001819	synonymous_variant	64849	exon2			GGGGAAGAGGACG	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.207C>G	20.37:g.45242269G>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	152	80	0.526316	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	37	CCDS13400.1																																																																																			G|0.680;C|0.320	0.320	strong		0.612	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
C11orf21	29125	hgsc.bcm.edu	37	11	2323022	2323022	+	Missense_Mutation	SNP	C	C	T	rs12276847	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:2323022C>T	ENST00000381153.3	-	1	268	c.17G>A	c.(16-18)tGt>tAt	p.C6Y	TSPAN32_ENST00000182290.4_5'Flank|TSPAN32_ENST00000451520.2_5'Flank|TSPAN32_ENST00000381121.3_5'Flank|C11orf21_ENST00000470369.1_5'UTR			Q9P2W6	CK021_HUMAN	chromosome 11 open reading frame 21	6						cytoplasm (GO:0005737)											CCACATCCCACACCAGGTCCT	0.642											OREG0003773	type=REGULATORY REGION|Gene=TSPAN32|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1052	0.210064	0.0802	0.2637	5008	,	,		16273	0.1399		0.3588	False		,,,				2504	0.2669				p.V24M		Atlas-SNP	.											.	C11orf21	11	.	0			c.G70A						PASS	.	C	MET/VAL	171,1213		16,139,537	90.0	99.0	96.0		70	-0.9	0.0	11	dbSNP_120	96	1092,2090		192,708,691	yes	missense	C11orf21	NM_001142946.1	21	208,847,1228	TT,TC,CC		34.318,12.3555,27.661	benign	24/179	2323022	1263,3303	692	1591	2283	SO:0001583	missense	29125	exon1			ATCCCACACCAGG	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.17G>A	11.37:g.2323022C>T	ENSP00000370545:p.Cys6Tyr	Somatic	61	0	0	602	WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_001142946		Missense_Mutation	SNP	ENST00000381153.3	37		521|521	0.23855311355311357|0.23855311355311357	45|45	0.09146341463414634|0.09146341463414634	117|117	0.32320441988950277|0.32320441988950277	81|81	0.14160839160839161|0.14160839160839161	278|278	0.36675461741424803|0.36675461741424803	C|C	2.389|2.389	-0.340270|-0.340270	0.05243|0.05243	0.123555|0.123555	0.34318|0.34318	ENSG00000110665|ENSG00000110665	ENST00000381153|ENST00000456145	.|.	.|.	.|.	1.85|1.85	-0.933|-0.933	0.10431|0.10431	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.04013	0.0|0.001	T|T	0.41770|0.41770	-0.9490|-0.9490	7|7	0.02654|0.87932	T|D	1|0	.|.	4.636|4.636	0.12525|0.12525	0.0:0.4842:0.0:0.5158|0.0:0.4842:0.0:0.5158	rs12276847|rs12276847	6|24	Q9P2W6|E9PAM5	CK021_HUMAN|.	Y|M	6|24	.|.	ENSP00000370545:C6Y|ENSP00000406541:V24M	C|V	-|-	2|1	0|0	C11orf21|C11orf21	2279598|2279598	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.563000|-0.563000	0.05943|0.05943	-0.238000|-0.238000	0.09724|0.09724	-0.521000|-0.521000	0.04368|0.04368	TGT|GTG	C|0.750;T|0.250	0.250	strong		0.642	C11orf21-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000026908.2	NM_001142946	
PRG2	5553	hgsc.bcm.edu	37	11	57157405	57157405	+	Silent	SNP	A	A	G	rs490358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57157405A>G	ENST00000311862.5	-	2	86	c.13T>C	c.(13-15)Tta>Cta	p.L5L	PRG2_ENST00000525955.1_Silent_p.L5L|PRG2_ENST00000533605.1_Silent_p.L5L|RP11-872D17.8_ENST00000529411.1_Silent_p.L110L	NM_001243245.1|NM_002728.4	NP_001230174.1|NP_002719.3	P13727	PRG2_HUMAN	proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein)	5					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)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)	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)	Sargramostim(DB00020)	GCCAGAAGTAAGGGGAGTTTC	0.423													G|||	3767	0.752196	0.6241	0.8343	5008	,	,		21396	0.7718		0.7406	False		,,,				2504	0.8589				p.L5L		Atlas-SNP	.											.	PRG2	65	.	0			c.T13C						PASS	.	G		2764,1638	498.8+/-364.2	869,1026,306	184.0	171.0	175.0		13	2.8	0.9	11	dbSNP_83	175	6281,2311	384.9+/-341.3	2283,1715,298	no	coding-synonymous	PRG2	NM_002728.4		3152,2741,604	GG,GA,AA		26.8971,37.2104,30.3909		5/223	57157405	9045,3949	2201	4296	6497	SO:0001819	synonymous_variant	5553	exon2			GAAGTAAGGGGAG	BC005929	CCDS7955.1, CCDS58133.1	11q12	2005-11-25				ENSG00000186652			9362	protein-coding gene	gene with protein product		605601				1565101	Standard	NM_001243245		Approved	MBP, BMPG		P13727		ENST00000311862.5:c.13T>C	11.37:g.57157405A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001243245	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000311862.5	37	CCDS7955.1																																																																																			A|0.292;G|0.708	0.708	strong		0.423	PRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392468.1	NM_002728	
RASAL3	64926	hgsc.bcm.edu	37	19	15569378	15569378	+	Missense_Mutation	SNP	G	G	C	rs58123634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	125	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	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	
MGMT	4255	hgsc.bcm.edu	37	10	131265545	131265545	+	Silent	SNP	C	C	T	rs16906252	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:131265545C>T	ENST00000306010.7	+	1	98	c.66C>T	c.(64-66)cgC>cgT	p.R22R		NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	0					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	L-Cysteine(DB00151)	TCGCGGTGCGCACCGTTTGCG	0.731								Direct reversal of damage					C|||	123	0.0245607	0.0015	0.0288	5008	,	,		9189	0.0		0.0616	False		,,,				2504	0.0399				p.R22R		Atlas-SNP	.											.	MGMT	32	.	0			c.C66T	GRCh37	CR075258	MGMT	R	rs16906252	PASS	.	C		22,2814		0,22,1396	6.0	7.0	7.0		66	3.2	0.0	10	dbSNP_123	7	390,6204		5,380,2912	no	coding-synonymous	MGMT	NM_002412.3		5,402,4308	TT,TC,CC		5.9145,0.7757,4.369		22/239	131265545	412,9018	1418	3297	4715	SO:0001819	synonymous_variant	4255	exon1			GGTGCGCACCGTT	M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.66C>T	10.37:g.131265545C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_002412	Q5VY78	Silent	SNP	ENST00000306010.7	37	CCDS7660.2																																																																																			C|0.966;T|0.034	0.034	strong		0.731	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412	
TARBP1	6894	hgsc.bcm.edu	37	1	234529519	234529519	+	Silent	SNP	C	C	T	rs1802871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	211	0	0		WXS	Illumina HiSeq	Phase_I	178	60	0.337079	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	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68024134	68024134	+	Splice_Site	SNP	A	A	T	rs3825723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:68024134A>T	ENST00000329153.5	+	4	470	c.338A>T	c.(337-339)cAg>cTg	p.Q113L		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	113			Q -> L (in dbSNP:rs3825723).			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)		CTGGAGAAGCAGGTAAGGGCT	0.567													A|||	790	0.157748	0.0484	0.1383	5008	,	,		19248	0.2937		0.1491	False		,,,				2504	0.1881				p.Q113L		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.A338T						PASS	.	A	LEU/GLN	269,3779		9,251,1764	60.0	61.0	61.0		338	5.4	1.0	14	dbSNP_107	61	1227,7161		93,1041,3060	yes	missense-near-splice	PLEKHH1	NM_020715.2	113	102,1292,4824	TT,TA,AA		14.628,6.6453,12.0296	possibly-damaging	113/1365	68024134	1496,10940	2024	4194	6218	SO:0001630	splice_region_variant	57475	exon4			AGAAGCAGGTAAG	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.339+1A>T	14.37:g.68024134A>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	366	0.16758241758241757	30	0.06097560975609756	47	0.1298342541436464	172	0.3006993006993007	117	0.15435356200527706	A	24.6	4.550030	0.86127	0.066453	0.14628	ENSG00000054690	ENST00000329153	T	0.32753	1.44	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.73962	2.25	0.09310	P	1.0	D	0.76494	0.999	D	0.78314	0.991	T	0.15037	-1.0451	9	0.36615	T	0.2	.	13.0709	0.59061	1.0:0.0:0.0:0.0	rs3825723;rs52813401;rs3825723	113	Q9ULM0	PKHH1_HUMAN	L	113	ENSP00000330278:Q113L	ENSP00000330278:Q113L	Q	+	2	0	PLEKHH1	67093887	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.541000	0.82084	2.279000	0.76181	0.459000	0.35465	CAG	A|0.828;T|0.172	0.172	strong		0.567	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	Missense_Mutation
CLDN20	49861	hgsc.bcm.edu	37	6	155597147	155597147	+	Silent	SNP	C	C	T	rs1555774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:155597147C>T	ENST00000367165.3	+	2	674	c.294C>T	c.(292-294)tcC>tcT	p.S98S	TFB1M_ENST00000367166.4_Intron	NM_001001346.3	NP_001001346.1	P56880	CLD20_HUMAN	claudin 20	98					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(1)|lung(2)	3				OV - Ovarian serous cystadenocarcinoma(155;7.82e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0114)		TCTGCACTTCCACAGTAGGAA	0.532													C|||	1993	0.397963	0.2572	0.5159	5008	,	,		22057	0.6528		0.2535	False		,,,				2504	0.3906				p.S98S		Atlas-SNP	.											.	CLDN20	10	.	0			c.C294T						PASS	.	C	,	1192,3214	414.6+/-336.9	166,860,1177	133.0	116.0	121.0		294,	0.2	0.0	6	dbSNP_88	121	2290,6310	386.5+/-341.9	312,1666,2322	no	coding-synonymous,intron	CLDN20,TFB1M	NM_001001346.3,NM_016020.3	,	478,2526,3499	TT,TC,CC		26.6279,27.054,26.7723	,	98/220,	155597147	3482,9524	2203	4300	6503	SO:0001819	synonymous_variant	49861	exon2			CACTTCCACAGTA	BC020838	CCDS5249.1	6q25	2008-08-01			ENSG00000171217	ENSG00000171217		"""Claudins"""	2042	protein-coding gene	gene with protein product						16836752	Standard	NM_001001346		Approved		uc003qql.2	P56880	OTTHUMG00000015882	ENST00000367165.3:c.294C>T	6.37:g.155597147C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_001001346		Silent	SNP	ENST00000367165.3	37	CCDS5249.1																																																																																			C|0.681;T|0.319	0.319	strong		0.532	CLDN20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042818.1	NM_001001346	
KRT32	3882	hgsc.bcm.edu	37	17	39622068	39622068	+	Missense_Mutation	SNP	G	G	T	rs2071561	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39622068G>T	ENST00000225899.3	-	3	768	c.665C>A	c.(664-666)tCc>tAc	p.S222Y	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	222	Coil 1B.|Rod.		S -> Y (in dbSNP:rs2071561).		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)				CTCCTTCAGGGACTCAACCTG	0.617													G|||	2502	0.499601	0.2413	0.5187	5008	,	,		18777	0.6369		0.4761	False		,,,				2504	0.7178				p.S222Y		Atlas-SNP	.											.	KRT32	57	.	0			c.C665A						PASS	.	G	TYR/SER	1268,3138	434.1+/-343.8	181,906,1116	82.0	70.0	74.0		665	4.1	1.0	17	dbSNP_96	74	4288,4312	576.5+/-390.4	1072,2144,1084	yes	missense	KRT32	NM_002278.3	144	1253,3050,2200	TT,TG,GG		49.8605,28.7789,42.7187	probably-damaging	222/449	39622068	5556,7450	2203	4300	6503	SO:0001583	missense	3882	exon3			TTCAGGGACTCAA	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.665C>A	17.37:g.39622068G>T	ENSP00000225899:p.Ser222Tyr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	65	0.439189	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	1016	0.4652014652014652	121	0.2459349593495935	205	0.5662983425414365	339	0.5926573426573427	351	0.4630606860158311	G	17.95	3.513733	0.64522	0.287789	0.498605	ENSG00000108759	ENST00000225899	D	0.90844	-2.74	5.1	4.12	0.48240	Filament (1);	0.000000	0.38720	N	0.001589	T	0.00012	0.0000	H	0.95816	3.725	0.30879	P	0.731614	D	0.58620	0.983	D	0.72338	0.977	T	0.10222	-1.0639	9	0.87932	D	0	.	9.1393	0.36894	0.0786:0.1455:0.7759:0.0	rs2071561;rs52794180;rs60448298;rs2071561	222	Q14532	K1H2_HUMAN	Y	222	ENSP00000225899:S222Y	ENSP00000225899:S222Y	S	-	2	0	KRT32	36875594	0.000000	0.05858	1.000000	0.80357	0.995000	0.86356	0.600000	0.24104	1.285000	0.44548	0.558000	0.71614	TCC	G|0.553;T|0.445	0.445	strong		0.617	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
GPC6	10082	hgsc.bcm.edu	37	13	95034749	95034749	+	Missense_Mutation	SNP	G	G	A	rs1535692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:95034749G>A	ENST00000377047.4	+	7	1849	c.1234G>A	c.(1234-1236)Gtg>Atg	p.V412M		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	412			V -> M (in dbSNP:rs1535692). {ECO:0000269|PubMed:14702039}.		carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GGACGAGAGCGTGACAGCGGG	0.527													G|||	856	0.170927	0.0598	0.2695	5008	,	,		21317	0.2093		0.1918	False		,,,				2504	0.1902				p.V412M		Atlas-SNP	.											GPC6,NS,carcinoma,0,1	GPC6	102	1	0			c.G1234A						PASS	.	G	MET/VAL	353,4053	182.6+/-210.3	20,313,1870	152.0	136.0	141.0		1234	4.0	0.8	13	dbSNP_88	141	1637,6963	303.0+/-306.2	166,1305,2829	yes	missense	GPC6	NM_005708.3	21	186,1618,4699	AA,AG,GG		19.0349,8.0118,15.3006	benign	412/556	95034749	1990,11016	2203	4300	6503	SO:0001583	missense	10082	exon7			GAGAGCGTGACAG	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1234G>A	13.37:g.95034749G>A	ENSP00000366246:p.Val412Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	406	0.1858974358974359	32	0.06504065040650407	90	0.24861878453038674	136	0.23776223776223776	148	0.19525065963060687	G	2.075	-0.412013	0.04799	0.080118	0.190349	ENSG00000183098	ENST00000377047	T	0.50001	0.76	5.74	3.97	0.46021	.	0.284066	0.33916	N	0.004424	T	0.00012	0.0000	N	0.02802	-0.49	0.34299	P	0.31582299999999996	B	0.24823	0.112	B	0.25884	0.064	T	0.23404	-1.0189	9	0.10636	T	0.68	.	10.4396	0.44457	0.1561:0.0:0.8439:0.0	rs1535692;rs17791864;rs52821250;rs57981092;rs1535692	412	Q9Y625	GPC6_HUMAN	M	412	ENSP00000366246:V412M	ENSP00000366246:V412M	V	+	1	0	GPC6	93832750	1.000000	0.71417	0.821000	0.32701	0.597000	0.36814	5.119000	0.64679	0.734000	0.32515	-0.133000	0.14855	GTG	G|0.835;A|0.165	0.165	strong		0.527	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	
STYXL1	51657	hgsc.bcm.edu	37	7	75634687	75634687	+	Silent	SNP	G	G	A	rs1044484	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:75634687G>A	ENST00000248600.1	-	6	831	c.489C>T	c.(487-489)atC>atT	p.I163I	STYXL1_ENST00000340062.5_Silent_p.I67I|STYXL1_ENST00000360591.3_3'UTR|STYXL1_ENST00000431581.1_Silent_p.I163I|STYXL1_ENST00000451157.1_Silent_p.I163I|STYXL1_ENST00000359697.3_Silent_p.I163I	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	163	Tyrosine-protein phosphatase.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						TCCCTGGCACGATTTCAATGG	0.473													g|||	257	0.0513179	0.0053	0.1052	5008	,	,		13912	0.001		0.1551	False		,,,				2504	0.0204				p.I163I		Atlas-SNP	.											.	STYXL1	35	.	0			c.C489T						PASS	.	G		137,4269	97.6+/-136.3	3,131,2069	124.0	112.0	116.0		489	-2.4	0.0	7	dbSNP_86	116	1438,7162	277.4+/-292.8	112,1214,2974	no	coding-synonymous	STYXL1	NM_016086.2		115,1345,5043	AA,AG,GG		16.7209,3.1094,12.1098		163/314	75634687	1575,11431	2203	4300	6503	SO:0001819	synonymous_variant	51657	exon6			TGGCACGATTTCA	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	18165	protein-coding gene	gene with protein product			"""dual specificity phosphatase 24 (putative)"""	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.489C>T	7.37:g.75634687G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_016086	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Silent	SNP	ENST00000248600.1	37	CCDS5580.1																																																																																			G|0.900;A|0.100	0.100	strong		0.473	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086	
TGM1	7051	hgsc.bcm.edu	37	14	24728294	24728294	+	Silent	SNP	G	G	T	rs1126432	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24728294G>T	ENST00000206765.6	-	7	1269	c.1146C>A	c.(1144-1146)ggC>ggA	p.G382G	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	382			G -> R (in ARCI1).		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	TGGTGGTCACGCCAGCAAAGA	0.632													G|||	778	0.155351	0.1815	0.1657	5008	,	,		18927	0.0853		0.2028	False		,,,				2504	0.136				p.G382G		Atlas-SNP	.											.	TGM1	73	.	0			c.C1146A						PASS	.	G		774,3632	314.1+/-293.5	74,626,1503	80.0	62.0	68.0		1146	-2.0	1.0	14	dbSNP_86	68	1680,6920	308.5+/-308.9	153,1374,2773	no	coding-synonymous	TGM1	NM_000359.2		227,2000,4276	TT,TG,GG		19.5349,17.567,18.8682		382/818	24728294	2454,10552	2203	4300	6503	SO:0001819	synonymous_variant	7051	exon7			GGTCACGCCAGCA	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"""Transglutaminases"""	11777	protein-coding gene	gene with protein product	"""K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"""	190195	"""transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"""	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.1146C>A	14.37:g.24728294G>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_000359	B4DWR7|Q197M4	Silent	SNP	ENST00000206765.6	37	CCDS9622.1																																																																																			G|0.828;T|0.172	0.172	strong		0.632	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412561	105412561	+	Missense_Mutation	SNP	C	C	T	rs3000771	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	205	0	0		WXS	Illumina HiSeq	Phase_I	94	91	0.968085	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	
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	494	5	0.0101215		WXS	Illumina HiSeq	Phase_I	374	6	0.0160428	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	
ACSM6	142827	hgsc.bcm.edu	37	10	96954360	96954360	+	Missense_Mutation	SNP	T	T	A	rs11188225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:96954360T>A	ENST00000394005.3	+	1	127	c.118T>A	c.(118-120)Tgc>Agc	p.C40S	C10orf129_ENST00000430183.1_5'UTR|C10orf129_ENST00000341686.3_Missense_Mutation_p.C40S			Q6P461	ACSM6_HUMAN		40			C -> S (in dbSNP:rs11188225). {ECO:0000269|PubMed:15489334}.		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)|kidney(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		TGACTCCAGGTGCCTAGTCCA	0.468													T|||	988	0.197284	0.0416	0.1916	5008	,	,		19742	0.0456		0.3648	False		,,,				2504	0.3957				p.C40S		Atlas-SNP	.											.	C10orf129	52	.	0			c.T118A						PASS	.	T	SER/CYS	130,1254		5,120,567	109.0	97.0	100.0		118	-4.4	0.0	10	dbSNP_120	100	1167,2015		206,755,630	yes	missense	C10orf129	NM_207321.2	112	211,875,1197	AA,AT,TT		36.675,9.3931,28.4056	benign	40/481	96954360	1297,3269	692	1591	2283	SO:0001583	missense	142827	exon2			TCCAGGTGCCTAG																												ENST00000394005.3:c.118T>A	10.37:g.96954360T>A	ENSP00000377573:p.Cys40Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_207321	A4FU95|A4IF38|Q5VZX2|Q6ZTX1	Missense_Mutation	SNP	ENST00000394005.3	37	CCDS7440.2	409	0.18727106227106227	23	0.046747967479674794	83	0.2292817679558011	28	0.04895104895104895	275	0.3627968337730871	T	5.686	0.311204	0.10789	0.093931	0.36675	ENSG00000173124	ENST00000539707;ENST00000341686;ENST00000394005	T;T	0.17854	2.25;2.25	2.18	-4.37	0.03633	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	1.0000000000287557E-6	B	0.19706	0.038	B	0.12156	0.007	T	0.47959	-0.9076	8	0.09338	T	0.73	.	1.1151	0.01712	0.2626:0.3873:0.1711:0.179	rs11188225;rs17451841;rs11188225	40	Q6P461	ACSM6_HUMAN	S	40	ENSP00000340296:C40S;ENSP00000377573:C40S	ENSP00000328491:C40S	C	+	1	0	C10orf129	96944350	0.002000	0.14202	0.000000	0.03702	0.024000	0.10985	-0.509000	0.06336	-1.234000	0.02548	0.391000	0.25812	TGC	A|0.198;N|0.001	0.198	strong		0.468	C10orf129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049506.2		
OR10T2	128360	hgsc.bcm.edu	37	1	158369064	158369064	+	Missense_Mutation	SNP	A	A	G	rs41488350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158369064A>G	ENST00000334438.1	-	1	192	c.193T>C	c.(193-195)Ttc>Ctc	p.F65L		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	65			F -> L (in dbSNP:rs41488350).			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)					GAAAGGATGAATAGAAAGCCA	0.488													A|||	544	0.108626	0.0272	0.0807	5008	,	,		20087	0.1369		0.1113	False		,,,				2504	0.2065				p.F65L		Atlas-SNP	.											OR10T2,NS,carcinoma,+2,1	OR10T2	76	1	0			c.T193C						PASS	.	A	LEU/PHE	240,4166	140.8+/-176.2	4,232,1967	78.0	79.0	79.0		193	3.6	0.1	1	dbSNP_127	79	859,7741	196.1+/-241.1	46,767,3487	yes	missense	OR10T2	NM_001004475.1	22	50,999,5454	GG,GA,AA		9.9884,5.4471,8.4499	probably-damaging	65/315	158369064	1099,11907	2203	4300	6503	SO:0001583	missense	128360	exon1			GGATGAATAGAAA	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.193T>C	1.37:g.158369064A>G	ENSP00000334115:p.Phe65Leu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	214	0.09798534798534798	16	0.032520325203252036	30	0.08287292817679558	95	0.1660839160839161	73	0.09630606860158311	A	7.655	0.683694	0.14907	0.054471	0.099884	ENSG00000186306	ENST00000334438	T	0.00543	6.68	4.73	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41001	U	0.000977	T	0.00144	0.0004	L	0.28192	0.835	0.80722	P	0.0	P	0.34977	0.478	B	0.32583	0.148	T	0.50311	-0.8843	9	0.40728	T	0.16	.	5.6709	0.17721	0.6878:0.1452:0.1669:0.0	rs41488350;rs55642766;rs61818751;rs41488350	65	Q8NGX3	O10T2_HUMAN	L	65	ENSP00000334115:F65L	ENSP00000334115:F65L	F	-	1	0	OR10T2	156635688	0.000000	0.05858	0.132000	0.22025	0.008000	0.06430	-0.163000	0.09997	0.304000	0.22809	-1.162000	0.01777	TTC	A|0.905;G|0.095	0.095	strong		0.488	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
PRND	23627	hgsc.bcm.edu	37	20	4705274	4705274	+	Missense_Mutation	SNP	C	C	T	rs41279424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:4705274C>T	ENST00000305817.2	+	2	148	c.77C>T	c.(76-78)aCg>aTg	p.T26M		NM_012409.2	NP_036541.2	Q9UKY0	PRND_HUMAN	prion protein 2 (dublet)	26			T -> P. {ECO:0000269|PubMed:10825657}.		protein homooligomerization (GO:0051260)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	13						GCGGTCCAGACGAGGGGCATC	0.622													C|||	37	0.00738818	0.0	0.0072	5008	,	,		17886	0.0		0.0199	False		,,,				2504	0.0123				p.T26M		Atlas-SNP	.											PRND,caecum,carcinoma,-1,1	PRND	34	1	0			c.C77T						PASS	.	C	MET/THR	24,4382	30.8+/-60.4	0,24,2179	63.0	57.0	59.0		77	5.5	0.1	20	dbSNP_127	59	191,8409	84.2+/-146.7	2,187,4111	yes	missense	PRND	NM_012409.2	81	2,211,6290	TT,TC,CC		2.2209,0.5447,1.6531	benign	26/177	4705274	215,12791	2203	4300	6503	SO:0001583	missense	23627	exon2			TCCAGACGAGGGG	AF106918	CCDS13081.1	20p13	2013-09-19			ENSG00000171864	ENSG00000171864			15748	protein-coding gene	gene with protein product	"""prion-like protein doppel"""	604263				10525406, 10577243	Standard	NM_012409		Approved	DPL, dJ1068H6.4, DOPPEL, PrPLP	uc002wkz.3	Q9UKY0	OTTHUMG00000031789	ENST00000305817.2:c.77C>T	20.37:g.4705274C>T	ENSP00000306900:p.Thr26Met	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	146	80	0.547945	NM_012409	A7U7M5|Q9H311|Q9H312|Q9NTM4	Missense_Mutation	SNP	ENST00000305817.2	37	CCDS13081.1	14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	C	9.089	1.001333	0.19121	0.005447	0.022209	ENSG00000171864	ENST00000305817	T	0.22134	1.97	5.47	5.47	0.80525	.	0.000000	0.44483	D	0.000451	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B	0.23591	0.088	B	0.16722	0.016	T	0.19160	-1.0314	10	0.87932	D	0	-16.7517	14.8253	0.70107	0.0:1.0:0.0:0.0	rs41279424	26	Q9UKY0	PRND_HUMAN	M	26	ENSP00000306900:T26M	ENSP00000306900:T26M	T	+	2	0	PRND	4653274	0.601000	0.26907	0.054000	0.19295	0.018000	0.09664	3.545000	0.53648	2.560000	0.86352	0.557000	0.71058	ACG	C|0.985;T|0.015	0.015	strong		0.622	PRND-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077827.2	NM_012409	
RMND1	55005	hgsc.bcm.edu	37	6	151766552	151766552	+	Missense_Mutation	SNP	G	G	A	rs3734800	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151766552G>A	ENST00000367303.4	-	2	517	c.395C>T	c.(394-396)aCg>aTg	p.T132M	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)	132			T -> M (in dbSNP:rs3734800). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		AAATGTTTCCGTTGATACAGA	0.418													G|||	1017	0.203075	0.1589	0.1311	5008	,	,		19301	0.3879		0.1133	False		,,,				2504	0.2157				p.T132M		Atlas-SNP	.											.	RMND1	32	.	0			c.C395T						PASS	.	G	MET/THR	653,3753	272.2+/-270.6	52,549,1602	104.0	108.0	107.0		395	3.6	0.0	6	dbSNP_107	107	873,7727	197.5+/-242.1	39,795,3466	no	missense	RMND1	NM_017909.2	81	91,1344,5068	AA,AG,GG		10.1512,14.8207,11.733	probably-damaging	132/450	151766552	1526,11480	2203	4300	6503	SO:0001583	missense	55005	exon2			GTTTCCGTTGATA	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.395C>T	6.37:g.151766552G>A	ENSP00000356272:p.Thr132Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	99	58	0.585859	NM_017909	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Missense_Mutation	SNP	ENST00000367303.4	37	CCDS5232.1	381	0.17445054945054944	67	0.13617886178861788	44	0.12154696132596685	187	0.3269230769230769	83	0.10949868073878628	G	9.605	1.129644	0.21041	0.148207	0.101512	ENSG00000155906	ENST00000367303	T	0.51325	0.71	5.46	3.63	0.41609	.	0.311865	0.29699	N	0.011436	T	0.35422	0.0931	L	0.29908	0.895	0.46609	P	8.770000000000167E-4	D;D	0.89917	1.0;0.996	P;B	0.61003	0.882;0.432	T	0.38628	-0.9652	9	0.62326	D	0.03	-2.5649	8.5436	0.33408	0.0785:0.0:0.7655:0.156	rs3734800	132;132	Q9NWS8-3;Q9NWS8	.;RMND1_HUMAN	M	132	ENSP00000356272:T132M	ENSP00000356272:T132M	T	-	2	0	RMND1	151808245	0.917000	0.31117	0.005000	0.12908	0.306000	0.27790	4.530000	0.60595	0.638000	0.30545	-0.214000	0.12660	ACG	G|0.867;A|0.133	0.133	strong		0.418	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	
PIEZO1	9780	hgsc.bcm.edu	37	16	88791458	88791458	+	Missense_Mutation	SNP	G	G	A	rs11645197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88791458G>A	ENST00000301015.9	-	30	4439	c.4193C>T	c.(4192-4194)cCa>cTa	p.P1398L		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1398					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CTGCCTCCGTGGCGGGGAGGA	0.701													G|||	878	0.175319	0.0121	0.1643	5008	,	,		17170	0.0873		0.3171	False		,,,				2504	0.3487				p.P1398L		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C4193T						PASS	.						5.0	11.0	9.0					16																	88791458		644	1514	2158	SO:0001583	missense	9780	exon30			CTCCGTGGCGGGG	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.4193C>T	16.37:g.88791458G>A	ENSP00000301015:p.Pro1398Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	356	0.163003663003663	12	0.024390243902439025	72	0.19889502762430938	46	0.08041958041958042	226	0.29815303430079154	G	13.18	2.159529	0.38119	.	.	ENSG00000103335	ENST00000301015	T	0.71934	-0.61	4.33	4.33	0.51752	.	0.581104	0.16407	N	0.215765	T	0.00012	0.0000	L	0.54323	1.7	0.53688	P	2.4000000000024002E-5	B	0.29716	0.255	B	0.26614	0.071	T	0.06391	-1.0829	9	0.36615	T	0.2	-9.1253	11.3569	0.49621	0.0:0.0:0.8181:0.1819	rs11645197;rs11645197	1398	Q92508	PIEZ1_HUMAN	L	1398	ENSP00000301015:P1398L	ENSP00000301015:P1398L	P	-	2	0	FAM38A	87318959	.	.	0.902000	0.35471	0.960000	0.62799	.	.	2.406000	0.81754	0.462000	0.41574	CCA	G|0.827;A|0.173	0.173	strong		0.701	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
KIRREL2	84063	hgsc.bcm.edu	37	19	36349752	36349752	+	Missense_Mutation	SNP	G	G	A	rs404299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36349752G>A	ENST00000360202.5	+	4	706	c.508G>A	c.(508-510)Gcc>Acc	p.A170T	KIRREL2_ENST00000347900.6_Missense_Mutation_p.A120T|KIRREL2_ENST00000262625.7_Missense_Mutation_p.A170T|KIRREL2_ENST00000592409.1_Missense_Mutation_p.A170T|NPHS1_ENST00000591817.1_Intron	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	233	0	0		WXS	Illumina HiSeq	Phase_I	231	90	0.38961	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	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103158278	103158278	+	Missense_Mutation	SNP	C	C	T	rs10895391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	217	0	0		WXS	Illumina HiSeq	Phase_I	184	69	0.375	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	
OR2H1	26716	hgsc.bcm.edu	37	6	29429732	29429732	+	Silent	SNP	T	T	C	rs61732184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000473369.1_Intron|OR2H1_ENST00000377133.1_Silent_p.S62S|OR2H1_ENST00000396792.2_Silent_p.S62S			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	231	0	0		WXS	Illumina HiSeq	Phase_I	253	121	0.478261	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		
FLG	2312	hgsc.bcm.edu	37	1	152283862	152283862	+	Missense_Mutation	SNP	G	G	C	rs58001094	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152283862G>C	ENST00000368799.1	-	3	3535	c.3500C>G	c.(3499-3501)gCa>gGa	p.A1167G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_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	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	281	136	0.483986	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	
SI	6476	hgsc.bcm.edu	37	3	164730804	164730804	+	Silent	SNP	T	T	C	rs74648160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:164730804T>C	ENST00000264382.3	-	34	4088	c.4026A>G	c.(4024-4026)acA>acG	p.T1342T		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1342	Sucrase.				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)	TTTTATCTATTGTTATGTTGG	0.338										HNSCC(35;0.089)			T|||	494	0.0986422	0.0703	0.0706	5008	,	,		14762	0.0794		0.1083	False		,,,				2504	0.1667				p.T1342T		Atlas-SNP	.											SI,NS,haematopoietic_neoplasm,-1,1	SI	500	1	0			c.A4026G						PASS	.	T		355,4051	185.0+/-212.2	20,315,1868	126.0	123.0	124.0		4026	1.8	1.0	3	dbSNP_132	124	1040,7560	222.2+/-259.3	58,924,3318	no	coding-synonymous	SI	NM_001041.3		78,1239,5186	CC,CT,TT		12.093,8.0572,10.7258		1342/1828	164730804	1395,11611	2203	4300	6503	SO:0001819	synonymous_variant	6476	exon34			ATCTATTGTTATG	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.4026A>G	3.37:g.164730804T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																			T|0.892;C|0.108	0.108	strong		0.338	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
AMZ1	155185	hgsc.bcm.edu	37	7	2748758	2748758	+	Silent	SNP	G	G	C	rs59438885	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2748758G>C	ENST00000312371.4	+	5	1019	c.651G>C	c.(649-651)tcG>tcC	p.S217S	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	217							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		TCCCGAAGTCGGGGCCCAGCG	0.677													G|||	1284	0.25639	0.1974	0.1124	5008	,	,		15442	0.5754		0.1123	False		,,,				2504	0.2577				p.S217S		Atlas-SNP	.											.	AMZ1	41	.	0			c.G651C						PASS	.	G		775,3619		75,625,1497	18.0	22.0	21.0		651	-2.4	0.0	7	dbSNP_129	21	1053,7545		61,931,3307	no	coding-synonymous	AMZ1	NM_133463.1		136,1556,4804	CC,CG,GG		12.247,17.6377,14.0702		217/499	2748758	1828,11164	2197	4299	6496	SO:0001819	synonymous_variant	155185	exon5			GAAGTCGGGGCCC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.651G>C	7.37:g.2748758G>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1																																																																																			A|0.000;C|0.164;G|0.836	0.164	strong		0.677	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
CPAMD8	27151	hgsc.bcm.edu	37	19	17025292	17025292	+	Missense_Mutation	SNP	G	G	A	rs706761	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	146	0	0		WXS	Illumina HiSeq	Phase_I	152	61	0.401316	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	
CACNA1H	8912	hgsc.bcm.edu	37	16	1270162	1270162	+	Missense_Mutation	SNP	G	G	A	rs1054645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1270162G>A	ENST00000348261.5	+	35	6478	c.6230G>A	c.(6229-6231)cGc>cAc	p.R2077H	CACNA1H_ENST00000358590.4_Missense_Mutation_p.R2071H|CACNA1H_ENST00000565831.1_Missense_Mutation_p.R2071H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2077			R -> H (in dbSNP:rs1054645). {ECO:0000269|PubMed:12891677, ECO:0000269|PubMed:9930755, ECO:0000269|Ref.7}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TTCGGACAGCGCTGCGTCTCC	0.741													G|||	3509	0.700679	0.7262	0.7075	5008	,	,		12781	0.8681		0.6441	False		,,,				2504	0.547				p.R2077H		Atlas-SNP	.											CACNA1H_ENST00000358590,NS,carcinoma,0,2	CACNA1H	317	2	0			c.G6230A						PASS	.	G	HIS/ARG,HIS/ARG	2894,1084		1068,758,163	10.0	13.0	12.0		6212,6230	0.8	1.0	16	dbSNP_86	12	5031,3243		1584,1863,690	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	29,29	2652,2621,853	AA,AG,GG		39.1951,27.2499,35.3167	benign,benign	2071/2348,2077/2354	1270162	7925,4327	1989	4137	6126	SO:0001583	missense	8912	exon35			GACAGCGCTGCGT	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.6230G>A	16.37:g.1270162G>A	ENSP00000334198:p.Arg2077His	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	1589	0.7275641025641025	346	0.7032520325203252	245	0.6767955801104972	519	0.9073426573426573	479	0.6319261213720316	G	7.681	0.689039	0.14973	0.727501	0.608049	ENSG00000196557	ENST00000348261;ENST00000358590	T;T	0.32988	1.43;1.43	4.02	0.758	0.18432	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.54753	P	1.799999999996249E-5	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.14172	-1.0482	8	0.28530	T	0.3	.	8.2472	0.31695	0.4591:0.0:0.5409:0.0	rs1054645;rs3195163;rs3751890;rs17745303;rs60109536;rs1054645	2071;2077	O95180-2;O95180	.;CAC1H_HUMAN	H	2077;2071	ENSP00000334198:R2077H;ENSP00000351401:R2071H	ENSP00000334198:R2077H	R	+	2	0	CACNA1H	1210163	0.000000	0.05858	0.956000	0.39512	0.169000	0.22640	-0.663000	0.05299	0.095000	0.17434	0.306000	0.20318	CGC	G|0.269;A|0.731	0.731	strong		0.741	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291160	1291160	+	Missense_Mutation	SNP	G	G	T	rs141519544		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1291160G>T	ENST00000338844.3	+	3	101	c.68G>T	c.(67-69)gGc>gTc	p.G23V	TPSAB1_ENST00000461509.2_Missense_Mutation_p.G30V	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	23			G -> V (in allele alpha; dbSNP:rs1141965). {ECO:0000269|PubMed:10898108}.		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G23V(1)		NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				CCAGCCCCAGGCCAGGCCCTG	0.711																																					p.G23V		Atlas-SNP	.											TPSAB1,NS,lymphoid_neoplasm,0,2	TPSAB1	24	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G68T						scavenged	.						21.0	23.0	22.0					16																	1291160		2193	4291	6484	SO:0001583	missense	7177	exon3			CCCCAGGCCAGGC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.68G>T	16.37:g.1291160G>T	ENSP00000343577:p.Gly23Val	Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	745	0.3411172161172161	111	0.22560975609756098	106	0.292817679558011	262	0.458041958041958	266	0.35092348284960423	G	9.934	1.215703	0.22373	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.86497	-2.13;-2.13	2.84	0.752	0.18398	.	0.709020	0.11654	N	0.542536	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.56287	0.975	P	0.45660	0.489	T	0.17868	-1.0355	9	0.39692	T	0.17	.	4.3463	0.11134	0.1498:0.3033:0.5468:0.0	.	23	Q15661	TRYB1_HUMAN	V	23;30	ENSP00000343577:G23V;ENSP00000418247:G30V	ENSP00000343577:G23V	G	+	2	0	TPSAB1	1231161	0.001000	0.12720	0.035000	0.18076	0.629000	0.37895	0.668000	0.25127	0.237000	0.21200	0.479000	0.44913	GGC	G|0.658;T|0.342	0.342	strong		0.711	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
ECM2	1842	hgsc.bcm.edu	37	9	95279985	95279985	+	Silent	SNP	C	C	A	rs968040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:95279985C>A	ENST00000344604.5	-	3	614	c.465G>T	c.(463-465)ccG>ccT	p.P155P	ECM2_ENST00000375540.1_Silent_p.P155P|CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.P155P	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	155	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						CGGAGCAGACCGGGCAGCATT	0.423													C|||	1676	0.334665	0.7557	0.2421	5008	,	,		18956	0.0893		0.2932	False		,,,				2504	0.1268				p.P155P		Atlas-SNP	.											.	ECM2	147	.	0			c.G465T						PASS	.	C	,,,	2918,1488	678.6+/-403.6	969,980,254	152.0	162.0	158.0		,465,465,465	-10.7	0.0	9	dbSNP_86	158	2496,6104	411.9+/-350.6	371,1754,2175	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	1340,2734,2429	AA,AC,CC		29.0233,33.7721,41.6269	,,,	,155/678,155/644,155/700	95279985	5414,7592	2203	4300	6503	SO:0001819	synonymous_variant	1842	exon3			GCAGACCGGGCAG	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.465G>T	9.37:g.95279985C>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			C|0.602;A|0.398	0.398	strong		0.423	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
PTCH1	5727	hgsc.bcm.edu	37	9	98231084	98231084	+	Silent	SNP	T	T	C	rs2227970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:98231084T>C	ENST00000331920.6	-	14	2498	c.2199A>G	c.(2197-2199)tcA>tcG	p.S733S	PTCH1_ENST00000429896.2_Silent_p.S582S|PTCH1_ENST00000421141.1_Silent_p.S582S|PTCH1_ENST00000375274.2_Silent_p.S732S|PTCH1_ENST00000437951.1_Silent_p.S667S|PTCH1_ENST00000418258.1_Silent_p.S582S|PTCH1_ENST00000430669.2_Silent_p.S667S	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	733					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CAGCAAAAGATGAGAGTGTCC	0.512													t|||	69	0.013778	0.0	0.0029	5008	,	,		18253	0.0278		0.0119	False		,,,				2504	0.0276				p.S733S		Atlas-SNP	.											PTCH1_ENST00000430669,NS,carcinoma,-1,4	PTCH1	1850	4	0			c.A2199G						PASS	.		,,,,,,	8,4398	14.3+/-33.2	0,8,2195	125.0	138.0	134.0		2199,2001,2196,1746,1746,1746,1746	-8.6	0.7	9	dbSNP_132	134	131,8469	67.3+/-129.8	0,131,4169	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	0,139,6364	CC,CT,TT		1.5233,0.1816,1.0687	,,,,,,	733/1448,667/1382,732/1447,582/1297,582/1297,582/1297,582/1297	98231084	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon14			AAAAGATGAGAGT	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2199A>G	9.37:g.98231084T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	98	68	0.693878	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			T|0.987;C|0.013	0.013	strong		0.512	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
PLB1	151056	hgsc.bcm.edu	37	2	28761981	28761981	+	Missense_Mutation	SNP	G	G	C	rs6753929	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:28761981G>C	ENST00000327757.5	+	11	678	c.634G>C	c.(634-636)Gta>Cta	p.V212L	PLB1_ENST00000422425.2_Missense_Mutation_p.V223L	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	212	4 X 308-326 AA approximate repeats.		V -> L (in dbSNP:rs6753929).		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)					CAGAGCATTTGTAAACCTGGT	0.557													G|||	999	0.199481	0.0923	0.304	5008	,	,		19379	0.2232		0.2425	False		,,,				2504	0.2014				p.V223L		Atlas-SNP	.											.	PLB1	255	.	0			c.G667C						PASS	.	G	LEU/VAL,LEU/VAL	591,3815	259.2+/-262.9	47,497,1659	129.0	105.0	113.0		667,634	5.7	1.0	2	dbSNP_116	113	2244,6356	380.3+/-339.6	280,1684,2336	yes	missense,missense	PLB1	NM_001170585.1,NM_153021.4	32,32	327,2181,3995	CC,CG,GG		26.093,13.4135,21.7976	probably-damaging,probably-damaging	223/1448,212/1459	28761981	2835,10171	2203	4300	6503	SO:0001583	missense	151056	exon11			GCATTTGTAAACC		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.634G>C	2.37:g.28761981G>C	ENSP00000330442:p.Val212Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	173	85	0.491329	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	463|463	0.211996336996337|0.211996336996337	52|52	0.10569105691056911|0.10569105691056911	113|113	0.31215469613259667|0.31215469613259667	114|114	0.1993006993006993|0.1993006993006993	184|184	0.24274406332453827|0.24274406332453827	G|G	19.90|19.90	3.912156|3.912156	0.72983|0.72983	0.134135|0.134135	0.26093|0.26093	ENSG00000163803|ENSG00000163803	ENST00000404858|ENST00000416713;ENST00000327757;ENST00000422425	.|T;T;T	.|0.41400	.|1.0;2.21;2.01	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.075093	.|0.52532	.|D	.|0.000077	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.90145|0.90145	3.09|3.09	0.09310|0.09310	P|P	1.0|1.0	.|D;D	.|0.89917	.|1.0;0.995	.|D;D	.|0.87578	.|0.998;0.957	T|T	0.02313|0.02313	-1.1178|-1.1178	4|9	.|0.56958	.|D	.|0.05	-23.1992|-23.1992	15.3191|15.3191	0.74105|0.74105	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs6753929;rs52831699;rs59816904;rs6753929|rs6753929;rs52831699;rs59816904;rs6753929	.|223;212	.|Q6P1J6-3;Q6P1J6	.|.;PLB1_HUMAN	F|L	221|167;212;223	.|ENSP00000407076:V167L;ENSP00000330442:V212L;ENSP00000416440:V223L	.|ENSP00000330442:V212L	L|V	+|+	3|1	2|0	PLB1|PLB1	28615485|28615485	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.596000|0.596000	0.36781|0.36781	3.117000|3.117000	0.50407|0.50407	2.688000|2.688000	0.91661|0.91661	0.591000|0.591000	0.81541|0.81541	TTG|GTA	A|0.000;C|0.213;G|0.787	0.213	strong		0.557	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
ZNF845	91664	hgsc.bcm.edu	37	19	53856702	53856702	+	Missense_Mutation	SNP	G	G	A	rs200114728	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53856702G>A	ENST00000595091.1	+	5	2993	c.2774G>A	c.(2773-2775)cGt>cAt	p.R925H	ZNF845_ENST00000458035.1_Missense_Mutation_p.R925H			Q96IR2	ZN845_HUMAN	zinc finger protein 845	925					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R925H(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AAAACCTTCCGTCACAATTCA	0.363													.|||	267	0.0533147	0.0484	0.0562	5008	,	,		21751	0.0466		0.0915	False		,,,				2504	0.0256				p.R925H		Atlas-SNP	.											ZNF845,NS,carcinoma,0,6	ZNF845	101	6	3	Substitution - Missense(3)	kidney(3)	c.G2774A						scavenged	.						33.0	30.0	31.0					19																	53856702		692	1591	2283	SO:0001583	missense	91664	exon4			CCTTCCGTCACAA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2774G>A	19.37:g.53856702G>A	ENSP00000470005:p.Arg925His	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	139	13	0.0935252	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	G	5.812	0.334080	0.11013	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.36157	1.27	2.0	-4.0	0.04057	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42585	0.1209	L	0.58302	1.8	0.09310	N	1	D	0.55800	0.973	P	0.53760	0.734	T	0.43925	-0.9361	9	0.51188	T	0.08	.	10.7803	0.46374	0.0:0.6804:0.1821:0.1375	.	925	Q96IR2	ZN845_HUMAN	H	925;841	ENSP00000388311:R925H	ENSP00000412086:R841H	R	+	2	0	ZNF845	58548514	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.662000	0.00032	-1.603000	0.01597	-0.499000	0.04595	CGT	.	.	weak		0.363	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
KANSL1	284058	hgsc.bcm.edu	37	17	44248837	44248837	+	Missense_Mutation	SNP	T	T	C	rs553586616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44248837T>C	ENST00000262419.6	-	2	1143	c.673A>G	c.(673-675)Aat>Gat	p.N225D	KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Missense_Mutation_p.N225D|KANSL1_ENST00000572904.1_Missense_Mutation_p.N225D|KANSL1_ENST00000575318.1_Missense_Mutation_p.N225D|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000432791.1_Missense_Mutation_p.N225D	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	225			N -> D (in dbSNP:rs35643216).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GTGCTATTATTGCTATACAAA	0.443													T|||	364	0.0726837	0.0113	0.1398	5008	,	,		24410	0.001		0.1998	False		,,,				2504	0.0511				p.N225D		Atlas-SNP	.											.	.	.	.	0			c.A673G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	167,4239		0,167,2036	132.0	164.0	154.0		673,673,673	5.0	1.0	17	dbSNP_126	154	1565,7035		0,1565,2735	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	23,23,23	0,1732,4771	CC,CT,TT		18.1977,3.7903,13.3169	benign,benign,benign	225/1105,225/1106,225/1106	44248837	1732,11274	2203	4300	6503	SO:0001583	missense	284058	exon2			TATTATTGCTATA	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.673A>G	17.37:g.44248837T>C	ENSP00000262419:p.Asn225Asp	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	288	93	0.322917	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	215	0.09844322344322344	10	0.02032520325203252	58	0.16022099447513813	1	0.0017482517482517483	146	0.19261213720316622	T	12.33	1.907105	0.33628	0.037903	0.181977	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.10668	2.85;2.85	6.04	4.97	0.65823	.	0.224065	0.47455	D	0.000233	T	0.00012	0.0000	N	0.12182	0.205	0.80722	D	1	B;B	0.33637	0.011;0.42	B;B	0.31337	0.007;0.128	T	0.61222	-0.7106	10	0.44086	T	0.13	-16.177	9.254	0.37573	0.0:0.0809:0.0:0.9191	rs35643216	225;225	C9JHY2;Q7Z3B3	.;K1267_HUMAN	D	225	ENSP00000262419:N225D;ENSP00000387393:N225D	ENSP00000262419:N225D	N	-	1	0	KIAA1267	41604614	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.265000	0.51561	2.317000	0.78254	0.459000	0.35465	AAT	T|0.857;C|0.143	0.143	strong		0.443	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
TMEM171	134285	hgsc.bcm.edu	37	5	72424269	72424269	+	Silent	SNP	T	T	G	rs34728034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:72424269T>G	ENST00000454765.2	+	3	1166	c.693T>G	c.(691-693)tcT>tcG	p.S231S	TMEM171_ENST00000287773.5_Silent_p.S231S			Q8WVE6	TM171_HUMAN	transmembrane protein 171	231						integral component of membrane (GO:0016021)				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		TTCCTGAATCTTCAGCTTCTG	0.418													T|||	82	0.0163738	0.0545	0.0144	5008	,	,		17554	0.0		0.0	False		,,,				2504	0.0				p.S231S	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.T693G						PASS	.	T	,	229,4177	138.0+/-173.8	6,217,1980	193.0	194.0	194.0		693,693	4.1	1.0	5	dbSNP_126	194	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	TMEM171	NM_001161342.1,NM_173490.6	,	6,219,6278	GG,GT,TT		0.0233,5.1975,1.7761	,	231/324,231/325	72424269	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	134285	exon3			TGAATCTTCAGCT	BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.693T>G	5.37:g.72424269T>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	187	95	0.508021	NM_173490	Q8N0S1|Q8TDT7	Silent	SNP	ENST00000454765.2	37	CCDS4017.1																																																																																			T|0.980;G|0.020	0.020	strong		0.418	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
ZNF181	339318	hgsc.bcm.edu	37	19	35232368	35232368	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:35232368G>C	ENST00000492450.1	+	4	1171	c.1082G>C	c.(1081-1083)aGg>aCg	p.R361T	ZNF181_ENST00000459757.2_Missense_Mutation_p.R360T|ZNF181_ENST00000392232.3_Missense_Mutation_p.R405T			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	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)	p.R297T(1)		endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTCATTCATAGGTCATCTCTC	0.393																																					p.R361T		Atlas-SNP	.											ZNF181,NS,carcinoma,0,1	ZNF181	65	1	1	Substitution - Missense(1)	endometrium(1)	c.G1082C						scavenged	.						58.0	58.0	58.0					19																	35232368		2203	4300	6503	SO:0001583	missense	339318	exon4			TTCATAGGTCATC	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"""Zinc fingers, C2H2-type"", ""-"""	12971	protein-coding gene	gene with protein product		606741	"""zinc finger protein 181 (HHZ181)"""				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.1082G>C	19.37:g.35232368G>C	ENSP00000420727:p.Arg361Thr	Somatic	101	3	0.029703		WXS	Illumina HiSeq	Phase_I	100	6	0.06	NM_001029997	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	G	4.274	0.050021	0.08243	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	T;T;T	0.07114	3.22;3.22;3.22	2.84	2.84	0.33178	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05731	0.0150	L	0.37897	1.145	0.09310	N	1	B;B	0.31790	0.34;0.288	B;B	0.24269	0.052;0.045	T	0.31998	-0.9923	9	0.22109	T	0.4	.	5.8316	0.18584	0.1455:0.0:0.8545:0.0	.	360;361	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	T	405;360;361;360	ENSP00000376065:R405T;ENSP00000420727:R361T;ENSP00000419435:R360T	ENSP00000376065:R405T	R	+	2	0	ZNF181	39924208	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.914000	0.04038	1.876000	0.54355	0.561000	0.74099	AGG	.	.	none		0.393	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997	
DLC1	10395	hgsc.bcm.edu	37	8	12950315	12950315	+	Silent	SNP	G	G	T	rs568182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:12950315G>T	ENST00000276297.4	-	13	3955	c.3546C>A	c.(3544-3546)cgC>cgA	p.R1182R	DLC1_ENST00000510318.1_5'UTR|DLC1_ENST00000520226.1_Silent_p.R671R|DLC1_ENST00000358919.2_Silent_p.R745R|DLC1_ENST00000512044.2_Silent_p.R779R	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						scavenged	.	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	50	1	0.02		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	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	
PNPLA6	10908	hgsc.bcm.edu	37	19	7606908	7606908	+	Missense_Mutation	SNP	G	G	C	rs17854645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7606908G>C	ENST00000221249.6	+	13	1521	c.1090G>C	c.(1090-1092)Gcc>Ccc	p.A364P	PNPLA6_ENST00000600737.1_Missense_Mutation_p.A403P|PNPLA6_ENST00000545201.2_Missense_Mutation_p.A364P|PNPLA6_ENST00000450331.3_Missense_Mutation_p.A364P|PNPLA6_ENST00000414982.3_Missense_Mutation_p.A412P	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	403					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						AACCCCCTCGGCCCCTCTGCT	0.627													G|||	593	0.118411	0.1036	0.1268	5008	,	,		14735	0.002		0.2087	False		,,,				2504	0.1595				p.A412P		Atlas-SNP	.											.	PNPLA6	163	.	0			c.G1234C						PASS	.	G	PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	454,3952	211.8+/-231.9	27,400,1776	53.0	53.0	53.0		1234,1090,1090,1207,1090	4.6	1.0	19	dbSNP_123	53	1863,6737	321.2+/-315.0	188,1487,2625	yes	missense,missense,missense,missense,missense	PNPLA6	NM_001166111.1,NM_001166112.1,NM_001166113.1,NM_001166114.1,NM_006702.4	27,27,27,27,27	215,1887,4401	CC,CG,GG		21.6628,10.3041,17.8149	benign,benign,benign,benign,benign	412/1376,364/1301,364/1328,403/1366,364/1328	7606908	2317,10689	2203	4300	6503	SO:0001583	missense	10908	exon12			CCCTCGGCCCCTC	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1090G>C	19.37:g.7606908G>C	ENSP00000221249:p.Ala364Pro	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	37	CCDS32891.1	267	0.12225274725274725	54	0.10975609756097561	55	0.15193370165745856	0	0.0	158	0.20844327176781002	G	13.94	2.387933	0.42308	0.103041	0.216628	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000544207;ENST00000450331	T;T;T;T	0.04194	3.7;3.7;3.68;3.7	5.63	4.57	0.56435	.	0.331114	0.32548	N	0.005947	T	0.00012	0.0000	N	0.16478	0.41	0.27854	P	0.9406483	B;B;B;B	0.11235	0.003;0.004;0.002;0.004	B;B;B;B	0.15052	0.001;0.012;0.007;0.003	T	0.51236	-0.8731	9	0.26408	T	0.33	.	12.376	0.55281	0.0:0.1695:0.8305:0.0	rs17854645	403;364;403;364	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	P	364;364;412;301;364	ENSP00000221249:A364P;ENSP00000443323:A364P;ENSP00000407509:A412P;ENSP00000394348:A364P	ENSP00000221249:A364P	A	+	1	0	PNPLA6	7512908	0.246000	0.23909	0.960000	0.40013	0.961000	0.63080	2.817000	0.48034	1.343000	0.45638	0.655000	0.94253	GCC	G|0.837;C|0.163	0.163	strong		0.627	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
COQ5	84274	hgsc.bcm.edu	37	12	120966921	120966921	+	Silent	SNP	A	A	G	rs3742052	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120966921A>G	ENST00000288532.6	-	1	64	c.24T>C	c.(22-24)gcT>gcC	p.A8A	COQ5_ENST00000445328.2_Silent_p.A8A	NM_032314.3	NP_115690.3	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase (S. cerevisiae)	8					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)					AGCTCCATAGAGCACAGCTCC	0.667													A|||	1325	0.264577	0.0809	0.2579	5008	,	,		14695	0.4921		0.2783	False		,,,				2504	0.2689				p.A8A		Atlas-SNP	.											.	COQ5	26	.	0			c.T24C						PASS	.	A		466,3938		24,418,1760	18.0	21.0	20.0		24	-1.4	0.0	12	dbSNP_107	20	2678,5920		424,1830,2045	no	coding-synonymous	COQ5	NM_032314.3		448,2248,3805	GG,GA,AA		31.1468,10.5813,24.1809		8/328	120966921	3144,9858	2202	4299	6501	SO:0001819	synonymous_variant	84274	exon1			CCATAGAGCACAG	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.24T>C	12.37:g.120966921A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	57	0.619565	NM_032314	B4DEJ4|Q32Q28|Q53HH0|Q96LV1|Q9BSP8	Silent	SNP	ENST00000288532.6	37	CCDS31912.1																																																																																			A|0.748;G|0.252	0.252	strong		0.667	COQ5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403767.2	NM_032314	
STAT5A	6776	hgsc.bcm.edu	37	17	40459737	40459737	+	Silent	SNP	C	C	T	rs1135669	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40459737C>T	ENST00000345506.4	+	16	2544	c.1902C>T	c.(1900-1902)gaC>gaT	p.D634D	STAT5A_ENST00000452307.2_Silent_p.D631D|STAT5A_ENST00000588868.1_Silent_p.D603D|STAT5A_ENST00000546010.2_Silent_p.D604D|STAT5A_ENST00000587646.1_Silent_p.D122D|STAT5A_ENST00000590949.1_Silent_p.D634D	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	634	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GGAAGTTTGACTCCCGTGAGT	0.602													C|||	1207	0.241014	0.1967	0.0908	5008	,	,		15460	0.371		0.1889	False		,,,				2504	0.3272				p.D634D		Atlas-SNP	.											.	STAT5A	49	.	0			c.C1902T						PASS	.	C		855,3551	335.5+/-303.9	83,689,1431	61.0	53.0	56.0		1902	4.8	1.0	17	dbSNP_86	56	1474,7126	280.6+/-294.6	142,1190,2968	no	coding-synonymous	STAT5A	NM_003152.3		225,1879,4399	TT,TC,CC		17.1395,19.4054,17.9071		634/795	40459737	2329,10677	2203	4300	6503	SO:0001819	synonymous_variant	6776	exon16			GTTTGACTCCCGT	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"""SH2 domain containing"""	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1902C>T	17.37:g.40459737C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_003152	Q1KLZ6	Silent	SNP	ENST00000345506.4	37	CCDS11424.1																																																																																			C|0.802;T|0.198	0.198	strong		0.602	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152	
TCF25	22980	hgsc.bcm.edu	37	16	89965055	89965055	+	Silent	SNP	G	G	A	rs11648433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89965055G>A	ENST00000263346.8	+	10	1169	c.1113G>A	c.(1111-1113)ctG>ctA	p.L371L	TCF25_ENST00000263347.7_Silent_p.L136L	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	371					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)		AGCTCATCCTGAGGTGAGTGT	0.622													G|||	393	0.0784744	0.0045	0.0231	5008	,	,		17571	0.2837		0.0666	False		,,,				2504	0.0184				p.L371L		Atlas-SNP	.											.	TCF25	61	.	0			c.G1113A						PASS	.	G		89,4307	72.5+/-110.5	0,89,2109	64.0	70.0	68.0		1113	-0.7	1.0	16	dbSNP_120	68	746,7854	179.6+/-228.7	34,678,3588	no	coding-synonymous	TCF25	NM_014972.2		34,767,5697	AA,AG,GG		8.6744,2.0246,6.4251		371/677	89965055	835,12161	2198	4300	6498	SO:0001819	synonymous_variant	22980	exon10			CATCCTGAGGTGA	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.1113G>A	16.37:g.89965055G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_014972	Q2MK75|Q9UPV3	Silent	SNP	ENST00000263346.8	37	CCDS10987.1																																																																																			G|0.932;A|0.068	0.068	strong		0.622	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972	
SPTB	6710	hgsc.bcm.edu	37	14	65241228	65241228	+	Silent	SNP	A	A	G	rs229592	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:65241228A>G	ENST00000389721.5	-	23	4892	c.4860T>C	c.(4858-4860)atT>atC	p.I1620I	SPTB_ENST00000556626.1_Silent_p.I1620I|SPTB_ENST00000389722.3_Silent_p.I1620I|SPTB_ENST00000542895.1_Silent_p.I1620I|SPTB_ENST00000389720.3_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	86	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	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		
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331625	21331625	+	Silent	SNP	C	C	T	rs2291075	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21331625C>T	ENST00000256958.2	+	6	693	c.597C>T	c.(595-597)ttC>ttT	p.F199F		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	199					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TTGATGATTTCGCTAAAGAAG	0.358													T|||	2081	0.415535	0.5598	0.3314	5008	,	,		15258	0.5109		0.3966	False		,,,				2504	0.2014				p.F199F		Atlas-SNP	.											SLCO1B1,NS,carcinoma,+2,1	SLCO1B1	151	1	0			c.C597T						PASS	.	T		2401,2005	559.9+/-380.3	649,1103,451	122.0	113.0	116.0		597	2.5	1.0	12	dbSNP_100	116	3438,5162	636.0+/-399.1	695,2048,1557	yes	coding-synonymous	SLCO1B1	NM_006446.4		1344,3151,2008	TT,TC,CC		39.9767,45.5061,44.8947		199/692	21331625	5839,7167	2203	4300	6503	SO:0001819	synonymous_variant	10599	exon6			TGATTTCGCTAAA		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.597C>T	12.37:g.21331625C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	191	87	0.455497	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			C|0.548;T|0.452	0.452	strong		0.358	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
FCRL5	83416	hgsc.bcm.edu	37	1	157494106	157494106	+	Silent	SNP	C	C	T	rs34273689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:157494106C>T	ENST00000361835.3	-	10	2359	c.2202G>A	c.(2200-2202)gaG>gaA	p.E734E	FCRL5_ENST00000356953.4_Silent_p.E734E|FCRL5_ENST00000368190.3_Silent_p.E734E|FCRL5_ENST00000461387.1_5'Flank|FCRL5_ENST00000368191.3_Silent_p.E649E	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	734	Ig-like C2-type 7.				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)				TGCGCTGGGCCTCCAGACCAT	0.567													c|||	632	0.126198	0.3306	0.0231	5008	,	,		20608	0.0893		0.0109	False		,,,				2504	0.0798				p.E734E		Atlas-SNP	.											.	FCRL5	177	.	0			c.G2202A						PASS	.	C	,	1185,3221	411.1+/-335.6	163,859,1181	53.0	58.0	56.0		2202,2202	-7.6	0.0	1	dbSNP_126	56	71,8529	41.7+/-99.0	1,69,4230	no	coding-synonymous,coding-synonymous	FCRL5	NM_001195388.1,NM_031281.2	,	164,928,5411	TT,TC,CC		0.8256,26.8951,9.6571	,	734/999,734/978	157494106	1256,11750	2203	4300	6503	SO:0001819	synonymous_variant	83416	exon10			CTGGGCCTCCAGA	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.2202G>A	1.37:g.157494106C>T		Somatic	314	1	0.00318471		WXS	Illumina HiSeq	Phase_I	335	178	0.531343	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			C|0.902;T|0.098	0.098	strong		0.567	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
FMN2	56776	hgsc.bcm.edu	37	1	240371085	240371085	+	Silent	SNP	A	A	T	rs71646826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	91	3	0.032967		WXS	Illumina HiSeq	Phase_I	131	15	0.114504	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	
KRT20	54474	hgsc.bcm.edu	37	17	39041309	39041309	+	Silent	SNP	G	G	A	rs17567558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39041309G>A	ENST00000167588.3	-	1	170	c.129C>T	c.(127-129)ggC>ggT	p.G43G		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	43	Head.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				AGATGCGGATGCCCCGGCCTC	0.607													G|||	380	0.0758786	0.0779	0.111	5008	,	,		17304	0.0149		0.1014	False		,,,				2504	0.0849				p.G43G		Atlas-SNP	.											.	KRT20	38	.	0			c.C129T						PASS	.	G		315,4091	169.1+/-199.8	18,279,1906	69.0	64.0	66.0		129	1.0	0.9	17	dbSNP_123	66	724,7876	175.2+/-225.3	31,662,3607	no	coding-synonymous	KRT20	NM_019010.2		49,941,5513	AA,AG,GG		8.4186,7.1493,7.9886		43/425	39041309	1039,11967	2203	4300	6503	SO:0001819	synonymous_variant	54474	exon1			GCGGATGCCCCGG	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.129C>T	17.37:g.39041309G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_019010	B2R6W7	Silent	SNP	ENST00000167588.3	37	CCDS11379.1																																																																																			G|0.922;A|0.078	0.078	strong		0.607	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
DHX37	57647	hgsc.bcm.edu	37	12	125467158	125467158	+	Missense_Mutation	SNP	C	C	T	rs11558556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:125467158C>T	ENST00000308736.2	-	3	386	c.288G>A	c.(286-288)atG>atA	p.M96I	DHX37_ENST00000544745.1_5'Flank	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	96			M -> I (in dbSNP:rs11558556).				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)		GCTTCTGTAGCATCTCTGCTC	0.458													C|||	1873	0.374002	0.4123	0.2507	5008	,	,		21166	0.4147		0.339	False		,,,				2504	0.4039				p.M96I		Atlas-SNP	.											.	DHX37	114	.	0			c.G288A						PASS	.	C	ILE/MET	1730,2676	518.1+/-369.6	347,1036,820	204.0	191.0	195.0		288	4.1	1.0	12	dbSNP_120	195	2985,5615	461.9+/-365.5	511,1963,1826	yes	missense	DHX37	NM_032656.3	10	858,2999,2646	TT,TC,CC		34.7093,39.2646,36.2525	benign	96/1158	125467158	4715,8291	2203	4300	6503	SO:0001583	missense	57647	exon3			CTGTAGCATCTCT	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.288G>A	12.37:g.125467158C>T	ENSP00000311135:p.Met96Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	808	0.36996336996337	207	0.42073170731707316	99	0.27348066298342544	235	0.41083916083916083	267	0.35224274406332456	C	12.17	1.858647	0.32791	0.392646	0.347093	ENSG00000150990	ENST00000308736	T	0.10288	2.89	5.15	4.05	0.47172	.	0.275088	0.41097	D	0.000941	T	0.00012	0.0000	L	0.41236	1.265	0.38155	P	0.061158000000000046	B	0.02656	0.0	B	0.01281	0.0	T	0.47018	-0.9149	9	0.56958	D	0.05	-10.2958	13.4808	0.61334	0.0:0.9067:0.0:0.0933	rs11558556;rs12427062;rs52793255;rs60943078;rs12427062	96	Q8IY37	DHX37_HUMAN	I	96	ENSP00000311135:M96I	ENSP00000311135:M96I	M	-	3	0	DHX37	124033111	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	1.912000	0.39946	2.382000	0.81193	0.462000	0.41574	ATG	T|0.288;G|0.120;C|0.514;A|0.078	0.288	strong		0.458	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037626	33037626	+	Silent	SNP	C	C	G	rs1042174	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	143	0	0		WXS	Illumina HiSeq	Phase_I	98	33	0.336735	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	
SLIT2	9353	hgsc.bcm.edu	37	4	20552510	20552510	+	Silent	SNP	A	A	C	rs17542486	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:20552510A>C	ENST00000504154.1	+	25	2802	c.2550A>C	c.(2548-2550)gcA>gcC	p.A850A	SLIT2_ENST00000503823.1_Silent_p.A842A|SLIT2_ENST00000273739.5_Silent_p.A854A|SLIT2_ENST00000503837.1_Silent_p.A846A|SLIT2_ENST00000509394.2_3'UTR	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	850					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						ATCTTTCTGCATTATCACATC	0.338													A|||	320	0.0638978	0.0567	0.183	5008	,	,		17440	0.0		0.0895	False		,,,				2504	0.0286				p.A850A		Atlas-SNP	.											.	SLIT2	290	.	0			c.A2550C						PASS	.	A		328,4078	172.7+/-202.6	17,294,1892	182.0	169.0	173.0		2550	-1.7	0.4	4	dbSNP_123	173	933,7667	204.9+/-247.5	61,811,3428	no	coding-synonymous	SLIT2	NM_004787.1		78,1105,5320	CC,CA,AA		10.8488,7.4444,9.6955		850/1530	20552510	1261,11745	2203	4300	6503	SO:0001819	synonymous_variant	9353	exon25			TTCTGCATTATCA	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.2550A>C	4.37:g.20552510A>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			A|0.917;C|0.083	0.083	strong		0.338	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
SRRT	51593	hgsc.bcm.edu	37	7	100486110	100486110	+	Silent	SNP	C	C	T	rs11171	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100486110C>T	ENST00000347433.4	+	20	2729	c.2571C>T	c.(2569-2571)gaC>gaT	p.D857D	SRRT_ENST00000457580.2_Silent_p.D853D|SRRT_ENST00000388793.4_Silent_p.D856D|SRRT_ENST00000432932.1_Silent_p.D852D			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	240	0	0		WXS	Illumina HiSeq	Phase_I	274	137	0.5	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	
FLG	2312	hgsc.bcm.edu	37	1	152284854	152284854	+	Silent	SNP	A	A	G	rs3120653	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152284854A>G	ENST00000368799.1	-	3	2543	c.2508T>C	c.(2506-2508)gaT>gaC	p.D836D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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	341	0	0		WXS	Illumina HiSeq	Phase_I	362	180	0.497238	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	
FAM86C1	55199	hgsc.bcm.edu	37	11	71504464	71504464	+	Silent	SNP	C	C	T	rs139287982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:71504464C>T	ENST00000359244.4	+	3	221	c.198C>T	c.(196-198)taC>taT	p.Y66Y	FAM86C1_ENST00000346333.6_Intron|FAM86C1_ENST00000426628.2_Intron	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	66										lung(1)	1						ATGAGCTGTACGAGGTGCTGG	0.567													.|||	316	0.063099	0.0499	0.0591	5008	,	,		19080	0.0933		0.0577	False		,,,				2504	0.0583				p.Y66Y		Atlas-SNP	.											.	FAM86C1	27	.	0			c.C198T						PASS	.	C	,,	79,4231		2,75,2078	41.0	39.0	40.0		,198,	-0.8	0.3	11	dbSNP_134	40	211,8365		3,205,4080	no	intron,coding-synonymous,intron	FAM86C1	NM_001099653.1,NM_018172.2,NM_152563.2	,,	5,280,6158	TT,TC,CC		2.4604,1.8329,2.2505	,,	,66/166,	71504464	290,12596	2155	4288	6443	SO:0001819	synonymous_variant	55199	exon3			GCTGTACGAGGTG	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.198C>T	11.37:g.71504464C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	160	49	0.30625	NM_018172	Q8N5D3	Silent	SNP	ENST00000359244.4	37	CCDS41686.1																																																																																			C|0.959;T|0.041	0.041	strong		0.567	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563	
MUC4	4585	hgsc.bcm.edu	37	3	195509572	195509572	+	Missense_Mutation	SNP	G	G	A	rs554783249		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195509572G>A	ENST00000463781.3	-	2	9338	c.8879C>T	c.(8878-8880)tCt>tTt	p.S2960F	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S2960F	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.P2960L(1)|p.S2960F(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)		GACAGGAAGAGAGGTGGCGTG	0.582													.|||	1	0.000199681	0.0	0.0	5008	,	,		9532	0.0		0.0	False		,,,				2504	0.001				p.S2960F		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	skin(2)	c.C8879T						scavenged	.						8.0	8.0	8.0					3																	195509572		596	1430	2026	SO:0001583	missense	4585	exon2			GGAAGAGAGGTGG	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.8879C>T	3.37:g.195509572G>A	ENSP00000417498:p.Ser2960Phe	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	249	8	0.0321285	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	3.963	-0.009937	0.07727	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37584	1.19;1.26	.	.	.	.	.	.	.	.	T	0.33876	0.0878	N	0.14661	0.345	0.09310	N	1	D	0.71674	0.998	D	0.69824	0.966	T	0.13656	-1.0501	7	.	.	.	.	4.2698	0.10780	0.0:0.0:0.6087:0.3913	.	2832	E7ESK3	.	F	2960	ENSP00000417498:S2960F;ENSP00000420243:S2960F	.	S	-	2	0	MUC4	196994351	0.069000	0.21087	0.006000	0.13384	0.000000	0.00434	1.672000	0.37523	0.482000	0.27582	0.000000	0.15137	TCT	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CTNS	1497	hgsc.bcm.edu	37	17	3563963	3563963	+	3'UTR	SNP	C	C	G	rs2873624	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3563963C>G	ENST00000046640.3	+	0	1997				CTNS_ENST00000381870.3_Missense_Mutation_p.P380A|CTNS_ENST00000414524.2_3'UTR|RP11-235E17.6_ENST00000575741.1_RNA|CTNS_ENST00000441220.2_Missense_Mutation_p.P272A	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter						adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)			NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	GGACTGGGCACCAAGCTTGCA	0.617													C|||	1145	0.228634	0.0129	0.2882	5008	,	,		19046	0.503		0.2167	False		,,,				2504	0.2076				p.P380A		Atlas-SNP	.											.	CTNS	42	.	0			c.C1138G						PASS	.	C	ALA/PRO,	237,4169	138.8+/-174.5	12,213,1978	71.0	65.0	67.0		1138,	1.4	0.0	17	dbSNP_101	67	2240,6360	379.5+/-339.3	285,1670,2345	yes	missense,utr-3	CTNS	NM_001031681.2,NM_004937.2	27,	297,1883,4323	GG,GC,CC		26.0465,5.379,19.0451	benign,	380/401,	3563963	2477,10529	2203	4300	6503	SO:0001624	3_prime_UTR_variant	1497	exon13			TGGGCACCAAGCT	AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"""cystinosis, nephropathic"""			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.*300C>G	17.37:g.3563963C>G		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	281	140	0.498221	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Missense_Mutation	SNP	ENST00000046640.3	37	CCDS11031.1	535	0.24496336996336995	9	0.018292682926829267	103	0.2845303867403315	272	0.4755244755244755	151	0.19920844327176782	c	0.551	-0.849610	0.02651	0.05379	0.260465	ENSG00000040531	ENST00000381870;ENST00000441220	D;D	0.96491	-3.56;-4.03	4.56	1.44	0.22558	.	1.261780	0.05896	N	0.629221	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.26950	-1.0088	9	0.12103	T	0.63	6.5659	4.5312	0.12006	0.1738:0.6411:0.0:0.1851	rs2873624;rs3826498	272;380	F8W6Z1;O60931-2	.;.	A	380;272	ENSP00000371294:P380A;ENSP00000411465:P272A	ENSP00000371294:P380A	P	+	1	0	CTNS	3510712	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.328000	0.19681	0.408000	0.25621	-0.268000	0.10319	CCA	C|0.789;G|0.211	0.211	strong		0.617	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937	
DNAH17	8632	hgsc.bcm.edu	37	17	76433899	76433899	+	Missense_Mutation	SNP	G	G	A	rs386799532|rs61742072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:76433899G>A	ENST00000585328.1	-	74	11966	c.11842C>T	c.(11842-11844)Cac>Tac	p.H3948Y	DNAH17_ENST00000389840.5_Missense_Mutation_p.H3947Y|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3947	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|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)			GTGCTGTAGTGCTCCAGCTTC	0.617													G|||	530	0.105831	0.0257	0.1095	5008	,	,		17133	0.1012		0.1889	False		,,,				2504	0.1309				p.H3953Y		Atlas-SNP	.											DNAH17,NS,carcinoma,+1,1	DNAH17	347	1	0			c.C11857T						PASS	.	G	TYR/HIS	203,4201		5,193,2004	48.0	49.0	49.0		11857	3.0	1.0	17	dbSNP_129	49	1438,7158		136,1166,2996	yes	missense	DNAH17	NM_173628.3	83	141,1359,5000	AA,AG,GG		16.7287,4.6094,12.6231	benign	3953/4463	76433899	1641,11359	2202	4298	6500	SO:0001583	missense	8632	exon74			TGTAGTGCTCCAG	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.11842C>T	17.37:g.76433899G>A	ENSP00000465516:p.His3948Tyr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		278	0.12728937728937728	30	0.06097560975609756	46	0.1270718232044199	59	0.10314685314685315	143	0.18865435356200527	G	12.35	1.912274	0.33721	0.046094	0.167287	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.08282	3.11	5.07	2.96	0.34315	.	0.000000	0.53938	D	0.000049	T	0.00012	0.0000	L	0.43554	1.36	0.51767	P	6.60000000000105E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.37337	-0.9710	9	0.33940	T	0.23	.	14.0729	0.64870	0.0:0.0:0.6129:0.387	.	3948	E7EUM8	.	Y	3948;3947	ENSP00000374490:H3947Y	ENSP00000300671:H3948Y	H	-	1	0	DNAH17	73945494	0.997000	0.39634	0.997000	0.53966	0.720000	0.41350	2.564000	0.45931	1.112000	0.41740	0.561000	0.74099	CAC	G|0.865;A|0.135	0.135	strong		0.617	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
RAB3GAP1	22930	hgsc.bcm.edu	37	2	135893372	135893372	+	Missense_Mutation	SNP	A	A	G	rs10445686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:135893372A>G	ENST00000264158.8	+	17	1836	c.1793A>G	c.(1792-1794)aAt>aGt	p.N598S	RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.N554S|SNORA40_ENST00000385573.1_RNA|ZRANB3_ENST00000412849.1_5'Flank|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.N598S|RAB3GAP1_ENST00000487003.1_3'UTR	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	598			N -> S (in dbSNP:rs10445686). {ECO:0000269|PubMed:15489334}.		brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		CTTAAAGGAAATGGACAAGAG	0.433													A|||	1074	0.214457	0.0204	0.2003	5008	,	,		18540	0.3859		0.1909	False		,,,				2504	0.3344				p.N598S		Atlas-SNP	.											.	RAB3GAP1	87	.	0			c.A1793G						PASS	.	A	SER/ASN,SER/ASN	138,4268	98.9+/-137.6	3,132,2068	84.0	84.0	84.0		1793,1793	4.3	1.0	2	dbSNP_119	84	1324,7276	260.2+/-283.1	134,1056,3110	yes	missense,missense	RAB3GAP1	NM_001172435.1,NM_012233.2	46,46	137,1188,5178	GG,GA,AA		15.3953,3.1321,11.241	benign,benign	598/989,598/982	135893372	1462,11544	2203	4300	6503	SO:0001583	missense	22930	exon17			AAGGAAATGGACA	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.1793A>G	2.37:g.135893372A>G	ENSP00000264158:p.Asn598Ser	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	NM_001172435	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	37	CCDS33294.1	470	0.21520146520146521	13	0.026422764227642278	73	0.20165745856353592	242	0.4230769230769231	142	0.18733509234828497	A	11.59	1.682973	0.29872	0.031321	0.153953	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.42900	0.96;0.96;0.96	5.4	4.26	0.50523	.	0.301526	0.39274	N	0.001405	T	0.00012	0.0000	N	0.11560	0.145	0.33124	P	0.45778300000000005	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.40251	-0.9573	9	0.07813	T	0.8	-25.553	8.0603	0.30629	0.8474:0.0:0.1526:0.0	rs10445686;rs17845714;rs17858662;rs52816789;rs59620553;rs10445686	598;598	C9J837;Q15042	.;RB3GP_HUMAN	S	598;554;598	ENSP00000264158:N598S;ENSP00000444306:N554S;ENSP00000411418:N598S	ENSP00000264158:N598S	N	+	2	0	RAB3GAP1	135609842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.026000	0.64103	2.051000	0.60960	0.482000	0.46254	AAT	A|0.834;G|0.166	0.166	strong		0.433	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233	
CEACAM18	729767	hgsc.bcm.edu	37	19	51983673	51983673	+	Missense_Mutation	SNP	G	G	A	rs61743859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51983673G>A	ENST00000396477.4	+	2	160	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	CEACAM18_ENST00000451626.1_Missense_Mutation_p.V108M	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	47										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCGGACTGTCGTGGCCCTGGA	0.552													c|||	926	0.184904	0.171	0.1628	5008	,	,		19388	0.1111		0.2594	False		,,,				2504	0.2188				p.V108M		Atlas-SNP	.											.	CEACAM18	96	.	0			c.G322A						PASS	.	C	MET/VAL	733,3265		78,577,1344	54.0	51.0	52.0		322	1.7	0.0	19	dbSNP_129	52	2069,6239		245,1579,2330	yes	missense	CEACAM18	NM_001080405.1	21	323,2156,3674	AA,AG,GG		24.9037,18.3342,22.7694	benign	108/399	51983673	2802,9504	1999	4154	6153	SO:0001583	missense	729767	exon3			ACTGTCGTGGCCC			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.139G>A	19.37:g.51983673G>A	ENSP00000379738:p.Val47Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		386	0.17673992673992675	82	0.16666666666666666	65	0.17955801104972377	57	0.09965034965034965	182	0.24010554089709762	.	14.64	2.595023	0.46318	0.183342	0.249037	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.05580	3.42	2.78	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.34226	0.443	B	0.17722	0.019	T	0.50180	-0.8858	8	0.87932	D	0	-3.1057	5.3435	0.15996	0.2361:0.5348:0.2291:0.0	rs61743859	108	A8MTB9	CEA18_HUMAN	M	108;47;47	ENSP00000402203:V108M	ENSP00000379738:V47M	V	+	1	0	CEACAM18	56675485	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-0.097000	0.11042	0.264000	0.21851	-0.857000	0.03018	GTG	G|0.806;A|0.194	0.194	strong		0.552	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
MAP7D1	55700	hgsc.bcm.edu	37	1	36644874	36644874	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:36644874G>A	ENST00000373151.2	+	13	2358	c.2142G>A	c.(2140-2142)gaG>gaA	p.E714E	MAP7D1_ENST00000316156.4_Silent_p.E677E|MAP7D1_ENST00000373150.4_Silent_p.E682E|MAP7D1_ENST00000373148.4_Silent_p.E251E	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	714					microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				GTCTGGAGGAGATCATGAAGA	0.597																																					p.E714E		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G2142A						PASS	.						31.0	35.0	34.0					1																	36644874		2203	4300	6503	SO:0001819	synonymous_variant	55700	exon13			GGAGGAGATCATG	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.2142G>A	1.37:g.36644874G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	138	75	0.543478	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			.	.	none		0.597	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
TTN	7273	hgsc.bcm.edu	37	2	179575511	179575511	+	Missense_Mutation	SNP	C	C	T	rs72648998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179575511C>T	ENST00000591111.1	-	96	27586	c.27362G>A	c.(27361-27363)cGa>cAa	p.R9121Q	TTN_ENST00000589042.1_Missense_Mutation_p.R9438Q|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R8194Q|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13252	Ig-like 74.				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)			TCCGCCACTTCGTATTTCTCT	0.498													C|||	137	0.0273562	0.0	0.0807	5008	,	,		17461	0.0		0.0547	False		,,,				2504	0.0266				p.R9438Q		Atlas-SNP	.											TTN_ENST00000342992,colon,carcinoma,-1,1	TTN	18412	1	0			c.G28313A						PASS	.	C	,,,GLN/ARG	56,3912		1,54,1929	142.0	137.0	139.0		,,,24581	5.3	1.0	2	dbSNP_130	139	476,7872		14,448,3712	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,43	15,502,5641	TT,TC,CC		5.702,1.4113,4.3196	,,,benign	,,,8194/33424	179575511	532,11784	1984	4174	6158	SO:0001583	missense	7273	exon98			CCACTTCGTATTT	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.27362G>A	2.37:g.179575511C>T	ENSP00000465570:p.Arg9121Gln	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	172	77	0.447674	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		59	0.027014652014652016	0	0.0	18	0.049723756906077346	0	0.0	41	0.05408970976253298	C	16.23	3.064896	0.55432	0.014113	0.05702	ENSG00000155657	ENST00000342992	T	0.67171	-0.25	6.17	5.3	0.74995	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14830	0.0358	L	0.52823	1.66	0.09310	P	1.0	B	0.27316	0.175	B	0.21151	0.033	T	0.58792	-0.7574	8	0.87932	D	0	.	9.9548	0.41660	0.0:0.798:0.0:0.202	.	9121	Q8WZ42	TITIN_HUMAN	Q	8194	ENSP00000343764:R8194Q	ENSP00000343764:R8194Q	R	-	2	0	TTN	179283756	0.999000	0.42202	1.000000	0.80357	0.925000	0.55904	2.133000	0.42093	1.631000	0.50456	0.655000	0.94253	CGA	C|0.966;T|0.034	0.034	strong		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LAMB1	3912	hgsc.bcm.edu	37	7	107626770	107626770	+	Silent	SNP	G	G	A	rs25659	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:107626770G>A	ENST00000222399.6	-	6	692	c.462C>T	c.(460-462)tcC>tcT	p.S154S	LAMB1_ENST00000393561.1_Silent_p.S178S|LAMB1_ENST00000393560.1_Silent_p.S154S	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	154	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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						TCCCAAAGTCGGACGATCGTT	0.428													G|||	457	0.091254	0.059	0.134	5008	,	,		19024	0.0675		0.1203	False		,,,				2504	0.0992				p.S154S		Atlas-SNP	.											.	LAMB1	185	.	0			c.C462T						PASS	.	G		322,4084	173.7+/-203.5	14,294,1895	83.0	83.0	83.0		462	-7.5	0.3	7	dbSNP_72	83	1073,7527	226.4+/-262.1	67,939,3294	no	coding-synonymous	LAMB1	NM_002291.2		81,1233,5189	AA,AG,GG		12.4767,7.3082,10.7258		154/1787	107626770	1395,11611	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon6			AAAGTCGGACGAT	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.462C>T	7.37:g.107626770G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			G|0.898;A|0.102	0.102	strong		0.428	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
BBOX1	8424	hgsc.bcm.edu	37	11	27114788	27114788	+	Silent	SNP	C	C	T	rs3183973	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:27114788C>T	ENST00000529202.1	+	4	747	c.408C>T	c.(406-408)caC>caT	p.H136H	BBOX1_ENST00000525090.1_Silent_p.H136H|BBOX1_ENST00000263182.3_Silent_p.H136H|RP11-1L12.3_ENST00000526061.1_RNA|BBOX1_ENST00000527505.1_Intron|RP11-1L12.3_ENST00000525302.1_RNA|BBOX1_ENST00000528583.1_Silent_p.H136H|RP11-1L12.3_ENST00000530430.1_RNA			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	136					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)	p.H136H(1)		breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	ATGATGAACACGCATACAAGT	0.423													T|||	1463	0.292133	0.68	0.1686	5008	,	,		19165	0.0516		0.2237	False		,,,				2504	0.1738				p.H136H		Atlas-SNP	.											BBOX1,NS,carcinoma,0,1	BBOX1	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C408T						PASS	.	T		2551,1853	535.6+/-374.3	734,1083,385	93.0	92.0	92.0		408	0.5	0.2	11	dbSNP_105	92	2022,6574	720.2+/-406.3	229,1564,2505	no	coding-synonymous	BBOX1	NM_003986.2		963,2647,2890	TT,TC,CC		23.5226,42.0754,35.1769		136/388	27114788	4573,8427	2202	4298	6500	SO:0001819	synonymous_variant	8424	exon5			TGAACACGCATAC	AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.408C>T	11.37:g.27114788C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Silent	SNP	ENST00000529202.1	37	CCDS7862.1																																																																																			C|0.675;T|0.325	0.325	strong		0.423	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986	
NT5C1B	93034	hgsc.bcm.edu	37	2	18768850	18768850	+	Silent	SNP	A	A	G	rs16985306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:18768850A>G	ENST00000359846.2	-	2	116	c.39T>C	c.(37-39)ccT>ccC	p.P13P	NT5C1B_ENST00000460052.1_5'UTR|NT5C1B_ENST00000600945.1_Silent_p.P13P|NT5C1B-RDH14_ENST00000532967.1_Silent_p.P13P|NT5C1B_ENST00000304081.4_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	89	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	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		
DENND2C	163259	hgsc.bcm.edu	37	1	115168600	115168600	+	Missense_Mutation	SNP	A	A	T	rs7541738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:115168600A>T	ENST00000393274.1	-	4	631	c.6T>A	c.(4-6)gaT>gaA	p.D2E	DENND2C_ENST00000393277.1_Missense_Mutation_p.D2E|DENND2C_ENST00000481894.1_5'Flank|DENND2C_ENST00000393276.3_Missense_Mutation_p.D2E	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	2			D -> E (in dbSNP:rs7541738). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAAAACCAACATCCATGTTCC	0.363													A|||	572	0.114217	0.0182	0.1441	5008	,	,		18969	0.002		0.2863	False		,,,				2504	0.1616				p.D2E		Atlas-SNP	.											.	DENND2C	105	.	0			c.T6A						PASS	.	A	GLU/ASP	271,4135	145.0+/-179.8	16,239,1948	73.0	74.0	73.0		6	4.5	1.0	1	dbSNP_116	73	2373,6225	378.3+/-338.9	312,1749,2238	yes	missense	DENND2C	NM_198459.3	45	328,1988,4186	TT,TA,AA		27.5994,6.1507,20.3322	benign	2/872	115168600	2644,10360	2203	4299	6502	SO:0001583	missense	163259	exon4			ACCAACATCCATG		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.6T>A	1.37:g.115168600A>T	ENSP00000376955:p.Asp2Glu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	37	CCDS58018.1	290	0.13278388278388278	8	0.016260162601626018	65	0.17955801104972377	0	0.0	217	0.2862796833773087	A	12.69	2.012818	0.35511	0.061507	0.275994	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	T;T;T	0.09630	3.46;3.61;2.96	5.71	4.54	0.55810	.	0.439888	0.26556	N	0.023706	T	0.02807	0.0084	L	0.43152	1.355	0.31952	P	0.6095729999999999	B;B	0.23377	0.084;0.024	B;B	0.19148	0.024;0.016	T	0.34700	-0.9818	9	0.38643	T	0.18	.	1.8171	0.03102	0.5684:0.1674:0.1034:0.1607	rs7541738;rs17529624;rs52833856;rs7541738	2;2	Q68D51;Q68D51-3	DEN2C_HUMAN;.	E	2	ENSP00000376957:D2E;ENSP00000376955:D2E;ENSP00000376958:D2E	ENSP00000358553:D2E	D	-	3	2	DENND2C	114970123	0.277000	0.24220	1.000000	0.80357	0.998000	0.95712	0.645000	0.24782	2.187000	0.69744	0.524000	0.50904	GAT	A|0.824;T|0.176	0.176	strong		0.363	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
ADAM12	8038	hgsc.bcm.edu	37	10	128019025	128019025	+	Missense_Mutation	SNP	C	C	G	rs3740199	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:128019025C>G	ENST00000368679.4	-	2	451	c.142G>C	c.(142-144)Ggg>Cgg	p.G48R	ADAM12_ENST00000368676.4_Missense_Mutation_p.G48R	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	48			G -> R (in dbSNP:rs3740199). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417060, ECO:0000269|Ref.5}.		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)	p.G48R(3)		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)		TCCCCACTCCCAACAGAGGCA	0.468													G|||	2621	0.523363	0.5802	0.5965	5008	,	,		17512	0.4772		0.5398	False		,,,				2504	0.4254				p.G48R		Atlas-SNP	.											ADAM12_ENST00000368679,NS,carcinoma,0,3	ADAM12	388	3	3	Substitution - Missense(3)	prostate(3)	c.G142C						PASS	.	G	ARG/GLY,ARG/GLY	2589,1817	531.5+/-373.2	755,1079,369	128.0	133.0	131.0		142,142	-3.9	0.0	10	dbSNP_107	131	4850,3750	534.1+/-382.5	1384,2082,834	yes	missense,missense	ADAM12	NM_003474.4,NM_021641.3	125,125	2139,3161,1203	GG,GC,CC		43.6047,41.2392,42.8033	benign,benign	48/910,48/739	128019025	7439,5567	2203	4300	6503	SO:0001583	missense	8038	exon2			CACTCCCAACAGA	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.142G>C	10.37:g.128019025C>G	ENSP00000357668:p.Gly48Arg	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	206	100	0.485437	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Missense_Mutation	SNP	ENST00000368679.4	37	CCDS7653.1	1195	0.5471611721611722	289	0.5873983739837398	205	0.5662983425414365	278	0.486013986013986	423	0.558047493403694	G	0.695	-0.793114	0.02862	0.587608	0.563953	ENSG00000148848	ENST00000368679;ENST00000368676;ENST00000448723	T;T;T	0.20200	4.87;2.09;3.81	4.93	-3.88	0.04205	.	1.821900	0.05342	N	0.530222	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	0.44483	-0.9325	9	0.22109	T	0.4	.	6.3149	0.21184	0.3822:0.2372:0.3806:0.0	rs3740199;rs56748698;rs3740199	48;48;48;48	O43184-3;O43184-2;O43184-4;O43184	.;.;.;ADA12_HUMAN	R	48	ENSP00000357668:G48R;ENSP00000357665:G48R;ENSP00000391268:G48R	ENSP00000357665:G48R	G	-	1	0	ADAM12	128009015	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.308000	0.01131	-1.216000	0.02607	-0.701000	0.03672	GGG	A|0.000;C|0.444;G|0.555;N|0.001	0.555	strong		0.468	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
USP17L2	377630	hgsc.bcm.edu	37	8	11994957	11994957	+	Missense_Mutation	SNP	T	T	C	rs12543578	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11994957T>C	ENST00000333796.3	-	1	1629	c.1313A>G	c.(1312-1314)aAa>aGa	p.K438R	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	438	Mediates interaction with SUDS3.		K -> R (in dbSNP:rs12543578).		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						TTGGGGGAATTTCCAGTGGTC	0.517													T|||	2118	0.422923	0.3381	0.536	5008	,	,		21160	0.4018		0.4662	False		,,,				2504	0.4346				p.K438R		Atlas-SNP	.											.	USP17L2	47	.	0			c.A1313G						PASS	.	T	ARG/LYS	774,1884		128,518,683	63.0	69.0	67.0		1313	-0.5	0.0	8	dbSNP_120	67	2435,3579		435,1565,1007	no	missense	USP17L2	NM_201402.2	26	563,2083,1690	CC,CT,TT		40.4889,29.1196,37.0042	benign	438/531	11994957	3209,5463	1329	3007	4336	SO:0001583	missense	377630	exon1			GGGAATTTCCAGT	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.1313A>G	8.37:g.11994957T>C	ENSP00000333329:p.Lys438Arg	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	853	0.39056776556776557	157	0.31910569105691056	169	0.46685082872928174	197	0.34440559440559443	330	0.43535620052770446	T	4.323	0.059326	0.08339	0.291196	0.404889	ENSG00000223443	ENST00000333796	T	0.58210	0.35	0.745	-0.523	0.11924	Hyaluronan/mRNA-binding protein (1);	0.190186	0.30930	N	0.008591	T	0.00012	0.0000	L	0.31371	0.925	0.80722	P	0.0	B	0.27882	0.192	B	0.43018	0.405	T	0.43621	-0.9380	9	0.12766	T	0.61	.	2.725	0.05211	0.0:0.3869:0.0:0.6131	rs12543578	438	Q6R6M4	U17L2_HUMAN	R	438	ENSP00000333329:K438R	ENSP00000333329:K438R	K	-	2	0	USP17L2	12032366	0.633000	0.27181	0.003000	0.11579	0.008000	0.06430	-0.137000	0.10389	-0.155000	0.11098	0.386000	0.25728	AAA	.	.	weak		0.517	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
C9orf84	158401	hgsc.bcm.edu	37	9	114454544	114454544	+	Missense_Mutation	SNP	T	T	C	rs7869279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114454544T>C	ENST00000318737.4	-	25	3649	c.3521A>G	c.(3520-3522)gAa>gGa	p.E1174G	C9orf84_ENST00000394777.4_Missense_Mutation_p.E1100G|C9orf84_ENST00000374287.3_Missense_Mutation_p.E1174G|C9orf84_ENST00000394779.3_Missense_Mutation_p.E1135G	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1174			E -> G (in dbSNP:rs7869279).							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						ACTTGAGATTTCTTTTAGTTC	0.358													T|||	2489	0.497005	0.3911	0.5994	5008	,	,		18606	0.7728		0.4404	False		,,,				2504	0.3415				p.E1174G		Atlas-SNP	.											.	C9orf84	207	.	0			c.A3521G						PASS	.	T	GLY/GLU,GLY/GLU	1817,2589	531.9+/-373.3	402,1013,788	94.0	96.0	95.0		3404,3521	4.2	0.1	9	dbSNP_116	95	3834,4766	539.0+/-383.5	867,2100,1333	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	98,98	1269,3113,2121	CC,CT,TT		44.5814,41.2392,43.4492	benign,benign	1135/1406,1174/1445	114454544	5651,7355	2203	4300	6503	SO:0001583	missense	158401	exon25			GAGATTTCTTTTA	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.3521A>G	9.37:g.114454544T>C	ENSP00000322108:p.Glu1174Gly	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	1144	0.5238095238095238	178	0.3617886178861789	211	0.5828729281767956	427	0.7465034965034965	328	0.43271767810026385	T	11.24	1.580204	0.28180	0.412392	0.445814	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.05996	3.37;3.36;3.38;3.38	5.4	4.24	0.50183	.	0.672855	0.13625	N	0.374124	T	0.00012	0.0000	L	0.29908	0.895	0.49130	P	2.4599999999996847E-4	P;P;P	0.47302	0.893;0.893;0.893	P;P;P	0.47981	0.563;0.563;0.563	T	0.00138	-1.2003	9	0.54805	T	0.06	-1.1518	10.7936	0.46447	0.0:0.0:0.1584:0.8416	rs7869279;rs57126656;rs7869279	1100;1174;1135	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	G	1135;1100;788;1174;1174	ENSP00000378259:E1135G;ENSP00000378257:E1100G;ENSP00000363405:E1174G;ENSP00000322108:E1174G	ENSP00000322108:E1174G	E	-	2	0	C9orf84	113494365	0.986000	0.35501	0.074000	0.20217	0.050000	0.14768	2.033000	0.41136	0.955000	0.37878	0.383000	0.25322	GAA	T|0.528;C|0.472	0.472	strong		0.358	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
SLC7A4	6545	hgsc.bcm.edu	37	22	21386019	21386019	+	Missense_Mutation	SNP	G	G	A	rs2072550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21386019G>A	ENST00000382932.2	-	2	150	c.83C>T	c.(82-84)aCc>aTc	p.T28I	AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.T28I|MIR649_ENST00000384843.1_RNA	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	97	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	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	
VWDE	221806	hgsc.bcm.edu	37	7	12409263	12409263	+	Missense_Mutation	SNP	C	C	A	rs17165906	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	196	0	0		WXS	Illumina HiSeq	Phase_I	213	116	0.544601	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	
ADAMTS15	170689	hgsc.bcm.edu	37	11	130339312	130339312	+	Silent	SNP	T	T	C	rs731446	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:130339312T>C	ENST00000299164.2	+	5	1698	c.1698T>C	c.(1696-1698)aaT>aaC	p.N566N		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	566	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					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)		GATCCTGCAATCTGGAGCCCT	0.677													C|||	2832	0.565495	0.8011	0.4207	5008	,	,		18416	0.3552		0.6262	False		,,,				2504	0.5041				p.N566N		Atlas-SNP	.											.	ADAMTS15	103	.	0			c.T1698C						PASS	.	C		3376,1026	365.6+/-317.5	1293,790,118	43.0	33.0	37.0		1698	5.5	1.0	11	dbSNP_86	37	5327,3267	477.2+/-369.6	1669,1989,639	no	coding-synonymous	ADAMTS15	NM_139055.2		2962,2779,757	CC,CT,TT		38.0149,23.3076,33.0332		566/951	130339312	8703,4293	2201	4297	6498	SO:0001819	synonymous_variant	170689	exon5			CTGCAATCTGGAG	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.1698T>C	11.37:g.130339312T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_139055	Q32MI6	Silent	SNP	ENST00000299164.2	37	CCDS8488.1																																																																																			T|0.365;C|0.635	0.635	strong		0.677	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055	
TTN	7273	hgsc.bcm.edu	37	2	179429612	179429612	+	Missense_Mutation	SNP	A	A	G	rs186273940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179429612A>G	ENST00000591111.1	-	276	76548	c.76324T>C	c.(76324-76326)Tca>Cca	p.S25442P	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S27083P|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S18143P|TTN_ENST00000460472.2_Missense_Mutation_p.S18018P|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S18210P|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S24515P|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25442	Fibronectin type-III 85. {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)			TTTGAGATTGATGTCACAAAA	0.408													A|||	3	0.000599042	0.0	0.0	5008	,	,		21196	0.0		0.003	False		,,,				2504	0.0				p.S27083P		Atlas-SNP	.											.	TTN	18412	.	0			c.T81247C						PASS	.	A	PRO/SER,PRO/SER,PRO/SER,PRO/SER	0,3750		0,0,1875	77.0	73.0	74.0		54052,73543,54427,54628	4.8	1.0	2		74	6,8210		1,4,4103	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	74,74,74,74	1,4,5978	GG,GA,AA		0.073,0.0,0.0501	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	18018/26927,24515/33424,18143/27052,18210/27119	179429612	6,11960	1875	4108	5983	SO:0001583	missense	7273	exon326			AGATTGATGTCAC	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.76324T>C	2.37:g.179429612A>G	ENSP00000465570:p.Ser25442Pro	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	122	73	0.598361	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	8.744	0.919583	0.17982	0.0	7.3E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	6.02	4.85	0.62838	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.51907	0.1702	L	0.53617	1.68	0.44207	D	0.997039	P;P;P;P	0.42584	0.784;0.784;0.784;0.662	P;P;P;P	0.48368	0.575;0.575;0.575;0.478	T	0.55617	-0.8113	9	0.87932	D	0	.	4.0826	0.09932	0.5754:0.2427:0.0654:0.1165	.	18018;18143;18210;25442	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	24515;18018;18210;18143;18016	ENSP00000343764:S24515P;ENSP00000434586:S18018P;ENSP00000340554:S18210P;ENSP00000352154:S18143P	ENSP00000340554:S18210P	S	-	1	0	TTN	179137858	1.000000	0.71417	0.960000	0.40013	0.993000	0.82548	1.448000	0.35112	1.063000	0.40649	0.528000	0.53228	TCA	A|0.999;G|0.001	0.001	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KPTN	11133	hgsc.bcm.edu	37	19	47987230	47987230	+	Missense_Mutation	SNP	C	C	T	rs142867197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47987230C>T	ENST00000338134.3	-	1	295	c.188G>A	c.(187-189)cGg>cAg	p.R63Q	NAPA-AS1_ENST00000593284.1_RNA|KPTN_ENST00000536339.1_5'UTR|KPTN_ENST00000595484.1_5'UTR|NAPA-AS1_ENST00000594367.1_RNA	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	63					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		GGCCACTGGCCGGATTTTCTG	0.667											OREG0025593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0	0.0	5008	,	,		14783	0.0		0.002	False		,,,				2504	0.0				p.R63Q		Atlas-SNP	.											.	KPTN	34	.	0			c.G188A						PASS	.	C	GLN/ARG	1,3881		0,1,1940	42.0	48.0	46.0		188	4.6	1.0	19	dbSNP_134	46	13,8253		0,13,4120	yes	missense	KPTN	NM_007059.2	43	0,14,6060	TT,TC,CC		0.1573,0.0258,0.1152	possibly-damaging	63/437	47987230	14,12134	1941	4133	6074	SO:0001583	missense	11133	exon1			ACTGGCCGGATTT	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"""kaptin (actin-binding protein)"""			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.188G>A	19.37:g.47987230C>T	ENSP00000337850:p.Arg63Gln	Somatic	25	0	0	951	WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	37	CCDS42583.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	22.0	4.231215	0.79688	2.58E-4	0.001573	ENSG00000118162	ENST00000338134	.	.	.	4.59	4.59	0.56863	.	0.128494	0.50627	D	0.000103	T	0.57388	0.2050	L	0.56396	1.775	0.80722	D	1	B	0.30281	0.275	B	0.23716	0.048	T	0.58053	-0.7704	9	0.33940	T	0.23	-22.8261	16.3101	0.82865	0.0:1.0:0.0:0.0	.	63	Q9Y664	KPTN_HUMAN	Q	63	.	ENSP00000337850:R63Q	R	-	2	0	KPTN	52679042	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.799000	0.75160	2.390000	0.81377	0.313000	0.20887	CGG	C|0.998;T|0.002	0.002	strong		0.667	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2		
DIP2C	22982	hgsc.bcm.edu	37	10	323283	323283	+	Silent	SNP	A	A	G	rs3740304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:323283A>G	ENST00000280886.6	-	37	4740	c.4653T>C	c.(4651-4653)taT>taC	p.Y1551Y	AL603831.1_ENST00000579524.1_RNA	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1551						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TGTAGGCCACATAGATGGGGT	0.547													A|||	1423	0.284145	0.3116	0.2594	5008	,	,		19382	0.2381		0.2575	False		,,,				2504	0.3395				p.Y1551Y		Atlas-SNP	.											.	DIP2C	195	.	0			c.T4653C						PASS	.	A		1287,3119	437.2+/-344.9	181,925,1097	117.0	100.0	106.0		4653	-3.9	1.0	10	dbSNP_107	106	2153,6447	369.8+/-335.6	274,1605,2421	no	coding-synonymous	DIP2C	NM_014974.2		455,2530,3518	GG,GA,AA		25.0349,29.2102,26.4493		1551/1557	323283	3440,9566	2203	4300	6503	SO:0001819	synonymous_variant	22982	exon37			GGCCACATAGATG	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.4653T>C	10.37:g.323283A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																			A|0.732;G|0.268	0.268	strong		0.547	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
DPYSL4	10570	hgsc.bcm.edu	37	10	134013906	134013906	+	Silent	SNP	C	C	T	rs56326856	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:134013906C>T	ENST00000338492.4	+	9	1022	c.858C>T	c.(856-858)gaC>gaT	p.D286D	DPYSL4_ENST00000368627.1_Silent_p.D186D|DPYSL4_ENST00000368629.1_Silent_p.D186D	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	286					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)	p.D286D(3)		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)		TGGGCACCGACGGTTCACACT	0.672													T|||	751	0.14996	0.2708	0.098	5008	,	,		15549	0.001		0.159	False		,,,				2504	0.1677				p.D286D		Atlas-SNP	.											DPYSL4,caecum,carcinoma,+1,8	DPYSL4	91	8	3	Substitution - Missense(3)	central_nervous_system(2)|endometrium(1)	c.C858T						PASS	.	T		1004,3402	727.6+/-409.9	119,766,1318	119.0	107.0	112.0		858	-3.2	0.1	10	dbSNP_129	112	1324,7276	756.8+/-407.5	92,1140,3068	no	coding-synonymous	DPYSL4	NM_006426.2		211,1906,4386	TT,TC,CC		15.3953,22.7871,17.8994		286/573	134013906	2328,10678	2203	4300	6503	SO:0001819	synonymous_variant	10570	exon9			CACCGACGGTTCA	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.858C>T	10.37:g.134013906C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	37	CCDS7665.1																																																																																			C|0.833;T|0.167	0.167	strong		0.672	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2		
SBK2	646643	hgsc.bcm.edu	37	19	56042540	56042540	+	Silent	SNP	G	G	A	rs45520537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56042540G>A	ENST00000413299.1	-	3	463	c.426C>T	c.(424-426)caC>caT	p.H142H	SBK2_ENST00000344158.3_Silent_p.H142H	NM_001101401.2	NP_001094871.2	P0C263	SBK2_HUMAN	SH3 domain binding kinase family, member 2	142	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9						TGAGGTCCCCGTGCAGGACGG	0.677													G|||	286	0.0571086	0.0703	0.1326	5008	,	,		16563	0.0139		0.0557	False		,,,				2504	0.0317				p.H142H		Atlas-SNP	.											.	SBK2	26	.	0			c.C426T						PASS	.	G		287,4041		11,265,1888	44.0	50.0	48.0		426	-9.7	0.2	19	dbSNP_127	48	401,8099		10,381,3859	no	coding-synonymous	SBK2	NM_001101401.2		21,646,5747	AA,AG,GG		4.7176,6.6312,5.3633		142/349	56042540	688,12140	2164	4250	6414	SO:0001819	synonymous_variant	646643	exon3			GTCCCCGTGCAGG		CCDS42631.1	19q13.42	2013-09-27	2013-09-27		ENSG00000187550	ENSG00000187550			34416	protein-coding gene	gene with protein product			"""SH3-binding domain kinase family, member 2"""				Standard	NM_001101401		Approved	SGK069	uc010ygc.2	P0C263	OTTHUMG00000155830	ENST00000413299.1:c.426C>T	19.37:g.56042540G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_001101401		Silent	SNP	ENST00000413299.1	37	CCDS42631.1																																																																																			G|0.942;A|0.058	0.058	strong		0.677	SBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341919.1	NM_001101401	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086377	46086377	+	Missense_Mutation	SNP	A	A	G	rs2838622	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46086377A>G	ENST00000360770.3	-	1	467	c.427T>C	c.(427-429)Tct>Cct	p.S143P	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	143			S -> P (in dbSNP:rs2838622).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						CAGCAGGAAGAGATACTGTAG	0.602													G|||	2918	0.582668	0.6967	0.5403	5008	,	,		19253	0.5655		0.492	False		,,,				2504	0.5695				p.S143P		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.T427C						PASS	.	G	,PRO/SER	2893,1387		1004,885,251	54.0	59.0	57.0		,427	1.8	0.0	21	dbSNP_100	57	3867,4609		924,2019,1295	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,74	1928,2904,1546	GG,GA,AA		45.6229,32.4065,47.0053	,benign	,143/147	46086377	6760,5996	2140	4238	6378	SO:0001583	missense	353323	exon1			AGGAAGAGATACT	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.427T>C	21.37:g.46086377A>G	ENSP00000354001:p.Ser143Pro	Somatic	334	2	0.00598802		WXS	Illumina HiSeq	Phase_I	340	340	1	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1234	0.565018315018315	353	0.717479674796748	203	0.5607734806629834	303	0.5297202797202797	375	0.4947229551451187	g	0.003	-2.494097	0.00159	0.675935	0.456229	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02067	4.47	3.62	1.78	0.24846	.	.	.	.	.	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	0.15780	-1.0425	8	0.02654	T	1	.	5.8109	0.18465	0.3543:0.0:0.6457:0.0	rs2838622;rs61048872;rs2838622	143	P59991	KR122_HUMAN	P	143;93	ENSP00000354001:S143P	ENSP00000354001:S143P	S	-	1	0	KRTAP12-2	44910805	0.003000	0.15002	0.002000	0.10522	0.008000	0.06430	-0.301000	0.08232	-0.049000	0.13379	-0.355000	0.07637	TCT	A|0.429;G|0.571	0.571	strong		0.602	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
CENPF	1063	hgsc.bcm.edu	37	1	214811244	214811244	+	Missense_Mutation	SNP	C	C	G	rs2070065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214811244C>G	ENST00000366955.3	+	11	1650	c.1482C>G	c.(1480-1482)caC>caG	p.H494Q		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0			H -> Q (in dbSNP:rs2070065).		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)		TTAAGAGTCACTCTGAGCAAA	0.393													G|||	1512	0.301917	0.6921	0.2118	5008	,	,		18271	0.1597		0.0964	False		,,,				2504	0.1963				p.H494Q	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.C1482G						PASS	.	G	GLN/HIS	2678,1728	516.7+/-369.2	821,1036,346	79.0	81.0	81.0		1482	3.1	1.0	1	dbSNP_96	81	817,7783	782.0+/-407.6	42,733,3525	yes	missense	CENPF	NM_016343.3	24	863,1769,3871	GG,GC,CC		9.5,39.2192,26.8722	benign	494/3115	214811244	3495,9511	2203	4300	6503	SO:0001583	missense	1063	exon11			GAGTCACTCTGAG	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.1482C>G	1.37:g.214811244C>G	ENSP00000355922:p.His494Gln	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	228	104	0.45614	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	589	0.2696886446886447	332	0.6747967479674797	87	0.24033149171270718	99	0.17307692307692307	71	0.09366754617414248	G	1.265	-0.614716	0.03663	0.607808	0.095	ENSG00000117724	ENST00000366955	T	0.01767	4.65	5.9	3.06	0.35304	.	0.000000	0.36002	N	0.002843	T	0.00012	0.0000	.	.	.	0.54753	P	1.0999999999983245E-5	B	0.14012	0.009	B	0.01281	0.0	T	0.25187	-1.0139	8	0.02654	T	1	.	7.6719	0.28463	0.2448:0.1082:0.647:0.0	rs2070065;rs52809323;rs61607734;rs2070065	494	P49454	CENPF_HUMAN	Q	494	ENSP00000355922:H494Q	ENSP00000355922:H494Q	H	+	3	2	CENPF	212877867	1.000000	0.71417	0.995000	0.50966	0.805000	0.45488	0.783000	0.26802	0.136000	0.18733	-0.754000	0.03487	CAC	C|0.715;G|0.285	0.285	strong		0.393	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
CCDC7	79741	hgsc.bcm.edu	37	10	32745262	32745262	+	Splice_Site	SNP	T	T	C	rs7897978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:32745262T>C	ENST00000362006.5	+	4	999	c.456T>C	c.(454-456)aaT>aaC	p.N152N	CCDC7_ENST00000537047.1_Splice_Site_p.N152N|CCDC7_ENST00000535327.1_Splice_Site_p.N152N|CCDC7_ENST00000545067.1_Splice_Site_p.N152N|CCDC7_ENST00000277657.6_Splice_Site_p.N152N|CCDC7_ENST00000539197.1_Splice_Site_p.N152N	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	152										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				AAGAACAAAATGTATGTATTC	0.318													T|||	806	0.160942	0.2829	0.1095	5008	,	,		14777	0.1627		0.1034	False		,,,				2504	0.09				p.N152N		Atlas-SNP	.											.	CCDC7	47	.	0			c.T456C						PASS	.	T	,	997,3407	373.9+/-321.0	116,765,1321	74.0	72.0	73.0		456,456	2.1	0.6	10	dbSNP_116	73	843,7745	193.4+/-239.1	36,771,3487	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CCDC7	NM_001026383.1,NM_145023.4	,	152,1536,4808	CC,CT,TT		9.816,22.6385,14.1626	,	152/487,152/487	32745262	1840,11152	2202	4294	6496	SO:0001630	splice_region_variant	221016	exon4			ACAAAATGTATGT	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.456+1T>C	10.37:g.32745262T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	128	73	0.570312	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Silent	SNP	ENST00000362006.5	37	CCDS7173.1																																																																																			T|0.858;C|0.142	0.142	strong		0.318	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	Silent
APOBEC3H	164668	hgsc.bcm.edu	37	22	39498038	39498038	+	Missense_Mutation	SNP	G	G	C	rs139302	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39498038G>C	ENST00000401756.1	+	4	610	c.534G>C	c.(532-534)gaG>gaC	p.E178D	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.E178D|APOBEC3H_ENST00000421988.2_Intron|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.E178D	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	178			E -> D (in allele A3H-Var; haplotype 2; allele presenting a higher expression and more effective in retrotransposons and HIV-1 restriction; dbSNP:rs139302). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					GACGGCTTGAGAGGATAAAGG	0.562													G|||	2582	0.515575	0.8472	0.3458	5008	,	,		13390	0.3313		0.4632	False		,,,				2504	0.4315				p.E178D		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G534C						PASS	.	G	ASP/GLU,ASP/GLU,,ASP/GLU	3461,945		1362,737,104	55.0	46.0	49.0		534,534,,534	-6.1	0.0	22	dbSNP_78	49	3964,4636		887,2190,1223	yes	missense,missense,intron,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	45,45,,45	2249,2927,1327	CC,CG,GG		46.093,21.448,42.911	possibly-damaging,possibly-damaging,,possibly-damaging	178/183,178/201,,178/184	39498038	7425,5581	2203	4300	6503	SO:0001583	missense	164668	exon4			GCTTGAGAGGATA	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.534G>C	22.37:g.39498038G>C	ENSP00000385741:p.Glu178Asp	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	1082	0.49542124542124544	411	0.8353658536585366	122	0.3370165745856354	186	0.32517482517482516	363	0.4788918205804749	.	2.255	-0.370687	0.05069	0.78552	0.46093	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000401756	T;T;T	0.64438	-0.08;-0.08;-0.1	3.06	-6.12	0.02124	.	.	.	.	.	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.12630	0.006	B	0.16722	0.016	T	0.25710	-1.0124	8	0.30078	T	0.28	.	1.9922	0.03448	0.1454:0.3233:0.309:0.2223	rs139302;rs52796542;rs58930549;rs139302	178	B7TQM3	.	D	178	ENSP00000216123:E178D;ENSP00000411754:E178D;ENSP00000385741:E178D	ENSP00000216123:E178D	E	+	3	2	APOBEC3H	37827984	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.286000	0.02788	-2.277000	0.00677	-2.185000	0.00314	GAG	G|0.460;C|0.540	0.540	strong		0.562	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
STON1	11037	hgsc.bcm.edu	37	2	48808898	48808898	+	Silent	SNP	C	C	T	rs3749145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48808898C>T	ENST00000406226.1	+	3	1321	c.1126C>T	c.(1126-1128)Ctg>Ttg	p.L376L	STON1-GTF2A1L_ENST00000405008.1_Silent_p.L376L|STON1-GTF2A1L_ENST00000394754.1_Silent_p.L376L|STON1-GTF2A1L_ENST00000402114.2_Silent_p.L376L|STON1-GTF2A1L_ENST00000394751.3_Silent_p.L376L|STON1_ENST00000309835.3_Silent_p.L376L|STON1-GTF2A1L_ENST00000309827.2_Silent_p.L376L|STON1_ENST00000404752.1_Silent_p.L376L	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	376	SHD. {ECO:0000255|PROSITE- ProRule:PRU00403}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGAGCAGATGCTGAAGTTGGG	0.408													C|||	1673	0.334065	0.2791	0.3098	5008	,	,		21013	0.3879		0.3191	False		,,,				2504	0.3855				p.L376L		Atlas-SNP	.											.	STON1	100	.	0			c.C1126T						PASS	.	C	,,,,	1311,3095	437.6+/-345.0	195,921,1087	69.0	69.0	69.0		1126,1126,1126,1126,1126	2.2	1.0	2	dbSNP_107	69	2751,5849	437.4+/-358.6	456,1839,2005	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	651,2760,3092	TT,TC,CC		31.9884,29.7549,31.2317	,,,,	376/1159,376/1136,376/736,376/736,376/1183	48808898	4062,8944	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			CAGATGCTGAAGT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1126C>T	2.37:g.48808898C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			C|0.681;T|0.319	0.319	strong		0.408	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
LHX3	8022	hgsc.bcm.edu	37	9	139092571	139092571	+	Silent	SNP	C	C	T	rs33998096	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139092571C>T	ENST00000371748.5	-	2	204	c.108G>A	c.(106-108)caG>caA	p.Q36Q	LHX3_ENST00000371746.3_Silent_p.Q41Q	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	36	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)		CCAGGATGTGCTGGTCACAGC	0.632													C|||	32	0.00638978	0.0068	0.0058	5008	,	,		19156	0.0		0.0189	False		,,,				2504	0.0				p.Q41Q		Atlas-SNP	.											.	LHX3	23	.	0			c.G123A						PASS	.	C	,	19,4387	26.2+/-53.5	0,19,2184	72.0	70.0	71.0		123,108	4.7	1.0	9	dbSNP_126	71	140,8460	69.0+/-131.5	2,136,4162	no	coding-synonymous,coding-synonymous	LHX3	NM_014564.3,NM_178138.4	,	2,155,6346	TT,TC,CC		1.6279,0.4312,1.2225	,	41/403,36/398	139092571	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	8022	exon2			GATGTGCTGGTCA	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.108G>A	9.37:g.139092571C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_014564	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Silent	SNP	ENST00000371748.5	37	CCDS6994.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3		
COL4A3	1285	hgsc.bcm.edu	37	2	228128568	228128568	+	Missense_Mutation	SNP	G	G	A	rs34505188	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228128568G>A	ENST00000396578.3	+	21	1385	c.1223G>A	c.(1222-1224)cGc>cAc	p.R408H	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	408	Triple-helical region.		R -> H (in dbSNP:rs34505188). {ECO:0000269|PubMed:11134255}.		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)		GAACGAGGCCGCCCAGGAAAG	0.562													G|||	504	0.100639	0.028	0.1772	5008	,	,		15959	0.1577		0.0686	False		,,,				2504	0.1186				p.R408H		Atlas-SNP	.											COL4A3_ENST00000328380,NS,carcinoma,+1,2	COL4A3	293	2	0			c.G1223A						PASS	.	G	HIS/ARG	123,3603		3,117,1743	40.0	45.0	44.0		1223	2.1	1.0	2	dbSNP_126	44	630,7548		21,588,3480	yes	missense	COL4A3	NM_000091.4	29	24,705,5223	AA,AG,GG		7.7036,3.3011,6.3256	probably-damaging	408/1671	228128568	753,11151	1863	4089	5952	SO:0001583	missense	1285	exon21			GAGGCCGCCCAGG		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.1223G>A	2.37:g.228128568G>A	ENSP00000379823:p.Arg408His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	133	72	0.541353	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	210	0.09615384615384616	16	0.032520325203252036	58	0.16022099447513813	87	0.1520979020979021	49	0.06464379947229551	G	8.597	0.885960	0.17540	0.033011	0.077036	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.94000	-3.33	6.02	2.07	0.26955	.	0.318892	0.27522	N	0.018999	T	0.03608	0.0103	L	0.33093	0.98	0.44937	P	0.0020459999999999923	D;D;D;D	0.76494	0.998;0.998;0.998;0.999	P;P;P;D	0.63192	0.731;0.731;0.856;0.912	T	0.60662	-0.7219	9	0.28530	T	0.3	.	2.6414	0.04972	0.1368:0.4371:0.2739:0.1523	rs34505188	408;408;408;408	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	H	408	ENSP00000379823:R408H	ENSP00000323334:R408H	R	+	2	0	COL4A3	227836812	0.994000	0.37717	0.989000	0.46669	0.043000	0.13939	0.671000	0.25172	0.456000	0.26937	-0.783000	0.03347	CGC	G|0.907;A|0.093	0.093	strong		0.562	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
DSPP	1834	hgsc.bcm.edu	37	4	88537268	88537268	+	Missense_Mutation	SNP	G	G	A	rs62651555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537268G>A	ENST00000282478.7	+	4	3487	c.3454G>A	c.(3454-3456)Gac>Aac	p.D1152N	DSPP_ENST00000399271.1_Missense_Mutation_p.D1152N|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1152	Asp/Ser-rich.			D -> N (in Ref. 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgaaagcagcgacagcagtga	0.557													G|||	745	0.148762	0.0144	0.3372	5008	,	,		27589	0.1776		0.2147	False		,,,				2504	0.0992				p.D1152N		Atlas-SNP	.											.	DSPP	174	.	0			c.G3454A						PASS	.	G	ASN/ASP	162,3000		5,152,1424	46.0	60.0	55.0		3454	1.5	0.4	4	dbSNP_134	55	1296,4426		118,1060,1683	no	missense	DSPP	NM_014208.3	23	123,1212,3107	AA,AG,GG		22.6494,5.1233,16.4115	probably-damaging	1152/1302	88537268	1458,7426	1581	2861	4442	SO:0001583	missense	1834	exon5			AGCAGCGACAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3454G>A	4.37:g.88537268G>A	ENSP00000282478:p.Asp1152Asn	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	164	87	0.530488	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	G	2.285	-0.363699	0.05103	0.051233	0.226494	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90444	-2.67;-2.67	1.52	1.52	0.23074	.	0.483859	0.15263	N	0.271667	T	0.00271	0.0008	L	0.29908	0.895	0.52501	P	4.199999999998649E-5	D	0.89917	1.0	D	0.74348	0.983	T	0.09640	-1.0665	9	0.44086	T	0.13	.	6.5429	0.22390	0.0:0.0:1.0:0.0	rs62651555	1152	Q9NZW4	DSPP_HUMAN	N	1152	ENSP00000382213:D1152N;ENSP00000282478:D1152N	ENSP00000282478:D1152N	D	+	1	0	DSPP	88756292	0.924000	0.31332	0.365000	0.25901	0.010000	0.07245	1.465000	0.35299	1.179000	0.42884	0.298000	0.19748	GAC	.	.	weak		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
DHRS4	10901	hgsc.bcm.edu	37	14	24423090	24423090	+	Silent	SNP	A	A	G	rs2273944	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24423090A>G	ENST00000313250.5	+	1	296	c.93A>G	c.(91-93)gcA>gcG	p.A31A	DHRS4_ENST00000558263.1_Silent_p.A31A|DHRS4_ENST00000543741.2_Silent_p.A31A|DHRS4_ENST00000421831.1_Silent_p.A13A|DHRS4_ENST00000382761.3_Silent_p.A13A|DHRS4_ENST00000397074.3_Silent_p.A31A|DHRS4_ENST00000397075.3_Silent_p.A31A|DHRS4_ENST00000558581.1_Silent_p.A31A|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000308178.8_Silent_p.A13A|DHRS4_ENST00000559632.1_Silent_p.A31A|DHRS4_ENST00000397073.2_Silent_p.A13A	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	31			A -> T (in dbSNP:rs1043442).		alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	ACCCGCTCGCAAATAAGGTGG	0.662													.|||	1415	0.282548	0.7973	0.1254	5008	,	,		15599	0.1359		0.0875	False		,,,				2504	0.0501				p.A31A		Atlas-SNP	.											.	DHRS4	22	.	0			c.A93G						PASS	.	G		3004,1398		1049,906,246	28.0	36.0	33.0		93	0.5	0.5	14	dbSNP_100	33	810,7782		36,738,3522	no	coding-synonymous	DHRS4	NM_021004.2		1085,1644,3768	GG,GA,AA		9.4274,31.7583,29.352		31/279	24423090	3814,9180	2201	4296	6497	SO:0001819	synonymous_variant	10901	exon1			GCTCGCAAATAAG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.93A>G	14.37:g.24423090A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	47	0.618421	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		
DOCK10	55619	hgsc.bcm.edu	37	2	225719693	225719693	+	Silent	SNP	G	G	A	rs16866236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:225719693G>A	ENST00000258390.7	-	16	1942	c.1875C>T	c.(1873-1875)ccC>ccT	p.P625P	DOCK10_ENST00000409592.3_Silent_p.P619P	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	625					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GATGCTCCAAGGGAACGTTGT	0.438													G|||	228	0.0455272	0.0166	0.0591	5008	,	,		15983	0.001		0.1382	False		,,,				2504	0.0256				p.P625P		Atlas-SNP	.											.	DOCK10	308	.	0			c.C1875T						PASS	.	G		129,3801		1,127,1837	96.0	95.0	95.0		1875	-0.1	1.0	2	dbSNP_123	95	1140,7140		84,972,3084	no	coding-synonymous	DOCK10	NM_014689.2		85,1099,4921	AA,AG,GG		13.7681,3.2824,10.3931		625/2187	225719693	1269,10941	1965	4140	6105	SO:0001819	synonymous_variant	55619	exon16			CTCCAAGGGAACG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.1875C>T	2.37:g.225719693G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			G|0.922;A|0.078	0.078	strong		0.438	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
DNAJA1	3301	hgsc.bcm.edu	37	9	33026572	33026572	+	Silent	SNP	T	T	C	rs20583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33026572T>C	ENST00000330899.4	+	2	273	c.90T>C	c.(88-90)gcT>gcC	p.A30A	DNAJA1_ENST00000495015.1_Intron|DNAJA1_ENST00000544625.1_5'UTR|APTX_ENST00000473270.1_5'Flank	NM_001539.2	NP_001530.1	P31689	DNJA1_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 1	30	J.				androgen receptor signaling pathway (GO:0030521)|DNA damage response, detection of DNA damage (GO:0042769)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of apoptotic process (GO:0043065)|protein folding (GO:0006457)|protein localization to mitochondrion (GO:0070585)|regulation of protein transport (GO:0051223)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasmic side of endoplasmic reticulum membrane (GO:0098554)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|G-protein coupled receptor binding (GO:0001664)|Hsp70 protein binding (GO:0030544)|low-density lipoprotein particle receptor binding (GO:0050750)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(2)|ovary(1)|skin(3)	6			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.102)		GGAAACTGGCTTTGAAGTACC	0.388													C|||	2994	0.597843	0.857	0.4784	5008	,	,		18511	0.5744		0.5119	False		,,,				2504	0.4448				p.A30A		Atlas-SNP	.											.	DNAJA1	26	.	0			c.T90C						PASS	.	C		3496,910	351.1+/-311.1	1396,704,103	81.0	80.0	80.0		90	3.0	1.0	9	dbSNP_67	80	4443,4157	564.5+/-388.3	1159,2125,1016	no	coding-synonymous	DNAJA1	NM_001539.2		2555,2829,1119	CC,CT,TT		48.3372,20.6537,38.9589		30/398	33026572	7939,5067	2203	4300	6503	SO:0001819	synonymous_variant	3301	exon2			ACTGGCTTTGAAG	L08069	CCDS6533.1	9p13.3	2011-09-02			ENSG00000086061	ENSG00000086061		"""Heat shock proteins / DNAJ (HSP40)"""	5229	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 7"""	602837		HSJ2		8334160, 11147971	Standard	NM_001539		Approved	HSPF4, hdj-2, dj-2, NEDD7	uc003zsd.1	P31689	OTTHUMG00000019760	ENST00000330899.4:c.90T>C	9.37:g.33026572T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_001539	Q5T7Q0|Q86TL9	Silent	SNP	ENST00000330899.4	37	CCDS6533.1																																																																																			A|0.004;C|0.607	0.607	strong		0.388	DNAJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052031.1		
TTN	7273	hgsc.bcm.edu	37	2	179543217	179543217	+	Silent	SNP	C	C	T	rs35112591	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179543217C>T	ENST00000591111.1	-	142	33107	c.32883G>A	c.(32881-32883)gaG>gaA	p.E10961E	TTN_ENST00000589042.1_Silent_p.E11278E|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.E10034E|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33597	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.E10034E(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTGGGTACCTCTGGCACTT	0.373													C|||	1194	0.238419	0.1362	0.183	5008	,	,		13346	0.4454		0.1581	False		,,,				2504	0.2853				p.E11278E		Atlas-SNP	.											TTN_ENST00000356127,NS,carcinoma,0,1	TTN	18412	1	1	Substitution - coding silent(1)	prostate(1)	c.G33834A						scavenged	.	C	,,,	498,3178		42,414,1382	36.0	33.0	34.0		,30102,,	1.4	1.0	2	dbSNP_126	34	1313,6871		103,1107,2882	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	145,1521,4264	TT,TC,CC		16.0435,13.5473,15.2698	,,,	,10034/33424,,	179543217	1811,10049	1838	4092	5930	SO:0001819	synonymous_variant	7273	exon144			GGGTACCTCTGGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32883G>A	2.37:g.179543217C>T		Somatic	149	2	0.0134228		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.788;T|0.212	0.212	strong		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF98	148198	hgsc.bcm.edu	37	19	22575784	22575784	+	Splice_Site	SNP	C	C	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:22575784C>A	ENST00000357774.5	-	4	375		c.e4-1			NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98						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)				GAATATACAACTGAAAGAAAT	0.289																																					.		Atlas-SNP	.											.	ZNF98	230	.	0			c.254-1G>T						PASS	.						19.0	16.0	17.0					19																	22575784		1812	4087	5899	SO:0001630	splice_region_variant	148198	exon5			ATACAACTGAAAG		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.254-1G>T	19.37:g.22575784C>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	55	12	0.218182	NM_001098626		Splice_Site	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	0.621	-0.821207	0.02755	.	.	ENSG00000197360	ENST00000357774	.	.	.	1.56	-3.12	0.05282	.	.	.	.	.	.	.	.	.	.	.	0.20307	N	0.999913	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.0148	0.03496	0.2997:0.4494:0.0:0.2509	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF98	22367624	0.009000	0.17119	0.018000	0.16275	0.149000	0.21700	-0.035000	0.12205	-0.408000	0.07565	0.195000	0.17529	.	.	.	none		0.289	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	Intron
TARS	6897	hgsc.bcm.edu	37	5	33461355	33461355	+	Silent	SNP	G	G	A	rs2270905	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:33461355G>A	ENST00000265112.3	+	13	1817	c.1506G>A	c.(1504-1506)ccG>ccA	p.P502P	TARS_ENST00000502553.1_Silent_p.P502P|TARS_ENST00000509410.1_3'UTR|TARS_ENST00000414361.2_Silent_p.P381P|TARS_ENST00000455217.2_Silent_p.P535P|TARS_ENST00000541634.1_Silent_p.P398P	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	502					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)			NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	CTACTCGCCCGGAAAAATTCC	0.353													G|||	692	0.138179	0.1256	0.1441	5008	,	,		18644	0.127		0.2356	False		,,,				2504	0.0624				p.P535P		Atlas-SNP	.											TARS,NS,carcinoma,+1,1	TARS	66	1	0			c.G1605A						PASS	.	G		624,3782	262.5+/-264.9	43,538,1622	85.0	91.0	89.0		1506	-4.8	1.0	5	dbSNP_100	89	1892,6708	331.8+/-319.8	201,1490,2609	no	coding-synonymous	TARS	NM_152295.3		244,2028,4231	AA,AG,GG		22.0,14.1625,19.3449		502/724	33461355	2516,10490	2203	4300	6503	SO:0001819	synonymous_variant	6897	exon14			TCGCCCGGAAAAA	AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	11572	protein-coding gene	gene with protein product	"""threonine tRNA ligase 1, cytoplasmic"""	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.1506G>A	5.37:g.33461355G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001258438	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Silent	SNP	ENST00000265112.3	37	CCDS3899.1																																																																																			G|0.816;A|0.184	0.184	strong		0.353	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295	
OR5L1	219437	hgsc.bcm.edu	37	11	55578987	55578987	+	Silent	SNP	T	T	C	rs386753698|rs67727364	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	92	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	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	
TTI1	9675	hgsc.bcm.edu	37	20	36624780	36624780	+	Missense_Mutation	SNP	C	C	T	rs34900517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36624780C>T	ENST00000373448.2	-	8	3321	c.3083G>A	c.(3082-3084)aGg>aAg	p.R1028K	TTI1_ENST00000449821.1_Missense_Mutation_p.R1028K|TTI1_ENST00000373447.3_Missense_Mutation_p.R1028K	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	1028			R -> K (in dbSNP:rs34900517).		regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						GACGTACCTCCTGGCAGCCTC	0.458													C|||	82	0.0163738	0.0	0.0202	5008	,	,		20369	0.0		0.0348	False		,,,				2504	0.0337				p.R1028K		Atlas-SNP	.											.	TTI1	104	.	0			c.G3083A						PASS	.	C	LYS/ARG	30,4376	35.2+/-66.4	0,30,2173	97.0	90.0	93.0		3083	5.3	1.0	20	dbSNP_126	93	289,8311	106.6+/-167.4	6,277,4017	yes	missense	TTI1	NM_014657.1	26	6,307,6190	TT,TC,CC		3.3605,0.6809,2.4527	benign	1028/1090	36624780	319,12687	2203	4300	6503	SO:0001583	missense	9675	exon8			TACCTCCTGGCAG	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"""smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	614425	"""KIAA0406"", ""Tel2 interacting protein 1 homolog (S. pombe)"""	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.3083G>A	20.37:g.36624780C>T	ENSP00000362547:p.Arg1028Lys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	42	0.019230769230769232	0	0.0	13	0.03591160220994475	0	0.0	29	0.03825857519788918	C	7.314	0.615633	0.14129	0.006809	0.033605	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.65732	-0.17;-0.17;-0.17	5.3	5.3	0.74995	Armadillo-type fold (1);	0.315894	0.35970	N	0.002874	T	0.22085	0.0532	M	0.63428	1.95	0.33917	D	0.640416	B	0.02656	0.0	B	0.06405	0.002	T	0.50750	-0.8791	10	0.29301	T	0.29	.	6.2312	0.20736	0.1868:0.7196:0.0:0.0936	rs34900517	1028	O43156	TTI1_HUMAN	K	1028	ENSP00000362547:R1028K;ENSP00000362546:R1028K;ENSP00000407270:R1028K	ENSP00000362546:R1028K	R	-	2	0	TTI1	36058194	0.984000	0.35163	1.000000	0.80357	0.970000	0.65996	0.975000	0.29449	2.756000	0.94617	0.563000	0.77884	AGG	C|0.975;T|0.025	0.025	strong		0.458	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657	
CUBN	8029	hgsc.bcm.edu	37	10	16918997	16918997	+	Missense_Mutation	SNP	T	T	C	rs1801240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:16918997T>C	ENST00000377833.4	-	57	9070	c.9005A>G	c.(9004-9006)gAg>gGg	p.E3002G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3002	CUB 22. {ECO:0000255|PROSITE- ProRule:PRU00059}.		E -> G (in dbSNP:rs1801240). {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)	AGCTGGCATCTCATCCCCACA	0.517													T|||	586	0.117013	0.2156	0.0922	5008	,	,		17499	0.002		0.0915	False		,,,				2504	0.1462				p.E3002G		Atlas-SNP	.											.	CUBN	515	.	0			c.A9005G						PASS	.	T	GLY/GLU	899,3507	347.2+/-309.4	83,733,1387	123.0	101.0	108.0		9005	5.8	0.1	10	dbSNP_89	108	902,7698	201.0+/-244.6	50,802,3448	yes	missense	CUBN	NM_001081.3	98	133,1535,4835	CC,CT,TT		10.4884,20.404,13.8475	benign	3002/3624	16918997	1801,11205	2203	4300	6503	SO:0001583	missense	8029	exon57			GGCATCTCATCCC	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.9005A>G	10.37:g.16918997T>C	ENSP00000367064:p.Glu3002Gly	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	103	58	0.563107	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	200	0.09157509157509157	98	0.1991869918699187	34	0.09392265193370165	0	0.0	68	0.08970976253298153	T	11.71	1.720131	0.30503	0.20404	0.104884	ENSG00000107611	ENST00000377833	T	0.18338	2.22	5.8	5.8	0.92144	CUB (5);	0.282943	0.25052	N	0.033504	T	0.00012	0.0000	L	0.50847	1.595	0.44918	P	0.0020689999999999875	B	0.12630	0.006	B	0.10450	0.005	T	0.23762	-1.0179	9	0.32370	T	0.25	.	6.2647	0.20919	0.0:0.0801:0.1624:0.7575	rs1801240	3002	O60494	CUBN_HUMAN	G	3002	ENSP00000367064:E3002G	ENSP00000367064:E3002G	E	-	2	0	CUBN	16959003	0.273000	0.24181	0.096000	0.21009	0.061000	0.15899	2.418000	0.44662	2.209000	0.71365	0.533000	0.62120	GAG	T|0.878;C|0.122	0.122	strong		0.517	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MUC16	94025	hgsc.bcm.edu	37	19	9060059	9060059	+	Missense_Mutation	SNP	A	A	C	rs12977368	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9060059A>C	ENST00000397910.4	-	3	27590	c.27387T>G	c.(27385-27387)gaT>gaG	p.D9129E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9131	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCCATGGCACATCTCCAGGAG	0.483													A|||	897	0.179113	0.1445	0.2061	5008	,	,		23138	0.0099		0.3121	False		,,,				2504	0.2444				p.D9129E		Atlas-SNP	.											.	MUC16	4315	.	0			c.T27387G						PASS	.	A	GLU/ASP	610,3382		40,530,1426	79.0	75.0	76.0		27387	-1.2	0.0	19	dbSNP_121	76	2806,5520		497,1812,1854	yes	missense	MUC16	NM_024690.2	45	537,2342,3280	CC,CA,AA		33.7017,15.2806,27.7318	possibly-damaging	9129/14508	9060059	3416,8902	1996	4163	6159	SO:0001583	missense	94025	exon3			TGGCACATCTCCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27387T>G	19.37:g.9060059A>C	ENSP00000381008:p.Asp9129Glu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	161	77	0.478261	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	390	0.17857142857142858	68	0.13821138211382114	78	0.2154696132596685	5	0.008741258741258742	239	0.3153034300791557	a	6.593	0.477708	0.12521	0.152806	0.337017	ENSG00000181143	ENST00000397910	T	0.23348	1.91	2.34	-1.19	0.09585	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	P	0.41041	0.736	B	0.44224	0.444	T	0.40887	-0.9539	8	0.87932	D	0	.	2.9933	0.05990	0.4644:0.2373:0.2983:0.0	rs12977368;rs12977368	9129	B5ME49	.	E	9129	ENSP00000381008:D9129E	ENSP00000381008:D9129E	D	-	3	2	MUC16	8921059	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-2.522000	0.00950	-0.409000	0.07553	-0.775000	0.03384	GAT	A|0.794;C|0.206	0.206	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KRT1	3848	hgsc.bcm.edu	37	12	53070145	53070145	+	Silent	SNP	G	G	A	rs60447237|rs936958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53070145G>A	ENST00000252244.3	-	7	1447	c.1389C>T	c.(1387-1389)cgC>cgT	p.R463R		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	463	Coil 2.|Rod.		Missing (in palmoplantar keratoderma; and mild ichthyosis largely limited to the flexural areas).	R -> C (in Ref. 9; AAA36153). {ECO:0000305}.	complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CCTGGTAGTCGCGCAGCAGGC	0.597													a|||	2131	0.425519	0.4939	0.4424	5008	,	,		19067	0.2411		0.4523	False		,,,				2504	0.4836				p.R463R		Atlas-SNP	.											KRT1,NS,carcinoma,-2,1	KRT1	110	1	0			c.C1389T						PASS	.	A		2047,2359		466,1115,622	84.0	69.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1389	-10.1	0.5	12	dbSNP_86	74	4067,4533		964,2139,1197	no	coding-synonymous	KRT1	NM_006121.3		1430,3254,1819	AA,AG,GG		47.2907,46.4594,47.0091		463/645	53070145	6114,6892	2203	4300	6503	SO:0001819	synonymous_variant	3848	exon7			GTAGTCGCGCAGC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1389C>T	12.37:g.53070145G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	193	191	0.989637	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	37	CCDS8836.1																																																																																			G|0.554;A|0.446	0.446	strong		0.597	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
CDK4	1019	hgsc.bcm.edu	37	12	58142983	58142983	+	Silent	SNP	C	C	T	rs201744062		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:58142983C>T	ENST00000257904.6	-	7	1166	c.801G>A	c.(799-801)tcG>tcA	p.S267S	CDK4_ENST00000540325.1_Silent_p.S147S|TSPAN31_ENST00000547992.1_3'UTR|CDK4_ENST00000551888.1_5'UTR|CDK4_ENST00000549606.1_Silent_p.S4S|CDK4_ENST00000312990.6_3'UTR	NM_000075.3	NP_000066.1	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	267	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|circadian rhythm (GO:0007623)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle arrest (GO:0071157)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of translation (GO:0045727)|protein phosphorylation (GO:0006468)|regulation of gene expression (GO:0010468)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to lead ion (GO:0010288)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.S267S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	21	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			GCTGTGCTCCCGACTCCTCCA	0.607			Mis			melanoma			Hereditary Melanoma																												p.S267S		Atlas-SNP	.	yes	Dom		Familial malignant melanoma	12	12q14	1019	cyclin-dependent kinase 4		E	CDK4,caecum,carcinoma,-2,1	CDK4	36	1	1	Substitution - coding silent(1)	lung(1)	c.G801A						scavenged	.						65.0	72.0	70.0					12																	58142983		2203	4299	6502	SO:0001819	synonymous_variant	1019	exon7	Familial Cancer Database	Familial Atypical Multiple Mole Melanoma sydrome, FAMMM, Familial Dysplastic Nevus syndrome	TGCTCCCGACTCC	M14505	CCDS8953.1	12q13	2014-09-17				ENSG00000135446		"""Cyclin-dependent kinases"""	1773	protein-coding gene	gene with protein product		123829				8275715	Standard	NM_000075		Approved	PSK-J3	uc001spv.3	P11802		ENST00000257904.6:c.801G>A	12.37:g.58142983C>T		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	293	3	0.0102389	NM_000075	B2R9A0|B4DNF9|O00576|Q6FG61	Silent	SNP	ENST00000257904.6	37	CCDS8953.1																																																																																			C|1.000;T|0.000	0.000	strong		0.607	CDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408790.2	NM_000075	
PPIP5K2	23262	hgsc.bcm.edu	37	5	102520400	102520400	+	Silent	SNP	A	A	C	rs26821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:102520400A>C	ENST00000358359.3	+	26	3633	c.3124A>C	c.(3124-3126)Aga>Cga	p.R1042R	PPIP5K2_ENST00000321521.9_Silent_p.R1042R|PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000414217.1_Silent_p.R1042R	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	1042					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TAATTACCTGAGAACACCAAG	0.353													C|||	1540	0.307508	0.3873	0.2378	5008	,	,		19466	0.4454		0.2813	False		,,,				2504	0.1339				p.R1042R		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.A3124C						PASS	.	C		1646,2760	658.2+/-400.4	298,1050,855	109.0	106.0	107.0		3124	-0.2	0.5	5	dbSNP_76	107	2629,5971	686.9+/-404.2	405,1819,2076	no	coding-synonymous	PPIP5K2	NM_015216.2		703,2869,2931	CC,CA,AA		30.5698,37.3581,32.8694		1042/1223	102520400	4275,8731	2203	4300	6503	SO:0001819	synonymous_variant	23262	exon25			TACCTGAGAACAC	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"""histidine acid phosphatase domain containing 1"""	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.3124A>C	5.37:g.102520400A>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_015216	A1NI53|A6NGS8|Q8TB50	Silent	SNP	ENST00000358359.3	37																																																																																				A|0.660;C|0.340	0.340	strong		0.353	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216	
ZFHX3	463	hgsc.bcm.edu	37	16	72993622	72993622	+	Silent	SNP	C	C	T	rs62053190	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72993622C>T	ENST00000268489.5	-	2	1095	c.423G>A	c.(421-423)gcG>gcA	p.A141A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	141					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCACAATGTACGCGGAGCCGT	0.667													C|||	219	0.04373	0.0507	0.0317	5008	,	,		13453	0.003		0.0616	False		,,,				2504	0.0665				p.A141A		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,2	ZFHX3	404	2	0			c.G423A						PASS	.	C	,	276,4120	146.9+/-181.5	9,258,1931	35.0	39.0	38.0		,423	-10.2	0.4	16	dbSNP_129	38	604,7996	152.8+/-207.3	25,554,3721	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	34,812,5652	TT,TC,CC		7.0233,6.2784,6.7713	,	,141/3704	72993622	880,12116	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			AATGTACGCGGAG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.423G>A	16.37:g.72993622C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	67	0.563025	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			C|0.941;T|0.059	0.059	strong		0.667	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
ZNF112	7771	hgsc.bcm.edu	37	19	44831989	44831989	+	Missense_Mutation	SNP	T	T	G	rs2609881	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	211	0	0		WXS	Illumina HiSeq	Phase_I	228	225	0.986842	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	
WDR45B	56270	hgsc.bcm.edu	37	17	80579609	80579609	+	Missense_Mutation	SNP	T	T	C	rs74895287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80579609T>C	ENST00000392325.4	-	6	688	c.494A>G	c.(493-495)cAt>cGt	p.H165R	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	165																	AAGCTGCACATGGCCCGTGTG	0.587													T|||	66	0.0131789	0.0348	0.0043	5008	,	,		18302	0.0		0.0109	False		,,,				2504	0.0061				p.H165R		Atlas-SNP	.											.	.	.	.	0			c.A494G						PASS	.	T	ARG/HIS	154,4252	106.5+/-144.9	4,146,2053	71.0	57.0	62.0		494	4.8	1.0	17	dbSNP_131	62	151,8449	72.6+/-135.2	2,147,4151	yes	missense	WDR45L	NM_019613.3	29	6,293,6204	CC,CT,TT		1.7558,3.4952,2.3451	benign	165/345	80579609	305,12701	2203	4300	6503	SO:0001583	missense	56270	exon6			TGCACATGGCCCG	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"""WD repeat domain containing"""	25072	protein-coding gene	gene with protein product		609226	"""WDR45-like"""	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.494A>G	17.37:g.80579609T>C	ENSP00000376139:p.His165Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	89	54	0.606742	NM_019613	O95328|Q2MCP6|Q6IBN2	Missense_Mutation	SNP	ENST00000392325.4	37	CCDS11815.2	51	0.023351648351648352	21	0.042682926829268296	2	0.0055248618784530384	8	0.013986013986013986	20	0.026385224274406333	T	16.74	3.205660	0.58234	0.034952	0.017558	ENSG00000141580	ENST00000392325;ENST00000539012	T	0.76578	-1.03	4.82	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.44393	0.1291	M	0.64404	1.975	0.80722	D	1	B	0.31910	0.346	B	0.30316	0.114	T	0.64453	-0.6404	10	0.37606	T	0.19	-25.5227	14.6708	0.68942	0.0:0.0:0.0:1.0	.	165	Q5MNZ6	WIPI3_HUMAN	R	165;137	ENSP00000376139:H165R	ENSP00000376139:H165R	H	-	2	0	WDR45L	78172898	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.503000	0.81632	1.935000	0.56089	0.460000	0.39030	CAT	T|0.977;C|0.023	0.023	strong		0.587	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613	
GTPBP4	23560	hgsc.bcm.edu	37	10	1060218	1060218	+	Missense_Mutation	SNP	G	G	A	rs3207775	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:1060218G>A	ENST00000360803.4	+	15	1656	c.1574G>A	c.(1573-1575)cGt>cAt	p.R525H	GTPBP4_ENST00000538293.1_Missense_Mutation_p.R409H|GTPBP4_ENST00000545048.1_Missense_Mutation_p.R478H	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	525			R -> H (in dbSNP:rs3207775). {ECO:0000269|PubMed:14702039}.		GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		AAGGAGATGCGTAGTCTTGGT	0.388													G|||	398	0.0794728	0.0477	0.0576	5008	,	,		18069	0.0972		0.0795	False		,,,				2504	0.1196				p.R525H		Atlas-SNP	.											.	GTPBP4	57	.	0			c.G1574A						PASS	.	G	HIS/ARG	290,4116	161.4+/-193.6	12,266,1925	195.0	156.0	169.0		1574	4.3	0.9	10	dbSNP_105	169	830,7770	191.3+/-237.5	42,746,3512	yes	missense	GTPBP4	NM_012341.2	29	54,1012,5437	AA,AG,GG		9.6512,6.5819,8.6114	benign	525/635	1060218	1120,11886	2203	4300	6503	SO:0001583	missense	23560	exon15			AGATGCGTAGTCT	AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"""G protein-binding protein CRFG"", "" GTP-binding protein"""					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.1574G>A	10.37:g.1060218G>A	ENSP00000354040:p.Arg525His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	147	66	0.44898	NM_012341	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Missense_Mutation	SNP	ENST00000360803.4	37	CCDS31132.1	154	0.07051282051282051	29	0.05894308943089431	21	0.058011049723756904	49	0.08566433566433566	55	0.07255936675461741	G	10.04	1.242768	0.22796	0.065819	0.096512	ENSG00000107937	ENST00000360803;ENST00000538293;ENST00000545048	T;T;T	0.32023	1.47;1.47;1.47	5.27	4.35	0.52113	.	0.310452	0.36628	N	0.002498	T	0.00637	0.0021	L	0.46157	1.445	0.27426	N	0.954168	B	0.09022	0.002	B	0.06405	0.002	T	0.04178	-1.0971	10	0.51188	T	0.08	-8.6994	8.0377	0.30502	0.1474:0.1953:0.6573:0.0	rs3207775;rs52837854;rs3207775	525	Q9BZE4	NOG1_HUMAN	H	525;409;478	ENSP00000354040:R525H;ENSP00000444277:R409H;ENSP00000445473:R478H	ENSP00000354040:R525H	R	+	2	0	GTPBP4	1050218	0.986000	0.35501	0.926000	0.36857	0.150000	0.21749	2.006000	0.40874	1.345000	0.45676	0.650000	0.86243	CGT	G|0.917;A|0.083	0.083	strong		0.388	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341	
COL4A2	1284	hgsc.bcm.edu	37	13	111156250	111156250	+	Missense_Mutation	SNP	G	G	A	rs45520539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:111156250G>A	ENST00000360467.5	+	44	4501	c.4195G>A	c.(4195-4197)Gtc>Atc	p.V1399I	COL4A2-AS1_ENST00000417970.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1399	Triple-helical region.		V -> I (in dbSNP:rs45520539). {ECO:0000269|PubMed:22209247, ECO:0000269|PubMed:3582677}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GAAGATTGCCGTCCAACCAGG	0.677													G|||	72	0.014377	0.0	0.0259	5008	,	,		14057	0.001		0.0398	False		,,,				2504	0.0133				p.V1399I		Atlas-SNP	.											COL4A2,colon,carcinoma,-1,1	COL4A2	178	1	0			c.G4195A						PASS	.	G	ILE/VAL	24,3606		0,24,1791	47.0	50.0	49.0		4195	-5.6	0.0	13	dbSNP_127	49	340,7790		8,324,3733	yes	missense	COL4A2	NM_001846.2	29	8,348,5524	AA,AG,GG		4.182,0.6612,3.0952	benign	1399/1713	111156250	364,11396	1815	4065	5880	SO:0001583	missense	1284	exon44			ATTGCCGTCCAAC	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.4195G>A	13.37:g.111156250G>A	ENSP00000353654:p.Val1399Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	155	88	0.567742	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	42	0.019230769230769232	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	31	0.040897097625329816	G	9.499	1.102704	0.20632	0.006612	0.04182	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93366	-3.21	5.2	-5.56	0.02529	.	1.658900	0.03478	N	0.214603	T	0.61035	0.2315	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.34452	0.183	T	0.72484	-0.4279	10	0.20519	T	0.43	.	10.777	0.46356	0.1784:0.1897:0.6319:0.0	rs45520539	1399	P08572	CO4A2_HUMAN	I	1399	ENSP00000353654:V1399I	ENSP00000257309:V1399I	V	+	1	0	COL4A2	109954251	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.527000	0.06200	-0.766000	0.04639	-1.149000	0.01842	GTC	G|0.971;A|0.029	0.029	strong		0.677	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
CACNA1S	779	hgsc.bcm.edu	37	1	201052310	201052310	+	Missense_Mutation	SNP	A	A	T	rs12742169|rs386638457	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201052310A>T	ENST00000362061.3	-	10	1599	c.1373T>A	c.(1372-1374)cTc>cAc	p.L458H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.L458H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	458			L -> H (in dbSNP:rs12742169). {ECO:0000269|PubMed:7713519, ECO:0000269|PubMed:9199552}.		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)	GGTCAGCCAGAGAGGCTGGTT	0.557													A|||	637	0.127196	0.0257	0.2032	5008	,	,		17427	0.001		0.34	False		,,,				2504	0.1217				p.L458H		Atlas-SNP	.											.	CACNA1S	249	.	0			c.T1373A						PASS	.	A	HIS/LEU	337,4069	176.6+/-205.7	18,301,1884	98.0	81.0	87.0		1373	3.4	1.0	1	dbSNP_121	87	3235,5365	488.1+/-372.3	645,1945,1710	yes	missense	CACNA1S	NM_000069.2	99	663,2246,3594	TT,TA,AA		37.6163,7.6487,27.4642	benign	458/1874	201052310	3572,9434	2203	4300	6503	SO:0001583	missense	779	exon10			AGCCAGAGAGGCT	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.1373T>A	1.37:g.201052310A>T	ENSP00000355192:p.Leu458His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	379	0.17353479853479853	20	0.04065040650406504	96	0.26519337016574585	1	0.0017482517482517483	262	0.34564643799472294	A	12.50	1.955446	0.34471	0.076487	0.376163	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.97642	-4.47;-4.47	4.53	3.39	0.38822	.	1.216240	0.05908	N	0.631142	T	0.00012	0.0000	L	0.43923	1.385	0.54753	P	1.8999999999991246E-5	P	0.44429	0.835	P	0.44990	0.466	T	0.30001	-0.9993	9	0.29301	T	0.29	.	4.02	0.09662	0.5648:0.0:0.1007:0.3345	rs12742169	458	Q13698	CAC1S_HUMAN	H	458	ENSP00000355192:L458H;ENSP00000356307:L458H	ENSP00000355192:L458H	L	-	2	0	CACNA1S	199318933	0.997000	0.39634	0.984000	0.44739	0.917000	0.54804	4.578000	0.60929	1.786000	0.52430	0.523000	0.50628	CTC	A|0.769;T|0.231	0.231	strong		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628414	60628414	+	Silent	SNP	G	G	T	rs111274143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	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	
ZPLD1	131368	hgsc.bcm.edu	37	3	102157365	102157365	+	Missense_Mutation	SNP	A	A	T	rs6784362	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:102157365A>T	ENST00000491959.1	+	9	916	c.34A>T	c.(34-36)Att>Ttt	p.I12F	ZPLD1_ENST00000306176.1_Missense_Mutation_p.I28F|ZPLD1_ENST00000466937.1_Missense_Mutation_p.I12F			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	12			I -> F (in dbSNP:rs6784362).			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						GCTTCTAACAATTAGAGTGCT	0.438													A|||	484	0.0966454	0.09	0.1585	5008	,	,		18750	0.0357		0.1372	False		,,,				2504	0.0828				p.I28F		Atlas-SNP	.											ZPLD1,NS,carcinoma,-2,1	ZPLD1	82	1	0			c.A82T						PASS	.	A	PHE/ILE	404,4002	201.8+/-224.7	18,368,1817	151.0	134.0	140.0		82	3.8	1.0	3	dbSNP_116	140	1330,7270	260.8+/-283.4	95,1140,3065	yes	missense	ZPLD1	NM_175056.1	21	113,1508,4882	TT,TA,AA		15.4651,9.1693,13.3323	benign	28/432	102157365	1734,11272	2203	4300	6503	SO:0001583	missense	131368	exon2			CTAACAATTAGAG	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.34A>T	3.37:g.102157365A>T	ENSP00000420265:p.Ile12Phe	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		219	0.10027472527472528	40	0.08130081300813008	58	0.16022099447513813	16	0.027972027972027972	105	0.13852242744063326	A	10.93	1.490772	0.26774	0.091693	0.154651	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	T;T;T	0.80653	-1.4;-1.4;-1.4	5.0	3.81	0.43845	.	0.357489	0.34484	N	0.003924	T	0.00328	0.0010	N	0.08118	0	0.31825	P	0.625469	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04128	-1.0975	9	0.10902	T	0.67	-11.2344	6.1708	0.20416	0.7811:0.0:0.0772:0.1417	rs6784362;rs17771116;rs52789307;rs6784362	28;12	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	F	12;28;12	ENSP00000420265:I12F;ENSP00000307801:I28F;ENSP00000418253:I12F	ENSP00000307801:I28F	I	+	1	0	ZPLD1	103640055	0.003000	0.15002	0.972000	0.41901	0.976000	0.68499	1.147000	0.31602	0.723000	0.32274	0.482000	0.46254	ATT	A|0.881;N|0.000	.	strong		0.438	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464046	39464046	+	Missense_Mutation	SNP	G	G	C	rs2074286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	125	124	0.992	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	
HADHB	3032	hgsc.bcm.edu	37	2	26502875	26502875	+	Silent	SNP	T	T	C	rs1056389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:26502875T>C	ENST00000317799.5	+	10	929	c.825T>C	c.(823-825)gtT>gtC	p.V275V	HADHB_ENST00000405867.3_Silent_p.V152V|HADHB_ENST00000545822.1_Silent_p.V253V|HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000537713.1_Silent_p.V260V	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	275					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGATACAGTTACCAAAGATA	0.363													T|||	729	0.145567	0.0303	0.1585	5008	,	,		15976	0.1458		0.2087	False		,,,				2504	0.227				p.V275V		Atlas-SNP	.											.	HADHB	50	.	0			c.T825C						PASS	.	T		272,4134	152.5+/-186.2	9,254,1940	87.0	80.0	82.0		825	1.6	1.0	2	dbSNP_86	82	1861,6739	332.8+/-320.3	204,1453,2643	no	coding-synonymous	HADHB	NM_000183.2		213,1707,4583	CC,CT,TT		21.6395,6.1734,16.4001		275/475	26502875	2133,10873	2203	4300	6503	SO:0001819	synonymous_variant	3032	exon10			TACAGTTACCAAA		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"""mitochondrial trifunctional protein, beta subunit"""	143450	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"""			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.825T>C	2.37:g.26502875T>C		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	273	123	0.450549	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	37	CCDS1722.1																																																																																			T|0.834;C|0.166	0.166	strong		0.363	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183	
OR7A10	390892	hgsc.bcm.edu	37	19	14951898	14951898	+	Silent	SNP	G	G	T	rs3752195	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14951898G>T	ENST00000248058.1	-	1	791	c.792C>A	c.(790-792)gcC>gcA	p.A264A		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	264						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)					AATTGTGGGTGGCAGCAGAAC	0.478													.|||	1159	0.23143	0.1694	0.2464	5008	,	,		19853	0.1776		0.2097	False		,,,				2504	0.3824				p.A264A		Atlas-SNP	.											OR7A10,NS,carcinoma,-2,1	OR7A10	33	1	0			c.C792A						PASS	.	T		829,3577	747.7+/-411.9	90,649,1464	96.0	87.0	90.0		792	-3.8	0.0	19	dbSNP_107	90	1967,6633	723.8+/-406.5	208,1551,2541	no	coding-synonymous	OR7A10	NM_001005190.1		298,2200,4005	TT,TG,GG		22.8721,18.8153,21.4978		264/310	14951898	2796,10210	2203	4300	6503	SO:0001819	synonymous_variant	390892	exon1			GTGGGTGGCAGCA		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.792C>A	19.37:g.14951898G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_001005190	Q6IFP0|Q96R97	Silent	SNP	ENST00000248058.1	37	CCDS32936.1																																																																																			G|0.787;T|0.213	0.213	strong		0.478	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
SPEF2	79925	hgsc.bcm.edu	37	5	35646784	35646784	+	Missense_Mutation	SNP	A	A	G	rs80010329	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:35646784A>G	ENST00000356031.3	+	5	755	c.601A>G	c.(601-603)Aga>Gga	p.R201G	SPEF2_ENST00000282469.6_Missense_Mutation_p.R201G|SPEF2_ENST00000440995.2_Missense_Mutation_p.R201G|SPEF2_ENST00000509059.1_Missense_Mutation_p.R201G	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	201					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTTAAACAGAAGACGACAAAA	0.318													A|||	44	0.00878594	0.0008	0.0043	5008	,	,		16656	0.001		0.007	False		,,,				2504	0.0327				p.R201G		Atlas-SNP	.											.	SPEF2	324	.	0			c.A601G						PASS	.	A	GLY/ARG,GLY/ARG	9,4397	14.3+/-33.2	0,9,2194	104.0	111.0	109.0		601,601	5.8	1.0	5	dbSNP_131	109	66,8532	39.8+/-96.3	0,66,4233	yes	missense,missense	SPEF2	NM_024867.3,NM_144722.3	125,125	0,75,6427	GG,GA,AA		0.7676,0.2043,0.5767	probably-damaging,probably-damaging	201/1823,201/515	35646784	75,12929	2203	4299	6502	SO:0001583	missense	79925	exon5			AACAGAAGACGAC	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.601A>G	5.37:g.35646784A>G	ENSP00000348314:p.Arg201Gly	Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	239	127	0.531381	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	18.98	3.738481	0.69304	0.002043	0.007676	ENSG00000152582	ENST00000282469;ENST00000356031;ENST00000509059;ENST00000510777;ENST00000440995	T;T;T;T;T	0.23147	2.44;3.29;3.14;1.92;3.29	5.76	5.76	0.90799	.	0.106914	0.64402	D	0.000010	T	0.38374	0.1038	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.999	D;D;D	0.78314	0.991;0.931;0.936	T	0.37033	-0.9723	10	0.62326	D	0.03	.	11.5326	0.50618	0.8504:0.1496:0.0:0.0	.	201;201;201	D6REZ4;Q9C093;Q9C093-3	.;SPEF2_HUMAN;.	G	201;201;201;144;201	ENSP00000282469:R201G;ENSP00000348314:R201G;ENSP00000421593:R201G;ENSP00000426259:R144G;ENSP00000412125:R201G	ENSP00000282469:R201G	R	+	1	2	SPEF2	35682541	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.892000	0.63193	2.209000	0.71365	0.533000	0.62120	AGA	A|0.995;G|0.005	0.005	strong		0.318	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
PXDN	7837	hgsc.bcm.edu	37	2	1652660	1652660	+	Silent	SNP	G	G	A	rs3811613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:1652660G>A	ENST00000252804.4	-	17	2942	c.2892C>T	c.(2890-2892)aaC>aaT	p.N964N		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	964					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGGGGCTCTCGTTCTCGTCCC	0.721													G|||	1226	0.244808	0.1218	0.2709	5008	,	,		14999	0.2847		0.2823	False		,,,				2504	0.3129				p.N964N		Atlas-SNP	.											.	PXDN	255	.	0			c.C2892T						PASS	.	G		635,3533		56,523,1505	15.0	16.0	16.0		2892	-0.3	1.0	2	dbSNP_107	16	2507,5881		385,1737,2072	no	coding-synonymous	PXDN	NM_012293.1		441,2260,3577	AA,AG,GG		29.8879,15.2351,25.0239		964/1480	1652660	3142,9414	2084	4194	6278	SO:0001819	synonymous_variant	7837	exon17			GCTCTCGTTCTCG	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2892C>T	2.37:g.1652660G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																			G|0.761;A|0.239	0.239	strong		0.721	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
FLG2	388698	hgsc.bcm.edu	37	1	152325866	152325866	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152325866C>T	ENST00000388718.5	-	3	4468	c.4396G>A	c.(4396-4398)Gga>Aga	p.G1466R	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1466					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)			TGAGTAGTTCCGTGTCTCCCA	0.507																																					p.G1466R		Atlas-SNP	.											FLG2,NS,carcinoma,+1,1	FLG2	431	1	0			c.G4396A						scavenged	.						438.0	389.0	406.0					1																	152325866		2203	4300	6503	SO:0001583	missense	388698	exon3			TAGTTCCGTGTCT	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.4396G>A	1.37:g.152325866C>T	ENSP00000373370:p.Gly1466Arg	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	310	5	0.016129	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	c	0.354	-0.943270	0.02322	.	.	ENSG00000143520	ENST00000388718	T	0.13538	2.58	2.82	-5.65	0.02459	.	.	.	.	.	T	0.02807	0.0084	L	0.60455	1.87	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.42632	-0.9440	9	0.30854	T	0.27	-1.5691	1.1555	0.01795	0.1509:0.3416:0.15:0.3576	.	1466	Q5D862	FILA2_HUMAN	R	1466	ENSP00000373370:G1466R	ENSP00000373370:G1466R	G	-	1	0	FLG2	150592490	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-4.354000	0.00247	-1.205000	0.02645	-1.326000	0.01283	GGA	.	.	none		0.507	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
CCDC158	339965	hgsc.bcm.edu	37	4	77255210	77255210	+	Silent	SNP	C	C	T	rs113022439	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77255210C>T	ENST00000388914.3	-	18	2927	c.2775G>A	c.(2773-2775)aaG>aaA	p.K925K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	925										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						CTTCCTCTGTCTTGCTCAGAG	0.483													C|||	32	0.00638978	0.0015	0.0072	5008	,	,		17210	0.0		0.0239	False		,,,				2504	0.001				p.K925K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2775A						PASS	.	C		15,4101		0,15,2043	158.0	159.0	159.0		2775	3.8	0.6	4	dbSNP_132	159	300,8128		4,292,3918	no	coding-synonymous	CCDC158	NM_001042784.1		4,307,5961	TT,TC,CC		3.5596,0.3644,2.5112		925/1114	77255210	315,12229	2058	4214	6272	SO:0001819	synonymous_variant	339965	exon18			CTCTGTCTTGCTC	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.2775G>A	4.37:g.77255210C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	177	93	0.525424	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			C|0.984;T|0.016	0.016	strong		0.483	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
MCC	4163	hgsc.bcm.edu	37	5	112406862	112406862	+	Silent	SNP	G	G	A	rs2227950	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:112406862G>A	ENST00000302475.4	-	10	1847	c.1284C>T	c.(1282-1284)gcC>gcT	p.A428A	MCC_ENST00000408903.3_Silent_p.A618A|MCC_ENST00000515367.2_Silent_p.A365A|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	199	0	0		WXS	Illumina HiSeq	Phase_I	192	189	0.984375	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	
COL15A1	1306	hgsc.bcm.edu	37	9	101748356	101748356	+	Missense_Mutation	SNP	A	A	G	rs2075663	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	62	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	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	
GPRIN3	285513	hgsc.bcm.edu	37	4	90169925	90169925	+	Missense_Mutation	SNP	A	A	G	rs7653897	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	112	0	0		WXS	Illumina HiSeq	Phase_I	145	60	0.413793	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	
OR5I1	10798	hgsc.bcm.edu	37	11	55703247	55703247	+	Silent	SNP	G	G	A	rs4465383	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:55703247G>A	ENST00000301532.3	-	1	629	c.630C>T	c.(628-630)atC>atT	p.I210I		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	210					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						TAAAACAAATGATTTCCACTG	0.423													A|||	843	0.168331	0.2958	0.0893	5008	,	,		19082	0.0913		0.1849	False		,,,				2504	0.1145				p.I210I		Atlas-SNP	.											.	OR5I1	110	.	0			c.C630T						PASS	.	A		1098,3304	702.4+/-406.9	163,772,1266	41.0	46.0	44.0		630	-7.2	0.0	11	dbSNP_111	44	1406,7182	743.1+/-407.2	115,1176,3003	no	coding-synonymous	OR5I1	NM_006637.1		278,1948,4269	AA,AG,GG		16.3717,24.9432,19.2764		210/315	55703247	2504,10486	2201	4294	6495	SO:0001819	synonymous_variant	10798	exon1			ACAAATGATTTCC	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.630C>T	11.37:g.55703247G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_006637	Q6IEU4	Silent	SNP	ENST00000301532.3	37	CCDS7949.1																																																																																			G|0.817;A|0.183	0.183	strong		0.423	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
LPAR2	9170	hgsc.bcm.edu	37	19	19737992	19737992	+	Silent	SNP	G	G	A	rs150741448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19737992G>A	ENST00000542587.1	-	5	1004	c.102C>T	c.(100-102)gtC>gtT	p.V34V	LPAR2_ENST00000589311.1_5'Flank|LPAR2_ENST00000407877.3_Silent_p.V34V|LPAR2_ENST00000586703.1_Silent_p.V34V			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	34					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						GTGCCACCACGACCACATCCT	0.592													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18269	0.0		0.005	False		,,,				2504	0.0				p.V34V		Atlas-SNP	.											.	LPAR2	28	.	0			c.C102T						PASS	.	G		4,4400	6.2+/-15.9	0,4,2198	33.0	32.0	33.0		102	-8.9	0.4	19	dbSNP_134	33	39,8561	24.0+/-70.4	0,39,4261	no	coding-synonymous	LPAR2	NM_004720.5		0,43,6459	AA,AG,GG		0.4535,0.0908,0.3307		34/352	19737992	43,12961	2202	4300	6502	SO:0001819	synonymous_variant	9170	exon2			CACCACGACCACA	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	3168	protein-coding gene	gene with protein product		605110	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"""	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.102C>T	19.37:g.19737992G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	37	CCDS12407.1																																																																																			G|0.997;A|0.003	0.003	strong		0.592	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21200089	21200089	+	Missense_Mutation	SNP	A	A	G	rs11045681	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21200089A>G	ENST00000421593.2	+	7	932	c.932A>G	c.(931-933)tAt>tGt	p.Y311C	LST3_ENST00000540229.1_Intron|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.Y358C|LST3_ENST00000381541.3_Missense_Mutation_p.Y358C|SLCO1B3_ENST00000553473.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TCTCTTACTTATATCATTAAA	0.333													A|||	379	0.0756789	0.0083	0.1354	5008	,	,		15229	0.003		0.1869	False		,,,				2504	0.0849				p.Y311C		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.A932G						PASS	.	A	CYS/TYR	170,4136		5,160,1988	112.0	113.0	112.0		932	3.4	0.7	12	dbSNP_120	112	1683,6879		164,1355,2762	yes	missense	SLCO1B7	NM_001009562.4	194	169,1515,4750	GG,GA,AA		19.6566,3.948,14.4001		311/641	21200089	1853,11015	2153	4281	6434	SO:0001583	missense	338821	exon7			TTACTTATATCAT	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.932A>G	12.37:g.21200089A>G	ENSP00000394168:p.Tyr311Cys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	167	76	0.45509	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	188	0.08608058608058608	6	0.012195121951219513	47	0.1298342541436464	1	0.0017482517482517483	134	0.17678100263852242	.	14.21	2.467159	0.43839	0.03948	0.196566	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.48522	0.81;0.81;0.81	3.36	3.36	0.38483	.	0.262265	0.38720	N	0.001594	T	0.00178	0.0005	M	0.88570	2.965	0.24286	P	0.9951805	D;D	0.76494	0.996;0.999	D;D	0.70016	0.967;0.967	T	0.19712	-1.0297	9	0.87932	D	0	.	9.6342	0.39798	1.0:0.0:0.0:0.0	rs11045681;rs11045681	311;358	G3V0H7;F5H094	.;.	C	358;358;311	ENSP00000370952:Y358C;ENSP00000452013:Y358C;ENSP00000394168:Y311C	ENSP00000370952:Y358C	Y	+	2	0	SLCO1B7;RP11-545J16.1	21091356	0.777000	0.28628	0.652000	0.29579	0.010000	0.07245	1.339000	0.33885	1.510000	0.48803	0.377000	0.23210	TAT	A|0.896;G|0.104	0.104	strong		0.333	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
MAN2A1	4124	hgsc.bcm.edu	37	5	109181682	109181682	+	Silent	SNP	A	A	T	rs3186988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:109181682A>T	ENST00000261483.4	+	18	3869	c.2817A>T	c.(2815-2817)tcA>tcT	p.S939S		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	939					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		CTGCTCAGTCATTAGGGGTTT	0.418													T|||	3740	0.746805	0.9047	0.6369	5008	,	,		16728	0.8819		0.6093	False		,,,				2504	0.6135				p.S939S		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A2817T						PASS	.	T		3767,637	273.1+/-271.2	1619,529,54	246.0	229.0	235.0		2817	0.2	0.1	5	dbSNP_105	235	5340,3260	490.6+/-372.9	1663,2014,623	no	coding-synonymous	MAN2A1	NM_002372.2		3282,2543,677	TT,TA,AA		37.907,14.4641,29.9677		939/1145	109181682	9107,3897	2202	4300	6502	SO:0001819	synonymous_variant	4124	exon18			TCAGTCATTAGGG		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2817A>T	5.37:g.109181682A>T		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	193	85	0.440415	NM_002372	Q16767	Silent	SNP	ENST00000261483.4	37	CCDS34209.1																																																																																			A|0.293;T|0.707	0.707	strong		0.418	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
RETSAT	54884	hgsc.bcm.edu	37	2	85570849	85570849	+	Missense_Mutation	SNP	C	C	T	rs4832168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:85570849C>T	ENST00000295802.4	-	10	1718	c.1606G>A	c.(1606-1608)Ggg>Agg	p.G536R	RETSAT_ENST00000457495.2_Missense_Mutation_p.G475R|RETSAT_ENST00000263854.6_Missense_Mutation_p.R480Q|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	235	0	0		WXS	Illumina HiSeq	Phase_I	310	39	0.125806	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	
OR51F1	256892	hgsc.bcm.edu	37	11	4790951	4790951	+	Missense_Mutation	SNP	A	A	G	rs11033801	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790951A>G	ENST00000380383.1	-	1	217	c.218T>C	c.(217-219)tTc>tCc	p.F73S	OR51F1_ENST00000343430.3_Missense_Mutation_p.F66S|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			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	81	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	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	
ITIH2	3698	hgsc.bcm.edu	37	10	7759679	7759679	+	Silent	SNP	G	G	A	rs35076349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:7759679G>A	ENST00000358415.4	+	6	724	c.558G>A	c.(556-558)gtG>gtA	p.V186V	ITIH2_ENST00000379587.4_Silent_p.V175V|ITIH2_ENST00000480387.1_3'UTR	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	186					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						ACCAGGAGGTGAAGTGGAGGA	0.517													G|||	210	0.0419329	0.0045	0.1037	5008	,	,		21135	0.0119		0.0716	False		,,,				2504	0.0491				p.V186V		Atlas-SNP	.											.	ITIH2	144	.	0			c.G558A						PASS	.	G		48,4358	48.9+/-83.8	0,48,2155	158.0	155.0	156.0		558	3.5	1.0	10	dbSNP_126	156	534,8066	148.9+/-204.1	14,506,3780	no	coding-synonymous	ITIH2	NM_002216.2		14,554,5935	AA,AG,GG		6.2093,1.0894,4.4749		186/947	7759679	582,12424	2203	4300	6503	SO:0001819	synonymous_variant	3698	exon6			GGAGGTGAAGTGG	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.558G>A	10.37:g.7759679G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	138	72	0.521739	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																			G|0.952;A|0.048	0.048	strong		0.517	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
TNIP3	79931	hgsc.bcm.edu	37	4	122075739	122075739	+	Silent	SNP	T	T	C	rs17051298	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:122075739T>C	ENST00000509841.1	-	8	768	c.690A>G	c.(688-690)gaA>gaG	p.E230E	TNIP3_ENST00000057513.3_Silent_p.E153E|TNIP3_ENST00000507879.1_Silent_p.E223E|TNIP3_ENST00000454328.1_Silent_p.E153E	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3											NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						ATTCGTAATGTTCCTTTTCCT	0.348													T|||	639	0.127596	0.0862	0.0403	5008	,	,		18458	0.0665		0.0686	False		,,,				2504	0.3691				p.E230E		Atlas-SNP	.											.	TNIP3	58	.	0			c.A690G						PASS	.	T	,	351,4055	182.9+/-210.6	15,321,1867	188.0	172.0	177.0		459,459	-2.9	0.7	4	dbSNP_123	177	569,8031	154.8+/-208.9	18,533,3749	no	coding-synonymous,coding-synonymous	TNIP3	NM_001128843.2,NM_024873.5	,	33,854,5616	CC,CT,TT		6.6163,7.9664,7.0737	,	153/326,153/326	122075739	920,12086	2203	4300	6503	SO:0001819	synonymous_variant	79931	exon8			GTAATGTTCCTTT	AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.690A>G	4.37:g.122075739T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	46	0.386555	NM_001244764		Silent	SNP	ENST00000509841.1	37	CCDS58926.1																																																																																			T|0.924;C|0.076	0.076	strong		0.348	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873	
VPS41	27072	hgsc.bcm.edu	37	7	38785204	38785204	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:38785204T>C	ENST00000310301.4	-	23	1990	c.1936A>G	c.(1936-1938)Atc>Gtc	p.I646V	VPS41_ENST00000395969.2_Missense_Mutation_p.I621V	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	646					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						TGTTGACAGATCTCAAGAGCC	0.328																																					p.I646V		Atlas-SNP	.											.	VPS41	102	.	0			c.A1936G						PASS	.						112.0	114.0	113.0					7																	38785204		2203	4300	6503	SO:0001583	missense	27072	exon23			GACAGATCTCAAG	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.1936A>G	7.37:g.38785204T>C	ENSP00000309457:p.Ile646Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290379	0.40494	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.19105	2.17;2.17	5.35	5.35	0.76521	Tetratricopeptide-like helical (1);	0.252290	0.45126	D	0.000390	T	0.19725	0.0474	L	0.41236	1.265	0.58432	D	0.999996	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.02617	-1.1133	10	0.30078	T	0.28	-15.5727	15.6427	0.77020	0.0:0.0:0.0:1.0	.	646;621;646	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	V	646;621	ENSP00000309457:I646V;ENSP00000379297:I621V	ENSP00000309457:I646V	I	-	1	0	VPS41	38751729	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.923000	0.63412	2.152000	0.67230	0.455000	0.32223	ATC	.	.	none		0.328	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
EXTL1	2134	hgsc.bcm.edu	37	1	26357667	26357667	+	Silent	SNP	G	G	A	rs11247848	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26357667G>A	ENST00000374280.3	+	5	2013	c.1146G>A	c.(1144-1146)ctG>ctA	p.L382L	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	382					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)	p.L382L(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		ACCCCTCACTGCTGTGGAACA	0.567													G|||	748	0.149361	0.1513	0.1484	5008	,	,		18563	0.1845		0.1859	False		,,,				2504	0.0736				p.L382L		Atlas-SNP	.											EXTL1,NS,carcinoma,0,1	EXTL1	61	1	1	Substitution - coding silent(1)	stomach(1)	c.G1146A						PASS	.	G		702,3704	291.5+/-281.6	54,594,1555	108.0	105.0	106.0		1146	-0.4	0.0	1	dbSNP_120	106	1751,6849	317.9+/-313.4	173,1405,2722	no	coding-synonymous	EXTL1	NM_004455.2		227,1999,4277	AA,AG,GG		20.3605,15.9328,18.8605		382/677	26357667	2453,10553	2203	4300	6503	SO:0001819	synonymous_variant	2134	exon5			CTCACTGCTGTGG	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.1146G>A	1.37:g.26357667G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_004455	Q6GSC1	Silent	SNP	ENST00000374280.3	37	CCDS271.1																																																																																			G|0.819;A|0.181	0.181	strong		0.567	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291831	1291831	+	Missense_Mutation	SNP	G	G	C	rs202156919		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1291831G>C	ENST00000338844.3	+	5	536	c.503G>C	c.(502-504)cGc>cCc	p.R168P	TPSAB1_ENST00000461509.2_Missense_Mutation_p.R175P	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	168	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> P (in allele alpha; dbSNP:rs1141969).		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				CCTGCAGAGCGCCTCCCACCG	0.632																																					p.R168P		Atlas-SNP	.											TPSAB1,NS,carcinoid-endocrine_tumour,0,1	TPSAB1	24	1	0			c.G503C						scavenged	.						1.0	1.0	1.0					16																	1291831		839	2074	2913	SO:0001583	missense	7177	exon5			CAGAGCGCCTCCC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.503G>C	16.37:g.1291831G>C	ENSP00000343577:p.Arg168Pro	Somatic	538	6	0.0111524		WXS	Illumina HiSeq	Phase_I	402	128	0.318408	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	367	0.16804029304029305	73	0.1483739837398374	58	0.16022099447513813	91	0.1590909090909091	145	0.19129287598944592	N	0.005	-2.227160	0.00280	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	T;T	0.81163	-1.46;-1.46	3.67	-7.34	0.01427	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	2.170790	0.01914	N	0.040075	T	0.00144	0.0004	N	0.11023	0.085	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37888	-0.9686	9	0.02654	T	1	.	7.2213	0.25988	0.2688:0.1211:0.5338:0.0763	.	159;168	Q15661-2;Q15661	.;TRYB1_HUMAN	P	168;175	ENSP00000343577:R168P;ENSP00000418247:R175P	ENSP00000343577:R168P	R	+	2	0	TPSAB1	1231832	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.446000	0.00232	-2.203000	0.00744	-4.814000	0.00003	CGC	.	.	strong		0.632	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
RNF17	56163	hgsc.bcm.edu	37	13	25378476	25378476	+	Missense_Mutation	SNP	A	A	G	rs9511451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25378476A>G	ENST00000255324.5	+	15	2052	c.2000A>G	c.(1999-2001)cAc>cGc	p.H667R	RNF17_ENST00000381921.1_Missense_Mutation_p.H667R|RNF17_ENST00000255325.6_Intron	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	667			H -> R (in dbSNP:rs9511451).		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)		ACTACTTTACACTATCATCCA	0.348													A|||	1064	0.21246	0.0847	0.2219	5008	,	,		20210	0.3244		0.2913	False		,,,				2504	0.182				p.H667R		Atlas-SNP	.											RNF17_ENST00000255324,NS,carcinoma,+1,1	RNF17	259	1	0			c.A2000G						PASS	.	A	ARG/HIS,ARG/HIS	526,3874	239.0+/-250.2	34,458,1708	92.0	91.0	91.0		2000,2000	0.3	0.1	13	dbSNP_119	91	2517,6083	409.5+/-349.8	346,1825,2129	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	29,29	380,2283,3837	GG,GA,AA		29.2674,11.9545,23.4077	benign,benign	667/1620,667/1624	25378476	3043,9957	2200	4300	6500	SO:0001583	missense	56163	exon15			CTTTACACTATCA	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.2000A>G	13.37:g.25378476A>G	ENSP00000255324:p.His667Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	493	0.22573260073260074	40	0.08130081300813008	82	0.2265193370165746	155	0.270979020979021	216	0.2849604221635884	A	0.018	-1.480284	0.01027	0.119545	0.292674	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047	T;T	0.20069	2.1;2.1	5.5	0.308	0.15815	.	1.211800	0.05578	N	0.572397	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	0.43782	-0.9370	9	0.11485	T	0.65	.	5.0512	0.14508	0.3981:0.1682:0.4338:0.0	rs9511451;rs9511451	667;667	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	R	667;667;526	ENSP00000255324:H667R;ENSP00000371346:H667R	ENSP00000255324:H667R	H	+	2	0	RNF17	24276476	0.001000	0.12720	0.054000	0.19295	0.249000	0.25844	0.214000	0.17541	0.061000	0.16311	0.482000	0.46254	CAC	A|0.776;G|0.224	0.224	strong		0.348	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
RIC3	79608	hgsc.bcm.edu	37	11	8159884	8159884	+	Missense_Mutation	SNP	C	C	G	rs80168649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8159884C>G	ENST00000309737.6	-	3	361	c.362G>C	c.(361-363)gGg>gCg	p.G121A	RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000425599.2_Missense_Mutation_p.G121A|RIC3_ENST00000539720.1_Missense_Mutation_p.G72A|RIC3_ENST00000343202.4_Missense_Mutation_p.G121A|RIC3_ENST00000335425.7_Intron			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	121					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)		AGTTGTTTTCCCCTTTGAGAG	0.438													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		16568	0.0		0.0149	False		,,,				2504	0.0				p.G121A		Atlas-SNP	.											.	RIC3	42	.	0			c.G362C						PASS	.	C	,ALA/GLY,ALA/GLY,ALA/GLY	12,4390	19.1+/-41.9	0,12,2189	224.0	215.0	218.0		,362,362,362	5.8	1.0	11	dbSNP_131	218	114,8478	60.6+/-122.4	0,114,4182	yes	intron,missense,missense,missense	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	,60,60,60	0,126,6371	GG,GC,CC		1.3268,0.2726,0.9697	,probably-damaging,probably-damaging,probably-damaging	,121/370,121/289,121/369	8159884	126,12868	2201	4296	6497	SO:0001583	missense	79608	exon3			GTTTTCCCCTTTG		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.362G>C	11.37:g.8159884C>G	ENSP00000308820:p.Gly121Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	0	0.0	14	0.018469656992084433	C	21.8	4.195192	0.78902	0.002726	0.013268	ENSG00000166405	ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.38639	0.1048	M	0.68317	2.08	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;0.999;0.999	T	0.25606	-1.0127	10	0.32370	T	0.25	.	18.1955	0.89820	0.0:1.0:0.0:0.0	.	121;121;121;121	B7Z1U4;B0B1U0;Q7Z5B4;Q7Z5B4-5	.;.;RIC3_HUMAN;.	A	121;121;121;72;121;121	ENSP00000344904:G121A;ENSP00000308820:G121A;ENSP00000443871:G72A;ENSP00000395320:G121A;ENSP00000431658:G121A	ENSP00000308820:G121A	G	-	2	0	RIC3	8116460	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.457000	0.53007	2.738000	0.93877	0.609000	0.83330	GGG	C|0.992;G|0.008	0.008	strong		0.438	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
SYNRG	11276	hgsc.bcm.edu	37	17	35956391	35956391	+	Splice_Site	SNP	G	G	C	rs12944821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:35956391G>C	ENST00000339208.6	-	3	259	c.119C>G	c.(118-120)gCa>gGa	p.A40G	SYNRG_ENST00000394378.2_Splice_Site_p.A40G|SYNRG_ENST00000345615.4_Splice_Site_p.A40G|SYNRG_ENST00000591288.1_Splice_Site_p.A40G|SYNRG_ENST00000346661.4_Splice_Site_p.A40G|SYNRG_ENST00000585472.1_Intron|SYNRG_ENST00000502449.2_Splice_Site_p.A40G	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	40			A -> G (in dbSNP:rs12944821).		endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CATCAGGCCTGCTGAAAATAT	0.383													G|||	1009	0.201478	0.1203	0.3372	5008	,	,		21269	0.251		0.1789	False		,,,				2504	0.1871				p.A40G		Atlas-SNP	.											SYNRG,rectum,carcinoma,0,1	SYNRG	101	1	0			c.C119G						PASS	.	G	GLY/ALA,,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	564,3842	251.8+/-258.4	39,486,1678	83.0	78.0	80.0		119,,119,119,119,119,119	3.7	1.0	17	dbSNP_121	80	1587,7013	295.7+/-302.5	151,1285,2864	yes	missense-near-splice,intron,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	60,,60,60,60,60,60	190,1771,4542	CC,CG,GG		18.4535,12.8007,16.5385	benign,,benign,benign,benign,benign,benign	40/1237,,40/1180,40/1109,40/1315,40/1225,40/1260	35956391	2151,10855	2203	4300	6503	SO:0001630	splice_region_variant	11276	exon3			AGGCCTGCTGAAA	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.119-1C>G	17.37:g.35956391G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_001163544	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	440	0.20146520146520147	55	0.11178861788617886	116	0.32044198895027626	139	0.243006993006993	130	0.17150395778364116	G	13.47	2.246510	0.39697	0.128007	0.184535	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378;ENST00000394379	T;T;T;T;T	0.46451	1.53;1.53;0.87;0.87;0.87	6.07	3.74	0.42951	.	0.470274	0.20873	N	0.084129	T	0.00012	0.0000	L	0.27053	0.805	0.29416	P	0.860872	B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001;0.001	T	0.34477	-0.9827	9	0.24483	T	0.36	.	12.9222	0.58239	0.0721:0.1192:0.8088:0.0	rs12944821;rs12944821	40;40;40;40;40;40;40	A8MYE0;B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;.;SYNRG_HUMAN	G	40	ENSP00000005279:A40G;ENSP00000343610:A40G;ENSP00000315722:A40G;ENSP00000424893:A40G;ENSP00000377903:A40G	ENSP00000343610:A40G	A	-	2	0	SYNRG	33030504	1.000000	0.71417	0.995000	0.50966	0.973000	0.67179	3.224000	0.51238	1.548000	0.49413	0.655000	0.94253	GCA	G|0.825;C|0.175	0.175	strong		0.383	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	Missense_Mutation
ABCD4	5826	hgsc.bcm.edu	37	14	74759066	74759066	+	Missense_Mutation	SNP	G	G	A	rs147795328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74759066G>A	ENST00000356924.4	-	11	1185	c.1042C>T	c.(1042-1044)Cgg>Tgg	p.R348W	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000298816.7_Missense_Mutation_p.R244W	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	348					cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		AGCGTCTCCCGAAGCTGCCCA	0.562													G|||	17	0.00339457	0.0008	0.0014	5008	,	,		21281	0.001		0.001	False		,,,				2504	0.0133				p.R348W		Atlas-SNP	.											.	ABCD4	54	.	0			c.C1042T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	56.0	53.0	54.0		1042	4.2	1.0	14	dbSNP_134	54	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ABCD4	NM_005050.3	101	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	348/607	74759066	3,13003	2203	4300	6503	SO:0001583	missense	5826	exon11			TCTCCCGAAGCTG	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.1042C>T	14.37:g.74759066G>A	ENSP00000349396:p.Arg348Trp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	12.58	1.981289	0.34942	0.0	3.49E-4	ENSG00000119688	ENST00000356924;ENST00000298816;ENST00000537629	D;D	0.94457	-3.43;-3.12	5.1	4.2	0.49525	ABC transporter, transmembrane domain, type 1 (1);	0.326291	0.37437	N	0.002086	D	0.91068	0.7189	L	0.34521	1.04	0.28094	N	0.931705	P;B;P;B	0.44241	0.829;0.004;0.738;0.012	B;B;B;B	0.42798	0.398;0.007;0.394;0.007	D	0.86008	0.1499	10	0.38643	T	0.18	.	14.4627	0.67462	0.0:0.1467:0.8533:0.0	.	244;244;348;348	F8W7M4;B7Z4V6;A8K5L7;O14678	.;.;.;ABCD4_HUMAN	W	348;244;85	ENSP00000349396:R348W;ENSP00000298816:R244W	ENSP00000298816:R244W	R	-	1	2	ABCD4	73828819	1.000000	0.71417	0.998000	0.56505	0.580000	0.36256	2.853000	0.48317	1.487000	0.48415	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.562	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
CRISP1	167	hgsc.bcm.edu	37	6	49814379	49814379	+	Missense_Mutation	SNP	T	T	C	rs3209304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:49814379T>C	ENST00000335847.4	-	5	390	c.289A>G	c.(289-291)Acc>Gcc	p.T97A	CRISP1_ENST00000355791.2_Missense_Mutation_p.T97A|CRISP1_ENST00000536021.1_Missense_Mutation_p.T97A|CRISP1_ENST00000329411.5_Missense_Mutation_p.T97A|CRISP1_ENST00000505118.1_Missense_Mutation_p.T97A|CRISP1_ENST00000507853.1_Missense_Mutation_p.T97A	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	97	SCP.			T -> A (in Ref. 2; AAB35899 and 3; BAA07483). {ECO:0000305}.	binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)			endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					CCACAAAAGGTATCTGAAATG	0.368													T|||	220	0.0439297	0.0091	0.0504	5008	,	,		21396	0.0		0.1272	False		,,,				2504	0.046				p.T97A		Atlas-SNP	.											.	CRISP1	45	.	0			c.A289G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	144,4262	100.7+/-139.4	2,140,2061	134.0	119.0	124.0		289,289,289	2.8	0.2	6	dbSNP_105	124	1278,7322	255.0+/-280.0	106,1066,3128	yes	missense,missense,missense	CRISP1	NM_001131.2,NM_001205220.1,NM_170609.1	58,58,58	108,1206,5189	CC,CT,TT		14.8605,3.2683,10.9334	possibly-damaging,possibly-damaging,possibly-damaging	97/250,97/250,97/179	49814379	1422,11584	2203	4300	6503	SO:0001583	missense	167	exon5			AAAAGGTATCTGA	D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"""acidic epididymal glycoprotein-like 1"""	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.289A>G	6.37:g.49814379T>C	ENSP00000338276:p.Thr97Ala	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	172	81	0.47093	NM_001205220	B5BU98|O00698|Q13248|Q14082|Q96SF6	Missense_Mutation	SNP	ENST00000335847.4	37	CCDS4931.1	124	0.056776556776556776	7	0.014227642276422764	22	0.06077348066298342	0	0.0	95	0.12532981530343007	T	10.34	1.323035	0.24080	0.032683	0.148605	ENSG00000124812	ENST00000507853;ENST00000335847;ENST00000355791;ENST00000329411;ENST00000505118;ENST00000536021	T;T;T;T;T;T	0.07216	3.21;3.21;3.21;3.21;3.21;3.21	5.34	2.77	0.32553	CAP domain (3);	0.790058	0.11938	N	0.514962	T	0.06280	0.0162	L	0.58669	1.825	0.80722	P	0.0	P;D	0.57571	0.793;0.98	B;P	0.52454	0.256;0.699	T	0.28902	-1.0029	8	.	.	.	.	4.5062	0.11889	0.0:0.1067:0.1945:0.6988	rs3209304;rs12205497;rs17410390;rs17663949;rs52831968;rs12205497	97;97	P54107-2;P54107	.;CRIS1_HUMAN	A	97	ENSP00000425020:T97A;ENSP00000338276:T97A;ENSP00000348044:T97A;ENSP00000331317:T97A;ENSP00000427589:T97A;ENSP00000441798:T97A	.	T	-	1	0	CRISP1	49922338	0.001000	0.12720	0.220000	0.23810	0.052000	0.14988	0.287000	0.18920	0.842000	0.35045	0.528000	0.53228	ACC	T|0.762;G|0.006;C|0.078;A|0.154	0.078	strong		0.368	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131	
KLHL13	90293	hgsc.bcm.edu	37	X	117032973	117032973	+	Silent	SNP	C	C	G	rs6645983	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:117032973C>G	ENST00000262820.3	-	7	2775	c.1866G>C	c.(1864-1866)ctG>ctC	p.L622L	KLHL13_ENST00000469946.1_Silent_p.L571L|KLHL13_ENST00000371882.1_Silent_p.L571L|KLHL13_ENST00000541812.1_Silent_p.L606L|KLHL13_ENST00000539496.1_Silent_p.L625L|KLHL13_ENST00000371876.1_Silent_p.L571L|KLHL13_ENST00000545703.1_Silent_p.L580L|KLHL13_ENST00000371878.1_Silent_p.L571L|KLHL13_ENST00000540167.1_Silent_p.L606L	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	622					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						GGGATTCTGGCAGATCAAAAA	0.438													G|||	720	0.190728	0.4433	0.0605	3775	,	,		15075	0.0		0.0557	False		,,,				2504	0.0368				p.L625L		Atlas-SNP	.											.	KLHL13	87	.	0			c.G1875C						PASS	.	G	,,,,,	1860,1975		386,815,273,431,298	192.0	169.0	177.0		1875,1848,1818,1818,1740,1866	1.4	1.0	X	dbSNP_116	177	513,6215		20,320,153,2088,1719	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	,,,,,	406,1135,426,2519,2017	GG,GC,G,CC,C		7.6249,48.5007,22.4652	,,,,,	625/659,616/650,606/640,606/640,580/614,622/656	117032973	2373,8190	2203	4300	6503	SO:0001819	synonymous_variant	90293	exon8			TTCTGGCAGATCA	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.1866G>C	X.37:g.117032973C>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	120	0.983607	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	37	CCDS14571.1																																																																																			C|0.757;0|0.013	.	strong		0.438	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495	
DFNA5	1687	hgsc.bcm.edu	37	7	24758818	24758818	+	Missense_Mutation	SNP	G	G	T	rs754554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:24758818G>T	ENST00000342947.3	-	4	849	c.424C>A	c.(424-426)Cct>Act	p.P142T	DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR|DFNA5_ENST00000409775.3_Missense_Mutation_p.P142T|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	142			P -> T (in dbSNP:rs754554). {ECO:0000269|PubMed:12690205}.		apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						TGGAGCACAGGGTTTCTCAGA	0.483													G|||	1298	0.259185	0.1982	0.1383	5008	,	,		22470	0.4444		0.1501	False		,,,				2504	0.3487				p.P142T	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											DFNA5,colon,carcinoma,+1,1	DFNA5	51	1	0			c.C424A						PASS	.	G	THR/PRO,,THR/PRO	925,3481	355.1+/-312.9	106,713,1384	110.0	106.0	107.0		424,,424	0.2	0.0	7	dbSNP_86	107	1230,7370	246.8+/-275.1	79,1072,3149	yes	missense,utr-5,missense	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	38,,38	185,1785,4533	TT,TG,GG		14.3023,20.9941,16.5693	possibly-damaging,,possibly-damaging	142/497,,142/497	24758818	2155,10851	2203	4300	6503	SO:0001583	missense	1687	exon4			GCACAGGGTTTCT	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.424C>A	7.37:g.24758818G>T	ENSP00000339587:p.Pro142Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	37	CCDS5389.1	527	0.2413003663003663	90	0.18292682926829268	47	0.1298342541436464	276	0.4825174825174825	114	0.1503957783641161	G	4.384	0.070890	0.08436	0.209941	0.143023	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.20881	2.04;2.04	5.17	0.252	0.15545	.	0.885835	0.10104	N	0.715585	T	0.00012	0.0000	M	0.65975	2.015	0.47905	P	4.6000000000001595E-4	B;B	0.30068	0.267;0.267	B;B	0.32805	0.153;0.153	T	0.45264	-0.9273	9	0.16420	T	0.52	-2.0218	8.6313	0.33922	0.4149:0.0:0.5851:0.0	rs754554;rs16873696;rs52826337;rs754554	142;142	A4FTY0;O60443	.;DFNA5_HUMAN	T	142	ENSP00000339587:P142T;ENSP00000386670:P142T	ENSP00000339587:P142T	P	-	1	0	DFNA5	24725343	0.035000	0.19736	0.000000	0.03702	0.002000	0.02628	0.711000	0.25764	-0.022000	0.13986	-0.150000	0.13652	CCT	G|0.798;T|0.202	0.202	strong		0.483	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
OR1S1	219959	hgsc.bcm.edu	37	11	57982832	57982832	+	Missense_Mutation	SNP	T	T	A	rs2867400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57982832T>A	ENST00000309433.6	+	1	616	c.616T>A	c.(616-618)Ttg>Atg	p.L206M		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	206			L -> M (in dbSNP:rs2867400).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L206M(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTCAGATACATTGATCAATGA	0.438													t|||	2629	0.52496	0.2829	0.5403	5008	,	,		19594	0.8046		0.4225	False		,,,				2504	0.6585				p.L206M		Atlas-SNP	.											OR1S1,NS,carcinoma,0,1	OR1S1	139	1	1	Substitution - Missense(1)	stomach(1)	c.T616A						PASS	.						179.0	140.0	153.0					11																	57982832		2201	4294	6495	SO:0001583	missense	219959	exon1			GATACATTGATCA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.616T>A	11.37:g.57982832T>A	ENSP00000311688:p.Leu206Met	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	128	46	0.359375	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	980	0.44871794871794873	120	0.24390243902439024	175	0.48342541436464087	413	0.722027972027972	272	0.35883905013192613	T	0.120	-1.126825	0.01770	.	.	ENSG00000172774	ENST00000309433	T	0.00115	8.71	3.23	0.689	0.18033	GPCR, rhodopsin-like superfamily (1);	1.756970	0.02885	N	0.133431	T	0.00012	0.0000	L	0.56280	1.765	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23583	-1.0184	9	0.49607	T	0.09	.	1.1022	0.01686	0.3279:0.1471:0.1014:0.4237	rs2867400;rs2867400	206	Q8NH92	OR1S1_HUMAN	M	206	ENSP00000311688:L206M	ENSP00000311688:L206M	L	+	1	2	OR1S1	57739408	0.000000	0.05858	0.005000	0.12908	0.171000	0.22731	-1.315000	0.02713	0.339000	0.23719	-0.562000	0.04174	TTG	T|0.703;A|0.297	0.297	strong		0.438	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
RAB38	23682	hgsc.bcm.edu	37	11	87908502	87908502	+	Silent	SNP	G	G	A	rs36074402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:87908502G>A	ENST00000243662.6	-	1	133	c.51C>T	c.(49-51)gaC>gaT	p.D17D	MIR3166_ENST00000577344.1_RNA	NM_022337.2	NP_071732.1	P57729	RAB38_HUMAN	RAB38, member RAS oncogene family	17					endosome to melanosome transport (GO:0035646)|GTP catabolic process (GO:0006184)|melanosome organization (GO:0032438)|phagosome acidification (GO:0090383)|platelet dense granule organization (GO:0060155)|protein localization to membrane (GO:0072657)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|early endosome (GO:0005769)|melanosome (GO:0042470)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	AP-1 adaptor complex binding (GO:0035650)|AP-3 adaptor complex binding (GO:0035651)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)			large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CCACGCCCAGGTCGCCAATCA	0.637													G|||	29	0.00579073	0.0008	0.0115	5008	,	,		10588	0.0		0.0139	False		,,,				2504	0.0061				p.D17D		Atlas-SNP	.											.	RAB38	20	.	0			c.C51T						PASS	.	G		10,4392	16.8+/-37.8	0,10,2191	105.0	81.0	89.0		51	4.2	1.0	11	dbSNP_126	89	116,8482	60.6+/-122.4	0,116,4183	no	coding-synonymous	RAB38	NM_022337.2		0,126,6374	AA,AG,GG		1.3492,0.2272,0.9692		17/212	87908502	126,12874	2201	4299	6500	SO:0001819	synonymous_variant	23682	exon1			GCCCAGGTCGCCA	AF235022	CCDS8281.1	11q14	2008-05-14			ENSG00000123892	ENSG00000123892		"""RAB, member RAS oncogene"""	9776	protein-coding gene	gene with protein product		606281				10910072	Standard	NM_022337		Approved	NY-MEL-1	uc001pcj.2	P57729	OTTHUMG00000167288	ENST00000243662.6:c.51C>T	11.37:g.87908502G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_022337	Q53XK7	Silent	SNP	ENST00000243662.6	37	CCDS8281.1	18|18	0.008241758241758242|0.008241758241758242	1|1	0.0020325203252032522|0.0020325203252032522	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	12|12	0.0158311345646438|0.0158311345646438	G|G	11.31|11.31	1.600127|1.600127	0.28534|0.28534	0.002272|0.002272	0.013492|0.013492	ENSG00000123892|ENSG00000123892	ENST00000531138|ENST00000526372	.|.	.|.	.|.	5.1|5.1	4.19|4.19	0.49359|0.49359	.|.	.|.	.|.	.|.	.|.	T|T	0.54013|0.54013	0.1832|0.1832	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.63220|0.63220	-0.6686|-0.6686	4|4	.|.	.|.	.|.	-7.4398|-7.4398	13.7122|13.7122	0.62675|0.62675	0.0738:0.0:0.9262:0.0|0.0738:0.0:0.9262:0.0	rs36074402|rs36074402	.|.	.|.	.|.	S|I	34|34	.|.	.|.	P|T	-|-	1|2	0|0	RAB38|RAB38	87548150|87548150	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.014000|0.014000	0.08584|0.08584	2.521000|2.521000	0.45563|0.45563	1.378000|1.378000	0.46305|0.46305	-0.140000|-0.140000	0.14226|0.14226	CCT|ACC	G|0.991;A|0.009	0.009	strong		0.637	RAB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394015.2		
OSBPL10	114884	hgsc.bcm.edu	37	3	31725316	31725316	+	Silent	SNP	G	G	A	rs2278959	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:31725316G>A	ENST00000396556.2	-	8	1658	c.1536C>T	c.(1534-1536)caC>caT	p.H512H	OSBPL10_ENST00000438237.2_Silent_p.H448H	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	512					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		TTGGGTGTTCGTGACAGCTGG	0.537													G|||	1175	0.234625	0.0983	0.2853	5008	,	,		19004	0.3234		0.3141	False		,,,				2504	0.2096				p.H512H		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C1536T						PASS	.	G	,	576,3830	256.4+/-261.2	41,494,1668	142.0	126.0	132.0		1344,1536	-11.4	0.0	3	dbSNP_100	132	2420,6180	401.6+/-347.2	332,1756,2212	no	coding-synonymous,coding-synonymous	OSBPL10	NM_001174060.1,NM_017784.4	,	373,2250,3880	AA,AG,GG		28.1395,13.0731,23.0355	,	448/701,512/765	31725316	2996,10010	2203	4300	6503	SO:0001819	synonymous_variant	114884	exon8			GTGTTCGTGACAG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1536C>T	3.37:g.31725316G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	151	66	0.437086	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1	585	0.26785714285714285	48	0.0975609756097561	115	0.31767955801104975	197	0.34440559440559443	225	0.29683377308707126	G	0.013	-1.643961	0.00792	0.130731	0.281395	ENSG00000144645	ENST00000429492	.	.	.	5.68	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.08432	-1.0722	3	.	.	.	-2.2597	11.7127	0.51635	0.0745:0.0716:0.711:0.1428	rs2278959;rs17383217;rs60439437;rs2278959	.	.	.	M	281	.	.	T	-	2	0	OSBPL10	31700320	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.905000	0.00171	-3.447000	0.00161	-1.076000	0.02234	ACG	G|0.754;A|0.246	0.246	strong		0.537	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
ZNF608	57507	hgsc.bcm.edu	37	5	123984763	123984763	+	Silent	SNP	C	C	T	rs7708070	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:123984763C>T	ENST00000306315.5	-	4	1749	c.1314G>A	c.(1312-1314)gcG>gcA	p.A438A	ZNF608_ENST00000504926.1_Silent_p.A11A	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	438							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CAGCAGACCTCGCTCTCTTCC	0.592													T|||	3812	0.761182	0.885	0.5951	5008	,	,		16392	0.7609		0.7505	False		,,,				2504	0.7229				p.A438A		Atlas-SNP	.											.	ZNF608	117	.	0			c.G1314A						PASS	.	T		3820,584		1666,488,48	31.0	34.0	33.0		1314	-10.5	0.1	5	dbSNP_116	33	6393,2197		2403,1587,305	yes	coding-synonymous	ZNF608	NM_020747.2		4069,2075,353	TT,TC,CC		25.5763,13.2607,21.4022		438/1513	123984763	10213,2781	2202	4295	6497	SO:0001819	synonymous_variant	57507	exon4			AGACCTCGCTCTC	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"""Zinc fingers, C2H2-type"""	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.1314G>A	5.37:g.123984763C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	37	CCDS34219.1																																																																																			C|0.228;T|0.772	0.772	strong		0.592	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
USP19	10869	hgsc.bcm.edu	37	3	49148980	49148980	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49148980A>G	ENST00000398888.2	-	20	3179	c.2861T>C	c.(2860-2862)aTt>aCt	p.I954T	USP19_ENST00000434032.2_Missense_Mutation_p.I1055T|USP19_ENST00000398896.1_Missense_Mutation_p.I762T|USP19_ENST00000453664.1_Missense_Mutation_p.I1045T|USP19_ENST00000398898.2_Missense_Mutation_p.I994T|USP19_ENST00000398892.3_Missense_Mutation_p.I994T|USP19_ENST00000417901.1_Missense_Mutation_p.I1057T	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	954	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)		GCCAACCTCAATGGGCCCACT	0.627																																					p.I1057T		Atlas-SNP	.											.	USP19	158	.	0			c.T3170C						PASS	.						35.0	36.0	36.0					3																	49148980		1888	4115	6003	SO:0001583	missense	10869	exon21			ACCTCAATGGGCC	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.2861T>C	3.37:g.49148980A>G	ENSP00000381863:p.Ile954Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	A	2.782	-0.253241	0.05829	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.18174	2.23;2.24;2.34;2.34;2.24;2.33;2.34	6.04	-9.85	0.00476	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.404660	0.03866	N	0.274854	T	0.05640	0.0148	N	0.05414	-0.055	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	0.06405	0.001;0.001;0.002;0.0;0.0	T	0.24977	-1.0145	10	0.14252	T	0.57	11.2509	3.8486	0.08945	0.2931:0.3067:0.3169:0.0833	.	1055;1045;954;994;762	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	T	762;994;1057;1045;994;954;1055	ENSP00000381870:I762T;ENSP00000381872:I994T;ENSP00000395260:I1057T;ENSP00000400090:I1045T;ENSP00000381867:I994T;ENSP00000381863:I954T;ENSP00000401197:I1055T	ENSP00000381863:I954T	I	-	2	0	USP19	49123984	0.000000	0.05858	0.000000	0.03702	0.819000	0.46315	-1.946000	0.01536	-1.572000	0.01661	-0.450000	0.05554	ATT	.	.	none		0.627	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
COL4A2	1284	hgsc.bcm.edu	37	13	111160304	111160304	+	Silent	SNP	G	G	A	rs391859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:111160304G>A	ENST00000360467.5	+	47	4923	c.4617G>A	c.(4615-4617)gcG>gcA	p.A1539A	COL4A2-AS1_ENST00000417970.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1539	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			CCTGCCTGGCGCGGTTCAGCA	0.632													G|||	505	0.100839	0.0711	0.1974	5008	,	,		17295	0.128		0.0915	False		,,,				2504	0.0542				p.A1539A		Atlas-SNP	.											.	COL4A2	178	.	0			c.G4617A						PASS	.	G		309,3977		14,281,1848	66.0	72.0	70.0		4617	-9.9	0.0	13	dbSNP_80	70	807,7701		39,729,3486	no	coding-synonymous	COL4A2	NM_001846.2		53,1010,5334	AA,AG,GG		9.4852,7.2095,8.7228		1539/1713	111160304	1116,11678	2143	4254	6397	SO:0001819	synonymous_variant	1284	exon47			CCTGGCGCGGTTC	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.4617G>A	13.37:g.111160304G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			G|0.890;A|0.110	0.110	strong		0.632	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
JARID2	3720	hgsc.bcm.edu	37	6	15513482	15513482	+	Silent	SNP	G	G	A	rs2235258	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:15513482G>A	ENST00000341776.2	+	16	3523	c.3279G>A	c.(3277-3279)ctG>ctA	p.L1093L	JARID2_ENST00000397311.3_Silent_p.L921L	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1093					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)				ATACAGAGCTGCGGCAGCGCA	0.667													G|||	2929	0.584864	0.3003	0.6513	5008	,	,		16258	0.6667		0.7465	False		,,,				2504	0.6718				p.L1093L		Atlas-SNP	.											JARID2,NS,carcinoma,0,1	JARID2	135	1	0			c.G3279A						PASS	.	G		1670,2696		354,962,867	16.0	15.0	15.0		3279	2.5	1.0	6	dbSNP_98	15	6569,1975		2569,1431,272	no	coding-synonymous	JARID2	NM_004973.2		2923,2393,1139	AA,AG,GG		23.1156,38.2501,36.1813		1093/1247	15513482	8239,4671	2183	4272	6455	SO:0001819	synonymous_variant	3720	exon16			AGAGCTGCGGCAG	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.3279G>A	6.37:g.15513482G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			G|0.410;A|0.590	0.590	strong		0.667	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
CCDC86	79080	hgsc.bcm.edu	37	11	60610065	60610065	+	Silent	SNP	G	G	A	rs141728952|rs2074420	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60610065G>A	ENST00000227520.5	+	1	522	c.468G>A	c.(466-468)ccG>ccA	p.P156P	RP11-804A23.4_ENST00000538705.1_RNA|RP11-804A23.2_ENST00000539897.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	156	Pro-rich.				viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						AGCTACCGCCGGTCCCAGGAT	0.662													G|||	1707	0.340855	0.1664	0.2752	5008	,	,		14318	0.6806		0.1899	False		,,,				2504	0.4284				p.P156P		Atlas-SNP	.											CCDC86,NS,carcinoma,0,1	CCDC86	24	1	0			c.G468A						scavenged	.						25.0	31.0	29.0					11																	60610065		2196	4289	6485	SO:0001819	synonymous_variant	79080	exon1			ACCGCCGGTCCCA	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.468G>A	11.37:g.60610065G>A		Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_024098	B4DY99	Silent	SNP	ENST00000227520.5	37	CCDS7993.1																																																																																			G|0.725;A|0.275	0.275	strong		0.662	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
CCDC88B	283234	hgsc.bcm.edu	37	11	64111738	64111738	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:64111738C>T	ENST00000356786.5	+	14	1769	c.1725C>T	c.(1723-1725)tcC>tcT	p.S575S	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	575						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CAGACTGGTCCCCGCAAGAGT	0.642																																					p.S575S		Atlas-SNP	.											CCDC88B,NS,carcinoma,+1,1	CCDC88B	89	1	0			c.C1725T						scavenged	.						41.0	47.0	45.0					11																	64111738		2201	4297	6498	SO:0001819	synonymous_variant	283234	exon14			CTGGTCCCCGCAA	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1725C>T	11.37:g.64111738C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	102	2	0.0196078	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			.	.	none		0.642	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
AGGF1	55109	hgsc.bcm.edu	37	5	76342447	76342447	+	Silent	SNP	T	T	C	rs61736982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:76342447T>C	ENST00000312916.7	+	6	1528	c.1146T>C	c.(1144-1146)taT>taC	p.Y382Y		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	382					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)		AGGATAGTTATGACGAAGCCA	0.373													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19817	0.0		0.005	False		,,,				2504	0.0				p.Y382Y		Atlas-SNP	.											.	AGGF1	71	.	0			c.T1146C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	128.0	130.0	129.0		1146	-3.2	0.0	5	dbSNP_129	129	54,8546	34.3+/-88.2	0,54,4246	no	coding-synonymous	AGGF1	NM_018046.4		0,55,6448	CC,CT,TT		0.6279,0.0227,0.4229		382/715	76342447	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	55109	exon6			TAGTTATGACGAA	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.1146T>C	5.37:g.76342447T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	37	CCDS4035.1																																																																																			T|0.998;C|0.002	0.002	strong		0.373	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
TYW1	55253	hgsc.bcm.edu	37	7	66660242	66660242	+	Missense_Mutation	SNP	A	A	G	rs2949097		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	200	0	0		WXS	Illumina HiSeq	Phase_I	161	51	0.31677	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	
IL17F	112744	hgsc.bcm.edu	37	6	52101739	52101739	+	Missense_Mutation	SNP	T	T	C	rs763780	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:52101739T>C	ENST00000336123.4	-	3	589	c.482A>G	c.(481-483)cAt>cGt	p.H161R		NM_052872.3	NP_443104.1	Q96PD4	IL17F_HUMAN	interleukin 17F	161			H -> R (in dbSNP:rs763780). {ECO:0000269|PubMed:15489334}.		cartilage development (GO:0051216)|cytokine biosynthetic process (GO:0042089)|inflammatory response (GO:0006954)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045423)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of interleukin-8 biosynthetic process (GO:0045414)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine binding (GO:0019955)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)	14	Lung NSC(77;0.116)					TTACTGCACATGGTGGATGAC	0.547													T|||	468	0.0934505	0.087	0.0605	5008	,	,		18360	0.1627		0.0577	False		,,,				2504	0.091				p.H161R		Atlas-SNP	.											.	IL17F	28	.	0			c.A482G	GRCh37	CM068187	IL17F	M	rs763780	PASS	.	T	ARG/HIS	395,4011	195.7+/-220.2	17,361,1825	82.0	73.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	482	2.8	0.0	6	dbSNP_86	76	425,8175	131.7+/-189.4	8,409,3883	yes	missense	IL17F	NM_052872.3	29	25,770,5708	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	4.9419,8.965,6.3048	benign	161/164	52101739	820,12186	2203	4300	6503	SO:0001583	missense	112744	exon3			TGCACATGGTGGA	AF384857	CCDS4938.1	6p12	2014-09-17			ENSG00000112116	ENSG00000112116		"""Interleukins and interleukin receptors"""	16404	protein-coding gene	gene with protein product		606496				11591732, 11591768	Standard	NM_052872		Approved	IL-17F, ML-1, ML1	uc003pam.1	Q96PD4	OTTHUMG00000014845	ENST00000336123.4:c.482A>G	6.37:g.52101739T>C	ENSP00000337432:p.His161Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_052872	Q6NSI0|Q7Z6P4|Q96PI8|Q9NUE6	Missense_Mutation	SNP	ENST00000336123.4	37	CCDS4938.1	175	0.08012820512820513	24	0.04878048780487805	24	0.06629834254143646	79	0.1381118881118881	48	0.0633245382585752	T	9.258	1.042456	0.19748	0.08965	0.049419	ENSG00000112116	ENST00000336123	T	0.44083	0.93	5.2	2.78	0.32641	.	1.364500	0.04188	N	0.327799	T	0.14743	0.0356	L	0.38953	1.18	0.80722	P	0.0	B	0.20780	0.048	B	0.12837	0.008	T	0.13124	-1.0521	9	0.40728	T	0.16	-1.0401	4.9296	0.13910	0.0:0.0974:0.2029:0.6997	rs763780;rs56499381;rs57501176;rs763780	161	Q96PD4	IL17F_HUMAN	R	161	ENSP00000337432:H161R	ENSP00000337432:H161R	H	-	2	0	IL17F	52209698	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	0.520000	0.22878	1.002000	0.39104	-0.290000	0.09829	CAT	A|0.012;C|0.071	0.071	strong		0.547	IL17F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040901.3	NM_052872	
PRR21	643905	hgsc.bcm.edu	37	2	240982228	240982228	+	Missense_Mutation	SNP	C	C	T	rs10439373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:240982228C>T	ENST00000408934.1	-	1	171	c.172G>A	c.(172-174)Ggc>Agc	p.G58S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	58	Pro-rich.		G -> S (in dbSNP:rs10439373).							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						GATGAAGGGCCGTGGGTGAAG	0.602													N|||	2614	0.521965	0.6157	0.4481	5008	,	,		17559	0.506		0.502	False		,,,				2504	0.4847				p.G58S		Atlas-SNP	.											.	PRR21	53	.	0			c.G172A						PASS	.	C	SER/GLY	2651,1755		769,1113,321	133.0	117.0	122.0		172	-3.0	0.0	2	dbSNP_119	122	3699,4901		748,2203,1349	no	missense	PRR21	NM_001080835.1	56	1517,3316,1670	TT,TC,CC		43.0116,39.832,48.8236	possibly-damaging	58/390	240982228	6350,6656	2203	4300	6503	SO:0001583	missense	643905	exon1			AAGGGCCGTGGGT	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.172G>A	2.37:g.240982228C>T	ENSP00000386166:p.Gly58Ser	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	28	19	0.678571	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	N	0.155	-1.087546	0.01873	0.60168	0.430116	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.37584	1.19;1.19	1.5	-3.0	0.05480	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.27679	0.185	B	0.23275	0.045	T	0.41980	-0.9478	8	0.17832	T	0.49	.	4.1525	0.10245	0.1588:0.3931:0.0:0.4481	rs10439373;rs10439373	58	Q8WXC7	PRR21_HUMAN	S	58	ENSP00000386166:G58S;ENSP00000418240:G58S	ENSP00000386166:G58S	G	-	1	0	PRR21	240630901	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.681000	0.01937	-2.086000	0.00863	-1.281000	0.01382	GGC	C|0.491;T|0.509	0.509	strong		0.602	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
APOC4	346	hgsc.bcm.edu	37	19	45448036	45448036	+	Missense_Mutation	SNP	T	T	C	rs1132899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45448036T>C	ENST00000592954.1	+	2	147	c.107T>C	c.(106-108)cTg>cCg	p.L36P	APOC2_ENST00000590360.1_5'Flank|APOC4-APOC2_ENST00000589057.1_Missense_Mutation_p.L36P|APOC2_ENST00000252490.4_5'Flank|APOC2_ENST00000592257.1_5'Flank|APOC4_ENST00000419266.2_Missense_Mutation_p.L36P|APOC4_ENST00000591600.1_Missense_Mutation_p.L36P|APOC2_ENST00000591597.1_5'Flank	NM_001646.2	NP_001637.1	P55056	APOC4_HUMAN	apolipoprotein C-IV	36			L -> P (in dbSNP:rs1132899). {ECO:0000269|PubMed:10996355, ECO:0000269|Ref.2}.		lipid metabolic process (GO:0006629)|positive regulation of sequestering of triglyceride (GO:0010890)|triglyceride homeostasis (GO:0070328)	high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|lung(2)	4	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		GAAGGAACCCTGAGCCCCCCA	0.607													C|||	3327	0.664337	0.7307	0.7248	5008	,	,		14986	0.7262		0.498	False		,,,				2504	0.6391				p.L36P		Atlas-SNP	.											.	APOC4	6	.	0			c.T107C						PASS	.	C	PRO/LEU	3152,1252	415.2+/-337.1	1134,884,184	47.0	49.0	49.0		107	-4.9	0.0	19	dbSNP_86	49	4412,4188	547.6+/-385.2	1147,2118,1035	yes	missense	APOC4	NM_001646.2	98	2281,3002,1219	CC,CT,TT		48.6977,28.4287,41.8333	benign	36/128	45448036	7564,5440	2202	4300	6502	SO:0001583	missense	346	exon2			GAACCCTGAGCCC	U32576	CCDS12649.1	19q13.2	2013-09-30			ENSG00000267467	ENSG00000267467		"""Apolipoproteins"""	611	protein-coding gene	gene with protein product		600745				8530039	Standard	NM_001646		Approved			P55056	OTTHUMG00000180845	ENST00000592954.1:c.107T>C	19.37:g.45448036T>C	ENSP00000468236:p.Leu36Pro	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_001646	B3KWY6|Q53YY8	Missense_Mutation	SNP	ENST00000592954.1	37	CCDS12649.1	1435	0.657051282051282	380	0.7723577235772358	250	0.6906077348066298	417	0.7290209790209791	388	0.5118733509234829	C	2.272	-0.366865	0.05069	0.715713	0.513023	ENSG00000224916	ENST00000419266;ENST00000436871	T;T	0.24151	1.87;1.87	2.44	-4.88	0.03113	.	1.295300	0.05865	N	0.623646	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	0.29912	-0.9996	9	0.36615	T	0.2	-1.3808	6.3134	0.21176	0.1493:0.1684:0.0:0.6823	rs1132899;rs2304180;rs3194191;rs17251065;rs17257866;rs17561696;rs59271342;rs1132899	36	P55056	APOC4_HUMAN	P	36	ENSP00000406381:L36P;ENSP00000412935:L36P	ENSP00000406381:L36P	L	+	2	0	APOC4	50139876	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.990000	0.01479	-1.844000	0.01178	-2.059000	0.00401	CTG	T|0.387;C|0.613	0.613	strong		0.607	APOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453255.1	NM_001646	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21377717	21377717	+	Silent	SNP	C	C	G	rs143812591		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21377717C>G	ENST00000256958.2	+	14	1905	c.1809C>G	c.(1807-1809)tcC>tcG	p.S603S		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	603					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)	TAAAGTGGTCCACCAACAACT	0.358																																					p.S603S		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.C1809G						PASS	.	C		0,4406		0,0,2203	148.0	143.0	145.0		1809	-3.8	0.0	12	dbSNP_134	145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLCO1B1	NM_006446.4		0,2,6501	GG,GC,CC		0.0233,0.0,0.0154		603/692	21377717	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10599	exon14			GTGGTCCACCAAC		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.1809C>G	12.37:g.21377717C>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			C|1.000;G|0.000	0.000	weak		0.358	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
SBNO1	55206	hgsc.bcm.edu	37	12	123810873	123810873	+	Silent	SNP	G	G	A	rs61388686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:123810873G>A	ENST00000602398.1	-	14	1828	c.1701C>T	c.(1699-1701)atC>atT	p.I567I	SBNO1_ENST00000267176.4_Silent_p.I566I|SBNO1_ENST00000602750.1_Silent_p.I566I|SBNO1_ENST00000420886.2_Silent_p.I567I			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	567					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)		GCTCTCTGGCGATGACCCACT	0.408													G|||	2471	0.493411	0.0567	0.5836	5008	,	,		16493	0.7004		0.664	False		,,,				2504	0.6309				p.I567I		Atlas-SNP	.											.	SBNO1	138	.	0			c.C1701T						PASS	.	G	,	693,3713	290.1+/-280.8	67,559,1577	121.0	110.0	113.0		1701,1698	-2.2	0.6	12	dbSNP_129	113	5970,2630	687.2+/-404.2	2086,1798,416	no	coding-synonymous,coding-synonymous	SBNO1	NM_001167856.1,NM_018183.3	,	2153,2357,1993	AA,AG,GG		30.5814,15.7286,48.7698	,	567/1394,566/1393	123810873	6663,6343	2203	4300	6503	SO:0001819	synonymous_variant	55206	exon13			TCTGGCGATGACC	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.1701C>T	12.37:g.123810873G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																			G|0.483;A|0.517	0.517	strong		0.408	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
GPR20	2843	hgsc.bcm.edu	37	8	142367246	142367246	+	Missense_Mutation	SNP	G	G	A	rs36092215	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	53	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	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	
TRAK1	22906	hgsc.bcm.edu	37	3	42251329	42251329	+	Silent	SNP	C	C	T	rs2290133	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42251329C>T	ENST00000327628.5	+	14	2215	c.1815C>T	c.(1813-1815)ccC>ccT	p.P605P	TRAK1_ENST00000396175.1_Silent_p.P547P|TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000341421.3_Silent_p.P547P	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	605					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						ACCCCCGGCCCGGTGTGGTCA	0.582													C|||	1811	0.361621	0.2428	0.5346	5008	,	,		17180	0.4663		0.2793	False		,,,				2504	0.3763				p.P605P	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.C1815T						PASS	.	C	,	1134,3272	404.4+/-333.1	152,830,1221	79.0	79.0	79.0		1815,1641	-8.8	0.4	3	dbSNP_100	79	2611,5989	423.1+/-354.3	405,1801,2094	no	coding-synonymous,coding-synonymous	TRAK1	NM_001042646.1,NM_014965.3	,	557,2631,3315	TT,TC,CC		30.3605,25.7376,28.7944	,	605/954,547/687	42251329	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	22906	exon14			CCGGCCCGGTGTG		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.1815C>T	3.37:g.42251329C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Silent	SNP	ENST00000327628.5	37	CCDS43072.1																																																																																			C|0.681;T|0.319	0.319	strong		0.582	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
PER3	8863	hgsc.bcm.edu	37	1	7887579	7887579	+	Missense_Mutation	SNP	C	C	G	rs228697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:7887579C>G	ENST00000361923.2	+	17	2741	c.2566C>G	c.(2566-2568)Cct>Gct	p.P856A	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.P864A	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	856	Pro-rich.		P -> A (in dbSNP:rs228697). {ECO:0000269|PubMed:11306557}.		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTGACCCCCCTGTCTGTCC	0.547													C|||	302	0.0603035	0.0098	0.0692	5008	,	,		19911	0.0427		0.0964	False		,,,				2504	0.1033				p.P856A		Atlas-SNP	.											.	PER3	95	.	0			c.C2566G						PASS	.	C	ALA/PRO	102,4304	80.4+/-118.8	0,102,2101	201.0	197.0	198.0		2566	-2.6	0.0	1	dbSNP_79	198	897,7703	201.4+/-244.9	51,795,3454	yes	missense	PER3	NM_016831.1	27	51,897,5555	GG,GC,CC		10.4302,2.315,7.6811	benign	856/1202	7887579	999,12007	2203	4300	6503	SO:0001583	missense	8863	exon17			GACCCCCCTGTCT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2566C>G	1.37:g.7887579C>G	ENSP00000355031:p.Pro856Ala	Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	239	124	0.518828	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	141	0.06456043956043957	3	0.006097560975609756	29	0.08011049723756906	30	0.05244755244755245	79	0.10422163588390501	C	9.849	1.193105	0.21954	0.02315	0.104302	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.10763	2.84;2.85	4.32	-2.59	0.06209	.	3.975590	0.00837	N	0.001717	T	0.00241	0.0007	L	0.46157	1.445	0.80722	P	0.0	B;B;B;B	0.30914	0.199;0.199;0.3;0.199	B;B;B;B	0.31290	0.06;0.06;0.127;0.06	T	0.20042	-1.0287	9	0.24483	T	0.36	.	0.4792	0.00545	0.2482:0.2832:0.243:0.2255	rs228697;rs480069;rs52826465;rs228697	856;864;864;856	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	A	864;856;67	ENSP00000366755:P864A;ENSP00000355031:P856A	ENSP00000355031:P856A	P	+	1	0	PER3	7810166	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.057000	0.14279	-0.823000	0.04301	-0.263000	0.10527	CCT	C|0.925;G|0.075	0.075	strong		0.547	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
GAS8	2622	hgsc.bcm.edu	37	16	90095561	90095561	+	Intron	SNP	C	C	T	rs3785183	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90095561C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.V64I|GAS8_ENST00000536122.1_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)		p.V64I(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)		gggcagcctacggggcaggct	0.672													N|||	1658	0.33107	0.3638	0.3127	5008	,	,		16091	0.1687		0.335	False		,,,				2504	0.4632				p.V64I		Atlas-SNP	.											C16orf3,NS,carcinoma,0,1	C16orf3	14	1	1	Substitution - Missense(1)	prostate(1)	c.G190A						scavenged	.						23.0	19.0	21.0					16																	90095561		2193	4300	6493	SO:0001627	intron_variant	750	exon1			AGCCTACGGGGCA	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+1431C>T	16.37:g.90095561C>T		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	200	70	0.35	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	638	0.29212454212454214	196	0.3983739837398374	106	0.292817679558011	103	0.18006993006993008	233	0.3073878627968338	N	2.174	-0.389260	0.04932	.	.	ENSG00000221819	ENST00000408886	T	0.55052	0.54	1.41	0.438	0.16560	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.25609	0.13	B	0.08055	0.003	T	0.46091	-0.9216	7	.	.	.	.	5.5547	0.17109	0.0:0.6469:0.3531:0.0	rs3785183;rs57727995;rs3785183	72	O95177	CP003_HUMAN	I	64	ENSP00000386218:V64I	.	V	-	1	0	C16orf3	88623062	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.385000	0.07379	0.197000	0.20387	-0.486000	0.04755	GTA	C|0.676;T|0.324	0.324	strong		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
TACC2	10579	hgsc.bcm.edu	37	10	123846860	123846860	+	Silent	SNP	C	C	T	rs11599291	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123846860C>T	ENST00000369005.1	+	4	5185	c.4845C>T	c.(4843-4845)ccC>ccT	p.P1615P	TACC2_ENST00000334433.3_Silent_p.P1615P|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.P1615P|TACC2_ENST00000453444.2_Silent_p.P1615P|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.P1615P	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1615					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)				AAGATGGTCCCGGGGACTTTG	0.567													C|||	996	0.198882	0.2859	0.1844	5008	,	,		21091	0.1002		0.2107	False		,,,				2504	0.181				p.P1615P		Atlas-SNP	.											TACC2,colon,carcinoma,0,1	TACC2	271	1	0			c.C4845T						scavenged	.	C	,	1406,3000	460.9+/-352.8	223,960,1020	82.0	81.0	81.0		,4845	1.6	0.0	10	dbSNP_120	81	1930,6670	340.3+/-323.5	214,1502,2584	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	437,2462,3604	TT,TC,CC		22.4419,31.911,25.6497	,	,1615/2949	123846860	3336,9670	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			TGGTCCCGGGGAC	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.4845C>T	10.37:g.123846860C>T		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	104	59	0.567308	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			C|0.767;T|0.233	0.233	strong		0.567	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
CSNK1G2	1455	hgsc.bcm.edu	37	19	1979386	1979386	+	Silent	SNP	C	C	T	rs11550450	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1979386C>T	ENST00000255641.8	+	8	1332	c.837C>T	c.(835-837)ctC>ctT	p.L279L		NM_001319.6	NP_001310.3	P78368	KC1G2_HUMAN	casein kinase 1, gamma 2	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|peptide binding (GO:0042277)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|lung(3)|prostate(1)|skin(1)|stomach(1)	8		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)		TCGAGGTGCTCTGCGAGAACT	0.726													c|||	904	0.180511	0.4221	0.0605	5008	,	,		3701	0.0843		0.0875	False		,,,				2504	0.1339				p.L279L	Ovarian(91;880 1392 21236 36928 37598)	Atlas-SNP	.											.	CSNK1G2	28	.	0			c.C837T						PASS	.	C		1571,2779		263,1045,867	14.0	13.0	13.0		837	-4.3	1.0	19	dbSNP_120	13	713,7855		31,651,3602	no	coding-synonymous	CSNK1G2	NM_001319.6		294,1696,4469	TT,TC,CC		8.3217,36.1149,17.6808		279/416	1979386	2284,10634	2175	4284	6459	SO:0001819	synonymous_variant	1455	exon8			GGTGCTCTGCGAG	AF001177	CCDS12077.1	19p13.3	2013-01-17			ENSG00000133275	ENSG00000133275			2455	protein-coding gene	gene with protein product		602214				9403068	Standard	NM_001319		Approved	CK1g2	uc002lul.4	P78368		ENST00000255641.8:c.837C>T	19.37:g.1979386C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	NM_001319	B5BU42|O00704|Q8WUB1	Silent	SNP	ENST00000255641.8	37	CCDS12077.1																																																																																			C|0.820;T|0.180	0.180	strong		0.726	CSNK1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449287.1	NM_001319	
CPB2	1361	hgsc.bcm.edu	37	13	46648094	46648094	+	Missense_Mutation	SNP	C	C	T	rs3742264	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46648094C>T	ENST00000181383.4	-	6	521	c.505G>A	c.(505-507)Gca>Aca	p.A169T	CPB2-AS1_ENST00000606351.1_RNA|CPB2_ENST00000439329.3_Missense_Mutation_p.A169T|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606991.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	169			A -> T (in dbSNP:rs3742264). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1939207}.		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)			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)		TTTTTGGCTGCTTGTTCTTTT	0.378													T|||	1539	0.307308	0.4251	0.304	5008	,	,		17258	0.256		0.336	False		,,,				2504	0.1738				p.A169T		Atlas-SNP	.											.	CPB2	60	.	0			c.G505A	GRCh37	CM063919	CPB2	M	rs3742264	PASS	.	T	THR/ALA,THR/ALA	1714,2692	650.9+/-399.1	329,1056,818	110.0	97.0	102.0		505,505	2.7	0.0	13	dbSNP_107	102	2782,5818	677.6+/-403.4	441,1900,1959	yes	missense,missense	CPB2	NM_001872.3,NM_016413.3	58,58	770,2956,2777	TT,TC,CC		32.3488,38.9015,34.5687	benign,benign	169/424,169/361	46648094	4496,8510	2203	4300	6503	SO:0001583	missense	1361	exon6			TGGCTGCTTGTTC	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.505G>A	13.37:g.46648094C>T	ENSP00000181383:p.Ala169Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	37	CCDS9401.1	744	0.34065934065934067	205	0.4166666666666667	114	0.3149171270718232	158	0.2762237762237762	267	0.35224274406332456	T	4.510	0.094684	0.08681	0.389015	0.323488	ENSG00000080618	ENST00000181383;ENST00000439329	T;T	0.29397	1.57;2.83	5.17	2.66	0.31614	Peptidase M14, carboxypeptidase A (2);	0.842873	0.10925	N	0.619022	T	0.00012	0.0000	N	0.04686	-0.185	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48714	-0.9011	9	0.11485	T	0.65	.	4.6888	0.12771	0.1407:0.1611:0.0:0.6983	rs3742264;rs52803778;rs57767929;rs3742264	169;169	Q96IY4-2;Q96IY4	.;CBPB2_HUMAN	T	169	ENSP00000181383:A169T;ENSP00000400714:A169T	ENSP00000181383:A169T	A	-	1	0	CPB2	45546095	0.000000	0.05858	0.046000	0.18839	0.841000	0.47740	0.765000	0.26546	0.049000	0.15920	-0.360000	0.07572	GCA	C|0.653;T|0.347	0.347	strong		0.378	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872	
TTN	7273	hgsc.bcm.edu	37	2	179406191	179406191	+	Missense_Mutation	SNP	C	C	T	rs3731749	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179406191C>T	ENST00000591111.1	-	300	92914	c.92690G>A	c.(92689-92691)cGc>cAc	p.R30897H	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R32538H|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R23598H|TTN_ENST00000460472.2_Missense_Mutation_p.R23473H|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R23665H|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R29970H|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588716.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000450692.2_RNA			Q8WZ42	TITIN_HUMAN	titin	30897	Fibronectin type-III 125. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H. {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)			CACTTCTTTGCGCTCCACAAT	0.468													C|||	1048	0.209265	0.0666	0.1484	5008	,	,		15530	0.4514		0.1382	False		,,,				2504	0.2689				p.R32538H		Atlas-SNP	.											.	TTN	18412	.	0			c.G97613A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	289,3661		10,269,1696	129.0	122.0	125.0		70418,89909,70793,70994	5.7	1.0	2	dbSNP_107	125	1206,7092		90,1026,3033	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	100,1295,4729	TT,TC,CC		14.5336,7.3165,12.2061	probably-damaging,probably-damaging,probably-damaging,probably-damaging	23473/26927,29970/33424,23598/27052,23665/27119	179406191	1495,10753	1975	4149	6124	SO:0001583	missense	7273	exon350			TCTTTGCGCTCCA	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.92690G>A	2.37:g.179406191C>T	ENSP00000465570:p.Arg30897His	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	252	110	0.436508	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		415	0.190018315018315	30	0.06097560975609756	43	0.11878453038674033	238	0.4160839160839161	104	0.13720316622691292	C	34	5.412118	0.96072	0.073165	0.145336	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.72	5.72	0.89469	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.71206	2.165	0.09310	P	0.9999999321613	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.17899	-1.0354	8	0.87932	D	0	.	19.8706	0.96849	0.0:1.0:0.0:0.0	rs3731749;rs58471840;rs3731749	23473;23598;23665;30897	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	29970;23473;23665;23598;23470	ENSP00000343764:R29970H;ENSP00000434586:R23473H;ENSP00000340554:R23665H;ENSP00000352154:R23598H	ENSP00000340554:R23665H	R	-	2	0	TTN	179114437	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.814000	0.86154	2.692000	0.91855	0.561000	0.74099	CGC	C|0.822;T|0.178	0.178	strong		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MCF2L2	23101	hgsc.bcm.edu	37	3	182897920	182897920	+	Missense_Mutation	SNP	A	A	G	rs35070271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:182897920A>G	ENST00000328913.3	-	28	3341	c.3044T>C	c.(3043-3045)aTg>aCg	p.M1015T	MCF2L2_ENST00000473233.1_Missense_Mutation_p.M1015T|MCF2L2_ENST00000468976.1_5'Flank	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	1015			M -> T (in dbSNP:rs35070271).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			AAAGGTGTCCATGGAGCTAAA	0.527													A|||	954	0.190495	0.0953	0.3559	5008	,	,		21609	0.3056		0.171	False		,,,				2504	0.1033				p.M1015T		Atlas-SNP	.											.	MCF2L2	164	.	0			c.T3044C						PASS	.	A	THR/MET	546,3860	247.5+/-255.7	29,488,1686	187.0	186.0	186.0		3044	-4.0	0.0	3	dbSNP_126	186	1164,7436	238.2+/-269.8	81,1002,3217	yes	missense	MCF2L2	NM_015078.2	81	110,1490,4903	GG,GA,AA		13.5349,12.3922,13.1478	benign	1015/1115	182897920	1710,11296	2203	4300	6503	SO:0001583	missense	23101	exon28			GTGTCCATGGAGC	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.3044T>C	3.37:g.182897920A>G	ENSP00000328118:p.Met1015Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	486	0.22252747252747251	48	0.0975609756097561	109	0.3011049723756906	189	0.3304195804195804	140	0.18469656992084432	A	7.970	0.748863	0.15710	0.123922	0.135349	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.01725	4.67;4.7	4.3	-3.98	0.04082	.	1.830950	0.02686	N	0.110136	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47262	-0.9131	9	0.13853	T	0.58	.	10.7505	0.46207	0.4031:0.0:0.5969:0.0	rs35070271;rs61750383;rs35070271	1015	Q86YR7	MF2L2_HUMAN	T	1015	ENSP00000328118:M1015T;ENSP00000420070:M1015T	ENSP00000328118:M1015T	M	-	2	0	MCF2L2	184380614	0.000000	0.05858	0.001000	0.08648	0.645000	0.38454	-0.999000	0.03697	-1.047000	0.03242	-0.534000	0.04291	ATG	A|0.833;G|0.167	0.167	strong		0.527	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
PSMD13	5719	hgsc.bcm.edu	37	11	244167	244167	+	Silent	SNP	C	C	T	rs1128320	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244167C>T	ENST00000532097.1	+	4	720	c.216C>T	c.(214-216)aaC>aaT	p.N72N	PSMD13_ENST00000431206.2_Silent_p.N74N|PSMD13_ENST00000352303.5_Silent_p.N72N	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	72					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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.N72N(1)|p.N74N(1)		NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCAGGGTGAACCCTTTGTCCC	0.418													T|||	4083	0.815296	0.8918	0.83	5008	,	,		16356	0.8036		0.7306	False		,,,				2504	0.8006				p.N74N		Atlas-SNP	.											PSMD13_ENST00000431206,colon,carcinoma,0,2	PSMD13	53	2	2	Substitution - coding silent(2)	large_intestine(2)	c.C222T						PASS	.	T	,	3855,551	224.3+/-240.5	1713,429,61	57.0	62.0	60.0		216,222	-2.1	1.0	11	dbSNP_86	60	6312,2288	364.1+/-333.4	2371,1570,359	no	coding-synonymous,coding-synonymous	PSMD13	NM_002817.3,NM_175932.2	,	4084,1999,420	TT,TC,CC		26.6047,12.5057,21.8284	,	72/377,74/379	244167	10167,2839	2203	4300	6503	SO:0001819	synonymous_variant	5719	exon2			GGTGAACCCTTTG	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.216C>T	11.37:g.244167C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Silent	SNP	ENST00000532097.1	37	CCDS7692.1																																																																																			C|0.207;T|0.793	0.793	strong		0.418	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
CDH23	64072	hgsc.bcm.edu	37	10	73406504	73406504	+	Silent	SNP	T	T	C	rs2305209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73406504T>C	ENST00000461841.3	+	14	1967	c.1714T>C	c.(1714-1716)Ttg>Ctg	p.L572L	CDH23_ENST00000224721.6_Intron|CDH23_ENST00000299366.7_Intron|CDH23_ENST00000398842.3_Silent_p.L527L|CDH23_ENST00000398809.4_Silent_p.L527L			Q9H251	CAD23_HUMAN	cadherin-related 23	0	Cadherin 6. {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						TGAGCTGTGTTTGTTGGTGTA	0.527													T|||	604	0.120607	0.1036	0.1066	5008	,	,		19843	0.0516		0.1779	False		,,,				2504	0.1656				p.L527L		Atlas-SNP	.											.	CDH23	365	.	0			c.T1579C						PASS	.	T	,,,	423,3367		32,359,1504	31.0	32.0	32.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,,1579	-7.0	0.0	10	dbSNP_100	32	1376,6844		124,1128,2858	no	intron,intron,intron,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5,NM_052836.3	,,,	156,1487,4362	CC,CT,TT		16.7397,11.1609,14.9792	,,,	,,,527/531	73406504	1799,10211	1895	4110	6005	SO:0001819	synonymous_variant	64072	exon13			CTGTGTTTGTTGG	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	ENST00000461841.3:c.1714T>C	10.37:g.73406504T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	135	74	0.548148	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000461841.3	37																																																																																				T|0.878;C|0.122	0.122	strong		0.527	CDH23-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051228.4	NM_052836	
CNKSR1	10256	hgsc.bcm.edu	37	1	26515956	26515956	+	Missense_Mutation	SNP	C	C	A	rs1045105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26515956C>A	ENST00000374253.5	+	21	2119	c.2080C>A	c.(2080-2082)Cac>Aac	p.H694N	CNKSR1_ENST00000531191.1_Missense_Mutation_p.H429N|CATSPER4_ENST00000456354.2_5'Flank|CNKSR1_ENST00000361530.6_Missense_Mutation_p.H687N	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	694				H -> N (in Ref. 1; AAC80558). {ECO:0000305}.	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)	p.H687Y(1)		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)		ACAGTCCCCCCACTCCCTGCC	0.637													C|||	591	0.118011	0.0779	0.0821	5008	,	,		17563	0.0962		0.1223	False		,,,				2504	0.2157				p.H687N	NSCLC(180;1396 2109 28270 30756 34275)	Atlas-SNP	.											CNKSR1,colon,carcinoma,0,3	CNKSR1	66	3	1	Substitution - Missense(1)	kidney(1)	c.C2059A						PASS	.	C	ASN/HIS	384,4022	191.6+/-217.2	38,308,1857	132.0	134.0	133.0		2059	2.8	0.0	1	dbSNP_86	133	1162,7438	237.9+/-269.6	87,988,3225	yes	missense	CNKSR1	NM_006314.2	68	125,1296,5082	AA,AC,CC		13.5116,8.7154,11.8868	benign	687/714	26515956	1546,11460	2203	4300	6503	SO:0001583	missense	10256	exon21			TCCCCCCACTCCC	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.2080C>A	1.37:g.26515956C>A	ENSP00000363371:p.His694Asn	Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	236	110	0.466102	NM_006314	B1AMW9|O95381	Missense_Mutation	SNP	ENST00000374253.5	37		212	0.09706959706959707	41	0.08333333333333333	31	0.0856353591160221	57	0.09965034965034965	83	0.10949868073878628	C	4.741	0.137816	0.09032	0.087154	0.135116	ENSG00000142675	ENST00000361530;ENST00000374253;ENST00000531191	T;T;T	0.13538	2.59;2.6;2.58	4.66	2.77	0.32553	.	1.288580	0.04684	N	0.412844	T	0.00109	0.0003	L	0.44542	1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31308	-0.9948	9	0.27082	T	0.32	-0.9495	6.9902	0.24751	0.1255:0.6606:0.1346:0.0793	rs1045105;rs3184920;rs57946802;rs1045105	694;687	Q969H4;Q53GM7	CNKR1_HUMAN;.	N	687;694;429	ENSP00000354609:H687N;ENSP00000363371:H694N;ENSP00000431817:H429N	ENSP00000354609:H687N	H	+	1	0	CNKSR1	26388543	0.000000	0.05858	0.005000	0.12908	0.007000	0.05969	0.030000	0.13688	0.660000	0.30964	-0.808000	0.03180	CAC	A|0.120;C|0.880;T|0.000	0.120	strong		0.637	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
FCRL5	83416	hgsc.bcm.edu	37	1	157489535	157489535	+	Silent	SNP	G	G	A	rs3827757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:157489535G>A	ENST00000361835.3	-	13	2815	c.2658C>T	c.(2656-2658)gcC>gcT	p.A886A	FCRL5_ENST00000356953.4_Silent_p.A886A|FCRL5_ENST00000461387.1_5'UTR	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	886					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)				GCTCTTACCTGGCGGGGTCAG	0.502													g|||	718	0.143371	0.3986	0.0245	5008	,	,		19995	0.0893		0.0099	False		,,,				2504	0.0757				p.A886A		Atlas-SNP	.											.	FCRL5	177	.	0			c.C2658T						PASS	.	G	,	1418,2988	463.0+/-353.4	231,956,1016	63.0	63.0	63.0		2658,2658	4.2	0.9	1	dbSNP_107	63	70,8530	40.8+/-97.7	1,68,4231	no	coding-synonymous,coding-synonymous	FCRL5	NM_001195388.1,NM_031281.2	,	232,1024,5247	AA,AG,GG		0.814,32.1834,11.4409	,	886/999,886/978	157489535	1488,11518	2203	4300	6503	SO:0001819	synonymous_variant	83416	exon13			TTACCTGGCGGGG	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.2658C>T	1.37:g.157489535G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	235	114	0.485106	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			G|0.879;A|0.121	0.121	strong		0.502	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
LAMC1	3915	hgsc.bcm.edu	37	1	183093875	183093875	+	Silent	SNP	T	T	C	rs20557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:183093875T>C	ENST00000258341.4	+	14	2768	c.2511T>C	c.(2509-2511)aaT>aaC	p.N837N		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	837	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TCGATCCCAATGCAGTTGGAA	0.507													C|||	2663	0.531749	0.3321	0.6254	5008	,	,		20434	0.628		0.5636	False		,,,				2504	0.6033				p.N837N		Atlas-SNP	.											.	LAMC1	176	.	0			c.T2511C						PASS	.	C		1650,2756	659.6+/-400.6	334,982,887	123.0	105.0	111.0		2511	-8.2	0.0	1	dbSNP_67	111	4898,3702	529.7+/-381.6	1352,2194,754	no	coding-synonymous	LAMC1	NM_002293.3		1686,3176,1641	CC,CT,TT		43.0465,37.4489,49.654		837/1610	183093875	6548,6458	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon14			TCCCAATGCAGTT	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.2511T>C	1.37:g.183093875T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			A|0.000;C|0.515;G|0.000;T|0.485	0.515	strong		0.507	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
SLC17A4	10050	hgsc.bcm.edu	37	6	25773809	25773809	+	Silent	SNP	A	A	G	rs2275906	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25773809A>G	ENST00000377905.4	+	8	1013	c.894A>G	c.(892-894)ttA>ttG	p.L298L	SLC17A4_ENST00000397076.2_Silent_p.L68L|SLC17A4_ENST00000439485.2_Intron	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	298					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GGGCCATTTTAGTCTCTTATT	0.453													A|||	485	0.096845	0.0295	0.111	5008	,	,		19912	0.0546		0.1421	False		,,,				2504	0.1748				p.L298L		Atlas-SNP	.											.	SLC17A4	79	.	0			c.A894G						PASS	.	A		181,4225	117.1+/-155.0	6,169,2028	171.0	151.0	158.0		894	-2.7	0.0	6	dbSNP_100	158	1251,7349	249.6+/-276.8	85,1081,3134	no	coding-synonymous	SLC17A4	NM_005495.2		91,1250,5162	GG,GA,AA		14.5465,4.108,11.0103		298/498	25773809	1432,11574	2203	4300	6503	SO:0001819	synonymous_variant	10050	exon8			CATTTTAGTCTCT	AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"""Solute carriers"""	10932	protein-coding gene	gene with protein product		604216	"""solute carrier family 17 (sodium phosphate), member 4"""			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.894A>G	6.37:g.25773809A>G		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	228	112	0.491228	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Silent	SNP	ENST00000377905.4	37	CCDS4564.1																																																																																			A|0.903;G|0.097	0.097	strong		0.453	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1		
DNAJB12	54788	hgsc.bcm.edu	37	10	74098037	74098037	+	Silent	SNP	A	A	G	rs138477026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:74098037A>G	ENST00000444643.2	-	6	1088	c.756T>C	c.(754-756)ccT>ccC	p.P252P	DNAJB12_ENST00000461919.1_Silent_p.P47P|DNAJB12_ENST00000394903.2_Silent_p.P286P|DNAJB12_ENST00000338820.3_Silent_p.P286P			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	252						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						GGATGAGGATAGGCATCAGCT	0.582													A|||	8	0.00159744	0.0	0.0014	5008	,	,		18106	0.0		0.001	False		,,,				2504	0.0061				p.P286P		Atlas-SNP	.											.	DNAJB12	22	.	0			c.T858C						PASS	.	A	,	0,4406		0,0,2203	111.0	96.0	101.0		858,858	4.9	1.0	10	dbSNP_134	101	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	DNAJB12	NM_001002762.2,NM_017626.4	,	0,7,6496	GG,GA,AA		0.0814,0.0,0.0538	,	286/410,286/410	74098037	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	54788	exon6			GAGGATAGGCATC	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"""Heat shock proteins / DNAJ (HSP40)"""	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.756T>C	10.37:g.74098037A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_017626	B7Z7I3|Q9H6H0	Silent	SNP	ENST00000444643.2	37																																																																																				A|1.000;G|0.000	0.000	strong		0.582	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2		
CD1A	909	hgsc.bcm.edu	37	1	158224904	158224904	+	Missense_Mutation	SNP	C	C	T	rs2269714	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158224904C>T	ENST00000289429.5	+	2	622	c.89C>T	c.(88-90)aCc>aTc	p.T30I		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	30			T -> I (in dbSNP:rs2269714). {ECO:0000269|PubMed:11600221, ECO:0000269|PubMed:2701945}.		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	TTCCATGTCACCTGGATCGCA	0.488													c|||	823	0.164337	0.0363	0.0908	5008	,	,		20620	0.3948		0.0577	False		,,,				2504	0.2618				p.T30I		Atlas-SNP	.											.	CD1A	88	.	0			c.C89T	GRCh37	CM067655	CD1A	M	rs2269714	PASS	.	C	ILE/THR	224,4182	134.5+/-170.7	7,210,1986	133.0	113.0	120.0		89	-4.8	0.0	1	dbSNP_100	120	496,8104	143.0+/-199.1	13,470,3817	yes	missense	CD1A	NM_001763.2	89	20,680,5803	TT,TC,CC		5.7674,5.084,5.5359	benign	30/328	158224904	720,12286	2203	4300	6503	SO:0001583	missense	909	exon2			ATGTCACCTGGAT	M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1634	protein-coding gene	gene with protein product		188370	"""CD1A antigen, a polypeptide"", ""CD1a antigen"""	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.89C>T	1.37:g.158224904C>T	ENSP00000289429:p.Thr30Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	37	CCDS1174.1	301	0.13782051282051283	22	0.044715447154471545	32	0.08839779005524862	207	0.3618881118881119	40	0.052770448548812667	c	0.016	-1.513795	0.00975	0.05084	0.057674	ENSG00000158477	ENST00000289429	T	0.12984	2.63	4.54	-4.82	0.03171	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.454567	0.16291	N	0.220890	T	0.00496	0.0016	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32052	-0.9921	9	0.02654	T	1	-5.1416	1.8947	0.03255	0.1399:0.3555:0.1436:0.3611	rs2269714;rs52806754;rs2269714	30	P06126	CD1A_HUMAN	I	30	ENSP00000289429:T30I	ENSP00000289429:T30I	T	+	2	0	CD1A	156491528	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.396000	0.07278	-0.666000	0.05310	-1.310000	0.01310	ACC	C|0.902;T|0.098	0.098	strong		0.488	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763	
CENPF	1063	hgsc.bcm.edu	37	1	214816224	214816224	+	Missense_Mutation	SNP	G	G	A	rs2666839	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214816224G>A	ENST00000366955.3	+	12	4711	c.4543G>A	c.(4543-4545)Gct>Act	p.A1515T		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1611	2 X 96 AA approximate tandem repeats.		A -> T (in dbSNP:rs2666839).		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)		TTTAGAAGGGGCTGTTTCAGC	0.478													A|||	1494	0.298323	0.6785	0.2104	5008	,	,		19612	0.1597		0.0974	False		,,,				2504	0.1963				p.A1515T	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.G4543A						PASS	.	A	THR/ALA	2620,1786	516.5+/-369.2	788,1044,371	47.0	47.0	47.0		4543	2.8	0.0	1	dbSNP_100	47	816,7784	764.0+/-407.6	43,730,3527	yes	missense	CENPF	NM_016343.3	58	831,1774,3898	AA,AG,GG		9.4884,40.5356,26.4186	benign	1515/3115	214816224	3436,9570	2203	4300	6503	SO:0001583	missense	1063	exon12			GAAGGGGCTGTTT	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.4543G>A	1.37:g.214816224G>A	ENSP00000355922:p.Ala1515Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	586	0.2683150183150183	328	0.6666666666666666	87	0.24033149171270718	99	0.17307692307692307	72	0.09498680738786279	A	0.005	-2.154013	0.00325	0.594644	0.094884	ENSG00000117724	ENST00000366955	T	0.33438	1.41	5.14	2.83	0.33086	.	2.006080	0.02906	N	0.136142	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.41945	-0.9480	9	0.09084	T	0.74	.	8.1673	0.31235	0.69:0.0:0.31:0.0	rs2666839;rs3795515;rs52815072;rs58250271;rs2666839	1515	P49454	CENPF_HUMAN	T	1515	ENSP00000355922:A1515T	ENSP00000355922:A1515T	A	+	1	0	CENPF	212882847	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-0.456000	0.06754	0.015000	0.14971	-0.982000	0.02568	GCT	G|0.721;A|0.279	0.279	strong		0.478	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
CD109	135228	hgsc.bcm.edu	37	6	74497152	74497152	+	Missense_Mutation	SNP	G	G	A	rs5023688	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:74497152G>A	ENST00000287097.5	+	21	2645	c.2533G>A	c.(2533-2535)Gtc>Atc	p.V845I	CD109_ENST00000437994.2_Missense_Mutation_p.V845I|CD109_ENST00000422508.2_Missense_Mutation_p.V768I			Q6YHK3	CD109_HUMAN	CD109 molecule	845			V -> I (in dbSNP:rs5023688). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTCTGATGCTGTCACCCAGAT	0.403													A|||	1861	0.371605	0.4644	0.4049	5008	,	,		18074	0.4087		0.339	False		,,,				2504	0.2178				p.V845I		Atlas-SNP	.											.	CD109	170	.	0			c.G2533A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	2043,2363	610.5+/-391.6	492,1059,652	94.0	92.0	93.0		2533,2302,2533	-9.1	0.0	6	dbSNP_113	93	3057,5543	660.7+/-401.8	552,1953,1795	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	29,29,29	1044,3012,2447	AA,AG,GG		35.5465,46.3686,39.2127	benign,benign,benign	845/1429,768/1369,845/1446	74497152	5100,7906	2203	4300	6503	SO:0001583	missense	135228	exon21			GATGCTGTCACCC	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2533G>A	6.37:g.74497152G>A	ENSP00000287097:p.Val845Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	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	
DAK	26007	hgsc.bcm.edu	37	11	61111346	61111346	+	Missense_Mutation	SNP	C	C	G	rs35723406	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:61111346C>G	ENST00000394900.3	+	12	1230	c.1001C>G	c.(1000-1002)gCa>gGa	p.A334G		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	334	DhaK. {ECO:0000255|PROSITE- ProRule:PRU00814}.		A -> G (in dbSNP:rs35723406).		carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						ACCACTGCAGCAGCCTGGCCT	0.617													C|||	194	0.038738	0.0038	0.0648	5008	,	,		19467	0.001		0.1213	False		,,,				2504	0.0215				p.A334G		Atlas-SNP	.											.	DAK	52	.	0			c.C1001G						PASS	.	C	GLY/ALA	109,4297	83.4+/-121.9	1,107,2095	84.0	92.0	89.0		1001	-0.7	0.0	11	dbSNP_126	89	1029,7569	218.7+/-257.0	61,907,3331	yes	missense	DAK	NM_015533.3	60	62,1014,5426	GG,GC,CC		11.9679,2.4739,8.7512	benign	334/576	61111346	1138,11866	2203	4299	6502	SO:0001583	missense	26007	exon12			CTGCAGCAGCCTG		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"""dihydroxyacetone kinase 2 homolog (yeast)"""				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1001C>G	11.37:g.61111346C>G	ENSP00000378360:p.Ala334Gly	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_015533	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Missense_Mutation	SNP	ENST00000394900.3	37	CCDS8003.1	106	0.048534798534798536	2	0.0040650406504065045	24	0.06629834254143646	1	0.0017482517482517483	79	0.10422163588390501	C	12.44	1.938144	0.34189	0.024739	0.119679	ENSG00000149476	ENST00000394900;ENST00000529479	T;T	0.30448	1.53;1.53	5.84	-0.714	0.11219	Dak kinase (2);	0.692145	0.14877	N	0.293164	T	0.00328	0.0010	L	0.43152	1.355	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.10450	0.002;0.005	T	0.07309	-1.0779	9	0.66056	D	0.02	3.3223	8.2482	0.31702	0.099:0.5216:0.0:0.3794	rs35723406	334;334	Q2L9C1;Q3LXA3	.;DHAK_HUMAN	G	334;333	ENSP00000378360:A334G;ENSP00000432539:A333G	ENSP00000378360:A334G	A	+	2	0	DAK	60867922	0.000000	0.05858	0.044000	0.18714	0.914000	0.54420	0.683000	0.25349	-0.346000	0.08312	-0.797000	0.03246	GCA	C|0.923;G|0.077	0.077	strong		0.617	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533	
PDE11A	50940	hgsc.bcm.edu	37	2	178762824	178762824	+	Silent	SNP	T	T	C	rs71423514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:178762824T>C	ENST00000286063.6	-	4	1580	c.1263A>G	c.(1261-1263)gaA>gaG	p.E421E	PDE11A_ENST00000358450.4_Silent_p.E171E|PDE11A_ENST00000449286.2_Silent_p.E63E|PDE11A_ENST00000409504.1_Silent_p.E63E|PDE11A_ENST00000497003.1_5'UTR	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	421	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)	CAGAACAGCGTTCACATTTCA	0.378									Primary Pigmented Nodular Adrenocortical Disease, Familial				T|||	301	0.0601038	0.0061	0.0735	5008	,	,		15586	0.0149		0.1362	False		,,,				2504	0.092				p.E421E		Atlas-SNP	.											.	PDE11A	283	.	0			c.A1263G						PASS	.	T	,,	137,4269	98.0+/-136.7	4,129,2070	142.0	134.0	137.0		513,189,1263	1.7	1.0	2	dbSNP_130	137	1324,7276	260.3+/-283.2	92,1140,3068	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE11A	NM_001077197.1,NM_001077358.1,NM_016953.3	,,	96,1269,5138	CC,CT,TT		15.3953,3.1094,11.2333	,,	171/684,63/576,421/934	178762824	1461,11545	2203	4300	6503	SO:0001819	synonymous_variant	50940	exon4	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	ACAGCGTTCACAT	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.1263A>G	2.37:g.178762824T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	170	74	0.435294	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1	159	0.07280219780219781	6	0.012195121951219513	29	0.08011049723756906	14	0.024475524475524476	110	0.14511873350923482	T	9.875	1.199996	0.22121	0.031094	0.153953	ENSG00000128655	ENST00000433879	.	.	.	5.89	1.66	0.24008	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11036	-1.0604	3	.	.	.	.	10.0467	0.42190	0.0:0.3364:0.0:0.6636	.	.	.	.	S	60	.	.	N	-	2	0	PDE11A	178471070	0.994000	0.37717	1.000000	0.80357	0.998000	0.95712	0.296000	0.19083	0.431000	0.26258	0.533000	0.62120	AAC	T|0.895;C|0.105	0.105	strong		0.378	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
KIAA1755	85449	hgsc.bcm.edu	37	20	36850988	36850988	+	Silent	SNP	C	C	T	rs35524973	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36850988C>T	ENST00000279024.4	-	10	2551	c.2280G>A	c.(2278-2280)agG>agA	p.R760R		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	760										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)				TGCTCAGGCACCTGGTAGCCT	0.657											OREG0025921	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	113	0.0225639	0.0507	0.013	5008	,	,		17572	0.002		0.0159	False		,,,				2504	0.0194				p.R760R		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G2280A						PASS	.	C		274,4132	150.7+/-184.7	12,250,1941	39.0	35.0	37.0		2280	3.0	1.0	20	dbSNP_126	37	143,8457	68.4+/-130.8	3,137,4160	no	coding-synonymous	KIAA1755	NM_001029864.1		15,387,6101	TT,TC,CC		1.6628,6.2188,3.2062		760/1201	36850988	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon10			CAGGCACCTGGTA	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.2280G>A	20.37:g.36850988C>T		Somatic	30	0	0	866	WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			A|0.000;C|0.971;T|0.029	0.029	strong		0.657	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
JMJD8	339123	hgsc.bcm.edu	37	16	733424	733424	+	Missense_Mutation	SNP	C	C	G	rs72773413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:733424C>G	ENST00000293882.4	-	6	618	c.619G>C	c.(619-621)Ggg>Cgg	p.G207R	JMJD8_ENST00000609261.1_Missense_Mutation_p.G137R|JMJD8_ENST00000454700.1_Missense_Mutation_p.G177R|JMJD8_ENST00000562111.1_Missense_Mutation_p.G137R|JMJD8_ENST00000562824.1_Missense_Mutation_p.G107R|JMJD8_ENST00000412368.2_Missense_Mutation_p.G158R			Q96S16	JMJD8_HUMAN	jumonji domain containing 8	207	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.					extracellular vesicular exosome (GO:0070062)				breast(1)	1						TTGTTGTCCCCGAAGAAGTAC	0.627													C|||	18	0.00359425	0.0008	0.0029	5008	,	,		16613	0.0		0.0129	False		,,,				2504	0.002				p.G158R		Atlas-SNP	.											.	JMJD8	14	.	0			c.G472C						PASS	.	C	ARG/GLY	5,3865		0,5,1930	37.0	44.0	42.0		472	2.8	0.9	16	dbSNP_130	42	42,8076		2,38,4019	yes	missense	JMJD8	NM_001005920.2	125	2,43,5949	GG,GC,CC		0.5174,0.1292,0.3921	probably-damaging	158/286	733424	47,11941	1935	4059	5994	SO:0001583	missense	339123	exon6			TGTCCCCGAAGAA		CCDS45369.1	16p13.3	2008-07-28	2008-07-28	2008-07-28		ENSG00000161999			14148	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 20"""	C16orf20			Standard	NM_001005920		Approved		uc002ciw.1	Q96S16		ENST00000293882.4:c.619G>C	16.37:g.733424C>G	ENSP00000293882:p.Gly207Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001005920	B2RNS7|D3DU58|Q4PKE3|Q4VBY1|Q6GMW5|Q71RB8	Missense_Mutation	SNP	ENST00000293882.4	37		10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	14.31	2.497766	0.44455	0.001292	0.005174	ENSG00000161999	ENST00000412368;ENST00000293882;ENST00000454700	T;T;T	0.71461	-0.57;-0.57;-0.57	3.75	2.77	0.32553	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.78660	0.4318	M	0.82630	2.6	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82208	-0.0571	10	0.72032	D	0.01	-17.4867	11.1688	0.48558	0.1859:0.8141:0.0:0.0	.	177;207	Q96S16-2;Q96S16	.;JMJD8_HUMAN	R	158;207;177	ENSP00000399475:G158R;ENSP00000293882:G207R;ENSP00000394147:G177R	ENSP00000293882:G207R	G	-	1	0	JMJD8	673425	1.000000	0.71417	0.913000	0.36048	0.015000	0.08874	6.993000	0.76245	0.772000	0.33382	-0.181000	0.13052	GGG	C|0.996;G|0.004	0.004	strong		0.627	JMJD8-201	KNOWN	basic	protein_coding	protein_coding		NM_001005920	
C1orf168	199920	hgsc.bcm.edu	37	1	57257914	57257914	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:57257914G>A	ENST00000343433.6	-	2	652	c.572C>T	c.(571-573)gCc>gTc	p.A191V	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	191										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						AAGAGTCTGGGCTCCTTTTGT	0.468																																					p.A191V		Atlas-SNP	.											C1orf168,caecum,carcinoma,+1,1	C1orf168	102	1	0			c.C572T						PASS	.						102.0	104.0	104.0					1																	57257914		2203	4300	6503	SO:0001583	missense	199920	exon2			GTCTGGGCTCCTT	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.572C>T	1.37:g.57257914G>A	ENSP00000345972:p.Ala191Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001004303	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	37	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.949546	0.73787	.	.	ENSG00000187889	ENST00000343433	T	0.32988	1.43	4.55	1.41	0.22369	.	0.483859	0.18959	N	0.126441	T	0.18882	0.0453	L	0.32530	0.975	0.09310	N	1	P;B	0.37955	0.612;0.176	B;B	0.37692	0.256;0.067	T	0.09997	-1.0649	10	0.49607	T	0.09	0.0321	2.8636	0.05594	0.1004:0.1808:0.5323:0.1865	.	191;191	Q5VWT5-2;Q5VWT5	.;CA168_HUMAN	V	191	ENSP00000345972:A191V	ENSP00000345972:A191V	A	-	2	0	C1orf168	57030502	0.000000	0.05858	0.213000	0.23690	0.813000	0.45954	0.139000	0.16036	0.642000	0.30620	0.563000	0.77884	GCC	.	.	none		0.468	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
TFAM	7019	hgsc.bcm.edu	37	10	60145363	60145363	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:60145363C>T	ENST00000487519.1	+	1	582	c.56C>T	c.(55-57)gCa>gTa	p.A19V	TFAM_ENST00000373895.3_Missense_Mutation_p.A19V|TFAM_ENST00000373899.3_3'UTR	NM_001270782.1|NM_003201.2	NP_001257711.1|NP_003192.1	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial	19					DNA-dependent DNA replication (GO:0006261)|gene expression (GO:0010467)|mitochondrial respiratory chain complex assembly (GO:0033108)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|mitochondrial light strand promoter sense binding (GO:0070363)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						AGGTCTGGAGCAGAGCTGTGC	0.667											OREG0020196	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A19V		Atlas-SNP	.											.	TFAM	52	.	0			c.C56T						PASS	.						75.0	62.0	66.0					10																	60145363		2201	4289	6490	SO:0001583	missense	7019	exon1			CTGGAGCAGAGCT	BC018628	CCDS7253.1, CCDS59217.1	10q21	2010-09-24			ENSG00000108064	ENSG00000108064			11741	protein-coding gene	gene with protein product		600438		TCF6, TCF6L2		7789991	Standard	NM_003201		Approved		uc001jkf.4	Q00059	OTTHUMG00000018270	ENST00000487519.1:c.56C>T	10.37:g.60145363C>T	ENSP00000420588:p.Ala19Val	Somatic	78	0	0	1043	WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_003201	A8MRB2|A9QXC6|B5BU05|Q5U0C6	Missense_Mutation	SNP	ENST00000487519.1	37	CCDS7253.1	.	.	.	.	.	.	.	.	.	.	C	9.457	1.092160	0.20471	.	.	ENSG00000108064	ENST00000487519;ENST00000373895	T;T	0.14516	2.53;2.5	4.31	1.43	0.22495	.	0.907854	0.09398	N	0.807600	T	0.09598	0.0236	L	0.32530	0.975	0.09310	N	0.999999	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.003	T	0.42965	-0.9420	10	0.17832	T	0.49	.	6.2181	0.20665	0.0:0.6834:0.0:0.3166	.	19;19	A8MRB2;Q00059	.;TFAM_HUMAN	V	19	ENSP00000420588:A19V;ENSP00000363002:A19V	ENSP00000363002:A19V	A	+	2	0	TFAM	59815369	0.048000	0.20356	0.198000	0.23420	0.309000	0.27889	0.110000	0.15437	0.333000	0.23563	-0.123000	0.14984	GCA	.	.	none		0.667	TFAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048146.1	NM_003201	
TRPV2	51393	hgsc.bcm.edu	37	17	16336992	16336992	+	Silent	SNP	C	C	G	rs14039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	75	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	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	
SLC9C1	285335	hgsc.bcm.edu	37	3	111996554	111996554	+	Missense_Mutation	SNP	T	T	C	rs9828502	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:111996554T>C	ENST00000305815.5	-	5	724	c.472A>G	c.(472-474)Ata>Gta	p.I158V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I158V|SLC9C1_ENST00000467397.1_5'Flank	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	158			I -> V (in dbSNP:rs9828502). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										AGGTCTCTTATAGCAGCTGCG	0.333													T|||	1557	0.310903	0.3116	0.4006	5008	,	,		17507	0.2976		0.2346	False		,,,				2504	0.3384				p.I158V		Atlas-SNP	.											.	.	.	.	0			c.A472G						PASS	.	T	VAL/ILE	1392,3014	448.5+/-348.7	219,954,1030	72.0	77.0	75.0		472	-1.3	0.3	3	dbSNP_119	75	2333,6267	386.0+/-341.7	321,1691,2288	yes	missense	SLC9A10	NM_183061.1	29	540,2645,3318	CC,CT,TT		27.1279,31.5933,28.6406	possibly-damaging	158/1178	111996554	3725,9281	2203	4300	6503	SO:0001583	missense	285335	exon5			CTCTTATAGCAGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.472A>G	3.37:g.111996554T>C	ENSP00000306627:p.Ile158Val	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	649	0.29716117216117216	157	0.31910569105691056	137	0.3784530386740331	173	0.30244755244755245	182	0.24010554089709762	T	0.080	-1.185856	0.01620	0.315933	0.271279	ENSG00000172139	ENST00000305815;ENST00000487372;ENST00000486574	T;T;T	0.13420	2.59;2.59;3.95	5.45	-1.34	0.09143	Cation/H+ exchanger (1);	0.188565	0.36854	N	0.002361	T	0.00012	0.0000	L	0.53249	1.67	0.58432	P	6.999999999979245E-6	B;B	0.10296	0.002;0.003	B;B	0.14578	0.005;0.011	T	0.44174	-0.9345	9	0.56958	D	0.05	.	5.697	0.17861	0.1198:0.302:0.0:0.5782	rs9828502;rs9828502	158;158	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	158;158;85	ENSP00000306627:I158V;ENSP00000420688:I158V;ENSP00000417274:I85V	ENSP00000306627:I158V	I	-	1	0	SLC9A10	113479244	0.992000	0.36948	0.281000	0.24762	0.037000	0.13140	0.134000	0.15932	-0.872000	0.04037	-2.485000	0.00197	ATA	T|0.713;C|0.287	0.287	strong		0.333	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
ZNF786	136051	hgsc.bcm.edu	37	7	148777770	148777770	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:148777770C>T	ENST00000491431.1	-	2	122	c.58G>A	c.(58-60)Gag>Aag	p.E20K	ZNF786_ENST00000316286.9_Intron|ZNF786_ENST00000451334.3_5'UTR	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	20	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(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			CATTCTTGCTCGGAGAAATAA	0.418																																					p.E20K		Atlas-SNP	.											ZNF786,NS,carcinoma,0,1	ZNF786	69	1	0			c.G58A						scavenged	.						104.0	103.0	104.0					7																	148777770		1948	4130	6078	SO:0001583	missense	136051	exon2			CTTGCTCGGAGAA	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"""Zinc fingers, C2H2-type"", ""-"""	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.58G>A	7.37:g.148777770C>T	ENSP00000417470:p.Glu20Lys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	198	3	0.0151515	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	37	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.163796	0.78226	.	.	ENSG00000197362	ENST00000491431	T	0.01745	4.66	4.75	4.75	0.60458	Krueppel-associated box (4);	0.198630	0.25156	N	0.032717	T	0.04497	0.0123	L	0.37800	1.135	0.80722	D	1	D	0.76494	0.999	D	0.64776	0.929	T	0.59059	-0.7525	10	0.27785	T	0.31	-23.6693	10.638	0.45575	0.1913:0.8087:0.0:0.0	.	20	Q8N393	ZN786_HUMAN	K	20	ENSP00000417470:E20K	ENSP00000417470:E20K	E	-	1	0	ZNF786	148408703	0.000000	0.05858	0.958000	0.39756	0.982000	0.71751	0.084000	0.14891	2.636000	0.89361	0.557000	0.71058	GAG	.	.	none		0.418	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249552	3249552	+	Missense_Mutation	SNP	C	C	T	rs4391795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	28	0	0		WXS	Illumina HiSeq	Phase_I	29	21	0.724138	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	
SLC7A13	157724	hgsc.bcm.edu	37	8	87241847	87241847	+	Silent	SNP	G	G	A	rs7814198	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87241847G>A	ENST00000297524.3	-	1	763	c.660C>T	c.(658-660)ggC>ggT	p.G220G	SLC7A13_ENST00000419776.2_Splice_Site|SLC7A13_ENST00000520624.1_Intron	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	220						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						AGCATGCCCCGCCTGAATATG	0.353													G|||	2232	0.445687	0.4932	0.4481	5008	,	,		21344	0.502		0.2296	False		,,,				2504	0.544				p.G220G		Atlas-SNP	.											.	SLC7A13	97	.	0			c.C660T						PASS	.	G		1947,2459	552.0+/-378.4	443,1061,699	140.0	134.0	136.0		660	-9.4	0.0	8	dbSNP_116	136	2012,6588	352.7+/-328.8	237,1538,2525	no	coding-synonymous	SLC7A13	NM_138817.2		680,2599,3224	AA,AG,GG		23.3953,44.1897,30.4398		220/471	87241847	3959,9047	2203	4300	6503	SO:0001819	synonymous_variant	157724	exon1			TGCCCCGCCTGAA	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.660C>T	8.37:g.87241847G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	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	
PDHX	8050	hgsc.bcm.edu	37	11	34969112	34969112	+	Missense_Mutation	SNP	A	A	G	rs11539202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:34969112A>G	ENST00000227868.4	+	3	385	c.301A>G	c.(301-303)Acc>Gcc	p.T101A	PDHX_ENST00000448838.3_Missense_Mutation_p.T86A|PDHX_ENST00000430469.2_Missense_Mutation_p.T101A			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	101	Lipoyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.		T -> A (in dbSNP:rs11539202).		cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			AGCTGTGGTTACCTTAGATGC	0.353													A|||	545	0.108826	0.0257	0.1527	5008	,	,		15764	0.0		0.3191	False		,,,				2504	0.0859				p.T101A		Atlas-SNP	.											.	PDHX	40	.	0			c.A301G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	381,4023	191.9+/-217.4	10,361,1831	200.0	186.0	191.0		256,301,301	4.9	1.0	11	dbSNP_120	191	2764,5832	440.6+/-359.6	429,1906,1963	yes	missense,missense,missense	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	58,58,58	439,2267,3794	GG,GA,AA		32.1545,8.6512,24.1923	possibly-damaging,possibly-damaging,possibly-damaging	86/487,101/275,101/502	34969112	3145,9855	2202	4298	6500	SO:0001583	missense	8050	exon3			GTGGTTACCTTAG	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.301A>G	11.37:g.34969112A>G	ENSP00000227868:p.Thr101Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	328	0.15018315018315018	17	0.034552845528455285	58	0.16022099447513813	0	0.0	253	0.3337730870712401	A	16.82	3.228063	0.58777	0.086512	0.321545	ENSG00000110435	ENST00000533550;ENST00000448838;ENST00000227868;ENST00000430469;ENST00000533262	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	6.06	4.93	0.64822	Single hybrid motif (1);Biotin/lipoyl attachment (2);	0.151252	0.64402	D	0.000017	T	0.00012	0.0000	N	0.04994	-0.135	0.29635	P	0.845129	D;P;B	0.76494	0.999;0.843;0.246	D;B;B	0.83275	0.996;0.336;0.241	T	0.47169	-0.9138	9	0.26408	T	0.33	-21.7084	11.872	0.52525	0.8689:0.0:0.0:0.131	rs11539202;rs52812226;rs60066295;rs11539202	101;86;101	E9PBP7;E9PB14;O00330	.;.;ODPX_HUMAN	A	41;86;101;101;74	ENSP00000431281:T41A;ENSP00000389404:T86A;ENSP00000227868:T101A;ENSP00000415695:T101A;ENSP00000432277:T74A	ENSP00000227868:T101A	T	+	1	0	PDHX	34925688	1.000000	0.71417	0.998000	0.56505	0.747000	0.42532	8.129000	0.89597	1.091000	0.41335	0.528000	0.53228	ACC	A|0.800;G|0.200	0.200	strong		0.353	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
CNBD2	140894	hgsc.bcm.edu	37	20	34596371	34596371	+	Missense_Mutation	SNP	C	C	T	rs6060750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34596371C>T	ENST00000373973.3	+	9	1296	c.1123C>T	c.(1123-1125)Ccc>Tcc	p.P375S	CNBD2_ENST00000538900.1_Missense_Mutation_p.P375S|CNBD2_ENST00000349339.1_Missense_Mutation_p.P375S			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	375			P -> S (in dbSNP:rs6060750). {ECO:0000269|PubMed:14702039}.														AGACACTCTCCCCAAGATGCT	0.507													C|||	1552	0.309904	0.3359	0.1859	5008	,	,		18022	0.3135		0.2018	False		,,,				2504	0.4703				p.P375S		Atlas-SNP	.											.	.	.	.	0			c.C1123T						PASS	.	C	SER/PRO,SER/PRO	1337,3069	445.9+/-347.8	208,921,1074	53.0	53.0	53.0		1123,1123	4.5	1.0	20	dbSNP_114	53	1737,6863	314.5+/-311.8	168,1401,2731	yes	missense,missense	C20orf152	NM_001207076.1,NM_080834.2	74,74	376,2322,3805	TT,TC,CC		20.1977,30.345,23.6352	probably-damaging,probably-damaging	375/424,375/573	34596371	3074,9932	2203	4300	6503	SO:0001583	missense	140894	exon9			ACTCTCCCCAAGA	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 152"", ""cyclic nucleotide (cNMP) binding domain containing 1"""	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.1123C>T	20.37:g.34596371C>T	ENSP00000363084:p.Pro375Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Missense_Mutation	SNP	ENST00000373973.3	37		523	0.23946886446886448	151	0.30691056910569103	80	0.22099447513812154	144	0.2517482517482518	148	0.19525065963060687	C	11.72	1.723698	0.30593	0.30345	0.201977	ENSG00000149646	ENST00000373973;ENST00000349339;ENST00000538900	T;T;T	0.12255	2.75;2.74;2.7	4.5	4.5	0.54988	Cyclic nucleotide-binding-like (1);	0.185586	0.36591	N	0.002515	T	0.00012	0.0000	M	0.67953	2.075	0.29895	P	0.824906	B;B	0.33637	0.15;0.42	B;B	0.28465	0.027;0.09	T	0.45906	-0.9229	9	0.25751	T	0.34	-12.0748	13.0094	0.58724	0.0:1.0:0.0:0.0	rs6060750;rs6579272;rs52810685;rs60984638;rs6060750	375;375	Q96M20;Q96M20-2	CT152_HUMAN;.	S	375	ENSP00000363084:P375S;ENSP00000340954:P375S;ENSP00000442729:P375S	ENSP00000340954:P375S	P	+	1	0	C20orf152	34059785	0.810000	0.29049	0.968000	0.41197	0.010000	0.07245	2.944000	0.49034	2.797000	0.96272	0.561000	0.74099	CCC	C|0.746;T|0.254	0.254	strong		0.507	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834	
CUBN	8029	hgsc.bcm.edu	37	10	16870912	16870912	+	Missense_Mutation	SNP	G	G	T	rs1801232	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:16870912G>T	ENST00000377833.4	-	66	10721	c.10656C>A	c.(10654-10656)aaC>aaA	p.N3552K		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3552	CUB 27. {ECO:0000255|PROSITE- ProRule:PRU00059}.		N -> K (in dbSNP:rs1801232). {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)	TGAAGTAGAAGTTGATGGTGA	0.532													G|||	412	0.0822684	0.0061	0.036	5008	,	,		16914	0.1458		0.1004	False		,,,				2504	0.1339				p.N3552K		Atlas-SNP	.											.	CUBN	515	.	0			c.C10656A						PASS	.	G	LYS/ASN	78,4328	68.1+/-105.8	0,78,2125	186.0	147.0	161.0		10656	4.0	0.9	10	dbSNP_89	161	646,7954	166.1+/-218.1	32,582,3686	yes	missense	CUBN	NM_001081.3	94	32,660,5811	TT,TG,GG		7.5116,1.7703,5.5667	benign	3552/3624	16870912	724,12282	2203	4300	6503	SO:0001583	missense	8029	exon66			GTAGAAGTTGATG	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.10656C>A	10.37:g.16870912G>T	ENSP00000367064:p.Asn3552Lys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	127	50	0.393701	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	176	0.08058608058608059	9	0.018292682926829267	18	0.049723756906077346	76	0.13286713286713286	73	0.09630606860158311	G	2.114	-0.402953	0.04865	0.017703	0.075116	ENSG00000107611	ENST00000377833;ENST00000545090	T	0.16897	2.31	5.94	4.04	0.47022	CUB (5);	0.788702	0.11136	N	0.595861	T	0.00109	0.0003	L	0.31752	0.955	0.09310	P	1.0	P	0.35872	0.525	B	0.34590	0.186	T	0.07520	-1.0768	9	0.06236	T	0.91	.	7.8064	0.29204	0.1397:0.139:0.7214:0.0	rs1801232;rs17334699;rs52824857;rs1801232	3552	O60494	CUBN_HUMAN	K	3552;393	ENSP00000367064:N3552K	ENSP00000367064:N3552K	N	-	3	2	CUBN	16910918	1.000000	0.71417	0.890000	0.34922	0.008000	0.06430	2.190000	0.42630	1.486000	0.48398	0.561000	0.74099	AAC	T|0.070;G|0.929	0.070	strong		0.532	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
THBS2	7058	hgsc.bcm.edu	37	6	169621536	169621536	+	Silent	SNP	A	A	G	rs1132742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	101	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	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	
TMED5	50999	hgsc.bcm.edu	37	1	93620393	93620393	+	Missense_Mutation	SNP	G	G	A	rs1060622	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:93620393G>A	ENST00000370282.3	-	4	1009	c.524C>T	c.(523-525)aCt>aTt	p.T175I	TMED5_ENST00000479918.1_Silent_p.N191N|TMED5_ENST00000483033.1_5'UTR	NM_016040.4	NP_057124.3	Q9Y3A6	TMED5_HUMAN	transmembrane emp24 protein transport domain containing 5	175			T -> I (in dbSNP:rs1060622). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		Golgi ribbon formation (GO:0090161)|protein transport (GO:0015031)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6		all_lung(203;0.0223)|Lung NSC(277;0.071)|Melanoma(281;0.147)|Glioma(108;0.188)		all cancers(265;0.00108)|GBM - Glioblastoma multiforme(16;0.00407)|Epithelial(280;0.0797)		TCTAAGCAGAGTTTGTATGTG	0.353													G|||	2456	0.490415	0.0696	0.5836	5008	,	,		18336	0.6438		0.6302	False		,,,				2504	0.6912				p.T175I		Atlas-SNP	.											.	TMED5	16	.	0			c.C524T						PASS	.	G	,ILE/THR	734,3672	304.4+/-288.4	62,610,1531	158.0	146.0	150.0		573,524	3.9	1.0	1	dbSNP_86	150	5383,3217	652.4+/-400.9	1713,1957,630	yes	coding-synonymous,missense	TMED5	NM_001167830.1,NM_016040.4	,89	1775,2567,2161	AA,AG,GG		37.407,16.6591,47.0321	,possibly-damaging	191/194,175/230	93620393	6117,6889	2203	4300	6503	SO:0001583	missense	50999	exon4			AGCAGAGTTTGTA	BC070051	CCDS743.1, CCDS53342.1	1p22.1	2013-09-19			ENSG00000117500	ENSG00000117500			24251	protein-coding gene	gene with protein product						10810093	Standard	NM_016040		Approved	CGI-100	uc001dpn.3	Q9Y3A6	OTTHUMG00000010162	ENST00000370282.3:c.524C>T	1.37:g.93620393G>A	ENSP00000359305:p.Thr175Ile	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	175	77	0.44	NM_016040	B1AKT4|B2R703|D3DT38|Q96AX8	Missense_Mutation	SNP	ENST00000370282.3	37	CCDS743.1	1112	0.5091575091575091	43	0.08739837398373984	212	0.585635359116022	376	0.6573426573426573	481	0.6345646437994723	G	24.5	4.543293	0.86022	0.166591	0.62593	ENSG00000117500	ENST00000370282;ENST00000535517	T	0.16196	2.36	5.9	3.94	0.45596	GOLD (1);	0.042911	0.85682	D	0.000000	T	0.24314	0.0589	M	0.87682	2.9	0.09310	P	1.0	P	0.51449	0.945	P	0.52823	0.71	T	0.18304	-1.0341	9	0.54805	T	0.06	-20.1247	10.8543	0.46789	0.0675:0.0:0.8021:0.1304	rs1060622;rs3201522;rs17851401;rs52819149;rs60258163;rs1060622	175	Q9Y3A6	TMED5_HUMAN	I	175;124	ENSP00000359305:T175I	ENSP00000359305:T175I	T	-	2	0	TMED5	93392981	1.000000	0.71417	0.997000	0.53966	0.952000	0.60782	7.850000	0.86915	1.510000	0.48803	0.655000	0.94253	ACT	G|0.516;A|0.484	0.484	strong		0.353	TMED5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028076.3	NM_016040	
MMP27	64066	hgsc.bcm.edu	37	11	102567207	102567207	+	Missense_Mutation	SNP	T	T	A	rs1276286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102567207T>A	ENST00000260229.4	-	6	888	c.797A>T	c.(796-798)gAa>gTa	p.E266V		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	266			E -> V (in dbSNP:rs1276286). {ECO:0000269|PubMed:12975309}.		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	CTTAGCAGGTTCCTTAGGCAG	0.413													A|||	2191	0.4375	0.1725	0.5043	5008	,	,		18588	0.629		0.4443	False		,,,				2504	0.544				p.E266V		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	0			c.A797T						PASS	.	A	VAL/GLU	1066,3340	723.7+/-409.4	113,840,1250	151.0	154.0	153.0		797	-1.3	0.0	11	dbSNP_87	153	3904,4694	606.3+/-395.1	863,2178,1258	yes	missense	MMP27	NM_022122.2	121	976,3018,2508	AA,AT,TT		45.4059,24.1943,38.219	benign	266/514	102567207	4970,8034	2203	4299	6502	SO:0001583	missense	64066	exon6			GCAGGTTCCTTAG	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.797A>T	11.37:g.102567207T>A	ENSP00000260229:p.Glu266Val	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	931	0.42628205128205127	84	0.17073170731707318	169	0.46685082872928174	336	0.5874125874125874	342	0.45118733509234826	A	0.065	-1.215502	0.01542	0.241943	0.454059	ENSG00000137675	ENST00000260229	T	0.14266	2.52	5.89	-1.3	0.09259	.	3.758110	0.00837	N	0.001700	T	0.00012	0.0000	N	0.02830	-0.485	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44467	-0.9326	9	0.20046	T	0.44	.	5.2352	0.15443	0.4414:0.0:0.2808:0.2778	rs1276286;rs17800318;rs52815827;rs56490119;rs1276286	266	Q9H306	MMP27_HUMAN	V	266	ENSP00000260229:E266V	ENSP00000260229:E266V	E	-	2	0	MMP27	102072417	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.450000	0.06803	-0.348000	0.08286	-1.349000	0.01238	GAA	T|0.600;A|0.400	0.400	strong		0.413	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
CASR	846	hgsc.bcm.edu	37	3	122003769	122003769	+	Missense_Mutation	SNP	A	A	G	rs1042636	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:122003769A>G	ENST00000490131.1	+	7	3340	c.2968A>G	c.(2968-2970)Agg>Ggg	p.R990G	AC068754.1_ENST00000408547.1_RNA|CASR_ENST00000296154.5_Missense_Mutation_p.R990G|CASR_ENST00000498619.1_Missense_Mutation_p.R1000G	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	990			R -> G (associated with low serum level of calcium; dbSNP:rs1042636). {ECO:0000269|PubMed:12050233, ECO:0000269|PubMed:14985373, ECO:0000269|PubMed:15531522, ECO:0000269|PubMed:15551332, ECO:0000269|PubMed:17698911, ECO:0000269|PubMed:18756473, ECO:0000269|PubMed:7759551, ECO:0000269|Ref.5}.		anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	CATGGCCCACAGGAATTCTAC	0.577													A|||	1034	0.20647	0.0303	0.1988	5008	,	,		19982	0.5198		0.0736	False		,,,				2504	0.2638				p.R1000G		Atlas-SNP	.											.	CASR	190	.	0			c.A2998G	GRCh37	CM044584	CASR	M	rs1042636	PASS	.	A	GLY/ARG,GLY/ARG	189,4217	118.4+/-156.1	4,181,2018	64.0	61.0	62.0		2968,2998	3.3	1.0	3	dbSNP_86	62	629,7971	163.6+/-216.1	20,589,3691	yes	missense,missense	CASR	NM_000388.3,NM_001178065.1	125,125	24,770,5709	GG,GA,AA		7.314,4.2896,6.2894	benign,benign	990/1079,1000/1089	122003769	818,12188	2203	4300	6503	SO:0001583	missense	846	exon7			GCCCACAGGAATT	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"""GPCR / Class C : Calcium-sensing receptors"""	1514	protein-coding gene	gene with protein product	"""severe neonatal hyperparathyroidism"""	601199	"""hypocalciuric hypercalcemia 1"""	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.2968A>G	3.37:g.122003769A>G	ENSP00000418685:p.Arg990Gly	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	271	123	0.453875	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	453	0.20741758241758243	14	0.028455284552845527	62	0.1712707182320442	315	0.5506993006993007	62	0.08179419525065963	A	10.86	1.469071	0.26335	0.042896	0.07314	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.89746	-2.56;-2.52;-2.56	5.79	3.26	0.37387	.	0.065488	0.56097	D	0.000022	T	0.00012	0.0000	L	0.27053	0.805	0.25725	P	0.9853387	B;B	0.31318	0.319;0.155	B;B	0.24155	0.051;0.051	T	0.43940	-0.9360	9	0.87932	D	0	.	11.8665	0.52496	0.7239:0.2761:0.0:0.0	rs1042636;rs3804596;rs52829576;rs59615814;rs1042636	1000;990	E7ENE0;P41180	.;CASR_HUMAN	G	990;1000;990	ENSP00000418685:R990G;ENSP00000420194:R1000G;ENSP00000296154:R990G	ENSP00000296154:R990G	R	+	1	2	CASR	123486459	1.000000	0.71417	0.996000	0.52242	0.582000	0.36321	2.918000	0.48829	1.004000	0.39156	0.459000	0.35465	AGG	A|0.871;G|0.129	0.129	strong		0.577	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388	
TRIM45	80263	hgsc.bcm.edu	37	1	117660754	117660754	+	Missense_Mutation	SNP	C	C	T	rs749902	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:117660754C>T	ENST00000256649.4	-	2	1650	c.1124G>A	c.(1123-1125)tGt>tAt	p.C375Y	TRIM45_ENST00000369464.3_Missense_Mutation_p.C375Y|TRIM45_ENST00000369461.3_Missense_Mutation_p.C318Y	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	375			C -> Y (in dbSNP:rs749902). {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)		CTCCTGAGGACAGAAGCGTAT	0.468													C|||	1125	0.224641	0.2103	0.3674	5008	,	,		21820	0.0327		0.3529	False		,,,				2504	0.2086				p.C375Y		Atlas-SNP	.											.	TRIM45	55	.	0			c.G1124A						PASS	.	C	TYR/CYS,TYR/CYS	1014,3392	379.7+/-323.4	123,768,1312	127.0	127.0	127.0		1124,1124	0.7	0.9	1	dbSNP_86	127	2832,5768	447.2+/-361.5	470,1892,1938	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	194,194	593,2660,3250	TT,TC,CC		32.9302,23.0141,29.571	benign,benign	375/563,375/581	117660754	3846,9160	2203	4300	6503	SO:0001583	missense	80263	exon2			TGAGGACAGAAGC		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.1124G>A	1.37:g.117660754C>T	ENSP00000256649:p.Cys375Tyr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	190	101	0.531579	NM_001145635	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	509	0.23305860805860806	103	0.20934959349593496	125	0.3453038674033149	17	0.02972027972027972	264	0.3482849604221636	C	0.003	-2.538963	0.00143	0.230141	0.329302	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	T;D;T	0.81996	-1.38;-1.56;-1.09	4.75	0.722	0.18225	.	0.676676	0.15867	N	0.240719	T	0.31918	0.0812	N	0.03608	-0.345	0.47698	P	5.020000000000024E-4	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.03945	-1.0990	9	0.07482	T	0.82	-0.4557	5.3998	0.16288	0.2396:0.2863:0.4741:0.0	rs749902;rs52795064;rs58937492;rs749902	375;375	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	Y	375;375;318	ENSP00000256649:C375Y;ENSP00000358476:C375Y;ENSP00000358473:C318Y	ENSP00000256649:C375Y	C	-	2	0	TRIM45	117462277	0.990000	0.36364	0.888000	0.34837	0.040000	0.13550	1.358000	0.34102	-0.013000	0.14199	-0.165000	0.13383	TGT	C|0.742;T|0.258	0.258	strong		0.468	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
SPHKAP	80309	hgsc.bcm.edu	37	2	228884530	228884530	+	Missense_Mutation	SNP	G	G	A	rs61752225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228884530G>A	ENST00000392056.3	-	7	1086	c.1040C>T	c.(1039-1041)tCc>tTc	p.S347F	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S347F	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	347						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)		ATCCATCATGGAGAAATAAGC	0.428													G|||	12	0.00239617	0.0015	0.0058	5008	,	,		11672	0.0		0.004	False		,,,				2504	0.002				p.S347F		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,-1,4	SPHKAP	750	4	0			c.C1040T						PASS	.	G	PHE/SER,PHE/SER	1,4405	2.1+/-5.4	0,1,2202	140.0	133.0	135.0		1040,1040	3.8	0.5	2	dbSNP_129	135	40,8560	26.8+/-75.7	0,40,4260	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	155,155	0,41,6462	AA,AG,GG		0.4651,0.0227,0.3152	benign,benign	347/1701,347/1672	228884530	41,12965	2203	4300	6503	SO:0001583	missense	80309	exon7			ATCATGGAGAAAT		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.1040C>T	2.37:g.228884530G>A	ENSP00000375909:p.Ser347Phe	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	264	119	0.450758	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	11	0.005036630036630037	4	0.008130081300813009	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	10.13	1.267055	0.23136	2.27E-4	0.004651	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12984	2.63;2.63	5.78	3.84	0.44239	.	1.477610	0.03572	N	0.228681	T	0.20007	0.0481	M	0.62723	1.935	0.09310	N	1	P;P	0.42993	0.612;0.797	B;P	0.47528	0.259;0.549	T	0.25293	-1.0136	10	0.72032	D	0.01	.	10.8001	0.46483	0.0:0.1313:0.7185:0.1502	rs61752225	347;347	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	F	347	ENSP00000375909:S347F;ENSP00000339886:S347F	ENSP00000339886:S347F	S	-	2	0	SPHKAP	228592774	0.820000	0.29190	0.537000	0.28052	0.062000	0.15995	2.710000	0.47169	2.742000	0.94016	0.650000	0.86243	TCC	G|0.997;A|0.003	0.003	strong		0.428	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
ATP12A	479	hgsc.bcm.edu	37	13	25272833	25272833	+	Missense_Mutation	SNP	G	G	A	rs41288280	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25272833G>A	ENST00000381946.3	+	12	1717	c.1550G>A	c.(1549-1551)cGc>cAc	p.R517H	ATP12A_ENST00000218548.6_Missense_Mutation_p.R523H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	517					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)	p.R517L(1)		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)		CACGGCAAGCGCTTCCTCATG	0.547													G|||	73	0.0145767	0.0242	0.0115	5008	,	,		20369	0.0		0.0209	False		,,,				2504	0.0123				p.R523H	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											ATP12A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ATP12A	172	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1568A						PASS	.	G	HIS/ARG,HIS/ARG	122,4284	91.1+/-129.8	3,116,2084	70.0	67.0	68.0		1568,1550	5.9	0.9	13	dbSNP_127	68	114,8486	61.0+/-122.8	2,110,4188	yes	missense,missense	ATP12A	NM_001185085.1,NM_001676.5	29,29	5,226,6272	AA,AG,GG		1.3256,2.769,1.8145	probably-damaging,probably-damaging	523/1046,517/1040	25272833	236,12770	2203	4300	6503	SO:0001583	missense	479	exon12			GCAAGCGCTTCCT	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.1550G>A	13.37:g.25272833G>A	ENSP00000371372:p.Arg517His	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	34	0.015567765567765568	11	0.022357723577235773	6	0.016574585635359115	1	0.0017482517482517483	16	0.021108179419525065	G	14.11	2.437143	0.43224	0.02769	0.013256	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.79845	-1.31;-1.31	5.87	5.87	0.94306	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.46464	0.1394	L	0.35341	1.055	0.58432	D	0.999999	P;P	0.43287	0.802;0.79	B;B	0.29524	0.103;0.076	T	0.67452	-0.5667	10	0.49607	T	0.09	.	17.713	0.88327	0.0:0.0:1.0:0.0	rs41288280;rs61739333	523;517	P54707-2;P54707	.;AT12A_HUMAN	H	523;517	ENSP00000218548:R523H;ENSP00000371372:R517H	ENSP00000218548:R523H	R	+	2	0	ATP12A	24170833	1.000000	0.71417	0.937000	0.37676	0.087000	0.18053	6.891000	0.75639	2.780000	0.95670	0.655000	0.94253	CGC	G|0.984;A|0.016	0.016	strong		0.547	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
VILL	50853	hgsc.bcm.edu	37	3	38047954	38047954	+	Missense_Mutation	SNP	G	G	C	rs9816693	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:38047954G>C	ENST00000283713.6	+	19	2486	c.2220G>C	c.(2218-2220)ttG>ttC	p.L740F	VILL_ENST00000383759.2_Missense_Mutation_p.L740F|VILL_ENST00000465644.1_Missense_Mutation_p.L458F			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						PASS	.	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	141	0	0		WXS	Illumina HiSeq	Phase_I	141	49	0.347518	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	
BEST2	54831	hgsc.bcm.edu	37	19	12863429	12863429	+	Missense_Mutation	SNP	G	G	A	rs79300835	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12863429G>A	ENST00000549706.1	+	2	347	c.23G>A	c.(22-24)cGa>cAa	p.R8Q	BEST2_ENST00000042931.1_Missense_Mutation_p.R8Q|BEST2_ENST00000553030.1_Missense_Mutation_p.R8Q			Q8NFU1	BEST2_HUMAN	bestrophin 2	8					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						TACACAGCCCGAGTGGCGAAC	0.672													G|||	146	0.0291534	0.0023	0.0476	5008	,	,		9341	0.0		0.0775	False		,,,				2504	0.0327				p.R8Q		Atlas-SNP	.											.	BEST2	35	.	0			c.G23A						PASS	.	G	GLN/ARG	53,4111		0,53,2029	52.0	53.0	53.0		23	3.5	0.9	19	dbSNP_131	53	682,7748		26,630,3559	yes	missense	BEST2	NM_017682.2	43	26,683,5588	AA,AG,GG		8.0902,1.2728,5.8361	possibly-damaging	8/510	12863429	735,11859	2082	4215	6297	SO:0001583	missense	54831	exon1			CAGCCCGAGTGGC	AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17107	protein-coding gene	gene with protein product		607335	"""vitelliform macular dystrophy 2-like 1"""	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.23G>A	19.37:g.12863429G>A	ENSP00000448310:p.Arg8Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_017682	Q53YQ8|Q9NXP0	Missense_Mutation	SNP	ENST00000549706.1	37	CCDS42506.1	88	0.040293040293040296	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	60	0.079155672823219	G	16.60	3.169513	0.57584	0.012728	0.080902	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	D;D;D	0.98512	-4.97;-4.97;-4.97	3.55	3.55	0.40652	.	0.000000	0.49305	U	0.000148	T	0.61702	0.2368	N	0.19112	0.55	0.43364	D	0.995448	B	0.33739	0.422	B	0.34452	0.183	T	0.80106	-0.1521	10	0.27082	T	0.32	-17.5452	14.7592	0.69593	0.0:0.0:1.0:0.0	.	8	Q8NFU1	BEST2_HUMAN	Q	8	ENSP00000448310:R8Q;ENSP00000447203:R8Q;ENSP00000042931:R8Q	ENSP00000042931:R8Q	R	+	2	0	BEST2	12724429	0.141000	0.22595	0.919000	0.36401	0.717000	0.41224	2.748000	0.47483	1.944000	0.56390	0.313000	0.20887	CGA	G|0.937;A|0.063	0.063	strong		0.672	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682	
FCRL3	115352	hgsc.bcm.edu	37	1	157648543	157648543	+	Missense_Mutation	SNP	T	T	C	rs2282284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:157648543T>C	ENST00000368184.3	-	15	2453	c.2162A>G	c.(2161-2163)aAc>aGc	p.N721S	FCRL3_ENST00000368186.5_Missense_Mutation_p.N721S|FCRL3_ENST00000473231.1_5'UTR	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	721			N -> S (in dbSNP:rs2282284).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					ATTCTCATAGTTTTCTTCATC	0.498													T|||	287	0.0573083	0.0635	0.049	5008	,	,		20156	0.0486		0.0457	False		,,,				2504	0.0757				p.N721S		Atlas-SNP	.											.	FCRL3	163	.	0			c.A2162G						PASS	.	T	SER/ASN	271,4135	153.7+/-187.2	8,255,1940	182.0	158.0	166.0		2162	1.0	0.1	1	dbSNP_100	166	443,8157	133.6+/-191.1	13,417,3870	yes	missense	FCRL3	NM_052939.3	46	21,672,5810	CC,CT,TT		5.1512,6.1507,5.4898	benign	721/735	157648543	714,12292	2203	4300	6503	SO:0001583	missense	115352	exon15			TCATAGTTTTCTT	AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.2162A>G	1.37:g.157648543T>C	ENSP00000357167:p.Asn721Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_052939	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	117	0.05357142857142857	34	0.06910569105691057	20	0.055248618784530384	26	0.045454545454545456	37	0.048812664907651716	T	9.809	1.182609	0.21870	0.061507	0.051512	ENSG00000160856	ENST00000368186;ENST00000368184	T;T	0.48201	0.83;0.82	3.37	1.02	0.19986	.	.	.	.	.	T	0.13628	0.0330	L	0.31294	0.92	0.58432	P	1.0000000000287557E-6	B;P;B	0.37330	0.227;0.59;0.297	B;B;B	0.31686	0.043;0.113;0.134	T	0.04579	-1.0941	8	0.87932	D	0	.	5.3752	0.16162	0.0:0.2236:0.0:0.7764	rs2282284;rs52789839;rs57694319;rs2282284	721;626;721	Q96P31;D3DVD1;Q96P31-6	FCRL3_HUMAN;.;.	S	721	ENSP00000357169:N721S;ENSP00000357167:N721S	ENSP00000357167:N721S	N	-	2	0	FCRL3	155915167	0.183000	0.23186	0.125000	0.21846	0.018000	0.09664	0.068000	0.14531	0.182000	0.20032	0.533000	0.62120	AAC	T|0.948;C|0.052	0.052	strong		0.498	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939	
CENPF	1063	hgsc.bcm.edu	37	1	214819328	214819328	+	Missense_Mutation	SNP	G	G	A	rs3748695	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214819328G>A	ENST00000366955.3	+	13	6583	c.6415G>A	c.(6415-6417)Gca>Aca	p.A2139T		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2235	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)		GCTGCACATCGCAGAGAAACT	0.478													G|||	532	0.10623	0.1089	0.1066	5008	,	,		19428	0.1151		0.0507	False		,,,				2504	0.1503				p.A2139T	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,1	CENPF	321	1	0			c.G6415A						PASS	.	G	THR/ALA	435,3971	208.2+/-229.3	22,391,1790	67.0	65.0	66.0		6415	-10.9	0.0	1	dbSNP_107	66	467,8133	136.8+/-193.9	12,443,3845	yes	missense	CENPF	NM_016343.3	58	34,834,5635	AA,AG,GG		5.4302,9.8729,6.9353	benign	2139/3115	214819328	902,12104	2203	4300	6503	SO:0001583	missense	1063	exon13			CACATCGCAGAGA	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.6415G>A	1.37:g.214819328G>A	ENSP00000355922:p.Ala2139Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	223	0.1021062271062271	64	0.13008130081300814	40	0.11049723756906077	77	0.1346153846153846	42	0.055408970976253295	G	0.555	-0.847583	0.02651	0.098729	0.054302	ENSG00000117724	ENST00000366955	T	0.43294	0.95	5.46	-10.9	0.00192	Centromere protein Cenp-F, leucine-rich repeat-containing domain (1);	1.161280	0.06766	N	0.782730	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	B	0.21309	0.054	B	0.09377	0.004	T	0.06127	-1.0844	9	0.20046	T	0.44	.	0.6715	0.00859	0.3498:0.2526:0.2008:0.1969	rs3748695;rs52791429;rs3748695	2235	P49454	CENPF_HUMAN	T	2139	ENSP00000355922:A2139T	ENSP00000355922:A2139T	A	+	1	0	CENPF	212885951	0.001000	0.12720	0.000000	0.03702	0.042000	0.13812	0.069000	0.14552	-2.264000	0.00689	-0.192000	0.12808	GCA	G|0.915;A|0.085	0.085	strong		0.478	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
G6PC3	92579	hgsc.bcm.edu	37	17	42152103	42152103	+	Silent	SNP	G	G	A	rs3815076	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42152103G>A	ENST00000269097.4	+	3	612	c.381G>A	c.(379-381)acG>acA	p.T127T		NM_138387.3	NP_612396.1	Q9BUM1	G6PC3_HUMAN	glucose 6 phosphatase, catalytic, 3	127					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucose-6-phosphatase activity (GO:0004346)			endometrium(2)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	11		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CCATAATGACGGCCCTGTCTT	0.587													G|||	1352	0.269968	0.0908	0.3213	5008	,	,		18006	0.7093		0.0825	False		,,,				2504	0.2157				p.T127T		Atlas-SNP	.											.	G6PC3	26	.	0			c.G381A						PASS	.	G		469,3937	219.7+/-237.4	28,413,1762	39.0	38.0	38.0		381	-10.1	0.2	17	dbSNP_107	38	641,7959	163.5+/-216.0	27,587,3686	no	coding-synonymous	G6PC3	NM_138387.3		55,1000,5448	AA,AG,GG		7.4535,10.6446,8.5345		127/347	42152103	1110,11896	2203	4300	6503	SO:0001819	synonymous_variant	92579	exon3			AATGACGGCCCTG	BC021574	CCDS11476.1	17q21.31	2014-09-17				ENSG00000141349			24861	protein-coding gene	gene with protein product		611045				12370122, 12965222	Standard	NM_138387		Approved	UGRP	uc002iex.3	Q9BUM1		ENST00000269097.4:c.381G>A	17.37:g.42152103G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_138387	Q8WU15	Silent	SNP	ENST00000269097.4	37	CCDS11476.1																																																																																			G|0.834;A|0.166	0.166	strong		0.587	G6PC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457675.1	NM_138387	
ARAP2	116984	hgsc.bcm.edu	37	4	36069805	36069805	+	Silent	SNP	G	G	A	rs7657166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:36069805G>A	ENST00000303965.4	-	33	5328	c.4839C>T	c.(4837-4839)gcC>gcT	p.A1613A		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1613					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						CCAGGCAGTGGGCCACCATGG	0.517													G|||	778	0.155351	0.0204	0.2061	5008	,	,		18703	0.0913		0.2803	False		,,,				2504	0.2393				p.A1613A		Atlas-SNP	.											.	ARAP2	210	.	0			c.C4839T						PASS	.	G		314,4092	168.3+/-199.2	12,290,1901	102.0	103.0	103.0		4839	3.4	1.0	4	dbSNP_116	103	2765,5835	438.1+/-358.8	474,1817,2009	no	coding-synonymous	ARAP2	NM_015230.3		486,2107,3910	AA,AG,GG		32.1512,7.1266,23.6737		1613/1705	36069805	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	116984	exon33			GCAGTGGGCCACC	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.4839C>T	4.37:g.36069805G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	37	CCDS3441.1																																																																																			G|0.777;A|0.223	0.223	strong		0.517	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
PPP4R1	9989	hgsc.bcm.edu	37	18	9562042	9562042	+	Missense_Mutation	SNP	C	C	T	rs2306134	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	172	0	0		WXS	Illumina HiSeq	Phase_I	171	93	0.54386	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	
GAL3ST2	64090	hgsc.bcm.edu	37	2	242742875	242742875	+	Missense_Mutation	SNP	C	C	T	rs62620233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242742875C>T	ENST00000192314.6	+	4	622	c.491C>T	c.(490-492)gCc>gTc	p.A164V	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	164					biosynthetic process (GO:0009058)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TTCCGGGGCGCCCCGAGCCTG	0.607													C|||	790	0.157748	0.1581	0.2032	5008	,	,		14441	0.1964		0.1044	False		,,,				2504	0.1401				p.A164V		Atlas-SNP	.											GAL3ST2,colon,carcinoma,+1,1	GAL3ST2	34	1	0			c.C491T						PASS	.	C	VAL/ALA	700,3702	252.4+/-258.8	62,576,1563	31.0	32.0	31.0		491	-1.0	0.0	2	dbSNP_129	31	827,7769	176.5+/-226.3	40,747,3511	yes	missense	GAL3ST2	NM_022134.2	64	102,1323,5074	TT,TC,CC		9.6208,15.9019,11.748	benign	164/399	242742875	1527,11471	2201	4298	6499	SO:0001583	missense	64090	exon4			GGGGCGCCCCGAG	AB040610	CCDS33427.1	2q37.2	2014-05-19			ENSG00000154252	ENSG00000154252		"""Sulfotransferases, membrane-bound"""	24869	protein-coding gene	gene with protein product		608237				11029462	Standard	NM_022134		Approved	GP3ST	uc002wcj.1	Q9H3Q3	OTTHUMG00000151473	ENST00000192314.6:c.491C>T	2.37:g.242742875C>T	ENSP00000192314:p.Ala164Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_022134	Q17RK0|Q57Z52	Missense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	307	0.14056776556776557	74	0.15040650406504066	59	0.16298342541436464	103	0.18006993006993008	71	0.09366754617414248	C	11.77	1.737866	0.30774	0.159019	0.096208	ENSG00000154252	ENST00000192314	T	0.12147	2.71	4.39	-0.998	0.10212	.	1.225170	0.05750	N	0.602914	T	0.00012	0.0000	N	0.11870	0.19	0.80722	P	0.0	B	0.14805	0.011	B	0.16289	0.015	T	0.45205	-0.9277	9	0.23891	T	0.37	-7.5969	8.759	0.34663	0.0:0.5757:0.0:0.4243	rs62620233	164	Q9H3Q3	G3ST2_HUMAN	V	164	ENSP00000192314:A164V	ENSP00000192314:A164V	A	+	2	0	GAL3ST2	242391548	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.125000	0.10579	-0.193000	0.10415	-0.391000	0.06502	GCC	C|0.884;T|0.116	0.116	strong		0.607	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134	
OR5H2	79310	hgsc.bcm.edu	37	3	98002587	98002587	+	Missense_Mutation	SNP	A	A	G	rs16839611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:98002587A>G	ENST00000355273.2	+	1	856	c.856A>G	c.(856-858)Ata>Gta	p.I286V	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	286			I -> V (in dbSNP:rs16839611).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						TTATACAATCATAATTCCTTT	0.328													A|||	2547	0.508586	0.6626	0.4524	5008	,	,		17384	0.75		0.2296	False		,,,				2504	0.3783				p.I286V		Atlas-SNP	.											.	OR5H2	63	.	0			c.A856G						PASS	.	A	VAL/ILE	2689,1717	644.4+/-398.0	815,1059,329	53.0	51.0	51.0		856	-1.4	0.0	3	dbSNP_123	51	2102,6498	358.0+/-331.0	273,1556,2471	yes	missense	OR5H2	NM_001005482.1	29	1088,2615,2800	GG,GA,AA		24.4419,38.9696,36.8368	possibly-damaging	286/315	98002587	4791,8215	2203	4300	6503	SO:0001583	missense	79310	exon1			ACAATCATAATTC		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"""GPCR / Class A : Olfactory receptors"""	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.856A>G	3.37:g.98002587A>G	ENSP00000347418:p.Ile286Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	1099	0.5032051282051282	316	0.6422764227642277	152	0.4198895027624309	451	0.7884615384615384	180	0.23746701846965698	A	0	-2.745156	0.00087	0.610304	0.244419	ENSG00000197938	ENST00000355273	T	0.00018	9.07	3.03	-1.37	0.09056	GPCR, rhodopsin-like superfamily (1);	0.337021	0.21263	N	0.077457	T	0.00012	0.0000	N	0.02403	-0.565	0.80722	P	0.0	P	0.46706	0.883	P	0.50570	0.644	T	0.48502	-0.9030	9	0.02654	T	1	.	4.6526	0.12603	0.4826:0.3037:0.2137:0.0	rs16839611;rs52809881;rs61556920;rs16839611	286	Q8NGV7	OR5H2_HUMAN	V	286	ENSP00000347418:I286V	ENSP00000347418:I286V	I	+	1	0	OR5H2	99485277	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	-0.054000	0.11826	-0.778000	0.04566	-1.509000	0.00949	ATA	A|0.567;G|0.433	0.433	strong		0.328	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
UGT2A1	10941	hgsc.bcm.edu	37	4	70512801	70512801	+	Missense_Mutation	SNP	A	A	G	rs55864295	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70512801A>G	ENST00000503640.1	-	1	617	c.562T>C	c.(562-564)Tac>Cac	p.Y188H	UGT2A1_ENST00000514019.1_Missense_Mutation_p.Y188H|UGT2A1_ENST00000512704.1_Missense_Mutation_p.Y188H|UGT2A1_ENST00000286604.4_Missense_Mutation_p.Y188H	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	188					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						GAAGGAGGGTATGGTACCTTC	0.418													A|||	351	0.0700879	0.0038	0.0807	5008	,	,		19321	0.001		0.161	False		,,,				2504	0.1299				p.Y188H		Atlas-SNP	.											.	UGT2A1	131	.	0			c.T562C						PASS	.	A	HIS/TYR	167,4237	110.4+/-148.6	4,159,2039	98.0	84.0	89.0		562	3.3	0.1	4	dbSNP_129	89	1586,7012	295.7+/-302.5	139,1308,2852	yes	missense	UGT2A1	NM_006798.2	83	143,1467,4891	GG,GA,AA		18.4462,3.792,13.4825	benign	188/528	70512801	1753,11249	2202	4299	6501	SO:0001583	missense	10941	exon2			GAGGGTATGGTAC	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.562T>C	4.37:g.70512801A>G	ENSP00000424478:p.Tyr188His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	149	0.06822344322344322	3	0.006097560975609756	31	0.0856353591160221	0	0.0	115	0.1517150395778364	A	2.661	-0.279681	0.05642	0.03792	0.184462	ENSG00000173610	ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T	0.60424	0.19;0.19;0.19;0.28	5.78	3.26	0.37387	.	0.757353	0.13093	N	0.414354	T	0.00109	0.0003	N	0.08118	0	.	.	.	B;P;B;B	0.46142	0.003;0.873;0.001;0.0	B;P;B;B	0.49140	0.007;0.601;0.001;0.001	T	0.02275	-1.1184	9	0.15952	T	0.53	.	7.6491	0.28337	0.7146:0.146:0.0:0.1394	rs55864295	188;188;188;188	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1	.;.;.;UD2A1_HUMAN	H	188	ENSP00000424478:Y188H;ENSP00000421432:Y188H;ENSP00000425497:Y188H;ENSP00000286604:Y188H	ENSP00000286604:Y188H	Y	-	1	0	UGT2A1	70547390	0.001000	0.12720	0.064000	0.19789	0.570000	0.35934	0.773000	0.26661	0.419000	0.25927	0.482000	0.46254	TAC	A|0.882;G|0.118	0.118	strong		0.418	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410775	105410775	+	Silent	SNP	A	A	G	rs2819424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	188	0	0		WXS	Illumina HiSeq	Phase_I	197	197	1	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	
TMCO3	55002	hgsc.bcm.edu	37	13	114152755	114152755	+	Silent	SNP	C	C	T	rs2260218	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:114152755C>T	ENST00000434316.2	+	3	902	c.543C>T	c.(541-543)gaC>gaT	p.D181D	TMCO3_ENST00000474393.1_3'UTR|TMCO3_ENST00000375391.1_Silent_p.D181D	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	78	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	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	
CELSR2	1952	hgsc.bcm.edu	37	1	109811522	109811522	+	Missense_Mutation	SNP	G	G	A	rs148006855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109811522G>A	ENST00000271332.3	+	19	6584	c.6523G>A	c.(6523-6525)Gac>Aac	p.D2175N		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2175					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		AGTGCGCTTGGACAAAGGGAA	0.622													G|||	25	0.00499201	0.0	0.0	5008	,	,		19345	0.0		0.002	False		,,,				2504	0.0235				p.D2175N	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											CELSR2,NS,neuroblastoma,-2,1	CELSR2	228	1	0			c.G6523A						PASS	.	G	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	71.0	76.0	74.0		6523	4.4	1.0	1	dbSNP_134	74	9,8591	7.1+/-27.0	0,9,4291	yes	missense	CELSR2	NM_001408.2	23	0,11,6492	AA,AG,GG		0.1047,0.0454,0.0846	benign	2175/2924	109811522	11,12995	2203	4300	6503	SO:0001583	missense	1952	exon19			CGCTTGGACAAAG	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6523G>A	1.37:g.109811522G>A	ENSP00000271332:p.Asp2175Asn	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	168	68	0.404762	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.84	2.356070	0.41700	4.54E-4	0.001047	ENSG00000143126	ENST00000271332	T	0.10860	2.83	4.36	4.36	0.52297	Domain of unknown function DUF3497 (1);	.	.	.	.	T	0.05410	0.0143	L	0.48642	1.525	0.34853	D	0.741849	B	0.26935	0.164	B	0.28709	0.093	T	0.09443	-1.0674	9	0.52906	T	0.07	.	10.689	0.45860	0.0898:0.0:0.9102:0.0	.	2175	Q9HCU4	CELR2_HUMAN	N	2175	ENSP00000271332:D2175N	ENSP00000271332:D2175N	D	+	1	0	CELSR2	109613045	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.180000	0.50895	2.430000	0.82344	0.462000	0.41574	GAC	G|0.999;A|0.001	0.001	strong		0.622	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
RRP12	23223	hgsc.bcm.edu	37	10	99141484	99141484	+	Silent	SNP	C	C	T	rs12218483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99141484C>T	ENST00000370992.4	-	11	1419	c.1308G>A	c.(1306-1308)acG>acA	p.T436T	RRP12_ENST00000315563.6_Silent_p.T336T|RRP12_ENST00000536831.1_Silent_p.T154T|RRP12_ENST00000414986.1_Silent_p.T375T	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	436						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TGAGGCTCTGCGTAGCAGCAG	0.602													C|||	1316	0.26278	0.1377	0.2579	5008	,	,		18072	0.3125		0.2604	False		,,,				2504	0.3865				p.T436T		Atlas-SNP	.											RRP12,colon,carcinoma,0,8	RRP12	97	8	0			c.G1308A						PASS	.	C	,	662,3744	283.4+/-277.1	50,562,1591	67.0	56.0	60.0		1125,1308	1.6	1.0	10	dbSNP_120	60	2179,6421	371.9+/-336.4	281,1617,2402	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	331,2179,3993	TT,TC,CC		25.3372,15.025,21.8438	,	375/1237,436/1298	99141484	2841,10165	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon11			GCTCTGCGTAGCA		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.1308G>A	10.37:g.99141484C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	314	150	0.477707	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			C|0.769;T|0.231	0.231	strong		0.602	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
ABCC12	94160	hgsc.bcm.edu	37	16	48164777	48164777	+	Silent	SNP	T	T	C	rs12149826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:48164777T>C	ENST00000311303.3	-	8	1503	c.1158A>G	c.(1156-1158)gtA>gtG	p.V386V	ABCC12_ENST00000416054.1_Silent_p.V386V|ABCC12_ENST00000448542.1_Silent_p.V386V	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	386	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				AAAACTTCATTACATTAAACA	0.408													T|||	605	0.120807	0.0091	0.1931	5008	,	,		23511	0.0		0.2714	False		,,,				2504	0.1902				p.V386V		Atlas-SNP	.											.	ABCC12	190	.	0			c.A1158G						PASS	.	T		270,4132	150.3+/-184.3	10,250,1941	84.0	75.0	78.0		1158	-1.4	1.0	16	dbSNP_120	78	2634,5966	425.1+/-354.9	409,1816,2075	no	coding-synonymous	ABCC12	NM_033226.2		419,2066,4016	CC,CT,TT		30.6279,6.1336,22.335		386/1360	48164777	2904,10098	2201	4300	6501	SO:0001819	synonymous_variant	94160	exon8			CTTCATTACATTA	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.1158A>G	16.37:g.48164777T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			T|0.827;C|0.173	0.173	strong		0.408	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
POLR1D	51082	hgsc.bcm.edu	37	13	28239940	28239940	+	Silent	SNP	G	G	C	rs11029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28239940G>C	ENST00000399697.3	+	3	337	c.219G>C	c.(217-219)gcG>gcC	p.A73A	POLR1D_ENST00000465887.1_3'UTR	NM_001206559.1|NM_152705.2	NP_001193488.1|NP_689918.1	Q9Y2S0	RPAC2_HUMAN	polymerase (RNA) I polypeptide D, 16kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.A73A(1)		endometrium(1)|large_intestine(1)|lung(4)|stomach(2)	8		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0758)|OV - Ovarian serous cystadenocarcinoma(117;0.1)|Epithelial(112;0.213)		AGGAACCAGCGAAGAGCCAGG	0.468													G|||	1291	0.257788	0.0424	0.5245	5008	,	,		18058	0.2381		0.336	False		,,,				2504	0.2996				p.A73A		Atlas-SNP	.											POLR1D,caecum,carcinoma,0,2	POLR1D	31	2	1	Substitution - coding silent(1)	stomach(1)	c.G219C						PASS	.	G	,	406,4000	201.5+/-224.5	26,354,1823	101.0	101.0	101.0		135,219	-3.2	0.0	13	dbSNP_52	101	3050,5550	468.2+/-367.2	527,1996,1777	no	coding-synonymous,coding-synonymous	POLR1D	NM_001206559.1,NM_152705.2	,	553,2350,3600	CC,CG,GG		35.4651,9.2147,26.5724	,	45/95,73/123	28239940	3456,9550	2203	4300	6503	SO:0001819	synonymous_variant	51082	exon3			ACCAGCGAAGAGC	AF077044, BC018528	CCDS9324.1, CCDS9325.1, CCDS73555.1	13q12.2	2013-01-21			ENSG00000186184	ENSG00000186184		"""RNA polymerase subunits"""	20422	protein-coding gene	gene with protein product		613715				11042152, 12391170	Standard	NM_015972		Approved	RPAC2, RPA16, RPO1-3, RPA9, MGC9850	uc001urp.3	Q9Y2S0	OTTHUMG00000016635	ENST00000399697.3:c.219G>C	13.37:g.28239940G>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_152705	Q5TBX2|Q96BR3	Silent	SNP	ENST00000399697.3	37	CCDS9324.1																																																																																			G|0.739;C|0.261	0.261	strong		0.468	POLR1D-004	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044306.1	NM_015972, NM_152705	
TPSD1	23430	hgsc.bcm.edu	37	16	1306921	1306921	+	Silent	SNP	G	G	A	rs78324915	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306921G>A	ENST00000211076.3	+	3	526	c.378G>A	c.(376-378)ggG>ggA	p.G126G	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.G119G	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	126	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G126G(2)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TCCAGACCGGGGCGGACATCG	0.647																																					p.G126G		Atlas-SNP	.											TPSD1,NS,carcinoma,0,2	TPSD1	47	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.G378A						PASS	.						77.0	75.0	76.0					16																	1306921		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			GACCGGGGCGGAC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.378G>A	16.37:g.1306921G>A		Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	603	210	0.348259	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			G|0.643;A|0.357	0.357	strong		0.647	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
GALNTL6	442117	hgsc.bcm.edu	37	4	173232805	173232805	+	Silent	SNP	G	G	A	rs9312524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:173232805G>A	ENST00000506823.1	+	4	945	c.288G>A	c.(286-288)gaG>gaA	p.E96E	GALNTL6_ENST00000508122.1_Silent_p.E79E|GALNTL6_ENST00000457021.1_3'UTR	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	96					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)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TTACTGAAGAGGACCATGATG	0.388													G|||	522	0.104233	0.1558	0.0879	5008	,	,		15998	0.0089		0.1859	False		,,,				2504	0.0603				p.E96E		Atlas-SNP	.											.	GALNTL6	102	.	0			c.G288A						PASS	.	G		666,3740	283.1+/-276.9	50,566,1587	131.0	131.0	131.0		288	0.1	1.0	4	dbSNP_119	131	1609,6991	297.8+/-303.6	160,1289,2851	no	coding-synonymous	GALNTL6	NM_001034845.2		210,1855,4438	AA,AG,GG		18.7093,15.1158,17.4919		96/602	173232805	2275,10731	2203	4300	6503	SO:0001819	synonymous_variant	442117	exon4			TGAAGAGGACCAT		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"""Glycosyltransferase family 2 domain containing"""	33844	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 6"""	615138	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"""				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.288G>A	4.37:g.173232805G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	184	88	0.478261	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	37	CCDS34104.1																																																																																			G|0.852;A|0.148	0.148	strong		0.388	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	
CHGB	1114	hgsc.bcm.edu	37	20	5903192	5903192	+	Silent	SNP	G	G	A	rs78101688	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:5903192G>A	ENST00000378961.4	+	4	606	c.402G>A	c.(400-402)gcG>gcA	p.A134A		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	134						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GAGAGCGAGCGGATGAGCCCC	0.612													G|||	103	0.0205671	0.0023	0.0418	5008	,	,		14179	0.0		0.0557	False		,,,				2504	0.0153				p.A134A		Atlas-SNP	.											.	CHGB	112	.	0			c.G402A						PASS	.	G		51,4355	50.2+/-85.5	0,51,2152	27.0	30.0	29.0		402	-10.5	0.0	20	dbSNP_132	29	467,8133	134.4+/-191.8	13,441,3846	no	coding-synonymous	CHGB	NM_001819.2		13,492,5998	AA,AG,GG		5.4302,1.1575,3.9828		134/678	5903192	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			GCGAGCGGATGAG		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.402G>A	20.37:g.5903192G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	37	CCDS13092.1																																																																																			A|0.036;C|0.000;G|0.964	0.036	strong		0.612	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
CHRDL2	25884	hgsc.bcm.edu	37	11	74413843	74413843	+	Silent	SNP	T	T	C	rs34695217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:74413843T>C	ENST00000376332.3	-	9	1612	c.1116A>G	c.(1114-1116)gtA>gtG	p.V372V	CHRDL2_ENST00000263671.5_Silent_p.V372V|CHRDL2_ENST00000534159.1_5'UTR	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	372					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)					ACTCACCTTTTACCAGCTTCC	0.612											OREG0021223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	203	0.0405351	0.0605	0.0173	5008	,	,		17089	0.0208		0.0338	False		,,,				2504	0.0573				p.V372V		Atlas-SNP	.											.	CHRDL2	47	.	0			c.A1116G						PASS	.	T		198,4202	124.5+/-161.8	5,188,2007	98.0	95.0	96.0		1116	-7.1	0.6	11	dbSNP_126	96	365,8221	122.0+/-181.0	7,351,3935	no	coding-synonymous	CHRDL2	NM_015424.3		12,539,5942	CC,CT,TT		4.2511,4.5,4.3354		372/452	74413843	563,12423	2200	4293	6493	SO:0001819	synonymous_variant	25884	exon9			ACCTTTTACCAGC	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.1116A>G	11.37:g.74413843T>C		Somatic	50	0	0	1152	WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_015424	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Silent	SNP	ENST00000376332.3	37																																																																																				T|0.957;C|0.043	0.043	strong		0.612	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1		
TTC22	55001	hgsc.bcm.edu	37	1	55266797	55266797	+	Missense_Mutation	SNP	G	G	C	rs671108	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:55266797G>C	ENST00000371276.4	-	1	143	c.40C>G	c.(40-42)Ctc>Gtc	p.L14V	TTC22_ENST00000371274.4_Missense_Mutation_p.L14V	NM_001114108.1	NP_001107580.1	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22	14			L -> V (in dbSNP:rs671108).							kidney(1)|large_intestine(1)|lung(7)|skin(1)	10						TCGTCGATGAGGGCGTCTAGA	0.662													G|||	769	0.153554	0.0265	0.2334	5008	,	,		13377	0.2639		0.2356	False		,,,				2504	0.0706				p.L14V		Atlas-SNP	.											.	TTC22	40	.	0			c.C40G						PASS	.	G	VAL/LEU,VAL/LEU	251,4141		11,229,1956	28.0	26.0	27.0		40,40	4.1	1.0	1	dbSNP_83	27	1735,6841		178,1379,2731	yes	missense,missense	TTC22	NM_001114108.1,NM_017904.3	32,32	189,1608,4687	CC,CG,GG		20.2309,5.7149,15.3146	probably-damaging,probably-damaging	14/570,14/373	55266797	1986,10982	2196	4288	6484	SO:0001583	missense	55001	exon1			CGATGAGGGCGTC	AK000626	CCDS598.1, CCDS44152.1	1p32.3	2013-01-11			ENSG00000006555	ENSG00000006555		"""Tetratricopeptide (TTC) repeat domain containing"""	26067	protein-coding gene	gene with protein product							Standard	NM_017904		Approved	FLJ20619	uc009vzt.1	Q5TAA0	OTTHUMG00000009916	ENST00000371276.4:c.40C>G	1.37:g.55266797G>C	ENSP00000360323:p.Leu14Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_001114108	Q9NWT4	Missense_Mutation	SNP	ENST00000371276.4	37	CCDS44152.1	435	0.19917582417582416	24	0.04878048780487805	87	0.24033149171270718	157	0.2744755244755245	167	0.22031662269129287	G	15.92	2.974554	0.53720	0.057149	0.202309	ENSG00000006555	ENST00000371276;ENST00000371274	T;T	0.60920	0.17;0.15	4.13	4.13	0.48395	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.61703	1.905	0.20489	P	0.999899774	D;D	0.76494	0.999;0.996	D;D	0.80764	0.987;0.994	T	0.01015	-1.1480	9	0.56958	D	0.05	-10.3499	15.6739	0.77300	0.0:0.0:1.0:0.0	rs671108;rs671108	14;14	Q5TAA0;Q5TAA0-2	TTC22_HUMAN;.	V	14	ENSP00000360323:L14V;ENSP00000360321:L14V	ENSP00000360321:L14V	L	-	1	0	TTC22	55039385	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.057000	0.41365	2.279000	0.76181	0.491000	0.48974	CTC	G|0.830;C|0.170	0.170	strong		0.662	TTC22-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027438.1	NM_017904	
AHNAK2	113146	hgsc.bcm.edu	37	14	105407208	105407208	+	Silent	SNP	T	T	C	rs11851053	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	73	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	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	
TXNL1	9352	hgsc.bcm.edu	37	18	54281790	54281790	+	Silent	SNP	T	T	C	rs655539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:54281790T>C	ENST00000217515.6	-	6	804	c.600A>G	c.(598-600)ctA>ctG	p.L200L	TXNL1_ENST00000590954.1_Silent_p.L200L|TXNL1_ENST00000540155.1_Silent_p.L77L	NM_004786.2	NP_004777.1	O43396	TXNL1_HUMAN	thioredoxin-like 1	200	PITH. {ECO:0000255|PROSITE- ProRule:PRU00864}.				cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		TAGATCGGGGTAGGTTGATAA	0.353													T|||	93	0.0185703	0.003	0.0216	5008	,	,		17755	0.0		0.0606	False		,,,				2504	0.0133				p.L200L		Atlas-SNP	.											.	TXNL1	30	.	0			c.A600G						PASS	.	T		56,4350	54.9+/-90.9	0,56,2147	95.0	90.0	92.0		600	-3.5	1.0	18	dbSNP_83	92	528,8072	148.2+/-203.4	13,502,3785	no	coding-synonymous	TXNL1	NM_004786.2		13,558,5932	CC,CT,TT		6.1395,1.271,4.4902		200/290	54281790	584,12422	2203	4300	6503	SO:0001819	synonymous_variant	9352	exon6			TCGGGGTAGGTTG	AF003938	CCDS11961.1	18q21.31	2011-01-17	2004-05-06	2004-05-07	ENSG00000091164	ENSG00000091164			12436	protein-coding gene	gene with protein product	"""thioredoxin-like, 32kD"""	603049	"""thioredoxin-like, 32kDa"""	TXNL		9473519, 9668102	Standard	NM_004786		Approved	Txl, TRP32	uc002lgg.3	O43396	OTTHUMG00000132722	ENST00000217515.6:c.600A>G	18.37:g.54281790T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_004786		Silent	SNP	ENST00000217515.6	37	CCDS11961.1																																																																																			T|0.962;C|0.038	0.038	strong		0.353	TXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256064.2		
NUF2	83540	hgsc.bcm.edu	37	1	163309219	163309219	+	Silent	SNP	A	A	T	rs1509022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:163309219A>T	ENST00000271452.3	+	8	837	c.558A>T	c.(556-558)ggA>ggT	p.G186G	NUF2_ENST00000524800.1_Silent_p.G186G|NUF2_ENST00000367900.3_Silent_p.G186G	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	186	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					TTTCAGATGGAATTCAGGAGC	0.338													T|||	2146	0.428514	0.32	0.4352	5008	,	,		18185	0.3512		0.4374	False		,,,				2504	0.6411				p.G186G		Atlas-SNP	.											.	NUF2	138	.	0			c.A558T						PASS	.	T	,	1515,2891	672.9+/-402.7	252,1011,940	95.0	93.0	94.0		558,558	-2.7	0.0	1	dbSNP_88	94	3907,4693	605.8+/-395.0	887,2133,1280	no	coding-synonymous,coding-synonymous	NUF2	NM_031423.3,NM_145697.2	,	1139,3144,2220	TT,TA,AA		45.4302,34.3849,41.6885	,	186/465,186/465	163309219	5422,7584	2203	4300	6503	SO:0001819	synonymous_variant	83540	exon8			AGATGGAATTCAG	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.558A>T	1.37:g.163309219A>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Silent	SNP	ENST00000271452.3	37	CCDS1245.1																																																																																			A|0.599;T|0.401	0.401	strong		0.338	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	
RNF123	63891	hgsc.bcm.edu	37	3	49751585	49751585	+	Silent	SNP	C	C	T	rs2291542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49751585C>T	ENST00000327697.6	+	31	3132	c.2988C>T	c.(2986-2988)gaC>gaT	p.D996D	RNF123_ENST00000433785.1_Silent_p.D108D	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	996					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)		AACTTGAGGACGCCAATTTGC	0.597													C|||	1254	0.250399	0.2519	0.2061	5008	,	,		19901	0.1538		0.3091	False		,,,				2504	0.319				p.D996D		Atlas-SNP	.											RNF123,caecum,carcinoma,0,1	RNF123	100	1	0			c.C2988T						PASS	.	C		1113,3293	399.2+/-331.1	143,827,1233	90.0	90.0	90.0		2988	-4.6	0.9	3	dbSNP_100	90	2588,6012	421.6+/-353.8	391,1806,2103	no	coding-synonymous	RNF123	NM_022064.2		534,2633,3336	TT,TC,CC		30.093,25.261,28.4561		996/1315	49751585	3701,9305	2203	4300	6503	SO:0001819	synonymous_variant	63891	exon31			TGAGGACGCCAAT	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.2988C>T	3.37:g.49751585C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1																																																																																			C|0.736;T|0.264	0.264	strong		0.597	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125826059	125826059	+	Missense_Mutation	SNP	T	T	C	rs1127717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:125826059T>C	ENST00000393434.2	-	21	2727	c.2378A>G	c.(2377-2379)gAc>gGc	p.D793G	ALDH1L1_ENST00000452905.2_Missense_Mutation_p.D692G|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.D803G|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.D793G	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	793	Aldehyde dehydrogenase.		D -> G (in dbSNP:rs1127717).		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)	GTCTTCCACGTCTGTGAAAAC	0.527													T|||	992	0.198083	0.2284	0.1571	5008	,	,		20773	0.126		0.2167	False		,,,				2504	0.2413				p.D803G		Atlas-SNP	.											ALDH1L1,caecum,carcinoma,-1,1	ALDH1L1	138	1	0			c.A2408G						PASS	.	T	GLY/ASP	940,3466	357.1+/-313.8	91,758,1354	160.0	139.0	146.0		2378	4.0	0.1	3	dbSNP_86	146	1855,6745	332.8+/-320.3	208,1439,2653	yes	missense	ALDH1L1	NM_012190.2	94	299,2197,4007	CC,CT,TT		21.5698,21.3345,21.4901	benign	793/903	125826059	2795,10211	2203	4300	6503	SO:0001583	missense	10840	exon21			TCCACGTCTGTGA	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.2378A>G	3.37:g.125826059T>C	ENSP00000377083:p.Asp793Gly	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	406	0.1858974358974359	112	0.22764227642276422	68	0.1878453038674033	66	0.11538461538461539	160	0.21108179419525067	T	10.41	1.342416	0.24339	0.213345	0.215698	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	3.98	3.98	0.46160	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.341755	0.29668	N	0.011517	T	0.00073	0.0002	N	0.25426	0.745	0.20403	P	0.9999034691	B;B;B	0.18741	0.011;0.03;0.003	B;B;B	0.31495	0.058;0.131;0.04	T	0.12091	-1.0561	9	0.48119	T	0.1	.	10.8723	0.46891	0.0:0.0:0.0:1.0	rs1127717;rs16837129;rs1127717	692;328;793	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	G	803;793;692;793	ENSP00000273450:D803G;ENSP00000420293:D793G;ENSP00000395881:D692G;ENSP00000377083:D793G	ENSP00000273450:D803G	D	-	2	0	ALDH1L1	127308749	0.928000	0.31464	0.149000	0.22428	0.533000	0.34776	3.804000	0.55568	1.677000	0.50941	0.260000	0.18958	GAC	T|0.800;C|0.200	0.200	strong		0.527	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
DNAH3	55567	hgsc.bcm.edu	37	16	21151913	21151913	+	Missense_Mutation	SNP	G	G	T	rs72780891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:21151913G>T	ENST00000261383.3	-	5	639	c.640C>A	c.(640-642)Cag>Aag	p.Q214K	DNAH3_ENST00000415178.1_Missense_Mutation_p.Q214K|DNAH3_ENST00000575491.1_5'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	214	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		ATCTCCTGCTGTAACATGACA	0.488													G|||	856	0.170927	0.0968	0.2954	5008	,	,		22605	0.129		0.1869	False		,,,				2504	0.2096				p.Q214K		Atlas-SNP	.											DNAH3_ENST00000261383,colon,carcinoma,0,2	DNAH3	1142	2	0			c.C640A						PASS	.	G	LYS/GLN	531,3871	240.6+/-251.3	33,465,1703	275.0	222.0	240.0		640	4.1	1.0	16	dbSNP_130	240	1751,6849	319.2+/-314.1	183,1385,2732	yes	missense	DNAH3	NM_017539.1	53	216,1850,4435	TT,TG,GG		20.3605,12.0627,17.5511	benign	214/4117	21151913	2282,10720	2201	4300	6501	SO:0001583	missense	55567	exon5			CCTGCTGTAACAT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.640C>A	16.37:g.21151913G>T	ENSP00000261383:p.Gln214Lys	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	179	90	0.502793	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	355	0.16254578754578755	45	0.09146341463414634	90	0.24861878453038674	65	0.11363636363636363	155	0.20448548812664907	G	8.534	0.871685	0.17322	0.120627	0.203605	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.20881	2.04;2.21	5.07	4.1	0.47936	.	0.771253	0.12304	N	0.480826	T	0.00012	0.0000	L	0.42245	1.32	0.40662	P	0.017862000000000045	B;B	0.26363	0.001;0.147	B;B	0.25506	0.001;0.061	T	0.35574	-0.9783	9	0.05525	T	0.97	.	3.8791	0.09071	0.0866:0.1655:0.5763:0.1716	.	214;185	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	K	214;214;185	ENSP00000261383:Q214K;ENSP00000394245:Q214K	ENSP00000261383:Q214K	Q	-	1	0	DNAH3	21059414	0.540000	0.26410	1.000000	0.80357	0.906000	0.53458	0.697000	0.25556	1.318000	0.45170	0.655000	0.94253	CAG	G|0.825;T|0.175	0.175	strong		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
SETBP1	26040	hgsc.bcm.edu	37	18	42529996	42529996	+	Missense_Mutation	SNP	G	G	C	rs11082414	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:42529996G>C	ENST00000282030.5	+	4	987	c.691G>C	c.(691-693)Gtc>Ctc	p.V231L		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	231			V -> L (in dbSNP:rs11082414).			nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CAGCGGACCCGTCACTCAGAA	0.547									Schinzel-Giedion syndrome				G|||	785	0.156749	0.1664	0.1859	5008	,	,		18933	0.0139		0.2028	False		,,,				2504	0.2229				p.V231L		Atlas-SNP	.											.	SETBP1	577	.	0			c.G691C						PASS	.	G	LEU/VAL	652,3754	279.6+/-274.9	45,562,1596	85.0	79.0	81.0		691	-5.5	0.1	18	dbSNP_120	81	1758,6842	318.0+/-313.5	190,1378,2732	yes	missense	SETBP1	NM_015559.2	32	235,1940,4328	CC,CG,GG		20.4419,14.798,18.5299	benign	231/1597	42529996	2410,10596	2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	GGACCCGTCACTC	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.691G>C	18.37:g.42529996G>C	ENSP00000282030:p.Val231Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	313	0.1433150183150183	91	0.18495934959349594	63	0.17403314917127072	6	0.01048951048951049	153	0.20184696569920843	G	6.120	0.390461	0.11581	0.14798	0.204419	ENSG00000152217	ENST00000282030	T	0.35048	1.33	5.61	-5.47	0.02600	.	0.815246	0.11620	N	0.545835	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12630	0.006	B	0.14023	0.01	T	0.26052	-1.0114	9	0.42905	T	0.14	.	10.5593	0.45135	0.6081:0.0:0.305:0.0868	rs11082414;rs17794146;rs52816645;rs57788366;rs11082414	231	Q9Y6X0	SETBP_HUMAN	L	231	ENSP00000282030:V231L	ENSP00000282030:V231L	V	+	1	0	SETBP1	40783994	0.002000	0.14202	0.091000	0.20842	0.449000	0.32228	-0.123000	0.10611	-1.076000	0.03125	-0.768000	0.03414	GTC	A|0.000;C|0.168;G|0.832	0.168	strong		0.547	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
BRINP1	1620	hgsc.bcm.edu	37	9	121930416	121930416	+	Missense_Mutation	SNP	C	C	T	rs141766717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:121930416C>T	ENST00000265922.3	-	8	1693	c.1232G>A	c.(1231-1233)cGg>cAg	p.R411Q	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	411					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.R411Q(1)									CACGCAGCTCCGCTGGCTCTC	0.597													C|||	5	0.000998403	0.0015	0.0	5008	,	,		19155	0.002		0.0	False		,,,				2504	0.001				p.R411Q		Atlas-SNP	.											DBC1,NS,carcinoma,0,2	DBC1	194	2	1	Substitution - Missense(1)	lung(1)	c.G1232A						PASS	.	C	GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	20.0	18.0	19.0		1232	5.7	1.0	9	dbSNP_134	19	9,8591	7.1+/-27.0	0,9,4291	yes	missense	DBC1	NM_014618.2	43	0,15,6488	TT,TC,CC		0.1047,0.1362,0.1153	probably-damaging	411/762	121930416	15,12991	2203	4300	6503	SO:0001583	missense	1620	exon8			CAGCTCCGCTGGC	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.1232G>A	9.37:g.121930416C>T	ENSP00000265922:p.Arg411Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	24.4	4.525548	0.85600	0.001362	0.001047	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.62364	0.03	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.62588	0.2440	L	0.41824	1.3	0.80722	D	1	D	0.63880	0.993	P	0.47134	0.539	T	0.63296	-0.6669	10	0.46703	T	0.11	-21.7784	19.8211	0.96595	0.0:1.0:0.0:0.0	.	411	O60477	DBC1_HUMAN	Q	411	ENSP00000265922:R411Q	ENSP00000265922:R411Q	R	-	2	0	DBC1	120970237	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.890000	0.63178	2.687000	0.91594	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.597	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
PRRC2B	84726	hgsc.bcm.edu	37	9	134351770	134351770	+	Silent	SNP	G	G	A	rs78591540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134351770G>A	ENST00000357304.4	+	15	4309	c.4254G>A	c.(4252-4254)aaG>aaA	p.K1418K	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1418							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AGCTGGCCAAGAGGAGCTTCT	0.652											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	487	0.0972444	0.1778	0.0735	5008	,	,		13836	0.004		0.163	False		,,,				2504	0.0337				p.K1418K		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G4254A						PASS	.	G		504,3354		23,458,1448	15.0	17.0	16.0		4254	4.9	1.0	9	dbSNP_132	16	1094,7126		70,954,3086	no	coding-synonymous	PRRC2B	NM_013318.3		93,1412,4534	AA,AG,GG		13.309,13.0638,13.2307		1418/2230	134351770	1598,10480	1929	4110	6039	SO:0001819	synonymous_variant	84726	exon15			GGCCAAGAGGAGC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4254G>A	9.37:g.134351770G>A		Somatic	50	0	0	1610	WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	219	0.10027472527472528	68	0.13821138211382114	29	0.08011049723756906	1	0.0017482517482517483	121	0.15963060686015831	G	7.262	0.605446	0.14002	0.130638	0.13309	ENSG00000130723	ENST00000451855	.	.	.	5.93	4.94	0.65067	.	.	.	.	.	T	0.00412	0.0013	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06463	-1.0825	3	.	.	.	.	12.4476	0.55659	0.1081:0.0:0.8919:0.0	.	.	.	.	K	152	.	.	E	+	1	0	PRRC2B	133341591	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	3.787000	0.55439	2.814000	0.96858	0.655000	0.94253	GAG	A|0.104;C|0.000;G|0.895	0.104	strong		0.652	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
YPEL1	29799	hgsc.bcm.edu	37	22	22049783	22049783	+	IGR	SNP	C	C	T	rs12484060	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:22049783C>T	ENST00000339468.3	-	0	4329				PPIL2_ENST00000456792.2_Missense_Mutation_p.A467V|PPIL2_ENST00000412327.1_Silent_p.S521S|PPIL2_ENST00000492445.2_3'UTR|PPIL2_ENST00000446951.1_3'UTR|PPIL2_ENST00000335025.8_3'UTR|PPIL2_ENST00000398831.3_3'UTR|PPIL2_ENST00000406385.1_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	215	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	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	
PADI6	353238	hgsc.bcm.edu	37	1	17707601	17707601	+	RNA	SNP	T	T	C	rs6669650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17707601T>C	ENST00000434762.2	+	0	545							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	ATTGCAACCCTGCTGATGTGG	0.498													T|||	812	0.162141	0.1029	0.1196	5008	,	,		19632	0.2788		0.1292	False		,,,				2504	0.1861				p.P165P		Atlas-SNP	.											.	PADI6	51	.	0			c.T495C						PASS	.	T		361,3521		13,335,1593	75.0	79.0	78.0		495	-2.6	0.0	1	dbSNP_116	78	1351,6935		132,1087,2924	no	coding-synonymous	PADI6	NM_207421.3		145,1422,4517	CC,CT,TT		16.3046,9.2993,14.0697		165/695	17707601	1712,10456	1941	4143	6084			353238	exon5			CAACCCTGCTGAT	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"""Peptidyl arginine deiminases"""	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17707601T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_207421	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	37																																																																																				T|0.832;C|0.168	0.168	strong		0.498	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421	
SLC7A9	11136	hgsc.bcm.edu	37	19	33353464	33353464	+	Silent	SNP	G	G	A	rs11084673	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33353464G>A	ENST00000023064.4	-	5	698	c.507C>T	c.(505-507)agC>agT	p.S169S	SLC7A9_ENST00000587772.1_Silent_p.S169S|SLC7A9_ENST00000590341.1_Silent_p.S169S|RN7SKP22_ENST00000365097.1_RNA	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	169					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)	CCAGCCGCACGCTCAGTGAGT	0.542													G|||	1402	0.279952	0.3026	0.1816	5008	,	,		15500	0.3046		0.3738	False		,,,				2504	0.1973				p.S169S	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.C507T						PASS	.	G	,	1382,3024	454.9+/-350.8	215,952,1036	72.0	63.0	66.0		507,507	-3.1	1.0	19	dbSNP_120	66	2958,5642	460.3+/-365.1	490,1978,1832	no	coding-synonymous,coding-synonymous	SLC7A9	NM_001126335.1,NM_014270.4	,	705,2930,2868	AA,AG,GG		34.3953,31.3663,33.3692	,	169/488,169/488	33353464	4340,8666	2203	4300	6503	SO:0001819	synonymous_variant	11136	exon5			CCGCACGCTCAGT	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.507C>T	19.37:g.33353464G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																			G|0.692;A|0.308	0.308	strong		0.542	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
FMN2	56776	hgsc.bcm.edu	37	1	240371328	240371328	+	Silent	SNP	G	G	A	rs71646895	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.						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	76	0	0		WXS	Illumina HiSeq	Phase_I	90	24	0.266667	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	
RP11-93K22.13	0	hgsc.bcm.edu	37	3	129810158	129810158	+	lincRNA	SNP	C	C	T	rs6803922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:129810158C>T	ENST00000514010.1	-	0	248				ALG1L2_ENST00000507643.1_RNA																							CACCTCTGGACCTGCAGCACC	0.587													c|||	924	0.184505	0.239	0.1758	5008	,	,		18754	0.005		0.3042	False		,,,				2504	0.1789				p.D25D		Atlas-SNP	.											.	.	.	.	0			c.C75T						PASS	.																																					644974	exon2			TCTGGACCTGCAG																													3.37:g.129810158C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_001136152		Silent	SNP	ENST00000514010.1	37																																																																																				C|0.798;T|0.202	0.202	strong		0.587	RP11-93K22.13-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000358040.1		
DDX51	317781	hgsc.bcm.edu	37	12	132624669	132624669	+	Silent	SNP	G	G	A	rs12312005	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:132624669G>A	ENST00000397333.3	-	12	1787	c.1749C>T	c.(1747-1749)ccC>ccT	p.P583P		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	583	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		TCAGGTACTGGGGGGCGTCGT	0.667													G|||	29	0.00579073	0.0	0.0043	5008	,	,		15476	0.0		0.006	False		,,,				2504	0.0204				p.P583P		Atlas-SNP	.											.	DDX51	33	.	0			c.C1749T						PASS	.	G		7,4287		0,7,2140	55.0	63.0	60.0		1749	-6.2	0.4	12	dbSNP_120	60	51,8417		0,51,4183	no	coding-synonymous	DDX51	NM_175066.3		0,58,6323	AA,AG,GG		0.6023,0.163,0.4545		583/667	132624669	58,12704	2147	4234	6381	SO:0001819	synonymous_variant	317781	exon12			GTACTGGGGGGCG	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.1749C>T	12.37:g.132624669G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																			G|0.994;A|0.006	0.006	strong		0.667	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
CDCA7L	55536	hgsc.bcm.edu	37	7	21956405	21956405	+	Silent	SNP	G	G	A	rs1128250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:21956405G>A	ENST00000406877.3	-	2	411	c.132C>T	c.(130-132)tgC>tgT	p.C44C	CDCA7L_ENST00000356195.5_Silent_p.C10C|CDCA7L_ENST00000465490.1_5'UTR|CDCA7L_ENST00000373934.4_Silent_p.C44C	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	44					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						CAAAACTATCGCAGCTCTCCT	0.468													G|||	1548	0.309105	0.1074	0.4179	5008	,	,		17366	0.5784		0.1779	False		,,,				2504	0.362				p.C44C		Atlas-SNP	.											CDCA7L,caecum,carcinoma,0,1	CDCA7L	56	1	0			c.C132T						PASS	.	G	,,	581,3825	258.6+/-262.5	35,511,1657	173.0	164.0	167.0		30,132,132	-9.0	0.5	7	dbSNP_86	167	1598,7002	297.5+/-303.5	156,1286,2858	no	coding-synonymous,coding-synonymous,coding-synonymous	CDCA7L	NM_001127370.2,NM_001127371.2,NM_018719.4	,,	191,1797,4515	AA,AG,GG		18.5814,13.1866,16.7538	,,	10/421,44/409,44/455	21956405	2179,10827	2203	4300	6503	SO:0001819	synonymous_variant	55536	exon2			ACTATCGCAGCTC		CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.132C>T	7.37:g.21956405G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_018719	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Silent	SNP	ENST00000406877.3	37	CCDS5374.1																																																																																			G|0.773;A|0.227	0.227	strong		0.468	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719	
BLMH	642	hgsc.bcm.edu	37	17	28612448	28612448	+	Silent	SNP	G	G	C	rs7342921	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28612448G>C	ENST00000261714.6	-	6	777	c.603C>G	c.(601-603)acC>acG	p.T201T	BLMH_ENST00000394819.3_Silent_p.T114T|RNU6-1267P_ENST00000410747.1_RNA|BLMH_ENST00000582669.1_5'UTR	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	201					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	TTTCTCCTTTGGTTGCTCCAC	0.428													G|||	1346	0.26877	0.2557	0.3746	5008	,	,		18907	0.1746		0.329	False		,,,				2504	0.2464				p.T201T	Pancreas(127;628 1772 12912 33293 36203)	Atlas-SNP	.											.	BLMH	42	.	0			c.C603G						PASS	.	G		1133,3273	403.5+/-332.8	142,849,1212	161.0	145.0	150.0		603	2.4	1.0	17	dbSNP_116	150	2776,5824	439.9+/-359.4	463,1850,1987	no	coding-synonymous	BLMH	NM_000386.3		605,2699,3199	CC,CG,GG		32.2791,25.7149,30.0554		201/456	28612448	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	642	exon6			TCCTTTGGTTGCT	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.603C>G	17.37:g.28612448G>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	149	82	0.550336	NM_000386	B2R796|Q53F86|Q9UER9	Silent	SNP	ENST00000261714.6	37	CCDS32604.1																																																																																			G|0.708;C|0.292	0.292	strong		0.428	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386	
COL18A1	80781	hgsc.bcm.edu	37	21	46876083	46876083	+	Silent	SNP	A	A	G	rs2236451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46876083A>G	ENST00000359759.4	+	1	660	c.639A>G	c.(637-639)ccA>ccG	p.P213P	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Silent_p.P213P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	213					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)		TGCCACCACCATCTTCAGGTA	0.697													G|||	1881	0.375599	0.5673	0.2997	5008	,	,		14080	0.3284		0.326	False		,,,				2504	0.2699				p.P213P		Atlas-SNP	.											.	COL18A1	129	.	0			c.A639G						PASS	.	G	,	2040,2022		519,1002,510	27.0	35.0	32.0		639,	-6.4	0.0	21	dbSNP_98	32	2719,5647		469,1781,1933	no	coding-synonymous,intron	COL18A1	NM_030582.3,NM_130445.2	,	988,2783,2443	GG,GA,AA		32.5006,49.7784,38.2926	,	213/1520,	46876083	4759,7669	2031	4183	6214	SO:0001819	synonymous_variant	80781	exon1			ACCACCATCTTCA		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.639A>G	21.37:g.46876083A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				A|0.628;G|0.372	0.372	strong		0.697	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
LRP1B	53353	hgsc.bcm.edu	37	2	141259283	141259283	+	Silent	SNP	G	G	A	rs35296183	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:141259283G>A	ENST00000389484.3	-	55	9794	c.8823C>T	c.(8821-8823)gaC>gaT	p.D2941D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2941	EGF-like 11. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GGTCTTGACAGTCTTGAGAAC	0.378										TSP Lung(27;0.18)			G|||	523	0.104433	0.0401	0.1066	5008	,	,		16546	0.0188		0.1988	False		,,,				2504	0.181				p.D2941D	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C8823T						PASS	.	G		283,4123	158.5+/-191.2	7,269,1927	115.0	118.0	117.0		8823	1.2	1.0	2	dbSNP_126	117	1947,6653	343.9+/-325.1	215,1517,2568	no	coding-synonymous	LRP1B	NM_018557.2		222,1786,4495	AA,AG,GG		22.6395,6.4231,17.1459		2941/4600	141259283	2230,10776	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon55			TTGACAGTCTTGA	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.8823C>T	2.37:g.141259283G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.847;A|0.153	0.153	strong		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
RASA3	22821	hgsc.bcm.edu	37	13	114780764	114780764	+	Silent	SNP	A	A	G	rs2274717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:114780764A>G	ENST00000334062.7	-	14	1447	c.1326T>C	c.(1324-1326)acT>acC	p.T442T	RASA3_ENST00000389544.4_Silent_p.T410T	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	442	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			CCCCAGACTCAGTGATGGCGT	0.642													N|||	3635	0.725839	0.9183	0.6585	5008	,	,		16916	0.6558		0.6461	False		,,,				2504	0.6677				p.T442T		Atlas-SNP	.											.	RASA3	83	.	0			c.T1326C						PASS	.	G		3787,619	267.1+/-267.6	1636,515,52	120.0	103.0	109.0		1326	-1.8	0.1	13	dbSNP_100	109	5445,3155	478.5+/-369.9	1715,2015,570	no	coding-synonymous	RASA3	NM_007368.2		3351,2530,622	GG,GA,AA		36.686,14.049,29.0174		442/835	114780764	9232,3774	2203	4300	6503	SO:0001819	synonymous_variant	22821	exon14			AGACTCAGTGATG		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1326T>C	13.37:g.114780764A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_007368	A6NL15|F8W6X8|Q8IUY2	Silent	SNP	ENST00000334062.7	37	CCDS32016.1																																																																																			A|0.286;G|0.714	0.714	strong		0.642	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189616	11189616	+	Missense_Mutation	SNP	G	G	A	rs200495954		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11189616G>A	ENST00000382435.4	+	1	1220	c.1001G>A	c.(1000-1002)gGg>gAg	p.G334E		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	334						integral component of membrane (GO:0016021)											GAGAGGACAGGGAAGGTGGAG	0.498																																					p.G334E		Atlas-SNP	.											AMAC1L2,right_upper_lobe,carcinoma,+1,1	.	.	1	0			c.G1001A						scavenged	.						55.0	58.0	57.0					8																	11189616		2203	4300	6503	SO:0001583	missense	83650	exon1			GGACAGGGAAGGT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.1001G>A	8.37:g.11189616G>A	ENSP00000371872:p.Gly334Glu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	147	9	0.0612245	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	g	5.777	0.327688	0.10956	.	.	ENSG00000177710	ENST00000382435	T	0.38560	1.13	.	.	.	.	0.350088	0.20838	N	0.084754	T	0.26484	0.0647	L	0.50333	1.59	0.28172	N	0.928524	B	0.06786	0.001	B	0.04013	0.001	T	0.35574	-0.9783	8	0.02654	T	1	-1.4658	.	.	.	.	334	Q96KT7	S35G5_HUMAN	E	334	ENSP00000371872:G334E	ENSP00000371872:G334E	G	+	2	0	SLC35G5	11227026	0.086000	0.21541	0.277000	0.24703	0.278000	0.26855	-0.233000	0.09041	0.064000	0.16427	0.064000	0.15345	GGG	G|0.999;A|0.001	0.001	weak		0.498	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
COL3A1	1281	hgsc.bcm.edu	37	2	189858790	189858790	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:189858790T>C	ENST00000304636.3	+	17	1346	c.1176T>C	c.(1174-1176)ccT>ccC	p.P392P	COL3A1_ENST00000317840.5_Silent_p.P392P	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	392	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	ATGGTAGTCCTGGTGGTAAAG	0.383																																					p.P392P		Atlas-SNP	.											.	COL3A1	292	.	0			c.T1176C						PASS	.						129.0	127.0	128.0					2																	189858790		2203	4300	6503	SO:0001819	synonymous_variant	1281	exon17			TAGTCCTGGTGGT	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.1176T>C	2.37:g.189858790T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	T	9.959	1.222154	0.22457	.	.	ENSG00000168542	ENST00000450867	.	.	.	5.86	3.44	0.39384	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46830	-0.9163	4	.	.	.	.	5.9517	0.19250	0.1242:0.1382:0.0:0.7376	.	.	.	.	R	59	.	.	W	+	1	0	COL3A1	189567035	0.989000	0.36119	1.000000	0.80357	0.974000	0.67602	0.128000	0.15810	0.540000	0.28808	0.528000	0.53228	TGG	.	.	none		0.383	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
CRB2	286204	hgsc.bcm.edu	37	9	126134542	126134542	+	Silent	SNP	G	G	A	rs61740213	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:126134542G>A	ENST00000373631.3	+	9	2524	c.2523G>A	c.(2521-2523)acG>acA	p.T841T	CRB2_ENST00000373629.2_Silent_p.T509T|CRB2_ENST00000359999.3_Silent_p.T841T	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	841	EGF-like 11. {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						CGGGGCCTACGTGTGCCCAGC	0.612													G|||	1648	0.329073	0.0658	0.3963	5008	,	,		20199	0.377		0.5298	False		,,,				2504	0.3814				p.T841T		Atlas-SNP	.											.	CRB2	86	.	0			c.G2523A						PASS	.	G		535,3871		36,463,1704	136.0	103.0	114.0		2523	-5.1	0.8	9	dbSNP_129	114	4684,3916		1264,2156,880	yes	coding-synonymous	CRB2	NM_173689.5		1300,2619,2584	AA,AG,GG		45.5349,12.1425,40.1276		841/1286	126134542	5219,7787	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon9			GCCTACGTGTGCC	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.2523G>A	9.37:g.126134542G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			G|0.606;A|0.394	0.394	strong		0.612	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73205382	73205382	+	Missense_Mutation	SNP	A	A	G	rs200976886	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73205382A>G	ENST00000426542.2	+	33	4327	c.4307A>G	c.(4306-4308)gAg>gGg	p.E1436G	ARHGEF28_ENST00000437974.1_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.E356G|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.E1123G|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.E1392G			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1436	Interaction with microtubules. {ECO:0000250}.				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)										CAGCATGAGGAGCTGGCCAAT	0.677													A|||	6	0.00119808	0.0	0.0014	5008	,	,		17397	0.0		0.005	False		,,,				2504	0.0				p.E1436G		Atlas-SNP	.											.	.	.	.	0			c.A4307G						PASS	.	A	GLY/GLU,GLY/GLU	0,4202		0,0,2101	10.0	11.0	11.0		4307,4307	2.7	1.0	5		11	4,8440		0,4,4218	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	98,98	0,4,6319	GG,GA,AA		0.0474,0.0,0.0316	probably-damaging,probably-damaging	1436/1732,1436/1706	73205382	4,12642	2101	4222	6323	SO:0001583	missense	64283	exon34			ATGAGGAGCTGGC		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.4307A>G	5.37:g.73205382A>G	ENSP00000412175:p.Glu1436Gly	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	166	92	0.554217	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.209869	0.58343	0.0	4.74E-4	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.34	2.73	0.32206	.	1.144270	0.07072	U	0.835626	T	0.62109	0.2401	M	0.81942	2.565	0.42236	D	0.991911	D;D;D;D;D	0.71674	0.996;0.998;0.997;0.997;0.998	P;D;D;D;D	0.67382	0.894;0.947;0.947;0.951;0.944	T	0.55698	-0.8100	10	0.87932	D	0	.	11.6878	0.51497	0.7192:0.2808:0.0:0.0	.	1123;1436;1436;356;1436	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	G	1436;1436;1436;1392;1436;1436;1123;356	ENSP00000296794:E1436G;ENSP00000441913:E1436G;ENSP00000441436:E1436G;ENSP00000287898:E1392G;ENSP00000411459:E1436G;ENSP00000412175:E1436G;ENSP00000296799:E1123G;ENSP00000421081:E356G	ENSP00000287898:E1392G	E	+	2	0	RP11-428C6.1	73241138	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	4.810000	0.62598	0.841000	0.35020	0.454000	0.30748	GAG	A|0.997;G|0.003	0.003	weak		0.677	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
TTN	7273	hgsc.bcm.edu	37	2	179455207	179455207	+	Silent	SNP	T	T	C	rs2163009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179455207T>C	ENST00000591111.1	-	254	56546	c.56322A>G	c.(56320-56322)acA>acG	p.T18774T	TTN_ENST00000589042.1_Silent_p.T20415T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Silent_p.T11475T|TTN_ENST00000460472.2_Silent_p.T11350T|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.T11542T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.T17847T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18774	Fibronectin type-III 36. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCATTGTGCTGTGCCAGGTT	0.433													t|||	2566	0.51238	0.5688	0.4078	5008	,	,		22493	0.7232		0.2545	False		,,,				2504	0.5583				p.T20415T		Atlas-SNP	.											.	TTN	18412	.	0			c.A61245G						PASS	.	C	,,,	2033,1861		544,945,458	109.0	110.0	110.0		34050,53541,34425,34626	-12.2	0.0	2	dbSNP_96	110	1857,6427		195,1467,2480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	739,2412,2938	CC,CT,TT		22.4167,47.7915,31.9428	,,,	11350/26927,17847/33424,11475/27052,11542/27119	179455207	3890,8288	1947	4142	6089	SO:0001819	synonymous_variant	7273	exon304			TTGTGCTGTGCCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.56322A>G	2.37:g.179455207T>C		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	264	130	0.492424	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.557;C|0.443	0.443	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501514	90501514	+	Missense_Mutation	SNP	C	C	G	rs4076794	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	69	0	0		WXS	Illumina HiSeq	Phase_I	73	48	0.657534	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	
FLG	2312	hgsc.bcm.edu	37	1	152281948	152281948	+	Missense_Mutation	SNP	G	G	A	rs12405241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281948G>A	ENST00000368799.1	-	3	5449	c.5414C>T	c.(5413-5415)gCg>gTg	p.A1805V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1805	Ser-rich.		A -> V (in dbSNP:rs12405241).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTTGGGACGCTGAGTGCCT	0.592									Ichthyosis				G|||	1440	0.28754	0.0113	0.3905	5008	,	,		20549	0.5843		0.1421	False		,,,				2504	0.4315				p.A1805V		Atlas-SNP	.											.	FLG	900	.	0			c.C5414T						PASS	.	G	VAL/ALA	161,4245	108.2+/-146.6	2,157,2044	311.0	321.0	317.0		5414	-3.6	0.0	1	dbSNP_120	317	1240,7356	248.9+/-276.4	97,1046,3155	no	missense	FLG	NM_002016.1	64	99,1203,5199	AA,AG,GG		14.4253,3.6541,10.7753	probably-damaging	1805/4062	152281948	1401,11601	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGACGCTGAGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5414C>T	1.37:g.152281948G>A	ENSP00000357789:p.Ala1805Val	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	361	179	0.495845	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	574	0.26282051282051283	9	0.018292682926829267	118	0.3259668508287293	335	0.5856643356643356	112	0.14775725593667546	G	9.606	1.130070	0.21041	0.036541	0.144253	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01821	4.62	2.68	-3.56	0.04626	.	.	.	.	.	T	0.01254	0.0041	L	0.49350	1.555	0.80722	P	0.0	D	0.76494	0.999	D	0.68621	0.959	T	0.36383	-0.9750	8	0.25106	T	0.35	.	0.7622	0.01009	0.3595:0.1924:0.2946:0.1534	rs12405241;rs57429267	1805	P20930	FILA_HUMAN	V	1805;40	ENSP00000357789:A1805V	ENSP00000271820:A40V	A	-	2	0	FLG	150548572	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.623000	0.00109	-0.903000	0.03881	-1.464000	0.01018	GCG	G|0.839;A|0.161	0.161	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PRDM14	63978	hgsc.bcm.edu	37	8	70980738	70980738	+	Missense_Mutation	SNP	T	T	C	rs3750228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:70980738T>C	ENST00000276594.2	-	3	931	c.730A>G	c.(730-732)Aaa>Gaa	p.K244E		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	244			K -> E (in dbSNP:rs3750228). {ECO:0000269|PubMed:15489334}.		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)			AGGGAGTCTTTATCCAGAGTT	0.403													T|||	999	0.199481	0.1649	0.2507	5008	,	,		20938	0.2956		0.1362	False		,,,				2504	0.1759				p.K244E	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.A730G						PASS	.	T	GLU/LYS	700,3706	293.3+/-282.5	50,600,1553	96.0	93.0	94.0		730	1.3	0.9	8	dbSNP_107	94	1127,7473	233.6+/-266.8	77,973,3250	yes	missense	PRDM14	NM_024504.2	56	127,1573,4803	CC,CT,TT		13.1047,15.8874,14.0474	benign	244/572	70980738	1827,11179	2203	4300	6503	SO:0001583	missense	63978	exon3			AGTCTTTATCCAG	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.730A>G	8.37:g.70980738T>C	ENSP00000276594:p.Lys244Glu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_024504	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	37	CCDS6206.1	418	0.19139194139194138	95	0.19308943089430894	88	0.2430939226519337	133	0.23251748251748253	102	0.1345646437994723	T	14.68	2.606447	0.46527	0.158874	0.131047	ENSG00000147596	ENST00000276594	T	0.11821	2.74	5.05	1.3	0.21679	.	0.330774	0.20918	N	0.083340	T	0.00012	0.0000	M	0.67953	2.075	0.38261	P	0.05810800000000005	B	0.13145	0.007	B	0.08055	0.003	T	0.31024	-0.9958	9	0.31617	T	0.26	-1.464	8.168	0.31239	0.0:0.0732:0.4275:0.4993	rs3750228;rs52814557;rs57157953;rs3750228	244	Q9GZV8	PRD14_HUMAN	E	244	ENSP00000276594:K244E	ENSP00000276594:K244E	K	-	1	0	PRDM14	71143292	0.981000	0.34729	0.931000	0.37212	0.965000	0.64279	0.981000	0.29526	0.064000	0.16427	0.402000	0.26972	AAA	C|0.167;N|0.000	0.167	strong		0.403	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79092750	79092750	+	Silent	SNP	G	G	C	rs7173267	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79092750G>C	ENST00000388820.4	-	2	450	c.240C>G	c.(238-240)gcC>gcG	p.A80A	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	80					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						GCTCGTAGAAGGCGGGCGCGT	0.692													G|||	1245	0.248602	0.1044	0.2968	5008	,	,		12618	0.1518		0.4284	False		,,,				2504	0.3241				p.A80A		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C240G						PASS	.	G		628,3716		55,518,1599	11.0	12.0	11.0		240	1.1	0.9	15	dbSNP_116	11	3580,4914		781,2018,1448	no	coding-synonymous	ADAMTS7	NM_014272.3		836,2536,3047	CC,CG,GG		42.1474,14.4567,32.7777		80/1687	79092750	4208,8630	2172	4247	6419	SO:0001819	synonymous_variant	11173	exon2			GTAGAAGGCGGGC	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.240C>G	15.37:g.79092750G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			G|0.752;C|0.248	0.248	strong		0.692	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
USP6	9098	hgsc.bcm.edu	37	17	5037281	5037281	+	Missense_Mutation	SNP	T	T	C	rs114991387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5037281T>C	ENST00000574788.1	+	15	2714	c.484T>C	c.(484-486)Tat>Cat	p.Y162H	USP6_ENST00000332776.4_Missense_Mutation_p.Y162H|USP6_ENST00000250066.6_Missense_Mutation_p.Y162H|USP6_ENST00000304328.5_5'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	162	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						TAGGGATCGATATGGAGCCAA	0.572			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								T|||	357	0.0712859	0.0386	0.0389	5008	,	,		18774	0.1448		0.0557	False		,,,				2504	0.0787				p.Y162H		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.T484C						PASS	.	T	HIS/TYR	244,4162	144.6+/-179.5	11,222,1970	145.0	112.0	123.0		484	0.9	0.1	17	dbSNP_132	123	508,8092	145.4+/-201.1	30,448,3822	yes	missense	USP6	NM_004505.2	83	41,670,5792	CC,CT,TT		5.907,5.5379,5.7819	probably-damaging	162/1407	5037281	752,12254	2203	4300	6503	SO:0001583	missense	9098	exon7			GATCGATATGGAG	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.484T>C	17.37:g.5037281T>C	ENSP00000460380:p.Tyr162His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	154	0.07051282051282051	20	0.04065040650406504	14	0.03867403314917127	73	0.12762237762237763	47	0.06200527704485488	T	15.68	2.905963	0.52333	0.055379	0.05907	ENSG00000129204	ENST00000332776;ENST00000250066	T;T	0.37915	1.17;1.17	0.862	0.862	0.19056	Rab-GAP/TBC domain (4);	0.087488	0.85682	D	0.000000	T	0.00468	0.0015	M	0.62209	1.925	0.09310	P	1.0	D;D	0.63880	0.985;0.993	P;P	0.54401	0.685;0.751	T	0.06338	-1.0832	9	0.87932	D	0	.	4.181	0.10376	0.0:0.0:0.0:1.0	.	162;162	B9A6N0;P35125	.;UBP6_HUMAN	H	162	ENSP00000328010:Y162H;ENSP00000250066:Y162H	ENSP00000250066:Y162H	Y	+	1	0	USP6	4978005	1.000000	0.71417	0.063000	0.19743	0.063000	0.16089	4.579000	0.60936	0.115000	0.18071	0.113000	0.15668	TAT	T|0.943;C|0.057	0.057	strong		0.572	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
ZNF880	400713	hgsc.bcm.edu	37	19	52888048	52888048	+	Silent	SNP	G	G	A	rs324124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	19	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	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	
CLTCL1	8218	hgsc.bcm.edu	37	22	19184095	19184095	+	Missense_Mutation	SNP	T	T	C	rs1061325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:19184095T>C	ENST00000263200.10	-	25	4018	c.3946A>G	c.(3946-3948)Atg>Gtg	p.M1316V	CLTCL1_ENST00000353891.5_Missense_Mutation_p.M1316V|CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000427926.1_Missense_Mutation_p.M1316V	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1316	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.		M -> V (in dbSNP:rs1061325).		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)					TCAGTGAACATGCCCATGTGG	0.577			T	?	ALCL								T|||	2021	0.403554	0.2277	0.4568	5008	,	,		17804	0.3075		0.5149	False		,,,				2504	0.5879				p.M1316V		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.A3946G						PASS	.	T	VAL/MET,VAL/MET	1092,3080		157,778,1151	41.0	45.0	43.0		3946,3946	3.5	1.0	22	dbSNP_86	43	4183,4233		1040,2103,1065	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	21,21	1197,2881,2216	CC,CT,TT		49.7029,26.1745,41.905	probably-damaging,probably-damaging	1316/1584,1316/1641	19184095	5275,7313	2086	4208	6294	SO:0001583	missense	8218	exon25			TGAACATGCCCAT		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.3946A>G	22.37:g.19184095T>C	ENSP00000445677:p.Met1316Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	829	0.37957875457875456	121	0.2459349593495935	150	0.4143646408839779	165	0.28846153846153844	393	0.5184696569920845	T	17.71	3.457621	0.63401	0.261745	0.497029	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.13901	2.55;2.55;2.55	3.5	3.5	0.40072	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.75264	2.295	0.09310	P	0.99999827883	B;D;D	0.56287	0.176;0.975;0.975	B;D;D	0.80764	0.314;0.994;0.994	T	0.48714	-0.9011	9	0.42905	T	0.14	-20.4924	12.1517	0.54053	0.0:0.0:0.0:1.0	rs1061325;rs1633401;rs3202383;rs57127986;rs1061325	1316;139;1316	P53675-2;B7Z2Y4;P53675	.;.;CLH2_HUMAN	V	1316	ENSP00000439662:M1316V;ENSP00000445677:M1316V;ENSP00000441158:M1316V	ENSP00000445677:M1316V	M	-	1	0	CLTCL1	17564095	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	7.144000	0.77357	1.469000	0.48083	0.402000	0.26972	ATG	A|0.008;C|0.387	0.387	strong		0.577	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
FIBCD1	84929	hgsc.bcm.edu	37	9	133787225	133787225	+	Silent	SNP	A	A	G	rs6597650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133787225A>G	ENST00000372338.4	-	5	1142	c.900T>C	c.(898-900)gaT>gaC	p.D300D	FIBCD1_ENST00000448616.1_Silent_p.D300D|FIBCD1_ENST00000372337.2_Silent_p.D142D|FIBCD1_ENST00000253018.4_Silent_p.D142D	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	85	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	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	
ADNP2	22850	hgsc.bcm.edu	37	18	77891039	77891039	+	Silent	SNP	T	T	A	rs1064058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:77891039T>A	ENST00000262198.4	+	3	617	c.162T>A	c.(160-162)ggT>ggA	p.G54G		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	54					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		CATCATGGGGTGATGTTTCTC	0.348													A|||	626	0.125	0.1248	0.1499	5008	,	,		21138	0.0347		0.2068	False		,,,				2504	0.1166				p.G54G		Atlas-SNP	.											.	ADNP2	102	.	0			c.T162A						PASS	.	A		551,3855	775.5+/-414.1	33,485,1685	161.0	142.0	149.0		162	2.5	1.0	18	dbSNP_86	149	1813,6787	732.2+/-406.8	199,1415,2686	no	coding-synonymous	ADNP2	NM_014913.3		232,1900,4371	AA,AT,TT		21.0814,12.5057,18.1762		54/1132	77891039	2364,10642	2203	4300	6503	SO:0001819	synonymous_variant	22850	exon3			ATGGGGTGATGTT	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	23803	protein-coding gene	gene with protein product			"""zinc finger protein 508"""	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.162T>A	18.37:g.77891039T>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	134	53	0.395522	NM_014913	A8K951|O94943|Q9H9P3	Silent	SNP	ENST00000262198.4	37	CCDS32853.1																																																																																			T|0.838;A|0.162	0.162	strong		0.348	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913	
MICAL1	64780	hgsc.bcm.edu	37	6	109768295	109768295	+	Silent	SNP	G	G	A	rs910730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:109768295G>A	ENST00000358807.3	-	17	2519	c.2208C>T	c.(2206-2208)taC>taT	p.Y736Y	MICAL1_ENST00000368952.4_Silent_p.Y755Y|MICAL1_ENST00000358577.3_Silent_p.Y650Y	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	58	0	0		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	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	
BTNL3	10917	hgsc.bcm.edu	37	5	180432416	180432416	+	Silent	SNP	C	C	T	rs7726150	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180432416C>T	ENST00000342868.6	+	8	1129	c.945C>T	c.(943-945)ccC>ccT	p.P315P	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	315	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GAAAAGCTCCCCAGGAGGTGC	0.547													C|||	2313	0.461861	0.6135	0.4856	5008	,	,		19347	0.3621		0.4414	False		,,,				2504	0.364				p.P315P		Atlas-SNP	.											BTNL3,NS,carcinoma,+1,1	BTNL3	55	1	0			c.C945T						scavenged	.						57.0	63.0	61.0					5																	180432416		2193	4295	6488	SO:0001819	synonymous_variant	10917	exon8			AGCTCCCCAGGAG	AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1143	protein-coding gene	gene with protein product	"""butyrophilin-like receptor"""	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.945C>T	5.37:g.180432416C>T		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	161	81	0.503106	NM_197975	Q496L7|Q9Y2C7	Silent	SNP	ENST00000342868.6	37	CCDS47358.1																																																																																			T|1.000;|0.000	1.000	weak		0.547	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975	
RRP12	23223	hgsc.bcm.edu	37	10	99126249	99126249	+	Silent	SNP	G	G	A	rs2275581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99126249G>A	ENST00000370992.4	-	28	3456	c.3345C>T	c.(3343-3345)gaC>gaT	p.D1115D	RRP12_ENST00000315563.6_Silent_p.D1015D|RRP12_ENST00000536831.1_Silent_p.D833D|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000414986.1_Silent_p.D1054D	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1115						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TGAGGGGCTCGTCCCCACCGC	0.617													G|||	1367	0.272963	0.1815	0.2622	5008	,	,		15986	0.3095		0.2584	False		,,,				2504	0.3814				p.D1115D		Atlas-SNP	.											.	RRP12	97	.	0			c.C3345T						PASS	.	G	,	805,3601	323.7+/-298.2	75,655,1473	110.0	104.0	106.0		3162,3345	-10.4	0.0	10	dbSNP_100	106	2153,6447	368.9+/-335.3	279,1595,2426	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	354,2250,3899	AA,AG,GG		25.0349,18.2705,22.7433	,	1054/1237,1115/1298	99126249	2958,10048	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon28			GGGCTCGTCCCCA		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3345C>T	10.37:g.99126249G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.762;A|0.238	0.238	strong		0.617	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
PGM2L1	283209	hgsc.bcm.edu	37	11	74053547	74053547	+	Missense_Mutation	SNP	C	C	T	rs592644	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:74053547C>T	ENST00000298198.4	-	12	1902	c.1591G>A	c.(1591-1593)Gtt>Att	p.V531I		NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	531			V -> I (in dbSNP:rs592644). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					CCAGTGGTAACGTCCCGTACA	0.333													T|||	3708	0.740415	0.7632	0.7133	5008	,	,		16619	0.7956		0.6849	False		,,,				2504	0.729				p.V531I		Atlas-SNP	.											.	PGM2L1	59	.	0			c.G1591A						PASS	.	T	ILE/VAL	3361,1039	381.8+/-324.2	1285,791,124	68.0	72.0	70.0		1591	-5.5	0.0	11	dbSNP_83	70	5917,2667	427.2+/-355.5	2041,1835,416	yes	missense	PGM2L1	NM_173582.3	29	3326,2626,540	TT,TC,CC		31.0694,23.6136,28.5428	benign	531/623	74053547	9278,3706	2200	4292	6492	SO:0001583	missense	283209	exon12			TGGTAACGTCCCG	AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"""glucose-1,6-bisphosphate synthase"""	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.1591G>A	11.37:g.74053547C>T	ENSP00000298198:p.Val531Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_173582	Q96MQ7|Q9UIK3	Missense_Mutation	SNP	ENST00000298198.4	37	CCDS8231.1	1586	0.7261904761904762	367	0.7459349593495935	247	0.6823204419889503	454	0.7937062937062938	518	0.683377308707124	T	12.36	1.914689	0.33815	0.763864	0.689306	ENSG00000165434	ENST00000298198	T	0.29655	1.56	5.8	-5.47	0.02600	.	0.565274	0.18147	N	0.150212	T	0.00012	0.0000	L	0.45422	1.42	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.36696	-0.9737	9	0.49607	T	0.09	-1.9454	15.9114	0.79475	0.0:0.4914:0.0:0.5086	rs592644;rs3855385;rs17857481;rs52836395;rs60966471	531	Q6PCE3	PGM2L_HUMAN	I	531	ENSP00000298198:V531I	ENSP00000298198:V531I	V	-	1	0	PGM2L1	73731195	0.000000	0.05858	0.024000	0.17045	0.970000	0.65996	-2.754000	0.00790	-1.312000	0.02306	-0.360000	0.07572	GTT	C|0.285;T|0.715	0.715	strong		0.333	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582	
BSPRY	54836	hgsc.bcm.edu	37	9	116132092	116132092	+	Missense_Mutation	SNP	G	G	C	rs818711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:116132092G>C	ENST00000374183.4	+	6	918	c.879G>C	c.(877-879)caG>caC	p.Q293H	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	293	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		Q -> H (in dbSNP:rs818711).		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						TGAATGTCCAGAACAGTTGTG	0.622													G|||	301	0.0601038	0.0045	0.0476	5008	,	,		18997	0.0734		0.0646	False		,,,				2504	0.1258				p.Q293H		Atlas-SNP	.											.	BSPRY	21	.	0			c.G879C						PASS	.	G	HIS/GLN	56,4062		0,56,2003	59.0	62.0	61.0		879	1.5	1.0	9	dbSNP_86	61	485,7871		17,451,3710	yes	missense	BSPRY	NM_017688.2	24	17,507,5713	CC,CG,GG		5.8042,1.3599,4.337	benign	293/403	116132092	541,11933	2059	4178	6237	SO:0001583	missense	54836	exon6			TGTCCAGAACAGT	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.879G>C	9.37:g.116132092G>C	ENSP00000363298:p.Gln293His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	114	0.0521978021978022	3	0.006097560975609756	18	0.049723756906077346	46	0.08041958041958042	47	0.06200527704485488	G	12.03	1.814651	0.32053	0.013599	0.058042	ENSG00000119411	ENST00000374183	T	0.13901	2.55	5.54	1.49	0.22878	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.273375	0.41938	N	0.000784	T	0.00468	0.0015	L	0.34521	1.04	0.39021	P	0.040259000000000045	B	0.14012	0.009	B	0.11329	0.006	T	0.10706	-1.0618	9	0.72032	D	0.01	-11.3344	4.8002	0.13292	0.3242:0.1496:0.5262:0.0	rs818711;rs3750530;rs17765453;rs52795781;rs818711	293	Q5W0U4	BSPRY_HUMAN	H	293	ENSP00000363298:Q293H	ENSP00000363298:Q293H	Q	+	3	2	BSPRY	115171913	1.000000	0.71417	0.959000	0.39883	0.936000	0.57629	0.918000	0.28678	0.255000	0.21593	0.561000	0.74099	CAG	G|0.930;C|0.070	0.070	strong		0.622	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
DNMT3A	1788	hgsc.bcm.edu	37	2	25536827	25536827	+	Silent	SNP	G	G	A	rs41284843	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:25536827G>A	ENST00000264709.3	-	2	364	c.27C>T	c.(25-27)ccC>ccT	p.P9P	DNMT3A_ENST00000321117.5_Silent_p.P9P|DNMT3A_ENST00000406659.3_Silent_p.P9P	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	9					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)					TGGTGTCCCCGGGGCCGCTGG	0.721			"""Mis, F, N, S"""		AML								G|||	475	0.0948482	0.0575	0.0533	5008	,	,		13310	0.1121		0.1034	False		,,,				2504	0.1483				p.P9P		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.C27T						PASS	.	G	,,	221,3953		7,207,1873	8.0	9.0	8.0		27,27,27	3.9	1.0	2	dbSNP_127	8	715,7337		33,649,3344	no	coding-synonymous,coding-synonymous,coding-synonymous	DNMT3A	NM_022552.3,NM_175629.1,NM_175630.1	,,	40,856,5217	AA,AG,GG		8.8798,5.2947,7.6558	,,	9/913,9/913,9/167	25536827	936,11290	2087	4026	6113	SO:0001819	synonymous_variant	1788	exon2			GTCCCCGGGGCCG		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.27C>T	2.37:g.25536827G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_175630	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	37	CCDS33157.1																																																																																			G|0.915;A|0.085	0.085	strong		0.721	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
CD207	50489	hgsc.bcm.edu	37	2	71062648	71062648	+	Missense_Mutation	SNP	G	G	A	rs10489990	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71062648G>A	ENST00000410009.3	-	2	209	c.164C>T	c.(163-165)gCc>gTc	p.A55V		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	55			A -> V (in dbSNP:rs10489990).		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)	p.A55V(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						CAGGACGGAGGCGACCAGGAC	0.602													G|||	1424	0.284345	0.1346	0.3963	5008	,	,		19468	0.3075		0.3608	False		,,,				2504	0.3047				p.A55V		Atlas-SNP	.											CD207,NS,carcinoma,0,1	CD207	47	1	1	Substitution - Missense(1)	stomach(1)	c.C164T						scavenged	.	G	VAL/ALA	640,3582		45,550,1516	68.0	77.0	74.0		164	4.0	0.0	2	dbSNP_119	74	2952,5510		522,1908,1801	yes	missense	CD207	NM_015717.3	64	567,2458,3317	AA,AG,GG		34.8854,15.1587,28.3191	possibly-damaging	55/329	71062648	3592,9092	2111	4231	6342	SO:0001583	missense	50489	exon2			ACGGAGGCGACCA	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.164C>T	2.37:g.71062648G>A	ENSP00000386378:p.Ala55Val	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	111	65	0.585586	NM_015717		Missense_Mutation	SNP	ENST00000410009.3	37		645	0.29532967032967034	66	0.13414634146341464	137	0.3784530386740331	181	0.31643356643356646	261	0.34432717678100266	G	16.18	3.049152	0.55110	0.151587	0.348854	ENSG00000116031	ENST00000410009	T	0.04156	3.69	4.87	4.0	0.46444	.	0.407067	0.21670	N	0.070893	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.30068	0.267	B	0.30401	0.115	T	0.42464	-0.9450	9	0.11182	T	0.66	.	9.7514	0.40478	0.0984:0.0:0.9016:0.0	rs10489990;rs52834864;rs59407760;rs10489990	55	Q9UJ71	CLC4K_HUMAN	V	55	ENSP00000386378:A55V	ENSP00000386378:A55V	A	-	2	0	CD207	70916156	0.695000	0.27747	0.024000	0.17045	0.048000	0.14542	2.131000	0.42074	1.365000	0.46057	-0.136000	0.14681	GCC	G|0.716;A|0.284	0.284	strong		0.602	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
TNFAIP6	7130	hgsc.bcm.edu	37	2	152226570	152226570	+	Missense_Mutation	SNP	A	A	G	rs1046668	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:152226570A>G	ENST00000243347.3	+	4	506	c.431A>G	c.(430-432)cAa>cGa	p.Q144R	RN7SL124P_ENST00000498656.2_RNA|MIR4773-1_ENST00000585225.1_RNA	NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	144	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.		Q -> R (in dbSNP:rs1046668). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1730767}.		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	GATCCAAAGCAAATTTTTAAA	0.383													G|||	887	0.177117	0.3033	0.1138	5008	,	,		17071	0.1329		0.1382	False		,,,				2504	0.137				p.Q144R		Atlas-SNP	.											.	TNFAIP6	98	.	0			c.A431G						PASS	.	G	ARG/GLN	1301,3105	695.6+/-406.0	199,903,1101	112.0	113.0	113.0		431	3.5	1.0	2	dbSNP_86	113	1188,7412	763.4+/-407.6	77,1034,3189	yes	missense	TNFAIP6	NM_007115.3	43	276,1937,4290	GG,GA,AA		13.814,29.5279,19.1373	benign	144/278	152226570	2489,10517	2203	4300	6503	SO:0001583	missense	7130	exon4			CAAAGCAAATTTT		CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.431A>G	2.37:g.152226570A>G	ENSP00000243347:p.Gln144Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	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	
IL17RC	84818	hgsc.bcm.edu	37	3	9960070	9960070	+	Missense_Mutation	SNP	C	C	T	rs708567	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:9960070C>T	ENST00000295981.3	+	4	763	c.545C>T	c.(544-546)tCa>tTa	p.S182L	RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000413608.1_Missense_Mutation_p.S111L|IL17RC_ENST00000403601.3_Missense_Mutation_p.S111L|IL17RC_ENST00000416074.2_Intron|IL17RC_ENST00000383812.4_Missense_Mutation_p.S111L|IL17RC_ENST00000455057.1_Missense_Mutation_p.S111L|IL17RC_ENST00000498214.1_3'UTR	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	182			S -> L (in dbSNP:rs708567). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GCAGCTGACTCAGGGGTGGAG	0.642													C|||	1938	0.386981	0.4955	0.4683	5008	,	,		17282	0.0933		0.5437	False		,,,				2504	0.3241				p.S182L		Atlas-SNP	.											.	IL17RC	55	.	0			c.C545T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	2150,2254	558.2+/-379.9	533,1084,585	60.0	65.0	64.0		332,332,332,332,332,545	-0.3	0.0	3	dbSNP_86	64	4574,4026	572.6+/-389.7	1199,2176,925	yes	missense,missense,missense,missense,missense,missense	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	145,145,145,145,145,145	1732,3260,1510	TT,TC,CC		46.814,48.8193,48.2928	benign,benign,benign,benign,benign,benign	111/708,111/691,111/689,111/706,111/721,182/792	9960070	6724,6280	2202	4300	6502	SO:0001583	missense	84818	exon4			CTGACTCAGGGGT	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.545C>T	3.37:g.9960070C>T	ENSP00000295981:p.Ser182Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	856	0.39194139194139194	239	0.48577235772357724	170	0.4696132596685083	38	0.06643356643356643	409	0.5395778364116095	C	3.436	-0.115044	0.06881	0.488193	0.53186	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000403601;ENST00000455057;ENST00000413608	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	5.07	-0.28	0.12886	.	0.950409	0.08755	N	0.898547	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B;B;B;B	0.23937	0.0;0.0;0.0;0.025;0.0;0.094;0.043	B;B;B;B;B;B;B	0.20767	0.0;0.0;0.0;0.014;0.001;0.014;0.031	T	0.43572	-0.9383	9	0.36615	T	0.2	0.7799	4.0234	0.09677	0.301:0.4467:0.0:0.2523	rs708567;rs1695435;rs11546398;rs17775675;rs61446752;rs708567	111;111;111;111;111;182;111	Q8NAC3-4;E9PHG1;A8BWD5;E9PHJ6;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;I17RC_HUMAN;.	L	111;182;111;111;111	ENSP00000373323:S111L;ENSP00000295981:S182L;ENSP00000384969:S111L;ENSP00000407894:S111L;ENSP00000396064:S111L	ENSP00000295981:S182L	S	+	2	0	IL17RC	9935070	0.000000	0.05858	0.005000	0.12908	0.015000	0.08874	-0.564000	0.05936	0.232000	0.21100	-0.397000	0.06425	TCA	T|0.437;G|0.004	0.437	strong		0.642	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
CENPF	1063	hgsc.bcm.edu	37	1	214818945	214818945	+	Missense_Mutation	SNP	A	A	C	rs3790647	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214818945A>C	ENST00000366955.3	+	13	6200	c.6032A>C	c.(6031-6033)gAa>gCa	p.E2011A		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2107			E -> A (in dbSNP:rs3790647).		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)		GAGGTGAAGGAAAAGACGGAA	0.438													A|||	552	0.110224	0.1142	0.1095	5008	,	,		19400	0.126		0.0507	False		,,,				2504	0.1503				p.E2011A	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A6032C						PASS	.	A	ALA/GLU	457,3949	215.5+/-234.4	23,411,1769	81.0	80.0	80.0		6032	4.1	0.0	1	dbSNP_107	80	467,8133	138.1+/-194.9	12,443,3845	yes	missense	CENPF	NM_016343.3	107	35,854,5614	CC,CA,AA		5.4302,10.3722,7.1044	probably-damaging	2011/3115	214818945	924,12082	2203	4300	6503	SO:0001583	missense	1063	exon13			TGAAGGAAAAGAC	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.6032A>C	1.37:g.214818945A>C	ENSP00000355922:p.Glu2011Ala	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	233	0.10668498168498168	67	0.13617886178861788	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	A	0.412	-0.912756	0.02415	0.103722	0.054302	ENSG00000117724	ENST00000366955	T	0.02916	4.11	5.21	4.05	0.47172	.	0.934195	0.08782	N	0.894580	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.12013	0.005	B	0.08055	0.003	T	0.43163	-0.9408	9	0.15499	T	0.54	.	8.1287	0.31014	0.4169:0.4611:0.0:0.122	rs3790647;rs3790647	2107	P49454	CENPF_HUMAN	A	2011	ENSP00000355922:E2011A	ENSP00000355922:E2011A	E	+	2	0	CENPF	212885568	0.050000	0.20438	0.003000	0.11579	0.007000	0.05969	0.933000	0.28897	0.793000	0.33875	0.496000	0.49642	GAA	A|0.916;C|0.083;T|0.000	0.083	strong		0.438	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
PROC	5624	hgsc.bcm.edu	37	2	128183690	128183690	+	Missense_Mutation	SNP	C	C	T	rs146922325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:128183690C>T	ENST00000234071.3	+	7	652	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	PROC_ENST00000422777.3_Missense_Mutation_p.R189W|MIR4783_ENST00000580343.1_RNA|PROC_ENST00000453608.2_Missense_Mutation_p.R244W|PROC_ENST00000409048.1_Missense_Mutation_p.R223W	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	189			R -> W (in patients with PROC deficiency; La Jolla-3; dbSNP:rs146922325).		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	GCCCTGGAAGCGGATGGAGAA	0.592													C|||	20	0.00399361	0.0	0.0	5008	,	,		18726	0.0198		0.0	False		,,,				2504	0.0				p.R189W		Atlas-SNP	.											.	PROC	31	.	0			c.C565T	GRCh37	CM951003	PROC	M	rs146922325	PASS	.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	115.0	95.0	102.0		565	-0.9	0.0	2	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PROC	NM_000312.3	101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	189/462	128183690	2,13004	2203	4300	6503	SO:0001583	missense	5624	exon7			TGGAAGCGGATGG	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"""Endogenous ligands"""	9451	protein-coding gene	gene with protein product	"""prepro-protein C"""	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.565C>T	2.37:g.128183690C>T	ENSP00000234071:p.Arg189Trp	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	177	77	0.435028	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Missense_Mutation	SNP	ENST00000234071.3	37	CCDS2145.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	10.19	1.280794	0.23392	2.27E-4	1.16E-4	ENSG00000115718	ENST00000234071;ENST00000537436;ENST00000442644;ENST00000453608;ENST00000409048;ENST00000422777	D;D;D;D;D	0.99677	-3.02;-6.37;-3.04;-3.04;-3.02	3.6	-0.86	0.10680	.	1.646220	0.04119	N	0.316035	D	0.97589	0.9210	L	0.41824	1.3	0.09310	N	1	B;B;B;B	0.28082	0.029;0.2;0.108;0.182	B;B;B;B	0.17098	0.003;0.01;0.017;0.011	D	0.98565	1.0643	10	0.52906	T	0.07	.	3.9352	0.09302	0.3472:0.4457:0.0:0.2071	.	244;245;223;189	B4DPQ7;B4DPQ3;E7END6;P04070	.;.;.;PROC_HUMAN	W	189;148;170;244;223;189	ENSP00000234071:R189W;ENSP00000411241:R170W;ENSP00000404030:R244W;ENSP00000386679:R223W;ENSP00000409543:R189W	ENSP00000234071:R189W	R	+	1	2	PROC	127900160	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.258000	0.18387	-0.050000	0.13356	0.561000	0.74099	CGG	C|0.999;T|0.001	0.001	strong		0.592	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312	
FRAS1	80144	hgsc.bcm.edu	37	4	79371474	79371474	+	Silent	SNP	C	C	T	rs17003235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79371474C>T	ENST00000264895.6	+	45	6884	c.6444C>T	c.(6442-6444)acC>acT	p.T2148T		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2148					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						GAAGTTTCACCCAGGCAGACA	0.483													C|||	749	0.149561	0.2943	0.1354	5008	,	,		17712	0.002		0.2018	False		,,,				2504	0.0624				p.T2148T		Atlas-SNP	.											.	FRAS1	779	.	0			c.C6444T						PASS	.	C		1021,2773		154,713,1030	82.0	82.0	82.0		6444	-1.9	1.0	4	dbSNP_123	82	1783,6435		199,1385,2525	no	coding-synonymous	FRAS1	NM_025074.6		353,2098,3555	TT,TC,CC		21.6963,26.9109,23.3433		2148/4013	79371474	2804,9208	1897	4109	6006	SO:0001819	synonymous_variant	80144	exon45			TTTCACCCAGGCA	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.6444C>T	4.37:g.79371474C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	349	0.15979853479853479	141	0.2865853658536585	54	0.14917127071823205	1	0.0017482517482517483	153	0.20184696569920843	C	2.179	-0.387955	0.04932	0.269109	0.216963	ENSG00000138759	ENST00000512123	.	.	.	6.01	-1.87	0.07737	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39921	-0.9590	3	.	.	.	.	2.4182	0.04441	0.2145:0.2259:0.3813:0.1784	rs17003235	.	.	.	S	377	.	.	P	+	1	0	FRAS1	79590498	0.134000	0.22483	0.980000	0.43619	0.223000	0.24884	-0.585000	0.05794	-0.433000	0.07286	0.650000	0.86243	CCA	C|0.828;T|0.172	0.172	strong		0.483	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SOS2	6655	hgsc.bcm.edu	37	14	50616878	50616878	+	Silent	SNP	G	G	A	rs2229869	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:50616878G>A	ENST00000216373.5	-	14	2506	c.2232C>T	c.(2230-2232)aaC>aaT	p.N744N	SOS2_ENST00000543680.1_Silent_p.N711N	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	744					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					GGCTTACTCCGTTTGCCTGAG	0.393													g|||	2596	0.518371	0.4024	0.647	5008	,	,		20617	0.4276		0.67	False		,,,				2504	0.5215				p.N744N		Atlas-SNP	.											.	SOS2	195	.	0			c.C2232T						PASS	.	A		2018,2388	562.1+/-380.9	463,1092,648	291.0	247.0	262.0		2232	1.7	1.0	14	dbSNP_98	262	5889,2711	682.4+/-403.8	2013,1863,424	no	coding-synonymous	SOS2	NM_006939.2		2476,2955,1072	AA,AG,GG		31.5233,45.8012,39.205		744/1333	50616878	7907,5099	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon14			TACTCCGTTTGCC	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.2232C>T	14.37:g.50616878G>A		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			G|0.426;A|0.574	0.574	strong		0.393	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
TSHZ3	57616	hgsc.bcm.edu	37	19	31770009	31770009	+	Silent	SNP	C	C	T	rs28609894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:31770009C>T	ENST00000240587.4	-	2	1017	c.690G>A	c.(688-690)acG>acA	p.T230T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	230					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)					TCATGTGCACCGTCAACTCCA	0.597													C|||	1576	0.314696	0.4304	0.2651	5008	,	,		19559	0.2331		0.2187	False		,,,				2504	0.3763				p.T230T		Atlas-SNP	.											.	TSHZ3	549	.	0			c.G690A						PASS	.	C		1793,2613	529.0+/-372.6	385,1023,795	194.0	174.0	181.0		690	-7.6	0.9	19	dbSNP_125	181	1893,6707	336.8+/-322.0	214,1465,2621	no	coding-synonymous	TSHZ3	NM_020856.2		599,2488,3416	TT,TC,CC		22.0116,40.6945,28.3408		230/1082	31770009	3686,9320	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			GTGCACCGTCAAC	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.690G>A	19.37:g.31770009C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	74	45	0.608108	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			C|0.717;T|0.283	0.283	strong		0.597	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
VNN1	8876	hgsc.bcm.edu	37	6	133035098	133035098	+	Missense_Mutation	SNP	G	G	A	rs2294757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	91	0	0		WXS	Illumina HiSeq	Phase_I	101	57	0.564356	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		
MYO7A	4647	hgsc.bcm.edu	37	11	76919478	76919478	+	Missense_Mutation	SNP	C	C	A	rs948962	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76919478C>A	ENST00000409709.3	+	43	6132	c.5860C>A	c.(5860-5862)Ctc>Atc	p.L1954I	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000458637.2_Missense_Mutation_p.L1916I|MYO7A_ENST00000409619.2_Missense_Mutation_p.L1905I	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1954	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.		L -> I (in dbSNP:rs948962). {ECO:0000269|PubMed:8622919, ECO:0000269|PubMed:8884267}.		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						ACCCCAGGTCCTCAGCGTTCC	0.527													A|||	2499	0.499002	0.7572	0.549	5008	,	,		22715	0.3343		0.5	False		,,,				2504	0.2832				p.L1954I		Atlas-SNP	.											.	MYO7A	164	.	0			c.C5860A						PASS	.	A	ILE/LEU,ILE/LEU	2851,1287		1005,841,223	64.0	68.0	67.0		5860,5746	4.3	1.0	11	dbSNP_86	67	4046,4374		989,2068,1153	yes	missense,missense	MYO7A	NM_000260.3,NM_001127180.1	5,5	1994,2909,1376	AA,AC,CC		48.0523,31.102,45.0788	benign,benign	1954/2216,1916/2176	76919478	6897,5661	2069	4210	6279	SO:0001583	missense	4647	exon43			CAGGTCCTCAGCG	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.5860C>A	11.37:g.76919478C>A	ENSP00000386331:p.Leu1954Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	1142	0.5228937728937729	376	0.7642276422764228	199	0.5497237569060773	188	0.32867132867132864	379	0.5	A	0.836	-0.743420	0.03088	0.68898	0.480523	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	4.29	4.29	0.51040	.	0.257857	0.38272	N	0.001753	T	0.00012	0.0000	.	.	.	0.40727	P	0.017290000000000028	B	0.02656	0.0	B	0.04013	0.001	T	0.42481	-0.9449	8	0.02654	T	1	.	11.0982	0.48157	0.8444:0.1556:0.0:0.0	rs948962;rs58377123;rs948962	1916	F8VUN5	.	I	1954;1916;1905;1127;1953;1923;1830;1096;569	ENSP00000386331:L1954I;ENSP00000392185:L1916I;ENSP00000386635:L1905I;ENSP00000417017:L1096I	ENSP00000345075:L1830I	L	+	1	0	MYO7A	76597126	1.000000	0.71417	1.000000	0.80357	0.269000	0.26545	5.790000	0.69038	0.699000	0.31761	-0.512000	0.04463	CTC	C|0.478;A|0.522	0.522	strong		0.527	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
ZNF99	7652	hgsc.bcm.edu	37	19	22952111	22952111	+	Missense_Mutation	SNP	A	A	G	rs34726149	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	86	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	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	
TTN	7273	hgsc.bcm.edu	37	2	179413110	179413110	+	Silent	SNP	G	G	A	rs3731748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179413110G>A	ENST00000591111.1	-	289	88544	c.88320C>T	c.(88318-88320)gcC>gcT	p.A29440A	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.A31081A|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.A22141A|TTN_ENST00000460472.2_Silent_p.A22016A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.A22208A|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.A28513A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29440	Fibronectin type-III 114. {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)			GAACACCTTCGGCCAGGTCAT	0.468													G|||	1173	0.234225	0.1483	0.1571	5008	,	,		23794	0.4514		0.1382	False		,,,				2504	0.2802				p.A31081A		Atlas-SNP	.											.	TTN	18412	.	0			c.C93243T						PASS	.	G	,,,	563,3493		40,483,1505	221.0	222.0	222.0		66048,85539,66423,66624	2.0	0.9	2	dbSNP_107	222	1222,7148		92,1038,3055	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	132,1521,4560	AA,AG,GG		14.5998,13.8807,14.365	,,,	22016/26927,28513/33424,22141/27052,22208/27119	179413110	1785,10641	2028	4185	6213	SO:0001819	synonymous_variant	7273	exon339			ACCTTCGGCCAGG	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.88320C>T	2.37:g.179413110G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	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|0.798;A|0.202	0.202	strong		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
AGL	178	hgsc.bcm.edu	37	1	100358103	100358103	+	Missense_Mutation	SNP	C	C	T	rs3753494	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:100358103C>T	ENST00000294724.4	+	24	3677	c.3199C>T	c.(3199-3201)Cct>Tct	p.P1067S	AGL_ENST00000370163.3_Missense_Mutation_p.P1067S|AGL_ENST00000361522.4_Missense_Mutation_p.P1050S|AGL_ENST00000361302.3_Missense_Mutation_p.P1051S|AGL_ENST00000361915.3_Missense_Mutation_p.P1067S|AGL_ENST00000370165.3_Missense_Mutation_p.P1067S|AGL_ENST00000370161.2_Missense_Mutation_p.P1051S	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1067			P -> S (in dbSNP:rs3753494).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AATGGATGTACCTTATAGGTT	0.378													C|||	554	0.110623	0.1203	0.0951	5008	,	,		15854	0.0278		0.1551	False		,,,				2504	0.1483				p.P1067S		Atlas-SNP	.											.	AGL	137	.	0			c.C3199T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	557,3849	249.0+/-256.6	36,485,1682	99.0	94.0	96.0		3199,3199,3199,3199,3148,3151	5.2	0.4	1	dbSNP_107	96	1257,7343	251.5+/-278.0	96,1065,3139	yes	missense,missense,missense,missense,missense,missense	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	74,74,74,74,74,74	132,1550,4821	TT,TC,CC		14.6163,12.6419,13.9474	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1067/1533,1067/1533,1067/1533,1067/1533,1050/1516,1051/1517	100358103	1814,11192	2203	4300	6503	SO:0001583	missense	178	exon24			GATGTACCTTATA	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3199C>T	1.37:g.100358103C>T	ENSP00000294724:p.Pro1067Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	237	0.10851648351648352	69	0.1402439024390244	43	0.11878453038674033	13	0.022727272727272728	112	0.14775725593667546	C	13.10	2.137783	0.37728	0.126419	0.146163	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.74947	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.89	5.2	5.2	0.72013	.	0.111526	0.64402	D	0.000006	T	0.66703	0.2816	M	0.67953	2.075	0.09310	P	0.999999999670201	B;B;B	0.26318	0.12;0.12;0.146	B;B;B	0.29353	0.047;0.047;0.101	T	0.66460	-0.5918	9	0.37606	T	0.19	.	19.1022	0.93277	0.0:1.0:0.0:0.0	rs3753494;rs17449932;rs52793848;rs56862711;rs3753494	1050;1051;1067	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	S	1067;1067;1067;1067;1051;1051;1050	ENSP00000355106:P1067S;ENSP00000359184:P1067S;ENSP00000359182:P1067S;ENSP00000294724:P1067S;ENSP00000354971:P1051S;ENSP00000359180:P1051S;ENSP00000354635:P1050S	ENSP00000294724:P1067S	P	+	1	0	AGL	100130691	1.000000	0.71417	0.412000	0.26496	0.008000	0.06430	7.230000	0.78097	2.553000	0.86117	0.573000	0.79308	CCT	C|0.869;T|0.131	0.131	strong		0.378	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232596859	232596859	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:232596859C>T	ENST00000366630.1	-	9	3227	c.2869G>A	c.(2869-2871)Ggg>Agg	p.G957R	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.G31R|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.G957R			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	957	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TGGCCCAGCCCGTTCCTCCTC	0.562																																					p.G957R		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G2869A						PASS	.						129.0	137.0	135.0					1																	232596859		2130	4269	6399	SO:0001583	missense	57568	exon8			CCAGCCCGTTCCT	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.2869G>A	1.37:g.232596859C>T	ENSP00000355589:p.Gly957Arg	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	173	90	0.520231	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424498	0.83667	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.28069	1.63;1.63;1.63	5.94	5.94	0.96194	PDZ/DHR/GLGF (3);	0.108992	0.64402	D	0.000005	T	0.55465	0.1922	L	0.59436	1.845	0.54753	D	0.999985	D;D	0.89917	1.0;0.996	D;D	0.80764	0.994;0.927	T	0.52132	-0.8616	10	0.66056	D	0.02	-32.9946	20.3594	0.98849	0.0:1.0:0.0:0.0	.	957;31	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	R	957;957;31	ENSP00000355589:G957R;ENSP00000262861:G957R;ENSP00000309102:G31R	ENSP00000262861:G957R	G	-	1	0	SIPA1L2	230663482	0.997000	0.39634	0.993000	0.49108	0.957000	0.61999	3.845000	0.55880	2.816000	0.96949	0.563000	0.77884	GGG	.	.	none		0.562	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
ACSS1	84532	hgsc.bcm.edu	37	20	25011423	25011423	+	Silent	SNP	T	T	C	rs6050259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:25011423T>C	ENST00000323482.4	-	3	682	c.603A>G	c.(601-603)gcA>gcG	p.A201A	ACSS1_ENST00000542618.1_Silent_p.A80A|ACSS1_ENST00000537502.1_Silent_p.A118A|ACSS1_ENST00000432802.2_Silent_p.A201A	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	201					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)	CCAAGGACTCTGCACTGAAGC	0.592													C|||	1115	0.222644	0.2806	0.2305	5008	,	,		20056	0.0873		0.3072	False		,,,				2504	0.1912				p.A201A		Atlas-SNP	.											.	ACSS1	46	.	0			c.A603G						PASS	.	C		1309,3097	698.3+/-406.3	192,925,1086	103.0	87.0	92.0		603	-11.9	0.1	20	dbSNP_114	92	2663,5937	684.7+/-404.0	416,1831,2053	no	coding-synonymous	ACSS1	NM_032501.2		608,2756,3139	CC,CT,TT		30.9651,29.7095,30.5398		201/690	25011423	3972,9034	2203	4300	6503	SO:0001819	synonymous_variant	84532	exon3			GGACTCTGCACTG		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.603A>G	20.37:g.25011423T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			T|0.725;C|0.275	0.275	strong		0.592	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
FHL5	9457	hgsc.bcm.edu	37	6	97063522	97063522	+	Missense_Mutation	SNP	C	C	G	rs9373985	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:97063522C>G	ENST00000326771.2	+	7	1109	c.729C>G	c.(727-729)agC>agG	p.S243R	FHL5_ENST00000541107.1_Missense_Mutation_p.S243R	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	243	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.		S -> R (in dbSNP:rs9373985).		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)		TTCAAGACAGCCAGTGGCATA	0.438													C|||	1913	0.381989	0.497	0.2997	5008	,	,		20721	0.3502		0.3479	False		,,,				2504	0.3528				p.S243R		Atlas-SNP	.											.	FHL5	73	.	0			c.C729G						PASS	.	C	ARG/SER,ARG/SER	2137,2269	579.2+/-384.9	517,1103,583	111.0	109.0	109.0		729,729	3.9	1.0	6	dbSNP_119	109	2868,5732	450.2+/-362.3	476,1916,1908	yes	missense,missense	FHL5	NM_001170807.1,NM_020482.4	110,110	993,3019,2491	GG,GC,CC		33.3488,48.502,38.4822	benign,benign	243/285,243/285	97063522	5005,8001	2203	4300	6503	SO:0001583	missense	9457	exon7			AGACAGCCAGTGG	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.729C>G	6.37:g.97063522C>G	ENSP00000326022:p.Ser243Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	136	72	0.529412	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	837	0.38324175824175827	259	0.5264227642276422	123	0.3397790055248619	200	0.34965034965034963	255	0.33641160949868076	C	2.233	-0.375731	0.05034	0.48502	0.333488	ENSG00000112214	ENST00000541107;ENST00000326771	D;D	0.87029	-2.2;-2.2	5.66	3.9	0.45041	Zinc finger, LIM-type (5);	0.179999	0.27362	N	0.019718	T	0.30792	0.0776	N	0.00227	-1.8	0.33206	P	0.44715099999999997	B	0.02656	0.0	B	0.04013	0.001	T	0.17868	-1.0355	9	0.02654	T	1	.	8.5385	0.33377	0.0:0.6902:0.0:0.3098	rs9373985;rs52808781;rs9373985	243	Q5TD97	FHL5_HUMAN	R	243	ENSP00000442357:S243R;ENSP00000326022:S243R	ENSP00000326022:S243R	S	+	3	2	FHL5	97170243	0.906000	0.30813	1.000000	0.80357	0.989000	0.77384	0.065000	0.14466	0.750000	0.32877	-0.136000	0.14681	AGC	C|0.612;G|0.388	0.388	strong		0.438	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
SCNN1B	6338	hgsc.bcm.edu	37	16	23379279	23379279	+	Splice_Site	SNP	C	C	T	rs250563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	121	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	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
SVIL	6840	hgsc.bcm.edu	37	10	29777558	29777558	+	Silent	SNP	G	G	A	rs61737742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:29777558G>A	ENST00000355867.4	-	23	5072	c.4320C>T	c.(4318-4320)taC>taT	p.Y1440Y	PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000535393.1_Silent_p.Y354Y|SVIL_ENST00000375400.3_Silent_p.Y1014Y|SVIL_ENST00000538146.1_Silent_p.Y232Y|SVIL_ENST00000375398.2_Silent_p.Y1440Y	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1440	Interaction with NEB.				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)				TCAGCCTCTTGTAGGGCACGG	0.547													G|||	254	0.0507188	0.0378	0.0533	5008	,	,		19469	0.001		0.1362	False		,,,				2504	0.0297				p.Y1440Y		Atlas-SNP	.											.	SVIL	226	.	0			c.C4320T						PASS	.	G	,	223,4183	132.5+/-169.0	0,223,1980	88.0	69.0	76.0		3042,4320	2.9	1.0	10	dbSNP_129	76	1125,7475	230.7+/-264.9	79,967,3254	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	79,1190,5234	AA,AG,GG		13.0814,5.0613,10.3644	,	1014/1789,1440/2215	29777558	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon23			CCTCTTGTAGGGC	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.4320C>T	10.37:g.29777558G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.911;A|0.089	0.089	strong		0.547	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
GYPC	2995	hgsc.bcm.edu	37	2	127453664	127453664	+	Silent	SNP	A	A	C	rs1050967	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:127453664A>C	ENST00000259254.4	+	4	664	c.333A>C	c.(331-333)ggA>ggC	p.G111G	GYPC_ENST00000356887.7_Silent_p.G90G|GYPC_ENST00000409836.3_Silent_p.G92G|GYPC_ENST00000464053.1_3'UTR	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	143	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	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	
LRRC8B	23507	hgsc.bcm.edu	37	1	90049040	90049040	+	Silent	SNP	A	A	G	rs36084789	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:90049040A>G	ENST00000330947.2	+	5	1191	c.831A>G	c.(829-831)ccA>ccG	p.P277P	LRRC8B_ENST00000358200.4_Silent_p.P277P|LRRC8B_ENST00000439853.1_Silent_p.P277P|RP5-1007M22.2_ENST00000443562.1_RNA	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	277					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)		CTTATGTTCCATATTTTTTAA	0.378													A|||	809	0.161542	0.034	0.1225	5008	,	,		22995	0.1677		0.2117	False		,,,				2504	0.3037				p.P277P		Atlas-SNP	.											.	LRRC8B	49	.	0			c.A831G						PASS	.	A	,	341,4065	180.5+/-208.7	12,317,1874	120.0	116.0	117.0		831,831	-10.6	0.3	1	dbSNP_126	117	2230,6370	377.5+/-338.5	281,1668,2351	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	293,1985,4225	GG,GA,AA		25.9302,7.7394,19.7678	,	277/804,277/804	90049040	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			TGTTCCATATTTT	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.831A>G	1.37:g.90049040A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			A|0.813;G|0.187	0.187	strong		0.378	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
PSG8	440533	hgsc.bcm.edu	37	19	43269705	43269705	+	Missense_Mutation	SNP	G	G	A	rs71337226|rs34129574|rs7245423	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43269705G>A	ENST00000306511.4	-	1	126	c.29C>T	c.(28-30)aCa>aTa	p.T10I	PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.T10I|PSG8_ENST00000406636.3_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	24	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	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		
IKBKAP	8518	hgsc.bcm.edu	37	9	111659483	111659483	+	Missense_Mutation	SNP	T	T	G	rs2230793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111659483T>G	ENST00000374647.5	-	23	2753	c.2446A>C	c.(2446-2448)Ata>Cta	p.I816L	IKBKAP_ENST00000537196.1_Missense_Mutation_p.I467L	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	816			I -> L (in dbSNP:rs2230793).		chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						ACAAGGTCTATTTTATTCCCG	0.463													G|||	1491	0.297724	0.4803	0.2507	5008	,	,		20905	0.2599		0.1998	False		,,,				2504	0.2239				p.I816L		Atlas-SNP	.											IKBKAP,NS,carcinoma,+2,1	IKBKAP	122	1	0			c.A2446C						PASS	.	G	LEU/ILE	1945,2461	622.6+/-394.0	436,1073,694	202.0	170.0	181.0		2446	3.4	0.2	9	dbSNP_98	181	1575,7025	744.7+/-407.2	146,1283,2871	yes	missense	IKBKAP	NM_003640.3	5	582,2356,3565	GG,GT,TT		18.314,44.1443,27.0644	benign	816/1333	111659483	3520,9486	2203	4300	6503	SO:0001583	missense	8518	exon23			GGTCTATTTTATT	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2446A>C	9.37:g.111659483T>G	ENSP00000363779:p.Ile816Leu	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	624	0.2857142857142857	225	0.4573170731707317	98	0.27071823204419887	158	0.2762237762237762	143	0.18865435356200527	G	11.24	1.581764	0.28180	0.441443	0.18314	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.27402	1.67;1.67	5.24	3.39	0.38822	.	0.128507	0.52532	N	0.000080	T	0.00012	0.0000	N	0.24115	0.695	0.52501	P	4.700000000001925E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46512	-0.9186	9	0.41790	T	0.15	-3.3164	10.2342	0.43273	0.0:0.6919:0.2107:0.0974	rs2230793;rs10759326;rs57174619;rs2230793	816	O95163	ELP1_HUMAN	L	816;467	ENSP00000363779:I816L;ENSP00000439367:I467L	ENSP00000363779:I816L	I	-	1	0	IKBKAP	110699304	0.999000	0.42202	0.203000	0.23512	0.394000	0.30568	1.614000	0.36911	0.304000	0.22809	-0.352000	0.07741	ATA	T|0.728;G|0.272	0.272	strong		0.463	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
PHLDB3	653583	hgsc.bcm.edu	37	19	44001379	44001379	+	Missense_Mutation	SNP	T	T	C	rs11083711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44001379T>C	ENST00000292140.5	-	6	1076	c.716A>G	c.(715-717)cAg>cGg	p.Q239R	PHLDB3_ENST00000599242.1_Missense_Mutation_p.Q239R	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	239			Q -> R (in dbSNP:rs11083711). {ECO:0000269|PubMed:15489334}.				enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				CTCCAGTTGCTGGAACTCCAG	0.617													T|||	403	0.0804712	0.0507	0.1859	5008	,	,		18254	0.1131		0.0596	False		,,,				2504	0.0337				p.Q239R		Atlas-SNP	.											.	PHLDB3	30	.	0			c.A716G						PASS	.	T	ARG/GLN	214,4192	128.2+/-165.1	5,204,1994	41.0	39.0	40.0		716	4.5	1.0	19	dbSNP_120	40	468,8132	136.0+/-193.2	15,438,3847	yes	missense	PHLDB3	NM_198850.3	43	20,642,5841	CC,CT,TT		5.4419,4.857,5.2437	possibly-damaging	239/641	44001379	682,12324	2203	4300	6503	SO:0001583	missense	653583	exon6			AGTTGCTGGAACT		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.716A>G	19.37:g.44001379T>C	ENSP00000292140:p.Gln239Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	166	0.076007326007326	13	0.026422764227642278	52	0.143646408839779	57	0.09965034965034965	44	0.05804749340369393	T	16.09	3.025064	0.54683	0.04857	0.054419	ENSG00000176531	ENST00000292140	T	0.53423	0.62	4.51	4.51	0.55191	.	0.316381	0.25414	N	0.030847	T	0.00845	0.0028	M	0.66297	2.02	0.37189	P	0.09614599999999995	D;D	0.67145	0.996;0.981	D;D	0.75484	0.986;0.932	T	0.35699	-0.9778	9	0.66056	D	0.02	.	10.5883	0.45296	0.0:0.0:0.0:1.0	rs11083711;rs52805800;rs60922596;rs11083711	239;239	Q6NSJ2-2;Q6NSJ2	.;PHLB3_HUMAN	R	239	ENSP00000292140:Q239R	ENSP00000292140:Q239R	Q	-	2	0	PHLDB3	48693219	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.385000	0.59613	1.817000	0.53016	0.254000	0.18369	CAG	T|0.939;C|0.061	0.061	strong		0.617	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
POU5F1	5460	hgsc.bcm.edu	37	6	31138310	31138310	+	Missense_Mutation	SNP	C	C	T	rs41257954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31138310C>T	ENST00000259915.8	-	1	160	c.88G>A	c.(88-90)Gtt>Att	p.V30I	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	30					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	CGAGGATCAACCCAGCCCGGC	0.687			T	EWSR1	sarcoma								C|||	59	0.0117812	0.0015	0.0043	5008	,	,		13351	0.0149		0.0278	False		,,,				2504	0.0112				p.V30I		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	.	POU5F1	25	.	0			c.G88A						PASS	.	C	ILE/VAL	10,2778		0,10,1384	4.0	5.0	5.0		88	1.9	1.0	6	dbSNP_127	5	72,4952		0,72,2440	no	missense	POU5F1	NM_002701.4	29	0,82,3824	TT,TC,CC		1.4331,0.3587,1.0497	benign	30/361	31138310	82,7730	1394	2512	3906	SO:0001583	missense	5460	exon1			GATCAACCCAGCC	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.88G>A	6.37:g.31138310C>T	ENSP00000259915:p.Val30Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Missense_Mutation	SNP	ENST00000259915.8	37	CCDS34391.1	42	0.019230769230769232	2	0.0040650406504065045	2	0.0055248618784530384	14	0.024475524475524476	24	0.0316622691292876	C	15.63	2.891065	0.52014	0.003587	0.014331	ENSG00000204531	ENST00000259915;ENST00000448657	T	0.61742	0.08	3.7	1.92	0.25849	.	0.791726	0.10706	N	0.643431	T	0.34600	0.0903	M	0.61703	1.905	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	10	0.66056	D	0.02	.	5.9515	0.19248	0.0:0.7594:0.0:0.2406	rs41257954	30	Q01860	PO5F1_HUMAN	I	30	ENSP00000259915:V30I	ENSP00000259915:V30I	V	-	1	0	POU5F1	31246289	0.985000	0.35326	0.998000	0.56505	0.952000	0.60782	0.124000	0.15728	0.553000	0.29044	0.549000	0.68633	GTT	C|0.974;T|0.026	0.026	strong		0.687	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
PPIF	10105	hgsc.bcm.edu	37	10	81109458	81109458	+	Silent	SNP	C	C	T	rs2233719	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:81109458C>T	ENST00000225174.3	+	3	335	c.264C>T	c.(262-264)ttC>ttT	p.F88F	PPIF_ENST00000492149.1_3'UTR|PPIF_ENST00000394579.3_Silent_p.F88F	NM_005729.3	NP_005720.1	P30405	PPIF_HUMAN	peptidylprolyl isomerase F	88	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				apoptotic mitochondrial changes (GO:0008637)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ATPase activity (GO:0032780)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of oxidative phosphorylation uncoupler activity (GO:2000276)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein folding (GO:0006457)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of necrotic cell death (GO:0010939)|regulation of proton-transporting ATPase activity, rotational mechanism (GO:0010849)|response to ischemia (GO:0002931)	membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(2)|lung(2)|skin(2)	6	all_cancers(46;0.0893)|Breast(12;8.52e-05)|all_epithelial(25;0.00449)|Prostate(51;0.00985)		Epithelial(14;0.00242)|all cancers(16;0.0069)|Colorectal(32;0.229)		Cyclosporine(DB00091)|L-Proline(DB00172)	AGAAGGGCTTCGGCTACAAAG	0.552													C|||	104	0.0207668	0.003	0.0331	5008	,	,		21390	0.0		0.0656	False		,,,				2504	0.0112				p.F88F		Atlas-SNP	.											.	PPIF	15	.	0			c.C264T						PASS	.	C		36,4370	40.8+/-73.8	0,36,2167	113.0	91.0	99.0		264	-4.6	0.8	10	dbSNP_98	99	449,8151	134.9+/-192.2	14,421,3865	no	coding-synonymous	PPIF	NM_005729.3		14,457,6032	TT,TC,CC		5.2209,0.8171,3.729		88/208	81109458	485,12521	2203	4300	6503	SO:0001819	synonymous_variant	10105	exon3			GGGCTTCGGCTAC	M80254	CCDS7358.1	10q22-q23	2008-10-24	2008-10-24		ENSG00000108179	ENSG00000108179	5.2.1.8		9259	protein-coding gene	gene with protein product	"""cyclophilin D"""	604486	"""peptidylprolyl isomerase F (cyclophilin F)"""			1744118	Standard	NM_005729		Approved	hCyP3, Cyp-D	uc001kai.3	P30405	OTTHUMG00000018562	ENST00000225174.3:c.264C>T	10.37:g.81109458C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	144	59	0.409722	NM_005729	Q2YDB7|Q5W131	Silent	SNP	ENST00000225174.3	37	CCDS7358.1	65	0.02976190476190476	1	0.0020325203252032522	15	0.04143646408839779	0	0.0	49	0.06464379947229551	C	6.163	0.398292	0.11696	0.008171	0.052209	ENSG00000108179	ENST00000448165	.	.	.	5.4	-4.61	0.03380	.	.	.	.	.	T	0.18551	0.0445	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56908	-0.7901	4	.	.	.	-25.8689	16.2424	0.82423	0.0:0.2631:0.0:0.7369	rs2233719	.	.	.	L	52	.	.	S	+	2	0	PPIF	80779464	0.018000	0.18449	0.755000	0.31263	0.585000	0.36419	-1.041000	0.03542	-1.342000	0.02222	-2.069000	0.00389	TCG	C|0.964;T|0.036	0.036	strong		0.552	PPIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048949.1	NM_005729	
GAK	2580	hgsc.bcm.edu	37	4	860192	860192	+	Silent	SNP	A	A	G	rs1064207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:860192A>G	ENST00000314167.4	-	22	3113	c.3003T>C	c.(3001-3003)agT>agC	p.S1001S	GAK_ENST00000511163.1_Silent_p.S922S|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1001					cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GGGGCGGAGCACTGTGGGCAG	0.632													G|||	3269	0.652756	0.5772	0.585	5008	,	,		16289	0.6567		0.6252	False		,,,				2504	0.8272				p.S1001S		Atlas-SNP	.											.	GAK	104	.	0			c.T3003C						PASS	.	G		2687,1719	514.5+/-368.7	821,1045,337	78.0	75.0	76.0		3003	-4.8	0.8	4	dbSNP_86	76	5440,3160	479.4+/-370.1	1745,1950,605	no	coding-synonymous	GAK	NM_005255.2		2566,2995,942	GG,GA,AA		36.7442,39.015,37.5135		1001/1312	860192	8127,4879	2203	4300	6503	SO:0001819	synonymous_variant	2580	exon22			CGGAGCACTGTGG	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3003T>C	4.37:g.860192A>G		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	1308|1308	0.5989010989010989|0.5989010989010989	265|265	0.5386178861788617|0.5386178861788617	208|208	0.574585635359116|0.574585635359116	361|361	0.6311188811188811|0.6311188811188811	474|474	0.6253298153034301|0.6253298153034301	G|G	1.579|1.579	-0.532196|-0.532196	0.04112|0.04112	0.60985|0.60985	0.632558|0.632558	ENSG00000178950|ENSG00000178950	ENST00000510799|ENST00000511980	.|.	.|.	.|.	5.24|5.24	-4.8|-4.8	0.03190|0.03190	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999555762|0.99999555762	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.11591|0.11591	-1.0581|-1.0581	3|3	.|.	.|.	.|.	-34.3133|-34.3133	15.233|15.233	0.73407|0.73407	0.6304:0.0:0.3696:0.0|0.6304:0.0:0.3696:0.0	rs1064207;rs60937528;rs1064207|rs1064207;rs60937528;rs1064207	.|.	.|.	.|.	R|A	121|113	.|.	.|.	C|V	-|-	1|2	0|0	GAK|GAK	850192|850192	0.032000|0.032000	0.19561|0.19561	0.765000|0.765000	0.31456|0.31456	0.005000|0.005000	0.04900|0.04900	-1.084000|-1.084000	0.03393|0.03393	-1.390000|-1.390000	0.02087|0.02087	-2.599000|-2.599000	0.00162|0.00162	TGC|GTG	A|0.389;G|0.611	0.611	strong		0.632	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
OR13J1	392309	hgsc.bcm.edu	37	9	35870225	35870225	+	Silent	SNP	G	G	A	rs72727089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35870225G>A	ENST00000377981.2	-	1	236	c.174C>T	c.(172-174)ccC>ccT	p.P58P		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	58						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(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			AGAAGTACACGGGCGTGTGCA	0.582													G|||	890	0.177716	0.0272	0.2608	5008	,	,		22168	0.0804		0.3091	False		,,,				2504	0.2873				p.P58P		Atlas-SNP	.											.	OR13J1	37	.	0			c.C174T						PASS	.	G		330,4076	173.4+/-203.2	12,306,1885	119.0	105.0	110.0		174	4.8	1.0	9	dbSNP_130	110	2665,5935	428.6+/-355.9	411,1843,2046	no	coding-synonymous	OR13J1	NM_001004487.1		423,2149,3931	AA,AG,GG		30.9884,7.4898,23.0278		58/313	35870225	2995,10011	2203	4300	6503	SO:0001819	synonymous_variant	392309	exon1			GTACACGGGCGTG		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"""GPCR / Class A : Olfactory receptors"""	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.174C>T	9.37:g.35870225G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_001004487	B2RN66|Q6IF20|Q96R40	Silent	SNP	ENST00000377981.2	37	CCDS35011.1																																																																																			G|0.779;A|0.221	0.221	strong		0.582	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1		
ELF1	1997	hgsc.bcm.edu	37	13	41515286	41515286	+	Missense_Mutation	SNP	T	T	A	rs1056820	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:41515286T>A	ENST00000239882.3	-	8	1341	c.1027A>T	c.(1027-1029)Aca>Tca	p.T343S	ELF1_ENST00000442101.1_Missense_Mutation_p.T319S|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	343			T -> S (in dbSNP:rs1056820). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TTTAGAACTGTAGTGGCTCCT	0.473													T|||	2071	0.413538	0.152	0.6657	5008	,	,		17563	0.1538		0.7097	False		,,,				2504	0.5511				p.T343S		Atlas-SNP	.											ELF1,colon,carcinoma,0,1	ELF1	65	1	0			c.A1027T						PASS	.	T	SER/THR,SER/THR	972,3434	363.6+/-316.6	103,766,1334	167.0	155.0	159.0		955,1027	4.3	1.0	13	dbSNP_86	159	5834,2766	679.4+/-403.6	1961,1912,427	yes	missense,missense	ELF1	NM_001145353.1,NM_172373.3	58,58	2064,2678,1761	AA,AT,TT		32.1628,22.0608,47.6703	possibly-damaging,possibly-damaging	319/596,343/620	41515286	6806,6200	2203	4300	6503	SO:0001583	missense	1997	exon8			GAACTGTAGTGGC	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1027A>T	13.37:g.41515286T>A	ENSP00000239882:p.Thr343Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	130	52	0.4	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	955	0.43727106227106227	82	0.16666666666666666	229	0.6325966850828729	93	0.16258741258741258	551	0.7269129287598944	T	10.55	1.382206	0.24944	0.220608	0.678372	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.53640	0.61;0.61	5.47	4.3	0.51218	.	0.614496	0.17112	N	0.186597	T	0.00012	0.0000	L	0.36672	1.1	0.29711	P	0.839398	B;B	0.13594	0.004;0.008	B;B	0.16722	0.011;0.016	T	0.41378	-0.9512	9	0.07175	T	0.84	.	5.6684	0.17709	0.1273:0.1416:0.0:0.7311	rs1056820;rs3197446;rs17447529;rs1056820	319;343	E9PDQ9;P32519	.;ELF1_HUMAN	S	319;85;343	ENSP00000405580:T319S;ENSP00000239882:T343S	ENSP00000239882:T343S	T	-	1	0	ELF1	40413286	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.626000	0.24492	1.026000	0.39733	0.533000	0.62120	ACA	T|0.513;A|0.487	0.487	strong		0.473	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
PIGO	84720	hgsc.bcm.edu	37	9	35091880	35091880	+	Silent	SNP	C	C	T	rs10814196	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35091880C>T	ENST00000378617.3	-	7	2398	c.2004G>A	c.(2002-2004)ttG>ttA	p.L668L	PIGO_ENST00000361778.2_Intron|PIGO_ENST00000298004.5_Intron|PIGO_ENST00000341666.3_Silent_p.L668L	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	668					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CTCCATACCACAAATTCTTGG	0.592													C|||	981	0.195887	0.1891	0.2046	5008	,	,		17772	0.0774		0.2048	False		,,,				2504	0.3119				p.L668L		Atlas-SNP	.											.	PIGO	86	.	0			c.G2004A						PASS	.	C	,,	835,3571	331.2+/-301.9	82,671,1450	49.0	51.0	50.0		,2004,	2.5	1.0	9	dbSNP_120	50	1748,6852	316.2+/-312.6	181,1386,2733	no	intron,coding-synonymous,intron	PIGO	NM_001201484.1,NM_032634.3,NM_152850.3	,,	263,2057,4183	TT,TC,CC		20.3256,18.9514,19.8601	,,	,668/1090,	35091880	2583,10423	2203	4300	6503	SO:0001819	synonymous_variant	84720	exon7			ATACCACAAATTC	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.2004G>A	9.37:g.35091880C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	64	23	0.359375	NM_032634	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Silent	SNP	ENST00000378617.3	37	CCDS6575.1																																																																																			C|0.816;T|0.184	0.184	strong		0.592	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634	
SPHK1	8877	hgsc.bcm.edu	37	17	74383601	74383601	+	Silent	SNP	C	C	T	rs346802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74383601C>T	ENST00000545180.1	+	8	1898	c.1089C>T	c.(1087-1089)agC>agT	p.S363S	SPHK1_ENST00000392496.3_Silent_p.S363S|SPHK1_ENST00000592299.1_Silent_p.S363S|SPHK1_ENST00000323374.4_Silent_p.S449S|SPHK1_ENST00000590959.1_Silent_p.S377S			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	363					'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)	GGATGGTCAGCGGTTGCGTGG	0.612													T|||	495	0.0988419	0.0946	0.1124	5008	,	,		17655	0.1111		0.0487	False		,,,				2504	0.1339				p.S449S	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.C1347T						PASS	.	T	,,,	368,4038	781.7+/-414.5	15,338,1850	48.0	50.0	49.0		1089,1089,1131,1347	-0.9	0.1	17	dbSNP_79	49	281,8319	800.7+/-407.4	7,267,4026	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	,,,	22,605,5876	TT,TC,CC		3.2674,8.3522,4.99	,,,	363/385,363/385,377/399,449/471	74383601	649,12357	2203	4300	6503	SO:0001819	synonymous_variant	8877	exon6			GGTCAGCGGTTGC	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.1089C>T	17.37:g.74383601C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Silent	SNP	ENST00000545180.1	37	CCDS45785.1																																																																																			C|0.943;T|0.057	0.057	strong		0.612	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
PGC	5225	hgsc.bcm.edu	37	6	41710111	41710111	+	Silent	SNP	G	G	A	rs61731757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:41710111G>A	ENST00000373025.3	-	5	626	c.564C>T	c.(562-564)tcC>tcT	p.S188S	PGC_ENST00000425343.2_Silent_p.S188S	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	188					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			CCTCATCCACGGACAGAGCAG	0.602													G|||	12	0.00239617	0.0	0.0043	5008	,	,		18988	0.0		0.0089	False		,,,				2504	0.0				p.S188S		Atlas-SNP	.											.	PGC	56	.	0			c.C564T						PASS	.	G	,	7,4399	12.9+/-30.5	0,7,2196	130.0	94.0	106.0		564,564	-3.7	0.0	6	dbSNP_129	106	81,8519	47.2+/-106.3	0,81,4219	no	coding-synonymous,coding-synonymous	PGC	NM_001166424.1,NM_002630.3	,	0,88,6415	AA,AG,GG		0.9419,0.1589,0.6766	,	188/316,188/389	41710111	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	5225	exon5			ATCCACGGACAGA		CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.564C>T	6.37:g.41710111G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Silent	SNP	ENST00000373025.3	37	CCDS4859.1																																																																																			G|0.994;A|0.006	0.006	strong		0.602	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2		
AQP8	343	hgsc.bcm.edu	37	16	25239805	25239805	+	Missense_Mutation	SNP	G	G	C	rs2287798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:25239805G>C	ENST00000219660.5	+	6	903	c.778G>C	c.(778-780)Gct>Cct	p.A260P	AQP8_ENST00000566125.1_Missense_Mutation_p.A254P	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	260			A -> P (in dbSNP:rs2287798).		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)	p.A260P(2)		NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		CATCCTGAAGGCTCGGTGAAG	0.592													G|||	2074	0.414137	0.4077	0.4308	5008	,	,		19369	0.5298		0.3459	False		,,,				2504	0.362				p.A260P		Atlas-SNP	.											AQP8_ENST00000219660,NS,carcinoma,0,2	AQP8	75	2	2	Substitution - Missense(2)	stomach(2)	c.G778C						scavenged	.	G	PRO/ALA	1822,2572	533.3+/-373.7	378,1066,753	97.0	84.0	88.0		778	-1.5	0.0	16	dbSNP_100	88	3191,5409	482.4+/-370.9	578,2035,1687	yes	missense	AQP8	NM_001169.2	27	956,3101,2440	CC,CG,GG		37.1047,41.4656,38.5793	benign	260/262	25239805	5013,7981	2197	4300	6497	SO:0001583	missense	343	exon6			CTGAAGGCTCGGT	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.778G>C	16.37:g.25239805G>C	ENSP00000219660:p.Ala260Pro	Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_001169	Q8IUU3|Q9UIA4	Missense_Mutation	SNP	ENST00000219660.5	37	CCDS10626.1	903	0.41346153846153844	203	0.41260162601626016	146	0.40331491712707185	291	0.5087412587412588	263	0.3469656992084433	G	9.751	1.167366	0.21621	0.414656	0.371047	ENSG00000103375	ENST00000219660	D	0.90844	-2.74	4.71	-1.46	0.08800	Aquaporin-like (1);	2.407790	0.01641	N	0.024060	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.26975	0.165	B	0.23018	0.043	T	0.21449	-1.0245	9	0.40728	T	0.16	1.6603	8.6705	0.34147	0.0:0.1258:0.4556:0.4186	rs2287798;rs56573772;rs2287798	260	O94778	AQP8_HUMAN	P	260	ENSP00000219660:A260P	ENSP00000219660:A260P	A	+	1	0	AQP8	25147306	0.174000	0.23070	0.003000	0.11579	0.003000	0.03518	0.297000	0.19101	-0.007000	0.14345	-0.831000	0.03077	GCT	G|0.599;C|0.401	0.401	strong		0.592	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169	
SCN4A	6329	hgsc.bcm.edu	37	17	62018931	62018931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62018931G>A	ENST00000435607.1	-	24	4787	c.4711C>T	c.(4711-4713)Ccc>Tcc	p.P1571S	SCN4A_ENST00000578147.1_Missense_Mutation_p.P1571S	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1571					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)	CCGATGGAGGGGTTGCCGCAG	0.577																																					p.P1571S		Atlas-SNP	.											.	SCN4A	205	.	0			c.C4711T						PASS	.						46.0	52.0	50.0					17																	62018931		2149	4263	6412	SO:0001583	missense	6329	exon24			TGGAGGGGTTGCC	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.4711C>T	17.37:g.62018931G>A	ENSP00000396320:p.Pro1571Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	g	17.38	3.376136	0.61735	.	.	ENSG00000007314	ENST00000435607	D	0.98178	-4.77	3.9	3.9	0.45041	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98210	0.9408	L	0.46670	1.46	0.58432	D	0.999998	D	0.89917	1.0	D	0.81914	0.995	D	0.98880	1.0769	10	0.62326	D	0.03	.	15.4266	0.75055	0.0:0.0:1.0:0.0	.	1571	P35499	SCN4A_HUMAN	S	1571	ENSP00000396320:P1571S	ENSP00000396320:P1571S	P	-	1	0	SCN4A	59372663	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.601000	0.98297	2.177000	0.69029	0.556000	0.70494	CCC	.	.	none		0.577	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
C12orf5	57103	hgsc.bcm.edu	37	12	4461485	4461485	+	Silent	SNP	G	G	A	rs7133330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4461485G>A	ENST00000179259.4	+	6	508	c.441G>A	c.(439-441)gcG>gcA	p.A147A	C12orf5_ENST00000537251.1_3'UTR	NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	147					intestinal epithelial cell development (GO:0060576)|negative regulation of macromitophagy (GO:1901525)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|response to gamma radiation (GO:0010332)|response to xenobiotic stimulus (GO:0009410)	intracellular (GO:0005622)	fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			endometrium(1)|large_intestine(1)|lung(5)|skin(3)	10			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			TGAAAGAAGCGGATCAAAAAG	0.333													G|||	918	0.183307	0.0832	0.2839	5008	,	,		19855	0.1577		0.2714	False		,,,				2504	0.183				p.A147A	Colon(1;100 192 35375 49454 52532)	Atlas-SNP	.											.	C12orf5	28	.	0			c.G441A						PASS	.	G		494,3912	223.6+/-240.1	32,430,1741	56.0	57.0	57.0		441	-1.5	0.1	12	dbSNP_116	57	2302,6298	383.6+/-340.8	306,1690,2304	no	coding-synonymous	C12orf5	NM_020375.2		338,2120,4045	AA,AG,GG		26.7674,11.212,21.4978		147/271	4461485	2796,10210	2203	4300	6503	SO:0001819	synonymous_variant	57103	exon6			AGAAGCGGATCAA	AJ272206	CCDS8525.1	12p13.32	2014-05-29	2009-11-24	2009-11-24	ENSG00000078237	ENSG00000078237	3.1.3.46		1185	protein-coding gene	gene with protein product	"""TP53-induced glycolysis and apoptosis regulator"""	610775				16140933, 16839880, 18945750, 19713938	Standard	NM_020375		Approved	TIGAR	uc001qmp.3	Q9NQ88		ENST00000179259.4:c.441G>A	12.37:g.4461485G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_020375	B2R840	Silent	SNP	ENST00000179259.4	37	CCDS8525.1																																																																																			G|0.799;A|0.201	0.201	strong		0.333	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375	
OR2J3	442186	hgsc.bcm.edu	37	6	29080386	29080386	+	Missense_Mutation	SNP	T	T	C	rs79293918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	318	1	0.00314465		WXS	Illumina HiSeq	Phase_I	345	152	0.44058	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		
TRIM14	9830	hgsc.bcm.edu	37	9	100857170	100857170	+	Silent	SNP	A	A	G	rs150211153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100857170A>G	ENST00000341469.2	-	4	688	c.679T>C	c.(679-681)Ttg>Ctg	p.L227L	TRIM14_ENST00000342043.3_Silent_p.L227L|TRIM14_ENST00000375098.3_Silent_p.L227L|TRIM14_ENST00000538344.1_5'Flank	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	227					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				CGAATGTCCAATGGCGTCTGT	0.532													A|||	2	0.000399361	0.0	0.0	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.0				p.L227L	Colon(14;460 597 13826 51781)	Atlas-SNP	.											.	TRIM14	24	.	0			c.T679C						PASS	.	A	,,	2,4404	4.2+/-10.8	0,2,2201	128.0	111.0	117.0		679,679,679	-0.0	0.3	9	dbSNP_134	117	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM14	NM_014788.2,NM_033219.1,NM_033220.1	,,	0,13,6490	GG,GA,AA		0.1279,0.0454,0.1	,,	227/443,227/443,227/443	100857170	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	9830	exon4			TGTCCAATGGCGT	AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"""Tripartite motif containing / Tripartite motif containing"""	16283	protein-coding gene	gene with protein product		606556	"""tripartite motif-containing 14"""			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.679T>C	9.37:g.100857170A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_033219	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Silent	SNP	ENST00000341469.2	37	CCDS6734.1																																																																																			A|0.999;G|0.001	0.001	strong		0.532	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788	
PCNT	5116	hgsc.bcm.edu	37	21	47786524	47786524	+	Missense_Mutation	SNP	A	A	G	rs2839227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47786524A>G	ENST00000359568.5	+	15	2742	c.2635A>G	c.(2635-2637)Acc>Gcc	p.T879A	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	879			T -> A (in dbSNP:rs2839227). {ECO:0000269|PubMed:11171385}.		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)					TAAAGAGATCACCGAGAAATT	0.522													A|||	1586	0.316693	0.5787	0.2464	5008	,	,		20280	0.2014		0.1521	False		,,,				2504	0.3006				p.T879A		Atlas-SNP	.											.	PCNT	283	.	0			c.A2635G						PASS	.	A	ALA/THR	2199,2189		545,1109,540	63.0	60.0	61.0		2635	1.8	0.0	21	dbSNP_100	61	1168,7408		82,1004,3202	yes	missense	PCNT	NM_006031.5	58	627,2113,3742	GG,GA,AA		13.6194,49.8861,25.9719	possibly-damaging	879/3337	47786524	3367,9597	2194	4288	6482	SO:0001583	missense	5116	exon15			GAGATCACCGAGA	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.2635A>G	21.37:g.47786524A>G	ENSP00000352572:p.Thr879Ala	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	258	120	0.465116	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	584	0.2673992673992674	275	0.5589430894308943	71	0.19613259668508287	121	0.21153846153846154	117	0.15435356200527706	A	7.766	0.706433	0.15239	0.501139	0.136194	ENSG00000160299	ENST00000359568	T	0.01560	4.77	5.61	1.81	0.25067	.	0.919056	0.08883	N	0.879765	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B;B	0.29988	0.264;0.172	B;B	0.17722	0.019;0.009	T	0.12760	-1.0535	9	0.19590	T	0.45	.	4.1456	0.10214	0.689:0.0:0.1615:0.1495	rs2839227;rs59744350;rs2839227	761;879	O95613-2;O95613	.;PCNT_HUMAN	A	879	ENSP00000352572:T879A	ENSP00000352572:T879A	T	+	1	0	PCNT	46610952	0.044000	0.20184	0.002000	0.10522	0.099000	0.18886	2.418000	0.44662	0.438000	0.26450	0.533000	0.62120	ACC	A|0.704;C|0.002	.	strong		0.522	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
DNAAF1	123872	hgsc.bcm.edu	37	16	84203612	84203612	+	Missense_Mutation	SNP	A	A	G	rs17856705	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:84203612A>G	ENST00000378553.5	+	8	1302	c.1178A>G	c.(1177-1179)aAg>aGg	p.K393R	DNAAF1_ENST00000334315.5_Missense_Mutation_p.K393R|DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	393	Pro-rich.		K -> R (in dbSNP:rs17856705). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)	p.K393R(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						TGCCCGGAAAAGCCAAGTGGA	0.577													A|||	1608	0.321086	0.1853	0.4063	5008	,	,		18118	0.3403		0.4473	False		,,,				2504	0.2945				p.K393R		Atlas-SNP	.											DNAAF1,NS,carcinoma,0,1	DNAAF1	81	1	1	Substitution - Missense(1)	stomach(1)	c.A1178G						PASS	.	A	ARG/LYS	991,3409	369.1+/-318.9	105,781,1314	61.0	67.0	65.0		1178	0.1	0.0	16	dbSNP_123	65	3932,4666	546.9+/-385.1	897,2138,1264	yes	missense	DNAAF1	NM_178452.4	26	1002,2919,2578	GG,GA,AA		45.7316,22.5227,37.8751	benign	393/726	84203612	4923,8075	2200	4299	6499	SO:0001583	missense	123872	exon8			CGGAAAAGCCAAG	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1178A>G	16.37:g.84203612A>G	ENSP00000367815:p.Lys393Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	94	59	0.62766	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	795	0.364010989010989	99	0.20121951219512196	145	0.4005524861878453	209	0.36538461538461536	342	0.45118733509234826	A	9.460	1.092818	0.20471	0.225227	0.457316	ENSG00000154099	ENST00000334315;ENST00000378553	T;T	0.34472	1.36;1.78	5.18	0.133	0.14766	.	1.732920	0.03435	N	0.208365	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.003	T	0.44682	-0.9312	9	0.18710	T	0.47	-2.2671	1.0174	0.01510	0.5219:0.1476:0.1697:0.1609	rs17856705;rs17856705	157;393	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	R	393	ENSP00000334593:K393R;ENSP00000367815:K393R	ENSP00000334593:K393R	K	+	2	0	DNAAF1	82761113	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.630000	0.24553	-0.189000	0.10482	-1.652000	0.00757	AAG	A|0.639;G|0.361	0.361	strong		0.577	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
CFTR	1080	hgsc.bcm.edu	37	7	117306991	117306991	+	Silent	SNP	C	C	T	rs1800135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:117306991C>T	ENST00000003084.6	+	27	4404	c.4272C>T	c.(4270-4272)taC>taT	p.Y1424Y	CFTR_ENST00000454343.1_Silent_p.Y1363Y	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1424	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)	TGCGGCAGTACGATTCCATCC	0.542									Cystic Fibrosis				C|||	21	0.00419329	0.0	0.0058	5008	,	,		17076	0.0		0.0139	False		,,,				2504	0.0031				p.Y1424Y		Atlas-SNP	.											.	CFTR	171	.	0			c.C4272T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	59.0	51.0	54.0		4272	-9.6	0.0	7	dbSNP_89	54	58,8542	36.9+/-92.0	1,56,4243	no	coding-synonymous	CFTR	NM_000492.3		1,65,6437	TT,TC,CC		0.6744,0.2043,0.5151		1424/1481	117306991	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	1080	exon27	Familial Cancer Database	CF	GCAGTACGATTCC	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.4272C>T	7.37:g.117306991C>T		Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	191	92	0.481675	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																			C|0.994;T|0.006	0.006	strong		0.542	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
NHSL1	57224	hgsc.bcm.edu	37	6	138745299	138745299	+	Silent	SNP	G	G	A	rs9495082	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:138745299G>A	ENST00000427025.2	-	7	5380	c.4752C>T	c.(4750-4752)ccC>ccT	p.P1584P	NHSL1_ENST00000343505.5_Silent_p.P1580P	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1584										breast(2)|endometrium(4)|kidney(1)	7						CCACAGGGCCGGGGGCCTGGG	0.682													G|||	632	0.126198	0.3222	0.0865	5008	,	,		15615	0.0139		0.0845	False		,,,				2504	0.0481				p.P1584P		Atlas-SNP	.											.	NHSL1	99	.	0			c.C4752T						PASS	.	G	,	308,1010		41,226,392	5.0	9.0	7.0		4740,4752	-5.0	0.0	6	dbSNP_119	7	218,2872		5,208,1332	no	coding-synonymous,coding-synonymous	NHSL1	NM_001144060.1,NM_020464.1	,	46,434,1724	AA,AG,GG		7.055,23.3687,11.9328	,	1580/1607,1584/1611	138745299	526,3882	659	1545	2204	SO:0001819	synonymous_variant	57224	exon7			AGGGCCGGGGGCC	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.4752C>T	6.37:g.138745299G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	28	10	0.357143	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Silent	SNP	ENST00000427025.2	37	CCDS55063.1																																																																																			G|0.893;A|0.107	0.107	strong		0.682	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
MYBPC3	4607	hgsc.bcm.edu	37	11	47354787	47354787	+	Silent	SNP	C	C	T	rs1052373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47354787C>T	ENST00000545968.1	-	30	3342	c.3288G>A	c.(3286-3288)gaG>gaA	p.E1096E	MYBPC3_ENST00000399249.2_Silent_p.E1096E|MYBPC3_ENST00000256993.4_Silent_p.E1095E	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	1096	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		ACCCCCAGAGCTCCGTGTTGC	0.637													C|||	2385	0.476238	0.5083	0.3329	5008	,	,		19715	0.7202		0.3072	False		,,,				2504	0.4571				p.E1096E		Atlas-SNP	.											.	MYBPC3	102	.	0			c.G3288A						PASS	.	C		1833,2133		433,967,583	41.0	47.0	45.0		3288	2.4	0.7	11	dbSNP_86	45	2524,5782		385,1754,2014	yes	coding-synonymous	MYBPC3	NM_000256.3		818,2721,2597	TT,TC,CC		30.3877,46.2179,35.5036		1096/1275	47354787	4357,7915	1983	4153	6136	SO:0001819	synonymous_variant	4607	exon29			CCAGAGCTCCGTG	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.3288G>A	11.37:g.47354787C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Silent	SNP	ENST00000545968.1	37	CCDS53621.1																																																																																			C|0.557;T|0.443	0.443	strong		0.637	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
KIF19	124602	hgsc.bcm.edu	37	17	72346855	72346855	+	Silent	SNP	T	T	C	rs11077744	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72346855T>C	ENST00000389916.4	+	12	1536	c.1398T>C	c.(1396-1398)caT>caC	p.H466H		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	466					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						GCTGGAAGCATGAGAAGTCCC	0.627													t|||	3017	0.602436	0.1566	0.7493	5008	,	,		17064	0.7421		0.7843	False		,,,				2504	0.7699				p.H466H		Atlas-SNP	.											.	KIF19	102	.	0			c.T1398C						PASS	.			1102,3304	379.7+/-323.4	134,834,1235	47.0	46.0	46.0		1398	-11.5	0.0	17	dbSNP_120	46	6848,1752	719.5+/-406.3	2720,1408,172	no	coding-synonymous	KIF19	NM_153209.3		2854,2242,1407	CC,CT,TT		20.3721,25.0113,38.8744		466/999	72346855	7950,5056	2203	4300	6503	SO:0001819	synonymous_variant	124602	exon12			GAAGCATGAGAAG	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.1398T>C	17.37:g.72346855T>C		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			T|0.397;C|0.603	0.603	strong		0.627	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
DPP7	29952	hgsc.bcm.edu	37	9	140008934	140008934	+	Silent	SNP	A	A	G	rs11145999	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140008934A>G	ENST00000371579.2	-	2	166	c.162T>C	c.(160-162)ccT>ccC	p.P54P		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	54						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)		GGAAGCGCTGAGGGAAGGTCT	0.731													G|||	1247	0.249002	0.1263	0.3242	5008	,	,		5355	0.129		0.3757	False		,,,				2504	0.3548				p.P54P		Atlas-SNP	.											.	DPP7	22	.	0			c.T162C						PASS	.	G		689,3603		76,537,1533	8.0	9.0	9.0		162	-0.4	0.1	9	dbSNP_120	9	3168,5246		639,1890,1678	no	coding-synonymous	DPP7	NM_013379.2		715,2427,3211	GG,GA,AA		37.6515,16.0531,30.3557		54/493	140008934	3857,8849	2146	4207	6353	SO:0001819	synonymous_variant	29952	exon2			GCGCTGAGGGAAG	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.162T>C	9.37:g.140008934A>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_013379	A8K7U7|Q5VSF1|Q969X4	Silent	SNP	ENST00000371579.2	37	CCDS7030.1	592	0.27106227106227104	97	0.19715447154471544	124	0.3425414364640884	68	0.11888111888111888	303	0.3997361477572559	G	4.691	0.128560	0.08981	0.160531	0.376515	ENSG00000176978	ENST00000443858	.	.	.	3.89	-0.399	0.12415	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.23277	P	0.99799006	B	0.02656	0.0	B	0.01281	0.0	T	0.47235	-0.9133	5	.	.	.	-3.1938	4.3537	0.11167	0.3006:0.3159:0.3836:0.0	rs11145999;rs11547762;rs17850819	78	E7EQS4	.	P	78	.	.	S	-	1	0	DPP7	139128755	0.001000	0.12720	0.055000	0.19348	0.319000	0.28217	-0.471000	0.06631	-0.268000	0.09312	-0.215000	0.12644	TCA	A|0.728;G|0.272;T|0.000	0.272	strong		0.731	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379	
SMCO3	440087	hgsc.bcm.edu	37	12	14959006	14959006	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:14959006T>G	ENST00000316048.2	-	2	681	c.609A>C	c.(607-609)aaA>aaC	p.K203N	C12orf60_ENST00000330828.2_Intron|WBP11_ENST00000261167.2_5'Flank|C12orf60_ENST00000527783.1_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	203						integral component of membrane (GO:0016021)											CTGAGGCTGATTTGAACTCCA	0.403																																					p.K203N		Atlas-SNP	.											.	.	.	.	0			c.A609C						PASS	.						135.0	132.0	133.0					12																	14959006		1900	4122	6022	SO:0001583	missense	0	exon2			GGCTGATTTGAAC		CCDS41759.1	12p12.3	2013-03-11	2013-03-11	2013-03-11	ENSG00000179256	ENSG00000179256			34401	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 69"""	C12orf69			Standard	NM_001013698		Approved	LOC440087	uc001rck.1	A2RU48	OTTHUMG00000167474	ENST00000316048.2:c.609A>C	12.37:g.14959006T>G	ENSP00000381895:p.Lys203Asn	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	243	104	0.427984	NM_001013698	Q8NAI5	Missense_Mutation	SNP	ENST00000316048.2	37	CCDS41759.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.652321	0.47362	.	.	ENSG00000179256	ENST00000316048	T	0.16743	2.32	4.38	-0.586	0.11694	.	0.000000	0.41712	U	0.000829	T	0.10465	0.0256	L	0.27053	0.805	0.25005	N	0.991445	B	0.23185	0.081	B	0.25884	0.064	T	0.21042	-1.0257	10	0.72032	D	0.01	-3.6815	7.1498	0.25604	0.0:0.4745:0.0:0.5255	.	203	A2RU48	CL069_HUMAN	N	203	ENSP00000381895:K203N	ENSP00000381895:K203N	K	-	3	2	C12orf69	14850273	0.960000	0.32886	0.981000	0.43875	0.772000	0.43724	0.877000	0.28106	-0.010000	0.14271	-1.017000	0.02453	AAA	.	.	none		0.403	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698	
MYH9	4627	hgsc.bcm.edu	37	22	36691691	36691691	+	Silent	SNP	T	T	C	rs875725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36691691T>C	ENST00000216181.5	-	26	3575	c.3345A>G	c.(3343-3345)gaA>gaG	p.E1115E		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1115					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CTTCCTGGAGTTCAGAGATCT	0.522			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				T|||	128	0.0255591	0.0696	0.0159	5008	,	,		20546	0.0		0.0199	False		,,,				2504	0.0051				p.E1115E		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.A3345G						PASS	.	T		346,4060	177.3+/-206.3	15,316,1872	51.0	48.0	49.0		3345	-1.8	0.9	22	dbSNP_86	49	106,8494	57.9+/-119.4	1,104,4195	no	coding-synonymous	MYH9	NM_002473.4		16,420,6067	CC,CT,TT		1.2326,7.8529,3.4753		1115/1961	36691691	452,12554	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon26	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CTGGAGTTCAGAG		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.3345A>G	22.37:g.36691691T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			T|0.965;C|0.035	0.035	strong		0.522	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
TRPC6	7225	hgsc.bcm.edu	37	11	101359750	101359750	+	Missense_Mutation	SNP	G	G	A	rs36111323	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:101359750G>A	ENST00000344327.3	-	4	1635	c.1211C>T	c.(1210-1212)gCg>gTg	p.A404V	TRPC6_ENST00000360497.4_Intron|TRPC6_ENST00000532133.1_Missense_Mutation_p.A404V|TRPC6_ENST00000348423.4_Intron	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	404			A -> V (in dbSNP:rs36111323).		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)		GAACTTGACCGCCATTGTCTG	0.478													G|||	322	0.0642971	0.0023	0.0764	5008	,	,		15909	0.0268		0.1382	False		,,,				2504	0.1022				p.A404V	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											TRPC6,right_lower_lobe,carcinoma,+1,1	TRPC6	132	1	0			c.C1211T						PASS	.	G	VAL/ALA	100,4306	81.4+/-119.9	1,98,2104	95.0	87.0	90.0		1211	3.9	0.8	11	dbSNP_126	90	1047,7551	220.6+/-258.3	65,917,3317	yes	missense	TRPC6	NM_004621.5	64	66,1015,5421	AA,AG,GG		12.1773,2.2696,8.8204	benign	404/932	101359750	1147,11857	2203	4299	6502	SO:0001583	missense	7225	exon4			TTGACCGCCATTG	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.1211C>T	11.37:g.101359750G>A	ENSP00000340913:p.Ala404Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	159	0.07280219780219781	1	0.0020325203252032522	27	0.07458563535911603	18	0.03146853146853147	113	0.14907651715039577	G	14.00	2.405544	0.42715	0.022696	0.121773	ENSG00000137672	ENST00000344327;ENST00000532133	T;T	0.68624	-0.34;-0.34	5.77	3.92	0.45320	.	0.046747	0.85682	N	0.000000	T	0.00936	0.0031	L	0.47716	1.5	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	T	0.37244	-0.9714	9	0.12103	T	0.63	-12.0206	12.4707	0.55785	0.1347:0.0:0.8653:0.0	rs36111323	404	Q9Y210	TRPC6_HUMAN	V	404	ENSP00000340913:A404V;ENSP00000435574:A404V	ENSP00000340913:A404V	A	-	2	0	TRPC6	100864960	1.000000	0.71417	0.805000	0.32314	0.988000	0.76386	4.690000	0.61731	0.815000	0.34398	-0.143000	0.13931	GCG	A|0.083;G|0.917	0.083	strong		0.478	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621	
MEP1B	4225	hgsc.bcm.edu	37	18	29795101	29795101	+	Missense_Mutation	SNP	T	T	C	rs233223	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:29795101T>C	ENST00000269202.6	+	12	1683	c.1636T>C	c.(1636-1638)Tct>Cct	p.S546P	MEP1B_ENST00000581447.1_Missense_Mutation_p.S546P	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	546	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.			S -> P (in Ref. 2; AAU05377 and 3; AAI36560/AAI44245). {ECO:0000305}.	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						GGCTTTGTTCTCTAATGGAAC	0.393													C|||	4164	0.83147	0.8238	0.8372	5008	,	,		16693	0.995		0.7425	False		,,,				2504	0.7607				p.S546P		Atlas-SNP	.											.	MEP1B	54	.	0			c.T1636C						PASS	.	C	PRO/SER	2994,686		1214,566,60	106.0	105.0	106.0		1636	4.1	1.0	18	dbSNP_79	106	5868,2296		2118,1632,332	yes	missense	MEP1B	NM_005925.2	74	3332,2198,392	CC,CT,TT		28.1235,18.6413,25.1773	benign	546/702	29795101	8862,2982	1840	4082	5922	SO:0001583	missense	4225	exon12			TTGTTCTCTAATG	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.1636T>C	18.37:g.29795101T>C	ENSP00000269202:p.Ser546Pro	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	150	63	0.42	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	1844	0.8443223443223443	418	0.8495934959349594	296	0.8176795580110497	570	0.9965034965034965	560	0.7387862796833773	C	7.323	0.617371	0.14129	0.813587	0.718765	ENSG00000141434	ENST00000269202	T	0.19938	2.11	5.97	4.14	0.48551	TRAF-type (1);TRAF-like (1);MATH (3);	0.048376	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00109	-2.105	0.49213	P	2.3399999999995647E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.38650	-0.9651	9	0.21014	T	0.42	-9.6266	9.1155	0.36755	0.1275:0.7455:0.0:0.127	rs233223;rs52805518;rs57939154;rs233223	546	Q16820	MEP1B_HUMAN	P	546	ENSP00000269202:S546P	ENSP00000269202:S546P	S	+	1	0	MEP1B	28049099	0.017000	0.18338	0.998000	0.56505	0.439000	0.31926	-0.020000	0.12525	0.388000	0.25054	-0.119000	0.15052	TCT	T|0.171;C|0.829	0.829	strong		0.393	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
MTNR1A	4543	hgsc.bcm.edu	37	4	187454951	187454951	+	Silent	SNP	T	T	C	rs8192551	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187454951T>C	ENST00000307161.5	-	2	1146	c.945A>G	c.(943-945)acA>acG	p.T315T	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	315					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	ACACCCTGGCTGTACAGAGCG	0.448													T|||	334	0.0666933	0.1135	0.049	5008	,	,		20852	0.0784		0.0408	False		,,,				2504	0.0307				p.T315T		Atlas-SNP	.											.	MTNR1A	46	.	0			c.A945G						PASS	.	T		473,3933	223.9+/-240.3	22,429,1752	137.0	136.0	136.0		945	-1.6	0.1	4	dbSNP_117	136	387,8213	125.6+/-184.2	15,357,3928	no	coding-synonymous	MTNR1A	NM_005958.3		37,786,5680	CC,CT,TT		4.5,10.7354,6.6123		315/351	187454951	860,12146	2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			CCTGGCTGTACAG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.945A>G	4.37:g.187454951T>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	199	89	0.447236	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	37	CCDS3848.1																																																																																			T|0.936;C|0.064	0.064	strong		0.448	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
L1TD1	54596	hgsc.bcm.edu	37	1	62676612	62676612	+	Silent	SNP	A	A	G	rs66958136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:62676612A>G	ENST00000498273.1	+	4	2461	c.2166A>G	c.(2164-2166)aaA>aaG	p.K722K	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	722								p.K722K(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						acataattaaagaaataattg	0.358													G|||	792	0.158147	0.0825	0.3199	5008	,	,		20205	0.0704		0.2922	False		,,,				2504	0.0982				p.K722K		Atlas-SNP	.											L1TD1,NS,carcinoma,0,2	L1TD1	114	2	2	Substitution - coding silent(2)	ovary(1)|stomach(1)	c.A2166G						PASS	.	G	,	314,2912		19,276,1318	36.0	38.0	37.0		2166,2166	-4.0	0.0	1	dbSNP_130	37	1482,4316		190,1102,1607	no	coding-synonymous,coding-synonymous	L1TD1	NM_001164835.1,NM_019079.4	,	209,1378,2925	GG,GA,AA		25.5605,9.7334,19.9025	,	722/866,722/866	62676612	1796,7228	1613	2899	4512	SO:0001819	synonymous_variant	54596	exon5			AATTAAAGAAATA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.2166A>G	1.37:g.62676612A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	221	117	0.529412	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	37	CCDS619.1																																																																																			A|0.804;G|0.196	0.196	strong		0.358	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
DSPP	1834	hgsc.bcm.edu	37	4	88535785	88535785	+	Silent	SNP	C	C	T	rs111215813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88535785C>T	ENST00000282478.7	+	4	2004	c.1971C>T	c.(1969-1971)agC>agT	p.S657S	DSPP_ENST00000399271.1_Silent_p.S657S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	657	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.S657S(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)		gtgatagcagcgacagcagca	0.493													C|||	758	0.151358	0.0522	0.2435	5008	,	,		36985	0.1002		0.2714	False		,,,				2504	0.1493				p.S657S		Atlas-SNP	.											DSPP,NS,carcinoma,0,1	DSPP	174	1	1	Substitution - coding silent(1)	stomach(1)	c.C1971T						scavenged	.	C		290,3230		8,274,1478	117.0	137.0	130.0		1971	-3.2	0.2	4	dbSNP_132	130	1396,5034		133,1130,1952	no	coding-synonymous	DSPP	NM_014208.3		141,1404,3430	TT,TC,CC		21.7107,8.2386,16.9447		657/1302	88535785	1686,8264	1760	3215	4975	SO:0001819	synonymous_variant	1834	exon5			TAGCAGCGACAGC	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.1971C>T	4.37:g.88535785C>T		Somatic	195	7	0.0358974		WXS	Illumina HiSeq	Phase_I	226	114	0.504425	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			C|0.828;T|0.172	0.172	strong		0.493	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
LILRB4	11006	hgsc.bcm.edu	37	19	55174498	55174498	+	Missense_Mutation	SNP	T	T	C	rs28366008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55174498T>C	ENST00000391736.1	+	3	328	c.13T>C	c.(13-15)Ttc>Ctc	p.F5L	LILRB4_ENST00000391733.3_Missense_Mutation_p.F5L|LILRB4_ENST00000391734.3_Missense_Mutation_p.F5L|LILRB4_ENST00000270452.2_Missense_Mutation_p.F5L|LILRB4_ENST00000430952.2_Missense_Mutation_p.F5L	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	5			F -> L (in dbSNP:rs28366008). {ECO:0000269|PubMed:10941837}.		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.F5L(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		GATCCCCACCTTCACGGCTCT	0.602											OREG0003670	type=REGULATORY REGION|Gene=LILRB4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1525	0.304513	0.4955	0.2334	5008	,	,		14806	0.2331		0.2386	False		,,,				2504	0.2382				p.F5L		Atlas-SNP	.											LILRB4,NS,carcinoma,0,1	LILRB4	86	1	1	Substitution - Missense(1)	stomach(1)	c.T13C						scavenged	.	C	LEU/PHE,LEU/PHE	1861,2545	627.9+/-395.0	392,1077,734	52.0	55.0	54.0		13,13	0.5	0.0	19	dbSNP_125	54	2156,6444	711.8+/-405.9	282,1592,2426	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	22,22	674,2669,3160	CC,CT,TT		25.0698,42.2379,30.8857	benign,benign	5/448,5/449	55174498	4017,8989	2203	4300	6503	SO:0001583	missense	11006	exon1			CCCACCTTCACGG	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.13T>C	19.37:g.55174498T>C	ENSP00000375616:p.Phe5Leu	Somatic	47	1	0.0212766	1005	WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	641	0.2934981684981685	244	0.4959349593495935	84	0.23204419889502761	127	0.22202797202797203	186	0.24538258575197888	C	0.070	-1.203873	0.01581	0.422379	0.250698	ENSG00000186818	ENST00000420271;ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00438	7.44;7.44;7.44;7.43;7.46;7.42	2.87	0.476	0.16779	.	.	.	.	.	T	0.00012	0.0000	N	0.00029	-2.625	0.80722	P	0.0	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.06405	0.002;0.001;0.001;0.001;0.0;0.0	T	0.34675	-0.9819	8	0.02654	T	1	.	3.4403	0.07461	0.0:0.5078:0.2147:0.2775	rs28366008;rs36220281	5;5;5;5;5;46	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6;C9JHA6	.;.;.;.;LIRB4_HUMAN;.	L	46;5;5;5;5;5;5	ENSP00000375616:F5L;ENSP00000270452:F5L;ENSP00000408995:F5L;ENSP00000375614:F5L;ENSP00000375613:F5L;ENSP00000401962:F5L	ENSP00000270452:F5L	F	+	1	0	LILRB4	59866310	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.282000	0.08445	-0.466000	0.06943	-0.479000	0.04858	TTC	T|0.700;C|0.300	0.300	strong		0.602	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
RASSF3	283349	hgsc.bcm.edu	37	12	65004520	65004520	+	Silent	SNP	A	A	G	rs77813527	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:65004520A>G	ENST00000542104.1	+	1	228	c.108A>G	c.(106-108)caA>caG	p.Q36Q	RP11-338E21.1_ENST00000546135.1_RNA|RASSF3_ENST00000540088.1_3'UTR|RASSF3_ENST00000336061.2_Silent_p.Q36Q	NM_178169.3	NP_835463.1	Q86WH2	RASF3_HUMAN	Ras association (RalGDS/AF-6) domain family member 3	36					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)		GCTCCGGCCAACAAGTGAGTG	0.726													G|||	624	0.124601	0.1755	0.121	5008	,	,		9170	0.0089		0.2078	False		,,,				2504	0.092				p.Q36Q		Atlas-SNP	.											RASSF3,brain,glioma,0,4	RASSF3	18	4	0			c.A108G						PASS	.	G	,	823,3551		97,629,1461	14.0	16.0	16.0		108,108	2.5	1.0	12	dbSNP_131	16	1644,6926		160,1324,2801	no	coding-synonymous,coding-synonymous	RASSF3	NM_001242691.1,NM_178169.3	,	257,1953,4262	GG,GA,AA		19.1832,18.8157,19.059	,	36/91,36/239	65004520	2467,10477	2187	4285	6472	SO:0001819	synonymous_variant	283349	exon1			CGGCCAACAAGTG		CCDS8969.1	12q14.2	2008-02-22	2008-02-22		ENSG00000153179	ENSG00000153179			14271	protein-coding gene	gene with protein product		607019					Standard	NM_178169		Approved		uc001ssd.3	Q86WH2	OTTHUMG00000168812	ENST00000542104.1:c.108A>G	12.37:g.65004520A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_178169	Q86WH1	Silent	SNP	ENST00000542104.1	37	CCDS8969.1																																																																																			A|0.835;G|0.165	0.165	strong		0.726	RASSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401161.1		
TTBK1	84630	hgsc.bcm.edu	37	6	43251118	43251118	+	Silent	SNP	C	C	T	rs45515398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43251118C>T	ENST00000259750.4	+	14	2723	c.2640C>T	c.(2638-2640)gaC>gaT	p.D880D		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	880					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)			GCCAGCTGGACGTATCTGAGC	0.721													C|||	780	0.155751	0.2632	0.1009	5008	,	,		14101	0.1121		0.0885	False		,,,				2504	0.1636				p.D880D		Atlas-SNP	.											TTBK1,NS,carcinoma,0,1	TTBK1	124	1	0			c.C2640T						PASS	.	C		984,3394		100,784,1305	9.0	12.0	11.0		2640	-6.6	0.8	6	dbSNP_127	11	712,7850		29,654,3598	yes	coding-synonymous	TTBK1	NM_032538.1		129,1438,4903	TT,TC,CC		8.3158,22.476,13.1066		880/1322	43251118	1696,11244	2189	4281	6470	SO:0001819	synonymous_variant	84630	exon14			GCTGGACGTATCT	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.2640C>T	6.37:g.43251118C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	37	CCDS34455.1																																																																																			C|0.863;T|0.137	0.137	strong		0.721	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
C11orf86	254439	hgsc.bcm.edu	37	11	66743098	66743098	+	Missense_Mutation	SNP	C	C	T	rs118060724|rs137983778	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66743098C>T	ENST00000308963.4	+	1	351	c.265C>T	c.(265-267)Cgg>Tgg	p.R89W		NM_001136485.1	NP_001129957.1	A6NJI1	CK086_HUMAN	chromosome 11 open reading frame 86	89										NS(1)|skin(1)	2						GTGGCTGAGGCGGTACCAACA	0.652													C|||	110	0.0219649	0.0015	0.0548	5008	,	,		17871	0.0		0.0507	False		,,,				2504	0.0194				p.R89W		Atlas-SNP	.											.	C11orf86	7	.	0			c.C265T						PASS	.						19.0	30.0	27.0					11																	66743098		692	1591	2283	SO:0001583	missense	254439	exon1			CTGAGGCGGTACC	AK026328, AP003176	CCDS44656.1	11q13.1	2012-08-10			ENSG00000173237	ENSG00000173237			34442	protein-coding gene	gene with protein product							Standard	NM_001136485		Approved	FLJ22675	uc010rpm.2	A6NJI1	OTTHUMG00000153671	ENST00000308963.4:c.265C>T	11.37:g.66743098C>T	ENSP00000311479:p.Arg89Trp	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_001136485		Missense_Mutation	SNP	ENST00000308963.4	37	CCDS44656.1	67	0.030677655677655676	2	0.0040650406504065045	23	0.06353591160220995	1	0.0017482517482517483	41	0.05408970976253298	.	2.776	-0.254606	0.05829	.	.	ENSG00000173237	ENST00000308963	.	.	.	4.95	0.873	0.19118	.	0.748097	0.12110	N	0.498652	T	0.01387	0.0045	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.16276	-1.0408	9	0.42905	T	0.14	-13.8993	4.008	0.09610	0.1637:0.5651:0.0:0.2712	.	89	A6NJI1	CK086_HUMAN	W	89	.	ENSP00000311479:R89W	R	+	1	2	C11orf86	66499674	0.026000	0.19158	0.004000	0.12327	0.069000	0.16628	0.454000	0.21827	-0.025000	0.13918	-1.018000	0.02450	CGG	C|0.969;T|0.031	0.031	strong		0.652	C11orf86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332022.2	NM_001136485	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33406556	33406556	+	Silent	SNP	A	A	G	rs7759963|rs587780471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33406556A>G	ENST00000418600.2	+	10	1637	c.1536A>G	c.(1534-1536)gaA>gaG	p.E512E	MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000428982.2_Silent_p.E453E|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Silent_p.E512E	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	512	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)			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						CCCCAGGAGAATTCATCCGTG	0.552													G|||	346	0.0690895	0.1952	0.0216	5008	,	,		16126	0.0208		0.0258	False		,,,				2504	0.0266				p.E512E		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.A1536G						PASS	.	G		821,3585	749.2+/-412.0	71,679,1453	116.0	119.0	118.0		1536	1.9	1.0	6	dbSNP_116	118	203,8397	810.4+/-407.1	0,203,4097	no	coding-synonymous	SYNGAP1	NM_006772.2		71,882,5550	GG,GA,AA		2.3605,18.6337,7.8733		512/1344	33406556	1024,11982	2203	4300	6503	SO:0001819	synonymous_variant	8831	exon10			AGGAGAATTCATC	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.1536A>G	6.37:g.33406556A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			A|0.933;G|0.067	0.067	strong		0.552	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
MMP2	4313	hgsc.bcm.edu	37	16	55519535	55519535	+	Silent	SNP	G	G	C	rs1132896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:55519535G>C	ENST00000219070.4	+	5	1187	c.678G>C	c.(676-678)ggG>ggC	p.G226G	MMP2_ENST00000437642.2_Silent_p.G176G|MMP2_ENST00000570308.1_Silent_p.G150G|MMP2_ENST00000543485.1_Silent_p.G150G	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	226	Collagen-binding.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	TGAAGTATGGGAACGCCGATG	0.537													G|||	1002	0.20008	0.031	0.3919	5008	,	,		20547	0.13		0.3469	False		,,,				2504	0.2137				p.G226G		Atlas-SNP	.											.	MMP2	119	.	0			c.G678C						PASS	.	G	,	369,4027	188.5+/-214.9	12,345,1841	129.0	108.0	115.0		528,678	1.1	0.9	16	dbSNP_86	115	2968,5632	461.0+/-365.3	528,1912,1860	no	coding-synonymous,coding-synonymous	MMP2	NM_001127891.1,NM_004530.4	,	540,2257,3701	CC,CG,GG		34.5116,8.394,25.6771	,	176/611,226/661	55519535	3337,9659	2198	4300	6498	SO:0001819	synonymous_variant	4313	exon5			GTATGGGAACGCC		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.678G>C	16.37:g.55519535G>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	37	CCDS10752.1																																																																																			G|0.738;C|0.262	0.262	strong		0.537	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
HDC	3067	hgsc.bcm.edu	37	15	50555544	50555544	+	Missense_Mutation	SNP	G	G	A	rs17740607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:50555544G>A	ENST00000267845.3	-	2	494	c.92C>T	c.(91-93)aCg>aTg	p.T31M	HDC_ENST00000543581.1_Missense_Mutation_p.T31M	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0	Ala/Gly-rich.				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)		CACGTCTGGCGTCACACGTCT	0.567													G|||	238	0.047524	0.0053	0.085	5008	,	,		20228	0.0466		0.0974	False		,,,				2504	0.0276				p.T31M	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.C92T						PASS	.	G	MET/THR	113,4279	86.8+/-125.4	2,109,2085	96.0	85.0	89.0		92	3.0	0.9	15	dbSNP_123	89	972,7618	212.1+/-252.5	62,848,3385	yes	missense	HDC	NM_002112.3	81	64,957,5470	AA,AG,GG		11.3155,2.5729,8.3577	possibly-damaging	31/663	50555544	1085,11897	2196	4295	6491	SO:0001583	missense	3067	exon2			TCTGGCGTCACAC		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.92C>T	15.37:g.50555544G>A	ENSP00000267845:p.Thr31Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	132	0.06043956043956044	5	0.01016260162601626	29	0.08011049723756906	24	0.04195804195804196	74	0.09762532981530343	G	11.65	1.701572	0.30142	0.025729	0.113155	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.37915	1.17;1.17	6.05	3.03	0.35002	Pyridoxal phosphate-dependent transferase, major domain (1);	0.429863	0.26836	N	0.022249	T	0.00384	0.0012	L	0.32530	0.975	0.50467	P	1.2299999999998423E-4	D;D	0.54397	0.966;0.966	B;B	0.38562	0.276;0.276	T	0.08330	-1.0727	9	0.36615	T	0.2	-9.5804	6.2745	0.20973	0.1366:0.0:0.6087:0.2548	rs17740607;rs34750797;rs52799745;rs17740607	31;31	B7ZM01;P19113	.;DCHS_HUMAN	M	31	ENSP00000267845:T31M;ENSP00000440252:T31M	ENSP00000267845:T31M	T	-	2	0	HDC	48342836	0.781000	0.28676	0.893000	0.35052	0.476000	0.33039	1.241000	0.32743	0.896000	0.36366	0.650000	0.86243	ACG	G|0.928;A|0.072	0.072	strong		0.567	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
MDM2	4193	hgsc.bcm.edu	37	12	69222634	69222634	+	Silent	SNP	C	C	T	rs1795480	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:69222634C>T	ENST00000350057.5	+	6	514	c.514C>T	c.(514-516)Ctg>Ttg	p.L172L	MDM2_ENST00000393413.3_Intron|MDM2_ENST00000348801.2_Intron|RP11-611O2.1_ENST00000544710.1_RNA|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000428863.2_Intron|MDM2_ENST00000356290.4_Intron|MDM2_ENST00000544561.1_Intron|MDM2_ENST00000360430.2_Intron|MDM2_ENST00000299252.4_Intron|MDM2_ENST00000393410.1_Intron|MDM2_ENST00000258149.5_Silent_p.L142L|MDM2_ENST00000258148.7_Silent_p.L148L|MDM2_ENST00000540827.1_Intron|MDM2_ENST00000517852.1_Intron|MDM2_ENST00000393412.3_Intron|MDM2_ENST00000462284.1_Silent_p.L203L|MDM2_ENST00000478070.1_Intron			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	197	Interaction with MTBP. {ECO:0000250}.|Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34. {ECO:0000269|PubMed:16479015, ECO:0000269|PubMed:18382127}.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TGATGAAAGCCTGGCTCTGTG	0.388			A		"""sarcoma, glioma, colorectal, other"""								C|||	64	0.0127796	0.0287	0.0086	5008	,	,		18795	0.0		0.0159	False		,,,				2504	0.0041				p.L203L		Atlas-SNP	.		Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"""M, O, E, L"""	.	MDM2	92	.	0			c.C607T						PASS	.	C		104,3670		1,102,1784	156.0	149.0	151.0		607	3.8	1.0	12	dbSNP_89	151	136,8082		2,132,3975	no	coding-synonymous	MDM2	NM_002392.3		3,234,5759	TT,TC,CC		1.6549,2.7557,2.0013		203/498	69222634	240,11752	1887	4109	5996	SO:0001819	synonymous_variant	4193	exon8			GAAAGCCTGGCTC		CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"""mouse double minute 2, human homolog of; p53-binding protein"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)"", ""Mdm2 p53 binding protein homolog (mouse)"""			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000350057.5:c.514C>T	12.37:g.69222634C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_002392	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Silent	SNP	ENST00000350057.5	37																																																																																				C|0.983;T|0.017	0.017	strong		0.388	MDM2-033	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000402665.1	NM_006880	
GC	2638	hgsc.bcm.edu	37	4	72620788	72620788	+	Silent	SNP	C	C	T	rs76803094	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:72620788C>T	ENST00000273951.8	-	9	1414	c.1071G>A	c.(1069-1071)ccG>ccA	p.P357P	GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Silent_p.P376P|GC_ENST00000513476.1_Silent_p.P357P	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	357	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)	p.P357P(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	45		all_hematologic(202;0.107)	Lung(101;0.148)		Alfacalcidol(DB01436)|Cholecalciferol(DB00169)	GGAATACTTCCGGAAGATGAG	0.343													C|||	45	0.00898562	0.0008	0.0159	5008	,	,		15213	0.0		0.0288	False		,,,				2504	0.0041				p.P376P		Atlas-SNP	.											GC,NS,carcinoma,0,1	GC	132	1	1	Substitution - coding silent(1)	pancreas(1)	c.G1128A						PASS	.	C	,,	18,4388	26.2+/-53.5	0,18,2185	119.0	112.0	114.0		1071,1071,1128	0.9	1.0	4	dbSNP_132	114	198,8402	86.9+/-149.2	2,194,4104	no	coding-synonymous,coding-synonymous,coding-synonymous	GC	NM_000583.3,NM_001204306.1,NM_001204307.1	,,	2,212,6289	TT,TC,CC		2.3023,0.4085,1.6608	,,	357/475,357/475,376/494	72620788	216,12790	2203	4300	6503	SO:0001819	synonymous_variant	2638	exon10			TACTTCCGGAAGA	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.1071G>A	4.37:g.72620788C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	164	70	0.426829	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Silent	SNP	ENST00000273951.8	37	CCDS3550.1																																																																																			C|0.981;T|0.019	0.019	strong		0.343	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2		
SEMA3D	223117	hgsc.bcm.edu	37	7	84628989	84628989	+	Missense_Mutation	SNP	T	T	G	rs7800072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:84628989T>G	ENST00000284136.6	-	17	2144	c.2101A>C	c.(2101-2103)Aag>Cag	p.K701Q	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	701			K -> Q (in dbSNP:rs7800072). {ECO:0000269|PubMed:12975309}.		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						TCCTTGACCTTCCCCTCCTCA	0.473													G|||	1430	0.285543	0.351	0.2421	5008	,	,		17893	0.2718		0.3201	False		,,,				2504	0.2065				p.K701Q	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											SEMA3D,rectum,carcinoma,0,1	SEMA3D	177	1	0			c.A2101C						PASS	.	G	GLN/LYS	1642,2764	659.1+/-400.5	314,1014,875	144.0	119.0	128.0		2101	3.8	1.0	7	dbSNP_116	128	2814,5786	676.5+/-403.3	459,1896,1945	yes	missense	SEMA3D	NM_152754.2	53	773,2910,2820	GG,GT,TT		32.7209,37.2674,34.2611	benign	701/778	84628989	4456,8550	2203	4300	6503	SO:0001583	missense	223117	exon17			TGACCTTCCCCTC	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.2101A>C	7.37:g.84628989T>G	ENSP00000284136:p.Lys701Gln	Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	225	116	0.515556	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	667	0.30540293040293043	191	0.3882113821138211	94	0.2596685082872928	139	0.243006993006993	243	0.32058047493403696	G	5.817	0.334982	0.11013	0.372674	0.327209	ENSG00000153993	ENST00000284136	T	0.30981	1.51	5.73	3.82	0.43975	.	0.959042	0.08767	N	0.896847	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999611851	B	0.02656	0.0	B	0.01281	0.0	T	0.44620	-0.9316	9	0.13108	T	0.6	.	15.0253	0.71667	0.0:0.0:0.6279:0.3721	rs7800072;rs10365892;rs7800072	701	O95025	SEM3D_HUMAN	Q	701	ENSP00000284136:K701Q	ENSP00000284136:K701Q	K	-	1	0	SEMA3D	84466925	0.865000	0.29922	0.998000	0.56505	0.986000	0.74619	1.502000	0.35704	0.759000	0.33084	-0.121000	0.15023	AAG	T|0.671;G|0.329	0.329	strong		0.473	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
COMMD10	51397	hgsc.bcm.edu	37	5	115428381	115428381	+	Missense_Mutation	SNP	T	T	G	rs1129495	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	92	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	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	
ADA	100	hgsc.bcm.edu	37	20	43254298	43254298	+	Silent	SNP	C	C	T	rs61737144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:43254298C>T	ENST00000372874.4	-	5	524	c.390G>A	c.(388-390)gtG>gtA	p.V130V	ADA_ENST00000537820.1_Silent_p.V130V|ADA_ENST00000464097.1_5'UTR	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	130					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	CCACTAGGGCCACCACCTCGT	0.647									Adenosine Deaminase Deficiency				C|||	153	0.0305511	0.0643	0.0231	5008	,	,		18564	0.0		0.0378	False		,,,				2504	0.0143				p.V130V		Atlas-SNP	.											ADA,caecum,carcinoma,0,1	ADA	42	1	0			c.G390A						PASS	.	C		251,4125		5,241,1942	25.0	20.0	22.0		390	3.7	0.7	20	dbSNP_129	22	297,8287		5,287,4000	no	coding-synonymous	ADA	NM_000022.2		10,528,5942	TT,TC,CC		3.4599,5.7358,4.2284		130/364	43254298	548,12412	2188	4292	6480	SO:0001819	synonymous_variant	100	exon5	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	TAGGGCCACCACC	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.390G>A	20.37:g.43254298C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_000022	Q53F92|Q6LA59	Silent	SNP	ENST00000372874.4	37	CCDS13335.1																																																																																			C|0.960;T|0.040	0.040	strong		0.647	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
ENPP7	339221	hgsc.bcm.edu	37	17	77710990	77710990	+	Missense_Mutation	SNP	C	C	T	rs139719997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:77710990C>T	ENST00000328313.5	+	4	1398	c.1177C>T	c.(1177-1179)Cgg>Tgg	p.R393W		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GCTCATGTGCCGGCTGCTGGG	0.647													C|||	7	0.00139776	0.0	0.0029	5008	,	,		18712	0.0		0.002	False		,,,				2504	0.0031				p.R393W		Atlas-SNP	.											ENPP7,NS,carcinoma,-2,1	ENPP7	63	1	0			c.C1177T						PASS	.	C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	61.0	51.0	55.0		1177	0.8	0.7	17	dbSNP_134	55	30,8570	20.4+/-63.3	0,30,4270	yes	missense	ENPP7	NM_178543.3	101	0,33,6470	TT,TC,CC		0.3488,0.0681,0.2537	possibly-damaging	393/459	77710990	33,12973	2203	4300	6503	SO:0001583	missense	339221	exon4			ATGTGCCGGCTGC	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.1177C>T	17.37:g.77710990C>T	ENSP00000332656:p.Arg393Trp	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	13.24	2.177465	0.38413	6.81E-4	0.003488	ENSG00000182156	ENST00000328313	T	0.75589	-0.95	3.07	0.824	0.18818	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.824992	0.10969	N	0.614092	T	0.69088	0.3072	L	0.42245	1.32	0.25279	N	0.989453	D	0.54047	0.964	P	0.48677	0.586	T	0.59043	-0.7528	10	0.72032	D	0.01	-10.5339	5.5668	0.17175	0.3222:0.4528:0.225:0.0	.	393	Q6UWV6	ENPP7_HUMAN	W	393	ENSP00000332656:R393W	ENSP00000332656:R393W	R	+	1	2	ENPP7	75325585	0.000000	0.05858	0.698000	0.30274	0.382000	0.30200	-0.066000	0.11598	0.075000	0.16796	0.561000	0.74099	CGG	C|0.997;T|0.003	0.003	strong		0.647	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
LRRC6	23639	hgsc.bcm.edu	37	8	133584558	133584558	+	Missense_Mutation	SNP	A	A	G	rs9297853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133584558A>G	ENST00000519595.1	-	12	1495	c.1397T>C	c.(1396-1398)aTt>aCt	p.I466T	LRRC6_ENST00000518642.1_3'UTR|LRRC6_ENST00000250173.1_Missense_Mutation_p.I466T			Q86X45	TILB_HUMAN	leucine rich repeat containing 6	466			I -> T (in dbSNP:rs9297853).		cilium movement (GO:0003341)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|inner dynein arm assembly (GO:0036159)|male gonad development (GO:0008584)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|reproductive system development (GO:0061458)|sperm motility (GO:0030317)	cilium (GO:0005929)|cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|urinary_tract(2)	34	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			GATGTTTCAAATCAGCGGAGG	0.468													A|||	721	0.14397	0.326	0.0893	5008	,	,		17839	0.0466		0.0875	False		,,,				2504	0.0951				p.I466T		Atlas-SNP	.											.	LRRC6	58	.	0			c.T1397C						PASS	.	A	THR/ILE	1297,3109	439.2+/-345.6	198,901,1104	225.0	206.0	212.0		1397	5.7	0.6	8	dbSNP_119	212	832,7768	192.1+/-238.2	38,756,3506	yes	missense	LRRC6	NM_012472.3	89	236,1657,4610	GG,GA,AA		9.6744,29.4371,16.3694	probably-damaging	466/467	133584558	2129,10877	2203	4300	6503	SO:0001583	missense	23639	exon12			TTTCAAATCAGCG	U60666	CCDS6365.1	8q24	2013-02-22			ENSG00000129295	ENSG00000129295			16725	protein-coding gene	gene with protein product	"""leucine rich testes protein"""	614930				10775177, 23122586	Standard	NM_012472		Approved	TSLRP, LRTP, CILD19	uc003ytk.4	Q86X45	OTTHUMG00000164646	ENST00000519595.1:c.1397T>C	8.37:g.133584558A>G	ENSP00000429791:p.Ile466Thr	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	287	140	0.487805	NM_012472	Q13648|Q4G183	Missense_Mutation	SNP	ENST00000519595.1	37		286	0.13095238095238096	153	0.31097560975609756	36	0.09944751381215469	23	0.04020979020979021	74	0.09762532981530343	A	15.36	2.810633	0.50421	0.294371	0.096744	ENSG00000129295	ENST00000519595;ENST00000522789;ENST00000250173	T;T;T	0.60040	0.22;0.34;0.22	5.69	5.69	0.88448	.	0.250357	0.41294	D	0.000910	T	0.00012	0.0000	M	0.72894	2.215	0.27459	P	0.9531937	D	0.54964	0.969	P	0.52856	0.711	T	0.08391	-1.0724	9	0.87932	D	0	.	12.3338	0.55054	1.0:0.0:0.0:0.0	rs9297853;rs52822837;rs57953540;rs9297853	466	Q86X45	LRRC6_HUMAN	T	466;206;466	ENSP00000429791:I466T;ENSP00000428015:I206T;ENSP00000250173:I466T	ENSP00000250173:I466T	I	-	2	0	LRRC6	133653740	0.999000	0.42202	0.576000	0.28549	0.116000	0.19942	5.469000	0.66749	2.162000	0.67917	0.533000	0.62120	ATT	A|0.843;G|0.157	0.157	strong		0.468	LRRC6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379578.1	NM_012472	
GP6	51206	hgsc.bcm.edu	37	19	55526373	55526373	+	Silent	SNP	G	G	C	rs2304166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55526373G>C	ENST00000417454.1	-	8	963	c.936C>G	c.(934-936)ctC>ctG	p.L312L	GP6_ENST00000333884.2_Silent_p.L294L|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.7_ENST00000586845.1_RNA|GP6_ENST00000310373.3_Missense_Mutation_p.P314A	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	312					blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		GGAGGGGCGGGAGGGGCGGAA	0.657													G|||	1926	0.384585	0.2012	0.5663	5008	,	,		13801	0.2411		0.6093	False		,,,				2504	0.4202				p.P314A		Atlas-SNP	.											GP6,colon,carcinoma,0,1	GP6	55	1	0			c.C940G						PASS	.	G	ALA/PRO,	916,2878		125,666,1106	15.0	18.0	17.0		940,936	2.7	0.9	19	dbSNP_100	17	4939,3277		1506,1927,675	yes	missense,coding-synonymous	GP6	NM_001083899.1,NM_016363.4	27,	1631,2593,1781	CC,CG,GG		39.8856,24.1434,48.751	probably-damaging,	314/621,312/340	55526373	5855,6155	1897	4108	6005	SO:0001819	synonymous_variant	51206	exon8			GGGCGGGAGGGGC	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.936C>G	19.37:g.55526373G>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	29	8	0.275862	NM_001083899	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	925	0.42353479853479853	131	0.266260162601626	214	0.5911602209944752	124	0.21678321678321677	456	0.6015831134564644	g	13.95	2.391030	0.42410	0.241434	0.601144	ENSG00000088053	ENST00000310373	T	0.00566	6.55	2.65	2.65	0.31530	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999677	D	0.89917	1.0	D	0.83275	0.996	T	0.00341	-1.1804	7	0.27082	T	0.32	.	8.9559	0.35818	0.0:0.0:1.0:0.0	rs2304166;rs60037271	314	Q9HCN6-3	.	A	314	ENSP00000308782:P314A	ENSP00000308782:P314A	P	-	1	0	GP6	60218185	0.742000	0.28228	0.944000	0.38274	0.034000	0.12701	0.423000	0.21313	1.778000	0.52293	0.561000	0.74099	CCC	G|0.538;C|0.462	0.462	strong		0.657	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
GOLGA6C	653641	hgsc.bcm.edu	37	15	75562495	75562495	+	Silent	SNP	G	G	T	rs138154232	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:75562495G>T	ENST00000300576.5	+	18	2037	c.2037G>T	c.(2035-2037)ccG>ccT	p.P679P	RN7SL489P_ENST00000486185.2_RNA	NM_001164404.1	NP_001157876.1	A6NDK9	GOG6C_HUMAN	golgin A6 family, member C	679						Golgi apparatus (GO:0005794)				ovary(1)	1						ACAACCCCCCGGTACAGCAGA	0.602													N|||	184	0.0367412	0.1339	0.0086	5008	,	,		17187	0.0		0.001	False		,,,				2504	0.0				p.P679P		Atlas-SNP	.											GOLGA6C_ENST00000300576,bladder,carcinoma,0,3	GOLGA6C	12	3	0			c.G2037T						scavenged	.						52.0	65.0	61.0					15																	75562495		652	1575	2227	SO:0001819	synonymous_variant	653641	exon18			CCCCCCGGTACAG		CCDS58388.1	15q24.2	2014-02-12	2010-02-12		ENSG00000167195	ENSG00000167195			32206	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6C"""				Standard	NM_001164404		Approved		uc002azs.2	A6NDK9	OTTHUMG00000172671	ENST00000300576.5:c.2037G>T	15.37:g.75562495G>T		Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	353	5	0.0141643	NM_001164404		Silent	SNP	ENST00000300576.5	37	CCDS58388.1																																																																																			.	.	weak		0.602	GOLGA6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419797.1	NM_001164404	
LRRC6	23639	hgsc.bcm.edu	37	8	133637659	133637659	+	Missense_Mutation	SNP	G	G	A	rs2293979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133637659G>A	ENST00000519595.1	-	6	793	c.695C>T	c.(694-696)aCa>aTa	p.T232I	LRRC6_ENST00000520446.1_5'UTR|LRRC6_ENST00000518642.1_Missense_Mutation_p.T232I|LRRC6_ENST00000250173.1_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	182	0	0		WXS	Illumina HiSeq	Phase_I	202	90	0.445545	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	
RGPD3	653489	hgsc.bcm.edu	37	2	107049714	107049714	+	Missense_Mutation	SNP	C	C	G	rs62152468		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:107049714C>G	ENST00000409886.3	-	16	2320	c.2233G>C	c.(2233-2235)Gag>Cag	p.E745Q	RGPD3_ENST00000304514.7_Missense_Mutation_p.E745Q	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	745					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTAAGCATCTCTTTTACAGAC	0.343																																					p.E745Q		Atlas-SNP	.											RGPD3_ENST00000304514,right_upper_lobe,carcinoma,0,2	RGPD3	316	2	0			c.G2233C						scavenged	.						15.0	28.0	24.0					2																	107049714		673	1545	2218	SO:0001583	missense	653489	exon16			GCATCTCTTTTAC		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.2233G>C	2.37:g.107049714C>G	ENSP00000386588:p.Glu745Gln	Somatic	581	1	0.00172117		WXS	Illumina HiSeq	Phase_I	642	181	0.281931	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	4.999	0.185488	0.09495	.	.	ENSG00000153165	ENST00000409886;ENST00000452099;ENST00000304514	T;T	0.24908	1.83;1.83	2.34	2.34	0.29019	.	.	.	.	.	T	0.21841	0.0526	M	0.62723	1.935	0.26104	N	0.980775	P	0.35700	0.516	B	0.20955	0.032	T	0.10405	-1.0631	9	0.42905	T	0.14	-11.6791	10.3857	0.44138	0.0:1.0:0.0:0.0	.	745	A6NKT7	RGPD3_HUMAN	Q	745;503;745	ENSP00000386588:E745Q;ENSP00000303659:E745Q	ENSP00000303659:E745Q	E	-	1	0	RGPD3	106416146	1.000000	0.71417	0.998000	0.56505	0.191000	0.23601	5.692000	0.68256	1.308000	0.44962	0.173000	0.16961	GAG	C|0.250;G|0.750	0.750	weak		0.343	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
MUC2	4583	hgsc.bcm.edu	37	11	1093296	1093296	+	Silent	SNP	T	T	C	rs200837746|rs56068864		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093296T>C	ENST00000441003.2	+	30	5142	c.5115T>C	c.(5113-5115)acT>acC	p.T1705T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1672T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccactacggtgaccc	0.642																																					p.T1705T		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,+1,2	MUC2	614	2	0			c.T5115C						scavenged	.						111.0	159.0	142.0					11																	1093296		1883	3466	5349	SO:0001819	synonymous_variant	4583	exon30			CACCACTACGGTG	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.5115T>C	11.37:g.1093296T>C		Somatic	45	5	0.111111		WXS	Illumina HiSeq	Phase_I	67	14	0.208955	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	weak		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
IFNAR1	3454	hgsc.bcm.edu	37	21	34715699	34715699	+	Missense_Mutation	SNP	G	G	C	rs2257167	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	125	0	0		WXS	Illumina HiSeq	Phase_I	114	43	0.377193	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		
SPTA1	6708	hgsc.bcm.edu	37	1	158592901	158592901	+	Missense_Mutation	SNP	C	C	G	rs77877855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592901C>G	ENST00000368147.4	-	43	6172	c.5992G>C	c.(5992-5994)Gct>Cct	p.A1998P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1998					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)					TTGTGTTGAGCAGAAATCAGT	0.507													C|||	270	0.0539137	0.1407	0.0303	5008	,	,		16400	0.0		0.0229	False		,,,				2504	0.0409				p.A1998P		Atlas-SNP	.											.	SPTA1	720	.	0			c.G5992C						PASS	.	C	PRO/ALA	550,3340		26,498,1421	323.0	325.0	324.0		5992	3.9	0.4	1	dbSNP_131	324	126,8146		2,122,4012	yes	missense	SPTA1	NM_003126.2	27	28,620,5433	GG,GC,CC		1.5232,14.1388,5.5583	probably-damaging	1998/2420	158592901	676,11486	1945	4136	6081	SO:0001583	missense	6708	exon43			GTTGAGCAGAAAT	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.5992G>C	1.37:g.158592901C>G	ENSP00000357129:p.Ala1998Pro	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	221	100	0.452489	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	101	0.04624542124542125	75	0.1524390243902439	10	0.027624309392265192	0	0.0	16	0.021108179419525065	C	15.33	2.800750	0.50315	0.141388	0.015232	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53423	0.62;0.62	4.78	3.86	0.44501	.	.	.	.	.	T	0.54175	0.1842	M	0.72118	2.19	0.36867	D	0.888732	D	0.53462	0.96	P	0.62885	0.908	T	0.60944	-0.7162	9	0.54805	T	0.06	.	13.0889	0.59156	0.1622:0.8378:0.0:0.0	.	1998	P02549	SPTA1_HUMAN	P	1998;1995	ENSP00000357130:A1998P;ENSP00000357129:A1995P	ENSP00000357129:A1995P	A	-	1	0	SPTA1	156859525	0.996000	0.38824	0.362000	0.25862	0.025000	0.11179	3.441000	0.52893	1.203000	0.43233	0.655000	0.94253	GCT	C|0.961;G|0.039	0.039	strong		0.507	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
GNRH1	2796	hgsc.bcm.edu	37	8	25280800	25280800	+	Missense_Mutation	SNP	C	C	G	rs6185	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:25280800C>G	ENST00000276414.4	-	1	1370	c.47G>C	c.(46-48)tGg>tCg	p.W16S	GNRH1_ENST00000421054.2_Missense_Mutation_p.W16S|RP11-395I14.2_ENST00000523840.1_lincRNA	NM_000825.3	NP_000816.4	P01148	GON1_HUMAN	gonadotropin-releasing hormone 1 (luteinizing-releasing hormone)	16			W -> S (in dbSNP:rs6185). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:6090951}.		cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|ovulation cycle (GO:0042698)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|response to corticosteroid (GO:0031960)|response to ethanol (GO:0045471)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	gonadotropin hormone-releasing hormone activity (GO:0005183)|hormone activity (GO:0005179)			large_intestine(1)	1		all_cancers(63;0.0423)|Ovarian(32;0.000626)|all_epithelial(46;0.0186)|Hepatocellular(4;0.114)|Breast(100;0.14)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0201)|Epithelial(17;1.25e-12)|Colorectal(74;0.0113)|COAD - Colon adenocarcinoma(73;0.0385)		TTCCACGCACCAAGTCAGTAG	0.448													C|||	1123	0.224241	0.0552	0.1931	5008	,	,		17847	0.5476		0.2425	False		,,,				2504	0.1227				p.W20S		Atlas-SNP	.											.	GNRH1	8	.	0			c.G59C						PASS	.	C	SER/TRP,SER/TRP	348,3418		14,320,1549	79.0	78.0	78.0		47,47	2.9	0.0	8	dbSNP_52	78	2064,6144		272,1520,2312	yes	missense,missense	GNRH1	NM_000825.3,NM_001083111.1	177,177	286,1840,3861	GG,GC,CC		25.1462,9.2406,20.1436	benign,benign	16/93,16/93	25280800	2412,9562	1883	4104	5987	SO:0001583	missense	2796	exon1			ACGCACCAAGTCA	X01059	CCDS43725.1	8p21-p11.2	2013-02-26	2004-10-13		ENSG00000147437	ENSG00000147437		"""Endogenous ligands"""	4419	protein-coding gene	gene with protein product		152760	"""gonadotropin-releasing hormone 1 (leutinizing-releasing hormone)"""	GRH, GNRH, LHRH		6090951	Standard	NM_000825		Approved		uc003xem.4	P01148	OTTHUMG00000163852	ENST00000276414.4:c.47G>C	8.37:g.25280800C>G	ENSP00000276414:p.Trp16Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_000825	A0AVP0	Missense_Mutation	SNP	ENST00000276414.4	37	CCDS43725.1	593	0.2715201465201465	20	0.04065040650406504	80	0.22099447513812154	307	0.5367132867132867	186	0.24538258575197888	C	6.004	0.369183	0.11352	0.092406	0.251462	ENSG00000147437	ENST00000421054;ENST00000276414	T;T	0.40476	1.03;1.03	5.29	2.9	0.33743	.	1.973800	0.02558	N	0.096387	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.46261	-0.9204	8	0.51188	T	0.08	-0.0022	4.5292	0.11997	0.6642:0.1675:0.1683:0.0	rs6185;rs3191535;rs6185	16	P01148	GON1_HUMAN	S	16	ENSP00000391280:W16S;ENSP00000276414:W16S	ENSP00000276414:W16S	W	-	2	0	GNRH1	25336717	0.022000	0.18835	0.000000	0.03702	0.000000	0.00434	3.083000	0.50136	0.457000	0.26962	-1.092000	0.02172	TGG	C|0.738;G|0.262	0.262	strong		0.448	GNRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375982.1	NM_001083111	
NOMO2	283820	hgsc.bcm.edu	37	16	18532182	18532182	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:18532182A>T	ENST00000381474.3	-	19	2243	c.2178T>A	c.(2176-2178)aaT>aaA	p.N726K	NOMO2_ENST00000330537.6_Missense_Mutation_p.N726K|NOMO2_ENST00000543392.1_Missense_Mutation_p.N559K	NM_001004060.1	NP_001004060.1	Q5JPE7	NOMO2_HUMAN	NODAL modulator 2	726			N -> K (in dbSNP:rs370986).			endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(4)|kidney(1)|large_intestine(2)|liver(3)|lung(5)|ovary(3)|prostate(1)|skin(1)	20						CACCTTCCTCATTGCCGTTTT	0.562																																					p.N726K		Atlas-SNP	.											NOMO2,NS,carcinoma,0,1	NOMO2	36	1	0			c.T2178A						scavenged	.						224.0	232.0	229.0					16																	18532182		2196	4297	6493	SO:0001583	missense	283820	exon19			TTCCTCATTGCCG	AL512687	CCDS10570.1, CCDS32394.1	16p12.3	2008-02-05			ENSG00000185164	ENSG00000185164			22652	protein-coding gene	gene with protein product		609158				15257293	Standard	NM_001004060		Approved	NOMO, PM5	uc002dfe.3	Q5JPE7	OTTHUMG00000131366	ENST00000381474.3:c.2178T>A	16.37:g.18532182A>T	ENSP00000370883:p.Asn726Lys	Somatic	1094	5	0.00457038		WXS	Illumina HiSeq	Phase_I	936	34	0.0363248	NM_173614	Q4G177	Missense_Mutation	SNP	ENST00000381474.3	37	CCDS32394.1	.	.	.	.	.	.	.	.	.	.	.	0.004	-2.260122	0.00262	.	.	ENSG00000185164	ENST00000330537;ENST00000381474;ENST00000543392	T;T;T	0.03663	3.87;3.86;3.85	3.37	-2.16	0.07080	.	0.796012	0.12016	N	0.507432	T	0.01523	0.0049	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	0.46190	-0.9209	10	0.05351	T	0.99	1.8419	2.0563	0.03582	0.1237:0.3142:0.1267:0.4354	.	559;726	Q4G177;Q5JPE7	.;NOMO2_HUMAN	K	726;726;559	ENSP00000331851:N726K;ENSP00000370883:N726K;ENSP00000439970:N559K	ENSP00000331851:N726K	N	-	3	2	NOMO2	18439683	0.000000	0.05858	0.000000	0.03702	0.180000	0.23129	-1.326000	0.02685	-1.117000	0.02965	-0.545000	0.04230	AAT	.	.	weak		0.562	NOMO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435858.1	NM_001004060	
RPTN	126638	hgsc.bcm.edu	37	1	152129087	152129087	+	Missense_Mutation	SNP	T	T	C	rs78544048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152129087T>C	ENST00000316073.3	-	3	552	c.488A>G	c.(487-489)aAa>aGa	p.K163R		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	163	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TCTGTCTTGTTTCTCAGACTG	0.498													T|||	1376	0.27476	0.2216	0.4741	5008	,	,		19446	0.2996		0.1779	False		,,,				2504	0.2791				p.K163R		Atlas-SNP	.											.	RPTN	123	.	1	Deletion - In frame(1)	stomach(1)	c.A488G						PASS	.	T	ARG/LYS	221,2911		36,149,1381	461.0	402.0	420.0		488	-4.1	0.0	1	dbSNP_131	420	403,6741		69,265,3238	yes	missense	RPTN	NM_001122965.1	26	105,414,4619	CC,CT,TT		5.6411,7.0562,6.0724	benign	163/785	152129087	624,9652	1566	3572	5138	SO:0001583	missense	126638	exon3			TCTTGTTTCTCAG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.488A>G	1.37:g.152129087T>C	ENSP00000317895:p.Lys163Arg	Somatic	329	1	0.00303951		WXS	Illumina HiSeq	Phase_I	297	113	0.380471	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	499	0.22847985347985347	90	0.18292682926829268	127	0.35082872928176795	156	0.2727272727272727	126	0.1662269129287599	T	0.693	-0.793571	0.02862	0.070562	0.056411	ENSG00000215853	ENST00000316073	T	0.12984	2.63	4.82	-4.06	0.03986	.	0.724647	0.11240	N	0.584740	T	0.00468	0.0015	N	0.00092	-2.175	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39251	-0.9623	9	0.10377	T	0.69	-0.1041	5.4828	0.16733	0.0:0.3687:0.2434:0.388	.	163	Q6XPR3	RPTN_HUMAN	R	163	ENSP00000317895:K163R	ENSP00000317895:K163R	K	-	2	0	RPTN	150395711	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-1.098000	0.03346	-1.459000	0.01914	-1.225000	0.01585	AAA	T|0.756;C|0.244	0.244	strong		0.498	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
VPS33B	26276	hgsc.bcm.edu	37	15	91543761	91543761	+	Missense_Mutation	SNP	C	C	T	rs11073964	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:91543761C>T	ENST00000333371.3	-	20	1893	c.1540G>A	c.(1540-1542)Ggt>Agt	p.G514S	VPS33B_ENST00000535906.1_Missense_Mutation_p.G487S|VPS33B_ENST00000535843.1_Missense_Mutation_p.G423S	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	514			G -> S (in dbSNP:rs11073964). {ECO:0000269|PubMed:10894945, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)					TAAGCACCACCGAAGACGTAA	0.493													T|||	3845	0.767772	0.9607	0.6686	5008	,	,		20263	0.996		0.3986	False		,,,				2504	0.7219				p.G514S		Atlas-SNP	.											.	VPS33B	42	.	0			c.G1540A						PASS	.	T	SER/GLY	3870,526	240.6+/-251.3	1709,452,37	118.0	96.0	104.0		1540	5.8	1.0	15	dbSNP_120	104	3422,5174	637.6+/-399.2	670,2082,1546	yes	missense	VPS33B	NM_018668.3	56	2379,2534,1583	TT,TC,CC		39.8092,11.9654,43.8732	benign	514/618	91543761	7292,5700	2198	4298	6496	SO:0001583	missense	26276	exon20			CACCACCGAAGAC	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.1540G>A	15.37:g.91543761C>T	ENSP00000327650:p.Gly514Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	37	CCDS10369.1	1573	0.7202380952380952	469	0.9532520325203252	218	0.6022099447513812	571	0.9982517482517482	315	0.4155672823218997	T	10.36	1.328511	0.24167	0.880346	0.398092	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.74737	-0.87;-0.87;-0.87	5.83	5.83	0.93111	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00303	-1.675	0.39820	P	0.027178999999999953	B;B	0.12630	0.006;0.002	B;B	0.08055	0.002;0.003	T	0.44559	-0.9320	9	0.02654	T	1	-15.2107	11.7519	0.51853	0.0:0.0695:0.0:0.9305	rs11073964;rs17515382;rs17845495;rs17858380;rs57245246;rs11073964	487;514	F5H008;Q9H267	.;VP33B_HUMAN	S	514;487;423;469	ENSP00000327650:G514S;ENSP00000444053:G487S;ENSP00000446267:G423S	ENSP00000327650:G514S	G	-	1	0	VPS33B	89344765	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	4.267000	0.58877	1.028000	0.39785	-0.269000	0.10298	GGT	C|0.359;T|0.641	0.641	strong		0.493	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668	
MKI67	4288	hgsc.bcm.edu	37	10	129902131	129902131	+	Missense_Mutation	SNP	T	T	C	rs146439186		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:129902131T>C	ENST00000368654.3	-	13	8348	c.7973A>G	c.(7972-7974)gAa>gGa	p.E2658G	MKI67_ENST00000368653.3_Missense_Mutation_p.E2298G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2658	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)				GGGTTCCTCTTCTACTGGGTT	0.517													T|||	1	0.000199681	0.0	0.0	5008	,	,		19173	0.0		0.0	False		,,,				2504	0.001				p.E2658G		Atlas-SNP	.											.	MKI67	363	.	0			c.A7973G						PASS	.	T	GLY/GLU,GLY/GLU	3,4403	6.2+/-15.9	0,3,2200	163.0	171.0	168.0		6893,7973	-7.3	0.0	10	dbSNP_134	168	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	98,98	0,21,6482	CC,CT,TT		0.2093,0.0681,0.1615	possibly-damaging,possibly-damaging	2298/2897,2658/3257	129902131	21,12985	2203	4300	6503	SO:0001583	missense	4288	exon13			TCCTCTTCTACTG	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.7973A>G	10.37:g.129902131T>C	ENSP00000357643:p.Glu2658Gly	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	213	88	0.413146	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	4.259	0.047198	0.08243	6.81E-4	0.002093	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02216	4.39;4.39	3.68	-7.35	0.01422	.	0.726931	0.11842	N	0.524155	T	0.02156	0.0067	M	0.62723	1.935	0.09310	N	1	B;B;B	0.34290	0.11;0.11;0.447	B;B;B	0.33846	0.027;0.075;0.171	T	0.06373	-1.0830	10	0.33141	T	0.24	.	2.5101	0.04654	0.1564:0.0851:0.3995:0.3589	.	2657;2298;2658	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	G	2658;2298;2657	ENSP00000357643:E2658G;ENSP00000357642:E2298G	ENSP00000357642:E2298G	E	-	2	0	MKI67	129792121	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-4.528000	0.00044	-1.301000	0.01330	GAA	T|0.998;C|0.002	0.002	strong		0.517	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
NOTCH2	4853	hgsc.bcm.edu	37	1	120468425	120468425	+	Silent	SNP	G	G	A	rs17024525	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:120468425G>A	ENST00000256646.2	-	25	4233	c.4014C>T	c.(4012-4014)tcC>tcT	p.S1338S	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1338	EGF-like 34. {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)		ACCTTGCCCCGGAAAATCCCT	0.512			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				g|||	179	0.0357428	0.0151	0.0159	5008	,	,		19191	0.1399		0.001	False		,,,				2504	0.0061				p.S1338S		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C4014T						PASS	.	A		51,4351		0,51,2150	25.0	23.0	24.0		4014	-11.7	0.2	1	dbSNP_123	24	16,8568		0,16,4276	no	coding-synonymous	NOTCH2	NM_024408.3		0,67,6426	AA,AG,GG		0.1864,1.1586,0.5159		1338/2472	120468425	67,12919	2201	4292	6493	SO:0001819	synonymous_variant	4853	exon25	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	TGCCCCGGAAAAT	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.4014C>T	1.37:g.120468425G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	153	70	0.457516	NM_024408	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																			A|0.027;G|0.973	0.027	strong		0.512	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
SLC45A4	57210	hgsc.bcm.edu	37	8	142228809	142228809	+	Silent	SNP	T	T	C	rs753779	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:142228809T>C	ENST00000024061.3	-	4	1084	c.777A>G	c.(775-777)gcA>gcG	p.A259A	SLC45A4_ENST00000519067.1_Silent_p.A259A|SLC45A4_ENST00000433583.2_Silent_p.A252A|SLC45A4_ENST00000517878.1_Silent_p.A310A	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)			GCACGTGCAATGCCGAGTCGC	0.667													C|||	3563	0.711462	0.8238	0.5879	5008	,	,		16667	0.8194		0.6024	False		,,,				2504	0.6483				p.A259A		Atlas-SNP	.											.	SLC45A4	71	.	0			c.A777G						PASS	.	C		3559,847	316.3+/-294.6	1446,667,90	74.0	77.0	76.0		777	2.6	1.0	8	dbSNP_86	76	4925,3675	510.2+/-377.4	1414,2097,789	no	coding-synonymous	SLC45A4	NM_001080431.1		2860,2764,879	CC,CT,TT		42.7326,19.2238,34.7686		259/799	142228809	8484,4522	2203	4300	6503	SO:0001819	synonymous_variant	57210	exon4			GTGCAATGCCGAG	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.777A>G	8.37:g.142228809T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	199	92	0.462312	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	37	CCDS34948.1																																																																																			T|0.319;C|0.681	0.681	strong		0.667	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
RFPL3	10738	hgsc.bcm.edu	37	22	32754286	32754286	+	Silent	SNP	G	G	A	rs9621426	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:32754286G>A	ENST00000249007.4	+	1	433	c.228G>A	c.(226-228)ctG>ctA	p.L76L	RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000382088.3_Silent_p.L47L|RFPL3_ENST00000397468.1_Silent_p.L47L	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	76							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GGGAGGATCTGCTTTGCTGTT	0.537													a|||	62	0.0123802	0.0015	0.0216	5008	,	,		19556	0.0		0.0378	False		,,,				2504	0.0072				p.L76L		Atlas-SNP	.											.	RFPL3	91	.	0			c.G228A						PASS	.	A	,	20,4386	824.5+/-416.5	0,20,2183	127.0	119.0	122.0		228,141	-0.6	0.0	22	dbSNP_119	122	264,8336	807.6+/-407.2	4,256,4040	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	4,276,6223	AA,AG,GG		3.0698,0.4539,2.1836	,	76/318,47/289	32754286	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	10738	exon1			GGATCTGCTTTGC	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.228G>A	22.37:g.32754286G>A		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	271	137	0.505535	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			G|0.979;A|0.021	0.021	strong		0.537	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
TTLL2	83887	hgsc.bcm.edu	37	6	167754721	167754721	+	Missense_Mutation	SNP	G	G	A	rs9457304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:167754721G>A	ENST00000239587.5	+	3	1421	c.1333G>A	c.(1333-1335)Ggt>Agt	p.G445S		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	445			G -> S (in dbSNP:rs9457304).		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)		AAGTGACAGAGGTGGGCTTGA	0.443													G|||	312	0.0623003	0.1362	0.0432	5008	,	,		22397	0.0		0.0676	False		,,,				2504	0.0348				p.G445S		Atlas-SNP	.											.	TTLL2	82	.	0			c.G1333A						PASS	.	G	SER/GLY	607,3799	266.5+/-267.3	45,517,1641	105.0	96.0	99.0		1333	-0.7	0.0	6	dbSNP_119	99	693,7907	172.6+/-223.3	26,641,3633	yes	missense	TTLL2	NM_031949.4	56	71,1158,5274	AA,AG,GG		8.0581,13.7767,9.9954	benign	445/593	167754721	1300,11706	2203	4300	6503	SO:0001583	missense	83887	exon3			GACAGAGGTGGGC	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.1333G>A	6.37:g.167754721G>A	ENSP00000239587:p.Gly445Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	126	0.057692307692307696	63	0.12804878048780488	13	0.03591160220994475	0	0.0	50	0.06596306068601583	G	8.051	0.765961	0.15983	0.137767	0.080581	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02197	4.4	3.61	-0.681	0.11342	.	1.067990	0.07329	N	0.878983	T	0.00384	0.0012	N	0.24115	0.695	0.80722	P	0.0	B	0.30326	0.276	B	0.25614	0.062	T	0.43310	-0.9399	9	0.06891	T	0.86	.	1.3265	0.02126	0.1249:0.1981:0.2658:0.4112	rs9457304;rs52802447;rs61221763;rs9457304	445	Q9BWV7	TTLL2_HUMAN	S	445;372	ENSP00000239587:G445S	ENSP00000239587:G445S	G	+	1	0	TTLL2	167674711	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.822000	0.04448	0.024000	0.15214	0.491000	0.48974	GGT	G|0.915;A|0.085	0.085	strong		0.443	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
GLB1L2	89944	hgsc.bcm.edu	37	11	134226278	134226278	+	Silent	SNP	C	C	T	rs3802928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134226278C>T	ENST00000535456.2	+	6	830	c.642C>T	c.(640-642)taC>taT	p.Y214Y	GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.Y214Y|GLB1L2_ENST00000389881.3_Silent_p.Y214Y	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	214					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)	p.Y214Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		ACATGCCCTACGTCAAGAAGG	0.458													C|||	634	0.126597	0.2027	0.0677	5008	,	,		17955	0.1944		0.0596	False		,,,				2504	0.0644				p.Y214Y		Atlas-SNP	.											GLB1L2,NS,carcinoma,0,1	GLB1L2	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C642T						PASS	.	C		833,3569	330.7+/-301.6	85,663,1453	128.0	135.0	132.0		642	-1.6	0.0	11	dbSNP_107	132	415,8179	130.2+/-188.1	15,385,3897	no	coding-synonymous	GLB1L2	NM_138342.3		100,1048,5350	TT,TC,CC		4.829,18.9232,9.603		214/637	134226278	1248,11748	2201	4297	6498	SO:0001819	synonymous_variant	89944	exon6			GCCCTACGTCAAG		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.642C>T	11.37:g.134226278C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	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	
APLP1	333	hgsc.bcm.edu	37	19	36370011	36370011	+	Silent	SNP	G	G	A	rs2227909	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	36	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	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	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671575	31671575	+	Missense_Mutation	SNP	T	T	G	rs144272671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31671575T>G	ENST00000375483.3	+	3	572	c.572T>G	c.(571-573)cTc>cGc	p.L191R		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	191	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										GGTGGCCTGCTCGGCGGAGGT	0.662													T|||	23	0.00459265	0.0	0.0	5008	,	,		15553	0.001		0.0	False		,,,				2504	0.0225				p.L191R		Atlas-SNP	.											.	.	.	.	0			c.T572G						PASS	.	T	ARG/LEU	0,4400		0,0,2200	26.0	32.0	30.0		572	3.3	1.0	20	dbSNP_134	30	17,8581		0,17,4282	yes	missense	BPIFB4	NM_182519.2	102	0,17,6482	GG,GT,TT		0.1977,0.0,0.1308	probably-damaging	191/615	31671575	17,12981	2200	4299	6499	SO:0001583	missense	149954	exon3			GCCTGCTCGGCGG	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.572T>G	20.37:g.31671575T>G	ENSP00000364632:p.Leu191Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	127	74	0.582677	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	T	13.01	2.109728	0.37242	0.0	0.001977	ENSG00000186191	ENST00000375483	T	0.01430	4.9	3.33	3.33	0.38152	.	0.672431	0.13031	N	0.419352	T	0.03695	0.0105	L	0.29908	0.895	0.36259	D	0.854418	D	0.65815	0.995	D	0.72982	0.979	T	0.57039	-0.7879	10	0.62326	D	0.03	-15.6488	8.2721	0.31851	0.0:0.0:0.0:1.0	.	191	P59827	BPIB4_HUMAN	R	191	ENSP00000364632:L191R	ENSP00000364632:L191R	L	+	2	0	BPIFB4	31135236	0.999000	0.42202	0.992000	0.48379	0.309000	0.27889	3.953000	0.56699	1.516000	0.48900	0.334000	0.21626	CTC	T|0.998;G|0.002	0.002	strong		0.662	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
POLRMT	5442	hgsc.bcm.edu	37	19	619021	619021	+	Silent	SNP	G	G	C	rs14155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:619021G>C	ENST00000588649.2	-	15	3327	c.3243C>G	c.(3241-3243)ccC>ccG	p.P1081P	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1081	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)	p.P1081P(1)		cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGCGATAGGGCTGGATGA	0.637													C|||	3117	0.622404	0.7352	0.4006	5008	,	,		13997	0.5823		0.5119	False		,,,				2504	0.7822				p.P1081P		Atlas-SNP	.											POLRMT,colon,carcinoma,0,2	POLRMT	91	2	1	Substitution - coding silent(1)	stomach(1)	c.C3243G						PASS	.	C		2965,1429		999,967,231	59.0	50.0	53.0		3243	-2.7	1.0	19	dbSNP_52	53	4220,4378		1005,2210,1084	no	coding-synonymous	POLRMT	NM_005035.3		2004,3177,1315	CC,CG,GG		49.0812,32.5216,44.6967		1081/1231	619021	7185,5807	2197	4299	6496	SO:0001819	synonymous_variant	5442	exon15			GCGATAGGGCTGG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.3243C>G	19.37:g.619021G>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	232	110	0.474138	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.442;C|0.558	0.558	strong		0.637	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
ACOXL	55289	hgsc.bcm.edu	37	2	111666368	111666368	+	Missense_Mutation	SNP	G	G	A	rs116012262	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:111666368G>A	ENST00000389811.4	+	11	1015	c.791G>A	c.(790-792)cGg>cAg	p.R264Q	ACOXL_ENST00000439055.1_Missense_Mutation_p.R264Q			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	264					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						CCCTCTAGCCGGAGGCAGTTT	0.527													g|||	4	0.000798722	0.0	0.0	5008	,	,		19159	0.001		0.003	False		,,,				2504	0.0				p.R264Q		Atlas-SNP	.											.	ACOXL	93	.	0			c.G791A						PASS	.		GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	89.0	86.0	87.0		791	3.2	1.0	2	dbSNP_132	87	25,8575	17.9+/-57.8	0,25,4275	yes	missense	ACOXL	NM_001142807.1	43	0,27,6476	AA,AG,GG		0.2907,0.0454,0.2076	probably-damaging	264/581	111666368	27,12979	2203	4300	6503	SO:0001583	missense	55289	exon11			CTAGCCGGAGGCA		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"""acyl-Coenzyme A oxidase-like"""				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.791G>A	2.37:g.111666368G>A	ENSP00000374461:p.Arg264Gln	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	g	15.47	2.842370	0.51057	4.54E-4	0.002907	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000422487;ENST00000417074	D;D;D	0.89810	-2.57;-2.57;-2.57	5.02	3.2	0.36748	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.339475	0.23160	N	0.051250	D	0.94122	0.8115	M	0.87097	2.86	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.968;0.947;1.0	D	0.93087	0.6496	10	0.87932	D	0	-44.5563	9.5964	0.39576	0.1755:0.0:0.8245:0.0	.	264;264;264	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	Q	264;264;115;102	ENSP00000374461:R264Q;ENSP00000407761:R264Q;ENSP00000387832:R102Q	ENSP00000374461:R264Q	R	+	2	0	ACOXL	111382839	1.000000	0.71417	0.993000	0.49108	0.173000	0.22820	3.379000	0.52440	0.509000	0.28195	0.558000	0.71614	CGG	G|0.999;A|0.001	0.001	strong		0.527	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
GNB4	59345	hgsc.bcm.edu	37	3	179137273	179137273	+	Silent	SNP	A	A	G	rs1362650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:179137273A>G	ENST00000232564.3	-	4	403	c.117T>C	c.(115-117)tcT>tcC	p.S39S	GNB4_ENST00000468623.1_Silent_p.S39S	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	39					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			TTCGACCCACAGAGTCCATAT	0.383													G|||	2369	0.473043	0.4455	0.5058	5008	,	,		17180	0.4365		0.5	False		,,,				2504	0.4969				p.S39S	Melanoma(105;1405 1491 7265 20440 33721)	Atlas-SNP	.											.	GNB4	37	.	0			c.T117C						PASS	.	G		2021,2385	614.5+/-392.4	461,1099,643	180.0	171.0	174.0		117	-2.8	0.9	3	dbSNP_88	174	4036,4564	597.2+/-393.7	948,2140,1212	no	coding-synonymous	GNB4	NM_021629.3		1409,3239,1855	GG,GA,AA		46.9302,45.8693,46.5708		39/341	179137273	6057,6949	2203	4300	6503	SO:0001819	synonymous_variant	59345	exon4			ACCCACAGAGTCC	AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"""WD repeat domain containing"""	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.117T>C	3.37:g.179137273A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_021629	B3KMH5|D3DNR8	Silent	SNP	ENST00000232564.3	37	CCDS3230.1																																																																																			A|0.538;G|0.462	0.462	strong		0.383	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629	
ITGA11	22801	hgsc.bcm.edu	37	15	68653946	68653946	+	Missense_Mutation	SNP	C	C	T	rs148886354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:68653946C>T	ENST00000315757.7	-	5	540	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	ITGA11_ENST00000562826.1_5'UTR|ITGA11_ENST00000423218.2_Missense_Mutation_p.V152M	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	152					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						GCTGGGGCCACGGTCTTGGAG	0.557													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20919	0.001		0.001	False		,,,				2504	0.0				p.V152M		Atlas-SNP	.											.	ITGA11	110	.	0			c.G454A						PASS	.	C	MET/VAL	0,3976		0,0,1988	74.0	74.0	74.0		454	4.7	1.0	15	dbSNP_134	74	12,8308		0,12,4148	yes	missense	ITGA11	NM_001004439.1	21	0,12,6136	TT,TC,CC		0.1442,0.0,0.0976	probably-damaging	152/1189	68653946	12,12284	1988	4160	6148	SO:0001583	missense	22801	exon5			GGGCCACGGTCTT	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.454G>A	15.37:g.68653946C>T	ENSP00000327290:p.Val152Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	C	14.81	2.646911	0.47258	0.0	0.001442	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.60040	0.22;0.22	4.66	4.66	0.58398	.	0.063133	0.64402	D	0.000004	T	0.52996	0.1769	M	0.61703	1.905	0.43050	D	0.994657	P;P	0.43607	0.812;0.809	B;B	0.34489	0.163;0.184	T	0.62812	-0.6775	10	0.49607	T	0.09	.	16.915	0.86149	0.0:1.0:0.0:0.0	.	152;152	A8K8T0;Q9UKX5	.;ITA11_HUMAN	M	152	ENSP00000327290:V152M;ENSP00000403392:V152M	ENSP00000327290:V152M	V	-	1	0	ITGA11	66441000	0.998000	0.40836	0.999000	0.59377	0.993000	0.82548	3.185000	0.50934	2.282000	0.76494	0.555000	0.69702	GTG	C|0.999;T|0.001	0.001	strong		0.557	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
STAB2	55576	hgsc.bcm.edu	37	12	104048446	104048446	+	Missense_Mutation	SNP	G	G	T	rs149524008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:104048446G>T	ENST00000388887.2	+	13	1725	c.1521G>T	c.(1519-1521)aaG>aaT	p.K507N	RP11-341G23.2_ENST00000551905.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CCATGGACAAGTTAGAACCCA	0.443													G|||	22	0.00439297	0.0008	0.0029	5008	,	,		21467	0.0		0.0159	False		,,,				2504	0.0031				p.K507N		Atlas-SNP	.											.	STAB2	370	.	0			c.G1521T						PASS	.	G	ASN/LYS	6,4400	14.3+/-33.2	0,6,2197	103.0	93.0	96.0		1521	0.5	0.0	12	dbSNP_134	96	85,8515	48.9+/-108.6	2,81,4217	yes	missense	STAB2	NM_017564.9	94	2,87,6414	TT,TG,GG		0.9884,0.1362,0.6997	benign	507/2552	104048446	91,12915	2203	4300	6503	SO:0001583	missense	55576	exon13			GGACAAGTTAGAA	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.1521G>T	12.37:g.104048446G>T	ENSP00000373539:p.Lys507Asn	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	G	1.712	-0.498842	0.04291	0.001362	0.009884	ENSG00000136011	ENST00000388887	T	0.63580	-0.05	5.8	0.469	0.16741	FAS1 domain (2);	0.583558	0.18587	N	0.136838	T	0.25494	0.0620	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.11421	-1.0588	10	0.24483	T	0.36	.	7.5112	0.27575	0.0643:0.4925:0.2505:0.1927	.	507	Q8WWQ8	STAB2_HUMAN	N	507	ENSP00000373539:K507N	ENSP00000373539:K507N	K	+	3	2	STAB2	102572576	0.991000	0.36638	0.000000	0.03702	0.002000	0.02628	0.356000	0.20181	-0.171000	0.10797	-0.257000	0.10917	AAG	G|0.992;T|0.008	0.008	strong		0.443	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
COLEC12	81035	hgsc.bcm.edu	37	18	335099	335099	+	Missense_Mutation	SNP	T	T	C	rs8098850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:335099T>C	ENST00000400256.3	-	6	1666	c.1459A>G	c.(1459-1461)Att>Gtt	p.I487V		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	487	Collagen-like 2.		I -> V (in dbSNP:rs8098850).		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)				GCTGGTCCAATTGGGCCTCTC	0.667													T|||	223	0.0445288	0.0643	0.049	5008	,	,		14094	0.001		0.0686	False		,,,				2504	0.0348				p.I487V		Atlas-SNP	.											.	COLEC12	121	.	0			c.A1459G						PASS	.	T	VAL/ILE	292,4100		9,274,1913	32.0	34.0	33.0		1459	-7.9	0.0	18	dbSNP_116	33	489,8077		7,475,3801	yes	missense	COLEC12	NM_130386.2	29	16,749,5714	CC,CT,TT		5.7086,6.6485,6.0272	benign	487/743	335099	781,12177	2196	4283	6479	SO:0001583	missense	81035	exon6			GTCCAATTGGGCC	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.1459A>G	18.37:g.335099T>C	ENSP00000383115:p.Ile487Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	106	0.048534798534798536	30	0.06097560975609756	19	0.052486187845303865	0	0.0	57	0.07519788918205805	T	0.004	-2.266847	0.00259	0.066485	0.057086	ENSG00000158270	ENST00000400256	T	0.16457	2.34	5.67	-7.86	0.01187	.	0.805279	0.11648	N	0.543031	T	0.00440	0.0014	N	0.16903	0.455	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28267	-1.0049	10	0.21014	T	0.42	0.0071	13.5974	0.61998	0.0:0.5516:0.166:0.2824	rs8098850;rs52809593;rs8098850	487	Q5KU26	COL12_HUMAN	V	487	ENSP00000383115:I487V	ENSP00000383115:I487V	I	-	1	0	COLEC12	325099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.377000	0.07456	-2.159000	0.00787	-1.139000	0.01908	ATT	T|0.944;C|0.056	0.056	strong		0.667	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		
UNC79	57578	hgsc.bcm.edu	37	14	93994954	93994954	+	Silent	SNP	G	G	A	rs28420706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:93994954G>A	ENST00000393151.2	+	9	1014	c.1014G>A	c.(1012-1014)ccG>ccA	p.P338P	UNC79_ENST00000553484.1_Silent_p.P338P|UNC79_ENST00000555664.1_Silent_p.P338P|UNC79_ENST00000256339.4_Silent_p.P161P			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	338					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)		p.P161P(1)		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						AACCACCCCCGTTGTATCTCT	0.408													G|||	2442	0.48762	0.534	0.6931	5008	,	,		18987	0.2431		0.5636	False		,,,				2504	0.453				p.P161P		Atlas-SNP	.											KIAA1409,NS,carcinoma,0,1	UNC79	366	1	1	Substitution - coding silent(1)	stomach(1)	c.G483A						PASS	.	G		2294,2112	601.1+/-389.6	597,1100,506	115.0	111.0	113.0		483	-6.0	0.1	14	dbSNP_125	113	4866,3734	617.5+/-396.7	1391,2084,825	no	coding-synonymous	UNC79	NM_020818.3		1988,3184,1331	AA,AG,GG		43.4186,47.9346,44.9485		161/2459	93994954	7160,5846	2203	4300	6503	SO:0001819	synonymous_variant	57578	exon9			ACCCCCGTTGTAT	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.1014G>A	14.37:g.93994954G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	150	89	0.593333	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																				G|0.462;A|0.538	0.538	strong		0.408	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
ZNF778	197320	hgsc.bcm.edu	37	16	89294595	89294595	+	Silent	SNP	C	C	T	rs74466939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89294595C>T	ENST00000433976.2	+	6	2147	c.1815C>T	c.(1813-1815)atC>atT	p.I605I	ZNF778_ENST00000306502.6_Silent_p.I563I|RP11-46C24.6_ENST00000563182.1_RNA	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	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	70	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	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	
GAMT	2593	hgsc.bcm.edu	37	19	1397443	1397443	+	Missense_Mutation	SNP	G	G	A	rs17851582	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1397443G>A	ENST00000252288.2	-	6	692	c.626C>T	c.(625-627)aCg>aTg	p.T209M	AC005329.7_ENST00000589734.1_RNA|AC005329.7_ENST00000585596.1_RNA|AC005329.7_ENST00000501448.1_RNA	NM_000156.5	NP_000147.1	Q14353	GAMT_HUMAN	guanidinoacetate N-methyltransferase	209	RMT2. {ECO:0000255|PROSITE- ProRule:PRU00892}.		T -> M (in dbSNP:rs17851582). {ECO:0000269|PubMed:15489334}.		cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|organ morphogenesis (GO:0009887)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	guanidinoacetate N-methyltransferase activity (GO:0030731)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|upper_aerodigestive_tract(1)	6		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Lung NSC(49;0.000195)|Breast(49;0.000231)|all_lung(49;0.000247)|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)	Creatine(DB00148)|Guanidine(DB00536)	CATCACCTCCGTACGGATGTT	0.692													G|||	183	0.0365415	0.003	0.0648	5008	,	,		14054	0.0		0.0825	False		,,,				2504	0.0521				p.T209M	Colon(167;1531 1939 13427 28842 31956)	Atlas-SNP	.											.	GAMT	39	.	0			c.C626T	GRCh37	CM024106	GAMT	M	rs17851582	PASS	.	G	MET/THR	90,4314	72.0+/-110.0	2,86,2114	82.0	75.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	626	5.1	0.1	19	dbSNP_123	77	836,7764	192.0+/-238.1	38,760,3502	yes	missense	GAMT	NM_000156.4	81	40,846,5616	AA,AG,GG		9.7209,2.0436,7.1209		209/237	1397443	926,12078	2202	4300	6502	SO:0001583	missense	2593	exon6			ACCTCCGTACGGA	Z49878	CCDS12064.1, CCDS45897.1	19p13.3	2008-02-05							4136	protein-coding gene	gene with protein product		601240				9570966, 8547310	Standard	NM_000156		Approved	PIG2, TP53I2	uc002lsk.4	Q14353		ENST00000252288.2:c.626C>T	19.37:g.1397443G>A	ENSP00000252288:p.Thr209Met	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_000156	A8K0A0|Q53Y34|Q8WVJ1	Missense_Mutation	SNP	ENST00000252288.2	37	CCDS12064.1	83	0.038003663003663	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	70	0.09234828496042216	G	14.89	2.671302	0.47781	0.020436	0.097209	ENSG00000130005	ENST00000252288	D	0.88509	-2.39	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.26738	0.0654	L	0.54323	1.7	0.80722	D	1	D	0.71674	0.998	P	0.52159	0.691	T	0.63323	-0.6663	10	0.34782	T	0.22	.	15.9511	0.79840	0.0:0.0:1.0:0.0	rs17851582	209	Q14353	GAMT_HUMAN	M	209	ENSP00000252288:T209M	ENSP00000252288:T209M	T	-	2	0	GAMT	1348443	0.999000	0.42202	0.100000	0.21137	0.035000	0.12851	2.733000	0.47360	2.365000	0.80145	0.561000	0.74099	ACG	G|0.939;A|0.061	0.061	strong		0.692	GAMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449739.1	NM_138924	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2410332	2410332	+	Silent	SNP	T	T	C	rs3848635	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2410332T>C	ENST00000332578.3	+	8	1092	c.1092T>C	c.(1090-1092)caT>caC	p.H364H		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	364	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)		TGTACGGCCATTCACTCACTG	0.597													C|||	1968	0.392971	0.5893	0.2896	5008	,	,		16394	0.3581		0.2575	False		,,,				2504	0.3763				p.H364H		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.T1092C						PASS	.	C		2455,1951	551.7+/-378.3	701,1053,449	92.0	80.0	84.0		1092	3.7	1.0	19	dbSNP_108	84	2286,6314	706.1+/-405.5	310,1666,2324	yes	coding-synonymous	TMPRSS9	NM_182973.1		1011,2719,2773	CC,CT,TT		26.5814,44.2805,36.4524		364/1060	2410332	4741,8265	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon8			CGGCCATTCACTC	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.1092T>C	19.37:g.2410332T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	51	0.593023	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			T|0.629;C|0.371	0.371	strong		0.597	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
OR51F1	256892	hgsc.bcm.edu	37	11	4790268	4790268	+	Missense_Mutation	SNP	C	C	A	rs1030726	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790268C>A	ENST00000380383.1	-	1	900	c.901G>T	c.(901-903)Gac>Tac	p.D301Y	OR51F1_ENST00000343430.3_Missense_Mutation_p.D294Y|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	301			D -> Y (in dbSNP:rs1030726).			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)		TTTACACTGTCGATGATGGGG	0.448													A|||	1080	0.215655	0.4569	0.2017	5008	,	,		21026	0.0		0.2704	False		,,,				2504	0.0654				p.D294Y		Atlas-SNP	.											.	OR51F1	60	.	0			c.G880T						PASS	.	A	TYR/ASP	1967,2435	618.7+/-393.2	444,1079,678	95.0	92.0	93.0		880	5.4	1.0	11	dbSNP_86	93	2178,6418	712.3+/-405.9	291,1596,2411	yes	missense	OR51F1	NM_001004752.1	160	735,2675,3089	AA,AC,CC		25.3374,44.6842,31.8895	benign	294/313	4790268	4145,8853	2201	4298	6499	SO:0001583	missense	256892	exon1			CACTGTCGATGAT	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.901G>T	11.37:g.4790268C>A	ENSP00000369744:p.Asp301Tyr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		494	0.2261904761904762	225	0.4573170731707317	82	0.2265193370165746	0	0.0	187	0.24670184696569922	A	1.713	-0.498507	0.04291	0.446842	0.253374	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.15718	2.4;2.4	5.43	5.43	0.79202	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	N	0.000106	T	0.00012	0.0000	N	0.00000	-3.91	0.38500	P	0.05178700000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.47911	-0.9080	9	0.02654	T	1	.	11.8333	0.52307	0.8531:0.1469:0.0:0.0	rs1030726;rs52801059;rs60846270;rs1030726	301	A6NGY5	O51F1_HUMAN	Y	294;301	ENSP00000345163:D294Y;ENSP00000369744:D301Y	ENSP00000345163:D294Y	D	-	1	0	OR51F1	4746844	1.000000	0.71417	0.992000	0.48379	0.617000	0.37484	6.611000	0.74183	1.085000	0.41206	-0.256000	0.11100	GAC	C|0.712;A|0.288	0.288	strong		0.448	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
CC2D1B	200014	hgsc.bcm.edu	37	1	52828384	52828384	+	Missense_Mutation	SNP	A	A	G	rs11555349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:52828384A>G	ENST00000371586.2	-	3	242	c.104T>C	c.(103-105)aTg>aCg	p.M35T	CC2D1B_ENST00000438831.1_5'UTR|CC2D1B_ENST00000460261.1_5'Flank|CC2D1B_ENST00000284376.3_Missense_Mutation_p.M35T	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	35			M -> T (in dbSNP:rs11555349).			nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						GCCCAGCAGCATGTCCTCAGG	0.577													A|||	362	0.0722843	0.1369	0.0418	5008	,	,		20658	0.003		0.0507	False		,,,				2504	0.1002				p.M35T		Atlas-SNP	.											.	CC2D1B	73	.	0			c.T104C						PASS	.	A	THR/MET	523,3883	239.6+/-250.7	26,471,1706	143.0	142.0	143.0		104	4.8	1.0	1	dbSNP_120	143	466,8134	138.4+/-195.2	12,442,3846	yes	missense	CC2D1B	NM_032449.2	81	38,913,5552	GG,GA,AA		5.4186,11.8702,7.6042	benign	35/859	52828384	989,12017	2203	4300	6503	SO:0001583	missense	200014	exon3			AGCAGCATGTCCT	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.104T>C	1.37:g.52828384A>G	ENSP00000360642:p.Met35Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	134	0.06135531135531135	78	0.15853658536585366	14	0.03867403314917127	1	0.0017482517482517483	41	0.05408970976253298	A	14.90	2.673409	0.47781	0.118702	0.054186	ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371575	T;T	0.22945	1.93;1.93	4.85	4.85	0.62838	.	0.204155	0.47455	D	0.000235	T	0.00109	0.0003	M	0.62723	1.935	0.09310	P	1.0	P	0.36282	0.546	B	0.26770	0.073	T	0.10730	-1.0617	9	0.72032	D	0.01	-9.6858	11.9234	0.52806	1.0:0.0:0.0:0.0	rs11555349;rs60350082	35	Q5T0F9	C2D1B_HUMAN	T	35	ENSP00000360642:M35T;ENSP00000284376:M35T	ENSP00000284376:M35T	M	-	2	0	CC2D1B	52600972	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.201000	0.65163	2.028000	0.59812	0.533000	0.62120	ATG	A|0.928;G|0.072	0.072	strong		0.577	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
GABRA6	2559	hgsc.bcm.edu	37	5	161113004	161113004	+	Silent	SNP	G	G	A	rs13188991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:161113004G>A	ENST00000274545.5	+	1	442	c.9G>A	c.(7-9)tcG>tcA	p.S3S	GABRA6_ENST00000522269.1_Intron|GABRA6_ENST00000523217.1_Silent_p.S3S|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	3					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	GGATGGCGTCGTCTCTGCCCT	0.468										TCGA Ovarian(5;0.080)			G|||	497	0.0992412	0.0083	0.1124	5008	,	,		19854	0.0655		0.2664	False		,,,				2504	0.0757				p.S3S		Atlas-SNP	.											GABRA6,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	GABRA6	139	1	0			c.G9A						PASS	.	G		192,4214	121.7+/-159.2	5,182,2016	167.0	143.0	151.0		9	-8.4	0.0	5	dbSNP_121	151	2249,6351	381.6+/-340.1	295,1659,2346	no	coding-synonymous	GABRA6	NM_000811.2		300,1841,4362	AA,AG,GG		26.1512,4.3577,18.7683		3/454	161113004	2441,10565	2203	4300	6503	SO:0001819	synonymous_variant	2559	exon1			GGCGTCGTCTCTG		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.9G>A	5.37:g.161113004G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	197	94	0.477157	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	37	CCDS4356.1																																																																																			G|0.841;A|0.159	0.159	strong		0.468	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
PPFIBP2	8495	hgsc.bcm.edu	37	11	7662732	7662732	+	Silent	SNP	C	C	T	rs4643071	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7662732C>T	ENST00000299492.4	+	16	1786	c.1398C>T	c.(1396-1398)gaC>gaT	p.D466D	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000530181.1_Silent_p.D323D|PPFIBP2_ENST00000528883.1_Silent_p.D354D|PPFIBP2_ENST00000533792.1_Silent_p.D308D	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	144	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	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	
MDGA1	266727	hgsc.bcm.edu	37	6	37631768	37631768	+	Missense_Mutation	SNP	A	A	G	rs10947690	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:37631768A>G	ENST00000434837.3	-	2	1360	c.182T>C	c.(181-183)cTt>cCt	p.L61P	MDGA1_ENST00000505425.1_Missense_Mutation_p.L61P|MDGA1_ENST00000297153.7_Missense_Mutation_p.L61P	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	61	Ig-like 1.		L -> P (in dbSNP:rs10947690).		brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CCCTGTTACAAGGCACTGCAG	0.607													A|||	425	0.0848642	0.0068	0.1412	5008	,	,		19734	0.006		0.2147	False		,,,				2504	0.0982				p.L61P		Atlas-SNP	.											.	MDGA1	104	.	0			c.T182C						PASS	.	A	PRO/LEU	183,4065		7,169,1948	70.0	72.0	72.0		182	5.2	1.0	6	dbSNP_120	72	1997,6447		254,1489,2479	yes	missense	MDGA1	NM_153487.3	98	261,1658,4427	GG,GA,AA		23.6499,4.3079,17.1762	probably-damaging	61/956	37631768	2180,10512	2124	4222	6346	SO:0001583	missense	266727	exon2			GTTACAAGGCACT	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.182T>C	6.37:g.37631768A>G	ENSP00000402584:p.Leu61Pro	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	213	0.09752747252747253	6	0.012195121951219513	55	0.15193370165745856	2	0.0034965034965034965	150	0.19788918205804748	A	22.5	4.294354	0.81025	0.043079	0.236499	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425;ENST00000515437;ENST00000508399	T;T;T;T;T	0.66638	0.3;0.3;0.3;-0.22;-0.22	5.25	5.25	0.73442	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40908	D	0.000981	T	0.60183	0.2249	N	0.21508	0.67	0.09310	P	0.999999999653738	D	0.69078	0.997	D	0.68621	0.959	T	0.63395	-0.6647	9	0.31617	T	0.26	.	14.3559	0.66738	1.0:0.0:0.0:0.0	rs10947690;rs60791866;rs10947690	61	Q8NFP4	MDGA1_HUMAN	P	61;61;61;5;5	ENSP00000402584:L61P;ENSP00000297153:L61P;ENSP00000422042:L61P;ENSP00000421510:L5P;ENSP00000427645:L5P	ENSP00000297153:L61P	L	-	2	0	MDGA1	37739746	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	1.994000	0.58287	0.533000	0.62120	CTT	A|0.894;G|0.106	0.106	strong		0.607	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
OPN3	23596	hgsc.bcm.edu	37	1	241755348	241755348	+	IGR	SNP	C	C	T	rs1053230	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:241755348C>T	ENST00000366554.2	-	0	2620				KMO_ENST00000366558.3_Missense_Mutation_p.R439C|KMO_ENST00000366559.4_Missense_Mutation_p.R452C|KMO_ENST00000366557.4_Missense_Mutation_p.R418C|OPN3_ENST00000469376.1_5'Flank	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	94	42	0.446809	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	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455976	5455976	+	Silent	SNP	C	C	T	rs386806230|rs61740902	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5455976C>T	ENST00000222033.4	+	1	551	c.474C>T	c.(472-474)atC>atT	p.I158I		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	158	PA.			AIV -> SIA (in Ref. 4; AAH17592). {ECO:0000305}.		cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		TGGGCGCCATCGTGCTGATCC	0.682													C|||	596	0.11901	0.0477	0.1729	5008	,	,		15731	0.004		0.2296	False		,,,				2504	0.182				p.I158I		Atlas-SNP	.											.	ZNRF4	59	.	0			c.C474T						PASS	.	C		259,3999		8,243,1878	28.0	31.0	30.0		474	-9.3	0.0	19	dbSNP_129	30	1616,6844		228,1160,2842	no	coding-synonymous	ZNRF4	NM_181710.3		236,1403,4720	TT,TC,CC		19.1017,6.0827,14.7429		158/430	5455976	1875,10843	2129	4230	6359	SO:0001819	synonymous_variant	148066	exon1			CGCCATCGTGCTG	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.474C>T	19.37:g.5455976C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_181710	A8K886|O75866	Silent	SNP	ENST00000222033.4	37	CCDS42475.1																																																																																			C|0.851;T|0.149	0.149	strong		0.682	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
GALNT8	26290	hgsc.bcm.edu	37	12	4830000	4830000	+	Missense_Mutation	SNP	T	T	G	rs10849133	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4830000T>G	ENST00000252318.2	+	1	494	c.157T>G	c.(157-159)Tac>Gac	p.Y53D	RP11-234B24.2_ENST00000527518.1_lincRNA|RP11-234B24.6_ENST00000544741.2_Intron	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	53			Y -> D (in dbSNP:rs10849133).|Y -> N. {ECO:0000269|PubMed:10767557}.		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.Y53D(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						GAATAAACGCTACGGGGCAGT	0.468													G|||	1913	0.381989	0.4977	0.415	5008	,	,		19958	0.3611		0.3777	False		,,,				2504	0.228				p.Y53D	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											GALNT8,NS,carcinoma,0,2	GALNT8	89	2	1	Substitution - Missense(1)	prostate(1)	c.T157G						PASS	.	G	ASP/TYR	2050,2356	609.2+/-391.3	481,1088,634	88.0	92.0	91.0		157	0.5	0.0	12	dbSNP_120	91	3284,5316	647.2+/-400.4	612,2060,1628	yes	missense	GALNT8	NM_017417.1	160	1093,3148,2262	GG,GT,TT		38.186,46.5275,41.0118	benign	53/638	4830000	5334,7672	2203	4300	6503	SO:0001583	missense	26290	exon1			AAACGCTACGGGG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.157T>G	12.37:g.4830000T>G	ENSP00000252318:p.Tyr53Asp	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	897	0.4107142857142857	249	0.5060975609756098	143	0.39502762430939226	226	0.3951048951048951	279	0.36807387862796836	G	0.963	-0.702517	0.03255	0.465275	0.38186	ENSG00000130035	ENST00000252318	T	0.51817	0.69	3.74	0.482	0.16815	.	104.897000	0.00166	N	0.000000	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	0.43589	-0.9382	9	0.11794	T	0.64	.	0.2754	0.00237	0.3052:0.2005:0.2915:0.2028	rs10849133;rs10849133	53	Q9NY28	GALT8_HUMAN	D	53	ENSP00000252318:Y53D	ENSP00000252318:Y53D	Y	+	1	0	GALNT8	4700261	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.341000	0.19909	-0.294000	0.08973	-1.720000	0.00707	TAC	G|0.410;N|0.000	0.410	strong		0.468	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
TDRD9	122402	hgsc.bcm.edu	37	14	104497543	104497543	+	Silent	SNP	C	C	T	rs10135507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104497543C>T	ENST00000409874.4	+	29	3429	c.3381C>T	c.(3379-3381)ctC>ctT	p.L1127L	TDRD9_ENST00000339063.5_Intron	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	1127					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L1127L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				AGAAATATCTCATCCGGATTT	0.393													C|||	1599	0.319289	0.2776	0.3429	5008	,	,		13729	0.3353		0.3469	False		,,,				2504	0.3139				p.L1127L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	1	Substitution - coding silent(1)	stomach(1)	c.C3381T						PASS	.	C		424,960		63,298,331	128.0	110.0	115.0		3381	4.2	0.0	14	dbSNP_119	115	1047,2135		162,723,706	no	coding-synonymous	TDRD9	NM_153046.2		225,1021,1037	TT,TC,CC		32.9038,30.6358,32.2164		1127/1383	104497543	1471,3095	692	1591	2283	SO:0001819	synonymous_variant	122402	exon29			ATATCTCATCCGG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.3381C>T	14.37:g.104497543C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2																																																																																			C|0.684;T|0.316	0.316	strong		0.393	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
TCTN2	79867	hgsc.bcm.edu	37	12	124171538	124171538	+	Silent	SNP	C	C	G	rs149430216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124171538C>G	ENST00000303372.5	+	6	848	c.720C>G	c.(718-720)ccC>ccG	p.P240P	TCTN2_ENST00000426174.2_Silent_p.P239P	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	240					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		TGCAGTCCCCCCTTGCCAACA	0.572													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18850	0.0		0.002	False		,,,				2504	0.0				p.P240P		Atlas-SNP	.											.	TCTN2	50	.	0			c.C720G						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	308.0	279.0	289.0		717,720	-4.8	0.0	12	dbSNP_134	289	55,8545	33.8+/-87.4	0,55,4245	no	coding-synonymous,coding-synonymous	TCTN2	NM_001143850.1,NM_024809.3	,	0,60,6443	GG,GC,CC		0.6395,0.1135,0.4613	,	239/697,240/698	124171538	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	79867	exon6			GTCCCCCCTTGCC	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.720C>G	12.37:g.124171538C>G		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	209	98	0.4689	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																			C|0.996;G|0.004	0.004	strong		0.572	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
LRFN2	57497	hgsc.bcm.edu	37	6	40360465	40360465	+	Silent	SNP	A	A	G	rs3734557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:40360465A>G	ENST00000338305.6	-	3	2129	c.1587T>C	c.(1585-1587)atT>atC	p.I529I		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	529						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)					TGCCGCCCAGAATCTGGCTGT	0.602													g|||	3020	0.603035	0.671	0.3905	5008	,	,		15932	0.5278		0.5835	False		,,,				2504	0.7597				p.I529I		Atlas-SNP	.											.	LRFN2	133	.	0			c.T1587C						PASS	.			2884,1522	479.5+/-358.5	943,998,262	83.0	59.0	67.0		1587	1.4	1.0	6	dbSNP_107	67	5009,3591	518.9+/-379.4	1493,2023,784	no	coding-synonymous	LRFN2	NM_020737.1		2436,3021,1046	GG,GA,AA		41.7558,34.5438,39.3126		529/790	40360465	7893,5113	2203	4300	6503	SO:0001819	synonymous_variant	57497	exon3			GCCCAGAATCTGG	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.1587T>C	6.37:g.40360465A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	37	CCDS34443.1																																																																																			A|0.395;G|0.605	0.605	strong		0.602	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
KANSL1	284058	hgsc.bcm.edu	37	17	44110532	44110532	+	Silent	SNP	G	G	A	rs36076725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44110532G>A	ENST00000262419.6	-	13	3221	c.2751C>T	c.(2749-2751)ttC>ttT	p.F917F	KANSL1_ENST00000393476.3_Silent_p.F211F|KANSL1_ENST00000574590.1_Silent_p.F917F|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000572904.1_Silent_p.F917F|KANSL1_ENST00000575318.1_Silent_p.F853F|KANSL1_ENST00000432791.1_Silent_p.F917F	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	917	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GCAGGGCGGCGAAGGCTGCGT	0.602													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19745	0.001		0.2406	False		,,,				2504	0.0613				p.F917F		Atlas-SNP	.											.	.	.	.	0			c.C2751T						PASS	.	G	,,	201,4205	118.8+/-156.5	5,191,2007	59.0	59.0	59.0		2748,2751,2751	-5.2	0.9	17	dbSNP_126	59	1915,6685	305.0+/-307.2	214,1487,2599	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	219,1678,4606	AA,AG,GG		22.2674,4.562,16.2694	,,	916/1105,917/1106,917/1106	44110532	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon13			GGCGGCGAAGGCT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2751C>T	17.37:g.44110532G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	180	178	0.988889	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.143;C|0.000;G|0.856;T|0.000	0.143	strong		0.602	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
ARMC10	83787	hgsc.bcm.edu	37	7	102715804	102715804	+	Missense_Mutation	SNP	C	C	T	rs7798381	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:102715804C>T	ENST00000323716.3	+	1	477	c.85C>T	c.(85-87)Cgg>Tgg	p.R29W	FBXL13_ENST00000379306.3_5'Flank|FBXL13_ENST00000379305.3_5'Flank|FBXL13_ENST00000313221.4_5'Flank|FBXL13_ENST00000455112.2_5'Flank|FBXL13_ENST00000456695.1_5'Flank|FBXL13_ENST00000471074.1_5'Flank|FBXL13_ENST00000393772.2_5'Flank|ARMC10_ENST00000541300.1_Missense_Mutation_p.R29W|FBXL13_ENST00000379308.3_5'Flank|ARMC10_ENST00000454559.1_Missense_Mutation_p.R29W|ARMC10_ENST00000425331.1_Missense_Mutation_p.R29W|ARMC10_ENST00000428183.2_Missense_Mutation_p.R29W|ARMC10_ENST00000441711.2_Missense_Mutation_p.R29W	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	29					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						CAGGCTGACCCGGGGTCGGCG	0.771													C|||	368	0.0734824	0.0159	0.0245	5008	,	,		7637	0.131		0.0427	False		,,,				2504	0.1585				p.R29W		Atlas-SNP	.											.	ARMC10	25	.	0			c.C85T						PASS	.						3.0	5.0	4.0					7																	102715804		1373	3170	4543	SO:0001583	missense	83787	exon1			CTGACCCGGGGTC	AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"""Armadillo repeat containing"""	21706	protein-coding gene	gene with protein product	"""specific Splicing Variant involved in Hepatocarcinogenesis"""	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.85C>T	7.37:g.102715804C>T	ENSP00000319412:p.Arg29Trp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_001161012	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	37	CCDS5728.1	146	0.06684981684981685	9	0.018292682926829267	10	0.027624309392265192	91	0.1590909090909091	36	0.047493403693931395	C	11.96	1.795812	0.31777	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153	T;T;T;T;T;T	0.49139	0.79;1.39;0.81;1.39;0.83;0.84	4.56	2.58	0.30949	.	0.630262	0.15842	N	0.241977	T	0.00300	0.0009	L	0.46614	1.455	0.38143	P	0.06149099999999996	D;D;P;P;D;D	0.89917	0.999;1.0;0.95;0.956;0.994;0.996	P;D;B;B;P;P	0.79108	0.857;0.992;0.261;0.343;0.721;0.53	T	0.07809	-1.0753	9	0.33141	T	0.24	-0.5968	5.6462	0.17590	0.0:0.7472:0.0:0.2528	rs7798381	29;29;29;29;29;29	B4DWJ8;F5GX65;Q8N2F6-4;Q8N2F6-3;Q8N2F6-2;Q8N2F6	.;.;.;.;.;ARM10_HUMAN	W	29	ENSP00000319412:R29W;ENSP00000413619:R29W;ENSP00000405612:R29W;ENSP00000397969:R29W;ENSP00000440463:R29W;ENSP00000398201:R29W	ENSP00000305395:R29W	R	+	1	2	ARMC10	102503040	0.297000	0.24408	0.960000	0.40013	0.063000	0.16089	0.408000	0.21065	1.145000	0.42336	0.491000	0.48974	CGG	C|0.933;T|0.067	0.067	strong		0.771	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905	
RNF32	140545	hgsc.bcm.edu	37	7	156469179	156469179	+	Missense_Mutation	SNP	C	C	T	rs2302146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:156469179C>T	ENST00000405335.1	+	10	1328	c.919C>T	c.(919-921)Cgc>Tgc	p.R307C	RNF32_ENST00000311822.8_3'UTR|LMBR1_ENST00000430825.2_5'UTR|RNF32_ENST00000317955.5_Missense_Mutation_p.R307C|RNF32_ENST00000432459.2_Missense_Mutation_p.R307C|RNF32_ENST00000392743.2_Missense_Mutation_p.R307C|RNF32_ENST00000343665.4_Missense_Mutation_p.R283C			Q9H0A6	RNF32_HUMAN	ring finger protein 32	307			R -> C (in dbSNP:rs2302146).			aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TGGCGGTCAGCGCGTGGGTGC	0.672													C|||	2016	0.402556	0.531	0.415	5008	,	,		12678	0.4058		0.3559	False		,,,				2504	0.2648				p.R307C		Atlas-SNP	.											.	RNF32	77	.	0			c.C919T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	2153,2253	578.9+/-384.8	551,1051,601	45.0	40.0	41.0		919,919,919	-0.6	0.0	7	dbSNP_100	41	2967,5633	457.6+/-364.4	519,1929,1852	yes	missense,missense,missense	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	180,180,180	1070,2980,2453	TT,TC,CC		34.5,48.8652,39.3664	probably-damaging,probably-damaging,probably-damaging	307/363,307/363,307/363	156469179	5120,7886	2203	4300	6503	SO:0001583	missense	140545	exon9			GGTCAGCGCGTGG		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.919C>T	7.37:g.156469179C>T	ENSP00000385285:p.Arg307Cys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_001184996	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Missense_Mutation	SNP	ENST00000405335.1	37	CCDS5944.1	919	0.4207875457875458	263	0.5345528455284553	136	0.3756906077348066	233	0.40734265734265734	287	0.3786279683377309	C	13.73	2.323027	0.41096	0.488652	0.345	ENSG00000105982	ENST00000432459;ENST00000317955;ENST00000405335;ENST00000392743;ENST00000343665	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	3.66	-0.589	0.11683	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	2.027620	0.02567	N	0.097404	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.59767	0.986	P	0.48901	0.594	T	0.29579	-1.0007	9	0.59425	D	0.04	0.3209	2.1958	0.03910	0.1602:0.4725:0.1589:0.2083	rs2302146;rs10372978;rs2302146	307	Q9H0A6	RNF32_HUMAN	C	307;307;307;307;283	ENSP00000405588:R307C;ENSP00000315950:R307C;ENSP00000385285:R307C;ENSP00000376499:R307C;ENSP00000341185:R283C	ENSP00000315950:R307C	R	+	1	0	RNF32	156161940	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.486000	0.22340	-0.157000	0.11059	0.563000	0.77884	CGC	C|0.600;T|0.400	0.400	strong		0.672	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	
PRPS2	5634	hgsc.bcm.edu	37	X	12809661	12809661	+	Silent	SNP	G	G	A	rs1731469	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:12809661G>A	ENST00000380668.5	+	1	173	c.45G>A	c.(43-45)ctG>ctA	p.L15L	PRPS2_ENST00000398491.2_Silent_p.L15L|PRPS2_ENST00000489404.1_Silent_p.L15L	NM_001039091.2|NM_002765.4	NP_001034180.1|NP_002756.1	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	15					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|AMP biosynthetic process (GO:0006167)|nucleobase-containing compound metabolic process (GO:0006139)|organ regeneration (GO:0031100)	extracellular vesicular exosome (GO:0070062)|ribose phosphate diphosphokinase complex (GO:0002189)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|carbohydrate binding (GO:0030246)|GDP binding (GO:0019003)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	16						ATCAGGACCTGTCCCAGCGCG	0.721													g|||	2182	0.578013	0.3079	0.4769	3775	,	,		5715	0.6101		0.4662	False		,,,				2504	0.3681				p.L15L		Atlas-SNP	.											.	PRPS2	41	.	0			c.G45A						PASS	.		,	1726,2063		348,786,244,485,307	16.0	14.0	15.0		45,45	3.8	1.0	X	dbSNP_89	15	4189,2453		968,1104,1149,338,673	no	coding-synonymous,coding-synonymous	PRPS2	NM_001039091.2,NM_002765.4	,	1316,1890,1393,823,980	AA,AG,A,GG,G		36.9316,45.5529,43.294	,	15/322,15/319	12809661	5915,4516	2170	4232	6402	SO:0001819	synonymous_variant	5634	exon1			GGACCTGTCCCAG	Y00971	CCDS14150.1, CCDS43918.1	Xp22.2	2012-10-02			ENSG00000101911	ENSG00000101911	2.7.6.1		9465	protein-coding gene	gene with protein product	"""PRS II"", ""ribose-phosphate diphosphokinase 2"""	311860				1962753	Standard	NM_002765		Approved		uc004cva.3	P11908	OTTHUMG00000021139	ENST00000380668.5:c.45G>A	X.37:g.12809661G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001039091	Q0VDH9|Q0VDI0|Q15245|Q2TAK7	Silent	SNP	ENST00000380668.5	37	CCDS14150.1																																																																																			G|0.430;A|0.570	0.570	strong		0.721	PRPS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055772.2	NM_002765	
LRRC75A	388341	hgsc.bcm.edu	37	17	16347001	16347001	+	Silent	SNP	C	C	T	rs200702301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16347001C>T	ENST00000470794.1	-	4	963	c.936G>A	c.(934-936)cgG>cgA	p.R312R	C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000481898.1_RNA|FAM211A_ENST00000409083.3_3'UTR|C17orf76-AS1_ENST00000582911.1_RNA|RP11-138I1.3_ENST00000585048.1_lincRNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA	NM_001113567.2	NP_001107039.1														lung(1)	1						CTGTCCCTTCCCGGACCTCCT	0.667													C|||	3	0.000599042	0.0008	0.0	5008	,	,		17848	0.0		0.002	False		,,,				2504	0.0				p.R312R		Atlas-SNP	.											.	FAM211A	21	.	0			c.G936A						PASS	.						28.0	33.0	31.0					17																	16347001		692	1591	2283	SO:0001819	synonymous_variant	388341	exon4			CCCTTCCCGGACC																												ENST00000470794.1:c.936G>A	17.37:g.16347001C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_001113567		Silent	SNP	ENST00000470794.1	37	CCDS45620.1																																																																																			C|0.996;T|0.004	0.004	weak		0.667	FAM211A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130463.3		
LRRC43	254050	hgsc.bcm.edu	37	12	122674780	122674780	+	Missense_Mutation	SNP	C	C	A	rs11060094	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	145	0	0		WXS	Illumina HiSeq	Phase_I	159	76	0.477987	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	
IGSF1	3547	hgsc.bcm.edu	37	X	130410965	130410965	+	Silent	SNP	A	A	G	rs4830219	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:130410965A>G	ENST00000361420.3	-	14	2635	c.2556T>C	c.(2554-2556)taT>taC	p.Y852Y	IGSF1_ENST00000370910.1_Silent_p.Y843Y|IGSF1_ENST00000370903.3_Silent_p.Y857Y|IGSF1_ENST00000370904.1_Silent_p.Y843Y|IGSF1_ENST00000467244.1_5'UTR			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	852	Ig-like C2-type 8.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						TAGAAAAGTCATAATATCGGC	0.567													A|||	920	0.243709	0.3253	0.2406	3775	,	,		12325	0.002		0.2525	False		,,,				2504	0.0685				p.Y857Y		Atlas-SNP	.											.	IGSF1	231	.	0			c.T2571C						PASS	.	A	,,	1675,2160		318,787,252,527,319	153.0	154.0	154.0		2571,2529,2556	-2.5	1.0	X	dbSNP_111	154	2336,4392		295,1082,664,1051,1208	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF1	NM_001170961.1,NM_001170962.1,NM_001555.4	,,	613,1869,916,1578,1527	GG,GA,G,AA,A		34.7206,43.6767,37.9722	,,	857/1342,843/1328,852/1337	130410965	4011,6552	2203	4300	6503	SO:0001819	synonymous_variant	3547	exon14			AAAGTCATAATAT	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.2556T>C	X.37:g.130410965A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001170961	B5MEG2|H9KV64|O15070|Q9NTC8	Silent	SNP	ENST00000361420.3	37	CCDS14629.1																																																																																			A|0.663;0|0.005	.	strong		0.567	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1		
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23049292	23049292	+	Missense_Mutation	SNP	C	C	T	rs2230229	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:23049292C>T	ENST00000221132.3	-	10	1386	c.1322G>A	c.(1321-1323)aGa>aAa	p.R441K	RP11-1149O23.2_ENST00000518308.1_RNA	NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	441	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.		R -> K (in dbSNP:rs2230229). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9082980, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|signal transduction (GO:0007165)|TRAIL-activated apoptotic signaling pathway (GO:0036462)	integral component of membrane (GO:0016021)	death receptor activity (GO:0005035)|protease binding (GO:0002020)|receptor activity (GO:0004872)|TRAIL binding (GO:0045569)|transcription factor binding (GO:0008134)			NS(2)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|skin(1)	16		Prostate(55;0.0421)|Breast(100;0.14)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)		AATCTTCTCTCTTGCATGTCT	0.488													T|||	4570	0.91254	0.8759	0.902	5008	,	,		14055	0.9772		0.8628	False		,,,				2504	0.954				p.R441K		Atlas-SNP	.											.	TNFRSF10A	40	.	0			c.G1322A						PASS	.	T	LYS/ARG	3773,633	273.1+/-271.2	1614,545,44	137.0	121.0	127.0		1322	-2.6	0.0	8	dbSNP_98	127	7273,1327	261.0+/-283.6	3079,1115,106	yes	missense	TNFRSF10A	NM_003844.3	26	4693,1660,150	TT,TC,CC		15.4302,14.3668,15.07	benign	441/469	23049292	11046,1960	2203	4300	6503	SO:0001583	missense	8797	exon10			TTCTCTCTTGCAT	U90875	CCDS6039.1	8p21	2006-02-22			ENSG00000104689	ENSG00000104689		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11904	protein-coding gene	gene with protein product		603611				9311998, 9082980	Standard	NM_003844		Approved	DR4, Apo2, TRAILR-1, CD261	uc003xda.3	O00220	OTTHUMG00000097843	ENST00000221132.3:c.1322G>A	8.37:g.23049292C>T	ENSP00000221132:p.Arg441Lys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	1965	0.8997252747252747	437	0.8882113821138211	321	0.8867403314917127	558	0.9755244755244755	649	0.8562005277044855	T	0.546	-0.851516	0.02651	0.856332	0.845698	ENSG00000104689	ENST00000221132	D	0.85556	-2.0	3.43	-2.61	0.06171	Death (3);DEATH-like (2);	0.681612	0.12988	N	0.422740	T	0.00012	0.0000	N	0.00408	-1.53	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32214	-0.9915	9	0.02654	T	1	.	6.4331	0.21809	0.2135:0.6077:0.0:0.1788	rs2230229;rs17856410;rs52803224;rs59918525;rs2230229	441	O00220	TR10A_HUMAN	K	441	ENSP00000221132:R441K	ENSP00000221132:R441K	R	-	2	0	TNFRSF10A	23105237	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.512000	0.06313	-0.983000	0.03511	-0.521000	0.04368	AGA	C|0.120;T|0.880	0.880	strong		0.488	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137901	32137901	+	Missense_Mutation	SNP	A	A	C	rs3759296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32137901A>C	ENST00000312561.4	+	4	4426	c.4012A>C	c.(4012-4014)Aca>Cca	p.T1338P	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1338			T -> A (in dbSNP:rs3759296).					p.T1338A(1)									AAAAACAAAAACAGCTTTTTT	0.348																																					p.T1338P		Atlas-SNP	.											C12orf35,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A4012C						PASS	.						86.0	90.0	88.0					12																	32137901		2203	4300	6503	SO:0001583	missense	55196	exon4			ACAAAAACAGCTT	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.4012A>C	12.37:g.32137901A>C	ENSP00000310338:p.Thr1338Pro	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	10.15	1.271497	0.23221	.	.	ENSG00000174718	ENST00000312561	T	0.12465	2.68	5.3	-8.75	0.00834	.	2.186560	0.01601	N	0.022031	T	0.06280	0.0162	N	0.14661	0.345	0.80722	P	0.0	B	0.24882	0.113	B	0.23275	0.045	T	0.21690	-1.0238	8	.	.	.	.	5.0984	0.14747	0.216:0.2115:0.4686:0.1039	.	1338	Q9HCM1	CL035_HUMAN	P	1338	ENSP00000310338:T1338P	.	T	+	1	0	C12orf35	32029168	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.164000	0.01275	-1.463000	0.01904	0.460000	0.39030	ACA	A|0.986;G|0.014	.	alt		0.348	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411153	105411153	+	Silent	SNP	G	G	A	rs34499888	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105411153G>A	ENST00000333244.5	-	7	10754	c.10635C>T	c.(10633-10635)ccC>ccT	p.P3545P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3545						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)			CCTCGGGCACGGGGCCCTCCA	0.617													.|||	1205	0.240615	0.0787	0.2968	5008	,	,		16477	0.0873		0.4553	False		,,,				2504	0.3569				p.P3545P		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	0			c.C10635T						PASS	.	G		568,3200		51,466,1367	88.0	96.0	93.0		10635	-7.9	0.0	14	dbSNP_126	93	3905,4301		931,2043,1129	no	coding-synonymous	AHNAK2	NM_138420.2		982,2509,2496	AA,AG,GG		47.5871,15.0743,37.3559		3545/5796	105411153	4473,7501	1884	4103	5987	SO:0001819	synonymous_variant	113146	exon7			GGGCACGGGGCCC	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.10635C>T	14.37:g.105411153G>A		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	237	237	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.688;A|0.312	0.312	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MED11	400569	hgsc.bcm.edu	37	17	4638484	4638484	+	IGR	SNP	T	T	C	rs1876444	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4638484T>C	ENST00000293777.5	+	0	833				RP11-314A20.5_ENST00000570493.2_RNA|CXCL16_ENST00000574412.1_Silent_p.P226P|CXCL16_ENST00000293778.6_Silent_p.P226P|CXCL16_ENST00000576153.1_5'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.P226P(1)		lung(2)|ovary(2)	4						GGCACAGGACTGGCACTGTGG	0.612													C|||	2658	0.530751	0.3555	0.5764	5008	,	,		19019	0.5933		0.5765	False		,,,				2504	0.6237				p.P226P		Atlas-SNP	.											CXCL16_ENST00000293778,NS,carcinoma,0,1	CXCL16	30	1	1	Substitution - coding silent(1)	stomach(1)	c.A678G						PASS	.	C	,	1717,2689	650.6+/-399.1	336,1045,822	64.0	55.0	58.0		678,678	-11.2	0.0	17	dbSNP_92	58	4866,3734	532.8+/-382.3	1366,2134,800	no	coding-synonymous,coding-synonymous	CXCL16	NM_001100812.1,NM_022059.2	,	1702,3179,1622	CC,CT,TT		43.4186,38.9696,49.3849	,	226/274,226/274	4638484	6583,6423	2203	4300	6503	SO:0001628	intergenic_variant	58191	exon4			CAGGACTGGCACT	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638484T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	94	91	0.968085	NM_022059	Q6NS89	Silent	SNP	ENST00000293777.5	37	CCDS32533.1																																																																																			T|0.485;C|0.515	0.515	strong		0.612	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
ZFP69	339559	hgsc.bcm.edu	37	1	40961449	40961449	+	Silent	SNP	T	T	C	rs3795348	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40961449T>C	ENST00000372706.1	+	6	2305	c.1299T>C	c.(1297-1299)caT>caC	p.H433H	RP11-656D10.3_ENST00000450713.1_RNA|ZFP69_ENST00000372705.3_Silent_p.H433H			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										AGAGAATCCATACTGGGGAGA	0.413													T|||	220	0.0439297	0.0598	0.0331	5008	,	,		21816	0.0218		0.0328	False		,,,				2504	0.0644				p.H433H		Atlas-SNP	.											.	.	.	.	0			c.T1299C						PASS	.	T		247,4159	143.1+/-178.2	9,229,1965	73.0	75.0	75.0		1299	-3.9	1.0	1	dbSNP_107	75	300,8300	109.0+/-169.6	5,290,4005	no	coding-synonymous	ZNF642	NM_198494.2		14,519,5970	CC,CT,TT		3.4884,5.606,4.2058		433/527	40961449	547,12459	2203	4300	6503	SO:0001819	synonymous_variant	339559	exon6			AATCCATACTGGG	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.1299T>C	1.37:g.40961449T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_198494	Q5SWM5|Q6ZWK8	Silent	SNP	ENST00000372706.1	37	CCDS30686.1																																																																																			T|0.960;C|0.040	0.040	strong		0.413	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494	
TTN	7273	hgsc.bcm.edu	37	2	179582537	179582537	+	Splice_Site	SNP	G	G	T	rs2627043	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179582537G>T	ENST00000591111.1	-	85	24337	c.24113C>A	c.(24112-24114)gCg>gAg	p.A8038E	TTN_ENST00000589042.1_Splice_Site_p.A8355E|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Splice_Site_p.A7111E|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12230				A -> E (in Ref. 3; CAD12456). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGTTTGCGCGCTGTAAAGAA	0.378													T|||	2228	0.444888	0.4637	0.379	5008	,	,		21070	0.6577		0.2247	False		,,,				2504	0.4734				p.A8355E		Atlas-SNP	.											TTN_ENST00000356127,NS,carcinoma,+1,2	TTN	18412	2	0			c.C25064A						scavenged	.	T	GLU/ALA,,,	1507,2191		316,875,658	34.0	34.0	34.0		21332,,,	5.9	1.0	2	dbSNP_100	34	1653,6537		157,1339,2599	yes	missense-near-splice,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	107,,,	473,2214,3257	TT,TG,GG		20.1832,40.7518,26.5814	possibly-damaging,,,	7111/33424,,,	179582537	3160,8728	1849	4095	5944	SO:0001630	splice_region_variant	7273	exon87			TTGCGCGCTGTAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24113-1C>A	2.37:g.179582537G>T		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		859	0.3933150183150183	213	0.4329268292682927	113	0.31215469613259667	367	0.6416083916083916	166	0.21899736147757257	T	12.02	1.811212	0.32053	0.407518	0.201832	ENSG00000155657	ENST00000342992	T	0.62639	0.01	5.87	5.87	0.94306	.	.	.	.	.	T	0.00012	0.0000	N	0.01019	-1.045	0.09310	P	1.0	.	.	.	.	.	.	T	0.32666	-0.9898	6	0.87932	D	0	.	13.6839	0.62504	0.0:0.0:0.129:0.871	rs2627043;rs52818239;rs57224311;rs2627043	.	.	.	E	7111	ENSP00000343764:A7111E	ENSP00000343764:A7111E	A	-	2	0	TTN	179290782	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.236000	0.72339	1.157000	0.42530	-0.256000	0.11100	GCG	G|0.606;T|0.394	0.394	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	Missense_Mutation
MUC5B	727897	hgsc.bcm.edu	37	11	1272245	1272245	+	Missense_Mutation	SNP	C	C	T	rs2943511	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1272245C>T	ENST00000529681.1	+	31	14193	c.14135C>T	c.(14134-14136)aCg>aTg	p.T4712M	MUC5B_ENST00000447027.1_Missense_Mutation_p.T4715M|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)		ctgaccagcacggccaccaca	0.617													c|||	356	0.0710863	0.0295	0.1138	5008	,	,		18081	0.0496		0.0974	False		,,,				2504	0.092				p.T4712M		Atlas-SNP	.											MUC5B,colon,carcinoma,0,2	MUC5B	473	2	0			c.C14135T						PASS	.	C	MET/THR	77,4207		2,73,2067	110.0	141.0	131.0		14135	-3.3	0.0	11	dbSNP_101	131	629,7823		39,551,3636	yes	missense	MUC5B	NM_002458.2	81	41,624,5703	TT,TC,CC		7.442,1.7974,5.5433		4712/5763	1272245	706,12030	2142	4226	6368	SO:0001583	missense	727897	exon31			CCAGCACGGCCAC	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.14135C>T	11.37:g.1272245C>T	ENSP00000436812:p.Thr4712Met	Somatic	360	1	0.00277778		WXS	Illumina HiSeq	Phase_I	451	217	0.481153	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	154	0.07051282051282051	9	0.018292682926829267	38	0.10497237569060773	43	0.07517482517482517	64	0.08443271767810026	-	2.685	-0.274526	0.05679	0.017974	0.07442	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000535652	T;T	0.19394	2.15;2.33	1.65	-3.31	0.04988	.	.	.	.	.	T	0.00412	0.0013	M	0.75264	2.295	0.80722	P	0.0	D	0.60160	0.987	B	0.35413	0.202	T	0.06023	-1.0850	8	0.87932	D	0	.	2.2239	0.03979	0.177:0.497:0.176:0.1499	rs2943511	4715	E9PBJ0	.	M	4712;4715;4656;485	ENSP00000436812:T4712M;ENSP00000415793:T4715M	ENSP00000343037:T4656M	T	+	2	0	MUC5B	1228821	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-5.903000	0.00091	-0.636000	0.05524	0.194000	0.17425	ACG	C|0.930;T|0.070	0.070	strong		0.617	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CPNE1	8904	hgsc.bcm.edu	37	20	34219480	34219480	+	Silent	SNP	G	G	A	rs2230219	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34219480G>A	ENST00000317619.3	-	10	1042	c.648C>T	c.(646-648)gaC>gaT	p.D216D	CPNE1_ENST00000397442.1_Silent_p.D216D|CPNE1_ENST00000397443.1_Silent_p.D216D|CPNE1_ENST00000397446.1_Silent_p.D216D|CPNE1_ENST00000317677.5_Silent_p.D221D|CPNE1_ENST00000397445.1_Silent_p.D216D|CPNE1_ENST00000352393.4_Silent_p.D216D			Q99829	CPNE1_HUMAN	copine I	216	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			ACCCGTCACTGTCATAATCGG	0.557													G|||	237	0.0473243	0.0008	0.0202	5008	,	,		20674	0.002		0.0507	False		,,,				2504	0.1728				p.D221D		Atlas-SNP	.											.	CPNE1	44	.	0			c.C663T						PASS	.	G	,,,,,	37,4369	41.6+/-74.8	0,37,2166	70.0	51.0	57.0		648,663,648,648,648,648	3.5	1.0	20	dbSNP_98	57	418,8182	130.2+/-188.1	14,390,3896	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	,,,,,	14,427,6062	AA,AG,GG		4.8605,0.8398,3.4984	,,,,,	216/537,221/543,216/538,216/538,216/538,216/538	34219480	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	8904	exon8			GTCACTGTCATAA	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.648C>T	20.37:g.34219480G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Silent	SNP	ENST00000317619.3	37	CCDS13260.1																																																																																			G|0.969;A|0.031	0.031	strong		0.557	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
KBTBD8	84541	hgsc.bcm.edu	37	3	67054649	67054649	+	Missense_Mutation	SNP	T	T	C	rs13096789	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:67054649T>C	ENST00000417314.2	+	3	1307	c.1258T>C	c.(1258-1260)Tgt>Cgt	p.C420R	KBTBD8_ENST00000460576.1_Intron|KBTBD8_ENST00000295568.4_Missense_Mutation_p.C394R			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	420			C -> R (in dbSNP:rs13096789).			cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		TAGAGAGAATTGTTGGACGAC	0.423													T|||	468	0.0934505	0.0522	0.2305	5008	,	,		20779	0.0179		0.1352	False		,,,				2504	0.0869				p.C420R		Atlas-SNP	.											.	KBTBD8	101	.	0			c.T1258C						PASS	.	T	ARG/CYS	270,4136	149.5+/-183.7	11,248,1944	193.0	180.0	184.0		1258	2.7	0.9	3	dbSNP_121	184	1167,7433	236.4+/-268.6	69,1029,3202	yes	missense	KBTBD8	NM_032505.2	180	80,1277,5146	CC,CT,TT		13.5698,6.128,11.0487	probably-damaging	420/602	67054649	1437,11569	2203	4300	6503	SO:0001583	missense	84541	exon3			GAGAATTGTTGGA	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"""BTB/POZ domain containing"""	30691	protein-coding gene	gene with protein product	"""T-cell activation kelch repeat protein"""					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.1258T>C	3.37:g.67054649T>C	ENSP00000401878:p.Cys420Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_032505	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	37	CCDS2906.2	208	0.09523809523809523	24	0.04878048780487805	68	0.1878453038674033	12	0.02097902097902098	104	0.13720316622691292	T	10.04	1.242106	0.22796	0.06128	0.135698	ENSG00000163376	ENST00000295568;ENST00000417314	T;T	0.76839	-1.05;-1.05	5.07	2.69	0.31865	Kelch-type beta propeller (1);	0.084638	0.85682	N	0.000000	T	0.00109	0.0003	N	0.05306	-0.075	0.09310	P	0.99999999876442	B	0.10296	0.003	B	0.10450	0.005	T	0.02625	-1.1132	8	.	.	.	.	9.3807	0.38311	0.0:0.145:0.0:0.855	rs13096789;rs17798278;rs52819173;rs58414813;rs13096789	420	Q8NFY9	KBTB8_HUMAN	R	394;420	ENSP00000295568:C394R;ENSP00000401878:C420R	.	C	+	1	0	KBTBD8	67137339	1.000000	0.71417	0.863000	0.33907	0.731000	0.41821	4.094000	0.57721	0.369000	0.24510	0.455000	0.32223	TGT	C|0.097;N|0.000	0.097	strong		0.423	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505	
PALD1	27143	hgsc.bcm.edu	37	10	72326400	72326400	+	Missense_Mutation	SNP	G	G	A	rs10999406	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:72326400G>A	ENST00000263563.6	+	20	2750	c.2482G>A	c.(2482-2484)Ggg>Agg	p.G828R		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	828			G -> R (in dbSNP:rs10999406).			cytosol (GO:0005829)											GCTGGAGAGCGGGGAGGACCA	0.647													G|||	378	0.0754792	0.0234	0.0764	5008	,	,		17312	0.0288		0.1491	False		,,,				2504	0.1176				p.G828R		Atlas-SNP	.											.	.	.	.	0			c.G2482A						PASS	.	G	ARG/GLY	193,4213	113.3+/-151.4	6,181,2016	30.0	28.0	29.0		2482	-7.8	0.0	10	dbSNP_120	29	1288,7310	233.2+/-266.6	100,1088,3111	yes	missense	KIAA1274	NM_014431.2	125	106,1269,5127	AA,AG,GG		14.9802,4.3804,11.3888	benign	828/857	72326400	1481,11523	2203	4299	6502	SO:0001583	missense	27143	exon20			GAGAGCGGGGAGG	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.2482G>A	10.37:g.72326400G>A	ENSP00000263563:p.Gly828Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	33	0.6875	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	172|172	0.07875457875457875|0.07875457875457875	11|11	0.022357723577235773|0.022357723577235773	32|32	0.08839779005524862|0.08839779005524862	13|13	0.022727272727272728|0.022727272727272728	116|116	0.15303430079155672|0.15303430079155672	G|G	9.319|9.319	1.057547|1.057547	0.19907|0.19907	0.043804|0.043804	0.149802|0.149802	ENSG00000107719|ENSG00000107719	ENST00000263563;ENST00000373214|ENST00000426268	T|.	0.44482|.	0.92|.	5.08|5.08	-7.82|-7.82	0.01205|0.01205	.|.	1.358810|.	0.04479|.	N|.	0.377400|.	T|T	0.00241|0.00241	0.0007|0.0007	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	P|P	0.0|0.0	P|.	0.39847|.	0.691|.	B|.	0.35550|.	0.205|.	T|T	0.15925|0.15925	-1.0420|-1.0420	9|4	0.16420|.	T|.	0.52|.	0.0|0.0	10.7075|10.7075	0.45962|0.45962	0.6714:0.2172:0.1114:0.0|0.6714:0.2172:0.1114:0.0	rs10999406|rs10999406	828|.	Q9ULE6|.	PALD_HUMAN|.	R|Q	828;804|208	ENSP00000263563:G828R|.	ENSP00000263563:G828R|.	G|R	+|+	1|2	0|0	KIAA1274|KIAA1274	71996406|71996406	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.882000|0.882000	0.50991|0.50991	-0.076000|-0.076000	0.11412|0.11412	-1.591000|-1.591000	0.01621|0.01621	-0.339000|-0.339000	0.08088|0.08088	GGG|CGG	G|0.900;A|0.100	0.100	strong		0.647	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415745	105415745	+	Missense_Mutation	SNP	C	C	G	rs117379881	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105415745C>G	ENST00000333244.5	-	7	6162	c.6043G>C	c.(6043-6045)Gca>Cca	p.A2015P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2015						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)			ACCTTGGGTGCAGGCACATCC	0.602													.|||	1388	0.277157	0.0734	0.3573	5008	,	,		16098	0.0813		0.5477	False		,,,				2504	0.4192				p.A2015P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G6043C						PASS	.	C	PRO/ALA	567,3291		79,409,1441	136.0	117.0	123.0		6043	-5.7	0.0	14	dbSNP_132	123	4464,3654		1440,1584,1035	no	missense	AHNAK2	NM_138420.2	27	1519,1993,2476	GG,GC,CC		45.0111,14.6967,42.009	possibly-damaging	2015/5796	105415745	5031,6945	1929	4059	5988	SO:0001583	missense	113146	exon7			TGGGTGCAGGCAC	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.6043G>C	14.37:g.105415745C>G	ENSP00000353114:p.Ala2015Pro	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	586	0.2683150183150183	47	0.09552845528455285	123	0.3397790055248619	30	0.05244755244755245	386	0.5092348284960422	-	9.172	1.021440	0.19433	0.146967	0.549889	ENSG00000185567	ENST00000333244	T	0.00912	5.55	3.72	-5.67	0.02444	.	.	.	.	.	T	0.00012	0.0000	M	0.66939	2.045	0.80722	P	0.0	D	0.76494	0.999	D	0.67725	0.953	T	0.16958	-1.0385	8	0.30078	T	0.28	0.0986	7.2742	0.26275	0.0:0.2807:0.4681:0.2512	.	2015	Q8IVF2	AHNK2_HUMAN	P	2015	ENSP00000353114:A2015P	ENSP00000353114:A2015P	A	-	1	0	AHNAK2	104486790	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.139000	0.01302	-1.107000	0.03004	0.485000	0.47835	GCA	C|0.667;G|0.333	0.333	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CNBD2	140894	hgsc.bcm.edu	37	20	34560609	34560609	+	Missense_Mutation	SNP	G	G	A	rs17347958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34560609G>A	ENST00000373973.3	+	2	283	c.110G>A	c.(109-111)cGc>cAc	p.R37H	CNBD2_ENST00000538900.1_Missense_Mutation_p.R37H|CNBD2_ENST00000349339.1_Missense_Mutation_p.R37H			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	37			R -> H (in dbSNP:rs17347958).														AAAATGTTCCGCCAAGGCCTC	0.463													G|||	253	0.0505192	0.0015	0.0231	5008	,	,		22174	0.002		0.0467	False		,,,				2504	0.1902				p.R37H		Atlas-SNP	.											.	.	.	.	0			c.G110A						PASS	.	G	HIS/ARG,HIS/ARG	40,4366	43.8+/-77.6	0,40,2163	170.0	156.0	161.0		110,110	5.9	1.0	20	dbSNP_123	161	420,8180	130.5+/-188.4	12,396,3892	yes	missense,missense	C20orf152	NM_001207076.1,NM_080834.2	29,29	12,436,6055	AA,AG,GG		4.8837,0.9079,3.5368	probably-damaging,probably-damaging	37/424,37/573	34560609	460,12546	2203	4300	6503	SO:0001583	missense	140894	exon2			TGTTCCGCCAAGG	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 152"", ""cyclic nucleotide (cNMP) binding domain containing 1"""	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.110G>A	20.37:g.34560609G>A	ENSP00000363084:p.Arg37His	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	142	65	0.457746	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Missense_Mutation	SNP	ENST00000373973.3	37		50	0.022893772893772892	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	39	0.051451187335092345	G	28.4	4.914985	0.92178	0.009079	0.048837	ENSG00000149646	ENST00000373973;ENST00000349339;ENST00000538900	T;T;T	0.14391	2.51;2.51;2.53	5.9	5.9	0.94986	.	0.000000	0.64402	D	0.000009	T	0.07593	0.0191	M	0.66939	2.045	0.39928	D	0.97424	D;D	0.89917	1.0;1.0	D;D	0.76071	0.971;0.987	T	0.00142	-1.1997	10	0.87932	D	0	-18.62	15.779	0.78246	0.0:0.0:1.0:0.0	rs17347958;rs52836568;rs17347958	37;37	Q96M20;Q96M20-2	CT152_HUMAN;.	H	37	ENSP00000363084:R37H;ENSP00000340954:R37H;ENSP00000442729:R37H	ENSP00000340954:R37H	R	+	2	0	C20orf152	34024023	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.788000	0.62439	2.788000	0.95919	0.650000	0.86243	CGC	G|0.966;A|0.034	0.034	strong		0.463	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834	
VPS26B	112936	hgsc.bcm.edu	37	11	134109924	134109924	+	Silent	SNP	T	T	C	rs35378544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134109924T>C	ENST00000281187.5	+	3	898	c.420T>C	c.(418-420)gaT>gaC	p.D140D	VPS26B_ENST00000525095.2_Silent_p.D140D|VPS26B_ENST00000530402.1_3'UTR	NM_052875.3	NP_443107.1	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B (S. pombe)	140					protein transport (GO:0015031)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)	14	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-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;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		GCCTCAATGATGTTGTCAAAG	0.473													T|||	144	0.028754	0.0598	0.0202	5008	,	,		21578	0.0		0.0417	False		,,,				2504	0.0092				p.D140D	Colon(171;1263 1952 15904 45703 47982)	Atlas-SNP	.											.	VPS26B	30	.	0			c.T420C						PASS	.	T		158,4244	106.5+/-144.9	3,152,2046	148.0	123.0	131.0		420	-2.8	0.8	11	dbSNP_126	131	365,8229	121.3+/-180.4	18,329,3950	no	coding-synonymous	VPS26B	NM_052875.3		21,481,5996	CC,CT,TT		4.2471,3.5893,4.0243		140/337	134109924	523,12473	2201	4297	6498	SO:0001819	synonymous_variant	112936	exon3			CAATGATGTTGTC		CCDS8495.1	11q25	2008-02-05	2007-01-12		ENSG00000151502	ENSG00000151502			28119	protein-coding gene	gene with protein product		610027	"""vacuolar protein sorting 26 homolog B (yeast)"""			16190980	Standard	NM_052875		Approved	MGC10485, Pep8b	uc001qhe.3	Q4G0F5	OTTHUMG00000167175	ENST00000281187.5:c.420T>C	11.37:g.134109924T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	138	67	0.485507	NM_052875	Q96A55	Silent	SNP	ENST00000281187.5	37	CCDS8495.1																																																																																			T|0.963;C|0.037	0.037	strong		0.473	VPS26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393591.1	NM_052875	
KRT1	3848	hgsc.bcm.edu	37	12	53070121	53070121	+	Silent	SNP	T	T	G	rs698170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53070121T>G	ENST00000252244.3	-	7	1471	c.1413A>C	c.(1411-1413)acA>acC	p.T471T		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	471	Coil 2.|Rod.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						GGGCCAGCTTTGTGTTCATCA	0.587													g|||	4012	0.801118	0.7897	0.7219	5008	,	,		19549	0.8284		0.8221	False		,,,				2504	0.8231				p.T471T		Atlas-SNP	.											.	KRT1	110	.	0			c.A1413C						PASS	.	C		3479,927		1380,719,104	97.0	75.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1413	1.9	0.1	12	dbSNP_86	82	7015,1585		2874,1267,159	no	coding-synonymous	KRT1	NM_006121.3		4254,1986,263	GG,GT,TT		18.4302,21.0395,19.3142		471/645	53070121	10494,2512	2203	4300	6503	SO:0001819	synonymous_variant	3848	exon7			CAGCTTTGTGTTC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1413A>C	12.37:g.53070121T>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	37	CCDS8836.1																																																																																			G|0.806;N|0.000	0.806	strong		0.587	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
DMRT2	10655	hgsc.bcm.edu	37	9	1056959	1056959	+	Missense_Mutation	SNP	G	G	C	rs17641078	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:1056959G>C	ENST00000358146.2	+	3	1372	c.1372G>C	c.(1372-1374)Gaa>Caa	p.E458Q	DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000302441.6_Missense_Mutation_p.E458Q|DMRT2_ENST00000382251.3_Missense_Mutation_p.E458Q			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	458			E -> Q (in dbSNP:rs17641078).		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)		GATCAGCAAAGAAAACACCAG	0.493													G|||	609	0.121605	0.0492	0.0548	5008	,	,		21108	0.1389		0.161	False		,,,				2504	0.2086				p.E458Q		Atlas-SNP	.											DMRT2_ENST00000302441,colon,carcinoma,0,2	DMRT2	70	2	0			c.G1372C						PASS	.	G	,,GLN/GLU	231,4175	135.3+/-171.4	8,215,1980	107.0	104.0	105.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,,1372	5.8	1.0	9	dbSNP_123	105	1008,7592	216.0+/-255.2	51,906,3343	yes	utr-3,utr-3,missense	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,29	59,1121,5323	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.7209,5.2429,9.5264	,,possibly-damaging	,,458/562	1056959	1239,11767	2203	4300	6503	SO:0001583	missense	10655	exon4			AGCAAAGAAAACA	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.1372G>C	9.37:g.1056959G>C	ENSP00000350865:p.Glu458Gln	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	147	64	0.435374	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	257	0.11767399267399267	22	0.044715447154471545	25	0.06906077348066299	77	0.1346153846153846	133	0.17546174142480211	G	18.21	3.572513	0.65765	0.052429	0.117209	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.27720	1.65;1.65;1.65	5.84	5.84	0.93424	.	0.168665	0.53938	D	0.000045	T	0.00109	0.0003	L	0.53249	1.67	0.22521	P	0.999021945	D;D	0.63880	0.988;0.993	P;P	0.59424	0.723;0.857	T	0.00686	-1.1610	9	0.72032	D	0.01	-22.743	14.3174	0.66460	0.0725:0.0:0.9275:0.0	rs17641078;rs52807456;rs17641078	458;302	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	Q	458	ENSP00000371686:E458Q;ENSP00000305785:E458Q;ENSP00000350865:E458Q	ENSP00000305785:E458Q	E	+	1	0	DMRT2	1046959	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.155000	0.77445	2.748000	0.94277	0.650000	0.86243	GAA	G|0.896;C|0.104	0.104	strong		0.493	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
FMO3	2328	hgsc.bcm.edu	37	1	171085413	171085413	+	Missense_Mutation	SNP	C	C	T	rs149551557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171085413C>T	ENST00000367755.4	+	8	1360	c.1249C>T	c.(1249-1251)Cgc>Tgc	p.R417C	FMO3_ENST00000392085.2_Missense_Mutation_p.R417C|FMO3_ENST00000538429.1_Missense_Mutation_p.R354C|FMO3_ENST00000542847.1_Missense_Mutation_p.R397C	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	417					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)	GGAGAAAAAGCGCAAATGGTA	0.328													C|||	3	0.000599042	0.0	0.0	5008	,	,		18812	0.0		0.0	False		,,,				2504	0.0031				p.R417C		Atlas-SNP	.											FMO3,NS,carcinoma,0,2	FMO3	73	2	0			c.C1249T						scavenged	.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	134.0	133.0	134.0		1249,1249	0.5	0.0	1	dbSNP_134	134	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	FMO3	NM_001002294.2,NM_006894.5	180,180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	417/533,417/533	171085413	2,13004	2203	4300	6503	SO:0001583	missense	2328	exon8			AAAAAGCGCAAAT	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.1249C>T	1.37:g.171085413C>T	ENSP00000356729:p.Arg417Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	120	2	0.0166667	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	C	3.924	-0.017629	0.07681	0.0	2.33E-4	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	4.71	0.484	0.16825	.	1.116300	0.06681	N	0.767918	T	0.35248	0.0925	L	0.45137	1.4	0.09310	N	1	P;P;P	0.50943	0.94;0.901;0.6	B;P;P	0.49140	0.398;0.594;0.601	T	0.18840	-1.0324	10	0.52906	T	0.07	-0.3399	3.8448	0.08930	0.3761:0.3755:0.0:0.2484	.	354;397;417	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	C	417;417;397;354	ENSP00000356729:R417C;ENSP00000375935:R417C;ENSP00000444073:R397C;ENSP00000439500:R354C	ENSP00000356729:R417C	R	+	1	0	FMO3	169352037	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.251000	0.08818	0.174000	0.19809	-0.147000	0.13772	CGC	C|1.000;T|0.000	0.000	weak		0.328	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
SYK	6850	hgsc.bcm.edu	37	9	93640009	93640009	+	Silent	SNP	G	G	A	rs2290887	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:93640009G>A	ENST00000375754.4	+	10	1486	c.1338G>A	c.(1336-1338)ctG>ctA	p.L446L	SYK_ENST00000375747.1_Silent_p.L423L|SYK_ENST00000375751.4_Silent_p.L423L|SYK_ENST00000375746.1_Silent_p.L446L	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	446	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CCTGGATGCTGGTTATGGAGA	0.502			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								G|||	982	0.196086	0.2095	0.366	5008	,	,		20829	0.2321		0.1362	False		,,,				2504	0.0818				p.L446L		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.G1338A						PASS	.	G	,,,	928,3478	355.1+/-312.9	91,746,1366	138.0	116.0	123.0		1269,1338,1269,1338	3.7	1.0	9	dbSNP_100	123	1215,7385	245.3+/-274.2	88,1039,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	179,1785,4539	AA,AG,GG		14.1279,21.0622,16.477	,,,	423/613,446/636,423/613,446/636	93640009	2143,10863	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon10			GATGCTGGTTATG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1338G>A	9.37:g.93640009G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	183	89	0.486339	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			G|0.824;A|0.176	0.176	strong		0.502	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
GTF2F2	2963	hgsc.bcm.edu	37	13	45841502	45841502	+	Silent	SNP	G	G	A	rs7331090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:45841502G>A	ENST00000340473.6	+	7	762	c.621G>A	c.(619-621)aaG>aaA	p.K207K		NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa	207					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|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)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		ACATCACAAAGCAACCTGTGG	0.368													A|||	1599	0.319289	0.7542	0.2205	5008	,	,		19072	0.0565		0.2296	False		,,,				2504	0.1646				p.K207K		Atlas-SNP	.											.	GTF2F2	13	.	0			c.G621A						PASS	.	A		2985,1421	464.0+/-353.7	1003,979,221	136.0	140.0	139.0		621	-0.3	1.0	13	dbSNP_116	139	2126,6474	715.7+/-406.1	266,1594,2440	no	coding-synonymous	GTF2F2	NM_004128.2		1269,2573,2661	AA,AG,GG		24.7209,32.2515,39.2972		207/250	45841502	5111,7895	2203	4300	6503	SO:0001819	synonymous_variant	2963	exon7			CACAAAGCAACCT	X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342		"""General transcription factors"""	4653	protein-coding gene	gene with protein product		189969	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			8162052	Standard	NM_004128		Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.621G>A	13.37:g.45841502G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_004128	A6NNS5|Q5W0H3	Silent	SNP	ENST00000340473.6	37	CCDS9395.1																																																																																			G|0.639;A|0.361	0.361	strong		0.368	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044767.2	NM_004128	
IRG1	730249	hgsc.bcm.edu	37	13	77531361	77531361	+	Silent	SNP	C	C	T	rs41287034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:77531361C>T	ENST00000377462.1	+	5	749	c.687C>T	c.(685-687)ctC>ctT	p.L229L	IRG1_ENST00000449753.1_Silent_p.L229L	NM_001258406.1	NP_001245335.1	A6NK06	IRG1_HUMAN	immunoresponsive 1 homolog (mouse)	229					cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to progesterone stimulus (GO:0071393)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of type I interferon production (GO:0032480)|positive regulation of antimicrobial humoral response (GO:0002760)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|propionate catabolic process (GO:0019543)|tolerance induction to lipopolysaccharide (GO:0072573)	mitochondrion (GO:0005739)	2-methylcitrate dehydratase activity (GO:0047547)|aconitate decarboxylase activity (GO:0047613)										TGTTGGGTCTCCAAGGAAACA	0.527													C|||	112	0.0223642	0.0015	0.0605	5008	,	,		22273	0.0		0.0557	False		,,,				2504	0.0123				p.L225L		Atlas-SNP	.											.	IRG1	1	.	0			c.C675T						PASS	.																																			SO:0001819	synonymous_variant	730249	exon4			GGGTCTCCAAGGA		CCDS58299.1	13q22.3	2013-04-29			ENSG00000102794	ENSG00000102794			33904	protein-coding gene	gene with protein product		615275				23610393	Standard	NM_001258406		Approved		uc031qmi.1	A6NK06	OTTHUMG00000017098	ENST00000377462.1:c.687C>T	13.37:g.77531361C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_001258406		Silent	SNP	ENST00000377462.1	37	CCDS58299.1																																																																																			C|0.960;T|0.040	0.040	strong		0.527	IRG1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045311.1	XM_001133269	
ODF4	146852	hgsc.bcm.edu	37	17	8243469	8243469	+	Missense_Mutation	SNP	T	T	C	rs12943505	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:8243469T>C	ENST00000328248.2	+	1	288	c.100T>C	c.(100-102)Tgg>Cgg	p.W34R	RP11-849F2.4_ENST00000585275.1_lincRNA|ODF4_ENST00000584943.1_Missense_Mutation_p.W34R	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	34			W -> R (in dbSNP:rs12943505). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						GGAGGCAGGATGGGGCACAGG	0.572													T|||	897	0.179113	0.0151	0.3963	5008	,	,		18988	0.0675		0.3469	False		,,,				2504	0.1892				p.W34R		Atlas-SNP	.											.	ODF4	23	.	0			c.T100C						PASS	.	T	ARG/TRP	261,4145	148.4+/-182.8	6,249,1948	85.0	80.0	82.0		100	-2.7	0.0	17	dbSNP_121	82	2589,6011	418.0+/-352.6	410,1769,2121	yes	missense	ODF4	NM_153007.4	101	416,2018,4069	CC,CT,TT		30.1047,5.9237,21.913	benign	34/258	8243469	2850,10156	2203	4300	6503	SO:0001583	missense	146852	exon1			GCAGGATGGGGCA	AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"""cancer/testis antigen 136"""	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.100T>C	17.37:g.8243469T>C	ENSP00000331086:p.Trp34Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_153007	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	455	0.20833333333333334	10	0.02032520325203252	136	0.3756906077348066	46	0.08041958041958042	263	0.3469656992084433	T	4.163	0.028769	0.08054	0.059237	0.301047	ENSG00000184650	ENST00000328248	T	0.27557	1.66	3.68	-2.74	0.05932	.	2.012190	0.02669	N	0.108369	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.14438	0.01	B	0.17098	0.017	T	0.36187	-0.9758	9	0.07175	T	0.84	3.2504	5.4871	0.16755	0.0:0.4853:0.1835:0.3312	rs12943505;rs12943505	34	Q2M2E3	ODFP4_HUMAN	R	34	ENSP00000331086:W34R	ENSP00000331086:W34R	W	+	1	0	ODF4	8184194	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.952000	0.01528	-0.593000	0.05844	0.533000	0.62120	TGG	T|0.790;C|0.210	0.210	strong		0.572	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1		
GRIN3B	116444	hgsc.bcm.edu	37	19	1005531	1005531	+	Silent	SNP	G	G	C	rs12973948	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1005531G>C	ENST00000234389.3	+	3	2050	c.2031G>C	c.(2029-2031)ctG>ctC	p.L677L	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	677					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)	TCGAGGAGCTGTCGGGGATCC	0.697													g|||	1175	0.234625	0.1293	0.2291	5008	,	,		11122	0.1706		0.3738	False		,,,				2504	0.3037				p.L677L		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G2031C						PASS	.	G		733,3665		74,585,1540	22.0	22.0	22.0		2031	3.3	1.0	19	dbSNP_121	22	3190,5408		595,2000,1704	no	coding-synonymous	GRIN3B	NM_138690.1		669,2585,3244	CC,CG,GG		37.1017,16.6667,30.1862		677/1044	1005531	3923,9073	2199	4299	6498	SO:0001819	synonymous_variant	116444	exon3			GGAGCTGTCGGGG		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.2031G>C	19.37:g.1005531G>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			C|0.264;G|0.736;T|0.000	0.264	strong		0.697	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
IGDCC4	57722	hgsc.bcm.edu	37	15	65676617	65676617	+	Silent	SNP	T	T	C	rs2292933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	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	
CLIP1	6249	hgsc.bcm.edu	37	12	122817580	122817580	+	Missense_Mutation	SNP	A	A	G	rs17883517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:122817580A>G	ENST00000540338.1	-	14	2862	c.2821T>C	c.(2821-2823)Tct>Cct	p.S941P	CLIP1_ENST00000361654.4_Missense_Mutation_p.S819P|CLIP1_ENST00000545889.1_Missense_Mutation_p.S516P|CLIP1_ENST00000537178.1_Missense_Mutation_p.S895P|CLIP1_ENST00000302528.7_Missense_Mutation_p.S930P|CLIP1_ENST00000358808.2_Missense_Mutation_p.S930P			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	941			S -> P (in dbSNP:rs17883517). {ECO:0000269|PubMed:15489334}.		microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		AGCTGAGAAGAGTTATCTCCT	0.388													A|||	157	0.0313498	0.003	0.0591	5008	,	,		18646	0.001		0.1034	False		,,,				2504	0.0072				p.S941P		Atlas-SNP	.											.	CLIP1	126	.	0			c.T2821C						PASS	.	A	PRO/SER,PRO/SER	75,4331	67.0+/-104.6	1,73,2129	191.0	164.0	173.0		2788,2683	5.6	1.0	12	dbSNP_124	173	848,7748	193.0+/-238.8	37,774,3487	yes	missense,missense	CLIP1	NM_002956.2,NM_198240.1	74,74	38,847,5616	GG,GA,AA		9.8651,1.7022,7.0989	probably-damaging,probably-damaging	930/1428,895/1393	122817580	923,12079	2203	4298	6501	SO:0001583	missense	6249	exon15			GAGAAGAGTTATC		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.2821T>C	12.37:g.122817580A>G	ENSP00000439093:p.Ser941Pro	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	256	101	0.394531	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	90	0.04120879120879121	1	0.0020325203252032522	20	0.055248618784530384	1	0.0017482517482517483	68	0.08970976253298153	A	27.9	4.876504	0.91664	0.017022	0.098651	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304	T;T;T;T;T;T	0.78126	2.31;-1.15;-1.15;0.29;0.29;-1.0	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	M	0.72894	2.215	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.74348	0.983;0.97;0.961	T	0.63269	-0.6675	10	0.56958	D	0.05	-9.4204	15.837	0.78805	1.0:0.0:0.0:0.0	rs17883517;rs17883517	895;930;941	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	P	516;930;930;660;895;941;788	ENSP00000438743:S516P;ENSP00000303585:S930P;ENSP00000351665:S930P;ENSP00000445531:S895P;ENSP00000439093:S941P;ENSP00000437786:S788P	ENSP00000303585:S930P	S	-	1	0	CLIP1	121383533	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.663000	0.91134	2.140000	0.66376	0.460000	0.39030	TCT	A|0.939;G|0.061	0.061	strong		0.388	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
BDP1	55814	hgsc.bcm.edu	37	5	70800475	70800475	+	Missense_Mutation	SNP	C	C	T	rs3761966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	282	279	0.989362	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	
WDR35	57539	hgsc.bcm.edu	37	2	20175312	20175312	+	Silent	SNP	G	G	A	rs34169020	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:20175312G>A	ENST00000345530.3	-	6	664	c.549C>T	c.(547-549)taC>taT	p.Y183Y	WDR35_ENST00000281405.4_Silent_p.Y183Y|WDR35_ENST00000416055.2_De_novo_Start_OutOfFrame	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	183					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)					CTTGATTATCGTAAATGTGTA	0.338													A|||	319	0.0636981	0.0514	0.0231	5008	,	,		18428	0.1915		0.0278	False		,,,				2504	0.0143				p.Y183Y		Atlas-SNP	.											.	WDR35	92	.	0			c.C549T						PASS	.	A	,	152,4254	810.0+/-416.0	2,148,2053	95.0	84.0	88.0		549,549	5.2	1.0	2	dbSNP_126	88	270,8330	805.4+/-407.3	5,260,4035	no	coding-synonymous,coding-synonymous	WDR35	NM_001006657.1,NM_020779.3	,	7,408,6088	AA,AG,GG		3.1395,3.4498,3.2447	,	183/1182,183/1171	20175312	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	57539	exon6			ATTATCGTAAATG	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.549C>T	2.37:g.20175312G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_020779	B3KVI5|Q4ZG01|Q8NE11	Silent	SNP	ENST00000345530.3	37	CCDS33152.1																																																																																			G|0.952;A|0.048	0.048	strong		0.338	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
PLEKHG3	26030	hgsc.bcm.edu	37	14	65209867	65209867	+	Missense_Mutation	SNP	C	C	T	rs229649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:65209867C>T	ENST00000394691.1	+	17	3253	c.3106C>T	c.(3106-3108)Cgg>Tgg	p.R1036W	PLEKHG3_ENST00000471182.2_Missense_Mutation_p.R569W|PLEKHG3_ENST00000484731.2_Missense_Mutation_p.R541W|PLEKHG3_ENST00000492928.1_Intron|PLEKHG3_ENST00000247226.7_Missense_Mutation_p.R980W			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	1036			R -> W (in dbSNP:rs229649). {ECO:0000269|PubMed:15489334}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		GCCCTCCGCCCGGAGCCCCCT	0.687													C|||	416	0.0830671	0.1596	0.0634	5008	,	,		14831	0.002		0.0805	False		,,,				2504	0.0798				p.R980W		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.C2938T						PASS	.	C	TRP/ARG	618,3788	250.9+/-257.8	42,534,1627	54.0	64.0	61.0		2938	3.8	0.0	14	dbSNP_79	61	777,7819	176.2+/-226.1	41,695,3562	yes	missense	PLEKHG3	NM_015549.1	101	83,1229,5189	TT,TC,CC		9.0391,14.0263,10.7291	probably-damaging	980/1164	65209867	1395,11607	2203	4298	6501	SO:0001583	missense	26030	exon15			TCCGCCCGGAGCC	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20364	protein-coding gene	gene with protein product			"""KIAA0599"""	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.3106C>T	14.37:g.65209867C>T	ENSP00000378183:p.Arg1036Trp	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Missense_Mutation	SNP	ENST00000394691.1	37		159	0.07280219780219781	72	0.14634146341463414	28	0.07734806629834254	1	0.0017482517482517483	58	0.07651715039577836	C	13.90	2.373988	0.42105	0.140263	0.090391	ENSG00000126822	ENST00000247226;ENST00000394691;ENST00000471182;ENST00000484731	T;T;T;T	0.65178	0.31;-0.14;1.19;1.2	5.66	3.81	0.43845	.	0.314051	0.25055	N	0.033482	T	0.01156	0.0038	M	0.69823	2.125	0.80722	P	0.0	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.73380	0.95;0.971;0.956;0.98	T	0.41574	-0.9501	9	0.62326	D	0.03	.	12.9469	0.58376	0.4224:0.5776:0.0:0.0	rs229649;rs1695766;rs17846643;rs17859738	569;541;1036;980	A1L390-2;G3V311;A1L390;A1L390-3	.;.;PKHG3_HUMAN;.	W	980;1036;569;541	ENSP00000247226:R980W;ENSP00000378183:R1036W;ENSP00000450945:R569W;ENSP00000450973:R541W	ENSP00000247226:R980W	R	+	1	2	PLEKHG3	64279620	0.001000	0.12720	0.034000	0.17996	0.043000	0.13939	0.092000	0.15066	0.711000	0.32018	0.655000	0.94253	CGG	C|0.906;T|0.094	0.094	strong		0.687	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549	
AKAP13	11214	hgsc.bcm.edu	37	15	86125304	86125304	+	Silent	SNP	C	C	T	rs7179919	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:86125304C>T	ENST00000394518.2	+	7	4100	c.4005C>T	c.(4003-4005)atC>atT	p.I1335I	AKAP13_ENST00000361243.2_Silent_p.I1335I|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1335					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						CAGAGAAGATCATTTTACCTG	0.512													T|||	963	0.192292	0.0613	0.2075	5008	,	,		20438	0.2966		0.166	False		,,,				2504	0.2781				p.I1335I	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C4005T						PASS	.	T	,	370,4032		18,334,1849	46.0	42.0	43.0		4005,4005	-1.1	0.0	15	dbSNP_116	43	1269,7327		94,1081,3123	no	coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3	,	112,1415,4972	TT,TC,CC		14.7627,8.4053,12.6096	,	1335/2818,1335/2814	86125304	1639,11359	2201	4298	6499	SO:0001819	synonymous_variant	11214	exon7			GAAGATCATTTTA	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.4005C>T	15.37:g.86125304C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																			C|0.849;T|0.151	0.151	strong		0.512	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
NPAS2	4862	hgsc.bcm.edu	37	2	101554236	101554236	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:101554236G>T	ENST00000335681.5	+	5	580	c.295G>T	c.(295-297)Gca>Tca	p.A99S	NPAS2_ENST00000542504.1_Missense_Mutation_p.A164S|NPAS2_ENST00000486017.1_3'UTR	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	99	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTTCATTATCGCAGTGACAAC	0.468																																					p.A99S		Atlas-SNP	.											NPAS2,colon,carcinoma,0,1	NPAS2	88	1	0			c.G295T						scavenged	.						259.0	223.0	235.0					2																	101554236		2203	4300	6503	SO:0001583	missense	4862	exon5			ATTATCGCAGTGA	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.295G>T	2.37:g.101554236G>T	ENSP00000338283:p.Ala99Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.0|24.0	4.485775|4.485775	0.84854|0.84854	.|.	.|.	ENSG00000170485|ENSG00000170485	ENST00000335681;ENST00000542504;ENST00000451740|ENST00000448812	T;T;T|.	0.17691|.	2.26;2.26;2.26|.	5.93|5.93	5.93|5.93	0.95920|0.95920	PAS (3);PAS fold (1);|.	0.053408|.	0.85682|.	D|.	0.000000|.	T|T	0.82153|0.82153	0.4975|0.4975	M|M	0.81497|0.81497	2.545|2.545	0.54753|0.54753	D|D	0.999983|0.999983	D;D|.	0.67145|.	0.996;0.981|.	D;D|.	0.68353|.	0.928;0.957|.	T|T	0.81512|0.81512	-0.0899|-0.0899	10|5	0.72032|.	D|.	0.01|.	.|.	19.9457|19.9457	0.97181|0.97181	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	164;99|.	F5H027;Q99743|.	.;NPAS2_HUMAN|.	S|L	99;164;85|88	ENSP00000338283:A99S;ENSP00000438428:A164S;ENSP00000395265:A85S|.	ENSP00000338283:A99S|.	A|R	+|+	1|2	0|0	NPAS2|NPAS2	100920668|100920668	1.000000|1.000000	0.71417|0.71417	0.940000|0.940000	0.37924|0.37924	0.984000|0.984000	0.73092|0.73092	8.902000|8.902000	0.92568|0.92568	2.808000|2.808000	0.96608|0.96608	0.655000|0.655000	0.94253|0.94253	GCA|CGC	.	.	none		0.468	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387503	46387503	+	Silent	SNP	T	T	C	rs3745926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	34	16	0.470588	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	
DAPP1	27071	hgsc.bcm.edu	37	4	100787233	100787233	+	Silent	SNP	C	C	A	rs77036069	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100787233C>A	ENST00000512369.1	+	8	797	c.729C>A	c.(727-729)acC>acA	p.T243T	DAPP1_ENST00000296414.7_Silent_p.T243T	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	243	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		GTGCAAAGACCGGAGTAGAAG	0.333													C|||	77	0.0153754	0.0023	0.0216	5008	,	,		10762	0.0		0.0567	False		,,,				2504	0.002				p.T243T		Atlas-SNP	.											.	DAPP1	47	.	0			c.C729A						PASS	.	C		39,3665		0,39,1813	90.0	82.0	84.0		729	-6.3	0.9	4	dbSNP_132	84	545,7645		18,509,3568	no	coding-synonymous	DAPP1	NM_014395.2		18,548,5381	AA,AC,CC		6.6545,1.0529,4.91		243/281	100787233	584,11310	1852	4095	5947	SO:0001819	synonymous_variant	27071	exon8			AAAGACCGGAGTA	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.729C>A	4.37:g.100787233C>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_014395	Q8TCK5|Q9UHF2	Silent	SNP	ENST00000512369.1	37	CCDS47112.1																																																																																			C|0.971;A|0.029	0.029	strong		0.333	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1		
SEPT1	1731	hgsc.bcm.edu	37	16	30387148	30387148	+	IGR	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:30387148A>G	ENST00000571393.1	-	0	1589				MYLPF_ENST00000322861.7_Missense_Mutation_p.K4R			Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			CAGGCACCCAAGAGGGCCAAG	0.572																																					p.K4R		Atlas-SNP	.											.	MYLPF	12	.	0			c.A11G						PASS	.						46.0	50.0	48.0					16																	30387148		2197	4300	6497	SO:0001628	intergenic_variant	29895	exon2			CACCCAAGAGGGC	AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984		16.37:g.30387148A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_013292	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Missense_Mutation	SNP	ENST00000571393.1	37		.	.	.	.	.	.	.	.	.	.	A	11.07	1.529847	0.27387	.	.	ENSG00000180209	ENST00000322861	T	0.75154	-0.91	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.71324	0.3326	N	0.10809	0.05	0.58432	D	0.999999	D	0.58268	0.982	D	0.67548	0.952	T	0.68914	-0.5283	10	0.15499	T	0.54	.	14.7308	0.69379	1.0:0.0:0.0:0.0	.	4	Q96A32	MLRS_HUMAN	R	4	ENSP00000325239:K4R	ENSP00000325239:K4R	K	+	2	0	MYLPF	30294649	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	8.674000	0.91191	2.120000	0.65058	0.372000	0.22366	AAG	.	.	none		0.572	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	
MED11	400569	hgsc.bcm.edu	37	17	4636385	4636385	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4636385C>T	ENST00000293777.5	+	3	313	c.257C>T	c.(256-258)tCg>tTg	p.S86L	RP11-314A20.5_ENST00000570493.2_RNA|CXCL16_ENST00000576153.1_5'Flank|MED11_ENST00000575284.1_3'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11	86						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						AGCTACTCTTCGAGGAAGGAC	0.557																																					p.S86L		Atlas-SNP	.											.	MED11	5	.	0			c.C257T						PASS	.						94.0	80.0	85.0					17																	4636385		2203	4300	6503	SO:0001583	missense	400569	exon3			ACTCTTCGAGGAA	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086		ENST00000293777.5:c.257C>T	17.37:g.4636385C>T	ENSP00000293777:p.Ser86Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	154	64	0.415584	NM_001001683	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	CCDS32533.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816690	0.70912	.	.	ENSG00000161920	ENST00000293777	.	.	.	5.74	4.74	0.60224	.	0.163543	0.37669	N	0.001992	T	0.47040	0.1424	L	0.38175	1.15	0.41743	D	0.989629	B	0.34313	0.448	B	0.29440	0.102	T	0.51631	-0.8681	9	0.66056	D	0.02	-22.7906	14.2205	0.65823	0.0:0.8492:0.1508:0.0	.	86	Q9P086	MED11_HUMAN	L	86	.	ENSP00000293777:S86L	S	+	2	0	MED11	4583134	0.999000	0.42202	0.893000	0.35052	0.967000	0.64934	4.595000	0.61048	1.365000	0.46057	0.655000	0.94253	TCG	.	.	none		0.557	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
MUC2	4583	hgsc.bcm.edu	37	11	1075920	1075920	+	Splice_Site	SNP	G	G	A	rs11825977	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	68	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	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
AHNAK2	113146	hgsc.bcm.edu	37	14	105412009	105412009	+	Missense_Mutation	SNP	A	A	G	rs28714612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	171	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	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	
COBLL1	22837	hgsc.bcm.edu	37	2	165551201	165551201	+	Missense_Mutation	SNP	T	T	C	rs7607980	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:165551201T>C	ENST00000392717.2	-	13	2933	c.2929A>G	c.(2929-2931)Aat>Gat	p.N977D	COBLL1_ENST00000194871.6_Missense_Mutation_p.N1006D|COBLL1_ENST00000409184.3_Missense_Mutation_p.N939D|COBLL1_ENST00000342193.4_Missense_Mutation_p.N939D|COBLL1_ENST00000375458.2_Missense_Mutation_p.N901D			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	977						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						GCCTCTTTATTTGTCAGTTCT	0.463													T|||	538	0.107428	0.1861	0.0821	5008	,	,		17891	0.001		0.1541	False		,,,				2504	0.0808				p.N939D		Atlas-SNP	.											.	COBLL1	122	.	0			c.A2815G						PASS	.	T	ASP/ASN	687,3719	285.5+/-278.2	58,571,1574	51.0	52.0	52.0		2815	-2.7	0.0	2	dbSNP_116	52	1074,7526	222.6+/-259.6	72,930,3298	yes	missense	COBLL1	NM_014900.3	23	130,1501,4872	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	12.4884,15.5924,13.5399	benign	939/1167	165551201	1761,11245	2203	4300	6503	SO:0001583	missense	22837	exon12			CTTTATTTGTCAG	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.2929A>G	2.37:g.165551201T>C	ENSP00000376478:p.Asn977Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		249	0.11401098901098901	102	0.2073170731707317	34	0.09392265193370165	0	0.0	113	0.14907651715039577	T	5.776	0.327468	0.10956	0.155924	0.124884	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	5.49	-2.65	0.06095	.	0.747690	0.12754	N	0.441935	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P;P	0.43352	0.704;0.804	B;B	0.39840	0.165;0.311	T	0.26018	-1.0115	8	0.12766	T	0.61	0.0091	6.0314	0.19683	0.097:0.0642:0.4336:0.4052	rs7607980;rs52821863;rs59793124;rs7607980	977;939	Q53SF7;Q53SF7-2	COBL1_HUMAN;.	D	901;939;939;977;1006	.	ENSP00000194871:N1006D	N	-	1	0	COBLL1	165259447	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.534000	0.23098	-0.224000	0.09928	0.533000	0.62120	AAT	T|0.872;C|0.128	0.128	strong		0.463	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
SLC25A48	153328	hgsc.bcm.edu	37	5	135178142	135178142	+	Silent	SNP	A	A	G	rs6596270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:135178142A>G	ENST00000420621.1	+	2	256	c.84A>G	c.(82-84)acA>acG	p.T28T	SLC25A48_ENST00000433282.2_5'UTR|SLC25A48_ENST00000425402.1_Silent_p.T28T|SLC25A48_ENST00000274513.5_Silent_p.T28T|SLC25A48_ENST00000412661.2_Silent_p.T28T			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	28					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						CTCTGGACACAGTCAAGGTAC	0.507													G|||	691	0.137979	0.208	0.1225	5008	,	,		17766	0.0099		0.2117	False		,,,				2504	0.1104				p.T28T		Atlas-SNP	.											.	SLC25A48	37	.	0			c.A84G						PASS	.	G		740,3508		73,594,1457	132.0	143.0	140.0		84	-1.4	1.0	5	dbSNP_116	140	1786,6722		184,1418,2652	no	coding-synonymous	SLC25A48	NM_145282.4		257,2012,4109	GG,GA,AA		20.992,17.42,19.8024		28/158	135178142	2526,10230	2124	4254	6378	SO:0001819	synonymous_variant	153328	exon2			GGACACAGTCAAG		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"""Solute carriers"""	30451	protein-coding gene	gene with protein product	"""HCC-down-regulated mitochondrial carrier protein"""					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.84A>G	5.37:g.135178142A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_145282	Q8TAV9	Silent	SNP	ENST00000420621.1	37																																																																																				A|0.820;G|0.180	0.180	strong		0.507	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282	
SPATA22	84690	hgsc.bcm.edu	37	17	3352294	3352294	+	Missense_Mutation	SNP	A	A	G	rs1488689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3352294A>G	ENST00000573128.1	-	6	962	c.479T>C	c.(478-480)aTa>aCa	p.I160T	SPATA22_ENST00000541913.1_Missense_Mutation_p.I144T|SPATA22_ENST00000397168.3_Missense_Mutation_p.I160T|SPATA22_ENST00000572969.1_Missense_Mutation_p.I160T|SPATA22_ENST00000575375.1_Missense_Mutation_p.I160T|SPATA22_ENST00000355380.4_Missense_Mutation_p.I117T|SPATA22_ENST00000268981.5_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	265	0	0		WXS	Illumina HiSeq	Phase_I	246	136	0.552846	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	
CCDC57	284001	hgsc.bcm.edu	37	17	80136418	80136418	+	Missense_Mutation	SNP	C	C	T	rs7209474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80136418C>T	ENST00000389641.4	-	10	1474	c.1438G>A	c.(1438-1440)Gtg>Atg	p.V480M	CCDC57_ENST00000392347.1_Missense_Mutation_p.V480M|CCDC57_ENST00000392343.3_Missense_Mutation_p.V480M|CCDC57_ENST00000327026.3_5'UTR			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	480			V -> M (in dbSNP:rs7209474). {ECO:0000269|PubMed:15489334}.							endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TCCAGGGTCACGGCCTTCAGC	0.612													C|||	2868	0.572684	0.4145	0.6239	5008	,	,		18881	0.8631		0.4841	False		,,,				2504	0.5419				p.V480M		Atlas-SNP	.											.	CCDC57	102	.	0			c.G1438A						PASS	.	C	MET/VAL	1658,2652		328,1002,825	50.0	58.0	55.0		1438	-4.4	0.0	17	dbSNP_116	55	3644,4838		814,2016,1411	yes	missense	CCDC57	NM_198082.2	21	1142,3018,2236	TT,TC,CC		42.9616,38.4687,41.4478	probably-damaging	480/916	80136418	5302,7490	2155	4241	6396	SO:0001583	missense	284001	exon10			GGGTCACGGCCTT	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.1438G>A	17.37:g.80136418C>T	ENSP00000374292:p.Val480Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Missense_Mutation	SNP	ENST00000389641.4	37		1299	0.5947802197802198	232	0.4715447154471545	215	0.5939226519337016	494	0.8636363636363636	358	0.47229551451187335	C	10.89	1.477704	0.26511	0.384687	0.429616	ENSG00000176155	ENST00000389641;ENST00000392347;ENST00000392343	T;T;T	0.27890	2.82;2.82;1.64	4.71	-4.43	0.03568	.	0.901682	0.09424	N	0.804002	T	0.00012	0.0000	L	0.47716	1.5	0.52501	P	4.199999999998649E-5	P;P	0.41624	0.757;0.757	B;B	0.33960	0.173;0.173	T	0.32903	-0.9889	9	0.45353	T	0.12	-13.8907	1.2328	0.01946	0.4183:0.1894:0.2337:0.1586	rs7209474;rs52834366;rs60192273;rs7209474	480;480	Q2TAC2-2;Q2TAC2	.;CCD57_HUMAN	M	480	ENSP00000374292:V480M;ENSP00000376158:V480M;ENSP00000376154:V480M	ENSP00000374292:V480M	V	-	1	0	CCDC57	77729707	0.001000	0.12720	0.031000	0.17742	0.015000	0.08874	-1.103000	0.03329	-0.582000	0.05929	-0.181000	0.13052	GTG	C|0.422;N|0.002	.	strong		0.612	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
OPA3	80207	hgsc.bcm.edu	37	19	46057081	46057081	+	Silent	SNP	A	A	G	rs3826860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46057081A>G	ENST00000263275.4	-	2	285	c.231T>C	c.(229-231)gcT>gcC	p.A77A	OPA3_ENST00000544371.1_Silent_p.A24A|OPA3_ENST00000323060.3_Intron	NM_025136.3	NP_079412.1	Q9H6K4	OPA3_HUMAN	optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)	77					growth (GO:0040007)|mitochondrion morphogenesis (GO:0070584)|neuromuscular process (GO:0050905)|regulation of lipid metabolic process (GO:0019216)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	mitochondrion (GO:0005739)				cervix(1)|large_intestine(1)|lung(2)	4		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00778)|GBM - Glioblastoma multiforme(486;0.0976)|Epithelial(262;0.242)		CGCCCAGCTCAGCTGCCGCCT	0.662													G|||	3841	0.766973	0.7806	0.8055	5008	,	,		16229	0.8869		0.664	False		,,,				2504	0.7035				p.A77A		Atlas-SNP	.											OPA3_ENST00000263275,NS,carcinoma,0,1	OPA3	19	1	0			c.T231C						PASS	.		,	3339,1053		1291,757,148	17.0	20.0	19.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,231	-5.2	0.8	19	dbSNP_107	19	5522,3068		1813,1896,586	no	intron,coding-synonymous	OPA3	NM_001017989.2,NM_025136.3	,	3104,2653,734	GG,GA,AA		35.7159,23.9754,31.744	,	,77/180	46057081	8861,4121	2196	4295	6491	SO:0001819	synonymous_variant	80207	exon2			CAGCTCAGCTGCC	AK025840	CCDS12668.1, CCDS33052.1	19q13.2-q13.3	2014-01-28				ENSG00000125741			8142	protein-coding gene	gene with protein product		606580				9097959, 11668429	Standard	NM_001017989		Approved	FLJ22187, MGA3	uc002pcj.4	Q9H6K4		ENST00000263275.4:c.231T>C	19.37:g.46057081A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	61	38	0.622951	NM_025136	Q6P384|Q8N784	Silent	SNP	ENST00000263275.4	37	CCDS12668.1																																																																																			A|0.295;G|0.705	0.705	strong		0.662	OPA3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459601.1		
HS3ST3A1	9955	hgsc.bcm.edu	37	17	13399616	13399616	+	Silent	SNP	A	A	T	rs62057033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:13399616A>T	ENST00000284110.1	-	2	1916	c.1119T>A	c.(1117-1119)ccT>ccA	p.P373P	HS3ST3A1_ENST00000578576.1_Silent_p.P171P	NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	373					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 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGTCGATCTCAGGATGGGTCC	0.607													A|||	2091	0.417532	0.1823	0.5144	5008	,	,		13730	0.5585		0.3459	False		,,,				2504	0.5951				p.P373P		Atlas-SNP	.											.	HS3ST3A1	39	.	0			c.T1119A						PASS	.						20.0	21.0	20.0					17																	13399616		2194	4261	6455	SO:0001819	synonymous_variant	9955	exon2			GATCTCAGGATGG	AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.1119T>A	17.37:g.13399616A>T		Somatic	406	0	0		WXS	Illumina HiSeq	Phase_I	383	245	0.639687	NM_006042	A8K7N2	Silent	SNP	ENST00000284110.1	37	CCDS11165.1																																																																																			A|0.615;T|0.385	0.385	strong		0.607	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042	
FANCA	2175	hgsc.bcm.edu	37	16	89807233	89807233	+	Silent	SNP	C	C	G	rs11649210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	174	0	0		WXS	Illumina HiSeq	Phase_I	179	92	0.513967	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		
PSAPL1	768239	hgsc.bcm.edu	37	4	7435721	7435721	+	Missense_Mutation	SNP	C	C	T	rs6850206	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:7435721C>T	ENST00000319098.4	-	1	979	c.886G>A	c.(886-888)Gtg>Atg	p.V296M	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)	296	Saposin B-type 3. {ECO:0000255|PROSITE- ProRule:PRU00415}.		V -> M (in dbSNP:rs6850206).		sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						TTCATGCACACCTCACAGGTC	0.587													C|||	647	0.129193	0.1044	0.1383	5008	,	,		20561	0.0764		0.1948	False		,,,				2504	0.1431				p.V296M		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G886A						PASS	.	C	MET/VAL,	547,3769		33,481,1644	55.0	60.0	58.0		886,	0.7	0.5	4	dbSNP_116	58	1659,6879		161,1337,2771	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	21,	194,1818,4415	TT,TC,CC		19.4308,12.6738,17.162	possibly-damaging,	296/522,	7435721	2206,10648	2158	4269	6427	SO:0001583	missense	768239	exon1			TGCACACCTCACA	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.886G>A	4.37:g.7435721C>T	ENSP00000317445:p.Val296Met	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	285	0.1304945054945055	53	0.10772357723577236	53	0.1464088397790055	33	0.057692307692307696	146	0.19261213720316622	C	10.15	1.271609	0.23221	0.126738	0.194308	ENSG00000178597	ENST00000319098	D	0.85411	-1.98	3.8	0.671	0.17929	Saposin-like (2);Saposin-like type B, 1 (1);Saposin B (2);	0.339732	0.29924	N	0.010851	T	0.00784	0.0026	L	0.56340	1.77	0.35994	P	0.16310100000000005	D	0.76494	0.999	D	0.72338	0.977	T	0.44205	-0.9343	9	0.48119	T	0.1	-1.1881	11.0437	0.47846	0.0:0.4309:0.5691:0.0	rs6850206;rs60725764;rs6850206	296	Q6NUJ1	SAPL1_HUMAN	M	296	ENSP00000317445:V296M	ENSP00000317445:V296M	V	-	1	0	PSAPL1	7486622	0.031000	0.19500	0.520000	0.27837	0.033000	0.12548	0.050000	0.14120	0.356000	0.24157	-0.305000	0.09177	GTG	C|0.871;T|0.129	0.129	strong		0.587	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
MORC3	23515	hgsc.bcm.edu	37	21	37741352	37741352	+	Silent	SNP	G	G	A	rs61739936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:37741352G>A	ENST00000400485.1	+	15	1762	c.1686G>A	c.(1684-1686)caG>caA	p.Q562Q	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	562					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						TGAGTAGTCAGTTTGAAAATT	0.328													G|||	312	0.0623003	0.0121	0.0749	5008	,	,		19872	0.0298		0.0905	False		,,,				2504	0.1258				p.Q562Q		Atlas-SNP	.											MORC3,NS,carcinoma,+2,1	MORC3	78	1	0			c.G1686A						PASS	.	G		69,3671		1,67,1802	77.0	69.0	71.0		1686	-4.4	0.1	21	dbSNP_129	71	823,7403		46,731,3336	no	coding-synonymous	MORC3	NM_015358.2		47,798,5138	AA,AG,GG		10.0049,1.8449,7.4545		562/940	37741352	892,11074	1870	4113	5983	SO:0001819	synonymous_variant	23515	exon15			TAGTCAGTTTGAA	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.1686G>A	21.37:g.37741352G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	151	61	0.403974	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	37	CCDS42924.1																																																																																			G|0.919;A|0.081	0.081	strong		0.328	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
PRSS1	5644	hgsc.bcm.edu	37	7	142458437	142458437	+	Silent	SNP	C	C	T	rs372637371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142458437C>T	ENST00000311737.7	+	2	78	c.72C>T	c.(70-72)atC>atT	p.I24I	PRSS1_ENST00000486171.1_Silent_p.I24I	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	24	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)	ATGACAAGATCGTTGGGGGCT	0.542													C|||	2	0.000399361	0.0	0.0	5008	,	,		19985	0.002		0.0	False		,,,				2504	0.0				p.I24I		Atlas-SNP	.											PRSS1,NS,carcinoma,0,1	PRSS1	68	1	0			c.C72T						scavenged	.						158.0	156.0	157.0					7																	142458437		2203	4300	6503	SO:0001819	synonymous_variant	5644	exon2			CAAGATCGTTGGG	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.72C>T	7.37:g.142458437C>T		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	201	11	0.0547264	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Silent	SNP	ENST00000311737.7	37	CCDS5872.1																																																																																			.	.	weak		0.542	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
CLPTM1	1209	hgsc.bcm.edu	37	19	45490570	45490570	+	Silent	SNP	A	A	G	rs3786505	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	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	
SLC39A7	7922	hgsc.bcm.edu	37	6	33169895	33169895	+	Silent	SNP	C	C	G	rs1547387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33169895C>G	ENST00000374677.3	+	3	1000	c.627C>G	c.(625-627)tcC>tcG	p.S209S	RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000374680.3_5'Flank|RXRB_ENST00000544186.1_5'Flank|RXRB_ENST00000413614.2_5'Flank|RNY4P10_ENST00000365571.1_RNA|HSD17B8_ENST00000374662.3_5'Flank|SLC39A7_ENST00000374675.3_Silent_p.S209S	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	209					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						ATGGACACTCCCACAGTGGTG	0.552													C|||	428	0.0854633	0.0287	0.0533	5008	,	,		20191	0.0486		0.1044	False		,,,				2504	0.2035				p.S209S		Atlas-SNP	.											.	SLC39A7	32	.	0			c.C627G						PASS	.	C	,	100,2440		5,90,1175	69.0	71.0	70.0		627,627	-0.5	1.0	6	dbSNP_88	70	545,4569		27,491,2039	yes	coding-synonymous,coding-synonymous	SLC39A7	NM_001077516.1,NM_006979.2	,	32,581,3214	GG,GC,CC		10.657,3.937,8.427	,	209/470,209/470	33169895	645,7009	1270	2557	3827	SO:0001819	synonymous_variant	7922	exon3			ACACTCCCACAGT	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"""Solute carriers"""	4927	protein-coding gene	gene with protein product		601416	"""HLA class II region expressed gene KE4"""	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.627C>G	6.37:g.33169895C>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	213	109	0.511737	NM_006979	B0UXF6|Q5STP8|Q9UIQ0	Silent	SNP	ENST00000374677.3	37	CCDS43453.1																																																																																			C|0.881;G|0.119	0.119	strong		0.552	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979	
PHF3	23469	hgsc.bcm.edu	37	6	64394121	64394121	+	Silent	SNP	A	A	G	rs35294942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:64394121A>G	ENST00000262043.3	+	4	838	c.498A>G	c.(496-498)gtA>gtG	p.V166V	PHF3_ENST00000509330.1_Silent_p.V166V|PHF3_ENST00000393387.1_Silent_p.V166V			Q92576	PHF3_HUMAN	PHD finger protein 3	166					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GGAAGACTGTATCTACTGCTA	0.403													A|||	45	0.00898562	0.031	0.0029	5008	,	,		17216	0.0		0.002	False		,,,				2504	0.0				p.V166V	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.A498G						PASS	.	A		118,4288	87.8+/-126.4	2,114,2087	176.0	183.0	180.0		498	-4.4	0.5	6	dbSNP_126	180	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	PHF3	NM_015153.2		2,114,6387	GG,GA,AA		0.0,2.6782,0.9073		166/2040	64394121	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	23469	exon3			GACTGTATCTACT	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.498A>G	6.37:g.64394121A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Silent	SNP	ENST00000262043.3	37	CCDS4966.1																																																																																			A|0.990;G|0.010	0.010	strong		0.403	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237388	239237388	+	Missense_Mutation	SNP	G	G	A	rs61742338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:239237388G>A	ENST00000373327.4	+	4	638	c.416G>A	c.(415-417)cGg>cAg	p.R139Q	TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.R139Q|TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.R139Q	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	139	Abolishes microtubules-binding when missing.				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)		GTGAAAGGCCGGGCCTCACTG	0.478													G|||	97	0.019369	0.0023	0.0187	5008	,	,		16176	0.0		0.0517	False		,,,				2504	0.0297				p.R139Q		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.G416A						PASS	.	G	GLN/ARG,GLN/ARG	37,4369	42.3+/-75.8	0,37,2166	75.0	77.0	76.0		416,416	0.2	0.0	2	dbSNP_129	76	343,8257	117.9+/-177.5	4,335,3961	yes	missense,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	43,43	4,372,6127	AA,AG,GG		3.9884,0.8398,2.9217	benign,benign	139/626,139/692	239237388	380,12626	2203	4300	6503	SO:0001583	missense	26146	exon4			AAGGCCGGGCCTC	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.416G>A	2.37:g.239237388G>A	ENSP00000362424:p.Arg139Gln	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	51	0.023351648351648352	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	39	0.051451187335092345	G	17.19	3.325671	0.60743	0.008398	0.039884	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.14640	2.49;2.49;2.49	4.65	0.171	0.15026	.	0.145903	0.64402	N	0.000014	T	0.01661	0.0053	M	0.63843	1.955	0.09310	N	1	B;B	0.24576	0.086;0.106	B;B	0.19148	0.008;0.024	T	0.20874	-1.0262	10	0.30854	T	0.27	-21.8073	7.13	0.25496	0.6846:0.0:0.3154:0.0	rs61742338	139;139	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	Q	139	ENSP00000375851:R139Q;ENSP00000362424:R139Q;ENSP00000375852:R139Q	ENSP00000362424:R139Q	R	+	2	0	TRAF3IP1	238902127	0.009000	0.17119	0.000000	0.03702	0.035000	0.12851	1.836000	0.39191	0.169000	0.19679	-0.748000	0.03510	CGG	G|0.971;A|0.029	0.029	strong		0.478	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
INPP5E	56623	hgsc.bcm.edu	37	9	139326304	139326304	+	Silent	SNP	G	G	A	rs10870188	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139326304G>A	ENST00000371712.3	-	7	1923	c.1521C>T	c.(1519-1521)caC>caT	p.H507H		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		TGAGCTGGTCGTGCTGCAGCA	0.701													g|||	608	0.121406	0.0151	0.2435	5008	,	,		8607	0.1429		0.1213	False		,,,				2504	0.1564				p.H507H		Atlas-SNP	.											INPP5E,NS,carcinoma,0,1	INPP5E	18	1	0			c.C1521T						PASS	.	G		168,4224		2,164,2030	24.0	24.0	24.0		1521	-10.2	0.0	9	dbSNP_120	24	1145,7439		72,1001,3219	no	coding-synonymous	INPP5E	NM_019892.4		74,1165,5249	AA,AG,GG		13.3388,3.8251,10.1187		507/645	139326304	1313,11663	2196	4292	6488	SO:0001819	synonymous_variant	56623	exon7			CTGGTCGTGCTGC	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1521C>T	9.37:g.139326304G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	97	62	0.639175	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			G|0.898;A|0.102	0.102	strong		0.701	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
BOD1L1	259282	hgsc.bcm.edu	37	4	13615174	13615174	+	Missense_Mutation	SNP	G	G	A	rs2035820	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:13615174G>A	ENST00000040738.5	-	5	1421	c.1286C>T	c.(1285-1287)aCg>aTg	p.T429M		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	429	Lys-rich.		T -> M (in dbSNP:rs2035820).			nucleus (GO:0005634)	DNA binding (GO:0003677)										GCTATCAGACGTTACAACTTC	0.383													A|||	688	0.13738	0.1558	0.2147	5008	,	,		11755	0.003		0.1501	False		,,,				2504	0.183				p.T429M		Atlas-SNP	.											BOD1L,NS,carcinoma,+1,1	.	.	1	0			c.C1286T						PASS	.	A	MET/THR	691,3715	761.7+/-413.1	44,603,1556	168.0	158.0	161.0		1286	4.0	0.7	4	dbSNP_94	161	1295,7305	758.9+/-407.5	86,1123,3091	yes	missense	BOD1L	NM_148894.2	81	130,1726,4647	AA,AG,GG		15.0581,15.6832,15.2699	benign	429/3052	13615174	1986,11020	2203	4300	6503	SO:0001583	missense	259282	exon5			TCAGACGTTACAA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.1286C>T	4.37:g.13615174G>A	ENSP00000040738:p.Thr429Met	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	324	162	0.5	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	269	0.12316849816849818	85	0.17276422764227642	73	0.20165745856353592	0	0.0	111	0.14643799472295516	A	0.018	-1.474986	0.01035	0.156832	0.150581	ENSG00000038219	ENST00000040738	T	0.06371	3.31	5.18	3.99	0.46301	.	0.580206	0.15617	N	0.253098	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.27082	T	0.32	-3.2621	9.6555	0.39923	0.8567:0.0:0.1433:0.0	rs2035820;rs17807749;rs58395303;rs2035820	429	Q8NFC6	BOD1L_HUMAN	M	429	ENSP00000040738:T429M	ENSP00000040738:T429M	T	-	2	0	BOD1L	13224272	0.969000	0.33509	0.676000	0.29932	0.496000	0.33645	2.391000	0.44424	0.387000	0.25024	-1.120000	0.02017	ACG	G|0.852;A|0.148	0.148	strong		0.383	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
OR10H2	26538	hgsc.bcm.edu	37	19	15839081	15839081	+	Silent	SNP	C	C	T	rs2067083	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	390	0	0		WXS	Illumina HiSeq	Phase_I	338	141	0.41716	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		
KIRREL2	84063	hgsc.bcm.edu	37	19	36352024	36352024	+	Splice_Site	SNP	G	G	A	rs35423326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36352024G>A	ENST00000360202.5	+	9	1255	c.1057G>A	c.(1057-1059)Gtg>Atg	p.V353M	KIRREL2_ENST00000347900.6_Splice_Site_p.V303M|KIRREL2_ENST00000262625.7_Splice_Site_p.V353M|KIRREL2_ENST00000592409.1_Splice_Site_p.V353M|NPHS1_ENST00000591817.1_Intron	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	353	Ig-like C2-type 4.		V -> M (in dbSNP:rs35423326).		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)			CCTGTCGCAGGTGCTGGGCTC	0.672													G|||	118	0.0235623	0.025	0.0144	5008	,	,		15018	0.0119		0.0249	False		,,,				2504	0.0389				p.V353M		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G1057A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	123,4279		0,123,2078	14.0	17.0	16.0		1057,907,1057	3.1	1.0	19	dbSNP_126	16	259,8339		1,257,4041	yes	missense-near-splice,missense-near-splice,missense-near-splice	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	21,21,21	1,380,6119	AA,AG,GG		3.0123,2.7942,2.9385	probably-damaging,probably-damaging,probably-damaging	353/634,303/584,353/709	36352024	382,12618	2201	4299	6500	SO:0001630	splice_region_variant	84063	exon9			TCGCAGGTGCTGG	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.1057-1G>A	19.37:g.36352024G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	45	0.020604395604395604	14	0.028455284552845527	7	0.019337016574585635	4	0.006993006993006993	20	0.026385224274406333	G	17.89	3.500405	0.64298	0.027942	0.030123	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.13089	2.62;2.62;2.62	4.24	3.14	0.36123	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.184475	0.27306	N	0.019967	T	0.08223	0.0205	M	0.65498	2.005	0.41537	D	0.98849	P;P;P;D;D	0.57571	0.949;0.937;0.949;0.98;0.963	P;P;P;P;P	0.55455	0.776;0.668;0.776;0.668;0.668	T	0.00293	-1.1841	9	.	.	.	-17.2249	6.2505	0.20843	0.139:0.0:0.861:0.0	rs35423326	353;333;353;303;353	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	M	353;303;353;333	ENSP00000262625:V353M;ENSP00000345067:V303M;ENSP00000353331:V353M	.	V	+	1	0	KIRREL2	41043864	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	4.598000	0.61069	2.223000	0.72356	0.499000	0.49734	GTG	G|0.972;A|0.028	0.028	strong		0.672	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	Missense_Mutation
CDH23	64072	hgsc.bcm.edu	37	10	73550117	73550117	+	Missense_Mutation	SNP	C	C	G	rs11592462	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73550117C>G	ENST00000224721.6	+	45	6016	c.6011C>G	c.(6010-6012)aCc>aGc	p.T2004S		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1999	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GCCGTGGTGACCTACCAGCTG	0.632													c|||	1729	0.345248	0.2625	0.317	5008	,	,		17889	0.1597		0.499	False		,,,				2504	0.5102				p.T1999S		Atlas-SNP	.											.	CDH23	365	.	0			c.C5996G						PASS	.		SER/THR	1130,3052		168,794,1129	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5996	4.1	1.0	10	dbSNP_120	52	4091,4325		998,2095,1115	yes	missense	CDH23	NM_022124.5	58	1166,2889,2244	GG,GC,CC		48.6098,27.0206,41.4431	benign	1999/3355	73550117	5221,7377	2091	4208	6299	SO:0001583	missense	64072	exon44			TGGTGACCTACCA	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.6011C>G	10.37:g.73550117C>G	ENSP00000224721:p.Thr2004Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		721	0.3301282051282051	115	0.23373983739837398	133	0.3674033149171271	96	0.16783216783216784	377	0.4973614775725594	c	11.52	1.663782	0.29515	0.270206	0.486098	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.06	4.14	0.48551	Cadherin (3);Cadherin-like (1);	0.248227	0.38897	N	0.001535	T	0.00012	0.0000	N	0.05534	-0.03	0.09310	P	0.9999999999999997	B	0.02656	0.0	B	0.06405	0.002	T	0.38265	-0.9669	8	0.08837	T	0.75	.	15.6194	0.76793	0.0:0.8623:0.1377:0.0	rs11592462;rs11592462	1999	Q9H251	CAD23_HUMAN	S	2004;1999;2002	.	ENSP00000224721:T2004S	T	+	2	0	CDH23	73220123	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.661000	0.37408	1.096000	0.41439	0.556000	0.70494	ACC	C|0.672;G|0.328	0.328	strong		0.632	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
RELL2	285613	hgsc.bcm.edu	37	5	141019830	141019830	+	Missense_Mutation	SNP	C	C	G	rs11742646	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:141019830C>G	ENST00000297164.3	+	5	2047	c.847C>G	c.(847-849)Cag>Gag	p.Q283E	FCHSD1_ENST00000435817.2_3'UTR|RELL2_ENST00000444782.1_Missense_Mutation_p.Q283E|RELL2_ENST00000521367.1_Missense_Mutation_p.Q217E|RELL2_ENST00000518856.1_Missense_Mutation_p.Q217E|RELL2_ENST00000518025.1_3'UTR|FCHSD1_ENST00000523856.1_5'UTR	NM_173828.4	NP_776189.3	Q8NC24	RELL2_HUMAN	RELT-like 2	283			Q -> E (in dbSNP:rs11742646). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAAATGGGCAGCCAAGCAA	0.597																																					p.Q283E		Atlas-SNP	.											.	RELL2	24	.	0			c.C847G						PASS	.	C	GLU/GLN,,GLU/GLN	613,3793	264.7+/-266.2	44,525,1634	65.0	68.0	67.0		847,,847	4.7	1.0	5	dbSNP_120	67	1693,6907	309.3+/-309.3	173,1347,2780	yes	missense,utr-3,missense	FCHSD1,RELL2	NM_001130029.1,NM_033449.2,NM_173828.4	29,,29	217,1872,4414	GG,GC,CC		19.686,13.9128,17.7303	benign,,benign	283/304,,283/304	141019830	2306,10700	2203	4300	6503	SO:0001583	missense	285613	exon5			AATGGGCAGCCAA	AK054889	CCDS4265.1	5q31.3	2011-10-11	2007-06-15	2007-06-15	ENSG00000164620	ENSG00000164620			26902	protein-coding gene	gene with protein product		611213	"""chromosome 5 open reading frame 16"""	C5orf16		12975309, 16389068	Standard	NM_173828		Approved	FLJ90583	uc003lli.3	Q8NC24	OTTHUMG00000129612	ENST00000297164.3:c.847C>G	5.37:g.141019830C>G	ENSP00000297164:p.Gln283Glu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_173828	D3DQE2|Q6P4E7|Q6UXY2	Missense_Mutation	SNP	ENST00000297164.3	37	CCDS4265.1	353	0.16163003663003664	68	0.13821138211382114	78	0.2154696132596685	76	0.13286713286713286	131	0.17282321899736147	C	11.99	1.802654	0.31869	0.139128	0.19686	ENSG00000164620	ENST00000444782;ENST00000521367;ENST00000297164;ENST00000518856	T;T;T;T	0.16196	2.43;2.36;2.43;2.37	5.54	4.66	0.58398	.	0.148021	0.44688	D	0.000434	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	0.9999999999999987	B;B	0.22683	0.073;0.005	B;B	0.21917	0.037;0.003	T	0.40905	-0.9538	9	0.25106	T	0.35	-1.5045	12.254	0.54613	0.0:0.8288:0.1712:0.0	rs11742646;rs17855843;rs56623708;rs11742646	217;283	E5RHA7;Q8NC24	.;RELL2_HUMAN	E	283;217;283;217	ENSP00000409443:Q283E;ENSP00000430948:Q217E;ENSP00000297164:Q283E;ENSP00000427992:Q217E	ENSP00000297164:Q283E	Q	+	1	0	RELL2	141000014	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	2.418000	0.44662	1.312000	0.45043	0.655000	0.94253	CAG	C|0.826;G|0.174	0.174	strong		0.597	RELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251807.2	NM_173828	
ZNF845	91664	hgsc.bcm.edu	37	19	53854948	53854948	+	Silent	SNP	A	A	C	rs73935563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53854948A>C	ENST00000595091.1	+	5	1239	c.1020A>C	c.(1018-1020)tcA>tcC	p.S340S	ZNF845_ENST00000458035.1_Silent_p.S340S			Q96IR2	ZN845_HUMAN	zinc finger protein 845	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTCAAACGTCATACCTTGTGT	0.378													.|||	246	0.0491214	0.1316	0.0317	5008	,	,		24413	0.0159		0.0249	False		,,,				2504	0.0092				p.S340S		Atlas-SNP	.											.	ZNF845	101	.	0			c.A1020C						PASS	.	A		173,1211		11,151,530	56.0	50.0	52.0		1020	-0.6	0.0	19	dbSNP_130	52	50,3132		0,50,1541	no	coding-synonymous	ZNF845	NM_138374.1		11,201,2071	CC,CA,AA		1.5713,12.5,4.8839		340/971	53854948	223,4343	692	1591	2283	SO:0001819	synonymous_variant	91664	exon4			AACGTCATACCTT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.1020A>C	19.37:g.53854948A>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			A|0.955;C|0.045	0.045	strong		0.378	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
OGDHL	55753	hgsc.bcm.edu	37	10	50950976	50950976	+	Missense_Mutation	SNP	G	G	A	rs11101224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50950976G>A	ENST00000374103.4	-	15	1995	c.1910C>T	c.(1909-1911)aCg>aTg	p.T637M	OGDHL_ENST00000419399.1_Missense_Mutation_p.T580M|OGDHL_ENST00000432695.1_Missense_Mutation_p.T428M	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	637			T -> M (in dbSNP:rs11101224). {ECO:0000269|PubMed:14702039}.		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						CCAGTCCACCGTCCGGTTCTT	0.652													g|||	1045	0.208666	0.3048	0.2565	5008	,	,		20432	0.0407		0.1958	False		,,,				2504	0.2311				p.T637M		Atlas-SNP	.											.	OGDHL	149	.	0			c.C1910T						PASS	.	G	MET/THR,MET/THR,MET/THR	1199,3207	419.1+/-338.5	166,867,1170	86.0	70.0	75.0		1739,1283,1910	0.0	0.0	10	dbSNP_120	75	1581,7019	296.7+/-303.1	136,1309,2855	yes	missense,missense,missense	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	81,81,81	302,2176,4025	AA,AG,GG		18.3837,27.2129,21.3748	benign,benign,benign	580/954,428/802,637/1011	50950976	2780,10226	2203	4300	6503	SO:0001583	missense	55753	exon15			TCCACCGTCCGGT	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.1910C>T	10.37:g.50950976G>A	ENSP00000363216:p.Thr637Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	410	0.18772893772893773	151	0.30691056910569103	84	0.23204419889502761	28	0.04895104895104895	147	0.19393139841688653	g	6.119	0.390152	0.11581	0.272129	0.183837	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	D;D;D	0.91577	-2.87;-2.87;-2.87	5.22	0.0223	0.14133	Transketolase-like, pyrimidine-binding domain (1);	0.792037	0.12112	N	0.498421	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B;B;B	0.18461	0.016;0.006;0.028	B;B;B	0.20184	0.017;0.017;0.028	T	0.05273	-1.0895	9	0.56958	D	0.05	.	5.7086	0.17923	0.3992:0.0:0.4704:0.1304	rs11101224;rs61669512;rs11101224	580;428;637	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	M	637;580;428	ENSP00000363216:T637M;ENSP00000401356:T580M;ENSP00000390240:T428M	ENSP00000363216:T637M	T	-	2	0	OGDHL	50620982	0.000000	0.05858	0.000000	0.03702	0.156000	0.22039	-0.513000	0.06305	0.028000	0.15324	-0.141000	0.14075	ACG	G|0.792;A|0.208	0.208	strong		0.652	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
ZNF761	388561	hgsc.bcm.edu	37	19	53959804	53959804	+	RNA	SNP	T	T	C	rs4803129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53959804T>C	ENST00000454407.1	+	0	2496							Q86XN6	ZN761_HUMAN	zinc finger protein 761						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.H627H(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TATGCCATCATAGACTTCATA	0.393													t|||	731	0.145966	0.1914	0.1066	5008	,	,		22447	0.1349		0.165	False		,,,				2504	0.1043				p.H681H		Atlas-SNP	.											ZNF761,NS,carcinoma,0,1	ZNF761	104	1	1	Substitution - coding silent(1)	stomach(1)	c.T2043C						PASS	.	T		683,3723	286.0+/-278.5	50,583,1570	89.0	93.0	91.0		2044	-0.7	0.0	19	dbSNP_111	91	1572,7028	291.7+/-300.5	131,1310,2859	no	coding-synonymous	ZNF761	NM_001008401.3		181,1893,4429	CC,CT,TT		18.2791,15.5016,17.3382		681/747	53959804	2255,10751	2203	4300	6503			388561	exon7			CCATCATAGACTT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959804T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_001008401	Q6ZNB9	Silent	SNP	ENST00000454407.1	37																																																																																				T|0.823;C|0.177	0.177	strong		0.393	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
OR52J3	119679	hgsc.bcm.edu	37	11	5068177	5068177	+	Missense_Mutation	SNP	A	A	T	rs2500018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	239	0	0		WXS	Illumina HiSeq	Phase_I	277	144	0.519856	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	
HAP1	9001	hgsc.bcm.edu	37	17	39884065	39884065	+	Missense_Mutation	SNP	C	C	A	rs35612698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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|HAP1_ENST00000341193.5_Intron|HAP1_ENST00000393939.2_Intron|RN7SL399P_ENST00000471648.2_RNA|JUP_ENST00000540235.1_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	64	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	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	
CNR2	1269	hgsc.bcm.edu	37	1	24201094	24201094	+	Silent	SNP	G	G	C	rs2229581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201094G>C	ENST00000374472.4	-	2	1175	c.1014C>G	c.(1012-1014)acC>acG	p.T338T	CNR2_ENST00000536471.1_Silent_p.T338T	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	338					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)	p.T338T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	CCTCTGTCTCGGTGACTGAGG	0.532													G|||	3272	0.653355	0.7943	0.6383	5008	,	,		21376	0.502		0.5875	False		,,,				2504	0.6973				p.T338T		Atlas-SNP	.											CNR2,NS,carcinoma,0,1	CNR2	78	1	1	Substitution - coding silent(1)	stomach(1)	c.C1014G						PASS	.	G		3313,1093	719.6+/-409.0	1263,787,153	96.0	107.0	103.0		1014	-7.3	0.1	1	dbSNP_98	103	4935,3665	622.6+/-397.3	1402,2131,767	no	coding-synonymous	CNR2	NM_001841.2		2665,2918,920	CC,CG,GG		42.6163,24.8071,36.5831		338/361	24201094	8248,4758	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			TGTCTCGGTGACT	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.1014C>G	1.37:g.24201094G>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	213	98	0.460094	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			G|0.370;C|0.630	0.630	strong		0.532	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
CMYA5	202333	hgsc.bcm.edu	37	5	79086883	79086883	+	Missense_Mutation	SNP	G	G	A	rs1129770	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79086883G>A	ENST00000446378.2	+	11	11811	c.11780G>A	c.(11779-11781)cGg>cAg	p.R3927Q	CTC-431G16.2_ENST00000421252.2_RNA	NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3927	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> Q (in dbSNP:rs1129770). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAGAGGAGACGGCTGACGGAG	0.517													G|||	596	0.11901	0.0726	0.1066	5008	,	,		18826	0.0942		0.2018	False		,,,				2504	0.1309				p.R3927Q		Atlas-SNP	.											.	CMYA5	643	.	0			c.G11780A						PASS	.	G	GLN/ARG	404,3684		16,372,1656	62.0	60.0	61.0		11780	6.1	1.0	5	dbSNP_86	61	1515,6905		138,1239,2833	yes	missense	CMYA5	NM_153610.3	43	154,1611,4489	AA,AG,GG		17.9929,9.8826,15.3422	probably-damaging	3927/4070	79086883	1919,10589	2044	4210	6254	SO:0001583	missense	202333	exon11			GGAGACGGCTGAC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.11780G>A	5.37:g.79086883G>A	ENSP00000394770:p.Arg3927Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	267	0.12225274725274725	27	0.054878048780487805	38	0.10497237569060773	59	0.10314685314685315	143	0.18865435356200527	G	24.3	4.511938	0.85389	0.098826	0.179929	ENSG00000164309	ENST00000446378	T	0.20463	2.07	6.06	6.06	0.98353	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00039	0.0001	L	0.49350	1.555	0.39798	P	0.027464000000000044	D	0.89917	1.0	D	0.66497	0.944	T	0.25710	-1.0124	8	0.72032	D	0.01	.	5.9675	0.19332	0.1701:0.1628:0.6671:0.0	rs1129770;rs2287675;rs3188025;rs17392236;rs17412292;rs52809107;rs59804203;rs1129770	3927	Q8N3K9	CMYA5_HUMAN	Q	3927	ENSP00000394770:R3927Q	ENSP00000394770:R3927Q	R	+	2	0	CMYA5	79122639	0.941000	0.31946	1.000000	0.80357	0.927000	0.56198	3.175000	0.50855	2.882000	0.98803	0.655000	0.94253	CGG	G|0.884;A|0.116	0.116	strong		0.517	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ZFYVE1	53349	hgsc.bcm.edu	37	14	73465003	73465003	+	Silent	SNP	A	A	G	rs997667	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:73465003A>G	ENST00000556143.1	-	3	1224	c.504T>C	c.(502-504)ttT>ttC	p.F168F	ZFYVE1_ENST00000553891.1_Silent_p.F168F|ZFYVE1_ENST00000318876.5_Silent_p.F168F	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	168					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		ATTTTCTAATAAAGTCTTCTT	0.353													G|||	1444	0.288339	0.23	0.2233	5008	,	,		15127	0.3542		0.3628	False		,,,				2504	0.2689				p.F168F		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.T504C						PASS	.	G		1112,3248		150,812,1218	34.0	34.0	34.0		504	-0.9	1.0	14	dbSNP_86	34	2916,5610		509,1898,1856	yes	coding-synonymous	ZFYVE1	NM_021260.2		659,2710,3074	GG,GA,AA		34.2013,25.5046,31.2587		168/778	73465003	4028,8858	2180	4263	6443	SO:0001819	synonymous_variant	53349	exon3			TCTAATAAAGTCT	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.504T>C	14.37:g.73465003A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																			A|0.678;G|0.322	0.322	strong		0.353	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
TPH2	121278	hgsc.bcm.edu	37	12	72372862	72372862	+	Silent	SNP	A	A	G	rs7305115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	77	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	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	
DSC3	1825	hgsc.bcm.edu	37	18	28610988	28610988	+	Missense_Mutation	SNP	C	C	T	rs276938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	136	136	1	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	
GIMAP7	168537	hgsc.bcm.edu	37	7	150217335	150217335	+	Silent	SNP	G	G	T	rs3735079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150217335G>T	ENST00000313543.4	+	2	430	c.273G>T	c.(271-273)ggG>ggT	p.G91G		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	91	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)		CCTGCCCAGGGCCCCATGCTA	0.547													G|||	549	0.109625	0.0416	0.1138	5008	,	,		19563	0.1855		0.1272	False		,,,				2504	0.1022				p.G91G		Atlas-SNP	.											.	GIMAP7	47	.	0			c.G273T						PASS	.	G		215,4191	130.6+/-167.2	2,211,1990	47.0	48.0	48.0		273	-6.0	0.8	7	dbSNP_107	48	1111,7489	231.2+/-265.3	78,955,3267	no	coding-synonymous	GIMAP7	NM_153236.3		80,1166,5257	TT,TG,GG		12.9186,4.8797,10.1953		91/301	150217335	1326,11680	2203	4300	6503	SO:0001819	synonymous_variant	168537	exon2			CCCAGGGCCCCAT	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.273G>T	7.37:g.150217335G>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	30	0.361446	NM_153236		Silent	SNP	ENST00000313543.4	37	CCDS5903.1																																																																																			G|0.893;T|0.107	0.107	strong		0.547	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520567	72520567	+	Silent	SNP	A	A	G	rs10823616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:72520567A>G	ENST00000373207.1	+	22	3630	c.3630A>G	c.(3628-3630)agA>agG	p.R1210R	ADAMTS14_ENST00000373208.1_Silent_p.R1213R	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1210	Pro-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						AAGACCTGAGACATCCCGGCA	0.647													G|||	1217	0.243011	0.3283	0.2709	5008	,	,		17130	0.1687		0.1899	False		,,,				2504	0.2393				p.R1213R		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.A3639G						PASS	.	G	,	1318,3088	692.2+/-405.5	208,902,1093	57.0	54.0	55.0		3630,3639	1.1	0.0	10	dbSNP_120	55	1981,6619	722.1+/-406.4	238,1505,2557	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	446,2407,3650	GG,GA,AA		23.0349,29.9138,25.3652	,	1210/1224,1213/1227	72520567	3299,9707	2203	4300	6503	SO:0001819	synonymous_variant	140766	exon22			CCTGAGACATCCC	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.3630A>G	10.37:g.72520567A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			A|0.756;G|0.244	0.244	strong		0.647	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
STARD3	10948	hgsc.bcm.edu	37	17	37815749	37815749	+	Silent	SNP	G	G	A	rs73296109	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:37815749G>A	ENST00000336308.5	+	9	956	c.738G>A	c.(736-738)acG>acA	p.T246T	STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000544210.2_Silent_p.T246T|STARD3_ENST00000394250.4_Silent_p.T228T|STARD3_ENST00000580611.1_Silent_p.T220T	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	246	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AGGAGGCCACGGCAGTGGTGG	0.597													A|||	144	0.028754	0.059	0.0274	5008	,	,		14528	0.0		0.0437	False		,,,				2504	0.0031				p.T246T		Atlas-SNP	.											STARD3,colon,carcinoma,0,1	STARD3	33	1	0			c.G738A						PASS	.	A	,,	248,4158	803.1+/-415.7	12,224,1967	77.0	78.0	78.0		738,684,738	-0.1	0.2	17	dbSNP_130	78	487,8113	797.7+/-407.4	18,451,3831	no	coding-synonymous,coding-synonymous,coding-synonymous	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	,,	30,675,5798	AA,AG,GG		5.6628,5.6287,5.6512	,,	246/446,228/428,246/446	37815749	735,12271	2203	4300	6503	SO:0001819	synonymous_variant	10948	exon9			GGCCACGGCAGTG		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.738G>A	17.37:g.37815749G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Silent	SNP	ENST00000336308.5	37	CCDS11341.1																																																																																			A|0.046;C|0.000;G|0.954;T|0.000	0.046	strong		0.597	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		
CCDC157	550631	hgsc.bcm.edu	37	22	30772686	30772686	+	Silent	SNP	C	C	T	rs2286442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:30772686C>T	ENST00000405659.1	+	12	2920	c.2211C>T	c.(2209-2211)ggC>ggT	p.G737G	RP1-130H16.16_ENST00000332468.4_RNA|CCDC157_ENST00000338306.3_Silent_p.G737G			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	737										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						TGTCACCTGGCCGGGGACAGG	0.647													C|||	640	0.127796	0.0287	0.219	5008	,	,		16862	0.1895		0.1133	False		,,,				2504	0.1483				p.G737G		Atlas-SNP	.											.	CCDC157	86	.	0			c.C2211T						PASS	.	C		219,4185		9,201,1992	28.0	29.0	29.0		2211	2.6	0.0	22	dbSNP_100	29	914,7680		41,832,3424	no	coding-synonymous	CCDC157	NM_001017437.2		50,1033,5416	TT,TC,CC		10.6353,4.9728,8.7167		737/753	30772686	1133,11865	2202	4297	6499	SO:0001819	synonymous_variant	550631	exon12			ACCTGGCCGGGGA	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.2211C>T	22.37:g.30772686C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	155	77	0.496774	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			C|0.898;T|0.102	0.102	strong		0.647	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
FLG	2312	hgsc.bcm.edu	37	1	152277822	152277822	+	Silent	SNP	T	T	C	rs3126069	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152277822T>C	ENST00000368799.1	-	3	9575	c.9540A>G	c.(9538-9540)tcA>tcG	p.S3180S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3180	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)			CATGGTGACGTGACACTGAGT	0.557									Ichthyosis				C|||	1121	0.223842	0.0378	0.2709	5008	,	,		17239	0.4831		0.0944	False		,,,				2504	0.3078				p.S3180S		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.A9540G						scavenged	.						291.0	281.0	285.0					1																	152277822		2201	4293	6494	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGACGTGACACT	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.9540A>G	1.37:g.152277822T>C		Somatic	401	1	0.00249377		WXS	Illumina HiSeq	Phase_I	254	28	0.110236	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.777;C|0.223	0.223	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SLC30A4	7782	hgsc.bcm.edu	37	15	45779810	45779810	+	Silent	SNP	G	G	A	rs2453531	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:45779810G>A	ENST00000261867.4	-	6	1229	c.915C>T	c.(913-915)gaC>gaT	p.D305D	RP11-519G16.3_ENST00000558536.1_RNA|RP11-519G16.3_ENST00000560647.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	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	63	0	0		WXS	Illumina HiSeq	Phase_I	72	72	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		
GLRA3	8001	hgsc.bcm.edu	37	4	175598280	175598280	+	Silent	SNP	A	A	G	rs12648678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	133	0	0		WXS	Illumina HiSeq	Phase_I	157	71	0.452229	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		
MTMR10	54893	hgsc.bcm.edu	37	15	31246972	31246972	+	Missense_Mutation	SNP	C	C	T	rs142149917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:31246972C>T	ENST00000435680.1	-	10	1157	c.1060G>A	c.(1060-1062)Gtt>Att	p.V354I	RNU6-466P_ENST00000391224.1_RNA|MTMR10_ENST00000563714.1_Missense_Mutation_p.V272I|MTMR10_ENST00000314404.8_Missense_Mutation_p.V106I|MTMR10_ENST00000425768.1_3'UTR	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	354	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						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)		TTACCATTAACGCATAGCTGC	0.333													C|||	19	0.00379393	0.0	0.0043	5008	,	,		17377	0.0		0.007	False		,,,				2504	0.0092				p.V354I		Atlas-SNP	.											MTMR10_ENST00000435680,NS,carcinoma,0,2	MTMR10	74	2	0			c.G1060A						PASS	.	C	ILE/VAL	7,3651		0,7,1822	83.0	75.0	77.0		1060	4.4	0.9	15	dbSNP_134	77	58,8108		0,58,4025	yes	missense	MTMR10	NM_017762.2	29	0,65,5847	TT,TC,CC		0.7103,0.1914,0.5497	benign	354/778	31246972	65,11759	1829	4083	5912	SO:0001583	missense	54893	exon10			CATTAACGCATAG	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.1060G>A	15.37:g.31246972C>T	ENSP00000402537:p.Val354Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_017762	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	13.17	2.158574	0.38119	0.001914	0.007103	ENSG00000166912	ENST00000435680;ENST00000314404;ENST00000340566	D;D	0.89415	-2.51;-2.51	5.32	4.4	0.53042	Myotubularin phosphatase domain (1);	0.121057	0.56097	N	0.000032	T	0.79730	0.4496	M	0.65320	2	0.80722	D	1	B;B;P;P	0.37688	0.256;0.066;0.605;0.522	B;B;B;B	0.21151	0.024;0.017;0.033;0.031	T	0.80266	-0.1454	10	0.33940	T	0.23	.	13.6029	0.62031	0.0:0.9259:0.0:0.0741	.	123;272;272;354	Q0IJ45;Q9NXD2-2;A6NGL9;Q9NXD2	.;.;.;MTMRA_HUMAN	I	354;106;272	ENSP00000402537:V354I;ENSP00000313788:V106I	ENSP00000313788:V106I	V	-	1	0	MTMR10	29034264	0.990000	0.36364	0.863000	0.33907	0.849000	0.48306	2.209000	0.42806	1.249000	0.43950	0.650000	0.86243	GTT	C|0.996;T|0.004	0.004	strong		0.333	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
LIMK2	3985	hgsc.bcm.edu	37	22	31663842	31663842	+	Silent	SNP	C	C	G	rs2228619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31663842C>G	ENST00000331728.4	+	10	1323	c.1209C>G	c.(1207-1209)ctC>ctG	p.L403L	LIMK2_ENST00000406516.1_Silent_p.L325L|LIMK2_ENST00000444929.2_Silent_p.L157L|LIMK2_ENST00000340552.4_Silent_p.L382L|LIMK2_ENST00000333611.4_Silent_p.L382L	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	403	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						AGCTGAACCTCCTGACAGAGT	0.552													G|||	4232	0.845048	0.9856	0.7478	5008	,	,		20970	0.876		0.7266	False		,,,				2504	0.8139				p.L403L		Atlas-SNP	.											.	LIMK2	101	.	0			c.C1209G						PASS	.	G	,,	4165,241		1971,223,9	88.0	78.0	82.0		1146,1209,1146	3.6	1.0	22	dbSNP_98	82	6233,2367		2258,1717,325	no	coding-synonymous,coding-synonymous,coding-synonymous	LIMK2	NM_001031801.1,NM_005569.3,NM_016733.2	,,	4229,1940,334	GG,GC,CC		27.5233,5.4698,20.0523	,,	382/687,403/639,382/618	31663842	10398,2608	2203	4300	6503	SO:0001819	synonymous_variant	3985	exon10			GAACCTCCTGACA	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1209C>G	22.37:g.31663842C>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_005569	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Silent	SNP	ENST00000331728.4	37	CCDS13891.1																																																																																			C|0.189;G|0.811	0.811	strong		0.552	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733	
MORC3	23515	hgsc.bcm.edu	37	21	37741439	37741439	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:37741439T>C	ENST00000400485.1	+	15	1849	c.1773T>C	c.(1771-1773)gaT>gaC	p.D591D	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	591					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						CTGCAGTAGATCATGATATTG	0.408																																					p.D591D		Atlas-SNP	.											MORC3,colon,carcinoma,+2,1	MORC3	78	1	0			c.T1773C						scavenged	.						213.0	206.0	209.0					21																	37741439		2125	4234	6359	SO:0001819	synonymous_variant	23515	exon15			AGTAGATCATGAT	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.1773T>C	21.37:g.37741439T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	260	4	0.0153846	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	37	CCDS42924.1																																																																																			.	.	none		0.408	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
FRMD6	122786	hgsc.bcm.edu	37	14	52186966	52186966	+	Silent	SNP	G	G	A	rs2277495	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:52186966G>A	ENST00000344768.5	+	11	1414	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	FRMD6_ENST00000554167.1_Silent_p.T329T|FRMD6_ENST00000553556.1_Silent_p.T48T|FRMD6_ENST00000395718.2_Silent_p.T398T|FRMD6_ENST00000356218.4_Silent_p.T398T			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	68	31	0.455882	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	
FAM118A	55007	hgsc.bcm.edu	37	22	45723807	45723807	+	Missense_Mutation	SNP	G	G	C	rs11556482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45723807G>C	ENST00000216214.3	+	5	1219	c.385G>C	c.(385-387)Gtg>Ctg	p.V129L	FAM118A_ENST00000405548.3_5'Flank|FAM118A_ENST00000405673.1_Missense_Mutation_p.V129L|FAM118A_ENST00000441876.2_Missense_Mutation_p.V129L	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	128	0	0		WXS	Illumina HiSeq	Phase_I	133	74	0.556391	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	
TBC1D4	9882	hgsc.bcm.edu	37	13	75866284	75866284	+	Missense_Mutation	SNP	G	G	A	rs9600455	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:75866284G>A	ENST00000377636.3	-	19	3786	c.3440C>T	c.(3439-3441)aCg>aTg	p.T1147M	TBC1D4_ENST00000377625.2_Missense_Mutation_p.T1084M|TBC1D4_ENST00000425511.1_Missense_Mutation_p.T311M|TBC1D4_ENST00000478591.1_5'Flank|TBC1D4_ENST00000431480.2_Missense_Mutation_p.T1139M	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1147			T -> M (in dbSNP:rs9600455).		cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)	p.T1147M(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		ATCAGGTAGCGTGTTTTTAAG	0.323													G|||	182	0.0363419	0.0023	0.0706	5008	,	,		15425	0.0		0.1133	False		,,,				2504	0.0164				p.T1147M		Atlas-SNP	.											TBC1D4,NS,lymphoid_neoplasm,0,1	TBC1D4	142	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C3440T						PASS	.	G	MET/THR	76,3552		1,74,1739	76.0	74.0	74.0		3440	3.9	0.0	13	dbSNP_119	74	979,7167		68,843,3162	yes	missense	TBC1D4	NM_014832.2	81	69,917,4901	AA,AG,GG		12.0182,2.0948,8.9604	possibly-damaging	1147/1299	75866284	1055,10719	1814	4073	5887	SO:0001583	missense	9882	exon19			GGTAGCGTGTTTT	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3440C>T	13.37:g.75866284G>A	ENSP00000366863:p.Thr1147Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	120	0.054945054945054944	0	0.0	33	0.09116022099447514	0	0.0	87	0.11477572559366754	G	14.20	2.463807	0.43736	0.020948	0.120182	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	5.63	3.87	0.44632	Rab-GAP/TBC domain (1);	0.079267	0.53938	D	0.000052	T	0.00210	0.0006	L	0.60455	1.87	0.33130	P	0.45700799999999997	B;P;B;B	0.42785	0.135;0.79;0.26;0.166	B;B;B;B	0.29353	0.016;0.101;0.038;0.02	T	0.14200	-1.0481	9	0.56958	D	0.05	-9.219	7.0733	0.25191	0.141:0.0:0.7189:0.1401	rs9600455;rs52825604;rs9600455	311;1084;1139;1147	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	M	1147;1139;1084;311	ENSP00000366863:T1147M;ENSP00000395986:T1139M;ENSP00000366852:T1084M;ENSP00000390654:T311M	ENSP00000366852:T1084M	T	-	2	0	TBC1D4	74764285	1.000000	0.71417	0.003000	0.11579	0.992000	0.81027	4.605000	0.61119	0.695000	0.31675	0.650000	0.86243	ACG	G|0.929;A|0.071	0.071	strong		0.323	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254058	39254058	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254058G>T	ENST00000333822.4	-	1	335	c.279C>A	c.(277-279)agC>agA	p.S93R		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	93	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						agatgcagcagcTAGGGTGGC	0.677																																					p.S93R		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,2	KRTAP4-8	57	2	0			c.C279A						scavenged	.						8.0	11.0	10.0					17																	39254058		683	1581	2264	SO:0001583	missense	728224	exon1			GCAGCAGCTAGGG	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.279C>A	17.37:g.39254058G>T	ENSP00000328444:p.Ser93Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	89	9	0.101124	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	12.38	1.921689	0.33908	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01629	4.72	2.84	0.649	0.17806	.	1.381260	0.05066	U	0.480753	T	0.03220	0.0094	M	0.69823	2.125	0.19575	N	0.999964	B	0.13145	0.007	B	0.14578	0.011	T	0.47249	-0.9132	10	0.36615	T	0.2	.	5.5258	0.16957	0.4095:0.0:0.5905:0.0	.	93	Q9BYQ9	KRA48_HUMAN	R	93;78	ENSP00000328444:S93R	ENSP00000414561:S78R	S	-	3	2	KRTAP4-8	36507584	0.001000	0.12720	0.112000	0.21494	0.752000	0.42762	-0.433000	0.06948	0.063000	0.16370	0.456000	0.33151	AGC	.	.	none		0.677	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
TSPEAR	54084	hgsc.bcm.edu	37	21	45948342	45948342	+	Silent	SNP	C	C	T	rs201202780		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45948342C>T	ENST00000323084.4	-	6	980	c.915G>A	c.(913-915)gtG>gtA	p.V305V	TSPEAR_ENST00000397916.1_Silent_p.V237V	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	305					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						CACCTGCTAACACGGAGACCC	0.642																																					p.V305V		Atlas-SNP	.											.	TSPEAR	110	.	0			c.G915A						PASS	.						152.0	141.0	144.0					21																	45948342		2203	4300	6503	SO:0001819	synonymous_variant	54084	exon6			TGCTAACACGGAG	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.915G>A	21.37:g.45948342C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			C|0.999;T|0.001	0.001	weak		0.642	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
NOL8	55035	hgsc.bcm.edu	37	9	95068046	95068046	+	Silent	SNP	C	C	T	rs1133908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:95068046C>T	ENST00000535387.1	-	10	2777	c.2778G>A	c.(2776-2778)aaG>aaA	p.K926K	NOL8_ENST00000442668.2_Silent_p.K964K|NOL8_ENST00000542053.1_Silent_p.K896K|NOL8_ENST00000358855.4_Silent_p.K896K|NOL8_ENST00000545558.1_Silent_p.K964K					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTTCTTTTGGCTTATCATCTC	0.348													T|||	2173	0.433906	0.8933	0.2968	5008	,	,		19457	0.1508		0.3549	False		,,,				2504	0.2832				p.K964K		Atlas-SNP	.											.	NOL8	118	.	0			c.G2892A						PASS	.	T		2958,738		1198,562,88	156.0	155.0	156.0		2892	0.5	1.0	9	dbSNP_86	156	3098,5096		592,1914,1591	no	coding-synonymous	NOL8	NM_017948.5		1790,2476,1679	TT,TC,CC		37.8082,19.9675,49.0664		964/1168	95068046	6056,5834	1848	4097	5945	SO:0001819	synonymous_variant	55035	exon12			TTTTGGCTTATCA	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.2778G>A	9.37:g.95068046C>T		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	256	131	0.511719	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			T|0.382;G|0.057	0.382	strong		0.348	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
FRMD4A	55691	hgsc.bcm.edu	37	10	13779898	13779898	+	Silent	SNP	C	C	T	rs61755072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:13779898C>T	ENST00000357447.2	-	12	1073	c.705G>A	c.(703-705)ctG>ctA	p.L235L	FRMD4A_ENST00000342409.2_Silent_p.L251L|FRMD4A_ENST00000378503.1_Silent_p.L235L|FRMD4A_ENST00000358621.4_Silent_p.L220L|RP11-353M9.1_ENST00000449462.1_RNA	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	235	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						CTTTGTAGCTCAGGCCCAGCC	0.468													C|||	8	0.00159744	0.0008	0.0014	5008	,	,		19078	0.0		0.006	False		,,,				2504	0.0				p.L235L		Atlas-SNP	.											.	FRMD4A	108	.	0			c.G705A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	156.0	116.0	130.0		705	1.5	1.0	10	dbSNP_129	130	90,8510	51.1+/-111.2	0,90,4210	no	coding-synonymous	FRMD4A	NM_018027.3		0,99,6404	TT,TC,CC		1.0465,0.2043,0.7612		235/1040	13779898	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	55691	exon12			GTAGCTCAGGCCC	AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"""FERM domain containing 4"""	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.705G>A	10.37:g.13779898C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_018027	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	37	CCDS7101.1																																																																																			C|0.994;T|0.006	0.006	strong		0.468	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027	
TAS2R7	50837	hgsc.bcm.edu	37	12	10954258	10954258	+	Missense_Mutation	SNP	C	C	T	rs619381	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:10954258C>T	ENST00000240687.2	-	1	968	c.912G>A	c.(910-912)atG>atA	p.M304I		NM_023919.2	NP_076408.1	Q9NYW3	TA2R7_HUMAN	taste receptor, type 2, member 7	304			M -> I (in dbSNP:rs619381).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.M304I(1)		kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(3)	10						TTAGAATAGACATTACTTTCC	0.313													C|||	455	0.0908546	0.0098	0.111	5008	,	,		20774	0.0893		0.0855	False		,,,				2504	0.1933				p.M304I		Atlas-SNP	.											TAS2R7,NS,carcinoma,0,1	TAS2R7	35	1	1	Substitution - Missense(1)	stomach(1)	c.G912A						PASS	.	C	ILE/MET	122,4284	89.7+/-128.4	2,118,2083	81.0	79.0	79.0		912	-0.7	0.0	12	dbSNP_83	79	1043,7557	220.1+/-257.9	65,913,3322	yes	missense	TAS2R7	NM_023919.2	10	67,1031,5405	TT,TC,CC		12.1279,2.769,8.9574	benign	304/319	10954258	1165,11841	2203	4300	6503	SO:0001583	missense	50837	exon1			AATAGACATTACT	AF227133	CCDS8631.1	12p13	2012-08-22			ENSG00000121377	ENSG00000121377		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14913	protein-coding gene	gene with protein product		604793				10761934, 10766242	Standard	NM_023919		Approved	T2R7, TRB4	uc001qyv.3	Q9NYW3	OTTHUMG00000168505	ENST00000240687.2:c.912G>A	12.37:g.10954258C>T	ENSP00000240687:p.Met304Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_023919	Q645Y1	Missense_Mutation	SNP	ENST00000240687.2	37	CCDS8631.1	152	0.0695970695970696	3	0.006097560975609756	33	0.09116022099447514	55	0.09615384615384616	61	0.08047493403693931	C	11.32	1.603087	0.28534	0.02769	0.121279	ENSG00000121377	ENST00000240687	T	0.36340	1.26	5.72	-0.705	0.11252	.	0.410373	0.21537	N	0.072955	T	0.00210	0.0006	N	0.08118	0	0.80722	P	0.0	B	0.29886	0.26	B	0.27796	0.083	T	0.11108	-1.0601	9	0.87932	D	0	.	4.6703	0.12685	0.2335:0.4905:0.0:0.276	rs619381;rs1663405;rs52812680;rs57496493;rs619381	304	Q9NYW3	TA2R7_HUMAN	I	304	ENSP00000240687:M304I	ENSP00000240687:M304I	M	-	3	0	TAS2R7	10845525	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.526000	0.06207	-0.148000	0.11234	-0.162000	0.13425	ATG	C|0.919;T|0.081	0.081	strong		0.313	TAS2R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399931.1		
SPRR2F	6705	hgsc.bcm.edu	37	1	153085152	153085152	+	Missense_Mutation	SNP	C	C	T	rs151137674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153085152C>T	ENST00000468739.1	-	2	118	c.58G>A	c.(58-60)Gcg>Acg	p.A20T	SPRR2B_ENST00000368752.4_Intron	NM_001014450.1	NP_001014450.1	Q96RM1	SPR2F_HUMAN	small proline-rich protein 2F	20					epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	4	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CACTTTGGCGCGGGGCACACA	0.572													t|||	76	0.0151757	0.0182	0.0231	5008	,	,		16303	0.001		0.0338	False		,,,				2504	0.001				p.A20T		Atlas-SNP	.											SPRR2F,caecum,carcinoma,+2,1	SPRR2F	12	1	0			c.G58A						scavenged	.	T	THR/ALA	56,4350	819.2+/-416.3	0,56,2147	106.0	94.0	98.0		58	-3.5	0.0	1	dbSNP_134	98	105,8489	809.3+/-407.2	1,103,4193	no	missense	SPRR2F	NM_001014450.1	58	1,159,6340	TT,TC,CC		1.2218,1.271,1.2385	benign	20/73	153085152	161,12839	2203	4297	6500	SO:0001583	missense	6705	exon2			TTGGCGCGGGGCA	AF333956	CCDS30867.1	1q21-q22	2008-02-05			ENSG00000244094	ENSG00000244094			11266	protein-coding gene	gene with protein product						8325635, 11279051	Standard	NM_001014450		Approved		uc001fbi.3	Q96RM1	OTTHUMG00000014398	ENST00000468739.1:c.58G>A	1.37:g.153085152C>T	ENSP00000418193:p.Ala20Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	121	22	0.181818	NM_001014450	Q5T9T3	Missense_Mutation	SNP	ENST00000468739.1	37	CCDS30867.1	25	0.011446886446886446	8	0.016260162601626018	3	0.008287292817679558	1	0.0017482517482517483	13	0.017150395778364115	T	2.586	-0.296265	0.05532	0.01271	0.012218	ENSG00000244094	ENST00000468739	T	0.26810	1.71	2.66	-3.46	0.04767	.	0.891598	0.09133	N	0.844110	T	0.05640	0.0148	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40327	-0.9569	9	0.87932	D	0	.	5.6027	0.17363	0.0:0.4524:0.2541:0.2935	.	20	Q96RM1	SPR2F_HUMAN	T	20	ENSP00000418193:A20T	ENSP00000418193:A20T	A	-	1	0	SPRR2F	151351776	0.006000	0.16342	0.006000	0.13384	0.150000	0.21749	-0.639000	0.05446	-1.375000	0.02129	-0.848000	0.03037	GCG	.	.	weak		0.572	SPRR2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040056.1		
GP1BA	2811	hgsc.bcm.edu	37	17	4837243	4837243	+	Silent	SNP	C	C	T	rs41466145|rs574786279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4837243C>T	ENST00000329125.5	+	2	1419	c.1344C>T	c.(1342-1344)acC>acT	p.T448T		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	448	Pro/Thr-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						ccagcccgaccaccccggagc	0.677													C|||	731	0.145966	0.0469	0.1182	5008	,	,		5451	0.1746		0.1243	False		,,,				2504	0.2924				p.T448T		Atlas-SNP	.											.	GP1BA	53	.	0			c.C1344T						PASS	.	C		170,3284		4,162,1561	11.0	13.0	12.0		1344	-1.1	0.0	17	dbSNP_127	12	853,6979		41,771,3104	no	coding-synonymous	GP1BA	NM_000173.5		45,933,4665	TT,TC,CC		10.8912,4.9218,9.0643		448/653	4837243	1023,10263	1727	3916	5643	SO:0001819	synonymous_variant	2811	exon2			CCCGACCACCCCG		CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.1344C>T	17.37:g.4837243C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_000173	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Silent	SNP	ENST00000329125.5	37	CCDS54068.1																																																																																			C|0.882;T|0.118	0.118	strong		0.677	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
ZBBX	79740	hgsc.bcm.edu	37	3	167051726	167051726	+	Silent	SNP	A	A	G	rs10936530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000469220.1_Intron|ZBBX_ENST00000392767.2_Silent_p.F192F	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						scavenged	.	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	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	103	61	0.592233	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	
CNTNAP2	26047	hgsc.bcm.edu	37	7	147092861	147092861	+	Silent	SNP	G	G	A	rs34592169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:147092861G>A	ENST00000361727.3	+	10	2175	c.1659G>A	c.(1657-1659)gcG>gcA	p.A553A		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	553					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ACATGTGTGCGATCATAGACA	0.428										HNSCC(39;0.1)			G|||	469	0.0936502	0.0197	0.1599	5008	,	,		16618	0.006		0.2207	False		,,,				2504	0.1063				p.A553A		Atlas-SNP	.											CNTNAP2,colon,carcinoma,0,1	CNTNAP2	392	1	0			c.G1659A						PASS	.	G		246,4160	145.0+/-179.8	6,234,1963	139.0	123.0	128.0		1659	3.5	1.0	7	dbSNP_126	128	2020,6578	353.4+/-329.1	238,1544,2517	no	coding-synonymous	CNTNAP2	NM_014141.5		244,1778,4480	AA,AG,GG		23.4938,5.5833,17.4254		553/1332	147092861	2266,10738	2203	4299	6502	SO:0001819	synonymous_variant	26047	exon10			GTGTGCGATCATA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1659G>A	7.37:g.147092861G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																			G|0.845;A|0.155	0.155	strong		0.428	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
RRP1	8568	hgsc.bcm.edu	37	21	45220483	45220483	+	Missense_Mutation	SNP	A	A	G	rs915770	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	125	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	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	
GAS8	2622	hgsc.bcm.edu	37	16	90103659	90103659	+	Missense_Mutation	SNP	G	G	A	rs17178299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90103659G>A	ENST00000268699.4	+	7	898	c.776G>A	c.(775-777)cGg>cAg	p.R259Q	GAS8_ENST00000540721.1_3'UTR|GAS8_ENST00000536122.1_Missense_Mutation_p.R234Q	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	259			R -> Q (in dbSNP:rs17178299).		cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		GAGGACATGCGGAAGAAGGAG	0.637													G|||	240	0.0479233	0.0038	0.013	5008	,	,		21050	0.1488		0.0507	False		,,,				2504	0.0256				p.R259Q		Atlas-SNP	.											.	GAS8	29	.	0			c.G776A						PASS	.	G	GLN/ARG	50,4346	50.2+/-85.5	0,50,2148	58.0	56.0	57.0		776	4.4	1.0	16	dbSNP_123	57	516,8084	144.7+/-200.5	15,486,3799	yes	missense	GAS8	NM_001481.2	43	15,536,5947	AA,AG,GG		6.0,1.1374,4.3552	possibly-damaging	259/479	90103659	566,12430	2198	4300	6498	SO:0001583	missense	2622	exon7			ACATGCGGAAGAA	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.776G>A	16.37:g.90103659G>A	ENSP00000268699:p.Arg259Gln	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	198	97	0.489899	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	100	0.045787545787545784	3	0.006097560975609756	7	0.019337016574585635	47	0.08216783216783216	43	0.05672823218997362	G	19.36	3.812005	0.70797	0.011374	0.06	ENSG00000141013	ENST00000536122;ENST00000268699;ENST00000540721	T;T	0.46451	0.87;0.87	5.49	4.44	0.53790	.	0.258952	0.37955	N	0.001866	T	0.01558	0.0050	L	0.45352	1.415	0.22918	P	0.99856096	P;P	0.46656	0.882;0.774	B;B	0.40228	0.323;0.126	T	0.15321	-1.0441	8	.	.	.	-37.1049	3.5798	0.07947	0.3568:0.0:0.6432:0.0	rs17178299;rs17178299	230;259	B7Z1X3;O95995	.;GAS8_HUMAN	Q	234;259;230	ENSP00000440977:R234Q;ENSP00000268699:R259Q	.	R	+	2	0	GAS8	88631160	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.732000	0.68563	2.578000	0.87016	0.563000	0.77884	CGG	G|0.958;A|0.042	0.042	strong		0.637	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
NKTR	4820	hgsc.bcm.edu	37	3	42679497	42679497	+	Silent	SNP	C	C	T	rs35890296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42679497C>T	ENST00000232978.8	+	13	2489	c.2301C>T	c.(2299-2301)agC>agT	p.S767S	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	767	Arg/Ser-rich.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		AAAAAAATAGCGTTTCACATA	0.388													T|||	971	0.19389	0.32	0.0735	5008	,	,		20890	0.1101		0.1402	False		,,,				2504	0.2505				p.S767S		Atlas-SNP	.											.	NKTR	116	.	0			c.C2301T						PASS	.	T		1276,3130	698.4+/-406.3	182,912,1109	88.0	89.0	89.0		2301	-1.2	0.0	3	dbSNP_126	89	1061,7539	769.1+/-407.6	58,945,3297	no	coding-synonymous	NKTR	NM_005385.3		240,1857,4406	TT,TC,CC		12.3372,28.9605,17.9686		767/1463	42679497	2337,10669	2203	4300	6503	SO:0001819	synonymous_variant	4820	exon13			AAATAGCGTTTCA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.2301C>T	3.37:g.42679497C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_005385		Silent	SNP	ENST00000232978.8	37	CCDS2702.1																																																																																			C|0.823;T|0.177	0.177	strong		0.388	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
PLEKHA3	65977	hgsc.bcm.edu	37	2	179358665	179358665	+	Silent	SNP	A	A	G	rs2303536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179358665A>G	ENST00000234453.5	+	4	801	c.399A>G	c.(397-399)acA>acG	p.T133T	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	133						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AAGTTCATACAATACAGGAAT	0.403													G|||	1527	0.304912	0.2095	0.1945	5008	,	,		20258	0.63		0.1551	False		,,,				2504	0.3313				p.T133T		Atlas-SNP	.											PLEKHA3,NS,carcinoma,+1,1	PLEKHA3	25	1	0			c.A399G						PASS	.	G		883,3523	741.1+/-411.2	90,703,1410	126.0	118.0	120.0		399	-11.7	0.4	2	dbSNP_100	120	1271,7329	760.0+/-407.6	99,1073,3128	no	coding-synonymous	PLEKHA3	NM_019091.3		189,1776,4538	GG,GA,AA		14.7791,20.0409,16.5616		133/301	179358665	2154,10852	2203	4300	6503	SO:0001819	synonymous_variant	65977	exon4			TCATACAATACAG	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.399A>G	2.37:g.179358665A>G		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	248	118	0.475806	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Silent	SNP	ENST00000234453.5	37	CCDS33336.1																																																																																			A|1.000;|0.000	.	weak		0.403	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	
CCDC144NL	339184	hgsc.bcm.edu	37	17	20798992	20798992	+	Silent	SNP	C	C	T	rs8073465	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:20798992C>T	ENST00000327925.5	-	1	461	c.342G>A	c.(340-342)aaG>aaA	p.K114K	RP11-344E13.3_ENST00000577537.1_RNA|RNU6-1178P_ENST00000516674.1_RNA|RP11-344E13.3_ENST00000582324.1_RNA|RP11-344E13.3_ENST00000583962.1_RNA|RP11-344E13.3_ENST00000577860.1_RNA|RP11-344E13.3_ENST00000439794.2_RNA|RP11-344E13.3_ENST00000417232.2_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	114										large_intestine(3)|lung(3)|skin(1)	7						GCCATTACCTCTTCTTCCTAT	0.652													c|||	497	0.0992412	0.0212	0.0865	5008	,	,		14967	0.1766		0.1501	False		,,,				2504	0.0818				p.K114K		Atlas-SNP	.											.	CCDC144NL	34	.	0			c.G342A						PASS	.	C		228,4178	130.2+/-166.9	12,204,1987	74.0	79.0	77.0		342	-1.8	0.0	17	dbSNP_116	77	1217,7383	229.0+/-263.8	74,1069,3157	no	coding-synonymous	CCDC144NL	NM_001004306.1		86,1273,5144	TT,TC,CC		14.1512,5.1748,11.1103		114/222	20798992	1445,11561	2203	4300	6503	SO:0001819	synonymous_variant	339184	exon1			TTACCTCTTCTTC		CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.342G>A	17.37:g.20798992C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	208	91	0.4375	NM_001004306		Silent	SNP	ENST00000327925.5	37	CCDS32591.1																																																																																			C|0.883;T|0.117	0.117	strong		0.652	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306	
OR8G5	219865	hgsc.bcm.edu	37	11	124135215	124135215	+	Missense_Mutation	SNP	T	T	G	rs11219544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124135215T>G	ENST00000524943.2	+	1	493	c.493T>G	c.(493-495)Ttg>Gtg	p.L165V	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	165						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)		CTGTAGCCCCTTGCTGTACAG	0.448													t|||	429	0.0856629	0.1415	0.0346	5008	,	,		22984	0.0516		0.0169	False		,,,				2504	0.1524				p.L165V	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.T493G						PASS	.	T	VAL/LEU	506,3758		30,446,1656	212.0	207.0	209.0		493	-1.0	1.0	11	dbSNP_120	209	230,8306		4,222,4042	yes	missense	OR8G5	NM_001005198.1	32	34,668,5698	GG,GT,TT		2.6945,11.8668,5.75		165/347	124135215	736,12064	2132	4268	6400	SO:0001583	missense	219865	exon1			AGCCCCTTGCTGT	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.493T>G	11.37:g.124135215T>G	ENSP00000477014:p.Leu165Val	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	298	146	0.489933	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				T|0.947;G|0.053	0.053	strong		0.448	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
RIPK3	11035	hgsc.bcm.edu	37	14	24807221	24807221	+	Silent	SNP	G	G	A	rs56337365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24807221G>A	ENST00000216274.5	-	6	908	c.690C>T	c.(688-690)taC>taT	p.Y230Y	RP11-934B9.3_ENST00000555591.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		ACACTGCTTCGTACACGAGTG	0.547													A|||	274	0.0547125	0.0953	0.0403	5008	,	,		21403	0.001		0.0577	False		,,,				2504	0.0624				p.Y230Y	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C690T						PASS	.	A		438,3968	784.4+/-414.7	12,414,1777	77.0	71.0	73.0		690	-3.0	0.0	14	dbSNP_129	73	409,8191	799.1+/-407.4	19,371,3910	no	coding-synonymous	RIPK3	NM_006871.3		31,785,5687	AA,AG,GG		4.7558,9.941,6.5124		230/519	24807221	847,12159	2203	4300	6503	SO:0001819	synonymous_variant	11035	exon6			TGCTTCGTACACG	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.690C>T	14.37:g.24807221G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	37	CCDS9628.1																																																																																			G|0.933;A|0.067	0.067	strong		0.547	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
PTGR2	145482	hgsc.bcm.edu	37	14	74340797	74340797	+	Silent	SNP	A	A	T	rs11159042	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74340797A>T	ENST00000555661.1	+	4	373	c.228A>T	c.(226-228)ggA>ggT	p.G76G	RP5-1021I20.4_ENST00000556551.2_Silent_p.G76G|PTGR2_ENST00000267568.4_Silent_p.G76G|PTGR2_ENST00000555228.1_Silent_p.G76G|PTGR2_ENST00000553813.1_De_novo_Start_OutOfFrame			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	76					prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)			NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	TCGTTGATGGAGGAGGTATTG	0.368													T|||	2529	0.504992	0.4024	0.4827	5008	,	,		17866	0.5079		0.5129	False		,,,				2504	0.6483				p.G76G	Esophageal Squamous(98;1155 1417 16452 47043 47872)	Atlas-SNP	.											.	PTGR2	21	.	0			c.A228T						PASS	.	T	,,	1726,2680	650.3+/-399.0	337,1052,814	105.0	105.0	105.0		228,228,228	3.0	1.0	14	dbSNP_120	105	4417,4183	568.1+/-388.9	1134,2149,1017	no	coding-synonymous,coding-synonymous,coding-synonymous	PTGR2	NM_001146154.1,NM_001146155.1,NM_152444.2	,,	1471,3201,1831	TT,TA,AA		48.6395,39.1739,47.232	,,	76/352,76/352,76/352	74340797	6143,6863	2203	4300	6503	SO:0001819	synonymous_variant	145482	exon4			TGATGGAGGAGGT	AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043			20149	protein-coding gene	gene with protein product		608642	"""zinc binding alcohol dehydrogenase domain containing 1"""	ZADH1		17449869	Standard	NM_152444		Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.228A>T	14.37:g.74340797A>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	148	69	0.466216	NM_152444	Q3L8A4|Q6MZH8	Silent	SNP	ENST00000555661.1	37	CCDS9820.1																																																																																			A|0.507;N|0.000	.	strong		0.368	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412575.1		
KDM5A	5927	hgsc.bcm.edu	37	12	406292	406292	+	Silent	SNP	G	G	A	rs2229351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:406292G>A	ENST00000399788.2	-	25	4511	c.4149C>T	c.(4147-4149)tcC>tcT	p.S1383S	KDM5A_ENST00000382815.4_Silent_p.S1383S	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1383					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CCACCTCCTCGGATTTGATGG	0.418			T	NUP98	AML								G|||	1766	0.352636	0.3306	0.3199	5008	,	,		18093	0.5109		0.2326	False		,,,				2504	0.3661				p.S1383S		Atlas-SNP	.		Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	KDM5A_ENST00000399788,trunk,malignant_melanoma,-1,2	KDM5A	307	2	0			c.C4149T						PASS	.	G		1187,2579		201,785,897	65.0	64.0	64.0		4149	-3.8	1.0	12	dbSNP_98	64	2087,6129		276,1535,2297	no	coding-synonymous	KDM5A	NM_001042603.1		477,2320,3194	AA,AG,GG		25.4017,31.5189,27.3243		1383/1691	406292	3274,8708	1883	4108	5991	SO:0001819	synonymous_variant	5927	exon25			CTCCTCGGATTTG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4149C>T	12.37:g.406292G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Silent	SNP	ENST00000399788.2	37	CCDS41736.1																																																																																			T|0.139;G|0.444;C|0.211;A|0.206	0.206	strong		0.418	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	
SLC7A3	84889	hgsc.bcm.edu	37	X	70146398	70146398	+	Silent	SNP	A	A	G	rs4360450	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:70146398A>G	ENST00000374299.3	-	10	1743	c.1599T>C	c.(1597-1599)agT>agC	p.S533S	SLC7A3_ENST00000298085.4_Silent_p.S533S			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	533					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GGGGAGTGGAACTCTGTGGCT	0.468													G|||	3066	0.812185	0.5658	0.6081	3775	,	,		14725	0.754		0.4791	False		,,,				2504	0.6687				p.S533S		Atlas-SNP	.											.	SLC7A3	76	.	0			c.T1599C						PASS	.	G	,	2907,924		934,598,441,99,128	47.0	39.0	42.0		1599,1599	1.1	0.1	X	dbSNP_111	42	4337,2385		992,1138,1215,297,653	no	coding-synonymous,coding-synonymous	SLC7A3	NM_001048164.2,NM_032803.5	,	1926,1736,1656,396,781	GG,GA,G,AA,A		35.4805,24.119,31.356	,	533/620,533/620	70146398	7244,3309	2200	4295	6495	SO:0001819	synonymous_variant	84889	exon10			AGTGGAACTCTGT	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1599T>C	X.37:g.70146398A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Silent	SNP	ENST00000374299.3	37	CCDS14404.1																																																																																			A|0.284;G|0.716	0.716	strong		0.468	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
ZNF133	7692	hgsc.bcm.edu	37	20	18295861	18295861	+	Silent	SNP	G	G	A	rs2228274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:18295861G>A	ENST00000316358.4	+	4	463	c.366G>A	c.(364-366)ccG>ccA	p.P122P	ZNF133_ENST00000535822.1_Silent_p.P27P|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000402618.2_Silent_p.P59P|ZNF133_ENST00000377671.3_Silent_p.P121P|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000396026.3_Silent_p.P125P|ZNF133_ENST00000538547.1_Silent_p.P27P|ZNF133_ENST00000401790.1_Silent_p.P122P	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	122					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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						CTGGGGATCCGGGCCCAGGGG	0.557													G|||	283	0.0565096	0.0484	0.062	5008	,	,		18611	0.0139		0.0706	False		,,,				2504	0.093				p.P121P		Atlas-SNP	.											.	ZNF133	63	.	0			c.G363A						PASS	.	G	,	199,4207	124.5+/-161.8	4,191,2008	88.0	91.0	90.0		363,363	-8.2	0.0	20	dbSNP_98	90	703,7897	172.6+/-223.3	36,631,3633	no	coding-synonymous,coding-synonymous	ZNF133	NM_001083330.1,NM_003434.4	,	40,822,5641	AA,AG,GG		8.1744,4.5166,6.9353	,	121/654,121/654	18295861	902,12104	2203	4300	6503	SO:0001819	synonymous_variant	7692	exon4			GGATCCGGGCCCA	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.366G>A	20.37:g.18295861G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Silent	SNP	ENST00000316358.4	37																																																																																				G|0.928;A|0.072	0.072	strong		0.557	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240794	39240794	+	Silent	SNP	C	C	A	rs9894106|rs553572799	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39240794C>A	ENST00000391417.4	+	1	336	c.336C>A	c.(334-336)ccC>ccA	p.P112P		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	137	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.P112P(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						gctgccgccccagctgctgcc	0.667																																					p.P112P		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,0,3	KRTAP4-7	49	3	3	Unknown(1)|Substitution - coding silent(1)|Deletion - In frame(1)	NS(2)|prostate(1)	c.C336A						scavenged	.						13.0	14.0	14.0					17																	39240794		691	1589	2280	SO:0001819	synonymous_variant	100132476	exon1			CCGCCCCAGCTGC	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.336C>A	17.37:g.39240794C>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	58	11	0.189655	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
PROSER3	148137	hgsc.bcm.edu	37	19	36258721	36258721	+	Missense_Mutation	SNP	C	C	T	rs73592448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36258721C>T	ENST00000544099.1	+	9	1037	c.974C>T	c.(973-975)gCc>gTc	p.A325V	AC002398.13_ENST00000589397.1_RNA|C19orf55_ENST00000396908.4_Missense_Mutation_p.A325V			Q2NL68	PRSR3_HUMAN		325										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	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)			TCTCTGAAAGCCAAGGCCTTG	0.627													C|||	445	0.0888578	0.059	0.0922	5008	,	,		13002	0.0744		0.1064	False		,,,				2504	0.1237				p.A325V		Atlas-SNP	.											.	C19orf55	39	.	0			c.C974T						PASS	.	C	VAL/ALA	249,3507		6,237,1635	21.0	24.0	23.0		974	-0.5	0.0	19	dbSNP_130	23	747,7433		27,693,3370	yes	missense	C19orf55	NM_001039887.2	64	33,930,5005	TT,TC,CC		9.132,6.6294,8.3445	probably-damaging	325/481	36258721	996,10940	1878	4090	5968	SO:0001583	missense	148137	exon9			TGAAAGCCAAGGC																												ENST00000544099.1:c.974C>T	19.37:g.36258721C>T	ENSP00000467267:p.Ala325Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	37		184	0.08424908424908426	30	0.06097560975609756	34	0.09392265193370165	38	0.06643356643356643	82	0.10817941952506596	C	11.71	1.720944	0.30503	0.066294	0.09132	ENSG00000167595	ENST00000396908	T	0.32515	1.45	3.04	-0.484	0.12071	.	.	.	.	.	T	0.00412	0.0013	L	0.51422	1.61	0.80722	P	0.0	B	0.19331	0.035	B	0.14023	0.01	T	0.14254	-1.0479	8	0.56958	D	0.05	-0.5768	3.3343	0.07096	0.0:0.4894:0.2358:0.2748	.	325	E5RFB9	.	V	325	ENSP00000380116:A325V	ENSP00000380116:A325V	A	+	2	0	C19orf55	40950561	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.452000	0.21795	0.008000	0.14787	-0.490000	0.04691	GCC	C|0.916;T|0.084	0.084	strong		0.627	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		
UBQLNL	143630	hgsc.bcm.edu	37	11	5537045	5537045	+	Silent	SNP	T	T	G	rs872751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5537045T>G	ENST00000380184.1	-	1	890	c.627A>C	c.(625-627)ccA>ccC	p.P209P	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	209										endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		GGGAAACTTCTGGGTTCTGCT	0.468													T|||	1608	0.321086	0.3472	0.3487	5008	,	,		21098	0.375		0.2644	False		,,,				2504	0.2689				p.P209P		Atlas-SNP	.											.	UBQLNL	74	.	0			c.A627C						PASS	.	T		1484,2918	476.3+/-357.6	258,968,975	129.0	131.0	130.0		627	1.2	1.0	11	dbSNP_86	130	2364,6230	394.6+/-344.7	338,1688,2271	no	coding-synonymous	UBQLNL	NM_145053.4		596,2656,3246	GG,GT,TT		27.5076,33.7119,29.6091		209/476	5537045	3848,9148	2201	4297	6498	SO:0001819	synonymous_variant	143630	exon1			AACTTCTGGGTTC	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.627A>C	11.37:g.5537045T>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	37	CCDS31385.1																																																																																			T|0.688;G|0.312	0.312	strong		0.468	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
SPTB	6710	hgsc.bcm.edu	37	14	65246623	65246623	+	Silent	SNP	T	T	C	rs1626923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:65246623T>C	ENST00000389721.5	-	20	4325	c.4293A>G	c.(4291-4293)cgA>cgG	p.R1431R	SPTB_ENST00000556626.1_Silent_p.R1431R|SPTB_ENST00000389722.3_Silent_p.R1431R|SPTB_ENST00000542895.1_Silent_p.R1431R|SPTB_ENST00000389720.3_Silent_p.R1431R	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1431					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GCTCCTCTTTTCGCACATTCA	0.582													C|||	2229	0.445088	0.7057	0.2176	5008	,	,		21086	0.377		0.326	False		,,,				2504	0.4468				p.R1431R		Atlas-SNP	.											SPTB_ENST00000542895,NS,malignant_melanoma,-1,6	SPTB	378	6	0			c.A4293G						PASS	.	C	,	2747,1659	505.9+/-366.3	858,1031,314	112.0	109.0	110.0		4293,4293	1.2	1.0	14	dbSNP_89	110	2762,5838	677.8+/-403.4	453,1856,1991	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1311,2887,2305	CC,CT,TT		32.1163,37.6532,42.3574	,	1431/2138,1431/2329	65246623	5509,7497	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon20			CTCTTTTCGCACA		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4293A>G	14.37:g.65246623T>C		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			T|0.575;C|0.425	0.425	strong		0.582	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
CD48	962	hgsc.bcm.edu	37	1	160681508	160681508	+	Silent	SNP	G	G	A	rs11541827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160681508G>A	ENST00000368046.3	-	1	133	c.46C>T	c.(46-48)Ctg>Ttg	p.L16L	CD48_ENST00000368045.3_Silent_p.L16L	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	16					blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			AGAGGCAGCAGTAGCAATTCC	0.522													G|||	92	0.0183706	0.0	0.0072	5008	,	,		17698	0.0119		0.0139	False		,,,				2504	0.0624				p.L16L		Atlas-SNP	.											.	CD48	31	.	0			c.C46T						PASS	.	G		16,4390	23.3+/-48.9	0,16,2187	116.0	93.0	101.0		46	1.3	0.0	1	dbSNP_120	101	186,8414	84.0+/-146.5	2,182,4116	no	coding-synonymous	CD48	NM_001778.2		2,198,6303	AA,AG,GG		2.1628,0.3631,1.5531		16/244	160681508	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	962	exon1			GCAGCAGTAGCAA	BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1683	protein-coding gene	gene with protein product		109530	"""CD48 antigen (B-cell membrane protein)"", ""CD48 molecule """	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.46C>T	1.37:g.160681508G>A		Somatic	363	0	0		WXS	Illumina HiSeq	Phase_I	326	166	0.509202	NM_001256030	Q5U055|Q8MGR0	Silent	SNP	ENST00000368046.3	37	CCDS1208.1																																																																																			G|0.986;A|0.014	0.014	strong		0.522	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778	
VWA8	23078	hgsc.bcm.edu	37	13	42385446	42385446	+	Missense_Mutation	SNP	T	T	C	rs9562353	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42385446T>C	ENST00000379310.3	-	17	2046	c.1978A>G	c.(1978-1980)Aga>Gga	p.R660G	VWA8_ENST00000281496.6_Missense_Mutation_p.R660G	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	660			R -> G (in dbSNP:rs9562353).			extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										AACAGTTGTCTGGTAGAAAGT	0.388													T|||	365	0.0728834	0.0877	0.0476	5008	,	,		7178	0.1349		0.0358	False		,,,				2504	0.045				p.R660G		Atlas-SNP	.											KIAA0564,lymph_node,lymphoid_neoplasm,0,1	.	.	1	0			c.A1978G						PASS	.	T	GLY/ARG,GLY/ARG	508,3898	233.9+/-246.9	28,452,1723	125.0	127.0	126.0		1978,1978	3.1	1.0	13	dbSNP_119	126	367,8233	122.7+/-181.7	11,345,3944	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	125,125	39,797,5667	CC,CT,TT		4.2674,11.5297,6.7277	probably-damaging,probably-damaging	660/1040,660/1906	42385446	875,12131	2203	4300	6503	SO:0001583	missense	23078	exon17			GTTGTCTGGTAGA	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.1978A>G	13.37:g.42385446T>C	ENSP00000368612:p.Arg660Gly	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	148	0.06776556776556776	43	0.08739837398373984	16	0.04419889502762431	64	0.11188811188811189	25	0.032981530343007916	T	15.34	2.805700	0.50315	0.115297	0.042674	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.66995	-0.24;-0.24	5.27	3.08	0.35506	.	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54503	-0.8284	10	0.87932	D	0	.	12.9555	0.58425	0.0:0.0:0.4004:0.5996	rs9562353;rs52800556;rs9562353	660	A3KMH1	K0564_HUMAN	G	564;660;660	ENSP00000368612:R660G;ENSP00000281496:R660G	ENSP00000251030:R564G	R	-	1	2	KIAA0564	41283446	0.999000	0.42202	1.000000	0.80357	0.501000	0.33797	1.280000	0.33202	0.898000	0.36418	0.477000	0.44152	AGA	T|0.931;C|0.069	0.069	strong		0.388	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
OTOP1	133060	hgsc.bcm.edu	37	4	4199083	4199083	+	Missense_Mutation	SNP	T	T	G	rs34666677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:4199083T>G	ENST00000296358.4	-	5	1502	c.1478A>C	c.(1477-1479)aAg>aCg	p.K493T		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	493			K -> T (in dbSNP:rs34666677).		biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TGGCATGTCCTTGCCCTGGGG	0.592													t|||	304	0.0607029	0.0113	0.0591	5008	,	,		15180	0.0298		0.1093	False		,,,				2504	0.1104				p.K493T		Atlas-SNP	.											.	OTOP1	118	.	0			c.A1478C						PASS	.	T	THR/LYS	140,4266	90.6+/-129.3	2,136,2065	51.0	54.0	53.0		1478	-0.2	0.0	4	dbSNP_126	53	951,7649	193.7+/-239.3	68,815,3417	yes	missense	OTOP1	NM_177998.1	78	70,951,5482	GG,GT,TT		11.0581,3.1775,8.3884	benign	493/613	4199083	1091,11915	2203	4300	6503	SO:0001583	missense	133060	exon5			ATGTCCTTGCCCT	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1478A>C	4.37:g.4199083T>G	ENSP00000296358:p.Lys493Thr	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	201	199	0.99005	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	128	0.05860805860805861	8	0.016260162601626018	21	0.058011049723756904	18	0.03146853146853147	81	0.10686015831134564	t	4.779	0.144914	0.09134	0.031775	0.110581	ENSG00000163982	ENST00000296358	T	0.08458	3.09	4.92	-0.201	0.13212	.	2.641920	0.01146	N	0.006318	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	B	0.21071	0.051	B	0.16722	0.016	T	0.36456	-0.9747	10	0.13470	T	0.59	-0.0401	3.7221	0.08460	0.2674:0.4424:0.0:0.2903	rs34666677	493	Q7RTM1	OTOP1_HUMAN	T	493	ENSP00000296358:K493T	ENSP00000296358:K493T	K	-	2	0	OTOP1	4249984	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.700000	0.25601	-0.303000	0.08856	-0.308000	0.09152	AAG	T|0.925;G|0.075	0.075	strong		0.592	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
OR11H6	122748	hgsc.bcm.edu	37	14	20691888	20691888	+	Missense_Mutation	SNP	C	C	A	rs10140652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20691888C>A	ENST00000315519.2	+	1	98	c.20C>A	c.(19-21)tCt>tAt	p.S7Y		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	7			S -> Y (in dbSNP:rs10140652).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		attattCATTCTTTGGTTACT	0.373													c|||	498	0.0994409	0.121	0.049	5008	,	,		21282	0.0903		0.0815	False		,,,				2504	0.1339				p.S7Y		Atlas-SNP	.											.	OR11H6	60	.	0			c.C20A						PASS	.	C	TYR/SER	427,3979	198.7+/-222.5	18,391,1794	70.0	75.0	73.0		20	-4.8	0.0	14	dbSNP_119	73	620,7980	153.0+/-207.5	34,552,3714	yes	missense	OR11H6	NM_001004480.1	144	52,943,5508	AA,AC,CC		7.2093,9.6913,8.0501	benign	7/331	20691888	1047,11959	2203	4300	6503	SO:0001583	missense	122748	exon1			TTCATTCTTTGGT		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.20C>A	14.37:g.20691888C>A	ENSP00000319071:p.Ser7Tyr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	204	0.09340659340659341	72	0.14634146341463414	17	0.04696132596685083	53	0.09265734265734266	62	0.08179419525065963	c	8.427	0.847651	0.17034	0.096913	0.072093	ENSG00000176219	ENST00000315519	T	0.00554	6.64	4.53	-4.82	0.03171	.	2.033520	0.02979	U	0.145446	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.20671	0.047	B	0.16289	0.015	T	0.39461	-0.9613	9	0.38643	T	0.18	.	7.818	0.29271	0.0:0.2525:0.129:0.6185	rs10140652;rs52838202;rs58829059;rs10140652	7	Q8NGC7	O11H6_HUMAN	Y	7	ENSP00000319071:S7Y	ENSP00000319071:S7Y	S	+	2	0	OR11H6	19761728	0.000000	0.05858	0.001000	0.08648	0.129000	0.20672	-1.346000	0.02634	-0.847000	0.04168	-0.417000	0.06048	TCT	C|0.909;A|0.091	0.091	strong		0.373	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
ZNF83	55769	hgsc.bcm.edu	37	19	53116939	53116939	+	Silent	SNP	C	C	T	rs78207921	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53116939C>T	ENST00000597597.1	-	2	3132	c.879G>A	c.(877-879)gaG>gaA	p.E293E	ZNF83_ENST00000391789.4_Intron|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Silent_p.E293E|ZNF83_ENST00000301096.3_Silent_p.E293E|ZNF83_ENST00000544146.1_Silent_p.E293E|ZNF83_ENST00000545872.1_Silent_p.E293E|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Silent_p.E293E			P51522	ZNF83_HUMAN	zinc finger protein 83	293					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		CCTTGCCACACTCATTACATT	0.403													C|||	1367	0.272963	0.1634	0.4294	5008	,	,		2257	0.499		0.2137	False		,,,				2504	0.138				p.E293E		Atlas-SNP	.											.	ZNF83	73	.	0			c.G879A						PASS	.						84.0	84.0	84.0					19																	53116939		2201	4300	6501	SO:0001819	synonymous_variant	55769	exon3			GCCACACTCATTA	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.879G>A	19.37:g.53116939C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	65	22	0.338462	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	37	CCDS12854.1																																																																																			.	.	weak		0.403	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
SIK1	150094	hgsc.bcm.edu	37	21	44839263	44839263	+	Missense_Mutation	SNP	C	C	T	rs34987632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44839263C>T	ENST00000270162.6	-	10	1347	c.1215G>A	c.(1213-1215)atG>atA	p.M405I		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	405					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	GCTCACAGTCCATCTCGGCCT	0.682													C|||	7	0.00139776	0.0	0.0029	5008	,	,		16988	0.0		0.003	False		,,,				2504	0.002				p.M405I		Atlas-SNP	.											.	SIK1	65	.	0			c.G1215A						PASS	.	C	ILE/MET	8,4394	15.5+/-35.6	0,8,2193	40.0	42.0	41.0		1215	4.3	1.0	21	dbSNP_126	41	60,8540	36.9+/-92.0	0,60,4240	yes	missense	SIK1	NM_173354.3	10	0,68,6433	TT,TC,CC		0.6977,0.1817,0.523	benign	405/784	44839263	68,12934	2201	4300	6501	SO:0001583	missense	150094	exon10			ACAGTCCATCTCG	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1215G>A	21.37:g.44839263C>T	ENSP00000270162:p.Met405Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	11.67	1.707255	0.30322	0.001817	0.006977	ENSG00000142178	ENST00000270162	T	0.71222	-0.55	5.16	4.26	0.50523	.	0.469281	0.25310	N	0.031582	T	0.50531	0.1621	L	0.38838	1.175	0.29858	N	0.827879	B	0.06786	0.001	B	0.04013	0.001	T	0.52682	-0.8543	10	0.36615	T	0.2	.	10.2121	0.43147	0.0:0.9064:0.0:0.0936	rs34987632	405	P57059	SIK1_HUMAN	I	405	ENSP00000270162:M405I	ENSP00000270162:M405I	M	-	3	0	SIK1	43663691	1.000000	0.71417	0.970000	0.41538	0.589000	0.36550	2.583000	0.46094	1.140000	0.42260	0.561000	0.74099	ATG	C|0.996;T|0.004	0.004	strong		0.682	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
MTNR1A	4543	hgsc.bcm.edu	37	4	187454972	187454972	+	Silent	SNP	T	T	C	rs8192550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187454972T>C	ENST00000307161.5	-	2	1125	c.924A>G	c.(922-924)agA>agG	p.R308R	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	308					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	AGACTATAATTCTCCTGTATT	0.468													T|||	155	0.0309505	0.0008	0.0274	5008	,	,		20615	0.0675		0.0398	False		,,,				2504	0.0276				p.R308R		Atlas-SNP	.											.	MTNR1A	46	.	0			c.A924G						PASS	.	T		46,4360	48.9+/-83.8	0,46,2157	128.0	130.0	129.0		924	-5.6	0.0	4	dbSNP_117	129	375,8225	123.6+/-182.4	15,345,3940	no	coding-synonymous	MTNR1A	NM_005958.3		15,391,6097	CC,CT,TT		4.3605,1.044,3.237		308/351	187454972	421,12585	2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			TATAATTCTCCTG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.924A>G	4.37:g.187454972T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	182	86	0.472527	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	37	CCDS3848.1																																																																																			T|0.964;C|0.036	0.036	strong		0.468	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
OR4K14	122740	hgsc.bcm.edu	37	14	20482919	20482919	+	Missense_Mutation	SNP	A	A	C	rs17308108	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20482919A>C	ENST00000305045.2	-	1	433	c.434T>G	c.(433-435)cTg>cGg	p.L145R		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	145			L -> R (in dbSNP:rs17308108).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		AGCCAGCACCAGCCTGATGCA	0.488													A|||	465	0.0928514	0.0461	0.0836	5008	,	,		22273	0.1647		0.0686	False		,,,				2504	0.1135				p.L145R		Atlas-SNP	.											.	OR4K14	86	.	0			c.T434G						PASS	.	A	ARG/LEU	242,4164		4,234,1965	74.0	73.0	73.0		434	4.0	0.2	14	dbSNP_123	73	652,7948		28,596,3676	yes	missense	OR4K14	NM_001004712.1	102	32,830,5641	CC,CA,AA		7.5814,5.4925,6.8738	probably-damaging	145/311	20482919	894,12112	2203	4300	6503	SO:0001583	missense	122740	exon1			AGCACCAGCCTGA		CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"""GPCR / Class A : Olfactory receptors"""	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.434T>G	14.37:g.20482919A>C	ENSP00000305011:p.Leu145Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_001004712	Q6IEU1|Q96R71	Missense_Mutation	SNP	ENST00000305045.2	37	CCDS32027.1	199	0.09111721611721611	26	0.052845528455284556	32	0.08839779005524862	85	0.1486013986013986	56	0.07387862796833773	.	12.44	1.937602	0.34189	0.054925	0.075814	ENSG00000169484	ENST00000305045	T	0.44881	0.91	4.04	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.270951	0.20350	N	0.094073	T	0.00998	0.0033	H	0.97186	3.955	0.45762	P	0.0013480000000000159	D	0.64830	0.994	D	0.71414	0.973	T	0.55798	-0.8084	9	0.87932	D	0	.	12.097	0.53761	1.0:0.0:0.0:0.0	rs17308108;rs52813083;rs17308108	145	Q8NGD5	OR4KE_HUMAN	R	145	ENSP00000305011:L145R	ENSP00000305011:L145R	L	-	2	0	OR4K14	19552759	0.783000	0.28701	0.198000	0.23420	0.111000	0.19643	5.417000	0.66423	1.695000	0.51148	0.413000	0.27773	CTG	A|0.922;C|0.078	0.078	strong		0.488	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1		
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679268	37679268	+	Missense_Mutation	SNP	G	G	T	rs9576175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	53	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	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	
PLCG2	5336	hgsc.bcm.edu	37	16	81819768	81819768	+	Silent	SNP	T	T	C	rs1143685	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:81819768T>C	ENST00000359376.3	+	2	388	c.174T>C	c.(172-174)gcT>gcC	p.A58A		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	58	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						GCAAGACCGCTGACAAGATCG	0.632													T|||	3672	0.733227	0.6422	0.7277	5008	,	,		16454	0.8591		0.6859	False		,,,				2504	0.7791				p.A58A		Atlas-SNP	.											PLCG2_ENST00000359376,NS,carcinoma,+2,2	PLCG2	276	2	0			c.T174C						PASS	.	T		2627,1547		840,947,300	39.0	47.0	44.0		174	-6.6	0.8	16	dbSNP_111	44	5775,2629		1991,1793,418	no	coding-synonymous	PLCG2	NM_002661.3		2831,2740,718	CC,CT,TT		31.2827,37.0628,33.2008		58/1266	81819768	8402,4176	2087	4202	6289	SO:0001819	synonymous_variant	5336	exon2			GACCGCTGACAAG		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.174T>C	16.37:g.81819768T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			T|0.273;C|0.727	0.727	strong		0.632	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
MACC1	346389	hgsc.bcm.edu	37	7	20180717	20180717	+	Missense_Mutation	SNP	C	C	G	rs3735615	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20180717C>G	ENST00000400331.5	-	7	2719	c.2411G>C	c.(2410-2412)aGa>aCa	p.R804T	MACC1_ENST00000332878.4_Missense_Mutation_p.R804T|MACC1-AS1_ENST00000439285.1_RNA|MACC1_ENST00000589011.1_Missense_Mutation_p.R804T	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	804			R -> T (in dbSNP:rs3735615). {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						TAACACATCTCTGTAGTTATT	0.358													C|||	3022	0.603435	0.3911	0.5764	5008	,	,		16212	0.8194		0.5815	False		,,,				2504	0.7096				p.R804T		Atlas-SNP	.											MACC1,tonsil,carcinoma,0,1	MACC1	99	1	0			c.G2411C						PASS	.	C	THR/ARG	1811,2595	524.4+/-371.3	380,1051,772	83.0	85.0	85.0		2411	4.9	1.0	7	dbSNP_107	85	5002,3598	624.7+/-397.6	1471,2060,769	yes	missense	MACC1	NM_182762.3	71	1851,3111,1541	GG,GC,CC		41.8372,41.103,47.6165	probably-damaging	804/853	20180717	6813,6193	2203	4300	6503	SO:0001583	missense	346389	exon7			ACATCTCTGTAGT		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.2411G>C	7.37:g.20180717C>G	ENSP00000383185:p.Arg804Thr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	1366	0.6254578754578755	224	0.45528455284552843	219	0.6049723756906077	482	0.8426573426573427	441	0.5817941952506597	C	20.4	3.983394	0.74474	0.41103	0.581628	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.37752	1.18;1.18	5.74	4.87	0.63330	.	0.130847	0.64402	D	0.000002	T	0.00012	0.0000	M	0.81497	2.545	0.21184	P	0.999767261	D	0.76494	0.999	D	0.64144	0.922	T	0.07790	-1.0754	9	0.66056	D	0.02	-15.5312	14.8695	0.70444	0.0:0.9311:0.0:0.0689	rs3735615;rs52825803;rs3735615	804	Q6ZN28	MACC1_HUMAN	T	804	ENSP00000383185:R804T;ENSP00000328410:R804T	ENSP00000328410:R804T	R	-	2	0	MACC1	20147242	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	3.200000	0.51051	1.426000	0.47256	0.655000	0.94253	AGA	C|0.430;G|0.570	0.570	strong		0.358	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762	
INHA	3623	hgsc.bcm.edu	37	2	220439916	220439916	+	Missense_Mutation	SNP	G	G	A	rs12720062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220439916G>A	ENST00000243786.2	+	2	949	c.769G>A	c.(769-771)Gct>Act	p.A257T		NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	257			A -> T (either a rare polymorphism or may play a role in premature ovarian failure; dbSNP:rs12720062). {ECO:0000269|PubMed:11098038}.		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)		GGAGGAACCGGCTGCCCATGC	0.617													G|||	75	0.014976	0.0015	0.0115	5008	,	,		20641	0.0		0.0149	False		,,,				2504	0.0511				p.A257T		Atlas-SNP	.											.	INHA	30	.	0			c.G769A	GRCh37	CM004796	INHA	M	rs12720062	PASS	.	G	THR/ALA	20,4386	28.1+/-56.4	0,20,2183	92.0	94.0	93.0		769	-2.1	0.0	2	dbSNP_121	93	216,8384	91.9+/-153.9	3,210,4087	yes	missense	INHA	NM_002191.3	58	3,230,6270	AA,AG,GG		2.5116,0.4539,1.8145	possibly-damaging	257/367	220439916	236,12770	2203	4300	6503	SO:0001583	missense	3623	exon2			GAACCGGCTGCCC		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.769G>A	2.37:g.220439916G>A	ENSP00000243786:p.Ala257Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	173	80	0.462428	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	20	0.009157509157509158	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	11	0.014511873350923483	G	9.248	1.039895	0.19669	0.004539	0.025116	ENSG00000123999	ENST00000243786	D	0.89196	-2.48	5.47	-2.11	0.07187	Transforming growth factor-beta, C-terminal (1);	0.533866	0.19261	N	0.118676	T	0.72128	0.3422	M	0.83953	2.67	0.09310	N	1	P	0.39940	0.696	B	0.40702	0.338	T	0.73924	-0.3829	9	.	.	.	0.4131	4.7307	0.12962	0.3167:0.0:0.4619:0.2214	rs12720062	257	P05111	INHA_HUMAN	T	257	ENSP00000243786:A257T	.	A	+	1	0	INHA	220148160	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	0.078000	0.14761	-0.525000	0.06391	0.555000	0.69702	GCT	G|0.983;A|0.017	0.017	strong		0.617	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1		
OR51F1	256892	hgsc.bcm.edu	37	11	4790881	4790881	+	Silent	SNP	A	A	G	rs111736749	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790881A>G	ENST00000380383.1	-	1	287	c.288T>C	c.(286-288)ttT>ttC	p.F96F	OR51F1_ENST00000343430.3_Silent_p.F89F|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	96						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)		CACGTGCCTCAAACCAGAGGA	0.428													A|||	301	0.0601038	0.0537	0.0749	5008	,	,		22910	0.0		0.1272	False		,,,				2504	0.0511				p.F89F		Atlas-SNP	.											OR51F1,NS,carcinoma,-2,1	OR51F1	60	1	0			c.T267C						PASS	.	A		316,4086	167.3+/-198.3	15,286,1900	76.0	73.0	74.0		267	4.9	0.9	11	dbSNP_132	74	997,7599	213.4+/-253.3	72,853,3373	no	coding-synonymous	OR51F1	NM_001004752.1		87,1139,5273	GG,GA,AA		11.5984,7.1786,10.1016		89/313	4790881	1313,11685	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			TGCCTCAAACCAG	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.288T>C	11.37:g.4790881A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.903;G|0.097	0.097	strong		0.428	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
PTK2B	2185	hgsc.bcm.edu	37	8	27277537	27277537	+	Silent	SNP	G	G	A	rs1030526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:27277537G>A	ENST00000397501.1	+	8	1138	c.330G>A	c.(328-330)acG>acA	p.T110T	PTK2B_ENST00000346049.5_Silent_p.T110T|PTK2B_ENST00000517339.1_Silent_p.T110T|PTK2B_ENST00000544172.1_Silent_p.T110T|PTK2B_ENST00000338238.4_Silent_p.T110T|PTK2B_ENST00000420218.2_Silent_p.T110T	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	110	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|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 cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	CACAGATGACGGTGGGTGAGG	0.582													G|||	1936	0.386581	0.4228	0.2738	5008	,	,		19922	0.2718		0.4076	False		,,,				2504	0.5143				p.T110T		Atlas-SNP	.											.	PTK2B	304	.	0			c.G330A						PASS	.	G	,,,	1867,2539	540.1+/-375.4	400,1067,736	100.0	84.0	90.0		330,330,330,330	-10.3	0.2	8	dbSNP_86	90	3484,5116	508.9+/-377.2	727,2030,1543	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	1127,3097,2279	AA,AG,GG		40.5116,42.374,41.1425	,,,	110/1010,110/1010,110/968,110/1010	27277537	5351,7655	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon8			GATGACGGTGGGT	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.330G>A	8.37:g.27277537G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	181	94	0.519337	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			G|0.621;A|0.379	0.379	strong		0.582	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
ZNF845	91664	hgsc.bcm.edu	37	19	53856730	53856730	+	Silent	SNP	G	G	A	rs201351032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53856730G>A	ENST00000595091.1	+	5	3021	c.2802G>A	c.(2800-2802)aaG>aaA	p.K934K	ZNF845_ENST00000458035.1_Silent_p.K934K			Q96IR2	ZN845_HUMAN	zinc finger protein 845	934					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K934K(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TAATTCATAAGACAATTCATA	0.368													.|||	271	0.0541134	0.0507	0.0576	5008	,	,		22260	0.0456		0.0924	False		,,,				2504	0.0256				p.K934K		Atlas-SNP	.											ZNF845,NS,carcinoma,0,5	ZNF845	101	5	3	Substitution - coding silent(3)	kidney(3)	c.G2802A						scavenged	.																																			SO:0001819	synonymous_variant	91664	exon4			TCATAAGACAATT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2802G>A	19.37:g.53856730G>A		Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	132	13	0.0984849	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			.	.	weak		0.368	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
TC2N	123036	hgsc.bcm.edu	37	14	92251587	92251587	+	Silent	SNP	A	A	G	rs61990064	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:92251587A>G	ENST00000435962.2	-	11	1604	c.1281T>C	c.(1279-1281)ctT>ctC	p.L427L	TC2N_ENST00000556018.1_Silent_p.L363L|TC2N_ENST00000340892.5_Silent_p.L427L|TC2N_ENST00000360594.5_Silent_p.L427L	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	427	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		CACTCTGTATAAGTGGAAAAA	0.383													A|||	557	0.111222	0.0582	0.121	5008	,	,		14404	0.1151		0.173	False		,,,				2504	0.1084				p.L427L		Atlas-SNP	.											TC2N,NS,adenoma,0,2	TC2N	49	2	0			c.T1281C						PASS	.	A	,,	307,4099	165.4+/-196.9	9,289,1905	167.0	182.0	177.0		1281,1281,1281	-3.5	0.4	14	dbSNP_129	177	1436,7164	274.9+/-291.5	119,1198,2983	no	coding-synonymous,coding-synonymous,coding-synonymous	TC2N	NM_001128595.1,NM_001128596.1,NM_152332.4	,,	128,1487,4888	GG,GA,AA		16.6977,6.9678,13.4015	,,	427/491,427/491,427/491	92251587	1743,11263	2203	4300	6503	SO:0001819	synonymous_variant	123036	exon11			CTGTATAAGTGGA	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"""C2 calcium-dependent domain containing 1"""		"""chromosome 14 open reading frame 47"", ""membrane targeting (tandem) C2 domain containing 1"""	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.1281T>C	14.37:g.92251587A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	19	0.287879	NM_001128596		Silent	SNP	ENST00000435962.2	37	CCDS9897.1																																																																																			A|0.864;G|0.136	0.136	strong		0.383	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332	
GPR123	84435	hgsc.bcm.edu	37	10	134942166	134942166	+	Silent	SNP	A	A	G	rs2806452	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	78	0	0		WXS	Illumina HiSeq	Phase_I	53	53	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		
KRT6C	286887	hgsc.bcm.edu	37	12	52866060	52866060	+	Missense_Mutation	SNP	C	C	T	rs11608915	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	134	0	0		WXS	Illumina HiSeq	Phase_I	267	123	0.460674	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	
IL6R	3570	hgsc.bcm.edu	37	1	154401679	154401679	+	Silent	SNP	G	G	A	rs2228144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154401679G>A	ENST00000368485.3	+	2	530	c.93G>A	c.(91-93)gcG>gcA	p.A31A	IL6R_ENST00000344086.4_Silent_p.A31A	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	31	Ig-like C2-type.				acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	CAGAGGTGGCGAGAGGCGTGC	0.607													G|||	590	0.117812	0.0484	0.1023	5008	,	,		18314	0.1042		0.1789	False		,,,				2504	0.1738				p.A31A		Atlas-SNP	.											.	IL6R	47	.	0			c.G93A						PASS	.	G	,,	288,4118	158.5+/-191.2	6,276,1921	73.0	74.0	74.0		93,93,93	-9.7	0.0	1	dbSNP_117	74	1399,7201	267.1+/-287.1	135,1129,3036	no	coding-synonymous,coding-synonymous,coding-synonymous	IL6R	NM_000565.3,NM_001206866.1,NM_181359.2	,,	141,1405,4957	AA,AG,GG		16.2674,6.5365,12.9709	,,	31/469,31/353,31/366	154401679	1687,11319	2203	4300	6503	SO:0001819	synonymous_variant	3570	exon2			GGTGGCGAGAGGC	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.93G>A	1.37:g.154401679G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Silent	SNP	ENST00000368485.3	37	CCDS1067.1																																																																																			G|0.876;A|0.124	0.124	strong		0.607	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565	
ARMS2	387715	hgsc.bcm.edu	37	10	124214251	124214251	+	Missense_Mutation	SNP	G	G	A	rs10490923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:124214251G>A	ENST00000528446.1	+	1	83	c.8G>A	c.(7-9)cGc>cAc	p.R3H		NM_001099667.1	NP_001093137.1	P0C7Q2	ARMS2_HUMAN	age-related maculopathy susceptibility 2	3			R -> H (in dbSNP:rs10490923).		retina homeostasis (GO:0001895)	mitochondrion (GO:0005739)|photoreceptor inner segment (GO:0001917)				ovary(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TACATGCTGCGCCTATACCCA	0.562													G|||	376	0.0750799	0.0272	0.0749	5008	,	,		19034	0.0119		0.1302	False		,,,				2504	0.1483				p.R3H		Atlas-SNP	.											ARMS2_ENST00000528446,caecum,carcinoma,0,2	ARMS2	7	2	0			c.G8A						PASS	.	G	HIS/ARG	148,3996		4,140,1928	88.0	93.0	91.0		8	-0.7	0.0	10	dbSNP_119	91	1091,7319		73,945,3187	yes	missense	ARMS2	NM_001099667.1	29	77,1085,5115	AA,AG,GG		12.9727,3.5714,9.8694	benign	3/108	124214251	1239,11315	2072	4205	6277	SO:0001583	missense	387715	exon1			TGCTGCGCCTATA	BC066349	CCDS53585.1	10q26.13	2013-01-23			ENSG00000254636	ENSG00000254636			32685	protein-coding gene	gene with protein product		611313				16080115, 16174643	Standard	NM_001099667		Approved	LOC387715, ARMD8	uc001lgi.3	P0C7Q2	OTTHUMG00000048232	ENST00000528446.1:c.8G>A	10.37:g.124214251G>A	ENSP00000436682:p.Arg3His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_001099667	B2Y7I5	Missense_Mutation	SNP	ENST00000528446.1	37	CCDS53585.1	159	0.07280219780219781	12	0.024390243902439025	38	0.10497237569060773	6	0.01048951048951049	103	0.1358839050131926	G	2.548	-0.304798	0.05495	0.035714	0.129727	ENSG00000254636	ENST00000528446	T	0.40225	1.04	1.78	-0.729	0.11158	.	.	.	.	.	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	0.27191	-1.0081	8	0.16420	T	0.52	.	4.4187	0.11470	0.6256:0.0:0.3744:0.0	rs10490923;rs52837685;rs10490923	3	P0C7Q2	ARMS2_HUMAN	H	3	ENSP00000436682:R3H	ENSP00000436682:R3H	R	+	2	0	ARMS2	124204241	0.000000	0.05858	0.003000	0.11579	0.008000	0.06430	-0.547000	0.06055	-0.202000	0.10268	-0.295000	0.09555	CGC	G|0.919;A|0.081	0.081	strong		0.562	ARMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109727.2		
FAT2	2196	hgsc.bcm.edu	37	5	150905398	150905398	+	Silent	SNP	C	C	T	rs3734051	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150905398C>T	ENST00000261800.5	-	17	10449	c.10437G>A	c.(10435-10437)ccG>ccA	p.P3479P		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3479	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCCATCCATCCGGGGTCACTC	0.577													C|||	872	0.174121	0.2005	0.196	5008	,	,		19464	0.1319		0.2624	False		,,,				2504	0.0757				p.P3479P		Atlas-SNP	.											FAT2,colon,carcinoma,-1,2	FAT2	465	2	0			c.G10437A						PASS	.	C		900,3506	345.7+/-308.6	90,720,1393	81.0	74.0	76.0		10437	-4.5	1.0	5	dbSNP_107	76	2263,6337	383.8+/-340.9	313,1637,2350	no	coding-synonymous	FAT2	NM_001447.2		403,2357,3743	TT,TC,CC		26.314,20.4267,24.3195		3479/4350	150905398	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon17			TCCATCCGGGGTC	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.10437G>A	5.37:g.150905398C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	477	0.2184065934065934	115	0.23373983739837398	82	0.2265193370165746	87	0.1520979020979021	193	0.2546174142480211	C	9.298	1.052233	0.19827	0.204267	0.26314	ENSG00000086570	ENST00000520200	.	.	.	5.11	-4.53	0.03462	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998391	.	.	.	.	.	.	T	0.38950	-0.9637	3	.	.	.	.	4.0147	0.09639	0.3573:0.2731:0.0:0.3695	rs3734051;rs17404132;rs56590107;rs60495232;rs3734051	.	.	.	R	338	.	.	G	-	1	0	FAT2	150885591	0.296000	0.24398	0.993000	0.49108	0.831000	0.47069	-0.350000	0.07721	-0.238000	0.09724	-1.028000	0.02416	GGA	C|0.776;N|0.000	.	strong		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
ZNFX1	57169	hgsc.bcm.edu	37	20	47874005	47874005	+	Silent	SNP	A	A	G	rs3021	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	185	0	0		WXS	Illumina HiSeq	Phase_I	189	73	0.386243	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	
CNTN6	27255	hgsc.bcm.edu	37	3	1262474	1262474	+	Silent	SNP	T	T	C	rs2013828	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:1262474T>C	ENST00000446702.2	+	3	786	c.159T>C	c.(157-159)aaT>aaC	p.N53N	CNTN6_ENST00000539053.1_5'UTR|CNTN6_ENST00000350110.2_Silent_p.N53N			Q9UQ52	CNTN6_HUMAN	contactin 6	53	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GTGCTGCTAATGGTTACCCTT	0.383													C|||	2354	0.470048	0.466	0.4813	5008	,	,		15116	0.5119		0.3419	False		,,,				2504	0.5562				p.N53N		Atlas-SNP	.											.	CNTN6	245	.	0			c.T159C						PASS	.	C		1938,2468	623.5+/-394.1	418,1102,683	156.0	147.0	150.0		159	-6.6	0.0	3	dbSNP_92	150	3024,5576	663.4+/-402.1	552,1920,1828	no	coding-synonymous	CNTN6	NM_014461.2		970,3022,2511	CC,CT,TT		35.1628,43.9855,38.1516		53/1029	1262474	4962,8044	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon3			TGCTAATGGTTAC	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.159T>C	3.37:g.1262474T>C		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	199	98	0.492462	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			T|0.584;C|0.416	0.416	strong		0.383	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
ZNF57	126295	hgsc.bcm.edu	37	19	2917842	2917842	+	Missense_Mutation	SNP	G	G	A	rs149690257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917842G>A	ENST00000306908.5	+	4	1371	c.1223G>A	c.(1222-1224)cGa>cAa	p.R408Q	ZNF57_ENST00000523428.1_Missense_Mutation_p.R376Q|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	408					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		AGATCATTCCGAGGTCATTTG	0.428													G|||	2	0.000399361	0.0	0.0	5008	,	,		22693	0.0		0.0	False		,,,				2504	0.002				p.R408Q	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											ZNF57,NS,carcinoma,0,3	ZNF57	57	3	0			c.G1223A						scavenged	.						95.0	86.0	89.0					19																	2917842		2203	4300	6503	SO:0001583	missense	126295	exon4			CATTCCGAGGTCA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.1223G>A	19.37:g.2917842G>A	ENSP00000303696:p.Arg408Gln	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	152	4	0.0263158	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	G	2.637	-0.285137	0.05605	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.04275	3.66;3.66	2.25	-4.5	0.03493	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01976	0.0062	N	0.05050	-0.12	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47368	-0.9123	9	0.20046	T	0.44	.	5.4761	0.16695	0.2484:0.0:0.5675:0.1841	.	408	Q68EA5	ZNF57_HUMAN	Q	408;410;376	ENSP00000303696:R408Q;ENSP00000430223:R376Q	ENSP00000303696:R408Q	R	+	2	0	ZNF57	2868842	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.935000	0.01550	-1.296000	0.02353	-0.514000	0.04452	CGA	.	.	weak		0.428	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
C3orf20	84077	hgsc.bcm.edu	37	3	14755572	14755572	+	Missense_Mutation	SNP	A	A	G	rs6765537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:14755572A>G	ENST00000253697.3	+	8	1671	c.1219A>G	c.(1219-1221)Atc>Gtc	p.I407V	C3orf20_ENST00000412910.1_Missense_Mutation_p.I285V|C3orf20_ENST00000495387.1_3'UTR|C3orf20_ENST00000435614.1_Missense_Mutation_p.I285V	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	407			I -> V (in dbSNP:rs6765537). {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						AGGGAGAACCATCACCTGCCT	0.483													A|||	1894	0.378195	0.4244	0.4524	5008	,	,		20247	0.3244		0.4155	False		,,,				2504	0.2802				p.I407V		Atlas-SNP	.											.	C3orf20	109	.	0			c.A1219G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	1899,2507	544.6+/-376.6	426,1047,730	120.0	108.0	112.0		853,853,1219	4.4	1.0	3	dbSNP_116	112	3639,4961	525.2+/-380.7	776,2087,1437	yes	missense,missense,missense	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	29,29,29	1202,3134,2167	GG,GA,AA		42.314,43.1003,42.5803	possibly-damaging,possibly-damaging,possibly-damaging	285/783,285/783,407/905	14755572	5538,7468	2203	4300	6503	SO:0001583	missense	84077	exon8			AGAACCATCACCT	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.1219A>G	3.37:g.14755572A>G	ENSP00000253697:p.Ile407Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	159	67	0.421384	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	888	0.4065934065934066	231	0.4695121951219512	155	0.4281767955801105	186	0.32517482517482516	316	0.41688654353562005	A	16.44	3.123451	0.56613	0.431003	0.42314	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	T;T;T	0.11821	2.74;2.74;2.74	5.56	4.41	0.53225	.	0.123786	0.36740	N	0.002433	T	0.00012	0.0000	M	0.68317	2.08	0.39104	P	0.03865099999999999	P	0.35507	0.506	B	0.36464	0.225	T	0.46775	-0.9167	9	0.24483	T	0.36	-25.0529	8.2326	0.31608	0.9099:0.0:0.0901:0.0	rs6765537;rs17856868;rs59250263;rs6765537	407	Q8ND61	CC020_HUMAN	V	407;285;285	ENSP00000253697:I407V;ENSP00000402933:I285V;ENSP00000396081:I285V	ENSP00000253697:I407V	I	+	1	0	C3orf20	14730576	0.962000	0.33011	0.988000	0.46212	0.726000	0.41606	2.190000	0.42630	0.942000	0.37525	0.482000	0.46254	ATC	A|0.590;G|0.410	0.410	strong		0.483	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
ATP13A4	84239	hgsc.bcm.edu	37	3	193209178	193209178	+	Missense_Mutation	SNP	T	T	C	rs6788448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	73	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	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	
TIAM1	7074	hgsc.bcm.edu	37	21	32638550	32638550	+	Missense_Mutation	SNP	C	C	T	rs2070418|rs386817934	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:32638550C>T	ENST00000286827.3	-	5	1210	c.739G>A	c.(739-741)Ggg>Agg	p.G247R	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.G247R	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	247			G -> R (in dbSNP:rs2070418).|G -> V (in dbSNP:rs2070417).	G -> M (in Ref. 1; AAA98443). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CCCGGCCCCCCGTTTGCTGTC	0.537													C|||	1069	0.213458	0.0159	0.2594	5008	,	,		16363	0.4107		0.1133	False		,,,				2504	0.3476				p.G247R		Atlas-SNP	.											.	TIAM1	522	.	0			c.G739A						PASS	.	C	ARG/GLY	148,4258	88.2+/-126.9	6,136,2061	69.0	73.0	71.0		739	4.5	1.0	21	dbSNP_96	71	730,7870	141.4+/-197.7	39,652,3609	yes	missense	TIAM1	NM_003253.2	125	45,788,5670	TT,TC,CC		8.4884,3.3591,6.7507	probably-damaging	247/1592	32638550	878,12128	2203	4300	6503	SO:0001583	missense	7074	exon5			GCCCCCCGTTTGC		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.739G>A	21.37:g.32638550C>T	ENSP00000286827:p.Gly247Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	351	0.16071428571428573	7	0.014227642276422764	80	0.22099447513812154	196	0.34265734265734266	68	0.08970976253298153	C	13.23	2.176241	0.38413	0.033591	0.084884	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.39229	1.11;1.09	5.4	4.49	0.54785	.	0.367039	0.30869	N	0.008718	T	0.00012	0.0000	L	0.36672	1.1	0.25471	P	0.9878204	P;P;P	0.46656	0.882;0.813;0.813	B;B;B	0.34824	0.19;0.093;0.093	T	0.42050	-0.9474	9	0.44086	T	0.13	.	17.6719	0.88221	0.0:0.8674:0.1326:0.0	rs2070418;rs56928974;rs2070418	247;247;247	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	R	247;88;247	ENSP00000286827:G247R;ENSP00000441570:G247R	ENSP00000286827:G247R	G	-	1	0	TIAM1	31560421	0.911000	0.30947	0.998000	0.56505	0.993000	0.82548	2.031000	0.41117	2.803000	0.96430	0.585000	0.79938	GGG	C|0.874;A|0.001	.	strong		0.537	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
ACHE	43	hgsc.bcm.edu	37	7	100490077	100490077	+	Silent	SNP	G	G	A	rs7636	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100490077G>A	ENST00000412389.1	-	2	1586	c.1431C>T	c.(1429-1431)ccC>ccT	p.P477P	ACHE_ENST00000241069.5_Silent_p.P477P|ACHE_ENST00000411582.1_Silent_p.P477P|ACHE_ENST00000302913.4_Silent_p.P477P|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000428317.1_Silent_p.P477P|ACHE_ENST00000419336.2_Silent_p.P389P			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	96	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	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	
MYH4	4622	hgsc.bcm.edu	37	17	10355763	10355763	+	Missense_Mutation	SNP	T	T	C	rs917361	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10355763T>C	ENST00000255381.2	-	26	3428	c.3318A>G	c.(3316-3318)atA>atG	p.I1106M	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1106			I -> M (in dbSNP:rs917361). {ECO:0000269|PubMed:10388558}.		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)			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						TTTGTAGCTGTATTGCAAGGG	0.353													C|||	2674	0.533946	0.3442	0.5187	5008	,	,		18291	0.8631		0.3698	False		,,,				2504	0.6309				p.I1106M		Atlas-SNP	.											.	MYH4	349	.	0			c.A3318G						PASS	.	C	MET/ILE	1585,2821	666.0+/-401.6	281,1023,899	150.0	138.0	142.0		3318	4.6	1.0	17	dbSNP_86	142	3577,5023	628.0+/-398.0	760,2057,1483	yes	missense	MYH4	NM_017533.2	10	1041,3080,2382	CC,CT,TT		41.593,35.9737,39.6894	benign	1106/1940	10355763	5162,7844	2203	4300	6503	SO:0001583	missense	4622	exon26			TAGCTGTATTGCA		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.3318A>G	17.37:g.10355763T>C	ENSP00000255381:p.Ile1106Met	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1125	0.5151098901098901	162	0.32926829268292684	181	0.5	498	0.8706293706293706	284	0.37467018469656993	C	7.093	0.572480	0.13623	0.359737	0.41593	ENSG00000141048	ENST00000255381	D	0.82984	-1.67	5.6	4.63	0.57726	Myosin tail (1);	0.000000	0.45361	N	0.000374	T	0.00012	0.0000	N	0.03050	-0.425	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.08055	0.003	T	0.38950	-0.9637	9	0.34782	T	0.22	.	4.1163	0.10083	0.1302:0.6059:0.126:0.1378	rs917361;rs3744556;rs17811136;rs52820909;rs58019198;rs917361	1106	Q9Y623	MYH4_HUMAN	M	1106	ENSP00000255381:I1106M	ENSP00000255381:I1106M	I	-	3	3	MYH4	10296488	0.004000	0.15560	0.998000	0.56505	0.963000	0.63663	-0.314000	0.08092	0.854000	0.35336	-0.119000	0.15052	ATA	C|0.466;N|0.000	0.466	strong		0.353	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
C10orf54	64115	hgsc.bcm.edu	37	10	73533124	73533124	+	Missense_Mutation	SNP	C	C	T	rs146887444		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73533124C>T	ENST00000394957.3	-	1	131	c.73G>A	c.(73-75)Gcg>Acg	p.A25T	CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	25					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						CCTAGGGACGCAGCCAGGAAG	0.687													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14034	0.0		0.0	False		,,,				2504	0.0				p.A25T		Atlas-SNP	.											.	C10orf54	29	.	0			c.G73A						PASS	.	C	,THR/ALA	1,4385		0,1,2192	13.0	17.0	16.0		,73	3.0	1.0	10	dbSNP_134	16	5,8581		0,5,4288	yes	intron,missense	CDH23,C10orf54	NM_022124.5,NM_022153.1	,58	0,6,6480	TT,TC,CC		0.0582,0.0228,0.0463	,probably-damaging	,25/312	73533124	6,12966	2193	4293	6486	SO:0001583	missense	64115	exon1			GGGACGCAGCCAG	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.73G>A	10.37:g.73533124C>T	ENSP00000378409:p.Ala25Thr	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	285	145	0.508772	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Missense_Mutation	SNP	ENST00000394957.3	37	CCDS31218.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	21.8|21.8	4.199161|4.199161	0.79015|0.79015	2.28E-4|2.28E-4	5.82E-4|5.82E-4	ENSG00000107738|ENSG00000107738	ENST00000394957|ENST00000263569	T|.	0.47528|.	0.84|.	3.91|3.91	3.0|3.0	0.34707|0.34707	.|.	0.571467|.	0.17287|.	N|.	0.179798|.	T|T	0.34948|0.34948	0.0915|0.0915	N|N	0.24115|0.24115	0.695|0.695	0.28462|0.28462	N|N	0.915816|0.915816	B|.	0.30482|.	0.281|.	B|.	0.29440|.	0.102|.	T|T	0.32745|0.32745	-0.9895|-0.9895	10|6	0.29301|0.87932	T|D	0.29|0	-0.9608|-0.9608	9.7011|9.7011	0.40187|0.40187	0.0:0.7891:0.2109:0.0|0.0:0.7891:0.2109:0.0	.|.	25|.	Q9H7M9|.	GI24_HUMAN|.	T|Y	25|48	ENSP00000378409:A25T|.	ENSP00000378409:A25T|ENSP00000263569:C48Y	A|C	-|-	1|2	0|0	C10orf54|C10orf54	73203130|73203130	0.018000|0.018000	0.18449|0.18449	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	0.381000|0.381000	0.20619|0.20619	1.226000|1.226000	0.43582|0.43582	0.455000|0.455000	0.32223|0.32223	GCG|TGC	C|0.999;T|0.001	0.001	strong		0.687	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153	
USP8	9101	hgsc.bcm.edu	37	15	50769520	50769520	+	Missense_Mutation	SNP	G	G	A	rs61733869	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:50769520G>A	ENST00000396444.3	+	10	1380	c.1042G>A	c.(1042-1044)Gct>Act	p.A348T	USP8_ENST00000425032.3_Missense_Mutation_p.A271T|USP8_ENST00000433963.1_Missense_Mutation_p.A348T|USP8_ENST00000307179.4_Missense_Mutation_p.A348T	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	348					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)		TTCTAAACCTGCTGCCCAGAC	0.353													G|||	59	0.0117812	0.0023	0.0245	5008	,	,		16343	0.0		0.0358	False		,,,				2504	0.0031				p.A348T		Atlas-SNP	.											.	USP8	90	.	0			c.G1042A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	46,4346	46.7+/-81.2	0,46,2150	48.0	50.0	50.0		1042,1042,1042	-9.4	0.1	15	dbSNP_129	50	373,8215	123.2+/-182.1	9,355,3930	yes	missense,missense,missense	USP8	NM_001128610.1,NM_001128611.1,NM_005154.3	58,58,58	9,401,6080	AA,AG,GG		4.3433,1.0474,3.228	benign,benign,benign	348/1119,348/1119,348/1119	50769520	419,12561	2196	4294	6490	SO:0001583	missense	9101	exon10			AAACCTGCTGCCC	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.1042G>A	15.37:g.50769520G>A	ENSP00000379721:p.Ala348Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	42	0.019230769230769232	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	32	0.04221635883905013	G	0.879	-0.729342	0.03135	0.010474	0.043433	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.17370	2.28;2.28;2.28;2.29	4.72	-9.45	0.00600	.	1.505420	0.03406	N	0.204125	T	0.01730	0.0055	N	0.22421	0.69	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.17167	-1.0378	10	0.11485	T	0.65	0.0554	7.2057	0.25905	0.4933:0.2568:0.2499:0.0	rs61733869	271;348;348	B4DKA8;P40818;A8K8N5	.;UBP8_HUMAN;.	T	348;348;348;271	ENSP00000379721:A348T;ENSP00000405537:A348T;ENSP00000302239:A348T;ENSP00000412682:A271T	ENSP00000302239:A348T	A	+	1	0	USP8	48556812	0.306000	0.24490	0.093000	0.20910	0.259000	0.26198	-0.155000	0.10115	-2.533000	0.00490	-0.444000	0.05651	GCT	G|0.971;A|0.029	0.029	strong		0.353	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
PSPH	5723	hgsc.bcm.edu	37	7	56088780	56088780	+	Silent	SNP	G	G	A	rs75497420	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:56088780G>A	ENST00000395471.3	-	4	931	c.126C>T	c.(124-126)gaC>gaT	p.D42D	PSPH_ENST00000275605.3_Silent_p.D42D|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	42					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)			CTGACACCGCGTCCTCAACGC	0.423																																					p.D42D		Atlas-SNP	.											.	PSPH	23	.	0			c.C126T						PASS	.						153.0	116.0	129.0					7																	56088780		2203	4300	6503	SO:0001819	synonymous_variant	5723	exon4			CACCGCGTCCTCA	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.126C>T	7.37:g.56088780G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	136	24	0.176471	NM_004577	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	37	CCDS5522.1																																																																																			G|0.957;A|0.044	0.044	strong		0.423	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
BCR	613	hgsc.bcm.edu	37	22	23523630	23523630	+	Silent	SNP	C	C	A	rs5751602	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:23523630C>A	ENST00000305877.8	+	1	1234	c.483C>A	c.(481-483)atC>atA	p.I161I	BCR_ENST00000398512.5_Silent_p.I161I|BCR_ENST00000359540.3_Silent_p.I161I	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	161	Kinase.				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)	TCGAGCGGATCCGCAAGGGCC	0.721			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""								C|||	1460	0.291534	0.3238	0.3602	5008	,	,		9634	0.3542		0.2396	False		,,,				2504	0.1881				p.I161I		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.C483A						PASS	.	C	,	1202,3134		189,824,1155	29.0	35.0	33.0		483,483	3.4	1.0	22	dbSNP_114	33	2071,6389		269,1533,2428	no	coding-synonymous,coding-synonymous	BCR	NM_004327.3,NM_021574.2	,	458,2357,3583	AA,AC,CC		24.4799,27.7214,25.5783	,	161/1272,161/1228	23523630	3273,9523	2168	4230	6398	SO:0001819	synonymous_variant	613	exon1			GCGGATCCGCAAG		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.483C>A	22.37:g.23523630C>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1																																																																																			C|0.720;A|0.280	0.280	strong		0.721	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327	
CS	1431	hgsc.bcm.edu	37	12	56679751	56679751	+	Silent	SNP	A	A	G	rs1802236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56679751A>G	ENST00000351328.3	-	3	340	c.150T>C	c.(148-150)acT>acC	p.T50T	RP11-977G19.10_ENST00000549318.1_Silent_p.T246T|CS_ENST00000548567.1_5'UTR|CS_ENST00000542324.2_Silent_p.T37T	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	50					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)		GCTGCCTGAAAGTCTTAATTC	0.433													G|||	163	0.0325479	0.0015	0.0548	5008	,	,		21200	0.0357		0.0676	False		,,,				2504	0.0194				p.T50T		Atlas-SNP	.											.	CS	44	.	0			c.T150C						PASS	.	G		44,4362	822.4+/-416.4	1,42,2160	245.0	218.0	227.0		150	2.9	1.0	12	dbSNP_89	227	536,8064	794.9+/-407.5	22,492,3786	no	coding-synonymous	CS	NM_004077.2		23,534,5946	GG,GA,AA		6.2326,0.9986,4.4595		50/467	56679751	580,12426	2203	4300	6503	SO:0001819	synonymous_variant	1431	exon3			CCTGAAAGTCTTA		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.150T>C	12.37:g.56679751A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Silent	SNP	ENST00000351328.3	37	CCDS8913.1																																																																																			A|0.962;G|0.038	0.038	strong		0.433	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
IQGAP1	8826	hgsc.bcm.edu	37	15	91010776	91010776	+	Silent	SNP	T	T	C	rs1505936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:91010776T>C	ENST00000268182.5	+	18	2254	c.2130T>C	c.(2128-2130)ccT>ccC	p.P710P	IQGAP1_ENST00000560738.1_Silent_p.P138P	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	710	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGGatgaacctccaaattttg	0.438													C|||	2184	0.436102	0.7239	0.2695	5008	,	,		18199	0.377		0.328	False		,,,				2504	0.3374				p.P710P		Atlas-SNP	.											.	IQGAP1	140	.	0			c.T2130C						PASS	.	C		2993,1403	450.8+/-349.5	1021,951,226	83.0	90.0	88.0		2130	3.5	0.3	15	dbSNP_88	88	2795,5801	674.3+/-403.1	448,1899,1951	no	coding-synonymous	IQGAP1	NM_003870.3		1469,2850,2177	CC,CT,TT		32.5151,31.9154,44.5505		710/1658	91010776	5788,7204	2198	4298	6496	SO:0001819	synonymous_variant	8826	exon18			TGAACCTCCAAAT	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2130T>C	15.37:g.91010776T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_003870	A7MBM3	Silent	SNP	ENST00000268182.5	37	CCDS10362.1																																																																																			T|0.557;C|0.442	0.442	strong		0.438	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870	
PAPOLB	56903	hgsc.bcm.edu	37	7	4901385	4901385	+	Missense_Mutation	SNP	A	A	C	rs3750009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	34	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	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	
KIAA1217	56243	hgsc.bcm.edu	37	10	24721946	24721946	+	Silent	SNP	A	A	C	rs2274831	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:24721946A>C	ENST00000376454.3	+	4	606	c.576A>C	c.(574-576)ggA>ggC	p.G192G	KIAA1217_ENST00000430453.2_Silent_p.G113G|KIAA1217_ENST00000376462.1_Silent_p.G112G|KIAA1217_ENST00000458595.1_Silent_p.G192G|KIAA1217_ENST00000376452.3_Silent_p.G192G	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	192					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TCCAGTATGGAGATGAAACCA	0.483													A|||	945	0.188698	0.3124	0.121	5008	,	,		18323	0.1935		0.1531	False		,,,				2504	0.1012				p.G192G		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A576C						PASS	.	A	,,	1334,3072	448.5+/-348.7	214,906,1083	93.0	77.0	83.0		336,576,576	1.9	1.0	10	dbSNP_100	83	1361,7239	264.3+/-285.5	103,1155,3042	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	317,2061,4125	CC,CA,AA		15.8256,30.2769,20.7212	,,	112/1265,192/1310,192/1944	24721946	2695,10311	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon4			GTATGGAGATGAA	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.576A>C	10.37:g.24721946A>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			A|0.794;C|0.206	0.206	strong		0.483	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
INA	9118	hgsc.bcm.edu	37	10	105037958	105037958	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105037958C>T	ENST00000369849.4	+	1	1039	c.990C>T	c.(988-990)cgC>cgT	p.R330R		NM_032727.3	NP_116116.1	Q16352	AINX_HUMAN	internexin neuronal intermediate filament protein, alpha	330	Coil 2.|Rod.				cell differentiation (GO:0030154)|neurofilament cytoskeleton organization (GO:0060052)|substantia nigra development (GO:0021762)	cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular space (GO:0005615)|neurofilament (GO:0005883)	structural constituent of cytoskeleton (GO:0005200)	p.R330R(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)	13				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		AGGGCCTGCGCGGGGCCAACG	0.711																																					p.R330R		Atlas-SNP	.											INA,NS,carcinoma,0,2	INA	34	2	1	Substitution - coding silent(1)	endometrium(1)	c.C990T						scavenged	.						13.0	12.0	13.0					10																	105037958		2194	4296	6490	SO:0001819	synonymous_variant	9118	exon1			CCTGCGCGGGGCC	S78296	CCDS7545.1	10q24	2013-01-16			ENSG00000148798	ENSG00000148798		"""Intermediate filaments type IV"""	6057	protein-coding gene	gene with protein product		605338		NEF5		7769995	Standard	NM_032727		Approved	NF-66	uc001kws.3	Q16352	OTTHUMG00000018986	ENST00000369849.4:c.990C>T	10.37:g.105037958C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_032727	B1AQK0|Q9BRC5	Silent	SNP	ENST00000369849.4	37	CCDS7545.1																																																																																			.	.	none		0.711	INA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050145.1	NM_032727	
AGBL1	123624	hgsc.bcm.edu	37	15	86790997	86790997	+	Missense_Mutation	SNP	G	G	A	rs149477284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:86790997G>A	ENST00000441037.2	+	6	579	c.484G>A	c.(484-486)Gtg>Atg	p.V162M	AGBL1_ENST00000421325.2_Missense_Mutation_p.V162M	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	162					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						CAACGCCTACGTGCAGATCCG	0.642													G|||	14	0.00279553	0.0	0.0029	5008	,	,		19735	0.0		0.0119	False		,,,				2504	0.0				p.V162M		Atlas-SNP	.											.	AGBL1	151	.	0			c.G484A						PASS	.	G	MET/VAL	12,4312		0,12,2150	37.0	39.0	38.0		484	1.9	0.0	15	dbSNP_134	38	103,8421		1,101,4160	yes	missense	AGBL1	NM_152336.2	21	1,113,6310	AA,AG,GG		1.2084,0.2775,0.8951	probably-damaging	162/1067	86790997	115,12733	2162	4262	6424	SO:0001583	missense	123624	exon6			GCCTACGTGCAGA	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.484G>A	15.37:g.86790997G>A	ENSP00000413001:p.Val162Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	0.010	-1.782928	0.00634	0.002775	0.012084	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.33865	1.39	5.16	1.86	0.25419	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.09730	0.0239	L	0.31207	0.915	0.80722	D	1	P	0.39352	0.669	B	0.20955	0.032	T	0.25082	-1.0142	9	0.05525	T	0.97	-7.5937	5.0261	0.14385	0.4866:0.0:0.5134:0.0	.	162	Q96MI9	CBPC4_HUMAN	M	191;162	ENSP00000397173:V162M	ENSP00000397173:V162M	V	+	1	0	AGBL1	84592001	0.099000	0.21834	0.007000	0.13788	0.085000	0.17905	0.616000	0.24344	0.575000	0.29434	-0.258000	0.10820	GTG	G|0.995;A|0.005	0.005	strong		0.642	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
PRDM9	56979	hgsc.bcm.edu	37	5	23527472	23527472	+	Missense_Mutation	SNP	G	G	A	rs112666693		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:23527472G>A	ENST00000296682.3	+	11	2457	c.2275G>A	c.(2275-2277)Gat>Aat	p.D759N		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	759					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.D759N(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGCTTTCGCGATAAGTCACA	0.572										HNSCC(3;0.000094)																											p.D759N		Atlas-SNP	.											PRDM9,NS,carcinoma,0,2	PRDM9	344	2	1	Substitution - Missense(1)	kidney(1)	c.G2275A						scavenged	.						63.0	89.0	81.0					5																	23527472		2132	4296	6428	SO:0001583	missense	56979	exon11			TTTCGCGATAAGT	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2275G>A	5.37:g.23527472G>A	ENSP00000296682:p.Asp759Asn	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	149	6	0.0402685	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.937166	0.00484	.	.	ENSG00000164256	ENST00000296682	T	0.35605	1.3	2.65	-1.92	0.07618	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11324	0.0276	N	0.02275	-0.615	0.09310	N	1	P	0.35155	0.487	B	0.13407	0.009	T	0.13764	-1.0497	9	0.37606	T	0.19	.	9.3631	0.38208	0.0:0.3794:0.5202:0.1004	.	759	Q9NQV7	PRDM9_HUMAN	N	759	ENSP00000296682:D759N	ENSP00000296682:D759N	D	+	1	0	PRDM9	23563229	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-14.321000	0.00000	-0.886000	0.03966	-4.161000	0.00010	GAT	G|0.500;A|0.500	0.500	weak		0.572	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
PODXL	5420	hgsc.bcm.edu	37	7	131194255	131194255	+	Missense_Mutation	SNP	G	G	C	rs35893129|rs36086597	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:131194255G>C	ENST00000378555.3	-	4	1139	c.892C>G	c.(892-894)Ccc>Gcc	p.P298A	PODXL_ENST00000465001.1_5'Flank|PODXL_ENST00000541194.1_Missense_Mutation_p.P300A|PODXL_ENST00000537928.1_Missense_Mutation_p.P266A|PODXL_ENST00000322985.9_Missense_Mutation_p.P266A			O00592	PODXL_HUMAN	podocalyxin-like	298	Thr-rich.		P -> A (in dbSNP:rs35893129).		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)					GGGCTCGTGGGCTGCACTGTC	0.587													G|||	139	0.0277556	0.0083	0.0331	5008	,	,		18222	0.0		0.0795	False		,,,				2504	0.0256				p.P298A		Atlas-SNP	.											.	PODXL	53	.	0			c.C892G						PASS	.	G	ALA/PRO,ALA/PRO	74,4332	66.4+/-103.9	2,70,2131	221.0	206.0	211.0		892,796	2.7	0.0	7	dbSNP_126	211	659,7941	167.4+/-219.2	29,601,3670	yes	missense,missense	PODXL	NM_001018111.2,NM_005397.3	27,27	31,671,5801	CC,CG,GG		7.6628,1.6795,5.6359	probably-damaging,probably-damaging	298/559,266/527	131194255	733,12273	2203	4300	6503	SO:0001583	missense	5420	exon4			TCGTGGGCTGCAC		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.892C>G	7.37:g.131194255G>C	ENSP00000367817:p.Pro298Ala	Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	207	98	0.47343	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	74	0.03388278388278388	6	0.012195121951219513	10	0.027624309392265192	0	0.0	58	0.07651715039577836	G	14.36	2.513213	0.44660	0.016795	0.076628	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.12147	2.82;2.71;2.82;2.87	3.62	2.71	0.32032	.	48.005600	0.00166	N	0.000001	T	0.00754	0.0025	N	0.24115	0.695	0.09310	N	1	P;P	0.51057	0.932;0.941	P;B	0.47470	0.548;0.346	T	0.16247	-1.0409	10	0.48119	T	0.1	-11.6227	7.4932	0.27473	0.1195:0.0:0.8805:0.0	rs35893129	266;298	O00592-2;O00592	.;PODXL_HUMAN	A	300;266;256;298;266	ENSP00000440518:P300A;ENSP00000442655:P266A;ENSP00000367817:P298A;ENSP00000319782:P266A	ENSP00000319782:P266A	P	-	1	0	PODXL	130844795	0.003000	0.15002	0.014000	0.15608	0.019000	0.09904	0.352000	0.20113	1.076000	0.40961	0.650000	0.86243	CCC	G|0.949;C|0.051	0.051	strong		0.587	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
FANCA	2175	hgsc.bcm.edu	37	16	89809319	89809319	+	Silent	SNP	T	T	C	rs1800358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	62	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	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		
EPPK1	83481	hgsc.bcm.edu	37	8	144945792	144945792	+	Missense_Mutation	SNP	T	T	C	rs13255110	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144945792T>C	ENST00000525985.1	-	2	1701	c.1630A>G	c.(1630-1632)Aag>Gag	p.K544E				P58107	EPIPL_HUMAN	epiplakin 1	544				E -> K (in Ref. 2; BAC92750). {ECO:0000305}.		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)			GCGCTCAGCTTAGCGGCCAGC	0.632													C|||	2817	0.5625	0.5983	0.6844	5008	,	,		18696	0.2798		0.6809	False		,,,				2504	0.5971				p.K544E		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	1	0			c.A1630G						scavenged	.	C	GLU/LYS	2785,1489		943,899,295	20.0	24.0	23.0		1630	0.2	0.0	8	dbSNP_121	23	5912,2572		2082,1748,412	yes	missense	EPPK1	NM_031308.1	56	3025,2647,707	CC,CT,TT		30.3159,34.8386,31.831	benign	544/2420	144945792	8697,4061	2137	4242	6379	SO:0001583	missense	83481	exon1			TCAGCTTAGCGGC	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.1630A>G	8.37:g.144945792T>C	ENSP00000436337:p.Lys544Glu	Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		1227	0.5618131868131868	289	0.5873983739837398	253	0.6988950276243094	164	0.2867132867132867	521	0.6873350923482849	C	0.004	-2.333404	0.00227	0.651614	0.696841	ENSG00000227184	ENST00000525985	T	0.65549	-0.16	5.12	0.205	0.15204	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43540	-0.9385	7	0.02654	T	1	.	6.5371	0.22361	0.0:0.2197:0.3324:0.4479	rs13255110;rs57752496;rs13255110	544	E9PPU0	.	E	544	ENSP00000436337:K544E	ENSP00000436337:K544E	K	-	1	0	EPPK1	145017780	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.015000	0.12634	-0.412000	0.07519	-0.726000	0.03593	AAG	T|0.461;C|0.539	0.539	strong		0.632	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
PSPH	5723	hgsc.bcm.edu	37	7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	rs77329757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.						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	136	0	0		WXS	Illumina HiSeq	Phase_I	165	15	0.0909091	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	
MAEL	84944	hgsc.bcm.edu	37	1	166958601	166958601	+	Silent	SNP	T	T	C	rs2296837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:166958601T>C	ENST00000367872.4	+	1	256	c.12T>C	c.(10-12)cgT>cgC	p.R4R	MAEL_ENST00000367870.2_Silent_p.R4R	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	4					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						TGCCGAACCGTAAGGCCAGCC	0.617													C|||	1512	0.301917	0.559	0.1715	5008	,	,		16556	0.247		0.2247	False		,,,				2504	0.183				p.R4R		Atlas-SNP	.											.	MAEL	95	.	0			c.T12C						PASS	.	C		2297,2109	557.3+/-379.7	590,1117,496	51.0	45.0	47.0		12	4.3	1.0	1	dbSNP_100	47	2135,6465	696.9+/-404.9	255,1625,2420	no	coding-synonymous	MAEL	NM_032858.1		845,2742,2916	CC,CT,TT		24.8256,47.8665,34.0766		4/435	166958601	4432,8574	2203	4300	6503	SO:0001819	synonymous_variant	84944	exon1			GAACCGTAAGGCC	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"""cancer/testis antigen 128"", ""spermatogenesis associated 35"""	611368	"""maelstrom homolog (Drosophila)"""			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.12T>C	1.37:g.166958601T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Silent	SNP	ENST00000367872.4	37	CCDS1257.1																																																																																			T|0.682;G|0.000;C|0.317;A|0.000	0.317	strong		0.617	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858	
ZNF142	7701	hgsc.bcm.edu	37	2	219509618	219509618	+	Missense_Mutation	SNP	C	C	A	rs2230115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:219509618C>A	ENST00000449707.1	-	8	2042	c.1621G>T	c.(1621-1623)Gcc>Tcc	p.A541S	ZNF142_ENST00000411696.2_Missense_Mutation_p.A541S	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	541				A -> S (in Ref. 1; BAA13242). {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(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)		TAGAGTGGGGCCGGTGTGCCA	0.592													C|||	2586	0.516374	0.0711	0.5879	5008	,	,		16874	0.8194		0.5934	False		,,,				2504	0.6759				p.A541S	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.G1621T						PASS	.	C	SER/ALA	729,3641		72,585,1528	70.0	83.0	78.0		1621	5.1	0.5	2	dbSNP_98	78	4956,3626		1457,2042,792	yes	missense	ZNF142	NM_001105537.1	99	1529,2627,2320	AA,AC,CC		42.2512,16.6819,43.8928	benign	541/1688	219509618	5685,7267	2185	4291	6476	SO:0001583	missense	7701	exon8			GTGGGGCCGGTGT	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.1621G>T	2.37:g.219509618C>A	ENSP00000408643:p.Ala541Ser	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	201	188	0.935323	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	1164	0.532967032967033	36	0.07317073170731707	216	0.5966850828729282	454	0.7937062937062938	458	0.604221635883905	C	8.081	0.772438	0.16051	0.166819	0.577488	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.11385	2.78;2.78	5.95	5.08	0.68730	.	0.441671	0.24691	N	0.036400	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P;P	0.40909	0.732;0.647	B;P	0.46144	0.419;0.505	T	0.00668	-1.1618	9	0.15066	T	0.55	-14.1029	10.9014	0.47054	0.13:0.803:0.0:0.0671	rs2230115;rs3821034;rs2230115	541;378	P52746;A8MWU9	ZN142_HUMAN;.	S	541	ENSP00000408643:A541S;ENSP00000398798:A541S	ENSP00000398798:A541S	A	-	1	0	ZNF142	219217862	0.245000	0.23899	0.513000	0.27749	0.485000	0.33311	0.775000	0.26689	1.528000	0.49103	-0.150000	0.13652	GCC	C|0.484;A|0.516	0.516	strong		0.592	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
FSCB	84075	hgsc.bcm.edu	37	14	44974922	44974922	+	Missense_Mutation	SNP	A	A	T	rs3825632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:44974922A>T	ENST00000340446.4	-	1	1560	c.1269T>A	c.(1267-1269)gaT>gaA	p.D423E	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	423			D -> E (in dbSNP:rs3825632). {ECO:0000269|PubMed:11230166}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		GAGGCTGAACATCAGCAAGGG	0.517													T|||	2204	0.440096	0.4735	0.3977	5008	,	,		17653	0.3869		0.4553	False		,,,				2504	0.4642				p.D423E		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.T1269A						PASS	.	T	GLU/ASP	1907,2453		439,1029,712	27.0	29.0	29.0		1269	-1.9	0.0	14	dbSNP_107	29	4026,4554		996,2034,1260	yes	missense	FSCB	NM_032135.3	45	1435,3063,1972	TT,TA,AA		46.9231,43.7385,45.8501	benign	423/826	44974922	5933,7007	2180	4290	6470	SO:0001583	missense	84075	exon1			CTGAACATCAGCA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1269T>A	14.37:g.44974922A>T	ENSP00000344579:p.Asp423Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	944	0.43223443223443225	222	0.45121951219512196	136	0.3756906077348066	241	0.42132867132867136	345	0.4551451187335092	T	1.412	-0.575357	0.03882	0.437385	0.469231	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.11712	2.75	4.67	-1.88	0.07713	.	.	.	.	.	T	0.00012	0.0000	N	0.00152	-1.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43410	-0.9393	8	0.02654	T	1	1.2389	0.638	0.00806	0.3943:0.2492:0.135:0.2216	rs3825632;rs3825632	423	Q5H9T9	FSCB_HUMAN	E	423	ENSP00000344579:D423E	ENSP00000344579:D423E	D	-	3	2	FSCB	44044672	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-2.011000	0.01452	-0.509000	0.06532	-1.179000	0.01719	GAT	A|0.560;T|0.440	0.440	strong		0.517	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
MROH2B	133558	hgsc.bcm.edu	37	5	41061715	41061715	+	Nonsense_Mutation	SNP	C	C	T	rs1023840|rs386687544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:41061715C>T	ENST00000399564.4	-	6	1022	c.572G>A	c.(571-573)tGg>tAg	p.W191*		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	191			W -> R (in dbSNP:rs865093). {ECO:0000269|PubMed:15489334}.														CATTATATACCAGAACAGCAT	0.488													C|||	1043	0.208267	0.025	0.3329	5008	,	,		17005	0.2996		0.1819	False		,,,				2504	0.3006				p.W191X		Atlas-SNP	.											.	.	.	.	0			c.G572A						PASS	.	C	stop/TRP	210,3656		2,206,1725	175.0	168.0	170.0		572	2.9	1.0	5	dbSNP_86	170	1643,6603		176,1291,2656	yes	stop-gained	HEATR7B2	NM_173489.4		178,1497,4381	TT,TC,CC		19.9248,5.432,15.2989		191/1586	41061715	1853,10259	1933	4123	6056	SO:0001587	stop_gained	133558	exon6			ATATACCAGAACA		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.572G>A	5.37:g.41061715C>T	ENSP00000382476:p.Trp191*	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	149	60	0.402685	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Nonsense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	337	0.1543040293040293	10	0.02032520325203252	97	0.26795580110497236	142	0.24825174825174826	88	0.11609498680738786	C	40	8.282932	0.98742	0.05432	0.199248	ENSG00000171495	ENST00000399564	.	.	.	5.81	2.91	0.33838	.	0.249672	0.28257	N	0.016016	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	6.9332	0.24453	0.0:0.6857:0.0:0.3143	rs1023840;rs60925153;rs1023840	.	.	.	X	191	.	ENSP00000382476:W191X	W	-	2	0	HEATR7B2	41097472	0.586000	0.26782	0.992000	0.48379	0.991000	0.79684	-0.147000	0.10234	0.299000	0.22661	0.655000	0.94253	TGG	C|0.821;T|0.179	0.179	strong		0.488	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
CCDC30	728621	hgsc.bcm.edu	37	1	43042703	43042703	+	Silent	SNP	C	C	T	rs12049046	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:43042703C>T	ENST00000340612.4	+	6	868	c.868C>T	c.(868-870)Cta>Tta	p.L290L	CCDC30_ENST00000390640.4_Silent_p.L79L|CCDC30_ENST00000507855.1_Silent_p.L79L|CCDC30_ENST00000428554.2_Silent_p.L290L|CCDC30_ENST00000342022.4_Silent_p.L290L			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	290						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						AAAGATTGAACTAAAGCATGC	0.388													C|||	1430	0.285543	0.177	0.1571	5008	,	,		19876	0.4563		0.1879	False		,,,				2504	0.4479				p.L290L		Atlas-SNP	.											.	CCDC30	78	.	0			c.C868T						PASS	.	C		808,3598	322.3+/-297.6	79,650,1474	65.0	61.0	62.0		868	3.9	1.0	1	dbSNP_120	62	1707,6893	309.3+/-309.3	176,1355,2769	no	coding-synonymous	CCDC30	NM_001080850.2		255,2005,4243	TT,TC,CC		19.8488,18.3386,19.3372		290/784	43042703	2515,10491	2203	4300	6503	SO:0001819	synonymous_variant	728621	exon7			ATTGAACTAAAGC	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"""prefoldin 6-like"""					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.868C>T	1.37:g.43042703C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_001080850	Q14F06|Q5VVM5	Silent	SNP	ENST00000340612.4	37	CCDS30690.1																																																																																			C|0.778;T|0.222	0.222	strong		0.388	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030	
KMT2C	58508	hgsc.bcm.edu	37	7	151970899	151970899	+	Silent	SNP	T	T	C	rs577540910		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:151970899T>C	ENST00000262189.6	-	7	1121	c.903A>G	c.(901-903)aaA>aaG	p.K301K	KMT2C_ENST00000355193.2_Silent_p.K301K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	301					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)										TCTGGGTACATTTCTCTTCAC	0.438													T|||	1	0.000199681	0.0	0.0	5008	,	,		26142	0.0		0.0	False		,,,				2504	0.001				p.K301K		Atlas-SNP	.											.	MLL3	1564	.	0			c.A903G						PASS	.						135.0	129.0	131.0					7																	151970899		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon7			GGTACATTTCTCT	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.903A>G	7.37:g.151970899T>C		Somatic	385	0	0		WXS	Illumina HiSeq	Phase_I	360	23	0.0638889	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			.	.	none		0.438	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
BRD2	6046	hgsc.bcm.edu	37	6	32946133	32946133	+	Silent	SNP	T	T	C	rs206781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32946133T>C	ENST00000374825.4	+	10	3510	c.1809T>C	c.(1807-1809)tcT>tcC	p.S603S	BRD2_ENST00000449085.2_Silent_p.S556S|BRD2_ENST00000443797.2_Silent_p.S483S|BRD2_ENST00000395289.2_Silent_p.S603S|BRD2_ENST00000374831.4_Silent_p.S603S|BRD2_ENST00000395287.1_Silent_p.S603S	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	603					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						TAGGCCCTTCTGGCTTTGGAC	0.537													T|||	1323	0.264177	0.171	0.2911	5008	,	,		17525	0.1964		0.3748	False		,,,				2504	0.3272				p.S603S		Atlas-SNP	.											.	BRD2	70	.	0			c.T1809C						PASS	.	T	,,,	646,2372		62,522,925	153.0	164.0	160.0		1809,1809,1668,1809	1.5	1.0	6	dbSNP_79	160	2009,3409		381,1247,1081	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	443,1769,2006	CC,CT,TT		37.0801,21.4049,31.4723	,,,	603/802,603/837,556/755,603/802	32946133	2655,5781	1509	2709	4218	SO:0001819	synonymous_variant	6046	exon10			CCCTTCTGGCTTT	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1809T>C	6.37:g.32946133T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	597	0.2733516483516483	89	0.18089430894308944	100	0.27624309392265195	111	0.19405594405594406	297	0.391820580474934	T	10.96	1.499210	0.26861	0.214049	0.370801	ENSG00000204256	ENST00000449025	.	.	.	5.37	1.48	0.22813	.	.	.	.	.	T	0.12050	0.0293	.	.	.	0.09310	P	0.9999999999999775	.	.	.	.	.	.	T	0.20371	-1.0277	3	.	.	.	-6.2398	2.2795	0.04111	0.1549:0.0857:0.1614:0.5979	rs206781;rs209471;rs622332;rs1049374;rs1265601;rs2070267;rs3189519;rs6919815;rs17416379;rs17508857;rs17855228;rs206781	.	.	.	P	609	.	.	L	+	2	0	BRD2	33054111	0.445000	0.25657	0.993000	0.49108	0.968000	0.65278	-0.043000	0.12043	0.446000	0.26666	-0.307000	0.09154	CTG	T|0.705;C|0.295	0.295	strong		0.537	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
CBY1	25776	hgsc.bcm.edu	37	22	39069181	39069181	+	Silent	SNP	T	T	C	rs3747174	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	67	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	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	
GJA4	2701	hgsc.bcm.edu	37	1	35260202	35260202	+	Missense_Mutation	SNP	G	G	A	rs41266431	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:35260202G>A	ENST00000342280.4	+	2	476	c.388G>A	c.(388-390)Gta>Ata	p.V130I		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	130			V -> I (in dbSNP:rs41266431). {ECO:0000269|PubMed:8761439, 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)				GCTGGCGGCCGTAGAGCGTCA	0.657													G|||	271	0.0541134	0.0091	0.111	5008	,	,		15563	0.0		0.1421	False		,,,				2504	0.0399				p.V130I		Atlas-SNP	.											.	GJA4	25	.	0			c.G388A						PASS	.	G	ILE/VAL	161,4243	99.8+/-138.5	5,151,2046	23.0	26.0	25.0		388	-4.5	0.0	1	dbSNP_127	25	1181,7419	229.6+/-264.2	88,1005,3207	yes	missense	GJA4	NM_002060.2	29	93,1156,5253	AA,AG,GG		13.7326,3.6558,10.3199	benign	130/334	35260202	1342,11662	2202	4300	6502	SO:0001583	missense	2701	exon2			GCGGCCGTAGAGC	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.388G>A	1.37:g.35260202G>A	ENSP00000343676:p.Val130Ile	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	37	CCDS30669.1	164	0.07509157509157509	12	0.024390243902439025	46	0.1270718232044199	0	0.0	106	0.13984168865435356	G	0.007	-1.984776	0.00443	0.036558	0.137326	ENSG00000187513	ENST00000342280;ENST00000450137;ENST00000543143	D;D	0.97352	-4.29;-4.35	5.11	-4.46	0.03536	.	0.953379	0.08590	N	0.923240	T	0.04634	0.0126	N	0.02315	-0.6	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.62224	-0.6899	9	0.16420	T	0.52	.	7.6565	0.28379	0.5279:0.2003:0.2718:0.0	rs41266431;rs61738291	130;130	Q5JW71;P35212	.;CXA4_HUMAN	I	130	ENSP00000343676:V130I;ENSP00000409186:V130I	ENSP00000343676:V130I	V	+	1	0	GJA4	35032789	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-0.772000	0.04694	-0.912000	0.03837	-0.471000	0.05019	GTA	G|0.912;A|0.088	0.088	strong		0.657	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39497454	39497454	+	Missense_Mutation	SNP	G	G	C	rs139299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39497454G>C	ENST00000401756.1	+	3	439	c.363G>C	c.(361-363)aaG>aaC	p.K121N	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.K121N|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.K121N|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.K121N	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	121			K -> E (in allele A3H-Var; haplotype 2; allele presenting a higher expression and more effective in retrotransposons and HIV-1 restriction; dbSNP:rs139298).|K -> N (in dbSNP:rs139299).	K -> D (in Ref. 2; CAG30367). {ECO:0000305}.	cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					CCCAGCAGAAGGGGCTGCGGC	0.597													G|||	2653	0.529752	0.8752	0.3876	5008	,	,		6362	0.3155		0.4771	False		,,,				2504	0.4387				p.K121N		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G363C						PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	3564,842		1465,634,104	51.0	49.0	50.0		363,363,363,363	1.3	0.4	22	dbSNP_78	50	3932,4668		898,2136,1266	yes	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	94,94,94,94	2363,2770,1370	CC,CG,GG		45.7209,19.1103,42.3651	benign,benign,benign,benign	121/183,121/201,121/155,121/184	39497454	7496,5510	2203	4300	6503	SO:0001583	missense	164668	exon3			GCAGAAGGGGCTG	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.363G>C	22.37:g.39497454G>C	ENSP00000385741:p.Lys121Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	1098	0.5027472527472527	427	0.8678861788617886	129	0.356353591160221	172	0.3006993006993007	370	0.48812664907651715	.	11.64	1.698131	0.30142	0.808897	0.457209	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	3.33	1.26	0.21427	.	.	.	.	.	T	0.00012	0.0000	L	0.59436	1.845	0.58432	P	1.0000000000287557E-6	B	0.26602	0.154	B	0.36719	0.231	T	0.18209	-1.0344	8	0.72032	D	0.01	-5.078	5.5224	0.16939	0.2545:0.0:0.7455:0.0	rs139299;rs60075609	121	B7TQM3	.	N	121	ENSP00000216123:K121N;ENSP00000411754:K121N;ENSP00000393520:K121N;ENSP00000385741:K121N	ENSP00000216123:K121N	K	+	3	2	APOBEC3H	37827400	0.860000	0.29831	0.436000	0.26797	0.010000	0.07245	1.033000	0.30191	0.441000	0.26529	0.460000	0.39030	AAG	G|0.453;C|0.547	0.547	strong		0.597	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
AKR1B15	441282	hgsc.bcm.edu	37	7	134260595	134260595	+	Missense_Mutation	SNP	C	C	T	rs141101327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:134260595C>T	ENST00000457545.2	+	8	919	c.659C>T	c.(658-660)aCg>aTg	p.T220M	AKR1B15_ENST00000423958.1_Missense_Mutation_p.T192M	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	220							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						CCATACCTCACGCAGGAGAAA	0.537													C|||	31	0.0061901	0.0015	0.0072	5008	,	,		18433	0.0		0.0179	False		,,,				2504	0.0061				p.T220M		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C659T						PASS	.	C	MET/THR	15,4391	20.2+/-43.8	0,15,2188	152.0	118.0	129.0		659	3.0	0.7	7	dbSNP_134	129	137,8463	67.7+/-130.1	0,137,4163	no	missense	AKR1B15	NM_001080538.2	81	0,152,6351	TT,TC,CC		1.593,0.3404,1.1687	probably-damaging	220/345	134260595	152,12854	2203	4300	6503	SO:0001583	missense	441282	exon8			ACCTCACGCAGGA		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.659C>T	7.37:g.134260595C>T	ENSP00000389289:p.Thr220Met	Somatic	598	0	0		WXS	Illumina HiSeq	Phase_I	616	220	0.357143	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	19	0.0086996336996337	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	C	11.82	1.754067	0.31046	0.003404	0.01593	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.17854	2.25;2.25	3.87	2.98	0.34508	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.18173	0.0436	L	0.56199	1.76	0.39942	D	0.974421	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.01810	-1.1269	9	0.72032	D	0.01	.	8.189	0.31357	0.0:0.7958:0.0:0.2042	.	192;220	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	M	220;192	ENSP00000389289:T220M;ENSP00000397009:T192M	ENSP00000397009:T192M	T	+	2	0	AKR1B15	133911135	0.025000	0.19082	0.699000	0.30290	0.184000	0.23303	0.640000	0.24705	0.810000	0.34279	0.537000	0.68136	ACG	C|0.991;T|0.009	0.009	strong		0.537	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
TULP1	7287	hgsc.bcm.edu	37	6	35477032	35477032	+	Missense_Mutation	SNP	A	A	G	rs2064317	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35477032A>G	ENST00000229771.6	-	8	855	c.776T>C	c.(775-777)aTa>aCa	p.I259T	TULP1_ENST00000322263.4_Missense_Mutation_p.I206T	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	259			I -> T (in dbSNP:rs2064317). {ECO:0000269|PubMed:17962469}.		dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I259T(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						GCTCTTCTTTATCACCGTAGC	0.587													G|||	1973	0.39397	0.3449	0.3329	5008	,	,		19111	0.499		0.3648	False		,,,				2504	0.4254				p.I259T	GBM(55;1027 1091 11115 23439)	Atlas-SNP	.											TULP1,NS,carcinoma,0,1	TULP1	51	1	1	Substitution - Missense(1)	stomach(1)	c.T776C						PASS	.	G	THR/ILE	1564,2842	669.1+/-402.1	254,1056,893	371.0	345.0	354.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	776	3.6	0.3	6	dbSNP_94	354	3190,5410	653.8+/-401.1	609,1972,1719	yes	missense	TULP1	NM_003322.3	89	863,3028,2612	GG,GA,AA		37.093,35.497,36.5524	benign	259/543	35477032	4754,8252	2203	4300	6503	SO:0001583	missense	7287	exon8			TTCTTTATCACCG	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.776T>C	6.37:g.35477032A>G	ENSP00000229771:p.Ile259Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_003322	O43536|Q5TGM5|Q8N571	Missense_Mutation	SNP	ENST00000229771.6	37	CCDS4807.1	837	0.38324175824175827	172	0.34959349593495936	137	0.3784530386740331	256	0.44755244755244755	272	0.35883905013192613	G	0.004	-2.320881	0.00232	0.35497	0.37093	ENSG00000112041	ENST00000229771;ENST00000322263	T;T	0.79352	-1.25;-1.26	4.5	3.62	0.41486	.	0.891546	0.09851	N	0.747564	T	0.16128	0.0388	N	0.00413	-1.525	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.11966	-1.0566	9	0.02654	T	1	-11.6502	6.4263	0.21772	0.2277:0.0:0.7723:0.0	rs2064317;rs41539122;rs41539440;rs41539748;rs45630406;rs45632076;rs57520700;rs61726639;rs2064317	206;259	O00294-2;O00294	.;TULP1_HUMAN	T	259;206	ENSP00000229771:I259T;ENSP00000319414:I206T	ENSP00000229771:I259T	I	-	2	0	TULP1	35585010	0.662000	0.27439	0.260000	0.24451	0.137000	0.21094	0.696000	0.25541	0.513000	0.28278	-0.355000	0.07637	ATA	A|0.642;G|0.358	0.358	strong		0.587	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2		
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969507	99969507	+	Missense_Mutation	SNP	C	C	T	rs35122894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99969507C>T	ENST00000298999.3	+	5	1939	c.1636C>T	c.(1636-1638)Cct>Tct	p.P546S	R3HCC1L_ENST00000314594.5_5'UTR|R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000370584.3_Missense_Mutation_p.P546S	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	546			P -> S (in dbSNP:rs35122894).				nucleotide binding (GO:0000166)										TGTATCTTTTCCTGATAGGGA	0.428													C|||	48	0.00958466	0.0015	0.013	5008	,	,		19570	0.0		0.0258	False		,,,				2504	0.0112				p.P546S		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.C1636T						PASS	.	C	SER/PRO	23,4383	29.9+/-59.1	0,23,2180	138.0	133.0	134.0		1636	-0.9	0.4	10	dbSNP_126	134	271,8329	102.9+/-164.1	5,261,4034	yes	missense	C10orf28	NM_014472.4	74	5,284,6214	TT,TC,CC		3.1512,0.522,2.2605	benign	546/779	99969507	294,12712	2203	4300	6503	SO:0001583	missense	27291	exon4			TCTTTTCCTGATA	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1636C>T	10.37:g.99969507C>T	ENSP00000298999:p.Pro546Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	26	0.011904761904761904	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	18	0.023746701846965697	C	0.006	-2.029569	0.00410	0.00522	0.031512	ENSG00000166024	ENST00000370584;ENST00000298999	T;T	0.06142	3.34;3.34	4.85	-0.872	0.10638	.	0.467092	0.20282	N	0.095430	T	0.01558	0.0050	L	0.46741	1.465	0.19575	N	0.999967	B;B	0.26975	0.1;0.165	B;B	0.30855	0.032;0.121	T	0.36720	-0.9736	9	.	.	.	-3.1923	4.044	0.09764	0.0:0.3398:0.343:0.3172	rs35122894	546;546	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	S	546	ENSP00000359616:P546S;ENSP00000298999:P546S	.	P	+	1	0	C10orf28	99959497	0.975000	0.34042	0.373000	0.26003	0.026000	0.11368	0.183000	0.16919	0.153000	0.19213	0.491000	0.48974	CCT	C|0.980;T|0.020	0.020	strong		0.428	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
FLG	2312	hgsc.bcm.edu	37	1	152276626	152276626	+	Missense_Mutation	SNP	G	G	C	rs3126075	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276626G>C	ENST00000368799.1	-	3	10771	c.10736C>G	c.(10735-10737)aCg>aGg	p.T3579R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3579	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGATGGGACGTGGGGTGTCT	0.567									Ichthyosis				C|||	2393	0.477835	0.6074	0.4395	5008	,	,		15943	0.6498		0.1561	False		,,,				2504	0.4836				p.T3579R		Atlas-SNP	.											FLG,colon,carcinoma,-1,1	FLG	900	1	0			c.C10736G						scavenged	.	C	ARG/THR	1117,3267		429,259,1504	128.0	213.0	184.0		10736	-2.5	0.0	1	dbSNP_103	184	149,8435		32,85,4175	no	missense	FLG	NM_002016.1	71	461,344,5679	CC,CG,GG		1.7358,25.479,9.7625	benign	3579/4062	152276626	1266,11702	2192	4292	6484	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGACGTGGGGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10736C>G	1.37:g.152276626G>C	ENSP00000357789:p.Thr3579Arg	Somatic	458	0	0		WXS	Illumina HiSeq	Phase_I	284	61	0.214789	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	
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79.0	60.0	65.0					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	Somatic	228	7	0.0307018		WXS	Illumina HiSeq	Phase_I	247	8	0.0323887	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
CATSPER4	378807	hgsc.bcm.edu	37	1	26526439	26526439	+	Missense_Mutation	SNP	A	A	G	rs17257155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26526439A>G	ENST00000456354.2	+	7	944	c.877A>G	c.(877-879)Atc>Gtc	p.I293V		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	293			I -> V (in dbSNP:rs17257155).		calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		CTTCATCACCATCGGTGCCTT	0.522													A|||	664	0.132588	0.1823	0.0879	5008	,	,		21373	0.0119		0.1839	False		,,,				2504	0.1687				p.I293V		Atlas-SNP	.											.	CATSPER4	59	.	0			c.A877G						PASS	.	A	VAL/ILE	863,3543	339.1+/-305.6	95,673,1435	152.0	100.0	118.0		877	-6.3	0.0	1	dbSNP_123	118	1619,6981	299.7+/-304.6	153,1313,2834	yes	missense	CATSPER4	NM_198137.1	29	248,1986,4269	GG,GA,AA		18.8256,19.5869,19.0835	benign	293/473	26526439	2482,10524	2203	4300	6503	SO:0001583	missense	378807	exon7			ATCACCATCGGTG	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.877A>G	1.37:g.26526439A>G	ENSP00000390423:p.Ile293Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_198137	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	280	0.1282051282051282	95	0.19308943089430894	37	0.10220994475138122	9	0.015734265734265736	139	0.18337730870712401	A	10.21	1.287570	0.23478	0.195869	0.188256	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.98649	-5.05;-5.05	5.15	-6.3	0.02007	Ion transport (1);	0.828483	0.10515	N	0.665634	T	0.01287	0.0042	N	0.21545	0.675	0.80722	P	0.0	B;B	0.21071	0.051;0.041	B;B	0.21151	0.033;0.013	T	0.66468	-0.5916	9	0.46703	T	0.11	-2.5968	4.2766	0.10811	0.2033:0.5249:0.1593:0.1125	rs17257155;rs56610794;rs17257155	293;277	Q7RTX7;Q7RTX7-2	CTSR4_HUMAN;.	V	293	ENSP00000341006:I293V;ENSP00000390423:I293V	ENSP00000341006:I293V	I	+	1	0	CATSPER4	26399026	0.155000	0.22806	0.034000	0.17996	0.964000	0.63967	-0.170000	0.09897	-1.060000	0.03189	-0.644000	0.03951	ATC	A|0.836;G|0.164	0.164	strong		0.522	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
ZNF57	126295	hgsc.bcm.edu	37	19	2917287	2917287	+	Missense_Mutation	SNP	C	C	A	rs2288958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917287C>A	ENST00000306908.5	+	4	816	c.668C>A	c.(667-669)aCc>aAc	p.T223N	ZNF57_ENST00000523428.1_Missense_Mutation_p.T191N|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	223			T -> N (in dbSNP:rs2288958).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGAGAAAACCTACAAATGC	0.468													C|||	2345	0.468251	0.2398	0.5447	5008	,	,		22421	0.631		0.4642	False		,,,				2504	0.5593				p.T223N	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.C668A						PASS	.	C	ASN/THR	1204,3202	419.6+/-338.7	167,870,1166	104.0	89.0	94.0		668	-4.0	0.0	19	dbSNP_100	94	3845,4755	540.9+/-383.9	841,2163,1296	yes	missense	ZNF57	NM_173480.2	65	1008,3033,2462	AA,AC,CC		44.7093,27.3264,38.8205	benign	223/556	2917287	5049,7957	2203	4300	6503	SO:0001583	missense	126295	exon4			AGAAAACCTACAA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.668C>A	19.37:g.2917287C>A	ENSP00000303696:p.Thr223Asn	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	1026	0.4697802197802198	114	0.23170731707317074	187	0.5165745856353591	371	0.6486013986013986	354	0.46701846965699206	C	13.02	2.111658	0.37242	0.273264	0.447093	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.15372	2.43;2.43	2.02	-4.04	0.04010	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.25890	0.77	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.39272	-0.9622	8	0.66056	D	0.02	.	4.7224	0.12924	0.5138:0.3621:0.0:0.1241	rs2288958;rs61415421;rs2288958	223	Q68EA5	ZNF57_HUMAN	N	223;225;191	ENSP00000303696:T223N;ENSP00000430223:T191N	ENSP00000303696:T223N	T	+	2	0	ZNF57	2868287	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-2.633000	0.00869	-1.718000	0.01383	-0.535000	0.04281	ACC	C|0.581;A|0.419	0.419	strong		0.468	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
IKBKE	9641	hgsc.bcm.edu	37	1	206669465	206669465	+	Missense_Mutation	SNP	C	C	T	rs3748022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:206669465C>T	ENST00000367120.3	+	22	2511	c.2138C>T	c.(2137-2139)cCt>cTt	p.P713L	C1orf147_ENST00000367119.1_Intron|IKBKE_ENST00000537984.1_Missense_Mutation_p.P628L	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	713			P -> L (in dbSNP:rs3748022). {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)					GTCCCAGCACCTCCTGATGTC	0.532													C|||	742	0.148163	0.0182	0.3256	5008	,	,		22926	0.1935		0.2326	False		,,,				2504	0.0644				p.P713L		Atlas-SNP	.											IKBKE,NS,adenoma,0,1	IKBKE	77	1	0			c.C2138T						PASS	.	C	LEU/PRO,,LEU/PRO	195,4211	122.9+/-160.3	7,181,2015	132.0	107.0	116.0		1883,,2138	3.5	0.1	1	dbSNP_107	116	1876,6724	335.6+/-321.5	182,1512,2606	yes	missense,utr-3,missense	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	98,,98	189,1693,4621	TT,TC,CC		21.814,4.4258,15.9234	benign,,benign	628/632,,713/717	206669465	2071,10935	2203	4300	6503	SO:0001583	missense	9641	exon22			CAGCACCTCCTGA	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.2138C>T	1.37:g.206669465C>T	ENSP00000356087:p.Pro713Leu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_014002	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	407	0.18635531135531136	15	0.03048780487804878	105	0.2900552486187845	107	0.18706293706293706	180	0.23746701846965698	C	13.59	2.281232	0.40394	0.044258	0.21814	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.62639	0.01;0.16	4.38	3.45	0.39498	.	0.940554	0.08970	N	0.867304	T	0.00012	0.0000	N	0.14661	0.345	0.50632	P	1.1700000000003374E-4	B	0.18741	0.03	B	0.18561	0.022	T	0.11299	-1.0593	9	0.36615	T	0.2	1.8782	8.6908	0.34264	0.0:0.8967:0.0:0.1033	rs3748022;rs17434096;rs61028264;rs3748022	713	Q14164	IKKE_HUMAN	L	713;628	ENSP00000356087:P713L;ENSP00000444529:P628L	ENSP00000356087:P713L	P	+	2	0	IKBKE	204736088	0.003000	0.15002	0.057000	0.19452	0.813000	0.45954	1.861000	0.39438	1.401000	0.46761	0.655000	0.94253	CCT	C|0.844;T|0.156	0.156	strong		0.532	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
SGSH	6448	hgsc.bcm.edu	37	17	78184393	78184393	+	Missense_Mutation	SNP	C	C	T	rs7503034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78184393C>T	ENST00000326317.6	-	8	1453	c.1367G>A	c.(1366-1368)cGc>cAc	p.R456H	SGSH_ENST00000534910.1_Missense_Mutation_p.R253H	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	456			R -> H (does not affect enzyme activity; cells transfected with the mutant enzyme contain a 62 kDa precursor and a 56 kDa mature form as cells transfected with the wild-type enzyme; dbSNP:rs7503034). {ECO:0000269|PubMed:11182930, ECO:0000269|PubMed:12000360, ECO:0000269|PubMed:12702166, ECO:0000269|PubMed:15637719, ECO:0000269|PubMed:9158154, ECO:0000269|PubMed:9554748}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CTGAGCAAAGCGCGGGTCGGT	0.672													C|||	1732	0.345847	0.2126	0.4769	5008	,	,		18116	0.3998		0.3032	False		,,,				2504	0.4213				p.R456H		Atlas-SNP	.											.	SGSH	27	.	0			c.G1367A						PASS	.	C	HIS/ARG	973,3433	351.6+/-311.3	98,777,1328	32.0	34.0	33.0		1367	-6.9	0.0	17	dbSNP_116	33	2850,5750	435.0+/-357.9	447,1956,1897	yes	missense	SGSH	NM_000199.3	29	545,2733,3225	TT,TC,CC		33.1395,22.0835,29.3941	benign	456/503	78184393	3823,9183	2203	4300	6503	SO:0001583	missense	6448	exon8			GCAAAGCGCGGGT	BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	3.10.1.1		10818	protein-coding gene	gene with protein product	"""sulfamidase"", ""mucopolysaccharidosis type IIIA"""	605270				7493035	Standard	NM_000199		Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688		ENST00000326317.6:c.1367G>A	17.37:g.78184393C>T	ENSP00000314606:p.Arg456His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	50	0.549451	NM_000199	A8K5E2	Missense_Mutation	SNP	ENST00000326317.6	37	CCDS11770.1	713	0.32646520146520147	103	0.20934959349593496	161	0.4447513812154696	212	0.3706293706293706	237	0.31266490765171506	C	5.737	0.320438	0.10845	0.220835	0.331395	ENSG00000181523	ENST00000326317;ENST00000534910	T;T	0.77489	-1.1;-1.1	4.89	-6.91	0.01649	Alkaline-phosphatase-like, core domain (1);	1.486580	0.03365	N	0.198071	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.10730	-1.0617	9	0.45353	T	0.12	-3.0403	10.126	0.42649	0.0:0.3472:0.0928:0.56	rs7503034;rs52793683;rs60961709;rs7503034	456	P51688	SPHM_HUMAN	H	456;253	ENSP00000314606:R456H;ENSP00000437778:R253H	ENSP00000314606:R456H	R	-	2	0	SGSH	75798988	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.308000	0.08156	-1.268000	0.02439	-1.090000	0.02178	CGC	C|0.701;N|0.000	.	strong		0.672	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522387	144522387	+	Nonsense_Mutation	SNP	G	G	T	rs2272754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	90	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	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	
NOM1	64434	hgsc.bcm.edu	37	7	156742749	156742749	+	Silent	SNP	G	G	A	rs6969196	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:156742749G>A	ENST00000275820.3	+	1	333	c.318G>A	c.(316-318)caG>caA	p.Q106Q		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	106	Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.					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)		GCCCCGAACAGGGTCCCGGCC	0.706													.|||	1014	0.202476	0.2042	0.2392	5008	,	,		12063	0.2788		0.1511	False		,,,				2504	0.1483				p.Q106Q		Atlas-SNP	.											.	NOM1	73	.	0			c.G318A						PASS	.	G		436,2828		20,396,1216	2.0	3.0	3.0		318	2.5	0.0	7	dbSNP_116	3	717,6267		26,665,2801	no	coding-synonymous	NOM1	NM_138400.1		46,1061,4017	AA,AG,GG		10.2663,13.3578,11.251		106/861	156742749	1153,9095	1632	3492	5124	SO:0001819	synonymous_variant	64434	exon1			CGAACAGGGTCCC	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.318G>A	7.37:g.156742749G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	19	6	0.315789	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																			G|0.791;A|0.209	0.209	strong		0.706	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
COG1	9382	hgsc.bcm.edu	37	17	71197323	71197323	+	Missense_Mutation	SNP	G	G	C	rs62621249	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:71197323G>C	ENST00000299886.4	+	7	1437	c.1357G>C	c.(1357-1359)Gaa>Caa	p.E453Q		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	453					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			GCAGGAACTTGAAAGCAGCAC	0.468													G|||	252	0.0503195	0.0295	0.0663	5008	,	,		21462	0.0		0.0885	False		,,,				2504	0.0798				p.E453Q		Atlas-SNP	.											.	COG1	46	.	0			c.G1357C						PASS	.	G	GLN/GLU	153,4253	106.9+/-145.3	2,149,2052	121.0	117.0	118.0		1357	5.3	0.1	17	dbSNP_129	118	726,7874	176.5+/-226.3	38,650,3612	yes	missense	COG1	NM_018714.2	29	40,799,5664	CC,CG,GG		8.4419,3.4725,6.7584	possibly-damaging	453/981	71197323	879,12127	2203	4300	6503	SO:0001583	missense	9382	exon7			GAACTTGAAAGCA		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1357G>C	17.37:g.71197323G>C	ENSP00000299886:p.Glu453Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	121	0.0554029304029304	19	0.03861788617886179	33	0.09116022099447514	0	0.0	69	0.09102902374670185	G	10.37	1.331855	0.24167	0.034725	0.084419	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.24151	1.87;1.88	5.28	5.28	0.74379	.	0.098849	0.64402	D	0.000002	T	0.00998	0.0033	M	0.61703	1.905	0.09310	P	0.99999866012	P;P;P	0.44478	0.836;0.539;0.836	B;B;B	0.37267	0.245;0.135;0.245	T	0.12218	-1.0556	9	0.17369	T	0.5	-22.1809	19.2788	0.94042	0.0:0.0:1.0:0.0	rs62621249	453;453;453	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	Q	453	ENSP00000400111:E453Q;ENSP00000299886:E453Q	ENSP00000299886:E453Q	E	+	1	0	COG1	68708918	1.000000	0.71417	0.066000	0.19879	0.655000	0.38815	4.140000	0.58031	2.624000	0.88883	0.655000	0.94253	GAA	G|0.935;C|0.065	0.065	strong		0.468	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
NUP214	8021	hgsc.bcm.edu	37	9	134021630	134021630	+	Silent	SNP	A	A	G	rs2296710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134021630A>G	ENST00000359428.5	+	13	2028	c.1884A>G	c.(1882-1884)acA>acG	p.T628T	RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA|NUP214_ENST00000411637.2_Silent_p.T617T|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000586290.1_RNA|NUP214_ENST00000451030.1_Silent_p.T628T|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	628	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|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)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.T628T(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GCCACCCCACACCTCTCTCAG	0.552			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""								g|||	1735	0.346446	0.2821	0.2277	5008	,	,		18493	0.4276		0.3191	False		,,,				2504	0.4622				p.T628T	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	NUP214,NS,carcinoma,0,1	NUP214	166	1	1	Substitution - coding silent(1)	stomach(1)	c.A1884G						PASS	.			1195,3211	709.5+/-407.8	166,863,1174	357.0	314.0	328.0		1884	-1.5	0.0	9	dbSNP_100	328	2735,5865	681.0+/-403.7	446,1843,2011	no	coding-synonymous	NUP214	NM_005085.2		612,2706,3185	GG,GA,AA		31.8023,27.1221,30.2168		628/2091	134021630	3930,9076	2203	4300	6503	SO:0001819	synonymous_variant	8021	exon13			CCCCACACCTCTC	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1884A>G	9.37:g.134021630A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	141	138	0.978723	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	37	CCDS6940.1																																																																																			T|0.000;G|0.312;A|0.687	0.312	strong		0.552	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
MS4A5	64232	hgsc.bcm.edu	37	11	60198328	60198328	+	Silent	SNP	C	C	T	rs708229	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60198328C>T	ENST00000300190.2	+	2	299	c.213C>T	c.(211-213)acC>acT	p.T71T	MS4A5_ENST00000534071.1_Intron	NM_023945.2	NP_076434.2	Q9H3V2	MS4A5_HUMAN	membrane-spanning 4-domains, subfamily A, member 5	71						integral component of membrane (GO:0016021)				large_intestine(7)|lung(7)|ovary(1)|skin(1)	16						TCCTTTTCACCTTGTTAAAAC	0.363													C|||	1571	0.313698	0.4796	0.3069	5008	,	,		19758	0.2004		0.3131	False		,,,				2504	0.2117				p.T71T		Atlas-SNP	.											.	MS4A5	35	.	0			c.C213T						PASS	.	C		1836,2570	534.4+/-373.9	370,1096,737	211.0	207.0	208.0		213	-2.2	0.0	11	dbSNP_86	208	2667,5931	428.4+/-355.9	423,1821,2055	no	coding-synonymous	MS4A5	NM_023945.2		793,2917,2792	TT,TC,CC		31.0188,41.6704,34.6278		71/201	60198328	4503,8501	2203	4299	6502	SO:0001819	synonymous_variant	64232	exon2			TTTCACCTTGTTA	AB013103	CCDS7987.1	11q12	2008-03-25			ENSG00000166930	ENSG00000166930			13374	protein-coding gene	gene with protein product		606499				11245982, 11401424	Standard	NM_023945		Approved	CD20L2	uc001npo.3	Q9H3V2	OTTHUMG00000167613	ENST00000300190.2:c.213C>T	11.37:g.60198328C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	147	81	0.55102	NM_023945	Q9BZH1	Silent	SNP	ENST00000300190.2	37	CCDS7987.1	730	0.3342490842490842	230	0.46747967479674796	124	0.3425414364640884	143	0.25	233	0.3073878627968338	C	0.013	-1.612083	0.00835	0.416704	0.310188	ENSG00000166930	ENST00000528905	.	.	.	4.82	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47923	-0.9079	3	.	.	.	-0.0028	5.4591	0.16607	0.0:0.3876:0.1425:0.4698	rs708229;rs3168127;rs17433589;rs56628287;rs61544591;rs708229	.	.	.	F	45	.	.	L	+	1	0	MS4A5	59954904	0.007000	0.16637	0.000000	0.03702	0.006000	0.05464	-0.279000	0.08479	-0.301000	0.08882	-0.345000	0.07892	CTT	C|0.656;T|0.344	0.344	strong		0.363	MS4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395392.1		
EHHADH	1962	hgsc.bcm.edu	37	3	184910133	184910133	+	Missense_Mutation	SNP	G	G	T	rs11919970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184910133G>T	ENST00000231887.3	-	7	2128	c.2053C>A	c.(2053-2055)Cag>Aag	p.Q685K	EHHADH-AS1_ENST00000417720.1_RNA|EHHADH_ENST00000456310.1_Missense_Mutation_p.Q589K	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	685			Q -> K (in dbSNP:rs11919970).		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)			TCAGGGTTCTGCCTGTAATAT	0.493													G|||	890	0.177716	0.3903	0.1643	5008	,	,		18761	0.0665		0.0765	False		,,,				2504	0.1186				p.Q685K		Atlas-SNP	.											.	EHHADH	73	.	0			c.C2053A						PASS	.	G	LYS/GLN,LYS/GLN	1578,2828	488.7+/-361.3	292,994,917	74.0	82.0	79.0		1765,2053	3.9	1.0	3	dbSNP_120	79	718,7882	175.3+/-225.4	25,668,3607	yes	missense,missense	EHHADH	NM_001166415.1,NM_001966.3	53,53	317,1662,4524	TT,TG,GG		8.3488,35.8148,17.6534	benign,benign	589/628,685/724	184910133	2296,10710	2203	4300	6503	SO:0001583	missense	1962	exon7			GGTTCTGCCTGTA	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.2053C>A	3.37:g.184910133G>T	ENSP00000231887:p.Gln685Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	353	0.16163003663003664	192	0.3902439024390244	58	0.16022099447513813	41	0.07167832167832168	62	0.08179419525065963	G	5.397	0.258450	0.10239	0.358148	0.083488	ENSG00000113790	ENST00000231887;ENST00000456310	D;D	0.88896	-2.44;-2.44	5.91	3.9	0.45041	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.597524	0.17879	N	0.158930	T	0.00012	0.0000	N	0.11106	0.095	0.09310	P	0.9999999999297928	B	0.11235	0.004	B	0.08055	0.003	T	0.09773	-1.0659	9	0.20519	T	0.43	-10.6704	8.9521	0.35796	0.0:0.4174:0.335:0.2477	rs11919970;rs52831944;rs61245533;rs11919970	685	Q08426	ECHP_HUMAN	K	685;589	ENSP00000231887:Q685K;ENSP00000387746:Q589K	ENSP00000231887:Q685K	Q	-	1	0	EHHADH	186392827	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	2.777000	0.47717	1.447000	0.47661	0.655000	0.94253	CAG	G|0.822;T|0.178	0.178	strong		0.493	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
NEK1	4750	hgsc.bcm.edu	37	4	170428901	170428901	+	Missense_Mutation	SNP	C	C	T	rs33933790	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:170428901C>T	ENST00000439128.2	-	20	2432	c.1792G>A	c.(1792-1794)Gct>Act	p.A598T	NEK1_ENST00000511633.1_Missense_Mutation_p.A582T|NEK1_ENST00000507142.1_Missense_Mutation_p.A626T|NEK1_ENST00000512193.1_Missense_Mutation_p.A529T|NEK1_ENST00000510533.1_Missense_Mutation_p.A554T	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	598			A -> T (in dbSNP:rs33933790). {ECO:0000269|PubMed:17344846}.		cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		CTCATGTCAGCCTCTTCACTT	0.348													C|||	119	0.023762	0.0038	0.0346	5008	,	,		14938	0.0		0.0795	False		,,,				2504	0.0102				p.A626T		Atlas-SNP	.											.	NEK1	203	.	0			c.G1876A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	63,3621		1,61,1780	122.0	112.0	115.0		1876,1744,1585,1660,1792	1.8	1.0	4	dbSNP_126	115	655,7525		31,593,3466	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	58,58,58,58,58	32,654,5246	TT,TC,CC		8.0073,1.7101,6.0519	benign,benign,benign,benign,benign	626/1287,582/1243,529/1190,554/1215,598/1259	170428901	718,11146	1842	4090	5932	SO:0001583	missense	4750	exon22			TGTCAGCCTCTTC	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.1792G>A	4.37:g.170428901C>T	ENSP00000408020:p.Ala598Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	78	0.03571428571428571	3	0.006097560975609756	10	0.027624309392265192	0	0.0	65	0.08575197889182058	C	15.63	2.889056	0.52014	0.017101	0.080073	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.72282	-0.6;-0.6;-0.53;-0.64;-0.57	5.53	1.79	0.24919	.	0.307929	0.27495	N	0.019103	T	0.04318	0.0119	L	0.39397	1.21	0.38085	D	0.936805	B;B;B;B;B	0.26318	0.146;0.069;0.146;0.069;0.09	B;B;B;B;B	0.31337	0.128;0.056;0.128;0.056;0.06	T	0.06127	-1.0844	10	0.28530	T	0.3	.	7.5477	0.27777	0.1188:0.6787:0.0:0.2025	rs33933790;rs57604515	529;582;626;554;598	Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;NEK1_HUMAN	T	598;582;554;626;529	ENSP00000408020:A598T;ENSP00000423332:A582T;ENSP00000427653:A554T;ENSP00000424757:A626T;ENSP00000424938:A529T	ENSP00000408020:A598T	A	-	1	0	NEK1	170665476	0.151000	0.22747	0.998000	0.56505	0.884000	0.51177	0.194000	0.17135	0.363000	0.24346	0.655000	0.94253	GCT	C|0.961;T|0.039	0.039	strong		0.348	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
TIMM23	100287932	hgsc.bcm.edu	37	10	51620361	51620361	+	Missense_Mutation	SNP	G	G	C	rs148307270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:51620361G>C	ENST00000260867.4	-	2	251	c.128C>G	c.(127-129)tCt>tGt	p.S43C	TIMM23_ENST00000374064.3_Missense_Mutation_p.S43C|TIMM23_ENST00000374065.3_Missense_Mutation_p.S43C	NM_006327.3	NP_006318.1	O14925	TIM23_HUMAN	translocase of inner mitochondrial membrane 23 homolog (yeast)	43					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)	p.S43C(1)		endometrium(1)|large_intestine(1)|pancreas(1)	3						TAAATAAGGAGACAGAGGGTT	0.348																																					p.S43C		Atlas-SNP	.											TIMM23,NS,other,0,1	TIMM23	4	1	1	Substitution - Missense(1)	pancreas(1)	c.C128G						scavenged	.						10.0	12.0	12.0					10																	51620361		2136	4217	6353	SO:0001583	missense	100287932	exon2			TAAGGAGACAGAG	AF030162	CCDS73091.1	10q11.21-q11.23	2010-03-17			ENSG00000138297				17312	protein-coding gene	gene with protein product		605034				10339406	Standard	NM_006327		Approved	TIM23	uc010qha.2	O14925	OTTHUMG00000018213	ENST00000260867.4:c.128C>G	10.37:g.51620361G>C	ENSP00000260867:p.Ser43Cys	Somatic	1077	1	0.000928505		WXS	Illumina HiSeq	Phase_I	936	490	0.523504	NM_006327	Q53FF8|Q5T1E6|Q6P5S5	Missense_Mutation	SNP	ENST00000260867.4	37	CCDS7238.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841243	0.71488	.	.	ENSG00000138297	ENST00000260867;ENST00000374064;ENST00000374065	.	.	.	4.12	4.12	0.48240	.	0.117031	0.64402	D	0.000011	T	0.67382	0.2887	M	0.76727	2.345	0.58432	D	0.999995	B;B	0.15473	0.011;0.013	B;B	0.17433	0.018;0.007	T	0.69914	-0.5016	9	0.62326	D	0.03	-0.1752	15.0602	0.71947	0.0:0.0:1.0:0.0	.	43;43	B1APJ0;O14925	.;TIM23_HUMAN	C	43	.	ENSP00000260867:S43C	S	-	2	0	TIMM23	51290367	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.507000	0.90522	2.301000	0.77427	0.536000	0.68110	TCT	G|0.984;C|0.016	0.016	strong		0.348	TIMM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048040.1	NM_006327.2	
SNAPC4	6621	hgsc.bcm.edu	37	9	139272502	139272502	+	Silent	SNP	T	T	C	rs3812565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139272502T>C	ENST00000298532.2	-	21	4145	c.3777A>G	c.(3775-3777)ctA>ctG	p.L1259L		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)		CAGGCTGGGGTAGGGGCGGCT	0.746													N|||	1642	0.327875	0.2935	0.5648	5008	,	,		12956	0.1885		0.3549	False		,,,				2504	0.3221				p.L1259L		Atlas-SNP	.											SNAPC4,caecum,carcinoma,0,1	SNAPC4	82	1	0			c.A3777G						scavenged	.			899,2601		168,563,1019	4.0	5.0	4.0		3777	-2.4	0.0	9	dbSNP_107	4	2448,4658		514,1420,1619	no	coding-synonymous	SNAPC4	NM_003086.2		682,1983,2638	CC,CT,TT		34.4498,25.6857,31.5576		1259/1470	139272502	3347,7259	1750	3553	5303	SO:0001819	synonymous_variant	6621	exon21			CTGGGGTAGGGGC	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.3777A>G	9.37:g.139272502T>C		Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	47	13	0.276596	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			T|0.670;C|0.330	0.330	strong		0.746	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
SMCHD1	23347	hgsc.bcm.edu	37	18	2763697	2763697	+	Silent	SNP	C	C	T	rs483547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:2763697C>T	ENST00000320876.6	+	37	4967	c.4629C>T	c.(4627-4629)ggC>ggT	p.G1543G	SMCHD1_ENST00000261598.8_Silent_p.G1543G|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1543					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						CCATTAAAGGCTCTAATGAGG	0.358													C|||	1381	0.275759	0.264	0.317	5008	,	,		18800	0.1895		0.4612	False		,,,				2504	0.1605				p.G1543G		Atlas-SNP	.											SMCHD1,colon,carcinoma,0,3	SMCHD1	88	3	0			c.C4629T						PASS	.	C		1096,2578		176,744,917	86.0	83.0	84.0		4629	-2.0	1.0	18	dbSNP_83	84	3607,4579		805,1997,1291	no	coding-synonymous	SMCHD1	NM_015295.2		981,2741,2208	TT,TC,CC		44.063,29.8312,39.6543		1543/2006	2763697	4703,7157	1837	4093	5930	SO:0001819	synonymous_variant	23347	exon37			TAAAGGCTCTAAT	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.4629C>T	18.37:g.2763697C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			C|0.685;T|0.315	0.315	strong		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
GPR45	11250	hgsc.bcm.edu	37	2	105859249	105859249	+	Missense_Mutation	SNP	C	C	T	rs35946826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:105859249C>T	ENST00000258456.1	+	1	1050	c.934C>T	c.(934-936)Ctc>Ttc	p.L312F		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	312			L -> F (in dbSNP:rs35946826). {ECO:0000269|PubMed:10036181}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						CGTCCTGTGGCTCAGTTACCT	0.557													C|||	415	0.0828674	0.0424	0.1225	5008	,	,		19983	0.0218		0.159	False		,,,				2504	0.0941				p.L312F		Atlas-SNP	.											GPR45,colon,carcinoma,0,1	GPR45	73	1	0			c.C934T						PASS	.	C	PHE/LEU	222,4184	134.1+/-170.4	2,218,1983	131.0	129.0	130.0		934	4.6	1.0	2	dbSNP_126	130	1253,7347	249.9+/-277.0	107,1039,3154	yes	missense	GPR45	NM_007227.3	22	109,1257,5137	TT,TC,CC		14.5698,5.0386,11.3409	probably-damaging	312/373	105859249	1475,11531	2203	4300	6503	SO:0001583	missense	11250	exon1			CTGTGGCTCAGTT	AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"""GPCR / Class A : Orphans"""	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.934C>T	2.37:g.105859249C>T	ENSP00000258456:p.Leu312Phe	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	NM_007227	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	37	CCDS2066.1	209	0.09569597069597069	27	0.054878048780487805	45	0.12430939226519337	14	0.024475524475524476	123	0.16226912928759896	C	18.83	3.706211	0.68615	0.050386	0.145698	ENSG00000135973	ENST00000258456	T	0.47528	0.84	4.63	4.63	0.57726	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.00580	0.0019	M	0.85710	2.77	0.09310	P	0.99999885138	D	0.89917	1.0	D	0.83275	0.996	T	0.18053	-1.0349	9	0.51188	T	0.08	-31.7966	13.8309	0.63380	0.1534:0.8465:0.0:0.0	rs35946826	312	Q9Y5Y3	GPR45_HUMAN	F	312	ENSP00000258456:L312F	ENSP00000258456:L312F	L	+	1	0	GPR45	105225681	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.759000	0.62227	2.586000	0.87340	0.456000	0.33151	CTC	C|0.891;T|0.109	0.109	strong		0.557	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227	
SMARCA5	8467	hgsc.bcm.edu	37	4	144442735	144442735	+	Silent	SNP	C	C	T	rs11541117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:144442735C>T	ENST00000283131.3	+	3	868	c.406C>T	c.(406-408)Cta>Tta	p.L136L		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	136					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					GCAGAACTTACTATCCGTTGG	0.378													C|||	2603	0.519768	0.5129	0.4251	5008	,	,		15820	0.744		0.4175	False		,,,				2504	0.4703				p.L136L		Atlas-SNP	.											.	SMARCA5	73	.	0			c.C406T						PASS	.	C		2287,2119	594.5+/-388.2	596,1095,512	42.0	41.0	42.0		406	1.1	0.1	4	dbSNP_120	42	3646,4954	517.0+/-378.9	789,2068,1443	no	coding-synonymous	SMARCA5	NM_003601.3		1385,3163,1955	TT,TC,CC		42.3953,48.0935,45.6174		136/1053	144442735	5933,7073	2203	4300	6503	SO:0001819	synonymous_variant	8467	exon3			AACTTACTATCCG	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.406C>T	4.37:g.144442735C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	130	80	0.615385	NM_003601		Silent	SNP	ENST00000283131.3	37	CCDS3761.1																																																																																			C|0.512;T|0.488	0.488	strong		0.378	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3		
TEKT4	150483	hgsc.bcm.edu	37	2	95537501	95537501	+	Silent	SNP	C	C	T	rs11889464	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:95537501C>T	ENST00000295201.4	+	1	314	c.177C>T	c.(175-177)cgC>cgT	p.R59R	TEKT4_ENST00000427593.2_Silent_p.R59R|AC097374.2_ENST00000568768.1_RNA	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	50	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	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	
RHO	6010	hgsc.bcm.edu	37	3	129251142	129251142	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:129251142G>A	ENST00000296271.3	+	3	673	c.579G>A	c.(577-579)acG>acA	p.T193T		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	193					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)	p.T193T(2)		breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	ACTACTACACGCTCAAGCCGG	0.547																																					p.T193T	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											RHO,caecum,carcinoma,0,2	RHO	57	2	2	Substitution - coding silent(2)	large_intestine(2)	c.G579A						scavenged	.						275.0	217.0	236.0					3																	129251142		2203	4300	6503	SO:0001819	synonymous_variant	6010	exon3			CTACACGCTCAAG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.579G>A	3.37:g.129251142G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	185	2	0.0108108	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	37	CCDS3063.1																																																																																			.	.	none		0.547	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	
ZNF92	168374	hgsc.bcm.edu	37	7	64864607	64864607	+	Missense_Mutation	SNP	G	G	A	rs10239197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:64864607G>A	ENST00000328747.7	+	4	1779	c.1580G>A	c.(1579-1581)cGt>cAt	p.R527H	ZNF92_ENST00000431504.1_Missense_Mutation_p.R451H|ZNF92_ENST00000450302.2_Missense_Mutation_p.R458H|ZNF92_ENST00000357512.2_Missense_Mutation_p.R495H	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	527			R -> H (in dbSNP:rs10239197).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				CTTACTGCACGTAAGATAATT	0.323													a|||	1745	0.348442	0.5809	0.4251	5008	,	,		19397	0.3145		0.162	False		,,,				2504	0.2065				p.R527H		Atlas-SNP	.											.	ZNF92	68	.	0			c.G1580A						PASS	.	A	HIS/ARG,HIS/ARG	2174,2232	580.2+/-385.1	558,1058,587	44.0	52.0	49.0		1373,1580	0.4	0.0	7	dbSNP_119	49	1418,7182	745.3+/-407.3	132,1154,3014	no	missense,missense	ZNF92	NM_007139.2,NM_152626.2	29,29	690,2212,3601	AA,AG,GG		16.4884,49.3418,27.618	benign,benign	458/518,527/587	64864607	3592,9414	2203	4300	6503	SO:0001583	missense	168374	exon4			CTGCACGTAAGAT	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"""Zinc fingers, C2H2-type"", ""-"""	13168	protein-coding gene	gene with protein product		603974	"""zinc finger protein 92 (HTF12)"""			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.1580G>A	7.37:g.64864607G>A	ENSP00000332595:p.Arg527His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_152626	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	37	CCDS34646.1	700	0.32051282051282054	283	0.5752032520325203	128	0.35359116022099446	178	0.3111888111888112	111	0.14643799472295516	A	0.038	-1.295299	0.01375	0.493418	0.164884	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.06218	3.33;3.33;3.33;3.33	0.418	0.418	0.16429	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00007	-3.17	0.53688	P	2.999999999997449E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37549	-0.9701	8	0.02654	T	1	.	4.0144	0.09637	0.7235:0.0:0.2765:0.0	rs10239197;rs10239197	495;527	Q03936-3;Q03936	.;ZNF92_HUMAN	H	527;451;495;458	ENSP00000332595:R527H;ENSP00000400495:R451H;ENSP00000350113:R495H;ENSP00000396126:R458H	ENSP00000332595:R527H	R	+	2	0	ZNF92	64502042	0.974000	0.33945	0.002000	0.10522	0.002000	0.02628	3.533000	0.53561	-0.525000	0.06391	-0.550000	0.04213	CGT	G|0.717;A|0.283	0.283	strong		0.323	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626	
COL20A1	57642	hgsc.bcm.edu	37	20	61945439	61945439	+	Missense_Mutation	SNP	G	G	C	rs147670144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61945439G>C	ENST00000358894.6	+	19	2474	c.2374G>C	c.(2374-2376)Gcc>Ccc	p.A792P	COL20A1_ENST00000326996.6_Missense_Mutation_p.A792P|COL20A1_ENST00000422202.1_Missense_Mutation_p.A799P|COL20A1_ENST00000435874.1_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	139	0	0		WXS	Illumina HiSeq	Phase_I	173	58	0.33526	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	
RAB6C	84084	hgsc.bcm.edu	37	2	130738163	130738163	+	Missense_Mutation	SNP	G	G	A	rs144773989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:130738163G>A	ENST00000410061.2	+	1	929	c.475G>A	c.(475-477)Gct>Act	p.A159T	AC079776.7_ENST00000412425.1_RNA	NM_032144.2	NP_115520.2	Q9H0N0	RAB6C_HUMAN	RAB6C, member RAS oncogene family	159	Required for centrosome localization.		A -> T. {ECO:0000269|PubMed:11054569, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12007787, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell cycle process (GO:0022402)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of centrosome duplication (GO:0010824)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	5	Colorectal(110;0.1)					TAGGGCAAAAGCTGGATACAA	0.458													.|||	2890	0.577077	0.3366	0.6859	5008	,	,		23155	0.6101		0.6928	False		,,,				2504	0.6718				p.A159T		Atlas-SNP	.											RAB6C,NS,carcinoma,-1,1	RAB6C	28	1	0			c.G475A						PASS	.						108.0	95.0	99.0					2																	130738163		2203	4297	6500	SO:0001583	missense	84084	exon1			GCAAAAGCTGGAT	AF124200	CCDS46408.1	2q21.1	2012-07-02			ENSG00000222014	ENSG00000222014		"""RAB, member RAS oncogene"""	16525	protein-coding gene	gene with protein product		612909				11054569, 17426708	Standard	NM_032144		Approved	WTH3	uc002tpx.1	Q9H0N0	OTTHUMG00000153487	ENST00000410061.2:c.475G>A	2.37:g.130738163G>A	ENSP00000387307:p.Ala159Thr	Somatic	511	0	0		WXS	Illumina HiSeq	Phase_I	460	318	0.691304	NM_032144	Q53RU3|Q6FIF7|Q9P128	Missense_Mutation	SNP	ENST00000410061.2	37	CCDS46408.1	.	.	.	.	.	.	.	.	.	.	.	9.294	1.051337	0.19827	.	.	ENSG00000222014	ENST00000410061	T	0.76578	-1.03	0.652	-0.869	0.10649	Small GTP-binding protein domain (1);	.	.	.	.	T	0.33789	0.0875	N	0.00149	-1.99	0.24763	P	0.99291617	B	0.10296	0.003	B	0.11329	0.006	T	0.42430	-0.9452	8	0.11485	T	0.65	-6.1379	5.2636	0.15588	0.2646:0.0:0.7354:0.0	.	159	Q9H0N0	RAB6C_HUMAN	T	159	ENSP00000387307:A159T	ENSP00000387307:A159T	A	+	1	0	RAB6C	130454633	0.960000	0.32886	0.004000	0.12327	0.305000	0.27757	0.594000	0.24014	-0.306000	0.08818	0.121000	0.15741	GCT	G|0.417;A|0.583	0.583	strong		0.458	RAB6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331384.1	NM_032144	
RASEF	158158	hgsc.bcm.edu	37	9	85613354	85613354	+	Silent	SNP	A	A	G	rs34303676	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:85613354A>G	ENST00000376447.3	-	13	1991	c.1731T>C	c.(1729-1731)gaT>gaC	p.D577D		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	577					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(4)|liver(1)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TCATTTGGAAATCAACTCCTG	0.443													A|||	156	0.0311502	0.0461	0.0187	5008	,	,		17788	0.0		0.0308	False		,,,				2504	0.0521				p.D577D		Atlas-SNP	.											.	RASEF	69	.	0			c.T1731C						PASS	.	A		139,4267	97.6+/-136.3	1,137,2065	147.0	137.0	141.0		1731	0.6	1.0	9	dbSNP_126	141	320,8280	113.1+/-173.2	2,316,3982	no	coding-synonymous	RASEF	NM_152573.2		3,453,6047	GG,GA,AA		3.7209,3.1548,3.5291		577/741	85613354	459,12547	2203	4300	6503	SO:0001819	synonymous_variant	158158	exon13			TTGGAAATCAACT	AK056176	CCDS6662.1	9q21.33	2014-05-09	2004-06-11	2004-06-16	ENSG00000165105	ENSG00000165105		"""EF-hand domain containing"", ""RAB, member RAS oncogene"""	26464	protein-coding gene	gene with protein product		611344	"""RAB45, member RAS oncogene family"""	RAB45		17448446	Standard	NM_152573		Approved	FLJ31614	uc004amo.2	Q8IZ41	OTTHUMG00000020100	ENST00000376447.3:c.1731T>C	9.37:g.85613354A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_152573	A6NC29|Q96N04	Silent	SNP	ENST00000376447.3	37	CCDS6662.1																																																																																			A|0.966;G|0.034	0.034	strong		0.443	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573	
TRIM15	89870	hgsc.bcm.edu	37	6	30131515	30131515	+	Silent	SNP	C	C	A	rs2523733	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30131515C>A	ENST00000376694.4	+	1	523	c.54C>A	c.(52-54)ctC>ctA	p.L18L	TRIM10_ENST00000449742.2_5'Flank|TRIM15_ENST00000376688.1_Silent_p.L18L|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	110	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	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	
DAP3	7818	hgsc.bcm.edu	37	1	155699118	155699118	+	Silent	SNP	T	T	C	rs4933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:155699118T>C	ENST00000368336.5	+	9	928	c.804T>C	c.(802-804)ctT>ctC	p.L268L	MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000421487.2_Silent_p.L234L|DAP3_ENST00000471642.2_Silent_p.L227L|DAP3_ENST00000343043.3_Silent_p.L268L|MSTO1_ENST00000538143.1_Intron|DAP3_ENST00000535183.1_Silent_p.L227L	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	268					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TCAATGCTCTTTGGGGAAGAA	0.453													T|||	292	0.0583067	0.1316	0.0418	5008	,	,		18175	0.0		0.0557	False		,,,				2504	0.0337				p.L268L		Atlas-SNP	.											.	DAP3	46	.	0			c.T804C						PASS	.	T	,,,,	454,3952	211.8+/-231.9	22,410,1771	103.0	101.0	101.0		804,702,681,804,804	1.3	1.0	1	dbSNP_52	101	429,8171	130.5+/-188.4	9,411,3880	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DAP3	NM_001199849.1,NM_001199850.1,NM_001199851.1,NM_004632.3,NM_033657.2	,,,,	31,821,5651	CC,CT,TT		4.9884,10.3041,6.7892	,,,,	268/399,234/365,227/358,268/399,268/399	155699118	883,12123	2203	4300	6503	SO:0001819	synonymous_variant	7818	exon9			TGCTCTTTGGGGA	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"""Mitochondrial ribosomal proteins / small subunits"""	2673	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S29"""	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.804T>C	1.37:g.155699118T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	166	91	0.548193	NM_033657	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Silent	SNP	ENST00000368336.5	37	CCDS1120.1																																																																																			A|0.000;C|0.066;G|0.000;T|0.934	0.066	strong		0.453	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632	
TATDN2	9797	hgsc.bcm.edu	37	3	10302172	10302172	+	Missense_Mutation	SNP	G	G	A	rs394558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:10302172G>A	ENST00000287652.4	+	3	1817	c.766G>A	c.(766-768)Gtc>Atc	p.V256I	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Missense_Mutation_p.V256I	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	256			V -> I (in dbSNP:rs394558). {ECO:0000269|PubMed:15489334}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						AACCCCAGAGGTCAGCATGGA	0.552													A|||	2986	0.596246	0.3737	0.4207	5008	,	,		19472	0.9643		0.4304	False		,,,				2504	0.8129				p.V256I		Atlas-SNP	.											.	TATDN2	59	.	0			c.G766A						PASS	.	A	ILE/VAL	1647,2759	657.7+/-400.3	312,1023,868	64.0	60.0	61.0		766	0.8	0.0	3	dbSNP_80	61	3466,5134	635.5+/-399.0	697,2072,1531	yes	missense	TATDN2	NM_014760.3	29	1009,3095,2399	AA,AG,GG		40.3023,37.3808,39.3126	possibly-damaging	256/762	10302172	5113,7893	2203	4300	6503	SO:0001583	missense	9797	exon3			CCAGAGGTCAGCA	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.766G>A	3.37:g.10302172G>A	ENSP00000287652:p.Val256Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	1222	0.5595238095238095	195	0.39634146341463417	154	0.425414364640884	559	0.9772727272727273	314	0.41424802110817943	A	3.840	-0.034032	0.07543	0.373808	0.403023	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.25250	1.81;1.81	4.81	0.786	0.18590	.	0.557126	0.13504	N	0.382984	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.18310	0.027	B	0.11329	0.006	T	0.42344	-0.9457	9	0.08837	T	0.75	-7.8544	5.5043	0.16846	0.2461:0.0:0.6091:0.1447	rs394558;rs52804764;rs59440092;rs394558	256	Q93075	TATD2_HUMAN	I	256	ENSP00000287652:V256I;ENSP00000408736:V256I	ENSP00000287652:V256I	V	+	1	0	TATDN2	10277172	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.634000	0.24614	0.055000	0.16094	-1.822000	0.00598	GTC	G|0.518;A|0.482	0.482	strong		0.552	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
CDHR4	389118	hgsc.bcm.edu	37	3	49836707	49836707	+	Silent	SNP	G	G	A	rs7629936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49836707G>A	ENST00000412678.2	-	2	221	c.213C>T	c.(211-213)gcC>gcT	p.A71A	CDHR4_ENST00000343366.4_Silent_p.A71A|CDHR4_ENST00000487256.1_Silent_p.A71A	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	71					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						CTTGCCACCTGGCCAAGCTGG	0.567													G|||	1168	0.233227	0.2632	0.1844	5008	,	,		19701	0.1488		0.2386	False		,,,				2504	0.3088				p.A71A		Atlas-SNP	.											CDHR4,caecum,carcinoma,0,1	CDHR4	37	1	0			c.C213T						PASS	.	G		938,3054		111,716,1169	74.0	78.0	76.0		213	-3.8	0.0	3	dbSNP_116	76	1927,6429		212,1503,2463	no	coding-synonymous	CDHR4	NM_001007540.2		323,2219,3632	AA,AG,GG		23.0613,23.497,23.2021		71/789	49836707	2865,9483	1996	4178	6174	SO:0001819	synonymous_variant	389118	exon2			CCACCTGGCCAAG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.213C>T	3.37:g.49836707G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	220	220	1	NM_001007540	Q6UXT0	Silent	SNP	ENST00000412678.2	37	CCDS46829.1																																																																																			G|0.775;A|0.225	0.225	strong		0.567	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
MPP1	4354	hgsc.bcm.edu	37	X	154020114	154020114	+	Silent	SNP	C	C	A	rs1126762	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:154020114C>A	ENST00000369534.3	-	3	402	c.255G>T	c.(253-255)acG>acT	p.T85T	MPP1_ENST00000393531.1_Silent_p.T85T|MPP1_ENST00000462825.1_Intron|MPP1_ENST00000413259.3_Silent_p.T55T	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	85	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	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)					TCAGCTTCAGCGTGATTCCCT	0.423													A|||	2054	0.544106	0.1573	0.4914	3775	,	,		14052	0.5605		0.5964	False		,,,				2504	0.3476				p.T85T		Atlas-SNP	.											.	MPP1	52	.	0			c.G255T						PASS	.	A	,,,	978,2857		123,597,135,912,436	114.0	88.0	97.0		204,255,165,255	-1.0	0.9	X	dbSNP_86	97	4861,1867		1257,966,1381,205,491	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MPP1	NM_001166460.1,NM_001166461.1,NM_001166462.1,NM_002436.3	,,,	1380,1563,1516,1117,927	AA,AC,A,CC,C		27.7497,25.502,44.7221	,,,	68/450,85/447,55/437,85/467	154020114	5839,4724	2203	4300	6503	SO:0001819	synonymous_variant	4354	exon3			CTTCAGCGTGATT		CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"""membrane protein, palmitoylated 1 (55kD)"""	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.255G>T	X.37:g.154020114C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001166461	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Silent	SNP	ENST00000369534.3	37	CCDS14762.1																																																																																			C|0.440;0|0.014	.	strong		0.423	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436	
FAM129C	199786	hgsc.bcm.edu	37	19	17660300	17660300	+	Missense_Mutation	SNP	G	G	A	rs11666267	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17660300G>A	ENST00000335393.4	+	15	1945	c.1807G>A	c.(1807-1809)Ggc>Agc	p.G603S	FAM129C_ENST00000599164.1_Missense_Mutation_p.G572S|FAM129C_ENST00000595684.1_Missense_Mutation_p.G603S|FAM129C_ENST00000599124.1_Missense_Mutation_p.G536S|FAM129C_ENST00000600871.1_Intron|FAM129C_ENST00000332386.5_Missense_Mutation_p.G603S|FAM129C_ENST00000449408.2_Missense_Mutation_p.G329S|FAM129C_ENST00000352727.3_Missense_Mutation_p.G567S|FAM129C_ENST00000601861.1_Missense_Mutation_p.G572S	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	603			G -> S (in dbSNP:rs11666267).					p.G603S(1)		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						CACTCTGGACGGCTGCTTGGA	0.562													G|||	2018	0.402955	0.3427	0.3818	5008	,	,		19109	0.3651		0.5537	False		,,,				2504	0.3834				p.G603S		Atlas-SNP	.											FAM129C,NS,carcinoma,0,1	FAM129C	110	1	1	Substitution - Missense(1)	stomach(1)	c.G1807A						PASS	.	G	SER/GLY,SER/GLY	1659,2747	504.9+/-366.0	311,1037,855	119.0	116.0	117.0		1807,1807	1.7	0.0	19	dbSNP_120	117	4833,3767	615.5+/-396.4	1375,2083,842	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	56,56	1686,3120,1697	AA,AG,GG		43.8023,37.6532,49.9154	possibly-damaging,possibly-damaging	603/652,603/698	17660300	6492,6514	2203	4300	6503	SO:0001583	missense	199786	exon15			CTGGACGGCTGCT	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.1807G>A	19.37:g.17660300G>A	ENSP00000335040:p.Gly603Ser	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	77	27	0.350649	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	906	0.41483516483516486	167	0.3394308943089431	149	0.4116022099447514	178	0.3111888111888112	412	0.5435356200527705	G	7.374	0.627412	0.14257	0.376532	0.561977	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000449408	T;T;T;T	0.24350	2.21;2.3;1.96;1.86	2.73	1.68	0.24146	.	0.676700	0.12241	N	0.486478	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	P;P;P;P	0.40230	0.708;0.708;0.708;0.708	B;B;B;B	0.31946	0.138;0.087;0.087;0.087	T	0.40924	-0.9537	9	0.06494	T	0.89	-11.9487	5.6065	0.17383	0.154:0.0:0.846:0.0	rs11666267;rs17710528;rs52789437;rs57563079;rs11666267	603;603;567;603	Q86XR2;Q86XR2-3;Q86XR2-4;Q86XR2-2	NIBL2_HUMAN;.;.;.	S	603;603;567;329	ENSP00000335040:G603S;ENSP00000333447:G603S;ENSP00000341067:G567S;ENSP00000394929:G329S	ENSP00000333447:G603S	G	+	1	0	FAM129C	17521300	0.007000	0.16637	0.002000	0.10522	0.003000	0.03518	1.228000	0.32588	0.729000	0.32403	0.557000	0.71058	GGC	G|0.543;A|0.456	0.456	strong		0.562	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
ZNF492	57615	hgsc.bcm.edu	37	19	22846623	22846623	+	Missense_Mutation	SNP	G	G	A	rs71355986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	73	0	0		WXS	Illumina HiSeq	Phase_I	58	20	0.344828	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	
MRGPRF	116535	hgsc.bcm.edu	37	11	68777323	68777323	+	Splice_Site	SNP	T	T	C	rs11544721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:68777323T>C	ENST00000309099.6	-	2	429	c.47A>G	c.(46-48)aAg>aGg	p.K16R	RP11-554A11.6_ENST00000569432.1_RNA|MRGPRF_ENST00000441623.1_Splice_Site_p.K16R|MRGPRF_ENST00000320913.6_Missense_Mutation_p.K16R|RP11-554A11.6_ENST00000569428.1_RNA|RP11-554A11.6_ENST00000538407.2_RNA	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	16			K -> R (in dbSNP:rs11544721). {ECO:0000269|PubMed:16303743}.			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)			GGCACTTACCTTGTTCCTGTT	0.682													T|||	1534	0.30631	0.3563	0.2594	5008	,	,		16522	0.2887		0.3012	False		,,,				2504	0.2955				p.K16R		Atlas-SNP	.											.	MRGPRF	22	.	0			c.A47G						PASS	.	T	ARG/LYS,ARG/LYS	1443,2957	465.5+/-354.2	246,951,1003	77.0	69.0	72.0		47,47	3.5	1.0	11	dbSNP_120	72	2492,6096	406.4+/-348.8	370,1752,2172	yes	missense-near-splice,missense-near-splice	MRGPRF	NM_001098515.1,NM_145015.4	26,26	616,2703,3175	CC,CT,TT		29.0172,32.7955,30.2972	benign,benign	16/344,16/344	68777323	3935,9053	2200	4294	6494	SO:0001630	splice_region_variant	116535	exon2			CTTACCTTGTTCC	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.48+1A>G	11.37:g.68777323T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_001098515	B3KV43|Q8NBK8	Missense_Mutation	SNP	ENST00000309099.6	37	CCDS8188.1	671	0.30723443223443225	191	0.3882113821138211	94	0.2596685082872928	174	0.3041958041958042	212	0.2796833773087071	T	10.04	1.242268	0.22796	0.327955	0.290172	ENSG00000172935	ENST00000441623;ENST00000309099;ENST00000421543;ENST00000320913	T;T;T	0.55930	3.35;3.35;0.49	3.47	3.47	0.39725	.	0.000000	0.40469	N	0.001100	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	1.0	B	0.27823	0.19	B	0.24701	0.055	T	0.41963	-0.9479	9	0.16420	T	0.52	-17.2217	8.5952	0.33712	0.0:0.0:0.0:1.0	rs11544721;rs12361947	16	Q96AM1	MRGRF_HUMAN	R	16	ENSP00000403660:K16R;ENSP00000309782:K16R;ENSP00000323414:K16R	ENSP00000309782:K16R	K	-	2	0	MRGPRF	68533899	1.000000	0.71417	0.996000	0.52242	0.363000	0.29612	1.181000	0.32017	1.597000	0.50072	0.374000	0.22700	AAG	T|0.700;C|0.300	0.300	strong		0.682	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	Missense_Mutation
STK17A	9263	hgsc.bcm.edu	37	7	43647879	43647879	+	Silent	SNP	C	C	T	rs11555026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:43647879C>T	ENST00000319357.5	+	3	623	c.444C>T	c.(442-444)gaC>gaT	p.D148D	STK17A_ENST00000462448.1_3'UTR	NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						AAATCTTTGACCAGTGTGTTG	0.373													C|||	456	0.0910543	0.0091	0.1354	5008	,	,		17699	0.0119		0.2167	False		,,,				2504	0.1227				p.D148D		Atlas-SNP	.											.	STK17A	31	.	0			c.C444T						PASS	.	C		173,4233	113.3+/-151.4	5,163,2035	92.0	91.0	92.0		444	2.9	1.0	7	dbSNP_120	92	1816,6784	326.4+/-317.4	194,1428,2678	no	coding-synonymous	STK17A	NM_004760.2		199,1591,4713	TT,TC,CC		21.1163,3.9265,15.2929		148/415	43647879	1989,11017	2203	4300	6503	SO:0001819	synonymous_variant	9263	exon3			CTTTGACCAGTGT	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 1"""	604726	"""serine/threonine kinase 17a (apoptosis-inducing)"""			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.444C>T	7.37:g.43647879C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_004760	A4D1V6|Q8IVC8	Silent	SNP	ENST00000319357.5	37	CCDS5470.1																																																																																			C|0.858;T|0.142	0.142	strong		0.373	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
FMN2	56776	hgsc.bcm.edu	37	1	240371484	240371484	+	Silent	SNP	A	A	T	rs202006855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371484A>T	ENST00000319653.9	+	5	3602	c.3372A>T	c.(3370-3372)ctA>ctT	p.L1124L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1124	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)			CTCCCCCTCTACCCGGAGCGG	0.711																																					p.L1124L		Atlas-SNP	.											FMN2,rectum,carcinoma,0,3	FMN2	451	3	0			c.A3372T						scavenged	.						8.0	10.0	9.0					1																	240371484		2106	4139	6245	SO:0001819	synonymous_variant	56776	exon5			CCCTCTACCCGGA	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.3372A>T	1.37:g.240371484A>T		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	88	12	0.136364	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.975;T|0.026	0.026	strong		0.711	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
FAM217A	222826	hgsc.bcm.edu	37	6	4069685	4069685	+	Missense_Mutation	SNP	C	C	T	rs639905	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:4069685C>T	ENST00000274673.3	-	7	1175	c.772G>A	c.(772-774)Gct>Act	p.A258T	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	258			A -> T (in dbSNP:rs639905).														AAGTCTAGAGCACTGAAAGGA	0.418													T|||	1486	0.296725	0.4107	0.2997	5008	,	,		18758	0.3542		0.1889	False		,,,				2504	0.1922				p.A258T		Atlas-SNP	.											.	.	.	.	0			c.G772A						PASS	.	T	THR/ALA	1735,2671	647.9+/-398.6	345,1045,813	82.0	83.0	83.0		772	-1.1	0.0	6	dbSNP_83	83	1508,7092	747.9+/-407.3	138,1232,2930	yes	missense	C6orf146	NM_173563.2	58	483,2277,3743	TT,TC,CC		17.5349,39.3781,24.9346	benign	258/509	4069685	3243,9763	2203	4300	6503	SO:0001583	missense	222826	exon7			CTAGAGCACTGAA	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 146"""	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.772G>A	6.37:g.4069685C>T	ENSP00000274673:p.Ala258Thr	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	670	0.3067765567765568	210	0.4268292682926829	100	0.27624309392265195	212	0.3706293706293706	148	0.19525065963060687	T	0.078	-1.188431	0.01607	0.393781	0.175349	ENSG00000145975	ENST00000274673;ENST00000538080;ENST00000470599	T	0.19105	2.17	5.43	-1.11	0.09840	.	0.614820	0.16862	N	0.196476	T	0.00695	0.0023	N	0.00104	-2.125	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.35798	-0.9774	9	0.02654	T	1	-1.6331	5.6412	0.17565	0.1471:0.4406:0.0:0.4123	rs639905;rs57001715;rs639905	258	Q8IXS0	CF146_HUMAN	T	258;105;386	ENSP00000274673:A258T	ENSP00000274673:A258T	A	-	1	0	C6orf146	4014684	0.004000	0.15560	0.002000	0.10522	0.672000	0.39443	0.226000	0.17776	-0.624000	0.05611	-2.248000	0.00284	GCT	C|0.732;T|0.268	0.268	strong		0.418	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	
PIP5K1C	23396	hgsc.bcm.edu	37	19	3653525	3653525	+	Silent	SNP	C	C	T	rs2074957	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3653525C>T	ENST00000335312.3	-	7	772	c.684G>A	c.(682-684)tcG>tcA	p.S228S	PIP5K1C_ENST00000589578.1_Silent_p.S228S|PIP5K1C_ENST00000539785.1_Silent_p.S228S|PIP5K1C_ENST00000537021.1_Silent_p.S228S|PIP5K1C_ENST00000587482.1_5'UTR	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	228	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		TCTTGCCCCCCGACTGCACGC	0.627													C|||	2719	0.542931	0.4463	0.6513	5008	,	,		17959	0.6865		0.5636	False		,,,				2504	0.4274				p.S228S	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-SNP	.											PIP5K1C_ENST00000335312,NS,carcinoma,-1,1	PIP5K1C	63	1	0			c.G684A						PASS	.	C	,	2030,2376	562.1+/-380.9	462,1106,635	117.0	90.0	99.0		684,684	-8.1	0.9	19	dbSNP_96	99	4856,3744	616.2+/-396.5	1373,2110,817	no	coding-synonymous,coding-synonymous	PIP5K1C	NM_001195733.1,NM_012398.2	,	1835,3216,1452	TT,TC,CC		43.5349,46.0735,47.0552	,	228/641,228/669	3653525	6886,6120	2203	4300	6503	SO:0001819	synonymous_variant	23396	exon7			GCCCCCCGACTGC	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.684G>A	19.37:g.3653525C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_001195733	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Silent	SNP	ENST00000335312.3	37	CCDS32872.1																																																																																			C|0.455;T|0.545	0.545	strong		0.627	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398	
DAAM2	23500	hgsc.bcm.edu	37	6	39855288	39855288	+	Silent	SNP	C	C	A	rs35383047	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:39855288C>A	ENST00000398904.2	+	16	2162	c.1980C>A	c.(1978-1980)atC>atA	p.I660I	RP11-61I13.3_ENST00000606829.1_RNA|RP11-61I13.3_ENST00000420293.1_RNA|DAAM2_ENST00000538976.1_Silent_p.I660I|RP11-61I13.3_ENST00000607675.1_RNA|RP11-61I13.3_ENST00000607215.1_RNA|RP11-61I13.3_ENST00000430595.1_RNA|DAAM2_ENST00000274867.4_Silent_p.I660I			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	660	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				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)					CTGAAGACATCTACCTGGCTT	0.537													C|||	793	0.158347	0.2753	0.1009	5008	,	,		18699	0.1806		0.0626	False		,,,				2504	0.1166				p.I660I		Atlas-SNP	.											.	DAAM2	101	.	0			c.C1980A						PASS	.	C	,	853,3023		90,673,1175	64.0	69.0	67.0		1980,1980	4.5	1.0	6	dbSNP_126	67	406,7864		12,382,3741	no	coding-synonymous,coding-synonymous	DAAM2	NM_001201427.1,NM_015345.3	,	102,1055,4916	AA,AC,CC		4.9093,22.0072,10.3656	,	660/1069,660/1068	39855288	1259,10887	1938	4135	6073	SO:0001819	synonymous_variant	23500	exon16			AGACATCTACCTG	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.1980C>A	6.37:g.39855288C>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Silent	SNP	ENST00000398904.2	37	CCDS56426.1																																																																																			C|0.882;A|0.118	0.118	strong		0.537	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
UEVLD	55293	hgsc.bcm.edu	37	11	18600283	18600283	+	Missense_Mutation	SNP	T	T	C	rs61752314	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:18600283T>C	ENST00000541984.1	-	2	177	c.115A>G	c.(115-117)Atg>Gtg	p.M39V	UEVLD_ENST00000379387.4_Missense_Mutation_p.M39V|UEVLD_ENST00000396197.3_Missense_Mutation_p.M39V|UEVLD_ENST00000300038.7_Missense_Mutation_p.M39V|UEVLD_ENST00000535484.1_Start_Codon_SNP_p.M1V|UEVLD_ENST00000540666.1_Intron|UEVLD_ENST00000320750.6_Missense_Mutation_p.M39V|UEVLD_ENST00000543987.1_Missense_Mutation_p.M39V	NM_001261386.1	NP_001248315.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TAGGTGTCCATGGAATATTTG	0.328													T|||	196	0.0391374	0.1157	0.0115	5008	,	,		18474	0.0149		0.0159	False		,,,				2504	0.0041				p.M39V		Atlas-SNP	.											.	UEVLD	58	.	0			c.A115G						PASS	.	T	VAL/MET,VAL/MET	434,3964	209.2+/-230.0	21,392,1786	116.0	111.0	113.0		115,115	0.5	1.0	11	dbSNP_129	113	154,8432	74.5+/-137.1	0,154,4139	yes	missense,missense	UEVLD	NM_001040697.1,NM_018314.3	21,21	21,546,5925	CC,CT,TT		1.7936,9.8681,4.5287	benign,benign	39/472,39/380	18600283	588,12396	2199	4293	6492	SO:0001583	missense	55293	exon2			TGTCCATGGAATA	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000541984.1:c.115A>G	11.37:g.18600283T>C	ENSP00000437538:p.Met39Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	22	0.372881	NM_001040697		Missense_Mutation	SNP	ENST00000541984.1	37	CCDS58125.1	76	0.0347985347985348	56	0.11382113821138211	4	0.011049723756906077	5	0.008741258741258742	11	0.014511873350923483	T	12.24	1.880002	0.33162	0.098681	0.017936	ENSG00000151116	ENST00000543987;ENST00000535484;ENST00000396197;ENST00000320750;ENST00000379387;ENST00000541984;ENST00000300038	D;D;T;D;T;T	0.82711	-1.52;-1.59;-0.66;-1.64;-0.78;-1.04	5.83	0.493	0.16878	Ubiquitin E2 variant, N-terminal (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.336293	0.42172	N	0.000751	T	0.03136	0.0092	N	0.25332	0.735	0.32523	N	0.535977	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.12837	0.001;0.008;0.001;0.001;0.001	T	0.15838	-1.0423	10	0.27785	T	0.31	-5.6767	6.128	0.20189	0.1121:0.1743:0.0:0.7137	rs61752314	39;39;39;39;39	Q8IX04-5;B4DL43;Q8IX04-3;Q8IX04-2;Q8IX04	.;.;.;.;UEVLD_HUMAN	V	39;1;39;39;39;39;39	ENSP00000442974:M39V;ENSP00000441092:M1V;ENSP00000379500:M39V;ENSP00000323353:M39V;ENSP00000368697:M39V;ENSP00000437538:M39V	ENSP00000300038:M39V	M	-	1	0	UEVLD	18556859	1.000000	0.71417	0.989000	0.46669	0.978000	0.69477	1.481000	0.35476	-0.125000	0.11703	0.459000	0.35465	ATG	T|0.959;C|0.041	0.041	strong		0.328	UEVLD-015	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000395928.1	NM_018314	
EDDM3A	10876	hgsc.bcm.edu	37	14	21215923	21215923	+	Missense_Mutation	SNP	G	G	T	rs34552133	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21215923G>T	ENST00000326842.2	+	2	311	c.184G>T	c.(184-186)Ggc>Tgc	p.G62C		NM_006683.4	NP_006674.2	Q14507	EP3A_HUMAN	epididymal protein 3A	62			G -> C (in dbSNP:rs34552133).		sperm displacement (GO:0007321)	extracellular space (GO:0005615)				breast(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						GGCTCTGAAAGGCAAGAGCTT	0.378													G|||	566	0.113019	0.062	0.0519	5008	,	,		21696	0.1627		0.1064	False		,,,				2504	0.181				p.G62C		Atlas-SNP	.											.	EDDM3A	15	.	0			c.G184T						PASS	.	G	CYS/GLY	286,4120	157.0+/-190.0	12,262,1929	106.0	107.0	107.0		184	0.2	0.0	14	dbSNP_126	107	922,7678	204.8+/-247.4	49,824,3427	yes	missense	EDDM3A	NM_006683.4	159	61,1086,5356	TT,TG,GG		10.7209,6.4911,9.288	probably-damaging	62/148	21215923	1208,11798	2203	4300	6503	SO:0001583	missense	10876	exon2			CTGAAAGGCAAGA	X76383	CCDS9556.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181562	ENSG00000181562			16978	protein-coding gene	gene with protein product		611580	"""family with sequence similarity 12, member A"""	FAM12A		7514008	Standard	NM_006683		Approved	HE3-ALPHA	uc001vyc.3	Q14507	OTTHUMG00000029581	ENST00000326842.2:c.184G>T	14.37:g.21215923G>T	ENSP00000315098:p.Gly62Cys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_006683	Q4KN33	Missense_Mutation	SNP	ENST00000326842.2	37	CCDS9556.1	225	0.10302197802197802	27	0.054878048780487805	26	0.0718232044198895	94	0.16433566433566432	78	0.10290237467018469	G	11.97	1.797746	0.31777	0.064911	0.107209	ENSG00000181562	ENST00000326842	T	0.41758	0.99	2.46	0.182	0.15077	Ribonuclease A, domain (2);	1.031530	0.07726	N	0.944462	T	0.00241	0.0007	L	0.40543	1.245	0.80722	P	0.0	D	0.67145	0.996	P	0.62813	0.907	T	0.05225	-1.0898	9	0.62326	D	0.03	.	3.8521	0.08959	0.1757:0.3849:0.4394:0.0	rs34552133	62	Q14507	EP3A_HUMAN	C	62	ENSP00000315098:G62C	ENSP00000315098:G62C	G	+	1	0	EDDM3A	20285763	0.001000	0.12720	0.000000	0.03702	0.129000	0.20672	0.484000	0.22308	-0.138000	0.11434	0.313000	0.20887	GGC	T|0.100;G|0.900;A|0.000	0.100	strong		0.378	EDDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073742.3		
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464779	39464779	+	Missense_Mutation	SNP	T	T	C	rs72828119	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39464779T>C	ENST00000391352.1	-	1	726	c.727A>G	c.(727-729)Agc>Ggc	p.S243G		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	243	11 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						GCCTGGCAGCTACTGGTCACA	0.602													T|||	335	0.066893	0.1188	0.0403	5008	,	,		23172	0.0506		0.0775	False		,,,				2504	0.0215				p.S243G		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.A727G						PASS	.																																			SO:0001583	missense	100505753	exon1			GGCAGCTACTGGT	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.727A>G	17.37:g.39464779T>C	ENSP00000375147:p.Ser243Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	179	0.08195970695970696	65	0.13211382113821138	18	0.049723756906077346	31	0.05419580419580419	65	0.08575197889182058	T	1.360	-0.588992	0.03799	.	.	ENSG00000212657	ENST00000391352	T	0.00760	5.73	4.18	1.95	0.26073	.	.	.	.	.	T	0.00039	0.0001	M	0.61703	1.905	0.48975	P	2.6999999999999247E-4	.	.	.	.	.	.	T	0.46911	-0.9157	6	0.45353	T	0.12	.	8.022	0.30415	0.0:0.2704:0.0:0.7296	.	.	.	.	G	243	ENSP00000375147:S243G	ENSP00000375147:S243G	S	-	1	0	KRTAP16-1	36718305	0.168000	0.22989	0.309000	0.25155	0.761000	0.43186	0.168000	0.16622	0.072000	0.16694	-1.447000	0.01057	AGC	T|0.917;C|0.083	0.083	strong		0.602	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
HOMER3	9454	hgsc.bcm.edu	37	19	19049194	19049194	+	Silent	SNP	G	G	A	rs11540741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19049194G>A	ENST00000539827.1	-	3	923	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	AC005932.1_ENST00000601106.1_RNA|HOMER3_ENST00000594439.1_Silent_p.L91L|HOMER3_ENST00000594794.1_Intron|HOMER3_ENST00000392351.3_Silent_p.L91L|HOMER3_ENST00000542541.2_Silent_p.L91L|HOMER3_ENST00000221222.11_Silent_p.L91L|HOMER3_ENST00000355887.6_Silent_p.L91L|HOMER3_ENST00000433218.2_Silent_p.L91L			Q9NSC5	HOME3_HUMAN	homer homolog 3 (Drosophila)	91	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				G-protein coupled glutamate receptor signaling pathway (GO:0007216)|protein targeting (GO:0006605)	basal part of cell (GO:0045178)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(3)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10			Epithelial(12;0.0107)			GCAAAGCCCAGGCCGTAGACT	0.597													G|||	331	0.0660942	0.0091	0.0951	5008	,	,		15228	0.0565		0.1451	False		,,,				2504	0.0511				p.L91L		Atlas-SNP	.											.	HOMER3	19	.	0			c.C271T						PASS	.	G	,,,	132,4274	96.7+/-135.4	3,126,2074	106.0	100.0	102.0		271,271,271,271	3.2	0.8	19	dbSNP_120	102	1325,7275	254.6+/-279.8	108,1109,3083	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HOMER3	NM_001145721.1,NM_001145722.1,NM_001145724.1,NM_004838.3	,,,	111,1235,5157	AA,AG,GG		15.407,2.9959,11.2025	,,,	91/359,91/362,91/326,91/362	19049194	1457,11549	2203	4300	6503	SO:0001819	synonymous_variant	9454	exon4			AGCCCAGGCCGTA	Y18894	CCDS12391.1, CCDS46022.1, CCDS46023.1	19p13.1	2008-02-05				ENSG00000051128			17514	protein-coding gene	gene with protein product		604800				10653696, 9808459	Standard	NM_004838		Approved	HOMER-3	uc002nkv.2	Q9NSC5		ENST00000539827.1:c.271C>T	19.37:g.19049194G>A		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	130	77	0.592308	NM_001145722	E9PCW9|O14580|O95350|Q9NSB9|Q9NSC0|Q9NSC1	Silent	SNP	ENST00000539827.1	37	CCDS12391.1																																																																																			G|0.895;A|0.105	0.105	strong		0.597	HOMER3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464607.1		
FLG	2312	hgsc.bcm.edu	37	1	152279019	152279019	+	Silent	SNP	G	G	A	rs57670307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152279019G>A	ENST00000368799.1	-	3	8378	c.8343C>T	c.(8341-8343)gaC>gaT	p.D2781D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2781	Ser-rich.		D -> Y (in dbSNP:rs2065958).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCCTGACCGTCTTGGGATG	0.607									Ichthyosis																												p.D2781D		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.C8343T						PASS	.	C		87,4307		0,87,2110	459.0	597.0	550.0		8343	-6.8	0.0	1	dbSNP_129	550	660,7940		0,660,3640	no	coding-synonymous	FLG	NM_002016.1		0,747,5750	AA,AG,GG		7.6744,1.98,5.7488		2781/4062	152279019	747,12247	2197	4300	6497	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCGTCTTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8343C>T	1.37:g.152279019G>A		Somatic	663	1	0.0015083		WXS	Illumina HiSeq	Phase_I	1064	203	0.190789	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			G|0.939;A|0.061	0.061	strong		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458476	39458476	+	Missense_Mutation	SNP	A	A	T	rs1001191	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	101	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	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		
PDZD2	23037	hgsc.bcm.edu	37	5	32091076	32091076	+	Missense_Mutation	SNP	G	G	A	rs377748174		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:32091076G>A	ENST00000438447.1	+	20	7910	c.7522G>A	c.(7522-7524)Gtg>Atg	p.V2508M	PDZD2_ENST00000282493.3_Missense_Mutation_p.V2508M			O15018	PDZD2_HUMAN	PDZ domain containing 2	2508					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						GCCGAGCGCCGTGCTCTTCAA	0.637																																					p.V2508M		Atlas-SNP	.											PDZD2,NS,carcinoma,0,1	PDZD2	306	1	0			c.G7522A						scavenged	.	G	MET/VAL	0,4406		0,0,2203	55.0	56.0	56.0		7522	-1.8	0.0	5		56	1,8599	1.2+/-3.3	0,1,4299	no	missense	PDZD2	NM_178140.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	2508/2840	32091076	1,13005	2203	4300	6503	SO:0001583	missense	23037	exon19			AGCGCCGTGCTCT	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.7522G>A	5.37:g.32091076G>A	ENSP00000402033:p.Val2508Met	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	196	3	0.0153061	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	3.318	-0.139282	0.06669	0.0	1.16E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.07327	3.2;3.2	5.32	-1.78	0.07957	.	0.981044	0.08314	N	0.964822	T	0.06600	0.0169	L	0.38838	1.175	0.09310	N	1	B	0.26775	0.159	B	0.20955	0.032	T	0.38243	-0.9670	10	0.42905	T	0.14	.	6.9628	0.24608	0.5512:0.1305:0.3183:0.0	.	2508	O15018	PDZD2_HUMAN	M	2508;2309;2508	ENSP00000402033:V2508M;ENSP00000282493:V2508M	ENSP00000282493:V2508M	V	+	1	0	PDZD2	32126833	0.000000	0.05858	0.004000	0.12327	0.061000	0.15899	0.143000	0.16115	-0.487000	0.06735	-1.069000	0.02264	GTG	.	.	weak		0.637	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
METTL21C	196541	hgsc.bcm.edu	37	13	103339365	103339365	+	Silent	SNP	A	A	G	rs660207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103339365A>G	ENST00000267273.6	-	3	330	c.325T>C	c.(325-327)Ttg>Ctg	p.L109L		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	109					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						TGGAAATTCAATTCCTCGGCA	0.393													G|||	2396	0.478435	0.6286	0.3847	5008	,	,		19452	0.4544		0.4712	False		,,,				2504	0.3742				p.L109L		Atlas-SNP	.											METTL21C,NS,carcinoma,+2,1	METTL21C	23	1	0			c.T325C						PASS	.	G		2717,1689	512.9+/-368.2	821,1075,307	83.0	77.0	79.0		325	-0.1	0.9	13	dbSNP_83	79	4128,4472	590.2+/-392.6	955,2218,1127	no	coding-synonymous	METTL21C	NM_001010977.1		1776,3293,1434	GG,GA,AA		48.0,38.3341,47.3704		109/265	103339365	6845,6161	2203	4300	6503	SO:0001819	synonymous_variant	196541	exon3			AATTCAATTCCTC		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"""chromosome 13 open reading frame 39"""	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.325T>C	13.37:g.103339365A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_001010977		Silent	SNP	ENST00000267273.6	37	CCDS32003.1																																																																																			A|0.483;G|0.517	0.517	strong		0.393	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977	
TTF2	8458	hgsc.bcm.edu	37	1	117635413	117635413	+	Missense_Mutation	SNP	A	A	G	rs80076283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:117635413A>G	ENST00000369466.4	+	18	2910	c.2866A>G	c.(2866-2868)Agt>Ggt	p.S956G	MIR942_ENST00000401111.1_RNA	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	956					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)		AGAACAGCTCAGTGCTTTGAC	0.502													A|||	44	0.00878594	0.0	0.0072	5008	,	,		19861	0.0		0.0239	False		,,,				2504	0.0153				p.S956G		Atlas-SNP	.											.	TTF2	92	.	0			c.A2866G						PASS	.	A	GLY/SER	16,4390	23.3+/-48.9	0,16,2187	199.0	167.0	178.0		2866	1.5	0.6	1	dbSNP_131	178	227,8373	93.5+/-155.5	4,219,4077	yes	missense	TTF2	NM_003594.3	56	4,235,6264	GG,GA,AA		2.6395,0.3631,1.8684	benign	956/1163	117635413	243,12763	2203	4300	6503	SO:0001583	missense	8458	exon18			CAGCTCAGTGCTT	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.2866A>G	1.37:g.117635413A>G	ENSP00000358478:p.Ser956Gly	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	21	0.009615384615384616	0	0.0	1	0.0027624309392265192	0	0.0	20	0.026385224274406333	A	9.898	1.206042	0.22205	0.003631	0.026395	ENSG00000116830	ENST00000369466	T	0.75704	-0.96	5.06	1.51	0.23008	.	0.164529	0.29185	N	0.012882	T	0.48554	0.1506	M	0.64997	1.995	0.33498	D	0.589534	B	0.23735	0.09	B	0.18263	0.021	T	0.21177	-1.0253	10	0.38643	T	0.18	-0.497	6.5752	0.22562	0.7164:0.0:0.2836:0.0	.	956	Q9UNY4	TTF2_HUMAN	G	956	ENSP00000358478:S956G	ENSP00000358478:S956G	S	+	1	0	TTF2	117436936	1.000000	0.71417	0.646000	0.29493	0.339000	0.28857	2.188000	0.42612	0.092000	0.17331	0.528000	0.53228	AGT	A|0.987;G|0.013	0.013	strong		0.502	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
MYO1G	64005	hgsc.bcm.edu	37	7	45009723	45009723	+	Silent	SNP	G	G	A	rs11555636	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:45009723G>A	ENST00000258787.7	-	10	1384	c.1248C>T	c.(1246-1248)aaC>aaT	p.N416N		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	416	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						GCAGCTTCTCGTTGCAGTAGT	0.582													G|||	2923	0.583666	0.4667	0.611	5008	,	,		18789	0.7619		0.5596	False		,,,				2504	0.5634				p.N416N		Atlas-SNP	.											.	MYO1G	86	.	0			c.C1248T						PASS	.	G		2151,2255	580.2+/-385.1	533,1085,585	74.0	67.0	69.0		1248	-8.5	0.1	7	dbSNP_120	69	4974,3626	623.0+/-397.4	1451,2072,777	no	coding-synonymous	MYO1G	NM_033054.2		1984,3157,1362	AA,AG,GG		42.1628,48.8198,45.2176		416/1019	45009723	7125,5881	2203	4300	6503	SO:0001819	synonymous_variant	64005	exon10			CTTCTCGTTGCAG	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.1248C>T	7.37:g.45009723G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Silent	SNP	ENST00000258787.7	37	CCDS34629.1																																																																																			G|0.439;A|0.561	0.561	strong		0.582	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
NOP56	10528	hgsc.bcm.edu	37	20	2637071	2637071	+	Silent	SNP	T	T	C	rs8958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:2637071T>C	ENST00000329276.5	+	9	1551	c.1035T>C	c.(1033-1035)acT>acC	p.T345T	SNORD56_ENST00000413522.1_RNA|SNORD57_ENST00000448188.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORD86_ENST00000391196.1_RNA|NOP56_ENST00000492135.1_3'UTR|SNORA51_ENST00000606420.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	345	Nop. {ECO:0000255|PROSITE- ProRule:PRU00690}.				cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GGGGTAACACTCCAAAATATG	0.483													T|||	3374	0.673722	0.7549	0.683	5008	,	,		18133	0.626		0.6064	False		,,,				2504	0.6759				p.T345T		Atlas-SNP	.											.	NOP56	73	.	0			c.T1035C						PASS	.	T		3217,1189	709.5+/-407.8	1171,875,157	74.0	74.0	74.0		1035	-1.6	1.0	20	dbSNP_52	74	5248,3352	643.1+/-399.9	1614,2020,666	no	coding-synonymous	NOP56	NM_006392.3		2785,2895,823	CC,CT,TT		38.9767,26.9859,34.9147		345/595	2637071	8465,4541	2203	4300	6503	SO:0001819	synonymous_variant	10528	exon9			TAACACTCCAAAA	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1035T>C	20.37:g.2637071T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	116	114	0.982759	NM_006392	Q2M3T6|Q9NQ05	Silent	SNP	ENST00000329276.5	37	CCDS13030.1	1438	0.6584249084249084	387	0.7865853658536586	246	0.6795580110497238	346	0.6048951048951049	459	0.6055408970976254	T	7.754	0.703984	0.15172	0.730141	0.610233	ENSG00000101361	ENST00000415272	.	.	.	5.91	-1.64	0.08318	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.24512	-1.0158	3	.	.	.	-24.3311	2.0915	0.03658	0.175:0.2571:0.0948:0.4731	rs8958;rs742841;rs1043187;rs1043410;rs17353776;rs60430678	.	.	.	P	86	.	.	L	+	2	0	NOP56	2585071	0.597000	0.26874	0.975000	0.42487	0.995000	0.86356	-0.124000	0.10595	-0.621000	0.05633	-0.275000	0.10095	CTC	T|0.349;C|0.651	0.651	strong		0.483	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
UBC	7316	hgsc.bcm.edu	37	12	125397244	125397244	+	Silent	SNP	A	A	G	rs71458876	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:125397244A>G	ENST00000536769.1	-	1	2650	c.1074T>C	c.(1072-1074)cgT>cgC	p.R358R	UBC_ENST00000538617.1_Intron|UBC_ENST00000536661.1_5'Flank|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000546120.1_Silent_p.R282R|UBC_ENST00000339647.5_Silent_p.R358R			P0CG48	UBC_HUMAN	ubiquitin C	358	Ubiquitin-like 5. {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)			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)		CAGACAGGGTACGACCATCTT	0.512													G|||	64	0.0127796	0.028	0.0231	5008	,	,		28475	0.0		0.0099	False		,,,				2504	0.001				p.R358R		Atlas-SNP	.											.	UBC	79	.	0			c.T1074C						PASS	.	G		123,4283	812.8+/-416.1	6,111,2086	181.0	168.0	172.0		1074	1.2	1.0	12	dbSNP_130	172	71,8523	813.9+/-407.0	2,67,4228	no	coding-synonymous	UBC	NM_021009.5		8,178,6314	GG,GA,AA		0.8262,2.7916,1.4923		358/686	125397244	194,12806	2203	4297	6500	SO:0001819	synonymous_variant	7316	exon2			CAGGGTACGACCA		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		ENST00000536769.1:c.1074T>C	12.37:g.125397244A>G		Somatic	371	1	0.00269542		WXS	Illumina HiSeq	Phase_I	317	168	0.529968	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	37	CCDS9260.1																																																																																			A|0.985;G|0.015	0.015	strong		0.512	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009	
LRP8	7804	hgsc.bcm.edu	37	1	53716416	53716416	+	Silent	SNP	G	G	A	rs3737983	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:53716416G>A	ENST00000306052.6	-	17	2723	c.2622C>T	c.(2620-2622)gaC>gaT	p.D874D	LRP8_ENST00000354412.3_Silent_p.D670D|LRP8_ENST00000465675.1_Silent_p.D427D|LRP8_ENST00000371454.2_Silent_p.D874D|LRP8_ENST00000347547.2_Silent_p.D704D	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	874					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						GCTCATCTTCGTCTTCTTCTT	0.453													A|||	1857	0.370807	0.2466	0.2867	5008	,	,		21922	0.6984		0.4076	False		,,,				2504	0.2229				p.D874D		Atlas-SNP	.											LRP8,NS,carcinoma,-2,1	LRP8	58	1	0			c.C2622T						PASS	.	A	,,,	1178,3228	711.3+/-408.0	167,844,1192	376.0	308.0	331.0		2622,2622,2010,2112	-2.7	0.9	1	dbSNP_107	331	3536,5064	630.9+/-398.4	733,2070,1497	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRP8	NM_001018054.2,NM_004631.4,NM_017522.4,NM_033300.3	,,,	900,2914,2689	AA,AG,GG		41.1163,26.7363,36.2448	,,,	874/905,874/964,670/701,704/794	53716416	4714,8292	2203	4300	6503	SO:0001819	synonymous_variant	7804	exon17			ATCTTCGTCTTCT	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"""Low density lipoprotein receptors"""	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.2622C>T	1.37:g.53716416G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	179	90	0.502793	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Silent	SNP	ENST00000306052.6	37	CCDS578.1																																																																																			G|0.603;A|0.397	0.397	strong		0.453	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631	
SETD1B	23067	hgsc.bcm.edu	37	12	122248047	122248047	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:122248047C>T	ENST00000604567.1	+	6	1264	c.1196C>T	c.(1195-1197)cCg>cTg	p.P399L	SETD1B_ENST00000267197.5_Missense_Mutation_p.P399L|SETD1B_ENST00000542440.1_Missense_Mutation_p.P399L			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	399	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						GCTTTCTCTCCGTATCAGACC	0.642																																					p.P399L		Atlas-SNP	.											.	SETD1B	105	.	0			c.C1196T						PASS	.						4.0	6.0	5.0					12																	122248047		685	1573	2258	SO:0001583	missense	23067	exon5			TCTCTCCGTATCA	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.1196C>T	12.37:g.122248047C>T	ENSP00000474253:p.Pro399Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	113	5	0.0442478	NM_015048	F6MFW1	Missense_Mutation	SNP	ENST00000604567.1	37		.	.	.	.	.	.	.	.	.	.	C	12.85	2.060661	0.36373	.	.	ENSG00000139718	ENST00000542440;ENST00000267197	D;D	0.94576	-3.46;-3.46	4.78	4.78	0.61160	.	.	.	.	.	D	0.96250	0.8777	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.64506	0.926	D	0.96855	0.9628	9	0.72032	D	0.01	.	17.8068	0.88604	0.0:1.0:0.0:0.0	.	399	Q9UPS6	SET1B_HUMAN	L	399	ENSP00000442924:P399L;ENSP00000267197:P399L	ENSP00000267197:P399L	P	+	2	0	SETD1B	120732430	1.000000	0.71417	0.821000	0.32701	0.484000	0.33280	5.401000	0.66326	2.196000	0.70406	0.467000	0.42956	CCG	.	.	none		0.642	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
AKAP12	9590	hgsc.bcm.edu	37	6	151673074	151673074	+	Missense_Mutation	SNP	C	C	G	rs41289375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151673074C>G	ENST00000253332.1	+	3	3737	c.3548C>G	c.(3547-3549)cCa>cGa	p.P1183R	AKAP12_ENST00000354675.6_Missense_Mutation_p.P1085R|AKAP12_ENST00000359755.5_Missense_Mutation_p.P1078R|AKAP12_ENST00000402676.2_Missense_Mutation_p.P1183R			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1183					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)		TTTGACGCACCAGGCACAACC	0.562													C|||	95	0.0189696	0.0015	0.0144	5008	,	,		19502	0.001		0.0427	False		,,,				2504	0.0399				p.P1183R	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.C3548G						PASS	.	C	ARG/PRO,ARG/PRO	58,4348	54.9+/-90.9	0,58,2145	109.0	105.0	106.0		3548,3254	-10.2	0.0	6	dbSNP_127	106	448,8152	134.3+/-191.7	12,424,3864	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	103,103	12,482,6009	GG,GC,CC		5.2093,1.3164,3.8905	benign,benign	1183/1783,1085/1685	151673074	506,12500	2203	4300	6503	SO:0001583	missense	9590	exon4			ACGCACCAGGCAC	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.3548C>G	6.37:g.151673074C>G	ENSP00000253332:p.Pro1183Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	37	0.01694139194139194	0	0.0	11	0.03038674033149171	1	0.0017482517482517483	25	0.032981530343007916	C	8.327	0.825517	0.16749	0.013164	0.052093	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07021	3.23;3.23;3.23;3.23	5.08	-10.2	0.00374	.	1.298180	0.05918	N	0.633016	T	0.01061	0.0035	N	0.19112	0.55	0.09310	N	1	B;B;B	0.23128	0.078;0.078;0.08	B;B;B	0.27608	0.081;0.081;0.037	T	0.42865	-0.9426	10	0.16420	T	0.52	.	5.5532	0.17101	0.1541:0.4816:0.1776:0.1868	rs41289375	1078;1085;1183	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	R	1183;1183;1085;1078	ENSP00000384537:P1183R;ENSP00000253332:P1183R;ENSP00000346702:P1085R;ENSP00000352794:P1078R	ENSP00000253332:P1183R	P	+	2	0	AKAP12	151714767	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.032000	0.01426	-2.125000	0.00821	-0.693000	0.03709	CCA	C|0.968;G|0.032	0.032	strong		0.562	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
ABCA4	24	hgsc.bcm.edu	37	1	94544234	94544234	+	Missense_Mutation	SNP	T	T	C	rs3112831	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:94544234T>C	ENST00000370225.3	-	10	1354	c.1268A>G	c.(1267-1269)cAc>cGc	p.H423R	ABCA4_ENST00000535735.1_Missense_Mutation_p.H423R	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	423			H -> R (in dbSNP:rs3112831). {ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11527935, ECO:0000269|PubMed:12111378}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CTTCCTAACGTGTTCCAGTTC	0.453													C|||	1106	0.220847	0.1316	0.3026	5008	,	,		14062	0.254		0.2913	False		,,,				2504	0.1769				p.H423R		Atlas-SNP	.											ABCA4,NS,carcinoma,-1,2	ABCA4	275	2	0			c.A1268G	GRCh37	CM015072|CM032802	ABCA4	M	rs3112831	PASS	.	C	ARG/HIS	729,3677	757.8+/-412.8	63,603,1537	196.0	184.0	188.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1268	5.5	0.2	1	dbSNP_103	188	2661,5939	685.7+/-404.1	395,1871,2034	yes	missense	ABCA4	NM_000350.2	29	458,2474,3571	CC,CT,TT		30.9419,16.5456,26.0649	benign	423/2274	94544234	3390,9616	2203	4300	6503	SO:0001583	missense	24	exon10			CTAACGTGTTCCA	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1268A>G	1.37:g.94544234T>C	ENSP00000359245:p.His423Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	179	177	0.988827	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	538	0.24633699633699635	77	0.1565040650406504	106	0.292817679558011	133	0.23251748251748253	222	0.2928759894459103	C	11.96	1.795287	0.31777	0.165456	0.309419	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.83591	-1.74;-1.74	5.49	5.49	0.81192	.	0.000000	0.85682	N	0.000000	T	0.30135	0.0755	N	0.00074	-2.255	0.47245	P	6.399999999999739E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08994	-1.0695	9	0.22706	T	0.39	.	14.5395	0.67982	0.0:0.9297:0.0:0.0703	rs3112831;rs17461660;rs60698303;rs3112831	423;423	F5H6E5;P78363	.;ABCA4_HUMAN	R	423	ENSP00000359245:H423R;ENSP00000437682:H423R	ENSP00000359245:H423R	H	-	2	0	ABCA4	94316822	0.950000	0.32346	0.222000	0.23844	0.141000	0.21300	2.204000	0.42761	1.341000	0.45600	-0.215000	0.12644	CAC	T|0.748;C|0.251;N|0.001	0.251	strong		0.453	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
LIG4	3981	hgsc.bcm.edu	37	13	108863609	108863609	+	Missense_Mutation	SNP	G	G	A	rs1805389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:108863609G>A	ENST00000356922.4	-	2	280	c.8C>T	c.(7-9)gCc>gTc	p.A3V	LIG4_ENST00000405925.1_Missense_Mutation_p.A3V|LIG4_ENST00000442234.1_Missense_Mutation_p.A3V	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	3			A -> V (associated with resistance to multiple myeloma; dbSNP:rs1805389). {ECO:0000269|PubMed:12471202}.		cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					AGTTTGTGAGGCAGCCATCAA	0.328								Non-homologous end-joining					G|||	271	0.0541134	0.0015	0.0793	5008	,	,		17139	0.1002		0.0586	False		,,,				2504	0.0552				p.A3V		Atlas-SNP	.											.	LIG4	91	.	0			c.C8T	GRCh37	CM023642	LIG4	M	rs1805389	PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	53,4315		0,53,2131	27.0	28.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8,8,8	5.8	1.0	13	dbSNP_92	27	429,7989		10,409,3790	yes	missense,missense,missense	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	64,64,64	10,462,5921	AA,AG,GG		5.0962,1.2134,3.7697	benign,benign,benign	3/912,3/912,3/912	108863609	482,12304	2184	4209	6393	SO:0001583	missense	3981	exon3			TGTGAGGCAGCCA	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.8C>T	13.37:g.108863609G>A	ENSP00000349393:p.Ala3Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	124	0.056776556776556776	4	0.008130081300813009	21	0.058011049723756904	54	0.0944055944055944	45	0.059366754617414245	G	15.10	2.732522	0.48939	0.012134	0.050962	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.61980	0.06;0.06;0.06	5.82	5.82	0.92795	DNA ligase, ATP-dependent, N-terminal (1);	0.448521	0.24037	N	0.042138	T	0.02267	0.0070	N	0.08118	0	0.38382	P	0.054835999999999996	B	0.32573	0.376	B	0.28465	0.09	T	0.29458	-1.0011	9	0.59425	D	0.04	.	19.0813	0.93182	0.0:0.0:1.0:0.0	rs1805389;rs1805389	3	P49917	DNLI4_HUMAN	V	3	ENSP00000385955:A3V;ENSP00000402030:A3V;ENSP00000349393:A3V	ENSP00000349393:A3V	A	-	2	0	LIG4	107661610	0.991000	0.36638	0.997000	0.53966	0.436000	0.31835	4.221000	0.58574	2.761000	0.94854	0.643000	0.83706	GCC	G|0.955;A|0.045	0.045	strong		0.328	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
MDH2	4191	hgsc.bcm.edu	37	7	75677504	75677504	+	Missense_Mutation	SNP	C	C	T	rs6720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:75677504C>T	ENST00000315758.5	+	1	120	c.26C>T	c.(25-27)gCc>gTc	p.A9V	MDH2_ENST00000443006.1_5'UTR|MDH2_ENST00000432020.2_Missense_Mutation_p.A9V|STYXL1_ENST00000460184.2_5'Flank|STYXL1_ENST00000340062.5_5'Flank|STYXL1_ENST00000360591.3_5'Flank|STYXL1_ENST00000431581.1_5'Flank|STYXL1_ENST00000248600.1_5'Flank|MDH2_ENST00000490105.1_3'UTR|MDH2_ENST00000461263.2_Missense_Mutation_p.A9V|STYXL1_ENST00000451157.1_5'Flank|STYXL1_ENST00000359697.3_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	8	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	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		
LOR	4014	hgsc.bcm.edu	37	1	153234295	153234295	+	Silent	SNP	G	G	A	rs12043009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153234295G>A	ENST00000368742.3	+	2	927	c.870G>A	c.(868-870)ggG>ggA	p.G290G		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	290					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	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)			GTGGCTCCGGGAGTGGCAAGG	0.692													G|||	973	0.194289	0.3828	0.1542	5008	,	,		9988	0.0685		0.2326	False		,,,				2504	0.0583				p.G290G		Atlas-SNP	.											.	LOR	19	.	0			c.G870A						PASS	.	G		953,2271		129,695,788	6.0	8.0	7.0		870	-1.5	0.0	1	dbSNP_120	7	1211,5851		114,983,2434	no	coding-synonymous	LOR	NM_000427.2		243,1678,3222	AA,AG,GG		17.1481,29.5596,21.0383		290/313	153234295	2164,8122	1612	3531	5143	SO:0001819	synonymous_variant	4014	exon2			CTCCGGGAGTGGC	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.870G>A	1.37:g.153234295G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	65	0.942029	NM_000427	Q5T869|Q5XKF8	Silent	SNP	ENST00000368742.3	37	CCDS30870.1	490	0.22435897435897437	195	0.39634146341463417	66	0.18232044198895028	47	0.08216783216783216	182	0.24010554089709762	G	8.025	0.760514	0.15914	0.295596	0.171481	ENSG00000203782	ENST00000392652	.	.	.	4.24	-1.45	0.08828	.	.	.	.	.	T	0.25158	0.0611	.	.	.	0.43613	P	0.0040120000000000156	.	.	.	.	.	.	T	0.25710	-1.0124	4	0.87932	D	0	1.8651	4.3283	0.11051	0.3272:0.3631:0.3097:0.0	rs12043009;rs12043009	.	.	.	K	290	.	ENSP00000376422:E290K	E	+	1	0	LOR	151500919	0.019000	0.18553	0.010000	0.14722	0.844000	0.47949	-0.788000	0.04614	-0.548000	0.06199	0.563000	0.77884	GAG	G|0.777;A|0.223	0.223	strong		0.692	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274206	39274206	+	Missense_Mutation	SNP	C	C	T	rs79388709		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39274206C>T	ENST00000391413.2	-	1	400	c.362G>A	c.(361-363)aGa>aAa	p.R121K		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	121	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.R121K(5)		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)			gcactggggtctgcagcagct	0.652																																					p.R121K		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,9	KRTAP4-11	94	9	5	Substitution - Missense(5)	lung(2)|prostate(1)|kidney(1)|skin(1)	c.G362A						PASS	.						5.0	9.0	8.0					17																	39274206		644	1533	2177	SO:0001583	missense	653240	exon1			TGGGGTCTGCAGC	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.362G>A	17.37:g.39274206C>T	ENSP00000375232:p.Arg121Lys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	96	10	0.104167	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	4.782	0.145483	0.09134	.	.	ENSG00000212721	ENST00000391413	T	0.01455	4.87	3.34	-4.84	0.03151	.	.	.	.	.	T	0.01905	0.0060	M	0.73962	2.25	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.50276	-0.8847	9	0.11794	T	0.64	.	2.2508	0.04042	0.1417:0.1925:0.1396:0.5262	.	121	Q9BYQ6	KR411_HUMAN	K	121	ENSP00000375232:R121K	ENSP00000375232:R121K	R	-	2	0	KRTAP4-11	36527732	0.000000	0.05858	0.009000	0.14445	0.065000	0.16274	-1.602000	0.02079	-0.525000	0.06391	-1.218000	0.01608	AGA	T|1.000;|0.000	1.000	weak		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
CATSPER4	378807	hgsc.bcm.edu	37	1	26517267	26517267	+	Missense_Mutation	SNP	A	A	G	rs41284333	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26517267A>G	ENST00000456354.2	+	1	216	c.149A>G	c.(148-150)cAc>cGc	p.H50R		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	50					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		AGTACCATTCACGAGTCCTAC	0.632													A|||	617	0.123203	0.2269	0.0908	5008	,	,		15690	0.0089		0.1879	False		,,,				2504	0.0573				p.H50R		Atlas-SNP	.											CATSPER4,NS,carcinoma,0,1	CATSPER4	59	1	0			c.A149G						PASS	.	A	ARG/HIS	980,3426	356.6+/-313.6	123,734,1346	37.0	41.0	40.0		149	1.2	0.0	1	dbSNP_127	40	1629,6971	294.4+/-301.9	152,1325,2823	yes	missense	CATSPER4	NM_198137.1	29	275,2059,4169	GG,GA,AA		18.9419,22.2424,20.06	benign	50/473	26517267	2609,10397	2203	4300	6503	SO:0001583	missense	378807	exon1			CCATTCACGAGTC	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.149A>G	1.37:g.26517267A>G	ENSP00000390423:p.His50Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	NM_198137	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	300	0.13736263736263737	114	0.23170731707317074	38	0.10497237569060773	7	0.012237762237762238	141	0.18601583113456466	A	10.33	1.319305	0.23994	0.222424	0.189419	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97256	-4.31;-4.29	5.05	1.19	0.21007	.	1.497430	0.04299	N	0.347079	T	0.00468	0.0015	L	0.43152	1.355	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.56920	-0.7899	9	0.49607	T	0.09	-0.57	1.9246	0.03314	0.5768:0.169:0.0915:0.1627	rs41284333;rs61776646	50	Q7RTX7	CTSR4_HUMAN	R	50	ENSP00000341006:H50R;ENSP00000390423:H50R	ENSP00000341006:H50R	H	+	2	0	CATSPER4	26389854	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.742000	0.26216	0.354000	0.24105	-0.461000	0.05368	CAC	A|0.826;G|0.174	0.174	strong		0.632	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
ZNF792	126375	hgsc.bcm.edu	37	19	35449760	35449760	+	Silent	SNP	G	G	C	rs2651080	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	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	
CAMTA2	23125	hgsc.bcm.edu	37	17	4883045	4883045	+	Silent	SNP	C	C	T	rs79255821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4883045C>T	ENST00000348066.3	-	9	1695	c.1572G>A	c.(1570-1572)ccG>ccA	p.P524P	CAMTA2_ENST00000572543.1_Silent_p.P529P|CAMTA2_ENST00000414043.3_Silent_p.P547P|CAMTA2_ENST00000381311.5_Silent_p.P526P|CAMTA2_ENST00000358183.4_Silent_p.P524P|CAMTA2_ENST00000361571.5_Silent_p.P523P|CAMTA2_ENST00000571831.1_5'Flank	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	524					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GCTGGGGGGTCGGAGCAGGGA	0.572													C|||	440	0.0878594	0.0257	0.1527	5008	,	,		12833	0.1935		0.0169	False		,,,				2504	0.09				p.P547P		Atlas-SNP	.											.	CAMTA2	93	.	0			c.G1641A						PASS	.	C	,,,	141,4265	99.4+/-138.0	1,139,2063	120.0	121.0	120.0		1578,1641,1569,1572	-4.3	0.0	17	dbSNP_131	120	223,8377	93.3+/-155.3	5,213,4082	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMTA2	NM_001171166.1,NM_001171167.1,NM_001171168.1,NM_015099.3	,,,	6,352,6145	TT,TC,CC		2.593,3.2002,2.7987	,,,	526/1198,547/1242,523/1202,524/1203	4883045	364,12642	2203	4300	6503	SO:0001819	synonymous_variant	23125	exon9			GGGGGTCGGAGCA	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1572G>A	17.37:g.4883045C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Silent	SNP	ENST00000348066.3	37	CCDS11063.1																																																																																			C|0.957;T|0.043	0.043	strong		0.572	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
TFB1M	51106	hgsc.bcm.edu	37	6	155606325	155606325	+	Silent	SNP	C	C	T	rs324356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:155606325C>T	ENST00000367166.4	-	5	688	c.633G>A	c.(631-633)acG>acA	p.T211T		NM_016020.3	NP_057104.2	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	211			T -> A. {ECO:0000269|PubMed:19096125}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		GTCCTGGAATCGTAAAGATGT	0.448													T|||	3365	0.671925	0.6846	0.7104	5008	,	,		22209	0.8333		0.5328	False		,,,				2504	0.6043				p.T211T		Atlas-SNP	.											.	TFB1M	30	.	0			c.G633A						PASS	.	T		2894,1512	481.9+/-359.3	941,1012,250	145.0	127.0	133.0		633	-11.8	0.0	6	dbSNP_79	133	4269,4331	579.6+/-390.9	1072,2125,1103	no	coding-synonymous	TFB1M	NM_016020.3		2013,3137,1353	TT,TC,CC		49.6395,34.3168,44.9254		211/347	155606325	7163,5843	2203	4300	6503	SO:0001819	synonymous_variant	51106	exon5			TGGAATCGTAAAG	AF151833	CCDS5248.1	6q25.1-q25.3	2011-01-28			ENSG00000029639	ENSG00000029639			17037	protein-coding gene	gene with protein product	"""dimethyladenosine transferase 1, mitochondrial"""	607033				10810093, 11809803	Standard	NM_016020		Approved	mtTFB, CGI-75	uc003qqj.4	Q8WVM0	OTTHUMG00000015881	ENST00000367166.4:c.633G>A	6.37:g.155606325C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_016020	Q05DR0|Q9Y384	Silent	SNP	ENST00000367166.4	37	CCDS5248.1																																																																																			C|0.338;T|0.662	0.662	strong		0.448	TFB1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042809.1		
ITGA4	3676	hgsc.bcm.edu	37	2	182395345	182395345	+	Missense_Mutation	SNP	G	G	A	rs1143676	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:182395345G>A	ENST00000397033.2	+	24	3063	c.2633G>A	c.(2632-2634)cGg>cAg	p.R878Q		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	878			R -> Q (in dbSNP:rs1143676). {ECO:0000269|PubMed:8643114, ECO:0000269|Ref.5}.		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)	GGCATAGTCCGGTTCTTGTCC	0.403													A|||	3959	0.790535	0.7542	0.8026	5008	,	,		20207	0.8413		0.669	False		,,,				2504	0.9039				p.R878Q		Atlas-SNP	.											.	ITGA4	142	.	0			c.G2633A						PASS	.	A	GLN/ARG	2847,937		1080,687,125	202.0	181.0	188.0		2633	-10.9	0.0	2	dbSNP_86	188	5596,2654		1908,1780,437	yes	missense	ITGA4	NM_000885.4	43	2988,2467,562	AA,AG,GG		32.1697,24.7622,29.8405	benign	878/1033	182395345	8443,3591	1892	4125	6017	SO:0001583	missense	3676	exon24			TAGTCCGGTTCTT		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.2633G>A	2.37:g.182395345G>A	ENSP00000380227:p.Arg878Gln	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	181	181	1	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	1619	0.7413003663003663	362	0.7357723577235772	277	0.7651933701657458	480	0.8391608391608392	500	0.6596306068601583	A	10.58	1.390478	0.25118	0.752378	0.678303	ENSG00000115232	ENST00000397033	T	0.44083	0.93	5.45	-10.9	0.00192	.	1.265470	0.05097	N	0.486427	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22003	0.063	B	0.22753	0.041	T	0.21211	-1.0252	9	0.18276	T	0.48	.	1.4346	0.02341	0.3668:0.2961:0.1653:0.1718	rs1143676;rs2305579;rs4667319;rs17484822;rs52836429;rs58692589;rs4667319	878	P13612	ITA4_HUMAN	Q	878	ENSP00000380227:R878Q	ENSP00000380227:R878Q	R	+	2	0	ITGA4	182103590	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-3.957000	0.00325	-3.283000	0.00196	-0.360000	0.07572	CGG	G|0.258;A|0.742	0.742	strong		0.403	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
ERAP1	51752	hgsc.bcm.edu	37	5	96127833	96127833	+	Silent	SNP	G	G	A	rs3213809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:96127833G>A	ENST00000443439.2	-	8	1317	c.1251C>T	c.(1249-1251)caC>caT	p.H417H	ERAP1_ENST00000296754.3_Silent_p.H417H	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	417					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TAGACACAGGGTGTGAGGAAT	0.363													G|||	485	0.096845	0.0144	0.2507	5008	,	,		18650	0.0268		0.1481	False		,,,				2504	0.1186				p.H417H		Atlas-SNP	.											.	ERAP1	59	.	0			c.C1251T						PASS	.	G	,,	141,4265	98.0+/-136.7	1,139,2063	138.0	135.0	136.0		1251,1251,1251	4.8	1.0	5	dbSNP_106	136	1240,7360	248.6+/-276.2	72,1096,3132	no	coding-synonymous,coding-synonymous,coding-synonymous	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	,,	73,1235,5195	AA,AG,GG		14.4186,3.2002,10.6182	,,	417/942,417/942,417/949	96127833	1381,11625	2203	4300	6503	SO:0001819	synonymous_variant	51752	exon8			CACAGGGTGTGAG	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.1251C>T	5.37:g.96127833G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			G|0.905;A|0.095	0.095	strong		0.363	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
KRT38	8687	hgsc.bcm.edu	37	17	39595539	39595539	+	Silent	SNP	A	A	G	rs117668654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39595539A>G	ENST00000246646.3	-	3	647	c.648T>C	c.(646-648)gaT>gaC	p.D216D		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	216	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)				CCAGGGTCGCATCATCCAGGA	0.632													G|||	58	0.0115815	0.0008	0.0043	5008	,	,		17656	0.0278		0.0089	False		,,,				2504	0.0174				p.D216D		Atlas-SNP	.											KRT38,rectum,carcinoma,0,1	KRT38	63	1	0			c.T648C						scavenged	.						85.0	77.0	79.0					17																	39595539		2203	4300	6503	SO:0001819	synonymous_variant	8687	exon3			GGTCGCATCATCC	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.648T>C	17.37:g.39595539A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	90	7	0.0777778	NM_006771	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	37	CCDS11392.1																																																																																			A|0.999;G|0.001	0.001	weak		0.632	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73090261	73090261	+	Silent	SNP	T	T	C	rs7716253	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73090261T>C	ENST00000426542.2	+	7	965	c.945T>C	c.(943-945)gcT>gcC	p.A315A	ARHGEF28_ENST00000437974.1_Silent_p.A315A|ARHGEF28_ENST00000296794.6_Silent_p.A315A|ARHGEF28_ENST00000513042.2_Silent_p.A315A|ARHGEF28_ENST00000545377.1_Silent_p.A315A|ARHGEF28_ENST00000287898.5_Silent_p.A315A			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	315					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)										GATCAGCAGCTGAAAAGGAAG	0.343													C|||	3072	0.613419	0.8215	0.5346	5008	,	,		16966	0.5327		0.508	False		,,,				2504	0.5798				p.A315A		Atlas-SNP	.											.	.	.	.	0			c.T945C						PASS	.	C	,	2932,776		1161,610,83	66.0	72.0	70.0		945,945	-11.4	0.0	5	dbSNP_116	70	4269,3947		1142,1985,981	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	2303,2595,1064	CC,CT,TT		48.0404,20.9277,39.6092	,	315/1732,315/1706	73090261	7201,4723	1854	4108	5962	SO:0001819	synonymous_variant	64283	exon8			AGCAGCTGAAAAG		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.945T>C	5.37:g.73090261T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	113	112	0.99115	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			T|0.404;C|0.596	0.596	strong		0.343	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
FAM222B	55731	hgsc.bcm.edu	37	17	27085564	27085564	+	Silent	SNP	A	A	G	rs2043031	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:27085564A>G	ENST00000341217.5	-	3	1628	c.1413T>C	c.(1411-1413)ctT>ctC	p.L471L	FAM222B_ENST00000452648.3_Silent_p.L471L|FAM222B_ENST00000581407.1_Silent_p.L471L|FAM222B_ENST00000582266.1_3'UTR	NM_018182.2	NP_060652.2	Q8WU58	F222B_HUMAN	family with sequence similarity 222, member B	471			L -> S (in dbSNP:rs2043031).														ACGGCATGGCAAGGTCCTGAG	0.657													G|||	1064	0.21246	0.1422	0.2349	5008	,	,		17804	0.1786		0.1938	False		,,,				2504	0.3456				p.L471L		Atlas-SNP	.											.	.	.	.	0			c.T1413C						PASS	.	G	,	557,3407		54,449,1479	40.0	41.0	41.0		1413,1413	0.7	0.3	17	dbSNP_94	41	1603,6699		152,1299,2700	no	coding-synonymous,coding-synonymous	C17orf63	NM_001077498.1,NM_018182.2	,	206,1748,4179	GG,GA,AA		19.3086,14.0515,17.6097	,	471/563,471/563	27085564	2160,10106	1982	4151	6133	SO:0001819	synonymous_variant	55731	exon4			CATGGCAAGGTCC	AK001562	CCDS45637.1, CCDS74022.1	17q11.2	2012-04-27	2012-04-27	2012-04-27	ENSG00000173065	ENSG00000173065			25563	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 63"""	C17orf63			Standard	NM_001288631		Approved	FLJ10700	uc010way.1	Q8WU58		ENST00000341217.5:c.1413T>C	17.37:g.27085564A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_018182	Q9H6F3|Q9NVJ4|Q9NXN6	Silent	SNP	ENST00000341217.5	37	CCDS45637.1																																																																																			A|0.808;G|0.192	0.192	strong		0.657	FAM222B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446703.1	NM_018182	
NEUROG1	4762	hgsc.bcm.edu	37	5	134870913	134870913	+	Silent	SNP	G	G	A	rs8192559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:134870913G>A	ENST00000314744.4	-	1	726	c.468C>T	c.(466-468)ccC>ccT	p.P156P		NM_006161.2	NP_006152.2	Q92886	NGN1_HUMAN	neurogenin 1	156					cell fate commitment (GO:0045165)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perikaryon (GO:0043204)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			endometrium(1)|liver(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CACCGCCTCCGGGCAGCCCTT	0.706													G|||	162	0.0323482	0.0053	0.0807	5008	,	,		11444	0.0		0.0825	False		,,,				2504	0.0164				p.P156P		Atlas-SNP	.											.	NEUROG1	18	.	0			c.C468T						PASS	.	G		97,4291		3,91,2100	21.0	24.0	23.0		468	0.3	1.0	5	dbSNP_117	23	785,7791		23,739,3526	no	coding-synonymous	NEUROG1	NM_006161.2		26,830,5626	AA,AG,GG		9.1535,2.2106,6.8035		156/238	134870913	882,12082	2194	4288	6482	SO:0001819	synonymous_variant	4762	exon1			GCCTCCGGGCAGC	U63842	CCDS4187.1	5q23-q31	2013-05-21			ENSG00000181965	ENSG00000181965		"""Basic helix-loop-helix proteins"""	7764	protein-coding gene	gene with protein product	"""neurogenic differentiation 3"""	601726		NEUROD3		9119405	Standard	NM_006161		Approved	AKA, Math4C, ngn1, bHLHa6	uc003lax.3	Q92886	OTTHUMG00000129138	ENST00000314744.4:c.468C>T	5.37:g.134870913G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	NM_006161	Q5U0Q9|Q96HE1	Silent	SNP	ENST00000314744.4	37	CCDS4187.1																																																																																			G|0.941;A|0.059	0.059	strong		0.706	NEUROG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251192.1	NM_006161	
ELMOD2	255520	hgsc.bcm.edu	37	4	141464666	141464666	+	Missense_Mutation	SNP	G	G	A	rs148286208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:141464666G>A	ENST00000323570.3	+	8	794	c.662G>A	c.(661-663)aGt>aAt	p.S221N		NM_153702.3	NP_714913.1	Q8IZ81	ELMD2_HUMAN	ELMO/CED-12 domain containing 2	221	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				defense response to virus (GO:0051607)|phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)|regulation of defense response to virus (GO:0050688)	cytoskeleton (GO:0005856)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	7	all_hematologic(180;0.162)					TTACTGAAGAGTGAAGCTTTG	0.338													G|||	3	0.000599042	0.0	0.0	5008	,	,		14795	0.0		0.003	False		,,,				2504	0.0				p.S221N		Atlas-SNP	.											.	ELMOD2	16	.	0			c.G662A						PASS	.	G	ASN/SER	3,4403	6.2+/-15.9	0,3,2200	114.0	114.0	114.0		662	5.3	1.0	4	dbSNP_134	114	11,8573	7.7+/-29.5	0,11,4281	yes	missense	ELMOD2	NM_153702.3	46	0,14,6481	AA,AG,GG		0.1281,0.0681,0.1078	benign	221/294	141464666	14,12976	2203	4292	6495	SO:0001583	missense	255520	exon8			TGAAGAGTGAAGC	BX648349	CCDS3752.1	4q31.1	2006-10-24	2006-01-20		ENSG00000179387	ENSG00000179387			28111	protein-coding gene	gene with protein product		610196	"""ELMO domain containing 2"""			16773575	Standard	NM_153702		Approved	MGC10084	uc003iik.3	Q8IZ81	OTTHUMG00000133417	ENST00000323570.3:c.662G>A	4.37:g.141464666G>A	ENSP00000326342:p.Ser221Asn	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	94	36	0.382979	NM_153702	B2R712|D3DNZ0	Missense_Mutation	SNP	ENST00000323570.3	37	CCDS3752.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.68	2.905457	0.52333	6.81E-4	0.001281	ENSG00000179387	ENST00000323570	T	0.30448	1.53	6.16	5.33	0.75918	Engulfment/cell motility, ELMO (2);	0.159239	0.64402	N	0.000001	T	0.26991	0.0661	L	0.51914	1.62	0.42822	D	0.993998	B	0.17038	0.02	B	0.22601	0.04	T	0.08493	-1.0719	10	0.18276	T	0.48	-4.9602	10.0032	0.41942	0.1887:0.0:0.8113:0.0	.	221	Q8IZ81	ELMD2_HUMAN	N	221	ENSP00000326342:S221N	ENSP00000326342:S221N	S	+	2	0	ELMOD2	141684116	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.898000	0.39809	1.631000	0.50456	0.650000	0.86243	AGT	A|0.001;G|0.999	0.001	strong		0.338	ELMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257277.2	NM_153702	
VWDE	221806	hgsc.bcm.edu	37	7	12376811	12376811	+	Missense_Mutation	SNP	A	A	C	rs2192828	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:12376811A>C	ENST00000275358.3	-	25	4642	c.4454T>G	c.(4453-4455)tTc>tGc	p.F1485C		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1485	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.		F -> C (in dbSNP:rs2192828). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						ACTTTTTTGGAATCTCCTACC	0.393													C|||	3497	0.698283	0.9448	0.7017	5008	,	,		20755	0.6151		0.5885	False		,,,				2504	0.5613				p.F1485C		Atlas-SNP	.											.	VWDE	123	.	0			c.T4454G						PASS	.	C	CYS/PHE	1222,162		539,144,9	198.0	156.0	169.0		4454	4.9	1.0	7	dbSNP_96	169	1802,1380		514,774,303	yes	missense	VWDE	NM_001135924.1	205	1053,918,312	CC,CA,AA		43.369,11.7052,33.7714	benign	1485/1591	12376811	3024,1542	692	1591	2283	SO:0001583	missense	221806	exon25			TTTTGGAATCTCC		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.4454T>G	7.37:g.12376811A>C	ENSP00000275358:p.Phe1485Cys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	145	71	0.489655	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	1539	0.7046703296703297	464	0.943089430894309	254	0.7016574585635359	371	0.6486013986013986	450	0.5936675461741425	C	6.674	0.492883	0.12702	0.882948	0.56631	ENSG00000146530	ENST00000275358;ENST00000536307	T	0.57907	0.37	4.86	4.86	0.63082	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00000	-4.73	0.37090	P	0.10061900000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.50608	-0.8808	9	0.02654	T	1	.	14.8064	0.69959	0.1453:0.8546:0.0:0.0	rs2192828;rs10382186;rs17670328;rs52819048;rs2192828	1485	Q8N2E2	VWDE_HUMAN	C	1485;939	ENSP00000275358:F1485C	ENSP00000275358:F1485C	F	-	2	0	VWDE	12343336	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.640000	0.67875	1.281000	0.44480	-0.127000	0.14921	TTC	A|0.306;C|0.694	0.694	strong		0.393	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
ARFGEF2	10564	hgsc.bcm.edu	37	20	47626847	47626847	+	Silent	SNP	T	T	C	rs2295580	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	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	
PPAT	5471	hgsc.bcm.edu	37	4	57268328	57268328	+	Silent	SNP	T	T	C	rs2271924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	82	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	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	
CDC25B	994	hgsc.bcm.edu	37	20	3784110	3784110	+	Silent	SNP	C	C	T	rs1056720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3784110C>T	ENST00000245960.5	+	14	2113	c.1416C>T	c.(1414-1416)atC>atT	p.I472I	CDC25B_ENST00000340833.4_Silent_p.I431I|CDC25B_ENST00000379598.5_Silent_p.I381I|CDC25B_ENST00000439880.2_Silent_p.I458I|CDC25B_ENST00000344256.6_Silent_p.I408I|CDC25B_ENST00000467519.1_3'UTR	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	472	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				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						AGAGCCCCATCGCGCCCTGTA	0.622													C|||	1152	0.230032	0.1036	0.2925	5008	,	,		19448	0.377		0.2207	False		,,,				2504	0.2147				p.I472I		Atlas-SNP	.											.	CDC25B	76	.	0			c.C1416T						PASS	.	C	,,	557,3849	251.5+/-258.2	37,483,1683	115.0	100.0	105.0		1374,1293,1416	-0.8	0.1	20	dbSNP_86	105	2109,6491	365.2+/-333.8	259,1591,2450	yes	coding-synonymous,coding-synonymous,coding-synonymous	CDC25B	NM_004358.3,NM_021872.2,NM_021873.2	,,	296,2074,4133	TT,TC,CC		24.5233,12.6419,20.4982	,,	458/567,431/540,472/581	3784110	2666,10340	2203	4300	6503	SO:0001819	synonymous_variant	994	exon14			CCCCATCGCGCCC		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.1416C>T	20.37:g.3784110C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	161	75	0.465839	NM_021873	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	Silent	SNP	ENST00000245960.5	37	CCDS13067.1																																																																																			C|0.781;T|0.219	0.219	strong		0.622	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077779.2	NM_021874	
FERMT1	55612	hgsc.bcm.edu	37	20	6093177	6093177	+	Missense_Mutation	SNP	A	A	G	rs16991866	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:6093177A>G	ENST00000217289.4	-	4	1267	c.479T>C	c.(478-480)aTa>aCa	p.I160T	FERMT1_ENST00000536936.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	160	FERM.		I -> T (in dbSNP:rs16991866).		cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ATCTTCAATTATGGGTTCCTT	0.343													A|||	416	0.0830671	0.1172	0.0519	5008	,	,		15189	0.0794		0.0905	False		,,,				2504	0.0552				p.I160T		Atlas-SNP	.											.	FERMT1	106	.	0			c.T479C						PASS	.	A	THR/ILE	546,3860	245.6+/-254.5	41,464,1698	132.0	134.0	133.0		479	5.8	0.0	20	dbSNP_123	133	807,7793	189.0+/-235.8	33,741,3526	yes	missense	FERMT1	NM_017671.4	89	74,1205,5224	GG,GA,AA		9.3837,12.3922,10.4029	benign	160/678	6093177	1353,11653	2203	4300	6503	SO:0001583	missense	55612	exon4			TCAATTATGGGTT	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.479T>C	20.37:g.6093177A>G	ENSP00000217289:p.Ile160Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	37	CCDS13098.1	193	0.08836996336996338	68	0.13821138211382114	16	0.04419889502762431	45	0.07867132867132867	64	0.08443271767810026	A	9.186	1.024830	0.19433	0.123922	0.093837	ENSG00000101311	ENST00000217289;ENST00000339538	T	0.41758	0.99	5.77	5.77	0.91146	FERM, N-terminal (1);Band 4.1 domain (1);	0.968169	0.08542	N	0.930408	T	0.00210	0.0006	N	0.08118	0	0.28873	P	0.894859	B;B	0.18968	0.007;0.032	B;B	0.20955	0.026;0.032	T	0.09509	-1.0671	9	0.13108	T	0.6	-13.0329	12.212	0.54386	0.9318:0.0:0.0682:0.0	rs16991866;rs52791370;rs16991866	160;160	Q9BQL6-4;Q9BQL6	.;FERM1_HUMAN	T	160	ENSP00000217289:I160T	ENSP00000217289:I160T	I	-	2	0	FERMT1	6041177	0.093000	0.21703	0.013000	0.15412	0.754000	0.42855	3.679000	0.54634	2.326000	0.78906	0.533000	0.62120	ATA	A|0.898;G|0.102	0.102	strong		0.343	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
ATP1A4	480	hgsc.bcm.edu	37	1	160121899	160121899	+	Silent	SNP	A	A	G	rs77332724	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160121899A>G	ENST00000368081.4	+	1	540	c.69A>G	c.(67-69)aaA>aaG	p.K23K		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	23					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)	p.G24fs*28(1)		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)			GACCTAAAAAAGGGCTTATCA	0.507													A|||	332	0.0662939	0.0068	0.1225	5008	,	,		18851	0.0456		0.1173	False		,,,				2504	0.0757				p.K23K		Atlas-SNP	.											.	ATP1A4	167	.	1	Insertion - Frameshift(1)	breast(1)	c.A69G						PASS	.	A		103,4303		0,103,2100	84.0	80.0	81.0		69	-2.1	0.0	1	dbSNP_131	81	1100,7500		82,936,3282	no	coding-synonymous	ATP1A4	NM_144699.3		82,1039,5382	GG,GA,AA		12.7907,2.3377,9.2496		23/1030	160121899	1203,11803	2203	4300	6503	SO:0001819	synonymous_variant	480	exon1			TAAAAAAGGGCTT	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.69A>G	1.37:g.160121899A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	32	22	0.6875	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																			A|0.910;G|0.090	0.090	strong		0.507	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
KLK7	5650	hgsc.bcm.edu	37	19	51483620	51483620	+	Silent	SNP	G	G	C	rs35354640	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51483620G>C	ENST00000391807.1	-	4	446	c.345C>G	c.(343-345)ctC>ctG	p.L115L	KLK7_ENST00000336317.4_Silent_p.L2L|KLK7_ENST00000595820.1_Silent_p.L115L|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000595638.1_5'Flank|KLK7_ENST00000597707.1_Silent_p.L43L	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	115	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)		TGAGCTTCACGAGCATGAGGT	0.587													G|||	45	0.00898562	0.0008	0.0187	5008	,	,		14158	0.0		0.0258	False		,,,				2504	0.0051				p.L115L		Atlas-SNP	.											.	KLK7	40	.	0			c.C345G						PASS	.	G	,,	14,4392	21.2+/-45.6	0,14,2189	122.0	93.0	103.0		129,345,345	-9.2	0.0	19	dbSNP_126	103	181,8419	83.1+/-145.7	1,179,4120	no	coding-synonymous,coding-synonymous,coding-synonymous	KLK7	NM_001207053.1,NM_005046.3,NM_139277.2	,,	1,193,6309	CC,CG,GG		2.1047,0.3177,1.4993	,,	43/182,115/254,115/254	51483620	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	5650	exon4			CTTCACGAGCATG	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.345C>G	19.37:g.51483620G>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	200	85	0.425	NM_139277	A8K0U5|Q8N5N9|Q8NFV7	Silent	SNP	ENST00000391807.1	37	CCDS12812.1																																																																																			G|0.986;C|0.014	0.014	strong		0.587	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046	
NAALADL2	254827	hgsc.bcm.edu	37	3	174814738	174814738	+	Missense_Mutation	SNP	G	G	A	rs9823911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:174814738G>A	ENST00000454872.1	+	2	330	c.202G>A	c.(202-204)Ggt>Agt	p.G68S	NAALADL2-AS3_ENST00000453180.1_RNA|NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	68			G -> S (in dbSNP:rs9823911). {ECO:0000269|PubMed:15168106, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		CCAGCTAGACGGTGCTGAGAA	0.463													A|||	1893	0.377995	0.2852	0.4179	5008	,	,		14330	0.4375		0.3926	False		,,,				2504	0.3988				p.G68S		Atlas-SNP	.											.	NAALADL2	86	.	0			c.G202A						PASS	.	A	SER/GLY	1024,2766		148,728,1019	77.0	73.0	74.0		202	1.0	0.0	3	dbSNP_119	74	3188,5052		627,1934,1559	yes	missense	NAALADL2	NM_207015.2	56	775,2662,2578	AA,AG,GG		38.6893,27.0185,35.0125	benign	68/796	174814738	4212,7818	1895	4120	6015	SO:0001583	missense	254827	exon2			CTAGACGGTGCTG		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.202G>A	3.37:g.174814738G>A	ENSP00000404705:p.Gly68Ser	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	180	79	0.438889	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	828	0.3791208791208791	145	0.29471544715447157	161	0.4447513812154696	236	0.4125874125874126	286	0.37730870712401055	A	7.764	0.706087	0.15172	0.270185	0.386893	ENSG00000177694	ENST00000434257;ENST00000454872	T;T	0.30182	1.62;1.54	5.72	0.957	0.19613	.	0.757199	0.12476	N	0.465639	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46541	-0.9184	9	0.02654	T	1	-0.2147	5.8982	0.18951	0.4966:0.2423:0.2611:0.0	rs9823911;rs52835565;rs58142944;rs9823911	51;68	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	S	51;68	ENSP00000409858:G51S;ENSP00000404705:G68S	ENSP00000409858:G51S	G	+	1	0	NAALADL2	176297432	0.007000	0.16637	0.018000	0.16275	0.704000	0.40688	0.523000	0.22925	-0.042000	0.13535	-0.269000	0.10298	GGT	G|0.642;A|0.358	0.358	strong		0.463	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
PFN4	375189	hgsc.bcm.edu	37	2	24344060	24344060	+	Silent	SNP	T	T	G	rs33913065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:24344060T>G	ENST00000313213.4	-	3	599	c.228A>C	c.(226-228)gcA>gcC	p.A76A	FAM228B_ENST00000407625.1_5'Flank|FAM228B_ENST00000420135.2_5'Flank|PFN4_ENST00000465360.1_5'UTR	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	115	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	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	
SCN4A	6329	hgsc.bcm.edu	37	17	62036738	62036738	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62036738C>T	ENST00000435607.1	-	12	1982	c.1906G>A	c.(1906-1908)Gag>Aag	p.E636K	SCN4A_ENST00000578147.1_Missense_Mutation_p.E636K	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	636					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)	TGGAAATACTCGTAGGGGTCC	0.562																																					p.E636K		Atlas-SNP	.											.	SCN4A	205	.	0			c.G1906A						PASS	.						83.0	85.0	85.0					17																	62036738		2063	4230	6293	SO:0001583	missense	6329	exon12			AATACTCGTAGGG	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.1906G>A	17.37:g.62036738C>T	ENSP00000396320:p.Glu636Lys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	141	69	0.489362	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.810092	0.70797	.	.	ENSG00000007314	ENST00000435607	D	0.98362	-4.89	4.74	4.74	0.60224	Ion transport (1);	0.119294	0.56097	D	0.000022	D	0.94258	0.8156	N	0.20530	0.585	0.39768	D	0.972125	B	0.30281	0.275	B	0.24541	0.054	D	0.93435	0.6789	10	0.44086	T	0.13	.	12.1023	0.53792	0.1716:0.8284:0.0:0.0	.	636	P35499	SCN4A_HUMAN	K	636	ENSP00000396320:E636K	ENSP00000396320:E636K	E	-	1	0	SCN4A	59390470	0.996000	0.38824	1.000000	0.80357	0.927000	0.56198	3.358000	0.52284	2.481000	0.83766	0.556000	0.70494	GAG	.	.	none		0.562	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726788	32726788	+	Missense_Mutation	SNP	T	T	C	rs56536369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32726788T>C	ENST00000437316.2	-	3	548	c.485A>G	c.(484-486)gAc>gGc	p.D162G	HLA-DQB2_ENST00000435145.2_Missense_Mutation_p.D162G|HLA-DQB2_ENST00000411527.1_Missense_Mutation_p.D162G			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	166	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						CTCCTCCTGGTCATTCCGAAA	0.552																																					p.D162G		Atlas-SNP	.											HLA-DQB2,NS,carcinoma,-1,1	HLA-DQB2	22	1	0			c.A485G						scavenged	.																																			SO:0001583	missense	3120	exon3			TCCTGGTCATTCC	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.485A>G	6.37:g.32726788T>C	ENSP00000396330:p.Asp162Gly	Somatic	193	2	0.0103627		WXS	Illumina HiSeq	Phase_I	210	47	0.22381	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Missense_Mutation	SNP	ENST00000437316.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.080|0.080	-1.184652|-1.184652	0.01620|0.01620	.|.	.|.	ENSG00000232629|ENSG00000232629	ENST00000437316;ENST00000435145;ENST00000411527|ENST00000427449	T;T;T|.	0.00529|.	6.78;6.78;6.78|.	3.43|3.43	-2.29|-2.29	0.06805|0.06805	.|.	0.329988|.	0.26616|.	N|.	0.023396|.	T|T	0.03348|0.03348	0.0097|0.0097	N|N	0.01631|0.01631	-0.79|-0.79	0.22412|0.22412	N|N	0.999124|0.999124	B;B|.	0.18461|.	0.005;0.028|.	B;B|.	0.26517|.	0.044;0.07|.	T|T	0.43196|0.43196	-0.9406|-0.9406	10|5	0.02654|.	T|.	1|.	.|.	10.6182|10.6182	0.45462|0.45462	0.0:0.7307:0.0:0.2693|0.0:0.7307:0.0:0.2693	rs56536369|rs56536369	162;162|.	A2ADX3;Q5SR06|.	.;.|.	G|A	162|161	ENSP00000396330:D162G;ENSP00000410512:D162G;ENSP00000390431:D162G|.	ENSP00000390431:D162G|.	D|T	-|-	2|1	0|0	HLA-DQB2|HLA-DQB2	32834766|32834766	0.962000|0.962000	0.33011|0.33011	0.994000|0.994000	0.49952|0.49952	0.583000|0.583000	0.36354|0.36354	0.529000|0.529000	0.23019|0.23019	-0.289000|-0.289000	0.09038|0.09038	-0.415000|-0.415000	0.06103|0.06103	GAC|ACC	T|0.992;C|0.008	0.008	strong		0.552	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
TRAPPC11	60684	hgsc.bcm.edu	37	4	184612553	184612553	+	Missense_Mutation	SNP	G	G	C	rs67383011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:184612553G>C	ENST00000334690.6	+	19	2180	c.1978G>C	c.(1978-1980)Gtt>Ctt	p.V660L	TRAPPC11_ENST00000512476.1_Missense_Mutation_p.V266L|TRAPPC11_ENST00000357207.4_Missense_Mutation_p.V660L	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	660				V -> L (in Ref. 2; AAH51724). {ECO:0000305}.	vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											GATGTGCCTAGTTCCTGGCAA	0.318													G|||	308	0.0615016	0.0363	0.0937	5008	,	,		16635	0.0625		0.0835	False		,,,				2504	0.0491				p.V660L		Atlas-SNP	.											.	.	.	.	0			c.G1978C						PASS	.	G	LEU/VAL,LEU/VAL	231,4175	137.3+/-173.1	5,221,1977	76.0	76.0	76.0		1978,1978	3.3	1.0	4	dbSNP_130	76	898,7702	201.1+/-244.7	54,790,3456	yes	missense,missense	C4orf41	NM_021942.4,NM_199053.1	32,32	59,1011,5433	CC,CG,GG		10.4419,5.2429,8.6806	benign,benign	660/1134,660/1087	184612553	1129,11877	2203	4300	6503	SO:0001583	missense	60684	exon19			TGCCTAGTTCCTG		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.1978G>C	4.37:g.184612553G>C	ENSP00000335371:p.Val660Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Missense_Mutation	SNP	ENST00000334690.6	37	CCDS34112.1	142	0.06501831501831502	12	0.024390243902439025	27	0.07458563535911603	33	0.057692307692307696	70	0.09234828496042216	G	12.05	1.821490	0.32237	0.052429	0.104419	ENSG00000168538	ENST00000334690;ENST00000357207;ENST00000360109;ENST00000512476	.	.	.	5.1	3.31	0.37934	.	0.245457	0.32802	N	0.005630	T	0.00724	0.0024	N	0.19112	0.55	0.22601	P	0.99894973	B;B;B;B	0.11235	0.003;0.003;0.004;0.001	B;B;B;B	0.12156	0.007;0.005;0.004;0.002	T	0.10382	-1.0632	8	0.19147	T	0.46	.	7.7243	0.28750	0.1495:0.1358:0.7147:0.0	.	391;266;660;660	B3KR79;D6RHE5;Q7Z392;Q7Z392-3	.;.;TPC11_HUMAN;.	L	660;660;660;266	.	ENSP00000335371:V660L	V	+	1	0	C4orf41	184849547	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	4.277000	0.58939	0.612000	0.30071	0.467000	0.42956	GTT	G|0.916;C|0.084	0.084	strong		0.318	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
NLRP4	147945	hgsc.bcm.edu	37	19	56369914	56369914	+	Silent	SNP	C	C	T	rs113444208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56369914C>T	ENST00000301295.6	+	3	1577	c.1155C>T	c.(1153-1155)gcC>gcT	p.A385A	NLRP4_ENST00000346986.5_Silent_p.A385A|NLRP4_ENST00000587891.1_Silent_p.A310A	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	385	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)		CTGAGGGTGCCGAGGGCCCGA	0.557													C|||	21	0.00419329	0.0008	0.0	5008	,	,		17743	0.0		0.006	False		,,,				2504	0.0143				p.A385A		Atlas-SNP	.											.	NLRP4	331	.	0			c.C1155T						PASS	.	C		15,4391	23.3+/-48.9	0,15,2188	55.0	52.0	53.0		1155	-7.7	0.0	19	dbSNP_132	53	50,8550	31.7+/-84.0	0,50,4250	no	coding-synonymous	NLRP4	NM_134444.4		0,65,6438	TT,TC,CC		0.5814,0.3404,0.4998		385/995	56369914	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			GGGTGCCGAGGGC	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.1155C>T	19.37:g.56369914C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.996;T|0.004	0.004	strong		0.557	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
ADCY8	114	hgsc.bcm.edu	37	8	132052342	132052342	+	Missense_Mutation	SNP	C	C	T	rs2228949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:132052342C>T	ENST00000286355.5	-	1	2330	c.238G>A	c.(238-240)Gcg>Acg	p.A80T	ADCY8_ENST00000377928.3_Missense_Mutation_p.A80T	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	80			A -> T (in dbSNP:rs2228949).		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)			AGCTGCGGCGCGTGGTGGTTG	0.726										HNSCC(32;0.087)			C|||	90	0.0179712	0.0015	0.0187	5008	,	,		11522	0.0		0.0338	False		,,,				2504	0.0419				p.A80T		Atlas-SNP	.											.	ADCY8	291	.	0			c.G238A						PASS	.	C	THR/ALA	20,3732		0,20,1856	3.0	3.0	3.0		238	4.6	1.0	8	dbSNP_98	3	227,7205		0,227,3489	no	missense	ADCY8	NM_001115.2	58	0,247,5345	TT,TC,CC		3.0544,0.533,2.2085	benign	80/1252	132052342	247,10937	1876	3716	5592	SO:0001583	missense	114	exon1			GCGGCGCGTGGTG	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.238G>A	8.37:g.132052342C>T	ENSP00000286355:p.Ala80Thr	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	6	5	0.833333	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	43	0.019688644688644688	4	0.008130081300813009	8	0.022099447513812154	4	0.006993006993006993	27	0.03562005277044855	C	18.88	3.716491	0.68844	0.00533	0.030544	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.65916	-0.18;-0.18	4.55	4.55	0.56014	.	0.116934	0.38605	N	0.001630	T	0.12817	0.0311	L	0.36672	1.1	0.29715	N	0.839078	B;B	0.32731	0.076;0.382	B;B	0.15052	0.012;0.012	T	0.09596	-1.0667	10	0.13470	T	0.59	.	6.3928	0.21595	0.0:0.7154:0.187:0.0976	rs2228949	80;80	E7EVL1;P40145	.;ADCY8_HUMAN	T	80	ENSP00000286355:A80T;ENSP00000367161:A80T	ENSP00000286355:A80T	A	-	1	0	ADCY8	132121524	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.772000	0.38552	2.383000	0.81215	0.462000	0.41574	GCG	C|0.979;T|0.021	0.021	strong		0.726	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
HMOX2	3163	hgsc.bcm.edu	37	16	4556911	4556911	+	Silent	SNP	G	G	A	rs25685	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4556911G>A	ENST00000570646.1	+	3	707	c.102G>A	c.(100-102)tcG>tcA	p.S34S	HMOX2_ENST00000458134.3_Silent_p.S34S|HMOX2_ENST00000406590.2_Silent_p.S34S|HMOX2_ENST00000575120.1_Silent_p.S5S|HMOX2_ENST00000398595.3_Silent_p.S34S|HMOX2_ENST00000219700.6_Silent_p.S34S|HMOX2_ENST00000414777.1_Silent_p.S34S	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	34					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						CTGACCTCTCGGAGCTCCTGA	0.493											OREG0023582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	411	0.0820687	0.2103	0.1081	5008	,	,		19674	0.003		0.0457	False		,,,				2504	0.0092				p.S34S		Atlas-SNP	.											.	HMOX2	22	.	0			c.G102A						PASS	.	G	,,,	718,3676	297.3+/-284.7	54,610,1533	142.0	151.0	148.0		102,102,102,102	-8.3	0.9	16	dbSNP_72	148	315,8285	111.4+/-171.7	3,309,3988	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HMOX2	NM_001127204.1,NM_001127205.1,NM_001127206.1,NM_002134.3	,,,	57,919,5521	AA,AG,GG		3.6628,16.3405,7.9498	,,,	34/317,34/317,34/317,34/317	4556911	1033,11961	2197	4300	6497	SO:0001819	synonymous_variant	3163	exon3			CCTCTCGGAGCTC		CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.102G>A	16.37:g.4556911G>A		Somatic	103	0	0	619	WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_001127205	A8MT35|D3DUD5|I3L430|O60605	Silent	SNP	ENST00000570646.1	37	CCDS10517.1																																																																																			G|0.921;A|0.079	0.079	strong		0.493	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2		
HERPUD2	64224	hgsc.bcm.edu	37	7	35709842	35709842	+	Missense_Mutation	SNP	C	C	T	rs3779234	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:35709842C>T	ENST00000396081.1	-	3	1126	c.322G>A	c.(322-324)Gca>Aca	p.A108T	HERPUD2_ENST00000311350.3_Missense_Mutation_p.A108T|HERPUD2_ENST00000426180.1_5'Flank	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	108	Ser-rich.		A -> T (in dbSNP:rs3779234). {ECO:0000269|PubMed:15489334}.		response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						CTGCTGGATGCCAATGCTTCA	0.383													C|||	1339	0.267372	0.1203	0.3156	5008	,	,		19078	0.2649		0.3678	False		,,,				2504	0.3313				p.A108T		Atlas-SNP	.											.	HERPUD2	47	.	0			c.G322A						PASS	.	C	THR/ALA	775,3631	313.0+/-292.9	71,633,1499	144.0	135.0	138.0		322	2.2	0.9	7	dbSNP_107	138	3319,5281	494.2+/-373.8	651,2017,1632	yes	missense	HERPUD2	NM_022373.4	58	722,2650,3131	TT,TC,CC		38.593,17.5897,31.4778	benign	108/407	35709842	4094,8912	2203	4300	6503	SO:0001583	missense	64224	exon4			TGGATGCCAATGC	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"""homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"""						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.322G>A	7.37:g.35709842C>T	ENSP00000379390:p.Ala108Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_022373	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	37	CCDS5446.1	605	0.27701465201465203	63	0.12804878048780488	120	0.3314917127071823	141	0.2465034965034965	281	0.370712401055409	C	12.44	1.937260	0.34189	0.175897	0.38593	ENSG00000122557	ENST00000396081;ENST00000311350;ENST00000413517	T;T;T	0.24723	2.81;2.81;1.84	5.57	2.24	0.28232	.	0.600215	0.18491	N	0.139623	T	0.00012	0.0000	N	0.08118	0	0.31015	P	0.718757	B	0.14438	0.01	B	0.12156	0.007	T	0.47995	-0.9073	9	0.28530	T	0.3	-5.4519	8.905	0.35519	0.0:0.6726:0.1285:0.1989	rs3779234;rs17849911;rs17851785;rs59517106;rs3779234	108	Q9BSE4	HERP2_HUMAN	T	108;108;82	ENSP00000379390:A108T;ENSP00000310729:A108T;ENSP00000391015:A82T	ENSP00000310729:A108T	A	-	1	0	HERPUD2	35676367	0.990000	0.36364	0.901000	0.35422	0.891000	0.51852	0.811000	0.27198	0.681000	0.31386	0.460000	0.39030	GCA	C|0.703;T|0.297	0.297	strong		0.383	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373	
FCRLB	127943	hgsc.bcm.edu	37	1	161697072	161697072	+	Missense_Mutation	SNP	G	G	C	rs72704099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161697072G>C	ENST00000367948.2	+	8	1116	c.901G>C	c.(901-903)Gct>Cct	p.A301P	FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367944.3_Missense_Mutation_p.S259T|FCRLB_ENST00000367946.3_Missense_Mutation_p.Q252H|FCRLB_ENST00000392158.1_Missense_Mutation_p.A301P|FCRLB_ENST00000336830.5_Missense_Mutation_p.S266T|FCRLB_ENST00000367945.1_Missense_Mutation_p.Q245H			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						PASS	.	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	72	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	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	
MAGI2	9863	hgsc.bcm.edu	37	7	78119109	78119109	+	Silent	SNP	C	C	T	rs3735442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:78119109C>T	ENST00000354212.4	-	6	1267	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K	MAGI2_ENST00000535697.1_Silent_p.K175K|MAGI2_ENST00000536571.1_Silent_p.K170K|MAGI2_ENST00000419488.1_Silent_p.K338K|MAGI2_ENST00000522391.1_Silent_p.K338K	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	338	Interaction with DDN.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GAGGTTTAGCCTTTTTCGCAA	0.373													C|||	1618	0.323083	0.4864	0.2334	5008	,	,		20046	0.2321		0.2952	False		,,,				2504	0.2883				p.K338K		Atlas-SNP	.											.	MAGI2	246	.	0			c.G1014A						PASS	.	C		1882,2524	542.0+/-375.9	408,1066,729	204.0	207.0	206.0		1014	5.5	1.0	7	dbSNP_107	206	2611,5989	420.6+/-353.4	405,1801,2094	no	coding-synonymous	MAGI2	NM_012301.3		813,2867,2823	TT,TC,CC		30.3605,42.7145,34.5456		338/1456	78119109	4493,8513	2203	4300	6503	SO:0001819	synonymous_variant	9863	exon6			TTTAGCCTTTTTC	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1014G>A	7.37:g.78119109C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	171	169	0.988304	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	37	CCDS5594.1																																																																																			C|0.670;T|0.330	0.330	strong		0.373	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301	
KNDC1	85442	hgsc.bcm.edu	37	10	134973995	134973995	+	Silent	SNP	G	G	A	rs71503783	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:134973995G>A	ENST00000304613.3	+	1	45	c.24G>A	c.(22-24)gcG>gcA	p.A8A	KNDC1_ENST00000368572.2_Silent_p.A8A			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	8					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)		ACCCGGCCGCGGCGGATCTTT	0.751													g|||	1255	0.250599	0.2663	0.379	5008	,	,		6772	0.0883		0.2952	False		,,,				2504	0.2597				p.A8A		Atlas-SNP	.											.	KNDC1	155	.	0			c.G24A						PASS	.	G		1227,3105		179,869,1118	13.0	13.0	13.0		24	-0.1	0.0	10	dbSNP_130	13	2413,6115		377,1659,2228	no	coding-synonymous	KNDC1	NM_152643.6		556,2528,3346	AA,AG,GG		28.295,28.3241,28.3048		8/1750	134973995	3640,9220	2166	4264	6430	SO:0001819	synonymous_variant	85442	exon1			GGCCGCGGCGGAT	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.24G>A	10.37:g.134973995G>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	7	4	0.571429	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	CCDS7674.1																																																																																			G|0.736;A|0.264	0.264	strong		0.751	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
PTPRS	5802	hgsc.bcm.edu	37	19	5212482	5212482	+	Silent	SNP	G	G	A	rs2230611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5212482G>A	ENST00000587303.1	-	30	4734	c.4635C>T	c.(4633-4635)cgC>cgT	p.R1545R	PTPRS_ENST00000588012.1_Silent_p.R1507R|PTPRS_ENST00000353284.2_Silent_p.R1098R|PTPRS_ENST00000348075.2_Silent_p.R1507R|PTPRS_ENST00000592099.1_Silent_p.R1098R|PTPRS_ENST00000357368.4_Silent_p.R1545R|PTPRS_ENST00000262963.6_Silent_p.R1525R|PTPRS_ENST00000372412.4_Silent_p.R1546R|PTPRS_ENST00000588552.1_5'UTR			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1545	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)	p.R1545R(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GGCGGACCTCGCGTTTCTCAC	0.612													G|||	724	0.144569	0.115	0.2795	5008	,	,		16496	0.0565		0.1243	False		,,,				2504	0.2004				p.R1545R		Atlas-SNP	.											PTPRS,NS,carcinoma,0,1	PTPRS	169	1	1	Substitution - coding silent(1)	stomach(1)	c.C4635T						PASS	.	G	,,,	450,3954		29,392,1781	50.0	43.0	46.0		4635,3294,4521,3306	-4.0	1.0	19	dbSNP_98	46	964,7622		44,876,3373	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	73,1268,5154	AA,AG,GG		11.2276,10.218,10.8853	,,,	1545/1949,1098/1502,1507/1911,1102/1506	5212482	1414,11576	2202	4293	6495	SO:0001819	synonymous_variant	5802	exon31			GACCTCGCGTTTC	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.4635C>T	19.37:g.5212482G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			G|0.889;A|0.111	0.111	strong		0.612	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
GEN1	348654	hgsc.bcm.edu	37	2	17962450	17962450	+	Silent	SNP	A	A	G	rs300168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:17962450A>G	ENST00000381254.2	+	14	2185	c.1971A>G	c.(1969-1971)gaA>gaG	p.E657E	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Silent_p.E657E	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	657					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)					TTAGTCCTGAAGAGCATCTAC	0.363								Homologous recombination					A|||	2874	0.573882	0.1536	0.6354	5008	,	,		19873	0.9226		0.5249	False		,,,				2504	0.7894				p.E657E		Atlas-SNP	.											.	GEN1	79	.	0			c.A1971G						PASS	.	A	,	1084,3322	389.8+/-327.4	148,788,1267	72.0	70.0	71.0		1971,1971	1.6	1.0	2	dbSNP_79	71	4458,4142	585.7+/-391.9	1162,2134,1004	no	coding-synonymous,coding-synonymous	GEN1	NM_001130009.1,NM_182625.3	,	1310,2922,2271	GG,GA,AA		48.1628,24.6028,42.6111	,	657/909,657/909	17962450	5542,7464	2203	4300	6503	SO:0001819	synonymous_variant	348654	exon14			TCCTGAAGAGCAT	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.1971A>G	2.37:g.17962450A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	37	CCDS1691.1																																																																																			A|0.505;G|0.495	0.495	strong		0.363	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
PCDHA2	56146	hgsc.bcm.edu	37	5	140176592	140176592	+	Silent	SNP	G	G	A	rs149822412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140176592G>A	ENST00000526136.1	+	1	2043	c.2043G>A	c.(2041-2043)cgG>cgA	p.R681R	PCDHA2_ENST00000520672.2_Silent_p.R681R|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Silent_p.R681R|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	681					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)			CCTCGTCGCGGGCGTGGGTGG	0.647													.|||	47	0.00938498	0.0	0.0115	5008	,	,		16817	0.0		0.0249	False		,,,				2504	0.0143				p.R681R		Atlas-SNP	.											.	PCDHA2	404	.	0			c.G2043A						PASS	.	G	,,,	36,4370	37.6+/-69.7	0,36,2167	72.0	76.0	75.0		,2043,,2043	0.7	0.0	5	dbSNP_134	75	391,8207	123.6+/-182.4	5,381,3913	no	intron,coding-synonymous,intron,coding-synonymous	PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_031411.1,NM_031495.1	,,,	5,417,6080	AA,AG,GG		4.5476,0.8171,3.2836	,,,	,681/949,,681/825	140176592	427,12577	2203	4299	6502	SO:0001819	synonymous_variant	56146	exon1			GTCGCGGGCGTGG	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.2043G>A	5.37:g.140176592G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	161	75	0.465839	NM_031495	O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	37	CCDS54914.1																																																																																			G|0.975;A|0.025	0.025	strong		0.647	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905	
PIGN	23556	hgsc.bcm.edu	37	18	59781800	59781800	+	Silent	SNP	A	A	G	rs13381627	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:59781800A>G	ENST00000357637.5	-	15	1660	c.1245T>C	c.(1243-1245)gaT>gaC	p.D415D	PIGN_ENST00000400334.3_Silent_p.D415D	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	415					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TTACCACTTCATCAAACTTTC	0.338													G|||	479	0.095647	0.0144	0.1239	5008	,	,		15310	0.0069		0.2694	False		,,,				2504	0.0982				p.D415D		Atlas-SNP	.											.	PIGN	62	.	0			c.T1245C						PASS	.	G	,	165,3269		4,157,1556	75.0	65.0	68.0		1245,1245	-2.8	0.8	18	dbSNP_121	68	1611,6081		152,1307,2387	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	156,1464,3943	GG,GA,AA		20.9438,4.8049,15.9626	,	415/932,415/932	59781800	1776,9350	1717	3846	5563	SO:0001819	synonymous_variant	23556	exon15			CACTTCATCAAAC	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1245T>C	18.37:g.59781800A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			A|0.876;G|0.124	0.124	strong		0.338	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
APOL1	8542	hgsc.bcm.edu	37	22	36661330	36661330	+	Missense_Mutation	SNP	G	G	A	rs2239785	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36661330G>A	ENST00000397278.3	+	6	677	c.448G>A	c.(448-450)Gag>Aag	p.E150K	APOL1_ENST00000397279.4_Missense_Mutation_p.E150K|APOL1_ENST00000440669.2_3'UTR|APOL1_ENST00000426053.1_Missense_Mutation_p.E132K|APOL1_ENST00000319136.4_Missense_Mutation_p.E166K|APOL1_ENST00000422706.1_Missense_Mutation_p.E150K|APOL1_ENST00000347595.7_Missense_Mutation_p.E29K	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	150			E -> K (in dbSNP:rs2239785). {ECO:0000269|PubMed:11290834, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9325276}.		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						GTTGAAAAGTGAGCTTGAGGA	0.478													g|||	3396	0.678115	0.3064	0.8401	5008	,	,		21489	0.7956		0.7813	False		,,,				2504	0.8384				p.E166K		Atlas-SNP	.											.	APOL1	35	.	0			c.G496A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1647,2759	505.2+/-366.1	301,1045,857	116.0	105.0	109.0	http://www.ncbi.nlm.nih.gov/pubmed?term	448,394,448,496	-2.2	0.0	22	dbSNP_98	109	6844,1756	735.7+/-407.0	2715,1414,171	yes	missense,missense,missense,missense	APOL1	NM_001136540.1,NM_001136541.1,NM_003661.3,NM_145343.2	56,56,56,56	3016,2459,1028	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	20.4186,37.3808,34.7147	probably-damaging,probably-damaging,probably-damaging,probably-damaging	150/399,132/381,150/399,166/415	36661330	8491,4515	2203	4300	6503	SO:0001583	missense	8542	exon7			AAAAGTGAGCTTG	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.448G>A	22.37:g.36661330G>A	ENSP00000380448:p.Glu150Lys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	146	61	0.417808	NM_145343	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Missense_Mutation	SNP	ENST00000397278.3	37	CCDS13926.1	1539	0.7046703296703297	188	0.3821138211382114	297	0.8204419889502762	464	0.8111888111888111	590	0.7783641160949868	g	13.36	2.214382	0.39102	0.373808	0.795814	ENSG00000100342	ENST00000397278;ENST00000422706;ENST00000426053;ENST00000319136;ENST00000427990;ENST00000347595;ENST00000397279	T;T;T;T;T;T;T	0.03524	3.9;3.9;3.9;3.9;3.9;3.9;3.9	3.38	-2.18	0.07037	.	0.413252	0.28533	N	0.015009	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	D;D;D	0.59767	0.986;0.986;0.982	P;P;P	0.59595	0.86;0.86;0.78	T	0.45293	-0.9271	9	0.11182	T	0.66	.	3.8103	0.08793	0.3625:0.1847:0.4528:0.0	rs2239785;rs52809722;rs60256333;rs2239785	132;150;166	E9PF24;O14791;O14791-2	.;APOL1_HUMAN;.	K	150;150;132;166;150;29;150	ENSP00000380448:E150K;ENSP00000411507:E150K;ENSP00000388477:E132K;ENSP00000317674:E166K;ENSP00000391302:E150K;ENSP00000216178:E29K;ENSP00000380449:E150K	ENSP00000317674:E166K	E	+	1	0	APOL1	34991276	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.987000	0.03743	-0.146000	0.11274	0.194000	0.17425	GAG	G|0.329;A|0.671	0.671	strong		0.478	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343	
OR1S1	219959	hgsc.bcm.edu	37	11	57982584	57982584	+	Missense_Mutation	SNP	T	T	C	rs1966835	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57982584T>C	ENST00000309433.6	+	1	368	c.368T>C	c.(367-369)aTt>aCt	p.I123T		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	123			I -> T (in dbSNP:rs1966835).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTTGTCGTCATTGACAATTTG	0.448													T|||	2620	0.523163	0.2844	0.5418	5008	,	,		22315	0.8036		0.4225	False		,,,				2504	0.6472				p.I123T		Atlas-SNP	.											.	OR1S1	139	.	0			c.T368C						PASS	.	T	THR/ILE	1323,3079	445.3+/-347.6	197,929,1075	183.0	172.0	176.0		368	-2.6	0.4	11	dbSNP_92	176	3643,4949	524.4+/-380.5	785,2073,1438	no	missense	OR1S1	NM_001004458.1	89	982,3002,2513	CC,CT,TT		42.3999,30.0545,38.2176	benign	123/326	57982584	4966,8028	2201	4296	6497	SO:0001583	missense	219959	exon1			TCGTCATTGACAA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.368T>C	11.37:g.57982584T>C	ENSP00000311688:p.Ile123Thr	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	323	157	0.486068	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1080	0.4945054945054945	147	0.29878048780487804	187	0.5165745856353591	432	0.7552447552447552	314	0.41424802110817943	T	0.360	-0.939776	0.02322	0.300545	0.423999	ENSG00000172774	ENST00000309433	T	0.01685	4.69	3.27	-2.56	0.06268	GPCR, rhodopsin-like superfamily (1);	0.522752	0.16164	N	0.226633	T	0.00012	0.0000	N	0.01515	-0.825	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.16394	-1.0404	9	0.62326	D	0.03	.	1.4226	0.02315	0.1409:0.3037:0.1431:0.4123	rs1966835;rs52810501;rs1966835	123	Q8NH92	OR1S1_HUMAN	T	123	ENSP00000311688:I123T	ENSP00000311688:I123T	I	+	2	0	OR1S1	57739160	0.000000	0.05858	0.354000	0.25760	0.142000	0.21351	-1.070000	0.03440	-0.406000	0.07588	-1.267000	0.01435	ATT	T|0.569;C|0.431	0.431	strong		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
RNF17	56163	hgsc.bcm.edu	37	13	25440318	25440318	+	Missense_Mutation	SNP	G	G	A	rs9507425	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25440318G>A	ENST00000255324.5	+	30	4190	c.4138G>A	c.(4138-4140)Gaa>Aaa	p.E1380K	RNF17_ENST00000381921.1_Missense_Mutation_p.E1338K|RNF17_ENST00000339524.3_Missense_Mutation_p.E390K	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1380			E -> K (in dbSNP:rs9507425). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		GTATGAAGAGGAACAATGGGA	0.313													G|||	1062	0.212061	0.0847	0.2205	5008	,	,		17485	0.3254		0.2903	False		,,,				2504	0.181				p.E1380K		Atlas-SNP	.											.	RNF17	259	.	0			c.G4138A						PASS	.	G	LYS/GLU,LYS/GLU	539,3867	240.3+/-251.1	35,469,1699	108.0	107.0	107.0		4126,4138	3.9	0.3	13	dbSNP_119	107	2506,6088	405.8+/-348.6	345,1816,2136	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	56,56	380,2285,3835	AA,AG,GG		29.1599,12.2333,23.4231	benign,benign	1376/1620,1380/1624	25440318	3045,9955	2203	4297	6500	SO:0001583	missense	56163	exon30			GAAGAGGAACAAT	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.4138G>A	13.37:g.25440318G>A	ENSP00000255324:p.Glu1380Lys	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	220	105	0.477273	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	489	0.2239010989010989	37	0.07520325203252033	82	0.2265193370165746	155	0.270979020979021	215	0.2836411609498681	G	9.703	1.155106	0.21371	0.122333	0.291599	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000418120;ENST00000339524	T;T;T;T	0.23552	3.52;3.41;2.73;1.9	4.74	3.9	0.45041	.	0.094831	0.46442	D	0.000286	T	0.00012	0.0000	L	0.41236	1.265	0.25451	P	0.988003	B;B;B;B	0.09022	0.001;0.0;0.0;0.002	B;B;B;B	0.09377	0.003;0.0;0.004;0.003	T	0.34354	-0.9832	9	0.07644	T	0.81	-20.6408	9.2271	0.37414	0.0994:0.0:0.9006:0.0	rs9507425;rs17480121;rs52806297;rs59442158;rs9507425	1376;390;1374;1380	B7Z7S1;Q5T6R1;Q9BXT8-5;Q9BXT8	.;.;.;RNF17_HUMAN	K	1380;1338;704;390	ENSP00000255324:E1380K;ENSP00000371346:E1338K;ENSP00000388892:E704K;ENSP00000344776:E390K	ENSP00000255324:E1380K	E	+	1	0	RNF17	24338318	0.968000	0.33430	0.343000	0.25615	0.557000	0.35523	3.135000	0.50546	1.367000	0.46095	-0.254000	0.11334	GAA	G|0.778;A|0.222	0.222	strong		0.313	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
CENPF	1063	hgsc.bcm.edu	37	1	214816142	214816142	+	Silent	SNP	T	T	G	rs3795516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214816142T>G	ENST00000366955.3	+	12	4629	c.4461T>G	c.(4459-4461)ctT>ctG	p.L1487L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1583	2 X 96 AA approximate tandem repeats.				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)		GCTCTAGTCTTAGCAGTTTGG	0.478													T|||	528	0.105431	0.1014	0.1052	5008	,	,		18311	0.126		0.0517	False		,,,				2504	0.1452				p.L1487L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T4461G						PASS	.	T		399,4007	199.1+/-222.7	17,365,1821	62.0	61.0	62.0		4461	2.5	0.0	1	dbSNP_107	62	467,8133	139.0+/-195.8	12,443,3845	no	coding-synonymous	CENPF	NM_016343.3		29,808,5666	GG,GT,TT		5.4302,9.0558,6.6585		1487/3115	214816142	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	1063	exon12			TAGTCTTAGCAGT	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.4461T>G	1.37:g.214816142T>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			T|0.915;G|0.085	0.085	strong		0.478	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
ART1	417	hgsc.bcm.edu	37	11	3681115	3681115	+	Silent	SNP	A	A	G	rs35136756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:3681115A>G	ENST00000250693.1	+	3	467	c.366A>G	c.(364-366)acA>acG	p.T122T		NM_004314.2	NP_004305.2	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1	122					innate immune response (GO:0045087)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|skin(1)	8		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)		TGGCCTACACAGCCAACAGCC	0.662													G|||	791	0.157947	0.2776	0.1124	5008	,	,		16719	0.0417		0.1312	False		,,,				2504	0.1759				p.T122T		Atlas-SNP	.											.	ART1	21	.	0			c.A366G						PASS	.	G		1149,3253	697.9+/-406.3	159,831,1211	30.0	32.0	31.0		366	-11.1	0.1	11	dbSNP_126	31	1152,7442	756.8+/-407.5	95,962,3240	no	coding-synonymous	ART1	NM_004314.2		254,1793,4451	GG,GA,AA		13.4047,26.1018,17.7054		122/328	3681115	2301,10695	2201	4297	6498	SO:0001819	synonymous_variant	417	exon3			CTACACAGCCAAC	S74683	CCDS7744.1	11p15	2006-02-23			ENSG00000129744	ENSG00000129744		"""CD molecules"""	723	protein-coding gene	gene with protein product		601625				8812442	Standard	NM_004314		Approved	ART2, CD296	uc001lye.1	P52961	OTTHUMG00000011845	ENST00000250693.1:c.366A>G	11.37:g.3681115A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_004314	Q6NTD2|Q96KT9	Silent	SNP	ENST00000250693.1	37	CCDS7744.1																																																																																			A|0.842;G|0.158	0.158	strong		0.662	ART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032765.1	NM_004314	
TMEM140	55281	hgsc.bcm.edu	37	7	134849213	134849213	+	Missense_Mutation	SNP	G	G	A	rs3800592	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:134849213G>A	ENST00000275767.3	+	2	243	c.20G>A	c.(19-21)cGg>cAg	p.R7Q	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	7			R -> Q (in dbSNP:rs3800592). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						CCAAGGCCTCGGTGGCGCGAC	0.592													G|||	2283	0.455871	0.4009	0.4798	5008	,	,		19594	0.2589		0.4821	False		,,,				2504	0.6892				p.R7Q		Atlas-SNP	.											.	TMEM140	18	.	0			c.G20A						PASS	.	G	GLN/ARG	1933,2473	550.6+/-378.1	435,1063,705	116.0	103.0	108.0		20	-5.3	0.0	7	dbSNP_107	108	4372,4228	583.5+/-391.6	1125,2122,1053	yes	missense	TMEM140	NM_018295.3	43	1560,3185,1758	AA,AG,GG		49.1628,43.872,48.4776	possibly-damaging	7/186	134849213	6305,6701	2203	4300	6503	SO:0001583	missense	55281	exon2			GGCCTCGGTGGCG	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.20G>A	7.37:g.134849213G>A	ENSP00000275767:p.Arg7Gln	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_018295	A4D1P9|Q8WUC3	Missense_Mutation	SNP	ENST00000275767.3	37	CCDS5837.1	908	0.4157509157509158	210	0.4268292682926829	165	0.4558011049723757	153	0.2674825174825175	380	0.5013192612137203	G	13.65	2.299389	0.40694	0.43872	0.508372	ENSG00000146859	ENST00000275767;ENST00000456488	T	0.19806	2.12	5.68	-5.31	0.02730	.	0.964256	0.08571	N	0.926035	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B	0.21381	0.055	B	0.12837	0.008	T	0.44757	-0.9307	9	0.34782	T	0.22	-2.082	9.0454	0.36343	0.5179:0.0:0.3867:0.0955	rs3800592;rs10337077;rs11558287;rs17851848;rs3800592	7	Q9NV12	TM140_HUMAN	Q	7	ENSP00000275767:R7Q	ENSP00000275767:R7Q	R	+	2	0	TMEM140	134499753	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.042000	0.12063	-1.042000	0.03262	-1.326000	0.01283	CGG	G|0.536;A|0.464	0.464	strong		0.592	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295	
MVD	4597	hgsc.bcm.edu	37	16	88724347	88724347	+	Silent	SNP	G	G	T	rs2279258	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88724347G>T	ENST00000301012.3	-	3	261	c.232C>A	c.(232-234)Cgg>Agg	p.R78R	MVD_ENST00000568709.1_5'UTR	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	78					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GCCTGCAGCCGCGGCTGCCCC	0.602													G|||	2496	0.498403	0.264	0.7089	5008	,	,		17747	0.6438		0.6441	False		,,,				2504	0.3661				p.R78R		Atlas-SNP	.											.	MVD	27	.	0			c.C232A						PASS	.	G		1479,2917	463.8+/-353.7	268,943,987	48.0	55.0	52.0		232	5.1	0.2	16	dbSNP_100	52	5675,2923	662.1+/-401.9	1853,1969,477	no	coding-synonymous	MVD	NM_002461.1		2121,2912,1464	TT,TG,GG		33.9963,33.6442,44.9438		78/401	88724347	7154,5840	2198	4299	6497	SO:0001819	synonymous_variant	4597	exon3			GCAGCCGCGGCTG	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"""mevalonate pyrophosphate decarboxylase"""	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.232C>A	16.37:g.88724347G>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	NM_002461	Q53Y65	Silent	SNP	ENST00000301012.3	37	CCDS10968.1																																																																																			G|0.443;T|0.557	0.557	strong		0.602	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925331	47925331	+	Missense_Mutation	SNP	C	C	G	rs10274334	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	99	0	0		WXS	Illumina HiSeq	Phase_I	95	95	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	
RNASE1	6035	hgsc.bcm.edu	37	14	21269811	21269811	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21269811T>A	ENST00000397967.4	-	2	923	c.417A>T	c.(415-417)gaA>gaT	p.E139D	RNASE1_ENST00000412779.2_Missense_Mutation_p.E139D|RNASE1_ENST00000555698.1_Missense_Mutation_p.E99D|RNASE1_ENST00000397970.4_Missense_Mutation_p.E139D|RNASE1_ENST00000340900.3_Missense_Mutation_p.E139D	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	139					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	ATGGGCTCCCTTCACAGGCCA	0.567																																					p.E139D		Atlas-SNP	.											.	RNASE1	14	.	0			c.A417T						PASS	.						151.0	132.0	138.0					14																	21269811		2203	4300	6503	SO:0001583	missense	6035	exon3			GCTCCCTTCACAG	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"""Ribonucleases, RNase A"""	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.417A>T	14.37:g.21269811T>A	ENSP00000381057:p.Glu139Asp	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	194	105	0.541237	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Missense_Mutation	SNP	ENST00000397967.4	37	CCDS9559.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.877944	0.33162	.	.	ENSG00000129538	ENST00000397967;ENST00000340900;ENST00000412779;ENST00000555698;ENST00000397970	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.21	1.28	0.21552	Ribonuclease A, domain (4);	0.527449	0.18611	N	0.136179	T	0.31888	0.0811	L	0.50333	1.59	0.30340	N	0.785825	B	0.02656	0.0	B	0.04013	0.001	T	0.21586	-1.0241	10	0.51188	T	0.08	-29.0622	5.056	0.14533	0.0:0.4831:0.3303:0.1866	.	139	P07998	RNAS1_HUMAN	D	139;139;139;99;139	ENSP00000381057:E139D;ENSP00000344193:E139D;ENSP00000399493:E139D;ENSP00000451058:E99D;ENSP00000381060:E139D	ENSP00000344193:E139D	E	-	3	2	RNASE1	20339651	0.268000	0.24133	0.971000	0.41717	0.601000	0.36947	-0.503000	0.06383	0.056000	0.16144	-0.248000	0.11899	GAA	.	.	none		0.567	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3		
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552812	43552812	+	Silent	SNP	A	A	G	rs71227520	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43552812A>G	ENST00000430334.3	-	4	710	c.577T>C	c.(577-579)Ttg>Ctg	p.L193L	PLEKHM1_ENST00000421073.2_Silent_p.L104L	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	193					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)					GACAGGGCCAATGGGGTGAGC	0.552													G|||	378	0.0754792	0.034	0.1412	5008	,	,		21329	0.001		0.1819	False		,,,				2504	0.0521				p.L193L		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.T577C						PASS	.						66.0	58.0	60.0					17																	43552812		2199	4249	6448	SO:0001819	synonymous_variant	9842	exon4			GGGCCAATGGGGT	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.577T>C	17.37:g.43552812A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			A|0.925;G|0.075	0.075	strong		0.552	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
MTAP	4507	hgsc.bcm.edu	37	9	21816758	21816758	+	Missense_Mutation	SNP	G	G	A	rs7023954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21816758G>A	ENST00000460874.2	+	3	442	c.217G>A	c.(217-219)Gtc>Atc	p.V73I	MTAP_ENST00000380172.4_Missense_Mutation_p.V56I|MTAP_ENST00000427788.2_3'UTR|MTAP_ENST00000580900.1_Missense_Mutation_p.V56I|RP11-145E5.5_ENST00000404796.2_Missense_Mutation_p.V56I					methylthioadenosine phosphorylase									p.0(1)|p.0?(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|lung(3)|pancreas(1)	10		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)		TGTTGATTGCGTCCTCCTTGC	0.313													G|||	1944	0.388179	0.4334	0.4438	5008	,	,		18888	0.4375		0.3946	False		,,,				2504	0.2301				p.V56I		Atlas-SNP	.											.	MTAP	23	.	2	Whole gene deletion(2)	lung(2)	c.G166A						PASS	.	G	ILE/VAL	1916,2490	547.2+/-377.2	407,1102,694	233.0	228.0	230.0		166	5.4	1.0	9	dbSNP_116	230	3569,5031	518.1+/-379.2	735,2099,1466	yes	missense	MTAP	NM_002451.3	29	1142,3201,2160	AA,AG,GG		41.5,43.4862,42.1728	benign	56/284	21816758	5485,7521	2203	4300	6503	SO:0001583	missense	4507	exon3			GATTGCGTCCTCC	AB062485	CCDS6509.1	9p21	2013-05-29			ENSG00000099810	ENSG00000099810	2.4.2.28		7413	protein-coding gene	gene with protein product	"""S-methyl-5'-thioadenosine phosphorylase"""	156540				11126361	Standard	NM_002451		Approved	MSAP, c86fus	uc003zph.3	Q13126	OTTHUMG00000019690	ENST00000460874.2:c.217G>A	9.37:g.21816758G>A	ENSP00000461932:p.Val73Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_002451		Missense_Mutation	SNP	ENST00000460874.2	37		897	0.4107142857142857	218	0.44308943089430897	149	0.4116022099447514	230	0.4020979020979021	300	0.39577836411609496	G	17.50	3.405531	0.62288	0.434862	0.415	ENSG00000099810	ENST00000380172	D	0.90004	-2.6	5.44	5.44	0.79542	Nucleoside phosphorylase domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.77616	2.38	0.09310	P	0.999999999893112	B;B;B	0.27450	0.179;0.052;0.006	B;B;B	0.34418	0.182;0.072;0.027	T	0.01956	-1.1240	9	0.49607	T	0.09	-17.3118	18.3922	0.90487	0.0:0.0:1.0:0.0	rs7023954;rs11555745;rs17755881;rs17852350;rs52809882;rs56427578;rs56666707;rs7023954	73;56;56	B4DUC8;F2Z2F3;Q13126	.;.;MTAP_HUMAN	I	56	ENSP00000369519:V56I	ENSP00000369519:V56I	V	+	1	0	MTAP	21806758	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	6.620000	0.74224	2.711000	0.92665	0.561000	0.74099	GTC	G|0.589;A|0.411	0.411	strong		0.313	MTAP-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000051929.2	NM_002451	
OR5P2	120065	hgsc.bcm.edu	37	11	7817959	7817959	+	Silent	SNP	G	G	A	rs73406603	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7817959G>A	ENST00000329434.2	-	1	561	c.531C>T	c.(529-531)ttC>ttT	p.F177F	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GTAAGGGAGCGAAATCACAGA	0.388													G|||	1185	0.236621	0.3472	0.2911	5008	,	,		20101	0.128		0.2763	False		,,,				2504	0.1196				p.F177F		Atlas-SNP	.											OR5P2,brain,glioma,0,1	OR5P2	68	1	0			c.C531T						PASS	.	G		1366,2838		399,568,1135	69.0	81.0	77.0		531	3.2	1.0	11	dbSNP_130	77	2424,6160		392,1640,2260	no	coding-synonymous	OR5P2	NM_153444.1		791,2208,3395	AA,AG,GG		28.2386,32.4929,29.6372		177/323	7817959	3790,8998	2102	4292	6394	SO:0001819	synonymous_variant	120065	exon1			GGGAGCGAAATCA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.531C>T	11.37:g.7817959G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			G|0.739;A|0.261	0.261	strong		0.388	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
VPS13C	54832	hgsc.bcm.edu	37	15	62259637	62259637	+	Missense_Mutation	SNP	C	C	T	rs3784634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:62259637C>T	ENST00000261517.5	-	29	2994	c.2921G>A	c.(2920-2922)aGg>aAg	p.R974K	VPS13C_ENST00000249837.3_Missense_Mutation_p.R931K|VPS13C_ENST00000395898.3_Missense_Mutation_p.R931K|VPS13C_ENST00000395896.4_Missense_Mutation_p.R974K	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						AAGGGGCTTCCTTTTGGATCC	0.269													T|||	3783	0.755391	0.9228	0.6052	5008	,	,		15751	0.8542		0.5636	False		,,,				2504	0.7311				p.R974K		Atlas-SNP	.											.	VPS13C	506	.	0			c.G2921A						PASS	.	T	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	3738,664		1600,538,63	53.0	61.0	58.0		2921,2792,2792,2921	1.6	1.0	15	dbSNP_107	58	4936,3652		1449,2038,807	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	26,26,26,26	3049,2576,870	TT,TC,CC		42.5245,15.0841,33.2256	benign,benign,benign,benign	974/3629,931/3711,931/3586,974/3754	62259637	8674,4316	2201	4294	6495	SO:0001583	missense	54832	exon29			GGCTTCCTTTTGG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.2921G>A	15.37:g.62259637C>T	ENSP00000261517:p.Arg974Lys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	103	103	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	
BAZ1B	9031	hgsc.bcm.edu	37	7	72891754	72891754	+	Silent	SNP	C	C	T	rs2074754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:72891754C>T	ENST00000339594.4	-	7	2375	c.2037G>A	c.(2035-2037)tcG>tcA	p.S679S	BAZ1B_ENST00000404251.1_Silent_p.S679S	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	679					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				AGGGGATTTCCGACAGCTTCA	0.488													C|||	1741	0.347644	0.0431	0.4784	5008	,	,		21713	0.4395		0.4682	False		,,,				2504	0.4479				p.S679S	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.G2037A						PASS	.	C		542,3864	246.2+/-254.9	39,464,1700	129.0	120.0	123.0		2037	-12.0	0.1	7	dbSNP_96	123	4035,4565	557.3+/-387.0	934,2167,1199	no	coding-synonymous	BAZ1B	NM_032408.3		973,2631,2899	TT,TC,CC		46.9186,12.3014,35.1915		679/1484	72891754	4577,8429	2203	4300	6503	SO:0001819	synonymous_variant	9031	exon7			GATTTCCGACAGC	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2037G>A	7.37:g.72891754C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	160	71	0.44375	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																			T|0.350;C|0.650	0.350	strong		0.488	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
METTL2B	55798	hgsc.bcm.edu	37	7	128119514	128119514	+	Missense_Mutation	SNP	G	G	A	rs1065267	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128119514G>A	ENST00000262432.8	+	3	542	c.505G>A	c.(505-507)Gaa>Aaa	p.E169K	RP11-212P7.3_ENST00000462662.1_RNA|METTL2B_ENST00000480046.1_Missense_Mutation_p.E104K	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	169			E -> K (in dbSNP:rs1065267).		tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TAGTGACCTGGAAATTTGTGC	0.408																																					p.E169K		Atlas-SNP	.											.	METTL2B	34	.	0			c.G505A						PASS	.						91.0	108.0	102.0					7																	128119514		2203	4299	6502	SO:0001583	missense	55798	exon3			GACCTGGAAATTT	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"""methyltransferase like 2"""	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.505G>A	7.37:g.128119514G>A	ENSP00000262432:p.Glu169Lys	Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	405	124	0.306173	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	37	CCDS5803.2	188	0.08608058608058608	11	0.022357723577235773	46	0.1270718232044199	0	0.0	131	0.17282321899736147	G	5.147	0.212742	0.09757	.	.	ENSG00000165055	ENST00000462662;ENST00000262432;ENST00000480046	T;T;T	0.17691	2.26;2.8;2.79	2.65	1.7	0.24286	.	0.906623	0.09774	N	0.757606	T	0.00039	0.0001	L	0.31664	0.95	0.80722	P	0.0	B;B	0.14805	0.001;0.011	B;B	0.14578	0.006;0.011	T	0.40813	-0.9543	9	0.09590	T	0.72	-1.7228	7.2315	0.26045	0.0:0.2783:0.7217:0.0	rs1065267;rs1065267	104;169	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	K	163;169;104	ENSP00000418634:E163K;ENSP00000262432:E169K;ENSP00000418402:E104K	ENSP00000262432:E169K	E	+	1	0	METTL2B	127906750	0.652000	0.27349	0.721000	0.30653	0.035000	0.12851	1.379000	0.34340	0.405000	0.25532	0.405000	0.27470	GAA	G|0.906;A|0.094	0.094	strong		0.408	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	
SLC45A3	85414	hgsc.bcm.edu	37	1	205628425	205628425	+	Silent	SNP	G	G	A	rs143282781		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205628425G>A	ENST00000367145.3	-	5	1894	c.1599C>T	c.(1597-1599)gtC>gtT	p.V533V	SLC45A3_ENST00000460934.1_5'UTR	NM_033102.2	NP_149093.1	Q96JT2	S45A3_HUMAN	solute carrier family 45, member 3	533					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)			SLC45A3/BRAF(2)|SLC45A3/ELK4(18)|SLC45A3/ETV1(3)|SLC45A3/ETV5_ENST00000306376(2)|SLC45A3/ERG(50)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|ovary(3)|prostate(5)	21	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			AGTAAATGGCGACCAGACCCA	0.547			T	"""ETV1, ETV5, ELK4, ERG"""	prostate						OREG0014161	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		20108	0.0		0.0	False		,,,				2504	0.001				p.V533V		Atlas-SNP	.		Dom	yes		1	1q32	85414	"""solute carrier family 45, member 3"""		E	.	SLC45A3	54	.	0			c.C1599T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	79.0	78.0	78.0		1599	-11.3	0.8	1	dbSNP_134	78	11,8589	9.1+/-34.3	0,11,4289	no	coding-synonymous	SLC45A3	NM_033102.2		0,14,6489	AA,AG,GG		0.1279,0.0681,0.1076		533/554	205628425	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	85414	exon5			AATGGCGACCAGA	AF109301	CCDS1458.1	1q32.1	2013-05-22	2005-10-04	2005-10-04	ENSG00000158715	ENSG00000158715		"""Solute carriers"""	8642	protein-coding gene	gene with protein product		605097	"""prostate cancer associated protein 6"", ""prostate cancer associated protein 2"", ""prostate cancer associated protein 8"""	PCANAP6, PCANAP2, PCANAP8		10613842, 11245466	Standard	XM_005245556		Approved	IPCA-6, prostein, IPCA-2, IPCA-8	uc001hda.1	Q96JT2	OTTHUMG00000037223	ENST00000367145.3:c.1599C>T	1.37:g.205628425G>A		Somatic	202	0	0	2153	WXS	Illumina HiSeq	Phase_I	196	98	0.5	NM_033102	A8K2U9	Silent	SNP	ENST00000367145.3	37	CCDS1458.1																																																																																			G|0.998;A|0.002	0.002	strong		0.547	SLC45A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090619.1	NM_033102	
COL5A1	1289	hgsc.bcm.edu	37	9	137707834	137707834	+	Splice_Site	SNP	G	G	A	rs3827848	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	228	0	0		WXS	Illumina HiSeq	Phase_I	223	223	1	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
C8A	731	hgsc.bcm.edu	37	1	57333312	57333312	+	Silent	SNP	A	A	G	rs34047108	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:57333312A>G	ENST00000361249.3	+	2	204	c.108A>G	c.(106-108)gcA>gcG	p.A36A		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	36					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						CACCCGCAGCAGTTACCTGCC	0.468													A|||	38	0.00758786	0.0015	0.0115	5008	,	,		17399	0.0		0.0229	False		,,,				2504	0.0051				p.A36A		Atlas-SNP	.											.	C8A	103	.	0			c.A108G						PASS	.	A		17,4389	24.3+/-50.5	0,17,2186	76.0	69.0	72.0		108	-3.3	0.0	1	dbSNP_126	72	155,8445	74.5+/-137.1	1,153,4146	no	coding-synonymous	C8A	NM_000562.2		1,170,6332	GG,GA,AA		1.8023,0.3858,1.3225		36/585	57333312	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	731	exon2			CGCAGCAGTTACC	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.108A>G	1.37:g.57333312A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Silent	SNP	ENST00000361249.3	37	CCDS606.1																																																																																			A|0.987;G|0.013	0.013	strong		0.468	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
ZNF880	400713	hgsc.bcm.edu	37	19	52888050	52888050	+	Missense_Mutation	SNP	A	A	G	rs76053634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:52888050A>G	ENST00000422689.2	+	4	1232	c.1217A>G	c.(1216-1218)cAa>cGa	p.Q406R		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	406					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						ACGGGAGAGCAACCTTACAAA	0.398																																					p.Q406R		Atlas-SNP	.											ZNF880,colon,carcinoma,0,2	ZNF880	45	2	0			c.A1217G						scavenged	.						70.0	64.0	66.0					19																	52888050		1568	3582	5150	SO:0001583	missense	400713	exon4			GAGAGCAACCTTA	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.1217A>G	19.37:g.52888050A>G	ENSP00000406318:p.Gln406Arg	Somatic	21	4	0.190476		WXS	Illumina HiSeq	Phase_I	38	9	0.236842	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	A	4.567	0.105370	0.08731	.	.	ENSG00000221923	ENST00000422689	T	0.15718	2.4	1.84	1.84	0.25277	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04182	0.0116	N	0.00392	-1.555	0.19775	N	0.999952	B	0.17667	0.023	B	0.23150	0.044	T	0.43360	-0.9396	8	.	.	.	.	8.4442	0.32833	1.0:0.0:0.0:0.0	.	406	Q6PDB4	ZN880_HUMAN	R	406	ENSP00000406318:Q406R	.	Q	+	2	0	ZNF880	57579862	0.002000	0.14202	0.418000	0.26571	0.177000	0.22998	0.149000	0.16243	0.834000	0.34852	0.450000	0.29827	CAA	A|0.867;G|0.133	0.133	strong		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
JPH2	57158	hgsc.bcm.edu	37	20	42747247	42747247	+	Missense_Mutation	SNP	C	C	T	rs3810510	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:42747247C>T	ENST00000372980.3	-	3	2058	c.1186G>A	c.(1186-1188)Gcc>Acc	p.A396T		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	396	Ala-rich.		A -> T (in dbSNP:rs3810510).		calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGCTTTGGCCTTGGCGTGG	0.592													C|||	1354	0.270367	0.3933	0.1009	5008	,	,		19145	0.3571		0.1163	False		,,,				2504	0.2935				p.A396T		Atlas-SNP	.											JPH2,caecum,carcinoma,0,1	JPH2	86	1	0			c.G1186A						PASS	.	C	THR/ALA	1455,2951	470.0+/-355.6	249,957,997	90.0	91.0	90.0		1186	3.8	1.0	20	dbSNP_107	90	1109,7491	231.1+/-265.2	78,953,3269	yes	missense	JPH2	NM_020433.4	58	327,1910,4266	TT,TC,CC		12.8953,33.0232,19.714	probably-damaging	396/697	42747247	2564,10442	2203	4300	6503	SO:0001583	missense	57158	exon3			CTTTGGCCTTGGC	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.1186G>A	20.37:g.42747247C>T	ENSP00000362071:p.Ala396Thr	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	23	0.638889	NM_020433	E1P5X1|O95913|Q5JY74|Q9UJN4	Missense_Mutation	SNP	ENST00000372980.3	37	CCDS13325.1	527	0.2413003663003663	185	0.37601626016260165	39	0.10773480662983426	217	0.3793706293706294	86	0.11345646437994723	C	21.7	4.194721	0.78902	0.330232	0.128953	ENSG00000149596	ENST00000372980	T	0.61980	0.06	4.78	3.84	0.44239	.	0.516515	0.20203	N	0.097052	T	0.00012	0.0000	L	0.48877	1.53	0.09310	P	1.0	D	0.54601	0.967	P	0.49276	0.605	T	0.29640	-1.0005	9	0.37606	T	0.19	.	11.654	0.51306	0.0:0.9117:0.0:0.0883	rs3810510;rs60986665;rs3810510	396	Q9BR39	JPH2_HUMAN	T	396	ENSP00000362071:A396T	ENSP00000362071:A396T	A	-	1	0	JPH2	42180661	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	4.050000	0.57404	1.005000	0.39183	0.561000	0.74099	GCC	C|0.772;T|0.228	0.228	strong		0.592	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1		
CLUH	23277	hgsc.bcm.edu	37	17	2606715	2606715	+	Silent	SNP	G	G	A	rs1065479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2606715G>A	ENST00000570628.2	-	3	363	c.258C>T	c.(256-258)cgC>cgT	p.R86R	CLUH_ENST00000538975.1_Silent_p.R86R|CLUH_ENST00000435359.1_Silent_p.R86R			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	86					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											AGAAGCAGGTGCGGTGACACG	0.662													G|||	2448	0.488818	0.2882	0.6354	5008	,	,		17901	0.5248		0.5696	False		,,,				2504	0.5358				p.R86R		Atlas-SNP	.											.	.	.	.	0			c.C258T						PASS	.	G		1485,2865		242,1001,932	41.0	50.0	47.0		258	1.9	1.0	17	dbSNP_86	47	5315,3219		1679,1957,631	no	coding-synonymous	KIAA0664	NM_015229.3		1921,2958,1563	AA,AG,GG		37.7197,34.1379,47.2214		86/1310	2606715	6800,6084	2175	4267	6442	SO:0001819	synonymous_variant	23277	exon3			GCAGGTGCGGTGA	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.258C>T	17.37:g.2606715G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	37	CCDS45572.1																																																																																			G|0.481;A|0.519	0.519	strong		0.662	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549362	32549362	+	Silent	SNP	G	G	A	rs199704140	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32549362G>A	ENST00000360004.5	-	3	729	c.624C>T	c.(622-624)agC>agT	p.S208S		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	208	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|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						GGCTTGTCACGCTTGGGTGCT	0.532										Multiple Myeloma(14;0.17)			G|||	507	0.101238	0.0885	0.1427	5008	,	,		16004	0.0506		0.1531	False		,,,				2504	0.0879				p.S208S		Atlas-SNP	.											HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	0			c.C624T						scavenged	.						125.0	112.0	117.0					6																	32549362		1504	2686	4190	SO:0001819	synonymous_variant	3123	exon3			TGTCACGCTTGGG	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.624C>T	6.37:g.32549362G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	155	29	0.187097	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.410;A|0.590	0.590	strong		0.532	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SEMA4D	10507	hgsc.bcm.edu	37	9	91978783	91978783	+	Silent	SNP	G	G	A	rs45515192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:91978783G>A	ENST00000420987.1	-	18	2411	c.1965C>T	c.(1963-1965)ccC>ccT	p.P655P	SEMA4D_ENST00000469653.1_5'UTR|SEMA4D_ENST00000420101.2_Silent_p.P40P|SEMA4D_ENST00000339861.4_Silent_p.P655P|SEMA4D_ENST00000343780.4_Silent_p.P655P|SEMA4D_ENST00000455551.2_Silent_p.P655P	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						CCCTGCCATCGGGCAGTGCAT	0.597													G|||	765	0.152756	0.0091	0.3646	5008	,	,		21139	0.2331		0.1203	False		,,,				2504	0.1472				p.P655P		Atlas-SNP	.											.	SEMA4D	81	.	0			c.C1965T						PASS	.	G		133,4273	95.3+/-134.0	3,127,2073	88.0	77.0	81.0		1965	-6.7	0.0	9	dbSNP_127	81	1143,7457	235.7+/-268.2	83,977,3240	no	coding-synonymous	SEMA4D	NM_001142287.1		86,1104,5313	AA,AG,GG		13.2907,3.0186,9.8109		655/739	91978783	1276,11730	2203	4300	6503	SO:0001819	synonymous_variant	10507	exon19			GCCATCGGGCAGT	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.1965C>T	9.37:g.91978783G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Silent	SNP	ENST00000420987.1	37	CCDS47991.1																																																																																			G|0.883;A|0.117	0.117	strong		0.597	SEMA4D-203	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402418.2	NM_006378	
DDI2	84301	hgsc.bcm.edu	37	1	15959977	15959977	+	Silent	SNP	C	C	T	rs3795763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15959977C>T	ENST00000480945.1	+	4	720	c.549C>T	c.(547-549)gcC>gcT	p.A183A		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	183							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|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;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AGGACCGAGCCCGGAGAGAGC	0.403													C|||	1257	0.250998	0.4493	0.2176	5008	,	,		18022	0.0317		0.2684	False		,,,				2504	0.2147				p.A183A		Atlas-SNP	.											.	DDI2	38	.	0			c.C549T						PASS	.	C		1831,2575	535.8+/-374.3	406,1019,778	186.0	222.0	210.0		549	2.7	1.0	1	dbSNP_107	210	2428,6172	401.3+/-347.1	326,1776,2198	no	coding-synonymous	DDI2	NM_032341.4		732,2795,2976	TT,TC,CC		28.2326,41.557,32.7464		183/400	15959977	4259,8747	2203	4300	6503	SO:0001819	synonymous_variant	84301	exon4			CCGAGCCCGGAGA		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"""				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.549C>T	1.37:g.15959977C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_032341	A8KAE1|Q7RTZ0|Q9BRT1	Silent	SNP	ENST00000480945.1	37	CCDS30607.1																																																																																			C|0.707;T|0.293	0.293	strong		0.403	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341	
DNM2	1785	hgsc.bcm.edu	37	19	10939792	10939792	+	Silent	SNP	T	T	C	rs2229920	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10939792T>C	ENST00000355667.6	+	19	2219	c.2139T>C	c.(2137-2139)gcT>gcC	p.A713A	DNM2_ENST00000585892.1_Silent_p.A713A|DNM2_ENST00000389253.4_Silent_p.A713A|DNM2_ENST00000408974.4_Silent_p.A709A|DNM2_ENST00000314646.5_Silent_p.A713A|DNM2_ENST00000359692.6_Silent_p.A709A	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	713	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			AGGAGTCGGCTGACCAGGCAC	0.627			"""F, N, Splice, Mis, O"""		ETP ALL								C|||	1694	0.338259	0.2617	0.2695	5008	,	,		19235	0.5595		0.2873	False		,,,				2504	0.3149				p.A713A		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.T2139C						PASS	.	C	,,,,	1148,3258	698.6+/-406.4	143,862,1198	46.0	36.0	39.0		2139,2139,2127,2139,2127	-10.1	0.1	19	dbSNP_98	39	2504,6096	679.1+/-403.5	370,1764,2166	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DNM2	NM_001005360.2,NM_001005361.2,NM_001005362.2,NM_001190716.1,NM_004945.3	,,,,	513,2626,3364	CC,CT,TT		29.1163,26.0554,28.0793	,,,,	713/871,713/871,709/867,713/870,709/867	10939792	3652,9354	2203	4300	6503	SO:0001819	synonymous_variant	1785	exon19			GTCGGCTGACCAG		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.2139T>C	19.37:g.10939792T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	158	55	0.348101	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Silent	SNP	ENST00000355667.6	37	CCDS45968.1																																																																																			T|0.682;C|0.318	0.318	strong		0.627	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	
DDX59	83479	hgsc.bcm.edu	37	1	200635617	200635617	+	Silent	SNP	G	G	A	rs78479136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:200635617G>A	ENST00000331314.6	-	2	465	c.252C>T	c.(250-252)agC>agT	p.S84S	DDX59_ENST00000447706.2_Silent_p.S84S|DDX59_ENST00000367348.3_Silent_p.S84S	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	84						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						CAGAAGGATGGCTGTCCTTCG	0.532													G|||	148	0.0295527	0.0061	0.0418	5008	,	,		18164	0.0		0.0934	False		,,,				2504	0.0174				p.S84S		Atlas-SNP	.											.	DDX59	117	.	0			c.C252T						PASS	.	G		75,4331	67.6+/-105.2	1,73,2129	94.0	86.0	88.0		252	3.0	0.0	1	dbSNP_132	88	876,7724	198.5+/-242.8	43,790,3467	no	coding-synonymous	DDX59	NM_001031725.4		44,863,5596	AA,AG,GG		10.186,1.7022,7.312		84/620	200635617	951,12055	2203	4300	6503	SO:0001819	synonymous_variant	83479	exon2			AGGATGGCTGTCC	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.252C>T	1.37:g.200635617G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	204	106	0.519608	NM_001031725	Q6PJL2|Q8IVW3|Q9H0W3	Silent	SNP	ENST00000331314.6	37	CCDS30964.1																																																																																			G|0.942;A|0.058	0.058	strong		0.532	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4	
ARHGAP15	55843	hgsc.bcm.edu	37	2	144194565	144194565	+	Silent	SNP	C	C	T	rs17230746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:144194565C>T	ENST00000295095.6	+	8	824	c.657C>T	c.(655-657)taC>taT	p.Y219Y	AC096558.1_ENST00000550516.1_RNA|AC096558.1_ENST00000442794.1_RNA|RP11-570L15.2_ENST00000546678.1_RNA|AC096558.1_ENST00000549032.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	219					positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)			endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		TAAGTCACTACGACAGTGATA	0.348													C|||	461	0.0920527	0.0325	0.0879	5008	,	,		18129	0.003		0.2058	False		,,,				2504	0.1503				p.Y219Y		Atlas-SNP	.											.	ARHGAP15	99	.	0			c.C657T						PASS	.	C		265,4141	147.6+/-182.1	9,247,1947	76.0	74.0	75.0		657	-3.3	0.4	2	dbSNP_123	75	1956,6644	343.2+/-324.8	242,1472,2586	no	coding-synonymous	ARHGAP15	NM_018460.3		251,1719,4533	TT,TC,CC		22.7442,6.0145,17.0767		219/476	144194565	2221,10785	2203	4300	6503	SO:0001819	synonymous_variant	55843	exon8			TCACTACGACAGT	AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.657C>T	2.37:g.144194565C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	227	102	0.449339	NM_018460	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Silent	SNP	ENST00000295095.6	37	CCDS2184.1																																																																																			C|0.853;T|0.147	0.147	strong		0.348	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460	
DCLK3	85443	hgsc.bcm.edu	37	3	36779992	36779992	+	Silent	SNP	G	G	A	rs55888784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:36779992G>A	ENST00000416516.2	-	2	649	c.159C>T	c.(157-159)cgC>cgT	p.R53R		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	53						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						TCTCCCCACAGCGGTGGTCTC	0.617													G|||	44	0.00878594	0.0008	0.013	5008	,	,		16590	0.001		0.0298	False		,,,				2504	0.0031				p.R53R		Atlas-SNP	.											DCLK3,NS,carcinoma,-2,1	DCLK3	95	1	0			c.C159T						PASS	.	G		12,3870		0,12,1929	75.0	78.0	77.0		159	1.1	0.1	3	dbSNP_129	77	220,8064		4,212,3926	no	coding-synonymous	DCLK3	NM_033403.1		4,224,5855	AA,AG,GG		2.6557,0.3091,1.907		53/649	36779992	232,11934	1941	4142	6083	SO:0001819	synonymous_variant	85443	exon2			CCCACAGCGGTGG	AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.159C>T	3.37:g.36779992G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_033403		Silent	SNP	ENST00000416516.2	37	CCDS43064.1																																																																																			G|0.982;A|0.018	0.018	strong		0.617	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355	
LPL	4023	hgsc.bcm.edu	37	8	19809435	19809435	+	Silent	SNP	G	G	A	rs1121923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:19809435G>A	ENST00000311322.8	+	3	875	c.405G>A	c.(403-405)gtG>gtA	p.V135V		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	135					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)	p.V135V(1)		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)	GACAGGATGTGGCCCGGTTTA	0.522													G|||	246	0.0491214	0.1392	0.0274	5008	,	,		16747	0.0		0.0398	False		,,,				2504	0.0031				p.V135V		Atlas-SNP	.											.	LPL	78	.	1	Substitution - coding silent(1)	lung(1)	c.G405A						PASS	.	G		502,3904	233.6+/-246.7	25,452,1726	88.0	81.0	84.0		405	-1.7	1.0	8	dbSNP_86	84	352,8248	119.2+/-178.6	12,328,3960	no	coding-synonymous	LPL	NM_000237.2		37,780,5686	AA,AG,GG		4.093,11.3936,6.5662		135/476	19809435	854,12152	2203	4300	6503	SO:0001819	synonymous_variant	4023	exon3			GGATGTGGCCCGG		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.405G>A	8.37:g.19809435G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Silent	SNP	ENST00000311322.8	37	CCDS6012.1																																																																																			G|0.937;A|0.063	0.063	strong		0.522	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3		
MROH2B	133558	hgsc.bcm.edu	37	5	41008780	41008780	+	Missense_Mutation	SNP	A	A	G	rs2271704	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:41008780A>G	ENST00000399564.4	-	33	3986	c.3536T>C	c.(3535-3537)cTc>cCc	p.L1179P	MROH2B_ENST00000506092.2_Missense_Mutation_p.L734P	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1179			L -> P (in dbSNP:rs2271704). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.5}.														GGGACAAGTGAGCATCTTCTG	0.552													G|||	3914	0.78155	0.8669	0.8343	5008	,	,		18299	0.5913		0.8141	False		,,,				2504	0.7914				p.L1179P		Atlas-SNP	.											.	.	.	.	0			c.T3536C						PASS	.	G	PRO/LEU	3635,491		1598,439,26	79.0	81.0	80.0		3536	4.2	0.7	5	dbSNP_100	80	6876,1534		2811,1254,140	yes	missense	HEATR7B2	NM_173489.4	98	4409,1693,166	GG,GA,AA		18.2402,11.9001,16.1535	benign	1179/1586	41008780	10511,2025	2063	4205	6268	SO:0001583	missense	133558	exon33			CAAGTGAGCATCT		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.3536T>C	5.37:g.41008780A>G	ENSP00000382476:p.Leu1179Pro	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	1702	0.7793040293040293	427	0.8678861788617886	310	0.856353591160221	348	0.6083916083916084	617	0.8139841688654353	G	0.164	-1.078163	0.01903	0.880999	0.817598	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.01406	4.93;5.18	5.97	4.18	0.49190	Armadillo-type fold (1);	0.483862	0.19509	N	0.112547	T	0.00012	0.0000	N	0.01874	-0.695	0.32236	P	0.573264	B	0.02656	0.0	B	0.01281	0.0	T	0.18178	-1.0345	9	0.02654	T	1	.	7.49	0.27456	0.2555:0.0:0.7445:0.0	rs2271704;rs17857416;rs58763466;rs2271704	1179	Q7Z745	HTRB2_HUMAN	P	734;884;1179	ENSP00000441504:L734P;ENSP00000382476:L1179P	ENSP00000296803:L884P	L	-	2	0	HEATR7B2	41044537	0.995000	0.38212	0.655000	0.29622	0.482000	0.33219	1.511000	0.35801	0.875000	0.35847	-0.215000	0.12644	CTC	A|0.219;G|0.781	0.781	strong		0.552	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
FAM135B	51059	hgsc.bcm.edu	37	8	139165273	139165273	+	Missense_Mutation	SNP	G	G	A	rs71505459|rs13280444	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:139165273G>A	ENST00000395297.1	-	13	1615	c.1445C>T	c.(1444-1446)cCa>cTa	p.P482L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	482										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)			ATTCTCACCTGGCTCTGGACA	0.388										HNSCC(54;0.14)			G|||	1804	0.360224	0.1399	0.415	5008	,	,		18502	0.5298		0.3757	False		,,,				2504	0.4284				p.P482L		Atlas-SNP	.											.	FAM135B	423	.	0			c.C1445T						PASS	.	G	LEU/PRO	683,3153		63,557,1298	117.0	111.0	113.0		1445	0.8	0.0	8	dbSNP_121	113	2831,5447		499,1833,1807	yes	missense	FAM135B	NM_015912.3	98	562,2390,3105	AA,AG,GG		34.1991,17.805,29.0078	benign	482/1407	139165273	3514,8600	1918	4139	6057	SO:0001583	missense	51059	exon13			TCACCTGGCTCTG	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.1445C>T	8.37:g.139165273G>A	ENSP00000378710:p.Pro482Leu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	191	107	0.560209	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	701	0.320970695970696	87	0.17682926829268292	108	0.2983425414364641	269	0.47027972027972026	237	0.31266490765171506	G	4.611	0.113469	0.08831	0.17805	0.341991	ENSG00000147724	ENST00000395297	T	0.14022	2.54	5.75	0.762	0.18454	.	1.828030	0.02172	N	0.059783	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.003;0.002;0.0	T	0.47535	-0.9110	9	0.08599	T	0.76	0.0139	3.4649	0.07547	0.2837:0.1058:0.5027:0.1079	rs13280444	482;482;482	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	L	482	ENSP00000378710:P482L	ENSP00000276737:P482L	P	-	2	0	FAM135B	139234455	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.461000	0.21940	0.073000	0.16731	-0.940000	0.02684	CCA	G|0.670;A|0.330	0.330	strong		0.388	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
PXK	54899	hgsc.bcm.edu	37	3	58376938	58376938	+	Silent	SNP	G	G	A	rs55962533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58376938G>A	ENST00000356151.2	+	6	640	c.531G>A	c.(529-531)gtG>gtA	p.V177V	PXK_ENST00000302779.5_Silent_p.V160V|PXK_ENST00000383716.3_Silent_p.V144V|PXK_ENST00000536660.1_Silent_p.V40V|PXK_ENST00000484288.1_Silent_p.V177V|PXK_ENST00000479241.1_Silent_p.V160V|PXK_ENST00000383715.4_Silent_p.V160V|PXK_ENST00000463280.1_Silent_p.V144V	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		AACGGCTAGTGTTAAGCTGGG	0.373													G|||	16	0.00319489	0.0	0.0029	5008	,	,		17947	0.0		0.0129	False		,,,				2504	0.001				p.V177V		Atlas-SNP	.											.	PXK	89	.	0			c.G531A						PASS	.	G		19,4387	26.2+/-53.5	0,19,2184	90.0	95.0	93.0		531	1.8	1.0	3	dbSNP_129	93	110,8490	59.5+/-121.1	1,108,4191	no	coding-synonymous	PXK	NM_017771.3		1,127,6375	AA,AG,GG		1.2791,0.4312,0.9918		177/579	58376938	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	54899	exon6			GCTAGTGTTAAGC	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.531G>A	3.37:g.58376938G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_017771		Silent	SNP	ENST00000356151.2	37	CCDS2889.1																																																																																			G|0.991;A|0.009	0.009	strong		0.373	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771	
SH3BP2	6452	hgsc.bcm.edu	37	4	2822467	2822467	+	Silent	SNP	G	G	T	rs231402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2822467G>T	ENST00000356331.5	+	2	384	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SH3BP2_ENST00000511747.1_Silent_p.L41L|SH3BP2_ENST00000435136.2_Silent_p.L41L|SH3BP2_ENST00000503393.2_Silent_p.L98L|SH3BP2_ENST00000389838.2_Silent_p.L41L|SH3BP2_ENST00000442312.2_Silent_p.L69L|SH3BP2_ENST00000452765.2_Silent_p.L41L	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	41	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GTACCCAGCTGCAGCTGCTGA	0.612									Cherubism				G|||	1863	0.372005	0.1097	0.487	5008	,	,		21198	0.4603		0.4324	False		,,,				2504	0.4918				p.L98L		Atlas-SNP	.											.	SH3BP2	43	.	0			c.G294T						PASS	.	G	,,,	714,3692	297.0+/-284.5	64,586,1553	46.0	46.0	46.0		123,207,294,123	4.3	1.0	4	dbSNP_79	46	3834,4764	537.9+/-383.3	879,2076,1344	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	943,2662,2897	TT,TG,GG		44.5918,16.2052,34.9739	,,,	41/562,69/590,98/619,41/562	2822467	4548,8456	2203	4299	6502	SO:0001819	synonymous_variant	6452	exon2	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CCAGCTGCAGCTG	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	10825	protein-coding gene	gene with protein product		602104	"""Cherubism"""			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.123G>T	4.37:g.2822467G>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			G|0.647;T|0.353	0.353	strong		0.612	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
RUNDC3A	10900	hgsc.bcm.edu	37	17	42392622	42392622	+	Silent	SNP	T	T	C	rs708386	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42392622T>C	ENST00000426726.3	+	7	1003	c.729T>C	c.(727-729)gaT>gaC	p.D243D	RUNDC3A_ENST00000590941.1_Silent_p.D238D|RUNDC3A_ENST00000225441.7_Silent_p.D243D|AC003102.3_ENST00000588097.1_RNA	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	58	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	
CALCR	799	hgsc.bcm.edu	37	7	93116299	93116299	+	Missense_Mutation	SNP	A	A	G	rs2301680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:93116299A>G	ENST00000359558.2	-	4	348	c.49T>C	c.(49-51)Tca>Cca	p.S17P	CALCR_ENST00000421592.1_5'UTR|CALCR_ENST00000360249.4_5'UTR|CALCR_ENST00000394441.1_5'UTR|MIR489_ENST00000384923.1_RNA|CALCR_ENST00000426151.1_5'UTR	NM_001164737.1	NP_001158209.1	P30988	CALCR_HUMAN	calcitonin receptor	17					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CTCATTTTTGATTTTTGAAGA	0.299													G|||	2883	0.575679	0.643	0.3934	5008	,	,		17003	0.7103		0.4791	False		,,,				2504	0.5746				p.S17P		Atlas-SNP	.											CALCR_ENST00000359558,NS,malignant_melanoma,+1,3	CALCR	200	3	0			c.T49C						PASS	.	G	PRO/SER,,	2677,1727	507.3+/-366.6	834,1009,359	81.0	87.0	85.0		49,,	0.1	0.0	7	dbSNP_100	85	4341,4257	570.2+/-389.3	1119,2103,1077	yes	missense,utr-5,utr-5	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	74,,	1953,3112,1436	GG,GA,AA		49.5115,39.2144,46.0237	,,	17/509,,	93116299	7018,5984	2202	4299	6501	SO:0001583	missense	799	exon4			TTTTTGATTTTTG	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000359558.2:c.49T>C	7.37:g.93116299A>G	ENSP00000352561:p.Ser17Pro	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000359558.2	37	CCDS55125.1	1206	0.5521978021978022	304	0.6178861788617886	144	0.39779005524861877	401	0.701048951048951	357	0.470976253298153	G	0.013	-1.627601	0.00813	0.607856	0.504885	ENSG00000004948	ENST00000359558	T	0.48836	0.8	3.92	0.0933	0.14476	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.46954	P	7.399999999999629E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.43766	-0.9371	8	0.02654	T	1	.	4.1206	0.10104	0.4019:0.1716:0.4266:0.0	rs2301680;rs3181599;rs17788498;rs58492476;rs2301680	17	F5H605	.	P	17	ENSP00000352561:S17P	ENSP00000352561:S17P	S	-	1	0	CALCR	92954235	0.005000	0.15991	0.010000	0.14722	0.112000	0.19704	-0.320000	0.08028	-0.202000	0.10268	-1.758000	0.00672	TCA	A|0.450;G|0.550	0.550	strong		0.299	CALCR-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001742	
ZKSCAN7	55888	hgsc.bcm.edu	37	3	44611896	44611896	+	Missense_Mutation	SNP	A	A	G	rs9835485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:44611896A>G	ENST00000273320.3	+	6	1723	c.1294A>G	c.(1294-1296)Acc>Gcc	p.T432A	RP11-944L7.5_ENST00000419137.1_Intron|RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000431636.1_Intron|ZKSCAN7_ENST00000426540.1_Missense_Mutation_p.T432A|ZKSCAN7_ENST00000341840.3_Intron	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	432			T -> A (in dbSNP:rs9835485).		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)										TCATCTCAGAACCCACACAGG	0.483													.|||	1102	0.220048	0.441	0.1758	5008	,	,		16561	0.001		0.335	False		,,,				2504	0.0603				p.T432A		Atlas-SNP	.											ZNF167,colon,carcinoma,0,1	.	.	1	0			c.A1294G						scavenged	.	A	ALA/THR,	1794,2610		359,1076,767	38.0	40.0	39.0		1294,	3.0	0.8	3	dbSNP_119	39	2768,5830		435,1898,1966	no	missense,intron	ZNF167	NM_018651.2,NM_025169.1	58,	794,2974,2733	GG,GA,AA		32.1935,40.7357,35.0869	benign,	432/755,	44611896	4562,8440	2202	4299	6501	SO:0001583	missense	55888	exon6			CTCAGAACCCACA	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12955	protein-coding gene	gene with protein product			"""zinc finger protein 64"", ""zinc finger protein 448"", ""zinc finger protein 167"""	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.1294A>G	3.37:g.44611896A>G	ENSP00000273320:p.Thr432Ala	Somatic	48	1	0.0208333		WXS	Illumina HiSeq	Phase_I	49	35	0.714286	NM_018651	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Missense_Mutation	SNP	ENST00000273320.3	37	CCDS2715.1	520	0.23809523809523808	212	0.43089430894308944	70	0.19337016574585636	1	0.0017482517482517483	237	0.31266490765171506	.	10.56	1.383923	0.25031	0.407357	0.321935	ENSG00000196345	ENST00000426540;ENST00000273320;ENST00000447279	T;T;T	0.11930	2.73;2.73;5.49	4.24	3.04	0.35103	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.241759	0.21426	N	0.074738	T	0.00012	0.0000	L	0.38692	1.165	0.43199	P	0.004956999999999989	B;B	0.22746	0.074;0.015	B;B	0.23018	0.043;0.03	T	0.46020	-0.9221	9	0.66056	D	0.02	-0.1894	7.2275	0.26024	0.8222:0.0:0.1778:0.0	rs9835485;rs58906783	302;432	A7MAY2;Q9P0L1	.;ZN167_HUMAN	A	432;432;281	ENSP00000395524:T432A;ENSP00000273320:T432A;ENSP00000405034:T281A	ENSP00000273320:T432A	T	+	1	0	ZNF167	44586900	0.107000	0.21998	0.772000	0.31596	0.933000	0.57130	1.749000	0.38319	1.782000	0.52362	0.528000	0.53228	ACC	A|0.700;G|0.300	0.300	strong		0.483	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651	
NEB	4703	hgsc.bcm.edu	37	2	152500449	152500449	+	Missense_Mutation	SNP	C	C	G	rs13013209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:152500449C>G	ENST00000172853.10	-	57	7986	c.7839G>C	c.(7837-7839)aaG>aaC	p.K2613N	NEB_ENST00000604864.1_Missense_Mutation_p.K2613N|NEB_ENST00000427231.2_Missense_Mutation_p.K2613N|NEB_ENST00000603639.1_Missense_Mutation_p.K2613N|NEB_ENST00000397345.3_Missense_Mutation_p.K2613N|NEB_ENST00000409198.1_Missense_Mutation_p.K2613N			P20929	NEBU_HUMAN	nebulin	2613			K -> N (in dbSNP:rs13013209).	K -> Y (in Ref. 1; CAA58788). {ECO:0000305}.	muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTGGCACTTCTTGGCCAACA	0.562													C|||	1469	0.293331	0.031	0.4438	5008	,	,		19755	0.2609		0.4662	False		,,,				2504	0.3967				p.K2613N		Atlas-SNP	.											.	NEB	1697	.	0			c.G7839C						PASS	.	C	ASN/LYS,ASN/LYS,ASN/LYS	407,3733		27,353,1690	360.0	346.0	351.0		7839,7839,7839	5.8	1.0	2	dbSNP_121	351	3979,4421		941,2097,1162	no	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	94,94,94	968,2450,2852	GG,GC,CC		47.369,9.8309,34.9761	probably-damaging,probably-damaging,probably-damaging	2613/8526,2613/8526,2613/6670	152500449	4386,8154	2070	4200	6270	SO:0001583	missense	4703	exon57			GCACTTCTTGGCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.7839G>C	2.37:g.152500449C>G	ENSP00000172853:p.Lys2613Asn	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	357	355	0.994398	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		656	0.30036630036630035	16	0.032520325203252036	140	0.3867403314917127	154	0.2692307692307692	346	0.45646437994722955	C	22.7	4.323892	0.81580	0.098309	0.47369	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.88775	2.98	0.09310	P	1.0	D	0.76494	0.999	D	0.87578	0.998	T	0.35847	-0.9772	9	0.66056	D	0.02	.	19.9941	0.97377	0.0:1.0:0.0:0.0	rs13013209;rs52797571	2613	P20929	NEBU_HUMAN	N	2613	ENSP00000386259:K2613N;ENSP00000380505:K2613N;ENSP00000416578:K2613N;ENSP00000172853:K2613N	ENSP00000172853:K2613N	K	-	3	2	NEB	152208695	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.897000	0.63231	2.729000	0.93468	0.557000	0.71058	AAG	C|0.678;G|0.322	0.322	strong		0.562	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
DMP1	1758	hgsc.bcm.edu	37	4	88584160	88584160	+	Silent	SNP	G	G	A	rs2615497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000507894.1_RNA|RP11-742B18.1_ENST00000506480.1_RNA|RP11-742B18.1_ENST00000506814.1_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	111	0	0		WXS	Illumina HiSeq	Phase_I	114	68	0.596491	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		
TECPR2	9895	hgsc.bcm.edu	37	14	102901023	102901023	+	Silent	SNP	G	G	A	rs45605932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:102901023G>A	ENST00000359520.7	+	9	2095	c.1869G>A	c.(1867-1869)ggG>ggA	p.G623G	TECPR2_ENST00000558678.1_Silent_p.G623G	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	623					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						GCTCTCCTGGGGCGCATGATG	0.562													G|||	517	0.103235	0.2753	0.0519	5008	,	,		21086	0.001		0.0775	False		,,,				2504	0.0389				p.G623G		Atlas-SNP	.											.	TECPR2	114	.	0			c.G1869A						PASS	.	G	,	1086,3320	391.9+/-328.3	123,840,1240	72.0	51.0	58.0		1869,1869	2.8	0.0	14	dbSNP_127	58	696,7904	172.3+/-223.0	28,640,3632	no	coding-synonymous,coding-synonymous	TECPR2	NM_001172631.1,NM_014844.3	,	151,1480,4872	AA,AG,GG		8.093,24.6482,13.7014	,	623/1268,623/1412	102901023	1782,11224	2203	4300	6503	SO:0001819	synonymous_variant	9895	exon9			TCCTGGGGCGCAT	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.1869G>A	14.37:g.102901023G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Silent	SNP	ENST00000359520.7	37	CCDS32162.1																																																																																			G|0.880;A|0.120	0.120	strong		0.562	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
TPP2	7174	hgsc.bcm.edu	37	13	103275386	103275386	+	Silent	SNP	T	T	C	rs2230854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103275386T>C	ENST00000376065.4	+	6	816	c.780T>C	c.(778-780)agT>agC	p.S260S	TPP2_ENST00000376052.3_Silent_p.S260S	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	260	Peptidase S8.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)			breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTGTGACCAGTGGAGGTATCC	0.403													C|||	2372	0.473642	0.618	0.3804	5008	,	,		18693	0.4474		0.4742	False		,,,				2504	0.3712				p.S260S		Atlas-SNP	.											.	TPP2	124	.	0			c.T780C						PASS	.	C		2655,1751	522.7+/-370.9	786,1083,334	139.0	145.0	143.0		780	-1.7	1.0	13	dbSNP_98	143	4154,4446	588.2+/-392.3	969,2216,1115	no	coding-synonymous	TPP2	NM_003291.2		1755,3299,1449	CC,CT,TT		48.3023,39.7413,47.6472		260/1250	103275386	6809,6197	2203	4300	6503	SO:0001819	synonymous_variant	7174	exon6			GACCAGTGGAGGT	M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.780T>C	13.37:g.103275386T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_003291	Q5VZU8	Silent	SNP	ENST00000376065.4	37	CCDS9502.1																																																																																			A|0.097;C|0.415	0.415	strong		0.403	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2		
THEMIS2	9473	hgsc.bcm.edu	37	1	28209305	28209305	+	Silent	SNP	A	A	G	rs3766398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:28209305A>G	ENST00000373921.3	+	4	1474	c.1470A>G	c.(1468-1470)ctA>ctG	p.L490L	THEMIS2_ENST00000328928.7_Silent_p.L361L|THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	490	CABIT 2.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TGGTGAGCCTAGACTCTGAGC	0.617													G|||	2366	0.472444	0.1445	0.5086	5008	,	,		17331	0.5099		0.6322	False		,,,				2504	0.6871				p.L490L		Atlas-SNP	.											.	.	.	.	0			c.A1470G						PASS	.	G	,,	1052,3112		124,804,1154	115.0	111.0	112.0		,1470,	1.9	0.9	1	dbSNP_107	112	5478,2944		1796,1886,529	no	intron,coding-synonymous,intron	C1orf38	NM_001039477.1,NM_001105556.1,NM_004848.2	,,	1920,2690,1683	GG,GA,AA		34.9561,25.2642,48.117	,,	,490/644,	28209305	6530,6056	2082	4211	6293	SO:0001819	synonymous_variant	9473	exon4			GAGCCTAGACTCT	AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"""induced by contact to basement membrane 1"""		"""chromosome 1 open reading frame 38"""	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.1470A>G	1.37:g.28209305A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_001105556	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Silent	SNP	ENST00000373921.3	37	CCDS41290.1	1036	0.47435897435897434	85	0.17276422764227642	192	0.5303867403314917	283	0.49475524475524474	476	0.6279683377308707	G	5.708	0.315067	0.10789	0.252642	0.650439	ENSG00000130775	ENST00000456990	.	.	.	4.98	1.89	0.25635	.	.	.	.	.	.	.	.	.	.	.	0.34916	P	0.252003	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.0731	4.182	0.10380	0.141:0.3327:0.4131:0.1132	rs3766398;rs61688279;rs3766398	.	.	.	W	238	.	.	X	+	2	0	C1orf38	28081892	0.001000	0.12720	0.940000	0.37924	0.785000	0.44390	-0.261000	0.08694	0.216000	0.20781	-0.227000	0.12334	TAG	A|0.498;G|0.502	0.502	strong		0.617	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848	
UEVLD	55293	hgsc.bcm.edu	37	11	18568542	18568542	+	Silent	SNP	A	A	T	rs34242612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:18568542A>T	ENST00000396197.3	-	8	799	c.771T>A	c.(769-771)ggT>ggA	p.G257G	UEVLD_ENST00000379387.4_Silent_p.G235G|UEVLD_ENST00000535484.1_Silent_p.G219G|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000541984.1_Intron|UEVLD_ENST00000320750.6_Silent_p.G235G|UEVLD_ENST00000543987.1_Silent_p.G257G	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						ACTGAGAACTACCCAAAGAGT	0.458													A|||	288	0.057508	0.1785	0.0231	5008	,	,		18611	0.0149		0.0169	False		,,,				2504	0.0041				p.G257G		Atlas-SNP	.											.	UEVLD	58	.	0			c.T771A						PASS	.	A	,	705,3693	294.1+/-283.0	54,597,1548	129.0	117.0	121.0		771,771	0.0	1.0	11	dbSNP_126	121	163,8423	77.8+/-140.4	0,163,4130	yes	coding-synonymous,coding-synonymous	UEVLD	NM_001040697.1,NM_018314.3	,	54,760,5678	TT,TA,AA		1.8984,16.03,6.6852	,	257/472,257/380	18568542	868,12116	2199	4293	6492	SO:0001819	synonymous_variant	55293	exon8			AGAACTACCCAAA	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.771T>A	11.37:g.18568542A>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001040697		Silent	SNP	ENST00000396197.3	37	CCDS41624.1																																																																																			A|0.941;T|0.059	0.059	strong		0.458	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314	
NBPF14	25832	hgsc.bcm.edu	37	1	148009437	148009437	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:148009437C>T	ENST00000369219.1	-	16	1886	c.1870G>A	c.(1870-1872)Ggt>Agt	p.G624S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	624	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					TCAAGACAACCTGAAGGAGTT	0.483																																					p.G624S		Atlas-SNP	.											.	NBPF14	107	.	0			c.G1870A						PASS	.						128.0	260.0	221.0					1																	148009437		1703	4065	5768	SO:0001583	missense	25832	exon16			GACAACCTGAAGG	AK092351		1q21.1	2013-01-17			ENSG00000122497			"""neuroblastoma breakpoint family"""	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1870G>A	1.37:g.148009437C>T	ENSP00000358221:p.Gly624Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	262	17	0.0648855	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	c	1.168	-0.641686	0.03531	.	.	ENSG00000122497	ENST00000369219;ENST00000434489	T	0.05382	3.45	.	.	.	DUF1220 (2);	.	.	.	.	T	0.01124	0.0037	L	0.33792	1.035	0.09310	N	1	.	.	.	.	.	.	T	0.46247	-0.9205	4	0.06625	T	0.88	.	.	.	.	.	624	Q5TI25	NBPFE_HUMAN	S	624;214	ENSP00000358221:G624S	ENSP00000358221:G624S	G	-	1	0	NBPF14	146476061	0.982000	0.34865	.	.	.	.	-1.256000	0.02869	.	.	.	.	GGT	.	.	none		0.483	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421054	29421054	+	Missense_Mutation	SNP	C	C	T	rs2306933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29421054C>T	ENST00000261275.4	-	8	940	c.941G>A	c.(940-942)gGt>gAt	p.G314D		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	314	Pro-rich.		G -> D (in dbSNP:rs2306933).			integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						CACCTGCTGACCTATACTTGT	0.552													T|||	677	0.135184	0.1263	0.1138	5008	,	,		16994	0.2093		0.0706	False		,,,				2504	0.1524				p.G314D		Atlas-SNP	.											.	FAM189A1	20	.	0			c.G941A						PASS	.	T	ASP/GLY	160,1224		10,140,542	53.0	54.0	54.0		941	2.7	0.0	15	dbSNP_100	54	230,2952		11,208,1372	yes	missense	FAM189A1	NM_015307.1	94	21,348,1914	TT,TC,CC		7.2282,11.5607,8.5414	benign	314/540	29421054	390,4176	692	1591	2283	SO:0001583	missense	23359	exon8			TGCTGACCTATAC		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.941G>A	15.37:g.29421054C>T	ENSP00000261275:p.Gly314Asp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	51	17	0.333333	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	260	0.11904761904761904	56	0.11382113821138211	35	0.09668508287292818	121	0.21153846153846154	48	0.0633245382585752	T	0.011	-1.701260	0.00725	0.115607	0.072282	ENSG00000104059	ENST00000261275	T	0.02737	4.18	5.07	2.73	0.32206	.	0.239743	0.41001	N	0.000968	T	0.00012	0.0000	N	0.00159	-1.955	0.53005	P	3.2999999999949736E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42582	-0.9443	9	0.02654	T	1	-16.8578	7.6984	0.28608	0.0:0.2482:0.0:0.7518	rs2306933;rs59289923;rs2306933	314	O60320	F1891_HUMAN	D	314	ENSP00000261275:G314D	ENSP00000261275:G314D	G	-	2	0	FAM189A1	27208346	0.944000	0.32072	0.004000	0.12327	0.014000	0.08584	1.419000	0.34793	0.048000	0.15891	-0.254000	0.11334	GGT	C|0.877;T|0.123	0.123	strong		0.552	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
KANSL1	284058	hgsc.bcm.edu	37	17	44248769	44248769	+	Silent	SNP	T	T	C	rs566672630	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44248769T>C	ENST00000262419.6	-	2	1211	c.741A>G	c.(739-741)agA>agG	p.R247R	KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.R247R|KANSL1_ENST00000572904.1_Silent_p.R247R|KANSL1_ENST00000575318.1_Silent_p.R247R|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000432791.1_Silent_p.R247R	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	247					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CAGGTGATAATCTACTGCTTC	0.438													C|||	437	0.0872604	0.0182	0.1571	5008	,	,		24930	0.001		0.2406	False		,,,				2504	0.0624				p.R247R		Atlas-SNP	.											.	.	.	.	0			c.A741G						PASS	.	C	,,	226,4180	805.7+/-415.8	6,214,1983	92.0	118.0	109.0		741,741,741	5.0	1.0	17	dbSNP_92	109	1936,6664	725.7+/-406.6	220,1496,2584	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	226,1710,4567	CC,CT,TT		22.5116,5.1294,16.6231	,,	247/1105,247/1106,247/1106	44248769	2162,10844	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			TGATAATCTACTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.741A>G	17.37:g.44248769T>C		Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	333	333	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			T|0.841;C|0.159	0.159	strong		0.438	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
KANK3	256949	hgsc.bcm.edu	37	19	8389405	8389405	+	Silent	SNP	G	G	A	rs12981073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	116	0	0		WXS	Illumina HiSeq	Phase_I	146	80	0.547945	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	
MYPOP	339344	hgsc.bcm.edu	37	19	46394322	46394322	+	Silent	SNP	G	G	A	rs114387602	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46394322G>A	ENST00000322217.5	-	3	845	c.759C>T	c.(757-759)ctC>ctT	p.L253L		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	253	Pro-rich.					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 negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						ctgaggccgagagcgtgggtg	0.721													G|||	445	0.0888578	0.1475	0.085	5008	,	,		3566	0.001		0.1024	False		,,,				2504	0.089				p.L253L		Atlas-SNP	.											.	MYPOP	23	.	0			c.C759T						PASS	.	G		426,3480		26,374,1553	3.0	3.0	3.0		759	1.3	0.1	19	dbSNP_132	3	744,6954		37,670,3142	no	coding-synonymous	MYPOP	NM_001012643.2		63,1044,4695	AA,AG,GG		9.6648,10.9063,10.0827		253/400	46394322	1170,10434	1953	3849	5802	SO:0001819	synonymous_variant	339344	exon3			GGCCGAGAGCGTG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"""p42 Myb-related transcription factor, partner of profilin"""					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.759C>T	19.37:g.46394322G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_001012643		Silent	SNP	ENST00000322217.5	37	CCDS33055.1																																																																																			G|0.923;A|0.077	0.077	strong		0.721	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643	
ARSB	411	hgsc.bcm.edu	37	5	78135201	78135201	+	Silent	SNP	C	C	T	rs25413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:78135201C>T	ENST00000264914.4	-	6	1727	c.1191G>A	c.(1189-1191)ccG>ccA	p.P397P	ARSB_ENST00000396151.3_Silent_p.P397P|ARSB_ENST00000565165.1_Silent_p.P397P	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	397					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		CCACGAAGTTCGGGTCAATAT	0.433													C|||	1298	0.259185	0.5628	0.1513	5008	,	,		19055	0.0486		0.1799	False		,,,				2504	0.2239				p.P397P	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											ARSB,NS,carcinoma,-1,1	ARSB	47	1	0			c.G1191A						PASS	.	C	,	2188,2218	586.5+/-386.5	546,1096,561	139.0	137.0	138.0		1191,1191	-8.9	0.0	5	dbSNP_71	138	1607,6993	298.3+/-303.9	153,1301,2846	no	coding-synonymous,coding-synonymous	ARSB	NM_000046.3,NM_198709.2	,	699,2397,3407	TT,TC,CC		18.686,49.6596,29.1788	,	397/534,397/414	78135201	3795,9211	2203	4300	6503	SO:0001819	synonymous_variant	411	exon7			GAAGTTCGGGTCA	M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"""Arylsulfatase family"""	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.1191G>A	5.37:g.78135201C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	152	66	0.434211	NM_198709	B2RC20|Q8N322|Q9UDI9	Silent	SNP	ENST00000264914.4	37	CCDS4043.1																																																																																			C|0.727;T|0.273	0.273	strong		0.433	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
LAIR1	3903	hgsc.bcm.edu	37	19	54867572	54867572	+	Silent	SNP	C	C	T	rs7257187	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54867572C>T	ENST00000391742.2	-	9	860	c.708G>A	c.(706-708)acG>acA	p.T236T	LAIR1_ENST00000391743.3_Silent_p.T218T|LAIR1_ENST00000463489.1_5'Flank|LAIR1_ENST00000313038.6_Silent_p.T229T|LAIR1_ENST00000474878.1_Silent_p.T218T|LAIR1_ENST00000348231.4_Silent_p.T219T|LAIR1_ENST00000434277.2_Silent_p.T235T|CTD-2587H19.1_ENST00000596234.1_lincRNA			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	236					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)		CCGAGGTGTCCGTCTCTCTGT	0.468													C|||	1172	0.234026	0.1006	0.2695	5008	,	,		17217	0.2808		0.3708	False		,,,				2504	0.2004				p.T236T		Atlas-SNP	.											.	LAIR1	44	.	0			c.G708A						PASS	.	C	,	579,3827		47,485,1671	131.0	127.0	128.0		708,657	0.4	0.0	19	dbSNP_116	128	3027,5573		543,1941,1816	no	coding-synonymous,coding-synonymous	LAIR1	NM_002287.3,NM_021706.2	,	590,2426,3487	TT,TC,CC		35.1977,13.1412,27.7257	,	236/288,219/271	54867572	3606,9400	2203	4300	6503	SO:0001819	synonymous_variant	3903	exon9			GGTGTCCGTCTCT	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.708G>A	19.37:g.54867572C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_002287		Silent	SNP	ENST00000391742.2	37	CCDS12891.1																																																																																			C|0.734;T|0.266	0.266	strong		0.468	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1		
TMEM86B	255043	hgsc.bcm.edu	37	19	55739689	55739689	+	Silent	SNP	G	G	A	rs10413828	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55739689G>A	ENST00000327042.4	-	2	690	c.168C>T	c.(166-168)ccC>ccT	p.P56P	AC010327.2_ENST00000598855.1_3'UTR	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	56					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		GGCAGAGGACGGGCAGGCACT	0.652													G|||	2167	0.432708	0.3222	0.4582	5008	,	,		17485	0.5992		0.4175	False		,,,				2504	0.408				p.P56P		Atlas-SNP	.											.	TMEM86B	12	.	0			c.C168T						PASS	.	G		1323,3079		187,949,1065	56.0	49.0	51.0		168	-10.0	0.0	19	dbSNP_119	51	3319,5279		632,2055,1612	no	coding-synonymous	TMEM86B	NM_173804.4		819,3004,2677	AA,AG,GG		38.602,30.0545,35.7077		56/227	55739689	4642,8358	2201	4299	6500	SO:0001819	synonymous_variant	255043	exon2			GAGGACGGGCAGG	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.168C>T	19.37:g.55739689G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_173804		Silent	SNP	ENST00000327042.4	37	CCDS12920.1																																																																																			G|0.620;A|0.380	0.380	strong		0.652	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804	
FSCB	84075	hgsc.bcm.edu	37	14	44975147	44975147	+	Silent	SNP	A	A	G	rs11623175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:44975147A>G	ENST00000340446.4	-	1	1335	c.1044T>C	c.(1042-1044)gcT>gcC	p.A348A	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	348	Pro-rich.					sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		GCAGAATTTCAGCCAGAAGCT	0.507													A|||	346	0.0690895	0.0817	0.0504	5008	,	,		18067	0.001		0.1044	False		,,,				2504	0.0992				p.A348A		Atlas-SNP	.											.	FSCB	173	.	0			c.T1044C						PASS	.	A		379,4027	175.1+/-204.6	22,335,1846	72.0	84.0	80.0		1044	-2.2	0.0	14	dbSNP_120	80	900,7700	197.5+/-242.1	53,794,3453	no	coding-synonymous	FSCB	NM_032135.3		75,1129,5299	GG,GA,AA		10.4651,8.6019,9.8339		348/826	44975147	1279,11727	2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			AATTTCAGCCAGA	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.1044T>C	14.37:g.44975147A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	37	CCDS9679.1																																																																																			A|0.914;G|0.086	0.086	strong		0.507	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
IL17C	27189	hgsc.bcm.edu	37	16	88706330	88706330	+	Silent	SNP	C	C	T	rs11076688	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88706330C>T	ENST00000244241.4	+	3	493	c.444C>T	c.(442-444)tcC>tcT	p.S148S		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C	148					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|neutrophil differentiation (GO:0030223)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			large_intestine(1)|lung(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0477)		CGCTCAACTCCGTGCGGCTGC	0.692													C|||	307	0.0613019	0.0484	0.1066	5008	,	,		15275	0.004		0.0865	False		,,,				2504	0.0798				p.S148S		Atlas-SNP	.											.	IL17C	6	.	0			c.C444T						PASS	.	C		209,3935		8,193,1871	24.0	30.0	28.0		444	-8.9	0.2	16	dbSNP_120	28	768,7612		44,680,3466	no	coding-synonymous	IL17C	NM_013278.3		52,873,5337	TT,TC,CC		9.1647,5.0434,7.801		148/198	88706330	977,11547	2072	4190	6262	SO:0001819	synonymous_variant	27189	exon3			CAACTCCGTGCGG	AF152099	CCDS42217.1	16q24	2011-07-14			ENSG00000124391	ENSG00000124391		"""Interleukins and interleukin receptors"""	5983	protein-coding gene	gene with protein product		604628				10639155	Standard	NM_013278		Approved	IL-17C, CX2, IL-21, MGC126884, MGC138401	uc002fla.3	Q9P0M4		ENST00000244241.4:c.444C>T	16.37:g.88706330C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	28	17	0.607143	NM_013278	Q3MIG8|Q9HC75	Silent	SNP	ENST00000244241.4	37	CCDS42217.1																																																																																			C|0.932;T|0.068	0.068	strong		0.692	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	NM_013278	
COL6A3	1293	hgsc.bcm.edu	37	2	238249630	238249630	+	Silent	SNP	C	C	T	rs4433949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238249630C>T	ENST00000295550.4	-	38	8381	c.7929G>A	c.(7927-7929)gcG>gcA	p.A2643A	COL6A3_ENST00000347401.3_Silent_p.A2442A|COL6A3_ENST00000353578.4_Silent_p.A2437A|COL6A3_ENST00000346358.4_Silent_p.A2443A|COL6A3_ENST00000472056.1_Silent_p.A2036A|COL6A3_ENST00000409809.1_Silent_p.A2437A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2643	Nonhelical region.|VWFA 12. {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)		TGACCAGGTACGCTATGTACT	0.567													C|||	1715	0.342452	0.2133	0.3329	5008	,	,		21379	0.4802		0.4284	False		,,,				2504	0.2935				p.A2643A		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7929A						PASS	.	C	,,	1138,3268	405.1+/-333.4	155,828,1220	158.0	146.0	150.0		7929,6108,7311	-5.4	0.0	2	dbSNP_111	150	3646,4954	524.7+/-380.6	769,2108,1423	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	924,2936,2643	TT,TC,CC		42.3953,25.8284,36.783	,,	2643/3178,2036/2571,2437/2972	238249630	4784,8222	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			CAGGTACGCTATG	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.7929G>A	2.37:g.238249630C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	232	109	0.469828	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.625;T|0.375	0.375	strong		0.567	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
AKR7A3	22977	hgsc.bcm.edu	37	1	19615062	19615062	+	Missense_Mutation	SNP	C	C	G	rs199504000		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19615062C>G	ENST00000361640.4	-	1	682	c.142G>C	c.(142-144)Gtg>Ctg	p.V48L		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	48					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)		TCGCTGTACACGAAGGCCGTG	0.711																																					p.V48L		Atlas-SNP	.											AKR7A3,NS,carcinoma,0,1	AKR7A3	30	1	0			c.G142C						PASS	.	G	LEU/VAL	0,4402		0,0,2201	24.0	25.0	25.0		142	-6.3	0.0	1		25	3,8595	2.2+/-6.3	0,3,4296	no	missense	AKR7A3	NM_012067.2	32	0,3,6497	GG,GC,CC		0.0349,0.0,0.0231	benign	48/332	19615062	3,12997	2201	4299	6500	SO:0001583	missense	22977	exon1			TGTACACGAAGGC	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.142G>C	1.37:g.19615062C>G	ENSP00000355377:p.Val48Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	185	39	0.210811	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Missense_Mutation	SNP	ENST00000361640.4	37	CCDS193.1	.	.	.	.	.	.	.	.	.	.	c	2.715	-0.267819	0.05754	0.0	3.49E-4	ENSG00000162482	ENST00000361640	T	0.24538	1.85	3.17	-6.35	0.01975	NADP-dependent oxidoreductase domain (3);	0.086043	0.85682	D	0.000000	T	0.10035	0.0246	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09164	-1.0687	9	0.27082	T	0.32	.	3.0874	0.06283	0.1202:0.1309:0.1206:0.6283	.	48	O95154	ARK73_HUMAN	L	48	ENSP00000355377:V48L	ENSP00000355377:V48L	V	-	1	0	AKR7A3	19487649	0.026000	0.19158	0.001000	0.08648	0.030000	0.12068	-1.205000	0.03014	-2.004000	0.00961	-0.700000	0.03674	GTG	C|0.998;G|0.002	0.002	weak		0.711	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
CD93	22918	hgsc.bcm.edu	37	20	23065342	23065342	+	Silent	SNP	A	A	G	rs3746732	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:23065342A>G	ENST00000246006.4	-	1	1635	c.1488T>C	c.(1486-1488)cgT>cgC	p.R496R		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	496				R -> Q (in Ref. 1; AA sequence). {ECO:0000305}.	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)					CTGTTGCAGCACGGGGCACGG	0.627													G|||	3905	0.779752	0.7731	0.8156	5008	,	,		14036	0.8036		0.7435	False		,,,				2504	0.7761				p.R496R		Atlas-SNP	.											CD93,NS,carcinoma,-2,1	CD93	84	1	0			c.T1488C						PASS	.	G		3303,1097		1235,833,132	36.0	42.0	40.0		1488	1.7	0.0	20	dbSNP_107	40	6492,2106		2454,1584,261	no	coding-synonymous	CD93	NM_012072.3		3689,2417,393	GG,GA,AA		24.4941,24.9318,24.6423		496/653	23065342	9795,3203	2200	4299	6499	SO:0001819	synonymous_variant	22918	exon1			TGCAGCACGGGGC	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.1488T>C	20.37:g.23065342A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_012072	O00274	Silent	SNP	ENST00000246006.4	37	CCDS13149.1																																																																																			A|0.233;G|0.766	0.766	strong		0.627	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994488	45994488	+	Missense_Mutation	SNP	G	G	T	rs396912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45994488G>T	ENST00000400374.3	+	1	883	c.853G>T	c.(853-855)Ggc>Tgc	p.G285C	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	285	36 X 5 AA repeats of C-C-X(3).		G -> C (in dbSNP:rs396912).			keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAAGCCTGTCGGCTCTGTGCC	0.642													.|||	931	0.185903	0.3812	0.0937	5008	,	,		22814	0.2054		0.0368	False		,,,				2504	0.1207				p.G285C		Atlas-SNP	.											KRTAP10-4,colon,carcinoma,-1,1	KRTAP10-4	44	1	0			c.G853T						PASS	.	T	,CYS/GLY	1527,2879	669.8+/-402.2	259,1009,935	115.0	120.0	118.0		,853	1.9	0.0	21	dbSNP_80	118	266,8334	803.6+/-407.3	4,258,4038	no	intron,missense	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,159	263,1267,4973	TT,TG,GG		3.093,34.6573,13.7859	,benign	,285/402	45994488	1793,11213	2203	4300	6503	SO:0001583	missense	386672	exon1			CCTGTCGGCTCTG	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.853G>T	21.37:g.45994488G>T	ENSP00000383225:p.Gly285Cys	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	230	117	0.508696	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	
YLPM1	56252	hgsc.bcm.edu	37	14	75230837	75230837	+	Silent	SNP	A	A	G	rs12885527	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:75230837A>G	ENST00000552421.1	+	1	769	c.645A>G	c.(643-645)caA>caG	p.Q215Q	YLPM1_ENST00000325680.7_Silent_p.Q215Q|YLPM1_ENST00000238571.3_Silent_p.Q215Q			P49750	YLPM1_HUMAN	YLP motif containing 1	215					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CTTCCTCGCAATCCTATTTGA	0.587													A|||	125	0.0249601	0.0045	0.0403	5008	,	,		15842	0.0		0.0815	False		,,,				2504	0.0092				p.Q215Q		Atlas-SNP	.											.	YLPM1	298	.	0			c.A645G						PASS	.	A		79,3947		1,77,1935	99.0	105.0	103.0		645	-2.3	1.0	14	dbSNP_121	103	720,7622		37,646,3488	no	coding-synonymous	YLPM1	NM_019589.2		38,723,5423	GG,GA,AA		8.631,1.9622,6.4602		215/2147	75230837	799,11569	2013	4171	6184	SO:0001819	synonymous_variant	56252	exon1			CTCGCAATCCTAT	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.645A>G	14.37:g.75230837A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_019589	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000552421.1	37																																																																																				A|0.958;G|0.042	0.042	strong		0.587	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589	
VWDE	221806	hgsc.bcm.edu	37	7	12428803	12428803	+	Missense_Mutation	SNP	G	G	A	rs848016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:12428803G>A	ENST00000275358.3	-	3	613	c.425C>T	c.(424-426)tCt>tTt	p.S142F		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	142						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TAAGTATACAGAAAAGTTCCC	0.418													A|||	3441	0.687101	0.9319	0.6758	5008	,	,		18556	0.6171		0.5537	False		,,,				2504	0.5736				p.S142F		Atlas-SNP	.											.	VWDE	123	.	0			c.C425T						PASS	.	A	PHE/SER	1212,172		528,156,8	102.0	103.0	103.0		425	3.5	0.4	7	dbSNP_86	103	1718,1464		464,790,337	yes	missense	VWDE	NM_001135924.1	155	992,946,345	AA,AG,GG		46.0088,12.4277,35.83	benign	142/1591	12428803	2930,1636	692	1591	2283	SO:0001583	missense	221806	exon3			TATACAGAAAAGT		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.425C>T	7.37:g.12428803G>A	ENSP00000275358:p.Ser142Phe	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	1481	0.6781135531135531	457	0.9288617886178862	245	0.6767955801104972	353	0.6171328671328671	426	0.5620052770448549	A	0.005	-2.132119	0.00338	0.875723	0.539912	ENSG00000146530	ENST00000275358;ENST00000541006	T	0.64085	-0.08	4.68	3.5	0.40072	.	0.501867	0.22766	N	0.055898	T	0.00012	0.0000	N	0.00079	-2.23	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38908	-0.9639	9	0.02654	T	1	.	6.8821	0.24179	0.7927:0.0:0.0737:0.1336	rs848016;rs971938;rs1638226;rs17540002;rs52819655;rs57187888;rs848016	142	Q8N2E2	VWDE_HUMAN	F	142	ENSP00000275358:S142F	ENSP00000275358:S142F	S	-	2	0	VWDE	12395328	0.940000	0.31905	0.358000	0.25811	0.300000	0.27592	1.711000	0.37930	0.369000	0.24510	-0.360000	0.07572	TCT	G|0.324;A|0.676	0.676	strong		0.418	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
BRCA2	675	hgsc.bcm.edu	37	13	32911888	32911888	+	Silent	SNP	A	A	G	rs1801406	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:32911888A>G	ENST00000380152.3	+	11	3629	c.3396A>G	c.(3394-3396)aaA>aaG	p.K1132K	BRCA2_ENST00000544455.1_Silent_p.K1132K			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1132					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)		AGTTTAGAAAACCAAGCTACA	0.358			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1336	0.266773	0.2095	0.2378	5008	,	,		19807	0.3681		0.2753	False		,,,				2504	0.2515				p.K1132K	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.A3396G						PASS	.	A		996,3410	351.1+/-311.1	107,782,1314	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3396	-3.1	0.7	13	dbSNP_89	61	2643,5955	415.9+/-351.9	400,1843,2056	no	coding-synonymous	BRCA2	NM_000059.3		507,2625,3370	GG,GA,AA		30.7397,22.6055,27.9837		1132/3419	32911888	3639,9365	2203	4299	6502	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)	TAGAAAACCAAGC	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.3396A>G	13.37:g.32911888A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			A|0.722;G|0.278	0.278	strong		0.358	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
CIB2	10518	hgsc.bcm.edu	37	15	78401620	78401620	+	Silent	SNP	C	C	T	rs77370542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:78401620C>T	ENST00000258930.3	-	4	631	c.303G>A	c.(301-303)tcG>tcA	p.S101S	CIB2_ENST00000539011.1_Silent_p.S58S|CIB2_ENST00000557846.1_Silent_p.S52S|CIB2_ENST00000560618.1_Silent_p.S58S	NM_006383.2	NP_006374.1	O75838	CIB2_HUMAN	calcium and integrin binding family member 2	101	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion homeostasis (GO:0055074)|photoreceptor cell maintenance (GO:0045494)	blood microparticle (GO:0072562)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|photoreceptor inner segment (GO:0001917)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	11						CTCGGGGAGCCGACTCGCAGA	0.552													C|||	59	0.0117812	0.0015	0.0187	5008	,	,		17572	0.0		0.0417	False		,,,				2504	0.002				p.S101S		Atlas-SNP	.											CIB2,NS,carcinoma,-1,1	CIB2	24	1	0			c.G303A						PASS	.	C		23,4369	29.9+/-59.1	0,23,2173	99.0	86.0	90.0		303	-6.4	0.2	15	dbSNP_132	90	308,8278	110.8+/-171.2	6,296,3991	no	coding-synonymous	CIB2	NM_006383.2		6,319,6164	TT,TC,CC		3.5872,0.5237,2.5505		101/188	78401620	331,12647	2196	4293	6489	SO:0001819	synonymous_variant	10518	exon4			GGGAGCCGACTCG	BC047381	CCDS10296.1, CCDS61722.1, CCDS61723.1	15q24	2013-01-10			ENSG00000136425	ENSG00000136425		"""EF-hand domain containing"""	24579	protein-coding gene	gene with protein product		605564	"""deafness, autosomal recessive 48"", ""Usher syndrome 1J (autosomal recessive)"""	DFNB48, USH1J		9931475, 23023331	Standard	NM_006383		Approved	KIP2	uc002bdb.2	O75838	OTTHUMG00000143731	ENST00000258930.3:c.303G>A	15.37:g.78401620C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_006383	B4DDF0|H0YM71|Q05BT6	Silent	SNP	ENST00000258930.3	37	CCDS10296.1																																																																																			C|0.978;T|0.022	0.022	strong		0.552	CIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289798.1	NM_006383	
MCC	4163	hgsc.bcm.edu	37	5	112823998	112823998	+	Silent	SNP	C	C	T	rs348943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:112823998C>T	ENST00000408903.3	-	1	529	c.114G>A	c.(112-114)gaG>gaA	p.E38E		NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					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)		GCCGCATCCTCTCCTCCTCGC	0.716													C|||	2519	0.502995	0.3298	0.4524	5008	,	,		10097	0.6726		0.494	False		,,,				2504	0.6074				p.E38E		Atlas-SNP	.											.	MCC	234	.	0			c.G114A						PASS	.	C		1293,2851		203,887,982	39.0	45.0	43.0		114	3.5	1.0	5	dbSNP_79	43	4052,4332		972,2108,1112	yes	coding-synonymous	MCC	NM_001085377.1		1175,2995,2094	TT,TC,CC		48.3302,31.2017,42.6644		38/1020	112823998	5345,7183	2072	4192	6264	SO:0001819	synonymous_variant	4163	exon1			CATCCTCTCCTCC		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	ENST00000408903.3:c.114G>A	5.37:g.112823998C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000408903.3	37	CCDS43351.1																																																																																			C|0.505;T|0.495	0.495	strong		0.716	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	NM_001085377	
TCHH	7062	hgsc.bcm.edu	37	1	152084216	152084216	+	Missense_Mutation	SNP	C	C	G	rs201131683	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152084216C>G	ENST00000368804.1	-	2	1476	c.1477G>C	c.(1477-1479)Gag>Cag	p.E493Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	493	9 X 28 AA approximate 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)			CTCTCCTCCTCCTCGAGCTTC	0.672																																					p.E493Q		Atlas-SNP	.											TCHH,NS,lymphoid_neoplasm,0,1	TCHH	275	1	0			c.G1477C						PASS	.		GLN/GLU	0,4218		0,0,2109	64.0	71.0	69.0		1477	-1.7	0.0	1		69	17,8419		0,17,4201	no	missense	TCHH	NM_007113.2	29	0,17,6310	GG,GC,CC		0.2015,0.0,0.1343	benign	493/1944	152084216	17,12637	2109	4218	6327	SO:0001583	missense	7062	exon3			CCTCCTCCTCGAG	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.1477G>C	1.37:g.152084216C>G	ENSP00000357794:p.Glu493Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	174	20	0.114943	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	7.158	0.585028	0.13749	0.0	0.002015	ENSG00000159450	ENST00000368804	T	0.04551	3.6	3.42	-1.67	0.08238	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43147	-0.9409	9	0.12103	T	0.63	.	11.5902	0.50941	0.1022:0.7375:0.1603:0.0	.	493	Q07283	TRHY_HUMAN	Q	493	ENSP00000357794:E493Q	ENSP00000357794:E493Q	E	-	1	0	TCHH	150350840	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.797000	0.04570	-0.858000	0.04110	-0.574000	0.04147	GAG	C|0.986;G|0.013	0.013	strong		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
TNC	3371	hgsc.bcm.edu	37	9	117797597	117797597	+	Silent	SNP	T	T	C	rs12347433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:117797597T>C	ENST00000350763.4	-	22	6084	c.5673A>G	c.(5671-5673)agA>agG	p.R1891R	TNC_ENST00000535648.1_Silent_p.R1436R|TNC_ENST00000537320.1_Silent_p.R1254R|TNC_ENST00000542877.1_Silent_p.R1528R|TNC_ENST00000341037.4_Silent_p.R1709R|TNC_ENST00000340094.3_Silent_p.R1527R|TNC_ENST00000423613.2_Silent_p.R1618R|TNC_ENST00000345230.3_Silent_p.R1254R|TNC_ENST00000346706.3_Silent_p.R1345R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1891	Fibronectin type-III 15. {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)	p.R1891R(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						CAGTCAAGTCTCTTGGAGAAT	0.512													T|||	773	0.154353	0.0666	0.1484	5008	,	,		19335	0.129		0.2793	False		,,,				2504	0.1748				p.R1891R		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	1	1	Substitution - coding silent(1)	stomach(1)	c.A5673G						PASS	.	T		404,4002	199.4+/-223.0	21,362,1820	72.0	72.0	72.0		5673	6.0	1.0	9	dbSNP_120	72	2313,6287	389.1+/-342.8	320,1673,2307	no	coding-synonymous	TNC	NM_002160.3		341,2035,4127	CC,CT,TT		26.8953,9.1693,20.8904		1891/2202	117797597	2717,10289	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon22			CAAGTCTCTTGGA		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.5673A>G	9.37:g.117797597T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	383	0.17536630036630035	40	0.08130081300813008	46	0.1270718232044199	85	0.1486013986013986	212	0.2796833773087071	T	10.49	1.365894	0.24684	0.091693	0.268953	ENSG00000041982	ENST00000544972	T	0.57436	0.4	5.97	5.97	0.96955	.	0.206129	0.51477	D	0.000084	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22034	-1.0228	6	0.48119	T	0.1	.	10.4647	0.44600	0.0:0.1145:0.0:0.8855	rs12347433;rs17240303;rs12347433	.	.	.	G	454	ENSP00000445380:R454G	ENSP00000445380:R454G	R	-	1	2	TNC	116837418	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.042000	0.49815	2.274000	0.75844	0.533000	0.62120	AGA	T|0.813;C|0.187	0.187	strong		0.512	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
AK2	204	hgsc.bcm.edu	37	1	33478841	33478841	+	Missense_Mutation	SNP	C	C	T	rs201817938		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:33478841C>T	ENST00000373449.2	-	6	702	c.661G>A	c.(661-663)Gca>Aca	p.A221T	AK2_ENST00000491241.1_5'UTR|AK2_ENST00000354858.6_Missense_Mutation_p.A221T|RP1-117O3.2_ENST00000427524.1_RNA|AK2_ENST00000548033.1_Missense_Mutation_p.A179T|AK2_ENST00000480134.1_3'UTR|AK2_ENST00000467905.1_Missense_Mutation_p.A221T	NM_001199199.1|NM_013411.4	NP_001186128.1|NP_037543.1			adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				AGGATGCTTGCGAACACGACA	0.507																																					p.A221T		Atlas-SNP	.											.	AK2	27	.	0			c.G661A						PASS	.						161.0	147.0	152.0					1																	33478841		2203	4300	6503	SO:0001583	missense	204	exon6			TGCTTGCGAACAC	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"""Adenylate kinases"""	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000373449.2:c.661G>A	1.37:g.33478841C>T	ENSP00000362548:p.Ala221Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	147	54	0.367347	NM_013411		Missense_Mutation	SNP	ENST00000373449.2	37	CCDS373.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685133	0.47991	.	.	ENSG00000004455	ENST00000373449;ENST00000548033;ENST00000467905;ENST00000354858	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.17	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.66257	0.2771	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.22480	0.006;0.07;0.004;0.003	B;B;B;B	0.19148	0.003;0.024;0.001;0.002	T	0.64433	-0.6409	10	0.51188	T	0.08	-11.7289	14.769	0.69662	0.0:0.9289:0.0:0.0711	.	213;179;221;221	P54819-5;F8VY04;P54819;P54819-2	.;.;KAD2_HUMAN;.	T	221;179;221;221	ENSP00000362548:A221T;ENSP00000449003:A179T;ENSP00000447082:A221T;ENSP00000346921:A221T	ENSP00000346921:A221T	A	-	1	0	AK2	33251428	1.000000	0.71417	0.957000	0.39632	0.542000	0.35054	6.063000	0.71162	1.499000	0.48617	0.563000	0.77884	GCA	.	.	weak		0.507	AK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011884.1	NM_001625	
C4BPA	722	hgsc.bcm.edu	37	1	207304900	207304900	+	Missense_Mutation	SNP	T	T	C	rs4844573	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:207304900T>C	ENST00000367070.3	+	8	1093	c.899T>C	c.(898-900)aTt>aCt	p.I300T		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	300	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> T (in dbSNP:rs4844573).		complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						GATAGTTGTATTAATTTACCA	0.433													C|||	2453	0.489816	0.8374	0.4625	5008	,	,		19901	0.2679		0.3767	False		,,,				2504	0.3845				p.I300T		Atlas-SNP	.											.	C4BPA	70	.	0			c.T899C						PASS	.	C	THR/ILE	3316,1090	394.2+/-329.2	1254,808,141	99.0	74.0	83.0		899	-8.9	0.0	1	dbSNP_111	83	2980,5620	665.4+/-402.3	534,1912,1854	no	missense	C4BPA	NM_000715.3	89	1788,2720,1995	CC,CT,TT		34.6512,24.739,48.4084	benign	300/598	207304900	6296,6710	2203	4300	6503	SO:0001583	missense	722	exon8			GTTGTATTAATTT	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.899T>C	1.37:g.207304900T>C	ENSP00000356037:p.Ile300Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_000715	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	1022	0.46794871794871795	401	0.8150406504065041	156	0.430939226519337	187	0.3269230769230769	278	0.36675461741424803	C	0.513	-0.865722	0.02590	0.75261	0.346512	ENSG00000123838	ENST00000367070	T	0.62498	0.02	4.51	-8.9	0.00782	Complement control module (2);Sushi/SCR/CCP (3);	1.917680	0.02627	N	0.103873	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.39702	-0.9601	9	0.08599	T	0.76	.	16.2134	0.82186	0.0:0.6809:0.0:0.3191	rs4844573;rs17258788;rs56540637;rs58565781;rs4844573	300	P04003	C4BPA_HUMAN	T	300	ENSP00000356037:I300T	ENSP00000356037:I300T	I	+	2	0	C4BPA	205371523	0.000000	0.05858	0.000000	0.03702	0.394000	0.30568	-2.583000	0.00904	-2.717000	0.00390	-0.119000	0.15052	ATT	T|0.519;C|0.481	0.481	strong		0.433	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		
AAMDC	28971	hgsc.bcm.edu	37	11	77583266	77583266	+	Missense_Mutation	SNP	G	G	A	rs2186564	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:77583266G>A	ENST00000526415.1	+	5	447	c.274G>A	c.(274-276)Gtg>Atg	p.V92M	RP11-91P24.6_ENST00000530972.1_RNA|AAMDC_ENST00000527134.1_Intron|AAMDC_ENST00000393427.2_Missense_Mutation_p.V92M|AAMDC_ENST00000304716.8_Intron|AAMDC_ENST00000525409.1_Missense_Mutation_p.V60M|AAMDC_ENST00000525034.1_Missense_Mutation_p.V111M|RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000533193.1_Missense_Mutation_p.V138M|AAMDC_ENST00000532481.1_Intron			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	92	MTH138-like domain. {ECO:0000250}.		V -> M (in dbSNP:rs2186564).		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.V92M(1)									TGGCATTGATGTGCGGGTCCT	0.552													G|||	706	0.140974	0.1286	0.1888	5008	,	,		20307	0.1766		0.1004	False		,,,				2504	0.1288				p.V92M		Atlas-SNP	.											C11orf67,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.G274A						scavenged	.	G	MET/VAL	526,3874	239.9+/-250.9	28,470,1702	114.0	103.0	107.0		274	5.3	1.0	11	dbSNP_96	107	827,7757	191.1+/-237.4	37,753,3502	yes	missense	C11orf67	NM_024684.2	21	65,1223,5204	AA,AG,GG		9.6342,11.9545,10.4205	probably-damaging	92/123	77583266	1353,11631	2200	4292	6492	SO:0001583	missense	28971	exon4			ATTGATGTGCGGG	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.274G>A	11.37:g.77583266G>A	ENSP00000431808:p.Val92Met	Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	132	51	0.386364	NM_024684	Q96AQ4|Q9Y6B1	Missense_Mutation	SNP	ENST00000526415.1	37	CCDS8254.1	320	0.14652014652014653	76	0.15447154471544716	56	0.15469613259668508	112	0.1958041958041958	76	0.10026385224274406	G	22.1	4.244571	0.79912	0.119545	0.096342	ENSG00000087884	ENST00000526415;ENST00000393427;ENST00000525409;ENST00000533193;ENST00000525034	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.00552	0.0018	M	0.74881	2.28	0.20074	P	0.9999344981	D	0.71674	0.998	D	0.67725	0.953	T	0.03887	-1.0995	9	0.54805	T	0.06	-10.6555	14.3405	0.66622	0.0:0.1481:0.8519:0.0	rs2186564;rs52804138;rs57349472;rs2186564	92	Q9H7C9	CK067_HUMAN	M	92;92;60;138;111	ENSP00000431808:V92M;ENSP00000377078:V92M;ENSP00000433956:V60M;ENSP00000436086:V138M;ENSP00000432830:V111M	ENSP00000377078:V92M	V	+	1	0	C11orf67	77260914	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	6.493000	0.73658	2.746000	0.94184	0.655000	0.94253	GTG	G|0.876;N|0.000	.	strong		0.552	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684	
CDC42EP1	11135	hgsc.bcm.edu	37	22	37962583	37962583	+	Missense_Mutation	SNP	G	G	A	rs61739954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37962583G>A	ENST00000249014.4	+	2	647	c.227G>A	c.(226-228)cGc>cAc	p.R76H		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	76					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					AGCACCCATCGCTCACCCCGC	0.701													G|||	69	0.013778	0.0477	0.0043	5008	,	,		14619	0.0		0.003	False		,,,				2504	0.0				p.R76H		Atlas-SNP	.											CDC42EP1,colon,carcinoma,0,1	CDC42EP1	53	1	0			c.G227A						PASS	.	G	HIS/ARG	235,4171	133.3+/-169.7	4,227,1972	31.0	31.0	31.0		227	4.7	1.0	22	dbSNP_129	31	33,8565	21.6+/-65.8	0,33,4266	yes	missense	CDC42EP1	NM_152243.2	29	4,260,6238	AA,AG,GG		0.3838,5.3336,2.0609	probably-damaging	76/392	37962583	268,12736	2203	4299	6502	SO:0001583	missense	11135	exon2			CCCATCGCTCACC	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.227G>A	22.37:g.37962583G>A	ENSP00000249014:p.Arg76His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	37	CCDS13949.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	17.07	3.295024	0.60086	0.053336	0.003838	ENSG00000128283	ENST00000249014	T	0.32515	1.45	4.7	4.7	0.59300	.	0.376263	0.27331	N	0.019849	T	0.04092	0.0114	L	0.29908	0.895	0.31658	N	0.64598	D	0.58620	0.983	P	0.46208	0.507	T	0.03545	-1.1026	10	0.42905	T	0.14	-24.6436	8.6301	0.33915	0.0834:0.2361:0.6805:0.0	rs61739954	76	Q00587	BORG5_HUMAN	H	76	ENSP00000249014:R76H	ENSP00000249014:R76H	R	+	2	0	CDC42EP1	36292529	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.119000	0.31258	2.429000	0.82318	0.563000	0.77884	CGC	G|0.980;A|0.020	0.020	strong		0.701	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291308	1291308	+	Silent	SNP	A	A	G	rs201568970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1291308A>G	ENST00000338844.3	+	3	249	c.216A>G	c.(214-216)gcA>gcG	p.A72A	TPSAB1_ENST00000461509.2_Silent_p.A79A	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	72	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				TGCTGACCGCAGCGCACTGCG	0.706																																					p.A72A		Atlas-SNP	.											TPSAB1,NS,carcinoma,+2,1	TPSAB1	24	1	0			c.A216G						scavenged	.						43.0	43.0	43.0					16																	1291308		2198	4298	6496	SO:0001819	synonymous_variant	7177	exon3			GACCGCAGCGCAC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.216A>G	16.37:g.1291308A>G		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	240	58	0.241667	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Silent	SNP	ENST00000338844.3	37	CCDS10431.1																																																																																			G|1.000;|0.000	1.000	weak		0.706	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
PDLIM5	10611	hgsc.bcm.edu	37	4	95506827	95506827	+	Silent	SNP	G	G	A	rs11722955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:95506827G>A	ENST00000317968.4	+	6	958	c.822G>A	c.(820-822)agG>agA	p.R274R	PDLIM5_ENST00000538141.1_Silent_p.R151R|PDLIM5_ENST00000380176.3_3'UTR|PDLIM5_ENST00000542407.1_Silent_p.R152R|PDLIM5_ENST00000380180.3_Silent_p.R171R|PDLIM5_ENST00000437932.1_Silent_p.R165R|PDLIM5_ENST00000508216.1_Silent_p.R171R|PDLIM5_ENST00000318007.5_Silent_p.R151R|PDLIM5_ENST00000450793.1_Silent_p.R171R|PDLIM5_ENST00000514743.1_Silent_p.R171R	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	274					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)		GGCGTCCAAGGACTGGAACAA	0.448													G|||	430	0.0858626	0.1339	0.0403	5008	,	,		13491	0.0466		0.0676	False		,,,				2504	0.1125				p.R274R		Atlas-SNP	.											.	PDLIM5	76	.	0			c.G822A						PASS	.	G	,,,	527,3879	240.9+/-251.5	37,453,1713	113.0	97.0	102.0		495,513,453,822	2.6	0.9	4	dbSNP_120	102	489,8111	142.3+/-198.5	14,461,3825	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,	51,914,5538	AA,AG,GG		5.686,11.961,7.8118	,,,	165/488,171/235,151/215,274/597	95506827	1016,11990	2203	4300	6503	SO:0001819	synonymous_variant	10611	exon6			TCCAAGGACTGGA	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.822G>A	4.37:g.95506827G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Silent	SNP	ENST00000317968.4	37	CCDS3641.1	163	0.07463369963369963	69	0.1402439024390244	14	0.03867403314917127	26	0.045454545454545456	54	0.0712401055408971	G	9.459	1.092598	0.20471	0.11961	0.05686	ENSG00000163110	ENST00000513341	.	.	.	5.31	2.56	0.30785	.	.	.	.	.	T	0.00468	0.0015	.	.	.	0.09310	P	0.9999999999996523	.	.	.	.	.	.	T	0.09292	-1.0681	3	.	.	.	.	9.1901	0.37193	0.136:0.4684:0.3956:0.0	rs11722955;rs11722955	.	.	.	E	133	.	.	G	+	2	0	PDLIM5	95725850	0.996000	0.38824	0.926000	0.36857	0.859000	0.49053	0.326000	0.19646	0.280000	0.22209	-0.172000	0.13284	GGA	G|0.921;A|0.079	0.079	strong		0.448	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
SOWAHD	347454	hgsc.bcm.edu	37	X	118893413	118893413	+	Silent	SNP	T	T	C	rs2782225		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:118893413T>C	ENST00000343905.3	+	1	838	c.783T>C	c.(781-783)agT>agC	p.S261S		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	261																	ACAACAGCAGTGGCACCACTG	0.687													C|||	2433	0.644503	0.559	0.5072	3775	,	,		11187	0.374		0.495	False		,,,				2504	0.4775				p.S261S		Atlas-SNP	.											.	.	.	.	0			c.T783C						PASS	.	C		2802,848		940,530,392,82,154	8.0	11.0	10.0		783	2.1	0.2	X	dbSNP_100	10	4152,2337		967,1078,1140,321,617	no	coding-synonymous	ANKRD58	NM_001105576.2		1907,1608,1532,403,771	CC,CT,C,TT,T		36.0148,23.2329,31.4134		261/316	118893413	6954,3185	2098	4123	6221	SO:0001819	synonymous_variant	347454	exon1			CAGCAGTGGCACC		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.783T>C	X.37:g.118893413T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_001105576		Silent	SNP	ENST00000343905.3	37	CCDS43984.1																																																																																			T|0.366;C|0.634	0.634	strong		0.687	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576	
TRPM6	140803	hgsc.bcm.edu	37	9	77436641	77436641	+	Silent	SNP	G	G	A	rs7018994	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:77436641G>A	ENST00000360774.1	-	8	1191	c.954C>T	c.(952-954)ggC>ggT	p.G318G	TRPM6_ENST00000376871.3_Silent_p.G318G|TRPM6_ENST00000376864.4_Silent_p.G318G|TRPM6_ENST00000451710.3_Silent_p.G318G|TRPM6_ENST00000376872.3_Silent_p.G318G|TRPM6_ENST00000483186.1_5'UTR|TRPM6_ENST00000361255.3_Silent_p.G313G|TRPM6_ENST00000449912.2_Silent_p.G313G	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	318					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						CCCTACCTGTGCCCTCACACA	0.572													G|||	1797	0.358826	0.0673	0.4438	5008	,	,		17635	0.5536		0.3787	False		,,,				2504	0.4714				p.G318G		Atlas-SNP	.											.	TRPM6	377	.	0			c.C954T						PASS	.	G	,,	512,3894	234.6+/-247.4	26,460,1717	143.0	105.0	118.0		939,939,954	4.6	1.0	9	dbSNP_116	118	3043,5557	467.6+/-367.1	549,1945,1806	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	575,2405,3523	AA,AG,GG		35.3837,11.6205,27.3335	,,	313/2018,313/2018,318/2023	77436641	3555,9451	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon8			ACCTGTGCCCTCA	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.954C>T	9.37:g.77436641G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			G|0.701;A|0.299	0.299	strong		0.572	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
APOC4	346	hgsc.bcm.edu	37	19	45448465	45448465	+	Missense_Mutation	SNP	T	T	G	rs5167	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45448465T>G	ENST00000592954.1	+	3	327	c.287T>G	c.(286-288)cTc>cGc	p.L96R	APOC2_ENST00000590360.1_5'Flank|APOC4-APOC2_ENST00000589057.1_Intron|APOC2_ENST00000252490.4_5'Flank|APOC2_ENST00000592257.1_5'Flank|APOC4_ENST00000419266.2_Missense_Mutation_p.L96R|APOC2_ENST00000591597.1_5'Flank	NM_001646.2	NP_001637.1	P55056	APOC4_HUMAN	apolipoprotein C-IV	96			L -> R (in dbSNP:rs5167). {ECO:0000269|PubMed:10996355}.		lipid metabolic process (GO:0006629)|positive regulation of sequestering of triglyceride (GO:0010890)|triglyceride homeostasis (GO:0070328)	high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|lung(2)	4	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		CTGGGTCCGCTCACCAAGGCC	0.587													G|||	2200	0.439297	0.4569	0.4553	5008	,	,		16354	0.5724		0.3668	False		,,,				2504	0.3415				p.L96R		Atlas-SNP	.											.	APOC4	6	.	0			c.T287G	GRCh37	CM065970	APOC4	M	rs5167	PASS	.	G	ARG/LEU	2023,2383	612.3+/-391.9	476,1071,656	179.0	177.0	177.0		287	2.1	0.0	19	dbSNP_52	177	3080,5520	659.3+/-401.7	558,1964,1778	yes	missense	APOC4	NM_001646.2	102	1034,3035,2434	GG,GT,TT		35.814,45.9147,39.2357	benign	96/128	45448465	5103,7903	2203	4300	6503	SO:0001583	missense	346	exon3			GTCCGCTCACCAA	U32576	CCDS12649.1	19q13.2	2013-09-30			ENSG00000267467	ENSG00000267467		"""Apolipoproteins"""	611	protein-coding gene	gene with protein product		600745				8530039	Standard	NM_001646		Approved			P55056	OTTHUMG00000180845	ENST00000592954.1:c.287T>G	19.37:g.45448465T>G	ENSP00000468236:p.Leu96Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_001646	B3KWY6|Q53YY8	Missense_Mutation	SNP	ENST00000592954.1	37	CCDS12649.1	1033	0.47298534798534797	253	0.5142276422764228	170	0.4696132596685083	330	0.5769230769230769	280	0.36939313984168864	G	0.003	-2.515632	0.00151	0.459147	0.35814	ENSG00000224916	ENST00000419266;ENST00000436871	T;T	0.18174	2.23;2.23	4.26	2.07	0.26955	.	0.168114	0.28821	N	0.014031	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	0.41980	-0.9478	9	0.02654	T	1	-18.197	4.6363	0.12527	0.195:0.0:0.6327:0.1723	rs5167;rs17257587;rs17257887;rs52812385;rs56784720;rs5167	96	P55056	APOC4_HUMAN	R	96	ENSP00000406381:L96R;ENSP00000412935:L96R	ENSP00000406381:L96R	L	+	2	0	APOC4	50140305	0.042000	0.20092	0.006000	0.13384	0.060000	0.15804	1.155000	0.31700	0.176000	0.19873	-0.702000	0.03669	CTC	G|0.427;N|0.000	0.427	strong		0.587	APOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453255.1	NM_001646	
CNR2	1269	hgsc.bcm.edu	37	1	24201448	24201448	+	Silent	SNP	C	C	T	rs3003336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201448C>T	ENST00000374472.4	-	2	821	c.660G>A	c.(658-660)gtG>gtA	p.V220V	CNR2_ENST00000536471.1_Silent_p.V220V	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	220					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)	p.V220V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	ACAAGCTGGCCACATGCTGAT	0.572													T|||	3272	0.653355	0.7943	0.6383	5008	,	,		23489	0.502		0.5875	False		,,,				2504	0.6973				p.V220V		Atlas-SNP	.											CNR2,NS,carcinoma,0,1	CNR2	78	1	1	Substitution - coding silent(1)	stomach(1)	c.G660A						PASS	.	T		3313,1093	393.7+/-329.0	1263,787,153	64.0	59.0	61.0		660	2.2	1.0	1	dbSNP_101	61	4940,3660	523.3+/-380.3	1408,2124,768	no	coding-synonymous	CNR2	NM_001841.2		2671,2911,921	TT,TC,CC		42.5581,24.8071,36.5447		220/361	24201448	8253,4753	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			GCTGGCCACATGC	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.660G>A	1.37:g.24201448C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			C|0.364;T|0.636	0.636	strong		0.572	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163099	163099	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:163099C>T	ENST00000283426.6	+	11	1894	c.1844C>T	c.(1843-1845)gCc>gTc	p.A615V		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	615							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)		CCGCCCCTTGCCCAGAGCCCC	0.657																																					p.A615V		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C1844T						PASS	.						14.0	14.0	14.0					5																	163099		2168	4267	6435	SO:0001583	missense	153478	exon11			CCCTTGCCCAGAG	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.1844C>T	5.37:g.163099C>T	ENSP00000283426:p.Ala615Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	138	76	0.550725	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	C	7.808	0.715147	0.15306	.	.	ENSG00000153404	ENST00000283426	D	0.92099	-2.97	2.71	-5.43	0.02632	.	.	.	.	.	T	0.75874	0.3909	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.62671	-0.6805	9	0.27785	T	0.31	.	0.5644	0.00684	0.2612:0.3176:0.2217:0.1994	.	615	Q96PX9	PKH4B_HUMAN	V	615	ENSP00000283426:A615V	ENSP00000283426:A615V	A	+	2	0	PLEKHG4B	216099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.238000	0.01199	-1.825000	0.01207	-0.670000	0.03821	GCC	.	.	none		0.657	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
OR52E2	119678	hgsc.bcm.edu	37	11	5080337	5080337	+	Missense_Mutation	SNP	T	T	C	rs61746343	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5080337T>C	ENST00000321522.2	-	1	520	c.521A>G	c.(520-522)cAt>cGt	p.H174R		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		GGGAATTACATGATTCCCACA	0.398													T|||	1048	0.209265	0.2746	0.3559	5008	,	,		22989	0.0873		0.2237	False		,,,				2504	0.1278				p.H174R		Atlas-SNP	.											.	OR52E2	63	.	0			c.A521G						PASS	.	T	ARG/HIS	1160,3242	409.5+/-335.0	154,852,1195	86.0	80.0	82.0		521	-1.2	0.1	11	dbSNP_129	82	1773,6823	320.7+/-314.7	174,1425,2699	yes	missense	OR52E2	NM_001005164.2	29	328,2277,3894	CC,CT,TT		20.6259,26.3517,22.565	benign	174/326	5080337	2933,10065	2201	4298	6499	SO:0001583	missense	119678	exon1			ATTACATGATTCC	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.521A>G	11.37:g.5080337T>C	ENSP00000322088:p.His174Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	466	0.21336996336996336	136	0.2764227642276423	104	0.287292817679558	62	0.10839160839160839	164	0.21635883905013192	T	0.098	-1.156324	0.01686	0.263517	0.206259	ENSG00000176787	ENST00000321522	T	0.00063	8.78	3.76	-1.16	0.09678	GPCR, rhodopsin-like superfamily (1);	1.067990	0.07299	N	0.873832	T	0.00012	0.0000	L	0.33189	0.99	0.58432	P	1.0000000000287557E-6	B	0.09022	0.002	B	0.15484	0.013	T	0.00330	-1.1812	9	0.10111	T	0.7	.	8.6192	0.33851	0.0:0.3152:0.0:0.6848	rs61746343	174	Q8NGJ4	O52E2_HUMAN	R	174	ENSP00000322088:H174R	ENSP00000322088:H174R	H	-	2	0	OR52E2	5036913	0.000000	0.05858	0.149000	0.22428	0.832000	0.47134	-0.595000	0.05727	-0.211000	0.10124	-0.262000	0.10625	CAT	T|0.770;C|0.230	0.230	strong		0.398	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
KRT84	3890	hgsc.bcm.edu	37	12	52777578	52777578	+	Missense_Mutation	SNP	C	C	T	rs386763043|rs1613931	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	99	40	0.40404	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	
NLN	57486	hgsc.bcm.edu	37	5	65108215	65108215	+	Silent	SNP	A	A	G	rs2254485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	43	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	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		
DISP1	84976	hgsc.bcm.edu	37	1	223177574	223177574	+	Silent	SNP	A	A	G	rs2609355	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:223177574A>G	ENST00000284476.6	+	8	2999	c.2835A>G	c.(2833-2835)aaA>aaG	p.K945K		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	945					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		AGTTTTATAAAGAGGTGGACT	0.463													A|||	1209	0.241414	0.1581	0.3084	5008	,	,		21088	0.2232		0.2793	False		,,,				2504	0.2863				p.K945K		Atlas-SNP	.											.	DISP1	145	.	0			c.A2835G						PASS	.	A		823,3583	327.2+/-299.9	79,665,1459	76.0	70.0	72.0		2835	-6.3	0.0	1	dbSNP_100	72	2582,6018	418.9+/-352.9	390,1802,2108	no	coding-synonymous	DISP1	NM_032890.3		469,2467,3567	GG,GA,AA		30.0233,18.6791,26.1802		945/1525	223177574	3405,9601	2203	4300	6503	SO:0001819	synonymous_variant	84976	exon10			TTATAAAGAGGTG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.2835A>G	1.37:g.223177574A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	160	86	0.5375	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	37	CCDS1536.1																																																																																			A|0.752;G|0.248	0.248	strong		0.463	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
FCGBP	8857	hgsc.bcm.edu	37	19	40368330	40368330	+	Missense_Mutation	SNP	C	C	T	rs74540349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	241	0	0		WXS	Illumina HiSeq	Phase_I	169	74	0.43787	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	
LSS	4047	hgsc.bcm.edu	37	21	47614443	47614443	+	Silent	SNP	A	A	G	rs2254522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	58	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	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		
ANKRD11	29123	hgsc.bcm.edu	37	16	89350911	89350911	+	Missense_Mutation	SNP	G	G	C	rs145694621	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89350911G>C	ENST00000301030.4	-	9	2499	c.2039C>G	c.(2038-2040)aCt>aGt	p.T680S	ANKRD11_ENST00000378330.2_Missense_Mutation_p.T680S	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	680	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CTTGTTTTCAGTGGAAAGATC	0.353													G|||	22	0.00439297	0.0	0.0014	5008	,	,		20305	0.0		0.0139	False		,,,				2504	0.0072				p.T680S		Atlas-SNP	.											.	ANKRD11	195	.	0			c.C2039G						PASS	.	G	SER/THR	14,4382	21.2+/-45.6	0,14,2184	168.0	162.0	164.0		2039	-3.3	0.0	16	dbSNP_134	164	166,8434	78.4+/-141.0	2,162,4136	yes	missense	ANKRD11	NM_013275.4	58	2,176,6320	CC,CG,GG		1.9302,0.3185,1.385	benign	680/2664	89350911	180,12816	2198	4300	6498	SO:0001583	missense	29123	exon9			TTTTCAGTGGAAA	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.2039C>G	16.37:g.89350911G>C	ENSP00000301030:p.Thr680Ser	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	G	0.015	-1.565862	0.00903	0.003185	0.019302	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000330736	T;T	0.35789	1.29;1.29	5.81	-3.35	0.04928	.	1.352090	0.04637	N	0.404613	T	0.09291	0.0229	N	0.25647	0.755	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.08055	0.003;0.001	T	0.12218	-1.0556	10	0.09338	T	0.73	.	1.9402	0.03345	0.2983:0.3974:0.171:0.1333	.	299;680	Q7Z5E5;Q6UB99	.;ANR11_HUMAN	S	680;680;299	ENSP00000301030:T680S;ENSP00000367581:T680S	ENSP00000301030:T680S	T	-	2	0	ANKRD11	87878412	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.687000	0.25407	-0.366000	0.08064	-0.273000	0.10243	ACT	G|0.988;C|0.012	0.012	strong		0.353	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
ZNF385D	79750	hgsc.bcm.edu	37	3	21462754	21462754	+	Silent	SNP	A	A	G	rs451242	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:21462754A>G	ENST00000281523.2	-	8	1658	c.1140T>C	c.(1138-1140)ccT>ccC	p.P380P		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	380						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						GAATGGGTCCAGGAGCTGGCC	0.502													A|||	4012	0.801118	0.7368	0.8098	5008	,	,		11101	0.8988		0.7584	False		,,,				2504	0.8252				p.P380P		Atlas-SNP	.											.	ZNF385D	93	.	0			c.T1140C						PASS	.	A		3339,1067	722.3+/-409.3	1281,777,145	48.0	46.0	46.0		1140	-11.6	0.0	3	dbSNP_80	46	6497,2103	714.6+/-406.0	2461,1575,264	no	coding-synonymous	ZNF385D	NM_024697.2		3742,2352,409	GG,GA,AA		24.4535,24.217,24.3734		380/396	21462754	9836,3170	2203	4300	6503	SO:0001819	synonymous_variant	79750	exon8			GGGTCCAGGAGCT	BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"""zinc finger protein 659"""	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.1140T>C	3.37:g.21462754A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_024697		Silent	SNP	ENST00000281523.2	37	CCDS2636.1																																																																																			G|0.765;A|0.235	0.765	strong		0.502	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
PRUNE2	158471	hgsc.bcm.edu	37	9	79320847	79320847	+	Missense_Mutation	SNP	G	G	C	rs2077181	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79320847G>C	ENST00000376718.3	-	8	6466	c.6343C>G	c.(6343-6345)Caa>Gaa	p.Q2115E	PRUNE2_ENST00000428286.1_Missense_Mutation_p.Q1756E	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2115					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						TCAGTCTCTTGCTTTGCTTCA	0.478													G|||	1190	0.23762	0.2103	0.1599	5008	,	,		21742	0.4653		0.1551	False		,,,				2504	0.18				p.Q2115E		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C6343G						PASS	.	G	GLU/GLN	628,2508		49,530,989	175.0	161.0	166.0		6343	5.1	0.9	9	dbSNP_96	166	882,6282		50,782,2750	yes	missense	PRUNE2	NM_015225.2	29	99,1312,3739	CC,CG,GG		12.3116,20.0255,14.6602	benign	2115/3089	79320847	1510,8790	1568	3582	5150	SO:0001583	missense	158471	exon8			TCTCTTGCTTTGC	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.6343C>G	9.37:g.79320847G>C	ENSP00000365908:p.Gln2115Glu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	560|560	0.2564102564102564|0.2564102564102564	109|109	0.22154471544715448|0.22154471544715448	51|51	0.1408839779005525|0.1408839779005525	285|285	0.4982517482517482|0.4982517482517482	115|115	0.1517150395778364|0.1517150395778364	G|G	3.328|3.328	-0.137372|-0.137372	0.06711|0.06711	0.200255|0.200255	0.123116|0.123116	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.45668	.|0.89;0.89	6.03|6.03	5.09|5.09	0.68999|0.68999	.|.	.|0.395169	.|0.22156	.|N	.|0.063843	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	P|P	0.99999999999985|0.99999999999985	.|B	.|0.21381	.|0.055	.|B	.|0.15052	.|0.012	T|T	0.43360|0.43360	-0.9396|-0.9396	4|9	.|0.37606	.|T	.|0.19	-3.3243|-3.3243	12.2965|12.2965	0.54849|0.54849	0.0691:0.1312:0.7997:0.0|0.0691:0.1312:0.7997:0.0	rs2077181;rs17786845;rs57039615;rs2077181|rs2077181;rs17786845;rs57039615;rs2077181	.|2115	.|Q8WUY3	.|PRUN2_HUMAN	G|E	1436|2115;1756;2114	.|ENSP00000365908:Q2115E;ENSP00000397425:Q1756E	.|ENSP00000365908:Q2115E	A|Q	-|-	2|1	0|0	PRUNE2|PRUNE2	78510667|78510667	1.000000|1.000000	0.71417|0.71417	0.885000|0.885000	0.34714|0.34714	0.023000|0.023000	0.10783|0.10783	0.801000|0.801000	0.27055|0.27055	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	GCA|CAA	G|0.744;C|0.256	0.256	strong		0.478	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
CLDN16	10686	hgsc.bcm.edu	37	3	190106074	190106074	+	Missense_Mutation	SNP	G	G	C	rs386669518|rs3214506	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:190106074G>C	ENST00000264734.2	+	1	414	c.166G>C	c.(166-168)Gct>Cct	p.A56P	CLDN16_ENST00000456423.1_Missense_Mutation_p.A56P|CLDN16_ENST00000468220.1_Intron	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	209	0	0		WXS	Illumina HiSeq	Phase_I	218	218	1	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	
CDHR1	92211	hgsc.bcm.edu	37	10	85978958	85978958	+	IGR	SNP	G	G	A	rs529093147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85978958G>A	ENST00000372117.3	+	0	5428				CDHR1_ENST00000332904.3_Missense_Mutation_p.E722K	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1						cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						TCCCCACTGCGAAATTGCCTT	0.403													G|||	6	0.00119808	0.0	0.0	5008	,	,		18511	0.0		0.0	False		,,,				2504	0.0061				p.E722K		Atlas-SNP	.											CDHR1_ENST00000332904,colon,carcinoma,0,3	CDHR1	122	3	0			c.G2164A						PASS	.																																			SO:0001628	intergenic_variant	92211	exon17			CACTGCGAAATTG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634		10.37:g.85978958G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	8.654	0.898947	0.17686	.	.	ENSG00000148600	ENST00000332904	T	0.56776	0.44	2.11	1.17	0.20885	.	.	.	.	.	T	0.24392	0.0591	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.24728	-1.0152	8	0.06099	T	0.92	.	6.5893	0.22638	0.0:0.6863:0.3137:0.0	.	722	Q96JP9-2	.	K	722	ENSP00000331063:E722K	ENSP00000331063:E722K	E	+	1	0	CDHR1	85968938	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.065000	0.11617	0.445000	0.26639	-0.147000	0.13772	GAA	.	.	none		0.403	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
NIPAL4	348938	hgsc.bcm.edu	37	5	156899925	156899925	+	Missense_Mutation	SNP	C	C	T	rs61743233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:156899925C>T	ENST00000311946.7	+	6	1474	c.1358C>T	c.(1357-1359)tCa>tTa	p.S453L	NIPAL4_ENST00000435489.2_Missense_Mutation_p.S434L|ADAM19_ENST00000430702.2_Intron	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	41	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	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	
RP1	6101	hgsc.bcm.edu	37	8	55540141	55540141	+	Silent	SNP	C	C	T	rs114557304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:55540141C>T	ENST00000220676.1	+	4	3847	c.3699C>T	c.(3697-3699)tcC>tcT	p.S1233S		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1233					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAGGAATCTCCTCTTTGGATG	0.443													C|||	117	0.0233626	0.0635	0.0231	5008	,	,		23602	0.001		0.0099	False		,,,				2504	0.0061				p.S1233S	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C3699T						PASS	.	C		286,4120	160.0+/-192.4	9,268,1926	128.0	124.0	125.0		3699	-1.2	0.0	8	dbSNP_132	125	141,8459	70.0+/-132.6	0,141,4159	no	coding-synonymous	RP1	NM_006269.1		9,409,6085	TT,TC,CC		1.6395,6.4911,3.2831		1233/2157	55540141	427,12579	2203	4300	6503	SO:0001819	synonymous_variant	6101	exon4			AATCTCCTCTTTG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3699C>T	8.37:g.55540141C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	210	98	0.466667	NM_006269		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			C|0.970;T|0.030	0.030	strong		0.443	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
PDE10A	10846	hgsc.bcm.edu	37	6	165895824	165895824	+	Silent	SNP	T	T	C	rs9459421	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:165895824T>C	ENST00000366882.1	-	4	328	c.174A>G	c.(172-174)tcA>tcG	p.S58S	PDE10A_ENST00000539869.2_Silent_p.S68S|PDE10A_ENST00000354448.4_Silent_p.S58S			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	58					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)	CCTTAGGAGCTGATTCATCTG	0.358													C|||	562	0.11222	0.0938	0.147	5008	,	,		19502	0.2421		0.0537	False		,,,				2504	0.0389				p.S68S	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.A204G						PASS	.	C	,	402,4004	789.7+/-415.0	13,376,1814	133.0	142.0	139.0		204,174	-0.8	1.0	6	dbSNP_119	139	542,8058	794.9+/-407.5	13,516,3771	no	coding-synonymous,coding-synonymous	PDE10A	NM_001130690.1,NM_006661.2	,	26,892,5585	CC,CT,TT		6.3023,9.1239,7.2582	,	68/790,58/780	165895824	944,12062	2203	4300	6503	SO:0001819	synonymous_variant	10846	exon3			AGGAGCTGATTCA	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.174A>G	6.37:g.165895824T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	142	62	0.43662	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Silent	SNP	ENST00000366882.1	37																																																																																				T|0.906;C|0.094	0.094	strong		0.358	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		
ANK1	286	hgsc.bcm.edu	37	8	41553928	41553928	+	Silent	SNP	C	C	G	rs504574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:41553928C>G	ENST00000347528.4	-	26	2996	c.2913G>C	c.(2911-2913)ctG>ctC	p.L971L	ANK1_ENST00000352337.4_Silent_p.L971L|ANK1_ENST00000289734.7_Silent_p.L971L|ANK1_ENST00000379758.2_Silent_p.L971L|ANK1_ENST00000396942.1_Silent_p.L971L|ANK1_ENST00000265709.8_Silent_p.L1012L|ANK1_ENST00000396945.1_Silent_p.L971L	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	971	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)			TCCTGCTGGCCAGGCCCTCCT	0.716													C|||	2039	0.407149	0.1082	0.5461	5008	,	,		16503	0.5079		0.494	False		,,,				2504	0.5194				p.L1012L		Atlas-SNP	.											ANK1_ENST00000265709,NS,carcinoma,0,4	ANK1	497	4	0			c.G3036C						PASS	.	C	,,,,	646,3758		49,548,1605	34.0	37.0	36.0		2913,3036,2913,2913,2913	2.7	1.0	8	dbSNP_83	36	4071,4525		973,2125,1200	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	,,,,	1022,2673,2805	GG,GC,CC		47.3592,14.6685,36.2846	,,,,	971/1881,1012/1898,971/1857,971/1882,971/1720	41553928	4717,8283	2202	4298	6500	SO:0001819	synonymous_variant	286	exon27			GCTGGCCAGGCCC	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.2913G>C	8.37:g.41553928C>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	908	0.4157509157509158	54	0.10975609756097561	191	0.5276243093922652	281	0.49125874125874125	382	0.503957783641161	C	9.971	1.225504	0.22457	0.146685	0.473592	ENSG00000029534	ENST00000520299	.	.	.	5.53	2.7	0.31948	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48833	-0.9000	3	.	.	.	.	7.5449	0.27761	0.1353:0.72:0.0:0.1447	rs504574;rs504574	.	.	.	R	293	.	.	G	-	1	0	ANK1	41673085	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.076000	0.41548	0.267000	0.21916	0.561000	0.74099	GGC	C|0.627;G|0.373	0.373	strong		0.716	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
SLC26A8	116369	hgsc.bcm.edu	37	6	35911856	35911856	+	Missense_Mutation	SNP	G	G	A	rs61741366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35911856G>A	ENST00000490799.1	-	20	3087	c.2734C>T	c.(2734-2736)Ccc>Tcc	p.P912S	SLC26A8_ENST00000355574.2_Missense_Mutation_p.P912S|SLC26A8_ENST00000394602.2_Missense_Mutation_p.P807S	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						TTGGGGTTGGGCTCCATCTCA	0.572													G|||	13	0.00259585	0.0008	0.0043	5008	,	,		18402	0.0		0.006	False		,,,				2504	0.0031				p.P912S		Atlas-SNP	.											.	SLC26A8	95	.	0			c.C2734T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	13,4393	20.2+/-43.8	0,13,2190	179.0	156.0	164.0		2734,2734,2419	0.5	0.0	6	dbSNP_129	164	101,8499	56.0+/-117.1	1,99,4200	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	74,74,74	1,112,6390	AA,AG,GG		1.1744,0.2951,0.8765	probably-damaging,probably-damaging,probably-damaging	912/971,912/971,807/866	35911856	114,12892	2203	4300	6503	SO:0001583	missense	116369	exon20			GGTTGGGCTCCAT	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.2734C>T	6.37:g.35911856G>A	ENSP00000417638:p.Pro912Ser	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	303	138	0.455446	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	9.857	1.195367	0.22037	0.002951	0.011744	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	T;T;T	0.61274	0.12;0.12;0.12	3.3	0.505	0.16953	.	0.691418	0.12766	N	0.440964	T	0.19005	0.0456	L	0.29908	0.895	0.09310	N	1	B;B;B	0.26602	0.079;0.06;0.154	B;B;B	0.28784	0.014;0.056;0.094	T	0.24083	-1.0170	10	0.24483	T	0.36	.	5.426	0.16425	0.3874:0.0:0.6126:0.0	.	912;807;494	Q96RN1;Q96RN1-2;Q96RN1-3	S26A8_HUMAN;.;.	S	912;807;912	ENSP00000417638:P912S;ENSP00000378100:P807S;ENSP00000347778:P912S	ENSP00000347778:P912S	P	-	1	0	SLC26A8	36019834	0.365000	0.25006	0.009000	0.14445	0.037000	0.13140	1.727000	0.38095	0.080000	0.16959	-0.150000	0.13652	CCC	G|0.993;A|0.007	0.007	strong		0.572	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
METTL2B	55798	hgsc.bcm.edu	37	7	128117227	128117227	+	Splice_Site	SNP	G	G	A	rs2288557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128117227G>A	ENST00000262432.8	+	2	239	c.202G>A	c.(202-204)Gtt>Att	p.V68I	RP11-212P7.3_ENST00000462662.1_RNA|METTL2B_ENST00000480046.1_Intron	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	68			V -> I (in dbSNP:rs2288557). {ECO:0000269|PubMed:15489334}.		tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GGAGAAACAAGGTGCGCTTAA	0.592											OREG0018295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	733	0.146366	0.0386	0.1484	5008	,	,		16242	0.3363		0.0795	False		,,,				2504	0.1636				p.V68I		Atlas-SNP	.											.	METTL2B	34	.	0			c.G202A						PASS	.	G	ILE/VAL	180,4226	114.2+/-152.2	7,166,2030	72.0	83.0	79.0		202	2.5	1.0	7	dbSNP_100	79	566,8034	149.7+/-204.7	9,548,3743	no	missense-near-splice	METTL2B	NM_018396.2	29	16,714,5773	AA,AG,GG		6.5814,4.0853,5.7358	benign	68/379	128117227	746,12260	2203	4300	6503	SO:0001630	splice_region_variant	55798	exon2			AAACAAGGTGCGC	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"""methyltransferase like 2"""	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.202+1G>A	7.37:g.128117227G>A		Somatic	129	0	0	1562	WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	37	CCDS5803.2	312	0.14285714285714285	20	0.04065040650406504	45	0.12430939226519337	180	0.3146853146853147	67	0.08839050131926121	G	13.75	2.330569	0.41297	0.040853	0.065814	ENSG00000165055	ENST00000262432	T	0.03889	3.77	2.45	2.45	0.29901	.	0.353056	0.31427	N	0.007671	T	0.00012	0.0000	L	0.43152	1.355	0.09310	P	1.0	B	0.09022	0.002	B	0.14578	0.011	T	0.47222	-0.9134	9	0.37606	T	0.19	-5.7359	10.6374	0.45573	0.0:0.0:1.0:0.0	rs2288557;rs12672154	68	Q6P1Q9	MTL2B_HUMAN	I	68	ENSP00000262432:V68I	ENSP00000262432:V68I	V	+	1	0	METTL2B	127904463	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	9.004000	0.93583	1.371000	0.46172	0.405000	0.27470	GTT	G|0.942;A|0.058	0.058	strong		0.592	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	Missense_Mutation
PCDHA7	56141	hgsc.bcm.edu	37	5	140214361	140214361	+	Silent	SNP	G	G	A	rs17844307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140214361G>A	ENST00000525929.1	+	1	393	c.393G>A	c.(391-393)ccG>ccA	p.P131P	PCDHA7_ENST00000378125.3_Silent_p.P131P|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	131	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(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)			ACAACCCTCCGGTGTTCCCAG	0.582																																					p.P131P	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											PCDHA7_ENST00000525929,NS,carcinoma,+1,4	PCDHA7	367	4	0			c.G393A						PASS	.						111.0	108.0	109.0					5																	140214361		2203	4300	6503	SO:0001819	synonymous_variant	56141	exon1			CCCTCCGGTGTTC	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.393G>A	5.37:g.140214361G>A		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	470	81	0.17234	NM_031852	O75282	Silent	SNP	ENST00000525929.1	37	CCDS54918.1																																																																																			G|0.981;A|0.019	0.019	strong		0.582	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
OSBPL5	114879	hgsc.bcm.edu	37	11	3141744	3141744	+	Silent	SNP	C	C	T	rs34950527	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:3141744C>T	ENST00000263650.7	-	6	672	c.513G>A	c.(511-513)ctG>ctA	p.L171L	OSBPL5_ENST00000389989.3_Intron|OSBPL5_ENST00000525498.1_Intron|OSBPL5_ENST00000542243.1_Intron|OSBPL5_ENST00000348039.5_Intron	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	171	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CGCAGCAGTGCAGCAGCACCG	0.642													T|||	611	0.122005	0.1558	0.1297	5008	,	,		17968	0.0258		0.1451	False		,,,				2504	0.1462				p.L171L		Atlas-SNP	.											OSBPL5,NS,carcinoma,0,1	OSBPL5	78	1	0			c.G513A						PASS	.	T	,,	673,3731	761.0+/-413.0	46,581,1575	74.0	64.0	67.0		,513,	2.4	1.0	11	dbSNP_126	67	1076,7520	768.1+/-407.6	79,918,3301	no	intron,coding-synonymous,intron	OSBPL5	NM_001144063.1,NM_020896.3,NM_145638.2	,,	125,1499,4876	TT,TC,CC		12.5174,15.2816,13.4538	,,	,171/880,	3141744	1749,11251	2202	4298	6500	SO:0001819	synonymous_variant	114879	exon6			GCAGTGCAGCAGC	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.513G>A	11.37:g.3141744C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	37	CCDS31344.1																																																																																			C|0.870;T|0.130	0.130	strong		0.642	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		
MS4A13	503497	hgsc.bcm.edu	37	11	60296879	60296879	+	Silent	SNP	C	C	T	rs11230364	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60296879C>T	ENST00000378186.2	+	6	671	c.348C>T	c.(346-348)taC>taT	p.Y116Y	MS4A13_ENST00000527948.1_Intron|MS4A13_ENST00000437058.2_Silent_p.Y57Y|MS4A13_ENST00000378185.2_Silent_p.Y76Y	NM_001012417.2	NP_001012417.2	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 13	123						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(1)|lung(2)|skin(2)	8						TGTTCTTCTACGGTTTGGAAT	0.353													C|||	539	0.107628	0.0613	0.098	5008	,	,		15834	0.129		0.0825	False		,,,				2504	0.181				p.Y116Y		Atlas-SNP	.											.	MS4A13	27	.	0			c.C348T						PASS	.	C	,	294,4112	161.1+/-193.3	11,272,1920	199.0	197.0	198.0		348,228	1.5	0.0	11	dbSNP_120	198	770,7828	181.9+/-230.5	25,720,3554	no	coding-synonymous,coding-synonymous	MS4A13	NM_001012417.2,NM_001100909.1	,	36,992,5474	TT,TC,CC		8.9556,6.6727,8.1821	,	116/153,76/113	60296879	1064,11940	2203	4299	6502	SO:0001819	synonymous_variant	503497	exon6			CTTCTACGGTTTG	AY324188	CCDS31571.1, CCDS41653.1, CCDS60801.1	11q12.2	2005-12-05	2005-12-05		ENSG00000204979	ENSG00000204979			16674	protein-coding gene	gene with protein product							Standard	NM_001012417		Approved		uc001nps.3	Q5J8X5	OTTHUMG00000167615	ENST00000378186.2:c.348C>T	11.37:g.60296879C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_001012417	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Silent	SNP	ENST00000378186.2	37	CCDS31571.1																																																																																			C|0.906;T|0.094	0.094	strong		0.353	MS4A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395408.1	NM_001012417	
RTTN	25914	hgsc.bcm.edu	37	18	67718688	67718688	+	Missense_Mutation	SNP	A	A	G	rs4891392	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:67718688A>G	ENST00000255674.6	-	39	5568	c.5282T>C	c.(5281-5283)tTt>tCt	p.F1761S	RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1761			F -> S (in dbSNP:rs4891392). {ECO:0000269|PubMed:14702039}.		determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CACGGTAACAAACGGGAGTGT	0.433													G|||	3960	0.790735	0.3147	0.9121	5008	,	,		16921	1.0		0.9513	False		,,,				2504	0.9673				p.F1761S		Atlas-SNP	.											.	RTTN	184	.	0			c.T5282C						PASS	.	G	SER/PHE	1758,2078		411,936,571	101.0	90.0	94.0		5282	-1.2	0.0	18	dbSNP_111	94	7961,311		3829,303,4	yes	missense	RTTN	NM_173630.3	155	4240,1239,575	GG,GA,AA		3.7597,45.829,19.7308	benign	1761/2227	67718688	9719,2389	1918	4136	6054	SO:0001583	missense	25914	exon39			GTAACAAACGGGA	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.5282T>C	18.37:g.67718688A>G	ENSP00000255674:p.Phe1761Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	1813	0.8301282051282052	182	0.3699186991869919	333	0.919889502762431	572	1.0	726	0.9577836411609498	G	7.364	0.625456	0.14257	0.45829	0.962403	ENSG00000176225	ENST00000255674	T	0.44083	0.93	5.42	-1.23	0.09465	.	0.923761	0.09361	N	0.812763	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.18967	-1.0320	9	0.15066	T	0.55	.	4.7664	0.13134	0.4604:0.0:0.2905:0.2492	rs4891392;rs52803403;rs61190252;rs4891392	1761	Q86VV8	RTTN_HUMAN	S	1761	ENSP00000255674:F1761S	ENSP00000255674:F1761S	F	-	2	0	RTTN	65869668	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.402000	0.02499	-0.576000	0.05974	-1.115000	0.02055	TTT	A|0.188;G|0.812	0.812	strong		0.433	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
RABEP1	9135	hgsc.bcm.edu	37	17	5284770	5284770	+	Silent	SNP	G	G	A	rs1065483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5284770G>A	ENST00000546142.2	+	17	2644	c.2457G>A	c.(2455-2457)agG>agA	p.R819R	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000408982.2_Silent_p.R786R|RABEP1_ENST00000262477.6_Silent_p.R819R|RABEP1_ENST00000537505.1_Silent_p.R776R|RABEP1_ENST00000341923.6_Silent_p.R786R			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	819					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						AAGTCCAGAGGGATTTTGTAA	0.443													A|||	3393	0.677516	0.6301	0.5187	5008	,	,		20225	0.9623		0.4553	False		,,,				2504	0.7894				p.R819R		Atlas-SNP	.											.	RABEP1	59	.	0			c.G2457A						PASS	.	A	,	2224,1532		648,928,302	86.0	88.0	87.0		2358,2457	1.3	1.0	17	dbSNP_86	87	3360,4856		684,1992,1432	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	1332,2920,1734	AA,AG,GG		40.8958,40.7881,46.6422	,	786/830,819/863	5284770	5584,6388	1878	4108	5986	SO:0001819	synonymous_variant	9135	exon17			CCAGAGGGATTTT	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.2457G>A	17.37:g.5284770G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			G|0.390;A|0.610	0.610	strong		0.443	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
MYO1H	283446	hgsc.bcm.edu	37	12	109838954	109838954	+	Silent	SNP	C	C	T	rs138935511	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109838954C>T	ENST00000431443.2	+	5	579	c.579C>T	c.(577-579)gtC>gtT	p.V193V	MYO1H_ENST00000310903.5_Silent_p.V193V	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	193	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						CCCGAGTTGTCTACCAAAACG	0.512													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17341	0.0		0.0	False		,,,				2504	0.0				p.V193V		Atlas-SNP	.											.	MYO1H	98	.	0			c.C579T						PASS	.	C		3,4061		0,3,2029	69.0	72.0	71.0		579	2.5	1.0	12	dbSNP_134	71	1,8387		0,1,4193	no	coding-synonymous	MYO1H	NM_001101421.3		0,4,6222	TT,TC,CC		0.0119,0.0738,0.0321		193/1023	109838954	4,12448	2032	4194	6226	SO:0001819	synonymous_variant	283446	exon5			AGTTGTCTACCAA		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.579C>T	12.37:g.109838954C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				C|0.999;T|0.001	0.001	strong		0.512	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
DUOX1	53905	hgsc.bcm.edu	37	15	45446156	45446156	+	Missense_Mutation	SNP	C	C	T	rs2458236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:45446156C>T	ENST00000321429.4	+	28	3939	c.3532C>T	c.(3532-3534)Ctc>Ttc	p.L1178F	DUOX1_ENST00000389037.3_Missense_Mutation_p.L1178F|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000559221.1_3'UTR|DUOX1_ENST00000561166.1_Missense_Mutation_p.L824F	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1178	Ferric oxidoreductase.|Interaction with TXNDC11. {ECO:0000250}.		L -> F (in dbSNP:rs2458236). {ECO:0000269|PubMed:11514595}.		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)	p.L1178F(1)		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)		CAGGTCTGAGCTCCCCCAGAA	0.498													T|||	2771	0.553315	0.388	0.5029	5008	,	,		19796	0.4911		0.661	False		,,,				2504	0.7658				p.L1178F		Atlas-SNP	.											DUOX1,NS,carcinoma,0,1	DUOX1	125	1	1	Substitution - Missense(1)	stomach(1)	c.C3532T						PASS	.	T	PHE/LEU,PHE/LEU	1870,2526	630.7+/-395.5	409,1052,737	99.0	88.0	92.0		3532,3532	3.3	1.0	15	dbSNP_100	92	5814,2782	441.3+/-359.8	1972,1870,456	yes	missense,missense	DUOX1	NM_017434.3,NM_175940.1	22,22	2381,2922,1193	TT,TC,CC		32.3639,42.5387,40.8559	benign,benign	1178/1552,1178/1552	45446156	7684,5308	2198	4298	6496	SO:0001583	missense	53905	exon28			TCTGAGCTCCCCC	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.3532C>T	15.37:g.45446156C>T	ENSP00000317997:p.Leu1178Phe	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	97	0.979798	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	1186	0.543040293040293	209	0.4247967479674797	207	0.5718232044198895	265	0.4632867132867133	505	0.6662269129287599	T	10.41	1.342094	0.24339	0.425387	0.676361	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.91011	-2.77;-2.77	4.47	3.35	0.38373	Flavoprotein transmembrane component (1);	0.305319	0.36444	N	0.002588	T	0.00012	0.0000	N	0.20845	0.615	0.46678	P	8.439999999999559E-4	B	0.09022	0.002	B	0.17722	0.019	T	0.48234	-0.9053	9	0.14252	T	0.57	-18.9469	6.2577	0.20884	0.0:0.296:0.0:0.704	rs2458236;rs3817195;rs52801292;rs58186531;rs2458236	1178	Q9NRD9	DUOX1_HUMAN	F	1178	ENSP00000317997:L1178F;ENSP00000373689:L1178F	ENSP00000317997:L1178F	L	+	1	0	DUOX1	43233448	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	0.792000	0.26929	0.354000	0.24105	-0.254000	0.11334	CTC	C|0.431;N|0.000	.	strong		0.498	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
FLG	2312	hgsc.bcm.edu	37	1	152284505	152284505	+	Missense_Mutation	SNP	C	C	G	rs201137357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152284505C>G	ENST00000368799.1	-	3	2892	c.2857G>C	c.(2857-2859)Gag>Cag	p.E953Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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						scavenged	.	G	GLN/GLU	442,3964		4,434,1765	302.0	283.0	290.0		2857	2.1	0.0	1	dbSNP_134	290	5,8595		0,5,4295	no	missense	FLG	NM_002016.1	29	4,439,6060	GG,GC,CC		0.0581,10.0318,3.4369	probably-damaging	953/4062	152284505	447,12559	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCCCTCACTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2857G>C	1.37:g.152284505C>G	ENSP00000357789:p.Glu953Gln	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	384	24	0.0625	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	
CENPF	1063	hgsc.bcm.edu	37	1	214814582	214814582	+	Silent	SNP	G	G	A	rs3795520	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214814582G>A	ENST00000366955.3	+	12	3069	c.2901G>A	c.(2899-2901)agG>agA	p.R967R		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)		TAAATAAAAGGGAAATTGAAG	0.363													A|||	527	0.105232	0.1006	0.1052	5008	,	,		18055	0.126		0.0517	False		,,,				2504	0.1452				p.R967R	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.G2901A						PASS	.	A		361,3977		12,337,1820	54.0	61.0	58.0		2901	1.7	0.0	1	dbSNP_107	58	451,8129		10,431,3849	no	coding-synonymous	CENPF	NM_016343.3		22,768,5669	AA,AG,GG		5.2564,8.3218,6.2858		967/3115	214814582	812,12106	2169	4290	6459	SO:0001819	synonymous_variant	1063	exon12			TAAAAGGGAAATT	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.2901G>A	1.37:g.214814582G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			G|0.914;A|0.086	0.086	strong		0.363	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
AKAP12	9590	hgsc.bcm.edu	37	6	151672812	151672812	+	Missense_Mutation	SNP	G	G	A	rs3734797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151672812G>A	ENST00000253332.1	+	3	3475	c.3286G>A	c.(3286-3288)Gta>Ata	p.V1096I	AKAP12_ENST00000354675.6_Missense_Mutation_p.V998I|AKAP12_ENST00000359755.5_Missense_Mutation_p.V991I|AKAP12_ENST00000402676.2_Missense_Mutation_p.V1096I			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1096			V -> I (in dbSNP:rs3734797).		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)		AGTGTTGAAAGTAGATGCTCA	0.507													G|||	288	0.057508	0.0234	0.1138	5008	,	,		20825	0.129		0.0189	False		,,,				2504	0.0297				p.V1096I	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G3286A						PASS	.	G	ILE/VAL,ILE/VAL	92,4314	71.4+/-109.4	2,88,2113	50.0	51.0	51.0		3286,2992	5.3	0.0	6	dbSNP_107	51	176,8424	79.8+/-142.4	3,170,4127	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	29,29	5,258,6240	AA,AG,GG		2.0465,2.0881,2.0606	benign,benign	1096/1783,998/1685	151672812	268,12738	2203	4300	6503	SO:0001583	missense	9590	exon4			TTGAAAGTAGATG	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.3286G>A	6.37:g.151672812G>A	ENSP00000253332:p.Val1096Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	142	0.06501831501831502	17	0.034552845528455285	34	0.09392265193370165	75	0.13111888111888112	16	0.021108179419525065	G	14.02	2.410267	0.42715	0.020881	0.020465	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.06933	3.24;3.24;3.25;3.25	5.26	5.26	0.73747	.	1.371780	0.05591	N	0.574666	T	0.02688	0.0081	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.28850	0.225;0.225;0.144	B;B;B	0.24394	0.053;0.053;0.024	T	0.23261	-1.0193	9	0.38643	T	0.18	.	11.927	0.52825	0.0803:0.0:0.9197:0.0	rs3734797;rs17261769;rs59746410;rs3734797	991;998;1096	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	I	1096;1096;998;991	ENSP00000384537:V1096I;ENSP00000253332:V1096I;ENSP00000346702:V998I;ENSP00000352794:V991I	ENSP00000253332:V1096I	V	+	1	0	AKAP12	151714505	0.215000	0.23574	0.004000	0.12327	0.095000	0.18619	2.485000	0.45250	2.462000	0.83206	0.455000	0.32223	GTA	G|0.961;A|0.039	0.039	strong		0.507	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
ITGA2	3673	hgsc.bcm.edu	37	5	52351413	52351413	+	Silent	SNP	G	G	A	rs1062535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:52351413G>A	ENST00000296585.5	+	8	968	c.825G>A	c.(823-825)acG>acA	p.T275T		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	275	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GAAGTGCTACGAAAGTAATGG	0.368																																					p.T275T		Atlas-SNP	.											.	ITGA2	211	.	0			c.G825A	GRCh37	CM993454	ITGA2	M	rs1062535	PASS	.	A		1442,2964	467.6+/-354.9	240,962,1001	165.0	157.0	160.0		825	0.4	0.9	5	dbSNP_86	160	3426,5174	504.5+/-376.2	655,2116,1529	no	coding-synonymous	ITGA2	NM_002203.3		895,3078,2530	AA,AG,GG		39.8372,32.7281,37.4289		275/1182	52351413	4868,8138	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon8			TGCTACGAAAGTA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.825G>A	5.37:g.52351413G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			G|0.627;A|0.373	0.373	strong		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
CTDP1	9150	hgsc.bcm.edu	37	18	77473086	77473086	+	Silent	SNP	G	G	A	rs599554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:77473086G>A	ENST00000299543.7	+	7	1125	c.978G>A	c.(976-978)acG>acA	p.T326T	CTDP1_ENST00000075430.7_Silent_p.T326T	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	326	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				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)		TCCAGGGCACGGGTGATATGA	0.448													G|||	1046	0.208866	0.3147	0.2205	5008	,	,		15472	0.1389		0.175	False		,,,				2504	0.1646				p.T326T		Atlas-SNP	.											.	CTDP1	67	.	0			c.G978A						PASS	.	G	,,	1272,3134	435.3+/-344.3	200,872,1131	77.0	74.0	75.0		621,978,978	-9.6	0.0	18	dbSNP_83	75	1463,7135	278.0+/-293.2	134,1195,2970	no	coding-synonymous,coding-synonymous,coding-synonymous	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,,	334,2067,4101	AA,AG,GG		17.0156,28.8697,21.032	,,	207/843,326/962,326/868	77473086	2735,10269	2203	4299	6502	SO:0001819	synonymous_variant	9150	exon7			GGGCACGGGTGAT	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.978G>A	18.37:g.77473086G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																			A|0.215;C|0.003	0.215	strong		0.448	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
UMODL1	89766	hgsc.bcm.edu	37	21	43546509	43546509	+	Missense_Mutation	SNP	G	G	A	rs111996953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43546509G>A	ENST00000408910.2	+	18	3202	c.3202G>A	c.(3202-3204)Ggc>Agc	p.G1068S	UMODL1_ENST00000400427.1_Missense_Mutation_p.G1124S|UMODL1_ENST00000400424.2_Missense_Mutation_p.G996S|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000408989.2_Missense_Mutation_p.G1196S	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1068	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		G -> S (in dbSNP:rs111996953). {ECO:0000269|PubMed:16026467}.		adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GTCCCAGGAGGGCATCATCCA	0.617													G|||	173	0.0345447	0.0045	0.0432	5008	,	,		18579	0.001		0.1014	False		,,,				2504	0.0348				p.G1196S	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.G3586A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY,SER/GLY	74,4252		1,72,2090	91.0	98.0	95.0		3202,3370,2986,3586	2.8	0.1	21	dbSNP_132	95	717,7791		39,639,3576	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	56,56,56,56	40,711,5666	AA,AG,GG		8.4274,1.7106,6.1633	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1068/1319,1124/1375,996/1247,1196/1447	43546509	791,12043	2163	4254	6417	SO:0001583	missense	89766	exon17			CAGGAGGGCATCA		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.3202G>A	21.37:g.43546509G>A	ENSP00000386147:p.Gly1068Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	89	0.04075091575091575	1	0.0020325203252032522	24	0.06629834254143646	1	0.0017482517482517483	63	0.08311345646437995	G	12.56	1.974616	0.34848	0.017106	0.084274	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	3.74	2.85	0.33270	Zona pellucida sperm-binding protein (3);	0.147837	0.30210	N	0.010143	T	0.36193	0.0958	M	0.77103	2.36	0.47659	P	5.110000000000392E-4	P;D	0.89917	0.94;1.0	P;D	0.85130	0.734;0.997	T	0.74490	-0.3648	8	.	.	.	-17.8657	10.0958	0.42475	0.0964:0.0:0.9036:0.0	.	1196;1068	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	S	1124;996;1196;1068	ENSP00000383279:G1124S;ENSP00000383276:G996S;ENSP00000386126:G1196S;ENSP00000386147:G1068S	.	G	+	1	0	UMODL1	42419578	0.998000	0.40836	0.076000	0.20297	0.029000	0.11900	2.787000	0.47798	1.145000	0.42336	0.561000	0.74099	GGC	G|0.943;A|0.057	0.057	strong		0.617	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
FAT2	2196	hgsc.bcm.edu	37	5	150901597	150901597	+	Silent	SNP	G	G	C	rs3734047	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150901597G>C	ENST00000261800.5	-	18	10569	c.10557C>G	c.(10555-10557)gtC>gtG	p.V3519V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3519	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGTGACATGGACACGGACAG	0.542													G|||	488	0.0974441	0.0083	0.1585	5008	,	,		20790	0.126		0.1948	False		,,,				2504	0.045				p.V3519V		Atlas-SNP	.											.	FAT2	465	.	0			c.C10557G						PASS	.	G		164,4242	107.8+/-146.2	6,152,2045	57.0	51.0	53.0		10557	2.3	0.1	5	dbSNP_107	53	1829,6771	328.1+/-318.2	206,1417,2677	no	coding-synonymous	FAT2	NM_001447.2		212,1569,4722	CC,CG,GG		21.2674,3.7222,15.3237		3519/4350	150901597	1993,11013	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon18			GACATGGACACGG	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.10557C>G	5.37:g.150901597G>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	290	0.13278388278388278	6	0.012195121951219513	65	0.17955801104972377	82	0.14335664335664336	137	0.18073878627968337	G	0.017	-1.494745	0.01009	0.037222	0.212674	ENSG00000086570	ENST00000520200	.	.	.	5.14	2.3	0.28687	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999996599	.	.	.	.	.	.	T	0.14531	-1.0469	3	.	.	.	.	4.8548	0.13554	0.0715:0.1279:0.5208:0.2799	rs3734047;rs3734047	.	.	.	A	378	.	.	P	-	1	0	FAT2	150881790	0.998000	0.40836	0.059000	0.19551	0.012000	0.07955	0.818000	0.27295	0.246000	0.21394	-0.261000	0.10672	CCA	G|0.858;C|0.142	0.142	strong		0.542	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
NCKAP5	344148	hgsc.bcm.edu	37	2	133971307	133971307	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133971307C>T	ENST00000409261.1	-	5	561	c.188G>A	c.(187-189)aGa>aAa	p.R63K	NCKAP5_ENST00000405974.3_Missense_Mutation_p.R63K|NCKAP5_ENST00000317721.6_Missense_Mutation_p.R63K|NCKAP5_ENST00000409213.1_Missense_Mutation_p.R63K	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	63										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						CTCACTTGTTCTTTGGGCAAC	0.493																																					p.R63K		Atlas-SNP	.											NCKAP5,NS,carcinoma,0,2	NCKAP5	322	2	0			c.G188A						scavenged	.						103.0	108.0	107.0					2																	133971307		1918	4110	6028	SO:0001583	missense	344148	exon5			CTTGTTCTTTGGG	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.188G>A	2.37:g.133971307C>T	ENSP00000387128:p.Arg63Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	115	4	0.0347826	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.49|13.49	2.251732|2.251732	0.39797|0.39797	.|.	.|.	ENSG00000176771|ENSG00000176771	ENST00000427594|ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834;ENST00000358991	.|T;T;T;T	.|0.43294	.|2.96;0.95;2.96;0.95	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	.|.	.|.	.|.	.|.	T|T	0.37046|0.37046	0.0989|0.0989	N|N	0.19112|0.19112	0.55|0.55	0.28888|0.28888	N|N	0.893999|0.893999	.|B;B;P;D	.|0.61697	.|0.033;0.373;0.663;0.99	.|B;B;B;P	.|0.48334	.|0.015;0.117;0.269;0.574	T|T	0.23368|0.23368	-1.0190|-1.0190	5|9	.|0.51188	.|T	.|0.08	.|.	14.17|14.17	0.65503|0.65503	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|63;38;63;63	.|F5GYX5;O14513-3;O14513-2;O14513	.|.;.;.;NCKP5_HUMAN	K|K	59|63;63;63;63;63;38;63	.|ENSP00000387128:R63K;ENSP00000386952:R63K;ENSP00000380603:R63K;ENSP00000385692:R63K	.|ENSP00000380603:R63K	E|R	-|-	1|2	0|0	NCKAP5|NCKAP5	133687777|133687777	0.989000|0.989000	0.36119|0.36119	0.985000|0.985000	0.45067|0.45067	0.963000|0.963000	0.63663|0.63663	2.343000|2.343000	0.44001|0.44001	2.708000|2.708000	0.92522|0.92522	0.650000|0.650000	0.86243|0.86243	GAA|AGA	.	.	none		0.493	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
IQGAP3	128239	hgsc.bcm.edu	37	1	156499969	156499969	+	Silent	SNP	T	T	C	rs386635735|rs1171566	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156499969T>C	ENST00000361170.2	-	34	4342	c.4332A>G	c.(4330-4332)ctA>ctG	p.L1444L	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1444					activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAAGTCGGCGTAGGTTCCGCA	0.647													C|||	3033	0.605631	0.8449	0.4424	5008	,	,		406	0.6022		0.33	False		,,,				2504	0.6851				p.L1444L		Atlas-SNP	.											IQGAP3,NS,carcinoma,0,1	IQGAP3	146	1	0			c.A4332G						PASS	.	C		3226,1180	404.0+/-332.9	1179,868,156	52.0	46.0	48.0		4332	4.5	1.0	1	dbSNP_87	48	2795,5805	665.5+/-402.3	475,1845,1980	no	coding-synonymous	IQGAP3	NM_178229.4		1654,2713,2136	CC,CT,TT		32.5,26.7817,46.294		1444/1632	156499969	6021,6985	2203	4300	6503	SO:0001819	synonymous_variant	128239	exon34			TCGGCGTAGGTTC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4332A>G	1.37:g.156499969T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																			T|0.489;C|0.511	0.511	strong		0.647	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
PIGZ	80235	hgsc.bcm.edu	37	3	196674307	196674307	+	Missense_Mutation	SNP	C	C	T	rs17855662	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:196674307C>T	ENST00000412723.1	-	3	1607	c.1461G>A	c.(1459-1461)atG>atA	p.M487I		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	487			M -> I (in dbSNP:rs17855662). {ECO:0000269|PubMed:15489334}.		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)		CAGTCCCCCCCATGTCCACCA	0.637													C|||	152	0.0303514	0.0023	0.0476	5008	,	,		17221	0.0		0.0775	False		,,,				2504	0.0389				p.M487I		Atlas-SNP	.											.	PIGZ	34	.	0			c.G1461A						PASS	.	C	ILE/MET	59,4347	56.2+/-92.4	0,59,2144	63.0	63.0	63.0		1461	4.9	1.0	3	dbSNP_123	63	629,7971	159.5+/-212.8	25,579,3696	yes	missense	PIGZ	NM_025163.2	10	25,638,5840	TT,TC,CC		7.314,1.3391,5.2899	benign	487/580	196674307	688,12318	2203	4300	6503	SO:0001583	missense	80235	exon3			CCCCCCCATGTCC	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.1461G>A	3.37:g.196674307C>T	ENSP00000413405:p.Met487Ile	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	37	CCDS3324.1	89	0.04075091575091575	1	0.0020325203252032522	19	0.052486187845303865	0	0.0	69	0.09102902374670185	C	11.93	1.785043	0.31593	0.013391	0.07314	ENSG00000119227	ENST00000412723	T	0.11277	2.79	4.93	4.93	0.64822	.	0.234837	0.30193	N	0.010190	T	0.00300	0.0009	L	0.27053	0.805	0.80722	D	1	P	0.35844	0.524	B	0.28849	0.095	T	0.47799	-0.9089	10	0.45353	T	0.12	-23.6546	12.6033	0.56509	0.1657:0.8343:0.0:0.0	rs17855662	487	Q86VD9	PIGZ_HUMAN	I	487	ENSP00000413405:M487I	ENSP00000413405:M487I	M	-	3	0	PIGZ	198158704	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	1.825000	0.39081	2.472000	0.83506	0.561000	0.74099	ATG	C|0.948;T|0.052	0.052	strong		0.637	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
LRRN2	10446	hgsc.bcm.edu	37	1	204589101	204589101	+	Missense_Mutation	SNP	G	G	A	rs3789044	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204589101G>A	ENST00000367175.1	-	1	2232	c.20C>T	c.(19-21)cCa>cTa	p.P7L	LRRN2_ENST00000496057.1_5'UTR|LRRN2_ENST00000367176.3_Missense_Mutation_p.P7L|LRRN2_ENST00000367177.3_Missense_Mutation_p.P7L			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	7			P -> L (in dbSNP:rs3789044).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TAGCAAGAGTGGGGCCACGAG	0.622													G|||	895	0.178714	0.0446	0.0908	5008	,	,		17566	0.3085		0.2247	False		,,,				2504	0.2413				p.P7L		Atlas-SNP	.											LRRN2,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,2	LRRN2	81	2	0			c.C20T						PASS	.	G	LEU/PRO,LEU/PRO	306,4064		13,280,1892	14.0	16.0	16.0		20,20	3.8	1.0	1	dbSNP_107	16	1859,6727		196,1467,2630	yes	missense,missense	LRRN2	NM_201630.1,NM_006338.2	98,98	209,1747,4522	AA,AG,GG		21.6515,7.0023,16.7104	benign,benign	7/714,7/714	204589101	2165,10791	2185	4293	6478	SO:0001583	missense	10446	exon3			AAGAGTGGGGCCA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.20C>T	1.37:g.204589101G>A	ENSP00000356143:p.Pro7Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	415	0.190018315018315	33	0.06707317073170732	38	0.10497237569060773	174	0.3041958041958042	170	0.22427440633245382	G	0.632	-0.816888	0.02776	0.070023	0.216515	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.20881	2.04;2.04;2.04	5.79	3.8	0.43715	.	0.360808	0.20218	N	0.096750	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.43376	-0.9395	9	0.15952	T	0.53	.	10.3029	0.43663	0.0:0.1355:0.7092:0.1552	rs3789044;rs59340562;rs3789044	7	O75325	LRRN2_HUMAN	L	7	ENSP00000356144:P7L;ENSP00000356145:P7L;ENSP00000356143:P7L	ENSP00000356143:P7L	P	-	2	0	LRRN2	202855724	0.519000	0.26242	0.968000	0.41197	0.317000	0.28152	0.541000	0.23207	2.746000	0.94184	0.650000	0.86243	CCA	G|0.822;A|0.178	0.178	strong		0.622	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
TNK1	8711	hgsc.bcm.edu	37	17	7286326	7286326	+	Silent	SNP	T	T	A	rs1554948	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7286326T>A	ENST00000576812.1	+	2	450	c.81T>A	c.(79-81)ctT>ctA	p.L27L	TNK1_ENST00000570896.1_Silent_p.L27L|TNK1_ENST00000311668.2_Silent_p.L27L	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				GGCCCATCCTTGAGGAGCTTA	0.592													.|||	1926	0.384585	0.2965	0.3314	5008	,	,		19751	0.2579		0.4533	False		,,,				2504	0.6012				p.L27L		Atlas-SNP	.											.	TNK1	31	.	0			c.T81A						PASS	.	T		1350,2944		239,872,1036	58.0	62.0	61.0		81	-10.1	0.4	17	dbSNP_88	61	3920,4584		935,2050,1267	no	coding-synonymous	TNK1	NM_003985.3		1174,2922,2303	AA,AT,TT		46.096,31.4392,41.1783		27/662	7286326	5270,7528	2147	4252	6399	SO:0001819	synonymous_variant	8711	exon2			CATCCTTGAGGAG	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.81T>A	17.37:g.7286326T>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			T|0.623;A|0.377	0.377	strong		0.592	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108053	17108053	+	Missense_Mutation	SNP	C	C	T	rs12974937	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17108053C>T	ENST00000443236.1	-	11	1135	c.1104G>A	c.(1102-1104)atG>atA	p.M368I	CPAMD8_ENST00000388925.4_Missense_Mutation_p.M321I	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	321						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						CACTGGTCACCATGGCCCAGA	0.642													c|||	893	0.178315	0.3601	0.1009	5008	,	,		18768	0.1012		0.159	False		,,,				2504	0.0869				p.M368I		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G1104A						PASS	.	C	ILE/MET	1167,2641		185,797,922	22.0	24.0	23.0		1104	-4.0	0.0	19	dbSNP_121	23	1236,6920		88,1060,2930	no	missense	CPAMD8	NM_015692.2	10	273,1857,3852	TT,TC,CC		15.1545,30.646,20.0853	benign	368/1933	17108053	2403,9561	1904	4078	5982	SO:0001583	missense	27151	exon11			GGTCACCATGGCC	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.1104G>A	19.37:g.17108053C>T	ENSP00000402505:p.Met368Ile	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	242	104	0.429752	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	367|367	0.16804029304029305|0.16804029304029305	164|164	0.3333333333333333|0.3333333333333333	33|33	0.09116022099447514|0.09116022099447514	52|52	0.09090909090909091|0.09090909090909091	118|118	0.15567282321899736|0.15567282321899736	c|c	3.308|3.308	-0.141438|-0.141438	0.06669|0.06669	0.30646|0.30646	0.151545|0.151545	ENSG00000160111|ENSG00000160111	ENST00000291440;ENST00000388925|ENST00000443236	T;T|.	0.50548|.	0.74;0.75|.	3.0|3.0	-3.97|-3.97	0.04094|0.04094	.|.	3.567220|.	0.01429|.	N|.	0.014647|.	T|.	0.00012|.	0.0000|.	N|N	0.02539|0.02539	-0.55|-0.55	0.58432|0.58432	P|P	2.9999999999752447E-6|2.9999999999752447E-6	B|.	0.15141|.	0.012|.	B|.	0.12156|.	0.007|.	T|.	0.43196|.	-0.9406|.	9|.	0.26408|.	T|.	0.33|.	.|.	1.2097|1.2097	0.01902|0.01902	0.2197:0.3481:0.1087:0.3235|0.2197:0.3481:0.1087:0.3235	rs12974937;rs57120169|rs12974937;rs57120169	321|.	Q8IZJ3|.	CPMD8_HUMAN|.	I|X	368;321|379	ENSP00000291440:M368I;ENSP00000373577:M321I|.	ENSP00000291440:M368I|.	M|W	-|-	3|2	0|0	CPAMD8|CPAMD8	16969053|16969053	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.083000|0.083000	0.17756|0.17756	-4.497000|-4.497000	0.00225|0.00225	-1.305000|-1.305000	0.02327|0.02327	-1.164000|-1.164000	0.01763|0.01763	ATG|TGG	C|0.750;T|0.250	0.250	strong		0.642	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
TRIM48	79097	hgsc.bcm.edu	37	11	55032663	55032663	+	Missense_Mutation	SNP	T	T	C	rs200778682	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:55032663T>C	ENST00000417545.2	+	2	418	c.332T>C	c.(331-333)aTt>aCt	p.I111T		NM_024114.3	NP_077019.2	Q8IWZ4	TRI48_HUMAN	tripartite motif containing 48	95						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(13)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						ATGTGTGGCATTCACAGGGAG	0.498																																					p.I111T		Atlas-SNP	.											TRIM48_ENST00000417545,NS,carcinoma,0,4	TRIM48	149	4	0			c.T332C						scavenged	.						98.0	90.0	93.0					11																	55032663		2188	4256	6444	SO:0001583	missense	79097	exon2			GTGGCATTCACAG	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.332T>C	11.37:g.55032663T>C	ENSP00000402414:p.Ile111Thr	Somatic	651	13	0.0199693		WXS	Illumina HiSeq	Phase_I	689	17	0.0246734	NM_024114	Q9BUW4	Missense_Mutation	SNP	ENST00000417545.2	37	CCDS7947.2	.	.	.	.	.	.	.	.	.	.	c	0	-2.612529	0.00120	.	.	ENSG00000150244	ENST00000417545	T	0.40476	1.03	0.596	0.596	0.17496	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, B-box (3);	.	.	.	.	T	0.13114	0.0318	N	0.03324	-0.35	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28038	-1.0056	9	0.02654	T	1	.	1.7225	0.02915	0.3221:0.4182:0.0:0.2597	.	95	Q8IWZ4	TRI48_HUMAN	T	111	ENSP00000402414:I111T	ENSP00000402414:I111T	I	+	2	0	TRIM48	54789239	0.000000	0.05858	0.154000	0.22540	0.130000	0.20726	-4.117000	0.00292	-0.174000	0.10743	-1.141000	0.01876	ATT	T|0.996;C|0.004	0.004	strong		0.498	TRIM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347088.1		
CENPF	1063	hgsc.bcm.edu	37	1	214814995	214814995	+	Missense_Mutation	SNP	C	C	T	rs12067133	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214814995C>T	ENST00000366955.3	+	12	3482	c.3314C>T	c.(3313-3315)aCa>aTa	p.T1105I		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0			T -> I (in dbSNP:rs12067133).		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)		GAGTTGGAGACAGTGCAGCAA	0.383													C|||	526	0.105032	0.1006	0.1052	5008	,	,		19775	0.126		0.0507	False		,,,				2504	0.1452				p.T1105I	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.C3314T						PASS	.	C	ILE/THR	399,4007	198.4+/-222.2	17,365,1821	80.0	81.0	80.0		3314	-0.5	0.0	1	dbSNP_120	80	466,8134	138.7+/-195.5	12,442,3846	yes	missense	CENPF	NM_016343.3	89	29,807,5667	TT,TC,CC		5.4186,9.0558,6.6508	benign	1105/3115	214814995	865,12141	2203	4300	6503	SO:0001583	missense	1063	exon12			TGGAGACAGTGCA	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.3314C>T	1.37:g.214814995C>T	ENSP00000355922:p.Thr1105Ile	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	212	90	0.424528	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	229	0.10485347985347986	63	0.12804878048780488	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	C	2.061	-0.415333	0.04766	0.090558	0.054186	ENSG00000117724	ENST00000366955	T	0.03272	3.99	4.92	-0.487	0.12060	.	1.109350	0.07116	N	0.843007	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.26744	0.158	B	0.17433	0.018	T	0.48163	-0.9059	8	0.36615	T	0.2	.	5.8445	0.18659	0.0:0.6556:0.1713:0.1731	rs12067133;rs52800597;rs56956048;rs12067133	1105	P49454	CENPF_HUMAN	I	1105	ENSP00000355922:T1105I	ENSP00000355922:T1105I	T	+	2	0	CENPF	212881618	0.001000	0.12720	0.000000	0.03702	0.658000	0.38924	0.572000	0.23684	0.005000	0.14708	0.609000	0.83330	ACA	C|0.915;T|0.085	0.085	strong		0.383	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
TGFBI	7045	hgsc.bcm.edu	37	5	135391374	135391374	+	Silent	SNP	C	C	T	rs1133170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:135391374C>T	ENST00000442011.2	+	11	1577	c.1416C>T	c.(1414-1416)ctC>ctT	p.L472L	TGFBI_ENST00000305126.8_Silent_p.L472L	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	472	FAS1 3. {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)			TGCAGAGCCTCTGCATTGAGA	0.562													G|||	1403	0.280152	0.3011	0.2133	5008	,	,		17398	0.247		0.2565	False		,,,				2504	0.3579				p.L472L		Atlas-SNP	.											TGFBI,NS,carcinoma,+2,1	TGFBI	76	1	0			c.C1416T						PASS	.	G		1182,2662		173,836,913	40.0	40.0	40.0		1416	3.4	1.0	5	dbSNP_86	40	2201,6035		306,1589,2223	no	coding-synonymous	TGFBI	NM_000358.2		479,2425,3136	TT,TC,CC		26.7241,30.7492,28.005		472/684	135391374	3383,8697	1922	4118	6040	SO:0001819	synonymous_variant	7045	exon11			GAGCCTCTGCATT	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.1416C>T	5.37:g.135391374C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1																																																																																			C|0.738;T|0.262	0.262	strong		0.562	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
OR10H2	26538	hgsc.bcm.edu	37	19	15838972	15838972	+	Missense_Mutation	SNP	T	T	A	rs4569397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	295	0	0		WXS	Illumina HiSeq	Phase_I	242	107	0.442149	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		
DRD5	1816	hgsc.bcm.edu	37	4	9784550	9784550	+	Silent	SNP	G	G	A	rs2227844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:9784550G>A	ENST00000304374.2	+	1	1293	c.897G>A	c.(895-897)tcG>tcA	p.S299S		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	299					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)	AGACCCTGTCGGTGATCATGG	0.632																																					p.S299S		Atlas-SNP	.											DRD5,colon,carcinoma,0,2	DRD5	119	2	0			c.G897A						scavenged	.						55.0	52.0	53.0					4																	9784550		2203	4297	6500	SO:0001819	synonymous_variant	1816	exon1			CCTGTCGGTGATC	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.897G>A	4.37:g.9784550G>A		Somatic	34	1	0.0294118		WXS	Illumina HiSeq	Phase_I	33	3	0.0909091	NM_000798	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			G|0.885;A|0.115	0.115	strong		0.632	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
CNN2	1265	hgsc.bcm.edu	37	19	1032689	1032689	+	Silent	SNP	G	G	T	rs1141534	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1032689G>T	ENST00000263097.4	+	4	747	c.384G>T	c.(382-384)gcG>gcT	p.A128A	CNN2_ENST00000565096.2_Intron|CNN2_ENST00000606983.1_3'UTR|CNN2_ENST00000348419.3_Silent_p.A128A|CNN2_ENST00000562958.2_Silent_p.A128A	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	128	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		tcgccctggcggggaaggtga	0.572													G|||	636	0.126997	0.028	0.1354	5008	,	,		20053	0.1429		0.1948	False		,,,				2504	0.1687				p.A128A		Atlas-SNP	.											.	CNN2	26	.	0			c.G384T						PASS	.	G	,	259,4143		9,241,1951	24.0	20.0	21.0		384,384	-8.1	0.6	19	dbSNP_86	21	1763,6833		184,1395,2719	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	193,1636,4670	TT,TG,GG		20.5095,5.8837,15.5562	,	128/310,128/271	1032689	2022,10976	2201	4298	6499	SO:0001819	synonymous_variant	1265	exon4			CCTGGCGGGGAAG	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.384G>T	19.37:g.1032689G>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	34	0.708333	NM_201277	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			G|0.862;T|0.138	0.138	strong		0.572	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
CYP11B2	1585	hgsc.bcm.edu	37	8	143996553	143996553	+	Silent	SNP	G	G	A	rs4546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:143996553G>A	ENST00000323110.2	-	3	506	c.504C>T	c.(502-504)ttC>ttT	p.F168F		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	168					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)	GGGCCTGGGAGAAGTCCCTGG	0.622									Familial Hyperaldosteronism type I				.|||	1730	0.345447	0.1838	0.4697	5008	,	,		19590	0.2867		0.4841	False		,,,				2504	0.3937				p.F168F		Atlas-SNP	.											CYP11B2,rectum,carcinoma,0,1	CYP11B2	107	1	0			c.C504T						PASS	.	G		1021,3385		122,777,1304	43.0	39.0	41.0		504	1.6	0.0	8	dbSNP_52	41	3861,4735		876,2109,1313	no	coding-synonymous	CYP11B2	NM_000498.3		998,2886,2617	AA,AG,GG		44.9162,23.1729,37.5481		168/504	143996553	4882,8120	2203	4298	6501	SO:0001819	synonymous_variant	1585	exon3	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CTGGGAGAAGTCC	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.504C>T	8.37:g.143996553G>A		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	197	193	0.979695	NM_000498	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	37	CCDS6393.1																																																																																			G|0.655;A|0.345	0.345	strong		0.622	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
C6orf201	404220	hgsc.bcm.edu	37	6	4087934	4087934	+	Missense_Mutation	SNP	G	G	C	rs619483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:4087934G>C	ENST00000380175.4	+	2	824	c.59G>C	c.(58-60)cGc>cCc	p.R20P	C6orf201_ENST00000360378.6_3'UTR|C6orf201_ENST00000333388.5_Intron|FAM217A_ENST00000380188.2_5'Flank|C6orf201_ENST00000430835.2_Missense_Mutation_p.R20P	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	20			R -> P (in dbSNP:rs619483). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				CTTTATTCCCGCAAGAGTGAA	0.478													A|||	1348	0.269169	0.3427	0.2896	5008	,	,		16422	0.3591		0.1938	False		,,,				2504	0.1401				p.R20P		Atlas-SNP	.											.	C6orf201	17	.	0			c.G59C						PASS	.	A	PRO/ARG	1246,2576		195,856,860	179.0	191.0	187.0		59	0.2	0.0	6	dbSNP_83	187	1439,6843		128,1183,2830	yes	missense	C6orf201	NM_001085401.1	103	323,2039,3690	CC,CG,GG		17.375,32.6007,22.1827	benign	20/141	4087934	2685,9419	1911	4141	6052	SO:0001583	missense	404220	exon2			ATTCCCGCAAGAG	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.59G>C	6.37:g.4087934G>C	ENSP00000420610:p.Arg20Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001085401	A6NLI6|Q6NXN5	Missense_Mutation	SNP	ENST00000380175.4	37	CCDS43419.1	657	0.3008241758241758	194	0.3943089430894309	97	0.26795580110497236	215	0.3758741258741259	151	0.19920844327176782	A	10.38	1.335190	0.24253	0.326007	0.17375	ENSG00000185689	ENST00000541127;ENST00000380175;ENST00000451679;ENST00000436110;ENST00000430835	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	4.28	0.147	0.14838	.	0.842845	0.09961	N	0.733497	T	0.02649	0.0080	N	0.08118	0	0.80722	P	0.0	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.42310	-0.9459	9	0.48119	T	0.1	.	2.5131	0.04661	0.4552:0.0:0.204:0.3408	rs619483;rs52815722;rs619483	20;20	B4DXB2;Q7Z4U5	.;CF201_HUMAN	P	20	ENSP00000420610:R20P;ENSP00000420763:R20P;ENSP00000417981:R20P;ENSP00000396912:R20P	ENSP00000420610:R20P	R	+	2	0	C6orf201	4032933	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.090000	0.15025	-0.010000	0.14271	-0.360000	0.07572	CGC	G|0.746;C|0.254	0.254	strong		0.478	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	
C8orf44	56260	hgsc.bcm.edu	37	8	67592152	67592152	+	Missense_Mutation	SNP	T	T	C	rs1057463	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:67592152T>C	ENST00000519561.1	+	3	594	c.443T>C	c.(442-444)tTc>tCc	p.F148S	C8orf44-SGK3_ENST00000519289.1_5'UTR|C8orf44_ENST00000518860.1_3'UTR|C8orf44_ENST00000390159.3_Missense_Mutation_p.F148S|C8orf44-SGK3_ENST00000520044.1_3'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	61	0	0		WXS	Illumina HiSeq	Phase_I	73	45	0.616438	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	
C3orf20	84077	hgsc.bcm.edu	37	3	14755617	14755617	+	Missense_Mutation	SNP	C	C	G	rs6790129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:14755617C>G	ENST00000253697.3	+	8	1716	c.1264C>G	c.(1264-1266)Cta>Gta	p.L422V	C3orf20_ENST00000412910.1_Missense_Mutation_p.L300V|C3orf20_ENST00000495387.1_3'UTR|C3orf20_ENST00000435614.1_Missense_Mutation_p.L300V	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	153	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	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	
OPLAH	26873	hgsc.bcm.edu	37	8	145112983	145112983	+	Missense_Mutation	SNP	C	C	T	rs55916375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145112983C>T	ENST00000426825.1	-	8	1099	c.1018G>A	c.(1018-1020)Gtc>Atc	p.V340I	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	340					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGGAGGGTGACGCCAGCTGTG	0.662													C|||	167	0.0333466	0.0174	0.0461	5008	,	,		16267	0.001		0.0835	False		,,,				2504	0.0276				p.V340I		Atlas-SNP	.											.	OPLAH	78	.	0			c.G1018A						PASS	.	C	ILE/VAL	107,4003		0,107,1948	41.0	49.0	46.0		1018	0.4	0.5	8	dbSNP_129	46	562,7804		15,532,3636	yes	missense	OPLAH	NM_017570.3	29	15,639,5584	TT,TC,CC		6.7177,2.6034,5.3623	benign	340/1289	145112983	669,11807	2055	4183	6238	SO:0001583	missense	26873	exon8			GGGTGACGCCAGC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1018G>A	8.37:g.145112983C>T	ENSP00000475943:p.Val340Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	92	55	0.597826	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		94	0.04304029304029304	12	0.024390243902439025	19	0.052486187845303865	1	0.0017482517482517483	62	0.08179419525065963	C	1.905	-0.452126	0.04540	0.026034	0.067177	ENSG00000178814	ENST00000426825	.	.	.	4.7	0.388	0.16264	.	0.121832	0.52532	D	0.000064	T	0.01353	0.0044	.	.	.	0.36301	D	0.857047	B;B	0.29766	0.143;0.256	B;B	0.29598	0.104;0.096	T	0.13602	-1.0503	7	0.15952	T	0.53	.	7.5772	0.27944	0.0:0.5138:0.0:0.4862	rs55916375	340;340	A7E261;O14841	.;OPLA_HUMAN	I	340	.	ENSP00000412071:V340I	V	-	1	0	OPLAH	145184971	0.005000	0.15991	0.508000	0.27688	0.050000	0.14768	0.061000	0.14366	0.291000	0.22468	-0.444000	0.05651	GTC	C|0.947;T|0.053	0.053	strong		0.662	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
CWC27	10283	hgsc.bcm.edu	37	5	64097145	64097145	+	Missense_Mutation	SNP	C	C	G	rs7735338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:64097145C>G	ENST00000381070.3	+	9	983	c.766C>G	c.(766-768)Cca>Gca	p.P256A	CWC27_ENST00000508024.1_Missense_Mutation_p.P256A	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	256			P -> A (in dbSNP:rs7735338). {ECO:0000269|PubMed:9610721}.		mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						AGGTGATGCACCAGATTTAGT	0.219													G|||	2068	0.412939	0.5023	0.2161	5008	,	,		14340	0.5069		0.341	False		,,,				2504	0.409				p.P256A		Atlas-SNP	.											.	CWC27	47	.	0			c.C766G						PASS	.	G	ALA/PRO	1832,2476		420,992,742	22.0	24.0	23.0		766	0.3	0.0	5	dbSNP_116	23	2614,5830		451,1712,2059	yes	missense	CWC27	NM_005869.2	27	871,2704,2801	GG,GC,CC		30.9569,42.5255,34.8651	benign	256/473	64097145	4446,8306	2154	4222	6376	SO:0001583	missense	10283	exon9			GATGCACCAGATT	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"""serologically defined colon cancer antigen 10"""	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.766C>G	5.37:g.64097145C>G	ENSP00000370460:p.Pro256Ala	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_005869	O60529|O60530|Q96EM3	Missense_Mutation	SNP	ENST00000381070.3	37	CCDS3982.2	888	0.4065934065934066	252	0.5121951219512195	90	0.24861878453038674	280	0.48951048951048953	266	0.35092348284960423	G	0.003	-2.554159	0.00138	0.425255	0.309569	ENSG00000153015	ENST00000381070;ENST00000508024;ENST00000538793	T;T	0.38401	1.14;1.14	4.77	0.351	0.16042	.	1.357770	0.04661	N	0.408922	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	0.04013	0.0;0.0;0.0;0.001	T	0.44892	-0.9298	9	0.09084	T	0.74	.	0.394	0.00415	0.2246:0.159:0.2921:0.3243	rs7735338;rs52792258;rs7735338	256;256;256;256	Q6UX04-2;Q6UX04;F5H636;D6REK3	.;CWC27_HUMAN;.;.	A	256	ENSP00000370460:P256A;ENSP00000426802:P256A	ENSP00000370460:P256A	P	+	1	0	CWC27	64132901	0.995000	0.38212	0.032000	0.17829	0.000000	0.00434	0.229000	0.17833	-0.290000	0.09025	-1.721000	0.00707	CCA	C|0.646;G|0.354	0.354	strong		0.219	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
LPAR1	1902	hgsc.bcm.edu	37	9	113637854	113637854	+	Silent	SNP	G	G	A	rs3739709	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:113637854G>A	ENST00000374431.3	-	5	1325	c.942C>T	c.(940-942)cgC>cgT	p.R314R	LPAR1_ENST00000358883.4_Silent_p.R314R|LPAR1_ENST00000538760.1_Silent_p.R315R|LPAR1_ENST00000374430.2_Silent_p.R314R|LPAR1_ENST00000541779.1_Silent_p.R315R	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	314					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						TTTCTTTGTCGCGGTAGGAGT	0.562													G|||	670	0.133786	0.0113	0.1643	5008	,	,		17668	0.1905		0.1988	False		,,,				2504	0.1524				p.R314R	NSCLC(115;661 2323 9836 34256)	Atlas-SNP	.											LPAR1,NS,carcinoma,-1,2	LPAR1	48	2	0			c.C942T						PASS	.	G	,	198,4208	124.1+/-161.4	5,188,2010	169.0	166.0	167.0		942,942	-9.9	0.6	9	dbSNP_107	167	1657,6943	306.2+/-307.8	153,1351,2796	no	coding-synonymous,coding-synonymous	LPAR1	NM_001401.3,NM_057159.2	,	158,1539,4806	AA,AG,GG		19.2674,4.4939,14.2626	,	314/365,314/365	113637854	1855,11151	2203	4300	6503	SO:0001819	synonymous_variant	1902	exon4			TTTGTCGCGGTAG	U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	3166	protein-coding gene	gene with protein product		602282	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"""	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.942C>T	9.37:g.113637854G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	169	80	0.473373	NM_001401	B4DK36|O00656|O00722|P78351	Silent	SNP	ENST00000374431.3	37	CCDS6777.1																																																																																			G|0.863;A|0.137	0.137	strong		0.562	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159	
FLG	2312	hgsc.bcm.edu	37	1	152276699	152276699	+	Missense_Mutation	SNP	A	A	G	rs12728605		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276699A>G	ENST00000368799.1	-	3	10698	c.10663T>C	c.(10663-10665)Tgg>Cgg	p.W3555R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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	384	0	0		WXS	Illumina HiSeq	Phase_I	300	68	0.226667	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	
SLC25A27	9481	hgsc.bcm.edu	37	6	46632594	46632594	+	Missense_Mutation	SNP	T	T	C	rs35884480	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:46632594T>C	ENST00000371347.5	+	5	842	c.590T>C	c.(589-591)aTa>aCa	p.I197T	SLC25A27_ENST00000411689.2_Missense_Mutation_p.I197T|SLC25A27_ENST00000604908.1_Intron|SLC25A27_ENST00000452689.2_Missense_Mutation_p.I111T	NM_001204051.1|NM_004277.4	NP_001190980.1|NP_004268.3	O95847	UCP4_HUMAN	solute carrier family 25, member 27	197			I -> T (in dbSNP:rs35884480).		cellular triglyceride homeostasis (GO:0035356)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|negative regulation of mitochondrial membrane potential (GO:0010917)|neuron death (GO:0070997)|positive regulation of cell proliferation (GO:0008284)|regulation of glucose import (GO:0046324)|transport (GO:0006810)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)				central_nervous_system(1)|kidney(1)|lung(4)|prostate(1)|urinary_tract(1)	8			Lung(136;0.192)			GTACCCAATATACAAAGAGCA	0.378													T|||	147	0.029353	0.0038	0.036	5008	,	,		13909	0.0		0.0577	False		,,,				2504	0.0603				p.I197T		Atlas-SNP	.											.	SLC25A27	22	.	0			c.T590C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE	40,3668		1,38,1815	86.0	84.0	84.0		590,590,590	5.1	1.0	6	dbSNP_126	84	522,7670		24,474,3598	yes	missense,missense,missense	SLC25A27	NM_001204051.1,NM_001204052.1,NM_004277.4	89,89,89	25,512,5413	CC,CT,TT		6.3721,1.0787,4.7227	benign,benign,benign	197/301,197/246,197/324	46632594	562,11338	1854	4096	5950	SO:0001583	missense	9481	exon5			CCAATATACAAAG	AK090871	CCDS43470.1, CCDS56431.1	6p12.3	2013-05-22			ENSG00000153291	ENSG00000153291		"""Solute carriers"""	21065	protein-coding gene	gene with protein product		613725				10025957, 10772343	Standard	NM_004277		Approved	UCP4, FLJ33552	uc003oyh.3	O95847	OTTHUMG00000014786	ENST00000371347.5:c.590T>C	6.37:g.46632594T>C	ENSP00000360398:p.Ile197Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	84	29	0.345238	NM_001204051	F5GWR4|Q5VTS9|Q8N518	Missense_Mutation	SNP	ENST00000371347.5	37	CCDS43470.1	69	0.03159340659340659	3	0.006097560975609756	18	0.049723756906077346	0	0.0	48	0.0633245382585752	T	13.48	2.250203	0.39797	0.010787	0.063721	ENSG00000153291	ENST00000371347;ENST00000411689;ENST00000355073;ENST00000452689;ENST00000425120	T;T;T	0.80738	-1.41;-1.41;-1.41	5.13	5.13	0.70059	Mitochondrial carrier domain (2);	0.229133	0.33916	N	0.004432	T	0.56891	0.2016	N	0.25201	0.72	0.37212	D	0.904839	B;B;B;B	0.21071	0.028;0.051;0.051;0.01	B;B;B;B	0.25405	0.042;0.06;0.06;0.015	T	0.58120	-0.7692	10	0.35671	T	0.21	-12.6418	12.9054	0.58149	0.0:0.0:0.0:1.0	rs35884480;rs62401180	111;197;197;197	B4DZG4;Q5VTS9;O95847;F5GWR4	.;.;UCP4_HUMAN;.	T	197;197;41;111;127	ENSP00000360398:I197T;ENSP00000412024:I197T;ENSP00000412223:I111T	ENSP00000347185:I41T	I	+	2	0	SLC25A27	46740553	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	5.876000	0.69667	1.929000	0.55896	0.533000	0.62120	ATA	T|0.951;C|0.049	0.049	strong		0.378	SLC25A27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040791.1	NM_004277	
AKAP12	9590	hgsc.bcm.edu	37	6	151674593	151674593	+	Missense_Mutation	SNP	G	G	T	rs3734795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151674593G>T	ENST00000253332.1	+	3	5256	c.5067G>T	c.(5065-5067)gaG>gaT	p.E1689D	AKAP12_ENST00000354675.6_Missense_Mutation_p.E1591D|AKAP12_ENST00000359755.5_Missense_Mutation_p.E1584D|AKAP12_ENST00000402676.2_Missense_Mutation_p.E1689D			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1689			E -> D (in dbSNP:rs3734795).		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)		AAAGAATAGAGAAGTCACTAG	0.483													G|||	753	0.150359	0.3502	0.1427	5008	,	,		22657	0.1379		0.0219	False		,,,				2504	0.0307				p.E1689D	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G5067T						PASS	.	G	ASP/GLU,ASP/GLU	1224,3182	422.5+/-339.8	169,886,1148	77.0	67.0	70.0		5067,4773	0.4	0.2	6	dbSNP_107	70	195,8405	85.6+/-148.0	3,189,4108	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	45,45	172,1075,5256	TT,TG,GG		2.2674,27.7803,10.9103	benign,benign	1689/1783,1591/1685	151674593	1419,11587	2203	4300	6503	SO:0001583	missense	9590	exon4			AATAGAGAAGTCA	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.5067G>T	6.37:g.151674593G>T	ENSP00000253332:p.Glu1689Asp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	305	0.13965201465201466	164	0.3333333333333333	43	0.11878453038674033	80	0.13986013986013987	18	0.023746701846965697	G	11.25	1.583112	0.28268	0.277803	0.022674	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07021	3.23;3.23;3.24;3.24	5.06	0.385	0.16249	.	0.235141	0.21940	N	0.066896	T	0.01254	0.0041	N	0.17082	0.46	0.80722	P	0.0	B;B;B	0.14805	0.011;0.011;0.006	B;B;B	0.14578	0.011;0.011;0.005	T	0.46219	-0.9207	9	0.37606	T	0.19	.	2.9113	0.05738	0.1485:0.2151:0.4774:0.159	rs3734795;rs52836225;rs57700368;rs3734795	1584;1591;1689	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	D	1689;1689;1591;1584	ENSP00000384537:E1689D;ENSP00000253332:E1689D;ENSP00000346702:E1591D;ENSP00000352794:E1584D	ENSP00000253332:E1689D	E	+	3	2	AKAP12	151716286	0.000000	0.05858	0.152000	0.22495	0.175000	0.22909	0.071000	0.14594	0.240000	0.21263	0.555000	0.69702	GAG	G|0.873;T|0.127	0.127	strong		0.483	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
G6PC2	57818	hgsc.bcm.edu	37	2	169764176	169764176	+	Missense_Mutation	SNP	G	G	C	rs492594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:169764176G>C	ENST00000375363.3	+	5	747	c.655G>C	c.(655-657)Gtt>Ctt	p.V219L	G6PC2_ENST00000429379.2_3'UTR|SPC25_ENST00000472216.2_Intron|G6PC2_ENST00000461586.1_3'UTR|G6PC2_ENST00000421979.1_3'UTR	NM_021176.2	NP_066999.1	Q9NQR9	G6PC2_HUMAN	glucose-6-phosphatase, catalytic, 2	219			V -> L (in dbSNP:rs492594).		carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)	p.V219L(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	13						CCTGTTTGCAGTTGGCTTTTA	0.527													C|||	2321	0.463458	0.3101	0.5634	5008	,	,		21028	0.4335		0.4443	False		,,,				2504	0.6503				p.V219L		Atlas-SNP	.											G6PC2,NS,carcinoma,0,1	G6PC2	44	1	1	Substitution - Missense(1)	stomach(1)	c.G655C						PASS	.	C	,LEU/VAL	1416,2990	685.6+/-404.6	221,974,1008	216.0	171.0	186.0		,655	3.1	0.9	2	dbSNP_83	186	3923,4677	605.1+/-394.9	899,2125,1276	yes	utr-3,missense	G6PC2	NM_001081686.1,NM_021176.2	,32	1120,3099,2284	CC,CG,GG		45.6163,32.138,41.0503	,benign	,219/356	169764176	5339,7667	2203	4300	6503	SO:0001583	missense	57818	exon5			TTTGCAGTTGGCT	AF283575	CCDS2230.1, CCDS46443.1	2q24-q31	2008-02-05			ENSG00000152254	ENSG00000152254			28906	protein-coding gene	gene with protein product	"""islet specific glucose 6 phosphatase catalytic subunit related protein"""	608058				10078553, 10078554	Standard	NM_021176		Approved	IGRP	uc002uem.3	Q9NQR9	OTTHUMG00000132182	ENST00000375363.3:c.655G>C	2.37:g.169764176G>C	ENSP00000364512:p.Val219Leu	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	375	179	0.477333	NM_021176	E9PAX2|Q6AHZ0	Missense_Mutation	SNP	ENST00000375363.3	37	CCDS2230.1	958	0.43864468864468864	166	0.33739837398373984	204	0.56353591160221	249	0.4353146853146853	339	0.4472295514511873	C	2.235	-0.375122	0.05034	0.32138	0.456163	ENSG00000152254	ENST00000375363	T	0.74315	-0.83	5.86	3.06	0.35304	.	0.500214	0.19206	N	0.120047	T	0.00012	0.0000	N	0.01656	-0.775	0.09310	P	0.9999999999999954	B	0.02656	0.0	B	0.01281	0.0	T	0.43814	-0.9368	9	0.02654	T	1	-19.5491	5.6207	0.17455	0.1171:0.6455:0.1129:0.1245	rs492594;rs3732032;rs52825832;rs492594	219	Q9NQR9	G6PC2_HUMAN	L	219	ENSP00000364512:V219L	ENSP00000364512:V219L	V	+	1	0	G6PC2	169472422	0.973000	0.33851	0.882000	0.34594	0.655000	0.38815	2.141000	0.42168	0.398000	0.25338	-0.824000	0.03097	GTT	G|0.584;C|0.416	0.416	strong		0.527	G6PC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255234.2	NM_021176	
ROM1	6094	hgsc.bcm.edu	37	11	62381808	62381808	+	Silent	SNP	G	G	C	rs1801144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:62381808G>C	ENST00000278833.3	+	2	1210	c.669G>C	c.(667-669)cgG>cgC	p.R223R	EML3_ENST00000494176.2_5'Flank|ROM1_ENST00000534093.1_Missense_Mutation_p.G14A|EML3_ENST00000278845.4_5'Flank|EML3_ENST00000394773.2_5'Flank|EML3_ENST00000529309.1_5'Flank	NM_000327.3	NP_000318	Q03395	ROM1_HUMAN	retinal outer segment membrane protein 1	223					camera-type eye photoreceptor cell differentiation (GO:0060219)|cell adhesion (GO:0007155)|regulation of gene expression (GO:0010468)|retina vasculature development in camera-type eye (GO:0061298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	8						ACTCACCCCGGCCTTGCCTGC	0.597													G|||	863	0.172324	0.1203	0.1988	5008	,	,		17343	0.0427		0.3161	False		,,,				2504	0.2096				p.R223R		Atlas-SNP	.											ROM1,rectum,carcinoma,0,1	ROM1	32	1	0			c.G669C						scavenged	.	G		689,3715	287.8+/-279.5	51,587,1564	130.0	125.0	127.0		669	1.5	1.0	11	dbSNP_89	127	3096,5502	473.0+/-368.5	562,1972,1765	no	coding-synonymous	ROM1	NM_000327.3		613,2559,3329	CC,CG,GG		36.0084,15.6449,29.1109		223/352	62381808	3785,9217	2202	4299	6501	SO:0001819	synonymous_variant	6094	exon2			ACCCCGGCCTTGC	L07894	CCDS8024.1	11q13	2013-02-14				ENSG00000149489		"""Tetraspanins"""	10254	protein-coding gene	gene with protein product		180721				8504299	Standard	NM_000327		Approved	TSPAN23, ROM	uc001ntv.3	Q03395		ENST00000278833.3:c.669G>C	11.37:g.62381808G>C		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	122	45	0.368852	NM_000327	B2R978	Silent	SNP	ENST00000278833.3	37	CCDS8024.1	419	0.19184981684981686	69	0.1402439024390244	85	0.23480662983425415	28	0.04895104895104895	237	0.31266490765171506	G	11.13	1.548416	0.27652	0.156449	0.360084	ENSG00000149489	ENST00000525801;ENST00000534093;ENST00000525947	.	.	.	5.38	1.46	0.22682	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.29058	-1.0024	4	0.87932	D	0	-15.2781	8.048	0.30562	0.3405:0.0:0.6595:0.0	rs1801144;rs17845151;rs17857955;rs61654907;rs1801144	.	.	.	A	14	.	ENSP00000433566:G14A	G	+	2	0	ROM1	62138384	0.997000	0.39634	1.000000	0.80357	0.939000	0.58152	0.287000	0.18920	0.266000	0.21894	0.462000	0.41574	GGC	G|0.727;C|0.273	0.273	strong		0.597	ROM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394929.1	NM_000327	
CDON	50937	hgsc.bcm.edu	37	11	125889526	125889526	+	Missense_Mutation	SNP	C	C	T	rs3740909	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	125	1	0.008		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	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	
MCM3AP	8888	hgsc.bcm.edu	37	21	47704896	47704896	+	Missense_Mutation	SNP	G	G	A	rs9975588	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47704896G>A	ENST00000397708.1	-	2	559	c.305C>T	c.(304-306)tCa>tTa	p.S102L	YBEY_ENST00000397701.4_5'Flank|YBEY_ENST00000329319.3_5'Flank|MCM3AP_ENST00000291688.1_Missense_Mutation_p.S102L|YBEY_ENST00000397692.1_5'Flank|YBEY_ENST00000339195.6_5'Flank|YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000397694.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	102	FG-repeats.		S -> L (in dbSNP:rs9975588). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CAGCACAGATGAACTTGAAGG	0.473													G|||	1245	0.248602	0.1982	0.232	5008	,	,		18278	0.1488		0.4085	False		,,,				2504	0.2669				p.S102L		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C305T	GRCh37	CM065300	MCM3AP	M	rs9975588	PASS	.	G	LEU/SER	940,3466	357.1+/-313.8	91,758,1354	75.0	74.0	75.0		305	4.6	1.0	21	dbSNP_119	75	3371,5229	500.2+/-375.2	664,2043,1593	yes	missense	MCM3AP	NM_003906.3	145	755,2801,2947	AA,AG,GG		39.1977,21.3345,33.1462	probably-damaging	102/1981	47704896	4311,8695	2203	4300	6503	SO:0001583	missense	8888	exon1			ACAGATGAACTTG	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.305C>T	21.37:g.47704896G>A	ENSP00000380820:p.Ser102Leu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	578	0.26465201465201466	102	0.2073170731707317	101	0.27900552486187846	72	0.1258741258741259	303	0.3997361477572559	G	18.71	3.682683	0.68157	0.213345	0.391977	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.19250	2.16;2.16	5.47	4.59	0.56863	.	0.290888	0.31612	N	0.007357	T	0.00012	0.0000	L	0.29908	0.895	0.33270	P	0.439095	P	0.44816	0.844	B	0.39904	0.313	T	0.47799	-0.9089	9	0.66056	D	0.02	-13.7559	12.4261	0.55548	0.0815:0.0:0.9185:0.0	rs9975588;rs17176138;rs52809897;rs60025591;rs9975588	102	O60318	MCM3A_HUMAN	L	102	ENSP00000380820:S102L;ENSP00000291688:S102L	ENSP00000291688:S102L	S	-	2	0	MCM3AP	46529324	0.887000	0.30362	0.992000	0.48379	0.974000	0.67602	4.224000	0.58593	2.561000	0.86390	0.561000	0.74099	TCA	G|0.707;A|0.293	0.293	strong		0.473	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
PPEF2	5470	hgsc.bcm.edu	37	4	76811175	76811175	+	Missense_Mutation	SNP	G	G	T	rs28436183	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	229	0	0		WXS	Illumina HiSeq	Phase_I	228	101	0.442982	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	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350374	65350374	+	Silent	SNP	A	A	G	rs36303	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:65350374A>G	ENST00000284037.5	+	21	3617	c.3228A>G	c.(3226-3228)cgA>cgG	p.R1076R	ERBB2IP_ENST00000511297.1_Silent_p.R1072R|ERBB2IP_ENST00000380943.2_Silent_p.R1076R|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000506030.1_Silent_p.R1076R|ERBB2IP_ENST00000380939.2_Silent_p.R1076R|ERBB2IP_ENST00000380935.1_Silent_p.R1076R|ERBB2IP_ENST00000380936.1_Silent_p.R1076R|ERBB2IP_ENST00000508515.1_Silent_p.R1076R|ERBB2IP_ENST00000380938.2_Silent_p.R1076R	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1076					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		CAATCCAGCGACAAAGTAGTG	0.473													A|||	1050	0.209665	0.09	0.2968	5008	,	,		19190	0.4623		0.1203	False		,,,				2504	0.1411				p.R1076R		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.A3228G						PASS	.	A	,	418,3988	205.2+/-227.1	11,396,1796	128.0	123.0	125.0		3228,3228	0.3	1.0	5	dbSNP_76	125	1191,7409	241.0+/-271.5	84,1023,3193	no	coding-synonymous,coding-synonymous	ERBB2IP	NM_001006600.1,NM_018695.2	,	95,1419,4989	GG,GA,AA		13.8488,9.4871,12.3712	,	1076/1303,1076/1372	65350374	1609,11397	2203	4300	6503	SO:0001819	synonymous_variant	55914	exon21			CCAGCGACAAAGT		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.3228A>G	5.37:g.65350374A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	37	CCDS58953.1																																																																																			A|0.830;G|0.170	0.170	strong		0.473	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
TMEM127	55654	hgsc.bcm.edu	37	2	96919642	96919642	+	Silent	SNP	C	C	T	rs3852673	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:96919642C>T	ENST00000258439.3	-	4	877	c.621G>A	c.(619-621)gcG>gcA	p.A207A	TMEM127_ENST00000435268.1_Silent_p.A123A|TMEM127_ENST00000432959.1_Silent_p.A207A	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	155	0	0		WXS	Illumina HiSeq	Phase_I	154	77	0.5	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	
CEP72	55722	hgsc.bcm.edu	37	5	639231	639231	+	Missense_Mutation	SNP	C	C	A	rs12522955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:639231C>A	ENST00000264935.5	+	8	1324	c.1234C>A	c.(1234-1236)Ccc>Acc	p.P412T	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	412			P -> T (in dbSNP:rs12522955).		G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CTCGGCTCTACCCGGGAAGAA	0.647													C|||	453	0.0904553	0.0045	0.1138	5008	,	,		17828	0.0099		0.1928	False		,,,				2504	0.1677				p.P412T		Atlas-SNP	.											.	CEP72	53	.	0			c.C1234A						PASS	.	C	THR/PRO	169,4237	106.5+/-144.9	0,169,2034	37.0	42.0	40.0		1234	3.6	0.0	5	dbSNP_120	40	1709,6891	299.8+/-304.6	175,1359,2766	yes	missense	CEP72	NM_018140.3	38	175,1528,4800	AA,AC,CC		19.8721,3.8357,14.4395	probably-damaging	412/648	639231	1878,11128	2203	4300	6503	SO:0001583	missense	55722	exon8			GCTCTACCCGGGA	BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.1234C>A	5.37:g.639231C>A	ENSP00000264935:p.Pro412Thr	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	185	103	0.556757	NM_018140	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	210	0.09615384615384616	2	0.0040650406504065045	50	0.13812154696132597	5	0.008741258741258742	153	0.20184696569920843	C	10.31	1.314332	0.23908	0.038357	0.198721	ENSG00000112877	ENST00000264935	T	0.32753	1.44	4.45	3.58	0.41010	.	0.286634	0.29266	N	0.012641	T	0.00039	0.0001	M	0.65975	2.015	0.44694	P	0.0023140000000000382	D	0.60160	0.987	P	0.54544	0.755	T	0.16129	-1.0413	9	0.08599	T	0.76	-10.98	8.9781	0.35948	0.0:0.8928:0.0:0.1072	rs12522955;rs12522955	412	Q9P209	CEP72_HUMAN	T	412	ENSP00000264935:P412T	ENSP00000264935:P412T	P	+	1	0	CEP72	692231	0.003000	0.15002	0.007000	0.13788	0.003000	0.03518	1.019000	0.30014	1.171000	0.42768	0.462000	0.41574	CCC	C|0.877;A|0.123	0.123	strong		0.647	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140	
ABCB5	340273	hgsc.bcm.edu	37	7	20768077	20768077	+	Splice_Site	SNP	A	A	T	rs117497357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20768077A>T	ENST00000404938.2	+	23	3518	c.2866A>T	c.(2866-2868)Ata>Tta	p.I956L	ABCB5_ENST00000258738.6_Splice_Site_p.I511L	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	956	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						GGGCATGTTCATGTAAGTCGT	0.483													a|||	70	0.0139776	0.0023	0.0259	5008	,	,		17795	0.001		0.0378	False		,,,				2504	0.0102				p.I956L		Atlas-SNP	.											.	ABCB5	357	.	0			c.A2866T						PASS	.	G	LEU/ILE,LEU/ILE	40,4366	44.6+/-78.6	1,38,2164	74.0	71.0	72.0		2866,1531	-1.1	0.8	7	dbSNP_132	72	397,8203	126.3+/-184.8	12,373,3915	yes	missense-near-splice,missense-near-splice	ABCB5	NM_001163941.1,NM_178559.5	5,5	13,411,6079	TT,TA,AA		4.6163,0.9079,3.36	benign,benign	956/1258,511/813	20768077	437,12569	2203	4300	6503	SO:0001630	splice_region_variant	340273	exon23			ATGTTCATGTAAG	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.2867+1A>T	7.37:g.20768077A>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	47	0.02152014652014652	1	0.0020325203252032522	9	0.024861878453038673	1	0.0017482517482517483	36	0.047493403693931395	a	1.008	-0.688653	0.03328	0.009079	0.046163	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.88975	-2.45;-2.45	3.91	-1.13	0.09775	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.909681	0.09236	N	0.829960	T	0.21881	0.0527	N	0.00746	-1.225	0.21105	N	0.999783	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.50750	-0.8791	10	0.02654	T	1	.	5.7593	0.18190	0.3169:0.1826:0.5004:0.0	.	956;511	A7BKA4;Q2M3G0	.;ABCB5_HUMAN	L	956;511	ENSP00000384881:I956L;ENSP00000258738:I511L	ENSP00000258738:I511L	I	+	1	0	ABCB5	20734602	0.211000	0.23529	0.789000	0.31954	0.678000	0.39670	-0.287000	0.08388	-0.196000	0.10366	-0.253000	0.11424	ATA	A|0.970;T|0.030	0.030	strong		0.483	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	Missense_Mutation
TTN	7273	hgsc.bcm.edu	37	2	179457147	179457147	+	Missense_Mutation	SNP	G	G	A	rs16866406	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179457147G>A	ENST00000591111.1	-	251	54886	c.54662C>T	c.(54661-54663)cCa>cTa	p.P18221L	TTN_ENST00000589042.1_Missense_Mutation_p.P19862L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P10922L|TTN_ENST00000460472.2_Missense_Mutation_p.P10797L|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P10989L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P17294L|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18221	Ig-like 105.		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)			TGAACCAGCTGGATTCTCCAC	0.333													G|||	1067	0.213059	0.0666	0.1527	5008	,	,		19552	0.4573		0.1392	False		,,,				2504	0.2781				p.P19862L		Atlas-SNP	.											.	TTN	18412	.	0			c.C59585T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	283,3415		10,263,1576	153.0	147.0	149.0		32966,32765,51881,32390	5.2	1.0	2	dbSNP_123	149	1205,6973		91,1023,2975	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	98,98,98,98	101,1286,4551	AA,AG,GG		14.7347,7.6528,12.5295	benign,benign,benign,benign	10989/27119,10922/27052,17294/33424,10797/26927	179457147	1488,10388	1849	4089	5938	SO:0001583	missense	7273	exon301			CCAGCTGGATTCT	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.54662C>T	2.37:g.179457147G>A	ENSP00000465570:p.Pro18221Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	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		425	0.1945970695970696	30	0.06097560975609756	46	0.1270718232044199	244	0.42657342657342656	105	0.13852242744063326	G	11.43	1.636872	0.29157	0.076528	0.147347	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	6.03	5.16	0.70880	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	0.00012	0.0000	L	0.55213	1.73	0.21878	P	0.999490043	B;B;B;B	0.13594	0.008;0.008;0.008;0.008	B;B;B;B	0.20767	0.031;0.031;0.031;0.031	T	0.28839	-1.0031	8	0.87932	D	0	.	12.5317	0.56120	0.1336:0.0:0.8664:0.0	rs16866406;rs52804325;rs16866406	10797;10922;10989;18221	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	17294;10797;10989;10922;10795	ENSP00000343764:P17294L;ENSP00000434586:P10797L;ENSP00000340554:P10989L;ENSP00000352154:P10922L	ENSP00000340554:P10989L	P	-	2	0	TTN	179165393	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.667000	0.61561	1.568000	0.49683	0.557000	0.71058	CCA	G|0.808;A|0.191	0.191	strong		0.333	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LPA	4018	hgsc.bcm.edu	37	6	161007496	161007496	+	Missense_Mutation	SNP	G	G	C	rs7765781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	90	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	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	
GRK7	131890	hgsc.bcm.edu	37	3	141535558	141535558	+	Missense_Mutation	SNP	A	A	G	rs36009541	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:141535558A>G	ENST00000264952.2	+	4	1465	c.1328A>G	c.(1327-1329)gAa>gGa	p.E443G		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	443	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> G (in dbSNP:rs36009541). {ECO:0000269|PubMed:17344846}.		protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CTTCACAGAGAAAAGTCTGAT	0.403													A|||	281	0.0561102	0.0522	0.0663	5008	,	,		17513	0.0139		0.1054	False		,,,				2504	0.047				p.E443G		Atlas-SNP	.											.	GRK7	65	.	0			c.A1328G						PASS	.	A	GLY/GLU	286,4120	140.4+/-175.9	10,266,1927	61.0	63.0	62.0		1328	5.4	1.0	3	dbSNP_126	62	1083,7517	200.9+/-244.5	66,951,3283	yes	missense	GRK7	NM_139209.2	98	76,1217,5210	GG,GA,AA		12.593,6.4911,10.5259	benign	443/554	141535558	1369,11637	2203	4300	6503	SO:0001583	missense	131890	exon4			ACAGAGAAAAGTC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.1328A>G	3.37:g.141535558A>G	ENSP00000264952:p.Glu443Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	155	0.07097069597069597	32	0.06504065040650407	33	0.09116022099447514	5	0.008741258741258742	85	0.11213720316622691	A	5.489	0.275185	0.10403	0.064911	0.12593	ENSG00000114124	ENST00000264952	T	0.69806	-0.43	5.4	5.4	0.78164	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.347524	0.29205	N	0.012835	T	0.00384	0.0012	N	0.04297	-0.235	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.12811	-1.0533	9	0.02654	T	1	-8.9791	5.9235	0.19096	0.7242:0.1522:0.1236:0.0	rs36009541	443	Q8WTQ7	GRK7_HUMAN	G	443	ENSP00000264952:E443G	ENSP00000264952:E443G	E	+	2	0	GRK7	143018248	0.006000	0.16342	0.997000	0.53966	0.946000	0.59487	0.459000	0.21908	2.052000	0.61016	0.383000	0.25322	GAA	A|0.903;G|0.097	0.097	strong		0.403	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
ACTN4	81	hgsc.bcm.edu	37	19	39196745	39196745	+	Silent	SNP	C	C	T	rs3745859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39196745C>T	ENST00000252699.2	+	5	622	c.546C>T	c.(544-546)aaC>aaT	p.N182N	ACTN4_ENST00000390009.3_Intron|ACTN4_ENST00000424234.2_Intron	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	182	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Polyphosphoinositide (PIP2)-binding. {ECO:0000255}.				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)			CGTATAAGAACGTCAATGTGC	0.527													C|||	1699	0.339257	0.2322	0.2853	5008	,	,		21014	0.4276		0.4364	False		,,,				2504	0.3313				p.N182N	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.C546T						PASS	.	C		1122,3284	401.9+/-332.2	135,852,1216	120.0	102.0	108.0		546	-0.2	1.0	19	dbSNP_107	108	3981,4619	552.5+/-386.1	925,2131,1244	no	coding-synonymous	ACTN4	NM_004924.4		1060,2983,2460	TT,TC,CC		46.2907,25.4653,39.2357		182/912	39196745	5103,7903	2203	4300	6503	SO:0001819	synonymous_variant	81	exon5			TAAGAACGTCAAT	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.546C>T	19.37:g.39196745C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_004924	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	37	CCDS12518.1																																																																																			C|0.617;T|0.383	0.383	strong		0.527	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
BNIP1	662	hgsc.bcm.edu	37	5	172578595	172578595	+	Intron	SNP	T	T	C	rs180928619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:172578595T>C	ENST00000351486.5	+	3	208				BNIP1_ENST00000352523.6_Silent_p.I68I|BNIP1_ENST00000231668.9_Silent_p.I68I|BNIP1_ENST00000393770.4_Intron	NM_001205.2	NP_001196.2	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 1						apoptotic process (GO:0006915)|autophagy (GO:0006914)|endoplasmic reticulum membrane fusion (GO:0016320)|endoplasmic reticulum organization (GO:0007029)|execution phase of apoptosis (GO:0097194)|negative regulation of apoptotic process (GO:0043066)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	11	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGGCATTTATTTGGACTGCTT	0.368													T|||	2	0.000399361	0.0015	0.0	5008	,	,		16395	0.0		0.0	False		,,,				2504	0.0				p.I68I		Atlas-SNP	.											.	BNIP1	30	.	0			c.T204C						PASS	.						108.0	103.0	105.0					5																	172578595		2203	4300	6503	SO:0001627	intron_variant	662	exon3			ATTTATTTGGACT	AF083957	CCDS4384.1, CCDS4385.1, CCDS4386.1, CCDS43400.1	5q33-q34	2008-02-05	2002-08-29		ENSG00000113734	ENSG00000113734			1082	protein-coding gene	gene with protein product		603291	"""BCL2/adenovirus E1B 19kD-interacting protein 1"""			7954800, 15272311	Standard	NM_013979		Approved	Nip1, SEC20	uc003mcj.4	Q12981	OTTHUMG00000130521	ENST00000351486.5:c.178-2730T>C	5.37:g.172578595T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	121	55	0.454545	NM_013979	D3DQM3|D3DQM4|D3DQM5|D3DQM6|O75622|O75623|O75624|Q6K044|Q96FG4	Silent	SNP	ENST00000351486.5	37	CCDS4384.1																																																																																			T|0.999;C|0.001	0.001	strong		0.368	BNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252939.1	NM_013979	
GOLGA6C	653641	hgsc.bcm.edu	37	15	75562493	75562493	+	Missense_Mutation	SNP	C	C	A	rs201864661		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:75562493C>A	ENST00000300576.5	+	18	2035	c.2035C>A	c.(2035-2037)Ccg>Acg	p.P679T	RN7SL489P_ENST00000486185.2_RNA	NM_001164404.1	NP_001157876.1	A6NDK9	GOG6C_HUMAN	golgin A6 family, member C	679						Golgi apparatus (GO:0005794)				ovary(1)	1						TGACAACCCCCCGGTACAGCA	0.602																																					p.P679T		Atlas-SNP	.											GOLGA6C_ENST00000300576,bladder,carcinoma,-2,3	GOLGA6C	12	3	0			c.C2035A						scavenged	.																																			SO:0001583	missense	653641	exon18			AACCCCCCGGTAC		CCDS58388.1	15q24.2	2014-02-12	2010-02-12		ENSG00000167195	ENSG00000167195			32206	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6C"""				Standard	NM_001164404		Approved		uc002azs.2	A6NDK9	OTTHUMG00000172671	ENST00000300576.5:c.2035C>A	15.37:g.75562493C>A	ENSP00000300576:p.Pro679Thr	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	356	6	0.0168539	NM_001164404		Missense_Mutation	SNP	ENST00000300576.5	37	CCDS58388.1	.	.	.	.	.	.	.	.	.	.	-	0.005	-2.235243	0.00277	.	.	ENSG00000167195	ENST00000300576	T	0.12465	2.68	.	.	.	.	.	.	.	.	T	0.01254	0.0041	N	0.00012	-2.95	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.34179	-0.9839	8	0.02654	T	1	.	4.0506	0.09793	0.6453:0.3546:1.0E-4:0.0	.	679	A6NDK9	GOG6C_HUMAN	T	679	ENSP00000300576:P679T	ENSP00000300576:P679T	P	+	1	0	GOLGA6C	73349546	1.000000	0.71417	0.004000	0.12327	0.004000	0.04260	3.804000	0.55568	-1.404000	0.02050	-1.477000	0.00996	CCG	.	.	weak		0.602	GOLGA6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419797.1	NM_001164404	
ME3	10873	hgsc.bcm.edu	37	11	86267678	86267678	+	Silent	SNP	G	G	A	rs4943943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:86267678G>A	ENST00000393324.3	-	3	637	c.384C>T	c.(382-384)gaC>gaT	p.D128D	RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000359636.2_Silent_p.D128D|ME3_ENST00000323418.6_Silent_p.D66D|ME3_ENST00000543262.1_Silent_p.D128D	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	128					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)				ACTTCTCCACGTCCGAAGTCA	0.547													G|||	744	0.148562	0.0416	0.1974	5008	,	,		19617	0.0496		0.2873	False		,,,				2504	0.2178				p.D128D		Atlas-SNP	.											.	ME3	70	.	0			c.C384T						PASS	.	G	,,	383,4021	194.0+/-219.0	21,341,1840	118.0	94.0	102.0		384,384,384	-4.4	0.6	11	dbSNP_111	102	2692,5906	432.1+/-357.0	414,1864,2021	yes	coding-synonymous,coding-synonymous,coding-synonymous	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	,,	435,2205,3861	AA,AG,GG		31.3096,8.6966,23.6502	,,	128/605,128/605,128/605	86267678	3075,9927	2202	4299	6501	SO:0001819	synonymous_variant	10873	exon4			CTCCACGTCCGAA	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.384C>T	11.37:g.86267678G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_006680	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																			G|0.799;A|0.201	0.201	strong		0.547	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
SPATA6	54558	hgsc.bcm.edu	37	1	48764419	48764419	+	Missense_Mutation	SNP	C	C	T	rs1056042	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:48764419C>T	ENST00000371847.3	-	13	1597	c.1433G>A	c.(1432-1434)tGt>tAt	p.C478Y	SPATA6_ENST00000371843.3_Missense_Mutation_p.C462Y|SPATA6_ENST00000396199.3_Missense_Mutation_p.C406Y	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	478			C -> F (in dbSNP:rs1056042).|C -> S (in dbSNP:rs1056042).|C -> Y (in dbSNP:rs1056042).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)		p.C478Y(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						AGCAGAACTACAGGCCTTTTT	0.423													C|||	1372	0.273962	0.025	0.3329	5008	,	,		16906	0.3492		0.4254	False		,,,				2504	0.3354				p.C478Y		Atlas-SNP	.											SPATA6,NS,carcinoma,0,1	SPATA6	45	1	1	Substitution - Missense(1)	stomach(1)	c.G1433A						PASS	.	C	TYR/CYS	392,4014	195.0+/-219.7	15,362,1826	162.0	159.0	160.0		1433	4.8	1.0	1	dbSNP_86	160	3624,4976	522.3+/-380.1	755,2114,1431	yes	missense	SPATA6	NM_019073.2	194	770,2476,3257	TT,TC,CC		42.1395,8.897,30.8781	probably-damaging	478/489	48764419	4016,8990	2203	4300	6503	SO:0001583	missense	54558	exon13			GAACTACAGGCCT	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"""spermatogenesis-related factor-1"""	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.1433G>A	1.37:g.48764419C>T	ENSP00000360913:p.Cys478Tyr	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	245	107	0.436735	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	682	0.31227106227106227	23	0.046747967479674794	125	0.3453038674033149	205	0.3583916083916084	329	0.4340369393139842	C	19.54	3.846395	0.71603	0.08897	0.421395	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199	T;T;T	0.13089	2.64;2.63;2.62	4.78	4.78	0.61160	.	0.064498	0.64402	D	0.000008	T	0.00012	0.0000	N	0.22421	0.69	0.28859	P	0.895616	D;D	0.69078	0.997;0.997	D;D	0.80764	0.994;0.994	T	0.51872	-0.8650	9	0.41790	T	0.15	.	13.1884	0.59695	0.0:1.0:0.0:0.0	rs1056042;rs3196668;rs52835803;rs56856507;rs1056042	462;478	Q9NWH7-2;Q9NWH7	.;SPAT6_HUMAN	Y	478;462;406	ENSP00000360913:C478Y;ENSP00000360909:C462Y;ENSP00000379502:C406Y	ENSP00000360909:C462Y	C	-	2	0	SPATA6	48537006	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.488000	0.35551	2.474000	0.83562	0.563000	0.77884	TGT	T|0.304;C|0.696	0.304	strong		0.423	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
TEX33	339669	hgsc.bcm.edu	37	22	37387257	37387257	+	Missense_Mutation	SNP	T	T	C	rs9610624	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37387257T>C	ENST00000405091.2	-	7	1057	c.806A>G	c.(805-807)tAt>tGt	p.Y269C	TEX33_ENST00000381821.1_Missense_Mutation_p.Y269C|TEX33_ENST00000402860.3_Missense_Mutation_p.Y184C			O43247	TEX33_HUMAN	testis expressed 33	269																	GTTTTCTCCATATTTCTCTTC	0.438													T|||	585	0.116813	0.1369	0.1801	5008	,	,		21699	0.0813		0.0885	False		,,,				2504	0.1104				p.Y269C		Atlas-SNP	.											.	TEX33	25	.	0			c.A806G						PASS	.	T	CYS/TYR,CYS/TYR	661,3745	281.6+/-276.1	52,557,1594	181.0	174.0	176.0		806,551	0.9	0.1	22	dbSNP_119	176	671,7929	168.4+/-220.0	28,615,3657	yes	missense,missense	C22orf33	NM_001163857.1,NM_178552.3	194,194	80,1172,5251	CC,CT,TT		7.8023,15.0023,10.2414	probably-damaging,probably-damaging	269/281,184/196	37387257	1332,11674	2203	4300	6503	SO:0001583	missense	339669	exon6			TCTCCATATTTCT	BC042635	CCDS13937.1, CCDS54524.1	22q12.3	2013-10-11	2012-02-16	2012-02-16	ENSG00000185264	ENSG00000185264			28568	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 33"""	C22orf33		22332119	Standard	NM_178552		Approved	MGC35206, EAN57	uc003aqf.3	O43247	OTTHUMG00000150531	ENST00000405091.2:c.806A>G	22.37:g.37387257T>C	ENSP00000386118:p.Tyr269Cys	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	252	119	0.472222	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Missense_Mutation	SNP	ENST00000405091.2	37	CCDS54524.1	229|229	0.10485347985347986|0.10485347985347986	68|68	0.13821138211382114|0.13821138211382114	56|56	0.15469613259668508|0.15469613259668508	39|39	0.06818181818181818|0.06818181818181818	66|66	0.0870712401055409|0.0870712401055409	T|T	10.31|10.31	1.315712|1.315712	0.23908|0.23908	0.150023|0.150023	0.078023|0.078023	ENSG00000185264|ENSG00000185264	ENST00000442538|ENST00000402860;ENST00000405091;ENST00000381821	.|.	.|.	.|.	4.43|4.43	0.878|0.878	0.19150|0.19150	.|.	.|1.510860	.|0.04364	.|N	.|0.357914	T|T	0.00210|0.00210	0.0006|0.0006	L|L	0.27053|0.27053	0.805|0.805	0.49798|0.49798	P|P	1.7800000000001148E-4|1.7800000000001148E-4	.|D	.|0.61697	.|0.99	.|P	.|0.50192	.|0.634	T|T	0.08371|0.08371	-1.0725|-1.0725	4|8	.|0.59425	.|D	.|0.04	2.9586|2.9586	8.6414|8.6414	0.33978|0.33978	0.7144:0.0:0.0:0.2856|0.7144:0.0:0.0:0.2856	rs9610624;rs52812150;rs58780254;rs9610624|rs9610624;rs52812150;rs58780254;rs9610624	.|269	.|O43247	.|EAN57_HUMAN	M|C	127|184;269;269	.|.	.|ENSP00000371243:Y269C	I|Y	-|-	3|2	3|0	C22orf33|C22orf33	35717203|35717203	0.022000|0.022000	0.18835|0.18835	0.062000|0.062000	0.19696|0.19696	0.175000|0.175000	0.22909|0.22909	0.127000|0.127000	0.15790|0.15790	-0.141000|-0.141000	0.11374|0.11374	0.460000|0.460000	0.39030|0.39030	ATA|TAT	T|0.899;C|0.101	0.101	strong		0.438	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552	
GRID1	2894	hgsc.bcm.edu	37	10	87489288	87489288	+	Silent	SNP	A	A	G	rs3812646	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:87489288A>G	ENST00000327946.7	-	9	1402	c.1317T>C	c.(1315-1317)ctT>ctC	p.L439L	GRID1_ENST00000536331.1_Silent_p.L10L	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	439					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						TCACCACTTTAAGAGTCAATC	0.512										Multiple Myeloma(13;0.14)			G|||	335	0.066893	0.1573	0.0173	5008	,	,		17298	0.0516		0.0239	False		,,,				2504	0.0399				p.L439L		Atlas-SNP	.											GRID1,NS,carcinoma,-1,1	GRID1	204	1	0			c.T1317C						PASS	.	G		682,3724	762.7+/-413.1	46,590,1567	96.0	93.0	94.0		1317	4.5	1.0	10	dbSNP_107	94	174,8426	811.8+/-407.1	0,174,4126	no	coding-synonymous	GRID1	NM_017551.2		46,764,5693	GG,GA,AA		2.0233,15.4789,6.5816		439/1010	87489288	856,12150	2203	4300	6503	SO:0001819	synonymous_variant	2894	exon9			CACTTTAAGAGTC	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.1317T>C	10.37:g.87489288A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																			A|0.937;G|0.063	0.063	strong		0.512	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
CLTCL1	8218	hgsc.bcm.edu	37	22	19213091	19213091	+	Silent	SNP	C	C	T	rs367815723		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:19213091C>T	ENST00000263200.10	-	13	2085	c.2013G>A	c.(2011-2013)ctG>ctA	p.L671L	CLTCL1_ENST00000353891.5_Silent_p.L671L|CLTCL1_ENST00000427926.1_Silent_p.L671L	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	671	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)					TGTTAGCAGACAGCATGGCAT	0.532			T	?	ALCL																																p.L671L		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.G2013A						PASS	.	C	,	0,4168		0,0,2084	46.0	47.0	47.0		2013,2013	0.6	0.9	22		47	1,8459		0,1,4229	no	coding-synonymous,coding-synonymous	CLTCL1	NM_001835.3,NM_007098.3	,	0,1,6313	TT,TC,CC		0.0118,0.0,0.0079	,	671/1584,671/1641	19213091	1,12627	2084	4230	6314	SO:0001819	synonymous_variant	8218	exon13			AGCAGACAGCATG		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.2013G>A	22.37:g.19213091C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			.	.	weak		0.532	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
FMN2	56776	hgsc.bcm.edu	37	1	240370941	240370941	+	Silent	SNP	T	T	C	rs71170718|rs4997329|rs562038978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240370941T>C	ENST00000319653.9	+	5	3059	c.2829T>C	c.(2827-2829)ccT>ccC	p.P943P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	943	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGAATACCTCCTCCGCCCC	0.697													C|||	1375	0.274561	0.357	0.1902	5008	,	,		7400	0.3105		0.2286	False		,,,				2504	0.2331				p.P943P		Atlas-SNP	.											FMN2,caecum,carcinoma,0,1	FMN2	451	1	0			c.T2829C						scavenged	.	C		371,3909		68,235,1837	23.0	29.0	27.0		2829	-8.0	0.0	1	dbSNP_113	27	396,8032		78,240,3896	no	coding-synonymous	FMN2	NM_020066.4		146,475,5733	CC,CT,TT		4.6986,8.6682,6.0356		943/1723	240370941	767,11941	2140	4214	6354	SO:0001819	synonymous_variant	56776	exon5			AATACCTCCTCCG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2829T>C	1.37:g.240370941T>C		Somatic	156	3	0.0192308		WXS	Illumina HiSeq	Phase_I	138	38	0.275362	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			T|0.863;C|0.137	0.137	strong		0.697	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
GRHPR	9380	hgsc.bcm.edu	37	9	37422763	37422763	+	Missense_Mutation	SNP	C	C	T	rs147185003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:37422763C>T	ENST00000318158.6	+	1	101	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F	GRHPR_ENST00000607784.1_Missense_Mutation_p.L6F|GRHPR_ENST00000493368.1_3'UTR	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	6					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		ACCGGTGCGACTCATGAAGGT	0.701													C|||	17	0.00339457	0.0	0.0	5008	,	,		11840	0.0		0.001	False		,,,				2504	0.0164				p.L6F		Atlas-SNP	.											.	GRHPR	35	.	0			c.C16T						PASS	.	C	PHE/LEU	0,4382		0,0,2191	15.0	16.0	16.0		16	4.0	0.9	9	dbSNP_134	16	15,8557		0,15,4271	yes	missense	GRHPR	NM_012203.1	22	0,15,6462	TT,TC,CC		0.175,0.0,0.1158	possibly-damaging	6/329	37422763	15,12939	2191	4286	6477	SO:0001583	missense	9380	exon1			GTGCGACTCATGA	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"""primary hyperoxaluria type 2"""	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.16C>T	9.37:g.37422763C>T	ENSP00000313432:p.Leu6Phe	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	65	23	0.353846	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	ENST00000318158.6	37	CCDS6609.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.32	3.359027	0.61403	0.0	0.00175	ENSG00000137106	ENST00000377824;ENST00000318158	D;D	0.89050	-1.61;-2.46	4.9	3.99	0.46301	.	0.629307	0.15669	N	0.250520	D	0.86117	0.5856	L	0.40543	1.245	0.35594	D	0.807311	B	0.30664	0.289	B	0.36030	0.216	D	0.86917	0.2064	10	0.40728	T	0.16	.	14.397	0.67018	0.0:0.8509:0.1491:0.0	.	6	Q9UBQ7	GRHPR_HUMAN	F	6	ENSP00000367055:L6F;ENSP00000313432:L6F	ENSP00000313432:L6F	L	+	1	0	GRHPR	37412763	0.994000	0.37717	0.871000	0.34182	0.043000	0.13939	1.025000	0.30090	1.422000	0.47177	-0.518000	0.04402	CTC	C|0.999;T|0.001	0.001	strong		0.701	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203	
SYNE2	23224	hgsc.bcm.edu	37	14	64656855	64656855	+	Silent	SNP	T	T	C	rs2256191	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64656855T>C	ENST00000344113.4	+	99	18150	c.17938T>C	c.(17938-17940)Ttg>Ctg	p.L5980L	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.L2614L|SYNE2_ENST00000358025.3_Silent_p.L5980L|SYNE2_ENST00000394768.2_Silent_p.L2365L|SYNE2_ENST00000554584.1_Silent_p.L5843L|SYNE2_ENST00000357395.3_Silent_p.L2365L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5980					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)		GGGTGACCAGTTGATCAAGGC	0.413													T|||	2439	0.487021	0.8048	0.4006	5008	,	,		18466	0.3552		0.3698	False		,,,				2504	0.3753				p.L5980L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T17938C						PASS	.	T	,	3284,1122	717.7+/-408.7	1236,812,155	128.0	112.0	117.0		17938,17938	-4.1	0.7	14	dbSNP_100	117	3113,5487	475.6+/-369.2	571,1971,1758	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	1807,2783,1913	CC,CT,TT		36.1977,25.4653,49.185	,	5980/6886,5980/6908	64656855	6397,6609	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon99			GACCAGTTGATCA	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.17938T>C	14.37:g.64656855T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			T|0.498;C|0.502	0.502	strong		0.413	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
KIAA2013	90231	hgsc.bcm.edu	37	1	11983041	11983041	+	Silent	SNP	G	G	A	rs33910280	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11983041G>A	ENST00000376572.3	-	2	1724	c.1539C>T	c.(1537-1539)tcC>tcT	p.S513S	KIAA2013_ENST00000376576.3_Silent_p.S513S	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	513						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCTGGCCACGGGACTCCACGG	0.627													G|||	116	0.0231629	0.0098	0.0144	5008	,	,		17294	0.0288		0.0358	False		,,,				2504	0.0286				p.S513S		Atlas-SNP	.											.	KIAA2013	25	.	0			c.C1539T						PASS	.	G		55,4349	51.6+/-87.1	0,55,2147	33.0	32.0	32.0		1539	0.5	0.9	1	dbSNP_126	32	477,8119	132.8+/-190.4	13,451,3834	no	coding-synonymous	KIAA2013	NM_138346.2		13,506,5981	AA,AG,GG		5.5491,1.2489,4.0923		513/635	11983041	532,12468	2202	4298	6500	SO:0001819	synonymous_variant	90231	exon2			GCCACGGGACTCC	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.1539C>T	1.37:g.11983041G>A		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	360	170	0.472222	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Silent	SNP	ENST00000376572.3	37	CCDS141.1																																																																																			G|0.500;A|0.500	0.500	strong		0.627	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346	
DNM1L	10059	hgsc.bcm.edu	37	12	32886672	32886672	+	Silent	SNP	A	A	G	rs79393011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32886672A>G	ENST00000549701.1	+	13	1544	c.1470A>G	c.(1468-1470)gaA>gaG	p.E490E	YARS2_ENST00000551673.1_Intron|DNM1L_ENST00000553257.1_Silent_p.E503E|DNM1L_ENST00000547312.1_Silent_p.E490E|DNM1L_ENST00000358214.5_Silent_p.E503E|DNM1L_ENST00000452533.2_Silent_p.E490E|DNM1L_ENST00000266481.6_Silent_p.E490E|DNM1L_ENST00000381000.4_Silent_p.E503E|DNM1L_ENST00000414834.2_Silent_p.E287E			O00429	DNM1L_HUMAN	dynamin 1-like	490	Interaction with GSK3B.				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)					TGGCAATTGAACTGGCTTATA	0.294													A|||	27	0.00539137	0.003	0.0029	5008	,	,		17660	0.0		0.0169	False		,,,				2504	0.0041				p.E490E		Atlas-SNP	.											.	DNM1L	52	.	0			c.A1470G						PASS	.	A	,,	8,4398	14.3+/-33.2	0,8,2195	204.0	212.0	209.0		1470,1470,1470	0.4	0.4	12	dbSNP_133	209	93,8507	52.3+/-112.8	1,91,4208	no	coding-synonymous,coding-synonymous,coding-synonymous	DNM1L	NM_005690.3,NM_012062.3,NM_012063.2	,,	1,99,6403	GG,GA,AA		1.0814,0.1816,0.7766	,,	490/700,490/737,490/711	32886672	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	10059	exon13			AATTGAACTGGCT	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.1470A>G	12.37:g.32886672A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	37	CCDS8729.1																																																																																			A|0.993;G|0.007	0.007	strong		0.294	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	
MOGAT1	116255	hgsc.bcm.edu	37	2	223574546	223574546	+	Silent	SNP	A	A	G	rs142300173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:223574546A>G	ENST00000446656.3	+	6	945	c.945A>G	c.(943-945)aaA>aaG	p.K315K		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	315					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|cervix(1)|endometrium(1)|lung(5)|urinary_tract(1)	9		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		AACTTAGGAAATTGTTTGAGG	0.393													A|||	17	0.00339457	0.0113	0.0029	5008	,	,		17048	0.0		0.0	False		,,,				2504	0.0				p.K315K	Ovarian(93;205 1446 2385 11581 25911)	Atlas-SNP	.											.	MOGAT1	47	.	0			c.A945G						PASS	.	A		46,3662		0,46,1808	102.0	101.0	101.0		945	-4.6	0.0	2	dbSNP_134	101	0,8196		0,0,4098	no	coding-synonymous	MOGAT1	NM_058165.2		0,46,5906	GG,GA,AA		0.0,1.2406,0.3864		315/336	223574546	46,11858	1854	4098	5952	SO:0001819	synonymous_variant	116255	exon6			TAGGAAATTGTTT	AF384163	CCDS46524.1	2q36.2	2006-10-06	2004-05-28	2004-05-28	ENSG00000124003	ENSG00000124003			18210	protein-coding gene	gene with protein product		610268	"""diacylglycerol O-acyltransferase 2 like 1"""	DGAT2L1		14970677	Standard	NM_058165		Approved	DGAT2L, MGAT1	uc010fws.1	Q96PD6	OTTHUMG00000153394	ENST00000446656.3:c.945A>G	2.37:g.223574546A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_058165	Q6IEE5	Silent	SNP	ENST00000446656.3	37	CCDS46524.1																																																																																			A|0.998;G|0.002	0.002	strong		0.393	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165	
LRIG1	26018	hgsc.bcm.edu	37	3	66431280	66431280	+	Missense_Mutation	SNP	C	C	T	rs9877201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:66431280C>T	ENST00000273261.3	-	18	3300	c.2776G>A	c.(2776-2778)Ggt>Agt	p.G926S	SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000496559.2_5'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	69	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	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	
AKR1E2	83592	hgsc.bcm.edu	37	10	4872930	4872930	+	Missense_Mutation	SNP	G	G	A	rs61745201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:4872930G>A	ENST00000298375.7	+	2	174	c.103G>A	c.(103-105)Gac>Aac	p.D35N	AKR1E2_ENST00000334019.4_Missense_Mutation_p.D35N|AKR1E2_ENST00000345253.5_Missense_Mutation_p.D35N|AKR1E2_ENST00000525281.1_3'UTR|AKR1E2_ENST00000532248.1_Missense_Mutation_p.D35N	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	35						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)			NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						CCGGCACTTCGACTGTGCTTA	0.517													G|||	136	0.0271565	0.025	0.0231	5008	,	,		19096	0.001		0.0656	False		,,,				2504	0.0204				p.D35N	NSCLC(43;343 1097 20371 28813 45509)	Atlas-SNP	.											.	AKR1E2	30	.	0			c.G103A						PASS	.	G	ASN/ASP	156,4250	106.0+/-144.5	1,154,2048	186.0	156.0	166.0		103	3.0	0.9	10	dbSNP_129	166	566,8034	153.3+/-207.7	18,530,3752	yes	missense	AKR1E2	NM_001040177.1	23	19,684,5800	AA,AG,GG		6.5814,3.5406,5.5513	benign	35/321	4872930	722,12284	2203	4300	6503	SO:0001583	missense	83592	exon2			CACTTCGACTGTG	AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"""Aldo-keto reductases"""	23437	protein-coding gene	gene with protein product			"""aldo-keto reductase family 1, member C-like 2"""	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.103G>A	10.37:g.4872930G>A	ENSP00000298375:p.Asp35Asn	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	216	134	0.62037	NM_001271025	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Missense_Mutation	SNP	ENST00000298375.7	37	CCDS31134.1	79	0.036172161172161175	10	0.02032520325203252	13	0.03591160220994475	0	0.0	56	0.07387862796833773	G	10.48	1.361941	0.24684	0.035406	0.065814	ENSG00000165568	ENST00000533295;ENST00000298375;ENST00000532248;ENST00000334019;ENST00000345253	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	3.95	3.03	0.35002	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);	0.053894	0.64402	N	0.000001	T	0.29716	0.0742	H	0.96833	3.89	0.20975	P	0.999816377	D;P;B;B;P	0.57899	0.981;0.568;0.282;0.09;0.666	P;B;B;B;B	0.53689	0.732;0.12;0.127;0.221;0.348	T	0.77411	-0.2598	9	0.72032	D	0.01	.	13.0178	0.58768	0.0922:0.0:0.9078:0.0	rs61745201	35;35;35;35;35	B7Z7K2;Q96JD6-5;Q96JD6-2;Q96JD6;Q96JD6-3	.;.;.;AKCL2_HUMAN;.	N	39;35;35;35;35	ENSP00000435436:D39N;ENSP00000298375:D35N;ENSP00000432947:D35N;ENSP00000335034:D35N;ENSP00000335603:D35N	ENSP00000298375:D35N	D	+	1	0	AKR1E2	4862930	1.000000	0.71417	0.921000	0.36526	0.117000	0.20001	6.926000	0.75835	0.639000	0.30564	-1.134000	0.01955	GAC	A|0.048;C|0.000;G|0.952	0.048	strong		0.517	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436	
EPPK1	83481	hgsc.bcm.edu	37	8	144946345	144946345	+	Silent	SNP	G	G	A	rs34753358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144946345G>A	ENST00000525985.1	-	2	1148	c.1077C>T	c.(1075-1077)gcC>gcT	p.A359A				P58107	EPIPL_HUMAN	epiplakin 1	359						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)			CGGCCTGCTCGGCCACCAGGA	0.657													G|||	1465	0.292532	0.0242	0.4409	5008	,	,		16339	0.2381		0.4801	False		,,,				2504	0.4131				p.A359A		Atlas-SNP	.											EPPK1,NS,carcinoma,-1,2	EPPK1	199	2	0			c.C1077T						PASS	.	G		371,3515		34,303,1606	11.0	14.0	13.0		1077	-3.5	1.0	8	dbSNP_126	13	3992,4228		1037,1918,1155	no	coding-synonymous	EPPK1	NM_031308.1		1071,2221,2761	AA,AG,GG		48.5645,9.5471,36.04		359/2420	144946345	4363,7743	1943	4110	6053	SO:0001819	synonymous_variant	83481	exon1			CTGCTCGGCCACC	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.1077C>T	8.37:g.144946345G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.685;A|0.315	0.315	strong		0.657	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ADI1	55256	hgsc.bcm.edu	37	2	3504687	3504687	+	Silent	SNP	A	A	G	rs9950	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:3504687A>G	ENST00000327435.6	-	3	566	c.318T>C	c.(316-318)gaT>gaC	p.D106D	ADI1_ENST00000382093.5_Silent_p.D100D	NM_018269.3	NP_060739.2			acireductone dioxygenase 1									p.D106D(1)		breast(2)|large_intestine(2)|lung(4)|ovary(1)|stomach(1)	10	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		TGTCCCTCACATCGAAGTACC	0.537													A|||	2672	0.533546	0.8918	0.451	5008	,	,		19687	0.4484		0.3887	False		,,,				2504	0.3446				p.D106D		Atlas-SNP	.											ADI1,NS,carcinoma,0,1	ADI1	12	1	1	Substitution - coding silent(1)	stomach(1)	c.T318C						PASS	.	A		3535,871	743.8+/-411.5	1431,673,99	221.0	165.0	184.0		318	-7.0	0.2	2	dbSNP_52	184	3057,5543	469.8+/-367.7	558,1941,1801	no	coding-synonymous	ADI1	NM_018269.3		1989,2614,1900	GG,GA,AA		35.5465,19.7685,49.3157		106/180	3504687	6592,6414	2203	4300	6503	SO:0001819	synonymous_variant	55256	exon3			CCTCACATCGAAG		CCDS1653.1	2p25.2	2013-05-29			ENSG00000182551	ENSG00000182551	1.13.11.54		30576	protein-coding gene	gene with protein product	"""membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1"""	613400				14718544, 15938715	Standard	NM_018269		Approved	SIPL, MTCBP-1, ARD, APL1, FLJ10913, HMFT1638, mtnD	uc002qxp.4	Q9BV57	OTTHUMG00000112441	ENST00000327435.6:c.318T>C	2.37:g.3504687A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	162	75	0.462963	NM_018269		Silent	SNP	ENST00000327435.6	37	CCDS1653.1																																																																																			A|0.473;G|0.527	0.527	strong		0.537	ADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000231914.6	NM_018269	
POTEE	445582	hgsc.bcm.edu	37	2	132021946	132021946	+	Missense_Mutation	SNP	G	G	A	rs62178369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:132021946G>A	ENST00000356920.5	+	15	3012	c.2918G>A	c.(2917-2919)gGc>gAc	p.G973D	PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	973	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GAATCCTGTGGCATCCATGAA	0.572																																					p.G973D		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,0,4	.	.	4	0			c.G2918A						scavenged	.						2.0	1.0	1.0					2																	132021946		585	948	1533	SO:0001583	missense	445582	exon15			CCTGTGGCATCCA	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.2918G>A	2.37:g.132021946G>A	ENSP00000439189:p.Gly973Asp	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	262	33	0.125954	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	15.99	2.994529	0.54041	.	.	ENSG00000188219	ENST00000356920	D	0.97352	-4.35	.	.	.	.	.	.	.	.	D	0.99074	0.9682	H	0.99946	5.015	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96048	0.9029	8	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	973	Q6S8J3	POTEE_HUMAN	D	973	ENSP00000439189:G973D	ENSP00000439189:G973D	G	+	2	0	AC131180.1	131738416	1.000000	0.71417	0.305000	0.25099	0.308000	0.27856	6.504000	0.73704	0.119000	0.18210	0.121000	0.15741	GGC	A|1.000;|0.000	1.000	weak		0.572	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
UBXN11	91544	hgsc.bcm.edu	37	1	26608867	26608867	+	Missense_Mutation	SNP	C	C	A	rs193142354		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26608867C>A	ENST00000374222.1	-	16	1950	c.1486G>T	c.(1486-1488)Ggt>Tgt	p.G496C	UBXN11_ENST00000357089.4_Missense_Mutation_p.G463C|UBXN11_ENST00000314675.7_Missense_Mutation_p.G376C|UBXN11_ENST00000374217.2_Missense_Mutation_p.G463C|UBXN11_ENST00000374221.3_Missense_Mutation_p.G496C|UBXN11_ENST00000374223.1_Missense_Mutation_p.G253C			Q5T124	UBX11_HUMAN	UBX domain protein 11	496	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			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						ggaccgggaccgggactgggg	0.721																																					p.G496C		Atlas-SNP	.											UBXN11,colon,carcinoma,0,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1486T						PASS	.						25.0	29.0	28.0					1																	26608867		1765	4016	5781	SO:0001583	missense	91544	exon16			CGGGACCGGGACT	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.1486G>T	1.37:g.26608867C>A	ENSP00000363339:p.Gly496Cys	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	36	8	0.222222	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	261	0.11950549450549451	72	0.14634146341463414	35	0.09668508287292818	16	0.027972027972027972	138	0.1820580474934037	A	8.132	0.783217	0.16189	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.23950	1.88;1.96;2.3;2.24;2.24;2.3	.	.	.	.	.	.	.	.	T	0.00073	0.0002	N	0.22421	0.69	0.58432	P	2.9999999999752447E-6	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	D;D;D;P	0.65323	0.934;0.934;0.934;0.861	T	0.12578	-1.0542	7	0.66056	D	0.02	.	6.1326	0.20213	0.0:0.6805:0.3194:0.0	.	463;458;376;496	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	C	376;253;463;496;496;463	ENSP00000324721:G376C;ENSP00000363340:G253C;ENSP00000349601:G463C;ENSP00000363338:G496C;ENSP00000363339:G496C;ENSP00000363334:G463C	ENSP00000324721:G376C	G	-	1	0	UBXN11	26481454	0.000000	0.05858	0.121000	0.21740	0.128000	0.20619	-1.193000	0.03049	0.392000	0.25172	0.391000	0.25812	GGT	C|0.880;A|0.120	0.120	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
MYEOV2	150678	hgsc.bcm.edu	37	2	241066280	241066280	+	Silent	SNP	C	C	T	rs4292120	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241066280C>T	ENST00000307266.3	-	5	458	c.459G>A	c.(457-459)gaG>gaA	p.E153E		NM_138336.1	NP_612209.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	0										breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		ACATTAGCGCCTCCGCCCCCT	0.542													T|||	3605	0.719848	0.9705	0.6744	5008	,	,		18094	0.7252		0.5696	False		,,,				2504	0.5624				p.E153E		Atlas-SNP	.											.	MYEOV2	20	.	0			c.G459A						PASS	.	T		3975,431	209.2+/-230.0	1788,399,16	166.0	174.0	171.0		459	-0.1	0.0	2	dbSNP_111	171	4761,3839	540.2+/-383.8	1344,2073,883	no	coding-synonymous	MYEOV2	NM_138336.1		3132,2472,899	TT,TC,CC		44.6395,9.7821,32.831		153/253	241066280	8736,4270	2203	4300	6503	SO:0001819	synonymous_variant	150678	exon5			TAGCGCCTCCGCC	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000307266.3:c.459G>A	2.37:g.241066280C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_138336	Q8N110	Silent	SNP	ENST00000307266.3	37	CCDS2532.1																																																																																			C|0.304;T|0.696	0.696	strong		0.542	MYEOV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257182.2	NM_138336	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54674963	54674963	+	Silent	SNP	T	T	C	rs139182599	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54674963T>C	ENST00000230640.5	+	18	2246	c.1992T>C	c.(1990-1992)aaT>aaC	p.N664N	SKIV2L2_ENST00000545714.1_Silent_p.N563N	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	664					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				AGGTAAAGAATGAAGGAGATG	0.308													T|||	6	0.00119808	0.0	0.0	5008	,	,		15869	0.0		0.005	False		,,,				2504	0.001				p.N664N	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T1992C						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	46.0	51.0	50.0		1992	5.6	1.0	5	dbSNP_134	50	42,8552	26.8+/-75.7	0,42,4255	no	coding-synonymous	SKIV2L2	NM_015360.4		0,48,6452	CC,CT,TT		0.4887,0.1362,0.3692		664/1043	54674963	48,12952	2203	4297	6500	SO:0001819	synonymous_variant	23517	exon18			AAAGAATGAAGGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1992T>C	5.37:g.54674963T>C		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	9	8	0.888889	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	37	CCDS3967.1																																																																																			T|0.997;C|0.003	0.003	strong		0.308	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
C6orf118	168090	hgsc.bcm.edu	37	6	165703523	165703523	+	Missense_Mutation	SNP	C	C	T	rs17856754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:165703523C>T	ENST00000230301.8	-	7	1174	c.1154G>A	c.(1153-1155)cGa>cAa	p.R385Q	C6orf118_ENST00000494696.2_5'UTR|C6orf118_ENST00000543069.1_3'UTR	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	385			R -> Q (in dbSNP:rs17856754). {ECO:0000269|PubMed:15489334}.							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)		AAGAGTAAGTCGGTTTTCATC	0.294													C|||	142	0.0283546	0.0204	0.0288	5008	,	,		13922	0.001		0.0815	False		,,,				2504	0.0123				p.R385Q		Atlas-SNP	.											.	C6orf118	116	.	0			c.G1154A						PASS	.	C	GLN/ARG	159,4247	105.2+/-143.6	1,157,2045	64.0	63.0	63.0		1154	-1.7	0.0	6	dbSNP_123	63	642,7950	162.0+/-214.8	19,604,3673	no	missense	C6orf118	NM_144980.3	43	20,761,5718	TT,TC,CC		7.4721,3.6087,6.1625	benign	385/470	165703523	801,12197	2203	4296	6499	SO:0001583	missense	168090	exon7			GTAAGTCGGTTTT		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.1154G>A	6.37:g.165703523C>T	ENSP00000230301:p.Arg385Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	91	0.041666666666666664	15	0.03048780487804878	14	0.03867403314917127	0	0.0	62	0.08179419525065963	C	5.143	0.212043	0.09757	0.036087	0.074721	ENSG00000112539	ENST00000230301	T	0.10960	2.82	5.44	-1.67	0.08238	.	2.307610	0.01382	N	0.012960	T	0.00695	0.0023	N	0.00583	-1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42932	-0.9422	10	0.11485	T	0.65	1.532	4.8881	0.13713	0.1349:0.3268:0.0:0.5382	rs17856754;rs17856754	385	Q5T5N4	CF118_HUMAN	Q	385	ENSP00000230301:R385Q	ENSP00000230301:R385Q	R	-	2	0	C6orf118	165623513	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.044000	0.12023	-0.100000	0.12241	-0.295000	0.09555	CGA	C|0.947;T|0.053	0.053	strong		0.294	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
LRP8	7804	hgsc.bcm.edu	37	1	53732315	53732315	+	Silent	SNP	G	G	T	rs2297660	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:53732315G>T	ENST00000306052.6	-	9	1358	c.1257C>A	c.(1255-1257)ggC>ggA	p.G419G	LRP8_ENST00000354412.3_Silent_p.G290G|LRP8_ENST00000465675.1_5'UTR|LRP8_ENST00000371454.2_Silent_p.G419G|RP4-784A16.1_ENST00000432653.1_RNA|LRP8_ENST00000347547.2_Silent_p.G249G	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	419					ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						ATGGGCTCTTGCCAGCTGTCA	0.567													G|||	1679	0.335264	0.2042	0.2824	5008	,	,		19507	0.6319		0.3956	False		,,,				2504	0.182				p.G419G		Atlas-SNP	.											.	LRP8	58	.	0			c.C1257A	GRCh37	CM061103	LRP8	M	rs2297660	PASS	.	G	,,,	1004,3402	374.6+/-321.3	120,764,1319	139.0	121.0	127.0	http://omim.org/entry/602600	1257,1257,870,747	4.9	1.0	1	dbSNP_100	127	3451,5149	507.5+/-376.8	700,2051,1549	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRP8	NM_001018054.2,NM_004631.4,NM_017522.4,NM_033300.3	,,,	820,2815,2868	TT,TG,GG		40.1279,22.7871,34.2534	,,,	419/905,419/964,290/701,249/794	53732315	4455,8551	2203	4300	6503	SO:0001819	synonymous_variant	7804	exon9			GCTCTTGCCAGCT	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"""Low density lipoprotein receptors"""	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.1257C>A	1.37:g.53732315G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Silent	SNP	ENST00000306052.6	37	CCDS578.1	877	0.4015567765567766	115	0.23373983739837398	94	0.2596685082872928	369	0.6451048951048951	299	0.3944591029023747	G	9.243	1.038713	0.19669	0.227871	0.401279	ENSG00000157193	ENST00000475501	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.49093	-0.8975	3	.	.	.	.	7.7546	0.28917	0.0808:0.0:0.686:0.2332	rs2297660;rs57601779;rs2297660	.	.	.	E	108	.	.	A	-	2	0	LRP8	53504903	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.007000	0.29860	2.550000	0.86006	0.462000	0.41574	GCA	G|0.633;T|0.367	0.367	strong		0.567	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631	
RNASE3	6037	hgsc.bcm.edu	37	14	21359987	21359987	+	Missense_Mutation	SNP	C	C	G	rs202232277		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21359987C>G	ENST00000304639.3	+	2	200	c.142C>G	c.(142-144)Cct>Gct	p.P48A		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	48	Required for nearly all of the bactericidal activity; partially involved in LPS-binding and bacterial membrane depolarization.				antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	TCTGAACCCCCCTCGATGCAC	0.478																																					p.P48A		Atlas-SNP	.											.	RNASE3	24	.	0			c.C142G						PASS	.	C	ALA/PRO	0,4382		0,0,2191	111.0	117.0	115.0		142	-4.0	0.0	14		115	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RNASE3	NM_002935.2	27	0,1,6490	GG,GC,CC		0.0116,0.0,0.0077	benign	48/161	21359987	1,12981	2191	4300	6491	SO:0001583	missense	6037	exon2			AACCCCCCTCGAT	X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"""Ribonucleases, RNase A"""	10046	protein-coding gene	gene with protein product	"""eosinophil cationic protein"""	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.142C>G	14.37:g.21359987C>G	ENSP00000302324:p.Pro48Ala	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_002935	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Missense_Mutation	SNP	ENST00000304639.3	37	CCDS9560.1	.	.	.	.	.	.	.	.	.	.	c	0.010	-1.759799	0.00657	0.0	1.16E-4	ENSG00000169397	ENST00000304639	T	0.72051	-0.62	2.56	-3.95	0.04118	Ribonuclease A, domain (4);	1.415800	0.04852	U	0.442561	T	0.55401	0.1918	L	0.53249	1.67	0.09310	N	1	B	0.22983	0.078	B	0.17433	0.018	T	0.30621	-0.9972	10	0.09590	T	0.72	.	1.8936	0.03253	0.4903:0.2296:0.1619:0.1183	.	48	P12724	ECP_HUMAN	A	48	ENSP00000302324:P48A	ENSP00000302324:P48A	P	+	1	0	RNASE3	20429827	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.611000	0.00110	-0.998000	0.03446	-0.415000	0.06103	CCT	C|0.999;G|0.001	0.001	weak		0.478	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935	
RPH3A	22895	hgsc.bcm.edu	37	12	113319600	113319600	+	Silent	SNP	C	C	T	rs2240194	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:113319600C>T	ENST00000389385.4	+	15	1772	c.1275C>T	c.(1273-1275)aaC>aaT	p.N425N	RPH3A_ENST00000447659.2_Silent_p.N376N|RPH3A_ENST00000548866.1_Silent_p.N376N|RPH3A_ENST00000543106.2_Silent_p.N425N|RPH3A_ENST00000551052.1_Silent_p.N421N|RPH3A_ENST00000415485.3_Silent_p.N425N|RPH3A_ENST00000420983.2_Silent_p.N425N|RPH3A_ENST00000549913.2_3'UTR	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	425	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		TGGATTCAAACGGCTTGGCTG	0.612													C|||	2846	0.568291	0.7148	0.6066	5008	,	,		19674	0.6181		0.4264	False		,,,				2504	0.4376				p.N425N		Atlas-SNP	.											.	RPH3A	98	.	0			c.C1275T						PASS	.	C	,	2914,1492	677.4+/-403.4	969,976,258	110.0	102.0	105.0		1275,1263	-9.4	0.5	12	dbSNP_98	105	3534,5066	513.9+/-378.3	785,1964,1551	no	coding-synonymous,coding-synonymous	RPH3A	NM_001143854.1,NM_014954.3	,	1754,2940,1809	TT,TC,CC		41.093,33.8629,49.5771	,	425/695,421/691	113319600	6448,6558	2203	4300	6503	SO:0001819	synonymous_variant	22895	exon15			TTCAAACGGCTTG	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"""Synaptotagmins"""	17056	protein-coding gene	gene with protein product		612159	"""rabphilin 3A homolog (mouse)"""			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1275C>T	12.37:g.113319600C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_001143854	B7Z3C3|Q96AE0	Silent	SNP	ENST00000389385.4	37	CCDS44979.1																																																																																			C|0.479;T|0.521	0.521	strong		0.612	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954	
MUC2	4583	hgsc.bcm.edu	37	11	1093054	1093054	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093054C>G	ENST00000441003.2	+	30	4900	c.4873C>G	c.(4873-4875)Cag>Gag	p.Q1625E	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cactggcacacagaccccaac	0.637																																					p.Q1625E		Atlas-SNP	.											.	MUC2	614	.	0			c.C4873G						PASS	.						130.0	168.0	155.0					11																	1093054		1880	3616	5496	SO:0001583	missense	4583	exon30			GGCACACAGACCC	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.4873C>G	11.37:g.1093054C>G	ENSP00000415183:p.Gln1625Glu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	4	0.0869565	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.029	-1.348877	0.01266	.	.	ENSG00000198788	ENST00000441003	T	0.11277	2.79	1.61	-3.22	0.05125	.	.	.	.	.	T	0.02888	0.0086	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.35450	-0.9788	8	0.02654	T	1	.	0.7509	0.00990	0.2924:0.2671:0.2831:0.1573	.	1625	E7EUV1	.	E	1625	ENSP00000415183:Q1625E	ENSP00000415183:Q1625E	Q	+	1	0	MUC2	1083054	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-0.356000	0.07661	-2.888000	0.00316	0.121000	0.15741	CAG	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FNDC1	84624	hgsc.bcm.edu	37	6	159688948	159688948	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:159688948T>C	ENST00000297267.9	+	22	5759	c.5559T>C	c.(5557-5559)ccT>ccC	p.P1853P	FNDC1_ENST00000340366.6_Silent_p.P1790P	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1853					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)		AAGCCCTCCCTACTATTCAAG	0.463																																					p.P1853P		Atlas-SNP	.											FNDC1,colon,carcinoma,+1,1	FNDC1	250	1	0			c.T5559C						scavenged	.						84.0	77.0	79.0					6																	159688948		1883	4116	5999	SO:0001819	synonymous_variant	84624	exon22			CCTCCCTACTATT	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.5559T>C	6.37:g.159688948T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	125	2	0.016	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	T	7.313	0.615326	0.14129	.	.	ENSG00000164694	ENST00000329629	.	.	.	5.58	-0.814	0.10846	.	.	.	.	.	T	0.44052	0.1275	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44711	-0.9310	4	.	.	.	-20.5987	11.261	0.49083	0.0:0.4544:0.0:0.5456	.	.	.	.	H	1749	.	.	Y	+	1	0	FNDC1	159608938	0.001000	0.12720	0.007000	0.13788	0.991000	0.79684	-0.161000	0.10026	-0.368000	0.08040	0.402000	0.26972	TAC	.	.	none		0.463	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
CILP2	148113	hgsc.bcm.edu	37	19	19655670	19655670	+	Silent	SNP	C	C	T	rs11669558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	12	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	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	
ANKMY1	51281	hgsc.bcm.edu	37	2	241451351	241451351	+	Missense_Mutation	SNP	G	G	A	rs35044862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241451351G>A	ENST00000272972.3	-	10	2160	c.1946C>T	c.(1945-1947)aCg>aTg	p.T649M	ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000373318.2_Missense_Mutation_p.T508M|ANKMY1_ENST00000406958.1_Missense_Mutation_p.T410M|ANKMY1_ENST00000401804.1_Missense_Mutation_p.T738M|ANKMY1_ENST00000391987.1_Missense_Mutation_p.T649M|ANKMY1_ENST00000373320.4_Missense_Mutation_p.T419M|ANKMY1_ENST00000403283.1_Missense_Mutation_p.T587M	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	649			T -> M (in dbSNP:rs35044862).				metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		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;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		GGCTGTGTCCGTGCTGTAGTA	0.672													G|||	889	0.177516	0.2821	0.2392	5008	,	,		18735	0.1855		0.1034	False		,,,				2504	0.0603				p.T649M		Atlas-SNP	.											.	ANKMY1	112	.	0			c.C1946T						PASS	.	G	MET/THR,	1061,3345	386.5+/-326.1	133,795,1275	61.0	61.0	61.0		1946,	-1.8	0.0	2	dbSNP_126	61	855,7745	193.8+/-239.4	42,771,3487	yes	missense,intron	ANKMY1	NM_016552.2,NM_017844.2	81,	175,1566,4762	AA,AG,GG		9.9419,24.0808,14.7317	benign,	649/942,	241451351	1916,11090	2203	4300	6503	SO:0001583	missense	51281	exon10			GTGTCCGTGCTGT	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1946C>T	2.37:g.241451351G>A	ENSP00000272972:p.Thr649Met	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	398	0.18223443223443223	150	0.3048780487804878	83	0.2292817679558011	98	0.17132867132867133	67	0.08839050131926121	G	5.362	0.252081	0.10185	0.240808	0.099419	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804	T;T;T;T;T;T;T	0.71579	-0.15;3.55;-0.58;-0.58;4.31;-0.15;0.44	3.43	-1.77	0.07982	Ankyrin repeat-containing domain (3);	3.829500	0.01322	N	0.010978	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B;P;B	0.44195	0.023;0.155;0.004;0.828;0.023	B;B;B;B;B	0.39738	0.01;0.014;0.005;0.308;0.01	T	0.02288	-1.1182	9	0.48119	T	0.1	-17.1302	2.1176	0.03718	0.1713:0.1121:0.4833:0.2333	rs35044862	649;419;508;410;649	Q4ZFV3;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6	.;.;.;.;ANKY1_HUMAN	M	508;410;649;649;419;587;738	ENSP00000362415:T508M;ENSP00000384555:T410M;ENSP00000272972:T649M;ENSP00000375847:T649M;ENSP00000362417:T419M;ENSP00000383968:T587M;ENSP00000385887:T738M	ENSP00000272972:T649M	T	-	2	0	ANKMY1	241100024	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.061000	0.00623	-0.925000	0.03775	-1.628000	0.00784	ACG	G|0.841;A|0.159	0.159	strong		0.672	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
EPS8L2	64787	hgsc.bcm.edu	37	11	721931	721931	+	Silent	SNP	C	C	T	rs7949926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:721931C>T	ENST00000533256.1	+	12	1299	c.924C>T	c.(922-924)ccC>ccT	p.P308P	EPS8L2_ENST00000318562.8_Silent_p.P308P|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000530636.1_Silent_p.P308P|EPS8L2_ENST00000526198.1_Silent_p.P324P			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	308					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)	p.P308P(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		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;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGCACGGCCCCCCTCTGAGG	0.667													c|||	538	0.107428	0.2474	0.0692	5008	,	,		12327	0.0357		0.0815	False		,,,				2504	0.046				p.P308P		Atlas-SNP	.											EPS8L2,NS,carcinoma,0,1	EPS8L2	42	1	1	Substitution - coding silent(1)	prostate(1)	c.C924T						PASS	.			950,3438		98,754,1342	30.0	28.0	29.0		924	2.5	1.0	11	dbSNP_116	29	767,7823		44,679,3572	no	coding-synonymous	EPS8L2	NM_022772.3		142,1433,4914	TT,TC,CC		8.929,21.65,13.2301		308/716	721931	1717,11261	2194	4295	6489	SO:0001819	synonymous_variant	64787	exon11			ACGGCCCCCCTCT	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.924C>T	11.37:g.721931C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			C|0.874;T|0.126	0.126	strong		0.667	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
ABCA13	154664	hgsc.bcm.edu	37	7	48314798	48314798	+	Silent	SNP	G	G	T	rs13233225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:48314798G>T	ENST00000435803.1	+	17	5559	c.5535G>T	c.(5533-5535)ggG>ggT	p.G1845G		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1845					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATGTCCATGGGCTCATGTCTT	0.443													G|||	1084	0.216454	0.261	0.2147	5008	,	,		18298	0.0119		0.3926	False		,,,				2504	0.1871				p.G1845G		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G5535T						PASS	.	G		1098,2664		166,766,949	60.0	59.0	59.0		5535	2.6	0.0	7	dbSNP_121	59	2908,5328		509,1890,1719	no	coding-synonymous	ABCA13	NM_152701.3		675,2656,2668	TT,TG,GG		35.3084,29.1866,33.3889		1845/5059	48314798	4006,7992	1881	4118	5999	SO:0001819	synonymous_variant	154664	exon17			CCATGGGCTCATG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5535G>T	7.37:g.48314798G>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			G|0.750;T|0.250	0.250	strong		0.443	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ZNF410	57862	hgsc.bcm.edu	37	14	74388908	74388908	+	Splice_Site	SNP	T	T	C	rs1127392	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74388908T>C	ENST00000555044.1	+	10	1463	c.1269T>C	c.(1267-1269)gaT>gaC	p.D423D	RP5-1021I20.4_ENST00000556551.2_3'UTR|ZNF410_ENST00000540593.1_Splice_Site_p.D350D|ZNF410_ENST00000334521.4_Splice_Site_p.D370D|ZNF410_ENST00000442160.3_Splice_Site_p.D440D|RP5-1021I20.5_ENST00000555916.1_RNA|RP5-1021I20.5_ENST00000554009.1_RNA|ZNF410_ENST00000324593.6_Intron	NM_001242928.1|NM_021188.2	NP_001229857.1|NP_067011.1	Q86VK4	ZN410_HUMAN	zinc finger protein 410	423					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.00369)		GAGTTGATGATGGTAAGACTT	0.438													T|||	1142	0.228035	0.1626	0.3357	5008	,	,		16968	0.0476		0.4105	False		,,,				2504	0.2382				p.D440D		Atlas-SNP	.											.	ZNF410	25	.	0			c.T1320C						PASS	.	T	,,,,	854,3552	332.8+/-302.6	84,686,1433	60.0	52.0	55.0		1320,,1050,681,1269	3.8	1.0	14	dbSNP_86	55	3570,5030	517.6+/-379.1	735,2100,1465	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ZNF410	NM_001242924.1,NM_001242926.1,NM_001242927.1,NM_001242928.1,NM_021188.2	,,,,	819,2786,2898	CC,CT,TT		41.5116,19.3827,34.0151	,,,,	440/517,,350/406,227/313,423/479	74388908	4424,8582	2203	4300	6503	SO:0001630	splice_region_variant	57862	exon11			TGATGATGGTAAG	U90919	CCDS9821.1, CCDS55929.1, CCDS55930.1, CCDS55931.1	14q24.3	2013-01-08				ENSG00000119725		"""Zinc fingers, C2H2-type"""	20144	protein-coding gene	gene with protein product						12370286	Standard	NM_001242924		Approved	APA1, APA-1	uc010arz.2	Q86VK4		ENST00000555044.1:c.1270+1T>C	14.37:g.74388908T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_001242924	B4DDV5|B4DR78|O00153|Q9BQ19	Silent	SNP	ENST00000555044.1	37	CCDS9821.1	557	0.25503663003663	74	0.15040650406504066	129	0.356353591160221	35	0.06118881118881119	319	0.420844327176781	T	11.90	1.776962	0.31411	0.193827	0.415116	ENSG00000119725	ENST00000557214	.	.	.	5.0	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999702	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7001	0.17877	0.1499:0.0:0.2294:0.6207	rs1127392;rs1804842;rs3177095;rs3183290;rs11540491;rs17182692;rs17423892;rs3177095	.	.	.	R	84	.	.	X	+	1	0	ZNF410	73458661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.363000	0.44178	2.222000	0.72286	0.477000	0.44152	TGA	A|0.000;C|0.298;T|0.702	0.298	strong		0.438	ZNF410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412597.1	NM_021188	Silent
METTL7A	25840	hgsc.bcm.edu	37	12	51319238	51319238	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:51319238T>C	ENST00000548553.1	+	2	1398	c.417T>C	c.(415-417)gaT>gaC	p.D139D	METTL7A_ENST00000332160.4_Silent_p.D139D			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	139						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GCTCTGTGGATGTGGTGGTCT	0.567																																					p.D139D		Atlas-SNP	.											.	METTL7A	19	.	0			c.T417C						PASS	.						74.0	65.0	68.0					12																	51319238		2203	4300	6503	SO:0001819	synonymous_variant	25840	exon1			TGTGGATGTGGTG		CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.417T>C	12.37:g.51319238T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_014033	Q9H7R3|Q9UHZ7|Q9Y422	Silent	SNP	ENST00000548553.1	37	CCDS8804.1																																																																																			.	.	none		0.567	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033	
MVB12A	93343	hgsc.bcm.edu	37	19	17534540	17534540	+	Missense_Mutation	SNP	G	G	T	rs147706400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17534540G>T	ENST00000317040.7	+	6	1627	c.572G>T	c.(571-573)gGc>gTc	p.G191V	CTD-2521M24.6_ENST00000593957.1_RNA|MVB12A_ENST00000529939.1_Missense_Mutation_p.G191V|MVB12A_ENST00000392702.2_Missense_Mutation_p.G151V|MVB12A_ENST00000543795.1_Missense_Mutation_p.G191V|MVB12A_ENST00000528515.1_Missense_Mutation_p.A149S			Q96EY5	MB12A_HUMAN	multivesicular body subunit 12A	191					protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|vesicle (GO:0031982)	lipid binding (GO:0008289)|ubiquitin binding (GO:0043130)										TCAAGGCTGGGCTCTCGGGCA	0.622													G|||	4	0.000798722	0.0008	0.0014	5008	,	,		15707	0.0		0.001	False		,,,				2504	0.001				p.G191V		Atlas-SNP	.											.	.	.	.	0			c.G572T						PASS	.	G	VAL/GLY	3,4403		0,3,2200	56.0	56.0	56.0		572	5.1	1.0	19	dbSNP_134	56	7,8593		0,7,4293	yes	missense	FAM125A	NM_138401.2	109	0,10,6493	TT,TG,GG		0.0814,0.0681,0.0769	possibly-damaging	191/274	17534540	10,12996	2203	4300	6503	SO:0001583	missense	93343	exon6			GGCTGGGCTCTCG	BC011840	CCDS12359.1	19p13.11	2013-10-11	2012-12-03	2012-12-03	ENSG00000141971	ENSG00000141971			25153	protein-coding gene	gene with protein product			"""family with sequence similarity 125, member A"""	FAM125A		18005716, 20654576, 22232651	Standard	NM_138401		Approved	FLJ32495	uc002ngo.1	Q96EY5	OTTHUMG00000166252	ENST00000317040.7:c.572G>T	19.37:g.17534540G>T	ENSP00000324810:p.Gly191Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_138401	Q96I18	Missense_Mutation	SNP	ENST00000317040.7	37	CCDS12359.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	.|.	10.70|10.70	1.424914|1.424914	0.25639|0.25639	6.81E-4|6.81E-4	8.14E-4|8.14E-4	ENSG00000141971|ENSG00000141971	ENST00000528515|ENST00000528911;ENST00000528604;ENST00000317040;ENST00000392702;ENST00000529939;ENST00000543795	.|T;T;T;T;T	.|0.44482	.|0.94;0.96;1.02;0.92;0.96	5.1|5.1	5.1|5.1	0.69264|0.69264	.|.	.|0.319630	.|0.37483	.|N	.|0.002062	T|T	0.36441|0.36441	0.0967|0.0967	L|L	0.44542|0.44542	1.39|1.39	0.58432|0.58432	D|D	0.999998|0.999998	.|P	.|0.37914	.|0.611	.|B	.|0.35114	.|0.196	T|T	0.34601|0.34601	-0.9822|-0.9822	6|10	0.54805|0.66056	T|D	0.06|0.02	-28.1606|-28.1606	14.0584|14.0584	0.64784|0.64784	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|191	.|Q96EY5	.|F125A_HUMAN	S|V	149|99;52;191;151;191;191	.|ENSP00000433280:G99V;ENSP00000324810:G191V;ENSP00000376466:G151V;ENSP00000432526:G191V;ENSP00000444653:G191V	ENSP00000433677:A149S|ENSP00000324810:G191V	A|G	+|+	1|2	0|0	FAM125A|FAM125A	17395540|17395540	0.998000|0.998000	0.40836|0.40836	0.978000|0.978000	0.43139|0.43139	0.183000|0.183000	0.23260|0.23260	4.163000|4.163000	0.58183|0.58183	2.371000|2.371000	0.80710|0.80710	0.558000|0.558000	0.71614|0.71614	GCT|GGC	G|0.999;T|0.001	0.001	strong		0.622	MVB12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388723.2	NM_138401	
C19orf48	84798	hgsc.bcm.edu	37	19	51301456	51301456	+	Missense_Mutation	SNP	G	G	A	rs4802741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51301456G>A	ENST00000598463.1	-	5	1348	c.250C>T	c.(250-252)Cgc>Tgc	p.R84C	C19orf48_ENST00000391812.1_Missense_Mutation_p.R84C|SNORD88B_ENST00000408454.1_RNA|C19orf48_ENST00000596655.1_Missense_Mutation_p.R84C|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000595794.1_5'Flank|C19orf48_ENST00000345523.4_Missense_Mutation_p.R84C			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48	84			R -> C (in dbSNP:rs4802741).							endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		TCACGGTGGCGTATGGACAGC	0.637													G|||	1652	0.329872	0.1309	0.2161	5008	,	,		19818	0.6538		0.3012	False		,,,				2504	0.3753				p.R84C		Atlas-SNP	.											.	C19orf48	11	.	0			c.C250T						PASS	.	G	CYS/ARG,CYS/ARG	682,3724		45,592,1566	110.0	100.0	103.0		250,250	0.9	0.0	19	dbSNP_111	103	2414,6186		350,1714,2236	yes	missense,missense	C19orf48	NM_199250.1,NM_199249.1	180,180	395,2306,3802	AA,AG,GG		28.0698,15.4789,23.8044	benign,benign	84/118,84/118	51301456	3096,9910	2203	4300	6503	SO:0001583	missense	84798	exon5			GGTGGCGTATGGA	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"""multidrug resistance-related protein"""					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		ENST00000598463.1:c.250C>T	19.37:g.51301456G>A	ENSP00000471463:p.Arg84Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_199249		Missense_Mutation	SNP	ENST00000598463.1	37	CCDS12803.1	769	0.35210622710622713	71	0.1443089430894309	80	0.22099447513812154	383	0.6695804195804196	235	0.3100263852242744	N	1.803	-0.476478	0.04414	0.154789	0.280698	ENSG00000167747	ENST00000391812;ENST00000345523	T;T	0.32023	1.47;1.47	1.92	0.845	0.18950	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.31779	-0.9931	8	0.44086	T	0.13	.	7.3421	0.26644	0.1625:0.0:0.8375:0.0	rs4802741;rs17657799;rs60128113;rs4802741	84	Q6RUI8	CS048_HUMAN	C	84	ENSP00000375688:R84C;ENSP00000301419:R84C	ENSP00000301419:R84C	R	-	1	0	C19orf48	55993268	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.160000	0.16462	-0.004000	0.14419	-1.786000	0.00637	CGC	G|0.713;A|0.287	0.287	strong		0.637	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712	
CENPF	1063	hgsc.bcm.edu	37	1	214818223	214818223	+	Missense_Mutation	SNP	T	T	A	rs3748693	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214818223T>A	ENST00000366955.3	+	13	5478	c.5310T>A	c.(5308-5310)caT>caA	p.H1770Q		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1866					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)		AAGATATCCATAATCTTCAAC	0.378													A|||	1218	0.243211	0.4788	0.1945	5008	,	,		19626	0.1597		0.0954	False		,,,				2504	0.1973				p.H1770Q	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T5310A						PASS	.	A	GLN/HIS	1870,2536	620.6+/-393.6	396,1078,729	44.0	46.0	45.0		5310	2.7	0.9	1	dbSNP_107	45	769,7831	779.8+/-407.7	36,697,3567	yes	missense	CENPF	NM_016343.3	24	432,1775,4296	AA,AT,TT		8.9419,42.4421,20.2906	benign	1770/3115	214818223	2639,10367	2203	4300	6503	SO:0001583	missense	1063	exon13			TATCCATAATCTT	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.5310T>A	1.37:g.214818223T>A	ENSP00000355922:p.His1770Gln	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	128	48	0.375	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	475	0.2174908424908425	225	0.4573170731707317	80	0.22099447513812154	99	0.17307692307692307	71	0.09366754617414248	A	0.007	-1.997615	0.00435	0.424421	0.089419	ENSG00000117724	ENST00000366955	T	0.02369	4.32	5.56	2.69	0.31865	.	0.458295	0.16309	N	0.220097	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	0.39354	-0.9618	9	0.02654	T	1	.	0.7918	0.01059	0.3627:0.1566:0.3199:0.1608	rs3748693;rs52837651;rs3748693	1866	P49454	CENPF_HUMAN	Q	1770	ENSP00000355922:H1770Q	ENSP00000355922:H1770Q	H	+	3	2	CENPF	212884846	0.177000	0.23109	0.908000	0.35775	0.059000	0.15707	0.463000	0.21972	0.329000	0.23460	-0.970000	0.02610	CAT	T|0.799;A|0.201	0.201	strong		0.378	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
KDM7A	80853	hgsc.bcm.edu	37	7	139797431	139797431	+	Missense_Mutation	SNP	G	G	T	rs6950119	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:139797431G>T	ENST00000397560.2	-	15	2027	c.1930C>A	c.(1930-1932)Cgt>Agt	p.R644S	JHDM1D_ENST00000006967.5_Missense_Mutation_p.R644S|Y_RNA_ENST00000515919.1_RNA	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		644			R -> S (in dbSNP:rs6950119). {ECO:0000269|PubMed:11214970}.		histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|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)|zinc ion binding (GO:0008270)	p.R644S(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					GATTTCACACGTGTAAAAAAC	0.433													G|||	1640	0.327476	0.4039	0.2767	5008	,	,		20930	0.245		0.334	False		,,,				2504	0.3384				p.R644S		Atlas-SNP	.											JHDM1D,NS,carcinoma,0,1	JHDM1D	54	1	1	Substitution - Missense(1)	lung(1)	c.C1930A						PASS	.	G	SER/ARG	1415,2283		266,883,700	67.0	64.0	65.0		1930	3.2	1.0	7	dbSNP_116	65	2782,5404		475,1832,1786	yes	missense	JHDM1D	NM_030647.1	110	741,2715,2486	TT,TG,GG		33.9849,38.2639,35.3164	benign	644/942	139797431	4197,7687	1849	4093	5942	SO:0001583	missense	80853	exon15			TCACACGTGTAAA																												ENST00000397560.2:c.1930C>A	7.37:g.139797431G>T	ENSP00000380692:p.Arg644Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Missense_Mutation	SNP	ENST00000397560.2	37	CCDS43658.1	664	0.304029304029304	188	0.3821138211382114	103	0.2845303867403315	137	0.2395104895104895	236	0.3113456464379947	G	4.224	0.040418	0.08148	0.382639	0.339849	ENSG00000006459	ENST00000397560;ENST00000006967	T;T	0.12465	2.92;2.68	5.53	3.18	0.36537	.	0.323397	0.40469	N	0.001093	T	0.00012	0.0000	N	0.00146	-1.995	0.34970	P	0.24697000000000002	B	0.02656	0.0	B	0.01281	0.0	T	0.43147	-0.9409	9	0.20519	T	0.43	-3.5099	8.5295	0.33326	0.1204:0.0:0.1557:0.7239	rs6950119;rs52801179;rs60741643;rs6950119	644	Q6ZMT4	KDM7_HUMAN	S	644	ENSP00000380692:R644S;ENSP00000006967:R644S	ENSP00000006967:R644S	R	-	1	0	JHDM1D	139443900	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.472000	0.45136	0.399000	0.25367	-0.237000	0.12165	CGT	A|0.000;G|0.670;T|0.330	0.330	strong		0.433	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1		
IL1RL2	8808	hgsc.bcm.edu	37	2	102851470	102851470	+	Missense_Mutation	SNP	G	G	A	rs75091099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102851470G>A	ENST00000264257.2	+	11	1537	c.1411G>A	c.(1411-1413)Gcg>Acg	p.A471T	IL1RL2_ENST00000539491.1_Missense_Mutation_p.A471T|IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000441515.2_Missense_Mutation_p.A353T	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	471	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						AGAACAAATCGCGGTCTACAG	0.488													G|||	144	0.028754	0.0	0.0072	5008	,	,		19953	0.0724		0.006	False		,,,				2504	0.0613				p.A471T		Atlas-SNP	.											IL1RL2,NS,carcinoma,-1,1	IL1RL2	118	1	0			c.G1411A						PASS	.	G	THR/ALA	9,4397	15.5+/-35.6	0,9,2194	132.0	120.0	124.0		1411	3.4	0.2	2	dbSNP_132	124	38,8562	25.1+/-72.6	0,38,4262	yes	missense	IL1RL2	NM_003854.2	58	0,47,6456	AA,AG,GG		0.4419,0.2043,0.3614	possibly-damaging	471/576	102851470	47,12959	2203	4300	6503	SO:0001583	missense	8808	exon11			CAAATCGCGGTCT	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.1411G>A	2.37:g.102851470G>A	ENSP00000264257:p.Ala471Thr	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	49	0.022435897435897436	0	0.0	3	0.008287292817679558	42	0.07342657342657342	4	0.005277044854881266	G	17.94	3.510555	0.64522	0.002043	0.004419	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	T;T;T	0.11712	2.75;2.75;2.75	5.43	3.4	0.38934	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.467616	0.23395	N	0.048647	T	0.01353	0.0044	M	0.69823	2.125	0.32198	N	0.57825	P;D	0.54047	0.924;0.964	P;P	0.48921	0.495;0.595	T	0.04115	-1.0976	10	0.59425	D	0.04	.	12.4276	0.55556	0.1128:0.0:0.8872:0.0	.	353;471	A4FU63;Q9HB29	.;ILRL2_HUMAN	T	471;353;471	ENSP00000264257:A471T;ENSP00000413348:A353T;ENSP00000442184:A471T	ENSP00000264257:A471T	A	+	1	0	IL1RL2	102217902	0.568000	0.26635	0.238000	0.24106	0.767000	0.43475	3.205000	0.51090	1.140000	0.42260	0.591000	0.81541	GCG	G|0.991;A|0.009	0.009	strong		0.488	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854	
C9orf117	286207	hgsc.bcm.edu	37	9	130475011	130475011	+	Silent	SNP	T	T	C	rs522328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130475011T>C	ENST00000373295.2	+	7	1201	c.1161T>C	c.(1159-1161)agT>agC	p.S387S	C9orf117_ENST00000373293.5_Silent_p.S36S|C9orf117_ENST00000464092.1_3'UTR	NM_001012502.2	NP_001012520.2	Q5JU67	CI117_HUMAN	chromosome 9 open reading frame 117	387										breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AAGAGGACAGTGACGTTGACG	0.602													C|||	3192	0.63738	0.9039	0.6066	5008	,	,		21362	0.3651		0.6054	False		,,,				2504	0.6125				p.S387S		Atlas-SNP	.											.	C9orf117	21	.	0			c.T1161C						PASS	.	C		3719,675	245.6+/-254.5	1584,551,62	89.0	96.0	94.0		1161	-1.1	0.0	9	dbSNP_83	94	4878,3684	513.0+/-378.1	1394,2090,797	no	coding-synonymous	C9orf117	NM_001012502.2		2978,2641,859	CC,CT,TT		43.0273,15.3619,33.6446		387/521	130475011	8597,4359	2197	4281	6478	SO:0001819	synonymous_variant	286207	exon7			GGACAGTGACGTT	AK094948	CCDS43878.1	9q34.11	2012-04-02			ENSG00000160401	ENSG00000160401			27843	protein-coding gene	gene with protein product							Standard	NM_001012502		Approved		uc004brn.1	Q5JU67	OTTHUMG00000020709	ENST00000373295.2:c.1161T>C	9.37:g.130475011T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_001012502	A5D8T9	Silent	SNP	ENST00000373295.2	37	CCDS43878.1																																																																																			T|0.374;C|0.626	0.626	strong		0.602	C9orf117-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054215.2	NM_001012502	
TPTE2	93492	hgsc.bcm.edu	37	13	20056679	20056679	+	Missense_Mutation	SNP	T	T	G	rs200244531		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:20056679T>G	ENST00000400230.2	-	4	172	c.128A>C	c.(127-129)gAa>gCa	p.E43A	TPTE2_ENST00000400103.2_Missense_Mutation_p.E43A|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000457266.2_Missense_Mutation_p.E43A|TPTE2_ENST00000382977.4_Missense_Mutation_p.E43A|TPTE2_ENST00000382978.1_Missense_Mutation_p.E43A|TPTE2_ENST00000382975.4_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	348	1	0.00287356		WXS	Illumina HiSeq	Phase_I	361	5	0.0138504	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	
USP34	9736	hgsc.bcm.edu	37	2	61450409	61450409	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:61450409C>G	ENST00000398571.2	-	63	7694	c.7618G>C	c.(7618-7620)Gac>Cac	p.D2540H	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2540					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)			GCTGCCATGTCAGTCTGTGAT	0.308																																					p.D2540H		Atlas-SNP	.											USP34,NS,carcinoma,+2,1	USP34	334	1	0			c.G7618C						PASS	.						137.0	128.0	131.0					2																	61450409		1847	4096	5943	SO:0001583	missense	9736	exon63			CCATGTCAGTCTG	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.7618G>C	2.37:g.61450409C>G	ENSP00000381577:p.Asp2540His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	78	5	0.0641026	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.5|25.5	4.646274|4.646274	0.87958|0.87958	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571|ENST00000411912	T|.	0.11169|.	2.8|.	5.72|5.72	5.72|5.72	0.89469|0.89469	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.74473|.	0.3721|.	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	D|.	0.69078|.	0.997|.	D|.	0.71870|.	0.975|.	T|.	0.71062|.	-0.4701|.	10|.	0.72032|.	D|.	0.01|.	.|.	19.8938|19.8938	0.96942|0.96942	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2540|.	Q70CQ2|.	UBP34_HUMAN|.	H|S	2388;2388;2540|299	ENSP00000381577:D2540H|.	ENSP00000263989:D2388H|.	D|X	-|-	1|2	0|2	USP34|USP34	61303913|61303913	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.348000|7.348000	0.79366|0.79366	2.703000|2.703000	0.92315|0.92315	0.460000|0.460000	0.39030|0.39030	GAC|TGA	.	.	none		0.308	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
SHROOM4	57477	hgsc.bcm.edu	37	X	50350674	50350674	+	Silent	SNP	T	T	C	rs3747282	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:50350674T>C	ENST00000289292.7	-	6	3751	c.3468A>G	c.(3466-3468)gaA>gaG	p.E1156E	SHROOM4_ENST00000376020.2_Silent_p.E1156E|SHROOM4_ENST00000460112.3_Silent_p.E1040E			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	50	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	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	
C16orf62	57020	hgsc.bcm.edu	37	16	19680546	19680546	+	Silent	SNP	T	T	C	rs957676	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:19680546T>C	ENST00000251143.5	+	27	2298	c.2286T>C	c.(2284-2286)gaT>gaC	p.D762D	C16orf62_ENST00000543152.1_Silent_p.D511D|C16orf62_ENST00000438132.3_Silent_p.D851D|C16orf62_ENST00000417362.2_Silent_p.D669D|C16orf62_ENST00000448695.1_Silent_p.D612D|C16orf62_ENST00000542263.1_Silent_p.D758D			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	762						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						TTAATATTGATGGGAAGATGC	0.408													C|||	1627	0.32488	0.3729	0.3098	5008	,	,		19645	0.2887		0.34	False		,,,				2504	0.2924				p.D851D		Atlas-SNP	.											.	C16orf62	164	.	0			c.T2553C						PASS	.	C		1628,2764	659.7+/-400.6	290,1048,858	118.0	117.0	118.0		2553	-2.5	0.6	16	dbSNP_86	118	2851,5749	674.3+/-403.1	467,1917,1916	no	coding-synonymous	C16orf62	NM_020314.5		757,2965,2774	CC,CT,TT		33.1512,37.0674,34.4751		851/1053	19680546	4479,8513	2196	4300	6496	SO:0001819	synonymous_variant	57020	exon27			TATTGATGGGAAG		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.2286T>C	16.37:g.19680546T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																				T|0.656;C|0.344	0.344	strong		0.408	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314	
LAMA5	3911	hgsc.bcm.edu	37	20	60897721	60897721	+	Missense_Mutation	SNP	C	C	T	rs3737137	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:60897721C>T	ENST00000252999.3	-	46	6224	c.6158G>A	c.(6157-6159)cGc>cAc	p.R2053H		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2053	Laminin EGF-like 20. {ECO:0000255|PROSITE-ProRule:PRU00460}.		R -> H (in dbSNP:rs3737137).		angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TACCTGGCAGCGGTCACAGCG	0.682													.|||	749	0.149561	0.0091	0.1571	5008	,	,		8221	0.127		0.2425	False		,,,				2504	0.2618				p.R2053H		Atlas-SNP	.											.	LAMA5	268	.	0			c.G6158A						PASS	.	C	HIS/ARG	173,3877		11,151,1863	6.0	6.0	6.0		6158	-4.9	0.9	20	dbSNP_107	6	1643,6367		144,1355,2506	yes	missense	LAMA5	NM_005560.3	29	155,1506,4369	TT,TC,CC		20.5119,4.2716,15.058	benign	2053/3696	60897721	1816,10244	2025	4005	6030	SO:0001583	missense	3911	exon46			TGGCAGCGGTCAC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.6158G>A	20.37:g.60897721C>T	ENSP00000252999:p.Arg2053His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	136	77	0.566176	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	317	0.14514652014652016	9	0.018292682926829267	64	0.17679558011049723	64	0.11188811188811189	180	0.23746701846965698	c	9.823	1.186240	0.21870	0.042716	0.205119	ENSG00000130702	ENST00000252999	T	0.37058	1.22	4.12	-4.95	0.03048	EGF-like, laminin (4);	0.294485	0.33691	N	0.004660	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	B	0.21452	0.056	B	0.17433	0.018	T	0.15093	-1.0449	9	0.42905	T	0.14	.	7.5599	0.27845	0.1022:0.4074:0.0:0.4904	rs3737137;rs60521636;rs3737137	2053	O15230	LAMA5_HUMAN	H	2053	ENSP00000252999:R2053H	ENSP00000252999:R2053H	R	-	2	0	LAMA5	60331116	0.806000	0.28996	0.855000	0.33649	0.027000	0.11550	0.110000	0.15437	-0.895000	0.03920	-1.199000	0.01669	CGC	C|0.858;T|0.142	0.142	strong		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SLC7A8	23428	hgsc.bcm.edu	37	14	23598976	23598976	+	Silent	SNP	G	G	A	rs17183863	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23598976G>A	ENST00000316902.7	-	9	1871	c.1146C>T	c.(1144-1146)agC>agT	p.S382S	SLC7A8_ENST00000422941.2_Silent_p.S158S|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000453702.1_Silent_p.S179S|SLC7A8_ENST00000529705.2_Silent_p.S277S	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	382					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	TGTACATGTCGCTGGTGACCA	0.498													G|||	524	0.104633	0.1331	0.0778	5008	,	,		20700	0.1438		0.0606	False		,,,				2504	0.09				p.S382S		Atlas-SNP	.											.	SLC7A8	54	.	0			c.C1146T						PASS	.	G	,	598,3808	262.2+/-264.8	43,512,1648	226.0	195.0	206.0		1146,537	-9.6	0.6	14	dbSNP_123	206	578,8022	154.9+/-209.1	19,540,3741	no	coding-synonymous,coding-synonymous	SLC7A8	NM_012244.2,NM_182728.1	,	62,1052,5389	AA,AG,GG		6.7209,13.5724,9.042	,	382/536,179/333	23598976	1176,11830	2203	4300	6503	SO:0001819	synonymous_variant	23428	exon9			CATGTCGCTGGTG	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"""Solute carriers"""	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.1146C>T	14.37:g.23598976G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	59	0.621053	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000316902.7	37	CCDS9590.1	235	0.10760073260073261	78	0.15853658536585366	26	0.0718232044198895	87	0.1520979020979021	44	0.05804749340369393	G	9.529	1.110304	0.20714	0.135724	0.067209	ENSG00000092068	ENST00000334354	.	.	.	5.86	-9.58	0.00559	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	20.7128	0.99707	0.8442:0.0:0.1558:0.0	rs17183863;rs17854736;rs52824765;rs58569778;rs17183863	.	.	.	X	179	.	ENSP00000334744:R179X	R	-	1	2	SLC7A8	22668816	0.000000	0.05858	0.616000	0.29078	0.953000	0.61014	-2.118000	0.01325	-2.000000	0.00965	-1.727000	0.00703	CGA	G|0.901;A|0.099	0.099	strong		0.498	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3		
LAMA1	284217	hgsc.bcm.edu	37	18	6997818	6997818	+	Missense_Mutation	SNP	A	A	C	rs12961939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:6997818A>C	ENST00000389658.3	-	33	4822	c.4729T>G	c.(4729-4731)Tct>Gct	p.S1577A		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1577	Domain II and I.		S -> A (in dbSNP:rs12961939).		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)				AGGTTCAGAGAAAGAACGGCA	0.398													A|||	749	0.149561	0.1513	0.1758	5008	,	,		23170	0.0575		0.2684	False		,,,				2504	0.1012				p.S1577A		Atlas-SNP	.											.	LAMA1	458	.	0			c.T4729G						PASS	.	A	ALA/SER	658,3748	279.9+/-275.1	52,554,1597	205.0	187.0	193.0		4729	4.2	0.5	18	dbSNP_121	193	2311,6289	388.3+/-342.5	307,1697,2296	yes	missense	LAMA1	NM_005559.3	99	359,2251,3893	CC,CA,AA		26.8721,14.9342,22.8279	possibly-damaging	1577/3076	6997818	2969,10037	2203	4300	6503	SO:0001583	missense	284217	exon33			TCAGAGAAAGAAC	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.4729T>G	18.37:g.6997818A>C	ENSP00000374309:p.Ser1577Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	399	0.18269230769230768	76	0.15447154471544716	74	0.20441988950276244	40	0.06993006993006994	209	0.2757255936675462	A	10.49	1.363916	0.24684	0.149342	0.268721	ENSG00000101680	ENST00000389658	T	0.12039	2.72	5.36	4.18	0.49190	Laminin I (1);	0.281539	0.35615	N	0.003085	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	B	0.32324	0.364	B	0.33295	0.161	T	0.42816	-0.9429	9	0.14656	T	0.56	.	11.7865	0.52045	0.9275:0.0:0.0725:0.0	rs12961939;rs52825785;rs58740747;rs12961939	1577	P25391	LAMA1_HUMAN	A	1577	ENSP00000374309:S1577A	ENSP00000374309:S1577A	S	-	1	0	LAMA1	6987818	0.997000	0.39634	0.506000	0.27664	0.067000	0.16453	4.299000	0.59073	2.160000	0.67779	0.533000	0.62120	TCT	A|0.790;C|0.210	0.210	strong		0.398	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
MYOM3	127294	hgsc.bcm.edu	37	1	24393563	24393563	+	Missense_Mutation	SNP	C	C	T	rs16829071	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24393563C>T	ENST00000374434.3	-	28	3533	c.3371G>A	c.(3370-3372)cGg>cAg	p.R1124Q	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Missense_Mutation_p.R1124Q|MYOM3_ENST00000330966.7_Missense_Mutation_p.R1127Q|MYOM3_ENST00000338909.5_5'Flank|RP11-293P20.4_ENST00000429191.1_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1124	Ig-like C2-type 3.		R -> Q (in dbSNP:rs16829071). {ECO:0000269|PubMed:15489334}.			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CTGCAACGGCCGCTCAAAATA	0.637													T|||	1404	0.280351	0.4871	0.1599	5008	,	,		16492	0.1964		0.1421	False		,,,				2504	0.3149				p.R1124Q		Atlas-SNP	.											.	MYOM3	131	.	0			c.G3371A						PASS	.	T	GLN/ARG	1438,2592		264,910,841	19.0	21.0	20.0		3371	5.5	0.8	1	dbSNP_123	20	1155,7167		85,985,3091	yes	missense	MYOM3	NM_152372.3	43	349,1895,3932	TT,TC,CC		13.8789,35.6824,20.9926	benign	1124/1438	24393563	2593,9759	2015	4161	6176	SO:0001583	missense	127294	exon28			AACGGCCGCTCAA	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.3371G>A	1.37:g.24393563C>T	ENSP00000363557:p.Arg1124Gln	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	159	71	0.446541	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	469	0.21474358974358973	196	0.3983739837398374	61	0.1685082872928177	109	0.19055944055944055	103	0.1358839050131926	T	14.02	2.411762	0.42817	0.356824	0.138789	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.54071	0.64;0.59;0.64	5.53	5.53	0.82687	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.166494	0.52532	N	0.000073	T	0.00012	0.0000	N	0.08118	0	0.58432	P	9.000000000036756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34900	-0.9810	9	0.54805	T	0.06	.	11.5382	0.50651	0.0:0.0703:0.0:0.9297	rs16829071;rs52795219;rs16829071	1124;1124	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	Q	1124;1127;1124	ENSP00000363557:R1124Q;ENSP00000332670:R1127Q;ENSP00000328415:R1124Q	ENSP00000328415:R1124Q	R	-	2	0	MYOM3	24266150	1.000000	0.71417	0.793000	0.32043	0.105000	0.19272	5.362000	0.66098	0.941000	0.37499	-0.490000	0.04691	CGG	C|0.765;T|0.235	0.235	strong		0.637	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
RAB3A	5864	hgsc.bcm.edu	37	19	18313515	18313515	+	Silent	SNP	C	C	T	rs2280342	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18313515C>T	ENST00000222256.4	-	2	214	c.36G>A	c.(34-36)aaG>aaA	p.K12K	AC068499.10_ENST00000596473.1_RNA|AC068499.10_ENST00000594805.3_RNA|RAB3A_ENST00000464076.3_Intron|AC068499.10_ENST00000599416.2_RNA	NM_002866.4	NP_002857.1	P20336	RAB3A_HUMAN	RAB3A, member RAS oncogene family	12					axonogenesis (GO:0007409)|constitutive secretory pathway (GO:0045054)|glutamate secretion (GO:0014047)|GTP catabolic process (GO:0006184)|lung development (GO:0030324)|maintenance of presynaptic active zone structure (GO:0048790)|mitochondrion organization (GO:0007005)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|post-embryonic development (GO:0009791)|protein transport (GO:0015031)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|respiratory system process (GO:0003016)|response to electrical stimulus (GO:0051602)|sensory perception of touch (GO:0050975)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle recycling (GO:0036465)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	8						CCGAGGACTCCTTCTGCCCAT	0.577											OREG0025360	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	309	0.0617013	0.0113	0.1282	5008	,	,		18670	0.1498		0.004	False		,,,				2504	0.0511				p.K12K		Atlas-SNP	.											.	RAB3A	23	.	0			c.G36A						PASS	.	C		55,4351	52.3+/-87.9	0,55,2148	216.0	183.0	194.0		36	3.4	1.0	19	dbSNP_100	194	51,8549	32.3+/-84.9	1,49,4250	no	coding-synonymous	RAB3A	NM_002866.4		1,104,6398	TT,TC,CC		0.593,1.2483,0.815		12/221	18313515	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	5864	exon2			GGACTCCTTCTGC		CCDS12372.1	19p13.2	2008-07-17			ENSG00000105649	ENSG00000105649		"""RAB, member RAS oncogene"""	9777	protein-coding gene	gene with protein product	"""RAS-associated protein RAB3A"""	179490				2687157, 7532276	Standard	NM_002866		Approved		uc002nie.2	P20336	OTTHUMG00000137378	ENST00000222256.4:c.36G>A	19.37:g.18313515C>T		Somatic	200	0	0	724	WXS	Illumina HiSeq	Phase_I	215	114	0.530233	NM_002866	A8K0J4|Q9NYE1	Silent	SNP	ENST00000222256.4	37	CCDS12372.1																																																																																			C|0.966;T|0.034	0.034	strong		0.577	RAB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268056.2	NM_002866	
BCO1	53630	hgsc.bcm.edu	37	16	81279120	81279120	+	Missense_Mutation	SNP	T	T	C	rs28370522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:81279120T>C	ENST00000425577.2	+	2	325	c.28T>C	c.(28-30)Tgg>Cgg	p.W10R	BCMO1_ENST00000258168.2_Silent_p.N35N|BCMO1_ENST00000564552.1_Silent_p.N35N														p.N35N(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						TGCTCCGCAATGGGCCTGGGA	0.537													C|||	1901	0.379593	0.5484	0.366	5008	,	,		21216	0.3472		0.341	False		,,,				2504	0.2342				p.N35N		Atlas-SNP	.											BCMO1,NS,carcinoma,0,1	BCMO1	53	1	1	Substitution - coding silent(1)	stomach(1)	c.T105C						PASS	.	C		2281,2123	576.8+/-384.3	582,1117,503	152.0	147.0	149.0		105	-7.8	0.0	16	dbSNP_125	149	2758,5842	680.0+/-403.6	466,1826,2008	no	coding-synonymous	BCMO1	NM_017429.2		1048,2943,2511	CC,CT,TT		32.0698,48.2062,38.7496		35/548	81279120	5039,7965	2202	4300	6502	SO:0001583	missense	53630	exon2			CCGCAATGGGCCT																												ENST00000425577.2:c.28T>C	16.37:g.81279120T>C	ENSP00000400586:p.Trp10Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_017429		Silent	SNP	ENST00000425577.2	37		839	0.3841575091575092	271	0.5508130081300813	138	0.3812154696132597	178	0.3111888111888112	252	0.3324538258575198	C	7.118	0.577439	0.13686	0.517938	0.320698	ENSG00000135697	ENST00000425577	D	0.93247	-3.19	4.89	-7.85	0.01192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49798	P	1.7100000000003224E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.17077	-1.0381	7	0.87932	D	0	-34.7449	17.4964	0.87718	0.0:0.2133:0.0:0.7867	rs28370522	10	E7EM88	.	R	10	ENSP00000400586:W10R	ENSP00000400586:W10R	W	+	1	0	BCMO1	79836621	0.000000	0.05858	0.029000	0.17559	0.549000	0.35272	-2.127000	0.01315	-2.283000	0.00672	-1.551000	0.00897	TGG	T|0.605;C|0.395	0.395	strong		0.537	BCMO1-201	KNOWN	basic	protein_coding	protein_coding			
RRP36	88745	hgsc.bcm.edu	37	6	42992825	42992825	+	Missense_Mutation	SNP	C	C	G	rs3749903	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42992825C>G	ENST00000244496.5	+	2	243	c.233C>G	c.(232-234)gCt>gGt	p.A78G		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	78			A -> G (in dbSNP:rs3749903).		ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						AAGAAACAAGCTTCTAGACCA	0.433													G|||	1721	0.34365	0.7133	0.2421	5008	,	,		22689	0.2123		0.1223	False		,,,				2504	0.2791				p.A78G		Atlas-SNP	.											.	RRP36	20	.	0			c.C233G						PASS	.	G	GLY/ALA	2782,1624	499.5+/-364.4	882,1018,303	132.0	118.0	122.0		233	-2.4	0.0	6	dbSNP_107	122	1118,7482	767.9+/-407.6	65,988,3247	yes	missense	RRP36	NM_033112.2	60	947,2006,3550	GG,GC,CC		13.0,36.8588,29.9862	benign	78/260	42992825	3900,9106	2203	4300	6503	SO:0001583	missense	88745	exon2			AACAAGCTTCTAG	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.233C>G	6.37:g.42992825C>G	ENSP00000244496:p.Ala78Gly	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_033112	Q9BRF6|Q9P0C8	Missense_Mutation	SNP	ENST00000244496.5	37	CCDS34453.1	642	0.29395604395604397	343	0.6971544715447154	80	0.22099447513812154	121	0.21153846153846154	98	0.12928759894459102	G	0.013	-1.630591	0.00813	0.631412	0.13	ENSG00000124541	ENST00000244496	T	0.48201	0.82	4.82	-2.4	0.06583	.	1.291000	0.04995	N	0.468096	T	0.07052	0.0179	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11991	-1.0565	9	0.20046	T	0.44	.	1.8773	0.03221	0.2792:0.3881:0.201:0.1316	rs3749903;rs52827172;rs58983673;rs3749903	78	Q96EU6	RRP36_HUMAN	G	78	ENSP00000244496:A78G	ENSP00000244496:A78G	A	+	2	0	RRP36	43100803	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.006000	0.13152	-0.500000	0.06614	-1.130000	0.01982	GCT	C|0.705;G|0.295	0.295	strong		0.433	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
SOCS7	30837	hgsc.bcm.edu	37	17	36552190	36552190	+	Missense_Mutation	SNP	A	A	G	rs55687042	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:36552190A>G	ENST00000577233.1	+	9	1715	c.1715A>G	c.(1714-1716)aAa>aGa	p.K572R	SOCS7_ENST00000331159.5_Missense_Mutation_p.K538R	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	572					fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					CTCATTTCCAAACAGAAGCAA	0.502													A|||	66	0.0131789	0.0008	0.0159	5008	,	,		18836	0.001		0.0348	False		,,,				2504	0.0184				p.K572R		Atlas-SNP	.											.	SOCS7	22	.	0			c.A1715G						PASS	.	A	ARG/LYS	37,4369	40.8+/-73.8	0,37,2166	61.0	59.0	60.0		1715	5.9	1.0	17	dbSNP_129	60	381,8219	124.3+/-183.0	6,369,3925	yes	missense	SOCS7	NM_014598.2	26	6,406,6091	GG,GA,AA		4.4302,0.8398,3.2139	benign	572/582	36552190	418,12588	2203	4300	6503	SO:0001583	missense	30837	exon9			TTTCCAAACAGAA	AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	29846	protein-coding gene	gene with protein product	"""Nck, Ash and phospholipase C binding protein"", ""NCK-associated protein 4"""	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.1715A>G	17.37:g.36552190A>G	ENSP00000464034:p.Lys572Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_014598	A2VCU2|Q0IJ63	Missense_Mutation	SNP	ENST00000577233.1	37	CCDS32637.1	38	0.0173992673992674	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	29	0.03825857519788918	A	13.56	2.274571	0.40194	0.008398	0.044302	ENSG00000174111	ENST00000331159	.	.	.	5.93	5.93	0.95920	.	0.208574	0.41396	D	0.000884	T	0.06142	0.0159	N	0.14661	0.345	0.32131	N	0.586711	P;P	0.44734	0.842;0.842	B;B	0.34536	0.185;0.185	T	0.07986	-1.0744	9	0.31617	T	0.26	-8.9747	15.3769	0.74615	1.0:0.0:0.0:0.0	rs55687042;rs61746210	288;572	B5MDS8;O14512	.;SOCS7_HUMAN	R	572	.	ENSP00000330659:K572R	K	+	2	0	SOCS7	33805716	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.180000	0.50895	2.281000	0.76405	0.533000	0.62120	AAA	A|0.971;G|0.029	0.029	strong		0.502	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052	
DTL	51514	hgsc.bcm.edu	37	1	212273606	212273606	+	Missense_Mutation	SNP	G	G	A	rs35137676	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:212273606G>A	ENST00000366991.4	+	14	1588	c.1274G>A	c.(1273-1275)aGt>aAt	p.S425N	DTL_ENST00000542077.1_Missense_Mutation_p.S383N|RN7SKP98_ENST00000517070.1_RNA|DTL_ENST00000475419.1_3'UTR	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	425			S -> N (in dbSNP:rs35137676).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|chromosome (GO:0005694)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)		ACAGTAACGAGTAGCCAGAGT	0.473													G|||	52	0.0103834	0.0015	0.0245	5008	,	,		17943	0.0		0.0308	False		,,,				2504	0.002				p.S425N		Atlas-SNP	.											DTL,NS,carcinoma,-1,1	DTL	52	1	0			c.G1274A						PASS	.	G	ASN/SER	36,4370	40.8+/-73.8	0,36,2167	71.0	75.0	74.0		1274	-0.9	0.1	1	dbSNP_126	74	335,8265	115.0+/-174.9	6,323,3971	yes	missense	DTL	NM_016448.2	46	6,359,6138	AA,AG,GG		3.8953,0.8171,2.8525	benign	425/731	212273606	371,12635	2203	4300	6503	SO:0001583	missense	51514	exon14			TAACGAGTAGCCA	AF195765	CCDS1502.1, CCDS65778.1	1q32	2013-01-10	2012-02-23		ENSG00000143476	ENSG00000143476		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"""	30288	protein-coding gene	gene with protein product	"""RA regulated nuclear matrix associated protein"", ""DDB1 and CUL4 associated factor 2"""	610617	"""denticleless homolog (Drosophila)"""			11278750	Standard	NM_001286229		Approved	RAMP, L2DTL, DCAF2	uc009xdc.3	Q9NZJ0	OTTHUMG00000037133	ENST00000366991.4:c.1274G>A	1.37:g.212273606G>A	ENSP00000355958:p.Ser425Asn	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	214	95	0.443925	NM_016448	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Missense_Mutation	SNP	ENST00000366991.4	37	CCDS1502.1	25	0.011446886446886446	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	9.046	0.990938	0.18966	0.008171	0.038953	ENSG00000143476	ENST00000366991;ENST00000542077;ENST00000420235	T;T	0.72051	-0.54;-0.62	5.54	-0.925	0.10458	.	0.462024	0.25628	N	0.029378	T	0.16642	0.0400	N	0.21448	0.665	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	0.06516	-1.0822	10	0.18276	T	0.48	-43.4432	5.751	0.18146	0.3171:0.225:0.458:0.0	rs35137676;rs61733817	383;425;383	F5GZ90;Q9NZJ0;B4E0E6	.;DTL_HUMAN;.	N	425;383;104	ENSP00000355958:S425N;ENSP00000443870:S383N	ENSP00000355958:S425N	S	+	2	0	DTL	210340229	0.901000	0.30685	0.079000	0.20413	0.953000	0.61014	0.515000	0.22801	-0.349000	0.08274	0.655000	0.94253	AGT	G|0.975;A|0.025	0.025	strong		0.473	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	NM_016448	
IGFALS	3483	hgsc.bcm.edu	37	16	1838703	1838703	+	IGR	SNP	G	G	A	rs11540961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1838703G>A	ENST00000215539.3	-	0	2116				NUBP2_ENST00000262302.9_Silent_p.A268A|NUBP2_ENST00000568706.1_Silent_p.A127A|NUBP2_ENST00000565987.1_Silent_p.A208A|NUBP2_ENST00000543305.1_Silent_p.A127A			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						CGACGCCCGCGTGCCTCCCCT	0.657													G|||	144	0.028754	0.0061	0.0591	5008	,	,		15636	0.002		0.0716	False		,,,				2504	0.0215				p.A268A		Atlas-SNP	.											NUBP2,NS,carcinoma,+2,2	NUBP2	25	2	0			c.G804A						PASS	.	G		87,4307	69.8+/-107.6	2,83,2112	26.0	26.0	26.0		804	-9.9	0.0	16	dbSNP_120	26	624,7968	158.0+/-211.6	20,584,3692	no	coding-synonymous	NUBP2	NM_012225.2		22,667,5804	AA,AG,GG		7.2626,1.98,5.4751		268/272	1838703	711,12275	2197	4296	6493	SO:0001628	intergenic_variant	10101	exon7			GCCCGCGTGCCTC	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.1838703G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_012225	B4DZY8|E9PGU3	Silent	SNP	ENST00000215539.3	37	CCDS10446.1																																																																																			G|0.949;A|0.051	0.051	strong		0.657	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
GGTLC2	91227	hgsc.bcm.edu	37	22	22989256	22989256	+	Missense_Mutation	SNP	A	A	G	rs2904923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:22989256A>G	ENST00000480559.1	+	2	209	c.209A>G	c.(208-210)gAg>gGg	p.E70G	GGTLC2_ENST00000448514.1_Missense_Mutation_p.E70G|POM121L1P_ENST00000402027.1_RNA	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	70			E -> G (in dbSNP:rs2904923). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8830654}.		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)	p.E70G(1)		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)		CCGGTCAGCGAGATCCTGTTC	0.587													.|||	4773	0.953075	0.9955	0.9452	5008	,	,		9320	1.0		0.8519	False		,,,				2504	0.9571				p.E70G		Atlas-SNP	.											GGTLC2,NS,carcinoma,0,2	GGTLC2	20	2	1	Substitution - Missense(1)	prostate(1)	c.A209G						scavenged	.	G	GLY/GLU	4265,141		2073,119,11	70.0	74.0	73.0		209		0.0	22	dbSNP_101	73	7122,1468		3136,850,309	no	missense	GGTLC2	NM_199127.2	98	5209,969,320	GG,GA,AA		17.0896,3.2002,12.3807	benign	70/219	22989256	11387,1609	2203	4295	6498	SO:0001583	missense	91227	exon2			TCAGCGAGATCCT	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.209A>G	22.37:g.22989256A>G	ENSP00000419751:p.Glu70Gly	Somatic	303	3	0.00990099		WXS	Illumina HiSeq	Phase_I	286	143	0.5	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Missense_Mutation	SNP	ENST00000480559.1	37	CCDS13802.2	1870	0.8562271062271062	438	0.8902439024390244	303	0.8370165745856354	547	0.9562937062937062	582	0.7678100263852242	N	0.035	-1.312951	0.01331	0.967998	0.829104	ENSG00000100121	ENST00000480559;ENST00000448514	T;T	0.00591	6.35;6.35	.	.	.	.	0.058434	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00000	-4.51	0.51482	P	7.100000000004325E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45571	-0.9252	8	0.02654	T	1	-35.6147	2.6652	0.05046	0.5:0.0:0.5:0.0	rs2904923;rs56798571	70;70	Q14390;B7WND7	GGTL2_HUMAN;.	G	70	ENSP00000419751:E70G;ENSP00000415676:E70G	ENSP00000415676:E70G	E	+	2	0	GGTLC2	21319256	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	4.302000	0.59092	-0.000000	0.14550	0.000000	0.15137	GAG	A|0.151;G|0.849	0.849	strong		0.587	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
EHMT2	10919	hgsc.bcm.edu	37	6	31851172	31851172	+	Silent	SNP	G	G	A	rs148424397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31851172G>A	ENST00000375537.4	-	23	2967	c.2961C>T	c.(2959-2961)tgC>tgT	p.C987C	EHMT2-AS1_ENST00000434689.1_RNA|EHMT2_ENST00000395728.3_Silent_p.C1044C|EHMT2_ENST00000375528.4_Silent_p.C1010C|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375530.4_Silent_p.C953C	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	987	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						TGAGCTGGCCGCACAGGCAGT	0.632													G|||	6	0.00119808	0.0	0.0043	5008	,	,		20855	0.0		0.003	False		,,,				2504	0.0				p.C987C		Atlas-SNP	.											.	EHMT2	45	.	0			c.C2961T						PASS	.	G	,	0,3018		0,0,1509	51.0	39.0	43.0		2961,2859	-9.0	0.7	6	dbSNP_134	43	8,5410		0,8,2701	yes	coding-synonymous,coding-synonymous	EHMT2	NM_006709.3,NM_025256.5	,	0,8,4210	AA,AG,GG		0.1477,0.0,0.0948	,	987/1211,953/1177	31851172	8,8428	1509	2709	4218	SO:0001819	synonymous_variant	10919	exon23			CTGGCCGCACAGG	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	14129	protein-coding gene	gene with protein product		604599	"""chromosome 6 open reading frame 30"", ""HLA-B associated transcript 8"""	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.2961C>T	6.37:g.31851172G>A		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	269	145	0.539033	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Silent	SNP	ENST00000375537.4	37	CCDS4725.1																																																																																			G|0.999;A|0.001	0.001	strong		0.632	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709	
DOT1L	84444	hgsc.bcm.edu	37	19	2222327	2222327	+	Silent	SNP	G	G	A	rs373960110		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2222327G>A	ENST00000398665.3	+	24	3195	c.3159G>A	c.(3157-3159)gcG>gcA	p.A1053A		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1053					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		CCACTGGTGCGGGCAGTGCCA	0.662																																					p.A1053A		Atlas-SNP	.											.	DOT1L	205	.	0			c.G3159A						PASS	.	G		0,4246		0,0,2123	26.0	32.0	30.0		3159	-8.4	0.0	19		30	1,8471		0,1,4235	no	coding-synonymous	DOT1L	NM_032482.2		0,1,6358	AA,AG,GG		0.0118,0.0,0.0079		1053/1538	2222327	1,12717	2123	4236	6359	SO:0001819	synonymous_variant	84444	exon24			TGGTGCGGGCAGT	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.3159G>A	19.37:g.2222327G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	80	0.606061	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042205	0.01997	0.0	1.18E-4	ENSG00000104885	ENST00000440640	.	.	.	4.21	-8.42	0.00957	.	.	.	.	.	T	0.14657	0.0354	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.19257	-1.0311	4	.	.	.	-2.2	0.8379	0.01143	0.3872:0.2217:0.212:0.1791	.	.	.	.	Q	840	.	.	R	+	2	0	DOT1L	2173327	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.688000	0.05150	-1.857000	0.01159	-0.379000	0.06801	CGG	.	.	weak		0.662	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
ZNF880	400713	hgsc.bcm.edu	37	19	52887282	52887282	+	Missense_Mutation	SNP	A	A	G	rs324125	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	153	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	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	
DGAT1	8694	hgsc.bcm.edu	37	8	145542021	145542021	+	Silent	SNP	G	G	A	rs56180335	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145542021G>A	ENST00000332324.4	-	7	852	c.579C>T	c.(577-579)ggC>ggT	p.G193G	DGAT1_ENST00000527438.1_5'Flank|DGAT1_ENST00000531896.1_Silent_p.G193G	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	193					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	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;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			CCAGCAGGGAGCCCACTGCAG	0.682													G|||	117	0.0233626	0.0023	0.0331	5008	,	,		17380	0.0		0.0825	False		,,,				2504	0.0082				p.G193G		Atlas-SNP	.											.	DGAT1	26	.	0			c.C579T						PASS	.	G		58,4348	52.3+/-87.9	0,58,2145	30.0	29.0	29.0		579	3.7	1.0	8	dbSNP_129	29	640,7950	155.2+/-209.3	35,570,3690	no	coding-synonymous	DGAT1	NM_012079.4		35,628,5835	AA,AG,GG		7.4505,1.3164,5.3709		193/489	145542021	698,12298	2203	4295	6498	SO:0001819	synonymous_variant	8694	exon7			CAGGGAGCCCACT	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"""diacylglycerol O-acyltransferase homolog 1 (mouse)"""			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.579C>T	8.37:g.145542021G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	41	0.37963	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Silent	SNP	ENST00000332324.4	37	CCDS6420.1																																																																																			G|0.956;A|0.044	0.044	strong		0.682	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079	
OR1S1	219959	hgsc.bcm.edu	37	11	57982896	57982896	+	Missense_Mutation	SNP	G	G	T	rs2903566	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57982896G>T	ENST00000309433.6	+	1	680	c.680G>T	c.(679-681)aGc>aTc	p.S227I		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	227			S -> I (in dbSNP:rs2903566).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTTACACTCAGCTTCTTTTCC	0.448													T|||	2616	0.522364	0.2814	0.5418	5008	,	,		21979	0.8036		0.4225	False		,,,				2504	0.6472				p.S227I		Atlas-SNP	.											.	OR1S1	139	.	0			c.G680T						PASS	.	T	ILE/SER	1299,3103	697.4+/-406.2	195,909,1097	157.0	124.0	135.0		680	2.1	0.1	11	dbSNP_101	135	3641,4949	623.4+/-397.5	784,2073,1438	yes	missense	OR1S1	NM_001004458.1	142	979,2982,2535	TT,TG,GG		42.3865,29.5093,38.0234	benign	227/326	57982896	4940,8052	2201	4295	6496	SO:0001583	missense	219959	exon1			CACTCAGCTTCTT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.680G>T	11.37:g.57982896G>T	ENSP00000311688:p.Ser227Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	136	61	0.448529	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1080	0.4945054945054945	146	0.2967479674796748	186	0.5138121546961326	433	0.756993006993007	315	0.4155672823218997	T	0.003	-2.561584	0.00136	0.295093	0.423865	ENSG00000172774	ENST00000309433	T	0.00010	9.43	3.23	2.08	0.27032	GPCR, rhodopsin-like superfamily (1);	0.128568	0.34828	N	0.003657	T	0.00012	0.0000	N	0.00008	-3.13	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46569	-0.9182	9	0.02654	T	1	.	4.0934	0.09980	0.0:0.3043:0.1798:0.516	rs2903566;rs17463613;rs52823244;rs2903566	227	Q8NH92	OR1S1_HUMAN	I	227	ENSP00000311688:S227I	ENSP00000311688:S227I	S	+	2	0	OR1S1	57739472	0.027000	0.19231	0.078000	0.20375	0.442000	0.32017	1.851000	0.39338	-0.026000	0.13895	-0.527000	0.04329	AGC	G|0.565;T|0.435	0.435	strong		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
ADAM33	80332	hgsc.bcm.edu	37	20	3650205	3650205	+	Missense_Mutation	SNP	G	G	A	rs2280090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3650205G>A	ENST00000356518.2	-	20	2561	c.2320C>T	c.(2320-2322)Ccc>Tcc	p.P774S	ADAM33_ENST00000379861.4_Missense_Mutation_p.P774S|ADAM33_ENST00000350009.2_Missense_Mutation_p.P748S|ADAM33_ENST00000466620.1_5'UTR	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	110	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	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	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084191	31084191	+	Intron	SNP	T	T	C	rs33941312	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31084191T>C	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.S401G	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						ATGCTAGAACTGCTGGGGACT	0.647													T|||	60	0.0119808	0.0008	0.0058	5008	,	,		15616	0.0149		0.0288	False		,,,				2504	0.0112				p.S401G		Atlas-SNP	.											.	CDSN	48	.	0			c.A1201G						PASS	.	T	GLY/SER,	18,4382		0,18,2182	36.0	42.0	40.0		1201,	3.7	0.3	6	dbSNP_126	40	169,8425		3,163,4131	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	56,	3,181,6313	CC,CT,TT		1.9665,0.4091,1.4391	possibly-damaging,	401/530,	31084191	187,12807	2200	4297	6497	SO:0001627	intron_variant	1041	exon2			TAGAACTGCTGGG	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+1523T>C	6.37:g.31084191T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	40	0.018315018315018316	0	0.0	2	0.0055248618784530384	14	0.024475524475524476	24	0.0316622691292876	T	9.761	1.170009	0.21621	0.004091	0.019665	ENSG00000204539	ENST00000376288	T	0.08807	3.05	3.74	3.74	0.42951	.	0.140133	0.32901	N	0.005510	T	0.06690	0.0171	N	0.24115	0.695	0.09310	N	0.999995	P	0.49696	0.927	D	0.67725	0.953	T	0.14755	-1.0461	10	0.52906	T	0.07	-3.9289	8.9816	0.35968	0.0:0.0:0.0:1.0	rs33941312	401	Q15517	CDSN_HUMAN	G	401	ENSP00000365465:S401G	ENSP00000365465:S401G	S	-	1	0	CDSN	31192170	0.006000	0.16342	0.252000	0.24328	0.287000	0.27160	-0.141000	0.10327	1.683000	0.51011	0.386000	0.25728	AGT	T|0.985;C|0.015	0.015	strong		0.647	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
HADHA	3030	hgsc.bcm.edu	37	2	26455127	26455127	+	Silent	SNP	G	G	A	rs11552518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:26455127G>A	ENST00000380649.3	-	6	603	c.474C>T	c.(472-474)taC>taT	p.Y158Y	HADHA_ENST00000461025.1_5'UTR|HADHA_ENST00000457468.2_Silent_p.Y71Y	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	158					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGCTATTCTGTATTGGCATG	0.398													G|||	713	0.142372	0.0219	0.1571	5008	,	,		16530	0.1458		0.2087	False		,,,				2504	0.2229				p.Y158Y		Atlas-SNP	.											.	HADHA	87	.	0			c.C474T						PASS	.	G		237,4169	138.8+/-174.5	8,221,1974	99.0	92.0	94.0		474	4.8	1.0	2	dbSNP_120	94	1862,6738	332.1+/-320.0	205,1452,2643	no	coding-synonymous	HADHA	NM_000182.4		213,1673,4617	AA,AG,GG		21.6512,5.379,16.1387		158/764	26455127	2099,10907	2203	4300	6503	SO:0001819	synonymous_variant	3030	exon6			TATTCTGTATTGG	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"""gastrin-binding protein"", ""long-chain-3-hydroxyacyl-CoA dehydrogenase"", ""long-chain 2-enoyl-CoA hydratase"", ""mitochondrial trifunctional protein, alpha subunit"""	600890	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"""			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.474C>T	2.37:g.26455127G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	67	27	0.402985	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Silent	SNP	ENST00000380649.3	37	CCDS1721.1																																																																																			G|0.834;C|0.000;A|0.165	0.165	strong		0.398	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182	
THEMIS2	9473	hgsc.bcm.edu	37	1	28209366	28209366	+	Missense_Mutation	SNP	A	A	G	rs3766400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:28209366A>G	ENST00000373921.3	+	4	1535	c.1531A>G	c.(1531-1533)Aag>Gag	p.K511E	THEMIS2_ENST00000328928.7_Missense_Mutation_p.K382E|THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	511	CABIT 2.		K -> E (in dbSNP:rs3766400). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACTGTTGTGAAGGCCAAGGG	0.567													G|||	2256	0.450479	0.0711	0.5029	5008	,	,		18066	0.501		0.6322	False		,,,				2504	0.6871				p.K511E		Atlas-SNP	.											.	.	.	.	0			c.A1531G						PASS	.	G	,GLU/LYS,	623,3461		45,533,1464	107.0	100.0	102.0		,1531,	4.0	0.9	1	dbSNP_107	102	5354,2994		1733,1888,553	yes	intron,missense,intron	C1orf38	NM_001039477.1,NM_001105556.1,NM_004848.2	,56,	1778,2421,2017	GG,GA,AA		35.8649,15.2547,48.0775	,benign,	,511/644,	28209366	5977,6455	2042	4174	6216	SO:0001583	missense	9473	exon4			GTTGTGAAGGCCA	AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"""induced by contact to basement membrane 1"""		"""chromosome 1 open reading frame 38"""	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.1531A>G	1.37:g.28209366A>G	ENSP00000363031:p.Lys511Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_001105556	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	993|993	0.45467032967032966|0.45467032967032966	46|46	0.09349593495934959|0.09349593495934959	191|191	0.5276243093922652|0.5276243093922652	280|280	0.48951048951048953|0.48951048951048953	476|476	0.6279683377308707|0.6279683377308707	G|G	1.629|1.629	-0.519377|-0.519377	0.04171|0.04171	0.152547|0.152547	0.641351|0.641351	ENSG00000130775|ENSG00000130775	ENST00000328928;ENST00000373921|ENST00000456990	T;T|.	0.12672|.	2.66;2.66|.	4.98|4.98	4.0|4.0	0.46444|0.46444	.|.	0.222353|.	0.47093|.	N|.	0.000246|.	T|.	0.00012|.	0.0000|.	N|N	0.00085|0.00085	-2.2|-2.2	0.51012|0.51012	P|P	9.599999999998499E-5|9.599999999998499E-5	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|.	0.44452|.	-0.9327|.	9|.	0.29301|.	T|.	0.29|.	-17.262|-17.262	3.2225|3.2225	0.06720|0.06720	0.085:0.2146:0.4511:0.2493|0.085:0.2146:0.4511:0.2493	rs3766400;rs59383226;rs3766400|rs3766400;rs59383226;rs3766400	382;315;511|.	Q5TEJ8-5;Q5TEJ8-6;Q5TEJ8|.	.;.;THMS2_HUMAN|.	E|W	382;511|258	ENSP00000329862:K382E;ENSP00000363031:K511E|.	ENSP00000329862:K382E|.	K|X	+|+	1|3	0|0	C1orf38|C1orf38	28081953|28081953	0.998000|0.998000	0.40836|0.40836	0.876000|0.876000	0.34364|0.34364	0.009000|0.009000	0.06853|0.06853	1.850000|1.850000	0.39328|0.39328	1.258000|1.258000	0.44101|0.44101	-0.227000|-0.227000	0.12334|0.12334	AAG|TGA	A|0.521;G|0.479	0.479	strong		0.567	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848	
TPSB2	64499	hgsc.bcm.edu	37	16	1279714	1279714	+	RNA	SNP	A	A	G	rs192643610	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1279714A>G	ENST00000339687.6	-	0	108				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				AACGATGCCCACTCGCTGCAG	0.711																																					p.V29A		Atlas-SNP	.											TPSB2,rectum,carcinoma,0,1	TPSB2	8	1	0			c.T86C						scavenged	.						25.0	32.0	29.0					16																	1279714		2180	4295	6475			64499	exon3			ATGCCCACTCGCT	AF099143		16p13.3	2009-11-20	2009-11-18		ENSG00000197253	ENSG00000197253			14120	protein-coding gene	gene with protein product	"""tryptase beta II"", ""tryptase beta III"""	191081	"""tryptase beta 2"""			19748655	Standard	NM_024164		Approved		uc002cky.3	P20231	OTTHUMG00000155926		16.37:g.1279714A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	83	53	0.638554	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Missense_Mutation	SNP	ENST00000339687.6	37		171	0.0782967032967033	39	0.07926829268292683	28	0.07734806629834254	44	0.07692307692307693	60	0.079155672823219	a	8.603	0.887339	0.17540	.	.	ENSG00000197253	ENST00000430512	T	0.81078	-1.45	4.02	-8.04	0.01110	.	1.382050	0.04868	N	0.445430	T	0.05090	0.0136	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32375	-0.9909	9	0.07644	T	0.81	.	3.7543	0.08579	0.5801:0.1008:0.1165:0.2027	.	29	P20231	TRYB2_HUMAN	A	29	ENSP00000412409:V29A	ENSP00000412409:V29A	V	-	2	0	TPSB2	1219715	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.520000	0.00221	-2.364000	0.00607	-1.306000	0.01317	GTG	A|0.924;G|0.076	0.076	strong		0.711	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
ABCB1	5243	hgsc.bcm.edu	37	7	87179601	87179601	+	Silent	SNP	A	A	G	rs1128503	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:87179601A>G	ENST00000265724.3	-	13	1653	c.1236T>C	c.(1234-1236)ggT>ggC	p.G412G	ABCB1_ENST00000543898.1_Silent_p.G348G	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	412	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)	TCAGGTTCAGACCCTTCAAGA	0.488													G|||	2924	0.583866	0.8638	0.5965	5008	,	,		18810	0.373		0.5845	False		,,,				2504	0.4131				p.G412G		Atlas-SNP	.											.	ABCB1	263	.	0			c.T1236C	GRCh37	CM084696	ABCB1	M	rs1128503	PASS	.	G		3454,952	361.6+/-315.8	1347,760,96	88.0	76.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1236	1.0	1.0	7	dbSNP_86	80	4901,3699	527.7+/-381.2	1394,2113,793	no	coding-synonymous	ABCB1	NM_000927.4		2741,2873,889	GG,GA,AA		43.0116,21.6069,35.7604		412/1281	87179601	8355,4651	2203	4300	6503	SO:0001819	synonymous_variant	5243	exon13			GTTCAGACCCTTC	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.1236T>C	7.37:g.87179601A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_000927	A8K294|B5AK60|Q12755|Q14812	Silent	SNP	ENST00000265724.3	37	CCDS5608.1																																																																																			A|0.384;G|0.616	0.616	strong		0.488	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
ARSH	347527	hgsc.bcm.edu	37	X	2928125	2928125	+	Silent	SNP	C	C	T	rs79487908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:2928125C>T	ENST00000381130.2	+	2	147	c.147C>T	c.(145-147)ctC>ctT	p.L49L		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	49					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CCCAGCATCTCGCAGCTGCTT	0.517													C|||	101	0.026755	0.0045	0.0159	3775	,	,		12432	0.0079		0.0507	False		,,,				2504	0.0256				p.L49L		Atlas-SNP	.											.	ARSH	72	.	0			c.C147T						PASS	.	C		58,3777		0,45,13,1587,558	87.0	68.0	74.0		147	0.7	0.1	X	dbSNP_131	74	444,6284		7,312,118,2109,1754	no	coding-synonymous	ARSH	NM_001011719.1		7,357,131,3696,2312	TT,TC,T,CC,C		6.5993,1.5124,4.7524		49/563	2928125	502,10061	2203	4300	6503	SO:0001819	synonymous_variant	347527	exon2			GCATCTCGCAGCT	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"""Arylsulfatase family"""	32488	protein-coding gene	gene with protein product		300586	"""arylsulfatase H"""			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.147C>T	X.37:g.2928125C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001011719		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																			C|0.959;T|0.041	0.041	strong		0.517	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
C9orf117	286207	hgsc.bcm.edu	37	9	130475442	130475442	+	Missense_Mutation	SNP	A	A	C	rs497632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130475442A>C	ENST00000373295.2	+	8	1488	c.1448A>C	c.(1447-1449)tAt>tCt	p.Y483S	PTRH1_ENST00000429848.1_5'Flank|C9orf117_ENST00000373293.5_Intron|C9orf117_ENST00000464092.1_Intron|TTC16_ENST00000393748.4_5'Flank|TTC16_ENST00000373289.3_5'Flank	NM_001012502.2	NP_001012520.2	Q5JU67	CI117_HUMAN	chromosome 9 open reading frame 117	483			Y -> S (in dbSNP:rs497632).							breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						CTGCTGTCATATATCACCCGT	0.637													A|||	2688	0.536741	0.5923	0.5807	5008	,	,		19266	0.2966		0.6014	False		,,,				2504	0.6115				p.Y483S		Atlas-SNP	.											.	C9orf117	21	.	0			c.A1448C						PASS	.	A	SER/TYR	2376,1532		746,884,324	39.0	42.0	41.0		1448	0.4	0.0	9	dbSNP_83	41	4704,3578		1335,2034,772	yes	missense	C9orf117	NM_001012502.2	144	2081,2918,1096	CC,CA,AA		43.2021,39.2016,41.9196	benign	483/521	130475442	7080,5110	1954	4141	6095	SO:0001583	missense	286207	exon8			TGTCATATATCAC	AK094948	CCDS43878.1	9q34.11	2012-04-02			ENSG00000160401	ENSG00000160401			27843	protein-coding gene	gene with protein product							Standard	NM_001012502		Approved		uc004brn.1	Q5JU67	OTTHUMG00000020709	ENST00000373295.2:c.1448A>C	9.37:g.130475442A>C	ENSP00000362392:p.Tyr483Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_001012502	A5D8T9	Missense_Mutation	SNP	ENST00000373295.2	37	CCDS43878.1	1153	0.5279304029304029	304	0.6178861788617886	207	0.5718232044198895	178	0.3111888111888112	464	0.6121372031662269	A	1.713	-0.498692	0.04291	0.607984	0.567979	ENSG00000160401	ENST00000373295	T	0.40225	1.04	4.35	0.369	0.16151	.	0.700195	0.13302	N	0.398166	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.15719	0.014	B	0.15870	0.014	T	0.43507	-0.9387	9	0.21014	T	0.42	-2.7759	3.1375	0.06443	0.6231:0.0:0.2012:0.1758	rs497632;rs1755995;rs497632	483	Q5JU67	CI117_HUMAN	S	483	ENSP00000362392:Y483S	ENSP00000362392:Y483S	Y	+	2	0	C9orf117	129515263	0.000000	0.05858	0.001000	0.08648	0.224000	0.24922	0.660000	0.25009	-0.029000	0.13827	0.454000	0.30748	TAT	A|0.466;C|0.534	0.534	strong		0.637	C9orf117-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054215.2	NM_001012502	
SIRPB1	10326	hgsc.bcm.edu	37	20	1600524	1600524	+	Missense_Mutation	SNP	T	T	C	rs1535882	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:1600524T>C	ENST00000381605.4	-	1	131	c.67A>G	c.(67-69)Aga>Gga	p.R23G	SIRPB1_ENST00000279477.7_Missense_Mutation_p.R23G|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000568365.1_Missense_Mutation_p.R23G|RP4-576H24.4_ENST00000564763.1_Missense_Mutation_p.R23G|SIRPB1_ENST00000381603.3_Missense_Mutation_p.R23G	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	23			R -> G (in dbSNP:rs1535882).		cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTGTGAGTCTCCCCAGCAGT	0.562													-|||	1217	0.243011	0.1263	0.4164	5008	,	,		19223	0.2212		0.3499	False		,,,				2504	0.1902				p.R23G		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,adenoma,0,2	SIRPB1	83	2	0			c.A67G						PASS	.	-	GLY/ARG,GLY/ARG,GLY/ARG	714,3692		67,580,1556	97.0	87.0	90.0		67,67,67	0.2	0.0	20	dbSNP_88	90	2946,5654		513,1920,1867	yes	missense,missense,missense	SIRPB1	NM_001083910.2,NM_001135844.2,NM_006065.3	125,125,125	580,2500,3423	CC,CT,TT		34.2558,16.2052,28.1409	benign,benign,benign	23/182,23/399,23/399	1600524	3660,9346	2203	4300	6503	SO:0001583	missense	10326	exon1			TGAGTCTCCCCAG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.67A>G	20.37:g.1600524T>C	ENSP00000371018:p.Arg23Gly	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_001083910	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	606	0.2774725274725275	71	0.1443089430894309	134	0.3701657458563536	131	0.229020979020979	270	0.3562005277044855	.	0.502	-0.870473	0.02570	0.162052	0.342558	ENSG00000101307	ENST00000381605;ENST00000381603;ENST00000279477;ENST00000381596	T;T;T	0.09630	4.47;4.83;2.96	0.15	0.15	0.14883	Immunoglobulin-like (2);	3.043770	0.01395	N	0.013381	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48917	-0.8992	8	0.25106	T	0.35	.	.	.	.	rs1535882;rs52800175;rs60047757;rs1535882	23;23;23	O00241;Q5TFQ8;O00241-2	SIRB1_HUMAN;SIRBL_HUMAN;.	G	23	ENSP00000371018:R23G;ENSP00000371016:R23G;ENSP00000279477:R23G	ENSP00000279477:R23G	R	-	1	2	SIRPB1	1548524	0.145000	0.22656	0.006000	0.13384	0.002000	0.02628	-0.970000	0.03810	-1.047000	0.03242	-1.042000	0.02369	AGA	T|0.729;C|0.271	0.271	strong		0.562	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
TP53BP1	7158	hgsc.bcm.edu	37	15	43712823	43712823	+	Missense_Mutation	SNP	C	C	T	rs28903077	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43712823C>T	ENST00000263801.3	-	21	4598	c.4346G>A	c.(4345-4347)cGa>cAa	p.R1449Q	TP53BP1_ENST00000382044.4_Missense_Mutation_p.R1454Q|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R1404Q|TP53BP1_ENST00000450115.2_Missense_Mutation_p.R1454Q	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1449					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)		CACATCTGTTCGTCTGGTGGA	0.552								Other conserved DNA damage response genes					C|||	2	0.000399361	0.0	0.0	5008	,	,		18672	0.0		0.002	False		,,,				2504	0.0				p.R1454Q		Atlas-SNP	.											.	TP53BP1	157	.	0			c.G4361A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4402		0,0,2201	66.0	64.0	64.0		4361,4361,4346	5.4	0.4	15	dbSNP_125	64	17,8579	11.9+/-42.8	0,17,4281	yes	missense,missense,missense	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	43,43,43	0,17,6482	TT,TC,CC		0.1978,0.0,0.1308	probably-damaging,probably-damaging,probably-damaging	1454/1976,1454/1978,1449/1973	43712823	17,12981	2201	4298	6499	SO:0001583	missense	7158	exon21			TCTGTTCGTCTGG	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.4346G>A	15.37:g.43712823C>T	ENSP00000263801:p.Arg1449Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	18.64	3.666759	0.67814	0.0	0.001978	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.04194	3.68;3.68;3.73;3.68	5.45	5.45	0.79879	.	0.347316	0.27735	N	0.018061	T	0.11239	0.0274	L	0.29908	0.895	0.09310	N	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.72625	0.978;0.945;0.975;0.975	T	0.33574	-0.9863	10	0.21014	T	0.42	-8.3136	14.178	0.65555	0.159:0.8409:0.0:0.0	rs28903077;rs28903077	1454;1449;1454;1454	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	Q	1449;1454;1404;1454	ENSP00000263801:R1449Q;ENSP00000371475:R1454Q;ENSP00000371470:R1404Q;ENSP00000393497:R1454Q	ENSP00000263801:R1449Q	R	-	2	0	TP53BP1	41500115	0.970000	0.33590	0.397000	0.26308	0.982000	0.71751	4.145000	0.58065	2.717000	0.92951	0.585000	0.79938	CGA	C|0.998;T|0.002	0.002	strong		0.552	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
FIG4	9896	hgsc.bcm.edu	37	6	110107517	110107517	+	Missense_Mutation	SNP	T	T	C	rs9885672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:110107517T>C	ENST00000230124.3	+	18	2085	c.1961T>C	c.(1960-1962)gTg>gCg	p.V654A	FIG4_ENST00000441478.2_Missense_Mutation_p.V377A	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	654			V -> A (in dbSNP:rs9885672). {ECO:0000269|Ref.2}.		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)		ATCTGTGCTGTGAACTTAAAG	0.353													C|||	2243	0.447883	0.7708	0.2608	5008	,	,		21565	0.4077		0.163	False		,,,				2504	0.4785				p.V654A		Atlas-SNP	.											.	FIG4	77	.	0			c.T1961C						PASS	.	C	ALA/VAL	2945,1461	469.4+/-355.4	995,955,253	91.0	94.0	93.0		1961	1.3	0.5	6	dbSNP_119	93	1304,7294	758.0+/-407.5	111,1082,3106	yes	missense	FIG4	NM_014845.5	64	1106,2037,3359	CC,CT,TT		15.1663,33.1593,32.6746	benign	654/908	110107517	4249,8755	2203	4299	6502	SO:0001583	missense	9896	exon18			GTGCTGTGAACTT	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.1961T>C	6.37:g.110107517T>C	ENSP00000230124:p.Val654Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	NM_014845	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	37	CCDS5078.1	818	0.37454212454212454	385	0.782520325203252	75	0.20718232044198895	230	0.4020979020979021	128	0.16886543535620052	C	3.418	-0.118856	0.06838	0.668407	0.151663	ENSG00000112367	ENST00000441478;ENST00000230124	T;T	0.49139	2.06;0.79	5.71	1.32	0.21799	.	0.221668	0.46145	N	0.000308	T	0.06645	0.0170	N	0.08118	0	0.41080	P	0.01448499999999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33471	-0.9867	9	0.06891	T	0.86	-7.4345	6.7708	0.23593	0.1887:0.5553:0.0:0.2561	rs9885672;rs52802097;rs56423865;rs58469958;rs9885672	377;654	F5H8L9;Q92562	.;FIG4_HUMAN	A	377;654	ENSP00000399443:V377A;ENSP00000230124:V654A	ENSP00000230124:V654A	V	+	2	0	FIG4	110214210	0.997000	0.39634	0.467000	0.27180	0.852000	0.48524	3.520000	0.53465	-0.033000	0.13736	-1.820000	0.00599	GTG	T|0.638;C|0.362	0.362	strong		0.353	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	
EFTUD2	9343	hgsc.bcm.edu	37	17	42953409	42953409	+	Silent	SNP	A	A	G	rs2289674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42953409A>G	ENST00000426333.2	-	10	1059	c.762T>C	c.(760-762)acT>acC	p.T254T	EFTUD2_ENST00000592576.1_Silent_p.T244T|EFTUD2_ENST00000591382.1_Silent_p.T254T|EFTUD2_ENST00000402521.3_Silent_p.T219T	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	254	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				TGATGCACACAGTGACTGCCA	0.512													A|||	854	0.170527	0.2526	0.121	5008	,	,		15775	0.1369		0.1958	False		,,,				2504	0.1033				p.T254T	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.T762C						PASS	.	A	,	1151,3255	407.3+/-334.2	150,851,1202	166.0	144.0	151.0		657,762	-4.6	0.9	17	dbSNP_100	151	1704,6896	311.3+/-310.3	164,1376,2760	no	coding-synonymous,coding-synonymous	EFTUD2	NM_001142605.1,NM_004247.3	,	314,2227,3962	GG,GA,AA		19.814,26.1235,21.9514	,	219/938,254/973	42953409	2855,10151	2203	4300	6503	SO:0001819	synonymous_variant	9343	exon10			GCACACAGTGACT	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 116 kD"""	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.762T>C	17.37:g.42953409A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Silent	SNP	ENST00000426333.2	37	CCDS11489.1																																																																																			A|0.799;G|0.201	0.201	strong		0.512	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247	
SEL1L2	80343	hgsc.bcm.edu	37	20	13912309	13912309	+	Missense_Mutation	SNP	G	G	A	rs41275404	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:13912309G>A	ENST00000284951.5	-	3	297	c.223C>T	c.(223-225)Cgt>Tgt	p.R75C	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.R75C			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	75						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CTTATTTTACGTTGATTCTTC	0.249													G|||	271	0.0541134	0.0083	0.0922	5008	,	,		15442	0.001		0.1471	False		,,,				2504	0.0481				p.R75C		Atlas-SNP	.											SEL1L2,colon,carcinoma,0,1	SEL1L2	103	1	0			c.C223T						PASS	.	G	CYS/ARG	99,3455		1,97,1679	59.0	52.0	54.0		223	1.9	0.0	20	dbSNP_127	54	1041,7023		65,911,3056	yes	missense	SEL1L2	NM_025229.1	180	66,1008,4735	AA,AG,GG		12.9092,2.7856,9.8124	possibly-damaging	75/689	13912309	1140,10478	1777	4032	5809	SO:0001583	missense	80343	exon3			TTTTACGTTGATT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.223C>T	20.37:g.13912309G>A	ENSP00000284951:p.Arg75Cys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	50	0.387597	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		151	0.06913919413919414	7	0.014227642276422764	34	0.09392265193370165	0	0.0	110	0.14511873350923482	G	6.852	0.526474	0.13066	0.027856	0.129092	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.24723	1.84;2.16	5.11	1.92	0.25849	.	1.668320	0.03077	N	0.157986	T	0.00073	0.0002	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21861	-1.0233	9	0.37606	T	0.19	3.976	2.2167	0.03962	0.1072:0.1386:0.4371:0.3171	rs41275404	75;75	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	C	75	ENSP00000367312:R75C;ENSP00000284951:R75C	ENSP00000284951:R75C	R	-	1	0	SEL1L2	13860309	0.627000	0.27129	0.000000	0.03702	0.309000	0.27889	1.730000	0.38125	0.222000	0.20900	0.655000	0.94253	CGT	G|0.910;A|0.090	0.090	strong		0.249	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
STON1	11037	hgsc.bcm.edu	37	2	48807796	48807796	+	Missense_Mutation	SNP	A	A	C	rs17039250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48807796A>C	ENST00000406226.1	+	3	219	c.24A>C	c.(22-24)aaA>aaC	p.K8N	STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.K8N|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.K8N|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.K8N|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.K8N|STON1_ENST00000309835.3_Missense_Mutation_p.K8N|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.K8N|STON1_ENST00000404752.1_Missense_Mutation_p.K8N	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	8			K -> N (in dbSNP:rs17039250).		endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATCCAGGCAAATGGGTCACCT	0.373													C|||	1672	0.333866	0.2784	0.3127	5008	,	,		19374	0.378		0.3181	False		,,,				2504	0.3947				p.K8N		Atlas-SNP	.											.	STON1	100	.	0			c.A24C						PASS	.	C	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	1309,3097	697.0+/-406.2	192,925,1086	93.0	88.0	90.0		24,24,24,24,24	1.6	1.0	2	dbSNP_123	90	2749,5851	679.6+/-403.6	457,1835,2008	yes	missense,missense,missense,missense,missense	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	94,94,94,94,94	649,2760,3094	CC,CA,AA		31.9651,29.7095,31.201	benign,benign,benign,benign,benign	8/1159,8/1136,8/736,8/736,8/1183	48807796	4058,8948	2203	4300	6503	SO:0001583	missense	11037	exon3			AGGCAAATGGGTC	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.24A>C	2.37:g.48807796A>C	ENSP00000384615:p.Lys8Asn	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	103	58	0.563107	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	37	CCDS1841.1	723	0.33104395604395603	141	0.2865853658536585	101	0.27900552486187846	228	0.3986013986013986	253	0.3337730870712401	C	0.701	-0.790630	0.02884	0.297095	0.319651	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.06687	3.27;3.27;3.27;3.32;3.31;3.32;3.32;3.48	5.35	1.6	0.23607	.	0.245586	0.46442	N	0.000289	T	0.00012	0.0000	N	0.00368	-1.59	0.45261	P	0.0017340000000000133	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.39921	-0.9590	9	0.09338	T	0.73	.	5.4175	0.16382	0.1226:0.5548:0.0:0.3226	rs17039250;rs52800575;rs17039250	8;8;8	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	N	8	ENSP00000385273:K8N;ENSP00000384615:K8N;ENSP00000310969:K8N;ENSP00000385499:K8N;ENSP00000385701:K8N;ENSP00000378236:K8N;ENSP00000311493:K8N;ENSP00000378234:K8N	ENSP00000310969:K8N	K	+	3	2	STON1-GTF2A1L;STON1	48661300	0.940000	0.31905	0.996000	0.52242	0.992000	0.81027	0.080000	0.14802	-0.006000	0.14370	-0.121000	0.15023	AAA	A|0.675;C|0.325	0.325	strong		0.373	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
CRYGB	1419	hgsc.bcm.edu	37	2	209010558	209010558	+	Silent	SNP	A	A	G	rs2854723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:209010558A>G	ENST00000260988.4	-	2	239	c.192T>C	c.(190-192)ccT>ccC	p.P64P		NM_005210.3	NP_005201.2	P07316	CRGB_HUMAN	crystallin, gamma B	64	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens fiber cell morphogenesis (GO:0070309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)	14				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		GCTGGTAGTCAGGGTACTCCC	0.602													G|||	2013	0.401957	0.382	0.2997	5008	,	,		13612	0.2659		0.5209	False		,,,				2504	0.5194				p.P64P		Atlas-SNP	.											.	CRYGB	24	.	0			c.T192C						PASS	.	G		1894,2512	608.6+/-391.2	408,1078,717	45.0	48.0	47.0		192	-0.8	1.0	2	dbSNP_100	47	4619,3981	533.1+/-382.3	1278,2063,959	no	coding-synonymous	CRYGB	NM_005210.3		1686,3141,1676	GG,GA,AA		46.2907,42.9868,49.9231		64/176	209010558	6513,6493	2203	4300	6503	SO:0001819	synonymous_variant	1419	exon2			GTAGTCAGGGTAC		CCDS2380.1	2q34	2013-02-14			ENSG00000182187	ENSG00000182187			2409	protein-coding gene	gene with protein product		123670	"""crystallin, gamma 1-2"""	CRYG2			Standard	NM_005210		Approved		uc002vcp.4	P07316	OTTHUMG00000132941	ENST00000260988.4:c.192T>C	2.37:g.209010558A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_005210	Q17RB5|Q53ST2	Silent	SNP	ENST00000260988.4	37	CCDS2380.1																																																																																			A|0.526;G|0.474	0.474	strong		0.602	CRYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256473.2	NM_005210	
DENND2A	27147	hgsc.bcm.edu	37	7	140227293	140227293	+	Missense_Mutation	SNP	A	A	G	rs6464833	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:140227293A>G	ENST00000275884.6	-	14	2747	c.2330T>C	c.(2329-2331)aTc>aCc	p.I777T	DENND2A_ENST00000537639.1_Missense_Mutation_p.I777T|DENND2A_ENST00000496613.1_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	113	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	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	
PCDH15	65217	hgsc.bcm.edu	37	10	55582905	55582905	+	Silent	SNP	G	G	T	rs10825114	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:55582905G>T	ENST00000320301.6	-	33	4975	c.4581C>A	c.(4579-4581)ccC>ccA	p.P1527P	PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000437009.1_Silent_p.P1458P|PCDH15_ENST00000361849.3_Silent_p.P1529P|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395432.2_Silent_p.P1487P|PCDH15_ENST00000395433.1_Silent_p.P1504P|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395430.1_Silent_p.P1524P|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1527					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CCTTATAAAGGGGATTATGGG	0.368										HNSCC(58;0.16)			G|||	1421	0.283746	0.1755	0.2277	5008	,	,		20280	0.7014		0.0447	False		,,,				2504	0.2853				p.P1534P		Atlas-SNP	.											PCDH15_ENST00000417177,NS,malignant_melanoma,-2,4	PCDH15	1715	4	0			c.C4602A						PASS	.	G	,,,,,,,,,,,	778,3628	311.4+/-292.0	73,632,1498	82.0	88.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4602,4587,4374,4572,4461,4521,,,,,4512,4581	-2.6	0.0	10	dbSNP_120	86	387,8211	122.4+/-181.4	10,367,3922	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	83,999,5420	TT,TG,GG		4.501,17.6577,8.9588	,,,,,,,,,,,	1534/1963,1529/1958,1458/1887,1524/1953,1487/1916,1507/1936,,,,,1504/1933,1527/1956	55582905	1165,11839	2203	4299	6502	SO:0001819	synonymous_variant	65217	exon35			ATAAAGGGGATTA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4581C>A	10.37:g.55582905G>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			G|0.809;T|0.191	0.191	strong		0.368	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
GALNS	2588	hgsc.bcm.edu	37	16	88884466	88884466	+	Silent	SNP	C	C	T	rs2303271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88884466C>T	ENST00000268695.5	-	13	1519	c.1431G>A	c.(1429-1431)gaG>gaA	p.E477E	GALNS_ENST00000542788.1_Silent_p.E402E	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	477					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		GGACCAAGGCCTCCTGGTGCT	0.672													C|||	2375	0.474241	0.4947	0.4265	5008	,	,		16578	0.627		0.3827	False		,,,				2504	0.4172				p.E477E	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.G1431A						PASS	.	C		2024,2324		475,1074,625	61.0	45.0	51.0		1431	-0.9	0.0	16	dbSNP_100	51	3140,5450		563,2014,1718	no	coding-synonymous	GALNS	NM_000512.4		1038,3088,2343	TT,TC,CC		36.5541,46.5501,39.9134		477/523	88884466	5164,7774	2174	4295	6469	SO:0001819	synonymous_variant	2588	exon13			CAAGGCCTCCTGG	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.1431G>A	16.37:g.88884466C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_000512	Q86VK3	Silent	SNP	ENST00000268695.5	37	CCDS10970.1																																																																																			C|0.573;T|0.427	0.427	strong		0.672	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
UTP14C	9724	hgsc.bcm.edu	37	13	52603896	52603896	+	Missense_Mutation	SNP	G	G	A	rs17402034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:52603896G>A	ENST00000521776.2	+	2	1689	c.956G>A	c.(955-957)cGc>cAc	p.R319H		NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	319			R -> H (in dbSNP:rs17402034).		cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)				breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		CTGGAGGCTCGCCAAGCTATG	0.483													G|||	153	0.0305511	0.0038	0.0346	5008	,	,		19323	0.0		0.0994	False		,,,				2504	0.0245				p.R319H		Atlas-SNP	.											.	UTP14C	67	.	0			c.G956A						PASS	.	G	HIS/ARG	98,4308	78.8+/-117.2	1,96,2106	120.0	123.0	122.0		956	0.7	0.0	13	dbSNP_123	122	914,7686	203.0+/-246.1	50,814,3436	yes	missense	UTP14C	NM_021645.5	29	51,910,5542	AA,AG,GG		10.6279,2.2242,7.781	probably-damaging	319/767	52603896	1012,11994	2203	4300	6503	SO:0001583	missense	9724	exon2			AGGCTCGCCAAGC	D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"""KIAA0266"""	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.956G>A	13.37:g.52603896G>A	ENSP00000428619:p.Arg319His	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	264	127	0.481061	NM_021645	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	98	0.04487179487179487	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	79	0.10422163588390501	G	13.30	2.197270	0.38806	0.022242	0.106279	ENSG00000253797	ENST00000521776	T	0.38401	1.14	2.58	0.736	0.18307	.	0.103239	0.64402	N	0.000002	T	0.02267	0.0070	M	0.92268	3.29	0.48830	D	0.999717	D	0.89917	1.0	D	0.97110	1.0	T	0.03344	-1.1046	9	.	.	.	-9.4065	6.3491	0.21365	0.2764:0.0:0.7236:0.0	rs17402034;rs52791623;rs17402034	319	Q5TAP6	UT14C_HUMAN	H	319	ENSP00000428619:R319H	.	R	+	2	0	UTP14C	51501897	1.000000	0.71417	0.028000	0.17463	0.912000	0.54170	5.938000	0.70170	0.021000	0.15133	0.448000	0.29417	CGC	G|0.934;A|0.066	0.066	strong		0.483	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645	
MECOM	2122	hgsc.bcm.edu	37	3	168810874	168810874	+	Silent	SNP	C	C	T	rs17466625	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:168810874C>T	ENST00000464456.1	-	12	3645	c.2445G>A	c.(2443-2445)tcG>tcA	p.S815S	MECOM_ENST00000460814.1_Silent_p.S815S|MECOM_ENST00000433243.2_Silent_p.S825S|MECOM_ENST00000472280.1_Silent_p.S825S|MECOM_ENST00000494292.1_Silent_p.S1003S|MECOM_ENST00000392736.3_Silent_p.S824S|MECOM_ENST00000468789.1_Silent_p.S824S|MECOM_ENST00000264674.3_Silent_p.S889S	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						CAGAATGAGGCGACGATGTTG	0.393													C|||	455	0.0908546	0.0159	0.1037	5008	,	,		18533	0.0694		0.2008	False		,,,				2504	0.092				p.S1012S		Atlas-SNP	.											.	MECOM	216	.	0			c.G3036A						PASS	.	C	,,,,,,	206,4200	127.8+/-164.7	5,196,2002	111.0	100.0	104.0		2667,2472,2448,2445,2472,3036,2472	-1.1	1.0	3	dbSNP_123	104	1750,6850	317.2+/-313.1	180,1390,2730	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MECOM	NM_001105077.3,NM_001105078.3,NM_001163999.1,NM_001164000.1,NM_001205194.1,NM_004991.3,NM_005241.3	,,,,,,	185,1586,4732	TT,TC,CC		20.3488,4.6754,15.0392	,,,,,,	889/1117,824/1052,816/1044,815/1043,824/1052,1012/1240,824/1052	168810874	1956,11050	2203	4300	6503	SO:0001819	synonymous_variant	2122	exon14			ATGAGGCGACGAT	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.2445G>A	3.37:g.168810874C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_004991	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	37	CCDS54669.1																																																																																			C|0.871;T|0.129	0.129	strong		0.393	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
EXO1	9156	hgsc.bcm.edu	37	1	242042301	242042301	+	Missense_Mutation	SNP	G	G	A	rs1047840	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:242042301G>A	ENST00000366548.3	+	13	2358	c.1765G>A	c.(1765-1767)Gag>Aag	p.E589K	EXO1_ENST00000348581.5_Missense_Mutation_p.E589K|EXO1_ENST00000518483.1_Missense_Mutation_p.E589K	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	589			E -> K (in dbSNP:rs1047840). {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9685493, ECO:0000269|PubMed:9788596, ECO:0000269|PubMed:9823303, ECO:0000269|Ref.5}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)	p.E589K(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			CTACTCTTTTGAGAGCAGCAA	0.408								Editing and processing nucleases					A|||	1761	0.351637	0.4781	0.3876	5008	,	,		20720	0.2312		0.3688	False		,,,				2504	0.2618				p.E589K		Atlas-SNP	.											EXO1,NS,carcinoma,0,1	EXO1	103	1	1	Substitution - Missense(1)	stomach(1)	c.G1765A	GRCh37	CM065155	EXO1	M	rs1047840	PASS	.	A	LYS/GLU,LYS/GLU,LYS/GLU	2093,2313	604.7+/-390.4	493,1107,603	134.0	132.0	133.0		1765,1765,1765	-3.3	0.0	1	dbSNP_86	133	3223,5377	651.7+/-400.9	611,2001,1688	yes	missense,missense,missense	EXO1	NM_003686.4,NM_006027.4,NM_130398.3	56,56,56	1104,3108,2291	AA,AG,GG		37.4767,47.5034,40.8734	benign,benign,benign	589/804,589/847,589/847	242042301	5316,7690	2203	4300	6503	SO:0001583	missense	9156	exon11			TCTTTTGAGAGCA	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1765G>A	1.37:g.242042301G>A	ENSP00000355506:p.Glu589Lys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	37	CCDS1620.1	787	0.36034798534798534	261	0.5304878048780488	123	0.3397790055248619	131	0.229020979020979	272	0.35883905013192613	A	4.889	0.165313	0.09339	0.475034	0.374767	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.36699	1.24;1.24;1.24	5.2	-3.34	0.04943	.	0.543637	0.20184	N	0.097444	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.43686	-0.9376	9	0.10377	T	0.69	-9.2144	10.0913	0.42449	0.23:0.1425:0.6274:0.0	rs1047840;rs3187846;rs12734501;rs16842258;rs52829990;rs56561721;rs59734256;rs1047840	588;589;589	A8K5H6;Q9UQ84-4;Q9UQ84	.;.;EXO1_HUMAN	K	589	ENSP00000355506:E589K;ENSP00000311873:E589K;ENSP00000430251:E589K	ENSP00000311873:E589K	E	+	1	0	EXO1	240108924	0.011000	0.17503	0.000000	0.03702	0.006000	0.05464	-0.006000	0.12833	-0.841000	0.04200	-1.172000	0.01736	GAG	G|0.616;A|0.384	0.384	strong		0.408	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
UNC13D	201294	hgsc.bcm.edu	37	17	73826120	73826120	+	Silent	SNP	C	C	T	rs35628234	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73826120C>T	ENST00000207549.4	-	30	3322	c.2943G>A	c.(2941-2943)gaG>gaA	p.E981E	UNC13D_ENST00000412096.2_Silent_p.E981E	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	981	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			ATTCAAAGGTCTCATCAAACA	0.607									Familial Hemophagocytic Lymphohistiocytosis				C|||	402	0.0802716	0.171	0.0504	5008	,	,		17369	0.0258		0.0368	False		,,,				2504	0.0798				p.E981E		Atlas-SNP	.											.	UNC13D	68	.	0			c.G2943A						PASS	.	C		575,3805		34,507,1649	89.0	77.0	81.0		2943	1.9	1.0	17	dbSNP_126	81	370,8208		7,356,3926	no	coding-synonymous	UNC13D	NM_199242.2		41,863,5575	TT,TC,CC		4.3134,13.1279,7.2928		981/1091	73826120	945,12013	2190	4289	6479	SO:0001819	synonymous_variant	201294	exon30	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AAAGGTCTCATCA	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.2943G>A	17.37:g.73826120C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	168	66	0.392857	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			C|0.923;T|0.077	0.077	strong		0.607	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
FMO3	2328	hgsc.bcm.edu	37	1	171083174	171083174	+	Silent	SNP	C	C	T	rs909530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171083174C>T	ENST00000367755.4	+	7	966	c.855C>T	c.(853-855)aaC>aaT	p.N285N	FMO3_ENST00000392085.2_Silent_p.N285N|FMO3_ENST00000538429.1_Silent_p.N222N|FMO3_ENST00000542847.1_Silent_p.N265N	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	285					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)	p.N285N(1)		endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CTGTATTTAACGATGAGCTCC	0.413													T|||	1671	0.333666	0.4576	0.3487	5008	,	,		19836	0.3452		0.2356	False		,,,				2504	0.2444				p.N285N		Atlas-SNP	.											FMO3,NS,carcinoma,0,1	FMO3	73	1	1	Substitution - coding silent(1)	stomach(1)	c.C855T						PASS	.	T	,	1905,2501	627.8+/-395.0	406,1093,704	84.0	76.0	79.0		855,855	0.8	1.0	1	dbSNP_86	79	2094,6506	717.2+/-406.1	263,1568,2469	no	coding-synonymous,coding-synonymous	FMO3	NM_001002294.2,NM_006894.5	,	669,2661,3173	TT,TC,CC		24.3488,43.2365,30.7473	,	285/533,285/533	171083174	3999,9007	2203	4300	6503	SO:0001819	synonymous_variant	2328	exon7			ATTTAACGATGAG	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.855C>T	1.37:g.171083174C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	181	77	0.425414	NM_006894	B2R816|Q14854|Q8N5N5	Silent	SNP	ENST00000367755.4	37	CCDS1292.1																																																																																			C|0.665;T|0.335	0.335	strong		0.413	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
TTN	7273	hgsc.bcm.edu	37	2	179605180	179605180	+	Silent	SNP	C	C	T	rs746578	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179605180C>T	ENST00000591111.1	-	46	12053	c.11829G>A	c.(11827-11829)gcG>gcA	p.A3943A	TTN_ENST00000589042.1_Silent_p.A4260A|TTN_ENST00000359218.5_Silent_p.A4022A|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000460472.2_Silent_p.A3897A|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Silent_p.A4089A|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAAGATGAGCGCACTTTGTG	0.483													C|||	1196	0.238818	0.1846	0.1585	5008	,	,		20859	0.4702		0.1382	False		,,,				2504	0.2342				p.A4260A		Atlas-SNP	.											TTN_ENST00000359218,colon,carcinoma,-1,1	TTN	18412	1	0			c.G12780A						PASS	.	C	,,,	585,3313		44,497,1408	106.0	99.0	101.0		11691,,12066,12267	-1.9	0.0	2	dbSNP_86	101	1064,7228		80,904,3162	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	124,1401,4570	TT,TC,CC		12.8316,15.0077,13.5275	,,,	3897/26927,,4022/27052,4089/27119	179605180	1649,10541	1949	4146	6095	SO:0001819	synonymous_variant	7273	exon48			GATGAGCGCACTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11829G>A	2.37:g.179605180C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	195	102	0.523077	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.233;C|0.757;A|0.010	0.233	strong		0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OR5L1	219437	hgsc.bcm.edu	37	11	55579419	55579419	+	Silent	SNP	T	T	C	rs34948392	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	431	1	0.00232019		WXS	Illumina HiSeq	Phase_I	406	193	0.475369	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	
DIAPH3	81624	hgsc.bcm.edu	37	13	60240829	60240829	+	Silent	SNP	C	C	T	rs41293422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:60240829C>T	ENST00000400324.4	-	28	3691	c.3471G>A	c.(3469-3471)gcG>gcA	p.A1157A	DIAPH3_ENST00000400320.1_Silent_p.A1111A|DIAPH3_ENST00000400319.1_Silent_p.A1087A|DIAPH3_ENST00000400330.1_Silent_p.A1157A|DIAPH3_ENST00000377908.2_Silent_p.A1146A	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	1157					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CTACATTACACGCTTCCTTCT	0.428													C|||	209	0.0417332	0.0492	0.0231	5008	,	,		14693	0.0228		0.0586	False		,,,				2504	0.047				p.A1157A		Atlas-SNP	.											.	DIAPH3	139	.	0			c.G3471A						PASS	.	C		194,3602		4,186,1708	179.0	168.0	172.0		3471	3.7	1.0	13	dbSNP_127	172	439,7797		18,403,3697	no	coding-synonymous	DIAPH3	NM_001042517.1		22,589,5405	TT,TC,CC		5.3303,5.1106,5.261		1157/1194	60240829	633,11399	1898	4118	6016	SO:0001819	synonymous_variant	81624	exon28			ATTACACGCTTCC	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.3471G>A	13.37:g.60240829C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	178	95	0.533708	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																			C|0.955;T|0.045	0.045	strong		0.428	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
HPN	3249	hgsc.bcm.edu	37	19	35550878	35550878	+	Silent	SNP	C	C	T	rs45512696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:35550878C>T	ENST00000262626.2	+	6	1216	c.391C>T	c.(391-393)Ctg>Ttg	p.L131L	HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000600675.1_3'UTR|HPN_ENST00000392226.1_Silent_p.L131L|HPN_ENST00000597419.1_Intron	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	131	SRCR.				basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	CACCCAGAGGCTGCTGGAGGT	0.667													C|||	323	0.0644968	0.0045	0.072	5008	,	,		13357	0.0109		0.162	False		,,,				2504	0.0951				p.L131L		Atlas-SNP	.											.	HPN	45	.	0			c.C391T						PASS	.	C	,	163,4241	101.2+/-139.8	6,151,2045	29.0	31.0	30.0		391,391	3.0	1.0	19	dbSNP_127	30	1379,7221	255.5+/-280.4	113,1153,3034	no	coding-synonymous,coding-synonymous	HPN	NM_002151.2,NM_182983.2	,	119,1304,5079	TT,TC,CC		16.0349,3.7012,11.8579	,	131/418,131/418	35550878	1542,11462	2202	4300	6502	SO:0001819	synonymous_variant	3249	exon6			CAGAGGCTGCTGG		CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"""Serine peptidases / Transmembrane"""	5155	protein-coding gene	gene with protein product	"""transmembrane protease, serine 1"""	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.391C>T	19.37:g.35550878C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_182983	B2RDS4	Silent	SNP	ENST00000262626.2	37	CCDS32993.1																																																																																			C|0.904;T|0.096	0.096	strong		0.667	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151	
SPECC1L	23384	hgsc.bcm.edu	37	22	24717518	24717518	+	Silent	SNP	G	G	A	rs3747113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:24717518G>A	ENST00000314328.9	+	5	855	c.570G>A	c.(568-570)acG>acA	p.T190T	SPECC1L_ENST00000416735.1_Intron|SPECC1L-ADORA2A_ENST00000358654.2_Silent_p.T190T|SPECC1L_ENST00000437398.1_Silent_p.T190T|SPECC1L_ENST00000541492.1_Silent_p.T190T	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	190			T -> M (no effect on the stabilization of microtubules; dbSNP:rs142144652). {ECO:0000269|PubMed:21703590}.		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)		p.T190T(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						ATCTTCTCACGCTGGCAAAAA	0.453													G|||	1037	0.207069	0.1127	0.317	5008	,	,		20502	0.2302		0.2654	False		,,,				2504	0.1728				p.T190T		Atlas-SNP	.											SPECC1L,NS,carcinoma,0,1	SPECC1L	85	1	1	Substitution - coding silent(1)	stomach(1)	c.G570A						scavenged	.	G	,	603,3803	263.8+/-265.7	40,523,1640	62.0	61.0	62.0		570,570	-8.3	0.5	22	dbSNP_107	62	2172,6428	372.6+/-336.7	292,1588,2420	no	coding-synonymous,coding-synonymous	SPECC1L	NM_001145468.1,NM_015330.2	,	332,2111,4060	AA,AG,GG		25.2558,13.6859,21.3363	,	190/1118,190/1118	24717518	2775,10231	2203	4300	6503	SO:0001819	synonymous_variant	23384	exon4			TCTCACGCTGGCA	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.570G>A	22.37:g.24717518G>A		Somatic	70	2	0.0285714		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_001145468	B7Z758|F5H1H6|O15081	Silent	SNP	ENST00000314328.9	37	CCDS33619.1																																																																																			G|0.777;A|0.223	0.223	strong		0.453	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
DOCK10	55619	hgsc.bcm.edu	37	2	225684166	225684166	+	Silent	SNP	A	A	G	rs7572725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:225684166A>G	ENST00000258390.7	-	29	3331	c.3264T>C	c.(3262-3264)ctT>ctC	p.L1088L	DOCK10_ENST00000409592.3_Silent_p.L1082L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1088					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TTCTTACCTTAAGGTCACCGG	0.373													G|||	1250	0.249601	0.6641	0.1196	5008	,	,		18217	0.0228		0.1511	False		,,,				2504	0.1166				p.L1088L		Atlas-SNP	.											.	DOCK10	308	.	0			c.T3264C						PASS	.	G		2120,1644		587,946,349	109.0	106.0	107.0		3264	2.0	0.9	2	dbSNP_116	107	1089,7123		77,935,3094	no	coding-synonymous	DOCK10	NM_014689.2		664,1881,3443	GG,GA,AA		13.2611,43.6769,26.7953		1088/2187	225684166	3209,8767	1882	4106	5988	SO:0001819	synonymous_variant	55619	exon29			TACCTTAAGGTCA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3264T>C	2.37:g.225684166A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			A|0.757;G|0.243	0.243	strong		0.373	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
ATP1B1	481	hgsc.bcm.edu	37	1	169094216	169094216	+	Silent	SNP	G	G	A	rs61742560	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:169094216G>A	ENST00000367816.1	+	4	850	c.321G>A	c.(319-321)agG>agA	p.R107R	ATP1B1_ENST00000367815.4_Silent_p.R107R|ATP1B1_ENST00000499679.3_Silent_p.R51R|ATP1B1_ENST00000367813.3_Silent_p.R99R			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	107					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					ACATAGTTAGGTTCCTGGAAA	0.408													G|||	19	0.00379393	0.0	0.0043	5008	,	,		18037	0.0		0.008	False		,,,				2504	0.0082				p.R107R		Atlas-SNP	.											.	ATP1B1	29	.	0			c.G321A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	171.0	165.0	167.0		321	2.2	1.0	1	dbSNP_129	167	90,8510	50.6+/-110.7	0,90,4210	no	coding-synonymous	ATP1B1	NM_001677.3		0,95,6408	AA,AG,GG		1.0465,0.1135,0.7304		107/304	169094216	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	481	exon3			AGTTAGGTTCCTG	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"""ATPases / P-type"""	804	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit beta-1"", ""sodium pump subunit beta-1"", ""sodium-potassium ATPase subunit beta 1 (non-catalytic)"""	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.321G>A	1.37:g.169094216G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	146	76	0.520548	NM_001677	Q5TGZ3	Silent	SNP	ENST00000367816.1	37	CCDS1276.1																																																																																			G|0.994;A|0.006	0.006	strong		0.408	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1		
SHROOM3	57619	hgsc.bcm.edu	37	4	77661017	77661017	+	Missense_Mutation	SNP	A	A	C	rs76656494	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77661017A>C	ENST00000296043.6	+	5	2644	c.1691A>C	c.(1690-1692)gAa>gCa	p.E564A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	564					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)			TCAGTGCCTGAAAATGAGGAG	0.502													A|||	33	0.00658946	0.0	0.013	5008	,	,		21550	0.0		0.0229	False		,,,				2504	0.001				p.E564A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1691C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	168.0	168.0	168.0		1691	4.4	1.0	4	dbSNP_131	168	145,8455	70.7+/-133.2	2,141,4157	yes	missense	SHROOM3	NM_020859.3	107	2,155,6346	CC,CA,AA		1.686,0.3177,1.2225	probably-damaging	564/1997	77661017	159,12847	2203	4300	6503	SO:0001583	missense	57619	exon5			TGCCTGAAAATGA	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.1691A>C	4.37:g.77661017A>C	ENSP00000296043:p.Glu564Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	15.10	2.733513	0.48939	0.003177	0.01686	ENSG00000138771	ENST00000296043	T	0.26660	1.72	5.59	4.39	0.52855	.	0.093877	0.44902	D	0.000410	T	0.31009	0.0783	M	0.71581	2.175	0.35431	D	0.794093	D;P;P	0.76494	0.999;0.89;0.8	D;B;B	0.65987	0.94;0.382;0.153	T	0.57688	-0.7768	10	0.72032	D	0.01	-7.8779	12.7677	0.57401	0.8629:0.1371:0.0:0.0	.	388;564;342	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	A	564	ENSP00000296043:E564A	ENSP00000296043:E564A	E	+	2	0	SHROOM3	77880041	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	1.907000	0.39897	0.925000	0.37094	0.460000	0.39030	GAA	A|0.988;C|0.012	0.012	strong		0.502	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
LRFN3	79414	hgsc.bcm.edu	37	19	36430368	36430368	+	Missense_Mutation	SNP	C	C	T	rs34933126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36430368C>T	ENST00000588831.1	+	3	1095	c.41C>T	c.(40-42)gCc>gTc	p.A14V	LRFN3_ENST00000246529.3_Missense_Mutation_p.A14V			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	14			A -> V (in dbSNP:rs34933126).		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)			CTGCCGCTGGCCCCTGCCTCA	0.701													C|||	325	0.0648962	0.1672	0.0231	5008	,	,		12900	0.0109		0.0249	False		,,,				2504	0.0532				p.A14V		Atlas-SNP	.											.	LRFN3	43	.	0			c.C41T						PASS	.	C	VAL/ALA	604,3662		38,528,1567	27.0	31.0	30.0		41	3.0	1.0	19	dbSNP_126	30	250,8078		1,248,3915	no	missense	LRFN3	NM_024509.1	64	39,776,5482	TT,TC,CC		3.0019,14.1585,6.781	benign	14/629	36430368	854,11740	2133	4164	6297	SO:0001583	missense	79414	exon2			CGCTGGCCCCTGC	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.41C>T	19.37:g.36430368C>T	ENSP00000466989:p.Ala14Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_024509	Q6UY10	Missense_Mutation	SNP	ENST00000588831.1	37	CCDS12483.1	94	0.04304029304029304	62	0.12601626016260162	8	0.022099447513812154	5	0.008741258741258742	19	0.025065963060686015	C	10.88	1.474987	0.26511	0.141585	0.030019	ENSG00000126243	ENST00000246529	T	0.52983	0.64	4.09	3.05	0.35203	.	0.000000	0.36482	N	0.002580	T	0.00241	0.0007	L	0.43923	1.385	0.37256	P	0.09323400000000004	B	0.09022	0.002	B	0.09377	0.004	T	0.04178	-1.0971	9	0.16896	T	0.51	.	5.0431	0.14469	0.0:0.6658:0.2187:0.1155	rs34933126	14	Q9BTN0	LRFN3_HUMAN	V	14	ENSP00000246529:A14V	ENSP00000246529:A14V	A	+	2	0	LRFN3	41122208	0.118000	0.22208	1.000000	0.80357	0.697000	0.40408	0.797000	0.26999	2.235000	0.73313	0.455000	0.32223	GCC	C|0.938;T|0.062	0.062	strong		0.701	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457403.2	NM_024509	
MUC2	4583	hgsc.bcm.edu	37	11	1084821	1084821	+	Silent	SNP	T	T	C	rs10794288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1084821T>C	ENST00000441003.2	+	20	2643	c.2616T>C	c.(2614-2616)gaT>gaC	p.D872D	MUC2_ENST00000359061.5_Silent_p.D872D	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	872	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)				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)	TCACCTTTGATGGGAAGTACT	0.592													C|||	1697	0.338858	0.4259	0.3646	5008	,	,		18680	0.3919		0.2167	False		,,,				2504	0.274				p.D872D		Atlas-SNP	.											.	MUC2	614	.	0			c.T2616C						PASS	.	C		1735,2589		356,1023,783	86.0	88.0	87.0		2616	-6.2	0.1	11	dbSNP_120	87	1719,6787		185,1349,2719	no	coding-synonymous	MUC2	NM_002457.2		541,2372,3502	CC,CT,TT		20.2093,40.1249,26.9213		872/2813	1084821	3454,9376	2162	4253	6415	SO:0001819	synonymous_variant	4583	exon20			CTTTGATGGGAAG	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.2616T>C	11.37:g.1084821T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	129	55	0.426357	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.699;C|0.301	0.301	strong		0.592	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR1E1	8387	hgsc.bcm.edu	37	17	3301549	3301549	+	Silent	SNP	G	G	A	rs150988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3301549G>A	ENST00000322608.2	-	1	155	c.156C>T	c.(154-156)gaC>gaT	p.D52D		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	52					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						GGAGATGGGAGTCCAGTCGAA	0.498													G|||	2235	0.446286	0.3464	0.5663	5008	,	,		20648	0.4315		0.4016	False		,,,				2504	0.5573				p.D52D		Atlas-SNP	.											.	OR1E1	37	.	0			c.C156T						PASS	.	G		1631,2775	501.5+/-365.0	309,1013,881	127.0	119.0	122.0		156	3.3	1.0	17	dbSNP_79	122	3357,5243	498.3+/-374.7	651,2055,1594	no	coding-synonymous	OR1E1	NM_003553.2		960,3068,2475	AA,AG,GG		39.0349,37.0177,38.3515		52/315	3301549	4988,8018	2203	4300	6503	SO:0001819	synonymous_variant	8387	exon1			ATGGGAGTCCAGT	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.156C>T	17.37:g.3301549G>A		Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	342	186	0.54386	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Silent	SNP	ENST00000322608.2	37	CCDS11024.1																																																																																			G|0.602;A|0.398	0.398	strong		0.498	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553	
TSHR	7253	hgsc.bcm.edu	37	14	81574959	81574959	+	Silent	SNP	A	A	G	rs3783942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:81574959A>G	ENST00000342443.6	+	9	946	c.696A>G	c.(694-696)ctA>ctG	p.L232L	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000554263.1_3'UTR|TSHR_ENST00000298171.2_Intron|TSHR_ENST00000541158.2_Intron|TSHR_ENST00000554435.1_Silent_p.L253L	NM_001018036.2|NM_001142626.2	NP_001018046.1|NP_001136098.1	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	0					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)			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)	TGTATAGGCTACCTCTTGGAA	0.488			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism						A|||	3061	0.611222	0.6369	0.6268	5008	,	,		15374	0.3889		0.671	False		,,,				2504	0.7331				p.L253L		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	.	TSHR	462	.	0			c.A759G						PASS	.	A	,,	2726,1680	655.4+/-399.9	856,1014,333	158.0	150.0	152.0		,696,759	-0.9	0.0	14	dbSNP_107	152	5647,2953	668.1+/-402.5	1871,1905,524	yes	intron,coding-synonymous,coding-synonymous	TSHR	NM_000369.2,NM_001018036.2,NM_001142626.2	,,	2727,2919,857	GG,GA,AA		34.3372,38.1298,35.622	,,	,232/254,253/275	81574959	8373,4633	2203	4300	6503	SO:0001819	synonymous_variant	7253	exon9			TAGGCTACCTCTT	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		ENST00000342443.6:c.696A>G	14.37:g.81574959A>G		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001142626	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Silent	SNP	ENST00000342443.6	37	CCDS32131.1																																																																																			A|0.387;G|0.613	0.613	strong		0.488	TSHR-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413366.1	NM_000369	
INSL5	10022	hgsc.bcm.edu	37	1	67266756	67266756	+	Missense_Mutation	SNP	T	T	A	rs549148	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:67266756T>A	ENST00000304526.2	-	1	183	c.149A>T	c.(148-150)cAg>cTg	p.Q50L		NM_005478.4	NP_005469.2	Q9Y5Q6	INSL5_HUMAN	insulin-like 5	50			Q -> L (in dbSNP:rs549148). {ECO:0000269|PubMed:10458910, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				breast(2)|endometrium(1)|lung(5)	8						GATCCCCTCCTGATGCCTTCT	0.448													A|||	4363	0.871206	0.7821	0.8919	5008	,	,		19756	0.9901		0.83	False		,,,				2504	0.8967				p.Q50L		Atlas-SNP	.											.	INSL5	26	.	0			c.A149T						PASS	.	A	LEU/GLN	3560,846	335.5+/-303.9	1441,678,84	114.0	101.0	106.0		149	-5.7	0.0	1	dbSNP_83	106	7399,1201	243.3+/-273.0	3191,1017,92	yes	missense	INSL5	NM_005478.4	113	4632,1695,176	AA,AT,TT		13.9651,19.2011,15.7389	benign	50/136	67266756	10959,2047	2203	4300	6503	SO:0001583	missense	10022	exon1			CCCTCCTGATGCC	AF133816	CCDS634.1	1p31.3	2013-02-26			ENSG00000172410	ENSG00000172410		"""Endogenous ligands"""	6088	protein-coding gene	gene with protein product	"""prepro-INSL5"""	606413				10458910	Standard	NM_005478		Approved		uc001dcw.3	Q9Y5Q6	OTTHUMG00000009164	ENST00000304526.2:c.149A>T	1.37:g.67266756T>A	ENSP00000302724:p.Gln50Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_005478	Q3MIY4|Q5VYD8	Missense_Mutation	SNP	ENST00000304526.2	37	CCDS634.1	1915	0.8768315018315018	397	0.806910569105691	313	0.8646408839779005	571	0.9982517482517482	634	0.8364116094986808	A	4.175	0.030974	0.08101	0.807989	0.860349	ENSG00000172410	ENST00000304526	D	0.89270	-2.49	4.49	-5.74	0.02391	Insulin-like (4);	2.235770	0.02505	N	0.090913	T	0.30262	0.0759	N	0.00313	-1.665	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48747	-0.9008	9	0.02654	T	1	-4.9009	6.5183	0.22260	0.3164:0.0:0.4578:0.2258	rs549148;rs17495476;rs52811901;rs549148	50	Q9Y5Q6	INSL5_HUMAN	L	50	ENSP00000302724:Q50L	ENSP00000302724:Q50L	Q	-	2	0	INSL5	67039344	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.361000	0.07612	-2.118000	0.00828	-2.188000	0.00313	CAG	T|0.146;A|0.854	0.854	strong		0.448	INSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025403.1	NM_005478	
ASPM	259266	hgsc.bcm.edu	37	1	197072420	197072420	+	Silent	SNP	T	T	C	rs41310925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:197072420T>C	ENST00000367409.4	-	18	6217	c.5961A>G	c.(5959-5961)caA>caG	p.Q1987Q	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1987	IQ 13. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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						TCCACTTCTTTTGTTGCACAT	0.333													t|||	1067	0.213059	0.0386	0.2262	5008	,	,		21160	0.1637		0.4115	False		,,,				2504	0.2863				p.Q1987Q		Atlas-SNP	.											.	ASPM	444	.	0			c.A5961G						PASS	.		,	440,3966	211.2+/-231.4	24,392,1787	147.0	147.0	147.0		,5961	-8.9	0.0	1	dbSNP_127	147	3738,4858	529.5+/-381.6	817,2104,1377	no	intron,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	841,2496,3164	CC,CT,TT		43.4853,9.9864,32.1335	,	,1987/3478	197072420	4178,8824	2203	4298	6501	SO:0001819	synonymous_variant	259266	exon18			CTTCTTTTGTTGC	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.5961A>G	1.37:g.197072420T>C		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	213	107	0.502347	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			T|0.699;C|0.301	0.301	strong		0.333	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
AHCTF1	25909	hgsc.bcm.edu	37	1	247006051	247006051	+	Missense_Mutation	SNP	G	G	C	rs12410563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:247006051G>C	ENST00000391829.2	-	35	6676	c.6553C>G	c.(6553-6555)Ctg>Gtg	p.L2185V	AHCTF1_ENST00000326225.3_Missense_Mutation_p.L2194V|AHCTF1_ENST00000470300.1_Intron|AHCTF1_ENST00000366508.1_Missense_Mutation_p.L2220V			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	2185	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.		L -> V (in dbSNP:rs12410563).		cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GGCTTTCCCAGAGTTTCTACT	0.343													C|||	1079	0.215455	0.2201	0.3357	5008	,	,		14969	0.1706		0.2197	False		,,,				2504	0.1656				p.L2194V	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C6580G						PASS	.	C	VAL/LEU	918,3488	738.7+/-411.0	83,752,1368	226.0	206.0	213.0		6580	-0.1	0.0	1	dbSNP_120	213	1848,6752	730.1+/-406.7	202,1444,2654	yes	missense	AHCTF1	NM_015446.4	32	285,2196,4022	CC,CG,GG		21.4884,20.8352,21.2671	benign	2194/2276	247006051	2766,10240	2203	4300	6503	SO:0001583	missense	25909	exon35			TTCCCAGAGTTTC		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.6553C>G	1.37:g.247006051G>C	ENSP00000375705:p.Leu2185Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		503	0.2303113553113553	107	0.21747967479674796	118	0.3259668508287293	112	0.1958041958041958	166	0.21899736147757257	C	0	-2.750109	0.00086	0.208352	0.214884	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.22743	1.94;1.94;1.94	5.06	-0.129	0.13502	.	0.730444	0.12588	N	0.455812	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45220	-0.9276	9	0.12766	T	0.61	0.0995	5.9971	0.19499	0.0:0.5018:0.1262:0.372	rs12410563;rs12410563	2220;2185	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	V	2220;2194;2185	ENSP00000355464:L2220V;ENSP00000355465:L2194V;ENSP00000375705:L2185V	ENSP00000355465:L2194V	L	-	1	2	AHCTF1	245072674	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.286000	0.08399	-0.188000	0.10499	-1.295000	0.01343	CTG	G|0.784;C|0.216	0.216	strong		0.343	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2307121	2307121	+	Missense_Mutation	SNP	G	G	A	rs61742112	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2307121G>A	ENST00000290974.2	-	8	1285	c.946C>T	c.(946-948)Cct>Tct	p.P316S	ZFYVE28_ENST00000515312.1_Missense_Mutation_p.P246S|ZFYVE28_ENST00000511071.1_Missense_Mutation_p.P286S|RP11-478C1.7_ENST00000510632.1_RNA	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	316					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						GGCCCCTCAGGGGGGAGAGGG	0.657													G|||	211	0.0421326	0.0091	0.0663	5008	,	,		18981	0.0		0.1272	False		,,,				2504	0.0256				p.P316S		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.C946T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	119,4287	81.9+/-120.4	3,113,2087	38.0	42.0	41.0		856,736,946	1.1	0.0	4	dbSNP_129	41	1107,7489	216.4+/-255.5	70,967,3261	yes	missense,missense,missense	ZFYVE28	NM_001172656.1,NM_001172659.1,NM_020972.2	74,74,74	73,1080,5348	AA,AG,GG		12.8781,2.7009,9.4293	benign,benign,benign	286/858,246/818,316/888	2307121	1226,11776	2203	4298	6501	SO:0001583	missense	57732	exon8			CCTCAGGGGGGAG	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.946C>T	4.37:g.2307121G>A	ENSP00000290974:p.Pro316Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	37	CCDS33942.1	140	0.0641025641025641	8	0.016260162601626018	35	0.09668508287292818	0	0.0	97	0.1279683377308707	G	2.740	-0.262423	0.05791	0.027009	0.128781	ENSG00000159733	ENST00000290974;ENST00000511071;ENST00000515312	T;T;T	0.58060	0.37;0.36;0.37	4.85	1.12	0.20585	.	0.391533	0.28618	N	0.014715	T	0.00412	0.0013	L	0.47716	1.5	0.23483	P	0.99758385	B;B	0.10296	0.003;0.0	B;B	0.12156	0.007;0.001	T	0.03887	-1.0995	9	0.34782	T	0.22	.	3.6557	0.08220	0.1448:0.3585:0.3743:0.1224	.	286;316	Q9HCC9-2;Q9HCC9	.;LST2_HUMAN	S	316;286;246	ENSP00000290974:P316S;ENSP00000425706:P286S;ENSP00000426299:P246S	ENSP00000290974:P316S	P	-	1	0	ZFYVE28	2276919	0.276000	0.24211	0.001000	0.08648	0.005000	0.04900	0.232000	0.17891	0.007000	0.14760	-0.949000	0.02662	CCT	A|0.086;C|0.000;G|0.914	0.086	strong		0.657	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
EFCAB5	374786	hgsc.bcm.edu	37	17	28407861	28407861	+	Silent	SNP	G	G	A	rs147629201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28407861G>A	ENST00000394835.3	+	17	3480	c.3288G>A	c.(3286-3288)aaG>aaA	p.K1096K	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Silent_p.K972K	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1096							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						CCCGTAATAAGCATGATTATA	0.448													G|||	50	0.00998403	0.0348	0.0029	5008	,	,		19986	0.0		0.002	False		,,,				2504	0.0				p.K1096K		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3288A						PASS	.	G		73,3703		0,73,1815	82.0	78.0	79.0		3288	4.1	0.1	17	dbSNP_134	79	10,8210		0,10,4100	no	coding-synonymous	EFCAB5	NM_198529.3		0,83,5915	AA,AG,GG		0.1217,1.9333,0.6919		1096/1504	28407861	83,11913	1888	4110	5998	SO:0001819	synonymous_variant	374786	exon17			TAATAAGCATGAT	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.3288G>A	17.37:g.28407861G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			G|0.990;A|0.010	0.010	strong		0.448	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
SNAPC4	6621	hgsc.bcm.edu	37	9	139279173	139279173	+	Splice_Site	SNP	G	G	A	rs10781510	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139279173G>A	ENST00000298532.2	-	13	1787	c.1419C>T	c.(1417-1419)gtC>gtT	p.V473V		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)		GCAACTTACCGACACCATATT	0.353													A|||	1831	0.365615	0.2557	0.5692	5008	,	,		19230	0.3165		0.3867	False		,,,				2504	0.3988				p.V473V		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C1419T						PASS	.	A		1233,3173	700.6+/-406.6	169,895,1139	114.0	112.0	113.0		1419	-10.0	0.0	9	dbSNP_120	113	3521,5077	630.5+/-398.4	714,2093,1492	yes	coding-synonymous-near-splice	SNAPC4	NM_003086.2		883,2988,2631	AA,AG,GG		40.9514,27.9846,36.558		473/1470	139279173	4754,8250	2203	4299	6502	SO:0001630	splice_region_variant	6621	exon13			CTTACCGACACCA	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.1420+1C>T	9.37:g.139279173G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			G|0.640;A|0.360	0.360	strong		0.353	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	Silent
OR10H3	26532	hgsc.bcm.edu	37	19	15853150	15853150	+	Silent	SNP	C	C	T	rs16980824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	80	43	0.5375	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		
HN1	51155	hgsc.bcm.edu	37	17	73132265	73132265	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73132265C>T	ENST00000409753.3	-	5	682	c.397G>A	c.(397-399)Gtg>Atg	p.V133M	RP11-649A18.5_ENST00000584339.1_RNA|HN1_ENST00000482348.1_Missense_Mutation_p.V87M|HN1_ENST00000476258.1_Missense_Mutation_p.V87M|HN1_ENST00000405458.3_Missense_Mutation_p.V87M|HN1_ENST00000481647.1_Missense_Mutation_p.V87M|HN1_ENST00000470924.1_Missense_Mutation_p.V87M|HN1_ENST00000392566.2_Missense_Mutation_p.V87M|HN1_ENST00000356033.4_Silent_p.R126R	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	133					developmental process (GO:0032502)	nucleus (GO:0005634)		p.R126R(1)|p.V133L(1)	HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					GCCGGGGCCACCGGGCTGGGC	0.597																																					p.V133M		Atlas-SNP	.											HN1_ENST00000409753,NS,carcinoma,0,3	HN1	17	3	2	Substitution - Missense(1)|Substitution - coding silent(1)	breast(2)	c.G397A						scavenged	.						48.0	52.0	51.0					17																	73132265		2203	4300	6503	SO:0001583	missense	51155	exon5			GGGCCACCGGGCT	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"""androgen-regulated protein 2"""					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.397G>A	17.37:g.73132265C>T	ENSP00000387059:p.Val133Met	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.250015	0.80024	.	.	ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000392566	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	T	0.80889	0.4710	.	.	.	0.40999	D	0.984916	D	0.76494	0.999	D	0.87578	0.998	T	0.83263	-0.0047	7	0.66056	D	0.02	4.4765	17.8012	0.88587	0.0:1.0:0.0:0.0	.	133	Q9UK76	HN1_HUMAN	M	87;133;87	.	ENSP00000440912:V87M	V	-	1	0	HN1	70643860	0.995000	0.38212	0.930000	0.37139	0.989000	0.77384	3.499000	0.53310	2.624000	0.88883	0.643000	0.83706	GTG	.	.	none		0.597	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032	
SEMA3E	9723	hgsc.bcm.edu	37	7	83037731	83037731	+	Missense_Mutation	SNP	C	C	G	rs61729612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:83037731C>G	ENST00000307792.3	-	6	1090	c.623G>C	c.(622-624)cGa>cCa	p.R208P	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R148P	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	208	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)				ATGGGCCAGTCGCCCCATGCT	0.468													C|||	489	0.0976438	0.0651	0.1081	5008	,	,		15618	0.1528		0.1243	False		,,,				2504	0.0501				p.R208P		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G623C						PASS	.	C	PRO/ARG,PRO/ARG	346,4060	178.3+/-207.1	23,300,1880	68.0	63.0	64.0		443,623	1.9	0.0	7	dbSNP_129	64	1106,7494	230.5+/-264.8	89,928,3283	yes	missense,missense	SEMA3E	NM_001178129.1,NM_012431.2	103,103	112,1228,5163	GG,GC,CC		12.8605,7.8529,11.1641	benign,benign	148/716,208/776	83037731	1452,11554	2203	4300	6503	SO:0001583	missense	9723	exon6			GCCAGTCGCCCCA	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.623G>C	7.37:g.83037731C>G	ENSP00000303212:p.Arg208Pro	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	196	94	0.479592	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	259	0.11858974358974358	35	0.07113821138211382	36	0.09944751381215469	92	0.16083916083916083	96	0.1266490765171504	C	7.232	0.599571	0.13939	0.078529	0.128605	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514;ENST00000442159	T;T;T	0.11063	2.81;2.81;2.81	5.9	1.88	0.25563	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.528179	0.20402	N	0.093037	T	0.00039	0.0001	N	0.16201	0.385	0.80722	P	0.0	B	0.02656	0.0	B	0.13407	0.009	T	0.44605	-0.9317	9	0.13853	T	0.58	.	4.4154	0.11454	0.1454:0.5388:0.0:0.3158	rs61729612	208	O15041	SEM3E_HUMAN	P	208;148;208;148	ENSP00000303212:R208P;ENSP00000405052:R148P;ENSP00000412867:R148P	ENSP00000303212:R208P	R	-	2	0	SEMA3E	82875667	0.206000	0.23470	0.001000	0.08648	0.636000	0.38137	1.147000	0.31602	0.325000	0.23359	0.591000	0.81541	CGA	C|0.877;G|0.123	0.123	strong		0.468	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18776784	18776784	+	Missense_Mutation	SNP	G	G	A	rs2060362	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:18776784G>A	ENST00000380548.4	+	19	2896	c.2557G>A	c.(2557-2559)Ggg>Agg	p.G853R		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	853						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)		TCCAGGGCCCGGGCGGCCATC	0.617													G|||	129	0.0257588	0.0008	0.0375	5008	,	,		15494	0.0		0.0517	False		,,,				2504	0.0511				p.G853R		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.G2557A						PASS	.	G	ARG/GLY	37,3657		0,37,1810	5.0	6.0	6.0		2557	4.1	0.5	9	dbSNP_94	6	389,7511		9,371,3570	yes	missense	ADAMTSL1	NM_001040272.5	125	9,408,5380	AA,AG,GG		4.9241,1.0016,3.6743	benign	853/1763	18776784	426,11168	1847	3950	5797	SO:0001583	missense	92949	exon19			GGGCCCGGGCGGC	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.2557G>A	9.37:g.18776784G>A	ENSP00000369921:p.Gly853Arg	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	56	0.02564102564102564	0	0.0	18	0.049723756906077346	0	0.0	38	0.05013192612137203	G	7.223	0.597810	0.13875	0.010016	0.049241	ENSG00000178031	ENST00000380548	T	0.62232	0.04	5.23	4.13	0.48395	.	0.000000	0.08080	U	1.000000	T	0.06645	0.0170	N	0.08118	0	0.23620	N	0.997276	B	0.32731	0.382	B	0.23018	0.043	T	0.06935	-1.0799	10	0.13108	T	0.6	.	4.8989	0.13764	0.1998:0.2072:0.593:0.0	rs2060362;rs17232039;rs2060362	853	Q8N6G6	ATL1_HUMAN	R	853	ENSP00000369921:G853R	ENSP00000369921:G853R	G	+	1	0	ADAMTSL1	18766784	0.850000	0.29656	0.495000	0.27527	0.090000	0.18270	2.049000	0.41288	2.448000	0.82819	0.558000	0.71614	GGG	G|0.973;A|0.027	0.027	strong		0.617	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
LAMC1	3915	hgsc.bcm.edu	37	1	183085755	183085755	+	Missense_Mutation	SNP	A	A	G	rs20563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:183085755A>G	ENST00000258341.4	+	7	1629	c.1372A>G	c.(1372-1374)Att>Gtt	p.I458V		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	458	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.		I -> V (in dbSNP:rs20563). {ECO:0000269|PubMed:1985895, ECO:0000269|PubMed:3360804}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TGAATGTAATATTGAAACAGG	0.383													G|||	2663	0.531749	0.3321	0.6254	5008	,	,		19531	0.628		0.5636	False		,,,				2504	0.6033				p.I458V		Atlas-SNP	.											.	LAMC1	176	.	0			c.A1372G						PASS	.	G	VAL/ILE	1650,2756	659.4+/-400.6	334,982,887	206.0	192.0	197.0		1372	-4.2	0.2	1	dbSNP_67	197	4898,3702	529.7+/-381.6	1352,2194,754	yes	missense	LAMC1	NM_002293.3	29	1686,3176,1641	GG,GA,AA		43.0465,37.4489,49.654	benign	458/1610	183085755	6548,6458	2203	4300	6503	SO:0001583	missense	3915	exon7			TGTAATATTGAAA	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1372A>G	1.37:g.183085755A>G	ENSP00000258341:p.Ile458Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	1166	0.5338827838827839	189	0.38414634146341464	211	0.5828729281767956	331	0.5786713286713286	435	0.5738786279683378	G	1.444	-0.566876	0.03910	0.374489	0.569535	ENSG00000135862	ENST00000258341	T	0.60920	0.15	4.5	-4.2	0.03823	EGF-like, laminin (3);	0.339165	0.30134	N	0.010325	T	0.00012	0.0000	N	0.00608	-1.33	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16217	-1.0410	9	0.02654	T	1	.	6.7303	0.23379	0.5027:0.0:0.308:0.1892	rs20563;rs7556132;rs60661931;rs20563	458	P11047	LAMC1_HUMAN	V	458	ENSP00000258341:I458V	ENSP00000258341:I458V	I	+	1	0	LAMC1	181352378	0.002000	0.14202	0.230000	0.23976	0.961000	0.63080	-0.034000	0.12225	-1.286000	0.02384	-0.186000	0.12905	ATT	A|0.491;G|0.509	0.509	strong		0.383	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
CDH2	1000	hgsc.bcm.edu	37	18	25543387	25543387	+	Silent	SNP	G	G	A	rs1041985	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:25543387G>A	ENST00000269141.3	-	15	2871	c.2448C>T	c.(2446-2448)gcC>gcT	p.A816A	AC015933.2_ENST00000423367.1_RNA|CDH2_ENST00000399380.3_Silent_p.A785A	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	816					adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.A816A(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACTGGGGCTCGGCGTGGATGG	0.537													G|||	1640	0.327476	0.1498	0.464	5008	,	,		15977	0.4216		0.3419	False		,,,				2504	0.3589				p.A816A		Atlas-SNP	.											CDH2,colon,carcinoma,-2,2	CDH2	194	2	1	Substitution - coding silent(1)	stomach(1)	c.C2448T						PASS	.	G		785,3621	316.9+/-294.8	80,625,1498	90.0	71.0	78.0		2448	-11.7	0.1	18	dbSNP_86	78	2690,5910	432.0+/-357.0	405,1880,2015	no	coding-synonymous	CDH2	NM_001792.3		485,2505,3513	AA,AG,GG		31.2791,17.8166,26.7184		816/907	25543387	3475,9531	2203	4300	6503	SO:0001819	synonymous_variant	1000	exon15			GGGCTCGGCGTGG	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.2448C>T	18.37:g.25543387G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	132	58	0.439394	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Silent	SNP	ENST00000269141.3	37	CCDS11891.1																																																																																			G|0.706;A|0.294	0.294	strong		0.537	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
GNLY	10578	hgsc.bcm.edu	37	2	85924729	85924729	+	Missense_Mutation	SNP	C	C	T	rs11127	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:85924729C>T	ENST00000263863.4	+	4	484	c.356C>T	c.(355-357)aCc>aTc	p.T119I	GNLY_ENST00000524600.1_Missense_Mutation_p.T146I|GNLY_ENST00000409696.3_Missense_Mutation_p.T104I	NM_006433.3	NP_006424.2	P22749	GNLY_HUMAN	granulysin	119	Saposin B-type. {ECO:0000255|PROSITE- ProRule:PRU00415}.		T -> I (in dbSNP:rs11127). {ECO:0000269|PubMed:2434598, ECO:0000269|PubMed:8423048}.		cellular defense response (GO:0006968)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular space (GO:0005615)				endometrium(4)|kidney(10)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	19						TCTAGAGTTACCCAGGGCCTC	0.557													C|||	1721	0.34365	0.0628	0.402	5008	,	,		20486	0.5933		0.4046	False		,,,				2504	0.362				p.T119I		Atlas-SNP	.											.	GNLY	29	.	0			c.C356T						PASS	.	C	ILE/THR,ILE/THR	491,3915	228.1+/-243.1	25,441,1737	89.0	81.0	84.0		356,311	0.3	0.0	2	dbSNP_52	84	3285,5315	492.0+/-373.2	630,2025,1645	yes	missense,missense	GNLY	NM_006433.3,NM_012483.2	89,89	655,2466,3382	TT,TC,CC		38.1977,11.1439,29.0328	benign,benign	119/146,104/131	85924729	3776,9230	2203	4300	6503	SO:0001583	missense	10578	exon4			GAGTTACCCAGGG	X54101	CCDS1984.1, CCDS46354.1	2p12-q11	2008-02-05			ENSG00000115523	ENSG00000115523			4414	protein-coding gene	gene with protein product	"""T-lymphocyte activation gene 519"""	188855		LAG2		2212946, 2434598	Standard	NM_012483		Approved	NKG5, LAG-2, D2S69E, TLA519	uc002sql.4	P22749	OTTHUMG00000130179	ENST00000263863.4:c.356C>T	2.37:g.85924729C>T	ENSP00000263863:p.Thr119Ile	Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_006433	P09325|Q6GU08	Missense_Mutation	SNP	ENST00000263863.4	37	CCDS1984.1	813|813	0.37225274725274726|0.37225274725274726	24|24	0.04878048780487805|0.04878048780487805	146|146	0.40331491712707185|0.40331491712707185	334|334	0.583916083916084|0.583916083916084	309|309	0.4076517150395778|0.4076517150395778	C|C	5.252|5.252	0.231888|0.231888	0.09969|0.09969	0.111439|0.111439	0.381977|0.381977	ENSG00000115523|ENSG00000115523	ENST00000526018|ENST00000263863;ENST00000524600;ENST00000409696	.|T;T;T	.|0.64991	.|-0.13;-0.13;-0.13	2.2|2.2	0.274|0.274	0.15654|0.15654	.|Saposin-like (2);Saposin-like type B, 2 (1);Saposin B (2);	.|0.639229	.|0.13105	.|U	.|0.413423	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	.|B;B	.|0.18166	.|0.021;0.026	.|B;B	.|0.19148	.|0.014;0.024	T|T	0.46952|0.46952	-0.9154|-0.9154	4|9	.|0.19147	.|T	.|0.46	.|.	3.4508|3.4508	0.07498|0.07498	0.0:0.566:0.2686:0.1655|0.0:0.566:0.2686:0.1655	rs11127;rs1053034;rs3193524;rs58379359;rs11127|rs11127;rs1053034;rs3193524;rs58379359;rs11127	.|146;119	.|B4E3H9;P22749	.|.;GNLY_HUMAN	S|I	86|119;146;104	.|ENSP00000263863:T119I;ENSP00000436423:T146I;ENSP00000387116:T104I	.|ENSP00000263863:T119I	P|T	+|+	1|2	0|0	GNLY|GNLY	85778240|85778240	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	0.577000|0.577000	0.23758|0.23758	0.060000|0.060000	0.16281|0.16281	-0.459000|-0.459000	0.05422|0.05422	CCC|ACC	C|0.678;N|0.000	.	strong		0.557	GNLY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252497.1	NM_006433	
SOAT1	6646	hgsc.bcm.edu	37	1	179310439	179310439	+	Silent	SNP	C	C	T	rs7547733	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:179310439C>T	ENST00000367619.3	+	7	917	c.774C>T	c.(772-774)ttC>ttT	p.F258F	SOAT1_ENST00000540564.1_Silent_p.F200F|SOAT1_ENST00000539888.1_Silent_p.F193F|SOAT1_ENST00000535686.1_5'UTR	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	258					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)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	TCATTATATTCGAGCAGGTAA	0.373													C|||	331	0.0660942	0.0061	0.1167	5008	,	,		17814	0.0		0.2087	False		,,,				2504	0.0327				p.F258F		Atlas-SNP	.											.	SOAT1	53	.	0			c.C774T						PASS	.	C		179,4227	112.1+/-150.2	3,173,2027	130.0	129.0	129.0		774	-6.3	0.0	1	dbSNP_116	129	1684,6914	287.5+/-298.3	163,1358,2778	no	coding-synonymous	SOAT1	NM_003101.4		166,1531,4805	TT,TC,CC		19.586,4.0626,14.3264		258/551	179310439	1863,11141	2203	4299	6502	SO:0001819	synonymous_variant	6646	exon7			TATATTCGAGCAG	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.774C>T	1.37:g.179310439C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	CCDS1330.1																																																																																			C|0.881;T|0.119	0.119	strong		0.373	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
GABBR2	9568	hgsc.bcm.edu	37	9	101068580	101068580	+	Silent	SNP	G	G	A	rs2304389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	273	135	0.494505	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		
PIEZO2	63895	hgsc.bcm.edu	37	18	10672782	10672782	+	Silent	SNP	T	T	A	rs34134242	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:10672782T>A	ENST00000503781.3	-	51	7910	c.7911A>T	c.(7909-7911)ggA>ggT	p.G2637G	PIEZO2_ENST00000285141.4_Silent_p.G429G|PIEZO2_ENST00000538948.1_Silent_p.G594G|PIEZO2_ENST00000581680.1_5'UTR|PIEZO2_ENST00000302079.6_Silent_p.G2574G|PIEZO2_ENST00000580640.1_Silent_p.G2662G	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2637					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										ATATTCTGTTTCCAGTCAGGT	0.438													T|||	35	0.00698882	0.0023	0.0216	5008	,	,		18731	0.0		0.0169	False		,,,				2504	0.0				p.G2637G		Atlas-SNP	.											.	.	.	.	0			c.A7911T						PASS	.	T		19,4387	26.2+/-53.5	0,19,2184	132.0	122.0	125.0		7911	0.7	0.9	18	dbSNP_126	125	118,8482	62.4+/-124.4	1,116,4183	no	coding-synonymous	PIEZO2	NM_022068.2		1,135,6367	AA,AT,TT		1.3721,0.4312,1.0534		2637/2753	10672782	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	63895	exon51			TCTGTTTCCAGTC	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.7911A>T	18.37:g.10672782T>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Silent	SNP	ENST00000503781.3	37																																																																																				T|0.990;A|0.010	0.010	strong		0.438	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068	
P2RY12	64805	hgsc.bcm.edu	37	3	151056616	151056616	+	Silent	SNP	G	G	A	rs6785930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:151056616G>A	ENST00000302632.3	-	3	317	c.18C>T	c.(16-18)aaC>aaT	p.N6N	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	6					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	CAGAGGTGAGGTTGTCGACGG	0.458													G|||	1211	0.241813	0.1672	0.2781	5008	,	,		17210	0.2113		0.3151	False		,,,				2504	0.273				p.N6N		Atlas-SNP	.											P2RY12,NS,malignant_melanoma,-1,1	P2RY12	36	1	0			c.C18T						PASS	.	G	,,	836,3570	333.1+/-302.8	80,676,1447	72.0	68.0	69.0		18,,18	4.1	0.9	3	dbSNP_116	69	2721,5879	433.3+/-357.4	427,1867,2006	no	coding-synonymous,intron,coding-synonymous	P2RY12,MED12L	NM_022788.3,NM_053002.4,NM_176876.1	,,	507,2543,3453	AA,AG,GG		31.6395,18.9741,27.3489	,,	6/343,,6/343	151056616	3557,9449	2203	4300	6503	SO:0001819	synonymous_variant	64805	exon3			GGTGAGGTTGTCG	AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.18C>T	3.37:g.151056616G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_022788	D3DNJ5|Q546J7	Silent	SNP	ENST00000302632.3	37	CCDS3159.1																																																																																			G|0.736;A|0.264	0.264	strong		0.458	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1		
OR51D1	390038	hgsc.bcm.edu	37	11	4661826	4661826	+	Missense_Mutation	SNP	T	T	C	rs79020081	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4661826T>C	ENST00000357605.2	+	1	882	c.806T>C	c.(805-807)aTt>aCt	p.I269T	OR51E1_ENST00000396952.5_5'Flank	NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTACCCCTCATTGGGCTCTCG	0.557													T|||	193	0.0385383	0.0113	0.0677	5008	,	,		20314	0.001		0.0835	False		,,,				2504	0.047				p.I269T		Atlas-SNP	.											.	OR51D1	49	.	0			c.T806C						PASS	.	T	THR/ILE	98,4304	77.8+/-116.1	3,92,2106	136.0	130.0	132.0		806	4.6	1.0	11	dbSNP_131	132	786,7810	186.0+/-233.6	32,722,3544	yes	missense	OR51D1	NM_001004751.2	89	35,814,5650	CC,CT,TT		9.1438,2.2263,6.801	probably-damaging	269/325	4661826	884,12114	2201	4298	6499	SO:0001583	missense	390038	exon1			CCCTCATTGGGCT	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"""GPCR / Class A : Olfactory receptors"""	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.806T>C	11.37:g.4661826T>C	ENSP00000350222:p.Ile269Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	37	CCDS31357.1	105	0.04807692307692308	6	0.012195121951219513	35	0.09668508287292818	1	0.0017482517482517483	63	0.08311345646437995	T	8.942	0.966004	0.18659	0.022263	0.091438	ENSG00000197428	ENST00000357605	T	0.00152	8.66	4.58	4.58	0.56647	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45606	D	0.000350	T	0.00039	0.0001	M	0.85945	2.785	0.80722	P	0.0	D	0.67145	0.996	D	0.74348	0.983	T	0.66344	-0.5947	9	0.72032	D	0.01	.	13.2106	0.59822	0.0:0.0:0.0:1.0	.	269	Q8NGF3	O51D1_HUMAN	T	269	ENSP00000350222:I269T	ENSP00000350222:I269T	I	+	2	0	OR51D1	4618402	0.011000	0.17503	0.964000	0.40570	0.005000	0.04900	1.995000	0.40767	2.044000	0.60594	0.460000	0.39030	ATT	T|0.938;C|0.062	0.062	strong		0.557	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751	
FANCA	2175	hgsc.bcm.edu	37	16	89857935	89857935	+	Missense_Mutation	SNP	G	G	A	rs11646374	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89857935G>A	ENST00000389301.3	-	14	1265	c.1235C>T	c.(1234-1236)gCg>gTg	p.A412V	FANCA_ENST00000568369.1_Missense_Mutation_p.A412V	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	412			A -> V (in dbSNP:rs11646374). {ECO:0000269|PubMed:18987736}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CATCAAACGCGCCACCCAGTC	0.567			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	353	0.0704872	0.0038	0.0187	5008	,	,		19935	0.254		0.0626	False		,,,				2504	0.0164				p.A412V		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C1235T						PASS	.	G	VAL/ALA	76,4320	64.7+/-102.0	0,76,2122	65.0	51.0	56.0		1235	5.1	0.1	16	dbSNP_120	56	698,7902	172.5+/-223.2	26,646,3628	yes	missense	FANCA	NM_000135.2	64	26,722,5750	AA,AG,GG		8.1163,1.7288,5.9557	possibly-damaging	412/1456	89857935	774,12222	2198	4300	6498	SO:0001583	missense	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAACGCGCCACCC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1235C>T	16.37:g.89857935G>A	ENSP00000373952:p.Ala412Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	180	0.08241758241758242	3	0.006097560975609756	10	0.027624309392265192	117	0.20454545454545456	50	0.06596306068601583	G	14.47	2.546014	0.45383	0.017288	0.081163	ENSG00000187741	ENST00000389301	D	0.98585	-5.01	5.13	5.13	0.70059	.	0.801903	0.11032	N	0.607099	T	0.03220	0.0094	M	0.65975	2.015	0.09310	P	0.9999999999981521	P;P	0.52316	0.952;0.952	B;B	0.41174	0.349;0.349	T	0.11155	-1.0599	9	0.46703	T	0.11	-1.967	12.244	0.54560	0.0:0.1854:0.8146:0.0	rs11646374;rs17226204;rs52813493;rs58856001;rs11646374	412;412	B4DRI7;O15360	.;FANCA_HUMAN	V	412	ENSP00000373952:A412V	ENSP00000373952:A412V	A	-	2	0	FANCA	88385436	1.000000	0.71417	0.128000	0.21923	0.016000	0.09150	4.990000	0.63876	2.417000	0.82017	0.650000	0.86243	GCG	G|0.932;A|0.068	0.068	strong		0.567	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ATP12A	479	hgsc.bcm.edu	37	13	25272807	25272807	+	Silent	SNP	C	C	T	rs148844496	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25272807C>T	ENST00000381946.3	+	12	1691	c.1524C>T	c.(1522-1524)caC>caT	p.H508H	ATP12A_ENST00000218548.6_Silent_p.H514H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	508					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)		TCTCCATCCACGAGATGGATG	0.517																																					p.H514H	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C1542T						PASS	.	C	,	0,4406		0,0,2203	56.0	50.0	52.0		1542,1524	-2.1	0.0	13	dbSNP_134	52	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	0,6,6497	TT,TC,CC		0.0698,0.0,0.0461	,	514/1046,508/1040	25272807	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	479	exon12			CATCCACGAGATG	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.1524C>T	13.37:g.25272807C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
SLC35E2	9906	hgsc.bcm.edu	37	1	1670432	1670432	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:1670432T>C	ENST00000246421.4	-	3	802	c.387A>G	c.(385-387)ttA>ttG	p.L129L	SLC35E2_ENST00000355439.2_Silent_p.L129L|SLC35E2_ENST00000400924.1_Silent_p.L129L|RP1-283E3.8_ENST00000598846.1_RNA	NM_182838.2	NP_878258.1	P0CK97	S35E2_HUMAN	solute carrier family 35, member E2	129						integral component of membrane (GO:0016021)				endometrium(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGTGCTGATATAAACAGCAAG	0.537																																					p.L129L		Atlas-SNP	.											SLC35E2,NS,carcinoma,0,1	SLC35E2	13	1	0			c.A387G						scavenged	.						108.0	140.0	129.0					1																	1670432		2203	4298	6501	SO:0001819	synonymous_variant	9906	exon3			CTGATATAAACAG	AB007916	CCDS33.1, CCDS55560.1	1p36.33	2013-05-22			ENSG00000215790	ENSG00000215790		"""Solute carriers"""	20863	protein-coding gene	gene with protein product							Standard	NM_182838		Approved	KIAA0447	uc001aia.2	P0CK97	OTTHUMG00000000823	ENST00000246421.4:c.387A>G	1.37:g.1670432T>C		Somatic	930	0	0		WXS	Illumina HiSeq	Phase_I	987	34	0.0344478	NM_182838	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q5QPR8|Q9Y3J8	Silent	SNP	ENST00000246421.4	37	CCDS33.1																																																																																			T|1.000;|0.000	.	weak		0.537	SLC35E2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000002210.3	XM_049733	
ARNTL2	56938	hgsc.bcm.edu	37	12	27553566	27553566	+	Missense_Mutation	SNP	A	A	G	rs1037921	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000311001.5_Missense_Mutation_p.N326S|ARNTL2_ENST00000261178.5_Missense_Mutation_p.N292S|ARNTL2_ENST00000542388.1_Missense_Mutation_p.N255S|ARNTL2_ENST00000395901.2_Missense_Mutation_p.N303S|ARNTL2_ENST00000544915.1_Missense_Mutation_p.N306S|ARNTL2_ENST00000546179.1_Missense_Mutation_p.N303S			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	109	0	0		WXS	Illumina HiSeq	Phase_I	127	65	0.511811	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	
PRR27	401137	hgsc.bcm.edu	37	4	71024463	71024463	+	Missense_Mutation	SNP	G	G	C	rs142405912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024463G>C	ENST00000344526.5	+	3	683	c.494G>C	c.(493-495)gGa>gCa	p.G165A	C4orf40_ENST00000502294.1_Missense_Mutation_p.G165A|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		165	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						GCACCTGTTGGAGCTGAGCCT	0.632													G|||	26	0.00519169	0.0038	0.0043	5008	,	,		16092	0.001		0.0139	False		,,,				2504	0.0031				p.G165A		Atlas-SNP	.											.	C4orf40	19	.	0			c.G494C						PASS	.	G	ALA/GLY	8,4398		0,8,2195	29.0	30.0	30.0		494	1.3	0.0	4	dbSNP_134	30	114,8482		2,110,4186	no	missense	C4orf40	NM_214711.3	60	2,118,6381	CC,CG,GG		1.3262,0.1816,0.9383	benign	165/220	71024463	122,12880	2203	4298	6501	SO:0001583	missense	401137	exon3			CTGTTGGAGCTGA																												ENST00000344526.5:c.494G>C	4.37:g.71024463G>C	ENSP00000343172:p.Gly165Ala	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	107	9	0.0841122	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	6.439	0.449185	0.12223	0.001816	0.013262	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.29917	1.55;1.55	4.43	1.28	0.21552	.	.	.	.	.	T	0.05318	0.0141	N	0.01874	-0.695	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.33343	-0.9872	9	0.02654	T	1	0.4193	1.7036	0.02877	0.1887:0.2762:0.391:0.1441	.	165	Q6MZM9	CD040_HUMAN	A	165	ENSP00000426249:G165A;ENSP00000343172:G165A	ENSP00000343172:G165A	G	+	2	0	C4orf40	71059052	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.053000	0.11846	-0.013000	0.14199	-0.241000	0.12123	GGA	G|0.993;C|0.007	0.007	strong		0.632	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
LEFTY1	10637	hgsc.bcm.edu	37	1	226076669	226076669	+	Missense_Mutation	SNP	C	C	T	rs41310561	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226076669C>T	ENST00000272134.5	-	1	177	c.98G>A	c.(97-99)cGg>cAg	p.R33Q	RP4-559A3.7_ENST00000432920.2_Intron|LEFTY1_ENST00000492457.1_Intron	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	33					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)					CTGCAGCTGCCGCAGCAGGCT	0.706													C|||	328	0.0654952	0.0008	0.0735	5008	,	,		15639	0.1458		0.0497	False		,,,				2504	0.0808				p.R33Q		Atlas-SNP	.											LEFTY1,NS,carcinoma,0,1	LEFTY1	30	1	0			c.G98A						PASS	.	C	GLN/ARG	29,4257		0,29,2114	11.0	12.0	12.0		98	-5.9	0.7	1	dbSNP_127	12	348,8060		8,332,3864	no	missense	LEFTY1	NM_020997.3	43	8,361,5978	TT,TC,CC		4.1389,0.6766,2.9699	benign	33/367	226076669	377,12317	2143	4204	6347	SO:0001583	missense	10637	exon1			AGCTGCCGCAGCA	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.98G>A	1.37:g.226076669C>T	ENSP00000272134:p.Arg33Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	145	0.06639194139194139	0	0.0	20	0.055248618784530384	85	0.1486013986013986	40	0.052770448548812667	c	0.016	-1.515749	0.00975	0.006766	0.041389	ENSG00000243709	ENST00000272134	T	0.65916	-0.18	4.18	-5.9	0.02275	Transforming growth factor-beta, N-terminal (1);	0.596957	0.18283	N	0.145963	T	0.00109	0.0003	N	0.00972	-1.085	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.13072	-1.0523	9	0.06236	T	0.91	.	12.5504	0.56223	0.0:0.5422:0.0:0.4578	rs41310561;rs61995950	33;33	B2R7U0;O75610	.;LFTY1_HUMAN	Q	33	ENSP00000272134:R33Q	ENSP00000272134:R33Q	R	-	2	0	LEFTY1	224143292	0.011000	0.17503	0.705000	0.30386	0.126000	0.20510	-0.619000	0.05572	-1.087000	0.03081	-2.087000	0.00375	CGG	C|0.955;T|0.045	0.045	strong		0.706	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
BMPR1A	657	hgsc.bcm.edu	37	10	88635779	88635779	+	Missense_Mutation	SNP	C	C	A	rs11528010	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:88635779C>A	ENST00000372037.3	+	3	541	c.4C>A	c.(4-6)Cct>Act	p.P2T	BMPR1A_ENST00000480152.1_3'UTR	NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	2			P -> T (in dbSNP:rs11528010). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8397373}.		BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						TTGAACAATGCCTCAGCTATA	0.328			"""Mis, N, F"""			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2				A|||	2503	0.4998	0.7239	0.3617	5008	,	,		19725	0.7093		0.2753	False		,,,				2504	0.3098				p.P2T	Ovarian(190;603 2086 22044 30335 47971)	Atlas-SNP	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"""bone morphogenetic protein receptor, type IA"""		E	.	BMPR1A	118	.	0			c.C4A						PASS	.	A	THR/PRO	2863,1543	485.5+/-360.3	941,981,281	197.0	195.0	196.0		4	5.3	1.0	10	dbSNP_120	196	2203,6397	709.9+/-405.7	280,1643,2377	no	missense	BMPR1A	NM_004329.2	38	1221,2624,2658	AA,AC,CC		25.6163,35.0204,38.9513	benign	2/533	88635779	5066,7940	2203	4300	6503	SO:0001583	missense	657	exon3	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	ACAATGCCTCAGC	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"""CD molecules"""	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.4C>A	10.37:g.88635779C>A	ENSP00000361107:p.Pro2Thr	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	206	205	0.995146	NM_004329	A8K6U9|Q8NEN8	Missense_Mutation	SNP	ENST00000372037.3	37	CCDS7378.1	987	0.4519230769230769	292	0.5934959349593496	117	0.32320441988950277	391	0.6835664335664335	187	0.24670184696569922	A	1.311	-0.602108	0.03744	0.649796	0.256163	ENSG00000107779	ENST00000224764;ENST00000372037	D	0.81499	-1.5	5.3	5.3	0.74995	.	0.301588	0.34200	N	0.004161	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	1.7000000000044757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41016	-0.9532	9	0.02654	T	1	.	11.256	0.49054	0.8467:0.1533:0.0:0.0	rs11528010	2	P36894	BMR1A_HUMAN	T	2	ENSP00000361107:P2T	ENSP00000224764:P2T	P	+	1	0	BMPR1A	88625759	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	3.768000	0.55295	0.956000	0.37904	-0.374000	0.07098	CCT	.	.	weak		0.328	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329	
COPS2	9318	hgsc.bcm.edu	37	15	49429410	49429410	+	Silent	SNP	A	A	G	rs17473148	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:49429410A>G	ENST00000388901.5	-	6	550	c.477T>C	c.(475-477)taT>taC	p.Y159Y	COPS2_ENST00000299259.6_Silent_p.Y166Y|Y_RNA_ENST00000363250.1_RNA|COPS2_ENST00000542928.1_Silent_p.Y95Y	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	159					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		CTCGTTCTAAATATAATTTTC	0.328													A|||	553	0.110423	0.0174	0.1441	5008	,	,		13666	0.006		0.2356	False		,,,				2504	0.1912				p.Y166Y	NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)	Atlas-SNP	.											.	COPS2	41	.	0			c.T498C						PASS	.	A	,	194,4196	110.8+/-149.0	6,182,2007	38.0	41.0	40.0		498,477	3.2	1.0	15	dbSNP_123	40	1717,6871	306.4+/-307.9	178,1361,2755	no	coding-synonymous,coding-synonymous	COPS2	NM_001143887.1,NM_004236.3	,	184,1543,4762	GG,GA,AA		19.993,4.4191,14.7249	,	166/451,159/444	49429410	1911,11067	2195	4294	6489	SO:0001819	synonymous_variant	9318	exon6			TTCTAAATATAAT	AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"""COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"""			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.477T>C	15.37:g.49429410A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_001143887	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Silent	SNP	ENST00000388901.5	37	CCDS32235.1																																																																																			A|0.868;G|0.132	0.132	strong		0.328	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236	
SLIT3	6586	hgsc.bcm.edu	37	5	168114030	168114030	+	Missense_Mutation	SNP	C	C	T	rs148887706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:168114030C>T	ENST00000519560.1	-	30	3687	c.3268G>A	c.(3268-3270)Gtg>Atg	p.V1090M	SLIT3_ENST00000404867.3_Missense_Mutation_p.V1090M|SLIT3_ENST00000332966.8_Missense_Mutation_p.V1097M	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1090	EGF-like 5. {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)			ATTGTGTCCACGCACTGGGCC	0.622													c|||	4	0.000798722	0.0	0.0043	5008	,	,		20234	0.0		0.0	False		,,,				2504	0.001				p.V1097M	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.G3289A						PASS	.	T	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	75.0	68.0	70.0		3268	0.6	0.9	5	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLIT3	NM_003062.2	21	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging	1090/1524	168114030	2,13004	2203	4300	6503	SO:0001583	missense	6586	exon30			TGTCCACGCACTG	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.3268G>A	5.37:g.168114030C>T	ENSP00000430333:p.Val1090Met	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	326	165	0.506135	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	2.527	-0.309415	0.05458	2.27E-4	1.16E-4	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	D;D;D	0.95103	-3.61;-3.61;-3.61	4.59	0.628	0.17681	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.373727	0.29707	N	0.011409	D	0.92264	0.7546	M	0.76574	2.34	0.38397	D	0.945565	P	0.43352	0.804	B	0.42163	0.378	D	0.87702	0.2561	10	0.42905	T	0.14	.	7.0594	0.25117	0.1166:0.6:0.0:0.2834	.	1090	O75094	SLIT3_HUMAN	M	1090;1097;1090	ENSP00000430333:V1090M;ENSP00000332164:V1097M;ENSP00000384890:V1090M	ENSP00000332164:V1097M	V	-	1	0	SLIT3	168046608	0.000000	0.05858	0.949000	0.38748	0.003000	0.03518	-0.190000	0.09615	-0.086000	0.12550	-4.011000	0.00013	GTG	C|1.000;T|0.000	0.000	strong		0.622	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
PHLDB3	653583	hgsc.bcm.edu	37	19	43990438	43990438	+	Missense_Mutation	SNP	G	G	A	rs201337364		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43990438G>A	ENST00000292140.5	-	13	1825	c.1465C>T	c.(1465-1467)Cct>Tct	p.P489S		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	489							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGAACAGCAGGGCCTGAGGAA	0.582																																					p.P489S		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1465T						PASS	.	G	SER/PRO	0,4164		0,0,2082	53.0	68.0	63.0		1465	-2.1	0.0	19		63	4,8378		0,4,4187	yes	missense	PHLDB3	NM_198850.3	74	0,4,6269	AA,AG,GG		0.0477,0.0,0.0319	possibly-damaging	489/641	43990438	4,12542	2082	4191	6273	SO:0001583	missense	653583	exon13			CAGCAGGGCCTGA		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1465C>T	19.37:g.43990438G>A	ENSP00000292140:p.Pro489Ser	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	G	6.513	0.462872	0.12402	0.0	4.77E-4	ENSG00000176531	ENST00000292140	T	0.45276	0.9	4.29	-2.07	0.07276	.	2.063540	0.02567	N	0.097370	T	0.27419	0.0673	L	0.29908	0.895	0.09310	N	1	B;B	0.14438	0.006;0.01	B;B	0.10450	0.005;0.003	T	0.07616	-1.0763	10	0.17369	T	0.5	.	3.9887	0.09527	0.4359:0.1828:0.3813:0.0	.	193;489	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	S	489	ENSP00000292140:P489S	ENSP00000292140:P489S	P	-	1	0	PHLDB3	48682278	0.668000	0.27493	0.028000	0.17463	0.253000	0.25986	0.582000	0.23834	-0.045000	0.13468	-0.385000	0.06624	CCT	.	.	weak		0.582	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
SNX29	92017	hgsc.bcm.edu	37	16	12145791	12145791	+	Missense_Mutation	SNP	G	G	C	rs118191509	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12145791G>C	ENST00000566228.1	+	8	905	c.836G>C	c.(835-837)gGg>gCg	p.G279A	SNX29_ENST00000323433.4_5'Flank|SNX29_ENST00000306030.3_5'Flank	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	279						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						CAGAACTCTGGGGACGTGTTT	0.473													G|||	34	0.00678914	0.0008	0.0014	5008	,	,		17949	0.001		0.0229	False		,,,				2504	0.0082				p.G279A		Atlas-SNP	.											.	SNX29	60	.	0			c.G836C						PASS	.	G	ALA/GLY	29,4365	32.6+/-62.9	0,29,2168	73.0	82.0	79.0		836	4.8	0.2	16	dbSNP_132	79	247,8353	96.6+/-158.3	3,241,4056	no	missense	SNX29	NM_032167.3	60	3,270,6224	CC,CG,GG		2.8721,0.66,2.1241	benign	279/376	12145791	276,12718	2197	4300	6497	SO:0001583	missense	92017	exon8			ACTCTGGGGACGT	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.836G>C	16.37:g.12145791G>C	ENSP00000456480:p.Gly279Ala	Somatic	504	0	0		WXS	Illumina HiSeq	Phase_I	499	217	0.43487	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	21	0.009615384615384616	0	0.0	0	0.0	0	0.0	21	0.027704485488126648	G	4.332	0.060912	0.08339	0.0066	0.028721	ENSG00000140660	ENST00000268271	.	.	.	5.78	4.82	0.62117	.	0.280809	0.33235	N	0.005122	T	0.24547	0.0595	L	0.29908	0.895	0.80722	D	1	.	.	.	.	.	.	T	0.18147	-1.0346	7	0.07175	T	0.84	-11.8625	14.9466	0.71035	0.0:0.2704:0.7296:0.0	.	.	.	.	A	279	.	ENSP00000268271:G279A	G	+	2	0	RUNDC2A	12053292	1.000000	0.71417	0.231000	0.23993	0.455000	0.32408	3.912000	0.56386	1.447000	0.47661	0.313000	0.20887	GGG	G|0.983;C|0.017	0.017	strong		0.473	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
CCDC38	120935	hgsc.bcm.edu	37	12	96292170	96292170	+	Missense_Mutation	SNP	C	C	G	rs75959092	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:96292170C>G	ENST00000344280.3	-	7	1164	c.607G>C	c.(607-609)Gtg>Ctg	p.V203L	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	203										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CACCTTTTCACTGCTTGTACC	0.428													C|||	282	0.0563099	0.0045	0.0706	5008	,	,		19368	0.0278		0.1342	False		,,,				2504	0.0654				p.V203L		Atlas-SNP	.											.	CCDC38	45	.	0			c.G607C						PASS	.	C	LEU/VAL	102,4304	80.9+/-119.3	2,98,2103	346.0	261.0	290.0		607	0.7	0.1	12	dbSNP_132	290	1073,7527	225.1+/-261.3	70,933,3297	yes	missense	CCDC38	NM_182496.2	32	72,1031,5400	GG,GC,CC		12.4767,2.315,9.0343	benign	203/564	96292170	1175,11831	2203	4300	6503	SO:0001583	missense	120935	exon7			TTTTCACTGCTTG	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.607G>C	12.37:g.96292170C>G	ENSP00000345470:p.Val203Leu	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	445	183	0.411236	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	139	0.06364468864468864	6	0.012195121951219513	24	0.06629834254143646	10	0.017482517482517484	99	0.13060686015831136	C	5.900	0.350137	0.11182	0.02315	0.124767	ENSG00000165972	ENST00000344280	T	0.07688	3.17	5.4	0.671	0.17929	.	0.361234	0.28062	N	0.016743	T	0.00039	0.0001	L	0.28556	0.865	0.42212	P	0.008184999999999998	B	0.23128	0.08	B	0.23419	0.046	T	0.42749	-0.9433	9	0.07325	T	0.83	-3.5442	4.7641	0.13123	0.0:0.3797:0.1564:0.4638	.	203	Q502W7	CCD38_HUMAN	L	203	ENSP00000345470:V203L	ENSP00000345470:V203L	V	-	1	0	CCDC38	94816301	0.010000	0.17322	0.129000	0.21949	0.024000	0.10985	-0.125000	0.10579	0.055000	0.16094	-0.424000	0.05967	GTG	C|0.917;G|0.083	0.083	strong		0.428	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
RETSAT	54884	hgsc.bcm.edu	37	2	85570857	85570857	+	Missense_Mutation	SNP	G	G	A	rs4832169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:85570857G>A	ENST00000295802.4	-	10	1710	c.1598C>T	c.(1597-1599)gCc>gTc	p.A533V	RETSAT_ENST00000457495.2_Missense_Mutation_p.A472V|RETSAT_ENST00000263854.6_Silent_p.C477C|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	239	0	0		WXS	Illumina HiSeq	Phase_I	308	43	0.13961	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	
CENPE	1062	hgsc.bcm.edu	37	4	104117191	104117191	+	Silent	SNP	A	A	G	rs2290943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	56	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	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			
MYO18B	84700	hgsc.bcm.edu	37	22	26388337	26388337	+	Silent	SNP	C	C	T	rs916425	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26388337C>T	ENST00000407587.2	+	40	6337	c.6168C>T	c.(6166-6168)taC>taT	p.Y2056Y	MYO18B_ENST00000536101.1_Silent_p.Y2055Y|MYO18B_ENST00000335473.7_Silent_p.Y2055Y			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2055	Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AGGAGAAGTACGTGGAGGAAC	0.577													C|||	571	0.114018	0.1997	0.1066	5008	,	,		21990	0.001		0.1759	False		,,,				2504	0.0562				p.Y2055Y		Atlas-SNP	.											.	MYO18B	322	.	0			c.C6165T						PASS	.	C		770,3384		72,626,1379	61.0	64.0	63.0		6165	-6.9	0.7	22	dbSNP_86	63	1363,7089		110,1143,2973	no	coding-synonymous	MYO18B	NM_032608.5		182,1769,4352	TT,TC,CC		16.1264,18.5364,16.9205		2055/2568	26388337	2133,10473	2077	4226	6303	SO:0001819	synonymous_variant	84700	exon40			GAAGTACGTGGAG	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.6168C>T	22.37:g.26388337C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	18	0.295082	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		268	0.1227106227106227	92	0.18699186991869918	42	0.11602209944751381	1	0.0017482517482517483	133	0.17546174142480211	C	1.337	-0.595152	0.03771	0.185364	0.161264	ENSG00000133454	ENST00000543971	.	.	.	5.17	-6.94	0.01633	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999883998	.	.	.	.	.	.	T	0.13361	-1.0512	3	.	.	.	.	11.1467	0.48434	0.0:0.3209:0.088:0.5911	rs916425;rs916425	.	.	.	M	20	.	.	T	+	2	0	MYO18B	24718337	0.149000	0.22717	0.692000	0.30179	0.288000	0.27193	-0.838000	0.04372	-1.610000	0.01583	-1.934000	0.00508	ACG	C|0.866;T|0.134	0.134	strong		0.577	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
NMT1	4836	hgsc.bcm.edu	37	17	43171154	43171154	+	Silent	SNP	C	C	T	rs1132898	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43171154C>T	ENST00000592782.1	+	5	618	c.487C>T	c.(487-489)Ctg>Ttg	p.L163L	NMT1_ENST00000590114.1_3'UTR|NMT1_ENST00000258960.2_Silent_p.L163L			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	116	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	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	
KLKB1	3818	hgsc.bcm.edu	37	4	187178473	187178473	+	Missense_Mutation	SNP	G	G	A	rs4253325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187178473G>A	ENST00000264690.6	+	14	1866	c.1679G>A	c.(1678-1680)cGg>cAg	p.R560Q	KLKB1_ENST00000513864.1_Intron	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	560	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> Q (in dbSNP:rs4253325). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		ATAACCCAACGGATGGTCTGT	0.343													.|||	1143	0.228235	0.2564	0.2305	5008	,	,		10375	0.3095		0.1153	False		,,,				2504	0.2209				p.R560Q		Atlas-SNP	.											.	KLKB1	155	.	0			c.G1679A	GRCh37	CM071826	KLKB1	M	rs4253325	PASS	.	G	GLN/ARG	998,3404	354.6+/-312.7	115,768,1318	96.0	113.0	108.0		1679	2.1	0.9	4	dbSNP_111	108	920,7676	202.3+/-245.6	44,832,3422	yes	missense	KLKB1	NM_000892.3	43	159,1600,4740	AA,AG,GG		10.7027,22.6715,14.7561	benign	560/639	187178473	1918,11080	2201	4298	6499	SO:0001583	missense	3818	exon14			CCCAACGGATGGT	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.1679G>A	4.37:g.187178473G>A	ENSP00000264690:p.Arg560Gln	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	462|462	0.21153846153846154|0.21153846153846154	118|118	0.23983739837398374|0.23983739837398374	75|75	0.20718232044198895|0.20718232044198895	186|186	0.32517482517482516|0.32517482517482516	83|83	0.10949868073878628|0.10949868073878628	G|G	8.074|8.074	0.770879|0.770879	0.15983|0.15983	0.226715|0.226715	0.107027|0.107027	ENSG00000164344|ENSG00000164344	ENST00000511608|ENST00000264690	.|D	.|0.93019	.|-3.15	5.97|5.97	2.08|2.08	0.27032|0.27032	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.|0.672704	.|0.14563	.|N	.|0.311923	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.46819|0.46819	1.47|1.47	0.19575|0.19575	P|P	0.9999605521|0.9999605521	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.04737|0.04737	-1.0930|-1.0930	4|9	.|0.18710	.|T	.|0.47	.|.	9.4553|9.4553	0.38751|0.38751	0.7979:0.0:0.2021:0.0|0.7979:0.0:0.2021:0.0	rs4253325;rs17691327;rs52791824;rs59026632;rs4253325|rs4253325;rs17691327;rs52791824;rs59026632;rs4253325	.|560;560	.|A8K9A9;P03952	.|.;KLKB1_HUMAN	R|Q	608|560	.|ENSP00000264690:R560Q	.|ENSP00000264690:R560Q	G|R	+|+	1|2	0|0	KLKB1|KLKB1	187415467|187415467	0.733000|0.733000	0.28132|0.28132	0.856000|0.856000	0.33681|0.33681	0.451000|0.451000	0.32288|0.32288	2.324000|2.324000	0.43831|0.43831	0.498000|0.498000	0.27948|0.27948	-0.290000|-0.290000	0.09829|0.09829	GGA|CGG	G|0.817;A|0.183	0.183	strong		0.343	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	
SIRT5	23408	hgsc.bcm.edu	37	6	13599303	13599303	+	Silent	SNP	C	C	T	rs3757261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:13599303C>T	ENST00000606117.1	+	8	953	c.657C>T	c.(655-657)caC>caT	p.H219H	SIRT5_ENST00000359782.3_Silent_p.H201H|SIRT5_ENST00000379262.4_Silent_p.H219H|SIRT5_ENST00000397350.2_Silent_p.H111H	NM_012241.4	NP_036373.1			sirtuin 5											breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	11	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)			TGCGACCTCACGTCGTGTGGT	0.577													C|||	860	0.171725	0.0461	0.1787	5008	,	,		15440	0.2054		0.2425	False		,,,				2504	0.229				p.H219H		Atlas-SNP	.											SIRT5_ENST00000379262,caecum,carcinoma,0,2	SIRT5	45	2	0			c.C657T						PASS	.	C	,,,	307,4099	166.2+/-197.5	13,281,1909	124.0	111.0	116.0		603,333,657,657	-2.3	0.8	6	dbSNP_107	116	2002,6598	349.7+/-327.5	216,1570,2514	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SIRT5	NM_001193267.2,NM_001242827.1,NM_012241.4,NM_031244.3	,,,	229,1851,4423	TT,TC,CC		23.2791,6.9678,17.7533	,,,	201/293,111/203,219/311,219/300	13599303	2309,10697	2203	4300	6503	SO:0001819	synonymous_variant	23408	exon8			ACCTCACGTCGTG	AF083110	CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1	6p23	2010-08-05	2010-06-25		ENSG00000124523	ENSG00000124523			14933	protein-coding gene	gene with protein product		604483	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5"", ""sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)"""			10381378	Standard	NM_012241		Approved		uc003nay.3	Q9NXA8	OTTHUMG00000014278	ENST00000606117.1:c.657C>T	6.37:g.13599303C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_012241		Silent	SNP	ENST00000606117.1	37	CCDS4526.1																																																																																			C|0.829;T|0.171	0.171	strong		0.577	SIRT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039908.2		
TMEM171	134285	hgsc.bcm.edu	37	5	72419267	72419267	+	Missense_Mutation	SNP	T	T	C	rs638333	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:72419267T>C	ENST00000454765.2	+	2	540	c.67T>C	c.(67-69)Ttc>Ctc	p.F23L	TMEM171_ENST00000287773.5_Missense_Mutation_p.F23L			Q8WVE6	TM171_HUMAN	transmembrane protein 171	23			F -> L (in dbSNP:rs638333). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		CAAACTCATCTTCTGCTTCTT	0.592													T|||	846	0.16893	0.0855	0.3458	5008	,	,		18441	0.0962		0.2883	False		,,,				2504	0.1084				p.F23L	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.T67C						PASS	.	T	LEU/PHE,LEU/PHE	512,3894	235.2+/-247.8	35,442,1726	124.0	117.0	120.0		67,67	5.1	1.0	5	dbSNP_83	120	2437,6163	404.7+/-348.2	336,1765,2199	yes	missense,missense	TMEM171	NM_001161342.1,NM_173490.6	22,22	371,2207,3925	CC,CT,TT		28.3372,11.6205,22.6742	probably-damaging,probably-damaging	23/324,23/325	72419267	2949,10057	2203	4300	6503	SO:0001583	missense	134285	exon2			CTCATCTTCTGCT	BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.67T>C	5.37:g.72419267T>C	ENSP00000415030:p.Phe23Leu	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	370	165	0.445946	NM_173490	Q8N0S1|Q8TDT7	Missense_Mutation	SNP	ENST00000454765.2	37	CCDS4017.1	456	0.2087912087912088	47	0.09552845528455285	122	0.3370165745856354	67	0.11713286713286714	220	0.29023746701846964	T	22.2	4.257271	0.80246	0.116205	0.283372	ENSG00000157111	ENST00000454765;ENST00000287773	T;T	0.34072	1.38;1.38	5.09	5.09	0.68999	.	0.074689	0.56097	N	0.000028	T	0.00012	0.0000	M	0.76002	2.32	0.23933	P	0.99642717	B;B	0.23540	0.087;0.087	B;B	0.19946	0.027;0.027	T	0.19943	-1.0290	9	0.66056	D	0.02	-23.8583	14.8705	0.70453	0.0:0.0:0.0:1.0	rs638333;rs17851615;rs59015469;rs638333	23;23	Q8WVE6-2;Q8WVE6	.;TM171_HUMAN	L	23	ENSP00000415030:F23L;ENSP00000287773:F23L	ENSP00000287773:F23L	F	+	1	0	TMEM171	72455023	1.000000	0.71417	0.990000	0.47175	0.720000	0.41350	5.398000	0.66308	1.922000	0.55676	0.379000	0.24179	TTC	T|0.791;C|0.209	0.209	strong		0.592	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
RNF145	153830	hgsc.bcm.edu	37	5	158603839	158603839	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:158603839A>G	ENST00000424310.2	-	5	781	c.422T>C	c.(421-423)aTg>aCg	p.M141T	RNF145_ENST00000521606.2_Missense_Mutation_p.M158T|RNF145_ENST00000520638.1_Missense_Mutation_p.M155T|RNF145_ENST00000519865.1_Missense_Mutation_p.M141T|RNF145_ENST00000518802.1_Missense_Mutation_p.M171T|RNF145_ENST00000274542.2_Missense_Mutation_p.M169T	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	141						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.M169T(4)		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)			CTTTGTTTTCATGACACAGGA	0.363																																					p.M171T		Atlas-SNP	.											RNF145,NS,carcinoma,0,4	RNF145	110	4	4	Substitution - Missense(4)	endometrium(3)|lung(1)	c.T512C						scavenged	.						35.0	33.0	34.0					5																	158603839		2201	4298	6499	SO:0001583	missense	153830	exon5			GTTTTCATGACAC	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.422T>C	5.37:g.158603839A>G	ENSP00000409064:p.Met141Thr	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	291	4	0.0137457	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.282699	0.80692	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.77229	-1.08;-1.06;-1.06;-1.07;-1.07;-1.08;-1.07	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.81725	0.4883	L	0.44542	1.39	0.80722	D	1	D;D;D;D;D;D	0.57257	0.979;0.979;0.979;0.979;0.979;0.974	P;P;P;P;P;P	0.57846	0.828;0.828;0.828;0.828;0.76;0.736	D	0.83797	0.0234	10	0.72032	D	0.01	-20.3428	15.6548	0.77124	1.0:0.0:0.0:0.0	.	157;158;155;171;141;169	E7EW26;B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;.;RN145_HUMAN;.	T	169;141;141;157;158;171;141;155	ENSP00000274542:M169T;ENSP00000430397:M141T;ENSP00000409064:M141T;ENSP00000430753:M157T;ENSP00000445115:M158T;ENSP00000430955:M171T;ENSP00000429071:M155T	ENSP00000274542:M169T	M	-	2	0	RNF145	158536417	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.162000	0.67917	0.377000	0.23210	ATG	.	.	none		0.363	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
TRIM65	201292	hgsc.bcm.edu	37	17	73886888	73886888	+	Missense_Mutation	SNP	A	A	G	rs3760128	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73886888A>G	ENST00000269383.3	-	6	1591	c.1526T>C	c.(1525-1527)cTg>cCg	p.L509P		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	509			L -> P (in dbSNP:rs3760128). {ECO:0000269|PubMed:15489334}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGGGGCCCCAGAGGGAACAC	0.627													G|||	2328	0.464856	0.9032	0.3141	5008	,	,		17564	0.2222		0.3499	False		,,,				2504	0.3476				p.L509P		Atlas-SNP	.											TRIM65,NS,carcinoma,0,1	TRIM65	23	1	0			c.T1526C						PASS	.	G	PRO/LEU	3605,787		1492,621,83	19.0	19.0	19.0		1526	3.7	0.0	17	dbSNP_107	19	2944,5646		541,1862,1892	yes	missense	TRIM65	NM_173547.2	98	2033,2483,1975	GG,GA,AA		34.2724,17.9189,49.5532	benign	509/518	73886888	6549,6433	2196	4295	6491	SO:0001583	missense	201292	exon6			GGCCCCAGAGGGA	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.1526T>C	17.37:g.73886888A>G	ENSP00000269383:p.Leu509Pro	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	37	CCDS11732.1	961	0.440018315018315	441	0.8963414634146342	128	0.35359116022099446	147	0.256993006993007	245	0.3232189973614776	G	0	-2.811358	0.00073	0.820811	0.342724	ENSG00000141569	ENST00000269383	T	0.57595	0.39	4.69	3.69	0.42338	Concanavalin A-like lectin/glucanase (1);	0.337845	0.21595	N	0.072024	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32481	-0.9905	9	0.11182	T	0.66	.	5.6825	0.17784	0.079:0.1377:0.6412:0.1422	rs3760128;rs57250342;rs3760128	509	Q6PJ69	TRI65_HUMAN	P	509	ENSP00000269383:L509P	ENSP00000269383:L509P	L	-	2	0	TRIM65	71398483	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	1.022000	0.30052	0.395000	0.25257	-0.215000	0.12644	CTG	A|0.500;G|0.500	0.500	strong		0.627	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
STYK1	55359	hgsc.bcm.edu	37	12	10782116	10782116	+	Silent	SNP	G	G	A	rs4763567	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:10782116G>A	ENST00000075503.3	-	6	1129	c.609C>T	c.(607-609)ctC>ctT	p.L203L		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	203	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						AGAGAAAGCTGAGCAGGTCCC	0.527										HNSCC(73;0.22)			G|||	215	0.0429313	0.0038	0.0317	5008	,	,		17862	0.0317		0.0467	False		,,,				2504	0.1115				p.L203L		Atlas-SNP	.											.	STYK1	55	.	0			c.C609T						PASS	.	G		45,4361	48.9+/-83.8	0,45,2158	56.0	47.0	50.0		609	4.7	1.0	12	dbSNP_111	50	410,8190	129.0+/-187.1	10,390,3900	yes	coding-synonymous	STYK1	NM_018423.2		10,435,6058	AA,AG,GG		4.7674,1.0213,3.4984		203/423	10782116	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	55359	exon6			AAAGCTGAGCAGG	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.609C>T	12.37:g.10782116G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Silent	SNP	ENST00000075503.3	37	CCDS8629.1	79	0.036172161172161175	3	0.006097560975609756	11	0.03038674033149171	22	0.038461538461538464	43	0.05672823218997362	G	9.582	1.123925	0.20959	0.010213	0.047674	ENSG00000060140	ENST00000542924	.	.	.	5.58	4.67	0.58626	.	.	.	.	.	T	0.13670	0.0331	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.13124	-1.0521	4	.	.	.	-14.0949	8.5143	0.33237	0.0855:0.158:0.7565:0.0	rs4763567;rs4763567	.	.	.	L	41	.	.	S	-	2	0	STYK1	10673383	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.361000	0.44160	2.782000	0.95742	0.655000	0.94253	TCA	G|0.963;A|0.037	0.037	strong		0.527	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423	
PRUNE2	158471	hgsc.bcm.edu	37	9	79320431	79320431	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79320431G>T	ENST00000376718.3	-	8	6882	c.6759C>A	c.(6757-6759)gaC>gaA	p.D2253E	PRUNE2_ENST00000428286.1_Missense_Mutation_p.D1894E	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2253					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						GAGAAAAGCTGTCTGATATCC	0.448																																					p.D2253E		Atlas-SNP	.											PRUNE2_ENST00000376718,NS,carcinoma,-2,1	PRUNE2	331	1	0			c.C6759A						scavenged	.						53.0	51.0	51.0					9																	79320431		1568	3582	5150	SO:0001583	missense	158471	exon8			AAAGCTGTCTGAT	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.6759C>A	9.37:g.79320431G>T	ENSP00000365908:p.Asp2253Glu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	175	2	0.0114286	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.033|1.033	-0.681293|-0.681293	0.03353|0.03353	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.39997|.	1.05;1.06|.	5.92|5.92	-7.0|-7.0	0.01599|0.01599	.|.	0.601995|.	0.15997|.	N|.	0.234504|.	T|T	0.06781|0.06781	0.0173|0.0173	N|N	0.01576|0.01576	-0.805|-0.805	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.28138|0.28138	-1.0053|-1.0053	10|5	0.02654|.	T|.	1|.	-4.753|-4.753	0.2877|0.2877	0.00253|0.00253	0.2228:0.222:0.2341:0.3211|0.2228:0.222:0.2341:0.3211	.|.	2253|.	Q8WUY3|.	PRUN2_HUMAN|.	E|K	2253;1894;2252|1575	ENSP00000365908:D2253E;ENSP00000397425:D1894E|.	ENSP00000365908:D2253E|.	D|Q	-|-	3|1	2|0	PRUNE2|PRUNE2	78510251|78510251	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.088000|0.088000	0.18126|0.18126	-1.542000|-1.542000	0.02196|0.02196	-0.982000|-0.982000	0.03515|0.03515	-1.053000|-1.053000	0.02334|0.02334	GAC|CAG	.	.	none		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
IL17RE	132014	hgsc.bcm.edu	37	3	9956279	9956279	+	Silent	SNP	G	G	A	rs455863	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:9956279G>A	ENST00000383814.3	+	14	1449	c.1344G>A	c.(1342-1344)ccG>ccA	p.P448P	IL17RC_ENST00000413608.1_5'Flank|IL17RE_ENST00000295980.3_Silent_p.P448P|IL17RC_ENST00000403601.3_5'Flank|IL17RE_ENST00000454190.2_Missense_Mutation_p.G473R|IL17RE_ENST00000421412.1_Silent_p.P481P|IL17RC_ENST00000416074.2_5'Flank|IL17RC_ENST00000295981.3_5'Flank|IL17RC_ENST00000383812.4_5'Flank|IL17RC_ENST00000455057.1_5'Flank	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	448					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		TCTTGTGTCCGGATGGTGAGT	0.607													G|||	1813	0.362021	0.4054	0.4625	5008	,	,		19167	0.0933		0.5447	False		,,,				2504	0.3211				p.G473R		Atlas-SNP	.											IL17RE,NS,haematopoietic_neoplasm,+1,1	IL17RE	62	1	0			c.G1417A						PASS	.	G	ARG/GLY,,	1829,2577	533.4+/-373.7	391,1047,765	121.0	123.0	122.0		1417,1344,1464	-9.9	0.0	3	dbSNP_80	122	4579,4021	597.6+/-393.8	1205,2169,926	yes	missense,coding-synonymous,coding-synonymous	IL17RE	NM_001193380.1,NM_153480.1,NM_153483.2	125,,	1596,3216,1691	AA,AG,GG		46.7558,41.5116,49.2696	,,	473/534,448/668,488/708	9956279	6408,6598	2203	4300	6503	SO:0001819	synonymous_variant	132014	exon14			GTGTCCGGATGGT	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"""Interleukins and interleukin receptors"""	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.1344G>A	3.37:g.9956279G>A		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_001193380	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Missense_Mutation	SNP	ENST00000383814.3	37	CCDS2589.1	809	0.37042124542124544	192	0.3902439024390244	168	0.46408839779005523	38	0.06643356643356643	411	0.5422163588390502	G	3.940	-0.014333	0.07681	0.415116	0.532442	ENSG00000163701	ENST00000454190	T	0.30714	1.52	4.94	-9.87	0.00470	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21861	P	0.999502608	B	0.02656	0.0	B	0.01281	0.0	T	0.31724	-0.9933	7	0.87932	D	0	-12.6119	6.2348	0.20756	0.0884:0.1602:0.4815:0.27	rs455863;rs1300549;rs52806952;rs61674331;rs455863	473	Q8NFR9-3	.	R	473	ENSP00000388086:G473R	ENSP00000388086:G473R	G	+	1	0	IL17RE	9931279	0.000000	0.05858	0.011000	0.14972	0.478000	0.33099	-5.110000	0.00150	-4.926000	0.00027	-2.560000	0.00174	GGA	A|0.424;C|0.006	0.424	strong		0.607	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480	
AFAP1	60312	hgsc.bcm.edu	37	4	7857230	7857230	+	Silent	SNP	C	C	T	rs61742221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:7857230C>T	ENST00000360265.4	-	3	531	c.297G>A	c.(295-297)ccG>ccA	p.P99P	AFAP1_ENST00000382543.3_Silent_p.P99P|AFAP1_ENST00000358461.2_Silent_p.P99P|AFAP1_ENST00000420658.1_Silent_p.P99P			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	99	Pro-rich.					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						CGGGGCTCAGCGGCACAGCTT	0.552													C|||	892	0.178115	0.0477	0.2464	5008	,	,		18081	0.0645		0.4443	False		,,,				2504	0.1493				p.P99P		Atlas-SNP	.											.	AFAP1	93	.	0			c.G297A						PASS	.	C	,	441,3965	213.8+/-233.3	20,401,1782	90.0	77.0	81.0		297,297	-9.3	0.6	4	dbSNP_129	81	3760,4840	535.6+/-382.8	836,2088,1376	no	coding-synonymous,coding-synonymous	AFAP1	NM_001134647.1,NM_198595.2	,	856,2489,3158	TT,TC,CC		43.7209,10.0091,32.3005	,	99/815,99/731	7857230	4201,8805	2203	4300	6503	SO:0001819	synonymous_variant	60312	exon4			GCTCAGCGGCACA	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.297G>A	4.37:g.7857230C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	47	0.423423	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			C|0.700;T|0.300	0.300	strong		0.552	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
POMT1	10585	hgsc.bcm.edu	37	9	134385435	134385435	+	Nonsense_Mutation	SNP	C	C	T	rs386738991|rs3887873	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134385435C>T	ENST00000372228.3	+	8	930	c.751C>T	c.(751-753)Cag>Tag	p.Q251*	POMT1_ENST00000404875.2_Intron|POMT1_ENST00000419118.2_Intron|POMT1_ENST00000402686.3_Intron|POMT1_ENST00000354713.4_Intron|POMT1_ENST00000341012.7_Intron|POMT1_ENST00000541219.1_Intron|POMT1_ENST00000423007.1_Intron	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	251			Q -> R (in dbSNP:rs2296949). {ECO:0000269|PubMed:10366449, ECO:0000269|PubMed:14702039}.|Q -> W (requires 2 nucleotide substitutions; dbSNP:rs3887873).		carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GGGGCAGATGCAGATGTCACA	0.572													C|||	394	0.0786741	0.1248	0.0793	5008	,	,		19038	0.001		0.1461	False		,,,				2504	0.0266				p.Q251X		Atlas-SNP	.											.	POMT1	59	.	0			c.C751T						PASS	.	C	,,,,stop/GLN	395,4011		22,351,1830	72.0	61.0	65.0		,,,,751	-1.1	0.0	9	dbSNP_108	65	871,7729		65,741,3494	yes	intron,intron,intron,intron,stop-gained	POMT1	NM_001077365.1,NM_001077366.1,NM_001136113.1,NM_001136114.1,NM_007171.3	,,,,	87,1092,5324	TT,TC,CC		10.1279,8.965,9.734	,,,,	,,,,251/748	134385435	1266,11740	2203	4300	6503	SO:0001587	stop_gained	10585	exon8			CAGATGCAGATGT	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.751C>T	9.37:g.134385435C>T	ENSP00000361302:p.Gln251*	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Nonsense_Mutation	SNP	ENST00000372228.3	37	CCDS6943.1	147	0.0673076923076923	34	0.06910569105691057	29	0.08011049723756906	1	0.0017482517482517483	83	0.10949868073878628	C	12.05	1.821679	0.32237	0.08965	0.101279	ENSG00000130714	ENST00000441334;ENST00000372228;ENST00000448212	.	.	.	2.2	-1.1	0.09872	.	4.494090	0.00649	U	0.000543	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.2385	2.8102	0.05440	0.3724:0.2516:0.376:0.0	rs3887873;rs52806687;rs57618284;rs3887873	.	.	.	X	134;251;197	.	.	Q	+	1	0	POMT1	133375256	0.274000	0.24191	0.001000	0.08648	0.049000	0.14656	-0.097000	0.11042	-0.288000	0.09051	-0.234000	0.12200	CAG	C|0.904;T|0.096	0.096	strong		0.572	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
FARSA	2193	hgsc.bcm.edu	37	19	13041442	13041442	+	Missense_Mutation	SNP	G	G	A	rs33925420	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:13041442G>A	ENST00000314606.4	-	2	287	c.269C>T	c.(268-270)gCc>gTc	p.A90V	FARSA_ENST00000423140.2_Missense_Mutation_p.A90V|FARSA_ENST00000588025.1_Missense_Mutation_p.A130V|CTC-425F1.2_ENST00000592636.1_RNA	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	90					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	CTCGCTCTGGGCCAGGCCCTC	0.627													G|||	19	0.00379393	0.0008	0.0029	5008	,	,		18747	0.0		0.0159	False		,,,				2504	0.0				p.A90V		Atlas-SNP	.											.	FARSA	46	.	0			c.C269T						PASS	.	G	VAL/ALA	22,4384	29.9+/-59.1	0,22,2181	60.0	50.0	53.0		269	0.4	1.0	19	dbSNP_126	53	174,8426	79.2+/-141.9	3,168,4129	yes	missense	FARSA	NM_004461.2	64	3,190,6310	AA,AG,GG		2.0233,0.4993,1.507	benign	90/509	13041442	196,12810	2203	4300	6503	SO:0001583	missense	2193	exon2			CTCTGGGCCAGGC	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	3592	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, alpha, cytoplasmic"""	602918	"""phenylalanine-tRNA synthetase-like"", ""phenylalanyl-tRNA synthetase-like, alpha subunit"""	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.269C>T	19.37:g.13041442G>A	ENSP00000320309:p.Ala90Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Missense_Mutation	SNP	ENST00000314606.4	37	CCDS12287.1	17	0.007783882783882784	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	G	12.58	1.982087	0.34942	0.004993	0.020233	ENSG00000179115	ENST00000314606;ENST00000423140	T;T	0.64085	-0.08;0.5	5.51	0.38	0.16222	.	0.423532	0.26812	N	0.022363	T	0.17619	0.0423	N	0.05230	-0.09	0.28950	N	0.89048	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.0	T	0.05767	-1.0865	10	0.30854	T	0.27	-19.0265	4.0896	0.09963	0.4105:0.0:0.4299:0.1596	rs33925420	90;90	B4E363;Q9Y285	.;SYFA_HUMAN	V	90	ENSP00000320309:A90V;ENSP00000396548:A90V	ENSP00000320309:A90V	A	-	2	0	FARSA	12902442	1.000000	0.71417	0.982000	0.44146	0.846000	0.48090	3.130000	0.50508	0.274000	0.22072	0.561000	0.74099	GCC	G|0.986;A|0.014	0.014	strong		0.627	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
IQCE	23288	hgsc.bcm.edu	37	7	2646796	2646796	+	Missense_Mutation	SNP	G	G	A	rs555122760|rs61729413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2646796G>A	ENST00000402050.2	+	21	2088	c.1904G>A	c.(1903-1905)aGg>aAg	p.R635K	IQCE_ENST00000404984.1_Missense_Mutation_p.R584K|IQCE_ENST00000438376.2_Missense_Mutation_p.R619K|IQCE_ENST00000325979.7_Missense_Mutation_p.R570K	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	635						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)		GCTTCTACCAGGAGGAGATCG	0.522													G|||	512	0.102236	0.087	0.1542	5008	,	,		18956	0.0526		0.171	False		,,,				2504	0.0665				p.R635K		Atlas-SNP	.											.	IQCE	66	.	0			c.G1904A						PASS	.	G	LYS/ARG,LYS/ARG	297,3515		11,275,1620	84.0	92.0	90.0		1856,1904	-3.6	0.0	7	dbSNP_129	90	1203,7041		96,1011,3015	yes	missense,missense	IQCE	NM_001100390.1,NM_152558.3	26,26	107,1286,4635	AA,AG,GG		14.5924,7.7912,12.4419	benign,benign	619/680,635/696	2646796	1500,10556	1906	4122	6028	SO:0001583	missense	23288	exon21			CTACCAGGAGGAG	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.1904G>A	7.37:g.2646796G>A	ENSP00000385597:p.Arg635Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	257	0.11767399267399267	36	0.07317073170731707	48	0.13259668508287292	40	0.06993006993006994	133	0.17546174142480211	G	6.341	0.431038	0.12045	0.077912	0.145924	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979;ENST00000423196	T;T;T;T;T	0.26067	2.74;2.74;2.74;2.75;1.76	4.38	-3.56	0.04626	.	1.611890	0.03793	N	0.263181	T	0.00039	0.0001	L	0.29908	0.895	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	0.22765	-1.0207	9	0.08179	T	0.78	-0.4083	5.5866	0.17277	0.4151:0.1535:0.4314:0.0	rs61729413	570;619;635;635;619	B4DXN1;B4DDX4;Q6IPM2;B3KRY4;Q6IPM2-4	.;.;IQCE_HUMAN;.;.	K	635;584;619;570;215	ENSP00000385597:R635K;ENSP00000385945:R584K;ENSP00000396178:R619K;ENSP00000313772:R570K;ENSP00000405982:R215K	ENSP00000313772:R570K	R	+	2	0	IQCE	2613322	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.682000	0.05185	-0.903000	0.03881	-0.294000	0.09567	AGG	G|0.869;A|0.131	0.131	strong		0.522	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
CCDC91	55297	hgsc.bcm.edu	37	12	28412372	28412372	+	Missense_Mutation	SNP	G	G	A	rs11049488	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:28412372G>A	ENST00000545336.1	+	6	525	c.106G>A	c.(106-108)Gca>Aca	p.A36T	CCDC91_ENST00000539107.1_Missense_Mutation_p.A36T|CCDC91_ENST00000381256.1_Missense_Mutation_p.A36T|CCDC91_ENST00000381259.1_Missense_Mutation_p.A36T			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	36				A -> T (in Ref. 1; AAP42284). {ECO:0000305}.	protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					TGCCTTTCCTGCAGGTATTGG	0.388													A|||	624	0.124601	0.0182	0.1239	5008	,	,		14041	0.0427		0.2972	False		,,,				2504	0.1759				p.A36T		Atlas-SNP	.											.	CCDC91	63	.	0			c.G106A						PASS	.	A	THR/ALA	243,4163	803.2+/-415.7	8,227,1968	112.0	93.0	100.0		106	-0.5	1.0	12	dbSNP_120	100	2641,5957	685.6+/-404.1	403,1835,2061	yes	missense	CCDC91	NM_018318.3	58	411,2062,4029	AA,AG,GG		30.7164,5.5152,22.1778	benign	36/442	28412372	2884,10120	2203	4299	6502	SO:0001583	missense	55297	exon2			TTTCCTGCAGGTA	AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"""GGA binding partner"""					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.106G>A	12.37:g.28412372G>A	ENSP00000438040:p.Ala36Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_018318	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	331	0.15155677655677655	16	0.032520325203252036	50	0.13812154696132597	31	0.05419580419580419	234	0.3087071240105541	A	5.392	0.257578	0.10239	0.055152	0.307164	ENSG00000123106	ENST00000538586;ENST00000539107;ENST00000536442;ENST00000545336;ENST00000543534;ENST00000545737;ENST00000381259;ENST00000381256	T;T;T;T;T;T	0.30448	1.56;1.53;1.54;1.53;1.54;1.56	5.57	-0.515	0.11954	.	0.204155	0.34268	N	0.004109	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999920092	B	0.02656	0.0	B	0.08055	0.003	T	0.38373	-0.9664	9	0.09843	T	0.71	-2.8834	1.3506	0.02172	0.4348:0.1422:0.2856:0.1374	rs11049488;rs52814885;rs58237387;rs11049488	36	Q7Z6B0	CCD91_HUMAN	T	36	ENSP00000440513:A36T;ENSP00000445660:A36T;ENSP00000438040:A36T;ENSP00000442544:A36T;ENSP00000370658:A36T;ENSP00000370655:A36T	ENSP00000370655:A36T	A	+	1	0	CCDC91	28303639	0.388000	0.25197	0.992000	0.48379	0.931000	0.56810	-0.115000	0.10741	-0.272000	0.09259	-0.254000	0.11334	GCA	G|0.816;A|0.184	0.184	strong		0.388	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318	
HSPB2	3316	hgsc.bcm.edu	37	11	111784229	111784229	+	Silent	SNP	C	C	T	rs4252588	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:111784229C>T	ENST00000304298.3	+	2	747	c.159C>T	c.(157-159)gcC>gcT	p.A53A	CRYAB_ENST00000533280.1_5'Flank|CRYAB_ENST00000525823.1_5'Flank|CRYAB_ENST00000227251.3_5'Flank|CRYAB_ENST00000533475.1_Intron|HSPB2_ENST00000537382.1_Silent_p.A53A|HSPB2-C11orf52_ENST00000534100.1_Intron|CRYAB_ENST00000533971.1_5'Flank|CRYAB_ENST00000526180.1_5'Flank|CRYAB_ENST00000531198.1_5'Flank|CRYAB_ENST00000527950.1_Intron	NM_001541.3	NP_001532.1	Q16082	HSPB2_HUMAN	heat shock 27kDa protein 2	53					positive regulation of catalytic activity (GO:0043085)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)	p.A53A(1)		large_intestine(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(61;3.75e-11)|all_epithelial(67;2.33e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)		GGCCTCGGGCCGCCCCAGCTG	0.622													C|||	341	0.0680911	0.1293	0.0461	5008	,	,		16397	0.001		0.0577	False		,,,				2504	0.0808				p.A53A		Atlas-SNP	.											.	HSPB2	20	.	1	Substitution - coding silent(1)	lung(1)	c.C159T						PASS	.	C		504,3898	233.6+/-246.7	33,438,1730	112.0	124.0	120.0		159	-4.8	0.0	11	dbSNP_111	120	608,7986	158.6+/-212.1	22,564,3711	no	coding-synonymous	HSPB2	NM_001541.3		55,1002,5441	TT,TC,CC		7.0747,11.4493,8.5565		53/183	111784229	1112,11884	2201	4297	6498	SO:0001819	synonymous_variant	3316	exon2			TCGGGCCGCCCCA	U75898	CCDS8352.1	11q22-q23	2011-09-02	2002-08-29			ENSG00000170276		"""Heat shock proteins / HSPB"""	5247	protein-coding gene	gene with protein product		602179	"""heat shock 27kD protein 2"""			9344664, 9490724	Standard	NM_001541		Approved	Hs.78846, MKBP	uc001pmg.2	Q16082		ENST00000304298.3:c.159C>T	11.37:g.111784229C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_001541	Q6I9U7	Silent	SNP	ENST00000304298.3	37	CCDS8352.1																																																																																			C|0.914;T|0.086	0.086	strong		0.622	HSPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391669.1		
KANSL1	284058	hgsc.bcm.edu	37	17	44108906	44108906	+	Missense_Mutation	SNP	A	A	G	rs34579536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44108906A>G	ENST00000262419.6	-	15	3724	c.3254T>C	c.(3253-3255)aTt>aCt	p.I1085T	KANSL1_ENST00000393476.3_Missense_Mutation_p.I379T|KANSL1_ENST00000574590.1_Missense_Mutation_p.I1085T|KANSL1_ENST00000572904.1_Missense_Mutation_p.I1085T|KANSL1_ENST00000575318.1_Missense_Mutation_p.I1021T|KANSL1_ENST00000432791.1_Missense_Mutation_p.I1085T	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1085	Sufficient for interaction with KAT8.		I -> T (in dbSNP:rs34579536).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GAGGGGGACAATGGGAGGCGA	0.627													G|||	432	0.086262	0.0151	0.1571	5008	,	,		15744	0.001		0.2406	False		,,,				2504	0.0613				p.I1085T		Atlas-SNP	.											KIAA1267,colon,carcinoma,0,1	.	.	1	0			c.T3254C						PASS	.	G	THR/ILE,THR/ILE,THR/ILE	203,4203	780.9+/-414.5	6,191,2006	29.0	26.0	27.0		3251,3254,3254	2.3	0.0	17	dbSNP_126	27	1914,6686	697.4+/-404.9	220,1474,2606	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	89,89,89	226,1665,4612	GG,GA,AA		22.2558,4.6074,16.2771	benign,benign,benign	1084/1105,1085/1106,1085/1106	44108906	2117,10889	2203	4300	6503	SO:0001583	missense	284058	exon15			GGGACAATGGGAG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3254T>C	17.37:g.44108906A>G	ENSP00000262419:p.Ile1085Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	3.452	-0.111802	0.06881	0.046074	0.222558	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.25085	2.63;2.63;1.82	5.72	2.34	0.29019	.	1.538450	0.03719	N	0.251449	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37979	-0.9682	9	0.12766	T	0.61	3.041	9.2051	0.37285	0.7644:0.0:0.2356:0.0	rs34579536	416;1085	Q7Z3B3-2;Q7Z3B3	.;K1267_HUMAN	T	1085;1085;379	ENSP00000262419:I1085T;ENSP00000387393:I1085T;ENSP00000377117:I379T	ENSP00000262419:I1085T	I	-	2	0	KIAA1267	41464753	0.000000	0.05858	0.001000	0.08648	0.426000	0.31534	0.910000	0.28571	-0.087000	0.12528	-1.163000	0.01768	ATT	A|0.860;G|0.140	0.140	strong		0.627	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38652993	38652993	+	Silent	SNP	C	C	T	rs332864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	186	0	0		WXS	Illumina HiSeq	Phase_I	205	91	0.443902	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	
SAE1	10055	hgsc.bcm.edu	37	19	47700611	47700611	+	Silent	SNP	C	C	T	rs11083864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47700611C>T	ENST00000270225.7	+	7	923	c.855C>T	c.(853-855)gaC>gaT	p.D285D	SAE1_ENST00000413379.3_Intron|SAE1_ENST00000598840.1_Silent_p.D204D|SAE1_ENST00000392776.3_Intron|SAE1_ENST00000540850.1_Silent_p.D111D	NM_005500.2	NP_005491.1	Q9UBE0	SAE1_HUMAN	SUMO1 activating enzyme subunit 1	285					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitotic cell cycle (GO:0007346)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP-dependent protein binding (GO:0043008)|enzyme activator activity (GO:0008047)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|ubiquitin activating enzyme activity (GO:0004839)			endometrium(3)|large_intestine(5)|lung(4)|ovary(1)	13		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TTAGTCCTGACCTGCTTCCTG	0.403													C|||	49	0.00978435	0.0008	0.0101	5008	,	,		18031	0.0		0.0288	False		,,,				2504	0.0123				p.D285D		Atlas-SNP	.											.	SAE1	50	.	0			c.C855T						PASS	.	C	,,	12,4394	19.1+/-41.9	0,12,2191	233.0	201.0	212.0		,,855	1.3	1.0	19	dbSNP_120	212	206,8394	88.1+/-150.5	4,198,4098	no	intron,intron,coding-synonymous	SAE1	NM_001145713.1,NM_001145714.1,NM_005500.2	,,	4,210,6289	TT,TC,CC		2.3953,0.2724,1.6761	,,	,,285/347	47700611	218,12788	2203	4300	6503	SO:0001819	synonymous_variant	10055	exon7			TCCTGACCTGCTT	BC018271	CCDS12696.1, CCDS54284.1, CCDS54285.1	19q13.32	2013-09-26				ENSG00000142230		"""Ubiquitin-like modifier activating enzymes"""	30660	protein-coding gene	gene with protein product	"""activator Of sumo 1"""	613294				10187858, 9920803, 10217437	Standard	NM_005500		Approved	AOS1, FLJ3091, Sua1	uc002pgc.3	Q9UBE0		ENST00000270225.7:c.855C>T	19.37:g.47700611C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	157	79	0.503185	NM_005500	B2RDP5|B3KMQ2|F5GXX7|G3XAK6|O95717|Q9P020	Silent	SNP	ENST00000270225.7	37	CCDS12696.1																																																																																			C|0.988;T|0.012	0.012	strong		0.403	SAE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466775.1	NM_005500	
PTPRH	5794	hgsc.bcm.edu	37	19	55697889	55697889	+	Silent	SNP	G	G	A	rs1136578	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55697889G>A	ENST00000376350.3	-	15	2608	c.2586C>T	c.(2584-2586)ccC>ccT	p.P862P	PTPRH_ENST00000263434.5_Silent_p.P684P	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	862	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TGGGCTTCAGGGGCACCCGGG	0.592													G|||	383	0.0764776	0.1551	0.0778	5008	,	,		16388	0.0		0.0954	False		,,,				2504	0.0286				p.P862P		Atlas-SNP	.											.	PTPRH	139	.	0			c.C2586T						PASS	.	G	,	705,3701	294.1+/-283.0	56,593,1554	68.0	69.0	69.0		2052,2586	3.1	1.0	19	dbSNP_86	69	899,7701	201.0+/-244.6	53,793,3454	no	coding-synonymous,coding-synonymous	PTPRH	NM_001161440.1,NM_002842.3	,	109,1386,5008	AA,AG,GG		10.4535,16.0009,12.3328	,	684/938,862/1116	55697889	1604,11402	2203	4300	6503	SO:0001819	synonymous_variant	5794	exon15			CTTCAGGGGCACC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2586C>T	19.37:g.55697889G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	37	CCDS33110.1																																																																																			G|0.891;A|0.109	0.109	strong		0.592	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
GPRC6A	222545	hgsc.bcm.edu	37	6	117114223	117114223	+	Silent	SNP	T	T	A	rs6924002	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	155	0	0		WXS	Illumina HiSeq	Phase_I	163	84	0.515337	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		
FABP6	2172	hgsc.bcm.edu	37	5	159659262	159659262	+	Missense_Mutation	SNP	G	G	A	rs116237330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:159659262G>A	ENST00000402432.3	+	2	353	c.225G>A	c.(223-225)atG>atA	p.M75I	FABP6_ENST00000393982.1_Missense_Mutation_p.M124I|FABP6_ENST00000393980.4_Missense_Mutation_p.M124I	NM_001445.2	NP_001436.1	P51161	FABP6_HUMAN	fatty acid binding protein 6, ileal	75					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(1)|lung(2)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TACAGACAATGGGGGGCAAGA	0.582													G|||	58	0.0115815	0.0023	0.0288	5008	,	,		16940	0.0		0.0298	False		,,,				2504	0.0051				p.M124I	Colon(29;562 677 12756 16385 20992)	Atlas-SNP	.											.	FABP6	37	.	0			c.G372A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET	24,4382	29.9+/-59.1	0,24,2179	46.0	34.0	38.0		372,372,225	0.4	0.2	5	dbSNP_132	38	271,8329	97.0+/-158.7	7,257,4036	yes	missense,missense,missense	FABP6	NM_001040442.1,NM_001130958.1,NM_001445.2	10,10,10	7,281,6215	AA,AG,GG		3.1512,0.5447,2.2682	benign,benign,benign	124/178,124/178,75/129	159659262	295,12711	2203	4300	6503	SO:0001583	missense	2172	exon5			GACAATGGGGGGC	U19869	CCDS4349.1, CCDS43393.1	5q23-q35	2013-03-01	2008-08-01		ENSG00000170231	ENSG00000170231		"""Fatty acid binding protein family"""	3561	protein-coding gene	gene with protein product	"""illeal lipid-binding protein"", ""ileal bile acid binding protein"", ""gastrotropin"""	600422				7894165, 7619861	Standard	NM_001130958		Approved	I-15P, ILLBP, I-BAP, ILBP3, I-BABP, ILBP, I-BALB	uc003lxx.1	P51161	OTTHUMG00000130329	ENST00000402432.3:c.225G>A	5.37:g.159659262G>A	ENSP00000385433:p.Met75Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	78	0.573529	NM_001130958	Q07DR7|Q8TBI3|Q9UGI7	Missense_Mutation	SNP	ENST00000402432.3	37	CCDS4349.1	39	0.017857142857142856	0	0.0	14	0.03867403314917127	0	0.0	25	0.032981530343007916	G	3.196	-0.164671	0.06502	0.005447	0.031512	ENSG00000170231	ENST00000393980;ENST00000393982;ENST00000402432	T;T;T	0.12879	2.64;2.64;2.64	4.64	0.398	0.16319	Calycin-like (1);Cytosolic fatty-acid binding (1);Calycin (1);	0.451193	0.28365	N	0.015612	T	0.01254	0.0041	N	0.17474	0.49	0.41661	D	0.989181	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.42632	-0.9440	10	0.36615	T	0.2	-7.4418	2.4291	0.04467	0.1891:0.1424:0.5224:0.1461	.	75;124	P51161;P51161-2	FABP6_HUMAN;.	I	124;124;75	ENSP00000377549:M124I;ENSP00000377551:M124I;ENSP00000385433:M75I	ENSP00000377549:M124I	M	+	3	0	FABP6	159591840	0.986000	0.35501	0.228000	0.23943	0.234000	0.25298	0.163000	0.16520	-0.117000	0.11872	-0.379000	0.06801	ATG	G|0.976;A|0.024	0.024	strong		0.582	FABP6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320505.2	NM_001040442	
MMP7	4316	hgsc.bcm.edu	37	11	102398593	102398593	+	Missense_Mutation	SNP	C	C	T	rs10502001	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102398593C>T	ENST00000260227.4	-	2	282	c.230G>A	c.(229-231)cGc>cAc	p.R77H		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	77			R -> H (in dbSNP:rs10502001). {ECO:0000269|Ref.4}.		antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	TTCTATGACGCGGGAGTTTAA	0.413													C|||	669	0.133586	0.0076	0.1484	5008	,	,		17923	0.248		0.2237	False		,,,				2504	0.0828				p.R77H		Atlas-SNP	.											.	MMP7	27	.	0			c.G230A						PASS	.	C	HIS/ARG	203,4203	126.1+/-163.2	8,187,2008	93.0	101.0	99.0		230	-7.8	0.0	11	dbSNP_119	99	1884,6714	335.1+/-321.3	198,1488,2613	yes	missense	MMP7	NM_002423.3	29	206,1675,4621	TT,TC,CC		21.9121,4.6074,16.0489	benign	77/268	102398593	2087,10917	2203	4299	6502	SO:0001583	missense	4316	exon2			ATGACGCGGGAGT	Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"""matrix metalloproteinase 7 (matrilysin, uterine)"""	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.230G>A	11.37:g.102398593C>T	ENSP00000260227:p.Arg77His	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	164	80	0.487805	NM_002423	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	37	CCDS8317.1	388	0.17765567765567766	6	0.012195121951219513	58	0.16022099447513813	164	0.2867132867132867	160	0.21108179419525067	C	9.161	1.018645	0.19355	0.046074	0.219121	ENSG00000137673	ENST00000260227	T	0.36340	1.26	5.39	-7.85	0.01192	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	1.979870	0.02198	N	0.062020	T	0.00012	0.0000	L	0.39147	1.195	0.80722	P	0.0	B;B	0.17268	0.021;0.012	B;B	0.12156	0.004;0.007	T	0.08764	-1.0706	9	0.39692	T	0.17	-8.0814	18.316	0.90221	0.0:0.1279:0.0:0.8721	rs10502001;rs17849786;rs17880557;rs57314446;rs10502001	77;77	B4DDW4;P09237	.;MMP7_HUMAN	H	77	ENSP00000260227:R77H	ENSP00000260227:R77H	R	-	2	0	MMP7	101903803	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.363000	0.07593	-1.561000	0.01684	0.563000	0.77884	CGC	C|0.837;N|0.000	.	strong		0.413	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2		
TRIOBP	11078	hgsc.bcm.edu	37	22	38164106	38164106	+	Silent	SNP	C	C	T	rs4821708	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	127	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	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		
HLA-A	3105	hgsc.bcm.edu	37	6	29911227	29911227	+	Nonsense_Mutation	SNP	G	G	T	rs1059537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29911227G>T	ENST00000396634.1	+	5	867	c.526G>T	c.(526-528)Gag>Tag	p.E176*	HLA-A_ENST00000376809.5_Nonsense_Mutation_p.E176*|HLA-A_ENST00000376806.5_Nonsense_Mutation_p.E176*|HLA-A_ENST00000376802.2_Nonsense_Mutation_p.E176*			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	176	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						GGCGGCCCATGAGGCGGAGCA	0.647									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	141	0.028155	0.0741	0.013	5008	,	,		12195	0.0149		0.0109	False		,,,				2504	0.0082				p.E176X		Atlas-SNP	.											.	HLA-A	89	.	0			c.G526T						PASS	.						37.0	29.0	31.0					6																	29911227		1506	2704	4210	SO:0001587	stop_gained	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCCCATGAGGCGG	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.526G>T	6.37:g.29911227G>T	ENSP00000379873:p.Glu176*	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	220	94	0.427273	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Nonsense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	35|35	5.554389|5.554389	0.96501|0.96501	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	.|.	.|.	.|.	3.78|3.78	-0.78|-0.78	0.10969|0.10969	.|.	17.376800|.	0.00944|.	U|.	0.002869|.	.|T	.|0.45175	.|0.1329	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.53287	.|-0.8460	.|4	0.59425|0.87932	D|D	0.04|0	.|.	11.7413|11.7413	0.51794|0.51794	0.0:0.0:0.4323:0.5677|0.0:0.0:0.4323:0.5677	rs1059537;rs41560012|rs1059537;rs41560012	.|.	.|.	.|.	X|I	176|150	.|.	ENSP00000365998:E176X|ENSP00000348012:M150I	E|M	+|+	1|3	0|0	HLA-A|HLA-A	30019206|30019206	0.268000|0.268000	0.24133|0.24133	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	1.211000|1.211000	0.32382|0.32382	0.028000|0.028000	0.15324|0.15324	-0.335000|-0.335000	0.08231|0.08231	GAG|ATG	C|0.002;G|0.992;T|0.006	0.006	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34826921	34826921	+	Missense_Mutation	SNP	G	G	C	rs61732793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:34826921G>C	ENST00000192788.5	+	14	2959	c.2788G>C	c.(2788-2790)Gag>Cag	p.E930Q	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.E930Q	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	930							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						AGCAAGCCCTGAGAAGGTCTT	0.522													G|||	127	0.0253594	0.0015	0.0346	5008	,	,		24340	0.005		0.0557	False		,,,				2504	0.0409				p.E930Q		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.G2788C						PASS	.	G	GLN/GLU	33,3907		1,31,1938	40.0	41.0	41.0		2788	2.5	0.2	6	dbSNP_129	41	378,7956		11,356,3800	yes	missense	UHRF1BP1	NM_017754.3	29	12,387,5738	CC,CG,GG		4.5356,0.8376,3.3485	possibly-damaging	930/1441	34826921	411,11863	1970	4167	6137	SO:0001583	missense	54887	exon14			AGCCCTGAGAAGG	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.2788G>C	6.37:g.34826921G>C	ENSP00000192788:p.Glu930Gln	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	61	0.027930402930402932	3	0.006097560975609756	15	0.04143646408839779	3	0.005244755244755245	40	0.052770448548812667	G	2.174	-0.389201	0.04932	0.008376	0.045356	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.08720	3.06;3.06	5.7	2.5	0.30297	.	1.138310	0.06182	N	0.679576	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B	0.20671	0.047	B	0.19148	0.024	T	0.46898	-0.9158	10	0.25751	T	0.34	-1.3808	4.63	0.12496	0.3302:0.0:0.5186:0.1512	rs61732793	930	Q6BDS2	URFB1_HUMAN	Q	930	ENSP00000192788:E930Q;ENSP00000400628:E930Q	ENSP00000192788:E930Q	E	+	1	0	UHRF1BP1	34934899	0.006000	0.16342	0.197000	0.23402	0.596000	0.36781	1.242000	0.32755	0.758000	0.33059	0.591000	0.81541	GAG	G|0.962;C|0.038	0.038	strong		0.522	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
TJP3	27134	hgsc.bcm.edu	37	19	3750615	3750615	+	Missense_Mutation	SNP	T	T	C	rs1046268	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3750615T>C	ENST00000541714.2	+	21	3155	c.2693T>C	c.(2692-2694)aTg>aCg	p.M898T	TJP3_ENST00000587641.1_3'UTR|TJP3_ENST00000262968.9_Missense_Mutation_p.M931T|TJP3_ENST00000589378.1_Missense_Mutation_p.M907T|TJP3_ENST00000587686.1_Missense_Mutation_p.M917T|TJP3_ENST00000382008.3_Missense_Mutation_p.M912T|TJP3_ENST00000539908.2_Missense_Mutation_p.M862T	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	898			M -> T (in dbSNP:rs1046268). {ECO:0000269|PubMed:15489334}.		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)		AAAAAGTTTATGCGAGTACAT	0.532													C|||	2671	0.533347	0.2958	0.6873	5008	,	,		17353	0.6389		0.5636	False		,,,				2504	0.6053				p.M907T		Atlas-SNP	.											.	TJP3	79	.	0			c.T2720C						PASS	.	C	THR/MET	1563,2843	654.4+/-399.7	274,1015,914	73.0	66.0	69.0		2792	2.4	0.0	19	dbSNP_86	69	4762,3834	527.2+/-381.1	1294,2174,830	yes	missense	TJP3	NM_014428.1	81	1568,3189,1744	CC,CT,TT		44.6021,35.4744,48.6464	benign	931/953	3750615	6325,6677	2203	4298	6501	SO:0001583	missense	27134	exon21			AGTTTATGCGAGT	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.2693T>C	19.37:g.3750615T>C	ENSP00000439278:p.Met898Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	1178	0.5393772893772893	137	0.2784552845528455	241	0.6657458563535912	387	0.6765734265734266	413	0.5448548812664907	C	0.001	-2.886655	0.00061	0.354744	0.553979	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.05786	3.39;3.57;3.42;3.52	4.59	2.44	0.29823	.	0.434355	0.23887	N	0.043595	T	0.00012	0.0000	N	0.00138	-2.015	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	0.29181	-1.0020	9	0.02654	T	1	.	4.9094	0.13814	0.1456:0.6153:0.0:0.2392	rs1046268;rs3186244;rs17016672;rs52820107;rs58327102;rs1046268	917;931;912;898	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	T	898;862;912;931	ENSP00000439278:M898T;ENSP00000439991:M862T;ENSP00000371438:M912T;ENSP00000262968:M931T	ENSP00000262968:M931T	M	+	2	0	TJP3	3701615	0.806000	0.28996	0.009000	0.14445	0.012000	0.07955	1.347000	0.33975	0.153000	0.19213	-1.319000	0.01295	ATG	T|0.505;C|0.495	0.495	strong		0.532	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
NIF3L1	60491	hgsc.bcm.edu	37	2	201768238	201768238	+	Missense_Mutation	SNP	C	C	T	rs7917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:201768238C>T	ENST00000409020.1	+	7	1265	c.971C>T	c.(970-972)aCt>aTt	p.T324I	NIF3L1_ENST00000416651.1_Missense_Mutation_p.T324I|NIF3L1_ENST00000359683.4_Missense_Mutation_p.T297I|NIF3L1_ENST00000409588.1_Missense_Mutation_p.L278F|NIF3L1_ENST00000409357.1_Missense_Mutation_p.T324I			Q9GZT8	GTPC1_HUMAN	NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)	324			T -> I (in dbSNP:rs7917).		7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|metal ion binding (GO:0046872)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(2)	13						CATCATGATACTTTGGATGCT	0.413													T|||	1419	0.283347	0.6694	0.1772	5008	,	,		20225	0.0149		0.2555	False		,,,				2504	0.1421				p.T324I		Atlas-SNP	.											.	NIF3L1	51	.	0			c.C971T						PASS	.	T	ILE/THR,ILE/THR,PHE/LEU,ILE/THR	2196,1598		645,906,346	156.0	150.0	152.0		971,890,832,890	5.3	0.6	2	dbSNP_52	152	1824,6416		184,1456,2480	yes	missense,missense,missense,missense	NIF3L1	NM_001136039.2,NM_001142355.1,NM_001142356.1,NM_021824.3	89,89,22,89	829,2362,2826	TT,TC,CC		22.1359,42.1191,33.4054	benign,benign,benign,benign	324/378,297/351,278/286,297/351	201768238	4020,8014	1897	4120	6017	SO:0001583	missense	60491	exon7			ATGATACTTTGGA	AB038949	CCDS42797.1, CCDS46485.1, CCDS46486.1	2q33	2011-11-10	2011-11-10		ENSG00000196290	ENSG00000196290			13390	protein-coding gene	gene with protein product		605778	"""NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1"", ""NIF3 NGG1 interacting factor 3-like 1 (S. pombe)"""	ALS2CR1		11124544, 11161814, 12522100	Standard	NM_001136039		Approved	CALS-7, MDS015	uc002uwm.2	Q9GZT8	OTTHUMG00000154588	ENST00000409020.1:c.971C>T	2.37:g.201768238C>T	ENSP00000386394:p.Thr324Ile	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	224	97	0.433036	NM_001136039	Q53TX4|Q6X735|Q9H2D2|Q9HC18	Missense_Mutation	SNP	ENST00000409020.1	37	CCDS46485.1	577|577	0.2641941391941392|0.2641941391941392	305|305	0.6199186991869918|0.6199186991869918	72|72	0.19889502762430938|0.19889502762430938	3|3	0.005244755244755245|0.005244755244755245	197|197	0.2598944591029024|0.2598944591029024	T|T	7.341|7.341	0.620919|0.620919	0.14193|0.14193	0.578809|0.578809	0.221359|0.221359	ENSG00000196290|ENSG00000196290	ENST00000409588|ENST00000416651;ENST00000409020;ENST00000359683;ENST00000409357	.|T;T;T;T	.|0.39592	.|1.07;1.07;1.07;1.07	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.167825	.|0.52532	.|N	.|0.000073	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.54753|0.54753	P|P	1.4999999999987246E-5|1.4999999999987246E-5	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.41448|0.41448	-0.9508|-0.9508	6|8	0.87932|0.23891	D|T	0|0.37	-3.6914|-3.6914	11.5287|11.5287	0.50595|0.50595	0.0:0.0708:0.0:0.9292|0.0:0.0708:0.0:0.9292	rs7917;rs1128563;rs3177342;rs3185643;rs11555980;rs13396213;rs17349459;rs52807793;rs58476980;rs7917|rs7917;rs1128563;rs3177342;rs3185643;rs11555980;rs13396213;rs17349459;rs52807793;rs58476980;rs7917	278|324	Q6X735|Q9GZT8	.|NIF3L_HUMAN	F|I	278|324;324;297;324	.|ENSP00000400787:T324I;ENSP00000386394:T324I;ENSP00000352711:T297I;ENSP00000387315:T324I	ENSP00000387021:L278F|ENSP00000352711:T297I	L|T	+|+	1|2	0|0	NIF3L1|NIF3L1	201476483|201476483	1.000000|1.000000	0.71417|0.71417	0.577000|0.577000	0.28562|0.28562	0.920000|0.920000	0.55202|0.55202	5.883000|5.883000	0.69721|0.69721	0.968000|0.968000	0.38212|0.38212	-0.381000|-0.381000	0.06696|0.06696	CTT|ACT	C|0.715;T|0.285	0.285	strong		0.413	NIF3L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336201.1	NM_021824	
TPGS2	25941	hgsc.bcm.edu	37	18	34398914	34398914	+	Silent	SNP	C	C	T	rs1045781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:34398914C>T	ENST00000334295.4	-	2	535	c.108G>A	c.(106-108)gaG>gaA	p.E36E	TPGS2_ENST00000593035.1_Silent_p.E36E|TPGS2_ENST00000383056.3_Silent_p.E36E|TPGS2_ENST00000587129.1_Silent_p.E36E|TPGS2_ENST00000589049.1_Silent_p.E36E|TPGS2_ENST00000590842.1_Silent_p.E36E	NM_015476.2	NP_056291.2	Q68CL5	TPGS2_HUMAN	tubulin polyglutamylase complex subunit 2	36						cytoplasm (GO:0005737)|microtubule (GO:0005874)											TGATGGTCACCTCAGTCACAC	0.443													C|||	619	0.123602	0.0091	0.2277	5008	,	,		20417	0.004		0.2644	False		,,,				2504	0.183				p.E36E		Atlas-SNP	.											.	.	.	.	0			c.G108A						PASS	.	C		268,4138	150.3+/-184.3	13,242,1948	147.0	140.0	142.0		108	-0.0	1.0	18	dbSNP_86	142	2418,6182	400.1+/-346.7	360,1698,2242	no	coding-synonymous	C18orf10	NM_015476.2		373,1940,4190	TT,TC,CC		28.1163,6.0826,20.652		36/301	34398914	2686,10320	2203	4300	6503	SO:0001819	synonymous_variant	25941	exon2			GGTCACCTCAGTC	BC015178	CCDS32817.1, CCDS62421.1, CCDS62422.1, CCDS62423.1, CCDS62424.1, CCDS74214.1, CCDS74215.1	18q12.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134779	ENSG00000134779			24561	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 10"""	C18orf10		12477932	Standard	NM_015476		Approved	DKFZP586M1523, HsT3006	uc031rhw.1	Q68CL5		ENST00000334295.4:c.108G>A	18.37:g.34398914C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_001271954	B4DIX2|K7EIJ9|Q4KN59|Q8WTU3|Q96BT9|Q9Y435	Silent	SNP	ENST00000334295.4	37	CCDS32817.1																																																																																			C|0.830;T|0.170	0.170	strong		0.443	TPGS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440410.2	NM_015476	
CAMK2B	816	hgsc.bcm.edu	37	7	44282868	44282868	+	Silent	SNP	A	A	G	rs11542228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:44282868A>G	ENST00000395749.2	-	8	658	c.582T>C	c.(580-582)ccT>ccC	p.P194P	CAMK2B_ENST00000358707.3_Silent_p.P194P|CAMK2B_ENST00000457475.1_Silent_p.P194P|CAMK2B_ENST00000350811.3_Silent_p.P194P|CAMK2B_ENST00000353625.4_Silent_p.P194P|CAMK2B_ENST00000346990.4_Silent_p.P194P|CAMK2B_ENST00000347193.4_Silent_p.P194P|CAMK2B_ENST00000395747.2_Silent_p.P194P|CAMK2B_ENST00000440254.2_Silent_p.P194P|CAMK2B_ENST00000258682.6_Silent_p.P194P|CAMK2B_ENST00000502837.2_Silent_p.P65P	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						AGATGTCCACAGGCTTGCCAT	0.617													.|||	1681	0.335663	0.2852	0.317	5008	,	,		20349	0.2222		0.4245	False		,,,				2504	0.4427				p.P194P		Atlas-SNP	.											.	CAMK2B	56	.	0			c.T582C						PASS	.	G	,,,,,,,	1367,3039	687.5+/-404.9	203,961,1039	82.0	72.0	76.0		582,582,582,582,582,582,582,582	-7.1	0.8	7	dbSNP_120	76	3823,4777	611.0+/-395.8	827,2169,1304	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2B	NM_001220.4,NM_172078.2,NM_172079.2,NM_172080.2,NM_172081.2,NM_172082.2,NM_172083.2,NM_172084.2	,,,,,,,	1030,3130,2343	GG,GA,AA		44.4535,31.0259,39.9047	,,,,,,,	194/667,194/543,194/519,194/518,194/504,194/493,194/480,194/450	44282868	5190,7816	2203	4300	6503	SO:0001819	synonymous_variant	816	exon8			GTCCACAGGCTTG	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"""CaM-kinase II beta chain"", ""calcium/calmodulin-dependent protein kinase type II beta chain"", ""CaM kinase II beta subunit"", ""proline rich calmodulin-dependent protein kinase"""	607707	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"""	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.582T>C	7.37:g.44282868A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	139	51	0.366906	NM_172081	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Silent	SNP	ENST00000395749.2	37	CCDS5483.1																																																																																			G|0.378;N|0.001	0.378	strong		0.617	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
ZNF273	10793	hgsc.bcm.edu	37	7	64389089	64389089	+	Missense_Mutation	SNP	A	A	C	rs2017252	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:64389089A>C	ENST00000476120.1	+	4	1454	c.1383A>C	c.(1381-1383)gaA>gaC	p.E461D	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.E396D	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	461			E -> D (in dbSNP:rs2017252). {ECO:0000269|PubMed:7865130}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				ACAAATGTGAAGAATGTGGCA	0.373													A|||	2283	0.455871	0.3502	0.5101	5008	,	,		20786	0.4911		0.4722	False		,,,				2504	0.5072				p.E461D	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.A1383C						PASS	.	A	ASP/GLU	1695,2707		312,1071,818	37.0	39.0	38.0		1383	-2.3	0.6	7	dbSNP_92	38	4183,4415		1034,2115,1150	yes	missense	ZNF273	NM_021148.2	45	1346,3186,1968	CC,CA,AA		48.6508,38.5052,45.2154	benign	461/570	64389089	5878,7122	2201	4299	6500	SO:0001583	missense	10793	exon4			ATGTGAAGAATGT	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"""Zinc fingers, C2H2-type"", ""-"""	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1383A>C	7.37:g.64389089A>C	ENSP00000418719:p.Glu461Asp	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	997	0.4565018315018315	175	0.3556910569105691	181	0.5	290	0.506993006993007	351	0.4630606860158311	.	12.53	1.964849	0.34659	0.385052	0.486508	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.16897	2.31;2.31	1.16	-2.32	0.06745	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.16166	0.38	0.80722	P	0.0	B	0.27823	0.19	B	0.40375	0.327	T	0.48043	-0.9069	8	0.42905	T	0.14	.	1.9366	0.03338	0.4312:0.2844:0.0:0.2844	rs2017252;rs59597540;rs2017252	461	Q14593	ZN273_HUMAN	D	461;396	ENSP00000418719:E461D;ENSP00000324518:E396D	ENSP00000324518:E396D	E	+	3	2	ZNF273	64026524	0.000000	0.05858	0.567000	0.28434	0.567000	0.35839	-5.647000	0.00107	0.175000	0.19841	0.172000	0.16884	GAA	A|0.544;C|0.456	0.456	strong		0.373	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1272684	1272684	+	IGR	SNP	C	C	G	rs4984638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1272684C>G	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.W160S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCCGGTCACCCAGCACCGGAT	0.682													c|||	612	0.122204	0.0401	0.1412	5008	,	,		16523	0.1637		0.1918	False		,,,				2504	0.1053				p.W160S		Atlas-SNP	.											.	TPSG1	19	.	0			c.G479C						PASS	.		SER/TRP	243,4153	135.7+/-171.8	8,227,1963	66.0	82.0	77.0		479	2.5	0.8	16	dbSNP_111	77	1656,6942	292.7+/-301.0	154,1348,2797	yes	missense	TPSG1	NM_012467.3	177	162,1575,4760	GG,GC,CC		19.2603,5.5278,14.6144	probably-damaging	160/322	1272684	1899,11095	2198	4299	6497	SO:0001628	intergenic_variant	25823	exon4			GTCACCCAGCACC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180			16.37:g.1272684C>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	304	0.1391941391941392	16	0.032520325203252036	50	0.13812154696132597	91	0.1590909090909091	147	0.19393139841688653	c	10.85	1.466579	0.26335	0.055278	0.192603	ENSG00000116176	ENST00000234798	D	0.92805	-3.11	3.47	2.48	0.30137	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.01387	0.0045	L	0.35487	1.065	0.24027	P	0.99612212	D	0.89917	1.0	D	0.80764	0.994	T	0.45527	-0.9255	8	0.52906	T	0.07	.	9.8621	0.41120	0.2067:0.7933:0.0:0.0	rs4984638	160	Q9NRR2	TRYG1_HUMAN	S	160	ENSP00000234798:W160S	ENSP00000234798:W160S	W	-	2	0	TPSG1	1212685	0.000000	0.05858	0.753000	0.31225	0.255000	0.26057	0.279000	0.18771	0.517000	0.28361	0.556000	0.70494	TGG	C|0.853;G|0.147	0.147	strong		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25268368	25268368	+	Silent	SNP	A	A	G	rs4787310	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:25268368A>G	ENST00000328086.7	-	1	884	c.81T>C	c.(79-81)ccT>ccC	p.P27P		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	27					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)	p.P27P(1)		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)		ATGCCCACTCAGGGTCCTTTT	0.557											OREG0023690	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2309	0.461062	0.6346	0.4481	5008	,	,		19215	0.4722		0.338	False		,,,				2504	0.3507				p.P27P		Atlas-SNP	.											ZKSCAN2,NS,carcinoma,0,1	ZKSCAN2	90	1	1	Substitution - coding silent(1)	stomach(1)	c.T81C						PASS	.	G		2596,1798	516.7+/-369.2	775,1046,376	73.0	79.0	77.0		81	2.0	0.9	16	dbSNP_111	77	3045,5555	655.5+/-401.3	540,1965,1795	no	coding-synonymous	ZKSCAN2	NM_001012981.4		1315,3011,2171	GG,GA,AA		35.407,40.9194,43.4123		27/968	25268368	5641,7353	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon1			CCACTCAGGGTCC	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.81T>C	16.37:g.25268368A>G		Somatic	84	0	0	777	WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			A|0.562;G|0.438	0.438	strong		0.557	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
BBS12	166379	hgsc.bcm.edu	37	4	123664919	123664919	+	Silent	SNP	A	A	G	rs13102440	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123664919A>G	ENST00000314218.3	+	2	2065	c.1872A>G	c.(1870-1872)caA>caG	p.Q624Q	BBS12_ENST00000542236.1_Silent_p.Q624Q	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	624					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ATCATCTGCAAAATGCCACAG	0.353									Bardet-Biedl syndrome				A|||	460	0.091853	0.0484	0.1052	5008	,	,		20993	0.0		0.2127	False		,,,				2504	0.1115				p.Q624Q		Atlas-SNP	.											.	BBS12	63	.	0			c.A1872G						PASS	.	A	,	289,4117	159.6+/-192.1	15,259,1929	85.0	82.0	83.0		1872,1872	-1.3	0.1	4	dbSNP_121	83	1940,6660	341.7+/-324.1	230,1480,2590	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	245,1739,4519	GG,GA,AA		22.5581,6.5592,17.1382	,	624/711,624/711	123664919	2229,10777	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TCTGCAAAATGCC	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1872A>G	4.37:g.123664919A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			A|0.856;G|0.144	0.144	strong		0.353	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
ABCB5	340273	hgsc.bcm.edu	37	7	20687604	20687604	+	Missense_Mutation	SNP	A	A	G	rs61732039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20687604A>G	ENST00000404938.2	+	11	1761	c.1109A>G	c.(1108-1110)gAt>gGt	p.D370G	ABCB5_ENST00000258738.6_5'UTR|ABCB5_ENST00000406935.1_5'UTR|ABCB5_ENST00000443026.2_5'UTR|ABCB5_ENST00000477094.1_3'UTR	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	370					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						CCCAGTATAGATAACTTTTCC	0.313													A|||	226	0.0451278	0.0083	0.0591	5008	,	,		18245	0.0		0.1441	False		,,,				2504	0.0297				p.D370G		Atlas-SNP	.											.	ABCB5	357	.	0			c.A1109G						PASS	.	A	GLY/ASP,,,	89,3047		2,85,1481	47.0	43.0	44.0		1109,,,	4.2	1.0	7	dbSNP_129	44	962,6196		73,816,2690	yes	missense,utr-5,utr-5,utr-5	ABCB5	NM_001163941.1,NM_001163942.1,NM_001163993.1,NM_178559.5	94,,,	75,901,4171	GG,GA,AA		13.4395,2.838,10.2098	probably-damaging,,,	370/1258,,,	20687604	1051,9243	1568	3579	5147	SO:0001583	missense	340273	exon11			GTATAGATAACTT	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.1109A>G	7.37:g.20687604A>G	ENSP00000384881:p.Asp370Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	43	0.373913	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	135	0.061813186813186816	7	0.014227642276422764	23	0.06353591160220995	0	0.0	105	0.13852242744063326	A	18.12	3.553314	0.65425	0.02838	0.134395	ENSG00000004846	ENST00000404938	D	0.88586	-2.4	5.3	4.15	0.48705	.	.	.	.	.	T	0.13286	0.0322	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.54840	-0.8233	9	0.72032	D	0.01	.	10.3928	0.44184	0.9213:0.0:0.0787:0.0	rs61732039	370	A7BKA4	.	G	370	ENSP00000384881:D370G	ENSP00000384881:D370G	D	+	2	0	ABCB5	20654129	1.000000	0.71417	1.000000	0.80357	0.674000	0.39518	6.314000	0.72848	1.108000	0.41662	0.533000	0.62120	GAT	A|0.924;G|0.076	0.076	strong		0.313	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
MAGEB2	4113	hgsc.bcm.edu	37	X	30236913	30236913	+	Silent	SNP	G	G	A	rs5973792	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:30236913G>A	ENST00000378988.4	+	2	317	c.216G>A	c.(214-216)gcG>gcA	p.A72A		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	72										breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						CCGCTGCTGCGGCTGCGGGTG	0.557													G|||	646	0.171126	0.1679	0.1499	3775	,	,		12005	0.0218		0.2087	False		,,,				2504	0.09				p.A72A		Atlas-SNP	.											.	MAGEB2	133	.	0			c.G216A						PASS	.	G		874,2947		88,563,135,980,424	12.0	11.0	12.0		216	-1.7	0.0	X	dbSNP_114	12	1906,4790		189,1006,522,1230,1324	no	coding-synonymous	MAGEB2	NM_002364.4		277,1569,657,2210,1748	AA,AG,A,GG,G		28.4648,22.8736,26.4334		72/320	30236913	2780,7737	2190	4271	6461	SO:0001819	synonymous_variant	4113	exon2			TGCTGCGGCTGCG	AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 6"", ""melanoma-associated antigen B2"", ""cancer/testis antigen family 3, member 2"""	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.216G>A	X.37:g.30236913G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_002364	O75860	Silent	SNP	ENST00000378988.4	37	CCDS14219.1																																																																																			G|0.782;A|0.218	0.218	strong		0.557	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364	
ANGPTL4	51129	hgsc.bcm.edu	37	19	8436164	8436164	+	Missense_Mutation	SNP	C	C	T	rs1044250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8436164C>T	ENST00000301455.2	+	6	968	c.797C>T	c.(796-798)aCg>aTg	p.T266M	ANGPTL4_ENST00000541807.1_Missense_Mutation_p.T99M|ANGPTL4_ENST00000393962.2_Missense_Mutation_p.T228M	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	266	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		T -> M (in dbSNP:rs1044250). {ECO:0000269|PubMed:10698685, ECO:0000269|PubMed:17322881, ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						CATAGCATCACGGGGGACCGC	0.667													C|||	1200	0.239617	0.2564	0.3285	5008	,	,		18038	0.0595		0.331	False		,,,				2504	0.2454				p.T266M		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.C797T	GRCh37	CM086232	ANGPTL4	M	rs1044250	PASS	.	C	MET/THR,MET/THR	1123,3283	393.7+/-329.0	132,859,1212	43.0	44.0	44.0		683,797	-1.3	0.0	19	dbSNP_86	44	2667,5933	418.0+/-352.6	419,1829,2052	yes	missense,missense	ANGPTL4	NM_001039667.1,NM_139314.1	81,81	551,2688,3264	TT,TC,CC		31.0116,25.488,29.1404	benign,benign	228/369,266/407	8436164	3790,9216	2203	4300	6503	SO:0001583	missense	51129	exon6			GCATCACGGGGGA	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"""Fibrinogen C domain containing"""	16039	protein-coding gene	gene with protein product	"""fasting-induced adipose factor"", ""hepatic angiopoietin-related protein"", ""PPARG angiopoietin related protein"", ""hepatic fibrinogen/angiopoietin-related protein"", ""peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein"", ""angiopoietin-related protein 4"""	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.797C>T	19.37:g.8436164C>T	ENSP00000301455:p.Thr266Met	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	555	0.2541208791208791	139	0.28252032520325204	116	0.32044198895027626	44	0.07692307692307693	256	0.33773087071240104	C	6.884	0.532489	0.13127	0.25488	0.310116	ENSG00000167772	ENST00000301455;ENST00000393962;ENST00000541807	T;T;T	0.33865	1.39;1.39;1.39	5.09	-1.27	0.09347	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.836750	0.02798	N	0.122905	T	0.00012	0.0000	M	0.92412	3.305	0.80722	P	0.0	B;B	0.25563	0.129;0.129	B;B	0.24848	0.056;0.056	T	0.36383	-0.9750	9	0.51188	T	0.08	.	6.5885	0.22634	0.112:0.6775:0.0:0.2105	rs1044250;rs3183947;rs17305531;rs52807441;rs59900793;rs1044250	228;266	A8MY84;Q9BY76	.;ANGL4_HUMAN	M	266;228;99	ENSP00000301455:T266M;ENSP00000377534:T228M;ENSP00000439833:T99M	ENSP00000301455:T266M	T	+	2	0	ANGPTL4	8342164	0.001000	0.12720	0.000000	0.03702	0.239000	0.25481	0.761000	0.26489	-0.515000	0.06479	-0.263000	0.10527	ACG	C|0.730;T|0.270	0.270	strong		0.667	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314	
KDM3B	51780	hgsc.bcm.edu	37	5	137754695	137754695	+	Silent	SNP	T	T	C	rs7726234	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137754695T>C	ENST00000314358.5	+	14	3689	c.3489T>C	c.(3487-3489)ggT>ggC	p.G1163G	KDM3B_ENST00000394866.1_Silent_p.G819G|KDM3B_ENST00000542866.1_Silent_p.G195G|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	196	0	0		WXS	Illumina HiSeq	Phase_I	229	115	0.502183	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	
OTUD6B	51633	hgsc.bcm.edu	37	8	92097062	92097062	+	Missense_Mutation	SNP	G	G	A	rs3210518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:92097062G>A	ENST00000285420.4	+	7	1037	c.938G>A	c.(937-939)cGg>cAg	p.R313Q	OTUD6B_ENST00000404789.3_Missense_Mutation_p.R182Q	NM_016023.3	NP_057107.3	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B	283							cysteine-type peptidase activity (GO:0008234)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11			BRCA - Breast invasive adenocarcinoma(11;0.0187)			TCGGTTACACGGTTGGTAAAC	0.289													G|||	203	0.0405351	0.087	0.0288	5008	,	,		15666	0.0437		0.0189	False		,,,				2504	0.0051				p.R313Q		Atlas-SNP	.											.	OTUD6B	28	.	0			c.G938A						PASS	.	G	GLN/ARG	311,4095	159.2+/-191.8	10,291,1902	85.0	80.0	81.0		938	-7.1	0.6	8	dbSNP_105	81	280,8312	100.1+/-161.6	2,276,4018	yes	missense	OTUD6B	NM_016023.3	43	12,567,5920	AA,AG,GG		3.2588,7.0586,4.5469	benign	313/324	92097062	591,12407	2203	4296	6499	SO:0001583	missense	51633	exon7			TTACACGGTTGGT		CCDS6253.2, CCDS69513.1	8q21.3	2013-01-21			ENSG00000155100	ENSG00000155100		"""OTU domain containing"""	24281	protein-coding gene	gene with protein product		612021					Standard	NM_016023		Approved	CGI-77, DUBA5	uc003yeu.4	Q8N6M0	OTTHUMG00000150758	ENST00000285420.4:c.938G>A	8.37:g.92097062G>A	ENSP00000285420:p.Arg313Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	123	67	0.544715	NM_016023	A8K6I1|B4DEY0|Q9NTA4|Q9Y387	Missense_Mutation	SNP	ENST00000285420.4	37	CCDS6253.2	97	0.044413919413919416	47	0.09552845528455285	14	0.03867403314917127	24	0.04195804195804196	12	0.0158311345646438	G	8.675	0.903743	0.17760	0.070586	0.032588	ENSG00000155100	ENST00000285420;ENST00000404789	T;T	0.44881	0.91;0.91	5.98	-7.05	0.01573	Ovarian tumour, otubain (1);	1.463720	0.03677	N	0.244978	T	0.00524	0.0017	N	0.25245	0.725	0.09310	N	0.999993	B;B	0.10296	0.002;0.003	B;B	0.04013	0.0;0.001	T	0.08269	-1.0730	10	0.10902	T	0.67	3.7178	3.9119	0.09207	0.5123:0.2449:0.1098:0.133	rs3210518;rs17297951;rs52830475;rs3210518	182;283	B4DEY0;Q8N6M0	.;OTU6B_HUMAN	Q	313;182	ENSP00000285420:R313Q;ENSP00000384190:R182Q	ENSP00000285420:R313Q	R	+	2	0	OTUD6B	92166238	0.001000	0.12720	0.579000	0.28588	0.969000	0.65631	-1.801000	0.01743	-1.300000	0.02341	-0.218000	0.12543	CGG	G|0.954;A|0.046	0.046	strong		0.289	OTUD6B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319968.1	NM_016023	
CENPF	1063	hgsc.bcm.edu	37	1	214814733	214814733	+	Missense_Mutation	SNP	T	T	G	rs3795519	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214814733T>G	ENST00000366955.3	+	12	3220	c.3052T>G	c.(3052-3054)Tac>Gac	p.Y1018D		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0			Y -> D (in dbSNP:rs3795519).		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)		ATCTGATCAGTACAAGCAAGA	0.328													T|||	527	0.105232	0.1006	0.1052	5008	,	,		18946	0.126		0.0517	False		,,,				2504	0.1452				p.Y1018D	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T3052G						PASS	.	T	ASP/TYR	373,4005		16,341,1832	61.0	68.0	66.0		3052	3.9	1.0	1	dbSNP_107	66	461,8125		10,441,3842	yes	missense	CENPF	NM_016343.3	160	26,782,5674	GG,GT,TT		5.3692,8.5199,6.4332	possibly-damaging	1018/3115	214814733	834,12130	2189	4293	6482	SO:0001583	missense	1063	exon12			GATCAGTACAAGC	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.3052T>G	1.37:g.214814733T>G	ENSP00000355922:p.Tyr1018Asp	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	229	0.10485347985347986	63	0.12804878048780488	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	T	10.88	1.474736	0.26511	0.085199	0.053692	ENSG00000117724	ENST00000366955	T	0.03301	3.98	5.16	3.92	0.45320	.	0.238077	0.21899	N	0.067479	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	P	0.52842	0.956	B	0.44224	0.444	T	0.48636	-0.9018	8	0.40728	T	0.16	.	7.2766	0.26288	0.1428:0.0853:0.0:0.7718	rs3795519;rs59237992;rs3795519	1018	P49454	CENPF_HUMAN	D	1018	ENSP00000355922:Y1018D	ENSP00000355922:Y1018D	Y	+	1	0	CENPF	212881356	0.017000	0.18338	0.986000	0.45419	0.972000	0.66771	0.901000	0.28445	1.947000	0.56498	0.496000	0.49642	TAC	T|0.916;G|0.084	0.084	strong		0.328	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240790	39240790	+	Missense_Mutation	SNP	G	G	A	rs11650261|rs553572799	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39240790G>A	ENST00000391417.4	+	1	332	c.332G>A	c.(331-333)cGc>cAc	p.R111H		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	136	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						acctgctgccgccccagctgc	0.657													g|||	343	0.0684904	0.0272	0.1196	5008	,	,		10689	0.0685		0.1153	False		,,,				2504	0.0399				p.R111H		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,3	KRTAP4-7	49	3	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G332A						scavenged	.						11.0	13.0	12.0					17																	39240790		682	1579	2261	SO:0001583	missense	100132476	exon1			GCTGCCGCCCCAG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.332G>A	17.37:g.39240790G>A	ENSP00000375236:p.Arg111His	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	55	9	0.163636	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	148	0.06776556776556776	22	0.044715447154471545	32	0.08839779005524862	22	0.038461538461538464	72	0.09498680738786279	.	6.498	0.460116	0.12342	.	.	ENSG00000240871	ENST00000391417	T	0.00612	6.22	3.95	-0.91	0.10511	.	8.977930	0.00616	U	0.000420	T	0.00039	0.0001	.	.	.	0.09310	N	1	D	0.60575	0.988	P	0.46389	0.515	T	0.44050	-0.9353	9	0.48119	T	0.1	.	3.4362	0.07446	0.2202:0.0:0.299:0.4808	rs11650261	166	Q9BYR0	KRA47_HUMAN	H	111	ENSP00000375236:R111H	ENSP00000375236:R111H	R	+	2	0	KRTAP4-7	36494316	0.000000	0.05858	0.005000	0.12908	0.119000	0.20118	0.218000	0.17622	0.230000	0.21059	-0.391000	0.06502	CGC	G|0.932;A|0.068	0.068	strong		0.657	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
RHPN2	85415	hgsc.bcm.edu	37	19	33498978	33498978	+	Silent	SNP	A	A	G	rs2163807	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	94	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	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	
VCAN	1462	hgsc.bcm.edu	37	5	82815408	82815408	+	Missense_Mutation	SNP	G	G	A	rs2287926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:82815408G>A	ENST00000265077.3	+	7	1848	c.1283G>A	c.(1282-1284)gGc>gAc	p.G428D	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.G428D|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.G380D	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	428	GAG-alpha (glucosaminoglycan attachment domain).		G -> D (in dbSNP:rs2287926).		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)	ACACCTACTGGCAGTACCAAG	0.463													G|||	1066	0.212859	0.3275	0.1412	5008	,	,		20371	0.1796		0.1173	False		,,,				2504	0.2413				p.G428D		Atlas-SNP	.											.	VCAN	498	.	0			c.G1283A						PASS	.	G	,,ASP/GLY,ASP/GLY	1229,3177	414.4+/-336.8	175,879,1149	82.0	84.0	83.0		,,1283,1283	0.9	0.0	5	dbSNP_100	83	984,7616	211.3+/-251.9	55,874,3371	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,94,94	230,1753,4520	AA,AG,GG		11.4419,27.8938,17.0152	,,probably-damaging,probably-damaging	,,428/1643,428/3397	82815408	2213,10793	2203	4300	6503	SO:0001583	missense	1462	exon7			CTACTGGCAGTAC	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.1283G>A	5.37:g.82815408G>A	ENSP00000265077:p.Gly428Asp	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	196	99	0.505102	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	407	0.18635531135531136	163	0.3313008130081301	51	0.1408839779005525	103	0.18006993006993008	90	0.11873350923482849	G	6.902	0.535981	0.13188	0.278938	0.114419	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.85702	-1.91;-1.99;-2.02	5.92	0.918	0.19386	.	0.421595	0.22627	N	0.057628	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	P;D	0.61697	0.939;0.99	P;P	0.54889	0.66;0.763	T	0.09530	-1.0670	9	0.35671	T	0.21	.	1.2917	0.02061	0.2548:0.2651:0.3444:0.1357	rs2287926;rs52819906;rs57562090;rs2287926	428;428	P13611-3;P13611	.;CSPG2_HUMAN	D	428;428;380	ENSP00000265077:G428D;ENSP00000342768:G428D;ENSP00000425959:G380D	ENSP00000265077:G428D	G	+	2	0	VCAN	82851164	0.049000	0.20398	0.000000	0.03702	0.025000	0.11179	0.632000	0.24583	-0.114000	0.11936	-0.175000	0.13238	GGC	G|0.819;A|0.181	0.181	strong		0.463	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
UGDH	7358	hgsc.bcm.edu	37	4	39515736	39515736	+	Silent	SNP	A	A	G	rs10019532	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:39515736A>G	ENST00000316423.6	-	3	573	c.231T>C	c.(229-231)gaT>gaC	p.D77D	UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000501493.2_Silent_p.D77D|UGDH_ENST00000507089.1_5'UTR|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	180	0	0		WXS	Illumina HiSeq	Phase_I	181	83	0.458564	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	
FLG2	388698	hgsc.bcm.edu	37	1	152325732	152325732	+	Silent	SNP	G	G	A	rs12022217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152325732G>A	ENST00000388718.5	-	3	4602	c.4530C>T	c.(4528-4530)caC>caT	p.H1510H	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1510					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)			AGCCCCCTGAGTGCACTTCAC	0.498													G|||	1585	0.316494	0.2905	0.4049	5008	,	,		25998	0.4534		0.1421	False		,,,				2504	0.3272				p.H1510H		Atlas-SNP	.											.	FLG2	431	.	0			c.C4530T						PASS	.	G		1149,3257	407.5+/-334.3	129,891,1183	331.0	319.0	323.0		4530	-9.1	0.0	1	dbSNP_120	323	1367,7233	266.8+/-286.9	135,1097,3068	no	coding-synonymous	FLG2	NM_001014342.2		264,1988,4251	AA,AG,GG		15.8953,26.0781,19.3449		1510/2392	152325732	2516,10490	2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			CCCTGAGTGCACT	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.4530C>T	1.37:g.152325732G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	302	148	0.490066	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			G|0.773;A|0.227	0.227	strong		0.498	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
FAM90A1	55138	hgsc.bcm.edu	37	12	8377348	8377348	+	Silent	SNP	T	T	C	rs199649765		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8377348T>C	ENST00000538603.1	-	4	639	c.81A>G	c.(79-81)ccA>ccG	p.P27P	FAM90A1_ENST00000307435.6_Silent_p.P27P	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	27							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)		TTGGCCCAACTGGGGCCCTCC	0.642																																					p.P27P		Atlas-SNP	.											FAM90A1,NS,neuroblastoma,0,1	FAM90A1	68	1	0			c.A81G						scavenged	.						12.0	16.0	15.0					12																	8377348		2192	4271	6463	SO:0001819	synonymous_variant	55138	exon4			CCCAACTGGGGCC	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.81A>G	12.37:g.8377348T>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	41	13	0.317073	NM_018088	D3DUU9|Q9NVZ6	Silent	SNP	ENST00000538603.1	37	CCDS31738.1																																																																																			.	.	weak		0.642	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
MYH2	4620	hgsc.bcm.edu	37	17	10450816	10450816	+	Silent	SNP	T	T	C	rs12600539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10450816T>C	ENST00000245503.5	-	4	708	c.324A>G	c.(322-324)gaA>gaG	p.E108E	CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000532183.2_Silent_p.E108E|MYH2_ENST00000397183.2_Silent_p.E108E	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	108	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CTGCATAACGTTCTTTGAGGT	0.483													C|||	2722	0.54353	0.3797	0.5216	5008	,	,		20805	0.8492		0.3917	False		,,,				2504	0.6217				p.E108E		Atlas-SNP	.											MYH2,NS,carcinoma,-2,1	MYH2	390	1	0			c.A324G						PASS	.	C	,	1764,2642	645.7+/-398.2	344,1076,783	330.0	280.0	297.0		324,324	5.9	1.0	17	dbSNP_120	297	3548,5052	630.3+/-398.3	747,2054,1499	no	coding-synonymous,coding-synonymous	MYH2	NM_001100112.1,NM_017534.5	,	1091,3130,2282	CC,CT,TT		41.2558,40.0363,40.8427	,	108/1942,108/1942	10450816	5312,7694	2203	4300	6503	SO:0001819	synonymous_variant	4620	exon4			ATAACGTTCTTTG		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.324A>G	17.37:g.10450816T>C		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	340	186	0.547059	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			T|0.540;C|0.460	0.460	strong		0.483	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
TCTN2	79867	hgsc.bcm.edu	37	12	124172643	124172643	+	Silent	SNP	C	C	T	rs144567556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124172643C>T	ENST00000303372.5	+	7	938	c.810C>T	c.(808-810)gaC>gaT	p.D270D	TCTN2_ENST00000426174.2_Silent_p.D269D	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	270					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		TGGATACTGACGCAAAAGACT	0.368													c|||	8	0.00159744	0.0	0.0043	5008	,	,		20396	0.0		0.005	False		,,,				2504	0.0				p.D270D		Atlas-SNP	.											.	TCTN2	50	.	0			c.C810T						PASS	.		,	6,4400	11.4+/-27.6	0,6,2197	133.0	137.0	136.0		807,810	-11.2	0.0	12	dbSNP_134	136	64,8536	38.3+/-94.2	0,64,4236	no	coding-synonymous,coding-synonymous	TCTN2	NM_001143850.1,NM_024809.3	,	0,70,6433	TT,TC,CC		0.7442,0.1362,0.5382	,	269/697,270/698	124172643	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	79867	exon7			TACTGACGCAAAA	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.810C>T	12.37:g.124172643C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	43	0.355372	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																			C|0.994;T|0.006	0.006	strong		0.368	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
RNF213	57674	hgsc.bcm.edu	37	17	78261730	78261730	+	Silent	SNP	G	G	A	rs17853714	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78261730G>A	ENST00000582970.1	+	4	521	c.378G>A	c.(376-378)ccG>ccA	p.P126P	RNF213_ENST00000456466.1_Silent_p.P126P|RNF213_ENST00000319921.4_Silent_p.P126P|RNF213_ENST00000508628.2_Silent_p.P175P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	126					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)			TTTCAAACCCGTGGCCTCAGG	0.632													G|||	584	0.116613	0.0862	0.0893	5008	,	,		13894	0.0655		0.162	False		,,,				2504	0.183				p.P126P		Atlas-SNP	.											.	RNF213	766	.	0			c.G378A						PASS	.	G	,	451,3923		26,399,1762	30.0	28.0	28.0		525,378	-7.2	0.0	17	dbSNP_123	28	1547,7007		142,1263,2872	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	168,1662,4634	AA,AG,GG		18.0851,10.3109,15.4548	,	175/5257,126/1064	78261730	1998,10930	2187	4277	6464	SO:0001819	synonymous_variant	57674	exon4			AAACCCGTGGCCT	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.378G>A	17.37:g.78261730G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	115	44	0.382609	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|0.861;A|0.139	0.139	strong		0.632	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744844	23744844	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23744844C>T	ENST00000357460.5	-	2	1757	c.1593G>A	c.(1591-1593)gaG>gaA	p.E531E	HOMEZ_ENST00000431326.2_Silent_p.E533E|HOMEZ_ENST00000561013.1_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	107	0	0		WXS	Illumina HiSeq	Phase_I	117	7	0.0598291	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	
MACROD2	140733	hgsc.bcm.edu	37	20	15967390	15967390	+	Missense_Mutation	SNP	C	C	T	rs41275442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:15967390C>T	ENST00000310348.4	+	14	1004	c.1004C>T	c.(1003-1005)aCg>aTg	p.T335M	MACROD2_ENST00000378058.3_Missense_Mutation_p.T100M|MACROD2_ENST00000402914.1_Missense_Mutation_p.T100M|MACROD2_ENST00000407045.3_5'UTR|MACROD2_ENST00000217246.4_Missense_Mutation_p.T335M			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	335	Glu-rich.		T -> M (in dbSNP:rs41275442).		brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				AATGATTCAACGAAGAATGAA	0.338													C|||	384	0.0766773	0.0076	0.121	5008	,	,		19157	0.0238		0.167	False		,,,				2504	0.1002				p.T335M		Atlas-SNP	.											.	MACROD2	34	.	0			c.C1004T						PASS	.	C	MET/THR,MET/THR	189,4217	118.0+/-155.7	6,177,2020	62.0	59.0	60.0		299,1004	-6.7	0.0	20	dbSNP_127	60	1609,6991	294.4+/-301.9	156,1297,2847	yes	missense,missense	MACROD2	NM_001033087.1,NM_080676.5	81,81	162,1474,4867	TT,TC,CC		18.7093,4.2896,13.8244	probably-damaging,probably-damaging	100/214,335/426	15967390	1798,11208	2203	4300	6503	SO:0001583	missense	140733	exon14			ATTCAACGAAGAA	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.1004C>T	20.37:g.15967390C>T	ENSP00000309809:p.Thr335Met	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	193	0.08836996336996338	5	0.01016260162601626	52	0.143646408839779	8	0.013986013986013986	128	0.16886543535620052	C	3.983	-0.005976	0.07773	0.042896	0.187093	ENSG00000172264	ENST00000217246;ENST00000310348;ENST00000402914;ENST00000378058	T;T;T;T	0.46063	2.48;2.5;0.88;0.88	5.92	-6.69	0.01772	.	1.480440	0.03889	N	0.278341	T	0.00039	0.0001	L	0.44542	1.39	0.80722	P	0.0	B;B	0.15719	0.008;0.014	B;B	0.11329	0.002;0.006	T	0.12656	-1.0539	9	0.30078	T	0.28	1.507	6.8409	0.23963	0.103:0.1336:0.102:0.6614	rs41275442	335;335	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	M	335;335;100;100	ENSP00000217246:T335M;ENSP00000309809:T335M;ENSP00000385290:T100M;ENSP00000367297:T100M	ENSP00000217246:T335M	T	+	2	0	MACROD2	15915390	0.000000	0.05858	0.000000	0.03702	0.349000	0.29174	-3.589000	0.00422	-1.070000	0.03149	-0.941000	0.02677	ACG	C|0.869;T|0.131	0.131	strong		0.338	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
OAS3	4940	hgsc.bcm.edu	37	12	113405328	113405328	+	Missense_Mutation	SNP	G	G	A	rs61732395	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:113405328G>A	ENST00000228928.7	+	13	2974	c.2795G>A	c.(2794-2796)cGg>cAg	p.R932Q	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	932	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						GAGCTACAACGGGACTTCATC	0.572													G|||	21	0.00419329	0.0008	0.0	5008	,	,		21937	0.0		0.0149	False		,,,				2504	0.0051				p.R932Q		Atlas-SNP	.											.	OAS3	63	.	0			c.G2795A						PASS	.	G	GLN/ARG	7,4279		1,5,2137	60.0	63.0	62.0		2795	4.2	0.2	12	dbSNP_129	62	115,8425		1,113,4156	yes	missense	OAS3	NM_006187.2	43	2,118,6293	AA,AG,GG		1.3466,0.1633,0.9512	probably-damaging	932/1088	113405328	122,12704	2143	4270	6413	SO:0001583	missense	4940	exon13			TACAACGGGACTT	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.2795G>A	12.37:g.113405328G>A	ENSP00000228928:p.Arg932Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	15|15	0.006868131868131868|0.006868131868131868	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	15|15	0.01978891820580475|0.01978891820580475	G|G	10.02|10.02	1.236677|1.236677	0.22711|0.22711	0.001633|0.001633	0.013466|0.013466	ENSG00000111331|ENSG00000111331	ENST00000546973|ENST00000228928;ENST00000323881	.|T	.|0.47528	.|0.84	4.16|4.16	4.16|4.16	0.48862|0.48862	.|-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.|0.335208	.|0.16372	.|U	.|0.217282	T|T	0.42200|0.42200	0.1192|0.1192	L|L	0.41824|0.41824	1.3|1.3	0.58432|0.58432	D|D	0.999995|0.999995	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	T|T	0.50491|0.50491	-0.8822|-0.8822	5|10	.|0.51188	.|T	.|0.08	.|.	12.1898|12.1898	0.54264|0.54264	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs61732395|rs61732395	.|932	.|Q9Y6K5	.|OAS3_HUMAN	R|Q	104|932;931	.|ENSP00000228928:R932Q	.|ENSP00000228928:R932Q	G|R	+|+	1|2	0|0	OAS3|OAS3	111889711|111889711	0.850000|0.850000	0.29656|0.29656	0.159000|0.159000	0.22649|0.22649	0.005000|0.005000	0.04900|0.04900	3.354000|3.354000	0.52254|0.52254	2.313000|2.313000	0.78055|0.78055	0.558000|0.558000	0.71614|0.71614	GGG|CGG	G|0.993;A|0.007	0.007	strong		0.572	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
FAM205A	259308	hgsc.bcm.edu	37	9	34724987	34724987	+	Silent	SNP	A	A	G	rs1697617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:34724987A>G	ENST00000378788.3	-	4	2289	c.2250T>C	c.(2248-2250)gcT>gcC	p.A750A		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	750						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						TACCTGGTAAAGCCTGTTGCT	0.527																																					p.A750A		Atlas-SNP	.											FAM205A_ENST00000378788,colon,carcinoma,-1,2	FAM205A	45	2	0			c.T2250C						scavenged	.						50.0	37.0	41.0					9																	34724987		692	1591	2283	SO:0001819	synonymous_variant	259308	exon4			TGGTAAAGCCTGT		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.2250T>C	9.37:g.34724987A>G		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	337	46	0.136499	NM_001141917	A8MVW7	Silent	SNP	ENST00000378788.3	37	CCDS55305.1																																																																																			A|0.870;G|0.130	0.130	strong		0.527	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
NMRK1	54981	hgsc.bcm.edu	37	9	77684690	77684690	+	Silent	SNP	A	A	C	rs3752955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:77684690A>C	ENST00000361092.4	-	6	593	c.357T>G	c.(355-357)acT>acG	p.T119T	NMRK1_ENST00000376811.1_Silent_p.T123T|NMRK1_ENST00000482537.1_5'Flank|NMRK1_ENST00000376808.4_Intron	NM_017881.2	NP_060351.1	Q9NWW6	NRK1_HUMAN	nicotinamide riboside kinase 1	119					NAD biosynthetic process (GO:0009435)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)										CATATGGAATAGTCAGGAAAT	0.363													A|||	3106	0.620208	0.7398	0.5893	5008	,	,		18362	0.6776		0.5268	False		,,,				2504	0.5174				p.T119T		Atlas-SNP	.											.	.	.	.	0			c.T357G						PASS	.	A	,	3125,1281	698.5+/-406.4	1102,921,180	90.0	86.0	87.0		,357	-0.4	0.8	9	dbSNP_107	87	4674,3926	602.7+/-394.5	1274,2126,900	no	intron,coding-synonymous	C9orf95	NM_001127603.1,NM_017881.2	,	2376,3047,1080	CC,CA,AA		45.6512,29.074,40.0354	,	,119/200	77684690	7799,5207	2203	4300	6503	SO:0001819	synonymous_variant	54981	exon6			TGGAATAGTCAGG	AK097144	CCDS6650.1, CCDS47981.1	9q21.31	2012-03-30	2012-03-30	2012-03-30	ENSG00000106733	ENSG00000106733			26057	protein-coding gene	gene with protein product		608704	"""chromosome 9 open reading frame 95"""	C9orf95		15137942	Standard	NM_017881		Approved	FLJ20559, NRK1, bA235O14.2	uc004ajr.4	Q9NWW6	OTTHUMG00000020034	ENST00000361092.4:c.357T>G	9.37:g.77684690A>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_017881	Q5W124|Q8N430	Silent	SNP	ENST00000361092.4	37	CCDS6650.1																																																																																			A|0.396;C|0.604	0.604	strong		0.363	NMRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052705.1	NM_017881	
CELSR1	9620	hgsc.bcm.edu	37	22	46760481	46760481	+	Missense_Mutation	SNP	C	C	G	rs9615351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	100	1	0.01		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	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	
FUT10	84750	hgsc.bcm.edu	37	8	33246591	33246591	+	Missense_Mutation	SNP	G	G	C	rs17855838	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:33246591G>C	ENST00000327671.5	-	4	1733	c.1102C>G	c.(1102-1104)Ctc>Gtc	p.L368V	FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Missense_Mutation_p.L306V|FUT10_ENST00000524021.1_Missense_Mutation_p.L340V|FUT10_ENST00000518672.1_Missense_Mutation_p.L340V	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	368			L -> V (in dbSNP:rs17855838). {ECO:0000269|PubMed:11698403, ECO:0000269|PubMed:15489334}.		embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.L368V(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CGTTCCCTGAGAGCTGTCAGA	0.473													G|||	1367	0.272963	0.0855	0.1671	5008	,	,		21753	0.4683		0.1938	False		,,,				2504	0.4816				p.L368V		Atlas-SNP	.											FUT10,NS,carcinoma,0,1	FUT10	62	1	1	Substitution - Missense(1)	stomach(1)	c.C1102G						PASS	.	G	VAL/LEU	530,3876	238.0+/-249.6	22,486,1695	211.0	181.0	191.0		1102	4.1	1.0	8	dbSNP_123	191	1745,6855	316.6+/-312.8	176,1393,2731	yes	missense	FUT10	NM_032664.3	32	198,1879,4426	CC,CG,GG		20.2907,12.0291,17.4919	possibly-damaging	368/480	33246591	2275,10731	2203	4300	6503	SO:0001583	missense	84750	exon4			CCCTGAGAGCTGT	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1102C>G	8.37:g.33246591G>C	ENSP00000332757:p.Leu368Val	Somatic	391	0	0		WXS	Illumina HiSeq	Phase_I	407	190	0.46683	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	37	CCDS6088.1	473	0.21657509157509158	33	0.06707317073170732	56	0.15469613259668508	250	0.4370629370629371	134	0.17678100263852242	G	15.32	2.799234	0.50208	0.120291	0.202907	ENSG00000172728	ENST00000327671;ENST00000380081;ENST00000518672;ENST00000524021;ENST00000335589	T;T;T;T	0.44083	0.93;0.94;0.94;1.81	5.04	4.09	0.47781	.	0.262237	0.33110	N	0.005264	T	0.00012	0.0000	M	0.86343	2.81	0.21675	P	0.999592885	P;P;P;P;P;B	0.48998	0.861;0.498;0.918;0.638;0.684;0.443	P;B;P;B;B;B	0.48952	0.562;0.23;0.596;0.272;0.422;0.395	T	0.48559	-0.9025	9	0.51188	T	0.08	-19.205	10.2443	0.43332	0.0:0.0:0.6866:0.3134	rs17855838;rs17855838	418;368;340;306;368;410	B4E056;Q6P4F1-5;Q6P4F1-4;Q6P4F1-3;Q6P4F1;E7EU36	.;.;.;.;FUT10_HUMAN;.	V	368;410;340;340;306	ENSP00000332757:L368V;ENSP00000430428:L340V;ENSP00000429870:L340V;ENSP00000334997:L306V	ENSP00000332757:L368V	L	-	1	0	FUT10	33366133	0.981000	0.34729	0.996000	0.52242	0.989000	0.77384	1.797000	0.38804	2.493000	0.84123	0.557000	0.71058	CTC	G|0.815;C|0.185	0.185	strong		0.473	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
CES5A	221223	hgsc.bcm.edu	37	16	55905676	55905676	+	Splice_Site	SNP	C	C	T	rs72810507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:55905676C>T	ENST00000290567.9	-	3	400		c.e3-1		CES5A_ENST00000520435.1_Splice_Site|CES5A_ENST00000319165.9_Splice_Site|CES5A_ENST00000541580.1_Intron|CES5A_ENST00000521992.1_Splice_Site|CES5A_ENST00000518005.1_Splice_Site	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A							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						CTGGAGGCACCTTGGAGAAGG	0.517													C|||	239	0.0477236	0.0121	0.0504	5008	,	,		18627	0.0327		0.1233	False		,,,				2504	0.0317				.		Atlas-SNP	.											.	CES5A	206	.	0			c.279-1G>A						PASS	.	C	,,	128,4268	91.6+/-130.3	2,124,2072	55.0	48.0	51.0		,,	4.9	1.0	16	dbSNP_130	51	980,7620	209.6+/-250.7	52,876,3372	yes	splice-3,splice-3,splice-3	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	,,	54,1000,5444	TT,TC,CC		11.3953,2.9117,8.5257	,,	,,	55905676	1108,11888	2198	4300	6498	SO:0001630	splice_region_variant	221223	exon4			AGGCACCTTGGAG	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.279-1G>A	16.37:g.55905676C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_001143685	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Splice_Site	SNP	ENST00000290567.9	37	CCDS45490.1	134	0.06135531135531135	6	0.012195121951219513	17	0.04696132596685083	18	0.03146853146853147	93	0.12269129287598944	C	15.45	2.836059	0.50951	0.029117	0.113953	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000290567;ENST00000520435	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2926	0.66289	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CES5A	54463177	1.000000	0.71417	0.991000	0.47740	0.219000	0.24729	5.842000	0.69417	2.633000	0.89246	0.655000	0.94253	.	C|0.922;T|0.078	0.078	strong		0.517	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	Intron
SEZ6L	23544	hgsc.bcm.edu	37	22	26702015	26702015	+	Silent	SNP	A	A	C	rs1210894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26702015A>C	ENST00000248933.6	+	6	1514	c.1419A>C	c.(1417-1419)acA>acC	p.T473T	SEZ6L_ENST00000529632.2_Silent_p.T473T|SEZ6L_ENST00000403121.1_Silent_p.T246T|SEZ6L_ENST00000343706.4_Silent_p.T473T|SEZ6L_ENST00000404234.3_Silent_p.T473T|SEZ6L_ENST00000360929.3_Silent_p.T473T|SEZ6L_ENST00000402979.1_Silent_p.T246T			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	473	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.T473T(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CTGAAAACACAAATGGGAGCC	0.557													C|||	1817	0.362819	0.6611	0.3386	5008	,	,		15893	0.1042		0.4433	False		,,,				2504	0.1605				p.T473T		Atlas-SNP	.											SEZ6L,NS,carcinoma,0,1	SEZ6L	174	1	1	Substitution - coding silent(1)	stomach(1)	c.A1419C						scavenged	.	C	,,,,,	2748,1658	506.6+/-366.4	852,1044,307	75.0	69.0	71.0		1419,1419,1419,1419,1419,1419	3.6	0.6	22	dbSNP_87	71	3722,4878	618.1+/-396.7	831,2060,1409	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	1683,3104,1716	CC,CA,AA		43.2791,37.6305,49.7463	,,,,,	473/1024,473/1014,473/1012,473/950,473/949,473/1025	26702015	6470,6536	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon6			AAACACAAATGGG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1419A>C	22.37:g.26702015A>C		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			A|0.555;C|0.445	0.445	strong		0.557	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
ARHGAP33	115703	hgsc.bcm.edu	37	19	36268771	36268771	+	Silent	SNP	C	C	T	rs231228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36268771C>T	ENST00000007510.4	+	3	294	c.150C>T	c.(148-150)gcC>gcT	p.A50A	ARHGAP33_ENST00000378944.5_5'UTR|ARHGAP33_ENST00000221905.1_3'UTR|ARHGAP33_ENST00000314737.5_Silent_p.A50A			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	50					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						CTGACTGCGCCCATTTCCACT	0.592													C|||	1450	0.289537	0.3828	0.3674	5008	,	,		17834	0.2907		0.2038	False		,,,				2504	0.1953				p.A50A		Atlas-SNP	.											ARHGAP33,NS,carcinoma,+2,1	ARHGAP33	102	1	0			c.C150T						scavenged	.	C	,	1551,2855	487.1+/-360.8	278,995,930	91.0	93.0	92.0		,150	4.0	1.0	19	dbSNP_79	92	1724,6876	316.4+/-312.7	181,1362,2757	no	utr-5,coding-synonymous	ARHGAP33	NM_001172630.1,NM_052948.3	,	459,2357,3687	TT,TC,CC		20.0465,35.202,25.1807	,	,50/1127	36268771	3275,9731	2203	4300	6503	SO:0001819	synonymous_variant	115703	exon3			CTGCGCCCATTTC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.150C>T	19.37:g.36268771C>T		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				C|0.743;T|0.257	0.257	strong		0.592	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
KIAA2013	90231	hgsc.bcm.edu	37	1	11983206	11983206	+	Silent	SNP	A	A	G	rs3795408	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11983206A>G	ENST00000376572.3	-	2	1559	c.1374T>C	c.(1372-1374)ttT>ttC	p.F458F	KIAA2013_ENST00000376576.3_Silent_p.F458F	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	458						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGCCCCCCAAAGCTGAGCA	0.617													G|||	3382	0.675319	0.8321	0.5317	5008	,	,		19110	0.6796		0.5537	False		,,,				2504	0.6861				p.F458F		Atlas-SNP	.											.	KIAA2013	25	.	0			c.T1374C						PASS	.	G		3262,1106		1314,634,236	22.0	27.0	25.0		1374	0.3	1.0	1	dbSNP_107	25	4410,4152		1343,1724,1214	no	coding-synonymous	KIAA2013	NM_138346.2		2657,2358,1450	GG,GA,AA		48.4933,25.3205,40.6651		458/635	11983206	7672,5258	2184	4281	6465	SO:0001819	synonymous_variant	90231	exon2			CCCCCCAAAGCTG	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.1374T>C	1.37:g.11983206A>G		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	355	162	0.456338	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Silent	SNP	ENST00000376572.3	37	CCDS141.1																																																																																			A|0.385;G|0.615	0.615	strong		0.617	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346	
TAT	6898	hgsc.bcm.edu	37	16	71610276	71610276	+	Missense_Mutation	SNP	G	G	A	rs74344827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71610276G>A	ENST00000355962.4	-	2	176	c.43C>T	c.(43-45)Ccc>Tcc	p.P15S	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	15					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)	AGAATTGAGGGGAGGTTGCCT	0.522													G|||	719	0.14357	0.1831	0.0836	5008	,	,		19385	0.0516		0.163	False		,,,				2504	0.2076				p.P15S	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.C43T						PASS	.	G	SER/PRO	864,3532	331.8+/-302.1	98,668,1432	115.0	114.0	114.0		43	2.7	0.1	16	dbSNP_131	114	1420,7180	270.2+/-288.9	121,1178,3001	yes	missense	TAT	NM_000353.2	74	219,1846,4433	AA,AG,GG		16.5116,19.6542,17.5746	benign	15/455	71610276	2284,10712	2198	4300	6498	SO:0001583	missense	6898	exon2			TTGAGGGGAGGTT		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.43C>T	16.37:g.71610276G>A	ENSP00000348234:p.Pro15Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	145	71	0.489655	NM_000353	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	37	CCDS10903.1	276	0.12637362637362637	72	0.14634146341463414	38	0.10497237569060773	33	0.057692307692307696	133	0.17546174142480211	G	6.429	0.447277	0.12223	0.196542	0.165116	ENSG00000198650	ENST00000355962	T	0.79554	-1.28	6.07	2.74	0.32292	Tyrosine aminotransferase ubiquitination region (1);	0.541440	0.22314	N	0.061700	T	0.00109	0.0003	N	0.12182	0.205	0.80722	P	0.0	B;B	0.29552	0.248;0.0	B;B	0.26202	0.067;0.002	T	0.04454	-1.0950	9	0.32370	T	0.25	-5.5369	7.8185	0.29274	0.2519:0.1309:0.6172:0.0	.	15;15	Q8WW92;P17735	.;ATTY_HUMAN	S	15	ENSP00000348234:P15S	ENSP00000348234:P15S	P	-	1	0	TAT	70167777	0.851000	0.29673	0.130000	0.21974	0.173000	0.22820	1.152000	0.31663	0.885000	0.36088	0.655000	0.94253	CCC	G|0.838;A|0.162	0.162	strong		0.522	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		
NUP88	4927	hgsc.bcm.edu	37	17	5289580	5289580	+	Silent	SNP	A	A	G	rs11209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	212	0	0		WXS	Illumina HiSeq	Phase_I	241	106	0.439834	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	
ZNF627	199692	hgsc.bcm.edu	37	19	11725413	11725413	+	Silent	SNP	G	G	A	rs12151212	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11725413G>A	ENST00000361113.5	+	2	283	c.75G>A	c.(73-75)caG>caA	p.Q25Q	ZNF627_ENST00000588174.1_Silent_p.Q25Q	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	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)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						ATCCTTCCCAGAAGAATCTCT	0.498													G|||	610	0.121805	0.0832	0.1167	5008	,	,		16866	0.0258		0.169	False		,,,				2504	0.228				p.Q25Q	Melanoma(112;173 1614 10731 17751 23322)	Atlas-SNP	.											ZNF627,NS,carcinoma,0,1	ZNF627	43	1	0			c.G75A						PASS	.	G		422,3984	203.8+/-226.2	17,388,1798	107.0	112.0	110.0		75	-0.9	0.5	19	dbSNP_120	110	1689,6911	306.1+/-307.8	164,1361,2775	no	coding-synonymous	ZNF627	NM_145295.3		181,1749,4573	AA,AG,GG		19.6395,9.5778,16.231		25/462	11725413	2111,10895	2203	4300	6503	SO:0001819	synonymous_variant	199692	exon2			TTCCCAGAAGAAT	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"""Zinc fingers, C2H2-type"", ""-"""	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.75G>A	19.37:g.11725413G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Silent	SNP	ENST00000361113.5	37	CCDS42502.1																																																																																			G|0.865;A|0.135	0.135	strong		0.498	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295	
APOBR	55911	hgsc.bcm.edu	37	16	28507452	28507452	+	Missense_Mutation	SNP	G	G	T	rs370148393		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:28507452G>T	ENST00000431282.1	+	3	1073	c.1063G>T	c.(1063-1065)Ggg>Tgg	p.G355W	CLN3_ENST00000567160.1_5'Flank|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000328423.5_Missense_Mutation_p.G355W|APOBR_ENST00000564831.1_Missense_Mutation_p.G364W			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	355	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GGAGGAGGCCGGGACAGCCTC	0.672																																					p.G364W		Atlas-SNP	.											APOBR,caecum,carcinoma,0,1	APOBR	89	1	0			c.G1090T						scavenged	.						14.0	17.0	16.0					16																	28507452		1944	4097	6041	SO:0001583	missense	55911	exon2			GAGGCCGGGACAG	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1063G>T	16.37:g.28507452G>T	ENSP00000416094:p.Gly355Trp	Somatic	21	3	0.142857		WXS	Illumina HiSeq	Phase_I	19	2	0.105263	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		.	.	.	.	.	.	.	.	.	.	G	11.71	1.718826	0.30503	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.60548	0.18;0.18	3.86	-2.49	0.06403	.	.	.	.	.	T	0.33059	0.0850	N	0.19112	0.55	0.09310	N	1	B	0.33777	0.425	B	0.27715	0.082	T	0.13980	-1.0489	9	0.72032	D	0.01	.	3.7884	0.08710	0.5999:0.0:0.2159:0.1841	.	355	Q9NS13	.	W	355	ENSP00000327669:G355W;ENSP00000416094:G355W	ENSP00000327669:G355W	G	+	1	0	APOBR	28414953	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.825000	0.04433	-0.783000	0.04534	-0.487000	0.04747	GGG	.	.	alt		0.672	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
HELZ	9931	hgsc.bcm.edu	37	17	65199433	65199433	+	Splice_Site	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:65199433A>G	ENST00000358691.5	-	6	539		c.e6+1		HELZ_ENST00000580168.1_Splice_Site|HELZ_ENST00000580662.1_Splice_Site	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger							membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TTATCAACATACCAGGGACTC	0.398																																					.		Atlas-SNP	.											.	HELZ	160	.	0			c.372+2T>C						PASS	.						100.0	99.0	99.0					17																	65199433		1898	4122	6020	SO:0001630	splice_region_variant	9931	exon7			CAACATACCAGGG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.372+1T>C	17.37:g.65199433A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	5	0.0574713	NM_014877	I6L9H4	Splice_Site	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.255640	0.80135	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8543	0.70323	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HELZ	62629895	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	6.429000	0.73387	2.323000	0.78572	0.528000	0.53228	.	.	.	none		0.398	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	Intron
MUC5B	727897	hgsc.bcm.edu	37	11	1264772	1264772	+	Missense_Mutation	SNP	T	T	C	rs2943500		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1264772T>C	ENST00000529681.1	+	31	6720	c.6662T>C	c.(6661-6663)aTc>aCc	p.I2221T	MUC5B_ENST00000447027.1_Missense_Mutation_p.I2224T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2221	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.I2224T(1)		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)		ACCTCGGGCATCTTGGGCACC	0.662																																					p.I2221T		Atlas-SNP	.											MUC5B,NS,neuroblastoma,0,3	MUC5B	473	3	1	Substitution - Missense(1)	skin(1)	c.T6662C						scavenged	.						94.0	111.0	105.0					11																	1264772		2080	4181	6261	SO:0001583	missense	727897	exon31			CGGGCATCTTGGG	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.6662T>C	11.37:g.1264772T>C	ENSP00000436812:p.Ile2221Thr	Somatic	243	2	0.00823045		WXS	Illumina HiSeq	Phase_I	406	30	0.0738916	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	5.754	0.323450	0.10900	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21191	2.02;2.21	2.39	1.4	0.22301	.	.	.	.	.	T	0.06325	0.0163	N	0.00729	-1.24	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34204	-0.9838	9	0.87932	D	0	.	6.6171	0.22782	0.0:0.7019:0.1804:0.1177	rs2943500	2859;2224	A7Y9J9;E9PBJ0	.;.	T	2221;2224;2222;2236	ENSP00000436812:I2221T;ENSP00000415793:I2224T	ENSP00000343037:I2222T	I	+	2	0	MUC5B	1221348	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.044000	0.13992	-0.095000	0.12351	-0.684000	0.03749	ATC	.	.	weak		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
FAT1	2195	hgsc.bcm.edu	37	4	187540918	187540918	+	Missense_Mutation	SNP	G	G	C	rs3796648	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187540918G>C	ENST00000441802.2	-	10	7031	c.6822C>G	c.(6820-6822)gaC>gaG	p.D2274E		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2274	Cadherin 20. {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						CATTGATGTCGTCTACTATGA	0.498										HNSCC(5;0.00058)			C|||	342	0.0682907	0.003	0.1499	5008	,	,		21577	0.1796		0.0338	False		,,,				2504	0.0194				p.D2274E	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C6822G						PASS	.	C	GLU/ASP	38,4004		0,38,1983	121.0	123.0	122.0		6822	-1.3	0.4	4	dbSNP_107	122	254,8124		4,246,3939	yes	missense	FAT1	NM_005245.3	45	4,284,5922	CC,CG,GG		3.0317,0.9401,2.351	benign	2274/4589	187540918	292,12128	2021	4189	6210	SO:0001583	missense	2195	exon10			GATGTCGTCTACT	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.6822C>G	4.37:g.187540918G>C	ENSP00000406229:p.Asp2274Glu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	189	0.08653846153846154	3	0.006097560975609756	40	0.11049723756906077	115	0.20104895104895104	31	0.040897097625329816	C	0.003	-2.411580	0.00191	0.009401	0.030317	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01685	4.69	5.23	-1.29	0.09288	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.048707	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00746	-1.225	0.52501	P	4.4000000000044004E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.37731	-0.9693	9	0.02654	T	1	.	7.3679	0.26783	0.0:0.3426:0.1145:0.543	rs3796648;rs52829050;rs3796648	2274	Q14517	FAT1_HUMAN	E	2274;2276	ENSP00000406229:D2274E	ENSP00000260147:D2276E	D	-	3	2	FAT1	187777912	0.997000	0.39634	0.441000	0.26858	0.003000	0.03518	0.347000	0.20014	-0.653000	0.05401	-2.664000	0.00146	GAC	G|0.922;C|0.078	0.078	strong		0.498	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
LRRN2	10446	hgsc.bcm.edu	37	1	204588140	204588140	+	Silent	SNP	G	G	A	rs3747630	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204588140G>A	ENST00000367175.1	-	1	3193	c.981C>T	c.(979-981)caC>caT	p.H327H	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367176.3_Silent_p.H327H|LRRN2_ENST00000367177.3_Silent_p.H327H			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	327					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			AGGCGCGGGGGTGGATGAAGG	0.602													G|||	1055	0.210663	0.0847	0.1153	5008	,	,		18119	0.3234		0.2545	False		,,,				2504	0.2873				p.H327H		Atlas-SNP	.											.	LRRN2	81	.	0			c.C981T						PASS	.	G	,	486,3920	226.5+/-242.0	27,432,1744	85.0	63.0	71.0		981,981	2.8	1.0	1	dbSNP_107	71	2109,6491	359.4+/-331.5	249,1611,2440	no	coding-synonymous,coding-synonymous	LRRN2	NM_006338.2,NM_201630.1	,	276,2043,4184	AA,AG,GG		24.5233,11.0304,19.9523	,	327/714,327/714	204588140	2595,10411	2203	4300	6503	SO:0001819	synonymous_variant	10446	exon3			GCGGGGGTGGATG	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.981C>T	1.37:g.204588140G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Silent	SNP	ENST00000367175.1	37	CCDS1448.1																																																																																			G|0.800;A|0.200	0.200	strong		0.602	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
RTL1	388015	hgsc.bcm.edu	37	14	101350298	101350298	+	Silent	SNP	T	T	C	rs3825569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:101350298T>C	ENST00000534062.1	-	1	886	c.828A>G	c.(826-828)gaA>gaG	p.E276E	MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	276					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						ACTCAAACACTTCGGACATGG	0.577													C|||	2565	0.512181	0.6089	0.4337	5008	,	,		19025	0.4206		0.6402	False		,,,				2504	0.3998				p.E276E		Atlas-SNP	.											.	RTL1	120	.	0			c.A828G						PASS	.	C		874,510		284,306,102	58.0	53.0	55.0		828	-6.3	0.0	14	dbSNP_107	55	2017,1165		647,723,221	yes	coding-synonymous	RTL1	NM_001134888.2		931,1029,323	CC,CT,TT		36.6122,36.8497,36.6842		276/1359	101350298	2891,1675	692	1591	2283	SO:0001819	synonymous_variant	388015	exon1			AAACACTTCGGAC		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.828A>G	14.37:g.101350298T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001134888	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																			T|0.456;C|0.544	0.544	strong		0.577	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
THBS2	7058	hgsc.bcm.edu	37	6	169622490	169622490	+	Silent	SNP	G	G	A	rs9505895	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	99	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	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	
MYO15A	51168	hgsc.bcm.edu	37	17	18047189	18047189	+	Missense_Mutation	SNP	G	G	A	rs2272571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:18047189G>A	ENST00000205890.5	+	28	6390	c.6052G>A	c.(6052-6054)Ggg>Agg	p.G2018R	snoU13_ENST00000459354.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2018	Neck or regulatory domain.		G -> R (in dbSNP:rs2272571).		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)					CACAGGCCTCGGGCTGGCCCA	0.657													G|||	1193	0.238219	0.1452	0.2695	5008	,	,		17612	0.5179		0.1213	False		,,,				2504	0.1738				p.G2018R		Atlas-SNP	.											.	MYO15A	268	.	0			c.G6052A						PASS	.	G	ARG/GLY	566,3560		41,484,1538	21.0	24.0	23.0		6052	2.7	0.6	17	dbSNP_100	23	967,7431		54,859,3286	yes	missense	MYO15A	NM_016239.3	125	95,1343,4824	AA,AG,GG		11.5146,13.7179,12.2405	benign	2018/3531	18047189	1533,10991	2063	4199	6262	SO:0001583	missense	51168	exon27			GGCCTCGGGCTGG	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.6052G>A	17.37:g.18047189G>A	ENSP00000205890:p.Gly2018Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	546	0.25	72	0.14634146341463414	75	0.20718232044198895	303	0.5297202797202797	96	0.1266490765171504	G	0.031	-1.333383	0.01298	0.137179	0.115146	ENSG00000091536	ENST00000205890	D	0.86769	-2.17	4.98	2.73	0.32206	.	.	.	.	.	T	0.00012	0.0000	N	0.00210	-1.845	0.21950	P	0.999455902	B	0.02656	0.0	B	0.01281	0.0	T	0.38887	-0.9640	8	0.02654	T	1	.	7.9865	0.30216	0.8356:0.0:0.1644:0.0	rs2272571;rs60920238;rs2272571	2018	Q9UKN7	MYO15_HUMAN	R	2018	ENSP00000205890:G2018R	ENSP00000205890:G2018R	G	+	1	0	MYO15A	17987914	0.046000	0.20272	0.650000	0.29550	0.075000	0.17131	1.152000	0.31663	0.341000	0.23771	-0.487000	0.04747	GGG	G|0.745;A|0.255	0.255	strong		0.657	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
GPR39	2863	hgsc.bcm.edu	37	2	133174764	133174764	+	Missense_Mutation	SNP	C	C	T	rs2241764	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133174764C>T	ENST00000329321.3	+	1	618	c.149C>T	c.(148-150)gCc>gTc	p.A50V		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	50			A -> V (in dbSNP:rs2241764). {ECO:0000269|PubMed:14702039}.		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGGAACAGCGCCACCATTCGG	0.532													T|||	1894	0.378195	0.5295	0.3429	5008	,	,		20511	0.2361		0.327	False		,,,				2504	0.3978				p.A50V		Atlas-SNP	.											.	GPR39	60	.	0			c.C149T						PASS	.	T	VAL/ALA	2200,2206	588.0+/-386.8	541,1118,544	150.0	134.0	139.0		149	5.3	1.0	2	dbSNP_98	139	2810,5790	676.5+/-403.3	477,1856,1967	yes	missense	GPR39	NM_001508.2	64	1018,2974,2511	TT,TC,CC		32.6744,49.9319,38.5207	benign	50/454	133174764	5010,7996	2203	4300	6503	SO:0001583	missense	2863	exon1			ACAGCGCCACCAT	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.149C>T	2.37:g.133174764C>T	ENSP00000327417:p.Ala50Val	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	167	75	0.449102	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Missense_Mutation	SNP	ENST00000329321.3	37	CCDS2170.1	786	0.3598901098901099	256	0.5203252032520326	127	0.35082872928176795	151	0.263986013986014	252	0.3324538258575198	T	5.771	0.326541	0.10900	0.499319	0.326744	ENSG00000183840	ENST00000329321	T	0.36157	1.27	5.34	5.34	0.76211	GPCR, rhodopsin-like superfamily (1);	0.264420	0.36628	N	0.002497	T	0.00012	0.0000	N	0.00677	-1.265	0.47123	P	6.789999999999852E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.42999	-0.9418	9	0.06099	T	0.92	.	11.4538	0.50169	0.0:0.0701:0.0:0.9299	rs2241764;rs2241764	50	O43194	GPR39_HUMAN	V	50	ENSP00000327417:A50V	ENSP00000327417:A50V	A	+	2	0	GPR39	132891234	1.000000	0.71417	0.989000	0.46669	0.839000	0.47603	4.958000	0.63660	1.064000	0.40671	-0.391000	0.06502	GCC	C|0.618;T|0.381	0.381	strong		0.532	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
FAM126A	84668	hgsc.bcm.edu	37	7	23015831	23015831	+	Silent	SNP	T	T	C	rs3735231	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:23015831T>C	ENST00000432176.2	-	7	856	c.624A>G	c.(622-624)tcA>tcG	p.S208S	FAM126A_ENST00000409923.1_Silent_p.S208S	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	208					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						TACTTTACCTTGAACAAATTT	0.318													T|||	1877	0.3748	0.3578	0.33	5008	,	,		18391	0.4663		0.3628	False		,,,				2504	0.3476				p.S208S		Atlas-SNP	.											FAM126A,NS,carcinoma,-1,1	FAM126A	53	1	0			c.A624G						PASS	.	T		1514,2892	479.2+/-358.4	276,962,965	86.0	84.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	624	5.5	1.0	7	dbSNP_107	85	2966,5632	460.2+/-365.1	518,1930,1851	no	coding-synonymous	FAM126A	NM_032581.3		794,2892,2816	CC,CT,TT		34.4964,34.3622,34.4509		208/522	23015831	4480,8524	2203	4299	6502	SO:0001819	synonymous_variant	84668	exon7			TTACCTTGAACAA	BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"""down regulated by Ctnnb1, a"""	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.624A>G	7.37:g.23015831T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Silent	SNP	ENST00000432176.2	37	CCDS5377.1	823	0.3768315018315018	154	0.3130081300813008	130	0.35911602209944754	269	0.47027972027972026	270	0.3562005277044855	T	12.31	1.900832	0.33535	0.343622	0.344964	ENSG00000122591	ENST00000440481	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43653	-0.9378	3	.	.	.	-16.156	15.587	0.76491	0.0:0.0:0.0:1.0	rs3735231;rs10368120;rs17147509;rs58350469;rs3735231	.	.	.	R	260	.	.	Q	-	2	0	FAM126A	22982356	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	1.643000	0.37217	2.092000	0.63282	0.374000	0.22700	CAA	T|0.643;C|0.357	0.357	strong		0.318	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581	
KIAA1244	57221	hgsc.bcm.edu	37	6	138615148	138615148	+	Silent	SNP	G	G	A	rs203145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:138615148G>A	ENST00000251691.4	+	20	3553	c.3387G>A	c.(3385-3387)acG>acA	p.T1129T		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)		AAGATGCTACGGATAAGTTGA	0.398													G|||	650	0.129792	0.0726	0.1427	5008	,	,		22044	0.1577		0.1362	False		,,,				2504	0.1626				p.T1129T		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G3387A						PASS	.	G		316,4090	169.8+/-200.3	14,288,1901	155.0	142.0	147.0		3387	-11.1	0.3	6	dbSNP_79	147	923,7677	205.2+/-247.7	57,809,3434	no	coding-synonymous	KIAA1244	NM_020340.4		71,1097,5335	AA,AG,GG		10.7326,7.172,9.5264		1129/2178	138615148	1239,11767	2203	4300	6503	SO:0001819	synonymous_variant	57221	exon20			TGCTACGGATAAG	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.3387G>A	6.37:g.138615148G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																			G|0.898;A|0.102	0.102	strong		0.398	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
UGT2B28	54490	hgsc.bcm.edu	37	4	70160342	70160342	+	Missense_Mutation	SNP	T	T	C	rs72552704	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70160342T>C	ENST00000335568.5	+	6	1407	c.1405T>C	c.(1405-1407)Tgc>Cgc	p.C469R	UGT2B28_ENST00000511240.1_3'UTR	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	469					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						ATTTGTGATGTGCCACAAAGG	0.453													N|||	1197	0.239018	0.2511	0.2147	5008	,	,		12534	0.2034		0.2813	False		,,,				2504	0.2331				p.C469R		Atlas-SNP	.											.	UGT2B28	101	.	0			c.T1405C						PASS	.	C	,ARG/CYS	300,3818		120,60,1879	74.0	84.0	81.0		,1405	1.9	1.0	4	dbSNP_130	81	524,7924		221,82,3921	no	utr-3,missense	UGT2B28	NM_001207004.1,NM_053039.1	,180	341,142,5800	CC,CT,TT		6.2027,7.2851,6.5574	,benign	,469/530	70160342	824,11742	2059	4224	6283	SO:0001583	missense	54490	exon6			GTGATGTGCCACA	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1405T>C	4.37:g.70160342T>C	ENSP00000334276:p.Cys469Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	111	38	0.342342	NM_053039	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	430	0.19688644688644688	110	0.22357723577235772	74	0.20441988950276244	96	0.16783216783216784	150	0.19788918205804748	-	0	-2.851034	0.00066	0.072851	0.062027	ENSG00000135226	ENST00000335568	T	0.36340	1.26	1.85	1.85	0.25348	.	0.000000	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00008	-3.1	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46020	-0.9221	10	0.02654	T	1	.	6.3969	0.21616	0.0:0.8267:0.0:0.1733	.	469	Q9BY64	UDB28_HUMAN	R	469	ENSP00000334276:C469R	ENSP00000334276:C469R	C	+	1	0	UGT2B28	70194931	0.997000	0.39634	0.975000	0.42487	0.016000	0.09150	0.435000	0.21510	0.124000	0.18369	-1.160000	0.01791	TGC	T|0.865;C|0.135	0.135	strong		0.453	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
OR5L2	26338	hgsc.bcm.edu	37	11	55595116	55595116	+	Missense_Mutation	SNP	G	G	C	rs75822385|rs35214936|rs386753701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	272	0	0		WXS	Illumina HiSeq	Phase_I	243	112	0.460905	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	
PALM	5064	hgsc.bcm.edu	37	19	731144	731144	+	Missense_Mutation	SNP	A	A	G	rs1050457	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:731144A>G	ENST00000338448.5	+	5	365	c.319A>G	c.(319-321)Act>Gct	p.T107A	PALM_ENST00000264560.7_Missense_Mutation_p.T107A|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	107			T -> A (in dbSNP:rs1050457). {ECO:0000269|PubMed:9615234}.		cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		CGCCCCAGCCACTGCCAAGGA	0.657													G|||	2736	0.546326	0.7315	0.4942	5008	,	,		13926	0.5446		0.4394	False		,,,				2504	0.4448				p.T107A		Atlas-SNP	.											.	PALM	26	.	0			c.A319G						PASS	.	G	ALA/THR,ALA/THR	2971,1427		1013,945,241	24.0	26.0	25.0		319,319	-0.3	0.0	19	dbSNP_86	25	3856,4724		869,2118,1303	yes	missense,missense	PALM	NM_001040134.1,NM_002579.2	58,58	1882,3063,1544	GG,GA,AA		44.9417,32.4466,47.3956	benign,benign	107/344,107/388	731144	6827,6151	2199	4290	6489	SO:0001583	missense	5064	exon5			CCAGCCACTGCCA	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.319A>G	19.37:g.731144A>G	ENSP00000341911:p.Thr107Ala	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	117	48	0.410256	NM_002579	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Missense_Mutation	SNP	ENST00000338448.5	37	CCDS32857.1	1144	0.5238095238095238	325	0.6605691056910569	186	0.5138121546961326	305	0.5332167832167832	328	0.43271767810026385	G	0.174	-1.068560	0.01934	0.675534	0.449417	ENSG00000099864	ENST00000338448;ENST00000264560	T;T	0.15256	2.44;2.44	4.06	-0.33	0.12683	.	1.296050	0.05908	N	0.631180	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.13407	0.001;0.001;0.009	T	0.40327	-0.9569	9	0.02654	T	1	-0.7764	4.8321	0.13445	0.6145:0.1804:0.2051:0.0	rs1050457;rs3190775;rs1050457	107;107;107	B7Z649;O75781-2;O75781	.;.;PALM_HUMAN	A	107	ENSP00000341911:T107A;ENSP00000264560:T107A	ENSP00000264560:T107A	T	+	1	0	PALM	682144	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.358000	0.01085	-0.100000	0.12241	-0.282000	0.10007	ACT	A|0.468;G|0.532	0.532	strong		0.657	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579	
OR10H3	26532	hgsc.bcm.edu	37	19	15852544	15852544	+	Silent	SNP	C	C	T	rs11670326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15852544C>T	ENST00000305892.1	+	1	342	c.342C>T	c.(340-342)ttC>ttT	p.F114F		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	114						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						CTCACTCCTTCCTTCTCATGG	0.512													c|||	1309	0.261382	0.4327	0.2752	5008	,	,		21200	0.0119		0.3131	False		,,,				2504	0.2239				p.F114F		Atlas-SNP	.											.	OR10H3	53	.	0			c.C342T						PASS	.	C		1798,2608		373,1052,778	405.0	330.0	355.0		342	1.2	0.9	19	dbSNP_120	355	2470,6130		378,1714,2208	no	coding-synonymous	OR10H3	NM_013938.1		751,2766,2986	TT,TC,CC		28.7209,40.808,32.8156		114/317	15852544	4268,8738	2203	4300	6503	SO:0001819	synonymous_variant	26532	exon1			CTCCTTCCTTCTC		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.342C>T	19.37:g.15852544C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	205	94	0.458537	NM_013938	Q2HIZ3|Q6IFQ0	Silent	SNP	ENST00000305892.1	37	CCDS12334.1																																																																																			C|0.700;T|0.300	0.300	strong		0.512	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
MOK	5891	hgsc.bcm.edu	37	14	102729881	102729881	+	Splice_Site	SNP	A	A	G	rs56377169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:102729881A>G	ENST00000361847.2	-	4	515		c.e4+1		MOK_ENST00000193029.6_Splice_Site|MOK_ENST00000522874.1_Splice_Site|MOK_ENST00000524214.1_Splice_Site	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase						protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										TATTCTACGTACCTCGTATTA	0.318													A|||	278	0.0555112	0.0166	0.049	5008	,	,		18341	0.003		0.0785	False		,,,				2504	0.1431				.		Atlas-SNP	.											.	.	.	.	0			c.283+2T>C						PASS	.	A		121,4281	87.3+/-125.9	1,119,2081	108.0	109.0	108.0			5.8	1.0	14	dbSNP_129	108	613,7987	157.7+/-211.4	17,579,3704	yes	splice-5	MOK	NM_014226.1		18,698,5785	GG,GA,AA		7.1279,2.7488,5.6453			102729881	734,12268	2201	4300	6501	SO:0001630	splice_region_variant	5891	exon5			CTACGTACCTCGT	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.283+1T>C	14.37:g.102729881A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Splice_Site	SNP	ENST00000361847.2	37	CCDS9971.1	80	0.03663003663003663	10	0.02032520325203252	20	0.055248618784530384	2	0.0034965034965034965	48	0.0633245382585752	A	19.54	3.847364	0.71603	0.027488	0.071279	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3848	0.66938	1.0:0.0:0.0:0.0	rs56377169	.	.	.	.	-1	.	.	.	-	.	.	RAGE	101799634	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	7.256000	0.78350	2.209000	0.71365	0.533000	0.62120	.	A|0.954;G|0.046	0.046	strong		0.318	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		Intron
MAT1A	4143	hgsc.bcm.edu	37	10	82033594	82033594	+	Silent	SNP	G	G	A	rs2993763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:82033594G>A	ENST00000372213.3	-	9	1391	c.1131C>T	c.(1129-1131)taC>taT	p.Y377Y	MAT1A_ENST00000485270.1_5'UTR	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	377					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)	CGAAATGGCCGTAGCATGCTG	0.552													G|||	2939	0.586861	0.7874	0.5187	5008	,	,		17763	0.4861		0.4245	False		,,,				2504	0.635				p.Y377Y		Atlas-SNP	.											.	MAT1A	52	.	0			c.C1131T						PASS	.	G		3186,1220	707.5+/-407.5	1155,876,172	189.0	176.0	180.0		1131	-8.9	0.5	10	dbSNP_101	180	3810,4790	539.6+/-383.6	817,2176,1307	no	coding-synonymous	MAT1A	NM_000429.2		1972,3052,1479	AA,AG,GG		44.3023,27.6895,46.2094		377/396	82033594	6996,6010	2203	4300	6503	SO:0001819	synonymous_variant	4143	exon9			ATGGCCGTAGCAT		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.1131C>T	10.37:g.82033594G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	188	99	0.526596	NM_000429	D3DWD5|Q5QP09	Silent	SNP	ENST00000372213.3	37	CCDS7365.1																																																																																			G|0.458;A|0.542	0.542	strong		0.552	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
DIS3L	115752	hgsc.bcm.edu	37	15	66612965	66612965	+	Silent	SNP	T	T	C	rs17851970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:66612965T>C	ENST00000319212.4	+	9	1271	c.1221T>C	c.(1219-1221)aaT>aaC	p.N407N	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Silent_p.N324N|DIS3L_ENST00000441424.2_Missense_Mutation_p.W217R	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	407					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						TGTATCCAAATGGACATTTTG	0.443													T|||	941	0.187899	0.0393	0.1686	5008	,	,		19029	0.1855		0.2614	False		,,,				2504	0.3292				p.N407N		Atlas-SNP	.											.	DIS3L	175	.	0			c.T1221C						PASS	.	T	,	353,4049	185.3+/-212.5	16,321,1864	163.0	150.0	155.0		1221,972	-4.5	0.8	15	dbSNP_123	155	2308,6290	387.7+/-342.3	306,1696,2297	no	coding-synonymous,coding-synonymous	DIS3L	NM_001143688.1,NM_133375.3	,	322,2017,4161	CC,CT,TT		26.8435,8.0191,20.4692	,	407/1055,324/972	66612965	2661,10339	2201	4299	6500	SO:0001819	synonymous_variant	115752	exon9			TCCAAATGGACAT		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.1221T>C	15.37:g.66612965T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	171	81	0.473684	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	37	CCDS45286.1	367	0.16804029304029305	17	0.034552845528455285	80	0.22099447513812154	76	0.13286713286713286	194	0.2559366754617414	T	14.64	2.594292	0.46214	0.080191	0.268435	ENSG00000166938	ENST00000441424	T	0.54279	0.58	5.11	-4.54	0.03452	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40347	P	0.020901999999999976	.	.	.	.	.	.	T	0.26189	-1.0110	5	0.52906	T	0.07	-0.1593	8.8639	0.35274	0.1103:0.4874:0.0:0.4023	rs17851970;rs56437794;rs17851970	.	.	.	R	217	ENSP00000388980:W217R	ENSP00000388980:W217R	W	+	1	0	DIS3L	64400019	0.992000	0.36948	0.815000	0.32552	0.995000	0.86356	0.232000	0.17891	-0.986000	0.03498	0.459000	0.35465	TGG	T|0.806;C|0.194	0.194	strong		0.443	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
HAUS6	54801	hgsc.bcm.edu	37	9	19076673	19076673	+	Silent	SNP	G	G	C	rs13286328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:19076673G>C	ENST00000380502.3	-	11	1688	c.1221C>G	c.(1219-1221)ccC>ccG	p.P407P	HAUS6_ENST00000380496.1_Silent_p.P271P|RNU6-264P_ENST00000517134.1_RNA	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	407					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						CAAACGAAAGGGGAGACATTG	0.333													G|||	1808	0.361022	0.2163	0.4049	5008	,	,		16282	0.3681		0.4493	False		,,,				2504	0.4274				p.P407P		Atlas-SNP	.											.	HAUS6	66	.	0			c.C1221G						PASS	.	G		1053,3353	380.6+/-323.8	139,775,1289	81.0	76.0	78.0		1221	-6.5	0.6	9	dbSNP_121	78	3905,4695	541.0+/-383.9	879,2147,1274	no	coding-synonymous	HAUS6	NM_017645.3		1018,2922,2563	CC,CG,GG		45.407,23.8992,38.1209		407/956	19076673	4958,8048	2203	4300	6503	SO:0001819	synonymous_variant	54801	exon11			CGAAAGGGGAGAC	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.1221C>G	9.37:g.19076673G>C		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	242	108	0.446281	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			G|0.633;C|0.367	0.367	strong		0.333	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
GPSM1	26086	hgsc.bcm.edu	37	9	139235415	139235415	+	Missense_Mutation	SNP	C	C	T	rs60980157	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139235415C>T	ENST00000440944.1	+	9	1392	c.1172C>T	c.(1171-1173)tCa>tTa	p.S391L	GPSM1_ENST00000392945.3_Missense_Mutation_p.S391L	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	391	Interaction with STK11/LKB1. {ECO:0000250}.|Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		CCGGCAGCCTCAGAGAAGCCT	0.697													C|||	965	0.192692	0.2239	0.2795	5008	,	,		14069	0.0476		0.2406	False		,,,				2504	0.1892				p.S391L		Atlas-SNP	.											.	GPSM1	50	.	0			c.C1172T						PASS	.	C	LEU/SER,LEU/SER	940,3334		99,742,1296	10.0	12.0	11.0		1172,1172	1.9	0.0	9	dbSNP_129	11	1981,6465		250,1481,2492	yes	missense,missense	GPSM1	NM_001145638.1,NM_015597.4	145,145	349,2223,3788	TT,TC,CC		23.4549,21.9934,22.9638	benign,benign	391/676,391/458	139235415	2921,9799	2137	4223	6360	SO:0001583	missense	26086	exon9			CAGCCTCAGAGAA	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1172C>T	9.37:g.139235415C>T	ENSP00000392828:p.Ser391Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Missense_Mutation	SNP	ENST00000440944.1	37	CCDS48055.1	423	0.1936813186813187	124	0.25203252032520324	82	0.2265193370165746	40	0.06993006993006994	177	0.23350923482849603	C	10.47	1.359825	0.24598	0.219934	0.234549	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	D;D;D	0.90788	-2.68;-2.73;-2.73	3.91	1.93	0.25924	.	0.534882	0.18457	N	0.140643	T	0.00073	0.0002	L	0.38175	1.15	0.80722	P	0.0	B;B	0.25609	0.025;0.13	B;B	0.29077	0.024;0.098	T	0.09552	-1.0669	9	0.11182	T	0.66	-9.4294	3.261	0.06849	0.0:0.5347:0.2683:0.1969	rs60980157;rs61731951	391;391	Q86YR5;Q86YR5-3	GPSM1_HUMAN;.	L	391;391;368	ENSP00000376674:S391L;ENSP00000392828:S391L;ENSP00000346797:S368L	ENSP00000346797:S368L	S	+	2	0	GPSM1	138355236	0.000000	0.05858	0.032000	0.17829	0.378000	0.30076	-0.005000	0.12855	2.028000	0.59812	0.462000	0.41574	TCA	C|0.803;T|0.197	0.197	strong		0.697	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
ZNF99	7652	hgsc.bcm.edu	37	19	22941191	22941191	+	Missense_Mutation	SNP	T	T	A	rs11667397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:22941191T>A	ENST00000596209.1	-	4	1610	c.1520A>T	c.(1519-1521)aAa>aTa	p.K507I	ZNF99_ENST00000397104.3_Missense_Mutation_p.K416I	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	507					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTGCAAGGTTTCTCTTCCAT	0.348													T|||	749	0.149561	0.118	0.1931	5008	,	,		19973	0.1716		0.1421	False		,,,				2504	0.1462				p.K507I		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1520T						PASS	.	T	ILE/LYS	504,3640		26,452,1594	43.0	45.0	44.0		1247	-0.1	0.0	19	dbSNP_120	44	1372,7068		93,1186,2941	no	missense	ZNF99	NM_001080409.2	102	119,1638,4535	AA,AT,TT		16.2559,12.1622,14.9078	probably-damaging	416/912	22941191	1876,10708	2072	4220	6292	SO:0001583	missense	7652	exon4			CAAGGTTTCTCTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1520A>T	19.37:g.22941191T>A	ENSP00000472969:p.Lys507Ile	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	344	0.1575091575091575	62	0.12601626016260162	65	0.17955801104972377	103	0.18006993006993008	114	0.1503957783641161	-	11.30	1.596585	0.28445	0.121622	0.162559	ENSG00000213973	ENST00000397104	T	0.33654	1.4	1.16	-0.143	0.13444	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00144	0.0004	H	0.94734	3.575	0.39932	P	0.025704999999999978	P	0.45902	0.868	P	0.46452	0.517	T	0.04115	-1.0976	8	0.87932	D	0	.	5.0822	0.14663	0.0:0.1911:0.0:0.8089	rs11667397;rs35159026	416	A8MXY4	ZNF99_HUMAN	I	416	ENSP00000380293:K416I	ENSP00000380293:K416I	K	-	2	0	ZNF99	22733031	0.001000	0.12720	0.004000	0.12327	0.075000	0.17131	-0.278000	0.08490	-0.345000	0.08325	0.163000	0.16589	AAA	T|0.834;A|0.166	0.166	strong		0.348	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ACPT	93650	hgsc.bcm.edu	37	19	51297825	51297825	+	Missense_Mutation	SNP	G	G	A	rs55716643|rs386810263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51297825G>A	ENST00000270593.1	+	9	973	c.973G>A	c.(973-975)Gcc>Acc	p.A325T	CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Missense_Mutation_p.A232T	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	325						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GGGGAATCCCGCCAAAGATGG	0.617													g|||	1652	0.329872	0.1309	0.2161	5008	,	,		17338	0.6538		0.3012	False		,,,				2504	0.3753				p.A325T		Atlas-SNP	.											.	ACPT	43	.	0			c.G973A						PASS	.	G	THR/ALA	673,3733	271.6+/-270.3	44,585,1574	40.0	39.0	39.0		973	1.7	0.0	19	dbSNP_129	39	2385,6215	365.6+/-334.0	349,1687,2264	yes	missense	ACPT	NM_033068.2	58	393,2272,3838	AA,AG,GG		27.7326,15.2746,23.5122	benign	325/427	51297825	3058,9948	2203	4300	6503	SO:0001583	missense	93650	exon9			AATCCCGCCAAAG	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.973G>A	19.37:g.51297825G>A	ENSP00000270593:p.Ala325Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	37	CCDS12802.1	641	0.2934981684981685	50	0.1016260162601626	71	0.19613259668508287	330	0.5769230769230769	190	0.25065963060686014	g	6.161	0.397948	0.11696	0.152746	0.277326	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.76448	2.98;-1.02	3.9	1.74	0.24563	.	0.642945	0.14811	N	0.297051	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.14805	0.011	B	0.04013	0.001	T	0.45512	-0.9256	9	0.28530	T	0.3	-10.0341	4.3799	0.11288	0.2057:0.1884:0.6059:0.0	rs55716643;rs60842760	325	Q9BZG2	PPAT_HUMAN	T	325;232	ENSP00000270593:A325T;ENSP00000270594:A232T	ENSP00000270593:A325T	A	+	1	0	ACPT	55989637	0.001000	0.12720	0.009000	0.14445	0.000000	0.00434	0.419000	0.21247	0.468000	0.27243	-0.931000	0.02705	GCC	G|0.751;A|0.249	0.249	strong		0.617	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	
RNF213	57674	hgsc.bcm.edu	37	17	78293189	78293189	+	Intron	SNP	A	A	T	rs55996424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78293189A>T	ENST00000582970.1	+	17	3167				RNF213_ENST00000456466.1_Intron|RNF213_ENST00000319921.4_Missense_Mutation_p.K1034M|CTD-2047H16.2_ENST00000576808.1_RNA|RNF213_ENST00000508628.2_Intron	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213						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)			AGGGCTATGAAGCACCCGCTG	0.587													a|||	1651	0.329673	0.2663	0.3588	5008	,	,		19655	0.6121		0.1451	False		,,,				2504	0.2935				p.K1034M		Atlas-SNP	.											.	RNF213	766	.	0			c.A3101T						PASS	.		,MET/LYS	1071,3335	388.6+/-327.0	135,801,1267	88.0	77.0	81.0		,3101	1.4	0.0	17	dbSNP_129	81	1393,7207	269.6+/-288.5	104,1185,3011	yes	intron,missense	RNF213	NM_020914.4,NM_020954.2	,95	239,1986,4278	TT,TA,AA		16.1977,24.3078,18.9451	,	,1034/1064	78293189	2464,10542	2203	4300	6503	SO:0001627	intron_variant	57674	exon17			CTATGAAGCACCC	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.3024+77A>T	17.37:g.78293189A>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_020954	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	739	0.3383699633699634	153	0.31097560975609756	123	0.3397790055248619	360	0.6293706293706294	103	0.1358839050131926	a	12.53	1.964889	0.34659	0.243078	0.161977	ENSG00000173821	ENST00000319921	.	.	.	2.43	1.35	0.21983	.	0.427242	0.19832	N	0.105078	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.52996	0.957	B	0.40375	0.327	T	0.39210	-0.9625	7	.	.	.	.	4.0068	0.09605	0.8234:0.0:0.1766:0.0	rs55996424	1034	Q9HCF4-2	.	M	1034	.	.	K	+	2	0	RNF213	75907784	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.150000	0.16263	0.381000	0.24851	0.373000	0.22412	AAG	A|0.768;T|0.232	0.232	strong		0.587	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
ZNF85	7639	hgsc.bcm.edu	37	19	21131728	21131728	+	Silent	SNP	A	A	G	rs12972502	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:21131728A>G	ENST00000328178.8	+	4	521	c.408A>G	c.(406-408)caA>caG	p.Q136Q	ZNF85_ENST00000601023.1_Silent_p.Q77Q|ZNF85_ENST00000345030.6_Silent_p.Q103Q	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	136					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						GACTTAACCAATGTCTCACAG	0.328													.|||	278	0.0555112	0.0053	0.0634	5008	,	,		17503	0.001		0.1402	False		,,,				2504	0.0869				p.Q166Q		Atlas-SNP	.											.	ZNF85	72	.	0			c.A498G						PASS	.	A		100,4306		2,96,2105	67.0	70.0	69.0		408	-2.5	0.0	19	dbSNP_121	69	1039,7561		53,933,3314	no	coding-synonymous	ZNF85	NM_003429.4		55,1029,5419	GG,GA,AA		12.0814,2.2696,8.7575		136/596	21131728	1139,11867	2203	4300	6503	SO:0001819	synonymous_variant	7639	exon5			TAACCAATGTCTC	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"""Zinc fingers, C2H2-type"", ""-"""	13160	protein-coding gene	gene with protein product		603899	"""zinc finger protein 85 (HPF4, HTF1)"""			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.408A>G	19.37:g.21131728A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_001256171	B9ZVP4|Q6NVI0	Silent	SNP	ENST00000328178.8	37	CCDS32977.1																																																																																			A|0.919;G|0.081	0.081	strong		0.328	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
CDC25C	995	hgsc.bcm.edu	37	5	137621421	137621421	+	Missense_Mutation	SNP	C	C	T	rs139145068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137621421C>T	ENST00000323760.6	-	14	1660	c.1382G>A	c.(1381-1383)cGg>cAg	p.R461Q	CDC25C_ENST00000415130.2_Missense_Mutation_p.R388Q|CDC25C_ENST00000348983.3_Missense_Mutation_p.R388Q|CDC25C_ENST00000357274.3_Missense_Mutation_p.R418Q|CDC25C_ENST00000356505.3_Missense_Mutation_p.R431Q|CDC25C_ENST00000514555.1_Missense_Mutation_p.R431Q|CDC25C_ENST00000513970.1_Missense_Mutation_p.R461Q	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	461					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)	p.R461Q(1)		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)			AATCTGCTCCCGCAGCTGCCG	0.542													C|||	7	0.00139776	0.0	0.0043	5008	,	,		18171	0.0		0.001	False		,,,				2504	0.0031				p.R461Q		Atlas-SNP	.											CDC25C,NS,carcinoma,0,1	CDC25C	37	1	1	Substitution - Missense(1)	lung(1)	c.G1382A						PASS	.	C	GLN/ARG,GLN/ARG	5,4401	8.1+/-20.4	0,5,2198	92.0	83.0	86.0		1382,1163	-0.7	0.3	5	dbSNP_134	86	41,8559	27.9+/-77.7	0,41,4259	yes	missense,missense	CDC25C	NM_001790.3,NM_022809.2	43,43	0,46,6457	TT,TC,CC		0.4767,0.1135,0.3537	benign,benign	461/474,388/401	137621421	46,12960	2203	4300	6503	SO:0001583	missense	995	exon14			TGCTCCCGCAGCT	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.1382G>A	5.37:g.137621421C>T	ENSP00000321656:p.Arg461Gln	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	142	82	0.577465	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	12.41	1.928653	0.34002	0.001135	0.004767	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555	T;T;T;T;T;T;T	0.27256	2.26;2.28;1.68;1.68;1.68;2.26;2.28	5.08	-0.722	0.11184	.	0.630192	0.14121	N	0.340066	T	0.10895	0.0266	N	0.22421	0.69	0.19575	N	0.999965	B;B;B;B	0.20261	0.043;0.024;0.03;0.014	B;B;B;B	0.10450	0.005;0.003;0.005;0.002	T	0.17776	-1.0358	10	0.38643	T	0.18	0.8534	10.1514	0.42796	0.0:0.4294:0.0:0.5706	.	478;431;388;461	G3V1P6;P30307-2;P30307-4;P30307	.;.;.;MPIP3_HUMAN	Q	461;431;418;388;388;461;478;431	ENSP00000321656:R461Q;ENSP00000348898:R431Q;ENSP00000349821:R418Q;ENSP00000345205:R388Q;ENSP00000392631:R388Q;ENSP00000424795:R461Q;ENSP00000425470:R431Q	ENSP00000321656:R461Q	R	-	2	0	CDC25C	137649320	0.009000	0.17119	0.268000	0.24571	0.929000	0.56500	-0.472000	0.06623	-0.288000	0.09051	0.655000	0.94253	CGG	C|0.997;T|0.003	0.003	strong		0.542	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254133	39254133	+	Missense_Mutation	SNP	G	G	T	rs200462175		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254133G>T	ENST00000333822.4	-	1	260	c.204C>A	c.(202-204)agC>agA	p.S68R		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	68	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						ACACACAGCAGCTGGGGCGAC	0.667																																					p.S68R		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C204A						PASS	.						6.0	9.0	8.0					17																	39254133		616	1426	2042	SO:0001583	missense	728224	exon1			ACAGCAGCTGGGG	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.204C>A	17.37:g.39254133G>T	ENSP00000328444:p.Ser68Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	12	0.196721	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	13.88	2.368333	0.42003	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01963	4.53	3.73	-3.02	0.05446	.	2.601200	0.02242	U	0.065854	T	0.05135	0.0137	M	0.89658	3.05	0.20307	N	0.999915	B	0.11235	0.004	B	0.10450	0.005	T	0.47774	-0.9091	10	0.46703	T	0.11	.	0.2646	0.00223	0.277:0.1441:0.2848:0.2941	.	68	Q9BYQ9	KRA48_HUMAN	R	68	ENSP00000328444:S68R	ENSP00000414561:S68R	S	-	3	2	KRTAP4-8	36507659	0.949000	0.32298	0.011000	0.14972	0.444000	0.32077	1.355000	0.34068	-0.877000	0.04012	0.449000	0.29647	AGC	.	.	weak		0.667	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
MYO5B	4645	hgsc.bcm.edu	37	18	47398549	47398549	+	Silent	SNP	G	G	A	rs3826579	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:47398549G>A	ENST00000285039.7	-	27	3890	c.3591C>T	c.(3589-3591)taC>taT	p.Y1197Y	MYO5B_ENST00000587895.1_5'UTR|Y_RNA_ENST00000364798.1_RNA|MYO5B_ENST00000324581.6_Silent_p.Y338Y	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	141	0	0		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	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		
IL27RA	9466	hgsc.bcm.edu	37	19	14153293	14153293	+	Missense_Mutation	SNP	T	T	C	rs35026308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14153293T>C	ENST00000263379.2	+	5	688	c.563T>C	c.(562-564)cTg>cCg	p.L188P		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	188	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						ACCATACCCCTGACCCCTGTT	0.542											OREG0025302	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	710	0.141773	0.0212	0.1311	5008	,	,		17339	0.2659		0.1968	False		,,,				2504	0.1278				p.L188P	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											IL27RA,NS,carcinoma,-1,1	IL27RA	56	1	0			c.T563C						PASS	.	T	PRO/LEU	192,4214	119.6+/-157.3	5,182,2016	113.0	119.0	117.0		563	2.5	0.0	19	dbSNP_126	117	1606,6994	297.1+/-303.3	153,1300,2847	yes	missense	IL27RA	NM_004843.2	98	158,1482,4863	CC,CT,TT		18.6744,4.3577,13.8244	probably-damaging	188/637	14153293	1798,11208	2203	4300	6503	SO:0001583	missense	9466	exon5			TACCCCTGACCCC	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.563T>C	19.37:g.14153293T>C	ENSP00000263379:p.Leu188Pro	Somatic	91	0	0	692	WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_004843	A0N0L1|O60624	Missense_Mutation	SNP	ENST00000263379.2	37	CCDS12303.1	352	0.16117216117216118	12	0.024390243902439025	51	0.1408839779005525	147	0.256993006993007	142	0.18733509234828497	T	11.67	1.708448	0.30322	0.043577	0.186744	ENSG00000104998	ENST00000263379	T	0.55413	0.52	4.69	2.52	0.30459	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.707453	0.11708	N	0.537196	T	0.00012	0.0000	L	0.32530	0.975	0.49915	P	1.7000000000000348E-4	D	0.56968	0.978	P	0.52267	0.694	T	0.08289	-1.0729	9	0.30854	T	0.27	-6.9541	7.5593	0.27843	0.3435:0.0:0.0:0.6565	rs35026308;rs62122121;rs35026308	188	Q6UWB1	I27RA_HUMAN	P	188	ENSP00000263379:L188P	ENSP00000263379:L188P	L	+	2	0	IL27RA	14014293	0.040000	0.19996	0.004000	0.12327	0.016000	0.09150	1.225000	0.32551	0.330000	0.23485	-0.333000	0.08304	CTG	T|0.853;C|0.147	0.147	strong		0.542	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	
HYKK	123688	hgsc.bcm.edu	37	15	78825917	78825917	+	Missense_Mutation	SNP	A	A	G	rs3885951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:78825917A>G	ENST00000569878.1	+	4	1027	c.1027A>G	c.(1027-1029)Aaa>Gaa	p.K343E	HYKK_ENST00000563233.1_Intron|HYKK_ENST00000388988.4_Missense_Mutation_p.K343E|HYKK_ENST00000408962.2_Intron			A2RU49	HYKK_HUMAN	hydroxylysine kinase	343						cytoplasm (GO:0005737)	hydroxylysine kinase activity (GO:0047992)										AACCGGGTGGAAACACTTACA	0.433													A|||	214	0.0427316	0.0061	0.0836	5008	,	,		19902	0.001		0.1064	False		,,,				2504	0.0409				p.K343E		Atlas-SNP	.											.	AGPHD1	22	.	0			c.A1027G						PASS	.	A	GLU/LYS,	67,3615		0,67,1774	131.0	112.0	118.0		1027,	5.8	1.0	15	dbSNP_108	118	855,7347		47,761,3293	yes	missense,intron	AGPHD1	NM_001013619.2,NM_001083612.1	56,	47,828,5067	GG,GA,AA		10.4243,1.8197,7.7583	benign,	343/374,	78825917	922,10962	1841	4101	5942	SO:0001583	missense	123688	exon5			GGGTGGAAACACT	BC132753, BC144383, BM045979	CCDS42063.1, CCDS45318.1	15q25.1	2013-06-11	2013-06-11	2013-06-11	ENSG00000188266	ENSG00000188266	2.7.1.81		34403	protein-coding gene	gene with protein product	"""5-hydroxylysine kinase"""	614681	"""aminoglycoside phosphotransferase domain containing 1"""	AGPHD1		18780872, 22241472	Standard	NM_001013619		Approved	LOC123688	uc010unc.2	A2RU49		ENST00000569878.1:c.1027A>G	15.37:g.78825917A>G	ENSP00000455459:p.Lys343Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_001013619	B7ZMA5|F8W6X5|Q6ZTN0	Missense_Mutation	SNP	ENST00000569878.1	37	CCDS42063.1	111	0.050824175824175824	2	0.0040650406504065045	30	0.08287292817679558	0	0.0	79	0.10422163588390501	A	14.62	2.590886	0.46214	0.018197	0.104243	ENSG00000188266	ENST00000388988	T	0.29655	1.56	5.85	5.85	0.93711	.	0.164381	0.53938	D	0.000058	T	0.00754	0.0025	L	0.51853	1.615	0.09310	P	1.0	B	0.12630	0.006	B	0.10450	0.005	T	0.12811	-1.0533	9	0.09338	T	0.73	-1.6435	16.2303	0.82332	1.0:0.0:0.0:0.0	rs3885951;rs17407196;rs52789359;rs59690284;rs3885951	343	A2RU49	AGPD1_HUMAN	E	343	ENSP00000373640:K343E	ENSP00000373640:K343E	K	+	1	0	AGPHD1	76612972	0.972000	0.33761	1.000000	0.80357	0.955000	0.61496	2.290000	0.43531	2.233000	0.73108	0.533000	0.62120	AAA	A|0.934;G|0.066	0.066	strong		0.433	HYKK-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435834.1	NM_001013619	
DPT	1805	hgsc.bcm.edu	37	1	168698173	168698173	+	Silent	SNP	C	C	T	rs1052591	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:168698173C>T	ENST00000367817.3	-	1	329	c.240G>A	c.(238-240)acG>acA	p.T80T		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	80	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					GGCTCTGTGGCGTGGGCATGC	0.612													c|||	1590	0.317492	0.2519	0.3141	5008	,	,		21034	0.1637		0.5129	False		,,,				2504	0.3661				p.T80T		Atlas-SNP	.											DPT,NS,carcinoma,-1,2	DPT	29	2	0			c.G240A						PASS	.	T		1438,2968	467.2+/-354.7	253,932,1018	158.0	126.0	137.0		240	-10.0	0.4	1	dbSNP_86	137	4658,3942	603.9+/-394.7	1281,2096,923	no	coding-synonymous	DPT	NM_001937.4		1534,3028,1941	TT,TC,CC		45.8372,32.6373,46.8707		80/202	168698173	6096,6910	2203	4300	6503	SO:0001819	synonymous_variant	1805	exon1			CTGTGGCGTGGGC	BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.240G>A	1.37:g.168698173C>T		Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	307	140	0.456026	NM_001937	A8K981|Q8N4R2|Q9UIX8	Silent	SNP	ENST00000367817.3	37	CCDS1275.1																																																																																			C|0.599;T|0.401	0.401	strong		0.612	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937	
OBSCN	84033	hgsc.bcm.edu	37	1	228481854	228481854	+	Splice_Site	SNP	C	C	T	rs199641194		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228481854C>T	ENST00000422127.1	+	42	11177	c.11133C>T	c.(11131-11133)gcC>gcT	p.A3711A	RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000359599.6_Splice_Site_p.A2558A|OBSCN_ENST00000570156.2_Splice_Site_p.A4140A|OBSCN_ENST00000366709.4_Splice_Site_p.A830A|OBSCN_ENST00000284548.11_Splice_Site_p.A3711A|OBSCN_ENST00000366707.4_Splice_Site_p.A830A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3711					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)				CCTCCCCAGCCATGCCTTCCA	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		23606	0.0		0.0	False		,,,				2504	0.001				p.A4140A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C12420T						PASS	.	C	,	0,3994		0,0,1997	104.0	106.0	105.0		11133,11133	1.8	1.0	1		105	3,8351		0,3,4174	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	OBSCN	NM_001098623.1,NM_052843.2	,	0,3,6171	TT,TC,CC		0.0359,0.0,0.0243	,	3711/7969,3711/6621	228481854	3,12345	1997	4177	6174	SO:0001630	splice_region_variant	84033	exon47			CCCAGCCATGCCT	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.11132-1C>T	1.37:g.228481854C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	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|0.998;T|0.002	0.002	weak		0.527	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	Silent
TRIM65	201292	hgsc.bcm.edu	37	17	73888354	73888354	+	Silent	SNP	G	G	A	rs34974290	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73888354G>A	ENST00000269383.3	-	3	803	c.738C>T	c.(736-738)ttC>ttT	p.F246F		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	246						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCACCTGCAGGAAGGTCTGCT	0.652													G|||	1025	0.204673	0.3094	0.1715	5008	,	,		17118	0.129		0.1938	False		,,,				2504	0.1759				p.F246F		Atlas-SNP	.											.	TRIM65	23	.	0			c.C738T						PASS	.	G		1339,3067	406.2+/-333.8	215,909,1079	23.0	25.0	25.0		738	3.2	1.0	17	dbSNP_126	25	1643,6957	273.1+/-290.5	147,1349,2804	no	coding-synonymous	TRIM65	NM_173547.2		362,2258,3883	AA,AG,GG		19.1047,30.3904,22.9279		246/518	73888354	2982,10024	2203	4300	6503	SO:0001819	synonymous_variant	201292	exon3			CTGCAGGAAGGTC	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.738C>T	17.37:g.73888354G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Silent	SNP	ENST00000269383.3	37	CCDS11732.1	432|432	0.1978021978021978|0.1978021978021978	147|147	0.29878048780487804|0.29878048780487804	65|65	0.17955801104972377|0.17955801104972377	81|81	0.14160839160839161|0.14160839160839161	139|139	0.18337730870712401|0.18337730870712401	G|G	1.367|1.367	-0.587037|-0.587037	0.03827|0.03827	0.303904|0.303904	0.191047|0.191047	ENSG00000141569|ENSG00000141569	ENST00000540128|ENST00000543309	.|.	.|.	.|.	4.16|4.16	3.19|3.19	0.36642|0.36642	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999842|0.9999999999999842	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.21999|0.21999	-1.0229|-1.0229	3|3	.|.	.|.	.|.	.|.	9.2634|9.2634	0.37625|0.37625	0.1794:0.0:0.8206:0.0|0.1794:0.0:0.8206:0.0	rs34974290|rs34974290	.|.	.|.	.|.	S|F	238|120	.|.	.|.	P|S	-|-	1|2	0|0	TRIM65|TRIM65	71399949|71399949	0.899000|0.899000	0.30636|0.30636	0.967000|0.967000	0.41034|0.41034	0.226000|0.226000	0.24999|0.24999	0.320000|0.320000	0.19540|0.19540	0.979000|0.979000	0.38497|0.38497	0.407000|0.407000	0.27541|0.27541	CCT|TCC	G|0.787;A|0.213	0.213	strong		0.652	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
E2F4	1874	hgsc.bcm.edu	37	16	67235672	67235672	+	IGR	SNP	C	C	T	rs33948247	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:67235672C>T	ENST00000379378.3	+	0	2096				ELMO3_ENST00000360833.1_Missense_Mutation_p.R352C|ELMO3_ENST00000477898.1_Missense_Mutation_p.R203C|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000393997.2_Missense_Mutation_p.R369C	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	75	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	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	
EML2	24139	hgsc.bcm.edu	37	19	46133251	46133251	+	Silent	SNP	C	C	T	rs7251952	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46133251C>T	ENST00000245925.3	-	7	614	c.564G>A	c.(562-564)tcG>tcA	p.S188S	EML2_ENST00000589876.1_Silent_p.S188S|EML2_ENST00000536630.1_Silent_p.S335S|EML2_ENST00000586902.1_5'UTR|EML2_ENST00000587152.1_Silent_p.S389S	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	188	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		AGTCCCACACCGAGAGCATGT	0.562													C|||	643	0.128395	0.1611	0.1282	5008	,	,		17260	0.1032		0.1074	False		,,,				2504	0.1319				p.S389S		Atlas-SNP	.											.	EML2	64	.	0			c.G1167A						PASS	.		,,	658,3748	279.6+/-274.9	61,536,1606	195.0	124.0	148.0		1167,1005,564	-8.1	0.7	19	dbSNP_116	148	1129,7471	232.5+/-266.1	78,973,3249	no	coding-synonymous,coding-synonymous,coding-synonymous	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,	139,1509,4855	TT,TC,CC		13.1279,14.9342,13.7398	,,	389/851,335/797,188/650	46133251	1787,11219	2203	4300	6503	SO:0001819	synonymous_variant	24139	exon10			CCACACCGAGAGC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.564G>A	19.37:g.46133251C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Silent	SNP	ENST00000245925.3	37	CCDS12670.1																																																																																			C|0.871;T|0.129	0.129	strong		0.562	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377029	168377029	+	lincRNA	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168377029G>A	ENST00000538528.1	-	0	590																											AAGACAGTGGGGGTCATTCCC	0.632																																					p.P102S		Atlas-SNP	.											.	.	.	.	0			c.C304T						PASS	.						8.0	8.0	8.0					6																	168377029		680	1544	2224			0	exon1			CAGTGGGGGTCAT																													6.37:g.168377029G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	217	29	0.133641	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				.	.	none		0.632	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464487	39464487	+	Missense_Mutation	SNP	G	G	C	rs2074285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	109	0	0		WXS	Illumina HiSeq	Phase_I	83	83	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	
SEC14L6	730005	hgsc.bcm.edu	37	22	30927975	30927975	+	Missense_Mutation	SNP	C	C	T	rs5749118	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:30927975C>T	ENST00000402034.2	-	6	433	c.434G>A	c.(433-435)aGg>aAg	p.R145K		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	145	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						TTTCTCCACCCTCTTCCCCAG	0.607													T|||	4409	0.880391	0.8729	0.7911	5008	,	,		19984	0.999		0.8082	False		,,,				2504	0.9059				p.R145K		Atlas-SNP	.											.	SEC14L6	6	.	0			c.G434A						PASS	.																																			SO:0001583	missense	730005	exon6			TCCACCCTCTTCC		CCDS54518.1	22q12.2	2011-05-06			ENSG00000214491	ENSG00000214491			40047	protein-coding gene	gene with protein product							Standard	NM_001193336		Approved		uc021wnu.1	B5MCN3	OTTHUMG00000151267	ENST00000402034.2:c.434G>A	22.37:g.30927975C>T	ENSP00000385695:p.Arg145Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001193336		Missense_Mutation	SNP	ENST00000402034.2	37	CCDS54518.1	1903	0.8713369963369964	424	0.8617886178861789	303	0.8370165745856354	569	0.9947552447552448	607	0.8007915567282322	.	1.798	-0.477785	0.04414	.	.	ENSG00000214491	ENST00000402034	T	0.74106	-0.81	3.21	2.16	0.27623	.	.	.	.	.	T	0.00012	0.0000	N	0.02412	-0.56	0.09310	P	0.999999999389428	.	.	.	.	.	.	T	0.35126	-0.9801	6	0.10377	T	0.69	-1.5081	6.792	0.23705	0.0:0.3043:0.0:0.6957	rs5749118;rs6518699;rs52797912;rs59166374;rs5749118	.	.	.	K	145	ENSP00000385695:R145K	ENSP00000385695:R145K	R	-	2	0	SEC14L6	29257975	0.954000	0.32549	0.870000	0.34147	0.172000	0.22775	1.446000	0.35090	0.019000	0.15079	-0.665000	0.03846	AGG	C|0.135;T|0.865	0.865	strong		0.607	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
ECD	11319	hgsc.bcm.edu	37	10	74890603	74890603	+	IGR	SNP	C	C	T	rs141533992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:74890603C>T	ENST00000372979.4	-	0	3069				NUDT13_ENST00000372997.3_3'UTR|NUDT13_ENST00000349051.5_Missense_Mutation_p.S245F|NUDT13_ENST00000357321.4_Missense_Mutation_p.S334F|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000544879.1_Missense_Mutation_p.S208F|NUDT13_ENST00000537969.1_Missense_Mutation_p.S137F	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)						cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					TTAGCCATCTCCCACCAACTG	0.517													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17492	0.0		0.002	False		,,,				2504	0.0				p.S334F		Atlas-SNP	.											.	NUDT13	16	.	0			c.C1001T						PASS	.	C	PHE/SER	3,4403	6.2+/-15.9	0,3,2200	78.0	71.0	73.0		1001	5.4	1.0	10	dbSNP_134	73	8,8592	6.4+/-24.3	0,8,4292	yes	missense	NUDT13	NM_015901.4	155	0,11,6492	TT,TC,CC		0.093,0.0681,0.0846	possibly-damaging	334/353	74890603	11,12995	2203	4300	6503	SO:0001628	intergenic_variant	25961	exon9			CCATCTCCCACCA	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905			10.37:g.74890603C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_015901	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.66	2.898957	0.52227	6.81E-4	9.3E-4	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000544879;ENST00000537969	T;T;T;T	0.42131	0.98;1.49;0.98;0.98	5.4	5.4	0.78164	NUDIX hydrolase domain (1);NUDIX hydrolase domain-like (1);	0.046479	0.85682	D	0.000000	T	0.27169	0.0666	N	0.08118	0	0.80722	D	1	B;P	0.44309	0.09;0.832	B;B	0.37387	0.058;0.248	T	0.29336	-1.0015	10	0.87932	D	0	-6.5638	19.1185	0.93351	0.0:1.0:0.0:0.0	.	245;334	Q86X67-2;Q86X67	.;NUD13_HUMAN	F	334;245;208;137	ENSP00000349874:S334F;ENSP00000335326:S245F;ENSP00000440760:S208F;ENSP00000438223:S137F	ENSP00000335326:S245F	S	+	2	0	NUDT13	74560609	1.000000	0.71417	1.000000	0.80357	0.250000	0.25880	6.910000	0.75741	2.692000	0.91855	0.650000	0.86243	TCC	C|0.999;T|0.001	0.001	strong		0.517	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
C1orf127	148345	hgsc.bcm.edu	37	1	11008695	11008695	+	Silent	SNP	T	T	C	rs17036032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11008695T>C	ENST00000377008.4	-	11	1442	c.996A>G	c.(994-996)ccA>ccG	p.P332P	C1orf127_ENST00000377004.4_Silent_p.P499P			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	332	Pro-rich.									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)		TTGGCAAGACTGGACGTGGCC	0.667													T|||	1061	0.211861	0.0522	0.2565	5008	,	,		16937	0.2321		0.1421	False		,,,				2504	0.4468				p.P499P		Atlas-SNP	.											.	C1orf127	134	.	0			c.A1497G						PASS	.	T		272,4134	151.4+/-185.3	5,262,1936	51.0	51.0	51.0		1497	-5.4	0.0	1	dbSNP_123	51	1164,7436	235.8+/-268.3	88,988,3224	no	coding-synonymous	C1orf127	NM_001170754.1		93,1250,5160	CC,CT,TT		13.5349,6.1734,11.0411		499/824	11008695	1436,11570	2203	4300	6503	SO:0001819	synonymous_variant	148345	exon12			CAAGACTGGACGT	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.996A>G	1.37:g.11008695T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		377	0.17261904761904762	33	0.06707317073170732	88	0.2430939226519337	142	0.24825174825174826	114	0.1503957783641161	T	6.065	0.380333	0.11466	0.061734	0.135349	ENSG00000175262	ENST00000418570;ENST00000520253	.	.	.	4.51	-5.45	0.02616	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49687	P	1.8899999999999473E-4	.	.	.	.	.	.	T	0.41034	-0.9531	3	.	.	.	-0.7605	0.2364	0.00186	0.2766:0.1805:0.2818:0.2611	rs17036032;rs17036032	.	.	.	R	334;451	.	.	Q	-	2	0	C1orf127	10931282	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.740000	0.01839	-0.824000	0.04295	0.402000	0.26972	CAG	T|0.858;C|0.142	0.142	strong		0.667	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
SP140L	93349	hgsc.bcm.edu	37	2	231256812	231256812	+	Silent	SNP	A	A	G	rs7559665|rs386656123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	149	0	0		WXS	Illumina HiSeq	Phase_I	150	150	1	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	
SUSD5	26032	hgsc.bcm.edu	37	3	33195309	33195309	+	Missense_Mutation	SNP	A	A	G	rs61743461	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:33195309A>G	ENST00000309558.3	-	5	1232	c.815T>C	c.(814-816)tTg>tCg	p.L272S		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	272				L -> S (in Ref. 1; BAA25453). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						AGCACCAGGCAAGCCTGTGGT	0.562													A|||	1006	0.200879	0.2239	0.1902	5008	,	,		19136	0.1925		0.1551	False		,,,				2504	0.2331				p.L272S		Atlas-SNP	.											.	SUSD5	53	.	0			c.T815C						PASS	.	A	SER/LEU	755,3049		80,595,1227	51.0	51.0	51.0		815	-3.0	0.0	3	dbSNP_129	51	1322,6924		105,1112,2906	yes	missense	SUSD5	NM_015551.1	145	185,1707,4133	GG,GA,AA		16.032,19.8475,17.2365	benign	272/630	33195309	2077,9973	1902	4123	6025	SO:0001583	missense	26032	exon5			CCAGGCAAGCCTG	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.815T>C	3.37:g.33195309A>G	ENSP00000308727:p.Leu272Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_015551		Missense_Mutation	SNP	ENST00000309558.3	37	CCDS46787.1	415|415	0.190018315018315|0.190018315018315	117|117	0.23780487804878048|0.23780487804878048	67|67	0.1850828729281768|0.1850828729281768	117|117	0.20454545454545456|0.20454545454545456	114|114	0.1503957783641161|0.1503957783641161	A|A	5.226|5.226	0.227208|0.227208	0.09916|0.09916	0.198475|0.198475	0.16032|0.16032	ENSG00000173705|ENSG00000173705	ENST00000412539|ENST00000309558	.|T	.|0.06687	.|3.27	6.02|6.02	-2.95|-2.95	0.05564|0.05564	.|.	.|1.433320	.|0.04002	.|N	.|0.296634	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.24721	.|0.11	.|B	.|0.16722	.|0.016	T|T	0.43814|0.43814	-0.9368|-0.9368	4|9	.|0.19147	.|T	.|0.46	-1.7866|-1.7866	6.6702|6.6702	0.23064|0.23064	0.3956:0.2344:0.3699:0.0|0.3956:0.2344:0.3699:0.0	.|.	.|272	.|O60279	.|SUSD5_HUMAN	R|S	208|272	.|ENSP00000308727:L272S	.|ENSP00000308727:L272S	C|L	-|-	1|2	0|0	SUSD5|SUSD5	33170313|33170313	0.073000|0.073000	0.21202|0.21202	0.008000|0.008000	0.14137|0.14137	0.110000|0.110000	0.19582|0.19582	-0.086000|-0.086000	0.11233|0.11233	-0.713000|-0.713000	0.04981|0.04981	0.533000|0.533000	0.62120|0.62120	TGC|TTG	A|0.820;G|0.180	0.180	strong		0.562	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054	
MYO1C	4641	hgsc.bcm.edu	37	17	1377943	1377943	+	Silent	SNP	A	A	G	rs2286873	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1377943A>G	ENST00000575158.1	-	17	1829	c.1653T>C	c.(1651-1653)ttT>ttC	p.F551F	MYO1C_ENST00000361007.2_Silent_p.F551F|MYO1C_ENST00000545534.2_Silent_p.F562F|MYO1C_ENST00000359786.5_Silent_p.F586F|MYO1C_ENST00000438665.2_Silent_p.F567F			Q12965	MYO1E_HUMAN	myosin IC	546	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CGCTCCGGTCAAAGCACTGGC	0.637													G|||	2091	0.417532	0.7126	0.3977	5008	,	,		14329	0.2093		0.3847	False		,,,				2504	0.2812				p.F586F		Atlas-SNP	.											.	MYO1C	57	.	0			c.T1758C						PASS	.	G	,,	2888,1518	480.8+/-358.9	956,976,271	108.0	109.0	108.0		1758,1701,1653	-2.0	1.0	17	dbSNP_100	108	2983,5617	666.3+/-402.4	522,1939,1839	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	1478,2915,2110	GG,GA,AA		34.686,34.453,45.1407	,,	586/1064,567/1045,551/1029	1377943	5871,7135	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon17			CCGGTCAAAGCAC	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"""Myosins / Myosin superfamily : Class I"""	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.1653T>C	17.37:g.1377943A>G		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			A|0.554;G|0.446	0.446	strong		0.637	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
PREPL	9581	hgsc.bcm.edu	37	2	44566479	44566479	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:44566479G>T	ENST00000409936.1	-	7	1213	c.776C>A	c.(775-777)aCa>aAa	p.T259K	PREPL_ENST00000378520.3_Missense_Mutation_p.T259K|PREPL_ENST00000260648.6_Missense_Mutation_p.T259K|PREPL_ENST00000541738.1_Missense_Mutation_p.T170K|PREPL_ENST00000409411.1_Missense_Mutation_p.T170K|PREPL_ENST00000378511.3_Missense_Mutation_p.T259K|PREPL_ENST00000410081.1_Missense_Mutation_p.T259K|PREPL_ENST00000409957.1_Missense_Mutation_p.T170K|PREPL_ENST00000409272.1_Missense_Mutation_p.T259K	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	259						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)				ACTGTCTTTTGTAAGATAAAG	0.408																																					p.T259K		Atlas-SNP	.											.	PREPL	69	.	0			c.C776A						PASS	.						60.0	58.0	59.0					2																	44566479		2203	4300	6503	SO:0001583	missense	9581	exon7			TCTTTTGTAAGAT	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.776C>A	2.37:g.44566479G>T	ENSP00000386543:p.Thr259Lys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475698	0.84640	.	.	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	T;T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.37	5.37	0.77165	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.055903	0.64402	D	0.000001	T	0.66336	0.2779	L	0.55481	1.735	0.52501	D	0.999955	D;D;D	0.89917	0.996;1.0;0.999	D;D;D	0.77557	0.99;0.983;0.984	T	0.68603	-0.5365	10	0.87932	D	0	-16.2408	19.0981	0.93263	0.0:0.0:1.0:0.0	.	259;259;259	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	K	170;170;170;259;259;259;259;259;259	ENSP00000439626:T170K;ENSP00000387095:T170K;ENSP00000387241:T170K;ENSP00000386543:T259K;ENSP00000260648:T259K;ENSP00000386909:T259K;ENSP00000386509:T259K;ENSP00000367781:T259K;ENSP00000367772:T259K	ENSP00000260648:T259K	T	-	2	0	PREPL	44419983	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.733000	0.74796	2.491000	0.84063	0.585000	0.79938	ACA	.	.	none		0.408	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036	
ADAM21	8747	hgsc.bcm.edu	37	14	70924693	70924693	+	Silent	SNP	T	T	C	rs45480894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:70924693T>C	ENST00000603540.1	+	2	735	c.477T>C	c.(475-477)taT>taC	p.Y159Y	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.Y159Y	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	141	0	0		WXS	Illumina HiSeq	Phase_I	85	24	0.282353	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		
PCNT	5116	hgsc.bcm.edu	37	21	47851753	47851753	+	Missense_Mutation	SNP	A	A	G	rs2073376	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47851753A>G	ENST00000359568.5	+	38	8482	c.8375A>G	c.(8374-8376)cAg>cGg	p.Q2792R	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2792			Q -> R (in dbSNP:rs2073376).		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)					GCTCTGCTGCAGAAGCTGAAG	0.617													G|||	3355	0.669928	0.8306	0.5447	5008	,	,		20201	0.619		0.6511	False		,,,				2504	0.6135				p.Q2792R		Atlas-SNP	.											.	PCNT	283	.	0			c.A8375G						PASS	.	G	ARG/GLN	3491,915	351.1+/-311.1	1379,733,91	45.0	46.0	46.0		8375	2.3	0.3	21	dbSNP_96	46	5507,3093	471.5+/-368.1	1765,1977,558	yes	missense	PCNT	NM_006031.5	43	3144,2710,649	GG,GA,AA		35.9651,20.7671,30.8165	benign	2792/3337	47851753	8998,4008	2203	4300	6503	SO:0001583	missense	5116	exon38			TGCTGCAGAAGCT	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.8375A>G	21.37:g.47851753A>G	ENSP00000352572:p.Gln2792Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	1478	0.6767399267399268	401	0.8150406504065041	203	0.5607734806629834	374	0.6538461538461539	500	0.6596306068601583	G	0.007	-1.982483	0.00448	0.792329	0.640349	ENSG00000160299	ENST00000359568	T	0.01335	5.0	5.32	2.32	0.28847	.	0.284430	0.19017	N	0.124923	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	0.01281	0.0;0.0	T	0.04128	-1.0975	9	0.08837	T	0.75	.	8.7059	0.34354	0.3348:0.0:0.6652:0.0	rs2073376;rs17299481;rs58436318;rs2073376	2674;2792	O95613-2;O95613	.;PCNT_HUMAN	R	2792	ENSP00000352572:Q2792R	ENSP00000352572:Q2792R	Q	+	2	0	PCNT	46676181	0.862000	0.29867	0.314000	0.25224	0.030000	0.12068	0.246000	0.18160	0.020000	0.15106	-0.119000	0.15052	CAG	A|0.303;G|0.697	0.697	strong		0.617	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
NSL1	25936	hgsc.bcm.edu	37	1	212965095	212965095	+	Missense_Mutation	SNP	G	G	A	rs17856201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:212965095G>A	ENST00000366977.3	-	1	29	c.11C>T	c.(10-12)tCt>tTt	p.S4F	NSL1_ENST00000473995.1_5'Flank|TATDN3_ENST00000366973.4_5'Flank|TATDN3_ENST00000526997.1_5'Flank|NSL1_ENST00000366976.1_Missense_Mutation_p.S4F|NSL1_ENST00000366975.6_Missense_Mutation_p.S4F|NSL1_ENST00000422588.2_Missense_Mutation_p.S4F|TATDN3_ENST00000532324.1_5'Flank|TATDN3_ENST00000366974.4_5'Flank|TATDN3_ENST00000531963.1_5'Flank|NSL1_ENST00000366978.1_5'Flank|TATDN3_ENST00000526641.1_5'Flank|TATDN3_ENST00000530441.1_5'Flank	NM_015471.3	NP_056286.3	Q96IY1	NSL1_HUMAN	NSL1, MIS12 kinetochore complex component	4			S -> F (in dbSNP:rs17856201). {ECO:0000269|PubMed:15489334}.		chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)		CAACTCAGGAGACCCCGCCAT	0.617													G|||	938	0.1873	0.2943	0.1081	5008	,	,		17447	0.1429		0.1441	False		,,,				2504	0.1892				p.S4F		Atlas-SNP	.											.	NSL1	24	.	0			c.C11T						PASS	.	G	PHE/SER,PHE/SER	1177,3229		168,841,1194	14.0	18.0	17.0		11,11	-0.6	0.0	1	dbSNP_123	17	1158,7426		71,1016,3205	yes	missense,missense	NSL1	NM_001042549.1,NM_015471.3	155,155	239,1857,4399	AA,AG,GG		13.4902,26.7136,17.9754	possibly-damaging,possibly-damaging	4/214,4/282	212965095	2335,10655	2203	4292	6495	SO:0001583	missense	25936	exon1			TCAGGAGACCCCG	AF255793	CCDS1509.1, CCDS73025.1	1q41	2013-07-03	2013-07-03	2006-11-07	ENSG00000117697	ENSG00000117697			24548	protein-coding gene	gene with protein product		609174	"""chromosome 1 open reading frame 48"", ""NSL1, MIND kinetochore complex component, homolog (S. cerevisiae)"""	C1orf48		20819937	Standard	NM_015471		Approved	DC8, DKFZP566O1646, MIS14	uc001hjn.3	Q96IY1	OTTHUMG00000036806	ENST00000366977.3:c.11C>T	1.37:g.212965095G>A	ENSP00000355944:p.Ser4Phe	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_015471	E7ETD5|Q5SY75|Q9H2M5|Q9NRN8|Q9Y415	Missense_Mutation	SNP	ENST00000366977.3	37	CCDS1509.1	398	0.18223443223443223	163	0.3313008130081301	46	0.1270718232044199	80	0.13986013986013987	109	0.1437994722955145	G	11.77	1.737654	0.30774	0.267136	0.134902	ENSG00000117697	ENST00000366977;ENST00000422588;ENST00000366975;ENST00000366976	T;T;T;T	0.50813	1.44;0.73;1.45;0.84	5.13	-0.561	0.11785	.	0.958527	0.08627	N	0.917615	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.40117	-0.9580	8	.	.	.	4.0511	4.2163	0.10537	0.3203:0.3257:0.354:0.0	rs17856201	4;4;4	B4E071;Q96IY1;E7ETD5	.;NSL1_HUMAN;.	F	4	ENSP00000355944:S4F;ENSP00000388406:S4F;ENSP00000355942:S4F;ENSP00000355943:S4F	.	S	-	2	0	NSL1	211031718	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.776000	0.04674	-0.262000	0.09392	-0.237000	0.12165	TCT	G|0.841;A|0.159	0.159	strong		0.617	NSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089398.2	NM_015471	
NDC80	10403	hgsc.bcm.edu	37	18	2616457	2616457	+	Missense_Mutation	SNP	G	G	C	rs9051	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:2616457G>C	ENST00000261597.4	+	17	1995	c.1813G>C	c.(1813-1815)Gct>Cct	p.A605P		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	605	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.		A -> P (in dbSNP:rs1983346).		attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GGAGCAGATTGCTAAAGTTGA	0.259													G|||	919	0.183506	0.1241	0.1354	5008	,	,		16739	0.125		0.2286	False		,,,				2504	0.3119				p.A605P		Atlas-SNP	.											.	NDC80	62	.	0			c.G1813C						PASS	.	G	PRO/ALA	664,3738	254.6+/-260.1	53,558,1590	44.0	47.0	46.0		1813	1.3	1.0	18	dbSNP_92	46	2000,6572	333.7+/-320.7	235,1530,2521	yes	missense	NDC80	NM_006101.2	27	288,2088,4111	CC,CG,GG		23.3318,15.0841,20.5334	benign	605/643	2616457	2664,10310	2201	4286	6487	SO:0001583	missense	10403	exon17			CAGATTGCTAAAG	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1813G>C	18.37:g.2616457G>C	ENSP00000261597:p.Ala605Pro	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	161	158	0.981366	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	383	0.17536630036630035	66	0.13414634146341464	61	0.1685082872928177	70	0.12237762237762238	186	0.24538258575197888	G	9.867	1.197860	0.22037	0.150841	0.233318	ENSG00000080986	ENST00000261597	T	0.48522	0.81	5.32	1.29	0.21616	.	1.211720	0.05314	N	0.525294	T	0.00012	0.0000	N	0.08118	0	0.49051	P	2.550000000000052E-4	B	0.26876	0.162	B	0.25614	0.062	T	0.20472	-1.0274	9	0.31617	T	0.26	-0.0998	5.5394	0.17030	0.24:0.247:0.513:0.0	rs9051	605	O14777	NDC80_HUMAN	P	605	ENSP00000261597:A605P	ENSP00000261597:A605P	A	+	1	0	NDC80	2606457	0.018000	0.18449	0.985000	0.45067	0.503000	0.33858	-0.152000	0.10159	0.332000	0.23536	0.555000	0.69702	GCT	G|0.806;C|0.194	0.194	strong		0.259	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
TTN	7273	hgsc.bcm.edu	37	2	179397561	179397561	+	Missense_Mutation	SNP	C	C	T	rs3829747	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179397561C>T	ENST00000591111.1	-	308	99082	c.98858G>A	c.(98857-98859)cGc>cAc	p.R32953H	TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R34594H|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R25654H|TTN_ENST00000460472.2_Missense_Mutation_p.R25529H|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R25721H|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R32026H|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000450692.2_RNA			Q8WZ42	TITIN_HUMAN	titin	32953			R -> H. {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)			AAGGCGGATGCGCTTGGGTCG	0.443													C|||	1045	0.208666	0.0666	0.1484	5008	,	,		22656	0.4484		0.1392	False		,,,				2504	0.2679				p.R34594H		Atlas-SNP	.											TTN_ENST00000359218,caecum,carcinoma,-1,7	TTN	18412	7	0			c.G103781A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	293,3679		10,273,1703	108.0	102.0	104.0		76586,96077,76961,77162	5.8	1.0	2	dbSNP_107	104	1201,7129		90,1021,3054	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	100,1294,4757	TT,TC,CC		14.4178,7.3766,12.1444	probably-damaging,probably-damaging,probably-damaging,probably-damaging	25529/26927,32026/33424,25654/27052,25721/27119	179397561	1494,10808	1986	4165	6151	SO:0001583	missense	7273	exon358			CGGATGCGCTTGG	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.98858G>A	2.37:g.179397561C>T	ENSP00000465570:p.Arg32953His	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	193	94	0.487047	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		414	0.18956043956043955	31	0.06300813008130081	43	0.11878453038674033	236	0.4125874125874126	104	0.13720316622691292	C	21.1	4.097774	0.76870	0.073766	0.144178	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66460	-0.21;0.02;0.0;-0.01	5.81	5.81	0.92471	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999927113	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	0.39210	-0.9625	8	0.87932	D	0	.	19.6737	0.95921	0.0:1.0:0.0:0.0	rs3829747;rs59855847;rs3829747	25529;25654;25721;32953	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	32026;25529;25721;25654;25526	ENSP00000343764:R32026H;ENSP00000434586:R25529H;ENSP00000340554:R25721H;ENSP00000352154:R25654H	ENSP00000340554:R25721H	R	-	2	0	TTN	179105807	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.794000	0.85869	2.757000	0.94681	0.462000	0.41574	CGC	C|0.813;T|0.187	0.187	strong		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OR5AR1	219493	hgsc.bcm.edu	37	11	56431618	56431618	+	Silent	SNP	C	C	T	rs77272836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56431618C>T	ENST00000302969.2	+	1	481	c.457C>T	c.(457-459)Cta>Tta	p.L153L		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L153I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						CCTGGCTGGTCTAGTGAGTTT	0.502													C|||	18	0.00359425	0.0008	0.0058	5008	,	,		21429	0.0		0.0129	False		,,,				2504	0.0				p.L153L		Atlas-SNP	.											OR5AR1,NS,carcinoma,0,1	OR5AR1	68	1	1	Substitution - Missense(1)	lung(1)	c.C457T						scavenged	.	C		14,4388	21.2+/-45.6	0,14,2187	204.0	181.0	189.0		457	4.0	1.0	11	dbSNP_132	189	100,8492	55.6+/-116.7	2,96,4198	no	coding-synonymous	OR5AR1	NM_001004730.1		2,110,6385	TT,TC,CC		1.1639,0.318,0.8773		153/311	56431618	114,12880	2201	4296	6497	SO:0001819	synonymous_variant	219493	exon1			GCTGGTCTAGTGA	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"""GPCR / Class A : Olfactory receptors"""	15260	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AR, member 1"""				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.457C>T	11.37:g.56431618C>T		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	209	102	0.488038	NM_001004730	Q6IF61	Silent	SNP	ENST00000302969.2	37	CCDS31535.1																																																																																			C|0.990;T|0.010	0.010	strong		0.502	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730	
APBA3	9546	hgsc.bcm.edu	37	19	3760027	3760027	+	Missense_Mutation	SNP	G	G	A	rs11556574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3760027G>A	ENST00000316757.3	-	2	436	c.236C>T	c.(235-237)gCc>gTc	p.A79V	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	79					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)		GGGACAGGGGGCTCCACCTGG	0.627													G|||	15	0.00299521	0.0008	0.0	5008	,	,		16690	0.0		0.0129	False		,,,				2504	0.001				p.A79V		Atlas-SNP	.											.	APBA3	28	.	0			c.C236T						PASS	.	G	VAL/ALA	7,4399	12.9+/-30.5	0,7,2196	39.0	42.0	41.0		236	-0.5	0.0	19	dbSNP_120	41	97,8503	51.9+/-112.3	0,97,4203	yes	missense	APBA3	NM_004886.3	64	0,104,6399	AA,AG,GG		1.1279,0.1589,0.7996	benign	79/576	3760027	104,12902	2203	4300	6503	SO:0001583	missense	9546	exon2			CAGGGGGCTCCAC	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.236C>T	19.37:g.3760027G>A	ENSP00000315136:p.Ala79Val	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	11	0.005036630036630037	1	0.0020325203252032522	0	0.0	0	0.0	10	0.013192612137203167	G	4.003	-0.002070	0.07819	0.001589	0.011279	ENSG00000011132	ENST00000316757	T	0.43688	0.94	4.73	-0.517	0.11947	.	1.883730	0.03191	N	0.173342	T	0.20495	0.0493	N	0.24115	0.695	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.15607	-1.0431	10	0.33940	T	0.23	.	3.9246	0.09257	0.0925:0.2707:0.4794:0.1574	rs11556574	79	O96018	APBA3_HUMAN	V	79	ENSP00000315136:A79V	ENSP00000315136:A79V	A	-	2	0	APBA3	3711027	0.001000	0.12720	0.043000	0.18650	0.078000	0.17371	0.002000	0.13061	0.389000	0.25086	0.561000	0.74099	GCC	G|0.993;A|0.007	0.007	strong		0.627	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036951	33036951	+	Missense_Mutation	SNP	A	A	G	rs386699855|rs2308930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	90	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	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	
ANKRD33	341405	hgsc.bcm.edu	37	12	52284483	52284483	+	Silent	SNP	A	A	G	rs7303030	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52284483A>G	ENST00000340970.4	+	5	749	c.378A>G	c.(376-378)caA>caG	p.Q126Q	ANKRD33_ENST00000301190.6_Silent_p.Q251Q|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Silent_p.Q57Q			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	126					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)		GGCGGCCCCAAGTGGAGCAGC	0.672													A|||	526	0.105032	0.0908	0.1153	5008	,	,		12941	0.0069		0.2197	False		,,,				2504	0.1002				p.Q251Q		Atlas-SNP	.											.	ANKRD33	33	.	0			c.A753G						PASS	.	A	,	417,3989		22,373,1808	26.0	27.0	27.0		378,753	-9.4	0.0	12	dbSNP_116	27	1826,6774		195,1436,2669	no	coding-synonymous,coding-synonymous	ANKRD33	NM_001130015.1,NM_182608.3	,	217,1809,4477	GG,GA,AA		21.2326,9.4644,17.2459	,	126/273,251/453	52284483	2243,10763	2203	4300	6503	SO:0001819	synonymous_variant	341405	exon5			GCCCCAAGTGGAG		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.378A>G	12.37:g.52284483A>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Silent	SNP	ENST00000340970.4	37	CCDS44892.1																																																																																			A|0.852;G|0.148	0.148	strong		0.672	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
DPCD	25911	hgsc.bcm.edu	37	10	103368654	103368654	+	Missense_Mutation	SNP	T	T	C	rs7006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103368654T>C	ENST00000370151.4	+	5	516	c.467T>C	c.(466-468)tTg>tCg	p.L156S	FBXW4_ENST00000470093.1_5'Flank|DPCD_ENST00000370148.2_Missense_Mutation_p.C170R|DPCD_ENST00000370147.1_Missense_Mutation_p.C170R	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	73	0	0		WXS	Illumina HiSeq	Phase_I	90	53	0.588889	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		
EFHB	151651	hgsc.bcm.edu	37	3	19975050	19975050	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:19975050A>G	ENST00000295824.9	-	1	622	c.461T>C	c.(460-462)gTa>gCa	p.V154A	EFHB_ENST00000498089.1_5'UTR|EFHB_ENST00000344838.4_Intron	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	154							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TAATTCCTCTACCCCTTCAGG	0.488																																					p.V154A		Atlas-SNP	.											EFHB_ENST00000295824,NS,carcinoma,-1,2	EFHB	186	2	0			c.T461C						scavenged	.						81.0	87.0	85.0					3																	19975050		2203	4300	6503	SO:0001583	missense	151651	exon1			TCCTCTACCCCTT	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.461T>C	3.37:g.19975050A>G	ENSP00000295824:p.Val154Ala	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	155	3	0.0193548	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	A	10.96	1.497854	0.26861	.	.	ENSG00000163576	ENST00000295824;ENST00000389256	T;T	0.25414	1.8;2.08	3.73	-3.79	0.04320	.	.	.	.	.	T	0.12817	0.0311	N	0.22421	0.69	0.09310	N	1	B	0.18461	0.028	B	0.10450	0.005	T	0.32534	-0.9903	8	.	.	.	0.7384	5.9996	0.19513	0.3278:0.1708:0.5015:0.0	.	154	Q8N7U6	EFHB_HUMAN	A	154	ENSP00000295824:V154A;ENSP00000373908:V154A	.	V	-	2	0	EFHB	19950054	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.012000	0.03649	-0.742000	0.04790	0.459000	0.35465	GTA	.	.	none		0.488	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
SAP130	79595	hgsc.bcm.edu	37	2	128757995	128757995	+	Silent	SNP	A	A	C	rs17015864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:128757995A>C	ENST00000259235.3	-	8	1110	c.981T>G	c.(979-981)tcT>tcG	p.S327S	SAP130_ENST00000259234.6_Silent_p.S301S|SAP130_ENST00000357702.5_Silent_p.S327S	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	327					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)		TGATTGCTGCAGATGGAGGAT	0.468													A|||	549	0.109625	0.0053	0.111	5008	,	,		22475	0.1379		0.0895	False		,,,				2504	0.2413				p.S327S		Atlas-SNP	.											.	SAP130	169	.	0			c.T981G						PASS	.	A	,	97,4309	80.4+/-118.8	1,95,2107	195.0	169.0	178.0		981,981	3.0	1.0	2	dbSNP_123	178	854,7746	194.2+/-239.7	51,752,3497	no	coding-synonymous,coding-synonymous	SAP130	NM_001145928.1,NM_024545.3	,	52,847,5604	CC,CA,AA		9.9302,2.2015,7.312	,	327/1084,327/1049	128757995	951,12055	2203	4300	6503	SO:0001819	synonymous_variant	79595	exon8			TGCTGCAGATGGA	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.981T>G	2.37:g.128757995A>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Silent	SNP	ENST00000259235.3	37	CCDS2153.1																																																																																			A|0.920;C|0.080	0.080	strong		0.468	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
TMEM5	10329	hgsc.bcm.edu	37	12	64173807	64173807	+	Missense_Mutation	SNP	G	G	A	rs61935924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:64173807G>A	ENST00000261234.6	+	1	225	c.67G>A	c.(67-69)Gct>Act	p.A23T	RP11-415I12.3_ENST00000509615.2_RNA|TMEM5_ENST00000537373.1_5'Flank	NM_014254.1	NP_055069.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	23						integral component of plasma membrane (GO:0005887)				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		CTCCCTCTACGCTGCCTACCA	0.716													G|||	262	0.0523163	0.0166	0.0562	5008	,	,		8945	0.0129		0.1044	False		,,,				2504	0.0849				p.A23T		Atlas-SNP	.											.	TMEM5	35	.	0			c.G67A						PASS	.	G	THR/ALA	125,4281	91.1+/-129.8	0,125,2078	51.0	48.0	49.0		67	2.5	1.0	12	dbSNP_129	49	903,7697	200.7+/-244.4	41,821,3438	yes	missense	TMEM5	NM_014254.1	58	41,946,5516	AA,AG,GG		10.5,2.837,7.904	possibly-damaging	23/444	64173807	1028,11978	2203	4300	6503	SO:0001583	missense	10329	exon1			CTCTACGCTGCCT	AB015633	CCDS8966.1, CCDS61179.1	12q14.1	2013-05-07			ENSG00000118600	ENSG00000118600			13530	protein-coding gene	gene with protein product		605862				10072769, 23217329	Standard	NM_014254		Approved	HP10481	uc001srq.2	Q9Y2B1	OTTHUMG00000168730	ENST00000261234.6:c.67G>A	12.37:g.64173807G>A	ENSP00000261234:p.Ala23Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_014254	A8K017|Q6PKD6	Missense_Mutation	SNP	ENST00000261234.6	37	CCDS8966.1	121	0.0554029304029304	12	0.024390243902439025	25	0.06906077348066299	6	0.01048951048951049	78	0.10290237467018469	G	24.5	4.540086	0.85917	0.02837	0.105	ENSG00000118600	ENST00000261234	T	0.32023	1.47	3.39	2.5	0.30297	.	0.000000	0.85682	D	0.000000	T	0.01353	0.0044	L	0.49350	1.555	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00123	-1.2026	9	.	.	.	-23.3885	6.7536	0.23501	0.1293:0.0:0.8707:0.0	rs61935924	23	Q9Y2B1	TMEM5_HUMAN	T	23	ENSP00000261234:A23T	.	A	+	1	0	TMEM5	62460074	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.363000	0.59473	1.009000	0.39289	0.462000	0.41574	GCT	G|0.927;A|0.073	0.073	strong		0.716	TMEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400821.1	NM_014254	
OR2B11	127623	hgsc.bcm.edu	37	1	247614386	247614386	+	Missense_Mutation	SNP	T	T	C	rs12070953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:247614386T>C	ENST00000318749.6	-	1	922	c.899A>G	c.(898-900)gAt>gGt	p.D300G		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	300			D -> G (in dbSNP:rs12070953).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CCCCTTCATATCTTTATTTCT	0.468													T|||	561	0.112021	0.1967	0.1758	5008	,	,		18632	0.001		0.1352	False		,,,				2504	0.0429				p.D300G		Atlas-SNP	.											.	OR2B11	102	.	0			c.A899G						PASS	.	T	GLY/ASP	880,3526	343.6+/-307.7	86,708,1409	189.0	203.0	199.0		899	2.7	0.3	1	dbSNP_120	199	1249,7351	248.9+/-276.4	89,1071,3140	yes	missense	OR2B11	NM_001004492.1	94	175,1779,4549	CC,CT,TT		14.5233,19.9728,16.3694	benign	300/318	247614386	2129,10877	2203	4300	6503	SO:0001583	missense	127623	exon1			TTCATATCTTTAT		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"""GPCR / Class A : Olfactory receptors"""	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.899A>G	1.37:g.247614386T>C	ENSP00000325682:p.Asp300Gly	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_001004492	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	37	CCDS31090.1	268	0.1227106227106227	106	0.21544715447154472	66	0.18232044198895028	1	0.0017482517482517483	95	0.12532981530343007	T	6.987	0.552289	0.13374	0.199728	0.145233	ENSG00000177535	ENST00000318749	T	0.39592	1.07	5.09	2.72	0.32119	.	0.114714	0.38720	N	0.001600	T	0.00039	0.0001	H	0.95224	3.64	0.30153	P	0.802859	B	0.06786	0.001	B	0.04013	0.001	T	0.06661	-1.0814	9	0.87932	D	0	.	5.6041	0.17369	0.1517:0.0844:0.0:0.7639	rs12070953;rs52795559;rs59137379;rs12070953	300	Q5JQS5	OR2BB_HUMAN	G	300	ENSP00000325682:D300G	ENSP00000325682:D300G	D	-	2	0	OR2B11	245681009	0.998000	0.40836	0.289000	0.24876	0.022000	0.10575	5.022000	0.64078	0.472000	0.27344	0.523000	0.50628	GAT	T|0.853;C|0.147	0.147	strong		0.468	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
RDH8	50700	hgsc.bcm.edu	37	19	10131999	10131999	+	Missense_Mutation	SNP	T	T	C	rs386806752|rs1644731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10131999T>C	ENST00000171214.1	+	5	854	c.605T>C	c.(604-606)aTg>aCg	p.M202T	RDH8_ENST00000591589.1_Missense_Mutation_p.M222T	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	202			M -> T (in dbSNP:rs1644731).		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)	CAGGTTTCTATGGCTGAGTTC	0.597													C|||	2953	0.589657	0.649	0.5648	5008	,	,		17249	0.5635		0.4563	False		,,,				2504	0.6912				p.M222T		Atlas-SNP	.											.	RDH8	51	.	0			c.T665C						PASS	.	C	THR/MET	2715,1691	510.6+/-367.6	844,1027,332	88.0	85.0	86.0		605	-2.0	0.0	19	dbSNP_89	86	3907,4693	600.4+/-394.2	903,2101,1296	yes	missense	RDH8	NM_015725.2	81	1747,3128,1628	CC,CT,TT		45.4302,38.3795,49.085	benign	202/312	10131999	6622,6384	2203	4300	6503	SO:0001583	missense	50700	exon5			TTTCTATGGCTGA	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.605T>C	19.37:g.10131999T>C	ENSP00000171214:p.Met202Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		1164	0.532967032967033	312	0.6341463414634146	181	0.5	338	0.5909090909090909	333	0.4393139841688654	C	2.288	-0.363067	0.05103	0.616205	0.454302	ENSG00000080511	ENST00000171214	D	0.92752	-3.1	5.17	-2.05	0.07321	NAD(P)-binding domain (1);	0.723471	0.13759	N	0.364760	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	0.42949	-0.9421	9	0.13853	T	0.58	.	3.2493	0.06808	0.4025:0.1776:0.3339:0.086	rs1644731;rs58353076;rs1644731	202	Q9NYR8	RDH8_HUMAN	T	202	ENSP00000171214:M202T	ENSP00000171214:M202T	M	+	2	0	RDH8	9992999	0.000000	0.05858	0.000000	0.03702	0.526000	0.34562	-0.457000	0.06745	-0.396000	0.07703	-0.355000	0.07637	ATG	T|0.467;C|0.533	0.533	strong		0.597	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
TMEM44	93109	hgsc.bcm.edu	37	3	194353875	194353875	+	Missense_Mutation	SNP	G	G	T	rs1675955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:194353875G>T	ENST00000392432.2	-	1	275	c.70C>A	c.(70-72)Cac>Aac	p.H24N	AC046143.3_ENST00000447139.1_RNA|TMEM44_ENST00000347147.4_Missense_Mutation_p.H24N|TMEM44_ENST00000273580.7_Missense_Mutation_p.H24N|TMEM44_ENST00000330115.3_Intron|TMEM44_ENST00000473092.1_Missense_Mutation_p.H24N|TMEM44_ENST00000381975.3_Missense_Mutation_p.H24N	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	24			H -> N (in dbSNP:rs1675955). {ECO:0000269|PubMed:15489334}.			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)		CAGACGCGGTGGCGGGCGAAG	0.771													G|||	1821	0.363618	0.3722	0.3127	5008	,	,		8730	0.2619		0.4771	False		,,,				2504	0.3763				p.H24N		Atlas-SNP	.											.	TMEM44	42	.	0			c.C70A						PASS	.	G	ASN/HIS,ASN/HIS,ASN/HIS,ASN/HIS	1585,2533		359,867,833	16.0	17.0	17.0		70,70,70,70	2.8	1.0	3	dbSNP_89	17	3754,4378		957,1840,1269	yes	missense,missense,missense,missense	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	68,68,68,68	1316,2707,2102	TT,TG,GG		46.1633,38.4896,43.5837	benign,benign,benign,benign	24/429,24/476,24/397,24/439	194353875	5339,6911	2059	4066	6125	SO:0001583	missense	93109	exon1			CGCGGTGGCGGGC	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.70C>A	3.37:g.194353875G>T	ENSP00000376227:p.His24Asn	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	774	0.3543956043956044	175	0.3556910569105691	105	0.2900552486187845	134	0.23426573426573427	360	0.47493403693931396	G	17.20	3.328680	0.60743	0.384896	0.461633	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000347147;ENST00000381975;ENST00000473092	T;T;T;T;T	0.29397	1.98;1.59;1.59;1.57;1.59	3.74	2.81	0.32909	.	0.381317	0.19732	N	0.107322	T	0.00012	0.0000	L	0.51422	1.61	0.45284	P	0.0017200000000000548	B;P;B;B;B	0.41848	0.187;0.763;0.341;0.187;0.187	B;B;B;B;B	0.42282	0.073;0.382;0.08;0.107;0.051	T	0.48293	-0.9048	9	0.17832	T	0.49	-7.5477	8.235	0.31620	0.0:0.2725:0.7275:0.0	rs1675955;rs59796673;rs1675955	24;24;24;24;24	E9PGA9;Q2T9K0;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.	N	24	ENSP00000376227:H24N;ENSP00000273580:H24N;ENSP00000333355:H24N;ENSP00000371402:H24N;ENSP00000418674:H24N	ENSP00000273580:H24N	H	-	1	0	TMEM44	195835164	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.517000	0.45529	1.918000	0.55548	0.467000	0.42956	CAC	G|0.652;T|0.348	0.348	strong		0.771	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
OR5L2	26338	hgsc.bcm.edu	37	11	55595012	55595012	+	Silent	SNP	A	A	T	rs35645945	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	127	0	0		WXS	Illumina HiSeq	Phase_I	115	30	0.26087	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	
ABCA4	24	hgsc.bcm.edu	37	1	94474328	94474328	+	Silent	SNP	T	T	C	rs4147857	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:94474328T>C	ENST00000370225.3	-	41	5900	c.5814A>G	c.(5812-5814)ttA>ttG	p.L1938L	ABCA4_ENST00000465352.1_5'UTR|ABCA4_ENST00000536513.1_Silent_p.L208L|ABCA4_ENST00000535881.1_Silent_p.L57L	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1938	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	p.L1938L(1)		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)		CATGTAGCCTTAAGATGTCAG	0.423													T|||	939	0.1875	0.2678	0.232	5008	,	,		23481	0.121		0.1879	False		,,,				2504	0.1155				p.L1938L		Atlas-SNP	.											ABCA4,NS,carcinoma,0,1	ABCA4	275	1	1	Substitution - coding silent(1)	stomach(1)	c.A5814G						PASS	.	T		1047,3359	384.4+/-325.3	137,773,1293	245.0	208.0	221.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5814	-1.0	1.0	1	dbSNP_110	221	1644,6956	304.1+/-306.8	156,1332,2812	no	coding-synonymous	ABCA4	NM_000350.2		293,2105,4105	CC,CT,TT		19.1163,23.7631,20.6905		1938/2274	94474328	2691,10315	2203	4300	6503	SO:0001819	synonymous_variant	24	exon41			TAGCCTTAAGATG	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.5814A>G	1.37:g.94474328T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	140	72	0.514286	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			T|0.795;C|0.205	0.205	strong		0.423	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
SGSM2	9905	hgsc.bcm.edu	37	17	2268311	2268311	+	Missense_Mutation	SNP	G	G	A	rs2248821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2268311G>A	ENST00000426855.2	+	10	1296	c.1121G>A	c.(1120-1122)cGg>cAg	p.R374Q	SGSM2_ENST00000574563.1_Missense_Mutation_p.R374Q|SGSM2_ENST00000268989.3_Missense_Mutation_p.R374Q	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	374			R -> Q (in dbSNP:rs2248821). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17509819}.		late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		CTGCTGCCTCGGGGACAGCTA	0.642													G|||	2824	0.563898	0.5393	0.3444	5008	,	,		18172	0.7619		0.4274	False		,,,				2504	0.6892				p.R374Q		Atlas-SNP	.											.	SGSM2	60	.	0			c.G1121A						PASS	.	G	GLN/ARG,GLN/ARG	2357,2049	582.9+/-385.7	631,1095,477	32.0	35.0	34.0		1121,1121	2.5	0.8	17	dbSNP_100	34	3950,4650	530.2+/-381.7	900,2150,1250	yes	missense,missense	SGSM2	NM_001098509.1,NM_014853.2	43,43	1531,3245,1727	AA,AG,GG		45.9302,46.5048,48.493	benign,benign	374/1007,374/1052	2268311	6307,6699	2203	4300	6503	SO:0001583	missense	9905	exon10			TGCCTCGGGGACA	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.1121G>A	17.37:g.2268311G>A	ENSP00000415107:p.Arg374Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001098509	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Missense_Mutation	SNP	ENST00000426855.2	37	CCDS45570.1	1152	0.5274725274725275	254	0.516260162601626	139	0.3839779005524862	426	0.7447552447552448	333	0.4393139841688654	G	19.03	3.748905	0.69533	0.534952	0.459302	ENSG00000141258	ENST00000268989;ENST00000426855	T;T	0.28895	1.59;1.59	5.52	2.47	0.30058	.	0.057886	0.64402	N	0.000001	T	0.00012	0.0000	L	0.50333	1.59	0.19775	P	0.9999556456	B;B;B	0.20052	0.041;0.029;0.002	B;B;B	0.20184	0.028;0.009;0.002	T	0.18681	-1.0329	9	0.54805	T	0.06	-7.7074	10.2336	0.43268	0.2152:0.0:0.7848:0.0	rs2248821;rs17857179;rs58247251;rs2248821	374;374;374	O43147-5;O43147;O43147-2	.;SGSM2_HUMAN;.	Q	374	ENSP00000268989:R374Q;ENSP00000415107:R374Q	ENSP00000268989:R374Q	R	+	2	0	SGSM2	2215061	0.983000	0.35010	0.831000	0.32960	0.997000	0.91878	2.258000	0.43249	0.303000	0.22785	0.655000	0.94253	CGG	G|0.492;A|0.508	0.508	strong		0.642	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
KDR	3791	hgsc.bcm.edu	37	4	55972974	55972974	+	Missense_Mutation	SNP	T	T	A	rs1870377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:55972974T>A	ENST00000263923.4	-	11	1711	c.1416A>T	c.(1414-1416)caA>caT	p.Q472H		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	472	Ig-like C2-type 5.		Q -> H (in dbSNP:rs1870377). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.Q472H(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGAGACAGCTTGGCTATAAG	0.343			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			T|||	1061	0.211861	0.09	0.1311	5008	,	,		17888	0.4653		0.2346	False		,,,				2504	0.1493				p.Q472H		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	stomach(1)	c.A1416T	GRCh37	CM074306	KDR	M	rs1870377	PASS	.	T	HIS/GLN	485,3921	221.0+/-238.3	28,429,1746	79.0	82.0	81.0		1416	-1.8	0.0	4	dbSNP_92	81	2037,6563	353.6+/-329.2	246,1545,2509	yes	missense	KDR	NM_002253.2	24	274,1974,4255	AA,AT,TT		23.686,11.0077,19.3911	benign	472/1357	55972974	2522,10484	2203	4300	6503	SO:0001583	missense	3791	exon11			GACAGCTTGGCTA	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.1416A>T	4.37:g.55972974T>A	ENSP00000263923:p.Gln472His	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	190	81	0.426316	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	513	0.2348901098901099	41	0.08333333333333333	52	0.143646408839779	248	0.43356643356643354	172	0.22691292875989447	T	4.227	0.041015	0.08196	0.110077	0.23686	ENSG00000128052	ENST00000263923	T	0.76448	-1.02	5.67	-1.82	0.07857	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.974058	0.08489	N	0.938324	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	P;B	0.52692	0.955;0.003	P;B	0.56514	0.8;0.011	T	0.14699	-1.0463	9	0.25106	T	0.35	.	5.5298	0.16978	0.0:0.2646:0.2451:0.4903	rs1870377;rs52810770;rs1870377	472;472	P35968-2;P35968	.;VGFR2_HUMAN	H	472	ENSP00000263923:Q472H	ENSP00000263923:Q472H	Q	-	3	2	KDR	55667731	0.011000	0.17503	0.005000	0.12908	0.006000	0.05464	-0.046000	0.11983	-0.160000	0.11002	-0.290000	0.09829	CAA	T|0.781;A|0.219	0.219	strong		0.343	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629889	32629889	+	Silent	SNP	G	G	A	rs1049087|rs386699585	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32629889G>A	ENST00000399082.3	-	2	290	c.246C>T	c.(244-246)gcC>gcT	p.A82A	XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399079.3_Silent_p.A172A|HLA-DQB1_ENST00000374943.4_Silent_p.A172A|HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.A172A|HLA-DQB1_ENST00000399084.1_Silent_p.A172A|HLA-DQB1_ENST00000460185.1_5'Flank			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	172	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	ACACAACGCCGGCTGTCTCCT	0.552									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	2257	0.450679	0.3185	0.5317	5008	,	,		15556	0.4931		0.4215	False		,,,				2504	0.5583				p.A172A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,colon,carcinoma,-1,1	HLA-DQB1	15	1	0			c.C516T						PASS	.	G		1448,2936		285,878,1029	46.0	48.0	48.0		516	-9.0	0.0	6	dbSNP_86	48	3438,5154		752,1934,1610	no	coding-synonymous	HLA-DQB1	NM_002123.4		1037,2812,2639	AA,AG,GG		40.014,33.0292,37.6541		172/262	32629889	4886,8090	2192	4296	6488	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AACGCCGGCTGTC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.246C>T	6.37:g.32629889G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	116	116	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																																																																																				G|0.576;A|0.424	0.424	strong		0.552	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
TENM1	10178	hgsc.bcm.edu	37	X	123540315	123540315	+	Silent	SNP	G	G	T	rs960869	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:123540315G>T	ENST00000371130.3	-	25	5049	c.4986C>A	c.(4984-4986)acC>acA	p.T1662T	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Silent_p.T1669T	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1662					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)										ACGTTGCATTGGTCAGGTGTC	0.483													G|||	1436	0.380397	0.2973	0.3069	3775	,	,		13411	0.2708		0.3241	False		,,,				2504	0.2362				p.T1669T		Atlas-SNP	.											.	.	.	.	0			c.C5007A						PASS	.	G	,,	1524,2311		260,779,225,593,346	136.0	120.0	126.0		5007,5004,4986	4.7	1.0	X	dbSNP_86	126	2837,3891		421,1206,789,801,1083	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	681,1985,1014,1394,1429	TT,TG,T,GG,G		42.1671,39.7392,41.2856	,,	1669/2733,1668/2732,1662/2726	123540315	4361,6202	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon26			TGCATTGGTCAGG	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.4986C>A	X.37:g.123540315G>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			G|0.579;0|0.024	.	strong		0.483	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
OR1S1	219959	hgsc.bcm.edu	37	11	57982229	57982229	+	Missense_Mutation	SNP	A	A	G	rs1966836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57982229A>G	ENST00000309433.6	+	1	13	c.13A>G	c.(13-15)Agt>Ggt	p.S5G		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	5			S -> G (in dbSNP:rs1966836).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GAAGACTTTTAGTTCCTTTCT	0.378													G|||	3330	0.664936	0.3759	0.7622	5008	,	,		21265	0.8681		0.662	False		,,,				2504	0.7802				p.S5G		Atlas-SNP	.											.	OR1S1	139	.	0			c.A13G						PASS	.	G	GLY/SER	1840,2562	633.2+/-396.0	383,1074,744	114.0	104.0	107.0		13	-0.8	0.0	11	dbSNP_92	107	5871,2721	435.2+/-358.0	2036,1799,461	yes	missense	OR1S1	NM_001004458.1	56	2419,2873,1205	GG,GA,AA		31.669,41.7992,40.6572	benign	5/326	57982229	7711,5283	2201	4296	6497	SO:0001583	missense	219959	exon1			ACTTTTAGTTCCT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.13A>G	11.37:g.57982229A>G	ENSP00000311688:p.Ser5Gly	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1421	0.6506410256410257	182	0.3699186991869919	262	0.7237569060773481	480	0.8391608391608392	497	0.6556728232189973	G	3.465	-0.109212	0.06924	0.417992	0.68331	ENSG00000172774	ENST00000309433	T	0.51817	0.69	3.1	-0.787	0.10943	.	1.086920	0.07475	N	0.902836	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.16166	0.016	B	0.12837	0.008	T	0.31779	-0.9931	9	0.26408	T	0.33	.	0.5763	0.00704	0.1698:0.2047:0.1803:0.4453	rs1966836;rs17152497;rs60905495;rs1966836	5	Q8NH92	OR1S1_HUMAN	G	5	ENSP00000311688:S5G	ENSP00000311688:S5G	S	+	1	0	OR1S1	57738805	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.762000	0.01803	-0.695000	0.05105	-2.467000	0.00204	AGT	G|0.613;N|0.000	0.613	strong		0.378	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
DZIP1	22873	hgsc.bcm.edu	37	13	96293631	96293631	+	Missense_Mutation	SNP	G	G	A	rs9561921	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:96293631G>A	ENST00000376829.2	-	5	1366	c.515C>T	c.(514-516)aCg>aTg	p.T172M	DZIP1_ENST00000347108.3_Missense_Mutation_p.T172M|DZIP1_ENST00000361396.2_Missense_Mutation_p.T172M|DZIP1_ENST00000466027.1_5'UTR|DZIP1_ENST00000361156.3_Missense_Mutation_p.T172M	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	172			T -> M (in dbSNP:rs9561921).		cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			TTCCTTGAGCGTCTTGATCTC	0.602													G|||	493	0.0984425	0.112	0.0922	5008	,	,		16754	0.1716		0.0656	False		,,,				2504	0.0429				p.T172M		Atlas-SNP	.											.	DZIP1	195	.	0			c.C515T						PASS	.	G	MET/THR,MET/THR	475,3931	223.9+/-240.3	30,415,1758	112.0	71.0	85.0		515,515	3.5	0.1	13	dbSNP_119	85	758,7842	181.3+/-230.0	34,690,3576	yes	missense,missense	DZIP1	NM_014934.3,NM_198968.2	81,81	64,1105,5334	AA,AG,GG		8.814,10.7808,9.4802	benign,benign	172/849,172/868	96293631	1233,11773	2203	4300	6503	SO:0001583	missense	22873	exon5			TTGAGCGTCTTGA	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.515C>T	13.37:g.96293631G>A	ENSP00000366025:p.Thr172Met	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	269	139	0.516729	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	265	0.12133699633699634	68	0.13821138211382114	43	0.11878453038674033	102	0.17832167832167833	52	0.06860158311345646	G	1.494	-0.553964	0.03996	0.107808	0.08814	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.68	3.49	0.39957	.	1.685550	0.02965	N	0.143627	T	0.00039	0.0001	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.09840	-1.0656	9	0.39692	T	0.17	-7.0E-4	4.2879	0.10863	0.5511:0.1859:0.263:0.0	rs9561921;rs57792076;rs9561921	172;172	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	M	172	ENSP00000257312:T172M;ENSP00000355018:T172M;ENSP00000355175:T172M;ENSP00000366025:T172M	ENSP00000257312:T172M	T	-	2	0	DZIP1	95091632	0.000000	0.05858	0.139000	0.22197	0.002000	0.02628	0.646000	0.24797	0.661000	0.30985	-0.238000	0.12139	ACG	G|0.895;A|0.105	0.105	strong		0.602	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
MCM8	84515	hgsc.bcm.edu	37	20	5948227	5948227	+	Missense_Mutation	SNP	G	G	A	rs16991615	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:5948227G>A	ENST00000378896.3	+	9	1398	c.1021G>A	c.(1021-1023)Gaa>Aaa	p.E341K	Y_RNA_ENST00000384650.1_RNA|MCM8_ENST00000265187.4_Missense_Mutation_p.E341K|MCM8_ENST00000378883.1_Missense_Mutation_p.E341K|MCM8_ENST00000378886.2_Missense_Mutation_p.E341K	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	341			E -> K (in dbSNP:rs16991615).		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						CTCAAATGCGGAAGAAGGTAG	0.393													G|||	133	0.0265575	0.0015	0.0562	5008	,	,		17588	0.0		0.0666	False		,,,				2504	0.0256				p.E341K		Atlas-SNP	.											.	MCM8	125	.	0			c.G1021A						PASS	.	G	LYS/GLU,LYS/GLU	53,4353	50.2+/-85.5	1,51,2151	141.0	126.0	131.0	http://omim.org/entry/612885|http://www.ncbi.nlm.nih.gov/pubmed?term	1021,1021	5.0	0.9	20	dbSNP_123	131	595,8005	157.9+/-211.5	21,553,3726	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	56,56	22,604,5877	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.9186,1.2029,4.9823	benign,benign	341/841,341/825	5948227	648,12358	2203	4300	6503	SO:0001583	missense	84515	exon9			AATGCGGAAGAAG	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.1021G>A	20.37:g.5948227G>A	ENSP00000368174:p.Glu341Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	76	0.0347985347985348	0	0.0	31	0.0856353591160221	0	0.0	45	0.059366754617414245	G	14.32	2.501641	0.44455	0.012029	0.069186	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.03745	3.82;3.82;3.82;4.27	5.96	5.02	0.67125	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.155443	0.48767	D	0.000162	T	0.00178	0.0005	L	0.41236	1.265	0.44201	D	0.997023	B;B;B;B	0.31383	0.321;0.215;0.09;0.215	B;B;B;B	0.31101	0.124;0.062;0.037;0.091	T	0.49390	-0.8945	10	0.07175	T	0.84	-26.3772	11.3858	0.49785	0.1381:0.0:0.8619:0.0	rs16991615;rs52791529;rs59632513;rs16991615	341;341;341;341	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	K	341	ENSP00000368174:E341K;ENSP00000368161:E341K;ENSP00000368164:E341K;ENSP00000265187:E341K	ENSP00000265187:E341K	E	+	1	0	MCM8	5896227	1.000000	0.71417	0.939000	0.37840	0.734000	0.41952	3.589000	0.53972	1.532000	0.49169	0.650000	0.86243	GAA	G|0.953;A|0.047	0.047	strong		0.393	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
NNT	23530	hgsc.bcm.edu	37	5	43613046	43613046	+	Missense_Mutation	SNP	A	A	G	rs35201656	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:43613046A>G	ENST00000264663.5	+	3	409	c.188A>G	c.(187-189)aAa>aGa	p.K63R	NNT_ENST00000512996.2_5'UTR|NNT_ENST00000344920.4_Missense_Mutation_p.K63R	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	63					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)	p.K63R(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					GGAGTCCCCAAAGAGATATTC	0.388													A|||	212	0.0423323	0.0015	0.0216	5008	,	,		17260	0.1062		0.0378	False		,,,				2504	0.0511				p.K63R		Atlas-SNP	.											NNT,NS,carcinoma,0,1	NNT	92	1	1	Substitution - Missense(1)	stomach(1)	c.A188G						PASS	.	A	ARG/LYS,ARG/LYS	44,4362	47.5+/-82.1	1,42,2160	125.0	131.0	129.0		188,188	2.0	1.0	5	dbSNP_126	129	361,8239	120.1+/-179.3	5,351,3944	yes	missense,missense	NNT	NM_012343.3,NM_182977.2	26,26	6,393,6104	GG,GA,AA		4.1977,0.9986,3.1139	benign,benign	63/1087,63/1087	43613046	405,12601	2203	4300	6503	SO:0001583	missense	23530	exon3			TCCCCAAAGAGAT	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.188A>G	5.37:g.43613046A>G	ENSP00000264663:p.Lys63Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	51	0.554348	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	37	CCDS3949.1	93	0.042582417582417584	1	0.0020325203252032522	7	0.019337016574585635	55	0.09615384615384616	30	0.0395778364116095	A	16.84	3.234226	0.58886	0.009986	0.041977	ENSG00000112992	ENST00000505678;ENST00000512422;ENST00000264663;ENST00000344920	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.7	1.95	0.26073	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-1 (1);Alanine dehydrogenase/PNT, N-terminal (1);	0.087586	0.85682	N	0.000000	T	0.06645	0.0170	L	0.35593	1.075	0.80722	D	1	P	0.47409	0.895	P	0.52881	0.712	T	0.12993	-1.0526	10	0.20046	T	0.44	-7.2108	9.8845	0.41253	0.805:0.0:0.195:0.0	rs35201656	63	Q13423	NNTM_HUMAN	R	63	ENSP00000427670:K63R;ENSP00000421886:K63R;ENSP00000264663:K63R;ENSP00000343873:K63R	ENSP00000264663:K63R	K	+	2	0	NNT	43648803	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	4.327000	0.59247	0.101000	0.17610	-0.274000	0.10170	AAA	A|0.964;G|0.036	0.036	strong		0.388	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
NOS1	4842	hgsc.bcm.edu	37	12	117669914	117669914	+	Silent	SNP	G	G	A	rs3741475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:117669914G>A	ENST00000338101.4	-	22	3364	c.3360C>T	c.(3358-3360)gaC>gaT	p.D1120D	NOS1_ENST00000317775.6_Silent_p.D1086D|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)		GGCGGAGCTCGTCTGTCCAGT	0.607													G|||	1294	0.258387	0.2821	0.2118	5008	,	,		6092	0.3304		0.2137	False		,,,				2504	0.2311				p.D1120D	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,colon,carcinoma,0,1	NOS1	240	1	0			c.C3360T						PASS	.	G	,,,	1041,3247		136,769,1239	62.0	69.0	67.0		3258,2250,2250,3360	-5.2	0.7	12	dbSNP_107	67	1712,6796		187,1338,2729	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	323,2107,3968	AA,AG,GG		20.1222,24.2771,21.5145	,,,	1086/1435,750/1099,750/1099,1120/1469	117669914	2753,10043	2144	4254	6398	SO:0001819	synonymous_variant	4842	exon23			GAGCTCGTCTGTC		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.3360C>T	12.37:g.117669914G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	75	0.568182	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.747;A|0.253	0.253	strong		0.607	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105409959	105409959	+	Silent	SNP	G	G	T	rs10152073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	199	198	0.994975	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	
YY1AP1	55249	hgsc.bcm.edu	37	1	155658085	155658085	+	Intron	SNP	T	T	C	rs2666826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:155658085T>C	ENST00000295566.4	-	2	71				MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000438245.2_5'UTR|YY1AP1_ENST00000368330.2_Intron|DAP3_ENST00000421487.2_5'Flank|DAP3_ENST00000471642.2_Intron|YY1AP1_ENST00000355499.4_Intron|DAP3_ENST00000465375.1_5'Flank|YY1AP1_ENST00000404643.1_Intron|DAP3_ENST00000343043.3_5'Flank|YY1AP1_ENST00000359205.5_Intron|DAP3_ENST00000368336.5_5'Flank|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000311573.5_5'UTR|YY1AP1_ENST00000407221.1_Intron|YY1AP1_ENST00000405763.3_Silent_p.E57E|DAP3_ENST00000535183.1_5'Flank|YY1AP1_ENST00000361831.5_Intron|YY1AP1_ENST00000476093.1_Intron|YY1AP1_ENST00000368340.5_Silent_p.E57E|YY1AP1_ENST00000368339.5_Silent_p.E57E|YY1AP1_ENST00000347088.5_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	62	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	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	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21207389	21207389	+	Missense_Mutation	SNP	T	T	C	rs11045699	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21207389T>C	ENST00000421593.2	+	10	1360	c.1360T>C	c.(1360-1362)Ttt>Ctt	p.F454L	LST3_ENST00000540229.1_Intron|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.F501L|RP11-125O5.2_ENST00000590779.1_5'Flank|LST3_ENST00000381541.3_Missense_Mutation_p.F501L|SLCO1B3_ENST00000553473.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	454	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TTTTTAGGTGTTTTATAACTG	0.338													T|||	358	0.0714856	0.0083	0.1354	5008	,	,		13478	0.003		0.1869	False		,,,				2504	0.0634				p.F454L		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.T1360C						PASS	.	T	LEU/PHE	163,4125		6,151,1987	81.0	86.0	84.0		1360	2.8	0.6	12	dbSNP_120	84	1686,6886		169,1348,2769	yes	missense	SLCO1B7	NM_001009562.4	22	175,1499,4756	CC,CT,TT		19.6687,3.8013,14.3779		454/641	21207389	1849,11011	2144	4286	6430	SO:0001583	missense	338821	exon10			TAGGTGTTTTATA	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.1360T>C	12.37:g.21207389T>C	ENSP00000394168:p.Phe454Leu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	127	53	0.417323	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	188	0.08608058608058608	6	0.012195121951219513	47	0.1298342541436464	1	0.0017482517482517483	134	0.17678100263852242	.	17.91	3.505516	0.64410	0.038013	0.196687	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.03831	3.79;3.79;3.79	2.8	2.8	0.32819	.	0.104622	0.64402	N	0.000003	T	0.00012	0.0000	M	0.76433	2.335	0.30917	P	0.728397	D;D	0.53885	0.963;0.963	P;P	0.59487	0.858;0.858	T	0.13019	-1.0525	9	0.62326	D	0.03	.	8.6398	0.33970	0.0:0.0:0.0:1.0	rs11045699;rs52795717;rs11045699	454;501	G3V0H7;F5H094	.;.	L	501;501;454	ENSP00000370952:F501L;ENSP00000452013:F501L;ENSP00000394168:F454L	ENSP00000370952:F501L	F	+	1	0	SLCO1B7;RP11-545J16.1	21098656	0.998000	0.40836	0.566000	0.28421	0.203000	0.24098	3.256000	0.51492	1.268000	0.44264	0.416000	0.27883	TTT	T|0.893;C|0.107	0.107	strong		0.338	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
STARD3	10948	hgsc.bcm.edu	37	17	37813338	37813338	+	Splice_Site	SNP	T	T	C	rs2941515	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:37813338T>C	ENST00000336308.5	+	3	515	c.297T>C	c.(295-297)ttT>ttC	p.F99F	STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000544210.2_Splice_Site_p.F99F|STARD3_ENST00000394250.4_Splice_Site_p.F99F|STARD3_ENST00000580611.1_Intron	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	99	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCGACATCTTTGTGAGTGGCC	0.507													C|||	156	0.0311502	0.0681	0.0274	5008	,	,		20299	0.0		0.0437	False		,,,				2504	0.0031				p.F99F		Atlas-SNP	.											.	STARD3	33	.	0			c.T297C						PASS	.	C	,,	300,4106	798.9+/-415.5	17,266,1920	108.0	98.0	102.0		297,297,297	2.0	1.0	17	dbSNP_101	102	486,8114	797.8+/-407.4	18,450,3832	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	,,	35,716,5752	CC,CT,TT		5.6512,6.8089,6.0434	,,	99/446,99/428,99/446	37813338	786,12220	2203	4300	6503	SO:0001630	splice_region_variant	10948	exon3			CATCTTTGTGAGT		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.297+1T>C	17.37:g.37813338T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Silent	SNP	ENST00000336308.5	37	CCDS11341.1																																																																																			T|0.952;C|0.048	0.048	strong		0.507	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		Silent
C7orf26	79034	hgsc.bcm.edu	37	7	6639953	6639953	+	Silent	SNP	G	G	A	rs34300529	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:6639953G>A	ENST00000344417.5	+	4	1341	c.1074G>A	c.(1072-1074)gtG>gtA	p.V358V	C7orf26_ENST00000359073.5_Silent_p.V261V|C7orf26_ENST00000472693.1_3'UTR	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	358										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		CTCTGCAGGTGGCCATGGCCT	0.662													G|||	380	0.0758786	0.0174	0.134	5008	,	,		13378	0.0278		0.1829	False		,,,				2504	0.0532				p.V358V		Atlas-SNP	.											C7orf26,NS,carcinoma,0,1	C7orf26	33	1	0			c.G1074A						PASS	.	G		177,4229	109.1+/-147.4	6,165,2032	28.0	28.0	28.0		1074	4.3	1.0	7	dbSNP_126	28	1502,7098	266.9+/-287.0	144,1214,2942	no	coding-synonymous	C7orf26	NM_024067.2		150,1379,4974	AA,AG,GG		17.4651,4.0172,12.9094		358/450	6639953	1679,11327	2203	4300	6503	SO:0001819	synonymous_variant	79034	exon4			GCAGGTGGCCATG	BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.1074G>A	7.37:g.6639953G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	NM_024067	Q9BQ43	Silent	SNP	ENST00000344417.5	37	CCDS5353.1	219	0.10027472527472528	12	0.024390243902439025	53	0.1464088397790055	9	0.015734265734265736	145	0.19129287598944592	G	9.926	1.213517	0.22289	0.040172	0.174651	ENSG00000146576	ENST00000445375	.	.	.	5.2	4.32	0.51571	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.13229	-1.0517	3	.	.	.	-33.9265	7.4662	0.27322	0.0865:0.0:0.7487:0.1647	rs34300529	.	.	.	S	96	.	.	G	+	1	0	C7orf26	6606478	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.646000	0.46630	1.515000	0.48885	0.555000	0.69702	GGC	G|0.883;A|0.117	0.117	strong		0.662	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067	
OR1Q1	158131	hgsc.bcm.edu	37	9	125377505	125377505	+	Missense_Mutation	SNP	A	A	G	rs1329957	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125377505A>G	ENST00000297913.2	+	1	558	c.489A>G	c.(487-489)atA>atG	p.I163M	RP11-64P14.7_ENST00000431442.1_RNA	NM_012364.1	NP_036496.1	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q, member 1	163			I -> M (in dbSNP:rs1329957). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:9119360}.		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)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	17						CCTTTCTCATAGGCCAACTAA	0.493													G|||	4416	0.881789	0.708	0.9323	5008	,	,		22919	0.9494		0.9245	False		,,,				2504	0.9673				p.I163M		Atlas-SNP	.											.	OR1Q1	46	.	0			c.A489G						PASS	.	G	MET/ILE	3303,1103	398.3+/-330.8	1227,849,127	184.0	160.0	168.0		489	5.6	0.7	9	dbSNP_88	168	7966,634	163.8+/-216.2	3689,588,23	yes	missense	OR1Q1	NM_012364.1	10	4916,1437,150	GG,GA,AA		7.3721,25.034,13.3554	benign	163/315	125377505	11269,1737	2203	4300	6503	SO:0001583	missense	158131	exon1			TCTCATAGGCCAA		CCDS35125.1	9q33.2	2013-09-20			ENSG00000165202	ENSG00000165202		"""GPCR / Class A : Olfactory receptors"""	8223	protein-coding gene	gene with protein product				OR1Q2, OR1Q3			Standard	NM_012364		Approved	OST226, OR9-A, HSTPCR106, OST226OR9-A, TPCR106	uc011lyy.2	Q15612	OTTHUMG00000020615	ENST00000297913.2:c.489A>G	9.37:g.125377505A>G	ENSP00000297913:p.Ile163Met	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	262	262	1	NM_012364	Q6IFN4|Q8NGR7|Q96R82	Missense_Mutation	SNP	ENST00000297913.2	37	CCDS35125.1	1928	0.8827838827838828	355	0.7215447154471545	331	0.914364640883978	545	0.9527972027972028	697	0.9195250659630607	G	0	-2.621630	0.00118	0.74966	0.926279	ENSG00000165202	ENST00000297913	T	0.00107	8.72	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.097993	0.45606	N	0.000359	T	0.00012	0.0000	N	0.03324	-0.35	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45920	-0.9228	9	0.02654	T	1	-0.2425	7.5273	0.27662	0.2376:0.0:0.7624:0.0	rs1329957;rs52834348;rs56746997;rs1329957	163	Q15612	OR1Q1_HUMAN	M	163	ENSP00000297913:I163M	ENSP00000297913:I163M	I	+	3	3	OR1Q1	124417326	0.000000	0.05858	0.740000	0.30986	0.019000	0.09904	-1.045000	0.03528	1.608000	0.50180	-0.128000	0.14901	ATA	A|0.129;G|0.871	0.871	strong		0.493	OR1Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053946.1		
KLHL40	131377	hgsc.bcm.edu	37	3	42733468	42733468	+	Missense_Mutation	SNP	T	T	C	rs123509	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42733468T>C	ENST00000287777.4	+	6	1949	c.1849T>C	c.(1849-1851)Tgc>Cgc	p.C617R		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	617			C -> R (in dbSNP:rs123509). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)											CAATGTGCTGTGCCTGACTAA	0.592													C|||	4506	0.89976	0.9448	0.8689	5008	,	,		19169	0.998		0.7714	False		,,,				2504	0.8916				p.C617R		Atlas-SNP	.											.	.	.	.	0			c.T1849C						PASS	.	C	ARG/CYS	3985,421	206.2+/-227.9	1802,381,20	116.0	92.0	100.0		1849	3.3	1.0	3	dbSNP_79	100	6487,2113	364.4+/-333.5	2436,1615,249	yes	missense	KBTBD5	NM_152393.2	180	4238,1996,269	CC,CT,TT		24.5698,9.5552,19.4833	benign	617/622	42733468	10472,2534	2203	4300	6503	SO:0001583	missense	131377	exon6			GTGCTGTGCCTGA	AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"""Kelch-like"", ""BTB/POZ domain containing"""	30372	protein-coding gene	gene with protein product	"""sarcosynapsin"", ""nemaline myopathy type 8"""	615340	"""kelch repeat and BTB (POZ) domain containing 5"", ""kelch-like 40 (Drosophila)"""	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.1849T>C	3.37:g.42733468T>C	ENSP00000287777:p.Cys617Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_152393	Q86SI1|Q96MR2	Missense_Mutation	SNP	ENST00000287777.4	37	CCDS2703.1	1928	0.8827838827838828	463	0.9410569105691057	313	0.8646408839779005	570	0.9965034965034965	582	0.7678100263852242	C	0.003	-2.546536	0.00140	0.904448	0.754302	ENSG00000157119	ENST00000287777;ENST00000452129	T	0.68903	-0.36	3.29	3.29	0.37713	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00186	-1.895	0.25136	P	0.99053258	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	9	0.02654	T	1	.	7.3787	0.26843	0.1647:0.7412:0.0:0.0941	rs123509;rs405466;rs17316418;rs57840414;rs123509	617	Q2TBA0	KBTB5_HUMAN	R	617;362	ENSP00000287777:C617R	ENSP00000287777:C617R	C	+	1	0	KBTBD5	42708472	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	1.237000	0.32695	0.685000	0.31468	-1.063000	0.02288	TGC	T|0.161;C|0.839	0.839	strong		0.592	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393	
RBM19	9904	hgsc.bcm.edu	37	12	114374887	114374887	+	Missense_Mutation	SNP	T	T	C	rs2290787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:114374887T>C	ENST00000545145.2	-	16	2071	c.1993A>G	c.(1993-1995)Aca>Gca	p.T665A	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.T665A|RBM19_ENST00000392561.3_Missense_Mutation_p.T665A	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	665			T -> A (in dbSNP:rs2290787). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T665A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TGTGGGGCTGTGCTGGAGAAG	0.527													C|||	579	0.115615	0.0514	0.0418	5008	,	,		17578	0.1885		0.1103	False		,,,				2504	0.1851				p.T665A		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1993G						scavenged	.	C	ALA/THR,ALA/THR,ALA/THR	194,4212		13,168,2022	130.0	129.0	129.0		1993,1993,1993	-7.4	0.1	12	dbSNP_100	129	875,7725		37,801,3462	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	58,58,58	50,969,5484	CC,CT,TT		10.1744,4.4031,8.2193	benign,benign,benign	665/961,665/961,665/961	114374887	1069,11937	2203	4300	6503	SO:0001583	missense	9904	exon16			GGGCTGTGCTGGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1993A>G	12.37:g.114374887T>C	ENSP00000442053:p.Thr665Ala	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	170	68	0.4	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	7.721	0.697212	0.15106	0.044031	0.101744	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05081	3.5;3.5;3.5	4.5	-7.42	0.01388	Nucleotide-binding, alpha-beta plait (1);	0.638273	0.16199	N	0.225012	T	0.00073	0.0002	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28522	-1.0041	10	0.07990	T	0.79	0.174	2.1166	0.03715	0.1533:0.1255:0.303:0.4182	rs2290787;rs17856103;rs17856172	665	Q9Y4C8	RBM19_HUMAN	A	665	ENSP00000442053:T665A;ENSP00000376344:T665A;ENSP00000261741:T665A	ENSP00000261741:T665A	T	-	1	0	RBM19	112859270	0.076000	0.21285	0.052000	0.19188	0.226000	0.24999	-0.181000	0.09740	-2.257000	0.00695	-1.557000	0.00889	ACA	A|0.076;C|0.019;T|0.905	0.019	strong		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
MUC4	4585	hgsc.bcm.edu	37	3	195511686	195511686	+	Silent	SNP	G	G	T	rs71291862|rs201950480		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195511686G>T	ENST00000463781.3	-	2	7224	c.6765C>A	c.(6763-6765)acC>acA	p.T2255T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2255T	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)		CAGGAAGAGGGGTGGTGTCAC	0.582																																					p.T2255T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C6765A						scavenged	.						30.0	28.0	29.0					3																	195511686		686	1584	2270	SO:0001819	synonymous_variant	4585	exon2			AAGAGGGGTGGTG	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.6765C>A	3.37:g.195511686G>T		Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	370	50	0.135135	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|0.998;T|0.002	0.002	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TLE3	7090	hgsc.bcm.edu	37	15	70352968	70352968	+	Silent	SNP	C	C	G	rs2228176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:70352968C>G	ENST00000558939.1	-	9	1992	c.615G>C	c.(613-615)tcG>tcC	p.S205S	TLE3_ENST00000557907.1_Silent_p.S205S|TLE3_ENST00000317509.8_Silent_p.S205S|TLE3_ENST00000557997.1_Silent_p.S205S|TLE3_ENST00000560589.1_Silent_p.S149S|TLE3_ENST00000559929.1_Silent_p.S215S|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000539550.1_Silent_p.S149S|TLE3_ENST00000442299.2_Silent_p.S205S|TLE3_ENST00000560939.1_Silent_p.S210S|TLE3_ENST00000559048.1_Silent_p.S210S|TLE3_ENST00000440567.3_Silent_p.S198S|TLE3_ENST00000451782.2_Silent_p.S205S|TLE3_ENST00000558201.1_Silent_p.S211S|TLE3_ENST00000558379.1_Silent_p.S205S	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	205	CCN domain.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GGAGGCTTTCCGAGGGTGACA	0.547													C|||	1056	0.210863	0.1354	0.3329	5008	,	,		15042	0.2321		0.2952	False		,,,				2504	0.1176				p.S205S		Atlas-SNP	.											.	TLE3	104	.	0			c.G615C						PASS	.	C	,,	571,3227		47,477,1375	78.0	77.0	77.0		615,615,615	-4.1	1.0	15	dbSNP_123	77	2355,5845		354,1647,2099	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	401,2124,3474	GG,GC,CC		28.7195,15.0342,24.3874	,,	205/770,205/773,205/761	70352968	2926,9072	1899	4100	5999	SO:0001819	synonymous_variant	7090	exon9			GCTTTCCGAGGGT	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.615G>C	15.37:g.70352968C>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	CCDS45293.1																																																																																			G|0.271;C|0.729;N|0.000;A|0.000	0.271	strong		0.547	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
PTCHD4	442213	hgsc.bcm.edu	37	6	47847401	47847401	+	Silent	SNP	A	A	G	rs2068006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:47847401A>G	ENST00000339488.4	-	3	1212	c.1179T>C	c.(1177-1179)gcT>gcC	p.A393A		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	393						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										CTAGTTGGCCAGCAAAGACCA	0.453													A|||	3250	0.648962	0.4592	0.7911	5008	,	,		19835	0.746		0.6769	False		,,,				2504	0.6759				p.A393A		Atlas-SNP	.											.	.	.	.	0			c.T1179C						PASS	.	A		2253,2153	594.9+/-388.3	577,1099,527	73.0	70.0	71.0		1179	-0.1	1.0	6	dbSNP_96	71	5888,2712	681.4+/-403.7	2016,1856,428	no	coding-synonymous	C6orf138	NM_001013732.3		2593,2955,955	GG,GA,AA		31.5349,48.8652,37.4058		393/847	47847401	8141,4865	2203	4300	6503	SO:0001819	synonymous_variant	442213	exon3			TTGGCCAGCAAAG		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 138"""	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1179T>C	6.37:g.47847401A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001013732	B0QZ29|B4DRK3|Q5T884	Silent	SNP	ENST00000339488.4	37	CCDS34473.2																																																																																			A|0.358;G|0.642	0.642	strong		0.453	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732	
TRIM66	9866	hgsc.bcm.edu	37	11	8646670	8646670	+	Missense_Mutation	SNP	T	T	G	rs7947230	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8646670T>G	ENST00000299550.6	-	11	2175	c.1981A>C	c.(1981-1983)Aac>Cac	p.N661H	TRIM66_ENST00000402157.2_Missense_Mutation_p.N659H	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	661						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						GCTGTCAGGTTGCTCACACTC	0.572													T|||	1377	0.27496	0.2587	0.2061	5008	,	,		20806	0.3621		0.1928	False		,,,				2504	0.3405				p.N661H		Atlas-SNP	.											.	TRIM66	45	.	0			c.A1981C						PASS	.	T	HIS/ASN	338,1046		34,270,388	26.0	26.0	26.0		1981	4.7	1.0	11	dbSNP_116	26	576,2606		49,478,1064	yes	missense	TRIM66	NM_014818.1	68	83,748,1452	GG,GT,TT		18.1018,24.422,20.0175	benign	661/1217	8646670	914,3652	692	1591	2283	SO:0001583	missense	9866	exon11			TCAGGTTGCTCAC	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.1981A>C	11.37:g.8646670T>G	ENSP00000299550:p.Asn661His	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		542	0.24816849816849818	116	0.23577235772357724	91	0.2513812154696133	192	0.3356643356643357	143	0.18865435356200527	T	13.37	2.216543	0.39201	0.24422	0.181018	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.64438	-0.1;-0.09	5.84	4.71	0.59529	.	0.258524	0.34628	N	0.003820	T	0.00012	0.0000	N	0.08118	0	0.45634	P	0.0014319999999999888	B	0.30709	0.291	B	0.28232	0.087	T	0.31530	-0.9940	9	0.36615	T	0.2	-3.3395	6.8564	0.24042	0.0:0.0772:0.1514:0.7714	rs7947230;rs52814841;rs7947230	661	O15016	TRI66_HUMAN	H	661;659	ENSP00000299550:N661H;ENSP00000384876:N659H	ENSP00000299550:N661H	N	-	1	0	TRIM66	8603246	0.991000	0.36638	0.999000	0.59377	0.789000	0.44602	0.430000	0.21428	1.025000	0.39708	0.533000	0.62120	AAC	T|0.743;G|0.257	0.257	strong		0.572	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
DEF8	54849	hgsc.bcm.edu	37	16	90025640	90025640	+	Intron	SNP	G	G	C	rs8166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90025640G>C	ENST00000268676.7	+	6	786				DEF8_ENST00000563594.1_Intron|DEF8_ENST00000563848.1_Intron|DEF8_ENST00000418391.2_Missense_Mutation_p.M197I|DEF8_ENST00000567874.1_Intron|DEF8_ENST00000570182.1_Intron|DEF8_ENST00000563795.1_Intron|DEF8_ENST00000569453.1_Intron	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)						intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		acattcAGATGtgagctatcc	0.507													C|||	609	0.121605	0.1021	0.0303	5008	,	,		20366	0.2688		0.0557	False		,,,				2504	0.1288				p.M197I		Atlas-SNP	.											.	DEF8	28	.	0			c.G591C						PASS	.	C	,,,,,ILE/MET,ILE/MET,ILE/MET,	278,2366		14,250,1058	23.0	33.0	29.0		,,,,,591,591,591,	-0.3	0.0	16	dbSNP_52	29	314,4304		9,296,2004	yes	intron,intron,intron,intron,intron,missense,missense,missense,intron	DEF8	NM_001242816.1,NM_001242817.1,NM_001242818.1,NM_001242819.1,NM_001242820.1,NM_001242821.1,NM_001242822.1,NM_017702.3,NM_207514.2	,,,,,10,10,10,	23,546,3062	CC,CG,GG		6.7995,10.5144,8.152	,,,,,,,,	,,,,,197/198,197/198,197/198,	90025640	592,6670	1322	2309	3631	SO:0001627	intron_variant	54849	exon6			TCAGATGTGAGCT	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.697+77G>C	16.37:g.90025640G>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_001242822	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Missense_Mutation	SNP	ENST00000268676.7	37	CCDS10989.1	235	0.10760073260073261	55	0.11178861788617886	13	0.03591160220994475	122	0.21328671328671328	45	0.059366754617414245	C	2.530	-0.308796	0.05458	0.105144	0.067995	ENSG00000140995	ENST00000418391	T	0.40476	1.03	1.8	-0.313	0.12754	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30090	-0.9990	6	.	.	.	.	2.9572	0.05881	0.0:0.4513:0.242:0.3067	rs8166;rs1130141;rs3188708	197	Q6ZN54-2	.	I	197	ENSP00000412784:M197I	.	M	+	3	0	DEF8	88553141	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.291000	0.02775	-0.402000	0.07633	-0.501000	0.04562	ATG	G|0.888;C|0.112	0.112	strong		0.507	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
LILRB5	10990	hgsc.bcm.edu	37	19	54755922	54755922	+	Missense_Mutation	SNP	C	C	T	rs34889610|rs12977062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000449561.2_Missense_Mutation_p.A542T|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	191	0	0		WXS	Illumina HiSeq	Phase_I	191	94	0.492147	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		
TRPM5	29850	hgsc.bcm.edu	37	11	2439542	2439542	+	Missense_Mutation	SNP	A	A	G	rs3986599	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:2439542A>G	ENST00000155858.6	-	6	769	c.761T>C	c.(760-762)gTa>gCa	p.V254A	TRPM5_ENST00000533060.1_Missense_Mutation_p.V254A|TRPM5_ENST00000452833.1_Missense_Mutation_p.V256A|TRPM5_ENST00000528453.1_Missense_Mutation_p.V254A	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)		CCCCGAGCCTACCAGGATCAG	0.652													G|||	4223	0.843251	0.9705	0.8444	5008	,	,		15415	0.9008		0.6561	False		,,,				2504	0.8037				p.V254A	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											TRPM5,NS,carcinoma,0,1	TRPM5	86	1	0			c.T761C						PASS	.	G	ALA/VAL	4013,329		1863,287,21	14.0	18.0	16.0		761	2.5	0.5	11	dbSNP_108	16	5658,2878		1881,1896,491	yes	missense	TRPM5	NM_014555.3	64	3744,2183,512	GG,GA,AA		33.716,7.5772,24.9029	benign	254/1166	2439542	9671,3207	2171	4268	6439	SO:0001583	missense	29850	exon6			GAGCCTACCAGGA	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.761T>C	11.37:g.2439542A>G	ENSP00000155858:p.Val254Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	1768	0.8095238095238095	470	0.9552845528455285	295	0.8149171270718232	520	0.9090909090909091	483	0.637203166226913	G	0.024	-1.393197	0.01185	0.924228	0.66284	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	3.42	2.47	0.30058	.	0.000000	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00094	-2.165	0.58432	P	8.000000000008E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25950	-1.0117	9	0.19147	T	0.46	-11.3073	6.9723	0.24656	0.0951:0.0:0.7335:0.1714	rs3986599	254;256;254	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	A	248;254;256;254;254;254	ENSP00000434383:V248A;ENSP00000155858:V254A;ENSP00000387965:V256A;ENSP00000434121:V254A;ENSP00000436809:V254A	ENSP00000155858:V254A	V	-	2	0	TRPM5	2396118	1.000000	0.71417	0.460000	0.27093	0.209000	0.24338	3.561000	0.53770	0.260000	0.21731	-0.320000	0.08662	GTA	A|0.209;G|0.791	0.791	strong		0.652	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
SLC4A11	83959	hgsc.bcm.edu	37	20	3218634	3218634	+	5'Flank	SNP	G	G	C	rs3810562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3218634G>C	ENST00000380056.3	-	0	0				SLC4A11_ENST00000539553.2_Intron|SLC4A11_ENST00000380059.3_Missense_Mutation_p.P26R	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11						bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)	p.P26R(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						CTCTCTCCTCGGATGCCAAGG	0.637													C|||	3213	0.641573	0.8215	0.5807	5008	,	,		15857	0.6766		0.5795	False		,,,				2504	0.4693				p.P26R	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											SLC4A11_ENST00000380059,NS,lymphoid_neoplasm,0,1	SLC4A11	188	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C77G						PASS	.																																			SO:0001631	upstream_gene_variant	83959	exon1			CTCCTCGGATGCC	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740		20.37:g.3218634G>C	Exception_encountered	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	1403	0.6423992673992674	385	0.782520325203252	209	0.5773480662983426	382	0.6678321678321678	427	0.5633245382585752	C	3.200	-0.163983	0.06502	.	.	ENSG00000088836	ENST00000380059	T	0.80909	-1.43	3.5	-1.98	0.07480	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38001	-0.9681	8	0.11182	T	0.66	.	4.6723	0.12694	0.1395:0.2058:0.5427:0.112	rs3810562	26	B4DKC8	.	R	26	ENSP00000369399:P26R	ENSP00000369399:P26R	P	-	2	0	SLC4A11	3166634	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.858000	0.04281	-0.398000	0.07679	-1.307000	0.01316	CCG	G|0.367;C|0.633	0.633	strong		0.637	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
C12orf56	115749	hgsc.bcm.edu	37	12	64746833	64746833	+	Missense_Mutation	SNP	C	C	T	rs73118352	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:64746833C>T	ENST00000543942.2	-	2	882	c.256G>A	c.(256-258)Gat>Aat	p.D86N	RPS11P6_ENST00000535684.1_RNA|C12orf56_ENST00000333722.5_Missense_Mutation_p.D86N|snoU13_ENST00000459220.1_RNA	NM_001170633.1	NP_001164104.1	Q8IXR9	CL056_HUMAN	chromosome 12 open reading frame 56	86										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)	15			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)		GGGTAATCATCAATCTGGAAA	0.328													c|||	828	0.165335	0.1014	0.1888	5008	,	,		14459	0.2669		0.1372	False		,,,				2504	0.1595				p.D86N		Atlas-SNP	.											.	C12orf56	42	.	0			c.G256A						PASS	.		ASN/ASP,ASN/ASP	340,3294		10,320,1487	83.0	78.0	80.0		256,256	3.8	1.0	12	dbSNP_130	80	958,7198		54,850,3174	yes	missense,missense	C12orf56	NM_001170633.1,NM_001099676.2	23,23	64,1170,4661	TT,TC,CC		11.746,9.3561,11.0093	benign,benign	86/623,86/463	64746833	1298,10492	1817	4078	5895	SO:0001583	missense	115749	exon2			AATCATCAATCTG		CCDS44935.1, CCDS61182.1	12q14.2	2012-08-15			ENSG00000185306	ENSG00000185306			26967	protein-coding gene	gene with protein product							Standard	NM_001099676		Approved		uc021qzu.1	Q8IXR9	OTTHUMG00000168782	ENST00000543942.2:c.256G>A	12.37:g.64746833C>T	ENSP00000446101:p.Asp86Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001170633		Missense_Mutation	SNP	ENST00000543942.2	37		330	0.1510989010989011	32	0.06504065040650407	55	0.15193370165745856	137	0.2395104895104895	106	0.13984168865435356	c	10.28	1.306739	0.23736	0.093561	0.11746	ENSG00000185306	ENST00000333722;ENST00000543942;ENST00000433716;ENST00000543259	.	.	.	3.83	3.83	0.44106	.	0.255375	0.30419	N	0.009668	T	0.00012	0.0000	L	0.41415	1.275	0.38962	P	0.041432000000000024	B	0.28470	0.213	B	0.31245	0.126	T	0.10359	-1.0633	7	.	.	.	-4.1125	11.5392	0.50657	0.0:1.0:0.0:0.0	.	86	Q8IXR9-2	.	N	86;86;86;73	.	.	D	-	1	0	C12orf56	63033100	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.873000	0.48475	2.439000	0.82584	0.651000	0.88453	GAT	C|0.854;T|0.146	0.146	strong		0.328	C12orf56-008	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000401058.2	NM_001099676	
BCL9	607	hgsc.bcm.edu	37	1	147091689	147091689	+	Silent	SNP	G	G	A	rs61751617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:147091689G>A	ENST00000234739.3	+	8	2468	c.1728G>A	c.(1726-1728)ccG>ccA	p.P576P		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	576	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					TGGAAGGGCCGAATGTCCCCA	0.567			T	"""IGH@, IGL@"""	B-ALL								G|||	75	0.014976	0.0045	0.0303	5008	,	,		19654	0.001		0.0348	False		,,,				2504	0.0123				p.P576P		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	BCL9_ENST00000234739,NS,carcinoma,+1,1	BCL9	150	1	0			c.G1728A						scavenged	.	G		24,4382	31.7+/-61.6	0,24,2179	82.0	89.0	86.0		1728	-10.8	0.0	1	dbSNP_129	86	333,8267	113.1+/-173.2	7,319,3974	no	coding-synonymous	BCL9	NM_004326.2		7,343,6153	AA,AG,GG		3.8721,0.5447,2.7449		576/1427	147091689	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	607	exon8			AGGGCCGAATGTC	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.1728G>A	1.37:g.147091689G>A		Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	84	49	0.583333	NM_004326	Q5T489	Silent	SNP	ENST00000234739.3	37	CCDS30833.1																																																																																			G|0.973;A|0.027	0.027	strong		0.567	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
CDH23	64072	hgsc.bcm.edu	37	10	73455201	73455201	+	Silent	SNP	T	T	C	rs3752752	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73455201T>C	ENST00000224721.6	+	21	2336	c.2331T>C	c.(2329-2331)aaT>aaC	p.N777N	CDH23_ENST00000299366.7_Silent_p.N817N	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	772	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TGGACATCAATGACAACCACC	0.592													C|||	2777	0.554513	0.5038	0.5187	5008	,	,		18623	0.4385		0.7068	False		,,,				2504	0.6115				p.N772N		Atlas-SNP	.											.	CDH23	365	.	0			c.T2316C						PASS	.	C	,,	2297,1867		652,993,437	108.0	115.0	113.0		2316,2316,2316	-9.3	0.3	10	dbSNP_107	113	6123,2303		2220,1683,310	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	,,	2872,2676,747	CC,CT,TT		27.3321,44.8367,33.1215	,,	772/1382,772/1062,772/3355	73455201	8420,4170	2082	4213	6295	SO:0001819	synonymous_variant	64072	exon21			CATCAATGACAAC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2331T>C	10.37:g.73455201T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				T|0.407;C|0.593	0.593	strong		0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
TEKT1	83659	hgsc.bcm.edu	37	17	6704071	6704071	+	Silent	SNP	G	G	A	rs17804647	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:6704071G>A	ENST00000338694.2	-	7	1173	c.1044C>T	c.(1042-1044)gtC>gtT	p.V348V	TEKT1_ENST00000535086.1_Silent_p.V202V	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	348						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				CCTACCTTGCGACATTGTGGG	0.552											OREG0024124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	269	0.0537141	0.0477	0.0749	5008	,	,		18937	0.002		0.1054	False		,,,				2504	0.047				p.V348V		Atlas-SNP	.											.	TEKT1	49	.	0			c.C1044T						PASS	.	A		221,4185	806.0+/-415.8	5,211,1987	165.0	144.0	151.0		1044	-2.0	0.0	17	dbSNP_123	151	976,7624	774.7+/-407.7	53,870,3377	no	coding-synonymous	TEKT1	NM_053285.1		58,1081,5364	AA,AG,GG		11.3488,5.0159,9.2034		348/419	6704071	1197,11809	2203	4300	6503	SO:0001819	synonymous_variant	83659	exon7			CCTTGCGACATTG		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.1044C>T	17.37:g.6704071G>A		Somatic	139	0	0	636	WXS	Illumina HiSeq	Phase_I	165	84	0.509091	NM_053285	D3DTM7	Silent	SNP	ENST00000338694.2	37	CCDS11083.1																																																																																			G|0.923;A|0.077	0.077	strong		0.552	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	
PCK2	5106	hgsc.bcm.edu	37	14	24572908	24572908	+	Missense_Mutation	SNP	G	G	A	rs149521304		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24572908G>A	ENST00000216780.4	+	10	1926	c.1658G>A	c.(1657-1659)cGg>cAg	p.R553Q	PCK2_ENST00000545054.2_Missense_Mutation_p.R419Q|PCK2_ENST00000559250.1_Intron|PCK2_ENST00000561286.1_Missense_Mutation_p.R419Q|PCK2_ENST00000558096.1_Missense_Mutation_p.R387Q|NRL_ENST00000561028.1_Intron	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	553					carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611)			breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)		GAGAATGCTCGGGTGCTAGAC	0.642																																					p.R553Q		Atlas-SNP	.											.	PCK2	66	.	0			c.G1658A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	68.0	74.0	72.0		1658	5.6	1.0	14	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	missense	PCK2	NM_004563.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	553/641	24572908	1,13005	2203	4300	6503	SO:0001583	missense	5106	exon10			ATGCTCGGGTGCT	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889	4.1.1.32		8725	protein-coding gene	gene with protein product		614095				8645161, 9657976	Standard	XM_005267726		Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000216780.4:c.1658G>A	14.37:g.24572908G>A	ENSP00000216780:p.Arg553Gln	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	156	71	0.455128	NM_004563	O43253|Q86U01|Q9BV62	Missense_Mutation	SNP	ENST00000216780.4	37	CCDS9609.1	.	.	.	.	.	.	.	.	.	.	G	36	5.616065	0.96649	0.0	1.16E-4	ENSG00000100889	ENST00000216780;ENST00000545054	T;T	0.07688	3.17;3.17	5.57	5.57	0.84162	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45135	0.1327	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62196	-0.6905	10	0.87932	D	0	-9.3642	17.4188	0.87508	0.0:0.0:1.0:0.0	.	419;553	B4DW73;Q16822	.;PCKGM_HUMAN	Q	553;419	ENSP00000216780:R553Q;ENSP00000441826:R419Q	ENSP00000216780:R553Q	R	+	2	0	PCK2	23642748	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	weak		0.642	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073	
KIF26A	26153	hgsc.bcm.edu	37	14	104642524	104642524	+	Silent	SNP	C	C	T	rs78184481	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104642524C>T	ENST00000423312.2	+	12	3399	c.3399C>T	c.(3397-3399)ttC>ttT	p.F1133F	KIF26A_ENST00000315264.7_Silent_p.F994F	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1133					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		AGCCCCGCTTCAGCCCCGACT	0.706													C|||	105	0.0209665	0.0045	0.0346	5008	,	,		13789	0.0		0.0577	False		,,,				2504	0.0174				p.F1133F		Atlas-SNP	.											.	KIF26A	84	.	0			c.C3399T						PASS	.	C		39,3513		0,39,1737	5.0	7.0	6.0		3399	2.8	0.2	14	dbSNP_132	6	445,7313		19,407,3453	no	coding-synonymous	KIF26A	NM_015656.1		19,446,5190	TT,TC,CC		5.736,1.098,4.2794		1133/1883	104642524	484,10826	1776	3879	5655	SO:0001819	synonymous_variant	26153	exon12			CCGCTTCAGCCCC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.3399C>T	14.37:g.104642524C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			C|0.971;T|0.029	0.029	strong		0.706	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
C15orf27	123591	hgsc.bcm.edu	37	15	76496232	76496232	+	Missense_Mutation	SNP	G	G	A	rs937732	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:76496232G>A	ENST00000388942.3	+	11	1448	c.1172G>A	c.(1171-1173)cGc>cAc	p.R391H		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	391			R -> H (in dbSNP:rs937732). {ECO:0000269|PubMed:14702039}.		calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						AGTGCCTCCCGCAGCTCAGTC	0.657													G|||	1874	0.374201	0.2284	0.3256	5008	,	,		17152	0.5794		0.2684	False		,,,				2504	0.5031				p.R391H		Atlas-SNP	.											.	C15orf27	32	.	0			c.G1172A						PASS	.	G	HIS/ARG	1063,3331	388.2+/-326.8	111,841,1245	77.0	74.0	75.0		1172	0.9	0.3	15	dbSNP_86	75	2242,6346	380.3+/-339.6	289,1664,2341	yes	missense	C15orf27	NM_152335.2	29	400,2505,3586	AA,AG,GG		26.1062,24.1921,25.4583	benign	391/532	76496232	3305,9677	2197	4294	6491	SO:0001583	missense	123591	exon11			CCTCCCGCAGCTC	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.1172G>A	15.37:g.76496232G>A	ENSP00000373594:p.Arg391His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	761	0.3484432234432234	119	0.241869918699187	124	0.3425414364640884	316	0.5524475524475524	202	0.26649076517150394	G	11.20	1.569114	0.28003	0.241921	0.261062	ENSG00000169758	ENST00000388942	T	0.37752	1.18	4.9	0.87	0.19102	.	1.238380	0.05458	N	0.550598	T	0.00012	0.0000	L	0.38531	1.155	0.28268	P	0.9245182	B;B	0.21309	0.054;0.003	B;B	0.14023	0.01;0.003	T	0.48031	-0.9070	9	0.38643	T	0.18	-16.2618	7.5721	0.27913	0.3391:0.0:0.6609:0.0	rs937732;rs61128976;rs937732	355;391	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	H	391	ENSP00000373594:R391H	ENSP00000373594:R391H	R	+	2	0	C15orf27	74283287	0.035000	0.19736	0.343000	0.25615	0.398000	0.30690	0.749000	0.26320	-0.104000	0.12154	0.455000	0.32223	CGC	G|0.704;A|0.296	0.296	strong		0.657	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335	
LPPR5	163404	hgsc.bcm.edu	37	1	99418647	99418647	+	Silent	SNP	G	G	C	rs309087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:99418647G>C	ENST00000263177.4	-	3	821	c.600C>G	c.(598-600)gtC>gtG	p.V200V	LPPR5_ENST00000370188.3_Silent_p.V200V	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		200						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										TAGCTGCATAGACACTGAGAG	0.393													G|||	1117	0.223043	0.2738	0.1571	5008	,	,		17020	0.2351		0.1789	False		,,,				2504	0.2342				p.V200V		Atlas-SNP	.											.	.	.	.	0			c.C600G						PASS	.	G	,	1181,3225	415.0+/-337.0	163,855,1185	116.0	106.0	109.0		600,600	2.1	1.0	1	dbSNP_79	109	1501,7099	285.4+/-297.1	118,1265,2917	no	coding-synonymous,coding-synonymous	LPPR5	NM_001010861.2,NM_001037317.1	,	281,2120,4102	CC,CG,GG		17.4535,26.8044,20.6213	,	200/317,200/322	99418647	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGCATAGACACTG																												ENST00000263177.4:c.600C>G	1.37:g.99418647G>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	129	48	0.372093	NM_001037317	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Silent	SNP	ENST00000263177.4	37	CCDS30778.1																																																																																			G|0.786;C|0.214	0.214	strong		0.393	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1		
CUL9	23113	hgsc.bcm.edu	37	6	43155718	43155718	+	Missense_Mutation	SNP	G	G	A	rs145911635	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43155718G>A	ENST00000252050.4	+	7	1933	c.1849G>A	c.(1849-1851)Gag>Aag	p.E617K	CUL9_ENST00000372647.2_Missense_Mutation_p.E617K|CUL9_ENST00000354495.3_Missense_Mutation_p.E507K	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	617					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						AGCAAAGGCCGAGGCCCCTAA	0.557													G|||	11	0.00219649	0.0	0.0043	5008	,	,		16267	0.0		0.007	False		,,,				2504	0.001				p.E617K		Atlas-SNP	.											.	CUL9	248	.	0			c.G1849A						PASS	.	G	LYS/GLU	9,4397	16.8+/-37.8	0,9,2194	63.0	61.0	62.0		1849	2.9	0.2	6	dbSNP_134	62	77,8523	44.0+/-102.2	0,77,4223	yes	missense	CUL9	NM_015089.2	56	0,86,6417	AA,AG,GG		0.8953,0.2043,0.6612	benign	617/2518	43155718	86,12920	2203	4300	6503	SO:0001583	missense	23113	exon7			AAGGCCGAGGCCC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1849G>A	6.37:g.43155718G>A	ENSP00000252050:p.Glu617Lys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	11.61	1.691091	0.30052	0.002043	0.008953	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.73258	-0.73;-0.7;-0.63	4.72	2.9	0.33743	.	1.879480	0.02107	N	0.054435	T	0.39937	0.1097	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.30909	-0.9962	10	0.87932	D	0	-5.0552	5.3876	0.16226	0.1878:0.1703:0.6419:0.0	.	617;617;617	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	K	617;507;617	ENSP00000252050:E617K;ENSP00000346490:E507K;ENSP00000361730:E617K	ENSP00000252050:E617K	E	+	1	0	CUL9	43263696	0.020000	0.18652	0.189000	0.23252	0.870000	0.49936	1.715000	0.37971	0.658000	0.30925	0.467000	0.42956	GAG	G|0.995;A|0.005	0.005	strong		0.557	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
HSPH1	10808	hgsc.bcm.edu	37	13	31729729	31729729	+	Silent	SNP	A	A	G	rs1047086	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:31729729A>G	ENST00000320027.5	-	3	572	c.228T>C	c.(226-228)aaT>aaC	p.N76N	HSPH1_ENST00000445273.2_Silent_p.N78N|HSPH1_ENST00000429785.2_5'UTR|HSPH1_ENST00000380406.5_Silent_p.N76N|HSPH1_ENST00000380405.4_Silent_p.N76N	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	76					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		TGAAGGGGTCATTGAATGCTC	0.338													A|||	1131	0.225839	0.2451	0.2723	5008	,	,		16489	0.0109		0.4642	False		,,,				2504	0.1431				p.N76N		Atlas-SNP	.											.	HSPH1	65	.	0			c.T228C						PASS	.	A		1261,3145	430.8+/-342.7	171,919,1113	118.0	116.0	117.0		228	3.3	0.9	13	dbSNP_86	117	4063,4537	557.6+/-387.1	952,2159,1189	no	coding-synonymous	HSPH1	NM_006644.2		1123,3078,2302	GG,GA,AA		47.2442,28.6201,40.935		76/859	31729729	5324,7682	2203	4300	6503	SO:0001819	synonymous_variant	10808	exon3			GGGGTCATTGAAT	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"""Heat shock proteins / HSP70"""	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.228T>C	13.37:g.31729729A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Silent	SNP	ENST00000320027.5	37	CCDS9340.1																																																																																			A|0.651;G|0.349	0.349	strong		0.338	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1		
PPIC	5480	hgsc.bcm.edu	37	5	122359640	122359640	+	Missense_Mutation	SNP	T	T	C	rs451195	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:122359640T>C	ENST00000306442.4	-	5	684	c.569A>G	c.(568-570)aAc>aGc	p.N190S	RN7SL689P_ENST00000577215.1_RNA	NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	190	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.		N -> S (in dbSNP:rs451195). {ECO:0000269|Ref.2}.		protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	GATCGAGCAGTTGGTGAGTGG	0.473													T|||	707	0.141174	0.0348	0.1902	5008	,	,		16612	0.0129		0.339	False		,,,				2504	0.1789				p.N190S	Ovarian(99;690 1502 20765 45543 49568)	Atlas-SNP	.											.	PPIC	18	.	0			c.A569G						PASS	.	T	SER/ASN	378,4028	189.9+/-215.9	14,350,1839	270.0	241.0	250.0		569	4.7	1.0	5	dbSNP_80	250	2982,5618	461.9+/-365.5	509,1964,1827	yes	missense	PPIC	NM_000943.4	46	523,2314,3666	CC,CT,TT		34.6744,8.5792,25.8342	benign	190/213	122359640	3360,9646	2203	4300	6503	SO:0001583	missense	5480	exon5			GAGCAGTTGGTGA	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.569A>G	5.37:g.122359640T>C	ENSP00000303057:p.Asn190Ser	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	233	112	0.480687	NM_000943	A4LBB5	Missense_Mutation	SNP	ENST00000306442.4	37	CCDS4133.1	344	0.1575091575091575	16	0.032520325203252036	71	0.19613259668508287	5	0.008741258741258742	252	0.3324538258575198	T	16.06	3.015510	0.54468	0.085792	0.346744	ENSG00000168938	ENST00000306442	T	0.35421	1.31	5.93	4.74	0.60224	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.087968	0.85682	D	0.000000	T	0.00012	0.0000	N	0.10837	0.055	0.35742	P	0.18126399999999998	B	0.06786	0.001	B	0.04013	0.001	T	0.38672	-0.9650	9	0.39692	T	0.17	.	13.2054	0.59793	0.0:0.0:0.133:0.867	rs451195;rs17388196;rs52837765;rs60389846;rs451195	190	P45877	PPIC_HUMAN	S	190	ENSP00000303057:N190S	ENSP00000303057:N190S	N	-	2	0	PPIC	122387539	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	4.760000	0.62235	1.035000	0.39972	0.533000	0.62120	AAC	A|0.005;C|0.208	0.208	strong		0.473	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943	
TMC3	342125	hgsc.bcm.edu	37	15	81625336	81625336	+	Silent	SNP	G	G	A	rs77430896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:81625336G>A	ENST00000359440.5	-	22	2862	c.2727C>T	c.(2725-2727)ttC>ttT	p.F909F	RP11-761I4.3_ENST00000559781.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Silent_p.F910F|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						CATCTATCTTGAAATGTCTTT	0.522													G|||	313	0.0625	0.0113	0.0346	5008	,	,		18639	0.1429		0.0408	False		,,,				2504	0.091				p.F909F		Atlas-SNP	.											.	TMC3	112	.	0			c.C2727T						PASS	.	G		60,3816		1,58,1879	77.0	76.0	77.0		2727	3.0	0.0	15	dbSNP_131	77	300,7988		1,298,3845	no	coding-synonymous	TMC3	NM_001080532.1		2,356,5724	AA,AG,GG		3.6197,1.548,2.9596		909/1101	81625336	360,11804	1938	4144	6082	SO:0001819	synonymous_variant	342125	exon22			TATCTTGAAATGT	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.2727C>T	15.37:g.81625336G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_001080532		Silent	SNP	ENST00000359440.5	37	CCDS45324.1																																																																																			G|0.946;A|0.054	0.054	strong		0.522	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
CPA6	57094	hgsc.bcm.edu	37	8	68536470	68536470	+	Missense_Mutation	SNP	A	A	G	rs10957393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:68536470A>G	ENST00000297770.4	-	2	348	c.133T>C	c.(133-135)Ttt>Ctt	p.F45L	CPA6_ENST00000518549.1_Missense_Mutation_p.F45L|CPA6_ENST00000297769.4_5'UTR	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	45			F -> L (in dbSNP:rs10957393).			proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			TTGGGAATAAATCTTATCACT	0.299													A|||	1163	0.232228	0.3449	0.2421	5008	,	,		15219	0.0923		0.2227	False		,,,				2504	0.227				p.F45L		Atlas-SNP	.											CPA6,NS,adenoma,0,1	CPA6	69	1	0			c.T133C						PASS	.	A	LEU/PHE	1408,2996	458.2+/-351.9	217,974,1011	157.0	136.0	143.0		133	4.5	1.0	8	dbSNP_120	143	2025,6573	352.6+/-328.8	220,1585,2494	yes	missense	CPA6	NM_020361.4	22	437,2559,3505	GG,GA,AA		23.552,31.9709,26.4036	benign	45/438	68536470	3433,9569	2202	4299	6501	SO:0001583	missense	57094	exon2			GAATAAATCTTAT	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.133T>C	8.37:g.68536470A>G	ENSP00000297770:p.Phe45Leu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	37	CCDS6200.1	477	0.2184065934065934	166	0.33739837398373984	84	0.23204419889502761	61	0.10664335664335664	166	0.21899736147757257	A	12.60	1.987604	0.35036	0.319709	0.23552	ENSG00000165078	ENST00000297770;ENST00000518549	T;T	0.35789	1.29;1.29	5.42	4.54	0.55810	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.211058	0.29646	N	0.011573	T	0.00012	0.0000	N	0.02011	-0.69	0.09310	P	0.9999999999999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39272	-0.9622	9	0.30078	T	0.28	.	9.7063	0.40218	0.0986:0.0:0.9014:0.0	rs10957393;rs52833473;rs57275145;rs10957393	45;45	Q8N4T0-2;Q8N4T0	.;CBPA6_HUMAN	L	45	ENSP00000297770:F45L;ENSP00000431112:F45L	ENSP00000297770:F45L	F	-	1	0	CPA6	68699024	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	2.986000	0.49370	1.398000	0.46701	-0.242000	0.12053	TTT	A|0.750;G|0.249	0.249	strong		0.299	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361	
L1TD1	54596	hgsc.bcm.edu	37	1	62673287	62673287	+	Missense_Mutation	SNP	A	A	C	rs2457828	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:62673287A>C	ENST00000498273.1	+	3	1282	c.987A>C	c.(985-987)aaA>aaC	p.K329N		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	329			K -> N (in dbSNP:rs2457828). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1}.							breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						gaggaagaaaatatggaattc	0.303													A|||	378	0.0754792	0.0567	0.1297	5008	,	,		18402	0.001		0.17	False		,,,				2504	0.0419				p.K329N		Atlas-SNP	.											.	L1TD1	114	.	0			c.A987C						PASS	.	A	ASN/LYS,ASN/LYS	203,2893		8,187,1353	30.0	30.0	30.0		987,987	1.0	0.0	1	dbSNP_100	30	783,4649		59,665,1992	yes	missense,missense	L1TD1	NM_019079.4,NM_001164835.1	94,94	67,852,3345	CC,CA,AA		14.4146,6.5568,11.5619	benign,benign	329/866,329/866	62673287	986,7542	1548	2716	4264	SO:0001583	missense	54596	exon4			AAGAAAATATGGA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.987A>C	1.37:g.62673287A>C	ENSP00000419901:p.Lys329Asn	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	212	0.09706959706959707	28	0.056910569105691054	49	0.13535911602209943	1	0.0017482517482517483	134	0.17678100263852242	A	8.877	0.950714	0.18431	0.065568	0.144146	ENSG00000240563	ENST00000498273	T	0.12879	2.64	2.2	1.01	0.19927	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.18310	0.027	B	0.25140	0.058	T	0.36625	-0.9740	8	0.62326	D	0.03	.	4.3241	0.11031	0.6995:0.0:0.0:0.3005	rs2457828;rs17379594;rs52791985;rs58639023;rs2457828	329	Q5T7N2	LITD1_HUMAN	N	329	ENSP00000419901:K329N	ENSP00000419901:K329N	K	+	3	2	L1TD1	62445875	0.003000	0.15002	0.019000	0.16419	0.003000	0.03518	-0.427000	0.06999	0.277000	0.22141	0.383000	0.25322	AAA	A|0.905;C|0.095	0.095	strong		0.303	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
ITPKA	3706	hgsc.bcm.edu	37	15	41793728	41793728	+	Missense_Mutation	SNP	A	A	G	rs143540732		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:41793728A>G	ENST00000260386.5	+	2	610	c.557A>G	c.(556-558)tAc>tGc	p.Y186C		NM_002220.2	NP_002211.1	P23677	IP3KA_HUMAN	inositol-trisphosphate 3-kinase A	186					actin cytoskeleton organization (GO:0030036)|dendritic spine maintenance (GO:0097062)|inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|positive regulation of dendritic spine morphogenesis (GO:0061003)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendritic spine (GO:0043197)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.Y186F(1)		kidney(1)|lung(3)|skin(1)	5		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		AAGAAGCGCTACGCCTGGGTG	0.637																																					p.Y186C		Atlas-SNP	.											ITPKA,NS,carcinoma,0,1	ITPKA	19	1	1	Substitution - Missense(1)	lung(1)	c.A557G						PASS	.	A	CYS/TYR	1,4403	2.1+/-5.4	0,1,2201	29.0	25.0	26.0		557	4.7	1.0	15	dbSNP_134	26	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ITPKA	NM_002220.2	194	0,5,6497	GG,GA,AA		0.0465,0.0227,0.0384	probably-damaging	186/462	41793728	5,12999	2202	4300	6502	SO:0001583	missense	3706	exon2			AGCGCTACGCCTG	X54938	CCDS10076.1	15q15.1	2011-04-28	2011-04-28		ENSG00000137825	ENSG00000137825	2.7.1.127		6178	protein-coding gene	gene with protein product		147521	"""inositol 1,4,5-trisphosphate 3-kinase A"""			1330886, 2175886	Standard	NM_002220		Approved	IP3KA, IP3-3KA	uc001znz.3	P23677	OTTHUMG00000130343	ENST00000260386.5:c.557A>G	15.37:g.41793728A>G	ENSP00000260386:p.Tyr186Cys	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	NM_002220	Q8TAN3	Missense_Mutation	SNP	ENST00000260386.5	37	CCDS10076.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207364	0.79240	2.27E-4	4.65E-4	ENSG00000137825	ENST00000425927;ENST00000260386	T	0.50548	0.74	4.71	4.71	0.59529	.	0.226565	0.38837	N	0.001556	T	0.66197	0.2765	M	0.70595	2.14	0.53688	D	0.999977	D	0.89917	1.0	D	0.81914	0.995	T	0.70457	-0.4866	10	0.87932	D	0	-10.9047	12.9023	0.58133	1.0:0.0:0.0:0.0	.	186	P23677	IP3KA_HUMAN	C	81;186	ENSP00000260386:Y186C	ENSP00000260386:Y186C	Y	+	2	0	ITPKA	39581020	0.997000	0.39634	0.996000	0.52242	0.995000	0.86356	3.558000	0.53749	1.972000	0.57404	0.379000	0.24179	TAC	A|1.000;G|0.000	0.000	weak		0.637	ITPKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252695.3	NM_002220	
FMO4	2329	hgsc.bcm.edu	37	1	171303836	171303836	+	Missense_Mutation	SNP	G	G	A	rs45599742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171303836G>A	ENST00000367749.3	+	8	1444	c.1114G>A	c.(1114-1116)Ggc>Agc	p.G372S		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	372			G -> S (in dbSNP:rs45599742). {ECO:0000269|Ref.2}.		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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CGGCCTTATCGGCCTTAAAGG	0.433													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		18706	0.0		0.005	False		,,,				2504	0.0				p.G372S	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											.	FMO4	64	.	0			c.G1114A						PASS	.	G	SER/GLY	4,4402	8.1+/-20.4	0,4,2199	74.0	73.0	73.0		1114	-11.3	0.0	1	dbSNP_127	73	37,8563	25.7+/-73.6	0,37,4263	yes	missense	FMO4	NM_002022.1	56	0,41,6462	AA,AG,GG		0.4302,0.0908,0.3152	benign	372/559	171303836	41,12965	2203	4300	6503	SO:0001583	missense	2329	exon8			CTTATCGGCCTTA	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.1114G>A	1.37:g.171303836G>A	ENSP00000356723:p.Gly372Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	151	88	0.582781	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	8.204	0.798723	0.16397	9.08E-4	0.004302	ENSG00000076258	ENST00000367749	T	0.66995	-0.24	5.63	-11.3	0.00108	.	0.989869	0.08259	N	0.973384	T	0.16385	0.0394	N	0.04746	-0.17	0.09310	N	1	B	0.13145	0.007	B	0.18561	0.022	T	0.42515	-0.9447	10	0.45353	T	0.12	0.8428	10.3207	0.43764	0.1423:0.2863:0.5002:0.0712	rs45599742	372	P31512	FMO4_HUMAN	S	372	ENSP00000356723:G372S	ENSP00000356723:G372S	G	+	1	0	FMO4	169570460	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.453000	0.06778	-3.204000	0.00216	-1.043000	0.02367	GGC	G|0.996;A|0.004	0.004	strong		0.433	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022	
AHNAK2	113146	hgsc.bcm.edu	37	14	105420927	105420927	+	Silent	SNP	A	A	G	rs879210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	80	80	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	
NPTXR	23467	hgsc.bcm.edu	37	22	39222652	39222652	+	Silent	SNP	G	G	A	rs5757299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39222652G>A	ENST00000333039.2	-	3	1074	c.951C>T	c.(949-951)taC>taT	p.Y317Y		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	317	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					CGGTGAATGCGTAGAGCTCGG	0.627													G|||	2305	0.460264	0.4107	0.2824	5008	,	,		18082	0.7589		0.3847	False		,,,				2504	0.4233				p.Y317Y	Pancreas(139;2521 3281 36965)	Atlas-SNP	.											.	NPTXR	34	.	0			c.C951T						PASS	.	G		1671,2735	509.3+/-367.2	325,1021,857	93.0	82.0	85.0		951	3.6	1.0	22	dbSNP_114	85	3442,5158	506.1+/-376.5	696,2050,1554	no	coding-synonymous	NPTXR	NM_014293.3		1021,3071,2411	AA,AG,GG		40.0233,37.9256,39.3126		317/501	39222652	5113,7893	2203	4300	6503	SO:0001819	synonymous_variant	23467	exon3			GAATGCGTAGAGC	AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.951C>T	22.37:g.39222652G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_014293		Silent	SNP	ENST00000333039.2	37	CCDS33647.1																																																																																			G|0.577;A|0.423	0.423	strong		0.627	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318194.2	NM_014293	
USP33	23032	hgsc.bcm.edu	37	1	78183670	78183670	+	Silent	SNP	G	G	T	rs41313399	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:78183670G>T	ENST00000370793.1	-	18	2239	c.1893C>A	c.(1891-1893)acC>acA	p.T631T	USP33_ENST00000370792.3_Silent_p.T623T|USP33_ENST00000357428.1_Silent_p.T631T|USP33_ENST00000370794.3_Silent_p.T600T	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	631	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						ATGAAACATGGGTACTGATTT	0.353													G|||	118	0.0235623	0.0227	0.0403	5008	,	,		17101	0.0		0.0417	False		,,,				2504	0.0184				p.T631T	Melanoma(152;72 1870 11110 26780 42647)	Atlas-SNP	.											.	USP33	87	.	0			c.C1893A						PASS	.	G	,,	79,4327	68.1+/-105.8	0,79,2124	117.0	124.0	122.0		1893,1800,1869	0.1	1.0	1	dbSNP_127	122	276,8324	104.4+/-165.4	8,260,4032	no	coding-synonymous,coding-synonymous,coding-synonymous	USP33	NM_015017.3,NM_201624.1,NM_201626.1	,,	8,339,6156	TT,TG,GG		3.2093,1.793,2.7295	,,	631/943,600/912,623/829	78183670	355,12651	2203	4300	6503	SO:0001819	synonymous_variant	23032	exon18			AACATGGGTACTG	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.1893C>A	1.37:g.78183670G>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_015017	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1	56	0.02564102564102564	9	0.018292682926829267	16	0.04419889502762431	0	0.0	31	0.040897097625329816	G	6.770	0.510913	0.12883	0.01793	0.032093	ENSG00000077254	ENST00000481579	.	.	.	4.7	0.0572	0.14322	.	.	.	.	.	T	0.33527	0.0866	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20009	-1.0288	4	.	.	.	.	4.6601	0.12637	0.3487:0.0:0.5144:0.1368	rs41313399;rs61734895	.	.	.	H	236	.	.	P	-	2	0	USP33	77956258	0.962000	0.33011	0.996000	0.52242	0.741000	0.42261	0.055000	0.14229	-0.184000	0.10567	0.563000	0.77884	CCC	G|0.973;T|0.027	0.027	strong		0.353	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017	
TDRD5	163589	hgsc.bcm.edu	37	1	179562740	179562740	+	Missense_Mutation	SNP	G	G	C	rs61310274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:179562740G>C	ENST00000367614.1	+	3	737	c.378G>C	c.(376-378)agG>agC	p.R126S	TDRD5_ENST00000444136.1_Missense_Mutation_p.R126S|RP11-545A16.4_ENST00000567150.1_RNA|TDRD5_ENST00000294848.8_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	2	0.00732601		WXS	Illumina HiSeq	Phase_I	306	304	0.993464	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	
UFL1	23376	hgsc.bcm.edu	37	6	96985311	96985311	+	Silent	SNP	T	T	C	rs55792562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:96985311T>C	ENST00000369278.4	+	9	930	c.864T>C	c.(862-864)taT>taC	p.Y288Y		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	288					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										AGAAAAGATATAAGACTACAC	0.373													T|||	65	0.0129792	0.0166	0.0259	5008	,	,		17079	0.0		0.0229	False		,,,				2504	0.002				p.Y288Y		Atlas-SNP	.											.	.	.	.	0			c.T864C						PASS	.	T		61,4345	58.1+/-94.6	0,61,2142	159.0	159.0	159.0		864	-6.8	0.9	6	dbSNP_129	159	247,8351	99.7+/-161.2	4,239,4056	no	coding-synonymous	UFL1	NM_015323.4		4,300,6198	CC,CT,TT		2.8728,1.3845,2.3685		288/795	96985311	308,12696	2203	4299	6502	SO:0001819	synonymous_variant	23376	exon9			AAGATATAAGACT	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.864T>C	6.37:g.96985311T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	141	76	0.539007	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																			T|0.978;C|0.022	0.022	strong		0.373	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
MROH2B	133558	hgsc.bcm.edu	37	5	41048533	41048533	+	Missense_Mutation	SNP	C	C	T	rs13173930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:41048533C>T	ENST00000399564.4	-	16	2027	c.1577G>A	c.(1576-1578)cGt>cAt	p.R526H	MROH2B_ENST00000506092.2_Missense_Mutation_p.R81H	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	526			R -> H (in dbSNP:rs13173930). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.														ACCAGCCCCACGTAACTCCCC	0.453													C|||	1177	0.235024	0.1573	0.3329	5008	,	,		17651	0.12		0.3787	False		,,,				2504	0.2413				p.R526H		Atlas-SNP	.											.	.	.	.	0			c.G1577A						PASS	.	C	HIS/ARG	701,3041		61,579,1231	88.0	81.0	83.0		1577	3.0	0.1	5	dbSNP_121	83	3138,5060		614,1910,1575	yes	missense	HEATR7B2	NM_173489.4	29	675,2489,2806	TT,TC,CC		38.2776,18.7333,32.1524	probably-damaging	526/1586	41048533	3839,8101	1871	4099	5970	SO:0001583	missense	133558	exon16			GCCCCACGTAACT		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1577G>A	5.37:g.41048533C>T	ENSP00000382476:p.Arg526His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	559	0.25595238095238093	78	0.15853658536585366	124	0.3425414364640884	64	0.11188811188811189	293	0.3865435356200528	C	8.610	0.888946	0.17540	0.187333	0.382776	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.09163	3.01;3.01	4.87	3.03	0.35002	Armadillo-type fold (1);	1.072850	0.07119	N	0.843613	T	0.00012	0.0000	L	0.54323	1.7	0.54753	P	2.0000000000020002E-5	B	0.09022	0.002	B	0.04013	0.001	T	0.43621	-0.9380	9	0.45353	T	0.12	.	5.8829	0.18866	0.2126:0.6886:0.0:0.0988	rs13173930;rs17854770;rs52825689;rs60763656;rs13173930	526	Q7Z745	HTRB2_HUMAN	H	81;230;526	ENSP00000441504:R81H;ENSP00000382476:R526H	ENSP00000296803:R230H	R	-	2	0	HEATR7B2	41084290	0.742000	0.28228	0.096000	0.21009	0.066000	0.16364	1.280000	0.33202	0.714000	0.32081	0.655000	0.94253	CGT	C|0.756;T|0.244	0.244	strong		0.453	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
TUBG1	7283	hgsc.bcm.edu	37	17	40766546	40766546	+	Silent	SNP	C	C	G	rs1045710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40766546C>G	ENST00000251413.3	+	10	1091	c.1029C>G	c.(1027-1029)cgC>cgG	p.R343R		NM_001070.4	NP_001061.2	P23258	TBG1_HUMAN	tubulin, gamma 1	343					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic spindle organization (GO:0000212)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	apical part of cell (GO:0045177)|cell leading edge (GO:0031252)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)|polar microtubule (GO:0005827)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Vinblastine(DB00570)	TCCGGGAACGCAAGTTGGCCA	0.657													c|||	2960	0.591054	0.7171	0.5159	5008	,	,		16066	0.4673		0.5239	False		,,,				2504	0.6708				p.R343R	Colon(20;114 698 11420 22864)	Atlas-SNP	.											.	TUBG1	25	.	0			c.C1029G						PASS	.	C		2995,1409		1053,889,260	37.0	44.0	42.0		1029	-2.2	0.7	17	dbSNP_86	42	4507,4079		1270,1967,1056	no	coding-synonymous	TUBG1	NM_001070.4		2323,2856,1316	GG,GC,CC		47.5076,31.9936,42.2479		343/452	40766546	7502,5488	2202	4293	6495	SO:0001819	synonymous_variant	7283	exon10			GGAACGCAAGTTG	BC000619	CCDS11433.1	17q21.31	2010-03-15	2000-01-20		ENSG00000131462	ENSG00000131462		"""Tubulins"""	12417	protein-coding gene	gene with protein product		191135	"""tubulin, gamma polypeptide"""	TUBG		1904010	Standard	NM_001070		Approved	TUBGCP1	uc002ian.3	P23258		ENST00000251413.3:c.1029C>G	17.37:g.40766546C>G		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	273	111	0.406593	NM_001070	Q53X79|Q9BW59	Silent	SNP	ENST00000251413.3	37	CCDS11433.1																																																																																			G|1.000;|0.000	1.000	weak		0.657	TUBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450548.1	NM_001070	
ZXDC	79364	hgsc.bcm.edu	37	3	126191011	126191011	+	Silent	SNP	G	G	A	rs62264721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:126191011G>A	ENST00000389709.3	-	2	1098	c.1045C>T	c.(1045-1047)Ctg>Ttg	p.L349L	ZXDC_ENST00000336332.5_Silent_p.L349L	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	349					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		TGGCTCCGCAGGTGAATTTTC	0.468													G|||	105	0.0209665	0.0061	0.0058	5008	,	,		18844	0.0665		0.0119	False		,,,				2504	0.0143				p.L349L		Atlas-SNP	.											.	ZXDC	87	.	0			c.C1045T						PASS	.	G	,	35,4239		0,35,2102	58.0	63.0	62.0		1045,1045	2.4	1.0	3	dbSNP_129	62	88,8460		0,88,4186	yes	coding-synonymous,coding-synonymous	ZXDC	NM_001040653.2,NM_025112.4	,	0,123,6288	AA,AG,GG		1.0295,0.8189,0.9593	,	349/711,349/859	126191011	123,12699	2137	4274	6411	SO:0001819	synonymous_variant	79364	exon2			TCCGCAGGTGAAT	AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"""Zinc fingers, C2H2-type"""	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.1045C>T	3.37:g.126191011G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Silent	SNP	ENST00000389709.3	37	CCDS43145.1																																																																																			G|0.982;A|0.018	0.018	strong		0.468	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112	
NUP88	4927	hgsc.bcm.edu	37	17	5326089	5326089	+	5'Flank	SNP	C	C	T	rs1071648	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5326089C>T	ENST00000573584.1	-	0	0				RPAIN_ENST00000574003.1_Splice_Site_p.L85L|CTC-524C5.2_ENST00000575890.1_RNA|RPAIN_ENST00000405578.4_Splice_Site_p.L85L|RPAIN_ENST00000327154.6_Splice_Site_p.L85L|RPAIN_ENST00000381208.5_Splice_Site_p.L85L|RPAIN_ENST00000381209.3_Splice_Site_p.L85L|RPAIN_ENST00000536255.2_Splice_Site_p.L85L	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa						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						TCTCTTCCAGCTGGAGGAGCT	0.473													T|||	2233	0.445887	0.1899	0.4193	5008	,	,		20883	0.7937		0.3052	False		,,,				2504	0.5971				p.L85L		Atlas-SNP	.											.	RPAIN	24	.	0			c.C253T						PASS	.	T	,,,,,	966,3440	734.1+/-410.5	87,792,1324	110.0	102.0	104.0		253,253,253,253,253,253	3.3	1.0	17	dbSNP_86	104	2362,6238	701.7+/-405.2	300,1762,2238	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	RPAIN	NM_001033002.3,NM_001160243.1,NM_001160244.1,NM_001160246.1,NM_001160266.1,NM_001160267.1	,,,,,	387,2554,3562	TT,TC,CC		27.4651,21.9246,25.5882	,,,,,	85/220,85/232,85/173,85/107,85/149,85/107	5326089	3328,9678	2203	4300	6503	SO:0001631	upstream_gene_variant	84268	exon3			TTCCAGCTGGAGG	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		17.37:g.5326089C>T	Exception_encountered	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	210	112	0.533333	NM_001160246	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			C|0.689;T|0.311	0.311	strong		0.473	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
OR51F1	256892	hgsc.bcm.edu	37	11	4790308	4790308	+	Silent	SNP	A	A	G	rs1030725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790308A>G	ENST00000380383.1	-	1	860	c.861T>C	c.(859-861)aaT>aaC	p.N287N	OR51F1_ENST00000343430.3_Silent_p.N280N|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	287						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)		GCAGGTATACATTAGCCATCA	0.478													A|||	1080	0.215655	0.4569	0.2017	5008	,	,		20536	0.0		0.2704	False		,,,				2504	0.0654				p.N280N		Atlas-SNP	.											.	OR51F1	60	.	0			c.T840C						PASS	.	A		1968,2434	556.1+/-379.4	445,1078,678	105.0	98.0	101.0		840	3.1	0.6	11	dbSNP_86	101	2178,6418	372.9+/-336.8	291,1596,2411	no	coding-synonymous	OR51F1	NM_001004752.1		736,2674,3089	GG,GA,AA		25.3374,44.707,31.8972		280/313	4790308	4146,8852	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			GTATACATTAGCC	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.861T>C	11.37:g.4790308A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.710;G|0.290	0.290	strong		0.478	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
MAP6	4135	hgsc.bcm.edu	37	11	75298797	75298797	+	Silent	SNP	A	A	G	rs1231128	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:75298797A>G	ENST00000304771.3	-	4	2499	c.1749T>C	c.(1747-1749)gaT>gaC	p.D583D	CTD-2530H12.4_ENST00000527803.1_RNA|MAP6_ENST00000526740.1_Silent_p.D254D|MAP6_ENST00000526689.1_5'Flank	NM_033063.1	NP_149052.1	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6	583	Pro-rich.				dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|microtubule cytoskeleton organization (GO:0000226)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	19	Ovarian(111;0.11)					TGGGACCTTCATCCTTGACAG	0.522													A|||	1884	0.376198	0.3041	0.5648	5008	,	,		21623	0.2579		0.3161	False		,,,				2504	0.5235				p.D583D	Esophageal Squamous(181;1115 2007 8647 17065 22697)	Atlas-SNP	.											.	MAP6	45	.	0			c.T1749C						PASS	.	A		1262,3138	432.2+/-343.2	192,878,1130	145.0	135.0	139.0		1749	-5.5	0.0	11	dbSNP_87	139	2625,5961	425.0+/-354.8	391,1843,2059	no	coding-synonymous	MAP6	NM_033063.1		583,2721,3189	GG,GA,AA		30.573,28.6818,29.9322		583/814	75298797	3887,9099	2200	4293	6493	SO:0001819	synonymous_variant	4135	exon4			ACCTTCATCCTTG	AK123340	CCDS31641.1, CCDS44686.1	11q13.5	2005-10-11			ENSG00000171533	ENSG00000171533			6868	protein-coding gene	gene with protein product		601783				10516426, 12231625	Standard	NM_207577		Approved	KIAA1878, STOP, FLJ41346	uc001owu.3	Q96JE9	OTTHUMG00000165343	ENST00000304771.3:c.1749T>C	11.37:g.75298797A>G		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	356	353	0.991573	NM_033063	A7E2A1|Q6P3T0|Q6ZWB8	Silent	SNP	ENST00000304771.3	37	CCDS31641.1																																																																																			A|0.685;G|0.315	0.315	strong		0.522	MAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383527.1	NM_033063	
CCDC171	203238	hgsc.bcm.edu	37	9	15571630	15571630	+	Missense_Mutation	SNP	T	T	A	rs443563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:15571630T>A	ENST00000380701.3	+	3	378	c.50T>A	c.(49-51)aTt>aAt	p.I17N	CCDC171_ENST00000297641.3_Missense_Mutation_p.I17N|CCDC171_ENST00000535968.1_Missense_Mutation_p.I17N	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	17			I -> N (in dbSNP:rs443563). {ECO:0000269|PubMed:15489334}.														AGGTTGAAGATTGCCTCATTG	0.279													A|||	380	0.0758786	0.1997	0.0519	5008	,	,		17906	0.004		0.0487	False		,,,				2504	0.0276				p.I17N		Atlas-SNP	.											.	.	.	.	0			c.T50A						PASS	.	A	ASN/ILE	818,3586	731.2+/-410.2	80,658,1464	63.0	72.0	69.0		50	-7.4	0.3	9	dbSNP_80	69	405,8179	792.4+/-407.5	11,383,3898	yes	missense	C9orf93	NM_173550.2	149	91,1041,5362	AA,AT,TT		4.7181,18.574,9.4164	benign	17/1327	15571630	1223,11765	2202	4292	6494	SO:0001583	missense	203238	exon3			TGAAGATTGCCTC	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.50T>A	9.37:g.15571630T>A	ENSP00000370077:p.Ile17Asn	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	150	0.06868131868131869	101	0.20528455284552846	15	0.04143646408839779	2	0.0034965034965034965	32	0.04221635883905013	A	0.642	-0.812776	0.02798	0.18574	0.047181	ENSG00000164989	ENST00000535968;ENST00000297641;ENST00000380701	T;T;T	0.28255	1.62;2.6;2.61	4.6	-7.39	0.01402	.	0.852819	0.09848	N	0.747982	T	0.00012	0.0000	N	0.02539	-0.55	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	0.29912	-0.9996	9	0.15499	T	0.54	-0.312	0.9958	0.01466	0.2121:0.3404:0.2255:0.222	rs443563;rs443563	17;17;17	Q6TFL3-3;Q6TFL3;Q7Z3F8	.;CI093_HUMAN;.	N	17	ENSP00000438838:I17N;ENSP00000297641:I17N;ENSP00000370077:I17N	ENSP00000297641:I17N	I	+	2	0	C9orf93	15561630	0.462000	0.25791	0.340000	0.25575	0.239000	0.25481	-0.235000	0.09016	-2.123000	0.00823	-1.644000	0.00765	ATT	T|0.908;A|0.092	0.092	strong		0.279	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
LRFN3	79414	hgsc.bcm.edu	37	19	36430798	36430798	+	Silent	SNP	A	A	G	rs1057265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	16	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	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	
NDST1	3340	hgsc.bcm.edu	37	5	149919778	149919778	+	Silent	SNP	G	G	A	rs61732050	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149919778G>A	ENST00000261797.6	+	8	2203	c.1701G>A	c.(1699-1701)gcG>gcA	p.A567A	NDST1_ENST00000523767.1_Silent_p.A567A	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	567	Heparan sulfate N-deacetylase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCAGTTGGCGCAGAAGTACT	0.637													g|||	120	0.0239617	0.0015	0.0519	5008	,	,		20869	0.001		0.0736	False		,,,				2504	0.0072				p.A567A		Atlas-SNP	.											.	NDST1	79	.	0			c.G1701A						PASS	.	A		51,4355	50.9+/-86.3	0,51,2152	57.0	54.0	55.0		1701	-2.3	1.0	5	dbSNP_129	55	490,8110	140.9+/-197.4	14,462,3824	no	coding-synonymous	NDST1	NM_001543.4		14,513,5976	AA,AG,GG		5.6977,1.1575,4.1596		567/883	149919778	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	3340	exon8			GTTGGCGCAGAAG	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"""Sulfotransferases, membrane-bound"""	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.1701G>A	5.37:g.149919778G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_001543	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																			G|0.958;A|0.042	0.042	strong		0.637	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
ROS1	6098	hgsc.bcm.edu	37	6	117622188	117622188	+	Missense_Mutation	SNP	T	T	G	rs529156	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:117622188T>G	ENST00000368508.3	-	42	6880	c.6682A>C	c.(6682-6684)Aag>Cag	p.K2228Q	RN7SKP51_ENST00000410781.1_RNA|RN7SKP18_ENST00000516005.1_RNA|ROS1_ENST00000368507.3_Missense_Mutation_p.K2222Q	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2228			K -> Q (in dbSNP:rs529156). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2352949}.		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)	p.K2228Q(1)	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)		TCTCTGGACTTATAAATGCTA	0.378			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								G|||	698	0.139377	0.0386	0.1657	5008	,	,		16450	0.1587		0.2197	False		,,,				2504	0.1544				p.K2228Q		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	ROS1_ENST00000368508,NS,carcinoma,0,1	ROS1	728	1	1	Substitution - Missense(1)	stomach(1)	c.A6682C						scavenged	.	G	GLN/LYS	327,4079	795.6+/-415.3	16,295,1892	82.0	82.0	82.0		6682	4.1	1.0	6	dbSNP_83	82	2234,6366	708.6+/-405.7	266,1702,2332	yes	missense	ROS1	NM_002944.2	53	282,1997,4224	GG,GT,TT		25.9767,7.4217,19.6909	benign	2228/2348	117622188	2561,10445	2203	4300	6503	SO:0001583	missense	6098	exon42			TGGACTTATAAAT	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.6682A>C	6.37:g.117622188T>G	ENSP00000357494:p.Lys2228Gln	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	348	0.15934065934065933	21	0.042682926829268296	62	0.1712707182320442	87	0.1520979020979021	178	0.23482849604221637	G	6.301	0.423609	0.11928	0.074217	0.259767	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.70631	-0.5;-0.5	5.02	4.07	0.47477	.	0.659654	0.14134	N	0.339182	T	0.20047	0.0482	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06770	-1.0808	9	0.21540	T	0.41	.	5.0983	0.14745	0.0979:0.0:0.5228:0.3793	rs529156;rs52813753;rs56890870;rs529156	2228	P08922	ROS1_HUMAN	Q	2228;2222	ENSP00000357494:K2228Q;ENSP00000357493:K2222Q	ENSP00000357493:K2222Q	K	-	1	0	ROS1	117728881	0.856000	0.29760	0.983000	0.44433	0.632000	0.37999	1.029000	0.30140	1.449000	0.47699	-0.121000	0.15023	AAG	T|0.824;G|0.176	0.176	strong		0.378	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
RPA1	6117	hgsc.bcm.edu	37	17	1795180	1795180	+	Silent	SNP	T	T	C	rs2230931	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	66	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	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	
CROT	54677	hgsc.bcm.edu	37	7	87021023	87021023	+	Missense_Mutation	SNP	G	G	C	rs7785206	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:87021023G>C	ENST00000331536.3	+	14	1605	c.1420G>C	c.(1420-1422)Gtc>Ctc	p.V474L	CROT_ENST00000419147.2_Missense_Mutation_p.V502L|CROT_ENST00000442291.1_Missense_Mutation_p.V474L	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	474			V -> L (in dbSNP:rs7785206).		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)	GGATCCTTCTGTCAATGTGAG	0.403													G|||	437	0.0872604	0.1021	0.0865	5008	,	,		18322	0.0129		0.0726	False		,,,				2504	0.1595				p.V502L		Atlas-SNP	.											.	CROT	81	.	0			c.G1504C						PASS	.	G	LEU/VAL,LEU/VAL	412,3994	204.1+/-226.4	15,382,1806	91.0	82.0	85.0		1504,1420	-11.2	0.0	7	dbSNP_116	85	672,7928	168.6+/-220.1	21,630,3649	yes	missense,missense	CROT	NM_001143935.1,NM_021151.3	32,32	36,1012,5455	CC,CG,GG		7.814,9.3509,8.3346	benign,benign	502/641,474/613	87021023	1084,11922	2203	4300	6503	SO:0001583	missense	54677	exon15			CCTTCTGTCAATG		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.1420G>C	7.37:g.87021023G>C	ENSP00000331981:p.Val474Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_001143935	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Missense_Mutation	SNP	ENST00000331536.3	37	CCDS5604.1	143	0.06547619047619048	60	0.12195121951219512	18	0.049723756906077346	4	0.006993006993006993	61	0.08047493403693931	G	4.653	0.121307	0.08881	0.093509	0.07814	ENSG00000005469	ENST00000419147;ENST00000331536;ENST00000442291	D;D;D	0.89050	-2.46;-2.46;-2.46	5.62	-11.2	0.00127	.	0.834673	0.11493	N	0.558566	T	0.03136	0.0092	N	0.24115	0.695	0.80722	P	0.0	B;B	0.22080	0.064;0.005	B;B	0.27380	0.079;0.03	T	0.39683	-0.9602	9	0.08599	T	0.76	0.6365	11.2	0.48736	0.1439:0.0:0.5074:0.3487	rs7785206;rs7785206	502;474	E7EQF2;Q9UKG9	.;OCTC_HUMAN	L	502;474;474	ENSP00000413575:V502L;ENSP00000331981:V474L;ENSP00000411983:V474L	ENSP00000331981:V474L	V	+	1	0	CROT	86858959	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-0.827000	0.04424	-2.259000	0.00693	-1.317000	0.01298	GTC	G|0.924;C|0.076	0.076	strong		0.403	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151	
HS3ST6	64711	hgsc.bcm.edu	37	16	1962047	1962047	+	Silent	SNP	G	G	A	rs1657140|rs386787777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1962047G>A	ENST00000293937.3	-	2	572	c.573C>T	c.(571-573)taC>taT	p.Y191Y	HS3ST6_ENST00000454677.2_Silent_p.Y208Y|HS3ST6_ENST00000443547.1_Silent_p.Y160Y			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	191					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						GCGTCTGGGCGTAGTCGGAGA	0.726													g|||	1961	0.391573	0.2345	0.3386	5008	,	,		13691	0.4643		0.3767	False		,,,				2504	0.5818				p.Y160Y		Atlas-SNP	.											.	HS3ST6	26	.	0			c.C480T						PASS	.	G		983,3403		118,747,1328	17.0	22.0	20.0		480	-7.8	0.3	16	dbSNP_89	20	2967,5625		541,1885,1870	no	coding-synonymous	HS3ST6	NM_001009606.2		659,2632,3198	AA,AG,GG		34.5321,22.4122,30.4361		160/312	1962047	3950,9028	2193	4296	6489	SO:0001819	synonymous_variant	64711	exon2			CTGGGCGTAGTCG			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.573C>T	16.37:g.1962047G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_001009606	Q96RX7	Silent	SNP	ENST00000293937.3	37																																																																																				G|0.664;A|0.336	0.336	strong		0.726	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
DND1	373863	hgsc.bcm.edu	37	5	140050940	140050940	+	Missense_Mutation	SNP	C	C	T	rs77880328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140050940C>T	ENST00000542735.1	-	4	1043	c.1000G>A	c.(1000-1002)Gag>Aag	p.E334K	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	334					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCCCAGACTCACTGAGTGCC	0.592																																					p.E334K		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	0			c.G1000A						scavenged	.						67.0	61.0	63.0					5																	140050940		2008	4046	6054	SO:0001583	missense	373863	exon4			CAGACTCACTGAG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1000G>A	5.37:g.140050940C>T	ENSP00000445366:p.Glu334Lys	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	961	164	0.170656	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.984700	0.35036	.	.	ENSG00000256453	ENST00000542735	T	0.32988	1.43	5.3	3.53	0.40419	.	0.429652	0.22940	N	0.053797	T	0.16769	0.0403	L	0.27053	0.805	0.27535	N	0.950973	B	0.02656	0.0	B	0.06405	0.002	T	0.29792	-1.0000	10	0.05620	T	0.96	-17.9422	9.0835	0.36567	0.0:0.7627:0.0:0.2373	.	334	Q8IYX4	DND1_HUMAN	K	334	ENSP00000445366:E334K	ENSP00000445366:E334K	E	-	1	0	DND1	140031124	0.995000	0.38212	0.998000	0.56505	0.721000	0.41392	1.914000	0.39966	0.821000	0.34540	0.551000	0.68910	GAG	A|0.029;G|0.971	.	alt		0.592	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
MOK	5891	hgsc.bcm.edu	37	14	102698131	102698131	+	Silent	SNP	G	G	A	rs7152550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:102698131G>A	ENST00000361847.2	-	10	1125	c.894C>T	c.(892-894)agC>agT	p.S298S	MOK_ENST00000561150.1_Intron|MOK_ENST00000517966.1_Intron|MOK_ENST00000522867.1_Intron|MOK_ENST00000523231.1_Intron|MOK_ENST00000522534.1_Intron|MOK_ENST00000520266.1_Intron|MOK_ENST00000524370.1_Intron|MOK_ENST00000193029.6_Intron|MOK_ENST00000519058.1_Intron|MOK_ENST00000522874.1_Silent_p.S297S|MOK_ENST00000524214.1_Silent_p.S268S	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	298					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)										CTTTTCTGTGGCTGCCCAGAG	0.567													G|||	279	0.0557109	0.0166	0.049	5008	,	,		17613	0.003		0.0795	False		,,,				2504	0.1431				p.S298S		Atlas-SNP	.											.	.	.	.	0			c.C894T						PASS	.	G		121,4285	89.7+/-128.4	1,119,2083	108.0	110.0	109.0		894	-1.0	0.0	14	dbSNP_116	109	617,7983	161.4+/-214.4	17,583,3700	no	coding-synonymous	MOK	NM_014226.1		18,702,5783	AA,AG,GG		7.1744,2.7463,5.6743		298/420	102698131	738,12268	2203	4300	6503	SO:0001819	synonymous_variant	5891	exon10			TCTGTGGCTGCCC	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.894C>T	14.37:g.102698131G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Silent	SNP	ENST00000361847.2	37	CCDS9971.1	81	0.03708791208791209	10	0.02032520325203252	21	0.058011049723756904	2	0.0034965034965034965	48	0.0633245382585752	G	4.163	0.028658	0.08054	0.027463	0.071744	ENSG00000080823	ENST00000521937	.	.	.	4.73	-1.03	0.10102	.	.	.	.	.	T	0.01661	0.0053	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.17531	-1.0366	4	.	.	.	-17.238	4.5829	0.12267	0.0905:0.4589:0.3077:0.1429	rs7152550;rs7152550	.	.	.	S	10	.	.	P	-	1	0	RAGE	101767884	0.002000	0.14202	0.000000	0.03702	0.025000	0.11179	0.206000	0.17375	-0.088000	0.12506	-0.391000	0.06502	CCA	G|0.951;A|0.049	0.049	strong		0.567	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
SH3BP1	23616	hgsc.bcm.edu	37	22	38046695	38046695	+	Missense_Mutation	SNP	C	C	A	rs12170939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38046695C>A	ENST00000357436.4	+	16	1874	c.1561C>A	c.(1561-1563)Ccg>Acg	p.P521T	SH3BP1_ENST00000599616.1_Missense_Mutation_p.P457T|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	521					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					agctccagctccggccccagc	0.657													C|||	664	0.132588	0.0756	0.2824	5008	,	,		14412	0.0635		0.1849	False		,,,				2504	0.1207				p.P521T		Atlas-SNP	.											.	SH3BP1	41	.	0			c.C1561A						PASS	.	C	THR/PRO	349,4055		16,317,1869	26.0	30.0	29.0		1561	0.3	0.0	22	dbSNP_120	29	1331,7267		102,1127,3070	yes	missense	SH3BP1	NM_018957.3	38	118,1444,4939	AA,AC,CC		15.4803,7.9246,12.9211	benign	521/702	38046695	1680,11322	2202	4299	6501	SO:0001583	missense	23616	exon16			CCAGCTCCGGCCC		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1561C>A	22.37:g.38046695C>A	ENSP00000350018:p.Pro521Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	144	77	0.534722	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	37	CCDS13952.2	304	0.1391941391941392	41	0.08333333333333333	98	0.27071823204419887	27	0.0472027972027972	138	0.1820580474934037	C	2.918	-0.223802	0.06061	0.079246	0.154803	ENSG00000100092	ENST00000357436;ENST00000397014	T	0.17854	2.25	0.312	0.312	0.15837	.	0.804139	0.10756	N	0.637701	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P;B;B	0.48350	0.063;0.909;0.022;0.063	B;P;B;B	0.50440	0.012;0.641;0.003;0.012	T	0.39143	-0.9628	8	0.13853	T	0.58	.	.	.	.	rs12170939	435;457;521;435	E7EUD3;Q6ZT62;Q9Y3L3;Q6ZTJ5	.;.;3BP1_HUMAN;.	T	521;435	ENSP00000350018:P521T	ENSP00000350018:P521T	P	+	1	0	SH3BP1	36376641	0.000000	0.05858	0.005000	0.12908	0.016000	0.09150	-0.295000	0.08298	0.420000	0.25954	0.089000	0.15464	CCG	C|0.871;A|0.129	0.129	strong		0.657	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
SLC44A4	80736	hgsc.bcm.edu	37	6	31838713	31838713	+	Silent	SNP	G	G	A	rs494620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31838713G>A	ENST00000229729.6	-	10	833	c.813C>T	c.(811-813)taC>taT	p.Y271Y	SLC44A4_ENST00000375562.4_Silent_p.Y229Y|SLC44A4_ENST00000544672.1_Silent_p.Y195Y	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	41	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	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		
OSER1	51526	hgsc.bcm.edu	37	20	42825929	42825929	+	Silent	SNP	C	C	T	rs8268	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	127	58	0.456693	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	
AMICA1	120425	hgsc.bcm.edu	37	11	118068752	118068752	+	Missense_Mutation	SNP	T	T	C	rs2298831	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:118068752T>C	ENST00000356289.5	-	8	1139	c.966A>G	c.(964-966)atA>atG	p.I322M	AMICA1_ENST00000526620.1_Missense_Mutation_p.I283M|AMICA1_ENST00000533261.1_Missense_Mutation_p.I311M|AMICA1_ENST00000292067.7_Missense_Mutation_p.I312M	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	322			I -> M (in dbSNP:rs2298831).		blood coagulation (GO:0007596)|gamma-delta T cell activation (GO:0046629)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte migration (GO:0050900)|monocyte extravasation (GO:0035696)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|stomach(2)	20	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		GTTTTTCTTTTATCTCTGGAT	0.448											OREG0021382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1021	0.203874	0.3714	0.2579	5008	,	,		19623	0.1161		0.175	False		,,,				2504	0.0593				p.I322M		Atlas-SNP	.											.	AMICA1	49	.	0			c.A966G						PASS	.	T	MET/ILE,MET/ILE	1559,2839	491.1+/-362.0	285,989,925	203.0	182.0	189.0		966,936	-2.5	0.4	11	dbSNP_100	189	1325,7267	260.3+/-283.2	116,1093,3087	yes	missense,missense	AMICA1	NM_001098526.1,NM_153206.2	10,10	401,2082,4012	CC,CT,TT		15.4213,35.4479,22.2017	benign,benign	322/395,312/385	118068752	2884,10106	2199	4296	6495	SO:0001583	missense	120425	exon8			TTCTTTTATCTCT	AY138965, AY358362	CCDS8391.1, CCDS41723.1, CCDS66240.1	11q23.3	2013-01-11				ENSG00000160593		"""Immunoglobulin superfamily / V-set domain containing"""	19084	protein-coding gene	gene with protein product		609770				12975309	Standard	NM_001098526		Approved	Gm638, AMICA	uc001psk.2	Q86YT9		ENST00000356289.5:c.966A>G	11.37:g.118068752T>C	ENSP00000348635:p.Ile322Met	Somatic	230	0	0	1485	WXS	Illumina HiSeq	Phase_I	259	107	0.413127	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Missense_Mutation	SNP	ENST00000356289.5	37	CCDS41723.1	490	0.22435897435897437	200	0.4065040650406504	92	0.2541436464088398	69	0.12062937062937062	129	0.17018469656992086	T	4.376	0.069268	0.08436	0.354479	0.154213	ENSG00000160593	ENST00000356289;ENST00000292067;ENST00000533261;ENST00000526620	D;D;D;D	0.98345	-4.3;-4.32;-4.3;-4.88	3.91	-2.48	0.06423	.	0.974614	0.08339	N	0.961138	T	0.00012	0.0000	N	0.03608	-0.345	0.51482	P	7.80000000000225E-5	B;B;B;B;B	0.17268	0.007;0.001;0.007;0.007;0.021	B;B;B;B;B	0.09377	0.002;0.002;0.002;0.002;0.004	T	0.13522	-1.0506	9	0.30078	T	0.28	6.3467	8.9085	0.35539	0.0:0.6209:0.0:0.3791	rs2298831;rs52812244;rs59197111;rs2298831	322;283;322;311;312	B4DVI6;E9PKK2;Q86YT9;E9PR26;Q86YT9-2	.;.;JAML1_HUMAN;.;.	M	322;312;311;283	ENSP00000348635:I322M;ENSP00000292067:I312M;ENSP00000436117:I311M;ENSP00000431218:I283M	ENSP00000292067:I312M	I	-	3	3	AMICA1	117573962	0.781000	0.28676	0.439000	0.26833	0.000000	0.00434	-0.891000	0.04135	-0.444000	0.07170	-1.069000	0.02264	ATA	T|0.772;C|0.228	0.228	strong		0.448	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206	
NUMB	8650	hgsc.bcm.edu	37	14	73743458	73743458	+	Missense_Mutation	SNP	C	C	T	rs17781919	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:73743458C>T	ENST00000355058.3	-	13	2062	c.1784G>A	c.(1783-1785)gGc>gAc	p.G595D	NUMB_ENST00000554546.1_Missense_Mutation_p.G536D|NUMB_ENST00000544991.3_Missense_Mutation_p.G400D|NUMB_ENST00000560335.1_Missense_Mutation_p.G449D|NUMB_ENST00000555238.1_Missense_Mutation_p.G595D|RP4-647C14.3_ENST00000556578.1_RNA|NUMB_ENST00000356296.4_Missense_Mutation_p.G547D|NUMB_ENST00000554521.2_Missense_Mutation_p.G389D|NUMB_ENST00000359560.3_Missense_Mutation_p.G584D|NUMB_ENST00000559312.1_Missense_Mutation_p.G400D|NUMB_ENST00000557597.1_Missense_Mutation_p.G584D|NUMB_ENST00000454166.4_Missense_Mutation_p.G449D|NUMB_ENST00000555394.1_Missense_Mutation_p.G547D|NUMB_ENST00000555738.2_Missense_Mutation_p.G438D|NUMB_ENST00000556772.1_Missense_Mutation_p.G451D|NUMB_ENST00000535282.1_Missense_Mutation_p.G584D			P49757	NUMB_HUMAN	numb homolog (Drosophila)	595			G -> D (in dbSNP:rs17781919).		adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		GGCCAACCTGCCATCATCTAC	0.527													C|||	55	0.0109824	0.0015	0.0115	5008	,	,		19916	0.001		0.0378	False		,,,				2504	0.0061				p.G595D		Atlas-SNP	.											.	NUMB	56	.	0			c.G1784A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	30,4376	36.0+/-67.5	0,30,2173	81.0	71.0	74.0		1784,1640,1607,1751	5.1	1.0	14	dbSNP_123	74	348,8252	118.8+/-178.2	6,336,3958	yes	missense,missense,missense,missense	NUMB	NM_001005743.1,NM_001005744.1,NM_001005745.1,NM_003744.5	94,94,94,94	6,366,6131	TT,TC,CC		4.0465,0.6809,2.9064	benign,benign,benign,benign	595/652,547/604,536/593,584/641	73743458	378,12628	2203	4300	6503	SO:0001583	missense	8650	exon13			AACCTGCCATCAT	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"""numb (Drosophila) homolog"", ""chromosome 14 open reading frame 41"""	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.1784G>A	14.37:g.73743458C>T	ENSP00000347169:p.Gly595Asp	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_001005743	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Missense_Mutation	SNP	ENST00000355058.3	37	CCDS32116.1	40	0.018315018315018316	2	0.0040650406504065045	4	0.011049723756906077	2	0.0034965034965034965	32	0.04221635883905013	C	12.73	2.024981	0.35701	0.006809	0.040465	ENSG00000133961	ENST00000554546;ENST00000356296;ENST00000557597;ENST00000555238;ENST00000556772;ENST00000355058;ENST00000359560;ENST00000555394;ENST00000544991;ENST00000454166;ENST00000555738;ENST00000554521;ENST00000535282	T;T;T;T;T;T;T;T;T;T;T;T;T	0.57752	0.43;0.38;0.83;0.83;1.44;0.83;0.83;0.38;0.4;0.39;0.4;0.41;0.83	5.14	5.14	0.70334	.	0.376195	0.32120	N	0.006545	T	0.10594	0.0259	N	0.08118	0	0.39784	D	0.972339	B;B;B;B;B;B;B;B;B	0.25904	0.093;0.137;0.137;0.137;0.137;0.063;0.063;0.043;0.032	B;B;B;B;B;B;B;B;B	0.31290	0.125;0.121;0.121;0.121;0.121;0.073;0.073;0.127;0.027	T	0.09422	-1.0675	10	0.33141	T	0.24	-2.0995	15.2044	0.73165	0.0:0.8591:0.1409:0.0	rs17781919;rs17781919	293;438;449;389;400;536;547;584;595	B1P2N9;B1P2N6;B1P2N5;B1P2N8;B1P2N7;P49757-4;P49757-2;P49757-3;P49757	.;.;.;.;.;.;.;.;NUMB_HUMAN	D	536;547;584;595;451;595;584;547;400;449;438;389;584	ENSP00000452416:G536D;ENSP00000348644:G547D;ENSP00000451117:G584D;ENSP00000451300:G595D;ENSP00000451513:G451D;ENSP00000347169:G595D;ENSP00000352563:G584D;ENSP00000451625:G547D;ENSP00000446001:G400D;ENSP00000394025:G449D;ENSP00000452069:G438D;ENSP00000450817:G389D;ENSP00000441258:G584D	ENSP00000347169:G595D	G	-	2	0	NUMB	72813211	0.761000	0.28439	0.984000	0.44739	0.975000	0.68041	2.858000	0.48356	2.681000	0.91329	0.561000	0.74099	GGC	C|0.975;T|0.025	0.025	strong		0.527	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1		
ARSH	347527	hgsc.bcm.edu	37	X	2928170	2928170	+	Silent	SNP	C	C	T	rs77183343	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:2928170C>T	ENST00000381130.2	+	2	192	c.192C>T	c.(190-192)acC>acT	p.T64T		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	64					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CCTTCCTGACCGGCCGGTACC	0.493													C|||	252	0.066755	0.0726	0.0317	3775	,	,		13559	0.0079		0.0835	False		,,,				2504	0.0429				p.T64T		Atlas-SNP	.											.	ARSH	72	.	0			c.C192T						PASS	.	C		416,3419		16,311,73,1305,498	57.0	43.0	48.0		192	-7.2	0.0	X	dbSNP_131	48	758,5970		30,498,200,1900,1672	no	coding-synonymous	ARSH	NM_001011719.1		46,809,273,3205,2170	TT,TC,T,CC,C		11.2663,10.8475,11.1143		64/563	2928170	1174,9389	2203	4300	6503	SO:0001819	synonymous_variant	347527	exon2			CCTGACCGGCCGG	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"""Arylsulfatase family"""	32488	protein-coding gene	gene with protein product		300586	"""arylsulfatase H"""			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.192C>T	X.37:g.2928170C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001011719		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																			C|0.899;T|0.101	0.101	strong		0.493	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
NHSL1	57224	hgsc.bcm.edu	37	6	138794490	138794490	+	Missense_Mutation	SNP	G	G	A	rs201780864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:138794490G>A	ENST00000427025.2	-	3	1064	c.436C>T	c.(436-438)Cca>Tca	p.P146S	NHSL1_ENST00000343505.5_Missense_Mutation_p.P98S|NHSL1_ENST00000479393.2_5'UTR	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	146										breast(2)|endometrium(4)|kidney(1)	7						TCACAGAATGGGCTGGCGTTG	0.517													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14373	0.0		0.003	False		,,,				2504	0.002				p.P146S		Atlas-SNP	.											.	NHSL1	99	.	0			c.C436T						PASS	.	G	SER/PRO,SER/PRO	3,1381		0,3,689	69.0	59.0	62.0		292,436	1.1	0.9	6		62	14,3168		0,14,1577	yes	missense,missense	NHSL1	NM_001144060.1,NM_020464.1	74,74	0,17,2266	AA,AG,GG		0.44,0.2168,0.3723	benign,benign	98/1607,146/1611	138794490	17,4549	692	1591	2283	SO:0001583	missense	57224	exon3			AGAATGGGCTGGC	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.436C>T	6.37:g.138794490G>A	ENSP00000394546:p.Pro146Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	167	79	0.473054	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Missense_Mutation	SNP	ENST00000427025.2	37	CCDS55063.1	.	.	.	.	.	.	.	.	.	.	G	8.796	0.931776	0.18131	0.002168	0.0044	ENSG00000135540	ENST00000427025;ENST00000343505;ENST00000342260;ENST00000533765	T;T	0.36878	1.23;1.75	5.13	1.12	0.20585	.	0.390782	0.29307	N	0.012534	T	0.06325	0.0163	L	0.31476	0.935	0.26206	N	0.979379	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.002;0.003;0.002	T	0.27502	-1.0072	10	0.18710	T	0.47	-13.1246	1.0418	0.01560	0.2696:0.1535:0.4184:0.1585	.	98;98;146	E2QRJ1;Q5SYE7-2;Q5SYE7	.;.;NHSL1_HUMAN	S	146;98;84;99	ENSP00000394546:P146S;ENSP00000344672:P98S	ENSP00000344582:P84S	P	-	1	0	NHSL1	138836183	1.000000	0.71417	0.872000	0.34217	0.369000	0.29798	0.910000	0.28571	0.668000	0.31126	-0.254000	0.11334	CCA	G|0.996;A|0.004	0.004	weak		0.517	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
KMT2B	9757	hgsc.bcm.edu	37	19	36224161	36224161	+	Silent	SNP	C	C	A	rs112013670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36224161C>A	ENST00000222270.7	+	28	6711	c.6711C>A	c.(6709-6711)ggC>ggA	p.G2237G	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Silent_p.G2237G	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2237					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)										TGCCCCCAGGCCCCCTCCTCG	0.731													C|||	523	0.104433	0.087	0.1037	5008	,	,		6096	0.0883		0.1223	False		,,,				2504	0.1268				p.G2237G		Atlas-SNP	.											.	MLL4	229	.	0			c.C6711A						PASS	.	C		236,3094		5,226,1434	17.0	18.0	18.0		6711	0.7	1.0	19	dbSNP_132	18	641,6845		21,599,3123	no	coding-synonymous	MLL4	NM_014727.1		26,825,4557	AA,AC,CC		8.5627,7.0871,8.1084		2237/2716	36224161	877,9939	1665	3743	5408	SO:0001819	synonymous_variant	8085	exon28			CCCAGGCCCCCTC	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.6711C>A	19.37:g.36224161C>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	74	46	0.621622	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																			C|0.894;A|0.106	0.106	strong		0.731	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
KDF1	126695	hgsc.bcm.edu	37	1	27278521	27278521	+	Silent	SNP	G	G	A	rs3010110	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:27278521G>A	ENST00000320567.5	-	2	439	c.351C>T	c.(349-351)gaC>gaT	p.D117D		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		117					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CCTCAGTGGAGTCCTCAGTAG	0.687													G|||	639	0.127596	0.0144	0.121	5008	,	,		15443	0.0288		0.2604	False		,,,				2504	0.2505				p.D117D		Atlas-SNP	.											.	C1orf172	38	.	0			c.C351T						PASS	.	G		223,4181		4,215,1983	17.0	19.0	18.0		351	4.9	1.0	1	dbSNP_101	18	2254,6346		286,1682,2332	no	coding-synonymous	C1orf172	NM_152365.2		290,1897,4315	AA,AG,GG		26.2093,5.0636,19.048		117/399	27278521	2477,10527	2202	4300	6502	SO:0001819	synonymous_variant	126695	exon2			AGTGGAGTCCTCA																												ENST00000320567.5:c.351C>T	1.37:g.27278521G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	186	94	0.505376	NM_152365	Q5QP32|Q8N0S7	Silent	SNP	ENST00000320567.5	37	CCDS293.1	279	0.12774725274725274	11	0.022357723577235773	49	0.13535911602209943	18	0.03146853146853147	201	0.26517150395778366	G	0.294	-0.978044	0.02197	0.050636	0.262093	ENSG00000175707	ENST00000374109	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.00015	-1.2392	4	0.46703	T	0.11	.	18.3122	0.90204	0.0:0.0:1.0:0.0	rs3010110;rs17356895;rs60594052;rs3010110	.	.	.	I	78	.	ENSP00000363223:T78I	T	-	2	0	C1orf172	27151108	1.000000	0.71417	1.000000	0.80357	0.124000	0.20399	3.711000	0.54868	2.547000	0.85894	0.557000	0.71058	ACT	G|0.848;A|0.152	0.152	strong		0.687	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1		
ZNF407	55628	hgsc.bcm.edu	37	18	72347482	72347482	+	Silent	SNP	T	T	C	rs12327359	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:72347482T>C	ENST00000299687.5	+	1	4507	c.4507T>C	c.(4507-4509)Tta>Cta	p.L1503L	ZNF407_ENST00000582337.1_Silent_p.L1503L|ZNF407_ENST00000577538.1_Silent_p.L1503L|ZNF407_ENST00000309902.6_Silent_p.L1503L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L1503L(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAATTTATTTTTACATATTAA	0.473													C|||	2123	0.423922	0.7201	0.3271	5008	,	,		19354	0.1845		0.4175	False		,,,				2504	0.3456				p.L1503L		Atlas-SNP	.											ZNF407,NS,carcinoma,0,1	ZNF407	231	1	1	Substitution - coding silent(1)	prostate(1)	c.T4507C						scavenged	.	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	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	100	60	0.6	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	
SNAPC4	6621	hgsc.bcm.edu	37	9	139272058	139272058	+	Silent	SNP	A	A	G	rs10781507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139272058A>G	ENST00000298532.2	-	21	4589	c.4221T>C	c.(4219-4221)agT>agC	p.S1407S		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa									p.S1407S(1)		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)		GTTCCAGCTCACTCAGGAGGT	0.667													G|||	1850	0.369409	0.2579	0.572	5008	,	,		15887	0.3214		0.3956	False		,,,				2504	0.3988				p.S1407S		Atlas-SNP	.											SNAPC4,NS,lymphoid_neoplasm,0,1	SNAPC4	82	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T4221C						PASS	.			1240,3166		172,896,1135	39.0	38.0	39.0		4221	-4.8	0.0	9	dbSNP_120	39	3584,5008		744,2096,1456	no	coding-synonymous	SNAPC4	NM_003086.2		916,2992,2591	GG,GA,AA		41.7132,28.1434,37.1134		1407/1470	139272058	4824,8174	2203	4296	6499	SO:0001819	synonymous_variant	6621	exon21			CAGCTCACTCAGG	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.4221T>C	9.37:g.139272058A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.635;G|0.365	0.365	strong		0.667	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
FIGF	2277	hgsc.bcm.edu	37	X	15381421	15381421	+	Silent	SNP	C	C	T	rs12011065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:15381421C>T	ENST00000297904.3	-	2	540	c.111G>A	c.(109-111)ttG>ttA	p.L37L		NM_004469.4	NP_004460.1	O43915	VEGFD_HUMAN	c-fos induced growth factor (vascular endothelial growth factor D)	37					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|induction of positive chemotaxis (GO:0050930)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell chemotaxis (GO:0060754)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor binding (GO:0005172)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17	Hepatocellular(33;0.183)					CAGATCGTTCCAATGTGGACT	0.383													T|||	435	0.115232	0.2141	0.0303	3775	,	,		15160	0.0079		0.0328	False		,,,				2504	0.092				p.L37L		Atlas-SNP	.											.	FIGF	39	.	0			c.G111A						PASS	.	T		863,2972		89,557,128,986,443	82.0	68.0	73.0		111	0.6	0.0	X	dbSNP_120	73	267,6461		1,184,81,2243,1791	no	coding-synonymous	FIGF	NM_004469.4		90,741,209,3229,2234	TT,TC,T,CC,C		3.9685,22.5033,10.6977		37/355	15381421	1130,9433	2203	4300	6503	SO:0001819	synonymous_variant	2277	exon2			TCGTTCCAATGTG	AJ000185	CCDS14166.1	Xp22.31	2008-02-05			ENSG00000165197	ENSG00000165197			3708	protein-coding gene	gene with protein product		300091		VEGFD		9479493	Standard	NM_004469		Approved	VEGF-D	uc004cwt.2	O43915	OTTHUMG00000021175	ENST00000297904.3:c.111G>A	X.37:g.15381421C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_004469	B2R7Z3	Silent	SNP	ENST00000297904.3	37	CCDS14166.1																																																																																			C|0.881;0|0.003	.	strong		0.383	FIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055859.1	NM_004469	
PYROXD2	84795	hgsc.bcm.edu	37	10	100167396	100167396	+	Silent	SNP	G	G	A	rs12763326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	57	0	0		WXS	Illumina HiSeq	Phase_I	44	27	0.613636	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	
FAT2	2196	hgsc.bcm.edu	37	5	150901630	150901630	+	Silent	SNP	G	G	T	rs3734049	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150901630G>T	ENST00000261800.5	-	18	10536	c.10524C>A	c.(10522-10524)atC>atA	p.I3508I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3508	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGAGGGGAGGGATGCCACTGT	0.572													G|||	488	0.0974441	0.0083	0.1585	5008	,	,		20709	0.126		0.1948	False		,,,				2504	0.045				p.I3508I		Atlas-SNP	.											.	FAT2	465	.	0			c.C10524A						PASS	.	G		161,4245	104.3+/-142.8	5,151,2047	39.0	34.0	35.0		10524	2.3	0.5	5	dbSNP_107	35	1819,6781	314.2+/-311.7	203,1413,2684	no	coding-synonymous	FAT2	NM_001447.2		208,1564,4731	TT,TG,GG		21.1512,3.6541,15.2237		3508/4350	150901630	1980,11026	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon18			GGGAGGGATGCCA	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.10524C>A	5.37:g.150901630G>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	290	0.13278388278388278	6	0.012195121951219513	65	0.17955801104972377	82	0.14335664335664336	137	0.18073878627968337	G	6.259	0.415816	0.11870	0.036541	0.211512	ENSG00000086570	ENST00000520200	.	.	.	5.14	2.28	0.28536	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18053	-1.0349	3	.	.	.	.	4.0795	0.09919	0.1445:0.1277:0.5961:0.1316	rs3734049;rs59902096;rs3734049	.	.	.	T	367	.	.	P	-	1	0	FAT2	150881823	0.930000	0.31532	0.496000	0.27539	0.869000	0.49853	1.367000	0.34204	0.652000	0.30806	0.563000	0.77884	CCC	G|0.872;T|0.128	0.128	strong		0.572	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
A2ML1	144568	hgsc.bcm.edu	37	12	9010671	9010671	+	Silent	SNP	G	G	A	rs11612600	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:9010671G>A	ENST00000299698.7	+	26	3417	c.3237G>A	c.(3235-3237)gtG>gtA	p.V1079V	A2ML1_ENST00000539547.1_Silent_p.V588V	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.V1079V(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						ATGCCAACGTGGGAAATCTCC	0.537													G|||	1274	0.254393	0.1944	0.2305	5008	,	,		-128	0.1696		0.3648	False		,,,				2504	0.3262				p.V1079V		Atlas-SNP	.											A2ML1,NS,carcinoma,0,1	A2ML1	199	1	1	Substitution - coding silent(1)	stomach(1)	c.G3237A						PASS	.	G		827,3139		96,635,1252	52.0	53.0	53.0		3237	2.2	0.9	12	dbSNP_120	53	2942,5388		526,1890,1749	yes	coding-synonymous	A2ML1	NM_144670.3		622,2525,3001	AA,AG,GG		35.3181,20.8522,30.6522		1079/1455	9010671	3769,8527	1983	4165	6148	SO:0001819	synonymous_variant	144568	exon26			CAACGTGGGAAAT	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.3237G>A	12.37:g.9010671G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_144670		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																			G|0.729;A|0.271	0.271	strong		0.537	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
CDK20	23552	hgsc.bcm.edu	37	9	90588970	90588970	+	Intron	SNP	C	C	A	rs28364935	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90588970C>A	ENST00000325303.8	-	2	381				CDK20_ENST00000375871.4_Intron|CDK20_ENST00000375883.3_Intron|CDK20_ENST00000605159.1_Intron|CDK20_ENST00000336654.5_Missense_Mutation_p.C32F	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20						cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			skin(1)	1						AGAAGGCAGACACTGCCAGCC	0.632													.|||	371	0.0740815	0.2141	0.0447	5008	,	,		17061	0.0		0.0507	False		,,,				2504	0.0061				p.C32F		Atlas-SNP	.											.	CDK20	52	.	0			c.G95T						PASS	.	C	,,,,PHE/CYS	813,3593		77,659,1467	47.0	47.0	47.0		,,,,95	1.6	0.0	9	dbSNP_125	47	365,8235		8,349,3943	yes	intron,intron,intron,intron,missense	CDK20	NM_001039803.2,NM_001170639.1,NM_001170640.1,NM_012119.4,NM_178432.3	,,,,205	85,1008,5410	AA,AC,CC		4.2442,18.4521,9.0574	,,,,	,,,,32/339	90588970	1178,11828	2203	4300	6503	SO:0001627	intron_variant	23552	exon2			GGCAGACACTGCC	AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"""Cyclin-dependent kinases"""	21420	protein-coding gene	gene with protein product		610076	"""cell cycle related kinase"""	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.76-20G>T	9.37:g.90588970C>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_178432	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Missense_Mutation	SNP	ENST00000325303.8	37	CCDS35060.1	168	0.07692307692307693	104	0.21138211382113822	22	0.06077348066298342	0	0.0	42	0.055408970976253295	.	1.147	-0.647886	0.03506	0.184521	0.042442	ENSG00000156345	ENST00000336654	T	0.66815	-0.23	4.55	1.56	0.23342	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06250	-1.0837	6	.	.	.	.	3.4873	0.07625	0.1726:0.5644:0.1672:0.0957	rs28364935	32	A2A390	.	F	32	ENSP00000338975:C32F	.	C	-	2	0	CDK20	89778790	0.014000	0.17966	0.002000	0.10522	0.013000	0.08279	0.096000	0.15147	0.099000	0.17552	-1.293000	0.01348	TGT	C|0.916;A|0.084	0.084	strong		0.632	CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119	
INPP5E	56623	hgsc.bcm.edu	37	9	139327439	139327439	+	Silent	SNP	A	A	G	rs10781542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139327439A>G	ENST00000371712.3	-	5	1650	c.1248T>C	c.(1246-1248)acT>acC	p.T416T		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		AGAGGAAGGAAGTGCCAAAAA	0.582													G|||	1895	0.378395	0.3896	0.6196	5008	,	,		17746	0.1935		0.4145	False		,,,				2504	0.3456				p.T416T		Atlas-SNP	.											.	INPP5E	18	.	0			c.T1248C						PASS	.	G		1747,2657	636.1+/-396.5	345,1057,800	189.0	168.0	175.0		1248	3.7	1.0	9	dbSNP_120	175	3922,4676	602.2+/-394.5	875,2172,1252	no	coding-synonymous	INPP5E	NM_019892.4		1220,3229,2052	GG,GA,AA		45.6153,39.6685,43.601		416/645	139327439	5669,7333	2202	4299	6501	SO:0001819	synonymous_variant	56623	exon5			GAAGGAAGTGCCA	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1248T>C	9.37:g.139327439A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			A|0.597;G|0.403	0.403	strong		0.582	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
RLN3	117579	hgsc.bcm.edu	37	19	14141666	14141666	+	Missense_Mutation	SNP	G	G	T	rs78161395	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14141666G>T	ENST00000431365.2	+	2	392	c.335G>T	c.(334-336)gGg>gTg	p.G112V	IL27RA_ENST00000263379.2_5'Flank|RLN3_ENST00000585987.1_3'UTR|CTB-55O6.4_ENST00000590528.1_RNA	NM_080864.2	NP_543140.1	Q8WXF3	REL3_HUMAN	relaxin 3	112						extracellular region (GO:0005576)				endometrium(1)|lung(4)	5						GGAACCCCTGGGGTTCTTCGG	0.612													G|||	951	0.189896	0.0469	0.17	5008	,	,		17645	0.2946		0.1511	False		,,,				2504	0.3292				p.G112V		Atlas-SNP	.											.	RLN3	10	.	0			c.G335T						PASS	.	G	VAL/GLY	355,4051	171.2+/-201.5	9,337,1857	44.0	49.0	47.0		335	1.2	0.0	19	dbSNP_131	47	1282,7318	241.0+/-271.5	88,1106,3106	yes	missense	RLN3	NM_080864.2	109	97,1443,4963	TT,TG,GG		14.907,8.0572,12.5865	possibly-damaging	112/143	14141666	1637,11369	2203	4300	6503	SO:0001583	missense	117579	exon2			CCCCTGGGGTTCT	AF447451	CCDS12302.1	19p13.2	2013-02-26	2004-11-15					"""Endogenous ligands"""	17135	protein-coding gene	gene with protein product	"""prorelaxin H3"""	606855	"""relaxin 3 (H3)"""				Standard	NM_080864		Approved	ZINS4, RXN3, H3	uc002mxw.1	Q8WXF3		ENST00000431365.2:c.335G>T	19.37:g.14141666G>T	ENSP00000397415:p.Gly112Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_080864	Q6UXW5	Missense_Mutation	SNP	ENST00000431365.2	37	CCDS12302.1	368	0.1684981684981685	23	0.046747967479674794	48	0.13259668508287292	174	0.3041958041958042	123	0.16226912928759896	G	11.28	1.591005	0.28357	0.080572	0.14907	ENSG00000171136	ENST00000431365	T	0.39056	1.1	4.62	1.21	0.21127	Insulin-like (3);	0.908383	0.09740	N	0.761990	T	0.00012	0.0000	L	0.46947	1.48	0.54753	P	1.3000000000040757E-5	B	0.13145	0.007	B	0.16289	0.015	T	0.25467	-1.0131	9	0.45353	T	0.12	-7.3272	6.2509	0.20845	0.1664:0.0:0.6851:0.1485	.	112	Q8WXF3	REL3_HUMAN	V	112	ENSP00000397415:G112V	ENSP00000397415:G112V	G	+	2	0	RLN3	14002666	0.009000	0.17119	0.004000	0.12327	0.003000	0.03518	0.842000	0.27627	0.059000	0.16252	-1.531000	0.00922	GGG	G|0.865;T|0.135	0.135	strong		0.612	RLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458529.1		
TPSB2	64499	hgsc.bcm.edu	37	16	1279623	1279623	+	RNA	SNP	G	G	A	rs72633259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1279623G>A	ENST00000339687.6	-	0	199				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				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	127	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	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	
MRPS27	23107	hgsc.bcm.edu	37	5	71519664	71519664	+	Missense_Mutation	SNP	C	C	T	rs3209157	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000522562.1_5'UTR|MRPS27_ENST00000513900.1_Missense_Mutation_p.G298D	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						PASS	.	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	95	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	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	
TYR	7299	hgsc.bcm.edu	37	11	89017961	89017961	+	Missense_Mutation	SNP	G	G	A	rs1126809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:89017961G>A	ENST00000263321.5	+	4	1707	c.1205G>A	c.(1204-1206)cGa>cAa	p.R402Q		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	402			R -> G (in OCA1B).|R -> L (in OCA1A). {ECO:0000269|PubMed:15146472}.|R -> Q (in dbSNP:rs1126809). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:15146472, ECO:0000269|PubMed:2342539, ECO:0000269|PubMed:7955413, ECO:0000269|PubMed:9158138}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CAGTGGCTCCGAAGGCACCGT	0.368													G|||	407	0.08127	0.0091	0.1254	5008	,	,		15773	0.001		0.2525	False		,,,				2504	0.0542				p.R402Q		Atlas-SNP	.											TYR,NS,carcinoma,+1,1	TYR	130	1	0			c.G1205A	GRCh37	CM041478|CM971555	TYR	M	rs1126809	PASS	.	G	GLN/ARG	223,4179	130.2+/-166.9	8,207,1986	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1205	4.7	1.0	11	dbSNP_86	61	2418,6180	399.1+/-346.3	322,1774,2203	yes	missense	TYR	NM_000372.4	43	330,1981,4189	AA,AG,GG		28.1228,5.0659,20.3154	probably-damaging	402/530	89017961	2641,10359	2201	4299	6500	SO:0001583	missense	7299	exon4			GGCTCCGAAGGCA	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1205G>A	11.37:g.89017961G>A	ENSP00000263321:p.Arg402Gln	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	257	141	0.548638	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	244	0.11172161172161173	5	0.01016260162601626	53	0.1464088397790055	0	0.0	186	0.24538258575197888	G	29.5	5.013726	0.93404	0.050659	0.281228	ENSG00000077498	ENST00000263321	D	0.98234	-4.81	4.68	4.68	0.58851	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.000000	0.85682	D	0.000000	T	0.00440	0.0014	M	0.66378	2.025	0.09310	P	0.999999826736	D	0.76494	0.999	D	0.80764	0.994	T	0.00000	-1.7609	8	.	.	.	.	17.6247	0.88091	0.0:0.0:1.0:0.0	rs62645918	402	P14679	TYRO_HUMAN	Q	402	ENSP00000263321:R402Q	.	R	+	2	0	TYR	88657609	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.499000	0.81566	2.166000	0.68216	0.555000	0.69702	CGA	G|0.831;A|0.169	0.169	strong		0.368	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
HLA-A	3105	hgsc.bcm.edu	37	6	29911115	29911115	+	Silent	SNP	G	G	A	rs66488547|rs1059498|rs12721717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29911115G>A	ENST00000396634.1	+	5	755	c.414G>A	c.(412-414)cgG>cgA	p.R138R	HLA-A_ENST00000376809.5_Silent_p.R138R|HLA-A_ENST00000376806.5_Silent_p.R138R|HLA-A_ENST00000376802.2_Silent_p.R138R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	138	Alpha-2.		Q -> R (in allele A*31:03, allele A*31:04 and allele A*31:06).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCGGGTACCGGCAGGACGCCT	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	273	0.0545128	0.1399	0.0461	5008	,	,		11640	0.0159		0.0308	False		,,,				2504	0.0092				p.R138R		Atlas-SNP	.											.	HLA-A	89	.	0			c.G414A						PASS	.						33.0	25.0	28.0					6																	29911115		1489	2696	4185	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTACCGGCAGGAC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.414G>A	6.37:g.29911115G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	180	60	0.333333	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	a	0.465	-0.887088	0.02511	.	.	ENSG00000206503	ENST00000355767	.	.	.	3.78	-7.56	0.01322	.	.	.	.	.	.	.	.	.	.	.	0.19300	N	0.999971	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.9334	0.19152	0.1782:0.1516:0.5545:0.1158	rs12721717;rs16896874;rs28749151;rs41556422	.	.	.	.	-1	.	.	.	+	.	.	HLA-A	30019094	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-12.409000	0.00002	-3.751000	0.00111	-2.593000	0.00164	.	A|0.005;C|0.418;G|0.576	0.005	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
EMILIN3	90187	hgsc.bcm.edu	37	20	39990700	39990700	+	Silent	SNP	T	T	C	rs41278104	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:39990700T>C	ENST00000332312.3	-	4	1701	c.1509A>G	c.(1507-1509)gtA>gtG	p.V503V		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	503						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				GCTCTGTCTGTACAAGGGGCC	0.632													C|||	764	0.152556	0.3132	0.147	5008	,	,		17537	0.003		0.1799	False		,,,				2504	0.0654				p.V503V		Atlas-SNP	.											.	EMILIN3	63	.	0			c.A1509G						PASS	.	C		1392,3014	683.9+/-404.3	220,952,1031	70.0	65.0	66.0		1509	4.2	0.9	20	dbSNP_127	66	1492,7108	746.0+/-407.3	141,1210,2949	no	coding-synonymous	EMILIN3	NM_052846.1		361,2162,3980	CC,CT,TT		17.3488,31.5933,22.1744		503/767	39990700	2884,10122	2203	4300	6503	SO:0001819	synonymous_variant	90187	exon4			TGTCTGTACAAGG	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1509A>G	20.37:g.39990700T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			T|0.802;C|0.198	0.198	strong		0.632	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
ZBBX	79740	hgsc.bcm.edu	37	3	167023624	167023624	+	Missense_Mutation	SNP	A	A	G	rs35190925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:167023624A>G	ENST00000392766.2	-	17	1872	c.1532T>C	c.(1531-1533)aTa>aCa	p.I511T	ZBBX_ENST00000307529.5_Missense_Mutation_p.I511T|ZBBX_ENST00000455345.2_Missense_Mutation_p.I511T|ZBBX_ENST00000392764.1_Missense_Mutation_p.I482T|ZBBX_ENST00000392767.2_Missense_Mutation_p.I511T	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	511			I -> T (in dbSNP:rs35190925).			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						TTCTAAACCTATATTTTTCTC	0.353													A|||	238	0.047524	0.0091	0.0677	5008	,	,		13576	0.001		0.1113	False		,,,				2504	0.0675				p.I511T		Atlas-SNP	.											.	ZBBX	299	.	0			c.T1532C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	101,3489		3,95,1697	58.0	51.0	53.0		1532,1445,1532	1.6	0.0	3	dbSNP_126	53	1000,7136		59,882,3127	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	89,89,89	62,977,4824	GG,GA,AA		12.2911,2.8134,9.3894	probably-damaging,probably-damaging,probably-damaging	511/840,482/772,511/801	167023624	1101,10625	1795	4068	5863	SO:0001583	missense	79740	exon17			AAACCTATATTTT	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.1532T>C	3.37:g.167023624A>G	ENSP00000376519:p.Ile511Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	118	0.05402930402930403	6	0.012195121951219513	30	0.08287292817679558	0	0.0	82	0.10817941952506596	A	12.60	1.986851	0.35036	0.028134	0.122911	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.10382	3.05;3.05;3.04;3.04;2.88	5.54	1.61	0.23674	.	0.421904	0.26355	N	0.024850	T	0.00144	0.0004	L	0.55481	1.735	0.80722	P	0.0	B;B	0.24721	0.077;0.11	B;B	0.21917	0.037;0.024	T	0.12604	-1.0541	9	0.62326	D	0.03	-2.0201	4.4261	0.11503	0.6568:0.1678:0.1753:0.0	rs35190925	511;511	A8MT70-2;A8MT70	.;ZBBX_HUMAN	T	511;511;511;511;482	ENSP00000376519:I511T;ENSP00000376520:I511T;ENSP00000390232:I511T;ENSP00000305065:I511T;ENSP00000376517:I482T	ENSP00000305065:I511T	I	-	2	0	ZBBX	168506318	0.003000	0.15002	0.005000	0.12908	0.034000	0.12701	0.240000	0.18042	0.477000	0.27464	0.528000	0.53228	ATA	A|0.918;G|0.082	0.082	strong		0.353	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
FLG	2312	hgsc.bcm.edu	37	1	152278555	152278555	+	Missense_Mutation	SNP	T	T	C	rs80221306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152278555T>C	ENST00000368799.1	-	3	8842	c.8807A>G	c.(8806-8808)gAc>gGc	p.D2936G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2936	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)			ACCAGCTCTGTCTTCTTGATG	0.552									Ichthyosis																												p.D2936G		Atlas-SNP	.											FLG,NS,haematopoietic_neoplasm,0,2	FLG	900	2	0			c.A8807G						scavenged	.	T	GLY/ASP	267,3373		3,261,1556	22.0	34.0	31.0		8807	1.3	0.0	1	dbSNP_131	31	809,7583		0,809,3387	no	missense	FLG	NM_002016.1	94	3,1070,4943	CC,CT,TT		9.6401,7.3352,8.9428	benign	2936/4062	152278555	1076,10956	1820	4196	6016	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCTGTCTTCTT	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.8807A>G	1.37:g.152278555T>C	ENSP00000357789:p.Asp2936Gly	Somatic	777	0	0		WXS	Illumina HiSeq	Phase_I	1020	194	0.190196	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	7.089	0.571862	0.13623	0.073352	0.096401	ENSG00000143631	ENST00000368799	T	0.01685	4.69	1.29	1.29	0.21616	.	.	.	.	.	T	0.00815	0.0027	M	0.70595	2.14	0.80722	P	0.0	B	0.17852	0.024	B	0.10450	0.005	T	0.39375	-0.9617	8	0.22706	T	0.39	.	4.7721	0.13160	0.0:0.0:0.0:1.0	.	2936	P20930	FILA_HUMAN	G	2936	ENSP00000357789:D2936G	ENSP00000357789:D2936G	D	-	2	0	FLG	150545179	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.386000	0.07370	0.851000	0.35264	0.248000	0.18094	GAC	T|0.972;C|0.028	0.028	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
EPPK1	83481	hgsc.bcm.edu	37	8	144941181	144941181	+	Missense_Mutation	SNP	G	G	C	rs7839934	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	90	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	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	
BCL6	604	hgsc.bcm.edu	37	3	187447032	187447032	+	Silent	SNP	G	G	A	rs1056932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:187447032G>A	ENST00000406870.2	-	5	1527	c.1161C>T	c.(1159-1161)aaC>aaT	p.N387N	BCL6_ENST00000232014.4_Silent_p.N387N|BCL6_ENST00000450123.2_Silent_p.N387N|RP11-211G3.3_ENST00000437407.1_Intron|RP11-211G3.3_ENST00000449623.1_Intron	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	387					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		TGGCATTCTGGTTGAGGCTGT	0.622			"""T, Mis"""	"""IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"""	"""NHL, CLL"""								G|||	2831	0.565296	0.1104	0.7536	5008	,	,		18031	0.7956		0.672	False		,,,				2504	0.6994				p.N387N		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.C1161T						PASS	.	G	,,	841,3565	332.3+/-302.4	106,629,1468	164.0	173.0	170.0		1161,1161,1161	2.8	1.0	3	dbSNP_86	170	5628,2972	667.0+/-402.4	1829,1970,501	no	coding-synonymous,coding-synonymous,coding-synonymous	BCL6	NM_001130845.1,NM_001134738.1,NM_001706.4	,,	1935,2599,1969	AA,AG,GG		34.5581,19.0876,49.7386	,,	387/707,387/651,387/707	187447032	6469,6537	2203	4300	6503	SO:0001819	synonymous_variant	604	exon4			ATTCTGGTTGAGG		CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1001	protein-coding gene	gene with protein product		109565	"""zinc finger protein 51"""	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.1161C>T	3.37:g.187447032G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	181	177	0.977901	NM_001134738	A7E241|B8PSA7|D3DNV5	Silent	SNP	ENST00000406870.2	37	CCDS3289.1																																																																																			G|0.471;A|0.529	0.529	strong		0.622	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931	
EML1	2009	hgsc.bcm.edu	37	14	100375707	100375707	+	Missense_Mutation	SNP	C	C	T	rs34198557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:100375707C>T	ENST00000262233.6	+	11	1269	c.1130C>T	c.(1129-1131)gCg>gTg	p.A377V	EML1_ENST00000334192.4_Missense_Mutation_p.A396V|EML1_ENST00000327921.9_Missense_Mutation_p.A365V	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	377	Tandem atypical propeller in EMLs.		A -> V (in dbSNP:rs34198557).		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)				GTGTTTGCTGCGGATTTCCAC	0.428													C|||	1253	0.2502	0.1006	0.3357	5008	,	,		20319	0.4673		0.1541	False		,,,				2504	0.2669				p.A396V		Atlas-SNP	.											EML1,colon,carcinoma,0,2	EML1	97	2	0			c.C1187T						PASS	.	C	VAL/ALA,VAL/ALA	478,3928	225.6+/-241.4	29,420,1754	175.0	172.0	173.0		1187,1130	2.4	0.7	14	dbSNP_126	173	1585,7015	296.5+/-302.9	151,1283,2866	yes	missense,missense	EML1	NM_001008707.1,NM_004434.2	64,64	180,1703,4620	TT,TC,CC		18.4302,10.8488,15.8619	benign,benign	396/835,377/816	100375707	2063,10943	2203	4300	6503	SO:0001583	missense	2009	exon12			TTGCTGCGGATTT	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.1130C>T	14.37:g.100375707C>T	ENSP00000262233:p.Ala377Val	Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	205	101	0.492683	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	538	0.24633699633699635	56	0.11382113821138211	108	0.2983425414364641	252	0.4405594405594406	122	0.16094986807387862	C	8.003	0.755862	0.15846	0.108488	0.184302	ENSG00000066629	ENST00000554479;ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T;T	0.21932	5.28;2.05;1.98;2.04	5.18	2.37	0.29283	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.215453	0.47455	N	0.000232	T	0.00012	0.0000	N	0.12920	0.275	0.09310	P	0.99999954605	B;B;B	0.18610	0.008;0.003;0.029	B;B;B	0.18871	0.014;0.001;0.023	T	0.46748	-0.9169	9	0.02654	T	1	-11.5461	10.4375	0.44443	0.0:0.7865:0.0:0.2135	rs34198557;rs60882024	365;377;396	F8W717;O00423;O00423-3	.;EMAL1_HUMAN;.	V	364;365;377;396;396	ENSP00000451346:A364V;ENSP00000327384:A365V;ENSP00000262233:A377V;ENSP00000334314:A396V	ENSP00000262233:A377V	A	+	2	0	EML1	99445460	0.971000	0.33674	0.740000	0.30986	0.917000	0.54804	2.132000	0.42083	0.209000	0.20645	0.655000	0.94253	GCG	C|0.813;T|0.187	0.187	strong		0.428	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707	
TEX14	56155	hgsc.bcm.edu	37	17	56690848	56690848	+	Silent	SNP	T	T	C	rs8077548	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	143	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	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		
TRIM38	10475	hgsc.bcm.edu	37	6	25966909	25966909	+	Missense_Mutation	SNP	G	G	T	rs41266771	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25966909G>T	ENST00000357085.3	+	3	635	c.159G>T	c.(157-159)agG>agT	p.R53S	TRIM38_ENST00000349458.3_Missense_Mutation_p.R53S	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	53					negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						AGCAACTGAGGCAGGAGACAT	0.498													G|||	11	0.00219649	0.0	0.0072	5008	,	,		20263	0.0		0.006	False		,,,				2504	0.0				p.R53S		Atlas-SNP	.											.	TRIM38	50	.	0			c.G159T						PASS	.	G	SER/ARG	7,4399	12.9+/-30.5	0,7,2196	83.0	80.0	81.0		159	-1.0	0.0	6	dbSNP_127	81	73,8527	44.0+/-102.2	0,73,4227	yes	missense	TRIM38	NM_006355.2	110	0,80,6423	TT,TG,GG		0.8488,0.1589,0.6151	benign	53/466	25966909	80,12926	2203	4300	6503	SO:0001583	missense	10475	exon3			ACTGAGGCAGGAG	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10059	protein-coding gene	gene with protein product			"""ring finger protein 15"", ""tripartite motif-containing 38"""	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.159G>T	6.37:g.25966909G>T	ENSP00000349596:p.Arg53Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_006355	B2R862	Missense_Mutation	SNP	ENST00000357085.3	37	CCDS4568.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	7.501	0.652721	0.14580	0.001589	0.008488	ENSG00000112343	ENST00000540262;ENST00000349458;ENST00000357085	T;T;T	0.53423	0.62;0.62;0.62	3.88	-0.956	0.10353	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	3.891910	0.00698	N	0.000762	T	0.07007	0.0178	N	0.12502	0.225	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.05241	-1.0897	10	0.07482	T	0.82	.	1.1526	0.01789	0.3016:0.152:0.392:0.1543	rs41266771	53;53	B2R862;O00635	.;TRI38_HUMAN	S	53	ENSP00000443976:R53S;ENSP00000230099:R53S;ENSP00000349596:R53S	ENSP00000230099:R53S	R	+	3	2	TRIM38	26074888	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.076000	0.14712	-0.198000	0.10333	0.585000	0.79938	AGG	G|0.995;T|0.005	0.005	strong		0.498	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2		
BPIFB2	80341	hgsc.bcm.edu	37	20	31609581	31609581	+	Silent	SNP	C	C	T	rs17124003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31609581C>T	ENST00000170150.3	+	15	1506	c.1311C>T	c.(1309-1311)gtC>gtT	p.V437V		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	437						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)	p.V437V(1)									TCCACTATGTCGCCCCTGAGA	0.582													C|||	1604	0.320288	0.4773	0.2118	5008	,	,		18493	0.1964		0.326	False		,,,				2504	0.3067				p.V437V		Atlas-SNP	.											BPIL1,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1311T						PASS	.	C		1934,2472	551.7+/-378.3	428,1078,697	159.0	144.0	149.0		1311	1.5	0.0	20	dbSNP_123	149	2459,6141	405.5+/-348.5	372,1715,2213	no	coding-synonymous	BPIFB2	NM_025227.1		800,2793,2910	TT,TC,CC		28.593,43.8947,33.7767		437/459	31609581	4393,8613	2203	4300	6503	SO:0001819	synonymous_variant	80341	exon15			CTATGTCGCCCCT	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.1311C>T	20.37:g.31609581C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Silent	SNP	ENST00000170150.3	37	CCDS13210.1																																																																																			C|0.672;N|0.000	.	strong		0.582	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
FSTL5	56884	hgsc.bcm.edu	37	4	162307060	162307060	+	Silent	SNP	G	G	T	rs17040984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:162307060G>T	ENST00000306100.5	-	16	2819	c.2383C>A	c.(2383-2385)Cgg>Agg	p.R795R	FSTL5_ENST00000427802.2_Silent_p.R785R|FSTL5_ENST00000536695.1_Silent_p.R794R|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000379164.4_Silent_p.R794R	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	795						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CTGTTTTTCCGGTTCCAAGGC	0.458													G|||	912	0.182109	0.0416	0.1657	5008	,	,		18093	0.3175		0.2256	False		,,,				2504	0.1994				p.R795R		Atlas-SNP	.											FSTL5,NS,carcinoma,+2,1	FSTL5	207	1	0			c.C2383A						PASS	.	G	,,	323,4083	171.6+/-201.8	12,299,1892	225.0	201.0	209.0		2380,2353,2383	1.6	0.0	4	dbSNP_123	209	2173,6427	372.0+/-336.5	273,1627,2400	no	coding-synonymous,coding-synonymous,coding-synonymous	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	,,	285,1926,4292	TT,TG,GG		25.2674,7.3309,19.1911	,,	794/847,785/838,795/848	162307060	2496,10510	2203	4300	6503	SO:0001819	synonymous_variant	56884	exon16			TTTTCCGGTTCCA	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.2383C>A	4.37:g.162307060G>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	263	141	0.536122	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			G|0.805;T|0.195	0.195	strong		0.458	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
CACNA1H	8912	hgsc.bcm.edu	37	16	1269029	1269029	+	Silent	SNP	T	T	C	rs2738893	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1269029T>C	ENST00000348261.5	+	34	6195	c.5947T>C	c.(5947-5949)Ttg>Ctg	p.L1983L	CACNA1H_ENST00000358590.4_Silent_p.L1977L|CACNA1H_ENST00000565831.1_Silent_p.L1977L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1983					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCAGATCCCATTGGCTGTGTC	0.687													t|||	3464	0.691693	0.6861	0.7075	5008	,	,		11649	0.8681		0.6441	False		,,,				2504	0.5552				p.L1983L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.T5947C						PASS	.		,	2390,1026		866,658,184	7.0	9.0	9.0		5929,5947	-5.6	0.0	16	dbSNP_100	9	4472,2502		1514,1444,529	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	2380,2102,713	CC,CT,TT		35.8761,30.0351,33.9557	,	1977/2348,1983/2354	1269029	6862,3528	1708	3487	5195	SO:0001819	synonymous_variant	8912	exon34			ATCCCATTGGCTG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5947T>C	16.37:g.1269029T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	210	210	1	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			T|0.277;C|0.723	0.723	strong		0.687	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TRIM56	81844	hgsc.bcm.edu	37	7	100732852	100732852	+	Silent	SNP	G	G	A	rs78537898	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100732852G>A	ENST00000306085.6	+	3	2556	c.2259G>A	c.(2257-2259)ccG>ccA	p.P753P		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	753					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)					TCCGTTCTCCGGACAGTTAAA	0.607													G|||	47	0.00938498	0.0008	0.0086	5008	,	,		17822	0.001		0.0179	False		,,,				2504	0.0215				p.P753P	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.G2259A						PASS	.	G		16,3958		0,16,1971	29.0	29.0	29.0		2259	-1.4	0.1	7	dbSNP_132	29	180,8116		5,170,3973	no	coding-synonymous	TRIM56	NM_030961.1		5,186,5944	AA,AG,GG		2.1697,0.4026,1.5974		753/756	100732852	196,12074	1987	4148	6135	SO:0001819	synonymous_variant	81844	exon3			TTCTCCGGACAGT	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.2259G>A	7.37:g.100732852G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			G|0.988;A|0.012	0.012	strong		0.607	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
OSER1	51526	hgsc.bcm.edu	37	20	42826350	42826350	+	Missense_Mutation	SNP	A	A	C	rs9346	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	40	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	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	
PASD1	139135	hgsc.bcm.edu	37	X	150840916	150840916	+	Silent	SNP	C	C	T	rs41299110	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:150840916C>T	ENST00000370357.4	+	14	1944	c.1699C>T	c.(1699-1701)Ctg>Ttg	p.L567L		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	567						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)					gaagcagcagctgcaagagca	0.547													T|||	732	0.193907	0.1074	0.2378	3775	,	,		13298	0.0536		0.1928	False		,,,				2504	0.181				p.L567L		Atlas-SNP	.											.	PASD1	286	.	0			c.C1699T						PASS	.	T		526,3309		34,381,77,1217,494	104.0	79.0	87.0		1699	-1.9	0.0	X	dbSNP_127	87	1626,5102		151,883,441,1394,1431	no	coding-synonymous	PASD1	NM_173493.2		185,1264,518,2611,1925	TT,TC,T,CC,C		24.1677,13.7158,20.373		567/774	150840916	2152,8411	2203	4300	6503	SO:0001819	synonymous_variant	139135	exon14			CAGCAGCTGCAAG	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.1699C>T	X.37:g.150840916C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	166	161	0.96988	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Silent	SNP	ENST00000370357.4	37	CCDS35431.1																																																																																			C|0.803;T|0.197	0.197	strong		0.547	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
MTOR	2475	hgsc.bcm.edu	37	1	11188142	11188142	+	Silent	SNP	C	C	T	rs192740864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11188142C>T	ENST00000361445.4	-	43	6028	c.5952G>A	c.(5950-5952)acG>acA	p.T1984T	MTOR_ENST00000376838.1_Silent_p.T189T	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1984					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)	GCCGGGCTGTCGTGGTAGACT	0.522													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18279	0.0		0.001	False		,,,				2504	0.0031				p.T1984T		Atlas-SNP	.											.	MTOR	327	.	0			c.G5952A						PASS	.	C		0,4406		0,0,2203	125.0	130.0	128.0		5952	-8.4	0.5	1		128	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTOR	NM_004958.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1984/2550	11188142	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon43			GGCTGTCGTGGTA	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.5952G>A	1.37:g.11188142C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			C|1.000;T|0.000	0.000	strong		0.522	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
GIMAP8	155038	hgsc.bcm.edu	37	7	150163837	150163837	+	Silent	SNP	A	A	G	rs2140595	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150163837A>G	ENST00000307271.3	+	2	625	c.51A>G	c.(49-51)ggA>ggG	p.G17G		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	17	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TCCTCCTGGGAAAATGCCGCT	0.512													G|||	1613	0.322085	0.3086	0.2334	5008	,	,		19150	0.4177		0.3708	False		,,,				2504	0.2546				p.G17G		Atlas-SNP	.											GIMAP8,trunk,malignant_melanoma,+1,1	GIMAP8	136	1	0			c.A51G						PASS	.	G		1393,3013		226,941,1036	58.0	60.0	59.0		51	-1.1	0.4	7	dbSNP_96	59	2989,5611		551,1887,1862	no	coding-synonymous	GIMAP8	NM_175571.2		777,2828,2898	GG,GA,AA		34.7558,31.616,33.6921		17/666	150163837	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon2			CCTGGGAAAATGC	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.51A>G	7.37:g.150163837A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	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	
TPSD1	23430	hgsc.bcm.edu	37	16	1306986	1306986	+	Missense_Mutation	SNP	C	C	T	rs72775467		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306986C>T	ENST00000211076.3	+	3	591	c.443C>T	c.(442-444)aCg>aTg	p.T148M	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.T141M	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	148	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CACACGGTCACGCTGCCCCCT	0.652																																					p.T148M		Atlas-SNP	.											TPSD1,NS,NS,0,1	TPSD1	47	1	0			c.C443T						scavenged	.						46.0	44.0	45.0					16																	1306986		2198	4299	6497	SO:0001583	missense	23430	exon3			CGGTCACGCTGCC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.443C>T	16.37:g.1306986C>T	ENSP00000211076:p.Thr148Met	Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	478	147	0.307531	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	772	0.3534798534798535	141	0.2865853658536585	112	0.30939226519337015	251	0.4388111888111888	268	0.35356200527704484	c	4.148	0.025917	0.08054	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.81659	-1.52;-1.52	2.55	1.57	0.23409	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.879151	0.09575	N	0.783735	T	0.00012	0.0000	L	0.49126	1.545	0.52501	P	4.099999999995774E-5	P;P	0.39250	0.468;0.665	B;B	0.32342	0.144;0.144	T	0.17899	-1.0354	9	0.52906	T	0.07	.	3.811	0.08796	0.0:0.5891:0.2553:0.1556	.	132;148	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	M	141;148	ENSP00000380668:T141M;ENSP00000211076:T148M	ENSP00000211076:T148M	T	+	2	0	TPSD1	1246987	0.000000	0.05858	0.004000	0.12327	0.060000	0.15804	0.429000	0.21412	0.384000	0.24942	0.185000	0.17295	ACG	C|0.646;T|0.354	0.354	strong		0.652	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
NEB	4703	hgsc.bcm.edu	37	2	152432311	152432311	+	Silent	SNP	T	T	C	rs33988153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:152432311T>C	ENST00000172853.10	-	79	11955	c.11808A>G	c.(11806-11808)ccA>ccG	p.P3936P	NEB_ENST00000604864.1_Silent_p.P5637P|NEB_ENST00000427231.2_Silent_p.P5637P|NEB_ENST00000603639.1_Silent_p.P5637P|NEB_ENST00000397345.3_Silent_p.P5637P|NEB_ENST00000409198.1_Silent_p.P3936P			P20929	NEBU_HUMAN	nebulin	3936					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)		CTCTGTACTTTGGCTGTGGAA	0.333													T|||	552	0.110224	0.0113	0.1282	5008	,	,		17816	0.004		0.2406	False		,,,				2504	0.2065				p.P5637P		Atlas-SNP	.											.	NEB	1697	.	0			c.A16911G						PASS	.	T	,,	166,3456		7,152,1652	243.0	237.0	239.0		16911,16911,11808	2.5	1.0	2	dbSNP_126	239	2064,6090		264,1536,2277	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	271,1688,3929	CC,CT,TT		25.3127,4.5831,18.9368	,,	5637/8526,5637/8526,3936/6670	152432311	2230,9546	1811	4077	5888	SO:0001819	synonymous_variant	4703	exon107			GTACTTTGGCTGT	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.11808A>G	2.37:g.152432311T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				T|0.853;C|0.147	0.147	strong		0.333	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
UNC119B	84747	hgsc.bcm.edu	37	12	121154784	121154784	+	Silent	SNP	C	C	T	rs117990192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:121154784C>T	ENST00000344651.4	+	4	622	c.582C>T	c.(580-582)atC>atT	p.I194I		NM_001080533.1	NP_001074002.1	A6NIH7	U119B_HUMAN	unc-119 homolog B (C. elegans)	194					cilium morphogenesis (GO:0060271)|lipoprotein transport (GO:0042953)	ciliary transition zone (GO:0035869)	lipid binding (GO:0008289)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GCTTCTGCATCCCCAGCAGTA	0.458													C|||	15	0.00299521	0.0015	0.0115	5008	,	,		21065	0.0		0.005	False		,,,				2504	0.0				p.I194I		Atlas-SNP	.											.	UNC119B	21	.	0			c.C582T						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	176.0	175.0	175.0		582	2.8	1.0	12	dbSNP_132	175	60,8540	37.4+/-92.8	0,60,4240	no	coding-synonymous	UNC119B	NM_001080533.1		0,66,6437	TT,TC,CC		0.6977,0.1362,0.5075		194/252	121154784	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	84747	exon4			CTGCATCCCCAGC		CCDS31914.1	12q24	2014-06-16	2001-11-28		ENSG00000175970	ENSG00000175970			16488	protein-coding gene	gene with protein product	"""POC7 centriolar protein homolog B (Chlamydomonas)"""		"""unc119 (C.elegans) homolog B"""				Standard	NM_001080533		Approved	MGC5139, POC7B	uc001tyz.4	A6NIH7	OTTHUMG00000169201	ENST00000344651.4:c.582C>T	12.37:g.121154784C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	183	96	0.52459	NM_001080533		Silent	SNP	ENST00000344651.4	37	CCDS31914.1																																																																																			C|0.994;T|0.006	0.006	strong		0.458	UNC119B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402857.1	NM_001080533	
FXYD5	53827	hgsc.bcm.edu	37	19	35648365	35648365	+	Missense_Mutation	SNP	T	T	G	rs1688005	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:35648365T>G	ENST00000342879.3	+	2	881	c.103T>G	c.(103-105)Tca>Gca	p.S35A	FXYD5_ENST00000392218.2_Missense_Mutation_p.S35A|FXYD5_ENST00000590686.1_Missense_Mutation_p.S35A|FXYD5_ENST00000423817.3_Missense_Mutation_p.S35A|FXYD5_ENST00000543307.1_Missense_Mutation_p.S35A|FXYD5_ENST00000392219.2_Missense_Mutation_p.S35A|FXYD5_ENST00000588699.1_Missense_Mutation_p.S35A|FXYD5_ENST00000541435.2_Missense_Mutation_p.S35A			Q96DB9	FXYD5_HUMAN	FXYD domain containing ion transport regulator 5	35			S -> A (in dbSNP:rs1688005).		microvillus assembly (GO:0030033)|negative regulation of calcium-dependent cell-cell adhesion (GO:0046588)	integral component of membrane (GO:0016021)	actin binding (GO:0003779)|cadherin binding (GO:0045296)|ion channel activity (GO:0005216)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)			TTCAGCAGACTCAACTATCAT	0.507													T|||	2065	0.41234	0.3359	0.3487	5008	,	,		18878	0.7976		0.2565	False		,,,				2504	0.3241				p.S35A		Atlas-SNP	.											.	FXYD5	41	.	0			c.T103G						PASS	.	T	ALA/SER,ALA/SER,ALA/SER	1434,2972	465.1+/-354.1	228,978,997	99.0	80.0	87.0		103,103,103	-4.6	0.0	19	dbSNP_89	87	2165,6435	370.2+/-335.8	276,1613,2411	yes	missense,missense,missense	FXYD5	NM_001164605.1,NM_014164.5,NM_144779.2	99,99,99	504,2591,3408	GG,GT,TT		25.1744,32.5465,27.6718	benign,benign,benign	35/179,35/179,35/179	35648365	3599,9407	2203	4300	6503	SO:0001583	missense	53827	exon3			GCAGACTCAACTA	AF161462	CCDS12447.1	19q13.12	2008-02-05	2002-01-14		ENSG00000089327	ENSG00000089327			4029	protein-coding gene	gene with protein product	"""dysadherin"""	606669	"""FXYD domain-containing ion transport regulator 5"""				Standard	NM_144779		Approved	OIT2	uc002nyg.2	Q96DB9	OTTHUMG00000048092	ENST00000342879.3:c.103T>G	19.37:g.35648365T>G	ENSP00000344254:p.Ser35Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_014164	B7WNZ8|Q6UW44|Q9HC34|Q9P039	Missense_Mutation	SNP	ENST00000342879.3	37	CCDS12447.1	980	0.44871794871794873	182	0.3699186991869919	138	0.3812154696132597	462	0.8076923076923077	198	0.2612137203166227	T	0.400	-0.918670	0.02396	0.325465	0.251744	ENSG00000089327	ENST00000543307;ENST00000392218;ENST00000392219;ENST00000541435;ENST00000342879;ENST00000423817	T;T;T;T;T;T	0.65549	-0.16;0.78;0.86;0.86;0.86;0.86	3.08	-4.58	0.03410	.	2.674210	0.01182	N	0.007109	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	0.40021	-0.9585	9	0.20046	T	0.44	5.8774	0.6587	0.00838	0.1711:0.2827:0.1683:0.3778	rs1688005;rs17719100;rs57430720;rs1688005	35;35	F5H4X8;Q96DB9	.;FXYD5_HUMAN	A	35	ENSP00000444839:S35A;ENSP00000376052:S35A;ENSP00000376053:S35A;ENSP00000443390:S35A;ENSP00000344254:S35A;ENSP00000393848:S35A	ENSP00000344254:S35A	S	+	1	0	FXYD5	40340205	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.286000	0.01152	-0.698000	0.05085	-0.783000	0.03347	TCA	T|0.646;G|0.354	0.354	strong		0.507	FXYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109443.1	NM_014164	
EVC	2121	hgsc.bcm.edu	37	4	5750003	5750003	+	Silent	SNP	A	A	G	rs33929747	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:5750003A>G	ENST00000264956.6	+	8	1252	c.1068A>G	c.(1066-1068)ctA>ctG	p.L356L	EVC_ENST00000382674.2_Silent_p.L356L|EVC_ENST00000509451.1_Silent_p.L356L	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	356					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)				CCGAAGGGCTATTGTGCGATT	0.498													A|||	1089	0.217452	0.0628	0.3444	5008	,	,		16139	0.2044		0.3608	False		,,,				2504	0.2025				p.L356L		Atlas-SNP	.											.	EVC	90	.	0			c.A1068G						PASS	.	A		480,3926	225.2+/-241.2	31,418,1754	69.0	68.0	68.0		1068	-6.0	0.0	4	dbSNP_126	68	3081,5519	473.8+/-368.7	543,1995,1762	no	coding-synonymous	EVC	NM_153717.2		574,2413,3516	GG,GA,AA		35.8256,10.8942,27.3797		356/993	5750003	3561,9445	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon8			AGGGCTATTGTGC	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.1068A>G	4.37:g.5750003A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			A|0.728;G|0.272	0.272	strong		0.498	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
PI4KA	5297	hgsc.bcm.edu	37	22	21065652	21065652	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21065652T>C	ENST00000572273.1	-	51	5956	c.5726A>G	c.(5725-5727)aAg>aGg	p.K1909R	PI4KA_ENST00000255882.6_Missense_Mutation_p.K1967R|PI4KA_ENST00000414196.3_Missense_Mutation_p.K719R			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1909	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ATGACCCTTCTTGTCCAGCAT	0.597																																					p.K1967R	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,+1,2	PI4KA	313	2	0			c.A5900G						scavenged	.						101.0	122.0	115.0					22																	21065652		2072	4111	6183	SO:0001583	missense	5297	exon51			CCCTTCTTGTCCA	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.5726A>G	22.37:g.21065652T>C	ENSP00000458238:p.Lys1909Arg	Somatic	375	2	0.00533333		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	T	16.62	3.174495	0.57692	.	.	ENSG00000241973	ENST00000255882;ENST00000414196;ENST00000399213	T;T	0.81330	-1.48;-1.48	5.04	5.04	0.67666	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.112508	0.64402	D	0.000001	T	0.71854	0.3389	L	0.28274	0.84	0.53005	D	0.999967	B;B	0.18166	0.001;0.026	B;B	0.29176	0.02;0.099	T	0.66204	-0.5982	10	0.21014	T	0.42	-24.001	15.0754	0.72074	0.0:0.0:0.0:1.0	.	300;1909	A8MTF1;P42356	.;PI4KA_HUMAN	R	1909;719;300	ENSP00000402981:K719R;ENSP00000382162:K300R	ENSP00000255882:K1909R	K	-	2	0	PI4KA	19395652	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.560000	0.60802	2.031000	0.59945	0.443000	0.29094	AAG	.	.	none		0.597	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
ASMTL	8623	hgsc.bcm.edu	37	X	1531648	1531648	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:1531648C>T	ENST00000381317.3	-	12	1654	c.1622G>A	c.(1621-1623)aGg>aAg	p.R541K	ASMTL_ENST00000416733.2_Missense_Mutation_p.R465K|ASMTL_ENST00000534940.1_Missense_Mutation_p.R483K|ASMTL_ENST00000381333.4_Missense_Mutation_p.R525K|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL-AS1_ENST00000425740.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	541	ASMT-like.		R -> K (in dbSNP:rs1127297). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9736779}.			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)				CTCGGCGACCCTGCTGAGTAA	0.552													c|||	1851	0.369609	0.3699	0.3026	5008	,	,		17773	0.4752		0.2227	False		,,,				2504	0.4591				p.R541K		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1622A						PASS	.		LYS/ARG,LYS/ARG,LYS/ARG	1426,2682		258,910,886	192.0	207.0	202.0		1448,1574,1622	0.3	0.0	X	dbSNP_134	202	1922,6478		209,1504,2487	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	26,26,26	467,2414,3373	TT,TC,CC		22.881,34.7128,26.7669	benign,benign,benign	483/564,525/606,541/622	1531648	3348,9160	2054	4200	6254	SO:0001583	missense	8623	exon12			GCGACCCTGCTGA	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.1622G>A	X.37:g.1531648C>T	ENSP00000370718:p.Arg541Lys	Somatic	488	0	0		WXS	Illumina HiSeq	Phase_I	566	258	0.45583	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	699	0.32005494505494503	200	0.4065040650406504	103	0.2845303867403315	239	0.4178321678321678	157	0.20712401055408972	-	4.451	0.083577	0.08533	0.347128	0.22881	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	1.43	0.299	0.15771	O-methyltransferase, family 2 (1);	0.365915	0.22202	U	0.063240	T	0.00012	0.0000	N	0.04335	-0.225	0.21604	N	0.999629	B;B;B	0.25351	0.021;0.124;0.076	B;B;B	0.19148	0.022;0.024;0.017	T	0.45789	-0.9237	10	0.02654	T	1	.	4.8051	0.13316	0.0:0.4377:0.0:0.5623	rs1127297;rs3183051;rs11553053;rs17855363;rs17855363	465;525;541	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	K	465;483;525;541	ENSP00000410578:R465K;ENSP00000446410:R483K;ENSP00000370734:R525K;ENSP00000370718:R541K	ENSP00000370718:R541K	R	-	2	0	ASMTL	1491648	0.855000	0.29742	0.004000	0.12327	0.000000	0.00434	1.192000	0.32150	0.518000	0.28383	-0.000000	0.15137	AGG	T|0.191;G|0.118	0.191	strong		0.552	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
CFLAR	8837	hgsc.bcm.edu	37	2	202006096	202006096	+	Intron	SNP	G	G	A	rs10190751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202006096G>A	ENST00000309955.3	+	5	1121				CFLAR_ENST00000341582.6_Intron|CFLAR-AS1_ENST00000598453.1_RNA|CFLAR-AS1_ENST00000415011.2_RNA|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000457277.1_Intron|CFLAR_ENST00000443227.1_Intron|CFLAR_ENST00000340870.5_Intron|RNU7-45P_ENST00000459460.1_RNA|CFLAR_ENST00000479953.2_Intron|CFLAR_ENST00000423241.2_Intron|CFLAR_ENST00000440180.1_Splice_Site|CFLAR_ENST00000342795.5_Intron|CFLAR_ENST00000341222.6_Splice_Site|CFLAR-AS1_ENST00000594911.1_RNA|CFLAR-AS1_ENST00000474886.2_RNA	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator						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						ctcttctacagatgataacac	0.338													A|||	1084	0.216454	0.4622	0.147	5008	,	,		18717	0.0516		0.2147	False		,,,				2504	0.1053				.	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.607-1G>A						PASS	.	A	,,,,,,,	1221,1891		265,691,600	115.0	94.0	100.0		,,,,,,,	-4.6	0.0	2	dbSNP_119	100	1377,5755		145,1087,2334	yes	intron,splice-3,intron,intron,intron,intron,intron,intron	CFLAR	NM_001127183.2,NM_001127184.2,NM_001202515.1,NM_001202516.1,NM_001202517.1,NM_001202518.1,NM_001202519.1,NM_003879.5	,,,,,,,	410,1778,2934	AA,AG,GG		19.3073,39.2352,25.3612	,,,,,,,	,,,,,,,	202006096	2598,7646	1556	3566	5122	SO:0001627	intron_variant	8837	exon6			TCTACAGATGATA	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.606+934G>A	2.37:g.202006096G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_001127184	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Splice_Site	SNP	ENST00000309955.3	37	CCDS2337.1																																																																																			G|0.764;A|0.236	0.236	strong		0.338	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879	
TRIP6	7205	hgsc.bcm.edu	37	7	100466441	100466441	+	Missense_Mutation	SNP	G	G	A	rs2075756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	108	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	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	
MUM1	84939	hgsc.bcm.edu	37	19	1357082	1357082	+	Silent	SNP	T	T	C	rs713042	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1357082T>C	ENST00000415183.3	+	2	161	c.135T>C	c.(133-135)tcT>tcC	p.S45S	MUM1_ENST00000591806.1_Silent_p.S45S|MUM1_ENST00000344663.3_Silent_p.S45S|MUM1_ENST00000311401.5_5'UTR			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	44					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAATCCTCTCTCTAGAGGAAA	0.373													C|||	3569	0.71266	0.7436	0.755	5008	,	,		18370	0.5565		0.7684	False		,,,				2504	0.7444				p.S45S		Atlas-SNP	.											.	MUM1	54	.	0			c.T135C						PASS	.	C		3297,1109	391.9+/-328.3	1245,807,151	144.0	147.0	146.0		135	-5.8	0.8	19	dbSNP_86	146	6862,1738	313.7+/-311.4	2729,1404,167	no	coding-synonymous	MUM1	NM_032853.3		3974,2211,318	CC,CT,TT		20.2093,25.1702,21.8899		45/712	1357082	10159,2847	2203	4300	6503	SO:0001819	synonymous_variant	84939	exon3			CCTCTCTCTAGAG	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.135T>C	19.37:g.1357082T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	170	169	0.994118	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Silent	SNP	ENST00000415183.3	37																																																																																				T|0.248;C|0.752	0.752	strong		0.373	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853	
PIGN	23556	hgsc.bcm.edu	37	18	59770033	59770033	+	Silent	SNP	C	C	T	rs12326381	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:59770033C>T	ENST00000357637.5	-	21	2377	c.1962G>A	c.(1960-1962)ctG>ctA	p.L654L	PIGN_ENST00000400334.3_Silent_p.L654L	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	654					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				TGACCTGTAACAGATGTACCA	0.333													T|||	478	0.0954473	0.0144	0.1239	5008	,	,		17245	0.0069		0.2684	False		,,,				2504	0.0982				p.L654L		Atlas-SNP	.											.	PIGN	62	.	0			c.G1962A						PASS	.	T	,	210,3464		6,198,1633	61.0	59.0	59.0		1962,1962	-6.9	0.0	18	dbSNP_120	59	1996,6176		231,1534,2321	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	237,1732,3954	TT,TC,CC		24.4249,5.7158,18.6223	,	654/932,654/932	59770033	2206,9640	1837	4086	5923	SO:0001819	synonymous_variant	23556	exon21			CTGTAACAGATGT	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1962G>A	18.37:g.59770033C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	60	36	0.6	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			C|0.880;T|0.120	0.120	strong		0.333	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
DUOX1	53905	hgsc.bcm.edu	37	15	45444133	45444133	+	Missense_Mutation	SNP	T	T	C	rs16939752	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:45444133T>C	ENST00000321429.4	+	25	3483	c.3076T>C	c.(3076-3078)Tgt>Cgt	p.C1026R	DUOX1_ENST00000389037.3_Missense_Mutation_p.C1026R|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000561166.1_Missense_Mutation_p.C672R	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1026	Interaction with TXNDC11. {ECO:0000250}.		C -> R (in dbSNP:rs16939752). {ECO:0000269|PubMed:14702039}.		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)	p.C1026R(1)		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)		CCAACGCAGCTGTCTCCACCA	0.587													C|||	1517	0.302915	0.3245	0.1945	5008	,	,		19840	0.4167		0.1292	False		,,,				2504	0.4121				p.C1026R		Atlas-SNP	.											DUOX1,NS,carcinoma,0,1	DUOX1	125	1	1	Substitution - Missense(1)	stomach(1)	c.T3076C						PASS	.	C	ARG/CYS,ARG/CYS	1175,3221	710.9+/-407.9	154,867,1177	75.0	72.0	73.0		3076,3076	3.2	1.0	15	dbSNP_123	73	996,7600	773.0+/-407.7	56,884,3358	yes	missense,missense	DUOX1	NM_017434.3,NM_175940.1	180,180	210,1751,4535	CC,CT,TT		11.5868,26.7288,16.7103	benign,benign	1026/1552,1026/1552	45444133	2171,10821	2198	4298	6496	SO:0001583	missense	53905	exon25			CGCAGCTGTCTCC	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.3076T>C	15.37:g.45444133T>C	ENSP00000317997:p.Cys1026Arg	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	200	93	0.465	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	597	0.2733516483516483	176	0.35772357723577236	77	0.212707182320442	251	0.4388111888111888	93	0.12269129287598944	C	10.54	1.378582	0.24944	0.267288	0.115868	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.84660	-1.88;-1.88	4.17	3.25	0.37280	.	0.264295	0.37304	N	0.002148	T	0.00012	0.0000	N	0.00583	-1.355	0.36558	P	0.127749	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39078	-0.9631	9	0.23891	T	0.37	-4.8419	3.8893	0.09111	0.1884:0.6075:0.0:0.2041	rs16939752;rs52810022;rs57005737;rs16939752	159;1026	Q9NT13;Q9NRD9	.;DUOX1_HUMAN	R	1026	ENSP00000317997:C1026R;ENSP00000373689:C1026R	ENSP00000317997:C1026R	C	+	1	0	DUOX1	43231425	0.998000	0.40836	0.956000	0.39512	0.973000	0.67179	2.047000	0.41269	0.519000	0.28406	-0.119000	0.15052	TGT	C|0.231;N|0.000	0.231	strong		0.587	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
KIAA1217	56243	hgsc.bcm.edu	37	10	24790393	24790393	+	Silent	SNP	A	A	G	rs1112284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:24790393A>G	ENST00000376454.3	+	9	1950	c.1920A>G	c.(1918-1920)tcA>tcG	p.S640S	KIAA1217_ENST00000376451.2_Silent_p.S323S|KIAA1217_ENST00000430453.2_Silent_p.S526S|KIAA1217_ENST00000376462.1_Silent_p.S560S|KIAA1217_ENST00000307544.6_Silent_p.S323S|KIAA1217_ENST00000458595.1_Silent_p.S605S|KIAA1217_ENST00000396445.1_Silent_p.S323S|KIAA1217_ENST00000376452.3_Silent_p.S605S|KIAA1217_ENST00000396446.1_Silent_p.S323S	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	640					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TGGGCACCTCAGCCATCCACA	0.617													G|||	2003	0.39996	0.6815	0.2983	5008	,	,		15614	0.2123		0.3439	False		,,,				2504	0.3425				p.S640S		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A1920G						PASS	.	G	,,	2768,1638	503.9+/-365.7	870,1028,305	73.0	64.0	67.0		1680,1815,1920	-7.3	0.0	10	dbSNP_86	67	2835,5765	674.9+/-403.2	470,1895,1935	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	1340,2923,2240	GG,GA,AA		32.9651,37.1766,43.0801	,,	560/1265,605/1310,640/1944	24790393	5603,7403	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon9			CACCTCAGCCATC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.1920A>G	10.37:g.24790393A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			A|0.581;C|0.007	.	strong		0.617	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
MAPT	4137	hgsc.bcm.edu	37	17	44061278	44061278	+	Missense_Mutation	SNP	C	C	T	rs17651549	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44061278C>T	ENST00000571987.1	+	5	1108	c.1108C>T	c.(1108-1110)Cgg>Tgg	p.R370W	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.R370W|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.R370W|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.R370W|MAPT_ENST00000535772.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	370			R -> W (in dbSNP:rs17651549).		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GCCCGTCAGCCGGGTCCCTCA	0.647													C|||	429	0.0856629	0.0129	0.1571	5008	,	,		15403	0.001		0.2406	False		,,,				2504	0.0613				p.R370W		Atlas-SNP	.											.	MAPT	135	.	0			c.C1108T						PASS	.	C	TRP/ARG,,,,,,TRP/ARG,	171,3947		5,161,1893	65.0	79.0	75.0		1108,,,,,,1108,	4.5	1.0	17	dbSNP_123	75	1750,6338		186,1378,2480	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	101,,,,,,101,	191,1539,4373	TT,TC,CC		21.637,4.1525,15.7382	probably-damaging,,,,,,probably-damaging,	370/777,,,,,,370/759,	44061278	1921,10285	2059	4044	6103	SO:0001583	missense	4137	exon6			GTCAGCCGGGTCC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1108C>T	17.37:g.44061278C>T	ENSP00000458742:p.Arg370Trp	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	253	0.11584249084249085	9	0.018292682926829267	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	18.18	3.567727	0.65651	0.041525	0.21637	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.15139	2.54;2.45;2.54	5.51	4.51	0.55191	.	0.000000	0.37857	N	0.001904	T	0.00012	0.0000	L	0.58101	1.795	0.09310	P	0.9999999999999999	D;D	0.71674	0.998;0.998	P;P	0.62491	0.903;0.774	T	0.07616	-1.0763	9	0.66056	D	0.02	-12.7384	12.1085	0.53825	0.0:0.827:0.173:0.0	rs17651549;rs52812169;rs17651549	370;370	P10636-9;P10636	.;TAU_HUMAN	W	370	ENSP00000340820:R370W;ENSP00000262410:R370W;ENSP00000410838:R370W	ENSP00000262410:R370W	R	+	1	2	MAPT	41417115	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	2.545000	0.45769	1.277000	0.44412	0.511000	0.50034	CGG	C|0.867;T|0.133	0.133	strong		0.647	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
ZFP69B	65243	hgsc.bcm.edu	37	1	40928145	40928145	+	Silent	SNP	G	G	A	rs61740805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40928145G>A	ENST00000411995.2	+	6	864	c.489G>A	c.(487-489)tcG>tcA	p.S163S	RP1-228H13.5_ENST00000565390.1_RNA|ZFP69B_ENST00000361584.3_Silent_p.S61S|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	116	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	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	
ATP8B2	57198	hgsc.bcm.edu	37	1	154320942	154320942	+	Silent	SNP	A	A	G	rs2297607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	98	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	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	
UBR5	51366	hgsc.bcm.edu	37	8	103311153	103311153	+	Silent	SNP	C	C	T	rs61752302	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:103311153C>T	ENST00000520539.1	-	25	3855	c.3249G>A	c.(3247-3249)gcG>gcA	p.A1083A	UBR5_ENST00000220959.4_Silent_p.A1083A|UBR5_ENST00000521922.1_Silent_p.A1077A	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	125	0	0		WXS	Illumina HiSeq	Phase_I	142	76	0.535211	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	
TG	7038	hgsc.bcm.edu	37	8	134144113	134144113	+	Silent	SNP	C	C	T	rs2294024	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:134144113C>T	ENST00000220616.4	+	46	7960	c.7920C>T	c.(7918-7920)taC>taT	p.Y2640Y	TG_ENST00000542445.1_Silent_p.Y1010Y|TG_ENST00000519543.1_Silent_p.Y773Y|TG_ENST00000377869.1_Silent_p.Y2583Y	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	159	0	0		WXS	Illumina HiSeq	Phase_I	130	51	0.392308	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	
POM121C	100101267	hgsc.bcm.edu	37	7	75051375	75051375	+	Silent	SNP	T	T	C	rs398016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:75051375T>C	ENST00000257665.5	-	11	2885	c.2886A>G	c.(2884-2886)ccA>ccG	p.P962P	POM121C_ENST00000453279.2_Silent_p.P720P|POM121C_ENST00000473168.1_5'Flank			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	962	Pore side. {ECO:0000255}.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						GGGTAAGGGCTGGCTTGGCGG	0.657													.|||	1448	0.289137	0.152	0.3069	5008	,	,		11153	0.2589		0.4702	False		,,,				2504	0.3067				p.P720P		Atlas-SNP	.											POM121C,NS,carcinoma,0,1	POM121C	46	1	0			c.A2160G						PASS	.	C		682,3536		76,530,1503	10.0	13.0	12.0		2160	-6.0	0.0	7	dbSNP_80	12	3609,4787		853,1903,1442	no	coding-synonymous	POM121C	NM_001099415.1		929,2433,2945	CC,CT,TT		42.9848,16.1688,34.0178		720/988	75051375	4291,8323	2109	4198	6307	SO:0001819	synonymous_variant	100101267	exon13			AAGGGCTGGCTTG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.2886A>G	7.37:g.75051375T>C		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	178	87	0.488764	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000257665.5	37																																																																																				T|0.701;C|0.299	0.299	strong		0.657	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
MUM1	84939	hgsc.bcm.edu	37	19	1370675	1370675	+	Silent	SNP	C	C	G	rs12608765	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1370675C>G	ENST00000415183.3	+	11	1613	c.1587C>G	c.(1585-1587)gtC>gtG	p.V529V	MUM1_ENST00000591806.1_Silent_p.V529V|MUM1_ENST00000344663.3_Silent_p.V529V|MUM1_ENST00000311401.5_Silent_p.V460V			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	528					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCAGGACGTCTTGGGGACCA	0.652													C|||	1644	0.328275	0.0582	0.3963	5008	,	,		14823	0.369		0.496	False		,,,				2504	0.4305				p.V529V		Atlas-SNP	.											MUM1,NS,carcinoma,0,2	MUM1	54	2	0			c.C1587G						PASS	.	C		560,3610		61,438,1586	13.0	12.0	12.0		1587	-9.4	0.0	19	dbSNP_120	12	3891,4325		1023,1845,1240	no	coding-synonymous	MUM1	NM_032853.3		1084,2283,2826	GG,GC,CC		47.3588,13.4293,35.9357		529/712	1370675	4451,7935	2085	4108	6193	SO:0001819	synonymous_variant	84939	exon12			GGACGTCTTGGGG	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1587C>G	19.37:g.1370675C>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Silent	SNP	ENST00000415183.3	37																																																																																				C|0.666;G|0.334	0.334	strong		0.652	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853	
QPCTL	54814	hgsc.bcm.edu	37	19	46206262	46206262	+	Silent	SNP	G	G	A	rs17850756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46206262G>A	ENST00000012049.5	+	7	1325	c.1104G>A	c.(1102-1104)ttG>ttA	p.L368L	QPCTL_ENST00000366382.4_Silent_p.L274L	NM_017659.3	NP_060129.2	Q9NXS2	QPCTL_HUMAN	glutaminyl-peptide cyclotransferase-like	368					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)	p.L368L(1)		breast(1)|cervix(2)|endometrium(1)|lung(5)|skin(1)|stomach(1)	11		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)		TACACAACTTGTGCCGCATTC	0.612													G|||	1178	0.235224	0.2163	0.1744	5008	,	,		18926	0.2133		0.2853	False		,,,				2504	0.2751				p.L368L		Atlas-SNP	.											QPCTL,NS,carcinoma,0,1	QPCTL	24	1	1	Substitution - coding silent(1)	stomach(1)	c.G1104A						PASS	.	G	,	973,3433	366.4+/-317.8	114,745,1344	171.0	125.0	140.0		822,1104	-8.7	0.8	19	dbSNP_123	140	2781,5819	441.0+/-359.7	472,1837,1991	no	coding-synonymous,coding-synonymous	QPCTL	NM_001163377.1,NM_017659.3	,	586,2582,3335	AA,AG,GG		32.3372,22.0835,28.8636	,	274/289,368/383	46206262	3754,9252	2203	4300	6503	SO:0001819	synonymous_variant	54814	exon7			CAACTTGTGCCGC	AK000091	CCDS12672.1, CCDS54282.1	19q13.32	2014-09-04			ENSG00000011478	ENSG00000011478			25952	protein-coding gene	gene with protein product	"""glutaminyl cyclase-like"""						Standard	NM_017659		Approved	FLJ20084	uc010xxr.2	Q9NXS2	OTTHUMG00000182131	ENST00000012049.5:c.1104G>A	19.37:g.46206262G>A		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	240	114	0.475	NM_017659	Q53HE4|Q96F74	Silent	SNP	ENST00000012049.5	37	CCDS12672.1																																																																																			G|0.727;A|0.273	0.273	strong		0.612	QPCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459656.1	NM_017659	
CD1C	911	hgsc.bcm.edu	37	1	158260984	158260984	+	Nonsense_Mutation	SNP	G	G	A	rs201073562		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158260984G>A	ENST00000368170.3	+	2	401	c.122G>A	c.(121-123)tGg>tAg	p.W41*		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	41					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					AACCAATCCTGGGCACGAGGT	0.493																																					p.W41X		Atlas-SNP	.											CD1C,NS,malignant_melanoma,0,1	CD1C	100	1	0			c.G122A						scavenged	.						86.0	75.0	79.0					1																	158260984		2203	4300	6503	SO:0001587	stop_gained	911	exon2			AATCCTGGGCACG	M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1636	protein-coding gene	gene with protein product		188340	"""CD1C antigen, c polypeptide"", ""CD1c antigen"""	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.122G>A	1.37:g.158260984G>A	ENSP00000357152:p.Trp41*	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	225	3	0.0133333	NM_001765	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Nonsense_Mutation	SNP	ENST00000368170.3	37	CCDS1175.1	.	.	.	.	.	.	.	.	.	.	-	26.4	4.735423	0.89482	.	.	ENSG00000158481	ENST00000368169;ENST00000368170	.	.	.	3.32	1.2	0.21068	.	0.000000	0.32190	N	0.006455	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.3512	0.07153	0.1561:0.0:0.6023:0.2416	.	.	.	.	X	41	.	ENSP00000357151:W41X	W	+	2	0	CD1C	156527608	0.534000	0.26362	0.200000	0.23457	0.044000	0.14063	1.446000	0.35090	0.318000	0.23185	-0.175000	0.13238	TGG	G|0.999;A|0.001	0.001	weak		0.493	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765	
ADAMTS4	9507	hgsc.bcm.edu	37	1	161161284	161161284	+	Missense_Mutation	SNP	G	G	C	rs41270041	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161161284G>C	ENST00000367996.5	-	9	2586	c.2158C>G	c.(2158-2160)Cct>Gct	p.P720A	ADAMTS4_ENST00000478394.1_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	720	Spacer.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	CGGTGGCCAGGGTTTCCCTGC	0.582													G|||	499	0.0996406	0.1157	0.0677	5008	,	,		20568	0.0665		0.0726	False		,,,				2504	0.1626				p.P720A		Atlas-SNP	.											.	ADAMTS4	171	.	0			c.C2158G						PASS	.	G	ALA/PRO	535,3871	244.7+/-253.9	37,461,1705	65.0	68.0	67.0		2158	0.3	0.0	1	dbSNP_127	67	696,7904	172.0+/-222.8	30,636,3634	yes	missense	ADAMTS4	NM_005099.4	27	67,1097,5339	CC,CG,GG		8.093,12.1425,9.4649	benign	720/838	161161284	1231,11775	2203	4300	6503	SO:0001583	missense	9507	exon9			GGCCAGGGTTTCC	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.2158C>G	1.37:g.161161284G>C	ENSP00000356975:p.Pro720Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	162	0.07417582417582418	49	0.09959349593495935	22	0.06077348066298342	35	0.06118881118881119	56	0.07387862796833773	G	2.807	-0.247892	0.05867	0.121425	0.08093	ENSG00000158859	ENST00000367996	T	0.48836	0.8	4.39	0.261	0.15592	ADAM-TS Spacer 1 (1);	0.307814	0.27782	N	0.017880	T	0.10937	0.0267	N	0.24115	0.695	0.49051	P	2.590000000000092E-4	B	0.06786	0.001	B	0.14023	0.01	T	0.07751	-1.0756	9	0.54805	T	0.06	.	1.5245	0.02523	0.274:0.1456:0.4318:0.1486	rs41270041;rs60958497;rs61737001	720	O75173	ATS4_HUMAN	A	720	ENSP00000356975:P720A	ENSP00000356975:P720A	P	-	1	0	ADAMTS4	159427908	0.000000	0.05858	0.007000	0.13788	0.218000	0.24690	0.003000	0.13083	0.182000	0.20032	0.561000	0.74099	CCT	G|0.910;C|0.090	0.090	strong		0.582	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
FAM135B	51059	hgsc.bcm.edu	37	8	139165068	139165068	+	Silent	SNP	C	C	T	rs3763590	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:139165068C>T	ENST00000395297.1	-	13	1820	c.1650G>A	c.(1648-1650)gtG>gtA	p.V550V		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	550										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)			TGTAGGTCAGCACTGGGGCCT	0.502										HNSCC(54;0.14)			C|||	1825	0.364417	0.1566	0.4135	5008	,	,		17906	0.5298		0.3757	False		,,,				2504	0.4284				p.V550V		Atlas-SNP	.											.	FAM135B	423	.	0			c.G1650A						PASS	.	C		741,3163		75,591,1286	83.0	82.0	82.0		1650	-9.9	0.0	8	dbSNP_107	82	2847,5445		498,1851,1797	no	coding-synonymous	FAM135B	NM_015912.3		573,2442,3083	TT,TC,CC		34.3343,18.9805,29.4195		550/1407	139165068	3588,8608	1952	4146	6098	SO:0001819	synonymous_variant	51059	exon13			GGTCAGCACTGGG	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.1650G>A	8.37:g.139165068C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			C|0.632;T|0.368	0.368	strong		0.502	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
CFAP46	54777	hgsc.bcm.edu	37	10	134624504	134624504	+	Silent	SNP	C	C	T	rs2274429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:134624504C>T	ENST00000368586.5	-	56	7633	c.7533G>A	c.(7531-7533)gcG>gcA	p.A2511A	TTC40_ENST00000263170.5_Silent_p.A672A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GGTAGGACCGCGCCAGGTCCA	0.662													C|||	1658	0.33107	0.0983	0.219	5008	,	,		17397	0.6181		0.3419	False		,,,				2504	0.4182				p.A2511A		Atlas-SNP	.											.	TTC40	100	.	0			c.G7533A						PASS	.	C		627,3775		51,525,1625	65.0	45.0	52.0		2469	-5.7	0.0	10	dbSNP_100	52	2894,5706		473,1948,1879	no	coding-synonymous	C10orf92	NM_001200049.1		524,2473,3504	TT,TC,CC		33.6512,14.2435,27.0804		823/1028	134624504	3521,9481	2201	4300	6501	SO:0001819	synonymous_variant	54777	exon56			GGACCGCGCCAGG																												ENST00000368586.5:c.7533G>A	10.37:g.134624504C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			C|0.701;T|0.299	0.299	strong		0.662	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
CDA	978	hgsc.bcm.edu	37	1	20915701	20915701	+	Missense_Mutation	SNP	A	A	C	rs2072671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:20915701A>C	ENST00000375071.3	+	1	261	c.79A>C	c.(79-81)Aag>Cag	p.K27Q	CDA_ENST00000461985.1_3'UTR	NM_001785.2	NP_001776.1	P32320	CDD_HUMAN	cytidine deaminase	27	CMP/dCMP deaminase zinc-binding.		K -> Q (in dbSNP:rs2072671). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8422236}.		cell surface receptor signaling pathway (GO:0007166)|cytidine deamination (GO:0009972)|cytosine metabolic process (GO:0019858)|negative regulation of cell growth (GO:0030308)|negative regulation of nucleotide metabolic process (GO:0045980)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine-containing compound salvage (GO:0008655)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular region (GO:0005576)	cytidine deaminase activity (GO:0004126)|nucleoside binding (GO:0001882)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)	GGAGGCCAAGAAGTCAGCCTA	0.627													A|||	965	0.192692	0.0673	0.3055	5008	,	,		18529	0.122		0.3141	False		,,,				2504	0.2301				p.K27Q	Pancreas(74;49 1356 2772 27818 40529)	Atlas-SNP	.											.	CDA	19	.	0			c.A79C	GRCh37	CM984152	CDA	M	rs2072671	PASS	.	A	GLN/LYS	456,3950	216.1+/-234.9	27,402,1774	65.0	58.0	60.0		79	4.0	1.0	1	dbSNP_96	60	2978,5622	462.3+/-365.7	511,1956,1833	yes	missense	CDA	NM_001785.2	53	538,2358,3607	CC,CA,AA		34.6279,10.3495,26.4032	benign	27/147	20915701	3434,9572	2203	4300	6503	SO:0001583	missense	978	exon1			GCCAAGAAGTCAG	BC054036	CCDS210.1	1p36.2-p35	2008-02-05			ENSG00000158825	ENSG00000158825	3.5.4.5		1712	protein-coding gene	gene with protein product		123920				8422236, 9878810	Standard	NM_001785		Approved	CDD	uc001bdk.3	P32320	OTTHUMG00000002845	ENST00000375071.3:c.79A>C	1.37:g.20915701A>C	ENSP00000364212:p.Lys27Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	173	82	0.473988	NM_001785		Missense_Mutation	SNP	ENST00000375071.3	37	CCDS210.1	467	0.21382783882783882	39	0.07926829268292683	103	0.2845303867403315	76	0.13286713286713286	249	0.32849604221635886	A	13.74	2.326085	0.41197	0.103495	0.346279	ENSG00000158825	ENST00000375071	T	0.42131	0.98	5.14	3.98	0.46160	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.280120	0.39544	N	0.001322	T	0.00012	0.0000	N	0.17248	0.465	0.21184	P	0.999763501	B	0.11235	0.004	B	0.10450	0.005	T	0.38824	-0.9643	9	0.21014	T	0.42	.	7.7946	0.29140	0.9042:0.0:0.0958:0.0	rs2072671;rs57221291;rs2072671	27	P32320	CDD_HUMAN	Q	27	ENSP00000364212:K27Q	ENSP00000364212:K27Q	K	+	1	0	CDA	20788288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.604000	0.36804	2.169000	0.68431	0.459000	0.35465	AAG	A|0.766;C|0.234	0.234	strong		0.627	CDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007965.1	NM_001785	
ADIPOQ	9370	hgsc.bcm.edu	37	3	186570892	186570892	+	Silent	SNP	T	T	G	rs2241766	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000444204.2_Silent_p.G15G|ADIPOQ-AS1_ENST00000422718.1_RNA			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	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	289	147	0.508651	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	
C2orf54	79919	hgsc.bcm.edu	37	2	241831005	241831005	+	Silent	SNP	C	C	T	rs10195453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	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	
MAGEC3	139081	hgsc.bcm.edu	37	X	140983103	140983103	+	Silent	SNP	C	C	T	rs176025	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:140983103C>T	ENST00000298296.1	+	5	958	c.958C>T	c.(958-960)Ctg>Ttg	p.L320L	MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000536088.1_Intron|MAGEC3_ENST00000409007.1_5'Flank|MAGEC3_ENST00000483584.1_3'UTR|MAGEC3_ENST00000544766.1_5'UTR|MAGEC3_ENST00000448920.1_Silent_p.L72L	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	320	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									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)					CCGACTTGCACTGTGGGAGTC	0.597													-|||	843	0.223311	0.3359	0.1354	3775	,	,		7497	0.0427		0.2058	False		,,,				2504	0.0562				p.L320L		Atlas-SNP	.											.	MAGEC3	228	.	0			c.C958T						PASS	.	T	,	1712,2123		318,812,264,502,307	123.0	112.0	116.0		958,	-1.4	0.0	X	dbSNP_79	116	1769,4959		188,910,483,1330,1389	no	coding-synonymous,utr-5	MAGEC3	NM_138702.1,NM_177456.2	,	506,1722,747,1832,1696	TT,TC,T,CC,C		26.2931,44.6415,32.9547	,	320/644,	140983103	3481,7082	2203	4300	6503	SO:0001819	synonymous_variant	139081	exon5			CTTGCACTGTGGG	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.958C>T	X.37:g.140983103C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	37	CCDS14676.1																																																																																			C|0.685;T|0.315	0.315	strong		0.597	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
AHNAK2	113146	hgsc.bcm.edu	37	14	105421050	105421050	+	Silent	SNP	T	T	G	rs879209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105421050T>G	ENST00000333244.5	-	7	857	c.738A>C	c.(736-738)ccA>ccC	p.P246P	AHNAK2_ENST00000557457.1_5'Flank	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	246						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)			TCCCCACCCTTGGTTTGGAGA	0.562													G|||	1551	0.309704	0.3192	0.2954	5008	,	,		18421	0.0754		0.4632	False		,,,				2504	0.3906				p.P246P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A738C						PASS	.	G		1230,2538		210,810,864	26.0	28.0	28.0		738	2.0	0.0	14	dbSNP_86	28	3787,4439		896,1995,1222	no	coding-synonymous	AHNAK2	NM_138420.2		1106,2805,2086	GG,GT,TT		46.037,32.6433,41.8292		246/5796	105421050	5017,6977	1884	4113	5997	SO:0001819	synonymous_variant	113146	exon7			CACCCTTGGTTTG	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.738A>C	14.37:g.105421050T>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			T|0.673;G|0.327	0.327	strong		0.562	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
GOLIM4	27333	hgsc.bcm.edu	37	3	167747022	167747022	+	Missense_Mutation	SNP	C	C	T	rs61743591	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:167747022C>T	ENST00000470487.1	-	11	2191	c.1502G>A	c.(1501-1503)gGa>gAa	p.G501E	GOLIM4_ENST00000309027.4_Missense_Mutation_p.G473E	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	501	Gln-rich.|Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TCCTTCCTCTCCTTGGATTCC	0.373													T|||	134	0.0267572	0.0068	0.0115	5008	,	,		15771	0.0308		0.0537	False		,,,				2504	0.0327				p.G501E		Atlas-SNP	.											GOLIM4,NS,carcinoma,-1,1	GOLIM4	71	1	0			c.G1502A						PASS	.	T	GLU/GLY	89,4317	818.1+/-416.3	0,89,2114	130.0	112.0	118.0		1502	5.0	1.0	3	dbSNP_129	118	556,8044	794.4+/-407.5	23,510,3767	yes	missense	GOLIM4	NM_014498.3	98	23,599,5881	TT,TC,CC		6.4651,2.02,4.9592	benign	501/697	167747022	645,12361	2203	4300	6503	SO:0001583	missense	27333	exon11			TCCTCTCCTTGGA	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"""golgi phosphoprotein 4"""	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1502G>A	3.37:g.167747022C>T	ENSP00000417354:p.Gly501Glu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	95	36	0.378947	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	63	0.028846153846153848	5	0.01016260162601626	4	0.011049723756906077	10	0.017482517482517484	44	0.05804749340369393	T	5.739	0.320877	0.10845	0.0202	0.064651	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	4.97	4.97	0.65823	.	0.222920	0.47455	N	0.000232	T	0.00552	0.0018	N	0.00069	-2.28	0.18873	N	0.999988	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33777	-0.9855	9	0.02654	T	1	-10.1009	10.7675	0.46303	0.0:0.0753:0.0:0.9246	.	473;501	F8W785;O00461	.;GOLI4_HUMAN	E	501;473	.	ENSP00000309893:G473E	G	-	2	0	GOLIM4	169229716	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	4.289000	0.59013	0.758000	0.33059	-0.391000	0.06502	GGA	C|0.956;T|0.044	0.044	strong		0.373	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2		
HPS6	79803	hgsc.bcm.edu	37	10	103825929	103825929	+	Missense_Mutation	SNP	T	T	G	rs36078476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103825929T>G	ENST00000299238.5	+	1	783	c.698T>G	c.(697-699)cTt>cGt	p.L233R		NM_024747.5	NP_079023.2	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome 6	233					blood coagulation (GO:0007596)|melanocyte differentiation (GO:0030318)|organelle organization (GO:0006996)|protein localization to membrane (GO:0072657)	BLOC-2 complex (GO:0031084)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|Rab GTPase binding (GO:0017137)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)	11		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)		GCCCCACGGCTTGGTCTCTCC	0.632									Hermansky-Pudlak syndrome				T|||	18	0.00359425	0.0	0.0058	5008	,	,		17583	0.0		0.0089	False		,,,				2504	0.0051				p.L233R		Atlas-SNP	.											.	HPS6	38	.	0			c.T698G						PASS	.	T	ARG/LEU	5,4401	8.1+/-20.4	0,5,2198	66.0	70.0	69.0		698	2.4	0.6	10	dbSNP_126	69	84,8516	44.9+/-103.4	1,82,4217	yes	missense	HPS6	NM_024747.5	102	1,87,6415	GG,GT,TT		0.9767,0.1135,0.6843	benign	233/776	103825929	89,12917	2203	4300	6503	SO:0001583	missense	79803	exon1	Familial Cancer Database	HPS, HPS1-8	CACGGCTTGGTCT	BC009258	CCDS7527.1	10q24.32	2014-06-18			ENSG00000166189	ENSG00000166189			18817	protein-coding gene	gene with protein product		607522				12548288	Standard	NM_024747		Approved	FLJ22501	uc001kuj.3	Q86YV9	OTTHUMG00000018945	ENST00000299238.5:c.698T>G	10.37:g.103825929T>G	ENSP00000299238:p.Leu233Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_024747	Q5VV69|Q9H685	Missense_Mutation	SNP	ENST00000299238.5	37	CCDS7527.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	T	0.028	-1.357288	0.01245	0.001135	0.009767	ENSG00000166189	ENST00000299238	T	0.76839	-1.05	4.9	2.39	0.29439	.	0.686580	0.14829	N	0.295985	T	0.50718	0.1632	L	0.41236	1.265	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31888	-0.9927	10	0.07644	T	0.81	-8.6793	1.0414	0.01559	0.2679:0.0946:0.2798:0.3577	rs36078476;rs36078476	233	Q86YV9	HPS6_HUMAN	R	233	ENSP00000299238:L233R	ENSP00000299238:L233R	L	+	2	0	HPS6	103815919	0.055000	0.20627	0.601000	0.28877	0.719000	0.41307	1.287000	0.33284	0.870000	0.35726	-0.429000	0.05907	CTT	T|0.993;G|0.007	0.007	strong		0.632	HPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050018.2	NM_024747	
FAT1	2195	hgsc.bcm.edu	37	4	187629896	187629896	+	Silent	SNP	G	G	A	rs11722204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187629896G>A	ENST00000441802.2	-	2	1295	c.1086C>T	c.(1084-1086)gcC>gcT	p.A362A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	362					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A362A(3)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TGACTGGCCCGGCTTTGAACT	0.448										HNSCC(5;0.00058)			G|||	76	0.0151757	0.0	0.0216	5008	,	,		20402	0.0		0.0537	False		,,,				2504	0.0072				p.A362A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,0,2	FAT1	500	2	3	Substitution - coding silent(3)	prostate(3)	c.C1086T						PASS	.	G		38,3692		0,38,1827	114.0	108.0	110.0		1086	-10.6	0.4	4	dbSNP_120	110	542,7672		14,514,3579	no	coding-synonymous	FAT1	NM_005245.3		14,552,5406	AA,AG,GG		6.5985,1.0188,4.856		362/4589	187629896	580,11364	1865	4107	5972	SO:0001819	synonymous_variant	2195	exon2			TGGCCCGGCTTTG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1086C>T	4.37:g.187629896G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.969;A|0.031	0.031	strong		0.448	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
SLC6A11	6538	hgsc.bcm.edu	37	3	10885920	10885920	+	Silent	SNP	T	T	C	rs2304725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	132	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	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	
GBP6	163351	hgsc.bcm.edu	37	1	89835209	89835209	+	Missense_Mutation	SNP	G	G	A	rs75966734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89835209G>A	ENST00000370456.4	+	3	388	c.295G>A	c.(295-297)Gaa>Aaa	p.E99K	GBP6_ENST00000535065.1_Intron	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	99	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		TCTGGACACCGAAGGTCTGGG	0.512													G|||	26	0.00519169	0.0015	0.0014	5008	,	,		20562	0.0		0.0199	False		,,,				2504	0.0031				p.E99K		Atlas-SNP	.											.	GBP6	87	.	0			c.G295A						PASS	.	G	LYS/GLU	7,4399	12.9+/-30.5	0,7,2196	81.0	75.0	77.0		295	4.6	0.9	1	dbSNP_132	77	74,8526	44.5+/-102.8	0,74,4226	yes	missense	GBP6	NM_198460.2	56	0,81,6422	AA,AG,GG		0.8605,0.1589,0.6228	probably-damaging	99/634	89835209	81,12925	2203	4300	6503	SO:0001583	missense	163351	exon3			GACACCGAAGGTC	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.295G>A	1.37:g.89835209G>A	ENSP00000359485:p.Glu99Lys	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	148	59	0.398649	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	17	0.007783882783882784	1	0.0020325203252032522	0	0.0	0	0.0	16	0.021108179419525065	G	20.9	4.059633	0.76074	0.001589	0.008605	ENSG00000183347	ENST00000544311;ENST00000370456	T	0.64803	-0.12	4.55	4.55	0.56014	Guanylate-binding protein, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85487	0.5708	H	0.98786	4.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91319	0.5080	10	0.87932	D	0	-32.7322	14.7834	0.69784	0.0:0.0:1.0:0.0	.	99	Q6ZN66	GBP6_HUMAN	K	70;99	ENSP00000359485:E99K	ENSP00000359485:E99K	E	+	1	0	GBP6	89607797	1.000000	0.71417	0.911000	0.35937	0.426000	0.31534	6.781000	0.75068	2.079000	0.62486	0.585000	0.79938	GAA	G|0.993;A|0.007	0.007	strong		0.512	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
NGFR	4804	hgsc.bcm.edu	37	17	47588000	47588000	+	Silent	SNP	C	C	T	rs11466155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:47588000C>T	ENST00000172229.3	+	4	920	c.795C>T	c.(793-795)ggC>ggT	p.G265G	RP5-1029K10.2_ENST00000514506.1_RNA|NGFR_ENST00000504201.1_Silent_p.G171G	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	265					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					TGGTTGTGGGCCTTGTGGCCT	0.582													C|||	1151	0.229832	0.0477	0.3141	5008	,	,		20799	0.0823		0.3231	False		,,,				2504	0.4724				p.G265G		Atlas-SNP	.											NGFR,colon,carcinoma,0,2	NGFR	46	2	0			c.C795T						scavenged	.	C		398,4008	197.7+/-221.8	15,368,1820	117.0	104.0	108.0		795	-0.8	1.0	17	dbSNP_120	108	2848,5752	448.3+/-361.8	484,1880,1936	no	coding-synonymous	NGFR	NM_002507.3		499,2248,3756	TT,TC,CC		33.1163,9.0331,24.9577		265/428	47588000	3246,9760	2203	4300	6503	SO:0001819	synonymous_variant	4804	exon4			TGTGGGCCTTGTG	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	7809	protein-coding gene	gene with protein product	"""low affinity nerve growth factor receptor"", ""TNFR superfamily, member 16"""	162010	"""nerve growth factor receptor (TNFR superfamily, member 16)"""			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.795C>T	17.37:g.47588000C>T		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	NM_002507	B2R961|B4E096	Silent	SNP	ENST00000172229.3	37	CCDS11549.1																																																																																			C|0.763;T|0.237	0.237	strong		0.582	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		
ZNF414	84330	hgsc.bcm.edu	37	19	8577924	8577924	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8577924C>T	ENST00000255616.8	-	2	406	c.305G>A	c.(304-306)cGc>cAc	p.R102H	ZNF414_ENST00000393927.4_Missense_Mutation_p.R102H	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	102					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(2)	2						TGGAGGTGGGCGTCGTCTGGG	0.617																																					p.R102H		Atlas-SNP	.											.	ZNF414	25	.	0			c.G305A						PASS	.						7.0	5.0	6.0					19																	8577924		1959	3887	5846	SO:0001583	missense	84330	exon2			GGTGGGCGTCGTC	AK074191	CCDS12205.1, CCDS54211.1	19p13.2	2008-02-05				ENSG00000133250		"""Zinc fingers, C2H2-type"""	20630	protein-coding gene	gene with protein product							Standard	NM_032370		Approved	MGC15716, Zfp414	uc002mke.4	Q96IQ9		ENST00000255616.8:c.305G>A	19.37:g.8577924C>T	ENSP00000255616:p.Arg102His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	83	54	0.650602	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.302311	0.81136	.	.	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.09817	2.94;2.94	4.52	3.4	0.38934	.	0.170242	0.37304	N	0.002141	T	0.23965	0.0580	L	0.61036	1.89	0.29293	N	0.869209	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.991	T	0.02893	-1.1097	10	0.15499	T	0.54	-24.3645	11.0252	0.47741	0.0:0.8107:0.1893:0.0	.	102;102	Q96IQ9;A8MY94	ZN414_HUMAN;.	H	102	ENSP00000377504:R102H;ENSP00000255616:R102H	ENSP00000255616:R102H	R	-	2	0	ZNF414	8483924	0.975000	0.34042	0.995000	0.50966	0.988000	0.76386	0.720000	0.25896	2.219000	0.72066	0.655000	0.94253	CGC	.	.	none		0.617	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370	
TENM2	57451	hgsc.bcm.edu	37	5	167631599	167631599	+	Missense_Mutation	SNP	G	G	A	rs141103827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:167631599G>A	ENST00000518659.1	+	19	3836	c.3797G>A	c.(3796-3798)cGa>cAa	p.R1266Q	TENM2_ENST00000520394.1_Missense_Mutation_p.R1034Q|TENM2_ENST00000519204.1_Missense_Mutation_p.R1145Q|TENM2_ENST00000403607.2_Missense_Mutation_p.R1090Q|TENM2_ENST00000545108.1_Missense_Mutation_p.R1266Q	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1266					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)										TTTCCCTCTCGAAATGTGACC	0.522													g|||	25	0.00499201	0.0008	0.0014	5008	,	,		18911	0.0		0.004	False		,,,				2504	0.0194				p.R1257Q		Atlas-SNP	.											.	.	.	.	0			c.G3770A						PASS	.	G	GLN/ARG	3,3911		0,3,1954	93.0	89.0	90.0		3770	4.0	1.0	5	dbSNP_134	90	38,8266		0,38,4114	yes	missense	ODZ2	NM_001122679.1	43	0,41,6068	AA,AG,GG		0.4576,0.0766,0.3356	possibly-damaging	1257/2766	167631599	41,12177	1957	4152	6109	SO:0001583	missense	57451	exon19			CCTCTCGAAATGT	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.3797G>A	5.37:g.167631599G>A	ENSP00000429430:p.Arg1266Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	154	89	0.577922	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	22.9	4.353549	0.82243	7.66E-4	0.004576	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61;-2.61	4.9	4.01	0.46588	Six-bladed beta-propeller, TolB-like (1);	0.229981	0.43579	D	0.000549	T	0.77164	0.4090	N	0.08118	0	0.32750	N	0.506584	D;P;P	0.53885	0.963;0.785;0.942	P;B;B	0.46850	0.529;0.166;0.149	D	0.85392	0.1126	10	0.87932	D	0	.	15.0945	0.72223	0.0:0.1425:0.8575:0.0	.	1266;1266;1034	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	Q	1266;1266;1145;1034;1090	ENSP00000429430:R1266Q;ENSP00000438635:R1266Q;ENSP00000428964:R1145Q;ENSP00000427874:R1034Q;ENSP00000384905:R1090Q	ENSP00000384905:R1090Q	R	+	2	0	ODZ2	167564177	1.000000	0.71417	0.986000	0.45419	0.986000	0.74619	5.887000	0.69751	1.025000	0.39708	0.550000	0.68814	CGA	G|0.997;A|0.003	0.003	strong		0.522	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
AQP11	282679	hgsc.bcm.edu	37	11	77301341	77301341	+	Missense_Mutation	SNP	G	G	A	rs2276415	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:77301341G>A	ENST00000313578.3	+	1	662	c.304G>A	c.(304-306)Ggc>Agc	p.G102S	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	102			G -> S (in dbSNP:rs2276415).		endosomal lumen acidification (GO:0048388)|protein homooligomerization (GO:0051260)|proximal tubule development (GO:0072014)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			kidney(2)|large_intestine(1)|lung(5)	8	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			CAACCCGTGCGGCGTGATGAT	0.637													G|||	731	0.145966	0.1377	0.1902	5008	,	,		19940	0.1825		0.0964	False		,,,				2504	0.1391				p.G102S		Atlas-SNP	.											.	AQP11	14	.	0			c.G304A						PASS	.	G	SER/GLY	594,3806	258.0+/-262.2	40,514,1646	72.0	62.0	66.0		304	3.7	1.0	11	dbSNP_100	66	801,7783	187.3+/-234.6	34,733,3525	yes	missense	AQP11	NM_173039.2	56	74,1247,5171	AA,AG,GG		9.3313,13.5,10.744	probably-damaging	102/272	77301341	1395,11589	2200	4292	6492	SO:0001583	missense	282679	exon1			CCGTGCGGCGTGA	AB028147	CCDS8251.1	11q13.5	2008-02-05			ENSG00000178301	ENSG00000178301		"""Ion channels / Aquaporins"""	19940	protein-coding gene	gene with protein product		609914				16107722	Standard	NM_173039		Approved		uc001oyj.3	Q8NBQ7	OTTHUMG00000165194	ENST00000313578.3:c.304G>A	11.37:g.77301341G>A	ENSP00000318770:p.Gly102Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	117	48	0.410256	NM_173039		Missense_Mutation	SNP	ENST00000313578.3	37	CCDS8251.1	316	0.1446886446886447	74	0.15040650406504066	57	0.1574585635359116	113	0.19755244755244755	72	0.09498680738786279	G	17.49	3.402396	0.62288	0.135	0.093313	ENSG00000178301	ENST00000313578	D	0.84944	-1.92	5.54	3.68	0.42216	Aquaporin-like (2);	0.218216	0.47852	N	0.000215	T	0.00300	0.0009	M	0.63843	1.955	0.21762	P	0.99955712	P	0.52316	0.952	B	0.40602	0.334	T	0.07481	-1.0770	9	0.27082	T	0.32	-12.8909	9.8641	0.41131	0.2177:0.0:0.7823:0.0	rs2276415;rs52797374;rs59985599;rs2276415	102	Q8NBQ7	AQP11_HUMAN	S	102	ENSP00000318770:G102S	ENSP00000318770:G102S	G	+	1	0	AQP11	76978989	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.719000	0.47244	0.715000	0.32103	0.491000	0.48974	GGC	G|0.873;A|0.127	0.127	strong		0.637	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039	
FER1L5	90342	hgsc.bcm.edu	37	2	97366088	97366088	+	RNA	SNP	T	T	C	rs61742095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97366088T>C	ENST00000457909.1	+	0	4453							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						CCCCTACTGTTCATGGTTTGG	0.577													T|||	399	0.0796725	0.0938	0.0591	5008	,	,		20706	0.121		0.0716	False		,,,				2504	0.0409				p.V1677V		Atlas-SNP	.											.	FER1L5	113	.	0			c.T5031C						PASS	.	T		315,3773		16,283,1745	96.0	107.0	103.0		5031	-3.2	0.0	2	dbSNP_129	103	582,7756		28,526,3615	no	coding-synonymous	FER1L5	NM_001113382.1		44,809,5360	CC,CT,TT		6.9801,7.7055,7.2187		1677/2094	97366088	897,11529	2044	4169	6213			90342	exon44			TACTGTTCATGGT	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"""fer-1-like 5 (C. elegans)"""				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		2.37:g.97366088T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	22	0.372881	NM_001113382	Q17RH2|Q6ZU24	Silent	SNP	ENST00000457909.1	37																																																																																				T|0.912;C|0.088	0.088	strong		0.577	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400	
TRPA1	8989	hgsc.bcm.edu	37	8	72984041	72984041	+	Missense_Mutation	SNP	C	C	G	rs16937976	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:72984041C>G	ENST00000262209.4	-	2	380	c.173G>C	c.(172-174)aGa>aCa	p.R58T		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	58			R -> T (in dbSNP:rs16937976). {ECO:0000269|PubMed:10066796}.		calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATCGTCACATCTTTTTAATTT	0.363													C|||	509	0.101637	0.0847	0.0749	5008	,	,		18505	0.0565		0.173	False		,,,				2504	0.1166				p.R58T		Atlas-SNP	.											TRPA1,right_upper_lobe,carcinoma,+1,2	TRPA1	256	2	0			c.G173C						PASS	.	C	THR/ARG	368,4038	187.4+/-214.1	14,340,1849	143.0	127.0	132.0		173	-4.1	0.0	8	dbSNP_123	132	1443,7157	277.2+/-292.7	119,1205,2976	yes	missense	TRPA1	NM_007332.2	71	133,1545,4825	GG,GC,CC		16.7791,8.3522,13.9243	benign	58/1120	72984041	1811,11195	2203	4300	6503	SO:0001583	missense	8989	exon2			TCACATCTTTTTA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.173G>C	8.37:g.72984041C>G	ENSP00000262209:p.Arg58Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	224	0.10256410256410256	26	0.052845528455284556	29	0.08011049723756906	40	0.06993006993006994	129	0.17018469656992086	C	5.574	0.290729	0.10567	0.083522	0.167791	ENSG00000104321	ENST00000262209	T	0.39056	1.1	5.08	-4.1	0.03940	.	1.264600	0.05255	N	0.514708	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.16158	-1.0412	9	0.16896	T	0.51	-0.2071	6.303	0.21123	0.0:0.2639:0.3009:0.4352	rs16937976;rs57019352;rs16937976	58	O75762	TRPA1_HUMAN	T	58	ENSP00000262209:R58T	ENSP00000262209:R58T	R	-	2	0	TRPA1	73146595	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.077000	0.11394	-0.237000	0.09739	-0.251000	0.11542	AGA	C|0.874;G|0.126	0.126	strong		0.363	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
CCDC39	339829	hgsc.bcm.edu	37	3	180359790	180359790	+	Missense_Mutation	SNP	T	T	C	rs200277460	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:180359790T>C	ENST00000442201.2	-	13	1984	c.1865A>G	c.(1864-1866)gAa>gGa	p.E622G	CCDC39_ENST00000273654.4_Missense_Mutation_p.E706G	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	622					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CCTTATGTTTTCCCGTTCTTG	0.378													T|||	3	0.000599042	0.0	0.0	5008	,	,		17354	0.0		0.003	False		,,,				2504	0.0				p.E622G		Atlas-SNP	.											.	CCDC39	242	.	0			c.A1865G						PASS	.	T	GLY/GLU	0,3678		0,0,1839	129.0	119.0	122.0		1865	4.9	1.0	3		122	11,8175		0,11,4082	yes	missense	CCDC39	NM_181426.1	98	0,11,5921	CC,CT,TT		0.1344,0.0,0.0927	benign	622/942	180359790	11,11853	1839	4093	5932	SO:0001583	missense	339829	exon13			ATGTTTTCCCGTT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1865A>G	3.37:g.180359790T>C	ENSP00000405708:p.Glu622Gly	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	207	95	0.458937	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	16.10	3.028257	0.54790	0.0	0.001344	ENSG00000145075	ENST00000273654;ENST00000442201	.	.	.	4.9	4.9	0.64082	.	0.169998	0.52532	D	0.000067	T	0.26412	0.0645	N	0.08118	0	0.26248	N	0.978768	B	0.24882	0.113	B	0.26094	0.066	T	0.24154	-1.0168	9	0.48119	T	0.1	-11.3381	14.5324	0.67936	0.0:0.0:0.0:1.0	.	622	Q9UFE4	CCD39_HUMAN	G	706;622	.	ENSP00000273654:E706G	E	-	2	0	CCDC39	181842484	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	6.020000	0.70826	1.961000	0.56991	0.472000	0.43445	GAA	T|0.999;C|0.001	0.001	strong		0.378	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
RIMBP2	23504	hgsc.bcm.edu	37	12	130912757	130912757	+	Silent	SNP	C	C	T	rs2277356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:130912757C>T	ENST00000261655.4	-	12	2491	c.2328G>A	c.(2326-2328)agG>agA	p.R776R		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	776					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CGCTGGGCCGCCTCCTTCCCC	0.617													C|||	1446	0.288738	0.2148	0.3429	5008	,	,		17168	0.4077		0.165	False		,,,				2504	0.3548				p.R776R		Atlas-SNP	.											RIMBP2,NS,carcinoma,0,2	RIMBP2	220	2	0			c.G2328A						PASS	.	C		938,3468	356.1+/-313.4	92,754,1357	78.0	60.0	66.0		2328	4.1	1.0	12	dbSNP_100	66	1116,7484	231.9+/-265.7	73,970,3257	no	coding-synonymous	RIMBP2	NM_015347.4		165,1724,4614	TT,TC,CC		12.9767,21.2892,15.7927		776/1053	130912757	2054,10952	2203	4300	6503	SO:0001819	synonymous_variant	23504	exon12			GGGCCGCCTCCTT	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2328G>A	12.37:g.130912757C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	107	41	0.383178	NM_015347	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																			C|0.786;T|0.214	0.214	strong		0.617	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
RTP4	64108	hgsc.bcm.edu	37	3	187088612	187088612	+	Silent	SNP	C	C	T	rs33927333	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:187088612C>T	ENST00000259030.2	+	2	302	c.192C>T	c.(190-192)tcC>tcT	p.S64S		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	64					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GTTGGGCTTCCGCCCAAGTGC	0.552													C|||	396	0.0790735	0.0113	0.1066	5008	,	,		19676	0.0159		0.168	False		,,,				2504	0.1247				p.S64S		Atlas-SNP	.											.	RTP4	20	.	0			c.C192T						PASS	.	C		151,4255	105.2+/-143.6	0,151,2052	51.0	47.0	48.0		192	-7.8	0.2	3	dbSNP_126	48	1419,7181	273.5+/-290.7	111,1197,2992	yes	coding-synonymous	RTP4	NM_022147.2		111,1348,5044	TT,TC,CC		16.5,3.4271,12.0714		64/247	187088612	1570,11436	2203	4300	6503	SO:0001819	synonymous_variant	64108	exon2			GGCTTCCGCCCAA	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"""Receptor transporter proteins"""	23992	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 4"""	609350	"""receptor transporter protein 4"""			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.192C>T	3.37:g.187088612C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	208	89	0.427885	NM_022147	Q9H4F3	Silent	SNP	ENST00000259030.2	37	CCDS33910.1																																																																																			C|0.885;T|0.115	0.115	strong		0.552	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
ZNF653	115950	hgsc.bcm.edu	37	19	11598224	11598224	+	Missense_Mutation	SNP	C	C	T	rs74552618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11598224C>T	ENST00000293771.5	-	4	1190	c.1054G>A	c.(1054-1056)Gag>Aag	p.E352K	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	352					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						GGCACCTCCTCGCCCAGTCCA	0.652													C|||	29	0.00579073	0.0015	0.0043	5008	,	,		16677	0.001		0.0129	False		,,,				2504	0.0102				p.E352K	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.G1054A						PASS	.	C	LYS/GLU	5,4401	9.9+/-24.2	0,5,2198	63.0	52.0	56.0		1054	4.1	1.0	19	dbSNP_131	56	120,8480	62.4+/-124.4	1,118,4181	yes	missense	ZNF653	NM_138783.3	56	1,123,6379	TT,TC,CC		1.3953,0.1135,0.9611	benign	352/616	11598224	125,12881	2203	4300	6503	SO:0001583	missense	115950	exon4			CCTCCTCGCCCAG	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.1054G>A	19.37:g.11598224C>T	ENSP00000293771:p.Glu352Lys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_138783	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	37	CCDS12261.1	17	0.007783882783882784	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	13	0.017150395778364115	C	20.3	3.959028	0.74016	0.001135	0.013953	ENSG00000161914	ENST00000293771	T	0.15487	2.42	4.14	4.14	0.48551	.	0.057370	0.64402	D	0.000002	T	0.09774	0.0240	L	0.32530	0.975	0.54753	D	0.999987	D	0.62365	0.991	P	0.47402	0.546	T	0.01819	-1.1267	10	0.87932	D	0	-13.1491	15.5534	0.76170	0.0:1.0:0.0:0.0	.	352	Q96CK0	ZN653_HUMAN	K	352	ENSP00000293771:E352K	ENSP00000293771:E352K	E	-	1	0	ZNF653	11459224	0.994000	0.37717	0.996000	0.52242	0.730000	0.41778	3.644000	0.54381	2.002000	0.58637	0.462000	0.41574	GAG	C|0.991;T|0.009	0.009	strong		0.652	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
KCNMB1	3779	hgsc.bcm.edu	37	5	169810796	169810796	+	Missense_Mutation	SNP	C	C	T	rs11739136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:169810796C>T	ENST00000274629.4	-	3	635	c.193G>A	c.(193-195)Gag>Aag	p.E65K	KCNIP1_ENST00000377360.4_Intron|KCNIP1_ENST00000518527.1_Intron|KCNMB1_ENST00000521859.1_Missense_Mutation_p.E65K	NM_004137.3	NP_004128.1	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 1	65			E -> K (has a protective effect against diastolic hypertension; dbSNP:rs11739136). {ECO:0000269|PubMed:15057310}.		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)	CCCTTCAGCTCCTCCTGGTCC	0.582													C|||	474	0.0946486	0.053	0.1412	5008	,	,		20766	0.1369		0.0964	False		,,,				2504	0.0726				p.S65T		Atlas-SNP	.											.	KCNMB1	38	.	0			c.T193A	GRCh37	CM041786	KCNMB1	M	rs11739136	PASS	.	C	,LYS/GLU	266,4140	149.5+/-183.7	12,242,1949	128.0	100.0	109.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,193	3.6	1.0	5	dbSNP_120	109	870,7730	197.5+/-242.1	50,770,3480	yes	intron,missense	KCNMB1,KCNIP1	NM_001034838.1,NM_004137.2	,56	62,1012,5429	TT,TC,CC		10.1163,6.0372,8.7344	,benign	,65/192	169810796	1136,11870	2203	4300	6503	SO:0001583	missense	3779	exon3			TCAGCTCCTCCTG	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.193G>A	5.37:g.169810796C>T	ENSP00000274629:p.Glu65Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_004137	O00707|O00708|P78475|Q53YR0|Q8TAX3|Q93005	Missense_Mutation	SNP	ENST00000274629.4	37	CCDS4373.1	212	0.09706959706959707	20	0.04065040650406504	51	0.1408839779005525	68	0.11888111888111888	73	0.09630606860158311	C	15.48	2.845846	0.51164	0.060372	0.101163	ENSG00000145936	ENST00000274629;ENST00000521859	T;T	0.10763	2.84;2.84	5.7	3.59	0.41128	.	0.102225	0.64402	D	0.000003	T	0.00073	0.0002	L	0.27053	0.805	0.34848	P	0.25866999999999996	B;B	0.21071	0.037;0.051	B;B	0.19946	0.027;0.012	T	0.35624	-0.9781	8	.	.	.	.	8.0511	0.30579	0.0:0.7393:0.1654:0.0952	rs11739136;rs52831846;rs60174556;rs11739136	65;65	Q16558-2;Q16558	.;KCMB1_HUMAN	K	65	ENSP00000274629:E65K;ENSP00000427940:E65K	.	E	-	1	0	KCNMB1	169743374	0.960000	0.32886	0.999000	0.59377	0.964000	0.63967	0.608000	0.24223	1.403000	0.46800	0.655000	0.94253	GAG	C|0.910;T|0.090	0.090	strong		0.582	KCNMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252830.3		
PARPBP	55010	hgsc.bcm.edu	37	12	102547741	102547741	+	Missense_Mutation	SNP	G	G	A	rs114546604	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102547741G>A	ENST00000358383.5	+	4	527	c.482G>A	c.(481-483)cGt>cAt	p.R161H	PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000541394.1_Missense_Mutation_p.R238H|PARPBP_ENST00000378128.3_Missense_Mutation_p.R161H|PARPBP_ENST00000543784.1_Intron|PARPBP_ENST00000392911.2_Missense_Mutation_p.R80H|PARPBP_ENST00000327680.2_Missense_Mutation_p.R80H			Q9NWS1	PARI_HUMAN	PARP1 binding protein	161					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						AAATACAACCGTGATAATGAA	0.353													A|||	153	0.0305511	0.0998	0.0058	5008	,	,		18353	0.0		0.006	False		,,,				2504	0.0112				p.R161H		Atlas-SNP	.											.	PARPBP	40	.	0			c.G482A						PASS	.	A	HIS/ARG	282,4124	800.4+/-415.6	15,252,1936	105.0	93.0	97.0		482	2.8	0.1	12	dbSNP_132	97	21,8577	817.4+/-406.9	0,21,4278	yes	missense	C12orf48	NM_017915.3	29	15,273,6214	AA,AG,GG		0.2442,6.4004,2.3301	benign	161/580	102547741	303,12701	2203	4299	6502	SO:0001583	missense	55010	exon4			ACAACCGTGATAA	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.482G>A	12.37:g.102547741G>A	ENSP00000351153:p.Arg161His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	53	0.024267399267399268	48	0.0975609756097561	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	2.534	-0.307796	0.05458	0.064004	0.002442	ENSG00000185480	ENST00000378128;ENST00000327680;ENST00000541394;ENST00000358383;ENST00000392911;ENST00000417507;ENST00000412715	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.46	2.79	0.32731	.	0.713371	0.14523	N	0.314304	T	0.00412	0.0013	N	0.08118	0	0.09310	N	1	B;B;P;B;B;B	0.35527	0.0;0.0;0.507;0.018;0.0;0.0	B;B;B;B;B;B	0.14023	0.0;0.0;0.01;0.002;0.0;0.0	T	0.07947	-1.0746	10	0.27785	T	0.31	2.3812	5.7553	0.18170	0.7054:0.0:0.1593:0.1353	.	238;161;161;161;161;80	B4DZ31;Q9NWS1-6;Q9NWS1-7;Q9NWS1-3;Q9NWS1;Q9NWS1-2	.;.;.;.;PR1BP_HUMAN;.	H	161;80;238;161;80;128;128	ENSP00000367368:R161H;ENSP00000332915:R80H;ENSP00000440850:R238H;ENSP00000351153:R161H;ENSP00000376643:R80H;ENSP00000411313:R128H;ENSP00000393867:R128H	ENSP00000332915:R80H	R	+	2	0	C12orf48	101071871	0.919000	0.31177	0.084000	0.20598	0.049000	0.14656	1.172000	0.31908	0.371000	0.24564	-0.361000	0.07541	CGT	G|0.976;A|0.024	0.024	strong		0.353	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178581859	178581859	+	Silent	SNP	G	G	A	rs2278221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:178581859G>A	ENST00000251582.7	-	7	1295	c.1194C>T	c.(1192-1194)gaC>gaT	p.D398D	ADAMTS2_ENST00000274609.5_Silent_p.D398D	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	398	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AGGAGAAGCCGTCCTCATGGT	0.642													G|||	1144	0.228435	0.0446	0.2925	5008	,	,		19306	0.3185		0.2475	False		,,,				2504	0.319				p.D398D		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C1194T						PASS	.	G	,	347,4059	177.6+/-206.5	13,321,1869	59.0	47.0	51.0		1194,1194	-3.6	1.0	5	dbSNP_100	51	2084,6516	354.4+/-329.5	269,1546,2485	no	coding-synonymous,coding-synonymous	ADAMTS2	NM_014244.4,NM_021599.2	,	282,1867,4354	AA,AG,GG		24.2326,7.8756,18.6914	,	398/1212,398/567	178581859	2431,10575	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon7			GAAGCCGTCCTCA	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.1194C>T	5.37:g.178581859G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	202	116	0.574257	NM_021599		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			G|0.802;A|0.198	0.198	strong		0.642	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
DCAF4	26094	hgsc.bcm.edu	37	14	73425462	73425462	+	Silent	SNP	G	G	A	rs12882409	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:73425462G>A	ENST00000358377.2	+	14	1657	c.1437G>A	c.(1435-1437)ccG>ccA	p.P479P	DCAF4_ENST00000509153.1_Silent_p.P419P|DCAF4_ENST00000555042.1_Silent_p.P473P|DCAF4_ENST00000394234.2_Silent_p.P379P|DCAF4_ENST00000353777.3_Silent_p.P309P	NM_001163509.1|NM_015604.3	NP_001156981.1|NP_056419.2	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4	479					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|skin(1)	22						GGGGCGCGCCGGGGCTGCTCA	0.627													G|||	713	0.142372	0.0847	0.1153	5008	,	,		16333	0.1548		0.175	False		,,,				2504	0.1933				p.P479P		Atlas-SNP	.											.	DCAF4	40	.	0			c.G1437A						PASS	.	G	,,,,	474,3932		35,404,1764	44.0	54.0	51.0		1419,1374,1437,1137,1257	-10.0	0.1	14	dbSNP_121	51	1533,7067		133,1267,2900	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCAF4	NM_001163508.1,NM_001163509.1,NM_015604.3,NM_181340.2,NM_181341.2	,,,,	168,1671,4664	AA,AG,GG		17.8256,10.7581,15.4313	,,,,	473/490,458/475,479/496,379/396,419/436	73425462	2007,10999	2203	4300	6503	SO:0001819	synonymous_variant	26094	exon14			CGCGCCGGGGCTG	BC018979	CCDS9809.1, CCDS9810.1, CCDS41968.1, CCDS41968.2, CCDS55926.1	14q24.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000119599		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20229	protein-coding gene	gene with protein product			"""WD repeat domain 21"", ""WD repeat domain 21A"""	WDR21, WDR21A			Standard	NM_015604		Approved	DKFZp434K114	uc010ttr.2	Q8WV16		ENST00000358377.2:c.1437G>A	14.37:g.73425462G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_015604	B4DUT6|G3V522|Q86U31|Q8IV10|Q96K22|Q9Y4P5	Silent	SNP	ENST00000358377.2	37	CCDS9809.1																																																																																			G|0.844;A|0.156	0.156	strong		0.627	DCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361058.1	NM_015604	
ZNF667	63934	hgsc.bcm.edu	37	19	56953272	56953272	+	Silent	SNP	G	G	A	rs3760850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56953272G>A	ENST00000504904.3	-	7	1811	c.1092C>T	c.(1090-1092)gaC>gaT	p.D364D	ZNF667_ENST00000292069.6_Silent_p.D364D|ZNF667_ENST00000342634.3_Silent_p.D492D|ZNF667_ENST00000591790.1_3'UTR			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	364					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)		TGAAGAACTTGTCACATTTAT	0.378													G|||	1008	0.201278	0.1868	0.1772	5008	,	,		17742	0.4266		0.0328	False		,,,				2504	0.1789				p.D364D		Atlas-SNP	.											.	ZNF667	95	.	0			c.C1092T						PASS	.	G		649,3757	265.6+/-266.7	41,567,1595	82.0	89.0	87.0		1092	0.4	0.0	19	dbSNP_107	87	186,8412	82.9+/-145.4	6,174,4119	no	coding-synonymous	ZNF667	NM_022103.3		47,741,5714	AA,AG,GG		2.1633,14.7299,6.4211		364/611	56953272	835,12169	2203	4299	6502	SO:0001819	synonymous_variant	63934	exon5			GAACTTGTCACAT		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.1092C>T	19.37:g.56953272G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			G|0.875;A|0.125	0.125	strong		0.378	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
RP11-93K22.13	0	hgsc.bcm.edu	37	3	129810128	129810128	+	lincRNA	SNP	G	G	A	rs6804080	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:129810128G>A	ENST00000514010.1	-	0	248				ALG1L2_ENST00000507643.1_RNA																							ACGACAAGCCGGCATCTTTCT	0.562													g|||	949	0.189497	0.2595	0.1758	5008	,	,		19352	0.004		0.3032	False		,,,				2504	0.1789				p.P15P		Atlas-SNP	.											.	.	.	.	0			c.G45A						PASS	.																																					644974	exon2			CAAGCCGGCATCT																													3.37:g.129810128G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001136152		Silent	SNP	ENST00000514010.1	37																																																																																				G|0.794;A|0.206	0.206	strong		0.562	RP11-93K22.13-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000358040.1		
FARP2	9855	hgsc.bcm.edu	37	2	242407746	242407746	+	Silent	SNP	A	A	G	rs10933559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242407746A>G	ENST00000264042.3	+	18	2255	c.2085A>G	c.(2083-2085)ctA>ctG	p.L695L		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	695	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		TGCGCCGCCTATGCGGACATT	0.622													A|||	677	0.135184	0.2148	0.1614	5008	,	,		18581	0.0		0.2356	False		,,,				2504	0.045				p.L695L		Atlas-SNP	.											.	FARP2	92	.	0			c.A2085G						PASS	.	A		998,3408	368.3+/-318.6	116,766,1321	46.0	40.0	42.0		2085	1.0	0.9	2	dbSNP_120	42	1818,6782	323.0+/-315.8	194,1430,2676	no	coding-synonymous	FARP2	NM_014808.2		310,2196,3997	GG,GA,AA		21.1395,22.6509,21.6515		695/1055	242407746	2816,10190	2203	4300	6503	SO:0001819	synonymous_variant	9855	exon18			CCGCCTATGCGGA	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.2085A>G	2.37:g.242407746A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	37	CCDS33424.1																																																																																			A|0.804;G|0.196	0.196	strong		0.622	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
MAGEC1	9947	hgsc.bcm.edu	37	X	140994591	140994591	+	Missense_Mutation	SNP	C	C	G	rs176048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:140994591C>G	ENST00000285879.4	+	4	1687	c.1401C>G	c.(1399-1401)caC>caG	p.H467Q	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	467				H -> Q (in Ref. 1; AAC18837). {ECO:0000305}.						breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGAACTCACAGTACTTTTG	0.488										HNSCC(15;0.026)			-|||	488	0.129272	0.1339	0.0994	3775	,	,		13251	0.002		0.1938	False		,,,				2504	0.046				p.H467Q		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C1401G						PASS	.	G	GLN/HIS	749,3086		71,496,111,1065,460	104.0	115.0	111.0		1401		0.0	X	dbSNP_79	111	1702,5021		158,902,484,1366,1387	no	missense	MAGEC1	NM_005462.4	24	229,1398,595,2431,1847	GG,GC,G,CC,C		25.3161,19.5306,23.2146	benign	467/1143	140994591	2451,8107	2203	4297	6500	SO:0001583	missense	9947	exon4			AACTCACAGTACT	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1401C>G	X.37:g.140994591C>G	ENSP00000285879:p.His467Gln	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	167	165	0.988024	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	246	0.14828209764918626	43	0.09347826086956522	27	0.08035714285714286	3	0.005263157894736842	99	0.14864864864864866	g	0.004	-2.241877	0.00274	0.195306	0.253161	ENSG00000155495	ENST00000285879	T	0.02737	4.18	.	.	.	.	.	.	.	.	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	0.47484	-0.9114	7	0.11794	T	0.64	.	0.1312	0.00074	0.25:0.25:0.2498:0.2502	rs176048;rs3195988	467	O60732	MAGC1_HUMAN	Q	467	ENSP00000285879:H467Q	ENSP00000285879:H467Q	H	+	3	2	MAGEC1	140822257	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-4.348000	0.00248	-3.635000	0.00129	-3.556000	0.00030	CAC	C|0.811;G|0.189	0.189	strong		0.488	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
FLG	2312	hgsc.bcm.edu	37	1	152281479	152281479	+	Missense_Mutation	SNP	G	G	T	rs3126079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281479G>T	ENST00000368799.1	-	3	5918	c.5883C>A	c.(5881-5883)caC>caA	p.H1961Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1961	Ser-rich.		H -> Q (in dbSNP:rs3126079).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTGTCTTCGTGATGGGACC	0.572									Ichthyosis				-|||	2695	0.538139	0.7897	0.4683	5008	,	,		26201	0.6607		0.1759	False		,,,				2504	0.4939				p.H1961Q		Atlas-SNP	.											.	FLG	900	.	0			c.C5883A						PASS	.	T	GLN/HIS	3032,1374	454.4+/-350.6	1056,920,227	293.0	278.0	283.0		5883	-4.8	0.0	1	dbSNP_103	283	1480,7120	749.5+/-407.4	129,1222,2949	no	missense	FLG	NM_002016.1	24	1185,2142,3176	TT,TG,GG		17.2093,31.1847,34.6917	benign	1961/4062	152281479	4512,8494	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCTTCGTGATGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5883C>A	1.37:g.152281479G>T	ENSP00000357789:p.His1961Gln	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	602	392	0.651163	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	1005	0.46016483516483514	366	0.7439024390243902	142	0.39226519337016574	362	0.6328671328671329	135	0.17810026385224276	t	0.268	-0.994755	0.02145	0.688153	0.172093	ENSG00000143631	ENST00000368799	T	0.00949	5.51	2.37	-4.75	0.03239	.	.	.	.	.	T	0.00144	0.0004	N	0.12746	0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40757	-0.9546	8	0.13470	T	0.59	-0.1204	2.7757	0.05347	0.1149:0.1132:0.4273:0.3447	rs3126079;rs28567722;rs35290811	1961	P20930	FILA_HUMAN	Q	1961	ENSP00000357789:H1961Q	ENSP00000357789:H1961Q	H	-	3	2	FLG	150548103	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.708000	0.00196	-3.868000	0.00097	-4.206000	0.00009	CAC	A|0.000;G|0.622;T|0.378	0.378	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
DNAH14	127602	hgsc.bcm.edu	37	1	225288534	225288534	+	Intron	SNP	A	A	C	rs3105571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225288534A>C	ENST00000445597.2	+	16	3051				DNAH14_ENST00000439375.2_Missense_Mutation_p.E1272A|DNAH14_ENST00000430092.1_Missense_Mutation_p.E1272A			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						GGAGTCCTTGAAATTCTGCAA	0.303													A|||	622	0.124201	0.0764	0.1916	5008	,	,		15617	0.2232		0.0427	False		,,,				2504	0.1227				p.E1272A		Atlas-SNP	.											.	DNAH14	300	.	0			c.A3815C						PASS	.	A	ALA/GLU	95,1289		6,83,603	39.0	38.0	38.0		3815	3.4	0.0	1	dbSNP_103	38	113,3063		4,105,1479	yes	missense	DNAH14	NM_001373.1	107	10,188,2082	CC,CA,AA		3.5579,6.8642,4.5614	possibly-damaging	1272/4516	225288534	208,4352	692	1588	2280	SO:0001627	intron_variant	127602	exon23			TCCTTGAAATTCT	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.3051+15043A>C	1.37:g.225288534A>C		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	286	143	0.5	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		259	0.11858974358974358	40	0.08130081300813008	66	0.18232044198895028	121	0.21153846153846154	32	0.04221635883905013	A	14.98	2.697085	0.48202	0.068642	0.035579	ENSG00000185842	ENST00000430092;ENST00000439375;ENST00000328556	T;T;T	0.62788	0.0;0.0;0.0	5.79	3.41	0.39046	.	.	.	.	.	T	0.00073	0.0002	L	0.54965	1.715	0.34154	P	0.332145	P	0.36909	0.573	B	0.36666	0.23	T	0.02437	-1.1159	8	0.49607	T	0.09	.	8.9907	0.36022	0.8448:0.0:0.1552:0.0	rs3105571;rs52819981;rs3105571	1272	Q0VDD8-4	.	A	1272;1272;350	ENSP00000414402:E1272A;ENSP00000392061:E1272A;ENSP00000332424:E350A	ENSP00000332424:E350A	E	+	2	0	DNAH14	223355157	1.000000	0.71417	0.003000	0.11579	0.747000	0.42532	3.046000	0.49846	0.423000	0.26033	0.491000	0.48974	GAA	A|0.893;C|0.107	0.107	strong		0.303	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
CD3EAP	10849	hgsc.bcm.edu	37	19	45911669	45911669	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45911669G>A	ENST00000309424.3	+	3	931	c.443G>A	c.(442-444)cGg>cAg	p.R148Q	ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000588738.1_5'Flank|PPP1R13L_ENST00000418234.2_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.R150Q|ERCC1_ENST00000423698.2_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	148					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)		CTGAGGCCTCGGTTCTGTGCC	0.617																																					p.R148Q		Atlas-SNP	.											.	CD3EAP	27	.	0			c.G443A						PASS	.						42.0	44.0	43.0					19																	45911669		2203	4299	6502	SO:0001583	missense	10849	exon3			GGCCTCGGTTCTG	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.443G>A	19.37:g.45911669G>A	ENSP00000310966:p.Arg148Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	.	.	.	.	.	.	.	.	.	.	G	32	5.145864	0.94603	.	.	ENSG00000117877	ENST00000309424	T	0.54279	0.58	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000003	T	0.70228	0.3200	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.73275	-0.4034	10	0.87932	D	0	-21.8983	14.3879	0.66958	0.0:0.0:1.0:0.0	.	150;148	O15446-2;O15446	.;RPA34_HUMAN	Q	148	ENSP00000310966:R148Q	ENSP00000310966:R148Q	R	+	2	0	CD3EAP	50603509	0.998000	0.40836	1.000000	0.80357	0.971000	0.66376	5.734000	0.68580	2.463000	0.83235	0.561000	0.74099	CGG	.	.	none		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
DHRS1	115817	hgsc.bcm.edu	37	14	24760764	24760764	+	Missense_Mutation	SNP	G	G	A	rs10134537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24760764G>A	ENST00000288111.7	-	7	998	c.722C>T	c.(721-723)aCa>aTa	p.T241I	DHRS1_ENST00000396813.1_Missense_Mutation_p.T241I|DHRS1_ENST00000559088.1_5'UTR	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	241			T -> I (in dbSNP:rs10134537).			endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		AACTTCACCTGTTGCCAAAGC	0.507													G|||	469	0.0936502	0.1384	0.0735	5008	,	,		21757	0.0893		0.0636	False		,,,				2504	0.0828				p.T241I		Atlas-SNP	.											.	DHRS1	21	.	0			c.C722T						PASS	.	G	ILE/THR,ILE/THR	545,3861	247.5+/-255.7	32,481,1690	234.0	233.0	234.0		722,722	6.0	1.0	14	dbSNP_119	234	602,7998	158.3+/-211.8	24,554,3722	yes	missense,missense	DHRS1	NM_001136050.2,NM_138452.2	89,89	56,1035,5412	AA,AG,GG		7.0,12.3695,8.819	possibly-damaging,possibly-damaging	241/314,241/314	24760764	1147,11859	2203	4300	6503	SO:0001583	missense	115817	exon7			TCACCTGTTGCCA	AK058159	CCDS9623.1	14q11.2	2011-09-14			ENSG00000157379	ENSG00000157379	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16445	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 19C, member 1"""	610410				12153138, 19027726	Standard	NM_138452		Approved	FLJ25430, MGC20204, SDR19C1	uc001wok.3	Q96LJ7	OTTHUMG00000029333	ENST00000288111.7:c.722C>T	14.37:g.24760764G>A	ENSP00000288111:p.Thr241Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Missense_Mutation	SNP	ENST00000288111.7	37	CCDS9623.1	181	0.08287545787545787	54	0.10975609756097561	30	0.08287292817679558	43	0.07517482517482517	54	0.0712401055408971	G	16.95	3.264429	0.59431	0.123695	0.07	ENSG00000157379	ENST00000288111;ENST00000396813	D;D	0.89746	-2.56;-2.56	5.97	5.97	0.96955	NAD(P)-binding domain (1);	0.108837	0.64402	D	0.000007	T	0.12774	0.0310	M	0.75264	2.295	0.23585	P	0.99735537	B	0.31752	0.338	B	0.33042	0.157	T	0.65265	-0.6210	9	0.48119	T	0.1	-7.9814	15.9136	0.79491	0.0:0.0:1.0:0.0	rs10134537;rs60832143;rs10134537	241	Q96LJ7	DHRS1_HUMAN	I	241	ENSP00000288111:T241I;ENSP00000380027:T241I	ENSP00000288111:T241I	T	-	2	0	DHRS1	23830604	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.736000	0.55052	2.835000	0.97688	0.591000	0.81541	ACA	G|0.913;A|0.087	0.087	strong		0.507	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452	
WDR43	23160	hgsc.bcm.edu	37	2	29129418	29129418	+	Silent	SNP	A	A	G	rs11688605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:29129418A>G	ENST00000407426.3	+	3	512	c.456A>G	c.(454-456)gaA>gaG	p.E152E		NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	152						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					ATATTGTGGAATGGAACGTAC	0.413													A|||	1860	0.371406	0.1732	0.4524	5008	,	,		18995	0.7907		0.2256	False		,,,				2504	0.2996				p.E152E		Atlas-SNP	.											.	WDR43	38	.	0			c.A456G						PASS	.	A		717,3275		61,595,1340	92.0	90.0	91.0		456	-0.9	1.0	2	dbSNP_120	91	1849,6505		196,1457,2524	no	coding-synonymous	WDR43	NM_015131.1		257,2052,3864	GG,GA,AA		22.1331,17.9609,20.7841		152/678	29129418	2566,9780	1996	4177	6173	SO:0001819	synonymous_variant	23160	exon3			TGTGGAATGGAAC	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"""WD repeat domain containing"""	28945	protein-coding gene	gene with protein product	"""UTP5, small subunit (SSU) processome component, homolog (yeast)"""					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.456A>G	2.37:g.29129418A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_015131	Q15395|Q92577	Silent	SNP	ENST00000407426.3	37	CCDS46251.1																																																																																			A|0.630;G|0.370	0.370	strong		0.413	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089	
KDELR3	11015	hgsc.bcm.edu	37	22	38877461	38877461	+	Missense_Mutation	SNP	T	T	G	rs12004	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38877461T>G	ENST00000216014.4	+	4	768	c.596T>G	c.(595-597)gTg>gGg	p.V199G	KDELR3_ENST00000471268.1_3'UTR|KDELR3_ENST00000409006.3_Missense_Mutation_p.V199G	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	199			V -> G (in dbSNP:rs12004). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		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)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					TACTTGTATGTGACCAAAGGT	0.438													T|||	1278	0.255192	0.1657	0.1974	5008	,	,		20556	0.3542		0.3062	False		,,,				2504	0.2628				p.V199G	Ovarian(11;103 529 24120 28493 32980)	Atlas-SNP	.											.	KDELR3	39	.	0			c.T596G						PASS	.	T	GLY/VAL,GLY/VAL	824,3582	325.3+/-299.0	73,678,1452	138.0	125.0	129.0		596,596	4.7	1.0	22	dbSNP_52	129	2634,5966	426.6+/-355.3	402,1830,2068	yes	missense,missense	KDELR3	NM_006855.2,NM_016657.1	109,109	475,2508,3520	GG,GT,TT		30.6279,18.7018,26.5877	possibly-damaging,possibly-damaging	199/215,199/221	38877461	3458,9548	2203	4300	6503	SO:0001583	missense	11015	exon4			TGTATGTGACCAA	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.596T>G	22.37:g.38877461T>G	ENSP00000216014:p.Val199Gly	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	185	103	0.556757	NM_016657	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation	SNP	ENST00000216014.4	37	CCDS13972.1	630	0.28846153846153844	89	0.18089430894308944	81	0.22375690607734808	219	0.38286713286713286	241	0.3179419525065963	T	16.69	3.193945	0.58017	0.187018	0.306279	ENSG00000100196	ENST00000216014;ENST00000409006	T;T	0.75704	-0.96;-0.96	4.65	4.65	0.58169	.	0.218747	0.39475	N	0.001353	T	0.00012	0.0000	M	0.81802	2.56	0.09310	P	0.999999999789922	B;P	0.43973	0.356;0.823	B;P	0.48141	0.197;0.568	T	0.01159	-1.1433	9	0.62326	D	0.03	-10.4461	14.226	0.65860	0.0:0.0:0.0:1.0	rs12004;rs3180098;rs17173760;rs17402570;rs52804343;rs57393871;rs12004	199;199	O43731;O43731-2	ERD23_HUMAN;.	G	199	ENSP00000216014:V199G;ENSP00000386918:V199G	ENSP00000216014:V199G	V	+	2	0	KDELR3	37207407	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.868000	0.87116	1.950000	0.56595	0.477000	0.44152	GTG	A|0.004;C|0.002	.	strong		0.438	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1		
GRIN3A	116443	hgsc.bcm.edu	37	9	104449098	104449098	+	Missense_Mutation	SNP	C	C	T	rs10989591	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:104449098C>T	ENST00000361820.3	-	2	1684	c.1084G>A	c.(1084-1086)Gtg>Atg	p.V362M		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	362			V -> M (in dbSNP:rs10989591). {ECO:0000269|PubMed:11880201}.		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)	AGTTCCTCCACATTCTGGGAA	0.507													C|||	1601	0.319688	0.5295	0.2824	5008	,	,		21591	0.1081		0.326	False		,,,				2504	0.274				p.V362M		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G1084A						PASS	.	C	MET/VAL	2091,2315	575.5+/-384.0	508,1075,620	76.0	66.0	69.0		1084	5.8	1.0	9	dbSNP_120	69	2703,5897	433.1+/-357.3	412,1879,2009	yes	missense	GRIN3A	NM_133445.2	21	920,2954,2629	TT,TC,CC		31.4302,47.458,36.8599	probably-damaging	362/1116	104449098	4794,8212	2203	4300	6503	SO:0001583	missense	116443	exon2			CCTCCACATTCTG		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.1084G>A	9.37:g.104449098C>T	ENSP00000355155:p.Val362Met	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	99	55	0.555556	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	655	0.2999084249084249	241	0.4898373983739837	102	0.281767955801105	66	0.11538461538461539	246	0.3245382585751979	C	21.1	4.103988	0.76983	0.47458	0.314302	ENSG00000198785	ENST00000361820	D	0.86366	-2.11	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.99999927067	B	0.33857	0.429	B	0.43990	0.438	T	0.14172	-1.0482	9	0.45353	T	0.12	.	20.1374	0.98035	0.0:1.0:0.0:0.0	rs10989591;rs52812520;rs59456765;rs10989591	362	Q8TCU5	NMD3A_HUMAN	M	362	ENSP00000355155:V362M	ENSP00000355155:V362M	V	-	1	0	GRIN3A	103488919	1.000000	0.71417	0.993000	0.49108	0.988000	0.76386	4.796000	0.62496	2.763000	0.94921	0.563000	0.77884	GTG	C|0.652;T|0.348	0.348	strong		0.507	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
COPE	11316	hgsc.bcm.edu	37	19	19011244	19011244	+	Silent	SNP	T	T	C	rs1127821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19011244T>C	ENST00000262812.4	-	8	798	c.750A>G	c.(748-750)ccA>ccG	p.P250P	COPE_ENST00000600932.1_Silent_p.P273P|COPE_ENST00000598969.1_5'UTR|COPE_ENST00000351079.4_Silent_p.P199P|COPE_ENST00000349893.4_Silent_p.P198P	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	250					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						CCAGCGTCTCTGGGTAGCCAC	0.662													C|||	1815	0.36242	0.3654	0.5994	5008	,	,		15588	0.1915		0.4841	False		,,,				2504	0.2413				p.P250P		Atlas-SNP	.											.	COPE	26	.	0			c.A750G						PASS	.	C	,,	1321,2265		262,797,734	31.0	26.0	28.0		750,597,594	-9.9	0.2	19	dbSNP_86	28	2857,3705		650,1557,1074	no	coding-synonymous,coding-synonymous,coding-synonymous	COPE	NM_007263.3,NM_199442.1,NM_199444.1	,,	912,2354,1808	CC,CT,TT		43.5386,36.8377,41.1707	,,	250/309,199/258,198/257	19011244	4178,5970	1793	3281	5074	SO:0001819	synonymous_variant	11316	exon8			CGTCTCTGGGTAG	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.750A>G	19.37:g.19011244T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Silent	SNP	ENST00000262812.4	37	CCDS12387.1																																																																																			T|0.421;G|0.095;C|0.305;A|0.179	0.305	strong		0.662	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
F12	2161	hgsc.bcm.edu	37	5	176831085	176831085	+	Missense_Mutation	SNP	G	G	A	rs2230939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:176831085G>A	ENST00000253496.3	-	10	1073	c.1025C>T	c.(1024-1026)cCg>cTg	p.P342L	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	342	Pro-rich.		P -> Q (in dbSNP:rs2230939).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_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)		Ethanolamine Oleate(DB06689)	CCGCTTCGCCGGCAAGGCTGT	0.721									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	4	0.000798722	0.0008	0.0014	5008	,	,		12509	0.0		0.002	False		,,,				2504	0.0				p.P342L		Atlas-SNP	.											.	F12	35	.	0			c.C1025T						PASS	.	G	LEU/PRO	0,4194		0,0,2097	9.0	12.0	11.0		1025	-5.3	0.0	5	dbSNP_98	11	13,8427		0,13,4207	yes	missense	F12	NM_000505.3	98	0,13,6304	AA,AG,GG		0.154,0.0,0.1029	benign	342/616	176831085	13,12621	2097	4220	6317	SO:0001583	missense	2161	exon10	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	TTCGCCGGCAAGG	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.1025C>T	5.37:g.176831085G>A	ENSP00000253496:p.Pro342Leu	Somatic	5	0	0	1934	WXS	Illumina HiSeq	Phase_I	15	11	0.733333	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	37	CCDS34302.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	9.062	0.994618	0.19043	0.0	0.00154	ENSG00000131187	ENST00000253496	D	0.88975	-2.45	4.9	-5.28	0.02755	.	3.606630	0.00899	N	0.002331	T	0.76898	0.4052	L	0.29908	0.895	0.09310	N	0.999996	B	0.06786	0.001	B	0.04013	0.001	T	0.65776	-0.6086	10	0.10902	T	0.67	.	0.9191	0.01311	0.1778:0.1964:0.325:0.3008	.	342	P00748	FA12_HUMAN	L	342	ENSP00000253496:P342L	ENSP00000253496:P342L	P	-	2	0	F12	176763691	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.303000	0.00519	-1.202000	0.02655	-0.367000	0.07326	CCG	T|0.005;G|0.993;A|0.001	0.001	strong		0.721	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1		
CDHR1	92211	hgsc.bcm.edu	37	10	85978939	85978939	+	IGR	SNP	G	G	A	rs4244947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85978939G>A	ENST00000372117.3	+	0	5428				CDHR1_ENST00000332904.3_Silent_p.L715L	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1						cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						gCCAGGGTCTGTTCTTGCATC	0.398													A|||	2775	0.554113	0.8185	0.5331	5008	,	,		18287	0.4107		0.4632	False		,,,				2504	0.453				p.L715L		Atlas-SNP	.											.	CDHR1	122	.	0			c.G2145A						PASS	.																																			SO:0001628	intergenic_variant	92211	exon17			GGGTCTGTTCTTG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634		10.37:g.85978939G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			G|0.460;A|0.540	0.540	strong		0.398	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
ANKRD24	170961	hgsc.bcm.edu	37	19	4200156	4200156	+	Missense_Mutation	SNP	G	G	A	rs2052191	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4200156G>A	ENST00000600132.1	+	5	607	c.331G>A	c.(331-333)Gcg>Acg	p.A111T	ANKRD24_ENST00000262970.5_Missense_Mutation_p.A201T|ANKRD24_ENST00000318934.4_Missense_Mutation_p.A111T	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	111			A -> T (in dbSNP:rs2052191). {ECO:0000269|PubMed:11853319}.							endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		TGTCATGAGCGCGGACGGGGC	0.657													A|||	2035	0.40635	0.5454	0.3228	5008	,	,		16174	0.3234		0.4632	False		,,,				2504	0.3047				p.A111T		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G331A						PASS	.	A	THR/ALA	2003,1899		519,965,467	20.0	22.0	21.0		331	2.0	0.2	19	dbSNP_94	21	3515,4749		775,1965,1392	no	missense	ANKRD24	NM_133475.1	58	1294,2930,1859	AA,AG,GG		42.5339,48.6674,45.3559	benign	111/1147	4200156	5518,6648	1951	4132	6083	SO:0001583	missense	170961	exon5			ATGAGCGCGGACG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.331G>A	19.37:g.4200156G>A	ENSP00000471252:p.Ala111Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	56	53	0.946429	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	889	0.40705128205128205	248	0.5040650406504065	114	0.3149171270718232	189	0.3304195804195804	338	0.44591029023746703	A	0.005	-2.235948	0.00277	0.513326	0.425339	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.28895	1.59;1.59	4.17	2.01	0.26516	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B;B	0.13145	0.0;0.007	B;B	0.01281	0.0;0.0	T	0.47861	-0.9084	8	0.05525	T	0.97	-9.5245	6.9181	0.24371	0.7004:0.0:0.2996:0.0	rs2052191;rs57740215;rs2052191	111;201	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	T	111;201	ENSP00000321731:A111T;ENSP00000262970:A201T	ENSP00000262970:A201T	A	+	1	0	ANKRD24	4151156	0.552000	0.26505	0.241000	0.24154	0.046000	0.14306	1.923000	0.40055	-0.245000	0.09625	-0.817000	0.03123	GCG	G|0.591;A|0.409	0.409	strong		0.657	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
ARMC3	219681	hgsc.bcm.edu	37	10	23297301	23297301	+	Silent	SNP	C	C	T	rs11817610	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:23297301C>T	ENST00000298032.5	+	15	2010	c.1926C>T	c.(1924-1926)aaC>aaT	p.N642N	ARMC3_ENST00000409049.3_Silent_p.N642N|ARMC3_ENST00000409983.3_Silent_p.N642N|ARMC3_ENST00000376528.4_Silent_p.N379N	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	642						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AAGAAAAGAACAAGTAAGAAA	0.313													c|||	2504	0.5	0.2958	0.5605	5008	,	,		16449	0.5476		0.6163	False		,,,				2504	0.5644				p.N642N		Atlas-SNP	.											.	ARMC3	102	.	0			c.C1926T						PASS	.	C		1500,2880		250,1000,940	31.0	28.0	29.0		1926	4.5	0.5	10	dbSNP_120	29	5199,3283		1643,1913,685	no	coding-synonymous	ARMC3	NM_173081.3		1893,2913,1625	TT,TC,CC		38.7055,34.2466,47.9163		642/873	23297301	6699,6163	2190	4241	6431	SO:0001819	synonymous_variant	219681	exon15			AAAGAACAAGTAA	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1926C>T	10.37:g.23297301C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Silent	SNP	ENST00000298032.5	37	CCDS7142.1																																																																																			C|0.513;T|0.487	0.487	strong		0.313	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081	
CD109	135228	hgsc.bcm.edu	37	6	74466377	74466377	+	Silent	SNP	C	C	T	rs6453696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:74466377C>T	ENST00000287097.5	+	6	757	c.645C>T	c.(643-645)taC>taT	p.Y215Y	CD109_ENST00000437994.2_Silent_p.Y215Y|CD109_ENST00000422508.2_Silent_p.Y138Y			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	312	0	0		WXS	Illumina HiSeq	Phase_I	216	98	0.453704	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	
TACC1	6867	hgsc.bcm.edu	37	8	38684853	38684853	+	Silent	SNP	T	T	C	rs2037204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:38684853T>C	ENST00000317827.4	+	5	1999	c.1620T>C	c.(1618-1620)ccT>ccC	p.P540P	TACC1_ENST00000520611.1_5'UTR|TACC1_ENST00000519416.1_Silent_p.P344P|TACC1_ENST00000379931.3_Silent_p.P552P|TACC1_ENST00000518415.1_Intron|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000330691.6_Silent_p.P114P|TACC1_ENST00000520615.1_Silent_p.P345P|TACC1_ENST00000520340.1_Intron|TACC1_ENST00000348567.4_Silent_p.P102P|TACC1_ENST00000443286.2_Intron|TACC1_ENST00000276520.8_Silent_p.P130P|TACC1_ENST00000520973.1_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	250	1	0.004		WXS	Illumina HiSeq	Phase_I	273	127	0.465201	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	
CCDC114	93233	hgsc.bcm.edu	37	19	48800914	48800914	+	Missense_Mutation	SNP	G	G	A	rs35461177	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48800914G>A	ENST00000315396.7	-	13	2085	c.1403C>T	c.(1402-1404)cCg>cTg	p.P468L		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	468			P -> L (in dbSNP:rs35461177).		outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)		p.P261L(1)		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)		CTCAAAACCCGGGGGGTCTTC	0.627													G|||	839	0.167532	0.1036	0.2277	5008	,	,		15478	0.1329		0.2803	False		,,,				2504	0.1309				p.P468L		Atlas-SNP	.											CCDC114,NS,carcinoma,0,1	CCDC114	100	1	1	Substitution - Missense(1)	stomach(1)	c.C1403T						PASS	.	G	LEU/PRO	567,3839		48,471,1684	20.0	22.0	21.0		1403	1.8	0.7	19	dbSNP_126	21	2455,6145		376,1703,2221	yes	missense	CCDC114	NM_144577.3	98	424,2174,3905	AA,AG,GG		28.5465,12.8688,23.2354	possibly-damaging	468/671	48800914	3022,9984	2203	4300	6503	SO:0001583	missense	93233	exon13			AAACCCGGGGGGT	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.1403C>T	19.37:g.48800914G>A	ENSP00000318429:p.Pro468Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	CCDS12714.2	428	0.19597069597069597	48	0.0975609756097561	101	0.27900552486187846	81	0.14160839160839161	198	0.2612137203166227	G	15.40	2.822657	0.50739	0.128688	0.285465	ENSG00000105479	ENST00000315396	T	0.21932	1.98	3.98	1.84	0.25277	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.34643	P	0.27919099999999997	P;B	0.37708	0.606;0.163	B;B	0.27170	0.077;0.019	T	0.45249	-0.9274	8	0.66056	D	0.02	-3.1936	5.4686	0.16658	0.2523:0.0:0.7477:0.0	rs35461177	468;468	Q96M63;Q96M63-5	CC114_HUMAN;.	L	468	ENSP00000318429:P468L	ENSP00000318429:P468L	P	-	2	0	CCDC114	53492726	0.967000	0.33354	0.700000	0.30305	0.760000	0.43138	1.490000	0.35573	0.965000	0.38133	-0.136000	0.14681	CCG	G|0.793;A|0.207	0.207	strong		0.627	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
PKDCC	91461	hgsc.bcm.edu	37	2	42275819	42275819	+	Silent	SNP	T	T	C	rs11897440	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	28	0	0		WXS	Illumina HiSeq	Phase_I	31	8	0.258065	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		
LRP1B	53353	hgsc.bcm.edu	37	2	141707868	141707868	+	Silent	SNP	G	G	T	rs6748626	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:141707868G>T	ENST00000389484.3	-	20	4043	c.3072C>A	c.(3070-3072)gcC>gcA	p.A1024A		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1024	LDL-receptor class A 7. {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)		CACCATCACAGGCCCAGTGGC	0.443										TSP Lung(27;0.18)			G|||	1381	0.275759	0.4735	0.2378	5008	,	,		16069	0.249		0.1402	False		,,,				2504	0.2025				p.A1024A	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C3072A						PASS	.	G		1721,2685	517.2+/-369.4	334,1053,816	89.0	64.0	73.0		3072	0.2	1.0	2	dbSNP_116	73	1182,7418	241.0+/-271.5	85,1012,3203	yes	coding-synonymous	LRP1B	NM_018557.2		419,2065,4019	TT,TG,GG		13.7442,39.0604,22.3205		1024/4600	141707868	2903,10103	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon20			ATCACAGGCCCAG	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.3072C>A	2.37:g.141707868G>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	158	75	0.474684	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.770;T|0.230	0.230	strong		0.443	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
OR5V1	81696	hgsc.bcm.edu	37	6	29323655	29323655	+	Silent	SNP	G	G	A	rs7761746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	104	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	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		
SFTPD	6441	hgsc.bcm.edu	37	10	81702210	81702210	+	Missense_Mutation	SNP	G	G	C	rs17878336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:81702210G>C	ENST00000372292.3	-	4	407	c.367C>G	c.(367-369)Ctg>Gtg	p.L123V		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	123	Collagen-like.		L -> V (in dbSNP:rs17878336). {ECO:0000269|PubMed:19100526, ECO:0000269|Ref.4}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			TGCTTCCCCAGGGGACCTTCT	0.602													g|||	88	0.0175719	0.0045	0.0418	5008	,	,		20297	0.0		0.0417	False		,,,				2504	0.0112				p.L123V		Atlas-SNP	.											.	SFTPD	43	.	0			c.C367G						PASS	.		VAL/LEU	48,4358	50.2+/-85.5	0,48,2155	77.0	71.0	73.0		367	-6.7	0.0	10	dbSNP_124	73	352,8248	119.4+/-178.7	9,334,3957	yes	missense	SFTPD	NM_003019.4	32	9,382,6112	CC,CG,GG		4.093,1.0894,3.0755	benign	123/376	81702210	400,12606	2203	4300	6503	SO:0001583	missense	6441	exon4			TCCCCAGGGGACC	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"""Collectins"""	10803	protein-coding gene	gene with protein product		178635	"""surfactant, pulmonary-associated protein D"""	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.367C>G	10.37:g.81702210G>C	ENSP00000361366:p.Leu123Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	45	0.642857	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Missense_Mutation	SNP	ENST00000372292.3	37	CCDS7362.1	52	0.023809523809523808	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	28	0.036939313984168866	g	9.197	1.027533	0.19512	0.010894	0.04093	ENSG00000133661	ENST00000372292;ENST00000444384	T;T	0.54071	0.59;0.59	5.02	-6.72	0.01755	.	0.859352	0.09835	N	0.749677	T	0.02156	0.0067	N	0.04994	-0.135	0.09310	N	1	B	0.16396	0.017	B	0.12156	0.007	T	0.07673	-1.0760	10	0.30854	T	0.27	-0.1717	2.491	0.04610	0.371:0.1274:0.3761:0.1255	rs17878336	123	P35247	SFTPD_HUMAN	V	123;136	ENSP00000361366:L123V;ENSP00000394325:L136V	ENSP00000361366:L123V	L	-	1	2	SFTPD	81692190	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	-0.386000	0.07370	-1.157000	0.02815	-1.486000	0.00981	CTG	G|0.972;C|0.028	0.028	strong		0.602	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		
EMC3	55831	hgsc.bcm.edu	37	3	10028294	10028294	+	Silent	SNP	G	G	A	rs11551739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:10028294G>A	ENST00000245046.2	-	1	510	c.52C>T	c.(52-54)Cta>Tta	p.L18L	EMC3_ENST00000429759.1_Silent_p.L18L|AC034193.5_ENST00000326237.3_RNA	NM_018447.2	NP_060917.1	Q9P0I2	EMC3_HUMAN	ER membrane protein complex subunit 3	18						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											ACGATGGGTAGGACCACCCAG	0.537													G|||	182	0.0363419	0.0053	0.0476	5008	,	,		19680	0.0		0.1163	False		,,,				2504	0.0256				p.L18L		Atlas-SNP	.											.	EMC3	2	.	0			c.C52T						PASS	.	G		49,4357		1,47,2155	143.0	118.0	127.0		52	4.8	1.0	3	dbSNP_120	127	756,7844		33,690,3577	no	coding-synonymous	TMEM111	NM_018447.2		34,737,5732	AA,AG,GG		8.7907,1.1121,6.1895		18/262	10028294	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	55831	exon1			TGGGTAGGACCAC	AF157321	CCDS2594.1	3p25.3	2012-05-23	2012-05-23	2012-05-23	ENSG00000125037	ENSG00000125037			23999	protein-coding gene	gene with protein product			"""transmembrane protein 111"""	TMEM111		19797678, 22119785	Standard	NM_018447		Approved		uc003bun.3	Q9P0I2	OTTHUMG00000128652	ENST00000245046.2:c.52C>T	3.37:g.10028294G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	159	75	0.471698	NM_018447	B2R4Z9|Q53GH8|Q6ZMC2	Silent	SNP	ENST00000245046.2	37	CCDS2594.1																																																																																			G|0.941;A|0.059	0.059	strong		0.537	EMC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250532.1	NM_018447	
ITSN2	50618	hgsc.bcm.edu	37	2	24524958	24524958	+	Missense_Mutation	SNP	C	C	T	rs7603997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	56	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	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	
POTEC	388468	hgsc.bcm.edu	37	18	14535001	14535001	+	Silent	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:14535001G>C	ENST00000358970.5	-	4	815	c.816C>G	c.(814-816)ggC>ggG	p.G272G	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	272										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GTGGTGTGAGGCCACACTGTA	0.313																																					p.G272G		Atlas-SNP	.											POTEC,NS,carcinoma,0,2	POTEC	129	2	0			c.C816G						scavenged	.						7.0	6.0	6.0					18																	14535001		666	1525	2191	SO:0001819	synonymous_variant	388468	exon4			TGTGAGGCCACAC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.816C>G	18.37:g.14535001G>C		Somatic	808	0	0		WXS	Illumina HiSeq	Phase_I	706	92	0.130312	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	weak		0.313	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
CYP27C1	339761	hgsc.bcm.edu	37	2	127961026	127961026	+	Missense_Mutation	SNP	A	A	G	rs139058558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:127961026A>G	ENST00000335247.7	-	2	230	c.100T>C	c.(100-102)Tac>Cac	p.Y34H	CYP27C1_ENST00000409327.1_Missense_Mutation_p.Y34H	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	34						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)			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)		CTGAGGAGGTAGATTCTTTTA	0.413													A|||	7	0.00139776	0.0	0.0014	5008	,	,		19995	0.0		0.003	False		,,,				2504	0.0031				p.Y34H		Atlas-SNP	.											.	CYP27C1	52	.	0			c.T100C						PASS	.	A	HIS/TYR	4,4402	8.1+/-20.4	0,4,2199	169.0	167.0	167.0		100	4.2	1.0	2	dbSNP_134	167	34,8566	24.0+/-70.4	0,34,4266	yes	missense	CYP27C1	NM_001001665.3	83	0,38,6465	GG,GA,AA		0.3953,0.0908,0.2922	benign	34/373	127961026	38,12968	2203	4300	6503	SO:0001583	missense	339761	exon2			GGAGGTAGATTCT	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.100T>C	2.37:g.127961026A>G	ENSP00000334128:p.Tyr34His	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_001001665	Q6ZNI7	Missense_Mutation	SNP	ENST00000335247.7	37	CCDS33285.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	A	10.37	1.332587	0.24167	9.08E-4	0.003953	ENSG00000186684	ENST00000335247;ENST00000409327	T;T	0.67523	-0.27;-0.27	4.23	4.23	0.50019	.	0.584729	0.17003	N	0.190842	T	0.51398	0.1672	L	0.31065	0.9	0.24644	N	0.993557	B	0.13145	0.007	B	0.18263	0.021	T	0.42430	-0.9452	10	0.45353	T	0.12	-0.1021	6.7049	0.23244	0.75:0.0:0.25:0.0	.	34	Q4G0S4	C27C1_HUMAN	H	34	ENSP00000334128:Y34H;ENSP00000387198:Y34H	ENSP00000334128:Y34H	Y	-	1	0	CYP27C1	127677496	0.954000	0.32549	0.998000	0.56505	0.949000	0.60115	0.657000	0.24963	1.564000	0.49628	0.402000	0.26972	TAC	A|0.997;G|0.003	0.003	strong		0.413	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665	
MEP1A	4224	hgsc.bcm.edu	37	6	46806809	46806809	+	Missense_Mutation	SNP	C	C	T	rs1804211	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:46806809C>T	ENST00000230588.4	+	14	2186	c.2177C>T	c.(2176-2178)aCg>aTg	p.T726M		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	726			T -> M (in dbSNP:rs1804211). {ECO:0000269|PubMed:14702039}.		digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			ATCGGAGGCACGGCTGGCGTG	0.602													C|||	1272	0.253994	0.09	0.3646	5008	,	,		18798	0.1944		0.3469	False		,,,				2504	0.363				p.T726M		Atlas-SNP	.											.	MEP1A	93	.	0			c.C2177T						PASS	.	C	MET/THR	547,3859	246.5+/-255.1	36,475,1692	124.0	104.0	111.0		2177	-1.3	0.0	6	dbSNP_89	111	3046,5554	470.1+/-367.7	541,1964,1795	no	missense	MEP1A	NM_005588.2	81	577,2439,3487	TT,TC,CC		35.4186,12.4149,27.6257	possibly-damaging	726/747	46806809	3593,9413	2203	4300	6503	SO:0001583	missense	4224	exon14			GAGGCACGGCTGG		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.2177C>T	6.37:g.46806809C>T	ENSP00000230588:p.Thr726Met	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	231	113	0.489177	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	37	CCDS4918.1	524	0.23992673992673993	40	0.08130081300813008	128	0.35359116022099446	83	0.1451048951048951	273	0.36015831134564646	C	14.06	2.423088	0.43020	0.124149	0.354186	ENSG00000112818	ENST00000230588	T	0.26373	1.74	5.8	-1.33	0.09172	.	0.909437	0.09810	N	0.752909	T	0.07007	0.0178	L	0.29908	0.895	0.80722	P	0.0	P;P	0.48998	0.918;0.918	B;B	0.39738	0.308;0.289	T	0.20907	-1.0261	9	0.66056	D	0.02	0.1704	8.2215	0.31543	0.0:0.3658:0.1088:0.5254	rs1804211;rs16875099;rs52810040	754;726	B7ZL91;Q16819	.;MEP1A_HUMAN	M	726	ENSP00000230588:T726M	ENSP00000230588:T726M	T	+	2	0	MEP1A	46914768	0.000000	0.05858	0.027000	0.17364	0.128000	0.20619	-0.788000	0.04614	-0.097000	0.12307	0.650000	0.86243	ACG	C|0.738;T|0.262	0.262	strong		0.602	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588	
KNDC1	85442	hgsc.bcm.edu	37	10	135012162	135012162	+	Missense_Mutation	SNP	T	T	C	rs2998139	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:135012162T>C	ENST00000304613.3	+	14	2171	c.2150T>C	c.(2149-2151)cTg>cCg	p.L717P	KNDC1_ENST00000368571.2_Missense_Mutation_p.L652P|KNDC1_ENST00000368572.2_Missense_Mutation_p.L717P			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	717			L -> P (in dbSNP:rs2998139). {ECO:0000269|Ref.1}.		cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		AAGCTCTCCCTGGAGGCCCAC	0.706													C|||	2794	0.557907	0.5182	0.4914	5008	,	,		12230	0.6121		0.5308	False		,,,				2504	0.6309				p.L717P		Atlas-SNP	.											KNDC1,NS,carcinoma,0,1	KNDC1	155	1	0			c.T2150C						PASS	.		PRO/LEU	2365,1941		685,995,473	7.0	10.0	9.0		2150	2.8	0.0	10	dbSNP_101	9	4790,3688		1424,1942,873	no	missense	KNDC1	NM_152643.6	98	2109,2937,1346	CC,CT,TT		43.5008,45.0766,44.0316	benign	717/1750	135012162	7155,5629	2153	4239	6392	SO:0001583	missense	85442	exon14			TCTCCCTGGAGGC	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2150T>C	10.37:g.135012162T>C	ENSP00000304437:p.Leu717Pro	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	1195	0.5471611721611722	233	0.4735772357723577	184	0.5082872928176796	364	0.6363636363636364	414	0.5461741424802111	C	7.498	0.652101	0.14580	0.549234	0.564992	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.15834	2.83;2.83;2.39	2.82	2.82	0.32997	.	1.232730	0.06215	N	0.685777	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38929	-0.9638	9	0.30854	T	0.27	5.8541	6.0141	0.19592	0.0:0.8532:0.0:0.1468	rs2998139;rs59625486;rs2998139	717;652;717	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	P	717;717;652	ENSP00000304437:L717P;ENSP00000357561:L717P;ENSP00000357560:L652P	ENSP00000304437:L717P	L	+	2	0	KNDC1	134862152	0.004000	0.15560	0.001000	0.08648	0.000000	0.00434	1.349000	0.33998	0.768000	0.33290	-0.674000	0.03794	CTG	T|0.452;C|0.548	0.548	strong		0.706	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
MUC4	4585	hgsc.bcm.edu	37	3	195511051	195511051	+	Missense_Mutation	SNP	C	C	A	rs74867514		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195511051C>A	ENST00000463781.3	-	2	7859	c.7400G>T	c.(7399-7401)gGc>gTc	p.G2467V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G2467V	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.G2467V(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)		AGTGTCGGTGCCAGGAAGAGG	0.582																																					p.G2467V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,5	MUC4	1505	5	3	Substitution - Missense(3)	stomach(2)|endometrium(1)	c.G7400T						scavenged	.						36.0	33.0	34.0					3																	195511051		657	1587	2244	SO:0001583	missense	4585	exon2			TCGGTGCCAGGAA	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.7400G>T	3.37:g.195511051C>A	ENSP00000417498:p.Gly2467Val	Somatic	377	25	0.066313		WXS	Illumina HiSeq	Phase_I	368	20	0.0543478	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	4.251	0.045673	0.08196	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27890	1.64;1.7	.	.	.	.	.	.	.	.	T	0.10121	0.0248	N	0.02539	-0.55	0.23765	N	0.996904	B	0.09022	0.002	B	0.01281	0.0	T	0.36237	-0.9756	7	.	.	.	.	5.8178	0.18506	0.0:0.999:0.0:0.001	.	2467	E7ESK3	.	V	2467	ENSP00000417498:G2467V;ENSP00000420243:G2467V	.	G	-	2	0	MUC4	196995446	0.001000	0.12720	0.021000	0.16686	0.000000	0.00434	-2.888000	0.00711	-0.000000	0.14550	0.000000	0.15137	GGC	C|0.500;A|0.500	0.500	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PPIH	10465	hgsc.bcm.edu	37	1	43131653	43131653	+	Silent	SNP	G	G	A	rs12244	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:43131653G>A	ENST00000304979.3	+	7	361	c.339G>A	c.(337-339)gcG>gcA	p.A113A	PPIH_ENST00000455203.2_Silent_p.A70A|PPIH_ENST00000372550.1_Silent_p.A70A	NM_006347.3	NP_006338.1	O43447	PPIH_HUMAN	peptidylprolyl isomerase H (cyclophilin H)	113	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|ribonucleoprotein complex binding (GO:0043021)			endometrium(1)|large_intestine(1)|lung(2)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)			L-Proline(DB00172)	TCCATCAGGCGAACAGTGGTC	0.463													G|||	753	0.150359	0.0363	0.0908	5008	,	,		21387	0.3185		0.1233	False		,,,				2504	0.2014				p.A113A	NSCLC(73;23 1942 10718 46854)	Atlas-SNP	.											PPIH,NS,carcinoma,+1,1	PPIH	15	1	0			c.G339A						PASS	.	G		228,4178	135.3+/-171.4	3,222,1978	253.0	219.0	230.0		339	0.4	1.0	1	dbSNP_52	230	1001,7599	215.2+/-254.6	85,831,3384	no	coding-synonymous	PPIH	NM_006347.3		88,1053,5362	AA,AG,GG		11.6395,5.1748,9.4495		113/178	43131653	1229,11777	2203	4300	6503	SO:0001819	synonymous_variant	10465	exon7			TCAGGCGAACAGT	AF016371	CCDS469.1	1p34.1	2012-06-07	2006-01-12		ENSG00000171960	ENSG00000171960			14651	protein-coding gene	gene with protein product	"""USA-CyP SnuCyp-20"", ""cyclophilin H"", ""U-snRNP-associated cyclophilin SunCyp-20"", ""small nuclear ribonucleoprotein particle-specific cyclophilin H"", ""rotamase H"", ""peptidyl-prolyl cis-trans isomerase H"", ""PPIase h"""	606095	"""peptidyl prolyl isomerase H (cyclophilin H)"""			9404889, 9570313	Standard	NM_006347		Approved	USA-CYP, CYP-20, SnuCyp-20, CYPH, MGC5016	uc001chq.3	O43447	OTTHUMG00000007520	ENST00000304979.3:c.339G>A	1.37:g.43131653G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	252	117	0.464286	NM_006347	A6NNE7	Silent	SNP	ENST00000304979.3	37	CCDS469.1																																																																																			A|0.124;C|0.000;G|0.876	0.124	strong		0.463	PPIH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019778.1	NM_006347	
PDLIM4	8572	hgsc.bcm.edu	37	5	131607096	131607096	+	Missense_Mutation	SNP	G	G	A	rs145687686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:131607096G>A	ENST00000253754.3	+	5	671	c.607G>A	c.(607-609)Gcg>Acg	p.A203T	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000379018.3_Missense_Mutation_p.A203T|PDLIM4_ENST00000484620.1_3'UTR	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	203							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)			GCCCGTGGCCGCGGAGCCCAA	0.697													G|||	6	0.00119808	0.0	0.0014	5008	,	,		13703	0.0		0.002	False		,,,				2504	0.0031				p.A203T		Atlas-SNP	.											.	PDLIM4	22	.	0			c.G607A						PASS	.	G	THR/ALA,THR/ALA	4,4400		0,4,2198	22.0	32.0	28.0		607,607	-4.2	0.0	5	dbSNP_134	28	24,8576		0,24,4276	yes	missense,missense	PDLIM4	NM_001131027.1,NM_003687.3	58,58	0,28,6474	AA,AG,GG		0.2791,0.0908,0.2153	benign,benign	203/247,203/331	131607096	28,12976	2202	4300	6502	SO:0001583	missense	8572	exon5			GTGGCCGCGGAGC	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.607G>A	5.37:g.131607096G>A	ENSP00000253754:p.Ala203Thr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	37	CCDS4152.1	.	.	.	.	.	.	.	.	.	.	G	6.078	0.382625	0.11524	9.08E-4	0.002791	ENSG00000131435	ENST00000253754;ENST00000379018	T;T	0.20332	2.71;2.08	5.14	-4.15	0.03881	.	0.616023	0.17450	N	0.173809	T	0.04003	0.0112	N	0.02539	-0.55	0.09310	N	1	P;B	0.37330	0.59;0.127	B;B	0.27887	0.084;0.038	T	0.45600	-0.9250	10	0.13853	T	0.58	-0.8003	4.3024	0.10930	0.1555:0.0814:0.1504:0.6127	.	203;203	P50479-2;P50479	.;PDLI4_HUMAN	T	203	ENSP00000253754:A203T;ENSP00000368303:A203T	ENSP00000253754:A203T	A	+	1	0	PDLIM4	131634995	0.000000	0.05858	0.000000	0.03702	0.281000	0.26958	0.017000	0.13399	-0.420000	0.07427	0.313000	0.20887	GCG	G|0.997;A|0.003	0.003	strong		0.697	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
MUC5B	727897	hgsc.bcm.edu	37	11	1263776	1263776	+	Missense_Mutation	SNP	C	C	T	rs2943510	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1263776C>T	ENST00000529681.1	+	31	5724	c.5666C>T	c.(5665-5667)cCa>cTa	p.P1889L	MUC5B_ENST00000447027.1_Missense_Mutation_p.P1892L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1889	7 X Cys-rich subdomain repeats.|Thr-rich.		P -> L (in dbSNP:rs2943510). {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)		CCCAGTACCCCAGCCACCAGC	0.592													C|||	595	0.11881	0.0998	0.2147	5008	,	,		18334	0.0526		0.1312	False		,,,				2504	0.1319				p.P1889L		Atlas-SNP	.											.	MUC5B	473	.	0			c.C5666T						PASS	.	C	LEU/PRO	421,3957	185.3+/-212.5	16,389,1784	78.0	99.0	92.0		5666	2.7	0.0	11	dbSNP_101	92	1067,7491	217.4+/-256.1	67,933,3279	yes	missense	MUC5B	NM_002458.2	98	83,1322,5063	TT,TC,CC		12.4679,9.6163,11.5028	probably-damaging	1889/5763	1263776	1488,11448	2189	4279	6468	SO:0001583	missense	727897	exon31			GTACCCCAGCCAC	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.5666C>T	11.37:g.1263776C>T	ENSP00000436812:p.Pro1889Leu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	243	125	0.514403	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	265	0.12133699633699634	45	0.09146341463414634	71	0.19613259668508287	43	0.07517482517482517	106	0.13984168865435356	C	10.98	1.504368	0.26949	0.096163	0.124679	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.19394	2.15;2.34	2.72	2.72	0.32119	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.29627	0.144;0.252	B;B	0.18561	0.022;0.022	T	0.23726	-1.0180	8	0.87932	D	0	.	9.1961	0.37228	0.0:0.8804:0.0:0.1196	rs2943510;rs58124603;rs2943510	2582;1892	A7Y9J9;E9PBJ0	.;.	L	1889;1892;1890;1959	ENSP00000436812:P1889L;ENSP00000415793:P1892L	ENSP00000343037:P1890L	P	+	2	0	MUC5B	1220352	0.000000	0.05858	0.001000	0.08648	0.142000	0.21351	0.339000	0.19875	1.534000	0.49203	0.089000	0.15464	CCA	C|0.873;T|0.127	0.127	strong		0.592	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CTNND1	1500	hgsc.bcm.edu	37	11	57563991	57563991	+	Silent	SNP	C	C	T	rs10896644	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57563991C>T	ENST00000399050.4	+	6	1019	c.483C>T	c.(481-483)gaC>gaT	p.D161D	CTNND1_ENST00000528232.1_Silent_p.D60D|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000528621.1_Silent_p.D107D|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000361391.6_Silent_p.D161D|CTNND1_ENST00000534579.1_Silent_p.D107D|CTNND1_ENST00000361332.4_Silent_p.D161D|CTNND1_ENST00000532844.1_Silent_p.D107D|CTNND1_ENST00000360682.6_Silent_p.D161D|CTNND1_ENST00000530094.1_Silent_p.D60D|CTNND1_ENST00000532463.1_Silent_p.D60D|CTNND1_ENST00000524630.1_Silent_p.D161D|CTNND1_ENST00000426142.2_Silent_p.D60D|CTNND1_ENST00000399039.4_Silent_p.D161D|CTNND1_ENST00000529919.1_Silent_p.D161D|CTNND1_ENST00000526357.1_Silent_p.D107D|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000358694.6_Silent_p.D161D|CTNND1_ENST00000529986.1_Silent_p.D60D|CTNND1_ENST00000530748.1_Silent_p.D107D|CTNND1_ENST00000428599.2_Silent_p.D161D|CTNND1_ENST00000532787.1_Silent_p.D60D|CTNND1_ENST00000532649.1_Silent_p.D107D|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000529526.1_Silent_p.D107D|CTNND1_ENST00000529873.1_Silent_p.D107D|CTNND1_ENST00000415361.2_Silent_p.D60D|CTNND1_ENST00000526938.1_Silent_p.D161D|CTNND1_ENST00000361796.4_Silent_p.D161D|CTNND1_ENST00000532245.1_Silent_p.D60D|CTNND1_ENST00000527467.1_Intron	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	129	0	0		WXS	Illumina HiSeq	Phase_I	112	63	0.5625	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	
CORT	1325	hgsc.bcm.edu	37	1	10511544	10511544	+	Silent	SNP	C	C	T	rs628462	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10511544C>T	ENST00000377049.3	+	2	715	c.210C>T	c.(208-210)gcC>gcT	p.A70A	CORT_ENST00000320498.4_Silent_p.A120A|APITD1_ENST00000602296.1_3'UTR|APITD1-CORT_ENST00000465026.1_3'UTR|APITD1-CORT_ENST00000400900.2_Silent_p.A129A|APITD1_ENST00000602787.1_Silent_p.A129A|APITD1-CORT_ENST00000470413.2_3'UTR	NM_001302.4	NP_001293.3	O00230	CORT_HUMAN	cortistatin	70					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)	G-protein coupled receptor binding (GO:0001664)|neuropeptide hormone activity (GO:0005184)			breast(1)|endometrium(1)|stomach(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-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)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0487)		GAGAGGAAGCCCGGGAGGTGG	0.627													C|||	1440	0.28754	0.0212	0.3112	5008	,	,		14123	0.4871		0.3907	False		,,,				2504	0.319				p.A129A		Atlas-SNP	.											CORT,colon,carcinoma,0,2	.	.	2	0			c.C387T						PASS	.	C	,,	351,4051		21,309,1871	24.0	30.0	28.0		210,387,	-2.3	0.0	1	dbSNP_83	28	3414,5182		682,2050,1566	no	coding-synonymous,coding-synonymous,utr-3	CORT,APITD1-CORT	NM_001302.4,NM_198544.3,NM_199006.2	,,	703,2359,3437	TT,TC,CC		39.7161,7.9736,28.966	,,	70/106,129/165,	10511544	3765,9233	2201	4298	6499	SO:0001819	synonymous_variant	100526739	exon5			GGAAGCCCGGGAG	AF013252	CCDS117.1, CCDS117.2	1p36.22	2013-02-25			ENSG00000241563	ENSG00000241563		"""Endogenous ligands"""	2257	protein-coding gene	gene with protein product	"""prepro-cortistatin"""	602784				9205124	Standard	NM_001302		Approved	MGC32686		O00230	OTTHUMG00000001906	ENST00000377049.3:c.210C>T	1.37:g.10511544C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_198544	Q5T6G0|Q6UX11	Silent	SNP	ENST00000377049.3	37	CCDS117.2																																																																																			C|0.685;T|0.315	0.315	strong		0.627	CORT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005410.3	NM_001302	
CENPF	1063	hgsc.bcm.edu	37	1	214814925	214814925	+	Missense_Mutation	SNP	C	C	T	rs61732031	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214814925C>T	ENST00000366955.3	+	12	3412	c.3244C>T	c.(3244-3246)Cac>Tac	p.H1082Y		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)		TGCAAAGGAACACCAAGAATT	0.358													C|||	59	0.0117812	0.0113	0.0072	5008	,	,		19835	0.0		0.0129	False		,,,				2504	0.0266				p.H1082Y	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.C3244T						PASS	.	C	TYR/HIS	73,4333	63.5+/-100.7	0,73,2130	61.0	64.0	63.0		3244	3.9	1.0	1	dbSNP_129	63	122,8478	62.8+/-124.8	1,120,4179	yes	missense	CENPF	NM_016343.3	83	1,193,6309	TT,TC,CC		1.4186,1.6568,1.4993	probably-damaging	1082/3115	214814925	195,12811	2203	4300	6503	SO:0001583	missense	1063	exon12			AAGGAACACCAAG	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.3244C>T	1.37:g.214814925C>T	ENSP00000355922:p.His1082Tyr	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	191	90	0.471204	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	20	0.009157509157509158	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	C	13.63	2.295772	0.40594	0.016568	0.014186	ENSG00000117724	ENST00000366955	T	0.03212	4.01	4.92	3.93	0.45458	.	0.189139	0.26173	N	0.025919	T	0.02012	0.0063	.	.	.	0.23876	N	0.996598	D	0.54601	0.967	B	0.44044	0.439	T	0.40701	-0.9549	9	0.46703	T	0.11	.	10.6502	0.45645	0.3009:0.6991:0.0:0.0	rs61732031	1082	P49454	CENPF_HUMAN	Y	1082	ENSP00000355922:H1082Y	ENSP00000355922:H1082Y	H	+	1	0	CENPF	212881548	0.407000	0.25352	1.000000	0.80357	0.982000	0.71751	1.213000	0.32407	2.437000	0.82529	0.609000	0.83330	CAC	C|0.987;T|0.013	0.013	strong		0.358	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
UBR2	23304	hgsc.bcm.edu	37	6	42532102	42532102	+	Silent	SNP	C	C	T	rs3749897	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42532102C>T	ENST00000372899.1	+	1	303	c.45C>T	c.(43-45)agC>agT	p.S15S	UBR2_ENST00000372903.2_Silent_p.S15S|UBR2_ENST00000372901.1_Silent_p.S15S	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	15					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCGACCGGAGCTTGCTGGAAT	0.692													T|||	2341	0.467452	0.5325	0.4179	5008	,	,		15673	0.4464		0.4046	False		,,,				2504	0.501				p.S15S		Atlas-SNP	.											.	UBR2	134	.	0			c.C45T						PASS	.	T	,	2221,2183	566.8+/-382.0	551,1119,532	68.0	65.0	66.0		45,45	4.9	1.0	6	dbSNP_107	66	3544,5056	613.3+/-396.1	745,2054,1501	no	coding-synonymous,coding-synonymous	UBR2	NM_001184801.1,NM_015255.2	,	1296,3173,2033	TT,TC,CC		41.2093,49.5686,44.3325	,	15/440,15/1756	42532102	5765,7239	2202	4300	6502	SO:0001819	synonymous_variant	23304	exon1			CCGGAGCTTGCTG	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.45C>T	6.37:g.42532102C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	211	97	0.459716	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			C|0.559;G|0.000;T|0.440	0.440	strong		0.692	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
UGT2B11	10720	hgsc.bcm.edu	37	4	70066376	70066376	+	Missense_Mutation	SNP	C	C	G	rs144149579	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70066376C>G	ENST00000446444.1	-	6	1380	c.1372G>C	c.(1372-1374)Gat>Cat	p.D458H	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	458					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.D458H(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						ACTGCTCGATCCAGGGGCTTT	0.408																																					p.D458H		Atlas-SNP	.											UGT2B11,trunk,malignant_melanoma,0,1	UGT2B11	92	1	1	Substitution - Missense(1)	skin(1)	c.G1372C						PASS	.						104.0	107.0	106.0					4																	70066376		2203	4298	6501	SO:0001583	missense	10720	exon6			CTCGATCCAGGGG	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.1372G>C	4.37:g.70066376C>G	ENSP00000387683:p.Asp458His	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	151	15	0.0993377	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	.	.	.	.	.	.	.	.	.	.	-	11.29	1.595749	0.28445	.	.	ENSG00000213759	ENST00000446444	T	0.73469	-0.75	1.27	1.27	0.21489	.	0.000000	0.64402	U	0.000002	D	0.88738	0.6518	H	0.97415	4	0.31420	N	0.674431	D	0.89917	1.0	D	0.81914	0.995	D	0.86564	0.1843	10	0.87932	D	0	.	8.4963	0.33130	0.0:1.0:0.0:0.0	.	458	O75310	UDB11_HUMAN	H	458	ENSP00000387683:D458H	ENSP00000387683:D458H	D	-	1	0	UGT2B11	70100965	0.997000	0.39634	0.937000	0.37676	0.142000	0.21351	3.075000	0.50073	1.023000	0.39654	0.184000	0.17185	GAT	C|0.959;G|0.041	0.041	strong		0.408	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
TAS1R2	80834	hgsc.bcm.edu	37	1	19180860	19180860	+	Silent	SNP	G	G	A	rs528216046		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19180860G>A	ENST00000375371.3	-	3	1125	c.1104C>T	c.(1102-1104)aaC>aaT	p.N368N	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	368					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)	ACAAGGTGGCGTTCAGGCAGT	0.622																																					p.N368N		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C1104T						PASS	.						128.0	114.0	119.0					1																	19180860		2203	4300	6503	SO:0001819	synonymous_variant	80834	exon3			GGTGGCGTTCAGG		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.1104C>T	1.37:g.19180860G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			.	.	none		0.622	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
PRG4	10216	hgsc.bcm.edu	37	1	186277989	186277989	+	Silent	SNP	A	A	G	rs3737940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:186277989A>G	ENST00000445192.2	+	7	3183	c.3138A>G	c.(3136-3138)ccA>ccG	p.P1046P	PRG4_ENST00000367483.4_Silent_p.P1005P|PRG4_ENST00000367484.3_Silent_p.P575P|PRG4_ENST00000367485.4_Silent_p.P953P|PRG4_ENST00000367486.3_Silent_p.P1003P|RNU6-1240P_ENST00000365155.1_RNA	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1046					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGAGAAAACCAAAGACGACAC	0.448													A|||	1108	0.221246	0.1142	0.402	5008	,	,		21201	0.125		0.33	False		,,,				2504	0.2249				p.P1046P		Atlas-SNP	.											.	PRG4	259	.	0			c.A3138G						PASS	.	A	,,,	658,3748	281.4+/-275.9	53,552,1598	164.0	175.0	171.0		3015,2859,2736,3138	-2.0	0.3	1	dbSNP_107	171	3044,5556	467.6+/-367.1	543,1958,1799	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRG4	NM_001127708.1,NM_001127709.1,NM_001127710.1,NM_005807.3	,,,	596,2510,3397	GG,GA,AA		35.3953,14.9342,28.4638	,,,	1005/1364,953/1312,912/1271,1046/1405	186277989	3702,9304	2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			AAAACCAAAGACG	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3138A>G	1.37:g.186277989A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	114	67	0.587719	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			A|0.735;G|0.265	0.265	strong		0.448	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
POLRMT	5442	hgsc.bcm.edu	37	19	621063	621063	+	Silent	SNP	A	A	G	rs76890343	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:621063A>G	ENST00000588649.2	-	10	2719	c.2635T>C	c.(2635-2637)Ttg>Ctg	p.L879L	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	879	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)		CCTACCGTCAAGGGTTGGTCC	0.756													A|||	1109	0.221446	0.1823	0.1499	5008	,	,		4907	0.249		0.172	False		,,,				2504	0.3476				p.L879L		Atlas-SNP	.											.	POLRMT	91	.	0			c.T2635C						PASS	.	A		667,3715		53,561,1577	17.0	20.0	19.0		2635	0.9	0.9	19	dbSNP_131	19	1367,7215		124,1119,3048	no	coding-synonymous	POLRMT	NM_005035.3		177,1680,4625	GG,GA,AA		15.9287,15.2214,15.6896		879/1231	621063	2034,10930	2191	4291	6482	SO:0001819	synonymous_variant	5442	exon10			CCGTCAAGGGTTG		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.2635T>C	19.37:g.621063A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			A|0.839;G|0.161	0.161	strong		0.756	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
SETD2	29072	hgsc.bcm.edu	37	3	47125385	47125385	+	Missense_Mutation	SNP	G	G	A	rs4082155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47125385G>A	ENST00000409792.3	-	12	5927	c.5885C>T	c.(5884-5886)cCc>cTc	p.P1962L	SETD2_ENST00000492397.1_5'UTR	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1962			P -> L (in dbSNP:rs4082155). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.P1962L(1)|p.P1459L(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GCTCTCTTTGGGCTCTATTTC	0.453			"""N, F, S, Mis"""		clear cell renal carcinoma								G|||	2353	0.469848	0.236	0.5187	5008	,	,		21360	0.5327		0.5825	False		,,,				2504	0.5706				p.P1962L		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	721	2	2	Substitution - Missense(2)	stomach(2)	c.C5885T						PASS	.	G	LEU/PRO	1261,3145	433.1+/-343.5	201,859,1143	248.0	213.0	225.0		5885	2.9	1.0	3	dbSNP_108	225	4869,3731	618.1+/-396.7	1380,2109,811	yes	missense	SETD2	NM_014159.6	98	1581,2968,1954	AA,AG,GG		43.3837,28.6201,47.1321	benign	1962/2565	47125385	6130,6876	2203	4300	6503	SO:0001583	missense	29072	exon12			TCTTTGGGCTCTA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5885C>T	3.37:g.47125385G>A	ENSP00000386759:p.Pro1962Leu	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	311	308	0.990354	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	1082	0.49542124542124544	143	0.29065040650406504	194	0.5359116022099447	304	0.5314685314685315	441	0.5817941952506597	G	11.54	1.669445	0.29693	0.286201	0.566163	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.21932	1.98	5.69	2.94	0.34122	.	0.827297	0.10610	N	0.654637	T	0.00012	0.0000	N	0.14661	0.345	0.28580	P	0.9101621	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.42207	-0.9465	9	0.13108	T	0.6	.	5.2839	0.15690	0.266:0.0:0.5927:0.1413	rs4082155;rs52814353;rs4082155	1962;1962	F2Z317;Q9BYW2	.;SETD2_HUMAN	L	1962	ENSP00000386759:P1962L	ENSP00000386759:P1962L	P	-	2	0	SETD2	47100389	0.764000	0.28473	0.986000	0.45419	0.925000	0.55904	0.529000	0.23019	0.333000	0.23563	-0.145000	0.13849	CCC	G|0.524;A|0.476	0.476	strong		0.453	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
CLEC18A	348174	hgsc.bcm.edu	37	16	69988473	69988473	+	Silent	SNP	G	G	A	rs80122082	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:69988473G>A	ENST00000288040.6	+	3	640	c.453G>A	c.(451-453)acG>acA	p.T151T	CLEC18A_ENST00000393701.2_Silent_p.T151T|CLEC18A_ENST00000449317.2_Silent_p.T151T|CLEC18A_ENST00000568461.1_Silent_p.T151T	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						CCCACTACACGCAGGTGAGTG	0.582																																					p.T151T		Atlas-SNP	.											.	CLEC18A	9	.	0			c.G453A						PASS	.						25.0	23.0	24.0					16																	69988473		2198	4298	6496	SO:0001819	synonymous_variant	348174	exon4			CTACACGCAGGTG	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.453G>A	16.37:g.69988473G>A		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	340	32	0.0941176	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Silent	SNP	ENST00000288040.6	37	CCDS10886.1																																																																																			G|0.997;A|0.003	0.003	strong		0.582	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
GABRG3	2567	hgsc.bcm.edu	37	15	27725917	27725917	+	Silent	SNP	C	C	T	rs77771286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:27725917C>T	ENST00000333743.6	+	6	950	c.696C>T	c.(694-696)atC>atT	p.I232I	RP11-100M12.3_ENST00000556642.1_RNA|GABRG3_ENST00000555083.1_Silent_p.I232I	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	232					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)	CCACAGAAATCGTGACAACGT	0.443													C|||	13	0.00259585	0.0	0.0029	5008	,	,		15354	0.0		0.008	False		,,,				2504	0.0031				p.I232I	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.C696T						PASS	.	C		7,3769		0,7,1881	54.0	54.0	54.0		696	-4.5	0.2	15	dbSNP_131	54	84,8170		1,82,4044	no	coding-synonymous	GABRG3	NM_033223.4		1,89,5925	TT,TC,CC		1.0177,0.1854,0.7564		232/468	27725917	91,11939	1888	4127	6015	SO:0001819	synonymous_variant	2567	exon6			AGAAATCGTGACA		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.696C>T	15.37:g.27725917C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001270873	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			C|0.994;T|0.006	0.006	strong		0.443	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
HGFAC	3083	hgsc.bcm.edu	37	4	3444593	3444593	+	Silent	SNP	G	G	A	rs2073504	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:3444593G>A	ENST00000382774.3	+	2	367	c.252G>A	c.(250-252)ccG>ccA	p.P84P	HGFAC_ENST00000511533.1_Silent_p.P84P	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	84					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGGGGCTCCCGCCCCCGCCCA	0.672													G|||	1155	0.230631	0.2057	0.2291	5008	,	,		15322	0.372		0.175	False		,,,				2504	0.1769				p.P84P		Atlas-SNP	.											HGFAC,NS,carcinoma,0,1	HGFAC	69	1	0			c.G252A						PASS	.	G		927,3473	330.4+/-301.5	90,747,1363	43.0	51.0	48.0		252	-1.1	0.0	4	dbSNP_96	48	1407,7191	265.7+/-286.3	119,1169,3011	yes	coding-synonymous	HGFAC	NM_001528.2		209,1916,4374	AA,AG,GG		16.3643,21.0682,17.9566		84/656	3444593	2334,10664	2200	4299	6499	SO:0001819	synonymous_variant	3083	exon2			GCTCCCGCCCCCG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.252G>A	4.37:g.3444593G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	37	CCDS3369.1																																																																																			G|0.806;A|0.194	0.194	strong		0.672	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
KRT38	8687	hgsc.bcm.edu	37	17	39595536	39595536	+	Silent	SNP	C	C	T	rs17494404	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	90	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	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	
EFS	10278	hgsc.bcm.edu	37	14	23826822	23826822	+	Silent	SNP	C	C	T	rs2231809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23826822C>T	ENST00000216733.3	-	6	1906	c.1299G>A	c.(1297-1299)ctG>ctA	p.L433L	RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000429593.2_Silent_p.L264L|EFS_ENST00000351354.3_Silent_p.L340L	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	433					cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		ACAGGAGCTGCAGATCTCCGG	0.592													T|||	2280	0.455272	0.8767	0.2493	5008	,	,		17090	0.3036		0.2734	False		,,,				2504	0.3753				p.L433L		Atlas-SNP	.											.	EFS	37	.	0			c.G1299A						PASS	.	T	,	3442,964	347.5+/-309.5	1350,742,111	34.0	38.0	37.0		1299,1020	-9.4	0.0	14	dbSNP_98	37	2599,5999	662.1+/-401.9	394,1811,2094	no	coding-synonymous,coding-synonymous	EFS	NM_005864.2,NM_032459.1	,	1744,2553,2205	TT,TC,CC		30.228,21.8793,46.4549	,	433/562,340/469	23826822	6041,6963	2203	4299	6502	SO:0001819	synonymous_variant	10278	exon6			GAGCTGCAGATCT	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.1299G>A	14.37:g.23826822C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	83	0.965116	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Silent	SNP	ENST00000216733.3	37	CCDS9595.1																																																																																			C|0.549;T|0.451	0.451	strong		0.592	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		
HJURP	55355	hgsc.bcm.edu	37	2	234749780	234749780	+	Missense_Mutation	SNP	G	G	C	rs3821238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:234749780G>C	ENST00000411486.2	-	8	1711	c.1646C>G	c.(1645-1647)tCt>tGt	p.S549C	HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000432087.1_Missense_Mutation_p.S495C|HJURP_ENST00000441687.1_Missense_Mutation_p.S464C	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	549			S -> C (in dbSNP:rs3821238). {ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)	p.S549C(1)		NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		AAATATTCCAGAACTATTTCC	0.468													G|||	832	0.166134	0.2375	0.1254	5008	,	,		19121	0.2827		0.0875	False		,,,				2504	0.0593				p.S549C		Atlas-SNP	.											HJURP,NS,carcinoma,0,1	HJURP	72	1	1	Substitution - Missense(1)	stomach(1)	c.C1646G						PASS	.	G	CYS/SER	864,3542	339.4+/-305.8	89,686,1428	117.0	121.0	119.0		1646	-1.1	0.0	2	dbSNP_107	119	825,7775	190.7+/-237.1	40,745,3515	yes	missense	HJURP	NM_018410.3	112	129,1431,4943	CC,CG,GG		9.593,19.6096,12.9863	probably-damaging	549/749	234749780	1689,11317	2203	4300	6503	SO:0001583	missense	55355	exon8			ATTCCAGAACTAT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1646C>G	2.37:g.234749780G>C	ENSP00000414109:p.Ser549Cys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	414	0.18956043956043955	116	0.23577235772357724	40	0.11049723756906077	186	0.32517482517482516	72	0.09498680738786279	G	14.36	2.510896	0.44660	0.196096	0.09593	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.11604	3.06;3.07;3.07;2.76	4.29	-1.13	0.09775	.	1.608680	0.03391	N	0.201811	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	D;D;D	0.69078	0.997;0.997;0.994	P;P;P	0.57468	0.821;0.821;0.667	T	0.32134	-0.9918	9	0.45353	T	0.12	-0.9977	6.5815	0.22596	0.1926:0.1639:0.6434:0.0	rs3821238;rs56481334;rs59494558;rs3821238	464;495;549	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	C	549;495;464;464	ENSP00000414109:S549C;ENSP00000407208:S495C;ENSP00000401944:S464C;ENSP00000393253:S464C	ENSP00000414109:S549C	S	-	2	0	HJURP	234414519	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.637000	0.05459	-0.209000	0.10156	0.563000	0.77884	TCT	G|0.832;C|0.168	0.168	strong		0.468	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
IL10RB	3588	hgsc.bcm.edu	37	21	34640788	34640788	+	Missense_Mutation	SNP	A	A	G	rs2834167	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:34640788A>G	ENST00000290200.2	+	2	247	c.139A>G	c.(139-141)Aaa>Gaa	p.K47E	IL10RB-AS1_ENST00000411998.1_RNA|AP000295.9_ENST00000433395.2_Silent_p.P174P	NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	47	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		K -> E (associated with susceptibility to HBV infection; higher cell surface levels; dbSNP:rs2834167). {ECO:0000269|PubMed:16757563, ECO:0000269|Ref.4}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						TGCTTTTGCCAAAGGGAACCT	0.493													A|||	1700	0.339457	0.0855	0.5014	5008	,	,		20653	0.5635		0.2684	False		,,,				2504	0.41				p.K47E	Melanoma(67;315 1275 21667 21943 44564)	Atlas-SNP	.											.	IL10RB	37	.	0			c.A139G	GRCh37	CM066574	IL10RB	M	rs2834167	PASS	.	A	GLU/LYS	576,3830	257.4+/-261.8	23,530,1650	96.0	88.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	139	2.6	1.0	21	dbSNP_100	91	2214,6386	376.3+/-338.1	290,1634,2376	yes	missense	IL10RB	NM_000628.3	56	313,2164,4026	GG,GA,AA		25.7442,13.0731,21.4516		47/326	34640788	2790,10216	2203	4300	6503	SO:0001583	missense	3588	exon2			TTTGCCAAAGGGA	U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646		"""Interleukins and interleukin receptors"", ""CD molecules"""	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66		8314576, 9312047	Standard	NM_000628		Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.139A>G	21.37:g.34640788A>G	ENSP00000290200:p.Lys47Glu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_000628	Q9BUU4	Missense_Mutation	SNP	ENST00000290200.2	37	CCDS13623.1	755	0.3456959706959707	47	0.09552845528455285	172	0.47513812154696133	323	0.5646853146853147	213	0.28100263852242746	A	15.76	2.927466	0.52759	0.130731	0.257442	ENSG00000243646	ENST00000290200;ENST00000539894	T	0.72835	-0.69	5.35	2.61	0.31194	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.428243	0.24405	N	0.038805	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	P;B	0.37122	0.583;0.392	B;B	0.38880	0.284;0.109	T	0.51779	-0.8662	9	0.25751	T	0.34	-16.1558	5.6759	0.17747	0.6598:0.1733:0.0:0.1669	rs2834167;rs52815411;rs61161628;rs2834167	47;47	Q08334;F5H766	I10R2_HUMAN;.	E	47	ENSP00000290200:K47E	ENSP00000290200:K47E	K	+	1	0	IL10RB	33562658	0.741000	0.28217	0.992000	0.48379	0.968000	0.65278	0.790000	0.26900	2.021000	0.59480	0.533000	0.62120	AAA	A|0.728;G|0.272	0.272	strong		0.493	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139831.3		
PTGER4	5734	hgsc.bcm.edu	37	5	40681254	40681254	+	Silent	SNP	C	C	T	rs2228058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:40681254C>T	ENST00000302472.3	+	2	1183	c.159C>T	c.(157-159)acC>acT	p.T53T	PTGER4_ENST00000514343.1_3'UTR	NM_000958.2	NP_000949.1	P35408	PE2R4_HUMAN	prostaglandin E receptor 4 (subtype EP4)	53					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|bone development (GO:0060348)|cellular response to mechanical stimulus (GO:0071260)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|JNK cascade (GO:0007254)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of eosinophil extravasation (GO:2000420)|negative regulation of inflammatory response (GO:0050728)|negative regulation of integrin activation (GO:0033624)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|regulation of ossification (GO:0030278)|regulation of stress fiber assembly (GO:0051492)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|T-helper cell differentiation (GO:0042093)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)			breast(1)|endometrium(3)|liver(1)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23					Dinoprostone(DB00917)|Misoprostol(DB00929)	AGGAGACGACCTTCTACACGC	0.612											OREG0016588	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	292	0.0583067	0.112	0.0562	5008	,	,		19308	0.0		0.0696	False		,,,				2504	0.0358				p.T53T		Atlas-SNP	.											.	PTGER4	49	.	0			c.C159T						PASS	.	C		459,3947	217.1+/-235.6	27,405,1771	75.0	64.0	68.0		159	2.6	1.0	5	dbSNP_98	68	638,7962	162.7+/-215.4	20,598,3682	no	coding-synonymous	PTGER4	NM_000958.2		47,1003,5453	TT,TC,CC		7.4186,10.4176,8.4346		53/489	40681254	1097,11909	2203	4300	6503	SO:0001819	synonymous_variant	5734	exon2			GACGACCTTCTAC	L28175	CCDS3930.1	5p13.1	2012-08-08			ENSG00000171522	ENSG00000171522		"""GPCR / Class A : Prostanoid receptors"""	9596	protein-coding gene	gene with protein product		601586				7759114, 8661119	Standard	NM_000958		Approved	EP4	uc003jlz.3	P35408	OTTHUMG00000094769	ENST00000302472.3:c.159C>T	5.37:g.40681254C>T		Somatic	161	0	0	895	WXS	Illumina HiSeq	Phase_I	173	80	0.462428	NM_000958	Q3MJ87	Silent	SNP	ENST00000302472.3	37	CCDS3930.1																																																																																			C|0.924;T|0.076	0.076	strong		0.612	PTGER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211578.2	NM_000958	
LEPR	3953	hgsc.bcm.edu	37	1	66058513	66058513	+	Missense_Mutation	SNP	A	A	G	rs1137101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:66058513A>G	ENST00000349533.6	+	6	853	c.668A>G	c.(667-669)cAg>cGg	p.Q223R	LEPR_ENST00000406510.3_Intron|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371060.3_Missense_Mutation_p.Q223R|LEPR_ENST00000371059.3_Missense_Mutation_p.Q223R|LEPR_ENST00000344610.8_Missense_Mutation_p.Q223R|LEPR_ENST00000371058.1_Missense_Mutation_p.Q223R	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		GTAATTTTCCAGTCACCTCTA	0.363													A|||	2926	0.584265	0.5923	0.4366	5008	,	,		18691	0.869		0.4692	False		,,,				2504	0.5031				p.Q223R		Atlas-SNP	.											.	LEPR	284	.	0			c.A668G	GRCh37	CM010905	LEPR	M	rs1137101	PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	2471,1935	623.5+/-394.1	694,1083,426	97.0	95.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	668,668,668,668,668,668	3.7	1.0	1	dbSNP_86	95	3906,4694	544.9+/-384.7	901,2104,1295	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	43,43,43,43,43,43	1595,3187,1721	GG,GA,AA		45.4186,43.9174,49.0312	benign,benign,benign,benign,benign,benign	223/897,223/959,223/959,223/907,223/897,223/1166	66058513	6377,6629	2203	4300	6503	SO:0001583	missense	3953	exon6			TTTTCCAGTCACC	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.668A>G	1.37:g.66058513A>G	ENSP00000330393:p.Gln223Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	130	57	0.438462	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	1287	0.5892857142857143	265	0.5386178861788617	153	0.42265193370165743	496	0.8671328671328671	373	0.4920844327176781	A	13.55	2.271131	0.40194	0.560826	0.454186	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.54675	0.57;0.56;0.58;0.56;0.57	5.96	3.66	0.41972	.	0.550372	0.19543	N	0.111741	T	0.20740	0.0499	L	0.42245	1.32	0.09310	P	0.999999999633346	B;B;P	0.44195	0.282;0.404;0.828	B;B;B	0.36845	0.081;0.109;0.234	T	0.03566	-1.1024	9	0.21540	T	0.41	-0.1619	9.2279	0.37418	0.7896:0.0:0.2104:0.0	rs1137101;rs1805093;rs2229418;rs3200842;rs9282885;rs12131454;rs17356624;rs52820808;rs59347832;rs1137101	223;223;223	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	R	223	ENSP00000340884:Q223R;ENSP00000330393:Q223R;ENSP00000360099:Q223R;ENSP00000360098:Q223R;ENSP00000360097:Q223R	ENSP00000340884:Q223R	Q	+	2	0	LEPR	65831101	1.000000	0.71417	0.999000	0.59377	0.899000	0.52679	2.850000	0.48294	0.513000	0.28278	0.528000	0.53228	CAG	A|0.463;G|0.537	0.537	strong		0.363	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410827	105410827	+	Missense_Mutation	SNP	C	C	T	rs28380382	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	183	0	0		WXS	Illumina HiSeq	Phase_I	197	197	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418344	105418344	+	Missense_Mutation	SNP	T	T	G	rs55791176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105418344T>G	ENST00000333244.5	-	7	3563	c.3444A>C	c.(3442-3444)gaA>gaC	p.E1148D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1148						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)			CCAGGGACAGTTCCCCCTCCA	0.627													.|||	9	0.00179712	0.003	0.0014	5008	,	,		19779	0.0		0.0	False		,,,				2504	0.0041				p.E1148D		Atlas-SNP	.											AHNAK2_ENST00000333244,rectum,carcinoma,-1,2	AHNAK2	719	2	0			c.A3444C						PASS	.	G	ASP/GLU	1588,2354		371,846,754	163.0	185.0	178.0		3444	-8.4	0.0	14	dbSNP_129	178	4406,3886		1211,1984,951	no	missense	AHNAK2	NM_138420.2	45	1582,2830,1705	GG,GT,TT		46.8644,40.2841,48.9946	benign	1148/5796	105418344	5994,6240	1971	4146	6117	SO:0001583	missense	113146	exon7			GGACAGTTCCCCC	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.3444A>C	14.37:g.105418344T>G	ENSP00000353114:p.Glu1148Asp	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	190	190	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	954	0.4368131868131868	209	0.4247967479674797	154	0.425414364640884	196	0.34265734265734266	395	0.521108179419525	N	0.155	-1.087652	0.01873	0.402841	0.531356	ENSG00000185567	ENST00000333244	T	0.00557	6.62	4.22	-8.45	0.00946	.	.	.	.	.	T	0.00012	0.0000	N	0.00894	-1.105	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40403	-0.9565	8	0.09338	T	0.73	.	0.4796	0.00546	0.2411:0.2568:0.1548:0.3473	.	1148	Q8IVF2	AHNK2_HUMAN	D	1148	ENSP00000353114:E1148D	ENSP00000353114:E1148D	E	-	3	2	AHNAK2	104489389	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.714000	0.00385	-2.769000	0.00366	-3.794000	0.00020	GAA	T|0.536;G|0.464	0.464	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NSUN4	387338	hgsc.bcm.edu	37	1	46810670	46810670	+	Silent	SNP	T	T	C	rs17361763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46810670T>C	ENST00000474844.1	+	2	941	c.291T>C	c.(289-291)gaT>gaC	p.D97D	NSUN4_ENST00000536062.1_Silent_p.D48D|NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_Silent_p.D48D	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	97					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)					GTGCCAAGGATTTTGTGAATG	0.547													C|||	660	0.131789	0.1331	0.147	5008	,	,		21008	0.0179		0.2724	False		,,,				2504	0.092				p.D97D		Atlas-SNP	.											.	NSUN4	26	.	0			c.T291C						PASS	.	C		673,3733	763.6+/-413.2	58,557,1588	117.0	105.0	109.0		291	2.2	1.0	1	dbSNP_123	109	2493,6107	695.1+/-404.8	360,1773,2167	no	coding-synonymous	NSUN4	NM_199044.2		418,2330,3755	CC,CT,TT		28.9884,15.2746,24.3426		97/385	46810670	3166,9840	2203	4300	6503	SO:0001819	synonymous_variant	387338	exon2			CAAGGATTTTGTG	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.291T>C	1.37:g.46810670T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Silent	SNP	ENST00000474844.1	37	CCDS534.1																																																																																			T|0.802;C|0.198	0.198	strong		0.547	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
TPSB2	64499	hgsc.bcm.edu	37	16	1279438	1279438	+	RNA	SNP	C	C	T	rs202041848	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1279438C>T	ENST00000339687.6	-	0	275				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				ACCCTGAGGGCGGCCAGATCC	0.667													C|||	1791	0.357628	0.267	0.2853	5008	,	,		12166	0.5149		0.3469	False		,,,				2504	0.3804				p.A85T		Atlas-SNP	.											TPSB2,NS,carcinoma,0,1	TPSB2	8	1	0			c.G253A						scavenged	.						2.0	2.0	2.0					16																	1279438		1068	2864	3932			64499	exon4			TGAGGGCGGCCAG	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.1279438C>T		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	128	46	0.359375	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Missense_Mutation	SNP	ENST00000339687.6	37		.	.	.	.	.	.	.	.	.	.	C	3.062	-0.193122	0.06259	.	.	ENSG00000197253	ENST00000430512	D	0.88975	-2.45	3.7	-6.35	0.01975	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	2.192380	0.02106	N	0.054344	T	0.71719	0.3373	.	.	.	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.65286	-0.6205	8	0.13470	T	0.59	.	0.1285	0.00071	0.2587:0.2665:0.1762:0.2985	.	85	P20231	TRYB2_HUMAN	T	85	ENSP00000412409:A85T	ENSP00000412409:A85T	A	-	1	0	TPSB2	1219439	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.877000	0.00344	-1.596000	0.01611	-0.448000	0.05591	GCC	.	.	weak		0.667	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
FLG	2312	hgsc.bcm.edu	37	1	152280788	152280788	+	Missense_Mutation	SNP	T	T	G	rs66954353	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280788T>G	ENST00000368799.1	-	3	6609	c.6574A>C	c.(6574-6576)Aaa>Caa	p.K2192Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2192	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCATATGTTTTTCTGCTTGCA	0.532									Ichthyosis																												p.K2192Q		Atlas-SNP	.											.	FLG	900	.	0			c.A6574C						PASS	.	G	GLN/LYS	1049,3357		0,1049,1154	476.0	402.0	427.0		6574	2.0	0.0	1	dbSNP_130	427	819,7781		4,811,3485	yes	missense	FLG	NM_002016.1	53	4,1860,4639	GG,GT,TT		9.5233,23.8084,14.3626	benign	2192/4062	152280788	1868,11138	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATGTTTTTCTGCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6574A>C	1.37:g.152280788T>G	ENSP00000357789:p.Lys2192Gln	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	492	146	0.296748	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	
MKNK2	2872	hgsc.bcm.edu	37	19	2039727	2039727	+	Missense_Mutation	SNP	C	C	T	rs34475638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2039727C>T	ENST00000591601.1	-	13	1318	c.1283G>A	c.(1282-1284)cGa>cAa	p.R428Q	MKNK2_ENST00000541165.1_Missense_Mutation_p.R297Q|MKNK2_ENST00000250896.3_Missense_Mutation_p.R428Q|MKNK2_ENST00000591142.1_Intron|MKNK2_ENST00000309340.7_Intron			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	428			R -> Q (in dbSNP:rs34475638).		cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(3)|large_intestine(3)|lung(3)	10		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAGGTAGCTCGGACCAGGAC	0.701													C|||	54	0.0107827	0.0	0.0159	5008	,	,		12095	0.0		0.0338	False		,,,				2504	0.0092				p.R428Q		Atlas-SNP	.											.	MKNK2	56	.	0			c.G1283A						PASS	.	C	,GLN/ARG	17,4389	23.3+/-48.9	0,17,2186	34.0	32.0	32.0		,1283	2.5	1.0	19	dbSNP_126	32	211,8385	88.1+/-150.5	1,209,4088	yes	intron,missense	MKNK2	NM_017572.3,NM_199054.2	,43	1,226,6274	TT,TC,CC		2.4546,0.3858,1.7536	,benign	,428/466	2039727	228,12774	2203	4298	6501	SO:0001583	missense	2872	exon14			GTAGCTCGGACCA	AF125532	CCDS12079.1, CCDS12080.1	19p13.3	2012-12-20			ENSG00000099875	ENSG00000099875			7111	protein-coding gene	gene with protein product	"""Putative map kinase interacting kinase"""	605069	"""G protein-coupled receptor kinase 7"""	GPRK7		11013076	Standard	NM_199054		Approved	MNK2	uc002lus.2	Q9HBH9	OTTHUMG00000180020	ENST00000591601.1:c.1283G>A	19.37:g.2039727C>T	ENSP00000467811:p.Arg428Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	54	0.586957	NM_199054	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	37	CCDS12080.1	32	0.014652014652014652	0	0.0	6	0.016574585635359115	0	0.0	26	0.03430079155672823	C	14.79	2.639543	0.47153	0.003858	0.024546	ENSG00000099875	ENST00000250896;ENST00000541165;ENST00000545627	T;T	0.69561	-0.22;-0.41	3.53	2.49	0.30216	.	0.314966	0.28510	N	0.015098	T	0.19208	0.0461	L	0.29908	0.895	0.80722	D	1	B	0.31837	0.342	B	0.19946	0.027	T	0.11131	-1.0600	10	0.20046	T	0.44	-0.181	3.8162	0.08817	0.0:0.6509:0.0:0.3491	rs34475638	428	Q9HBH9	MKNK2_HUMAN	Q	428;297;368	ENSP00000250896:R428Q;ENSP00000438904:R297Q	ENSP00000250896:R428Q	R	-	2	0	MKNK2	1990727	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.700000	0.47085	1.980000	0.57719	0.561000	0.74099	CGA	C|0.985;T|0.015	0.015	strong		0.701	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054	
MUC16	94025	hgsc.bcm.edu	37	19	8982266	8982266	+	Silent	SNP	G	G	A	rs76124866	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8982266G>A	ENST00000397910.4	-	70	42212	c.42009C>T	c.(42007-42009)agC>agT	p.S14003S	MUC16_ENST00000380951.5_Silent_p.S644S	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	14028	SEA 13. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GACCTGGGCCGCTGAGGGGCT	0.617													g|||	82	0.0163738	0.0212	0.0072	5008	,	,		15276	0.0218		0.0159	False		,,,				2504	0.0112				p.S14003S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C42009T						PASS	.	G		92,4022		0,92,1965	62.0	66.0	65.0		42009	-7.8	0.0	19	dbSNP_132	65	197,8213		0,197,4008	no	coding-synonymous	MUC16	NM_024690.2		0,289,5973	AA,AG,GG		2.3424,2.2363,2.3076		14003/14508	8982266	289,12235	2057	4205	6262	SO:0001819	synonymous_variant	94025	exon70			TGGGCCGCTGAGG	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.42009C>T	19.37:g.8982266G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	35	0.016025641025641024	12	0.024390243902439025	5	0.013812154696132596	8	0.013986013986013986	10	0.013192612137203167	G	2.769	-0.256115	0.05829	0.022363	0.023424	ENSG00000181143	ENST00000542240	.	.	.	3.89	-7.78	0.01223	.	.	.	.	.	T	0.13884	0.0336	.	.	.	.	.	.	.	.	.	.	.	.	T	0.23655	-1.0182	3	.	.	.	.	7.8284	0.29328	0.301:0.4142:0.2848:0.0	.	.	.	.	V	843	.	.	A	-	2	0	MUC16	8843266	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.305000	0.00256	-2.148000	0.00798	-2.947000	0.00085	GCG	G|0.982;A|0.018	0.018	strong		0.617	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KDM5B	10765	hgsc.bcm.edu	37	1	202718202	202718202	+	Silent	SNP	G	G	A	rs1892164	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:202718202G>A	ENST00000367265.3	-	14	3051	c.1887C>T	c.(1885-1887)caC>caT	p.H629H	KDM5B_ENST00000367264.2_Silent_p.H665H	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	629					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						TCATCTCATCGTGGGAAAACA	0.418													G|||	2605	0.520168	0.2352	0.6715	5008	,	,		20534	0.5208		0.7425	False		,,,				2504	0.5685				p.H629H		Atlas-SNP	.											.	KDM5B	166	.	0			c.C1887T						PASS	.	G		1361,3045	451.6+/-349.7	217,927,1059	121.0	104.0	110.0		1887	-8.2	0.8	1	dbSNP_92	110	6422,2178	712.6+/-405.9	2414,1594,292	no	coding-synonymous	KDM5B	NM_006618.3		2631,2521,1351	AA,AG,GG		25.3256,30.8897,40.1584		629/1545	202718202	7783,5223	2203	4300	6503	SO:0001819	synonymous_variant	10765	exon14			CTCATCGTGGGAA	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.1887C>T	1.37:g.202718202G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_006618	O95811|Q15752|Q9Y3Q5	Silent	SNP	ENST00000367265.3	37	CCDS30974.1																																																																																			G|0.415;A|0.585	0.585	strong		0.418	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
GAN	8139	hgsc.bcm.edu	37	16	81398635	81398635	+	Silent	SNP	C	C	T	rs2608555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	71	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	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		
CDC27	996	hgsc.bcm.edu	37	17	45234386	45234386	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45234386G>T	ENST00000066544.3	-	7	828	c.735C>A	c.(733-735)gtC>gtA	p.V245V	CDC27_ENST00000527547.1_Silent_p.V245V|CDC27_ENST00000446365.2_Silent_p.V184V|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Silent_p.V245V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	245					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.V245V(9)		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						TTCCCAGTGGGACAGTATCAG	0.358																																					p.V245V		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,8	CDC27	337	8	9	Substitution - coding silent(9)	prostate(9)	c.C735A						scavenged	.						48.0	53.0	51.0					17																	45234386		2196	4292	6488	SO:0001819	synonymous_variant	996	exon7			CAGTGGGACAGTA	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.735C>A	17.37:g.45234386G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	7	0.12069	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			.	.	none		0.358	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
CD207	50489	hgsc.bcm.edu	37	2	71058184	71058184	+	Silent	SNP	C	C	T	rs13421115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	111	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	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	
WDR81	124997	hgsc.bcm.edu	37	17	1636934	1636934	+	Missense_Mutation	SNP	A	A	G	rs587780503|rs3809870	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1636934A>G	ENST00000409644.1	+	7	4603	c.4603A>G	c.(4603-4605)Atg>Gtg	p.M1535V	WDR81_ENST00000545662.1_Missense_Mutation_p.M166V|WDR81_ENST00000437219.2_Missense_Mutation_p.M332V|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Missense_Mutation_p.M484V|WDR81_ENST00000446363.1_Missense_Mutation_p.M174V|WDR81_ENST00000419248.1_Missense_Mutation_p.M308V	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1535			M -> V (in dbSNP:rs3809870). {ECO:0000269|PubMed:14702039}.		negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GGAGCCCACCATGCCCGGCAC	0.672													G|||	1397	0.278954	0.177	0.2219	5008	,	,		15718	0.4861		0.2744	False		,,,				2504	0.2485				p.M1535V		Atlas-SNP	.											.	WDR81	180	.	0			c.A4603G						PASS	.	G	VAL/MET,VAL/MET,VAL/MET,VAL/MET	804,3596		59,686,1455	31.0	37.0	35.0		1450,922,4603,994	-1.0	0.0	17	dbSNP_107	35	2261,6319		300,1661,2329	yes	missense,missense,missense,missense	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	21,21,21,21	359,2347,3784	GG,GA,AA		26.352,18.2727,23.6133	benign,benign,benign,benign	484/891,308/715,1535/1942,332/739	1636934	3065,9915	2200	4290	6490	SO:0001583	missense	124997	exon7			CCCACCATGCCCG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.4603A>G	17.37:g.1636934A>G	ENSP00000386609:p.Met1535Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	662	0.3031135531135531	87	0.17682926829268292	86	0.23756906077348067	283	0.49475524475524474	206	0.2717678100263852	G	0.001	-3.187157	0.00026	0.182727	0.26352	ENSG00000167716	ENST00000437219;ENST00000309182;ENST00000446363;ENST00000419248;ENST00000418841;ENST00000409644;ENST00000354680;ENST00000545662	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	4.26	-1.04	0.10068	.	1.449160	0.03756	N	0.257327	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.22452	-1.0216	9	0.13108	T	0.6	.	9.6648	0.39977	0.5735:0.0:0.4265:0.0	rs3809870;rs61272730	166;332;662;484	B7Z6V3;B7Z579;Q8TEL1;Q562E7	.;.;.;WDR81_HUMAN	V	332;484;174;308;120;1535;286;166	ENSP00000391074:M332V;ENSP00000312074:M484V;ENSP00000401560:M174V;ENSP00000407845:M308V;ENSP00000395198:M120V;ENSP00000386609:M1535V;ENSP00000442726:M166V	ENSP00000312074:M484V	M	+	1	0	WDR81	1583684	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-0.684000	0.05173	-0.539000	0.06273	-0.971000	0.02607	ATG	A|0.743;G|0.257	0.257	strong		0.672	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
MMEL1	79258	hgsc.bcm.edu	37	1	2560882	2560882	+	Silent	SNP	G	G	A	rs4648658	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:2560882G>A	ENST00000378412.3	-	2	203	c.42C>T	c.(40-42)gcC>gcT	p.A14A	MMEL1_ENST00000288709.6_Silent_p.A5A|MMEL1_ENST00000502556.1_Silent_p.A14A|MMEL1_ENST00000511099.1_5'Flank			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	14						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)		CTGCACGGCCGGCGCTCTCCA	0.711													-|||	2311	0.461462	0.2693	0.5101	5008	,	,		11458	0.4633		0.672	False		,,,				2504	0.4683				p.A14A		Atlas-SNP	.											.	MMEL1	64	.	0			c.C42T						PASS	.	G		1386,2372		292,802,785	11.0	12.0	12.0		42	-4.6	0.0	1	dbSNP_111	12	5087,2117		1849,1389,364	no	coding-synonymous	MMEL1	NM_033467.3		2141,2191,1149	AA,AG,GG		29.3865,36.8813,40.9506		14/780	2560882	6473,4489	1879	3602	5481	SO:0001819	synonymous_variant	79258	exon2			ACGGCCGGCGCTC	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.42C>T	1.37:g.2560882G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2																																																																																			G|0.473;A|0.527	0.527	strong		0.711	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240795	39240795	+	Missense_Mutation	SNP	A	A	T	rs541163988|rs553572799|rs9894966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39240795A>T	ENST00000391417.4	+	1	337	c.337A>T	c.(337-339)Agc>Tgc	p.S113C		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	138	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.S113C(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						ctgccgccccagctgctgccg	0.667																																					p.S113C		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,0,1	KRTAP4-7	49	1	3	Substitution - Missense(1)|Unknown(1)|Deletion - In frame(1)	NS(2)|prostate(1)	c.A337T						scavenged	.						13.0	14.0	14.0					17																	39240795		692	1589	2281	SO:0001583	missense	100132476	exon1			CGCCCCAGCTGCT	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.337A>T	17.37:g.39240795A>T	ENSP00000375236:p.Ser113Cys	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	63	11	0.174603	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	2.613	-0.290379	0.05568	.	.	ENSG00000240871	ENST00000391417	T	0.00640	6.03	2.73	1.42	0.22433	.	2.038930	0.02697	N	0.111300	T	0.00666	0.0022	.	.	.	0.20403	N	0.999909	B	0.09022	0.002	B	0.12837	0.008	T	0.46190	-0.9209	9	0.56958	D	0.05	.	3.0387	0.06130	0.5149:0.2451:0.0:0.24	rs9894966	168	Q9BYR0	KRA47_HUMAN	C	113	ENSP00000375236:S113C	ENSP00000375236:S113C	S	+	1	0	KRTAP4-7	36494321	0.000000	0.05858	0.056000	0.19401	0.021000	0.10359	-0.332000	0.07904	0.986000	0.38683	0.240000	0.17902	AGC	.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
TUBB8	347688	hgsc.bcm.edu	37	10	93816	93816	+	Silent	SNP	C	C	T	rs9329305	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:93816C>T	ENST00000309812.4	-	4	578	c.516G>A	c.(514-516)tcG>tcA	p.S172S	TUBB8_ENST00000332708.5_3'UTR|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.S100S	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	172					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)	p.S172S(1)		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)		ACACCTTGGGCGAGGGCAGGA	0.557													c|||	1442	0.287939	0.2973	0.2378	5008	,	,		29261	0.2163		0.3549	False		,,,				2504	0.316				p.S172S	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,NS,carcinoma,0,1	TUBB8	62	1	1	Substitution - coding silent(1)	stomach(1)	c.G516A						PASS	.	C		1120,3284		32,1056,1114	97.0	88.0	91.0		516		0.6	10	dbSNP_119	91	2730,5864		199,2332,1766	no	coding-synonymous	TUBB8	NM_177987.2		231,3388,2880	TT,TC,CC		31.7663,25.4314,29.6199		172/445	93816	3850,9148	2202	4297	6499	SO:0001819	synonymous_variant	347688	exon4			CTTGGGCGAGGGC	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.516G>A	10.37:g.93816C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			C|0.751;T|0.249	0.249	strong		0.557	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
NBEAL1	65065	hgsc.bcm.edu	37	2	204058557	204058557	+	Missense_Mutation	SNP	C	C	G	rs114408639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:204058557C>G	ENST00000449802.1	+	46	7207	c.6874C>G	c.(6874-6876)Cag>Gag	p.Q2292E		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2292										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AGAAGCAGTGCAGAAGCCAAC	0.348													C|||	8	0.00159744	0.0	0.0	5008	,	,		15075	0.0		0.006	False		,,,				2504	0.002				p.Q2292E		Atlas-SNP	.											.	NBEAL1	266	.	0			c.C6874G						PASS	.	C	GLU/GLN	3,3747		0,3,1872	156.0	155.0	155.0		6874	5.4	1.0	2	dbSNP_132	155	81,8123		0,81,4021	yes	missense	NBEAL1	NM_001114132.1	29	0,84,5893	GG,GC,CC		0.9873,0.08,0.7027	benign	2292/2695	204058557	84,11870	1875	4102	5977	SO:0001583	missense	65065	exon46			GCAGTGCAGAAGC	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6874C>G	2.37:g.204058557C>G	ENSP00000399903:p.Gln2292Glu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	13.17	2.158032	0.38119	8.0E-4	0.009873	ENSG00000144426	ENST00000449802;ENST00000414576	T;T	0.52526	0.66;1.25	5.43	5.43	0.79202	.	0.155623	0.40818	U	0.001008	T	0.34279	0.0892	L	0.54323	1.7	0.30447	N	0.775613	B	0.27450	0.179	B	0.27170	0.077	T	0.37979	-0.9682	10	0.27785	T	0.31	.	12.2442	0.54560	0.0:0.9212:0.0:0.0788	.	2292	Q6ZS30	NBEL1_HUMAN	E	2292;307	ENSP00000399903:Q2292E;ENSP00000388466:Q307E	ENSP00000388466:Q307E	Q	+	1	0	NBEAL1	203766802	1.000000	0.71417	0.957000	0.39632	0.991000	0.79684	4.345000	0.59360	2.550000	0.86006	0.650000	0.86243	CAG	C|0.997;G|0.003	0.003	strong		0.348	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
SPATA21	374955	hgsc.bcm.edu	37	1	16736132	16736132	+	Missense_Mutation	SNP	T	T	C	rs4661746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16736132T>C	ENST00000335496.1	-	6	1033	c.551A>G	c.(550-552)cAg>cGg	p.Q184R	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Missense_Mutation_p.Q161R	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	184			Q -> R (in dbSNP:rs4661746).				calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		CTCGCTGCTCTGGTGCAAGAG	0.682													t|||	765	0.152756	0.0159	0.1686	5008	,	,		14091	0.1726		0.3161	False		,,,				2504	0.138				p.Q184R		Atlas-SNP	.											.	SPATA21	47	.	0			c.A551G						PASS	.		ARG/GLN	282,4124	149.2+/-183.4	9,264,1930	27.0	27.0	27.0		551	-1.8	0.0	1	dbSNP_111	27	2822,5778	425.0+/-354.8	512,1798,1990	yes	missense	SPATA21	NM_198546.1	43	521,2062,3920	CC,CT,TT		32.814,6.4004,23.8659	benign	184/470	16736132	3104,9902	2203	4300	6503	SO:0001583	missense	374955	exon6			CTGCTCTGGTGCA		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.551A>G	1.37:g.16736132T>C	ENSP00000335612:p.Gln184Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	436	0.19963369963369965	14	0.028455284552845527	72	0.19889502762430938	115	0.20104895104895104	235	0.3100263852242744	t	8.622	0.891646	0.17613	0.064004	0.32814	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.65732	-0.17;-0.15	4.03	-1.76	0.08006	.	1.538070	0.03919	N	0.283261	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.26195	0.144;0.037	B;B	0.18871	0.023;0.01	T	0.15321	-1.0441	9	0.38643	T	0.18	0.1062	2.3344	0.04243	0.3824:0.2539:0.0:0.3636	rs4661746;rs17453182;rs52812478;rs58066662;rs4661746	161;184	F5GXP5;Q7Z572	.;SPT21_HUMAN	R	184;161	ENSP00000335612:Q184R;ENSP00000440046:Q161R	ENSP00000335612:Q184R	Q	-	2	0	SPATA21	16608719	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-0.374000	0.07484	-0.066000	0.12998	0.358000	0.22013	CAG	T|0.794;C|0.206	0.206	strong		0.682	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
ZFHX3	463	hgsc.bcm.edu	37	16	72993706	72993706	+	Silent	SNP	G	G	A	rs62053191	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72993706G>A	ENST00000268489.5	-	2	1011	c.339C>T	c.(337-339)gcC>gcT	p.A113A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	113					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CGGTGTCGCTGGCGCTCTCCT	0.672													G|||	137	0.0273562	0.0061	0.0303	5008	,	,		12816	0.002		0.0596	False		,,,				2504	0.047				p.A113A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C339T						PASS	.	G	,	72,4324		1,70,2127	22.0	23.0	23.0		,339	-0.8	1.0	16	dbSNP_129	23	584,8000		21,542,3729	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	22,612,5856	AA,AG,GG		6.8034,1.6379,5.0539	,	,113/3704	72993706	656,12324	2198	4292	6490	SO:0001819	synonymous_variant	463	exon2			GTCGCTGGCGCTC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.339C>T	16.37:g.72993706G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			G|0.958;A|0.042	0.042	strong		0.672	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
ABHD16B	140701	hgsc.bcm.edu	37	20	62493978	62493978	+	Missense_Mutation	SNP	G	G	A	rs74444574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62493978G>A	ENST00000369916.3	+	1	1413	c.1085G>A	c.(1084-1086)cGa>cAa	p.R362Q	TPD52L2_ENST00000351424.4_5'Flank|C20ORF135_ENST00000601296.1_5'Flank|TPD52L2_ENST00000346249.4_5'Flank|TPD52L2_ENST00000352482.4_5'Flank|TPD52L2_ENST00000348257.5_5'Flank|TPD52L2_ENST00000369927.4_5'Flank|TPD52L2_ENST00000358548.4_5'Flank|TPD52L2_ENST00000217121.5_5'Flank	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	362							hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						GTGATGGCGCGAGAGGGCCGC	0.721													G|||	327	0.0652955	0.0136	0.0548	5008	,	,		15021	0.129		0.0686	False		,,,				2504	0.0736				p.R362Q		Atlas-SNP	.											.	ABHD16B	22	.	0			c.G1085A						PASS	.	G	GLN/ARG	71,4183		0,71,2056	9.0	10.0	10.0		1085	0.3	0.0	20	dbSNP_131	10	540,7768		10,520,3624	no	missense	ABHD16B	NM_080622.3	43	10,591,5680	AA,AG,GG		6.4998,1.669,4.8639	possibly-damaging	362/470	62493978	611,11951	2127	4154	6281	SO:0001583	missense	140701	exon1			TGGCGCGAGAGGG		CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"""Abhydrolase domain containing"""	16128	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 135"""	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.1085G>A	20.37:g.62493978G>A	ENSP00000358932:p.Arg362Gln	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	10	9	0.9	NM_080622		Missense_Mutation	SNP	ENST00000369916.3	37	CCDS13539.1	154	0.07051282051282051	8	0.016260162601626018	20	0.055248618784530384	72	0.1258741258741259	54	0.0712401055408971	G	3.748	-0.052279	0.07362	0.01669	0.064998	ENSG00000183260	ENST00000369916	T	0.42900	0.96	5.04	0.338	0.15974	.	0.763543	0.12093	N	0.500210	T	0.00241	0.0007	N	0.14661	0.345	0.80722	P	0.0	B	0.15141	0.012	B	0.20184	0.028	T	0.19192	-1.0313	9	0.26408	T	0.33	-5.0558	5.9365	0.19169	0.1925:0.2996:0.5079:0.0	.	362	Q9H3Z7	ABHGB_HUMAN	Q	362	ENSP00000358932:R362Q	ENSP00000358932:R362Q	R	+	2	0	ABHD16B	61964422	0.001000	0.12720	0.005000	0.12908	0.000000	0.00434	0.916000	0.28651	0.177000	0.19895	-1.273000	0.01405	CGA	G|0.929;A|0.071	0.071	strong		0.721	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1		
GBP6	163351	hgsc.bcm.edu	37	1	89847444	89847444	+	Missense_Mutation	SNP	A	A	G	rs4658146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89847444A>G	ENST00000370456.4	+	7	1156	c.1063A>G	c.(1063-1065)Atg>Gtg	p.M355V	GBP6_ENST00000535065.1_Missense_Mutation_p.M225V	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	355			M -> V (in dbSNP:rs4658146). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		GCTGCTGGACATGCATGCGGC	0.542													G|||	4039	0.80651	0.91	0.8429	5008	,	,		19474	0.7252		0.7485	False		,,,				2504	0.7843				p.M355V		Atlas-SNP	.											.	GBP6	87	.	0			c.A1063G						PASS	.	G	VAL/MET	3878,528	241.5+/-251.9	1713,452,38	82.0	75.0	77.0		1063	-4.2	0.0	1	dbSNP_111	77	6411,2189	374.6+/-337.4	2383,1645,272	no	missense	GBP6	NM_198460.2	21	4096,2097,310	GG,GA,AA		25.4535,11.9837,20.8904	benign	355/634	89847444	10289,2717	2203	4300	6503	SO:0001583	missense	163351	exon7			CTGGACATGCATG	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.1063A>G	1.37:g.89847444A>G	ENSP00000359485:p.Met355Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	1729	0.7916666666666666	447	0.9085365853658537	300	0.8287292817679558	423	0.7395104895104895	559	0.737467018469657	G	0.003	-2.440817	0.00180	0.880163	0.745465	ENSG00000183347	ENST00000544311;ENST00000370456;ENST00000535065	T;T	0.01725	4.67;4.67	4.75	-4.25	0.03766	Guanylate-binding protein, C-terminal (3);	0.663590	0.13413	N	0.389733	T	0.00109	0.0003	N	0.00082	-2.215	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24870	-1.0148	9	0.05833	T	0.94	-1.8221	3.178	0.06575	0.2617:0.3887:0.2527:0.0969	rs4658146;rs17437204;rs52837666;rs58257431;rs4658146	355	Q6ZN66	GBP6_HUMAN	V	326;355;225	ENSP00000359485:M355V;ENSP00000442530:M225V	ENSP00000359485:M355V	M	+	1	0	GBP6	89620032	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-2.447000	0.01010	-0.835000	0.04234	-2.224000	0.00294	ATG	A|0.210;G|0.790	0.790	strong		0.542	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
GNB5	10681	hgsc.bcm.edu	37	15	52446260	52446260	+	Silent	SNP	C	C	T	rs35581121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52446260C>T	ENST00000261837.7	-	4	317	c.252G>A	c.(250-252)gcG>gcA	p.A84A	GNB5_ENST00000560116.1_Silent_p.A42A|GNB5_ENST00000396335.4_Silent_p.A42A|GNB5_ENST00000358784.7_Silent_p.A42A	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	84					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)		CCACCCGCTCCGCCACCTGGT	0.562													C|||	84	0.0167732	0.0008	0.0389	5008	,	,		18869	0.001		0.0378	False		,,,				2504	0.0174				p.A84A		Atlas-SNP	.											.	GNB5	28	.	0			c.G252A						PASS	.	C	,	36,4354	40.0+/-72.8	1,34,2160	79.0	67.0	71.0		126,252	-11.1	0.0	15	dbSNP_126	71	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,343,6140	TT,TC,CC		3.6921,0.82,2.7204	,	42/354,84/396	52446260	353,12623	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			CCGCTCCGCCACC	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.252G>A	15.37:g.52446260C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;T|0.027	0.027	strong		0.562	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
FRAS1	80144	hgsc.bcm.edu	37	4	79403682	79403682	+	Silent	SNP	C	C	T	rs41327848	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79403682C>T	ENST00000264895.6	+	58	9185	c.8745C>T	c.(8743-8745)ttC>ttT	p.F2915F		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2911	Calx-beta 4.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ATGACACATTCCAAGATGGTA	0.413													C|||	806	0.160942	0.3449	0.1383	5008	,	,		21952	0.005		0.1938	False		,,,				2504	0.0552				p.F2915F		Atlas-SNP	.											.	FRAS1	779	.	0			c.C8745T						PASS	.	C		1237,2561		207,823,869	115.0	114.0	114.0		8745	3.9	1.0	4	dbSNP_127	114	1749,6499		192,1365,2567	no	coding-synonymous	FRAS1	NM_025074.6		399,2188,3436	TT,TC,CC		21.2051,32.5698,24.7883		2915/4013	79403682	2986,9060	1899	4124	6023	SO:0001819	synonymous_variant	80144	exon58			CACATTCCAAGAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.8745C>T	4.37:g.79403682C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	374	0.17124542124542125	173	0.3516260162601626	54	0.14917127071823205	2	0.0034965034965034965	145	0.19129287598944592	C	9.445	1.089100	0.20390	0.325698	0.212051	ENSG00000138759	ENST00000512123	.	.	.	5.9	3.86	0.44501	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27123	-1.0083	3	.	.	.	.	12.2097	0.54373	0.0:0.7952:0.0:0.2048	rs56181015;rs56526896;rs57256258	.	.	.	S	1144	.	.	P	+	1	0	FRAS1	79622706	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.199000	0.32235	1.503000	0.48686	0.585000	0.79938	CCA	C|0.828;T|0.172	0.172	strong		0.413	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPATA4	132851	hgsc.bcm.edu	37	4	177113836	177113836	+	Silent	SNP	C	C	T	rs6832177	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	160	0	0		WXS	Illumina HiSeq	Phase_I	205	82	0.4	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	
UMODL1	89766	hgsc.bcm.edu	37	21	43531085	43531085	+	Missense_Mutation	SNP	A	A	T	rs139776068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43531085A>T	ENST00000408910.2	+	11	1753	c.1753A>T	c.(1753-1755)Aac>Tac	p.N585Y	UMODL1_ENST00000400427.1_Missense_Mutation_p.N513Y|UMODL1_ENST00000400424.2_Missense_Mutation_p.N513Y|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000408989.2_Missense_Mutation_p.N585Y	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	585					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						CGGCCTAGAGAACTTCACCTT	0.662													A|||	27	0.00539137	0.0197	0.0014	5008	,	,		15612	0.0		0.0	False		,,,				2504	0.0				p.N585Y	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.A1753T						PASS	.	A	TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN	72,4004		0,72,1966	30.0	38.0	35.0		1753,1537,1537,1753	2.6	0.2	21	dbSNP_134	35	0,8368		0,0,4184	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	143,143,143,143	0,72,6150	TT,TA,AA		0.0,1.7664,0.5786	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	585/1319,513/1375,513/1247,585/1447	43531085	72,12372	2038	4184	6222	SO:0001583	missense	89766	exon11			CTAGAGAACTTCA		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.1753A>T	21.37:g.43531085A>T	ENSP00000386147:p.Asn585Tyr	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	193	94	0.487047	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	A	12.14	1.849160	0.32699	0.017664	0.0	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.72167	-0.63;-0.61;-0.63;-0.61	3.83	2.64	0.31445	.	0.534882	0.15278	N	0.270826	T	0.39572	0.1083	N	0.19112	0.55	0.21527	N	0.999656	D;P	0.64830	0.994;0.947	P;P	0.56751	0.805;0.453	T	0.43294	-0.9400	10	0.87932	D	0	-7.3138	3.9168	0.09227	0.6689:0.2198:0.1113:0.0	.	585;585	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	Y	513;513;585;585	ENSP00000383279:N513Y;ENSP00000383276:N513Y;ENSP00000386126:N585Y;ENSP00000386147:N585Y	ENSP00000383276:N513Y	N	+	1	0	UMODL1	42404154	0.482000	0.25948	0.191000	0.23289	0.007000	0.05969	0.802000	0.27069	0.780000	0.33566	0.533000	0.62120	AAC	A|0.992;T|0.008	0.008	strong		0.662	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
MPHOSPH9	10198	hgsc.bcm.edu	37	12	123645803	123645803	+	Silent	SNP	G	G	A	rs1051431	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:123645803G>A	ENST00000606320.1	-	22	3467	c.3261C>T	c.(3259-3261)taC>taT	p.Y1087Y	MPHOSPH9_ENST00000541076.2_Silent_p.Y1057Y|MPHOSPH9_ENST00000302349.5_Silent_p.Y935Y|MPHOSPH9_ENST00000392425.3_Silent_p.Y935Y			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	1087						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		TACACTGTTCGTAGCTAACTG	0.418													A|||	3171	0.633187	0.1415	0.7262	5008	,	,		16679	0.9772		0.7684	False		,,,				2504	0.7382				p.Y935Y		Atlas-SNP	.											.	MPHOSPH9	75	.	0			c.C2805T						PASS	.	A		1126,3280	717.2+/-408.7	142,842,1219	137.0	124.0	128.0		2805	-1.5	0.0	12	dbSNP_86	128	6757,1843	329.9+/-319.0	2637,1483,180	no	coding-synonymous	MPHOSPH9	NM_022782.2		2779,2325,1399	AA,AG,GG		21.4302,25.5561,39.3895		935/1032	123645803	7883,5123	2203	4300	6503	SO:0001819	synonymous_variant	10198	exon18			CTGTTCGTAGCTA	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.3261C>T	12.37:g.123645803G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Silent	SNP	ENST00000606320.1	37																																																																																				G|0.376;A|0.624	0.624	strong		0.418	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2		
CYB5R2	51700	hgsc.bcm.edu	37	11	7687715	7687715	+	Missense_Mutation	SNP	T	T	C	rs12801394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7687715T>C	ENST00000533558.1	-	8	1181	c.625A>G	c.(625-627)Aac>Gac	p.N209D	CYB5R2_ENST00000299498.6_Missense_Mutation_p.N209D|CYB5R2_ENST00000299497.9_Missense_Mutation_p.N209D|CYB5R2_ENST00000524790.1_Missense_Mutation_p.N209D|CYB5R2_ENST00000528585.1_Intron			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	129	0	0	643	WXS	Illumina HiSeq	Phase_I	137	63	0.459854	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	
APOB	338	hgsc.bcm.edu	37	2	21263900	21263900	+	Missense_Mutation	SNP	G	G	A	rs1367117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:21263900G>A	ENST00000233242.1	-	4	420	c.293C>T	c.(292-294)aCc>aTc	p.T98I	APOB_ENST00000399256.4_Missense_Mutation_p.T98I	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	98	Heparin-binding.|Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		T -> I (polymorphism that influences plasma concentrations of low density lipoprotein cholesterol; dbSNP:rs1367117). {ECO:0000269|PubMed:12551903, ECO:0000269|PubMed:20686565, ECO:0000269|PubMed:2115173, ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:3461454, ECO:0000269|PubMed:3759943}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.T98I(1)		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)					CTCTTTCAGGGTGCACTGGCT	0.507													G|||	848	0.169329	0.0779	0.2867	5008	,	,		20685	0.1151		0.2982	False		,,,				2504	0.1329				p.T98I		Atlas-SNP	.											APOB,NS,carcinoma,0,1	APOB	761	1	1	Substitution - Missense(1)	stomach(1)	c.C293T	GRCh37	CM020623	APOB	M	rs1367117	PASS	.	G	ILE/THR	559,3847	249.6+/-257.0	30,499,1674	67.0	61.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	293	2.9	1.0	2	dbSNP_88	63	2699,5901	432.4+/-357.1	448,1803,2049	yes	missense	APOB	NM_000384.2	89	478,2302,3723	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	31.3837,12.6872,25.05	benign	98/4564	21263900	3258,9748	2203	4300	6503	SO:0001583	missense	338	exon4			TTCAGGGTGCACT	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.293C>T	2.37:g.21263900G>A	ENSP00000233242:p.Thr98Ile	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	449	0.20558608058608058	48	0.0975609756097561	113	0.31215469613259667	70	0.12237762237762238	218	0.287598944591029	G	16.00	2.999255	0.54147	0.126872	0.313837	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.41400	1.0;1.0	4.86	2.93	0.34026	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.480621	0.19028	N	0.124629	T	0.00012	0.0000	M	0.69823	2.125	0.35685	P	0.18562900000000004	B	0.25390	0.125	B	0.28011	0.085	T	0.14839	-1.0458	9	0.48119	T	0.1	.	7.7562	0.28925	0.0942:0.3059:0.5999:0.0	rs1367117;rs17246849;rs57336814;rs1367117	98	P04114	APOB_HUMAN	I	98	ENSP00000233242:T98I;ENSP00000382200:T98I	ENSP00000233242:T98I	T	-	2	0	APOB	21117405	0.983000	0.35010	0.958000	0.39756	0.991000	0.79684	2.809000	0.47971	0.493000	0.27837	0.655000	0.94253	ACC	G|0.784;A|0.216	0.216	strong		0.507	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
SLAMF1	6504	hgsc.bcm.edu	37	1	160616703	160616703	+	Missense_Mutation	SNP	G	G	T	rs2295612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160616703G>T	ENST00000302035.6	-	1	382	c.33C>A	c.(31-33)ttC>ttA	p.F11L	SLAMF1_ENST00000355199.3_Missense_Mutation_p.F11L|SLAMF1_ENST00000538290.1_Missense_Mutation_p.F11L|SLAMF1_ENST00000235739.5_Missense_Mutation_p.F11L	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	11			F -> L (in dbSNP:rs2295612).		lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.F11F(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GAAACAGCACGAAGGTCAAGG	0.567													G|||	493	0.0984425	0.0061	0.2075	5008	,	,		19271	0.0347		0.2167	False		,,,				2504	0.09				p.F11L		Atlas-SNP	.											SLAMF1,colon,carcinoma,0,1	SLAMF1	74	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C33A						PASS	.	G	LEU/PHE	158,4248	105.6+/-144.1	3,152,2048	68.0	62.0	64.0		33	0.8	0.0	1	dbSNP_100	64	1748,6852	308.2+/-308.8	190,1368,2742	yes	missense	SLAMF1	NM_003037.2	22	193,1520,4790	TT,TG,GG		20.3256,3.586,14.6548	benign	11/336	160616703	1906,11100	2203	4300	6503	SO:0001583	missense	6504	exon1			CAGCACGAAGGTC	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10903	protein-coding gene	gene with protein product		603492	"""signaling lymphocytic activation molecule"""	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.33C>A	1.37:g.160616703G>T	ENSP00000306190:p.Phe11Leu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	167	75	0.449102	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	267	0.12225274725274725	6	0.012195121951219513	77	0.212707182320442	18	0.03146853146853147	166	0.21899736147757257	G	0.031	-1.336977	0.01287	0.03586	0.203256	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000392208;ENST00000538290;ENST00000355199	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	3.84	0.793	0.18632	Signaling lymphocytic activation molecule, N-terminal (2);	1.960650	0.02772	N	0.119850	T	0.07548	0.0190	N	0.20685	0.6	0.80722	P	0.0	B;B	0.12630	0.006;0.002	B;B	0.14023	0.01;0.006	T	0.07539	-1.0767	9	0.05833	T	0.94	-13.3109	5.3222	0.15887	0.2009:0.0:0.632:0.1672	rs2295612;rs58261892;rs2295612	11;11	B4E2E4;Q13291	.;SLAF1_HUMAN	L	11	ENSP00000306190:F11L;ENSP00000235739:F11L;ENSP00000438406:F11L;ENSP00000347333:F11L	ENSP00000235739:F11L	F	-	3	2	SLAMF1	158883327	0.062000	0.20869	0.006000	0.13384	0.001000	0.01503	-0.151000	0.10175	-0.038000	0.13624	-1.119000	0.02030	TTC	G|0.877;T|0.123	0.123	strong		0.567	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1		
PRSS3	5646	hgsc.bcm.edu	37	9	33798052	33798052	+	Silent	SNP	C	C	T	rs377380263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33798052C>T	ENST00000361005.5	+	3	597	c.597C>T	c.(595-597)tcC>tcT	p.S199S	PRSS3_ENST00000379405.3_Silent_p.S142S|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000429677.3_Silent_p.S135S|PRSS3_ENST00000342836.4_Silent_p.S156S	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	199	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.S142S(2)|p.S199S(1)		large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			GCCTCATCTCCGGCTGGGGCA	0.567													c|||	2	0.000399361	0.0	0.0	5008	,	,		20608	0.0		0.002	False		,,,				2504	0.0				p.S199S		Atlas-SNP	.											PRSS3_ENST00000361005,NS,carcinoma,0,3	PRSS3	79	3	3	Substitution - coding silent(3)	pancreas(2)|upper_aerodigestive_tract(1)	c.C597T						scavenged	.						144.0	118.0	127.0					9																	33798052		2203	4300	6503	SO:0001819	synonymous_variant	5646	exon3			CATCTCCGGCTGG		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.597C>T	9.37:g.33798052C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	129	6	0.0465116	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Silent	SNP	ENST00000361005.5	37	CCDS47958.1																																																																																			.	.	weak		0.567	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
B4GALNT3	283358	hgsc.bcm.edu	37	12	662412	662412	+	Missense_Mutation	SNP	G	G	C	rs35419938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:662412G>C	ENST00000266383.5	+	14	1336	c.1323G>C	c.(1321-1323)gaG>gaC	p.E441D		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	441					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TGGCAGAGGAGACCCCTGCCT	0.517													G|||	26	0.00519169	0.0015	0.0029	5008	,	,		18370	0.0		0.005	False		,,,				2504	0.0174				p.E441D		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G1323C						PASS	.	G	ASP/GLU	10,4396	16.8+/-37.8	0,10,2193	75.0	85.0	82.0		1323	1.8	1.0	12	dbSNP_126	82	67,8533	40.3+/-97.0	0,67,4233	yes	missense	B4GALNT3	NM_173593.3	45	0,77,6426	CC,CG,GG		0.7791,0.227,0.592	benign	441/999	662412	77,12929	2203	4300	6503	SO:0001583	missense	283358	exon14			AGAGGAGACCCCT	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1323G>C	12.37:g.662412G>C	ENSP00000266383:p.Glu441Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	10.18	1.278940	0.23307	0.00227	0.007791	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.33438	3.47;1.41	5.43	1.79	0.24919	.	0.513490	0.22886	N	0.054444	T	0.10981	0.0268	N	0.21448	0.665	0.34393	D	0.694362	B;B	0.21606	0.058;0.001	B;B	0.17098	0.017;0.001	T	0.19679	-1.0298	10	0.18276	T	0.48	-22.7032	4.7555	0.13082	0.2545:0.172:0.5735:0.0	rs35419938	344;441	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	D	441;344	ENSP00000266383:E441D;ENSP00000322953:E344D	ENSP00000266383:E441D	E	+	3	2	B4GALNT3	532673	0.002000	0.14202	0.953000	0.39169	0.426000	0.31534	-0.238000	0.08977	0.130000	0.18549	0.650000	0.86243	GAG	G|0.995;C|0.005	0.005	strong		0.517	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
HRNR	388697	hgsc.bcm.edu	37	1	152192555	152192555	+	Missense_Mutation	SNP	T	T	C	rs41266134	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152192555T>C	ENST00000368801.2	-	3	1625	c.1550A>G	c.(1549-1551)tAt>tGt	p.Y517C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	517			Y -> C (in dbSNP:rs41266134).		establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGCTGACCATAGCTGGAAGA	0.582													T|||	1464	0.292332	0.0242	0.3905	5008	,	,		23145	0.5962		0.1412	False		,,,				2504	0.4274				p.Y517C		Atlas-SNP	.											.	HRNR	403	.	0			c.A1550G						PASS	.	T	CYS/TYR	206,4200	126.6+/-163.6	3,200,2000	260.0	249.0	253.0		1550	-6.0	0.0	1	dbSNP_127	253	1241,7359	249.2+/-276.5	96,1049,3155	yes	missense	HRNR	NM_001009931.1	194	99,1249,5155	CC,CT,TT		14.4302,4.6754,11.1256	benign	517/2851	152192555	1447,11559	2203	4300	6503	SO:0001583	missense	388697	exon3			TGACCATAGCTGG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1550A>G	1.37:g.152192555T>C	ENSP00000357791:p.Tyr517Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	582	0.2664835164835165	13	0.026422764227642278	119	0.3287292817679558	338	0.5909090909090909	112	0.14775725593667546	T	2.829	-0.243134	0.05906	0.046754	0.144302	ENSG00000197915	ENST00000368801	T	0.01725	4.67	3.01	-6.02	0.02192	.	.	.	.	.	T	0.00300	0.0009	N	0.14661	0.345	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.46952	-0.9154	8	0.38643	T	0.18	.	0.3516	0.00350	0.3025:0.2331:0.2662:0.1982	rs41266134	517	Q86YZ3	HORN_HUMAN	C	517	ENSP00000357791:Y517C	ENSP00000357791:Y517C	Y	-	2	0	HRNR	150459179	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-6.023000	0.00085	-1.875000	0.01132	-0.515000	0.04445	TAT	T|0.836;C|0.164	0.164	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
SOWAHD	347454	hgsc.bcm.edu	37	X	118893054	118893054	+	Silent	SNP	C	C	A	rs2782223	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:118893054C>A	ENST00000343905.3	+	1	479	c.424C>A	c.(424-426)Cgg>Agg	p.R142R		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	142																	GCTGCTGCTGCGGGGCGACCC	0.692													c|||	2308	0.611391	0.4743	0.487	3775	,	,		10375	0.374		0.495	False		,,,				2504	0.4785				p.R142R		Atlas-SNP	.											.	.	.	.	0			c.C424A						PASS	.			2517,1128		803,578,333,178,194	5.0	8.0	7.0		424	1.9	1.0	X	dbSNP_100	7	4207,2293		1031,1011,1134,344,594	no	coding-synonymous	ANKRD58	NM_001105576.2		1834,1589,1467,522,788	AA,AC,A,CC,C		35.2769,30.9465,33.721		142/316	118893054	6724,3421	2086	4114	6200	SO:0001819	synonymous_variant	347454	exon1			CTGCTGCGGGGCG		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.424C>A	X.37:g.118893054C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	NM_001105576		Silent	SNP	ENST00000343905.3	37	CCDS43984.1																																																																																			C|0.399;A|0.601	0.601	strong		0.692	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576	
OSER1	51526	hgsc.bcm.edu	37	20	42826379	42826379	+	Splice_Site	SNP	C	C	T	rs11274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	27	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	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
B3GNT6	192134	hgsc.bcm.edu	37	11	76751608	76751608	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76751608C>T	ENST00000533140.1	+	2	1151	c.1013C>T	c.(1012-1014)cCt>cTt	p.P338L	B3GNT6_ENST00000354301.5_Missense_Mutation_p.P337L|B3GNT6_ENST00000421061.1_Missense_Mutation_p.P216L			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	357					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						TGCAGCTTGCCTGGCGCACAG	0.667																																					p.P337L		Atlas-SNP	.											.	B3GNT6	27	.	0			c.C1010T						PASS	.						12.0	12.0	12.0					11																	76751608		2111	4199	6310	SO:0001583	missense	192134	exon5			GCTTGCCTGGCGC	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"""Beta 3-glycosyltransferases"""	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.1013C>T	11.37:g.76751608C>T	ENSP00000435352:p.Pro338Leu	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	37	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586243	0.66105	.	.	ENSG00000198488	ENST00000533140;ENST00000354301;ENST00000421061	T;T;T	0.60672	1.5;0.17;2.66	2.9	2.9	0.33743	.	0.066129	0.64402	U	0.000007	T	0.76248	0.3961	M	0.86502	2.82	0.52501	D	0.999958	D	0.89917	1.0	D	0.97110	1.0	T	0.79522	-0.1769	10	0.51188	T	0.08	.	12.0142	0.53305	0.0:1.0:0.0:0.0	.	337	Q6ZMB0	B3GN6_HUMAN	L	338;337;216	ENSP00000435352:P338L;ENSP00000346256:P337L;ENSP00000403463:P216L	ENSP00000346256:P337L	P	+	2	0	B3GNT6	76429256	0.000000	0.05858	0.920000	0.36463	0.642000	0.38348	0.234000	0.17930	1.908000	0.55244	0.462000	0.41574	CCT	.	.	none		0.667	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706	
USP33	23032	hgsc.bcm.edu	37	1	78163080	78163080	+	Silent	SNP	C	C	T	rs34351666	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:78163080C>T	ENST00000370793.1	-	25	3097	c.2751G>A	c.(2749-2751)ctG>ctA	p.L917L	USP33_ENST00000357428.1_Silent_p.L917L|USP33_ENST00000370794.3_Silent_p.L886L	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	917	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				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						CCGGAGGTCGCAGGATAACTT	0.383													T|||	264	0.0527157	0.1278	0.049	5008	,	,		15421	0.0		0.0427	False		,,,				2504	0.0184				p.L917L	Melanoma(152;72 1870 11110 26780 42647)	Atlas-SNP	.											.	USP33	87	.	0			c.G2751A						PASS	.	T	,	454,3952	784.0+/-414.7	29,396,1778	105.0	110.0	108.0		2751,2658	-10.5	0.0	1	dbSNP_126	108	278,8322	807.0+/-407.2	8,262,4030	no	coding-synonymous,coding-synonymous	USP33	NM_015017.3,NM_201624.1	,	37,658,5808	TT,TC,CC		3.2326,10.3041,5.6282	,	917/943,886/912	78163080	732,12274	2203	4300	6503	SO:0001819	synonymous_variant	23032	exon25			AGGTCGCAGGATA	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.2751G>A	1.37:g.78163080C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	225	101	0.448889	NM_015017	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1																																																																																			C|0.947;T|0.053	0.053	strong		0.383	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017	
MRPL35	51318	hgsc.bcm.edu	37	2	86433240	86433240	+	Missense_Mutation	SNP	C	C	T	rs10901	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:86433240C>T	ENST00000337109.4	+	2	89	c.55C>T	c.(55-57)Ccc>Tcc	p.P19S	MRPL35_ENST00000605125.1_Missense_Mutation_p.P19S|MRPL35_ENST00000409180.1_Missense_Mutation_p.P19S|MRPL35_ENST00000254644.8_Missense_Mutation_p.P19S	NM_016622.3	NP_057706.2	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35	19			P -> S (in dbSNP:rs12714176). {ECO:0000269|PubMed:15489334}.		translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)	p.P19S(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(2)	14						AATCCTACGGCCCCTGAATAT	0.378													C|||	1225	0.244609	0.0552	0.2781	5008	,	,		17596	0.121		0.4751	False		,,,				2504	0.3671				p.P19S		Atlas-SNP	.											MRPL35,NS,adenoma,0,2	MRPL35	23	2	1	Substitution - Missense(1)	stomach(1)	c.C55T						scavenged	.	C	SER/PRO,SER/PRO	497,3909	231.0+/-245.0	30,437,1736	141.0	139.0	140.0		55,55	4.7	1.0	2	dbSNP_52	140	4343,4257	580.4+/-391.0	1090,2163,1047	yes	missense,missense	MRPL35	NM_016622.3,NM_145644.2	74,74	1120,2600,2783	TT,TC,CC		49.5,11.2801,37.2136	probably-damaging,probably-damaging	19/189,19/171	86433240	4840,8166	2203	4300	6503	SO:0001583	missense	51318	exon2			CTACGGCCCCTGA	AF208849	CCDS1987.1, CCDS1988.1	2p11.2	2012-09-13			ENSG00000132313	ENSG00000132313		"""Mitochondrial ribosomal proteins / large subunits"""	14489	protein-coding gene	gene with protein product		611841				11042152, 11551941	Standard	NM_016622		Approved		uc002srg.4	Q9NZE8	OTTHUMG00000037385	ENST00000337109.4:c.55C>T	2.37:g.86433240C>T	ENSP00000338389:p.Pro19Ser	Somatic	412	4	0.00970874		WXS	Illumina HiSeq	Phase_I	380	190	0.5	NM_016622	A6NKV6|B2RB93|Q658U7|Q8WWA2	Missense_Mutation	SNP	ENST00000337109.4	37	CCDS1988.1	571	0.26144688644688646	30	0.06097560975609756	121	0.3342541436464088	69	0.12062937062937062	351	0.4630606860158311	C	15.36	2.809597	0.50421	0.112801	0.505	ENSG00000132313	ENST00000254644;ENST00000337109;ENST00000409180	T;T;T	0.18174	2.24;2.65;2.23	5.62	4.74	0.60224	.	0.096882	0.64402	N	0.000001	T	0.00012	0.0000	M	0.75264	2.295	0.27111	P	0.9623878	B	0.27882	0.192	B	0.21151	0.033	T	0.43081	-0.9413	9	0.26408	T	0.33	-10.0043	10.6449	0.45615	0.0:0.912:0.0:0.088	rs12714176;rs17845611;rs17858541;rs52836017;rs57050204;rs12714176	19	Q9NZE8	RM35_HUMAN	S	19	ENSP00000254644:P19S;ENSP00000338389:P19S;ENSP00000386255:P19S	ENSP00000254644:P19S	P	+	1	0	MRPL35	86286751	0.330000	0.24705	0.987000	0.45799	0.922000	0.55478	2.399000	0.44495	1.527000	0.49086	0.650000	0.86243	CCC	T|0.269;G|0.143	0.269	strong		0.378	MRPL35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091002.2	NM_016622	
NIN	51199	hgsc.bcm.edu	37	14	51192659	51192659	+	Silent	SNP	G	G	A	rs1983764	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:51192659G>A	ENST00000382041.3	-	30	6394	c.6204C>T	c.(6202-6204)ccC>ccT	p.P2068P	RP11-248J18.3_ENST00000602615.1_RNA|NIN_ENST00000245441.5_Intron|NIN_ENST00000530997.2_Intron|NIN_ENST00000382043.4_Silent_p.P1355P|NIN_ENST00000389868.3_Intron|NIN_ENST00000324330.9_3'UTR	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	2068					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					AGAGATGACCGGGTAGGCTCA	0.398			T	PDGFRB	MPD								G|||	1225	0.244609	0.0303	0.2507	5008	,	,		20594	0.2966		0.3469	False		,,,				2504	0.3712				p.P2068P		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C6204T						PASS	.	G	,,	384,4022	195.7+/-220.2	17,350,1836	233.0	203.0	213.0		4065,,6204	-4.4	0.0	14	dbSNP_92	213	3053,5547	470.4+/-367.8	530,1993,1777	no	coding-synonymous,intron,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182946.1	,,	547,2343,3613	AA,AG,GG		35.5,8.7154,26.4263	,,	1355/1378,,2068/2091	51192659	3437,9569	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon30			ATGACCGGGTAGG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.6204C>T	14.37:g.51192659G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	232	232	1	NM_182946	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	564	0.25824175824175827	24	0.04878048780487805	86	0.23756906077348067	183	0.31993006993006995	271	0.3575197889182058	G	6.376	0.437532	0.12104	0.087154	0.355	ENSG00000100503	ENST00000389869	.	.	.	5.93	-4.4	0.03600	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44298	-0.9337	3	.	.	.	.	1.1314	0.01746	0.3536:0.2034:0.297:0.146	rs1983764;rs52794699;rs59283049;rs1983764	.	.	.	W	1559	.	.	R	-	1	2	NIN	50262409	0.000000	0.05858	0.001000	0.08648	0.213000	0.24496	-1.297000	0.02759	-1.103000	0.03019	-1.004000	0.02495	CGG	G|0.744;A|0.256	0.256	strong		0.398	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
ALMS1	7840	hgsc.bcm.edu	37	2	73828453	73828453	+	Missense_Mutation	SNP	C	C	T	rs200897773		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:73828453C>T	ENST00000264448.6	+	19	12112	c.12001C>T	c.(12001-12003)Cgg>Tgg	p.R4001W	ALMS1_ENST00000409009.1_Missense_Mutation_p.R3959W|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4001					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						GGAGCCACTGCGGGAGCAGAA	0.587																																					p.R4001W		Atlas-SNP	.											.	ALMS1	384	.	0			c.C12001T						PASS	.	C	TRP/ARG	1,4369		0,1,2184	74.0	85.0	81.0		12001	4.3	1.0	2		81	3,8579		0,3,4288	yes	missense	ALMS1	NM_015120.4	101	0,4,6472	TT,TC,CC		0.035,0.0229,0.0309	probably-damaging	4001/4168	73828453	4,12948	2185	4291	6476	SO:0001583	missense	7840	exon19			CCACTGCGGGAGC	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.12001C>T	2.37:g.73828453C>T	ENSP00000264448:p.Arg4001Trp	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	232	115	0.49569	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.112605	0.77210	2.29E-4	3.5E-4	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.09538	2.97;2.97	5.17	4.27	0.50696	.	0.000000	0.52532	D	0.000072	T	0.23410	0.0566	L	0.46157	1.445	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.65010	0.922;0.931	T	0.00780	-1.1569	10	0.87932	D	0	.	12.4318	0.55578	0.1748:0.8252:0.0:0.0	.	3959;4001	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	W	3959;4001	ENSP00000386627:R3959W;ENSP00000264448:R4001W	ENSP00000264448:R4001W	R	+	1	2	ALMS1	73681961	0.699000	0.27786	0.995000	0.50966	0.986000	0.74619	1.262000	0.32992	1.359000	0.45940	0.561000	0.74099	CGG	.	.	weak		0.587	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
PCSK5	5125	hgsc.bcm.edu	37	9	78506187	78506187	+	Silent	SNP	T	T	C	rs7040769	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:78506187T>C	ENST00000545128.1	+	1	628	c.90T>C	c.(88-90)tgT>tgC	p.C30C	PCSK5_ENST00000376767.3_Silent_p.C30C|PCSK5_ENST00000376752.4_Silent_p.C30C	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	30					anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						TCCCCGTGTGTCGGACGCGCG	0.672													C|||	962	0.192093	0.525	0.1124	5008	,	,		12372	0.0		0.1441	False		,,,				2504	0.046				p.C30C		Atlas-SNP	.											.	PCSK5	329	.	0			c.T90C						PASS	.	C	,	2039,2365	580.3+/-385.1	491,1057,654	43.0	52.0	49.0		90,90	3.9	1.0	9	dbSNP_116	49	1231,7369	738.2+/-407.0	86,1059,3155	no	coding-synonymous,coding-synonymous	PCSK5	NM_001190482.1,NM_006200.3	,	577,2116,3809	CC,CT,TT		14.314,46.2988,25.1461	,	30/1861,30/914	78506187	3270,9734	2202	4300	6502	SO:0001819	synonymous_variant	5125	exon1			CGTGTGTCGGACG		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.90T>C	9.37:g.78506187T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			T|0.760;C|0.240	0.240	strong		0.672	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TRANK1	9881	hgsc.bcm.edu	37	3	36897812	36897812	+	Missense_Mutation	SNP	T	T	C	rs11712950	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:36897812T>C	ENST00000429976.2	-	12	3516	c.3269A>G	c.(3268-3270)gAg>gGg	p.E1090G	TRANK1_ENST00000428977.2_Missense_Mutation_p.E540G|TRANK1_ENST00000301807.6_Missense_Mutation_p.E540G	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1090	Glu-rich.		E -> G (in dbSNP:rs11712950). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9205841}.				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						ctcttcctcctcctcttcctc	0.542													T|||	1407	0.28095	0.093	0.2493	5008	,	,		21575	0.5595		0.2604	False		,,,				2504	0.2914				p.E1090G		Atlas-SNP	.											.	TRANK1	398	.	0			c.A3269G						PASS	.	T	GLY/GLU	455,3557		34,387,1585	20.0	22.0	21.0		3269	-0.3	0.0	3	dbSNP_120	21	2044,6258		282,1480,2389	yes	missense	TRANK1	NM_014831.2	98	316,1867,3974	CC,CT,TT		24.6206,11.341,20.294	benign	1090/2926	36897812	2499,9815	2006	4151	6157	SO:0001583	missense	9881	exon12			TCCTCCTCCTCTT	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.3269A>G	3.37:g.36897812T>C	ENSP00000416168:p.Glu1090Gly	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	667	0.30540293040293043	52	0.10569105691056911	92	0.2541436464088398	325	0.5681818181818182	198	0.2612137203166227	T	3.277	-0.147776	0.06627	0.11341	0.246206	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.33216	1.42;1.83;1.42	3.61	-0.286	0.12862	.	0.450703	0.20184	N	0.097443	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22851	0.076	B	0.15870	0.014	T	0.42137	-0.9469	9	0.23891	T	0.37	.	3.2031	0.06656	0.2737:0.2456:0.0:0.4807	rs11712950;rs52808513;rs11712950	1090	O15050	TRNK1_HUMAN	G	540;1090;540	ENSP00000416826:E540G;ENSP00000416168:E1090G;ENSP00000301807:E540G	ENSP00000301807:E540G	E	-	2	0	TRANK1	36872816	0.000000	0.05858	0.000000	0.03702	0.742000	0.42306	0.007000	0.13174	-0.248000	0.09583	0.402000	0.26972	GAG	T|0.690;C|0.310	0.310	strong		0.542	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
WDFY4	57705	hgsc.bcm.edu	37	10	50038878	50038878	+	Missense_Mutation	SNP	G	G	C	rs41283281	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50038878G>C	ENST00000325239.5	+	37	6501	c.6474G>C	c.(6472-6474)gaG>gaC	p.E2158D	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2158						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						AGATTGAAGAGGTCACACCGC	0.557													G|||	169	0.033746	0.0212	0.0461	5008	,	,		21721	0.001		0.0855	False		,,,				2504	0.0225				p.E2158D		Atlas-SNP	.											.	WDFY4	205	.	0			c.G6474C						PASS	.	G	ASP/GLU	48,1336		0,48,644	90.0	89.0	89.0		6474	-1.9	1.0	10	dbSNP_127	89	210,2972		4,202,1385	yes	missense	WDFY4	NM_020945.1	45	4,250,2029	CC,CG,GG		6.5996,3.4682,5.6505	benign	2158/3185	50038878	258,4308	692	1591	2283	SO:0001583	missense	57705	exon38			TGAAGAGGTCACA	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.6474G>C	10.37:g.50038878G>C	ENSP00000320563:p.Glu2158Asp	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	264	113	0.42803	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	92|92|92	0.04212454212454213|0.04212454212454213|0.04212454212454213	8|8|8	0.016260162601626018|0.016260162601626018|0.016260162601626018	18|18|18	0.049723756906077346|0.049723756906077346|0.049723756906077346	0|0|0	0.0|0.0|0.0	66|66|66	0.0870712401055409|0.0870712401055409|0.0870712401055409	G|G|G	8.766|8.766|8.766	0.924841|0.924841|0.924841	0.18056|0.18056|0.18056	0.034682|0.034682|0.034682	0.065996|0.065996|0.065996	ENSG00000128815|ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002|ENST00000265453	T|.|.	0.55588|.|.	0.51|.|.	5.87|5.87|5.87	-1.88|-1.88|-1.88	0.07713|0.07713|0.07713	.|.|.	0.190175|.|.	0.45126|.|.	D|.|.	0.000400|.|.	T|T|T	0.02047|0.02047|0.02047	0.0064|0.0064|0.0064	L|L|L	0.46157|0.46157|0.46157	1.445|1.445|1.445	0.80722|0.80722|0.80722	D|D|D	1|1|1	B|.|.	0.12013|.|.	0.005|.|.	B|.|.	0.11329|.|.	0.006|.|.	T|T|T	0.12502|0.12502|0.12502	-1.0545|-1.0545|-1.0545	9|5|5	.|.|.	.|.|.	.|.|.	.|.|.	2.7635|2.7635|2.7635	0.05314|0.05314|0.05314	0.3072:0.1891:0.4076:0.0962|0.3072:0.1891:0.4076:0.0962|0.3072:0.1891:0.4076:0.0962	rs41283281;rs61733235|rs41283281;rs61733235|rs41283281;rs61733235	2158|.|.	Q6ZS81|.|.	WDFY4_HUMAN|.|.	D|R|T	2158|1249|245	ENSP00000320563:E2158D|.|.	.|.|.	E|G|R	+|+|+	3|1|2	2|0|0	WDFY4|WDFY4|WDFY4	49708884|49708884|49708884	0.971000|0.971000|0.971000	0.33674|0.33674|0.33674	0.953000|0.953000|0.953000	0.39169|0.39169|0.39169	0.979000|0.979000|0.979000	0.70002|0.70002|0.70002	0.057000|0.057000|0.057000	0.14279|0.14279|0.14279	-0.020000|-0.020000|-0.020000	0.14032|0.14032|0.14032	-0.175000|-0.175000|-0.175000	0.13238|0.13238|0.13238	GAG|GGT|AGG	G|0.954;C|0.046	0.046	strong		0.557	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
LRIT1	26103	hgsc.bcm.edu	37	10	85993910	85993910	+	Silent	SNP	G	G	A	rs3814206	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85993910G>A	ENST00000372105.3	-	3	835	c.814C>T	c.(814-816)Ctg>Ttg	p.L272L		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	272	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						CAGCGTAGCAGTGCTGTGCCA	0.612													A|||	2867	0.572484	0.8941	0.5418	5008	,	,		18907	0.4058		0.4722	False		,,,				2504	0.4346				p.L272L		Atlas-SNP	.											.	LRIT1	73	.	0			c.C814T						PASS	.	A		3585,821	327.5+/-300.1	1468,649,86	71.0	69.0	70.0		814	-5.1	0.0	10	dbSNP_107	70	3877,4723	607.6+/-395.3	903,2071,1326	no	coding-synonymous	LRIT1	NM_015613.2		2371,2720,1412	AA,AG,GG		45.0814,18.6337,42.6265		272/624	85993910	7462,5544	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon3			GTAGCAGTGCTGT	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.814C>T	10.37:g.85993910G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			G|0.431;A|0.569	0.569	strong		0.612	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
BTBD10	84280	hgsc.bcm.edu	37	11	13443250	13443250	+	Silent	SNP	C	C	T	rs3789325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:13443250C>T	ENST00000278174.5	-	3	482	c.237G>A	c.(235-237)acG>acA	p.T79T	BTBD10_ENST00000532261.1_5'UTR|BTBD10_ENST00000530907.1_Silent_p.T87T|BTBD10_ENST00000528120.1_Silent_p.T31T	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	79						nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		GCTGAGACTCCGTTCTTTCAT	0.418													T|||	702	0.140176	0.0545	0.2997	5008	,	,		18962	0.1687		0.1481	False		,,,				2504	0.1053				p.T79T		Atlas-SNP	.											.	BTBD10	43	.	0			c.G237A						PASS	.	T		292,4108	799.4+/-415.5	16,260,1924	152.0	125.0	134.0		237	3.8	1.0	11	dbSNP_107	134	1492,7096	747.9+/-407.3	117,1258,2919	no	coding-synonymous	BTBD10	NM_032320.5		133,1518,4843	TT,TC,CC		17.3731,6.6364,13.7358		79/476	13443250	1784,11204	2200	4294	6494	SO:0001819	synonymous_variant	84280	exon3			AGACTCCGTTCTT	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.237G>A	11.37:g.13443250C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_032320	B7Z228|Q86WG1	Silent	SNP	ENST00000278174.5	37	CCDS7811.1																																																																																			C|0.866;T|0.134	0.134	strong		0.418	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
APBA3	9546	hgsc.bcm.edu	37	19	3752874	3752874	+	Missense_Mutation	SNP	A	A	G	rs8102086	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3752874A>G	ENST00000316757.3	-	7	1326	c.1126T>C	c.(1126-1128)Tgc>Cgc	p.C376R	AC005954.4_ENST00000586503.1_RNA|AC005954.3_ENST00000591962.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	376	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.		C -> R (in dbSNP:rs8102086). {ECO:0000269|PubMed:18669648}.		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)		TGGAGGTGGCAGGCGCCTGGG	0.672													C|||	2701	0.539337	0.323	0.6916	5008	,	,		13976	0.63		0.5676	False		,,,				2504	0.6012				p.C376R		Atlas-SNP	.											.	APBA3	28	.	0			c.T1126C						PASS	.	C	ARG/CYS	1804,2600		456,892,854	36.0	40.0	39.0		1126	1.8	0.0	19	dbSNP_116	39	4742,3854		1291,2160,847	yes	missense	APBA3	NM_004886.3	180	1747,3052,1701	GG,GA,AA		44.8348,40.9628,49.6462	benign	376/576	3752874	6546,6454	2202	4298	6500	SO:0001583	missense	9546	exon7			GGTGGCAGGCGCC	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.1126T>C	19.37:g.3752874A>G	ENSP00000315136:p.Cys376Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	77	24	0.311688	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	1221	0.5590659340659341	180	0.36585365853658536	247	0.6823204419889503	377	0.6590909090909091	417	0.5501319261213721	C	10.35	1.325729	0.24080	0.409628	0.551652	ENSG00000011132	ENST00000316757	T	0.05996	3.36	4.02	1.84	0.25277	.	0.596537	0.16596	N	0.207529	T	0.00012	0.0000	N	0.03608	-0.345	0.40860	P	0.016175999999999968	B	0.02656	0.0	B	0.01281	0.0	T	0.12293	-1.0553	9	0.49607	T	0.09	.	2.6738	0.05075	0.1433:0.5361:0.1594:0.1611	rs8102086;rs58868831;rs8102086	376	O96018	APBA3_HUMAN	R	376	ENSP00000315136:C376R	ENSP00000315136:C376R	C	-	1	0	APBA3	3703874	0.618000	0.27051	0.002000	0.10522	0.004000	0.04260	0.931000	0.28871	-0.086000	0.12550	-0.358000	0.07595	TGC	A|0.470;C|0.000;G|0.530	0.530	strong		0.672	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
GPR55	9290	hgsc.bcm.edu	37	2	231775144	231775144	+	Silent	SNP	G	G	A	rs1992187	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:231775144G>A	ENST00000392040.1	-	2	726	c.534C>T	c.(532-534)agC>agT	p.S178S	GPR55_ENST00000392039.2_Silent_p.S178S|AC012507.4_ENST00000454890.1_RNA	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	178					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)	p.S178S(1)		endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		AGACCTTGGCGCTCCAGGTAT	0.552													G|||	267	0.0533147	0.0038	0.0576	5008	,	,		21432	0.0744		0.0596	False		,,,				2504	0.089				p.S178S		Atlas-SNP	.											GPR55,NS,carcinoma,-1,2	GPR55	46	2	1	Substitution - coding silent(1)	stomach(1)	c.C534T						PASS	.	G		47,4359	50.2+/-85.5	0,47,2156	131.0	135.0	134.0		534	-10.2	0.0	2	dbSNP_92	134	528,8072	147.6+/-202.9	15,498,3787	no	coding-synonymous	GPR55	NM_005683.3		15,545,5943	AA,AG,GG		6.1395,1.0667,4.421		178/320	231775144	575,12431	2203	4300	6503	SO:0001819	synonymous_variant	9290	exon2			CTTGGCGCTCCAG	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.534C>T	2.37:g.231775144G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	151	80	0.529801	NM_005683	Q8N580	Silent	SNP	ENST00000392040.1	37	CCDS2480.1																																																																																			G|0.954;A|0.046	0.046	strong		0.552	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
WDR16	146845	hgsc.bcm.edu	37	17	9511492	9511492	+	Silent	SNP	C	C	T	rs146548028		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:9511492C>T	ENST00000352665.5	+	7	879	c.810C>T	c.(808-810)gcC>gcT	p.A270A	WDR16_ENST00000396219.3_Silent_p.A202A|WDR16_ENST00000299764.5_Silent_p.A280A	NM_145054.4	NP_659491.4			WD repeat domain 16									p.A270A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						GCTCTGGAGCCGGACTGCTGG	0.507													c|||	1	0.000199681	0.0	0.0	5008	,	,		14489	0.0		0.001	False		,,,				2504	0.0				p.A270A		Atlas-SNP	.											WDR16,NS,carcinoma,0,1	WDR16	67	1	1	Substitution - coding silent(1)	endometrium(1)	c.C810T						PASS	.		,	1,4405	2.1+/-5.4	0,1,2202	76.0	76.0	76.0		606,810	-10.8	0.7	17	dbSNP_134	76	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	WDR16	NM_001080556.1,NM_145054.4	,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,	202/553,270/621	9511492	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	146845	exon7			TGGAGCCGGACTG	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"""WD repeat domain containing"""	16053	protein-coding gene	gene with protein product	"""WD40-repeat protein upregulated in HCC"""	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.810C>T	17.37:g.9511492C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	171	90	0.526316	NM_145054		Silent	SNP	ENST00000352665.5	37	CCDS11149.2																																																																																			C|0.999;T|0.001	0.001	strong		0.507	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054	
SOAT2	8435	hgsc.bcm.edu	37	12	53497402	53497402	+	Missense_Mutation	SNP	A	A	G	rs9658625	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53497402A>G	ENST00000301466.3	+	1	101	c.41A>G	c.(40-42)gAa>gGa	p.E14G		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	14			E -> G (in dbSNP:rs9658625).		cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)			endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	CAGAGGACAGAAGGGCTGGGA	0.697													A|||	525	0.104832	0.0408	0.1484	5008	,	,		16087	0.1617		0.0686	False		,,,				2504	0.1391				p.E14G		Atlas-SNP	.											.	SOAT2	44	.	0			c.A41G						PASS	.	A	GLY/GLU	152,3558		4,144,1707	10.0	13.0	12.0		41	1.2	0.3	12	dbSNP_119	12	415,6597		9,397,3100	yes	missense	SOAT2	NM_003578.3	98	13,541,4807	GG,GA,AA		5.9184,4.097,5.2882	benign	14/523	53497402	567,10155	1855	3506	5361	SO:0001583	missense	8435	exon1			GGACAGAAGGGCT	AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.41A>G	12.37:g.53497402A>G	ENSP00000301466:p.Glu14Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_003578	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Missense_Mutation	SNP	ENST00000301466.3	37	CCDS8847.1	216	0.0989010989010989	25	0.0508130081300813	48	0.13259668508287292	89	0.1555944055944056	54	0.0712401055408971	A	12.98	2.099804	0.37048	0.04097	0.059184	ENSG00000167780	ENST00000551896;ENST00000301466	T;T	0.50813	0.73;1.86	4.97	1.19	0.21007	.	1.602540	0.03660	N	0.242465	T	0.00144	0.0004	L	0.36672	1.1	0.36838	P	0.11273999999999995	B	0.06786	0.001	B	0.08055	0.003	T	0.04128	-1.0975	9	0.24483	T	0.36	-0.6279	4.3659	0.11225	0.6226:0.1931:0.1843:0.0	rs9658625;rs56674225;rs9658625	14	O75908	SOAT2_HUMAN	G	14	ENSP00000450120:E14G;ENSP00000301466:E14G	ENSP00000301466:E14G	E	+	2	0	SOAT2	51783669	0.989000	0.36119	0.316000	0.25252	0.027000	0.11550	0.657000	0.24963	0.105000	0.17753	0.460000	0.39030	GAA	A|0.901;G|0.099	0.099	strong		0.697	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1		
SIGLEC11	114132	hgsc.bcm.edu	37	19	50453317	50453317	+	Silent	SNP	C	C	T	rs9304690	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50453317C>T	ENST00000447370.2	-	11	2097	c.2007G>A	c.(2005-2007)tcG>tcA	p.S669S	CTC-326K19.6_ENST00000451973.1_Intron|U3_ENST00000408198.1_RNA|SIGLEC11_ENST00000426971.2_Silent_p.S573S	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	669					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		TCTTGATCTCCGAGTACTCGG	0.617													C|||	1027	0.205072	0.0779	0.1643	5008	,	,		16936	0.2619		0.2396	False		,,,				2504	0.3119				p.S669S		Atlas-SNP	.											SIGLEC11,colon,carcinoma,0,1	SIGLEC11	70	1	0			c.G2007A						PASS	.	C	,	455,3949	215.5+/-234.4	30,395,1777	42.0	40.0	41.0		1719,2007	-7.3	0.0	19	dbSNP_119	41	2058,6542	355.9+/-330.1	238,1582,2480	no	coding-synonymous,coding-synonymous	SIGLEC11	NM_001135163.1,NM_052884.2	,	268,1977,4257	TT,TC,CC		23.9302,10.3315,19.3248	,	573/603,669/699	50453317	2513,10491	2202	4300	6502	SO:0001819	synonymous_variant	114132	exon11			GATCTCCGAGTAC	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.2007G>A	19.37:g.50453317C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_052884		Silent	SNP	ENST00000447370.2	37	CCDS12790.2	473	0.21657509157509158	48	0.0975609756097561	75	0.20718232044198895	154	0.2692307692307692	196	0.25857519788918204	C	3.560	-0.089762	0.07053	0.103315	0.239302	ENSG00000161640	ENST00000426971	.	.	.	3.64	-7.29	0.01451	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27274	P	0.9582925	.	.	.	.	.	.	T	0.38178	-0.9673	3	.	.	.	.	1.0129	0.01501	0.2576:0.3395:0.1309:0.272	rs9304690;rs56579996;rs9304690	.	.	.	Q	563	.	.	R	-	2	0	SIGLEC11	55145129	0.000000	0.05858	0.005000	0.12908	0.026000	0.11368	-3.084000	0.00612	-1.620000	0.01564	-1.192000	0.01694	CGG	C|0.803;T|0.197	0.197	strong		0.617	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884	
PDE6C	5146	hgsc.bcm.edu	37	10	95395364	95395364	+	Silent	SNP	C	C	G	rs3737228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:95395364C>G	ENST00000371447.3	+	10	1518	c.1380C>G	c.(1378-1380)acC>acG	p.T460T		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	460					phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	TGAACCAAACCAAAGCCACTC	0.368													C|||	1178	0.235224	0.1112	0.3199	5008	,	,		19136	0.3661		0.2922	False		,,,				2504	0.1493				p.T460T		Atlas-SNP	.											.	PDE6C	97	.	0			c.C1380G						PASS	.	C		582,3824	258.9+/-262.7	36,510,1657	129.0	115.0	120.0		1380	2.4	1.0	10	dbSNP_107	120	2398,6202	397.8+/-345.9	310,1778,2212	no	coding-synonymous	PDE6C	NM_006204.3		346,2288,3869	GG,GC,CC		27.8837,13.2093,22.9125		460/859	95395364	2980,10026	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon10			CCAAACCAAAGCC	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1380C>G	10.37:g.95395364C>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			C|0.752;G|0.248	0.248	strong		0.368	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
KLC4	89953	hgsc.bcm.edu	37	6	43034850	43034850	+	Intron	SNP	C	C	T	rs4714660	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43034850C>T	ENST00000394056.2	+	7	1374				KLC4_ENST00000259708.3_Intron|KLC4_ENST00000394058.1_Intron|KLC4_ENST00000458460.2_Missense_Mutation_p.T303M|KLC4_ENST00000453940.2_Intron|KLC4_ENST00000347162.5_Intron|KLC4_ENST00000479388.1_Intron			Q9NSK0	KLC4_HUMAN	kinesin light chain 4							cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			CCCCACCCCACGCCCCGCACC	0.582													c|||	734	0.146565	0.1959	0.147	5008	,	,		8592	0.1647		0.0358	False		,,,				2504	0.1748				p.T303M		Atlas-SNP	.											.	KLC4	89	.	0			c.C908T						PASS	.	T	MET/THR,,,	846,3560	332.8+/-302.6	87,672,1444	48.0	41.0	43.0		908,,,	-0.8	0.0	6	dbSNP_111	43	347,8253	117.7+/-177.3	5,337,3958	yes	missense,intron,intron,intron	KLC4	NM_138343.2,NM_201521.1,NM_201522.1,NM_201523.1	81,,,	92,1009,5402	TT,TC,CC		4.0349,19.2011,9.1727	,,,	303/316,,,	43034850	1193,11813	2203	4300	6503	SO:0001627	intron_variant	89953	exon6			ACCCCACGCCCCG	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"""Tetratricopeptide (TTC) repeat domain containing"""	21624	protein-coding gene	gene with protein product			"""kinesin-like 8"""	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.879+29C>T	6.37:g.43034850C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	171	82	0.479532	NM_138343	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	256	0.11721611721611722	91	0.18495934959349594	47	0.1298342541436464	92	0.16083916083916083	26	0.03430079155672823	c	1.134	-0.651543	0.03506	0.192011	0.040349	ENSG00000137171	ENST00000458460	T	0.81078	-1.45	0.717	-0.787	0.10943	.	.	.	.	.	T	0.34571	0.0902	.	.	.	0.80722	P	0.0	B	0.19200	0.034	B	0.08055	0.003	T	0.07790	-1.0754	5	.	.	.	.	.	.	.	rs4714660;rs57133855;rs4714660	303	Q96EG6	.	M	303	ENSP00000410358:T303M	.	T	+	2	0	KLC4	43142828	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.730000	0.00805	-2.721000	0.00389	-3.274000	0.00048	ACG	C|0.869;T|0.131	0.131	strong		0.582	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343	
LYN	4067	hgsc.bcm.edu	37	8	56866452	56866452	+	Silent	SNP	G	G	A	rs2227980	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:56866452G>A	ENST00000519728.1	+	8	995	c.699G>A	c.(697-699)aaG>aaA	p.K233K	LYN_ENST00000520220.2_Silent_p.K212K	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	233					B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	AGCCACAGAAGCCATGGGATA	0.488													G|||	704	0.140575	0.4365	0.0749	5008	,	,		16314	0.0288		0.0219	False		,,,				2504	0.0245				p.K233K		Atlas-SNP	.											.	LYN	54	.	0			c.G699A						PASS	.	G	,	1712,2694	516.2+/-369.1	352,1008,843	79.0	82.0	81.0		636,699	2.0	1.0	8	dbSNP_98	81	248,8352	98.1+/-159.7	2,244,4054	no	coding-synonymous,coding-synonymous	LYN	NM_001111097.2,NM_002350.3	,	354,1252,4897	AA,AG,GG		2.8837,38.8561,15.07	,	212/492,233/513	56866452	1960,11046	2203	4300	6503	SO:0001819	synonymous_variant	4067	exon8			ACAGAAGCCATGG	M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"""SH2 domain containing"""	6735	protein-coding gene	gene with protein product		165120	"""v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"""			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.699G>A	8.37:g.56866452G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_002350	A0AVQ5	Silent	SNP	ENST00000519728.1	37	CCDS6162.1																																																																																			G|0.860;A|0.140	0.140	strong		0.488	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350	
COQ3	51805	hgsc.bcm.edu	37	6	99819379	99819379	+	Missense_Mutation	SNP	T	T	C	rs6925344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:99819379T>C	ENST00000254759.3	-	6	838	c.814A>G	c.(814-816)Agt>Ggt	p.S272G	COQ3_ENST00000369242.1_Missense_Mutation_p.S44G|COQ3_ENST00000369240.1_Missense_Mutation_p.S44G	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	272			S -> G (in dbSNP:rs6925344). {ECO:0000269|PubMed:10777520, ECO:0000269|PubMed:14702039, 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)		GGTACAATACTTGCAATTTGC	0.343													C|||	4187	0.836062	0.705	0.9121	5008	,	,		17099	0.8641		0.826	False		,,,				2504	0.9407				p.S272G		Atlas-SNP	.											.	COQ3	19	.	0			c.A814G						PASS	.	C	GLY/SER	3145,1261	431.4+/-342.9	1121,903,179	96.0	100.0	99.0		814	4.4	0.4	6	dbSNP_116	99	7186,1414	271.7+/-289.7	3025,1136,139	yes	missense	COQ3	NM_017421.3	56	4146,2039,318	CC,CT,TT		16.4419,28.6201,20.5674	benign	272/370	99819379	10331,2675	2203	4300	6503	SO:0001583	missense	51805	exon6			CAATACTTGCAAT	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.814A>G	6.37:g.99819379T>C	ENSP00000254759:p.Ser272Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	41	0.401961	NM_017421	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Missense_Mutation	SNP	ENST00000254759.3	37	CCDS5042.1	1771	0.8108974358974359	348	0.7073170731707317	323	0.8922651933701657	471	0.8234265734265734	629	0.8298153034300791	C	4.472	0.087491	0.08583	0.713799	0.835581	ENSG00000132423	ENST00000254759;ENST00000369242;ENST00000369240	T;T;T	0.26518	2.61;1.73;1.73	5.23	4.36	0.52297	.	0.113933	0.64402	N	0.000011	T	0.01092	0.0036	N	0.00038	-2.52	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41680	-0.9495	9	0.06365	T	0.9	-26.8618	11.9053	0.52708	0.0:0.8579:0.0:0.1421	rs6925344;rs17846638;rs17859729;rs52790991;rs57847888;rs6925344	272	Q9NZJ6	COQ3_HUMAN	G	272;44;44	ENSP00000254759:S272G;ENSP00000358245:S44G;ENSP00000358243:S44G	ENSP00000254759:S272G	S	-	1	0	COQ3	99926100	0.997000	0.39634	0.449000	0.26957	0.891000	0.51852	2.050000	0.41297	0.712000	0.32039	-0.213000	0.12676	AGT	T|0.206;C|0.794	0.794	strong		0.343	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421	
PCK1	5105	hgsc.bcm.edu	37	20	56137184	56137184	+	Silent	SNP	C	C	T	rs6070157	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:56137184C>T	ENST00000319441.4	+	3	446	c.282C>T	c.(280-282)atC>atT	p.I94I	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Intron	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	94					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			AGACGGTTATCGTCACCCAAG	0.547													C|||	612	0.122204	0.1483	0.1167	5008	,	,		19900	0.0159		0.174	False		,,,				2504	0.1472				p.I94I		Atlas-SNP	.											.	PCK1	95	.	0			c.C282T						PASS	.	C		588,3818	256.1+/-261.0	37,514,1652	102.0	89.0	94.0		282	2.5	0.2	20	dbSNP_114	94	1686,6914	309.6+/-309.4	176,1334,2790	no	coding-synonymous	PCK1	NM_002591.3		213,1848,4442	TT,TC,CC		19.6047,13.3454,17.4842		94/623	56137184	2274,10732	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon3			GGTTATCGTCACC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.282C>T	20.37:g.56137184C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			C|0.851;T|0.149	0.149	strong		0.547	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15586672	15586672	+	Missense_Mutation	SNP	A	A	T	rs892145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15586672A>T	ENST00000340880.4	-	2	1289	c.809T>A	c.(808-810)aTg>aAg	p.M270K	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.M270K	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	270			M -> K (in dbSNP:rs892145). {ECO:0000269|PubMed:12975309}.		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)	p.M270K(2)		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						GAGGAAGGCCATGGTTAACAG	0.612													A|||	1834	0.366214	0.4077	0.3444	5008	,	,		19085	0.3631		0.3917	False		,,,				2504	0.3027				p.M270K		Atlas-SNP	.											PGLYRP2_ENST00000292609,NS,carcinoma,0,4	PGLYRP2	116	4	2	Substitution - Missense(2)	prostate(2)	c.T809A						PASS	.	A	LYS/MET	1709,2697		339,1031,833	37.0	38.0	38.0		809	-1.1	0.9	19	dbSNP_86	38	3238,5362		641,1956,1703	yes	missense	PGLYRP2	NM_052890.3	95	980,2987,2536	TT,TA,AA		37.6512,38.788,38.0363	benign	270/577	15586672	4947,8059	2203	4300	6503	SO:0001583	missense	114770	exon2			AAGGCCATGGTTA	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.809T>A	19.37:g.15586672A>T	ENSP00000345968:p.Met270Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	815	0.3731684981684982	199	0.40447154471544716	115	0.31767955801104975	208	0.36363636363636365	293	0.3865435356200528	A	5.442	0.266646	0.10294	0.38788	0.376512	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.04194	3.69;3.68	5.31	-1.07	0.09968	.	1.255450	0.05643	N	0.583853	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B	0.25904	0.137;0.02	B;B	0.29598	0.104;0.013	T	0.45644	-0.9247	9	0.25751	T	0.34	-21.0741	12.7595	0.57356	0.8205:0.0:0.1795:0.0	rs892145;rs52816103;rs60008418;rs892145	270;270	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	K	270	ENSP00000345968:M270K;ENSP00000292609:M270K	ENSP00000292609:M270K	M	-	2	0	PGLYRP2	15447672	0.001000	0.12720	0.886000	0.34754	0.058000	0.15608	-0.159000	0.10056	-0.419000	0.07439	-1.447000	0.01057	ATG	A|0.632;T|0.368	0.368	strong		0.612	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
RIN1	9610	hgsc.bcm.edu	37	11	66099992	66099992	+	Missense_Mutation	SNP	G	G	A	rs139103405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66099992G>A	ENST00000311320.4	-	10	2233	c.2107C>T	c.(2107-2109)Cgg>Tgg	p.R703W	RIN1_ENST00000530056.1_Missense_Mutation_p.R537W|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Intron|RIN1_ENST00000524804.1_5'Flank	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	703	Ras and 14-3-3 protein binding region.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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						CACTCCGCCCGGCGGTAGACG	0.672																																					p.R703W		Atlas-SNP	.											.	RIN1	64	.	0			c.C2107T						PASS	.	G	TRP/ARG	0,4400		0,0,2200	73.0	84.0	80.0		2107	4.0	1.0	11	dbSNP_134	80	4,8586	3.7+/-12.6	0,4,4291	no	missense	RIN1	NM_004292.2	101	0,4,6491	AA,AG,GG		0.0466,0.0,0.0308	probably-damaging	703/784	66099992	4,12986	2200	4295	6495	SO:0001583	missense	9610	exon10			CCGCCCGGCGGTA	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.2107C>T	11.37:g.66099992G>A	ENSP00000310406:p.Arg703Trp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_004292	O15010|Q00427|Q96CC8	Missense_Mutation	SNP	ENST00000311320.4	37	CCDS31614.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451461	0.63290	0.0	4.66E-4	ENSG00000174791	ENST00000311320;ENST00000530056	T;T	0.19394	2.15;2.15	4.93	4.0	0.46444	Ras-association (3);	0.682458	0.13161	N	0.409069	T	0.39009	0.1062	M	0.61703	1.905	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.99	P;P;P	0.60609	0.849;0.877;0.571	T	0.12967	-1.0527	10	0.87932	D	0	-13.1701	10.7254	0.46066	0.0:0.0:0.7956:0.2044	.	537;334;703	E9PNR2;B4DW96;Q13671	.;.;RIN1_HUMAN	W	703;537	ENSP00000310406:R703W;ENSP00000432798:R537W	ENSP00000310406:R703W	R	-	1	2	RIN1	65856568	0.999000	0.42202	0.998000	0.56505	0.382000	0.30200	3.479000	0.53165	1.166000	0.42689	0.462000	0.41574	CGG	G|0.999;A|0.001	0.001	strong		0.672	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
NOC2L	26155	hgsc.bcm.edu	37	1	880502	880502	+	Missense_Mutation	SNP	C	C	T	rs74047418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:880502C>T	ENST00000327044.6	-	18	2127	c.2078G>A	c.(2077-2079)cGg>cAg	p.R693Q		NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	693	Asp/Glu-rich (acidic).				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)			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)		caccccATGCCGAGTGCTCAG	0.607													c|||	6	0.00119808	0.003	0.0014	5008	,	,		17544	0.0		0.001	False		,,,				2504	0.0				p.R693Q		Atlas-SNP	.											.	NOC2L	42	.	0			c.G2078A						PASS	.	C	GLN/ARG	9,4395	15.5+/-35.6	0,9,2193	88.0	81.0	84.0		2078	-6.8	0.0	1	dbSNP_130	84	15,8585	9.8+/-36.6	0,15,4285	yes	missense	NOC2L	NM_015658.3	43	0,24,6478	TT,TC,CC		0.1744,0.2044,0.1846	possibly-damaging	693/750	880502	24,12980	2202	4300	6502	SO:0001583	missense	26155	exon18			CCATGCCGAGTGC	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.2078G>A	1.37:g.880502C>T	ENSP00000317992:p.Arg693Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_015658	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	5	0.0022893772893772895	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	4.022	0.001552	0.07819	0.002044	0.001744	ENSG00000188976	ENST00000327044	T	0.22134	1.97	3.39	-6.79	0.01715	Armadillo-type fold (1);	2.092900	0.02013	N	0.047121	T	0.06735	0.0172	N	0.22421	0.69	0.09310	N	1	B;B;B	0.12630	0.005;0.005;0.006	B;B;B	0.04013	0.001;0.001;0.001	T	0.28996	-1.0026	10	0.11485	T	0.65	0.8905	0.9663	0.01406	0.221:0.1346:0.2196:0.4248	.	693;693;460	B3KNC3;Q9Y3T9;Q9H9J5	.;NOC2L_HUMAN;.	Q	693	ENSP00000317992:R693Q	ENSP00000317992:R693Q	R	-	2	0	NOC2L	870365	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.544000	0.00933	-2.506000	0.00507	0.448000	0.29417	CGG	C|0.998;T|0.002	0.002	strong		0.607	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658	
RAB17	64284	hgsc.bcm.edu	37	2	238494681	238494681	+	Silent	SNP	G	G	A	rs34052613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	243	0	0		WXS	Illumina HiSeq	Phase_I	245	108	0.440816	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		
PDGFRB	5159	hgsc.bcm.edu	37	5	149497228	149497228	+	Silent	SNP	G	G	A	rs2228440	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149497228G>A	ENST00000261799.4	-	22	3559	c.3090C>T	c.(3088-3090)ccC>ccT	p.P1030P		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	1030					adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCAACCTCGGGTTTGGGGT	0.612			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								G|||	310	0.061901	0.0794	0.0735	5008	,	,		16115	0.0		0.1103	False		,,,				2504	0.044				p.P1030P		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	PDGFRB	142	.	0			c.C3090T						PASS	.	G		367,4039	186.7+/-213.5	12,343,1848	73.0	72.0	73.0		3090	-6.3	0.5	5	dbSNP_98	73	934,7666	206.2+/-248.4	49,836,3415	no	coding-synonymous	PDGFRB	NM_002609.3		61,1179,5263	AA,AG,GG		10.8605,8.3296,10.0031		1030/1107	149497228	1301,11705	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon22			AACCTCGGGTTTG	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.3090C>T	5.37:g.149497228G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			G|0.910;A|0.091	0.091	strong		0.612	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
ATE1	11101	hgsc.bcm.edu	37	10	123662023	123662023	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123662023G>T	ENST00000224652.6	-	6	781	c.696C>A	c.(694-696)ttC>ttA	p.F232L	ATE1_ENST00000481784.1_5'UTR|ATE1_ENST00000543447.1_Missense_Mutation_p.F117L|ATE1_ENST00000369043.3_Missense_Mutation_p.F232L|ATE1_ENST00000540606.1_Missense_Mutation_p.F225L|ATE1_ENST00000535655.1_Intron|ATE1_ENST00000369040.3_Missense_Mutation_p.F136L	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	232					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				CTTGAGCCTGGAAACCCTCAA	0.423																																					p.F232L		Atlas-SNP	.											.	ATE1	67	.	0			c.C696A						PASS	.						162.0	146.0	151.0					10																	123662023		2203	4300	6503	SO:0001583	missense	11101	exon6			AGCCTGGAAACCC	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.696C>A	10.37:g.123662023G>T	ENSP00000224652:p.Phe232Leu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	166	77	0.463855	NM_001001976	O95261|Q5SQQ3|Q8WW04	Missense_Mutation	SNP	ENST00000224652.6	37	CCDS31300.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.679|0.679	-0.798913|-0.798913	0.02841|0.02841	.|.	.|.	ENSG00000107669|ENSG00000107669	ENST00000369043;ENST00000224652;ENST00000369040;ENST00000540606;ENST00000543447|ENST00000423243	.|.	.|.	.|.	4.58|4.58	3.66|3.66	0.41972|0.41972	.|.	0.913149|.	0.09305|.	N|.	0.820356|.	T|T	0.33644|0.33644	0.0870|0.0870	L|L	0.36672|0.36672	1.1|1.1	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|.	0.09377|.	0.004;0.001;0.002;0.001|.	T|T	0.20371|0.20371	-1.0277|-1.0277	9|5	0.23891|.	T|.	0.37|.	-7.5611|-7.5611	5.5146|5.5146	0.16900|0.16900	0.124:0.3975:0.4785:0.0|0.124:0.3975:0.4785:0.0	.|.	225;136;232;232|.	F5GXE4;B4E107;O95260;O95260-2|.	.;.;ATE1_HUMAN;.|.	L|T	232;232;136;225;117|229	.|.	ENSP00000224652:F232L|.	F|P	-|-	3|1	2|0	ATE1|ATE1	123652013|123652013	0.152000|0.152000	0.22762|0.22762	0.920000|0.920000	0.36463|0.36463	0.774000|0.774000	0.43823|0.43823	0.524000|0.524000	0.22940|0.22940	1.128000|1.128000	0.42052|0.42052	0.557000|0.557000	0.71058|0.71058	TTC|CCA	.	.	none		0.423	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	
UMODL1	89766	hgsc.bcm.edu	37	21	43531553	43531553	+	Intron	SNP	A	A	C	rs220128	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43531553A>C	ENST00000408910.2	+	12	1899				UMODL1_ENST00000400427.1_Missense_Mutation_p.T669P|UMODL1_ENST00000400424.2_Intron|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000408989.2_Missense_Mutation_p.T741P	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1						adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CCCGAAGGCTACTGGGTCAAC	0.662													C|||	2084	0.416134	0.1573	0.5101	5008	,	,		16788	0.5357		0.5318	False		,,,				2504	0.4571				p.T741P	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.A2221C						PASS	.	C	,PRO/THR,,PRO/THR	907,3045		122,663,1191	49.0	52.0	51.0		,2005,,2221	-0.8	0.0	21	dbSNP_79	51	4259,4025		1116,2027,999	yes	intron,missense,intron,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,38,,38	1238,2690,2190	CC,CA,AA		48.5876,22.9504,42.2197	,benign,,benign	,669/1375,,741/1447	43531553	5166,7070	1976	4142	6118	SO:0001627	intron_variant	89766	exon11			AAGGCTACTGGGT		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1900-63A>C	21.37:g.43531553A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	988	0.4523809523809524	94	0.1910569105691057	182	0.5027624309392266	290	0.506993006993007	422	0.5567282321899736	C	0.354	-0.943422	0.02322	0.229504	0.514124	ENSG00000177398	ENST00000400427;ENST00000408989	T;T	0.71934	-0.61;-0.61	4.41	-0.782	0.10961	.	0.261743	0.20395	N	0.093165	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	8	0.02654	T	1	-2.7542	3.3896	0.07283	0.2839:0.3702:0.0:0.3459	rs220128;rs481812;rs1153356;rs57873525;rs220128	741	Q5DID0-2	.	P	669;741	ENSP00000383279:T669P;ENSP00000386126:T741P	ENSP00000383279:T669P	T	+	1	0	UMODL1	42404622	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.444000	0.06854	-0.579000	0.05952	-1.544000	0.00907	ACT	A|0.568;C|0.432	0.432	strong		0.662	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
NCOA1	8648	hgsc.bcm.edu	37	2	24974958	24974958	+	Missense_Mutation	SNP	C	C	T	rs1804645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:24974958C>T	ENST00000406961.1	+	20	4466	c.3814C>T	c.(3814-3816)Cca>Tca	p.P1272S	NCOA1_ENST00000538539.1_Missense_Mutation_p.P1272S|NCOA1_ENST00000407230.1_Missense_Mutation_p.P1121S|NCOA1_ENST00000348332.3_Missense_Mutation_p.P1272S|NCOA1_ENST00000288599.5_Missense_Mutation_p.P1272S|NCOA1_ENST00000405141.1_Missense_Mutation_p.P1272S|NCOA1_ENST00000395856.3_Missense_Mutation_p.P1272S			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1272			P -> S (in dbSNP:rs1804645). {ECO:0000269|Ref.4}.		androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGCAAACTCCACCTGCCTC	0.532			T	PAX3	alveolar rhadomyosarcoma								C|||	40	0.00798722	0.0023	0.0159	5008	,	,		17295	0.0		0.0199	False		,,,				2504	0.0061				p.P1272S		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.C3814T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	31,4375	36.8+/-68.6	1,29,2173	70.0	66.0	68.0		3814,3814,3814	5.1	0.9	2	dbSNP_89	68	252,8348	100.3+/-161.8	3,246,4051	yes	missense,missense,missense	NCOA1	NM_003743.4,NM_147223.2,NM_147233.2	74,74,74	4,275,6224	TT,TC,CC		2.9302,0.7036,2.1759	probably-damaging,probably-damaging,probably-damaging	1272/1442,1272/1400,1272/1441	24974958	283,12723	2203	4300	6503	SO:0001583	missense	8648	exon18			CAAACTCCACCTG	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.3814C>T	2.37:g.24974958C>T	ENSP00000385216:p.Pro1272Ser	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	311	144	0.463023	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	23	0.010531135531135532	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	14.62	2.588512	0.46110	0.007036	0.029302	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02216	4.45;4.47;4.39;4.47;4.45;4.47;4.45	5.14	5.14	0.70334	.	0.191149	0.46145	D	0.000312	T	0.01124	0.0037	L	0.40543	1.245	0.52501	D	0.999952	B;B;B;B;B	0.27823	0.012;0.16;0.19;0.16;0.099	B;B;B;B;B	0.30646	0.015;0.118;0.055;0.118;0.055	T	0.58725	-0.7586	10	0.35671	T	0.21	.	18.3626	0.90380	0.0:1.0:0.0:0.0	rs1804645;rs17838346;rs1804645	1272;1272;1272;1272;1121	A8K1V4;Q15788-3;Q15788;Q15788-2;B5MCN7	.;.;NCOA1_HUMAN;.;.	S	1272;1272;1121;1272;1272;1272;1272	ENSP00000385216:P1272S;ENSP00000385097:P1272S;ENSP00000385195:P1121S;ENSP00000444039:P1272S;ENSP00000320940:P1272S;ENSP00000288599:P1272S;ENSP00000379197:P1272S	ENSP00000288599:P1272S	P	+	1	0	NCOA1	24828462	0.908000	0.30866	0.894000	0.35097	0.939000	0.58152	4.814000	0.62627	2.653000	0.90120	0.585000	0.79938	CCA	C|0.982;T|0.018	0.018	strong		0.532	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
CLEC2A	387836	hgsc.bcm.edu	37	12	10069302	10069302	+	Missense_Mutation	SNP	C	C	T	rs526680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:10069302C>T	ENST00000455827.1	-	4	458	c.407G>A	c.(406-408)gGt>gAt	p.G136D	CLEC2A_ENST00000339766.4_Missense_Mutation_p.G136D	NM_001130711.1	NP_001124183.1	Q6UVW9	CLC2A_HUMAN	C-type lectin domain family 2, member A	136	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		G -> D (in dbSNP:rs526680). {ECO:0000269|PubMed:18046548}.		natural killer cell mediated cytotoxicity (GO:0042267)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|protein homodimerization activity (GO:0042803)	p.G136D(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	4						AACTCACCAACCATTGAATGT	0.343													T|||	2633	0.525759	0.5106	0.5403	5008	,	,		18764	0.3085		0.675	False		,,,				2504	0.6063				p.G136D		Atlas-SNP	.											CLEC2A,NS,carcinoma,0,1	CLEC2A	12	1	1	Substitution - Missense(1)	kidney(1)	c.G407A						PASS	.	T	ASP/GLY	788,596		231,326,135	311.0	245.0	265.0		407	-4.9	0.0	12	dbSNP_83	265	2107,1075		697,713,181	yes	missense	CLEC2A	NM_001130711.1	94	928,1039,316	TT,TC,CC		33.7838,43.0636,36.5966	benign	136/175	10069302	2895,1671	692	1591	2283	SO:0001583	missense	387836	exon4			CACCAACCATTGA	AY359126	CCDS44829.1, CCDS8606.1	12p13.31	2010-06-30			ENSG00000188393	ENSG00000188393		"""C-type lectin domain containing"""	24191	protein-coding gene	gene with protein product	"""keratinocyte-associated C-type lectin"", ""proliferation-induced lymphocyte-associated receptor"""	612087				12975309	Standard	NM_001130711		Approved	UNQ5792, INPE5792, KACL, PILAR	uc009zhc.2	Q6UVW9	OTTHUMG00000140393	ENST00000455827.1:c.407G>A	12.37:g.10069302C>T	ENSP00000396163:p.Gly136Asp	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	223	220	0.986547	NM_001130711	A5Y4G5|A9QKS2|A9QKS3	Missense_Mutation	SNP	ENST00000455827.1	37	CCDS44829.1	1145	0.5242673992673993	251	0.5101626016260162	206	0.569060773480663	177	0.3094405594405594	511	0.6741424802110818	T	2.420	-0.333368	0.05278	0.569364	0.662162	ENSG00000188393	ENST00000339766;ENST00000455827	T;T	0.16743	2.32;2.32	3.14	-4.9	0.03094	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.564659	0.12009	N	0.508105	T	0.00012	0.0000	N	0.25332	0.735	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.10450	0.003;0.005	T	0.33394	-0.9870	9	0.27082	T	0.32	1.7061	6.3027	0.21121	0.0:0.2256:0.3781:0.3964	rs526680;rs1797509;rs59944859;rs526680	136;136	Q6UVW9;Q6UVW9-2	CLC2A_HUMAN;.	D	136	ENSP00000339732:G136D;ENSP00000396163:G136D	ENSP00000339732:G136D	G	-	2	0	CLEC2A	9960569	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.317000	0.01122	-1.547000	0.01715	-0.550000	0.04213	GGT	C|0.484;T|0.516	0.516	strong		0.343	CLEC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399919.1	NM_207375	
FCRL5	83416	hgsc.bcm.edu	37	1	157504422	157504422	+	Missense_Mutation	SNP	C	C	T	rs73011567	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:157504422C>T	ENST00000361835.3	-	8	1820	c.1663G>A	c.(1663-1665)Gtg>Atg	p.V555M	FCRL5_ENST00000356953.4_Missense_Mutation_p.V555M|FCRL5_ENST00000368190.3_Missense_Mutation_p.V555M|FCRL5_ENST00000368189.3_Missense_Mutation_p.V555M|FCRL5_ENST00000368191.3_Missense_Mutation_p.V470M	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	555	Ig-like C2-type 5.				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)				AAAAGGCTCACCACTTCACTG	0.502													c|||	627	0.1252	0.3268	0.0231	5008	,	,		20298	0.0893		0.0109	False		,,,				2504	0.0798				p.V555M		Atlas-SNP	.											.	FCRL5	177	.	0			c.G1663A						PASS	.	C	MET/VAL,MET/VAL	1165,3241	407.1+/-334.1	160,845,1198	48.0	50.0	50.0		1663,1663	-6.8	0.0	1	dbSNP_130	50	72,8528	41.2+/-98.3	1,70,4229	no	missense,missense	FCRL5	NM_001195388.1,NM_031281.2	21,21	161,915,5427	TT,TC,CC		0.8372,26.4412,9.511	probably-damaging,probably-damaging	555/999,555/978	157504422	1237,11769	2203	4300	6503	SO:0001583	missense	83416	exon8			GGCTCACCACTTC	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.1663G>A	1.37:g.157504422C>T	ENSP00000354691:p.Val555Met	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	225	0.10302197802197802	151	0.30691056910569103	7	0.019337016574585635	60	0.1048951048951049	7	0.009234828496042216	C	12.37	1.919121	0.33908	0.264412	0.008372	ENSG00000143297	ENST00000361835;ENST00000356953;ENST00000368190;ENST00000368191;ENST00000368189	T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38	3.39	-6.79	0.01715	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.300410	0.02487	N	0.089100	T	0.23014	0.0556	M	0.92077	3.27	0.80722	P	0.0	P;P;D;P;P;P	0.55800	0.877;0.892;0.973;0.784;0.86;0.784	P;P;P;P;P;P	0.58660	0.74;0.675;0.843;0.573;0.511;0.672	T	0.43147	-0.9409	9	0.42905	T	0.14	.	6.1042	0.20063	0.0:0.1552:0.3923:0.4525	.	586;470;555;555;555;555	B4DW39;F5GXJ2;Q96RD9-3;A6NJE8;Q96RD9-4;Q96RD9	.;.;.;.;.;FCRL5_HUMAN	M	555;555;555;470;555	ENSP00000354691:V555M;ENSP00000349434:V555M;ENSP00000357173:V555M;ENSP00000357174:V470M;ENSP00000357172:V555M	ENSP00000349434:V555M	V	-	1	0	FCRL5	155771046	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.463000	0.02361	-1.408000	0.02040	0.313000	0.20887	GTG	C|0.903;T|0.097	0.097	strong		0.502	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
BPI	671	hgsc.bcm.edu	37	20	36939052	36939052	+	Silent	SNP	G	G	C	rs5743507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36939052G>C	ENST00000262865.4	+	4	635	c.546G>C	c.(544-546)gtG>gtC	p.V182V	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	182					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)				AGAGCAAAGTGGGGTATGGAC	0.557													g|||	279	0.0557109	0.0061	0.1513	5008	,	,		20228	0.002		0.1193	False		,,,				2504	0.045				p.V182V		Atlas-SNP	.											BPI,caecum,carcinoma,0,1	BPI	67	1	0			c.G546C						PASS	.			90,4316	72.5+/-110.5	1,88,2114	107.0	87.0	94.0		546	2.6	1.0	20	dbSNP_114	94	1001,7599	215.6+/-254.9	61,879,3360	no	coding-synonymous	BPI	NM_001725.2		62,967,5474	CC,CG,GG		11.6395,2.0427,8.3884		182/488	36939052	1091,11915	2203	4300	6503	SO:0001819	synonymous_variant	671	exon4			CAAAGTGGGGTAT	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.546G>C	20.37:g.36939052G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	37	CCDS13303.1																																																																																			G|0.928;C|0.072	0.072	strong		0.557	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
FAM161B	145483	hgsc.bcm.edu	37	14	74402693	74402693	+	Silent	SNP	C	C	T	rs17182699	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74402693C>T	ENST00000534936.1	-	8	1869	c.1764G>A	c.(1762-1764)cgG>cgA	p.R588R	FAM161B_ENST00000286544.3_Silent_p.R651R|RP5-1021I20.5_ENST00000555916.1_RNA			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	588										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						CTTGAACAGCCCGGGTGCCTT	0.468													C|||	219	0.04373	0.0083	0.0648	5008	,	,		18871	0.0		0.1123	False		,,,				2504	0.0511				p.R651R		Atlas-SNP	.											.	FAM161B	67	.	0			c.G1953A						PASS	.	C		96,4310	78.3+/-116.7	2,92,2109	144.0	133.0	137.0		1953	-4.7	0.0	14	dbSNP_123	137	887,7713	199.4+/-243.5	56,775,3469	no	coding-synonymous	FAM161B	NM_152445.2		58,867,5578	TT,TC,CC		10.314,2.1788,7.5581		651/711	74402693	983,12023	2203	4300	6503	SO:0001819	synonymous_variant	145483	exon8			AACAGCCCGGGTG	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 44"""	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.1764G>A	14.37:g.74402693C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_152445	B7Z882|J3KNA2	Silent	SNP	ENST00000534936.1	37		119	0.05448717948717949	1	0.0020325203252032522	29	0.08011049723756906	0	0.0	89	0.11741424802110818	C	3.048	-0.196076	0.06259	0.021788	0.10314	ENSG00000156050	ENST00000556794	.	.	.	4.86	-4.65	0.03339	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.22487	-1.0215	3	.	.	.	20.474	1.6237	0.02719	0.2691:0.1841:0.099:0.4477	rs17182699;rs60311174;rs17182699	.	.	.	S	116	.	.	G	-	1	0	FAM161B	73472446	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.111000	0.01333	-0.712000	0.04988	-0.768000	0.03414	GGC	C|0.935;T|0.065	0.065	strong		0.468	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
DRD5	1816	hgsc.bcm.edu	37	4	9784631	9784631	+	Silent	SNP	C	C	T	rs6283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:9784631C>T	ENST00000304374.2	+	1	1374	c.978C>T	c.(976-978)ccC>ccT	p.P326P		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	326					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)	GTGGACACCCCGAAGGCCCTC	0.587													C|||	3050	0.609026	0.5946	0.6282	5008	,	,		19035	0.6121		0.6302	False		,,,				2504	0.59				p.P326P		Atlas-SNP	.											DRD5,NS,carcinoma,+2,1	DRD5	119	1	0			c.C978T						PASS	.						87.0	88.0	88.0					4																	9784631		2203	4300	6503	SO:0001819	synonymous_variant	1816	exon1			ACACCCCGAAGGC	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.978C>T	4.37:g.9784631C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_000798	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			C|0.407;T|0.593	0.593	strong		0.587	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
MYO1H	283446	hgsc.bcm.edu	37	12	109826535	109826535	+	Silent	SNP	G	G	A	rs61742038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109826535G>A	ENST00000431443.2	+	1	12	c.12G>A	c.(10-12)gcG>gcA	p.A4A	MYO1H_ENST00000310903.5_Silent_p.A4A	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	4						myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						TGGAAGGGGCGCTGACTGCCC	0.502													G|||	341	0.0680911	0.2474	0.0187	5008	,	,		18985	0.0		0.001	False		,,,				2504	0.0				p.A4A		Atlas-SNP	.											.	MYO1H	98	.	0			c.G12A						PASS	.	G		777,3405		61,655,1375	144.0	156.0	152.0		12	-2.6	0.8	12	dbSNP_129	152	12,8460		0,12,4224	no	coding-synonymous	MYO1H	NM_001101421.3		61,667,5599	AA,AG,GG		0.1416,18.5796,6.2352		4/1023	109826535	789,11865	2091	4236	6327	SO:0001819	synonymous_variant	283446	exon1			AGGGGCGCTGACT		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.12G>A	12.37:g.109826535G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	172	85	0.494186	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				G|0.947;A|0.053	0.053	strong		0.502	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
LAMC3	10319	hgsc.bcm.edu	37	9	133901819	133901819	+	Missense_Mutation	SNP	C	C	A	rs386738954|rs2275137	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133901819C>A	ENST00000361069.4	+	2	654	c.521C>A	c.(520-522)cCc>cAc	p.P174H	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	174	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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)		TACGGCCGGCCCGAGGGCCAG	0.682													C|||	1604	0.320288	0.6082	0.2997	5008	,	,		16491	0.1399		0.173	False		,,,				2504	0.2832				p.P174H		Atlas-SNP	.											.	LAMC3	167	.	0			c.C521A						PASS	.	C	HIS/PRO	2363,2043		680,1003,520	33.0	39.0	37.0		521	5.0	1.0	9	dbSNP_100	37	1331,7269		128,1075,3097	yes	missense	LAMC3	NM_006059.3	77	808,2078,3617	AA,AC,CC		15.4767,46.3686,28.4023	benign	174/1576	133901819	3694,9312	2203	4300	6503	SO:0001583	missense	10319	exon2			GCCGGCCCGAGGG	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.521C>A	9.37:g.133901819C>A	ENSP00000354360:p.Pro174His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	167	81	0.48503	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	617	0.2825091575091575	299	0.6077235772357723	100	0.27624309392265195	90	0.15734265734265734	128	0.16886543535620052	C	4.399	0.073716	0.08485	0.536314	0.154767	ENSG00000050555	ENST00000361069;ENST00000355048;ENST00000320021	T	0.75367	-0.93	5.93	4.97	0.65823	Laminin, N-terminal (3);	0.425661	0.26032	N	0.026760	T	0.00012	0.0000	L	0.45137	1.4	0.28175	P	0.9284276	B	0.28291	0.206	B	0.33196	0.159	T	0.52711	-0.8539	9	0.56958	D	0.05	.	3.6237	0.08105	0.1987:0.5665:0.1471:0.0877	rs2275137;rs61041091	174	Q9Y6N6	LAMC3_HUMAN	H	174	ENSP00000354360:P174H	ENSP00000325873:P174H	P	+	2	0	LAMC3	132891640	0.000000	0.05858	0.998000	0.56505	0.010000	0.07245	-0.487000	0.06505	2.826000	0.97356	0.655000	0.94253	CCC	C|0.716;A|0.284	0.284	strong		0.682	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
KIR3DL3	115653	hgsc.bcm.edu	37	19	55246812	55246812	+	Missense_Mutation	SNP	G	G	C	rs16985907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55246812G>C	ENST00000291860.1	+	6	1060	c.1042G>C	c.(1042-1044)Gcc>Ccc	p.A348P	KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	348			A -> P (in allele KIR3DL3*027, allele KIR3DL3*029 and allele KIR3DL3*031; dbSNP:rs16985907).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		TCGCTGGTGTGCCAACAAAAA	0.537													.|||	363	0.072484	0.1725	0.0562	5008	,	,		14126	0.0		0.0586	False		,,,				2504	0.0378				p.A348P		Atlas-SNP	.											.	KIR3DL3	46	.	0			c.G1042C						PASS	.	T	PRO/ALA	652,3306		194,264,1521	110.0	78.0	89.0		1042	-0.3	0.0	19	dbSNP_123	89	492,7318		123,246,3536	no	missense	KIR3DL3	NM_153443.3	27	317,510,5057	CC,CG,GG		6.2996,16.473,9.7213	benign	348/411	55246812	1144,10624	1979	3905	5884	SO:0001583	missense	115653	exon6			TGGTGTGCCAACA	AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.1042G>C	19.37:g.55246812G>C	ENSP00000291860:p.Ala348Pro	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	79	70	0.886076	NM_153443	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	37	CCDS12903.1	128	0.05860805860805861	64	0.13008130081300814	24	0.06629834254143646	0	0.0	40	0.052770448548812667	t	3.404	-0.121634	0.06838	0.16473	0.062996	ENSG00000242019	ENST00000291860	T	0.00473	7.18	0.929	-0.344	0.12628	.	62.167800	0.00166	N	0.000000	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.44019	-0.9355	9	0.62326	D	0.03	.	2.2391	0.04016	0.0:0.2431:0.3133:0.4437	rs16985907;rs45502995;rs16985907	348	Q8N743	KI3L3_HUMAN	P	348	ENSP00000291860:A348P	ENSP00000291860:A348P	A	+	1	0	KIR3DL3	59938624	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-3.000000	0.00653	-0.960000	0.03613	-1.448000	0.01049	GCC	.	.	strong		0.537	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443	
LAMC1	3915	hgsc.bcm.edu	37	1	183072590	183072590	+	Silent	SNP	T	T	C	rs2296288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:183072590T>C	ENST00000258341.4	+	2	803	c.546T>C	c.(544-546)tgT>tgC	p.C182C		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	182	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GTGGTTCCTGTGAGAACACCT	0.552													C|||	2664	0.531949	0.3321	0.6268	5008	,	,		19406	0.628		0.5646	False		,,,				2504	0.6022				p.C182C		Atlas-SNP	.											.	LAMC1	176	.	0			c.T546C						PASS	.	C		1657,2749	658.8+/-400.5	337,983,883	88.0	81.0	83.0		546	-3.3	1.0	1	dbSNP_100	83	4913,3687	528.5+/-381.4	1352,2209,739	no	coding-synonymous	LAMC1	NM_002293.3		1689,3192,1622	CC,CT,TT		42.8721,37.6078,49.4849		182/1610	183072590	6570,6436	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon2			TTCCTGTGAGAAC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.546T>C	1.37:g.183072590T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	191	98	0.513089	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			T|0.487;C|0.513	0.513	strong		0.552	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
RP1	6101	hgsc.bcm.edu	37	8	55539057	55539057	+	Missense_Mutation	SNP	G	G	A	rs444772	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:55539057G>A	ENST00000220676.1	+	4	2763	c.2615G>A	c.(2614-2616)cGt>cAt	p.R872H		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	872			R -> H (in dbSNP:rs444772). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11095597, ECO:0000269|PubMed:11527933, ECO:0000269|PubMed:15933747, ECO:0000269|PubMed:20664799}.		axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CAGAAAAAACGTAAAGGGGAT	0.358													G|||	1363	0.272165	0.1407	0.3055	5008	,	,		16799	0.4415		0.2714	False		,,,				2504	0.2526				p.R872H	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											RP1,caecum,carcinoma,0,1	RP1	429	1	0			c.G2615A						PASS	.	G	HIS/ARG	743,3653		64,615,1519	36.0	38.0	37.0		2615	1.4	1.0	8	dbSNP_80	37	2330,6262		305,1720,2271	yes	missense	RP1	NM_006269.1	29	369,2335,3790	AA,AG,GG		27.1182,16.9017,23.6603	benign	872/2157	55539057	3073,9915	2198	4296	6494	SO:0001583	missense	6101	exon4			AAAAACGTAAAGG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2615G>A	8.37:g.55539057G>A	ENSP00000220676:p.Arg872His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	657	0.3008241758241758	102	0.2073170731707317	109	0.3011049723756906	250	0.4370629370629371	196	0.25857519788918204	G	11.43	1.636342	0.29068	0.169017	0.271182	ENSG00000104237	ENST00000220676	T	0.43294	0.95	5.44	1.42	0.22433	.	0.938342	0.08875	N	0.881013	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.29253	0.239	B	0.22880	0.042	T	0.44997	-0.9291	9	0.56958	D	0.05	.	8.4605	0.32925	0.5628:0.37:0.0671:0.0	rs444772;rs52805057;rs57776921;rs444772	872	P56715	RP1_HUMAN	H	872	ENSP00000220676:R872H	ENSP00000220676:R872H	R	+	2	0	RP1	55701610	0.998000	0.40836	0.994000	0.49952	0.827000	0.46813	1.804000	0.38873	0.327000	0.23409	-0.294000	0.09567	CGT	G|0.735;A|0.265	0.265	strong		0.358	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
CAMTA1	23261	hgsc.bcm.edu	37	1	7723588	7723588	+	Silent	SNP	C	C	T	rs3737906	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:7723588C>T	ENST00000303635.7	+	9	1188	c.981C>T	c.(979-981)aaC>aaT	p.N327N	CAMTA1_ENST00000439411.2_Silent_p.N327N	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGAAGAGGAACGGCAAGGTGG	0.652			T	WWTR1	epitheliod hemangioendothelioma								C|||	298	0.0595048	0.0061	0.0735	5008	,	,		18971	0.0198		0.1431	False		,,,				2504	0.0767				p.N327N		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.C981T						PASS	.	C		135,4271	98.0+/-136.7	1,133,2069	97.0	94.0	95.0		981	-1.3	1.0	1	dbSNP_107	95	1224,7376	246.9+/-275.2	97,1030,3173	no	coding-synonymous	CAMTA1	NM_015215.2		98,1163,5242	TT,TC,CC		14.2326,3.064,10.449		327/1674	7723588	1359,11647	2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			GAGGAACGGCAAG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.981C>T	1.37:g.7723588C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	95	56	0.589474	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1																																																																																			C|0.901;T|0.099	0.099	strong		0.652	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
CLEC18B	497190	hgsc.bcm.edu	37	16	74451970	74451970	+	Missense_Mutation	SNP	G	G	C	rs201240581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:74451970G>C	ENST00000339953.5	-	3	564	c.443C>G	c.(442-444)aCc>aGc	p.T148S		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	148	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.T148S(1)		endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CGTGTAGTGGGTGCAGGTGGC	0.612																																					p.T148S		Atlas-SNP	.											CLEC18B,mouth,carcinoma,0,1	CLEC18B	45	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C443G						scavenged	.						10.0	11.0	11.0					16																	74451970		1710	3535	5245	SO:0001583	missense	497190	exon3			TAGTGGGTGCAGG	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"""C-type lectin domain containing"""	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.443C>G	16.37:g.74451970G>C	ENSP00000341051:p.Thr148Ser	Somatic	565	0	0		WXS	Illumina HiSeq	Phase_I	722	27	0.0373961	NM_001011880	B4DF90	Missense_Mutation	SNP	ENST00000339953.5	37	CCDS32484.1	.	.	.	.	.	.	.	.	.	.	g	3.129	-0.178796	0.06380	.	.	ENSG00000140839	ENST00000429489;ENST00000339953;ENST00000268492	T	0.07688	3.17	3.57	3.57	0.40892	CAP domain (3);	0.557277	0.19650	N	0.109248	T	0.05135	0.0137	N	0.25286	0.73	0.22342	N	0.999188	B;B	0.14012	0.005;0.009	B;B	0.13407	0.007;0.009	T	0.39702	-0.9601	10	0.07030	T	0.85	.	10.55	0.45083	0.0:0.0:1.0:0.0	.	148;148	C9JSV1;Q6UXF7	.;CL18B_HUMAN	S	148	ENSP00000341051:T148S	ENSP00000268492:T148S	T	-	2	0	CLEC18B	73009471	0.995000	0.38212	0.998000	0.56505	0.761000	0.43186	1.684000	0.37649	1.821000	0.53095	0.531000	0.56144	ACC	.	.	weak		0.612	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880	
EML3	256364	hgsc.bcm.edu	37	11	62378660	62378660	+	Silent	SNP	G	G	A	rs12808829	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:62378660G>A	ENST00000394773.2	-	3	658	c.351C>T	c.(349-351)agC>agT	p.S117S	EML3_ENST00000531557.1_5'Flank|EML3_ENST00000494176.2_Silent_p.S89S|ROM1_ENST00000534093.1_5'Flank|ROM1_ENST00000278833.3_5'Flank|EML3_ENST00000278845.4_Silent_p.S118S|EML3_ENST00000529309.1_Silent_p.S117S	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	117						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ATTGGGTCCCGCTAGGCTCTT	0.687													A|||	972	0.194089	0.1936	0.2032	5008	,	,		15245	0.0506		0.3161	False		,,,				2504	0.2106				p.S117S		Atlas-SNP	.											.	EML3	61	.	0			c.C351T						PASS	.	A		926,3418		102,722,1348	11.0	14.0	13.0		351	-5.5	0.1	11	dbSNP_121	13	2990,5538		549,1892,1823	no	coding-synonymous	EML3	NM_153265.2		651,2614,3171	AA,AG,GG		35.061,21.3168,30.4226		117/897	62378660	3916,8956	2172	4264	6436	SO:0001819	synonymous_variant	256364	exon3			GGTCCCGCTAGGC	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.351C>T	11.37:g.62378660G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_153265	Q6ZQW7|Q8NA55	Silent	SNP	ENST00000394773.2	37	CCDS8023.2	472	0.21611721611721613	112	0.22764227642276422	91	0.2513812154696133	32	0.055944055944055944	237	0.31266490765171506	A	4.052	0.007268	0.07866	0.213168	0.35061	ENSG00000149499	ENST00000394776	.	.	.	5.05	-5.49	0.02584	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999872094	.	.	.	.	.	.	T	0.37865	-0.9687	3	.	.	.	-0.0522	7.3335	0.26596	0.2996:0.2839:0.4165:0.0	rs12808829	.	.	.	W	112	.	.	R	-	1	2	EML3	62135236	0.008000	0.16893	0.095000	0.20976	0.334000	0.28698	-0.688000	0.05150	-1.005000	0.03417	-0.521000	0.04368	CGG	G|0.761;A|0.239	0.239	strong		0.687	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
NAGS	162417	hgsc.bcm.edu	37	17	42084067	42084067	+	Silent	SNP	T	T	C	rs55708447	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42084067T>C	ENST00000293404.3	+	4	1204	c.1086T>C	c.(1084-1086)ttT>ttC	p.F362F	PYY_ENST00000360085.2_5'Flank	NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	362	Amino-acid kinase domain (AAK).				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CTGAGCTCTTTAGCAACAAGG	0.682													T|||	535	0.106829	0.0915	0.111	5008	,	,		12642	0.0139		0.2097	False		,,,				2504	0.1145				p.F362F		Atlas-SNP	.											.	NAGS	25	.	0			c.T1086C						PASS	.	T		419,3957		26,367,1795	17.0	16.0	17.0		1086	1.9	1.0	17	dbSNP_129	17	1577,6951		162,1253,2849	no	coding-synonymous	NAGS	NM_153006.2		188,1620,4644	CC,CT,TT		18.492,9.575,15.4681		362/535	42084067	1996,10908	2188	4264	6452	SO:0001819	synonymous_variant	162417	exon4			GCTCTTTAGCAAC	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.1086T>C	17.37:g.42084067T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_153006	B2RAZ9|Q8IWR4	Silent	SNP	ENST00000293404.3	37	CCDS11473.1																																																																																			T|0.864;C|0.136	0.136	strong		0.682	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412347	105412347	+	Silent	SNP	C	C	T	rs55842266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105412347C>T	ENST00000333244.5	-	7	9560	c.9441G>A	c.(9439-9441)aaG>aaA	p.K3147K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3147						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCATCTTGAACTTGGGCATTT	0.602													.|||	305	0.0609026	0.0106	0.0778	5008	,	,		16789	0.0109		0.1491	False		,,,				2504	0.0777				p.K3147K		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,neuroblastoma,0,1	AHNAK2	719	1	0			c.G9441A						scavenged	.						199.0	143.0	161.0					14																	105412347		1924	4066	5990	SO:0001819	synonymous_variant	113146	exon7			CTTGAACTTGGGC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9441G>A	14.37:g.105412347C>T		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	weak		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ABCA4	24	hgsc.bcm.edu	37	1	94512565	94512565	+	Missense_Mutation	SNP	C	C	T	rs1801581|rs281865513	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:94512565C>T	ENST00000370225.3	-	19	2914	c.2828G>A	c.(2827-2829)cGg>cAg	p.R943Q	ABCA4_ENST00000535735.1_Missense_Mutation_p.R869Q	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	943	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> Q (in linkage disequilibrium with A- 863 in the European population; dbSNP:rs1801581). {ECO:0000269|PubMed:10746567, ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11385708, ECO:0000269|PubMed:11527935, ECO:0000269|PubMed:11594993, ECO:0000269|PubMed:9054934, ECO:0000269|Ref.5}.|R -> W (in STGD1 and FFM; dbSNP:rs61749446). {ECO:0000269|PubMed:11379881, 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)		CACAGCTGGCCGGCCACAGGG	0.517													C|||	77	0.0153754	0.0023	0.0086	5008	,	,		16564	0.0		0.0368	False		,,,				2504	0.0317				p.R943Q		Atlas-SNP	.											.	ABCA4	275	.	0			c.G2828A	GRCh37	CM024629	ABCA4	M	rs1801581	PASS	.	C	GLN/ARG	63,4343	59.3+/-96.0	0,63,2140	148.0	157.0	154.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2828	3.5	1.0	1	dbSNP_89	154	353,8247	119.4+/-178.7	8,337,3955	yes	missense	ABCA4	NM_000350.2	43	8,400,6095	TT,TC,CC		4.1047,1.4299,3.1985	probably-damaging	943/2274	94512565	416,12590	2203	4300	6503	SO:0001583	missense	24	exon19			GCTGGCCGGCCAC	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.2828G>A	1.37:g.94512565C>T	ENSP00000359245:p.Arg943Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	32	0.014652014652014652	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	27	0.03562005277044855	C	11.01	1.512669	0.27123	0.014299	0.041047	ENSG00000198691	ENST00000370225;ENST00000535735	D;D	0.93659	-3.26;-2.81	5.62	3.54	0.40534	ABC transporter-like (1);	0.312543	0.36134	N	0.002764	T	0.78477	0.4289	L	0.28458	0.855	0.21782	N	0.999548	P;B	0.35774	0.519;0.01	B;B	0.33392	0.163;0.012	T	0.70648	-0.4814	10	0.40728	T	0.16	.	7.5546	0.27817	0.0:0.6477:0.0:0.3523	rs1801581	869;943	F5H6E5;P78363	.;ABCA4_HUMAN	Q	943;869	ENSP00000359245:R943Q;ENSP00000437682:R869Q	ENSP00000359245:R943Q	R	-	2	0	ABCA4	94285153	0.767000	0.28508	0.992000	0.48379	0.372000	0.29890	1.065000	0.30592	1.294000	0.44707	0.655000	0.94253	CGG	C|0.975;T|0.025	0.025	strong		0.517	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
HPS3	84343	hgsc.bcm.edu	37	3	148858267	148858267	+	Missense_Mutation	SNP	A	A	G	rs199722122		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148858267A>G	ENST00000296051.2	+	2	834	c.694A>G	c.(694-696)Ata>Gta	p.I232V	HPS3_ENST00000460120.1_Intron	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	232					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)			CAACAATCGAATAAGACGGAC	0.393									Hermansky-Pudlak syndrome																												p.I232V		Atlas-SNP	.											.	HPS3	104	.	0			c.A694G						PASS	.						82.0	80.0	81.0					3																	148858267		2168	4282	6450	SO:0001583	missense	84343	exon2	Familial Cancer Database	HPS, HPS1-8	AATCGAATAAGAC	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.694A>G	3.37:g.148858267A>G	ENSP00000296051:p.Ile232Val	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	133	79	0.593985	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	5.521	0.281147	0.10458	.	.	ENSG00000163755	ENST00000296051	T	0.62498	0.02	5.46	-7.86	0.01187	.	2.003110	0.01674	N	0.025777	T	0.28962	0.0719	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	10	0.28530	T	0.3	2.052	7.5676	0.27887	0.0972:0.071:0.7585:0.0733	.	232	Q969F9	HPS3_HUMAN	V	232	ENSP00000296051:I232V	ENSP00000296051:I232V	I	+	1	0	HPS3	150340957	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.081000	0.11321	-2.013000	0.00949	-0.263000	0.10527	ATA	A|0.999;G|0.001	0.001	weak		0.393	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
MASP1	5648	hgsc.bcm.edu	37	3	186954324	186954324	+	Intron	SNP	G	G	A	rs3774268	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:186954324G>A	ENST00000337774.5	-	10	1693				MASP1_ENST00000392472.2_Silent_p.S332S|MASP1_ENST00000296280.6_Silent_p.S445S|MASP1_ENST00000495249.1_Intron	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	90	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	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	
DENND4B	9909	hgsc.bcm.edu	37	1	153909069	153909069	+	Silent	SNP	G	G	C	rs1043608	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153909069G>C	ENST00000361217.4	-	16	2806	c.2388C>G	c.(2386-2388)gcC>gcG	p.A796A		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	796					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GCACATGGTAGGCTGTGTGCA	0.627													g|||	1316	0.26278	0.0991	0.4063	5008	,	,		18571	0.2847		0.2913	False		,,,				2504	0.3303				p.A796A		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2388G						PASS	.	G		561,3657		28,505,1576	52.0	54.0	53.0		2388	0.3	1.0	1	dbSNP_86	53	2472,5982		359,1754,2114	no	coding-synonymous	DENND4B	NM_014856.2		387,2259,3690	CC,CG,GG		29.2406,13.3001,23.9347		796/1497	153909069	3033,9639	2109	4227	6336	SO:0001819	synonymous_variant	9909	exon16			ATGGTAGGCTGTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"""DENN/MADD domain containing"""	29044	protein-coding gene	gene with protein product			"""KIAA0476"""	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2388C>G	1.37:g.153909069G>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	196	107	0.545918	NM_014856	Q5T4K0	Silent	SNP	ENST00000361217.4	37	CCDS44228.1																																																																																			G|0.706;C|0.294	0.294	strong		0.627	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
COL14A1	7373	hgsc.bcm.edu	37	8	121210069	121210069	+	Silent	SNP	T	T	C	rs2305598	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:121210069T>C	ENST00000297848.3	+	7	882	c.612T>C	c.(610-612)ggT>ggC	p.G204G	COL14A1_ENST00000247781.3_Intron|COL14A1_ENST00000537875.1_Silent_p.G204G|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.G204G	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)			AGTATAGTGGTGACCCCAGAA	0.408													C|||	3177	0.634385	0.8192	0.6009	5008	,	,		16103	0.6597		0.4622	False		,,,				2504	0.5593				p.G204G		Atlas-SNP	.											COL14A1,rectum,carcinoma,0,1	COL14A1	292	1	0			c.T612C						PASS	.	C		3359,1047	385.1+/-325.6	1310,739,154	122.0	125.0	124.0		612	-6.2	0.6	8	dbSNP_100	124	4124,4476	590.4+/-392.7	1002,2120,1178	no	coding-synonymous	COL14A1	NM_021110.1		2312,2859,1332	CC,CT,TT		47.9535,23.7631,42.465		204/1797	121210069	7483,5523	2203	4300	6503	SO:0001819	synonymous_variant	7373	exon7			TAGTGGTGACCCC		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.612T>C	8.37:g.121210069T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	189	186	0.984127	NM_021110		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																			T|0.406;C|0.594	0.594	strong		0.408	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
TBATA	219793	hgsc.bcm.edu	37	10	72536936	72536936	+	Silent	SNP	A	A	G	rs2254433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	40	1	0.025		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	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	
ZNF462	58499	hgsc.bcm.edu	37	9	109691676	109691676	+	Missense_Mutation	SNP	A	A	G	rs3814538	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:109691676A>G	ENST00000277225.5	+	3	5772	c.5483A>G	c.(5482-5484)aAc>aGc	p.N1828S	ZNF462_ENST00000441147.2_Missense_Mutation_p.N673S|ZNF462_ENST00000457913.1_Missense_Mutation_p.N1828S			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1828			N -> S (in dbSNP:rs3814538).		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						GAGAGAGGCAACTTTGAGAAA	0.542													G|||	2802	0.559505	0.8623	0.4625	5008	,	,		19918	0.4782		0.3917	False		,,,				2504	0.4755				p.N1828S		Atlas-SNP	.											.	ZNF462	322	.	0			c.A5483G						PASS	.	G	SER/ASN	3402,1004	361.6+/-315.8	1329,744,130	83.0	73.0	77.0		5483	3.9	1.0	9	dbSNP_107	77	3126,5474	647.7+/-400.4	542,2042,1716	yes	missense	ZNF462	NM_021224.4	46	1871,2786,1846	GG,GA,AA		36.3488,22.7871,49.8078	benign	1828/2507	109691676	6528,6478	2203	4300	6503	SO:0001583	missense	58499	exon3			GAGGCAACTTTGA	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.5483A>G	9.37:g.109691676A>G	ENSP00000277225:p.Asn1828Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	1134	0.5192307692307693	411	0.8353658536585366	170	0.4696132596685083	258	0.45104895104895104	295	0.3891820580474934	G	0.006	-2.046486	0.00398	0.772129	0.363488	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.04654	3.58;4.03;4.14;4.16	5.92	3.86	0.44501	.	0.653773	0.17254	N	0.181055	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	0.19353	-1.0308	9	0.07030	T	0.85	.	5.0988	0.14749	0.4595:0.0:0.5405:0.0	rs3814538;rs17788089;rs17846198;rs17859213;rs52813323;rs57069281;rs3814538	1828;1828	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	S	1828;1828;711;673	ENSP00000277225:N1828S;ENSP00000414570:N1828S;ENSP00000363818:N711S;ENSP00000397306:N673S	ENSP00000277225:N1828S	N	+	2	0	ZNF462	108731497	0.013000	0.17824	0.991000	0.47740	0.824000	0.46624	1.305000	0.33493	0.858000	0.35431	-0.215000	0.12644	AAC	G|0.519;N|0.001	0.519	strong		0.542	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
FAM86B1	85002	hgsc.bcm.edu	37	8	12044010	12044010	+	Missense_Mutation	SNP	C	C	T	rs201876260	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:12044010C>T	ENST00000448228.2	-	5	540	c.491G>A	c.(490-492)cGa>cAa	p.R164Q	FAM86B1_ENST00000533513.1_3'UTR|FAM86B1_ENST00000533852.2_Missense_Mutation_p.R198Q|FAM86B1_ENST00000534520.1_Intron|FAM86B1_ENST00000321602.8_Intron	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	164										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		GACATTCCCTCGGAGCTGCTC	0.617																																					p.R164Q		Atlas-SNP	.											FAM86B1,NS,carcinoma,0,1	FAM86B1	7	1	0			c.G491A						scavenged	.						39.0	43.0	42.0					8																	12044010		1489	2646	4135	SO:0001583	missense	85002	exon5			TTCCCTCGGAGCT	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.491G>A	8.37:g.12044010C>T	ENSP00000407067:p.Arg164Gln	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	128	25	0.195312	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.	.	.	.	.	.	.	.	.	.	-	11.09	1.537041	0.27475	.	.	ENSG00000186523	ENST00000431227;ENST00000448228;ENST00000526708	T	0.20881	2.04	1.17	1.17	0.20885	.	.	.	.	.	T	0.12689	0.0308	L	0.33624	1.015	0.80722	D	1	B;B	0.32573	0.376;0.123	B;B	0.28385	0.089;0.046	T	0.13124	-1.0521	9	0.24483	T	0.36	.	8.2654	0.31810	0.0:1.0:0.0:0.0	.	164;198	Q8N7N1;E9PN63	F86B1_HUMAN;.	Q	198;164;198	ENSP00000407067:R164Q	ENSP00000444227:R198Q	R	-	2	0	FAM86B1	12081419	0.000000	0.05858	0.202000	0.23494	0.276000	0.26787	-0.432000	0.06956	0.950000	0.37743	0.173000	0.16961	CGA	C|0.983;T|0.016	0.016	strong		0.617	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
ABCB8	11194	hgsc.bcm.edu	37	7	150732812	150732812	+	Missense_Mutation	SNP	C	C	T	rs17545756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150732812C>T	ENST00000297504.6	+	7	1027	c.961C>T	c.(961-963)Cgc>Tgc	p.R321C	ABCB8_ENST00000477719.1_Missense_Mutation_p.R304C|ABCB8_ENST00000477092.1_Missense_Mutation_p.R304C|ABCB8_ENST00000542328.1_Missense_Mutation_p.R216C|ABCB8_ENST00000356058.4_Missense_Mutation_p.R341C|ABCB8_ENST00000358849.4_Missense_Mutation_p.R304C|ABCB8_ENST00000498578.1_Missense_Mutation_p.R304C			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	321	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	AAAATTGTCTCGCCAGTGTCA	0.622													C|||	136	0.0271565	0.0106	0.0418	5008	,	,		3043	0.0198		0.0606	False		,,,				2504	0.0123				p.R304C		Atlas-SNP	.											.	ABCB8	65	.	0			c.C910T						PASS	.	C	CYS/ARG	75,4331	66.4+/-103.9	0,75,2128	102.0	78.0	86.0		910	4.8	1.0	7	dbSNP_123	86	508,8092	144.8+/-200.6	12,484,3804	yes	missense	ABCB8	NM_007188.3	180	12,559,5932	TT,TC,CC		5.907,1.7022,4.4825	probably-damaging	304/719	150732812	583,12423	2203	4300	6503	SO:0001583	missense	11194	exon6			TTGTCTCGCCAGT	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.961C>T	7.37:g.150732812C>T	ENSP00000297504:p.Arg321Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		89|89	0.04075091575091575|0.04075091575091575	9|9	0.018292682926829267|0.018292682926829267	19|19	0.052486187845303865|0.052486187845303865	8|8	0.013986013986013986|0.013986013986013986	53|53	0.06992084432717678|0.06992084432717678	C|C	19.43|19.43	3.826831|3.826831	0.71143|0.71143	0.017022|0.017022	0.05907|0.05907	ENSG00000197150|ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092|ENST00000491920	D;D;D;D;D;D;D|D	0.90563|0.90069	-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69|-2.61	4.79|4.79	4.79|4.79	0.61399|0.61399	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67590|0.67590	0.2909|0.2909	M|M	0.87758|0.87758	2.905|2.905	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D|.	0.79784|.	0.975;0.985;0.978;0.985;0.975;0.985;0.993|.	T|T	0.80756|0.80756	-0.1240|-0.1240	10|7	0.87932|0.87932	D|D	0|0	0.8042|0.8042	15.3604|15.3604	0.74469|0.74469	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs17545756;rs60582410;rs17545756|rs17545756;rs60582410;rs17545756	216;304;134;321;304;304;341|.	G3XAP3;A5D8W3;B3KND2;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8|.	.;.;.;ABCB8_HUMAN;.;.;.|.	C|L	304;287;321;216;304;341;304;304|36	ENSP00000351717:R304C;ENSP00000297504:R321C;ENSP00000438776:R216C;ENSP00000418271:R304C;ENSP00000348353:R341C;ENSP00000419891:R304C;ENSP00000419558:R304C|ENSP00000420162:S36L	ENSP00000297504:R321C|ENSP00000420162:S36L	R|S	+|+	1|2	0|0	ABCB8|ABCB8	150363745|150363745	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	3.804000|3.804000	0.55568|0.55568	2.210000|2.210000	0.71456|0.71456	0.561000|0.561000	0.74099|0.74099	CGC|TCG	C|0.964;T|0.036	0.036	strong		0.622	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
POLR2A	5430	hgsc.bcm.edu	37	17	7399866	7399866	+	Silent	SNP	G	G	A	rs2301609	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7399866G>A	ENST00000322644.6	+	4	870	c.471G>A	c.(469-471)ggG>ggA	p.G157G	POLR2A_ENST00000572844.1_Silent_p.G157G	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	157					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				GCGAGGGTGGGGAGGAGATGG	0.532													G|||	859	0.171526	0.2186	0.0994	5008	,	,		19352	0.0278		0.1849	False		,,,				2504	0.2935				p.G157G		Atlas-SNP	.											.	POLR2A	157	.	0			c.G471A						PASS	.	G		913,3493	352.8+/-311.9	90,733,1380	143.0	148.0	146.0		471	-0.5	1.0	17	dbSNP_100	146	1798,6802	323.7+/-316.1	221,1356,2723	no	coding-synonymous	POLR2A	NM_000937.4		311,2089,4103	AA,AG,GG		20.907,20.7217,20.8442		157/1971	7399866	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon4			GGGTGGGGAGGAG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.471G>A	17.37:g.7399866G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	138	55	0.398551	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			G|0.810;A|0.190	0.190	strong		0.532	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253969	39253969	+	Missense_Mutation	SNP	T	T	G	rs147906218	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39253969T>G	ENST00000333822.4	-	1	424	c.368A>C	c.(367-369)aAc>aCc	p.N123T		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	123	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].			N -> T (in Ref. 2; CAC27579). {ECO:0000305}.	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						gcggcagcagttgggctggca	0.672													t|||	2493	0.497804	0.5408	0.5274	5008	,	,		15104	0.3234		0.6054	False		,,,				2504	0.4877				p.N123T		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,+1,1	KRTAP4-8	57	1	0			c.A368C						PASS	.						3.0	4.0	4.0					17																	39253969		499	1210	1709	SO:0001583	missense	728224	exon1			CAGCAGTTGGGCT	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.368A>C	17.37:g.39253969T>G	ENSP00000328444:p.Asn123Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	813	0.37225274725274726	189	0.38414634146341464	155	0.4281767955801105	135	0.23601398601398602	334	0.44063324538258575	.	7.852	0.724185	0.15439	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01252	5.1	3.06	-2.81	0.05805	.	1.269160	0.05476	N	0.553971	T	0.00012	0.0000	N	0.00465	-1.465	0.52501	P	4.4000000000044004E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41466	-0.9507	9	0.07482	T	0.82	.	0.8758	0.01223	0.148:0.3433:0.1829:0.3257	.	123	Q9BYQ9	KRA48_HUMAN	T	123;108	ENSP00000328444:N123T	ENSP00000414561:N108T	N	-	2	0	KRTAP4-8	36507495	0.000000	0.05858	0.212000	0.23672	0.805000	0.45488	-2.862000	0.00725	-0.915000	0.03823	-0.405000	0.06341	AAC	T|0.629;G|0.371	0.371	strong		0.672	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
IKBKAP	8518	hgsc.bcm.edu	37	9	111668652	111668652	+	Missense_Mutation	SNP	C	C	T	rs838827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111668652C>T	ENST00000374647.5	-	14	1881	c.1574G>A	c.(1573-1575)cGg>cAg	p.R525Q	IKBKAP_ENST00000537196.1_Missense_Mutation_p.R176Q	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	525			R -> Q (in dbSNP:rs838827).		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						AATGACAGACCGGGGGCTGAA	0.463													C|||	286	0.0571086	0.1324	0.0346	5008	,	,		19194	0.0		0.0686	False		,,,				2504	0.0184				p.R525Q		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G1574A						PASS	.	C	GLN/ARG	500,3906	232.3+/-245.9	26,448,1729	137.0	121.0	126.0		1574	0.3	0.3	9	dbSNP_86	126	547,8053	150.9+/-205.7	18,511,3771	yes	missense	IKBKAP	NM_003640.3	43	44,959,5500	TT,TC,CC		6.3605,11.3482,8.0501	benign	525/1333	111668652	1047,11959	2203	4300	6503	SO:0001583	missense	8518	exon14			ACAGACCGGGGGC	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.1574G>A	9.37:g.111668652C>T	ENSP00000363779:p.Arg525Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	125	0.05723443223443223	67	0.13617886178861788	11	0.03038674033149171	0	0.0	47	0.06200527704485488	C	1.540	-0.542007	0.04053	0.113482	0.063605	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.26067	2.14;1.76	5.6	0.32	0.15878	.	0.690799	0.14980	N	0.287310	T	0.00039	0.0001	N	0.00446	-1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39981	-0.9587	9	0.10902	T	0.67	-0.7265	8.2551	0.31751	0.0:0.343:0.0:0.657	rs838827;rs1556536;rs1772034;rs2230790;rs52818078;rs59641501;rs838827	525	O95163	ELP1_HUMAN	Q	525;176	ENSP00000363779:R525Q;ENSP00000439367:R176Q	ENSP00000363779:R525Q	R	-	2	0	IKBKAP	110708473	0.964000	0.33143	0.343000	0.25615	0.003000	0.03518	0.340000	0.19892	0.149000	0.19098	-0.321000	0.08615	CGG	C|0.924;T|0.076	0.076	strong		0.463	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
ZNF354B	117608	hgsc.bcm.edu	37	5	178294059	178294059	+	Silent	SNP	T	T	C	rs113633676|rs11952817|rs386695542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:178294059T>C	ENST00000322434.3	+	4	469	c.243T>C	c.(241-243)ggT>ggC	p.G81G		NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	81	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G81G(1)		breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGTTCTGGTGTCTCCTCTC	0.507													C|||	1517	0.302915	0.379	0.3055	5008	,	,		17700	0.1538		0.4254	False		,,,				2504	0.226				p.G81G		Atlas-SNP	.											ZNF354B,NS,carcinoma,0,1	ZNF354B	67	1	1	Substitution - coding silent(1)	stomach(1)	c.T243C						PASS	.	C		1588,2818		329,930,944	148.0	139.0	142.0		243	-2.0	0.0	5	dbSNP_120	142	3351,5249		699,1953,1648	no	coding-synonymous	ZNF354B	NM_058230.2		1028,2883,2592	CC,CT,TT		38.9651,36.0418,37.9748		81/613	178294059	4939,8067	2203	4300	6503	SO:0001819	synonymous_variant	117608	exon4			TTCTGGTGTCTCC	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.243T>C	5.37:g.178294059T>C		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	242	125	0.516529	NM_058230	A8K0V2|Q5U5Z4	Silent	SNP	ENST00000322434.3	37	CCDS4439.1																																																																																			T|0.635;C|0.365	0.365	strong		0.507	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
PKN1	5585	hgsc.bcm.edu	37	19	14578707	14578707	+	Missense_Mutation	SNP	G	G	A	rs35416389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14578707G>A	ENST00000242783.6	+	15	2069	c.1904G>A	c.(1903-1905)cGg>cAg	p.R635Q	PKN1_ENST00000342216.4_Missense_Mutation_p.R641Q	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	635	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in dbSNP:rs35416389). {ECO:0000269|PubMed:17344846}.		activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						TCCGAATTCCGGCCCAGTGGG	0.642													G|||	71	0.0141773	0.0023	0.0245	5008	,	,		15098	0.0		0.0457	False		,,,				2504	0.0051				p.R641Q	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.G1922A						PASS	.	G	GLN/ARG,GLN/ARG	37,3791		1,35,1878	48.0	51.0	50.0		1904,1922	-2.1	0.2	19	dbSNP_126	50	336,7914		10,316,3799	yes	missense,missense	PKN1	NM_002741.3,NM_213560.1	43,43	11,351,5677	AA,AG,GG		4.0727,0.9666,3.0883	benign,benign	635/943,641/949	14578707	373,11705	1914	4125	6039	SO:0001583	missense	5585	exon15			AATTCCGGCCCAG	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"""protein kinase C-like 1"""	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.1904G>A	19.37:g.14578707G>A	ENSP00000242783:p.Arg635Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	37	CCDS42513.1	47	0.02152014652014652	1	0.0020325203252032522	11	0.03038674033149171	1	0.0017482517482517483	34	0.044854881266490766	G	13.26	2.182803	0.38511	0.009666	0.040727	ENSG00000123143	ENST00000242783;ENST00000342216	T;T	0.65364	-0.15;-0.15	4.62	-2.13	0.07144	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.310995	0.26539	U	0.023818	T	0.15478	0.0373	L	0.46819	1.47	0.23076	N	0.998333	B;B	0.10296	0.002;0.003	B;B	0.04013	0.001;0.001	T	0.21827	-1.0234	10	0.72032	D	0.01	-32.0946	3.2848	0.06927	0.3476:0.0:0.3657:0.2868	rs35416389;rs52826627;rs61733709	641;635	Q16512-2;Q16512	.;PKN1_HUMAN	Q	635;641	ENSP00000242783:R635Q;ENSP00000343325:R641Q	ENSP00000242783:R635Q	R	+	2	0	PKN1	14439707	0.042000	0.20092	0.226000	0.23910	0.761000	0.43186	0.346000	0.19997	0.000000	0.14550	0.561000	0.74099	CGG	G|0.971;A|0.029	0.029	strong		0.642	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560	
DNAH14	127602	hgsc.bcm.edu	37	1	225380564	225380564	+	Missense_Mutation	SNP	A	A	G	rs191528375|rs144339803	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225380564A>G	ENST00000445597.2	+	25	4556	c.4556A>G	c.(4555-4557)aAg>aGg	p.K1519R	DNAH14_ENST00000439375.2_Missense_Mutation_p.K1924R|DNAH14_ENST00000430092.1_Missense_Mutation_p.K1924R			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1519					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						AAGAACACAAAGAAAGACATT	0.294													A|||	21	0.00419329	0.0	0.0086	5008	,	,		15476	0.0		0.0149	False		,,,				2504	0.0				p.K1924R		Atlas-SNP	.											.	DNAH14	300	.	0			c.A5771G						PASS	.						187.0	158.0	167.0					1																	225380564		692	1586	2278	SO:0001583	missense	127602	exon37			ACACAAAGAAAGA	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.4556A>G	1.37:g.225380564A>G	ENSP00000409472:p.Lys1519Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	179	75	0.418994	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		15	0.006868131868131868	0	0.0	5	0.013812154696132596	0	0.0	10	0.013192612137203167	A	13.33	2.205121	0.39003	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.31769	3.3;1.48;1.48	4.9	-0.189	0.13260	.	.	.	.	.	T	0.09069	0.0224	N	0.04090	-0.28	0.23304	N	0.997948	B	0.13594	0.008	B	0.14578	0.011	T	0.32134	-0.9918	9	0.22109	T	0.4	.	8.6113	0.33804	0.6451:0.0:0.3549:0.0	.	1924	Q0VDD8-4	.	R	1519;1924;1924	ENSP00000409472:K1519R;ENSP00000414402:K1924R;ENSP00000392061:K1924R	ENSP00000414402:K1924R	K	+	2	0	DNAH14	223447187	0.836000	0.29430	0.026000	0.17262	0.025000	0.11179	0.851000	0.27751	0.011000	0.14865	-0.520000	0.04383	AAG	A|0.993;G|0.007	0.007	strong		0.294	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97922875	97922875	+	Silent	SNP	G	G	A	rs13008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97922875G>A	ENST00000005260.8	-	14	1709	c.1494C>T	c.(1492-1494)cgC>cgT	p.R498R		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	498	Binds F-actin.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			TCACAGTCGGGCGGAGTTTCA	0.537													G|||	739	0.147564	0.0144	0.2637	5008	,	,		16327	0.001		0.4284	False		,,,				2504	0.1074				p.R498R		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.C1494T						PASS	.	G		433,3973	208.5+/-229.5	21,391,1791	129.0	127.0	128.0		1494	-4.7	0.0	7	dbSNP_52	128	4026,4574	556.9+/-386.9	945,2136,1219	no	coding-synonymous	BAIAP2L1	NM_018842.4		966,2527,3010	AA,AG,GG		46.814,9.8275,34.2842		498/512	97922875	4459,8547	2203	4300	6503	SO:0001819	synonymous_variant	55971	exon14			AGTCGGGCGGAGT	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1494C>T	7.37:g.97922875G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			G|0.717;A|0.283	0.283	strong		0.537	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
ABCC10	89845	hgsc.bcm.edu	37	6	43406501	43406501	+	Silent	SNP	C	C	T	rs2277122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43406501C>T	ENST00000372530.4	+	8	2310	c.2095C>T	c.(2095-2097)Cta>Tta	p.L699L	ABCC10_ENST00000244533.3_Silent_p.L671L	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	699	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)	CAAGGAGGTGCTAGAAGCCTG	0.542													C|||	401	0.0800719	0.0045	0.0692	5008	,	,		21051	0.1131		0.0487	False		,,,				2504	0.1881				p.L699L		Atlas-SNP	.											.	ABCC10	118	.	0			c.C2095T						PASS	.	C	,	50,4356	50.2+/-85.5	0,50,2153	138.0	122.0	127.0		2095,2011	2.3	0.9	6	dbSNP_100	127	406,8194	128.5+/-186.7	7,392,3901	no	coding-synonymous,coding-synonymous	ABCC10	NM_001198934.1,NM_033450.2	,	7,442,6054	TT,TC,CC		4.7209,1.1348,3.5061	,	699/1493,671/1465	43406501	456,12550	2203	4300	6503	SO:0001819	synonymous_variant	89845	exon8			GAGGTGCTAGAAG	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.2095C>T	6.37:g.43406501C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	130	63	0.484615	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			C|0.947;T|0.053	0.053	strong		0.542	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
OXER1	165140	hgsc.bcm.edu	37	2	42990522	42990522	+	Silent	SNP	C	C	T	rs12712859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:42990522C>T	ENST00000378661.2	-	1	879	c.798G>A	c.(796-798)gcG>gcA	p.A266A		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	266					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						AGAGGATGAGCGCCAGTGGCA	0.667													.|||	1714	0.342252	0.236	0.2363	5008	,	,		18313	0.5913		0.2396	False		,,,				2504	0.41				p.A266A		Atlas-SNP	.											.	OXER1	33	.	0			c.G798A						PASS	.	C		1112,3292		143,826,1233	15.0	17.0	16.0		798	-5.8	0.0	2	dbSNP_121	16	1794,6804		197,1400,2702	no	coding-synonymous	OXER1	NM_148962.4		340,2226,3935	TT,TC,CC		20.8653,25.2498,22.3504		266/424	42990522	2906,10096	2202	4299	6501	SO:0001819	synonymous_variant	165140	exon1			GATGAGCGCCAGT	AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"""GPCR / Class A : Leukotriene receptors"""	24884	protein-coding gene	gene with protein product	"""5-oxo-ETE acid G-protein-coupled receptor 1"""					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.798G>A	2.37:g.42990522C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_148962	Q86WP7|Q8NGW4	Silent	SNP	ENST00000378661.2	37	CCDS1810.1																																																																																			C|0.719;T|0.281	0.281	strong		0.667	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962	
FMN1	342184	hgsc.bcm.edu	37	15	33359370	33359370	+	Intron	SNP	C	C	T	rs11072170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33359370C>T	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Missense_Mutation_p.G239E|FMN1_ENST00000558197.1_Missense_Mutation_p.G239E|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G239E(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GTCTTGGGACCCTTCTTCTCC	0.512													C|||	1305	0.260583	0.1929	0.4337	5008	,	,		18120	0.1478		0.3569	False		,,,				2504	0.2464				p.G239E		Atlas-SNP	.											FMN1_ENST00000334528,NS,carcinoma,0,1	FMN1	174	1	1	Substitution - Missense(1)	stomach(1)	c.G716A						PASS	.	C	GLU/GLY	781,3349		69,643,1353	85.0	90.0	88.0		716	0.4	0.0	15	dbSNP_120	88	2934,5482		520,1894,1794	yes	missense	FMN1	NM_001103184.2	98	589,2537,3147	TT,TC,CC		34.8622,18.9104,29.611	benign	239/1197	33359370	3715,8831	2065	4208	6273	SO:0001627	intron_variant	342184	exon1			TGGGACCCTTCTT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2095G>A	15.37:g.33359370C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		617	0.2825091575091575	85	0.17276422764227642	154	0.425414364640884	96	0.16783216783216784	282	0.3720316622691293	C	0	-2.721836	0.00092	0.189104	0.348622	ENSG00000248905	ENST00000334528	T	0.34667	1.35	4.57	0.42	0.16444	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B;B	0.14012	0.009;0.001	B;B	0.10450	0.005;0.001	T	0.48019	-0.9071	7	0.27082	T	0.32	.	6.6807	0.23119	0.0:0.5879:0.1238:0.2883	rs11072170;rs52836692;rs61639257;rs11072170	239;239	Q68DA7-3;Q68DA7-5	.;.	E	239	ENSP00000333950:G239E	ENSP00000333950:G239E	G	-	2	0	FMN1	31146662	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.333000	0.07894	0.141000	0.18875	-0.136000	0.14681	GGG	C|0.730;T|0.270	0.270	strong		0.512	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
DNAAF3	352909	hgsc.bcm.edu	37	19	55672055	55672055	+	Missense_Mutation	SNP	A	A	G	rs890871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55672055A>G	ENST00000524407.2	-	9	1034	c.1001T>C	c.(1000-1002)cTg>cCg	p.L334P	DNAAF3_ENST00000455045.1_Missense_Mutation_p.L280P|TNNI3_ENST00000590463.1_5'Flank|DNAAF3_ENST00000527223.2_Missense_Mutation_p.L402P|DNAAF3_ENST00000587789.2_5'Flank|CTD-2587H24.4_ENST00000587871.1_5'Flank|TNNI3_ENST00000344887.5_5'Flank|DNAAF3_ENST00000391720.4_Missense_Mutation_p.L381P|CTD-2587H24.5_ENST00000591665.1_RNA			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	334					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											CTGCTCCTCCAGGTCCCCCCC	0.662											OREG0025678	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	587	0.117212	0.0651	0.2651	5008	,	,		12297	0.1994		0.0169	False		,,,				2504	0.1012				p.L402P		Atlas-SNP	.											.	.	.	.	0			c.T1205C						PASS	.	G	PRO/LEU	152,3708		3,146,1781	74.0	78.0	77.0		1142	1.5	0.0	19	dbSNP_86	77	176,8082		2,172,3955	yes	missense	C19orf51	NM_178837.3	98	5,318,5736	GG,GA,AA		2.1313,3.9378,2.7067	benign	381/589	55672055	328,11790	1930	4129	6059	SO:0001583	missense	352909	exon9			TCCTCCAGGTCCC	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.1001T>C	19.37:g.55672055A>G	ENSP00000432046:p.Leu334Pro	Somatic	39	0	0	1009	WXS	Illumina HiSeq	Phase_I	38	9	0.236842	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	37	CCDS59422.1	239	0.10943223443223443	35	0.07113821138211382	64	0.17679558011049723	130	0.22727272727272727	10	0.013192612137203167	G	9.598	1.128001	0.20959	0.039378	0.021313	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.16324	2.35;2.35	3.81	1.54	0.23209	.	0.950797	0.08719	N	0.903801	T	0.00012	0.0000	N	0.00760	-1.21	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	0.45600	-0.9250	9	0.25751	T	0.34	-5.6366	3.5043	0.07684	0.2373:0.0:0.5646:0.1981	rs890871;rs56832619	402;280;355;334	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	P	402;280;381	ENSP00000394343:L280P;ENSP00000375600:L381P	ENSP00000301249:L402P	L	-	2	0	C19orf51	60363867	0.002000	0.14202	0.000000	0.03702	0.018000	0.09664	0.013000	0.13310	0.035000	0.15519	-0.172000	0.13284	CTG	A|0.920;G|0.080	0.080	strong		0.662	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
DFNA5	1687	hgsc.bcm.edu	37	7	24758753	24758753	+	Silent	SNP	C	C	T	rs754555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:24758753C>T	ENST00000342947.3	-	4	914	c.489G>A	c.(487-489)acG>acA	p.T163T	DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR|DFNA5_ENST00000409775.3_Silent_p.T163T|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	163					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						TCTGCATCGTCGTGATCTTCT	0.517													C|||	1298	0.259185	0.1982	0.1383	5008	,	,		22645	0.4435		0.1501	False		,,,				2504	0.3497				p.T163T	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.G489A						PASS	.	C	,,	925,3481	355.1+/-312.9	106,713,1384	227.0	182.0	197.0		489,,489	4.3	0.2	7	dbSNP_86	197	1230,7370	247.4+/-275.4	79,1072,3149	no	coding-synonymous,utr-5,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	185,1785,4533	TT,TC,CC		14.3023,20.9941,16.5693	,,	163/497,,163/497	24758753	2155,10851	2203	4300	6503	SO:0001819	synonymous_variant	1687	exon4			CATCGTCGTGATC	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.489G>A	7.37:g.24758753C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1																																																																																			C|0.802;T|0.198	0.198	strong		0.517	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
COL6A5	256076	hgsc.bcm.edu	37	3	130104206	130104206	+	Splice_Site	SNP	A	A	G	rs10212372	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:130104206A>G	ENST00000432398.2	+	5	2354	c.1860A>G	c.(1858-1860)aaA>aaG	p.K620K	COL6A5_ENST00000265379.6_Splice_Site_p.K620K	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	620	Nonhelical region.				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						GCGCTGAAAAAGGTAAGCAAC	0.408													A|||	2012	0.401757	0.4871	0.4597	5008	,	,		22209	0.5198		0.2028	False		,,,				2504	0.3282				p.K620K		Atlas-SNP	.											.	COL6A5	205	.	0			c.A1860G						PASS	.						16.0	14.0	14.0					3																	130104206		692	1590	2282	SO:0001630	splice_region_variant	256076	exon5			TGAAAAAGGTAAG	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.1861+1A>G	3.37:g.130104206A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				A|0.613;G|0.387	0.387	strong		0.408	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	Silent
CMYA5	202333	hgsc.bcm.edu	37	5	79029594	79029594	+	Missense_Mutation	SNP	T	T	C	rs1019762	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79029594T>C	ENST00000446378.2	+	2	5037	c.5006T>C	c.(5005-5007)tTa>tCa	p.L1669S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1669			L -> S (in dbSNP:rs1019762).		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)		GATTCTGTTTTAGAAAAAGGC	0.403													T|||	555	0.110823	0.1172	0.1225	5008	,	,		19852	0.0188		0.164	False		,,,				2504	0.1339				p.L1669S		Atlas-SNP	.											.	CMYA5	643	.	0			c.T5006C						PASS	.	T	SER/LEU	469,3227		33,403,1412	59.0	60.0	60.0		5006	2.6	0.9	5	dbSNP_86	60	1272,6918		104,1064,2927	yes	missense	CMYA5	NM_153610.3	145	137,1467,4339	CC,CT,TT		15.5311,12.6894,14.6475	probably-damaging	1669/4070	79029594	1741,10145	1848	4095	5943	SO:0001583	missense	202333	exon2			CTGTTTTAGAAAA	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.5006T>C	5.37:g.79029594T>C	ENSP00000394770:p.Leu1669Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	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	242	0.1108058608058608	56	0.11382113821138211	48	0.13259668508287292	11	0.019230769230769232	127	0.16754617414248021	T	15.65	2.895293	0.52121	0.126894	0.155311	ENSG00000164309	ENST00000446378	T	0.61742	0.08	4.95	2.57	0.30868	.	0.488799	0.15222	N	0.273849	T	0.00300	0.0009	L	0.47190	1.495	0.80722	P	0.0	D	0.69078	0.997	P	0.59115	0.852	T	0.11991	-1.0565	9	0.87932	D	0	.	5.9191	0.19072	0.0:0.2058:0.0:0.7942	rs1019762;rs52808958;rs1019762	1669	Q8N3K9	CMYA5_HUMAN	S	1669	ENSP00000394770:L1669S	ENSP00000394770:L1669S	L	+	2	0	CMYA5	79065350	0.026000	0.19158	0.851000	0.33527	0.902000	0.53008	0.245000	0.18142	0.746000	0.32786	0.460000	0.39030	TTA	T|0.888;C|0.112	0.112	strong		0.403	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
NFKB1	4790	hgsc.bcm.edu	37	4	103505961	103505961	+	Silent	SNP	C	C	T	rs4648039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:103505961C>T	ENST00000505458.1	+	11	1324	c.1047C>T	c.(1045-1047)taC>taT	p.Y349Y	NFKB1_ENST00000394820.4_Silent_p.Y349Y|NFKB1_ENST00000600343.1_Silent_p.Y169Y|NFKB1_ENST00000226574.4_Silent_p.Y350Y			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	349	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				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)	CTTTCCTCTACTATCCTGAAA	0.303													C|||	26	0.00519169	0.0	0.0014	5008	,	,		18222	0.0		0.0219	False		,,,				2504	0.0031				p.Y350Y		Atlas-SNP	.											.	NFKB1	78	.	0			c.C1050T						PASS	.	C	,	27,4379	33.5+/-64.1	0,27,2176	55.0	57.0	56.0		1047,1050	4.0	1.0	4	dbSNP_111	56	211,8389	89.7+/-151.9	2,207,4091	no	coding-synonymous,coding-synonymous	NFKB1	NM_001165412.1,NM_003998.3	,	2,234,6267	TT,TC,CC		2.4535,0.6128,1.8299	,	349/969,350/970	103505961	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	4790	exon11			CCTCTACTATCCT	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.1047C>T	4.37:g.103505961C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	37	CCDS54783.1																																																																																			C|0.983;T|0.017	0.017	strong		0.303	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
DGKH	160851	hgsc.bcm.edu	37	13	42764564	42764564	+	Silent	SNP	C	C	G	rs7324235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42764564C>G	ENST00000337343.4	+	16	1959	c.1938C>G	c.(1936-1938)ccC>ccG	p.P646P	DGKH_ENST00000538674.1_Silent_p.P401P|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000379274.2_Silent_p.P510P|DGKH_ENST00000261491.5_Silent_p.P646P|DGKH_ENST00000540693.1_Silent_p.P646P|DGKH_ENST00000536612.1_Silent_p.P510P	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	646					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		CAGTTCACCCCTGTGAACCAG	0.388													C|||	871	0.173922	0.0643	0.2666	5008	,	,		15383	0.0942		0.2624	False		,,,				2504	0.2474				p.P646P		Atlas-SNP	.											DGKH,caecum,carcinoma,0,1	DGKH	106	1	0			c.C1938G						PASS	.	C	,,,,	445,3961	216.1+/-234.9	22,401,1780	121.0	117.0	119.0		1938,1530,1530,1938,1938	-2.6	0.1	13	dbSNP_116	119	2332,6268	390.9+/-343.5	335,1662,2303	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	357,2063,4083	GG,GC,CC		27.1163,10.0999,21.3517	,,,,	646/1165,510/1101,510/1085,646/1165,646/1221	42764564	2777,10229	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon17			TCACCCCTGTGAA	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.1938C>G	13.37:g.42764564C>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			C|0.796;G|0.204	0.204	strong		0.388	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
TRIM15	89870	hgsc.bcm.edu	37	6	30131527	30131527	+	Silent	SNP	G	G	T	rs11961941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30131527G>T	ENST00000376694.4	+	1	535	c.66G>T	c.(64-66)ccG>ccT	p.P22P	TRIM10_ENST00000449742.2_5'Flank|TRIM15_ENST00000376688.1_Silent_p.P22P|TRIM10_ENST00000376704.3_5'Flank	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	22					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						GTGCGGGGCCGCTGGAGGATG	0.677													G|||	137	0.0273562	0.0688	0.0144	5008	,	,		16858	0.0139		0.0139	False		,,,				2504	0.0082				p.P22P		Atlas-SNP	.											.	TRIM15	34	.	0			c.G66T						PASS	.	G		195,2827		5,185,1321	55.0	48.0	50.0		66	3.1	0.4	6	dbSNP_120	50	74,5342		0,74,2634	no	coding-synonymous	TRIM15	NM_033229.2		5,259,3955	TT,TG,GG		1.3663,6.4527,3.188		22/466	30131527	269,8169	1511	2708	4219	SO:0001819	synonymous_variant	89870	exon1			GGGGCCGCTGGAG	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.66G>T	6.37:g.30131527G>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	105	45	0.428571	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Silent	SNP	ENST00000376694.4	37	CCDS4677.1																																																																																			G|0.964;T|0.036	0.036	strong		0.677	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
NDUFAF2	91942	hgsc.bcm.edu	37	5	60241142	60241142	+	Silent	SNP	G	G	A	rs158921	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:60241142G>A	ENST00000296597.5	+	1	187	c.60G>A	c.(58-60)aaG>aaA	p.K20K	ERCC8_ENST00000426742.2_5'Flank|ERCC8_ENST00000543101.1_5'Flank|NDUFAF2_ENST00000511107.1_Silent_p.K20K|ERCC8_ENST00000265038.5_5'Flank	NM_174889.4	NP_777549.1	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 2	20					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)				GGGAAGTGAAGGAGCACGTGG	0.597													G|||	3470	0.692891	0.6074	0.6974	5008	,	,		18298	0.9484		0.5696	False		,,,				2504	0.6687				p.K20K		Atlas-SNP	.											.	NDUFAF2	10	.	0			c.G60A						PASS	.						77.0	65.0	69.0					5																	60241142		2203	4298	6501	SO:0001819	synonymous_variant	91942	exon1			AGTGAAGGAGCAC	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.60G>A	5.37:g.60241142G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	167	153	0.916168	NM_174889	A8K5I1	Silent	SNP	ENST00000296597.5	37	CCDS3979.1																																																																																			.	.	weak		0.597	NDUFAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253965.1	NM_174889	
PSG3	5671	hgsc.bcm.edu	37	19	43243217	43243217	+	Missense_Mutation	SNP	A	A	G	rs34721205|rs12185496	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	225	93	0.413333	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	
SYNE3	161176	hgsc.bcm.edu	37	14	95912388	95912388	+	Missense_Mutation	SNP	G	G	A	rs61749972	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:95912388G>A	ENST00000334258.5	-	8	1504	c.1490C>T	c.(1489-1491)aCg>aTg	p.T497M	SYNE3_ENST00000553340.1_Missense_Mutation_p.T497M|SYNE3_ENST00000554873.1_Missense_Mutation_p.T254M|SYNE3_ENST00000557275.1_Missense_Mutation_p.T497M	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	497					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CTGCAGCATCGTCAGCAGCTC	0.587													G|||	294	0.0587061	0.0424	0.0605	5008	,	,		20204	0.002		0.0895	False		,,,				2504	0.1063				p.T497M		Atlas-SNP	.											.	SYNE3	130	.	0			c.C1490T						PASS	.	G	MET/THR	252,4154	145.7+/-180.5	7,238,1958	115.0	118.0	117.0		1490	3.1	0.5	14	dbSNP_129	117	733,7867	178.5+/-227.8	30,673,3597	yes	missense	C14orf49	NM_152592.3	81	37,911,5555	AA,AG,GG		8.5233,5.7195,7.5734	benign	497/976	95912388	985,12021	2203	4300	6503	SO:0001583	missense	161176	exon8			AGCATCGTCAGCA	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1490C>T	14.37:g.95912388G>A	ENSP00000334308:p.Thr497Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	121	0.0554029304029304	25	0.0508130081300813	28	0.07734806629834254	1	0.0017482517482517483	67	0.08839050131926121	G	13.20	2.166674	0.38217	0.057195	0.085233	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.14266	3.53;2.52;3.52;2.93	5.31	3.12	0.35913	.	0.586050	0.14224	N	0.333221	T	0.00356	0.0011	L	0.50919	1.6	0.09310	N	1	P;P;P	0.39352	0.669;0.521;0.54	B;B;B	0.27500	0.08;0.08;0.036	T	0.33599	-0.9862	10	0.40728	T	0.16	-9.8178	4.6667	0.12670	0.2707:0.1827:0.5466:0.0	rs61749972	497;497;497	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	M	497;254;497;497	ENSP00000334308:T497M;ENSP00000452154:T254M;ENSP00000450562:T497M;ENSP00000450774:T497M	ENSP00000334308:T497M	T	-	2	0	C14orf49	94982141	0.303000	0.24463	0.527000	0.27925	0.492000	0.33523	0.954000	0.29175	1.239000	0.43787	0.561000	0.74099	ACG	G|0.929;A|0.071	0.071	strong		0.587	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
FBXO42	54455	hgsc.bcm.edu	37	1	16577908	16577908	+	Missense_Mutation	SNP	G	G	C	rs12069239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	193	0	0		WXS	Illumina HiSeq	Phase_I	179	179	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		
SLC6A5	9152	hgsc.bcm.edu	37	11	20623007	20623007	+	Silent	SNP	C	C	T	rs7109418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:20623007C>T	ENST00000525748.1	+	2	609	c.336C>T	c.(334-336)tcC>tcT	p.S112S		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	112					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CCGGGAGCTCCGGGCCCGGCA	0.682													C|||	953	0.190296	0.2534	0.1556	5008	,	,		15026	0.005		0.2853	False		,,,				2504	0.2229				p.S112S		Atlas-SNP	.											.	SLC6A5	151	.	0			c.C336T						PASS	.	C		1102,3298		131,840,1229	26.0	29.0	28.0		336	-5.6	0.0	11	dbSNP_116	28	2356,6238		332,1692,2273	no	coding-synonymous	SLC6A5	NM_004211.3		463,2532,3502	TT,TC,CC		27.4145,25.0455,26.6123		112/798	20623007	3458,9536	2200	4297	6497	SO:0001819	synonymous_variant	9152	exon2			GAGCTCCGGGCCC	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.336C>T	11.37:g.20623007C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			C|0.774;T|0.226	0.226	strong		0.682	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
TDRD9	122402	hgsc.bcm.edu	37	14	104452640	104452640	+	Silent	SNP	G	G	A	rs10143389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104452640G>A	ENST00000409874.4	+	8	1146	c.1098G>A	c.(1096-1098)ttG>ttA	p.L366L	TDRD9_ENST00000339063.5_Silent_p.L366L	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	366					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L366L(1)|p.L81L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TTGATGACTTGGATATGAAGG	0.348													G|||	1613	0.322085	0.2731	0.3516	5008	,	,		18906	0.3343		0.3588	False		,,,				2504	0.317				p.L366L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	2	Substitution - coding silent(2)	stomach(2)	c.G1098A						PASS	.	G		1326,3080	446.7+/-348.1	190,946,1067	113.0	104.0	107.0		1098	3.9	1.0	14	dbSNP_119	107	2984,5616	460.9+/-365.3	518,1948,1834	no	coding-synonymous	TDRD9	NM_153046.2		708,2894,2901	AA,AG,GG		34.6977,30.0953,33.1386		366/1383	104452640	4310,8696	2203	4300	6503	SO:0001819	synonymous_variant	122402	exon8			TGACTTGGATATG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1098G>A	14.37:g.104452640G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2	706	0.3232600732600733	131	0.266260162601626	118	0.3259668508287293	183	0.31993006993006995	274	0.36147757255936674	G	8.454	0.853663	0.17106	0.300953	0.346977	ENSG00000156414	ENST00000557332	.	.	.	5.71	3.9	0.45041	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38200	-0.9672	3	.	.	.	.	7.929	0.29891	0.25:0.0:0.75:0.0	rs10143389;rs58504835;rs10143389	.	.	.	R	93	.	.	G	+	1	0	TDRD9	103522393	1.000000	0.71417	0.986000	0.45419	0.988000	0.76386	1.987000	0.40687	0.772000	0.33382	0.650000	0.86243	GGA	G|0.674;A|0.326	0.326	strong		0.348	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
DIDO1	11083	hgsc.bcm.edu	37	20	61513649	61513649	+	Missense_Mutation	SNP	G	G	T	rs6011441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	133	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	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	
PLIN4	729359	hgsc.bcm.edu	37	19	4512669	4512669	+	Missense_Mutation	SNP	T	T	C	rs55901236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4512669T>C	ENST00000301286.3	-	3	1260	c.1261A>G	c.(1261-1263)Acc>Gcc	p.T421A		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	421	27 X 33 AA approximate tandem repeat.		T -> A (in dbSNP:rs55901236).			cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CTGCAGACGGTGTCCTTTGTA	0.557													T|||	2274	0.454073	0.118	0.4741	5008	,	,		19060	0.7153		0.5696	False		,,,				2504	0.5061				p.T421A		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1261G						PASS	.	T	ALA/THR	828,3146		215,398,1374	90.0	130.0	117.0		1261	0.1	0.0	19	dbSNP_129	117	4493,3881		1426,1641,1120	yes	missense	PLIN4	NM_001080400.1	58	1641,2039,2494	CC,CT,TT		46.3458,20.8354,43.092	possibly-damaging	421/1358	4512669	5321,7027	1987	4187	6174	SO:0001583	missense	729359	exon3			AGACGGTGTCCTT	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1261A>G	19.37:g.4512669T>C	ENSP00000301286:p.Thr421Ala	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	190	188	0.989474	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	1099	0.5032051282051282	73	0.1483739837398374	186	0.5138121546961326	407	0.7115384615384616	433	0.5712401055408971	T	9.686	1.150525	0.21371	0.208354	0.536542	ENSG00000167676	ENST00000301286	T	0.15139	2.45	4.69	0.0866	0.14447	.	0.115125	0.38837	N	0.001559	T	0.00012	0.0000	L	0.45422	1.42	0.80722	P	0.0	B	0.14012	0.009	B	0.12837	0.008	T	0.20140	-1.0284	9	0.40728	T	0.16	-9.8017	8.6452	0.34000	0.0:0.3322:0.0:0.6678	rs55901236;rs61730736	421	Q96Q06	PLIN4_HUMAN	A	421	ENSP00000301286:T421A	ENSP00000301286:T421A	T	-	1	0	PLIN4	4463669	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.441000	0.06879	-0.085000	0.12573	0.369000	0.22263	ACC	T|0.494;C|0.506	0.506	strong		0.557	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ABCB5	340273	hgsc.bcm.edu	37	7	20691219	20691219	+	Silent	SNP	G	G	A	rs61227829	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20691219G>A	ENST00000404938.2	+	13	2161	c.1509G>A	c.(1507-1509)gcG>gcA	p.A503A	ABCB5_ENST00000258738.6_Silent_p.A58A|ABCB5_ENST00000406935.1_Silent_p.A58A|ABCB5_ENST00000443026.2_Silent_p.A58A|ABCB5_ENST00000477094.1_3'UTR	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	503	ABC transporter 1. {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						AAGCAAATGCGTATGATTTTA	0.443													g|||	254	0.0507188	0.028	0.062	5008	,	,		20710	0.0		0.1441	False		,,,				2504	0.0297				p.A503A		Atlas-SNP	.											ABCB5_ENST00000443026,NS,carcinoma,+1,4	ABCB5	357	4	0			c.G1509A						PASS	.	G	,,,	191,4215	120.8+/-158.4	7,177,2019	264.0	219.0	234.0		1509,174,174,174	-1.6	1.0	7	dbSNP_129	234	1137,7463	235.1+/-267.8	83,971,3246	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCB5	NM_001163941.1,NM_001163942.1,NM_001163993.1,NM_178559.5	,,,	90,1148,5265	AA,AG,GG		13.2209,4.335,10.2107	,,,	503/1258,58/132,58/127,58/813	20691219	1328,11678	2203	4300	6503	SO:0001819	synonymous_variant	340273	exon13			AAATGCGTATGAT	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.1509G>A	7.37:g.20691219G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	174	77	0.442529	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			G|0.914;A|0.086	0.086	strong		0.443	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
ZNF646	9726	hgsc.bcm.edu	37	16	31090269	31090269	+	Missense_Mutation	SNP	C	C	T	rs75586809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31090269C>T	ENST00000394979.2	+	1	3047	c.2624C>T	c.(2623-2625)gCg>gTg	p.A875V	ZNF646_ENST00000300850.5_Missense_Mutation_p.A875V			O15015	ZN646_HUMAN	zinc finger protein 646	875					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						CCTGGGGAGGCGACCTCAGCA	0.642													C|||	24	0.00479233	0.0008	0.0115	5008	,	,		21323	0.0		0.0139	False		,,,				2504	0.001				p.A875V		Atlas-SNP	.											ZNF646,NS,haematopoietic_neoplasm,0,1	ZNF646	133	1	0			c.C2624T						PASS	.	C	VAL/ALA	20,4374	26.2+/-53.5	0,20,2177	51.0	54.0	53.0		2624	2.0	0.3	16	dbSNP_131	53	149,8451	71.3+/-133.9	1,147,4152	yes	missense	ZNF646	NM_014699.3	64	1,167,6329	TT,TC,CC		1.7326,0.4552,1.3006	benign	875/1833	31090269	169,12825	2197	4300	6497	SO:0001583	missense	9726	exon2			GGGAGGCGACCTC	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.2624C>T	16.37:g.31090269C>T	ENSP00000378429:p.Ala875Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	C	10.60	1.394311	0.25205	0.004552	0.017326	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.09538	2.97;2.99	5.1	2.01	0.26516	.	.	.	.	.	T	0.02533	0.0077	N	0.19112	0.55	0.21762	N	0.999553	B	0.24768	0.111	B	0.17722	0.019	T	0.44757	-0.9307	9	0.09590	T	0.72	-4.0386	7.7886	0.29106	0.0:0.6518:0.0:0.3482	.	875	O15015-2	.	V	875	ENSP00000300850:A875V;ENSP00000378429:A875V	ENSP00000300850:A875V	A	+	2	0	ZNF646	30997770	0.000000	0.05858	0.330000	0.25442	0.849000	0.48306	-1.042000	0.03539	0.163000	0.19507	0.563000	0.77884	GCG	C|0.989;T|0.011	0.011	strong		0.642	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739865	20739865	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:20739865G>T	ENST00000427390.2	-	8	1975	c.1885C>A	c.(1885-1887)Cgg>Agg	p.R629R		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	629	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						tcctgctcccgtatcttctcc	0.542																																					p.R629R		Atlas-SNP	.											GOLGA6L6,NS,carcinoma,+1,1	GOLGA6L6	37	1	0			c.C1885A						scavenged	.						7.0	4.0	5.0					15																	20739865		625	1376	2001	SO:0001819	synonymous_variant	727832	exon8			GCTCCCGTATCTT	AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1885C>A	15.37:g.20739865G>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	50	17	0.34	NM_001145004	D3YTC0	Silent	SNP	ENST00000427390.2	37	CCDS45184.1																																																																																			.	.	none		0.542	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3	NM_001145004	
APOL3	80833	hgsc.bcm.edu	37	22	36537725	36537725	+	Silent	SNP	G	G	A	rs61731692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36537725G>A	ENST00000349314.2	-	3	769	c.732C>T	c.(730-732)taC>taT	p.Y244Y	APOL3_ENST00000397287.2_Silent_p.Y44Y|APOL3_ENST00000487423.1_5'Flank|APOL3_ENST00000397293.2_Silent_p.Y173Y|APOL3_ENST00000361710.2_Silent_p.Y44Y|APOL3_ENST00000424878.2_Silent_p.Y44Y	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	244					inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						CTGATGATGTGTATGAGTGCT	0.537													G|||	472	0.0942492	0.0983	0.0735	5008	,	,		21525	0.0198		0.16	False		,,,				2504	0.1125				p.Y244Y		Atlas-SNP	.											.	APOL3	60	.	0			c.C732T						PASS	.	G	,,	385,4021	192.6+/-218.0	14,357,1832	65.0	55.0	59.0		732,132,132	-6.8	0.0	22	dbSNP_129	59	1324,7276	260.3+/-283.2	106,1112,3082	yes	coding-synonymous,coding-synonymous,coding-synonymous	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	,,	120,1469,4914	AA,AG,GG		15.3953,8.7381,13.1401	,,	244/403,44/203,44/203	36537725	1709,11297	2203	4300	6503	SO:0001819	synonymous_variant	80833	exon3			TGATGTGTATGAG	AF305227	CCDS13922.1, CCDS13924.1	22q13.1	2013-01-24			ENSG00000128284	ENSG00000128284		"""Apolipoproteins"""	14868	protein-coding gene	gene with protein product		607253				11374903	Standard	NM_145640		Approved	CG12-1, APOLIII	uc003aot.3	O95236	OTTHUMG00000150632	ENST00000349314.2:c.732C>T	22.37:g.36537725G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Silent	SNP	ENST00000349314.2	37	CCDS13922.1																																																																																			G|0.888;A|0.112	0.112	strong		0.537	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137852	32137852	+	Silent	SNP	C	C	G	rs3759297	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	70	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	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	
FCER2	2208	hgsc.bcm.edu	37	19	7754194	7754194	+	Missense_Mutation	SNP	C	C	T	rs8102872	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7754194C>T	ENST00000346664.5	-	11	1063	c.851G>A	c.(850-852)cGg>cAg	p.R284Q	FCER2_ENST00000597921.1_Missense_Mutation_p.R284Q|FCER2_ENST00000360067.4_Missense_Mutation_p.R283Q	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)	284	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		R -> Q (in dbSNP:rs8102872).		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						TGTGGCCAGCCGGTCGCACAC	0.697													C|||	25	0.00499201	0.0	0.0072	5008	,	,		12203	0.0		0.0179	False		,,,				2504	0.002				p.R284Q		Atlas-SNP	.											.	FCER2	19	.	0			c.G851A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	20,4374		1,18,2178	27.0	25.0	25.0		848,851,851	-2.4	0.2	19	dbSNP_116	25	233,8365		3,227,4069	yes	missense,missense,missense	FCER2	NM_001207019.2,NM_001220500.1,NM_002002.4	43,43,43	4,245,6247	TT,TC,CC		2.7099,0.4552,1.9474	possibly-damaging,possibly-damaging,possibly-damaging	283/321,284/322,284/322	7754194	253,12739	2197	4299	6496	SO:0001583	missense	2208	exon11			GCCAGCCGGTCGC	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.851G>A	19.37:g.7754194C>T	ENSP00000264072:p.Arg284Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	108	63	0.583333	NM_002002		Missense_Mutation	SNP	ENST00000346664.5	37	CCDS12184.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	4.968	0.179782	0.09443	0.004552	0.027099	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.18016	2.24;2.24	3.81	-2.37	0.06643	C-type lectin fold (1);C-type lectin-like (1);	.	.	.	.	T	0.04092	0.0114	L	0.51853	1.615	0.21105	N	0.999787	B	0.27013	0.166	B	0.12156	0.007	T	0.23404	-1.0189	9	0.28530	T	0.3	.	8.2769	0.31877	0.0:0.2358:0.0:0.7642	rs8102872	284	P06734	FCER2_HUMAN	Q	284;283	ENSP00000264072:R284Q;ENSP00000353178:R283Q	ENSP00000264072:R284Q	R	-	2	0	FCER2	7660194	0.004000	0.15560	0.243000	0.24186	0.007000	0.05969	-0.452000	0.06787	-0.500000	0.06614	-0.361000	0.07541	CGG	C|0.986;T|0.014	0.014	strong		0.697	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	
UGT2A1	10941	hgsc.bcm.edu	37	4	70512773	70512773	+	Missense_Mutation	SNP	A	A	G	rs41292307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70512773A>G	ENST00000503640.1	-	1	645	c.590T>C	c.(589-591)tTa>tCa	p.L197S	UGT2A1_ENST00000514019.1_Missense_Mutation_p.L197S|UGT2A1_ENST00000512704.1_Missense_Mutation_p.L197S|UGT2A1_ENST00000286604.4_Missense_Mutation_p.L197S	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	197					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						GAGTTCTGATAAAACAGCAGG	0.423													A|||	351	0.0700879	0.0038	0.0807	5008	,	,		18794	0.001		0.161	False		,,,				2504	0.1299				p.L197S		Atlas-SNP	.											.	UGT2A1	131	.	0			c.T590C						PASS	.	A	SER/LEU	167,4239	109.9+/-148.2	4,159,2040	92.0	80.0	84.0		590	5.8	0.4	4	dbSNP_127	84	1581,7017	294.8+/-302.1	136,1309,2854	yes	missense	UGT2A1	NM_006798.2	145	140,1468,4894	GG,GA,AA		18.388,3.7903,13.442	possibly-damaging	197/528	70512773	1748,11256	2203	4299	6502	SO:0001583	missense	10941	exon2			TCTGATAAAACAG	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.590T>C	4.37:g.70512773A>G	ENSP00000424478:p.Leu197Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	149	0.06822344322344322	3	0.006097560975609756	31	0.0856353591160221	0	0.0	115	0.1517150395778364	A	14.39	2.519890	0.44866	0.037903	0.18388	ENSG00000173610	ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T	0.64803	-0.12;0.02;-0.12;-0.12	5.78	5.78	0.91487	.	0.378699	0.25762	N	0.028474	T	0.00384	0.0012	L	0.49350	1.555	.	.	.	D;P;D;D	0.89917	1.0;0.92;1.0;0.999	D;B;D;D	0.79784	0.993;0.388;0.993;0.986	T	0.08146	-1.0736	9	0.54805	T	0.06	.	14.0552	0.64764	1.0:0.0:0.0:0.0	rs41292307	197;197;197;197	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1	.;.;.;UD2A1_HUMAN	S	197	ENSP00000424478:L197S;ENSP00000421432:L197S;ENSP00000425497:L197S;ENSP00000286604:L197S	ENSP00000286604:L197S	L	-	2	0	UGT2A1	70547362	0.949000	0.32298	0.364000	0.25888	0.503000	0.33858	4.429000	0.59901	2.215000	0.71742	0.482000	0.46254	TTA	A|0.882;G|0.118	0.118	strong		0.423	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
PIGN	23556	hgsc.bcm.edu	37	18	59774037	59774037	+	Silent	SNP	C	C	T	rs9319997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:59774037C>T	ENST00000357637.5	-	19	2167	c.1752G>A	c.(1750-1752)ctG>ctA	p.L584L	PIGN_ENST00000400334.3_Silent_p.L584L	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	584					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				CTCGAGTCCACAGCCGAGTGA	0.403													C|||	468	0.0934505	0.0061	0.1239	5008	,	,		19226	0.0069		0.2694	False		,,,				2504	0.0982				p.L584L		Atlas-SNP	.											.	PIGN	62	.	0			c.G1752A						PASS	.	C	,	191,3641		5,181,1730	52.0	50.0	51.0		1752,1752	2.2	1.0	18	dbSNP_119	51	2034,6216		242,1550,2333	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	247,1731,4063	TT,TC,CC		24.6545,4.9843,18.4158	,	584/932,584/932	59774037	2225,9857	1916	4125	6041	SO:0001819	synonymous_variant	23556	exon19			AGTCCACAGCCGA	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.1752G>A	18.37:g.59774037C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			C|0.912;T|0.088	0.088	strong		0.403	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
MUC2	4583	hgsc.bcm.edu	37	11	1081757	1081757	+	Missense_Mutation	SNP	G	G	C	rs57737240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1081757G>C	ENST00000441003.2	+	13	1712	c.1685G>C	c.(1684-1686)aGc>aCc	p.S562T	MUC2_ENST00000359061.5_Missense_Mutation_p.S562T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	562	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCACAGTCAAGCTGCCATGAC	0.647													G|||	1838	0.367013	0.4266	0.366	5008	,	,		18028	0.3889		0.2197	False		,,,				2504	0.4162				p.S562T		Atlas-SNP	.											.	MUC2	614	.	0			c.G1685C						PASS	.	G	THR/SER	1613,2501		331,951,775	36.0	41.0	39.0		1685	-0.0	0.0	11	dbSNP_129	39	1711,6651		188,1335,2658	yes	missense	MUC2	NM_002457.2	58	519,2286,3433	CC,CG,GG		20.4616,39.2076,26.6432	benign	562/2813	1081757	3324,9152	2057	4181	6238	SO:0001583	missense	4583	exon13			AGTCAAGCTGCCA	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.1685G>C	11.37:g.1081757G>C	ENSP00000415183:p.Ser562Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		690	0.3159340659340659	188	0.3821138211382114	110	0.30386740331491713	230	0.4020979020979021	162	0.21372031662269128	G	0.576	-0.839120	0.02692	0.392076	0.204616	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12984	2.67;2.63	3.06	-0.0447	0.13854	.	0.845665	0.10123	U	0.713130	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.25169	0.119	B	0.30716	0.119	T	0.45145	-0.9281	8	0.02654	T	1	.	6.6078	0.22735	0.1934:0.4181:0.3885:0.0	rs57737240;rs61732123	562	E7EUV1	.	T	562	ENSP00000415183:S562T;ENSP00000351956:S562T	ENSP00000351956:S562T	S	+	2	0	MUC2	1071757	0.003000	0.15002	0.031000	0.17742	0.321000	0.28281	0.085000	0.14912	-0.239000	0.09710	-0.258000	0.10820	AGC	G|0.707;C|0.293	0.293	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR51L1	119682	hgsc.bcm.edu	37	11	5020799	5020799	+	Missense_Mutation	SNP	C	C	T	rs10768448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5020799C>T	ENST00000321543.1	+	1	587	c.587C>T	c.(586-588)aCc>aTc	p.T196I		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	196			T -> I (in dbSNP:rs10768448).			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)		GATGCCAGGACCAACAGTATT	0.428													T|||	1223	0.244209	0.3502	0.1643	5008	,	,		25413	0.0694		0.3131	False		,,,				2504	0.2669				p.T196I		Atlas-SNP	.											.	OR51L1	60	.	0			c.C587T						PASS	.	T	ILE/THR	1520,2882	672.9+/-402.7	237,1046,918	225.0	192.0	203.0		587	4.0	0.0	11	dbSNP_120	203	2567,6029	690.3+/-404.4	383,1801,2114	yes	missense	OR51L1	NM_001004755.1	89	620,2847,3032	TT,TC,CC		29.8627,34.5298,31.4433	benign	196/316	5020799	4087,8911	2201	4298	6499	SO:0001583	missense	119682	exon1			CCAGGACCAACAG	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.587C>T	11.37:g.5020799C>T	ENSP00000322156:p.Thr196Ile	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	350	142	0.405714	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	37	CCDS31369.1	519	0.23763736263736263	169	0.3434959349593496	68	0.1878453038674033	41	0.07167832167832168	241	0.3179419525065963	T	0.001	-3.309023	0.00018	0.345298	0.298627	ENSG00000176798	ENST00000321543	T	0.00030	8.9	5.18	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.550755	0.15346	N	0.267206	T	0.00012	0.0000	N	0.00074	-2.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27706	-1.0066	9	0.02654	T	1	.	5.3792	0.16181	0.0:0.1584:0.1506:0.6911	rs10768448;rs52829062;rs57450622;rs10768448	196	Q8NGJ5	O51L1_HUMAN	I	196	ENSP00000322156:T196I	ENSP00000322156:T196I	T	+	2	0	OR51L1	4977375	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.673000	0.25203	0.411000	0.25702	-0.381000	0.06696	ACC	C|0.707;T|0.293	0.293	strong		0.428	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
TLN1	7094	hgsc.bcm.edu	37	9	35708425	35708425	+	Silent	SNP	T	T	C	rs35461988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35708425T>C	ENST00000314888.9	-	34	4736	c.4383A>G	c.(4381-4383)ctA>ctG	p.L1461L	TLN1_ENST00000464379.1_5'Flank|TLN1_ENST00000540444.1_Silent_p.L1461L	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1461	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGGGCTCCACTAGCCCTTGCT	0.562													T|||	40	0.00798722	0.0008	0.013	5008	,	,		19074	0.0		0.0288	False		,,,				2504	0.001				p.L1461L		Atlas-SNP	.											.	TLN1	185	.	0			c.A4383G						PASS	.	T		28,4378	35.2+/-66.4	0,28,2175	79.0	72.0	75.0		4383	0.9	1.0	9	dbSNP_126	75	302,8298	109.8+/-170.3	2,298,4000	no	coding-synonymous	TLN1	NM_006289.3		2,326,6175	CC,CT,TT		3.5116,0.6355,2.5373		1461/2542	35708425	330,12676	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon34			CTCCACTAGCCCT	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.4383A>G	9.37:g.35708425T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			T|0.978;C|0.022	0.022	strong		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
EPPK1	83481	hgsc.bcm.edu	37	8	144940474	144940474	+	Silent	SNP	C	C	T	rs56015972		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	147	0	0		WXS	Illumina HiSeq	Phase_I	191	8	0.0418848	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	
TPSD1	23430	hgsc.bcm.edu	37	16	1306918	1306918	+	Silent	SNP	C	C	T	rs74470113		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306918C>T	ENST00000211076.3	+	3	523	c.375C>T	c.(373-375)acC>acT	p.T125T	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.T118T	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	125	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.T125T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TCATCCAGACCGGGGCGGACA	0.652																																					p.T125T		Atlas-SNP	.											TPSD1,pharynx,carcinoma,0,1	TPSD1	47	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C375T						PASS	.						77.0	75.0	76.0					16																	1306918		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			CCAGACCGGGGCG	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.375C>T	16.37:g.1306918C>T		Somatic	404	0	0		WXS	Illumina HiSeq	Phase_I	618	216	0.349515	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			C|0.644;T|0.356	0.356	strong		0.652	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
KRT37	8688	hgsc.bcm.edu	37	17	39579059	39579059	+	Nonsense_Mutation	SNP	G	G	A	rs78158550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39579059G>A	ENST00000225550.3	-	3	702	c.703C>T	c.(703-705)Cag>Tag	p.Q235*	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	235	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				AGGGAGAGCTGCTCCTCCTTC	0.692													G|||	862	0.172125	0.034	0.1268	5008	,	,		17559	0.3214		0.1759	False		,,,				2504	0.2331				p.Q235X		Atlas-SNP	.											.	KRT37	61	.	0			c.C703T						PASS	.						53.0	45.0	48.0					17																	39579059		2203	4298	6501	SO:0001587	stop_gained	8688	exon3			AGAGCTGCTCCTC	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.703C>T	17.37:g.39579059G>A	ENSP00000225550:p.Gln235*	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	66	21	0.318182	NM_003770		Nonsense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	381	0.17445054945054944	21	0.042682926829268296	48	0.13259668508287292	178	0.3111888111888112	134	0.17678100263852242	.	25.9	4.682848	0.88542	.	.	ENSG00000108417	ENST00000225550	.	.	.	4.86	3.87	0.44632	.	0.713944	0.11971	N	0.511799	.	.	.	.	.	.	0.09310	P	0.9999999999999974	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.7517	0.62912	0.0:0.0:0.8457:0.1543	.	.	.	.	X	235	.	ENSP00000225550:Q235X	Q	-	1	0	KRT37	36832585	0.982000	0.34865	0.981000	0.43875	0.878000	0.50629	3.380000	0.52448	1.016000	0.39470	0.655000	0.94253	CAG	G|0.847;A|0.153	0.153	strong		0.692	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
CRHR1	1394	hgsc.bcm.edu	37	17	43910507	43910507	+	Silent	SNP	C	C	T	rs16940674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43910507C>T	ENST00000398285.3	+	10	861	c.861C>T	c.(859-861)tgC>tgT	p.C287C	CRHR1_ENST00000314537.5_Silent_p.C258C|CRHR1_ENST00000352855.5_Silent_p.C218C|CRHR1_ENST00000577353.1_Silent_p.C258C|CRHR1_ENST00000293493.7_Silent_p.C83C|CRHR1_ENST00000339069.5_Silent_p.C157C	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	287					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CTTCTAGGTGCTGGTTTGGCA	0.612													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		20400	0.001		0.2396	False		,,,				2504	0.0613				p.C287C	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.C861T	GRCh37	CM044865	CRHR1	M	rs16940674	PASS	.	C	,,,	173,3815		5,163,1826	123.0	128.0	127.0		861,654,774,774	4.2	1.0	17	dbSNP_123	127	1831,6495		203,1425,2535	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRHR1	NM_001145146.1,NM_001145147.1,NM_001145148.1,NM_004382.4	,,,	208,1588,4361	TT,TC,CC		21.9914,4.338,16.2742	,,,	287/445,218/376,258/402,258/416	43910507	2004,10310	1994	4163	6157	SO:0001819	synonymous_variant	1394	exon10			TAGGTGCTGGTTT	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2357	protein-coding gene	gene with protein product	"""corticotropin-releasing factor receptor"""	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.861C>T	17.37:g.43910507C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001145146	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	37	CCDS45712.1																																																																																			C|0.860;T|0.140	0.140	strong		0.612	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
STARD7	56910	hgsc.bcm.edu	37	2	96859034	96859034	+	Silent	SNP	A	A	G	rs997547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	240	0	0		WXS	Illumina HiSeq	Phase_I	231	91	0.393939	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		
ITPR2	3709	hgsc.bcm.edu	37	12	26648092	26648092	+	Silent	SNP	C	C	T	rs2230381	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:26648092C>T	ENST00000381340.3	-	38	5591	c.5175G>A	c.(5173-5175)caG>caA	p.Q1725Q		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1725					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)	TACCTCCCACCTGTGCAGTTT	0.363													C|||	446	0.0890575	0.0113	0.1412	5008	,	,		18270	0.0248		0.2346	False		,,,				2504	0.0736				p.Q1725Q		Atlas-SNP	.											.	ITPR2	270	.	0			c.G5175A						PASS	.	C		135,3625		1,133,1746	118.0	110.0	112.0		5175	0.4	0.2	12	dbSNP_98	112	1812,6412		199,1414,2499	no	coding-synonymous	ITPR2	NM_002223.2		200,1547,4245	TT,TC,CC		22.0331,3.5904,16.2467		1725/2702	26648092	1947,10037	1880	4112	5992	SO:0001819	synonymous_variant	3709	exon38			TCCCACCTGTGCA	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.5175G>A	12.37:g.26648092C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			C|0.868;T|0.132	0.132	strong		0.363	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048606	33048606	+	Missense_Mutation	SNP	G	G	C	rs1042133	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33048606G>C	ENST00000418931.2	+	2	374	c.258G>C	c.(256-258)gaG>gaC	p.E86D	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.E86D	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	86	Beta-1.		E -> D (in allele DPB1*03:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*09:01, allele DPB1*10:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*17:01, allele DPB1*20:01, allele DPB1*22:02, allele DPB1*29:01, allele DPB1*35:01, allele DPB1*44:01, allele DPB1*46:01, allele DPB1*50:01, allele DPB1*57:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*80:01, allele DPB1*86:01, allele DPB1*88:01, allele DPB1*91:01, allele DPB1*92:01 and allele DPB1*98:01; dbSNP:rs1042133).|E -> V (in allele DPB1*32:01; dbSNP:rs41545212).		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						CTGCTGCGGAGTACTGGAACA	0.647													.|||	861	0.171925	0.1672	0.2089	5008	,	,		13752	0.124		0.1869	False		,,,				2504	0.1861				p.E86D		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.G258C						PASS	.						54.0	55.0	55.0					6																	33048606		1511	2709	4220	SO:0001583	missense	3115	exon2			TGCGGAGTACTGG		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.258G>C	6.37:g.33048606G>C	ENSP00000408146:p.Glu86Asp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	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	341|341	0.15613553113553114|0.15613553113553114	71|71	0.1443089430894309|0.1443089430894309	60|60	0.16574585635359115|0.16574585635359115	84|84	0.14685314685314685|0.14685314685314685	126|126	0.1662269129287599|0.1662269129287599	G|G	10.32|10.32	1.317463|1.317463	0.23908|0.23908	.|.	.|.	ENSG00000223865|ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835|ENST00000416804	T;T;T|.	0.00316|.	8.13;8.13;8.13|.	4.02|4.02	2.22|2.22	0.28083|0.28083	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);|.	0.653702|.	0.13202|.	N|.	0.405940|.	T|T	0.24774|0.24774	0.0601|0.0601	L|L	0.49126|0.49126	1.545|1.545	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	0.15954|0.15954	-1.0419|-1.0419	9|4	0.62326|.	D|.	0.03|.	.|.	3.3331|3.3331	0.07092|0.07092	0.2185:0.0:0.5766:0.2049|0.2185:0.0:0.5766:0.2049	rs1042133;rs3173294;rs11551418;rs16868595;rs17214741;rs17845447;rs17858320|rs1042133;rs3173294;rs11551418;rs16868595;rs17214741;rs17845447;rs17858320	96;86|.	Q59GY1;P04440|.	.;DPB1_HUMAN|.	D|T	86;86;86;63|53	ENSP00000408146:E86D;ENSP00000439674:E86D;ENSP00000412654:E63D|.	ENSP00000389210:E86D|.	E|S	+|+	3|2	2|0	HLA-DPB1|HLA-DPB1	33156584|33156584	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.003000|0.003000	0.03518|0.03518	0.033000|0.033000	0.13754|0.13754	1.056000|1.056000	0.40484|0.40484	-0.134000|-0.134000	0.14843|0.14843	GAG|AGT	G|0.854;C|0.146	0.146	strong		0.647	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
KRT4	3851	hgsc.bcm.edu	37	12	53205757	53205757	+	Missense_Mutation	SNP	T	T	C	rs7959052	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53205757T>C	ENST00000551956.1	-	2	959	c.467A>G	c.(466-468)cAg>cGg	p.Q156R	KRT4_ENST00000458244.2_Missense_Mutation_p.Q136R|KRT4_ENST00000293774.4_Missense_Mutation_p.Q230R			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	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	287	140	0.487805	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	
CUEDC2	79004	hgsc.bcm.edu	37	10	104184081	104184081	+	Silent	SNP	G	G	A	rs1044476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:104184081G>A	ENST00000369937.4	-	5	496	c.351C>T	c.(349-351)ccC>ccT	p.P117P	PSD_ENST00000492902.2_5'Flank|CUEDC2_ENST00000465409.1_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	117						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.P117P(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TGAGCATTTCGGGCCGCTGCA	0.582													G|||	416	0.0830671	0.0121	0.0821	5008	,	,		17467	0.0923		0.1461	False		,,,				2504	0.1053				p.P117P		Atlas-SNP	.											CUEDC2,NS,carcinoma,0,1	CUEDC2	22	1	1	Substitution - coding silent(1)	stomach(1)	c.C351T						scavenged	.	G		127,3617		1,125,1746	77.0	81.0	80.0		351	-7.9	0.7	10	dbSNP_86	80	992,7210		61,870,3170	no	coding-synonymous	CUEDC2	NM_024040.2		62,995,4916	AA,AG,GG		12.0946,3.3921,9.3672		117/288	104184081	1119,10827	1872	4101	5973	SO:0001819	synonymous_variant	79004	exon5			CATTTCGGGCCGC	BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"""chromosome 10 open reading frame 66"""	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.351C>T	10.37:g.104184081G>A		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_024040	D3DR88|Q9BWG8	Silent	SNP	ENST00000369937.4	37	CCDS41566.1																																																																																			G|0.898;A|0.102	0.102	strong		0.582	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040	
AIM1L	55057	hgsc.bcm.edu	37	1	26673076	26673076	+	5'Flank	SNP	G	G	A	rs11247924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26673076G>A	ENST00000308182.5	-	0	0				AIM1L_ENST00000527815.1_5'Flank|RN7SL490P_ENST00000579210.1_RNA			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		GTGGGGGGCCGCTGCCGCCAT	0.622													G|||	899	0.179513	0.1505	0.1931	5008	,	,		15200	0.1458		0.1918	False		,,,				2504	0.2311				p.R25W		Atlas-SNP	.											.	AIM1L	98	.	0			c.C73T						PASS	.	G	TRP/ARG	524,3272		33,458,1407	13.0	15.0	14.0		73	3.0	1.0	1	dbSNP_120	14	1591,6607		162,1267,2670	yes	missense	AIM1L	NM_001039775.3	101	195,1725,4077	AA,AG,GG		19.4072,13.804,17.6338	benign	25/1662	26673076	2115,9879	1898	4099	5997	SO:0001631	upstream_gene_variant	55057	exon2			GGGGCCGCTGCCG			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490		1.37:g.26673076G>A	Exception_encountered	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	37		377	0.17261904761904762	71	0.1443089430894309	73	0.20165745856353592	101	0.17657342657342656	132	0.1741424802110818	G	18.91	3.724308	0.68959	0.13804	0.194072	ENSG00000176092	ENST00000538018;ENST00000475866	T	0.22134	1.97	5.04	3.01	0.34805	.	.	.	.	.	T	0.00039	0.0001	L	0.29908	0.895	0.41275	P	0.013122999999999996	D	0.89917	1.0	D	0.80764	0.994	T	0.10823	-1.0613	8	0.59425	D	0.04	.	9.8058	0.40792	0.0:0.0:0.6286:0.3714	rs11247924;rs60455159	25	E7ET48	.	W	25	ENSP00000428746:R25W	ENSP00000428746:R25W	R	-	1	2	AIM1L	26545663	0.127000	0.22367	1.000000	0.80357	0.970000	0.65996	0.700000	0.25601	1.096000	0.41439	0.655000	0.94253	CGG	G|0.828;A|0.172	0.172	strong		0.622	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
INPP5B	3633	hgsc.bcm.edu	37	1	38411445	38411445	+	Silent	SNP	G	G	A	rs871524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:38411445G>A	ENST00000373026.1	-	2	135	c.135C>T	c.(133-135)caC>caT	p.H45H	INPP5B_ENST00000373024.3_Silent_p.H45H|INPP5B_ENST00000373023.2_Silent_p.H45H|INPP5B_ENST00000373021.1_Silent_p.H45H			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	45	PH.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CCTGGCCGCCGTGCTCCAGGC	0.652													G|||	1011	0.201877	0.0431	0.2262	5008	,	,		15761	0.2401		0.3181	False		,,,				2504	0.2403				p.H45H		Atlas-SNP	.											.	INPP5B	76	.	0			c.C135T						PASS	.	G		351,3805		17,317,1744	54.0	65.0	62.0		135	-8.0	0.0	1	dbSNP_86	62	2590,5800		388,1814,1993	no	coding-synonymous	INPP5B	NM_005540.2		405,2131,3737	AA,AG,GG		30.8701,8.4456,23.4417		45/914	38411445	2941,9605	2078	4195	6273	SO:0001819	synonymous_variant	3633	exon3			GCCGCCGTGCTCC	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.135C>T	1.37:g.38411445G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	154	78	0.506494	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37																																																																																				G|0.734;A|0.266	0.266	strong		0.652	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
CLEC12B	387837	hgsc.bcm.edu	37	12	10163379	10163379	+	Silent	SNP	C	C	T	rs1359083|rs386760228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:10163379C>T	ENST00000338896.5	+	1	149	c.21C>T	c.(19-21)taC>taT	p.Y7Y	CLEC12B_ENST00000396502.1_Silent_p.Y7Y|CLEC1B_ENST00000428126.2_Intron	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	7						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						AAGTGACCTACGCGACACTCA	0.403													C|||	1332	0.265974	0.261	0.3487	5008	,	,		20658	0.1468		0.3966	False		,,,				2504	0.2025				p.Y7Y		Atlas-SNP	.											.	CLEC12B	25	.	0			c.C21T						PASS	.	C	,	1291,3115	431.4+/-342.9	185,921,1097	61.0	57.0	59.0		21,21	-4.1	0.3	12	dbSNP_88	59	2999,5601	458.5+/-364.6	528,1943,1829	no	coding-synonymous,coding-synonymous	CLEC12B	NM_001129998.1,NM_205852.2	,	713,2864,2926	TT,TC,CC		34.8721,29.301,32.9848	,	7/277,7/233	10163379	4290,8716	2203	4300	6503	SO:0001819	synonymous_variant	387837	exon1			GACCTACGCGACA	AK128243	CCDS8610.1, CCDS44830.1	12p13.2	2010-08-17			ENSG00000256660	ENSG00000256660		"""C-type lectin domain containing"""	31966	protein-coding gene	gene with protein product						17562706	Standard	NM_205852		Approved		uc001qwz.2	Q2HXU8	OTTHUMG00000168397	ENST00000338896.5:c.21C>T	12.37:g.10163379C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_001129998	Q6UWF2|Q6ZRG0	Silent	SNP	ENST00000338896.5	37	CCDS44830.1																																																																																			C|0.683;T|0.317	0.317	strong		0.403	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852	
AHNAK2	113146	hgsc.bcm.edu	37	14	105413223	105413223	+	Silent	SNP	A	A	G	rs55797226	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	181	0	0		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	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	
PRR21	643905	hgsc.bcm.edu	37	2	240981262	240981262	+	Missense_Mutation	SNP	A	A	C	rs6728493	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:240981262A>C	ENST00000408934.1	-	1	1137	c.1138T>G	c.(1138-1140)Tct>Gct	p.S380A		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	380			S -> A (in dbSNP:rs6728493).							NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						TACATGTTAGAAACAAGAAGA	0.463													a|||	2079	0.415136	0.4455	0.379	5008	,	,		22976	0.5754		0.332	False		,,,				2504	0.32				p.S380A		Atlas-SNP	.											.	PRR21	53	.	0			c.T1138G						PASS	.	A	ALA/SER	1685,2721	511.1+/-367.7	316,1053,834	74.0	72.0	73.0		1138	0.5	0.0	2	dbSNP_116	73	2727,5873	434.6+/-357.8	431,1865,2004	yes	missense	PRR21	NM_001080835.1	99	747,2918,2838	CC,CA,AA		31.7093,38.2433,33.9228	benign	380/390	240981262	4412,8594	2203	4300	6503	SO:0001583	missense	643905	exon1			TGTTAGAAACAAG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.1138T>G	2.37:g.240981262A>C	ENSP00000386166:p.Ser380Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	954	0.4368131868131868	233	0.4735772357723577	135	0.3729281767955801	322	0.5629370629370629	264	0.3482849604221636	a	6.816	0.519647	0.13005	0.382433	0.317093	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.32753	1.44;1.44	0.483	0.483	0.16820	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.999999999950489E-6	P	0.39424	0.673	B	0.32022	0.139	T	0.41052	-0.9530	8	0.87932	D	0	.	2.636	0.04958	0.6216:0.0:0.3784:0.0	rs6728493;rs52815143;rs60219994;rs6728493	380	Q8WXC7	PRR21_HUMAN	A	380	ENSP00000386166:S380A;ENSP00000418240:S380A	ENSP00000386166:S380A	S	-	1	0	PRR21	240629935	0.000000	0.05858	0.013000	0.15412	0.040000	0.13550	0.106000	0.15354	0.424000	0.26061	0.413000	0.27773	TCT	A|0.620;C|0.380	0.380	strong		0.463	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
WIPI2	26100	hgsc.bcm.edu	37	7	5257573	5257573	+	Silent	SNP	G	G	A	rs1134489	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:5257573G>A	ENST00000288828.4	+	7	829	c.597G>A	c.(595-597)ccG>ccA	p.P199P	WIPI2_ENST00000404704.3_Silent_p.P199P|WIPI2_ENST00000401525.3_Silent_p.P181P|WIPI2_ENST00000382384.2_Silent_p.P181P|WIPI2_ENST00000484262.1_Silent_p.P140P	NM_001033518.1|NM_001278299.1|NM_015610.3	NP_001028690.1|NP_001265228.1|NP_056425.1	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	199					autophagic vacuole assembly (GO:0000045)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|protein complex (GO:0043234)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)	16		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		ACATGATTCCGGCTCACGACA	0.577													G|||	237	0.0473243	0.0076	0.1037	5008	,	,		18725	0.002		0.1044	False		,,,				2504	0.0491				p.P199P		Atlas-SNP	.											WIPI2,NS,carcinoma,+1,1	WIPI2	41	1	0			c.G597A						PASS	.	G	,,,,	130,4276	96.2+/-134.9	3,124,2076	199.0	173.0	182.0		597,543,420,597,543	-4.4	0.4	7	dbSNP_86	182	1085,7515	226.9+/-262.5	64,957,3279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WIPI2	NM_001033518.1,NM_001033519.1,NM_001033520.1,NM_015610.3,NM_016003.3	,,,,	67,1081,5355	AA,AG,GG		12.6163,2.9505,9.3418	,,,,	199/444,181/426,140/385,199/455,181/437	5257573	1215,11791	2203	4300	6503	SO:0001819	synonymous_variant	26100	exon7			GATTCCGGCTCAC		CCDS5339.1, CCDS34593.1, CCDS47531.1, CCDS47532.1, CCDS47533.1	7p22.1	2014-02-12			ENSG00000157954	ENSG00000157954		"""WD repeat domain containing"""	32225	protein-coding gene	gene with protein product		609225				15602573	Standard	NM_001278299		Approved	Atg21, CGI-50, FLJ12979, FLJ14217, FLJ42984, DKFZP434J154, DKFZp686P02188, ATG18B	uc003snv.3	Q9Y4P8	OTTHUMG00000121179	ENST00000288828.4:c.597G>A	7.37:g.5257573G>A		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	293	110	0.375427	NM_015610	B3KNC2|Q5MNZ8|Q6FI96|Q75L50|Q96IE4|Q9Y364	Silent	SNP	ENST00000288828.4	37	CCDS5339.1																																																																																			G|0.927;A|0.073	0.073	strong		0.577	WIPI2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241669.2	NM_015610	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4452638	4452638	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4452638C>T	ENST00000254718.4	-	10	1725	c.1419G>A	c.(1417-1419)gaG>gaA	p.E473E	MYBBP1A_ENST00000381556.2_Silent_p.E473E			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	473	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						TGGCCACCTGCTCAGTCAAGG	0.592																																					p.E473E		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G1419A						PASS	.						87.0	59.0	69.0					17																	4452638		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon10			CACCTGCTCAGTC	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.1419G>A	17.37:g.4452638C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			.	.	none		0.592	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
NCKAP5	344148	hgsc.bcm.edu	37	2	133542545	133542545	+	Silent	SNP	G	G	A	rs10191147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133542545G>A	ENST00000409261.1	-	14	2212	c.1839C>T	c.(1837-1839)tcC>tcT	p.S613S	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Silent_p.S613S|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	613										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						GGTTCTCCACGGACTTATCGG	0.488													g|||	1771	0.353634	0.4395	0.2997	5008	,	,		19890	0.494		0.2555	False		,,,				2504	0.2321				p.S613S		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C1839T						PASS	.	G	,	1619,2279		361,897,691	64.0	66.0	65.0		1839,	-0.2	0.1	2	dbSNP_119	65	2185,6087		287,1611,2238	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	648,2508,2929	AA,AG,GG		26.4144,41.5341,31.2572	,	613/1910,	133542545	3804,8366	1949	4136	6085	SO:0001819	synonymous_variant	344148	exon14			CTCCACGGACTTA	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.1839C>T	2.37:g.133542545G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			G|0.628;A|0.372	0.372	strong		0.488	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
FUT5	2527	hgsc.bcm.edu	37	19	5867053	5867053	+	Silent	SNP	A	A	G	rs61730513	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5867053A>G	ENST00000588525.1	-	2	771	c.684T>C	c.(682-684)gcT>gcC	p.A228A	FUT5_ENST00000252675.5_Silent_p.A228A	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	228					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						CCTTGAGATGAGCCTGCAGGC	0.632													G|||	272	0.0543131	0.1467	0.0187	5008	,	,		15675	0.0367		0.0199	False		,,,				2504	0.0082				p.A228A		Atlas-SNP	.											.	FUT5	29	.	0			c.T684C						PASS	.	G		470,3936	774.2+/-414.0	28,414,1761	50.0	48.0	48.0		684	-4.3	0.0	19	dbSNP_132	48	163,8437	807.7+/-407.2	1,161,4138	no	coding-synonymous	FUT5	NM_002034.2		29,575,5899	GG,GA,AA		1.8953,10.6673,4.867		228/375	5867053	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	2527	exon2			GAGATGAGCCTGC		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.684T>C	19.37:g.5867053A>G		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	273	128	0.468864	NM_002034	A8K4X2	Silent	SNP	ENST00000588525.1	37	CCDS12154.1																																																																																			A|0.872;G|0.128	0.128	strong		0.632	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548550	32548550	+	Silent	SNP	G	G	A	rs574897295|rs1059362	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32548550G>A	ENST00000360004.5	-	4	841	c.736C>T	c.(736-738)Ctg>Ttg	p.L246L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	246					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						TAGATGAACAGCCCGGCCCCA	0.557										Multiple Myeloma(14;0.17)			G|||	491	0.0980431	0.0628	0.0951	5008	,	,		27449	0.0427		0.1262	False		,,,				2504	0.1759				p.L246L		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C736T						PASS	.						88.0	102.0	97.0					6																	32548550		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon4			TGAACAGCCCGGC	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.736C>T	6.37:g.32548550G>A		Somatic	473	1	0.00211416		WXS	Illumina HiSeq	Phase_I	428	231	0.53972	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.930;A|0.070	0.070	strong		0.557	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
MPC1	51660	hgsc.bcm.edu	37	6	166779464	166779464	+	Silent	SNP	G	G	A	rs12205572	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:166779464G>A	ENST00000360961.6	-	4	424	c.303C>T	c.(301-303)caC>caT	p.H101H	MPC1_ENST00000341756.6_Silent_p.H101H|MPC1_ENST00000487218.1_5'UTR	NM_001270879.1|NM_016098.3	NP_001257808.1|NP_057182.1	Q9Y5U8	MPC1_HUMAN	mitochondrial pyruvate carrier 1	101					cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	pyruvate transmembrane transporter activity (GO:0050833)										CTGCTTACTCGTGTTTGATAA	0.463													G|||	160	0.0319489	0.0023	0.0375	5008	,	,		19560	0.0		0.0606	False		,,,				2504	0.0716				p.H58H		Atlas-SNP	.											.	.	.	.	0			c.C174T						PASS	.	G		44,4362	46.7+/-81.2	0,44,2159	87.0	80.0	82.0		303	-3.1	0.0	6	dbSNP_120	82	504,8096	144.0+/-200.0	12,480,3808	yes	coding-synonymous	BRP44L	NM_016098.2		12,524,5967	AA,AG,GG		5.8605,0.9986,4.2134		101/110	166779464	548,12458	2203	4300	6503	SO:0001819	synonymous_variant	51660	exon4			TTACTCGTGTTTG	AF125101	CCDS5293.1, CCDS75547.1	6q27	2012-08-01	2012-07-30	2012-07-30	ENSG00000060762	ENSG00000060762			21606	protein-coding gene	gene with protein product		614738	"""brain protein 44-like"""	BRP44L		22628558	Standard	NM_016098		Approved	dJ68L15.3, CGI-129	uc031sra.1	Q9Y5U8	OTTHUMG00000015999	ENST00000360961.6:c.303C>T	6.37:g.166779464G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_001270879	B2R5I7|Q5TI66|Q9HB67|Q9UQN4	Silent	SNP	ENST00000360961.6	37	CCDS5293.1																																																																																			G|0.962;A|0.038	0.038	strong		0.463	MPC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043052.1	NM_016098	
MFI2	4241	hgsc.bcm.edu	37	3	196746629	196746629	+	Intron	SNP	T	T	C	rs1056664	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:196746629T>C	ENST00000296350.5	-	6	826				MFI2_ENST00000296351.4_Silent_p.E252E	NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5						cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		ACTCGCCTTCTTCCTCCTCAG	0.488													C|||	1334	0.266374	0.2844	0.3444	5008	,	,		20384	0.2847		0.2266	False		,,,				2504	0.2086				p.E252E		Atlas-SNP	.											.	MFI2	88	.	0			c.A756G						PASS	.	C	,	1202,3204	708.8+/-407.7	167,868,1168	112.0	87.0	96.0		,756	-2.4	0.0	3	dbSNP_86	96	1912,6688	726.6+/-406.6	216,1480,2604	no	intron,coding-synonymous	MFI2	NM_005929.5,NM_033316.3	,	383,2348,3772	CC,CT,TT		22.2326,27.281,23.9428	,	,252/303	196746629	3114,9892	2203	4300	6503	SO:0001627	intron_variant	4241	exon7			GCCTTCTTCCTCC		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.712+1645A>G	3.37:g.196746629T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	165	87	0.527273	NM_033316	Q9BQE2	Silent	SNP	ENST00000296350.5	37	CCDS3325.1																																																																																			T|0.742;C|0.258	0.258	strong		0.488	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
ILK	3611	hgsc.bcm.edu	37	11	6629665	6629665	+	Silent	SNP	C	C	T	rs1043388	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6629665C>T	ENST00000396751.2	+	3	753	c.297C>T	c.(295-297)caC>caT	p.H99H	ILK_ENST00000537806.1_5'UTR|ILK_ENST00000299421.4_Silent_p.H99H|ILK_ENST00000528995.1_Silent_p.H99H|ILK_ENST00000420936.2_Silent_p.H99H|TAF10_ENST00000531760.1_5'Flank|RP11-732A19.2_ENST00000527398.1_RNA	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	106	0	0		WXS	Illumina HiSeq	Phase_I	147	77	0.52381	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	
MAST2	23139	hgsc.bcm.edu	37	1	46499526	46499526	+	Missense_Mutation	SNP	A	A	G	rs1052607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46499526A>G	ENST00000361297.2	+	27	3873	c.3590A>G	c.(3589-3591)aAa>aGa	p.K1197R	MAST2_ENST00000372009.2_Missense_Mutation_p.K1104R	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)					ACATCCATTAAAGTGGGGCCA	0.572													A|||	122	0.024361	0.0038	0.0461	5008	,	,		18838	0.001		0.0795	False		,,,				2504	0.0041				p.K1197R		Atlas-SNP	.											.	MAST2	136	.	0			c.A3590G						PASS	.	A	ARG/LYS	62,3948		0,62,1943	49.0	52.0	51.0		3590	3.6	1.0	1	dbSNP_86	51	630,7732		18,594,3569	yes	missense	MAST2	NM_015112.2	26	18,656,5512	GG,GA,AA		7.5341,1.5461,5.5933	possibly-damaging	1197/1799	46499526	692,11680	2005	4181	6186	SO:0001583	missense	23139	exon27			CCATTAAAGTGGG	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.3590A>G	1.37:g.46499526A>G	ENSP00000354671:p.Lys1197Arg	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	227	118	0.519824	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	74	0.03388278388278388	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	51	0.06728232189973615	A	14.49	2.551723	0.45487	0.015461	0.075341	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.64803	-0.12;-0.1	4.73	3.58	0.41010	.	0.000000	0.85682	D	0.000000	T	0.04227	0.0117	L	0.43923	1.385	0.45541	D	0.99849	B;B	0.31599	0.289;0.33	B;B	0.29524	0.048;0.103	T	0.03086	-1.1074	10	0.26408	T	0.33	-13.9418	10.52	0.44914	0.9116:0.0:0.0884:0.0	rs1052607;rs3193053;rs57188416;rs1052607	1104;1197	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	R	1197;1104	ENSP00000354671:K1197R;ENSP00000361079:K1104R	ENSP00000354671:K1197R	K	+	2	0	MAST2	46272113	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.281000	0.78621	1.976000	0.57569	0.528000	0.53228	AAA	A|0.956;G|0.044	0.044	strong		0.572	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414810	105414810	+	Silent	SNP	C	C	G	rs10145032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105414810C>G	ENST00000333244.5	-	7	7097	c.6978G>C	c.(6976-6978)ctG>ctC	p.L2326L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2326						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)			CCCCAAACGACAGCATCTTGA	0.607													.|||	2666	0.532348	0.5431	0.5288	5008	,	,		20443	0.4276		0.5298	False		,,,				2504	0.6309				p.L2326L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G6978C						PASS	.	T		2450,1664		803,844,410	209.0	231.0	224.0		6978	-7.5	0.0	14	dbSNP_119	224	4568,3828		1270,2028,900	no	coding-synonymous	AHNAK2	NM_138420.2		2073,2872,1310	GG,GC,CC		45.5931,40.4473,43.9009		2326/5796	105414810	7018,5492	2057	4198	6255	SO:0001819	synonymous_variant	113146	exon7			AAACGACAGCATC	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.6978G>C	14.37:g.105414810C>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	194	194	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.495;G|0.505	0.505	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
FUT6	2528	hgsc.bcm.edu	37	19	5831840	5831840	+	Missense_Mutation	SNP	C	C	T	rs17855739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5831840C>T	ENST00000318336.4	-	3	1933	c.739G>A	c.(739-741)Gag>Aag	p.E247K	FUT6_ENST00000527106.1_Missense_Mutation_p.E247K|FUT6_ENST00000524754.1_Missense_Mutation_p.E247K|FUT6_ENST00000592563.1_Missense_Mutation_p.E247K|FUT6_ENST00000286955.5_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	351	0	0		WXS	Illumina HiSeq	Phase_I	303	124	0.409241	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	
A1CF	29974	hgsc.bcm.edu	37	10	52601702	52601702	+	Silent	SNP	A	A	G	rs141891504		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:52601702A>G	ENST00000373993.1	-	3	329	c.285T>C	c.(283-285)aaT>aaC	p.N95N	A1CF_ENST00000395495.1_Silent_p.N95N|A1CF_ENST00000395489.2_Silent_p.N88N|A1CF_ENST00000374001.2_Silent_p.N95N|A1CF_ENST00000373997.3_Silent_p.N95N|A1CF_ENST00000282641.2_Silent_p.N95N|A1CF_ENST00000373995.3_Silent_p.N103N			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	95	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CATATCCTCTATTGTTGCCAT	0.303													A|||	1	0.000199681	0.0	0.0	5008	,	,		19096	0.0		0.001	False		,,,				2504	0.0				p.N103N		Atlas-SNP	.											.	A1CF	190	.	0			c.T309C						PASS	.	A	,,,,,	2,4402	2.1+/-5.4	0,2,2200	141.0	135.0	137.0		285,309,309,285,285,309	0.4	1.0	10	dbSNP_134	137	14,8584	10.5+/-38.8	0,14,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	A1CF	NM_001198818.1,NM_001198819.1,NM_001198820.1,NM_014576.3,NM_138932.2,NM_138933.2	,,,,,	0,16,6485	GG,GA,AA		0.1628,0.0454,0.1231	,,,,,	95/587,103/603,103/595,95/587,95/595,103/595	52601702	16,12986	2202	4299	6501	SO:0001819	synonymous_variant	29974	exon6			TCCTCTATTGTTG	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.285T>C	10.37:g.52601702A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Silent	SNP	ENST00000373993.1	37	CCDS7242.1																																																																																			A|0.999;G|0.001	0.001	strong		0.303	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
CD1A	909	hgsc.bcm.edu	37	1	158225019	158225019	+	Missense_Mutation	SNP	C	C	G	rs2269715	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158225019C>G	ENST00000289429.5	+	2	737	c.204C>G	c.(202-204)tgC>tgG	p.C68W		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	68			C -> W (in dbSNP:rs2269715). {ECO:0000269|PubMed:11600221, ECO:0000269|PubMed:2701945}.		antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	TTTTCCTGTGCCCCTGGTCCA	0.473													G|||	823	0.164337	0.0363	0.0908	5008	,	,		21023	0.3948		0.0577	False		,,,				2504	0.2618				p.C68W		Atlas-SNP	.											.	CD1A	88	.	0			c.C204G	GRCh37	CM067656	CD1A	M	rs2269715	PASS	.	G	TRP/CYS	224,4182	806.1+/-415.8	7,210,1986	111.0	103.0	106.0		204	-1.9	0.0	1	dbSNP_100	106	496,8104	797.1+/-407.5	13,470,3817	yes	missense	CD1A	NM_001763.2	215	20,680,5803	GG,GC,CC		5.7674,5.084,5.5359	benign	68/328	158225019	720,12286	2203	4300	6503	SO:0001583	missense	909	exon2			CCTGTGCCCCTGG	M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1634	protein-coding gene	gene with protein product		188370	"""CD1A antigen, a polypeptide"", ""CD1a antigen"""	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.204C>G	1.37:g.158225019C>G	ENSP00000289429:p.Cys68Trp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	153	87	0.568627	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	37	CCDS1174.1	302	0.1382783882783883	22	0.044715447154471545	32	0.08839779005524862	208	0.36363636363636365	40	0.052770448548812667	G	7.133	0.580353	0.13686	0.05084	0.057674	ENSG00000158477	ENST00000289429	T	0.00705	5.81	4.54	-1.85	0.07784	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	2.242710	0.02150	N	0.057955	T	0.00109	0.0003	N	0.00125	-2.05	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48581	-0.9023	9	0.40728	T	0.16	14.3899	8.2031	0.31436	0.0:0.3547:0.2197:0.4255	rs2269715;rs2269715	68	P06126	CD1A_HUMAN	W	68	ENSP00000289429:C68W	ENSP00000289429:C68W	C	+	3	2	CD1A	156491643	0.024000	0.19004	0.001000	0.08648	0.013000	0.08279	-0.046000	0.11983	-0.459000	0.07013	-0.194000	0.12790	TGC	C|0.905;G|0.095	0.095	strong		0.473	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763	
APBA2	321	hgsc.bcm.edu	37	15	29390715	29390715	+	Missense_Mutation	SNP	C	C	T	rs371370074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29390715C>T	ENST00000558402.1	+	10	1873	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	APBA2_ENST00000411764.1_Missense_Mutation_p.T413M|APBA2_ENST00000558259.1_Missense_Mutation_p.T425M|APBA2_ENST00000558330.1_Missense_Mutation_p.T413M|APBA2_ENST00000561069.1_Missense_Mutation_p.T425M			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	425	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)		GATGCCCAGACGCTGACGGAA	0.423													C|||	2	0.000399361	0.0	0.0	5008	,	,		19432	0.002		0.0	False		,,,				2504	0.0				p.T425M		Atlas-SNP	.											.	APBA2	132	.	0			c.C1274T						PASS	.	C	MET/THR,MET/THR	0,4406		0,0,2203	110.0	106.0	108.0		1238,1274	4.0	0.8	15		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	APBA2	NM_001130414.1,NM_005503.3	81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	413/738,425/750	29390715	1,13005	2203	4300	6503	SO:0001583	missense	321	exon8			CCCAGACGCTGAC	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.1274C>T	15.37:g.29390715C>T	ENSP00000453293:p.Thr425Met	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	27	0.402985	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.461454	0.43736	0.0	1.16E-4	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.55760	0.5	4.93	4.02	0.46733	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.184551	0.45361	N	0.000369	T	0.51550	0.1681	N	0.14661	0.345	0.58432	D	0.999997	P;P;D;P	0.67145	0.637;0.66;0.996;0.462	B;B;P;B	0.61397	0.269;0.389;0.888;0.244	T	0.58457	-0.7633	10	0.87932	D	0	.	12.3957	0.55382	0.0:0.9183:0.0:0.0817	.	413;117;413;425	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	M	413;425;117	ENSP00000409312:T413M	ENSP00000219865:T425M	T	+	2	0	APBA2	27178007	1.000000	0.71417	0.776000	0.31678	0.297000	0.27493	4.750000	0.62162	1.177000	0.42855	0.655000	0.94253	ACG	.	.	weak		0.423	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
CHCHD6	84303	hgsc.bcm.edu	37	3	126451937	126451937	+	Missense_Mutation	SNP	G	G	T	rs2272487	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:126451937G>T	ENST00000290913.3	+	4	376	c.283G>T	c.(283-285)Gct>Tct	p.A95S	CHCHD6_ENST00000508789.1_Missense_Mutation_p.A95S	NM_032343.2	NP_115719.1	Q9BRQ6	MIC25_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 6	95			A -> S (in dbSNP:rs2272487).		cellular response to DNA damage stimulus (GO:0006974)|cristae formation (GO:0042407)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(3)|lung(3)	8						ACAGGAGCATGCTGCTATCCA	0.547													G|||	1426	0.284744	0.2511	0.2565	5008	,	,		22414	0.3522		0.165	False		,,,				2504	0.4039				p.A95S		Atlas-SNP	.											.	CHCHD6	18	.	0			c.G283T						PASS	.	G	SER/ALA	1087,3319	393.1+/-328.7	123,841,1239	81.0	70.0	74.0		283	2.6	0.7	3	dbSNP_100	74	1409,7191	272.0+/-289.9	127,1155,3018	yes	missense	CHCHD6	NM_032343.1	99	250,1996,4257	TT,TG,GG		16.3837,24.6709,19.1911	benign	95/236	126451937	2496,10510	2203	4300	6503	SO:0001583	missense	84303	exon4			GAGCATGCTGCTA	BC006123	CCDS3041.1	3q21.3	2012-04-17			ENSG00000159685	ENSG00000159685		"""Coiled-coil-helix-coiled-coil-helix domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28184	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 23"", ""coiled-coil-helix cristae morphology 1"""	615634				17624330, 22228767	Standard	NM_032343		Approved	MGC13016, PPP1R23, CHCM1	uc003ejf.2	Q9BRQ6	OTTHUMG00000159601	ENST00000290913.3:c.283G>T	3.37:g.126451937G>T	ENSP00000290913:p.Ala95Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	216	112	0.518519	NM_032343	D6R9U0|D6RIB4|H8Y0Y7	Missense_Mutation	SNP	ENST00000290913.3	37	CCDS3041.1	507|507	0.23214285714285715|0.23214285714285715	128|128	0.2601626016260163|0.2601626016260163	96|96	0.26519337016574585|0.26519337016574585	168|168	0.2937062937062937|0.2937062937062937	115|115	0.1517150395778364|0.1517150395778364	G|G	7.333|7.333	0.619243|0.619243	0.14129|0.14129	0.246709|0.246709	0.163837|0.163837	ENSG00000159685|ENSG00000159685	ENST00000290913;ENST00000508789|ENST00000513253	T;T|.	0.50813|.	0.73;0.73|.	4.48|4.48	2.64|2.64	0.31445|0.31445	.|.	0.252628|.	0.38217|.	N|.	0.001762|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.57536|0.57536	1.79|1.79	0.34928|0.34928	P|P	0.250926|0.250926	D;P|.	0.63046|.	0.992;0.684|.	P;P|.	0.59012|.	0.85;0.553|.	T|T	0.13629|0.13629	-1.0502|-1.0502	9|4	0.38643|.	T|.	0.18|.	-4.0401|-4.0401	7.1596|7.1596	0.25657|0.25657	0.0:0.1885:0.6163:0.1952|0.0:0.1885:0.6163:0.1952	rs2272487;rs11544130;rs52805448;rs59133559;rs2272487|rs2272487;rs11544130;rs52805448;rs59133559;rs2272487	95;95|.	D6R9U0;Q9BRQ6|.	.;CHCH6_HUMAN|.	S|I	95|28	ENSP00000290913:A95S;ENSP00000422912:A95S|.	ENSP00000290913:A95S|.	A|M	+|+	1|3	0|0	CHCHD6|CHCHD6	127934627|127934627	0.983000|0.983000	0.35010|0.35010	0.656000|0.656000	0.29637|0.29637	0.053000|0.053000	0.15095|0.15095	1.839000|1.839000	0.39220|0.39220	0.496000|0.496000	0.27904|0.27904	0.591000|0.591000	0.81541|0.81541	GCT|ATG	G|0.788;T|0.212	0.212	strong		0.547	CHCHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356432.1	NM_032343	
KRT80	144501	hgsc.bcm.edu	37	12	52566047	52566047	+	Silent	SNP	G	G	A	rs3741736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52566047G>A	ENST00000394815.2	-	7	1210	c.1113C>T	c.(1111-1113)aaC>aaT	p.N371N	KRT80_ENST00000313234.5_Silent_p.N371N	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	371	Coil 2.|Rod.					cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(2)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.108)		CCAGCTTGACGTTCATCAGCT	0.657													G|||	1661	0.331669	0.2852	0.2968	5008	,	,		19597	0.2907		0.4513	False		,,,				2504	0.3384				p.N371N	GBM(178;2309 2916 15678 35873)	Atlas-SNP	.											.	KRT80	68	.	0			c.C1113T						PASS	.	G	,	1315,3091	444.3+/-347.3	197,921,1085	101.0	90.0	94.0		1113,1113	-3.1	0.7	12	dbSNP_107	94	3352,5248	497.8+/-374.6	656,2040,1604	no	coding-synonymous,coding-synonymous	KRT80	NM_001081492.1,NM_182507.2	,	853,2961,2689	AA,AG,GG		38.9767,29.8457,35.8834	,	371/423,371/453	52566047	4667,8339	2203	4300	6503	SO:0001819	synonymous_variant	144501	exon7			CTTGACGTTCATC	BX537567	CCDS8821.2, CCDS41784.1	12q13.13	2013-01-16			ENSG00000167767	ENSG00000167767		"""-"", ""Intermediate filaments type II, keratins (basic)"""	27056	protein-coding gene	gene with protein product		611161				16831889	Standard	NM_001081492		Approved	KB20	uc001rzx.3	Q6KB66	OTTHUMG00000150193	ENST00000394815.2:c.1113C>T	12.37:g.52566047G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_182507	Q6P1A5|Q7Z3Q0	Silent	SNP	ENST00000394815.2	37	CCDS8821.2																																																																																			G|0.650;A|0.350	0.350	strong		0.657	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507	
STOML1	9399	hgsc.bcm.edu	37	15	74277666	74277666	+	Silent	SNP	C	C	T	rs34353835	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:74277666C>T	ENST00000316900.5	-	5	907	c.783G>A	c.(781-783)ccG>ccA	p.P261P	STOML1_ENST00000316911.6_Silent_p.P211P|STOML1_ENST00000561656.1_Silent_p.P174P|STOML1_ENST00000359750.4_Silent_p.P261P|STOML1_ENST00000541638.1_Silent_p.P219P|STOML1_ENST00000564777.1_Silent_p.P211P	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	261						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CACCTGGCCCCGGGGACGGGG	0.637													c|||	40	0.00798722	0.0008	0.0086	5008	,	,		17752	0.0		0.0298	False		,,,				2504	0.0031				p.P261P		Atlas-SNP	.											.	STOML1	22	.	0			c.G783A						PASS	.	T		31,4345		0,31,2157	14.0	15.0	15.0		783	-10.7	0.0	15	dbSNP_126	15	318,8242		8,302,3970	no	coding-synonymous	STOML1	NM_004809.3		8,333,6127	TT,TC,CC		3.715,0.7084,2.6979		261/399	74277666	349,12587	2188	4280	6468	SO:0001819	synonymous_variant	9399	exon5			TGGCCCCGGGGAC	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"""stomatin-like 1"", ""stomatin (EBP72)-like 1"""	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.783G>A	15.37:g.74277666C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	98	36	0.367347	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Silent	SNP	ENST00000316900.5	37	CCDS10254.1																																																																																			C|0.980;T|0.020	0.020	strong		0.637	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809	
TRAP1	10131	hgsc.bcm.edu	37	16	3721773	3721773	+	Missense_Mutation	SNP	G	G	C	rs1136948	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:3721773G>C	ENST00000246957.5	-	11	1273	c.1185C>G	c.(1183-1185)gaC>gaG	p.D395E	TRAP1_ENST00000538171.1_Missense_Mutation_p.D342E|TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000575671.1_Missense_Mutation_p.D186E	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	395			D -> E (in dbSNP:rs1136948). {ECO:0000269|PubMed:8756626}.		chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				TCAGGGGAATGTCCTCACTGT	0.652													G|||	542	0.108227	0.0189	0.085	5008	,	,		17423	0.0893		0.1839	False		,,,				2504	0.1871				p.D395E		Atlas-SNP	.											TRAP1,colon,carcinoma,-1,1	TRAP1	53	1	0			c.C1185G						PASS	.	G	GLU/ASP	161,4233	109.1+/-147.4	4,153,2040	56.0	49.0	51.0		1185	2.3	1.0	16	dbSNP_86	51	1583,7017	293.6+/-301.5	147,1289,2864	yes	missense	TRAP1	NM_016292.2	45	151,1442,4904	CC,CG,GG		18.407,3.6641,13.4216	probably-damaging	395/705	3721773	1744,11250	2197	4300	6497	SO:0001583	missense	10131	exon11			GGGAATGTCCTCA	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1185C>G	16.37:g.3721773G>C	ENSP00000246957:p.Asp395Glu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	37	CCDS10508.1	244	0.11172161172161173	14	0.028455284552845527	38	0.10497237569060773	48	0.08391608391608392	144	0.18997361477572558	G	17.54	3.416008	0.62511	0.036641	0.18407	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.22134	1.97;1.97	5.4	2.35	0.29111	Ribosomal protein S5 domain 2-type fold (1);	0.044222	0.85682	D	0.000000	T	0.00073	0.0002	M	0.87900	2.915	0.09310	P	0.99999893569	D;D	0.61697	0.987;0.99	D;D	0.69142	0.936;0.962	T	0.02942	-1.1091	9	0.72032	D	0.01	-49.732	7.3339	0.26599	0.4086:0.0:0.5914:0.0	rs1136948;rs11541716;rs12373018;rs17424284;rs52828896;rs1136948	342;395	F5H897;Q12931	.;TRAP1_HUMAN	E	395;342	ENSP00000246957:D395E;ENSP00000442070:D342E	ENSP00000246957:D395E	D	-	3	2	TRAP1	3661774	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.377000	0.44300	0.781000	0.33589	-0.140000	0.14226	GAC	G|0.864;C|0.136	0.136	strong		0.652	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
DTNB	1838	hgsc.bcm.edu	37	2	25754393	25754393	+	Missense_Mutation	SNP	T	T	C	rs199811406		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:25754393T>C	ENST00000406818.3	-	9	1199	c.950A>G	c.(949-951)cAt>cGt	p.H317R	DTNB_ENST00000545439.1_Missense_Mutation_p.H113R|DTNB_ENST00000405222.1_Missense_Mutation_p.H317R|DTNB_ENST00000407661.3_Missense_Mutation_p.H317R|DTNB_ENST00000404103.3_Missense_Mutation_p.H317R|DTNB_ENST00000496972.2_Missense_Mutation_p.H260R|DTNB_ENST00000407186.1_Missense_Mutation_p.H317R|DTNB_ENST00000407038.3_Missense_Mutation_p.H317R|DTNB_ENST00000288642.8_Missense_Mutation_p.H317R	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	317						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAAAACAGGATGCGGGGGTTC	0.463																																					p.H317R		Atlas-SNP	.											.	DTNB	43	.	0			c.A950G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	2,3750		0,2,1874	142.0	141.0	141.0		950,950,950,950,950	5.2	1.0	2		141	2,8196		0,2,4097	yes	missense,missense,missense,missense,missense	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	29,29,29,29,29	0,4,5971	CC,CT,TT		0.0244,0.0533,0.0335	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	317/628,317/598,317/568,317/610,317/561	25754393	4,11946	1876	4099	5975	SO:0001583	missense	1838	exon9			ACAGGATGCGGGG	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.950A>G	2.37:g.25754393T>C	ENSP00000384084:p.His317Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Missense_Mutation	SNP	ENST00000406818.3	37	CCDS46237.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586513	0.46110	5.33E-4	2.44E-4	ENSG00000138101	ENST00000496972;ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000545439;ENST00000535791	T;T;T;T;T;T;T;T;T	0.44083	2.28;2.28;2.28;2.28;2.31;2.31;2.31;2.28;0.93	5.15	5.15	0.70609	.	0.094216	0.64402	D	0.000001	T	0.46521	0.1397	M	0.80847	2.515	0.53005	D	0.99996	B;B;B;B;B;B;B;B;B;B;B;B	0.09022	0.001;0.001;0.002;0.002;0.001;0.001;0.0;0.001;0.0;0.002;0.002;0.001	B;B;B;B;B;B;B;B;B;B;B;B	0.17722	0.005;0.003;0.007;0.019;0.003;0.005;0.001;0.003;0.012;0.012;0.018;0.005	T	0.43523	-0.9386	10	0.34782	T	0.22	-16.4358	12.9424	0.58352	0.0:0.0:0.0:1.0	.	317;113;260;317;317;260;317;317;317;317;317;317	E7EVB6;B7Z202;F5GZG4;O60941-3;B7Z6A9;B7Z733;E9PEY4;Q96AW0;O60941-2;O60941-4;G5E9F6;O60941	.;.;.;.;.;.;.;.;.;.;.;DTNB_HUMAN	R	260;317;317;317;317;317;317;317;113;170	ENSP00000444463:H260R;ENSP00000384084:H317R;ENSP00000385482:H317R;ENSP00000385193:H317R;ENSP00000384767:H317R;ENSP00000384787:H317R;ENSP00000385784:H317R;ENSP00000288642:H317R;ENSP00000444961:H113R	ENSP00000288642:H317R	H	-	2	0	DTNB	25607897	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.025000	0.64097	1.930000	0.55929	0.383000	0.25322	CAT	.	.	weak		0.463	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147	
C15orf27	123591	hgsc.bcm.edu	37	15	76496340	76496340	+	Missense_Mutation	SNP	C	C	T	rs937733	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:76496340C>T	ENST00000388942.3	+	11	1556	c.1280C>T	c.(1279-1281)cCg>cTg	p.P427L		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	427			P -> L (in dbSNP:rs937733). {ECO:0000269|PubMed:14702039}.		calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						CCTTCTCCCCCGCCGCTGCCA	0.697													T|||	1871	0.373602	0.2269	0.3256	5008	,	,		15096	0.5794		0.2674	False		,,,				2504	0.5031				p.P427L		Atlas-SNP	.											.	C15orf27	32	.	0			c.C1280T						PASS	.	T	LEU/PRO	1018,3366		107,804,1281	15.0	17.0	16.0		1280	-3.3	0.2	15	dbSNP_86	16	2162,6418		287,1588,2415	no	missense	C15orf27	NM_152335.2	98	394,2392,3696	TT,TC,CC		25.1981,23.2208,24.5295	benign	427/532	76496340	3180,9784	2192	4290	6482	SO:0001583	missense	123591	exon11			CTCCCCCGCCGCT	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.1280C>T	15.37:g.76496340C>T	ENSP00000373594:p.Pro427Leu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	759	0.3475274725274725	118	0.23983739837398374	124	0.3425414364640884	316	0.5524475524475524	201	0.26517150395778366	T	2.116	-0.402548	0.04865	0.232208	0.251981	ENSG00000169758	ENST00000388942	T	0.30714	1.52	4.31	-3.27	0.05048	.	0.669305	0.15393	N	0.264739	T	0.00012	0.0000	N	0.12182	0.205	0.51233	P	8.699999999994823E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42965	-0.9420	9	0.06494	T	0.89	-13.482	0.4214	0.00456	0.2841:0.2834:0.1451:0.2874	rs937733;rs57604304	391;427	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	L	427	ENSP00000373594:P427L	ENSP00000373594:P427L	P	+	2	0	C15orf27	74283395	0.122000	0.22280	0.194000	0.23346	0.242000	0.25591	0.130000	0.15850	-0.611000	0.05709	-0.775000	0.03384	CCG	C|0.712;T|0.288	0.288	strong		0.697	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408182	105408182	+	Missense_Mutation	SNP	T	T	G	rs9672139	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	132	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	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	
THUMPD3	25917	hgsc.bcm.edu	37	3	9425911	9425911	+	Silent	SNP	G	G	A	rs1129170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:9425911G>A	ENST00000345094.3	+	9	1585	c.1251G>A	c.(1249-1251)aaG>aaA	p.K417K	SETD5-AS1_ENST00000519043.1_RNA|SETD5-AS1_ENST00000520629.1_RNA|SETD5-AS1_ENST00000468186.1_RNA|SETD5-AS1_ENST00000523354.1_RNA|THUMPD3_ENST00000515662.2_Silent_p.K417K|THUMPD3_ENST00000452837.2_Silent_p.K417K|SETD5-AS1_ENST00000521609.1_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	417						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		GATCCAAGAAGAGAAACTGGA	0.423													g|||	3027	0.604433	0.5371	0.5821	5008	,	,		18542	0.5655		0.5915	False		,,,				2504	0.7648				p.K417K		Atlas-SNP	.											.	THUMPD3	46	.	0			c.G1251A						PASS	.		,	2407,1999	615.1+/-392.5	664,1079,460	192.0	207.0	202.0		1251,1251	1.9	1.0	3	dbSNP_86	202	5096,3504	631.9+/-398.5	1504,2088,708	no	coding-synonymous,coding-synonymous	THUMPD3	NM_001114092.1,NM_015453.2	,	2168,3167,1168	AA,AG,GG		40.7442,45.37,42.3112	,	417/508,417/508	9425911	7503,5503	2203	4300	6503	SO:0001819	synonymous_variant	25917	exon9			CAAGAAGAGAAAC	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1251G>A	3.37:g.9425911G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Silent	SNP	ENST00000345094.3	37	CCDS2573.1	1234	0.565018315018315	262	0.532520325203252	206	0.569060773480663	327	0.5716783216783217	439	0.579155672823219	G	9.581	1.123543	0.20959	0.5463	0.592558	ENSG00000134077	ENST00000416603	.	.	.	5.66	1.89	0.25635	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48725	-0.9010	3	.	.	.	-22.952	8.9034	0.35507	0.4144:0.0:0.5856:0.0	rs1129170;rs2251595;rs3177482;rs3186764;rs17171661;rs17849508;rs60440721	.	.	.	K	188	.	.	E	+	1	0	THUMPD3	9400911	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.283000	0.33237	0.773000	0.33404	-0.143000	0.13931	GAG	G|0.425;A|0.575	0.575	strong		0.423	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
PAPL	390928	hgsc.bcm.edu	37	19	39589191	39589191	+	Missense_Mutation	SNP	T	T	A	rs566749338		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39589191T>A	ENST00000331256.5	+	3	489	c.215T>A	c.(214-216)cTc>cAc	p.L72H	PAPL_ENST00000594229.1_Missense_Mutation_p.L72H	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		72						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										CCCCTGCCCCTCCGCGCCCAG	0.642													t|||	1	0.000199681	0.0	0.0	5008	,	,		13097	0.0		0.001	False		,,,				2504	0.0				p.L72H		Atlas-SNP	.											.	.	.	.	0			c.T215A						PASS	.						35.0	33.0	34.0					19																	39589191		2203	4300	6503	SO:0001583	missense	0	exon3			TGCCCCTCCGCGC																												ENST00000331256.5:c.215T>A	19.37:g.39589191T>A	ENSP00000327557:p.Leu72His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_001004318	B2RN68	Missense_Mutation	SNP	ENST00000331256.5	37	CCDS33018.1	.	.	.	.	.	.	.	.	.	.	T	1.006	-0.689462	0.03328	.	.	ENSG00000183760	ENST00000331256	D	0.82711	-1.64	5.2	4.19	0.49359	Purple acid phosphatase-like, N-terminal (1);Purple acid phosphatase, N-terminal (1);	0.743246	0.12988	N	0.422733	T	0.73273	0.3566	L	0.39245	1.2	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.56613	-0.7950	10	0.14252	T	0.57	-12.7226	8.4714	0.32988	0.0:0.0927:0.0:0.9073	.	72	Q6ZNF0	PAPL_HUMAN	H	72	ENSP00000327557:L72H	ENSP00000327557:L72H	L	+	2	0	AC011443.1	44281031	0.001000	0.12720	0.249000	0.24280	0.063000	0.16089	0.986000	0.29590	1.956000	0.56807	0.533000	0.62120	CTC	.	.	none		0.642	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
OR5P2	120065	hgsc.bcm.edu	37	11	7818313	7818313	+	Silent	SNP	C	C	T	rs73406609	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7818313C>T	ENST00000329434.2	-	1	207	c.177G>A	c.(175-177)ctG>ctA	p.L59L	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, 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)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCAAGTGGCTCAGAAAGAAAT	0.408													C|||	1185	0.236621	0.348	0.2911	5008	,	,		18246	0.128		0.2763	False		,,,				2504	0.1186				p.L59L		Atlas-SNP	.											.	OR5P2	68	.	0			c.G177A						PASS	.	C		1363,2839		399,565,1137	67.0	84.0	79.0		177	1.4	1.0	11	dbSNP_130	79	2421,6163		389,1643,2260	no	coding-synonymous	OR5P2	NM_153444.1		788,2208,3397	TT,TC,CC		28.2036,32.4369,29.5949		59/323	7818313	3784,9002	2101	4292	6393	SO:0001819	synonymous_variant	120065	exon1			GTGGCTCAGAAAG	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.177G>A	11.37:g.7818313C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			C|0.741;T|0.259	0.259	strong		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274157	39274157	+	Silent	SNP	G	G	A	rs145503152		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39274157G>A	ENST00000391413.2	-	1	449	c.411C>T	c.(409-411)ccC>ccT	p.P137P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	137	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.P137P(3)		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)			tgctgcagctggggtggcagc	0.672																																					p.P137P		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,8	KRTAP4-11	94	8	3	Substitution - coding silent(3)	prostate(1)|lung(1)|endometrium(1)	c.C411T						PASS	.						8.0	13.0	12.0					17																	39274157		684	1586	2270	SO:0001819	synonymous_variant	653240	exon1			GCAGCTGGGGTGG	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.411C>T	17.37:g.39274157G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	115	20	0.173913	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			G|0.500;A|0.500	0.500	weak		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
MDH1B	130752	hgsc.bcm.edu	37	2	207603221	207603221	+	Missense_Mutation	SNP	T	T	C	rs2287632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:207603221T>C	ENST00000374412.3	-	12	1818	c.1543A>G	c.(1543-1545)Acc>Gcc	p.T515A	MDH1B_ENST00000449792.1_Missense_Mutation_p.T417A|MDH1B_ENST00000454776.2_Missense_Mutation_p.T514A	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	515			T -> A (in dbSNP:rs2287632).		carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		GATTCCACGGTTTTGCCTTCA	0.269													T|||	509	0.101637	0.1861	0.0764	5008	,	,		20164	0.0595		0.0716	False		,,,				2504	0.0798				p.T515A	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.A1543G						PASS	.	T	ALA/THR	708,3692	274.3+/-271.8	63,582,1555	81.0	84.0	83.0		1543	-3.5	0.0	2	dbSNP_100	83	763,7829	174.6+/-224.8	34,695,3567	yes	missense	MDH1B	NM_001039845.1	58	97,1277,5122	CC,CT,TT		8.8804,16.0909,11.3224	benign	515/519	207603221	1471,11521	2200	4296	6496	SO:0001583	missense	130752	exon12			CCACGGTTTTGCC		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.1543A>G	2.37:g.207603221T>C	ENSP00000363533:p.Thr515Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	197	0.0902014652014652	90	0.18292682926829268	28	0.07734806629834254	33	0.057692307692307696	46	0.06068601583113457	T	8.539	0.872777	0.17322	0.160909	0.088804	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.31510	1.51;1.49;1.5	4.02	-3.49	0.04724	.	2.417000	0.02095	N	0.053436	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.30090	-0.9990	9	0.87932	D	0	1.2602	5.4946	0.16795	0.0:0.1904:0.4747:0.3349	rs2287632;rs2287632	514;515	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	A	515;417;514	ENSP00000363533:T515A;ENSP00000416577:T417A;ENSP00000389916:T514A	ENSP00000363533:T515A	T	-	1	0	MDH1B	207311466	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	-0.209000	0.09358	-0.586000	0.05898	-0.478000	0.04885	ACC	T|0.898;C|0.102	0.102	strong		0.269	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	
TPCN2	219931	hgsc.bcm.edu	37	11	68840397	68840397	+	Silent	SNP	T	T	C	rs386754584|rs1466221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:68840397T>C	ENST00000294309.3	+	13	1259	c.1158T>C	c.(1156-1158)taT>taC	p.Y386Y	TPCN2_ENST00000442692.2_Intron|TPCN2_ENST00000542467.1_Silent_p.Y386Y	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	386					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGCGTTCCTATGGCAGTGTTC	0.612													C|||	1693	0.338059	0.3699	0.3329	5008	,	,		17514	0.2867		0.4851	False		,,,				2504	0.2004				p.Y386Y		Atlas-SNP	.											TPCN2,NS,carcinoma,0,1	TPCN2	63	1	0			c.T1158C						PASS	.	C		1761,2639	644.8+/-398.1	353,1055,792	101.0	97.0	98.0		1158	-10.5	0.0	11	dbSNP_88	98	4278,4310	578.6+/-390.8	1033,2212,1049	no	coding-synonymous	TPCN2	NM_139075.3		1386,3267,1841	CC,CT,TT		49.8137,40.0227,46.4968		386/753	68840397	6039,6949	2200	4294	6494	SO:0001819	synonymous_variant	219931	exon13			TTCCTATGGCAGT	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1158T>C	11.37:g.68840397T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_139075	Q9NT82	Silent	SNP	ENST00000294309.3	37	CCDS8189.1																																																																																			T|0.561;C|0.439	0.439	strong		0.612	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
FSD1	79187	hgsc.bcm.edu	37	19	4322990	4322990	+	Silent	SNP	G	G	A	rs67511110	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4322990G>A	ENST00000221856.6	+	11	1194	c.1047G>A	c.(1045-1047)acG>acA	p.T349T	FSD1_ENST00000597590.1_Silent_p.T349T|STAP2_ENST00000597593.1_5'Flank	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	349	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGGGACACGCTGATCGACG	0.682													g|||	249	0.0497204	0.0756	0.0692	5008	,	,		15399	0.0		0.0795	False		,,,				2504	0.0215				p.T349T		Atlas-SNP	.											.	FSD1	51	.	0			c.G1047A						PASS	.			376,4018		11,354,1832	16.0	17.0	17.0		1047	-6.8	0.0	19	dbSNP_130	17	643,7921		16,611,3655	no	coding-synonymous	FSD1	NM_024333.2		27,965,5487	AA,AG,GG		7.5082,8.5571,7.8639		349/497	4322990	1019,11939	2197	4282	6479	SO:0001819	synonymous_variant	79187	exon11			GGACACGCTGATC	AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"""Fibronectin type III domain containing"""	13745	protein-coding gene	gene with protein product		609828	"""fibronectin type 3 and SPRY domain containing 1"""			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.1047G>A	19.37:g.4322990G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_024333	B2RDT0|Q9BXN0|Q9HAG4	Silent	SNP	ENST00000221856.6	37	CCDS12127.1																																																																																			G|0.924;A|0.076	0.076	strong		0.682	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421014	29421014	+	Silent	SNP	G	G	C	rs2306934	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29421014G>C	ENST00000261275.4	-	8	980	c.981C>G	c.(979-981)acC>acG	p.T327T		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	327	Pro-rich.					integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						AGCCAGCACTGGTGTTTGGGT	0.537													G|||	690	0.13778	0.1271	0.1196	5008	,	,		18171	0.2103		0.0805	False		,,,				2504	0.1493				p.T327T		Atlas-SNP	.											.	FAM189A1	20	.	0			c.C981G						PASS	.	G		160,1224		9,142,541	60.0	62.0	61.0		981	1.8	0.0	15	dbSNP_100	61	249,2933		12,225,1354	no	coding-synonymous	FAM189A1	NM_015307.1		21,367,1895	CC,CG,GG		7.8253,11.5607,8.9575		327/540	29421014	409,4157	692	1591	2283	SO:0001819	synonymous_variant	23359	exon8			AGCACTGGTGTTT		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.981C>G	15.37:g.29421014G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_015307	A0PK09	Silent	SNP	ENST00000261275.4	37	CCDS45198.1																																																																																			G|0.869;C|0.131	0.131	strong		0.537	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
CCNB2	9133	hgsc.bcm.edu	37	15	59408904	59408904	+	Missense_Mutation	SNP	C	C	T	rs369137460		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:59408904C>T	ENST00000288207.2	+	6	804	c.613C>T	c.(613-615)Cgg>Tgg	p.R205W	CCNB2_ENST00000559622.1_Missense_Mutation_p.R124W	NM_004701.3	NP_004692.1	O95067	CCNB2_HUMAN	cyclin B2	205					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)		p.R205W(1)		kidney(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9						GCCAGTTTCCCGGAAGAAGCT	0.408																																					p.R205W		Atlas-SNP	.											CCNB2,NS,carcinoma,0,1	CCNB2	23	1	1	Substitution - Missense(1)	lung(1)	c.C613T						scavenged	.	C	TRP/ARG	0,4382		0,0,2191	89.0	87.0	88.0		613	5.3	0.9	15		88	1,8581	1.2+/-3.3	0,1,4290	no	missense	CCNB2	NM_004701.3	101	0,1,6481	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging	205/399	59408904	1,12963	2191	4291	6482	SO:0001583	missense	9133	exon6			GTTTCCCGGAAGA	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.613C>T	15.37:g.59408904C>T	ENSP00000288207:p.Arg205Trp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	165	4	0.0242424	NM_004701	B3KM93|Q6FI99	Missense_Mutation	SNP	ENST00000288207.2	37	CCDS10170.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.717330	0.68844	0.0	1.17E-4	ENSG00000157456	ENST00000288207	T	0.13901	2.55	5.28	5.28	0.74379	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.54240	0.1846	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.71045	-0.4706	10	0.87932	D	0	.	18.272	0.90071	0.0:1.0:0.0:0.0	.	205;205	Q53HG9;O95067	.;CCNB2_HUMAN	W	205	ENSP00000288207:R205W	ENSP00000288207:R205W	R	+	1	2	CCNB2	57196196	0.993000	0.37304	0.925000	0.36789	0.622000	0.37654	2.782000	0.47758	2.629000	0.89072	0.650000	0.86243	CGG	.	.	weak		0.408	CCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256016.1	NM_004701	
MOS	4342	hgsc.bcm.edu	37	8	57025762	57025762	+	Silent	SNP	G	G	T	rs55969078	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:57025762G>T	ENST00000311923.1	-	1	779	c.780C>A	c.(778-780)gcC>gcA	p.A260A		NM_005372.1	NP_005363.1	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene homolog	260	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|chromatin organization (GO:0006325)|establishment of meiotic spindle orientation (GO:0051296)|MAPK cascade (GO:0000165)|meiotic spindle organization (GO:0000212)|negative regulation of metaphase/anaphase transition of meiotic cell cycle (GO:1902103)|protein autophosphorylation (GO:0046777)|regulation of meiosis (GO:0040020)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(12)|ovary(1)|urinary_tract(2)	22			Epithelial(17;0.00117)|all cancers(17;0.00879)			AATAAATGTCGGCTTTAGGCG	0.582													G|||	147	0.029353	0.0408	0.036	5008	,	,		18912	0.006		0.0308	False		,,,				2504	0.0317				p.A260A	Esophageal Squamous(124;373 2870 4778)	Atlas-SNP	.											MOS,NS,carcinoma,-1,1	MOS	63	1	0			c.C780A						PASS	.	G		169,4237	110.4+/-148.6	4,161,2038	59.0	62.0	61.0		780	-11.6	0.4	8	dbSNP_129	61	299,8301	108.8+/-169.4	5,289,4006	no	coding-synonymous	MOS	NM_005372.1		9,450,6044	TT,TG,GG		3.4767,3.8357,3.5983		260/347	57025762	468,12538	2203	4300	6503	SO:0001819	synonymous_variant	4342	exon1			AATGTCGGCTTTA		CCDS6164.1	8q11	2012-10-02			ENSG00000172680	ENSG00000172680			7199	protein-coding gene	gene with protein product		190060				9552420	Standard	NM_005372		Approved		uc011leb.2	P00540	OTTHUMG00000164299	ENST00000311923.1:c.780C>A	8.37:g.57025762G>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_005372	Q3KPG9|Q3KPH0	Silent	SNP	ENST00000311923.1	37	CCDS6164.1																																																																																			G|0.967;T|0.033	0.033	strong		0.582	MOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378174.1	NM_005372	
SLC37A1	54020	hgsc.bcm.edu	37	21	43985958	43985958	+	Missense_Mutation	SNP	A	A	T	rs117821416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43985958A>T	ENST00000352133.2	+	15	2225	c.1243A>T	c.(1243-1245)Agc>Tgc	p.S415C	SLC37A1_ENST00000398341.3_Missense_Mutation_p.S415C			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	415					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						CTCCACCGTCAGCAAGATGGG	0.488													A|||	37	0.00738818	0.0	0.0115	5008	,	,		20272	0.0		0.0129	False		,,,				2504	0.0164				p.S415C		Atlas-SNP	.											.	SLC37A1	48	.	0			c.A1243T						PASS	.	A	CYS/SER	6,4400	11.4+/-27.6	0,6,2197	119.0	99.0	106.0		1243	4.1	1.0	21	dbSNP_132	106	60,8540	37.8+/-93.5	0,60,4240	yes	missense	SLC37A1	NM_018964.3	112	0,66,6437	TT,TA,AA		0.6977,0.1362,0.5075	possibly-damaging	415/534	43985958	66,12940	2203	4300	6503	SO:0001583	missense	54020	exon16			ACCGTCAGCAAGA	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.1243A>T	21.37:g.43985958A>T	ENSP00000344648:p.Ser415Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	37	CCDS13689.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	A	19.31	3.803880	0.70682	0.001362	0.006977	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.59906	0.23;0.23	4.12	4.12	0.48240	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.089981	0.85682	D	0.000000	T	0.64864	0.2637	M	0.69823	2.125	0.58432	D	0.999998	D	0.62365	0.991	D	0.64506	0.926	T	0.73248	-0.4043	10	0.87932	D	0	-11.1635	12.4259	0.55546	1.0:0.0:0.0:0.0	.	415	P57057	GLPT_HUMAN	C	415	ENSP00000381383:S415C;ENSP00000344648:S415C	ENSP00000344648:S415C	S	+	1	0	SLC37A1	42859027	1.000000	0.71417	0.999000	0.59377	0.802000	0.45316	7.095000	0.76952	1.637000	0.50538	0.460000	0.39030	AGC	A|0.994;T|0.006	0.006	strong		0.488	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
FAM13B	51306	hgsc.bcm.edu	37	5	137354665	137354665	+	Missense_Mutation	SNP	C	C	T	rs79543971	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137354665C>T	ENST00000033079.3	-	3	587	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	FAM13B_ENST00000420893.2_Missense_Mutation_p.V46M|FAM13B_ENST00000425075.2_Intron	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	46	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)			endometrium(4)|kidney(2)|lung(5)	11						ATATAGTCCACAACGTGGCGG	0.393													C|||	2	0.000399361	0.0	0.0	5008	,	,		19229	0.0		0.002	False		,,,				2504	0.0				p.V46M		Atlas-SNP	.											.	FAM13B	46	.	0			c.G136A						PASS	.	C	MET/VAL,,MET/VAL	3,4403	4.2+/-10.8	0,3,2200	92.0	88.0	89.0		136,,136	6.1	1.0	5	dbSNP_131	89	16,8584	11.9+/-42.8	0,16,4284	yes	missense,intron,missense	FAM13B	NM_001101800.1,NM_001101801.1,NM_016603.2	21,,21	0,19,6484	TT,TC,CC		0.186,0.0681,0.1461	probably-damaging,,probably-damaging	46/888,,46/916	137354665	19,12987	2203	4300	6503	SO:0001583	missense	51306	exon3			AGTCCACAACGTG	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.136G>A	5.37:g.137354665C>T	ENSP00000033079:p.Val46Met	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	153	82	0.535948	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	27.0	4.793716	0.90453	6.81E-4	0.00186	ENSG00000031003	ENST00000033079;ENST00000420893;ENST00000514310;ENST00000502471;ENST00000509596;ENST00000508403;ENST00000505961	T;T;T;T;T;T;T	0.46819	1.88;1.88;1.88;1.88;1.88;0.86;0.86	6.08	6.08	0.98989	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.72534	0.3472	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73275	-0.4034	10	0.87932	D	0	-7.2121	20.6634	0.99662	0.0:1.0:0.0:0.0	.	46;46	Q9NYF5-2;Q9NYF5	.;FA13B_HUMAN	M	46	ENSP00000033079:V46M;ENSP00000388521:V46M;ENSP00000425326:V46M;ENSP00000424785:V46M;ENSP00000422311:V46M;ENSP00000426863:V46M;ENSP00000422673:V46M	ENSP00000033079:V46M	V	-	1	0	FAM13B	137382564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.120000	0.77153	2.894000	0.99253	0.655000	0.94253	GTG	C|0.999;T|0.001	0.001	strong		0.393	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		
CEP57	9702	hgsc.bcm.edu	37	11	95555088	95555088	+	Silent	SNP	G	G	A	rs11742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:95555088G>A	ENST00000325542.5	+	7	991	c.753G>A	c.(751-753)ccG>ccA	p.P251P	CEP57_ENST00000538658.1_Silent_p.P251P|CEP57_ENST00000325486.5_Silent_p.P251P|CEP57_ENST00000537677.1_Silent_p.P224P|CEP57_ENST00000541150.1_Silent_p.P242P	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	251					fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGGCAACTCCGTGTGTTCCCA	0.363									Mosaic Variegated Aneuploidy Syndrome				G|||	76	0.0151757	0.0015	0.0259	5008	,	,		18904	0.0		0.0537	False		,,,				2504	0.002				p.P251P		Atlas-SNP	.											CEP57,NS,carcinoma,+1,1	CEP57	40	1	0			c.G753A						PASS	.	G		41,4361	43.8+/-77.6	0,41,2160	74.0	71.0	72.0		753	-3.2	0.0	11	dbSNP_52	72	435,8161	133.5+/-191.0	10,415,3873	no	coding-synonymous	CEP57	NM_014679.4		10,456,6033	AA,AG,GG		5.0605,0.9314,3.6621		251/501	95555088	476,12522	2201	4298	6499	SO:0001819	synonymous_variant	9702	exon7	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AACTCCGTGTGTT	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.753G>A	11.37:g.95555088G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001243777	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Silent	SNP	ENST00000325542.5	37	CCDS8304.1	43	0.019688644688644688	0	0.0	9	0.024861878453038673	0	0.0	34	0.044854881266490766	G	0.022	-1.415636	0.01136	0.009314	0.050605	ENSG00000166037	ENST00000535224	.	.	.	5.53	-3.16	0.05217	.	.	.	.	.	T	0.02688	0.0081	.	.	.	0.20638	N	0.999874	.	.	.	.	.	.	T	0.21177	-1.0253	4	.	.	.	0.0401	1.3638	0.02197	0.2131:0.1606:0.3608:0.2655	rs11742;rs1056578;rs3197165;rs11550730	.	.	.	M	67	.	.	V	+	1	0	CEP57	95194736	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-1.101000	0.03336	-0.424000	0.07382	-1.068000	0.02270	GTG	G|0.967;A|0.033	0.033	strong		0.363	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679	
TDRD9	122402	hgsc.bcm.edu	37	14	104394850	104394850	+	Silent	SNP	C	C	T	rs9324066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104394850C>T	ENST00000409874.4	+	1	52	c.4C>T	c.(4-6)Ctg>Ttg	p.L2L	TDRD9_ENST00000339063.5_Silent_p.L2L|C14orf2_ENST00000554880.1_5'Flank	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	2					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				CTTGAGGATGCTGCGGAAGCT	0.701													C|||	2308	0.460863	0.5946	0.5216	5008	,	,		5602	0.3869		0.4016	False		,,,				2504	0.3742				p.L2L		Atlas-SNP	.											TDRD9_ENST00000409874,colon,carcinoma,0,1	TDRD9	175	1	0			c.C4T						PASS	.	C		777,607		217,343,132	21.0	25.0	24.0		4	3.6	1.0	14	dbSNP_119	24	1212,1970		225,762,604	yes	coding-synonymous	TDRD9	NM_153046.2		442,1105,736	TT,TC,CC		38.0893,43.8584,43.5611		2/1383	104394850	1989,2577	692	1591	2283	SO:0001819	synonymous_variant	122402	exon1			AGGATGCTGCGGA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.4C>T	14.37:g.104394850C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2																																																																																			A|0.000;C|0.519;G|0.000;T|0.480	0.480	strong		0.701	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
CR1L	1379	hgsc.bcm.edu	37	1	207857254	207857254	+	Missense_Mutation	SNP	A	A	G	rs3085	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:207857254A>G	ENST00000508064.2	+	4	475	c.415A>G	c.(415-417)Atc>Gtc	p.I139V	CR1L_ENST00000530905.1_3'UTR	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	139	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> V (in dbSNP:rs3085).			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						CACATGCATCATCTCAGGCAA	0.358													N|||	807	0.161142	0.0189	0.0648	5008	,	,		20001	0.3601		0.1083	False		,,,				2504	0.271				p.I139V		Atlas-SNP	.											.	CR1L	97	.	0			c.A415G						PASS	.	A	VAL/ILE	141,3869		1,139,1865	175.0	168.0	170.0		415	-4.0	0.0	1	dbSNP_36	170	951,7415		55,841,3287	yes	missense	CR1L	NM_175710.1	29	56,980,5152	GG,GA,AA		11.3674,3.5162,8.8235	benign	139/570	207857254	1092,11284	2005	4183	6188	SO:0001583	missense	1379	exon4			TGCATCATCTCAG	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.415A>G	1.37:g.207857254A>G	ENSP00000421736:p.Ile139Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	323	0.1478937728937729	13	0.026422764227642278	21	0.058011049723756904	203	0.3548951048951049	86	0.11345646437994723	A	9.486	1.099475	0.20552	0.035162	0.113674	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.23552	1.9	2.81	-3.99	0.04069	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B	0.12013	0.005	B	0.26094	0.066	T	0.48864	-0.8997	8	0.21540	T	0.41	.	5.6438	0.17579	0.276:0.5862:0.1378:0.0	rs3085;rs52799932;rs3085	139	Q2VPA4	CR1L_HUMAN	V	139	ENSP00000421736:I139V	ENSP00000434864:I83V	I	+	1	0	CR1L	205923877	0.000000	0.05858	0.002000	0.10522	0.436000	0.31835	-2.954000	0.00676	-0.487000	0.06735	0.338000	0.21704	ATC	A|0.852;G|0.148	0.148	strong		0.358	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
CD8A	925	hgsc.bcm.edu	37	2	87017575	87017575	+	Silent	SNP	C	C	T	rs2229240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:87017575C>T	ENST00000409511.2	-	5	1309	c.279G>A	c.(277-279)agG>agA	p.R93R	CD8A_ENST00000456996.2_Silent_p.R93R|CD8A_ENST00000283635.3_Silent_p.R93R|CD8A_ENST00000352580.3_Silent_p.R93R|CD8A_ENST00000538832.1_Silent_p.R134R|CD8A_ENST00000409781.1_Silent_p.R93R	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	93	Ig-like V-type.				antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	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)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						TGTCCCCCAACCTCTTGCCCG	0.637													C|||	183	0.0365415	0.0696	0.0288	5008	,	,		12826	0.0		0.0626	False		,,,				2504	0.0082				p.R93R		Atlas-SNP	.											.	CD8A	28	.	0			c.G279A						PASS	.	C	,,	349,4057	179.7+/-208.2	15,319,1869	64.0	73.0	70.0		279,279,279	2.9	0.0	2	dbSNP_98	70	656,7944	166.2+/-218.2	26,604,3670	no	coding-synonymous,coding-synonymous,coding-synonymous	CD8A	NM_001145873.1,NM_001768.6,NM_171827.3	,,	41,923,5539	TT,TC,CC		7.6279,7.921,7.7272	,,	93/236,93/236,93/199	87017575	1005,12001	2203	4300	6503	SO:0001819	synonymous_variant	925	exon5			CCCCAACCTCTTG		CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1706	protein-coding gene	gene with protein product		186910	"""CD8 antigen, alpha polypeptide (p32)"", ""T-cell surface glycoprotein CD8 alpha chain"""	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.279G>A	2.37:g.87017575C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_001145873	B4DT80|D6W5M8|Q13970|Q4ZG17	Silent	SNP	ENST00000409511.2	37	CCDS1992.1																																																																																			C|0.931;T|0.069	0.069	strong		0.637	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768	
CACNG6	59285	hgsc.bcm.edu	37	19	54501527	54501527	+	Silent	SNP	G	G	A	rs34604090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54501527G>A	ENST00000252729.2	+	2	956	c.366G>A	c.(364-366)acG>acA	p.T122T	CACNG6_ENST00000346968.2_Silent_p.T122T|CACNG6_ENST00000352529.1_Intron	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	58	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	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		
SIRPD	128646	hgsc.bcm.edu	37	20	1538266	1538266	+	Silent	SNP	G	G	A	rs11697395	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:1538266G>A	ENST00000381623.3	-	1	1223	c.34C>T	c.(34-36)Ctg>Ttg	p.L12L	SIRPD_ENST00000381621.1_Silent_p.L12L|RP4-576H24.4_ENST00000564763.1_Intron			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	12						extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						AAGGAAGGCAGAGGTGGGTGG	0.577													G|||	476	0.0950479	0.0575	0.1023	5008	,	,		18036	0.003		0.2167	False		,,,				2504	0.1104				p.L12L		Atlas-SNP	.											.	SIRPD	34	.	0			c.C34T						PASS	.	G		395,4011		15,365,1823	241.0	182.0	202.0		34	1.4	0.0	20	dbSNP_120	202	1756,6844		189,1378,2733	no	coding-synonymous	SIRPD	NM_178460.2		204,1743,4556	AA,AG,GG		20.4186,8.965,16.5385		12/198	1538266	2151,10855	2203	4300	6503	SO:0001819	synonymous_variant	128646	exon1			AAGGCAGAGGTGG	AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"""Signal-regulatory proteins"", ""Immunoglobulin superfamily / V-set domain containing"""	16248	protein-coding gene	gene with protein product			"""protein tyrosine phosphatase, non-receptor type substrate 1-like 2"""	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.34C>T	20.37:g.1538266G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_178460	B3KS88|Q5TFQ6	Silent	SNP	ENST00000381623.3	37	CCDS13018.1																																																																																			G|0.853;A|0.147	0.147	strong		0.577	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460	
CACNA1H	8912	hgsc.bcm.edu	37	16	1268494	1268494	+	Silent	SNP	C	C	T	rs2745136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1268494C>T	ENST00000348261.5	+	33	5978	c.5730C>T	c.(5728-5730)gaC>gaT	p.D1910D	CACNA1H_ENST00000358590.4_Silent_p.D1904D|CACNA1H_ENST00000565831.1_Silent_p.D1904D	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1910					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCGCCAGGGACGCCCCAAACC	0.701													C|||	3501	0.699081	0.7156	0.7075	5008	,	,		14381	0.8661		0.6441	False		,,,				2504	0.5552				p.D1910D		Atlas-SNP	.											CACNA1H_ENST00000358590,NS,carcinoma,0,2	CACNA1H	317	2	0			c.C5730T						PASS	.	C	,	2908,1158		1072,764,197	23.0	30.0	28.0		5712,5730	-5.8	0.0	16	dbSNP_100	28	5076,3122		1657,1762,680	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	2729,2526,877	TT,TC,CC		38.0825,28.4801,34.8989	,	1904/2348,1910/2354	1268494	7984,4280	2033	4099	6132	SO:0001819	synonymous_variant	8912	exon33			CAGGGACGCCCCA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5730C>T	16.37:g.1268494C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.275;G|0.000;T|0.724	0.724	strong		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TNNT3	7140	hgsc.bcm.edu	37	11	1959707	1959707	+	Silent	SNP	C	C	T	rs4727	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1959707C>T	ENST00000397301.1	+	17	803	c.795C>T	c.(793-795)ggC>ggT	p.G265G	TNNT3_ENST00000381561.4_Silent_p.G257G|TNNT3_ENST00000381549.3_Silent_p.G246G|TNNT3_ENST00000381589.3_Silent_p.G252G|TNNT3_ENST00000446240.1_Silent_p.G235G|TNNT3_ENST00000278317.6_Silent_p.G254G|TNNT3_ENST00000397304.2_Silent_p.G235G|TNNT3_ENST00000381558.1_Silent_p.G246G|TNNT3_ENST00000381579.3_Silent_p.G246G|TNNT3_ENST00000360603.3_Silent_p.G248G|TNNT3_ENST00000381548.3_Silent_p.G256G			P45378	TNNT3_HUMAN	troponin T type 3 (skeletal, fast)	265					ATP catabolic process (GO:0006200)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)|regulation of striated muscle contraction (GO:0006942)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium-dependent protein binding (GO:0048306)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(4)|stomach(1)	19		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00253)|Lung(200;0.0333)|LUSC - Lung squamous cell carcinoma(625;0.0826)		GCAAAGTCGGCGGGCGCTGGA	0.652													C|||	686	0.136981	0.0212	0.0937	5008	,	,		16576	0.3214		0.1819	False		,,,				2504	0.0879				p.G254G		Atlas-SNP	.											TNNT3_ENST00000381589,NS,carcinoma,+2,2	TNNT3	68	2	0			c.C762T						PASS	.	C	,,,	160,4244		2,156,2044	45.0	56.0	52.0		738,756,738,762	-4.5	0.9	11	dbSNP_52	52	1328,7268		108,1112,3078	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNNT3	NM_001042780.2,NM_001042781.2,NM_001042782.2,NM_006757.3	,,,	110,1268,5122	TT,TC,CC		15.449,3.6331,11.4462	,,,	246/251,252/257,246/251,254/259	1959707	1488,11512	2202	4298	6500	SO:0001819	synonymous_variant	7140	exon16			AGTCGGCGGGCGC	M21984	CCDS7727.1, CCDS41594.1, CCDS41595.1, CCDS41596.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130595	ENSG00000130595			11950	protein-coding gene	gene with protein product	"""troponin-T3, skeletal, fast"""	600692	"""troponin T3, skeletal, fast"""			8172653	Standard	NM_001042782		Approved	AMCD2B, DA2B, FSSV, DKFZp779M2348	uc001lup.4	P45378	OTTHUMG00000012475	ENST00000397301.1:c.795C>T	11.37:g.1959707C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	184	90	0.48913	NM_006757	A8MQ76|A8MSW1|B3KPX3|B7WP64|B7ZL26|B7ZVV9|Q12975|Q12976|Q12977|Q12978|Q17RG9|Q6FH29|Q6N056|Q86TH6	Silent	SNP	ENST00000397301.1	37																																																																																				C|0.866;T|0.134	0.134	strong		0.652	TNNT3-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000142920.3	NM_006757	
ARAP1	116985	hgsc.bcm.edu	37	11	72408055	72408055	+	Missense_Mutation	SNP	G	G	C	rs56200889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:72408055G>C	ENST00000393609.3	-	22	3341	c.3139C>G	c.(3139-3141)Cag>Gag	p.Q1047E	ARAP1_ENST00000334211.8_Missense_Mutation_p.Q802E|ARAP1_ENST00000393605.3_Missense_Mutation_p.Q807E|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000359373.5_Missense_Mutation_p.Q1047E|ARAP1_ENST00000455638.2_Missense_Mutation_p.Q1047E|ARAP1_ENST00000426523.1_Missense_Mutation_p.Q802E|ARAP1_ENST00000429686.1_Missense_Mutation_p.Q741E	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1047	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.		Q -> E (in dbSNP:rs56200889). {ECO:0000269|Ref.6}.		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						GTTAGGCGCTGGGCGCGAGTG	0.672													G|||	1248	0.249201	0.2194	0.2147	5008	,	,		15059	0.2431		0.2624	False		,,,				2504	0.3067				p.Q1047E	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											ARAP1_ENST00000393609,NS,carcinoma,0,2	ARAP1	168	2	0			c.C3139G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN	920,3472		111,698,1387	20.0	22.0	22.0		3139,2221,2404	4.4	1.0	11	dbSNP_129	22	2135,6443		303,1529,2457	yes	missense,missense,missense	ARAP1	NM_001040118.2,NM_001135190.1,NM_015242.4	29,29,29	414,2227,3844	CC,CG,GG		24.8893,20.9472,23.5544	benign,benign,benign	1047/1451,741/1134,802/1206	72408055	3055,9915	2196	4289	6485	SO:0001583	missense	116985	exon22			GGCGCTGGGCGCG	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.3139C>G	11.37:g.72408055G>C	ENSP00000377233:p.Gln1047Glu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	499	0.22847985347985347	94	0.1910569105691057	73	0.20165745856353592	131	0.229020979020979	201	0.26517150395778366	G	13.17	2.158091	0.38119	0.209472	0.248893	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686	T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19	5.35	4.43	0.53597	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.321288	0.33161	N	0.005208	T	0.00012	0.0000	L	0.39633	1.23	0.58432	P	5.000000000032756E-6	B;B;B;B;B	0.21147	0.026;0.02;0.019;0.052;0.021	B;B;B;B;B	0.30401	0.017;0.009;0.026;0.115;0.01	T	0.24764	-1.0151	9	0.66056	D	0.02	.	9.4767	0.38875	0.1511:0.0:0.8489:0.0	rs56200889	802;741;1047;1047;807	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	E	1047;1047;807;802;1047;802;741	ENSP00000352332:Q1047E;ENSP00000390461:Q1047E;ENSP00000377230:Q807E;ENSP00000335506:Q802E;ENSP00000377233:Q1047E;ENSP00000392264:Q802E;ENSP00000403127:Q741E	ENSP00000335506:Q802E	Q	-	1	0	ARAP1	72085703	0.016000	0.18221	1.000000	0.80357	0.872000	0.50106	0.552000	0.23376	2.501000	0.84356	0.455000	0.32223	CAG	G|0.788;C|0.212	0.212	strong		0.672	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
FLG	2312	hgsc.bcm.edu	37	1	152280736	152280736	+	Missense_Mutation	SNP	T	T	C	rs66977240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280736T>C	ENST00000368799.1	-	3	6661	c.6626A>G	c.(6625-6627)cAt>cGt	p.H2209R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2209	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCATGATGATGCGACCCTGA	0.562									Ichthyosis																												p.H2209R		Atlas-SNP	.											.	FLG	900	.	0			c.A6626G						PASS	.						397.0	353.0	368.0					1																	152280736		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGATGATGCGACC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6626A>G	1.37:g.152280736T>C	ENSP00000357789:p.His2209Arg	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	529	90	0.170132	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	
OR6A2	8590	hgsc.bcm.edu	37	11	6816792	6816792	+	Missense_Mutation	SNP	T	T	C	rs61741824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6816792T>C	ENST00000332601.3	-	1	336	c.148A>G	c.(148-150)Att>Gtt	p.I50V		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	50					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(4)|pancreas(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	29		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGGTTCCTAATTGCCATAATG	0.463													t|||	83	0.0165735	0.0008	0.0101	5008	,	,		23756	0.0		0.0288	False		,,,				2504	0.047				p.I50V		Atlas-SNP	.											.	OR6A2	68	.	0			c.A148G						PASS	.	T	VAL/ILE	35,4367	40.0+/-72.8	0,35,2166	163.0	139.0	148.0		148	-6.0	0.0	11	dbSNP_129	148	291,8301	108.0+/-168.7	8,275,4013	yes	missense	OR6A2	NM_003696.2	29	8,310,6179	CC,CT,TT		3.3869,0.7951,2.5089	benign	50/328	6816792	326,12668	2201	4296	6497	SO:0001583	missense	8590	exon1			TCCTAATTGCCAT	AB065822	CCDS7772.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184933	ENSG00000184933		"""GPCR / Class A : Olfactory receptors"""	15301	protein-coding gene	gene with protein product		608495		OR6A2P, OR6A1			Standard	NM_003696		Approved	OR11-55	uc001mes.1	O95222	OTTHUMG00000165736	ENST00000332601.3:c.148A>G	11.37:g.6816792T>C	ENSP00000330384:p.Ile50Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	194	80	0.412371	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	37	CCDS7772.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	18	0.023746701846965697	t	0.031	-1.337374	0.01287	0.007951	0.033869	ENSG00000184933	ENST00000332601	T	0.06687	3.27	4.95	-6.02	0.02192	GPCR, rhodopsin-like superfamily (1);	0.397790	0.20442	N	0.092272	T	0.00967	0.0032	N	0.12663	0.25	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39482	-0.9612	10	0.02654	T	1	.	12.8703	0.57960	0.0:0.4366:0.0:0.5634	rs61741824	50	O95222	OR6A2_HUMAN	V	50	ENSP00000330384:I50V	ENSP00000330384:I50V	I	-	1	0	OR6A2	6773368	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.270000	0.02831	-0.806000	0.04398	-3.168000	0.00057	ATT	T|0.981;C|0.019	0.019	strong		0.463	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696	
MYOM3	127294	hgsc.bcm.edu	37	1	24416133	24416133	+	Silent	SNP	C	C	T	rs4276859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24416133C>T	ENST00000374434.3	-	14	1671	c.1509G>A	c.(1507-1509)ccG>ccA	p.P503P	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Silent_p.P503P|MYOM3_ENST00000330966.7_Silent_p.P504P|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	503	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CATTGGTTGGCGGTGAGGGGA	0.597													C|||	871	0.173922	0.1876	0.1254	5008	,	,		18991	0.1845		0.1143	False		,,,				2504	0.2403				p.P503P		Atlas-SNP	.											MYOM3,caecum,carcinoma,0,1	MYOM3	131	1	0			c.G1509A						PASS	.	C		619,3447		51,517,1465	35.0	40.0	38.0		1509	-3.8	0.0	1	dbSNP_111	38	899,7463		48,803,3330	no	coding-synonymous	MYOM3	NM_152372.3		99,1320,4795	TT,TC,CC		10.751,15.2238,12.2144		503/1438	24416133	1518,10910	2033	4181	6214	SO:0001819	synonymous_variant	127294	exon14			GGTTGGCGGTGAG	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.1509G>A	1.37:g.24416133C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			C|0.855;T|0.145	0.145	strong		0.597	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84606956	84606956	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:84606956G>A	ENST00000344803.2	+	4	1618	c.1571G>A	c.(1570-1572)gGc>gAc	p.G524D		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	524					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.G524V(2)									GTCCAACGTGGCCATTCCTCC	0.463																																					p.G524D		Atlas-SNP	.											FAM75D4,NS,carcinoma,0,4	.	.	4	2	Substitution - Missense(2)	endometrium(2)	c.G1571A						scavenged	.						101.0	91.0	94.0					9																	84606956		1959	4159	6118	SO:0001583	missense	389763	exon4			AACGTGGCCATTC		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.1571G>A	9.37:g.84606956G>A	ENSP00000341988:p.Gly524Asp	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	264	3	0.0113636	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.767931	0.00645	.	.	ENSG00000214929	ENST00000344803	T	0.05382	3.45	3.5	-0.943	0.10395	.	0.719533	0.12012	N	0.507801	T	0.03959	0.0111	L	0.28344	0.845	0.09310	N	1	B	0.31790	0.34	B	0.36808	0.233	T	0.40553	-0.9557	10	0.02654	T	1	-1.6963	6.5439	0.22394	0.5482:0.0:0.4518:0.0	.	524	Q6ZQQ2	F75D1_HUMAN	D	524	ENSP00000341988:G524D	ENSP00000341988:G524D	G	+	2	0	FAM75D1	83796776	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	1.248000	0.32827	-0.266000	0.09339	-0.218000	0.12543	GGC	.	.	none		0.463	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
C5orf60	285679	hgsc.bcm.edu	37	5	179072006	179072006	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:179072006A>G	ENST00000448248.2	-	1	41	c.16T>C	c.(16-18)Ttg>Ctg	p.L6L	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	6						integral component of membrane (GO:0016021)		p.L6L(1)		NS(1)|breast(1)|kidney(5)	7						TCCTCAGGCAACTGAGCCCTG	0.577																																					p.L6L		Atlas-SNP	.											C5orf60,NS,carcinoma,0,1	C5orf60	24	1	1	Substitution - coding silent(1)	kidney(1)	c.T16C						PASS	.						35.0	33.0	34.0					5																	179072006		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			CAGGCAACTGAGC	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.16T>C	5.37:g.179072006A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	194	35	0.180412	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			.	.	weak		0.577	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
FCRL6	343413	hgsc.bcm.edu	37	1	159778910	159778910	+	Missense_Mutation	SNP	G	G	A	rs72700615	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:159778910G>A	ENST00000368106.3	+	4	480	c.479G>A	c.(478-480)gGc>gAc	p.G160D	FCRL6_ENST00000392235.3_Intron|FCRL6_ENST00000321935.6_Missense_Mutation_p.G167D|FCRL6_ENST00000339348.5_Missense_Mutation_p.G160D	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	144	0	0		WXS	Illumina HiSeq	Phase_I	130	68	0.523077	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	
ZNF682	91120	hgsc.bcm.edu	37	19	20116963	20116963	+	Missense_Mutation	SNP	C	C	T	rs17679334	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:20116963C>T	ENST00000397165.2	-	4	1508	c.1348G>A	c.(1348-1350)Gtc>Atc	p.V450I	ZNF682_ENST00000358523.5_Missense_Mutation_p.V418I|ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000397162.1_Missense_Mutation_p.V418I|ZNF682_ENST00000595736.1_Missense_Mutation_p.V374I|ZNF682_ENST00000597972.1_Missense_Mutation_p.V456I	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	450			V -> I (in dbSNP:rs17679334).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TAGCGTTTGACGGCAGTATGA	0.388													c|||	975	0.194688	0.2897	0.1931	5008	,	,		20255	0.0754		0.1779	False		,,,				2504	0.2076				p.V450I		Atlas-SNP	.											.	ZNF682	51	.	0			c.G1348A						PASS	.	C	ILE/VAL,ILE/VAL	1183,3155		179,825,1165	88.0	97.0	94.0		1252,1348	-0.4	0.0	19	dbSNP_123	94	1474,7104		135,1204,2950	no	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	29,29	314,2029,4115	TT,TC,CC		17.1835,27.2706,20.5714	benign,benign	418/467,450/499	20116963	2657,10259	2169	4289	6458	SO:0001583	missense	91120	exon4			GTTTGACGGCAGT	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.1348G>A	19.37:g.20116963C>T	ENSP00000380351:p.Val450Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	398	0.18223443223443223	139	0.28252032520325204	77	0.212707182320442	39	0.06818181818181818	143	0.18865435356200527	c	8.091	0.774465	0.16051	0.272706	0.171835	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000341262;ENST00000358523	T;T;T	0.18502	2.21;2.21;2.21	1.09	-0.422	0.12329	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.26130	0.795	0.58432	P	2.9999999999752447E-6	B	0.11235	0.004	B	0.13407	0.009	T	0.40979	-0.9534	8	0.87932	D	0	.	8.1706	0.31252	0.0:0.8131:0.0:0.1869	rs17679334;rs52819789;rs61436554;rs17679334	450	O95780	ZN682_HUMAN	I	450;418;119;418	ENSP00000380351:V450I;ENSP00000380348:V418I;ENSP00000351324:V418I	ENSP00000340236:V119I	V	-	1	0	ZNF682	19977963	0.147000	0.22687	0.000000	0.03702	0.000000	0.00434	2.720000	0.47252	-1.571000	0.01663	-1.579000	0.00862	GTC	C|0.804;T|0.196	0.196	strong		0.388	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
CSMD3	114788	hgsc.bcm.edu	37	8	113395826	113395826	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:113395826T>C	ENST00000297405.5	-	37	6245	c.6001A>G	c.(6001-6003)Aac>Gac	p.N2001D	CSMD3_ENST00000343508.3_Missense_Mutation_p.N1961D|CSMD3_ENST00000455883.2_Missense_Mutation_p.N1897D|CSMD3_ENST00000352409.3_Missense_Mutation_p.N1931D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2001	CUB 11. {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						GGAGCATTGTTGTCTCCCCCA	0.323										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N2001D		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A6001G						PASS	.						84.0	82.0	83.0					8																	113395826		2203	4300	6503	SO:0001583	missense	114788	exon37			CATTGTTGTCTCC	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.6001A>G	8.37:g.113395826T>C	ENSP00000297405:p.Asn2001Asp	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	200	102	0.51	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543166	0.65198	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	4.42	4.42	0.53409	CUB (5);	0.269490	0.36409	N	0.002617	T	0.19046	0.0457	N	0.15975	0.35	0.39770	D	0.972152	P;B;D	0.60575	0.913;0.083;0.988	B;B;P	0.61201	0.431;0.174;0.885	T	0.07328	-1.0778	10	0.10636	T	0.68	.	14.1168	0.65159	0.0:0.0:0.0:1.0	.	1897;2001;1961	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	1961;2001;1271;1897;1931	ENSP00000345799:N1961D;ENSP00000297405:N2001D;ENSP00000341558:N1271D;ENSP00000412263:N1897D;ENSP00000343124:N1931D	ENSP00000297405:N2001D	N	-	1	0	CSMD3	113465002	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.040000	0.57333	1.975000	0.57531	0.383000	0.25322	AAC	.	.	none		0.323	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
MAGI3	260425	hgsc.bcm.edu	37	1	114196495	114196495	+	Silent	SNP	A	A	G	rs2359173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:114196495A>G	ENST00000307546.9	+	15	2559	c.2484A>G	c.(2482-2484)acA>acG	p.T828T	MAGI3_ENST00000369617.4_Silent_p.T853T|MAGI3_ENST00000369611.4_Silent_p.T828T|MAGI3_ENST00000369615.1_Silent_p.T828T	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	853	Interaction with BAI1.|PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCATTTCAACACAGAATGGAT	0.473													A|||	973	0.194289	0.0098	0.2032	5008	,	,		2608	0.0933		0.327	False		,,,				2504	0.4049				p.T828T		Atlas-SNP	.											.	MAGI3	181	.	0			c.A2484G						PASS	.	A	,	299,4107	162.5+/-194.5	12,275,1916	137.0	151.0	146.0		2484,2484	-4.9	0.2	1	dbSNP_100	146	2612,5988	423.1+/-354.3	400,1812,2088	no	coding-synonymous,coding-synonymous	MAGI3	NM_001142782.1,NM_152900.2	,	412,2087,4004	GG,GA,AA		30.3721,6.7862,22.382	,	828/1482,828/1126	114196495	2911,10095	2203	4300	6503	SO:0001819	synonymous_variant	260425	exon15			TTCAACACAGAAT	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.2484A>G	1.37:g.114196495A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	93	0.958763	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																			A|0.804;G|0.196	0.196	strong		0.473	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900	
JAK2	3717	hgsc.bcm.edu	37	9	5065003	5065003	+	Missense_Mutation	SNP	C	C	G	rs2230723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:5065003C>G	ENST00000381652.3	+	9	1671	c.1177C>G	c.(1177-1179)Ctt>Gtt	p.L393V	JAK2_ENST00000539801.1_Missense_Mutation_p.L393V|JAK2_ENST00000544510.1_Missense_Mutation_p.L244V	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	393			L -> V (in dbSNP:rs2230723). {ECO:0000269|PubMed:17344846}.		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)	TCCAGCCGTGCTTGAAAATAT	0.343		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				C|||	60	0.0119808	0.0272	0.0202	5008	,	,		17562	0.0		0.0099	False		,,,				2504	0.0				p.L393V		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C1177G						PASS	.	C	VAL/LEU	132,4274	94.8+/-133.5	4,124,2075	74.0	71.0	72.0		1177	5.2	0.9	9	dbSNP_98	72	52,8548	33.3+/-86.6	0,52,4248	yes	missense	JAK2	NM_004972.3	32	4,176,6323	GG,GC,CC		0.6047,2.9959,1.4147	benign	393/1133	5065003	184,12822	2203	4300	6503	SO:0001583	missense	3717	exon9	Familial Cancer Database		GCCGTGCTTGAAA		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.1177C>G	9.37:g.5065003C>G	ENSP00000371067:p.Leu393Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	29	0.013278388278388278	20	0.04065040650406504	7	0.019337016574585635	0	0.0	2	0.002638522427440633	C	7.763	0.705753	0.15172	0.029959	0.006047	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.59083	0.29;0.29;0.29	5.15	5.15	0.70609	.	0.221618	0.39020	N	0.001490	T	0.10809	0.0264	N	0.17764	0.52	0.53005	D	0.999966	B	0.29612	0.251	B	0.23150	0.044	T	0.08330	-1.0727	10	0.08599	T	0.76	-14.3001	12.0387	0.53440	0.0:0.9205:0.0:0.0795	rs2230723;rs35844880	393	O60674	JAK2_HUMAN	V	393;393;244	ENSP00000440387:L393V;ENSP00000371067:L393V;ENSP00000443103:L244V	ENSP00000371067:L393V	L	+	1	0	JAK2	5055003	0.633000	0.27181	0.933000	0.37362	0.824000	0.46624	1.199000	0.32235	2.412000	0.81896	0.313000	0.20887	CTT	C|0.986;G|0.014	0.014	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
DSCAML1	57453	hgsc.bcm.edu	37	11	117309603	117309603	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:117309603C>T	ENST00000321322.6	-	24	4422	c.4421G>A	c.(4420-4422)cGa>cAa	p.R1474Q	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R1204Q	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1414	Fibronectin type-III 5. {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)		CTCCTCACCTCGGATGGAGCT	0.607																																					p.R1474Q		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G4421A						PASS	.						44.0	42.0	43.0					11																	117309603		2201	4296	6497	SO:0001583	missense	57453	exon24			TCACCTCGGATGG		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.4421G>A	11.37:g.117309603C>T	ENSP00000315465:p.Arg1474Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182083	0.94885	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.56611	0.45;0.45	4.8	4.8	0.61643	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57975	0.2090	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63435	-0.6638	9	0.48119	T	0.1	.	18.0562	0.89365	0.0:1.0:0.0:0.0	.	1414	Q8TD84	DSCL1_HUMAN	Q	1204;1474;1181	ENSP00000434335:R1204Q;ENSP00000315465:R1474Q	ENSP00000315465:R1474Q	R	-	2	0	DSCAML1	116814813	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.635000	0.83286	2.503000	0.84419	0.561000	0.74099	CGA	.	.	none		0.607	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
PML	5371	hgsc.bcm.edu	37	15	74328141	74328141	+	Intron	SNP	G	G	T	rs743581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:74328141G>T	ENST00000268058.3	+	7	1806				PML_ENST00000435786.2_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000354026.6_Missense_Mutation_p.G732V|PML_ENST00000395132.2_Intron|PML_ENST00000564428.1_Intron|PML_ENST00000436891.3_3'UTR|PML_ENST00000395135.3_Intron|PML_ENST00000268059.6_Missense_Mutation_p.G780V|PML_ENST00000359928.4_Intron|PML_ENST00000565898.1_Intron|PML_ENST00000563500.1_3'UTR	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CTTGGAGCAGGTGTTCCCCCT	0.582			T	"""RARA, PAX5"""	"""APL, ALL"""								G|||	1759	0.351238	0.298	0.4481	5008	,	,		15253	0.4018		0.3837	False		,,,				2504	0.2689				p.G780V		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.G2339T						PASS	.	G	,,VAL/GLY,,,,,,VAL/GLY	1412,2984	428.5+/-341.9	230,952,1016	52.0	62.0	59.0		,,2339,,,,,,2195	-2.4	0.0	15	dbSNP_86	59	3088,5506	456.0+/-363.9	540,2008,1749	yes	intron,intron,missense,utr-3,utr-3,intron,intron,intron,missense	PML	NM_002675.3,NM_033238.2,NM_033239.2,NM_033240.2,NM_033244.3,NM_033246.2,NM_033247.2,NM_033249.2,NM_033250.2	,,109,,,,,,109	770,2960,2765	TT,TG,GG		35.932,32.1201,34.642	,,,,,,,,	,,780/830,,,,,,732/782	74328141	4500,8490	2198	4297	6495	SO:0001627	intron_variant	5371	exon8			GAGCAGGTGTTCC	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+1270G>T	15.37:g.74328141G>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_033239	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	37	CCDS10255.1	846	0.3873626373626374	151	0.30691056910569103	141	0.38950276243093923	253	0.4423076923076923	301	0.3970976253298153	G	3.117	-0.181346	0.06380	0.321201	0.35932	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	3.24	-2.39	0.06602	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.22909	0.077;0.077	B;B	0.19391	0.025;0.025	T	0.47711	-0.9096	6	0.32370	T	0.25	.	1.2769	0.02032	0.2141:0.3451:0.282:0.1587	rs743581;rs17855994;rs17856628	732;780	P29590-13;P29590-8	.;.	V	780;732	.	ENSP00000268059:G780V	G	+	2	0	PML	72115194	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.312000	0.19397	-0.518000	0.06452	-0.502000	0.04539	GGT	A|0.000;G|0.653;T|0.347	0.347	strong		0.582	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
LSG1	55341	hgsc.bcm.edu	37	3	194373832	194373832	+	Missense_Mutation	SNP	T	T	C	rs1675953|rs386669929|rs66771418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:194373832T>C	ENST00000265245.5	-	8	1113	c.799A>G	c.(799-801)Aag>Gag	p.K267E		NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	267	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.		K -> E (in dbSNP:rs1675953). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		TGTCCAAACTTGGTTGTGTTG	0.408													C|||	3178	0.634585	0.3253	0.6297	5008	,	,		22485	0.8651		0.7038	False		,,,				2504	0.7474				p.K267E		Atlas-SNP	.											.	LSG1	38	.	0			c.A799G						PASS	.	C	GLU/LYS	1770,2636	637.5+/-396.8	378,1014,811	118.0	95.0	102.0		799	4.3	0.0	3	dbSNP_89	102	5880,2720	421.6+/-353.8	2035,1810,455	yes	missense	LSG1	NM_018385.2	56	2413,2824,1266	CC,CT,TT		31.6279,40.1725,41.181	benign	267/659	194373832	7650,5356	2203	4300	6503	SO:0001583	missense	55341	exon8			CAAACTTGGTTGT		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.799A>G	3.37:g.194373832T>C	ENSP00000265245:p.Lys267Glu	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	249	127	0.51004	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	37	CCDS33922.1	1232	0.5641025641025641	127	0.258130081300813	207	0.5718232044198895	434	0.7587412587412588	464	0.6121372031662269	C	2.660	-0.280053	0.05642	0.401725	0.683721	ENSG00000041802	ENST00000265245	T	0.42131	0.98	4.34	4.34	0.51931	.	0.828691	0.10929	N	0.618622	T	0.00012	0.0000	N	0.00554	-1.385	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41197	-0.9522	9	0.02654	T	1	-4.2612	8.5768	0.33603	0.0:0.8977:0.0:0.1023	rs1675953;rs59067666;rs1675953	267	Q9H089	LSG1_HUMAN	E	267	ENSP00000265245:K267E	ENSP00000265245:K267E	K	-	1	0	LSG1	195855121	0.011000	0.17503	0.015000	0.15790	0.015000	0.08874	0.516000	0.22817	1.431000	0.47355	-0.119000	0.15052	AAG	T|0.413;C|0.587	0.587	strong		0.408	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	
MUC2	4583	hgsc.bcm.edu	37	11	1103873	1103873	+	Silent	SNP	C	C	T	rs11245957	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1103873C>T	ENST00000441003.2	+	48	8199	c.8172C>T	c.(8170-8172)taC>taT	p.Y2724Y		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5086					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	AGGTTTCGTACGCCGGCTGCA	0.657													c|||	753	0.150359	0.385	0.072	5008	,	,		14924	0.0357		0.0934	False		,,,				2504	0.0654				p.Y2720Y		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.C8160T						PASS	.	T		1236,2906		166,904,1001	26.0	30.0	28.0		8157	-7.6	0.0	11	dbSNP_120	28	693,7677		30,633,3522	no	coding-synonymous	MUC2	NM_002457.2		196,1537,4523	TT,TC,CC		8.2796,29.8407,15.4172		2719/2813	1103873	1929,10583	2071	4185	6256	SO:0001819	synonymous_variant	4583	exon49			TTCGTACGCCGGC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8172C>T	11.37:g.1103873C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.867;T|0.133	0.133	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
AASDH	132949	hgsc.bcm.edu	37	4	57204777	57204777	+	Missense_Mutation	SNP	A	A	C	rs8340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:57204777A>C	ENST00000205214.6	-	15	3268	c.3088T>G	c.(3088-3090)Tac>Gac	p.Y1030D	AASDH_ENST00000434343.2_Missense_Mutation_p.Y545D|AASDH_ENST00000513376.1_Missense_Mutation_p.Y930D|AASDH_ENST00000451613.1_3'UTR|AASDH_ENST00000602986.1_3'UTR	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	1030			Y -> D (in dbSNP:rs8340). {ECO:0000269|PubMed:15865210}.		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.Y1030D(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CTGCCATTGTAGTTATGGAAA	0.413													A|||	1130	0.225639	0.2231	0.379	5008	,	,		18086	0.2153		0.1302	False		,,,				2504	0.229				p.Y1030D		Atlas-SNP	.											AASDH,NS,carcinoma,0,1	AASDH	101	1	1	Substitution - Missense(1)	stomach(1)	c.T3088G						PASS	.	A	ASP/TYR	950,3456	360.6+/-315.3	103,744,1356	93.0	89.0	91.0		3088	2.3	0.0	4	dbSNP_52	91	1096,7504	228.2+/-263.3	69,958,3273	yes	missense	AASDH	NM_181806.2	160	172,1702,4629	CC,CA,AA		12.7442,21.5615,15.7312	benign	1030/1099	57204777	2046,10960	2203	4300	6503	SO:0001583	missense	132949	exon15			CATTGTAGTTATG	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.3088T>G	4.37:g.57204777A>C	ENSP00000205214:p.Tyr1030Asp	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	245	119	0.485714	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	434	0.1987179487179487	100	0.2032520325203252	118	0.3259668508287293	117	0.20454545454545456	99	0.13060686015831136	A	3.749	-0.051936	0.07362	0.215615	0.127442	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343	T;T;T	0.29142	1.58;1.58;1.58	5.9	2.31	0.28768	Quinonprotein alcohol dehydrogenase-like (2);	0.892392	0.10130	N	0.712160	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	0.46345	-0.9198	9	0.27785	T	0.31	4.1894	6.8594	0.24058	0.2768:0.1237:0.5996:0.0	rs8340;rs3193307;rs3733325;rs60987677;rs8340	1030	Q4L235	ACSF4_HUMAN	D	1030;930;545	ENSP00000205214:Y1030D;ENSP00000423760:Y930D;ENSP00000392158:Y545D	ENSP00000205214:Y1030D	Y	-	1	0	AASDH	56899534	0.098000	0.21812	0.000000	0.03702	0.103000	0.19146	1.387000	0.34430	0.125000	0.18397	-0.248000	0.11899	TAC	C|0.176;N|0.000	0.176	strong		0.413	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
ONECUT2	9480	hgsc.bcm.edu	37	18	55143766	55143766	+	Silent	SNP	C	C	T	rs3745074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:55143766C>T	ENST00000491143.2	+	2	1358	c.1326C>T	c.(1324-1326)ttC>ttT	p.F442F		NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	442					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)		GAACACTCTTCGCCATCTTCA	0.517													C|||	1965	0.392372	0.5136	0.4236	5008	,	,		18551	0.4673		0.2356	False		,,,				2504	0.2904				p.F442F		Atlas-SNP	.											ONECUT2,NS,carcinoma,+1,1	ONECUT2	42	1	0			c.C1326T						PASS	.	C		1811,2319		385,1041,639	62.0	69.0	66.0		1326	-10.2	0.4	18	dbSNP_107	66	1778,6648		177,1424,2612	no	coding-synonymous	ONECUT2	NM_004852.2		562,2465,3251	TT,TC,CC		21.1014,43.8499,28.5839		442/505	55143766	3589,8967	2065	4213	6278	SO:0001819	synonymous_variant	9480	exon2			ACTCTTCGCCATC	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.1326C>T	18.37:g.55143766C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_004852		Silent	SNP	ENST00000491143.2	37	CCDS42440.1	852	0.3901098901098901	240	0.4878048780487805	154	0.425414364640884	276	0.4825174825174825	182	0.24010554089709762	C	7.087	0.571487	0.13623	0.438499	0.211014	ENSG00000119547	ENST00000481727	.	.	.	6.02	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999699	.	.	.	.	.	.	T	0.11012	-1.0605	3	.	.	.	-10.8386	21.9508	0.99964	0.0:0.1873:0.0:0.8127	rs3745074;rs17831449;rs3745074	.	.	.	C	71	.	.	R	+	1	0	ONECUT2	53294764	0.000000	0.05858	0.399000	0.26333	0.993000	0.82548	-2.690000	0.00831	-2.195000	0.00752	-0.145000	0.13849	CGC	C|0.638;T|0.362	0.362	strong		0.517	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
XRCC4	7518	hgsc.bcm.edu	37	5	82648977	82648977	+	Silent	SNP	T	T	G	rs1056503	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:82648977T>G	ENST00000511817.1	+	8	1007	c.927T>G	c.(925-927)tcT>tcG	p.S309S	XRCC4_ENST00000338635.6_Silent_p.S309S|XRCC4_ENST00000396027.4_Silent_p.S307S|XRCC4_ENST00000282268.3_Silent_p.S307S			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	309					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		CTGAGACGTCTAAAAAGGAGC	0.338								Non-homologous end-joining					G|||	1881	0.375599	0.4758	0.3329	5008	,	,		17355	0.7063		0.1402	False		,,,				2504	0.1718				p.S309S		Atlas-SNP	.											.	XRCC4	37	.	0			c.T927G						PASS	.	G	,,	1942,2464	617.9+/-393.1	424,1094,685	113.0	123.0	120.0		921,927,921	1.1	0.0	5	dbSNP_86	120	1055,7543	768.5+/-407.6	63,929,3307	no	coding-synonymous,coding-synonymous,coding-synonymous	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	,,	487,2023,3992	GG,GT,TT		12.2703,44.0763,23.0468	,,	307/335,309/337,307/335	82648977	2997,10007	2203	4299	6502	SO:0001819	synonymous_variant	7518	exon8			GACGTCTAAAAAG	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.927T>G	5.37:g.82648977T>G		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	269	127	0.472119	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	
IMPG2	50939	hgsc.bcm.edu	37	3	100976502	100976502	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:100976502C>T	ENST00000193391.7	-	10	1211	c.1024G>A	c.(1024-1026)Gat>Aat	p.D342N		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	342	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	GGTTTATCATCCAGTTCCACA	0.438																																					p.D342N		Atlas-SNP	.											IMPG2,colon,carcinoma,+2,1	IMPG2	164	1	0			c.G1024A						scavenged	.						127.0	121.0	123.0					3																	100976502		2203	4300	6503	SO:0001583	missense	50939	exon10			TATCATCCAGTTC	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1024G>A	3.37:g.100976502C>T	ENSP00000193391:p.Asp342Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	2	0.0166667	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093233	0.76756	.	.	ENSG00000081148	ENST00000193391	T	0.26223	1.75	5.51	4.64	0.57946	SEA (1);	0.149852	0.45126	N	0.000381	T	0.24353	0.0590	L	0.44542	1.39	0.33587	D	0.600672	B;B	0.22146	0.065;0.024	B;B	0.24394	0.053;0.031	T	0.28870	-1.0030	10	0.62326	D	0.03	-10.9615	12.5939	0.56456	0.0:0.9231:0.0:0.0769	.	342;342	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	N	342	ENSP00000193391:D342N	ENSP00000193391:D342N	D	-	1	0	IMPG2	102459192	0.995000	0.38212	1.000000	0.80357	0.872000	0.50106	3.526000	0.53509	1.332000	0.45431	0.462000	0.41574	GAT	.	.	none		0.438	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3		
SYNE3	161176	hgsc.bcm.edu	37	14	95884323	95884323	+	Missense_Mutation	SNP	G	G	A	rs12434757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:95884323G>A	ENST00000334258.5	-	17	2782	c.2768C>T	c.(2767-2769)gCg>gTg	p.A923V	SYNE3_ENST00000554873.1_Missense_Mutation_p.A680V|SYNE3_ENST00000557275.1_Missense_Mutation_p.A918V	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	923	KASH. {ECO:0000255|PROSITE- ProRule:PRU00385}.		A -> V (in dbSNP:rs12434757). {ECO:0000269|PubMed:14702039}.		cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CACACAGCACGCCCTCCGGAA	0.672													A|||	2755	0.55012	0.5	0.5461	5008	,	,		14315	0.5		0.659	False		,,,				2504	0.5603				p.A923V		Atlas-SNP	.											SYNE3_ENST00000334258,NS,carcinoma,0,6	SYNE3	130	6	0			c.C2768T						PASS	.	A	VAL/ALA	2281,2125	574.6+/-383.8	587,1107,509	56.0	50.0	52.0		2768	2.3	0.7	14	dbSNP_120	52	5839,2761	437.0+/-358.5	1983,1873,444	yes	missense	C14orf49	NM_152592.3	64	2570,2980,953	AA,AG,GG		32.1047,48.2297,37.5673	benign	923/976	95884323	8120,4886	2203	4300	6503	SO:0001583	missense	161176	exon17			CAGCACGCCCTCC	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2768C>T	14.37:g.95884323G>A	ENSP00000334308:p.Ala923Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	77	0.950617	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	1226	0.5613553113553114	235	0.47764227642276424	201	0.5552486187845304	287	0.5017482517482518	503	0.6635883905013192	A	3.580	-0.085774	0.07097	0.517703	0.678953	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.19532	2.14;2.14;2.14	4.67	2.34	0.29019	Klarsicht/ANC-1/syne-1 homology (2);	0.365080	0.17018	N	0.190232	T	0.00012	0.0000	N	0.00621	-1.32	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.42716	-0.9435	9	0.02654	T	1	-7.063	8.5717	0.33574	0.5683:0.0:0.4317:0.0	rs12434757;rs58866555;rs12434757	918;923	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	V	923;680;918	ENSP00000334308:A923V;ENSP00000452154:A680V;ENSP00000450562:A918V	ENSP00000334308:A923V	A	-	2	0	C14orf49	94954076	0.532000	0.26346	0.703000	0.30354	0.897000	0.52465	1.201000	0.32259	-0.092000	0.12417	-1.115000	0.02055	GCG	G|0.410;A|0.590	0.590	strong		0.672	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
ZKSCAN1	7586	hgsc.bcm.edu	37	7	99627504	99627504	+	Missense_Mutation	SNP	C	C	G	rs148669042	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99627504C>G	ENST00000324306.6	+	4	835	c.601C>G	c.(601-603)Cct>Gct	p.P201A	ZKSCAN1_ENST00000535170.1_5'UTR|ZKSCAN1_ENST00000426572.1_Missense_Mutation_p.P165A	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TGCCCACATTCCTGCACCCCC	0.587													C|||	26	0.00519169	0.0	0.0043	5008	,	,		18311	0.001		0.0109	False		,,,				2504	0.0112				p.P201A		Atlas-SNP	.											.	ZKSCAN1	59	.	0			c.C601G						PASS	.	C	ALA/PRO	9,4397	15.5+/-35.6	0,9,2194	118.0	113.0	115.0		601	4.4	1.0	7	dbSNP_134	115	68,8532	43.6+/-101.6	0,68,4232	yes	missense	ZKSCAN1	NM_003439.1	27	0,77,6426	GG,GC,CC		0.7907,0.2043,0.592	possibly-damaging	201/564	99627504	77,12929	2203	4300	6503	SO:0001583	missense	7586	exon4			CACATTCCTGCAC	X52349	CCDS34698.1, CCDS69349.1, CCDS75640.1	7q22	2013-01-09	2004-11-16	2004-11-17	ENSG00000106261	ENSG00000106261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13101	protein-coding gene	gene with protein product		601260	"""zinc finger protein 36 (KOX 18)"""	ZNF139, ZNF36			Standard	NM_001287055		Approved	KOX18, PHZ-37, ZSCAN33	uc003usk.1	P17029	OTTHUMG00000156534	ENST00000324306.6:c.601C>G	7.37:g.99627504C>G	ENSP00000323148:p.Pro201Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_003439	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Missense_Mutation	SNP	ENST00000324306.6	37	CCDS34698.1	11	0.005036630036630037	0	0.0	0	0.0	1	0.0017482517482517483	10	0.013192612137203167	C	15.16	2.751185	0.49257	0.002043	0.007907	ENSG00000106261	ENST00000324306;ENST00000426572	T;T	0.08282	3.14;3.11	5.33	4.45	0.53987	.	0.134244	0.34676	N	0.003763	T	0.06371	0.0164	N	0.08118	0	0.80722	D	1	D	0.61697	0.99	P	0.57620	0.824	T	0.26849	-1.0091	10	0.52906	T	0.07	.	11.028	0.47757	0.0:0.9107:0.0:0.0893	.	201	P17029	ZKSC1_HUMAN	A	201;165	ENSP00000323148:P201A;ENSP00000409172:P165A	ENSP00000323148:P201A	P	+	1	0	ZKSCAN1	99465440	0.162000	0.22906	0.994000	0.49952	0.105000	0.19272	0.647000	0.24812	2.489000	0.83994	0.655000	0.94253	CCT	C|0.994;G|0.006	0.006	strong		0.587	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439	
MAP2	4133	hgsc.bcm.edu	37	2	210559960	210559960	+	Silent	SNP	G	G	T	rs2239672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	102	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	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	
APIP	51074	hgsc.bcm.edu	37	11	34916657	34916657	+	Splice_Site	SNP	C	C	T	rs61734605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:34916657C>T	ENST00000395787.3	-	2	272	c.58G>A	c.(58-60)Gac>Aac	p.D20N	APIP_ENST00000278359.5_Splice_Site_p.D37N|APIP_ENST00000527830.1_Intron	NM_015957.2	NP_057041.2			APAF1 interacting protein											kidney(2)|lung(1)|skin(1)	4	all_epithelial(35;0.161)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.000425)			TGCTCCTTGTCCTTAAAAAGA	0.373													C|||	574	0.114617	0.0204	0.1643	5008	,	,		20546	0.0		0.328	False		,,,				2504	0.1053				p.D20N		Atlas-SNP	.											.	APIP	21	.	0			c.G58A						PASS	.	C	ASN/ASP	366,4038	182.9+/-210.6	13,340,1849	81.0	77.0	78.0		58	5.2	1.0	11	dbSNP_129	78	2877,5719	449.3+/-362.1	467,1943,1888	yes	missense-near-splice	APIP	NM_015957.2	23	480,2283,3737	TT,TC,CC		33.4691,8.3106,24.9462	benign	20/243	34916657	3243,9757	2202	4298	6500	SO:0001630	splice_region_variant	51074	exon2			CCTTGTCCTTAAA	AF132963	CCDS7895.1	11p13	2014-05-12				ENSG00000149089	4.2.1.109		17581	protein-coding gene	gene with protein product	"""methylthioribulose-1-phosphate dehydratase"""	612491				10810093, 15262985, 24367089	Standard	NM_015957		Approved	CGI-29, Mmrp19, APIP2	uc001mvs.2	Q96GX9		ENST00000395787.3:c.58-1G>A	11.37:g.34916657C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_015957		Missense_Mutation	SNP	ENST00000395787.3	37	CCDS7895.1	334	0.15293040293040294	12	0.024390243902439025	63	0.17403314917127072	0	0.0	259	0.341688654353562	C	18.64	3.668045	0.67814	0.083106	0.334691	ENSG00000149089	ENST00000278359;ENST00000395787	T;T	0.30714	1.52;1.82	5.17	5.17	0.71159	Class II aldolase/adducin, N-terminal (1);	0.159136	0.56097	D	0.000037	T	0.00012	0.0000	L	0.37850	1.14	0.09310	P	0.99999778761	B	0.31752	0.338	B	0.28709	0.093	T	0.43829	-0.9367	9	0.40728	T	0.16	-24.48	18.6546	0.91448	0.0:1.0:0.0:0.0	rs61734605	20	Q96GX9	MTNB_HUMAN	N	37;20	ENSP00000278359:D37N;ENSP00000379133:D20N	ENSP00000278359:D37N	D	-	1	0	APIP	34873233	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.770000	0.74990	2.417000	0.82017	0.563000	0.77884	GAC	C|0.778;T|0.222	0.222	strong		0.373	APIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389864.1	NM_015957	Missense_Mutation
COX10	1352	hgsc.bcm.edu	37	17	13972955	13972955	+	Silent	SNP	C	C	T	rs8076787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:13972955C>T	ENST00000261643.3	+	1	110	c.33C>T	c.(31-33)cgC>cgT	p.R11R	COX10-AS1_ENST00000602743.1_RNA|COX10_ENST00000537334.1_5'UTR|COX10-AS1_ENST00000602539.1_RNA|COX10_ENST00000429152.2_Silent_p.R11R|COX10-AS1_ENST00000449363.1_RNA|COX10_ENST00000536205.1_5'UTR	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	11					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)		TCTCCTCACGCCTCCTGACAG	0.627													C|||	166	0.033147	0.0045	0.036	5008	,	,		16178	0.0288		0.0666	False		,,,				2504	0.0399				p.R11R		Atlas-SNP	.											.	COX10	36	.	0			c.C33T						PASS	.	C		49,4357	50.9+/-86.3	1,47,2155	54.0	47.0	49.0		33	4.3	1.0	17	dbSNP_116	49	579,8021	153.3+/-207.7	25,529,3746	no	coding-synonymous	COX10	NM_001303.3		26,576,5901	TT,TC,CC		6.7326,1.1121,4.8285		11/444	13972955	628,12378	2203	4300	6503	SO:0001819	synonymous_variant	1352	exon1			CTCACGCCTCCTG	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.33C>T	17.37:g.13972955C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	37	CCDS11166.1																																																																																			C|0.957;T|0.043	0.043	strong		0.627	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
WDR36	134430	hgsc.bcm.edu	37	5	110439509	110439509	+	Missense_Mutation	SNP	A	A	G	rs80306217|rs11241095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:110439509A>G	ENST00000513710.2	+	7	794	c.790A>G	c.(790-792)Att>Gtt	p.I264V	WDR36_ENST00000505303.1_Missense_Mutation_p.I208V|WDR36_ENST00000506538.2_Missense_Mutation_p.I264V			Q8NI36	WDR36_HUMAN	WD repeat domain 36	264			I -> V (in dbSNP:rs11241095). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15677485}.		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)		TGTTGTTGCTATTGGTCTTAT	0.313													A|||	1289	0.257388	0.0582	0.353	5008	,	,		16831	0.2728		0.3131	False		,,,				2504	0.3855				p.I264V		Atlas-SNP	.											.	WDR36	111	.	0			c.A790G	GRCh37	CM075046	WDR36	M	rs11241095	PASS	.	A	VAL/ILE	448,3954	210.8+/-231.2	20,408,1773	64.0	65.0	65.0		790	0.6	0.8	5	dbSNP_120	65	2652,5942	423.8+/-354.5	398,1856,2043	yes	missense	WDR36	NM_139281.2	29	418,2264,3816	GG,GA,AA		30.8587,10.1772,23.8535	benign	264/952	110439509	3100,9896	2201	4297	6498	SO:0001583	missense	134430	exon7			GTTGCTATTGGTC	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.790A>G	5.37:g.110439509A>G	ENSP00000424628:p.Ile264Val	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	210	115	0.547619	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	37	CCDS4102.1	540	0.24725274725274726	29	0.05894308943089431	130	0.35911602209944754	147	0.256993006993007	234	0.3087071240105541	A	1.229	-0.624726	0.03636	0.101772	0.308587	ENSG00000134987	ENST00000506538;ENST00000513710;ENST00000505303;ENST00000504122	T;T;T;T	0.32753	1.79;1.79;3.46;1.44	5.51	0.615	0.17608	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.231702	0.44097	N	0.000482	T	0.00012	0.0000	N	0.05487	-0.04	0.30639	P	0.756659	B	0.02656	0.0	B	0.01281	0.0	T	0.45848	-0.9233	9	0.87932	D	0	-10.1007	10.6201	0.45474	0.3359:0.0:0.6641:0.0	rs11241095;rs17552957;rs52808180;rs57821592;rs11241095	264	Q8NI36	WDR36_HUMAN	V	264;264;208;135	ENSP00000423067:I264V;ENSP00000424628:I264V;ENSP00000422158:I208V;ENSP00000426509:I135V	ENSP00000426509:I135V	I	+	1	0	WDR36	110467408	0.026000	0.19158	0.797000	0.32132	0.818000	0.46254	0.234000	0.17930	-0.184000	0.10567	-0.818000	0.03119	ATT	A|0.756;G|0.243	0.243	strong		0.313	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	
ARMC4	55130	hgsc.bcm.edu	37	10	28257852	28257852	+	Splice_Site	SNP	C	C	T	rs199740026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:28257852C>T	ENST00000305242.5	-	9	1330	c.1238G>A	c.(1237-1239)cGg>cAg	p.R413Q	ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000239715.3_Splice_Site_p.R270Q|ARMC4_ENST00000537576.1_Splice_Site_p.R105Q|ARMC4_ENST00000545014.1_Intron	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	413					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						AGAAACATACCGAAGTAATTG	0.458													C|||	557	0.111222	0.1884	0.0836	5008	,	,		18036	0.003		0.1213	False		,,,				2504	0.1278				p.R413Q		Atlas-SNP	.											ARMC4,rectum,NS,-1,1	ARMC4	177	1	0			c.G1238A						scavenged	.						4.0	3.0	3.0					10																	28257852		1459	3081	4540	SO:0001630	splice_region_variant	55130	exon9			ACATACCGAAGTA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1238+1G>A	10.37:g.28257852C>T		Somatic	787	1	0.00127065		WXS	Illumina HiSeq	Phase_I	830	207	0.249398	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	261	0.11950549450549451	136	0.2764227642276423	36	0.09944751381215469	3	0.005244755244755245	86	0.11345646437994723	C	7.770	0.707261	0.15239	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	3.89	2.05	0.26809	.	1.074070	0.07060	N	0.833582	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.35628	0.513	B	0.21360	0.034	T	0.26052	-1.0114	8	.	.	.	-2.5181	6.1142	0.20117	0.0:0.7713:0.0:0.2287	.	413	Q5T2S8	ARMC4_HUMAN	Q	105;413;105;307;270	ENSP00000443208:R105Q;ENSP00000306410:R413Q;ENSP00000398155:R307Q;ENSP00000239715:R270Q	.	R	-	2	0	ARMC4	28297858	0.423000	0.25482	0.063000	0.19743	0.008000	0.06430	0.554000	0.23407	0.620000	0.30215	0.557000	0.71058	CGG	C|0.500;T|0.500	0.500	weak		0.458	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	Missense_Mutation
PHYHD1	254295	hgsc.bcm.edu	37	9	131702891	131702891	+	Silent	SNP	A	A	G	rs2273866	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:131702891A>G	ENST00000372592.3	+	11	1533	c.600A>G	c.(598-600)agA>agG	p.R200R	PHYHD1_ENST00000308941.5_Missense_Mutation_p.E193G|PHYHD1_ENST00000487504.1_3'UTR|PHYHD1_ENST00000421063.2_Silent_p.R179R|RP11-101E3.5_ENST00000482796.1_5'Flank|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						scavenged	.	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	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	101	101	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	
METTL13	51603	hgsc.bcm.edu	37	1	171751236	171751236	+	Silent	SNP	T	T	C	rs2294720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171751236T>C	ENST00000361735.3	+	1	395	c.129T>C	c.(127-129)caT>caC	p.H43H	METTL13_ENST00000362019.3_Intron|METTL13_ENST00000458517.1_Silent_p.H42H|METTL13_ENST00000367737.5_Silent_p.H43H	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	43							methyltransferase activity (GO:0008168)	p.H43H(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GGGTGCTACATAAATATATCA	0.517													C|||	2673	0.533746	0.73	0.4395	5008	,	,		17775	0.6577		0.4443	False		,,,				2504	0.2996				p.H43H		Atlas-SNP	.											METTL13,NS,carcinoma,0,1	METTL13	67	1	1	Substitution - coding silent(1)	stomach(1)	c.T129C						PASS	.	C	,,	3080,1326	445.1+/-347.6	1091,898,214	74.0	79.0	77.0		129,,129	5.5	1.0	1	dbSNP_100	77	4046,4554	595.7+/-393.5	940,2166,1194	no	coding-synonymous,intron,coding-synonymous	METTL13	NM_001007239.1,NM_014955.2,NM_015935.4	,,	2031,3064,1408	CC,CT,TT		47.0465,30.0953,45.2099	,,	43/544,,43/700	171751236	7126,5880	2203	4300	6503	SO:0001819	synonymous_variant	51603	exon1			GCTACATAAATAT	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.129T>C	1.37:g.171751236T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Silent	SNP	ENST00000361735.3	37	CCDS1299.1																																																																																			T|0.439;C|0.561	0.561	strong		0.517	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
LRRC75A	388341	hgsc.bcm.edu	37	17	16346932	16346932	+	Silent	SNP	G	G	T	rs4792745	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16346932G>T	ENST00000470794.1	-	4	1032	c.1005C>A	c.(1003-1005)ggC>ggA	p.G335G	C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000481898.1_RNA|FAM211A_ENST00000409083.3_3'UTR|C17orf76-AS1_ENST00000582911.1_RNA|RP11-138I1.3_ENST00000585048.1_lincRNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA	NM_001113567.2	NP_001107039.1														lung(1)	1						CAGTCTCCTTGCCCTCATGGT	0.652													G|||	1372	0.273962	0.2655	0.3343	5008	,	,		18678	0.2212		0.3569	False		,,,				2504	0.2117				p.G335G		Atlas-SNP	.											.	FAM211A	21	.	0			c.C1005A						PASS	.	G	,	398,984		65,268,358	7.0	9.0	9.0		1005,	2.5	0.0	17	dbSNP_111	9	1183,1985		249,685,650	no	coding-synonymous,utr-3	C17orf76	NM_001113567.1,NM_207387.2	,	314,953,1008	TT,TG,GG		37.3422,28.7988,34.7473	,	335/345,	16346932	1581,2969	691	1584	2275	SO:0001819	synonymous_variant	388341	exon4			CTCCTTGCCCTCA																												ENST00000470794.1:c.1005C>A	17.37:g.16346932G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	35	0.380435	NM_001113567		Silent	SNP	ENST00000470794.1	37	CCDS45620.1																																																																																			G|0.691;T|0.309	0.309	strong		0.652	FAM211A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130463.3		
RPAP1	26015	hgsc.bcm.edu	37	15	41819367	41819367	+	Missense_Mutation	SNP	T	T	C	rs11630901	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:41819367T>C	ENST00000304330.4	-	13	1860	c.1744A>G	c.(1744-1746)Agg>Ggg	p.R582G	RPAP1_ENST00000561603.1_Missense_Mutation_p.R582G|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	582			R -> G (in dbSNP:rs11630901).			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)		TTTCTCACCCTTGTGGCTGAT	0.587													T|||	330	0.0658946	0.0098	0.1153	5008	,	,		19877	0.0		0.2008	False		,,,				2504	0.0358				p.R582G		Atlas-SNP	.											RPAP1,colon,carcinoma,0,1	RPAP1	111	1	0			c.A1744G						PASS	.	T	GLY/ARG	167,4239	109.9+/-148.2	6,155,2042	55.0	51.0	53.0		1744	3.4	1.0	15	dbSNP_120	53	1619,6981	289.4+/-299.3	158,1303,2839	yes	missense	RPAP1	NM_015540.2	125	164,1458,4881	CC,CT,TT		18.8256,3.7903,13.7321	possibly-damaging	582/1394	41819367	1786,11220	2203	4300	6503	SO:0001583	missense	26015	exon13			TCACCCTTGTGGC	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.1744A>G	15.37:g.41819367T>C	ENSP00000306123:p.Arg582Gly	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	207	0.09478021978021978	7	0.014227642276422764	42	0.11602209944751381	0	0.0	158	0.20844327176781002	T	15.93	2.977355	0.53720	0.037903	0.188256	ENSG00000103932	ENST00000304330	T	0.74737	-0.87	4.58	3.43	0.39272	.	0.289012	0.38959	N	0.001513	T	0.00073	0.0002	L	0.44542	1.39	0.30713	P	0.749065	P	0.40144	0.704	B	0.35182	0.197	T	0.10042	-1.0647	9	0.87932	D	0	-6.304	5.3683	0.16125	0.0:0.0908:0.3521:0.557	rs11630901;rs56425685;rs57768203;rs11630901	582	Q9BWH6	RPAP1_HUMAN	G	582	ENSP00000306123:R582G	ENSP00000306123:R582G	R	-	1	2	RPAP1	39606659	0.997000	0.39634	0.996000	0.52242	0.957000	0.61999	1.747000	0.38298	0.862000	0.35528	0.460000	0.39030	AGG	T|0.886;C|0.114	0.114	strong		0.587	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68257485	68257485	+	Silent	SNP	C	C	T	rs7143196	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:68257485C>T	ENST00000347230.4	-	15	2697	c.2559G>A	c.(2557-2559)ctG>ctA	p.L853L	ZFYVE26_ENST00000555452.1_Silent_p.L853L	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	853					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)		TGAACGTGAACAGCACCTGTC	0.527													C|||	374	0.0746805	0.0106	0.1095	5008	,	,		18439	0.0169		0.2217	False		,,,				2504	0.045				p.L853L		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.G2559A						PASS	.	C		184,4222	120.4+/-158.0	5,174,2024	120.0	106.0	111.0		2559	-4.3	0.9	14	dbSNP_116	111	1801,6799	323.7+/-316.1	203,1395,2702	no	coding-synonymous	ZFYVE26	NM_015346.3		208,1569,4726	TT,TC,CC		20.9419,4.1761,15.2622		853/2540	68257485	1985,11021	2203	4300	6503	SO:0001819	synonymous_variant	23503	exon15			CGTGAACAGCACC	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.2559G>A	14.37:g.68257485C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	154	78	0.506494	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	37	CCDS9788.1																																																																																			C|0.874;T|0.126	0.126	strong		0.527	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
DNAJC27	51277	hgsc.bcm.edu	37	2	25194741	25194741	+	Silent	SNP	G	G	A	rs7593864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:25194741G>A	ENST00000264711.2	-	1	222	c.33C>T	c.(31-33)ccC>ccT	p.P11P	DNAJC27-AS1_ENST00000422449.1_RNA|SNORD14_ENST00000365609.1_RNA|DNAJC27_ENST00000468467.1_5'Flank|DNAJC27-AS1_ENST00000421842.1_RNA|DNAJC27-AS1_ENST00000434897.1_RNA|DNAJC27-AS1_ENST00000428614.1_RNA|DNAJC27-AS1_ENST00000445389.1_RNA|DNAJC27-AS1_ENST00000451291.1_RNA|DNAJC27_ENST00000534855.1_5'Flank|DNAJC27-AS1_ENST00000421904.1_RNA	NM_001198559.1|NM_016544.2	NP_001185488.1|NP_057628.1	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27	11	Required for interaction with MAPK1. {ECO:0000250|UniProtKB:Q8CFP6}.				small GTPase mediated signal transduction (GO:0007264)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						GAGACCTGCCGGGCTCCTTCC	0.692													G|||	3570	0.712859	0.6324	0.8588	5008	,	,		14385	0.744		0.7873	False		,,,				2504	0.6094				p.P11P		Atlas-SNP	.											DNAJC27_ENST00000264711,NS,carcinoma,0,1	DNAJC27	37	1	0			c.C33T						PASS	.	G	,	2955,1451	672.5+/-402.6	1002,951,250	45.0	39.0	41.0		33,33	-11.6	0.0	2	dbSNP_116	41	6642,1958	714.2+/-406.0	2560,1522,218	no	coding-synonymous,coding-synonymous	DNAJC27	NM_001198559.1,NM_016544.2	,	3562,2473,468	AA,AG,GG		22.7674,32.9324,26.211	,	11/178,11/274	25194741	9597,3409	2203	4300	6503	SO:0001819	synonymous_variant	51277	exon1			CCTGCCGGGCTCC		CCDS1716.1, CCDS74493.1	2p23.3	2011-09-02	2008-08-20	2008-08-20	ENSG00000115137	ENSG00000115137		"""Heat shock proteins / DNAJ (HSP40)"""	30290	protein-coding gene	gene with protein product		613527	"""rab and DnaJ domain containing"""	RBJ		14980719	Standard	NM_016544		Approved	RabJS	uc002rft.2	Q9NZQ0	OTTHUMG00000125524	ENST00000264711.2:c.33C>T	2.37:g.25194741G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_016544	Q5JV88|Q86Y24	Silent	SNP	ENST00000264711.2	37	CCDS1716.1																																																																																			G|0.256;A|0.744	0.744	strong		0.692	DNAJC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246855.3	NM_016544	
C21orf2	755	hgsc.bcm.edu	37	21	45750346	45750346	+	Intron	SNP	C	C	A	rs2070573	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45750346C>A	ENST00000339818.4	-	7	850				C21orf2_ENST00000397956.3_Splice_Site_p.P333P|C21orf2_ENST00000325223.7_Intron|AP001062.7_ENST00000448927.1_RNA|AP001062.8_ENST00000422357.1_RNA|C21orf2_ENST00000496321.1_Intron	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2						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)		AGTGACTGACCGGCACACTCG	0.697													c|||	1322	0.263978	0.298	0.2089	5008	,	,		14117	0.3591		0.2107	False		,,,				2504	0.2137				p.P333P		Atlas-SNP	.											.	C21orf2	10	.	0			c.G999T						PASS	.																																			SO:0001627	intron_variant	755	exon6			ACTGACCGGCACA	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.643-137G>T	21.37:g.45750346C>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_001271441	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			C|0.728;A|0.272	0.272	strong		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
KDM5B	10765	hgsc.bcm.edu	37	1	202733178	202733178	+	Splice_Site	SNP	A	A	G	rs61749325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:202733178A>G	ENST00000367265.3	-	6	1971	c.807T>C	c.(805-807)aaT>aaC	p.N269N	KDM5B_ENST00000367264.2_Splice_Site_p.N305N	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	269					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						TTTTCTTACCATTTTCACATT	0.303													A|||	55	0.0109824	0.0023	0.0216	5008	,	,		16710	0.0		0.0298	False		,,,				2504	0.0072				p.N269N		Atlas-SNP	.											.	KDM5B	166	.	0			c.T807C						PASS	.	A		24,4382	29.0+/-57.7	1,22,2180	85.0	78.0	80.0		807	3.3	1.0	1	dbSNP_129	80	308,8292	111.2+/-171.5	5,298,3997	yes	coding-synonymous-near-splice	KDM5B	NM_006618.3		6,320,6177	GG,GA,AA		3.5814,0.5447,2.5527		269/1545	202733178	332,12674	2203	4300	6503	SO:0001630	splice_region_variant	10765	exon6			CTTACCATTTTCA	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.808+1T>C	1.37:g.202733178A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_006618	O95811|Q15752|Q9Y3Q5	Silent	SNP	ENST00000367265.3	37	CCDS30974.1																																																																																			A|0.978;G|0.022	0.022	strong		0.303	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	Silent
OPLAH	26873	hgsc.bcm.edu	37	8	145114924	145114924	+	Silent	SNP	G	G	C	rs7003860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145114924G>C	ENST00000426825.1	-	2	93	c.12C>G	c.(10-12)ccC>ccG	p.P4P	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	4					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGCGGCCCTCGGGGCTGCCCA	0.652													G|||	605	0.120807	0.3404	0.0663	5008	,	,		14509	0.001		0.0795	False		,,,				2504	0.0286				p.P4P		Atlas-SNP	.											.	OPLAH	78	.	0			c.C12G						PASS	.	G		1125,2657		172,781,938	15.0	17.0	17.0		12	-9.8	0.0	8	dbSNP_116	17	565,7665		17,531,3567	no	coding-synonymous	OPLAH	NM_017570.3		189,1312,4505	CC,CG,GG		6.8651,29.7462,14.0693		4/1289	145114924	1690,10322	1891	4115	6006	SO:0001819	synonymous_variant	26873	exon2			GCCCTCGGGGCTG	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.12C>G	8.37:g.145114924G>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	37																																																																																				G|0.894;C|0.106	0.106	strong		0.652	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
TTC23	64927	hgsc.bcm.edu	37	15	99762052	99762052	+	Silent	SNP	A	A	G	rs76007555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:99762052A>G	ENST00000394132.2	-	6	1015	c.198T>C	c.(196-198)caT>caC	p.H66H	TTC23_ENST00000394130.1_Silent_p.H66H|TTC23_ENST00000558663.1_Silent_p.H66H|TTC23_ENST00000262074.4_Silent_p.H66H|TTC23_ENST00000558613.1_Silent_p.H66H|TTC23_ENST00000394135.3_Silent_p.H66H|TTC23_ENST00000394136.1_Silent_p.H66H|TTC23_ENST00000394129.2_Silent_p.H66H			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	66										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)			GCACAAGCTCATGGACGGCCT	0.433													G|||	230	0.0459265	0.0703	0.0418	5008	,	,		19732	0.0089		0.0596	False		,,,				2504	0.0399				p.H66H		Atlas-SNP	.											.	TTC23	33	.	0			c.T198C						PASS	.	G	,,,,,,	384,4010	790.3+/-415.0	23,338,1836	107.0	89.0	95.0		198,198,198,198,198,198,198	-10.8	0.0	15	dbSNP_132	95	640,7954	790.5+/-407.6	21,598,3678	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	,,,,,,	44,936,5514	GG,GA,AA		7.4471,8.7392,7.8842	,,,,,,	66/448,66/448,66/448,66/448,66/448,66/448,66/448	99762052	1024,11964	2197	4297	6494	SO:0001819	synonymous_variant	64927	exon4			AAGCTCATGGACG		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.198T>C	15.37:g.99762052A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	49	0.563218	NM_001040657	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Silent	SNP	ENST00000394132.2	37	CCDS10379.2																																																																																			A|0.932;G|0.068	0.068	strong		0.433	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303953.2	NM_022905	
SDHA	6389	hgsc.bcm.edu	37	5	256455	256455	+	Missense_Mutation	SNP	C	C	G	rs1126697		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:256455C>G	ENST00000264932.6	+	15	2030	c.1915C>G	c.(1915-1917)Ctg>Gtg	p.L639V	SDHA_ENST00000504309.1_Missense_Mutation_p.L558V|SDHA_ENST00000510361.1_Missense_Mutation_p.L591V|SDHA_ENST00000507522.1_Intron	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	639					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	CAAGGTCACTCTGGAATATAG	0.418									Familial Paragangliomas																												p.L639V		Atlas-SNP	.											SDHA,NS,adenocarcinoma,0,1	SDHA	80	1	0			c.C1915G						scavenged	.						92.0	103.0	99.0					5																	256455		2203	4300	6503	SO:0001583	missense	6389	exon15	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	GTCACTCTGGAAT	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1915C>G	5.37:g.256455C>G	ENSP00000264932:p.Leu639Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	134	3	0.0223881	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	4.275|4.275	0.050102|0.050102	0.08243|0.08243	.|.	.|.	ENSG00000073578|ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361|ENST00000515815	D;D;D|.	0.82344|.	-1.6;-1.6;-1.6|.	4.12|4.12	-1.06|-1.06	0.10002|0.10002	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (1);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);|.	0.000000|.	0.64402|.	U|.	0.000014|.	T|T	0.53899|0.53899	0.1825|0.1825	L|L	0.50333|0.50333	1.59|1.59	0.50467|0.50467	D|D	0.999871|0.999871	B;B;D;B|.	0.57257|.	0.432;0.049;0.979;0.072|.	B;B;D;B|.	0.71414|.	0.344;0.085;0.973;0.063|.	T|T	0.47799|0.47799	-0.9089|-0.9089	10|5	0.72032|.	D|.	0.01|.	.|.	7.982|7.982	0.30190|0.30190	0.0:0.2524:0.0:0.7476|0.0:0.2524:0.0:0.7476	rs1126697;rs3181866;rs17414511|rs1126697;rs3181866;rs17414511	591;233;558;639|.	E9PBJ5;B3KYA5;D6RFM5;P31040|.	.;.;.;DHSA_HUMAN|.	V|C	639;494;558;591|121	ENSP00000264932:L639V;ENSP00000426514:L558V;ENSP00000427703:L591V|.	ENSP00000264932:L639V|.	L|S	+|+	1|2	2|0	SDHA|SDHA	309455|309455	0.152000|0.152000	0.22762|0.22762	0.492000|0.492000	0.27490|0.27490	0.237000|0.237000	0.25408|0.25408	0.546000|0.546000	0.23284|0.23284	-0.096000|-0.096000	0.12329|0.12329	-0.680000|-0.680000	0.03767|0.03767	CTG|TCT	C|0.998;G|0.002	0.002	weak		0.418	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
WDR27	253769	hgsc.bcm.edu	37	6	170070723	170070723	+	Missense_Mutation	SNP	A	A	G	rs4236176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170070723A>G	ENST00000448612.1	-	4	507	c.398T>C	c.(397-399)cTg>cCg	p.L133P	WDR27_ENST00000423258.1_Intron|WDR27_ENST00000420344.2_Missense_Mutation_p.L133P|WDR27_ENST00000333572.6_Missense_Mutation_p.L133P	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	133			L -> P (in dbSNP:rs4236176). {ECO:0000269|PubMed:15489334}.			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)		ATGATCATCCAGGCTCAACTG	0.468													a|||	2691	0.53734	0.4803	0.5548	5008	,	,		16862	0.9365		0.2922	False		,,,				2504	0.4427				p.L133P		Atlas-SNP	.											.	WDR27	129	.	0			c.T398C						PASS	.	A	,PRO/LEU	1677,2209		358,961,624	123.0	123.0	123.0		,398	0.7	0.0	6	dbSNP_111	123	2170,6136		294,1582,2277	yes	intron,missense	WDR27	NM_001202550.1,NM_182552.4	,98	652,2543,2901	GG,GA,AA		26.1257,43.1549,31.5535	,benign	,133/896	170070723	3847,8345	1943	4153	6096	SO:0001583	missense	253769	exon4			TCATCCAGGCTCA	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.398T>C	6.37:g.170070723A>G	ENSP00000416289:p.Leu133Pro	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	1132	0.5183150183150184	202	0.4105691056910569	179	0.494475138121547	524	0.916083916083916	227	0.2994722955145119	a	0.086	-1.174843	0.01646	0.431549	0.261257	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000420344	T;T;T	0.60299	1.73;2.37;0.2	5.52	0.661	0.17874	.	0.643068	0.15332	N	0.267927	T	0.05410	0.0143	N	0.00419	-1.52	0.51012	P	9.40000000000385E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38607	-0.9653	9	0.02654	T	1	-7.9112	9.8422	0.41006	0.3536:0.0:0.6464:0.0	rs4236176;rs17854047;rs17860914;rs61562734;rs4236176	133;133	F2Z2U5;C9JGV0	.;.	P	133	ENSP00000416289:L133P;ENSP00000330265:L133P;ENSP00000406114:L133P	ENSP00000330265:L133P	L	-	2	0	WDR27	169812648	0.509000	0.26163	0.000000	0.03702	0.050000	0.14768	0.527000	0.22987	-0.185000	0.10550	-0.362000	0.07510	CTG	A|0.485;G|0.515	0.515	strong		0.468	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
CDON	50937	hgsc.bcm.edu	37	11	125871735	125871735	+	Silent	SNP	C	C	T	rs516664	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:125871735C>T	ENST00000392693.3	-	11	2164	c.2037G>A	c.(2035-2037)gcG>gcA	p.A679A	CDON_ENST00000263577.7_Silent_p.A679A|CDON_ENST00000531738.1_Silent_p.A56A	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	679					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.A679A(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)		TTTTTGATGACGCTGTTTTTT	0.388													T|||	1515	0.302516	0.4017	0.3415	5008	,	,		16262	0.1617		0.337	False		,,,				2504	0.2505				p.A679A		Atlas-SNP	.											CDON,NS,carcinoma,0,2	CDON	137	2	1	Substitution - coding silent(1)	stomach(1)	c.G2037A						PASS	.	T		1697,2705	652.5+/-399.4	318,1061,822	112.0	112.0	112.0		2037	-7.2	0.4	11	dbSNP_83	112	2793,5805	676.8+/-403.3	473,1847,1979	no	coding-synonymous	CDON	NM_016952.4		791,2908,2801	TT,TC,CC		32.4843,38.5507,34.5385		679/1265	125871735	4490,8510	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon11			TGATGACGCTGTT	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.2037G>A	11.37:g.125871735C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	150	69	0.46	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			C|0.667;T|0.333	0.333	strong		0.388	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
USH2A	7399	hgsc.bcm.edu	37	1	216258194	216258194	+	Silent	SNP	G	G	T	rs56110889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:216258194G>T	ENST00000307340.3	-	25	5399	c.5013C>A	c.(5011-5013)ggC>ggA	p.G1671G	RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Silent_p.G1671G|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA	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	107	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	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	
GTF2H4	2968	hgsc.bcm.edu	37	6	30877760	30877760	+	Silent	SNP	A	A	C	rs1419693	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30877760A>C	ENST00000259895.4	+	4	517	c.294A>C	c.(292-294)acA>acC	p.T98T	GTF2H4_ENST00000376316.2_Silent_p.T98T|GTF2H4_ENST00000539324.1_Silent_p.T42T|RN7SL175P_ENST00000580375.1_RNA	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	98					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|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)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						TCTGGCACACACAGCTGCTCC	0.567								Nucleotide excision repair (NER)					C|||	2042	0.407748	0.2769	0.4294	5008	,	,		16351	0.6091		0.2217	False		,,,				2504	0.5532				p.T98T		Atlas-SNP	.											.	GTF2H4	38	.	0			c.A294C						PASS	.	C		789,2231		107,575,828	98.0	115.0	109.0		294	-1.8	1.0	6	dbSNP_96	109	963,4455		85,793,1831	no	coding-synonymous	GTF2H4	NM_001517.4		192,1368,2659	CC,CA,AA		17.7741,26.1258,20.7632		98/463	30877760	1752,6686	1510	2709	4219	SO:0001819	synonymous_variant	2968	exon4			GCACACACAGCTG	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	4658	protein-coding gene	gene with protein product		601760	"""general transcription factor IIH, polypeptide 4 (52kD subunit)"""			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.294A>C	6.37:g.30877760A>C		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001517	B4DTJ5|Q76KU4	Silent	SNP	ENST00000259895.4	37	CCDS34386.1																																																																																			A|0.740;C|0.260	0.260	strong		0.567	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517	
TMEM200A	114801	hgsc.bcm.edu	37	6	130761804	130761804	+	Silent	SNP	C	C	T	rs12200105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:130761804C>T	ENST00000296978.3	+	3	1108	c.237C>T	c.(235-237)gcC>gcT	p.A79A	TMEM200A_ENST00000392429.1_Silent_p.A79A|TMEM200A_ENST00000545622.1_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	121	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	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	
STXBP5L	9515	hgsc.bcm.edu	37	3	121100283	121100283	+	Missense_Mutation	SNP	G	G	A	rs17740066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:121100283G>A	ENST00000273666.6	+	23	2834	c.2563G>A	c.(2563-2565)Gtt>Att	p.V855I	STXBP5L_ENST00000492541.1_Missense_Mutation_p.V855I|STXBP5L_ENST00000497029.1_Missense_Mutation_p.V829I|STXBP5L_ENST00000471454.1_Missense_Mutation_p.V831I|STXBP5L_ENST00000472879.1_Missense_Mutation_p.V831I	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	855			V -> I (in dbSNP:rs17740066).		exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V855F(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		TTGTCTGTTCGTTGGAACCAG	0.413													G|||	337	0.0672923	0.0091	0.147	5008	,	,		17412	0.0675		0.0984	False		,,,				2504	0.0573				p.V855I		Atlas-SNP	.											.	STXBP5L	159	.	1	Substitution - Missense(1)	lung(1)	c.G2563A						PASS	.	G	ILE/VAL	79,3713		1,77,1818	189.0	177.0	180.0		2563	5.1	1.0	3	dbSNP_123	180	890,7358		58,774,3292	yes	missense	STXBP5L	NM_014980.2	29	59,851,5110	AA,AG,GG		10.7905,2.0833,8.0482	benign	855/1187	121100283	969,11071	1896	4124	6020	SO:0001583	missense	9515	exon23			CTGTTCGTTGGAA	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"""WD repeat domain containing"""	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2563G>A	3.37:g.121100283G>A	ENSP00000273666:p.Val855Ile	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	205	102	0.497561	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	154	0.07051282051282051	8	0.016260162601626018	49	0.13535911602209943	19	0.033216783216783216	78	0.10290237467018469	G	16.65	3.183023	0.57800	0.020833	0.107905	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37	5.1	5.1	0.69264	Lethal giant larvae (Lgl)-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00524	0.0017	L	0.60904	1.88	0.09310	P	0.99999639701	D;D	0.89917	0.958;1.0	P;D	0.81914	0.582;0.995	T	0.02781	-1.1111	9	0.27082	T	0.32	-8.4264	12.0804	0.53667	0.0781:0.0:0.9219:0.0	rs17740066;rs52790800;rs56442849;rs56887239;rs17740066	831;855	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	I	855;831;831;829;855;798	ENSP00000273666:V855I;ENSP00000420019:V831I;ENSP00000419627:V831I;ENSP00000420287:V829I;ENSP00000420666:V855I;ENSP00000420167:V798I	ENSP00000273666:V855I	V	+	1	0	STXBP5L	122582973	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.584000	0.82572	2.660000	0.90430	0.650000	0.86243	GTT	G|0.930;A|0.070	0.070	strong		0.413	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		
FBN3	84467	hgsc.bcm.edu	37	19	8203392	8203392	+	Missense_Mutation	SNP	G	G	C	rs61729623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8203392G>C	ENST00000600128.1	-	9	1336	c.922C>G	c.(922-924)Ctc>Gtc	p.L308V	FBN3_ENST00000270509.2_Missense_Mutation_p.L308V|FBN3_ENST00000601739.1_Missense_Mutation_p.L308V			Q75N90	FBN3_HUMAN	fibrillin 3	308	TB 2.					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						TGGCCGGCGAGGTCTCCAGCA	0.652													g|||	14	0.00279553	0.0015	0.0014	5008	,	,		15853	0.0		0.008	False		,,,				2504	0.0031				p.L308V		Atlas-SNP	.											.	FBN3	300	.	0			c.C922G						PASS	.		VAL/LEU	9,4393		0,9,2192	24.0	26.0	25.0		922	1.7	0.0	19	dbSNP_129	25	90,8510		0,90,4210	yes	missense	FBN3	NM_032447.3	32	0,99,6402	CC,CG,GG		1.0465,0.2045,0.7614	probably-damaging	308/2810	8203392	99,12903	2201	4300	6501	SO:0001583	missense	84467	exon8			CGGCGAGGTCTCC		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.922C>G	19.37:g.8203392G>C	ENSP00000470498:p.Leu308Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	g	10.79	1.450741	0.26074	0.002045	0.010465	ENSG00000142449	ENST00000270509	D	0.94828	-3.53	4.06	1.72	0.24424	Matrix fibril-associated (3);TGF-beta binding (1);	0.090982	0.45867	N	0.000325	D	0.87826	0.6275	M	0.65498	2.005	0.25192	N	0.990126	P	0.35192	0.489	B	0.30179	0.112	T	0.77624	-0.2518	10	0.20519	T	0.43	.	9.7313	0.40363	0.0:0.1538:0.6867:0.1595	rs61729623	308	Q75N90	FBN3_HUMAN	V	308	ENSP00000270509:L308V	ENSP00000270509:L308V	L	-	1	0	FBN3	8109392	0.994000	0.37717	0.001000	0.08648	0.000000	0.00434	1.255000	0.32909	0.235000	0.21160	-0.313000	0.08912	CTC	G|0.983;C|0.017	0.017	strong		0.652	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
ATF7IP	55729	hgsc.bcm.edu	37	12	14577524	14577524	+	Silent	SNP	C	C	T	rs146972131		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:14577524C>T	ENST00000540793.1	+	1	830	c.675C>T	c.(673-675)gcC>gcT	p.A225A	ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000544627.1_Silent_p.A233A|ATF7IP_ENST00000536444.1_Silent_p.A225A|ATF7IP_ENST00000261168.4_Silent_p.A225A|ATF7IP_ENST00000543189.1_Silent_p.A225A			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	225					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						GTGATTGTGCCGCTGATGATA	0.517																																					p.A225A		Atlas-SNP	.											.	ATF7IP	136	.	0			c.C675T						PASS	.	C		0,4406		0,0,2203	127.0	115.0	119.0		675	-0.9	0.0	12	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATF7IP	NM_018179.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		225/1271	14577524	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55729	exon2			TTGTGCCGCTGAT	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.675C>T	12.37:g.14577524C>T		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	280	135	0.482143	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																			C|1.000;T|0.000	0.000	weak		0.517	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
CSF1	1435	hgsc.bcm.edu	37	1	110466338	110466338	+	Silent	SNP	C	C	A	rs333970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:110466338C>A	ENST00000329608.6	+	6	1486	c.1095C>A	c.(1093-1095)acC>acA	p.T365T	CSF1_ENST00000420111.2_Intron|CSF1_ENST00000369802.3_Silent_p.T365T|CSF1_ENST00000369801.1_Intron|CSF1_ENST00000344188.5_Intron	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	365					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)		TAACTGGTACCGCCTTGCCCA	0.632											OREG0013645	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2154	0.430112	0.1067	0.5749	5008	,	,		17431	0.4018		0.6213	False		,,,				2504	0.5971				p.T365T		Atlas-SNP	.											.	CSF1	40	.	0			c.C1095A						PASS	.	C	,,,	843,3563	328.8+/-300.7	89,665,1449	55.0	56.0	56.0		1095,,,1095	-3.9	0.0	1	dbSNP_79	56	5200,3400	632.1+/-398.6	1572,2056,672	no	coding-synonymous,intron,intron,coding-synonymous	CSF1	NM_000757.5,NM_172210.2,NM_172211.2,NM_172212.2	,,,	1661,2721,2121	AA,AC,CC		39.5349,19.133,46.4632	,,,	365/555,,,365/555	110466338	6043,6963	2203	4300	6503	SO:0001819	synonymous_variant	1435	exon6			TGGTACCGCCTTG	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.1095C>A	1.37:g.110466338C>A		Somatic	127	0	0	1427	WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Silent	SNP	ENST00000329608.6	37	CCDS816.1																																																																																			C|0.554;A|0.446	0.446	strong		0.632	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757	
FMN2	56776	hgsc.bcm.edu	37	1	240371502	240371502	+	Silent	SNP	C	C	T	rs200984130		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371502C>T	ENST00000319653.9	+	5	3620	c.3390C>T	c.(3388-3390)ccC>ccT	p.P1130P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1130	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)			CGGGCATACCCCCTCCTCCCC	0.721																																					p.P1130P		Atlas-SNP	.											.	FMN2	451	.	0			c.C3390T						PASS	.						7.0	8.0	8.0					1																	240371502		2106	4124	6230	SO:0001819	synonymous_variant	56776	exon5			CATACCCCCTCCT	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.3390C>T	1.37:g.240371502C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	82	6	0.0731707	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.999;T|0.001	0.001	weak		0.721	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
PSMD13	5719	hgsc.bcm.edu	37	11	244197	244197	+	Silent	SNP	T	T	C	rs1128322	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244197T>C	ENST00000532097.1	+	4	750	c.246T>C	c.(244-246)caT>caC	p.H82H	PSMD13_ENST00000431206.2_Silent_p.H84H|PSMD13_ENST00000352303.5_Silent_p.H82H	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	82					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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCATTCTTCATGTAGTTAGAC	0.388													T|||	4083	0.815296	0.8918	0.83	5008	,	,		17996	0.8036		0.7306	False		,,,				2504	0.8006				p.H84H		Atlas-SNP	.											.	PSMD13	53	.	0			c.T252C						PASS	.	T	,	3878,528	765.4+/-413.4	1714,450,39	56.0	59.0	58.0		246,252	-3.6	1.0	11	dbSNP_86	58	6381,2217	704.7+/-405.4	2371,1639,289	no	coding-synonymous,coding-synonymous	PSMD13	NM_002817.3,NM_175932.2	,	4085,2089,328	CC,CT,TT		25.7851,11.9837,21.1089	,	82/377,84/379	244197	10259,2745	2203	4299	6502	SO:0001819	synonymous_variant	5719	exon2			TCTTCATGTAGTT	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.246T>C	11.37:g.244197T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Silent	SNP	ENST00000532097.1	37	CCDS7692.1																																																																																			T|0.198;C|0.802	0.802	strong		0.388	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
OR51B5	282763	hgsc.bcm.edu	37	11	5364493	5364493	+	Missense_Mutation	SNP	T	T	C	rs57900141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364493T>C	ENST00000300773.2	-	1	316	c.262A>G	c.(262-264)Agg>Ggg	p.R88G	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	88			R -> G (in dbSNP:rs57900141).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAATCTCCCTGTGATCCAGC	0.562													T|||	528	0.105431	0.3306	0.0519	5008	,	,		18694	0.0		0.0497	False		,,,				2504	0.0051				p.R88G		Atlas-SNP	.											.	OR51B5	60	.	0			c.A262G						PASS	.	T	GLY/ARG	1300,3102	434.3+/-343.9	182,936,1083	42.0	42.0	42.0		262	4.8	0.9	11	dbSNP_129	42	458,8136	134.7+/-192.1	14,430,3853	yes	missense	OR51B5	NM_001005567.2	125	196,1366,4936	CC,CT,TT		5.3293,29.532,13.5272	probably-damaging	88/313	5364493	1758,11238	2201	4297	6498	SO:0001583	missense	282763	exon5			TCTCCCTGTGATC	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.262A>G	11.37:g.5364493T>C	ENSP00000300773:p.Arg88Gly	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	209	0.09569597069597069	150	0.3048780487804878	23	0.06353591160220995	0	0.0	36	0.047493403693931395	T	14.56	2.573102	0.45902	0.29532	0.053293	ENSG00000242180	ENST00000300773	T	0.37752	1.18	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.186059	0.26532	N	0.023845	T	0.00012	0.0000	L	0.60845	1.875	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.18777	-1.0326	9	0.87932	D	0	.	9.6048	0.39626	0.0:0.0:0.1761:0.8239	rs57900141;rs61738479	88	Q9H339	O51B5_HUMAN	G	88	ENSP00000300773:R88G	ENSP00000300773:R88G	R	-	1	2	OR51B5	5321069	0.000000	0.05858	0.874000	0.34290	0.601000	0.36947	-0.007000	0.12810	2.017000	0.59298	0.529000	0.55759	AGG	T|0.879;C|0.121	0.121	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
DENND4A	10260	hgsc.bcm.edu	37	15	65957717	65957717	+	Silent	SNP	C	C	G	rs61751113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:65957717C>G	ENST00000431932.2	-	29	5401	c.5193G>C	c.(5191-5193)ccG>ccC	p.P1731P	DENND4A_ENST00000443035.3_Silent_p.P1774P	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1731					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AGGGCTGTCCCGGATCCTGAT	0.373													C|||	21	0.00419329	0.0008	0.0101	5008	,	,		16939	0.0		0.0089	False		,,,				2504	0.0041				p.P1774P		Atlas-SNP	.											.	DENND4A	217	.	0			c.G5322C						PASS	.	C	,	2,3794		0,2,1896	153.0	152.0	152.0		5322,5193	-6.4	0.9	15	dbSNP_129	152	123,8115		1,121,3997	no	coding-synonymous,coding-synonymous	DENND4A	NM_001144823.1,NM_005848.3	,	1,123,5893	GG,GC,CC		1.4931,0.0527,1.0387	,	1774/1907,1731/1864	65957717	125,11909	1898	4119	6017	SO:0001819	synonymous_variant	10260	exon30			CTGTCCCGGATCC	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.5193G>C	15.37:g.65957717C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	123	69	0.560976	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			C|0.991;G|0.009	0.009	strong		0.373	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
ANAPC2	29882	hgsc.bcm.edu	37	9	140077639	140077639	+	Silent	SNP	G	G	A	rs11549105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140077639G>A	ENST00000323927.2	-	6	1228	c.1224C>T	c.(1222-1224)cgC>cgT	p.R408R		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	408					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		GGTCCAGCACGCGCAGCGCCT	0.627													G|||	511	0.102037	0.0151	0.1095	5008	,	,		19560	0.002		0.2425	False		,,,				2504	0.1728				p.R408R		Atlas-SNP	.											ANAPC2,caecum,carcinoma,-2,1	ANAPC2	57	1	0			c.C1224T						PASS	.	G		211,4195	129.8+/-166.5	6,199,1998	135.0	134.0	135.0		1224	-10.0	0.0	9	dbSNP_120	135	2235,6365	378.2+/-338.8	278,1679,2343	no	coding-synonymous	ANAPC2	NM_013366.3		284,1878,4341	AA,AG,GG		25.9884,4.7889,18.8067		408/823	140077639	2446,10560	2203	4300	6503	SO:0001819	synonymous_variant	29882	exon6			CAGCACGCGCAGC	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"""Anaphase promoting complex subunits"""	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.1224C>T	9.37:g.140077639G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	151	84	0.556291	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Silent	SNP	ENST00000323927.2	37	CCDS7033.1																																																																																			G|0.835;A|0.165	0.165	strong		0.627	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366	
RNF213	57674	hgsc.bcm.edu	37	17	78261805	78261805	+	Silent	SNP	A	A	G	rs7215243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78261805A>G	ENST00000582970.1	+	4	596	c.453A>G	c.(451-453)ccA>ccG	p.P151P	RNF213_ENST00000456466.1_Silent_p.P151P|RNF213_ENST00000319921.4_Silent_p.P151P|RNF213_ENST00000508628.2_Silent_p.P200P	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						scavenged	.	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	1	0.0175439		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	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	
MSANTD1	345222	hgsc.bcm.edu	37	4	3257593	3257593	+	Silent	SNP	C	C	T	rs362287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:3257593C>T	ENST00000438480.2	+	3	2485	c.738C>T	c.(736-738)cgC>cgT	p.R246R	MSANTD1_ENST00000507492.1_Silent_p.R233R|MSANTD1_ENST00000510580.1_Silent_p.R246R	NM_001042690.1	NP_001036155.1	Q6ZTZ1	MSD1_HUMAN	Myb/SANT-like DNA-binding domain containing 1	246										endometrium(1)|lung(2)	3						AGGTGCGCCGCGTGCTGGACC	0.667													C|||	1288	0.257188	0.0802	0.3069	5008	,	,		14882	0.3343		0.3787	False		,,,				2504	0.2566				p.R246R		Atlas-SNP	.											.	MSANTD1	14	.	0			c.C738T						PASS	.	C		442,3382		40,362,1510	7.0	8.0	8.0		738	-0.3	1.0	4	dbSNP_79	8	2174,5164		319,1536,1814	no	coding-synonymous	C4orf44	NM_001042690.1		359,1898,3324	TT,TC,CC		29.6266,11.5586,23.4367		246/279	3257593	2616,8546	1912	3669	5581	SO:0001819	synonymous_variant	345222	exon3			GCGCCGCGTGCTG		CCDS47003.1	4p16.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000188981	ENSG00000188981			33741	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 44"""	C4orf44			Standard	NM_001042690		Approved	LOC345222	uc003ggs.3	Q6ZTZ1	OTTHUMG00000159977	ENST00000438480.2:c.738C>T	4.37:g.3257593C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_001042690	C9J6V0	Silent	SNP	ENST00000438480.2	37	CCDS47003.1																																																																																			C|0.700;T|0.300	0.300	strong		0.667	MSANTD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370924.1	NM_001012982	
RMDN1	51115	hgsc.bcm.edu	37	8	87519315	87519315	+	Missense_Mutation	SNP	T	T	G	rs6980476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87519315T>G	ENST00000406452.3	-	2	315	c.156A>C	c.(154-156)aaA>aaC	p.K52N	CPNE3_ENST00000198765.4_Intron|RMDN1_ENST00000523911.1_Missense_Mutation_p.K8N|RMDN1_ENST00000519966.1_Missense_Mutation_p.K52N|RMDN1_ENST00000518772.1_5'UTR|RMDN1_ENST00000430676.2_Missense_Mutation_p.K52N	NM_016033.2	NP_057117.2	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1	52			K -> N (in dbSNP:rs6980476). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:14702039}.			microtubule (GO:0005874)|mitochondrion (GO:0005739)											AAAGGCCTCTTTTGAAAGTTC	0.393													T|||	768	0.153355	0.1725	0.134	5008	,	,		16358	0.0496		0.2515	False		,,,				2504	0.1472				p.K52N		Atlas-SNP	.											.	.	.	.	0			c.A156C						PASS	.	T	ASN/LYS	900,3506	345.7+/-308.6	74,752,1377	116.0	126.0	123.0		156	3.3	1.0	8	dbSNP_116	123	2324,6276	390.4+/-343.3	315,1694,2291	yes	missense	FAM82B	NM_016033.2	94	389,2446,3668	GG,GT,TT		27.0233,20.4267,24.7886	benign	52/315	87519315	3224,9782	2203	4300	6503	SO:0001583	missense	51115	exon2			GCCTCTTTTGAAA	AK000672	CCDS34918.1, CCDS69509.1, CCDS69510.1	8q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000176623	ENSG00000176623			24285	protein-coding gene	gene with protein product		611871	"""family with sequence similarity 82, member B"""	FAM82B		10810093	Standard	NM_016033		Approved	CGI-90, FLJ20665, RMD1	uc003ydu.3	Q96DB5	OTTHUMG00000163692	ENST00000406452.3:c.156A>C	8.37:g.87519315T>G	ENSP00000385927:p.Lys52Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	32	0.376471	NM_016033	A9UMZ8|B4DNF5|B4DZW6|B5MC61|C9JSC6|E7EVI2|Q9Y398	Missense_Mutation	SNP	ENST00000406452.3	37	CCDS34918.1	375	0.1717032967032967	81	0.16463414634146342	62	0.1712707182320442	33	0.057692307692307696	199	0.262532981530343	T	12.62	1.991542	0.35131	0.204267	0.270233	ENSG00000176623	ENST00000406452;ENST00000523911;ENST00000519966;ENST00000430676;ENST00000521045	T;T;T;T;T	0.55760	1.15;1.31;0.54;0.5;0.83	4.4	3.26	0.37387	.	0.540958	0.20542	N	0.090295	T	0.00012	0.0000	L	0.50919	1.6	0.09310	P	0.9999999999497646	B;B;B	0.17268	0.021;0.021;0.002	B;B;B	0.15052	0.007;0.012;0.003	T	0.15065	-1.0450	8	.	.	.	-11.069	5.8521	0.18699	0.0:0.1214:0.0:0.8786	rs6980476;rs52814394;rs58444409;rs6980476	52;52;52	B4DZW6;E7EVI2;Q96DB5	.;.;RMD1_HUMAN	N	52;8;52;52;8	ENSP00000385927:K52N;ENSP00000429899:K8N;ENSP00000428661:K52N;ENSP00000409661:K52N;ENSP00000428743:K8N	.	K	-	3	2	FAM82B	87588431	1.000000	0.71417	0.955000	0.39395	0.906000	0.53458	2.340000	0.43974	0.747000	0.32809	0.533000	0.62120	AAA	T|0.790;G|0.210	0.210	strong		0.393	RMDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374770.2	NM_016033	
OR3A2	4995	hgsc.bcm.edu	37	17	3181384	3181384	+	Silent	SNP	C	C	T	rs769434	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3181384C>T	ENST00000408891.2	-	1	884	c.846G>A	c.(844-846)ggG>ggA	p.G282G	RP11-64J4.2_ENST00000573491.1_RNA	NM_002551.3	NP_002542.3	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A, member 2	282					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						AAACTCCAACCCCTTTATCCT	0.468													C|||	891	0.177915	0.0144	0.3112	5008	,	,		21872	0.25		0.1561	False		,,,				2504	0.2526				p.G282G	GBM(166;478 2018 3875 5042 31983)|Esophageal Squamous(77;407 1232 1405 14297 15272)	Atlas-SNP	.											.	OR3A2	36	.	0			c.G846A						PASS	.	C		167,4131		2,163,1984	73.0	76.0	75.0		846	-2.8	1.0	17	dbSNP_86	75	1217,7339		99,1019,3160	no	coding-synonymous	OR3A2	NM_002551.3		101,1182,5144	TT,TC,CC		14.2239,3.8855,10.7671		282/322	3181384	1384,11470	2149	4278	6427	SO:0001819	synonymous_variant	4995	exon1			TCCAACCCCTTTA	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.846G>A	17.37:g.3181384C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	136	72	0.529412	NM_002551	Q6IFM3|Q9P1Q3	Silent	SNP	ENST00000408891.2	37	CCDS42233.1																																																																																			C|0.838;T|0.162	0.162	strong		0.468	OR3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438370.1		
DNAH9	1770	hgsc.bcm.edu	37	17	11511457	11511457	+	Silent	SNP	C	C	T	rs11078022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:11511457C>T	ENST00000262442.4	+	2	497	c.429C>T	c.(427-429)ccC>ccT	p.P143P	DNAH9_ENST00000454412.2_Silent_p.P143P|DNAH9_ENST00000579828.1_Silent_p.P143P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	143	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TTGTTCTACCCGTCCTGGCCA	0.483													C|||	2220	0.443291	0.1664	0.5648	5008	,	,		18842	0.5417		0.4235	False		,,,				2504	0.6503				p.P143P		Atlas-SNP	.											.	DNAH9	695	.	0			c.C429T						PASS	.	C		940,3466	357.1+/-313.8	103,734,1366	137.0	136.0	136.0		429	-11.4	0.0	17	dbSNP_120	136	3560,5040	516.7+/-378.9	761,2038,1501	no	coding-synonymous	DNAH9	NM_001372.3		864,2772,2867	TT,TC,CC		41.3953,21.3345,34.5994		143/4487	11511457	4500,8506	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon2			TCTACCCGTCCTG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.429C>T	17.37:g.11511457C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.626;N|0.000	.	strong		0.483	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
POLR2D	5433	hgsc.bcm.edu	37	2	128608184	128608184	+	Silent	SNP	C	C	T	rs11556864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:128608184C>T	ENST00000272645.4	-	3	386	c.330G>A	c.(328-330)gaG>gaA	p.E110E	POLR2D_ENST00000409955.1_Intron|POLR2D_ENST00000409698.1_Silent_p.E72E|POLR2D_ENST00000487079.1_Intron	NM_004805.3	NP_004796.1	O15514	RPB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide D	110					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus in response to heat stress (GO:0031990)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleotide-excision repair (GO:0006289)|positive regulation of translational initiation (GO:0045948)|positive regulation of viral transcription (GO:0050434)|recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)|nucleotide binding (GO:0000166)|translation initiation factor binding (GO:0031369)			large_intestine(1)|lung(4)|urinary_tract(1)	6	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)		GAGCCTTGGACTCCTCAGCAG	0.388													C|||	532	0.10623	0.0484	0.0994	5008	,	,		16256	0.1399		0.1014	False		,,,				2504	0.1595				p.E110E		Atlas-SNP	.											.	POLR2D	13	.	0			c.G330A						PASS	.	C		253,4153	146.9+/-181.5	8,237,1958	78.0	86.0	83.0		330	3.4	1.0	2	dbSNP_120	83	789,7811	185.6+/-233.3	45,699,3556	no	coding-synonymous	POLR2D	NM_004805.3		53,936,5514	TT,TC,CC		9.1744,5.7422,8.0117		110/143	128608184	1042,11964	2203	4300	6503	SO:0001819	synonymous_variant	5433	exon3			CTTGGACTCCTCA	U85510	CCDS2151.1	2q21	2013-01-21			ENSG00000144231	ENSG00000144231		"""RNA polymerase subunits"""	9191	protein-coding gene	gene with protein product	"""RNA polymerase II subunit hsRBP4"""	606017				9528765	Standard	NM_004805		Approved	RBP4	uc002tpj.3	O15514	OTTHUMG00000131531	ENST00000272645.4:c.330G>A	2.37:g.128608184C>T		Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	239	112	0.468619	NM_004805	Q52LT4	Silent	SNP	ENST00000272645.4	37	CCDS2151.1																																																																																			C|0.907;T|0.093	0.093	strong		0.388	POLR2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254388.3	NM_004805	
CTDSP1	58190	hgsc.bcm.edu	37	2	219267781	219267781	+	Silent	SNP	C	C	T	rs2227255	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:219267781C>T	ENST00000273062.2	+	5	738	c.402C>T	c.(400-402)caC>caT	p.H134H	CTDSP1_ENST00000488627.1_3'UTR|MIR26B_ENST00000362251.2_RNA|CTDSP1_ENST00000443891.1_Silent_p.H133H	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	134	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCGTCCTCACGTGGATGAGT	0.672													C|||	2331	0.465455	0.0318	0.5764	5008	,	,		13304	0.6915		0.6163	False		,,,				2504	0.5849				p.H134H		Atlas-SNP	.											CTDSP1,colon,carcinoma,0,1	CTDSP1	19	1	0			c.C402T						scavenged	.	C	,,,	597,3809	262.8+/-265.1	39,519,1645	69.0	64.0	66.0		399,,402,399	-2.7	0.6	2	dbSNP_96	66	5248,3352	642.6+/-399.8	1604,2040,656	no	coding-synonymous,utr-5,coding-synonymous,coding-synonymous	CTDSP1	NM_001206878.1,NM_001206879.1,NM_021198.2,NM_182642.2	,,,	1643,2559,2301	TT,TC,CC		38.9767,13.5497,44.9408	,,,	133/261,,134/262,133/261	219267781	5845,7161	2203	4300	6503	SO:0001819	synonymous_variant	58190	exon5			TCCTCACGTGGAT	AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	21614	protein-coding gene	gene with protein product	"""nuclear LIM interactor-interacting factor"", ""small CTD phosphatase 1"""	605323				11950066, 12721286	Standard	NM_021198		Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.402C>T	2.37:g.219267781C>T		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	217	106	0.488479	NM_021198	C9IYG0|Q7Z5Q3|Q7Z5Q4	Silent	SNP	ENST00000273062.2	37	CCDS2416.1	1121	0.5132783882783882	26	0.052845528455284556	212	0.585635359116022	401	0.701048951048951	482	0.6358839050131926	C	6.359	0.434375	0.12045	0.135497	0.610233	ENSG00000144579	ENST00000452977;ENST00000428361	.	.	.	4.91	-2.71	0.05986	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999968	.	.	.	.	.	.	T	0.34403	-0.9830	3	.	.	.	-16.9965	12.043	0.53464	0.0:0.4326:0.0:0.5674	rs2227255;rs58989933;rs2227255	.	.	.	M	127;135	.	.	T	+	2	0	CTDSP1	218976025	0.000000	0.05858	0.627000	0.29227	0.863000	0.49368	-2.503000	0.00965	-0.677000	0.05231	-1.174000	0.01732	ACG	C|0.533;T|0.467	0.467	strong		0.672	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198	
THBS2	7058	hgsc.bcm.edu	37	6	169637847	169637847	+	Silent	SNP	G	G	A	rs35631991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:169637847G>A	ENST00000366787.3	-	9	1422	c.1173C>T	c.(1171-1173)acC>acT	p.T391T	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	391	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGGAGCACTGGGTCCACTCTG	0.652													g|||	105	0.0209665	0.0015	0.0202	5008	,	,		17613	0.0		0.0328	False		,,,				2504	0.0573				p.T391T	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C1173T						PASS	.			37,4369	40.8+/-73.8	0,37,2166	86.0	66.0	73.0		1173	-7.1	0.1	6	dbSNP_126	73	332,8268	114.4+/-174.4	7,318,3975	no	coding-synonymous	THBS2	NM_003247.2		7,355,6141	AA,AG,GG		3.8605,0.8398,2.8372		391/1173	169637847	369,12637	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon9			GCACTGGGTCCAC		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.1173C>T	6.37:g.169637847G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.975;A|0.025	0.025	strong		0.652	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
SYK	6850	hgsc.bcm.edu	37	9	93606309	93606309	+	Silent	SNP	G	G	A	rs35758162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:93606309G>A	ENST00000375754.4	+	2	277	c.129G>A	c.(127-129)caG>caA	p.Q43Q	SYK_ENST00000375747.1_Silent_p.Q43Q|SYK_ENST00000476708.1_3'UTR|SYK_ENST00000375751.4_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	84	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	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		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305820	39305820	+	Missense_Mutation	SNP	C	C	T	rs238830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39305820C>T	ENST00000343246.4	-	1	234	c.200G>A	c.(199-201)cGc>cAc	p.R67H		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	67	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		R -> H (in dbSNP:rs238830). {ECO:0000269|PubMed:15955084}.		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)			gcaataggggcggcagcagct	0.672													C|||	167	0.0333466	0.0076	0.0216	5008	,	,		16776	0.0516		0.0666	False		,,,				2504	0.0235				p.R67H		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.G200A						PASS	.	C	HIS/ARG	49,4195		0,49,2073	15.0	19.0	18.0		200	2.0	0.9	17	dbSNP_79	18	611,7763		13,585,3589	no	missense	KRTAP4-5	NM_033188.3	29	13,634,5662	TT,TC,CC		7.2964,1.1546,5.2306	benign	67/182	39305820	660,11958	2122	4187	6309	SO:0001583	missense	85289	exon1			TAGGGGCGGCAGC	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.200G>A	17.37:g.39305820C>T	ENSP00000340546:p.Arg67His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	81	25	0.308642	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	99	0.04532967032967033	7	0.014227642276422764	9	0.024861878453038673	28	0.04895104895104895	55	0.07255936675461741	.	8.099	0.776312	0.16051	0.011546	0.072964	ENSG00000198271	ENST00000343246	T	0.00575	6.46	4.15	2.05	0.26809	.	0.674572	0.10739	N	0.639706	T	0.00073	0.0002	M	0.72576	2.205	0.20074	N	0.999938	B	0.29232	0.238	B	0.25614	0.062	T	0.48151	-0.9060	10	0.72032	D	0.01	.	4.054	0.09808	0.0:0.5732:0.1936:0.2332	rs238830;rs542064	67	Q9BYR2	KRA45_HUMAN	H	67	ENSP00000340546:R67H	ENSP00000340546:R67H	R	-	2	0	KRTAP4-5	36559346	0.000000	0.05858	0.947000	0.38551	0.033000	0.12548	0.733000	0.26087	0.438000	0.26450	0.609000	0.83330	CGC	C|0.952;T|0.048	0.048	strong		0.672	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
PRDM16	63976	hgsc.bcm.edu	37	1	3328659	3328659	+	Missense_Mutation	SNP	C	C	T	rs2493292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3328659C>T	ENST00000270722.5	+	9	1947	c.1898C>T	c.(1897-1899)cCt>cTt	p.P633L	PRDM16_ENST00000511072.1_Missense_Mutation_p.P634L|PRDM16_ENST00000442529.2_Missense_Mutation_p.P633L|PRDM16_ENST00000378398.3_Missense_Mutation_p.P634L|PRDM16_ENST00000514189.1_Missense_Mutation_p.P634L|PRDM16_ENST00000441472.2_Missense_Mutation_p.P633L|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378391.2_Missense_Mutation_p.P633L			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	633			P -> L (in dbSNP:rs2493292).		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)		GACAGCGACCCTGACAAGGAC	0.697			T	EVI1	"""MDS, AML"""								C|||	531	0.10603	0.1634	0.121	5008	,	,		13011	0.006		0.166	False		,,,				2504	0.0593				p.P633L		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C1898T						PASS	.	C	LEU/PRO,LEU/PRO	659,3627		61,537,1545	55.0	66.0	62.0		1898,1898	4.2	0.9	1	dbSNP_100	62	1283,7181		100,1083,3049	yes	missense,missense	PRDM16	NM_199454.2,NM_022114.3	98,98	161,1620,4594	TT,TC,CC		15.1583,15.3756,15.2314	benign,benign	633/1258,633/1277	3328659	1942,10808	2143	4232	6375	SO:0001583	missense	63976	exon9			GCGACCCTGACAA	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.1898C>T	1.37:g.3328659C>T	ENSP00000270722:p.Pro633Leu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	242	0.1108058608058608	75	0.1524390243902439	52	0.143646408839779	4	0.006993006993006993	111	0.14643799472295516	C	15.56	2.871058	0.51695	0.153756	0.151583	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.04917	3.54;3.57;3.58;3.58;3.57;3.57;3.58;3.53;3.53	5.09	4.18	0.49190	.	0.125337	0.29046	N	0.013308	T	0.00039	0.0001	N	0.08118	0	0.28723	P	0.9029207	B;B;B;B	0.31383	0.039;0.066;0.321;0.039	B;B;B;B	0.26969	0.016;0.036;0.075;0.016	T	0.48163	-0.9059	9	0.52906	T	0.07	.	14.9602	0.71151	0.0:0.1609:0.8391:0.0	rs2493292;rs57392481;rs2493292	633;633;633;633	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	L	634;634;633;633;633;634;633;449;449;442	ENSP00000426975:P634L;ENSP00000367651:P634L;ENSP00000407968:P633L;ENSP00000405253:P633L;ENSP00000367643:P633L;ENSP00000421400:P634L;ENSP00000270722:P633L;ENSP00000422504:P449L;ENSP00000425796:P442L	ENSP00000270722:P633L	P	+	2	0	PRDM16	3318519	1.000000	0.71417	0.921000	0.36526	0.851000	0.48451	4.782000	0.62396	1.153000	0.42468	0.603000	0.83216	CCT	C|0.868;T|0.132	0.132	strong		0.697	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205308335	205308335	+	Silent	SNP	G	G	A	rs1105385	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205308335G>A	ENST00000367156.3	-	7	1560	c.744C>T	c.(742-744)ttC>ttT	p.F248F	KLHDC8A_ENST00000460687.1_Silent_p.F114F|KLHDC8A_ENST00000539253.1_Silent_p.F248F|KLHDC8A_ENST00000367155.3_Silent_p.F248F|KLHDC8A_ENST00000537168.1_Silent_p.F135F	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	248										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GTTCCATGTCGAACACGTCCA	0.612													G|||	918	0.183307	0.2247	0.1354	5008	,	,		18148	0.0317		0.2942	False		,,,				2504	0.2035				p.F248F		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.C744T						PASS	.	G		987,3419	369.1+/-318.9	109,769,1325	47.0	41.0	43.0		744	-6.8	0.8	1	dbSNP_86	43	2613,5987	420.9+/-353.5	364,1885,2051	no	coding-synonymous	KLHDC8A	NM_018203.1		473,2654,3376	AA,AG,GG		30.3837,22.4013,27.6795		248/351	205308335	3600,9406	2203	4300	6503	SO:0001819	synonymous_variant	55220	exon4			CATGTCGAACACG		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.744C>T	1.37:g.205308335G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_018203	B3KU70|Q9NVG5	Silent	SNP	ENST00000367156.3	37	CCDS30985.1																																																																																			A|0.232;C|0.004	0.232	strong		0.612	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
COL13A1	1305	hgsc.bcm.edu	37	10	71640267	71640267	+	Silent	SNP	C	C	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:71640267C>A	ENST00000398978.3	+	6	936	c.444C>A	c.(442-444)ccC>ccA	p.P148P	COL13A1_ENST00000398964.3_Intron|COL13A1_ENST00000520267.1_Intron|COL13A1_ENST00000357811.3_Silent_p.P148P|COL13A1_ENST00000354547.3_Silent_p.P148P|COL13A1_ENST00000522165.1_Silent_p.P148P|COL13A1_ENST00000520133.1_Intron|COL13A1_ENST00000356340.3_Silent_p.P148P|COL13A1_ENST00000517713.1_Silent_p.P148P|COL13A1_ENST00000398974.3_Silent_p.P136P|COL13A1_ENST00000398969.3_Intron|COL13A1_ENST00000398968.3_Silent_p.P148P|COL13A1_ENST00000398966.3_Silent_p.P148P|COL13A1_ENST00000398973.3_Silent_p.P148P|COL13A1_ENST00000398971.3_Silent_p.P148P|COL13A1_ENST00000398972.3_Silent_p.P148P	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1									p.P148P(1)		endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						AGGGGTCCCCCGGAGACGCTG	0.622																																					p.P148P		Atlas-SNP	.											COL13A1_ENST00000398978,NS,carcinoma,0,1	COL13A1	133	1	1	Substitution - coding silent(1)	endometrium(1)	c.C444A						PASS	.						33.0	34.0	34.0					10																	71640267		1821	4077	5898	SO:0001819	synonymous_variant	1305	exon6			GTCCCCCGGAGAC	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"""Collagens"""	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.444C>A	10.37:g.71640267C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	137	63	0.459854	NM_080802		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			.	.	none		0.622	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203	
VPS51	738	hgsc.bcm.edu	37	11	64877197	64877197	+	Silent	SNP	C	C	T	rs61736623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:64877197C>T	ENST00000279281.3	+	7	1772	c.1680C>T	c.(1678-1680)ccC>ccT	p.P560P	TM7SF2_ENST00000345348.5_5'Flank|TM7SF2_ENST00000540748.1_5'Flank|TM7SF2_ENST00000279263.7_5'Flank|AP003068.9_ENST00000528887.1_RNA|VPS51_ENST00000527646.1_3'UTR	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	560					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											CAGTGACGCCCGTGAGCACGC	0.642													c|||	140	0.0279553	0.003	0.0389	5008	,	,		19211	0.0655		0.0348	False		,,,				2504	0.0082				p.P560P		Atlas-SNP	.											.	.	.	.	0			c.C1680T						PASS	.	T		31,4361		0,31,2165	26.0	22.0	23.0		1680	-9.6	0.0	11	dbSNP_129	23	275,8299		3,269,4015	no	coding-synonymous	C11orf2	NM_013265.2		3,300,6180	TT,TC,CC		3.2074,0.7058,2.36		560/783	64877197	306,12660	2196	4287	6483	SO:0001819	synonymous_variant	738	exon7			GACGCCCGTGAGC	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"""fat-free homolog (zebrafish)"""	615738	"""chromosome 11 open reading frame 3"", ""chromosome 11 open reading frame 2"""	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.1680C>T	11.37:g.64877197C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_013265	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Silent	SNP	ENST00000279281.3	37	CCDS8093.1	64	0.029304029304029304	4	0.008130081300813009	13	0.03591160220994475	19	0.033216783216783216	28	0.036939313984168866	c	0.838	-0.743015	0.03088	0.007058	0.032074	ENSG00000149823	ENST00000526856	.	.	.	4.8	-9.61	0.00550	.	0.055231	0.85682	D	0.000000	T	0.16428	0.0395	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59364	-0.7468	6	0.24483	T	0.36	-15.4675	10.0775	0.42368	0.0824:0.124:0.0816:0.712	rs61736623	.	.	.	L	58	.	ENSP00000435629:P58L	P	+	2	0	C11orf2	64633773	0.000000	0.05858	0.014000	0.15608	0.127000	0.20565	-4.504000	0.00224	-2.406000	0.00574	-0.974000	0.02594	CCG	C|0.974;T|0.026	0.026	strong		0.642	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265	
CBX8	57332	hgsc.bcm.edu	37	17	77768654	77768654	+	Missense_Mutation	SNP	C	C	A	rs4889891|rs113547221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	53	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	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	
USP5	8078	hgsc.bcm.edu	37	12	6965194	6965194	+	Silent	SNP	A	A	G	rs2226955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6965194A>G	ENST00000229268.8	+	4	370	c.318A>G	c.(316-318)ggA>ggG	p.G106G	USP5_ENST00000389231.5_Silent_p.G106G	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	106					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						TTGAAGGCGGATTTGACCTTA	0.522													G|||	2521	0.503395	0.8517	0.3847	5008	,	,		-128	0.505		0.3181	False		,,,				2504	0.3057				p.G106G		Atlas-SNP	.											.	USP5	124	.	0			c.A318G						PASS	.	G	,	3297,1109	397.6+/-330.5	1231,835,137	183.0	181.0	182.0		318,318	-4.9	0.8	12	dbSNP_96	182	2636,5964	686.9+/-404.2	432,1772,2096	no	coding-synonymous,coding-synonymous	USP5	NM_001098536.1,NM_003481.2	,	1663,2607,2233	GG,GA,AA		30.6512,25.1702,45.6174	,	106/859,106/836	6965194	5933,7073	2203	4300	6503	SO:0001819	synonymous_variant	8078	exon4			AGGCGGATTTGAC	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"""Ubiquitin-specific peptidases"""	12628	protein-coding gene	gene with protein product		601447	"""ubiquitin specific protease 5 (isopeptidase T)"""			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.318A>G	12.37:g.6965194A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	149	67	0.449664	NM_003481	D3DUS7|D3DUS8|Q96J22	Silent	SNP	ENST00000229268.8	37	CCDS41743.1																																																																																			A|0.527;G|0.473	0.473	strong		0.522	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1		
SGPL1	8879	hgsc.bcm.edu	37	10	72604263	72604263	+	Missense_Mutation	SNP	G	G	T	rs12770335	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:72604263G>T	ENST00000373202.3	+	3	261	c.61G>T	c.(61-63)Gta>Tta	p.V21L		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	21			V -> L (in dbSNP:rs12770335).		androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)			large_intestine(4)	4						GATTTTGGAAGTATACTCCAC	0.388													G|||	245	0.0489217	0.025	0.072	5008	,	,		20812	0.001		0.1372	False		,,,				2504	0.0235				p.V21L	Colon(151;1054 2458 6676 40971)	Atlas-SNP	.											.	SGPL1	37	.	0			c.G61T						PASS	.	G	LEU/VAL	171,4235	112.9+/-151.0	5,161,2037	94.0	88.0	90.0		61	5.0	1.0	10	dbSNP_121	90	1186,7414	241.8+/-272.0	89,1008,3203	yes	missense	SGPL1	NM_003901.3	32	94,1169,5240	TT,TG,GG		13.7907,3.8811,10.4336	benign	21/569	72604263	1357,11649	2203	4300	6503	SO:0001583	missense	8879	exon3			TTGGAAGTATACT	AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224			10817	protein-coding gene	gene with protein product		603729				9464245, 17090686	Standard	NM_003901		Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.61G>T	10.37:g.72604263G>T	ENSP00000362298:p.Val21Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_003901	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Missense_Mutation	SNP	ENST00000373202.3	37	CCDS31216.1	142	0.06501831501831502	12	0.024390243902439025	30	0.08287292817679558	1	0.0017482517482517483	99	0.13060686015831136	G	12.11	1.840437	0.32513	0.038811	0.137907	ENSG00000166224	ENST00000373202;ENST00000299297	T;T	0.41400	1.0;1.07	5.87	4.97	0.65823	.	0.674521	0.15146	N	0.277964	T	0.00210	0.0006	N	0.17474	0.49	0.44477	P	0.002585999999999977	B	0.02656	0.0	B	0.01281	0.0	T	0.12553	-1.0543	9	0.18276	T	0.48	-2.0832	10.1108	0.42561	0.0:0.1481:0.6982:0.1536	rs12770335;rs52829513;rs57780087;rs12770335	21	O95470	SGPL1_HUMAN	L	21;4	ENSP00000362298:V21L;ENSP00000299297:V4L	ENSP00000299297:V4L	V	+	1	0	SGPL1	72274269	0.961000	0.32948	0.996000	0.52242	0.997000	0.91878	2.027000	0.41078	1.460000	0.47911	0.650000	0.86243	GTA	G|0.913;T|0.087	0.087	strong		0.388	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901	
MRPL38	64978	hgsc.bcm.edu	37	17	73900688	73900688	+	Silent	SNP	T	T	C	rs3744015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73900688T>C	ENST00000309352.3	-	2	717	c.180A>G	c.(178-180)cgA>cgG	p.R60R	MRPL38_ENST00000409963.3_5'UTR|MRPL38_ENST00000585475.1_5'UTR	NM_032478.3	NP_115867.2	Q96DV4	RM38_HUMAN	mitochondrial ribosomal protein L38	60						mitochondrion (GO:0005739)|ribosome (GO:0005840)				ovary(1)|pancreas(1)|prostate(2)|skin(1)	5			all cancers(21;0.000154)|Epithelial(20;0.000156)|BRCA - Breast invasive adenocarcinoma(9;0.00936)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCTGCTCTGCTCGGCGCCGGT	0.682													C|||	2236	0.446486	0.8411	0.3156	5008	,	,		8697	0.2123		0.3509	False		,,,				2504	0.3456				p.R60R		Atlas-SNP	.											.	MRPL38	26	.	0			c.A180G						PASS	.	C		3264,1106		1242,780,163	10.0	12.0	11.0		180	-2.7	0.6	17	dbSNP_107	11	2855,5713		524,1807,1953	yes	coding-synonymous	MRPL38	NM_032478.3		1766,2587,2116	CC,CT,TT		33.3217,25.3089,47.2948		60/381	73900688	6119,6819	2185	4284	6469	SO:0001819	synonymous_variant	64978	exon2			CTCTGCTCGGCGC	AB051345	CCDS11733.2	17q23-q25	2012-09-13			ENSG00000204316	ENSG00000204316		"""Mitochondrial ribosomal proteins / large subunits"""	14033	protein-coding gene	gene with protein product		611844				11543634	Standard	NM_032478		Approved	RPML3, MRP-L3, HSPC262, MGC4810	uc010wso.1	Q96DV4	OTTHUMG00000152977	ENST00000309352.3:c.180A>G	17.37:g.73900688T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_032478	B3KN96|Q96Q66|Q9P0B9	Silent	SNP	ENST00000309352.3	37	CCDS11733.2																																																																																			T|0.523;C|0.477	0.477	strong		0.682	MRPL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328829.1	NM_032478	
PRPF31	26121	hgsc.bcm.edu	37	19	54627915	54627915	+	Silent	SNP	C	C	T	rs11556769	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54627915C>T	ENST00000321030.4	+	8	1084	c.735C>T	c.(733-735)ccC>ccT	p.P245P	AC012314.8_ENST00000452097.1_RNA|PRPF31_ENST00000498612.1_3'UTR|PRPF31_ENST00000391755.1_Silent_p.P245P|PRPF31_ENST00000419967.1_Silent_p.P245P	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	245	Nop. {ECO:0000255|PROSITE- ProRule:PRU00690}.				mRNA splicing, via spliceosome (GO:0000398)|spliceosomal tri-snRNP complex assembly (GO:0000244)	Cajal body (GO:0015030)|MLL1 complex (GO:0071339)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|U2-type spliceosomal complex (GO:0005684)|U4 snRNP (GO:0005687)|U4/U6 x U5 tri-snRNP complex (GO:0046540)|U4atac snRNP (GO:0005690)	poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|snRNP binding (GO:0070990)			breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)|urinary_tract(3)	12	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCAAGATGCCCGCCTGCAACA	0.647													C|||	326	0.0650958	0.0454	0.0778	5008	,	,		14602	0.004		0.1064	False		,,,				2504	0.1033				p.P245P		Atlas-SNP	.											.	PRPF31	48	.	0			c.C735T						PASS	.	C		301,4105	164.0+/-195.7	11,279,1913	64.0	61.0	62.0		735	-7.1	1.0	19	dbSNP_120	62	803,7797	186.9+/-234.3	46,711,3543	no	coding-synonymous	PRPF31	NM_015629.3		57,990,5456	TT,TC,CC		9.3372,6.8316,8.4884		245/500	54627915	1104,11902	2203	4300	6503	SO:0001819	synonymous_variant	26121	exon8			GATGCCCGCCTGC	AL050369	CCDS12879.1	19q13.4	2013-07-16	2013-06-10		ENSG00000105618	ENSG00000105618			15446	protein-coding gene	gene with protein product		606419	"""PRP31 pre-mRNA processing factor 31 homolog (yeast)"", ""PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae)"""	RP11		11545739	Standard	NM_015629		Approved	NY-BR-99, PRP31, hPrp31, SNRNP61	uc002qdh.2	Q8WWY3	OTTHUMG00000066040	ENST00000321030.4:c.735C>T	19.37:g.54627915C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Silent	SNP	ENST00000321030.4	37	CCDS12879.1																																																																																			C|0.925;T|0.075	0.075	strong		0.647	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2		
CUBN	8029	hgsc.bcm.edu	37	10	17088006	17088006	+	Silent	SNP	T	T	C	rs1801228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:17088006T>C	ENST00000377833.4	-	24	3482	c.3417A>G	c.(3415-3417)ctA>ctG	p.L1139L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1139	CUB 6. {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)	ATTTTAACCATAGTTTGTTAC	0.393													T|||	345	0.0688898	0.0076	0.0288	5008	,	,		15865	0.0179		0.0527	False		,,,				2504	0.2495				p.L1139L		Atlas-SNP	.											.	CUBN	515	.	0			c.A3417G						PASS	.	T		65,4341	59.3+/-96.0	0,65,2138	135.0	127.0	130.0		3417	-3.0	0.9	10	dbSNP_89	130	337,8263	115.3+/-175.2	10,317,3973	no	coding-synonymous	CUBN	NM_001081.3		10,382,6111	CC,CT,TT		3.9186,1.4753,3.0909		1139/3624	17088006	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon24			TAACCATAGTTTG	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.3417A>G	10.37:g.17088006T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			T|0.968;C|0.032	0.032	strong		0.393	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
FLG	2312	hgsc.bcm.edu	37	1	152286032	152286032	+	Missense_Mutation	SNP	C	C	T	rs11588170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152286032C>T	ENST00000368799.1	-	3	1365	c.1330G>A	c.(1330-1332)Ggg>Agg	p.G444R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	444	Ser-rich.		G -> R (in dbSNP:rs11588170).		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)			TGTCTCAGCCCAGCCTTTCCG	0.582									Ichthyosis				-|||	1438	0.287141	0.0113	0.3905	5008	,	,		19918	0.5823		0.1421	False		,,,				2504	0.4315				p.G444R		Atlas-SNP	.											.	FLG	900	.	0			c.G1330A						PASS	.	C	ARG/GLY	161,4245		2,157,2044	201.0	196.0	198.0		1330	-0.6	0.0	1	dbSNP_120	198	1241,7359		97,1047,3156	yes	missense	FLG	NM_002016.1	125	99,1204,5200	TT,TC,CC		14.4302,3.6541,10.7796	probably-damaging	444/4062	152286032	1402,11604	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCAGCCCAGCCTT	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.1330G>A	1.37:g.152286032C>T	ENSP00000357789:p.Gly444Arg	Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	337	179	0.531157	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	571	0.26144688644688646	9	0.018292682926829267	118	0.3259668508287293	333	0.5821678321678322	111	0.14643799472295516	-	9.564	1.119273	0.20877	0.036541	0.144302	ENSG00000143631	ENST00000368799	T	0.00768	5.72	2.5	-0.615	0.11587	.	.	.	.	.	T	0.00552	0.0018	L	0.53671	1.685	0.80722	P	0.0	P	0.51147	0.942	P	0.57244	0.816	T	0.48175	-0.9058	8	0.14252	T	0.57	.	3.0061	0.06028	0.0:0.467:0.2361:0.2968	rs11588170	444	P20930	FILA_HUMAN	R	444	ENSP00000357789:G444R	ENSP00000357789:G444R	G	-	1	0	FLG	150552656	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.639000	0.05446	-0.107000	0.12088	-0.458000	0.05436	GGG	C|0.839;T|0.161	0.161	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CSNK1D	1453	hgsc.bcm.edu	37	17	80209282	80209282	+	Silent	SNP	G	G	A	rs56181605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80209282G>A	ENST00000314028.6	-	6	1207	c.858C>T	c.(856-858)taC>taT	p.Y286Y	CSNK1D_ENST00000398519.5_Silent_p.Y286Y|CSNK1D_ENST00000392334.2_Silent_p.Y286Y|CSNK1D_ENST00000578904.1_5'UTR	NM_001893.4	NP_001884.2	P48730	KC1D_HUMAN	casein kinase 1, delta	286	Centrosomal localization signal (CLS).				circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle (GO:0005819)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			breast(2)|large_intestine(2)|lung(7)	11	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			AGTCGAACACGTAGTCATAGG	0.557													G|||	18	0.00359425	0.0008	0.0029	5008	,	,		19676	0.0		0.007	False		,,,				2504	0.0082				p.Y286Y		Atlas-SNP	.											.	CSNK1D	118	.	0			c.C858T						PASS	.	G	,	15,4391	21.2+/-45.6	0,15,2188	92.0	79.0	83.0		858,858	-9.2	0.8	17	dbSNP_129	83	128,8472	66.3+/-128.7	0,128,4172	no	coding-synonymous,coding-synonymous	CSNK1D	NM_001893.4,NM_139062.2	,	0,143,6360	AA,AG,GG		1.4884,0.3404,1.0995	,	286/416,286/410	80209282	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	1453	exon6			GAACACGTAGTCA		CCDS11805.1, CCDS11806.1	17q25	2013-01-17				ENSG00000141551			2452	protein-coding gene	gene with protein product		600864				7797465	Standard	NM_001893		Approved	HCKID, CKID, CKIdelta	uc002kej.3	P48730		ENST00000314028.6:c.858C>T	17.37:g.80209282G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	72	40	0.555556	NM_001893	A2I2P2|Q96KZ6|Q9BTN5	Silent	SNP	ENST00000314028.6	37	CCDS11805.1																																																																																			G|0.990;A|0.010	0.010	strong		0.557	CSNK1D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442632.1	NM_139062	
TTC22	55001	hgsc.bcm.edu	37	1	55248074	55248074	+	Missense_Mutation	SNP	A	A	G	rs12144325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:55248074A>G	ENST00000371276.4	-	6	1200	c.1097T>C	c.(1096-1098)cTg>cCg	p.L366P		NM_001114108.1	NP_001107580.1	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22	366										kidney(1)|large_intestine(1)|lung(7)|skin(1)	10						GGCACAGGCCAGGTGGTTCCT	0.602													A|||	312	0.0623003	0.0151	0.0807	5008	,	,		20739	0.0198		0.1312	False		,,,				2504	0.0859				p.L366P		Atlas-SNP	.											.	TTC22	40	.	0			c.T1097C						PASS	.	A	PRO/LEU	56,1328		0,56,636	71.0	68.0	69.0		1097	5.1	1.0	1	dbSNP_120	69	517,2665		43,431,1117	yes	missense	TTC22	NM_001114108.1	98	43,487,1753	GG,GA,AA		16.2476,4.0462,12.5493	probably-damaging	366/570	55248074	573,3993	692	1591	2283	SO:0001583	missense	55001	exon6			CAGGCCAGGTGGT	AK000626	CCDS598.1, CCDS44152.1	1p32.3	2013-01-11			ENSG00000006555	ENSG00000006555		"""Tetratricopeptide (TTC) repeat domain containing"""	26067	protein-coding gene	gene with protein product							Standard	NM_017904		Approved	FLJ20619	uc009vzt.1	Q5TAA0	OTTHUMG00000009916	ENST00000371276.4:c.1097T>C	1.37:g.55248074A>G	ENSP00000360323:p.Leu366Pro	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_001114108	Q9NWT4	Missense_Mutation	SNP	ENST00000371276.4	37	CCDS44152.1	164	0.07509157509157509	9	0.018292682926829267	31	0.0856353591160221	12	0.02097902097902098	112	0.14775725593667546	A	22.3	4.274413	0.80580	0.040462	0.162476	ENSG00000006555	ENST00000371276	T	0.75050	-0.9	5.14	5.14	0.70334	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000005	T	0.01061	0.0035	L	0.36672	1.1	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	T	0.46176	-0.9210	9	0.87932	D	0	-26.6867	14.0909	0.64990	1.0:0.0:0.0:0.0	rs12144325	366	Q5TAA0	TTC22_HUMAN	P	366	ENSP00000360323:L366P	ENSP00000360323:L366P	L	-	2	0	TTC22	55020662	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.393000	0.79851	2.159000	0.67721	0.455000	0.32223	CTG	A|0.925;G|0.075	0.075	strong		0.602	TTC22-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027438.1	NM_017904	
SPTBN4	57731	hgsc.bcm.edu	37	19	41009982	41009982	+	Silent	SNP	C	C	T	rs71358911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41009982C>T	ENST00000352632.3	+	12	1694	c.1608C>T	c.(1606-1608)gcC>gcT	p.A536A	SPTBN4_ENST00000595535.1_Silent_p.A536A|SPTBN4_ENST00000598249.1_Silent_p.A536A|SPTBN4_ENST00000344104.3_Silent_p.A536A|SPTBN4_ENST00000338932.3_Silent_p.A536A			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	536					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGAACCTTGCCCTGCAGAAGG	0.677													c|||	122	0.024361	0.0061	0.0259	5008	,	,		11341	0.0		0.0865	False		,,,				2504	0.0092				p.A536A		Atlas-SNP	.											.	SPTBN4	213	.	0			c.C1608T						PASS	.			80,4326	68.1+/-105.8	0,80,2123	44.0	52.0	50.0		1608	1.0	1.0	19	dbSNP_130	50	933,7667	203.5+/-246.5	50,833,3417	no	coding-synonymous	SPTBN4	NM_020971.2		50,913,5540	TT,TC,CC		10.8488,1.8157,7.7887		536/2565	41009982	1013,11993	2203	4300	6503	SO:0001819	synonymous_variant	57731	exon12			CCTTGCCCTGCAG	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.1608C>T	19.37:g.41009982C>T		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	183	102	0.557377	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			C|0.938;T|0.062	0.062	strong		0.677	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
CACNA1H	8912	hgsc.bcm.edu	37	16	1268596	1268596	+	Silent	SNP	C	C	T	rs372529098		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1268596C>T	ENST00000348261.5	+	33	6080	c.5832C>T	c.(5830-5832)caC>caT	p.H1944H	CACNA1H_ENST00000358590.4_Silent_p.H1938H|CACNA1H_ENST00000565831.1_Silent_p.H1938H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1944					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)	CGGCGCCCCACCCCCGCCCGC	0.657																																					p.H1944H		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5832T						PASS	.	C	,	0,3962		0,0,1981	13.0	17.0	16.0		5814,5832	-2.1	0.0	16		16	2,8230		0,2,4114	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	0,2,6095	TT,TC,CC		0.0243,0.0,0.0164	,	1938/2348,1944/2354	1268596	2,12192	1981	4116	6097	SO:0001819	synonymous_variant	8912	exon33			GCCCCACCCCCGC	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.5832C>T	16.37:g.1268596C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			.	.	weak		0.657	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
AMACR	23600	hgsc.bcm.edu	37	5	33998768	33998768	+	Missense_Mutation	SNP	C	C	A	rs34677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:33998768C>A	ENST00000335606.6	-	4	805	c.717G>T	c.(715-717)caG>caT	p.Q239H	RP11-1084J3.4_ENST00000382079.3_3'UTR|AMACR_ENST00000441713.2_Missense_Mutation_p.V186F|AMACR_ENST00000502637.1_Missense_Mutation_p.Q224H|AMACR_ENST00000512079.1_Missense_Mutation_p.Q239H|AMACR_ENST00000382072.2_Missense_Mutation_p.V186F|AMACR_ENST00000514195.1_5'UTR|AMACR_ENST00000426255.2_Missense_Mutation_p.Q239H|AMACR_ENST00000382068.3_Missense_Mutation_p.V186F|AMACR_ENST00000382085.3_Missense_Mutation_p.Q239H	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	239			Q -> H (in dbSNP:rs34677).		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)	p.Q239H(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						GCTCGTAGAACTGGGGTTCTA	0.478													C|||	573	0.114417	0.0582	0.0749	5008	,	,		16572	0.1706		0.1382	False		,,,				2504	0.136				p.Q239H		Atlas-SNP	.											AMACR,NS,carcinoma,0,1	AMACR	38	1	1	Substitution - Missense(1)	stomach(1)	c.G717T						PASS	.	C	HIS/GLN,HIS/GLN,PHE/VAL	310,4096	166.5+/-197.7	8,294,1901	119.0	109.0	113.0		717,717,556	3.3	1.0	5	dbSNP_76	113	1250,7350	250.8+/-277.5	84,1082,3134	yes	missense,missense,missense	AMACR	NM_001167595.1,NM_014324.5,NM_203382.2	24,24,50	92,1376,5035	AA,AC,CC		14.5349,7.0359,11.9945	probably-damaging,probably-damaging,probably-damaging	239/395,239/383,186/199	33998768	1560,11446	2203	4300	6503	SO:0001583	missense	23600	exon4			GTAGAACTGGGGT	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.717G>T	5.37:g.33998768C>A	ENSP00000334424:p.Gln239His	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	194	89	0.458763	NM_014324	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	254|254	0.1163003663003663|0.1163003663003663	28|28	0.056910569105691054|0.056910569105691054	34|34	0.09392265193370165|0.09392265193370165	85|85	0.1486013986013986|0.1486013986013986	107|107	0.14116094986807387|0.14116094986807387	C|C	10.02|10.02	1.237003|1.237003	0.22711|0.22711	0.070359|0.070359	0.145349|0.145349	ENSG00000242110|ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637|ENST00000382072;ENST00000441713	T;T;T|T;T	0.50813|0.69561	0.73;0.73;0.73|-0.33;-0.41	5.34|5.34	3.26|3.26	0.37387|0.37387	CoA-transferase family III domain (2);|.	0.052954|.	0.85682|.	D|.	0.000000|.	T|T	0.01029|0.01029	0.0034|0.0034	L|L	0.58101|0.58101	1.795|1.795	0.09310|0.09310	P|P	1.0|1.0	P;P;P;P|D;D	0.41710|0.71674	0.76;0.654;0.703;0.703|0.998;0.992	B;B;B;B|D;P	0.40134|0.70487	0.275;0.287;0.32;0.32|0.969;0.9	T|T	0.37244|0.37244	-0.9714|-0.9714	9|8	0.66056|0.38643	D|T	0.02|0.18	-18.029|-18.029	8.5827|8.5827	0.33640|0.33640	0.0:0.6599:0.0:0.3401|0.0:0.6599:0.0:0.3401	rs34677;rs52819324;rs60234651;rs34677|rs34677;rs52819324;rs60234651;rs34677	239;239;224;239|186;186	B3KMU8;F8W9N1;D6RB81;Q9UHK6|Q6VRU4;Q9UHK6-4	.;.;.;AMACR_HUMAN|.;.	H|F	239;239;224|186	ENSP00000334424:Q239H;ENSP00000371517:Q239H;ENSP00000424351:Q224H|ENSP00000371504:V186F;ENSP00000403800:V186F	ENSP00000334424:Q239H|ENSP00000371504:V186F	Q|V	-|-	3|1	2|0	AMACR|AMACR	34034525|34034525	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.391000|0.391000	0.30476|0.30476	1.867000|1.867000	0.39499|0.39499	1.000000|1.000000	0.39049|0.39049	0.563000|0.563000	0.77884|0.77884	CAG|GTT	T|0.007;G|0.005	.	strong		0.478	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
SLC22A10	387775	hgsc.bcm.edu	37	11	63064887	63064887	+	Missense_Mutation	SNP	G	G	T	rs117447942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:63064887G>T	ENST00000332793.6	+	3	621	c.619G>T	c.(619-621)Ggt>Tgt	p.G207C	SLC22A10_ENST00000544661.1_Missense_Mutation_p.G52C|SLC22A10_ENST00000525620.1_3'UTR|SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000535888.1_5'UTR	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	207						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.G207C(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	CTTCTTGGCAGGTTTTTCTTC	0.393													G|||	66	0.0131789	0.003	0.0216	5008	,	,		17325	0.0		0.0318	False		,,,				2504	0.0153				p.G207C		Atlas-SNP	.											SLC22A10,NS,carcinoma,0,1	SLC22A10	79	1	1	Substitution - Missense(1)	pancreas(1)	c.G619T						PASS	.	G	CYS/GLY	18,3996		0,18,1989	159.0	158.0	158.0		619	3.3	0.0	11	dbSNP_132	158	272,8106		9,254,3926	yes	missense	SLC22A10	NM_001039752.3	159	9,272,5915	TT,TG,GG		3.2466,0.4484,2.3402	probably-damaging	207/542	63064887	290,12102	2007	4189	6196	SO:0001583	missense	387775	exon3			TTGGCAGGTTTTT	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"""Solute carriers"""	18057	protein-coding gene	gene with protein product		607580	"""solute carrier family 22 (organic anion/cation transporter), member 10"""			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.619G>T	11.37:g.63064887G>T	ENSP00000327569:p.Gly207Cys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_001039752	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	32	0.014652014652014652	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	20	0.026385224274406333	G	16.03	3.007376	0.54361	0.004484	0.032466	ENSG00000184999	ENST00000544661;ENST00000332793	D;D	0.91464	-2.85;-2.85	3.26	3.26	0.37387	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.064487	0.64402	U	0.000009	D	0.92293	0.7555	H	0.97783	4.075	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91822	0.5468	10	0.87932	D	0	.	12.5163	0.56034	0.0:0.0:1.0:0.0	.	207	Q63ZE4	S22AA_HUMAN	C	52;207	ENSP00000445667:G52C;ENSP00000327569:G207C	ENSP00000327569:G207C	G	+	1	0	SLC22A10	62821463	1.000000	0.71417	0.017000	0.16124	0.132000	0.20833	5.484000	0.66844	1.882000	0.54519	0.447000	0.29281	GGT	G|0.976;T|0.024	0.024	strong		0.393	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752	
RP1L1	94137	hgsc.bcm.edu	37	8	10470068	10470068	+	Missense_Mutation	SNP	C	C	T	rs74990397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10470068C>T	ENST00000382483.3	-	4	1763	c.1540G>A	c.(1540-1542)Ggc>Agc	p.G514S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	514				G -> S (in Ref. 2; CAD36957). {ECO:0000305}.	cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGCTCTGGGCCGCCCAGCCCT	0.682													C|||	1476	0.294728	0.348	0.3112	5008	,	,		14828	0.0208		0.5109	False		,,,				2504	0.271				p.G514S		Atlas-SNP	.											RP1L1,NS,haematopoietic_neoplasm,0,1	RP1L1	453	1	0			c.G1540A						PASS	.	C	SER/GLY	1311,2557		228,855,851	27.0	31.0	30.0		1540	-8.6	0.0	8	dbSNP_131	30	4110,4122		1087,1936,1093	yes	missense	RP1L1	NM_178857.5	56	1315,2791,1944	TT,TC,CC		49.9271,33.8935,44.8017	benign	514/2401	10470068	5421,6679	1934	4116	6050	SO:0001583	missense	94137	exon4			CTGGGCCGCCCAG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1540G>A	8.37:g.10470068C>T	ENSP00000371923:p.Gly514Ser	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	687	0.31456043956043955	171	0.3475609756097561	123	0.3397790055248619	13	0.022727272727272728	380	0.5013192612137203	C	0.510	-0.866735	0.02590	0.338935	0.499271	ENSG00000183638	ENST00000382483	T	0.03663	3.85	4.29	-8.57	0.00900	.	1.462110	0.04952	N	0.460442	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.16166	0.016	B	0.06405	0.002	T	0.44559	-0.9320	9	0.25106	T	0.35	0.7598	4.828	0.13427	0.1825:0.5318:0.1832:0.1026	.	514	A6NKC6	.	S	514	ENSP00000371923:G514S	ENSP00000371923:G514S	G	-	1	0	RP1L1	10507478	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-3.501000	0.00450	-3.027000	0.00267	-1.632000	0.00781	GGC	C|0.632;T|0.368	0.368	strong		0.682	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SSTR1	6751	hgsc.bcm.edu	37	14	38679473	38679473	+	Silent	SNP	C	C	T	rs2228497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	105	55	0.52381	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		
TRIM56	81844	hgsc.bcm.edu	37	7	100731829	100731829	+	Silent	SNP	T	T	C	rs6948536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100731829T>C	ENST00000306085.6	+	3	1533	c.1236T>C	c.(1234-1236)gcT>gcC	p.A412A		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	412					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)					AGCCCCAGGCTGGAGATGGAG	0.632													C|||	3548	0.708466	0.9614	0.5418	5008	,	,		15987	0.5496		0.7455	False		,,,				2504	0.6104				p.A412A	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											TRIM56_ENST00000306085,rectum,carcinoma,0,2	TRIM56	123	2	0			c.T1236C						PASS	.	C		3809,297		1776,257,20	50.0	67.0	62.0		1236	-7.1	0.0	7	dbSNP_116	62	6223,2179		2318,1587,296	no	coding-synonymous	TRIM56	NM_030961.1		4094,1844,316	CC,CT,TT		25.9343,7.2333,19.7953		412/756	100731829	10032,2476	2053	4201	6254	SO:0001819	synonymous_variant	81844	exon3			CCAGGCTGGAGAT	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.1236T>C	7.37:g.100731829T>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			T|0.261;C|0.739	0.739	strong		0.632	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
RMND1	55005	hgsc.bcm.edu	37	6	151766500	151766500	+	Silent	SNP	T	T	C	rs61739876	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151766500T>C	ENST00000367303.4	-	2	569	c.447A>G	c.(445-447)aaA>aaG	p.K149K	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)	149					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)		TCCTGGATGCTTTTAGTGGTC	0.443													T|||	471	0.0940495	0.3207	0.0288	5008	,	,		19103	0.0		0.008	False		,,,				2504	0.0194				p.K149K		Atlas-SNP	.											.	RMND1	32	.	0			c.A447G						PASS	.	T		1269,3137	417.2+/-337.8	172,925,1106	79.0	84.0	82.0		447	1.4	0.9	6	dbSNP_129	82	74,8526	41.7+/-99.0	1,72,4227	no	coding-synonymous	RMND1	NM_017909.2		173,997,5333	CC,CT,TT		0.8605,28.8016,10.326		149/450	151766500	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	55005	exon2			GGATGCTTTTAGT	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.447A>G	6.37:g.151766500T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	NM_017909	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Silent	SNP	ENST00000367303.4	37	CCDS5232.1																																																																																			T|0.910;C|0.090	0.090	strong		0.443	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	
VCX3B	425054	hgsc.bcm.edu	37	X	8434367	8434367	+	Silent	SNP	C	C	T	rs139169782		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:8434367C>T	ENST00000381032.1	+	3	991	c.684C>T	c.(682-684)agC>agT	p.S228S	VCX3B_ENST00000444481.1_Silent_p.S198S|VCX3B_ENST00000381029.4_Silent_p.S196S|VCX3B_ENST00000440654.2_Intron|VCX3B_ENST00000453306.1_Intron	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	228	14 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						GTCAGGAGAGCGAGATGGAAG	0.557													-|||	923	0.244503	0.0968	0.147	3775	,	,		6423	0.2887		0.1173	False		,,,				2504	0.2904				p.S228S		Atlas-SNP	.											.	VCX3B	34	.	0			c.C684T						PASS	.	C		600,2579		158,223,61,977,402	108.0	222.0	187.0		684	-0.6	0.0	X	dbSNP_134	187	808,5694		89,402,228,1896,1500	no	coding-synonymous	VCX3B	NM_001001888.3		247,625,289,2873,1902	TT,TC,T,CC,C		12.4269,18.8739,14.544		228/247	8434367	1408,8273	1821	4115	5936	SO:0001819	synonymous_variant	425054	exon3			GGAGAGCGAGATG		CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.684C>T	X.37:g.8434367C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	426	410	0.962441	NM_001001888	C9JS46|Q4KN12	Silent	SNP	ENST00000381032.1	37	CCDS48077.2																																																																																			C|0.777;T|0.223	0.223	strong		0.557	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1		
ALK	238	hgsc.bcm.edu	37	2	29543699	29543699	+	Silent	SNP	G	G	A	rs56165377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:29543699G>A	ENST00000389048.3	-	7	2370	c.1464C>T	c.(1462-1464)ggC>ggT	p.G488G	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	488	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				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)	CTTGGGTCCAGCCACAGAAGC	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				G|||	20	0.00399361	0.0	0.0202	5008	,	,		18892	0.0		0.006	False		,,,				2504	0.0				p.G488G		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C1464T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	189.0	167.0	175.0		1464	5.9	1.0	2	dbSNP_129	175	88,8512	49.4+/-109.1	0,88,4212	no	coding-synonymous	ALK	NM_004304.4		0,94,6409	AA,AG,GG		1.0233,0.1362,0.7227		488/1621	29543699	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGTCCAGCCACAG	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.1464C>T	2.37:g.29543699G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	149	85	0.57047	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.995;A|0.005	0.005	strong		0.532	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
OR4M2	390538	hgsc.bcm.edu	37	15	22369343	22369343	+	Silent	SNP	C	C	T	rs11259845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:22369343C>T	ENST00000332663.2	+	1	866	c.768C>T	c.(766-768)tcC>tcT	p.S256S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, 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)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TTGGGCCATCCATCTACATTT	0.418																																					p.S256S		Atlas-SNP	.											.	OR4M2	140	.	0			c.C768T						PASS	.			92,4314		0,92,2111	275.0	206.0	229.0		768	1.3	1.0	15	dbSNP_120	229	9,8591		0,9,4291	no	coding-synonymous	OR4M2	NM_001004719.2		0,101,6402	TT,TC,CC		0.1047,2.0881,0.7766		256/314	22369343	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	390538	exon1			GCCATCCATCTAC	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.768C>T	15.37:g.22369343C>T		Somatic	339	1	0.00294985		WXS	Illumina HiSeq	Phase_I	333	117	0.351351	NM_001004719	B9EH16|Q6IEY2	Silent	SNP	ENST00000332663.2	37	CCDS32172.1																																																																																			C|0.971;T|0.029	0.029	strong		0.418	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
KIAA1024	23251	hgsc.bcm.edu	37	15	79749261	79749261	+	Missense_Mutation	SNP	A	A	C	rs79982509	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79749261A>C	ENST00000305428.3	+	2	847	c.772A>C	c.(772-774)Aat>Cat	p.N258H		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	258						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						CCAGAAAAGGAATATCTTCAA	0.493													A|||	112	0.0223642	0.003	0.0187	5008	,	,		19414	0.002		0.0517	False		,,,				2504	0.0419				p.N258H		Atlas-SNP	.											.	KIAA1024	146	.	0			c.A772C						PASS	.	A	HIS/ASN	53,4339	52.3+/-87.9	3,47,2146	69.0	77.0	75.0		772	4.2	1.0	15	dbSNP_131	75	459,8127	136.8+/-193.9	16,427,3850	yes	missense	KIAA1024	NM_015206.2	68	19,474,5996	CC,CA,AA		5.3459,1.2067,3.9451	probably-damaging	258/917	79749261	512,12466	2196	4293	6489	SO:0001583	missense	23251	exon2			AAAAGGAATATCT	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.772A>C	15.37:g.79749261A>C	ENSP00000307461:p.Asn258His	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	52	0.023809523809523808	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	41	0.05408970976253298	A	15.38	2.815777	0.50527	0.012067	0.053459	ENSG00000169330	ENST00000305428	T	0.34472	1.36	5.29	4.17	0.49024	.	0.191921	0.53938	D	0.000052	T	0.12732	0.0309	M	0.71581	2.175	0.50171	D	0.999859	D	0.61080	0.989	P	0.54401	0.751	T	0.03773	-1.1005	9	.	.	.	.	10.679	0.45802	0.9247:0.0:0.0753:0.0	.	258	Q9UPX6	K1024_HUMAN	H	258	ENSP00000307461:N258H	.	N	+	1	0	KIAA1024	77536316	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.698000	0.74608	0.854000	0.35336	0.482000	0.46254	AAT	A|0.965;C|0.035	0.035	strong		0.493	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
EPCAM	4072	hgsc.bcm.edu	37	2	47601106	47601106	+	Missense_Mutation	SNP	T	T	C	rs1126497|rs111849096	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:47601106T>C	ENST00000263735.4	+	3	702	c.344T>C	c.(343-345)aTg>aCg	p.M115T	EPCAM_ENST00000405271.1_Missense_Mutation_p.M143T	NM_002354.2	NP_002345.2	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule	115	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.		M -> T (in dbSNP:rs1126497). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2108441, ECO:0000269|PubMed:2463074, ECO:0000269|PubMed:2469722}.		negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|stem cell differentiation (GO:0048863)|ureteric bud development (GO:0001657)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein complex binding (GO:0032403)	p.0?(2)|p.?(1)		endometrium(3)|large_intestine(1)|liver(2)|lung(7)|skin(1)|stomach(1)	15						GGCACCTCCATGTGCTGGTGT	0.532													C|||	3336	0.666134	0.8888	0.5159	5008	,	,		17137	0.8323		0.4692	False		,,,				2504	0.5031				p.M115T		Atlas-SNP	.											.	EPCAM	27	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.T344C						PASS	.	C	THR/MET	3649,757	305.5+/-289.0	1530,589,84	74.0	69.0	70.0		344	1.7	0.4	2	dbSNP_86	70	3722,4878	618.5+/-396.8	801,2120,1379	yes	missense	EPCAM	NM_002354.2	81	2331,2709,1463	CC,CT,TT		43.2791,17.1811,43.3262	benign	115/315	47601106	7371,5635	2203	4300	6503	SO:0001583	missense	4072	exon3			CCTCCATGTGCTG	M33011	CCDS1833.1	2p21	2014-09-17	2008-12-16	2008-12-16	ENSG00000119888	ENSG00000119888		"""CD molecules"""	11529	protein-coding gene	gene with protein product		185535	"""antigen identified by monoclonal antibody AUA1"", ""tumor-associated calcium signal transducer 1"""	M4S1, MIC18, TACSTD1		8382772, 11306819	Standard	NM_002354		Approved	Ly74, TROP1, GA733-2, EGP34, EGP40, EGP-2, KSA, CD326, Ep-CAM, HEA125, KS1/4, MK-1, MH99, MOC31, 323/A3, 17-1A, TACST-1, CO-17A, ESA	uc002rvx.3	P16422	OTTHUMG00000128853	ENST00000263735.4:c.344T>C	2.37:g.47601106T>C	ENSP00000263735:p.Met115Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_002354	P18180|Q6FG26|Q6FG49|Q96C47|Q9UCD0	Missense_Mutation	SNP	ENST00000263735.4	37	CCDS1833.1	1440	0.6593406593406593	437	0.8882113821138211	182	0.5027624309392266	460	0.8041958041958042	361	0.4762532981530343	C	3.317	-0.139650	0.06669	0.828189	0.432791	ENSG00000119888	ENST00000405271;ENST00000263735;ENST00000419334	T;T;T	0.62105	0.05;0.05;0.05	5.93	1.71	0.24356	Thyroglobulin type-1 (6);	0.527053	0.22416	N	0.060350	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	0.44251	-0.9340	9	0.02654	T	1	-4.742	11.8944	0.52648	0.0:0.6732:0.0:0.3268	rs1126497;rs3181550;rs17845436;rs17858308;rs52820371;rs57528354;rs1126497	115;143	P16422;B5MCA4	EPCAM_HUMAN;.	T	143;115;191	ENSP00000385476:M143T;ENSP00000263735:M115T;ENSP00000389028:M191T	ENSP00000263735:M115T	M	+	2	0	EPCAM	47454610	0.325000	0.24660	0.371000	0.25978	0.878000	0.50629	0.040000	0.13905	0.160000	0.19432	-0.119000	0.15052	ATG	T|0.385;C|0.615	0.615	strong		0.532	EPCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250792.2		
CYP2D6	1565	hgsc.bcm.edu	37	22	42523528	42523528	+	Missense_Mutation	SNP	C	C	T	rs1058172	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:42523528C>T	ENST00000360608.5	-	7	1208	c.1094G>A	c.(1093-1095)cGc>cAc	p.R365H	NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.R365H|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.R314H|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	365			R -> H (in dbSNP:rs1058172).		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GTCCCCAAAGCGCTGCACCTC	0.602																																					p.R365H		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	0			c.G1094A						PASS	.						106.0	85.0	92.0					22																	42523528		2202	4300	6502	SO:0001583	missense	1565	exon7			CCAAAGCGCTGCA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1094G>A	22.37:g.42523528C>T	ENSP00000353820:p.Arg365His	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	265	45	0.169811	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	154	0.07051282051282051	11	0.022357723577235773	39	0.10773480662983426	0	0.0	104	0.13720316622691292	C	34	5.359243	0.95854	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	D;D;D	0.97505	-4.41;-4.41;-4.41	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000001	T	0.61800	0.2376	H	0.99545	4.62	0.09310	P	0.99999999622316	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.978;0.999	T	0.49943	-0.8885	9	0.87932	D	0	.	17.7329	0.88383	0.0:1.0:0.0:0.0	rs1058172;rs1974456;rs4134603;rs17002850	365;314;365	C1ID54;Q6NXU8;Q6NWU0	.;.;.	H	365;365;311;314;314	ENSP00000353820:R365H;ENSP00000374620:R365H;ENSP00000351927:R314H	ENSP00000351927:R314H	R	-	2	0	CYP2D6	40853472	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.610000	0.82949	2.283000	0.76528	0.555000	0.69702	CGC	C|0.908;T|0.092	0.092	strong		0.602	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
GABBR2	9568	hgsc.bcm.edu	37	9	101151234	101151234	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:101151234G>C	ENST00000259455.2	-	10	1890	c.1431C>G	c.(1429-1431)atC>atG	p.I477M		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	477					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)	GAGGTAGGGAGATCTTCCGCA	0.502																																					p.I477M		Atlas-SNP	.											.	GABBR2	126	.	0			c.C1431G						PASS	.						336.0	253.0	281.0					9																	101151234		2203	4300	6503	SO:0001583	missense	9568	exon10			TAGGGAGATCTTC	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.1431C>G	9.37:g.101151234G>C	ENSP00000259455:p.Ile477Met	Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	273	118	0.432234	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399282	0.62177	.	.	ENSG00000136928	ENST00000259455	T	0.80304	-1.36	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	M	0.63843	1.955	0.80722	D	1	P	0.50617	0.937	P	0.49276	0.605	T	0.82902	-0.0227	10	0.87932	D	0	.	9.4371	0.38646	0.0978:0.0:0.9022:0.0	.	477	O75899	GABR2_HUMAN	M	477	ENSP00000259455:I477M	ENSP00000259455:I477M	I	-	3	3	GABBR2	100191055	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.035000	0.41155	2.389000	0.81357	0.655000	0.94253	ATC	.	.	none		0.502	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
KIAA1549L	25758	hgsc.bcm.edu	37	11	33604960	33604960	+	Silent	SNP	C	C	T	rs2273115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:33604960C>T	ENST00000321505.4	+	10	3768	c.3588C>T	c.(3586-3588)atC>atT	p.I1196I	KIAA1549L_ENST00000389726.3_Silent_p.I1202I|KIAA1549L_ENST00000265654.5_Silent_p.I1202I			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1196	Poly-Ile.					integral component of membrane (GO:0016021)											TCACGGTCATCATCATCATCA	0.547													C|||	888	0.177316	0.0166	0.2334	5008	,	,		21311	0.3591		0.2187	False		,,,				2504	0.1247				p.I1196I		Atlas-SNP	.											.	.	.	.	0			c.C3588T						PASS	.	C		180,4112		5,170,1971	43.0	46.0	45.0		3588	4.7	1.0	11	dbSNP_100	45	1964,6550		225,1514,2518	no	coding-synonymous	C11orf41	NM_012194.2		230,1684,4489	TT,TC,CC		23.0679,4.1938,16.7422		1196/1850	33604960	2144,10662	2146	4257	6403	SO:0001819	synonymous_variant	25758	exon10			GGTCATCATCATC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.3588C>T	11.37:g.33604960C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	471	0.21565934065934067	12	0.024390243902439025	79	0.21823204419889503	210	0.36713286713286714	170	0.22427440633245382	C	10.12	1.262125	0.23051	0.041938	0.230679	ENSG00000110427	ENST00000526400	.	.	.	5.57	4.65	0.58169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42999	-0.9418	3	.	.	.	-25.2471	8.8586	0.35242	0.1496:0.7757:0.0:0.0747	rs2273115	.	.	.	L	594	.	.	S	+	2	0	C11orf41	33561536	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	1.438000	0.35002	2.619000	0.88677	0.561000	0.74099	TCA	C|0.781;T|0.218	0.218	strong		0.547	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
DSPP	1834	hgsc.bcm.edu	37	4	88536880	88536880	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88536880C>T	ENST00000282478.7	+	4	3099	c.3066C>T	c.(3064-3066)agC>agT	p.S1022S	DSPP_ENST00000399271.1_Silent_p.S1022S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1022	Asp/Ser-rich.			S -> G (in Ref. 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaatagcagtg	0.517																																					p.S1022S		Atlas-SNP	.											.	DSPP	174	.	0			c.C3066T						PASS	.						43.0	36.0	39.0					4																	88536880		1598	2799	4397	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAATAGC	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.3066C>T	4.37:g.88536880C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	149	17	0.114094	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.517	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
AMZ2	51321	hgsc.bcm.edu	37	17	66253095	66253095	+	Silent	SNP	T	T	A	rs7105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:66253095T>A	ENST00000359904.3	+	7	2200	c.1068T>A	c.(1066-1068)gcT>gcA	p.A356A	AMZ2_ENST00000577866.1_Silent_p.A356A|AMZ2_ENST00000577985.1_Silent_p.A356A|AMZ2_ENST00000359783.4_Silent_p.A298A|AMZ2_ENST00000580753.1_Silent_p.A356A|AMZ2_ENST00000392720.2_Silent_p.A356A|ARSG_ENST00000448504.2_5'Flank|AMZ2_ENST00000577273.1_3'UTR	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	356							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			AATGCCTGGCTGTTCTCCAAA	0.393													.|||	1856	0.370607	0.3048	0.3588	5008	,	,		20327	0.4762		0.3131	False		,,,				2504	0.4182				p.A356A		Atlas-SNP	.											.	AMZ2	15	.	0			c.T1068A						PASS	.	T	,,,,,	1286,3120	437.4+/-345.0	197,892,1114	80.0	79.0	79.0		1068,1068,1068,1068,894,1068	1.1	1.0	17	dbSNP_52	79	2789,5811	441.0+/-359.7	476,1837,1987	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMZ2	NM_001033569.1,NM_001033570.1,NM_001033571.1,NM_001033572.1,NM_001033574.1,NM_016627.4	,,,,,	673,2729,3101	AA,AT,TT		32.4302,29.1875,31.3317	,,,,,	356/361,356/361,356/361,356/361,298/303,356/361	66253095	4075,8931	2203	4300	6503	SO:0001819	synonymous_variant	51321	exon8			CCTGGCTGTTCTC	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"""archaemetzincin-2"""	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.1068T>A	17.37:g.66253095T>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_001033572	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Silent	SNP	ENST00000359904.3	37	CCDS11674.1																																																																																			T|0.663;A|0.337	0.337	strong		0.393	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627	
PMFBP1	83449	hgsc.bcm.edu	37	16	72156842	72156842	+	Missense_Mutation	SNP	T	T	G	rs16973716	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72156842T>G	ENST00000537792.1	-	3	236	c.237A>C	c.(235-237)aaA>aaC	p.K79N	PMFBP1_ENST00000537465.1_Missense_Mutation_p.K918N|PMFBP1_ENST00000355636.6_Missense_Mutation_p.K768N|PMFBP1_ENST00000237353.10_Missense_Mutation_p.K913N			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	77	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	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	
EIF3L	51386	hgsc.bcm.edu	37	22	38273749	38273749	+	Silent	SNP	T	T	C	rs9466	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38273749T>C	ENST00000412331.2	+	11	1728	c.1146T>C	c.(1144-1146)atT>atC	p.I382I	EIF3L_ENST00000381683.6_Silent_p.I334I|EIF3L_ENST00000406934.1_Silent_p.I284I	NM_016091.3	NP_057175.1			eukaryotic translation initiation factor 3, subunit L											kidney(2)|large_intestine(3)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCATGCGTATTGATGAGAGCA	0.507													t|||	2018	0.402955	0.534	0.4294	5008	,	,		22143	0.1815		0.4215	False		,,,				2504	0.4162				p.I382I		Atlas-SNP	.											.	EIF3L	35	.	0			c.T1146C						PASS	.	C	,	2268,2138	597.9+/-389.0	587,1094,522	108.0	90.0	96.0		1002,1146	-7.0	0.7	22	dbSNP_52	96	3667,4933	526.4+/-380.9	752,2163,1385	yes	coding-synonymous,coding-synonymous	EIF3L	NM_001242923.1,NM_016091.3	,	1339,3257,1907	CC,CT,TT		42.6395,48.5247,45.6328	,	334/517,382/565	38273749	5935,7071	2203	4300	6503	SO:0001819	synonymous_variant	51386	exon11			GCGTATTGATGAG	AF083243	CCDS13960.1, CCDS56230.1	22q	2012-12-20	2009-01-07	2009-01-07	ENSG00000100129	ENSG00000100129			18138	protein-coding gene	gene with protein product			"""eukaryotic translation initiation factor 3, subunit 6 interacting protein"", ""eukaryotic translation initiation factor 3, subunit E interacting protein"""	EIF3S6IP, EIF3EIP		11042152, 11590142	Standard	NM_016091		Approved	HSPC021, HSPC025, EIF3S11	uc003auf.3	Q9Y262	OTTHUMG00000150671	ENST00000412331.2:c.1146T>C	22.37:g.38273749T>C		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	246	106	0.430894	NM_016091		Silent	SNP	ENST00000412331.2	37	CCDS13960.1																																																																																			T|0.574;C|0.426	0.426	strong		0.507	EIF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319551.2	NM_016091	
PLB1	151056	hgsc.bcm.edu	37	2	28827625	28827625	+	Splice_Site	SNP	C	C	T	rs34289907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:28827625C>T	ENST00000327757.5	+	41	3004	c.2960C>T	c.(2959-2961)gCg>gTg	p.A987V	PLB1_ENST00000422425.2_Splice_Site_p.A976V|PLB1_ENST00000541605.1_Intron	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	987	4 X 308-326 AA approximate repeats.		A -> V (in dbSNP:rs34289907).		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)					CCTGTCCTGGCGGTATGTCCC	0.552													C|||	216	0.043131	0.025	0.0634	5008	,	,		21432	0.0		0.1054	False		,,,				2504	0.0337				p.A987V		Atlas-SNP	.											.	PLB1	255	.	0			c.C2960T						PASS	.	C	VAL/ALA,VAL/ALA	142,4264	98.9+/-137.6	1,140,2062	127.0	102.0	110.0		2927,2960	-5.4	0.0	2	dbSNP_126	110	922,7678	204.2+/-247.0	44,834,3422	yes	missense-near-splice,missense-near-splice	PLB1	NM_001170585.1,NM_153021.4	64,64	45,974,5484	TT,TC,CC		10.7209,3.2229,8.1808	benign,benign	976/1448,987/1459	28827625	1064,11942	2203	4300	6503	SO:0001630	splice_region_variant	151056	exon41			TCCTGGCGGTATG		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.2961+1C>T	2.37:g.28827625C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	192	90	0.46875	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	128|128	0.05860805860805861|0.05860805860805861	9|9	0.018292682926829267|0.018292682926829267	32|32	0.08839779005524862|0.08839779005524862	0|0	0.0|0.0	87|87	0.11477572559366754|0.11477572559366754	C|C	17.14|17.14	3.314710|3.314710	0.60524|0.60524	0.032229|0.032229	0.107209|0.107209	ENSG00000163803|ENSG00000163803	ENST00000327757;ENST00000422425|ENST00000404858	T;T|.	0.55760|.	0.5;0.5|.	5.2|5.2	-5.37|-5.37	0.02681|0.02681	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);|.	1.608970|.	0.03951|.	N|.	0.288560|.	T|T	0.01124|0.01124	0.0037|0.0037	M|M	0.61703|0.61703	1.905|1.905	0.19300|0.19300	P|P	0.9999726284|0.9999726284	D;D|.	0.54397|.	0.962;0.966|.	B;P|.	0.46339|.	0.287;0.513|.	T|T	0.41858|0.41858	-0.9485|-0.9485	9|4	0.48119|.	T|.	0.1|.	-1.3643|-1.3643	8.8365|8.8365	0.35115|0.35115	0.6265:0.2297:0.0:0.1438|0.6265:0.2297:0.0:0.1438	rs34289907|rs34289907	976;987|.	Q6P1J6-3;Q6P1J6|.	.;PLB1_HUMAN|.	V|W	987;976|975	ENSP00000330442:A987V;ENSP00000416440:A976V|.	ENSP00000330442:A987V|.	A|R	+|+	2|1	0|2	PLB1|PLB1	28681129|28681129	0.007000|0.007000	0.16637|0.16637	0.048000|0.048000	0.18961|0.18961	0.354000|0.354000	0.29330|0.29330	-0.209000|-0.209000	0.09358|0.09358	-0.605000|-0.605000	0.05753|0.05753	-0.181000|-0.181000	0.13052|0.13052	GCG|CGG	C|0.927;T|0.073	0.073	strong		0.552	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		Missense_Mutation
C11orf84	144097	hgsc.bcm.edu	37	11	63585804	63585804	+	Silent	SNP	C	C	A	rs643634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:63585804C>A	ENST00000294244.4	+	3	873	c.574C>A	c.(574-576)Cgg>Agg	p.R192R		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	192	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						TAAAAGGAGCCGGCCCAGGGG	0.612													C|||	1966	0.392572	0.0734	0.6354	5008	,	,		14644	0.6944		0.4225	False		,,,				2504	0.3098				p.R192R		Atlas-SNP	.											.	C11orf84	33	.	0			c.C574A						PASS	.	C		609,3793	263.8+/-265.7	46,517,1638	51.0	62.0	58.0		574	5.5	1.0	11	dbSNP_83	58	4008,4588	554.1+/-386.4	935,2138,1225	no	coding-synonymous	C11orf84	NM_138471.1		981,2655,2863	AA,AC,CC		46.6263,13.8346,35.5208		192/382	63585804	4617,8381	2201	4298	6499	SO:0001819	synonymous_variant	144097	exon3			AGGAGCCGGCCCA	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.574C>A	11.37:g.63585804C>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Silent	SNP	ENST00000294244.4	37	CCDS31594.1																																																																																			C|0.623;A|0.377	0.377	strong		0.612	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471	
RSPH10B	222967	hgsc.bcm.edu	37	7	5983063	5983063	+	Missense_Mutation	SNP	C	C	T	rs148485394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:5983063C>T	ENST00000405415.1	-	14	2036	c.1650G>A	c.(1648-1650)atG>atA	p.M550I	RSPH10B_ENST00000539903.1_3'UTR|RSPH10B_ENST00000404406.1_Missense_Mutation_p.M550I|RSPH10B_ENST00000337579.3_Missense_Mutation_p.M550I|RSPH10B_ENST00000535104.1_5'UTR|RSPH10B_ENST00000441023.2_Missense_Mutation_p.M550I			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	550										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		TCATGTAACTCATAGAGTAGA	0.428																																					p.M550I		Atlas-SNP	.											RSPH10B,NS,carcinoma,-1,2	RSPH10B	28	2	0			c.G1650A						PASS	.						30.0	29.0	29.0					7																	5983063		2164	4268	6432	SO:0001583	missense	222967	exon15			GTAACTCATAGAG		CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.1650G>A	7.37:g.5983063C>T	ENSP00000385443:p.Met550Ile	Somatic	1163	1	0.000859845		WXS	Illumina HiSeq	Phase_I	1049	262	0.249762	NM_173565	A6NMW7|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000405415.1	37	CCDS34598.1	420	0.19230769230769232	86	0.17479674796747968	87	0.24033149171270718	42	0.07342657342657342	205	0.2704485488126649	C	2.557	-0.302794	0.05495	.	.	ENSG00000155026	ENST00000405415;ENST00000404406;ENST00000337579;ENST00000354951;ENST00000441023	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	3.38	2.48	0.30137	.	0.193985	0.44285	D	0.000471	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	0.99999528627	B;B;B	0.33288	0.406;0.068;0.112	B;B;B	0.28232	0.087;0.013;0.04	T	0.15378	-1.0439	9	0.40728	T	0.16	.	5.6003	0.17349	0.1944:0.6963:0.0:0.1094	.	251;550;409	B7Z298;P0C881;F5GXE3	.;R10B1_HUMAN;.	I	550;550;550;409;550	ENSP00000385443:M550I;ENSP00000384097:M550I;ENSP00000338556:M550I;ENSP00000400988:M550I	ENSP00000338556:M550I	M	-	3	0	RSPH10B	5949589	0.985000	0.35326	0.060000	0.19600	0.014000	0.08584	0.436000	0.21526	0.734000	0.32515	0.551000	0.68910	ATG	.	.	weak		0.428	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062065	64062065	+	Missense_Mutation	SNP	T	T	C	rs10878075	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	166	0	0		WXS	Illumina HiSeq	Phase_I	141	45	0.319149	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	
ZNF45	7596	hgsc.bcm.edu	37	19	44418775	44418775	+	Silent	SNP	C	C	T	rs61731635	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44418775C>T	ENST00000269973.5	-	10	1903	c.813G>A	c.(811-813)acG>acA	p.T271T	ZNF45_ENST00000589703.1_Silent_p.T271T|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	271					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	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(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						GTTTCTCTCCCGTATGAACTA	0.428													C|||	73	0.0145767	0.0008	0.0231	5008	,	,		21109	0.0		0.0417	False		,,,				2504	0.0143				p.T271T		Atlas-SNP	.											.	ZNF45	51	.	0			c.G813A						PASS	.	C		29,4377	34.3+/-65.2	0,29,2174	101.0	93.0	96.0		813	-4.8	0.0	19	dbSNP_129	96	240,8360	97.5+/-159.1	3,234,4063	no	coding-synonymous	ZNF45	NM_003425.3		3,263,6237	TT,TC,CC		2.7907,0.6582,2.0683		271/683	44418775	269,12737	2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			CTCTCCCGTATGA	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"""Zinc fingers, C2H2-type"", ""-"""	13111	protein-coding gene	gene with protein product		194554	"""zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)"", ""zinc finger protein 13"""	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.813G>A	19.37:g.44418775C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	37	CCDS12632.1																																																																																			C|0.978;T|0.022	0.022	strong		0.428	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
SAMD9L	219285	hgsc.bcm.edu	37	7	92760738	92760738	+	Missense_Mutation	SNP	T	T	G	rs10282508	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:92760738T>G	ENST00000318238.4	-	5	5763	c.4547A>C	c.(4546-4548)aAt>aCt	p.N1516T	SAMD9L_ENST00000437805.1_Missense_Mutation_p.N1516T|SAMD9L_ENST00000411955.1_Missense_Mutation_p.N1516T	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1516			N -> T (in dbSNP:rs10282508).		common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTGACTTCATTTTTTTTCCA	0.393													T|||	534	0.106629	0.2247	0.0461	5008	,	,		19427	0.1369		0.0467	False		,,,				2504	0.0204				p.N1516T		Atlas-SNP	.											.	SAMD9L	227	.	0			c.A4547C						PASS	.	T	THR/ASN	859,3547	337.6+/-304.9	86,687,1430	128.0	127.0	127.0		4547	-1.9	0.1	7	dbSNP_119	127	438,8162	132.6+/-190.3	22,394,3884	yes	missense	SAMD9L	NM_152703.2	65	108,1081,5314	GG,GT,TT		5.093,19.4961,9.9723	benign	1516/1585	92760738	1297,11709	2203	4300	6503	SO:0001583	missense	219285	exon5			ACTTCATTTTTTT	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4547A>C	7.37:g.92760738T>G	ENSP00000326247:p.Asn1516Thr	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	265	128	0.483019	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	267	0.12225274725274725	122	0.24796747967479674	16	0.04419889502762431	95	0.1660839160839161	34	0.044854881266490766	T	2.359	-0.347034	0.05208	0.194961	0.05093	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.21543	2.0;2.0;2.0	4.77	-1.89	0.07689	.	0.928117	0.09002	N	0.862767	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.43294	-0.9400	9	0.48119	T	0.1	0.0887	5.8963	0.18941	0.0:0.3078:0.1296:0.5625	rs10282508;rs10282508	1516	Q8IVG5	SAM9L_HUMAN	T	1516;1516;1516;338	ENSP00000326247:N1516T;ENSP00000405760:N1516T;ENSP00000408796:N1516T	ENSP00000326247:N1516T	N	-	2	0	SAMD9L	92598674	0.000000	0.05858	0.098000	0.21074	0.437000	0.31866	0.047000	0.14056	-0.193000	0.10415	0.383000	0.25322	AAT	T|0.887;G|0.113	0.113	strong		0.393	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
EXT1	2131	hgsc.bcm.edu	37	8	118847782	118847782	+	Silent	SNP	G	G	A	rs11546829	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:118847782G>A	ENST00000378204.2	-	3	1871	c.1065C>T	c.(1063-1065)tgC>tgT	p.C355C		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	355					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|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 development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|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)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)	p.C355C(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			TCACAGGGACGCAGGCAGCCT	0.478			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses				G|||	871	0.173922	0.0908	0.3069	5008	,	,		19602	0.0853		0.2684	False		,,,				2504	0.1861				p.C355C		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	EXT1,NS,carcinoma,0,1	EXT1	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C1065T						scavenged	.	G		556,3850	250.0+/-257.2	32,492,1679	93.0	80.0	85.0		1065	1.4	1.0	8	dbSNP_120	85	2644,5956	427.4+/-355.6	415,1814,2071	no	coding-synonymous	EXT1	NM_000127.2		447,2306,3750	AA,AG,GG		30.7442,12.6192,24.604		355/747	118847782	3200,9806	2203	4300	6503	SO:0001819	synonymous_variant	2131	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	AGGGACGCAGGCA	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3512	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608177	"""Langer-Giedion syndrome chromosome region"", ""exostoses (multiple) 1"", ""exostosin 1"""	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1065C>T	8.37:g.118847782G>A		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1	421	0.19276556776556777	46	0.09349593495934959	113	0.31215469613259667	50	0.08741258741258741	212	0.2796833773087071	g	10.46	1.356943	0.24598	0.126192	0.307442	ENSG00000182197	ENST00000436216	.	.	.	5.77	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.24905	-1.0147	3	.	.	.	-14.1796	10.3835	0.44125	0.6261:0.0:0.3739:0.0	rs11546829;rs17439875;rs17474651;rs17439875	.	.	.	C	145	.	.	R	-	1	0	EXT1	118916963	0.906000	0.30813	0.998000	0.56505	0.986000	0.74619	0.094000	0.15107	0.002000	0.14630	-0.137000	0.14449	CGT	G|0.774;A|0.226	0.226	strong		0.478	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769276	43769276	+	Silent	SNP	T	T	C	rs10880473	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	155	0	0		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	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	
OR10H3	26532	hgsc.bcm.edu	37	19	15852363	15852363	+	Missense_Mutation	SNP	G	G	A	rs11670007	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	246	2	0.00813008		WXS	Illumina HiSeq	Phase_I	253	125	0.494071	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		
NEDD4	4734	hgsc.bcm.edu	37	15	56208933	56208933	+	Missense_Mutation	SNP	T	T	C	rs1912403	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:56208933T>C	ENST00000508342.1	-	1	396	c.97A>G	c.(97-99)Atg>Gtg	p.M33V	NEDD4_ENST00000435532.3_Intron|NEDD4_ENST00000338963.2_Missense_Mutation_p.M33V|NEDD4_ENST00000506154.1_Missense_Mutation_p.M33V	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	33			M -> V (in dbSNP:rs1912403).		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)		TTGAAGCACATGTGAACATGG	0.438													T|||	160	0.0319489	0.0008	0.0562	5008	,	,		21769	0.002		0.0746	False		,,,				2504	0.044				p.M33V		Atlas-SNP	.											.	NEDD4	167	.	0			c.A97G						PASS	.	T	,VAL/MET	72,4314	65.3+/-102.7	0,72,2121	186.0	173.0	177.0		,97	4.0	1.0	15	dbSNP_92	177	778,7804	183.2+/-231.5	29,720,3542	yes	intron,missense	NEDD4	NM_006154.2,NM_198400.2	,21	29,792,5663	CC,CT,TT		9.0655,1.6416,6.5546	,possibly-damaging	,33/1248	56208933	850,12118	2193	4291	6484	SO:0001583	missense	4734	exon1			AGCACATGTGAAC	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.97A>G	15.37:g.56208933T>C	ENSP00000424827:p.Met33Val	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	170	99	0.582353	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		75	0.034340659340659344	0	0.0	17	0.04696132596685083	0	0.0	58	0.07651715039577836	T	11.02	1.515263	0.27123	0.016416	0.090655	ENSG00000069869	ENST00000508342;ENST00000338963;ENST00000506154	T;T;T	0.27256	1.73;1.68;1.75	5.17	4.04	0.47022	.	0.436159	0.17044	U	0.189200	T	0.00666	0.0022	.	.	.	0.22213	N	0.999288	B;B;B	0.11235	0.004;0.003;0.004	B;B;B	0.13407	0.009;0.004;0.009	T	0.09997	-1.0649	9	0.37606	T	0.19	.	10.2035	0.43099	0.0:0.0785:0.0:0.9215	rs1912403;rs52829449;rs57658180;rs1912403	33;33;33	P46934-2;P46934;P46934-3	.;NEDD4_HUMAN;.	V	33	ENSP00000424827:M33V;ENSP00000345530:M33V;ENSP00000422705:M33V	ENSP00000345530:M33V	M	-	1	0	NEDD4	53996225	0.999000	0.42202	0.952000	0.39060	0.998000	0.95712	1.331000	0.33793	0.928000	0.37168	0.482000	0.46254	ATG	T|0.945;C|0.055	0.055	strong		0.438	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
DIS3L	115752	hgsc.bcm.edu	37	15	66621346	66621346	+	Missense_Mutation	SNP	A	A	G	rs17258507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:66621346A>G	ENST00000319212.4	+	13	2290	c.2240A>G	c.(2239-2241)aAc>aGc	p.N747S	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Missense_Mutation_p.N664S	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	747			N -> S (in dbSNP:rs17258507).		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						GATAATGCGAACGACCCCCAC	0.502													A|||	181	0.0361422	0.0106	0.0346	5008	,	,		17493	0.001		0.1064	False		,,,				2504	0.0358				p.N747S		Atlas-SNP	.											.	DIS3L	175	.	0			c.A2240G						PASS	.	A	SER/ASN,SER/ASN	104,4298	81.4+/-119.9	3,98,2100	129.0	132.0	131.0		2240,1991	4.6	0.0	15	dbSNP_123	131	678,7920	170.4+/-221.6	30,618,3651	yes	missense,missense	DIS3L	NM_001143688.1,NM_133375.3	46,46	33,716,5751	GG,GA,AA		7.8856,2.3626,6.0154	benign,benign	747/1055,664/972	66621346	782,12218	2201	4299	6500	SO:0001583	missense	115752	exon13			ATGCGAACGACCC		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.2240A>G	15.37:g.66621346A>G	ENSP00000321711:p.Asn747Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	127	70	0.551181	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	37	CCDS45286.1	95	0.043498168498168496	6	0.012195121951219513	13	0.03591160220994475	0	0.0	76	0.10026385224274406	A	2.423	-0.332611	0.05314	0.023626	0.078856	ENSG00000166938	ENST00000319194;ENST00000319212	T;T	0.34472	1.36;1.36	5.76	4.63	0.57726	Ribonuclease II/R (2);	0.510762	0.24044	N	0.042062	T	0.00412	0.0013	N	0.03608	-0.345	0.30580	P	0.762574	B	0.11235	0.004	B	0.18263	0.021	T	0.12682	-1.0538	9	0.09590	T	0.72	-15.3575	10.9008	0.47051	0.9266:0.0:0.0734:0.0	rs17258507;rs52810849;rs17258507	747	Q8TF46	DI3L1_HUMAN	S	664;747	ENSP00000321583:N664S;ENSP00000321711:N747S	ENSP00000321583:N664S	N	+	2	0	DIS3L	64408400	0.605000	0.26941	0.004000	0.12327	0.467000	0.32768	4.699000	0.61796	1.004000	0.39156	0.460000	0.39030	AAC	A|0.946;G|0.054	0.054	strong		0.502	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
KIAA1804	84451	hgsc.bcm.edu	37	1	233498026	233498026	+	Silent	SNP	C	C	T	rs56052041	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:233498026C>T	ENST00000366624.3	+	5	1800	c.1539C>T	c.(1537-1539)atC>atT	p.I513I	MLK4_ENST00000366623.3_Silent_p.I513I	NM_032435.2	NP_115811.2																					GACATCGAATCAGTTTACCTT	0.368													C|||	81	0.0161741	0.0023	0.0403	5008	,	,		21925	0.0		0.0477	False		,,,				2504	0.002				p.I513I		Atlas-SNP	.											.	KIAA1804	129	.	0			c.C1539T						PASS	.	C		38,4368	41.6+/-74.8	0,38,2165	85.0	84.0	84.0		1539	2.8	1.0	1	dbSNP_129	84	369,8231	122.4+/-181.4	10,349,3941	no	coding-synonymous	KIAA1804	NM_032435.2		10,387,6106	TT,TC,CC		4.2907,0.8625,3.1293		513/1037	233498026	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	0	exon5			TCGAATCAGTTTA																												ENST00000366624.3:c.1539C>T	1.37:g.233498026C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_032435		Silent	SNP	ENST00000366624.3	37	CCDS1598.1																																																																																			C|0.972;T|0.028	0.028	strong		0.368	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
LRRC17	10234	hgsc.bcm.edu	37	7	102574715	102574715	+	Missense_Mutation	SNP	A	A	G	rs3800939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:102574715A>G	ENST00000339431.4	+	2	650	c.355A>G	c.(355-357)Aaa>Gaa	p.K119E	FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000456695.1_Intron|LRRC17_ENST00000249377.4_Missense_Mutation_p.K119E|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000455112.2_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	119			K -> E (in dbSNP:rs3800939).		bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						TGAGATCTCTAAAATTGAGAG	0.418													A|||	340	0.0678914	0.003	0.0231	5008	,	,		19899	0.13		0.0368	False		,,,				2504	0.1554				p.K119E		Atlas-SNP	.											.	LRRC17	45	.	0			c.A355G						PASS	.	A	GLU/LYS,,GLU/LYS,	61,4345	58.1+/-94.6	0,61,2142	74.0	73.0	73.0		355,,355,	4.4	1.0	7	dbSNP_107	73	554,8046	151.6+/-206.3	12,530,3758	yes	missense,intron,missense,intron	LRRC17,FBXL13	NM_001031692.2,NM_001111038.1,NM_005824.2,NM_145032.3	56,,56,	12,591,5900	GG,GA,AA		6.4419,1.3845,4.7286	probably-damaging,,probably-damaging,	119/442,,119/314,	102574715	615,12391	2203	4300	6503	SO:0001583	missense	10234	exon2			ATCTCTAAAATTG	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.355A>G	7.37:g.102574715A>G	ENSP00000344242:p.Lys119Glu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_005824	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	37	CCDS34721.1	129	0.059065934065934064	1	0.0020325203252032522	9	0.024861878453038673	89	0.1555944055944056	30	0.0395778364116095	A	11.54	1.669618	0.29693	0.013845	0.064419	ENSG00000128606	ENST00000339431;ENST00000249377	T;T	0.55052	0.54;0.54	5.52	4.37	0.52481	.	0.091368	0.47093	N	0.000243	T	0.00144	0.0004	N	0.05012	-0.13	0.22693	P	0.99884542	D;D	0.57257	0.979;0.974	P;P	0.52343	0.696;0.57	T	0.04115	-1.0976	9	0.02654	T	1	-31.9436	11.6688	0.51389	0.9303:0.0:0.0697:0.0	rs3800939;rs52824913;rs60404263;rs3800939	119;119	Q8N6Y2;Q8N6Y2-2	LRC17_HUMAN;.	E	119	ENSP00000344242:K119E;ENSP00000249377:K119E	ENSP00000249377:K119E	K	+	1	0	LRRC17	102361951	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.075000	0.50073	1.033000	0.39918	0.455000	0.32223	AAA	A|0.942;G|0.058	0.058	strong		0.418	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824	
FAT1	2195	hgsc.bcm.edu	37	4	187540654	187540654	+	Silent	SNP	T	T	A	rs3796647	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187540654T>A	ENST00000441802.2	-	10	7295	c.7086A>T	c.(7084-7086)gcA>gcT	p.A2362A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2362	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CACCATCAACTGCCCTCACAA	0.488										HNSCC(5;0.00058)			A|||	341	0.0680911	0.003	0.1499	5008	,	,		20319	0.1786		0.0338	False		,,,				2504	0.0194				p.A2362A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A7086T						PASS	.	A		41,4215		0,41,2087	106.0	109.0	108.0		7086	-0.2	0.1	4	dbSNP_107	108	255,8231		4,247,3992	no	coding-synonymous	FAT1	NM_005245.3		4,288,6079	AA,AT,TT		3.0049,0.9633,2.323		2362/4589	187540654	296,12446	2128	4243	6371	SO:0001819	synonymous_variant	2195	exon10			ATCAACTGCCCTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7086A>T	4.37:g.187540654T>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	140	54	0.385714	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.927;A|0.073	0.073	strong		0.488	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
KANSL1	284058	hgsc.bcm.edu	37	17	44111613	44111613	+	Silent	SNP	A	A	G	rs17574604	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44111613A>G	ENST00000262419.6	-	11	3050	c.2580T>C	c.(2578-2580)ttT>ttC	p.F860F	KANSL1_ENST00000393476.3_Silent_p.F154F|KANSL1_ENST00000574590.1_Silent_p.F860F|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000572904.1_Silent_p.F860F|KANSL1_ENST00000575318.1_Silent_p.F796F|KANSL1_ENST00000432791.1_Silent_p.F860F	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	860	Required for activation of KAT8 histone acetyltransferase activity.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.F860F(2)									TGTTAATATCAAATGAGCTCT	0.398													G|||	432	0.086262	0.0151	0.1571	5008	,	,		21592	0.001		0.2406	False		,,,				2504	0.0613				p.F860F		Atlas-SNP	.											KIAA1267,NS,carcinoma,0,1	.	.	1	2	Substitution - coding silent(2)	prostate(2)	c.T2580C						PASS	.	G	,,	202,4204	807.7+/-415.9	5,192,2006	187.0	157.0	167.0		2577,2580,2580	-6.8	0.2	17	dbSNP_123	167	1928,6672	726.2+/-406.6	220,1488,2592	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	225,1680,4598	GG,GA,AA		22.4186,4.5847,16.3771	,,	859/1105,860/1106,860/1106	44111613	2130,10876	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon11			AATATCAAATGAG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2580T>C	17.37:g.44111613A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.853;G|0.147	0.147	strong		0.398	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
DEGS2	123099	hgsc.bcm.edu	37	14	100615961	100615961	+	Missense_Mutation	SNP	C	C	T	rs4905937	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:100615961C>T	ENST00000305631.5	-	2	744	c.169G>A	c.(169-171)Gcc>Acc	p.A57T	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)				AGCCAGCAGGCCAGCATCTGC	0.672													C|||	713	0.142372	0.0749	0.1599	5008	,	,		16363	0.1825		0.167	False		,,,				2504	0.1544				p.A57T		Atlas-SNP	.											.	DEGS2	25	.	0			c.G169A						PASS	.	C	THR/ALA	380,4014		17,346,1834	23.0	26.0	25.0		169	4.4	1.0	14	dbSNP_111	25	1376,7212		105,1166,3023	no	missense	DEGS2	NM_206918.2	58	122,1512,4857	TT,TC,CC		16.0224,8.6482,13.5264	possibly-damaging	57/324	100615961	1756,11226	2197	4294	6491	SO:0001583	missense	123099	exon2			AGCAGGCCAGCAT		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.169G>A	14.37:g.100615961C>T	ENSP00000307126:p.Ala57Thr	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	26	20	0.769231	NM_206918		Missense_Mutation	SNP	ENST00000305631.5	37	CCDS9956.1	314	0.14377289377289376	37	0.07520325203252033	56	0.15469613259668508	97	0.16958041958041958	124	0.16358839050131926	C	17.99	3.521991	0.64747	0.086482	0.160224	ENSG00000168350	ENST00000305631	T	0.33216	1.42	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	L	0.48260	1.515	0.09310	P	1.0	P	0.48294	0.908	P	0.44422	0.449	T	0.11867	-1.0570	9	0.22706	T	0.39	-25.8571	17.3127	0.87214	0.0:1.0:0.0:0.0	rs4905937;rs17855855;rs4905937	57	Q6QHC5	DEGS2_HUMAN	T	57	ENSP00000307126:A57T	ENSP00000307126:A57T	A	-	1	0	DEGS2	99685714	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.961000	0.70356	2.154000	0.67381	0.561000	0.74099	GCC	C|0.864;T|0.136	0.136	strong		0.672	DEGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414003.1	NM_206918	
SORBS2	8470	hgsc.bcm.edu	37	4	186548067	186548067	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:186548067G>A	ENST00000284776.7	-	12	1350	c.841C>T	c.(841-843)Cga>Tga	p.R281*	SORBS2_ENST00000355634.5_Nonsense_Mutation_p.R381*|SORBS2_ENST00000431808.1_Nonsense_Mutation_p.R281*|SORBS2_ENST00000319471.9_Nonsense_Mutation_p.R439*|SORBS2_ENST00000418609.1_Nonsense_Mutation_p.R185*|SORBS2_ENST00000393528.3_Nonsense_Mutation_p.R374*|SORBS2_ENST00000449407.2_Nonsense_Mutation_p.R352*|SORBS2_ENST00000437304.2_Nonsense_Mutation_p.R532*|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000448662.2_Nonsense_Mutation_p.R369*	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	281					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)		AGGTCCACTCGGCCTGGGCTA	0.537																																					p.R532X	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											SORBS2_ENST00000448662,colon,carcinoma,0,4	SORBS2	300	4	0			c.C1594T						scavenged	.						137.0	132.0	134.0					4																	186548067		2203	4300	6503	SO:0001587	stop_gained	8470	exon15			CCACTCGGCCTGG		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.841C>T	4.37:g.186548067G>A	ENSP00000284776:p.Arg281*	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Nonsense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.102136|4.102136	0.76983|0.76983	.|.	.|.	ENSG00000154556|ENSG00000154556	ENST00000438278|ENST00000284776;ENST00000448662;ENST00000431808;ENST00000418609;ENST00000437304;ENST00000319471;ENST00000449407;ENST00000355634;ENST00000393528;ENST00000319454;ENST00000451974	.|.	.|.	.|.	5.22|5.22	3.43|3.43	0.39272|0.39272	.|.	.|0.333666	.|0.31636	.|N	.|0.007315	T|.	0.27241|.	0.0668|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.30851|.	-0.9964|.	3|.	.|0.02654	.|T	.|1	-5.5776|-5.5776	12.1231|12.1231	0.53903|0.53903	0.0:0.131:0.7326:0.1364|0.0:0.131:0.7326:0.1364	.|.	.|.	.|.	.|.	L|X	224|281;369;281;185;532;439;352;381;374;399;157	.|.	.|ENSP00000284776:R281X	P|R	-|-	2|1	0|2	SORBS2|SORBS2	186785061|186785061	0.012000|0.012000	0.17670|0.17670	0.001000|0.001000	0.08648|0.08648	0.004000|0.004000	0.04260|0.04260	1.767000|1.767000	0.38501|0.38501	0.640000|0.640000	0.30582|0.30582	0.655000|0.655000	0.94253|0.94253	CCG|CGA	.	.	none		0.537	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37507982	37507982	+	Silent	SNP	A	A	C	rs35138017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:37507982A>C	ENST00000602533.1	+	34	3273	c.3174A>C	c.(3172-3174)ctA>ctC	p.L1058L	ANKRD30A_ENST00000361713.1_Silent_p.L1058L|ANKRD30A_ENST00000374660.1_Silent_p.L1177L			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1114					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						TTGCCATGCTAAAACTGGAAA	0.294													A|||	114	0.0227636	0.0023	0.0101	5008	,	,		18988	0.001		0.0447	False		,,,				2504	0.0593				p.L1058L		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A3174C						PASS	.	A		23,3601		0,23,1789	55.0	54.0	54.0		3174	0.2	0.0	10	dbSNP_126	54	379,7745		4,371,3687	no	coding-synonymous	ANKRD30A	NM_052997.2		4,394,5476	CC,CA,AA		4.6652,0.6347,3.4219		1058/1342	37507982	402,11346	1812	4062	5874	SO:0001819	synonymous_variant	91074	exon34			CATGCTAAAACTG	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.3174A>C	10.37:g.37507982A>C		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	191	94	0.492147	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																				A|0.969;C|0.031	0.031	strong		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
ZNF732	654254	hgsc.bcm.edu	37	4	264941	264941	+	Missense_Mutation	SNP	A	A	G	rs11731285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:264941A>G	ENST00000419098.1	-	4	1715	c.1705T>C	c.(1705-1707)Tgg>Cgg	p.W569R		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	569					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(2)	3						TATGAGGACCACTTAAAGGCT	0.363													.|||	1330	0.265575	0.2821	0.3069	5008	,	,		18221	0.1825		0.2058	False		,,,				2504	0.3609				p.W568R		Atlas-SNP	.											.	ZNF732	117	.	0			c.T1702C						PASS	.	G	ARG/TRP	390,994		60,270,362	45.0	40.0	42.0		1705	-0.6	0.0	4	dbSNP_120	42	618,2564		66,486,1039	no	missense	ZNF732	NM_001137608.1	101	126,756,1401	GG,GA,AA		19.4217,28.1792,22.0762	benign	569/586	264941	1008,3558	692	1591	2283	SO:0001583	missense	654254	exon3			AGGACCACTTAAA	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"""Zinc fingers, C2H2-type"", ""-"""	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.1705T>C	4.37:g.264941A>G	ENSP00000415774:p.Trp569Arg	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	37	CCDS46990.1	525	0.2403846153846154	160	0.3252032520325203	109	0.3011049723756906	97	0.16958041958041958	159	0.20976253298153033	a	0	-2.667468	0.00105	0.281792	0.194217	ENSG00000186777	ENST00000419098	T	0.38722	1.12	0.977	-0.566	0.11767	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (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	0.38520	-0.9657	8	0.17369	T	0.5	.	4.5003	0.11860	0.5143:0.0:0.4857:0.0	rs11731285;rs57399843;rs11731285	569	B4DXR9	ZN732_HUMAN	R	569	ENSP00000415774:W569R	ENSP00000415774:W569R	W	-	1	0	ZNF732	254941	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.951000	0.00327	-1.522000	0.01769	-1.511000	0.00944	TGG	A|0.752;G|0.248	0.248	strong		0.363	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608	
NAAA	27163	hgsc.bcm.edu	37	4	76857388	76857388	+	Splice_Site	SNP	C	C	T	rs4859572	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:76857388C>T	ENST00000286733.4	-	3	473	c.372G>A	c.(370-372)gtG>gtA	p.V124V	NAAA_ENST00000399497.3_Splice_Site_p.V124V|NAAA_ENST00000507956.1_Splice_Site_p.V124V|NAAA_ENST00000507187.2_Splice_Site_p.V124V|NAAA_ENST00000505594.1_Splice_Site_p.V23V	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	124					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						TGGTGCAGAACCTGAGAAAAG	0.378													T|||	1091	0.217851	0.0832	0.2939	5008	,	,		8131	0.3581		0.2346	False		,,,				2504	0.184				p.V124V		Atlas-SNP	.											.	NAAA	26	.	0			c.G372A						PASS	.	T	,	406,3286		19,368,1459	133.0	123.0	126.0		372,372	-1.2	1.0	4	dbSNP_111	126	1903,6289		221,1461,2414	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	NAAA	NM_001042402.1,NM_014435.3	,	240,1829,3873	TT,TC,CC		23.23,10.9967,19.4295	,	124/324,124/360	76857388	2309,9575	1846	4096	5942	SO:0001630	splice_region_variant	27163	exon3			GCAGAACCTGAGA	M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"""N-acylsphingosine amidohydrolase (acid ceramidase)-like"""	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.372-1G>A	4.37:g.76857388C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_014435	Q5KTF2|Q96EY2|Q9BRA8	Silent	SNP	ENST00000286733.4	37	CCDS43239.1																																																																																			C|0.772;T|0.228	0.228	strong		0.378	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4		Silent
CEP290	80184	hgsc.bcm.edu	37	12	88505633	88505633	+	Silent	SNP	A	A	G	rs45465996	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:88505633A>G	ENST00000552810.1	-	21	2398	c.2055T>C	c.(2053-2055)gcT>gcC	p.A685A	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Silent_p.A687A	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	685					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTGATTCTATAGCCTAGCAAA	0.318													A|||	345	0.0688898	0.0227	0.1023	5008	,	,		12512	0.001		0.2008	False		,,,				2504	0.0419				p.A685A		Atlas-SNP	.											.	CEP290	195	.	0			c.T2055C						PASS	.	A		177,3379		7,163,1608	21.0	19.0	19.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2055	0.6	1.0	12	dbSNP_127	19	1438,6672		137,1164,2754	no	coding-synonymous	CEP290	NM_025114.3		144,1327,4362	GG,GA,AA		17.7312,4.9775,13.8436		685/2480	88505633	1615,10051	1778	4055	5833	SO:0001819	synonymous_variant	80184	exon21			TTCTATAGCCTAG	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2055T>C	12.37:g.88505633A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	37	CCDS55858.1	188	0.08608058608058608	6	0.012195121951219513	34	0.09392265193370165	1	0.0017482517482517483	147	0.19393139841688653	A	13.61	2.288974	0.40494	0.049775	0.177312	ENSG00000198707	ENST00000545139	.	.	.	5.79	0.62	0.17637	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17992	-1.0351	4	0.56958	D	0.05	.	0.5596	0.00676	0.2812:0.3026:0.2014:0.2148	rs45465996;rs62638181	.	.	.	H	540	.	ENSP00000444813:Y540H	Y	-	1	0	CEP290	87029764	0.971000	0.33674	0.996000	0.52242	0.956000	0.61745	0.004000	0.13106	-0.126000	0.11682	0.477000	0.44152	TAT	A|0.892;G|0.108	0.108	strong		0.318	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
RBM19	9904	hgsc.bcm.edu	37	12	114386639	114386639	+	Splice_Site	SNP	A	A	G	rs7966348|rs17849837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:114386639A>G	ENST00000545145.2	-	10	1353	c.1275T>C	c.(1273-1275)taT>taC	p.Y425Y	RBM19_ENST00000261741.5_Splice_Site_p.Y425Y|RBM19_ENST00000392561.3_Splice_Site_p.Y425Y	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	425	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y425Y(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					CACCCCTACCATATTTGGAGA	0.607													G|||	992	0.198083	0.3457	0.0764	5008	,	,		18272	0.1885		0.1133	False		,,,				2504	0.182				p.Y425Y		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.T1275C						PASS	.	G	,,	1441,2965	683.3+/-404.2	253,935,1015	76.0	66.0	69.0		1275,1275,1275	0.8	0.8	12	dbSNP_116	69	887,7713	778.8+/-407.7	38,811,3451	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	291,1746,4466	GG,GA,AA		10.314,32.7054,17.8994	,,	425/961,425/961,425/961	114386639	2328,10678	2203	4300	6503	SO:0001630	splice_region_variant	9904	exon10			CCTACCATATTTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1276+1T>C	12.37:g.114386639A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	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
CLIC5	53405	hgsc.bcm.edu	37	6	46047640	46047640	+	Missense_Mutation	SNP	T	T	C	rs723580	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:46047640T>C	ENST00000185206.6	-	1	492	c.340A>G	c.(340-342)Acc>Gcc	p.T114A		NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	114			T -> A (in dbSNP:rs723580).		auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						TGGTCCTGGGTTGATGAATAT	0.517													T|||	181	0.0361422	0.0378	0.0634	5008	,	,		21865	0.0		0.0656	False		,,,				2504	0.0215				p.T114A		Atlas-SNP	.											.	CLIC5	48	.	0			c.A340G						PASS	.	T	ALA/THR	58,1326		0,58,634	55.0	52.0	53.0		340	-9.3	0.0	6	dbSNP_86	53	145,3037		5,135,1451	yes	missense	CLIC5	NM_001114086.1	58	5,193,2085	CC,CT,TT		4.5569,4.1908,4.4459	benign	114/411	46047640	203,4363	692	1591	2283	SO:0001583	missense	53405	exon1			CCTGGGTTGATGA	AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"""Ion channels / Chloride channels : Intracellular"""	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.340A>G	6.37:g.46047640T>C	ENSP00000185206:p.Thr114Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_001114086	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Missense_Mutation	SNP	ENST00000185206.6	37	CCDS47438.1	83	0.038003663003663	15	0.03048780487804878	22	0.06077348066298342	0	0.0	46	0.06068601583113457	T	6.171	0.399710	0.11696	0.041908	0.045569	ENSG00000112782	ENST00000185206	T	0.18810	2.19	4.63	-9.26	0.00662	.	2.063700	0.02216	N	0.063585	T	0.01800	0.0057	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25152	-1.0140	10	0.02654	T	1	.	4.0922	0.09975	0.3095:0.4601:0.1041:0.1262	rs723580;rs52835530;rs61481276;rs723580	114	Q9NZA1	CLIC5_HUMAN	A	114	ENSP00000185206:T114A	ENSP00000185206:T114A	T	-	1	0	CLIC5	46155599	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.187000	0.03067	-2.855000	0.00329	-1.385000	0.01166	ACC	T|0.962;C|0.038	0.038	strong		0.517	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1		
ITGAD	3681	hgsc.bcm.edu	37	16	31418869	31418869	+	Silent	SNP	A	A	G	rs62001041	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31418869A>G	ENST00000389202.2	+	8	787	c.738A>G	c.(736-738)cgA>cgG	p.R246R	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	246	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ATGGGGCCCGAAAAAGTGCCA	0.478													a|||	229	0.0457268	0.0053	0.0317	5008	,	,		19588	0.0298		0.0467	False		,,,				2504	0.1258				p.R246R		Atlas-SNP	.											.	ITGAD	154	.	0			c.A738G						PASS	.	A		61,4333	53.6+/-89.4	0,61,2136	91.0	84.0	86.0		738	-10.6	0.0	16	dbSNP_129	86	519,8081	143.0+/-199.1	16,487,3797	no	coding-synonymous	ITGAD	NM_005353.2		16,548,5933	GG,GA,AA		6.0349,1.3883,4.4636		246/1162	31418869	580,12414	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon8			GGCCCGAAAAAGT	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.738A>G	16.37:g.31418869A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			A|0.961;G|0.039	0.039	strong		0.478	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
HCN2	610	hgsc.bcm.edu	37	19	603769	603769	+	Silent	SNP	T	T	C	rs55659726	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:603769T>C	ENST00000251287.2	+	2	911	c.858T>C	c.(856-858)taT>taC	p.Y286Y		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	286					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)		AGAAGAAGTATCTGCGCACGT	0.542													c|||	1195	0.238618	0.2368	0.0908	5008	,	,		14856	0.2897		0.0984	False		,,,				2504	0.4376				p.Y286Y	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.T858C						PASS	.	C		1121,3277		142,837,1220	192.0	153.0	166.0		858	2.0	1.0	19	dbSNP_129	166	902,7694		50,802,3446	no	coding-synonymous	HCN2	NM_001194.3		192,1639,4666	CC,CT,TT		10.4933,25.4889,15.5687		286/890	603769	2023,10971	2199	4298	6497	SO:0001819	synonymous_variant	610	exon2			GAAGTATCTGCGC	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.858T>C	19.37:g.603769T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			T|0.835;C|0.165	0.165	strong		0.542	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
GEMIN4	50628	hgsc.bcm.edu	37	17	649547	649547	+	Missense_Mutation	SNP	G	G	C	rs910925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:649547G>C	ENST00000319004.5	-	2	1854	c.1736C>G	c.(1735-1737)gCc>gGc	p.A579G	GEMIN4_ENST00000576778.1_Missense_Mutation_p.A568G	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	579			A -> G (in dbSNP:rs910925).		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)		GAGAATCTGGGCCAGGAACTT	0.567													G|||	3556	0.710064	0.8858	0.6412	5008	,	,		18371	0.7232		0.5885	False		,,,				2504	0.6329				p.A579G		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C1736G						PASS	.	G	GLY/ALA	3341,673		1395,551,61	73.0	81.0	78.0		1736	5.8	1.0	17	dbSNP_86	78	4705,3659		1333,2039,810	yes	missense	GEMIN4	NM_015721.2	60	2728,2590,871	CC,CG,GG		43.747,16.7663,34.9976	probably-damaging	579/1059	649547	8046,4332	2007	4182	6189	SO:0001583	missense	50628	exon2			ATCTGGGCCAGGA	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.1736C>G	17.37:g.649547G>C	ENSP00000321706:p.Ala579Gly	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	1507	0.690018315018315	431	0.8760162601626016	221	0.6104972375690608	407	0.7115384615384616	448	0.5910290237467019	G	23.7	4.442024	0.83993	0.832337	0.56253	ENSG00000179409	ENST00000319004	T	0.16324	2.35	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.68952	2.095	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	T	0.06972	-1.0797	9	0.62326	D	0.03	-12.4698	19.1348	0.93422	0.0:0.0:1.0:0.0	rs910925;rs17856597;rs52802872;rs57202710;rs910925	579	P57678	GEMI4_HUMAN	G	579	ENSP00000321706:A579G	ENSP00000321706:A579G	A	-	2	0	GEMIN4	596297	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	9.633000	0.98432	2.779000	0.95612	0.591000	0.81541	GCC	G|0.346;C|0.654	0.654	strong		0.567	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
MARVELD3	91862	hgsc.bcm.edu	37	16	71660404	71660404	+	Missense_Mutation	SNP	G	G	A	rs61753635	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71660404G>A	ENST00000268485.3	+	1	316	c.272G>A	c.(271-273)cGg>cAg	p.R91Q	MARVELD3_ENST00000567501.1_5'Flank|RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000299952.4_Missense_Mutation_p.R91Q|MARVELD3_ENST00000567566.1_Missense_Mutation_p.R91Q|MARVELD3_ENST00000565261.1_Missense_Mutation_p.R91Q	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	91	Arg-rich.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				GGCCCCCGCCGGGACACACAC	0.701													G|||	958	0.191294	0.2262	0.1758	5008	,	,		12826	0.0665		0.3002	False		,,,				2504	0.1718				p.R91Q		Atlas-SNP	.											.	MARVELD3	63	.	0			c.G272A						PASS	.	G	GLN/ARG,GLN/ARG	874,3032		107,660,1186	14.0	24.0	21.0		272,272	-5.0	0.0	16	dbSNP_129	21	1976,5686		265,1446,2120	yes	missense,missense	MARVELD3	NM_052858.3,NM_001017967.2	43,43	372,2106,3306	AA,AG,GG		25.7896,22.3758,24.6369	benign,benign	91/402,91/411	71660404	2850,8718	1953	3831	5784	SO:0001583	missense	91862	exon1			CCCGCCGGGACAC	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.272G>A	16.37:g.71660404G>A	ENSP00000268485:p.Arg91Gln	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_001017967	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	37	CCDS10904.1	462	0.21153846153846154	103	0.20934959349593496	77	0.212707182320442	43	0.07517482517482517	239	0.3153034300791557	G	14.45	2.538478	0.45176	0.223758	0.257896	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.40225	1.04;1.04	3.96	-4.97	0.03029	.	1.273640	0.05995	N	0.646785	T	0.00012	0.0000	N	0.00926	-1.1	0.35332	P	0.214275	B;B;B	0.12630	0.002;0.002;0.006	B;B;B	0.04013	0.001;0.001;0.001	T	0.26538	-1.0100	9	0.02654	T	1	-32.2938	0.9839	0.01442	0.2747:0.2817:0.2887:0.1549	rs61753635	91;91;114	Q96A59-2;Q96A59;Q9BSH2	.;MALD3_HUMAN;.	Q	91	ENSP00000268485:R91Q;ENSP00000299952:R91Q	ENSP00000268485:R91Q	R	+	2	0	MARVELD3	70217905	0.000000	0.05858	0.028000	0.17463	0.153000	0.21895	-1.014000	0.03641	-0.568000	0.06038	-0.516000	0.04426	CGG	G|0.784;A|0.216	0.216	strong		0.701	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858	
B4GALNT3	283358	hgsc.bcm.edu	37	12	670595	670595	+	Missense_Mutation	SNP	G	G	A	rs36078145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:670595G>A	ENST00000266383.5	+	20	2988	c.2975G>A	c.(2974-2976)cGt>cAt	p.R992H		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	992			R -> H (in dbSNP:rs36078145).		metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			ATGTGGAGCCGTCGCCAGATG	0.622													G|||	135	0.0269569	0.0015	0.0461	5008	,	,		19895	0.001		0.0527	False		,,,				2504	0.0481				p.R992H		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G2975A						PASS	.	G	HIS/ARG	49,4357	49.6+/-84.7	0,49,2154	55.0	50.0	51.0		2975	4.7	1.0	12	dbSNP_126	51	531,8069	147.4+/-202.8	17,497,3786	yes	missense	B4GALNT3	NM_173593.3	29	17,546,5940	AA,AG,GG		6.1744,1.1121,4.4595	probably-damaging	992/999	670595	580,12426	2203	4300	6503	SO:0001583	missense	283358	exon20			GGAGCCGTCGCCA	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2975G>A	12.37:g.670595G>A	ENSP00000266383:p.Arg992His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	66	0.03021978021978022	1	0.0020325203252032522	24	0.06629834254143646	0	0.0	41	0.05408970976253298	G	11.84	1.757723	0.31137	0.011121	0.061744	ENSG00000139044	ENST00000266383	T	0.05513	3.43	4.72	4.72	0.59763	.	0.242135	0.40554	N	0.001070	T	0.00875	0.0029	M	0.72118	2.19	0.49582	D	0.999805	B	0.25390	0.125	B	0.30572	0.117	T	0.06463	-1.0825	10	0.54805	T	0.06	-19.2132	17.6819	0.88246	0.0:0.0:1.0:0.0	rs36078145	992	Q6L9W6	B4GN3_HUMAN	H	992	ENSP00000266383:R992H	ENSP00000266383:R992H	R	+	2	0	B4GALNT3	540856	1.000000	0.71417	0.998000	0.56505	0.112000	0.19704	3.892000	0.56235	2.164000	0.68074	0.313000	0.20887	CGT	G|0.958;A|0.042	0.042	strong		0.622	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629193	32629193	+	Missense_Mutation	SNP	C	C	T	rs1049163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32629193C>T	ENST00000399084.1	-	5	881	c.703G>A	c.(703-705)Gtt>Att	p.V235I	XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399079.3_Intron|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.V235I|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.V235I|HLA-DQB1_ENST00000460185.1_5'Flank			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	235			I -> V (in allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:09, allele DQB1*06:12 and allele DQB1*06:36).		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)"""	AAGCCTCCAACGCCACTCAGC	0.557									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1871	0.373602	0.2663	0.4625	5008	,	,		11748	0.4385		0.3748	False		,,,				2504	0.3875				p.V235I	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,NS,chondrosarcoma,0,1	HLA-DQB1	15	1	0			c.G703A						scavenged	.						37.0	32.0	34.0					6																	32629193		1981	3920	5901	SO:0001583	missense	3119	exon4	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CTCCAACGCCACT		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.703G>A	6.37:g.32629193C>T	ENSP00000382034:p.Val235Ile	Somatic	6	2	0.333333		WXS	Illumina HiSeq	Phase_I	31	29	0.935484	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	882	0.40384615384615385	131	0.266260162601626	185	0.511049723756906	275	0.4807692307692308	291	0.3839050131926121	.	0.003	-2.498580	0.00157	.	.	ENSG00000179344	ENST00000374943;ENST00000434651;ENST00000399084	T;T;T	0.00682	5.91;5.86;5.86	4.77	-4.85	0.03142	.	0.658102	0.14223	N	0.333270	T	0.00241	0.0007	.	.	.	0.80722	P	0.0	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.10450	0.005;0.005;0.002	T	0.31308	-0.9948	8	0.19147	T	0.46	.	13.7889	0.63128	0.0:0.2378:0.0:0.7622	rs1049163;rs3189251;rs9273648;rs9273649;rs17412879	200;235;235	A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.	I	235	ENSP00000364080:V235I;ENSP00000407332:V235I;ENSP00000382034:V235I	ENSP00000364080:V235I	V	-	1	0	HLA-DQB1	32737171	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.043000	0.01413	-1.147000	0.02851	-2.035000	0.00420	GTT	T|0.404;C|0.596	0.404	strong		0.557	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
ATXN7	6314	hgsc.bcm.edu	37	3	63981635	63981635	+	Silent	SNP	C	C	T	rs3733125	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:63981635C>T	ENST00000295900.6	+	12	2687	c.2137C>T	c.(2137-2139)Ctg>Ttg	p.L713L	ATXN7_ENST00000487717.1_Silent_p.L713L|ATXN7_ENST00000484332.1_Silent_p.L568L|ATXN7_ENST00000398590.3_Silent_p.L713L|ATXN7_ENST00000538065.1_Silent_p.L713L	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	713	Ser-rich.				cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.L713L(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		CAGTTCCCCACTGTTGGTTCA	0.498													C|||	453	0.0904553	0.0061	0.0548	5008	,	,		18163	0.1925		0.1272	False		,,,				2504	0.0869				p.L713L		Atlas-SNP	.											ATXN7,NS,carcinoma,0,1	ATXN7	126	1	1	Substitution - coding silent(1)	stomach(1)	c.C2137T						PASS	.	C	,,	82,4234		2,78,2078	59.0	71.0	67.0		2137,1702,2137	2.2	0.1	3	dbSNP_107	67	888,7670		42,804,3433	no	coding-synonymous,coding-synonymous,coding-synonymous	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	,,	44,882,5511	TT,TC,CC		10.3763,1.8999,7.5346	,,	713/893,568/748,713/946	63981635	970,11904	2158	4279	6437	SO:0001819	synonymous_variant	6314	exon12			TCCCCACTGTTGG	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2137C>T	3.37:g.63981635C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_000333	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Silent	SNP	ENST00000295900.6	37	CCDS43102.1																																																																																			C|0.892;T|0.108	0.108	strong		0.498	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33589107	33589107	+	IGR	SNP	G	G	A	rs36003887	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:33589107G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Silent_p.K1887K			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)			AGGCCCTTAAGGGCGTGCGCA	0.662													G|||	874	0.174521	0.1664	0.134	5008	,	,		19585	0.1071		0.1938	False		,,,				2504	0.2638				p.K1887K		Atlas-SNP	.											.	MYH7B	145	.	0			c.G5661A						PASS	.	G		698,3544		50,598,1473	31.0	39.0	37.0		5661	2.4	1.0	20	dbSNP_126	37	1637,6837		159,1319,2759	no	coding-synonymous	MYH7B	NM_020884.3		209,1917,4232	AA,AG,GG		19.3179,16.4545,18.3627		1887/1984	33589107	2335,10381	2121	4237	6358	SO:0001628	intergenic_variant	57644	exon42			CCTTAAGGGCGTG	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.33589107G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			G|0.819;A|0.181	0.181	strong		0.662	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
STAB1	23166	hgsc.bcm.edu	37	3	52548818	52548818	+	Silent	SNP	C	C	T	rs740903	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:52548818C>T	ENST00000321725.6	+	35	3856	c.3780C>T	c.(3778-3780)tgC>tgT	p.C1260C		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1260					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CAAGTCGCTGCCTGCATAGCC	0.667													C|||	821	0.163938	0.0461	0.1412	5008	,	,		17171	0.2331		0.0934	False		,,,				2504	0.3405				p.C1260C		Atlas-SNP	.											.	STAB1	178	.	0			c.C3780T						PASS	.	C		298,4108	158.5+/-191.2	11,276,1916	42.0	46.0	45.0		3780	2.5	1.0	3	dbSNP_86	45	975,7625	210.1+/-251.1	53,869,3378	no	coding-synonymous	STAB1	NM_015136.2		64,1145,5294	TT,TC,CC		11.3372,6.7635,9.7878		1260/2571	52548818	1273,11733	2203	4300	6503	SO:0001819	synonymous_variant	23166	exon35			TCGCTGCCTGCAT	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.3780C>T	3.37:g.52548818C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			C|0.890;T|0.110	0.110	strong		0.667	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
JAM2	58494	hgsc.bcm.edu	37	21	27056250	27056250	+	Silent	SNP	A	A	G	rs8133602	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:27056250A>G	ENST00000480456.1	+	2	673	c.123A>G	c.(121-123)gtA>gtG	p.V41V	JAM2_ENST00000312957.5_Silent_p.V41V|JAM2_ENST00000400532.1_Silent_p.V41V|JAM2_ENST00000425221.2_Silent_p.V41V	NM_001270407.1|NM_021219.3	NP_001257336.1|NP_067042.1	P57087	JAM2_HUMAN	junctional adhesion molecule 2	41	Ig-like V-type.				blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.V41V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|stomach(1)|urinary_tract(1)	19						TCACAGCAGTAGAGTACCAAG	0.348													A|||	646	0.128994	0.0287	0.1167	5008	,	,		19226	0.3264		0.0775	False		,,,				2504	0.1227				p.V41V		Atlas-SNP	.											JAM2,NS,carcinoma,0,1	JAM2	33	1	1	Substitution - coding silent(1)	stomach(1)	c.A123G						PASS	.	A		151,3625		2,147,1739	74.0	72.0	73.0		123	-0.0	1.0	21	dbSNP_116	73	667,7573		23,621,3476	no	coding-synonymous	JAM2	NM_021219.2		25,768,5215	GG,GA,AA		8.0947,3.9989,6.8076		41/299	27056250	818,11198	1888	4120	6008	SO:0001819	synonymous_variant	58494	exon2			AGCAGTAGAGTAC	AF255910	CCDS42911.1, CCDS58787.1, CCDS58788.1	21q21.2	2013-01-11			ENSG00000154721	ENSG00000154721		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	14686	protein-coding gene	gene with protein product		606870		C21orf43		10779521, 10945976	Standard	NM_021219		Approved	VE-JAM, JAM-B, JAMB, CD322	uc031rvc.1	P57087	OTTHUMG00000078441	ENST00000480456.1:c.123A>G	21.37:g.27056250A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_021219	B2R6T9|B4DGT9|Q6UXG6|Q6YNC1	Silent	SNP	ENST00000480456.1	37	CCDS42911.1																																																																																			A|0.877;G|0.123	0.123	strong		0.348	JAM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171347.1		
PTPRB	5787	hgsc.bcm.edu	37	12	70953277	70953277	+	Silent	SNP	T	T	C	rs2303963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:70953277T>C	ENST00000261266.5	-	16	3935	c.3906A>G	c.(3904-3906)gcA>gcG	p.A1302A	PTPRB_ENST00000538708.1_Silent_p.A1212A|PTPRB_ENST00000451516.2_Silent_p.A1212A|PTPRB_ENST00000550857.1_Silent_p.A1212A|PTPRB_ENST00000551525.1_Silent_p.A1519A|PTPRB_ENST00000550358.1_Silent_p.A1432A|PTPRB_ENST00000334414.6_Silent_p.A1520A	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1302	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			AGACAGTAAGTGCATCTCTGG	0.488													T|||	1006	0.200879	0.1853	0.1499	5008	,	,		19030	0.1369		0.2147	False		,,,				2504	0.3098				p.A1520A		Atlas-SNP	.											.	PTPRB	676	.	0			c.A4560G						PASS	.	T	,,,	701,3281		62,577,1352	265.0	258.0	260.0		4560,3636,3636,3906	-12.2	0.1	12	dbSNP_100	260	1835,6513		217,1401,2556	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	,,,	279,1978,3908	CC,CT,TT		21.9813,17.6042,20.5677	,,,	1520/2216,1212/1908,1212/1908,1302/1998	70953277	2536,9794	1991	4174	6165	SO:0001819	synonymous_variant	5787	exon18			AGTAAGTGCATCT	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.3906A>G	12.37:g.70953277T>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	190	187	0.984211	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																			T|0.804;C|0.196	0.196	strong		0.488	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
SWT1	54823	hgsc.bcm.edu	37	1	185171869	185171869	+	Missense_Mutation	SNP	A	A	G	rs6698109	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:185171869A>G	ENST00000367500.4	+	11	1772	c.1607A>G	c.(1606-1608)cAc>cGc	p.H536R	SWT1_ENST00000367501.3_Missense_Mutation_p.H536R	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	536			H -> R (in dbSNP:rs6698109). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						GAGTTATTACACTTATCTCTG	0.353													A|||	1380	0.275559	0.2179	0.2464	5008	,	,		12733	0.1964		0.341	False		,,,				2504	0.3885				p.H536R		Atlas-SNP	.											.	SWT1	88	.	0			c.A1607G						PASS	.	A	ARG/HIS,ARG/HIS	1090,3316	393.3+/-328.8	138,814,1251	88.0	89.0	89.0		1607,1607	-0.0	0.0	1	dbSNP_116	89	3038,5562	466.1+/-366.7	551,1936,1813	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	29,29	689,2750,3064	GG,GA,AA		35.3256,24.739,31.7392	benign,benign	536/901,536/901	185171869	4128,8878	2203	4300	6503	SO:0001583	missense	54823	exon11			TATTACACTTATC	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1607A>G	1.37:g.185171869A>G	ENSP00000356470:p.His536Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	615	0.2815934065934066	130	0.26422764227642276	87	0.24033149171270718	140	0.24475524475524477	258	0.3403693931398417	A	7.659	0.684572	0.14973	0.24739	0.353256	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.16457	2.34;2.34	5.49	-0.0357	0.13891	.	0.525254	0.22752	N	0.056064	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49194	-0.8965	9	0.23302	T	0.38	.	4.8888	0.13717	0.5657:0.1491:0.2852:0.0	rs6698109;rs17856891;rs52826833;rs61051695;rs6698109	536	Q5T5J6	SWT1_HUMAN	R	536	ENSP00000356471:H536R;ENSP00000356470:H536R	ENSP00000356470:H536R	H	+	2	0	SWT1	183438492	0.844000	0.29557	0.003000	0.11579	0.720000	0.41350	0.715000	0.25822	-0.187000	0.10516	-0.274000	0.10170	CAC	A|0.699;G|0.301	0.301	strong		0.353	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
TTC16	158248	hgsc.bcm.edu	37	9	130493513	130493513	+	Silent	SNP	A	A	G	rs482095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130493513A>G	ENST00000373289.3	+	14	2531	c.2451A>G	c.(2449-2451)aaA>aaG	p.K817K	TTC16_ENST00000489226.1_3'UTR|TOR2A_ENST00000472723.1_5'Flank	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	817										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GCCTCAGCAAAACTGAGTATG	0.597													G|||	3106	0.620208	0.7859	0.6081	5008	,	,		20572	0.369		0.6173	False		,,,				2504	0.6667				p.K817K		Atlas-SNP	.											.	TTC16	55	.	0			c.A2451G						PASS	.	G		3267,1137	395.4+/-329.6	1217,833,152	40.0	43.0	42.0		2451	-9.1	0.0	9	dbSNP_83	42	5015,3585	515.0+/-378.5	1463,2089,748	no	coding-synonymous	TTC16	NM_144965.1		2680,2922,900	GG,GA,AA		41.686,25.8174,36.3119		817/874	130493513	8282,4722	2202	4300	6502	SO:0001819	synonymous_variant	158248	exon14			CAGCAAAACTGAG	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.2451A>G	9.37:g.130493513A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	186	85	0.456989	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Silent	SNP	ENST00000373289.3	37	CCDS6875.1																																																																																			A|0.372;G|0.628	0.628	strong		0.597	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
SLC22A14	9389	hgsc.bcm.edu	37	3	38357961	38357961	+	Missense_Mutation	SNP	C	C	G	rs240033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:38357961C>G	ENST00000273173.4	+	9	1770	c.1679C>G	c.(1678-1680)cCg>cGg	p.P560R	SLC22A14_ENST00000448498.1_Missense_Mutation_p.P560R	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	560			P -> R (in dbSNP:rs240033). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		TCCCTGCTGCCGGAAACGCGA	0.612													C|||	1282	0.25599	0.2504	0.2767	5008	,	,		19883	0.2599		0.2535	False		,,,				2504	0.2474				p.P560R		Atlas-SNP	.											.	SLC22A14	64	.	0			c.C1679G						PASS	.	C	ARG/PRO	1180,3226	415.0+/-337.0	147,886,1170	99.0	78.0	85.0		1679	2.4	0.0	3	dbSNP_79	85	2436,6164	401.1+/-347.0	351,1734,2215	yes	missense	SLC22A14	NM_004803.3	103	498,2620,3385	GG,GC,CC		28.3256,26.7817,27.8026	probably-damaging	560/595	38357961	3616,9390	2203	4300	6503	SO:0001583	missense	9389	exon9			TGCTGCCGGAAAC	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"""Solute carriers"""	8495	protein-coding gene	gene with protein product		604048	"""organic cationic transporter-like 4"", ""solute carrier family 22 (organic cation transporter), member 14"""	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.1679C>G	3.37:g.38357961C>G	ENSP00000273173:p.Pro560Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	131	73	0.557252	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	574	0.26282051282051283	115	0.23373983739837398	112	0.30939226519337015	158	0.2762237762237762	189	0.24934036939313983	C	12.47	1.948947	0.34377	0.267817	0.283256	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.79940	-1.32;-1.32	4.2	2.39	0.29439	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.88241	2.94	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.01159	-1.1433	9	0.62326	D	0.03	.	6.0188	0.19618	0.0:0.7052:0.1913:0.1035	rs240033;rs1618758;rs17732434;rs59679116;rs240033	560	Q9Y267	S22AE_HUMAN	R	560;545;560	ENSP00000396283:P560R;ENSP00000273173:P560R	ENSP00000273173:P560R	P	+	2	0	SLC22A14	38332965	0.995000	0.38212	0.006000	0.13384	0.000000	0.00434	2.693000	0.47027	0.699000	0.31761	-0.892000	0.02923	CCG	C|0.724;G|0.276	0.276	strong		0.612	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
CNGB1	1258	hgsc.bcm.edu	37	16	58001086	58001086	+	Silent	SNP	C	C	T	rs61997250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:58001086C>T	ENST00000251102.8	-	2	165	c.105G>A	c.(103-105)gcG>gcA	p.A35A	CNGB1_ENST00000564448.1_Silent_p.A35A|CNGB1_ENST00000311183.4_Silent_p.A35A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	35	Glu-rich.				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						GTTCCACCTCCGCCTCCATCT	0.647													C|||	41	0.0081869	0.0023	0.0072	5008	,	,		17304	0.0		0.0258	False		,,,				2504	0.0072				p.A35A	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G105A						PASS	.	C	,	32,3990		0,32,1979	96.0	101.0	99.0		105,105	-8.9	0.0	16	dbSNP_129	99	242,8090		4,234,3928	no	coding-synonymous,coding-synonymous	CNGB1	NM_001135639.1,NM_001297.4	,	4,266,5907	TT,TC,CC		2.9045,0.7956,2.2179	,	35/300,35/1252	58001086	274,12080	2011	4166	6177	SO:0001819	synonymous_variant	1258	exon2			CACCTCCGCCTCC	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.105G>A	16.37:g.58001086C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
MKX	283078	hgsc.bcm.edu	37	10	27964470	27964470	+	Silent	SNP	G	G	A	rs2253230	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:27964470G>A	ENST00000375790.5	-	6	1284	c.852C>T	c.(850-852)aaC>aaT	p.N284N	MKX_ENST00000419761.1_Silent_p.N284N			Q8IYA7	MKX_HUMAN	mohawk homeobox	284					collagen fibril organization (GO:0030199)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|positive regulation of collagen biosynthetic process (GO:0032967)|tendon cell differentiation (GO:0035990)|tendon sheath development (GO:0002932)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16						TATTGGATCCGTTTTCCAGAG	0.378													G|||	1428	0.285144	0.295	0.353	5008	,	,		19342	0.121		0.338	False		,,,				2504	0.3384				p.N284N		Atlas-SNP	.											.	MKX	43	.	0			c.C852T						PASS	.	G	,	1379,3027	457.5+/-351.6	235,909,1059	79.0	67.0	71.0		852,852	-2.1	1.0	10	dbSNP_100	71	2853,5747	447.7+/-361.6	469,1915,1916	no	coding-synonymous,coding-synonymous	MKX	NM_001242702.1,NM_173576.2	,	704,2824,2975	AA,AG,GG		33.1744,31.2982,32.5388	,	284/353,284/353	27964470	4232,8774	2203	4300	6503	SO:0001819	synonymous_variant	283078	exon6			GGATCCGTTTTCC	BC036207	CCDS7156.1	10p12.1	2011-06-20	2006-03-31	2006-03-31	ENSG00000150051	ENSG00000150051		"""Homeoboxes / TALE class"""	23729	protein-coding gene	gene with protein product		601332	"""chromosome 10 open reading frame 48"", ""iroquois homeobox protein-like 1"""	C10orf48, IRXL1		16408284	Standard	NM_173576		Approved	MGC39616	uc001itx.4	Q8IYA7	OTTHUMG00000017862	ENST00000375790.5:c.852C>T	10.37:g.27964470G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_001242702	B3KWM5	Silent	SNP	ENST00000375790.5	37	CCDS7156.1																																																																																			G|0.693;A|0.307	0.307	strong		0.378	MKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047332.3	NM_173576	
SNX31	169166	hgsc.bcm.edu	37	8	101608919	101608919	+	Missense_Mutation	SNP	T	T	C	rs2248609	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:101608919T>C	ENST00000311812.2	-	10	1076	c.926A>G	c.(925-927)cAg>cGg	p.Q309R	SNX31_ENST00000519521.1_5'UTR|SNX31_ENST00000428383.2_Missense_Mutation_p.Q210R	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	108	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	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	
ZFPM2	23414	hgsc.bcm.edu	37	8	106814656	106814656	+	Missense_Mutation	SNP	G	G	C	rs2920048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:106814656G>C	ENST00000407775.2	+	8	2596	c.2346G>C	c.(2344-2346)gaG>gaC	p.E782D	ZFPM2_ENST00000517361.1_Missense_Mutation_p.E650D|ZFPM2_ENST00000378472.4_Missense_Mutation_p.E513D|RP11-152P17.2_ENST00000521622.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.E650D|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000520594.1_RNA|ZFPM2_ENST00000522296.1_3'UTR	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	782			E -> D (in dbSNP:rs2920048). {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)			GGCTAGGAGAGTGCTACCACC	0.448													G|||	288	0.057508	0.0091	0.0893	5008	,	,		20934	0.0		0.1412	False		,,,				2504	0.0736				p.E782D		Atlas-SNP	.											ZFPM2,trunk,malignant_melanoma,+2,1	ZFPM2	219	1	0			c.G2346C						PASS	.	G	ASP/GLU	114,3722		4,106,1808	69.0	68.0	68.0		2346	-7.1	0.3	8	dbSNP_101	68	1135,7121		78,979,3071	yes	missense	ZFPM2	NM_012082.3	45	82,1085,4879	CC,CG,GG		13.7476,2.9718,10.3291	benign	782/1152	106814656	1249,10843	1918	4128	6046	SO:0001583	missense	23414	exon8			AGGAGAGTGCTAC	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.2346G>C	8.37:g.106814656G>C	ENSP00000384179:p.Glu782Asp	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	157	0.07188644688644688	8	0.016260162601626018	49	0.13535911602209943	0	0.0	100	0.13192612137203166	G	3.442	-0.113823	0.06881	0.029718	0.137476	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.18016	2.24;2.71;2.71;3.92	5.72	-7.08	0.01558	.	0.098912	0.64402	N	0.000002	T	0.00039	0.0001	N	0.08118	0	0.41228	P	0.013445999999999958	B	0.12013	0.005	B	0.09377	0.004	T	0.36237	-0.9756	9	0.12430	T	0.62	.	8.9578	0.35829	0.4583:0.3463:0.1954:0.0	rs2920048;rs17314327;rs52825994;rs2920048	782	Q8WW38	FOG2_HUMAN	D	782;650;650;513	ENSP00000384179:E782D;ENSP00000430757:E650D;ENSP00000428720:E650D;ENSP00000367733:E513D	ENSP00000367733:E513D	E	+	3	2	ZFPM2	106883832	0.004000	0.15560	0.265000	0.24526	0.993000	0.82548	-1.006000	0.03671	-1.181000	0.02730	0.561000	0.74099	GAG	G|0.927;C|0.073	0.073	strong		0.448	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
ZHX2	22882	hgsc.bcm.edu	37	8	123965193	123965193	+	Silent	SNP	C	C	T	rs111726812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:123965193C>T	ENST00000314393.4	+	3	2278	c.1443C>T	c.(1441-1443)agC>agT	p.S481S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	481	Required for interaction with NFYA.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TTGCCAGGAGCGAGATCAAGA	0.567													C|||	116	0.0231629	0.0439	0.0317	5008	,	,		18163	0.0		0.0298	False		,,,				2504	0.0061				p.S481S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											ZHX2,caecum,carcinoma,0,1	ZHX2	106	1	0			c.C1443T						scavenged	.	C		179,4227	116.7+/-154.6	5,169,2029	88.0	82.0	84.0		1443	-8.1	0.7	8	dbSNP_132	84	278,8322	105.4+/-166.3	6,266,4028	no	coding-synonymous	ZHX2	NM_014943.3		11,435,6057	TT,TC,CC		3.2326,4.0626,3.5138		481/838	123965193	457,12549	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CAGGAGCGAGATC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1443C>T	8.37:g.123965193C>T		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			C|0.965;T|0.035	0.035	strong		0.567	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
PSMC5	5705	hgsc.bcm.edu	37	17	61908271	61908271	+	Silent	SNP	C	C	T	rs968719	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:61908271C>T	ENST00000310144.6	+	7	963	c.655C>T	c.(655-657)Ctg>Ttg	p.L219L	PSMC5_ENST00000375812.4_Silent_p.L211L|PSMC5_ENST00000580864.1_Silent_p.L211L|PSMC5_ENST00000581882.1_Silent_p.L211L|FTSJ3_ENST00000580295.1_5'Flank	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	219	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TGGCTCTGAACTGGTACAGAA	0.507													T|||	3669	0.732628	0.9788	0.6816	5008	,	,		19973	0.5556		0.5984	False		,,,				2504	0.7566				p.L219L		Atlas-SNP	.											.	PSMC5	41	.	0			c.C655T						PASS	.	T	,	4014,392	196.0+/-220.5	1829,356,18	90.0	88.0	89.0		631,655	-3.3	0.5	17	dbSNP_86	89	5215,3385	501.6+/-375.5	1599,2017,684	no	coding-synonymous,coding-synonymous	PSMC5	NM_001199163.1,NM_002805.5	,	3428,2373,702	TT,TC,CC		39.3605,8.897,29.0404	,	211/399,219/407	61908271	9229,3777	2203	4300	6503	SO:0001819	synonymous_variant	5705	exon7			TCTGAACTGGTAC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.655C>T	17.37:g.61908271C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	37	CCDS11645.1																																																																																			T|0.696;G|0.002	0.696	strong		0.507	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
WFDC8	90199	hgsc.bcm.edu	37	20	44184498	44184498	+	Missense_Mutation	SNP	A	A	G	rs2272955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:44184498A>G	ENST00000357199.4	-	4	365	c.287T>C	c.(286-288)aTg>aCg	p.M96T	WFDC8_ENST00000289953.2_Missense_Mutation_p.M96T	NM_181510.2	NP_852611.2	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8	96	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.		M -> T (in dbSNP:rs2272955).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.M96T(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|stomach(1)|upper_aerodigestive_tract(1)	15		Myeloproliferative disorder(115;0.0122)				CACAGGTAGCATGCAGGGTTC	0.458													A|||	518	0.103435	0.1694	0.0634	5008	,	,		21266	0.1716		0.0567	False		,,,				2504	0.0204				p.M96T		Atlas-SNP	.											WFDC8,NS,carcinoma,0,1	WFDC8	28	1	1	Substitution - Missense(1)	stomach(1)	c.T287C						PASS	.	A	THR/MET,THR/MET	715,3691	295.3+/-283.6	60,595,1548	87.0	80.0	82.0		287,287	-3.8	0.0	20	dbSNP_100	82	507,8093	144.7+/-200.5	12,483,3805	yes	missense,missense	WFDC8	NM_130896.2,NM_181510.2	81,81	72,1078,5353	GG,GA,AA		5.8953,16.2279,9.3957	benign,benign	96/242,96/242	44184498	1222,11784	2203	4300	6503	SO:0001583	missense	90199	exon4			GGTAGCATGCAGG	AL031663	CCDS13361.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000158901	ENSG00000158901		"""WAP four-disulfide core domain containing"""	16163	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 170"""	C20orf170		12206714	Standard	NM_130896		Approved	dJ461P17.1, WAP8	uc002xow.3	Q8IUA0	OTTHUMG00000046342	ENST00000357199.4:c.287T>C	20.37:g.44184498A>G	ENSP00000361735:p.Met96Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_181510	E1P623|Q5TDV2|Q96A34	Missense_Mutation	SNP	ENST00000357199.4	37	CCDS13361.1	266	0.12179487179487179	92	0.18699186991869918	27	0.07458563535911603	105	0.18356643356643357	42	0.055408970976253295	A	0.030	-1.343661	0.01277	0.162279	0.058953	ENSG00000158901	ENST00000357199;ENST00000289953	T;T	0.56275	0.47;0.47	4.26	-3.81	0.04294	Proteinase inhibitor I2, Kunitz metazoa (6);	1.987250	0.02150	N	0.057931	T	0.00039	0.0001	N	0.16833	0.445	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.12811	-1.0533	9	0.06891	T	0.86	.	10.2379	0.43294	0.5409:0.0:0.4591:0.0	rs2272955;rs52829198;rs59271448;rs2272955	96	Q8IUA0	WFDC8_HUMAN	T	96	ENSP00000361735:M96T;ENSP00000289953:M96T	ENSP00000289953:M96T	M	-	2	0	WFDC8	43617912	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.262000	0.08682	-0.787000	0.04510	-0.755000	0.03482	ATG	A|0.897;G|0.103	0.103	strong		0.458	WFDC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106958.1		
POM121L12	285877	hgsc.bcm.edu	37	7	53103382	53103382	+	Silent	SNP	G	G	T	rs72598685	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	48	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	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	
OR51D1	390038	hgsc.bcm.edu	37	11	4661450	4661450	+	Missense_Mutation	SNP	C	C	T	rs529314887		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4661450C>T	ENST00000357605.2	+	1	506	c.430C>T	c.(430-432)Cgc>Tgc	p.R144C		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCACCCATTGCGCCATGCTTC	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		22933	0.001		0.0	False		,,,				2504	0.0				p.R144C		Atlas-SNP	.											OR51D1,NS,carcinoma,-1,2	OR51D1	49	2	0			c.C430T						scavenged	.						156.0	132.0	141.0					11																	4661450		2201	4298	6499	SO:0001583	missense	390038	exon1			CCATTGCGCCATG	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"""GPCR / Class A : Olfactory receptors"""	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.430C>T	11.37:g.4661450C>T	ENSP00000350222:p.Arg144Cys	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	162	2	0.0123457	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	37	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	C	12.48	1.950944	0.34471	.	.	ENSG00000197428	ENST00000357605	T	0.00922	5.54	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.319059	0.22876	N	0.054566	T	0.04634	0.0126	M	0.87617	2.895	0.46298	D	0.998973	D	0.71674	0.998	P	0.57244	0.816	T	0.02275	-1.1184	10	0.87932	D	0	.	11.3936	0.49827	0.181:0.819:0.0:0.0	.	144	Q8NGF3	O51D1_HUMAN	C	144	ENSP00000350222:R144C	ENSP00000350222:R144C	R	+	1	0	OR51D1	4618026	0.003000	0.15002	0.066000	0.19879	0.012000	0.07955	-0.069000	0.11542	2.433000	0.82419	0.563000	0.77884	CGC	.	.	none		0.552	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751	
ATP2B3	492	hgsc.bcm.edu	37	X	152823728	152823728	+	Silent	SNP	G	G	C	rs2269415	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:152823728G>C	ENST00000349466.2	+	16	2918	c.2592G>C	c.(2590-2592)gtG>gtC	p.V864V	ATP2B3_ENST00000370186.1_Silent_p.V850V|ATP2B3_ENST00000370181.2_Silent_p.V850V|ATP2B3_ENST00000460549.1_3'UTR|ATP2B3_ENST00000263519.4_Silent_p.V864V|ATP2B3_ENST00000393842.1_Silent_p.V850V|ATP2B3_ENST00000359149.3_Silent_p.V864V			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	864					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGTGGCTGTGATCGTGGCCT	0.572													G|||	1789	0.473907	0.0719	0.4914	3775	,	,		12276	0.4841		0.3867	False		,,,				2504	0.4867				p.V864V		Atlas-SNP	.											.	ATP2B3	552	.	0			c.G2592C						PASS	.	G	,	555,3280		39,406,71,1187,500	209.0	144.0	166.0		2592,2592	4.8	1.0	X	dbSNP_100	166	3558,3170		708,1174,968,546,904	no	coding-synonymous,coding-synonymous	ATP2B3	NM_001001344.2,NM_021949.3	,	747,1580,1039,1733,1404	CC,CG,C,GG,G		47.1165,14.472,38.9378	,	864/1221,864/1174	152823728	4113,6450	2203	4300	6503	SO:0001819	synonymous_variant	492	exon15			GGCTGTGATCGTG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2592G>C	X.37:g.152823728G>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																			0|0.002;C|0.416	0.416	strong		0.572	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
SPEF2	79925	hgsc.bcm.edu	37	5	35692775	35692775	+	Missense_Mutation	SNP	T	T	A	rs7710284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:35692775T>A	ENST00000356031.3	+	12	2002	c.1848T>A	c.(1846-1848)aaT>aaA	p.N616K	SPEF2_ENST00000440995.2_Missense_Mutation_p.N616K|CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000509059.1_Missense_Mutation_p.N616K	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	216	0	0		WXS	Illumina HiSeq	Phase_I	236	115	0.487288	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	
TEAD3	7005	hgsc.bcm.edu	37	6	35446225	35446225	+	Missense_Mutation	SNP	A	A	G	rs144697750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35446225A>G	ENST00000402886.3	-	4	439	c.286T>C	c.(286-288)Tcc>Ccc	p.S96P	TEAD3_ENST00000338863.7_Missense_Mutation_p.S156P			Q99594	TEAD3_HUMAN	TEA domain family member 3	156					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						GAGGAAGTGGAGAAGACGGCC	0.612													a|||	16	0.00319489	0.0008	0.0072	5008	,	,		17840	0.0		0.008	False		,,,				2504	0.002				p.S156P		Atlas-SNP	.											.	TEAD3	52	.	0			c.T466C						PASS	.		PRO/SER	7,4137		0,7,2065	54.0	65.0	62.0		466	3.3	1.0	6	dbSNP_134	62	49,8365		0,49,4158	yes	missense	TEAD3	NM_003214.3	74	0,56,6223	GG,GA,AA		0.5824,0.1689,0.4459	benign	156/436	35446225	56,12502	2072	4207	6279	SO:0001583	missense	7005	exon6			AAGTGGAGAAGAC	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	ENST00000402886.3:c.286T>C	6.37:g.35446225A>G	ENSP00000384577:p.Ser96Pro	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_003214	O95910|Q5BJG7|Q8N6Y4	Missense_Mutation	SNP	ENST00000402886.3	37		8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	a	3.061	-0.193152	0.06259	0.001689	0.005824	ENSG00000007866	ENST00000338863;ENST00000402886;ENST00000373905;ENST00000433586	T;T;T	0.56275	0.48;0.47;0.91	4.46	3.26	0.37387	.	0.213980	0.41097	N	0.000949	T	0.19485	0.0468	N	0.17082	0.46	0.35183	D	0.77268	B;B;P	0.41748	0.002;0.0;0.761	B;B;P	0.45377	0.011;0.001;0.478	T	0.03473	-1.1033	10	0.09843	T	0.71	-16.0678	9.8736	0.41189	0.847:0.0:0.0:0.153	.	96;172;156	B5MCM0;Q7Z6V0;Q99594	.;.;TEAD3_HUMAN	P	156;96;172;67	ENSP00000345772:S156P;ENSP00000384577:S96P;ENSP00000416400:S67P	ENSP00000345772:S156P	S	-	1	0	TEAD3	35554203	1.000000	0.71417	0.997000	0.53966	0.915000	0.54546	2.068000	0.41471	0.826000	0.34661	0.444000	0.29173	TCC	A|0.995;G|0.005	0.005	strong		0.612	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2		
MX1	4599	hgsc.bcm.edu	37	21	42824661	42824661	+	Silent	SNP	A	A	G	rs1050008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:42824661A>G	ENST00000398600.2	+	18	2648	c.1623A>G	c.(1621-1623)gcA>gcG	p.A541A	MX1_ENST00000455164.2_Silent_p.A541A|MX1_ENST00000288383.6_Silent_p.A518A|MX1_ENST00000398598.3_Silent_p.A541A	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	541	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)				ACAGGGGTGCATTGCAGAAGG	0.498													G|||	1311	0.261781	0.2368	0.1873	5008	,	,		18703	0.4474		0.1402	False		,,,				2504	0.2822				p.A541A		Atlas-SNP	.											.	MX1	58	.	0			c.A1623G						PASS	.	G	,,	1040,3366	726.9+/-409.8	119,802,1282	135.0	145.0	141.0		1623,1623,1623	-9.5	0.0	21	dbSNP_86	141	1120,7480	767.5+/-407.6	78,964,3258	no	coding-synonymous,coding-synonymous,coding-synonymous	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	,,	197,1766,4540	GG,GA,AA		13.0233,23.6042,16.6077	,,	541/663,541/663,541/663	42824661	2160,10846	2203	4300	6503	SO:0001819	synonymous_variant	4599	exon18			GGGTGCATTGCAG		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.1623A>G	21.37:g.42824661A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Silent	SNP	ENST00000398600.2	37	CCDS13673.1																																																																																			A|0.796;G|0.204	0.204	strong		0.498	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
GALR2	8811	hgsc.bcm.edu	37	17	74072923	74072923	+	Missense_Mutation	SNP	T	T	G	rs369779116		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74072923T>G	ENST00000329003.3	+	2	665	c.575T>G	c.(574-576)tTc>tGc	p.F192C	ZACN_ENST00000334586.5_5'Flank|ZACN_ENST00000392503.2_5'Flank	NM_003857.2	NP_003848.1	O43603	GALR2_HUMAN	galanin receptor 2	192					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell surface receptor signaling pathway (GO:0007166)|digestion (GO:0007586)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|negative regulation of adenylate cyclase activity (GO:0007194)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of large conductance calcium-activated potassium channel activity (GO:1902608)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|peptide hormone binding (GO:0017046)			cervix(1)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						ATCTGCACCTTCGTCTTCAGC	0.692																																					p.F192C		Atlas-SNP	.											.	GALR2	17	.	0			c.T575G						PASS	.	T	CYS/PHE	1,4399		0,1,2199	45.0	31.0	36.0		575	5.0	1.0	17		36	0,8596		0,0,4298	no	missense	GALR2	NM_003857.2	205	0,1,6497	GG,GT,TT		0.0,0.0227,0.0077	probably-damaging	192/388	74072923	1,12995	2200	4298	6498	SO:0001583	missense	8811	exon2			GCACCTTCGTCTT	AF040630	CCDS11739.1	17q25.3	2012-08-08			ENSG00000182687	ENSG00000182687		"""GPCR / Class A : Galanin receptors"""	4133	protein-coding gene	gene with protein product		603691				9685625, 9832121	Standard	NM_003857		Approved	GALNR2	uc002jqm.1	O43603	OTTHUMG00000167479	ENST00000329003.3:c.575T>G	17.37:g.74072923T>G	ENSP00000329684:p.Phe192Cys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_003857	A5JUU4|Q32MN8	Missense_Mutation	SNP	ENST00000329003.3	37	CCDS11739.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.752255	0.89753	2.27E-4	0.0	ENSG00000182687	ENST00000329003	T	0.72394	-0.65	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.87657	0.6232	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90899	0.4767	10	0.87932	D	0	.	14.3163	0.66452	0.0:0.0:0.0:1.0	.	192	O43603	GALR2_HUMAN	C	192	ENSP00000329684:F192C	ENSP00000329684:F192C	F	+	2	0	GALR2	71584518	1.000000	0.71417	0.978000	0.43139	0.984000	0.73092	7.925000	0.87563	1.871000	0.54225	0.379000	0.24179	TTC	.	.	weak		0.692	GALR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394760.1		
SEC16A	9919	hgsc.bcm.edu	37	9	139347953	139347953	+	Missense_Mutation	SNP	G	G	A	rs202042941		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139347953G>A	ENST00000371706.3	-	20	5585	c.5552C>T	c.(5551-5553)cCg>cTg	p.P1851L	SEC16A_ENST00000313050.7_Missense_Mutation_p.P2029L|SEC16A_ENST00000290037.6_Missense_Mutation_p.P1851L|SEC16A_ENST00000398335.1_5'Flank|SEC16A_ENST00000431893.2_Missense_Mutation_p.P1851L			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1851	Pro-rich.				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)		CGCCTCCTGCGGCACTATCCC	0.483																																					p.P2029L		Atlas-SNP	.											.	SEC16A	249	.	0			c.C6086T						PASS	.	G	LEU/PRO	4,3968		0,4,1982	75.0	79.0	78.0		6086	2.0	0.0	9		78	6,8312		0,6,4153	yes	missense	SEC16A	NM_014866.1	98	0,10,6135	AA,AG,GG		0.0721,0.1007,0.0814	benign	2029/2358	139347953	10,12280	1986	4159	6145	SO:0001583	missense	9919	exon22			TCCTGCGGCACTA	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.5552C>T	9.37:g.139347953G>A	ENSP00000360771:p.Pro1851Leu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	28	9	0.321429	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	G	15.41	2.825603	0.50739	0.001007	7.21E-4	ENSG00000148396	ENST00000313050;ENST00000277537;ENST00000453963;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925;ENST00000398348	T;T;T;T;T;T	0.44482	1.89;0.92;1.51;1.88;1.88;1.87	4.84	1.96	0.26148	.	0.491778	0.21508	N	0.073403	T	0.56321	0.1977	M	0.71581	2.175	0.25198	N	0.990071	D;D;P;B;P	0.76494	0.997;0.999;0.573;0.278;0.769	D;D;B;B;B	0.71870	0.926;0.975;0.213;0.035;0.106	T	0.44772	-0.9306	10	0.45353	T	0.12	-0.9711	7.4567	0.27270	0.278:0.0:0.722:0.0	.	2029;1851;1851;1419;1851	F1T0I1;O15027-5;O15027-4;A4QN19;O15027	.;.;.;.;SC16A_HUMAN	L	2029;423;751;1851;1851;1851;1419;387	ENSP00000325827:P2029L;ENSP00000277537:P423L;ENSP00000403525:P751L;ENSP00000360771:P1851L;ENSP00000290037:P1851L;ENSP00000387583:P1851L	ENSP00000277537:P423L	P	-	2	0	SEC16A	138467774	0.128000	0.22383	0.002000	0.10522	0.019000	0.09904	1.080000	0.30779	0.191000	0.20236	0.561000	0.74099	CCG	.	.	weak		0.483	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
FAM20A	54757	hgsc.bcm.edu	37	17	66538239	66538239	+	Missense_Mutation	SNP	G	G	T	rs2302234	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:66538239G>T	ENST00000592554.1	-	7	1718	c.996C>A	c.(994-996)aaC>aaA	p.N332K	AC079210.1_ENST00000600820.1_5'Flank|PRKAR1A_ENST00000588188.2_Intron|FAM20A_ENST00000226094.5_5'UTR	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	332			N -> K (in dbSNP:rs2302234). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					GCAGGTGTGGGTTGCCACAGA	0.602													G|||	1792	0.357827	0.2716	0.4481	5008	,	,		21446	0.5446		0.3121	False		,,,				2504	0.2648				p.N332K		Atlas-SNP	.											.	FAM20A	35	.	0			c.C996A						PASS	.	G	LYS/ASN	1208,3198	420.6+/-339.1	173,862,1168	116.0	89.0	98.0		996	5.0	1.0	17	dbSNP_100	98	2606,5994	421.5+/-353.7	385,1836,2079	yes	missense	FAM20A	NM_017565.3	94	558,2698,3247	TT,TG,GG		30.3023,27.4172,29.3249	benign	332/542	66538239	3814,9192	2203	4300	6503	SO:0001583	missense	54757	exon7			GTGTGGGTTGCCA	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.996C>A	17.37:g.66538239G>T	ENSP00000468308:p.Asn332Lys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_017565	B2RN47|B2RN49|Q9UF95	Missense_Mutation	SNP	ENST00000592554.1	37	CCDS11679.1	825	0.37774725274725274	135	0.27439024390243905	155	0.4281767955801105	304	0.5314685314685315	231	0.30474934036939316	G	12.14	1.848673	0.32699	0.274172	0.303023	ENSG00000108950	ENST00000226094	.	.	.	6.04	5.02	0.67125	.	0.377447	0.35708	N	0.003022	T	0.00012	0.0000	L	0.31845	0.965	0.09310	P	0.999999598965	P	0.43578	0.811	B	0.40825	0.341	T	0.33266	-0.9875	8	0.07990	T	0.79	-27.4593	16.8418	0.85971	0.0:0.1282:0.8718:0.0	rs2302234;rs60530867;rs2302234	332	Q96MK3	FA20A_HUMAN	K	332	.	ENSP00000226094:N332K	N	-	3	2	FAM20A	64049834	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.510000	0.45468	2.873000	0.98535	0.563000	0.77884	AAC	A|0.003;C|0.004	.	strong		0.602	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
CECR5	27440	hgsc.bcm.edu	37	22	17618937	17618937	+	Missense_Mutation	SNP	G	G	A	rs35327402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:17618937G>A	ENST00000336737.4	-	8	1271	c.1246C>T	c.(1246-1248)Cgc>Tgc	p.R416C	CECR5_ENST00000155674.5_Missense_Mutation_p.R386C|CECR5_ENST00000399852.3_Missense_Mutation_p.R216C	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	416			R -> C (in dbSNP:rs35327402).			mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				CCCTCCTTGCGGAAGACCAGC	0.632													G|||	15	0.00299521	0.0008	0.0043	5008	,	,		19931	0.0		0.008	False		,,,				2504	0.0031				p.R416C		Atlas-SNP	.											.	CECR5	46	.	0			c.C1246T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	98.0	85.0	90.0		1156,1246	2.2	0.6	22	dbSNP_126	90	32,8568	21.6+/-65.8	0,32,4268	yes	missense,missense	CECR5	NM_017829.5,NM_033070.2	180,180	0,34,6469	AA,AG,GG		0.3721,0.0454,0.2614	benign,benign	386/394,416/424	17618937	34,12972	2203	4300	6503	SO:0001583	missense	27440	exon8			CCTTGCGGAAGAC	AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.1246C>T	22.37:g.17618937G>A	ENSP00000337358:p.Arg416Cys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	113	64	0.566372	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Missense_Mutation	SNP	ENST00000336737.4	37	CCDS33595.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	10.55	1.382430	0.24944	4.54E-4	0.003721	ENSG00000069998	ENST00000155674;ENST00000336737;ENST00000399852	T;T;T	0.25250	1.81;1.81;1.81	4.47	2.2	0.27929	HAD-like domain (1);	0.532262	0.21527	N	0.073110	T	0.12475	0.0303	L	0.44542	1.39	0.22112	N	0.999352	B;B;B;B	0.24426	0.103;0.015;0.014;0.023	B;B;B;B	0.18263	0.021;0.008;0.006;0.008	T	0.15321	-1.0441	10	0.59425	D	0.04	-8.9079	3.6609	0.08238	0.0871:0.1262:0.4078:0.3789	rs35327402	386;216;416;280	Q9BXW7-2;A8MYZ9;Q9BXW7;B3KVW8	.;.;CECR5_HUMAN;.	C	386;416;216	ENSP00000155674:R386C;ENSP00000337358:R416C;ENSP00000382745:R216C	ENSP00000155674:R386C	R	-	1	0	CECR5	15998937	0.000000	0.05858	0.641000	0.29422	0.811000	0.45836	-0.486000	0.06513	1.065000	0.40693	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.632	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829	
FAT1	2195	hgsc.bcm.edu	37	4	187542316	187542316	+	Silent	SNP	T	T	C	rs2099854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187542316T>C	ENST00000441802.2	-	10	5633	c.5424A>G	c.(5422-5424)gtA>gtG	p.V1808V		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1808	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CAATGTGATATACAAGCAAAG	0.403										HNSCC(5;0.00058)			T|||	343	0.0684904	0.003	0.1499	5008	,	,		22440	0.1806		0.0338	False		,,,				2504	0.0194				p.V1808V	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A5424G						PASS	.	T		40,3880		0,40,1920	82.0	80.0	81.0		5424	-5.7	0.9	4	dbSNP_96	81	255,8057		4,247,3905	no	coding-synonymous	FAT1	NM_005245.3		4,287,5825	CC,CT,TT		3.0679,1.0204,2.4117		1808/4589	187542316	295,11937	1960	4156	6116	SO:0001819	synonymous_variant	2195	exon10			GTGATATACAAGC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5424A>G	4.37:g.187542316T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.923;C|0.077	0.077	strong		0.403	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CEP164	22897	hgsc.bcm.edu	37	11	117266312	117266312	+	Missense_Mutation	SNP	C	C	G	rs2305830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:117266312C>G	ENST00000278935.3	+	24	3110	c.2963C>G	c.(2962-2964)aCc>aGc	p.T988S	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	988			T -> S (in dbSNP:rs2305830). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		AAGGAGCACACCCACCTGTTG	0.567													C|||	1392	0.277955	0.267	0.2089	5008	,	,		18904	0.3046		0.3211	False		,,,				2504	0.2699				p.T991S		Atlas-SNP	.											.	CEP164	121	.	0			c.C2972G						PASS	.	C	SER/THR	1176,3226	411.3+/-335.7	155,866,1180	56.0	57.0	57.0		2963	0.9	0.0	11	dbSNP_100	57	2658,5934	425.8+/-355.1	405,1848,2043	yes	missense	CEP164	NM_014956.4	58	560,2714,3223	GG,GC,CC		30.9358,26.7151,29.5059	benign	988/1461	117266312	3834,9160	2201	4296	6497	SO:0001583	missense	22897	exon23			AGCACACCCACCT	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.2963C>G	11.37:g.117266312C>G	ENSP00000278935:p.Thr988Ser	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	635	0.2907509157509158	139	0.28252032520325204	87	0.24033149171270718	168	0.2937062937062937	241	0.3179419525065963	C	10.78	1.445822	0.25987	0.267151	0.309358	ENSG00000110274	ENST00000278935;ENST00000529538	T	0.27104	1.69	5.02	0.953	0.19590	.	0.702415	0.12990	N	0.422568	T	0.00012	0.0000	L	0.50919	1.6	0.80722	P	0.0	B;B;B;B	0.10296	0.002;0.003;0.003;0.003	B;B;B;B	0.10450	0.002;0.005;0.005;0.005	T	0.40664	-0.9551	9	0.29301	T	0.29	-0.0052	3.8141	0.08808	0.1203:0.3898:0.353:0.1368	rs2305830;rs17500832;rs52823446;rs2305830	962;762;988;991	E9PI34;Q9NTH6;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	S	988;962	ENSP00000278935:T988S	ENSP00000278935:T988S	T	+	2	0	CEP164	116771522	0.000000	0.05858	0.003000	0.11579	0.953000	0.61014	-0.116000	0.10724	-0.075000	0.12798	0.491000	0.48974	ACC	C|0.709;G|0.291	0.291	strong		0.567	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
CSPG4	1464	hgsc.bcm.edu	37	15	75982085	75982085	+	Missense_Mutation	SNP	C	C	T	rs79463888	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:75982085C>T	ENST00000308508.5	-	3	1413	c.1321G>A	c.(1321-1323)Gag>Aag	p.E441K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	441	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GTGCCCCCCTCGGCCACCACC	0.637																																					p.E441K		Atlas-SNP	.											CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	0			c.G1321A						PASS	.						43.0	42.0	43.0					15																	75982085		2197	4292	6489	SO:0001583	missense	1464	exon3			CCCCCTCGGCCAC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1321G>A	15.37:g.75982085C>T	ENSP00000312506:p.Glu441Lys	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	137	17	0.124088	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	18.26	3.584924	0.65992	.	.	ENSG00000173546	ENST00000308508	T	0.31510	1.49	5.26	5.26	0.73747	.	0.170667	0.41001	D	0.000974	T	0.48642	0.1511	M	0.78049	2.395	0.80722	D	1	D	0.71674	0.998	P	0.56278	0.795	T	0.52041	-0.8628	10	0.59425	D	0.04	.	11.3564	0.49617	0.0:0.9168:0.0:0.0831	.	441	Q6UVK1	CSPG4_HUMAN	K	441	ENSP00000312506:E441K	ENSP00000312506:E441K	E	-	1	0	CSPG4	73769140	1.000000	0.71417	0.998000	0.56505	0.513000	0.34164	4.634000	0.61325	2.463000	0.83235	0.555000	0.69702	GAG	C|0.878;T|0.122	0.122	strong		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
ARID3C	138715	hgsc.bcm.edu	37	9	34627940	34627940	+	Silent	SNP	C	C	T	rs13283357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:34627940C>T	ENST00000378909.2	-	1	164	c.72G>A	c.(70-72)ccG>ccA	p.P24P		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	24					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)		GTGGCAGCAGCGGGCATGCAG	0.687													c|||	936	0.186901	0.1104	0.2983	5008	,	,		14143	0.0615		0.3817	False		,,,				2504	0.1401				p.P24P		Atlas-SNP	.											.	ARID3C	33	.	0			c.G72A						PASS	.	C		595,3645		45,505,1570	6.0	6.0	6.0		72	-7.5	0.0	9	dbSNP_121	6	2796,5448		508,1780,1834	no	coding-synonymous	ARID3C	NM_001017363.1		553,2285,3404	TT,TC,CC		33.9156,14.033,27.1628		24/413	34627940	3391,9093	2120	4122	6242	SO:0001819	synonymous_variant	138715	exon1			CAGCAGCGGGCAT		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.72G>A	9.37:g.34627940C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_001017363		Silent	SNP	ENST00000378909.2	37	CCDS35006.1																																																																																			C|0.766;T|0.234	0.234	strong		0.687	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061	
ALX4	60529	hgsc.bcm.edu	37	11	44331509	44331509	+	Missense_Mutation	SNP	C	C	G	rs3824915	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:44331509C>G	ENST00000329255.3	-	1	207	c.104G>C	c.(103-105)aGg>aCg	p.R35T		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	35			R -> T (in dbSNP:rs3824915). {ECO:0000269|PubMed:11106354, ECO:0000269|PubMed:11137991}.		anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						GGGAAATGCCCTAAAAGGCGA	0.642													C|||	2367	0.472644	0.2443	0.3833	5008	,	,		12277	0.5079		0.4682	False		,,,				2504	0.8129				p.R35T		Atlas-SNP	.											.	ALX4	58	.	0			c.G104C						PASS	.		THR/ARG	1324,3076		198,928,1074	16.0	19.0	18.0		104	4.6	1.0	11	dbSNP_107	18	4189,4407		1013,2163,1122	yes	missense	ALX4	NM_021926.3	71	1211,3091,2196	GG,GC,CC		48.732,30.0909,42.4207	probably-damaging	35/412	44331509	5513,7483	2200	4298	6498	SO:0001583	missense	60529	exon1			AATGCCCTAAAAG	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.104G>C	11.37:g.44331509C>G	ENSP00000332744:p.Arg35Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_021926	Q96JN7|Q9H198|Q9HAY9	Missense_Mutation	SNP	ENST00000329255.3	37	CCDS31468.1	913	0.41804029304029305	126	0.25609756097560976	136	0.3756906077348066	280	0.48951048951048953	371	0.4894459102902375	c	28.2	4.901377	0.92035	0.300909	0.48732	ENSG00000052850	ENST00000329255	D	0.96427	-4.01	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.99999604534	B	0.34103	0.437	B	0.30401	0.115	T	0.00995	-1.1487	9	0.72032	D	0.01	.	17.4764	0.87660	0.0:1.0:0.0:0.0	rs3824915;rs3824915	35	Q9H161	ALX4_HUMAN	T	35	ENSP00000332744:R35T	ENSP00000332744:R35T	R	-	2	0	ALX4	44288085	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.269000	0.65542	2.108000	0.64289	0.457000	0.33378	AGG	C|0.594;G|0.406	0.406	strong		0.642	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
TYW1	55253	hgsc.bcm.edu	37	7	66660247	66660247	+	Silent	SNP	T	T	C	rs55673383		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	206	0	0		WXS	Illumina HiSeq	Phase_I	158	48	0.303797	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	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036853	33036853	+	Missense_Mutation	SNP	A	A	C	rs1042308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	129	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	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	
FAM129C	199786	hgsc.bcm.edu	37	19	17638144	17638144	+	Missense_Mutation	SNP	A	A	C	rs200304763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17638144A>C	ENST00000335393.4	+	2	226	c.88A>C	c.(88-90)Agc>Cgc	p.S30R	FAM129C_ENST00000300971.2_Missense_Mutation_p.S30R|FAM129C_ENST00000599164.1_5'UTR|FAM129C_ENST00000595684.1_Missense_Mutation_p.S30R|FAM129C_ENST00000599124.1_5'UTR|FAM129C_ENST00000600871.1_5'UTR|FAM129C_ENST00000332386.5_Missense_Mutation_p.S30R|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000352727.3_Missense_Mutation_p.S30R|FAM129C_ENST00000601861.1_5'UTR|FAM129C_ENST00000597887.1_3'UTR	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	30										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						GGGAGACGACAGCAGCATGGG	0.692													A|||	7	0.00139776	0.0	0.0014	5008	,	,		11745	0.0		0.0	False		,,,				2504	0.0061				p.S30R		Atlas-SNP	.											.	FAM129C	110	.	0			c.A88C						PASS	.	A	ARG/SER,ARG/SER	0,4044		0,0,2022	25.0	21.0	23.0		88,88	-3.7	0.0	19		23	1,7935		0,1,3967	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	110,110	0,1,5989	CC,CA,AA		0.0126,0.0,0.0083	probably-damaging,probably-damaging	30/652,30/698	17638144	1,11979	2022	3968	5990	SO:0001583	missense	199786	exon2			GACGACAGCAGCA	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.88A>C	19.37:g.17638144A>C	ENSP00000335040:p.Ser30Arg	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	208	89	0.427885	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	15.73	2.920339	0.52653	0.0	1.26E-4	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971	T;T;T;T	0.26810	1.93;2.03;1.71;1.72	3.98	-3.67	0.04476	.	0.829479	0.10133	N	0.711885	T	0.13756	0.0333	L	0.51422	1.61	0.19300	N	0.999979	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.23048	-1.0199	10	0.39692	T	0.17	.	6.6521	0.22967	0.3189:0.1624:0.5187:0.0	.	30;30	Q86XR2;Q86XR2-3	NIBL2_HUMAN;.	R	30	ENSP00000335040:S30R;ENSP00000333447:S30R;ENSP00000341067:S30R;ENSP00000300971:S30R	ENSP00000300971:S30R	S	+	1	0	FAM129C	17499144	0.004000	0.15560	0.001000	0.08648	0.023000	0.10783	-0.012000	0.12699	-0.984000	0.03507	-0.415000	0.06103	AGC	A|0.998;C|0.002	0.002	strong		0.692	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
C1orf189	388701	hgsc.bcm.edu	37	1	154178079	154178079	+	Silent	SNP	G	G	A	rs74957241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154178079G>A	ENST00000368525.3	-	2	94	c.69C>T	c.(67-69)gtC>gtT	p.V23V	C1orf43_ENST00000483282.1_5'Flank	NM_001010979.1	NP_001010979.1	Q5VU69	CA189_HUMAN	chromosome 1 open reading frame 189	23										kidney(1)|large_intestine(3)|lung(1)|skin(2)	7	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					ATTACCTGTCGACCGTCTTCT	0.473													G|||	192	0.0383387	0.003	0.0677	5008	,	,		18138	0.001		0.1163	False		,,,				2504	0.0235				p.V23V		Atlas-SNP	.											C1orf189,NS,carcinoma,-2,1	C1orf189	17	1	0			c.C69T						PASS	.	G		82,4324	71.4+/-109.4	2,78,2123	166.0	148.0	154.0		69	-2.7	0.1	1	dbSNP_132	154	926,7674	205.1+/-247.6	55,816,3429	no	coding-synonymous	C1orf189	NM_001010979.1		57,894,5552	AA,AG,GG		10.7674,1.8611,7.7503		23/102	154178079	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	388701	exon2			CCTGTCGACCGTC		CCDS30876.1	1q21.3	2012-07-27			ENSG00000163263	ENSG00000163263			32305	protein-coding gene	gene with protein product							Standard	NM_001010979		Approved		uc001fee.2	Q5VU69	OTTHUMG00000035982	ENST00000368525.3:c.69C>T	1.37:g.154178079G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	87	34	0.390805	NM_001010979	A1L4E3	Silent	SNP	ENST00000368525.3	37	CCDS30876.1																																																																																			G|0.926;A|0.074	0.074	strong		0.473	C1orf189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087672.1	NM_001010979	
KRT33A	3883	hgsc.bcm.edu	37	17	39502398	39502398	+	Silent	SNP	A	A	G	rs16966703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	162	0	0		WXS	Illumina HiSeq	Phase_I	166	88	0.53012	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	
CABIN1	23523	hgsc.bcm.edu	37	22	24468386	24468386	+	Missense_Mutation	SNP	G	G	A	rs17854874	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:24468386G>A	ENST00000398319.2	+	18	2943	c.2558G>A	c.(2557-2559)cGg>cAg	p.R853Q	CABIN1_ENST00000263119.5_Missense_Mutation_p.R853Q|CABIN1_ENST00000405822.2_Missense_Mutation_p.R803Q	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	853			R -> Q (in dbSNP:rs17854874). {ECO:0000269|PubMed:15489334}.		cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ATTCTACACCGGATCATCTGG	0.602													G|||	307	0.0613019	0.0038	0.0317	5008	,	,		23025	0.1587		0.0974	False		,,,				2504	0.0225				p.R853Q		Atlas-SNP	.											.	CABIN1	153	.	0			c.G2558A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	70,4336	62.3+/-99.4	3,64,2136	143.0	98.0	113.0		2558,2408,2558	4.6	1.0	22	dbSNP_123	113	613,7987	160.8+/-213.9	27,559,3714	yes	missense,missense,missense	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	43,43,43	30,623,5850	AA,AG,GG		7.1279,1.5887,5.2514	probably-damaging,probably-damaging,probably-damaging	853/2221,803/2171,853/2221	24468386	683,12323	2203	4300	6503	SO:0001583	missense	23523	exon18			TACACCGGATCAT	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.2558G>A	22.37:g.24468386G>A	ENSP00000381364:p.Arg853Gln	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	187	0.08562271062271062	1	0.0020325203252032522	16	0.04419889502762431	97	0.16958041958041958	73	0.09630606860158311	G	16.53	3.148196	0.57151	0.015887	0.071279	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.58358	0.34;0.34;0.34	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	L	0.59436	1.845	0.09310	P	1.0	D;D	0.67145	0.996;0.993	P;B	0.50352	0.638;0.435	T	0.01570	-1.1322	9	0.27785	T	0.31	.	16.8003	0.85612	0.0:0.0:1.0:0.0	rs17854874;rs17854874	803;853	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	Q	853;803;853	ENSP00000263119:R853Q;ENSP00000384694:R803Q;ENSP00000381364:R853Q	ENSP00000263119:R853Q	R	+	2	0	CABIN1	22798386	1.000000	0.71417	0.989000	0.46669	0.445000	0.32107	5.903000	0.69877	2.300000	0.77407	0.650000	0.86243	CGG	G|0.926;A|0.074	0.074	strong		0.602	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33564123	33564123	+	Silent	SNP	T	T	C	rs2076623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:33564123T>C	ENST00000321505.4	+	1	303	c.123T>C	c.(121-123)ggT>ggC	p.G41G	KIAA1549L_ENST00000389726.3_Silent_p.G41G|KIAA1549L_ENST00000265654.5_Silent_p.G41G			Q6ZVL6	K154L_HUMAN	KIAA1549-like	41						integral component of membrane (GO:0016021)											ATTCAGCAGGTTCATCCACAC	0.547													C|||	3490	0.696885	0.8918	0.6095	5008	,	,		18348	0.6617		0.6153	False		,,,				2504	0.6155				p.G41G		Atlas-SNP	.											.	.	.	.	0			c.T123C						PASS	.	C		3342,560		1431,480,40	96.0	97.0	97.0		123	1.9	0.0	11	dbSNP_96	97	5307,2989		1688,1931,529	no	coding-synonymous	C11orf41	NM_012194.2		3119,2411,569	CC,CT,TT		36.0294,14.3516,29.0949		41/1850	33564123	8649,3549	1951	4148	6099	SO:0001819	synonymous_variant	25758	exon1			AGCAGGTTCATCC	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.123T>C	11.37:g.33564123T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																			T|0.300;C|0.700	0.700	strong		0.547	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
MTMR8	55613	hgsc.bcm.edu	37	X	63488670	63488670	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:63488670G>T	ENST00000374852.3	-	14	1929	c.1862C>A	c.(1861-1863)gCc>gAc	p.A621D	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	621						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						GATATTTATGGCCCTAAGGCT	0.527																																					p.A621D		Atlas-SNP	.											.	MTMR8	178	.	2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	c.C1862A						PASS	.						83.0	65.0	71.0					X																	63488670		2203	4300	6503	SO:0001583	missense	55613	exon14			TTTATGGCCCTAA	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1862C>A	X.37:g.63488670G>T	ENSP00000363985:p.Ala621Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.088488	0.36855	.	.	ENSG00000102043	ENST00000374852;ENST00000247400	D	0.95272	-3.66	2.51	2.51	0.30379	.	0.460045	0.16633	U	0.205952	D	0.85969	0.5821	N	0.08118	0	0.09310	N	1	P	0.41232	0.743	B	0.40602	0.334	T	0.80162	-0.1497	10	0.87932	D	0	.	6.6727	0.23078	0.0:0.2931:0.7069:0.0	.	621	Q96EF0	MTMR8_HUMAN	D	621;507	ENSP00000363985:A621D	ENSP00000247400:A507D	A	-	2	0	MTMR8	63405395	0.859000	0.29813	0.004000	0.12327	0.057000	0.15508	1.348000	0.33987	1.541000	0.49316	0.436000	0.28706	GCC	.	.	none		0.527	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677	
MANSC4	100287284	hgsc.bcm.edu	37	12	27916224	27916224	+	Missense_Mutation	SNP	A	A	G	rs11049126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:27916224A>G	ENST00000381273.3	-	3	469	c.470T>C	c.(469-471)tTa>tCa	p.L157S		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	157						integral component of membrane (GO:0016021)				kidney(1)	1						TTGTTTATCTAAATTCATAGC	0.403													A|||	625	0.1248	0.0234	0.1023	5008	,	,		19740	0.2044		0.173	False		,,,				2504	0.1462				p.L157S		Atlas-SNP	.											.	MANSC4	9	.	0			c.T470C						PASS	.						249.0	211.0	222.0					12																	27916224		692	1591	2283	SO:0001583	missense	100287284	exon3			TTATCTAAATTCA		CCDS53770.1	12p11.22	2011-05-05			ENSG00000205693	ENSG00000205693			40023	protein-coding gene	gene with protein product							Standard	NM_001146221		Approved		uc010sjs.1	A6NHS7	OTTHUMG00000169216	ENST00000381273.3:c.470T>C	12.37:g.27916224A>G	ENSP00000370673:p.Leu157Ser	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	282	137	0.485816	NM_001146221		Missense_Mutation	SNP	ENST00000381273.3	37	CCDS53770.1	295	0.13507326007326007	17	0.034552845528455285	34	0.09392265193370165	112	0.1958041958041958	132	0.1741424802110818	A	16.47	3.131562	0.56828	.	.	ENSG00000205693	ENST00000381273	T	0.49139	0.79	5.41	-2.67	0.06059	.	1.334070	0.05107	N	0.488297	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.28760	0.221	B	0.22386	0.039	T	0.05869	-1.0859	9	0.17832	T	0.49	0.1944	5.4929	0.16787	0.4742:0.0:0.3901:0.1357	rs11049126;rs11049126	157	A6NHS7	MANS4_HUMAN	S	157	ENSP00000370673:L157S	ENSP00000370673:L157S	L	-	2	0	MANSC4	27807491	0.018000	0.18449	0.000000	0.03702	0.794000	0.44872	0.074000	0.14662	-0.497000	0.06641	0.460000	0.39030	TTA	A|0.859;G|0.141	0.141	strong		0.403	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
SEMA4B	10509	hgsc.bcm.edu	37	15	90768959	90768959	+	Silent	SNP	A	A	C	rs908044	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90768959A>C	ENST00000411539.2	+	12	1848	c.1588A>C	c.(1588-1590)Agg>Cgg	p.R530R	SEMA4B_ENST00000379122.3_Silent_p.R525R|SEMA4B_ENST00000332496.6_Silent_p.R530R	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	525	PSI.				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)			CAGCCTGTACAGGAGCTGTGG	0.662													C|||	1794	0.358227	0.6997	0.3026	5008	,	,		17449	0.1002		0.3628	False		,,,				2504	0.1973				p.R530R		Atlas-SNP	.											.	SEMA4B	51	.	0			c.A1588C						PASS	.	C	,	2591,1563		836,919,322	14.0	18.0	17.0		1588,1588	4.7	1.0	15	dbSNP_86	17	2856,5524		517,1822,1851	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	1353,2741,2173	CC,CA,AA		34.0811,37.6264,43.4578	,	530/838,530/838	90768959	5447,7087	2077	4190	6267	SO:0001819	synonymous_variant	10509	exon13			CTGTACAGGAGCT	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.1588A>C	15.37:g.90768959A>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	37	CCDS45347.1																																																																																			A|0.634;C|0.366	0.366	strong		0.662	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
ICAM3	3385	hgsc.bcm.edu	37	19	10449392	10449392	+	Silent	SNP	A	A	G	rs2304240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10449392A>G	ENST00000160262.5	-	2	517	c.309T>C	c.(307-309)tcT>tcC	p.S103S	ICAM3_ENST00000589261.1_Silent_p.S26S	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	103	Ig-like C2-type 1.				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)			CTGTTATCTGAGAGCCATTGC	0.572													G|||	4148	0.828275	0.9372	0.6671	5008	,	,		19717	0.8254		0.8231	False		,,,				2504	0.8037				p.S103S		Atlas-SNP	.											ICAM3,NS,carcinoma,-1,1	ICAM3	29	1	0			c.T309C						PASS	.	G		4022,384	193.6+/-218.7	1834,354,15	96.0	73.0	81.0		309	-6.4	0.0	19	dbSNP_100	81	7173,1427	275.4+/-291.8	3000,1173,127	no	coding-synonymous	ICAM3	NM_002162.3		4834,1527,142	GG,GA,AA		16.593,8.7154,13.9243		103/548	10449392	11195,1811	2203	4300	6503	SO:0001819	synonymous_variant	3385	exon2			TATCTGAGAGCCA		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.309T>C	19.37:g.10449392A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	154	76	0.493506	NM_002162	Q6PD68	Silent	SNP	ENST00000160262.5	37	CCDS12235.1																																																																																			A|0.149;G|0.851	0.851	strong		0.572	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73207372	73207372	+	Missense_Mutation	SNP	T	T	A	rs1478453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73207372T>A	ENST00000426542.2	+	34	4940	c.4920T>A	c.(4918-4920)caT>caA	p.H1640Q	ARHGEF28_ENST00000437974.1_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.H560Q|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.H1327Q|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.H1596Q			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	110	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	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		
CT45A5	441521	hgsc.bcm.edu	37	X	134948034	134948034	+	Silent	SNP	A	A	G	rs2034920	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:134948034A>G	ENST00000463085.2	-	3	380	c.291T>C	c.(289-291)aaT>aaC	p.N97N	CT45A4_ENST00000420087.2_Intron|CT45A5_ENST00000370724.3_Silent_p.N97N|CT45A5_ENST00000491480.1_Silent_p.N97N			Q6NSH3	CT455_HUMAN	cancer/testis antigen family 45, member A5	97										endometrium(1)|large_intestine(2)|lung(6)	9						TGCTGGTAACATTTCCTCCCA	0.433													.|||	3151	0.834702	0.6876	0.5937	3775	,	,		15275	0.6577		0.5487	False		,,,				2504	0.6288				p.N97N		Atlas-SNP	.											.	CT45A5	26	.	0			c.T291C						PASS	.	G	,	3268,552		1196,387,489,49,67	207.0	192.0	197.0		291,291	0.5	0.0	X	dbSNP_94	197	4926,1768		1325,883,1393,217,451	no	coding-synonymous,coding-synonymous	CT45A5	NM_001007551.3,NM_001172288.1	,	2521,1270,1882,266,518	GG,GA,G,AA,A		26.4117,14.4503,22.0658	,	97/190,97/190	134948034	8194,2320	2188	4269	6457	SO:0001819	synonymous_variant	441521	exon3			GGTAACATTTCCT	AY743713	CCDS35406.1	Xq26.3	2009-03-12				ENSG00000269586			33270	protein-coding gene	gene with protein product	"""cancer/testis antigen CT45-5"""	300796				15905330	Standard	XM_006724759		Approved	CT45-5, CT45.5	uc022ces.1	Q6NSH3		ENST00000463085.2:c.291T>C	X.37:g.134948034A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001007551	A8K842|B7ZMC5	Silent	SNP	ENST00000463085.2	37	CCDS35406.1																																																																																			0|0.004;G|0.789	0.789	strong		0.433	CT45A5-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472589.1	NM_001007551	
STON1	11037	hgsc.bcm.edu	37	2	48808882	48808882	+	Silent	SNP	T	T	A	rs3749144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48808882T>A	ENST00000406226.1	+	3	1305	c.1110T>A	c.(1108-1110)ccT>ccA	p.P370P	STON1-GTF2A1L_ENST00000405008.1_Silent_p.P370P|STON1-GTF2A1L_ENST00000394754.1_Silent_p.P370P|STON1-GTF2A1L_ENST00000402114.2_Silent_p.P370P|STON1-GTF2A1L_ENST00000394751.3_Silent_p.P370P|STON1_ENST00000309835.3_Silent_p.P370P|STON1-GTF2A1L_ENST00000309827.2_Silent_p.P370P|STON1_ENST00000404752.1_Silent_p.P370P	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	370	SHD. {ECO:0000255|PROSITE- ProRule:PRU00403}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCATGAACCTGACATAGAGC	0.428													A|||	1683	0.336062	0.2784	0.3112	5008	,	,		20805	0.3879		0.3201	False		,,,				2504	0.3947				p.P370P		Atlas-SNP	.											.	STON1	100	.	0			c.T1110A						PASS	.	A	,,,,	1308,3098	693.8+/-405.7	193,922,1088	68.0	68.0	68.0		1110,1110,1110,1110,1110	-4.4	0.0	2	dbSNP_107	68	2750,5850	678.0+/-403.4	457,1836,2007	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	650,2758,3095	AA,AT,TT		31.9767,29.6868,31.201	,,,,	370/1159,370/1136,370/736,370/736,370/1183	48808882	4058,8948	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			TGAACCTGACATA	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1110T>A	2.37:g.48808882T>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			T|0.678;A|0.322	0.322	strong		0.428	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
MICALCL	84953	hgsc.bcm.edu	37	11	12315335	12315335	+	Silent	SNP	C	C	A	rs79609470	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:12315335C>A	ENST00000256186.2	+	3	648	c.357C>A	c.(355-357)gcC>gcA	p.A119A		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	119					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)		CAGCAGAGGCCCCTCTTGGGG	0.597													C|||	295	0.0589058	0.0212	0.0159	5008	,	,		12716	0.1647		0.0239	False		,,,				2504	0.0675				p.A119A		Atlas-SNP	.											.	MICALCL	59	.	0			c.C357A						PASS	.	C		66,3798		0,66,1866	56.0	60.0	59.0		357	-1.1	0.0	11	dbSNP_132	59	147,8101		1,145,3978	no	coding-synonymous	MICALCL	NM_032867.2		1,211,5844	AA,AC,CC		1.7823,1.7081,1.7586		119/696	12315335	213,11899	1932	4124	6056	SO:0001819	synonymous_variant	84953	exon3			AGAGGCCCCTCTT	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.357C>A	11.37:g.12315335C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_032867	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	37	CCDS41620.1																																																																																			C|0.958;A|0.042	0.042	strong		0.597	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
UNC79	57578	hgsc.bcm.edu	37	14	94007075	94007075	+	Silent	SNP	C	C	T	rs1951716	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:94007075C>T	ENST00000393151.2	+	13	1422	c.1422C>T	c.(1420-1422)ggC>ggT	p.G474G	UNC79_ENST00000553484.1_Silent_p.G474G|UNC79_ENST00000555664.1_Silent_p.G474G|UNC79_ENST00000256339.4_Silent_p.G297G			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	474					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						GGCAGCTGGGCCTCTCCTCTT	0.498													C|||	2430	0.485224	0.4652	0.7147	5008	,	,		17559	0.2113		0.6193	False		,,,				2504	0.4939				p.G297G		Atlas-SNP	.											UNC79,NS,chondrosarcoma,+1,2	UNC79	366	2	0			c.C891T						PASS	.	C		2168,2238	584.7+/-386.1	533,1102,568	75.0	82.0	80.0		891	-1.6	1.0	14	dbSNP_92	80	5491,3109	658.5+/-401.6	1776,1939,585	no	coding-synonymous	UNC79	NM_020818.3		2309,3041,1153	TT,TC,CC		36.1512,49.2056,41.1118		297/2459	94007075	7659,5347	2203	4300	6503	SO:0001819	synonymous_variant	57578	exon13			GCTGGGCCTCTCC	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.1422C>T	14.37:g.94007075C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																				C|0.455;T|0.545	0.545	strong		0.498	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
CTBS	1486	hgsc.bcm.edu	37	1	85029077	85029077	+	Missense_Mutation	SNP	C	C	T	rs15911|rs35270754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:85029077C>T	ENST00000370630.5	-	6	868	c.820G>A	c.(820-822)Gtc>Atc	p.V274I	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	274			V -> I (in dbSNP:rs15911).		chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		CGGAAAGGGACTTTTGCAATG	0.373													C|||	742	0.148163	0.1082	0.1254	5008	,	,		12711	0.0298		0.2038	False		,,,				2504	0.2832				p.V274I		Atlas-SNP	.											.	CTBS	24	.	0			c.G820A						PASS	.	C	ILE/VAL	564,3840		42,480,1680	43.0	48.0	46.0		820	2.6	1.0	1	dbSNP_52	46	1870,6728		217,1436,2646	yes	missense	CTBS	NM_004388.2	29	259,1916,4326	TT,TC,CC		21.7492,12.8065,18.7202	possibly-damaging	274/386	85029077	2434,10568	2202	4299	6501	SO:0001583	missense	1486	exon6			AAGGGACTTTTGC	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.820G>A	1.37:g.85029077C>T	ENSP00000359664:p.Val274Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	133	54	0.406015	NM_004388	Q5VX50	Missense_Mutation	SNP	ENST00000370630.5	37	CCDS698.1	287	0.13141025641025642	50	0.1016260162601626	57	0.1574585635359116	21	0.03671328671328671	159	0.20976253298153033	C	17.50	3.403971	0.62288	0.128065	0.217492	ENSG00000117151	ENST00000370630	T	0.07216	3.21	5.5	2.56	0.30785	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.175582	0.49305	D	0.000141	T	0.05227	0.0139	M	0.85197	2.74	0.25967	P	0.9825421	P	0.35192	0.489	B	0.37731	0.257	T	0.16217	-1.0410	9	0.32370	T	0.25	-1.2041	5.7446	0.18112	0.2649:0.549:0.1192:0.067	rs15911;rs3177079;rs17297378;rs17359075;rs17374997;rs52800947;rs57212367;rs15911	274	Q01459	DIAC_HUMAN	I	274	ENSP00000359664:V274I	ENSP00000359659:V183I	V	-	1	0	CTBS	84801665	0.989000	0.36119	0.991000	0.47740	0.909000	0.53808	0.705000	0.25675	0.271000	0.22005	0.650000	0.86243	GTC	C|0.831;T|0.169	0.169	strong		0.373	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
DRC1	92749	hgsc.bcm.edu	37	2	26676395	26676395	+	Missense_Mutation	SNP	G	G	T	rs12623642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:26676395G>T	ENST00000288710.2	+	14	1971	c.1897G>T	c.(1897-1899)Gtc>Ttc	p.V633F		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	633			V -> F (in dbSNP:rs12623642).		axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											GGAGGCCTTCGTCATGGGTCT	0.617													G|||	971	0.19389	0.0257	0.2651	5008	,	,		17792	0.5873		0.0716	False		,,,				2504	0.091				p.V633F		Atlas-SNP	.											.	CCDC164	84	.	0			c.G1897T						PASS	.	G	PHE/VAL	143,4263	99.4+/-138.0	1,141,2061	52.0	54.0	54.0		1897	5.0	1.0	2	dbSNP_120	54	584,8016	155.4+/-209.4	22,540,3738	yes	missense	CCDC164	NM_145038.2	50	23,681,5799	TT,TG,GG		6.7907,3.2456,5.5897	probably-damaging	633/741	26676395	727,12279	2203	4300	6503	SO:0001583	missense	92749	exon14			GCCTTCGTCATGG	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.1897G>T	2.37:g.26676395G>T	ENSP00000288710:p.Val633Phe	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	508	0.2326007326007326	11	0.022357723577235773	76	0.20994475138121546	367	0.6416083916083916	54	0.0712401055408971	G	23.3	4.396076	0.83011	0.032456	0.067907	ENSG00000157856	ENST00000288710	T	0.20598	2.06	5.03	5.03	0.67393	.	0.302633	0.31747	N	0.007127	T	0.00012	0.0000	M	0.83012	2.62	0.25125	P	0.99061866	D	0.57257	0.979	P	0.61132	0.884	T	0.46289	-0.9202	9	0.87932	D	0	-28.8909	17.4982	0.87724	0.0:0.0:1.0:0.0	rs12623642;rs52797399;rs57231544;rs12623642	633	Q96MC2	CC164_HUMAN	F	633	ENSP00000288710:V633F	ENSP00000288710:V633F	V	+	1	0	CCDC164	26529899	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.667000	0.54547	2.506000	0.84524	0.609000	0.83330	GTC	G|0.875;T|0.125	0.125	strong		0.617	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
DOK2	9046	hgsc.bcm.edu	37	8	21767275	21767275	+	Silent	SNP	C	C	G	rs2242240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:21767275C>G	ENST00000276420.4	-	5	1044	c.786G>C	c.(784-786)gcG>gcC	p.A262A	DOK2_ENST00000544659.1_Silent_p.A108A	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	262	Pro-rich.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GGGGCAGCGACGCGGGGATTG	0.667													G|||	1031	0.205871	0.1021	0.0994	5008	,	,		14731	0.3819		0.172	False		,,,				2504	0.2751				p.A262A		Atlas-SNP	.											.	DOK2	51	.	0			c.G786C						PASS	.	G		466,3940	778.7+/-414.3	19,428,1756	48.0	56.0	54.0		786	-10.8	0.0	8	dbSNP_98	54	1309,7289	755.2+/-407.5	99,1111,3089	no	coding-synonymous	DOK2	NM_003974.2		118,1539,4845	GG,GC,CC		15.2245,10.5765,13.6496		262/413	21767275	1775,11229	2203	4299	6502	SO:0001819	synonymous_variant	9046	exon5			CAGCGACGCGGGG	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"""docking protein 2, 56kD"""			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.786G>C	8.37:g.21767275C>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	148	64	0.432432	NM_003974	Q8N5A4	Silent	SNP	ENST00000276420.4	37	CCDS6016.1																																																																																			C|0.846;G|0.154	0.154	strong		0.667	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974	
GNAQ	2776	hgsc.bcm.edu	37	9	80537112	80537112	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:80537112T>A	ENST00000286548.4	-	2	508	c.286A>T	c.(286-288)Aca>Tca	p.T96S		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	96					action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.T96S(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						ATCTTGAGTGTGTCCATGGCT	0.473			Mis		uveal melanoma																																p.T96S		Atlas-SNP	.		Dom	yes		9	9q21	2776	"""guanine nucleotide binding protein (G protein), q polypeptide"""		E	GNAQ,NS,carcinoma,0,2	GNAQ	384	2	1	Substitution - Missense(1)	prostate(1)	c.A286T						scavenged	.																																			SO:0001583	missense	2776	exon2			TGAGTGTGTCCAT		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052			4390	protein-coding gene	gene with protein product		600998				8825633	Standard	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.286A>T	9.37:g.80537112T>A	ENSP00000286548:p.Thr96Ser	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	152	9	0.0592105	NM_002072	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141103	0.37825	.	.	ENSG00000156052	ENST00000286548;ENST00000411677	D;D	0.87809	-2.3;-2.3	5.86	5.86	0.93980	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	L	0.52126	1.63	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.79122	-0.1933	10	0.29301	T	0.29	.	16.2652	0.82574	0.0:0.0:0.0:1.0	.	96	P50148	GNAQ_HUMAN	S	96;67	ENSP00000286548:T96S;ENSP00000391501:T67S	ENSP00000286548:T96S	T	-	1	0	GNAQ	79726932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.145000	0.64839	2.241000	0.73720	0.528000	0.53228	ACA	.	.	none		0.473	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1	NM_002072	
B4GALT3	8703	hgsc.bcm.edu	37	1	161143801	161143801	+	Silent	SNP	G	G	A	rs3813619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161143801G>A	ENST00000319769.5	-	5	750	c.528C>T	c.(526-528)aaC>aaT	p.N176N	PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000367998.1_Silent_p.N176N|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|B4GALT3_ENST00000470882.1_5'UTR	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	176					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	GCACCCCAACGTTCAACAGTT	0.507													G|||	320	0.0638978	0.0454	0.0533	5008	,	,		20572	0.0675		0.0666	False		,,,				2504	0.09				p.N176N		Atlas-SNP	.											.	B4GALT3	39	.	0			c.C528T						PASS	.	G	,,	186,4220	118.8+/-156.5	2,182,2019	107.0	88.0	94.0		528,528,528	-4.0	1.0	1	dbSNP_107	94	552,8048	152.1+/-206.7	20,512,3768	no	coding-synonymous,coding-synonymous,coding-synonymous	B4GALT3	NM_001199873.1,NM_001199874.1,NM_003779.3	,,	22,694,5787	AA,AG,GG		6.4186,4.2215,5.6743	,,	176/394,176/394,176/394	161143801	738,12268	2203	4300	6503	SO:0001819	synonymous_variant	8703	exon5			CCCAACGTTCAAC	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.528C>T	1.37:g.161143801G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Silent	SNP	ENST00000319769.5	37	CCDS1222.1																																																																																			G|0.946;A|0.054	0.054	strong		0.507	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
CES5A	221223	hgsc.bcm.edu	37	16	55883618	55883618	+	Silent	SNP	T	T	C	rs2160276	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:55883618T>C	ENST00000290567.9	-	11	1462	c.1341A>G	c.(1339-1341)ccA>ccG	p.P447P	CES5A_ENST00000520435.1_Silent_p.P417P|CES5A_ENST00000319165.9_Intron|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000521992.1_Silent_p.P476P|CES5A_ENST00000518005.1_Silent_p.P341P	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	447						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						TGACAAAAGCTGGCTTCGTGT	0.527													T|||	3449	0.688698	0.5968	0.7839	5008	,	,		18711	0.7768		0.7455	False		,,,				2504	0.5961				p.P476P		Atlas-SNP	.											.	CES5A	206	.	0			c.A1428G						PASS	.	T	,,	1975,1161		632,711,225	120.0	105.0	110.0		1341,1428,	-5.4	0.2	16	dbSNP_96	110	5207,1957		1899,1409,274	no	coding-synonymous,coding-synonymous,intron	CES5A	NM_001143685.1,NM_001190158.1,NM_145024.2	,,	2531,2120,499	CC,CT,TT		27.3171,37.0217,30.2718	,,	447/576,476/605,	55883618	7182,3118	1568	3582	5150	SO:0001819	synonymous_variant	221223	exon12			AAAAGCTGGCTTC	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.1341A>G	16.37:g.55883618T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Silent	SNP	ENST00000290567.9	37	CCDS45490.1																																																																																			T|0.282;C|0.718	0.718	strong		0.527	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
EFCAB7	84455	hgsc.bcm.edu	37	1	63991267	63991267	+	Silent	SNP	T	T	C	rs217478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:63991267T>C	ENST00000371088.4	+	2	270	c.24T>C	c.(22-24)gaT>gaC	p.D8D	ITGB3BP_ENST00000371092.3_5'Flank|ITGB3BP_ENST00000271002.10_5'Flank|ITGB3BP_ENST00000283568.8_5'Flank	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	8							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						CACGAAGCGATGCAACTTTCT	0.353													T|||	2012	0.401757	0.3026	0.4741	5008	,	,		14553	0.4812		0.326	False		,,,				2504	0.4806				p.D8D		Atlas-SNP	.											EFCAB7,colon,carcinoma,+2,1	EFCAB7	45	1	0			c.T24C						PASS	.	T		1444,2962	456.9+/-351.5	237,970,996	72.0	79.0	77.0		24	0.2	0.3	1	dbSNP_79	77	2736,5864	434.9+/-357.9	436,1864,2000	no	coding-synonymous	EFCAB7	NM_032437.2		673,2834,2996	CC,CT,TT		31.814,32.7735,32.139		8/630	63991267	4180,8826	2203	4300	6503	SO:0001819	synonymous_variant	84455	exon2			AAGCGATGCAACT	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.24T>C	1.37:g.63991267T>C		Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_032437	Q658P0|Q96B95|Q96JM6	Silent	SNP	ENST00000371088.4	37	CCDS30737.1																																																																																			C|0.347;N|0.000	0.347	strong		0.353	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
HECW1	23072	hgsc.bcm.edu	37	7	43519337	43519337	+	Silent	SNP	T	T	C	rs2304327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:43519337T>C	ENST00000395891.2	+	17	3833	c.3228T>C	c.(3226-3228)gcT>gcC	p.A1076A	HECW1_ENST00000453890.1_Silent_p.A1042A	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1076					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GTTACAGCGCTGGAGAGGTAA	0.552													T|||	479	0.095647	0.0635	0.134	5008	,	,		16763	0.0794		0.1441	False		,,,				2504	0.0787				p.A1076A		Atlas-SNP	.											.	HECW1	540	.	0			c.T3228C						PASS	.	T		245,3631		7,231,1700	118.0	114.0	116.0		3228	2.0	1.0	7	dbSNP_100	116	1019,7267		65,889,3189	no	coding-synonymous	HECW1	NM_015052.3		72,1120,4889	CC,CT,TT		12.2979,6.3209,10.393		1076/1607	43519337	1264,10898	1938	4143	6081	SO:0001819	synonymous_variant	23072	exon17			CAGCGCTGGAGAG	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3228T>C	7.37:g.43519337T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	59	0.59596	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2	233	0.10668498168498168	30	0.06097560975609756	41	0.1132596685082873	58	0.10139860139860139	104	0.13720316622691292	T	9.668	1.145930	0.21288	0.063209	0.122979	ENSG00000002746	ENST00000429529	.	.	.	5.66	2.01	0.26516	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09400	-1.0676	3	.	.	.	.	5.4614	0.16619	0.1373:0.1399:0.0:0.7228	rs2304327;rs2304327	.	.	.	P	29	.	.	L	+	2	0	HECW1	43485862	0.614000	0.27017	1.000000	0.80357	0.745000	0.42441	-0.242000	0.08928	0.410000	0.25675	-0.527000	0.04329	CTG	T|0.892;C|0.108	0.108	strong		0.552	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
ARL10	285598	hgsc.bcm.edu	37	5	175793532	175793532	+	Silent	SNP	C	C	T	rs2303666	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	78	41	0.525641	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	
NOM1	64434	hgsc.bcm.edu	37	7	156743264	156743264	+	Missense_Mutation	SNP	C	C	A	rs61747373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:156743264C>A	ENST00000275820.3	+	1	848	c.833C>A	c.(832-834)gCg>gAg	p.A278E		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	278	Glu-rich.					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)		gaagcagaagcgcagagcgag	0.542													C|||	1067	0.213059	0.2443	0.2406	5008	,	,		19373	0.2768		0.1511	False		,,,				2504	0.1493				p.A278E		Atlas-SNP	.											.	NOM1	73	.	0			c.C833A						PASS	.	C	GLU/ALA	1082,3320		127,828,1246	72.0	46.0	55.0		833	-2.6	0.0	7	dbSNP_129	55	1249,7347		81,1087,3130	yes	missense	NOM1	NM_138400.1	107	208,1915,4376	AA,AC,CC		14.53,24.5797,17.9335	possibly-damaging	278/861	156743264	2331,10667	2201	4298	6499	SO:0001583	missense	64434	exon1			CAGAAGCGCAGAG	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.833C>A	7.37:g.156743264C>A	ENSP00000275820:p.Ala278Glu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	461	0.21108058608058608	108	0.21951219512195122	68	0.1878453038674033	161	0.28146853146853146	124	0.16358839050131926	C	0.887	-0.726873	0.03158	0.245797	0.1453	ENSG00000146909	ENST00000275820	T	0.10763	2.84	3.69	-2.63	0.06133	.	1.150490	0.06756	U	0.780893	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.42275	-0.9461	9	0.02654	T	1	-0.2561	0.9805	0.01435	0.3286:0.2021:0.2974:0.172	rs61747373	278	Q5C9Z4	NOM1_HUMAN	E	278	ENSP00000275820:A278E	ENSP00000275820:A278E	A	+	2	0	NOM1	156436025	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.720000	0.04969	-0.389000	0.07786	-0.302000	0.09304	GCG	C|0.807;A|0.193	0.193	strong		0.542	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
CCDC71	64925	hgsc.bcm.edu	37	3	49200627	49200627	+	Missense_Mutation	SNP	A	A	G	rs4955418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49200627A>G	ENST00000321895.6	-	2	1121	c.1015T>C	c.(1015-1017)Tgg>Cgg	p.W339R		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	339			W -> R (in dbSNP:rs4955418). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		gccttggcccatgctgccatg	0.632													g|||	3726	0.74401	0.5651	0.719	5008	,	,		19982	0.9435		0.6461	False		,,,				2504	0.8988				p.W339R		Atlas-SNP	.											.	CCDC71	33	.	0			c.T1015C						PASS	.	-	ARG/TRP	2456,1950	548.2+/-377.5	695,1066,442	80.0	64.0	69.0		1015	2.9	0.0	3	dbSNP_111	69	5298,3302	492.8+/-373.4	1634,2030,636	yes	missense	CCDC71	NM_022903.3	101	2329,3096,1078	GG,GA,AA		38.3953,44.2578,40.3814	benign	339/468	49200627	7754,5252	2203	4300	6503	SO:0001583	missense	64925	exon2			TGGCCCATGCTGC	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.1015T>C	3.37:g.49200627A>G	ENSP00000319006:p.Trp339Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	37	CCDS2790.1	1550	0.7097069597069597	271	0.5508130081300813	259	0.7154696132596685	533	0.9318181818181818	487	0.6424802110817942	g	0.007	-1.976971	0.00452	0.557422	0.616047	ENSG00000177352	ENST00000321895	T	0.27557	1.66	4.75	2.87	0.33458	.	0.665589	0.12566	N	0.457767	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	0.22977	-1.0201	9	0.13853	T	0.58	-26.4193	5.0066	0.14291	0.185:0.0:0.6387:0.1763	rs4955418;rs17857065;rs59266848;rs4955418	339	Q8IV32	CCD71_HUMAN	R	339	ENSP00000319006:W339R	ENSP00000319006:W339R	W	-	1	0	CCDC71	49175631	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	-0.502000	0.06390	0.631000	0.30412	-0.224000	0.12420	TGG	A|0.347;G|0.653	0.653	strong		0.632	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903	
JMJD4	65094	hgsc.bcm.edu	37	1	227920103	227920103	+	Missense_Mutation	SNP	G	G	A	rs3087908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:227920103G>A	ENST00000366758.3	-	6	1381	c.1382C>T	c.(1381-1383)gCg>gTg	p.A461V	SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000438896.2_Missense_Mutation_p.A445V|SNAP47_ENST00000315781.5_5'Flank|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000480897.1_3'UTR|SNAP47_ENST00000366759.4_5'Flank	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	461			A -> V (in dbSNP:rs3087908).							endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				CTATGGGGCCGCAGCAGCATC	0.612													G|||	881	0.175919	0.1445	0.2723	5008	,	,		18954	0.2093		0.1531	False		,,,				2504	0.1391				p.A461V		Atlas-SNP	.											.	JMJD4	28	.	0			c.C1382T						PASS	.	G	VAL/ALA,VAL/ALA	668,3738	272.2+/-270.6	61,546,1596	38.0	41.0	40.0		1334,1382	-2.1	0.0	1	dbSNP_102	40	1621,6979	293.0+/-301.1	134,1353,2813	yes	missense,missense	JMJD4	NM_001161465.1,NM_023007.2	64,64	195,1899,4409	AA,AG,GG		18.8488,15.1611,17.5996	benign,benign	445/448,461/464	227920103	2289,10717	2203	4300	6503	SO:0001583	missense	65094	exon6			GGGGCCGCAGCAG	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.1382C>T	1.37:g.227920103G>A	ENSP00000355720:p.Ala461Val	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	293	150	0.511945	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Missense_Mutation	SNP	ENST00000366758.3	37	CCDS1561.1	427|427	0.1955128205128205|0.1955128205128205	80|80	0.16260162601626016|0.16260162601626016	87|87	0.24033149171270718|0.24033149171270718	144|144	0.2517482517482518|0.2517482517482518	116|116	0.15303430079155672|0.15303430079155672	G|G	6.713|6.713	0.500318|0.500318	0.12762|0.12762	0.151611|0.151611	0.188488|0.188488	ENSG00000081692|ENSG00000081692	ENST00000366758|ENST00000438896	T|T	0.18810|0.20738	2.19|2.05	4.6|4.6	-2.14|-2.14	0.07123|0.07123	.|.	1.649630|.	0.02955|.	N|.	0.142231|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.18968|.	0.032;0.002|.	B;B|.	0.08055|.	0.003;0.0|.	T|T	0.46965|0.46965	-0.9153|-0.9153	9|5	0.13108|.	T|.	0.6|.	4.2357|4.2357	5.9147|5.9147	0.19048|0.19048	0.4037:0.0:0.4699:0.1264|0.4037:0.0:0.4699:0.1264	rs3087908;rs17619568;rs3087908|rs3087908;rs17619568;rs3087908	445;461|.	Q9H9V9-2;Q9H9V9|.	.;JMJD4_HUMAN|.	V|W	461|438	ENSP00000355720:A461V|ENSP00000387830:R438W	ENSP00000355720:A461V|.	A|R	-|-	2|1	0|2	JMJD4|JMJD4	225986726|225986726	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.172000|-0.172000	0.09868|0.09868	-0.849000|-0.849000	0.04158|0.04158	-1.598000|-1.598000	0.00824|0.00824	GCG|CGG	G|0.818;N|0.001	.	strong		0.612	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45566276	45566276	+	Silent	SNP	G	G	A	rs45501996	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:45566276G>A	ENST00000588982.1	-	3	1704	c.1203C>T	c.(1201-1203)ttC>ttT	p.F401F	ZBTB7C_ENST00000332053.2_Silent_p.F401F|ZBTB7C_ENST00000590800.1_Silent_p.F401F|ZBTB7C_ENST00000535628.2_Silent_p.F401F|ZBTB7C_ENST00000586438.1_Silent_p.F401F			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	401							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						CGCACCTGGTGAAGCGGACCT	0.662													G|||	984	0.196486	0.2632	0.1988	5008	,	,		18158	0.2252		0.174	False		,,,				2504	0.0982				p.F401F		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.C1203T						PASS	.	G		1130,3276	394.7+/-329.4	161,808,1234	63.0	64.0	63.0		1203	1.5	1.0	18	dbSNP_130	63	1430,7170	271.9+/-289.8	114,1202,2984	yes	coding-synonymous	ZBTB7C	NM_001039360.2		275,2010,4218	AA,AG,GG		16.6279,25.6468,19.6832		401/620	45566276	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	201501	exon2			CCTGGTGAAGCGG	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.1203C>T	18.37:g.45566276G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			G|0.804;A|0.196	0.196	strong		0.662	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
VAV2	7410	hgsc.bcm.edu	37	9	136662928	136662928	+	Silent	SNP	A	A	G	rs7865299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136662928A>G	ENST00000371850.3	-	10	871	c.840T>C	c.(838-840)ctT>ctC	p.L280L	VAV2_ENST00000406606.3_Silent_p.L275L|VAV2_ENST00000371851.1_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	103	0	0		WXS	Illumina HiSeq	Phase_I	116	116	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		
ALOXE3	59344	hgsc.bcm.edu	37	17	7999957	7999957	+	Silent	SNP	G	G	A	rs3809881	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7999957G>A	ENST00000448843.2	-	16	2464	c.2124C>T	c.(2122-2124)agC>agT	p.S708S	ALOXE3_ENST00000380149.1_Silent_p.S864S|ALOXE3_ENST00000318227.3_Silent_p.S840S	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	708	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						AGATGGAGACGCTGTTCTCAA	0.582													G|||	2127	0.42472	0.2504	0.5735	5008	,	,		18332	0.6022		0.4205	False		,,,				2504	0.3763				p.S840S		Atlas-SNP	.											ALOXE3_ENST00000318227,NS,carcinoma,0,2	ALOXE3	145	2	0			c.C2520T						PASS	.	G	,	1211,3195	419.8+/-338.8	161,889,1153	183.0	167.0	172.0		2520,2124	-9.0	0.2	17	dbSNP_107	172	3581,5019	518.5+/-379.3	754,2073,1473	no	coding-synonymous,coding-synonymous	ALOXE3	NM_001165960.1,NM_021628.2	,	915,2962,2626	AA,AG,GG		41.6395,27.4852,36.8445	,	840/844,708/712	7999957	4792,8214	2203	4300	6503	SO:0001819	synonymous_variant	59344	exon16			GGAGACGCTGTTC	AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"""Arachidonate lipoxygenases"""	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.2124C>T	17.37:g.7999957G>A		Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	252	107	0.424603	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Silent	SNP	ENST00000448843.2	37	CCDS11130.1																																																																																			G|0.593;A|0.407	0.407	strong		0.582	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1		
TSSC1	7260	hgsc.bcm.edu	37	2	3261173	3261173	+	Silent	SNP	A	A	G	rs10188932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:3261173A>G	ENST00000382125.4	-	4	505	c.313T>C	c.(313-315)Ttg>Ctg	p.L105L	TSSC1_ENST00000443925.2_Silent_p.L105L|TSSC1_ENST00000398659.4_Silent_p.L132L|TSSC1_ENST00000478754.1_5'UTR	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	105										breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CCTGATTCCAATTCCTTCGGC	0.542													A|||	199	0.0397364	0.0635	0.0115	5008	,	,		18120	0.0079		0.0338	False		,,,				2504	0.0665				p.L105L	Colon(140;1261 1762 4183 34270 49743)	Atlas-SNP	.											.	TSSC1	39	.	0			c.T313C						PASS	.	A		270,4136	151.4+/-185.3	10,250,1943	109.0	96.0	100.0		313	-0.5	0.4	2	dbSNP_119	100	289,8311	106.2+/-167.1	5,279,4016	no	coding-synonymous	TSSC1	NM_003310.2		15,529,5959	GG,GA,AA		3.3605,6.128,4.298		105/388	3261173	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	7260	exon4			ATTCCAATTCCTT	AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"""WD repeat domain containing"""	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.313T>C	2.37:g.3261173A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_003310	D6W4Y1|O43179|Q53S19|Q53SG2	Silent	SNP	ENST00000382125.4	37	CCDS1651.1																																																																																			A|0.960;G|0.040	0.040	strong		0.542	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310	
SMCO2	341346	hgsc.bcm.edu	37	12	27648786	27648786	+	Silent	SNP	A	A	G	rs306646	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:27648786A>G	ENST00000535986.1	+	7	831	c.831A>G	c.(829-831)gcA>gcG	p.A277A	SMCO2_ENST00000298876.4_Silent_p.A227A|SMCO2_ENST00000416383.1_Silent_p.A277A			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	277						integral component of membrane (GO:0016021)											GCAATACAGCATGGTAAGTCA	0.468													G|||	1557	0.310903	0.5144	0.1801	5008	,	,		16172	0.4048		0.0825	False		,,,				2504	0.2669				p.A277A		Atlas-SNP	.											.	.	.	.	0			c.A831G						PASS	.	G		553,811		146,261,275	50.0	43.0	45.0		831	-0.6	0.1	12	dbSNP_79	45	286,2894		19,248,1323	no	coding-synonymous	C12orf70	NM_001145010.1		165,509,1598	GG,GA,AA		8.9937,40.5425,18.4639		277/344	27648786	839,3705	682	1590	2272	SO:0001819	synonymous_variant	0	exon8			TACAGCATGGTAA		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.831A>G	12.37:g.27648786A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_001145010		Silent	SNP	ENST00000535986.1	37	CCDS44852.1																																																																																			A|0.729;G|0.271	0.271	strong		0.468	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
COL24A1	255631	hgsc.bcm.edu	37	1	86590948	86590948	+	Silent	SNP	A	A	G	rs11161746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:86590948A>G	ENST00000370571.2	-	3	1437	c.1071T>C	c.(1069-1071)agT>agC	p.S357S	COL24A1_ENST00000436319.1_Silent_p.S357S	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	357					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)		TTTTTGCCTCACTGATGCGAT	0.408													A|||	692	0.138179	0.0794	0.1614	5008	,	,		18266	0.0605		0.165	False		,,,				2504	0.2536				p.S357S		Atlas-SNP	.											.	COL24A1	202	.	0			c.T1071C						PASS	.	A		333,3541		16,301,1620	147.0	129.0	135.0		1071	-5.3	0.0	1	dbSNP_120	135	1232,7022		102,1028,2997	no	coding-synonymous	COL24A1	NM_152890.5		118,1329,4617	GG,GA,AA		14.9261,8.5958,12.904		357/1715	86590948	1565,10563	1937	4127	6064	SO:0001819	synonymous_variant	255631	exon3			TGCCTCACTGATG	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.1071T>C	1.37:g.86590948A>G		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	197	91	0.461929	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	37	CCDS41353.1																																																																																			A|0.886;G|0.114	0.114	strong		0.408	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189184	11189184	+	Missense_Mutation	SNP	C	C	T	rs115295428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11189184C>T	ENST00000382435.4	+	1	788	c.569C>T	c.(568-570)aCc>aTc	p.T190I		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	190						integral component of membrane (GO:0016021)		p.T190I(1)									GTCTACACCACCCTGGGCTAT	0.587																																					p.T190I		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.C569T						scavenged	.						145.0	143.0	143.0					8																	11189184		2203	4300	6503	SO:0001583	missense	83650	exon1			ACACCACCCTGGG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.569C>T	8.37:g.11189184C>T	ENSP00000371872:p.Thr190Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	209	34	0.162679	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	C	6.076	0.382330	0.11524	.	.	ENSG00000177710	ENST00000382435	T	0.24151	1.87	.	.	.	.	0.138504	0.32287	N	0.006302	T	0.10937	0.0267	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	8	0.18276	T	0.48	-0.7964	.	.	.	.	190	Q96KT7	S35G5_HUMAN	I	190	ENSP00000371872:T190I	ENSP00000371872:T190I	T	+	2	0	SLC35G5	11226594	0.778000	0.28640	0.080000	0.20451	0.075000	0.17131	0.362000	0.20284	0.088000	0.17205	0.089000	0.15464	ACC	C|0.978;T|0.022	0.022	strong		0.587	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
ITPK1	3705	hgsc.bcm.edu	37	14	93412743	93412743	+	Silent	SNP	G	G	A	rs2295394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:93412743G>A	ENST00000267615.6	-	10	1007	c.834C>T	c.(832-834)ttC>ttT	p.F278F	ITPK1_ENST00000556954.1_5'UTR|ITPK1_ENST00000354313.3_Silent_p.F278F|ITPK1_ENST00000556603.2_Silent_p.F278F|ITPK1_ENST00000555495.1_Silent_p.F159F			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	278	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		TGTCGATGCCGAAGAGTGACA	0.647													G|||	545	0.108826	0.0756	0.0461	5008	,	,		20421	0.2133		0.0606	False		,,,				2504	0.1401				p.F278F		Atlas-SNP	.											.	ITPK1	53	.	0			c.C834T						PASS	.	G	,,	365,4041	186.4+/-213.3	17,331,1855	117.0	102.0	107.0		834,834,834	-5.1	0.5	14	dbSNP_100	107	544,8056	149.5+/-204.6	18,508,3774	no	coding-synonymous,coding-synonymous,coding-synonymous	ITPK1	NM_001142593.1,NM_001142594.1,NM_014216.4	,,	35,839,5629	AA,AG,GG		6.3256,8.2842,6.9891	,,	278/415,278/315,278/415	93412743	909,12097	2203	4300	6503	SO:0001819	synonymous_variant	3705	exon10			GATGCCGAAGAGT	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"""inositol 1,3,4-triphosphate 5/6 kinase"""			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.834C>T	14.37:g.93412743G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_001142593	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	37	CCDS9907.1																																																																																			G|0.914;A|0.086	0.086	strong		0.647	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216	
GEN1	348654	hgsc.bcm.edu	37	2	17942775	17942775	+	Missense_Mutation	SNP	T	T	A	rs1812152	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:17942775T>A	ENST00000381254.2	+	3	488	c.274T>A	c.(274-276)Tct>Act	p.S92T	GEN1_ENST00000317402.7_Missense_Mutation_p.S92T|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	92	N-domain.		S -> T (in dbSNP:rs1812152). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)					GAGGAATCAGTCTCGGTATGG	0.388								Homologous recombination					A|||	4075	0.813698	0.7708	0.781	5008	,	,		16335	0.9861		0.6382	False		,,,				2504	0.8978				p.S92T		Atlas-SNP	.											.	GEN1	79	.	0			c.T274A						PASS	.	A	THR/SER,THR/SER	3347,1059	386.3+/-326.1	1278,791,134	88.0	90.0	89.0		274,274	0.3	0.9	2	dbSNP_92	89	5383,3217	487.0+/-372.0	1671,2041,588	yes	missense,missense	GEN1	NM_001130009.1,NM_182625.3	58,58	2949,2832,722	AA,AT,TT		37.407,24.0354,32.8771	benign,benign	92/909,92/909	17942775	8730,4276	2203	4300	6503	SO:0001583	missense	348654	exon3			AATCAGTCTCGGT	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.274T>A	2.37:g.17942775T>A	ENSP00000370653:p.Ser92Thr	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	214	95	0.443925	NM_182625	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	37	CCDS1691.1	1716	0.7857142857142857	393	0.7987804878048781	271	0.7486187845303868	559	0.9772727272727273	493	0.6503957783641161	A	2.445	-0.327812	0.05314	0.759646	0.62593	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000524465;ENST00000532257	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.35	0.326	0.15908	XPG N-terminal (2);	0.471865	0.20871	N	0.084169	T	0.00012	0.0000	N	0.02865	-0.47	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.06405	0.002	T	0.28138	-1.0053	9	0.11794	T	0.64	-3.1421	6.29	0.21054	0.6128:0.0:0.2761:0.1111	rs1812152;rs17315562;rs52822022;rs56931969;rs1812152	92	Q17RS7	GEN_HUMAN	T	92	ENSP00000318977:S92T;ENSP00000370653:S92T;ENSP00000435143:S92T;ENSP00000433180:S92T	ENSP00000318977:S92T	S	+	1	0	GEN1	17806256	0.189000	0.23263	0.898000	0.35279	0.215000	0.24574	0.567000	0.23608	-0.076000	0.12775	-0.257000	0.10917	TCT	T|0.279;A|0.721	0.721	strong		0.388	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
PARVG	64098	hgsc.bcm.edu	37	22	44594584	44594584	+	Silent	SNP	C	C	G	rs139152	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:44594584C>G	ENST00000444313.3	+	12	1279	c.795C>G	c.(793-795)ccC>ccG	p.P265P	PARVG_ENST00000415224.1_Silent_p.P265P|PARVG_ENST00000422871.1_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	173	0	0		WXS	Illumina HiSeq	Phase_I	188	87	0.462766	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	
LIG4	3981	hgsc.bcm.edu	37	13	108861913	108861913	+	Silent	SNP	A	A	G	rs1805386	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:108861913A>G	ENST00000356922.4	-	2	1976	c.1704T>C	c.(1702-1704)gaT>gaC	p.D568D	LIG4_ENST00000405925.1_Silent_p.D568D|LIG4_ENST00000442234.1_Silent_p.D568D	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	568					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					TTTTATACATATCACTGGGTA	0.423								Non-homologous end-joining					A|||	344	0.0686901	0.0507	0.1326	5008	,	,		19957	0.001		0.1481	False		,,,				2504	0.0358				p.D568D		Atlas-SNP	.											.	LIG4	91	.	0			c.T1704C						PASS	.	A	,,	352,4054	182.6+/-210.3	12,328,1863	98.0	91.0	93.0		1704,1704,1704	-11.5	0.1	13	dbSNP_92	93	1581,7019	295.9+/-302.6	145,1291,2864	no	coding-synonymous,coding-synonymous,coding-synonymous	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	,,	157,1619,4727	GG,GA,AA		18.3837,7.9891,14.8624	,,	568/912,568/912,568/912	108861913	1933,11073	2203	4300	6503	SO:0001819	synonymous_variant	3981	exon3			ATACATATCACTG	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.1704T>C	13.37:g.108861913A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_206937	Q8IY66|Q8TEU5	Silent	SNP	ENST00000356922.4	37	CCDS9508.1																																																																																			A|0.870;G|0.130	0.130	strong		0.423	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
KIAA0586	9786	hgsc.bcm.edu	37	14	58910784	58910784	+	Missense_Mutation	SNP	G	G	A	rs193056942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:58910784G>A	ENST00000556134.1	+	7	927	c.653G>A	c.(652-654)aGg>aAg	p.R218K	KIAA0586_ENST00000261244.5_Missense_Mutation_p.R233K|Y_RNA_ENST00000516389.1_RNA|KIAA0586_ENST00000354386.6_Missense_Mutation_p.R286K|KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000423743.3_Missense_Mutation_p.R189K	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	218					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGCATTCAGAGGAAACAAGAG	0.353													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18841	0.0		0.001	False		,,,				2504	0.0				p.R286K		Atlas-SNP	.											.	KIAA0586	180	.	0			c.G857A						PASS	.	G	LYS/ARG	0,3876		0,0,1938	96.0	87.0	90.0		698	-2.7	0.2	14		90	24,8264		0,24,4120	yes	missense	KIAA0586	NM_014749.3	26	0,24,6058	AA,AG,GG		0.2896,0.0,0.1973	benign	233/1473	58910784	24,12140	1938	4144	6082	SO:0001583	missense	9786	exon8			TTCAGAGGAAACA	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.653G>A	14.37:g.58910784G>A	ENSP00000452351:p.Arg218Lys	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	290	129	0.444828	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	37	CCDS58321.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	8.870	0.949111	0.18356	0.0	0.002896	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000555833;ENST00000261244;ENST00000546216	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.84	-2.69	0.06022	.	1.131010	0.06384	N	0.715728	T	0.19565	0.0470	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.19706	0.0;0.0;0.038;0.0;0.0;0.0	B;B;B;B;B;B	0.15870	0.0;0.0;0.014;0.0;0.0;0.0	T	0.22417	-1.0217	10	0.51188	T	0.08	.	3.4716	0.07569	0.3834:0.1633:0.361:0.0922	.	93;93;286;233;218;189	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	K	286;218;189;148;233;93	ENSP00000346359:R286K;ENSP00000452351:R218K;ENSP00000399427:R189K;ENSP00000450855:R148K;ENSP00000261244:R233K	ENSP00000261244:R233K	R	+	2	0	KIAA0586	57980537	0.010000	0.17322	0.246000	0.24233	0.613000	0.37349	0.132000	0.15891	-0.090000	0.12462	-0.312000	0.09012	AGG	G|0.999;A|0.001	0.001	strong		0.353	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749	
DECR2	26063	hgsc.bcm.edu	37	16	460976	460976	+	Silent	SNP	G	G	A	rs140561403	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:460976G>A	ENST00000219481.5	+	7	699	c.561G>A	c.(559-561)gcG>gcA	p.A187A	DECR2_ENST00000461947.1_3'UTR|DECR2_ENST00000424398.2_Silent_p.A175A	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	187					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				GTGCAGACGCGATGACGCGGC	0.657													G|||	28	0.00559105	0.0008	0.0187	5008	,	,		16609	0.001		0.0119	False		,,,				2504	0.001				p.A187A		Atlas-SNP	.											DECR2,NS,carcinoma,+1,1	DECR2	47	1	0			c.G561A						PASS	.	G		37,4355		0,37,2159	43.0	41.0	42.0		561	-11.0	0.5	16	dbSNP_134	42	141,8453		1,139,4157	no	coding-synonymous	DECR2	NM_020664.3		1,176,6316	AA,AG,GG		1.6407,0.8424,1.3707		187/293	460976	178,12808	2196	4297	6493	SO:0001819	synonymous_variant	26063	exon7			AGACGCGATGACG	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	2754	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 17C, member 1"""	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.561G>A	16.37:g.460976G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_020664	Q6ZRS7|Q96ET0	Silent	SNP	ENST00000219481.5	37	CCDS10409.1																																																																																			G|0.988;A|0.012	0.012	strong		0.657	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664	
FBN2	2201	hgsc.bcm.edu	37	5	127638759	127638759	+	Silent	SNP	A	A	G	rs11955288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:127638759A>G	ENST00000508053.1	-	52	6797	c.5823T>C	c.(5821-5823)caT>caC	p.H1941H	FBN2_ENST00000262464.4_Silent_p.H1941H			P35556	FBN2_HUMAN	fibrillin 2	1941	EGF-like 32; 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)		TTCCACATGGATGCCGCTCGC	0.358													A|||	465	0.0928514	0.1029	0.0692	5008	,	,		16087	0.0655		0.0954	False		,,,				2504	0.1217				p.H1941H		Atlas-SNP	.											.	FBN2	858	.	0			c.T5823C						PASS	.	A		466,3940	220.4+/-237.8	18,430,1755	126.0	127.0	127.0		5823	1.5	1.0	5	dbSNP_120	127	888,7712	198.5+/-242.8	47,794,3459	no	coding-synonymous	FBN2	NM_001999.3		65,1224,5214	GG,GA,AA		10.3256,10.5765,10.4106		1941/2913	127638759	1354,11652	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon46			ACATGGATGCCGC	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.5823T>C	5.37:g.127638759A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			A|0.901;G|0.099	0.099	strong		0.358	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
MYPN	84665	hgsc.bcm.edu	37	10	69934012	69934012	+	Silent	SNP	C	C	A	rs71584491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:69934012C>A	ENST00000358913.5	+	11	2651	c.2163C>A	c.(2161-2163)gcC>gcA	p.A721A	MYPN_ENST00000540630.1_Silent_p.A721A|MYPN_ENST00000354393.2_Silent_p.A446A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	721					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TCAGCTTGGCCCGGCCGAAGT	0.537													C|||	215	0.0429313	0.1331	0.0173	5008	,	,		18309	0.0		0.0109	False		,,,				2504	0.0164				p.A721A		Atlas-SNP	.											.	MYPN	189	.	0			c.C2163A						PASS	.	C		458,3948	218.4+/-236.5	22,414,1767	117.0	120.0	119.0		2163	4.1	1.0	10	dbSNP_130	119	106,8494	57.2+/-118.5	0,106,4194	no	coding-synonymous	MYPN	NM_032578.2		22,520,5961	AA,AC,CC		1.2326,10.3949,4.3365		721/1321	69934012	564,12442	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon11			CTTGGCCCGGCCG	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2163C>A	10.37:g.69934012C>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	175	88	0.502857	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			C|0.956;A|0.044	0.044	strong		0.537	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
PCNT	5116	hgsc.bcm.edu	37	21	47855876	47855876	+	Silent	SNP	A	A	G	rs17371795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47855876A>G	ENST00000359568.5	+	39	8918	c.8811A>G	c.(8809-8811)acA>acG	p.T2937T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2937					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)					TTCAGCAGACAGTGAGAGACC	0.567													A|||	736	0.146965	0.0666	0.1801	5008	,	,		17570	0.1994		0.1252	False		,,,				2504	0.2004				p.T2937T		Atlas-SNP	.											.	PCNT	283	.	0			c.A8811G						PASS	.	A		280,4126	155.5+/-188.7	11,258,1934	91.0	96.0	95.0		8811	-6.5	0.0	21	dbSNP_123	95	1056,7544	223.0+/-259.9	63,930,3307	no	coding-synonymous	PCNT	NM_006031.5		74,1188,5241	GG,GA,AA		12.2791,6.355,10.2722		2937/3337	47855876	1336,11670	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon39			GCAGACAGTGAGA	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.8811A>G	21.37:g.47855876A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			A|0.881;G|0.119	0.119	strong		0.567	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
LMX1A	4009	hgsc.bcm.edu	37	1	165218679	165218679	+	Silent	SNP	C	C	T	rs9970062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:165218679C>T	ENST00000342310.3	-	4	844	c.462G>A	c.(460-462)ctG>ctA	p.L154L	LMX1A_ENST00000294816.2_Silent_p.L154L|LMX1A_ENST00000367893.4_Silent_p.L154L	NM_177398.3	NP_796372.1	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	154	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon guidance (GO:0007411)|central nervous system neuron differentiation (GO:0021953)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|dopaminergic neuron differentiation (GO:0071542)|midbrain development (GO:0030901)|negative regulation of neuron differentiation (GO:0045665)|regulation of cell growth (GO:0001558)|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(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35	all_hematologic(923;0.248)					CCAGGCTGAGCAGCTCCCGCT	0.622													C|||	1086	0.216853	0.2867	0.2032	5008	,	,		17592	0.0823		0.3181	False		,,,				2504	0.1667				p.L154L		Atlas-SNP	.											.	LMX1A	87	.	0			c.G462A						PASS	.	C	,	1313,3093	443.9+/-347.2	191,931,1081	68.0	64.0	65.0		462,462	0.4	1.0	1	dbSNP_119	65	2553,6047	416.3+/-352.1	386,1781,2133	no	coding-synonymous,coding-synonymous	LMX1A	NM_001174069.1,NM_177398.3	,	577,2712,3214	TT,TC,CC		29.686,29.8003,29.7247	,	154/383,154/383	165218679	3866,9140	2203	4300	6503	SO:0001819	synonymous_variant	4009	exon4			GCTGAGCAGCTCC	AY078391	CCDS1247.1	1q24.1	2011-06-20			ENSG00000162761	ENSG00000162761		"""Homeoboxes / LIM class"""	6653	protein-coding gene	gene with protein product		600298		LMX1		7698771	Standard	NM_177398		Approved	LMX1.1	uc001gcz.2	Q8TE12	OTTHUMG00000034575	ENST00000342310.3:c.462G>A	1.37:g.165218679C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_001174069	B3KXP6|Q0VDB5|Q5VWG4|Q8TE11	Silent	SNP	ENST00000342310.3	37	CCDS1247.1																																																																																			C|0.720;T|0.280	0.280	strong		0.622	LMX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083668.2	NM_177398	
POLR2A	5430	hgsc.bcm.edu	37	17	7411770	7411770	+	Silent	SNP	C	C	T	rs2228132	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7411770C>T	ENST00000322644.6	+	20	3840	c.3441C>T	c.(3439-3441)tcC>tcT	p.S1147S		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1147					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)				TGGGCCAGTCCGCTCGAGATG	0.527													c|||	790	0.157748	0.1725	0.098	5008	,	,		20256	0.0228		0.1849	False		,,,				2504	0.2914				p.S1147S		Atlas-SNP	.											POLR2A,caecum,carcinoma,0,1	POLR2A	157	1	0			c.C3441T						scavenged	.	T		726,3680	291.3+/-281.4	65,596,1542	65.0	39.0	48.0		3441	0.0	1.0	17	dbSNP_98	48	1796,6804	305.2+/-307.3	224,1348,2728	no	coding-synonymous	POLR2A	NM_000937.4		289,1944,4270	TT,TC,CC		20.8837,16.4775,19.3911		1147/1971	7411770	2522,10484	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon20			CCAGTCCGCTCGA			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.3441C>T	17.37:g.7411770C>T		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	209	103	0.492823	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			C|0.834;T|0.166	0.166	strong		0.527	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
CNN2	1265	hgsc.bcm.edu	37	19	1036468	1036468	+	Silent	SNP	A	A	G	rs1064411	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1036468A>G	ENST00000263097.4	+	6	924	c.561A>G	c.(559-561)agA>agG	p.R187R	CNN2_ENST00000565096.2_Silent_p.R176R|CNN2_ENST00000606983.1_3'UTR|CNN2_ENST00000348419.3_Silent_p.R148R|CNN2_ENST00000562958.2_Silent_p.R208R|AC011558.5_ENST00000585757.1_RNA	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	187				RRHLYDPKNHILPPMD -> AGISMTPRTISCPPWT (in Ref. 6; BAA20887). {ECO:0000305}.	actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGGCACGAGAAGGCATCTCT	0.602													G|||	570	0.113818	0.0855	0.0951	5008	,	,		17403	0.0962		0.1968	False		,,,				2504	0.0982				p.R187R		Atlas-SNP	.											.	CNN2	26	.	0			c.A561G						PASS	.	G	,	446,3960	783.9+/-414.7	24,398,1781	74.0	70.0	71.0		561,444	-0.7	0.0	19	dbSNP_86	71	1807,6793	731.6+/-406.8	178,1451,2671	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	202,1849,4452	GG,GA,AA		21.0116,10.1226,17.3228	,	187/310,148/271	1036468	2253,10753	2203	4300	6503	SO:0001819	synonymous_variant	1265	exon6			CACGAGAAGGCAT	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.561A>G	19.37:g.1036468A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	174	77	0.442529	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			A|0.837;G|0.163	0.163	strong		0.602	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
OR10H5	284433	hgsc.bcm.edu	37	19	15905414	15905414	+	Missense_Mutation	SNP	A	A	C	rs61741438	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15905414A>C	ENST00000308940.8	+	1	654	c.556A>C	c.(556-558)Aag>Cag	p.K186Q		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	186						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						ACCTCTGTTGAAGTTGGCCTG	0.567													.|||	13	0.00259585	0.0008	0.0101	5008	,	,		22292	0.0		0.005	False		,,,				2504	0.0				p.K186Q		Atlas-SNP	.											.	OR10H5	49	.	0			c.A556C						PASS	.	A	GLN/LYS	17,4389		0,17,2186	168.0	135.0	146.0		556	1.2	0.8	19	dbSNP_129	146	193,8407		3,187,4110	yes	missense	OR10H5	NM_001004466.1	53	3,204,6296	CC,CA,AA		2.2442,0.3858,1.6146	possibly-damaging	186/316	15905414	210,12796	2203	4300	6503	SO:0001583	missense	284433	exon1			CTGTTGAAGTTGG	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.556A>C	19.37:g.15905414A>C	ENSP00000310704:p.Lys186Gln	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	293	150	0.511945	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	12	0.005494505494505495	0	0.0	6	0.016574585635359115	0	0.0	6	0.0079155672823219	.	12.71	2.019337	0.35606	0.003858	0.022442	ENSG00000172519	ENST00000308940	T	0.00269	8.37	3.36	1.16	0.20824	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000077	T	0.00109	0.0003	L	0.47016	1.485	0.24994	N	0.991513	P	0.44195	0.828	P	0.48524	0.58	T	0.44967	-0.9293	10	0.52906	T	0.07	.	3.2481	0.06804	0.55:0.2136:0.2364:0.0	rs61741438	186	Q8NGA6	O10H5_HUMAN	Q	186	ENSP00000310704:K186Q	ENSP00000310704:K186Q	K	+	1	0	OR10H5	15766414	0.001000	0.12720	0.778000	0.31720	0.431000	0.31685	0.545000	0.23268	0.052000	0.16007	0.477000	0.44152	AAG	A|0.985;C|0.015	0.015	strong		0.567	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
ASIC3	9311	hgsc.bcm.edu	37	7	150747650	150747650	+	Silent	SNP	G	G	T	rs62001897	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150747650G>T	ENST00000349064.5	+	3	966	c.768G>T	c.(766-768)ggG>ggT	p.G256G	ASIC3_ENST00000357922.4_Silent_p.G256G|ASIC3_ENST00000297512.8_Silent_p.G256G	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3	256					cation transmembrane transport (GO:0098655)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ion transmembrane transport (GO:0034220)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|response to heat (GO:0009408)|sensory perception (GO:0007600)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|enterobactin transporter activity (GO:0042931)|ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)										TGGGCTTGGGGGTGTCCCCGG	0.622													G|||	148	0.0295527	0.0098	0.0432	5008	,	,		16390	0.0317		0.0606	False		,,,				2504	0.0123				p.G256G		Atlas-SNP	.											.	.	.	.	0			c.G768T						PASS	.	G	,,	75,4331	67.0+/-104.6	0,75,2128	79.0	85.0	83.0		768,768,768	3.0	1.0	7	dbSNP_129	83	508,8092	145.0+/-200.8	11,486,3803	no	coding-synonymous,coding-synonymous,coding-synonymous	ACCN3	NM_004769.2,NM_020321.2,NM_020322.2	,,	11,561,5931	TT,TG,GG		5.907,1.7022,4.4825	,,	256/532,256/550,256/544	150747650	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	9311	exon3			CTTGGGGGTGTCC	AB010575	CCDS5914.1, CCDS5915.1, CCDS5916.1	7q35	2012-02-23	2012-02-22	2012-02-22	ENSG00000213199	ENSG00000213199		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	101	protein-coding gene	gene with protein product	"""testis sodium channel 1"""	611741	"""amiloride-sensitive cation channel 3, testis"", ""amiloride-sensitive cation channel 3"""	ACCN3		9571199, 9744806	Standard	NM_004769		Approved	TNaC1, DRASIC	uc003wio.3	Q9UHC3	OTTHUMG00000158685	ENST00000349064.5:c.768G>T	7.37:g.150747650G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	119	68	0.571429	NM_020322	B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Silent	SNP	ENST00000349064.5	37	CCDS5916.1																																																																																			G|0.956;T|0.044	0.044	strong		0.622	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3672240	3672240	+	Silent	SNP	G	G	A	rs111969446	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3672240G>A	ENST00000344754.4	-	17	4337	c.4338C>T	c.(4336-4338)cgC>cgT	p.R1446R	SIGLEC1_ENST00000202578.4_Silent_p.R1446R	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1446	Ig-like C2-type 15.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CTGCCACCACGCGTGCACCTG	0.667													G|||	53	0.0105831	0.0023	0.0029	5008	,	,		17190	0.001		0.0268	False		,,,				2504	0.0204				p.R1446R		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4338T						PASS	.	G		18,4388		0,18,2185	29.0	33.0	32.0		4338	-1.5	0.2	20	dbSNP_132	32	210,8384		3,204,4090	no	coding-synonymous	SIGLEC1	NM_023068.3		3,222,6275	AA,AG,GG		2.4436,0.4085,1.7538		1446/1710	3672240	228,12772	2203	4297	6500	SO:0001819	synonymous_variant	6614	exon17			CACCACGCGTGCA	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4338C>T	20.37:g.3672240G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	22	0.010073260073260074	0	0.0	0	0.0	0	0.0	22	0.029023746701846966	G	0.070	-1.204057	0.01581	0.004085	0.024436	ENSG00000088827	ENST00000419548	T	0.11821	2.74	5.34	-1.48	0.08745	.	1.124510	0.06783	N	0.785547	T	0.04497	0.0123	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.41520	-0.9504	7	0.66056	D	0.02	.	5.4318	0.16458	0.3977:0.1713:0.4311:0.0	.	.	.	.	C	260	ENSP00000395778:R260C	ENSP00000395778:R260C	R	-	1	0	SIGLEC1	3620240	0.000000	0.05858	0.200000	0.23457	0.014000	0.08584	-1.386000	0.02537	0.048000	0.15891	-0.345000	0.07892	CGT	G|0.985;A|0.015	0.015	strong		0.667	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
PLEKHG7	440107	hgsc.bcm.edu	37	12	93147907	93147907	+	Silent	SNP	A	A	T	rs9669519	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	167	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	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	
GNPTAB	79158	hgsc.bcm.edu	37	12	102224436	102224436	+	Silent	SNP	C	C	T	rs4764655	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102224436C>T	ENST00000299314.7	-	1	280	c.18G>A	c.(16-18)ctG>ctA	p.L6L	GNPTAB_ENST00000549165.1_Silent_p.L6L|GNPTAB_ENST00000392919.4_Silent_p.L6L|GNPTAB_ENST00000549940.1_Silent_p.L6L	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	6					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TCTGTCTCTGCAGGAGCTTGA	0.662													C|||	490	0.0978435	0.0182	0.1657	5008	,	,		8386	0.1637		0.1133	False		,,,				2504	0.0736				p.L6L		Atlas-SNP	.											.	GNPTAB	120	.	0			c.G18A						PASS	.	C		176,4230	110.8+/-149.0	4,168,2031	90.0	70.0	77.0		18	-3.7	0.1	12	dbSNP_111	77	1019,7581	209.0+/-250.3	61,897,3342	no	coding-synonymous	GNPTAB	NM_024312.4		65,1065,5373	TT,TC,CC		11.8488,3.9946,9.1881		6/1257	102224436	1195,11811	2203	4300	6503	SO:0001819	synonymous_variant	79158	exon1			TCTCTGCAGGAGC	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.18G>A	12.37:g.102224436C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Silent	SNP	ENST00000299314.7	37	CCDS9088.1																																																																																			C|0.900;T|0.100	0.100	strong		0.662	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1		
KIAA1033	23325	hgsc.bcm.edu	37	12	105550565	105550565	+	Silent	SNP	C	C	T	rs35149056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:105550565C>T	ENST00000332180.5	+	27	2907	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						GCAGCAATGCCATTAGGTATG	0.308													C|||	217	0.0433307	0.0166	0.0692	5008	,	,		14135	0.001		0.0795	False		,,,				2504	0.0675				p.A940A		Atlas-SNP	.											.	KIAA1033	83	.	0			c.C2820T						PASS	.	C		82,3618		1,80,1769	208.0	186.0	193.0		2820	4.9	1.0	12	dbSNP_126	193	613,7575		27,559,3508	no	coding-synonymous	KIAA1033	NM_015275.1		28,639,5277	TT,TC,CC		7.4866,2.2162,5.8462		940/1174	105550565	695,11193	1850	4094	5944	SO:0001819	synonymous_variant	23325	exon27			CAATGCCATTAGG	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2820C>T	12.37:g.105550565C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_015275		Silent	SNP	ENST00000332180.5	37	CCDS41826.1																																																																																			C|0.946;T|0.054	0.054	strong		0.308	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275	
TEP1	7011	hgsc.bcm.edu	37	14	20872881	20872881	+	Missense_Mutation	SNP	G	G	T	rs1760898	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20872881G>T	ENST00000262715.5	-	5	961	c.921C>A	c.(919-921)aaC>aaA	p.N307K	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	307	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.		N -> K (in dbSNP:rs1760898).		RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TGGCCAAGATGTTATTGGCCA	0.557													T|||	1827	0.364816	0.4894	0.2781	5008	,	,		21010	0.4167		0.2247	False		,,,				2504	0.3487				p.N307K		Atlas-SNP	.											.	TEP1	224	.	0			c.C921A						PASS	.	T	LYS/ASN	1989,2417	616.8+/-392.8	467,1055,681	78.0	73.0	74.0		921	-1.0	0.0	14	dbSNP_89	74	1865,6735	729.4+/-406.7	206,1453,2641	yes	missense	TEP1	NM_007110.4	94	673,2508,3322	TT,TG,GG		21.686,45.143,29.6325	benign	307/2628	20872881	3854,9152	2203	4300	6503	SO:0001583	missense	7011	exon5			CAAGATGTTATTG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.921C>A	14.37:g.20872881G>T	ENSP00000262715:p.Asn307Lys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	112	67	0.598214	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	737	0.3374542124542125	230	0.46747967479674796	106	0.292817679558011	221	0.38636363636363635	180	0.23746701846965698	T	10.03	1.237915	0.22711	0.45143	0.21686	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.14022	2.54	5.55	-0.961	0.10337	TROVE (2);	1.009720	0.07938	N	0.978726	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	9	0.10377	T	0.69	0.7568	2.53	0.04701	0.1169:0.3087:0.3471:0.2273	rs1760898;rs59063415;rs1760898	307	Q99973	TEP1_HUMAN	K	307	ENSP00000262715:N307K	ENSP00000262715:N307K	N	-	3	2	TEP1	19942721	0.017000	0.18338	0.001000	0.08648	0.936000	0.57629	0.083000	0.14871	-0.293000	0.08986	-0.256000	0.11100	AAC	G|0.682;T|0.318	0.318	strong		0.557	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
BCAS1	8537	hgsc.bcm.edu	37	20	52573971	52573971	+	Splice_Site	SNP	T	T	G	rs35575210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:52573971T>G	ENST00000395961.3	-	10	1582	c.1416A>C	c.(1414-1416)caA>caC	p.Q472H	BCAS1_ENST00000434986.2_Intron|BCAS1_ENST00000371435.2_Intron|BCAS1_ENST00000371440.3_Intron	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	472			Q -> H (in dbSNP:rs35575210).			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)			GGTCACTTACTTGGCAGCTGG	0.433													T|||	662	0.132188	0.0265	0.1354	5008	,	,		20559	0.1429		0.1899	False		,,,				2504	0.2025				p.Q472H		Atlas-SNP	.											.	BCAS1	77	.	0			c.A1416C						PASS	.	T	HIS/GLN	205,4201	125.7+/-162.9	3,199,2001	225.0	181.0	196.0		1416	4.4	1.0	20	dbSNP_126	196	1645,6955	302.6+/-306.0	151,1343,2806	yes	missense-near-splice	BCAS1	NM_003657.2	24	154,1542,4807	GG,GT,TT		19.1279,4.6527,14.2242	probably-damaging	472/585	52573971	1850,11156	2203	4300	6503	SO:0001630	splice_region_variant	8537	exon10			ACTTACTTGGCAG	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.1416+1A>C	20.37:g.52573971T>G		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	238	118	0.495798	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	278|278	0.12728937728937728|0.12728937728937728	10|10	0.02032520325203252|0.02032520325203252	58|58	0.16022099447513813|0.16022099447513813	68|68	0.11888111888111888|0.11888111888111888	142|142	0.18733509234828497|0.18733509234828497	T|T	18.88|18.88	3.717957|3.717957	0.68844|0.68844	0.046527|0.046527	0.191279|0.191279	ENSG00000064787|ENSG00000064787	ENST00000422805|ENST00000395961	.|T	.|0.21361	.|2.01	5.55|5.55	4.43|4.43	0.53597|0.53597	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.58101|0.58101	1.795|1.795	0.09310|0.09310	P|P	0.9999999999999795|0.9999999999999795	.|P;P	.|0.35348	.|0.496;0.496	.|B;B	.|0.34242	.|0.178;0.178	T|T	0.21177|0.21177	-1.0253|-1.0253	4|7	.|.	.|.	.|.	.|.	6.56|6.56	0.22481|0.22481	0.1465:0.0:0.1745:0.679|0.1465:0.0:0.1745:0.679	rs35575210;rs61749686|rs35575210;rs61749686	.|472;472	.|A0AVG7;O75363	.|.;BCAS1_HUMAN	T|H	135|472	.|ENSP00000379290:Q472H	.|.	K|Q	-|-	2|3	0|2	BCAS1|BCAS1	52007378|52007378	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.912000|0.912000	0.54170|0.54170	1.178000|1.178000	0.31981|0.31981	0.908000|0.908000	0.36671|0.36671	0.459000|0.459000	0.35465|0.35465	AAA|CAA	T|0.857;G|0.143	0.143	strong		0.433	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	Missense_Mutation
RNF130	55819	hgsc.bcm.edu	37	5	179498595	179498595	+	Silent	SNP	C	C	T	rs3749821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:179498595C>T	ENST00000261947.4	-	1	506	c.108G>A	c.(106-108)acG>acA	p.T36T	RNF130_ENST00000522208.2_Silent_p.T36T|RNF130_ENST00000521389.1_Silent_p.T36T	NM_001280801.1	NP_001267730.1			ring finger protein 130											breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGATGAGCGCCGTGTAGTACT	0.751													C|||	2993	0.597644	0.4092	0.6758	5008	,	,		7633	0.621		0.6193	False		,,,				2504	0.7505				p.T36T	GBM(24;432 554 38471 39699 51728)	Atlas-SNP	.											.	RNF130	49	.	0			c.G108A						PASS	.	C		1858,2406		455,948,729	11.0	12.0	12.0		108	1.0	1.0	5	dbSNP_107	12	5377,3081		1751,1875,603	no	coding-synonymous	RNF130	NM_018434.4		2206,2823,1332	TT,TC,CC		36.4271,43.5741,43.13		36/420	179498595	7235,5487	2132	4229	6361	SO:0001819	synonymous_variant	55819	exon1			GAGCGCCGTGTAG	AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"""RING-type (C3HC4) zinc fingers"""	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.108G>A	5.37:g.179498595C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	29	22	0.758621	NM_018434		Silent	SNP	ENST00000261947.4	37																																																																																				T|0.569;C|0.431;A|0.000	0.569	strong		0.751	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434	
TTN	7273	hgsc.bcm.edu	37	2	179430997	179430997	+	Missense_Mutation	SNP	G	G	A	rs3731746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179430997G>A	ENST00000591111.1	-	276	75163	c.74939C>T	c.(74938-74940)aCg>aTg	p.T24980M	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T26621M|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T17681M|TTN_ENST00000460472.2_Missense_Mutation_p.T17556M|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T17748M|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T24053M|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24980	Ig-like 123.		T -> M. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GATCTCAGGCGTTGGACGACC	0.418													G|||	1714	0.342252	0.3442	0.2061	5008	,	,		22404	0.629		0.171	False		,,,				2504	0.317				p.T26621M		Atlas-SNP	.											.	TTN	18412	.	0			c.C79862T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	1257,2583		208,841,871	161.0	155.0	157.0		52667,72158,53042,53243	5.0	1.0	2	dbSNP_107	157	1385,6915		116,1153,2881	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	81,81,81,81	324,1994,3752	AA,AG,GG		16.6867,32.7344,21.7628	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	17556/26927,24053/33424,17681/27052,17748/27119	179430997	2642,9498	1920	4150	6070	SO:0001583	missense	7273	exon326			TCAGGCGTTGGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74939C>T	2.37:g.179430997G>A	ENSP00000465570:p.Thr24980Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	148	83	0.560811	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		693	0.3173076923076923	157	0.31910569105691056	68	0.1878453038674033	341	0.5961538461538461	127	0.16754617414248021	G	9.152	1.016420	0.19355	0.327344	0.166867	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.91	5.03	0.67393	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.80183	2.485	0.25672	P	0.9858806	P;P;P;P	0.48694	0.914;0.914;0.914;0.914	P;P;P;P	0.50270	0.636;0.636;0.636;0.636	T	0.50338	-0.8840	8	0.87932	D	0	.	11.7884	0.52055	0.1854:0.0:0.8146:0.0	rs3731746;rs52794037;rs56683294;rs3731746	17556;17681;17748;24980	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	24053;17556;17748;17681;17554	ENSP00000343764:T24053M;ENSP00000434586:T17556M;ENSP00000340554:T17748M;ENSP00000352154:T17681M	ENSP00000340554:T17748M	T	-	2	0	TTN	179139243	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	2.938000	0.48987	1.485000	0.48380	0.555000	0.69702	ACG	T|0.000;G|0.681;N|0.000;A|0.318	0.318	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
WDR11	55717	hgsc.bcm.edu	37	10	122663585	122663585	+	Silent	SNP	G	G	A	rs1652727	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:122663585G>A	ENST00000263461.6	+	24	3204	c.2958G>A	c.(2956-2958)ctG>ctA	p.L986L	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			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						GGGTTAATCTGCAGGAAGTGA	0.328													A|||	3388	0.676518	0.8752	0.6657	5008	,	,		16683	0.5179		0.6511	False		,,,				2504	0.6053				p.L986L		Atlas-SNP	.											.	WDR11	95	.	0			c.G2958A						PASS	.	A		3786,620	270.1+/-269.4	1634,518,51	97.0	98.0	98.0		2958	-11.7	0.2	10	dbSNP_89	98	5628,2972	459.8+/-365.0	1853,1922,525	no	coding-synonymous	WDR11	NM_018117.11		3487,2440,576	AA,AG,GG		34.5581,14.0717,27.618		986/1225	122663585	9414,3592	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon24			TAATCTGCAGGAA	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.2958G>A	10.37:g.122663585G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			G|0.301;A|0.699	0.699	strong		0.328	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
MRPL37	51253	hgsc.bcm.edu	37	1	54681920	54681920	+	Missense_Mutation	SNP	G	G	C	rs13571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:54681920G>C	ENST00000360840.5	+	6	1174	c.1097G>C	c.(1096-1098)tGt>tCt	p.C366S	MRPL37_ENST00000336230.6_Missense_Mutation_p.C235S|MRPL37_ENST00000605337.1_Missense_Mutation_p.C366S	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	366			C -> S (in dbSNP:rs13571). {ECO:0000269|PubMed:11042152, ECO:0000269|Ref.1, ECO:0000269|Ref.3}.		translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						GACCTGGACTGTAACGAGGGT	0.522													C|||	2921	0.583267	0.6135	0.6398	5008	,	,		19939	0.4028		0.7922	False		,,,				2504	0.4734				p.C366S		Atlas-SNP	.											.	MRPL37	36	.	0			c.G1097C						PASS	.	C	SER/CYS	2894,1512	480.6+/-358.9	956,982,265	143.0	120.0	128.0		1097	5.4	0.0	1	dbSNP_52	128	6730,1870	331.5+/-319.7	2620,1490,190	yes	missense	MRPL37	NM_016491.3	112	3576,2472,455	CC,CG,GG		21.7442,34.3168,26.0034	benign	366/424	54681920	9624,3382	2203	4300	6503	SO:0001583	missense	51253	exon6			TGGACTGTAACGA	AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"""Mitochondrial ribosomal proteins / large subunits"""	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.1097G>C	1.37:g.54681920G>C	ENSP00000354086:p.Cys366Ser	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	285	141	0.494737	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Missense_Mutation	SNP	ENST00000360840.5	37	CCDS589.1	1369|1369	0.6268315018315018|0.6268315018315018	289|289	0.5873983739837398|0.5873983739837398	235|235	0.649171270718232|0.649171270718232	248|248	0.43356643356643354|0.43356643356643354	597|597	0.787598944591029|0.787598944591029	C|C	0.005|0.005	-2.149684|-2.149684	0.00328|0.00328	0.656832|0.656832	0.782558|0.782558	ENSG00000116221|ENSG00000116221	ENST00000360840;ENST00000329505;ENST00000336230|ENST00000398219	T;T|.	0.14516|.	2.5;2.5|.	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	0.292058|.	0.38548|.	N|.	0.001646|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00069|0.00069	-2.28|-2.28	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.06786|.	0.0;0.001;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|T	0.32561|0.32561	-0.9902|-0.9902	9|4	0.02654|.	T|.	1|.	-8.8693|-8.8693	16.3029|16.3029	0.82831|0.82831	0.0:0.8674:0.1326:0.0|0.0:0.8674:0.1326:0.0	rs13571;rs1768479;rs3182527;rs17110127;rs52818360;rs57460603;rs13571|rs13571;rs1768479;rs3182527;rs17110127;rs52818360;rs57460603;rs13571	235;303;366|.	A6NHR2;E9PB99;Q9BZE1|.	.;.;RM37_HUMAN|.	S|L	366;303;235|151	ENSP00000354086:C366S;ENSP00000338526:C235S|.	ENSP00000328799:C303S|.	C|V	+|+	2|1	0|0	MRPL37|MRPL37	54454508|54454508	0.032000|0.032000	0.19561|0.19561	0.030000|0.030000	0.17652|0.17652	0.021000|0.021000	0.10359|0.10359	2.059000|2.059000	0.41384|0.41384	1.270000|1.270000	0.44297|0.44297	-0.371000|-0.371000	0.07208|0.07208	TGT|GTA	G|0.305;C|0.695	0.695	strong		0.522	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491	
TTN	7273	hgsc.bcm.edu	37	2	179458591	179458591	+	Missense_Mutation	SNP	C	C	T	rs2288569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179458591C>T	ENST00000591111.1	-	248	53737	c.53513G>A	c.(53512-53514)cGt>cAt	p.R17838H	TTN_ENST00000589042.1_Missense_Mutation_p.R19479H|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R10539H|TTN_ENST00000460472.2_Missense_Mutation_p.R10414H|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R10606H|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R16911H|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17838			R -> H. {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)			TGGTCCAGGACGGTCTGCAGA	0.388													C|||	1064	0.21246	0.0666	0.1513	5008	,	,		20497	0.4544		0.1402	False		,,,				2504	0.2781				p.R19479H		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,-1,5	TTN	18412	5	0			c.G58436A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	284,3428		10,264,1582	54.0	51.0	52.0		31241,50732,31616,31817	6.2	1.0	2	dbSNP_100	52	1208,6994		91,1026,2984	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	101,1290,4566	TT,TC,CC		14.7281,7.6509,12.5231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	10414/26927,16911/33424,10539/27052,10606/27119	179458591	1492,10422	1856	4101	5957	SO:0001583	missense	7273	exon298			CCAGGACGGTCTG	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.53513G>A	2.37:g.179458591C>T	ENSP00000465570:p.Arg17838His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	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		423	0.1936813186813187	30	0.06097560975609756	44	0.12154696132596685	244	0.42657342657342656	105	0.13852242744063326	C	18.43	3.621219	0.66787	0.076509	0.147281	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	6.16	6.16	0.99307	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.85859	2.78	0.09310	P	0.99999999872635	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	0.20472	-1.0274	8	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	rs2288569;rs52796288;rs59952436;rs2288569	10414;10539;10606;17838	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	16911;10414;10606;10539;10412	ENSP00000343764:R16911H;ENSP00000434586:R10414H;ENSP00000340554:R10606H;ENSP00000352154:R10539H	ENSP00000340554:R10606H	R	-	2	0	TTN	179166837	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.807000	0.86032	2.937000	0.99478	0.650000	0.86243	CGT	C|0.818;T|0.182	0.182	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MYO16	23026	hgsc.bcm.edu	37	13	109661359	109661359	+	Missense_Mutation	SNP	C	C	G	rs3825491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:109661359C>G	ENST00000357550.2	+	21	2532	c.2491C>G	c.(2491-2493)Cct>Gct	p.P831A	MYO16_ENST00000457511.2_Missense_Mutation_p.P343A|MYO16_ENST00000356711.2_Missense_Mutation_p.P831A|MYO16_ENST00000251041.5_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	87	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	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	
CACNA1S	779	hgsc.bcm.edu	37	1	201079344	201079344	+	Missense_Mutation	SNP	G	G	C	rs12406479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201079344G>C	ENST00000362061.3	-	2	432	c.206C>G	c.(205-207)gCc>gGc	p.A69G	CACNA1S_ENST00000367338.3_Missense_Mutation_p.A69G	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	69			A -> G (in dbSNP:rs12406479).		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)	CAGGTACACGGCCAGGGCCAC	0.587													G|||	113	0.0225639	0.003	0.0259	5008	,	,		22722	0.0		0.0527	False		,,,				2504	0.0389				p.A69G		Atlas-SNP	.											CACNA1S,NS,carcinoma,-1,1	CACNA1S	249	1	0			c.C206G						scavenged	.	G	GLY/ALA	45,4361	46.7+/-81.2	0,45,2158	164.0	128.0	140.0		206	4.9	1.0	1	dbSNP_120	140	465,8135	137.8+/-194.7	13,439,3848	yes	missense	CACNA1S	NM_000069.2	60	13,484,6006	CC,CG,GG		5.407,1.0213,3.9213	probably-damaging	69/1874	201079344	510,12496	2203	4300	6503	SO:0001583	missense	779	exon2			TACACGGCCAGGG	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.206C>G	1.37:g.201079344G>C	ENSP00000355192:p.Ala69Gly	Somatic	168	2	0.0119048		WXS	Illumina HiSeq	Phase_I	148	74	0.5	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	50	0.022893772893772892	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	38	0.05013192612137203	G	23.1	4.380201	0.82682	0.010213	0.05407	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.74737	-0.87;-0.87	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.52451	0.1735	M	0.76002	2.32	0.80722	D	1	P	0.46220	0.874	P	0.57283	0.817	T	0.73107	-0.4087	10	0.45353	T	0.12	.	17.9499	0.89050	0.0:0.0:1.0:0.0	rs12406479;rs52825963;rs12406479	69	Q13698	CAC1S_HUMAN	G	69	ENSP00000355192:A69G;ENSP00000356307:A69G	ENSP00000355192:A69G	A	-	2	0	CACNA1S	199345967	1.000000	0.71417	0.991000	0.47740	0.867000	0.49689	9.360000	0.97119	2.388000	0.81334	0.561000	0.74099	GCC	G|0.967;C|0.033	0.033	strong		0.587	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
EHHADH	1962	hgsc.bcm.edu	37	3	184911151	184911151	+	Silent	SNP	T	T	C	rs3732933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184911151T>C	ENST00000231887.3	-	7	1110	c.1035A>G	c.(1033-1035)gaA>gaG	p.E345E	EHHADH-AS1_ENST00000417720.1_RNA|EHHADH_ENST00000456310.1_Silent_p.E249E	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	345	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)			AGGCTTCTTTTTCCAAGACAG	0.458													T|||	367	0.0732827	0.0212	0.1239	5008	,	,		19478	0.0665		0.0716	False		,,,				2504	0.1166				p.E345E		Atlas-SNP	.											.	EHHADH	73	.	0			c.A1035G						PASS	.	T	,	164,4242	109.1+/-147.4	6,152,2045	139.0	142.0	141.0		747,1035	0.8	1.0	3	dbSNP_107	141	706,7894	174.3+/-224.6	25,656,3619	no	coding-synonymous,coding-synonymous	EHHADH	NM_001166415.1,NM_001966.3	,	31,808,5664	CC,CT,TT		8.2093,3.7222,6.6892	,	249/628,345/724	184911151	870,12136	2203	4300	6503	SO:0001819	synonymous_variant	1962	exon7			TTCTTTTTCCAAG	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.1035A>G	3.37:g.184911151T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	169	81	0.47929	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	37	CCDS33901.1																																																																																			T|0.934;C|0.066	0.066	strong		0.458	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
METTL25	84190	hgsc.bcm.edu	37	12	82752559	82752559	+	Missense_Mutation	SNP	T	T	G	rs113882703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:82752559T>G	ENST00000248306.3	+	1	284	c.215T>G	c.(214-216)cTg>cGg	p.L72R	CCDC59_ENST00000548126.1_5'UTR|METTL25_ENST00000547357.1_3'UTR|CCDC59_ENST00000256151.7_5'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	72							methyltransferase activity (GO:0008168)										ACGGAGGCCCTGCCCTCAGAG	0.657											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	212	0.0423323	0.0182	0.0591	5008	,	,		13342	0.002		0.0805	False		,,,				2504	0.0654				p.L72R		Atlas-SNP	.											.	.	.	.	0			c.T215G						PASS	.	T	ARG/LEU	139,4267	93.0+/-131.7	3,133,2067	42.0	41.0	41.0		215	-5.2	0.0	12	dbSNP_132	41	806,7794	179.0+/-228.3	43,720,3537	yes	missense	C12orf26	NM_032230.2	102	46,853,5604	GG,GT,TT		9.3721,3.1548,7.2659	benign	72/604	82752559	945,12061	2203	4300	6503	SO:0001583	missense	84190	exon1			AGGCCCTGCCCTC	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.215T>G	12.37:g.82752559T>G	ENSP00000248306:p.Leu72Arg	Somatic	205	1	0.00487805	1216	WXS	Illumina HiSeq	Phase_I	214	109	0.509346	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	88	0.040293040293040296	11	0.022357723577235773	22	0.06077348066298342	1	0.0017482517482517483	54	0.0712401055408971	T	4.504	0.093403	0.08632	0.031548	0.093721	ENSG00000127720	ENST00000248306;ENST00000548200	T	0.31510	1.49	5.0	-5.17	0.02849	.	1.825470	0.02815	N	0.124811	T	0.00271	0.0008	N	0.00500	-1.43	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12967	-1.0527	10	0.23302	T	0.38	.	1.2997	0.02077	0.4643:0.162:0.1738:0.1999	.	72	Q8N6Q8	CL026_HUMAN	R	72	ENSP00000248306:L72R	ENSP00000248306:L72R	L	+	2	0	C12orf26	81276690	.	.	0.000000	0.03702	0.019000	0.09904	.	.	-0.704000	0.05042	-0.767000	0.03436	CTG	T|0.939;G|0.061	0.061	strong		0.657	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
CIITA	4261	hgsc.bcm.edu	37	16	11001743	11001743	+	Silent	SNP	G	G	A	rs2229320	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:11001743G>A	ENST00000324288.8	+	11	2527	c.2394G>A	c.(2392-2394)ccG>ccA	p.P798P	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	798					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GGCTGCAGCCGGGGACACTGC	0.706			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	948	0.189297	0.0129	0.1499	5008	,	,		13143	0.3145		0.2217	False		,,,				2504	0.2935				p.P798P		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.G2394A						PASS	.	G		225,4113		12,201,1956	19.0	27.0	25.0		2394	-10.0	0.0	16	dbSNP_98	25	1715,6781		179,1357,2712	no	coding-synonymous	CIITA	NM_000246.3		191,1558,4668	AA,AG,GG		20.186,5.1867,15.1161		798/1131	11001743	1940,10894	2169	4248	6417	SO:0001819	synonymous_variant	4261	exon11			GCAGCCGGGGACA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2394G>A	16.37:g.11001743G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			G|0.820;A|0.180	0.180	strong		0.706	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
GALNT14	79623	hgsc.bcm.edu	37	2	31135184	31135184	+	Missense_Mutation	SNP	G	G	T	rs2288101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:31135184G>T	ENST00000349752.5	-	14	2044	c.1405C>A	c.(1405-1407)Cag>Aag	p.Q469K	GALNT14_ENST00000406653.1_Missense_Mutation_p.Q449K|GALNT14_ENST00000486564.1_5'UTR|GALNT14_ENST00000356174.3_Missense_Mutation_p.Q436K|GALNT14_ENST00000420311.2_Missense_Mutation_p.Q434K|GALNT14_ENST00000324589.5_Missense_Mutation_p.Q474K	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	469	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		Q -> K (in dbSNP:rs2288101).		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					TGGAGGATCTGCTGGGTGTAT	0.547													G|||	993	0.198283	0.1407	0.1844	5008	,	,		19413	0.1984		0.2614	False		,,,				2504	0.2209				p.Q474K		Atlas-SNP	.											.	GALNT14	103	.	0			c.C1420A						PASS	.	G	LYS/GLN	722,3684	298.7+/-285.4	62,598,1543	89.0	88.0	89.0		1405	5.0	1.0	2	dbSNP_100	89	2081,6519	360.9+/-332.1	253,1575,2472	yes	missense	GALNT14	NM_024572.2	53	315,2173,4015	TT,TG,GG		24.1977,16.3867,21.5516	benign	469/553	31135184	2803,10203	2203	4300	6503	SO:0001583	missense	79623	exon15			GGATCTGCTGGGT	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.1405C>A	2.37:g.31135184G>T	ENSP00000288988:p.Gln469Lys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	440	0.20146520146520147	58	0.11788617886178862	60	0.16574585635359115	120	0.2097902097902098	202	0.26649076517150394	G	12.20	1.867597	0.32977	0.163867	0.241977	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.04	5.04	0.67666	Ricin B-related lectin (1);Ricin B lectin (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.82056	2.57	0.09310	P	0.999999763259	B;D;B;P	0.53745	0.336;0.962;0.1;0.896	B;P;B;P	0.53313	0.268;0.723;0.14;0.649	T	0.02059	-1.1221	9	0.45353	T	0.12	.	17.1769	0.86844	0.0:0.0:1.0:0.0	rs2288101;rs52827502;rs57335829;rs2288101	434;474;469;449	F5H263;Q96FL9-3;Q96FL9;B3KV89	.;.;GLT14_HUMAN;.	K	469;474;449;436;434	ENSP00000288988:Q469K;ENSP00000314500:Q474K;ENSP00000385435:Q449K;ENSP00000348497:Q436K;ENSP00000415514:Q434K	ENSP00000314500:Q474K	Q	-	1	0	GALNT14	30988688	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	6.095000	0.71439	2.349000	0.79799	0.563000	0.77884	CAG	G|0.797;T|0.203	0.203	strong		0.547	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
KIAA1109	84162	hgsc.bcm.edu	37	4	123229132	123229132	+	Silent	SNP	C	C	T	rs7688384	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123229132C>T	ENST00000264501.4	+	58	10243	c.9870C>T	c.(9868-9870)gcC>gcT	p.A3290A	KIAA1109_ENST00000455637.1_Silent_p.A3290A|KIAA1109_ENST00000388738.3_Silent_p.A3290A			Q2LD37	K1109_HUMAN	KIAA1109	3290					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A3290A(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATTATAAGGCCGCCTATGACA	0.353													T|||	1388	0.277157	0.0333	0.3084	5008	,	,		18430	0.3611		0.3072	False		,,,				2504	0.4673				p.A3290A		Atlas-SNP	.											KIAA1109,NS,carcinoma,0,1	KIAA1109	424	1	1	Substitution - coding silent(1)	prostate(1)	c.C9870T						PASS	.	T		304,3376		13,278,1549	155.0	152.0	153.0		9870	4.7	1.0	4	dbSNP_116	153	2662,5532		414,1834,1849	no	coding-synonymous	KIAA1109	NM_015312.3		427,2112,3398	TT,TC,CC		32.4872,8.2609,24.9789		3290/5006	123229132	2966,8908	1840	4097	5937	SO:0001819	synonymous_variant	84162	exon56			TAAGGCCGCCTAT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9870C>T	4.37:g.123229132C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	159	61	0.383648	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	571	0.26144688644688646	22	0.044715447154471545	111	0.30662983425414364	199	0.3479020979020979	239	0.3153034300791557	T	9.403	1.078547	0.20227	0.082609	0.324872	ENSG00000138688	ENST00000419325	.	.	.	5.92	4.74	0.60224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44314	-0.9336	3	.	.	.	.	2.7244	0.05210	0.1185:0.1305:0.1235:0.6276	rs7688384;rs59976925;rs7688384	.	.	.	C	1248	.	.	R	+	1	0	KIAA1109	123448582	0.931000	0.31567	1.000000	0.80357	0.992000	0.81027	-0.047000	0.11963	0.503000	0.28060	-0.254000	0.11334	CGC	C|0.717;T|0.283	0.283	strong		0.353	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
SETD2	29072	hgsc.bcm.edu	37	3	47162661	47162661	+	Silent	SNP	A	A	G	rs6767907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47162661A>G	ENST00000409792.3	-	3	3507	c.3465T>C	c.(3463-3465)aaT>aaC	p.N1155N		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1155					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CAGGCAGGCGATTATCTATTT	0.403			"""N, F, S, Mis"""		clear cell renal carcinoma								G|||	3397	0.678315	0.7837	0.6816	5008	,	,		18708	0.6577		0.6074	False		,,,				2504	0.6278				p.N1155N		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.T3465C						PASS	.	G		3302,1104	376.1+/-321.9	1239,824,140	130.0	141.0	137.0		3465	-0.6	0.9	3	dbSNP_116	137	5084,3516	507.7+/-376.9	1505,2074,721	no	coding-synonymous	SETD2	NM_014159.6		2744,2898,861	GG,GA,AA		40.8837,25.0567,35.5221		1155/2565	47162661	8386,4620	2203	4300	6503	SO:0001819	synonymous_variant	29072	exon3			CAGGCGATTATCT	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3465T>C	3.37:g.47162661A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																			A|0.343;G|0.657	0.657	strong		0.403	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
C1orf127	148345	hgsc.bcm.edu	37	1	11015165	11015165	+	Missense_Mutation	SNP	A	A	G	rs75130475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11015165A>G	ENST00000377008.4	-	8	802	c.356T>C	c.(355-357)aTt>aCt	p.I119T	C1orf127_ENST00000377004.4_Missense_Mutation_p.I286T			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	119										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)		GGTTTCCTCAATGTAGGAACC	0.522													A|||	1143	0.228235	0.0991	0.2752	5008	,	,		20517	0.2341		0.164	False		,,,				2504	0.4294				p.I286T		Atlas-SNP	.											.	C1orf127	134	.	0			c.T857C						PASS	.	A	THR/ILE	441,3965	212.8+/-232.6	18,405,1780	130.0	121.0	124.0		857	-6.0	0.0	1	dbSNP_131	124	1305,7295	258.7+/-282.2	109,1087,3104	yes	missense	C1orf127	NM_001170754.1	89	127,1492,4884	GG,GA,AA		15.1744,10.0091,13.4246	possibly-damaging	286/824	11015165	1746,11260	2203	4300	6503	SO:0001583	missense	148345	exon9			TCCTCAATGTAGG	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.356T>C	1.37:g.11015165A>G	ENSP00000366207:p.Ile119Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		415	0.190018315018315	47	0.09552845528455285	95	0.26243093922651933	141	0.2465034965034965	132	0.1741424802110818	A	10.67	1.416568	0.25552	0.100091	0.151744	ENSG00000175262	ENST00000377004;ENST00000377008	T;T	0.23754	1.89;1.89	4.94	-6.01	0.02199	.	2.410650	0.01815	N	0.033671	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.33103	0.278;0.278;0.397	B;B;B	0.28139	0.086;0.086;0.086	T	0.28170	-1.0052	9	0.13470	T	0.59	2.0094	1.0442	0.01566	0.2004:0.2288:0.3268:0.2439	.	137;137;119	B7ZLG7;Q8N9H9-2;Q8N9H9	.;.;CA127_HUMAN	T	286;119	ENSP00000366203:I286T;ENSP00000366207:I119T	ENSP00000366203:I286T	I	-	2	0	C1orf127	10937752	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-1.247000	0.02893	-0.647000	0.05444	-0.361000	0.07541	ATT	A|0.843;G|0.157	0.157	strong		0.522	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
OR52E2	119678	hgsc.bcm.edu	37	11	5080359	5080359	+	Missense_Mutation	SNP	G	G	A	rs11035396	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5080359G>A	ENST00000321522.2	-	1	498	c.499C>T	c.(499-501)Cgg>Tgg	p.R167W		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	167			R -> W (in dbSNP:rs11035396).			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)		AAGGGCAACCGCAATATAAGA	0.418													G|||	380	0.0758786	0.0068	0.0893	5008	,	,		22491	0.1319		0.1173	False		,,,				2504	0.0593				p.R167W		Atlas-SNP	.											OR52E2,caecum,carcinoma,0,1	OR52E2	63	1	0			c.C499T						PASS	.	G	TRP/ARG	95,4307	76.2+/-114.5	2,91,2108	80.0	75.0	77.0		499	-7.5	0.0	11	dbSNP_120	77	946,7650	207.9+/-249.5	57,832,3409	yes	missense	OR52E2	NM_001005164.2	101	59,923,5517	AA,AG,GG		11.0051,2.1581,8.0089	benign	167/326	5080359	1041,11957	2201	4298	6499	SO:0001583	missense	119678	exon1			GCAACCGCAATAT	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.499C>T	11.37:g.5080359G>A	ENSP00000322088:p.Arg167Trp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	213	0.09752747252747253	3	0.006097560975609756	32	0.08839779005524862	82	0.14335664335664336	96	0.1266490765171504	G	3.388	-0.125008	0.06795	0.021581	0.110051	ENSG00000176787	ENST00000321522	T	0.00188	8.59	3.76	-7.52	0.01341	GPCR, rhodopsin-like superfamily (1);	0.149485	0.29087	N	0.013181	T	0.00012	0.0000	M	0.88775	2.98	0.80722	P	0.0	P	0.35011	0.48	B	0.38156	0.266	T	0.18366	-1.0339	9	0.51188	T	0.08	.	9.5528	0.39321	0.133:0.0:0.2178:0.6491	rs11035396;rs17260244;rs58899786;rs11035396	167	Q8NGJ4	O52E2_HUMAN	W	167	ENSP00000322088:R167W	ENSP00000322088:R167W	R	-	1	2	OR52E2	5036935	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.363000	0.02592	-1.706000	0.01404	-0.819000	0.03115	CGG	G|0.917;A|0.083	0.083	strong		0.418	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39274415C>T	ENST00000391413.2	-	1	191	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	51	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.R51R(6)		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)			AGCACTGGGGCCTGCAGCAGC	0.667																																					p.R51R		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-1,11	KRTAP4-11	94	11	6	Substitution - coding silent(6)	endometrium(3)|kidney(2)|lung(1)	c.G153A						scavenged	.						9.0	15.0	13.0					17																	39274415		682	1579	2261	SO:0001819	synonymous_variant	653240	exon1			CTGGGGCCTGCAG	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.153G>A	17.37:g.39274415C>T		Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	100	6	0.06	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	weak		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
DNAH17	8632	hgsc.bcm.edu	37	17	76535948	76535948	+	Silent	SNP	T	T	C	rs7221209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:76535948T>C	ENST00000585328.1	-	18	2671	c.2547A>G	c.(2545-2547)ctA>ctG	p.L849L	DNAH17_ENST00000389840.5_Silent_p.L849L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	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(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)			CTGCCCTGAATAGTTCTGCGT	0.488													C|||	3696	0.738019	0.7595	0.7161	5008	,	,		18396	0.7381		0.7545	False		,,,				2504	0.7076				p.L849L		Atlas-SNP	.											.	DNAH17	347	.	0			c.A2547G						PASS	.	C		3260,882		1280,700,91	60.0	60.0	60.0		2547	-2.0	0.4	17	dbSNP_116	60	6327,2077		2367,1593,242	no	coding-synonymous	DNAH17	NM_173628.3		3647,2293,333	CC,CT,TT		24.7144,21.2941,23.5852		849/4463	76535948	9587,2959	2071	4202	6273	SO:0001819	synonymous_variant	8632	exon18			CCTGAATAGTTCT	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.2547A>G	17.37:g.76535948T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	219	217	0.990868	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				T|0.240;C|0.760	0.760	strong		0.488	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
KCNQ1	3784	hgsc.bcm.edu	37	11	2797237	2797237	+	Silent	SNP	G	G	A	rs1057128|rs4151646	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:2797237G>A	ENST00000155840.5	+	13	1746	c.1638G>A	c.(1636-1638)tcG>tcA	p.S546S	KCNQ1_ENST00000335475.5_Silent_p.S419S	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	546			S -> L (in LQT1). {ECO:0000269|PubMed:15840476}.		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)	AGCAGTACTCGCAGGGCCACC	0.642													G|||	906	0.180911	0.0106	0.33	5008	,	,		18625	0.2927		0.1978	False		,,,				2504	0.1728				p.S546S		Atlas-SNP	.											KCNQ1,NS,carcinoma,0,1	KCNQ1	60	1	0			c.G1638A						scavenged	.	G	,	204,4188		2,200,1994	82.0	62.0	69.0		1638,1257	-5.7	0.9	11	dbSNP_86	69	1657,6919		168,1321,2799	no	coding-synonymous,coding-synonymous	KCNQ1	NM_000218.2,NM_181798.1	,	170,1521,4793	AA,AG,GG		19.3214,4.6448,14.3507	,	546/677,419/550	2797237	1861,11107	2196	4288	6484	SO:0001819	synonymous_variant	3784	exon13			GTACTCGCAGGGC	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.1638G>A	11.37:g.2797237G>A		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			G|0.838;A|0.162	0.162	strong		0.642	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
KXD1	79036	hgsc.bcm.edu	37	19	18679379	18679379	+	Missense_Mutation	SNP	C	C	G	rs7648	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18679379C>G	ENST00000602094.1	+	5	1929	c.469C>G	c.(469-471)Cct>Gct	p.P157A	KXD1_ENST00000595073.1_Missense_Mutation_p.P157A|KXD1_ENST00000539106.1_Missense_Mutation_p.P157A|KXD1_ENST00000601630.1_Missense_Mutation_p.P176A|AC005253.4_ENST00000593791.1_RNA|KXD1_ENST00000222307.4_Missense_Mutation_p.P157A|KXD1_ENST00000540691.1_Missense_Mutation_p.P157A|KXD1_ENST00000599319.1_Missense_Mutation_p.P157A			Q9BQD3	KXDL1_HUMAN	KxDL motif containing 1	157			P -> A (in dbSNP:rs7648). {ECO:0000269|PubMed:15489334}.		vesicle-mediated transport (GO:0016192)	BLOC-1 complex (GO:0031083)											CCATGTCCAGCCTGGCTCCCC	0.662													C|||	2316	0.46246	0.146	0.5533	5008	,	,		16763	0.6895		0.5606	False		,,,				2504	0.4908				p.P157A		Atlas-SNP	.											.	.	.	.	0			c.C469G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	886,3520	342.3+/-307.1	93,700,1410	94.0	87.0	89.0		469,469,469	2.4	0.0	19	dbSNP_52	89	4849,3751	616.3+/-396.5	1356,2137,807	yes	missense,missense,missense	C19orf50	NM_001171948.1,NM_001171949.1,NM_024069.3	27,27,27	1449,2837,2217	GG,GC,CC		43.6163,20.1089,44.095	benign,benign,benign	157/177,157/177,157/177	18679379	5735,7271	2203	4300	6503	SO:0001583	missense	79036	exon6			GTCCAGCCTGGCT	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.469C>G	19.37:g.18679379C>G	ENSP00000472836:p.Pro157Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001171948	O76098	Missense_Mutation	SNP	ENST00000602094.1	37	CCDS12381.1	1101	0.5041208791208791	83	0.16869918699186992	190	0.5248618784530387	391	0.6835664335664335	437	0.5765171503957783	C	2.533	-0.308095	0.05458	0.201089	0.563837	ENSG00000105700	ENST00000540691;ENST00000539106;ENST00000222307	T;T;T	0.41400	1.0;1.0;1.0	4.6	2.41	0.29592	.	0.417725	0.27645	N	0.018454	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.25667	0.131	B	0.22386	0.039	T	0.40156	-0.9578	9	0.10111	T	0.7	-6.4712	6.6392	0.22899	0.0:0.5966:0.0:0.4034	rs7648;rs3170472;rs17844882;rs17857599;rs17857882;rs60515468	157	Q9BQD3	CS050_HUMAN	A	157	ENSP00000443549:P157A;ENSP00000438903:P157A;ENSP00000222307:P157A	ENSP00000222307:P157A	P	+	1	0	C19orf50	18540379	0.000000	0.05858	0.003000	0.11579	0.038000	0.13279	0.467000	0.22035	0.346000	0.23899	0.561000	0.74099	CCT	C|0.536;G|0.464	0.464	strong		0.662	KXD1-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465107.1	NM_024069	
BCAS4	55653	hgsc.bcm.edu	37	20	49411689	49411689	+	Silent	SNP	G	G	T	rs117388674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:49411689G>T	ENST00000358791.5	+	1	259	c.159G>T	c.(157-159)ctG>ctT	p.L53L	BCAS4_ENST00000609336.1_Silent_p.L23L|BCAS4_ENST00000262591.5_Silent_p.L53L|BCAS4_ENST00000485049.1_3'UTR|BCAS4_ENST00000371608.2_Silent_p.L53L	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	53						cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						CGCTCTTCCTGACCCCCGAGC	0.736													G|||	168	0.0335463	0.0605	0.0101	5008	,	,		9022	0.0169		0.0298	False		,,,				2504	0.0348				p.L53L		Atlas-SNP	.											.	BCAS4	41	.	0			c.G159T						PASS	.	G	,,	67,2413		0,67,1173	1.0	2.0	2.0		159,159,159	1.5	1.0	20	dbSNP_132	2	106,5142		0,106,2518	no	coding-synonymous,coding-synonymous,coding-synonymous	BCAS4	NM_001010974.1,NM_017843.3,NM_198799.2	,,	0,173,3691	TT,TG,GG		2.0198,2.7016,2.2386	,,	53/159,53/212,53/204	49411689	173,7555	1240	2624	3864	SO:0001819	synonymous_variant	55653	exon1			CTTCCTGACCCCC	AK000502	CCDS13432.2, CCDS33487.1	20q13	2008-07-03			ENSG00000124243	ENSG00000124243			14367	protein-coding gene	gene with protein product		607471				12378525	Standard	NM_001010974		Approved	FLJ20495, CNOL	uc002xvq.3	Q8TDM0	OTTHUMG00000032735	ENST00000358791.5:c.159G>T	20.37:g.49411689G>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_198799	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	Silent	SNP	ENST00000358791.5	37	CCDS33487.1	80	0.03663003663003663	34	0.06910569105691057	5	0.013812154696132596	17	0.02972027972027972	24	0.0316622691292876	G	8.976	0.974160	0.18736	0.027016	0.020198	ENSG00000124243	ENST00000445038	.	.	.	4.77	1.51	0.23008	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.7382	3.8781	0.09066	0.0999:0.1588:0.5791:0.1622	.	.	.	.	L	28	.	.	X	+	2	2	BCAS4	48845096	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	0.689000	0.25437	1.004000	0.39156	0.484000	0.47621	TGA	G|0.963;T|0.037	0.037	strong		0.736	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079700.1	NM_017843	
CHRNA4	1137	hgsc.bcm.edu	37	20	61991017	61991017	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61991017C>T	ENST00000370263.4	-	2	332	c.111G>A	c.(109-111)gaG>gaA	p.E37E	CHRNA4_ENST00000463705.1_Intron|RP11-261N11.8_ENST00000370257.1_RNA	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	37					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)	GGAGCCGCTCCTCGGCGTGGG	0.672																																					p.E37E		Atlas-SNP	.											CHRNA4,NS,carcinoma,-1,1	CHRNA4	98	1	0			c.G111A						scavenged	.						65.0	64.0	64.0					20																	61991017		2193	4282	6475	SO:0001819	synonymous_variant	1137	exon2			CCGCTCCTCGGCG		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.111G>A	20.37:g.61991017C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	2	0.0377358	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Silent	SNP	ENST00000370263.4	37	CCDS13517.1																																																																																			.	.	none		0.672	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
CAPN2	824	hgsc.bcm.edu	37	1	223954080	223954080	+	Missense_Mutation	SNP	A	A	C	rs17599	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:223954080A>C	ENST00000295006.5	+	16	2011	c.1702A>C	c.(1702-1704)Aag>Cag	p.K568Q	CAPN2_ENST00000474026.1_3'UTR|CAPN2_ENST00000433674.2_Missense_Mutation_p.K490Q	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	568	Domain IV.		K -> Q (in dbSNP:rs17599). {ECO:0000269|Ref.4}.		blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)	p.K568Q(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CCAAGATATCAAGTCAGATGG	0.403													A|||	1038	0.207268	0.0983	0.2493	5008	,	,		22375	0.2698		0.2425	False		,,,				2504	0.2239				p.K568Q		Atlas-SNP	.											CAPN2,NS,carcinoma,0,1	CAPN2	69	1	1	Substitution - Missense(1)	stomach(1)	c.A1702C						PASS	.	A	GLN/LYS,GLN/LYS	554,3852	249.3+/-256.8	38,478,1687	142.0	126.0	132.0		1468,1702	5.5	1.0	1	dbSNP_63	132	2104,6496	362.6+/-332.8	269,1566,2465	yes	missense,missense	CAPN2	NM_001146068.1,NM_001748.4	53,53	307,2044,4152	CC,CA,AA		24.4651,12.5738,20.4367	probably-damaging,probably-damaging	490/623,568/701	223954080	2658,10348	2203	4300	6503	SO:0001583	missense	824	exon16			GATATCAAGTCAG	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"""EF-hand domain containing"""	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1702A>C	1.37:g.223954080A>C	ENSP00000295006:p.Lys568Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	466	0.21336996336996336	51	0.10365853658536585	91	0.2513812154696133	132	0.23076923076923078	192	0.2532981530343008	A	16.47	3.132564	0.56828	0.125738	0.244651	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	T;T	0.32988	1.43;1.43	5.47	5.47	0.80525	EF-hand-like domain (1);	0.154834	0.56097	D	0.000021	T	0.00012	0.0000	M	0.77712	2.385	0.09310	P	0.999999146384	B;B;B	0.17465	0.007;0.022;0.007	B;B;B	0.27796	0.032;0.083;0.02	T	0.07424	-1.0773	9	0.59425	D	0.04	.	15.5473	0.76112	1.0:0.0:0.0:0.0	rs17599;rs1130849;rs3190187;rs3738372;rs11547592;rs17318843;rs17398495;rs52809008;rs59544343;rs3738372	490;151;568	B7ZA96;B3KUH9;P17655	.;.;CAN2_HUMAN	Q	490;568;597	ENSP00000413158:K490Q;ENSP00000295006:K568Q	ENSP00000295006:K568Q	K	+	1	0	CAPN2	222020703	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.158000	0.77470	2.069000	0.61940	0.459000	0.35465	AAG	A|0.649;C|0.175;G|0.031;T|0.145	0.175	strong		0.403	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748	
TTYH2	94015	hgsc.bcm.edu	37	17	72240177	72240177	+	Missense_Mutation	SNP	T	T	G	rs35999669	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72240177T>G	ENST00000269346.4	+	6	867	c.793T>G	c.(793-795)Tct>Gct	p.S265A	TTYH2_ENST00000534346.1_3'UTR|TTYH2_ENST00000529107.1_Missense_Mutation_p.S244A	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	265			S -> A (in dbSNP:rs35999669). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						CGCTGATGGCTCTGCGGCAGT	0.657													G|||	1913	0.381989	0.6225	0.3055	5008	,	,		13747	0.0972		0.3579	False		,,,				2504	0.4294				p.S265A		Atlas-SNP	.											TTYH2,NS,carcinoma,0,1	TTYH2	63	1	0			c.T793G						scavenged	.	G	ALA/SER	2637,1769	523.1+/-371.0	789,1059,355	64.0	61.0	62.0		793	4.0	0.0	17	dbSNP_126	62	3331,5269	642.8+/-399.9	667,1997,1636	yes	missense	TTYH2	NM_032646.5	99	1456,3056,1991	GG,GT,TT		38.7326,40.1498,45.8865	benign	265/535	72240177	5968,7038	2203	4300	6503	SO:0001583	missense	94015	exon6			GATGGCTCTGCGG		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.793T>G	17.37:g.72240177T>G	ENSP00000269346:p.Ser265Ala	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	759	0.3475274725274725	308	0.6260162601626016	100	0.27624309392265195	61	0.10664335664335664	290	0.38258575197889183	G	4.610	0.113410	0.08831	0.598502	0.387326	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.07800	3.16;3.16	5.01	4.04	0.47022	.	0.053637	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00313	-1.665	0.09310	P	0.9999999999999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38802	-0.9644	9	0.02654	T	1	-1.8901	6.8875	0.24209	0.082:0.0:0.609:0.3089	rs35999669;rs62065675	244;265	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	A	265;244	ENSP00000269346:S265A;ENSP00000433089:S244A	ENSP00000269346:S265A	S	+	1	0	TTYH2	69751772	0.985000	0.35326	0.006000	0.13384	0.307000	0.27823	2.541000	0.45735	0.539000	0.28788	-0.401000	0.06369	TCT	T|0.580;G|0.420	0.420	strong		0.657	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
OR9G1	390174	hgsc.bcm.edu	37	11	56468258	56468258	+	Missense_Mutation	SNP	C	C	T	rs78340277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56468258C>T	ENST00000312153.1	+	1	395	c.395C>T	c.(394-396)gCc>gTc	p.A132V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CTGCTTTATGCCCAGGCCATG	0.498													C|||	31	0.0061901	0.0015	0.0029	5008	,	,		19708	0.0		0.0239	False		,,,				2504	0.0031				p.A132V		Atlas-SNP	.											.	.	.	.	0			c.C395T						PASS	.	C	VAL/ALA	16,4386	21.2+/-45.6	0,16,2185	186.0	171.0	176.0		395	4.4	0.8	11	dbSNP_131	176	171,8421	67.7+/-130.1	0,171,4125	yes	missense	OR9G1	NM_001005213.1	64	0,187,6310	TT,TC,CC		1.9902,0.3635,1.4391	possibly-damaging	132/306	56468258	187,12807	2201	4296	6497	SO:0001583	missense	504191	exon1			TTTATGCCCAGGC	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.395C>T	11.37:g.56468258C>T	ENSP00000309012:p.Ala132Val	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	305	72	0.236066	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	C	11.81	1.748637	0.30955	0.003635	0.019902	ENSG00000174914	ENST00000312153	T	0.01572	4.76	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.696787	0.13040	N	0.418614	T	0.00998	0.0033	L	0.31120	0.905	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40117	-0.9580	10	0.66056	D	0.02	-6.4294	10.827	0.46638	0.0:0.9106:0.0:0.0894	.	132	Q8NH87	OR9G1_HUMAN	V	132	ENSP00000309012:A132V	ENSP00000309012:A132V	A	+	2	0	OR9G1	56224834	0.000000	0.05858	0.813000	0.32504	0.681000	0.39784	-0.197000	0.09518	2.430000	0.82344	0.585000	0.79938	GCC	C|0.987;T|0.013	0.013	strong		0.498	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
DCPS	28960	hgsc.bcm.edu	37	11	126201403	126201403	+	Silent	SNP	T	T	C	rs616360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126201403T>C	ENST00000263579.4	+	3	809	c.480T>C	c.(478-480)aaT>aaC	p.N160N	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	160					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)		ACTACAGGAATATTACTTTAC	0.572													C|||	1157	0.23103	0.2171	0.2695	5008	,	,		18519	0.2054		0.2465	False		,,,				2504	0.2331				p.N160N		Atlas-SNP	.											.	DCPS	33	.	0			c.T480C						PASS	.	C		980,3422	732.1+/-410.3	108,764,1329	99.0	93.0	95.0		480	-0.0	0.0	11	dbSNP_83	95	2189,6407	712.3+/-405.9	290,1609,2399	no	coding-synonymous	DCPS	NM_014026.3		398,2373,3728	CC,CT,TT		25.4653,22.2626,24.3807		160/338	126201403	3169,9829	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon3			CAGGAATATTACT	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.480T>C	11.37:g.126201403T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			T|0.755;C|0.245	0.245	strong		0.572	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
ACACB	32	hgsc.bcm.edu	37	12	109692053	109692053	+	Missense_Mutation	SNP	C	C	T	rs17848835	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109692053C>T	ENST00000338432.7	+	44	6199	c.6080C>T	c.(6079-6081)aCt>aTt	p.T2027I	ACACB_ENST00000377854.5_Missense_Mutation_p.T1957I|ACACB_ENST00000377848.3_Missense_Mutation_p.T2027I|ACACB_ENST00000543201.1_Missense_Mutation_p.T693I			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2027	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)	ATCACACCCACTGACCCCATT	0.483													C|||	379	0.0756789	0.1188	0.0706	5008	,	,		18636	0.0188		0.1034	False		,,,				2504	0.0511				p.T2027I		Atlas-SNP	.											ACACB_ENST00000543201,colon,carcinoma,0,2	ACACB	330	2	0			c.C6080T						PASS	.	C	ILE/THR	555,3851	250.0+/-257.2	42,471,1690	250.0	237.0	242.0		6080	1.3	0.3	12	dbSNP_123	242	940,7660	207.2+/-249.0	48,844,3408	yes	missense	ACACB	NM_001093.3	89	90,1315,5098	TT,TC,CC		10.9302,12.5965,11.4947	benign	2027/2459	109692053	1495,11511	2203	4300	6503	SO:0001583	missense	32	exon43			CACCCACTGACCC	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.6080C>T	12.37:g.109692053C>T	ENSP00000341044:p.Thr2027Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	152	77	0.506579	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	180	0.08241758241758242	65	0.13211382113821138	29	0.08011049723756906	8	0.013986013986013986	78	0.10290237467018469	C	5.850	0.340949	0.11069	0.125965	0.109302	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201	D;D;D;D	0.97529	-4.42;-4.42;-4.42;-4.42	5.27	1.28	0.21552	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.446918	0.26207	N	0.025718	T	0.10594	0.0259	N	0.16743	0.435	0.80722	P	0.0	B	0.09022	0.002	B	0.14578	0.011	T	0.64106	-0.6485	9	0.31617	T	0.26	.	4.1405	0.10191	0.1222:0.351:0.396:0.1308	rs17848835	2027	O00763	ACACB_HUMAN	I	2027;2027;1957;1258;693	ENSP00000341044:T2027I;ENSP00000367079:T2027I;ENSP00000367085:T1957I;ENSP00000444075:T693I	ENSP00000341044:T2027I	T	+	2	0	ACACB	108176436	0.000000	0.05858	0.260000	0.24451	0.896000	0.52359	0.090000	0.15025	0.306000	0.22856	-0.122000	0.15005	ACT	C|0.894;T|0.106	0.106	strong		0.483	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
FAM71A	149647	hgsc.bcm.edu	37	1	212799535	212799535	+	Missense_Mutation	SNP	G	G	A	rs114509113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:212799535G>A	ENST00000294829.3	+	1	1747	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	439						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)		AGTTCCCATCGCCGCAGGACA	0.577													G|||	41	0.0081869	0.0	0.013	5008	,	,		15806	0.0		0.0268	False		,,,				2504	0.0051				p.R439H		Atlas-SNP	.											FAM71A,NS,carcinoma,+1,1	FAM71A	87	1	0			c.G1316A						PASS	.	G	HIS/ARG	18,4386	24.3+/-50.5	0,18,2184	56.0	68.0	64.0		1316	-4.1	0.0	1	dbSNP_132	64	177,8423	81.2+/-143.8	0,177,4123	yes	missense	FAM71A	NM_153606.3	29	0,195,6307	AA,AG,GG		2.0581,0.4087,1.4995	benign	439/595	212799535	195,12809	2202	4300	6502	SO:0001583	missense	149647	exon1			CCCATCGCCGCAG		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.1316G>A	1.37:g.212799535G>A	ENSP00000294829:p.Arg439His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_153606	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	37	CCDS1507.1	27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	G	6.037	0.375275	0.11409	0.004087	0.020581	ENSG00000162771	ENST00000294829;ENST00000545975	T	0.02974	4.09	4.86	-4.13	0.03904	.	.	.	.	.	T	0.00384	0.0012	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45308	-0.9270	9	0.02654	T	1	-5.5561	1.1428	0.01769	0.3171:0.2816:0.2647:0.1366	.	439	Q8IYT1	FA71A_HUMAN	H	439;214	ENSP00000294829:R439H	ENSP00000294829:R439H	R	+	2	0	FAM71A	210866158	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.642000	0.05427	-0.766000	0.04639	-0.290000	0.09829	CGC	G|0.986;A|0.014	0.014	strong		0.577	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606	
SOWAHD	347454	hgsc.bcm.edu	37	X	118893137	118893137	+	Silent	SNP	T	T	C	rs2782224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:118893137T>C	ENST00000343905.3	+	1	562	c.507T>C	c.(505-507)gaT>gaC	p.D169D		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	169																	TGGTACACGATTTCGCCCTAC	0.701													c|||	2308	0.611391	0.475	0.487	3775	,	,		10041	0.374		0.495	False		,,,				2504	0.4775				p.D169D		Atlas-SNP	.											.	.	.	.	0			c.T507C						PASS	.	G		2276,1133		673,594,336,171,197	5.0	6.0	6.0		507	2.1	0.3	X	dbSNP_100	6	4068,2279		984,1003,1097,346,584	no	coding-synonymous	ANKRD58	NM_001105576.2		1657,1597,1433,517,781	CC,CT,C,TT,T		35.9067,33.2356,34.9733		169/316	118893137	6344,3412	1971	4014	5985	SO:0001819	synonymous_variant	347454	exon1			ACACGATTTCGCC		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.507T>C	X.37:g.118893137T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_001105576		Silent	SNP	ENST00000343905.3	37	CCDS43984.1																																																																																			T|0.405;C|0.595	0.595	strong		0.701	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576	
VILL	50853	hgsc.bcm.edu	37	3	38038982	38038982	+	Silent	SNP	T	T	C	rs6809649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	97	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	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	
POM121L12	285877	hgsc.bcm.edu	37	7	53103371	53103371	+	Missense_Mutation	SNP	G	G	T	rs72598684	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	39	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	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	
PCNXL4	64430	hgsc.bcm.edu	37	14	60591887	60591887	+	Missense_Mutation	SNP	G	G	A	rs167437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:60591887G>A	ENST00000406854.1	+	9	3552	c.2998G>A	c.(2998-3000)Ggt>Agt	p.G1000S	PCNXL4_ENST00000317623.4_Missense_Mutation_p.G766S|PCNXL4_ENST00000535349.1_Missense_Mutation_p.G207S|PCNXL4_ENST00000406949.1_Missense_Mutation_p.G766S|PCNXL4_ENST00000404681.2_Missense_Mutation_p.G1000S			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1000			G -> S (in dbSNP:rs167437). {ECO:0000269|PubMed:17974005}.			integral component of membrane (GO:0016021)											GAGAGTTTACGGTGGTGTTTT	0.363													A|||	1747	0.348842	0.6082	0.1412	5008	,	,		19049	0.3472		0.1183	False		,,,				2504	0.3845				p.G766S		Atlas-SNP	.											.	.	.	.	0			c.G2296A						PASS	.	A	SER/GLY	2375,2031	558.0+/-379.9	630,1115,458	52.0	52.0	52.0		2296	5.2	1.0	14	dbSNP_79	52	1103,7497	763.8+/-407.6	75,953,3272	yes	missense	C14orf135	NM_022495.5	56	705,2068,3730	AA,AG,GG		12.8256,46.0962,26.7415	benign	766/939	60591887	3478,9528	2203	4300	6503	SO:0001583	missense	64430	exon8			GTTTACGGTGGTG	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.2998G>A	14.37:g.60591887G>A	ENSP00000384801:p.Gly1000Ser	Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	351	168	0.478632	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		610	0.2793040293040293	277	0.5630081300813008	57	0.1574585635359116	196	0.34265734265734266	80	0.10554089709762533	A	3.746	-0.052626	0.07362	0.539038	0.128256	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000535349	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.18	5.18	0.71444	.	0.472372	0.27100	N	0.020923	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	1.0000000000287557E-6	B;B	0.11235	0.004;0.0	B;B	0.06405	0.002;0.001	T	0.44892	-0.9298	9	0.07482	T	0.82	.	6.5552	0.22456	0.7897:0.0:0.0736:0.1367	rs167437;rs3737079;rs52795398;rs61537067;rs167437	1000;766	Q63HM2;B5MC47	CN135_HUMAN;.	S	766;1000;766;1000;207	ENSP00000317396:G766S;ENSP00000384801:G1000S;ENSP00000385201:G766S;ENSP00000385713:G1000S;ENSP00000445644:G207S	ENSP00000317396:G766S	G	+	1	0	C14orf135	59661640	0.999000	0.42202	0.998000	0.56505	0.729000	0.41735	4.470000	0.60175	0.914000	0.36822	-0.893000	0.02921	GGT	G|0.700;A|0.300	0.300	strong		0.363	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
SCFD2	152579	hgsc.bcm.edu	37	4	54011603	54011603	+	Silent	SNP	C	C	T	rs17082453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:54011603C>T	ENST00000401642.3	-	5	1591	c.1458G>A	c.(1456-1458)acG>acA	p.T486T	SCFD2_ENST00000388940.4_Silent_p.T486T	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	486					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CTTTGTCTACCGTGAGCTCTC	0.438													c|||	637	0.127196	0.0144	0.1715	5008	,	,		18655	0.2321		0.0765	False		,,,				2504	0.1922				p.T486T		Atlas-SNP	.											.	SCFD2	78	.	0			c.G1458A						PASS	.	C		104,4302	81.4+/-119.9	1,102,2100	128.0	121.0	123.0		1458	-8.8	0.0	4	dbSNP_123	123	586,8014	156.4+/-210.3	23,540,3737	no	coding-synonymous	SCFD2	NM_152540.3		24,642,5837	TT,TC,CC		6.814,2.3604,5.3052		486/685	54011603	690,12316	2203	4300	6503	SO:0001819	synonymous_variant	152579	exon5			GTCTACCGTGAGC	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1458G>A	4.37:g.54011603C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	140	84	0.6	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Silent	SNP	ENST00000401642.3	37	CCDS33984.1																																																																																			C|0.913;T|0.087	0.087	strong		0.438	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
MC1R	4157	hgsc.bcm.edu	37	16	89985940	89985940	+	Missense_Mutation	SNP	G	G	A	rs2228479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89985940G>A	ENST00000555147.1	+	1	1654	c.274G>A	c.(274-276)Gtg>Atg	p.V92M	RP11-566K11.7_ENST00000570217.1_RNA|RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Missense_Mutation_p.V92M|TUBB3_ENST00000556922.1_Missense_Mutation_p.V92M|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	92			V -> M (associated with a risk for developing melanoma; predominantly found in type I skin; shows a moderate and not significant decreased of cAMP production to NDP-MSH stimulation; dbSNP:rs2228479). {ECO:0000269|PubMed:10101176, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:8990005, ECO:0000269|PubMed:9302268, ECO:0000269|Ref.12}.		G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		CGGGAGCAACGTGCTGGAGAC	0.637									Melanoma, Familial Clustering of				G|||	399	0.0796725	0.0038	0.0231	5008	,	,		19874	0.2887		0.0686	False		,,,				2504	0.0184				p.V92M		Atlas-SNP	.											.	MC1R	20	.	0			c.G274A	GRCh37	CM014730	MC1R	M	rs2228479	PASS	.	G	MET/VAL	85,4299		0,85,2107	48.0	58.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	274	0.2	0.4	16	dbSNP_98	55	735,7833		33,669,3582	yes	missense	MC1R	NM_002386.3	21	33,754,5689	AA,AG,GG		8.5784,1.9389,6.3311		92/318	89985940	820,12132	2192	4284	6476	SO:0001583	missense	4157	exon1	Familial Cancer Database		AGCAACGTGCTGG		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.274G>A	16.37:g.89985940G>A	ENSP00000451605:p.Val92Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	120	49	0.408333	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Missense_Mutation	SNP	ENST00000555147.1	37	CCDS56011.1	200	0.09157509157509157	2	0.0040650406504065045	10	0.027624309392265192	135	0.23601398601398602	53	0.06992084432717678	G	4.971	0.180387	0.09443	0.019389	0.085784	ENSG00000258947;ENSG00000258947;ENSG00000258839	ENST00000555427;ENST00000556922;ENST00000555147	T;T;T	0.04970	3.52;3.52;3.52	4.86	0.165	0.14995	GPCR, rhodopsin-like superfamily (1);	0.270105	0.18936	U	0.127063	T	0.00012	0.0000	L	0.42245	1.32	0.38397	P	0.05443699999999996	B	0.15930	0.015	B	0.21360	0.034	T	0.45934	-0.9227	8	.	.	.	.	8.2022	0.31432	0.1814:0.3993:0.4193:0.0	rs2228479;rs2228479	92	Q01726	MSHR_HUMAN	M	92	ENSP00000451760:V92M;ENSP00000451560:V92M;ENSP00000451605:V92M	.	V	+	1	0	MC1R;RP11-566K11.2	88513441	0.750000	0.28316	0.359000	0.25824	0.182000	0.23217	1.008000	0.29872	0.100000	0.17581	-1.360000	0.01215	GTG	G|0.904;A|0.096	0.096	strong		0.637	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
PLG	5340	hgsc.bcm.edu	37	6	161162406	161162406	+	Silent	SNP	T	T	C	rs4252170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:161162406T>C	ENST00000308192.9	+	17	2145	c.2082T>C	c.(2080-2082)gcT>gcC	p.A694A		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	694	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	ATGTGGTCGCTGACCGGACCG	0.468													T|||	317	0.0632987	0.0197	0.0749	5008	,	,		21016	0.0923		0.0895	False		,,,				2504	0.0573				p.A694A		Atlas-SNP	.											PLG,NS,carcinoma,+2,1	PLG	150	1	0			c.T2082C						scavenged	.	T		92,4314		1,90,2112	115.0	98.0	104.0		2082	-3.4	0.1	6	dbSNP_111	104	696,7904		25,646,3629	no	coding-synonymous	PLG	NM_000301.3		26,736,5741	CC,CT,TT		8.093,2.0881,6.0587		694/811	161162406	788,12218	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon17			GGTCGCTGACCGG	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.2082T>C	6.37:g.161162406T>C		Somatic	365	2	0.00547945		WXS	Illumina HiSeq	Phase_I	374	169	0.451872	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.930;C|0.070	0.070	strong		0.468	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
ICE2	79664	hgsc.bcm.edu	37	15	60747576	60747576	+	Silent	SNP	G	G	A	rs61753854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:60747576G>A	ENST00000261520.4	-	7	966	c.732C>T	c.(730-732)gaC>gaT	p.D244D	NARG2_ENST00000439632.1_Silent_p.D107D|NARG2_ENST00000561114.1_Silent_p.D244D	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						TAGCTATATCGTCCTTTGACA	0.328													G|||	16	0.00319489	0.0	0.0014	5008	,	,		18300	0.0		0.002	False		,,,				2504	0.0133				p.D244D		Atlas-SNP	.											NARG2,NS,carcinoma,0,1	NARG2	82	1	0			c.C732T						PASS	.	G	,	2,4402	2.1+/-5.4	0,2,2200	193.0	175.0	181.0		321,732	-2.8	0.0	15	dbSNP_129	181	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous,coding-synonymous	NARG2	NM_001018089.1,NM_024611.4	,	0,21,6481	AA,AG,GG		0.2209,0.0454,0.1615	,	107/846,244/983	60747576	21,12983	2202	4300	6502	SO:0001819	synonymous_variant	79664	exon7			TATATCGTCCTTT																												ENST00000261520.4:c.732C>T	15.37:g.60747576G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_024611		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																			G|0.998;A|0.002	0.002	strong		0.328	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1		
PCNT	5116	hgsc.bcm.edu	37	21	47847547	47847547	+	Silent	SNP	C	C	T	rs150882711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47847547C>T	ENST00000359568.5	+	34	7439	c.7332C>T	c.(7330-7332)acC>acT	p.T2444T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2444					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)					AAGTGCCCACCGCGTGCCCCG	0.557													C|||	2	0.000399361	0.0	0.0	5008	,	,		21792	0.0		0.002	False		,,,				2504	0.0				p.T2444T		Atlas-SNP	.											.	PCNT	283	.	0			c.C7332T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	68.0	70.0	70.0		7332	-4.9	0.0	21	dbSNP_134	70	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	PCNT	NM_006031.5		0,11,6492	TT,TC,CC		0.093,0.0681,0.0846		2444/3337	47847547	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon34			GCCCACCGCGTGC	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.7332C>T	21.37:g.47847547C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.999;T|0.001	0.001	strong		0.557	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
INSC	387755	hgsc.bcm.edu	37	11	15243059	15243059	+	Missense_Mutation	SNP	G	G	A	rs17507577	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:15243059G>A	ENST00000379554.3	+	8	1043	c.997G>A	c.(997-999)Gac>Aac	p.D333N	INSC_ENST00000528567.1_Missense_Mutation_p.D286N|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000379556.3_Missense_Mutation_p.D286N|INSC_ENST00000530161.1_Missense_Mutation_p.D286N|INSC_ENST00000525218.1_Missense_Mutation_p.D244N|INSC_ENST00000424273.1_Missense_Mutation_p.D244N	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	333			D -> N (in dbSNP:rs17507577).		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						CATCCTGACCGACAACAGCCA	0.627													G|||	195	0.0389377	0.0038	0.049	5008	,	,		16966	0.002		0.0855	False		,,,				2504	0.0695				p.D333N		Atlas-SNP	.											.	INSC	104	.	0			c.G997A						PASS	.	G	ASN/ASP,ASN/ASP	58,4188		1,56,2066	53.0	61.0	59.0		997,856	5.5	0.4	11	dbSNP_123	59	703,7771		41,621,3575	yes	missense,missense	INSC	NM_001031853.3,NM_001042536.1	23,23	42,677,5641	AA,AG,GG		8.296,1.366,5.9827	probably-damaging,probably-damaging	333/580,286/533	15243059	761,11959	2123	4237	6360	SO:0001583	missense	387755	exon8			CTGACCGACAACA	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.997G>A	11.37:g.15243059G>A	ENSP00000368872:p.Asp333Asn	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	226	121	0.535398	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	95	0.043498168498168496	3	0.006097560975609756	30	0.08287292817679558	2	0.0034965034965034965	60	0.079155672823219	G	26.0	4.696204	0.88830	0.01366	0.08296	ENSG00000188487	ENST00000379554;ENST00000379556;ENST00000424273;ENST00000528567;ENST00000530161;ENST00000525218	T;T;T;T;T;T	0.55052	0.73;0.73;0.54;0.73;0.73;0.54	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.10937	0.0267	L	0.47716	1.5	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.983;0.989;0.989	T	0.45963	-0.9225	10	0.62326	D	0.03	-23.3127	19.3063	0.94164	0.0:0.0:1.0:0.0	rs17507577;rs52799478;rs17507577	321;244;286;333	Q1MX18-5;Q1MX18-4;A0PJX5;Q1MX18	.;.;.;INSC_HUMAN	N	333;286;244;286;286;244	ENSP00000368872:D333N;ENSP00000368874:D286N;ENSP00000389161:D244N;ENSP00000435022:D286N;ENSP00000436194:D286N;ENSP00000436113:D244N	ENSP00000368872:D333N	D	+	1	0	INSC	15199635	1.000000	0.71417	0.429000	0.26710	0.505000	0.33919	9.269000	0.95684	2.552000	0.86080	0.655000	0.94253	GAC	G|0.946;A|0.054	0.054	strong		0.627	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
KRT33B	3884	hgsc.bcm.edu	37	17	39521248	39521248	+	Missense_Mutation	SNP	A	A	C	rs71373411	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	138	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	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	
TUBD1	51174	hgsc.bcm.edu	37	17	57963537	57963537	+	Missense_Mutation	SNP	A	A	G	rs1292053	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:57963537A>G	ENST00000592426.1	-	2	227	c.227T>C	c.(226-228)aTg>aCg	p.M76T	TUBD1_ENST00000346141.6_Intron|TUBD1_ENST00000394239.3_Missense_Mutation_p.M76T|TUBD1_ENST00000376094.4_Missense_Mutation_p.M76T|TUBD1_ENST00000340993.6_Missense_Mutation_p.M76T|TUBD1_ENST00000539018.1_Intron|TUBD1_ENST00000325752.3_Missense_Mutation_p.M76T|TUBD1_ENST00000591611.1_5'UTR			Q9UJT1	TBD_HUMAN	tubulin, delta 1	76			M -> T (in dbSNP:rs1292053). {ECO:0000269|PubMed:10620804, ECO:0000269|PubMed:15081367}.		cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.M76T(1)		NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	CTTTGACAGCATTTGATTGAT	0.418													G|||	2410	0.48123	0.5204	0.4597	5008	,	,		17567	0.5754		0.4175	False		,,,				2504	0.4121				p.M76T		Atlas-SNP	.											TUBD1,NS,carcinoma,0,1	TUBD1	38	1	1	Substitution - Missense(1)	stomach(1)	c.T227C						PASS	.	G	THR/MET,THR/MET,THR/MET,,,THR/MET	2123,2283	599.7+/-389.3	520,1083,600	99.0	96.0	97.0		227,227,227,,,227	4.1	0.7	17	dbSNP_87	97	3751,4849	617.5+/-396.7	846,2059,1395	yes	missense,missense,missense,utr-5,intron,missense	TUBD1	NM_001193609.1,NM_001193610.1,NM_001193611.1,NM_001193612.1,NM_001193613.1,NM_016261.3	81,81,81,,,81	1366,3142,1995	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	43.6163,48.1843,45.1638	benign,benign,benign,,,benign	76/399,76/397,76/352,,,76/454	57963537	5874,7132	2203	4300	6503	SO:0001583	missense	51174	exon3			GACAGCATTTGAT	AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"""Tubulins"""	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.227T>C	17.37:g.57963537A>G	ENSP00000468518:p.Met76Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_016261	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Missense_Mutation	SNP	ENST00000592426.1	37	CCDS11620.1	1077	0.49313186813186816	261	0.5304878048780488	159	0.43922651933701656	342	0.5979020979020979	315	0.4155672823218997	G	2.326	-0.354555	0.05138	0.481843	0.436163	ENSG00000108423	ENST00000325752;ENST00000340993;ENST00000394239;ENST00000376094	T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47	6.08	4.1	0.47936	Tubulin/FtsZ, GTPase domain (4);	0.183702	0.64402	N	0.000019	T	0.00012	0.0000	N	0.00960	-1.095	0.52099	P	5.299999999996974E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.45425	-0.9262	9	0.11485	T	0.65	-1.7956	11.3011	0.49306	0.1943:0.0:0.8057:0.0	rs1292053;rs59005131;rs1292053	76;76;76;76	E9PCA7;E9PCQ8;Q9UJT1-2;Q9UJT1	.;.;.;TBD_HUMAN	T	76	ENSP00000320797:M76T;ENSP00000342399:M76T;ENSP00000377785:M76T;ENSP00000365262:M76T	ENSP00000320797:M76T	M	-	2	0	TUBD1	55318319	1.000000	0.71417	0.705000	0.30386	0.931000	0.56810	4.164000	0.58190	0.476000	0.27440	-0.119000	0.15052	ATG	A|0.522;G|0.478	0.478	strong		0.418	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448815.1	NM_016261	
NPSR1	387129	hgsc.bcm.edu	37	7	34874038	34874038	+	Missense_Mutation	SNP	C	C	G	rs727162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:34874038C>G	ENST00000360581.1	+	6	851	c.723C>G	c.(721-723)agC>agG	p.S241R	NPSR1_ENST00000531252.1_Missense_Mutation_p.S230R|NPSR1_ENST00000381542.1_Missense_Mutation_p.S175R|NPSR1_ENST00000359791.1_Missense_Mutation_p.S241R|NPSR1_ENST00000381539.3_Missense_Mutation_p.S241R	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	241			S -> R (in dbSNP:rs727162). {ECO:0000269|Ref.5}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	GGATTAAAAGCAAAACCTACG	0.423													C|||	1591	0.317692	0.2708	0.3516	5008	,	,		21956	0.3512		0.2177	False		,,,				2504	0.4254				p.S241R		Atlas-SNP	.											.	NPSR1	134	.	0			c.C723G						PASS	.	C	ARG/SER,ARG/SER	1179,3227	413.7+/-336.6	145,889,1169	193.0	172.0	179.0		723,723	4.8	1.0	7	dbSNP_86	179	1812,6788	325.5+/-317.0	209,1394,2697	yes	missense,missense	NPSR1	NM_207172.1,NM_207173.1	110,110	354,2283,3866	GG,GC,CC		21.0698,26.759,22.9971	probably-damaging,probably-damaging	241/372,241/378	34874038	2991,10015	2203	4300	6503	SO:0001583	missense	387129	exon6			TAAAAGCAAAACC	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.723C>G	7.37:g.34874038C>G	ENSP00000353788:p.Ser241Arg	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	199	95	0.477387	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	619	0.2834249084249084	149	0.30284552845528456	115	0.31767955801104975	189	0.3304195804195804	166	0.21899736147757257	C	13.02	2.111304	0.37242	0.26759	0.210698	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.145297	0.49305	D	0.000142	T	0.00012	0.0000	L	0.56124	1.755	0.23449	P	0.99765779	D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999;0.998	D;D;D;D;D;D	0.71656	0.966;0.974;0.943;0.973;0.974;0.973	T	0.30909	-0.9962	9	0.41790	T	0.15	-29.6163	10.1436	0.42749	0.0:0.908:0.0:0.092	rs727162;rs11489290;rs52823007;rs56605321;rs59161753;rs727162	175;230;175;241;241;241	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	R	241;175;241;230;241	ENSP00000353788:S241R;ENSP00000370953:S175R;ENSP00000352839:S241R;ENSP00000433258:S230R;ENSP00000370950:S241R	ENSP00000352839:S241R	S	+	3	2	NPSR1	34840563	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	1.415000	0.34748	2.456000	0.83038	0.555000	0.69702	AGC	C|0.744;G|0.256	0.256	strong		0.423	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
MLLT4	4301	hgsc.bcm.edu	37	6	168349011	168349011	+	Silent	SNP	C	C	T	rs9364371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168349011C>T	ENST00000447894.2	+	28	3663	c.3663C>T	c.(3661-3663)atC>atT	p.I1221I	MLLT4_ENST00000366806.2_Silent_p.I1221I|MLLT4_ENST00000392112.1_Silent_p.I1204I|MLLT4_ENST00000351017.4_Silent_p.I1228I|MLLT4_ENST00000400822.3_Silent_p.I1220I|MLLT4_ENST00000344191.4_Silent_p.I1221I|MLLT4_ENST00000392108.3_Silent_p.I1221I			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1221					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)	p.I1205I(1)		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)		CCTACCCCATCCCCACTCAGA	0.463			T	MLL	AL								C|||	1191	0.237819	0.1135	0.2493	5008	,	,		15837	0.3433		0.2296	False		,,,				2504	0.2975				p.I1221I		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	MLLT4,NS,carcinoma,0,1	MLLT4	351	1	1	Substitution - coding silent(1)	stomach(1)	c.C3663T						PASS	.	C	,	611,3795	265.0+/-266.4	41,529,1633	86.0	83.0	84.0		3663,3612	3.5	1.0	6	dbSNP_119	84	1972,6628	345.8+/-325.9	226,1520,2554	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	267,2049,4187	TT,TC,CC		22.9302,13.8675,19.8601	,	1221/1652,1204/1744	168349011	2583,10423	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon28			CCCCATCCCCACT	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.3663C>T	6.37:g.168349011C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				C|0.779;T|0.221	0.221	strong		0.463	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
GALNT8	26290	hgsc.bcm.edu	37	12	4835882	4835882	+	Silent	SNP	T	T	G	rs2286578	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4835882T>G	ENST00000252318.2	+	2	733	c.396T>G	c.(394-396)ctT>ctG	p.L132L	RP11-234B24.6_ENST00000544741.2_3'UTR	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	132					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)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						GCGAGGATCTTTCTGAGGCCC	0.522													T|||	1568	0.313099	0.1838	0.4179	5008	,	,		16829	0.3601		0.4274	False		,,,				2504	0.2474				p.L132L	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.T396G						PASS	.	T		1049,3357	385.8+/-325.9	140,769,1294	64.0	60.0	61.0		396	-6.1	0.0	12	dbSNP_100	61	3571,5029	517.6+/-379.1	741,2089,1470	no	coding-synonymous	GALNT8	NM_017417.1		881,2858,2764	GG,GT,TT		41.5233,23.8084,35.5221		132/638	4835882	4620,8386	2203	4300	6503	SO:0001819	synonymous_variant	26290	exon2			GGATCTTTCTGAG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.396T>G	12.37:g.4835882T>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_017417	B2RU02	Silent	SNP	ENST00000252318.2	37	CCDS8533.1																																																																																			T|0.649;G|0.351	0.351	strong		0.522	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
PZP	5858	hgsc.bcm.edu	37	12	9346792	9346792	+	Missense_Mutation	SNP	G	G	C	rs12230214	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:9346792G>C	ENST00000261336.2	-	11	1163	c.1135C>G	c.(1135-1137)Ctc>Gtc	p.L379V	PZP_ENST00000381997.2_Missense_Mutation_p.L248V	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	379			L -> V (in dbSNP:rs12230214).		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						ATGAAGAAGAGTTTATTGGGG	0.433													G|||	1391	0.277756	0.1876	0.232	5008	,	,		-128	0.3819		0.3072	False		,,,				2504	0.2945				p.L379V	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.C1135G						PASS	.	G	VAL/LEU	799,3607	319.6+/-296.2	62,675,1466	174.0	161.0	166.0		1135	0.4	0.0	12	dbSNP_120	166	2400,6200	398.1+/-346.0	343,1714,2243	yes	missense	PZP	NM_002864.2	32	405,2389,3709	CC,CG,GG		27.907,18.1344,24.5963	benign	379/1483	9346792	3199,9807	2203	4300	6503	SO:0001583	missense	5858	exon11			AGAAGAGTTTATT	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.1135C>G	12.37:g.9346792G>C	ENSP00000261336:p.Leu379Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	217	129	0.59447	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	658	0.30128205128205127	119	0.241869918699187	101	0.27900552486187846	219	0.38286713286713286	219	0.28891820580474936	G	0.653	-0.808602	0.02819	0.181344	0.27907	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.34472	1.56;1.36	3.53	0.366	0.16136	.	1.257310	0.06069	U	0.659789	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B;B	0.20052	0.041;0.0	B;B	0.20955	0.032;0.001	T	0.44483	-0.9325	9	0.18710	T	0.47	.	2.4418	0.04496	0.1151:0.1872:0.5056:0.1921	rs12230214;rs52810221;rs12230214	248;379	P20742-2;P20742	.;PZP_HUMAN	V	379;248	ENSP00000261336:L379V;ENSP00000371427:L248V	ENSP00000261336:L379V	L	-	1	0	PZP	9238059	0.000000	0.05858	0.009000	0.14445	0.469000	0.32828	-0.997000	0.03705	-0.038000	0.13624	-0.319000	0.08680	CTC	G|0.735;C|0.265	0.265	strong		0.433	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
KALRN	8997	hgsc.bcm.edu	37	3	124418846	124418846	+	Silent	SNP	C	C	T	rs2289427	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:124418846C>T	ENST00000291478.5	+	23	3034	c.2871C>T	c.(2869-2871)agC>agT	p.S957S	KALRN_ENST00000428018.2_Silent_p.S925S|AC080008.1_ENST00000584173.1_RNA|KALRN_ENST00000360013.3_Silent_p.S2654S	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2653					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						GCCTTCCCAGCGAGCCCTCGG	0.592													C|||	707	0.141174	0.0386	0.1311	5008	,	,		18156	0.1855		0.2256	False		,,,				2504	0.1544				p.S2654S		Atlas-SNP	.											.	KALRN	556	.	0			c.C7962T						PASS	.	C	,	275,4131	153.3+/-186.9	10,255,1938	160.0	144.0	149.0		7962,2871	-3.3	1.0	3	dbSNP_100	149	1804,6796	324.7+/-316.6	180,1444,2676	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	190,1699,4614	TT,TC,CC		20.9767,6.2415,15.9849	,	2654/2987,957/1290	124418846	2079,10927	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon56			TCCCAGCGAGCCC	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.2871C>T	3.37:g.124418846C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	364	0.16666666666666666	27	0.054878048780487805	51	0.1408839779005525	112	0.1958041958041958	174	0.22955145118733508	C	10.51	1.370871	0.24771	0.062415	0.209767	ENSG00000160145	ENST00000354186	.	.	.	6.02	-3.27	0.05048	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.24870	-1.0148	3	.	.	.	.	14.7569	0.69572	0.0:0.365:0.0:0.635	rs2289427;rs17308511	.	.	.	V	2623	.	.	A	+	2	0	KALRN	125901536	0.116000	0.22171	0.958000	0.39756	0.993000	0.82548	-0.672000	0.05244	-0.596000	0.05821	-0.136000	0.14681	GCG	C|0.844;T|0.156	0.156	strong		0.592	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
TFEB	7942	hgsc.bcm.edu	37	6	41658889	41658889	+	Silent	SNP	C	C	T	rs1015149	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:41658889C>T	ENST00000230323.4	-	3	364	c.63G>A	c.(61-63)caG>caA	p.Q21Q	TFEB_ENST00000373033.1_Silent_p.Q21Q|TFEB_ENST00000358871.2_Silent_p.Q35Q|TFEB_ENST00000403298.4_Silent_p.Q21Q|TFEB_ENST00000420312.1_Silent_p.Q21Q|TFEB_ENST00000394283.1_Silent_p.Q21Q	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	21	Gln-rich.				autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TGCGCTCCCGCTGCTCCTCCT	0.652			T	ALPHA	renal (childhood epithelioid)						OREG0004069	type=REGULATORY REGION|Gene=TFEB|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2313	0.461861	0.5703	0.4496	5008	,	,		17967	0.4355		0.4722	False		,,,				2504	0.3405				p.Q35Q		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	TFEB,rectum,carcinoma,0,1	TFEB	37	1	0			c.G105A						PASS	.	C	,	2462,1932		701,1060,436	16.0	14.0	15.0		63,63	5.1	1.0	6	dbSNP_86	15	4095,4487		987,2121,1183	no	coding-synonymous,coding-synonymous	TFEB	NM_001167827.1,NM_007162.2	,	1688,3181,1619	TT,TC,CC		47.7162,43.969,49.4682	,	21/477,21/477	41658889	6557,6419	2197	4291	6488	SO:0001819	synonymous_variant	7942	exon2			CTCCCGCTGCTCC	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.63G>A	6.37:g.41658889C>T		Somatic	57	0	0	902	WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Silent	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																			C|0.516;T|0.484	0.484	strong		0.652	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		
KIF9	64147	hgsc.bcm.edu	37	3	47282303	47282303	+	Missense_Mutation	SNP	G	G	A	rs2276853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47282303G>A	ENST00000265529.3	-	18	2592	c.1912C>T	c.(1912-1914)Cgg>Tgg	p.R638W	KIF9_ENST00000452770.2_Missense_Mutation_p.R638W|KIF9_ENST00000487440.1_5'UTR|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000335044.2_Missense_Mutation_p.R638W|KIF9_ENST00000352910.4_Missense_Mutation_p.R480W|KIF9_ENST00000444589.2_Missense_Mutation_p.R573W			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	638			R -> W (in dbSNP:rs2276853). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)	p.R638W(1)		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)		TGCTTCTCCCGTAGTGACTTC	0.527													g|||	2805	0.560104	0.5121	0.5504	5008	,	,		20179	0.5357		0.5994	False		,,,				2504	0.6166				p.R638W	Colon(44;962 1147 15977 24541)	Atlas-SNP	.											KIF9,NS,carcinoma,0,1	KIF9	59	1	1	Substitution - Missense(1)	stomach(1)	c.C1912T						PASS	.		TRP/ARG,TRP/ARG,TRP/ARG	2289,2117	601.1+/-389.6	618,1053,532	139.0	115.0	123.0		1912,1717,1912	2.0	0.7	3	dbSNP_100	123	5052,3548	630.5+/-398.4	1496,2060,744	yes	missense,missense,missense	KIF9	NM_001134878.1,NM_022342.4,NM_182902.3	101,101,101	2114,3113,1276	AA,AG,GG		41.2558,48.0481,43.5568	probably-damaging,probably-damaging,probably-damaging	638/791,573/726,638/791	47282303	7341,5665	2203	4300	6503	SO:0001583	missense	64147	exon17			TCTCCCGTAGTGA	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.1912C>T	3.37:g.47282303G>A	ENSP00000265529:p.Arg638Trp	Somatic	214	2	0.00934579		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_182902	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	37	CCDS2752.1	1222	0.5595238095238095	256	0.5203252032520326	206	0.569060773480663	306	0.534965034965035	454	0.5989445910290238	g	18.84	3.710110	0.68730	0.519519	0.587442	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000444589;ENST00000452770;ENST00000352910	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	6.06	1.97	0.26223	.	0.056425	0.64402	D	0.000002	T	0.00012	0.0000	M	0.63843	1.955	0.31784	P	0.630505	D;D	0.76494	0.995;0.999	P;P	0.55824	0.785;0.77	T	0.49597	-0.8923	9	0.62326	D	0.03	.	9.2321	0.37444	0.0:0.1398:0.3292:0.531	rs2276853;rs17845926;rs17858905;rs52812560;rs57442975;rs2276853	573;638	Q9HAQ2-2;Q9HAQ2	.;KIF9_HUMAN	W	638;638;573;638;480	ENSP00000333942:R638W;ENSP00000265529:R638W;ENSP00000414987:R573W;ENSP00000391100:R638W;ENSP00000292334:R480W	ENSP00000265529:R638W	R	-	1	2	KIF9	47257307	0.573000	0.26676	0.655000	0.29622	0.923000	0.55619	0.807000	0.27140	0.398000	0.25338	0.651000	0.88453	CGG	G|0.440;A|0.560	0.560	strong		0.527	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2		
EXOC6B	23233	hgsc.bcm.edu	37	2	72707874	72707874	+	Silent	SNP	A	A	G	rs653220	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	60	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	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	
C14orf159	80017	hgsc.bcm.edu	37	14	91671124	91671124	+	Missense_Mutation	SNP	G	G	A	rs2295524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:91671124G>A	ENST00000523771.1	+	12	2107	c.1504G>A	c.(1504-1506)Gat>Aat	p.D502N	C14orf159_ENST00000518868.1_Missense_Mutation_p.D507N|C14orf159_ENST00000520328.1_Intron|C14orf159_ENST00000523816.1_Missense_Mutation_p.D502N|C14orf159_ENST00000412671.2_Missense_Mutation_p.D507N|C14orf159_ENST00000256324.10_Missense_Mutation_p.D507N|C14orf159_ENST00000521077.2_Intron|C14orf159_ENST00000428926.2_Missense_Mutation_p.D502N|C14orf159_ENST00000525393.2_Missense_Mutation_p.D378N|C14orf159_ENST00000522322.1_Missense_Mutation_p.D502N			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	502			D -> N (in dbSNP:rs2295524).			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)		ACGGCACGGGGATGTCATCGC	0.627													G|||	924	0.184505	0.289	0.0908	5008	,	,		19941	0.2123		0.0915	False		,,,				2504	0.1769				p.D507N		Atlas-SNP	.											.	C14orf159	57	.	0			c.G1519A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,,ASN/ASP	1127,3279	404.4+/-333.1	134,859,1210	162.0	107.0	126.0		1504,1504,1519,,1504	5.0	0.9	14	dbSNP_100	126	697,7903	171.6+/-222.5	33,631,3636	yes	missense,missense,missense,intron,missense	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	23,23,23,,23	167,1490,4846	AA,AG,GG		8.1047,25.5788,14.0243	possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging	502/617,502/617,507/622,,502/617	91671124	1824,11182	2203	4300	6503	SO:0001583	missense	80017	exon12			CACGGGGATGTCA	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.1504G>A	14.37:g.91671124G>A	ENSP00000429655:p.Asp502Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	335	0.1533882783882784	125	0.2540650406504065	41	0.1132596685082873	100	0.17482517482517482	69	0.09102902374670185	G	17.51	3.407587	0.62399	0.255788	0.081047	ENSG00000133943	ENST00000256324;ENST00000518868;ENST00000523816;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	4.96	4.96	0.65561	.	0.660719	0.15819	N	0.243086	T	0.00012	0.0000	M	0.69523	2.12	0.27463	P	0.9531044	P;D	0.57571	0.891;0.98	P;P	0.53649	0.673;0.731	T	0.05954	-1.0854	9	0.56958	D	0.05	.	17.8327	0.88687	0.0:0.0:1.0:0.0	rs2295524;rs17188983;rs57590208;rs2295524	502;507	Q7Z3D6;Q7Z3D6-2	CN159_HUMAN;.	N	507;507;502;378;502;502;502;507	ENSP00000256324:D507N;ENSP00000428263:D507N;ENSP00000428974:D502N;ENSP00000435459:D378N;ENSP00000404343:D502N;ENSP00000427953:D502N;ENSP00000429655:D502N;ENSP00000404196:D507N	ENSP00000256324:D507N	D	+	1	0	C14orf159	90740877	1.000000	0.71417	0.916000	0.36221	0.146000	0.21551	3.311000	0.51919	2.296000	0.77279	0.591000	0.81541	GAT	G|0.835;A|0.165	0.165	strong		0.627	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
AHNAK2	113146	hgsc.bcm.edu	37	14	105407031	105407031	+	Silent	SNP	A	A	G	rs11623422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	49	0	0		WXS	Illumina HiSeq	Phase_I	77	77	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	
BOD1L1	259282	hgsc.bcm.edu	37	4	13604182	13604182	+	Missense_Mutation	SNP	T	T	C	rs17745676	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:13604182T>C	ENST00000040738.5	-	10	4477	c.4342A>G	c.(4342-4344)Aca>Gca	p.T1448A		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1448			T -> A (in dbSNP:rs17745676).			nucleus (GO:0005634)	DNA binding (GO:0003677)										TATTTTTCTGTATTCAGGCCT	0.358													T|||	665	0.132788	0.1415	0.2089	5008	,	,		24405	0.003		0.1501	False		,,,				2504	0.183				p.T1448A		Atlas-SNP	.											.	.	.	.	0			c.A4342G						PASS	.	T	ALA/THR	655,3751	279.0+/-274.6	40,575,1588	97.0	89.0	92.0		4342	2.9	0.0	4	dbSNP_123	92	1295,7305	255.5+/-280.4	86,1123,3091	yes	missense	BOD1L	NM_148894.2	58	126,1698,4679	CC,CT,TT		15.0581,14.8661,14.9931	probably-damaging	1448/3052	13604182	1950,11056	2203	4300	6503	SO:0001583	missense	259282	exon10			TTTCTGTATTCAG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4342A>G	4.37:g.13604182T>C	ENSP00000040738:p.Thr1448Ala	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	187	88	0.470588	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	261	0.11950549450549451	80	0.16260162601626016	70	0.19337016574585636	0	0.0	111	0.14643799472295516	T	9.995	1.231917	0.22626	0.148661	0.150581	ENSG00000038219	ENST00000040738	T	0.07444	3.19	5.37	2.86	0.33363	.	0.235838	0.29335	N	0.012456	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.14012	0.009	B	0.12156	0.007	T	0.40627	-0.9553	9	0.39692	T	0.17	-2.3293	7.9535	0.30029	0.0:0.2567:0.0:0.7433	rs17745676;rs52821402;rs17745676	1448	Q8NFC6	BOD1L_HUMAN	A	1448	ENSP00000040738:T1448A	ENSP00000040738:T1448A	T	-	1	0	BOD1L	13213280	0.000000	0.05858	0.023000	0.16930	0.006000	0.05464	-0.055000	0.11807	0.327000	0.23409	-0.263000	0.10527	ACA	T|0.855;C|0.145	0.145	strong		0.358	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
BPIFA3	128861	hgsc.bcm.edu	37	20	31805464	31805464	+	Missense_Mutation	SNP	C	C	A	rs17124391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31805464C>A	ENST00000375454.3	+	1	332	c.122C>A	c.(121-123)gCa>gAa	p.A41E	BPIFA3_ENST00000375452.3_Missense_Mutation_p.A41E|RP11-49G10.3_ENST00000419613.1_RNA|BPIFA3_ENST00000490499.1_3'UTR	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	41			A -> E (in dbSNP:rs17124391).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCACCCTGGCAAGAAGTAAG	0.627													C|||	41	0.0081869	0.0008	0.0115	5008	,	,		18861	0.001		0.0239	False		,,,				2504	0.0072				p.A41E		Atlas-SNP	.											.	.	.	.	0			c.C122A						PASS	.	C	GLU/ALA,GLU/ALA	20,4386	26.2+/-53.5	0,20,2183	73.0	67.0	69.0		122,122	1.0	1.0	20	dbSNP_123	69	231,8369	94.7+/-156.6	2,227,4071	yes	missense,missense	BPIFA3	NM_001042439.1,NM_178466.3	107,107	2,247,6254	AA,AC,CC		2.686,0.4539,1.9299	probably-damaging,probably-damaging	41/219,41/255	31805464	251,12755	2203	4300	6503	SO:0001583	missense	128861	exon1			CCCTGGCAAGAAG		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.122C>A	20.37:g.31805464C>A	ENSP00000364603:p.Ala41Glu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	26	0.011904761904761904	0	0.0	7	0.019337016574585635	0	0.0	19	0.025065963060686015	C	13.77	2.336467	0.41398	0.004539	0.02686	ENSG00000131059	ENST00000375454;ENST00000375452	T;T	0.30182	1.8;1.54	4.36	0.96	0.19631	.	0.156146	0.30277	N	0.009986	T	0.14442	0.0349	L	0.32530	0.975	0.30574	N	0.763233	D;B	0.76494	0.999;0.331	D;B	0.68192	0.956;0.064	T	0.09143	-1.0688	10	0.49607	T	0.09	-2.27	5.9352	0.19161	0.0:0.6056:0.0:0.3944	rs17124391;rs17124391	41;41	Q9BQP9-2;Q9BQP9	.;BPIA3_HUMAN	E	41	ENSP00000364603:A41E;ENSP00000364601:A41E	ENSP00000364601:A41E	A	+	2	0	BPIFA3	31269125	0.867000	0.29959	0.980000	0.43619	0.935000	0.57460	0.403000	0.20982	0.222000	0.20900	0.655000	0.94253	GCA	C|0.984;A|0.016	0.016	strong		0.627	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
KCNK6	9424	hgsc.bcm.edu	37	19	38817876	38817876	+	Missense_Mutation	SNP	G	G	A	rs34989303	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38817876G>A	ENST00000263372.3	+	3	882	c.775G>A	c.(775-777)Gtg>Atg	p.V259M		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	259			V -> M (in dbSNP:rs34989303).		negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	CTTCCGCCACGTGTCCGACCT	0.642													G|||	784	0.15655	0.0507	0.2378	5008	,	,		17801	0.1478		0.1829	False		,,,				2504	0.2239				p.V259M		Atlas-SNP	.											.	KCNK6	37	.	0			c.G775A						PASS	.	G	MET/VAL	327,4079	169.8+/-200.3	21,285,1897	74.0	57.0	63.0		775	0.6	0.0	19	dbSNP_126	63	1314,7286	255.5+/-280.4	101,1112,3087	yes	missense	KCNK6	NM_004823.1	21	122,1397,4984	AA,AG,GG		15.2791,7.4217,12.6173	benign	259/314	38817876	1641,11365	2203	4300	6503	SO:0001583	missense	9424	exon3			CGCCACGTGTCCG	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.775G>A	19.37:g.38817876G>A	ENSP00000263372:p.Val259Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_004823	Q9HB47	Missense_Mutation	SNP	ENST00000263372.3	37	CCDS12513.1	335	0.1533882783882784	24	0.04878048780487805	88	0.2430939226519337	83	0.1451048951048951	140	0.18469656992084432	G	12.43	1.936680	0.34189	0.074217	0.152791	ENSG00000099337	ENST00000263372	T	0.24350	1.86	5.45	0.581	0.17407	.	0.265585	0.37053	N	0.002279	T	0.00012	0.0000	N	0.11560	0.145	0.58432	P	1.0000000000287557E-6	P	0.43231	0.801	B	0.43658	0.426	T	0.34179	-0.9839	9	0.49607	T	0.09	.	3.8911	0.09119	0.1517:0.1274:0.5898:0.1311	rs34989303	259	Q9Y257	KCNK6_HUMAN	M	259	ENSP00000263372:V259M	ENSP00000263372:V259M	V	+	1	0	KCNK6	43509716	0.003000	0.15002	0.003000	0.11579	0.589000	0.36550	-0.109000	0.10840	0.228000	0.21019	0.561000	0.74099	GTG	G|0.865;A|0.135	0.135	strong		0.642	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
TGS1	96764	hgsc.bcm.edu	37	8	56708701	56708701	+	Missense_Mutation	SNP	T	T	C	rs10100659	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:56708701T>C	ENST00000260129.5	+	7	2009	c.1532T>C	c.(1531-1533)aTt>aCt	p.I511T		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	511			I -> T (in dbSNP:rs10100659).		7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			AAAAGCAAAATTCTGAGTAAG	0.299													C|||	720	0.14377	0.2784	0.121	5008	,	,		18664	0.0099		0.1103	False		,,,				2504	0.1503				p.I511T	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.T1532C						PASS	.	C	THR/ILE	1140,3266	696.3+/-406.1	160,820,1223	40.0	39.0	39.0		1532	4.4	0.4	8	dbSNP_119	39	923,7675	767.4+/-407.6	48,827,3424	yes	missense	TGS1	NM_024831.6	89	208,1647,4647	CC,CT,TT		10.7351,25.8738,15.8643	benign	511/854	56708701	2063,10941	2203	4299	6502	SO:0001583	missense	96764	exon7			GCAAAATTCTGAG	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.1532T>C	8.37:g.56708701T>C	ENSP00000260129:p.Ile511Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	281	0.12866300366300365	153	0.31097560975609756	43	0.11878453038674033	0	0.0	85	0.11213720316622691	C	1.497	-0.552964	0.03996	0.258738	0.107351	ENSG00000137574	ENST00000260129	T	0.37235	1.21	6.17	4.37	0.52481	.	0.572044	0.20332	N	0.094404	T	0.00012	0.0000	N	0.00104	-2.125	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40794	-0.9544	9	0.02654	T	1	-0.0665	9.9018	0.41353	0.0:0.7887:0.0:0.2113	rs10100659;rs52810778;rs59983864;rs10100659	511;511	B2RBJ7;Q96RS0	.;TGS1_HUMAN	T	511	ENSP00000260129:I511T	ENSP00000260129:I511T	I	+	2	0	TGS1	56871255	0.999000	0.42202	0.442000	0.26870	0.941000	0.58515	2.096000	0.41738	0.486000	0.27676	-0.766000	0.03442	ATT	T|0.847;C|0.153	0.153	strong		0.299	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
DSPP	1834	hgsc.bcm.edu	37	4	88536550	88536550	+	Silent	SNP	T	T	C	rs111215872|rs111456637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88536550T>C	ENST00000282478.7	+	4	2769	c.2736T>C	c.(2734-2736)agT>agC	p.S912S	DSPP_ENST00000399271.1_Silent_p.S912S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	912	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.S912S(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)		gcaacagcagtgacagcagtg	0.488													T|||	1014	0.202476	0.1982	0.2637	5008	,	,		33910	0.1111		0.2972	False		,,,				2504	0.1616				p.S912S		Atlas-SNP	.											DSPP,NS,carcinoma,0,1	DSPP	174	1	1	Substitution - coding silent(1)	stomach(1)	c.T2736C						PASS	.			276,2946		18,240,1353	65.0	93.0	83.0		2736	0.4	0.9	4	dbSNP_134	83	1274,4674		128,1018,1828	no	coding-synonymous	DSPP	NM_014208.3		146,1258,3181	CC,CT,TT		21.419,8.5661,16.9029		912/1302	88536550	1550,7620	1611	2974	4585	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.2736T>C	4.37:g.88536550T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	212	115	0.542453	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	
GLYATL2	219970	hgsc.bcm.edu	37	11	58602309	58602309	+	Splice_Site	SNP	C	C	T	rs11229651	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58602309C>T	ENST00000287275.1	-	6	868	c.478G>A	c.(478-480)Gaa>Aaa	p.E160K	GLYATL2_ENST00000532258.1_Splice_Site_p.E160K|GLYATL2_ENST00000533636.1_5'UTR	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	160			E -> K (in dbSNP:rs11229651). {ECO:0000269|Ref.1}.			endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.E160K(1)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	AAGTTTCCTTCCCTGTGAAGA	0.343													C|||	1670	0.333466	0.2852	0.3242	5008	,	,		20670	0.4841		0.2018	False		,,,				2504	0.3855				p.E160K		Atlas-SNP	.											GLYATL2,NS,carcinoma,0,1	GLYATL2	40	1	1	Substitution - Missense(1)	stomach(1)	c.G478A						PASS	.	C	LYS/GLU	994,2856		152,690,1083	35.0	33.0	34.0		478	-1.4	0.0	11	dbSNP_120	34	1556,6738		141,1274,2732	yes	missense-near-splice	GLYATL2	NM_145016.3	56	293,1964,3815	TT,TC,CC		18.7605,25.8182,20.998	benign	160/295	58602309	2550,9594	1925	4147	6072	SO:0001630	splice_region_variant	219970	exon6			TTCCTTCCCTGTG	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.477-1G>A	11.37:g.58602309C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_145016	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	37	CCDS41649.1	663	0.30357142857142855	132	0.2682926829268293	97	0.26795580110497236	261	0.4562937062937063	173	0.22823218997361477	C	0.061	-1.225198	0.01530	0.258182	0.187605	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.14022	2.54;2.54	2.79	-1.35	0.09114	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	1.319930	0.05354	N	0.532409	T	0.00012	0.0000	N	0.01705	-0.755	0.09310	P	0.99999999507813	B	0.02656	0.0	B	0.01281	0.0	T	0.44877	-0.9299	9	0.02654	T	1	.	5.6535	0.17631	0.0:0.4619:0.0:0.5381	rs11229651;rs17845505;rs17858392;rs52831818;rs58248646;rs11229651	160	Q8WU03	GLYL2_HUMAN	K	160	ENSP00000287275:E160K;ENSP00000434277:E160K	ENSP00000287275:E160K	E	-	1	0	GLYATL2	58358885	0.007000	0.16637	0.007000	0.13788	0.012000	0.07955	0.205000	0.17356	0.057000	0.16193	-0.405000	0.06341	GAA	C|0.732;T|0.268	0.268	strong		0.343	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016	Missense_Mutation
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163266	163266	+	Missense_Mutation	SNP	C	C	G	rs3810867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	87	0	0		WXS	Illumina HiSeq	Phase_I	116	46	0.396552	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	
RP1	6101	hgsc.bcm.edu	37	8	55541513	55541513	+	Missense_Mutation	SNP	T	T	C	rs414352	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:55541513T>C	ENST00000220676.1	+	4	5219	c.5071T>C	c.(5071-5073)Tct>Cct	p.S1691P		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1691	Poly-Ser.		S -> P (in dbSNP:rs414352). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11095597, ECO:0000269|PubMed:11527933, ECO:0000269|PubMed:20664799}.		axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TAGTAGTTCATCTATGTTGCA	0.403													C|||	1397	0.278954	0.1687	0.3069	5008	,	,		20686	0.4415		0.2714	False		,,,				2504	0.2485				p.S1691P	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.T5071C						PASS	.	C	PRO/SER	883,3523	740.2+/-411.2	91,701,1411	163.0	166.0	165.0		5071	3.7	0.5	8	dbSNP_80	165	2341,6259	702.6+/-405.3	304,1733,2263	yes	missense	RP1	NM_006269.1	74	395,2434,3674	CC,CT,TT		27.2209,20.0409,24.7886	benign	1691/2157	55541513	3224,9782	2203	4300	6503	SO:0001583	missense	6101	exon4			AGTTCATCTATGT	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.5071T>C	8.37:g.55541513T>C	ENSP00000220676:p.Ser1691Pro	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	665	0.30448717948717946	110	0.22357723577235772	109	0.3011049723756906	250	0.4370629370629371	196	0.25857519788918204	C	3.533	-0.095342	0.07010	0.200409	0.272209	ENSG00000104237	ENST00000220676	T	0.21734	1.99	5.64	3.7	0.42460	.	0.647529	0.13571	N	0.378089	T	0.00012	0.0000	L	0.41236	1.265	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47058	-0.9146	9	0.20519	T	0.43	.	4.4777	0.11752	0.1745:0.6254:0.0:0.2001	rs414352;rs16920625;rs52799326;rs57524481;rs414352	1691	P56715	RP1_HUMAN	P	1691	ENSP00000220676:S1691P	ENSP00000220676:S1691P	S	+	1	0	RP1	55704066	0.011000	0.17503	0.460000	0.27093	0.374000	0.29953	-0.231000	0.09069	0.230000	0.21059	-0.119000	0.15052	TCT	C|0.269;N|0.000	0.269	strong		0.403	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
FAT1	2195	hgsc.bcm.edu	37	4	187518874	187518874	+	Silent	SNP	G	G	A	rs116628547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187518874G>A	ENST00000441802.2	-	24	12539	c.12330C>T	c.(12328-12330)ggC>ggT	p.G4110G	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4110	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						GACAAACGGCGCCATCCAAAC	0.418										HNSCC(5;0.00058)			G|||	15	0.00299521	0.0008	0.0014	5008	,	,		18073	0.0		0.008	False		,,,				2504	0.0051				p.G4110G	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C12330T						PASS	.	G		7,3819		0,7,1906	74.0	66.0	68.0		12330	-3.1	1.0	4	dbSNP_132	68	51,8225		0,51,4087	no	coding-synonymous	FAT1	NM_005245.3		0,58,5993	AA,AG,GG		0.6162,0.183,0.4793		4110/4589	187518874	58,12044	1913	4138	6051	SO:0001819	synonymous_variant	2195	exon24			AACGGCGCCATCC	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.12330C>T	4.37:g.187518874G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	147	81	0.55102	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.995;A|0.005	0.005	strong		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
SPECC1	92521	hgsc.bcm.edu	37	17	20108184	20108184	+	Missense_Mutation	SNP	C	C	G	rs9908032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:20108184C>G	ENST00000261503.5	+	4	873	c.822C>G	c.(820-822)agC>agG	p.S274R	AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395527.4_Missense_Mutation_p.S274R|SPECC1_ENST00000395525.3_Missense_Mutation_p.S193R|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395522.2_Missense_Mutation_p.S193R|SPECC1_ENST00000395529.3_Missense_Mutation_p.S274R|SPECC1_ENST00000395530.2_Missense_Mutation_p.S193R|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	274	Ser-rich.		S -> R (in dbSNP:rs9908032). {ECO:0000269|Ref.1}.		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)		GCGACAGCAGCTGCCCAACAT	0.463													C|||	569	0.113618	0.093	0.1455	5008	,	,		18010	0.0942		0.1223	False		,,,				2504	0.1299				p.S274R		Atlas-SNP	.											.	SPECC1	100	.	0			c.C822G						PASS	.	C	ARG/SER,ARG/SER,ARG/SER,ARG/SER	506,3900	223.6+/-240.1	34,438,1731	66.0	75.0	72.0		822,579,579,822	5.4	1.0	17	dbSNP_119	72	1154,7446	234.6+/-267.5	86,982,3232	yes	missense,missense,missense,missense	SPECC1	NM_001033553.2,NM_001033554.2,NM_001033555.2,NM_152904.4	110,110,110,110	120,1420,4963	GG,GC,CC		13.4186,11.4843,12.7633	probably-damaging,probably-damaging,probably-damaging,probably-damaging	274/1069,193/710,193/988,274/791	20108184	1660,11346	2203	4300	6503	SO:0001583	missense	92521	exon4			CAGCAGCTGCCCA	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.822C>G	17.37:g.20108184C>G	ENSP00000261503:p.Ser274Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	37	CCDS32590.1	229	0.10485347985347986	43	0.08739837398373984	43	0.11878453038674033	47	0.08216783216783216	96	0.1266490765171504	C	20.7	4.031537	0.75504	0.114843	0.134186	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.67171	-0.25;2.74;2.77;2.76	5.38	5.38	0.77491	.	0.136950	0.64402	D	0.000004	T	0.03477	0.0100	M	0.65498	2.005	0.09310	P	1.0	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.961;0.999;0.999;0.999;0.979	T	0.39542	-0.9609	9	0.59425	D	0.04	-17.4801	17.0048	0.86390	0.0:1.0:0.0:0.0	rs9908032	274;193;193;274;274	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	R	274;274;274;193;193;193	ENSP00000261503:S274R;ENSP00000378900:S274R;ENSP00000378893:S193R;ENSP00000378896:S193R	ENSP00000261503:S274R	S	+	3	2	SPECC1	20048776	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.068000	0.50018	2.698000	0.92095	0.655000	0.94253	AGC	C|0.883;G|0.117	0.117	strong		0.463	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
RBAK	57786	hgsc.bcm.edu	37	7	5096958	5096958	+	Silent	SNP	T	T	C	rs11975068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:5096958T>C	ENST00000353796.3	+	4	372	c.48T>C	c.(46-48)gaT>gaC	p.D16D	RBAK-RBAKDN_ENST00000407184.1_Silent_p.D16D|RBAK-RBAKDN_ENST00000396904.2_Silent_p.D16D|RBAK_ENST00000396912.1_Silent_p.D16D	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	16	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TGGCTGTGGATTTCACCCAGG	0.473													T|||	1279	0.255391	0.1687	0.2277	5008	,	,		11943	0.379		0.2724	False		,,,				2504	0.2474				p.D16D		Atlas-SNP	.											RBAK_ENST00000396912,NS,carcinoma,0,1	.	.	1	0			c.T48C						PASS	.	T	,,	808,3598	322.9+/-297.8	75,658,1470	110.0	115.0	113.0		48,48,48	1.9	0.9	7	dbSNP_120	113	2200,6400	374.2+/-337.3	261,1678,2361	no	coding-synonymous,coding-synonymous,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	336,2336,3831	CC,CT,TT		25.5814,18.3386,23.1278	,,	16/715,16/114,16/715	5096958	3008,9998	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGTGGATTTCACC	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.48T>C	7.37:g.5096958T>C		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	202	113	0.559406	NM_001204513	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			T|0.756;C|0.244	0.244	strong		0.473	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
ORC4	5000	hgsc.bcm.edu	37	2	148716428	148716428	+	Missense_Mutation	SNP	T	T	C	rs2307394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:148716428T>C	ENST00000392857.5	-	5	340	c.233A>G	c.(232-234)aAt>aGt	p.N78S	ORC4_ENST00000264169.2_Missense_Mutation_p.N78S|ORC4_ENST00000392858.1_Missense_Mutation_p.N78S|ORC4_ENST00000540442.1_Missense_Mutation_p.N4S|ORC4_ENST00000542387.1_Intron|ORC4_ENST00000535373.1_Missense_Mutation_p.N78S|ORC4_ENST00000536575.1_5'UTR	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	78			N -> S (in dbSNP:rs2307394). {ECO:0000269|PubMed:9353276, ECO:0000269|Ref.2, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	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)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						CAAAGCATGATTTATTAACTA	0.259													T|||	1782	0.355831	0.2859	0.4611	5008	,	,		14669	0.4762		0.325	False		,,,				2504	0.2832				p.N78S		Atlas-SNP	.											.	ORC4	40	.	0			c.A233G						PASS	.	T	SER/ASN,,SER/ASN,SER/ASN,SER/ASN,SER/ASN	1354,3032		218,918,1057	47.0	45.0	46.0		233,,11,233,233,233	5.5	1.0	2	dbSNP_100	46	2678,5882		415,1848,2017	yes	missense,utr-5,missense,missense,missense,missense	ORC4	NM_001190879.2,NM_001190881.2,NM_001190882.2,NM_002552.4,NM_181741.3,NM_181742.3	46,,46,46,46,46	633,2766,3074	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	31.285,30.871,31.1448	benign,,benign,benign,benign,benign	78/437,,4/363,78/437,78/437,78/437	148716428	4032,8914	2193	4280	6473	SO:0001583	missense	5000	exon5			GCATGATTTATTA	AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"""ATPases / AAA-type"""	8490	protein-coding gene	gene with protein product		603056	"""origin recognition complex, subunit 4 (yeast homolog)-like"", ""origin recognition complex, subunit 4-like (yeast)"", ""origin recognition complex, subunit 4-like (S. cerevisiae)"", ""origin recognition complex, subunit 4 homolog (S. cerevisiae)"""	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.233A>G	2.37:g.148716428T>C	ENSP00000376597:p.Asn78Ser	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	265	133	0.501887	NM_002552	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	848	0.3882783882783883	148	0.3008130081300813	161	0.4447513812154696	277	0.48426573426573427	262	0.34564643799472294	T	13.60	2.286415	0.40494	0.30871	0.31285	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000540442;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;T;T;T;T;T	0.72615	0.45;0.45;0.45;-0.67;0.45;0.45;0.45;0.45	5.48	5.48	0.80851	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.490109	0.25768	N	0.028426	T	0.00012	0.0000	L	0.31476	0.935	0.09310	P	0.9999999999997147	B;B;B	0.23249	0.082;0.021;0.021	B;B;B	0.21151	0.033;0.009;0.021	T	0.41124	-0.9526	9	0.19147	T	0.46	-18.291	9.1469	0.36939	0.0:0.0831:0.0:0.9169	rs2307394;rs3768682;rs17225472;rs59475490;rs2307394	78;78;78	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	S	78;78;78;4;78;78;78;78	ENSP00000264169:N78S;ENSP00000441953:N78S;ENSP00000376598:N78S;ENSP00000438326:N4S;ENSP00000376597:N78S;ENSP00000413939:N78S;ENSP00000391484:N78S;ENSP00000403105:N78S	ENSP00000264169:N78S	N	-	2	0	ORC4	148432898	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.450000	0.44943	2.069000	0.61940	0.477000	0.44152	AAT	T|0.653;C|0.346	0.346	strong		0.259	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742	
SRRM1	10250	hgsc.bcm.edu	37	1	24995933	24995933	+	Missense_Mutation	SNP	C	C	T	rs149689871		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24995933C>T	ENST00000323848.9	+	14	2374	c.2059C>T	c.(2059-2061)Cgg>Tgg	p.R687W	SRRM1_ENST00000447431.2_Missense_Mutation_p.R699W|SRRM1_ENST00000374389.4_Missense_Mutation_p.R696W|SRRM1_ENST00000479034.1_3'UTR|snoU13_ENST00000459464.1_RNA	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	687	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		GCCCTCACCACGGCCTCGAGC	0.582																																					p.R687W	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.C2059T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	73.0	68.0	70.0		2059	5.8	1.0	1	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SRRM1	NM_005839.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	687/905	24995933	1,13005	2203	4300	6503	SO:0001583	missense	10250	exon14			TCACCACGGCCTC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2059C>T	1.37:g.24995933C>T	ENSP00000326261:p.Arg687Trp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.681006	0.68042	0.0	1.16E-4	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.37752	1.18;1.18;1.18	5.75	5.75	0.90469	.	0.000000	0.56097	D	0.000035	T	0.43433	0.1247	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.999;0.993	D;B	0.74348	0.983;0.265	T	0.55244	-0.8171	10	0.72032	D	0.01	-1.1771	19.9382	0.97149	0.0:1.0:0.0:0.0	.	699;687	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	W	687;699;696	ENSP00000326261:R687W;ENSP00000391430:R699W;ENSP00000363510:R696W	ENSP00000326261:R687W	R	+	1	2	SRRM1	24868520	0.999000	0.42202	0.999000	0.59377	0.987000	0.75469	3.471000	0.53107	2.720000	0.93068	0.563000	0.77884	CGG	C|1.000;T|0.000	0.000	weak		0.582	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
HERC5	51191	hgsc.bcm.edu	37	4	89380540	89380540	+	Missense_Mutation	SNP	A	A	G	rs75070724	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:89380540A>G	ENST00000264350.3	+	2	461	c.308A>G	c.(307-309)gAc>gGc	p.D103G	HERC5_ENST00000508695.1_3'UTR	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	103					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		CATTCCGTGGACCAAGGAGCA	0.368													a|||	6	0.00119808	0.0	0.0014	5008	,	,		15874	0.0		0.005	False		,,,				2504	0.0				p.D103G	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.A308G						PASS	.	A	GLY/ASP	4,4402	8.1+/-20.4	0,4,2199	133.0	127.0	129.0		308	2.4	1.0	4	dbSNP_131	129	24,8576	17.3+/-56.4	0,24,4276	yes	missense	HERC5	NM_016323.2	94	0,28,6475	GG,GA,AA		0.2791,0.0908,0.2153	benign	103/1025	89380540	28,12978	2203	4300	6503	SO:0001583	missense	51191	exon2			CCGTGGACCAAGG	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.308A>G	4.37:g.89380540A>G	ENSP00000264350:p.Asp103Gly	Somatic	483	0	0		WXS	Illumina HiSeq	Phase_I	490	258	0.526531	NM_016323	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	a	10.19	1.281261	0.23392	9.08E-4	0.002791	ENSG00000138646	ENST00000264350	T	0.80123	-1.34	3.62	2.4	0.29515	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.115379	0.34088	N	0.004267	T	0.59528	0.2200	N	0.25890	0.77	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.60037	-0.7341	10	0.59425	D	0.04	.	8.5302	0.33329	0.8048:0.1952:0.0:0.0	.	103	Q9UII4	HERC5_HUMAN	G	103	ENSP00000264350:D103G	ENSP00000264350:D103G	D	+	2	0	HERC5	89599563	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	2.018000	0.40991	0.730000	0.32425	0.529000	0.55759	GAC	A|0.998;G|0.002	0.002	strong		0.368	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
MOV10	4343	hgsc.bcm.edu	37	1	113236681	113236681	+	Silent	SNP	C	C	T	rs3748656	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:113236681C>T	ENST00000413052.2	+	8	1572	c.1182C>T	c.(1180-1182)ggC>ggT	p.G394G	MOV10_ENST00000369645.1_Silent_p.G394G|MOV10_ENST00000357443.2_Silent_p.G394G|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.G338G|RP11-426L16.3_ENST00000421943.1_RNA	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	394					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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		TGCTACGGGGCGACCACCTGT	0.582													C|||	1426	0.284744	0.1672	0.2911	5008	,	,		17209	0.5427		0.2346	False		,,,				2504	0.2249				p.G394G		Atlas-SNP	.											MOV10,NS,carcinoma,+1,1	MOV10	74	1	0			c.C1182T						scavenged	.	C	,	805,3601	321.3+/-297.0	83,639,1481	104.0	95.0	98.0		1182,1182	-10.5	0.4	1	dbSNP_107	98	1768,6832	321.1+/-314.9	181,1406,2713	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	264,2045,4194	TT,TC,CC		20.5581,18.2705,19.7832	,	394/1004,394/1004	113236681	2573,10433	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon8			ACGGGGCGACCAC	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1182C>T	1.37:g.113236681C>T		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	161	86	0.534162	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			C|0.752;T|0.248	0.248	strong		0.582	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919949	51919949	+	Missense_Mutation	SNP	G	G	A	rs9304711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51919949G>A	ENST00000339313.5	-	3	793	c.677C>T	c.(676-678)gCa>gTa	p.A226V	SIGLEC10_ENST00000439889.2_Missense_Mutation_p.A168V|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.A226V|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.A226V|SIGLEC10_ENST00000432469.2_Intron|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.A226V|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.A168V|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000442846.3_Missense_Mutation_p.A168V|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.A178V			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	226	Ig-like C2-type 1.		A -> V (in dbSNP:rs9304711). {ECO:0000269|PubMed:11284738, ECO:0000269|PubMed:11358961, ECO:0000269|PubMed:12163025, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		GGTCCTCTGTGCGCTCACACC	0.652													g|||	1357	0.270966	0.4841	0.2233	5008	,	,		16594	0.006		0.3012	False		,,,				2504	0.2587				p.A226V		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C677T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,,VAL/ALA,VAL/ALA	1956,2450		441,1074,688	116.0	93.0	101.0		503,677,533,503,,503,677	3.7	0.0	19	dbSNP_119	101	2484,6110		365,1754,2178	no	missense,missense,missense,missense,intron,missense,missense	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	64,64,64,64,,64,64	806,2828,2866	AA,AG,GG		28.9039,44.394,34.1538	benign,benign,benign,benign,,benign,benign	168/640,226/603,178/555,168/545,,168/455,226/698	51919949	4440,8560	2203	4297	6500	SO:0001583	missense	89790	exon3			CTCTGTGCGCTCA	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.677C>T	19.37:g.51919949G>A	ENSP00000345243:p.Ala226Val	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	277	127	0.458484	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	569	0.26053113553113555	252	0.5121951219512195	93	0.2569060773480663	3	0.005244755244755245	221	0.29155672823219	.	14.46	2.541723	0.45280	0.44394	0.289039	ENSG00000142512	ENST00000353836;ENST00000442846;ENST00000356298;ENST00000441969;ENST00000525998;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;D;T;D;T;D;D;T;D	0.85955	4.05;-2.05;4.05;-2.05;4.05;-2.05;-2.05;4.05;-2.05	4.69	3.65	0.41850	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.354249	0.24474	N	0.038202	T	0.00012	0.0000	L	0.28400	0.85	0.80722	P	0.0	B;B;B;B;B;B;B	0.31893	0.087;0.345;0.329;0.005;0.165;0.095;0.112	B;B;B;B;B;B;B	0.33392	0.097;0.163;0.127;0.007;0.075;0.061;0.091	T	0.41161	-0.9524	9	0.14252	T	0.57	.	8.6839	0.34225	0.1084:0.0:0.8916:0.0	rs9304711;rs60900575	178;226;168;226;168;168;226	C9JM10;E9PL79;C9JJ33;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;.;SIG10_HUMAN	V	226;168;226;168;226;168;178;226;40	ENSP00000342389:A226V;ENSP00000395475:A168V;ENSP00000348646:A226V;ENSP00000408387:A168V;ENSP00000431444:A226V;ENSP00000389132:A168V;ENSP00000414324:A178V;ENSP00000345243:A226V;ENSP00000435281:A40V	ENSP00000345243:A226V	A	-	2	0	SIGLEC10	56611761	0.000000	0.05858	0.002000	0.10522	0.153000	0.21895	0.645000	0.24782	0.961000	0.38030	0.313000	0.20887	GCA	G|0.682;A|0.318	0.318	strong		0.652	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
FAM83F	113828	hgsc.bcm.edu	37	22	40417571	40417571	+	Missense_Mutation	SNP	G	G	A	rs35823589	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:40417571G>A	ENST00000333407.6	+	4	1151	c.1057G>A	c.(1057-1059)Ggc>Agc	p.G353S	FAM83F_ENST00000473717.1_Missense_Mutation_p.G185S	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	353			G -> S (in dbSNP:rs35823589).							breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						GGAGGCGGGCGGCAACCCGGA	0.687													G|||	188	0.0375399	0.003	0.0303	5008	,	,		13506	0.0		0.0736	False		,,,				2504	0.091				p.G353S		Atlas-SNP	.											.	FAM83F	29	.	0			c.G1057A						PASS	.	G	SER/GLY	47,4343		3,41,2151	16.0	18.0	17.0		1057	-0.9	0.0	22	dbSNP_126	17	568,8000		20,528,3736	no	missense	FAM83F	NM_138435.2	56	23,569,5887	AA,AG,GG		6.6293,1.0706,4.7461	benign	353/501	40417571	615,12343	2195	4284	6479	SO:0001583	missense	113828	exon4			GCGGGCGGCAACC		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.1057G>A	22.37:g.40417571G>A	ENSP00000330432:p.Gly353Ser	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	37	CCDS14000.2	76	0.0347985347985348	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	59	0.07783641160949868	G	7.875	0.729019	0.15507	0.010706	0.066293	ENSG00000133477	ENST00000333407	T	0.08807	3.05	4.79	-0.879	0.10613	.	0.828414	0.11087	N	0.601180	T	0.00241	0.0007	N	0.20986	0.625	0.09310	N	1	B	0.26002	0.139	B	0.16289	0.015	T	0.45381	-0.9265	10	0.09338	T	0.73	-10.7881	6.0315	0.19683	0.2862:0.126:0.5878:0.0	rs35823589	353	Q8NEG4	FA83F_HUMAN	S	353	ENSP00000330432:G353S	ENSP00000330432:G353S	G	+	1	0	FAM83F	38747517	0.057000	0.20700	0.000000	0.03702	0.005000	0.04900	0.867000	0.27968	-0.213000	0.10094	-0.258000	0.10820	GGC	G|0.955;A|0.045	0.045	strong		0.687	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
TCHH	7062	hgsc.bcm.edu	37	1	152084221	152084221	+	Missense_Mutation	SNP	A	A	C	rs202112040		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152084221A>C	ENST00000368804.1	-	2	1471	c.1472T>G	c.(1471-1473)cTc>cGc	p.L491R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	491	9 X 28 AA approximate 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)			CTCCTCCTCGAGCTTCAGCCA	0.672																																					p.L491R		Atlas-SNP	.											.	TCHH	275	.	0			c.T1472G						PASS	.						63.0	70.0	68.0					1																	152084221		2106	4220	6326	SO:0001583	missense	7062	exon3			TCCTCGAGCTTCA	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.1472T>G	1.37:g.152084221A>C	ENSP00000357794:p.Leu491Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	181	20	0.110497	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	a	0.064	-1.216147	0.01542	.	.	ENSG00000159450	ENST00000368804	T	0.04603	3.59	2.11	-4.23	0.03789	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43491	-0.9388	9	0.12430	T	0.62	.	7.0185	0.24900	0.2982:0.5613:0.0:0.1406	.	491	Q07283	TRHY_HUMAN	R	491	ENSP00000357794:L491R	ENSP00000357794:L491R	L	-	2	0	TCHH	150350845	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-1.154000	0.03166	-2.764000	0.00368	-1.533000	0.00918	CTC	.	.	weak		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
OR8U1	219417	hgsc.bcm.edu	37	11	56143424	56143424	+	Missense_Mutation	SNP	A	A	G	rs12788990	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56143424A>G	ENST00000302270.1	+	1	325	c.325A>G	c.(325-327)Ata>Gta	p.I109V		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	109			I -> V (in dbSNP:rs12788990).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I109V(1)		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)					CACCTTCATGATATCAGAATC	0.408													A|||	519	0.103634	0.1725	0.036	5008	,	,		23035	0.0933		0.0934	False		,,,				2504	0.0798				p.I109V		Atlas-SNP	.											OR8U1,NS,carcinoma,0,1	OR8U1	59	1	1	Substitution - Missense(1)	stomach(1)	c.A325G						PASS	.	A	VAL/ILE	597,3563		46,505,1529	175.0	167.0	169.0		325	1.0	0.1	11	dbSNP_121	169	728,7764		31,666,3549	yes	missense	OR8U1	NM_001005204.1	29	77,1171,5078	GG,GA,AA		8.5728,14.351,10.4727	benign	109/310	56143424	1325,11327	2080	4246	6326	SO:0001583	missense	219417	exon1			TTCATGATATCAG	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.325A>G	11.37:g.56143424A>G	ENSP00000304188:p.Ile109Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	229	0.10485347985347986	104	0.21138211382113822	19	0.052486187845303865	40	0.06993006993006994	66	0.0870712401055409	A	0.006	-2.037402	0.00406	0.14351	0.085728	ENSG00000172199	ENST00000302270	T	0.02916	4.11	5.78	1.02	0.19986	GPCR, rhodopsin-like superfamily (1);	1.290760	0.05319	N	0.526262	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.47947	-0.9077	9	0.24483	T	0.36	.	8.9956	0.36050	0.4219:0.0:0.5781:0.0	rs12788990;rs12788990	109	Q8NH10	OR8U1_HUMAN	V	109	ENSP00000304188:I109V	ENSP00000304188:I109V	I	+	1	0	OR8U1	55900000	0.000000	0.05858	0.116000	0.21606	0.003000	0.03518	-3.335000	0.00508	0.146000	0.19002	0.523000	0.50628	ATA	A|0.893;G|0.107	0.107	strong		0.408	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
PCNXL4	64430	hgsc.bcm.edu	37	14	60591829	60591829	+	Silent	SNP	T	T	C	rs308990	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:60591829T>C	ENST00000406854.1	+	9	3494	c.2940T>C	c.(2938-2940)ttT>ttC	p.F980F	PCNXL4_ENST00000317623.4_Silent_p.F746F|PCNXL4_ENST00000535349.1_Silent_p.F187F|PCNXL4_ENST00000406949.1_Silent_p.F746F|PCNXL4_ENST00000404681.2_Silent_p.F980F			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	980						integral component of membrane (GO:0016021)											CTTGTTATTTTAGTTTATTTG	0.373													T|||	1635	0.326478	0.5787	0.1369	5008	,	,		20338	0.2946		0.1153	False		,,,				2504	0.3701				p.F746F		Atlas-SNP	.											.	.	.	.	0			c.T2238C						PASS	.	T		2207,2197	583.5+/-385.8	543,1121,538	74.0	76.0	76.0		2238	2.8	0.8	14	dbSNP_79	76	1097,7503	224.3+/-260.7	75,947,3278	no	coding-synonymous	C14orf135	NM_022495.5		618,2068,3816	CC,CT,TT		12.7558,49.8865,25.4076		746/939	60591829	3304,9700	2202	4300	6502	SO:0001819	synonymous_variant	64430	exon8			TTATTTTAGTTTA	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.2940T>C	14.37:g.60591829T>C		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	307	156	0.508143	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Silent	SNP	ENST00000406854.1	37																																																																																				T|0.723;C|0.277	0.277	strong		0.373	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
ACHE	43	hgsc.bcm.edu	37	7	100490797	100490797	+	Missense_Mutation	SNP	G	G	T	rs1799805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100490797G>T	ENST00000412389.1	-	1	1212	c.1057C>A	c.(1057-1059)Cac>Aac	p.H353N	ACHE_ENST00000241069.5_Missense_Mutation_p.H353N|ACHE_ENST00000411582.1_Missense_Mutation_p.H353N|ACHE_ENST00000302913.4_Missense_Mutation_p.H353N|ACHE_ENST00000428317.1_Missense_Mutation_p.H353N|ACHE_ENST00000419336.2_Missense_Mutation_p.H353N			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	353			H -> N (in Yt(b) antigen; dbSNP:rs1799805). {ECO:0000269|PubMed:8488842, ECO:0000269|Ref.6}.		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)	TGCAGGCCGTGGAAGTCTCCC	0.617													G|||	123	0.0245607	0.0	0.0375	5008	,	,		18861	0.002		0.0517	False		,,,				2504	0.044				p.H353N		Atlas-SNP	.											.	ACHE	80	.	0			c.C1057A	GRCh37	CM930006	ACHE	M	rs1799805	PASS	.	G	ASN/HIS,ASN/HIS	29,4377	32.6+/-62.9	1,27,2175	64.0	52.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1057,1057	4.1	0.8	7	dbSNP_89	56	407,8193	126.7+/-185.1	14,379,3907	yes	missense,missense	ACHE	NM_000665.3,NM_015831.2	68,68	15,406,6082	TT,TG,GG		4.7326,0.6582,3.3523	benign,benign	353/615,353/618	100490797	436,12570	2203	4300	6503	SO:0001583	missense	43	exon2			GGCCGTGGAAGTC		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.1057C>A	7.37:g.100490797G>T	ENSP00000394976:p.His353Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	37	CCDS5709.1	60	0.027472527472527472	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	44	0.05804749340369393	G	5.710	0.315442	0.10789	0.006582	0.047326	ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000302913;ENST00000412389;ENST00000426415;ENST00000430554;ENST00000411582;ENST00000422451	T;T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.03	4.08	0.47627	Carboxylesterase, type B (1);	0.390772	0.28958	N	0.013583	T	0.05410	0.0143	N	0.02420	-0.555	0.80722	D	1	B;B;B;B	0.28258	0.137;0.205;0.07;0.017	B;B;B;B	0.32677	0.047;0.15;0.045;0.029	T	0.10917	-1.0609	10	0.72032	D	0.01	.	10.0132	0.41999	0.0:0.0:0.7431:0.2569	rs1799805;rs2230945;rs17228595;rs17884516;rs1799805	353;353;353;353	B7WPI6;P22303-3;P22303-2;P22303	.;.;.;ACES_HUMAN	N	353	ENSP00000403474:H353N;ENSP00000241069:H353N;ENSP00000414858:H353N;ENSP00000303211:H353N;ENSP00000394976:H353N;ENSP00000397143:H353N;ENSP00000399725:H353N;ENSP00000404865:H353N	ENSP00000241069:H353N	H	-	1	0	ACHE	100328733	1.000000	0.71417	0.764000	0.31436	0.210000	0.24377	1.991000	0.40727	0.935000	0.37341	0.484000	0.47621	CAC	G|0.967;T|0.033	0.033	strong		0.617	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
PRR21	643905	hgsc.bcm.edu	37	2	240981487	240981487	+	Missense_Mutation	SNP	A	A	G	rs60617721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:240981487A>G	ENST00000408934.1	-	1	912	c.913T>C	c.(913-915)Tgc>Cgc	p.C305R		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	305	Pro-rich.									NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GTGAAGAGGCATGGACGAAGG	0.632													a|||	2078	0.414936	0.4455	0.3775	5008	,	,		16158	0.5744		0.332	False		,,,				2504	0.3211				p.C305R		Atlas-SNP	.											PRR21,rectum,carcinoma,0,2	PRR21	53	2	0			c.T913C						PASS	.						25.0	21.0	23.0					2																	240981487		1766	3570	5336	SO:0001583	missense	643905	exon1			AGAGGCATGGACG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.913T>C	2.37:g.240981487A>G	ENSP00000386166:p.Cys305Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	63	0.954545	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.707321	0.00096	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13420	2.59;2.59	0.623	-1.25	0.09405	.	.	.	.	.	T	0.04452	0.0122	N	0.08118	0	0.80722	P	0.0	B	0.19073	0.033	B	0.08055	0.003	T	0.43360	-0.9396	8	0.08381	T	0.77	.	2.6586	0.05019	0.2679:0.4862:0.0:0.2459	rs60617721;rs62184584	305	Q8WXC7	PRR21_HUMAN	R	305	ENSP00000386166:C305R;ENSP00000418240:C305R	ENSP00000386166:C305R	C	-	1	0	PRR21	240630160	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.193000	0.01244	-1.350000	0.02199	-1.198000	0.01671	TGC	A|0.695;G|0.305	0.305	strong		0.632	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
CASQ2	845	hgsc.bcm.edu	37	1	116243877	116243877	+	Silent	SNP	G	G	A	rs7413162|rs397516641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:116243877G>A	ENST00000261448.5	-	11	1424	c.1185C>T	c.(1183-1185)gaC>gaT	p.D395D	CASQ2_ENST00000456138.2_Silent_p.D324D	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	395	Asp/Glu-rich (acidic).				cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		catcatcatcgtcatcactgt	0.398													A|||	2132	0.425719	0.4599	0.464	5008	,	,		23773	0.3224		0.4135	False		,,,				2504	0.4714				p.D395D		Atlas-SNP	.											.	CASQ2	54	.	0			c.C1185T						PASS	.	A		1973,2433	619.6+/-393.4	458,1057,688	231.0	197.0	208.0		1185	-9.6	0.5	1	dbSNP_116	208	3073,5527	660.2+/-401.7	565,1943,1792	no	coding-synonymous	CASQ2	NM_001232.3		1023,3000,2480	AA,AG,GG		35.7326,44.7798,38.7975		395/400	116243877	5046,7960	2203	4300	6503	SO:0001819	synonymous_variant	845	exon11			ATCATCGTCATCA	BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"""Protein disulfide isomerases"""	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.1185C>T	1.37:g.116243877G>A		Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	322	143	0.444099	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Silent	SNP	ENST00000261448.5	37	CCDS884.1																																																																																			G|0.586;A|0.414	0.414	strong		0.398	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232	
PIGF	5281	hgsc.bcm.edu	37	2	46839477	46839477	+	Silent	SNP	T	T	C	rs1824050	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:46839477T>C	ENST00000281382.6	-	4	497	c.327A>G	c.(325-327)gcA>gcG	p.A109A	PIGF_ENST00000306465.4_Silent_p.A109A|PIGF_ENST00000495933.1_5'UTR	NM_002643.3	NP_002634.1	Q07326	PIGF_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class F	109					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ethanolaminephosphotransferase activity (GO:0004307)			breast(1)|endometrium(1)|lung(1)|stomach(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ATGTTTCCAATGCCAACCTAG	0.274													T|||	903	0.180312	0.0484	0.3213	5008	,	,		12823	0.121		0.2873	False		,,,				2504	0.2096				p.A109A		Atlas-SNP	.											.	PIGF	9	.	0			c.A327G						PASS	.	T	,	354,4006		19,316,1845	23.0	21.0	22.0		327,327	1.9	1.0	2	dbSNP_92	22	2457,6103		374,1709,2197	no	coding-synonymous,coding-synonymous	PIGF	NM_002643.3,NM_173074.2	,	393,2025,4042	CC,CT,TT		28.7033,8.1193,21.757	,	109/220,109/207	46839477	2811,10109	2180	4280	6460	SO:0001819	synonymous_variant	5281	exon4			TTCCAATGCCAAC		CCDS1827.1, CCDS1828.1	2p21-p16	2013-02-26	2006-06-28		ENSG00000151665	ENSG00000151665		"""Phosphatidylinositol glycan anchor biosynthesis"""	8962	protein-coding gene	gene with protein product		600153	"""phosphatidylinositol glycan, class F"""			8575782, 8463218	Standard	NM_173074		Approved		uc002rvd.3	Q07326	OTTHUMG00000128816	ENST00000281382.6:c.327A>G	2.37:g.46839477T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_002643	Q8WW20	Silent	SNP	ENST00000281382.6	37	CCDS1827.1																																																																																			T|0.798;C|0.202	0.202	strong		0.274	PIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250749.2	NM_173074	
OR10G7	390265	hgsc.bcm.edu	37	11	123909671	123909671	+	Missense_Mutation	SNP	G	G	A	rs11827843	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123909671G>A	ENST00000330487.5	-	1	46	c.38C>T	c.(37-39)aCg>aTg	p.T13M		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	13			T -> M (in dbSNP:rs11827843).			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)		GGGAAGGCCCGTGAGGATGAA	0.547													A|||	393	0.0784744	0.1558	0.0288	5008	,	,		17247	0.0744		0.0139	False		,,,				2504	0.0798				p.T13M		Atlas-SNP	.											.	OR10G7	103	.	0			c.C38T						PASS	.	A	MET/THR	632,3768	268.6+/-268.5	46,540,1614	99.0	90.0	93.0		38	-2.3	0.2	11	dbSNP_120	93	156,8442	73.5+/-136.2	2,152,4145	yes	missense	OR10G7	NM_001004463.1	81	48,692,5759	AA,AG,GG		1.8144,14.3636,6.0625	benign	13/312	123909671	788,12210	2200	4299	6499	SO:0001583	missense	390265	exon1			AGGCCCGTGAGGA	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.38C>T	11.37:g.123909671G>A	ENSP00000329689:p.Thr13Met	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	216	104	0.481481	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	141	0.06456043956043957	66	0.13414634146341464	10	0.027624309392265192	52	0.09090909090909091	13	0.017150395778364115	g	5.259	0.233252	0.09969	0.143636	0.018144	ENSG00000182634	ENST00000330487	T	0.00421	7.46	3.27	-2.34	0.06704	.	1.119520	0.06816	N	0.791289	T	0.00012	0.0000	N	0.12887	0.27	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.09684	-1.0663	9	0.36615	T	0.2	.	3.5223	0.07747	0.5545:0.0:0.2732:0.1724	rs11827843	13	Q8NGN6	O10G7_HUMAN	M	13	ENSP00000329689:T13M	ENSP00000329689:T13M	T	-	2	0	OR10G7	123414881	0.000000	0.05858	0.247000	0.24249	0.028000	0.11728	-1.233000	0.02934	-0.569000	0.06030	-1.158000	0.01797	ACG	G|0.939;A|0.061	0.061	strong		0.547	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
TTN	7273	hgsc.bcm.edu	37	2	179395958	179395958	+	Silent	SNP	T	T	C	rs3813250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179395958T>C	ENST00000591111.1	-	308	100685	c.100461A>G	c.(100459-100461)gcA>gcG	p.A33487A	TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Silent_p.A35128A|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000359218.5_Silent_p.A26188A|TTN_ENST00000460472.2_Silent_p.A26063A|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.A26255A|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.A32560A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000450692.2_RNA			Q8WZ42	TITIN_HUMAN	titin	33487					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAATTCTTGCTGCCAAAGTCG	0.463													C|||	2545	0.508187	0.5681	0.4049	5008	,	,		20546	0.7123		0.2535	False		,,,				2504	0.5521				p.A35128A		Atlas-SNP	.											.	TTN	18412	.	0			c.A105384G						PASS	.	C	,,,	2024,1820		550,924,448	158.0	169.0	166.0		78189,97680,78564,78765	-0.2	0.5	2	dbSNP_107	166	1845,6423		194,1457,2483	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	744,2381,2931	CC,CT,TT		22.3149,47.3465,31.9435	,,,	26063/26927,32560/33424,26188/27052,26255/27119	179395958	3869,8243	1922	4134	6056	SO:0001819	synonymous_variant	7273	exon358			TCTTGCTGCCAAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.100461A>G	2.37:g.179395958T>C		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	328	155	0.472561	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.562;C|0.438	0.438	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KRT37	8688	hgsc.bcm.edu	37	17	39580559	39580559	+	Missense_Mutation	SNP	T	T	A	rs9916475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39580559T>A	ENST00000225550.3	-	1	216	c.217A>T	c.(217-219)Agt>Tgt	p.S73C	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	73	Head.		S -> C (in dbSNP:rs9916475).			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)				GCAGTGTGACTGGTTGGGGGC	0.617													A|||	1960	0.391374	0.1846	0.3415	5008	,	,		21312	0.4067		0.4592	False		,,,				2504	0.6207				p.S73C		Atlas-SNP	.											.	KRT37	61	.	0			c.A217T						PASS	.	A	CYS/SER	985,3421		111,763,1329	49.0	46.0	47.0		217	4.7	0.7	17	dbSNP_119	47	4177,4423		1020,2137,1143	yes	missense	KRT37	NM_003770.4	112	1131,2900,2472	AA,AT,TT		48.5698,22.3559,39.6894	benign	73/450	39580559	5162,7844	2203	4300	6503	SO:0001583	missense	8688	exon1			TGTGACTGGTTGG	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.217A>T	17.37:g.39580559T>A	ENSP00000225550:p.Ser73Cys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	812	0.3717948717948718	101	0.20528455284552846	145	0.4005524861878453	227	0.3968531468531469	339	0.4472295514511873	.	5.406	0.260139	0.10239	0.223559	0.485698	ENSG00000108417	ENST00000225550	T	0.81415	-1.49	4.69	4.69	0.59074	.	0.000000	0.53938	N	0.000046	T	0.00012	0.0000	N	0.00065	-2.305	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45323	-0.9269	9	0.02654	T	1	.	2.6648	0.05041	0.6159:0.1533:0.0832:0.1475	rs9916475;rs52814129;rs59236563;rs9916475	73	O76014	KRT37_HUMAN	C	73	ENSP00000225550:S73C	ENSP00000225550:S73C	S	-	1	0	KRT37	36834085	0.952000	0.32445	0.665000	0.29768	0.002000	0.02628	1.043000	0.30316	0.661000	0.30985	-0.257000	0.10917	AGT	T|0.606;A|0.394	0.394	strong		0.617	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
TPSD1	23430	hgsc.bcm.edu	37	16	1306347	1306347	+	Silent	SNP	G	G	C	rs2005937	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306347G>C	ENST00000211076.3	+	1	214	c.66G>C	c.(64-66)ccG>ccC	p.P22P	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.P15P	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	22			P -> R (in dbSNP:rs3865205). {ECO:0000269|PubMed:9920877}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TGGCGAGCCCGGCCTACGTGG	0.721													-|||	1100	0.219649	0.112	0.1571	5008	,	,		14369	0.3641		0.1938	False		,,,				2504	0.2873				p.P22P		Atlas-SNP	.											TPSD1,rectum,carcinoma,+1,4	TPSD1	47	4	0			c.G66C						scavenged	.						31.0	38.0	36.0					16																	1306347		2197	4298	6495	SO:0001819	synonymous_variant	23430	exon1			GAGCCCGGCCTAC	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.66G>C	16.37:g.1306347G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	12	0.171429	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			G|1.000	.	weak		0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
ZNF98	148198	hgsc.bcm.edu	37	19	22575777	22575777	+	Missense_Mutation	SNP	T	T	C	rs200167484	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	49	0	0		WXS	Illumina HiSeq	Phase_I	66	15	0.227273	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	
MANEA	79694	hgsc.bcm.edu	37	6	96034612	96034612	+	Silent	SNP	G	G	A	rs62417813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:96034612G>A	ENST00000358812.4	+	2	431	c.297G>A	c.(295-297)ctG>ctA	p.L99L	MANEA_ENST00000369293.1_Silent_p.L99L	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	99	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		TACCACCTCTGAACAATTATC	0.338													G|||	174	0.0347444	0.0053	0.0317	5008	,	,		17517	0.003		0.1083	False		,,,				2504	0.0337				p.L99L		Atlas-SNP	.											.	MANEA	58	.	0			c.G297A						PASS	.	G		102,4304	75.7+/-113.9	5,92,2106	102.0	106.0	105.0		297	2.8	1.0	6	dbSNP_129	105	979,7621	210.7+/-251.5	66,847,3387	no	coding-synonymous	MANEA	NM_024641.3		71,939,5493	AA,AG,GG		11.3837,2.315,8.3115		99/463	96034612	1081,11925	2203	4300	6503	SO:0001819	synonymous_variant	79694	exon2			ACCTCTGAACAAT	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.297G>A	6.37:g.96034612G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Silent	SNP	ENST00000358812.4	37	CCDS5032.1																																																																																			G|0.929;A|0.070	0.070	strong		0.338	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
TNIK	23043	hgsc.bcm.edu	37	3	170811667	170811667	+	Silent	SNP	G	G	A	rs16855789	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:170811667G>A	ENST00000436636.2	-	23	3026	c.2682C>T	c.(2680-2682)agC>agT	p.S894S	TNIK_ENST00000341852.6_Silent_p.S810S|TNIK_ENST00000460047.1_Silent_p.S831S|TNIK_ENST00000475336.1_Silent_p.S802S|TNIK_ENST00000369326.5_Silent_p.S872S|TNIK_ENST00000470834.1_Silent_p.S857S|TNIK_ENST00000538048.1_Silent_p.S846S|TNIK_ENST00000284483.8_Silent_p.S886S|TNIK_ENST00000488470.1_Silent_p.S839S|TNIK_ENST00000357327.5_Silent_p.S865S	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	894	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)			AAATACTGCCGCTGAAACTGT	0.463													G|||	448	0.0894569	0.1467	0.0706	5008	,	,		16700	0.0109		0.0944	False		,,,				2504	0.1012				p.S894S		Atlas-SNP	.											.	TNIK	313	.	0			c.C2682T						PASS	.	G	,,,,,,,	502,3494		28,446,1524	110.0	109.0	109.0		2658,2595,2571,2517,2493,2430,2406,2682	4.5	1.0	3	dbSNP_123	109	742,7622		32,678,3472	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,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	,,,,,,,	60,1124,4996	AA,AG,GG		8.8714,12.5626,10.0647	,,,,,,,	886/1353,865/1332,857/1324,839/1306,831/1298,810/1277,802/1269,894/1361	170811667	1244,11116	1998	4182	6180	SO:0001819	synonymous_variant	23043	exon23			ACTGCCGCTGAAA	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.2682C>T	3.37:g.170811667G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Silent	SNP	ENST00000436636.2	37	CCDS46956.1																																																																																			G|0.908;A|0.092	0.092	strong		0.463	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
CCDC38	120935	hgsc.bcm.edu	37	12	96266035	96266035	+	Silent	SNP	T	T	C	rs2117914	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:96266035T>C	ENST00000344280.3	-	14	2039	c.1482A>G	c.(1480-1482)caA>caG	p.Q494Q	SNRPF_ENST00000552085.1_Intron|SNRPF_ENST00000553192.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	494										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GACTGTACTTTTGCCGCCATT	0.393													T|||	724	0.144569	0.2663	0.1153	5008	,	,		18037	0.0714		0.172	False		,,,				2504	0.0481				p.Q494Q		Atlas-SNP	.											.	CCDC38	45	.	0			c.A1482G						PASS	.	T		1123,3283	392.8+/-328.6	137,849,1217	216.0	194.0	202.0		1482	1.6	1.0	12	dbSNP_96	202	1345,7255	252.1+/-278.3	96,1153,3051	no	coding-synonymous	CCDC38	NM_182496.2		233,2002,4268	CC,CT,TT		15.6395,25.488,18.9759		494/564	96266035	2468,10538	2203	4300	6503	SO:0001819	synonymous_variant	120935	exon14			GTACTTTTGCCGC	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.1482A>G	12.37:g.96266035T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	176	87	0.494318	NM_182496	Q8N835	Silent	SNP	ENST00000344280.3	37	CCDS9056.1																																																																																			T|0.828;C|0.172	0.172	strong		0.393	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
TSR1	55720	hgsc.bcm.edu	37	17	2238675	2238675	+	Silent	SNP	A	A	G	rs61743762	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2238675A>G	ENST00000301364.5	-	4	1514	c.435T>C	c.(433-435)gtT>gtC	p.V145V	TSR1_ENST00000576112.2_Silent_p.V145V|SGSM2_ENST00000426855.2_5'Flank|SGSM2_ENST00000574563.1_5'Flank|SGSM2_ENST00000268989.3_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	145	Bms1-type G.				ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						TGTCTAACACAACGTGCAGAT	0.433													A|||	56	0.0111821	0.0023	0.0346	5008	,	,		18399	0.0		0.0249	False		,,,				2504	0.0041				p.V145V		Atlas-SNP	.											.	TSR1	57	.	0			c.T435C						PASS	.	A		23,4383	30.8+/-60.4	0,23,2180	99.0	87.0	91.0		435	-1.0	0.9	17	dbSNP_129	91	339,8261	116.5+/-176.2	5,329,3966	no	coding-synonymous	TSR1	NM_018128.4		5,352,6146	GG,GA,AA		3.9419,0.522,2.7833		145/805	2238675	362,12644	2203	4300	6503	SO:0001819	synonymous_variant	55720	exon4			TAACACAACGTGC	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.435T>C	17.37:g.2238675A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Silent	SNP	ENST00000301364.5	37	CCDS32525.1																																																																																			A|0.974;G|0.026	0.026	strong		0.433	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
ZNF208	7757	hgsc.bcm.edu	37	19	22155783	22155783	+	Missense_Mutation	SNP	C	C	T	rs199604702		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:22155783C>T	ENST00000397126.4	-	4	2201	c.2053G>A	c.(2053-2055)Gta>Ata	p.V685I	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	685					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)				GTATGAATTACCTTATGTTTA	0.383																																					p.V685I		Atlas-SNP	.											ZNF208_ENST00000428290,rectum,carcinoma,0,3	ZNF208	817	3	0			c.G2053A						scavenged	.						37.0	38.0	37.0					19																	22155783		1986	4182	6168	SO:0001583	missense	7757	exon4			GAATTACCTTATG	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.2053G>A	19.37:g.22155783C>T	ENSP00000380315:p.Val685Ile	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	21	4	0.190476	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	4.480	0.089023	0.08583	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.17054	2.3	2.43	-4.86	0.03132	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11024	0.0269	.	.	.	0.09310	N	1	B	0.25441	0.126	B	0.24701	0.055	T	0.29852	-0.9998	8	0.42905	T	0.14	.	9.3378	0.38060	0.0:0.3337:0.0:0.6663	.	585	O43345	ZN208_HUMAN	I	685;585	ENSP00000380315:V685I	ENSP00000380315:V685I	V	-	1	0	ZNF208	21947623	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-6.732000	0.00055	-1.081000	0.03105	-1.169000	0.01745	GTA	.	.	weak		0.383	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
SEC14L5	9717	hgsc.bcm.edu	37	16	5046919	5046919	+	Missense_Mutation	SNP	C	C	T	rs199609540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:5046919C>T	ENST00000251170.7	+	8	1024	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	282						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						GGACAAGGCCCGGGAAATGCT	0.567													C|||	2	0.000399361	0.0	0.0	5008	,	,		17171	0.001		0.001	False		,,,				2504	0.0				p.R282W		Atlas-SNP	.											SEC14L5,NS,lymphoid_neoplasm,0,1	SEC14L5	79	1	0			c.C844T						scavenged	.	C	TRP/ARG	3,3813		0,3,1905	55.0	54.0	54.0		844	3.5	1.0	16		54	8,8228		0,8,4110	yes	missense	SEC14L5	NM_014692.1	101	0,11,6015	TT,TC,CC		0.0971,0.0786,0.0913	benign	282/697	5046919	11,12041	1908	4118	6026	SO:0001583	missense	9717	exon8			AAGGCCCGGGAAA	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.844C>T	16.37:g.5046919C>T	ENSP00000251170:p.Arg282Trp	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_014692		Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.719825	0.48728	7.86E-4	9.71E-4	ENSG00000103184	ENST00000251170	D	0.85556	-2.0	4.51	3.48	0.39840	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.464358	0.19561	N	0.111327	D	0.84853	0.5564	M	0.80616	2.505	0.46654	D	0.999142	B	0.31054	0.306	B	0.30782	0.12	D	0.86408	0.1746	10	0.62326	D	0.03	-6.5997	12.6573	0.56793	0.2671:0.7329:0.0:0.0	.	282	O43304	S14L5_HUMAN	W	282	ENSP00000251170:R282W	ENSP00000251170:R282W	R	+	1	2	SEC14L5	4986920	0.598000	0.26882	1.000000	0.80357	0.994000	0.84299	0.860000	0.27871	2.492000	0.84095	0.491000	0.48974	CGG	C|0.996;T|0.004	0.004	strong		0.567	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
KRT4	3851	hgsc.bcm.edu	37	12	53202183	53202183	+	Silent	SNP	C	C	G	rs7956809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53202183C>G	ENST00000551956.1	-	6	1512	c.1020G>C	c.(1018-1020)tcG>tcC	p.S340S	KRT4_ENST00000458244.2_Silent_p.S320S|KRT4_ENST00000293774.4_Silent_p.S414S			P19013	K2C4_HUMAN	keratin 4	354	Coil 2.|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						GTTGGTCAACCGAGATCTGGA	0.493													C|||	258	0.0515176	0.0091	0.0533	5008	,	,		20620	0.001		0.1123	False		,,,				2504	0.0971				p.S340S	Pancreas(190;284 2995 41444 45903)	Atlas-SNP	.											.	KRT4	110	.	0			c.G1020C						PASS	.	C		103,4277	70.3+/-108.2	0,103,2087	98.0	99.0	98.0		1020	-10.9	0.1	12	dbSNP_116	98	1062,7532	215.3+/-254.7	72,918,3307	no	coding-synonymous	KRT4	NM_002272.3		72,1021,5394	GG,GC,CC		12.3575,2.3516,8.9795		340/521	53202183	1165,11809	2190	4297	6487	SO:0001819	synonymous_variant	3851	exon6			GTCAACCGAGATC		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.1020G>C	12.37:g.53202183C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Silent	SNP	ENST00000551956.1	37	CCDS41787.2																																																																																			C|0.913;G|0.087	0.087	strong		0.493	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
OBSCN	84033	hgsc.bcm.edu	37	1	228537608	228537608	+	Missense_Mutation	SNP	G	G	A	rs375733623		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228537608G>A	ENST00000422127.1	+	76	18210	c.18166G>A	c.(18166-18168)Gtg>Atg	p.V6056M	OBSCN_ENST00000570156.2_Missense_Mutation_p.V7013M|OBSCN_ENST00000366709.4_Missense_Mutation_p.V3175M|OBSCN_ENST00000284548.11_Missense_Mutation_p.V6056M|OBSCN_ENST00000366707.4_Missense_Mutation_p.V3690M	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6056	Ig-like 52.				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)				AGCAGTGCAGGTGGACCCCCA	0.632																																					p.V7013M		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G21037A						PASS	.	G	MET/VAL,MET/VAL	0,4170		0,0,2085	32.0	39.0	36.0		18166,18166	5.4	1.0	1		36	1,8301		0,1,4150	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	21,21	0,1,6235	AA,AG,GG		0.012,0.0,0.0080	probably-damaging,probably-damaging	6056/7969,6056/6621	228537608	1,12471	2085	4151	6236	SO:0001583	missense	84033	exon87			GTGCAGGTGGACC	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.18166G>A	1.37:g.228537608G>A	ENSP00000409493:p.Val6056Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	106	59	0.556604	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	33|33	5.205199|5.205199	0.95033|0.95033	0.0|0.0	1.2E-4|1.2E-4	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.67345	.|-0.26;-0.26;-0.26;-0.26	5.39|5.39	5.39|5.39	0.77823|0.77823	.|Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.168788	.|0.38837	.|N	.|0.001548	T|T	0.68686|0.68686	0.3028|0.3028	N|N	0.10945|0.10945	0.07|0.07	0.48571|0.48571	D|D	0.999676|0.999676	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.77004	.|0.989;0.98	T|T	0.72520|0.72520	-0.4268|-0.4268	5|10	.|0.39692	.|T	.|0.17	.|.	19.1538|19.1538	0.93502|0.93502	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|6056;6056	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	D|M	672|6056;6056;3690;3175	.|ENSP00000284548:V6056M;ENSP00000409493:V6056M;ENSP00000355668:V3690M;ENSP00000355670:V3175M	.|ENSP00000284548:V6056M	G|V	+|+	2|1	0|0	OBSCN|OBSCN	226604231|226604231	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.810000|0.810000	0.45777|0.45777	7.813000|7.813000	0.86123|0.86123	2.517000|2.517000	0.84864|0.84864	0.491000|0.491000	0.48974|0.48974	GGT|GTG	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CMYA5	202333	hgsc.bcm.edu	37	5	79095299	79095299	+	Missense_Mutation	SNP	A	A	G	rs115059007	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79095299A>G	ENST00000446378.2	+	13	12101	c.12070A>G	c.(12070-12072)Aac>Gac	p.N4024D	CTC-431G16.2_ENST00000421252.2_RNA	NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	4024	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TATCTTCATCAACGCAGAGAG	0.483													A|||	40	0.00798722	0.0015	0.0144	5008	,	,		18985	0.0		0.0219	False		,,,				2504	0.0061				p.N4024D		Atlas-SNP	.											.	CMYA5	643	.	0			c.A12070G						PASS	.	A	ASP/ASN	13,4055		0,13,2021	141.0	137.0	138.0		12070	6.2	0.3	5	dbSNP_132	138	143,8235		3,137,4049	yes	missense	CMYA5	NM_153610.3	23	3,150,6070	GG,GA,AA		1.7069,0.3196,1.2534	benign	4024/4070	79095299	156,12290	2034	4189	6223	SO:0001583	missense	202333	exon13			TTCATCAACGCAG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.12070A>G	5.37:g.79095299A>G	ENSP00000394770:p.Asn4024Asp	Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	164	100	0.609756	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	21	0.009615384615384616	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	17	0.022427440633245383	A	16.47	3.131843	0.56828	0.003196	0.017069	ENSG00000164309	ENST00000446378	T	0.13538	2.58	6.17	6.17	0.99709	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.15998	0.0385	L	0.35644	1.08	0.53688	D	0.999974	D	0.89917	1.0	D	0.97110	1.0	T	0.00299	-1.1836	9	0.46703	T	0.11	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	4024	Q8N3K9	CMYA5_HUMAN	D	4024	ENSP00000394770:N4024D	ENSP00000394770:N4024D	N	+	1	0	CMYA5	79131055	1.000000	0.71417	0.285000	0.24819	0.013000	0.08279	7.964000	0.87933	2.371000	0.80710	0.533000	0.62120	AAC	A|0.987;G|0.013	0.013	strong		0.483	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
FAM90A1	55138	hgsc.bcm.edu	37	12	8377415	8377415	+	Missense_Mutation	SNP	C	C	T	rs200454993		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8377415C>T	ENST00000538603.1	-	4	572	c.14G>A	c.(13-15)cGt>cAt	p.R5H	FAM90A1_ENST00000307435.6_Missense_Mutation_p.R5H	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	5							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R5H(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TTTGGGGTCACGACGTGCCAT	0.577													.|||	28	0.00559105	0.0045	0.0072	5008	,	,		14884	0.005		0.008	False		,,,				2504	0.0041				p.R5H		Atlas-SNP	.											FAM90A1,NS,carcinoma,0,2	FAM90A1	68	2	1	Substitution - Missense(1)	stomach(1)	c.G14A						scavenged	.						47.0	53.0	51.0					12																	8377415		2203	4300	6503	SO:0001583	missense	55138	exon4			GGGTCACGACGTG	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.14G>A	12.37:g.8377415C>T	ENSP00000445418:p.Arg5His	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	41	7	0.170732	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	5.040	0.193071	0.09599	.	.	ENSG00000171847	ENST00000307435;ENST00000538603;ENST00000442295	T;T	0.14022	2.54;2.54	0.408	-0.719	0.11201	.	.	.	.	.	T	0.05593	0.0147	N	0.11427	0.14	0.09310	N	1	B	0.15719	0.014	B	0.14023	0.01	T	0.44065	-0.9352	8	0.17832	T	0.49	1.8103	.	.	.	.	5	Q86YD7	F90A1_HUMAN	H	5	ENSP00000307798:R5H;ENSP00000445418:R5H	ENSP00000307798:R5H	R	-	2	0	FAM90A1	8268682	0.006000	0.16342	0.000000	0.03702	0.014000	0.08584	0.250000	0.18235	-0.410000	0.07542	0.196000	0.17591	CGT	.	.	weak		0.577	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
PCK1	5105	hgsc.bcm.edu	37	20	56138648	56138648	+	Missense_Mutation	SNP	G	G	A	rs11552145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:56138648G>A	ENST00000319441.4	+	6	990	c.826G>A	c.(826-828)Gag>Aag	p.E276K	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Missense_Mutation_p.E144K	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	276			E -> K (in dbSNP:rs11552145). {ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CCCTGAGGGTGAGAAGAAGTA	0.557													G|||	431	0.0860623	0.0272	0.1052	5008	,	,		17730	0.0079		0.172	False		,,,				2504	0.1442				p.E276K		Atlas-SNP	.											.	PCK1	95	.	0			c.G826A						PASS	.	G	LYS/GLU	229,4177	134.1+/-170.4	3,223,1977	62.0	63.0	63.0		826	-2.2	0.3	20	dbSNP_120	63	1673,6927	307.3+/-308.3	172,1329,2799	yes	missense	PCK1	NM_002591.3	56	175,1552,4776	AA,AG,GG		19.4535,5.1975,14.624	benign	276/623	56138648	1902,11104	2203	4300	6503	SO:0001583	missense	5105	exon6			GAGGGTGAGAAGA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.826G>A	20.37:g.56138648G>A	ENSP00000319814:p.Glu276Lys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	63	39	0.619048	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	189	0.08653846153846154	7	0.014227642276422764	53	0.1464088397790055	4	0.006993006993006993	125	0.16490765171503957	G	1.662	-0.511127	0.04231	0.051975	0.194535	ENSG00000124253	ENST00000319441;ENST00000535860	T;T	0.10005	2.92;2.92	5.27	-2.16	0.07080	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.289017	0.37530	N	0.002042	T	0.00012	0.0000	N	0.05078	-0.115	0.42755	P	0.006217999999999946	B	0.02656	0.0	B	0.08055	0.003	T	0.44128	-0.9348	9	0.02654	T	1	-18.3718	7.5477	0.27777	0.4186:0.2498:0.3316:0.0	rs11552145;rs28359545;rs52823511;rs11552145	276	P35558	PCKGC_HUMAN	K	276;144	ENSP00000319814:E276K;ENSP00000444342:E144K	ENSP00000319814:E276K	E	+	1	0	PCK1	55572054	0.008000	0.16893	0.257000	0.24404	0.272000	0.26649	0.080000	0.14802	-0.018000	0.14079	-0.254000	0.11334	GAG	G|0.881;A|0.119	0.119	strong		0.557	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
MYO5B	4645	hgsc.bcm.edu	37	18	47429022	47429022	+	Missense_Mutation	SNP	C	C	T	rs2298624	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:47429022C>T	ENST00000285039.7	-	21	3052	c.2753G>A	c.(2752-2754)cGt>cAt	p.R918H	MYO5B_ENST00000324581.6_Missense_Mutation_p.R59H	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	918			R -> H (in dbSNP:rs2298624).		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)		CACGTTGAGACGTTTCAGATG	0.607													C|||	678	0.135383	0.0204	0.1556	5008	,	,		20073	0.246		0.1372	False		,,,				2504	0.1605				p.R918H		Atlas-SNP	.											.	MYO5B	178	.	0			c.G2753A						PASS	.	C	HIS/ARG	149,3951		2,145,1903	73.0	78.0	77.0		2753	5.6	1.0	18	dbSNP_100	77	1125,7249		78,969,3140	yes	missense	MYO5B	NM_001080467.2	29	80,1114,5043	TT,TC,CC		13.4344,3.6341,10.2132	possibly-damaging	918/1849	47429022	1274,11200	2050	4187	6237	SO:0001583	missense	4645	exon21			TTGAGACGTTTCA	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.2753G>A	18.37:g.47429022C>T	ENSP00000285039:p.Arg918His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	21	0.33871	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	310	0.14194139194139194	12	0.024390243902439025	55	0.15193370165745856	140	0.24475524475524477	103	0.1358839050131926	C	21.3	4.128888	0.77549	0.036341	0.134344	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.19105	2.17;2.17	5.63	5.63	0.86233	.	0.227467	0.37715	N	0.001970	T	0.00012	0.0000	L	0.40543	1.245	0.25362	P	0.9887736	P;D	0.60160	0.803;0.987	B;P	0.47251	0.053;0.542	T	0.20571	-1.0271	9	0.72032	D	0.01	.	10.5402	0.45029	0.0:0.855:0.0:0.145	rs2298624;rs17800963;rs60240897;rs2298624	918;59	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	H	918;59	ENSP00000285039:R918H;ENSP00000315531:R59H	ENSP00000285039:R918H	R	-	2	0	MYO5B	45683020	0.999000	0.42202	0.999000	0.59377	0.984000	0.73092	3.012000	0.49575	2.826000	0.97356	0.655000	0.94253	CGT	C|0.861;N|0.000	.	strong		0.607	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
C2orf54	79919	hgsc.bcm.edu	37	2	241835379	241835379	+	Silent	SNP	G	G	A	rs12105122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	14	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	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	
NUP62	23636	hgsc.bcm.edu	37	19	50412217	50412217	+	Missense_Mutation	SNP	C	C	G	rs1062798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50412217C>G	ENST00000596217.1	-	2	2735	c.848G>C	c.(847-849)aGc>aCc	p.S283T	IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597723.1_Intron|NUP62_ENST00000352066.3_Missense_Mutation_p.S283T|NUP62_ENST00000597029.1_Missense_Mutation_p.S283T|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000422090.2_Missense_Mutation_p.S283T|NUP62_ENST00000413454.1_Missense_Mutation_p.S283T|IL4I1_ENST00000341114.3_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	283	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.		S -> T (in dbSNP:rs1062798). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:1915414}.		carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		gctgctgctgctggtggtggt	0.627													C|||	1584	0.316294	0.2383	0.379	5008	,	,		15105	0.3938		0.3827	False		,,,				2504	0.229				p.S283T		Atlas-SNP	.											NUP62,NS,carcinoma,0,2	NUP62	50	2	0			c.G848C						PASS	.	C	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,	997,3405		118,761,1322	31.0	29.0	30.0		848,848,848,848,848,	0.8	0.0	19	dbSNP_86	30	3113,5481		577,1959,1761	yes	missense,missense,missense,missense,missense,intron	NUP62,IL4I1	NM_001193357.1,NM_012346.4,NM_016553.4,NM_153718.3,NM_153719.3,NM_172374.1	58,58,58,58,58,	695,2720,3083	GG,GC,CC		36.2229,22.6488,31.6251	benign,benign,benign,benign,benign,	283/523,283/523,283/523,283/523,283/523,	50412217	4110,8886	2201	4297	6498	SO:0001583	missense	23636	exon3			CTGCTGCTGGTGG	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.848G>C	19.37:g.50412217C>G	ENSP00000471191:p.Ser283Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	ENST00000596217.1	37	CCDS12788.1	763	0.34935897435897434	103	0.20934959349593496	134	0.3701657458563536	230	0.4020979020979021	296	0.39050131926121373	C	0.016	-1.533751	0.00951	0.226488	0.362229	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.36157	1.27;1.27;1.27	4.24	0.801	0.18679	Nucleoporin, NSP1-like, C-terminal (1);	1.330530	0.05670	N	0.588508	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45366	-0.9266	8	.	.	.	-2.1099	13.4683	0.61268	0.0:0.2452:0.7548:0.0	rs1062798;rs3203778;rs3745497;rs4009638;rs5828420;rs17844993;rs17857752;rs52814004	283	P37198	NUP62_HUMAN	T	283	ENSP00000305503:S283T;ENSP00000407331:S283T;ENSP00000387991:S283T	.	S	-	2	0	NUP62	55104029	0.050000	0.20438	0.000000	0.03702	0.004000	0.04260	1.221000	0.32503	0.190000	0.20209	-1.162000	0.01777	AGC	C|0.677;G|0.323	0.323	strong		0.627	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
ANK1	286	hgsc.bcm.edu	37	8	41559609	41559609	+	Silent	SNP	G	G	A	rs2304880	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:41559609G>A	ENST00000347528.4	-	21	2432	c.2349C>T	c.(2347-2349)acC>acT	p.T783T	ANK1_ENST00000352337.4_Silent_p.T783T|ANK1_ENST00000289734.7_Silent_p.T783T|ANK1_ENST00000379758.2_Silent_p.T783T|ANK1_ENST00000396942.1_Silent_p.T783T|ANK1_ENST00000265709.8_Silent_p.T816T|ANK1_ENST00000396945.1_Silent_p.T783T	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	783	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TGAGCACGTCGGTGACAGAAA	0.607											OREG0018740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	905	0.180711	0.0159	0.2954	5008	,	,		18368	0.0794		0.2843	False		,,,				2504	0.32				p.T816T		Atlas-SNP	.											.	ANK1	497	.	0			c.C2448T						PASS	.	G	,,,,	250,4156	145.4+/-180.2	7,236,1960	122.0	110.0	114.0		2349,2448,2349,2349,2349	-3.0	0.7	8	dbSNP_100	114	2302,6298	387.0+/-342.0	319,1664,2317	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	326,1900,4277	AA,AG,GG		26.7674,5.6741,19.6217	,,,,	783/1881,816/1898,783/1857,783/1882,783/1720	41559609	2552,10454	2203	4300	6503	SO:0001819	synonymous_variant	286	exon21			CACGTCGGTGACA	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2349C>T	8.37:g.41559609G>A		Somatic	59	0	0	902	WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	370	0.16941391941391942	11	0.022357723577235773	100	0.27624309392265195	37	0.06468531468531469	222	0.2928759894459103	G	1.954	-0.440462	0.04636	0.056741	0.267674	ENSG00000029534	ENST00000520299	.	.	.	5.96	-2.95	0.05564	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.0165	0.06061	0.0902:0.1696:0.3084:0.4317	rs2304880;rs2304880	.	.	.	X	97	.	.	R	-	1	2	ANK1	41678766	0.006000	0.16342	0.704000	0.30370	0.001000	0.01503	-1.166000	0.03129	-0.110000	0.12022	-0.885000	0.02943	CGA	G|0.820;A|0.180	0.180	strong		0.607	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
CALR3	125972	hgsc.bcm.edu	37	19	16593318	16593318	+	Silent	SNP	C	C	T	rs118131979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:16593318C>T	ENST00000269881.3	-	7	923	c.861G>A	c.(859-861)acG>acA	p.T287T	CTD-3222D19.2_ENST00000409035.1_3'UTR|CALR3_ENST00000602234.1_5'UTR	NM_145046.4	NP_659483.2	Q96L12	CALR3_HUMAN	calreticulin 3	287	P-domain.				cell differentiation (GO:0030154)|protein folding (GO:0006457)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|prostate(1)|skin(1)	15						GGTCATACTGCGTCAAATAGT	0.423													C|||	27	0.00539137	0.0008	0.0029	5008	,	,		21729	0.0		0.0189	False		,,,				2504	0.0051				p.T287T		Atlas-SNP	.											.	CALR3	41	.	0			c.G861A						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	207.0	184.0	192.0		861	-10.5	0.0	19	dbSNP_132	192	144,8456	70.3+/-132.9	2,140,4158	no	coding-synonymous	CALR3	NM_145046.3		2,154,6347	TT,TC,CC		1.6744,0.3177,1.2148		287/385	16593318	158,12848	2203	4300	6503	SO:0001819	synonymous_variant	125972	exon7			ATACTGCGTCAAA	AK058084	CCDS12344.1	19p13.11	2014-09-17				ENSG00000269058			20407	protein-coding gene	gene with protein product	"""cancer/testis antigen 93"", ""calsperin"""	611414				12384296	Standard	NM_145046		Approved	CRT2, FLJ25355, MGC26577, CT93	uc002ned.3	Q96L12		ENST00000269881.3:c.861G>A	19.37:g.16593318C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_145046	D9N574|Q96LN3	Silent	SNP	ENST00000269881.3	37	CCDS12344.1																																																																																			C|0.990;T|0.010	0.010	strong		0.423	CALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461089.1	NM_145046	
TRIM22	10346	hgsc.bcm.edu	37	11	5719667	5719667	+	Silent	SNP	T	T	C	rs2291842	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5719667T>C	ENST00000379965.3	+	4	919	c.642T>C	c.(640-642)gaT>gaC	p.D214D	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	214					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)		ATGTGCTGGATAACCTGGCAG	0.522													T|||	1500	0.299521	0.3389	0.3127	5008	,	,		19662	0.2996		0.2107	False		,,,				2504	0.3282				p.D214D	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.T642C						PASS	.	T	,	1242,2934		191,860,1037	65.0	73.0	70.0		630,642	-7.1	0.0	11	dbSNP_100	70	1680,6762		179,1322,2720	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	370,2182,3757	CC,CT,TT		19.9005,29.7414,23.1574	,	210/495,214/499	5719667	2922,9696	2088	4221	6309	SO:0001819	synonymous_variant	10346	exon4			GCTGGATAACCTG	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.642T>C	11.37:g.5719667T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	212	99	0.466981	NM_006074	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			T|0.726;C|0.274	0.274	strong		0.522	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
DCXR	51181	hgsc.bcm.edu	37	17	79994600	79994600	+	Silent	SNP	C	C	T	rs61739740|rs9780	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79994600C>T	ENST00000306869.2	-	4	394	c.345G>A	c.(343-345)tcG>tcA	p.S115S	RP13-650J16.1_ENST00000582558.1_RNA|RP13-650J16.1_ENST00000584705.1_RNA|DCXR_ENST00000584318.1_5'UTR	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	74	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	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		
FRYL	285527	hgsc.bcm.edu	37	4	48588742	48588742	+	Silent	SNP	C	C	T	rs34558821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:48588742C>T	ENST00000503238.1	-	16	1643	c.1644G>A	c.(1642-1644)ggG>ggA	p.G548G	FRYL_ENST00000506685.1_Silent_p.G254G|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Silent_p.G548G|FRYL_ENST00000507711.1_Silent_p.G548G|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	70	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	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		
RSPO1	284654	hgsc.bcm.edu	37	1	38079517	38079517	+	Missense_Mutation	SNP	T	T	G	rs36043533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:38079517T>G	ENST00000401069.1	-	6	1196	c.484A>C	c.(484-486)Aag>Cag	p.K162Q	RSPO1_ENST00000373059.1_Missense_Mutation_p.K135Q|RSPO1_ENST00000401070.1_Intron|RSPO1_ENST00000356545.2_Missense_Mutation_p.K162Q|RSPO1_ENST00000401071.2_Intron|RSPO1_ENST00000401068.1_Missense_Mutation_p.K162Q	NM_001242908.1	NP_001229837.1	Q2MKA7	RSPO1_HUMAN	R-spondin 1	162	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				canonical Wnt signaling pathway (GO:0060070)|male meiosis (GO:0007140)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of non-canonical Wnt signaling pathway (GO:2000052)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of gene expression (GO:0010468)|regulation of male germ cell proliferation (GO:2000254)|regulation of receptor internalization (GO:0002090)	extracellular space (GO:0005615)|nucleus (GO:0005634)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)|receptor binding (GO:0005102)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGCTGCTGCTTCTTGGAGCAG	0.617													T|||	242	0.0483227	0.0045	0.0418	5008	,	,		19712	0.0476		0.0427	False		,,,				2504	0.1186				p.K162Q	GBM(122;680 2230 27822 42821)	Atlas-SNP	.											.	RSPO1	35	.	0			c.A484C						PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS,	45,3859		0,45,1907	56.0	60.0	59.0		484,484,403,	5.4	1.0	1	dbSNP_126	59	470,7816		13,444,3686	no	missense,missense,missense,intron	RSPO1	NM_001038633.3,NM_001242908.1,NM_001242909.1,NM_001242910.1	53,53,53,	13,489,5593	GG,GT,TT		5.6722,1.1527,4.2248	probably-damaging,probably-damaging,probably-damaging,	162/264,162/264,135/237,	38079517	515,11675	1952	4143	6095	SO:0001583	missense	284654	exon6			GCTGCTTCTTGGA	AK098225	CCDS41304.1, CCDS55590.1, CCDS55591.1	1p34.2	2014-01-30	2011-06-29		ENSG00000169218	ENSG00000169218		"""Endogenous ligands"""	21679	protein-coding gene	gene with protein product		609595	"""R-spondin homolog (Xenopus laevis)"""				Standard	NM_001038633		Approved	FLJ40906, RSPONDIN	uc001cbm.2	Q2MKA7	OTTHUMG00000004321	ENST00000401069.1:c.484A>C	1.37:g.38079517T>G	ENSP00000383847:p.Lys162Gln	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	213	90	0.422535	NM_001242908	A2A420|Q0H8S6|Q14C72|Q5T0F2|Q8N7L5	Missense_Mutation	SNP	ENST00000401069.1	37	CCDS41304.1	84	0.038461538461538464	3	0.006097560975609756	13	0.03591160220994475	35	0.06118881118881119	33	0.04353562005277045	T	21.6	4.171296	0.78452	0.011527	0.056722	ENSG00000169218	ENST00000373059;ENST00000356545;ENST00000401069;ENST00000401068	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.42	5.42	0.78866	.	0.100628	0.64402	D	0.000002	T	0.35624	0.0938	L	0.57536	1.79	0.09310	P	1.0	P;P	0.38677	0.589;0.642	B;B	0.39503	0.295;0.301	T	0.73418	-0.3989	9	0.56958	D	0.05	.	15.7743	0.78198	0.0:0.0:0.0:1.0	rs36043533	135;162	Q2MKA7-2;Q2MKA7	.;RSPO1_HUMAN	Q	135;162;162;162	ENSP00000362150:K135Q;ENSP00000348944:K162Q;ENSP00000383847:K162Q;ENSP00000383846:K162Q	ENSP00000348944:K162Q	K	-	1	0	RSPO1	37852104	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.283000	0.78640	2.189000	0.69895	0.533000	0.62120	AAG	T|0.954;G|0.046	0.046	strong		0.617	RSPO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012477.2	NM_173640	
POLRMT	5442	hgsc.bcm.edu	37	19	621070	621070	+	Silent	SNP	G	G	A	rs77809401	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:621070G>A	ENST00000588649.2	-	10	2712	c.2628C>T	c.(2626-2628)gaC>gaT	p.D876D	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	876	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)		TCAAGGGTTGGTCCGCGGAGT	0.746													G|||	1026	0.204872	0.1225	0.1441	5008	,	,		5027	0.25		0.171	False		,,,				2504	0.3476				p.D876D		Atlas-SNP	.											.	POLRMT	91	.	0			c.C2628T						PASS	.	G		582,3810		35,512,1649	19.0	22.0	21.0		2628	2.3	0.1	19	dbSNP_131	21	1532,7062		130,1272,2895	no	coding-synonymous	POLRMT	NM_005035.3		165,1784,4544	AA,AG,GG		17.8264,13.2514,16.2791		876/1231	621070	2114,10872	2196	4297	6493	SO:0001819	synonymous_variant	5442	exon10			GGGTTGGTCCGCG		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.2628C>T	19.37:g.621070G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.849;A|0.151	0.151	strong		0.746	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2418031	2418031	+	Silent	SNP	C	C	T	rs11084939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2418031C>T	ENST00000332578.3	+	12	1947	c.1947C>T	c.(1945-1947)tcC>tcT	p.S649S		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	649	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGAAGGCGTCCGTGGGCATCA	0.567													t|||	813	0.16234	0.1778	0.0677	5008	,	,		15323	0.3333		0.0447	False		,,,				2504	0.1534				p.S649S		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C1947T						PASS	.	T		778,3628	315.5+/-294.2	83,612,1508	185.0	181.0	182.0		1947	-8.5	0.0	19	dbSNP_120	182	388,8212	124.6+/-183.3	4,380,3916	no	coding-synonymous	TMPRSS9	NM_182973.1		87,992,5424	TT,TC,CC		4.5116,17.6577,8.9651		649/1060	2418031	1166,11840	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon12			GGCGTCCGTGGGC	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.1947C>T	19.37:g.2418031C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.876;T|0.124	0.124	strong		0.567	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
WDR87	83889	hgsc.bcm.edu	37	19	38376103	38376103	+	Silent	SNP	A	A	G	rs73027454	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38376103A>G	ENST00000303868.5	-	6	8315	c.8091T>C	c.(8089-8091)ttT>ttC	p.F2697F	WDR87_ENST00000447313.2_Silent_p.F2736F	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2697										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						GTTTATCCTTAAAATCCCAGA	0.423													A|||	961	0.191893	0.0998	0.2622	5008	,	,		20467	0.0298		0.3469	False		,,,				2504	0.274				p.F2697F		Atlas-SNP	.											.	WDR87	191	.	0			c.T8091C						PASS	.	A		197,1187		16,165,511	20.0	18.0	19.0		8091	-5.0	0.0	19	dbSNP_130	19	1123,2059		213,697,681	no	coding-synonymous	WDR87	NM_031951.3		229,862,1192	GG,GA,AA		35.2923,14.2341,28.9093		2697/2874	38376103	1320,3246	692	1591	2283	SO:0001819	synonymous_variant	83889	exon6			ATCCTTAAAATCC	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.8091T>C	19.37:g.38376103A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			A|0.775;G|0.225	0.225	strong		0.423	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
NLRP8	126205	hgsc.bcm.edu	37	19	56467375	56467375	+	Missense_Mutation	SNP	C	C	T	rs41481648	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56467375C>T	ENST00000291971.3	+	3	2022	c.1951C>T	c.(1951-1953)Cgg>Tgg	p.R651W	NLRP8_ENST00000590542.1_Missense_Mutation_p.R651W	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	651			R -> W (in dbSNP:rs41481648).		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)		TTGCCTGAAGCGGTGTCAATA	0.463													C|||	480	0.0958466	0.1309	0.0605	5008	,	,		19353	0.0685		0.0825	False		,,,				2504	0.1155				p.R651W		Atlas-SNP	.											.	NLRP8	225	.	0			c.C1951T						PASS	.	C	TRP/ARG	512,3894	235.2+/-247.8	29,454,1720	143.0	133.0	136.0		1951	-3.0	0.0	19	dbSNP_127	136	695,7905	172.0+/-222.8	21,653,3626	yes	missense	NLRP8	NM_176811.2	101	50,1107,5346	TT,TC,CC		8.0814,11.6205,9.2803	probably-damaging	651/1049	56467375	1207,11799	2203	4300	6503	SO:0001583	missense	126205	exon3			CTGAAGCGGTGTC	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.1951C>T	19.37:g.56467375C>T	ENSP00000291971:p.Arg651Trp	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	175	78	0.445714	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	183	0.08379120879120878	62	0.12601626016260162	27	0.07458563535911603	39	0.06818181818181818	55	0.07255936675461741	C	10.88	1.474675	0.26511	0.116205	0.080814	ENSG00000179709	ENST00000291971	D	0.88277	-2.36	2.03	-3.03	0.05429	.	.	.	.	.	T	0.06826	0.0174	L	0.40543	1.245	0.80722	P	0.0	D;D	0.76494	0.997;0.999	P;P	0.56700	0.804;0.786	T	0.63594	-0.6602	8	0.72032	D	0.01	.	6.6284	0.22843	0.0:0.3271:0.0:0.6729	rs41481648;rs61730439;rs41481648	651;651	Q86W28-2;Q86W28	.;NALP8_HUMAN	W	651	ENSP00000291971:R651W	ENSP00000291971:R651W	R	+	1	2	NLRP8	61159187	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.670000	0.01956	-0.773000	0.04596	-0.362000	0.07510	CGG	C|0.909;T|0.091	0.091	strong		0.463	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418166	105418166	+	Missense_Mutation	SNP	T	T	C	rs78116894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105418166T>C	ENST00000333244.5	-	7	3741	c.3622A>G	c.(3622-3624)Acc>Gcc	p.T1208A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1208						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)			AGGTCAGTGGTCTTGAGGTCC	0.662													.|||	1458	0.291134	0.1679	0.2911	5008	,	,		16454	0.1567		0.4761	False		,,,				2504	0.4059				p.T1208A		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.A3622G						PASS	.						110.0	86.0	94.0					14																	105418166		1936	3923	5859	SO:0001583	missense	113146	exon7			CAGTGGTCTTGAG	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.3622A>G	14.37:g.105418166T>C	ENSP00000353114:p.Thr1208Ala	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	364	0.16666666666666666	49	0.09959349593495935	79	0.21823204419889503	44	0.07692307692307693	192	0.2532981530343008	N	3.547	-0.092530	0.07053	.	.	ENSG00000185567	ENST00000333244	T	0.02916	4.11	4.46	-3.46	0.04767	.	.	.	.	.	T	0.00012	0.0000	N	0.21282	0.65	0.80722	P	0.0	B	0.28713	0.22	B	0.25614	0.062	T	0.41945	-0.9480	8	0.05351	T	0.99	.	2.0245	0.03516	0.121:0.3542:0.2452:0.2796	.	1208	Q8IVF2	AHNK2_HUMAN	A	1208	ENSP00000353114:T1208A	ENSP00000353114:T1208A	T	-	1	0	AHNAK2	104489211	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-1.338000	0.02655	-0.516000	0.06470	-0.489000	0.04712	ACC	T|0.790;C|0.210	0.210	strong		0.662	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ILDR1	286676	hgsc.bcm.edu	37	3	121712805	121712805	+	Missense_Mutation	SNP	G	G	C	rs3915061	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:121712805G>C	ENST00000344209.5	-	7	917	c.791C>G	c.(790-792)cCg>cGg	p.P264R	ILDR1_ENST00000393631.1_Missense_Mutation_p.P175R|ILDR1_ENST00000273691.3_Missense_Mutation_p.P220R|ILDR1_ENST00000460554.1_Intron|ILDR1_ENST00000462014.1_Missense_Mutation_p.P232R	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	264					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)		GAGGCTGGACGGCAGGGACAA	0.493													C|||	1763	0.352037	0.4304	0.2968	5008	,	,		20582	0.2083		0.2853	False		,,,				2504	0.502				p.P264R		Atlas-SNP	.											.	ILDR1	120	.	0			c.C791G						PASS	.	C	ARG/PRO,ARG/PRO,ARG/PRO	1760,2646	644.3+/-398.0	365,1030,808	41.0	41.0	41.0		791,524,659	1.0	0.8	3	dbSNP_108	41	2253,6347	707.9+/-405.6	294,1665,2341	yes	missense,missense,missense	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	103,103,103	659,2695,3149	CC,CG,GG		26.1977,39.9455,30.855	benign,benign,benign	264/547,175/458,220/503	121712805	4013,8993	2203	4300	6503	SO:0001583	missense	286676	exon7			CTGGACGGCAGGG	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.791C>G	3.37:g.121712805G>C	ENSP00000345667:p.Pro264Arg	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	652	0.29853479853479853	229	0.4654471544715447	111	0.30662983425414364	97	0.16958041958041958	215	0.2836411609498681	C	0.010	-1.770905	0.00645	0.399455	0.261977	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000383663;ENST00000393631;ENST00000462014	T;T;T;T	0.76968	-0.33;-0.46;-1.06;0.08	5.0	0.992	0.19819	.	0.634163	0.17583	N	0.169031	T	0.00012	0.0000	N	0.00358	-1.6	0.80722	P	0.0	B;B;B;B	0.11235	0.0;0.0;0.001;0.004	B;B;B;B	0.08055	0.001;0.0;0.002;0.003	T	0.44190	-0.9344	9	0.15952	T	0.53	-8.1726	1.1658	0.01815	0.1419:0.3315:0.2759:0.2507	rs3915061;rs58826274;rs3915061	175;264;220;232	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	R	220;264;147;175;232	ENSP00000273691:P220R;ENSP00000345667:P264R;ENSP00000377251:P175R;ENSP00000419414:P232R	ENSP00000273691:P220R	P	-	2	0	ILDR1	123195495	0.000000	0.05858	0.792000	0.32020	0.771000	0.43674	-0.192000	0.09587	0.294000	0.22547	-0.216000	0.12614	CCG	G|0.700;C|0.300	0.300	strong		0.493	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
EMR1	2015	hgsc.bcm.edu	37	19	6903920	6903920	+	Missense_Mutation	SNP	A	A	G	rs443658	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6903920A>G	ENST00000312053.4	+	7	798	c.761A>G	c.(760-762)aAt>aGt	p.N254S	EMR1_ENST00000381404.4_Missense_Mutation_p.N202S|EMR1_ENST00000250572.8_Missense_Mutation_p.N254S|EMR1_ENST00000381407.5_Missense_Mutation_p.N113S|EMR1_ENST00000450315.3_Intron	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	94	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	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		
LRP3	4037	hgsc.bcm.edu	37	19	33696897	33696897	+	Silent	SNP	C	C	T	rs11084712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	47	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	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		
MUC2	4583	hgsc.bcm.edu	37	11	1088815	1088815	+	Silent	SNP	A	A	G	rs7103978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1088815A>G	ENST00000441003.2	+	26	3627	c.3600A>G	c.(3598-3600)gcA>gcG	p.A1200A	MUC2_ENST00000359061.5_Silent_p.A1200A	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1200					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CACCTGGAGCATCGGTTCCCA	0.592													G|||	326	0.0650958	0.053	0.0591	5008	,	,		22307	0.0556		0.0974	False		,,,				2504	0.0624				p.A1200A		Atlas-SNP	.											.	MUC2	614	.	0			c.A3600G						PASS	.	G		223,3987		5,213,1887	59.0	64.0	62.0		3600	-7.2	0.0	11	dbSNP_116	62	784,7636		37,710,3463	no	coding-synonymous	MUC2	NM_002457.2		42,923,5350	GG,GA,AA		9.3112,5.2969,7.9731		1200/2813	1088815	1007,11623	2105	4210	6315	SO:0001819	synonymous_variant	4583	exon26			TGGAGCATCGGTT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3600A>G	11.37:g.1088815A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				A|0.939;G|0.061	0.061	strong		0.592	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
GRM4	2914	hgsc.bcm.edu	37	6	34003928	34003928	+	Silent	SNP	C	C	T	rs34858760	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:34003928C>T	ENST00000538487.2	-	9	2402	c.1959G>A	c.(1957-1959)tcG>tcA	p.S653S	GRM4_ENST00000544773.2_Silent_p.S484S|GRM4_ENST00000374177.3_Silent_p.S537S|GRM4_ENST00000535756.1_Silent_p.S520S|GRM4_ENST00000455714.2_Silent_p.S513S|GRM4_ENST00000609222.1_Silent_p.S520S|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000374181.4_Silent_p.S653S	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	653					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						TTCGGCGCAGCGAGCAGGTGC	0.607													C|||	136	0.0271565	0.0961	0.0072	5008	,	,		22264	0.0		0.004	False		,,,				2504	0.0				p.S653S		Atlas-SNP	.											.	GRM4	317	.	0			c.G1959A						PASS	.	C		292,4114	159.6+/-192.1	13,266,1924	100.0	92.0	94.0		1959	-7.7	0.7	6	dbSNP_126	94	37,8563	25.1+/-72.6	0,37,4263	no	coding-synonymous	GRM4	NM_000841.1		13,303,6187	TT,TC,CC		0.4302,6.6273,2.5296		653/913	34003928	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	2914	exon9			GCGCAGCGAGCAG	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.1959G>A	6.37:g.34003928C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	115	69	0.6	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Silent	SNP	ENST00000538487.2	37	CCDS4787.1																																																																																			C|0.975;T|0.025	0.025	strong		0.607	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
FCRLA	84824	hgsc.bcm.edu	37	1	161681780	161681780	+	Missense_Mutation	SNP	A	A	G	rs2275603	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161681780A>G	ENST00000236938.6	+	4	849	c.607A>G	c.(607-609)Agc>Ggc	p.S203G	FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000367950.1_Intron|FCRLA_ENST00000367959.2_Missense_Mutation_p.S209G|FCRLA_ENST00000367949.2_Intron|FCRLA_ENST00000367957.2_Missense_Mutation_p.S63G|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000309691.6_Missense_Mutation_p.S97G|FCRLA_ENST00000294796.4_Missense_Mutation_p.S52G|FCRLA_ENST00000546024.1_Missense_Mutation_p.S114G|FCRLA_ENST00000540521.1_Missense_Mutation_p.S69G|FCRLA_ENST00000367953.3_Missense_Mutation_p.S192G|FCRLA_ENST00000540926.1_Missense_Mutation_p.S192G|FCRLA_ENST00000349527.4_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	142	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	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	
ITGAE	3682	hgsc.bcm.edu	37	17	3631241	3631241	+	Missense_Mutation	SNP	A	A	G	rs2976230	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	227	0	0		WXS	Illumina HiSeq	Phase_I	260	112	0.430769	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	
BTNL8	79908	hgsc.bcm.edu	37	5	180338368	180338368	+	Missense_Mutation	SNP	A	A	G	rs386695827|rs2276995	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180338368A>G	ENST00000340184.4	+	3	633	c.427A>G	c.(427-429)Acg>Gcg	p.T143A	BTNL8_ENST00000231229.4_Missense_Mutation_p.T143A|BTNL8_ENST00000508408.1_Missense_Mutation_p.T143A|BTNL8_ENST00000533815.2_5'UTR|BTNL8_ENST00000511704.1_Missense_Mutation_p.T27A|BTNL8_ENST00000400707.3_Missense_Mutation_p.T18A|BTNL8_ENST00000505126.1_5'UTR|Y_RNA_ENST00000410920.1_RNA	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	143	Ig-like V-type 2.		T -> A (in dbSNP:rs2276995). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATTTCCATCACGGGATATGT	0.527													G|||	2166	0.432508	0.6702	0.4236	5008	,	,		20380	0.3462		0.3757	False		,,,				2504	0.2648				p.T143A		Atlas-SNP	.											BTNL8,colon,carcinoma,-2,1	BTNL8	114	1	0			c.A427G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR,ALA/THR,,ALA/THR	2834,1572	658.7+/-400.4	925,984,294	248.0	272.0	264.0		427,79,427,52,,427	-5.4	0.0	5	dbSNP_100	264	3247,5345	485.0+/-371.5	625,1997,1674	yes	missense,missense,missense,missense,utr-5,missense	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	58,58,58,58,,58	1550,2981,1968	GG,GA,AA		37.791,35.6786,46.7841	benign,benign,benign,benign,,benign	143/501,27/385,143/341,18/376,,143/348	180338368	6081,6917	2203	4296	6499	SO:0001583	missense	79908	exon3			TCCATCACGGGAT	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.427A>G	5.37:g.180338368A>G	ENSP00000342197:p.Thr143Ala	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	225	108	0.48	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	983	0.4500915750915751	338	0.6869918699186992	143	0.39502762430939226	204	0.35664335664335667	298	0.39313984168865435	a	7.914	0.737065	0.15574	0.643214	0.37791	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000400707;ENST00000508408;ENST00000511704	T;T;T;T;T	0.06371	3.31;3.31;3.31;3.31;3.31	3.86	-5.37	0.02681	.	.	.	.	.	T	0.00012	0.0000	N	0.25485	0.75	0.54753	P	1.4999999999987246E-5	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.26326	-1.0106	8	0.25751	T	0.34	.	6.8869	0.24208	0.5006:0.1261:0.3733:0.0	rs2276995;rs17704309;rs62406680;rs2276995	18;27;143;143;143	E9PG07;E9PEF6;F2Z2B2;A6NEX6;Q6UX41	.;.;.;.;BTNL8_HUMAN	A	143;143;18;143;27	ENSP00000231229:T143A;ENSP00000342197:T143A;ENSP00000383543:T18A;ENSP00000424585:T143A;ENSP00000425207:T27A	ENSP00000231229:T143A	T	+	1	0	BTNL8	180270974	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.743000	0.01834	-1.000000	0.03438	-2.568000	0.00172	ACG	A|0.529;G|0.471	0.471	strong		0.527	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
RAD51D	5892	hgsc.bcm.edu	37	17	33433487	33433487	+	Missense_Mutation	SNP	C	C	T	rs4796033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:33433487C>T	ENST00000345365.6	-	6	749	c.494G>A	c.(493-495)cGg>cAg	p.R165Q	RAD51L3-RFFL_ENST00000593039.1_Missense_Mutation_p.R6Q|RAD51D_ENST00000460118.2_Missense_Mutation_p.R46Q|RAD51D_ENST00000360276.3_Missense_Mutation_p.R120Q|RAD51D_ENST00000590016.1_Missense_Mutation_p.R185Q|RAD51D_ENST00000335858.7_Missense_Mutation_p.R53Q|RAD51D_ENST00000590380.1_5'UTR|RAD51D_ENST00000394589.4_Missense_Mutation_p.R165Q	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	165			R -> Q (in dbSNP:rs4796033). {ECO:0000269|Ref.4}.		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						CTGGATCCTCCGGAGAGCTTC	0.562								Direct reversal of damage					C|||	476	0.0950479	0.0136	0.2205	5008	,	,		23141	0.0407		0.1292	False		,,,				2504	0.137				p.R185Q		Atlas-SNP	.											.	RAD51D	53	.	0			c.G554A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	162,4244	107.8+/-146.2	4,154,2045	44.0	40.0	42.0		554,494,158	0.2	1.0	17	dbSNP_111	42	1227,7373	243.5+/-273.1	87,1053,3160	yes	missense,missense,missense	RAD51D	NM_001142571.1,NM_002878.3,NM_133629.2	43,43,43	91,1207,5205	TT,TC,CC		14.2674,3.6768,10.6797	,,	185/349,165/329,53/217	33433487	1389,11617	2203	4300	6503	SO:0001583	missense	5892	exon6			ATCCTCCGGAGAG	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.494G>A	17.37:g.33433487C>T	ENSP00000338790:p.Arg165Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001142571	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	37	CCDS11287.1	212	0.09706959706959707	10	0.02032520325203252	73	0.20165745856353592	24	0.04195804195804196	105	0.13852242744063326	C	12.22	1.871652	0.33069	0.036768	0.142674	ENSG00000185379	ENST00000345365;ENST00000394589;ENST00000335858;ENST00000360276;ENST00000345766;ENST00000418935;ENST00000415064	T;T	0.65916	-0.18;-0.18	4.96	0.253	0.15551	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.164310	0.56097	N	0.000032	T	0.00039	0.0001	N	0.00652	-1.29	0.09310	P	0.9999999999941145	B;B;B;B	0.16166	0.016;0.008;0.0;0.0	B;B;B;B	0.15484	0.013;0.001;0.001;0.0	T	0.19031	-1.0318	9	0.02654	T	1	-3.6654	8.0109	0.30353	0.0:0.3404:0.0:0.6596	rs4796033;rs52810365;rs59839357;rs4796033	185;53;165;165	B4DJU7;O75771-3;O75771;F8W8E6	.;.;RA51D_HUMAN;.	Q	165;185;165;120;53;165;168	ENSP00000338790:R165Q;ENSP00000353417:R120Q	ENSP00000338408:R165Q	R	-	2	0	RAD51D	30457600	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	1.326000	0.33735	-0.161000	0.10983	-0.383000	0.06682	CGG	C|0.903;T|0.097	0.097	strong		0.562	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878	
SLC6A3	6531	hgsc.bcm.edu	37	5	1443151	1443151	+	Silent	SNP	G	G	A	rs6351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:1443151G>A	ENST00000270349.9	-	2	289	c.162C>T	c.(160-162)ccC>ccT	p.P54P	SLC6A3_ENST00000453492.2_Silent_p.P54P	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	54					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)	GGGCCTCCACGGGGCTCTGCC	0.632													G|||	23	0.00459265	0.0008	0.0058	5008	,	,		18389	0.0		0.0099	False		,,,				2504	0.0082				p.P54P		Atlas-SNP	.											.	SLC6A3	102	.	0			c.C162T						PASS	.	G		7,4399	15.5+/-35.6	0,7,2196	69.0	67.0	68.0		162	-3.0	0.0	5	dbSNP_52	68	90,8510	50.6+/-110.7	1,88,4211	no	coding-synonymous	SLC6A3	NM_001044.4		1,95,6407	AA,AG,GG		1.0465,0.1589,0.7458		54/621	1443151	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	6531	exon2			CTCCACGGGGCTC		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.162C>T	5.37:g.1443151G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																			G|0.992;A|0.008	0.008	strong		0.632	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	
KIF24	347240	hgsc.bcm.edu	37	9	34306410	34306410	+	Missense_Mutation	SNP	C	C	A	rs17350674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:34306410C>A	ENST00000402558.2	-	2	677	c.653G>T	c.(652-654)tGg>tTg	p.W218L	KIF24_ENST00000379166.2_Missense_Mutation_p.W218L|KIF24_ENST00000379174.3_Missense_Mutation_p.W218L|KIF24_ENST00000345050.2_Missense_Mutation_p.W218L			Q5T7B8	KIF24_HUMAN	kinesin family member 24	218			W -> L (in dbSNP:rs17350674).		ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			CATCTCAGTCCAAGGATTCTG	0.363													C|||	452	0.0902556	0.0098	0.147	5008	,	,		18714	0.0069		0.2177	False		,,,				2504	0.1135				p.W218L		Atlas-SNP	.											.	KIF24	64	.	0			c.G653T						PASS	.	C	LEU/TRP	120,3498		1,118,1690	166.0	156.0	159.0		653	5.6	1.0	9	dbSNP_123	159	1565,6597		146,1273,2662	yes	missense	KIF24	NM_194313.2	61	147,1391,4352	AA,AC,CC		19.1742,3.3167,14.3039	possibly-damaging	218/1369	34306410	1685,10095	1809	4081	5890	SO:0001583	missense	347240	exon3			TCAGTCCAAGGAT	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.653G>T	9.37:g.34306410C>A	ENSP00000384433:p.Trp218Leu	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	242	107	0.442149	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	37	CCDS6551.2	212	0.09706959706959707	5	0.01016260162601626	52	0.143646408839779	3	0.005244755244755245	152	0.20052770448548812	C	24.2	4.510651	0.85389	0.033167	0.191742	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.6	5.6	0.85130	.	0.000000	0.40818	N	0.001017	T	0.00039	0.0001	M	0.66939	2.045	0.26078	P	0.9811238	D;D	0.57257	0.975;0.979	P;P	0.56788	0.806;0.644	T	0.10590	-1.0623	9	0.10111	T	0.7	.	19.6051	0.95577	0.0:1.0:0.0:0.0	rs17350674;rs17350674	218;218	Q5T7B8-4;Q5T7B8	.;KIF24_HUMAN	L	218	ENSP00000384433:W218L;ENSP00000368472:W218L;ENSP00000368464:W218L;ENSP00000340179:W218L	ENSP00000340179:W218L	W	-	2	0	KIF24	34296410	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.581000	0.67471	2.636000	0.89361	0.655000	0.94253	TGG	C|0.891;A|0.109	0.109	strong		0.363	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
NT5C1B	93034	hgsc.bcm.edu	37	2	18757501	18757501	+	Silent	SNP	G	G	C	rs3902946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:18757501G>C	ENST00000359846.2	-	9	1535	c.1458C>G	c.(1456-1458)ctC>ctG	p.L486L	NT5C1B_ENST00000600945.1_Silent_p.L486L|NT5C1B-RDH14_ENST00000532967.1_Silent_p.L486L|NT5C1B_ENST00000304081.4_Silent_p.L426L	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	323	1	0.00309598		WXS	Illumina HiSeq	Phase_I	356	354	0.994382	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		
OSBPL1A	114876	hgsc.bcm.edu	37	18	21891975	21891975	+	Silent	SNP	A	A	G	rs2337961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:21891975A>G	ENST00000319481.3	-	13	1271	c.1065T>C	c.(1063-1065)tcT>tcC	p.S355S	OSBPL1A_ENST00000357041.4_5'Flank	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	355					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					GGTCTGCAGCAGAAACCGTAT	0.408													a|||	1172	0.234026	0.4455	0.1527	5008	,	,		19330	0.0625		0.2336	False		,,,				2504	0.183				p.S355S		Atlas-SNP	.											OSBPL1A,colon,carcinoma,0,1	OSBPL1A	94	1	0			c.T1065C						PASS	.	G		1789,2617	528.2+/-372.3	372,1045,786	201.0	195.0	197.0		1065	-2.5	0.1	18	dbSNP_100	197	1940,6660	340.5+/-323.6	211,1518,2571	no	coding-synonymous	OSBPL1A	NM_080597.3		583,2563,3357	GG,GA,AA		22.5581,40.6037,28.6714		355/951	21891975	3729,9277	2203	4300	6503	SO:0001819	synonymous_variant	114876	exon13			TGCAGCAGAAACC	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1065T>C	18.37:g.21891975A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	156	67	0.429487	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																			A|0.731;G|0.269	0.269	strong		0.408	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
CABP5	56344	hgsc.bcm.edu	37	19	48537585	48537585	+	Missense_Mutation	SNP	A	A	G	rs3745746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48537585A>G	ENST00000293255.2	-	5	513	c.383T>C	c.(382-384)gTg>gCg	p.V128A		NM_019855.4	NP_062829.1	Q9NP86	CABP5_HUMAN	calcium binding protein 5	128	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.		V -> A (in dbSNP:rs3745746).		signal transduction (GO:0007165)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	11		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		CTGTAGCTCCACCAGGGTGAT	0.522													g|||	1113	0.222244	0.1399	0.281	5008	,	,		16208	0.0645		0.3569	False		,,,				2504	0.316				p.V128A		Atlas-SNP	.											.	CABP5	28	.	0			c.T383C						PASS	.	G	ALA/VAL	756,3650	754.6+/-412.5	68,620,1515	59.0	56.0	57.0		383	-5.2	0.3	19	dbSNP_107	57	3333,5267	644.2+/-400.0	647,2039,1614	yes	missense	CABP5	NM_019855.4	64	715,2659,3129	GG,GA,AA		38.7558,17.1584,31.4393	benign	128/174	48537585	4089,8917	2203	4300	6503	SO:0001583	missense	56344	exon5			AGCTCCACCAGGG	AF169159	CCDS12709.1	19q13.33	2014-08-12			ENSG00000105507	ENSG00000105507		"""EF-hand domain containing"""	13714	protein-coding gene	gene with protein product		607315	"""calcium binding protein 3"""	CABP3		10625670	Standard	NM_019855		Approved	CaBP3	uc002phu.2	Q9NP86	OTTHUMG00000183139	ENST00000293255.2:c.383T>C	19.37:g.48537585A>G	ENSP00000293255:p.Val128Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_019855	A0AUY4	Missense_Mutation	SNP	ENST00000293255.2	37	CCDS12709.1	508	0.2326007326007326	70	0.14227642276422764	120	0.3314917127071823	52	0.09090909090909091	266	0.35092348284960423	G	0.023	-1.402989	0.01165	0.171584	0.387558	ENSG00000105507	ENST00000293255	T	0.68765	-0.35	5.01	-5.16	0.02857	EF-hand-like domain (1);	0.442432	0.23732	N	0.045101	T	0.00012	0.0000	N	0.00300	-1.685	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.17258	-1.0375	9	0.02654	T	1	-9.6053	8.8389	0.35129	0.3967:0.2939:0.3094:0.0	rs3745746;rs17663756;rs52805288;rs60664550;rs3745746	128	Q9NP86	CABP5_HUMAN	A	128	ENSP00000293255:V128A	ENSP00000293255:V128A	V	-	2	0	CABP5	53229397	0.000000	0.05858	0.314000	0.25224	0.351000	0.29236	-2.822000	0.00748	-0.593000	0.05844	-0.930000	0.02707	GTG	G|0.275;N|0.000	0.275	strong		0.522	CABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465212.1	NM_019855	
PRSS3	5646	hgsc.bcm.edu	37	9	33798075	33798075	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33798075T>C	ENST00000361005.5	+	3	620	c.620T>C	c.(619-621)tTt>tCt	p.F207S	PRSS3_ENST00000379405.3_Missense_Mutation_p.F150S|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000429677.3_Missense_Mutation_p.F143S|PRSS3_ENST00000342836.4_Missense_Mutation_p.F164S	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	207	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			ACTCTGAGCTTTGGTGGTGAG	0.577																																					p.F207S		Atlas-SNP	.											PRSS3_ENST00000361005,brain,glioma,0,3	PRSS3	79	3	0			c.T620C						scavenged	.						121.0	104.0	109.0					9																	33798075		2203	4300	6503	SO:0001583	missense	5646	exon3			TGAGCTTTGGTGG		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.620T>C	9.37:g.33798075T>C	ENSP00000354280:p.Phe207Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	116	5	0.0431034	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	37	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	T	1.643	-0.516079	0.04200	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	T;D;D;T;D	0.92249	0.37;-2.35;-3.0;0.37;-3.0	3.61	-7.22	0.01485	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.710450	0.02946	N	0.141069	T	0.72630	0.3484	N	0.03224	-0.385	0.40775	D	0.983123	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.69907	-0.5018	10	0.02654	T	1	.	1.7451	0.02961	0.1264:0.1901:0.3621:0.3214	.	150;207;164	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	S	207;162;164;143;150	ENSP00000354280:F207S;ENSP00000401249:F162S;ENSP00000340889:F164S;ENSP00000401828:F143S;ENSP00000368715:F150S	ENSP00000340889:F164S	F	+	2	0	PRSS3	33788075	0.519000	0.26242	0.960000	0.40013	0.020000	0.10135	-0.135000	0.10420	-0.550000	0.06183	-1.390000	0.01156	TTT	.	.	none		0.577	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
MAML3	55534	hgsc.bcm.edu	37	4	140640703	140640703	+	Missense_Mutation	SNP	G	G	T	rs61747885	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	69	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	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		
SGSM2	9905	hgsc.bcm.edu	37	17	2275734	2275734	+	Silent	SNP	C	C	G	rs3213712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2275734C>G	ENST00000426855.2	+	14	1780	c.1605C>G	c.(1603-1605)tcC>tcG	p.S535S	RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000574563.1_Silent_p.S535S|SGSM2_ENST00000268989.3_Silent_p.S580S	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	535					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		CGGGGGCCTCCGCGGGCCTCA	0.687													C|||	1288	0.257188	0.5507	0.1124	5008	,	,		12916	0.1478		0.0954	False		,,,				2504	0.2423				p.S580S		Atlas-SNP	.											SGSM2,colon,carcinoma,0,1	SGSM2	60	1	0			c.C1740G						PASS	.	C	,	1915,2437		438,1039,699	9.0	13.0	12.0		1605,1740	-11.4	0.0	17	dbSNP_106	12	721,7807		34,653,3577	no	coding-synonymous,coding-synonymous	SGSM2	NM_001098509.1,NM_014853.2	,	472,1692,4276	GG,GC,CC		8.4545,44.0028,20.4658	,	535/1007,580/1052	2275734	2636,10244	2176	4264	6440	SO:0001819	synonymous_variant	9905	exon15			GGCCTCCGCGGGC	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.1605C>G	17.37:g.2275734C>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	174	69	0.396552	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	37	CCDS45570.1																																																																																			C|0.810;G|0.190	0.190	strong		0.687	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
SSTR4	6754	hgsc.bcm.edu	37	20	23016819	23016819	+	Silent	SNP	C	C	T	rs141700474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:23016819C>T	ENST00000255008.3	+	1	763	c.699C>T	c.(697-699)ctC>ctT	p.L233L	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	233					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|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 cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCTACCTGCTCATCGTGGGCA	0.657													C|||	34	0.00678914	0.0113	0.0072	5008	,	,		17179	0.0		0.006	False		,,,				2504	0.0082				p.L233L	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											.	SSTR4	83	.	0			c.C699T						PASS	.	C		50,4310		0,50,2130	78.0	85.0	83.0		699	-1.4	0.5	20	dbSNP_134	83	81,8495		0,81,4207	no	coding-synonymous	SSTR4	NM_001052.2		0,131,6337	TT,TC,CC		0.9445,1.1468,1.0127		233/389	23016819	131,12805	2180	4288	6468	SO:0001819	synonymous_variant	6754	exon1			CCTGCTCATCGTG		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.699C>T	20.37:g.23016819C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Silent	SNP	ENST00000255008.3	37	CCDS42856.1																																																																																			C|0.993;T|0.007	0.007	strong		0.657	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
ACSS1	84532	hgsc.bcm.edu	37	20	24994275	24994275	+	Silent	SNP	G	G	A	rs6115001	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:24994275G>A	ENST00000323482.4	-	10	1555	c.1476C>T	c.(1474-1476)aaC>aaT	p.N492N	ACSS1_ENST00000542618.1_Silent_p.N371N|ACSS1_ENST00000537502.1_Silent_p.N409N|ACSS1_ENST00000484396.1_5'Flank|ACSS1_ENST00000432802.2_Silent_p.N492N	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	492					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)	CCCCGGAGACGTTGCTGCCCT	0.627													G|||	379	0.0756789	0.1051	0.0677	5008	,	,		18970	0.003		0.0984	False		,,,				2504	0.093				p.N492N		Atlas-SNP	.											.	ACSS1	46	.	0			c.C1476T						PASS	.	G		477,3929	219.7+/-237.4	23,431,1749	38.0	37.0	37.0		1476	-4.5	0.1	20	dbSNP_114	37	876,7724	196.6+/-241.5	51,774,3475	no	coding-synonymous	ACSS1	NM_032501.2		74,1205,5224	AA,AG,GG		10.186,10.8261,10.4029		492/690	24994275	1353,11653	2203	4300	6503	SO:0001819	synonymous_variant	84532	exon10			GGAGACGTTGCTG		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.1476C>T	20.37:g.24994275G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			G|0.909;A|0.091	0.091	strong		0.627	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
GPR128	84873	hgsc.bcm.edu	37	3	100368546	100368546	+	Missense_Mutation	SNP	A	A	G	rs61730367	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:100368546A>G	ENST00000273352.3	+	11	1542	c.1274A>G	c.(1273-1275)aAa>aGa	p.K425R	GPR128_ENST00000475887.1_Missense_Mutation_p.K130R	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	425	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						CAGACTTTCAAAAAGGATTAT	0.353													A|||	609	0.121605	0.0802	0.1643	5008	,	,		19359	0.251		0.0497	False		,,,				2504	0.0879				p.K425R	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.A1274G						PASS	.	A	ARG/LYS	334,4070	166.9+/-198.0	10,314,1878	98.0	93.0	95.0		1274	-1.6	0.6	3	dbSNP_129	95	444,8156	127.7+/-186.0	10,424,3866	yes	missense	GPR128	NM_032787.2	26	20,738,5744	GG,GA,AA		5.1628,7.584,5.9828	benign	425/798	100368546	778,12226	2202	4300	6502	SO:0001583	missense	84873	exon11			CTTTCAAAAAGGA	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.1274A>G	3.37:g.100368546A>G	ENSP00000273352:p.Lys425Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_032787	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	284	0.13003663003663005	26	0.052845528455284556	63	0.17403314917127072	155	0.270979020979021	40	0.052770448548812667	A	10.44	1.351018	0.24512	0.07584	0.051628	ENSG00000144820	ENST00000273352;ENST00000475887	T;T	0.38240	1.15;1.46	5.49	-1.61	0.08399	GPS domain (2);	0.968711	0.08539	N	0.930924	T	0.00012	0.0000	N	0.21373	0.66	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.001	T	0.38178	-0.9673	9	0.08179	T	0.78	.	5.1415	0.14961	0.5914:0.0:0.286:0.1226	rs61730367	130;425	E9PHI0;Q96K78	.;GP128_HUMAN	R	425;130	ENSP00000273352:K425R;ENSP00000419788:K130R	ENSP00000273352:K425R	K	+	2	0	GPR128	101851236	0.001000	0.12720	0.560000	0.28344	0.455000	0.32408	-0.066000	0.11598	-0.200000	0.10300	-0.327000	0.08410	AAA	A|0.920;G|0.080	0.080	strong		0.353	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		
UGT2B28	54490	hgsc.bcm.edu	37	4	70160343	70160343	+	Missense_Mutation	SNP	G	G	C	rs72552705	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70160343G>C	ENST00000335568.5	+	6	1408	c.1406G>C	c.(1405-1407)tGc>tCc	p.C469S	UGT2B28_ENST00000511240.1_3'UTR	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	469					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						TTTGTGATGTGCCACAAAGGA	0.448													N|||	1197	0.239018	0.2511	0.2147	5008	,	,		12565	0.2034		0.2813	False		,,,				2504	0.2331				p.C469S		Atlas-SNP	.											.	UGT2B28	101	.	0			c.G1406C						PASS	.	G	,SER/CYS	342,3778		154,34,1872	75.0	85.0	81.0		,1406	1.9	1.0	4	dbSNP_130	81	583,7865		270,43,3911	no	utr-3,missense	UGT2B28	NM_001207004.1,NM_053039.1	,112	424,77,5783	CC,CG,GG		6.901,8.301,7.36	,benign	,469/530	70160343	925,11643	2060	4224	6284	SO:0001583	missense	54490	exon6			TGATGTGCCACAA	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1406G>C	4.37:g.70160343G>C	ENSP00000334276:p.Cys469Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	110	38	0.345455	NM_053039	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	423	0.1936813186813187	103	0.20934959349593496	74	0.20441988950276244	96	0.16783216783216784	150	0.19788918205804748	-	7.164	0.586361	0.13749	0.08301	0.06901	ENSG00000135226	ENST00000335568	T	0.58652	0.32	1.85	1.85	0.25348	.	0.000000	0.64402	U	0.000003	T	0.00039	0.0001	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.10823	-1.0613	10	0.87932	D	0	.	9.3109	0.37903	0.0:0.0:1.0:0.0	.	469	Q9BY64	UDB28_HUMAN	S	469	ENSP00000334276:C469S	ENSP00000334276:C469S	C	+	2	0	UGT2B28	70194932	1.000000	0.71417	0.971000	0.41717	0.017000	0.09413	5.429000	0.66495	1.023000	0.39654	0.184000	0.17185	TGC	G|0.867;C|0.133	0.133	strong		0.448	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
ASAH2	56624	hgsc.bcm.edu	37	10	52005153	52005153	+	Silent	SNP	A	A	G	rs7097319	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	153	0	0		WXS	Illumina HiSeq	Phase_I	143	51	0.356643	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	
MMP10	4319	hgsc.bcm.edu	37	11	102650424	102650424	+	Missense_Mutation	SNP	C	C	T	rs486055	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102650424C>T	ENST00000279441.4	-	2	194	c.158G>A	c.(157-159)aGa>aAa	p.R53K		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	53			R -> K (in dbSNP:rs486055). {ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	ACTGTCCTTTCTTCTAAACTG	0.378													C|||	227	0.0453275	0.0045	0.0663	5008	,	,		19174	0.001		0.1382	False		,,,				2504	0.0358				p.R53K		Atlas-SNP	.											.	MMP10	44	.	0			c.G158A						PASS	.	C	LYS/ARG	120,4286	87.8+/-126.4	2,116,2085	85.0	77.0	80.0		158	4.2	1.0	11	dbSNP_83	80	1343,7255	262.4+/-284.4	108,1127,3064	yes	missense	MMP10	NM_002425.2	26	110,1243,5149	TT,TC,CC		15.6199,2.7236,11.2504	benign	53/477	102650424	1463,11541	2203	4299	6502	SO:0001583	missense	4319	exon2			TCCTTTCTTCTAA	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.158G>A	11.37:g.102650424C>T	ENSP00000279441:p.Arg53Lys	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	138	0.06318681318681318	2	0.0040650406504065045	29	0.08011049723756906	0	0.0	107	0.14116094986807387	c	4.269	0.048987	0.08243	0.027236	0.156199	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.32753	1.44;1.44	4.25	4.25	0.50352	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.121332	0.37178	N	0.002214	T	0.00039	0.0001	N	0.13168	0.305	0.09310	N	1	B	0.19073	0.033	B	0.22152	0.038	T	0.34004	-0.9846	10	0.02654	T	1	.	8.6471	0.34011	0.0:0.7624:0.153:0.0845	rs486055;rs17359452;rs17860947;rs60436444;rs486055	53	P09238	MMP10_HUMAN	K	53	ENSP00000279441:R53K;ENSP00000441485:R53K	ENSP00000279441:R53K	R	-	2	0	MMP10	102155634	0.000000	0.05858	0.977000	0.42913	0.046000	0.14306	0.542000	0.23222	2.365000	0.80145	0.591000	0.81541	AGA	C|0.916;T|0.084	0.084	strong		0.378	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
PTCH2	8643	hgsc.bcm.edu	37	1	45292926	45292926	+	Silent	SNP	C	C	G	rs111471526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:45292926C>G	ENST00000372192.3	-	16	2557	c.2427G>C	c.(2425-2427)tcG>tcC	p.S809S	PTCH2_ENST00000447098.2_Silent_p.S809S	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	809					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)					CATTGCGGTACGAGTGGCGGG	0.627									Basal Cell Nevus syndrome				C|||	34	0.00678914	0.0008	0.0086	5008	,	,		17933	0.0		0.0249	False		,,,				2504	0.002				p.S809S		Atlas-SNP	.											.	PTCH2	96	.	0			c.G2427C						PASS	.	C	,	10,4396	16.8+/-37.8	0,10,2193	69.0	77.0	74.0		2427,2427	-9.9	0.8	1	dbSNP_132	74	153,8447	74.8+/-137.4	3,147,4150	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	3,157,6343	GG,GC,CC		1.7791,0.227,1.2533	,	809/1147,809/1204	45292926	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon16	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	GCGGTACGAGTGG	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.2427G>C	1.37:g.45292926C>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			C|0.988;G|0.012	0.012	strong		0.627	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
ITPR3	3710	hgsc.bcm.edu	37	6	33643558	33643558	+	Silent	SNP	G	G	A	rs2229637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33643558G>A	ENST00000374316.5	+	26	4267	c.3207G>A	c.(3205-3207)ccG>ccA	p.P1069P	ITPR3_ENST00000605930.1_Silent_p.P1069P			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1069					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACTATGCGCCGCTGGTCTCGG	0.647													G|||	890	0.177716	0.1906	0.245	5008	,	,		21343	0.0704		0.2843	False		,,,				2504	0.1135				p.P1069P		Atlas-SNP	.											ITPR3_ENST00000374316,NS,carcinoma,0,2	ITPR3	409	2	0			c.G3207A						PASS	.	G		862,3544	317.4+/-295.1	75,712,1416	40.0	30.0	34.0		3207	-11.3	0.0	6	dbSNP_98	34	2451,6149	382.4+/-340.4	357,1737,2206	no	coding-synonymous	ITPR3	NM_002224.3		432,2449,3622	AA,AG,GG		28.5,19.5642,25.4729		1069/2672	33643558	3313,9693	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon25			TGCGCCGCTGGTC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.3207G>A	6.37:g.33643558G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			G|0.786;A|0.214	0.214	strong		0.647	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
GNG8	94235	hgsc.bcm.edu	37	19	47137459	47137459	+	Silent	SNP	C	C	T	rs12974613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	78	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	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		
GGTLC2	91227	hgsc.bcm.edu	37	22	22988911	22988911	+	Silent	SNP	G	G	A	rs9612135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:22988911G>A	ENST00000480559.1	+	1	96	c.96G>A	c.(94-96)ccG>ccA	p.P32P	GGTLC2_ENST00000448514.1_Silent_p.P32P|POM121L1P_ENST00000402027.1_RNA	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	32					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)	p.P32P(1)		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)		TCTACACGCCGGTTGATGGGG	0.617													.|||	1847	0.36881	0.1505	0.6124	5008	,	,		7239	0.5109		0.4056	False		,,,				2504	0.3067				p.P32P		Atlas-SNP	.											GGTLC2,NS,carcinoma,0,1	GGTLC2	20	1	1	Substitution - coding silent(1)	prostate(1)	c.G96A						scavenged	.						32.0	17.0	22.0					22																	22988911		2173	3963	6136	SO:0001819	synonymous_variant	91227	exon1			CACGCCGGTTGAT	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.96G>A	22.37:g.22988911G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	148	15	0.101351	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Silent	SNP	ENST00000480559.1	37	CCDS13802.2																																																																																			G|0.631;A|0.369	0.369	strong		0.617	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
ZNF804A	91752	hgsc.bcm.edu	37	2	185801917	185801917	+	Silent	SNP	A	A	G	rs728534	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:185801917A>G	ENST00000302277.6	+	4	2388	c.1794A>G	c.(1792-1794)aaA>aaG	p.K598K		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	598							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						GAAAGAAAAAAAGAAAAAAGT	0.333													A|||	798	0.159345	0.0076	0.1326	5008	,	,		18012	0.2312		0.2147	False		,,,				2504	0.2526				p.K598K		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A1794G						PASS	.	A		180,4222		5,170,2026	47.0	55.0	52.0		1794	0.1	0.9	2	dbSNP_86	52	1683,6903		182,1319,2792	no	coding-synonymous	ZNF804A	NM_194250.1		187,1489,4818	GG,GA,AA		19.6017,4.0891,14.344		598/1210	185801917	1863,11125	2201	4293	6494	SO:0001819	synonymous_variant	91752	exon4			GAAAAAAAGAAAA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1794A>G	2.37:g.185801917A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			A|0.840;G|0.160	0.160	strong		0.333	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
BTBD16	118663	hgsc.bcm.edu	37	10	124089075	124089075	+	Missense_Mutation	SNP	G	G	A	rs986178|rs58204486	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:124089075G>A	ENST00000260723.4	+	11	1243	c.992G>A	c.(991-993)gGc>gAc	p.G331D	BTBD16_ENST00000368994.2_Missense_Mutation_p.G332D	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	331			G -> D (in dbSNP:rs986178).							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				CGTCTGCACGGCATCACCAAA	0.612													G|||	480	0.0958466	0.0113	0.0764	5008	,	,		17173	0.1687		0.1044	False		,,,				2504	0.1401				p.G331D		Atlas-SNP	.											BTBD16,NS,carcinoma,0,1	BTBD16	44	1	0			c.G992A						PASS	.	G	ASP/GLY	116,4290	89.2+/-127.9	3,110,2090	108.0	95.0	99.0		992	1.8	0.2	10	dbSNP_86	99	1093,7507	228.4+/-263.5	69,955,3276	yes	missense	BTBD16	NM_144587.2	94	72,1065,5366	AA,AG,GG		12.7093,2.6328,9.2957	probably-damaging	331/507	124089075	1209,11797	2203	4300	6503	SO:0001583	missense	118663	exon11			TGCACGGCATCAC	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.992G>A	10.37:g.124089075G>A	ENSP00000260723:p.Gly331Asp	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	207	0.09478021978021978	7	0.014227642276422764	33	0.09116022099447514	88	0.15384615384615385	79	0.10422163588390501	G	5.362	0.252126	0.10185	0.026328	0.127093	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.19250	2.16;2.16	5.77	1.79	0.24919	.	0.954977	0.08657	N	0.913061	T	0.00210	0.0006	L	0.56769	1.78	0.35328	P	0.21467999999999998	D;D	0.64830	0.994;0.994	P;P	0.60886	0.88;0.88	T	0.06232	-1.0838	9	0.36615	T	0.2	-4.1952	7.2653	0.26226	0.3742:0.0:0.6258:0.0	rs986178;rs60773779;rs986178	332;331	Q32M84-2;Q32M84	.;BTBDG_HUMAN	D	331;332	ENSP00000260723:G331D;ENSP00000357990:G332D	ENSP00000260723:G331D	G	+	2	0	BTBD16	124079065	0.363000	0.24989	0.161000	0.22692	0.039000	0.13416	0.487000	0.22356	0.062000	0.16340	-0.137000	0.14449	GGC	G|0.902;A|0.098	0.098	strong		0.612	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
CUL9	23113	hgsc.bcm.edu	37	6	43188940	43188940	+	Silent	SNP	C	C	T	rs6917902	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43188940C>T	ENST00000252050.4	+	34	6717	c.6633C>T	c.(6631-6633)gaC>gaT	p.D2211D	CUL9_ENST00000372647.2_Silent_p.D2183D|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000354495.3_Silent_p.D2101D	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	162	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	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	
HAVCR1	26762	hgsc.bcm.edu	37	5	156479426	156479426	+	Missense_Mutation	SNP	T	T	C	rs386693988|rs12522248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:156479426T>C	ENST00000339252.3	-	3	1151	c.619A>G	c.(619-621)Act>Gct	p.T207A	HAVCR1_ENST00000523175.1_Missense_Mutation_p.T207A|HAVCR1_ENST00000544197.1_Missense_Mutation_p.T207A|HAVCR1_ENST00000522693.1_Missense_Mutation_p.T207A|HAVCR1_ENST00000425854.1_Missense_Mutation_p.T207A	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0					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)			GTAGAGACAGTTGTTGTCACT	0.473													T|||	1133	0.226238	0.1362	0.3386	5008	,	,		25057	0.1478		0.3042	False		,,,				2504	0.2689				p.T207A		Atlas-SNP	.											.	HAVCR1	84	.	0			c.A619G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	698,3416		51,596,1410	313.0	303.0	306.0		619,619,619	1.0	0.0	5	dbSNP_120	306	2393,6013		348,1697,2158	yes	missense,missense,missense	HAVCR1	NM_012206.2,NM_001173393.1,NM_001099414.1	58,58,58	399,2293,3568	CC,CT,TT		28.4678,16.9665,24.6885	benign,benign,benign	207/365,207/365,207/365	156479426	3091,9429	2057	4203	6260	SO:0001583	missense	26762	exon4			AGACAGTTGTTGT	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.619A>G	5.37:g.156479426T>C	ENSP00000344844:p.Thr207Ala	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	348	159	0.456897	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	37	CCDS43392.1	503	0.2303113553113553	63	0.12804878048780488	127	0.35082872928176795	83	0.1451048951048951	230	0.3034300791556728	T	1.618	-0.522318	0.04141	0.169665	0.284678	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	T;T;T;T;T;T	0.14640	2.49;2.56;2.56;2.49;2.56;2.53	3.51	1.05	0.20165	.	1622.760000	0.00166	N	0.000001	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.08055	0.002;0.003;0.003	T	0.44544	-0.9321	9	0.07990	T	0.79	-1.1978	0.6206	0.00777	0.211:0.123:0.2184:0.4476	rs12522248;rs61365319;rs12522248	207;202;202	E9PFX0;F1CME6;Q96D42	.;.;HAVR1_HUMAN	A	207	ENSP00000428524:T207A;ENSP00000427898:T207A;ENSP00000344844:T207A;ENSP00000403333:T207A;ENSP00000440258:T207A;ENSP00000428422:T207A	ENSP00000344844:T207A	T	-	1	0	HAVCR1	156412004	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.117000	0.10708	0.509000	0.28195	0.443000	0.29094	ACT	T|0.756;C|0.244	0.244	strong		0.473	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
SLC45A4	57210	hgsc.bcm.edu	37	8	142228909	142228909	+	Missense_Mutation	SNP	G	G	A	rs753778	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:142228909G>A	ENST00000024061.3	-	4	984	c.677C>T	c.(676-678)cCg>cTg	p.P226L	SLC45A4_ENST00000519067.1_Missense_Mutation_p.P226L|SLC45A4_ENST00000433583.2_Missense_Mutation_p.P219L|SLC45A4_ENST00000517878.1_Missense_Mutation_p.P277L	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)			GACGCCGTGCGGCTCGCCCCC	0.682													G|||	1880	0.375399	0.3737	0.366	5008	,	,		15297	0.4038		0.2942	False		,,,				2504	0.4387				p.P226L		Atlas-SNP	.											.	SLC45A4	71	.	0			c.C677T						PASS	.	G	LEU/PRO	1732,2674	500.5+/-364.7	345,1042,816	64.0	69.0	68.0		677	-10.6	0.0	8	dbSNP_86	68	2448,6150	391.5+/-343.7	352,1744,2203	yes	missense	SLC45A4	NM_001080431.1	98	697,2786,3019	AA,AG,GG		28.4717,39.31,32.144	benign	226/799	142228909	4180,8824	2203	4299	6502	SO:0001583	missense	57210	exon4			CCGTGCGGCTCGC	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.677C>T	8.37:g.142228909G>A	ENSP00000024061:p.Pro226Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	766	0.3507326007326007	194	0.3943089430894309	136	0.3756906077348066	220	0.38461538461538464	216	0.2849604221635884	G	6.417	0.445021	0.12164	0.3931	0.284717	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061;ENST00000520137	T;T;T;T;T	0.42513	2.47;2.46;2.47;2.44;0.97	5.3	-10.6	0.00265	.	1.534320	0.03423	N	0.206591	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B;B;B	0.13594	0.004;0.008;0.001	B;B;B	0.09377	0.002;0.002;0.004	T	0.15549	-1.0433	9	0.36615	T	0.2	-4.4495	9.9976	0.41909	0.2636:0.0:0.5968:0.1396	rs753778;rs57687708;rs753778	277;226;226	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	L	226;277;219;226;84	ENSP00000429059:P226L;ENSP00000428137:P277L;ENSP00000400799:P219L;ENSP00000024061:P226L;ENSP00000429033:P84L	ENSP00000024061:P226L	P	-	2	0	SLC45A4	142298091	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.059000	0.14322	-1.756000	0.01318	-2.934000	0.00087	CCG	G|0.657;A|0.343	0.343	strong		0.682	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
PRDM1	639	hgsc.bcm.edu	37	6	106547372	106547372	+	Missense_Mutation	SNP	C	C	G	rs811925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:106547372C>G	ENST00000369096.4	+	4	843	c.609C>G	c.(607-609)gaC>gaG	p.D203E	RP1-134E15.3_ENST00000602426.1_RNA|PRDM1_ENST00000369091.2_Missense_Mutation_p.D167E|PRDM1_ENST00000369089.3_Missense_Mutation_p.D69E	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	203			D -> E (in dbSNP:rs811925).		cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		ATTGTCGGGACTTTGCAGAAA	0.443			"""D, N, Mis, F, S"""		DLBCL								C|||	752	0.15016	0.1558	0.1513	5008	,	,		19653	0.0208		0.2048	False		,,,				2504	0.2188				p.D203E		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.C609G						PASS	.	C	GLU/ASP,GLU/ASP	717,3689	296.7+/-284.4	62,593,1548	96.0	83.0	87.0		609,207	5.9	1.0	6	dbSNP_86	87	1457,7143	278.4+/-293.4	108,1241,2951	yes	missense,missense	PRDM1	NM_001198.3,NM_182907.1	45,45	170,1834,4499	GG,GC,CC		16.9419,16.2733,16.7154	probably-damaging,probably-damaging	203/826,69/692	106547372	2174,10832	2203	4300	6503	SO:0001583	missense	639	exon4			TCGGGACTTTGCA		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.609C>G	6.37:g.106547372C>G	ENSP00000358092:p.Asp203Glu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	297	0.13598901098901098	70	0.14227642276422764	61	0.1685082872928177	10	0.017482517482517484	156	0.20580474934036938	C	5.903	0.350657	0.11182	0.162733	0.169419	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000450060;ENST00000369089	D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5	5.94	5.94	0.96194	SET domain (2);	0.091905	0.85682	D	0.000000	T	0.64713	0.2623	N	0.02708	-0.52	0.22873	P	0.99862732	P;P	0.39116	0.66;0.568	B;B	0.35971	0.215;0.046	T	0.73972	-0.3814	9	0.09843	T	0.71	-48.4594	20.3736	0.98901	0.0:1.0:0.0:0.0	rs811925;rs17440760;rs811925	69;203	Q86WM7;O75626	.;PRDM1_HUMAN	E	167;203;167;82;69	ENSP00000358087:D167E;ENSP00000358092:D203E;ENSP00000399772:D82E;ENSP00000358085:D69E	ENSP00000358085:D69E	D	+	3	2	PRDM1	106654065	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.723000	0.38053	2.820000	0.97059	0.650000	0.86243	GAC	C|0.843;G|0.157	0.157	strong		0.443	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
ARHGAP24	83478	hgsc.bcm.edu	37	4	86844835	86844835	+	Silent	SNP	A	A	G	rs6824722	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:86844835A>G	ENST00000395184.1	+	4	769	c.303A>G	c.(301-303)gaA>gaG	p.E101E	ARHGAP24_ENST00000503995.1_Silent_p.E101E|ARHGAP24_ENST00000395183.2_Silent_p.E6E	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	101	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CAAATCATGAAAGCTACCTCC	0.493													G|||	1985	0.396366	0.4304	0.3689	5008	,	,		17440	0.3601		0.2744	False		,,,				2504	0.5327				p.E101E		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A303G						PASS	.	G	,	1765,2641	644.4+/-398.0	365,1035,803	101.0	92.0	95.0		303,18	3.4	1.0	4	dbSNP_116	95	2352,6248	703.2+/-405.3	329,1694,2277	no	coding-synonymous,coding-synonymous	ARHGAP24	NM_001025616.2,NM_001042669.1	,	694,2729,3080	GG,GA,AA		27.3488,40.059,31.6546	,	101/749,6/654	86844835	4117,8889	2203	4300	6503	SO:0001819	synonymous_variant	83478	exon4			TCATGAAAGCTAC	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.303A>G	4.37:g.86844835A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	37	CCDS34025.1																																																																																			A|0.669;G|0.331	0.331	strong		0.493	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
NOP56	10528	hgsc.bcm.edu	37	20	2633936	2633936	+	Silent	SNP	T	T	C	rs2073194	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:2633936T>C	ENST00000329276.5	+	3	621	c.105T>C	c.(103-105)tcT>tcC	p.S35S	SNORD110_ENST00000408189.1_RNA|SNORD86_ENST00000391196.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORA51_ENST00000606420.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	35					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TGGAGGAGTCTGTGCTCAACC	0.577													C|||	4313	0.861222	0.9228	0.8934	5008	,	,		18345	0.8462		0.8002	False		,,,				2504	0.8333				p.S35S		Atlas-SNP	.											.	NOP56	73	.	0			c.T105C						PASS	.	C		4014,392	196.4+/-220.7	1832,350,21	248.0	227.0	234.0		105	-0.8	1.0	20	dbSNP_96	234	6837,1763	319.1+/-314.0	2727,1383,190	no	coding-synonymous	NOP56	NM_006392.3		4559,1733,211	CC,CT,TT		20.5,8.897,16.5693		35/595	2633936	10851,2155	2203	4300	6503	SO:0001819	synonymous_variant	10528	exon3			GGAGTCTGTGCTC	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.105T>C	20.37:g.2633936T>C		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_006392	Q2M3T6|Q9NQ05	Silent	SNP	ENST00000329276.5	37	CCDS13030.1																																																																																			T|0.163;G|0.000;C|0.837;A|0.000	0.837	strong		0.577	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
OR5M11	219487	hgsc.bcm.edu	37	11	56310497	56310497	+	Silent	SNP	C	C	T	rs72913727	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56310497C>T	ENST00000528616.2	-	1	260	c.237G>A	c.(235-237)ccG>ccA	p.P79P		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						TCGACATCTGCGGGGTTGCAT	0.423													C|||	275	0.0549121	0.0265	0.0159	5008	,	,		23045	0.0942		0.0577	False		,,,				2504	0.0777				p.P79P		Atlas-SNP	.											OR5M11,right_upper_lobe,carcinoma,-1,1	OR5M11	60	1	0			c.G237A						PASS	.	C		121,4191		0,121,2035	119.0	118.0	119.0		237	-1.9	1.0	11	dbSNP_130	119	477,8067		14,449,3809	no	coding-synonymous	OR5M11	NM_001005245.1		14,570,5844	TT,TC,CC		5.5829,2.8061,4.6515		79/306	56310497	598,12258	2156	4272	6428	SO:0001819	synonymous_variant	219487	exon1			CATCTGCGGGGTT	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"""GPCR / Class A : Olfactory receptors"""	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.237G>A	11.37:g.56310497C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001005245	B2RNL5|B2RNL7	Silent	SNP	ENST00000528616.2	37	CCDS53629.1																																																																																			C|0.949;T|0.051	0.051	strong		0.423	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245	
CRNN	49860	hgsc.bcm.edu	37	1	152382120	152382120	+	Missense_Mutation	SNP	C	C	T	rs3829868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152382120C>T	ENST00000271835.3	-	3	1500	c.1438G>A	c.(1438-1440)Ggc>Agc	p.G480S	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	480			G -> S (in dbSNP:rs3829868).		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)			GCTGTGATGCCTCGCTTCTCT	0.537													C|||	1236	0.246805	0.0635	0.3689	5008	,	,		20964	0.4315		0.1441	False		,,,				2504	0.3231				p.G480S		Atlas-SNP	.											.	CRNN	78	.	0			c.G1438A						PASS	.	C	SER/GLY	363,4043	186.7+/-213.5	16,331,1856	180.0	138.0	152.0		1438	4.0	0.0	1	dbSNP_107	152	1307,7293	258.8+/-282.3	123,1061,3116	yes	missense	CRNN	NM_016190.2	56	139,1392,4972	TT,TC,CC		15.1977,8.2388,12.8402	benign	480/496	152382120	1670,11336	2203	4300	6503	SO:0001583	missense	49860	exon3			TGATGCCTCGCTT	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.1438G>A	1.37:g.152382120C>T	ENSP00000271835:p.Gly480Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	506	0.2316849816849817	31	0.06300813008130081	109	0.3011049723756906	256	0.44755244755244755	110	0.14511873350923482	C	12.77	2.037003	0.35893	0.082388	0.151977	ENSG00000143536	ENST00000271835	T	0.09163	3.01	4.92	4.01	0.46588	.	0.415407	0.21211	N	0.078302	T	0.03695	0.0105	L	0.37561	1.115	0.80722	P	0.0	B	0.27498	0.18	B	0.27380	0.079	T	0.20174	-1.0283	9	0.62326	D	0.03	.	8.9869	0.35999	0.0:0.9002:0.0:0.0998	rs3829868;rs52796135;rs58776316;rs3829868	480	Q9UBG3	CRNN_HUMAN	S	480	ENSP00000271835:G480S	ENSP00000271835:G480S	G	-	1	0	CRNN	150648744	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.082000	0.11304	1.289000	0.44618	0.650000	0.86243	GGC	C|0.821;T|0.179	0.179	strong		0.537	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190	
C14orf159	80017	hgsc.bcm.edu	37	14	91636532	91636532	+	Splice_Site	SNP	C	C	T	rs4900072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:91636532C>T	ENST00000523771.1	+	5	1044		c.e5+2		C14orf159_ENST00000518868.1_Missense_Mutation_p.A148V|C14orf159_ENST00000520328.1_Splice_Site|C14orf159_ENST00000523816.1_Splice_Site|C14orf159_ENST00000412671.2_Missense_Mutation_p.A148V|C14orf159_ENST00000256324.10_Missense_Mutation_p.A148V|C14orf159_ENST00000521077.2_Missense_Mutation_p.A148V|C14orf159_ENST00000428926.2_Splice_Site|C14orf159_ENST00000525393.2_Splice_Site_p.A19V|C14orf159_ENST00000522322.1_Splice_Site			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159							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)		CACAGCCAGGCGGGTGCATAC	0.592													C|||	837	0.167133	0.1036	0.2262	5008	,	,		18191	0.0585		0.3241	False		,,,				2504	0.1616				p.A148V		Atlas-SNP	.											.	C14orf159	57	.	0			c.C443T						PASS	.	C	,,VAL/ALA,,	711,3695	290.7+/-281.1	62,587,1554	37.0	37.0	37.0		,,443,,	-5.0	0.0	14	dbSNP_111	37	2897,5703	447.4+/-361.5	493,1911,1896	yes	splice-5,splice-5,missense,splice-5,splice-5	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,64,,	555,2498,3450	TT,TC,CC		33.686,16.1371,27.741	,,,,	,,148/622,,	91636532	3608,9398	2203	4300	6503	SO:0001630	splice_region_variant	80017	exon5			GCCAGGCGGGTGC	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.441+2C>T	14.37:g.91636532C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	425|425	0.1945970695970696|0.1945970695970696	51|51	0.10365853658536585|0.10365853658536585	88|88	0.2430939226519337|0.2430939226519337	36|36	0.06293706293706294|0.06293706293706294	250|250	0.32981530343007914|0.32981530343007914	C|C	1.312|1.312	-0.601802|-0.601802	0.03744|0.03744	0.161371|0.161371	0.33686|0.33686	ENSG00000133943|ENSG00000133943	ENST00000520328;ENST00000523816;ENST00000428926;ENST00000522322;ENST00000523771|ENST00000521334;ENST00000256324;ENST00000522170;ENST00000519950;ENST00000521077;ENST00000518868;ENST00000517518;ENST00000525393;ENST00000523894;ENST00000412671	.|T;T;T;T;T;T;T;T;T;T	.|0.49432	.|1.55;1.55;1.55;1.55;1.55;1.55;1.55;0.78;1.55;1.55	4.65|4.65	-5.0|-5.0	0.03001|0.03001	.|.	.|1.370970	.|0.04809	.|N	.|0.434989	.|T	.|0.00012	.|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;B	.|0.34226	.|0.443;0.022;0.004;0.004	.|B;B;B;B	.|0.36666	.|0.23;0.004;0.002;0.002	.|T	.|0.05937	.|-1.0855	.|9	.|0.02654	.|T	.|1	.|.	2.8008|2.8008	0.05414|0.05414	0.1309:0.1886:0.1299:0.5506|0.1309:0.1886:0.1299:0.5506	rs4900072;rs4900072|rs4900072;rs4900072	.|19;148;148;148	.|Q8NB88;B3KVU6;Q7Z3D6-2;Q7Z3D6-3	.|.;.;.;.	.|V	-1|148;148;148;148;148;148;148;19;148;148	.|ENSP00000430022:A148V;ENSP00000256324:A148V;ENSP00000430666:A148V;ENSP00000428296:A148V;ENSP00000430137:A148V;ENSP00000428263:A148V;ENSP00000428652:A148V;ENSP00000435459:A19V;ENSP00000429459:A148V;ENSP00000404196:A148V	.|ENSP00000256324:A148V	.|A	+|+	.|2	.|0	C14orf159|C14orf159	90706285|90706285	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	-0.492000|-0.492000	0.06467|0.06467	-0.830000|-0.830000	0.04262|0.04262	-0.258000|-0.258000	0.10820|0.10820	.|GCG	C|0.773;T|0.227	0.227	strong		0.592	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	Intron
CCDC85A	114800	hgsc.bcm.edu	37	2	56420006	56420006	+	Missense_Mutation	SNP	A	A	T	rs60028731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:56420006A>T	ENST00000407595.2	+	2	1173	c.671A>T	c.(670-672)cAc>cTc	p.H224L	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	224	His-rich.									breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGCCCGGACCACCACAAGCAC	0.697													A|||	421	0.0840655	0.0265	0.0504	5008	,	,		14315	0.1687		0.0746	False		,,,				2504	0.1084				p.H224L		Atlas-SNP	.											.	CCDC85A	70	.	0			c.A671T						PASS	.	A	LEU/HIS	103,4261		1,101,2080	25.0	35.0	32.0		671	5.2	1.0	2	dbSNP_129	32	562,7996		16,530,3733	yes	missense	CCDC85A	NM_001080433.1	99	17,631,5813	TT,TA,AA		6.567,2.3602,5.1463	probably-damaging	224/554	56420006	665,12257	2182	4279	6461	SO:0001583	missense	114800	exon2			CGGACCACCACAA	AB067499	CCDS46290.1	2p16.1	2006-03-29			ENSG00000055813	ENSG00000055813			29400	protein-coding gene	gene with protein product						11572484	Standard	NM_001080433		Approved	KIAA1912	uc002rzn.3	Q96PX6	OTTHUMG00000152033	ENST00000407595.2:c.671A>T	2.37:g.56420006A>T	ENSP00000384040:p.His224Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_001080433		Missense_Mutation	SNP	ENST00000407595.2	37	CCDS46290.1	188	0.08608058608058608	17	0.034552845528455285	24	0.06629834254143646	95	0.1660839160839161	52	0.06860158311345646	A	20.7	4.041324	0.75732	0.023602	0.06567	ENSG00000055813	ENST00000407595	.	.	.	5.18	5.18	0.71444	.	0.045599	0.85682	D	0.000000	T	0.00580	0.0019	M	0.62723	1.935	0.09310	P	1.0	D	0.76494	0.999	D	0.87578	0.998	T	0.08911	-1.0699	8	0.52906	T	0.07	1.2164	15.0278	0.71682	1.0:0.0:0.0:0.0	rs60028731	224	Q96PX6	CC85A_HUMAN	L	224	.	ENSP00000384040:H224L	H	+	2	0	CCDC85A	56273510	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	7.002000	0.76304	1.947000	0.56498	0.533000	0.62120	CAC	A|0.919;T|0.081	0.081	strong		0.697	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1		
KRT84	3890	hgsc.bcm.edu	37	12	52777580	52777580	+	Silent	SNP	A	A	C	rs386763043|rs1613929	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	95	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	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	
ZNF682	91120	hgsc.bcm.edu	37	19	20133846	20133846	+	Missense_Mutation	SNP	C	C	T	rs7255165	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:20133846C>T	ENST00000397165.2	-	3	353	c.193G>A	c.(193-195)Gtg>Atg	p.V65M	ZNF682_ENST00000358523.5_Missense_Mutation_p.V33M|ZNF682_ENST00000596019.1_Missense_Mutation_p.V65M|ZNF682_ENST00000397162.1_Missense_Mutation_p.V33M|ZNF682_ENST00000593468.1_Missense_Mutation_p.V65M|ZNF682_ENST00000595736.1_Intron|ZNF682_ENST00000597972.1_Missense_Mutation_p.V71M	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	65	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> M (in dbSNP:rs7255165).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TGTCTCTTCACATTCCAGGGC	0.453													N|||	1041	0.207867	0.3578	0.2003	5008	,	,		18567	0.0744		0.1759	False		,,,				2504	0.181				p.V65M		Atlas-SNP	.											.	ZNF682	51	.	0			c.G193A						PASS	.	C	MET/VAL,MET/VAL	1446,2768		257,932,918	152.0	159.0	156.0		97,193	0.9	0.3	19	dbSNP_116	156	1421,7093		132,1157,2968	yes	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	21,21	389,2089,3886	TT,TC,CC		16.6902,34.3142,22.5251	benign,benign	33/467,65/499	20133846	2867,9861	2107	4257	6364	SO:0001583	missense	91120	exon3			TCTTCACATTCCA	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.193G>A	19.37:g.20133846C>T	ENSP00000380351:p.Val65Met	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	149	62	0.416107	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	430	0.19688644688644688	168	0.34146341463414637	80	0.22099447513812154	39	0.06818181818181818	143	0.18865435356200527	c	0.634	-0.816113	0.02776	0.343142	0.166902	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000358523	T;T;T	0.06371	3.43;3.31;3.31	0.898	0.898	0.19264	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	L	0.43646	1.37	0.80722	P	0.0	B	0.12013	0.005	B	0.08055	0.003	T	0.46830	-0.9163	8	0.02654	T	1	.	4.929	0.13907	0.0:1.0:0.0:0.0	rs7255165;rs52797555;rs7255165	65	O95780	ZN682_HUMAN	M	65;33;33	ENSP00000380351:V65M;ENSP00000380348:V33M;ENSP00000351324:V33M	ENSP00000351324:V33M	V	-	1	0	ZNF682	19994846	0.051000	0.20477	0.300000	0.25030	0.305000	0.27757	0.727000	0.25999	0.284000	0.22305	0.289000	0.19496	GTG	C|0.801;T|0.199	0.199	strong		0.453	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
DIDO1	11083	hgsc.bcm.edu	37	20	61538601	61538601	+	Silent	SNP	C	C	T	rs34820000	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61538601C>T	ENST00000266070.4	-	5	1597	c.1272G>A	c.(1270-1272)gcG>gcA	p.A424A	DIDO1_ENST00000370371.4_Silent_p.A424A|DIDO1_ENST00000370366.1_Silent_p.A424A|DIDO1_ENST00000354665.4_Silent_p.A424A|DIDO1_ENST00000370368.1_Silent_p.A424A|DIDO1_ENST00000395335.2_Silent_p.A424A|DIDO1_ENST00000395343.1_Silent_p.A424A|DIDO1_ENST00000395340.1_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	239	0	0		WXS	Illumina HiSeq	Phase_I	237	118	0.49789	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	
FAM214A	56204	hgsc.bcm.edu	37	15	52905882	52905882	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52905882G>A	ENST00000261844.7	-	3	341	c.189C>T	c.(187-189)gaC>gaT	p.D63D	FAM214A_ENST00000546305.2_Silent_p.D70D	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	63																	GGGCCAGCTTGTCACTACATT	0.368																																					p.D63D		Atlas-SNP	.											.	.	.	.	0			c.C189T						PASS	.						125.0	117.0	119.0					15																	52905882		1915	4142	6057	SO:0001819	synonymous_variant	56204	exon3			CAGCTTGTCACTA	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.189C>T	15.37:g.52905882G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	97	32	0.329897	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			.	.	none		0.368	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
EMC1	23065	hgsc.bcm.edu	37	1	19565338	19565338	+	Missense_Mutation	SNP	C	C	T	rs709682	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19565338C>T	ENST00000477853.1	-	10	1082	c.1040G>A	c.(1039-1041)aGt>aAt	p.S347N	EMC1_ENST00000375208.3_Missense_Mutation_p.S325N|RP1-43E13.2_ENST00000437898.1_RNA|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						PASS	.	T	ASN/SER	1304,3102	697.9+/-406.3	204,896,1103	124.0	132.0	129.0		1040	-0.3	0.5	1	dbSNP_86	129	1192,7408	764.2+/-407.6	96,1000,3204	yes	missense	KIAA0090	NM_015047.1	46	300,1896,4307	TT,TC,CC		13.8605,29.596,19.1911	benign	347/994	19565338	2496,10510	2203	4300	6503	SO:0001583	missense	23065	exon10			TCAGAACTGCTAC		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"""KIAA0090"""	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.1040G>A	1.37:g.19565338C>T	ENSP00000420608:p.Ser347Asn	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	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	
PODXL2	50512	hgsc.bcm.edu	37	3	127379270	127379270	+	Silent	SNP	C	C	T	rs920232	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:127379270C>T	ENST00000342480.6	+	3	438	c.399C>T	c.(397-399)acC>acT	p.T133T		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	133	O-glycosylated at one site.				leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						TTGAAGACACCAGCCAGGCTC	0.473													C|||	846	0.16893	0.1755	0.1744	5008	,	,		20261	0.1766		0.1392	False		,,,				2504	0.1789				p.T133T		Atlas-SNP	.											.	PODXL2	53	.	0			c.C399T						PASS	.	C		690,3716	290.1+/-280.8	62,566,1575	83.0	77.0	79.0		399	-1.6	0.0	3	dbSNP_86	79	1384,7216	268.3+/-287.8	108,1168,3024	no	coding-synonymous	PODXL2	NM_015720.2		170,1734,4599	TT,TC,CC		16.093,15.6605,15.9465		133/606	127379270	2074,10932	2203	4300	6503	SO:0001819	synonymous_variant	50512	exon3			AGACACCAGCCAG	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.399C>T	3.37:g.127379270C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	160	91	0.56875	NM_015720	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	37	CCDS3044.1																																																																																			C|0.837;T|0.163	0.163	strong		0.473	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
TIMM13	26517	hgsc.bcm.edu	37	19	2427266	2427266	+	Silent	SNP	G	G	A	rs968688	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2427266G>A	ENST00000215570.3	-	2	537	c.177C>T	c.(175-177)gaC>gaT	p.D59D	LMNB2_ENST00000475819.1_5'Flank|TIMM13_ENST00000591871.1_Silent_p.D44D	NM_012458.2	NP_036590.1	Q9Y5L4	TIM13_HUMAN	translocase of inner mitochondrial membrane 13 homolog (yeast)	59					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space protein transporter complex (GO:0042719)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	zinc ion binding (GO:0008270)			endometrium(1)|prostate(1)	2		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)		GCTCGGAGTTGTCCAGGGAGC	0.652													G|||	633	0.126398	0.1324	0.0634	5008	,	,		14183	0.2371		0.0398	False		,,,				2504	0.138				p.D59D		Atlas-SNP	.											.	TIMM13	7	.	0			c.C177T						PASS	.	G		557,3849	249.0+/-256.6	44,469,1690	96.0	113.0	107.0		177	-0.1	1.0	19	dbSNP_86	107	372,8228	122.4+/-181.4	3,366,3931	no	coding-synonymous	TIMM13	NM_012458.2		47,835,5621	AA,AG,GG		4.3256,12.6419,7.1429		59/96	2427266	929,12077	2203	4300	6503	SO:0001819	synonymous_variant	26517	exon2			GGAGTTGTCCAGG	AF152352	CCDS12089.1	19p13.3	2008-07-04	2001-11-28	2002-03-17		ENSG00000099800			11816	protein-coding gene	gene with protein product		607383	"""translocase of inner mitochondrial membrane 13 (yeast) homolog B"""	TIMM13B		10552927, 17329230	Standard	NM_012458		Approved	Tim13	uc002lvx.1	Q9Y5L4		ENST00000215570.3:c.177C>T	19.37:g.2427266G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	19	0.333333	NM_012458	P62206|Q9UHL8|Q9WTL1	Silent	SNP	ENST00000215570.3	37	CCDS12089.1																																																																																			G|0.910;T|0.000	.	strong		0.652	TIMM13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451333.1		
CWC27	10283	hgsc.bcm.edu	37	5	64267595	64267595	+	Silent	SNP	T	T	C	rs2278351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:64267595T>C	ENST00000381070.3	+	12	1325	c.1108T>C	c.(1108-1110)Ttg>Ctg	p.L370L	CWC27_ENST00000545000.1_3'UTR	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	370					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						GTATGAAGCTTTGAGGAAGCA	0.373													T|||	1700	0.339457	0.4123	0.1772	5008	,	,		16092	0.4653		0.2435	False		,,,				2504	0.3252				p.L370L		Atlas-SNP	.											.	CWC27	47	.	0			c.T1108C						PASS	.	T		1483,2923	473.1+/-356.6	265,953,985	61.0	63.0	62.0		1108	1.0	1.0	5	dbSNP_100	62	1995,6605	347.4+/-326.6	240,1515,2545	no	coding-synonymous	CWC27	NM_005869.2		505,2468,3530	CC,CT,TT		23.1977,33.6586,26.7415		370/473	64267595	3478,9528	2203	4300	6503	SO:0001819	synonymous_variant	10283	exon12			GAAGCTTTGAGGA	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"""serologically defined colon cancer antigen 10"""	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.1108T>C	5.37:g.64267595T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	198	102	0.515152	NM_005869	O60529|O60530|Q96EM3	Silent	SNP	ENST00000381070.3	37	CCDS3982.2																																																																																			T|0.708;C|0.292	0.292	strong		0.373	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
GTF3C4	9329	hgsc.bcm.edu	37	9	135554566	135554566	+	Silent	SNP	G	G	A	rs371169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:135554566G>A	ENST00000372146.4	+	2	2124	c.1560G>A	c.(1558-1560)gaG>gaA	p.E520E	GTF3C4_ENST00000483873.2_3'UTR	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	520					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)	p.E520E(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		CCTTTGAAGAGGCAGCTGCTC	0.423													G|||	2568	0.51278	0.6498	0.4971	5008	,	,		19032	0.5714		0.4036	False		,,,				2504	0.3906				p.E520E	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											GTF3C4,colon,carcinoma,0,1	GTF3C4	53	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1560A						PASS	.	G		2680,1726	621.6+/-393.8	821,1038,344	75.0	84.0	81.0		1560	4.7	1.0	9	dbSNP_80	81	3325,5275	480.4+/-370.4	636,2053,1611	no	coding-synonymous	GTF3C4	NM_012204.2		1457,3091,1955	AA,AG,GG		38.6628,39.1739,46.171		520/823	135554566	6005,7001	2203	4300	6503	SO:0001819	synonymous_variant	9329	exon2			TGAAGAGGCAGCT	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""General transcription factors"""	4667	protein-coding gene	gene with protein product		604892	"""general transcription factor IIIC, polypeptide 4 (90kD)"""			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.1560G>A	9.37:g.135554566G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	168	92	0.547619	NM_012204	Q5VZJ7	Silent	SNP	ENST00000372146.4	37	CCDS6953.1																																																																																			G|0.531;A|0.469	0.469	strong		0.423	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1		
SCRIB	23513	hgsc.bcm.edu	37	8	144873475	144873475	+	Missense_Mutation	SNP	G	G	A	rs146664605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144873475G>A	ENST00000320476.3	-	36	4757	c.4751C>T	c.(4750-4752)cCg>cTg	p.P1584L	RP11-429J17.8_ENST00000532625.1_RNA|RP11-429J17.8_ENST00000534089.1_RNA|RP11-429J17.8_ENST00000527139.1_RNA|SCRIB_ENST00000546337.1_5'Flank|SCRIB_ENST00000356994.2_Missense_Mutation_p.P1609L|SCRIB_ENST00000377533.3_Missense_Mutation_p.P1503L	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1584					activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CTCCTCCTGCGGGCCTGGAGG	0.701													G|||	22	0.00439297	0.0	0.0072	5008	,	,		16816	0.0		0.007	False		,,,				2504	0.0102				p.P1609L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C4826T						PASS	.	G	LEU/PRO,LEU/PRO	23,4357		0,23,2167	21.0	22.0	22.0		4751,4826	0.9	0.5	8	dbSNP_134	22	167,8405		1,165,4120	yes	missense,missense	SCRIB	NM_015356.3,NM_182706.3	98,98	1,188,6287	AA,AG,GG		1.9482,0.5251,1.467	benign,benign	1584/1631,1609/1656	144873475	190,12762	2190	4286	6476	SO:0001583	missense	23513	exon37			TCCTGCGGGCCTG	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.4751C>T	8.37:g.144873475G>A	ENSP00000322938:p.Pro1584Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_182706	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	2.254	-0.370931	0.05034	0.005251	0.019482	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.34472	1.56;1.53;1.36	4.45	0.933	0.19471	.	.	.	.	.	T	0.04182	0.0116	N	0.01267	-0.92	0.27060	N	0.963571	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.32402	-0.9908	9	0.06757	T	0.87	.	2.6901	0.05118	0.4335:0.2621:0.3044:0.0	.	1584;1609;1503	Q14160;Q14160-3;Q14160-2	SCRIB_HUMAN;.;.	L	1609;1584;1503	ENSP00000349486:P1609L;ENSP00000322938:P1584L;ENSP00000366756:P1503L	ENSP00000322938:P1584L	P	-	2	0	SCRIB	144945463	0.007000	0.16637	0.531000	0.27976	0.692000	0.40212	-0.102000	0.10956	0.327000	0.23409	0.486000	0.48141	CCG	G|0.990;A|0.010	0.010	strong		0.701	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
SSTR5	6755	hgsc.bcm.edu	37	16	1129872	1129872	+	Missense_Mutation	SNP	C	C	T	rs169068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1129872C>T	ENST00000293897.4	+	1	1092	c.1004C>T	c.(1003-1005)cCg>cTg	p.P335L	SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000397547.2_Missense_Mutation_p.P335L|SSTR5_ENST00000562758.1_Intron	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	335			P -> L (in dbSNP:rs169068). {ECO:0000269|PubMed:11157797, ECO:0000269|PubMed:15616553}.		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)	GCCACGGAGCCGCGTCCAGAC	0.657													C|||	2595	0.518171	0.3366	0.5562	5008	,	,		15310	0.8085		0.5427	False		,,,				2504	0.4121				p.P335L		Atlas-SNP	.											.	SSTR5	36	.	0			c.C1004T						PASS	.	C	LEU/PRO,LEU/PRO	1671,2691	488.8+/-361.3	321,1029,831	31.0	29.0	30.0		1004,1004	2.2	0.6	16	dbSNP_79	30	4627,3955	576.5+/-390.4	1266,2095,930	yes	missense,missense	SSTR5	NM_001053.3,NM_001172560.1	98,98	1587,3124,1761	TT,TC,CC		46.0848,38.3081,48.6557	benign,benign	335/365,335/365	1129872	6298,6646	2181	4291	6472	SO:0001583	missense	6755	exon2			CGGAGCCGCGTCC	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.1004C>T	16.37:g.1129872C>T	ENSP00000293897:p.Pro335Leu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001172560	P34988|Q541E0|Q9UJI5	Missense_Mutation	SNP	ENST00000293897.4	37	CCDS10429.1	1229	0.5627289377289377	149	0.30284552845528456	197	0.5441988950276243	463	0.8094405594405595	420	0.554089709762533	C	3.347	-0.133417	0.06711	0.383081	0.539152	ENSG00000162009	ENST00000397547;ENST00000293897	T;T	0.71698	-0.59;-0.59	4.49	2.24	0.28232	.	0.636775	0.16012	N	0.233745	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B	0.21381	0.055	B	0.14578	0.011	T	0.37641	-0.9697	9	0.23891	T	0.37	.	6.5926	0.22656	0.2905:0.6025:0.0:0.107	rs169068;rs642192;rs169068	335	P35346	SSR5_HUMAN	L	335	ENSP00000380680:P335L;ENSP00000293897:P335L	ENSP00000293897:P335L	P	+	2	0	SSTR5	1069873	0.045000	0.20229	0.589000	0.28718	0.066000	0.16364	0.488000	0.22371	0.883000	0.36040	0.561000	0.74099	CCG	C|0.484;T|0.516	0.516	strong		0.657	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058060	46058060	+	Silent	SNP	C	C	T	rs13051517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46058060C>T	ENST00000380095.1	+	1	788	c.726C>T	c.(724-726)agC>agT	p.S242S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	242						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCTGCTACAGCCTCTGCTCTG	0.687													C|||	1782	0.355831	0.2799	0.4813	5008	,	,		18886	0.3333		0.4364	False		,,,				2504	0.3098				p.S242S		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C726T						PASS	.	C	,	1303,3099	389.3+/-327.3	187,929,1085	37.0	41.0	40.0		,726	2.0	0.0	21	dbSNP_121	40	3267,5325	463.0+/-365.8	638,1991,1667	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	825,2920,2752	TT,TC,CC		38.0237,29.6002,35.1701	,	,242/252	46058060	4570,8424	2201	4296	6497	SO:0001819	synonymous_variant	353333	exon1			CTACAGCCTCTGC	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.726C>T	21.37:g.46058060C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	163	80	0.490798	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			T|1.000;|0.000	1.000	weak		0.687	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
SYNPR	132204	hgsc.bcm.edu	37	3	63600905	63600905	+	Silent	SNP	T	T	C	rs150251873	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:63600905T>C	ENST00000295894.5	+	5	915	c.546T>C	c.(544-546)ttT>ttC	p.F182F	SYNPR_ENST00000479198.1_3'UTR|SYNPR_ENST00000478300.1_Silent_p.F202F|SYNPR_ENST00000460711.1_Silent_p.F193F|SYNPR_ENST00000465156.1_Silent_p.F118F	NM_144642.4	NP_653243.1	Q8TBG9	SYNPR_HUMAN	synaptoporin	182	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					cell junction (GO:0030054)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)	transporter activity (GO:0005215)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		TTCAGGTCTTTGGATTCTTGA	0.378													T|||	12	0.00239617	0.0	0.0029	5008	,	,		18918	0.0		0.002	False		,,,				2504	0.0082				p.F202F	NSCLC(29;1052 1116 20025 32519)	Atlas-SNP	.											.	SYNPR	38	.	0			c.T606C						PASS	.	T	,	2,3622		0,2,1810	45.0	40.0	41.0		606,546	-1.4	1.0	3	dbSNP_134	41	5,8139		0,5,4067	yes	coding-synonymous,coding-synonymous	SYNPR	NM_001130003.1,NM_144642.4	,	0,7,5877	CC,CT,TT		0.0614,0.0552,0.0595	,	202/286,182/266	63600905	7,11761	1812	4072	5884	SO:0001819	synonymous_variant	132204	exon6			GGTCTTTGGATTC	AF411860	CCDS46859.1, CCDS46860.1	3p14.3	2011-07-28			ENSG00000163630	ENSG00000163630			16507	protein-coding gene	gene with protein product						8034131, 12974474	Standard	NM_144642		Approved	MGC26651, SPO	uc003dlp.3	Q8TBG9	OTTHUMG00000158699	ENST00000295894.5:c.546T>C	3.37:g.63600905T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	186	103	0.553763	NM_001130003	B2R675|G5E9W4	Silent	SNP	ENST00000295894.5	37	CCDS46860.1																																																																																			T|0.998;C|0.002	0.002	strong		0.378	SYNPR-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351787.1		
ZDBF2	57683	hgsc.bcm.edu	37	2	207173390	207173390	+	Missense_Mutation	SNP	G	G	A	rs79484112	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:207173390G>A	ENST00000374423.3	+	5	4524	c.4138G>A	c.(4138-4140)Gag>Aag	p.E1380K		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1380							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGCAGCAGATGAGCTTCAAAA	0.373													G|||	52	0.0103834	0.0015	0.0115	5008	,	,		19713	0.0		0.0268	False		,,,				2504	0.0153				p.E1380K		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G4138A						PASS	.	G	LYS/GLU	30,3630		1,28,1801	46.0	44.0	45.0		4138	2.9	0.0	2	dbSNP_132	45	301,7895		11,279,3808	yes	missense	ZDBF2	NM_020923.1	56	12,307,5609	AA,AG,GG		3.6725,0.8197,2.7918	benign	1380/2355	207173390	331,11525	1830	4098	5928	SO:0001583	missense	57683	exon5			GCAGATGAGCTTC	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.4138G>A	2.37:g.207173390G>A	ENSP00000363545:p.Glu1380Lys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	27	0.012362637362637362	0	0.0	3	0.008287292817679558	0	0.0	24	0.0316622691292876	G	8.967	0.972082	0.18736	0.008197	0.036725	ENSG00000204186	ENST00000374423	T	0.43294	0.95	3.76	2.87	0.33458	.	.	.	.	.	T	0.04724	0.0128	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13764	-1.0497	9	0.11182	T	0.66	.	9.2517	0.37560	0.0:0.7634:0.2366:0.0	.	1380	Q9HCK1	ZDBF2_HUMAN	K	1380	ENSP00000363545:E1380K	ENSP00000363545:E1380K	E	+	1	0	ZDBF2	206881635	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.709000	0.25734	1.155000	0.42497	-0.171000	0.13296	GAG	G|0.981;A|0.019	0.019	strong		0.373	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
SPTBN4	57731	hgsc.bcm.edu	37	19	41038574	41038574	+	Missense_Mutation	SNP	G	G	A	rs814501	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41038574G>A	ENST00000352632.3	+	19	4077	c.3991G>A	c.(3991-3993)Ggc>Agc	p.G1331S	SPTBN4_ENST00000595535.1_Missense_Mutation_p.G1331S|SPTBN4_ENST00000598249.1_Missense_Mutation_p.G1331S|SPTBN4_ENST00000392025.1_Missense_Mutation_p.G74S|SPTBN4_ENST00000338932.3_Missense_Mutation_p.G1331S|SPTBN4_ENST00000392023.1_Missense_Mutation_p.G7S			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1331			G -> S (in dbSNP:rs814501). {ECO:0000269|PubMed:11294830}.		actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGCGCGGGATGGCACGCGGGA	0.607													G|||	1616	0.322684	0.441	0.2867	5008	,	,		18358	0.0595		0.4722	False		,,,				2504	0.3057				p.G1331S		Atlas-SNP	.											.	SPTBN4	213	.	0			c.G3991A						PASS	.	G	SER/GLY,SER/GLY	1933,2473	550.2+/-378.0	414,1105,684	76.0	64.0	68.0		3991,19	2.6	1.0	19	dbSNP_86	68	4448,4152	589.0+/-392.4	1121,2206,973	yes	missense,missense	SPTBN4	NM_020971.2,NM_025213.2	56,56	1535,3311,1657	AA,AG,GG		48.2791,43.872,49.062	benign,benign	1331/2565,7/679	41038574	6381,6625	2203	4300	6503	SO:0001583	missense	57731	exon19			CGGGATGGCACGC	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.3991G>A	19.37:g.41038574G>A	ENSP00000263373:p.Gly1331Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	757	0.3466117216117216	242	0.491869918699187	119	0.3287292817679558	34	0.05944055944055944	362	0.47757255936675463	G	9.364	1.068837	0.20147	0.43872	0.517209	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025;ENST00000392023	T;T;T;T	0.58358	0.78;0.78;0.78;0.34	4.86	2.62	0.31277	.	0.275219	0.29152	N	0.012981	T	0.00012	0.0000	N	0.12569	0.235	0.34208	P	0.32599599999999995	B;B;P;B;P;B	0.48089	0.057;0.041;0.659;0.004;0.905;0.033	B;B;B;B;B;B	0.43331	0.032;0.016;0.228;0.008;0.416;0.104	T	0.44574	-0.9319	9	0.31617	T	0.26	.	7.6838	0.28528	0.2814:0.0:0.7185:0.0	rs814501;rs52802515;rs814501	1331;74;74;7;1331;1331	E9PDB1;Q9H254-3;C9JY79;E9PGQ5;Q9H254;Q71S06	.;.;.;.;SPTN4_HUMAN;.	S	1331;1331;1331;74;7	ENSP00000263373:G1331S;ENSP00000340345:G1331S;ENSP00000375879:G74S;ENSP00000375877:G7S	ENSP00000340345:G1331S	G	+	1	0	SPTBN4	45730414	0.983000	0.35010	0.986000	0.45419	0.993000	0.82548	1.662000	0.37418	1.252000	0.44001	0.561000	0.74099	GGC	G|0.572;A|0.428	0.428	strong		0.607	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
OR10A6	390093	hgsc.bcm.edu	37	11	7949707	7949707	+	Missense_Mutation	SNP	A	A	G	rs111488559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7949707A>G	ENST00000309838.2	-	1	502	c.503T>C	c.(502-504)tTt>tCt	p.F168S		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAGGCCACAAAAGGGAAAACT	0.328													A|||	92	0.0183706	0.0015	0.0648	5008	,	,		19130	0.0		0.0258	False		,,,				2504	0.0194				p.F168S		Atlas-SNP	.											.	OR10A6	49	.	0			c.T503C						PASS	.	A	SER/PHE	43,4359	41.6+/-74.8	0,43,2158	41.0	44.0	43.0		503	3.2	1.0	11	dbSNP_132	43	338,8252	113.1+/-173.2	14,310,3971	yes	missense	OR10A6	NM_001004461.1	155	14,353,6129	GG,GA,AA		3.9348,0.9768,2.9326	possibly-damaging	168/315	7949707	381,12611	2201	4295	6496	SO:0001583	missense	390093	exon1			CCACAAAAGGGAA	AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"""GPCR / Class A : Olfactory receptors"""	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.503T>C	11.37:g.7949707A>G	ENSP00000312470:p.Phe168Ser	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_001004461	Q6IF59	Missense_Mutation	SNP	ENST00000309838.2	37	CCDS31420.1	34	0.015567765567765568	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	16	0.021108179419525065	A	12.07	1.828003	0.32329	0.009768	0.039348	ENSG00000175393	ENST00000309838	T	0.00193	8.58	4.41	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000440	T	0.00178	0.0005	H	0.94183	3.505	0.28076	N	0.93237	D	0.57899	0.981	P	0.58077	0.832	T	0.17018	-1.0383	10	0.87932	D	0	.	7.0241	0.24930	0.615:0.0:0.0:0.3849	.	168	Q8NH74	O10A6_HUMAN	S	168	ENSP00000312470:F168S	ENSP00000312470:F168S	F	-	2	0	OR10A6	7906283	0.999000	0.42202	0.997000	0.53966	0.171000	0.22731	1.052000	0.30429	0.792000	0.33850	0.533000	0.62120	TTT	A|0.976;G|0.024	0.024	strong		0.328	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461	
ERCC1	2067	hgsc.bcm.edu	37	19	45922389	45922389	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45922389G>C	ENST00000300853.3	-	5	1083	c.492C>G	c.(490-492)ttC>ttG	p.F164L	ERCC1_ENST00000340192.7_Missense_Mutation_p.F164L|ERCC1_ENST00000013807.5_Missense_Mutation_p.F164L|ERCC1_ENST00000591636.1_Missense_Mutation_p.F164L|ERCC1_ENST00000423698.2_Missense_Mutation_p.F92L|ERCC1_ENST00000589165.1_Missense_Mutation_p.F164L	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	164					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)		CCCGCAAGGCGAAGTTCTTCC	0.627								Nucleotide excision repair (NER)																													p.F164L		Atlas-SNP	.											.	ERCC1	46	.	0			c.C492G						PASS	.						68.0	55.0	59.0					19																	45922389		2202	4299	6501	SO:0001583	missense	2067	exon5			CAAGGCGAAGTTC		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.492C>G	19.37:g.45922389G>C	ENSP00000300853:p.Phe164Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499600	0.64298	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807	T;T;T;T	0.44482	0.94;0.92;0.95;0.92	4.71	1.33	0.21861	Restriction endonuclease, type II-like (1);	0.170692	0.51477	D	0.000090	T	0.47154	0.1430	M	0.74258	2.255	0.48040	D	0.999578	D;D;P;P	0.60575	0.984;0.988;0.898;0.95	P;B;B;B	0.50537	0.643;0.441;0.344;0.426	T	0.47699	-0.9097	10	0.72032	D	0.01	-17.7424	7.097	0.25315	0.3011:0.0:0.6989:0.0	.	164;92;164;164	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	L	164;164;92;164	ENSP00000300853:F164L;ENSP00000345203:F164L;ENSP00000394875:F92L;ENSP00000013807:F164L	ENSP00000013807:F164L	F	-	3	2	ERCC1	50614229	1.000000	0.71417	0.995000	0.50966	0.977000	0.68977	0.770000	0.26618	0.418000	0.25898	0.462000	0.41574	TTC	.	.	none		0.627	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
TAF5L	27097	hgsc.bcm.edu	37	1	229738170	229738170	+	Silent	SNP	T	T	G	rs3753886	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:229738170T>G	ENST00000366676.1	-	3	743	c.744A>C	c.(742-744)cgA>cgC	p.R248R	TAF5L_ENST00000258281.2_Silent_p.R248R|TAF5L_ENST00000366675.3_Silent_p.R248R			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	248					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CATCCTTGACTCGCTTAATGC	0.552													G|||	2873	0.573682	0.4887	0.5447	5008	,	,		19925	0.7639		0.5179	False		,,,				2504	0.5706				p.R248R		Atlas-SNP	.											.	TAF5L	76	.	0			c.A744C						PASS	.	G	,	2246,2160	581.4+/-385.4	571,1104,528	91.0	90.0	90.0		744,744	-11.6	0.0	1	dbSNP_107	90	4407,4193	569.8+/-389.2	1100,2207,993	no	coding-synonymous,coding-synonymous	TAF5L	NM_001025247.1,NM_014409.3	,	1671,3311,1521	GG,GT,TT		48.7558,49.0241,48.8467	,	248/326,248/590	229738170	6653,6353	2203	4300	6503	SO:0001819	synonymous_variant	27097	exon4			CTTGACTCGCTTA	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"""WD repeat domain containing"""	17304	protein-coding gene	gene with protein product	"""PCAF associated factor 65 beta"""		"""TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.744A>C	1.37:g.229738170T>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	174	80	0.45977	NM_001025247	Q5TDI5|Q5TDI6|Q8IW31	Silent	SNP	ENST00000366676.1	37	CCDS1581.1																																																																																			T|0.456;G|0.544	0.544	strong		0.552	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409	
TANGO6	79613	hgsc.bcm.edu	37	16	68893953	68893953	+	Silent	SNP	T	T	C	rs4597312	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:68893953T>C	ENST00000261778.1	+	2	273	c.261T>C	c.(259-261)tcT>tcC	p.S87S		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	87						integral component of membrane (GO:0016021)											CACAAAACTCTGTGGATGTCA	0.428													T|||	405	0.0808706	0.0756	0.0663	5008	,	,		20015	0.0883		0.1183	False		,,,				2504	0.0521				p.S87S		Atlas-SNP	.											.	.	.	.	0			c.T261C						PASS	.	T		318,3472		9,300,1586	122.0	115.0	117.0		261	0.3	1.0	16	dbSNP_111	117	1020,7232		65,890,3171	no	coding-synonymous	TMCO7	NM_024562.1		74,1190,4757	CC,CT,TT		12.3606,8.3905,11.1111		87/1095	68893953	1338,10704	1895	4126	6021	SO:0001819	synonymous_variant	79613	exon2			AAACTCTGTGGAT		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 7"""	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.261T>C	16.37:g.68893953T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	196	88	0.44898	NM_024562	Q569F9|Q9H9K1	Silent	SNP	ENST00000261778.1	37	CCDS45516.1																																																																																			T|0.895;C|0.105	0.105	strong		0.428	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2	
RP1	6101	hgsc.bcm.edu	37	8	55541617	55541617	+	Silent	SNP	A	A	G	rs441800	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:55541617A>G	ENST00000220676.1	+	4	5323	c.5175A>G	c.(5173-5175)caA>caG	p.Q1725Q		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1725					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)			GTACAAAACAAAATGATGATA	0.403													A|||	1206	0.240815	0.056	0.2709	5008	,	,		22859	0.4415		0.2604	False		,,,				2504	0.2423				p.Q1725Q	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A5175G						PASS	.	A		404,4002	199.1+/-222.7	20,364,1819	127.0	123.0	125.0		5175	0.9	0.0	8	dbSNP_80	125	2200,6400	373.5+/-337.0	274,1652,2374	no	coding-synonymous	RP1	NM_006269.1		294,2016,4193	GG,GA,AA		25.5814,9.1693,20.0215		1725/2157	55541617	2604,10402	2203	4300	6503	SO:0001819	synonymous_variant	6101	exon4			AAAACAAAATGAT	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.5175A>G	8.37:g.55541617A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_006269		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			A|0.776;G|0.224	0.224	strong		0.403	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
C1RL	51279	hgsc.bcm.edu	37	12	7249598	7249598	+	Missense_Mutation	SNP	T	T	C	rs3742089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:7249598T>C	ENST00000266542.4	-	6	945	c.853A>G	c.(853-855)Atc>Gtc	p.I285V	C1RL_ENST00000504702.2_Intron|C1RL_ENST00000545280.1_Intron|C1RL_ENST00000544702.1_Silent_p.P300P	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	285	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		I -> V (in dbSNP:rs3742089). {ECO:0000269|PubMed:15358180}.		complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTGGGGTAGATGGTGTGGGCA	0.587													T|||	2167	0.432708	0.4879	0.4914	5008	,	,		-128	0.3264		0.3171	False		,,,				2504	0.545				p.I285V		Atlas-SNP	.											.	C1RL	39	.	0			c.A853G						PASS	.	T	VAL/ILE	2121,2285	575.9+/-384.1	521,1079,603	117.0	96.0	103.0		853	0.9	1.0	12	dbSNP_107	103	3097,5503	474.3+/-368.8	544,2009,1747	no	missense	C1RL	NM_016546.2	29	1065,3088,2350	CC,CT,TT		36.0116,48.1389,40.1199	benign	285/488	7249598	5218,7788	2203	4300	6503	SO:0001583	missense	51279	exon6			GGTAGATGGTGTG	AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.853A>G	12.37:g.7249598T>C	ENSP00000266542:p.Ile285Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	133	66	0.496241	NM_016546	Q53GX9	Missense_Mutation	SNP	ENST00000266542.4	37	CCDS8573.1	825|825	0.37774725274725274|0.37774725274725274	255|255	0.5182926829268293|0.5182926829268293	164|164	0.4530386740331492|0.4530386740331492	173|173	0.30244755244755245|0.30244755244755245	233|233	0.3073878627968338|0.3073878627968338	T|T	8.944|8.944	0.966637|0.966637	0.18659|0.18659	0.481389|0.481389	0.360116|0.360116	ENSG00000139178|ENSG00000139178	ENST00000534950|ENST00000266542;ENST00000396661	.|D	.|0.86865	.|-2.18	4.94|4.94	0.886|0.886	0.19194|0.19194	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03903|0.03903	-0.33|-0.33	0.09310|0.09310	P|P	0.9999999999998921|0.9999999999998921	.|B	.|0.34349	.|0.45	.|B	.|0.38056	.|0.264	T|T	0.28681|0.28681	-1.0036|-1.0036	4|8	.|0.07482	.|T	.|0.82	.|.	5.1861|5.1861	0.15185|0.15185	0.0:0.1986:0.1565:0.6449|0.0:0.1986:0.1565:0.6449	rs3742089;rs17791022;rs60820280;rs3742089|rs3742089;rs17791022;rs60820280;rs3742089	.|285	.|Q9NZP8	.|C1RL_HUMAN	R|V	117|285	.|ENSP00000266542:I285V	.|ENSP00000266542:I285V	H|I	-|-	2|1	0|0	C1RL|C1RL	7140740|7140740	0.029000|0.029000	0.19370|0.19370	0.983000|0.983000	0.44433|0.44433	0.806000|0.806000	0.45545|0.45545	-0.914000|-0.914000	0.04038|0.04038	0.290000|0.290000	0.22444|0.22444	0.414000|0.414000	0.27820|0.27820	CAT|ATC	T|0.606;C|0.393	0.393	strong		0.587	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546	
TTN	7273	hgsc.bcm.edu	37	2	179454394	179454394	+	Silent	SNP	A	A	G	rs1560221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179454394A>G	ENST00000591111.1	-	254	57359	c.57135T>C	c.(57133-57135)taT>taC	p.Y19045Y	TTN_ENST00000589042.1_Silent_p.Y20686Y|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Silent_p.Y11746Y|TTN_ENST00000460472.2_Silent_p.Y11621Y|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.Y11813Y|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.Y18118Y|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19045	Fibronectin type-III 38. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCACTTTAGATAGACAAATG	0.448													G|||	2566	0.51238	0.5681	0.4092	5008	,	,		22023	0.7232		0.2545	False		,,,				2504	0.5583				p.Y20686Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T62058C						PASS	.	G	,,,	2027,1825		546,935,445	194.0	187.0	189.0		34863,54354,35238,35439	3.9	1.0	2	dbSNP_88	189	1858,6404		196,1466,2469	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	742,2401,2914	GG,GA,AA		22.4885,47.378,32.0703	,,,	11621/26927,18118/33424,11746/27052,11813/27119	179454394	3885,8229	1926	4131	6057	SO:0001819	synonymous_variant	7273	exon304			CTTTAGATAGACA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.57135T>C	2.37:g.179454394A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	204	104	0.509804	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.558;G|0.442	0.442	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FMN1	342184	hgsc.bcm.edu	37	15	33357262	33357262	+	Missense_Mutation	SNP	A	A	G	rs2306277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33357262A>G	ENST00000559047.1	-	3	2056	c.2057T>C	c.(2056-2058)cTg>cCg	p.L686P	FMN1_ENST00000334528.9_Missense_Mutation_p.L463P|FMN1_ENST00000558197.1_Missense_Mutation_p.L463P|FMN1_ENST00000559150.1_5'UTR|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1	686	Mediates interaction with alpha-catenin. {ECO:0000250}.		L -> P (in dbSNP:rs2306277). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L463P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CTGCTCAGTCAGGCTGTGGTC	0.458													G|||	2253	0.44988	0.4342	0.5634	5008	,	,		16299	0.2054		0.5646	False		,,,				2504	0.5245				p.L463P		Atlas-SNP	.											FMN1_ENST00000334528,NS,carcinoma,0,1	FMN1	174	1	1	Substitution - Missense(1)	stomach(1)	c.T1388C						PASS	.	G	PRO/LEU	1766,2068		396,974,547	147.0	142.0	143.0		1388	5.1	1.0	15	dbSNP_100	143	4721,3531		1352,2017,757	yes	missense	FMN1	NM_001103184.2	98	1748,2991,1304	GG,GA,AA		42.7896,46.0616,46.3263	benign	463/1197	33357262	6487,5599	1917	4126	6043	SO:0001583	missense	342184	exon2			TCAGTCAGGCTGT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2057T>C	15.37:g.33357262A>G	ENSP00000454047:p.Leu686Pro	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	161	161	1	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		960	0.43956043956043955	194	0.3943089430894309	212	0.585635359116022	127	0.22202797202797203	427	0.5633245382585752	G	2.387	-0.340750	0.05243	0.460616	0.572104	ENSG00000248905	ENST00000334528	T	0.31510	1.49	6.04	5.13	0.70059	.	0.052415	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01009	-1.055	.	.	.	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41610	-0.9499	9	0.06494	T	0.89	.	13.1464	0.59463	0.1287:0.0:0.8713:0.0	rs2306277;rs17235540;rs56901218;rs2306277	463;463	Q68DA7-3;Q68DA7-5	.;.	P	463	ENSP00000333950:L463P	ENSP00000333950:L463P	L	-	2	0	FMN1	31144554	1.000000	0.71417	0.999000	0.59377	0.474000	0.32979	6.540000	0.73861	0.916000	0.36871	-0.215000	0.12644	CTG	G|0.444;N|0.000	0.444	strong		0.458	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441197	39441197	+	Silent	SNP	G	G	A	rs200983508	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39441197G>A	ENST00000308521.5	+	3	780	c.423G>A	c.(421-423)ggG>ggA	p.G141G	APOBEC3G_ENST00000452957.2_Intron|APOBEC3F_ENST00000491387.1_3'UTR	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	141					base conversion or substitution editing (GO:0016553)|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 single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.G141G(2)		breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|skin(2)	16	Melanoma(58;0.04)					GTCAGGCAGGGGCCCGCGTGA	0.592																																					p.G141G		Atlas-SNP	.											APOBEC3F,NS,carcinoma,0,1	APOBEC3F	37	1	2	Substitution - coding silent(2)	lung(1)|endometrium(1)	c.G423A						scavenged	.						47.0	49.0	48.0					22																	39441197		2203	4300	6503	SO:0001819	synonymous_variant	200316	exon3			GGCAGGGGCCCGC	BC038808	CCDS33648.1, CCDS33649.1	22q13.1-q13.2	2008-05-15			ENSG00000128394	ENSG00000128394		"""Apolipoprotein B mRNA editing enzymes"""	17356	protein-coding gene	gene with protein product		608993				11863358, 17121840	Standard	NM_145298		Approved	ARP8, BK150C2.4.MRNA, KA6	uc003aww.3	Q8IUX4	OTTHUMG00000151080	ENST00000308521.5:c.423G>A	22.37:g.39441197G>A		Somatic	117	5	0.042735		WXS	Illumina HiSeq	Phase_I	135	4	0.0296296	NM_145298	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Silent	SNP	ENST00000308521.5	37	CCDS33648.1																																																																																			G|0.998;A|0.002	0.002	strong		0.592	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298	
GLTPD2	388323	hgsc.bcm.edu	37	17	4692559	4692559	+	Missense_Mutation	SNP	G	G	T	rs2304969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4692559G>T	ENST00000331264.7	+	2	198	c.145G>T	c.(145-147)Gtt>Ttt	p.V49F	VMO1_ENST00000416307.2_5'Flank|VMO1_ENST00000328739.5_5'Flank|VMO1_ENST00000354194.4_5'Flank|VMO1_ENST00000441199.2_5'Flank	NM_001014985.2	NP_001014985	A6NH11	GLTD2_HUMAN	glycolipid transfer protein domain containing 2	49						cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4						GCAGCCCTGCGTTCCAGGGGA	0.701													G|||	1370	0.273562	0.1369	0.1715	5008	,	,		13658	0.506		0.159	False		,,,				2504	0.409				p.V49F		Atlas-SNP	.											.	GLTPD2	15	.	0			c.G145T						PASS	.	G	PHE/VAL	630,3756		44,542,1607	10.0	12.0	12.0		145	-0.4	0.0	17	dbSNP_100	12	1217,7343		95,1027,3158	yes	missense	GLTPD2	NM_001014985.2	50	139,1569,4765	TT,TG,GG		14.2173,14.3639,14.267	benign	49/292	4692559	1847,11099	2193	4280	6473	SO:0001583	missense	388323	exon2			CCCTGCGTTCCAG	BC029290	CCDS32534.1	17p13.2	2007-12-19				ENSG00000182327			33756	protein-coding gene	gene with protein product							Standard	NM_001014985		Approved		uc002fza.2	A6NH11		ENST00000331264.7:c.145G>T	17.37:g.4692559G>T	ENSP00000328070:p.Val49Phe	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_001014985	A7E2T2	Missense_Mutation	SNP	ENST00000331264.7	37	CCDS32534.1	535	0.24496336996336995	72	0.14634146341463414	57	0.1574585635359116	276	0.4825174825174825	130	0.17150395778364116	G	15.52	2.857505	0.51376	0.143639	0.142173	ENSG00000182327	ENST00000331264	.	.	.	4.3	-0.367	0.12541	.	1.040650	0.07588	N	0.921514	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.45768	0.866	B	0.41691	0.364	T	0.45469	-0.9259	8	0.59425	D	0.04	-13.4729	7.1891	0.25816	0.5324:0.0:0.4676:0.0	rs2304969;rs2304969	49	A6NH11	GLTD2_HUMAN	F	49	.	ENSP00000328070:V49F	V	+	1	0	GLTPD2	4639299	0.000000	0.05858	0.006000	0.13384	0.016000	0.09150	-0.045000	0.12003	0.013000	0.14918	-0.367000	0.07326	GTT	G|0.753;T|0.247	0.247	strong		0.701	GLTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439781.1	NM_001014985	
DENND4C	55667	hgsc.bcm.edu	37	9	19346710	19346710	+	Missense_Mutation	SNP	A	A	G	rs17818730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:19346710A>G	ENST00000380432.2	+	18	3121	c.3088A>G	c.(3088-3090)Act>Gct	p.T1030A	DENND4C_ENST00000434457.2_Missense_Mutation_p.T1315A|DENND4C_ENST00000602925.1_Missense_Mutation_p.T1266A			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1030			T -> A (in dbSNP:rs17818730).		cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GTCTGGCATGACTACTGCATT	0.413													A|||	239	0.0477236	0.0053	0.1787	5008	,	,		19791	0.003		0.0835	False		,,,				2504	0.0215				p.T1266A		Atlas-SNP	.											.	DENND4C	120	.	0			c.A3796G						PASS	.	A	ALA/THR	79,4327	69.2+/-107.0	3,73,2127	95.0	94.0	94.0		3088	-2.1	0.0	9	dbSNP_123	94	697,7903	172.0+/-222.8	32,633,3635	yes	missense	DENND4C	NM_017925.4	58	35,706,5762	GG,GA,AA		8.1047,1.793,5.9665	benign	1030/1674	19346710	776,12230	2203	4300	6503	SO:0001583	missense	55667	exon22			GGCATGACTACTG	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3088A>G	9.37:g.19346710A>G	ENSP00000369797:p.Thr1030Ala	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		137	0.06272893772893773	6	0.012195121951219513	56	0.15469613259668508	3	0.005244755244755245	72	0.09498680738786279	A	1.138	-0.650347	0.03506	0.01793	0.081047	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T;T	0.21191	2.02;2.02;3.72	5.72	-2.13	0.07144	.	1.133050	0.06790	N	0.786893	T	0.00039	0.0001	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	0.04013	0.001;0.001;0.001;0.0	T	0.39742	-0.9599	9	0.19590	T	0.45	-0.0033	1.6169	0.02705	0.3438:0.2745:0.0779:0.3038	rs17818730;rs52803664;rs17818730	360;1030;212;1030	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	A	1030;503;212;360;503;212;27	ENSP00000305795:T503A;ENSP00000443804:T360A;ENSP00000369797:T503A	ENSP00000305795:T503A	T	+	1	0	DENND4C	19336710	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.082000	0.03400	-0.181000	0.10619	0.528000	0.53228	ACT	A|0.940;G|0.060	0.060	strong		0.413	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
NAV3	89795	hgsc.bcm.edu	37	12	78598891	78598891	+	Silent	SNP	G	G	A	rs9971904	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:78598891G>A	ENST00000397909.2	+	39	7184	c.7011G>A	c.(7009-7011)ccG>ccA	p.P2337P	NAV3_ENST00000228327.6_Silent_p.P2315P|NAV3_ENST00000536525.2_Silent_p.P2315P|NAV3_ENST00000541270.1_Silent_p.P167P|NAV3_ENST00000266692.7_Silent_p.P2138P			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	89	0	0		WXS	Illumina HiSeq	Phase_I	73	73	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	
INPP4A	3631	hgsc.bcm.edu	37	2	99172243	99172243	+	Silent	SNP	C	C	T	rs41486345	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:99172243C>T	ENST00000523221.1	+	15	1809	c.1809C>T	c.(1807-1809)tcC>tcT	p.S603S	INPP4A_ENST00000409540.3_Intron|INPP4A_ENST00000409016.4_Intron|INPP4A_ENST00000409851.3_Silent_p.S598S|INPP4A_ENST00000074304.5_Silent_p.S603S|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000545415.1_Intron			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	603					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						CCATGCCCTCCACTGCATGCC	0.557													C|||	127	0.0253594	0.0008	0.0187	5008	,	,		21584	0.0		0.0845	False		,,,				2504	0.0286				p.S603S		Atlas-SNP	.											.	INPP4A	205	.	0			c.C1809T						PASS	.	C	,,,	12,1372		0,12,680	207.0	211.0	210.0		1809,1794,,	0.2	0.2	2	dbSNP_127	210	244,2938		9,226,1356	no	coding-synonymous,coding-synonymous,intron,intron	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	9,238,2036	TT,TC,CC		7.6681,0.8671,5.6067	,,,	603/978,598/973,,	99172243	256,4310	692	1591	2283	SO:0001819	synonymous_variant	3631	exon17			GCCCTCCACTGCA	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.1809C>T	2.37:g.99172243C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			C|0.954;T|0.046	0.046	strong		0.557	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274087	39274087	+	Missense_Mutation	SNP	G	G	C	rs141357429		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39274087G>C	ENST00000391413.2	-	1	519	c.481C>G	c.(481-483)Ctg>Gtg	p.L161V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	161	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.L161V(1)		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)			ACTGGACGCAGGcagcagcag	0.657																																					p.L161V		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,7	KRTAP4-11	94	7	1	Substitution - Missense(1)	prostate(1)	c.C481G						scavenged	.						17.0	21.0	20.0					17																	39274087		692	1589	2281	SO:0001583	missense	653240	exon1			GACGCAGGCAGCA	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.481C>G	17.37:g.39274087G>C	ENSP00000375232:p.Leu161Val	Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	107	8	0.0747664	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	249	0.11401098901098901	67	0.13617886178861788	40	0.11049723756906077	104	0.18181818181818182	38	0.05013192612137203	.	1.347	-0.592411	0.03799	.	.	ENSG00000212721	ENST00000391413	T	0.00614	6.21	4.35	0.986	0.19784	.	.	.	.	.	T	0.00012	0.0000	L	0.31752	0.955	0.80722	P	0.0	B	0.30068	0.267	B	0.18871	0.023	T	0.19063	-1.0317	8	0.11794	T	0.64	.	5.8913	0.18915	0.1751:0.0:0.6569:0.168	.	161	Q9BYQ6	KR411_HUMAN	V	161	ENSP00000375232:L161V	ENSP00000375232:L161V	L	-	1	2	KRTAP4-11	36527613	0.671000	0.27521	0.912000	0.35992	0.970000	0.65996	0.971000	0.29396	0.348000	0.23949	0.609000	0.83330	CTG	G|0.500;C|0.500	0.500	weak		0.657	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
HOXC10	3226	hgsc.bcm.edu	37	12	54379670	54379670	+	Silent	SNP	C	C	T	rs4564384	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:54379670C>T	ENST00000303460.4	+	1	701	c.627C>T	c.(625-627)ccC>ccT	p.P209P	RP11-834C11.12_ENST00000513209.1_Silent_p.P14P|HOXC-AS3_ENST00000514702.1_RNA|HOXC-AS3_ENST00000513165.1_RNA|HOXC-AS3_ENST00000567780.1_RNA|HOXC-AS3_ENST00000509870.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	209					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						GCCAGACCCCCAGCCCCAATG	0.642													C|||	371	0.0740815	0.0174	0.1095	5008	,	,		14760	0.0893		0.0855	False		,,,				2504	0.0982				p.P209P		Atlas-SNP	.											.	HOXC10	42	.	0			c.C627T						PASS	.	C		132,4274		1,130,2072	26.0	31.0	29.0		627	-1.4	1.0	12	dbSNP_111	29	714,7884		27,660,3612	no	coding-synonymous	HOXC10	NM_017409.3		28,790,5684	TT,TC,CC		8.3043,2.9959,6.5057		209/343	54379670	846,12158	2203	4299	6502	SO:0001819	synonymous_variant	3226	exon1			GACCCCCAGCCCC		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.627C>T	12.37:g.54379670C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_017409	O15219|O15220|Q9BVD5	Silent	SNP	ENST00000303460.4	37	CCDS8868.1																																																																																			T|0.070;G|0.000;C|0.929	0.070	strong		0.642	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2		
INPP5E	56623	hgsc.bcm.edu	37	9	139328551	139328551	+	Silent	SNP	T	T	C	rs10870199	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139328551T>C	ENST00000371712.3	-	3	1374	c.972A>G	c.(970-972)ccA>ccG	p.P324P		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		CGGCCTCGGCTGGGAGCAGGA	0.677													T|||	620	0.123802	0.0068	0.245	5008	,	,		15559	0.1587		0.1292	False		,,,				2504	0.1544				p.P324P		Atlas-SNP	.											.	INPP5E	18	.	0			c.A972G						PASS	.	T		135,4261	92.5+/-131.2	1,133,2064	40.0	35.0	37.0		972	-5.7	0.0	9	dbSNP_120	37	1173,7419	222.2+/-259.3	73,1027,3196	no	coding-synonymous	INPP5E	NM_019892.4		74,1160,5260	CC,CT,TT		13.6522,3.071,10.0708		324/645	139328551	1308,11680	2198	4296	6494	SO:0001819	synonymous_variant	56623	exon3			CTCGGCTGGGAGC	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.972A>G	9.37:g.139328551T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			T|0.894;C|0.106	0.106	strong		0.677	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
ZNF492	57615	hgsc.bcm.edu	37	19	22846601	22846601	+	Splice_Site	SNP	G	G	T	rs71355985	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:22846601G>T	ENST00000456783.2	+	4	374		c.e4-1		CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ATTTCTTTCAGTTGTATGTTC	0.299													N|||	190	0.0379393	0.0295	0.0187	5008	,	,		14644	0.0813		0.0398	False		,,,				2504	0.0164				.		Atlas-SNP	.											.	ZNF492	129	.	0			c.131-1G>T						PASS	.						14.0	15.0	15.0					19																	22846601		1803	4084	5887	SO:0001630	splice_region_variant	57615	exon4			CTTTCAGTTGTAT	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.131-1G>T	19.37:g.22846601G>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_020855	Q08EI7|Q08EI8	Splice_Site	SNP	ENST00000456783.2	37	CCDS46032.1	109	0.04990842490842491	17	0.034552845528455285	10	0.027624309392265192	53	0.09265734265734266	29	0.03825857519788918	.	8.371	0.835363	0.16820	.	.	ENSG00000229676	ENST00000456783	.	.	.	1.12	1.12	0.20585	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2552	0.15544	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF492	22638441	0.029000	0.19370	0.383000	0.26132	0.378000	0.30076	0.233000	0.17911	0.269000	0.21961	0.274000	0.19336	.	G|0.955;T|0.045	0.045	strong		0.299	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	Intron
SSRP1	6749	hgsc.bcm.edu	37	11	57100225	57100225	+	Silent	SNP	A	A	G	rs2230650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57100225A>G	ENST00000278412.2	-	6	908	c.642T>C	c.(640-642)taT>taC	p.Y214Y		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	214					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						TCCGAATGTCATAACGACCAC	0.522													A|||	37	0.00738818	0.0008	0.0058	5008	,	,		22752	0.0		0.0258	False		,,,				2504	0.0061				p.Y214Y	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.T642C						PASS	.	A		32,4370	38.4+/-70.7	0,32,2169	93.0	89.0	90.0		642	-3.9	0.8	11	dbSNP_98	90	274,8318	104.8+/-165.8	4,266,4026	no	coding-synonymous	SSRP1	NM_003146.2		4,298,6195	GG,GA,AA		3.189,0.7269,2.3549		214/710	57100225	306,12688	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon6			AATGTCATAACGA	M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 80 kDa subunit"""	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.642T>C	11.37:g.57100225A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	97	37	0.381443	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			A|0.978;G|0.022	0.022	strong		0.522	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993642	140993642	+	Missense_Mutation	SNP	C	C	T	rs176037|rs200557748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:140993642C>T	ENST00000285879.4	+	4	738	c.452C>T	c.(451-453)aCt>aTt	p.T151I	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	151			T -> I (in dbSNP:rs176037). {ECO:0000269|PubMed:9485030, ECO:0000269|PubMed:9618514}.							breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CCTGAGAGTACTCAAAGTCCT	0.507										HNSCC(15;0.026)			-|||	1104	0.29245	0.1831	0.219	3775	,	,		13816	0.1438		0.3757	False		,,,				2504	0.1912				p.T151I		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C452T						PASS	.		ILE/THR	997,2838		113,628,143,891,428	81.0	81.0	81.0		452		0.0	X	dbSNP_79	81	3046,3682		468,1260,850,700,1022	no	missense	MAGEC1	NM_005462.4	89	581,1888,993,1591,1450	TT,TC,T,CC,C		45.2735,25.9974,38.2751	possibly-damaging	151/1143	140993642	4043,6520	2203	4300	6503	SO:0001583	missense	9947	exon4			AGAGTACTCAAAG	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.452C>T	X.37:g.140993642C>T	ENSP00000285879:p.Thr151Ile	Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	211	192	0.909953	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	548	0.3303194695599759	60	0.13452914798206278	58	0.19863013698630136	56	0.11023622047244094	196	0.34146341463414637	c	0.980	-0.697338	0.03279	0.259974	0.452735	ENSG00000155495	ENST00000285879	T	0.02709	4.19	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.54753	P	2.0000000000020002E-5	P	0.47604	0.898	B	0.31290	0.127	T	0.19192	-1.0313	7	0.20046	T	0.44	.	5.8318	0.18584	0.0:0.9991:0.0:9.0E-4	rs176037	151	O60732	MAGC1_HUMAN	I	151	ENSP00000285879:T151I	ENSP00000285879:T151I	T	+	2	0	MAGEC1	140821308	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.109000	0.15417	-0.000000	0.14550	-0.000000	0.15137	ACT	C|0.647;T|0.353	0.353	strong		0.507	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
SLC2A8	29988	hgsc.bcm.edu	37	9	130165973	130165973	+	Missense_Mutation	SNP	T	T	C	rs34064803	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130165973T>C	ENST00000373371.3	+	6	847	c.758T>C	c.(757-759)aTc>aCc	p.I253T	SLC2A8_ENST00000373360.3_Missense_Mutation_p.I253T|SLC2A8_ENST00000373352.1_5'UTR	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	253			I -> T (in dbSNP:rs34064803).		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						CAGCCCGGCATCTACAAGCCC	0.617													T|||	227	0.0453275	0.0272	0.0821	5008	,	,		18287	0.0		0.1054	False		,,,				2504	0.0286				p.I253T		Atlas-SNP	.											.	SLC2A8	27	.	0			c.T758C						PASS	.	T	THR/ILE	135,4271	96.7+/-135.4	2,131,2070	50.0	50.0	50.0		758	5.4	0.9	9	dbSNP_126	50	886,7714	198.7+/-243.0	41,804,3455	yes	missense	SLC2A8	NM_014580.3	89	43,935,5525	CC,CT,TT		10.3023,3.064,7.8502	benign	253/478	130165973	1021,11985	2203	4300	6503	SO:0001583	missense	29988	exon6			CCGGCATCTACAA	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.758T>C	9.37:g.130165973T>C	ENSP00000362469:p.Ile253Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_014580	Q8WUZ9|Q9NSC4	Missense_Mutation	SNP	ENST00000373371.3	37	CCDS6870.1	122	0.055860805860805864	13	0.026422764227642278	32	0.08839779005524862	0	0.0	77	0.10158311345646438	T	17.75	3.465299	0.63513	0.03064	0.103023	ENSG00000136856	ENST00000373371;ENST00000451404;ENST00000419917;ENST00000373360;ENST00000423934;ENST00000373350;ENST00000430147	T;T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82;-0.82	5.42	5.42	0.78866	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.437153	0.28135	N	0.016463	T	0.05868	0.0153	L	0.28014	0.82	0.21020	P	0.999809739	P;P	0.46457	0.878;0.739	P;B	0.51170	0.661;0.403	T	0.48502	-0.9030	9	0.23891	T	0.37	.	14.4605	0.67445	0.0:0.0:0.0:1.0	rs34064803	253;253	Q5VVV9;Q9NY64	.;GTR8_HUMAN	T	253;90;184;253;118;118;92	ENSP00000362469:I253T;ENSP00000392434:I90T;ENSP00000411726:I184T;ENSP00000362458:I253T;ENSP00000389070:I118T;ENSP00000391213:I92T	ENSP00000362448:I118T	I	+	2	0	SLC2A8	129205794	1.000000	0.71417	0.927000	0.36925	0.515000	0.34225	7.338000	0.79269	2.063000	0.61619	0.533000	0.62120	ATC	T|0.928;C|0.072	0.072	strong		0.617	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580	
LSS	4047	hgsc.bcm.edu	37	21	47611799	47611799	+	Missense_Mutation	SNP	G	G	A	rs17293705	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47611799G>A	ENST00000397728.3	-	21	2141	c.2063C>T	c.(2062-2064)cCg>cTg	p.P688L	AP001468.58_ENST00000415026.1_RNA|LSS_ENST00000457828.2_Missense_Mutation_p.P608L|LSS_ENST00000356396.4_Missense_Mutation_p.P688L|LSS_ENST00000522411.1_Missense_Mutation_p.P677L	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	688			P -> L (in dbSNP:rs17293705).		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)					GCATACCTGCGGCCAGTCGCC	0.602													G|||	41	0.0081869	0.0	0.0072	5008	,	,		18890	0.0		0.0189	False		,,,				2504	0.0174				p.P688L	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C2063T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	14,4392	21.2+/-45.6	0,14,2189	103.0	74.0	84.0		2063,2030,1823,2063	5.6	1.0	21	dbSNP_123	84	184,8416	81.8+/-144.4	1,182,4117	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	98,98,98,98	1,196,6306	AA,AG,GG		2.1395,0.3177,1.5224	probably-damaging,probably-damaging,probably-damaging,probably-damaging	688/733,677/722,608/653,688/733	47611799	198,12808	2203	4300	6503	SO:0001583	missense	4047	exon21			ACCTGCGGCCAGT	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.2063C>T	21.37:g.47611799G>A	ENSP00000380837:p.Pro688Leu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	28.6	4.935067	0.92458	0.003177	0.021395	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.23348	1.91;1.91;1.91;1.91	5.61	5.61	0.85477	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	L	0.47016	1.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.98	T	0.01771	-1.1277	10	0.23302	T	0.38	.	19.2326	0.93846	0.0:0.0:1.0:0.0	rs17293705;rs52803981;rs17293705	677;688	E9PEI9;P48449	.;ERG7_HUMAN	L	688;608;688;677	ENSP00000348762:P688L;ENSP00000409191:P608L;ENSP00000380837:P688L;ENSP00000429133:P677L	ENSP00000348762:P688L	P	-	2	0	LSS	46436227	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	6.766000	0.74970	2.647000	0.89833	0.557000	0.71058	CCG	G|0.986;A|0.014	0.014	strong		0.602	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
CLEC4F	165530	hgsc.bcm.edu	37	2	71043461	71043461	+	Missense_Mutation	SNP	C	C	T	rs722896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71043461C>T	ENST00000272367.2	-	4	1128	c.1052G>A	c.(1051-1053)cGt>cAt	p.R351H	CLEC4F_ENST00000426626.1_Missense_Mutation_p.R351H	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	351			R -> H (in dbSNP:rs722896).		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						CTGGTCCAGACGGCCATTTGC	0.403													C|||	1693	0.338059	0.1195	0.4006	5008	,	,		21626	0.5248		0.3101	False		,,,				2504	0.4254				p.R351H	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.G1052A						PASS	.	C	HIS/ARG	739,3667	303.5+/-288.0	60,619,1524	86.0	83.0	84.0		1052	-5.1	0.0	2	dbSNP_86	84	2597,6003	421.6+/-353.8	431,1735,2134	yes	missense	CLEC4F	NM_173535.2	29	491,2354,3658	TT,TC,CC		30.1977,16.7726,25.6497	benign	351/590	71043461	3336,9670	2203	4300	6503	SO:0001583	missense	165530	exon4			TCCAGACGGCCAT	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.1052G>A	2.37:g.71043461C>T	ENSP00000272367:p.Arg351His	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	205	107	0.521951	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	753	0.3447802197802198	58	0.11788617886178862	124	0.3425414364640884	343	0.5996503496503497	228	0.3007915567282322	C	7.700	0.692882	0.15039	0.167726	0.301977	ENSG00000152672	ENST00000272367;ENST00000426626	D;D	0.82893	-1.66;-1.66	3.79	-5.05	0.02955	.	1.546170	0.04013	N	0.298500	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.12630	0.002;0.006	B;B	0.04013	0.001;0.001	T	0.16600	-1.0397	9	0.13470	T	0.59	.	11.5395	0.50659	0.0:0.2236:0.0:0.7764	rs722896;rs59663124;rs722896	351;351	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	H	351	ENSP00000272367:R351H;ENSP00000390581:R351H	ENSP00000272367:R351H	R	-	2	0	CLEC4F	70896969	0.000000	0.05858	0.000000	0.03702	0.779000	0.44077	-1.034000	0.03567	-1.226000	0.02574	0.467000	0.42956	CGT	C|0.704;T|0.296	0.296	strong		0.403	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
PTCD1	26024	hgsc.bcm.edu	37	7	99032593	99032593	+	Silent	SNP	G	G	T	rs11555142	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99032593G>T	ENST00000292478.4	-	2	523	c.273C>A	c.(271-273)acC>acA	p.T91T	PTCD1_ENST00000555673.1_Silent_p.T140T|PTCD1_ENST00000485746.1_5'UTR|ATP5J2-PTCD1_ENST00000413834.1_Silent_p.T140T|ATP5J2-PTCD1_ENST00000437572.1_5'Flank	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	91					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TGTCAGAGAGGGTCCCAAAAC	0.582													G|||	474	0.0946486	0.1967	0.0807	5008	,	,		17877	0.005		0.1054	False		,,,				2504	0.0481				p.T140T		Atlas-SNP	.											.	.	.	.	0			c.C420A						PASS	.	G	,	826,3580	325.9+/-299.3	82,662,1459	100.0	106.0	104.0		420,273	-1.4	0.9	7	dbSNP_120	104	648,7952	165.1+/-217.3	28,592,3680	no	coding-synonymous,coding-synonymous	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	,	110,1254,5139	TT,TG,GG		7.5349,18.7472,11.3332	,	140/750,91/701	99032593	1474,11532	2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon3			AGAGAGGGTCCCA	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.273C>A	7.37:g.99032593G>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	37	CCDS34691.1																																																																																			G|0.892;T|0.108	0.108	strong		0.582	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
RIMS2	9699	hgsc.bcm.edu	37	8	105263979	105263979	+	Silent	SNP	C	C	T	rs10461	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000262231.10_Silent_p.A1166A|RIMS2_ENST00000507740.1_Silent_p.A1141A|RIMS2_ENST00000406091.3_Silent_p.A1327A			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	143	0	0		WXS	Illumina HiSeq	Phase_I	148	70	0.472973	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	
RNASE8	122665	hgsc.bcm.edu	37	14	21526079	21526079	+	Missense_Mutation	SNP	C	C	T	rs12437266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21526079C>T	ENST00000308227.2	+	1	99	c.28C>T	c.(28-30)Ccc>Tcc	p.P10S	NDRG2_ENST00000403829.3_Intron	NM_138331.1	NP_612204.1	Q8TDE3	RNAS8_HUMAN	ribonuclease, RNase A family, 8	10			P -> S (in dbSNP:rs12437266). {ECO:0000269|PubMed:15489334}.		RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;3.42e-11)|Epithelial(56;5.57e-09)|all cancers(55;2.36e-08)	GBM - Glioblastoma multiforme(265;0.0188)		AGGATGCTGCCCCCTGCTGCT	0.547													C|||	2736	0.546326	0.4024	0.5922	5008	,	,		15156	0.6151		0.6412	False		,,,				2504	0.5399				p.P10S		Atlas-SNP	.											.	RNASE8	11	.	0			c.C28T						PASS	.	C	SER/PRO	1842,2564	534.7+/-374.0	369,1104,730	64.0	55.0	58.0		28	-4.9	0.0	14	dbSNP_120	58	5287,3313	644.1+/-400.0	1626,2035,639	yes	missense	RNASE8	NM_138331.1	74	1995,3139,1369	TT,TC,CC		38.5233,41.8066,45.1868	possibly-damaging	10/155	21526079	7129,5877	2203	4300	6503	SO:0001583	missense	122665	exon1			TGCTGCCCCCTGC	AF473854	CCDS9567.1	14q11.1	2003-03-13			ENSG00000173431	ENSG00000173431		"""Ribonucleases, RNase A"""	19277	protein-coding gene	gene with protein product		612485				11861908	Standard	NM_138331		Approved		uc010tlm.2	Q8TDE3	OTTHUMG00000029645	ENST00000308227.2:c.28C>T	14.37:g.21526079C>T	ENSP00000311398:p.Pro10Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_138331	B2RPP6|B2RPP7	Missense_Mutation	SNP	ENST00000308227.2	37	CCDS9567.1	1229	0.5627289377289377	193	0.39227642276422764	206	0.569060773480663	350	0.6118881118881119	480	0.633245382585752	C	11.77	1.737464	0.30774	0.418066	0.614767	ENSG00000173431	ENST00000308227	T	0.78003	-1.14	4.32	-4.89	0.03103	.	1.069470	0.07227	N	0.861806	T	0.00012	0.0000	L	0.58810	1.83	0.80722	P	0.0	B	0.16603	0.018	B	0.17098	0.017	T	0.42699	-0.9436	9	0.49607	T	0.09	-7.0205	7.2534	0.26162	0.0:0.2374:0.1351:0.6275	rs12437266;rs59321589	10	Q8TDE3	RNAS8_HUMAN	S	10	ENSP00000311398:P10S	ENSP00000311398:P10S	P	+	1	0	RNASE8	20595919	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.080000	0.03407	-1.275000	0.02417	-1.109000	0.02080	CCC	C|0.481;T|0.519	0.519	strong		0.547	RNASE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073925.3	NM_138331	
OSBPL7	114881	hgsc.bcm.edu	37	17	45886796	45886796	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45886796A>C	ENST00000007414.3	-	19	2120	c.1929T>G	c.(1927-1929)aaT>aaG	p.N643K	OSBPL7_ENST00000392507.3_Missense_Mutation_p.N643K	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	643					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						CACTCAGGACATTGTGAATGC	0.547																																					p.N643K		Atlas-SNP	.											.	OSBPL7	65	.	0			c.T1929G						PASS	.						134.0	98.0	110.0					17																	45886796		2203	4300	6503	SO:0001583	missense	114881	exon19			CAGGACATTGTGA	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.1929T>G	17.37:g.45886796A>C	ENSP00000007414:p.Asn643Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	37	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.467556	0.63625	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.44881	0.91;0.91	4.91	3.89	0.44902	.	0.043933	0.85682	D	0.000000	T	0.73450	0.3588	H	0.96460	3.825	0.54753	D	0.999983	D	0.89917	1.0	D	0.87578	0.998	T	0.80894	-0.1178	10	0.87932	D	0	-37.8662	12.0721	0.53622	0.087:0.0:0.913:0.0	.	643	Q9BZF2	OSBL7_HUMAN	K	643	ENSP00000007414:N643K;ENSP00000376295:N643K	ENSP00000007414:N643K	N	-	3	2	OSBPL7	43241795	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	2.907000	0.48743	1.045000	0.40225	-0.337000	0.08149	AAT	.	.	none		0.547	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
NUGGC	389643	hgsc.bcm.edu	37	8	27925185	27925185	+	Missense_Mutation	SNP	G	G	A	rs74462442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:27925185G>A	ENST00000413272.2	-	6	699	c.557C>T	c.(556-558)gCg>gTg	p.A186V	NUGGC_ENST00000341513.6_Missense_Mutation_p.A186V	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	186					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)										CCTGTTCCACGCATCTGCCTC	0.542													G|||	196	0.0391374	0.0779	0.0274	5008	,	,		20680	0.0		0.0288	False		,,,				2504	0.046				p.A186V		Atlas-SNP	.											.	.	.	.	0			c.C557T						PASS	.	G	VAL/ALA	265,3885		10,245,1820	87.0	90.0	89.0		557	-3.0	0.0	8	dbSNP_131	89	239,8211		6,227,3992	yes	missense	C8orf80	NM_001010906.1	64	16,472,5812	AA,AG,GG		2.8284,6.3855,4.0	benign	186/797	27925185	504,12096	2075	4225	6300	SO:0001583	missense	389643	exon6			TTCCACGCATCTG	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.557C>T	8.37:g.27925185G>A	ENSP00000408697:p.Ala186Val	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	214	111	0.518692	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	73	0.033424908424908424	32	0.06504065040650407	14	0.03867403314917127	0	0.0	27	0.03562005277044855	G	8.207	0.799435	0.16397	0.063855	0.028284	ENSG00000189233	ENST00000413272;ENST00000341513	D;D	0.96619	-4.07;-4.07	6.1	-3.0	0.05480	Dynamin, GTPase domain (1);	2.161710	0.02043	N	0.049436	T	0.59689	0.2212	L	0.48642	1.525	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.76318	-0.3003	10	0.13853	T	0.58	5.8383	5.0363	0.14436	0.2399:0.0:0.2273:0.5328	.	186	Q68CJ6	SLIP_HUMAN	V	186	ENSP00000408697:A186V;ENSP00000345031:A186V	ENSP00000345031:A186V	A	-	2	0	C8orf80	27981104	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-0.734000	0.04893	-0.541000	0.06257	0.603000	0.83216	GCG	G|0.965;A|0.035	0.035	strong		0.542	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
COPE	11316	hgsc.bcm.edu	37	19	19023853	19023853	+	Silent	SNP	T	T	C	rs3177137	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19023853T>C	ENST00000262812.4	-	2	177	c.129A>G	c.(127-129)ctA>ctG	p.L43L	COPE_ENST00000600932.1_Silent_p.L43L|COPE_ENST00000598969.1_5'UTR|AC002985.3_ENST00000596918.1_3'UTR|COPE_ENST00000351079.4_Silent_p.L43L|COPE_ENST00000349893.4_Silent_p.L43L	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	43					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CTGGGCTTGATAGCTGTGGGA	0.617													C|||	1753	0.35004	0.3222	0.5836	5008	,	,		18947	0.1925		0.4871	False		,,,				2504	0.2434				p.L43L		Atlas-SNP	.											COPE,NS,adenoma,0,1	COPE	26	1	0			c.A129G						PASS	.	C	,,	1594,2812	663.6+/-401.2	303,988,912	127.0	91.0	103.0		129,129,129	-9.8	0.0	19	dbSNP_105	103	4168,4432	585.7+/-391.9	997,2174,1129	no	coding-synonymous,coding-synonymous,coding-synonymous	COPE	NM_007263.3,NM_199442.1,NM_199444.1	,,	1300,3162,2041	CC,CT,TT		48.4651,36.1779,44.3026	,,	43/309,43/258,43/257	19023853	5762,7244	2203	4300	6503	SO:0001819	synonymous_variant	11316	exon2			GCTTGATAGCTGT	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.129A>G	19.37:g.19023853T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Silent	SNP	ENST00000262812.4	37	CCDS12387.1																																																																																			T|0.586;C|0.414	0.414	strong		0.617	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
SFTPD	6441	hgsc.bcm.edu	37	10	81697818	81697818	+	Silent	SNP	A	A	G	rs1051246	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:81697818A>G	ENST00000372292.3	-	8	958	c.918T>C	c.(916-918)gcT>gcC	p.A306A		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	306	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			CCTCGTTCTTAGCTACGACCA	0.577													A|||	874	0.174521	0.2519	0.2406	5008	,	,		19687	0.0188		0.1342	False		,,,				2504	0.2249				p.A306A		Atlas-SNP	.											.	SFTPD	43	.	0			c.T918C						PASS	.	A		1010,3396	374.4+/-321.2	121,768,1314	137.0	132.0	134.0		918	-11.3	0.0	10	dbSNP_86	134	1174,7426	240.1+/-271.0	73,1028,3199	no	coding-synonymous	SFTPD	NM_003019.4		194,1796,4513	GG,GA,AA		13.6512,22.9233,16.7922		306/376	81697818	2184,10822	2203	4300	6503	SO:0001819	synonymous_variant	6441	exon8			GTTCTTAGCTACG	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"""Collectins"""	10803	protein-coding gene	gene with protein product		178635	"""surfactant, pulmonary-associated protein D"""	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.918T>C	10.37:g.81697818A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Silent	SNP	ENST00000372292.3	37	CCDS7362.1																																																																																			A|0.837;G|0.163	0.163	strong		0.577	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		
WDR11	55717	hgsc.bcm.edu	37	10	122645376	122645376	+	Silent	SNP	A	A	T	rs7899928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:122645376A>T	ENST00000263461.6	+	15	2145	c.1899A>T	c.(1897-1899)gcA>gcT	p.A633A	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.A633A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AGCAACTTGCAACTCGAGAGG	0.473													T|||	1981	0.395567	0.4297	0.4366	5008	,	,		18356	0.4177		0.334	False		,,,				2504	0.3609				p.A633A		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.A1899T						PASS	.	T		1846,2560	635.2+/-396.3	392,1062,749	138.0	133.0	135.0		1899	-5.2	0.9	10	dbSNP_116	135	2894,5706	671.5+/-402.8	471,1952,1877	no	coding-synonymous	WDR11	NM_018117.11		863,3014,2626	TT,TA,AA		33.6512,41.8974,36.4447		633/1225	122645376	4740,8266	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon15			ACTTGCAACTCGA	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.1899A>T	10.37:g.122645376A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	50	32	0.64	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			A|0.640;T|0.360	0.360	strong		0.473	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
SURF6	6838	hgsc.bcm.edu	37	9	136199466	136199466	+	Missense_Mutation	SNP	G	G	A	rs886089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136199466G>A	ENST00000372022.4	-	4	789	c.524C>T	c.(523-525)aCg>aTg	p.T175M	SURF6_ENST00000468290.1_5'UTR	NM_006753.4	NP_006744.2	O75683	SURF6_HUMAN	surfeit 6	175			T -> M (in dbSNP:rs886089).		ribosome biogenesis (GO:0042254)	granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	12				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)		CTGGGCCTCCGTGGCCTCCTC	0.657													G|||	1407	0.28095	0.0386	0.3501	5008	,	,		15252	0.2986		0.3569	False		,,,				2504	0.4632				p.T175M		Atlas-SNP	.											SURF6,rectum,carcinoma,0,1	SURF6	32	1	0			c.C524T						scavenged	.	G	MET/THR	372,4034	184.0+/-211.4	20,332,1851	88.0	92.0	90.0		524	-8.3	0.0	9	dbSNP_86	90	3017,5583	460.5+/-365.2	543,1931,1826	yes	missense	SURF6	NM_006753.4	81	563,2263,3677	AA,AG,GG		35.0814,8.443,26.0572	possibly-damaging	175/362	136199466	3389,9617	2203	4300	6503	SO:0001583	missense	6838	exon4			GCCTCCGTGGCCT	AF186772	CCDS6962.1	9q33-q34	2010-07-06			ENSG00000148296	ENSG00000148296			11478	protein-coding gene	gene with protein product	"""surfeit locus protein 6"""	185642				9740673, 15629442	Standard	NM_006753		Approved	FLJ30322, RRP14	uc004cdb.4	O75683	OTTHUMG00000020871	ENST00000372022.4:c.524C>T	9.37:g.136199466G>A	ENSP00000361092:p.Thr175Met	Somatic	41	1	0.0243902		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_006753	Q5T8U1|Q9BRK9|Q9BTZ5|Q9UK24	Missense_Mutation	SNP	ENST00000372022.4	37	CCDS6962.1	584	0.2673992673992674	31	0.06300813008130081	122	0.3370165745856354	154	0.2692307692307692	277	0.3654353562005277	G	8.549	0.875047	0.17395	0.08443	0.350814	ENSG00000148296	ENST00000372022	T	0.14516	2.5	4.14	-8.28	0.01013	.	1.762280	0.02976	N	0.145022	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36010	0.532	B	0.31191	0.125	T	0.25847	-1.0120	9	0.48119	T	0.1	.	1.6707	0.02811	0.2994:0.1487:0.0953:0.4565	rs886089;rs886089	175	O75683	SURF6_HUMAN	M	175	ENSP00000361092:T175M	ENSP00000361092:T175M	T	-	2	0	SURF6	135189287	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.892000	0.01610	-3.813000	0.00104	-1.250000	0.01514	ACG	A|0.255;C|0.000;G|0.745	0.255	strong		0.657	SURF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054905.1	NM_006753	
RTN4RL1	146760	hgsc.bcm.edu	37	17	1839976	1839976	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1839976A>G	ENST00000331238.6	-	2	1619	c.1140T>C	c.(1138-1140)taT>taC	p.Y380Y		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						AGTCTGGGGCATAGTCTGGCA	0.637																																					p.Y380Y	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											.	RTN4RL1	21	.	0			c.T1140C						PASS	.						33.0	36.0	35.0					17																	1839976		1939	4116	6055	SO:0001819	synonymous_variant	146760	exon2			TGGGGCATAGTCT	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.1140T>C	17.37:g.1839976A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	193	91	0.471503	NM_178568		Silent	SNP	ENST00000331238.6	37	CCDS45569.1																																																																																			.	.	none		0.637	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568	
GPR123	84435	hgsc.bcm.edu	37	10	134942832	134942832	+	Silent	SNP	G	G	A	rs45586231	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	27	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	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		
RERG	85004	hgsc.bcm.edu	37	12	15262273	15262273	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:15262273T>A	ENST00000256953.2	-	5	707	c.371A>T	c.(370-372)cAc>cTc	p.H124L	RERG_ENST00000536465.1_Missense_Mutation_p.H124L|RERG_ENST00000546331.1_Missense_Mutation_p.H105L|RERG_ENST00000538313.1_Missense_Mutation_p.H124L	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	124					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						CTGCCTGGAGTGGTCCAAGTC	0.473																																					p.H124L		Atlas-SNP	.											.	RERG	30	.	0			c.A371T						PASS	.						236.0	211.0	219.0					12																	15262273		2203	4300	6503	SO:0001583	missense	85004	exon5			CTGGAGTGGTCCA	AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.371A>T	12.37:g.15262273T>A	ENSP00000256953:p.His124Leu	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	219	99	0.452055	NM_032918	B2R9R0|B4DI02	Missense_Mutation	SNP	ENST00000256953.2	37	CCDS8673.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.792870	0.70452	.	.	ENSG00000134533	ENST00000256953;ENST00000538313;ENST00000536465;ENST00000546331	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.33	5.33	0.75918	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.74898	0.3777	L	0.45744	1.44	0.80722	D	1	B;B	0.26400	0.148;0.012	B;B	0.20577	0.03;0.018	T	0.72679	-0.4220	10	0.44086	T	0.13	.	14.4198	0.67175	0.0:0.0:0.0:1.0	.	105;124	B4DI02;Q96A58	.;RERG_HUMAN	L	124;124;124;105	ENSP00000256953:H124L;ENSP00000441505:H124L;ENSP00000438280:H124L;ENSP00000444485:H105L	ENSP00000256953:H124L	H	-	2	0	RERG	15153540	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.992000	0.88273	2.145000	0.66743	0.533000	0.62120	CAC	.	.	none		0.473	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781614	88781614	+	IGR	SNP	G	G	C	rs1058158	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88781614G>C	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Silent_p.R414R|CTU2_ENST00000453996.2_Silent_p.R501R|CTU2_ENST00000567949.1_Silent_p.R572R|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.G482R	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						AGGAGATCCGGGACTGTCTGA	0.662													G|||	967	0.193091	0.1021	0.1844	5008	,	,		13563	0.0913		0.3082	False		,,,				2504	0.3088				p.G482R		Atlas-SNP	.											.	CTU2	66	.	0			c.G1444C						PASS	.	G	,ARG/GLY	584,3800	254.0+/-259.7	35,514,1643	89.0	80.0	83.0		1503,1444	2.1	0.9	16	dbSNP_86	83	2639,5949	423.7+/-354.4	407,1825,2062	yes	coding-synonymous,missense	CTU2	NM_001012759.1,NM_001012762.1	,125	442,2339,3705	CC,CG,GG		30.7289,13.3212,24.8458	,	501/516,482/486	88781614	3223,9749	2192	4294	6486	SO:0001628	intergenic_variant	348180	exon14			GATCCGGGACTGT	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		16.37:g.88781614G>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_001012762	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	396	0.1813186813186813	53	0.10772357723577236	78	0.2154696132596685	48	0.08391608391608392	217	0.2862796833773087	G	7.321	0.616970	0.14129	0.133212	0.307289	ENSG00000174177	ENST00000312060	T	0.13901	2.55	5.19	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	B	0.31413	0.322	B	0.31812	0.136	T	0.49679	-0.8914	7	0.19147	T	0.46	.	9.0299	0.36252	0.2539:0.0:0.7461:0.0	rs1058158;rs3169255;rs17846640;rs17859735;rs56871681	482	Q2VPK5-5	.	R	482	ENSP00000308617:G482R	ENSP00000308617:G482R	G	+	1	0	CTU2	87309115	0.126000	0.22350	0.870000	0.34147	0.009000	0.06853	0.362000	0.20284	0.699000	0.31761	-0.258000	0.10820	GGA	C|0.228;G|0.772;T|0.000	0.228	strong		0.662	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
ATR	545	hgsc.bcm.edu	37	3	142217537	142217537	+	Silent	SNP	A	A	G	rs2227932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:142217537A>G	ENST00000350721.4	-	32	5581	c.5460T>C	c.(5458-5460)taT>taC	p.Y1820Y	ATR_ENST00000383101.3_Silent_p.Y1756Y	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1820	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						TCAGTGAGTCATAAAAAGCTG	0.383								Other conserved DNA damage response genes					A|||	335	0.066893	0.0015	0.072	5008	,	,		18070	0.003		0.1272	False		,,,				2504	0.1554				p.Y1820Y		Atlas-SNP	.											.	ATR	285	.	0			c.T5460C						PASS	.	A		86,4320	72.0+/-110.0	1,84,2118	84.0	80.0	81.0		5460	5.1	1.0	3	dbSNP_98	81	913,7687	201.8+/-245.2	56,801,3443	no	coding-synonymous	ATR	NM_001184.3		57,885,5561	GG,GA,AA		10.6163,1.9519,7.6811		1820/2645	142217537	999,12007	2203	4300	6503	SO:0001819	synonymous_variant	545	exon32			TGAGTCATAAAAA	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.5460T>C	3.37:g.142217537A>G		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																			T|0.074;G|0.067	0.067	strong		0.383	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45255637	45255637	+	Missense_Mutation	SNP	G	G	C	rs6007344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45255637G>C	ENST00000389774.2	+	12	1138	c.997G>C	c.(997-999)Ggc>Cgc	p.G333R	PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.G512R|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.G302R|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.G424R|ARHGAP8_ENST00000336963.4_Intron|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.G512R|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.G433R	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	333	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.		G -> R (in dbSNP:rs6007344).		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)		GCGTGTCACTGGCTGCCGCCA	0.667													C|||	1345	0.26857	0.3207	0.1297	5008	,	,		18585	0.4048		0.1899	False		,,,				2504	0.2372				p.G424R		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.G1270C						PASS	.	C	ARG/GLY,,ARG/GLY,ARG/GLY	1322,3084	692.5+/-405.5	199,924,1080	64.0	56.0	59.0		997,,1270,904	-2.7	0.0	22	dbSNP_114	59	1493,7107	747.3+/-407.3	129,1235,2936	yes	missense,intron,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	125,,125,125	328,2159,4016	CC,CG,GG		17.3605,30.0045,21.6439	benign,,benign,benign	333/465,,424/556,302/434	45255637	2815,10191	2203	4300	6503	SO:0001583	missense	553158	exon14			GTCACTGGCTGCC	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.997G>C	22.37:g.45255637G>C	ENSP00000374424:p.Gly333Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	600	0.27472527472527475	136	0.2764227642276423	59	0.16298342541436464	260	0.45454545454545453	145	0.19129287598944592	C	0.014	-1.573230	0.00887	0.300045	0.173605	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000356099	T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25	4.14	-2.67	0.06059	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.962577	0.08458	N	0.942827	T	0.00012	0.0000	N	0.01679	-0.765	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	0.47420	-0.9119	9	0.22109	T	0.4	.	1.8601	0.03187	0.1794:0.3824:0.0925:0.3457	rs6007344;rs17846432;rs17859481;rs59835638;rs6007344	355;338;333;512;433	B7ZMA4;A2RU51;P85298;B1AHC4;B1AHC3	.;.;RHG08_HUMAN;.;.	R	433;512;512;424;333;302	ENSP00000354732:G433R;ENSP00000262731:G512R;ENSP00000429240:G512R;ENSP00000374423:G424R;ENSP00000374424:G333R;ENSP00000348407:G302R	ENSP00000348407:G302R	G	+	1	0	PRR5-ARHGAP8;ARHGAP8	43634301	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.388000	0.07352	-0.532000	0.06332	-1.565000	0.00878	GGC	G|0.764;C|0.236	0.236	strong		0.667	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
TCHH	7062	hgsc.bcm.edu	37	1	152084213	152084213	+	Missense_Mutation	SNP	C	C	G	rs199978168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152084213C>G	ENST00000368804.1	-	2	1479	c.1480G>C	c.(1480-1482)Gag>Cag	p.E494Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	494	9 X 28 AA approximate 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)			CGCCTCTCCTCCTCCTCGAGC	0.667																																					p.E494Q		Atlas-SNP	.											.	TCHH	275	.	0			c.G1480C						PASS	.						63.0	71.0	68.0					1																	152084213		2108	4221	6329	SO:0001583	missense	7062	exon3			TCTCCTCCTCCTC	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.1480G>C	1.37:g.152084213C>G	ENSP00000357794:p.Glu494Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	177	25	0.141243	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	7.483	0.649136	0.14516	.	.	ENSG00000159450	ENST00000368804	T	0.05199	3.48	3.42	0.2	0.15181	.	.	.	.	.	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.26081	0.141	B	0.20767	0.031	T	0.47381	-0.9122	9	0.21014	T	0.42	.	7.1235	0.25458	0.0:0.3768:0.5138:0.1093	.	494	Q07283	TRHY_HUMAN	Q	494	ENSP00000357794:E494Q	ENSP00000357794:E494Q	E	-	1	0	TCHH	150350837	0.000000	0.05858	0.001000	0.08648	0.031000	0.12232	0.016000	0.13377	0.159000	0.19401	-0.742000	0.03525	GAG	C|0.978;G|0.023	0.023	strong		0.667	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
MLPH	79083	hgsc.bcm.edu	37	2	238449107	238449107	+	Silent	SNP	A	A	G	rs2271809|rs386656756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238449107A>G	ENST00000264605.3	+	10	1515	c.1221A>G	c.(1219-1221)gaA>gaG	p.E407E	MLPH_ENST00000338530.4_Silent_p.E379E|MLPH_ENST00000409373.1_Silent_p.E339E|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Silent_p.E407E|MLPH_ENST00000410032.1_Silent_p.E264E	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	407					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)	p.E407E(1)		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)		AGGAGGAGGAAGCCAAGGACG	0.622													G|||	2532	0.505591	0.8873	0.3573	5008	,	,		20291	0.4226		0.2485	False		,,,				2504	0.4448				p.E407E		Atlas-SNP	.											MLPH,NS,carcinoma,0,2	MLPH	41	2	1	Substitution - coding silent(1)	stomach(1)	c.A1221G						PASS	.	G	,	3403,1003		1421,561,221	77.0	74.0	75.0		1137,1221	0.8	0.0	2	dbSNP_100	75	2263,6335		360,1543,2396	no	coding-synonymous,coding-synonymous	MLPH	NM_001042467.1,NM_024101.5	,	1781,2104,2617	GG,GA,AA		26.3201,22.7644,43.5712	,	379/573,407/601	238449107	5666,7338	2203	4299	6502	SO:0001819	synonymous_variant	79083	exon10			GGAGGAAGCCAAG	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.1221A>G	2.37:g.238449107A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Silent	SNP	ENST00000264605.3	37	CCDS2518.1	952|952	0.4358974358974359|0.4358974358974359	427|427	0.8678861788617886|0.8678861788617886	117|117	0.32320441988950277|0.32320441988950277	225|225	0.39335664335664333|0.39335664335664333	183|183	0.24142480211081793|0.24142480211081793	G|G	0.093|0.093	-1.163772|-1.163772	0.01673|0.01673	0.772356|0.772356	0.263201|0.263201	ENSG00000115648|ENSG00000115648	ENST00000436965|ENST00000415753	.|.	.|.	.|.	2.76|2.76	0.838|0.838	0.18902|0.18902	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.48341|0.48341	P|P	3.630000000000022E-4|3.630000000000022E-4	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.15150|0.15150	-1.0447|-1.0447	3|3	.|.	.|.	.|.	-5.625|-5.625	4.1178|4.1178	0.10090|0.10090	0.2496:0.1953:0.5551:0.0|0.2496:0.1953:0.5551:0.0	rs2271809|rs2271809	.|.	.|.	.|.	R|G	128|95	.|.	.|.	K|S	+|+	2|1	0|0	MLPH|MLPH	238113846|238113846	0.209000|0.209000	0.23505|0.23505	0.015000|0.015000	0.15790|0.15790	0.028000|0.028000	0.11728|0.11728	0.760000|0.760000	0.26475|0.26475	-0.372000|-0.372000	0.07992|0.07992	-0.128000|-0.128000	0.14901|0.14901	AAG|AGC	A|0.549;C|0.000;G|0.450;T|0.000	0.450	strong		0.622	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
MYLK	4638	hgsc.bcm.edu	37	3	123419733	123419733	+	Missense_Mutation	SNP	A	A	G	rs3732486	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:123419733A>G	ENST00000475616.1	-	15	2581	c.2582T>C	c.(2581-2583)cTa>cCa	p.L861P	MYLK_ENST00000346322.5_Missense_Mutation_p.L792P|MYLK_ENST00000360772.3_Missense_Mutation_p.L861P|MYLK_ENST00000359169.1_Missense_Mutation_p.L861P|MYLK_ENST00000360304.3_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	30	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	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	
BAZ2B	29994	hgsc.bcm.edu	37	2	160310246	160310246	+	Missense_Mutation	SNP	A	A	G	rs10202670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160310246A>G	ENST00000392783.2	-	4	707	c.212T>C	c.(211-213)aTg>aCg	p.M71T	BAZ2B_ENST00000355831.2_Missense_Mutation_p.M71T|BAZ2B_ENST00000343439.5_Missense_Mutation_p.M71T|BAZ2B_ENST00000392782.1_Missense_Mutation_p.M71T	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	71			M -> T (in dbSNP:rs10202670). {ECO:0000269|PubMed:17974005}.		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						GTGGCTGACCATTGGGAAGGC	0.493													A|||	358	0.0714856	0.0287	0.0605	5008	,	,		14437	0.0129		0.1153	False		,,,				2504	0.1524				p.M71T		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T212C						PASS	.	A	THR/MET	135,3693		1,133,1780	84.0	80.0	82.0		212	5.5	1.0	2	dbSNP_119	82	1000,7238		57,886,3176	yes	missense	BAZ2B	NM_013450.2	81	58,1019,4956	GG,GA,AA		12.1389,3.5266,9.4066	benign	71/2169	160310246	1135,10931	1914	4119	6033	SO:0001583	missense	29994	exon4			CTGACCATTGGGA	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.212T>C	2.37:g.160310246A>G	ENSP00000376534:p.Met71Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	151	0.06913919413919414	21	0.042682926829268296	29	0.08011049723756906	7	0.012237762237762238	94	0.12401055408970976	A	17.00	3.276231	0.59649	0.035266	0.121389	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000437839	T;T;T;T;T	0.32515	2.79;2.79;2.79;2.79;1.45	5.46	5.46	0.80206	.	.	.	.	.	T	0.00468	0.0015	L	0.54323	1.7	0.32974	P	0.47727699999999995	B;B;B	0.27732	0.187;0.065;0.039	B;B;B	0.25291	0.059;0.037;0.016	T	0.06570	-1.0819	8	0.87932	D	0	-2.5228	14.5001	0.67716	1.0:0.0:0.0:0.0	rs10202670;rs17495474;rs10202670	71;71;71	Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;BAZ2B_HUMAN	T	71	ENSP00000376533:M71T;ENSP00000376534:M71T;ENSP00000348087:M71T;ENSP00000339670:M71T;ENSP00000415613:M71T	ENSP00000339670:M71T	M	-	2	0	BAZ2B	160018492	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.256000	0.89848	2.066000	0.61787	0.533000	0.62120	ATG	A|0.916;G|0.084	0.084	strong		0.493	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
CETP	1071	hgsc.bcm.edu	37	16	57016092	57016092	+	Missense_Mutation	SNP	G	G	A	rs5882	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57016092G>A	ENST00000566128.1	+	14	1336	c.1069G>A	c.(1069-1071)Gtc>Atc	p.V357I	CETP_ENST00000200676.3_Missense_Mutation_p.V422I|CETP_ENST00000379780.2_Missense_Mutation_p.V362I					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CTCCGAGTCCGTCCAGAGCTT	0.587													g|||	2674	0.533946	0.3623	0.5994	5008	,	,		19194	0.5635		0.669	False		,,,				2504	0.5501				p.V422I		Atlas-SNP	.											.	CETP	50	.	0			c.G1264A	GRCh37	CM994290	CETP	M	rs5882	PASS	.		ILE/VAL	1823,2573	532.3+/-373.4	381,1061,756	135.0	107.0	117.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1264	-6.7	0.0	16	dbSNP_52	117	5860,2740	680.4+/-403.6	2030,1800,470	yes	missense	CETP	NM_000078.2	29	2411,2861,1226	AA,AG,GG		31.8605,41.4695,40.8818	benign	422/494	57016092	7683,5313	2198	4300	6498	SO:0001583	missense	1071	exon14			GAGTCCGTCCAGA	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.1069G>A	16.37:g.57016092G>A	ENSP00000456276:p.Val357Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	97	0.97	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		1206	0.5521978021978022	179	0.3638211382113821	224	0.6187845303867403	297	0.5192307692307693	506	0.6675461741424802	g	0.227	-1.024059	0.02061	0.414695	0.681395	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.06068	3.35;3.35	3.66	-6.67	0.01783	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.138590	0.06726	N	0.775724	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.33445	-0.9868	9	0.23891	T	0.37	-0.3616	8.142	0.31089	0.6186:0.1265:0.2549:0.0	rs5882;rs289738;rs1131843;rs1613122;rs1801707;rs3192075;rs12720881;rs17231896;rs17414131;rs17845778;rs17858738;rs61212082;rs5882	362;422	P11597-2;P11597	.;CETP_HUMAN	I	422;362	ENSP00000200676:V422I;ENSP00000369106:V362I	ENSP00000200676:V422I	V	+	1	0	CETP	55573593	0.000000	0.05858	0.001000	0.08648	0.221000	0.24807	-2.553000	0.00927	-1.419000	0.02012	-0.461000	0.05368	GTC	G|0.426;A|0.574	0.574	strong		0.587	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
IKZF1	10320	hgsc.bcm.edu	37	7	50467767	50467767	+	Silent	SNP	C	C	A	rs61731355	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:50467767C>A	ENST00000331340.3	+	8	1157	c.1002C>A	c.(1000-1002)ccC>ccA	p.P334P	IKZF1_ENST00000439701.1_Silent_p.P292P|IKZF1_ENST00000343574.5_Silent_p.P247P|IKZF1_ENST00000438033.1_Silent_p.P247P|IKZF1_ENST00000359197.5_Silent_p.P292P|IKZF1_ENST00000349824.4_Silent_p.P191P|IKZF1_ENST00000357364.4_Silent_p.P247P|IKZF1_ENST00000346667.4_Silent_p.P104P|IKZF1_ENST00000440768.2_3'UTR	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	41	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	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	
TTN	7273	hgsc.bcm.edu	37	2	179587130	179587130	+	Missense_Mutation	SNP	C	C	G	rs12693166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179587130C>G	ENST00000591111.1	-	75	21657	c.21433G>C	c.(21433-21435)Gat>Cat	p.D7145H	TTN_ENST00000589042.1_Missense_Mutation_p.D7462H|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.D6218H|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12720	Ig-like 53.			D -> H (in Ref. 1; CAA62189). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGATTTTCATCGTCTCTTAAA	0.408													C|||	1237	0.247005	0.202	0.1844	5008	,	,		19242	0.4375		0.1581	False		,,,				2504	0.2474				p.D7462H		Atlas-SNP	.											.	TTN	18412	.	0			c.G22384C						PASS	.	C	HIS/ASP,,,	623,3087		52,519,1284	61.0	59.0	60.0		18652,,,	6.2	1.0	2	dbSNP_121	60	1252,6966		97,1058,2954	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	81,,,	149,1577,4238	GG,GC,CC		15.2349,16.7925,15.7193	probably-damaging,,,	6218/33424,,,	179587130	1875,10053	1855	4109	5964	SO:0001583	missense	7273	exon77			TTTCATCGTCTCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.21433G>C	2.37:g.179587130C>G	ENSP00000465570:p.Asp7145His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		513	0.2348901098901099	98	0.1991869918699187	55	0.15193370165745856	244	0.42657342657342656	116	0.15303430079155672	C	13.78	2.338338	0.41398	0.167925	0.152349	ENSG00000155657	ENST00000342992	T	0.73897	-0.79	6.16	6.16	0.99307	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.76328	2.33	0.09310	P	1.0	D	0.89917	1.0	D	0.81914	0.995	T	0.06698	-1.0812	8	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	rs12693166;rs56624981;rs12693166	7145	Q8WZ42	TITIN_HUMAN	H	6218	ENSP00000343764:D6218H	ENSP00000343764:D6218H	D	-	1	0	TTN	179295375	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.786000	0.85741	2.937000	0.99478	0.650000	0.86243	GAT	C|0.765;G|0.235	0.235	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MUC5B	727897	hgsc.bcm.edu	37	11	1269215	1269215	+	Missense_Mutation	SNP	C	C	T	rs34528873	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1269215C>T	ENST00000529681.1	+	31	11163	c.11105C>T	c.(11104-11106)aCg>aTg	p.T3702M	MUC5B_ENST00000447027.1_Missense_Mutation_p.T3705M|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3702	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACAGCCACTACGACTGAGTCC	0.667													c|||	421	0.0840655	0.028	0.0821	5008	,	,		15787	0.0208		0.1471	False		,,,				2504	0.1616				p.T3702M		Atlas-SNP	.											MUC5B,caecum,carcinoma,-1,2	MUC5B	473	2	0			c.C11105T						PASS	.	C	MET/THR	174,3914		13,148,1883	93.0	121.0	112.0		11105	-0.7	0.0	11	dbSNP_131	112	1311,7009		138,1035,2987	no	missense	MUC5B	NM_002458.2	81	151,1183,4870	TT,TC,CC		15.7572,4.2564,11.9681	possibly-damaging	3702/5763	1269215	1485,10923	2044	4160	6204	SO:0001583	missense	727897	exon31			CCACTACGACTGA	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.11105C>T	11.37:g.1269215C>T	ENSP00000436812:p.Thr3702Met	Somatic	505	0	0		WXS	Illumina HiSeq	Phase_I	474	207	0.436709	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	4.022	0.001605	0.07819	0.042564	0.157572	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.19105	2.17;2.29	2.73	-0.734	0.11140	.	.	.	.	.	T	0.00039	0.0001	L	0.39898	1.24	0.09310	N	1	P;D	0.56035	0.928;0.974	B;B	0.40134	0.211;0.32	T	0.21245	-1.0251	9	0.87932	D	0	.	3.9079	0.09190	0.0:0.4838:0.2226:0.2936	.	4230;3705	A7Y9J9;E9PBJ0	.;.	M	3702;3705;3674;3607	ENSP00000436812:T3702M;ENSP00000415793:T3705M	ENSP00000343037:T3674M	T	+	2	0	MUC5B	1225791	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.099000	0.11007	-0.112000	0.11979	-0.424000	0.05967	ACG	C|0.866;T|0.134	0.134	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
GRIK4	2900	hgsc.bcm.edu	37	11	120745874	120745874	+	Silent	SNP	C	C	T	rs2230297	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:120745874C>T	ENST00000527524.2	+	11	1373	c.1086C>T	c.(1084-1086)caC>caT	p.H362H	GRIK4_ENST00000438375.2_Silent_p.H362H|RP11-640N11.2_ENST00000505153.2_RNA	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	362					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)		TTACCGGCCACATTGAATTCA	0.488													c|||	1165	0.232628	0.1536	0.1513	5008	,	,		21003	0.4593		0.1262	False		,,,				2504	0.273				p.H362H		Atlas-SNP	.											.	GRIK4	149	.	0			c.C1086T						PASS	.	C		728,3678	302.1+/-287.2	65,598,1540	126.0	109.0	115.0		1086	4.9	1.0	11	dbSNP_98	115	1164,7434	237.1+/-269.0	77,1010,3212	no	coding-synonymous	GRIK4	NM_014619.2		142,1608,4752	TT,TC,CC		13.538,16.5229,14.5494		362/957	120745874	1892,11112	2203	4299	6502	SO:0001819	synonymous_variant	2900	exon9			CGGCCACATTGAA	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.1086C>T	11.37:g.120745874C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_014619	A8K9L1	Silent	SNP	ENST00000527524.2	37	CCDS8433.1																																																																																			C|0.818;T|0.182	0.182	strong		0.488	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
INPP5K	51763	hgsc.bcm.edu	37	17	1417231	1417231	+	Silent	SNP	A	A	C	rs61733750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1417231A>C	ENST00000421807.2	-	2	475	c.87T>G	c.(85-87)ccT>ccG	p.P29P	INPP5K_ENST00000542125.1_Silent_p.P29P|PITPNA-AS1_ENST00000425081.2_RNA|INPP5K_ENST00000397335.3_Intron|INPP5K_ENST00000320345.6_5'UTR|INPP5K_ENST00000406424.4_5'UTR	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	29	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|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)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						TGAGATCTAGAGGGGGCGCTG	0.542													A|||	131	0.0261581	0.0053	0.0288	5008	,	,		20788	0.0069		0.0646	False		,,,				2504	0.0327				p.P29P		Atlas-SNP	.											.	INPP5K	30	.	0			c.T87G						PASS	.	A	,,	95,4311	77.3+/-115.6	4,87,2112	119.0	93.0	102.0		,87,	0.6	0.5	17	dbSNP_129	102	634,7966	164.2+/-216.6	25,584,3691	no	utr-5,coding-synonymous,utr-5	INPP5K	NM_001135642.1,NM_016532.3,NM_130766.2	,,	29,671,5803	CC,CA,AA		7.3721,2.1562,5.6051	,,	,29/449,	1417231	729,12277	2203	4300	6503	SO:0001819	synonymous_variant	51763	exon2			ATCTAGAGGGGGC		CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"""skeletal muscle and kidney enriched inositol phosphatase"""	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.87T>G	17.37:g.1417231A>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_016532	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Silent	SNP	ENST00000421807.2	37	CCDS11004.1																																																																																			A|0.952;C|0.048	0.048	strong		0.542	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4		
SLC9C1	285335	hgsc.bcm.edu	37	3	111962851	111962851	+	Missense_Mutation	SNP	T	T	C	rs6768523	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:111962851T>C	ENST00000305815.5	-	11	1522	c.1270A>G	c.(1270-1272)Act>Gct	p.T424A	SLC9C1_ENST00000487372.1_Missense_Mutation_p.T376A	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	424			T -> A (in dbSNP:rs6768523). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CCTAGTATAGTAACTGCCACT	0.313													T|||	1627	0.32488	0.3427	0.3963	5008	,	,		17034	0.3304		0.2376	False		,,,				2504	0.3344				p.T424A		Atlas-SNP	.											.	.	.	.	0			c.A1270G						PASS	.	T	ALA/THR	1465,2941	465.1+/-354.1	249,967,987	69.0	74.0	72.0		1270	4.0	0.9	3	dbSNP_116	72	2328,6272	387.2+/-342.1	320,1688,2292	yes	missense	SLC9A10	NM_183061.1	58	569,2655,3279	CC,CT,TT		27.0698,33.2501,29.1635	benign	424/1178	111962851	3793,9213	2203	4300	6503	SO:0001583	missense	285335	exon11			GTATAGTAACTGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1270A>G	3.37:g.111962851T>C	ENSP00000306627:p.Thr424Ala	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	109	64	0.587156	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	669	0.30631868131868134	167	0.3394308943089431	134	0.3701657458563536	183	0.31993006993006995	185	0.24406332453825857	T	2.635	-0.285462	0.05605	0.332501	0.270698	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.76709	-1.04;-1.04	5.11	3.96	0.45880	.	1.027890	0.07726	N	0.944446	T	0.00012	0.0000	L	0.40543	1.245	0.38456	P	0.052908999999999984	B;P	0.34462	0.202;0.454	B;B	0.38755	0.281;0.192	T	0.09250	-1.0683	9	0.30078	T	0.28	-7.0031	7.6407	0.28292	0.0:0.0978:0.0:0.9022	rs6768523;rs52800559;rs56653457;rs6768523	376;424	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	A	424;376	ENSP00000306627:T424A;ENSP00000420688:T376A	ENSP00000306627:T424A	T	-	1	0	SLC9A10	113445541	0.185000	0.23213	0.936000	0.37596	0.290000	0.27261	0.071000	0.14594	0.896000	0.36366	0.352000	0.21897	ACT	T|0.708;C|0.292	0.292	strong		0.313	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
TDRD9	122402	hgsc.bcm.edu	37	14	104436931	104436931	+	Silent	SNP	C	C	T	rs11851097	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104436931C>T	ENST00000409874.4	+	6	867	c.819C>T	c.(817-819)ctC>ctT	p.L273L	TDRD9_ENST00000339063.5_Silent_p.L273L	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	273	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L273L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TCCGCAAACTCTTAAGAACAA	0.373													C|||	1760	0.351438	0.3631	0.3646	5008	,	,		19346	0.3353		0.3688	False		,,,				2504	0.3252				p.L273L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,0,1	TDRD9	175	1	1	Substitution - coding silent(1)	stomach(1)	c.C819T						PASS	.	C		516,868		96,324,272	206.0	176.0	185.0		819	3.3	0.9	14	dbSNP_120	185	1127,2055		198,731,662	no	coding-synonymous	TDRD9	NM_153046.2		294,1055,934	TT,TC,CC		35.418,37.2832,35.9834		273/1383	104436931	1643,2923	692	1591	2283	SO:0001819	synonymous_variant	122402	exon6			CAAACTCTTAAGA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.819C>T	14.37:g.104436931C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2																																																																																			C|0.648;T|0.352	0.352	strong		0.373	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
NEIL3	55247	hgsc.bcm.edu	37	4	178262784	178262784	+	Missense_Mutation	SNP	A	A	G	rs34193982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:178262784A>G	ENST00000264596.3	+	6	975	c.857A>G	c.(856-858)cAt>cGt	p.H286R	RP11-376O6.2_ENST00000506895.1_RNA	NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	286			H -> R (in dbSNP:rs34193982). {ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AATCCTCAACATGTTGACATA	0.363								Base excision repair (BER), DNA glycosylases					A|||	457	0.091254	0.0053	0.0533	5008	,	,		18278	0.1012		0.161	False		,,,				2504	0.1524				p.H286R		Atlas-SNP	.											.	NEIL3	89	.	0			c.A857G						PASS	.	A	ARG/HIS	118,4288	88.7+/-127.4	2,114,2087	85.0	76.0	79.0		857	-4.6	0.0	4	dbSNP_126	79	1324,7276	260.6+/-283.4	97,1130,3073	yes	missense	NEIL3	NM_018248.2	29	99,1244,5160	GG,GA,AA		15.3953,2.6782,11.0872	benign	286/606	178262784	1442,11564	2203	4300	6503	SO:0001583	missense	55247	exon6			CTCAACATGTTGA	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.857A>G	4.37:g.178262784A>G	ENSP00000264596:p.His286Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	223	0.1021062271062271	4	0.008130081300813009	33	0.09116022099447514	63	0.11013986013986014	123	0.16226912928759896	A	6.487	0.458106	0.12342	0.026782	0.153953	ENSG00000109674	ENST00000264596	T	0.03717	3.83	5.24	-4.55	0.03441	.	0.860608	0.10787	N	0.634143	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48875	-0.8996	9	0.13853	T	0.58	-1.6377	0.0153	0.00002	0.3143:0.1952:0.2021:0.2884	rs34193982	286	Q8TAT5	NEIL3_HUMAN	R	286	ENSP00000264596:H286R	ENSP00000264596:H286R	H	+	2	0	NEIL3	178499778	0.011000	0.17503	0.007000	0.13788	0.997000	0.91878	0.245000	0.18142	-0.480000	0.06803	0.533000	0.62120	CAT	A|0.894;G|0.106	0.106	strong		0.363	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062023	64062023	+	Missense_Mutation	SNP	A	A	C	rs10878073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	182	0	0		WXS	Illumina HiSeq	Phase_I	176	67	0.380682	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	
IDS	3423	hgsc.bcm.edu	37	X	148582549	148582549	+	Silent	SNP	G	G	A	rs1141608	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:148582549G>A	ENST00000340855.6	-	4	647	c.438C>T	c.(436-438)acC>acT	p.T146T	IDS_ENST00000370443.4_Silent_p.T146T|IDS_ENST00000427113.2_5'Flank|IDS_ENST00000370441.4_Silent_p.T146T|IDS_ENST00000541269.1_5'UTR|IDS_ENST00000422081.2_5'UTR|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	31	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	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		
ENTHD1	150350	hgsc.bcm.edu	37	22	40283427	40283427	+	Missense_Mutation	SNP	A	A	G	rs17319801	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:40283427A>G	ENST00000325157.6	-	2	576	c.326T>C	c.(325-327)aTa>aCa	p.I109T		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	109	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.		I -> T (in dbSNP:rs17319801).							breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					AGCTTCATCTATGTGCTGAAA	0.418													A|||	236	0.0471246	0.003	0.1124	5008	,	,		19715	0.001		0.0646	False		,,,				2504	0.09				p.I109T		Atlas-SNP	.											.	ENTHD1	83	.	0			c.T326C						PASS	.	A	THR/ILE	60,4346	56.8+/-93.2	0,60,2143	106.0	106.0	106.0		326	5.4	1.0	22	dbSNP_123	106	416,8184	130.3+/-188.3	11,394,3895	yes	missense	ENTHD1	NM_152512.3	89	11,454,6038	GG,GA,AA		4.8372,1.3618,3.6598	possibly-damaging	109/608	40283427	476,12530	2203	4300	6503	SO:0001583	missense	150350	exon2			TCATCTATGTGCT	AK093154	CCDS13998.1	22q13.1	2006-06-26			ENSG00000176177	ENSG00000176177			26352	protein-coding gene	gene with protein product						12477932	Standard	NM_152512		Approved	FLJ25421	uc003ayg.3	Q8IYW4	OTTHUMG00000151098	ENST00000325157.6:c.326T>C	22.37:g.40283427A>G	ENSP00000317431:p.Ile109Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_152512	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	37	CCDS13998.1	83	0.038003663003663	1	0.0020325203252032522	35	0.09668508287292818	0	0.0	47	0.06200527704485488	A	15.12	2.740547	0.49045	0.013618	0.048372	ENSG00000176177	ENST00000325157	T	0.47528	0.84	5.41	5.41	0.78517	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.463226	0.23358	N	0.049055	T	0.01558	0.0050	L	0.50919	1.6	0.31447	P	0.671288	P	0.36010	0.532	B	0.38755	0.281	T	0.38001	-0.9681	9	0.62326	D	0.03	-7.4004	11.6943	0.51534	0.9287:0.0:0.0713:0.0	rs17319801;rs17319801	109	Q8IYW4	ENTD1_HUMAN	T	109	ENSP00000317431:I109T	ENSP00000317431:I109T	I	-	2	0	ENTHD1	38613373	0.606000	0.26949	0.991000	0.47740	0.993000	0.82548	5.181000	0.65054	2.171000	0.68590	0.533000	0.62120	ATA	A|0.962;G|0.038	0.038	strong		0.418	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512	
ZRSR2	8233	hgsc.bcm.edu	37	X	15838411	15838411	+	Silent	SNP	C	C	T	rs148608893	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:15838411C>T	ENST00000307771.7	+	10	933	c.909C>T	c.(907-909)ccC>ccT	p.P303P		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	303	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					AATTCTGCCCCGTGACCCGGT	0.428			"""F, S, Mis"""		"""MDS, CLL"""								C|||	14	0.00370861	0.0008	0.0043	3775	,	,		15256	0.0		0.008	False		,,,				2504	0.002				p.P303P	NSCLC(197;1631 3042 5741 31152)	Atlas-SNP	.		Rec	yes		X	Xp22.1	8233	"""zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"""		L	.	ZRSR2	78	.	0			c.C909T						PASS	.	C		4,3831		0,4,0,1628,571	136.0	128.0	131.0		909	-8.0	0.8	X	dbSNP_134	131	70,6658		0,52,18,2376,1854	no	coding-synonymous	ZRSR2	NM_005089.3		0,56,18,4004,2425	TT,TC,T,CC,C		1.0404,0.1043,0.7006		303/483	15838411	74,10489	2203	4300	6503	SO:0001819	synonymous_variant	8233	exon10			CTGCCCCGTGACC	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	23019	protein-coding gene	gene with protein product		300028	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 2"", ""U2 small nuclear RNA auxiliary factor 1-like 2"""	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.909C>T	X.37:g.15838411C>T		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	280	279	0.996429	NM_005089	Q14D69	Silent	SNP	ENST00000307771.7	37	CCDS14172.1																																																																																			C|0.994;T|0.006	0.006	strong		0.428	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089	
B4GALNT4	338707	hgsc.bcm.edu	37	11	372700	372700	+	Silent	SNP	G	G	C	rs35475866	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	97	0.989796	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	
MUC7	4589	hgsc.bcm.edu	37	4	71347171	71347171	+	Missense_Mutation	SNP	C	C	T	rs147763101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71347171C>T	ENST00000304887.5	+	3	900	c.710C>T	c.(709-711)gCc>gTc	p.A237V	MUC7_ENST00000413702.1_Missense_Mutation_p.A237V|MUC7_ENST00000456088.1_Missense_Mutation_p.A237V	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	237	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.A237V(1)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			ACCACAGCTGCCCCACCCACA	0.587																																					p.A237V		Atlas-SNP	.											MUC7,trunk,malignant_melanoma,0,1	MUC7	91	1	1	Substitution - Missense(1)	skin(1)	c.C710T						PASS	.						387.0	316.0	340.0					4																	71347171		2203	4300	6503	SO:0001583	missense	4589	exon4			CAGCTGCCCCACC	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.710C>T	4.37:g.71347171C>T	ENSP00000302021:p.Ala237Val	Somatic	392	0	0		WXS	Illumina HiSeq	Phase_I	290	55	0.189655	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	c	9.877	1.200531	0.22121	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.59772	0.24;0.24;0.24	2.03	1.17	0.20885	.	.	.	.	.	T	0.39911	0.1096	N	0.19112	0.55	0.20975	N	0.999817	P	0.50943	0.94	B	0.43809	0.432	T	0.17198	-1.0377	8	.	.	.	-1.8774	6.8415	0.23965	0.0:0.8404:0.0:0.1596	.	237	Q8TAX7	MUC7_HUMAN	V	237	ENSP00000407422:A237V;ENSP00000400585:A237V;ENSP00000302021:A237V	.	A	+	2	0	MUC7	71381760	0.004000	0.15560	0.026000	0.17262	0.070000	0.16714	0.994000	0.29693	0.392000	0.25172	-0.150000	0.13652	GCC	C|0.991;T|0.010	0.010	strong		0.587	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
CPNE8	144402	hgsc.bcm.edu	37	12	39087609	39087609	+	Silent	SNP	G	G	A	rs3759139	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:39087609G>A	ENST00000331366.5	-	15	1089	c.993C>T	c.(991-993)taC>taT	p.Y331Y	CPNE8_ENST00000538596.2_5'UTR|CPNE8_ENST00000360449.3_Silent_p.Y319Y	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	331	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular vesicular exosome (GO:0070062)		p.Y331Y(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				AAGGATTCATGTAGTGGAGGG	0.378													G|||	1314	0.26238	0.0477	0.2997	5008	,	,		17328	0.2331		0.4493	False		,,,				2504	0.364				p.Y331Y		Atlas-SNP	.											CPNE8,NS,carcinoma,0,1	CPNE8	66	1	1	Substitution - coding silent(1)	stomach(1)	c.C993T						PASS	.	G		450,3956	215.1+/-234.2	21,408,1774	120.0	99.0	106.0		993	-0.0	1.0	12	dbSNP_107	106	3855,4745	543.3+/-384.4	843,2169,1288	no	coding-synonymous	CPNE8	NM_153634.2		864,2577,3062	AA,AG,GG		44.8256,10.2133,33.1001		331/565	39087609	4305,8701	2203	4300	6503	SO:0001819	synonymous_variant	144402	exon15			ATTCATGTAGTGG	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.993C>T	12.37:g.39087609G>A		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	234	232	0.991453	NM_153634	Q2TB41|Q86VY2	Silent	SNP	ENST00000331366.5	37	CCDS8733.1																																																																																			G|0.695;A|0.305	0.305	strong		0.378	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634	
AQP2	359	hgsc.bcm.edu	37	12	50348078	50348078	+	Silent	SNP	T	T	C	rs426496	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:50348078T>C	ENST00000199280.3	+	2	586	c.501T>C	c.(499-501)tcT>tcC	p.S167S	RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.8_ENST00000552806.1_RNA|RP11-469H8.6_ENST00000550530.1_RNA	NM_000486.5	NP_000477.1	P41181	AQP2_HUMAN	aquaporin 2 (collecting duct)	167					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						TAGGCTTCTCTGTGGCCCTGG	0.622													C|||	3341	0.667133	0.4334	0.8357	5008	,	,		16556	0.6796		0.8141	False		,,,				2504	0.6994				p.S167S		Atlas-SNP	.											.	AQP2	34	.	0			c.T501C						PASS	.	C		2106,2300	585.8+/-386.3	516,1074,613	32.0	38.0	36.0		501	-8.0	0.6	12	dbSNP_80	36	6911,1689	301.7+/-305.6	2798,1315,187	no	coding-synonymous	AQP2	NM_000486.5		3314,2389,800	CC,CT,TT		19.6395,47.7985,30.6705		167/272	50348078	9017,3989	2203	4300	6503	SO:0001819	synonymous_variant	359	exon2			CTTCTCTGTGGCC		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.501T>C	12.37:g.50348078T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_000486	Q9UD68	Silent	SNP	ENST00000199280.3	37	CCDS8792.1																																																																																			T|0.320;C|0.680	0.680	strong		0.622	AQP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405540.1	NM_000486	
OR10P1	121130	hgsc.bcm.edu	37	12	56031273	56031273	+	Missense_Mutation	SNP	G	G	A	rs7970885	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56031273G>A	ENST00000309675.2	+	1	630	c.598G>A	c.(598-600)Gtg>Atg	p.V200M	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	200			V -> M (in dbSNP:rs7970885). {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.V200M(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						CGAGATCTCCGTGATGACAGC	0.542													G|||	1358	0.271166	0.09	0.3905	5008	,	,		20445	0.2331		0.4901	False		,,,				2504	0.2454				p.V200M		Atlas-SNP	.											OR10P1,NS,carcinoma,0,1	OR10P1	48	1	1	Substitution - Missense(1)	stomach(1)	c.G598A						PASS	.	G	MET/VAL	694,3712	291.8+/-281.7	57,580,1566	121.0	97.0	106.0		598	2.5	0.0	12	dbSNP_116	106	3930,4670	547.8+/-385.2	909,2112,1279	yes	missense	OR10P1	NM_206899.1	21	966,2692,2845	AA,AG,GG		45.6977,15.7512,35.5528	possibly-damaging	200/314	56031273	4624,8382	2203	4300	6503	SO:0001583	missense	121130	exon1			ATCTCCGTGATGA	BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"""GPCR / Class A : Olfactory receptors"""	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.598G>A	12.37:g.56031273G>A	ENSP00000308082:p.Val200Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_206899	B9EGY4	Missense_Mutation	SNP	ENST00000309675.2	37	CCDS31828.1	702	0.32142857142857145	50	0.1016260162601626	153	0.42265193370165743	135	0.23601398601398602	364	0.48021108179419525	G	10.15	1.271097	0.23221	0.157512	0.456977	ENSG00000175398	ENST00000309675	T	0.00169	8.63	4.44	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	0.838841	0.10054	N	0.721873	T	0.00012	0.0000	N	0.01824	-0.7	0.80722	P	0.0	D	0.71674	0.998	P	0.59595	0.86	T	0.00234	-1.1893	9	0.25751	T	0.34	.	8.5889	0.33674	0.1914:0.0:0.8086:0.0	rs7970885;rs60103698;rs7970885	200	Q8NGE3	O10P1_HUMAN	M	200	ENSP00000308082:V200M	ENSP00000308082:V200M	V	+	1	0	OR10P1	54317540	0.000000	0.05858	0.007000	0.13788	0.002000	0.02628	-0.123000	0.10611	1.142000	0.42291	0.561000	0.74099	GTG	G|0.676;A|0.324	0.324	strong		0.542	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1		
RSF1	51773	hgsc.bcm.edu	37	11	77378505	77378505	+	Silent	SNP	A	A	G	rs28930682	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:77378505A>G	ENST00000308488.6	-	16	4085	c.3783T>C	c.(3781-3783)gaT>gaC	p.D1261D	RSF1_ENST00000480887.1_Silent_p.D1009D|RSF1_ENST00000360355.2_Silent_p.D1230D			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1261					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)			TAGCTAGCTCATCATCTTCAG	0.443													G|||	983	0.196286	0.329	0.2147	5008	,	,		19989	0.1736		0.0984	False		,,,				2504	0.1278				p.D1261D		Atlas-SNP	.											.	RSF1	105	.	0			c.T3783C						PASS	.	G		1327,3073		199,929,1072	57.0	59.0	58.0		3783	2.6	1.0	11	dbSNP_125	58	823,7761		36,751,3505	no	coding-synonymous	RSF1	NM_016578.3		235,1680,4577	GG,GA,AA		9.5876,30.1591,16.5588		1261/1442	77378505	2150,10834	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon16			TAGCTCATCATCT	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.3783T>C	11.37:g.77378505A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1																																																																																			A|0.816;G|0.184	0.184	strong		0.443	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
VWF	7450	hgsc.bcm.edu	37	12	6105387	6105387	+	Splice_Site	SNP	G	G	A	rs216902	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6105387G>A	ENST00000261405.5	-	35	6098	c.5844C>T	c.(5842-5844)tgC>tgT	p.C1948C		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1948					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)	CTGTGCACACGCCTGGACAGA	0.507													G|||	2284	0.45607	0.2784	0.4179	5008	,	,		20719	0.7252		0.3648	False		,,,				2504	0.5399				p.C1948C		Atlas-SNP	.											.	VWF	338	.	0			c.C5844T						PASS	.	G		1365,3041	448.5+/-348.7	201,963,1039	38.0	34.0	35.0		5844	0.5	1.0	12	dbSNP_79	35	3266,5334	480.2+/-370.3	615,2036,1649	yes	coding-synonymous-near-splice	VWF	NM_000552.3		816,2999,2688	AA,AG,GG		37.9767,30.9805,35.6066		1948/2814	6105387	4631,8375	2203	4300	6503	SO:0001630	splice_region_variant	7450	exon35			GCACACGCCTGGA		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.5843-1C>T	12.37:g.6105387G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			G|0.580;A|0.420	0.420	strong		0.507	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	Silent
C5	727	hgsc.bcm.edu	37	9	123783934	123783934	+	Silent	SNP	T	T	C	rs10985126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	262	0	0		WXS	Illumina HiSeq	Phase_I	256	115	0.449219	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	
FAM200A	221786	hgsc.bcm.edu	37	7	99145845	99145845	+	Silent	SNP	C	C	T	rs10238965	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99145845C>T	ENST00000449309.1	-	2	565	c.186G>A	c.(184-186)ttG>ttA	p.L62L		NM_145111.3	NP_659802.1	Q8TCP9	F200A_HUMAN	family with sequence similarity 200, member A	62						integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(5)|large_intestine(2)|ovary(2)|skin(1)	11						aatacgatgacaataaggctc	0.403													T|||	2314	0.462061	0.9342	0.2853	5008	,	,		22164	0.3353		0.165	False		,,,				2504	0.3855				p.L62L		Atlas-SNP	.											.	FAM200A	27	.	0			c.G186A						PASS	.	T		3473,929		1369,735,97	117.0	111.0	113.0		186	-4.1	0.0	7	dbSNP_119	113	1235,7361		102,1031,3165	no	coding-synonymous	FAM200A	NM_145111.3		1471,1766,3262	TT,TC,CC		14.3671,21.104,36.221		62/574	99145845	4708,8290	2201	4298	6499	SO:0001819	synonymous_variant	221786	exon2			CGATGACAATAAG		CCDS5668.1	7q22.1	2010-02-22	2010-02-22	2010-02-22	ENSG00000221909	ENSG00000221909			25401	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 38"""	C7orf38		10607616	Standard	NM_145111		Approved	FLJ36794, DKFZp727G131	uc003ura.3	Q8TCP9	OTTHUMG00000156723	ENST00000449309.1:c.186G>A	7.37:g.99145845C>T		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	255	100	0.392157	NM_145111	A4D293|A8K3V9|B2RD92|C9J6A8|D6W5T2|Q8N9P3	Silent	SNP	ENST00000449309.1	37	CCDS5668.1																																																																																			C|0.566;T|0.434	0.434	strong		0.403	FAM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345467.1	NM_145111	
DHX33	56919	hgsc.bcm.edu	37	17	5356913	5356913	+	Silent	SNP	C	C	T	rs16954697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	126	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	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	
CYP11B2	1585	hgsc.bcm.edu	37	8	143996539	143996539	+	Missense_Mutation	SNP	T	T	C	rs4539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:143996539T>C	ENST00000323110.2	-	3	520	c.518A>G	c.(517-519)aAg>aGg	p.K173R		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	173			K -> R (in dbSNP:rs4539). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:9931115}.		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)	CACCTTCTTCTTCAGGGCCTG	0.627									Familial Hyperaldosteronism type I				.|||	1735	0.346446	0.1876	0.4697	5008	,	,		19583	0.2867		0.4841	False		,,,				2504	0.3937				p.K173R		Atlas-SNP	.											.	CYP11B2	107	.	0			c.A518G	GRCh37	CM962423	CYP11B2	M	rs4539	PASS	.	C	ARG/LYS	1038,3368		127,784,1292	44.0	41.0	42.0		518	-4.2	0.0	8	dbSNP_52	42	3857,4735		877,2103,1316	no	missense	CYP11B2	NM_000498.3	26	1004,2887,2608	CC,CT,TT		44.8906,23.5588,37.6596	benign	173/504	143996539	4895,8103	2203	4296	6499	SO:0001583	missense	1585	exon3	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TTCTTCTTCAGGG	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.518A>G	8.37:g.143996539T>C	ENSP00000325822:p.Lys173Arg	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	192	186	0.96875	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	37	CCDS6393.1	793	0.3630952380952381	93	0.18902439024390244	156	0.430939226519337	179	0.3129370629370629	365	0.4815303430079156	.	0.007	-1.971021	0.00457	0.235588	0.448906	ENSG00000179142	ENST00000323110	T	0.66995	-0.24	3.44	-4.17	0.03857	.	0.947674	0.08784	N	0.894271	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.30149	-0.9988	9	0.06365	T	0.9	.	6.5262	0.22303	0.1184:0.3843:0.0:0.4973	rs4539;rs61617752	173	P19099	C11B2_HUMAN	R	173	ENSP00000325822:K173R	ENSP00000325822:K173R	K	-	2	0	CYP11B2	143993541	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.668000	0.05268	-1.541000	0.01727	-2.253000	0.00282	AAG	T|0.648;C|0.352	0.352	strong		0.627	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
DND1	373863	hgsc.bcm.edu	37	5	140050894	140050894	+	Missense_Mutation	SNP	G	G	C	rs201638404		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140050894G>C	ENST00000542735.1	-	4	1089	c.1046C>G	c.(1045-1047)aCc>aGc	p.T349S	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	349					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTAACCATGGTACCTGCCTC	0.602																																					p.T349S		Atlas-SNP	.											DND1,NS,carcinoma,-1,1	DND1	15	1	0			c.C1046G						scavenged	.						75.0	61.0	66.0					5																	140050894		1959	3964	5923	SO:0001583	missense	373863	exon4			ACCATGGTACCTG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1046C>G	5.37:g.140050894G>C	ENSP00000445366:p.Thr349Ser	Somatic	465	1	0.00215054		WXS	Illumina HiSeq	Phase_I	613	106	0.17292	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	G	9.262	1.043394	0.19748	.	.	ENSG00000256453	ENST00000542735	T	0.30182	1.54	4.97	0.117	0.14652	.	1.006470	0.07994	N	0.987573	T	0.16769	0.0403	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29518	-1.0009	10	0.27082	T	0.32	0.0017	3.9136	0.09213	0.3271:0.0:0.5115:0.1614	.	349	Q8IYX4	DND1_HUMAN	S	349	ENSP00000445366:T349S	ENSP00000445366:T349S	T	-	2	0	DND1	140031078	0.002000	0.14202	0.000000	0.03702	0.312000	0.27988	0.583000	0.23849	0.101000	0.17610	0.551000	0.68910	ACC	G|0.979;C|0.021	0.021	strong		0.602	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
ZFAND2B	130617	hgsc.bcm.edu	37	2	220072431	220072431	+	Missense_Mutation	SNP	C	C	A	rs61750009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220072431C>A	ENST00000289528.5	+	3	407	c.212C>A	c.(211-213)cCc>cAc	p.P71H	ZFAND2B_ENST00000409206.1_Missense_Mutation_p.P71H|ZFAND2B_ENST00000409319.1_Missense_Mutation_p.P71H|ZFAND2B_ENST00000409412.1_Missense_Mutation_p.P71H|ZFAND2B_ENST00000409594.1_Missense_Mutation_p.P71H|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000409097.1_Missense_Mutation_p.P71H|ZFAND2B_ENST00000444522.2_Missense_Mutation_p.P71H|ZFAND2B_ENST00000409217.1_Missense_Mutation_p.P71H|ZFAND2B_ENST00000409336.1_Missense_Mutation_p.P71H	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	71						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGGGGAGCCCCCTGACCGT	0.562													c|||	68	0.0135783	0.0008	0.0288	5008	,	,		21079	0.001		0.0358	False		,,,				2504	0.0102				p.P71H		Atlas-SNP	.											.	ZFAND2B	28	.	0			c.C212A						PASS	.	C	HIS/PRO	44,4362	46.0+/-80.4	0,44,2159	88.0	82.0	84.0		212	4.4	1.0	2	dbSNP_129	84	346,8254	117.6+/-177.1	7,332,3961	yes	missense	ZFAND2B	NM_138802.1	77	7,376,6120	AA,AC,CC		4.0233,0.9986,2.9986	benign	71/258	220072431	390,12616	2203	4300	6503	SO:0001583	missense	130617	exon3			GGGAGCCCCCTGA	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"""Zinc fingers, AN1-type domain containing"""	25206	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein-like"""	613474	"""zinc finger, AN1-type 2B"""			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.212C>A	2.37:g.220072431C>A	ENSP00000289528:p.Pro71His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_138802	Q8NB98	Missense_Mutation	SNP	ENST00000289528.5	37	CCDS2435.1	36	0.016483516483516484	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	24	0.0316622691292876	C	14.55	2.569120	0.45798	0.009986	0.040233	ENSG00000158552	ENST00000409206;ENST00000409594;ENST00000289528;ENST00000422255;ENST00000409412;ENST00000409097;ENST00000409336;ENST00000409217;ENST00000409319;ENST00000444522	T;T;T;T;T;T;T;T;T;T	0.42900	0.98;0.98;0.97;0.96;0.98;0.96;0.97;0.98;0.98;0.96	5.32	4.44	0.53790	Zinc finger, AN1-type (1);	0.289314	0.39407	N	0.001373	T	0.11153	0.0272	L	0.50333	1.59	0.32446	N	0.546034	B;P	0.47841	0.005;0.901	B;B	0.42882	0.017;0.401	T	0.40757	-0.9546	10	0.45353	T	0.12	-7.3112	8.9394	0.35720	0.0:0.7907:0.0:0.2093	rs61750009	71;71	Q8WV99;B4DEN4	ZFN2B_HUMAN;.	H	71	ENSP00000386824:P71H;ENSP00000386399:P71H;ENSP00000289528:P71H;ENSP00000409931:P71H;ENSP00000386847:P71H;ENSP00000387179:P71H;ENSP00000386898:P71H;ENSP00000386370:P71H;ENSP00000387312:P71H;ENSP00000411334:P71H	ENSP00000289528:P71H	P	+	2	0	ZFAND2B	219780675	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	4.509000	0.60448	1.471000	0.48121	0.655000	0.94253	CCC	C|0.974;A|0.026	0.026	strong		0.562	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802	
FSCB	84075	hgsc.bcm.edu	37	14	44975510	44975510	+	Silent	SNP	C	C	T	rs372153461|rs3809430	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:44975510C>T	ENST00000340446.4	-	1	972	c.681G>A	c.(679-681)ccG>ccA	p.P227P	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	227						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CTAAAAGTACCGGGGGACCTT	0.403													C|||	1625	0.324481	0.2284	0.33	5008	,	,		18394	0.3859		0.3479	False		,,,				2504	0.363				p.P227P		Atlas-SNP	.											.	FSCB	173	.	0			c.G681A						PASS	.	C		1065,3341	384.9+/-325.5	131,803,1269	96.0	99.0	98.0		681	-8.2	0.0	14	dbSNP_107	98	3204,5396	484.5+/-371.4	627,1950,1723	no	coding-synonymous	FSCB	NM_032135.3		758,2753,2992	TT,TC,CC		37.2558,24.1716,32.8233		227/826	44975510	4269,8737	2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			AAGTACCGGGGGA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.681G>A	14.37:g.44975510C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	37	CCDS9679.1																																																																																			C|0.674;T|0.326	0.326	strong		0.403	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036971	33036971	+	Silent	SNP	C	C	T	rs2308928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33036971C>T	ENST00000419277.1	-	4	582	c.453G>A	c.(451-453)acG>acA	p.T151T	HLA-DPA1_ENST00000428995.1_Silent_p.T151T|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	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	91	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	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	
FIG4	9896	hgsc.bcm.edu	37	6	110064928	110064928	+	Missense_Mutation	SNP	A	A	T	rs2295837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	105	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	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	
CENPF	1063	hgsc.bcm.edu	37	1	214813487	214813487	+	Silent	SNP	A	A	G	rs2070066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214813487A>G	ENST00000366955.3	+	12	1974	c.1806A>G	c.(1804-1806)ttA>ttG	p.L602L		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)		TGAGTGCTTTAGAGTTAAAAA	0.328													G|||	733	0.146366	0.2526	0.1124	5008	,	,		17394	0.126		0.0517	False		,,,				2504	0.1452				p.L602L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A1806G						PASS	.	G		949,3455	690.8+/-405.3	107,735,1360	45.0	51.0	49.0		1806	3.5	1.0	1	dbSNP_96	49	479,8117	784.7+/-407.6	13,453,3832	no	coding-synonymous	CENPF	NM_016343.3		120,1188,5192	GG,GA,AA		5.5724,21.5486,10.9846		602/3115	214813487	1428,11572	2202	4298	6500	SO:0001819	synonymous_variant	1063	exon12			TGCTTTAGAGTTA	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.1806A>G	1.37:g.214813487A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	104	35	0.336538	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			A|0.881;G|0.119	0.119	strong		0.328	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
POM121C	100101267	hgsc.bcm.edu	37	7	75051324	75051324	+	Silent	SNP	G	G	C	rs117499978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:75051324G>C	ENST00000257665.5	-	11	2936	c.2937C>G	c.(2935-2937)gcC>gcG	p.A979A	POM121C_ENST00000453279.2_Silent_p.A737A|POM121C_ENST00000473168.1_5'Flank			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	979	Pore side. {ECO:0000255}.			Missing (in Ref. 2; BC082993). {ECO:0000305}.	mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						CCGGGGCCGGGGCTGCAGAGT	0.662													.|||	289	0.0577077	0.025	0.0548	5008	,	,		13799	0.0099		0.1044	False		,,,				2504	0.1053				p.A737A		Atlas-SNP	.											.	POM121C	46	.	0			c.C2211G						PASS	.	-		174,4230		5,164,2033	25.0	29.0	28.0		2211	1.2	0.1	7	dbSNP_132	28	831,7767		39,753,3507	no	coding-synonymous	POM121C	NM_001099415.1		44,917,5540	CC,CG,GG		9.665,3.951,7.7296		737/988	75051324	1005,11997	2202	4299	6501	SO:0001819	synonymous_variant	100101267	exon13			GGCCGGGGCTGCA		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.2937C>G	7.37:g.75051324G>C		Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	269	118	0.438662	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000257665.5	37																																																																																				G|0.940;C|0.060	0.060	strong		0.662	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
GRHL3	57822	hgsc.bcm.edu	37	1	24669457	24669457	+	Missense_Mutation	SNP	C	C	T	rs41268753	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24669457C>T	ENST00000350501.5	+	11	1488	c.1361C>T	c.(1360-1362)aCg>aTg	p.T454M	GRHL3_ENST00000361548.4_Missense_Mutation_p.T454M|GRHL3_ENST00000342072.4_Missense_Mutation_p.T361M|GRHL3_ENST00000356046.2_Missense_Mutation_p.T408M|GRHL3_ENST00000236255.4_Missense_Mutation_p.T459M	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	454					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GACCTGGAGACGCCACCCGTG	0.637													C|||	49	0.00978435	0.0008	0.0115	5008	,	,		16921	0.0		0.0298	False		,,,				2504	0.0102				p.T459M		Atlas-SNP	.											GRHL3,NS,carcinoma,-1,1	GRHL3	69	1	0			c.C1376T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR	27,4379	32.6+/-62.9	0,27,2176	126.0	132.0	130.0		1223,1376,1361,1361	4.3	1.0	1	dbSNP_127	130	273,8327	104.6+/-165.6	5,263,4032	yes	missense,missense,missense,missense	GRHL3	NM_001195010.1,NM_021180.3,NM_198173.2,NM_198174.2	81,81,81,81	5,290,6208	TT,TC,CC		3.1744,0.6128,2.3066	probably-damaging,probably-damaging,probably-damaging,probably-damaging	408/557,459/608,454/603,454/627	24669457	300,12706	2203	4300	6503	SO:0001583	missense	57822	exon11			TGGAGACGCCACC	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.1361C>T	1.37:g.24669457C>T	ENSP00000288955:p.Thr454Met	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	228	101	0.442982	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	30	0.013736263736263736	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	26	0.03430079155672823	C	19.07	3.755400	0.69648	0.006128	0.031744	ENSG00000158055	ENST00000361548;ENST00000342072;ENST00000350501;ENST00000356046;ENST00000236255	T;T;T;T;T	0.13307	2.8;2.6;2.77;2.79;2.79	5.27	4.32	0.51571	.	0.096084	0.64402	D	0.000001	T	0.09598	0.0236	L	0.41492	1.28	0.58432	D	0.999991	D;D;D	0.76494	0.995;0.999;0.999	P;P;P	0.60886	0.685;0.88;0.88	T	0.00206	-1.1920	10	0.72032	D	0.01	-35.1333	16.4218	0.83760	0.0:0.8575:0.1425:0.0	rs41268753	408;459;454	A2A297;Q8TE85-2;G3XAF0	.;.;.	M	454;361;454;408;459	ENSP00000354943:T454M;ENSP00000340543:T361M;ENSP00000288955:T454M;ENSP00000348333:T408M;ENSP00000236255:T459M	ENSP00000236255:T459M	T	+	2	0	GRHL3	24542044	1.000000	0.71417	0.992000	0.48379	0.506000	0.33950	4.644000	0.61397	2.746000	0.94184	0.561000	0.74099	ACG	C|0.982;T|0.018	0.018	strong		0.637	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
SDCCAG3	10807	hgsc.bcm.edu	37	9	139299637	139299637	+	Missense_Mutation	SNP	C	C	T	rs3812577	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139299637C>T	ENST00000357365.3	-	7	1040	c.911G>A	c.(910-912)cGg>cAg	p.R304Q	SDCCAG3_ENST00000298537.7_Missense_Mutation_p.R281Q|SDCCAG3_ENST00000461693.1_5'UTR|SDCCAG3_ENST00000371725.3_Missense_Mutation_p.R231Q	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	304			R -> Q (in dbSNP:rs3812577). {ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		TTCTAACTTCCGCTCAAGCGT	0.463													C|||	548	0.109425	0.0098	0.2349	5008	,	,		19347	0.1359		0.1093	False		,,,				2504	0.1278				p.R304Q		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.G911A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	95,3699		1,93,1803	116.0	110.0	112.0		911,692,842	4.5	1.0	9	dbSNP_107	112	1032,7206		68,896,3155	yes	missense,missense,missense	SDCCAG3	NM_001039707.1,NM_001039708.1,NM_006643.3	43,43,43	69,989,4958	TT,TC,CC		12.5273,2.504,9.3667	probably-damaging,probably-damaging,probably-damaging	304/436,231/363,281/413	139299637	1127,10905	1897	4119	6016	SO:0001583	missense	10807	exon7			AACTTCCGCTCAA	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.911G>A	9.37:g.139299637C>T	ENSP00000349929:p.Arg304Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	37	CCDS43904.1	241|241	0.11034798534798534|0.11034798534798534	6|6	0.012195121951219513|0.012195121951219513	68|68	0.1878453038674033|0.1878453038674033	73|73	0.12762237762237763|0.12762237762237763	94|94	0.12401055408970976|0.12401055408970976	C|C	11.89|11.89	1.772521|1.772521	0.31411|0.31411	0.02504|0.02504	0.125273|0.125273	ENSG00000165689|ENSG00000165689	ENST00000417512|ENST00000357365;ENST00000298537;ENST00000371725	.|T;T;T	.|0.78595	.|-1.19;-1.19;-1.19	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	.|0.192442	.|0.43919	.|D	.|0.000513	T|T	0.00328|0.00328	0.0010|0.0010	L|L	0.58810|0.58810	1.83|1.83	0.28814|0.28814	P|P	0.89807|0.89807	.|P;D;D	.|0.59767	.|0.956;0.986;0.986	.|B;P;P	.|0.47941	.|0.408;0.562;0.562	T|T	0.09684|0.09684	-1.0663|-1.0663	4|9	.|0.37606	.|T	.|0.19	-15.0759|-15.0759	12.2017|12.2017	0.54331|0.54331	0.0:0.9132:0.0:0.0868|0.0:0.9132:0.0:0.0868	rs3812577;rs52833688;rs57736081;rs3812577|rs3812577;rs52833688;rs57736081;rs3812577	.|231;281;304	.|Q96C92-4;Q96C92-2;Q96C92	.|.;.;SDCG3_HUMAN	R|Q	45|304;281;231	.|ENSP00000349929:R304Q;ENSP00000298537:R281Q;ENSP00000360790:R231Q	.|ENSP00000298537:R281Q	G|R	-|-	1|2	0|0	SDCCAG3|SDCCAG3	138419458|138419458	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.291000|0.291000	0.27294|0.27294	1.174000|1.174000	0.31932|0.31932	2.218000|2.218000	0.71995|0.71995	0.563000|0.563000	0.77884|0.77884	GGA|CGG	C|0.886;T|0.114	0.114	strong		0.463	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	
STAM	8027	hgsc.bcm.edu	37	10	17756596	17756596	+	Silent	SNP	T	T	C	rs12221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:17756596T>C	ENST00000377524.3	+	14	1655	c.1440T>C	c.(1438-1440)taT>taC	p.Y480Y	STAM_ENST00000540523.1_Silent_p.Y369Y	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	480					endosomal transport (GO:0016197)|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)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)	p.Y480Y(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						CGCCAGTATATAGTCCTCCTC	0.463													T|||	763	0.152356	0.0787	0.1441	5008	,	,		14054	0.2262		0.2058	False		,,,				2504	0.1268				p.Y480Y		Atlas-SNP	.											STAM,NS,carcinoma,0,1	STAM	60	1	1	Substitution - coding silent(1)	stomach(1)	c.T1440C						PASS	.	T		483,3923	226.5+/-242.0	23,437,1743	71.0	69.0	70.0		1440	-4.4	0.4	10	dbSNP_52	70	1913,6687	341.0+/-323.9	223,1467,2610	no	coding-synonymous	STAM	NM_003473.3		246,1904,4353	CC,CT,TT		22.2442,10.9623,18.4223		480/541	17756596	2396,10610	2203	4300	6503	SO:0001819	synonymous_variant	8027	exon14			AGTATATAGTCCT	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.1440T>C	10.37:g.17756596T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	156	69	0.442308	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Silent	SNP	ENST00000377524.3	37	CCDS7122.1																																																																																			T|0.815;C|0.185	0.185	strong		0.463	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473	
PAX9	5083	hgsc.bcm.edu	37	14	37135753	37135753	+	Missense_Mutation	SNP	G	G	C	rs4904210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:37135753G>C	ENST00000361487.6	+	3	943	c.718G>C	c.(718-720)Gcg>Ccg	p.A240P	PAX9_ENST00000557107.1_3'UTR|PAX9_ENST00000402703.2_Missense_Mutation_p.A240P|PAX9_ENST00000554201.1_Missense_Mutation_p.A53P			P55771	PAX9_HUMAN	paired box 9	240			A -> P (in dbSNP:rs4904210).		cellular response to growth factor stimulus (GO:0071363)|endoderm development (GO:0007492)|face morphogenesis (GO:0060325)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|regulation of odontogenesis (GO:0042481)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(3)	12	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)		CGCCCCGCACGCGGTGAACGG	0.687													G|||	1661	0.331669	0.2126	0.2738	5008	,	,		13955	0.4315		0.3519	False		,,,				2504	0.41				p.A240P		Atlas-SNP	.											.	PAX9	34	.	0			c.G718C						PASS	.	G	PRO/ALA	995,3369		114,767,1301	21.0	14.0	16.0		718	3.4	1.0	14	dbSNP_111	16	3097,5459		592,1913,1773	yes	missense	PAX9	NM_006194.3	27	706,2680,3074	CC,CG,GG		36.1968,22.8002,31.6718	benign	240/342	37135753	4092,8828	2182	4278	6460	SO:0001583	missense	5083	exon4			CCGCACGCGGTGA	AJ238381	CCDS9662.1	14q13.3	2007-07-12	2007-07-12		ENSG00000198807	ENSG00000198807		"""Paired boxes"""	8623	protein-coding gene	gene with protein product		167416	"""paired box gene 9"""			7981748	Standard	NM_006194		Approved		uc001wty.4	P55771	OTTHUMG00000140251	ENST00000361487.6:c.718G>C	14.37:g.37135753G>C	ENSP00000355245:p.Ala240Pro	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_006194	Q99582|Q9UQR4	Missense_Mutation	SNP	ENST00000361487.6	37	CCDS9662.1	749	0.34294871794871795	114	0.23170731707317074	118	0.3259668508287293	245	0.42832167832167833	272	0.35883905013192613	G	11.49	1.653459	0.29425	0.228002	0.361968	ENSG00000198807	ENST00000402703;ENST00000361487;ENST00000554201;ENST00000543853	D;D;T	0.98968	-5.28;-5.28;0.74	5.33	3.38	0.38709	.	0.350029	0.32548	N	0.005950	T	0.00012	0.0000	L	0.34521	1.04	0.39677	P	0.029159000000000046	B	0.02656	0.0	B	0.01281	0.0	T	0.00286	-1.1847	9	0.49607	T	0.09	.	12.5398	0.56163	0.073:0.1277:0.7993:0.0	rs4904210	240	P55771	PAX9_HUMAN	P	240;240;53;29	ENSP00000384817:A240P;ENSP00000355245:A240P;ENSP00000450434:A53P	ENSP00000355245:A240P	A	+	1	0	PAX9	36205504	0.995000	0.38212	0.997000	0.53966	0.279000	0.26890	1.970000	0.40520	1.266000	0.44231	-0.221000	0.12465	GCG	G|0.689;C|0.311	0.311	strong		0.687	PAX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276733.2		
PYROXD2	84795	hgsc.bcm.edu	37	10	100147060	100147060	+	Silent	SNP	A	A	G	rs4345897	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	83	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	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	
PSMD13	5719	hgsc.bcm.edu	37	11	244106	244106	+	Intron	SNP	A	A	G	rs10902112|rs373900649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244106A>G	ENST00000532097.1	+	3	713				PSMD13_ENST00000431206.2_Missense_Mutation_p.E54G|PSMD13_ENST00000352303.5_Intron	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13						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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TTTCACTTTGAAAATGAGTGC	0.398													A|||	4083	0.815296	0.8918	0.83	5008	,	,		16031	0.8036		0.7306	False		,,,				2504	0.8006				p.E54G		Atlas-SNP	.											.	PSMD13	53	.	0			c.A161G						PASS	.	A	,GLY/GLU	3796,610		1714,368,121	58.0	63.0	61.0		,161	-5.3	0.0	11	dbSNP_120	61	6103,2495		2368,1367,564	yes	intron,missense	PSMD13	NM_002817.3,NM_175932.2	,98	4082,1735,685	GG,GA,AA		29.0184,13.8448,23.8773	,	,54/379	244106	9899,3105	2203	4299	6502	SO:0001627	intron_variant	5719	exon2			ACTTTGAAAATGA	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.209+31A>G	11.37:g.244106A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	1762	0.8067765567765568	440	0.8943089430894309	295	0.8149171270718232	471	0.8234265734265734	556	0.7335092348284961	A	9.283	1.048578	0.19827	0.861552	0.709816	ENSG00000185627	ENST00000431206	T	0.17854	2.25	5.94	-5.27	0.02763	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.19353	-1.0308	6	.	.	.	.	1.0839	0.01648	0.3642:0.2635:0.2065:0.1659	rs10902112;rs57101334;rs10902112	54	Q9UNM6-2	.	G	54	ENSP00000396937:E54G	.	E	+	2	0	PSMD13	234106	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.330000	0.07925	-1.087000	0.03081	-1.783000	0.00646	GAA	A|0.207;G|0.793	0.793	strong		0.398	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
ZNF99	7652	hgsc.bcm.edu	37	19	22942325	22942325	+	Missense_Mutation	SNP	G	G	C	rs7255780	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:22942325G>C	ENST00000596209.1	-	4	476	c.386C>G	c.(385-387)gCt>gGt	p.A129G	ZNF99_ENST00000397104.3_Missense_Mutation_p.A150G	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	129			A -> G (in dbSNP:rs7255780).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTATTATAAGCTTCTTCGTG	0.299													C|||	1840	0.367412	0.5386	0.3256	5008	,	,		16402	0.3462		0.2783	False		,,,				2504	0.2791				p.A129G		Atlas-SNP	.											.	ZNF99	273	.	0			c.C386G						PASS	.	C	GLY/ALA	1869,1871		455,959,456	101.0	98.0	99.0		449	-0.8	0.0	19	dbSNP_116	99	2332,5862		324,1684,2089	yes	missense	ZNF99	NM_001080409.2	60	779,2643,2545	CC,CG,GG		28.4598,49.9733,35.2019	benign	150/912	22942325	4201,7733	1870	4097	5967	SO:0001583	missense	7652	exon4			TTATAAGCTTCTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.386C>G	19.37:g.22942325G>C	ENSP00000472969:p.Ala129Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	802	0.36721611721611724	266	0.540650406504065	120	0.3314917127071823	207	0.3618881118881119	209	0.2757255936675462	N	0.175	-1.068074	0.01934	0.499733	0.284598	ENSG00000213973	ENST00000397104	T	0.06294	3.32	1.18	-0.806	0.10875	.	.	.	.	.	T	0.00012	0.0000	N	0.00057	-2.36	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	8	0.02654	T	1	.	4.3885	0.11328	0.2323:0.3046:0.4631:0.0	rs7255780;rs57975939;rs7255780	150	A8MXY4	ZNF99_HUMAN	G	150	ENSP00000380293:A150G	ENSP00000380293:A150G	A	-	2	0	ZNF99	22734165	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.658000	0.05329	-1.903000	0.01093	-1.120000	0.02017	GCT	G|0.635;C|0.364	0.364	strong		0.299	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
CHD7	55636	hgsc.bcm.edu	37	8	61767070	61767070	+	Silent	SNP	G	G	A	rs61733338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:61767070G>A	ENST00000423902.2	+	32	7403	c.6924G>A	c.(6922-6924)tcG>tcA	p.S2308S	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2308					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)	p.S2308S(2)		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)			TTGCCTTCTCGTTTTGGCCTA	0.423													G|||	12	0.00239617	0.0091	0.0	5008	,	,		19366	0.0		0.0	False		,,,				2504	0.0				p.S2308S		Atlas-SNP	.											CHD7_ENST00000423902,NS,carcinoma,0,2	CHD7	534	2	2	Substitution - coding silent(2)	prostate(2)	c.G6924A						PASS	.	G		22,3776		0,22,1877	220.0	199.0	206.0		6924	-4.3	1.0	8	dbSNP_129	206	0,8224		0,0,4112	no	coding-synonymous	CHD7	NM_017780.3		0,22,5989	AA,AG,GG		0.0,0.5793,0.183		2308/2998	61767070	22,12000	1899	4112	6011	SO:0001819	synonymous_variant	55636	exon32			CTTCTCGTTTTGG	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.6924G>A	8.37:g.61767070G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																			G|0.997;A|0.003	0.003	strong		0.423	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
TMEM99	147184	hgsc.bcm.edu	37	17	38991032	38991032	+	Silent	SNP	T	T	A	rs6694	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38991032T>A	ENST00000301665.3	+	3	568	c.264T>A	c.(262-264)ggT>ggA	p.G88G		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	88						integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				GTGCTTGCGGTCATCGGTTGA	0.458													A|||	2920	0.583067	0.6846	0.4539	5008	,	,		20037	0.4494		0.6064	False		,,,				2504	0.6513				p.G88G		Atlas-SNP	.											.	TMEM99	21	.	0			c.T264A						PASS	.	A	,,	2612,1240		891,830,205	223.0	221.0	221.0		264,264,264	-0.5	0.0	17	dbSNP_52	221	4948,3342		1454,2040,651	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	,,	2345,2870,856	AA,AT,TT		40.3136,32.1911,37.7368	,,	88/259,88/259,88/259	38991032	7560,4582	1926	4145	6071	SO:0001819	synonymous_variant	147184	exon3			TTGCGGTCATCGG	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	ENST00000301665.3:c.264T>A	17.37:g.38991032T>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	200	87	0.435	NM_001195386	B4DQ34|Q96BP9	Silent	SNP	ENST00000301665.3	37	CCDS42319.1																																																																																			T|0.426;A|0.574	0.574	strong		0.458	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
LINC00283	100874057	hgsc.bcm.edu	37	13	103392562	103392562	+	RNA	SNP	C	C	A	rs12585626	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103392562C>A	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		CTGATGATTTCATTCCTTTTG	0.333													C|||	371	0.0740815	0.1573	0.0159	5008	,	,		21018	0.1052		0.0268	False		,,,				2504	0.0194				p.M3495I		Atlas-SNP	.											.	.	.	.	0			c.G10485T						PASS	.	C	ILE/MET	187,1197		14,159,519	72.0	58.0	62.0		10485	0.3	0.0	13	dbSNP_120	62	68,3112		2,64,1524	yes	missense	CCDC168	NM_001146197.1	10	16,223,2043	AA,AC,CC		2.1384,13.5116,5.5872		3495/7082	103392562	255,4309	692	1590	2282			643677	exon4			TGATTTCATTCCT			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.103392562C>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.905;A|0.095	0.095	strong		0.333	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
OPLAH	26873	hgsc.bcm.edu	37	8	145111529	145111529	+	Silent	SNP	A	A	G	rs11993554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145111529A>G	ENST00000426825.1	-	13	1917	c.1836T>C	c.(1834-1836)ttT>ttC	p.F612F	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	612					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACCGCTCCACAAAGGCTGCCC	0.692													G|||	707	0.141174	0.3835	0.0735	5008	,	,		14960	0.001		0.0944	False		,,,				2504	0.0542				p.F612F		Atlas-SNP	.											.	OPLAH	78	.	0			c.T1836C						PASS	.	G		1378,2896		223,932,982	29.0	36.0	33.0		1836	-4.3	0.3	8	dbSNP_120	33	634,7876		18,598,3639	yes	coding-synonymous	OPLAH	NM_017570.3		241,1530,4621	GG,GA,AA		7.4501,32.2415,15.7384		612/1289	145111529	2012,10772	2137	4255	6392	SO:0001819	synonymous_variant	26873	exon13			CTCCACAAAGGCT	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1836T>C	8.37:g.145111529A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	37																																																																																				A|0.879;G|0.121	0.121	strong		0.692	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
TNS1	7145	hgsc.bcm.edu	37	2	218683139	218683139	+	Missense_Mutation	SNP	G	G	A	rs34291329	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:218683139G>A	ENST00000171887.4	-	24	4056	c.3604C>T	c.(3604-3606)Ccc>Tcc	p.P1202S	TNS1_ENST00000430930.1_Missense_Mutation_p.P1181S|TNS1_ENST00000419504.1_Missense_Mutation_p.P1189S	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	79	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	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	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36636008	36636008	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:36636008C>T	ENST00000431231.2	+	14	2581	c.2513C>T	c.(2512-2514)cCc>cTc	p.P838L	ARHGAP23_ENST00000443378.1_Missense_Mutation_p.P744L|ARHGAP23_ENST00000437668.3_Missense_Mutation_p.P838L	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	838					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)	p.P1163L(5)		breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						AGCTCTGGGCCCAAAGCTGAT	0.642																																					p.P838L		Atlas-SNP	.											ARHGAP23,NS,carcinoma,0,5	ARHGAP23	48	5	5	Substitution - Missense(5)	endometrium(5)	c.C2513T						scavenged	.						3.0	3.0	3.0					17																	36636008		635	1447	2082	SO:0001583	missense	57636	exon14			CTGGGCCCAAAGC	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.2513C>T	17.37:g.36636008C>T	ENSP00000393539:p.Pro838Leu	Somatic	511	0	0		WXS	Illumina HiSeq	Phase_I	524	22	0.0419847	NM_001199417		Missense_Mutation	SNP	ENST00000431231.2	37	CCDS56027.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166506	0.57476	.	.	ENSG00000225485	ENST00000437668;ENST00000431231;ENST00000443378	T;T;T	0.15718	2.4;2.77;2.73	4.88	4.88	0.63580	.	0.339007	0.31358	N	0.007798	T	0.12050	0.0293	N	0.22421	0.69	0.53688	D	0.999976	B;P	0.34587	0.288;0.458	B;B	0.31869	0.122;0.137	T	0.10268	-1.0637	10	0.38643	T	0.18	.	13.4088	0.60931	0.0:1.0:0.0:0.0	.	838;838	Q9P227;Q9P227-2	RHG23_HUMAN;.	L	838;838;744	ENSP00000394153:P838L;ENSP00000393539:P838L;ENSP00000407333:P744L	ENSP00000393539:P838L	P	+	2	0	ARHGAP23	33889534	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.077000	0.50089	2.544000	0.85801	0.650000	0.86243	CCC	.	.	none		0.642	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
SUGP1	57794	hgsc.bcm.edu	37	19	19390185	19390185	+	Silent	SNP	G	G	A	rs11555053	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19390185G>A	ENST00000247001.5	-	10	1712	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y		NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	455	Gln/Met-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						TGATCATGTCGTACATCTGCT	0.642													G|||	747	0.149161	0.295	0.1268	5008	,	,		19295	0.0		0.167	False		,,,				2504	0.1033				p.Y455Y		Atlas-SNP	.											SUGP1,NS,carcinoma,0,1	SUGP1	63	1	0			c.C1365T						PASS	.	G		1242,3162	411.7+/-335.8	171,900,1131	67.0	44.0	52.0		1365	-2.3	1.0	19	dbSNP_120	52	1363,7237	257.9+/-281.7	106,1151,3043	no	coding-synonymous	SUGP1	NM_172231.3		277,2051,4174	AA,AG,GG		15.8488,28.2016,20.0323		455/646	19390185	2605,10399	2202	4300	6502	SO:0001819	synonymous_variant	57794	exon10			CATGTCGTACATC	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.1365C>T	19.37:g.19390185G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Silent	SNP	ENST00000247001.5	37	CCDS12399.1																																																																																			G|0.805;A|0.195	0.195	strong		0.642	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	
IRGC	56269	hgsc.bcm.edu	37	19	44223125	44223125	+	Silent	SNP	C	C	T	rs346049	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	52	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	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	
PDE6B	5158	hgsc.bcm.edu	37	4	663878	663878	+	Silent	SNP	A	A	G	rs137864502		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:663878A>G	ENST00000496514.1	+	22	2568	c.2547A>G	c.(2545-2547)tcA>tcG	p.S849S	PDE6B_ENST00000429163.2_Silent_p.S570S|ATP5I_ENST00000506525.1_5'Flank|PDE6B_ENST00000255622.6_Silent_p.S848S			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	849					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)	CCAAGTCTTCAACCTGCTGTA	0.527																																					p.S849S	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A2547G						PASS	.	A	,,	1,4405	2.1+/-5.4	0,1,2202	165.0	163.0	164.0		2547,2544,1710	-8.7	0.5	4	dbSNP_134	164	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	,,	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	,,	849/855,848/854,570/576	663878	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5158	exon22			GTCTTCAACCTGC	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.2547A>G	4.37:g.663878A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_000283	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1																																																																																			A|1.000;G|0.000	0.000	weak		0.527	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	
CNR2	1269	hgsc.bcm.edu	37	1	24201643	24201643	+	Silent	SNP	G	G	A	rs2501431	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201643G>A	ENST00000374472.4	-	2	626	c.465C>T	c.(463-465)ggC>ggT	p.G155G	CNR2_ENST00000536471.1_Silent_p.G155G	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	155					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	CCCACATGATGCCCAGGGTCA	0.592													G|||	3272	0.653355	0.7943	0.6383	5008	,	,		21110	0.502		0.5875	False		,,,				2504	0.6973				p.G155G		Atlas-SNP	.											.	CNR2	78	.	0			c.C465T						PASS	.	G		3310,1096	719.8+/-409.0	1261,788,154	80.0	76.0	78.0	http://omim.org/entry/606928	465	-0.5	1.0	1	dbSNP_100	78	4935,3665	622.5+/-397.3	1402,2131,767	no	coding-synonymous	CNR2	NM_001841.2		2663,2919,921	AA,AG,GG		42.6163,24.8752,36.6062		155/361	24201643	8245,4761	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			CATGATGCCCAGG	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.465C>T	1.37:g.24201643G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			G|0.360;A|0.640	0.640	strong		0.592	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
ANO7	50636	hgsc.bcm.edu	37	2	242157241	242157241	+	Missense_Mutation	SNP	G	G	A	rs76832527	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242157241G>A	ENST00000274979.8	+	20	2378	c.2275G>A	c.(2275-2277)Gcc>Acc	p.A759T	ANO7_ENST00000402430.3_Missense_Mutation_p.A758T	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	759					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						GGCCGAGCGCGCCCAGGACAT	0.721													g|||	555	0.110823	0.0174	0.1758	5008	,	,		7845	0.1131		0.172	False		,,,				2504	0.1258				p.A759T		Atlas-SNP	.											ANO7,colon,carcinoma,-2,1	ANO7	136	1	0			c.G2275A						PASS	.		THR/ALA	215,4153		9,197,1978	16.0	17.0	17.0		2275	2.8	1.0	2	dbSNP_131	17	1483,7097		131,1221,2938	yes	missense	ANO7	NM_001001891.3	58	140,1418,4916	AA,AG,GG		17.2844,4.9222,13.114	possibly-damaging	759/934	242157241	1698,11250	2184	4290	6474	SO:0001583	missense	50636	exon20			GAGCGCGCCCAGG	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.2275G>A	2.37:g.242157241G>A	ENSP00000274979:p.Ala759Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	255|255	0.11675824175824176|0.11675824175824176	10|10	0.02032520325203252|0.02032520325203252	68|68	0.1878453038674033|0.1878453038674033	61|61	0.10664335664335664|0.10664335664335664	116|116	0.15303430079155672|0.15303430079155672	g|g	22.8|22.8	4.333562|4.333562	0.81801|0.81801	0.049222|0.049222	0.172844|0.172844	ENSG00000146205|ENSG00000146205	ENST00000274979;ENST00000402430|ENST00000451047	T;T|T	0.67171|0.69806	-0.25;-0.25|-0.43	2.84|2.84	2.84|2.84	0.33178|0.33178	.|.	0.152058|.	0.42821|.	N|.	0.000643|.	T|T	0.00241|0.00241	0.0007|0.0007	L|L	0.52011|0.52011	1.625|1.625	0.21499|0.21499	P|P	0.9996691|0.9996691	P|.	0.41673|.	0.759|.	B|.	0.38378|.	0.272|.	T|T	0.26087|0.26087	-1.0113|-1.0113	9|6	0.56958|0.87932	D|D	0.05|0	.|.	13.5641|13.5641	0.61807|0.61807	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	759|.	Q6IWH7|.	ANO7_HUMAN|.	T|H	759;758|71	ENSP00000274979:A759T;ENSP00000385418:A758T|ENSP00000403625:R71H	ENSP00000274979:A759T|ENSP00000403625:R71H	A|R	+|+	1|2	0|0	ANO7|ANO7	241805914|241805914	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	8.276000|8.276000	0.89894|0.89894	1.305000|1.305000	0.44909|0.44909	0.298000|0.298000	0.19748|0.19748	GCC|CGC	G|0.874;A|0.126	0.126	strong		0.721	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73072504	73072504	+	Silent	SNP	A	A	C	rs10473959	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73072504A>C	ENST00000426542.2	+	5	843	c.823A>C	c.(823-825)Aga>Cga	p.R275R	ARHGEF28_ENST00000437974.1_Silent_p.R275R|ARHGEF28_ENST00000296794.6_Silent_p.R275R|ARHGEF28_ENST00000513042.2_Silent_p.R275R|CTC-575I10.1_ENST00000506717.1_RNA|ARHGEF28_ENST00000545377.1_Silent_p.R275R|ARHGEF28_ENST00000287898.5_Silent_p.R275R			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	275					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)										CTTTTGGGATAGAGCCTTTCT	0.413													A|||	188	0.0375399	0.0855	0.0231	5008	,	,		16768	0.0		0.0308	False		,,,				2504	0.0286				p.R275R		Atlas-SNP	.											.	.	.	.	0			c.A823C						PASS	.	A	,	296,3626		9,278,1674	132.0	140.0	137.0		823,823	4.1	1.0	5	dbSNP_119	137	236,8084		1,234,3925	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	10,512,5599	CC,CA,AA		2.8365,7.5472,4.3457	,	275/1732,275/1706	73072504	532,11710	1961	4160	6121	SO:0001819	synonymous_variant	64283	exon6			TGGGATAGAGCCT		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.823A>C	5.37:g.73072504A>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	150	83	0.553333	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			A|0.965;C|0.035	0.035	strong		0.413	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
TMPRSS12	283471	hgsc.bcm.edu	37	12	51237816	51237816	+	Missense_Mutation	SNP	G	G	A	rs861204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:51237816G>A	ENST00000398458.3	+	2	411	c.379G>A	c.(379-381)Gct>Act	p.A127T	TMPRSS12_ENST00000551456.1_Missense_Mutation_p.A127T|RN7SL519P_ENST00000497925.2_RNA	NM_182559.2	NP_872365	Q86WS5	TMPSC_HUMAN	transmembrane (C-terminal) protease, serine 12	127	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> T (in dbSNP:rs861204).			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						CACTAAAGACGCTAGGTACGT	0.443													G|||	843	0.168331	0.1301	0.1974	5008	,	,		15756	0.0218		0.3519	False		,,,				2504	0.1616				p.A127T		Atlas-SNP	.											.	TMPRSS12	33	.	0			c.G379A						PASS	.	G	THR/ALA	675,3409		59,557,1426	40.0	41.0	41.0		379	-10.7	0.0	12	dbSNP_86	41	2825,5581		470,1885,1848	yes	missense	TMPRSS12	NM_182559.2	58	529,2442,3274	AA,AG,GG		33.6069,16.5279,28.0224	benign	127/349	51237816	3500,8990	2042	4203	6245	SO:0001583	missense	283471	exon2			AAAGACGCTAGGT	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.379G>A	12.37:g.51237816G>A	ENSP00000381476:p.Ala127Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_182559	B9ZVX2	Missense_Mutation	SNP	ENST00000398458.3	37	CCDS44881.1	442	0.20238095238095238	70	0.14227642276422764	80	0.22099447513812154	12	0.02097902097902098	280	0.36939313984168864	G	1.214	-0.628931	0.03610	0.165279	0.336069	ENSG00000186452	ENST00000551456;ENST00000398458	T;T	0.60040	0.22;0.23	5.34	-10.7	0.00240	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	2.201380	0.01533	N	0.018891	T	0.00012	0.0000	N	0.10707	0.03	0.80722	P	0.0	B;B	0.24651	0.108;0.032	B;B	0.22753	0.041;0.004	T	0.04140	-1.0974	9	0.20046	T	0.44	1.155	2.8105	0.05440	0.4254:0.125:0.3167:0.133	rs861204;rs1268905;rs17291950;rs56916041;rs861204	127;127	F8WBX2;Q86WS5	.;TMPSC_HUMAN	T	127	ENSP00000447259:A127T;ENSP00000381476:A127T	ENSP00000381476:A127T	A	+	1	0	TMPRSS12	49524083	0.000000	0.05858	0.000000	0.03702	0.578000	0.36192	-2.724000	0.00809	-5.489000	0.00013	-0.471000	0.05019	GCT	G|0.806;A|0.193	0.193	strong		0.443	TMPRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404289.1	NM_182559	
SVEP1	79987	hgsc.bcm.edu	37	9	113276356	113276356	+	Missense_Mutation	SNP	C	C	G	rs3818764	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:113276356C>G	ENST00000401783.2	-	4	1331	c.995G>C	c.(994-996)gGc>gCc	p.G332A	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.G309A|SVEP1_ENST00000374461.1_Missense_Mutation_p.G309A|SVEP1_ENST00000302728.8_Missense_Mutation_p.G332A	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	332			G -> A (in dbSNP:rs3818764). {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						TCCTGGTGAGCCTTCAGGTTT	0.502													C|||	723	0.144369	0.034	0.2666	5008	,	,		18784	0.1081		0.2008	False		,,,				2504	0.1861				p.G332A		Atlas-SNP	.											.	SVEP1	326	.	0			c.G995C						PASS	.	C	ALA/GLY	223,3805		7,209,1798	69.0	68.0	68.0		995	3.6	0.7	9	dbSNP_107	68	1658,6708		180,1298,2705	yes	missense	SVEP1	NM_153366.3	60	187,1507,4503	GG,GC,CC		19.8183,5.5362,15.1767	benign	332/3572	113276356	1881,10513	2014	4183	6197	SO:0001583	missense	79987	exon4			GGTGAGCCTTCAG	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.995G>C	9.37:g.113276356C>G	ENSP00000384917:p.Gly332Ala	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	194	85	0.438144	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	326	0.14926739926739926	28	0.056910569105691054	96	0.26519337016574585	63	0.11013986013986014	139	0.18337730870712401	C	12.03	1.814249	0.32053	0.055362	0.198183	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.58	3.61	0.41365	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.163234	0.53938	N	0.000055	T	0.00012	0.0000	N	0.04746	-0.17	0.40684	P	0.017664000000000013	B;B;B;B	0.22276	0.067;0.067;0.004;0.031	B;B;B;B	0.25291	0.044;0.059;0.026;0.026	T	0.47394	-0.9121	9	0.15066	T	0.55	.	16.1518	0.81626	0.0:0.6854:0.3146:0.0	rs3818764;rs17806854;rs52807409;rs3818764	332;332;332;332	E9PBN8;Q4LDE5;B3KV07;Q4LDE5-2	.;SVEP1_HUMAN;.;.	A	332;309;332;309	ENSP00000384917:G332A;ENSP00000363593:G309A;ENSP00000304118:G332A;ENSP00000363585:G309A	ENSP00000304118:G332A	G	-	2	0	SVEP1	112316177	0.904000	0.30761	0.656000	0.29637	0.908000	0.53690	1.705000	0.37867	0.678000	0.31325	0.650000	0.86243	GGC	C|0.847;G|0.153	0.153	strong		0.502	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SLIT3	6586	hgsc.bcm.edu	37	5	168093522	168093522	+	Silent	SNP	G	G	A	rs1048307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:168093522G>A	ENST00000519560.1	-	36	4928	c.4509C>T	c.(4507-4509)gaC>gaT	p.D1503D	CTC-558O2.2_ENST00000520041.1_RNA|SLIT3_ENST00000332966.8_Silent_p.D1510D	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1503	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				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)			ACGAGGAGCCGTCCGTGCACT	0.642													G|||	1032	0.20607	0.0431	0.2061	5008	,	,		14738	0.4206		0.174	False		,,,				2504	0.2382				p.D1510D	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C4530T						PASS	.	G		358,4048	182.9+/-210.6	20,318,1865	47.0	39.0	42.0		4509	2.3	1.0	5	dbSNP_86	42	1589,7011	293.4+/-301.3	153,1283,2864	no	coding-synonymous	SLIT3	NM_003062.2		173,1601,4729	AA,AG,GG		18.4767,8.1253,14.97		1503/1524	168093522	1947,11059	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon36			GGAGCCGTCCGTG	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.4509C>T	5.37:g.168093522G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			G|0.834;A|0.166	0.166	strong		0.642	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27834877	27834877	+	Missense_Mutation	SNP	T	T	C	rs11970638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:27834877T>C	ENST00000331442.3	-	1	482	c.431A>G	c.(430-432)aAg>aGg	p.K144R		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	144			K -> R (in dbSNP:rs11970638).		chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CCCTGCAGCCTTCTTGGCCTT	0.617													T|||	136	0.0271565	0.0802	0.0144	5008	,	,		15536	0.005		0.0119	False		,,,				2504	0.0031				p.K144R		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.A431G						PASS	.	T	ARG/LYS	380,4026		14,352,1837	95.0	111.0	106.0		431	5.2	0.9	6	dbSNP_120	106	51,8547		1,49,4249	yes	missense	HIST1H1B	NM_005322.2	26	15,401,6086	CC,CT,TT		0.5932,8.6246,3.3144	probably-damaging	144/227	27834877	431,12573	2203	4299	6502	SO:0001583	missense	3009	exon1			GCAGCCTTCTTGG	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.431A>G	6.37:g.27834877T>C	ENSP00000330074:p.Lys144Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	61	0.027930402930402932	40	0.08130081300813008	8	0.022099447513812154	4	0.006993006993006993	9	0.011873350923482849	T	15.08	2.726408	0.48833	0.086246	0.005932	ENSG00000184357	ENST00000331442	T	0.24538	1.85	5.19	5.19	0.71726	.	0.587579	0.17333	N	0.178040	T	0.20577	0.0495	N	0.08118	0	0.80722	D	1	D	0.63880	0.993	D	0.72625	0.978	T	0.29088	-1.0023	10	0.51188	T	0.08	-5.6028	14.5461	0.68032	0.0:0.0:0.0:1.0	rs11970638;rs11970638	144	P16401	H15_HUMAN	R	144	ENSP00000330074:K144R	ENSP00000330074:K144R	K	-	2	0	HIST1H1B	27942856	1.000000	0.71417	0.944000	0.38274	0.103000	0.19146	3.084000	0.50143	2.103000	0.63969	0.533000	0.62120	AAG	T|0.968;C|0.032	0.032	strong		0.617	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232581436	232581436	+	Silent	SNP	G	G	A	rs12757779	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:232581436G>A	ENST00000366630.1	-	10	3550	c.3192C>T	c.(3190-3192)acC>acT	p.T1064T	SIPA1L2_ENST00000308942.4_Silent_p.T138T|SIPA1L2_ENST00000262861.4_Silent_p.T1064T			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1064					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)				GGTGCCACGTGGTGTTCCTCC	0.637													G|||	447	0.0892572	0.0363	0.1657	5008	,	,		15750	0.001		0.1889	False		,,,				2504	0.0951				p.T1064T		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C3192T						PASS	.	G		258,3548		12,234,1657	58.0	65.0	63.0		3192	2.5	1.0	1	dbSNP_121	63	1708,6528		176,1356,2586	no	coding-synonymous	SIPA1L2	NM_020808.3		188,1590,4243	AA,AG,GG		20.7382,6.7788,16.3262		1064/1723	232581436	1966,10076	1903	4118	6021	SO:0001819	synonymous_variant	57568	exon9			CCACGTGGTGTTC	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.3192C>T	1.37:g.232581436G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	108	65	0.601852	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			G|0.886;A|0.114	0.114	strong		0.637	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
GABRA6	2559	hgsc.bcm.edu	37	5	161119125	161119125	+	Silent	SNP	C	C	G	rs13184586	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:161119125C>G	ENST00000274545.5	+	8	1438	c.1005C>G	c.(1003-1005)gcC>gcG	p.A335A	GABRA6_ENST00000523217.1_Silent_p.A325A|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	335					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CACAGAAGGCCAAAAGGAAGG	0.433										TCGA Ovarian(5;0.080)			C|||	2009	0.401158	0.3351	0.3732	5008	,	,		19042	0.3185		0.5736	False		,,,				2504	0.4182				p.A335A		Atlas-SNP	.											.	GABRA6	139	.	0			c.C1005G						PASS	.	C		1564,2842	491.3+/-362.1	273,1018,912	161.0	139.0	146.0		1005	-1.1	1.0	5	dbSNP_121	146	4784,3816	613.0+/-396.0	1320,2144,836	no	coding-synonymous	GABRA6	NM_000811.2		1593,3162,1748	GG,GC,CC		44.3721,35.497,48.8082		335/454	161119125	6348,6658	2203	4300	6503	SO:0001819	synonymous_variant	2559	exon8			GAAGGCCAAAAGG		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1005C>G	5.37:g.161119125C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	37	CCDS4356.1																																																																																			C|0.535;G|0.465	0.465	strong		0.433	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
ZNF839	55778	hgsc.bcm.edu	37	14	102808330	102808330	+	Silent	SNP	C	C	T	rs12590618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:102808330C>T	ENST00000558850.1	+	8	2600	c.2250C>T	c.(2248-2250)gtC>gtT	p.V750V	ZNF839_ENST00000442396.2_Silent_p.V866V|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000262236.5_Silent_p.V752V|ZNF839_ENST00000559185.1_Silent_p.V750V	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	750							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						TGGTTGCTGTCGGCGAAGCCA	0.522													C|||	1343	0.268171	0.0734	0.2594	5008	,	,		18246	0.496		0.337	False		,,,				2504	0.2321				p.V866V		Atlas-SNP	.											.	ZNF839	41	.	0			c.C2598T						PASS	.	C		441,3435		23,395,1520	42.0	44.0	43.0		2598	-10.6	0.0	14	dbSNP_120	43	2654,5638		433,1788,1925	no	coding-synonymous	ZNF839	NM_018335.3		456,2183,3445	TT,TC,CC		32.0068,11.3777,25.4356		866/928	102808330	3095,9073	1938	4146	6084	SO:0001819	synonymous_variant	55778	exon8			TGCTGTCGGCGAA	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.2250C>T	14.37:g.102808330C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	151	90	0.596026	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	37	CCDS58336.1																																																																																			C|0.703;T|0.297	0.297	strong		0.522	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387344	46387344	+	Silent	SNP	G	G	A	rs11550348	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	73	0	0	938	WXS	Illumina HiSeq	Phase_I	75	33	0.44	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	
TNNT2	7139	hgsc.bcm.edu	37	1	201334795	201334795	+	Silent	SNP	C	C	T	rs3729845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201334795C>T	ENST00000509001.1	-	8	493	c.207G>A	c.(205-207)tcG>tcA	p.S69S	TNNT2_ENST00000421663.2_Silent_p.S71S|TNNT2_ENST00000460780.1_5'Flank|TNNT2_ENST00000458432.2_Silent_p.S81S|TNNT2_ENST00000367317.4_Silent_p.S69S|TNNT2_ENST00000367315.2_Silent_p.S69S|TNNT2_ENST00000367322.1_Silent_p.S69S|TNNT2_ENST00000360372.4_Silent_p.S64S|TNNT2_ENST00000367318.5_Silent_p.S69S|TNNT2_ENST00000367320.2_Silent_p.S78S|TNNT2_ENST00000236918.7_Silent_p.S74S	NM_001276347.1	NP_001263276.1	P45379	TNNT2_HUMAN	troponin T type 2 (cardiac)	79					ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|muscle filament sliding (GO:0030049)|negative regulation of ATPase activity (GO:0032780)|positive regulation of ATPase activity (GO:0032781)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle thin filament (GO:0005865)|troponin complex (GO:0005861)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(9)	20						TGGGCATGAACGACCTGTTGG	0.572													C|||	413	0.0824681	0.1921	0.0562	5008	,	,		21375	0.001		0.0666	False		,,,				2504	0.0532				p.S79S		Atlas-SNP	.											.	TNNT2	43	.	0			c.G237A						PASS	.	C	,,,	651,3755	277.8+/-273.9	47,557,1599	128.0	113.0	118.0		237,207,207,192	-8.8	0.2	1	dbSNP_107	118	545,8055	150.0+/-205.0	16,513,3771	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNNT2	NM_000364.2,NM_001001430.1,NM_001001431.1,NM_001001432.1	,,,	63,1070,5370	TT,TC,CC		6.3372,14.7753,9.1958	,,,	79/296,69/289,69/286,64/283	201334795	1196,11810	2203	4300	6503	SO:0001819	synonymous_variant	7139	exon9			CATGAACGACCTG	X74819	CCDS30968.1, CCDS30969.1, CCDS60390.1, CCDS73002.1, CCDS73003.1	1q32	2014-09-17	2005-09-12		ENSG00000118194	ENSG00000118194			11949	protein-coding gene	gene with protein product		191045	"""troponin T2, cardiac"", ""cardiomyopathy, hypertrophic 2"", ""cardiomyopathy, dilated 1D (autosomal dominant)"""	CMH2, CMD1D		8088824, 8205619, 9482583	Standard	NM_001001430		Approved	CMPD2	uc001gwf.4	P45379	OTTHUMG00000035733	ENST00000509001.1:c.207G>A	1.37:g.201334795C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_001276345	A2TDB9|A8K3K6|O60214|Q99596|Q99597|Q9BUF6|Q9UM96	Silent	SNP	ENST00000509001.1	37	CCDS30969.1																																																																																			C|0.911;T|0.089	0.089	strong		0.572	TNNT2-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360358.1	NM_000364	
BLMH	642	hgsc.bcm.edu	37	17	28576076	28576076	+	Missense_Mutation	SNP	T	T	C	rs1050565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28576076T>C	ENST00000261714.6	-	12	1501	c.1327A>G	c.(1327-1329)Atc>Gtc	p.I443V	BLMH_ENST00000394819.3_Missense_Mutation_p.I356V|SNORD63_ENST00000516303.1_RNA|RP11-354P11.2_ENST00000577420.1_RNA	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	443			I -> V (common polymorphism; dbSNP:rs1050565). {ECO:0000269|PubMed:8639621, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	GCTGGCAGGATAATGGGTTCC	0.527													T|||	1271	0.253794	0.1989	0.3746	5008	,	,		18137	0.1736		0.329	False		,,,				2504	0.2474				p.I443V	Pancreas(127;628 1772 12912 33293 36203)	Atlas-SNP	.											.	BLMH	42	.	0			c.A1327G	GRCh37	CM980214	BLMH	M	rs1050565	PASS	.	T	VAL/ILE	941,3465	357.6+/-314.0	91,759,1353	161.0	129.0	140.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1327	1.5	0.6	17	dbSNP_86	140	2771,5829	439.7+/-359.3	460,1851,1989	yes	missense	BLMH	NM_000386.3	29	551,2610,3342	CC,CT,TT		32.2209,21.3572,28.5407	benign	443/456	28576076	3712,9294	2203	4300	6503	SO:0001583	missense	642	exon12			GCAGGATAATGGG	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.1327A>G	17.37:g.28576076T>C	ENSP00000261714:p.Ile443Val	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	131	50	0.381679	NM_000386	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	37	CCDS32604.1	598	0.27380952380952384	111	0.22560975609756098	128	0.35359116022099446	102	0.17832167832167833	257	0.3390501319261214	T	0.549	-0.850369	0.02651	0.213572	0.322209	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.39787	1.06;1.06	5.83	1.54	0.23209	.	0.449653	0.24960	N	0.034224	T	0.00012	0.0000	N	0.00109	-2.105	0.54753	P	1.2000000000012001E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45056	-0.9287	9	0.02654	T	1	-4.5757	9.4628	0.38796	0.0:0.7023:0.0:0.2977	rs1050565;rs3190883;rs17767244;rs52825124;rs59661471;rs1050565	356;443	E7EMN3;Q13867	.;BLMH_HUMAN	V	443;356	ENSP00000261714:I443V;ENSP00000378296:I356V	ENSP00000261714:I443V	I	-	1	0	BLMH	25600202	0.494000	0.26043	0.649000	0.29536	0.957000	0.61999	1.148000	0.31614	0.080000	0.16959	-1.125000	0.01998	ATC	T|0.728;C|0.272	0.272	strong		0.527	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386	
OPRM1	4988	hgsc.bcm.edu	37	6	154360797	154360797	+	Missense_Mutation	SNP	A	A	G	rs1799971	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:154360797A>G	ENST00000330432.7	+	1	355	c.118A>G	c.(118-120)Aac>Gac	p.N40D	OPRM1_ENST00000360422.4_Missense_Mutation_p.N40D|OPRM1_ENST00000428397.2_Missense_Mutation_p.N40D|OPRM1_ENST00000523520.1_3'UTR|OPRM1_ENST00000419506.2_Missense_Mutation_p.N40D|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000524163.1_Missense_Mutation_p.N40D|OPRM1_ENST00000452687.2_Missense_Mutation_p.N40D|OPRM1_ENST00000337049.4_Missense_Mutation_p.N40D|OPRM1_ENST00000435918.2_Missense_Mutation_p.N40D|OPRM1_ENST00000414028.2_Missense_Mutation_p.N40D|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000434900.2_Missense_Mutation_p.N133D|OPRM1_ENST00000229768.5_Missense_Mutation_p.N40D	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	40			N -> D (in 10% of the population; dbSNP:rs1799971). {ECO:0000269|PubMed:7957926, ECO:0000269|PubMed:9399694, ECO:0000269|PubMed:9689128, ECO:0000269|Ref.13}.		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)	CTTAGATGGCAACCTGTCCGA	0.632													A|||	1119	0.223442	0.0091	0.2003	5008	,	,		17457	0.3929		0.162	False		,,,				2504	0.4182				p.N133D		Atlas-SNP	.											.	OPRM1	241	.	0			c.A397G	GRCh37	CM003770	OPRM1	M	rs1799971	PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,,,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	122,3862		2,118,1872	57.0	61.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	118,118,118,118,397,,,118,118,118,118,118	5.8	1.0	6	dbSNP_89	60	1070,7238		73,924,3157	yes	missense,missense,missense,missense,missense,intron,intron,missense,missense,missense,missense,missense	OPRM1	NM_000914.3,NM_001008503.1,NM_001008504.2,NM_001008505.1,NM_001145279.2,NM_001145280.2,NM_001145281.1,NM_001145282.1,NM_001145283.1,NM_001145284.2,NM_001145285.1,NM_001145286.1	23,23,23,23,23,,,23,23,23,23,23	75,1042,5029	GG,GA,AA		12.8792,3.0622,9.6974	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	40/401,40/419,40/393,40/447,133/494,,,40/407,40/398,40/404,40/390,40/421	154360797	1192,11100	1992	4154	6146	SO:0001583	missense	4988	exon3			GATGGCAACCTGT	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.118A>G	6.37:g.154360797A>G	ENSP00000328264:p.Asn40Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	37	CCDS55070.1	414	0.18956043956043955	7	0.014227642276422764	68	0.1878453038674033	218	0.3811188811188811	121	0.15963060686015831	A	22.9	4.355925	0.82243	0.030622	0.128792	ENSG00000112038	ENST00000520282;ENST00000434900;ENST00000330432;ENST00000360422;ENST00000428397;ENST00000452687;ENST00000229768;ENST00000419506;ENST00000524163;ENST00000414028;ENST00000435918;ENST00000337049	T;T;T;T;T;T;T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16	5.75	5.75	0.90469	.	1.586080	0.02913	N	0.136978	T	0.15478	0.0373	N	0.08118	0	0.23747	P	0.99695109	P;B;B;P;B;B;B;B;P;P;B	0.52061	0.95;0.217;0.001;0.95;0.081;0.002;0.003;0.227;0.734;0.486;0.007	P;B;B;P;B;B;B;B;P;B;B	0.55391	0.775;0.098;0.005;0.775;0.021;0.007;0.007;0.098;0.535;0.138;0.008	T	0.33007	-0.9885	9	0.72032	D	0.01	.	15.0406	0.71788	1.0:0.0:0.0:0.0	rs1799971;rs17181017;rs52818856;rs61596185;rs1799971	40;40;40;40;133;40;40;40;40;40;40	P35372-4;P35372-8;P35372-11;P35372-9;P35372-10;P35372-6;P35372-5;P35372;P35372-7;P35372-3;P35372-2	.;.;.;.;.;.;.;OPRM_HUMAN;.;.;.	D	88;133;40;40;40;40;40;40;40;40;40;40	ENSP00000430247:N88D;ENSP00000394624:N133D;ENSP00000328264:N40D;ENSP00000353598:N40D;ENSP00000411903:N40D;ENSP00000410497:N40D;ENSP00000229768:N40D;ENSP00000403549:N40D;ENSP00000430097:N40D;ENSP00000399359:N40D;ENSP00000413752:N40D;ENSP00000338381:N40D	ENSP00000229768:N40D	N	+	1	0	OPRM1	154402490	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.322000	0.43814	2.200000	0.70718	0.477000	0.44152	AAC	A|0.815;G|0.185	0.185	strong		0.632	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914	
APMAP	57136	hgsc.bcm.edu	37	20	24973247	24973247	+	Silent	SNP	C	C	A	rs11550623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:24973247C>A	ENST00000217456.2	-	1	368	c.78G>T	c.(76-78)ccG>ccT	p.P26P	APMAP_ENST00000447138.1_Silent_p.P26P	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	26					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										CCTTAGCCTCCGGGGCCTGGC	0.726													C|||	335	0.066893	0.0915	0.0548	5008	,	,		13061	0.003		0.0825	False		,,,				2504	0.092				p.P26P		Atlas-SNP	.											.	APMAP	3	.	0			c.G78T						PASS	.	C		372,4006		14,344,1831	15.0	19.0	18.0		78	0.2	0.9	20	dbSNP_120	18	724,7840		31,662,3589	no	coding-synonymous	C20orf3	NM_020531.2		45,1006,5420	AA,AC,CC		8.454,8.497,8.4686		26/417	24973247	1096,11846	2189	4282	6471	SO:0001819	synonymous_variant	57136	exon1			AGCCTCCGGGGCC	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.78G>T	20.37:g.24973247C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Silent	SNP	ENST00000217456.2	37	CCDS13166.1	131	0.059981684981684984	49	0.09959349593495935	18	0.049723756906077346	1	0.0017482517482517483	63	0.08311345646437995	C	12.79	2.044610	0.36085	0.08497	0.08454	ENSG00000101474	ENST00000451442	.	.	.	4.56	0.184	0.15086	.	.	.	.	.	T	0.01454	0.0047	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02444	-1.1158	4	.	.	.	-13.7053	3.4229	0.07400	0.1598:0.4043:0.3417:0.0942	rs11698945;rs60434486;rs11698945	.	.	.	L	11	.	.	R	-	2	0	C20orf3	24921247	0.291000	0.24352	0.906000	0.35671	0.994000	0.84299	0.130000	0.15850	-0.017000	0.14103	0.467000	0.42956	CGG	C|0.925;A|0.075	0.075	strong		0.726	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
KRT38	8687	hgsc.bcm.edu	37	17	39594857	39594857	+	Silent	SNP	G	G	T	rs60786473	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39594857G>T	ENST00000246646.3	-	5	905	c.906C>A	c.(904-906)atC>atA	p.I302I		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	302	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)				CCTGCAGGCTGATGCCTTCAG	0.627													G|||	230	0.0459265	0.0477	0.0346	5008	,	,		18842	0.0496		0.0755	False		,,,				2504	0.0174				p.I302I		Atlas-SNP	.											.	KRT38	63	.	0			c.C906A						PASS	.	G		227,4179		5,217,1981	123.0	100.0	108.0		906	-0.3	0.0	17	dbSNP_129	108	753,7847		29,695,3576	no	coding-synonymous	KRT38	NM_006771.3		34,912,5557	TT,TG,GG		8.7558,5.1521,7.535		302/457	39594857	980,12026	2203	4300	6503	SO:0001819	synonymous_variant	8687	exon5			CAGGCTGATGCCT	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.906C>A	17.37:g.39594857G>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_006771	A2RRM5|Q6A164	Silent	SNP	ENST00000246646.3	37	CCDS11392.1																																																																																			G|0.928;T|0.072	0.072	strong		0.627	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
DDX11	1663	hgsc.bcm.edu	37	12	31256517	31256517	+	Silent	SNP	C	C	T	rs140335402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:31256517C>T	ENST00000407793.2	+	26	2789	c.2538C>T	c.(2536-2538)ggC>ggT	p.G846G	DDX11_ENST00000545668.1_Silent_p.G846G|DDX11_ENST00000350437.4_Missense_Mutation_p.A798V|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Missense_Mutation_p.A848V|DDX11_ENST00000228264.6_Missense_Mutation_p.A822V	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	846					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)					GCAGGCAGGGCCATCAGGCAC	0.642										Multiple Myeloma(12;0.14)			C|||	212	0.0423323	0.0098	0.0778	5008	,	,		15220	0.002		0.1113	False		,,,				2504	0.0317				p.A848V		Atlas-SNP	.											DDX11_ENST00000407793,NS,haematopoietic_neoplasm,0,2	DDX11	188	2	0			c.C2543T						PASS	.	C	VAL/ALA,VAL/ALA,	70,4300		2,66,2117	17.0	25.0	22.0		2393,2543,2538	3.1	1.0	12	dbSNP_134	22	852,7726		41,770,3478	no	missense,missense,coding-synonymous	DDX11	NM_004399.2,NM_030653.3,NM_152438.1	64,64,	43,836,5595	TT,TC,CC		9.9324,1.6018,7.1208	,,	798/857,848/907,846/971	31256517	922,12026	2185	4289	6474	SO:0001819	synonymous_variant	1663	exon26			GCAGGGCCATCAG	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.2538C>T	12.37:g.31256517C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	123	47	0.382114	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	114|114	0.0521978021978022|0.0521978021978022	8|8	0.016260162601626018|0.016260162601626018	29|29	0.08011049723756906|0.08011049723756906	1|1	0.0017482517482517483|0.0017482517482517483	76|76	0.10026385224274406|0.10026385224274406	C|C	4.403|4.403	0.074498|0.074498	0.08485|0.08485	0.016018|0.016018	0.099324|0.099324	ENSG00000013573|ENSG00000013573	ENST00000542838;ENST00000228264;ENST00000350437|ENST00000404673;ENST00000539702	T;T;D|.	0.91011|.	-0.8;-0.8;-2.77|.	3.14|3.14	3.14|3.14	0.36123|0.36123	.|.	0.768466|.	0.12220|.	N|.	0.488518|.	T|T	0.01627|0.01627	0.0052|0.0052	L|L	0.43923|0.43923	1.385|1.385	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;0.999;0.999|.	T|T	0.12915|0.12915	-1.0529|-1.0529	9|5	0.72032|0.08837	D|T	0.01|0.75	.|.	11.816|11.816	0.52211|0.52211	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	822;798;848|.	Q96FC9-3;Q96FC9-4;Q96FC9-2|.	.;.;.|.	V|S	848;822;798|547;114	ENSP00000443426:A848V;ENSP00000228264:A822V;ENSP00000309965:A798V|.	ENSP00000228264:A822V|ENSP00000385471:P547S	A|P	+|+	2|1	0|0	DDX11|DDX11	31147784|31147784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.804000|0.804000	0.45430|0.45430	6.568000|6.568000	0.73987|0.73987	1.582000|1.582000	0.49881|0.49881	0.430000|0.430000	0.28490|0.28490	GCC|CCA	C|0.931;T|0.069	0.069	strong		0.642	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
HCRTR2	3062	hgsc.bcm.edu	37	6	55147110	55147110	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:55147110G>A	ENST00000370862.3	+	7	1529	c.1193G>A	c.(1192-1194)cGa>cAa	p.R398Q		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	398					circadian sleep/wake cycle process (GO:0022410)|feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|orexin receptor activity (GO:0016499)			breast(3)|endometrium(2)|kidney(1)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	46	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACCAGGGGACGAACTAGCACA	0.468																																					p.R398Q		Atlas-SNP	.											HCRTR2,NS,carcinoma,+1,1	HCRTR2	112	1	0			c.G1193A						scavenged	.						86.0	78.0	81.0					6																	55147110		2203	4300	6503	SO:0001583	missense	3062	exon7			GGGGACGAACTAG	AF041245	CCDS4956.1	6p12.1	2012-09-20			ENSG00000137252	ENSG00000137252		"""GPCR / Class A : Hypocretin (orexin) receptors"""	4849	protein-coding gene	gene with protein product		602393				9491897	Standard	NM_001526		Approved	OX2R	uc003pcl.3	O43614	OTTHUMG00000016150	ENST00000370862.3:c.1193G>A	6.37:g.55147110G>A	ENSP00000359899:p.Arg398Gln	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	118	3	0.0254237	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	37	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.969055	0.92855	.	.	ENSG00000137252	ENST00000370862	T	0.37915	1.17	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.36138	0.0956	L	0.29908	0.895	0.37237	D	0.905954	D	0.76494	0.999	P	0.59948	0.866	T	0.06935	-1.0799	10	0.36615	T	0.2	.	19.3106	0.94186	0.0:0.0:1.0:0.0	.	398	O43614	OX2R_HUMAN	Q	398	ENSP00000359899:R398Q	ENSP00000359899:R398Q	R	+	2	0	HCRTR2	55255069	0.441000	0.25626	0.007000	0.13788	0.937000	0.57800	3.344000	0.52174	2.561000	0.86390	0.650000	0.86243	CGA	.	.	none		0.468	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1		
MYOM3	127294	hgsc.bcm.edu	37	1	24406647	24406647	+	Silent	SNP	G	G	A	rs4649175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24406647G>A	ENST00000374434.3	-	20	2607	c.2445C>T	c.(2443-2445)gcC>gcT	p.A815A	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Silent_p.A815A|MYOM3_ENST00000330966.7_Silent_p.A816A|MYOM3_ENST00000475306.1_5'Flank|RP11-293P20.4_ENST00000429191.1_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	815	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CCAGGGATGTGGCCCGCACCT	0.607													G|||	1774	0.354233	0.3238	0.3444	5008	,	,		18648	0.4276		0.4423	False		,,,				2504	0.2362				p.A815A		Atlas-SNP	.											.	MYOM3	131	.	0			c.C2445T						PASS	.	G		1246,2752		209,828,962	47.0	53.0	51.0		2445	4.5	1.0	1	dbSNP_111	51	3538,4792		746,2046,1373	yes	coding-synonymous	MYOM3	NM_152372.3		955,2874,2335	AA,AG,GG		42.473,31.1656,38.806		815/1438	24406647	4784,7544	1999	4165	6164	SO:0001819	synonymous_variant	127294	exon20			GGATGTGGCCCGC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.2445C>T	1.37:g.24406647G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			G|0.639;A|0.361	0.361	strong		0.607	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
HTR4	3360	hgsc.bcm.edu	37	5	147889348	147889348	+	Silent	SNP	A	A	G	rs55727780	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:147889348A>G	ENST00000377888.3	-	6	885	c.747T>C	c.(745-747)caT>caC	p.H249H	HTR4_ENST00000314512.6_Silent_p.H249H|HTR4_ENST00000362016.2_Silent_p.H263H|HTR4_ENST00000521735.1_Silent_p.H249H|HTR4_ENST00000360693.3_Silent_p.H249H|HTR4_ENST00000517929.1_Silent_p.H249H|HTR4_ENST00000520514.1_Silent_p.H249H|HTR4_ENST00000354217.2_Silent_p.H249H|HTR4_ENST00000521530.1_Silent_p.H249H	NM_000870.5	NP_000861.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	249					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)	TCCTCATGCGATGAGTGCTAT	0.542													G|||	88	0.0175719	0.0212	0.0216	5008	,	,		21511	0.001		0.0129	False		,,,				2504	0.0317				p.H249H	GBM(120;370 1604 14007 17804 41573)	Atlas-SNP	.											.	HTR4	161	.	0			c.T747C						PASS	.	G	,,,,	103,4303	817.0+/-416.3	0,103,2100	99.0	84.0	89.0		747,747,747,747,747	-0.6	1.0	5	dbSNP_129	89	106,8494	814.6+/-407.0	0,106,4194	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HTR4	NM_000870.5,NM_001040169.2,NM_001040172.2,NM_001040173.2,NM_199453.3	,,,,	0,209,6294	GG,GA,AA		1.2326,2.3377,1.607	,,,,	249/389,249/388,249/361,249/429,249/379	147889348	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	3360	exon5			CATGCGATGAGTG	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	ENST00000377888.3:c.747T>C	5.37:g.147889348A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001040169	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Silent	SNP	ENST00000377888.3	37	CCDS4291.1																																																																																			A|0.982;G|0.018	0.018	strong		0.542	HTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252187.2	NM_000870	
EFCAB13	124989	hgsc.bcm.edu	37	17	45451894	45451894	+	Missense_Mutation	SNP	G	G	A	rs4968318	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45451894G>A	ENST00000331493.2	+	12	1345	c.934G>A	c.(934-936)Gta>Ata	p.V312I	EFCAB13_ENST00000517484.1_Missense_Mutation_p.V216I	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	312			V -> I (in dbSNP:rs4968318). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										GTTATCAAGTGTAGCAGGATG	0.279													A|||	3114	0.621805	0.7519	0.5317	5008	,	,		16412	0.5903		0.6034	False		,,,				2504	0.5613				p.V312I		Atlas-SNP	.											.	.	.	.	0			c.G934A						PASS	.	A	ILE/VAL,ILE/VAL	3176,1208		1163,850,179	32.0	36.0	34.0		646,934	-8.0	0.0	17	dbSNP_111	34	5226,3300		1668,1890,705	yes	missense,missense	C17orf57	NM_001195192.1,NM_152347.4	29,29	2831,2740,884	AA,AG,GG		38.7051,27.5547,34.9187	benign,benign	216/785,312/974	45451894	8402,4508	2192	4263	6455	SO:0001583	missense	124989	exon12			TCAAGTGTAGCAG	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.934G>A	17.37:g.45451894G>A	ENSP00000332111:p.Val312Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	1372	0.6282051282051282	343	0.6971544715447154	216	0.5966850828729282	361	0.6311188811188811	452	0.5963060686015831	A	0.044	-1.272243	0.01421	0.724453	0.612949	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176	T;T	0.64438	0.26;-0.1	4.02	-8.04	0.01110	.	3.018340	0.01263	N	0.009260	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.33033	-0.9884	9	0.02654	T	1	-12.1637	1.6133	0.02698	0.4474:0.1675:0.2154:0.1697	rs4968318;rs52803438;rs60032644;rs4968318	264;312;216	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	I	312;216;264	ENSP00000332111:V312I;ENSP00000430048:V216I	ENSP00000332111:V312I	V	+	1	0	C17orf57	42806893	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-3.603000	0.00417	-3.238000	0.00207	-2.097000	0.00363	GTA	G|0.358;A|0.642	0.642	strong		0.279	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
PRPF31	26121	hgsc.bcm.edu	37	19	54634830	54634830	+	Silent	SNP	C	C	T	rs62144168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54634830C>T	ENST00000321030.4	+	14	1816	c.1467C>T	c.(1465-1467)gtC>gtT	p.V489V	PRPF31_ENST00000391755.1_Silent_p.V483V|PRPF31_ENST00000419967.1_3'UTR	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	489					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal tri-snRNP complex assembly (GO:0000244)	Cajal body (GO:0015030)|MLL1 complex (GO:0071339)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|U2-type spliceosomal complex (GO:0005684)|U4 snRNP (GO:0005687)|U4/U6 x U5 tri-snRNP complex (GO:0046540)|U4atac snRNP (GO:0005690)	poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|snRNP binding (GO:0070990)			breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)|urinary_tract(3)	12	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TCCTCAAGGTCAAGGGCGAGA	0.567													C|||	316	0.063099	0.0461	0.0735	5008	,	,		21475	0.004		0.1004	False		,,,				2504	0.1012				p.V489V		Atlas-SNP	.											.	PRPF31	48	.	0			c.C1467T						PASS	.	C		310,4096	166.9+/-198.0	12,286,1905	133.0	113.0	119.0		1467	3.0	1.0	19	dbSNP_129	119	748,7852	179.9+/-228.9	41,666,3593	no	coding-synonymous	PRPF31	NM_015629.3		53,952,5498	TT,TC,CC		8.6977,7.0359,8.1347		489/500	54634830	1058,11948	2203	4300	6503	SO:0001819	synonymous_variant	26121	exon14			CAAGGTCAAGGGC	AL050369	CCDS12879.1	19q13.4	2013-07-16	2013-06-10		ENSG00000105618	ENSG00000105618			15446	protein-coding gene	gene with protein product		606419	"""PRP31 pre-mRNA processing factor 31 homolog (yeast)"", ""PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae)"""	RP11		11545739	Standard	NM_015629		Approved	NY-BR-99, PRP31, hPrp31, SNRNP61	uc002qdh.2	Q8WWY3	OTTHUMG00000066040	ENST00000321030.4:c.1467C>T	19.37:g.54634830C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	178	72	0.404494	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Silent	SNP	ENST00000321030.4	37	CCDS12879.1	126	0.057692307692307696	23	0.046747967479674794	33	0.09116022099447514	0	0.0	70	0.09234828496042216	C	9.284	1.048990	0.19827	0.070359	0.086977	ENSG00000105618	ENST00000263436	.	.	.	4.1	3.02	0.34903	.	.	.	.	.	T	0.08846	0.0219	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42430	-0.9452	5	0.59425	D	0.04	-54.0321	12.3326	0.55048	0.0:0.5334:0.4666:0.0	rs62144168	.	.	.	L	353	.	ENSP00000263436:S353L	S	+	2	0	PRPF31	59326642	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.141000	0.31528	0.979000	0.38497	0.491000	0.48974	TCA	C|0.925;T|0.075	0.075	strong		0.567	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2		
MED24	9862	hgsc.bcm.edu	37	17	38179492	38179492	+	Silent	SNP	A	A	G	rs2302777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38179492A>G	ENST00000394128.2	-	20	2223	c.2142T>C	c.(2140-2142)atT>atC	p.I714I	MED24_ENST00000394126.1_Silent_p.I739I|MED24_ENST00000394127.2_Silent_p.I701I|MED24_ENST00000356271.3_Silent_p.I701I|MED24_ENST00000501516.3_Silent_p.I733I	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	714					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CCTTGGCAAAAATGTCCGTCA	0.597													G|||	1575	0.314497	0.0537	0.4135	5008	,	,		18077	0.4226		0.3668	False		,,,				2504	0.4315				p.I714I		Atlas-SNP	.											.	MED24	89	.	0			c.T2142C						PASS	.	G	,	462,3944	783.4+/-414.6	20,422,1761	67.0	62.0	64.0		2103,2142	1.1	1.0	17	dbSNP_100	64	3225,5375	649.3+/-400.6	590,2045,1665	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	610,2467,3426	GG,GA,AA		37.5,10.4857,28.3485	,	701/977,714/990	38179492	3687,9319	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon20			GGCAAAAATGTCC	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2142T>C	17.37:g.38179492A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			A|0.706;G|0.294	0.294	strong		0.597	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
TJP3	27134	hgsc.bcm.edu	37	19	3730041	3730041	+	Silent	SNP	C	C	T	rs7258176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3730041C>T	ENST00000541714.2	+	4	636	c.174C>T	c.(172-174)atC>atT	p.I58I	TJP3_ENST00000262968.9_Silent_p.I77I|TJP3_ENST00000589378.1_Silent_p.I67I|TJP3_ENST00000587686.1_Silent_p.I77I|TJP3_ENST00000382008.3_Silent_p.I58I|TJP3_ENST00000539908.2_Silent_p.I22I	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	58	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		GCGACCACATCGTCATGGTGA	0.602													C|||	3538	0.70647	0.7579	0.7997	5008	,	,		16653	0.6429		0.6421	False		,,,				2504	0.7025				p.I67I		Atlas-SNP	.											.	TJP3	79	.	0			c.C201T						PASS	.	C		3305,1101	720.1+/-409.0	1249,807,147	146.0	130.0	135.0		231	-6.3	0.2	19	dbSNP_116	135	5450,3150	655.6+/-401.3	1735,1980,585	no	coding-synonymous	TJP3	NM_014428.1		2984,2787,732	TT,TC,CC		36.6279,24.9887,32.6849		77/953	3730041	8755,4251	2203	4300	6503	SO:0001819	synonymous_variant	27134	exon4			CCACATCGTCATG	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.174C>T	19.37:g.3730041C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			C|0.314;T|0.686	0.686	strong		0.602	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
POLR1E	64425	hgsc.bcm.edu	37	9	37501752	37501752	+	Silent	SNP	T	T	C	rs17412622	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:37501752T>C	ENST00000377798.4	+	11	1124	c.1011T>C	c.(1009-1011)acT>acC	p.T337T	POLR1E_ENST00000442009.2_Silent_p.T267T|POLR1E_ENST00000377792.3_Silent_p.T399T	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		CGAAGATTACTGCATATGTGA	0.388													T|||	112	0.0223642	0.003	0.036	5008	,	,		23063	0.0		0.0676	False		,,,				2504	0.0153				p.T337T	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.T1011C						PASS	.	T		77,4329	67.6+/-105.2	1,75,2127	148.0	135.0	139.0		1011	-11.6	0.0	9	dbSNP_123	139	659,7941	167.1+/-218.9	23,613,3664	no	coding-synonymous	POLR1E	NM_022490.1		24,688,5791	CC,CT,TT		7.6628,1.7476,5.6589		337/420	37501752	736,12270	2203	4300	6503	SO:0001819	synonymous_variant	64425	exon11			GATTACTGCATAT	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.1011T>C	9.37:g.37501752T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	37	CCDS6611.1																																																																																			T|0.952;C|0.048	0.048	strong		0.388	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
ARHGAP11B	89839	hgsc.bcm.edu	37	15	30927750	30927750	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:30927750G>A	ENST00000428041.2	+	6	866	c.721G>A	c.(721-723)Gtg>Atg	p.V241M		NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	241	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)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		GATGGTCTCTGTGCTACTCCA	0.413																																					p.V241M		Atlas-SNP	.											ARHGAP11B,colon,carcinoma,-2,1	ARHGAP11B	14	1	0			c.G721A						PASS	.						150.0	150.0	150.0					15																	30927750		2202	4298	6500	SO:0001583	missense	89839	exon6			GTCTCTGTGCTAC	BC105788	CCDS32185.1	15q13.2	2011-07-13				ENSG00000187951		"""Rho GTPase activating proteins"""	15782	protein-coding gene	gene with protein product	"""GAP (1-8)"""		"""family with sequence similarity 7, member B1"""	FAM7B1		11829490	Standard	NM_001039841		Approved	B'-T	uc001zet.1	Q3KRB8		ENST00000428041.2:c.721G>A	15.37:g.30927750G>A	ENSP00000392760:p.Val241Met	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	252	97	0.384921	NM_001039841		Missense_Mutation	SNP	ENST00000428041.2	37	CCDS32185.1	.	.	.	.	.	.	.	.	.	.	.	5.293	0.239371	0.10023	.	.	ENSG00000187951	ENST00000428041	T	0.10763	2.84	1.49	1.49	0.22878	Rho GTPase-activating protein domain (1);	.	.	.	.	T	0.04407	0.0121	N	0.14661	0.345	0.18873	N	0.999987	P	0.43857	0.819	B	0.28991	0.097	T	0.35699	-0.9778	9	0.44086	T	0.13	.	6.461	0.21956	0.0:0.0:1.0:0.0	.	241	Q3KRB8	RHGBB_HUMAN	M	241	ENSP00000392760:V241M	ENSP00000392760:V241M	V	+	1	0	ARHGAP11B	28715042	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	1.574000	0.36482	1.121000	0.41925	0.162000	0.16502	GTG	.	.	none		0.413	ARHGAP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430729.1	NM_001039841	
OR51A2	401667	hgsc.bcm.edu	37	11	4976671	4976671	+	Silent	SNP	G	G	A	rs2595984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4976671G>A	ENST00000380371.1	-	1	272	c.273C>T	c.(271-273)gcC>gcT	p.A91A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A91A(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGTTTCAGGGGCATTGAACA	0.438													A|||	746	0.148962	0.1036	0.2061	5008	,	,		14045	0.2183		0.1918	False		,,,				2504	0.0542				p.A91A		Atlas-SNP	.											OR51A2,rectum,carcinoma,0,1	OR51A2	40	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C273T						scavenged	.						132.0	99.0	111.0					11																	4976671		1918	3466	5384	SO:0001819	synonymous_variant	401667	exon1			TTCAGGGGCATTG	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.273C>T	11.37:g.4976671G>A		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	371	5	0.0134771	NM_001004748		Silent	SNP	ENST00000380371.1	37	CCDS31368.1																																																																																			G|0.880;A|0.120	0.120	strong		0.438	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
SMIM11	54065	hgsc.bcm.edu	37	21	35757915	35757915	+	Missense_Mutation	SNP	A	A	G	rs34016792	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:35757915A>G	ENST00000399295.2	+	3	522	c.152A>G	c.(151-153)aAg>aGg	p.K51R	SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Missense_Mutation_p.K51R|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	51			K -> R (in dbSNP:rs34016792).			integral component of membrane (GO:0016021)											GAAAGGAAGAAGCAATCAGAG	0.433													A|||	81	0.0161741	0.0113	0.0231	5008	,	,		20372	0.002		0.0129	False		,,,				2504	0.0358				p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.	A	ARG/LYS	67,4339	61.1+/-98.1	0,67,2136	51.0	47.0	49.0		152	-3.9	0.0	21	dbSNP_126	49	269,8331	100.1+/-161.6	4,261,4035	yes	missense	FAM165B	NM_058182.4	26	4,328,6171	GG,GA,AA		3.1279,1.5207,2.5834	benign	51/59	35757915	336,12670	2203	4300	6503	SO:0001583	missense	54065	exon3			GGAAGAAGCAATC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.152A>G	21.37:g.35757915A>G	ENSP00000382234:p.Lys51Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_058182		Missense_Mutation	SNP	ENST00000399295.2	37	CCDS33550.1	26	0.011904761904761904	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	9	0.011873350923482849	A	10.26	1.300114	0.23650	0.015207	0.031279	ENSG00000205670	ENST00000399292;ENST00000399295	T;T	0.36520	1.25;1.25	5.64	-3.86	0.04230	.	.	.	.	.	T	0.04679	0.0127	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23691	-1.0181	8	0.15952	T	0.53	.	2.0315	0.03530	0.3294:0.3538:0.2024:0.1144	rs34016792	51	P58511	F165B_HUMAN	R	51	ENSP00000382231:K51R;ENSP00000382234:K51R	ENSP00000382231:K51R	K	+	2	0	FAM165B	34679785	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	0.555000	0.23422	-0.979000	0.03529	-0.371000	0.07208	AAG	A|0.979;G|0.021	0.021	strong		0.433	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
DOK2	9046	hgsc.bcm.edu	37	8	21767042	21767042	+	Missense_Mutation	SNP	C	C	T	rs372534431		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:21767042C>T	ENST00000276420.4	-	5	1277	c.1019G>A	c.(1018-1020)cGa>cAa	p.R340Q	DOK2_ENST00000544659.1_Missense_Mutation_p.R186Q	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	340	Pro-rich.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GTGGTCAGGTCGAGGGGGCAG	0.642																																					p.R340Q		Atlas-SNP	.											.	DOK2	51	.	0			c.G1019A						PASS	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	54.0	51.0	52.0		1019	-7.8	0.0	8		52	0,8600		0,0,4300	no	missense	DOK2	NM_003974.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	340/413	21767042	1,13005	2203	4300	6503	SO:0001583	missense	9046	exon5			TCAGGTCGAGGGG	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"""docking protein 2, 56kD"""			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.1019G>A	8.37:g.21767042C>T	ENSP00000276420:p.Arg340Gln	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_003974	Q8N5A4	Missense_Mutation	SNP	ENST00000276420.4	37	CCDS6016.1	.	.	.	.	.	.	.	.	.	.	C	6.665	0.491294	0.12702	2.27E-4	0.0	ENSG00000147443	ENST00000276420;ENST00000544659	T;T	0.31247	1.91;1.5	5.42	-7.8	0.01214	.	2.171590	0.01745	N	0.029603	T	0.15522	0.0374	L	0.27053	0.805	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.10823	-1.0613	10	0.27785	T	0.31	.	0.8219	0.01113	0.2645:0.1123:0.2445:0.3787	.	340;340	O60496;A8K7W1	DOK2_HUMAN;.	Q	340;186	ENSP00000276420:R340Q;ENSP00000443602:R186Q	ENSP00000276420:R340Q	R	-	2	0	DOK2	21822988	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.338000	0.07842	-1.129000	0.02918	-0.345000	0.07892	CGA	.	.	weak		0.642	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974	
AKNAD1	254268	hgsc.bcm.edu	37	1	109363232	109363232	+	Silent	SNP	T	T	C	rs1333130	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	69	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	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	
TPSD1	23430	hgsc.bcm.edu	37	16	1306681	1306681	+	Missense_Mutation	SNP	G	G	A	rs1141967	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306681G>A	ENST00000211076.3	+	2	395	c.247G>A	c.(247-249)Gtg>Atg	p.V83M	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.V76M	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	83	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		V -> M (in dbSNP:rs3993987). {ECO:0000269|PubMed:12391231, ECO:0000269|PubMed:18854315, ECO:0000269|PubMed:9920877}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				GGCGCACTGCGTGGAACCGTG	0.706													-|||	2212	0.441693	0.326	0.2983	5008	,	,		17934	0.7946		0.3221	False		,,,				2504	0.4591				p.V83M		Atlas-SNP	.											.	TPSD1	47	.	0			c.G247A						PASS	.	C	MET/VAL	1411,2987		210,991,998	39.0	47.0	44.0		247	-2.4	0.0	16	dbSNP_86	44	2540,6056		362,1816,2120	yes	missense	TPSD1	NM_012217.2	21	572,2807,3118	AA,AG,GG		29.5486,32.0828,30.4063	possibly-damaging	83/243	1306681	3951,9043	2199	4298	6497	SO:0001583	missense	23430	exon2			CACTGCGTGGAAC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.247G>A	16.37:g.1306681G>A	ENSP00000211076:p.Val83Met	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	187	103	0.550802	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	974	0.445970695970696	160	0.3252032520325203	98	0.27071823204419887	470	0.8216783216783217	246	0.3245382585751979	-	12.51	1.959770	0.34565	0.320828	0.295486	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.83992	-1.79;-1.79	2.89	-2.38	0.06622	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.525008	0.15921	N	0.238116	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	D;D	0.64830	0.994;0.991	P;P	0.58454	0.839;0.731	T	0.48581	-0.9023	9	0.66056	D	0.02	.	1.0121	0.01499	0.2287:0.3302:0.2737:0.1674	rs3993987;rs58194992	76;83	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	M	76;83	ENSP00000380668:V76M;ENSP00000211076:V83M	ENSP00000211076:V83M	V	+	1	0	TPSD1	1246682	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.832000	0.04400	-0.652000	0.05408	-1.097000	0.02148	GTG	C|1.000;|0.000	.	alt		0.706	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
SLC22A5	6584	hgsc.bcm.edu	37	5	131705949	131705949	+	Silent	SNP	T	T	C	rs2631365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:131705949T>C	ENST00000245407.3	+	1	506	c.285T>C	c.(283-285)ctT>ctC	p.L95L	AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000457998.2_RNA|SLC22A5_ENST00000435065.2_Silent_p.L95L	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	94	0	0	1589	WXS	Illumina HiSeq	Phase_I	97	40	0.412371	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	
ZNF99	7652	hgsc.bcm.edu	37	19	22941938	22941938	+	Missense_Mutation	SNP	T	T	G	rs6511379	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	13	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	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	
PSG3	5671	hgsc.bcm.edu	37	19	43243238	43243238	+	Missense_Mutation	SNP	A	A	G	rs11559136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	181	0	0		WXS	Illumina HiSeq	Phase_I	181	77	0.425414	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	
HELZ	9931	hgsc.bcm.edu	37	17	65212042	65212042	+	Missense_Mutation	SNP	C	C	T	rs57482031|rs8080100	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:65212042C>T	ENST00000358691.5	-	5	386	c.220G>A	c.(220-222)Gtg>Atg	p.V74M	HELZ_ENST00000580168.1_Missense_Mutation_p.V74M|HELZ_ENST00000580662.1_5'UTR	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	74			V -> M (in dbSNP:rs8080100).			membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TCAGCTTGCACATAATTTTTC	0.284													C|||	981	0.195887	0.2489	0.1614	5008	,	,		19637	0.1994		0.1769	False		,,,				2504	0.1646				p.V74M		Atlas-SNP	.											.	HELZ	160	.	0			c.G220A						PASS	.	C	MET/VAL	851,2751		107,637,1057	58.0	54.0	55.0		220	4.9	1.0	17	dbSNP_116	55	1313,6823		88,1137,2843	yes	missense	HELZ	NM_014877.3	21	195,1774,3900	TT,TC,CC		16.1382,23.6258,18.4358	benign	74/1943	65212042	2164,9574	1801	4068	5869	SO:0001583	missense	9931	exon5			CTTGCACATAATT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.220G>A	17.37:g.65212042C>T	ENSP00000351524:p.Val74Met	Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	387	170	0.439276	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	408	0.18681318681318682	108	0.21951219512195122	49	0.13535911602209943	112	0.1958041958041958	139	0.18337730870712401	C	14.46	2.543148	0.45280	0.236258	0.161382	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.73897	-0.79;-0.79	4.86	4.86	0.63082	.	0.116901	0.64402	D	0.000010	T	0.00039	0.0001	N	0.08118	0	0.39472	P	0.03226799999999996	B;D	0.57899	0.259;0.981	B;P	0.45195	0.075;0.473	T	0.12192	-1.0557	9	0.49607	T	0.09	-5.7503	18.0445	0.89328	0.0:1.0:0.0:0.0	rs8080100;rs58229173;rs8080100	74;74	F8WBX6;P42694	.;HELZ_HUMAN	M	74	ENSP00000351524:V74M;ENSP00000411144:V74M	ENSP00000351524:V74M	V	-	1	0	HELZ	62642504	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.095000	0.64529	2.260000	0.74910	0.539000	0.68188	GTG	C|0.831;T|0.169	0.169	strong		0.284	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
MUC4	4585	hgsc.bcm.edu	37	3	195507874	195507874	+	Missense_Mutation	SNP	G	G	T	rs199875073		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195507874G>T	ENST00000463781.3	-	2	11036	c.10577C>A	c.(10576-10578)aCt>aAt	p.T3526N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3526N	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)		TACTGAGGAAGTGTCGGTGAC	0.602																																					p.T3526N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C10577A						scavenged	.						44.0	36.0	38.0					3																	195507874		680	1586	2266	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.10577C>A	3.37:g.195507874G>T	ENSP00000417498:p.Thr3526Asn	Somatic	471	18	0.0382166		WXS	Illumina HiSeq	Phase_I	525	18	0.0342857	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	4.955	0.177484	0.09443	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.52;1.62	0.743	0.743	0.18347	.	.	.	.	.	T	0.11793	0.0287	N	0.08118	0	0.09310	N	1	B	0.22909	0.077	B	0.09377	0.004	T	0.29181	-1.0020	8	.	.	.	.	3.2552	0.06828	0.3579:0.0:0.6421:0.0	.	3398	E7ESK3	.	N	3526	ENSP00000417498:T3526N;ENSP00000420243:T3526N	.	T	-	2	0	MUC4	196992653	0.003000	0.15002	0.011000	0.14972	0.011000	0.07611	1.098000	0.31000	0.088000	0.17205	0.089000	0.15464	ACT	.	.	weak		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CPT1C	126129	hgsc.bcm.edu	37	19	50204843	50204843	+	Silent	SNP	G	G	A	rs12973248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50204843G>A	ENST00000392518.4	+	7	1017	c.645G>A	c.(643-645)tcG>tcA	p.S215S	CPT1C_ENST00000354199.5_Silent_p.S215S|CPT1C_ENST00000323446.5_Silent_p.S215S|CPT1C_ENST00000405931.2_Silent_p.S215S|CPT1C_ENST00000598293.1_Silent_p.S215S	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	215					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		TGCAGGCGTCGCTGCTGCAGT	0.637																																					p.S215S		Atlas-SNP	.											.	CPT1C	93	.	0			c.G645A						PASS	.	G	,,,	243,4163	139.2+/-174.8	8,227,1968	38.0	34.0	35.0		645,645,645,645	-4.4	0.2	19	dbSNP_121	35	1439,7161	268.7+/-288.0	127,1185,2988	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	,,,	135,1412,4956	AA,AG,GG		16.7326,5.5152,12.9325	,,,	215/793,215/804,215/804,215/804	50204843	1682,11324	2203	4300	6503	SO:0001819	synonymous_variant	126129	exon7			GGCGTCGCTGCTG	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.645G>A	19.37:g.50204843G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Silent	SNP	ENST00000392518.4	37	CCDS12779.1																																																																																			G|0.880;A|0.120	0.120	strong		0.637	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33905566	33905566	+	Missense_Mutation	SNP	C	C	T	rs1127732	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:33905566C>T	ENST00000307296.3	+	16	2566	c.2189C>T	c.(2188-2190)tCa>tTa	p.S730L	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.S735L			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	730	Interaction with EIAV p9.|Pro-rich.|Self-association.		S -> L (in dbSNP:rs1127732). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TATCAGTCCTCACCAGCAGGA	0.433													C|||	1241	0.247804	0.1581	0.3112	5008	,	,		18749	0.3889		0.1332	False		,,,				2504	0.2965				p.S735L		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.C2204T						PASS	.	C	LEU/SER,LEU/SER	693,3713	291.8+/-281.7	58,577,1568	79.0	75.0	76.0		2204,2189	5.9	1.0	3	dbSNP_86	76	1313,7287	259.0+/-282.4	98,1117,3085	yes	missense,missense	PDCD6IP	NM_001162429.1,NM_013374.4	145,145	156,1694,4653	TT,TC,CC		15.2674,15.7286,15.4237	benign,benign	735/874,730/869	33905566	2006,11000	2203	4300	6503	SO:0001583	missense	10015	exon16			AGTCCTCACCAGC	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.2189C>T	3.37:g.33905566C>T	ENSP00000307387:p.Ser730Leu	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	252	135	0.535714	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	504	0.23076923076923078	71	0.1443089430894309	109	0.3011049723756906	220	0.38461538461538464	104	0.13720316622691292	C	18.35	3.603869	0.66445	0.157286	0.152674	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.36157	1.27;1.27	5.94	5.94	0.96194	.	0.207357	0.40144	N	0.001180	T	0.00012	0.0000	L	0.47016	1.485	0.27577	P	0.9497123	P;B;P	0.36086	0.536;0.346;0.536	B;B;B	0.30943	0.115;0.122;0.115	T	0.48258	-0.9051	9	0.26408	T	0.33	-18.0067	16.5903	0.84763	0.0:0.8699:0.1301:0.0	rs1127732;rs52791786;rs61557319;rs1127732	511;735;730	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	L	730;735	ENSP00000307387:S730L;ENSP00000411825:S735L	ENSP00000307387:S730L	S	+	2	0	PDCD6IP	33880570	0.405000	0.25336	0.997000	0.53966	0.716000	0.41182	1.948000	0.40303	2.817000	0.96982	0.557000	0.71058	TCA	C|0.800;N|0.001	.	strong		0.433	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
TFPI	7035	hgsc.bcm.edu	37	2	188343497	188343497	+	Intron	SNP	T	T	C	rs7586970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:188343497T>C	ENST00000233156.3	-	6	923				TFPI_ENST00000409676.1_Missense_Mutation_p.N221S|AC007319.1_ENST00000453517.1_RNA|TFPI_ENST00000392365.1_Intron|TFPI_ENST00000339091.4_Missense_Mutation_p.N221S|AC007319.1_ENST00000412276.1_RNA	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)						blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.N221S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	ATGAGCCGCATTCTTCCAACC	0.343													T|||	1411	0.281749	0.385	0.2651	5008	,	,		19517	0.1438		0.3002	False		,,,				2504	0.2771				p.N221S		Atlas-SNP	.											TFPI_ENST00000409676,NS,carcinoma,0,1	TFPI	66	1	1	Substitution - Missense(1)	stomach(1)	c.A662G						scavenged	.	T	SER/ASN,	1528,2878	482.4+/-359.4	243,1042,918	158.0	138.0	145.0	http://www.ncbi.nlm.nih.gov/pubmed?term	662,	3.6	1.0	2	dbSNP_116	145	2670,5930	429.7+/-356.3	403,1864,2033	yes	missense,intron	TFPI	NM_001032281.2,NM_006287.4	46,	646,2906,2951	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	31.0465,34.68,32.2774	,	221/252,	188343497	4198,8808	2203	4300	6503	SO:0001627	intron_variant	7035	exon7			GCCGCATTCTTCC		CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"""extrinsic pathway inhibitor"""	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.628+5353A>G	2.37:g.188343497T>C		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001032281	O95103|Q53TS4	Missense_Mutation	SNP	ENST00000233156.3	37	CCDS2294.1	595	0.2724358974358974	187	0.3800813008130081	106	0.292817679558011	69	0.12062937062937062	233	0.3073878627968338	T	14.64	2.595545	0.46318	0.3468	0.310465	ENSG00000003436	ENST00000409676;ENST00000339091	T;T	0.63580	-0.05;-0.05	4.72	3.57	0.40892	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999519004	B	0.27932	0.194	B	0.23275	0.045	T	0.28586	-1.0039	7	0.06891	T	0.86	.	7.6447	0.28312	0.0:0.0962:0.0:0.9038	rs7586970;rs52792399;rs60842722;rs7586970	221	P10646-2	.	S	221	ENSP00000386344:N221S;ENSP00000342306:N221S	ENSP00000342306:N221S	N	-	2	0	TFPI	188051742	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.742000	0.38248	1.738000	0.51689	0.455000	0.32223	AAT	T|0.703;C|0.297	0.297	strong		0.343	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287	
TUSC1	286319	hgsc.bcm.edu	37	9	25677698	25677698	+	Missense_Mutation	SNP	A	A	C	rs72631815	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:25677698A>C	ENST00000358022.3	-	1	1158	c.622T>G	c.(622-624)Tct>Gct	p.S208A		NM_001004125.2	NP_001004125.1	Q2TAM9	TUSC1_HUMAN	tumor suppressor candidate 1	208										kidney(1)	1	all_hematologic(1;0.197)	all_neural(3;5.42e-18)|Glioma(3;5.54e-17)		GBM - Glioblastoma multiforme(1;1.51e-108)|Lung(42;2.88e-14)|LUSC - Lung squamous cell carcinoma(38;3.16e-11)		CAGGGCCCAGAGGGCTCCGAG	0.736													A|||	833	0.166334	0.034	0.1744	5008	,	,		11360	0.1577		0.326	False		,,,				2504	0.184				p.S208A	Pancreas(19;648 672 25630 30820 31331)	Atlas-SNP	.											.	TUSC1	7	.	0			c.T622G						PASS	.	A	ALA/SER	228,3728		13,202,1763	6.0	6.0	6.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	622	-1.1	0.0	9	dbSNP_130	6	2027,5715		281,1465,2125	no	missense	TUSC1	NM_001004125.2	99	294,1667,3888	CC,CA,AA		26.1819,5.7634,19.2768	benign	208/213	25677698	2255,9443	1978	3871	5849	SO:0001583	missense	286319	exon1			GCCCAGAGGGCTC	AY168647	CCDS34999.1	9p21.2	2014-05-22			ENSG00000198680	ENSG00000198680			31010	protein-coding gene	gene with protein product		610529				15208665	Standard	NM_001004125		Approved	TSG-9	uc003zpx.3	Q2TAM9	OTTHUMG00000159591	ENST00000358022.3:c.622T>G	9.37:g.25677698A>C	ENSP00000350716:p.Ser208Ala	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_001004125	A0PJ78|Q67GI3|Q86SS1|Q8TAH8	Missense_Mutation	SNP	ENST00000358022.3	37	CCDS34999.1	446	0.2042124542124542	35	0.07113821138211382	74	0.20441988950276244	96	0.16783216783216784	241	0.3179419525065963	A	3.000	-0.206320	0.06180	0.057634	0.261819	ENSG00000198680	ENST00000358022	T	0.48201	0.82	3.71	-1.1	0.09872	.	0.850927	0.09559	U	0.785795	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.14012	0.009	B	0.08055	0.003	T	0.34279	-0.9835	9	0.06757	T	0.87	0.0163	4.2113	0.10512	0.3572:0.3245:0.3183:0.0	.	208	Q2TAM9	TUSC1_HUMAN	A	208	ENSP00000350716:S208A	ENSP00000350716:S208A	S	-	1	0	TUSC1	25667698	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.236000	0.09003	-0.521000	0.06426	0.379000	0.24179	TCT	A|0.795;C|0.205	0.205	strong		0.736	TUSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356351.1	NM_001004125	
COBL	23242	hgsc.bcm.edu	37	7	51096036	51096036	+	Missense_Mutation	SNP	G	G	C	rs2240089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:51096036G>C	ENST00000265136.7	-	10	2922	c.2757C>G	c.(2755-2757)caC>caG	p.H919Q	COBL_ENST00000395542.2_Missense_Mutation_p.H1001Q	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	919			H -> Q (in dbSNP:rs2240089). {ECO:0000269|PubMed:17974005}.		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)					GTGTCTCTGAGTGTGGGCTGG	0.597													G|||	1006	0.200879	0.1104	0.1556	5008	,	,		20822	0.3095		0.1889	False		,,,				2504	0.2556				p.H919Q	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C2757G						PASS	.	G	GLN/HIS	473,3933	222.3+/-239.2	25,423,1755	111.0	80.0	90.0		2757	0.4	0.0	7	dbSNP_98	90	1496,7104	282.3+/-295.5	129,1238,2933	yes	missense	COBL	NM_015198.3	24	154,1661,4688	CC,CG,GG		17.3953,10.7354,15.1392	benign	919/1262	51096036	1969,11037	2203	4300	6503	SO:0001583	missense	23242	exon10			CTCTGAGTGTGGG	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.2757C>G	7.37:g.51096036G>C	ENSP00000265136:p.His919Gln	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	257	103	0.400778	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	435	0.19917582417582416	58	0.11788617886178862	63	0.17403314917127072	173	0.30244755244755245	141	0.18601583113456466	G	9.706	1.155696	0.21454	0.107354	0.173953	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542	T;T;T;T	0.11604	2.76;2.76;2.77;2.77	4.99	0.382	0.16234	.	3.467550	0.00861	N	0.001935	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B;B;P;P;P	0.44241	0.399;0.399;0.454;0.589;0.829	B;B;B;B;B	0.38985	0.134;0.134;0.105;0.272;0.287	T	0.43653	-0.9378	9	0.21540	T	0.41	.	8.1457	0.31110	0.4421:0.0:0.5579:0.0	rs2240089;rs17799087;rs2240089	919;976;919;1001;461	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	Q	919;811;804;1001	ENSP00000265136:H919Q;ENSP00000401204:H811Q;ENSP00000413498:H804Q;ENSP00000378912:H1001Q	ENSP00000265136:H919Q	H	-	3	2	COBL	51063530	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	0.090000	0.15025	0.139000	0.18822	0.563000	0.77884	CAC	G|0.814;C|0.186	0.186	strong		0.597	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
OR13D1	286365	hgsc.bcm.edu	37	9	107456763	107456763	+	Missense_Mutation	SNP	T	T	C	rs10991359	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:107456763T>C	ENST00000318763.5	+	1	104	c.61T>C	c.(61-63)Ttc>Ctc	p.F21L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	21			F -> L (in dbSNP:rs10991359).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F21L(1)		large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TCATGTCCTTTTCTATACTAC	0.368													T|||	1099	0.219449	0.0106	0.3631	5008	,	,		18835	0.4484		0.2425	False		,,,				2504	0.1401				p.F21L		Atlas-SNP	.											OR13D1,NS,carcinoma,0,1	OR13D1	42	1	1	Substitution - Missense(1)	prostate(1)	c.T61C						scavenged	.	T	LEU/PHE	238,4166	140.0+/-175.5	6,226,1970	65.0	61.0	63.0		61	-5.4	0.0	9	dbSNP_120	63	1834,6766	327.2+/-317.7	209,1416,2675	yes	missense	OR13D1	NM_001004484.1	22	215,1642,4645	CC,CT,TT		21.3256,5.4042,15.9336	benign	21/347	107456763	2072,10932	2202	4300	6502	SO:0001583	missense	286365	exon1			GTCCTTTTCTATA		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.61T>C	9.37:g.107456763T>C	ENSP00000317357:p.Phe21Leu	Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	37	CCDS35094.1	582	0.2664835164835165	7	0.014227642276422764	117	0.32320441988950277	261	0.4562937062937063	197	0.2598944591029024	T	10.34	1.323824	0.24080	0.054042	0.213256	ENSG00000179055	ENST00000318763	T	0.00003	9.83	4.08	-5.42	0.02640	.	.	.	.	.	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	0.04165	-1.0972	8	0.27785	T	0.31	.	1.5599	0.02593	0.5009:0.1979:0.1347:0.1665	rs10991359;rs52837362;rs10991359	21	Q8NGV5	O13D1_HUMAN	L	21	ENSP00000317357:F21L	ENSP00000317357:F21L	F	+	1	0	OR13D1	106496584	0.000000	0.05858	0.000000	0.03702	0.520000	0.34377	-1.980000	0.01492	-0.946000	0.03677	0.533000	0.62120	TTC	T|0.800;C|0.200	0.200	strong		0.368	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
VSIG10	54621	hgsc.bcm.edu	37	12	118508870	118508870	+	Missense_Mutation	SNP	C	C	G	rs150561165	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:118508870C>G	ENST00000359236.5	-	7	1609	c.1333G>C	c.(1333-1335)Gga>Cga	p.G445R		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	445						integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GAAGTGTTTCCTACTGAAGAG	0.393													C|||	10	0.00199681	0.0	0.0029	5008	,	,		20975	0.0		0.007	False		,,,				2504	0.001				p.G445R		Atlas-SNP	.											.	VSIG10	41	.	0			c.G1333C						PASS	.	C	ARG/GLY	6,3744		0,6,1869	106.0	109.0	108.0		1333	4.0	1.0	12	dbSNP_134	108	48,8154		0,48,4053	yes	missense	VSIG10	NM_019086.5	125	0,54,5922	GG,GC,CC		0.5852,0.16,0.4518	possibly-damaging	445/541	118508870	54,11898	1875	4101	5976	SO:0001583	missense	54621	exon7			TGTTTCCTACTGA		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.1333G>C	12.37:g.118508870C>G	ENSP00000352172:p.Gly445Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_019086	Q9NWQ7	Missense_Mutation	SNP	ENST00000359236.5	37	CCDS44992.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	11.19	1.566483	0.27915	0.0016	0.005852	ENSG00000176834	ENST00000359236	T	0.52526	0.66	4.9	4.01	0.46588	.	.	.	.	.	T	0.32496	0.0831	L	0.54323	1.7	0.35554	D	0.804104	B	0.14012	0.009	B	0.12156	0.007	T	0.41360	-0.9513	9	0.30078	T	0.28	-2.8366	9.3865	0.38347	0.0:0.8996:0.0:0.1004	.	445	Q8N0Z9	VSI10_HUMAN	R	445	ENSP00000352172:G445R	ENSP00000352172:G445R	G	-	1	0	VSIG10	116993253	1.000000	0.71417	0.977000	0.42913	0.839000	0.47603	2.009000	0.40903	1.187000	0.43000	0.551000	0.68910	GGA	C|0.996;G|0.004	0.004	strong		0.393	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
UBR2	23304	hgsc.bcm.edu	37	6	42627434	42627434	+	Missense_Mutation	SNP	G	G	A	rs6917033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42627434G>A	ENST00000372899.1	+	30	3541	c.3283G>A	c.(3283-3285)Gca>Aca	p.A1095T	UBR2_ENST00000372901.1_Missense_Mutation_p.A1095T|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1095			A -> P (in dbSNP:rs6917033).|A -> S (in dbSNP:rs6917033).|A -> T (in dbSNP:rs6917033). {ECO:0000269|PubMed:9205841}.		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)			ACTGGGCCCCGCACAAACTCA	0.408													G|||	2163	0.431909	0.5015	0.389	5008	,	,		16383	0.4385		0.3857	False		,,,				2504	0.409				p.A1095T		Atlas-SNP	.											.	UBR2	134	.	0			c.G3283A						PASS	.	G	THR/ALA	2124,2282	577.4+/-384.4	509,1106,588	88.0	81.0	83.0		3283	2.8	0.8	6	dbSNP_116	83	3370,5230	498.4+/-374.7	682,2006,1612	yes	missense	UBR2	NM_015255.2	58	1191,3112,2200	AA,AG,GG		39.186,48.207,42.242	benign	1095/1756	42627434	5494,7512	2203	4300	6503	SO:0001583	missense	23304	exon30			GGCCCCGCACAAA	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.3283G>A	6.37:g.42627434G>A	ENSP00000361990:p.Ala1095Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	952	0.4358974358974359	235	0.47764227642276424	152	0.4198895027624309	258	0.45104895104895104	307	0.4050131926121372	G	9.977	1.227046	0.22542	0.48207	0.39186	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.42131	0.98;0.98	5.56	2.77	0.32553	.	0.364840	0.34291	N	0.004086	T	0.10508	0.0257	N	0.22421	0.69	0.09310	P	0.9999999850984	B;B	0.29115	0.233;0.091	B;B	0.21708	0.036;0.025	T	0.14035	-1.0487	9	0.16896	T	0.51	3.3783	11.6187	0.51104	0.0687:0.2336:0.6977:0.0	rs6917033;rs60034483;rs6917033	1095;1095	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	T	1095	ENSP00000361990:A1095T;ENSP00000361992:A1095T	ENSP00000361990:A1095T	A	+	1	0	UBR2	42735412	0.962000	0.33011	0.836000	0.33094	0.428000	0.31595	1.338000	0.33873	0.290000	0.22444	-1.516000	0.00938	GCA	A|0.421;G|0.579	0.421	strong		0.408	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
ANKK1	255239	hgsc.bcm.edu	37	11	113266821	113266821	+	Missense_Mutation	SNP	G	G	A	rs7118900	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:113266821G>A	ENST00000303941.3	+	5	809	c.715G>A	c.(715-717)Gcg>Acg	p.A239T		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs7118900). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TATCCGAGTGGCGGCAGGCAT	0.607													G|||	1605	0.320487	0.3744	0.3069	5008	,	,		16275	0.4058		0.1819	False		,,,				2504	0.3119				p.A239T		Atlas-SNP	.											.	ANKK1	83	.	0			c.G715A						PASS	.	G	THR/ALA	1246,2802		199,848,977	61.0	65.0	63.0		715	2.5	0.0	11	dbSNP_116	63	1518,6826		149,1220,2803	yes	missense	ANKK1	NM_178510.1	58	348,2068,3780	AA,AG,GG		18.1927,30.7806,22.3047	possibly-damaging	239/766	113266821	2764,9628	2024	4172	6196	SO:0001583	missense	255239	exon5			CGAGTGGCGGCAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.715G>A	11.37:g.113266821G>A	ENSP00000306678:p.Ala239Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	634	0.2902930402930403	178	0.3617886178861789	98	0.27071823204419887	223	0.38986013986013984	135	0.17810026385224276	G	12.52	1.963618	0.34659	0.307806	0.181927	ENSG00000170209	ENST00000303941	D	0.82619	-1.63	4.44	2.55	0.30701	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.266529	0.24912	U	0.034605	T	0.00012	0.0000	L	0.31578	0.945	0.44006	P	0.0032879999999999576	B	0.26547	0.152	B	0.37304	0.246	T	0.21484	-1.0244	9	0.44086	T	0.13	-1.7695	12.3831	0.55317	0.157:0.0:0.843:0.0	rs7118900;rs59912012;rs7118900	239	Q8NFD2	ANKK1_HUMAN	T	239	ENSP00000306678:A239T	ENSP00000306678:A239T	A	+	1	0	ANKK1	112772031	0.948000	0.32251	0.002000	0.10522	0.001000	0.01503	2.088000	0.41663	0.150000	0.19136	-1.598000	0.00824	GCG	G|0.714;A|0.286	0.286	strong		0.607	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
KNSTRN	90417	hgsc.bcm.edu	37	15	40683702	40683702	+	Missense_Mutation	SNP	A	A	G	rs11541642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:40683702A>G	ENST00000249776.8	+	7	809	c.694A>G	c.(694-696)Agt>Ggt	p.S232G	KNSTRN_ENST00000448395.2_Intron|KNSTRN_ENST00000416151.2_Missense_Mutation_p.S232G|KNSTRN_ENST00000608100.1_Missense_Mutation_p.S154G	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		AGCTTTAGGCAGTGAGACCCT	0.468													A|||	144	0.028754	0.0038	0.0576	5008	,	,		18788	0.0		0.0865	False		,,,				2504	0.0123				p.S232G		Atlas-SNP	.											.	.	.	.	0			c.A694G						PASS	.	A	GLY/SER,,GLY/SER	78,3932		1,76,1928	128.0	118.0	121.0		694,,694	1.3	1.0	15	dbSNP_120	121	889,7475		47,795,3340	yes	missense,intron,missense	C15orf23	NM_001142761.1,NM_001142762.1,NM_033286.3	56,,56	48,871,5268	GG,GA,AA		10.6289,1.9451,7.8148	benign,,benign	232/287,,232/317	40683702	967,11407	2005	4182	6187	SO:0001583	missense	90417	exon7			TTAGGCAGTGAGA	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"""small kinetochore-associated protein"", ""kinetochore-localized astrin-binding protein"", ""TRAF4 associated factor 1"""	614718	"""chromosome 15 open reading frame 23"""	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.694A>G	15.37:g.40683702A>G	ENSP00000249776:p.Ser232Gly	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_033286		Missense_Mutation	SNP	ENST00000249776.8	37	CCDS42021.1	94	0.04304029304029304	2	0.0040650406504065045	22	0.06077348066298342	0	0.0	70	0.09234828496042216	A	10.95	1.494747	0.26774	0.019451	0.106289	ENSG00000128944	ENST00000249776;ENST00000416151	T;T	0.24723	1.84;1.84	5.18	1.33	0.21861	.	0.729330	0.13793	N	0.362374	T	0.00271	0.0008	L	0.27053	0.805	0.58432	D	0.999999	B;B	0.11235	0.004;0.0	B;B	0.09377	0.004;0.001	T	0.37842	-0.9688	10	0.26408	T	0.33	-3.1594	1.7894	0.03048	0.5654:0.1803:0.0932:0.1611	rs11541642	232;232	Q9Y448-2;Q9Y448	.;T4AF1_HUMAN	G	232	ENSP00000249776:S232G;ENSP00000391233:S232G	ENSP00000249776:S232G	S	+	1	0	C15orf23	38470994	0.057000	0.20700	0.978000	0.43139	0.394000	0.30568	0.296000	0.19083	0.047000	0.15862	0.533000	0.62120	AGT	A|0.933;G|0.067	0.067	strong		0.468	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761	
CENPF	1063	hgsc.bcm.edu	37	1	214813941	214813941	+	Missense_Mutation	SNP	C	C	G	rs3795523	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214813941C>G	ENST00000366955.3	+	12	2428	c.2260C>G	c.(2260-2262)Caa>Gaa	p.Q754E		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0			Q -> E (in dbSNP:rs3795523).		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)		CCGGTGTTACCAAGACTTGCA	0.408													C|||	526	0.105032	0.1006	0.1052	5008	,	,		20757	0.126		0.0507	False		,,,				2504	0.1452				p.Q754E	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.C2260G						PASS	.	C	GLU/GLN	400,4006	196.4+/-220.7	17,366,1820	58.0	59.0	58.0		2260	3.8	0.7	1	dbSNP_107	58	465,8135	136.7+/-193.7	11,443,3846	yes	missense	CENPF	NM_016343.3	29	28,809,5666	GG,GC,CC		5.407,9.0785,6.6508	benign	754/3115	214813941	865,12141	2203	4300	6503	SO:0001583	missense	1063	exon12			TGTTACCAAGACT	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.2260C>G	1.37:g.214813941C>G	ENSP00000355922:p.Gln754Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	71	0.596639	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	229	0.10485347985347986	63	0.12804878048780488	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	C	1.251	-0.618679	0.03663	0.090785	0.05407	ENSG00000117724	ENST00000366955	T	0.03094	4.05	5.81	3.82	0.43975	.	0.216684	0.23474	N	0.047791	T	0.00012	0.0000	.	.	.	0.46631	P	8.610000000000007E-4	B	0.26744	0.158	B	0.23275	0.045	T	0.48456	-0.9034	8	0.12430	T	0.62	.	11.4336	0.50056	0.0:0.7158:0.2094:0.0748	rs3795523;rs3795523	754	P49454	CENPF_HUMAN	E	754	ENSP00000355922:Q754E	ENSP00000355922:Q754E	Q	+	1	0	CENPF	212880564	1.000000	0.71417	0.674000	0.29902	0.326000	0.28443	1.869000	0.39519	1.463000	0.47967	0.609000	0.83330	CAA	C|0.885;G|0.115	0.115	strong		0.408	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
GALNT8	26290	hgsc.bcm.edu	37	12	4873163	4873163	+	Missense_Mutation	SNP	G	G	T	rs1468556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4873163G>T	ENST00000252318.2	+	9	1880	c.1543G>T	c.(1543-1545)Gtt>Ttt	p.V515F		NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	515	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		V -> F (in dbSNP:rs1468556). {ECO:0000269|PubMed:10767557}.		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)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						TCAGGGACCCGTTCCAGGCAA	0.502													G|||	1651	0.329673	0.2466	0.4251	5008	,	,		19640	0.3611		0.4225	False		,,,				2504	0.2464				p.V515F	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											GALNT8,NS,adenoma,0,1	GALNT8	89	1	0			c.G1543T						PASS	.	G	PHE/VAL	1305,3101	442.3+/-346.6	207,891,1105	196.0	174.0	182.0		1543	-7.6	0.0	12	dbSNP_88	182	3609,4991	521.6+/-379.9	761,2087,1452	yes	missense	GALNT8	NM_017417.1	50	968,2978,2557	TT,TG,GG		41.9651,29.6187,37.7826	possibly-damaging	515/638	4873163	4914,8092	2203	4300	6503	SO:0001583	missense	26290	exon9			GGACCCGTTCCAG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.1543G>T	12.37:g.4873163G>T	ENSP00000252318:p.Val515Phe	Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	227	107	0.471366	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	814	0.3727106227106227	124	0.25203252032520324	150	0.4143646408839779	223	0.38986013986013984	317	0.4182058047493404	G	8.342	0.828853	0.16749	0.296187	0.419651	ENSG00000130035	ENST00000252318	T	0.26957	1.7	4.43	-7.55	0.01327	Ricin B-related lectin (1);Ricin B lectin (3);	1.667950	0.02954	N	0.142084	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.31383	0.321	B	0.29716	0.106	T	0.18935	-1.0321	9	0.56958	D	0.05	.	8.9706	0.35903	0.596:0.0:0.3027:0.1014	rs1468556;rs17783619;rs59456221;rs1468556	515	Q9NY28	GALT8_HUMAN	F	515	ENSP00000252318:V515F	ENSP00000252318:V515F	V	+	1	0	GALNT8	4743424	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.158000	0.10070	-1.811000	0.01229	-0.751000	0.03497	GTT	G|0.627;T|0.373	0.373	strong		0.502	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
ST6GALNAC6	30815	hgsc.bcm.edu	37	9	130656800	130656800	+	Silent	SNP	G	G	A	rs11552227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130656800G>A	ENST00000373146.1	-	4	467	c.288C>T	c.(286-288)ctC>ctT	p.L96L	ST6GALNAC6_ENST00000373144.3_Silent_p.L62L|ST6GALNAC6_ENST00000373142.1_Silent_p.L96L|ST6GALNAC6_ENST00000373141.1_Silent_p.L62L|ST6GALNAC6_ENST00000485320.1_5'UTR|ST6GALNAC6_ENST00000542456.1_Missense_Mutation_p.S32L|ST6GALNAC6_ENST00000291839.5_Silent_p.L96L			Q969X2	SIA7F_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	96					cell-cell recognition (GO:0009988)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCTTGTTGCCGAGAATGGGGA	0.587																																					p.L96L		Atlas-SNP	.											.	ST6GALNAC6	36	.	0			c.C288T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	88.0	84.0	85.0		288	-9.8	0.1	9	dbSNP_120	85	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ST6GALNAC6	NM_013443.3		0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308		96/334	130656800	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	30815	exon4			GTTGCCGAGAATG	BC006564	CCDS6882.1, CCDS69668.1, CCDS69669.1, CCDS75908.1	9q34.13	2013-03-01		2005-02-07	ENSG00000160408	ENSG00000160408		"""Sialyltransferases"""	23364	protein-coding gene	gene with protein product		610135	"""sialytransferase 7 ((alpha-N-acetylneuraminyl 2,3-betagalactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialytransferase) F"""	SIAT7F		12668675	Standard	XM_005251952		Approved	ST6GALNACVI	uc004bso.1	Q969X2	OTTHUMG00000020718	ENST00000373146.1:c.288C>T	9.37:g.130656800G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_013443	B3KQ01|Q5T9C4|Q5T9C5|Q9H8A2|Q9ULB8	Silent	SNP	ENST00000373146.1	37	CCDS6882.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533692	0.27387	4.54E-4	2.33E-4	ENSG00000160408	ENST00000542456	T	0.42900	0.96	4.88	-9.76	0.00503	.	.	.	.	.	T	0.21881	0.0527	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19160	-1.0314	7	.	.	.	-18.7556	10.2126	0.43150	0.5137:0.3211:0.1652:0.0	rs11552227	32	B4DU80	.	L	32	ENSP00000438109:S32L	.	S	-	2	0	ST6GALNAC6	129696621	0.000000	0.05858	0.082000	0.20525	0.589000	0.36550	-2.451000	0.01006	-3.649000	0.00126	-1.224000	0.01588	TCG	G|0.999;A|0.001	0.001	strong		0.587	ST6GALNAC6-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054278.1	NM_013443	
OR51D1	390038	hgsc.bcm.edu	37	11	4661243	4661243	+	Missense_Mutation	SNP	T	T	C	rs61740347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4661243T>C	ENST00000357605.2	+	1	299	c.223T>C	c.(223-225)Ttc>Ctc	p.F75L		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		CATGTACCTCTTCCTGGCCAT	0.512													T|||	201	0.0401358	0.0174	0.0677	5008	,	,		22466	0.001		0.0835	False		,,,				2504	0.047				p.F75L		Atlas-SNP	.											.	OR51D1	49	.	0			c.T223C						PASS	.	T	LEU/PHE	143,4259	99.8+/-138.5	9,125,2067	197.0	147.0	164.0		223	3.7	1.0	11	dbSNP_129	164	786,7810	186.0+/-233.6	32,722,3544	yes	missense	OR51D1	NM_001004751.2	22	41,847,5611	CC,CT,TT		9.1438,3.2485,7.1473	benign	75/325	4661243	929,12069	2201	4298	6499	SO:0001583	missense	390038	exon1			TACCTCTTCCTGG	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"""GPCR / Class A : Olfactory receptors"""	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.223T>C	11.37:g.4661243T>C	ENSP00000350222:p.Phe75Leu	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	283	131	0.462898	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	37	CCDS31357.1	109	0.04990842490842491	10	0.02032520325203252	35	0.09668508287292818	1	0.0017482517482517483	63	0.08311345646437995	T	10.02	1.237100	0.22711	0.032485	0.091438	ENSG00000197428	ENST00000357605	T	0.13778	2.56	4.84	3.71	0.42584	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000255	T	0.00440	0.0014	M	0.73217	2.22	0.25628	P	0.9863318	B	0.24651	0.108	B	0.29353	0.101	T	0.03922	-1.0992	9	0.87932	D	0	.	7.3299	0.26575	0.0:0.1731:0.0:0.8269	rs61740347	75	Q8NGF3	O51D1_HUMAN	L	75	ENSP00000350222:F75L	ENSP00000350222:F75L	F	+	1	0	OR51D1	4617819	0.919000	0.31177	1.000000	0.80357	0.105000	0.19272	1.435000	0.34969	0.970000	0.38263	0.460000	0.39030	TTC	T|0.936;C|0.064	0.064	strong		0.512	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751	
EBLN2	55096	hgsc.bcm.edu	37	3	73111998	73111998	+	Missense_Mutation	SNP	C	C	T	rs1060584	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:73111998C>T	ENST00000533473.1	+	1	1189	c.766C>T	c.(766-768)Ctt>Ttt	p.L256F	PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	256										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						AATGTTCACACTTCTATTTGG	0.428													T|||	2634	0.525958	0.618	0.3689	5008	,	,		22212	0.4504		0.508	False		,,,				2504	0.6094				p.L256F		Atlas-SNP	.											.	EBLN2	18	.	0			c.C766T						PASS	.	T	PHE/LEU,	2428,1434		764,900,267	191.0	196.0	195.0		766,	-0.7	0.0	3	dbSNP_86	195	4235,4021		1083,2069,976	yes	missense,intron	EBLN2,PPP4R2	NM_018029.3,NM_174907.2	22,	1847,2969,1243	TT,TC,CC		48.704,37.131,45.0157	benign,	256/273,	73111998	6663,5455	1931	4128	6059	SO:0001583	missense	55096	exon1			TTCACACTTCTAT		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 2"""	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.766C>T	3.37:g.73111998C>T	ENSP00000432104:p.Leu256Phe	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_018029	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	1072	0.4908424908424908	301	0.6117886178861789	143	0.39502762430939226	248	0.43356643356643354	380	0.5013192612137203	T	1.100	-0.661497	0.03454	0.62869	0.51296	ENSG00000255423	ENST00000533473	.	.	.	0.468	-0.722	0.11184	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41680	-0.9495	6	0.24483	T	0.36	.	.	.	.	rs1060584;rs3172277;rs3732436;rs61042197;rs1060584	256	Q6P2I7	EBLN2_HUMAN	F	256	.	ENSP00000432104:L256F	L	+	1	0	EBLN2	73194688	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	-0.622000	0.05553	-1.287000	0.02381	-1.305000	0.01319	CTT	C|0.490;T|0.510	0.510	strong		0.428	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029	
GBP6	163351	hgsc.bcm.edu	37	1	89847411	89847411	+	Missense_Mutation	SNP	C	C	T	rs4658360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89847411C>T	ENST00000370456.4	+	7	1123	c.1030C>T	c.(1030-1032)Ctc>Ttc	p.L344F	GBP6_ENST00000535065.1_Missense_Mutation_p.L214F	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	344			L -> F (in dbSNP:rs4658360). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		GCGAGTGAAGCTCCCCACAGA	0.567													T|||	4036	0.805911	0.9092	0.8415	5008	,	,		18811	0.7262		0.7465	False		,,,				2504	0.7843				p.L344F		Atlas-SNP	.											.	GBP6	87	.	0			c.C1030T						PASS	.	T	PHE/LEU	3878,528	241.5+/-251.9	1713,452,38	81.0	75.0	77.0		1030	-9.5	0.0	1	dbSNP_111	77	6411,2189	374.6+/-337.4	2382,1647,271	yes	missense	GBP6	NM_198460.2	22	4095,2099,309	TT,TC,CC		25.4535,11.9837,20.8904	benign	344/634	89847411	10289,2717	2203	4300	6503	SO:0001583	missense	163351	exon7			GTGAAGCTCCCCA	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.1030C>T	1.37:g.89847411C>T	ENSP00000359485:p.Leu344Phe	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	1730	0.7921245421245421	447	0.9085365853658537	300	0.8287292817679558	424	0.7412587412587412	559	0.737467018469657	T	0.057	-1.234974	0.01505	0.880163	0.745465	ENSG00000183347	ENST00000544311;ENST00000370456;ENST00000535065	T;T	0.02395	4.31;4.31	4.75	-9.49	0.00587	Guanylate-binding protein, C-terminal (3);	0.895592	0.09526	N	0.790184	T	0.00754	0.0025	N	0.25201	0.72	0.80722	P	0.0	B	0.14438	0.01	B	0.19391	0.025	T	0.48570	-0.9024	9	0.26408	T	0.33	0.485	20.0877	0.97802	0.0:0.6365:0.0:0.3635	rs4658360;rs17490134;rs52836528;rs57718847;rs4658360	344	Q6ZN66	GBP6_HUMAN	F	315;344;214	ENSP00000359485:L344F;ENSP00000442530:L214F	ENSP00000359485:L344F	L	+	1	0	GBP6	89619999	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.839000	0.00738	-4.167000	0.00068	-3.209000	0.00053	CTC	C|0.206;T|0.794	0.794	strong		0.567	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
SAMD9	54809	hgsc.bcm.edu	37	7	92731902	92731902	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:92731902C>T	ENST00000379958.2	-	3	3778	c.3509G>A	c.(3508-3510)aGt>aAt	p.S1170N		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1170						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TCTATCTTCACTTTGCTGTTG	0.378																																					p.S1170N		Atlas-SNP	.											SAMD9,NS,carcinoma,0,1	SAMD9	239	1	0			c.G3509A						scavenged	.						214.0	218.0	217.0					7																	92731902		2203	4300	6503	SO:0001583	missense	54809	exon2			TCTTCACTTTGCT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.3509G>A	7.37:g.92731902C>T	ENSP00000369292:p.Ser1170Asn	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	273	3	0.010989	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	4.242	0.043787	0.08196	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.22539	1.95;2.76	4.54	-0.899	0.10547	.	0.244262	0.31542	N	0.007467	T	0.13329	0.0323	L	0.40543	1.245	0.20873	N	0.999832	B	0.09022	0.002	B	0.06405	0.002	T	0.16100	-1.0414	10	0.39692	T	0.17	-8.7696	6.0989	0.20035	0.0:0.2791:0.4458:0.2751	.	1170	Q5K651	SAMD9_HUMAN	N	1170	ENSP00000369292:S1170N;ENSP00000414529:S1170N	ENSP00000369292:S1170N	S	-	2	0	SAMD9	92569838	0.983000	0.35010	0.998000	0.56505	0.048000	0.14542	1.242000	0.32755	0.144000	0.18951	-0.409000	0.06214	AGT	.	.	none		0.378	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
ZNF488	118738	hgsc.bcm.edu	37	10	48370595	48370595	+	Silent	SNP	G	G	A	rs11204210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	52	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	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	
RALGDS	5900	hgsc.bcm.edu	37	9	135982088	135982088	+	Silent	SNP	A	A	C	rs2073822	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:135982088A>C	ENST00000372050.3	-	8	1482	c.1461T>G	c.(1459-1461)tcT>tcG	p.S487S	RALGDS_ENST00000372047.3_Silent_p.S475S|RALGDS_ENST00000542690.1_Silent_p.S558S|RALGDS_ENST00000372062.3_Silent_p.S458S|RALGDS_ENST00000393157.3_Silent_p.S486S|RALGDS_ENST00000393160.3_Silent_p.S432S|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	487	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				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)		TCTGCAGGGCAGAGAGGATGG	0.612			T	CIITA	"""PMBL, Hodgkin Lymphona, """								A|||	974	0.194489	0.1422	0.317	5008	,	,		20075	0.1577		0.2962	False		,,,				2504	0.1115				p.S487S	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.T1461G						PASS	.	A	,	750,3652	301.8+/-287.1	70,610,1521	75.0	66.0	69.0		1296,1461	-9.9	0.2	9	dbSNP_96	69	2595,6001	413.4+/-351.1	387,1821,2090	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	457,2431,3611	CC,CA,AA		30.1885,17.0377,25.7347	,	432/860,487/915	135982088	3345,9653	2201	4298	6499	SO:0001819	synonymous_variant	5900	exon8			CAGGGCAGAGAGG	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.1461T>G	9.37:g.135982088A>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			A|0.759;C|0.241	0.241	strong		0.612	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
MCM5	4174	hgsc.bcm.edu	37	22	35802661	35802661	+	Missense_Mutation	SNP	C	C	G	rs2307340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	30	0.508475	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		
ABHD16B	140701	hgsc.bcm.edu	37	20	62494027	62494027	+	Silent	SNP	G	G	C	rs2236152	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62494027G>C	ENST00000369916.3	+	1	1462	c.1134G>C	c.(1132-1134)gcG>gcC	p.A378A	TPD52L2_ENST00000351424.4_5'Flank|C20ORF135_ENST00000601296.1_5'Flank|TPD52L2_ENST00000346249.4_5'Flank|TPD52L2_ENST00000352482.4_5'Flank|TPD52L2_ENST00000348257.5_5'Flank|TPD52L2_ENST00000369927.4_5'Flank|TPD52L2_ENST00000358548.4_5'Flank|TPD52L2_ENST00000217121.5_5'Flank	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	378							hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						GCAGCTTGGCGCAGGAGGCCG	0.711													G|||	356	0.0710863	0.0348	0.0562	5008	,	,		14221	0.129		0.0686	False		,,,				2504	0.0736				p.A378A		Atlas-SNP	.											.	ABHD16B	22	.	0			c.G1134C						PASS	.	G		105,3939		0,105,1917	7.0	8.0	8.0		1134	-10.1	0.5	20	dbSNP_98	8	483,7297		9,465,3416	no	coding-synonymous	ABHD16B	NM_080622.3		9,570,5333	CC,CG,GG		6.2082,2.5964,4.9729		378/470	62494027	588,11236	2022	3890	5912	SO:0001819	synonymous_variant	140701	exon1			CTTGGCGCAGGAG		CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"""Abhydrolase domain containing"""	16128	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 135"""	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.1134G>C	20.37:g.62494027G>C		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	13	9	0.692308	NM_080622		Silent	SNP	ENST00000369916.3	37	CCDS13539.1																																																																																			G|0.925;C|0.075	0.075	strong		0.711	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1		
SHROOM3	57619	hgsc.bcm.edu	37	4	77662125	77662125	+	Silent	SNP	C	C	T	rs36036308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77662125C>T	ENST00000296043.6	+	5	3752	c.2799C>T	c.(2797-2799)tcC>tcT	p.S933S		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	933	ASD1. {ECO:0000255|PROSITE- ProRule:PRU00637}.				actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			ACGCACAGTCCCGTGTCTTGG	0.721													C|||	187	0.0373403	0.031	0.0375	5008	,	,		11231	0.004		0.0895	False		,,,				2504	0.0266				p.S933S		Atlas-SNP	.											.	SHROOM3	134	.	0			c.C2799T						PASS	.	C		133,4161		2,129,2016	9.0	10.0	10.0		2799	2.3	1.0	4	dbSNP_126	10	719,7635		31,657,3489	no	coding-synonymous	SHROOM3	NM_020859.3		33,786,5505	TT,TC,CC		8.6067,3.0973,6.7362		933/1997	77662125	852,11796	2147	4177	6324	SO:0001819	synonymous_variant	57619	exon5			ACAGTCCCGTGTC	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.2799C>T	4.37:g.77662125C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			C|0.951;T|0.049	0.049	strong		0.721	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
EHD2	30846	hgsc.bcm.edu	37	19	48244401	48244401	+	Silent	SNP	G	G	A	rs35910701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48244401G>A	ENST00000263277.3	+	6	1595	c.1344G>A	c.(1342-1344)aaG>aaA	p.K448K	EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.K312K	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	448					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		TGGTGACCAAGGACAAGTCCA	0.647													G|||	458	0.0914537	0.0416	0.1052	5008	,	,		16302	0.006		0.2187	False		,,,				2504	0.1063				p.K448K		Atlas-SNP	.											.	EHD2	59	.	0			c.G1344A						PASS	.	G		312,4094	164.4+/-196.0	10,292,1901	91.0	72.0	78.0		1344	4.1	1.0	19	dbSNP_126	78	1683,6917	307.4+/-308.4	146,1391,2763	no	coding-synonymous	EHD2	NM_014601.3		156,1683,4664	AA,AG,GG		19.5698,7.0813,15.3391		448/544	48244401	1995,11011	2203	4300	6503	SO:0001819	synonymous_variant	30846	exon6			GACCAAGGACAAG	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1344G>A	19.37:g.48244401G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1	229	0.10485347985347986	18	0.036585365853658534	45	0.12430939226519337	4	0.006993006993006993	162	0.21372031662269128	G	9.962	1.223109	0.22457	0.070813	0.195698	ENSG00000024422	ENST00000454483	.	.	.	4.13	4.13	0.48395	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.03202	-1.1061	4	0.29301	T	0.29	-34.6291	14.267	0.66126	0.0:0.0:1.0:0.0	rs35910701	.	.	.	R	118	.	ENSP00000391634:G118R	G	+	1	0	EHD2	52936213	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.995000	0.49441	2.024000	0.59613	0.561000	0.74099	GGA	A|0.141;C|0.000;G|0.858	0.141	strong		0.647	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
FAT1	2195	hgsc.bcm.edu	37	4	187539217	187539217	+	Silent	SNP	G	G	A	rs3733405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187539217G>A	ENST00000441802.2	-	10	8732	c.8523C>T	c.(8521-8523)aaC>aaT	p.N2841N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2841	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TAACTTGGCCGTTGGTTCCTG	0.428										HNSCC(5;0.00058)			G|||	344	0.0686901	0.003	0.1499	5008	,	,		20252	0.1796		0.0358	False		,,,				2504	0.0194				p.N2841N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C8523T						PASS	.	G		39,3851		0,39,1906	113.0	105.0	107.0		8523	-8.4	0.5	4	dbSNP_107	107	256,8062		4,248,3907	no	coding-synonymous	FAT1	NM_005245.3		4,287,5813	AA,AG,GG		3.0777,1.0026,2.4164		2841/4589	187539217	295,11913	1945	4159	6104	SO:0001819	synonymous_variant	2195	exon10			TTGGCCGTTGGTT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8523C>T	4.37:g.187539217G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.923;A|0.077	0.077	strong		0.428	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
MADCAM1	8174	hgsc.bcm.edu	37	19	501802	501802	+	Missense_Mutation	SNP	G	G	C	rs75905809		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:501802G>C	ENST00000215637.3	+	4	847	c.801G>C	c.(799-801)aaG>aaC	p.K267N	MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000382683.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.K48N|AC005775.2_ENST00000592413.1_RNA	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	267	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCCCGACAAGACCTCCCCGG	0.721																																					p.K267N		Atlas-SNP	.											MADCAM1,rectum,carcinoma,+1,1	MADCAM1	29	1	0			c.G801C						scavenged	.						12.0	14.0	13.0					19																	501802		2117	4139	6256	SO:0001583	missense	8174	exon4			CGACAAGACCTCC	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.801G>C	19.37:g.501802G>C	ENSP00000215637:p.Lys267Asn	Somatic	88	21	0.238636		WXS	Illumina HiSeq	Phase_I	93	26	0.27957	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	.	.	.	.	.	.	.	.	.	.	g	1.225	-0.625782	0.03610	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10573	2.86	3.12	-6.25	0.02039	.	2.146880	0.03414	N	0.205240	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34179	-0.9839	10	0.16896	T	0.51	.	3.4407	0.07462	0.2616:0.3054:0.3464:0.0866	.	267	Q13477	MADCA_HUMAN	N	291;283;275;267	ENSP00000215637:K267N	ENSP00000215637:K267N	K	+	3	2	MADCAM1	452802	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.864000	0.00347	-2.471000	0.00529	-1.635000	0.00777	AAG	G|0.500;C|0.500	0.500	weak		0.721	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
NSUN2	54888	hgsc.bcm.edu	37	5	6604787	6604787	+	Silent	SNP	C	C	T	rs13181449	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:6604787C>T	ENST00000264670.6	-	16	2060	c.1749G>A	c.(1747-1749)acG>acA	p.T583T	NSUN2_ENST00000539938.1_Silent_p.T347T|NSUN2_ENST00000506139.1_Silent_p.T548T	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	583					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTTTGATCCCCGTGTTAATAA	0.453													C|||	1112	0.222045	0.0371	0.1427	5008	,	,		19971	0.4623		0.1899	False		,,,				2504	0.3139				p.T583T		Atlas-SNP	.											.	NSUN2	82	.	0			c.G1749A						PASS	.	C	,	255,4151	145.0+/-179.8	8,239,1956	81.0	83.0	83.0		1644,1749	-10.7	0.0	5	dbSNP_121	83	1753,6847	316.6+/-312.8	186,1381,2733	yes	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	194,1620,4689	TT,TC,CC		20.3837,5.7876,15.439	,	548/733,583/768	6604787	2008,10998	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon16			GATCCCCGTGTTA	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.1749G>A	5.37:g.6604787C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			C|0.819;T|0.181	0.181	strong		0.453	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
BDNF	627	hgsc.bcm.edu	37	11	27720937	27720937	+	Intron	SNP	C	C	T	rs66866077	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:27720937C>T	ENST00000418212.1	-	1	325				RP11-587D21.4_ENST00000530663.1_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395986.2_Missense_Mutation_p.E6K|BDNF_ENST00000530861.1_Intron|BDNF_ENST00000395978.3_Intron|BDNF_ENST00000525950.1_Intron|BDNF_ENST00000584049.1_Intron|BDNF_ENST00000314915.6_Intron|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000532997.1_Intron|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000356660.4_Intron|BDNF_ENST00000420794.1_Intron|BDNF_ENST00000438929.1_Intron|BDNF_ENST00000395983.3_Intron|BDNF_ENST00000533131.1_Intron|BDNF_ENST00000395981.3_Intron|BDNF_ENST00000395980.2_Intron|BDNF_ENST00000533246.1_Intron	NM_001143814.1	NP_001137286.1	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						ACCCATTCCTCTTCCCGGCTC	0.537											OREG0020848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	76	0.0151757	0.0	0.0432	5008	,	,		13645	0.0		0.0368	False		,,,				2504	0.0092				p.E6K		Atlas-SNP	.											.	BDNF	63	.	0			c.G16A						PASS	.	C	,,,,,,,,,,,,,,LYS/GLU	47,3757		0,47,1855	146.0	155.0	152.0		,,,,,,,,,,,,,,16	0.2	0.0	11	dbSNP_130	152	390,7842		12,366,3738	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,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_001709.4,NM_170731.4,NM_170732.4,NM_170733.3,NM_170734.3	,,,,,,,,,,,,,,56	12,413,5593	TT,TC,CC		4.7376,1.2355,3.6308	,,,,,,,,,,,,,,	,,,,,,,,,,,,,,6/263	27720937	437,11599	1902	4116	6018	SO:0001627	intron_variant	627	exon1			ATTCCTCTTCCCG	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	ENST00000418212.1:c.127+773G>A	11.37:g.27720937C>T		Somatic	56	0	0	796	WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_170734	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000418212.1	37	CCDS7866.1	43	0.019688644688644688	0	0.0	19	0.052486187845303865	0	0.0	24	0.0316622691292876	C	11.95	1.792906	0.31685	0.012355	0.047376	ENSG00000176697	ENST00000395986	T	0.55413	0.52	4.01	0.204	0.15199	.	0.692359	0.10578	U	0.658293	T	0.07143	0.0181	.	.	.	0.09310	N	0.999999	P	0.50710	0.938	B	0.37387	0.248	T	0.08806	-1.0704	9	0.87932	D	0	.	3.7433	0.08539	0.0:0.5168:0.1899:0.2933	.	6	P23560-3	.	K	6	ENSP00000379309:E6K	ENSP00000379309:E6K	E	-	1	0	BDNF	27677513	0.000000	0.05858	0.000000	0.03702	0.216000	0.24613	0.277000	0.18734	-0.056000	0.13221	0.561000	0.74099	GAG	T|0.032;G|0.020;C|0.947;A|0.001	0.032	strong		0.537	BDNF-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388097.1	NM_170735	
LHCGR	3973	hgsc.bcm.edu	37	2	48915871	48915871	+	Silent	SNP	A	A	G	rs11125179	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48915871A>G	ENST00000294954.7	-	11	1086	c.1065T>C	c.(1063-1065)gaT>gaC	p.D355D	LHCGR_ENST00000405626.1_Silent_p.D328D|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000403273.1_Intron|LHCGR_ENST00000401907.1_Intron|LHCGR_ENST00000344775.3_Silent_p.D293D	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	355					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	AGCCCATAATATCTTCACAGG	0.438													A|||	2966	0.592252	0.2542	0.6643	5008	,	,		19323	0.9236		0.6382	False		,,,				2504	0.6094				p.D355D		Atlas-SNP	.											.	LHCGR	154	.	0			c.T1065C						PASS	.	A	,	1382,3024	454.9+/-350.8	224,934,1045	134.0	134.0	134.0		1065,	-0.9	1.0	2	dbSNP_120	134	5078,3522	631.5+/-398.5	1497,2084,719	no	coding-synonymous,intron	LHCGR,STON1-GTF2A1L	NM_000233.3,NM_001198593.1	,	1721,3018,1764	GG,GA,AA		40.9535,31.3663,49.6694	,	355/700,	48915871	6460,6546	2203	4300	6503	SO:0001819	synonymous_variant	3973	exon11			CATAATATCTTCA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.1065T>C	2.37:g.48915871A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	143	71	0.496504	NM_000233	Q14751|Q15996|Q9UEW9	Silent	SNP	ENST00000294954.7	37	CCDS1842.1																																																																																			A|0.453;G|0.547	0.547	strong		0.438	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
AKAP17A	8227	hgsc.bcm.edu	37	X	1713021	1713021	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:1713021C>T	ENST00000313871.3	+	2	862	c.666C>T	c.(664-666)cgC>cgT	p.R222R	AKAP17A_ENST00000381261.3_Silent_p.R222R	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	222	RRM.				B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						TGCAGTACCGCGAGTACATGG	0.607													c|||	2801	0.559305	0.5832	0.5115	5008	,	,		19903	0.5268		0.5875	False		,,,				2504	0.5654				p.R222R		Atlas-SNP	.											.	AKAP17A	46	.	0			c.C666T						PASS	.			2444,1962		683,1078,442	111.0	102.0	105.0		666	-0.7	0.0	X	dbSNP_134	105	4590,4002		1181,2228,887	no	coding-synonymous	AKAP17A	NM_005088.2		1864,3306,1329	TT,TC,CC		46.5782,44.5302,45.884		222/696	1713021	7034,5964	2203	4296	6499	SO:0001819	synonymous_variant	8227	exon2			GTACCGCGAGTAC	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"""Pseudoautosomal regions / PAR1"", ""A-kinase anchor proteins"""	18783	protein-coding gene	gene with protein product		312095, 465000	"""chromosome X and Y open reading frame 3"", ""splicing factor, arginine/serine-rich 17A"""	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.666C>T	X.37:g.1713021C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Silent	SNP	ENST00000313871.3	37	CCDS14116.1																																																																																			C|0.448;T|0.552	0.552	strong		0.607	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088	
SNPH	9751	hgsc.bcm.edu	37	20	1285933	1285933	+	Silent	SNP	G	G	A	rs3795139	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:1285933G>A	ENST00000381873.3	+	6	956	c.720G>A	c.(718-720)ggG>ggA	p.G240G	SNPH_ENST00000381867.1_Silent_p.G284G	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	240					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CTGAGGATGGGGCAGACAGTG	0.672													G|||	1973	0.39397	0.3979	0.3314	5008	,	,		17209	0.5407		0.3201	False		,,,				2504	0.3579				p.G240G		Atlas-SNP	.											.	SNPH	89	.	0			c.G720A						PASS	.	G		1676,2726		316,1044,841	27.0	27.0	27.0		720	-0.2	0.4	20	dbSNP_107	27	2477,6113		357,1763,2175	no	coding-synonymous	SNPH	NM_014723.2		673,2807,3016	AA,AG,GG		28.8359,38.0736,31.9658		240/495	1285933	4153,8839	2201	4295	6496	SO:0001819	synonymous_variant	9751	exon6			GGATGGGGCAGAC		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.720G>A	20.37:g.1285933G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_014723	Q8IYI3	Silent	SNP	ENST00000381873.3	37	CCDS13012.1																																																																																			G|0.650;A|0.350	0.350	strong		0.672	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723	
ZNF160	90338	hgsc.bcm.edu	37	19	53572059	53572059	+	Silent	SNP	T	T	C	rs78382850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53572059T>C	ENST00000429604.1	-	7	2143	c.1728A>G	c.(1726-1728)caA>caG	p.Q576Q	ZNF160_ENST00000599056.1_Silent_p.Q576Q|ZNF160_ENST00000418871.1_Silent_p.Q576Q|ZNF160_ENST00000601421.1_Silent_p.Q540Q	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	576					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		GTTGTGATGTTTGAGCGAAGA	0.413													T|||	184	0.0367412	0.0045	0.0259	5008	,	,		22098	0.0466		0.0805	False		,,,				2504	0.0327				p.Q576Q		Atlas-SNP	.											.	ZNF160	75	.	0			c.A1728G						PASS	.	T	,,	62,4344	59.9+/-96.7	1,60,2142	93.0	95.0	94.0		1728,1728,1728	-4.7	0.0	19	dbSNP_131	94	704,7896	172.5+/-223.2	19,666,3615	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF160	NM_001102603.1,NM_033288.3,NM_198893.2	,,	20,726,5757	CC,CT,TT		8.186,1.4072,5.8896	,,	576/819,576/819,576/819	53572059	766,12240	2203	4300	6503	SO:0001819	synonymous_variant	90338	exon7			TGATGTTTGAGCG	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1728A>G	19.37:g.53572059T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Silent	SNP	ENST00000429604.1	37	CCDS12859.1																																																																																			T|0.945;C|0.055	0.055	strong		0.413	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288	
IKZF2	22807	hgsc.bcm.edu	37	2	214012508	214012508	+	Silent	SNP	C	C	T	rs6709554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:214012508C>T	ENST00000434687.1	-	4	372	c.63G>A	c.(61-63)gaG>gaA	p.E21E	IKZF2_ENST00000374319.4_Silent_p.E21E|IKZF2_ENST00000451136.2_Silent_p.E21E|IKZF2_ENST00000374327.4_Silent_p.E21E|IKZF2_ENST00000442445.1_Silent_p.E27E|IKZF2_ENST00000421754.2_Silent_p.E21E|IKZF2_ENST00000413091.3_Silent_p.E21E|IKZF2_ENST00000342002.2_Silent_p.E27E|IKZF2_ENST00000457361.1_Silent_p.E21E			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	21					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(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		TATTGGAGTGCTCCCTTTCGG	0.383													C|||	765	0.152756	0.0522	0.2363	5008	,	,		19810	0.003		0.3509	False		,,,				2504	0.18				p.E21E		Atlas-SNP	.											.	IKZF2	71	.	0			c.G63A						PASS	.	C	,	372,4034	188.8+/-215.1	15,342,1846	388.0	333.0	352.0		63,63	-1.0	1.0	2	dbSNP_116	352	3223,5377	486.0+/-371.8	581,2061,1658	no	coding-synonymous,coding-synonymous	IKZF2	NM_001079526.1,NM_016260.2	,	596,2403,3504	TT,TC,CC		37.4767,8.443,27.6411	,	21/501,21/527	214012508	3595,9411	2203	4300	6503	SO:0001819	synonymous_variant	22807	exon4			GGAGTGCTCCCTT	AF130863	CCDS2395.1, CCDS46507.1	2q13.1	2013-01-08	2006-08-25	2006-08-25	ENSG00000030419	ENSG00000030419		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13177	protein-coding gene	gene with protein product		606234	"""zinc finger protein, subfamily 1A, 2 (Helios)"""	ZNFN1A2		9512513, 9560339	Standard	NM_001079526		Approved	Helios	uc002vem.3	Q9UKS7	OTTHUMG00000133005	ENST00000434687.1:c.63G>A	2.37:g.214012508C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	232	103	0.443966	NM_001079526	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Silent	SNP	ENST00000434687.1	37	CCDS2395.1																																																																																			C|0.771;T|0.229	0.229	strong		0.383	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260	
METTL11B	149281	hgsc.bcm.edu	37	1	170135765	170135765	+	Silent	SNP	T	T	C	rs6669514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:170135765T>C	ENST00000439373.2	+	3	560	c.453T>C	c.(451-453)ttT>ttC	p.F151F	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	151						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						TGGAATCCTTTCTCCTTGAAG	0.512													T|||	1330	0.265575	0.4758	0.2219	5008	,	,		18181	0.1349		0.2207	False		,,,				2504	0.1933				p.F151F		Atlas-SNP	.											.	METTL11B	18	.	0			c.T453C						PASS	.	T		599,785		131,337,224	111.0	101.0	104.0		453	2.3	1.0	1	dbSNP_116	104	752,2430		97,558,936	no	coding-synonymous	METTL11B	NM_001136107.1		228,895,1160	CC,CT,TT		23.6329,43.2803,29.5883		151/284	170135765	1351,3215	692	1591	2283	SO:0001819	synonymous_variant	149281	exon3			ATCCTTTCTCCTT	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.453T>C	1.37:g.170135765T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	172	75	0.436047	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			T|0.746;C|0.254	0.254	strong		0.512	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
OR10H1	26539	hgsc.bcm.edu	37	19	15918455	15918455	+	Silent	SNP	G	G	A	rs61739573	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15918455G>A	ENST00000334920.2	-	1	481	c.393C>T	c.(391-393)cgC>cgT	p.R131R		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						GCACGTTGTAGCGCAGGGGGT	0.637													.|||	964	0.192492	0.0416	0.2032	5008	,	,		19525	0.1905		0.3072	False		,,,				2504	0.273				p.R131R		Atlas-SNP	.											OR10H1,NS,carcinoma,-2,1	OR10H1	59	1	0			c.C393T						scavenged	.	G		326,4080		15,296,1892	68.0	56.0	60.0		393	3.7	1.0	19	dbSNP_129	60	2491,6109		372,1747,2181	no	coding-synonymous	OR10H1	NM_013940.2		387,2043,4073	AA,AG,GG		28.9651,7.399,21.6592		131/319	15918455	2817,10189	2203	4300	6503	SO:0001819	synonymous_variant	26539	exon1			GTTGTAGCGCAGG	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.393C>T	19.37:g.15918455G>A		Somatic	222	5	0.0225225		WXS	Illumina HiSeq	Phase_I	261	135	0.517241	NM_013940	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	37	CCDS12335.1																																																																																			G|0.794;A|0.206	0.206	strong		0.637	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
CCDC36	339834	hgsc.bcm.edu	37	3	49273996	49273996	+	Silent	SNP	C	C	T	rs12631989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49273996C>T	ENST00000438782.1	+	3	308	c.72C>T	c.(70-72)tcC>tcT	p.S24S	CCDC36_ENST00000296449.5_Silent_p.S24S|CCDC36_ENST00000452691.2_Silent_p.S24S|CCDC36_ENST00000451634.2_Silent_p.S14S|CCDC36_ENST00000366429.2_Silent_p.S24S|CCDC36_ENST00000493870.1_3'UTR			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	24										endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		AGAAGTCATCCAACTGGAATA	0.353													C|||	3533	0.705471	0.4281	0.7089	5008	,	,		20068	0.9415		0.6431	False		,,,				2504	0.8988				p.S24S		Atlas-SNP	.											.	CCDC36	77	.	0			c.C72T						PASS	.	C	,	1992,2414	551.5+/-378.3	456,1080,667	53.0	54.0	54.0		72,72	4.2	1.0	3	dbSNP_120	54	5294,3306	641.7+/-399.7	1633,2028,639	no	coding-synonymous,coding-synonymous	CCDC36	NM_001135197.1,NM_178173.3	,	2089,3108,1306	TT,TC,CC		38.4419,45.2111,43.9797	,	24/595,24/595	49273996	7286,5720	2203	4300	6503	SO:0001819	synonymous_variant	339834	exon3			GTCATCCAACTGG	AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"""cancer/testis antigen 74"""						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.72C>T	3.37:g.49273996C>T		Somatic	388	0	0		WXS	Illumina HiSeq	Phase_I	316	314	0.993671	NM_001135197	C9JJL0|Q05DG9|Q96LP7	Silent	SNP	ENST00000438782.1	37	CCDS33755.2																																																																																			C|0.390;T|0.610	0.610	strong		0.353	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173	
LSS	4047	hgsc.bcm.edu	37	21	47635627	47635627	+	Silent	SNP	C	C	G	rs9980968	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47635627C>G	ENST00000397728.3	-	8	942	c.864G>C	c.(862-864)ccG>ccC	p.P288P	LSS_ENST00000464357.1_5'UTR|LSS_ENST00000457828.2_Silent_p.P208P|LSS_ENST00000356396.4_Silent_p.P288P|LSS_ENST00000522411.1_Silent_p.P277P	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	288					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					GCCAGCTGTGCGGCGTGTACA	0.657													C|||	1808	0.361022	0.4675	0.2781	5008	,	,		13305	0.127		0.4235	False		,,,				2504	0.453				p.P288P	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G864C						PASS	.	C	,,,	1929,2477	524.1+/-371.2	429,1071,703	31.0	35.0	34.0		864,831,624,864	-10.4	0.3	21	dbSNP_119	34	3403,5197	478.6+/-369.9	680,2043,1577	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	1109,3114,2280	GG,GC,CC		39.5698,43.7812,40.9965	,,,	288/733,277/722,208/653,288/733	47635627	5332,7674	2203	4300	6503	SO:0001819	synonymous_variant	4047	exon8			GCTGTGCGGCGTG	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.864G>C	21.37:g.47635627C>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1																																																																																			C|0.618;G|0.382	0.382	strong		0.657	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
TAS2R1	50834	hgsc.bcm.edu	37	5	9629295	9629295	+	Silent	SNP	A	A	G	rs2234235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:9629295A>G	ENST00000382492.2	-	1	1168	c.850T>C	c.(850-852)Ttg>Ctg	p.L284L	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	284					chemosensory behavior (GO:0007635)|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)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						TTTTGTTTCAATTTAGGATTT	0.368													A|||	110	0.0219649	0.0129	0.0245	5008	,	,		20740	0.001		0.0457	False		,,,				2504	0.0297				p.L284L		Atlas-SNP	.											.	TAS2R1	84	.	0			c.T850C						PASS	.	A		91,4315	74.7+/-112.8	2,87,2114	95.0	97.0	96.0		850	1.6	1.0	5	dbSNP_98	96	313,8287	111.2+/-171.5	4,305,3991	no	coding-synonymous	TAS2R1	NM_019599.2		6,392,6105	GG,GA,AA		3.6395,2.0654,3.1063		284/300	9629295	404,12602	2203	4300	6503	SO:0001819	synonymous_variant	50834	exon1			GTTTCAATTTAGG	AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.850T>C	5.37:g.9629295A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_019599	Q646G8	Silent	SNP	ENST00000382492.2	37	CCDS3876.1																																																																																			A|0.971;G|0.029	0.029	strong		0.368	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2		
LTBP1	4052	hgsc.bcm.edu	37	2	33567971	33567971	+	Missense_Mutation	SNP	C	C	T	rs61751742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:33567971C>T	ENST00000404816.2	+	25	4150	c.3797C>T	c.(3796-3798)tCc>tTc	p.S1266F	LTBP1_ENST00000354476.3_Missense_Mutation_p.S1267F|LTBP1_ENST00000407925.1_Missense_Mutation_p.S940F|LTBP1_ENST00000272273.5_Intron|LTBP1_ENST00000418533.2_Intron|LTBP1_ENST00000390003.4_Missense_Mutation_p.S941F|LTBP1_ENST00000404525.1_Missense_Mutation_p.S887F|LTBP1_ENST00000402934.1_Missense_Mutation_p.S887F			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1266	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ACAGCTGGCTCCTTCCGCTGC	0.453													C|||	20	0.00399361	0.0	0.0072	5008	,	,		17041	0.0		0.0129	False		,,,				2504	0.002				p.S1266F		Atlas-SNP	.											LTBP1_ENST00000407925,NS,carcinoma,-1,2	LTBP1	317	2	0			c.C3797T						PASS	.	C	PHE/SER,,PHE/SER,,PHE/SER	15,4391	22.3+/-47.3	0,15,2188	124.0	105.0	111.0		2819,,2660,,3797	5.9	1.0	2	dbSNP_129	111	79,8521	46.7+/-105.8	0,79,4221	yes	missense,intron,missense,intron,missense	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	155,,155,,155	0,94,6409	TT,TC,CC		0.9186,0.3404,0.7227	probably-damaging,,probably-damaging,,probably-damaging	940/1396,,887/1343,,1266/1722	33567971	94,12912	2203	4300	6503	SO:0001583	missense	4052	exon25			CTGGCTCCTTCCG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3797C>T	2.37:g.33567971C>T	ENSP00000386043:p.Ser1266Phe	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	29.1|29.1	4.974955|4.974955	0.92919|0.92919	0.003404|0.003404	0.009186|0.009186	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000402934;ENST00000404525;ENST00000407925	.|D;D;D;D;D;D	.|0.95412	.|-3.7;-3.7;-3.7;-3.7;-3.7;-3.7	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	.|.	.|.	.|.	.|.	D|D	0.97961|0.97961	0.9329|0.9329	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.994;1.0;1.0;1.0	.|P;D;D;D	.|0.91635	.|0.88;0.999;0.999;0.999	D|D	0.96283|0.96283	0.9208|0.9208	5|9	.|0.87932	.|D	.|0	.|.	20.3045|20.3045	0.98621|0.98621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs61751742|rs61751742	.|887;940;941;1267	.|Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;.;.;.	S|F	228|1266;1267;941;887;887;940	.|ENSP00000386043:S1266F;ENSP00000346467:S1267F;ENSP00000374653:S941F;ENSP00000384373:S887F;ENSP00000385359:S887F;ENSP00000384091:S940F	.|ENSP00000346467:S1267F	P|S	+|+	1|2	0|0	LTBP1|LTBP1	33421475|33421475	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.485000|7.485000	0.81204|0.81204	2.807000|2.807000	0.96579|0.96579	0.557000|0.557000	0.71058|0.71058	CCT|TCC	C|0.991;T|0.009	0.009	strong		0.453	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
PRG4	10216	hgsc.bcm.edu	37	1	186276661	186276661	+	Missense_Mutation	SNP	A	A	G	rs61831150	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:186276661A>G	ENST00000445192.2	+	7	1855	c.1810A>G	c.(1810-1812)Act>Gct	p.T604A	PRG4_ENST00000367483.4_Missense_Mutation_p.T563A|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.T511A|PRG4_ENST00000367486.3_Missense_Mutation_p.T561A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	604	59 X 8 AA repeats of K-X-P-X-P-T-T-X.			T -> A (in Ref. 1; AAB09089). {ECO:0000305}.	cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGCACCCACCACTCCCAAAGA	0.657													-|||	1149	0.229433	0.1415	0.4078	5008	,	,		8224	0.125		0.33	False		,,,				2504	0.226				p.T604A		Atlas-SNP	.											PRG4,brain,glioma,0,1	PRG4	259	1	0			c.A1810G						scavenged	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR	826,3580	322.6+/-297.7	75,676,1452	77.0	74.0	75.0		1810,1408,1531,1687	-7.0	0.0	1	dbSNP_129	75	3037,5563	461.6+/-365.5	537,1963,1800	no	missense,missense,missense,missense	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	58,58,58,58	612,2639,3252	GG,GA,AA		35.314,18.7472,29.7017	benign,benign,benign,benign	604/1405,470/1271,511/1312,563/1364	186276661	3863,9143	2203	4300	6503	SO:0001583	missense	10216	exon7			CCCACCACTCCCA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1810A>G	1.37:g.186276661A>G	ENSP00000399679:p.Thr604Ala	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	125	52	0.416	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	533	0.24404761904761904	57	0.11585365853658537	143	0.39502762430939226	73	0.12762237762237763	260	0.34300791556728233	A	6.871	0.530050	0.13127	0.187472	0.35314	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05996	3.36;3.45;3.39;3.46	3.74	-6.98	0.01611	.	0.224316	0.21263	U	0.077456	T	0.00012	0.0000	L	0.55990	1.75	0.80722	P	0.0	B;B;B;B	0.17268	0.021;0.021;0.012;0.021	B;B;B;B	0.11329	0.006;0.006;0.003;0.006	T	0.46596	-0.9180	8	.	.	.	.	2.0325	0.03532	0.2526:0.1179:0.3962:0.2333	rs61831150	470;511;604;563	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	A	561;470;563;511;604	ENSP00000356456:T561A;ENSP00000356453:T563A;ENSP00000356455:T511A;ENSP00000399679:T604A	.	T	+	1	0	PRG4	184543284	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.345000	0.19979	-1.252000	0.02491	-0.486000	0.04755	ACT	A|0.713;G|0.287	0.287	strong		0.657	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
FBF1	85302	hgsc.bcm.edu	37	17	73919538	73919538	+	Missense_Mutation	SNP	G	G	A	rs7218738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73919538G>A	ENST00000586717.1	-	13	1384	c.1111C>T	c.(1111-1113)Cct>Tct	p.P371S	FBF1_ENST00000319129.5_Missense_Mutation_p.P370S|FBF1_ENST00000389570.4_Missense_Mutation_p.P371S			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	371			P -> S (in dbSNP:rs7218738).		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						GGCGTGACAGGCACTGAACTT	0.657													G|||	627	0.1252	0.2579	0.0865	5008	,	,		19008	0.0268		0.0577	False		,,,				2504	0.1442				p.P370S		Atlas-SNP	.											.	FBF1	48	.	0			c.C1108T						PASS	.	G	SER/PRO	919,3239		98,723,1258	28.0	33.0	31.0		1108	0.0	0.0	17	dbSNP_116	31	614,7794		20,574,3610	yes	missense	FBF1	NM_001080542.1	74	118,1297,4868	AA,AG,GG		7.3026,22.102,12.1996	benign	370/1134	73919538	1533,11033	2079	4204	6283	SO:0001583	missense	85302	exon13			TGACAGGCACTGA	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.1111C>T	17.37:g.73919538G>A	ENSP00000465132:p.Pro371Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		204	0.09340659340659341	115	0.23373983739837398	30	0.08287292817679558	17	0.02972027972027972	42	0.055408970976253295	G	2.960	-0.214912	0.06101	0.22102	0.073026	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.21031	2.03;2.03	3.75	-0.00302	0.14028	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.25105	0.118;0.003;0.066	B;B;B	0.23574	0.047;0.006;0.043	T	0.44298	-0.9337	8	0.25106	T	0.35	0.8444	5.5972	0.17333	0.1165:0.0:0.4638:0.4197	rs7218738;rs56431814;rs7218738	385;371;370	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	S	371;371;370;384	ENSP00000374221:P371S;ENSP00000324292:P370S	ENSP00000324292:P370S	P	-	1	0	FBF1	71431133	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.199000	0.17237	0.196000	0.20367	0.561000	0.74099	CCT	G|0.882;A|0.118	0.118	strong		0.657	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
AHNAK2	113146	hgsc.bcm.edu	37	14	105409907	105409907	+	Missense_Mutation	SNP	T	T	C	rs10141053	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105409907T>C	ENST00000333244.5	-	7	12000	c.11881A>G	c.(11881-11883)Atg>Gtg	p.M3961V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3961			M -> V (in dbSNP:rs10141053).			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)			TTGGCCGTCATGTCCTTGTCG	0.617													.|||	1231	0.245807	0.0635	0.2997	5008	,	,		19573	0.0863		0.4851	False		,,,				2504	0.3722				p.M3961V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A11881G						PASS	.	C	VAL/MET	541,3487		44,453,1517	219.0	213.0	215.0		11881	-1.3	0.0	14	dbSNP_119	215	4038,4280		1001,2036,1122	no	missense	AHNAK2	NM_138420.2	21	1045,2489,2639	CC,CT,TT		48.5453,13.431,37.0889	benign	3961/5796	105409907	4579,7767	2014	4159	6173	SO:0001583	missense	113146	exon7			CCGTCATGTCCTT	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.11881A>G	14.37:g.105409907T>C	ENSP00000353114:p.Met3961Val	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	221	221	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	574	0.26282051282051283	47	0.09552845528455285	117	0.32320441988950277	37	0.06468531468531469	373	0.4920844327176781	-	0.012	-1.652023	0.00785	0.13431	0.485453	ENSG00000185567	ENST00000333244	T	0.00666	5.91	4.0	-1.33	0.09172	.	.	.	.	.	T	0.00012	0.0000	N	0.00256	-1.76	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.19321	-1.0309	8	0.02654	T	1	.	5.6094	0.17396	0.1352:0.3515:0.0:0.5133	rs10141053;rs10141053	3961	Q8IVF2	AHNK2_HUMAN	V	3961	ENSP00000353114:M3961V	ENSP00000353114:M3961V	M	-	1	0	AHNAK2	104480952	.	.	0.002000	0.10522	0.001000	0.01503	.	.	-0.765000	0.04645	-1.803000	0.00618	ATG	T|0.678;C|0.322	0.322	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
VCAN	1462	hgsc.bcm.edu	37	5	82815170	82815170	+	Missense_Mutation	SNP	A	A	G	rs61749613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:82815170A>G	ENST00000265077.3	+	7	1610	c.1045A>G	c.(1045-1047)Aaa>Gaa	p.K349E	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.K349E|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.K301E	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	349	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TTTTCTAGCTAAAGAGGCTAC	0.368													A|||	100	0.0199681	0.0008	0.0317	5008	,	,		19029	0.001		0.0487	False		,,,				2504	0.0276				p.K349E		Atlas-SNP	.											.	VCAN	498	.	0			c.A1045G						PASS	.	A	,,GLU/LYS,GLU/LYS	40,4364	41.6+/-74.8	1,38,2163	66.0	69.0	68.0		,,1045,1045	5.6	1.0	5	dbSNP_129	68	358,8238	115.5+/-175.4	8,342,3948	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,56,56	9,380,6111	GG,GA,AA		4.1647,0.9083,3.0615	,,probably-damaging,probably-damaging	,,349/1643,349/3397	82815170	398,12602	2202	4298	6500	SO:0001583	missense	1462	exon7			CTAGCTAAAGAGG	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.1045A>G	5.37:g.82815170A>G	ENSP00000265077:p.Lys349Glu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	109	59	0.541284	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	53	0.024267399267399268	0	0.0	12	0.03314917127071823	1	0.0017482517482517483	40	0.052770448548812667	A	16.74	3.207760	0.58343	0.009083	0.041647	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.09350	2.99;2.99;2.99	5.64	5.64	0.86602	C-type lectin fold (1);C-type lectin-like (1);	0.000000	0.64402	D	0.000006	T	0.03651	0.0104	M	0.61703	1.905	0.44454	D	0.997384	P;P	0.42692	0.694;0.787	P;P	0.55545	0.778;0.512	T	0.04693	-1.0933	10	0.11794	T	0.64	.	13.3803	0.60762	1.0:0.0:0.0:0.0	rs61749613	349;349	P13611-3;P13611	.;CSPG2_HUMAN	E	349;349;301	ENSP00000265077:K349E;ENSP00000342768:K349E;ENSP00000425959:K301E	ENSP00000265077:K349E	K	+	1	0	VCAN	82850926	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.860000	0.48372	2.151000	0.67156	0.533000	0.62120	AAA	A|0.973;G|0.027	0.027	strong		0.368	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
TSR1	55720	hgsc.bcm.edu	37	17	2236404	2236404	+	Missense_Mutation	SNP	T	T	C	rs2281726	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2236404T>C	ENST00000301364.5	-	7	2235	c.1156A>G	c.(1156-1158)Agt>Ggt	p.S386G	SNORD91A_ENST00000390861.1_RNA	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	386			S -> G (in dbSNP:rs2281726). {ECO:0000269|PubMed:15489334}.		ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						ACCTTAGAACTTTCCTTCAAG	0.423													T|||	869	0.173522	0.0204	0.121	5008	,	,		17797	0.5208		0.1203	False		,,,				2504	0.1145				p.S386G		Atlas-SNP	.											.	TSR1	57	.	0			c.A1156G						PASS	.	T	GLY/SER	175,4231	109.5+/-147.8	4,167,2032	81.0	78.0	79.0		1156	-1.2	0.9	17	dbSNP_100	79	990,7610	206.1+/-248.3	53,884,3363	yes	missense	TSR1	NM_018128.4	56	57,1051,5395	CC,CT,TT		11.5116,3.9719,8.9574	benign	386/805	2236404	1165,11841	2203	4300	6503	SO:0001583	missense	55720	exon7			TAGAACTTTCCTT	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.1156A>G	17.37:g.2236404T>C	ENSP00000301364:p.Ser386Gly	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	149	68	0.456376	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	456	0.2087912087912088	14	0.028455284552845527	43	0.11878453038674033	305	0.5332167832167832	94	0.12401055408970976	T	10.93	1.489830	0.26686	0.039719	0.115116	ENSG00000167721	ENST00000301364	T	0.11712	2.75	5.16	-1.25	0.09405	.	0.569347	0.21013	N	0.081643	T	0.00012	0.0000	L	0.32530	0.975	0.51233	P	8.60000000000305E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.42699	-0.9436	9	0.20046	T	0.44	-0.013	6.6189	0.22792	0.0:0.1412:0.3911:0.4678	rs2281726;rs59136948;rs2281726	386	Q2NL82	TSR1_HUMAN	G	386	ENSP00000301364:S386G	ENSP00000301364:S386G	S	-	1	0	TSR1	2183154	0.013000	0.17824	0.937000	0.37676	0.810000	0.45777	0.599000	0.24089	-0.441000	0.07201	0.528000	0.53228	AGT	T|0.862;C|0.138	0.138	strong		0.423	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471778	39471778	+	Missense_Mutation	SNP	C	C	T	rs78413710|rs386797077	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39471778C>T	ENST00000334202.3	-	1	169	c.125G>A	c.(124-126)gGc>gAc	p.G42D		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	42						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			gcccccgcagccagagccccc	0.687													C|||	941	0.187899	0.1354	0.1354	5008	,	,		9853	0.3165		0.1809	False		,,,				2504	0.1708				p.G42D		Atlas-SNP	.											.	KRTAP17-1	14	.	0			c.G125A						PASS	.						10.0	13.0	12.0					17																	39471778		2170	4250	6420	SO:0001583	missense	83902	exon1			CCGCAGCCAGAGC	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"""Keratin associated proteins"""	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.125G>A	17.37:g.39471778C>T	ENSP00000333993:p.Gly42Asp	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	31	0.738095	NM_031964		Missense_Mutation	SNP	ENST00000334202.3	37	CCDS11387.1	399	0.18269230769230768	62	0.12601626016260162	49	0.13535911602209943	159	0.27797202797202797	129	0.17018469656992086	C	5.391	0.257268	0.10239	.	.	ENSG00000186860	ENST00000334202	.	.	.	4.26	3.29	0.37713	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.46586	P	8.879999999999999E-4	B	0.15930	0.015	B	0.17433	0.018	T	0.15809	-1.0424	7	0.87932	D	0	-10.805	7.6767	0.28490	0.0:0.8845:0.0:0.1155	.	42	Q9BYP8	KR171_HUMAN	D	42	.	ENSP00000333993:G42D	G	-	2	0	KRTAP17-1	36725304	0.664000	0.27457	0.310000	0.25168	0.312000	0.27988	1.496000	0.35638	1.004000	0.39156	0.462000	0.41574	GGC	C|0.818;T|0.182	0.182	strong		0.687	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1		
GPR97	222487	hgsc.bcm.edu	37	16	57707249	57707249	+	Silent	SNP	C	C	T	rs73552781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57707249C>T	ENST00000333493.4	+	2	236	c.75C>T	c.(73-75)acC>acT	p.T25T	GPR97_ENST00000450388.3_5'UTR|GPR97_ENST00000327655.6_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	25					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						AAAAGCCCACCGAAGGGCCAA	0.547													C|||	176	0.0351438	0.087	0.0187	5008	,	,		21297	0.001		0.0378	False		,,,				2504	0.0092				p.T25T		Atlas-SNP	.											.	GPR97	74	.	0			c.C75T						PASS	.	C		375,4021	190.5+/-216.4	14,347,1837	82.0	74.0	77.0		75	-6.8	0.0	16	dbSNP_130	77	318,8282	113.1+/-173.2	10,298,3992	no	coding-synonymous	GPR97	NM_170776.4		24,645,5829	TT,TC,CC		3.6977,8.5305,5.3324		25/550	57707249	693,12303	2198	4300	6498	SO:0001819	synonymous_variant	222487	exon2			GCCCACCGAAGGG	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.75C>T	16.37:g.57707249C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	CCDS10786.1																																																																																			C|0.957;T|0.043	0.043	strong		0.547	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
EPS8L1	54869	hgsc.bcm.edu	37	19	55598724	55598724	+	Missense_Mutation	SNP	A	A	G	rs1054940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55598724A>G	ENST00000201647.6	+	19	2062	c.2006A>G	c.(2005-2007)aAg>aGg	p.K669R	EPS8L1_ENST00000540810.1_Missense_Mutation_p.K605R|EPS8L1_ENST00000245618.5_Missense_Mutation_p.K542R|EPS8L1_ENST00000588359.1_Missense_Mutation_p.K355R|EPS8L1_ENST00000586329.1_Intron	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	669			K -> R (in dbSNP:rs1054940). {ECO:0000269|PubMed:12620401, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15498874}.		positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TCGCTGCAGAAGGAGGAGCTG	0.731													A|||	2342	0.467652	0.3419	0.4597	5008	,	,		13706	0.4514		0.506	False		,,,				2504	0.6207				p.K669R	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											EPS8L1_ENST00000245618,NS,carcinoma,0,2	EPS8L1	122	2	0			c.A2006G						PASS	.	A	ARG/LYS,ARG/LYS	1592,2812		310,972,920	26.0	28.0	27.0		1625,2006	4.0	1.0	19	dbSNP_86	27	4241,4353		1078,2085,1134	yes	missense,missense	EPS8L1	NM_017729.3,NM_133180.2	26,26	1388,3057,2054	GG,GA,AA		49.3484,36.149,44.8761	probably-damaging,probably-damaging	542/597,669/724	55598724	5833,7165	2202	4297	6499	SO:0001583	missense	54869	exon19			TGCAGAAGGAGGA	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.2006A>G	19.37:g.55598724A>G	ENSP00000201647:p.Lys669Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	983	0.4500915750915751	171	0.3475609756097561	170	0.4696132596685083	260	0.45454545454545453	382	0.503957783641161	A	27.8	4.868341	0.91587	0.36149	0.493484	ENSG00000131037	ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.25250	1.81;1.81;1.81	4.02	4.02	0.46733	.	0.121108	0.53938	D	0.000057	T	0.00012	0.0000	L	0.54908	1.71	0.09310	P	0.99999486196	D;D;P	0.89917	1.0;0.991;0.863	D;D;P	0.87578	0.998;0.927;0.73	T	0.50440	-0.8828	9	0.34782	T	0.22	-35.624	11.4935	0.50394	1.0:0.0:0.0:0.0	rs1054940;rs3195458;rs58630253;rs1054940	448;542;669	Q8TE68-4;Q8TE68-2;Q8TE68	.;.;ES8L1_HUMAN	R	669;605;542;355	ENSP00000201647:K669R;ENSP00000437541:K605R;ENSP00000245618:K542R	ENSP00000201647:K669R	K	+	2	0	EPS8L1	60290536	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.360000	0.66086	1.768000	0.52137	0.260000	0.18958	AAG	A|0.559;G|0.441	0.441	strong		0.731	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
VWDE	221806	hgsc.bcm.edu	37	7	12400783	12400783	+	Missense_Mutation	SNP	C	C	T	rs35171886	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	65	0	0		WXS	Illumina HiSeq	Phase_I	90	36	0.4	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	
FBXO30	84085	hgsc.bcm.edu	37	6	146126419	146126419	+	Missense_Mutation	SNP	C	C	T	rs9373475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:146126419C>T	ENST00000237281.4	-	2	1289	c.1123G>A	c.(1123-1125)Gtg>Atg	p.V375M		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	375	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.		V -> M (in dbSNP:rs9373475). {ECO:0000269|Ref.3}.				ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		ACATTCTTCACGTCCCCTAAG	0.398													c|||	1649	0.329273	0.2549	0.232	5008	,	,		23522	0.2341		0.4105	False		,,,				2504	0.5133				p.V375M		Atlas-SNP	.											.	FBXO30	56	.	0			c.G1123A						PASS	.	T	MET/VAL	1117,3289	401.0+/-331.8	152,813,1238	159.0	151.0	153.0		1123	-3.2	0.2	6	dbSNP_119	153	3553,5047	516.6+/-378.9	728,2097,1475	yes	missense	FBXO30	NM_032145.4	21	880,2910,2713	TT,TC,CC		41.314,25.3518,35.9065	benign	375/746	146126419	4670,8336	2203	4300	6503	SO:0001583	missense	84085	exon2			TCTTCACGTCCCC	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"""F-boxes /  ""other"""""	15600	protein-coding gene	gene with protein product		609101	"""F-box only protein, helicase, 18"""				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.1123G>A	6.37:g.146126419C>T	ENSP00000237281:p.Val375Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	246	245	0.995935	NM_032145	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	37	CCDS5208.1	674	0.3086080586080586	125	0.2540650406504065	90	0.24861878453038674	149	0.26048951048951047	310	0.40897097625329815	c	4.167	0.029502	0.08054	0.253518	0.41314	ENSG00000118496	ENST00000237281	T	0.18810	2.19	5.46	-3.18	0.05186	.	0.133607	0.51477	N	0.000086	T	0.02193	0.0068	N	0.08118	0	0.80722	P	0.0	B	0.20261	0.043	B	0.12156	0.007	T	0.33650	-0.9860	9	0.56958	D	0.05	-0.0044	2.7703	0.05332	0.2489:0.2465:0.3853:0.1193	rs9373475;rs17822286;rs52794580;rs57120223;rs9373475	375	Q8TB52	FBX30_HUMAN	M	375	ENSP00000237281:V375M	ENSP00000237281:V375M	V	-	1	0	FBXO30	146168112	0.104000	0.21937	0.186000	0.23195	0.512000	0.34134	-0.321000	0.08018	-0.720000	0.04935	-1.033000	0.02402	GTG	C|0.663;N|0.000	.	strong		0.398	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2		
AMPH	273	hgsc.bcm.edu	37	7	38431436	38431436	+	Silent	SNP	C	C	T	rs1058656	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:38431436C>T	ENST00000356264.2	-	19	2006	c.1791G>A	c.(1789-1791)acG>acA	p.T597T	AMPH_ENST00000428293.2_Silent_p.T555T|AMPH_ENST00000325590.5_Silent_p.T555T|AMPH_ENST00000471913.1_5'Flank	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	597					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GTGCAGAAGGCGTGGGCTGAG	0.612													C|||	896	0.178914	0.2322	0.2248	5008	,	,		13855	0.127		0.1759	False		,,,				2504	0.1309				p.T597T		Atlas-SNP	.											.	AMPH	157	.	0			c.G1791A						PASS	.	C	,	948,3458	360.1+/-315.1	99,750,1354	52.0	49.0	50.0		1791,1665	-1.8	0.0	7	dbSNP_86	50	1860,6740	330.3+/-319.2	197,1466,2637	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	296,2216,3991	TT,TC,CC		21.6279,21.5161,21.59	,	597/696,555/654	38431436	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			AGAAGGCGTGGGC		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1791G>A	7.37:g.38431436C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	50	0.406504	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	
MYSM1	114803	hgsc.bcm.edu	37	1	59127086	59127086	+	Silent	SNP	G	G	A	rs7523134	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:59127086G>A	ENST00000472487.1	-	18	2301	c.2262C>T	c.(2260-2262)ctC>ctT	p.L754L	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	754					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					ACCTATGGGAGAGCCTGTATT	0.353													G|||	1241	0.247804	0.1339	0.2421	5008	,	,		17586	0.3095		0.2843	False		,,,				2504	0.3047				p.L754L		Atlas-SNP	.											.	MYSM1	50	.	0			c.C2262T						PASS	.	G		636,3036		55,526,1255	179.0	164.0	168.0		2262	-10.3	0.1	1	dbSNP_116	168	2406,5750		365,1676,2037	no	coding-synonymous	MYSM1	NM_001085487.2		420,2202,3292	AA,AG,GG		29.4998,17.3203,25.7186		754/829	59127086	3042,8786	1836	4078	5914	SO:0001819	synonymous_variant	114803	exon18			ATGGGAGAGCCTG	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.2262C>T	1.37:g.59127086G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																			G|0.742;A|0.258	0.258	strong		0.353	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
DOCK8	81704	hgsc.bcm.edu	37	9	370244	370244	+	Silent	SNP	A	A	G	rs913703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:370244A>G	ENST00000453981.1	+	16	1924	c.1812A>G	c.(1810-1812)aaA>aaG	p.K604K	DOCK8_ENST00000382331.1_5'UTR|DOCK8_ENST00000382329.1_Silent_p.K71K|DOCK8_ENST00000432829.2_Silent_p.K536K|DOCK8_ENST00000469391.1_Silent_p.K536K			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	604	DHR-1.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TCTTTGGAAAATCCAGCGGGC	0.388													G|||	1081	0.215855	0.2859	0.2133	5008	,	,		20473	0.0804		0.2326	False		,,,				2504	0.2454				p.K604K		Atlas-SNP	.											.	DOCK8	401	.	0			c.A1812G						PASS	.	G	,,	1184,3222	711.3+/-408.0	150,884,1169	104.0	104.0	104.0		1608,1608,1812	1.8	1.0	9	dbSNP_86	104	2091,6509	717.4+/-406.2	253,1585,2462	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	403,2469,3631	GG,GA,AA		24.314,26.8724,25.1807	,,	536/2000,536/2032,604/2100	370244	3275,9731	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon16			TGGAAAATCCAGC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1812A>G	9.37:g.370244A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			A|0.770;G|0.230	0.230	strong		0.388	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
VPS13C	54832	hgsc.bcm.edu	37	15	62212781	62212781	+	Silent	SNP	T	T	C	rs17238189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:62212781T>C	ENST00000261517.5	-	56	7201	c.7128A>G	c.(7126-7128)caA>caG	p.Q2376Q	VPS13C_ENST00000249837.3_Silent_p.Q2333Q|VPS13C_ENST00000395898.3_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	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	227	117	0.515419	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	
MAPT	4137	hgsc.bcm.edu	37	17	44061036	44061036	+	Missense_Mutation	SNP	T	T	C	rs62063787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44061036T>C	ENST00000571987.1	+	5	866	c.866T>C	c.(865-867)gTa>gCa	p.V289A	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.V289A|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.V289A|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.V289A|MAPT_ENST00000535772.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	289			V -> A (risk factor for PSNP1; dbSNP:rs62063787). {ECO:0000269|PubMed:10534245, ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GGGCCCAGTGTAGGGCGGGCC	0.617													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		16077	0.001		0.2406	False		,,,				2504	0.0613				p.V289A		Atlas-SNP	.											.	MAPT	135	.	0			c.T866C						PASS	.	C	ALA/VAL,,,,,,ALA/VAL,	227,4179	791.3+/-415.1	7,213,1983	41.0	46.0	44.0		866,,,,,,866,	-1.4	0.0	17	dbSNP_129	44	1928,6672	716.3+/-406.1	221,1486,2593	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	64,,,,,,64,	228,1699,4576	CC,CT,TT		22.4186,5.1521,16.5693	benign,,,,,,benign,	289/777,,,,,,289/759,	44061036	2155,10851	2203	4300	6503	SO:0001583	missense	4137	exon6			CCAGTGTAGGGCG	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.866T>C	17.37:g.44061036T>C	ENSP00000458742:p.Val289Ala	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	0.533	-0.857132	0.02630	0.051521	0.224186	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.09723	2.95;2.95;2.95	4.68	-1.36	0.09085	.	1.284980	0.05582	N	0.573067	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43589	-0.9382	9	0.05620	T	0.96	1.7099	0.2163	0.00162	0.3062:0.2538:0.1395:0.3005	rs62063787	289;289	P10636-9;P10636	.;TAU_HUMAN	A	289	ENSP00000340820:V289A;ENSP00000262410:V289A;ENSP00000410838:V289A	ENSP00000262410:V289A	V	+	2	0	MAPT	41416873	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.211000	0.17474	-0.068000	0.12953	-1.163000	0.01768	GTA	T|0.849;C|0.151	0.151	strong		0.617	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
MUC16	94025	hgsc.bcm.edu	37	19	9048170	9048170	+	Missense_Mutation	SNP	G	G	A	rs10417600	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9048170G>A	ENST00000397910.4	-	5	33664	c.33461C>T	c.(33460-33462)tCt>tTt	p.S11154F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11156	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTGACCAGAGAGGTCACCAT	0.478													G|||	948	0.189297	0.1982	0.1988	5008	,	,		23687	0.0258		0.2813	False		,,,				2504	0.2444				p.S11154F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C33461T						PASS	.		PHE/SER	749,3069		69,611,1229	86.0	79.0	81.0		33461	2.4	0.0	19	dbSNP_119	81	2497,5763		399,1699,2032	yes	missense	MUC16	NM_024690.2	155	468,2310,3261	AA,AG,GG		30.23,19.6176,26.8753	probably-damaging	11154/14508	9048170	3246,8832	1909	4130	6039	SO:0001583	missense	94025	exon5			ACCAGAGAGGTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33461C>T	19.37:g.9048170G>A	ENSP00000381008:p.Ser11154Phe	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	406	0.1858974358974359	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	216	0.2849604221635884	g	6.853	0.526597	0.13066	0.196176	0.3023	ENSG00000181143	ENST00000397910	T	0.02737	4.18	3.43	2.39	0.29439	.	.	.	.	.	T	0.00012	0.0000	L	0.55481	1.735	.	.	.	D	0.76494	0.999	D	0.78314	0.991	T	0.48843	-0.8999	8	0.87932	D	0	.	6.5891	0.22636	0.1311:0.0:0.8689:0.0	rs10417600;rs52818682;rs10417600	11154	B5ME49	.	F	11154	ENSP00000381008:S11154F	ENSP00000381008:S11154F	S	-	2	0	MUC16	8909170	0.001000	0.12720	0.002000	0.10522	0.011000	0.07611	0.463000	0.21972	0.994000	0.38892	0.550000	0.68814	TCT	G|0.796;A|0.204	0.204	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TRIM55	84675	hgsc.bcm.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	A	G	rs7843605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:67064654A>G	ENST00000315962.4	+	8	1401	c.1028A>G	c.(1027-1029)aAa>aGa	p.K343R	TRIM55_ENST00000276573.7_Missense_Mutation_p.K343R|TRIM55_ENST00000353317.5_Missense_Mutation_p.K343R|TRIM55_ENST00000350034.4_Intron	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	36	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	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	
C17orf80	55028	hgsc.bcm.edu	37	17	71239087	71239087	+	Silent	SNP	G	G	T	rs1566290	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:71239087G>T	ENST00000535032.2	+	4	1787	c.1674G>T	c.(1672-1674)acG>acT	p.T558T	C17orf80_ENST00000582793.1_Silent_p.T27T|C17orf80_ENST00000268942.8_Silent_p.T522T|C17orf80_ENST00000359042.2_Silent_p.T558T|RP11-661C3.2_ENST00000579037.1_RNA|C17orf80_ENST00000577615.1_Silent_p.T522T|C17orf80_ENST00000255557.4_Silent_p.T522T|C17orf80_ENST00000426147.2_Silent_p.T558T			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	558						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T558T(1)		kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			GTGGCATCACGATGCTCTTCA	0.463													G|||	1103	0.220248	0.0408	0.3761	5008	,	,		17952	0.1558		0.331	False		,,,				2504	0.3047				p.T558T		Atlas-SNP	.											C17orf80,colon,carcinoma,+1,2	C17orf80	37	2	1	Substitution - coding silent(1)	stomach(1)	c.G1674T						PASS	.	G	,,	415,3991	206.5+/-228.1	18,379,1806	200.0	146.0	165.0		1566,1674,1674	-11.8	0.0	17	dbSNP_88	165	3138,5462	476.9+/-369.5	598,1942,1760	no	coding-synonymous,coding-synonymous,coding-synonymous	C17orf80	NM_001100621.1,NM_001100622.1,NM_017941.4	,,	616,2321,3566	TT,TG,GG		36.4884,9.419,27.3182	,,	522/574,558/584,558/610	71239087	3553,9453	2203	4300	6503	SO:0001819	synonymous_variant	55028	exon5			CATCACGATGCTC	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"""sperm-expressed protein 1"", ""migration-inducing protein 3"""					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.1674G>T	17.37:g.71239087G>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_017941	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Silent	SNP	ENST00000535032.2	37	CCDS11694.1																																																																																			G|0.750;T|0.250	0.250	strong		0.463	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941	
MST1L	11223	hgsc.bcm.edu	37	1	17085006	17085006	+	RNA	SNP	C	C	T	rs201784242	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17085006C>T	ENST00000455405.2	-	0	182							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CGGATGGCCCCCAGCCACGCG	0.607																																					p.G490E		Atlas-SNP	.											.	.	.	.	0			c.G1469A						PASS	.																																					11223	exon11			TGGCCCCCAGCCA	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085006C>T		Somatic	420	0	0		WXS	Illumina HiSeq	Phase_I	546	42	0.0769231	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	11.84	1.758278	0.31137	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (2);	0.000000	0.42964	D	0.000638	T	0.62636	0.2444	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.65524	-0.6147	6	0.35671	T	0.21	.	6.8326	0.23919	0.0:0.9999:0.0:1.0E-4	.	490;490	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	E	459;490;490	.	ENSP00000439273:G490E	G	-	2	0	MST1P9	16957593	0.982000	0.34865	0.000000	0.03702	0.000000	0.00434	2.313000	0.43735	-0.000000	0.14550	0.000000	0.15137	GGG	C|0.987;T|0.013	0.013	strong		0.607	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
SCRIB	23513	hgsc.bcm.edu	37	8	144895669	144895669	+	Silent	SNP	G	G	A	rs56748182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144895669G>A	ENST00000320476.3	-	5	480	c.474C>T	c.(472-474)ctC>ctT	p.L158L	MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000356994.2_Silent_p.L158L|SCRIB_ENST00000377533.3_Silent_p.L77L	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	158	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GGTTCTCCCGGAGCTCCAGGG	0.652													G|||	206	0.0411342	0.0106	0.0504	5008	,	,		18796	0.0248		0.0994	False		,,,				2504	0.0327				p.L158L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C474T						PASS	.	G	,	103,4303	79.3+/-117.8	3,97,2103	40.0	38.0	39.0		474,474	-3.9	1.0	8	dbSNP_129	39	783,7817	183.7+/-231.9	44,695,3561	no	coding-synonymous,coding-synonymous	SCRIB	NM_015356.3,NM_182706.3	,	47,792,5664	AA,AG,GG		9.1047,2.3377,6.8122	,	158/1631,158/1656	144895669	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	23513	exon5			CTCCCGGAGCTCC	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.474C>T	8.37:g.144895669G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1																																																																																			G|0.941;A|0.059	0.059	strong		0.652	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18435452	18435452	+	Missense_Mutation	SNP	C	C	T	rs11044004	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:18435452C>T	ENST00000266497.5	+	1	475	c.437C>T	c.(436-438)cCa>cTa	p.P146L	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.P146L|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.P146L|RERGL_ENST00000541632.1_Intron|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.P146L			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	146			P -> L (in dbSNP:rs11044004). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17991425, 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)				ATTTTAGCTCCATCATTCACA	0.343													.|||	1769	0.353235	0.3616	0.4078	5008	,	,		17858	0.3046		0.3917	False		,,,				2504	0.3139				p.P146L		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C437T	GRCh37	CM080496	PIK3C2G	M	rs11044004	PASS	.	C	LEU/PRO	1290,2336		230,830,753	59.0	60.0	60.0		437	3.9	0.0	12	dbSNP_120	60	3252,4892		633,1986,1453	yes	missense	PIK3C2G	NM_004570.4	98	863,2816,2206	TT,TC,CC		39.9312,35.5764,38.5896	benign	146/1446	18435452	4542,7228	1813	4072	5885	SO:0001583	missense	5288	exon2			TAGCTCCATCATT	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.437C>T	12.37:g.18435452C>T	ENSP00000266497:p.Pro146Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	751	0.34386446886446886	160	0.3252032520325203	130	0.35911602209944754	157	0.2744755244755245	304	0.40105540897097625	C	10.87	1.474091	0.26423	0.355764	0.399312	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.64085	1.22;-0.08;-0.08;-0.08	4.79	3.9	0.45041	.	3.153010	0.00559	N	0.000263	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.10296	0.003;0.002	B;B	0.13407	0.009;0.004	T	0.12656	-1.0539	9	0.23302	T	0.38	-0.9112	9.1747	0.37105	0.0:0.9038:0.0:0.0962	rs11044004;rs12822329;rs17475132;rs52825387;rs61288137;rs11044004	146;146	F5H369;O75747	.;P3C2G_HUMAN	L	146	ENSP00000443850:P146L;ENSP00000404845:P146L;ENSP00000266497:P146L;ENSP00000445381:P146L	ENSP00000266497:P146L	P	+	2	0	PIK3C2G	18326719	0.003000	0.15002	0.028000	0.17463	0.051000	0.14879	0.398000	0.20899	1.634000	0.50500	0.655000	0.94253	CCA	C|0.656;T|0.344	0.344	strong		0.343	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
KNSTRN	90417	hgsc.bcm.edu	37	15	40675443	40675443	+	Missense_Mutation	SNP	G	G	T	rs7169404	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:40675443G>T	ENST00000249776.8	+	2	339	c.224G>T	c.(223-225)cGc>cTc	p.R75L	KNSTRN_ENST00000448395.2_Missense_Mutation_p.R75L|KNSTRN_ENST00000416151.2_Missense_Mutation_p.R75L|KNSTRN_ENST00000608100.1_5'UTR	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein									p.R75L(1)									CAGCCGTGCCGCCTCGTTACG	0.662													G|||	224	0.0447284	0.0083	0.1081	5008	,	,		15189	0.0179		0.0974	False		,,,				2504	0.0225				p.R75L		Atlas-SNP	.											C15orf23,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.G224T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG	94,3866		2,90,1888	73.0	78.0	77.0		224,224,224	0.5	0.0	15	dbSNP_116	77	1001,7313		56,889,3212	yes	missense,missense,missense	C15orf23	NM_001142761.1,NM_001142762.1,NM_033286.3	102,102,102	58,979,5100	TT,TG,GG		12.0399,2.3737,8.9213	benign,benign,benign	75/287,75/242,75/317	40675443	1095,11179	1980	4157	6137	SO:0001583	missense	90417	exon2			CGTGCCGCCTCGT	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"""small kinetochore-associated protein"", ""kinetochore-localized astrin-binding protein"", ""TRAF4 associated factor 1"""	614718	"""chromosome 15 open reading frame 23"""	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.224G>T	15.37:g.40675443G>T	ENSP00000249776:p.Arg75Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_033286		Missense_Mutation	SNP	ENST00000249776.8	37	CCDS42021.1	126	0.057692307692307696	2	0.0040650406504065045	36	0.09944751381215469	12	0.02097902097902098	76	0.10026385224274406	G	16.97	3.268139	0.59540	0.023737	0.120399	ENSG00000128944	ENST00000249776;ENST00000416151;ENST00000448395	T;T;T	0.26067	1.76;1.76;1.76	4.71	0.511	0.16989	.	1.278600	0.05274	N	0.518125	T	0.00210	0.0006	L	0.29908	0.895	0.80722	P	0.0	B;P;B	0.35272	0.05;0.493;0.05	B;B;B	0.28232	0.061;0.087;0.061	T	0.17410	-1.0370	9	0.16420	T	0.52	-4.7812	4.2114	0.10514	0.2918:0.1708:0.5374:0.0	rs7169404;rs7169404	75;75;75	Q9Y448-2;Q9Y448-3;Q9Y448	.;.;T4AF1_HUMAN	L	75	ENSP00000249776:R75L;ENSP00000391233:R75L;ENSP00000393001:R75L	ENSP00000249776:R75L	R	+	2	0	C15orf23	38462735	0.000000	0.05858	0.029000	0.17559	0.345000	0.29048	-0.546000	0.06062	0.012000	0.14892	0.561000	0.74099	CGC	G|0.931;T|0.069	0.069	strong		0.662	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761	
NOP14	8602	hgsc.bcm.edu	37	4	2951804	2951804	+	Missense_Mutation	SNP	A	A	G	rs2515960	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2951804A>G	ENST00000314262.6	-	8	1187	c.1139T>C	c.(1138-1140)tTg>tCg	p.L380S	NOP14-AS1_ENST00000505731.1_RNA|NOP14_ENST00000502735.1_Missense_Mutation_p.L380S|NOP14_ENST00000416614.2_Missense_Mutation_p.L380S|NOP14_ENST00000398071.4_Missense_Mutation_p.L380S|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000503709.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	380			L -> S (in dbSNP:rs2515960). {ECO:0000269|Ref.2}.		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						TTCCAGGTCCAAGTGGCTATC	0.547													G|||	2041	0.407548	0.6815	0.415	5008	,	,		20210	0.1915		0.4433	False		,,,				2504	0.2178				p.L380S		Atlas-SNP	.											.	NOP14	69	.	0			c.T1139C						PASS	.	G	SER/LEU	2761,1645	505.2+/-366.1	862,1037,304	315.0	311.0	312.0		1139	5.4	1.0	4	dbSNP_100	312	3694,4906	621.0+/-397.1	826,2042,1432	yes	missense	NOP14	NM_003703.1	145	1688,3079,1736	GG,GA,AA		42.9535,37.3355,49.6309	benign	380/858	2951804	6455,6551	2203	4300	6503	SO:0001583	missense	8602	exon8			AGGTCCAAGTGGC	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.1139T>C	4.37:g.2951804A>G	ENSP00000315674:p.Leu380Ser	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	262	117	0.446565	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	925	0.42353479853479853	332	0.6747967479674797	153	0.42265193370165743	104	0.18181818181818182	336	0.44327176781002636	G	2.803	-0.248704	0.05867	0.626645	0.429535	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	5.43	5.43	0.79202	.	0.230549	0.37906	N	0.001898	T	0.00012	0.0000	N	0.00026	-2.66	0.41445	P	0.012051000000000034	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37384	-0.9708	9	0.87932	D	0	-5.1055	13.1764	0.59629	0.0771:0.0:0.9229:0.0	rs2515960;rs13126429;rs52813409;rs61659094;rs2515960	380;380	E9PFK5;P78316	.;NOP14_HUMAN	S	380;380;380;380;279	ENSP00000405068:L380S;ENSP00000315674:L380S;ENSP00000427415:L380S;ENSP00000381146:L380S	ENSP00000315674:L380S	L	-	2	0	NOP14	2921602	1.000000	0.71417	0.955000	0.39395	0.104000	0.19210	3.876000	0.56115	1.309000	0.44985	-0.119000	0.15052	TTG	A|0.537;G|0.463	0.463	strong		0.547	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703	
CHRD	8646	hgsc.bcm.edu	37	3	184103903	184103903	+	Missense_Mutation	SNP	A	A	C	rs16858780	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184103903A>C	ENST00000204604.1	+	15	2134	c.1888A>C	c.(1888-1890)Atg>Ctg	p.M630L	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_Missense_Mutation_p.M260L|CHRD_ENST00000450923.1_Missense_Mutation_p.M630L|CHRD_ENST00000348986.3_Missense_Mutation_p.M590L	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	630	CHRD 4. {ECO:0000255|PROSITE- ProRule:PRU00230}.		M -> L (in dbSNP:rs16858780). {ECO:0000269|PubMed:11472837, ECO:0000269|PubMed:9782094}.		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)			GGCCTCCCTGATGATCACCAC	0.632													C|||	1435	0.286542	0.3366	0.4121	5008	,	,		17107	0.3075		0.1511	False		,,,				2504	0.2474				p.M630L		Atlas-SNP	.											.	CHRD	149	.	0			c.A1888C						PASS	.	C	LEU/MET	1396,3010	688.8+/-405.0	242,912,1049	79.0	82.0	81.0		1888	1.1	1.0	3	dbSNP_123	81	1486,7114	749.1+/-407.4	121,1244,2935	yes	missense	CHRD	NM_003741.2	15	363,2156,3984	CC,CA,AA		17.2791,31.6841,22.159	benign	630/956	184103903	2882,10124	2203	4300	6503	SO:0001583	missense	8646	exon15			TCCCTGATGATCA	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.1888A>C	3.37:g.184103903A>C	ENSP00000204604:p.Met630Leu	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	239	119	0.497908	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	619	0.2834249084249084	171	0.3475609756097561	131	0.36187845303867405	203	0.3548951048951049	114	0.1503957783641161	C	0.068	-1.208173	0.01568	0.316841	0.172791	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	4.51	1.11	0.20524	CHRD (3);	0.072421	0.53938	N	0.000049	T	0.00012	0.0000	N	0.00729	-1.24	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	0.001;0.0;0.0;0.001	T	0.41716	-0.9493	9	0.02654	T	1	-7.8705	5.617	0.17436	0.1389:0.5637:0.0:0.2975	rs16858780;rs61045530;rs16858780	260;590;630;630	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	L	630;630;590;260;343	ENSP00000204604:M630L;ENSP00000408972:M630L;ENSP00000334036:M590L;ENSP00000442948:M260L	ENSP00000204604:M630L	M	+	1	0	CHRD	185586597	0.993000	0.37304	0.961000	0.40146	0.194000	0.23727	1.032000	0.30178	0.128000	0.18479	-0.121000	0.15023	ATG	A|0.751;C|0.249	0.249	strong		0.632	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39086836	39086836	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:39086836C>T	ENST00000297668.6	-	20	3304	c.3231G>A	c.(3229-3231)caG>caA	p.Q1077Q	CNTNAP3_ENST00000377656.2_Silent_p.Q996Q|CNTNAP3_ENST00000358144.2_Silent_p.Q989Q	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	1077	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TGTACCTAATCTGCAAACTTC	0.299																																					p.Q1077Q		Atlas-SNP	.											CNTNAP3,NS,malignant_melanoma,0,1	CNTNAP3	82	1	0			c.G3231A						scavenged	.						3.0	3.0	3.0					9																	39086836		1547	3315	4862	SO:0001819	synonymous_variant	79937	exon20			CCTAATCTGCAAA	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.3231G>A	9.37:g.39086836C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	274	2	0.00729927	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			.	.	none		0.299	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
RELL2	285613	hgsc.bcm.edu	37	5	141019110	141019110	+	Missense_Mutation	SNP	C	C	A	rs14251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:141019110C>A	ENST00000297164.3	+	4	1597	c.397C>A	c.(397-399)Ctc>Atc	p.L133I	FCHSD1_ENST00000435817.2_3'UTR|RELL2_ENST00000444782.1_Missense_Mutation_p.L133I|HDAC3_ENST00000305264.3_5'Flank|RELL2_ENST00000521367.1_Missense_Mutation_p.L67I|RELL2_ENST00000518856.1_Missense_Mutation_p.L67I|RELL2_ENST00000518025.1_3'UTR|FCHSD1_ENST00000523856.1_5'UTR	NM_173828.4	NP_776189.3	Q8NC24	RELL2_HUMAN	RELT-like 2	133			L -> I (in dbSNP:rs14251). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCCCTTGCCTCCATTGCAG	0.642													A|||	1991	0.397564	0.5772	0.379	5008	,	,		14976	0.1637		0.3807	False		,,,				2504	0.4264				p.L133I		Atlas-SNP	.											.	RELL2	24	.	0			c.C397A						PASS	.	A	ILE/LEU,,ILE/LEU	2265,2141	571.5+/-383.1	599,1067,537	43.0	45.0	44.0		397,,397	5.7	1.0	5	dbSNP_52	44	3593,5007	617.7+/-396.7	771,2051,1478	yes	missense,utr-3,missense	FCHSD1,RELL2	NM_001130029.1,NM_033449.2,NM_173828.4	5,,5	1370,3118,2015	AA,AC,CC		41.7791,48.5928,45.0408	benign,,benign	133/304,,133/304	141019110	5858,7148	2203	4300	6503	SO:0001583	missense	285613	exon4			CCTTGCCTCCATT	AK054889	CCDS4265.1	5q31.3	2011-10-11	2007-06-15	2007-06-15	ENSG00000164620	ENSG00000164620			26902	protein-coding gene	gene with protein product		611213	"""chromosome 5 open reading frame 16"""	C5orf16		12975309, 16389068	Standard	NM_173828		Approved	FLJ90583	uc003lli.3	Q8NC24	OTTHUMG00000129612	ENST00000297164.3:c.397C>A	5.37:g.141019110C>A	ENSP00000297164:p.Leu133Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_173828	D3DQE2|Q6P4E7|Q6UXY2	Missense_Mutation	SNP	ENST00000297164.3	37	CCDS4265.1	817	0.3740842490842491	295	0.5995934959349594	144	0.39779005524861877	89	0.1555944055944056	289	0.3812664907651715	A	5.924	0.354549	0.11239	0.514072	0.417791	ENSG00000164620	ENST00000444782;ENST00000521367;ENST00000297164;ENST00000518856	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.7	5.7	0.88788	.	0.064449	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00436	-1.5	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44787	-0.9305	9	0.02654	T	1	-5.8058	12.8604	0.57910	0.8636:0.1364:0.0:0.0	rs14251;rs251179;rs3191867;rs17855846;rs14251	67;133	E5RHA7;Q8NC24	.;RELL2_HUMAN	I	133;67;133;67	ENSP00000409443:L133I;ENSP00000430948:L67I;ENSP00000297164:L133I;ENSP00000427992:L67I	ENSP00000297164:L133I	L	+	1	0	RELL2	140999294	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.514000	0.53422	0.990000	0.38787	-0.256000	0.11100	CTC	C|0.567;A|0.433	0.433	strong		0.642	RELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251807.2	NM_173828	
CCDC176	80127	hgsc.bcm.edu	37	14	74516497	74516497	+	Silent	SNP	G	G	A	rs34076068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74516497G>A	ENST00000394009.3	+	8	1008	c.885G>A	c.(883-885)ttG>ttA	p.L295L	CCDC176_ENST00000553773.1_Silent_p.L20L|AC005484.5_ENST00000492026.1_RNA	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	295					motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											TAGTAAACTTGGAGACTGCTC	0.398													G|||	480	0.0958466	0.0076	0.232	5008	,	,		21736	0.0873		0.1312	False		,,,				2504	0.091				p.L295L		Atlas-SNP	.											.	.	.	.	0			c.G885A						PASS	.	G		145,4261	95.7+/-134.4	3,139,2061	60.0	61.0	60.0		885	4.9	1.0	14	dbSNP_126	60	1266,7332	245.6+/-274.3	82,1102,3115	no	coding-synonymous	C14orf45	NM_025057.2		85,1241,5176	AA,AG,GG		14.7244,3.291,10.8505		295/530	74516497	1411,11593	2203	4299	6502	SO:0001819	synonymous_variant	80127	exon8			AAACTTGGAGACT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.885G>A	14.37:g.74516497G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_025057	Q0P604|Q9H5P8	Silent	SNP	ENST00000394009.3	37	CCDS32119.2																																																																																			G|0.885;A|0.115	0.115	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
CENPF	1063	hgsc.bcm.edu	37	1	214819587	214819587	+	Missense_Mutation	SNP	A	A	G	rs12058704	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214819587A>G	ENST00000366955.3	+	13	6842	c.6674A>G	c.(6673-6675)cAg>cGg	p.Q2225R		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2321	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)		AAACAAGGTCAGTTGTCAGAA	0.358													A|||	532	0.10623	0.1089	0.1066	5008	,	,		19949	0.1151		0.0507	False		,,,				2504	0.1503				p.Q2225R	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A6674G						PASS	.	A	ARG/GLN	428,3974		21,386,1794	50.0	56.0	54.0		6674	-0.1	0.0	1	dbSNP_120	54	463,8137		12,439,3849	yes	missense	CENPF	NM_016343.3	43	33,825,5643	GG,GA,AA		5.3837,9.7229,6.8528	benign	2225/3115	214819587	891,12111	2201	4300	6501	SO:0001583	missense	1063	exon13			AAGGTCAGTTGTC	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.6674A>G	1.37:g.214819587A>G	ENSP00000355922:p.Gln2225Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	137	55	0.40146	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	223	0.1021062271062271	64	0.13008130081300814	40	0.11049723756906077	77	0.1346153846153846	42	0.055408970976253295	A	0.061	-1.223724	0.01530	0.097229	0.053837	ENSG00000117724	ENST00000366955	T	0.37411	1.2	4.8	-0.141	0.13452	Centromere protein Cenp-F, leucine-rich repeat-containing domain (1);	0.502121	0.14965	N	0.288149	T	0.00109	0.0003	N	0.01874	-0.695	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.34004	-0.9846	9	0.09338	T	0.73	.	8.0441	0.30538	0.6361:0.0:0.3639:0.0	rs12058704;rs52816125;rs12058704	2321	P49454	CENPF_HUMAN	R	2225	ENSP00000355922:Q2225R	ENSP00000355922:Q2225R	Q	+	2	0	CENPF	212886210	0.001000	0.12720	0.001000	0.08648	0.017000	0.09413	0.830000	0.27462	0.051000	0.15978	0.421000	0.28195	CAG	A|0.915;G|0.085	0.085	strong		0.358	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
CTTN	2017	hgsc.bcm.edu	37	11	70279766	70279766	+	Silent	SNP	C	C	T	rs643301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:70279766C>T	ENST00000301843.8	+	17	1664	c.1458C>T	c.(1456-1458)taC>taT	p.Y486Y	CTTN_ENST00000538675.1_Silent_p.Y170Y|CTTN_ENST00000376561.3_Silent_p.Y449Y|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	137	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	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	
LAMA1	284217	hgsc.bcm.edu	37	18	6999628	6999628	+	Silent	SNP	T	T	C	rs625106	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:6999628T>C	ENST00000389658.3	-	32	4572	c.4479A>G	c.(4477-4479)tcA>tcG	p.S1493S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1493	Laminin EGF-like 16. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CATAATAGCTTGAGGAGCACC	0.517													C|||	2335	0.466254	0.7806	0.3112	5008	,	,		19207	0.2708		0.4215	False		,,,				2504	0.3988				p.S1493S		Atlas-SNP	.											.	LAMA1	458	.	0			c.A4479G						PASS	.	C		3030,1376	450.6+/-349.4	1044,942,217	46.0	38.0	40.0		4479	-11.5	0.0	18	dbSNP_83	40	3761,4839	608.2+/-395.4	837,2087,1376	no	coding-synonymous	LAMA1	NM_005559.3		1881,3029,1593	CC,CT,TT		43.7326,31.2301,47.7856		1493/3076	6999628	6791,6215	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon32			ATAGCTTGAGGAG	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.4479A>G	18.37:g.6999628T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			T|0.500;C|0.500	0.500	strong		0.517	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
OR51E1	143503	hgsc.bcm.edu	37	11	4673788	4673788	+	Missense_Mutation	SNP	G	G	A	rs17224476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4673788G>A	ENST00000530215.1	+	1	73	c.32G>A	c.(31-33)aGt>aAt	p.S11N	OR51E1_ENST00000396952.5_Missense_Mutation_p.S11N			Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	10						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(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		AATGAATCCAGTGCTACATAC	0.493													G|||	242	0.0483227	0.0053	0.0749	5008	,	,		22108	0.002		0.1173	False		,,,				2504	0.0644				p.S11N		Atlas-SNP	.											.	OR51E1	67	.	0			c.G32A						PASS	.	G	ASN/SER	115,4287	86.3+/-125.0	6,103,2092	256.0	188.0	211.0		32	3.8	1.0	11	dbSNP_123	211	985,7611	213.8+/-253.6	66,853,3379	yes	missense	OR51E1	NM_152430.3	46	72,956,5471	AA,AG,GG		11.4588,2.6124,8.4628	benign	11/319	4673788	1100,11898	2201	4298	6499	SO:0001583	missense	143503	exon2			AATCCAGTGCTAC	AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"""GPCR / Class A : Olfactory receptors"""	15194	protein-coding gene	gene with protein product		611267	"""olfactory receptor, family 51, subfamily E, member 1 pseudogene"""	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000530215.1:c.32G>A	11.37:g.4673788G>A	ENSP00000431593:p.Ser11Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_152430	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000530215.1	37		125	0.05723443223443223	0	0.0	36	0.09944751381215469	1	0.0017482517482517483	88	0.11609498680738786	G	2.852	-0.238008	0.05944	0.026124	0.114588	ENSG00000180785	ENST00000396952;ENST00000530215	T;T	0.00520	6.85;6.85	4.74	3.83	0.44106	.	0.284144	0.29814	N	0.011134	T	0.00012	0.0000	L	0.37800	1.135	0.33231	P	0.44412700000000005	B	0.25272	0.122	B	0.20384	0.029	T	0.51741	-0.8667	9	0.28530	T	0.3	.	11.6531	0.51301	0.0871:0.0:0.9129:0.0	rs17224476;rs52821343;rs61396409;rs17224476	10	Q8TCB6	O51E1_HUMAN	N	11	ENSP00000380155:S11N;ENSP00000431593:S11N	ENSP00000380155:S11N	S	+	2	0	OR51E1	4630364	0.086000	0.21541	1.000000	0.80357	0.255000	0.26057	1.200000	0.32247	1.224000	0.43551	0.563000	0.77884	AGT	G|0.926;A|0.074	0.074	strong		0.493	OR51E1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000385957.1	NM_152430	
PM20D1	148811	hgsc.bcm.edu	37	1	205819039	205819039	+	Silent	SNP	C	C	T	rs11540016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205819039C>T	ENST00000367136.4	-	1	206	c.162G>A	c.(160-162)gcG>gcA	p.A54A	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	54					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)			CACCTTTCAGCGCCTCTTTCA	0.617													C|||	802	0.160144	0.053	0.0605	5008	,	,		17728	0.4246		0.0964	False		,,,				2504	0.1687				p.A54A		Atlas-SNP	.											.	PM20D1	56	.	0			c.G162A						PASS	.	C		265,4141	149.9+/-184.0	8,249,1946	78.0	86.0	83.0		162	-1.3	1.0	1	dbSNP_120	83	647,7953	165.7+/-217.8	20,607,3673	no	coding-synonymous	PM20D1	NM_152491.4		28,856,5619	TT,TC,CC		7.5233,6.0145,7.0121		54/503	205819039	912,12094	2203	4300	6503	SO:0001819	synonymous_variant	148811	exon1			TTTCAGCGCCTCT		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.162G>A	1.37:g.205819039C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_152491	Q6P4E3|Q96DM4	Silent	SNP	ENST00000367136.4	37	CCDS1460.1																																																																																			C|0.902;T|0.098	0.098	strong		0.617	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
FGFRL1	53834	hgsc.bcm.edu	37	4	1018271	1018271	+	Silent	SNP	T	T	C	rs4647946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:1018271T>C	ENST00000398484.2	+	7	1471	c.891T>C	c.(889-891)gaT>gaC	p.D297D	FGFRL1_ENST00000510644.1_Silent_p.D297D|FGFRL1_ENST00000264748.6_Silent_p.D297D|FGFRL1_ENST00000504138.1_Silent_p.D297D			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	297	Ig-like C2-type 3.				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)			CCACCATCGATGTGGGCGGCC	0.662													t|||	193	0.0385383	0.0068	0.0331	5008	,	,		10542	0.1012		0.0447	False		,,,				2504	0.0143				p.D297D		Atlas-SNP	.											FGFRL1_ENST00000542622,NS,carcinoma,0,2	FGFRL1	77	2	0			c.T891C						PASS	.		,,	66,4338	62.3+/-99.4	1,64,2137	48.0	49.0	49.0		891,891,891	-3.6	0.8	4	dbSNP_111	49	363,8233	116.8+/-176.5	5,353,3940	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	,,	6,417,6077	CC,CT,TT		4.2229,1.4986,3.3	,,	297/505,297/505,297/505	1018271	429,12571	2202	4298	6500	SO:0001819	synonymous_variant	53834	exon6			CATCGATGTGGGC		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.891T>C	4.37:g.1018271T>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	149	58	0.389262	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Silent	SNP	ENST00000398484.2	37	CCDS3344.1																																																																																			T|0.965;C|0.035	0.035	strong		0.662	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	
KDM5B	10765	hgsc.bcm.edu	37	1	202715284	202715284	+	Silent	SNP	G	G	A	rs1141108	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:202715284G>A	ENST00000367265.3	-	15	3348	c.2184C>T	c.(2182-2184)taC>taT	p.Y728Y	KDM5B_ENST00000367264.2_Silent_p.Y764Y	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	728					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						ATTTATATTTGTAAGGAGGAC	0.393													A|||	3201	0.639177	0.3222	0.8343	5008	,	,		20178	0.7837		0.7714	False		,,,				2504	0.6442				p.Y728Y		Atlas-SNP	.											.	KDM5B	166	.	0			c.C2184T						PASS	.	A		1658,2748	657.2+/-400.2	319,1020,864	110.0	96.0	101.0		2184	0.8	0.9	1	dbSNP_86	101	6687,1913	338.1+/-322.6	2613,1461,226	no	coding-synonymous	KDM5B	NM_006618.3		2932,2481,1090	AA,AG,GG		22.2442,37.6305,35.8373		728/1545	202715284	8345,4661	2203	4300	6503	SO:0001819	synonymous_variant	10765	exon15			ATATTTGTAAGGA	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.2184C>T	1.37:g.202715284G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_006618	O95811|Q15752|Q9Y3Q5	Silent	SNP	ENST00000367265.3	37	CCDS30974.1																																																																																			G|0.346;A|0.654	0.654	strong		0.393	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
MARCO	8685	hgsc.bcm.edu	37	2	119739063	119739063	+	Missense_Mutation	SNP	T	T	C	rs6761637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	64	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	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	
GATA2	2624	hgsc.bcm.edu	37	3	128204960	128204960	+	Missense_Mutation	SNP	G	G	C	rs34799090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:128204960G>C	ENST00000341105.2	-	3	812	c.481C>G	c.(481-483)Cct>Gct	p.P161A	GATA2_ENST00000487848.1_Missense_Mutation_p.P161A|GATA2_ENST00000430265.2_Missense_Mutation_p.P161A	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	161					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)		GCTGCTGTAGGGGTGAGGGAG	0.687			Mis		AML(CML blast transformation)								G|||	8	0.00159744	0.0008	0.0043	5008	,	,		13302	0.0		0.003	False		,,,				2504	0.001				p.P161A		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	GATA2	122	.	0			c.C481G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO	14,4392	21.2+/-45.6	0,14,2189	38.0	36.0	36.0		481,481,481	4.5	1.0	3	dbSNP_126	36	108,8492	52.3+/-112.8	0,108,4192	yes	missense,missense,missense	GATA2	NM_001145661.1,NM_001145662.1,NM_032638.4	27,27,27	0,122,6381	CC,CG,GG		1.2558,0.3177,0.938	probably-damaging,probably-damaging,probably-damaging	161/481,161/467,161/481	128204960	122,12884	2203	4300	6503	SO:0001583	missense	2624	exon3			CTGTAGGGGTGAG	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.481C>G	3.37:g.128204960G>C	ENSP00000345681:p.Pro161Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	129	76	0.589147	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	12.68	2.010340	0.35511	0.003177	0.012558	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97114	-4.25;-4.23;-4.25	4.46	4.46	0.54185	.	0.568431	0.17408	N	0.175271	D	0.93864	0.8037	N	0.08118	0	0.48452	D	0.999652	D;B	0.76494	0.999;0.03	D;B	0.83275	0.996;0.014	D	0.91294	0.5061	10	0.08599	T	0.76	-26.4928	16.6918	0.85323	0.0:0.0:1.0:0.0	rs34799090	161;161	P23769-2;P23769	.;GATA2_HUMAN	A	161	ENSP00000345681:P161A;ENSP00000400259:P161A;ENSP00000417074:P161A	ENSP00000345681:P161A	P	-	1	0	GATA2	129687650	1.000000	0.71417	0.988000	0.46212	0.945000	0.59286	5.112000	0.64634	2.022000	0.59522	0.484000	0.47621	CCT	G|0.992;C|0.008	0.008	strong		0.687	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	
MYO16	23026	hgsc.bcm.edu	37	13	109793246	109793246	+	Silent	SNP	G	G	C	rs80260507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:109793246G>C	ENST00000357550.2	+	31	4661	c.4620G>C	c.(4618-4620)ccG>ccC	p.P1540P	MYO16_ENST00000356711.2_Silent_p.P1540P	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CGCTGTCCCCGCAGTACTCCA	0.711													G|||	231	0.0461262	0.0272	0.0648	5008	,	,		5556	0.0		0.1083	False		,,,				2504	0.0419				p.P1562P		Atlas-SNP	.											MYO16,NS,carcinoma,0,2	MYO16	285	2	0			c.G4686C						PASS	.	G	,	129,4247		2,125,2061	16.0	20.0	18.0		4686,4620	-7.8	0.0	13	dbSNP_131	18	799,7773		42,715,3529	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	44,840,5590	CC,CG,GG		9.321,2.9479,7.1671	,	1562/1881,1540/1859	109793246	928,12020	2188	4286	6474	SO:0001819	synonymous_variant	23026	exon32			GTCCCCGCAGTAC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4620G>C	13.37:g.109793246G>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			G|0.933;C|0.067	0.067	strong		0.711	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
SLC45A4	57210	hgsc.bcm.edu	37	8	142222374	142222374	+	Silent	SNP	A	A	G	rs7017848	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:142222374A>G	ENST00000024061.3	-	7	2377	c.2070T>C	c.(2068-2070)ggT>ggC	p.G690G	SLC45A4_ENST00000519067.1_Silent_p.G690G|SLC45A4_ENST00000433583.2_Silent_p.G683G|SLC45A4_ENST00000517878.1_Silent_p.G741G	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)			CGCTGTTCCCACCGGCCCTGC	0.632													G|||	3438	0.686502	0.7542	0.5764	5008	,	,		10865	0.8036		0.5905	False		,,,				2504	0.6513				p.G690G		Atlas-SNP	.											.	SLC45A4	71	.	0			c.T2070C						PASS	.	G		3360,1042	370.5+/-319.6	1298,764,139	36.0	33.0	34.0		2070	-8.4	0.0	8	dbSNP_116	34	4889,3711	521.9+/-380.0	1389,2111,800	no	coding-synonymous	SLC45A4	NM_001080431.1		2687,2875,939	GG,GA,AA		43.1512,23.6711,36.5559		690/799	142222374	8249,4753	2201	4300	6501	SO:0001819	synonymous_variant	57210	exon7			GTTCCCACCGGCC	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.2070T>C	8.37:g.142222374A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	37	CCDS34948.1																																																																																			A|0.359;G|0.641	0.641	strong		0.632	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
CDC27	996	hgsc.bcm.edu	37	17	45234367	45234367	+	Missense_Mutation	SNP	A	A	T	rs200148949		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45234367A>T	ENST00000066544.3	-	7	847	c.754T>A	c.(754-756)Tcc>Acc	p.S252T	CDC27_ENST00000527547.1_Missense_Mutation_p.S252T|CDC27_ENST00000446365.2_Missense_Mutation_p.S191T|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Missense_Mutation_p.S252T	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	252					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.S252T(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						GATAATATGGAAGTTCCTGTT	0.383																																					p.S252T		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,4	CDC27	337	4	3	Substitution - Missense(3)	prostate(3)	c.T754A						scavenged	.						54.0	60.0	58.0					17																	45234367		2197	4295	6492	SO:0001583	missense	996	exon7			ATATGGAAGTTCC	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.754T>A	17.37:g.45234367A>T	ENSP00000066544:p.Ser252Thr	Somatic	62	1	0.016129		WXS	Illumina HiSeq	Phase_I	60	8	0.133333	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	11.88	1.770710	0.31320	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.26;0.01;-0.31;0.83	5.44	2.92	0.33932	.	0.295461	0.32687	N	0.005769	T	0.46425	0.1392	N	0.24115	0.695	0.34835	D	0.740078	B;B;B;B	0.09022	0.002;0.001;0.001;0.0	B;B;B;B	0.08055	0.001;0.003;0.002;0.001	T	0.45702	-0.9243	10	0.19590	T	0.45	-13.824	7.977	0.30161	0.7316:0.1283:0.0:0.1401	.	191;252;252;252	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	T	252;252;191;252;252	ENSP00000066544:S252T;ENSP00000434614:S252T;ENSP00000392802:S191T;ENSP00000437339:S252T;ENSP00000432105:S252T	ENSP00000066544:S252T	S	-	1	0	CDC27	42589366	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	2.784000	0.47774	0.864000	0.35578	0.377000	0.23210	TCC	.	.	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
C1orf87	127795	hgsc.bcm.edu	37	1	60505783	60505783	+	Missense_Mutation	SNP	G	G	C	rs12737449	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:60505783G>C	ENST00000371201.3	-	5	660	c.553C>G	c.(553-555)Ctc>Gtc	p.L185V	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	185			L -> V (in dbSNP:rs12737449).				calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						CGTGACTTGAGTTCTCTTCTG	0.428													G|||	595	0.11881	0.031	0.1974	5008	,	,		19254	0.2192		0.1252	False		,,,				2504	0.0716				p.L185V	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.C553G						PASS	.	G	VAL/LEU	189,4217	123.7+/-161.0	4,181,2018	99.0	108.0	105.0		553	3.2	1.0	1	dbSNP_121	105	1250,7350	249.9+/-277.0	105,1040,3155	yes	missense	C1orf87	NM_152377.2	32	109,1221,5173	CC,CG,GG		14.5349,4.2896,11.0641	possibly-damaging	185/547	60505783	1439,11567	2203	4300	6503	SO:0001583	missense	127795	exon5			ACTTGAGTTCTCT	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"""carcinoma-related EF-hand protein"""					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.553C>G	1.37:g.60505783G>C	ENSP00000360244:p.Leu185Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_152377	Q6ZU07|Q8IVS0	Missense_Mutation	SNP	ENST00000371201.3	37	CCDS614.1	329	0.15064102564102563	30	0.06097560975609756	72	0.19889502762430938	115	0.20104895104895104	112	0.14775725593667546	G	10.05	1.244424	0.22796	0.042896	0.145349	ENSG00000162598	ENST00000371201	T	0.27402	1.67	5.18	3.18	0.36537	.	0.139058	0.33457	N	0.004884	T	0.00039	0.0001	L	0.59436	1.845	0.09310	P	0.999999999762251	D	0.56035	0.974	P	0.54499	0.754	T	0.05146	-1.0903	9	0.54805	T	0.06	-4.5613	8.6836	0.34223	0.1995:0.0:0.8005:0.0	rs12737449;rs52823537;rs12737449	185	Q8N0U7	CA087_HUMAN	V	185	ENSP00000360244:L185V	ENSP00000360244:L185V	L	-	1	0	C1orf87	60278371	1.000000	0.71417	0.997000	0.53966	0.209000	0.24338	1.686000	0.37669	1.433000	0.47394	0.650000	0.86243	CTC	G|0.875;C|0.125	0.125	strong		0.428	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	
PRSS55	203074	hgsc.bcm.edu	37	8	10396056	10396056	+	Missense_Mutation	SNP	G	G	C	rs61743179	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10396056G>C	ENST00000328655.3	+	5	852	c.812G>C	c.(811-813)aGc>aCc	p.S271T	PRSS55_ENST00000522210.1_Intron|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	271	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						GGCATCATAAGCTGGGGAAAG	0.577													G|||	342	0.0682907	0.1808	0.0504	5008	,	,		17440	0.001		0.0616	False		,,,				2504	0.0051				p.S271T		Atlas-SNP	.											.	PRSS55	67	.	0			c.G812C						PASS	.	G	,THR/SER	811,3595	325.0+/-298.9	70,671,1462	90.0	97.0	94.0		,812	4.2	1.0	8	dbSNP_129	94	539,8061	149.1+/-204.2	15,509,3776	no	intron,missense	PRSS55	NM_001197020.1,NM_198464.3	,58	85,1180,5238	CC,CG,GG		6.2674,18.4067,10.3798	,probably-damaging	,271/353	10396056	1350,11656	2203	4300	6503	SO:0001583	missense	203074	exon5			TCATAAGCTGGGG	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.812G>C	8.37:g.10396056G>C	ENSP00000333003:p.Ser271Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_198464	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	138	0.06318681318681318	74	0.15040650406504066	17	0.04696132596685083	1	0.0017482517482517483	46	0.06068601583113457	G	18.85	3.711347	0.68730	0.184067	0.062674	ENSG00000184647	ENST00000328655	D	0.96136	-3.92	4.2	4.2	0.49525	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41605	D	0.000852	T	0.09642	0.0237	M	0.86573	2.825	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.00747	-1.1583	9	0.87932	D	0	.	12.2115	0.54381	0.0:0.0:1.0:0.0	rs61743179	271	Q6UWB4	PRS55_HUMAN	T	271	ENSP00000333003:S271T	ENSP00000333003:S271T	S	+	2	0	PRSS55	10433466	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	6.673000	0.74482	2.324000	0.78689	0.655000	0.94253	AGC	G|0.909;C|0.091	0.091	strong		0.577	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
C20orf85	128602	hgsc.bcm.edu	37	20	56735759	56735759	+	Missense_Mutation	SNP	A	A	G	rs17440813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:56735759A>G	ENST00000371168.3	+	4	356	c.295A>G	c.(295-297)Atc>Gtc	p.I99V		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	99			I -> V (in dbSNP:rs17440813).							kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)			CCAGGGCTTCATCGGCTGGAG	0.577													A|||	328	0.0654952	0.0582	0.1153	5008	,	,		18955	0.0258		0.0716	False		,,,				2504	0.0746				p.I99V		Atlas-SNP	.											.	C20orf85	35	.	0			c.A295G						PASS	.	A	VAL/ILE	254,4152	144.2+/-179.2	6,242,1955	46.0	40.0	42.0		295	5.4	1.0	20	dbSNP_123	42	629,7971	161.6+/-214.5	21,587,3692	yes	missense	C20orf85	NM_178456.2	29	27,829,5647	GG,GA,AA		7.314,5.7649,6.7892	benign	99/138	56735759	883,12123	2203	4300	6503	SO:0001583	missense	128602	exon4			GGCTTCATCGGCT	AL354776	CCDS13465.1	20q13.32	2012-10-29			ENSG00000124237	ENSG00000124237			16216	protein-coding gene	gene with protein product	"""Low in Lung Cancer 1"""						Standard	NM_178456		Approved	bA196N14.1, LLC1	uc002xyv.3	Q9H1P6	OTTHUMG00000032836	ENST00000371168.3:c.295A>G	20.37:g.56735759A>G	ENSP00000360210:p.Ile99Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_178456		Missense_Mutation	SNP	ENST00000371168.3	37	CCDS13465.1	132	0.06043956043956044	22	0.044715447154471545	45	0.12430939226519337	14	0.024475524475524476	51	0.06728232189973615	A	18.73	3.685669	0.68157	0.057649	0.07314	ENSG00000124237	ENST00000371168	T	0.29917	1.55	5.43	5.43	0.79202	.	0.075461	0.56097	D	0.000034	T	0.00815	0.0027	L	0.47716	1.5	0.40966	D	0.984661	D	0.61697	0.99	D	0.75484	0.986	T	0.00265	-1.1865	10	0.30078	T	0.28	-5.9236	13.7259	0.62759	1.0:0.0:0.0:0.0	rs17440813;rs56521958;rs17440813	99	Q9H1P6	CT085_HUMAN	V	99	ENSP00000360210:I99V	ENSP00000360210:I99V	I	+	1	0	C20orf85	56169165	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.793000	0.69060	2.072000	0.62099	0.459000	0.35465	ATC	A|0.936;G|0.064	0.064	strong		0.577	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456	
ASPM	259266	hgsc.bcm.edu	37	1	197070442	197070442	+	Missense_Mutation	SNP	G	G	T	rs3762271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:197070442G>T	ENST00000367409.4	-	18	8195	c.7939C>A	c.(7939-7941)Ctt>Att	p.L2647I	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2647	IQ 28. {ECO:0000255|PROSITE- ProRule:PRU00116}.		L -> I (in dbSNP:rs3762271). {ECO:0000269|PubMed:14574646, ECO:0000269|PubMed:18204051}.		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						GTTGCTCTAAGGTGGAGATAA	0.363													G|||	1073	0.214257	0.0431	0.2277	5008	,	,		18268	0.1637		0.4105	False		,,,				2504	0.2863				p.L2647I		Atlas-SNP	.											.	ASPM	444	.	0			c.C7939A						PASS	.	G	,ILE/LEU	460,3942	214.5+/-233.7	27,406,1768	66.0	60.0	62.0		,7939	-1.3	0.0	1	dbSNP_107	62	3737,4859	528.1+/-381.3	816,2105,1377	yes	intron,missense	ASPM	NM_001206846.1,NM_018136.4	,5	843,2511,3145	TT,TG,GG		43.4737,10.4498,32.2896	,possibly-damaging	,2647/3478	197070442	4197,8801	2201	4298	6499	SO:0001583	missense	259266	exon18			CTCTAAGGTGGAG	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.7939C>A	1.37:g.197070442G>T	ENSP00000356379:p.Leu2647Ile	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	536	0.2454212454212454	20	0.04065040650406504	101	0.27900552486187846	98	0.17132867132867133	317	0.4182058047493404	G	6.569	0.473256	0.12461	0.104498	0.434737	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.74315	-0.83	4.72	-1.27	0.09347	.	0.800098	0.11415	N	0.566379	T	0.00012	0.0000	L	0.59436	1.845	0.35493	P	0.20087	D;D	0.63046	0.989;0.992	D;P	0.74348	0.983;0.88	T	0.30297	-0.9983	9	0.40728	T	0.16	.	9.5274	0.39173	0.4285:0.0:0.5715:0.0	rs3762271;rs52822679;rs60619702;rs3762271	633;2647	E7EQ84;Q8IZT6	.;ASPM_HUMAN	I	2647;633	ENSP00000356379:L2647I	ENSP00000356376:L633I	L	-	1	0	ASPM	195337065	0.237000	0.23815	0.003000	0.11579	0.172000	0.22775	0.277000	0.18734	-0.167000	0.10871	0.557000	0.71058	CTT	G|0.722;T|0.278	0.278	strong		0.363	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
BDP1	55814	hgsc.bcm.edu	37	5	70858194	70858194	+	Silent	SNP	C	C	T	rs277941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	120	0	0		WXS	Illumina HiSeq	Phase_I	84	81	0.964286	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	
MPEG1	219972	hgsc.bcm.edu	37	11	58978434	58978434	+	Silent	SNP	C	C	A	rs180770562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58978434C>A	ENST00000361050.3	-	1	1990	c.1905G>T	c.(1903-1905)ccG>ccT	p.P635P		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	635						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				GCAGCTCTATCGGTTCTCCCA	0.567													C|||	10	0.00199681	0.0023	0.0014	5008	,	,		17979	0.0		0.005	False		,,,				2504	0.001				p.P635P		Atlas-SNP	.											.	MPEG1	72	.	0			c.G1905T						PASS	.	C		7,3897		0,7,1945	95.0	104.0	101.0		1905	-11.4	0.0	11	dbSNP_134	101	66,8194		0,66,4064	no	coding-synonymous	MPEG1	NM_001039396.1		0,73,6009	AA,AC,CC		0.799,0.1793,0.6001		635/717	58978434	73,12091	1952	4130	6082	SO:0001819	synonymous_variant	219972	exon1			CTCTATCGGTTCT	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1905G>T	11.37:g.58978434C>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			C|0.996;A|0.004	0.004	strong		0.567	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
DENND3	22898	hgsc.bcm.edu	37	8	142204326	142204326	+	Silent	SNP	C	C	G	rs1045248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:142204326C>G	ENST00000262585.2	+	23	3869	c.3591C>G	c.(3589-3591)ggC>ggG	p.G1197G	DENND3_ENST00000519811.1_Silent_p.G1277G|DENND3_ENST00000523308.1_Silent_p.G247G|DENND3_ENST00000424248.1_Silent_p.G1145G	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	1197					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)			TTTGGAAAGGCGAATAAACGT	0.617													G|||	2563	0.511781	0.4713	0.4625	5008	,	,		19319	0.6627		0.4085	False		,,,				2504	0.5521				p.G1197G		Atlas-SNP	.											.	DENND3	127	.	0			c.C3591G						PASS	.	G		2180,2226	582.3+/-385.5	540,1100,563	56.0	50.0	52.0		3591	-5.1	0.0	8	dbSNP_86	52	3283,5315	636.1+/-399.1	642,1999,1658	no	coding-synonymous	DENND3	NM_014957.2		1182,3099,2221	GG,GC,CC		38.1833,49.478,42.0102		1197/1199	142204326	5463,7541	2203	4299	6502	SO:0001819	synonymous_variant	22898	exon23			GAAAGGCGAATAA	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.3591C>G	8.37:g.142204326C>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	40	26	0.65	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	37	CCDS34947.1	1101	0.5041208791208791	236	0.4796747967479675	184	0.5082872928176796	386	0.6748251748251748	295	0.3891820580474934	G	0.178	-1.064887	0.01934	0.49478	0.381833	ENSG00000105339	ENST00000518668	.	.	.	5.29	-5.14	0.02875	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41963	-0.9479	3	.	.	.	-22.9582	2.163	0.03829	0.147:0.3307:0.2613:0.261	rs1045248;rs3185128;rs3739225;rs1045248	.	.	.	G	1202	.	.	R	+	1	2	DENND3	142273508	0.000000	0.05858	0.013000	0.15412	0.005000	0.04900	-3.114000	0.00598	-1.350000	0.02199	-2.316000	0.00254	CGA	C|0.550;G|0.450	0.450	strong		0.617	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
KDM3A	55818	hgsc.bcm.edu	37	2	86693826	86693826	+	Missense_Mutation	SNP	T	T	C	rs34605051	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:86693826T>C	ENST00000409556.1	+	11	1704	c.1339T>C	c.(1339-1341)Tcg>Ccg	p.S447P	KDM3A_ENST00000542128.1_Missense_Mutation_p.S395P|KDM3A_ENST00000409064.1_Missense_Mutation_p.S447P|KDM3A_ENST00000312912.5_Missense_Mutation_p.S447P|KDM3A_ENST00000485171.1_3'UTR			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	447			S -> P (in dbSNP:rs34605051). {ECO:0000269|PubMed:17974005}.		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						ACCTTCCCCATCGGATGTTTC	0.448													T|||	365	0.0728834	0.118	0.0677	5008	,	,		20783	0.0		0.1392	False		,,,				2504	0.0225				p.S447P	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.T1339C						PASS	.	T	PRO/SER,PRO/SER	562,3844	251.5+/-258.2	39,484,1680	111.0	109.0	109.0		1339,1339	1.8	0.0	2	dbSNP_126	109	1393,7207	269.8+/-288.6	101,1191,3008	yes	missense,missense	KDM3A	NM_001146688.1,NM_018433.5	74,74	140,1675,4688	CC,CT,TT		16.1977,12.7553,15.0315	benign,benign	447/1322,447/1322	86693826	1955,11051	2203	4300	6503	SO:0001583	missense	55818	exon10			TCCCCATCGGATG	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.1339T>C	2.37:g.86693826T>C	ENSP00000386660:p.Ser447Pro	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	37	CCDS1990.1	192	0.08791208791208792	63	0.12804878048780488	25	0.06906077348066299	0	0.0	104	0.13720316622691292	T	8.980	0.975208	0.18736	0.127553	0.161977	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.65	1.78	0.24846	.	0.170906	0.41712	N	0.000825	T	0.00178	0.0005	L	0.27053	0.805	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.03423	-1.1038	9	0.51188	T	0.08	.	5.5513	0.17091	0.0:0.1521:0.1449:0.7029	rs34605051;rs34605051	395;447	F5H070;Q9Y4C1	.;KDM3A_HUMAN	P	447;447;447;447;395	ENSP00000386660:S447P;ENSP00000323659:S447P;ENSP00000386516:S447P;ENSP00000438324:S395P	ENSP00000323659:S447P	S	+	1	0	KDM3A	86547337	0.444000	0.25649	0.018000	0.16275	0.264000	0.26372	1.598000	0.36740	0.060000	0.16281	0.460000	0.39030	TCG	T|0.867;C|0.133	0.133	strong		0.448	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
LPCAT1	79888	hgsc.bcm.edu	37	5	1466919	1466919	+	Silent	SNP	G	G	A	rs2277006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:1466919G>A	ENST00000283415.3	-	13	1497	c.1365C>T	c.(1363-1365)acC>acT	p.T455T	LPCAT1_ENST00000503252.1_5'UTR	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	455	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)	p.T455T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		GGTCGGTCACGGTGAGCTCTG	0.632																																					p.T455T		Atlas-SNP	.											LPCAT1,NS,carcinoma,0,1	LPCAT1	70	1	1	Substitution - coding silent(1)	prostate(1)	c.C1365T						PASS	.	G		1812,2594	532.3+/-373.4	381,1050,772	127.0	109.0	115.0		1365	-8.5	0.0	5	dbSNP_100	115	1722,6878	315.1+/-312.1	173,1376,2751	no	coding-synonymous	LPCAT1	NM_024830.3		554,2426,3523	AA,AG,GG		20.0233,41.1257,27.1721		455/535	1466919	3534,9472	2203	4300	6503	SO:0001819	synonymous_variant	79888	exon13			GGTCACGGTGAGC	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1365C>T	5.37:g.1466919G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																			G|0.696;A|0.304	0.304	strong		0.632	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
SDHD	6392	hgsc.bcm.edu	37	11	111965573	111965573	+	Missense_Mutation	SNP	T	T	C	rs200981457		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:111965573T>C	ENST00000375549.3	+	4	494	c.359T>C	c.(358-360)tTg>tCg	p.L120S	SDHD_ENST00000528021.1_Intron|SDHD_ENST00000532699.1_Intron|SDHD_ENST00000525291.1_Missense_Mutation_p.L81S|SDHD_ENST00000528048.1_Missense_Mutation_p.C72R|SDHD_ENST00000528182.1_Missense_Mutation_p.C118R|SDHD_ENST00000526592.1_3'UTR	NM_003002.2	NP_002993.1	O14521	DHSD_HUMAN	succinate dehydrogenase complex, subunit D, integral membrane protein	120					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|succinate dehydrogenase activity (GO:0000104)|ubiquinone binding (GO:0048039)	p.L120S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515)	Hexachlorophene(DB00756)|Succinic acid(DB00139)	GGGGATGCCTTGCAGAAAGCT	0.413			"""Mis, N, F, S"""			"""paraganglioma, pheochromocytoma"""			Familial Paragangliomas;Cowden syndrome;Carney-Stratakis syndrome																												p.A120A		Atlas-SNP	.	yes	Rec		Familial paraganglioma	11	11q23	6392	"""succinate dehydrogenase complex, subunit D, integral membrane protein"""		O	SDHD,NS,carcinoma,0,1	SDHD	19	1	1	Substitution - Missense(1)	prostate(1)	c.C359C						scavenged	.						74.0	73.0	73.0					11																	111965573		2201	4297	6498	SO:0001583	missense	6392	exon4	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;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	ATGCCTTGCAGAA	AB006202	CCDS31678.1, CCDS60958.1, CCDS60959.1, CCDS60960.1	11q23	2014-09-17				ENSG00000204370		"""Mitochondrial respiratory chain complex / Complex II"""	10683	protein-coding gene	gene with protein product		602690		PGL, PGL1		9533030, 1301144	Standard	NM_003002		Approved		uc001pmz.4	O14521		ENST00000375549.3:c.359T>C	11.37:g.111965573T>C	ENSP00000364699:p.Leu120Ser	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	206	4	0.0194175	NM_003002	A6ND90|B3KQQ8|E9PIC0|E9PIG3|E9PQI9|Q53XW5|Q6IRW2	Silent	SNP	ENST00000375549.3	37	CCDS31678.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.312|9.312	1.055807|1.055807	0.19907|0.19907	.|.	.|.	ENSG00000204370|ENSG00000204370	ENST00000528182;ENST00000528048|ENST00000375549;ENST00000525291	D;D|D;D	0.92249|0.98684	-3.0;-1.71|-5.07;-5.07	4.85|4.85	-2.22|-2.22	0.06952|0.06952	.|.	.|1.953400	.|0.02197	.|N	.|0.061887	D|D	0.97145|0.97145	0.9067|0.9067	M|M	0.61703|0.61703	1.905|1.905	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	D|D	0.90248|0.90248	0.4291|0.4291	7|10	0.87932|0.87932	D|D	0|0	-25.135|-25.135	6.6942|6.6942	0.23189|0.23189	0.1144:0.4174:0.0:0.4683|0.1144:0.4174:0.0:0.4683	.|.	.|120	.|O14521	.|DHSD_HUMAN	R|S	118;72|120;81	ENSP00000435475:C118R;ENSP00000436217:C72R|ENSP00000364699:L120S;ENSP00000436669:L81S	ENSP00000436217:C72R|ENSP00000364699:L120S	C|L	+|+	1|2	0|0	SDHD|SDHD	111470783|111470783	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.775000|0.775000	0.43874|0.43874	0.488000|0.488000	0.22371|0.22371	-0.268000|-0.268000	0.09312|0.09312	-0.146000|-0.146000	0.13790|0.13790	TGC|TTG	.	.	weak		0.413	SDHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392351.1	NM_003002	
BTNL9	153579	hgsc.bcm.edu	37	5	180472498	180472498	+	Silent	SNP	C	C	T	rs28677846	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180472498C>T	ENST00000327705.9	+	2	240	c.9C>T	c.(7-9)gaC>gaT	p.D3D	BTNL9_ENST00000376841.2_Silent_p.D3D|BTNL9_ENST00000376842.3_Silent_p.D3D|BTNL9_ENST00000515271.1_Intron	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	3						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGATGGTGGACCTCTCAGTCT	0.602													T|||	2495	0.498203	0.6422	0.5216	5008	,	,		17239	0.3909		0.5189	False		,,,				2504	0.3763				p.D3D		Atlas-SNP	.											.	BTNL9	58	.	0			c.C9T						PASS	.	T		2716,1688	510.1+/-367.4	842,1032,328	95.0	83.0	87.0		9	-5.5	0.0	5	dbSNP_125	87	4498,4100	561.5+/-387.8	1168,2162,969	no	coding-synonymous	BTNL9	NM_152547.4		2010,3194,1297	TT,TC,CC		47.6855,38.3288,44.5162		3/536	180472498	7214,5788	2202	4299	6501	SO:0001819	synonymous_variant	153579	exon2			GGTGGACCTCTCA	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.9C>T	5.37:g.180472498C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																			C|0.460;G|0.000;T|0.539	0.539	strong		0.602	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
OR4D11	219986	hgsc.bcm.edu	37	11	59271637	59271637	+	Missense_Mutation	SNP	T	T	C	rs7120079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:59271637T>C	ENST00000313253.1	+	1	589	c.589T>C	c.(589-591)Ttc>Ctc	p.F197L		NM_001004706.1	NP_001004706.1	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D, member 11	197			F -> L (in dbSNP:rs7120079).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F197L(1)		endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						TGCTCTTGAGTTCTTGATGAT	0.498													N|||	1515	0.302516	0.289	0.2219	5008	,	,		21137	0.2758		0.3091	False		,,,				2504	0.3988				p.F197L		Atlas-SNP	.											OR4D11,NS,carcinoma,0,1	OR4D11	62	1	1	Substitution - Missense(1)	stomach(1)	c.T589C						PASS	.	C	LEU/PHE	1225,3177		173,879,1149	221.0	211.0	214.0		589	1.1	0.7	11	dbSNP_116	214	2595,5995		396,1803,2096	yes	missense	OR4D11	NM_001004706.1	22	569,2682,3245	CC,CT,TT		30.2095,27.8283,29.4027	benign	197/312	59271637	3820,9172	2201	4295	6496	SO:0001583	missense	219986	exon1			CTTGAGTTCTTGA	AB065810	CCDS31563.1	11q12.1	2012-08-09		2004-03-10	ENSG00000176200	ENSG00000176200		"""GPCR / Class A : Olfactory receptors"""	15174	protein-coding gene	gene with protein product				OR4D11P			Standard	NM_001004706		Approved		uc001noa.1	Q8NGI4	OTTHUMG00000167342	ENST00000313253.1:c.589T>C	11.37:g.59271637T>C	ENSP00000320077:p.Phe197Leu	Somatic	410	1	0.00243902		WXS	Illumina HiSeq	Phase_I	405	200	0.493827	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	
LRP1	4035	hgsc.bcm.edu	37	12	57594552	57594552	+	Silent	SNP	C	C	T	rs139916336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57594552C>T	ENST00000243077.3	+	64	10645	c.10179C>T	c.(10177-10179)tgC>tgT	p.C3393C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3393	LDL-receptor class A 22. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCTTCATCTGCGATGGCGACA	0.617													C|||	14	0.00279553	0.0	0.0072	5008	,	,		12339	0.0		0.008	False		,,,				2504	0.001				p.C3393C		Atlas-SNP	.											.	LRP1	428	.	0			c.C10179T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	91.0	78.0	83.0		10179	0.9	1.0	12	dbSNP_134	83	73,8527	43.6+/-101.6	0,73,4227	no	coding-synonymous	LRP1	NM_002332.2		0,83,6420	TT,TC,CC		0.8488,0.227,0.6382		3393/4545	57594552	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon64			CATCTGCGATGGC	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.10179C>T	12.37:g.57594552C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	183	90	0.491803	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.995;T|0.005	0.005	strong		0.617	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291178	1291178	+	Missense_Mutation	SNP	T	T	C	rs112944038		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1291178T>C	ENST00000338844.3	+	3	119	c.86T>C	c.(85-87)gTg>gCg	p.V29A	TPSAB1_ENST00000461509.2_Missense_Mutation_p.V36A	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	29			V -> A (in allele alpha; dbSNP:rs1064771).		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				CTGCAGCGAGTGGGCATCGTC	0.716																																					p.V29A		Atlas-SNP	.											TPSAB1,rectum,carcinoma,0,1	TPSAB1	24	1	0			c.T86C						scavenged	.						32.0	32.0	32.0					16																	1291178		2196	4296	6492	SO:0001583	missense	7177	exon3			AGCGAGTGGGCAT	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.86T>C	16.37:g.1291178T>C	ENSP00000343577:p.Val29Ala	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	173	51	0.294798	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	734	0.3360805860805861	109	0.22154471544715448	102	0.281767955801105	276	0.4825174825174825	247	0.3258575197889182	C	3.007	-0.204833	0.06180	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	T;T	0.81078	-1.45;-1.45	3.38	-6.75	0.01738	.	1.382050	0.04868	N	0.445430	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.07849	-1.0751	9	0.07325	T	0.83	.	7.137	0.25533	0.1118:0.6191:0.113:0.156	.	29	Q15661	TRYB1_HUMAN	A	29;36	ENSP00000343577:V29A;ENSP00000418247:V36A	ENSP00000343577:V29A	V	+	2	0	TPSAB1	1231179	0.934000	0.31675	0.000000	0.03702	0.001000	0.01503	-0.611000	0.05622	-3.400000	0.00171	-1.842000	0.00583	GTG	.	.	strong		0.716	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
RSC1A1	6248	hgsc.bcm.edu	37	1	15986547	15986547	+	Missense_Mutation	SNP	T	T	C	rs3766163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15986547T>C	ENST00000345034.1	+	1	184	c.184T>C	c.(184-186)Ttc>Ctc	p.F62L	DDI2_ENST00000480945.1_3'UTR	NM_006511.1	NP_006502.1	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1, member 1	62			F -> L (in dbSNP:rs3766163). {ECO:0000269|PubMed:14702039}.		intestinal absorption (GO:0050892)|negative regulation of transport (GO:0051051)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	brush border (GO:0005903)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel inhibitor activity (GO:0008200)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)	11		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|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)		TTCAGCTGAATTCCAGCTAAA	0.458													T|||	1256	0.250799	0.4478	0.2176	5008	,	,		21772	0.0317		0.2694	False		,,,				2504	0.2147				p.F62L		Atlas-SNP	.											.	RSC1A1	29	.	0			c.T184C						PASS	.	T	LEU/PHE,	1830,2576	536.1+/-374.4	405,1020,778	125.0	131.0	129.0		184,	4.5	1.0	1	dbSNP_107	129	2425,6175	400.9+/-346.9	324,1777,2199	yes	missense,utr-3	RSC1A1,DDI2	NM_006511.1,NM_032341.4	22,	729,2797,2977	CC,CT,TT		28.1977,41.5343,32.7157	benign,	62/618,	15986547	4255,8751	2203	4300	6503	SO:0001583	missense	6248	exon1			GCTGAATTCCAGC	BN000122, X82877	CCDS161.1	1p36.1	1998-08-25			ENSG00000215695	ENSG00000215695			10458	protein-coding gene	gene with protein product		601966					Standard	NM_006511		Approved	RS1	uc010obn.2	Q92681	OTTHUMG00000067830	ENST00000345034.1:c.184T>C	1.37:g.15986547T>C	ENSP00000341963:p.Phe62Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_006511	B2RBP5	Missense_Mutation	SNP	ENST00000345034.1	37	CCDS161.1	536	0.2454212454212454	211	0.42886178861788615	102	0.281767955801105	23	0.04020979020979021	200	0.2638522427440633	T	3.705	-0.060682	0.07317	0.415343	0.281977	ENSG00000215695	ENST00000345034	T	0.39229	1.09	5.61	4.48	0.54585	.	0.276090	0.25971	N	0.027139	T	0.00012	0.0000	N	0.19112	0.55	0.36160	P	0.15193	B	0.17268	0.021	B	0.15484	0.013	T	0.40040	-0.9584	9	0.02654	T	1	-23.5652	8.289	0.31946	0.0:0.1583:0.0:0.8417	rs3766163;rs59513823;rs3766163	62	Q92681	RSCA1_HUMAN	L	62	ENSP00000341963:F62L	ENSP00000341963:F62L	F	+	1	0	RSC1A1	15859134	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	1.411000	0.34702	0.966000	0.38159	0.459000	0.35465	TTC	T|0.708;C|0.292	0.292	strong		0.458	RSC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145500.1	NM_006511	
MED12L	116931	hgsc.bcm.edu	37	3	151112568	151112568	+	Silent	SNP	G	G	A	rs3732768	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:151112568G>A	ENST00000474524.1	+	37	5666	c.5628G>A	c.(5626-5628)tcG>tcA	p.S1876S	MED12L_ENST00000273432.4_Silent_p.S1736S	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1876						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAATCACATCGCAGCAGCAGT	0.547													G|||	1497	0.298922	0.3707	0.2233	5008	,	,		16917	0.2778		0.2028	False		,,,				2504	0.3763				p.S1876S		Atlas-SNP	.											MED12L,NS,carcinoma,+1,2	MED12L	271	2	0			c.G5628A						PASS	.	G		1547,2859	487.8+/-361.0	282,983,938	90.0	90.0	90.0		5628	-11.8	0.0	3	dbSNP_107	90	1835,6765	327.5+/-317.9	210,1415,2675	no	coding-synonymous	MED12L	NM_053002.4		492,2398,3613	AA,AG,GG		21.3372,35.1112,26.0034		1876/2146	151112568	3382,9624	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon37			CACATCGCAGCAG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5628G>A	3.37:g.151112568G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			G|0.724;A|0.276	0.276	strong		0.547	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
NIN	51199	hgsc.bcm.edu	37	14	51227000	51227000	+	Silent	SNP	A	A	G	rs4901055	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000245441.5_Silent_p.H658H|NIN_ENST00000530997.2_Silent_p.H658H|NIN_ENST00000382043.4_Silent_p.H658H|NIN_ENST00000389868.3_Silent_p.H658H|NIN_ENST00000324330.9_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	35	12	0.342857	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105405599	105405599	+	Missense_Mutation	SNP	G	G	C	rs3742935	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	123	123	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	
CAPRIN2	65981	hgsc.bcm.edu	37	12	30881809	30881809	+	Missense_Mutation	SNP	T	T	C	rs2304630	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:30881809T>C	ENST00000395805.2	-	8	2102	c.1555A>G	c.(1555-1557)Atg>Gtg	p.M519V	CAPRIN2_ENST00000417045.1_Missense_Mutation_p.M519V|CAPRIN2_ENST00000308433.5_Missense_Mutation_p.M186V|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.M519V|CAPRIN2_ENST00000538387.1_5'UTR|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.M519V	NM_001206856.1	NP_001193785.1			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TCGCTCTGCATGGAAGGTGTC	0.463													c|||	2781	0.555312	0.8192	0.3732	5008	,	,		20637	0.369		0.5736	False		,,,				2504	0.501				p.M519V		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.A1555G						PASS	.	G	VAL/MET,VAL/MET,VAL/MET,VAL/MET	3464,942	357.9+/-314.1	1363,738,102	201.0	190.0	194.0		1555,1555,1555,1555	-4.5	0.0	12	dbSNP_100	194	5120,3480	509.4+/-377.3	1518,2084,698	yes	missense,missense,missense,missense	CAPRIN2	NM_001002259.1,NM_001206856.1,NM_023925.3,NM_032156.3	21,21,21,21	2881,2822,800	CC,CT,TT		40.4651,21.3799,33.9997	benign,benign,benign,benign	519/1128,519/906,519/1078,519/961	30881809	8584,4422	2203	4300	6503	SO:0001583	missense	65981	exon8			TCTGCATGGAAGG	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"""C1q domain containing 1"""	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.1555A>G	12.37:g.30881809T>C	ENSP00000379150:p.Met519Val	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	262	132	0.503817	NM_023925		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	1162	0.532051282051282	380	0.7723577235772358	137	0.3784530386740331	206	0.36013986013986016	439	0.579155672823219	c	0.001	-2.991367	0.00045	0.786201	0.595349	ENSG00000110888	ENST00000433722;ENST00000298892;ENST00000395805;ENST00000251071;ENST00000308433;ENST00000417045;ENST00000438006;ENST00000537108	T;T;T;T;T;T;T	0.72505	2.67;-0.37;3.08;-0.39;-0.66;3.08;2.68	4.52	-4.49	0.03504	.	1.744600	0.03738	N	0.254586	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	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.31223	-0.9951	9	0.02654	T	1	2.3831	10.3528	0.43945	0.0:0.2263:0.576:0.1977	rs2304630;rs52805437;rs60234803;rs2304630	519;245;519;519;519;519;519	Q6IMN6-6;E9PAU5;Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;.;.;CAPR2_HUMAN;.;.	V	265;519;519;519;186;519;245;438	ENSP00000415407:M265V;ENSP00000298892:M519V;ENSP00000379150:M519V;ENSP00000251071:M519V;ENSP00000309785:M186V;ENSP00000391479:M519V;ENSP00000438010:M438V	ENSP00000251071:M519V	M	-	1	0	CAPRIN2	30773076	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.854000	0.04299	-1.874000	0.01133	-2.841000	0.00105	ATG	T|0.384;C|0.616	0.616	strong		0.463	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925	
HDHD1	8226	hgsc.bcm.edu	37	X	6995417	6995417	+	Silent	SNP	C	C	T	rs2379207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	87	0	0		WXS	Illumina HiSeq	Phase_I	78	75	0.961538	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	
KDM3B	51780	hgsc.bcm.edu	37	5	137717213	137717213	+	Silent	SNP	G	G	A	rs10073922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137717213G>A	ENST00000314358.5	+	6	914	c.714G>A	c.(712-714)gaG>gaA	p.E238E		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	238					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)	p.E238E(1)		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						AGAGTGGTGAGATCAAGTCGG	0.383													G|||	1456	0.290735	0.1067	0.4179	5008	,	,		17869	0.2708		0.337	False		,,,				2504	0.4223				p.E238E		Atlas-SNP	.											KDM3B,NS,carcinoma,+2,2	KDM3B	177	2	1	Substitution - coding silent(1)	stomach(1)	c.G714A						PASS	.	G		715,3691	299.6+/-285.9	63,589,1551	142.0	122.0	129.0		714	2.0	1.0	5	dbSNP_119	129	3132,5468	478.0+/-369.8	591,1950,1759	no	coding-synonymous	KDM3B	NM_016604.3		654,2539,3310	AA,AG,GG		36.4186,16.2279,29.5787		238/1762	137717213	3847,9159	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon6			TGGTGAGATCAAG	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.714G>A	5.37:g.137717213G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			G|0.716;A|0.284	0.284	strong		0.383	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
FLG	2312	hgsc.bcm.edu	37	1	152280614	152280614	+	Missense_Mutation	SNP	C	C	G	rs3120645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280614C>G	ENST00000368799.1	-	3	6783	c.6748G>C	c.(6748-6750)Gag>Cag	p.E2250Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2250	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGTGTCCCTCACTGTCACTG	0.592									Ichthyosis																												p.E2250Q		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,+2,1	FLG	900	1	0			c.G6748C						scavenged	.						203.0	203.0	203.0					1																	152280614		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCCCTCACTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6748G>C	1.37:g.152280614C>G	ENSP00000357789:p.Glu2250Gln	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	387	20	0.0516796	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	
SFRP4	6424	hgsc.bcm.edu	37	7	37947103	37947103	+	Missense_Mutation	SNP	C	C	T	rs1802074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	276	0	0		WXS	Illumina HiSeq	Phase_I	258	124	0.48062	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	
IQGAP3	128239	hgsc.bcm.edu	37	1	156518379	156518379	+	Missense_Mutation	SNP	G	G	A	rs744224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156518379G>A	ENST00000361170.2	-	17	1997	c.1987C>T	c.(1987-1989)Cgt>Tgt	p.R663C		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	663			R -> C (in dbSNP:rs744224). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTACCTGGACGCTGTTTCTTT	0.607													G|||	2039	0.407149	0.2958	0.3646	5008	,	,		19167	0.5724		0.2575	False		,,,				2504	0.5716				p.R663C		Atlas-SNP	.											IQGAP3,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	IQGAP3	146	1	0			c.C1987T						PASS	.	G	CYS/ARG	1316,3090	443.9+/-347.2	196,924,1083	143.0	101.0	115.0		1987	1.9	0.0	1	dbSNP_86	115	2370,6230	394.8+/-344.8	341,1688,2271	yes	missense	IQGAP3	NM_178229.4	180	537,2612,3354	AA,AG,GG		27.5581,29.8684,28.3408	benign	663/1632	156518379	3686,9320	2203	4300	6503	SO:0001583	missense	128239	exon17			CTGGACGCTGTTT	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1987C>T	1.37:g.156518379G>A	ENSP00000354451:p.Arg663Cys	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	107	105	0.981308	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	758	0.34706959706959706	134	0.27235772357723576	123	0.3397790055248619	311	0.5437062937062938	190	0.25065963060686014	G	3.973	-0.007916	0.07773	0.298684	0.275581	ENSG00000183856	ENST00000361170	T	0.06849	3.25	4.85	1.89	0.25635	.	1.156880	0.06169	N	0.677301	T	0.02455	0.0075	L	0.29908	0.895	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.42085	-0.9472	9	0.48119	T	0.1	2.333	9.5002	0.39013	0.2415:0.0:0.7585:0.0	rs744224;rs1774954;rs17391814;rs57842273;rs744224	663	Q86VI3	IQGA3_HUMAN	C	663	ENSP00000354451:R663C	ENSP00000354451:R663C	R	-	1	0	IQGAP3	154785003	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.029000	0.12329	0.108000	0.17862	-0.258000	0.10820	CGT	G|0.683;A|0.317	0.317	strong		0.607	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
EPHX1	2052	hgsc.bcm.edu	37	1	226019653	226019653	+	Silent	SNP	G	G	A	rs1131873	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226019653G>A	ENST00000366837.4	+	3	553	c.357G>A	c.(355-357)aaG>aaA	p.K119K	EPHX1_ENST00000467015.1_3'UTR|EPHX1_ENST00000272167.5_Silent_p.K119K	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	119					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)					TCAAGACTAAGATTGAAGGTA	0.438													G|||	957	0.191094	0.1165	0.1484	5008	,	,		23249	0.2867		0.162	False		,,,				2504	0.2536				p.K119K		Atlas-SNP	.											.	EPHX1	57	.	0			c.G357A						PASS	.	G	,	643,3763	275.7+/-272.7	50,543,1610	88.0	80.0	83.0		357,357	3.7	1.0	1	dbSNP_100	83	1236,7364	247.8+/-275.7	82,1072,3146	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	132,1615,4756	AA,AG,GG		14.3721,14.5937,14.4472	,	119/456,119/456	226019653	1879,11127	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon3			GACTAAGATTGAA	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.357G>A	1.37:g.226019653G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			G|0.831;A|0.169	0.169	strong		0.438	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
IL17RE	132014	hgsc.bcm.edu	37	3	9952706	9952706	+	Silent	SNP	A	A	G	rs279572	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:9952706A>G	ENST00000383814.3	+	9	1065	c.960A>G	c.(958-960)acA>acG	p.T320T	IL17RE_ENST00000295980.3_Silent_p.T320T|IL17RE_ENST00000454190.2_Silent_p.T320T|IL17RE_ENST00000421412.1_Silent_p.T353T	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	320					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		CGAATGCCACAGCTCGAGAGT	0.617													G|||	2138	0.426917	0.6384	0.4683	5008	,	,		17881	0.0942		0.5527	False		,,,				2504	0.3252				p.T360T		Atlas-SNP	.											.	IL17RE	62	.	0			c.A1080G						PASS	.	G	,,	2733,1673	509.6+/-367.3	863,1007,333	59.0	60.0	59.0		960,960,1080	-6.6	0.3	3	dbSNP_79	59	4624,3976	552.1+/-386.1	1229,2166,905	no	coding-synonymous,coding-synonymous,coding-synonymous	IL17RE	NM_001193380.1,NM_153480.1,NM_153483.2	,,	2092,3173,1238	GG,GA,AA		46.2326,37.9709,43.4338	,,	320/534,320/668,360/708	9952706	7357,5649	2203	4300	6503	SO:0001819	synonymous_variant	132014	exon10			TGCCACAGCTCGA	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"""Interleukins and interleukin receptors"""	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.960A>G	3.37:g.9952706A>G		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Silent	SNP	ENST00000383814.3	37	CCDS2589.1																																																																																			A|0.492;G|0.508	0.508	strong		0.617	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480	
ADARB2	105	hgsc.bcm.edu	37	10	1230968	1230968	+	Missense_Mutation	SNP	C	C	T	rs2271275	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:1230968C>T	ENST00000381312.1	-	9	2201	c.1876G>A	c.(1876-1878)Gcc>Acc	p.A626T	ADARB2_ENST00000381305.1_Missense_Mutation_p.A28T|ADARB2_ENST00000381310.3_Missense_Mutation_p.A135T	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	626	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.		A -> T (in dbSNP:rs2271275). {ECO:0000269|PubMed:15489334}.		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)		CGCGCCTCGGCGTCACTCACG	0.667													C|||	2720	0.543131	0.2504	0.5115	5008	,	,		15505	0.6696		0.6809	False		,,,				2504	0.6892				p.A626T		Atlas-SNP	.											ADARB2,rectum,carcinoma,0,1	ADARB2	95	1	0			c.G1876A						PASS	.	C	THR/ALA	1422,2984		224,974,1005	22.0	23.0	23.0		1876	4.8	0.0	10	dbSNP_100	23	5866,2730		2007,1852,439	yes	missense	ADARB2	NM_018702.3	58	2231,2826,1444	TT,TC,CC		31.759,32.2742,43.9471	benign	626/740	1230968	7288,5714	2203	4298	6501	SO:0001583	missense	105	exon9			CCTCGGCGTCACT	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.1876G>A	10.37:g.1230968C>T	ENSP00000370713:p.Ala626Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	96	58	0.604167	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	1213	0.5554029304029304	119	0.241869918699187	203	0.5607734806629834	372	0.6503496503496503	519	0.6846965699208444	C	13.59	2.281430	0.40394	0.322742	0.68241	ENSG00000185736	ENST00000381312;ENST00000381310;ENST00000381305	D;D;D	0.93859	-3.3;-3.3;-3.3	4.81	4.81	0.61882	Adenosine deaminase/editase (3);	0.168400	0.51477	D	0.000099	T	0.00012	0.0000	L	0.53617	1.68	0.09310	P	0.99999836182	B;B;P	0.38223	0.158;0.416;0.623	B;B;B	0.42112	0.098;0.08;0.376	T	0.45454	-0.9260	9	0.34782	T	0.22	-20.7549	17.8992	0.88898	0.0:1.0:0.0:0.0	rs2271275;rs57620546;rs2271275	626;28;135	Q9NS39;Q5VW43;Q5VW42	RED2_HUMAN;.;.	T	626;135;28	ENSP00000370713:A626T;ENSP00000370711:A135T;ENSP00000370706:A28T	ENSP00000370706:A28T	A	-	1	0	ADARB2	1220968	0.631000	0.27164	0.046000	0.18839	0.138000	0.21146	1.502000	0.35704	2.220000	0.72140	0.561000	0.74099	GCC	C|0.458;T|0.542	0.542	strong		0.667	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
DAPL1	92196	hgsc.bcm.edu	37	2	159672252	159672252	+	Silent	SNP	G	G	A	rs61740878	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:159672252G>A	ENST00000309950.3	+	4	299	c.243G>A	c.(241-243)gcG>gcA	p.A81A	DAPL1_ENST00000409042.1_Intron	NM_001017920.2	NP_001017920.2	A0PJW8	DAPL1_HUMAN	death associated protein-like 1	81					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)					prostate(1)	1						TGCACATGGCGCATCAAAAAC	0.388													G|||	513	0.102436	0.0061	0.1556	5008	,	,		18301	0.0764		0.1541	False		,,,				2504	0.1687				p.A81A		Atlas-SNP	.											.	DAPL1	11	.	0			c.G243A						PASS	.	G		143,4263	101.2+/-139.8	2,139,2062	137.0	131.0	133.0		243	1.5	1.0	2	dbSNP_129	133	1515,7085	286.7+/-297.9	139,1237,2924	no	coding-synonymous	DAPL1	NM_001017920.2		141,1376,4986	AA,AG,GG		17.6163,3.2456,12.748		81/108	159672252	1658,11348	2203	4300	6503	SO:0001819	synonymous_variant	92196	exon4			CATGGCGCATCAA		CCDS33307.1	2q24	2007-06-26			ENSG00000163331	ENSG00000163331			21490	protein-coding gene	gene with protein product							Standard	NM_001017920		Approved		uc002uaf.3	A0PJW8	OTTHUMG00000153970	ENST00000309950.3:c.243G>A	2.37:g.159672252G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_001017920	A0PJW9|B9EIK6	Silent	SNP	ENST00000309950.3	37	CCDS33307.1																																																																																			G|0.880;A|0.120	0.120	strong		0.388	DAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333265.1	NM_001017920	
SMARCA4	6597	hgsc.bcm.edu	37	19	11170839	11170839	+	Silent	SNP	T	T	C	rs7275	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11170839T>C	ENST00000429416.3	+	35	5168	c.4887T>C	c.(4885-4887)gaT>gaC	p.D1629D	SMARCA4_ENST00000589677.1_Silent_p.D1598D|SMARCA4_ENST00000590574.1_Silent_p.D1596D|SMARCA4_ENST00000413806.3_Silent_p.D1599D|SMARCA4_ENST00000541122.2_Silent_p.D1599D|SMARCA4_ENST00000444061.3_Silent_p.D1595D|SMARCA4_ENST00000450717.3_Silent_p.D1598D|SMARCA4_ENST00000358026.2_Silent_p.D1661D|SMARCA4_ENST00000344626.4_Silent_p.D1629D	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1629					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TGAGTGACGATGACAGTGAGG	0.687			"""F, N, Mis"""		NSCLC								C|||	1251	0.2498	0.3094	0.1715	5008	,	,		14726	0.0724		0.2942	False		,,,				2504	0.362				p.D1661D		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	SMARCA4_ENST00000358026,caecum,carcinoma,0,2	SMARCA4	502	2	1	Unknown(1)	lung(1)	c.T4983C						PASS	.	C	,,,,,,	1060,2890		143,774,1058	26.0	31.0	29.0		4887,4797,4794,4788,4785,4983,4887	-5.1	0.0	19	dbSNP_52	29	1961,5729		253,1455,2137	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SMARCA4	NM_001128844.1,NM_001128845.1,NM_001128846.1,NM_001128847.1,NM_001128848.1,NM_001128849.1,NM_003072.3	,,,,,,	396,2229,3195	CC,CT,TT		25.5007,26.8354,25.9536	,,,,,,	1629/1648,1599/1618,1598/1617,1596/1615,1595/1614,1661/1680,1629/1648	11170839	3021,8619	1975	3845	5820	SO:0001819	synonymous_variant	6597	exon35			TGACGATGACAGT	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4887T>C	19.37:g.11170839T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_001128849	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																			T|0.776;C|0.224	0.224	strong		0.687	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
PTCH1	5727	hgsc.bcm.edu	37	9	98238379	98238379	+	Silent	SNP	A	A	G	rs1805155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:98238379A>G	ENST00000331920.6	-	12	1964	c.1665T>C	c.(1663-1665)aaT>aaC	p.N555N	PTCH1_ENST00000429896.2_Silent_p.N404N|PTCH1_ENST00000421141.1_Silent_p.N404N|PTCH1_ENST00000375274.2_Silent_p.N554N|PTCH1_ENST00000437951.1_Silent_p.N489N|PTCH1_ENST00000418258.1_Silent_p.N404N|PTCH1_ENST00000430669.2_Silent_p.N489N	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	555	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGGCTGTGACATTGCTGATGG	0.582													A|||	559	0.111621	0.1687	0.0764	5008	,	,		18339	0.1131		0.1093	False		,,,				2504	0.0603				p.N555N		Atlas-SNP	.											.	PTCH1	1850	.	0			c.T1665C						PASS	.	A	,,,,,,	813,3593	323.7+/-298.2	78,657,1468	86.0	63.0	71.0		1665,1467,1662,1212,1212,1212,1212	-4.1	1.0	9	dbSNP_89	71	890,7710	199.0+/-243.2	48,794,3458	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	126,1451,4926	GG,GA,AA		10.3488,18.4521,13.094	,,,,,,	555/1448,489/1382,554/1447,404/1297,404/1297,404/1297,404/1297	98238379	1703,11303	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon12			TGTGACATTGCTG	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1665T>C	9.37:g.98238379A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			A|0.874;G|0.126	0.126	strong		0.582	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
HHLA1	10086	hgsc.bcm.edu	37	8	133111181	133111181	+	Silent	SNP	G	G	A	rs72715366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133111181G>A	ENST00000414222.1	-	4	227	c.228C>T	c.(226-228)tcC>tcT	p.S76S	HHLA1_ENST00000434736.2_Silent_p.S112S	NM_001145095.1	NP_001138567.1	C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	76						extracellular region (GO:0005576)				endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						GGTTAAGCGCGGACAGATCGA	0.418													G|||	451	0.0900559	0.1634	0.098	5008	,	,		19557	0.0298		0.1004	False		,,,				2504	0.0368				p.S76S		Atlas-SNP	.											.	HHLA1	35	.	0			c.C228T						PASS	.	G		190,1194		13,164,515	124.0	116.0	118.0		228	-12.1	0.0	8	dbSNP_130	118	332,2850		16,300,1275	no	coding-synonymous	HHLA1	NM_001145095.1		29,464,1790	AA,AG,GG		10.4337,13.7283,11.4323		76/532	133111181	522,4044	692	1591	2283	SO:0001819	synonymous_variant	10086	exon4			AAGCGCGGACAGA	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.228C>T	8.37:g.133111181G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_001145095		Silent	SNP	ENST00000414222.1	37																																																																																				G|0.901;A|0.099	0.099	strong		0.418	HHLA1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XR_017860	
LRMP	4033	hgsc.bcm.edu	37	12	25243115	25243115	+	Missense_Mutation	SNP	G	G	C	rs1908946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:25243115G>C	ENST00000354454.3	+	13	1419	c.590G>C	c.(589-591)tGt>tCt	p.C197S	LRMP_ENST00000548766.1_Missense_Mutation_p.C197S|LRMP_ENST00000547044.1_Missense_Mutation_p.C197S	NM_006152.3	NP_006143.2	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	253			L -> V (in dbSNP:rs7969931). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8021504}.		immune system process (GO:0002376)|single fertilization (GO:0007338)|vesicle fusion (GO:0006906)|vesicle targeting (GO:0006903)	chromosome (GO:0005694)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					ATCACTAACTGTTTAAAACTA	0.418													G|||	2501	0.499401	0.1657	0.5231	5008	,	,		20220	0.8095		0.5189	False		,,,				2504	0.5941				p.C197S		Atlas-SNP	.											.	LRMP	51	.	0			c.G590C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS	1012,3394	361.9+/-315.9	120,772,1311	79.0	79.0	79.0		590,590,590	5.8	1.0	12	dbSNP_92	79	4574,4026	593.4+/-393.1	1204,2166,930	yes	missense,missense,missense	LRMP	NM_001204126.1,NM_001204127.1,NM_006152.3	112,112,112	1324,2938,2241	CC,CG,GG		46.814,22.9687,42.9494	probably-damaging,probably-damaging,probably-damaging	197/500,197/500,197/500	25243115	5586,7420	2203	4300	6503	SO:0001583	missense	4033	exon12			CTAACTGTTTAAA		CCDS8701.1	12p12.1	2012-05-16			ENSG00000118308	ENSG00000118308			6690	protein-coding gene	gene with protein product		602003				8021504	Standard	NM_006152		Approved	JAW1	uc010sja.2	Q12912	OTTHUMG00000170192	ENST00000354454.3:c.590G>C	12.37:g.25243115G>C	ENSP00000346442:p.Cys197Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001204126	A0AVM2|B4E077|Q8N301	Missense_Mutation	SNP	ENST00000354454.3	37	CCDS8701.1	1153|1153	0.5279304029304029|0.5279304029304029	104|104	0.21138211382113822|0.21138211382113822	202|202	0.5580110497237569|0.5580110497237569	444|444	0.7762237762237763|0.7762237762237763	403|403	0.5316622691292876|0.5316622691292876	G|G	27.5|27.5	4.832726|4.832726	0.91036|0.91036	0.229687|0.229687	0.53186|0.53186	ENSG00000118308|ENSG00000118308	ENST00000354454;ENST00000536173;ENST00000548766;ENST00000547044|ENST00000555885	T;T;T;T|.	0.15834|.	2.39;2.39;2.39;2.39|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.105878|.	0.64402|.	D|.	0.000003|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.72894|0.72894	2.215|2.215	0.09310|0.09310	P|P	0.9999999089398|0.9999999089398	P|.	0.51240|.	0.943|.	P|.	0.51582|.	0.674|.	T|T	0.45673|0.45673	-0.9245|-0.9245	9|4	0.52906|.	T|.	0.07|.	-13.6954|-13.6954	17.4676|17.4676	0.87638|0.87638	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs1908946;rs17327056;rs52802443;rs1908946|rs1908946;rs17327056;rs52802443;rs1908946	253|.	Q12912|.	LRMP_HUMAN|.	S|L	197;144;197;197|48	ENSP00000346442:C197S;ENSP00000444056:C144S;ENSP00000446496:C197S;ENSP00000450246:C197S|.	ENSP00000346442:C197S|.	C|V	+|+	2|1	0|0	LRMP|LRMP	25134382|25134382	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.996000|0.996000	0.88848|0.88848	5.897000|5.897000	0.69831|0.69831	2.732000|2.732000	0.93576|0.93576	0.655000|0.655000	0.94253|0.94253	TGT|GTT	G|0.535;C|0.465	0.465	strong		0.418	LRMP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407870.1	NM_006152	
KRT84	3890	hgsc.bcm.edu	37	12	52774158	52774158	+	Silent	SNP	G	G	A	rs951772	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	85	0	0	987	WXS	Illumina HiSeq	Phase_I	84	52	0.619048	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	
YLPM1	56252	hgsc.bcm.edu	37	14	75230953	75230953	+	Missense_Mutation	SNP	C	C	T	rs45599947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:75230953C>T	ENST00000552421.1	+	1	885	c.761C>T	c.(760-762)cCt>cTt	p.P254L	YLPM1_ENST00000325680.7_Missense_Mutation_p.P254L|YLPM1_ENST00000238571.3_Missense_Mutation_p.P254L			P49750	YLPM1_HUMAN	YLP motif containing 1	254					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		TCCGCCCCCCCTGGAAATAAG	0.577													C|||	134	0.0267572	0.0015	0.0288	5008	,	,		16457	0.001		0.0736	False		,,,				2504	0.0378				p.P254L		Atlas-SNP	.											.	YLPM1	298	.	0			c.C761T						PASS	.	C	LEU/PRO	61,3695		0,61,1817	61.0	64.0	63.0		761	4.3	1.0	14	dbSNP_127	63	606,7616		26,554,3531	yes	missense	YLPM1	NM_019589.2	98	26,615,5348	TT,TC,CC		7.3705,1.6241,5.5685	benign	254/2147	75230953	667,11311	1878	4111	5989	SO:0001583	missense	56252	exon1			CCCCCCCTGGAAA	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.761C>T	14.37:g.75230953C>T	ENSP00000447921:p.Pro254Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	37		73	0.033424908424908424	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	61	0.08047493403693931	C	3.571	-0.087629	0.07097	0.016241	0.073705	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571	T;T;T	0.20881	2.04;2.04;2.04	4.31	4.31	0.51392	.	0.416039	0.20587	N	0.089434	T	0.00496	0.0016	N	0.08118	0	0.27298	N	0.957662	B	0.11235	0.004	B	0.14023	0.01	T	0.20505	-1.0273	10	0.10377	T	0.69	-0.6095	12.1735	0.54172	0.0:1.0:0.0:0.0	rs45599947	254	P49750-4	.	L	254	ENSP00000447921:P254L;ENSP00000324463:P254L;ENSP00000238571:P254L	ENSP00000238571:P254L	P	+	2	0	YLPM1	74300706	0.963000	0.33076	0.980000	0.43619	0.010000	0.07245	2.015000	0.40961	2.218000	0.71995	0.655000	0.94253	CCT	C|0.959;T|0.041	0.041	strong		0.577	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589	
TTN	7273	hgsc.bcm.edu	37	2	179421694	179421694	+	Missense_Mutation	SNP	A	A	G	rs9808377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179421694A>G	ENST00000591111.1	-	280	83488	c.83264T>C	c.(83263-83265)aTc>aCc	p.I27755T	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I29396T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I20456T|TTN_ENST00000460472.2_Missense_Mutation_p.I20331T|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I20523T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I26828T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27755	Fibronectin type-III 102. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCAGAGATGATGAATTGAGT	0.463													G|||	2540	0.507188	0.5666	0.4049	5008	,	,		20211	0.7153		0.2495	False		,,,				2504	0.5501				p.I29396T		Atlas-SNP	.											.	TTN	18412	.	0			c.T88187C						PASS	.	G	THR/ILE,THR/ILE,THR/ILE,THR/ILE	2066,1878		556,954,462	92.0	95.0	94.0		61568,61367,80483,60992	-2.9	0.1	2	dbSNP_119	94	1831,6469		187,1457,2506	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	743,2411,2968	GG,GA,AA		22.0602,47.6166,31.8278	benign,benign,benign,benign	20523/27119,20456/27052,26828/33424,20331/26927	179421694	3897,8347	1972	4150	6122	SO:0001583	missense	7273	exon330			GAGATGATGAATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.83264T>C	2.37:g.179421694A>G	ENSP00000465570:p.Ile27755Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	183	81	0.442623	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		979	0.4482600732600733	282	0.573170731707317	129	0.356353591160221	385	0.6730769230769231	183	0.24142480211081793	G	3.223	-0.159019	0.06544	0.523834	0.220602	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.87	-2.9	0.05648	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00044	-2.455	0.51482	P	7.299999999998974E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.50617	-0.8807	8	0.87932	D	0	.	12.5594	0.56273	0.6079:0.0:0.3921:0.0	rs9808377;rs56743405;rs9808377	20331;20456;20523;27755	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	26828;20331;20523;20456;20328	ENSP00000343764:I26828T;ENSP00000434586:I20331T;ENSP00000340554:I20523T;ENSP00000352154:I20456T	ENSP00000340554:I20523T	I	-	2	0	TTN	179129940	0.202000	0.23423	0.094000	0.20943	0.170000	0.22686	0.686000	0.25392	-1.202000	0.02655	-0.726000	0.03593	ATC	A|0.549;G|0.451	0.451	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KIAA1755	85449	hgsc.bcm.edu	37	20	36869396	36869396	+	Silent	SNP	G	G	A	rs41282822	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36869396G>A	ENST00000279024.4	-	3	1408	c.1137C>T	c.(1135-1137)gaC>gaT	p.D379D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	379										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGTCCAGTGCGTCCTCAAGGA	0.547													G|||	161	0.0321486	0.0741	0.0231	5008	,	,		17811	0.002		0.0209	False		,,,				2504	0.0245				p.D379D		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1137T						PASS	.	G		328,4078	166.2+/-197.5	13,302,1888	112.0	118.0	116.0		1137	-0.8	0.0	20	dbSNP_127	116	215,8385	88.4+/-150.7	4,207,4089	no	coding-synonymous	KIAA1755	NM_001029864.1		17,509,5977	AA,AG,GG		2.5,7.4444,4.175		379/1201	36869396	543,12463	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			CAGTGCGTCCTCA	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1137C>T	20.37:g.36869396G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.961;A|0.039	0.039	strong		0.547	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
P2RY11	5032	hgsc.bcm.edu	37	19	10224526	10224526	+	Silent	SNP	C	C	T	rs3745600	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10224526C>T	ENST00000321826.4	+	2	421	c.237C>T	c.(235-237)gcC>gcT	p.A79A	PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.P520L|PPAN_ENST00000556468.1_Silent_p.A499A|PPAN-P2RY11_ENST00000393796.4_Silent_p.A499A	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	79					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)			TGCTCTGCGCCCTGACGCTGC	0.687											OREG0025230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1830	0.365415	0.149	0.5144	5008	,	,		16363	0.3462		0.4901	False		,,,				2504	0.4438				p.P520L		Atlas-SNP	.											PPAN-P2RY11,caecum,carcinoma,+2,2	PPAN-P2RY11	81	2	0			c.C1559T						PASS	.	C	,LEU/PRO,	972,3434	355.6+/-313.1	100,772,1331	34.0	32.0	33.0		1497,1559,237	-4.4	0.6	19	dbSNP_107	33	3890,4706	534.7+/-382.6	888,2114,1296	yes	coding-synonymous,missense,coding-synonymous	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_002566.4	,98,	988,2886,2627	TT,TC,CC		45.2536,22.0608,37.3942	,,	499/795,520/521,79/375	10224526	4862,8140	2203	4298	6501	SO:0001819	synonymous_variant	692312	exon13			CTGCGCCCTGACG	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.237C>T	19.37:g.10224526C>T		Somatic	69	0	0	663	WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001198690	B2R8X9|O43190|Q9BYU4|Q9H170	Missense_Mutation	SNP	ENST00000321826.4	37	CCDS12226.1	821	0.3759157509157509	82	0.16666666666666666	184	0.5082872928176796	193	0.3374125874125874	362	0.47757255936675463	C	16.94	3.261297	0.59431	0.220608	0.452536	ENSG00000243207	ENST00000428358	T	0.33865	1.39	4.33	-4.37	0.03633	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999716189	B	0.02656	0.0	B	0.06405	0.002	T	0.49293	-0.8955	7	0.87932	D	0	.	3.5462	0.07829	0.1206:0.3738:0.3544:0.1512	rs3745600	520	C9J3F9	.	L	520	ENSP00000411918:P520L	ENSP00000411918:P520L	P	+	2	0	PPAN-P2RY11	10085526	0.000000	0.05858	0.553000	0.28255	0.283000	0.27025	-0.364000	0.07583	-0.519000	0.06444	0.561000	0.74099	CCC	C|0.631;T|0.369	0.369	strong		0.687	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
RREB1	6239	hgsc.bcm.edu	37	6	7246998	7246998	+	Missense_Mutation	SNP	G	G	A	rs2281833	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:7246998G>A	ENST00000349384.6	+	11	4464	c.4150G>A	c.(4150-4152)Ggg>Agg	p.G1384R	RREB1_ENST00000379933.3_Missense_Mutation_p.G1384R|RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379938.2_Missense_Mutation_p.G1439R	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1384			G -> R (in dbSNP:rs2281833).		multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GGCAGGCGCCGGGGGCGCGGC	0.697													G|||	1075	0.214657	0.0809	0.2435	5008	,	,		11963	0.3532		0.1451	False		,,,				2504	0.3037				p.G1439R		Atlas-SNP	.											RREB1_ENST00000379938,NS,carcinoma,0,4	RREB1	242	4	0			c.G4315A						PASS	.	G	ARG/GLY,ARG/GLY,,ARG/GLY	386,3790		14,358,1716	9.0	11.0	10.0		4150,4315,,4150	0.3	0.0	6	dbSNP_100	10	968,7248		64,840,3204	no	missense,missense,intron,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	125,125,,125	78,1198,4920	AA,AG,GG		11.7819,9.2433,10.9264	probably-damaging,probably-damaging,,probably-damaging	1384/1688,1439/1743,,1384/1688	7246998	1354,11038	2088	4108	6196	SO:0001583	missense	6239	exon12			GGCGCCGGGGGCG	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4150G>A	6.37:g.7246998G>A	ENSP00000305560:p.Gly1384Arg	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	407	0.18635531135531136	53	0.10772357723577236	76	0.20994475138121546	167	0.291958041958042	111	0.14643799472295516	G	6.535	0.466891	0.12402	0.092433	0.117819	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384	T;T;T	0.09630	2.97;2.96;2.97	5.25	0.313	0.15842	.	1.071720	0.07262	N	0.867685	T	0.01730	0.0055	N	0.17082	0.46	0.48040	P	4.269999999999552E-4	B;B	0.31274	0.212;0.317	B;B	0.30179	0.052;0.112	T	0.48570	-0.9024	9	0.24483	T	0.36	-2.6678	5.2861	0.15702	0.3033:0.1369:0.5598:0.0	rs2281833	1384;1439	Q92766;Q92766-2	RREB1_HUMAN;.	R	1384;1439;1384	ENSP00000369265:G1384R;ENSP00000369270:G1439R;ENSP00000305560:G1384R	ENSP00000305560:G1384R	G	+	1	0	RREB1	7191997	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.791000	0.26915	-0.024000	0.13941	-0.140000	0.14226	GGG	G|0.815;A|0.185	0.185	strong		0.697	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
KCNH8	131096	hgsc.bcm.edu	37	3	19190241	19190241	+	Silent	SNP	G	G	C	rs34370450	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:19190241G>C	ENST00000328405.2	+	1	296	c.30G>C	c.(28-30)ccG>ccC	p.P10P		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	10					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	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(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						TACTGGCGCCGCAAAACACCT	0.463													G|||	290	0.0579073	0.0068	0.1037	5008	,	,		15573	0.0		0.166	False		,,,				2504	0.0429				p.P10P	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.G30C						PASS	.	G		141,4265	98.0+/-136.7	2,137,2064	152.0	139.0	143.0		30	1.4	1.0	3	dbSNP_126	143	1321,7279	258.8+/-282.3	106,1109,3085	no	coding-synonymous	KCNH8	NM_144633.2		108,1246,5149	CC,CG,GG		15.3605,3.2002,11.241		10/1108	19190241	1462,11544	2203	4300	6503	SO:0001819	synonymous_variant	131096	exon1			GGCGCCGCAAAAC	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.30G>C	3.37:g.19190241G>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	129	46	0.356589	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																			G|0.898;C|0.102	0.102	strong		0.463	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
PDIK1L	149420	hgsc.bcm.edu	37	1	26448849	26448849	+	Silent	SNP	T	T	C	rs17356867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26448849T>C	ENST00000374271.4	+	4	1094	c.807T>C	c.(805-807)taT>taC	p.Y269Y	PDIK1L_ENST00000374269.1_Silent_p.Y269Y	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	269	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		TGGGGAGTTATGTAAAACAAG	0.428													T|||	587	0.117212	0.1929	0.1052	5008	,	,		18706	0.0159		0.1789	False		,,,				2504	0.0644				p.Y269Y		Atlas-SNP	.											.	PDIK1L	19	.	0			c.T807C						PASS	.	T		895,3511	342.8+/-307.3	81,733,1389	96.0	100.0	98.0		807	-3.8	0.9	1	dbSNP_123	98	1535,7065	288.6+/-298.9	136,1263,2901	no	coding-synonymous	PDIK1L	NM_152835.4		217,1996,4290	CC,CT,TT		17.8488,20.3132,18.6837		269/342	26448849	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	149420	exon3			GAGTTATGTAAAA	AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.807T>C	1.37:g.26448849T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Silent	SNP	ENST00000374271.4	37	CCDS274.1																																																																																			T|0.836;C|0.164	0.164	strong		0.428	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835	
PELP1	27043	hgsc.bcm.edu	37	17	4576620	4576620	+	Silent	SNP	C	C	T	rs55677157	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4576620C>T	ENST00000574876.1	-	15	1787	c.1770G>A	c.(1768-1770)ccG>ccA	p.P590P	PELP1_ENST00000301396.4_Silent_p.P734P|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000436683.2_Silent_p.P443P|PELP1_ENST00000269230.7_Intron|PELP1_ENST00000572293.1_Silent_p.P640P			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	151	0	0		WXS	Illumina HiSeq	Phase_I	144	76	0.527778	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	
PLOD1	5351	hgsc.bcm.edu	37	1	12012748	12012748	+	Missense_Mutation	SNP	G	G	C	rs188165334		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12012748G>C	ENST00000196061.4	+	5	562	c.535G>C	c.(535-537)Gat>Cat	p.D179H	PLOD1_ENST00000376369.3_Missense_Mutation_p.D226H|PLOD1_ENST00000485046.1_3'UTR	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	179					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)	CAGCGACAGCGATCAGCTGTT	0.622																																					p.D179H		Atlas-SNP	.											PLOD1_ENST00000429000,colon,carcinoma,0,2	PLOD1	75	2	0			c.G535C						PASS	.						97.0	89.0	92.0					1																	12012748		2203	4300	6503	SO:0001583	missense	5351	exon5			GACAGCGATCAGC	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.535G>C	1.37:g.12012748G>C	ENSP00000196061:p.Asp179His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	37	CCDS142.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629555	0.87660	.	.	ENSG00000083444	ENST00000358133;ENST00000376369;ENST00000429000;ENST00000196061	T;T;T	0.40756	1.02;1.02;1.02	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.71005	0.3289	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78807	-0.2059	10	0.87932	D	0	.	16.5981	0.84802	0.0:0.0:1.0:0.0	.	226;179	B4DR87;Q02809	.;PLOD1_HUMAN	H	179;226;179;179	ENSP00000365548:D226H;ENSP00000405372:D179H;ENSP00000196061:D179H	ENSP00000196061:D179H	D	+	1	0	PLOD1	11935335	1.000000	0.71417	0.945000	0.38365	0.821000	0.46438	9.585000	0.98223	2.380000	0.81148	0.555000	0.69702	GAT	G|1.000;T|0.000	.	alt		0.622	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
LAMC1	3915	hgsc.bcm.edu	37	1	183094547	183094547	+	Missense_Mutation	SNP	T	T	C	rs20558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:183094547T>C	ENST00000258341.4	+	15	2920	c.2663T>C	c.(2662-2664)cTg>cCg	p.L888P	LAMC1_ENST00000466964.1_3'UTR	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	888	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.		L -> P (in dbSNP:rs20558). {ECO:0000269|PubMed:1985895, ECO:0000269|PubMed:3360804}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						AATTGCAATCTGTATGGGACC	0.473													C|||	2663	0.531749	0.3321	0.6254	5008	,	,		17798	0.628		0.5636	False		,,,				2504	0.6033				p.L888P		Atlas-SNP	.											.	LAMC1	176	.	0			c.T2663C						PASS	.	C	PRO/LEU	1650,2756	659.6+/-400.6	334,982,887	133.0	114.0	120.0		2663	5.6	0.1	1	dbSNP_67	120	4898,3702	529.7+/-381.6	1352,2194,754	yes	missense	LAMC1	NM_002293.3	98	1686,3176,1641	CC,CT,TT		43.0465,37.4489,49.654	benign	888/1610	183094547	6548,6458	2203	4300	6503	SO:0001583	missense	3915	exon15			GCAATCTGTATGG	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.2663T>C	1.37:g.183094547T>C	ENSP00000258341:p.Leu888Pro	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	1166	0.5338827838827839	189	0.38414634146341464	211	0.5828729281767956	331	0.5786713286713286	435	0.5738786279683378	C	6.370	0.436410	0.12104	0.374489	0.569535	ENSG00000135862	ENST00000258341	T	0.60040	0.22	5.64	5.64	0.86602	EGF-like, laminin (3);	0.047130	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00162	-1.95	0.22968	P	0.99849924	B	0.02656	0.0	B	0.01281	0.0	T	0.43261	-0.9402	9	0.02654	T	1	.	14.4753	0.67541	0.0:0.9287:0.0:0.0713	rs20558;rs7410919;rs17398651;rs52812858;rs20558	888	P11047	LAMC1_HUMAN	P	888	ENSP00000258341:L888P	ENSP00000258341:L888P	L	+	2	0	LAMC1	181361170	1.000000	0.71417	0.071000	0.20095	0.012000	0.07955	4.396000	0.59684	1.396000	0.46663	-0.119000	0.15052	CTG	T|0.490;C|0.510	0.510	strong		0.473	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
PRSS57	400668	hgsc.bcm.edu	37	19	687078	687078	+	Silent	SNP	G	G	A	rs72618587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:687078G>A	ENST00000329267.7	-	4	521	c.492C>T	c.(490-492)ttC>ttT	p.F164F		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	164	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						AGTCAGACACGAAGCCCCAGC	0.692													G|||	527	0.105232	0.0719	0.0317	5008	,	,		16125	0.2738		0.0557	False		,,,				2504	0.0798				p.F164F		Atlas-SNP	.											.	PRSS57	18	.	0			c.C492T						PASS	.	G		305,4099	162.2+/-194.2	8,289,1905	36.0	36.0	36.0		492	-2.5	0.0	19	dbSNP_130	36	453,8147	134.1+/-191.5	16,421,3863	no	coding-synonymous	PRSS57	NM_214710.3		24,710,5768	AA,AG,GG		5.2674,6.9255,5.829		164/284	687078	758,12246	2202	4300	6502	SO:0001819	synonymous_variant	400668	exon4			AGACACGAAGCCC	AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"""Serine peptidases / Serine peptidases"""	31397	protein-coding gene	gene with protein product			"""protease, serine-like 1"""	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.492C>T	19.37:g.687078G>A		Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	231	120	0.519481	NM_214710	B2RNW8	Silent	SNP	ENST00000329267.7	37	CCDS12041.1																																																																																			G|0.928;A|0.072	0.072	strong		0.692	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710	
SCNN1B	6338	hgsc.bcm.edu	37	16	23360199	23360199	+	Silent	SNP	T	T	C	rs238547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:23360199T>C	ENST00000343070.2	+	2	455	c.279T>C	c.(277-279)ccT>ccC	p.P93P	SCNN1B_ENST00000569789.1_3'UTR|SCNN1B_ENST00000568923.1_Silent_p.P93P|SCNN1B_ENST00000568085.1_Silent_p.P93P|SCNN1B_ENST00000307331.5_Silent_p.P138P	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	93					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)	TGGACTTCCCTGCCGTCACCA	0.592													C|||	3949	0.788538	0.969	0.4582	5008	,	,		17020	0.9831		0.5408	False		,,,				2504	0.8333				p.P93P		Atlas-SNP	.											.	SCNN1B	81	.	0			c.T279C						PASS	.	C		3889,505	215.5+/-234.4	1737,415,45	69.0	62.0	64.0		279	-5.0	1.0	16	dbSNP_79	64	4717,3883	528.5+/-381.4	1287,2143,870	no	coding-synonymous	SCNN1B	NM_000336.2		3024,2558,915	CC,CT,TT		45.1512,11.4929,33.7694		93/641	23360199	8606,4388	2197	4300	6497	SO:0001819	synonymous_variant	6338	exon2			CTTCCCTGCCGTC	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.279T>C	16.37:g.23360199T>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	170	92	0.541176	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Silent	SNP	ENST00000343070.2	37	CCDS10609.1																																																																																			T|0.281;C|0.719	0.719	strong		0.592	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2		
FBXL5	26234	hgsc.bcm.edu	37	4	15640168	15640168	+	Silent	SNP	C	C	T	rs3182730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:15640168C>T	ENST00000341285.3	-	4	670	c.546G>A	c.(544-546)aaG>aaA	p.K182K	FBXL5_ENST00000382358.4_Silent_p.K56K|FBXL5_ENST00000412094.2_Silent_p.K165K	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	182					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						ATTTAAAAAACTTCTGTCGCT	0.338													C|||	481	0.0960463	0.0696	0.0807	5008	,	,		17245	0.0337		0.1581	False		,,,				2504	0.1431				p.K182K		Atlas-SNP	.											.	FBXL5	52	.	0			c.G546A						PASS	.	C	,,	325,4079	169.8+/-200.3	11,303,1888	71.0	66.0	68.0		546,495,546	1.8	1.0	4	dbSNP_105	68	1251,7349	250.0+/-277.0	99,1053,3148	no	coding-synonymous,coding-synonymous,coding-synonymous	FBXL5	NM_001193534.1,NM_001193535.1,NM_012161.3	,,	110,1356,5036	TT,TC,CC		14.5465,7.3797,12.1193	,,	182/691,165/675,182/692	15640168	1576,11428	2202	4300	6502	SO:0001819	synonymous_variant	26234	exon4			AAAAAACTTCTGT	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.546G>A	4.37:g.15640168C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	34	0.333333	NM_001193534	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Silent	SNP	ENST00000341285.3	37	CCDS3415.1	212	0.09706959706959707	50	0.1016260162601626	35	0.09668508287292818	18	0.03146853146853147	109	0.1437994722955145	C	7.981	0.751222	0.15778	0.073797	0.145465	ENSG00000118564	ENST00000513163	.	.	.	5.49	1.79	0.24919	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09574	-1.0668	3	.	.	.	-22.075	10.3944	0.44192	0.0:0.6401:0.0:0.3599	rs3182730;rs17418670	.	.	.	I	103	.	.	V	-	1	0	FBXL5	15249266	0.999000	0.42202	0.996000	0.52242	0.856000	0.48823	0.528000	0.23002	0.080000	0.16959	-0.961000	0.02630	GTT	T|0.112;G|0.000;C|0.888	0.112	strong		0.338	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2		
LRIT3	345193	hgsc.bcm.edu	37	4	110791526	110791526	+	Missense_Mutation	SNP	A	A	G	rs35997283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:110791526A>G	ENST00000594814.1	+	4	1621	c.1621A>G	c.(1621-1623)Ata>Gta	p.I541V	LRIT3_ENST00000327908.3_Missense_Mutation_p.I358V|LRIT3_ENST00000409621.2_Missense_Mutation_p.I358V|LRIT3_ENST00000379920.3_Missense_Mutation_p.I496V	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	541	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)		CCAAGTAACCATAGATGGCTT	0.488													A|||	8	0.00159744	0.0015	0.0029	5008	,	,		20846	0.0		0.002	False		,,,				2504	0.002				p.I541V		Atlas-SNP	.											.	LRIT3	107	.	0			c.A1621G						PASS	.	A	VAL/ILE	3,4403	6.2+/-15.9	0,3,2200	104.0	99.0	101.0		1486	2.6	1.0	4	dbSNP_126	101	59,8541	36.4+/-91.3	0,59,4241	yes	missense	LRIT3	NM_198506.2	29	0,62,6441	GG,GA,AA		0.686,0.0681,0.4767	benign	496/635	110791526	62,12944	2203	4300	6503	SO:0001583	missense	345193	exon4			GTAACCATAGATG	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.1621A>G	4.37:g.110791526A>G	ENSP00000469759:p.Ile541Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	A	13.22	2.171157	0.38315	6.81E-4	0.00686	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.27557	1.66;1.66;1.66	5.16	2.63	0.31362	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.106920	0.64402	D	0.000004	T	0.31136	0.0787	M	0.76838	2.35	0.40389	D	0.979528	P;P	0.46277	0.802;0.875	B;P	0.45037	0.206;0.467	T	0.36286	-0.9754	10	0.72032	D	0.01	.	11.922	0.52797	0.7234:0.2765:0.0:0.0	rs35997283	496;358	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	V	358;496;358	ENSP00000328222:I358V;ENSP00000369252:I496V;ENSP00000386734:I358V	ENSP00000328222:I358V	I	+	1	0	LRIT3	111010975	1.000000	0.71417	0.982000	0.44146	0.969000	0.65631	1.641000	0.37197	0.266000	0.21894	-0.313000	0.08912	ATA	A|0.996;G|0.004	0.004	strong		0.488	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
FIBCD1	84929	hgsc.bcm.edu	37	9	133779563	133779563	+	Missense_Mutation	SNP	C	C	T	rs138892175		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133779563C>T	ENST00000372338.4	-	7	1516	c.1274G>A	c.(1273-1275)cGc>cAc	p.R425H	FIBCD1_ENST00000448616.1_Missense_Mutation_p.R425H|FIBCD1_ENST00000372337.2_Missense_Mutation_p.R267H|FIBCD1_ENST00000253018.4_Intron	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	425	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)		GTGCGCACCGCGCAGGTACTG	0.627																																					p.R425H		Atlas-SNP	.											FIBCD1,NS,carcinoma,+1,2	FIBCD1	34	2	0			c.G1274A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	133.0	112.0	119.0		1274,1274	3.8	0.9	9	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FIBCD1	NM_001145106.1,NM_032843.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	425/462,425/462	133779563	1,13005	2203	4300	6503	SO:0001583	missense	84929	exon8			GCACCGCGCAGGT	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.1274G>A	9.37:g.133779563C>T	ENSP00000361413:p.Arg425His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_001145106	A3KFK0|Q6UXK6|Q96SJ7	Missense_Mutation	SNP	ENST00000372338.4	37	CCDS6937.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.298660	0.60195	0.0	1.16E-4	ENSG00000130720	ENST00000448616;ENST00000372338;ENST00000372337	T;T;T	0.76060	-0.99;-0.99;-0.99	4.66	3.75	0.43078	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.108817	0.56097	D	0.000024	T	0.58566	0.2131	L	0.46614	1.455	0.48288	D	0.999625	P	0.40619	0.724	B	0.25291	0.059	T	0.64309	-0.6438	10	0.54805	T	0.06	.	8.3984	0.32570	0.0:0.8277:0.0:0.1723	.	425	Q8N539	FBCD1_HUMAN	H	425;425;267	ENSP00000414501:R425H;ENSP00000361413:R425H;ENSP00000361412:R267H	ENSP00000361412:R267H	R	-	2	0	FIBCD1	132769384	0.842000	0.29525	0.881000	0.34555	0.103000	0.19146	1.528000	0.35985	2.138000	0.66242	0.455000	0.32223	CGC	C|1.000;T|0.000	0.000	weak		0.627	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843	
SVOP	55530	hgsc.bcm.edu	37	12	109309571	109309571	+	Missense_Mutation	SNP	C	C	T	rs76609278	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109309571C>T	ENST00000299134.5	-	13	1231	c.1232G>A	c.(1231-1233)cGt>cAt	p.R411H		NM_018711.2	NP_061181.1	Q8N4V2	SVOP_HUMAN	SV2 related protein homolog (rat)	0						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	ion transmembrane transporter activity (GO:0015075)			breast(2)|lung(4)	6						GGGCGATGAACGGAGTGATGA	0.607													C|||	263	0.052516	0.0696	0.0288	5008	,	,		17615	0.0952		0.0229	False		,,,				2504	0.0327				p.P423P		Atlas-SNP	.											.	SVOP	16	.	0			c.G1269A						PASS	.	C		236,3898		4,228,1835	31.0	35.0	34.0		1246	-7.5	0.8	12	dbSNP_132	34	215,8169		3,209,3980	no	coding-synonymous	SVOP	NM_018711.2		7,437,5815	TT,TC,CC		2.5644,5.7088,3.6028		476/549	109309571	451,12067	2067	4192	6259	SO:0001583	missense	55530	exon14			GATGAACGGAGTG	BC033587	CCDS73520.1	12q24.11	2011-07-12				ENSG00000166111			25417	protein-coding gene	gene with protein product		611699					Standard	NM_018711		Approved	DKFZp761H039	uc010sxh.1	Q8N4V2		ENST00000299134.5:c.1232G>A	12.37:g.109309571C>T	ENSP00000299134:p.Arg411His	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_018711	Q9NPW5	Silent	SNP	ENST00000299134.5	37		110	0.05036630036630037	40	0.08130081300813008	12	0.03314917127071823	42	0.07342657342657342	16	0.021108179419525065	C	9.685	1.150287	0.21371	0.057088	0.025644	ENSG00000166111	ENST00000299134	.	.	.	5.8	-7.52	0.01341	.	.	.	.	.	T	0.01976	0.0062	.	.	.	.	.	.	.	.	.	.	.	.	T	0.27468	-1.0073	3	.	.	.	-36.3173	9.4547	0.38747	0.0:0.1337:0.363:0.5033	.	.	.	.	H	411	.	.	R	-	2	0	SVOP	107833700	0.000000	0.05858	0.825000	0.32803	0.921000	0.55340	-5.705000	0.00103	-1.124000	0.02936	-0.749000	0.03505	CGT	C|0.954;T|0.046	0.046	strong		0.607	SVOP-001	KNOWN	mRNA_start_NF|cds_start_NF|basic	protein_coding	protein_coding	OTTHUMT00000403982.1	NM_018711	
ZNF407	55628	hgsc.bcm.edu	37	18	72344509	72344509	+	Missense_Mutation	SNP	G	G	A	rs7227263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:72344509G>A	ENST00000299687.5	+	1	1534	c.1534G>A	c.(1534-1536)Ggg>Agg	p.G512R	ZNF407_ENST00000582337.1_Missense_Mutation_p.G512R|ZNF407_ENST00000577538.1_Missense_Mutation_p.G512R|ZNF407_ENST00000309902.6_Missense_Mutation_p.G512R	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	512			G -> R (in dbSNP:rs7227263).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCCGGACTCCGGGCTGCATTC	0.562													G|||	339	0.0676917	0.112	0.0663	5008	,	,		18648	0.001		0.1064	False		,,,				2504	0.0378				p.G512R		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1534A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	404,3640		17,370,1635	85.0	93.0	90.0		1534,1534,1534	-9.6	0.0	18	dbSNP_116	90	1156,7212		87,982,3115	yes	missense,missense,missense	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	125,125,125	104,1352,4750	AA,AG,GG		13.8145,9.9901,12.5685	benign,benign,benign	512/1816,512/1661,512/2249	72344509	1560,10852	2022	4184	6206	SO:0001583	missense	55628	exon1			GACTCCGGGCTGC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1534G>A	18.37:g.72344509G>A	ENSP00000299687:p.Gly512Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	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	
IQCE	23288	hgsc.bcm.edu	37	7	2645552	2645552	+	Missense_Mutation	SNP	A	A	G	rs2293407	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2645552A>G	ENST00000402050.2	+	20	1970	c.1786A>G	c.(1786-1788)Acg>Gcg	p.T596A	IQCE_ENST00000404984.1_Missense_Mutation_p.T545A|IQCE_ENST00000438376.2_Missense_Mutation_p.T580A|IQCE_ENST00000325979.7_Missense_Mutation_p.T531A	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	596			T -> A (in dbSNP:rs2293407).			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)		CGCCCAGGCCACGGGCAGCCC	0.692													G|||	2073	0.413938	0.4009	0.464	5008	,	,		12402	0.494		0.327	False		,,,				2504	0.4029				p.T596A		Atlas-SNP	.											.	IQCE	66	.	0			c.A1786G						PASS	.	G	ALA/THR,ALA/THR	1515,2685		290,935,875	29.0	36.0	34.0		1738,1786	2.9	0.0	7	dbSNP_100	34	2321,6091		309,1703,2194	yes	missense,missense	IQCE	NM_001100390.1,NM_152558.3	58,58	599,2638,3069	GG,GA,AA		27.5915,36.0714,30.4155	benign,benign	580/680,596/696	2645552	3836,8776	2100	4206	6306	SO:0001583	missense	23288	exon20			CAGGCCACGGGCA	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.1786A>G	7.37:g.2645552A>G	ENSP00000385597:p.Thr596Ala	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	201	88	0.437811	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	883	0.4043040293040293	192	0.3902439024390244	144	0.39779005524861877	297	0.5192307692307693	250	0.32981530343007914	G	3.916	-0.019104	0.07634	0.360714	0.275915	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979;ENST00000423196	T;T;T;T;T	0.21031	2.92;2.91;2.92;2.92;2.03	4.79	2.89	0.33648	.	0.571682	0.14933	N	0.289966	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.11235	0.0;0.0;0.0;0.004	B;B;B;B	0.11329	0.001;0.001;0.0;0.006	T	0.44847	-0.9301	9	0.10377	T	0.69	-3.6098	7.1807	0.25770	0.0939:0.3532:0.5529:0.0	rs2293407;rs56785395	531;580;596;580	B4DXN1;B4DDX4;Q6IPM2;Q6IPM2-4	.;.;IQCE_HUMAN;.	A	596;545;580;531;176	ENSP00000385597:T596A;ENSP00000385945:T545A;ENSP00000396178:T580A;ENSP00000313772:T531A;ENSP00000405982:T176A	ENSP00000313772:T531A	T	+	1	0	IQCE	2612078	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.318000	0.19504	0.150000	0.19136	-0.215000	0.12644	ACG	A|0.612;G|0.388	0.388	strong		0.692	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
SYNGR2	9144	hgsc.bcm.edu	37	17	76167047	76167047	+	Silent	SNP	C	C	T	rs1062668	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:76167047C>T	ENST00000225777.3	+	2	308	c.249C>T	c.(247-249)gcC>gcT	p.A83A	SYNGR2_ENST00000588282.1_Silent_p.A83A|SYNGR2_ENST00000592456.1_3'UTR|SYNGR2_ENST00000590201.1_Silent_p.A27A|SYNGR2_ENST00000585591.1_Silent_p.A83A|SYNGR2_ENST00000589711.1_Intron			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						PASS	.	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	135	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	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		
TAS2R16	50833	hgsc.bcm.edu	37	7	122635024	122635024	+	Missense_Mutation	SNP	C	C	T	rs860170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:122635024C>T	ENST00000249284.2	-	1	730	c.665G>A	c.(664-666)cGc>cAc	p.R222H		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	222			R -> H (in dbSNP:rs860170). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15496549}.		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						GGCAGTGAAGCGCGCTTTCAT	0.443													T|||	3652	0.729233	0.9531	0.7622	5008	,	,		21414	0.5218		0.6859	False		,,,				2504	0.6616				p.R222H		Atlas-SNP	.											.	TAS2R16	57	.	0			c.G665A						PASS	.	T	HIS/ARG	3984,422	205.5+/-227.4	1805,374,24	156.0	130.0	139.0		665	2.2	0.1	7	dbSNP_86	139	5822,2778	440.1+/-359.4	1975,1872,453	yes	missense	TAS2R16	NM_016945.2	29	3780,2246,477	TT,TC,CC		32.3023,9.5778,24.604	benign	222/292	122635024	9806,3200	2203	4300	6503	SO:0001583	missense	50833	exon1			GTGAAGCGCGCTT	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.665G>A	7.37:g.122635024C>T	ENSP00000249284:p.Arg222His	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	172	83	0.482558	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Missense_Mutation	SNP	ENST00000249284.2	37	CCDS5785.1	1565	0.7165750915750916	464	0.943089430894309	268	0.7403314917127072	304	0.5314685314685315	529	0.6978891820580475	T	0.415	-0.911212	0.02434	0.904222	0.676977	ENSG00000128519	ENST00000249284	T	0.00635	6.06	4.67	2.21	0.28008	.	0.141755	0.46758	N	0.000275	T	0.00012	0.0000	N	0.00026	-2.66	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.12319	-1.0552	9	0.02654	T	1	.	3.9492	0.09361	0.0:0.1937:0.182:0.6243	rs860170;rs10441366;rs52808112;rs59417867;rs860170	222	Q9NYV7	T2R16_HUMAN	H	222	ENSP00000249284:R222H	ENSP00000249284:R222H	R	-	2	0	TAS2R16	122422260	0.779000	0.28652	0.138000	0.22173	0.044000	0.14063	1.247000	0.32815	0.058000	0.16222	-0.254000	0.11334	CGC	T|0.736;G|0.005	0.736	strong		0.443	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945	
LSP1	4046	hgsc.bcm.edu	37	11	1902768	1902768	+	Missense_Mutation	SNP	G	G	A	rs621679	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1902768G>A	ENST00000311604.3	+	3	473	c.298G>A	c.(298-300)Gcc>Acc	p.A100T	LSP1_ENST00000405957.2_Missense_Mutation_p.A38T|LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000381775.1_Missense_Mutation_p.A228T|LSP1_ENST00000406638.2_Missense_Mutation_p.A38T	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	100			A -> T (in dbSNP:rs621679). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.	Missing (in Ref. 3; AAB29545). {ECO:0000305}.	cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GGCGCAGGGCGCCTTGGACAG	0.706													g|||	1988	0.396965	0.2595	0.5418	5008	,	,		14019	0.5863		0.3867	False		,,,				2504	0.2955				p.A228T		Atlas-SNP	.											.	LSP1	59	.	0			c.G682A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	1155,3175		182,791,1192	15.0	16.0	16.0		112,112,112,298	-6.0	0.0	11	dbSNP_83	16	3046,5380		606,1834,1773	no	missense,missense,missense,missense	LSP1	NM_001013253.1,NM_001013254.1,NM_001013255.1,NM_002339.2	58,58,58,58	788,2625,2965	AA,AG,GG		36.15,26.6744,32.9335	benign,benign,benign,benign	38/278,38/278,38/278,100/340	1902768	4201,8555	2165	4213	6378	SO:0001583	missense	4046	exon4			CAGGGCGCCTTGG	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.298G>A	11.37:g.1902768G>A	ENSP00000308383:p.Ala100Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	151	68	0.450331	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	37	CCDS31334.1	913	0.41804029304029305	134	0.27235772357723576	168	0.46408839779005523	327	0.5716783216783217	284	0.37467018469656993	.	0.009	-1.859750	0.00552	0.266744	0.3615	ENSG00000130592	ENST00000311604;ENST00000421485;ENST00000446808;ENST00000381775;ENST00000405957;ENST00000451814;ENST00000457279;ENST00000429923;ENST00000406638;ENST00000418975;ENST00000417766;ENST00000432093	T;T;T;T;T;T;T;T;T;T;T;T	0.49139	2.0;1.49;1.54;1.93;1.99;1.48;1.98;1.55;1.99;0.79;1.99;1.99	2.98	-5.97	0.02227	.	1.832530	0.03432	N	0.207919	T	0.00012	0.0000	N	0.01493	-0.835	0.80722	P	0.0	B;B	0.24920	0.114;0.01	B;B	0.13407	0.009;0.002	T	0.10660	-1.0620	9	0.02654	T	1	-1.6885	1.6488	0.02767	0.385:0.1022:0.3106:0.2021	rs621679;rs3188464;rs16927670;rs17855362;rs57739592	228;100	E9PFP3;P33241	.;LSP1_HUMAN	T	100;38;38;228;38;38;91;83;38;118;38;38	ENSP00000308383:A100T;ENSP00000411191:A38T;ENSP00000402543:A38T;ENSP00000371194:A228T;ENSP00000383932:A38T;ENSP00000414106:A38T;ENSP00000400346:A91T;ENSP00000400999:A83T;ENSP00000384022:A38T;ENSP00000403460:A118T;ENSP00000416363:A38T;ENSP00000412405:A38T	ENSP00000308383:A100T	A	+	1	0	LSP1	1859344	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.012000	0.01451	-4.340000	0.00055	-1.783000	0.00646	GCC	G|0.638;A|0.362	0.362	strong		0.706	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2408530	2408530	+	Missense_Mutation	SNP	G	G	A	rs62120714	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2408530G>A	ENST00000332578.3	+	7	917	c.917G>A	c.(916-918)cGg>cAg	p.R306Q		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	306	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)		CCTTTCGGCCGGCACATCCAG	0.637													G|||	710	0.141773	0.1831	0.0663	5008	,	,		13976	0.2351		0.0427	False		,,,				2504	0.1452				p.R306Q		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G917A						PASS	.	G	GLN/ARG	757,3649	307.5+/-290.0	72,613,1518	87.0	73.0	77.0		917	2.5	0.1	19	dbSNP_129	77	379,8221	122.7+/-181.7	3,373,3924	yes	missense	TMPRSS9	NM_182973.1	43	75,986,5442	AA,AG,GG		4.407,17.1811,8.7344	probably-damaging	306/1060	2408530	1136,11870	2203	4300	6503	SO:0001583	missense	360200	exon7			TCGGCCGGCACAT	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.917G>A	19.37:g.2408530G>A	ENSP00000330264:p.Arg306Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	309	0.14148351648351648	86	0.17479674796747968	32	0.08839779005524862	156	0.2727272727272727	35	0.04617414248021108	G	15.38	2.816003	0.50527	0.171811	0.04407	ENSG00000178297	ENST00000395264;ENST00000332578	T	0.59224	0.28	4.67	2.53	0.30540	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.356468	0.20452	U	0.092078	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;D	0.64830	0.951;0.994	P;P	0.57371	0.819;0.797	T	0.05733	-1.0867	9	0.28530	T	0.3	.	5.4493	0.16554	0.3895:0.0:0.6105:0.0	rs62120714	306;340	Q7Z410;E7EMP4	TMPS9_HUMAN;.	Q	340;306	ENSP00000330264:R306Q	ENSP00000330264:R306Q	R	+	2	0	TMPRSS9	2359530	0.000000	0.05858	0.148000	0.22405	0.420000	0.31355	-0.025000	0.12413	0.966000	0.38159	0.491000	0.48974	CGG	G|0.900;A|0.100	0.100	strong		0.637	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
DCSTAMP	81501	hgsc.bcm.edu	37	8	105361803	105361803	+	Silent	SNP	C	C	T	rs117086639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:105361803C>T	ENST00000297581.2	+	2	1072	c.1023C>T	c.(1021-1023)caC>caT	p.H341H	DCSTAMP_ENST00000517991.1_Intron|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	341					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											TGAAACTGCACGGAGAGGTAG	0.502													C|||	94	0.01877	0.0182	0.0086	5008	,	,		19755	0.0288		0.0169	False		,,,				2504	0.0184				p.H341H		Atlas-SNP	.											.	.	.	.	0			c.C1023T						PASS	.	C		39,4367	43.1+/-76.7	0,39,2164	99.0	100.0	100.0		1023	-2.0	0.6	8	dbSNP_132	100	69,8531	39.8+/-96.3	1,67,4232	no	coding-synonymous	TM7SF4	NM_030788.2		1,106,6396	TT,TC,CC		0.8023,0.8852,0.8304		341/471	105361803	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	81501	exon2			ACTGCACGGAGAG	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"""Dendritic cells (DC)-specific transmembrane protein"", ""IL-Four INDuced"""	605933	"""transmembrane 7 superfamily member 4"""	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.1023C>T	8.37:g.105361803C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_030788	B7ZVW2|E7ESG0|Q2M2D5	Silent	SNP	ENST00000297581.2	37	CCDS6301.1																																																																																			C|0.989;T|0.011	0.011	strong		0.502	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
FASN	2194	hgsc.bcm.edu	37	17	80041466	80041466	+	Silent	SNP	G	G	A	rs2229425	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80041466G>A	ENST00000306749.2	-	31	5486	c.5268C>T	c.(5266-5268)agC>agT	p.S1756S	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1756	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			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)	AGCACCTCACGCTGGCCTGCA	0.637													.|||	236	0.0471246	0.0068	0.0764	5008	,	,		16867	0.001		0.1322	False		,,,				2504	0.0409				p.S1756S	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C5268T						PASS	.	G		144,4242	94.4+/-133.1	7,130,2056	35.0	34.0	35.0		5268	-7.1	0.8	17	dbSNP_98	35	1297,7287	244.2+/-273.5	96,1105,3091	no	coding-synonymous	FASN	NM_004104.4		103,1235,5147	AA,AG,GG		15.1095,3.2832,11.1103		1756/2512	80041466	1441,11529	2193	4292	6485	SO:0001819	synonymous_variant	2194	exon31			CCTCACGCTGGCC	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.5268C>T	17.37:g.80041466G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			G|0.916;A|0.084	0.084	strong		0.637	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
WAPAL	23063	hgsc.bcm.edu	37	10	88277457	88277457	+	Missense_Mutation	SNP	C	C	T	rs10887621	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:88277457C>T	ENST00000298767.5	-	2	842	c.370G>A	c.(370-372)Gtt>Att	p.V124I		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	124	Mediates interaction with the cohesin complex.		V -> I (in dbSNP:rs10887621).		mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						GTGTCTTCAACGACCACATGA	0.408													C|||	964	0.192492	0.0643	0.1239	5008	,	,		18371	0.1776		0.2803	False		,,,				2504	0.3395				p.V124I		Atlas-SNP	.											.	WAPAL	81	.	0			c.G370A						PASS	.	C	ILE/VAL	462,3944	218.7+/-236.7	20,422,1761	136.0	124.0	128.0		370	1.1	0.4	10	dbSNP_120	128	2426,6174	402.3+/-347.4	348,1730,2222	yes	missense	WAPAL	NM_015045.2	29	368,2152,3983	TT,TC,CC		28.2093,10.4857,22.2051	benign	124/1191	88277457	2888,10118	2203	4300	6503	SO:0001583	missense	23063	exon2			CTTCAACGACCAC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.370G>A	10.37:g.88277457C>T	ENSP00000298767:p.Val124Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	397	0.18177655677655677	37	0.07520325203252033	48	0.13259668508287292	100	0.17482517482517482	212	0.2796833773087071	C	8.675	0.903750	0.17760	0.104857	0.282093	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.22336	1.96	5.57	1.12	0.20585	.	0.771843	0.11847	N	0.523732	T	0.00012	0.0000	N	0.08118	0	0.27768	P	0.9435937	B;B;B;B	0.21753	0.06;0.014;0.014;0.024	B;B;B;B	0.17979	0.02;0.005;0.002;0.01	T	0.41448	-0.9508	9	0.51188	T	0.08	.	10.0746	0.42353	0.0:0.5265:0.0:0.4735	rs10887621;rs52791504;rs60591557;rs10887621	209;124;124;167	Q7Z5K2-3;B2RTX8;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	I	209;124;209	ENSP00000298767:V124I	ENSP00000298767:V124I	V	-	1	0	WAPAL	88267437	0.966000	0.33281	0.383000	0.26132	0.254000	0.26022	1.529000	0.35996	0.323000	0.23307	0.655000	0.94253	GTT	C|0.796;T|0.204	0.204	strong		0.408	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	
CSF1R	1436	hgsc.bcm.edu	37	5	149460553	149460553	+	Silent	SNP	A	A	G	rs216123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149460553A>G	ENST00000286301.3	-	3	375	c.84T>C	c.(82-84)ccT>ccC	p.P28P	CSF1R_ENST00000543093.1_Silent_p.P28P	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	28	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)	CGACCAGCTCAGGGACACTGG	0.607													A|||	1679	0.335264	0.2587	0.353	5008	,	,		21664	0.0893		0.5527	False		,,,				2504	0.456				p.P28P		Atlas-SNP	.											.	CSF1R	250	.	0			c.T84C						PASS	.	A		1287,3119	437.2+/-344.9	183,921,1099	86.0	61.0	69.0		84	-8.2	0.9	5	dbSNP_79	69	4874,3726	618.5+/-396.8	1407,2060,833	no	coding-synonymous	CSF1R	NM_005211.3		1590,2981,1932	GG,GA,AA		43.3256,29.2102,47.3704		28/973	149460553	6161,6845	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			CAGCTCAGGGACA	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.84T>C	5.37:g.149460553A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			A|0.588;G|0.411	0.411	strong		0.607	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
CNTN5	53942	hgsc.bcm.edu	37	11	99690376	99690376	+	Nonsense_Mutation	SNP	C	C	T	rs12292659	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:99690376C>T	ENST00000524871.1	+	4	447	c.157C>T	c.(157-159)Cga>Tga	p.R53*	CNTN5_ENST00000528682.1_Nonsense_Mutation_p.R53*|CNTN5_ENST00000527185.1_Nonsense_Mutation_p.R53*|CNTN5_ENST00000279463.3_Nonsense_Mutation_p.R53*|CNTN5_ENST00000418526.2_Intron	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	53					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		AACCAGACCACGATACAGCAG	0.428																																					p.R53X		Atlas-SNP	.											.	CNTN5	324	.	0			c.C157T						PASS	.	C	stop/ARG,	827,2987		0,827,1080	115.0	115.0	115.0		157,	3.0	0.9	11	dbSNP_120	115	2016,6260		0,2016,2122	yes	stop-gained,intron	CNTN5	NM_014361.3,NM_175566.2	,	0,2843,3202	TT,TC,CC		24.3596,21.6833,23.5153	,	53/1101,	99690376	2843,9247	1907	4138	6045	SO:0001587	stop_gained	53942	exon3			AGACCACGATACA	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.157C>T	11.37:g.99690376C>T	ENSP00000435637:p.Arg53*	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	243	130	0.534979	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Nonsense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.456071	0.84209	0.216833	0.243596	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	.	.	.	5.06	2.96	0.34315	.	0.104565	0.37483	N	0.002068	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0077	0.47644	0.1446:0.7156:0.1398:0.0	rs12292659;rs12292659	.	.	.	X	53	.	ENSP00000279463:R53X	R	+	1	2	CNTN5	99195586	0.798000	0.28890	0.915000	0.36163	0.672000	0.39443	1.290000	0.33319	1.385000	0.46445	0.650000	0.86243	CGA	C|0.822;T|0.178	0.178	strong		0.428	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
VCAN	1462	hgsc.bcm.edu	37	5	82789647	82789647	+	Silent	SNP	A	A	G	rs4470745	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:82789647A>G	ENST00000265077.3	+	5	1210	c.645A>G	c.(643-645)gtA>gtG	p.V215V	VCAN_ENST00000513984.1_Silent_p.V215V|VCAN_ENST00000502527.2_Silent_p.V215V|VCAN_ENST00000342785.4_Silent_p.V215V|VCAN_ENST00000343200.5_Silent_p.V215V|VCAN_ENST00000512590.2_Silent_p.V167V	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	215	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CTCCCAGAGTAGGCTGTTATG	0.473													A|||	1194	0.238419	0.2292	0.281	5008	,	,		19615	0.0893		0.4135	False		,,,				2504	0.1943				p.V215V		Atlas-SNP	.											.	VCAN	498	.	0			c.A645G						PASS	.	A	,,,	1066,3340	387.5+/-326.5	120,826,1257	138.0	132.0	134.0		645,645,645,645	3.4	1.0	5	dbSNP_111	134	3493,5107	511.9+/-377.8	697,2099,1504	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	817,2925,2761	GG,GA,AA		40.6163,24.1943,35.0531	,,,	215/656,215/2410,215/1643,215/3397	82789647	4559,8447	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon5			CAGAGTAGGCTGT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.645A>G	5.37:g.82789647A>G		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	200	93	0.465	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			A|0.691;G|0.309	0.309	strong		0.473	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
ELOVL2	54898	hgsc.bcm.edu	37	6	11005686	11005686	+	Silent	SNP	G	G	A	rs2295601	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:11005686G>A	ENST00000354666.3	-	3	257	c.174C>T	c.(172-174)aaC>aaT	p.N58N		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2	58					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|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)	fatty acid elongase activity (GO:0009922)	p.N58N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(2)	14	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			GAGCAGGTCTGTTCTTCATAT	0.443													G|||	1160	0.231629	0.1732	0.2752	5008	,	,		21146	0.2738		0.2326	False		,,,				2504	0.2352				p.N58N		Atlas-SNP	.											ELOVL2,NS,carcinoma,0,1	ELOVL2	40	1	1	Substitution - coding silent(1)	stomach(1)	c.C174T						PASS	.	G		709,3697	294.4+/-283.1	57,595,1551	105.0	95.0	98.0		174	5.1	1.0	6	dbSNP_100	98	1955,6645	344.7+/-325.5	216,1523,2561	no	coding-synonymous	ELOVL2	NM_017770.3		273,2118,4112	AA,AG,GG		22.7326,16.0917,20.4829		58/297	11005686	2664,10342	2203	4300	6503	SO:0001819	synonymous_variant	54898	exon3			AGGTCTGTTCTTC	AK000341	CCDS4518.1	6p24.1	2011-05-25	2011-05-25		ENSG00000197977	ENSG00000197977			14416	protein-coding gene	gene with protein product		611814	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2"""			12371743, 16564093	Standard	NM_017770		Approved	Ssc2	uc003mzp.4	Q9NXB9	OTTHUMG00000014252	ENST00000354666.3:c.174C>T	6.37:g.11005686G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_017770	Q6P9E1|Q86W94	Silent	SNP	ENST00000354666.3	37	CCDS4518.1																																																																																			G|0.781;A|0.219	0.219	strong		0.443	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1		
PTPLA	9200	hgsc.bcm.edu	37	10	17636309	17636309	+	Missense_Mutation	SNP	G	G	A	rs1053926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:17636309G>A	ENST00000361271.3	-	6	716	c.679C>T	c.(679-681)Cat>Tat	p.H227Y		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	227			H -> Y (in dbSNP:rs1053926). {ECO:0000269|PubMed:10644438, ECO:0000269|PubMed:11054553}.		fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						TTCTTCACATGCGGCAAGGCA	0.323													A|||	994	0.198482	0.2542	0.1744	5008	,	,		15516	0.0685		0.3022	False		,,,				2504	0.1677				p.H227Y		Atlas-SNP	.											.	PTPLA	34	.	0			c.C679T						PASS	.	A	TYR/HIS	1118,3288	711.7+/-408.0	151,816,1236	68.0	69.0	69.0		679	5.7	0.6	10	dbSNP_86	69	2405,6183	696.0+/-404.8	358,1689,2247	yes	missense	PTPLA	NM_014241.3	83	509,2505,3483	AA,AG,GG		28.0042,25.3745,27.1125	benign	227/289	17636309	3523,9471	2203	4294	6497	SO:0001583	missense	9200	exon6			TCACATGCGGCAA	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"""cementum attachment protein"""	610467	"""protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"""			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.679C>T	10.37:g.17636309G>A	ENSP00000355308:p.His227Tyr	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	179	80	0.446927	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	435	0.19917582417582416	123	0.25	72	0.19889502762430938	26	0.045454545454545456	214	0.28232189973614774	A	0.881	-0.728885	0.03135	0.253745	0.280042	ENSG00000165996	ENST00000361271	T	0.28666	1.6	5.72	5.72	0.89469	.	0.165083	0.56097	N	0.000036	T	0.00012	0.0000	N	0.01410	-0.885	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	9	0.02654	T	1	-17.2091	9.2783	0.37714	0.8614:0.0:0.1386:0.0	rs1053926;rs3167994;rs52791621;rs1053926	227	B0YJ81	HACD1_HUMAN	Y	227	ENSP00000355308:H227Y	ENSP00000355308:H227Y	H	-	1	0	PTPLA	17676315	0.996000	0.38824	0.583000	0.28640	0.543000	0.35085	3.798000	0.55522	1.099000	0.41499	-0.269000	0.10298	CAT	G|0.764;A|0.236	0.236	strong		0.323	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241	
DENND2C	163259	hgsc.bcm.edu	37	1	115164554	115164554	+	Missense_Mutation	SNP	C	C	T	rs56861557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:115164554C>T	ENST00000393274.1	-	7	1814	c.1189G>A	c.(1189-1191)Ggt>Agt	p.G397S	DENND2C_ENST00000393277.1_Missense_Mutation_p.G397S|DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393276.3_Intron	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	397					positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCAACTTCACCAGCTCGGAAA	0.398													C|||	216	0.043131	0.0552	0.0519	5008	,	,		19072	0.001		0.0497	False		,,,				2504	0.0573				p.G397S		Atlas-SNP	.											.	DENND2C	105	.	0			c.G1189A						PASS	.																																			SO:0001583	missense	163259	exon7			CTTCACCAGCTCG		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1189G>A	1.37:g.115164554C>T	ENSP00000376955:p.Gly397Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	37	CCDS58018.1	75	0.034340659340659344	22	0.044715447154471545	14	0.03867403314917127	1	0.0017482517482517483	38	0.05013192612137203	C	15.74	2.922682	0.52653	.	.	ENSG00000175984	ENST00000393274;ENST00000369540;ENST00000393277	T;T	0.08634	3.71;3.07	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000004	T	0.02610	0.0079	.	.	.	0.32586	N	0.527836	D	0.53151	0.958	B	0.38378	0.272	T	0.50874	-0.8776	9	0.13853	T	0.58	.	19.736	0.96205	0.0:1.0:0.0:0.0	rs56861557	397	Q68D51	DEN2C_HUMAN	S	397	ENSP00000376955:G397S;ENSP00000376958:G397S	ENSP00000358553:G397S	G	-	1	0	DENND2C	114966077	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	5.000000	0.63940	2.732000	0.93576	0.557000	0.71058	GGT	C|0.960;T|0.040	0.040	strong		0.398	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
KCTD17	79734	hgsc.bcm.edu	37	22	37458571	37458571	+	Silent	SNP	C	C	T	rs142739650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37458571C>T	ENST00000403888.3	+	9	904	c.903C>T	c.(901-903)taC>taT	p.Y301Y	KCTD17_ENST00000402077.3_Silent_p.Y277Y	NM_001282684.1	NP_001269613.1	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerization domain containing 17	301	Pro-rich.				protein homooligomerization (GO:0051260)		identical protein binding (GO:0042802)			NS(1)|breast(1)|endometrium(1)|lung(1)|prostate(1)	5						CTAGCTGTTACAAGCCAGAGG	0.612																																					p.Y277Y		Atlas-SNP	.											.	KCTD17	17	.	0			c.C831T						PASS	.	C		0,4406		0,0,2203	48.0	48.0	48.0		831	3.8	1.0	22	dbSNP_134	48	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	KCTD17	NM_024681.2		0,7,6496	TT,TC,CC		0.0814,0.0,0.0538		277/298	37458571	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	79734	exon8			CTGTTACAAGCCA	BC025403	CCDS13940.2, CCDS74854.1, CCDS74855.1	22q12.3	2013-06-20	2013-06-20		ENSG00000100379	ENSG00000100379			25705	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 17"""			12477932	Standard	XM_005261741		Approved	FLJ12242	uc011amv.2	Q8N5Z5	OTTHUMG00000150532	ENST00000403888.3:c.903C>T	22.37:g.37458571C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_024681	B0QYA9|B0QYB0|O95517	Silent	SNP	ENST00000403888.3	37																																																																																				C|0.999;T|0.001	0.001	strong		0.612	KCTD17-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318781.1	NM_024681	
CER1	9350	hgsc.bcm.edu	37	9	14722477	14722477	+	Missense_Mutation	SNP	G	G	C	rs3747532	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	190	106	0.557895	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	
COL9A3	1299	hgsc.bcm.edu	37	20	61463522	61463522	+	Missense_Mutation	SNP	C	C	A	rs751557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	150	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	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	
TRPA1	8989	hgsc.bcm.edu	37	8	72987638	72987638	+	Missense_Mutation	SNP	G	G	A	rs13268757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:72987638G>A	ENST00000262209.4	-	1	214	c.7C>T	c.(7-9)Cgc>Tgc	p.R3C		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	3			R -> C (in dbSNP:rs13268757). {ECO:0000269|PubMed:10066796}.		calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CTCAGGCTGCGCTTCATTGAC	0.652													g|||	503	0.100439	0.0825	0.0735	5008	,	,		13603	0.0565		0.173	False		,,,				2504	0.1145				p.R3C		Atlas-SNP	.											.	TRPA1	256	.	0			c.C7T						PASS	.	A	CYS/ARG	365,4041	186.7+/-213.5	14,337,1852	66.0	69.0	68.0		7	2.7	1.0	8	dbSNP_121	68	1437,7163	276.4+/-292.3	117,1203,2980	yes	missense	TRPA1	NM_007332.2	180	131,1540,4832	AA,AG,GG		16.7093,8.2842,13.8551	probably-damaging	3/1120	72987638	1802,11204	2203	4300	6503	SO:0001583	missense	8989	exon1			GGCTGCGCTTCAT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.7C>T	8.37:g.72987638G>A	ENSP00000262209:p.Arg3Cys	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	223	0.1021062271062271	26	0.052845528455284556	28	0.07734806629834254	40	0.06993006993006994	129	0.17018469656992086	g	10.45	1.352754	0.24512	0.082842	0.167093	ENSG00000104321	ENST00000262209	T	0.42513	0.97	4.58	2.73	0.32206	.	0.173631	0.36134	N	0.002767	T	0.00109	0.0003	L	0.39147	1.195	0.25823	P	0.9842676	B	0.15141	0.012	B	0.04013	0.001	T	0.04723	-1.0931	9	0.87932	D	0	-1.0158	8.9297	0.35663	0.0844:0.0:0.7798:0.1358	rs13268757;rs58641623;rs13268757	3	O75762	TRPA1_HUMAN	C	3	ENSP00000262209:R3C	ENSP00000262209:R3C	R	-	1	0	TRPA1	73150192	0.997000	0.39634	0.999000	0.59377	0.224000	0.24922	0.071000	0.14594	0.256000	0.21614	-0.875000	0.02981	CGC	G|0.872;A|0.128	0.128	strong		0.652	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33419593	33419593	+	Silent	SNP	G	G	A	rs372190836		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33419593G>A	ENST00000418600.2	+	19	4043	c.3942G>A	c.(3940-3942)ccG>ccA	p.P1314P	ZBTB9_ENST00000395064.2_5'Flank|SYNGAP1_ENST00000428982.2_Silent_p.P1255P|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1314					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						TGGCCCCACCGTGGAATGGCC	0.642																																					p.P1314P		Atlas-SNP	.											SYNGAP1,caecum,carcinoma,0,1	SYNGAP1	202	1	0			c.G3942A						scavenged	.	A		0,4406		0,0,2203	16.0	15.0	15.0		3942	-0.8	1.0	6		15	1,8597		0,1,4298	no	coding-synonymous	SYNGAP1	NM_006772.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		1314/1344	33419593	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	8831	exon19			CCCACCGTGGAAT	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.3942G>A	6.37:g.33419593G>A		Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			.	.	weak		0.642	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
TNFAIP2	7127	hgsc.bcm.edu	37	14	103601637	103601637	+	Silent	SNP	C	C	T	rs2234147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:103601637C>T	ENST00000560869.1	+	12	2544	c.1905C>T	c.(1903-1905)gaC>gaT	p.D635D	TNFAIP2_ENST00000451723.2_Silent_p.D304D|TNFAIP2_ENST00000538222.1_Silent_p.D118D|TNFAIP2_ENST00000333007.1_Silent_p.D635D			Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	635					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|exocytosis (GO:0006887)	exocyst (GO:0000145)|extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	11		Melanoma(154;0.155)	Epithelial(46;0.191)			GCATCTTGGACGTCAGCATGG	0.577													c|||	59	0.0117812	0.0015	0.0159	5008	,	,		19498	0.0		0.0119	False		,,,				2504	0.0348				p.D635D		Atlas-SNP	.											.	TNFAIP2	53	.	0			c.C1905T						PASS	.			19,4387	26.2+/-53.5	0,19,2184	167.0	172.0	170.0		1905	0.2	0.5	14	dbSNP_98	170	87,8513	49.8+/-109.6	0,87,4213	no	coding-synonymous	TNFAIP2	NM_006291.2		0,106,6397	TT,TC,CC		1.0116,0.4312,0.815		635/655	103601637	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	7127	exon11			CTTGGACGTCAGC		CCDS9979.1	14q32	2011-01-31				ENSG00000185215			11895	protein-coding gene	gene with protein product	"""exocyst complex component 3-like 3"""	603300				1374453	Standard	NM_006291		Approved	B94, EXOC3L3	uc001ymm.1	Q03169		ENST00000560869.1:c.1905C>T	14.37:g.103601637C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_006291	Q86VI0	Silent	SNP	ENST00000560869.1	37	CCDS9979.1																																																																																			C|0.993;T|0.007	0.007	strong		0.577	TNFAIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415674.1	NM_006291	
BPIFB6	128859	hgsc.bcm.edu	37	20	31627291	31627291	+	Missense_Mutation	SNP	A	A	G	rs4911287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31627291A>G	ENST00000349552.1	+	10	1039	c.1039A>G	c.(1039-1041)Agc>Ggc	p.S347G		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	347			S -> G (in dbSNP:rs4911287).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCGGTGGCGGAGCAAGGCTCC	0.532													G|||	3037	0.60643	0.7716	0.4827	5008	,	,		20088	0.7421		0.3917	False		,,,				2504	0.5521				p.S347G		Atlas-SNP	.											BPIL3,NS,carcinoma,-2,1	.	.	1	0			c.A1039G						PASS	.	G	GLY/SER	3060,1346	446.5+/-348.0	1092,876,235	105.0	112.0	109.0		1039	2.0	0.0	20	dbSNP_111	109	3244,5356	650.1+/-400.7	612,2020,1668	yes	missense	BPIFB6	NM_174897.2	56	1704,2896,1903	GG,GA,AA		37.7209,30.5493,48.4699	benign	347/454	31627291	6304,6702	2203	4300	6503	SO:0001583	missense	128859	exon10			TGGCGGAGCAAGG	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.1039A>G	20.37:g.31627291A>G	ENSP00000344929:p.Ser347Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	1268	0.5805860805860806	394	0.8008130081300813	165	0.4558011049723757	414	0.7237762237762237	295	0.3891820580474934	G	0.460	-0.889715	0.02511	0.694507	0.377209	ENSG00000167104	ENST00000349552	T	0.06687	3.27	4.43	2.02	0.26589	.	0.707366	0.12342	N	0.477386	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09228	-1.0684	9	0.10902	T	0.67	.	5.9577	0.19283	0.39:0.0:0.61:0.0	rs4911287;rs57352515;rs4911287	347	Q8NFQ5	BPIB6_HUMAN	G	347	ENSP00000344929:S347G	ENSP00000344929:S347G	S	+	1	0	BPIFB6	31090952	0.500000	0.26091	0.015000	0.15790	0.003000	0.03518	0.538000	0.23160	0.396000	0.25283	-0.227000	0.12334	AGC	A|0.477;G|0.523	0.523	strong		0.532	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
ZFHX4	79776	hgsc.bcm.edu	37	8	77690563	77690563	+	Silent	SNP	T	T	C	rs16939357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:77690563T>C	ENST00000521891.2	+	4	3661	c.3213T>C	c.(3211-3213)caT>caC	p.H1071H	ZFHX4_ENST00000517683.1_3'UTR|ZFHX4_ENST00000050961.6_Silent_p.H1045H|ZFHX4_ENST00000455469.2_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	105	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	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	
MUC16	94025	hgsc.bcm.edu	37	19	8993383	8993383	+	Silent	SNP	G	G	C	rs117289107	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8993383G>C	ENST00000397910.4	-	66	41909	c.41706C>G	c.(41704-41706)ctC>ctG	p.L13902L	MUC16_ENST00000380951.5_Silent_p.L543L	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13905	SEA 12. {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						CATTGACATAGAGACTGTCCC	0.557													g|||	52	0.0103834	0.0	0.0043	5008	,	,		20085	0.0218		0.0159	False		,,,				2504	0.0112				p.L13902L		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-2,1	MUC16	4315	1	0			c.C41706G						PASS	.	G		23,4127		0,23,2052	156.0	144.0	148.0		41706	-1.6	0.0	19	dbSNP_132	148	199,8189		0,199,3995	no	coding-synonymous	MUC16	NM_024690.2		0,222,6047	CC,CG,GG		2.3724,0.5542,1.7706		13902/14508	8993383	222,12316	2075	4194	6269	SO:0001819	synonymous_variant	94025	exon66			GACATAGAGACTG	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.41706C>G	19.37:g.8993383G>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	21	0.009615384615384616	0	0.0	3	0.008287292817679558	8	0.013986013986013986	10	0.013192612137203167	.	1.563	-0.536118	0.04082	0.005542	0.023724	ENSG00000181143	ENST00000542240	.	.	.	3.61	-1.59	0.08453	.	.	.	.	.	T	0.15478	0.0373	.	.	.	.	.	.	.	.	.	.	.	.	T	0.31971	-0.9924	3	.	.	.	.	4.6347	0.12518	0.2125:0.3326:0.4549:0.0	.	.	.	.	C	742	.	.	S	-	2	0	MUC16	8854383	0.566000	0.26618	0.009000	0.14445	0.031000	0.12232	0.060000	0.14342	-0.249000	0.09569	-0.357000	0.07601	TCT	G|0.987;C|0.013	0.013	strong		0.557	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
C6orf118	168090	hgsc.bcm.edu	37	6	165713917	165713917	+	Missense_Mutation	SNP	C	C	T	rs17852379	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:165713917C>T	ENST00000230301.8	-	3	832	c.812G>A	c.(811-813)gGa>gAa	p.G271E	C6orf118_ENST00000543069.1_Missense_Mutation_p.G167E	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	271			G -> E (in dbSNP:rs17852379). {ECO:0000269|PubMed:15489334}.							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)		AAAGACTTTTCCAAAGACGTG	0.408													C|||	517	0.103235	0.3026	0.062	5008	,	,		16060	0.0		0.0636	False		,,,				2504	0.0102				p.G271E		Atlas-SNP	.											C6orf118,colon,carcinoma,0,1	C6orf118	116	1	0			c.G812A						PASS	.	C	GLU/GLY	1320,3086	439.6+/-345.7	189,942,1072	125.0	145.0	139.0		812	2.4	0.0	6	dbSNP_123	139	535,8065	147.9+/-203.2	17,501,3782	yes	missense	C6orf118	NM_144980.3	98	206,1443,4854	TT,TC,CC		6.2209,29.9591,14.2626	probably-damaging	271/470	165713917	1855,11151	2203	4300	6503	SO:0001583	missense	168090	exon3			ACTTTTCCAAAGA		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.812G>A	6.37:g.165713917C>T	ENSP00000230301:p.Gly271Glu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	214	0.09798534798534798	146	0.2967479674796748	22	0.06077348066298342	0	0.0	46	0.06068601583113457	C	10.64	1.408313	0.25378	0.299591	0.062209	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.13538	2.58;2.58	5.24	2.39	0.29439	.	0.428311	0.21908	N	0.067358	T	0.15696	0.0378	M	0.62723	1.935	0.80722	P	0.0	D	0.76494	0.999	D	0.69479	0.964	T	0.03212	-1.1060	9	0.41790	T	0.15	-10.206	8.192	0.31374	0.0:0.6174:0.3002:0.0823	rs17852379;rs17852379	271	Q5T5N4	CF118_HUMAN	E	271;167	ENSP00000230301:G271E;ENSP00000439288:G167E	ENSP00000230301:G271E	G	-	2	0	C6orf118	165633907	0.008000	0.16893	0.002000	0.10522	0.005000	0.04900	1.689000	0.37700	0.176000	0.19873	0.655000	0.94253	GGA	C|0.874;T|0.126	0.126	strong		0.408	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
CELSR2	1952	hgsc.bcm.edu	37	1	109807099	109807099	+	Silent	SNP	G	G	A	rs6689614	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109807099G>A	ENST00000271332.3	+	11	5374	c.5313G>A	c.(5311-5313)ccG>ccA	p.P1771P		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1771	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GCGATACGCCGGAGGGGGTTA	0.652													A|||	1768	0.353035	0.0764	0.4654	5008	,	,		14927	0.497		0.4751	False		,,,				2504	0.3732				p.P1771P	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											CELSR2,NS,adenoma,0,1	CELSR2	228	1	0			c.G5313A						PASS	.	A		582,3824	772.6+/-413.9	35,512,1656	115.0	101.0	105.0		5313	-10.0	0.0	1	dbSNP_116	105	4005,4595	598.8+/-394.0	929,2147,1224	no	coding-synonymous	CELSR2	NM_001408.2		964,2659,2880	AA,AG,GG		46.5698,13.2093,35.2683		1771/2924	109807099	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon11			TACGCCGGAGGGG	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.5313G>A	1.37:g.109807099G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			G|0.632;A|0.368	0.368	strong		0.652	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
TRPV3	162514	hgsc.bcm.edu	37	17	3446885	3446885	+	Missense_Mutation	SNP	T	T	C	rs322937	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3446885T>C	ENST00000576742.1	-	5	670	c.349A>G	c.(349-351)Agg>Ggg	p.R117G	TRPV3_ENST00000572519.1_Missense_Mutation_p.R117G|TRPV3_ENST00000301365.4_Missense_Mutation_p.R117G	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	117			R -> G (in dbSNP:rs322937). {ECO:0000269|PubMed:12077606}.		calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	TTCAGCCGCCTCTTTTTCCTC	0.547													T|||	1256	0.250799	0.115	0.2147	5008	,	,		19720	0.247		0.3996	False		,,,				2504	0.3108				p.R117G		Atlas-SNP	.											.	TRPV3	85	.	0			c.A349G						PASS	.	T	GLY/ARG	731,3675	301.3+/-286.8	72,587,1544	115.0	111.0	112.0		349	2.8	1.0	17	dbSNP_79	112	3431,5169	505.5+/-376.4	670,2091,1539	yes	missense	TRPV3	NM_145068.2	125	742,2678,3083	CC,CT,TT		39.8953,16.591,32.0006	benign	117/791	3446885	4162,8844	2203	4300	6503	SO:0001583	missense	162514	exon5			GCCGCCTCTTTTT	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.349A>G	17.37:g.3446885T>C	ENSP00000461518:p.Arg117Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	37	CCDS11029.1	571	0.26144688644688646	43	0.08739837398373984	89	0.24585635359116023	136	0.23776223776223776	303	0.3997361477572559	T	8.019	0.759106	0.15846	0.16591	0.398953	ENSG00000167723	ENST00000381913;ENST00000301365;ENST00000430263	D	0.87491	-2.26	5.12	2.83	0.33086	.	0.384610	0.26300	N	0.025163	T	0.00012	0.0000	L	0.45352	1.415	0.48288	P	3.769999999999607E-4	B;B;B;B	0.14012	0.007;0.007;0.009;0.007	B;B;B;B	0.19391	0.015;0.015;0.025;0.015	T	0.10894	-1.0610	9	0.39692	T	0.17	-6.117	10.6601	0.45698	0.0:0.0:0.3068:0.6932	rs322937;rs59567507;rs322937	101;117;117;117	E7EV24;Q8NET8-3;Q8NET8;Q8NET8-2	.;.;TRPV3_HUMAN;.	G	117;117;101	ENSP00000301365:R117G	ENSP00000301365:R117G	R	-	1	2	TRPV3	3393635	0.993000	0.37304	0.990000	0.47175	0.079000	0.17450	2.032000	0.41127	0.326000	0.23384	-0.429000	0.05907	AGG	T|0.714;C|0.286	0.286	strong		0.547	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
CDHR1	92211	hgsc.bcm.edu	37	10	85960395	85960395	+	Silent	SNP	A	A	G	rs4933975	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85960395A>G	ENST00000372117.3	+	6	580	c.477A>G	c.(475-477)gcA>gcG	p.A159A	CDHR1_ENST00000332904.3_Silent_p.A159A|CDHR1_ENST00000440770.2_5'Flank	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	159	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGGTCCATGCAGTGGACAGGG	0.597													G|||	2584	0.515974	0.711	0.5202	5008	,	,		19219	0.3948		0.4612	False		,,,				2504	0.4305				p.A159A		Atlas-SNP	.											CDHR1,NS,carcinoma,+2,1	CDHR1	122	1	0			c.A477G						PASS	.	G	,	2949,1457	466.0+/-354.4	1006,937,260	112.0	79.0	90.0		477,477	-10.6	0.0	10	dbSNP_111	90	3878,4722	604.6+/-394.8	859,2160,1281	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	1865,3097,1541	GG,GA,AA		45.093,33.0685,47.5088	,	159/746,159/860	85960395	6827,6179	2203	4300	6503	SO:0001819	synonymous_variant	92211	exon6			CCATGCAGTGGAC	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.477A>G	10.37:g.85960395A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	204	82	0.401961	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			A|0.487;G|0.513	0.513	strong		0.597	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
EPHA7	2045	hgsc.bcm.edu	37	6	94067981	94067981	+	Silent	SNP	C	C	T	rs164544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:94067981C>T	ENST00000369303.4	-	4	1165	c.981G>A	c.(979-981)gcG>gcA	p.A327A		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	327	Cys-rich.				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)		CACTTGTGCACGCAACGTATG	0.403													T|||	3658	0.730431	0.8911	0.6455	5008	,	,		13541	0.8294		0.5527	False		,,,				2504	0.6544				p.A327A		Atlas-SNP	.											.	EPHA7	251	.	0			c.G981A						PASS	.	T		3659,747	306.3+/-289.4	1528,603,72	99.0	97.0	97.0		981	-11.8	0.1	6	dbSNP_79	97	4616,3984	552.9+/-386.2	1237,2142,921	no	coding-synonymous	EPHA7	NM_004440.3		2765,2745,993	TT,TC,CC		46.3256,16.9542,36.3755		327/999	94067981	8275,4731	2203	4300	6503	SO:0001819	synonymous_variant	2045	exon4			TGTGCACGCAACG	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.981G>A	6.37:g.94067981C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	37	CCDS5031.1																																																																																			C|0.322;T|0.678	0.678	strong		0.403	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
SUPT5H	6829	hgsc.bcm.edu	37	19	39955533	39955533	+	Silent	SNP	G	G	A	rs2304217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39955533G>A	ENST00000599117.1	+	12	1087	c.720G>A	c.(718-720)gaG>gaA	p.E240E	SUPT5H_ENST00000359191.6_Silent_p.E236E|SUPT5H_ENST00000402194.2_Silent_p.E236E|SUPT5H_ENST00000432763.2_Silent_p.E240E|SUPT5H_ENST00000598725.1_Silent_p.E240E			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	240	Interaction with SUPT4H1.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGGCCATTGAGGGGGTGGGCA	0.577													G|||	687	0.137181	0.1619	0.1254	5008	,	,		17964	0.1111		0.171	False		,,,				2504	0.1043				p.E240E		Atlas-SNP	.											.	SUPT5H	119	.	0			c.G720A						PASS	.	G	,,,	715,3691	295.9+/-283.9	59,597,1547	97.0	83.0	88.0		720,720,708,720	2.3	1.0	19	dbSNP_100	88	1462,7138	278.2+/-293.3	130,1202,2968	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SUPT5H	NM_001111020.2,NM_001130824.1,NM_001130825.1,NM_003169.3	,,,	189,1799,4515	AA,AG,GG		17.0,16.2279,16.7384	,,,	240/1088,240/1088,236/1084,240/1088	39955533	2177,10829	2203	4300	6503	SO:0001819	synonymous_variant	6829	exon10			CATTGAGGGGGTG	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.720G>A	19.37:g.39955533G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_003169	O43279|Q59G52|Q99639	Silent	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																			G|0.846;A|0.154	0.154	strong		0.577	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
UGT1A6	54578	hgsc.bcm.edu	37	2	234652347	234652347	+	Intron	SNP	C	C	G	rs13009407	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:234652347C>G	ENST00000305139.6	+	2	1000				UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A3_ENST00000482026.1_Intron|DNAJB3_ENST00000449667.1_RNA	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6						cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	CGCCCTCCGCCCCCGCCTCGC	0.642													C|||	731	0.145966	0.0121	0.1628	5008	,	,		15622	0.0407		0.2356	False		,,,				2504	0.3313				p.G72G		Atlas-SNP	.											.	.	.	.	0			c.G216C						PASS	.	C	,,,,,,,,,	223,3791		17,189,1801	92.0	104.0	100.0		216,,,,,,,,,	-7.1	0.0	2	dbSNP_121	100	2166,6190		285,1596,2297	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3,DNAJB3	NM_001001394.3,NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,,,,	302,1785,4098	GG,GC,CC		25.9215,5.5556,19.3129	,,,,,,,,,	72/146,,,,,,,,,	234652347	2389,9981	2007	4178	6185	SO:0001627	intron_variant	414061	exon1			CTCCGCCCCCGCC	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.862-23333C>G	2.37:g.234652347C>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_001001394	A6NKK6|B8K289|Q96TE7	Silent	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			C|0.867;G|0.133	0.133	strong		0.642	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
DYM	54808	hgsc.bcm.edu	37	18	46623854	46623854	+	Missense_Mutation	SNP	T	T	C	rs146000214		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:46623854T>C	ENST00000269445.6	-	16	2235	c.1778A>G	c.(1777-1779)cAa>cGa	p.Q593R	DYM_ENST00000442713.2_Missense_Mutation_p.Q403R	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	593					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						AGCTCCAGCTTGCAGCAACCT	0.433													T|||	1	0.000199681	0.0	0.0014	5008	,	,		22199	0.0		0.0	False		,,,				2504	0.0				p.Q593R		Atlas-SNP	.											.	DYM	52	.	0			c.A1778G						PASS	.	T	ARG/GLN	0,4406		0,0,2203	86.0	78.0	81.0		1778	5.6	0.4	18	dbSNP_134	81	9,8591	7.1+/-27.0	0,9,4291	yes	missense	DYM	NM_017653.3	43	0,9,6494	CC,CT,TT		0.1047,0.0,0.0692	benign	593/670	46623854	9,12997	2203	4300	6503	SO:0001583	missense	54808	exon16			CCAGCTTGCAGCA	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1778A>G	18.37:g.46623854T>C	ENSP00000269445:p.Gln593Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	37	CCDS11937.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	14.50	2.554677	0.45487	0.0	0.001047	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.82619	-1.63;-1.63	5.61	5.61	0.85477	.	0.053248	0.85682	D	0.000000	D	0.87478	0.6187	L	0.49640	1.575	0.80722	D	1	P;D	0.59357	0.908;0.985	P;D	0.74023	0.888;0.982	D	0.84012	0.0349	10	0.15952	T	0.53	-13.7508	15.7757	0.78214	0.0:0.0:0.0:1.0	.	403;593	Q7RTS9-2;Q7RTS9	.;DYM_HUMAN	R	403;593	ENSP00000395942:Q403R;ENSP00000269445:Q593R	ENSP00000269445:Q593R	Q	-	2	0	DYM	44877852	1.000000	0.71417	0.351000	0.25721	0.899000	0.52679	7.142000	0.77339	2.254000	0.74563	0.533000	0.62120	CAA	T|0.999;C|0.001	0.001	strong		0.433	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653	
KRT6B	3854	hgsc.bcm.edu	37	12	52841179	52841179	+	Missense_Mutation	SNP	T	T	C	rs61746354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52841179T>C	ENST00000252252.3	-	9	1537	c.1490A>G	c.(1489-1491)tAt>tGt	p.Y497C		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	497	Tail.				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)		GGCACCGCCATAGCCACTGGA	0.612													T|||	128	0.0255591	0.003	0.0317	5008	,	,		20137	0.0		0.0427	False		,,,				2504	0.0603				p.Y497C		Atlas-SNP	.											.	KRT6B	90	.	0			c.A1490G						PASS	.	T	CYS/TYR	57,4349	53.6+/-89.4	0,57,2146	44.0	45.0	45.0		1490	2.0	0.4	12	dbSNP_129	45	459,8141	136.2+/-193.3	19,421,3860	no	missense	KRT6B	NM_005555.3	194	19,478,6006	CC,CT,TT		5.3372,1.2937,3.9674	benign	497/565	52841179	516,12490	2203	4300	6503	SO:0001583	missense	3854	exon9			CCGCCATAGCCAC	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.1490A>G	12.37:g.52841179T>C	ENSP00000252252:p.Tyr497Cys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_005555	P48669	Missense_Mutation	SNP	ENST00000252252.3	37	CCDS8828.1	58	0.026556776556776556	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	41	0.05408970976253298	T	4.060	0.008900	0.07912	0.012937	0.053372	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.86030	-2.06	3.2	2.04	0.26737	.	0.000000	0.49916	D	0.000127	T	0.40546	0.1121	L	0.58583	1.82	0.36687	D	0.879362	B	0.22414	0.069	B	0.14578	0.011	T	0.58329	-0.7655	10	0.12430	T	0.62	.	8.1187	0.30959	0.0:0.0998:0.0:0.9002	.	497	P04259	K2C6B_HUMAN	C	497;457	ENSP00000252252:Y497C	ENSP00000252252:Y497C	Y	-	2	0	KRT6B	51127446	0.005000	0.15991	0.400000	0.26346	0.160000	0.22226	0.547000	0.23299	0.451000	0.26802	0.254000	0.18369	TAT	T|0.961;C|0.039	0.039	strong		0.612	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67320920	67320920	+	Silent	SNP	C	C	T	rs785029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:67320920C>T	ENST00000360461.5	+	17	5478	c.2943C>T	c.(2941-2943)ctC>ctT	p.L981L	PLEKHG4_ENST00000427155.2_Silent_p.L981L|PLEKHG4_ENST00000379344.3_Silent_p.L981L|PLEKHG4_ENST00000450733.1_Silent_p.L900L	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	69	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	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	
SMIM11	54065	hgsc.bcm.edu	37	21	35757787	35757787	+	Silent	SNP	C	C	T	rs61747964	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:35757787C>T	ENST00000399295.2	+	3	394	c.24C>T	c.(22-24)caC>caT	p.H8H	SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Silent_p.H8H|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	8						integral component of membrane (GO:0016021)											TTCTTGAGCACGTGCCCCTGC	0.403													C|||	121	0.0241613	0.0408	0.0245	5008	,	,		20251	0.002		0.0129	False		,,,				2504	0.0358				p.H8H		Atlas-SNP	.											.	.	.	.	0			c.C24T						PASS	.	C		200,4206	126.1+/-163.2	2,196,2005	106.0	89.0	95.0		24	0.4	0.8	21	dbSNP_129	95	269,8331	103.8+/-164.8	4,261,4035	no	coding-synonymous	FAM165B	NM_058182.4		6,457,6040	TT,TC,CC		3.1279,4.5393,3.606		8/59	35757787	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	54065	exon3			TGAGCACGTGCCC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.24C>T	21.37:g.35757787C>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	263	135	0.513308	NM_058182		Silent	SNP	ENST00000399295.2	37	CCDS33550.1																																																																																			C|0.971;T|0.029	0.029	strong		0.403	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
ALG6	29929	hgsc.bcm.edu	37	1	63881583	63881583	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:63881583A>G	ENST00000371108.4	+	11	1247	c.942A>G	c.(940-942)atA>atG	p.I314M	ALG6_ENST00000263440.4_Missense_Mutation_p.I316M	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	314					cellular protein metabolic process (GO:0044267)|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)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CTGCATGCATAAAATTAATAC	0.294																																					p.I314M		Atlas-SNP	.											.	ALG6	33	.	0			c.A942G						PASS	.						63.0	67.0	66.0					1																	63881583		2202	4297	6499	SO:0001583	missense	29929	exon11			ATGCATAAAATTA	AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	604566	"""asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.942A>G	1.37:g.63881583A>G	ENSP00000360149:p.Ile314Met	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	294	138	0.469388	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513855	0.27123	.	.	ENSG00000088035	ENST00000371108;ENST00000263440	D;D	0.85339	-1.97;-1.97	5.06	2.55	0.30701	.	0.276621	0.39615	N	0.001314	T	0.78065	0.4225	M	0.86502	2.82	0.41346	D	0.987339	B	0.13145	0.007	B	0.21360	0.034	T	0.76713	-0.2858	10	0.45353	T	0.12	-4.5375	8.1541	0.31158	0.566:0.3205:0.0:0.1136	.	316	A2A2G4	.	M	314;316	ENSP00000360149:I314M;ENSP00000263440:I316M	ENSP00000263440:I316M	I	+	3	3	ALG6	63654171	0.999000	0.42202	0.266000	0.24541	0.836000	0.47400	0.610000	0.24253	0.870000	0.35726	0.533000	0.62120	ATA	.	.	none		0.294	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339	
PBK	55872	hgsc.bcm.edu	37	8	27667969	27667969	+	Silent	SNP	C	C	G	rs2294092	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:27667969C>G	ENST00000301905.4	-	8	1285	c.822G>C	c.(820-822)gcG>gcC	p.A274A	PBK_ENST00000522944.1_Silent_p.A285A|ESCO2_ENST00000397418.2_Intron	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TAGTTCCCAACGCTGCATAGT	0.348													G|||	2100	0.419329	0.4289	0.4179	5008	,	,		21634	0.3829		0.4592	False		,,,				2504	0.4039				p.A274A		Atlas-SNP	.											.	PBK	29	.	0			c.G822C						PASS	.	G		1863,2543	632.3+/-395.8	398,1067,738	119.0	108.0	112.0		822	-1.2	1.0	8	dbSNP_100	112	3804,4796	612.0+/-395.9	843,2118,1339	no	coding-synonymous	PBK	NM_018492.2		1241,3185,2077	GG,GC,CC		44.2326,42.2833,43.5722		274/323	27667969	5667,7339	2203	4300	6503	SO:0001819	synonymous_variant	55872	exon8			TCCCAACGCTGCA	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.822G>C	8.37:g.27667969C>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Silent	SNP	ENST00000301905.4	37	CCDS6063.1																																																																																			C|0.567;G|0.433	0.433	strong		0.348	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
C20orf194	25943	hgsc.bcm.edu	37	20	3285126	3285126	+	Silent	SNP	A	A	T	rs2254916	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3285126A>T	ENST00000252032.9	-	21	1810	c.1743T>A	c.(1741-1743)atT>atA	p.I581I	C20orf194_ENST00000453730.2_Silent_p.I319I|C20orf194_ENST00000498079.1_5'UTR	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	581										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						GATCCTTGGAAATGATGATAC	0.438													a|||	1279	0.255391	0.1823	0.3184	5008	,	,		21848	0.3492		0.2505	False		,,,				2504	0.2178				p.I581I		Atlas-SNP	.											.	C20orf194	83	.	0			c.T1743A						PASS	.			651,3161		49,553,1304	117.0	108.0	111.0		1743	2.0	1.0	20	dbSNP_100	111	2196,6052		278,1640,2206	no	coding-synonymous	C20orf194	NM_001009984.1		327,2193,3510	TT,TA,AA		26.6246,17.0776,23.607		581/1178	3285126	2847,9213	1906	4124	6030	SO:0001819	synonymous_variant	25943	exon21			CTTGGAAATGATG	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.1743T>A	20.37:g.3285126A>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Silent	SNP	ENST00000252032.9	37	CCDS42851.1																																																																																			A|0.732;T|0.268	0.268	strong		0.438	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
CDC25C	995	hgsc.bcm.edu	37	5	137654980	137654980	+	Silent	SNP	G	G	A	rs111911741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137654980G>A	ENST00000323760.6	-	7	821	c.543C>T	c.(541-543)aaC>aaT	p.N181N	CDC25C_ENST00000415130.2_Silent_p.N108N|CDC25C_ENST00000348983.3_Silent_p.N108N|CDC25C_ENST00000357274.3_Silent_p.N138N|CDC25C_ENST00000356505.3_Silent_p.N151N|CDC25C_ENST00000514555.1_Silent_p.N151N|CDC25C_ENST00000513970.1_Silent_p.N181N	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	181					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)			CTTCTCCTAGGTTTGGATTTT	0.378													G|||	2	0.000399361	0.0	0.0029	5008	,	,		16400	0.0		0.0	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	CDC25C	37	.	0			c.C543T						PASS	.	G	,	3,4403	4.2+/-10.8	0,3,2200	136.0	133.0	134.0		543,324	-4.2	0.0	5	dbSNP_132	134	26,8574	19.2+/-60.6	0,26,4274	no	coding-synonymous,coding-synonymous	CDC25C	NM_001790.3,NM_022809.2	,	0,29,6474	AA,AG,GG		0.3023,0.0681,0.223	,	181/474,108/401	137654980	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	995	exon7			TCCTAGGTTTGGA	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.543C>T	5.37:g.137654980G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	155	67	0.432258	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Silent	SNP	ENST00000323760.6	37	CCDS4202.1																																																																																			G|0.999;A|0.001	0.001	strong		0.378	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
DHX30	22907	hgsc.bcm.edu	37	3	47891036	47891036	+	Silent	SNP	C	C	T	rs9871162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47891036C>T	ENST00000445061.1	+	20	3590	c.3183C>T	c.(3181-3183)acC>acT	p.T1061T	MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000446256.2_Silent_p.T1022T|DHX30_ENST00000457607.1_Silent_p.T1089T|DHX30_ENST00000348968.4_Silent_p.T1033T	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	1061						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		ACAAGTCGACCATTAACAGGT	0.592													C|||	220	0.0439297	0.146	0.0231	5008	,	,		20762	0.0		0.0089	False		,,,				2504	0.002				p.T1061T		Atlas-SNP	.											.	DHX30	101	.	0			c.C3183T						PASS	.	C	,	653,3753	278.7+/-274.4	63,527,1613	97.0	87.0	90.0		3066,3183	4.4	1.0	3	dbSNP_119	90	117,8483	60.6+/-122.4	0,117,4183	no	coding-synonymous,coding-synonymous	DHX30	NM_014966.3,NM_138615.2	,	63,644,5796	TT,TC,CC		1.3605,14.8207,5.9203	,	1022/1156,1061/1195	47891036	770,12236	2203	4300	6503	SO:0001819	synonymous_variant	22907	exon20			GTCGACCATTAAC	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"""DEAH-boxes"""	16716	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 30"""	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.3183C>T	3.37:g.47891036C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	144	78	0.541667	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Silent	SNP	ENST00000445061.1	37	CCDS2759.1																																																																																			C|0.949;T|0.051	0.051	strong		0.592	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615	
WDFY2	115825	hgsc.bcm.edu	37	13	52313195	52313195	+	Silent	SNP	C	C	T	rs1885854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:52313195C>T	ENST00000298125.5	+	7	789	c.609C>T	c.(607-609)acC>acT	p.T203T		NM_052950.3	NP_443182.1	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	203							metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)		GTGGGGTGACCGCTCTCTGTT	0.522													C|||	628	0.125399	0.0045	0.0937	5008	,	,		18055	0.1706		0.1531	False		,,,				2504	0.2362				p.T203T		Atlas-SNP	.											.	WDFY2	36	.	0			c.C609T						PASS	.	C		142,4264	99.8+/-138.5	1,140,2062	160.0	150.0	153.0		609	-12.3	0.1	13	dbSNP_92	153	1350,7250	263.9+/-285.3	104,1142,3054	no	coding-synonymous	WDFY2	NM_052950.3		105,1282,5116	TT,TC,CC		15.6977,3.2229,11.4716		203/401	52313195	1492,11514	2203	4300	6503	SO:0001819	synonymous_variant	115825	exon7			GGTGACCGCTCTC	AF411978	CCDS9429.1	13q14.12	2013-01-09	2003-03-13		ENSG00000139668	ENSG00000139668		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20482	protein-coding gene	gene with protein product		610418	"""WD40 and FYVE domain containing 2"""				Standard	NM_052950		Approved	ZFYVE22	uc001vfp.3	Q96P53	OTTHUMG00000017407	ENST00000298125.5:c.609C>T	13.37:g.52313195C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_052950	B1AL86|Q96CS1	Silent	SNP	ENST00000298125.5	37	CCDS9429.1																																																																																			C|0.887;T|0.113	0.113	strong		0.522	WDFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045985.3	NM_052950	
TMEM143	55260	hgsc.bcm.edu	37	19	48836673	48836673	+	Silent	SNP	G	G	T	rs3826828	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48836673G>T	ENST00000293261.3	-	8	1499	c.1183C>A	c.(1183-1185)Cgg>Agg	p.R395R	TMEM143_ENST00000435956.3_Silent_p.R360R|TMEM143_ENST00000436660.2_Silent_p.R330R|TMEM143_ENST00000541566.1_Silent_p.R285R|TMEM143_ENST00000377431.2_Silent_p.R295R	NM_018273.2	NP_060743.2	Q96AN5	TM143_HUMAN	transmembrane protein 143	395					hematopoietic progenitor cell differentiation (GO:0002244)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	14		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)		ACCTCCGACCGGAGCCACCTG	0.627													G|||	1680	0.335463	0.2595	0.3847	5008	,	,		17868	0.3482		0.4175	False		,,,				2504	0.3057				p.R395R		Atlas-SNP	.											.	TMEM143	29	.	0			c.C1183A						PASS	.	G		1279,3127	423.6+/-340.2	197,885,1121	46.0	44.0	45.0		1183	4.5	1.0	19	dbSNP_107	45	3792,4808	520.4+/-379.7	839,2114,1347	no	coding-synonymous	TMEM143	NM_018273.2		1036,2999,2468	TT,TG,GG		44.093,29.0286,38.9897		395/460	48836673	5071,7935	2203	4300	6503	SO:0001819	synonymous_variant	55260	exon8			CCGACCGGAGCCA	AK129801	CCDS12716.1	19q13.32	2008-02-05				ENSG00000161558			25603	protein-coding gene	gene with protein product						12975309	Standard	NM_018273		Approved	FLJ10922	uc002pix.1	Q96AN5		ENST00000293261.3:c.1183C>A	19.37:g.48836673G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_018273	A8K656|Q6UXY4|Q9NV49	Silent	SNP	ENST00000293261.3	37	CCDS12716.1																																																																																			G|0.645;T|0.355	0.355	strong		0.627	TMEM143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465622.1	NM_018273	
CHML	1122	hgsc.bcm.edu	37	1	241797791	241797791	+	Silent	SNP	A	A	G	rs372360469		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:241797791A>G	ENST00000366553.1	-	1	1441	c.1278T>C	c.(1276-1278)ggT>ggC	p.G426G	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	426					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TTATTCTTTGACCAAAGTGAT	0.363																																					p.G426G		Atlas-SNP	.											.	CHML	82	.	0			c.T1278C						PASS	.	A	,	0,4406		0,0,2203	75.0	79.0	78.0		1278,	-0.2	1.0	1		78	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,intron	CHML,OPN3	NM_001821.3,NM_014322.2	,	0,1,6500	GG,GA,AA		0.0116,0.0,0.0077	,	426/657,	241797791	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	1122	exon1			TCTTTGACCAAAG	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1278T>C	1.37:g.241797791A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Silent	SNP	ENST00000366553.1	37	CCDS31073.1																																																																																			.	.	none		0.363	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
BRD3	8019	hgsc.bcm.edu	37	9	136915508	136915508	+	Silent	SNP	C	C	T	rs2301576	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136915508C>T	ENST00000303407.7	-	5	887	c.702G>A	c.(700-702)ccG>ccA	p.P234P	BRD3_ENST00000357885.2_Silent_p.P234P|BRD3_ENST00000371834.2_Silent_p.P234P	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	234					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)		TGACGACAGGCGGCGTAGGAG	0.697			T	C15orf55	lethal midline carcinoma of young people								C|||	452	0.0902556	0.0091	0.1383	5008	,	,		13483	0.1339		0.0775	False		,,,				2504	0.1339				p.P234P		Atlas-SNP	.		Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	BRD3	82	.	0			c.G702A						PASS	.	C		122,4284	89.2+/-127.9	4,114,2085	53.0	54.0	53.0		702	-2.3	0.7	9	dbSNP_100	53	862,7736	193.7+/-239.3	30,802,3467	no	coding-synonymous	BRD3	NM_007371.3		34,916,5552	TT,TC,CC		10.0256,2.769,7.5669		234/727	136915508	984,12020	2203	4299	6502	SO:0001819	synonymous_variant	8019	exon5			GACAGGCGGCGTA		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.702G>A	9.37:g.136915508C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Silent	SNP	ENST00000303407.7	37	CCDS6980.1																																																																																			C|0.923;T|0.077	0.077	strong		0.697	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371	
CCNY	219771	hgsc.bcm.edu	37	10	35772402	35772402	+	Silent	SNP	G	G	A	rs3802509	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:35772402G>A	ENST00000374704.4	+	2	405	c.225G>A	c.(223-225)acG>acA	p.T75T	CCNY_ENST00000374706.1_Silent_p.T21T|CCNY_ENST00000339497.5_Intron|CCNY_ENST00000265375.9_Silent_p.T21T|CCNY_ENST00000492478.1_3'UTR	NM_145012.4	NP_659449.3	Q8ND76	CCNY_HUMAN	cyclin Y	75					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	8						AATCTCAGACGGACGGTAGGT	0.343													A|||	2289	0.457069	0.6536	0.4539	5008	,	,		17108	0.4266		0.3241	False		,,,				2504	0.362				p.T75T		Atlas-SNP	.											CCNY,rectum,carcinoma,+1,1	CCNY	22	1	0			c.G225A						PASS	.	A	,	2720,1686	511.6+/-367.8	849,1022,332	86.0	82.0	83.0		225,63	-11.7	0.0	10	dbSNP_107	83	2772,5828	678.6+/-403.5	433,1906,1961	no	coding-synonymous,coding-synonymous	CCNY	NM_145012.4,NM_181698.2	,	1282,2928,2293	AA,AG,GG		32.2326,38.266,42.2267	,	75/342,21/288	35772402	5492,7514	2203	4300	6503	SO:0001819	synonymous_variant	219771	exon2			TCAGACGGACGGT	AF413522, AY504868	CCDS7189.1, CCDS7190.1, CCDS60513.1	10p11.22	2011-01-25	2007-02-09	2007-02-09	ENSG00000108100	ENSG00000108100			23354	protein-coding gene	gene with protein product		612786	"""chromosome 10 open reading frame 9"""	C10orf9		20441050	Standard	XM_005252388		Approved	CFP1, CBCP1	uc001iyw.4	Q8ND76	OTTHUMG00000017955	ENST00000374704.4:c.225G>A	10.37:g.35772402G>A		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	359	173	0.481894	NM_145012	B7ZKX9|D3DRY9|Q2M3V4|Q2TU96|Q6NT86|Q7Z4U7|Q8TEX2|Q8TEX3|Q96M99|Q96P45	Silent	SNP	ENST00000374704.4	37	CCDS7189.1																																																																																			G|0.564;A|0.436	0.436	strong		0.343	CCNY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047568.2	NM_181698	
MYOM3	127294	hgsc.bcm.edu	37	1	24413159	24413159	+	Silent	SNP	T	T	C	rs6424152	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24413159T>C	ENST00000374434.3	-	15	1935	c.1773A>G	c.(1771-1773)gaA>gaG	p.E591E	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Silent_p.E591E|MYOM3_ENST00000330966.7_Silent_p.E592E|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	591	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		AGGCGATGGGTTCGCTGGGCT	0.627													C|||	1877	0.3748	0.3646	0.353	5008	,	,		16925	0.4623		0.4463	False		,,,				2504	0.2403				p.E591E		Atlas-SNP	.											.	MYOM3	131	.	0			c.A1773G						PASS	.	C		1365,2533		253,859,837	55.0	58.0	57.0		1773	-0.2	1.0	1	dbSNP_116	57	3544,4742		750,2044,1349	no	coding-synonymous	MYOM3	NM_152372.3		1003,2903,2186	CC,CT,TT		42.7709,35.018,40.2905		591/1438	24413159	4909,7275	1949	4143	6092	SO:0001819	synonymous_variant	127294	exon15			GATGGGTTCGCTG	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.1773A>G	1.37:g.24413159T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			T|0.602;C|0.398	0.398	strong		0.627	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248309020G>A	ENST00000366476.1	+	1	571	c.571G>A	c.(571-573)Gac>Aac	p.D191N		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CTCATGCAATGACACATCAAT	0.418																																					p.D191N		Atlas-SNP	.											OR2M5,NS,carcinoma,0,2	OR2M5	117	2	0			c.G571A						scavenged	.						284.0	272.0	276.0					1																	248309020		2203	4300	6503	SO:0001583	missense	127059	exon1			TGCAATGACACAT		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.571G>A	1.37:g.248309020G>A	ENSP00000355432:p.Asp191Asn	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	407	11	0.027027	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	g	13.27	2.186763	0.38609	.	.	ENSG00000162727	ENST00000366476	T	0.00231	8.49	3.05	-0.584	0.11702	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33691	U	0.004660	T	0.00178	0.0005	M	0.63843	1.955	0.09310	N	1	B	0.20052	0.041	B	0.25405	0.06	T	0.40739	-0.9547	10	0.52906	T	0.07	.	6.3472	0.21355	0.2028:0.2355:0.5617:0.0	.	191	A3KFT3	OR2M5_HUMAN	N	191	ENSP00000355432:D191N	ENSP00000355432:D191N	D	+	1	0	OR2M5	246375643	0.002000	0.14202	0.001000	0.08648	0.566000	0.35808	0.608000	0.24223	-0.004000	0.14419	0.492000	0.49549	GAC	G|0.996;A|0.004	0.004	strong		0.418	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
CD226	10666	hgsc.bcm.edu	37	18	67531642	67531642	+	Missense_Mutation	SNP	T	T	C	rs763361	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:67531642T>C	ENST00000280200.4	-	7	1187	c.919A>G	c.(919-921)Agt>Ggt	p.S307G	CD226_ENST00000577287.1_Missense_Mutation_p.S152G|CD226_ENST00000581982.1_Missense_Mutation_p.S152G|CD226_ENST00000582621.1_Missense_Mutation_p.S307G	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	307			S -> G (in dbSNP:rs763361). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19690332, ECO:0000269|PubMed:8673704, ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				GTAGGTTGACTGGTAGAGATG	0.383													T|||	2351	0.469449	0.2632	0.5476	5008	,	,		19506	0.6121		0.5268	False		,,,				2504	0.4867				p.S307G	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											CD226,NS,adenoma,0,1	CD226	51	1	0			c.A919G						PASS	.	T	GLY/SER	1403,3003	460.2+/-352.5	222,959,1022	232.0	205.0	214.0	http://www.ncbi.nlm.nih.gov/pubmed?term	919	0.2	0.0	18	dbSNP_86	214	4477,4123	591.1+/-392.8	1185,2107,1008	yes	missense	CD226	NM_006566.2	56	1407,3066,2030	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	47.9419,31.8429,45.2099	benign	307/337	67531642	5880,7126	2203	4300	6503	SO:0001583	missense	10666	exon7			GTTGACTGGTAGA	U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	16961	protein-coding gene	gene with protein product		605397	"""CD226 antigen"""			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.919A>G	18.37:g.67531642T>C	ENSP00000280200:p.Ser307Gly	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_006566	B2R818	Missense_Mutation	SNP	ENST00000280200.4	37	CCDS11997.1	1075	0.49221611721611724	126	0.25609756097560976	200	0.5524861878453039	361	0.6311188811188811	388	0.5118733509234829	T	0.051	-1.250683	0.01469	0.318429	0.520581	ENSG00000150637	ENST00000280200	T	0.23552	1.9	0.225	0.225	0.15325	.	1.124220	0.06665	N	0.765093	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.43228	-0.9404	8	0.54805	T	0.06	.	.	.	.	rs763361;rs1790587;rs17800796;rs52822910;rs57176311;rs763361	307	Q15762	CD226_HUMAN	G	307	ENSP00000280200:S307G	ENSP00000280200:S307G	S	-	1	0	CD226	65682622	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-0.188000	0.09642	0.257000	0.21650	0.254000	0.18369	AGT	C|0.456;N|0.000	0.456	strong		0.383	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566	
MYOM3	127294	hgsc.bcm.edu	37	1	24409165	24409165	+	Silent	SNP	C	C	T	rs4320728	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24409165C>T	ENST00000374434.3	-	17	2172	c.2010G>A	c.(2008-2010)gaG>gaA	p.E670E	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Silent_p.E670E|MYOM3_ENST00000330966.7_Silent_p.E671E|MYOM3_ENST00000475306.1_5'UTR|RP11-293P20.4_ENST00000429191.1_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	670	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		TGACACAAAACTCGTACTCCT	0.572													C|||	924	0.184505	0.1929	0.1398	5008	,	,		19098	0.1925		0.1332	False		,,,				2504	0.2495				p.E670E		Atlas-SNP	.											.	MYOM3	131	.	0			c.G2010A						PASS	.	C		638,3500		48,542,1479	55.0	61.0	59.0		2010	2.5	1.0	1	dbSNP_111	59	1088,7332		63,962,3185	no	coding-synonymous	MYOM3	NM_152372.3		111,1504,4664	TT,TC,CC		12.9216,15.4181,13.7442		670/1438	24409165	1726,10832	2069	4210	6279	SO:0001819	synonymous_variant	127294	exon17			ACAAAACTCGTAC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.2010G>A	1.37:g.24409165C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			C|0.844;T|0.156	0.156	strong		0.572	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
COLEC11	78989	hgsc.bcm.edu	37	2	3673609	3673609	+	Intron	SNP	A	A	G	rs76490827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:3673609A>G	ENST00000349077.4	+	4	305				COLEC11_ENST00000382062.2_Intron|COLEC11_ENST00000402922.1_Intron|COLEC11_ENST00000402794.1_Intron|COLEC11_ENST00000236693.7_Silent_p.S40S|COLEC11_ENST00000418971.2_Intron|COLEC11_ENST00000404205.1_Intron|COLEC11_ENST00000487365.1_Intron|COLEC11_ENST00000403096.3_Intron	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11						developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		TCCAGCAGTCACAGCCAGTCG	0.438													A|||	66	0.0131789	0.0	0.0159	5008	,	,		21979	0.002		0.008	False		,,,				2504	0.046				p.S40S		Atlas-SNP	.											.	COLEC11	93	.	0			c.A120G						PASS	.	A	,	3,4403	6.2+/-15.9	0,3,2200	166.0	164.0	165.0		,120	-0.3	0.0	2	dbSNP_133	165	71,8529	42.6+/-100.3	0,71,4229	no	intron,coding-synonymous	COLEC11	NM_024027.3,NM_199235.1	,	0,74,6429	GG,GA,AA		0.8256,0.0681,0.569	,	,40/269	3673609	74,12932	2203	4300	6503	SO:0001627	intron_variant	78989	exon4			GCAGTCACAGCCA	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.203-11514A>G	2.37:g.3673609A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_199235	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	37	CCDS1649.1																																																																																			A|0.994;G|0.006	0.006	strong		0.438	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
BTBD16	118663	hgsc.bcm.edu	37	10	124096160	124096160	+	Missense_Mutation	SNP	A	A	G	rs10510108	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:124096160A>G	ENST00000260723.4	+	15	1666	c.1415A>G	c.(1414-1416)cAg>cGg	p.Q472R	BTBD16_ENST00000368994.2_Missense_Mutation_p.Q473R	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	472			Q -> R (in dbSNP:rs10510108).							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				CAGATCAAGCAGAAGTTTGGG	0.512													A|||	237	0.0473243	0.0015	0.0648	5008	,	,		18871	0.0804		0.0348	False		,,,				2504	0.0757				p.Q472R		Atlas-SNP	.											.	BTBD16	44	.	0			c.A1415G						PASS	.	A	ARG/GLN	41,4365	45.3+/-79.5	0,41,2162	151.0	110.0	124.0		1415	5.6	1.0	10	dbSNP_119	124	246,8354	98.6+/-160.1	5,236,4059	yes	missense	BTBD16	NM_144587.2	43	5,277,6221	GG,GA,AA		2.8605,0.9305,2.2067	possibly-damaging	472/507	124096160	287,12719	2203	4300	6503	SO:0001583	missense	118663	exon15			TCAAGCAGAAGTT	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1415A>G	10.37:g.124096160A>G	ENSP00000260723:p.Gln472Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	87	0.03983516483516483	2	0.0040650406504065045	20	0.055248618784530384	41	0.07167832167832168	24	0.0316622691292876	A	16.15	3.042171	0.55003	0.009305	0.028605	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.21932	1.98;1.98	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000010	T	0.02304	0.0071	L	0.34521	1.04	0.39000	D	0.959328	D;D	0.59767	0.986;0.986	P;P	0.58660	0.843;0.843	T	0.00775	-1.1571	10	0.39692	T	0.17	-26.0289	12.2648	0.54672	1.0:0.0:0.0:0.0	rs10510108;rs17562418;rs52793426;rs10510108	473;472	Q32M84-2;Q32M84	.;BTBDG_HUMAN	R	472;473	ENSP00000260723:Q472R;ENSP00000357990:Q473R	ENSP00000260723:Q472R	Q	+	2	0	BTBD16	124086150	1.000000	0.71417	0.991000	0.47740	0.103000	0.19146	4.603000	0.61105	2.155000	0.67459	0.533000	0.62120	CAG	A|0.970;G|0.030	0.030	strong		0.512	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
OAF	220323	hgsc.bcm.edu	37	11	120099791	120099791	+	Silent	SNP	C	C	T	rs2465654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:120099791C>T	ENST00000328965.4	+	4	1275	c.762C>T	c.(760-762)ttC>ttT	p.F254F	OAF_ENST00000531220.1_Silent_p.F138F	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	254						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)		GCTACAGCTTCGACTTCTACG	0.647													C|||	810	0.161741	0.2231	0.1585	5008	,	,		14973	0.129		0.0815	False		,,,				2504	0.1973				p.F254F		Atlas-SNP	.											.	OAF	12	.	0			c.C762T						PASS	.	C		899,3507	331.2+/-301.9	91,717,1395	55.0	53.0	54.0		762	-0.5	0.8	11	dbSNP_100	54	624,7976	157.2+/-210.9	21,582,3697	no	coding-synonymous	OAF	NM_178507.2		112,1299,5092	TT,TC,CC		7.2558,20.404,11.71		254/274	120099791	1523,11483	2203	4300	6503	SO:0001819	synonymous_variant	220323	exon4			CAGCTTCGACTTC	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.762C>T	11.37:g.120099791C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_178507		Silent	SNP	ENST00000328965.4	37	CCDS8430.1																																																																																			C|0.869;T|0.131	0.131	strong		0.647	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
C6orf118	168090	hgsc.bcm.edu	37	6	165706935	165706935	+	Missense_Mutation	SNP	C	C	G	rs9459350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:165706935C>G	ENST00000230301.8	-	6	1107	c.1087G>C	c.(1087-1089)Gtg>Ctg	p.V363L	C6orf118_ENST00000494696.2_5'Flank|C6orf118_ENST00000543069.1_Missense_Mutation_p.V259L	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	363			V -> L (in dbSNP:rs9459350).							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)		AGCAATGCCACCTCCATCTCC	0.443													G|||	554	0.110623	0.3147	0.0648	5008	,	,		18707	0.0		0.0815	False		,,,				2504	0.0112				p.V363L		Atlas-SNP	.											.	C6orf118	116	.	0			c.G1087C						PASS	.	G	LEU/VAL	1354,3052	691.8+/-405.5	200,954,1049	270.0	229.0	243.0		1087	-0.1	0.1	6	dbSNP_119	243	664,7936	789.5+/-407.6	21,622,3657	yes	missense	C6orf118	NM_144980.3	32	221,1576,4706	GG,GC,CC		7.7209,30.7308,15.5159	benign	363/470	165706935	2018,10988	2203	4300	6503	SO:0001583	missense	168090	exon6			ATGCCACCTCCAT		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.1087G>C	6.37:g.165706935C>G	ENSP00000230301:p.Val363Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	157	67	0.426752	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	240	0.10989010989010989	154	0.3130081300813008	24	0.06629834254143646	0	0.0	62	0.08179419525065963	G	3.354	-0.131897	0.06753	0.307308	0.077209	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.13420	2.86;2.59	4.02	-0.0557	0.13808	.	1.710450	0.02957	N	0.142585	T	0.01156	0.0038	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39603	-0.9606	9	0.30854	T	0.27	.	2.8212	0.05471	0.094:0.1451:0.2933:0.4676	rs9459350;rs52793539;rs9459350	363	Q5T5N4	CF118_HUMAN	L	363;259	ENSP00000230301:V363L;ENSP00000439288:V259L	ENSP00000230301:V363L	V	-	1	0	C6orf118	165626925	0.010000	0.17322	0.086000	0.20670	0.002000	0.02628	0.207000	0.17395	-0.255000	0.09486	-1.123000	0.02005	GTG	C|0.861;G|0.139	0.139	strong		0.443	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
OPRD1	4985	hgsc.bcm.edu	37	1	29189597	29189597	+	Silent	SNP	C	C	T	rs2234918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:29189597C>T	ENST00000234961.2	+	3	1163	c.921C>T	c.(919-921)ggC>ggT	p.G307G		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1	307					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adult locomotory behavior (GO:0008344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|negative regulation of gene expression (GO:0010629)|negative regulation of protein oligomerization (GO:0032460)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein import into nucleus, translocation (GO:0000060)|regulation of calcium ion transport (GO:0051924)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of sensory perception of pain (GO:0051930)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	enkephalin receptor activity (GO:0038046)|opioid receptor activity (GO:0004985)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	TCGCGCTGGGCTACGCCAATA	0.667													C|||	2911	0.58127	0.3056	0.7032	5008	,	,		15581	0.754		0.5726	False		,,,				2504	0.6984				p.G307G		Atlas-SNP	.											OPRD1,rectum,carcinoma,0,1	OPRD1	36	1	0			c.C921T						PASS	.	C		1507,2897		274,959,969	29.0	26.0	27.0	http://www.ncbi.nlm.nih.gov/omim/103780,165195|http://omim.org/entry/165195|http://omim.org/entry/103780	921	3.2	1.0	1	dbSNP_98	27	4618,3982		1248,2122,930	no	coding-synonymous	OPRD1	NM_000911.3		1522,3081,1899	TT,TC,CC		46.3023,34.2189,47.1009		307/373	29189597	6125,6879	2202	4300	6502	SO:0001819	synonymous_variant	4985	exon3			GCTGGGCTACGCC	U10504	CCDS329.1	1p36.1-p34.3	2012-08-08			ENSG00000116329	ENSG00000116329		"""GPCR / Class A : Opioid receptors"""	8153	protein-coding gene	gene with protein product		165195				8415697	Standard	NM_000911		Approved		uc001brf.1	P41143	OTTHUMG00000003646	ENST00000234961.2:c.921C>T	1.37:g.29189597C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	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	
CPSF1	29894	hgsc.bcm.edu	37	8	145623963	145623963	+	Silent	SNP	G	G	A	rs4317614	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145623963G>A	ENST00000349769.3	-	18	1798	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	568					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GTCTGCGGCCGTCGTCGTCTG	0.677													G|||	2299	0.459065	0.2383	0.5	5008	,	,		13266	0.6597		0.3668	False		,,,				2504	0.6166				p.D568D	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C1704T						PASS	.	G		1169,3237	411.3+/-335.7	163,843,1197	105.0	105.0	105.0		1704	-10.4	0.0	8	dbSNP_111	105	3073,5527	468.6+/-367.3	566,1941,1793	no	coding-synonymous	CPSF1	NM_013291.2		729,2784,2990	AA,AG,GG		35.7326,26.532,32.6157		568/1444	145623963	4242,8764	2203	4300	6503	SO:0001819	synonymous_variant	29894	exon18			GCGGCCGTCGTCG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1704C>T	8.37:g.145623963G>A		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	286	119	0.416084	NM_013291	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																			G|0.629;A|0.371	0.371	strong		0.677	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
SLC15A1	6564	hgsc.bcm.edu	37	13	99356612	99356612	+	Silent	SNP	A	A	G	rs1339067	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:99356612A>G	ENST00000376503.5	-	17	1402	c.1347T>C	c.(1345-1347)gcT>gcC	p.A449A		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	449					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CGTCAGTTACAGCAGTGACTG	0.468													G|||	3171	0.633187	0.8578	0.7349	5008	,	,		19272	0.3433		0.6342	False		,,,				2504	0.5552				p.A449A		Atlas-SNP	.											.	SLC15A1	92	.	0			c.T1347C						PASS	.	G		3594,812	324.2+/-298.5	1471,652,80	186.0	171.0	176.0		1347	-8.2	0.0	13	dbSNP_88	176	5692,2908	453.3+/-363.2	1888,1916,496	no	coding-synonymous	SLC15A1	NM_005073.3		3359,2568,576	GG,GA,AA		33.814,18.4294,28.6022		449/709	99356612	9286,3720	2203	4300	6503	SO:0001819	synonymous_variant	6564	exon17			AGTTACAGCAGTG	U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.1347T>C	13.37:g.99356612A>G		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	205	113	0.55122	NM_005073	Q5VW82	Silent	SNP	ENST00000376503.5	37	CCDS9489.1																																																																																			A|0.346;G|0.654	0.654	strong		0.468	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073	
MYOM3	127294	hgsc.bcm.edu	37	1	24421474	24421474	+	Missense_Mutation	SNP	G	G	A	rs6678540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24421474G>A	ENST00000374434.3	-	9	959	c.797C>T	c.(796-798)aCg>aTg	p.T266M	MYOM3_ENST00000329601.7_Missense_Mutation_p.T266M|MYOM3_ENST00000330966.7_Missense_Mutation_p.T267M|MYOM3_ENST00000475306.1_5'UTR	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	119	0	0		WXS	Illumina HiSeq	Phase_I	130	57	0.438462	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	
FHL2	2274	hgsc.bcm.edu	37	2	105977776	105977776	+	Silent	SNP	G	G	A	rs3087523	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:105977776G>A	ENST00000409807.1	-	6	1138	c.804C>T	c.(802-804)gaC>gaT	p.D268D	FHL2_ENST00000322142.8_Silent_p.D268D|FHL2_ENST00000344213.4_Silent_p.D378D|FHL2_ENST00000393353.3_Silent_p.D268D|FHL2_ENST00000409177.1_Silent_p.D384D|FHL2_ENST00000336660.5_3'UTR|AC012360.6_ENST00000457290.2_RNA|FHL2_ENST00000358129.4_Silent_p.D268D|FHL2_ENST00000393352.3_Silent_p.D268D|FHL2_ENST00000408995.1_Silent_p.D268D			Q14192	FHL2_HUMAN	four and a half LIM domains 2	268	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						ACAGGATGTCGTCCCTCTCTG	0.483													G|||	259	0.0517173	0.0068	0.1066	5008	,	,		20376	0.0238		0.1103	False		,,,				2504	0.0419				p.D268D		Atlas-SNP	.											FHL2,colon,carcinoma,0,1	FHL2	18	1	0			c.C804T						PASS	.	G	,,,	116,4290	88.2+/-126.9	1,114,2088	122.0	110.0	114.0		804,804,804,804	-11.0	0.0	2	dbSNP_102	114	1092,7508	227.9+/-263.1	63,966,3271	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FHL2	NM_001039492.2,NM_001450.3,NM_201555.1,NM_201557.3	,,,	64,1080,5359	AA,AG,GG		12.6977,2.6328,9.288	,,,	268/280,268/280,268/280,268/280	105977776	1208,11798	2203	4300	6503	SO:0001819	synonymous_variant	2274	exon7			GATGTCGTCCCTC		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.804C>T	2.37:g.105977776G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_001039492	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Silent	SNP	ENST00000409807.1	37	CCDS2070.1																																																																																			G|0.921;A|0.079	0.079	strong		0.483	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1		
OSBP2	23762	hgsc.bcm.edu	37	22	31266546	31266546	+	Silent	SNP	T	T	C	rs2301816	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31266546T>C	ENST00000332585.6	+	3	1088	c.984T>C	c.(982-984)gcT>gcC	p.A328A	OSBP2_ENST00000407373.1_Silent_p.A155A|OSBP2_ENST00000437268.2_Silent_p.A70A|OSBP2_ENST00000401475.1_5'UTR|OSBP2_ENST00000446658.2_Silent_p.A328A|OSBP2_ENST00000382310.3_Silent_p.A328A|OSBP2_ENST00000403222.3_Silent_p.A163A	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	328					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						AGCACGGCGCTGCACTCCAGC	0.597													C|||	3539	0.706669	0.7383	0.6686	5008	,	,		18461	0.8234		0.6252	False		,,,				2504	0.6544				p.A328A		Atlas-SNP	.											.	OSBP2	52	.	0			c.T984C						PASS	.	C		3146,1174		1162,822,176	67.0	73.0	71.0		984	-8.7	0.0	22	dbSNP_100	71	5265,3227		1664,1937,645	no	coding-synonymous	OSBP2	NM_030758.3		2826,2759,821	CC,CT,TT		38.0005,27.1759,34.3506		328/917	31266546	8411,4401	2160	4246	6406	SO:0001819	synonymous_variant	23762	exon3			CGGCGCTGCACTC		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.984T>C	22.37:g.31266546T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_030758	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Silent	SNP	ENST00000332585.6	37	CCDS43002.1																																																																																			T|0.307;C|0.693	0.693	strong		0.597	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758	
SPARCL1	8404	hgsc.bcm.edu	37	4	88403609	88403609	+	Silent	SNP	G	G	A	rs72654103	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88403609G>A	ENST00000282470.6	-	8	2105	c.1635C>T	c.(1633-1635)caC>caT	p.H545H	SPARCL1_ENST00000503414.1_Silent_p.H420H|SPARCL1_ENST00000418378.1_Silent_p.H545H	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	545					signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		GATAACCAGCGTGTTCAGAGT	0.428													g|||	69	0.013778	0.0015	0.0331	5008	,	,		20581	0.001		0.0408	False		,,,				2504	0.002				p.H545H		Atlas-SNP	.											.	SPARCL1	59	.	0			c.C1635T						PASS	.	G	,	20,4386	28.1+/-56.4	0,20,2183	92.0	87.0	89.0		1635,1635	-9.9	0.0	4	dbSNP_130	89	274,8326	104.0+/-165.0	4,266,4030	no	coding-synonymous,coding-synonymous	SPARCL1	NM_001128310.1,NM_004684.4	,	4,286,6213	AA,AG,GG		3.186,0.4539,2.2605	,	545/665,545/665	88403609	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	8404	exon8			ACCAGCGTGTTCA	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1635C>T	4.37:g.88403609G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_004684	B4E2Z0|E7ESU2|Q14800	Silent	SNP	ENST00000282470.6	37	CCDS3622.1																																																																																			G|0.976;A|0.024	0.024	strong		0.428	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
ASNS	440	hgsc.bcm.edu	37	7	97483921	97483921	+	Silent	SNP	G	G	C	rs1049677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97483921G>C	ENST00000394309.3	-	10	1680	c.1209C>G	c.(1207-1209)ctC>ctG	p.L403L	ASNS_ENST00000444334.1_Silent_p.L382L|ASNS_ENST00000455086.1_Silent_p.L320L|ASNS_ENST00000422745.1_Silent_p.L382L|ASNS_ENST00000175506.4_Silent_p.L403L|ASNS_ENST00000437628.1_Silent_p.L320L|ASNS_ENST00000394308.3_Silent_p.L403L	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	403	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	GATCTGCGCGGAGAACATCAA	0.393													G|||	115	0.0229633	0.0008	0.0562	5008	,	,		16181	0.0		0.0646	False		,,,				2504	0.0102				p.L403L	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	Atlas-SNP	.											.	ASNS	97	.	0			c.C1209G						PASS	.	G	,,,,,	65,4341	61.1+/-98.1	1,63,2139	81.0	85.0	83.0		1146,960,960,1209,1209,1209	2.4	1.0	7	dbSNP_86	83	619,7981	161.3+/-214.2	22,575,3703	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ASNS	NM_001178075.1,NM_001178076.1,NM_001178077.1,NM_001673.4,NM_133436.3,NM_183356.3	,,,,,	23,638,5842	CC,CG,GG		7.1977,1.4753,5.2591	,,,,,	382/541,320/479,320/479,403/562,403/562,403/562	97483921	684,12322	2203	4300	6503	SO:0001819	synonymous_variant	440	exon10			TGCGCGGAGAACA	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"""asparagine synthetase"""				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1209C>G	7.37:g.97483921G>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	183	93	0.508197	NM_133436	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Silent	SNP	ENST00000394309.3	37	CCDS5652.1																																																																																			G|0.942;C|0.058	0.058	strong		0.393	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415229	105415229	+	Missense_Mutation	SNP	T	T	C	rs10134675|rs386781096	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105415229T>C	ENST00000333244.5	-	7	6678	c.6559A>G	c.(6559-6561)Atg>Gtg	p.M2187V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2187						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.M2187V(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)			GGGAGACTCATGTCGGCCTCC	0.607													.|||	1414	0.282348	0.1664	0.2983	5008	,	,		17789	0.1042		0.4841	False		,,,				2504	0.4039				p.M2187V		Atlas-SNP	.											AHNAK2_ENST00000333244,brain,glioma,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A6559G						PASS	.						136.0	107.0	116.0					14																	105415229		1947	4106	6053	SO:0001583	missense	113146	exon7			GACTCATGTCGGC	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.6559A>G	14.37:g.105415229T>C	ENSP00000353114:p.Met2187Val	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	0.009	-1.849188	0.00563	.	.	ENSG00000185567	ENST00000333244	T	0.00669	5.9	3.88	-0.584	0.11702	.	.	.	.	.	T	0.00241	0.0007	N	0.00389	-1.56	0.80722	P	0.0	B	0.14012	0.009	B	0.10450	0.005	T	0.42224	-0.9464	8	0.02654	T	1	.	1.2383	0.01958	0.1276:0.3125:0.2514:0.3085	.	2187	Q8IVF2	AHNK2_HUMAN	V	2187	ENSP00000353114:M2187V	ENSP00000353114:M2187V	M	-	1	0	AHNAK2	104486274	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.234000	0.00546	-0.676000	0.05238	-1.504000	0.00955	ATG	G|0.002;T|0.998	.	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TBL3	10607	hgsc.bcm.edu	37	16	2028220	2028220	+	Splice_Site	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2028220A>G	ENST00000568546.1	+	20	2261	c.2133A>G	c.(2131-2133)aaA>aaG	p.K711K		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	711					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						GCGACCAGAAAGGTTGGCGGC	0.662																																					p.K711K	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A2133G						PASS	.						43.0	48.0	47.0					16																	2028220		2197	4296	6493	SO:0001630	splice_region_variant	10607	exon20			CCAGAAAGGTTGG	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.2134+1A>G	16.37:g.2028220A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			.	.	none		0.662	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	Silent
ALLC	55821	hgsc.bcm.edu	37	2	3729254	3729254	+	Missense_Mutation	SNP	C	C	T	rs13426642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	73	71	0.972603	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		
LRCH4	4034	hgsc.bcm.edu	37	7	100176362	100176362	+	Missense_Mutation	SNP	C	C	T	rs52833865	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100176362C>T	ENST00000310300.6	-	5	698	c.646G>A	c.(646-648)Gtc>Atc	p.V216I	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	216					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)					ATTCGGGAGACGCGGTTACAG	0.622													C|||	27	0.00539137	0.0	0.0058	5008	,	,		19150	0.002		0.008	False		,,,				2504	0.0133				p.V216I		Atlas-SNP	.											.	LRCH4	53	.	0			c.G646A						PASS	.	C	ILE/VAL	7,4399	12.9+/-30.5	0,7,2196	71.0	67.0	68.0		646	0.5	0.9	7	dbSNP_128	68	72,8528	44.9+/-103.4	0,72,4228	yes	missense	LRCH4	NM_002319.3	29	0,79,6424	TT,TC,CC		0.8372,0.1589,0.6074	benign	216/684	100176362	79,12927	2203	4300	6503	SO:0001583	missense	4034	exon5			GGGAGACGCGGTT	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.646G>A	7.37:g.100176362C>T	ENSP00000309689:p.Val216Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	37	CCDS34706.1	9	0.004120879120879121	0	0.0	0	0.0	2	0.0034965034965034965	7	0.009234828496042216	c	5.153	0.213864	0.09810	0.001589	0.008372	ENSG00000077454	ENST00000310300	T	0.28666	1.6	4.66	0.518	0.17030	.	0.284157	0.33327	N	0.005035	T	0.04770	0.0129	N	0.00483	-1.445	0.80722	D	1	B	0.12013	0.005	B	0.16289	0.015	T	0.26573	-1.0099	9	.	.	.	-7.2602	8.2707	0.31842	0.0:0.6194:0.0:0.3806	rs52833865	216	O75427	LRCH4_HUMAN	I	216	ENSP00000309689:V216I	.	V	-	1	0	LRCH4	100014298	0.001000	0.12720	0.945000	0.38365	0.821000	0.46438	-0.266000	0.08631	-0.087000	0.12528	-0.289000	0.09944	GTC	C|0.994;T|0.006	0.006	strong		0.622	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
HPS4	89781	hgsc.bcm.edu	37	22	26861473	26861473	+	Missense_Mutation	SNP	T	T	A	rs34962745	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26861473T>A	ENST00000398145.2	-	10	1367	c.751A>T	c.(751-753)Acc>Tcc	p.T251S	HPS4_ENST00000336873.5_Missense_Mutation_p.T251S|HPS4_ENST00000402105.3_Missense_Mutation_p.T246S|HPS4_ENST00000398141.1_Missense_Mutation_p.T264S|HPS4_ENST00000493455.2_5'Flank	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	251					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						TCCTCTTTGGTCACAAAAACA	0.527									Hermansky-Pudlak syndrome				T|||	18	0.00359425	0.0008	0.0058	5008	,	,		19893	0.0		0.0099	False		,,,				2504	0.0031				p.T251S		Atlas-SNP	.											.	HPS4	123	.	0			c.A751T						PASS	.	T	SER/THR,SER/THR	7,4399	12.9+/-30.5	0,7,2196	134.0	118.0	123.0		751,736	4.6	0.5	22	dbSNP_126	123	94,8506	52.3+/-112.8	1,92,4207	yes	missense,missense	HPS4	NM_022081.4,NM_152841.1	58,58	1,99,6403	AA,AT,TT		1.093,0.1589,0.7766	benign,benign	251/709,246/704	26861473	101,12905	2203	4300	6503	SO:0001583	missense	89781	exon10	Familial Cancer Database	HPS, HPS1-8	CTTTGGTCACAAA		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.751A>T	22.37:g.26861473T>A	ENSP00000381213:p.Thr251Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Missense_Mutation	SNP	ENST00000398145.2	37	CCDS13835.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	9.532	1.111176	0.20714	0.001589	0.01093	ENSG00000100099	ENST00000398145;ENST00000398141;ENST00000402105;ENST00000336873;ENST00000312736;ENST00000422379	T;D;T;T;D	0.87966	1.41;-2.32;1.4;1.41;-2.32	4.6	4.6	0.57074	.	0.237776	0.41712	N	0.000824	T	0.75860	0.3907	L	0.34521	1.04	0.21527	N	0.99966	B;B;B;B;B;B	0.26483	0.06;0.15;0.15;0.06;0.141;0.15	B;B;B;B;B;B	0.31245	0.028;0.126;0.072;0.028;0.041;0.072	T	0.67526	-0.5648	10	0.30078	T	0.28	-19.5193	12.0079	0.53270	0.0:0.0:0.0:1.0	rs34962745	251;251;251;251;264;246	Q6ICH6;Q6P1K3;Q9NQG7;A8K2E6;Q9NQG7-4;Q9NQG7-3	.;.;HPS4_HUMAN;.;.;.	S	251;264;246;251;269;269	ENSP00000381213:T251S;ENSP00000381210:T264S;ENSP00000384185:T246S;ENSP00000338457:T251S;ENSP00000415081:T269S	ENSP00000325840:T269S	T	-	1	0	HPS4	25191473	0.996000	0.38824	0.453000	0.27007	0.219000	0.24729	4.589000	0.61006	1.936000	0.56123	0.533000	0.62120	ACC	T|0.993;A|0.007	0.007	strong		0.527	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081	
INTS4	92105	hgsc.bcm.edu	37	11	77614592	77614592	+	Silent	SNP	C	C	T	rs565544206	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:77614592C>T	ENST00000534064.1	-	17	2125	c.2091G>A	c.(2089-2091)gcG>gcA	p.A697A	AAMDC_ENST00000532481.1_Intron|INTS4_ENST00000535943.1_Silent_p.A72A	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	697					snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.A697A(1)	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)			TTACCTGTTTCGCTGCTGCTG	0.483													C|||	7	0.00139776	0.0045	0.0	5008	,	,		22683	0.001		0.0	False		,,,				2504	0.0				p.A697A		Atlas-SNP	.											INTS4,NS,carcinoma,0,2	INTS4	89	2	1	Substitution - coding silent(1)	prostate(1)	c.G2091A						scavenged	.						63.0	54.0	57.0					11																	77614592		2200	4292	6492	SO:0001819	synonymous_variant	92105	exon17			CTGTTTCGCTGCT	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.2091G>A	11.37:g.77614592C>T		Somatic	210	8	0.0380952		WXS	Illumina HiSeq	Phase_I	206	8	0.038835	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Silent	SNP	ENST00000534064.1	37	CCDS31644.1																																																																																			.	.	weak		0.483	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547	
LAMA1	284217	hgsc.bcm.edu	37	18	7008591	7008591	+	Missense_Mutation	SNP	T	T	C	rs662471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:7008591T>C	ENST00000389658.3	-	28	4111	c.4018A>G	c.(4018-4020)Atg>Gtg	p.M1340V		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1340	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.		M -> V (in dbSNP:rs662471). {ECO:0000269|PubMed:1714537}.		axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CCAACCTCCATTGAAATGTCT	0.428													T|||	937	0.187101	0.2292	0.1945	5008	,	,		18687	0.0099		0.3012	False		,,,				2504	0.1902				p.M1340V		Atlas-SNP	.											.	LAMA1	458	.	0			c.A4018G						PASS	.	T	VAL/MET	1072,3334	387.9+/-326.7	136,800,1267	119.0	111.0	113.0		4018	-7.8	0.0	18	dbSNP_83	113	2578,6022	419.2+/-353.0	368,1842,2090	yes	missense	LAMA1	NM_005559.3	21	504,2642,3357	CC,CT,TT		29.9767,24.3305,28.064	possibly-damaging	1340/3076	7008591	3650,9356	2203	4300	6503	SO:0001583	missense	284217	exon28			CCTCCATTGAAAT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4018A>G	18.37:g.7008591T>C	ENSP00000374309:p.Met1340Val	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	426	0.19505494505494506	109	0.22154471544715448	84	0.23204419889502761	3	0.005244755244755245	230	0.3034300791556728	T	16.41	3.115673	0.56505	0.243305	0.299767	ENSG00000101680	ENST00000389658	T	0.36520	1.25	5.47	-7.83	0.01201	Laminin B type IV (2);Laminin B, subgroup (1);	0.264036	0.40908	N	0.000983	T	0.00012	0.0000	M	0.88450	2.955	0.43160	P	0.005055999999999949	P	0.36354	0.549	B	0.42625	0.393	T	0.04153	-1.0973	9	0.62326	D	0.03	.	5.1126	0.14817	0.094:0.122:0.4681:0.3159	rs662471;rs59106429;rs662471	1340	P25391	LAMA1_HUMAN	V	1340	ENSP00000374309:M1340V	ENSP00000374309:M1340V	M	-	1	0	LAMA1	6998591	0.009000	0.17119	0.006000	0.13384	0.427000	0.31564	-0.035000	0.12205	-0.925000	0.03775	-0.304000	0.09214	ATG	T|0.753;C|0.247	0.247	strong		0.428	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
PTGIR	5739	hgsc.bcm.edu	37	19	47126807	47126807	+	Missense_Mutation	SNP	G	G	T	rs138619017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47126807G>T	ENST00000291294.2	-	2	809	c.676C>A	c.(676-678)Cca>Aca	p.P226T	PTGIR_ENST00000598865.1_Missense_Mutation_p.P14T|PTGIR_ENST00000597185.1_Intron|PTGIR_ENST00000594275.1_5'UTR|PTGIR_ENST00000596260.1_Missense_Mutation_p.P226T	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	226					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)	CGCGGCCGTGGACCCAGAGAG	0.672													G|||	6	0.00119808	0.0	0.0029	5008	,	,		16491	0.0		0.003	False		,,,				2504	0.001				p.P226T		Atlas-SNP	.											.	PTGIR	31	.	0			c.C676A						PASS	.	G	THR/PRO	0,4362		0,0,2181	14.0	15.0	15.0		676	4.8	0.0	19	dbSNP_134	15	30,8496		0,30,4233	yes	missense	PTGIR	NM_000960.3	38	0,30,6414	TT,TG,GG		0.3519,0.0,0.2328	benign	226/387	47126807	30,12858	2181	4263	6444	SO:0001583	missense	5739	exon2			GCCGTGGACCCAG		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.676C>A	19.37:g.47126807G>T	ENSP00000291294:p.Pro226Thr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	0.270	-0.993357	0.02145	0.0	0.003519	ENSG00000160013	ENST00000291294	T	0.71341	-0.56	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.212063	0.37669	N	0.001994	T	0.57755	0.2075	L	0.34521	1.04	0.23156	N	0.998204	B	0.06786	0.001	B	0.11329	0.006	T	0.31971	-0.9924	10	0.09590	T	0.72	-14.1054	15.2825	0.73797	0.0:0.0:1.0:0.0	.	226	P43119	PI2R_HUMAN	T	226	ENSP00000291294:P226T	ENSP00000291294:P226T	P	-	1	0	PTGIR	51818647	0.995000	0.38212	0.012000	0.15200	0.002000	0.02628	3.196000	0.51020	2.454000	0.82982	0.563000	0.77884	CCA	G|0.999;T|0.001	0.001	strong		0.672	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
ANXA2	302	hgsc.bcm.edu	37	15	60653205	60653205	+	Missense_Mutation	SNP	C	C	A	rs17845226	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:60653205C>A	ENST00000396024.3	-	6	451	c.292G>T	c.(292-294)Gtg>Ttg	p.V98L	ANXA2_ENST00000421017.2_Missense_Mutation_p.V98L|ANXA2_ENST00000557937.1_5'Flank|ANXA2_ENST00000451270.2_Missense_Mutation_p.V98L|ANXA2_ENST00000332680.4_Missense_Mutation_p.V116L	NM_001136015.2	NP_001129487.1	P07355	ANXA2_HUMAN	annexin A2	98			V -> L (in dbSNP:rs17845226). {ECO:0000269|PubMed:15489334}.		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)			kidney(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9					Tenecteplase(DB00031)	CCCAAAATCACCGTCTCCAGG	0.403													C|||	243	0.0485224	0.0076	0.0951	5008	,	,		19555	0.0		0.1252	False		,,,				2504	0.0419				p.V116L		Atlas-SNP	.											.	ANXA2	28	.	0			c.G346T						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	105,4301	82.4+/-120.9	2,101,2100	72.0	69.0	70.0		292,346,292,292	5.4	1.0	15	dbSNP_123	70	1144,7450	234.4+/-267.4	89,966,3242	no	missense,missense,missense,missense	ANXA2	NM_001002857.1,NM_001002858.2,NM_001136015.2,NM_004039.2	32,32,32,32	91,1067,5342	AA,AC,CC		13.3116,2.3831,9.6077	benign,benign,benign,benign	98/340,116/358,98/340,98/340	60653205	1249,11751	2203	4297	6500	SO:0001583	missense	302	exon5			AAATCACCGTCTC	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.292G>T	15.37:g.60653205C>A	ENSP00000379342:p.Val98Leu	Somatic	420	0	0		WXS	Illumina HiSeq	Phase_I	416	186	0.447115	NM_001002858	Q567R4|Q6N0B3|Q8TBV2|Q96DD5|Q9UDH8	Missense_Mutation	SNP	ENST00000396024.3	37	CCDS10175.1	134	0.06135531135531135	6	0.012195121951219513	36	0.09944751381215469	0	0.0	92	0.12137203166226913	C	14.69	2.611899	0.46631	0.023831	0.133116	ENSG00000182718	ENST00000396024;ENST00000332680;ENST00000421017;ENST00000451270	T;T;T;T	0.02395	4.31;4.31;4.31;4.31	5.4	5.4	0.78164	Annexin repeat, conserved site (1);	0.295374	0.27447	U	0.019332	T	0.00039	0.0001	N	0.17345	0.48	0.21841	P	0.999512084	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.20184	0.028;0.001;0.002	T	0.39800	-0.9596	9	0.02654	T	1	.	7.4902	0.27458	0.1671:0.7492:0.0:0.0836	rs17845226;rs17858041	98;116;98	B4DNH8;P07355-2;P07355	.;.;ANXA2_HUMAN	L	98;116;98;98	ENSP00000379342:V98L;ENSP00000346032:V116L;ENSP00000411352:V98L;ENSP00000387545:V98L	ENSP00000346032:V116L	V	-	1	0	ANXA2	58440497	0.985000	0.35326	0.971000	0.41717	0.995000	0.86356	2.631000	0.46502	2.701000	0.92244	0.561000	0.74099	GTG	C|0.912;A|0.088	0.088	strong		0.403	ANXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256135.1	NM_001002857	
FAT1	2195	hgsc.bcm.edu	37	4	187522528	187522528	+	Silent	SNP	C	C	T	rs2289550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187522528C>T	ENST00000441802.2	-	21	11744	c.11535G>A	c.(11533-11535)acG>acA	p.T3845T	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3845	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTTCATTTTCCGTCAGACGGT	0.413										HNSCC(5;0.00058)			C|||	279	0.0557109	0.0023	0.1052	5008	,	,		17244	0.1558		0.0348	False		,,,				2504	0.0112				p.T3845T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,-1,3	FAT1	500	3	0			c.G11535A						PASS	.	C		32,3780		0,32,1874	139.0	137.0	137.0		11535	2.7	0.8	4	dbSNP_100	137	247,7991		3,241,3875	no	coding-synonymous	FAT1	NM_005245.3		3,273,5749	TT,TC,CC		2.9983,0.8395,2.3154		3845/4589	187522528	279,11771	1906	4119	6025	SO:0001819	synonymous_variant	2195	exon21			ATTTTCCGTCAGA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.11535G>A	4.37:g.187522528C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	168	70	0.416667	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			C|0.934;T|0.066	0.066	strong		0.413	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ATP5SL	55101	hgsc.bcm.edu	37	19	41944270	41944270	+	Missense_Mutation	SNP	T	T	C	rs2231939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41944270T>C	ENST00000221943.9	-	2	73	c.68A>G	c.(67-69)cAt>cGt	p.H23R	ATP5SL_ENST00000595425.1_Missense_Mutation_p.H23R|ATP5SL_ENST00000589970.1_Missense_Mutation_p.H23R|ATP5SL_ENST00000301183.11_Missense_Mutation_p.H29R|ATP5SL_ENST00000597457.1_Missense_Mutation_p.H23R|ATP5SL_ENST00000417807.3_Missense_Mutation_p.H29R|ATP5SL_ENST00000590641.2_Missense_Mutation_p.H29R|ATP5SL_ENST00000438807.3_Missense_Mutation_p.H23R|ATP5SL_ENST00000592922.2_Missense_Mutation_p.H23R	NM_018035.2	NP_060505.2	Q9NW81	AT5SL_HUMAN	ATP5S-like	23			H -> R (in dbSNP:rs2231939). {ECO:0000269|PubMed:14702039}.			mitochondrion (GO:0005739)				breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	11						ACCCAGGCGATGGATGCCCCT	0.602													T|||	10	0.00199681	0.0	0.0058	5008	,	,		18463	0.0		0.004	False		,,,				2504	0.002				p.H29R		Atlas-SNP	.											.	ATP5SL	20	.	0			c.A86G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	6,4400	11.4+/-27.6	0,6,2197	80.0	73.0	76.0		86,86,68,68,68,68	-1.9	0.0	19	dbSNP_98	76	95,8505	52.7+/-113.3	0,95,4205	yes	missense,missense,missense,missense,missense,missense	ATP5SL	NM_001167867.1,NM_001167868.1,NM_001167869.1,NM_001167870.1,NM_001167871.1,NM_018035.2	29,29,29,29,29,29	0,101,6402	CC,CT,TT		1.1047,0.1362,0.7766	benign,benign,benign,benign,benign,benign	29/264,29/192,23/186,23/159,23/231,23/258	41944270	101,12905	2203	4300	6503	SO:0001583	missense	55101	exon2			AGGCGATGGATGC	AK001103	CCDS33032.1, CCDS54269.1, CCDS54270.1, CCDS54271.1, CCDS59389.1, CCDS59390.1	19q13.2	2007-12-13				ENSG00000105341			25496	protein-coding gene	gene with protein product						12477932	Standard	NM_001167867		Approved	FLJ10241	uc002oqv.3	Q9NW81		ENST00000221943.9:c.68A>G	19.37:g.41944270T>C	ENSP00000221943:p.His23Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_001167867	B4DDC0|B4DMZ4|B4DP55|B4DXE8|F5H4W7|K7EMF6|Q96D43	Missense_Mutation	SNP	ENST00000221943.9	37	CCDS33032.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	4.961	0.178467	0.09443	0.001362	0.011047	ENSG00000105341	ENST00000221943;ENST00000438807;ENST00000417807;ENST00000301183;ENST00000507129	T;T;T;T	0.21191	3.29;2.07;3.26;2.02	3.28	-1.89	0.07689	.	0.628545	0.14348	N	0.325281	T	0.04998	0.0134	N	0.04705	-0.18	0.09310	N	1	B;B;B;B;B;B	0.09022	0.001;0.001;0.002;0.001;0.001;0.001	B;B;B;B;B;B	0.08055	0.002;0.001;0.001;0.003;0.003;0.003	T	0.40384	-0.9566	10	0.10377	T	0.69	-11.0354	8.2202	0.31537	0.0:0.6733:0.0:0.3267	rs2231939;rs2231939	29;29;23;23;23;29	B4DFT4;B4DDC0;Q9NW81-2;E9PDC6;Q9NW81;F5H4W7	.;.;.;.;AT5SL_HUMAN;.	R	23;23;29;29;99	ENSP00000221943:H23R;ENSP00000397413:H23R;ENSP00000403910:H29R;ENSP00000301183:H29R	ENSP00000221943:H23R	H	-	2	0	ATP5SL	46636110	0.101000	0.21875	0.002000	0.10522	0.018000	0.09664	0.329000	0.19698	-0.358000	0.08162	-0.250000	0.11733	CAT	T|0.996;C|0.004	0.004	strong		0.602	ATP5SL-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460602.1	NM_018035	
C21orf2	755	hgsc.bcm.edu	37	21	45751822	45751822	+	Missense_Mutation	SNP	G	G	A	rs2277809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45751822G>A	ENST00000339818.4	-	5	656	c.449C>T	c.(448-450)aCa>aTa	p.T150I	C21orf2_ENST00000397956.3_Missense_Mutation_p.T150I|C21orf2_ENST00000325223.7_Missense_Mutation_p.T150I|AP001062.7_ENST00000448927.1_RNA|AP001062.8_ENST00000422357.1_RNA|C21orf2_ENST00000496321.1_5'UTR	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	150			T -> I (in dbSNP:rs2277809). {ECO:0000269|Ref.2}.		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)		GCCGTGGCCTGTGCCCTCTCT	0.637													G|||	187	0.0373403	0.0015	0.0144	5008	,	,		19317	0.0635		0.0318	False		,,,				2504	0.0808				p.T150I		Atlas-SNP	.											.	C21orf2	10	.	0			c.C449T						PASS	.	G	ILE/THR	43,4363	46.0+/-80.4	1,41,2161	76.0	60.0	65.0		449	-3.3	0.0	21	dbSNP_100	65	241,8359	97.0+/-158.7	4,233,4063	yes	missense	C21orf2	NM_004928.2	89	5,274,6224	AA,AG,GG		2.8023,0.9759,2.1836	benign	150/257	45751822	284,12722	2203	4300	6503	SO:0001583	missense	755	exon5			TGGCCTGTGCCCT	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.449C>T	21.37:g.45751822G>A	ENSP00000344566:p.Thr150Ile	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	195	100	0.512821	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	67	0.030677655677655676	0	0.0	4	0.011049723756906077	37	0.06468531468531469	26	0.03430079155672823	G	11.90	1.776806	0.31411	0.009759	0.028023	ENSG00000160226	ENST00000339818;ENST00000380160;ENST00000397956;ENST00000325223	T;T;T	0.35789	1.64;1.29;1.59	4.59	-3.27	0.05048	.	1.966160	0.02514	N	0.091875	T	0.03136	0.0092	L	0.39898	1.24	0.09310	N	1	P;P;P;P	0.39424	0.673;0.546;0.544;0.673	B;B;B;B	0.37144	0.242;0.103;0.122;0.242	T	0.06826	-1.0805	10	0.37606	T	0.19	1.2129	5.4638	0.16632	0.4772:0.0:0.3915:0.1313	rs2277809;rs58801270	150;150;150;109	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	I	150;186;150;150	ENSP00000344566:T150I;ENSP00000381047:T150I;ENSP00000317302:T150I	ENSP00000317302:T150I	T	-	2	0	C21orf2	44576250	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.521000	0.22893	-1.089000	0.03073	-1.119000	0.02030	ACA	G|0.974;A|0.026	0.026	strong		0.637	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
ANKRD26	22852	hgsc.bcm.edu	37	10	27322306	27322306	+	Splice_Site	SNP	C	C	T	rs146819984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:27322306C>T	ENST00000376087.4	-	25	3820	c.3655G>A	c.(3655-3657)Gtt>Att	p.V1219I	ANKRD26_ENST00000376070.3_Splice_Site_p.V776I|ANKRD26_ENST00000436985.2_Splice_Site_p.V1235I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1218			V -> L (in dbSNP:rs12572862).		glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CTCACAACAACCTGATAAGAC	0.279													C|||	42	0.00838658	0.0045	0.0058	5008	,	,		14044	0.0		0.0129	False		,,,				2504	0.0194				p.V1219I		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G3655A						PASS	.	C	ILE/VAL	8,3660		0,8,1826	136.0	120.0	125.0		3655	4.5	0.5	10	dbSNP_134	125	90,8082		1,88,3997	no	missense-near-splice	ANKRD26	NM_014915.2	29	1,96,5823	TT,TC,CC		1.1013,0.2181,0.8277	benign	1219/1711	27322306	98,11742	1834	4086	5920	SO:0001630	splice_region_variant	22852	exon25			CAACAACCTGATA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3655-1G>A	10.37:g.27322306C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	53	0.602273	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	17	0.007783882783882784	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	11.08	1.534978	0.27475	0.002181	0.011013	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.34667	3.83;1.35;1.36	5.41	4.51	0.55191	.	0.433404	0.18085	N	0.152181	T	0.26919	0.0659	M	0.62209	1.925	0.28550	N	0.911682	B;B;B	0.11235	0.003;0.001;0.004	B;B;B	0.10450	0.005;0.002;0.004	T	0.23154	-1.0196	10	0.48119	T	0.1	.	8.3454	0.32270	0.0:0.8224:0.0:0.1776	.	1219;1218;1235	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	I	776;1219;1235	ENSP00000365238:V776I;ENSP00000365255:V1219I;ENSP00000405112:V1235I	ENSP00000365238:V776I	V	-	1	0	ANKRD26	27362312	0.551000	0.26497	0.507000	0.27676	0.934000	0.57294	1.015000	0.29963	1.320000	0.45209	0.586000	0.80456	GTT	C|0.991;T|0.009	0.009	strong		0.279	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		Missense_Mutation
MUC20	200958	hgsc.bcm.edu	37	3	195456561	195456561	+	Missense_Mutation	SNP	C	C	G	rs3762739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195456561C>G	ENST00000447234.2	+	3	2138	c.2012C>G	c.(2011-2013)tCc>tGc	p.S671C	MUC20_ENST00000445522.2_Missense_Mutation_p.S636C|MUC20_ENST00000436408.1_Missense_Mutation_p.S671C|MUC20_ENST00000320736.6_Missense_Mutation_p.S500C	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	671	Interaction with MET.		S -> C (in dbSNP:rs3762739).		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		AGTGTGGCTTCCCCGGAAGAC	0.587																																					p.S500C		Atlas-SNP	.											.	MUC20	84	.	0			c.C1499G						PASS	.						45.0	43.0	44.0					3																	195456561		1997	4174	6171	SO:0001583	missense	200958	exon4			TGGCTTCCCCGGA	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.2012C>G	3.37:g.195456561C>G	ENSP00000414350:p.Ser671Cys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	134	36	0.268657	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		532|532	0.24358974358974358|0.24358974358974358	101|101	0.20528455284552846|0.20528455284552846	98|98	0.27071823204419887|0.27071823204419887	229|229	0.40034965034965037|0.40034965034965037	104|104	0.13720316622691292|0.13720316622691292	c|c	15.24|15.24	2.775028|2.775028	0.49786|0.49786	.|.	.|.	ENSG00000176945|ENSG00000176945	ENST00000423938|ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	.|T;T;T;T	.|0.38401	.|1.66;1.98;2.23;1.14	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	.|0.187733	.|0.26528	.|N	.|0.023880	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.39245|0.39245	1.2|1.2	0.31261|0.31261	P|P	0.692931|0.692931	.|D	.|0.89917	.|1.0	.|D	.|0.79108	.|0.992	T|T	0.42582|0.42582	-0.9443|-0.9443	4|9	.|0.66056	.|D	.|0.02	-14.3302|-14.3302	12.8995|12.8995	0.58117|0.58117	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs3762739;rs59929965|rs3762739;rs59929965	.|500	.|E9PH32	.|.	L|C	82|482;671;500;671;636	.|ENSP00000414350:S671C;ENSP00000325431:S500C;ENSP00000396774:S671C;ENSP00000405629:S636C	.|ENSP00000325431:S500C	F|S	+|+	3|2	2|0	MUC20|MUC20	196942232|196942232	0.960000|0.960000	0.32886|0.32886	0.966000|0.966000	0.40874|0.40874	0.236000|0.236000	0.25371|0.25371	3.051000|3.051000	0.49885|0.49885	2.396000|2.396000	0.81511|0.81511	0.558000|0.558000	0.71614|0.71614	TTC|TCC	C|0.780;G|0.220	0.220	strong		0.587	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
EFCAB13	124989	hgsc.bcm.edu	37	17	45490251	45490251	+	Silent	SNP	C	C	T	rs3883318	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45490251C>T	ENST00000331493.2	+	22	2802	c.2391C>T	c.(2389-2391)ttC>ttT	p.F797F	CTD-2026D20.2_ENST00000523101.1_RNA|EFCAB13_ENST00000517484.1_Silent_p.F701F	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	797	EF-hand 5.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.F797F(1)									AGGAGGACTTCAATGAAGCCC	0.358													c|||	743	0.148363	0.0643	0.1037	5008	,	,		17659	0.3353		0.0815	False		,,,				2504	0.1697				p.F797F		Atlas-SNP	.											C17orf57,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C2391T						scavenged	.		,	314,4092	170.5+/-200.9	13,288,1902	131.0	129.0	130.0		2103,2391	-2.0	0.0	17	dbSNP_108	130	649,7951	166.1+/-218.1	26,597,3677	no	coding-synonymous,coding-synonymous	C17orf57	NM_001195192.1,NM_152347.4	,	39,885,5579	TT,TC,CC		7.5465,7.1266,7.4043	,	701/785,797/974	45490251	963,12043	2203	4300	6503	SO:0001819	synonymous_variant	124989	exon22			GGACTTCAATGAA	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.2391C>T	17.37:g.45490251C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	173	68	0.393064	NM_152347	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	37	CCDS11512.1																																																																																			C|0.885;T|0.115	0.115	strong		0.358	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
CARD14	79092	hgsc.bcm.edu	37	17	78178916	78178916	+	Silent	SNP	C	C	T	rs61757652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78178916C>T	ENST00000573882.1	+	20	3017	c.2481C>T	c.(2479-2481)ccC>ccT	p.P827P	RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|CARD14_ENST00000344227.2_Silent_p.P827P|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	827	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CCGCCCGGCCCCGGCCTGTGC	0.652													C|||	501	0.10004	0.0492	0.1369	5008	,	,		14544	0.1042		0.0746	False		,,,				2504	0.1646				p.P827P		Atlas-SNP	.											.	CARD14	98	.	0			c.C2481T						PASS	.	C		192,4214	114.2+/-152.2	7,178,2018	53.0	53.0	53.0		2481	-1.5	0.9	17	dbSNP_129	53	660,7940	165.8+/-217.9	26,608,3666	yes	coding-synonymous	CARD14	NM_024110.3		33,786,5684	TT,TC,CC		7.6744,4.3577,6.5508		827/1005	78178916	852,12154	2203	4300	6503	SO:0001819	synonymous_variant	79092	exon18			CCGGCCCCGGCCT	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2481C>T	17.37:g.78178916C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	115	65	0.565217	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			C|0.928;T|0.072	0.072	strong		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
RAD51AP2	729475	hgsc.bcm.edu	37	2	17698678	17698678	+	Silent	SNP	A	A	G	rs665312	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:17698678A>G	ENST00000399080.2	-	1	1028	c.1005T>C	c.(1003-1005)agT>agC	p.S335S		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	335										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TATTTTGGCTACTGAGTGATG	0.338													G|||	2999	0.598842	0.1611	0.6585	5008	,	,		19036	0.8839		0.6491	False		,,,				2504	0.8027				p.S335S		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.T1005C						PASS	.	G		1053,2575		167,719,928	74.0	68.0	69.0		1005	1.7	0.2	2	dbSNP_83	69	5373,2787		1773,1827,480	no	coding-synonymous	RAD51AP2	NM_001099218.2		1940,2546,1408	GG,GA,AA		34.1544,29.0243,45.4869		335/1160	17698678	6426,5362	1814	4080	5894	SO:0001819	synonymous_variant	729475	exon1			TTGGCTACTGAGT	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.1005T>C	2.37:g.17698678A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001099218		Silent	SNP	ENST00000399080.2	37	CCDS42656.1																																																																																			A|0.397;G|0.603	0.603	strong		0.338	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
POLR3E	55718	hgsc.bcm.edu	37	16	22319517	22319517	+	Missense_Mutation	SNP	T	T	G	rs2347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:22319517T>G	ENST00000299853.5	+	4	303	c.136T>G	c.(136-138)Tca>Gca	p.S46A	POLR3E_ENST00000564256.1_3'UTR|POLR3E_ENST00000564209.1_Missense_Mutation_p.S46A|POLR3E_ENST00000418581.2_Intron|POLR3E_ENST00000359210.4_Missense_Mutation_p.S46A	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	46			S -> A (in dbSNP:rs2347).		defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|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)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		TCCGCACCTCTCAGCCAAGAT	0.627													T|||	257	0.0513179	0.0106	0.0274	5008	,	,		19847	0.003		0.0716	False		,,,				2504	0.1524				p.S46A		Atlas-SNP	.											.	POLR3E	62	.	0			c.T136G						PASS	.	T	ALA/SER	68,4326	62.9+/-100.1	0,68,2129	92.0	70.0	77.0		136	5.6	1.0	16	dbSNP_36	77	491,8109	142.8+/-198.9	8,475,3817	yes	missense	POLR3E	NM_018119.2	99	8,543,5946	GG,GT,TT		5.7093,1.5476,4.302	benign	46/709	22319517	559,12435	2197	4300	6497	SO:0001583	missense	55718	exon4			CACCTCTCAGCCA	AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"""RNA polymerase subunits"""	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.136T>G	16.37:g.22319517T>G	ENSP00000299853:p.Ser46Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_001258033	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Missense_Mutation	SNP	ENST00000299853.5	37	CCDS10605.1	76	0.0347985347985348	7	0.014227642276422764	14	0.03867403314917127	1	0.0017482517482517483	54	0.0712401055408971	T	13.48	2.248808	0.39797	0.015476	0.057093	ENSG00000058600	ENST00000299853;ENST00000359210	T;T	0.47177	0.85;0.85	5.6	5.6	0.85130	.	0.453885	0.24213	N	0.040515	T	0.03305	0.0096	N	0.17872	0.535	0.38978	D	0.958888	B;B;B;B	0.26577	0.076;0.062;0.153;0.062	B;B;B;B	0.26517	0.07;0.028;0.065;0.042	T	0.05241	-1.0897	10	0.87932	D	0	-2.1779	14.8076	0.69968	0.0:0.0:0.0:1.0	rs2347;rs17627984;rs52818542;rs60754269;rs2347	46;46;46;46	B4DUP6;Q9NVU0-2;Q9NVU0;Q9NVU0-3	.;.;RPC5_HUMAN;.	A	46	ENSP00000299853:S46A;ENSP00000352140:S46A	ENSP00000299853:S46A	S	+	1	0	POLR3E	22227018	1.000000	0.71417	0.970000	0.41538	0.985000	0.73830	3.172000	0.50832	2.145000	0.66743	0.454000	0.30748	TCA	T|0.958;G|0.042	0.042	strong		0.627	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119	
PLOD3	8985	hgsc.bcm.edu	37	7	100850144	100850144	+	Silent	SNP	G	G	A	rs11546151	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100850144G>A	ENST00000223127.3	-	18	2375	c.1977C>T	c.(1975-1977)gaC>gaT	p.D659D		NM_001084.4	NP_001075.1	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	659	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				basement membrane assembly (GO:0070831)|cellular protein modification process (GO:0006464)|cellular response to hormone stimulus (GO:0032870)|collagen fibril organization (GO:0030199)|endothelial cell morphogenesis (GO:0001886)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|lung morphogenesis (GO:0060425)|neural tube development (GO:0021915)|protein localization (GO:0008104)|vasodilation (GO:0042311)	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 galactosyltransferase activity (GO:0050211)|procollagen glucosyltransferase activity (GO:0033823)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	31	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	ACGGCTGCTCGTCTGGCCGGT	0.632													G|||	163	0.0325479	0.028	0.0072	5008	,	,		13032	0.0952		0.001	False		,,,				2504	0.0245				p.D659D		Atlas-SNP	.											.	PLOD3	79	.	0			c.C1977T						PASS	.	G		78,4300		2,74,2113	96.0	61.0	73.0		1977	-0.6	0.8	7	dbSNP_120	73	60,8502		0,60,4221	no	coding-synonymous	PLOD3	NM_001084.4		2,134,6334	AA,AG,GG		0.7008,1.7816,1.0665		659/739	100850144	138,12802	2189	4281	6470	SO:0001819	synonymous_variant	8985	exon18			CTGCTCGTCTGGC	AF046889	CCDS5715.1	7q22.1	2011-08-24			ENSG00000106397	ENSG00000106397	1.14.11.4		9083	protein-coding gene	gene with protein product	"""lysyl hydroxlase 3"""	603066				9724729, 9582318	Standard	NM_001084		Approved	LH3	uc003uyd.3	O60568	OTTHUMG00000157111	ENST00000223127.3:c.1977C>T	7.37:g.100850144G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	138	74	0.536232	NM_001084	B2R6W6|Q540C3	Silent	SNP	ENST00000223127.3	37	CCDS5715.1	78	0.03571428571428571	18	0.036585365853658534	4	0.011049723756906077	56	0.0979020979020979	0	0.0	G	0.150	-1.092547	0.01858	0.017816	0.007008	ENSG00000106397	ENST00000454310	.	.	.	3.77	-0.604	0.11626	.	.	.	.	.	T	0.01189	0.0039	.	.	.	0.09310	P	0.9999999999999954	.	.	.	.	.	.	T	0.19712	-1.0297	3	.	.	.	-15.2026	7.9767	0.30159	0.6136:0.0:0.3864:0.0	rs11546151	.	.	.	M	185	.	.	T	-	2	0	PLOD3	100636864	0.002000	0.14202	0.831000	0.32960	0.003000	0.03518	-1.153000	0.03169	-0.503000	0.06586	-1.598000	0.00824	ACG	G|0.978;A|0.022	0.022	strong		0.632	PLOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347470.1		
ACP2	53	hgsc.bcm.edu	37	11	47270255	47270255	+	Missense_Mutation	SNP	C	C	T	rs2167079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47270255C>T	ENST00000256997.3	-	1	202	c.86G>A	c.(85-87)cGg>cAg	p.R29Q	NR1H3_ENST00000405576.1_5'Flank|ACP2_ENST00000529788.1_Missense_Mutation_p.R29Q|ACP2_ENST00000530453.1_Missense_Mutation_p.R29Q|ACP2_ENST00000533929.1_5'Flank|NR1H3_ENST00000529540.1_3'UTR|ACP2_ENST00000529444.1_Missense_Mutation_p.R29Q|NR1H3_ENST00000481889.2_5'Flank|ACP2_ENST00000537863.1_5'UTR|NR1H3_ENST00000395397.3_5'Flank|ACP2_ENST00000527256.1_Missense_Mutation_p.R29Q|NR1H3_ENST00000407404.1_5'Flank|ACP2_ENST00000444355.2_Missense_Mutation_p.R29Q	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	29			R -> Q (in dbSNP:rs2167079). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		dephosphorylation (GO:0016311)|lysosome organization (GO:0007040)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)	acid phosphatase activity (GO:0003993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10						ACTCCGGGCCCGGGTGGGCGG	0.622													T|||	2589	0.516973	0.6203	0.3458	5008	,	,		17244	0.7768		0.3002	False		,,,				2504	0.454				p.R29Q	Melanoma(90;262 1440 11488 44828 48531)	Atlas-SNP	.											.	ACP2	36	.	0			c.G86A						PASS	.	T	GLN/ARG,GLN/ARG	2452,1934		672,1108,413	20.0	22.0	22.0		86,86	5.7	1.0	11	dbSNP_96	22	2478,6114		353,1772,2171	yes	missense,missense	ACP2	NM_001131064.1,NM_001610.2	43,43	1025,2880,2584	TT,TC,CC		28.8408,44.0948,37.9874	benign,benign	29/161,29/424	47270255	4930,8048	2193	4296	6489	SO:0001583	missense	53	exon1			CGGGCCCGGGTGG	X15525	CCDS7928.1, CCDS44583.1	11p11.2	2008-02-05			ENSG00000134575	ENSG00000134575	3.1.3.2		123	protein-coding gene	gene with protein product		171650				975882	Standard	NM_001610		Approved		uc001nei.3	P11117	OTTHUMG00000166949	ENST00000256997.3:c.86G>A	11.37:g.47270255C>T	ENSP00000256997:p.Arg29Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_001610	E9PCI1|Q561W5|Q9BTU7	Missense_Mutation	SNP	ENST00000256997.3	37	CCDS7928.1	1078	0.4935897435897436	279	0.5670731707317073	139	0.3839779005524862	425	0.743006993006993	235	0.3100263852242744	T	17.86	3.491528	0.64074	0.559052	0.288408	ENSG00000134575	ENST00000256997;ENST00000529444;ENST00000527256;ENST00000540414;ENST00000529663;ENST00000530453;ENST00000444355;ENST00000529788	T;T;T;T;T;T;T	0.40476	3.19;3.02;3.31;2.82;1.61;1.6;1.03	5.69	5.69	0.88448	.	0.394063	0.27591	N	0.018686	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999999999996	B;B;B;B;B	0.10296	0.003;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	0.40496	-0.9560	9	0.02654	T	1	.	9.8795	0.41225	0.0:0.0786:0.0:0.9214	rs2167079;rs2228400;rs58523292;rs2167079	29;29;29;29;29	E9PCI1;E9PHY0;B7Z7D2;F5H1S6;P11117	.;.;.;.;PPAL_HUMAN	Q	29	ENSP00000256997:R29Q;ENSP00000436658:R29Q;ENSP00000432205:R29Q;ENSP00000436487:R29Q;ENSP00000434205:R29Q;ENSP00000414911:R29Q;ENSP00000436828:R29Q	ENSP00000256997:R29Q	R	-	2	0	ACP2	47226831	1.000000	0.71417	0.987000	0.45799	0.990000	0.78478	1.370000	0.34238	1.092000	0.41356	-0.254000	0.11334	CGG	C|0.559;T|0.441	0.441	strong		0.622	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610	
P2RX3	5024	hgsc.bcm.edu	37	11	57137371	57137371	+	Silent	SNP	G	G	A	rs2276039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57137371G>A	ENST00000263314.2	+	12	1129	c.1095G>A	c.(1093-1095)acG>acA	p.T365T		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	365					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|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 homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						ATGAGACTACGCTGAAAATCG	0.552													G|||	2060	0.411342	0.0756	0.4813	5008	,	,		20321	0.6319		0.3847	False		,,,				2504	0.6155				p.T365T		Atlas-SNP	.											P2RX3,NS,adenoma,0,1	P2RX3	55	1	0			c.G1095A						scavenged	.	G		572,3830	250.0+/-257.2	43,486,1672	106.0	88.0	94.0		1095	-7.2	0.0	11	dbSNP_100	94	3200,5392	477.5+/-369.7	605,1990,1701	yes	coding-synonymous	P2RX3	NM_002559.3		648,2476,3373	AA,AG,GG		37.2439,12.9941,29.0288		365/398	57137371	3772,9222	2201	4296	6497	SO:0001819	synonymous_variant	5024	exon12			GACTACGCTGAAA	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.1095G>A	11.37:g.57137371G>A		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	147	79	0.537415	NM_002559	Q6DK37|Q9UQB6	Silent	SNP	ENST00000263314.2	37	CCDS7953.1																																																																																			G|0.664;A|0.336	0.336	strong		0.552	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
PFN1	5216	hgsc.bcm.edu	37	17	4849284	4849284	+	Silent	SNP	G	G	A	rs13204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4849284G>A	ENST00000225655.5	-	3	953	c.334C>T	c.(334-336)Ctg>Ttg	p.L112L	PFN1_ENST00000574872.1_Silent_p.L76L	NM_005022.3	NP_005013.1	P07737	PROF1_HUMAN	profilin 1	112					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cell death (GO:0008219)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of ATPase activity (GO:0032781)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of ruffle assembly (GO:1900029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|adenyl-nucleotide exchange factor activity (GO:0000774)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|proline-rich region binding (GO:0070064)			NS(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5						CCCATCAGCAGGACTAGCGCT	0.562													G|||	442	0.0882588	0.0159	0.147	5008	,	,		16202	0.1954		0.0278	False		,,,				2504	0.0961				p.L112L		Atlas-SNP	.											.	PFN1	6	.	0			c.C334T						PASS	.	G		137,4269	97.1+/-135.8	1,135,2067	86.0	68.0	74.0		334	3.3	1.0	17	dbSNP_52	74	346,8254	118.1+/-177.6	9,328,3963	no	coding-synonymous	PFN1	NM_005022.2		10,463,6030	AA,AG,GG		4.0233,3.1094,3.7137		112/141	4849284	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	5216	exon3			TCAGCAGGACTAG	BC057828	CCDS11061.1	17p13.2	2010-07-09			ENSG00000108518	ENSG00000108518			8881	protein-coding gene	gene with protein product		176610				3356709, 1968707	Standard	NM_005022		Approved		uc002gaa.4	P07737	OTTHUMG00000099396	ENST00000225655.5:c.334C>T	17.37:g.4849284G>A		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	287	146	0.508711	NM_005022	Q53Y44	Silent	SNP	ENST00000225655.5	37	CCDS11061.1																																																																																			G|0.949;C|0.000;A|0.051	0.051	strong		0.562	PFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216853.1	NM_005022	
ZNF107	51427	hgsc.bcm.edu	37	7	64168806	64168806	+	Silent	SNP	T	T	C	rs4718103	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:64168806T>C	ENST00000395391.1	+	4	3499	c.2124T>C	c.(2122-2124)acT>acC	p.T708T	ZNF107_ENST00000423627.1_Silent_p.T708T|ZNF107_ENST00000344930.3_Silent_p.T708T			Q9UII5	ZN107_HUMAN	zinc finger protein 107	708					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)				CAAACCTTACTACACATAAGA	0.338													t|||	1649	0.329273	0.1505	0.3876	5008	,	,		19003	0.25		0.4314	False		,,,				2504	0.5061				p.T708T		Atlas-SNP	.											.	ZNF107	107	.	0			c.T2124C						PASS	.	T	,	923,3479		110,703,1388	28.0	31.0	30.0		2124,2124	1.3	0.0	7	dbSNP_111	30	3744,4850		849,2046,1402	no	coding-synonymous,coding-synonymous	ZNF107	NM_001013746.1,NM_016220.3	,	959,2749,2790	CC,CT,TT		43.5653,20.9677,35.911	,	708/784,708/784	64168806	4667,8329	2201	4297	6498	SO:0001819	synonymous_variant	51427	exon7			CCTTACTACACAT	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.2124T>C	7.37:g.64168806T>C		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_016220		Silent	SNP	ENST00000395391.1	37	CCDS5527.1																																																																																			T|0.629;C|0.371	0.371	strong		0.338	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
SARDH	1757	hgsc.bcm.edu	37	9	136573412	136573412	+	Silent	SNP	G	G	A	rs2073815	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136573412G>A	ENST00000371872.4	-	11	1724	c.1467C>T	c.(1465-1467)caC>caT	p.H489H	SARDH_ENST00000422262.2_Silent_p.H321H|SARDH_ENST00000439388.1_Silent_p.H489H	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	489					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		GCGTTACCTCGTGCAGCGGGT	0.637													G|||	2123	0.423922	0.2254	0.464	5008	,	,		17063	0.4891		0.5577	False		,,,				2504	0.4591				p.H489H		Atlas-SNP	.											SARDH,NS,carcinoma,0,2	SARDH	112	2	0			c.C1467T						PASS	.	G	,	1190,3216	415.0+/-337.0	157,876,1170	73.0	66.0	68.0		1467,1467	0.6	1.0	9	dbSNP_96	68	4982,3618	625.8+/-397.8	1437,2108,755	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	1594,2984,1925	AA,AG,GG		42.0698,27.0086,47.455	,	489/919,489/919	136573412	6172,6834	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon11			TACCTCGTGCAGC		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1467C>T	9.37:g.136573412G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.539;A|0.461	0.461	strong		0.637	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
MYOM3	127294	hgsc.bcm.edu	37	1	24394811	24394811	+	Missense_Mutation	SNP	A	A	G	rs12145360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24394811A>G	ENST00000374434.3	-	26	3359	c.3197T>C	c.(3196-3198)aTc>aCc	p.I1066T	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Missense_Mutation_p.I1066T|MYOM3_ENST00000330966.7_Missense_Mutation_p.I1067T|MYOM3_ENST00000338909.5_5'Flank|RP11-293P20.4_ENST00000429191.1_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1066			I -> T (in dbSNP:rs12145360).			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GTTCTGGATGATCACTTCCAC	0.478													A|||	982	0.196086	0.2262	0.1427	5008	,	,		16302	0.1964		0.1372	False		,,,				2504	0.2536				p.I1066T		Atlas-SNP	.											.	MYOM3	131	.	0			c.T3197C						PASS	.	A	THR/ILE	715,3291		61,593,1349	284.0	282.0	282.0		3197	4.7	1.0	1	dbSNP_120	282	1118,7206		69,980,3113	yes	missense	MYOM3	NM_152372.3	89	130,1573,4462	GG,GA,AA		13.431,17.8482,14.8662	benign	1066/1438	24394811	1833,10497	2003	4162	6165	SO:0001583	missense	127294	exon26			TGGATGATCACTT	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.3197T>C	1.37:g.24394811A>G	ENSP00000363557:p.Ile1066Thr	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	144	55	0.381944	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	352	0.16117216117216118	90	0.18292682926829268	52	0.143646408839779	109	0.19055944055944055	101	0.13324538258575197	A	12.56	1.975219	0.34848	0.178482	0.13431	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.04317	3.65;3.65;3.65	4.69	4.69	0.59074	Immunoglobulin-like fold (1);	0.245363	0.35936	N	0.002893	T	0.00012	0.0000	L	0.31578	0.945	0.27553	P	0.9504333	B;B	0.16166	0.004;0.016	B;B	0.17979	0.02;0.008	T	0.47446	-0.9117	9	0.19590	T	0.45	.	9.5611	0.39369	0.9152:0.0:0.0848:0.0	rs12145360;rs52790715;rs12145360	1066;1066	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	T	1066;1067;1066	ENSP00000363557:I1066T;ENSP00000332670:I1067T;ENSP00000328415:I1066T	ENSP00000328415:I1066T	I	-	2	0	MYOM3	24267398	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.548000	0.60718	1.887000	0.54652	0.379000	0.24179	ATC	A|0.836;G|0.164	0.164	strong		0.478	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
MUC4	4585	hgsc.bcm.edu	37	3	195507817	195507817	+	Missense_Mutation	SNP	A	A	G	rs200993341		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195507817A>G	ENST00000463781.3	-	2	11093	c.10634T>C	c.(10633-10635)gTa>gCa	p.V3545A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3545A	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)		ACCTGTGGATACTGAGGAAAG	0.602																																					p.V3545A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.T10634C						scavenged	.						23.0	22.0	23.0					3																	195507817		682	1577	2259	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.10634T>C	3.37:g.195507817A>G	ENSP00000417498:p.Val3545Ala	Somatic	398	10	0.0251256		WXS	Illumina HiSeq	Phase_I	425	17	0.04	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	1.383	-0.582833	0.03827	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.49432	0.98;0.78	0.743	-1.49	0.08718	.	0.435754	0.11199	U	0.589055	T	0.16041	0.0386	N	0.02539	-0.55	0.09310	N	1	B	0.26512	0.151	B	0.14023	0.01	T	0.11867	-1.0570	9	.	.	.	.	4.1685	0.10318	0.735:0.0:0.265:0.0	.	3417	E7ESK3	.	A	3545	ENSP00000417498:V3545A;ENSP00000420243:V3545A	.	V	-	2	0	MUC4	196992596	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-2.247000	0.01190	-1.995000	0.00971	-2.001000	0.00444	GTA	G|0.994;T|0.006	0.994	weak		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ABCC12	94160	hgsc.bcm.edu	37	16	48151202	48151202	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:48151202C>T	ENST00000311303.3	-	12	2100	c.1755G>A	c.(1753-1755)ctG>ctA	p.L585L	ABCC12_ENST00000416054.1_Intron|ABCC12_ENST00000448542.1_Silent_p.L585L	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	585	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.					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)				GGAGGTTGCTCAGGTCCTTCT	0.582																																					p.L585L		Atlas-SNP	.											.	ABCC12	190	.	0			c.G1755A						PASS	.						82.0	75.0	77.0					16																	48151202		2201	4300	6501	SO:0001819	synonymous_variant	94160	exon12			GTTGCTCAGGTCC	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.1755G>A	16.37:g.48151202C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			.	.	none		0.582	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
RIMBP3	85376	hgsc.bcm.edu	37	22	20457514	20457514	+	Missense_Mutation	SNP	T	T	G	rs200584390		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:20457514T>G	ENST00000426804.1	-	1	4272	c.3788A>C	c.(3787-3789)gAa>gCa	p.E1263A	SCARNA18_ENST00000516215.1_RNA|SCARNA17_ENST00000516762.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1263								p.E1263A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			ACATTCTCCTTCTGAGCCCAG	0.592																																					p.E1263A		Atlas-SNP	.											RIMBP3,colon,carcinoma,0,1	RIMBP3	42	1	1	Substitution - Missense(1)	large_intestine(1)	c.A3788C						scavenged	.																																			SO:0001583	missense	85376	exon1			TCTCCTTCTGAGC	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3788A>C	22.37:g.20457514T>G	ENSP00000391564:p.Glu1263Ala	Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	313	132	0.421725	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	37	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497585	0.44455	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.20069	2.1	3.38	3.38	0.38709	.	0.974387	0.08394	N	0.952473	T	0.13372	0.0324	L	0.29908	0.895	0.44221	P	0.002943000000000029	B	0.33694	0.421	B	0.25140	0.058	T	0.12477	-1.0546	9	0.18276	T	0.48	-1.0666	8.3984	0.32570	0.0:0.0:0.0:1.0	.	1169	Q9UFD9	RIM3A_HUMAN	A	1169;1263	ENSP00000391564:E1263A	ENSP00000347318:E1169A	E	-	2	0	RIMBP3	18837514	0.928000	0.31464	0.559000	0.28332	0.264000	0.26372	1.444000	0.35068	1.548000	0.49413	0.347000	0.21830	GAA	.	.	weak		0.592	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
D2HGDH	728294	hgsc.bcm.edu	37	2	242674803	242674803	+	Missense_Mutation	SNP	G	G	A	rs77940364	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242674803G>A	ENST00000321264.4	+	2	373	c.164G>A	c.(163-165)cGg>cAg	p.R55Q	D2HGDH_ENST00000342518.6_Missense_Mutation_p.R55Q|D2HGDH_ENST00000537090.1_Missense_Mutation_p.R55Q|AC114730.8_ENST00000400768.2_RNA|D2HGDH_ENST00000403782.1_Intron	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	22	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	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	
HELQ	113510	hgsc.bcm.edu	37	4	84364751	84364751	+	Silent	SNP	A	A	G	rs7665103	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:84364751A>G	ENST00000295488.3	-	6	1644	c.1482T>C	c.(1480-1482)atT>atC	p.I494I	HELQ_ENST00000510985.1_Silent_p.I427I	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	494	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						CACTCATACCAATAATTTGAG	0.294								Other identified genes with known or suspected DNA repair function					A|||	2543	0.507788	0.4493	0.5447	5008	,	,		18714	0.6736		0.3787	False		,,,				2504	0.5225				p.I494I		Atlas-SNP	.											.	HELQ	95	.	0			c.T1482C						PASS	.	A		1950,2446	539.4+/-375.3	460,1030,708	63.0	63.0	63.0		1482	0.6	1.0	4	dbSNP_116	63	3504,5094	502.8+/-375.8	713,2078,1508	no	coding-synonymous	HELQ	NM_133636.2		1173,3108,2216	GG,GA,AA		40.7537,44.3585,41.9732		494/1102	84364751	5454,7540	2198	4299	6497	SO:0001819	synonymous_variant	113510	exon6			CATACCAATAATT	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1482T>C	4.37:g.84364751A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	45	29	0.644444	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.558;G|0.442	0.442	strong		0.294	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
CD19	930	hgsc.bcm.edu	37	16	28944700	28944700	+	Silent	SNP	G	G	T	rs35979293	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:28944700G>T	ENST00000324662.3	+	4	749	c.705G>T	c.(703-705)ccG>ccT	p.P235P	CD19_ENST00000567541.1_Silent_p.P235P|CD19_ENST00000538922.1_Silent_p.P235P			P15391	CD19_HUMAN	CD19 molecule	235	Ig-like C2-type 2.				B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|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)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						ACGATCGCCCGGCCAGAGATA	0.587													G|||	937	0.187101	0.0711	0.2406	5008	,	,		17615	0.1726		0.3976	False		,,,				2504	0.1043				p.P235P		Atlas-SNP	.											.	CD19	65	.	0			c.G705T						PASS	.	G	,	509,3885	233.3+/-246.5	21,467,1709	67.0	65.0	66.0		705,705	-8.5	0.0	16	dbSNP_126	66	3069,5531	470.9+/-367.9	541,1987,1772	no	coding-synonymous,coding-synonymous	CD19	NM_001178098.1,NM_001770.5	,	562,2454,3481	TT,TG,GG		35.686,11.584,27.5358	,	235/558,235/557	28944700	3578,9416	2197	4300	6497	SO:0001819	synonymous_variant	930	exon4			TCGCCCGGCCAGA		CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1633	protein-coding gene	gene with protein product		107265	"""CD19 antigen"""				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.705G>T	16.37:g.28944700G>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Silent	SNP	ENST00000324662.3	37	CCDS10644.1																																																																																			G|0.736;T|0.264	0.264	strong		0.587	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2		
ZBBX	79740	hgsc.bcm.edu	37	3	167083758	167083758	+	Missense_Mutation	SNP	G	G	T	rs528713569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:167083758G>T	ENST00000392766.2	-	6	529	c.189C>A	c.(187-189)agC>agA	p.S63R	ZBBX_ENST00000307529.5_Missense_Mutation_p.S63R|ZBBX_ENST00000455345.2_Missense_Mutation_p.S63R|ZBBX_ENST00000392764.1_Missense_Mutation_p.S34R|ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392767.2_Missense_Mutation_p.S63R	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	63						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.S63S(2)		NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						AGTAATACTCGCTTGACCTTT	0.294																																					p.S63R		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,0,2	ZBBX	299	2	2	Substitution - coding silent(2)	breast(2)	c.C189A						scavenged	.						87.0	80.0	82.0					3																	167083758		1809	4057	5866	SO:0001583	missense	79740	exon6			ATACTCGCTTGAC	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.189C>A	3.37:g.167083758G>T	ENSP00000376519:p.Ser63Arg	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	190	2	0.0105263	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	G	8.894	0.954608	0.18431	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764;ENST00000474464	T;T;T;T;T;T	0.32023	3.0;3.0;3.0;3.0;2.82;1.47	5.26	2.79	0.32731	.	.	.	.	.	T	0.46444	0.1393	L	0.57536	1.79	0.22531	N	0.999013	D;D	0.76494	0.999;0.997	D;P	0.64410	0.925;0.842	T	0.24119	-1.0169	9	0.52906	T	0.07	-2.6669	9.5283	0.39178	0.9067:0.0:0.0933:0.0	.	63;63	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	63;63;63;63;34;63	ENSP00000376519:S63R;ENSP00000376520:S63R;ENSP00000390232:S63R;ENSP00000305065:S63R;ENSP00000376517:S34R;ENSP00000419307:S63R	ENSP00000305065:S63R	S	-	3	2	ZBBX	168566452	0.758000	0.28405	0.938000	0.37757	0.135000	0.20990	2.515000	0.45512	0.400000	0.25396	-1.338000	0.01255	AGC	.	.	none		0.294	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
LRRC16B	90668	hgsc.bcm.edu	37	14	24529260	24529260	+	Silent	SNP	C	C	T	rs58283036	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24529260C>T	ENST00000342740.5	+	23	2104	c.1950C>T	c.(1948-1950)gaC>gaT	p.D650D	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	650						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)		GCACCGAGGACGTCTGGCAGA	0.662													C|||	1594	0.318291	0.382	0.2478	5008	,	,		21073	0.5556		0.0924	False		,,,				2504	0.2699				p.D650D		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1950T						PASS	.	C		1461,2945	472.0+/-356.2	261,939,1003	120.0	105.0	110.0		1950	-4.8	0.9	14	dbSNP_129	110	777,7823	183.3+/-231.6	39,699,3562	no	coding-synonymous	LRRC16B	NM_138360.3		300,1638,4565	TT,TC,CC		9.0349,33.1593,17.2074		650/1373	24529260	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon23			CGAGGACGTCTGG	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.1950C>T	14.37:g.24529260C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.788;T|0.212	0.212	strong		0.662	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
KIAA1644	85352	hgsc.bcm.edu	37	22	44681612	44681612	+	Silent	SNP	A	A	G	rs135388	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:44681612A>G	ENST00000381176.4	-	4	427	c.295T>C	c.(295-297)Ttg>Ctg	p.L99L		NM_001099294.1	NP_001092764.1	Q3SXP7	K1644_HUMAN	KIAA1644	99						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				ACTCCCAACAAGGCGGTGTAA	0.502													A|||	2329	0.465056	0.4017	0.3674	5008	,	,		19009	0.3284		0.6163	False		,,,				2504	0.6053				p.L99L		Atlas-SNP	.											.	KIAA1644	39	.	0			c.T295C						PASS	.	A		1815,2275		423,969,653	131.0	124.0	126.0		295	-3.9	0.8	22	dbSNP_78	126	5269,3127		1689,1891,618	no	coding-synonymous	KIAA1644	NM_001099294.1		2112,2860,1271	GG,GA,AA		37.2439,44.3765,43.2645		99/200	44681612	7084,5402	2045	4198	6243	SO:0001819	synonymous_variant	85352	exon4			CCAACAAGGCGGT	AB051431	CCDS43025.1	22q13	2009-02-06	2009-02-06		ENSG00000138944	ENSG00000138944			29335	protein-coding gene	gene with protein product						11258795	Standard	NM_001099294		Approved		uc003bet.2	Q3SXP7	OTTHUMG00000030991	ENST00000381176.4:c.295T>C	22.37:g.44681612A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_001099294	A6NHP0|A9Z1Z0|Q3SXP8|Q5JZ71|Q9BYB5	Silent	SNP	ENST00000381176.4	37	CCDS43025.1																																																																																			A|0.509;G|0.491	0.491	strong		0.502	KIAA1644-006	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075879.2	NM_001099294	
FNBP1	23048	hgsc.bcm.edu	37	9	132662786	132662786	+	Missense_Mutation	SNP	C	C	T	rs1023000	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:132662786C>T	ENST00000446176.2	-	14	1655	c.1469G>A	c.(1468-1470)aGc>aAc	p.S490N	FNBP1_ENST00000355681.3_Missense_Mutation_p.S461N|FNBP1_ENST00000478129.1_5'UTR|FNBP1_ENST00000443566.2_Missense_Mutation_p.S118N|FNBP1_ENST00000420781.1_Missense_Mutation_p.S481N	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	490	Interaction with RND2. {ECO:0000250}.|Required for self-association and induction of membrane tubulation.		S -> N (in dbSNP:rs1023000). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)						Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		CGCCTGCTCGCTGCGTGCTGG	0.622			T	MLL	AML								c|||	3179	0.634784	0.5787	0.6527	5008	,	,		16546	0.7927		0.507	False		,,,				2504	0.6667				p.S490N		Atlas-SNP	.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	FNBP1_ENST00000372416,NS,carcinoma,0,2	FNBP1	51	2	0			c.G1469A						PASS	.	T	ASN/SER	2340,1616		694,952,332	27.0	30.0	29.0		1469	2.2	0.0	9	dbSNP_86	29	4354,3952		1131,2092,930	yes	missense	FNBP1	NM_015033.2	46	1825,3044,1262	TT,TC,CC		47.5801,40.8493,45.4086	benign	490/618	132662786	6694,5568	1978	4153	6131	SO:0001583	missense	23048	exon14			TGCTCGCTGCGTG	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.1469G>A	9.37:g.132662786C>T	ENSP00000413625:p.Ser490Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_015033	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	37	CCDS48040.1	1334|1334	0.6108058608058609|0.6108058608058609	308|308	0.6260162601626016|0.6260162601626016	218|218	0.6022099447513812|0.6022099447513812	433|433	0.756993006993007|0.756993006993007	375|375	0.4947229551451187|0.4947229551451187	c|c	0.609|0.609	-0.825795|-0.825795	0.02734|0.02734	0.591507|0.591507	0.524199|0.524199	ENSG00000187239|ENSG00000187239	ENST00000449089|ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000443566;ENST00000355681	.|T;T;T;T	.|0.73681	.|-0.77;-0.77;-0.77;-0.77	4.02|4.02	2.15|2.15	0.27550|0.27550	.|.	.|1.265410	.|0.05157	.|N	.|0.497001	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25144|0.25144	0.715|0.715	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B;B;B	.|0.15052	.|0.001;0.001;0.002;0.001;0.003;0.012;0.003;0.001	T|T	0.46679|0.46679	-0.9174|-0.9174	4|9	.|0.45353	.|T	.|0.12	-4.9808|-4.9808	5.5861|5.5861	0.17275|0.17275	0.0:0.5641:0.1482:0.2878|0.0:0.5641:0.1482:0.2878	rs1023000;rs3208771;rs17407396;rs58921965;rs1023000|rs1023000;rs3208771;rs17407396;rs58921965;rs1023000	.|485;480;118;424;461;441;485;490	.|B7ZL12;B7ZL13;E7EPB7;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3	.|.;.;.;.;.;.;.;FNBP1_HUMAN	T|N	442|490;490;481;490;118;461	.|ENSP00000413625:S490N;ENSP00000407548:S481N;ENSP00000389117:S118N;ENSP00000347907:S461N	.|ENSP00000347907:S461N	A|S	-|-	1|2	0|0	FNBP1|FNBP1	131702607|131702607	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.351000|0.351000	0.29236|0.29236	0.438000|0.438000	0.21559|0.21559	0.131000|0.131000	0.18576|0.18576	-1.924000|-1.924000	0.00514|0.00514	GCG|AGC	C|0.386;T|0.614	0.614	strong		0.622	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2		
A2ML1	144568	hgsc.bcm.edu	37	12	9009820	9009820	+	Missense_Mutation	SNP	G	G	A	rs1558526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:9009820G>A	ENST00000299698.7	+	24	3089	c.2909G>A	c.(2908-2910)tGt>tAt	p.C970Y	A2ML1_ENST00000539547.1_Missense_Mutation_p.C479Y	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CCCAGTGGCTGTGGCGAGCAG	0.562													G|||	557	0.111222	0.0159	0.1888	5008	,	,		-128	0.0		0.2684	False		,,,				2504	0.138				p.C970Y		Atlas-SNP	.											.	A2ML1	199	.	0			c.G2909A						PASS	.	G	TYR/CYS	189,3851		7,175,1838	132.0	139.0	137.0		2909	1.8	1.0	12	dbSNP_88	137	2167,6215		298,1571,2322	yes	missense	A2ML1	NM_144670.3	194	305,1746,4160	AA,AG,GG		25.853,4.6782,18.9664	probably-damaging	970/1455	9009820	2356,10066	2020	4191	6211	SO:0001583	missense	144568	exon24			GTGGCTGTGGCGA	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.2909G>A	12.37:g.9009820G>A	ENSP00000299698:p.Cys970Tyr	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	170	91	0.535294	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	300	0.13736263736263737	13	0.026422764227642278	83	0.2292817679558011	0	0.0	204	0.2691292875989446	G	17.04	3.286741	0.59867	0.046782	0.25853	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	D;D;D	0.81739	-1.53;-1.53;-1.53	3.73	1.81	0.25067	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);Alpha-2-macroglobulin, thiol-ester bond-forming (1);Alpha-2-macroglobulin, conserved site (1);	0.000000	0.64402	D	0.000017	T	0.00073	0.0002	H	0.95917	3.74	0.24571	P	0.99392864	D	0.89917	1.0	D	0.91635	0.999	T	0.02852	-1.1102	9	0.87932	D	0	.	7.8364	0.29371	0.0958:0.1631:0.741:0.0	rs1558526;rs52832831;rs60455871;rs1558526	970	A8K2U0	A2ML1_HUMAN	Y	970;970;520;479	ENSP00000299698:C970Y;ENSP00000443174:C520Y;ENSP00000438292:C479Y	ENSP00000299698:C970Y	C	+	2	0	A2ML1	8901087	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.380000	0.66202	0.333000	0.23563	0.462000	0.41574	TGT	G|0.843;A|0.157	0.157	strong		0.562	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
EHBP1	23301	hgsc.bcm.edu	37	2	63169975	63169975	+	Silent	SNP	G	G	A	rs138897020	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:63169975G>A	ENST00000263991.5	+	12	1895	c.1413G>A	c.(1411-1413)tcG>tcA	p.S471S	EHBP1_ENST00000405289.1_Silent_p.S436S|EHBP1_ENST00000431489.1_Silent_p.S436S|EHBP1_ENST00000354487.3_Silent_p.S436S|EHBP1_ENST00000405015.3_Silent_p.S436S	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	471	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.					cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TTACTACATCGTGGAGAAATG	0.343													g|||	98	0.0195687	0.0015	0.0576	5008	,	,		17001	0.0		0.0278	False		,,,				2504	0.0286				p.S471S		Atlas-SNP	.											EHBP1,NS,carcinoma,-2,1	EHBP1	127	1	0			c.G1413A						PASS	.	A	,,,	29,4377	35.2+/-66.4	0,29,2174	78.0	81.0	80.0		1308,1308,1308,1413	-12.0	0.7	2	dbSNP_134	80	251,8349	98.8+/-160.4	3,245,4052	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EHBP1	NM_001142614.1,NM_001142615.2,NM_001142616.1,NM_015252.3	,,,	3,274,6226	AA,AG,GG		2.9186,0.6582,2.1529	,,,	436/1197,436/1161,436/1161,471/1232	63169975	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	23301	exon12			TACATCGTGGAGA	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.1413G>A	2.37:g.63169975G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	136	72	0.529412	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Silent	SNP	ENST00000263991.5	37	CCDS1872.1																																																																																			G|0.978;A|0.022	0.022	strong		0.343	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
DBNDD1	79007	hgsc.bcm.edu	37	16	90076445	90076445	+	Intron	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90076445G>A	ENST00000002501.6	-	2	163				DBNDD1_ENST00000304733.3_Missense_Mutation_p.T4I|DBNDD1_ENST00000568838.1_Intron|DBNDD1_ENST00000392973.3_5'UTR	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1							cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		ATTCTTCCAGGTTTCTCCCAT	0.473																																					p.T4I		Atlas-SNP	.											.	DBNDD1	9	.	0			c.C11T						PASS	.						91.0	86.0	87.0					16																	90076445		1848	4097	5945	SO:0001627	intron_variant	79007	exon1			TTCCAGGTTTCTC	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.32-607C>T	16.37:g.90076445G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	156	71	0.455128	NM_024043	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	37	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624552	0.28889	.	.	ENSG00000003249	ENST00000304733	T	0.47177	0.85	1.92	0.867	0.19085	.	.	.	.	.	T	0.26557	0.0649	.	.	.	0.09310	N	1	B	0.30889	0.299	B	0.21546	0.035	T	0.12682	-1.0538	7	.	.	.	.	6.0374	0.19716	0.0:0.3279:0.6721:0.0	.	4	Q9H9R9-2	.	I	4	ENSP00000306407:T4I	.	T	-	2	0	DBNDD1	88603946	0.300000	0.24435	0.004000	0.12327	0.007000	0.05969	0.637000	0.24659	0.326000	0.23384	0.591000	0.81541	ACC	.	.	none		0.473	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043	
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38483174	38483174	+	Missense_Mutation	SNP	A	A	T	rs374089121|rs200930717|rs78489217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38483174A>T	ENST00000381669.3	-	11	1360	c.1216T>A	c.(1216-1218)Tcc>Acc	p.S406T	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	406					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)	p.M405_S406insTSM(1)		large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					gtcatgggggacatggaggtc	0.657													A|||	84	0.0167732	0.0076	0.0159	5008	,	,		13137	0.001		0.0278	False		,,,				2504	0.0348				p.S406T		Atlas-SNP	.											.	BAIAP2L2	39	.	1	Insertion - In frame(1)	ovary(1)	c.T1216A						PASS	.						32.0	38.0	36.0					22																	38483174		1925	4121	6046	SO:0001583	missense	80115	exon11			TGGGGGACATGGA	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1216T>A	22.37:g.38483174A>T	ENSP00000371085:p.Ser406Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	58	0.734177	NM_025045	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	37	CCDS43018.1	254	0.1163003663003663	58	0.11788617886178862	58	0.16022099447513813	32	0.055944055944055944	106	0.13984168865435356	A	0.010	-1.753658	0.00663	.	.	ENSG00000128298	ENST00000381669;ENST00000402500;ENST00000428572	T;T	0.21543	2.0;2.0	0.235	-0.47	0.12131	.	2.310980	0.01612	N	0.022579	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27434	-1.0074	9	0.18276	T	0.48	.	.	.	.	.	406	Q6UXY1	BI2L2_HUMAN	T	406;406;97	ENSP00000371085:S406T;ENSP00000410074:S97T	ENSP00000371085:S406T	S	-	1	0	BAIAP2L2	36813120	0.121000	0.22262	0.001000	0.08648	0.001000	0.01503	0.410000	0.21098	-2.434000	0.00554	-2.582000	0.00168	TCC	A|0.886;T|0.114	0.114	strong		0.657	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18775810	18775810	+	Missense_Mutation	SNP	C	C	A	rs934472	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	98	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	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		
FAT4	79633	hgsc.bcm.edu	37	4	126411594	126411594	+	Silent	SNP	G	G	A	rs62312781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	84	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	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	
ICAM3	3385	hgsc.bcm.edu	37	19	10446568	10446568	+	Missense_Mutation	SNP	T	T	C	rs2304237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	35	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	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		
TMEM232	642987	hgsc.bcm.edu	37	5	109973902	109973902	+	Silent	SNP	T	T	G	rs1422495	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:109973902T>G	ENST00000455884.2	-	5	548	c.498A>C	c.(496-498)gcA>gcC	p.A166A	TMEM232_ENST00000429839.2_Silent_p.A166A|TMEM232_ENST00000515518.2_5'UTR			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	171	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	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	
THUMPD2	80745	hgsc.bcm.edu	37	2	39997087	39997087	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:39997087C>T	ENST00000505747.1	-	3	462	c.435G>A	c.(433-435)aaG>aaA	p.K145K	THUMPD2_ENST00000454352.2_Silent_p.K115K|THUMPD2_ENST00000403537.3_5'UTR|THUMPD2_ENST00000260619.6_Silent_p.K115K	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	145							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				TTTTTAATTTCTTTGCAATGA	0.318																																					p.K145K		Atlas-SNP	.											THUMPD2,NS,carcinoma,0,1	THUMPD2	35	1	0			c.G435A						scavenged	.						67.0	61.0	63.0					2																	39997087		2202	4297	6499	SO:0001819	synonymous_variant	80745	exon3			TAATTTCTTTGCA	AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"""chromosome 2 open reading frame 8"""	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.435G>A	2.37:g.39997087C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	173	3	0.017341	NM_025264	A8K7I7|Q53TT8|Q53TV0	Silent	SNP	ENST00000505747.1	37	CCDS1805.2																																																																																			.	.	none		0.318	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264	
ZNF880	400713	hgsc.bcm.edu	37	19	52888042	52888042	+	Silent	SNP	G	G	T	rs75507701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:52888042G>T	ENST00000422689.2	+	4	1224	c.1209G>T	c.(1207-1209)acG>acT	p.T403T		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	403					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						GAATGCACACGGGAGAGCAAC	0.403																																					p.T403T		Atlas-SNP	.											ZNF880,caecum,carcinoma,0,1	ZNF880	45	1	0			c.G1209T						scavenged	.						65.0	59.0	61.0					19																	52888042		1568	3582	5150	SO:0001819	synonymous_variant	400713	exon4			GCACACGGGAGAG	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.1209G>T	19.37:g.52888042G>T		Somatic	19	3	0.157895		WXS	Illumina HiSeq	Phase_I	39	7	0.179487	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			G|0.910;T|0.090	0.090	strong		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
MUC17	140453	hgsc.bcm.edu	37	7	100679902	100679902	+	Silent	SNP	A	A	G	rs55974941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100679902A>G	ENST00000306151.4	+	3	5269	c.5205A>G	c.(5203-5205)gaA>gaG	p.E1735E		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1735	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.E1735E(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)					CAACTTCTGAAGGTACCAGCA	0.512													a|||	1933	0.385982	0.1392	0.3372	5008	,	,		24828	0.5595		0.4861	False		,,,				2504	0.4724				p.E1735E		Atlas-SNP	.											MUC17,rectum,carcinoma,0,2	MUC17	804	2	1	Substitution - coding silent(1)	stomach(1)	c.A5205G						PASS	.	A		858,3548	336.3+/-304.3	91,676,1436	252.0	259.0	256.0		5205	-1.6	0.0	7	dbSNP_129	256	4211,4389	570.1+/-389.3	1030,2151,1119	no	coding-synonymous	MUC17	NM_001040105.1		1121,2827,2555	GG,GA,AA		48.9651,19.4734,38.9743		1735/4494	100679902	5069,7937	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TTCTGAAGGTACC	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.5205A>G	7.37:g.100679902A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.600;G|0.400	0.400	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TBC1D26	353149	hgsc.bcm.edu	37	17	15640806	15640806	+	Missense_Mutation	SNP	A	A	C	rs200208182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:15640806A>C	ENST00000437605.2	+	5	417	c.167A>C	c.(166-168)gAg>gCg	p.E56A	TBC1D26_ENST00000579428.1_Missense_Mutation_p.E56A|AC005324.6_ENST00000433873.1_RNA|ZNF286A_ENST00000593105.1_3'UTR|AC005324.6_ENST00000434017.1_RNA|ZNF286A_ENST00000413242.2_3'UTR	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	56							Rab GTPase activator activity (GO:0005097)	p.E56A(1)		endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		AGTGAGATGGAGCTGCCCCAC	0.647																																					p.E56A		Atlas-SNP	.											TBC1D26,trunk,malignant_melanoma,0,1	TBC1D26	16	1	1	Substitution - Missense(1)	skin(1)	c.A167C						scavenged	.						35.0	39.0	37.0					17																	15640806		1942	4099	6041	SO:0001583	missense	353149	exon5			AGATGGAGCTGCC		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.167A>C	17.37:g.15640806A>C	ENSP00000410111:p.Glu56Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	286	58	0.202797	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1	.	.	.	.	.	.	.	.	.	.	a	8.747	0.920269	0.17982	.	.	ENSG00000214946	ENST00000437605	T	0.44881	0.91	0.888	-1.78	0.07957	.	0.321547	0.28187	U	0.016280	T	0.40067	0.1102	M	0.81682	2.555	0.09310	N	1	P;P	0.41710	0.76;0.481	B;B	0.44163	0.443;0.347	T	0.39292	-0.9621	10	0.51188	T	0.08	.	1.5879	0.02648	0.3144:0.2682:0.0:0.4174	.	56;56	Q86UD7;Q86UD7-2	TBC26_HUMAN;.	A	56	ENSP00000410111:E56A	ENSP00000410111:E56A	E	+	2	0	TBC1D26	15581531	0.176000	0.23096	0.000000	0.03702	0.001000	0.01503	0.354000	0.20146	-1.189000	0.02702	-0.811000	0.03165	GAG	A|0.500;C|0.500	0.500	strong		0.647	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571	
FAM118A	55007	hgsc.bcm.edu	37	22	45728370	45728370	+	Missense_Mutation	SNP	G	G	A	rs6007594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45728370G>A	ENST00000216214.3	+	7	1550	c.716G>A	c.(715-717)cGt>cAt	p.R239H	FAM118A_ENST00000405548.3_Missense_Mutation_p.R57H|FAM118A_ENST00000441876.2_Missense_Mutation_p.R239H	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	239			R -> H (in dbSNP:rs6007594). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)		p.R239H(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GAGACCCTTCGTGATCAGATA	0.458													G|||	2632	0.525559	0.8411	0.3905	5008	,	,		20074	0.5218		0.2724	False		,,,				2504	0.4591				p.R239H		Atlas-SNP	.											FAM118A,NS,carcinoma,0,1	FAM118A	32	1	1	Substitution - Missense(1)	stomach(1)	c.G716A						PASS	.	G	HIS/ARG,HIS/ARG	3274,1132	714.4+/-408.4	1225,824,154	129.0	138.0	135.0		716,716	5.8	0.2	22	dbSNP_114	135	2331,6269	391.1+/-343.5	318,1695,2287	yes	missense,missense	FAM118A	NM_001104595.1,NM_017911.2	29,29	1543,2519,2441	AA,AG,GG		27.1047,25.6922,43.0955	probably-damaging,probably-damaging	239/358,239/358	45728370	5605,7401	2203	4300	6503	SO:0001583	missense	55007	exon6			CCCTTCGTGATCA	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.716G>A	22.37:g.45728370G>A	ENSP00000216214:p.Arg239His	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	212	105	0.495283	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	
CATSPER4	378807	hgsc.bcm.edu	37	1	26517794	26517794	+	Missense_Mutation	SNP	A	A	G	rs11247866	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26517794A>G	ENST00000456354.2	+	2	297	c.230A>G	c.(229-231)cAg>cGg	p.Q77R		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	77			Q -> R (in dbSNP:rs11247866).		calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TGGGACATGCAGGAGTTCATC	0.577													A|||	611	0.122005	0.2216	0.0893	5008	,	,		18415	0.0109		0.1879	False		,,,				2504	0.0573				p.Q77R		Atlas-SNP	.											.	CATSPER4	59	.	0			c.A230G						PASS	.	A	ARG/GLN	968,3438	364.6+/-317.1	121,726,1356	78.0	64.0	69.0		230	5.5	1.0	1	dbSNP_120	69	1633,6967	302.0+/-305.7	154,1325,2821	yes	missense	CATSPER4	NM_198137.1	43	275,2051,4177	GG,GA,AA		18.9884,21.97,19.9985	probably-damaging	77/473	26517794	2601,10405	2203	4300	6503	SO:0001583	missense	378807	exon2			ACATGCAGGAGTT	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.230A>G	1.37:g.26517794A>G	ENSP00000390423:p.Gln77Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_198137	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	300	0.13736263736263737	112	0.22764227642276422	38	0.10497237569060773	9	0.015734265734265736	141	0.18601583113456466	A	14.30	2.493893	0.44352	0.2197	0.189884	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97378	-4.36;-4.35	5.54	5.54	0.83059	.	0.139310	0.32736	N	0.005703	T	0.00580	0.0019	L	0.54323	1.7	0.36729	P	0.118398	P	0.43094	0.799	B	0.40901	0.343	T	0.01480	-1.1344	9	0.23302	T	0.38	-8.2558	12.0609	0.53562	1.0:0.0:0.0:0.0	rs11247866;rs17257134;rs52811757;rs60723618;rs11247866	77	Q7RTX7	CTSR4_HUMAN	R	77	ENSP00000341006:Q77R;ENSP00000390423:Q77R	ENSP00000341006:Q77R	Q	+	2	0	CATSPER4	26390381	1.000000	0.71417	0.994000	0.49952	0.030000	0.12068	3.528000	0.53524	2.097000	0.63578	0.379000	0.24179	CAG	A|0.823;G|0.177	0.177	strong		0.577	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
ENC1	8507	hgsc.bcm.edu	37	5	73931246	73931246	+	Silent	SNP	T	T	C	rs442425	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73931246T>C	ENST00000302351.4	-	2	2195	c.1065A>G	c.(1063-1065)tcA>tcG	p.S355S	ENC1_ENST00000510316.1_Silent_p.S282S|ENC1_ENST00000537006.1_Silent_p.S355S	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	355					multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		AGACATCTTTTGAGACCCCAT	0.542													C|||	3780	0.754792	0.8578	0.8184	5008	,	,		18713	0.623		0.8131	False		,,,				2504	0.6462				p.S355S		Atlas-SNP	.											.	ENC1	56	.	0			c.A1065G						PASS	.	C		3682,724	299.3+/-285.7	1542,598,63	78.0	83.0	81.0		1065	-8.4	0.5	5	dbSNP_80	81	6670,1930	338.2+/-322.6	2580,1510,210	no	coding-synonymous	ENC1	NM_003633.2		4122,2108,273	CC,CT,TT		22.4419,16.4321,20.406		355/590	73931246	10352,2654	2203	4300	6503	SO:0001819	synonymous_variant	8507	exon2			ATCTTTTGAGACC	AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"""Kelch-like"", ""BTB/POZ domain containing"""	3345	protein-coding gene	gene with protein product	"""kelch-like family member 37"""	605173	"""ectodermal-neural cortex 1 (with BTB-like domain)"""	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1065A>G	5.37:g.73931246T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Silent	SNP	ENST00000302351.4	37	CCDS4021.1																																																																																			T|0.206;C|0.794	0.794	strong		0.542	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633	
WDR27	253769	hgsc.bcm.edu	37	6	170047902	170047902	+	Missense_Mutation	SNP	T	T	A	rs61740334	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170047902T>A	ENST00000448612.1	-	16	1733	c.1624A>T	c.(1624-1626)Acc>Tcc	p.T542S	WDR27_ENST00000423258.1_Missense_Mutation_p.T415S|WDR27_ENST00000333572.6_Missense_Mutation_p.T542S|WDR27_ENST00000546525.1_5'UTR	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	512						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)		CGTGTGCAGGTGGGGGCGGCA	0.617													T|||	287	0.0573083	0.0121	0.0418	5008	,	,		13579	0.0992		0.0726	False		,,,				2504	0.0706				p.T542S		Atlas-SNP	.											.	WDR27	129	.	0			c.A1624T						PASS	.	T	SER/THR,SER/THR	72,3958		0,72,1943	9.0	13.0	12.0		1624,1243	-7.6	0.0	6	dbSNP_129	12	578,7746		16,546,3600	yes	missense,missense	WDR27	NM_182552.4,NM_001202550.1	58,58	16,618,5543	AA,AT,TT		6.9438,1.7866,5.2615	benign,benign	542/896,415/731	170047902	650,11704	2015	4162	6177	SO:0001583	missense	253769	exon16			TGCAGGTGGGGGC	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.1624A>T	6.37:g.170047902T>A	ENSP00000416289:p.Thr542Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	172	77	0.447674	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	141	0.06456043956043957	8	0.016260162601626018	16	0.04419889502762431	62	0.10839160839160839	55	0.07255936675461741	T	1.713	-0.498641	0.04291	0.017866	0.069438	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258	T;T;D	0.95724	1.94;1.09;-3.79	3.79	-7.58	0.01313	.	3.278270	0.00991	N	0.003520	T	0.67924	0.2945	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.20887	0.013;0.009;0.049	B;B;B	0.18263	0.004;0.014;0.021	T	0.75079	-0.3444	9	0.08599	T	0.76	1.0724	8.3339	0.32202	0.0:0.5217:0.2596:0.2187	rs61740334	542;415;542	F2Z2U5;A2RRH5-2;C9JGV0	.;.;.	S	542;542;415	ENSP00000416289:T542S;ENSP00000330265:T542S;ENSP00000397869:T415S	ENSP00000330265:T542S	T	-	1	0	WDR27	169789827	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.815000	0.00096	-2.957000	0.00291	-0.959000	0.02639	ACC	T|0.912;A|0.088	0.088	strong		0.617	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
SLC39A12	221074	hgsc.bcm.edu	37	10	18266989	18266989	+	Missense_Mutation	SNP	G	G	A	rs2478568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:18266989G>A	ENST00000377369.2	+	5	1183	c.910G>A	c.(910-912)Gtt>Att	p.V304I	SLC39A12_ENST00000377371.3_Missense_Mutation_p.V304I|SLC39A12_ENST00000539911.1_Missense_Mutation_p.V170I|SLC39A12_ENST00000377374.4_Missense_Mutation_p.V304I	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	304			V -> I (in dbSNP:rs2478568). {ECO:0000269|PubMed:15489334}.		regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						GGATGGTCCAGTTTCCTGGGA	0.368													G|||	3329	0.664736	0.6195	0.6888	5008	,	,		18447	0.6627		0.6322	False		,,,				2504	0.7444				p.V304I		Atlas-SNP	.											.	SLC39A12	181	.	0			c.G910A						PASS	.	G	ILE/VAL,ILE/VAL	2758,1648	657.1+/-400.2	872,1014,317	75.0	75.0	75.0		910,910	-9.4	0.0	10	dbSNP_100	75	5431,3169	651.8+/-400.9	1732,1967,601	yes	missense,missense	SLC39A12	NM_001145195.1,NM_152725.3	29,29	2604,2981,918	AA,AG,GG		36.8488,37.4035,37.0368	benign,benign	304/692,304/655	18266989	8189,4817	2203	4300	6503	SO:0001583	missense	221074	exon5			GGTCCAGTTTCCT		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.910G>A	10.37:g.18266989G>A	ENSP00000366586:p.Val304Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	37	CCDS44362.1	1433	0.6561355311355311	315	0.6402439024390244	251	0.6933701657458563	387	0.6765734265734266	480	0.633245382585752	G	2.906	-0.226350	0.06022	0.625965	0.631512	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.61510	0.21;0.1;0.22;0.1	4.72	-9.43	0.00607	.	4.189790	0.00166	N	0.000001	T	0.00012	0.0000	N	0.02736	-0.51	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	0.28138	-1.0053	9	0.35671	T	0.21	3.6	5.1597	0.15054	0.5145:0.1544:0.2533:0.0777	rs2478568;rs52811040;rs56884282;rs2478568	304;304;304	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	I	304;304;304;170;224	ENSP00000366586:V304I;ENSP00000366591:V304I;ENSP00000366588:V304I;ENSP00000440445:V170I	ENSP00000366586:V304I	V	+	1	0	SLC39A12	18306995	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	-4.098000	0.00295	-3.949000	0.00088	-1.058000	0.02302	GTT	G|0.353;A|0.647	0.647	strong		0.368	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
MUC4	4585	hgsc.bcm.edu	37	3	195509623	195509623	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195509623G>A	ENST00000463781.3	-	2	9287	c.8828C>T	c.(8827-8829)aCc>aTc	p.T2943I	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2943I	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)		AGGAAGAGGGGTGGTGTCACC	0.592																																					p.T2943I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	0			c.C8828T						scavenged	.						11.0	9.0	9.0					3																	195509623		659	1522	2181	SO:0001583	missense	4585	exon2			AGAGGGGTGGTGT	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.8828C>T	3.37:g.195509623G>A	ENSP00000417498:p.Thr2943Ile	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	268	2	0.00746269	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	5.617	0.298501	0.10622	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.52	.	.	.	.	.	.	.	.	T	0.32194	0.0821	N	0.19112	0.55	0.09310	N	1	D	0.65815	0.995	D	0.68483	0.958	T	0.21759	-1.0236	7	.	.	.	.	6.8646	0.24086	1.0E-4:0.0:0.9999:0.0	.	2815	E7ESK3	.	I	2943	ENSP00000417498:T2943I;ENSP00000420243:T2943I	.	T	-	2	0	MUC4	196994402	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.045000	0.14013	-0.000000	0.14550	0.000000	0.15137	ACC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RDH8	50700	hgsc.bcm.edu	37	19	10132318	10132318	+	Missense_Mutation	SNP	T	T	C	rs45503592	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10132318T>C	ENST00000171214.1	+	6	1078	c.829T>C	c.(829-831)Tat>Cat	p.Y277H	RDH8_ENST00000591589.1_Missense_Mutation_p.Y297H	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	277					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TGGCAGCCTGTATGTGCGAAC	0.637													T|||	22	0.00439297	0.0015	0.0058	5008	,	,		18548	0.0		0.0139	False		,,,				2504	0.002				p.Y297H		Atlas-SNP	.											.	RDH8	51	.	0			c.T889C						PASS	.	T	HIS/TYR	11,4395	17.9+/-39.9	0,11,2192	113.0	107.0	109.0		829	3.4	0.7	19	dbSNP_127	109	111,8489	59.5+/-121.1	1,109,4190	yes	missense	RDH8	NM_015725.2	83	1,120,6382	CC,CT,TT		1.2907,0.2497,0.938	possibly-damaging	277/312	10132318	122,12884	2203	4300	6503	SO:0001583	missense	50700	exon6			AGCCTGTATGTGC	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	14423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 28C, member 2"""	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.829T>C	19.37:g.10132318T>C	ENSP00000171214:p.Tyr277His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	T	14.74	2.624219	0.46840	0.002497	0.012907	ENSG00000080511	ENST00000171214	D	0.82619	-1.63	4.41	3.39	0.38822	.	0.140657	0.49305	D	0.000154	T	0.75177	0.3814	M	0.73217	2.22	0.35526	D	0.80184	P	0.51240	0.943	P	0.46718	0.525	T	0.78534	-0.2167	10	0.16896	T	0.51	.	7.3638	0.26762	0.0:0.1066:0.0:0.8934	rs45503592	277	Q9NYR8	RDH8_HUMAN	H	277	ENSP00000171214:Y277H	ENSP00000171214:Y277H	Y	+	1	0	RDH8	9993318	1.000000	0.71417	0.654000	0.29608	0.185000	0.23345	3.477000	0.53151	1.629000	0.50426	0.247000	0.18012	TAT	T|0.990;C|0.010	0.010	strong		0.637	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
TULP3	7289	hgsc.bcm.edu	37	12	3046802	3046802	+	Silent	SNP	A	A	G	rs33973716	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:3046802A>G	ENST00000448120.2	+	9	981	c.930A>G	c.(928-930)acA>acG	p.T310T	TULP3_ENST00000397132.2_Silent_p.T310T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	310					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TCCAGGAAACAAACGTACTTG	0.378													a|||	1108	0.221246	0.2163	0.1801	5008	,	,		18091	0.2083		0.2048	False		,,,				2504	0.2873				p.T310T		Atlas-SNP	.											.	TULP3	45	.	0			c.A930G						PASS	.		,	899,3505	341.8+/-306.9	91,717,1394	48.0	44.0	45.0		930,930	-1.2	1.0	12	dbSNP_126	45	1784,6816	319.9+/-314.4	168,1448,2684	no	coding-synonymous,coding-synonymous	TULP3	NM_001160408.1,NM_003324.4	,	259,2165,4078	GG,GA,AA		20.7442,20.4133,20.6321	,	310/502,310/443	3046802	2683,10321	2202	4300	6502	SO:0001819	synonymous_variant	7289	exon9			GGAAACAAACGTA	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.930A>G	12.37:g.3046802A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	141	86	0.609929	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Silent	SNP	ENST00000448120.2	37	CCDS8519.1																																																																																			A|0.796;G|0.204	0.204	strong		0.378	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
SVEP1	79987	hgsc.bcm.edu	37	9	113166792	113166792	+	Missense_Mutation	SNP	A	A	T	rs3739451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:113166792A>T	ENST00000401783.2	-	39	9817	c.9481T>A	c.(9481-9483)Ttc>Atc	p.F3161I	SVEP1_ENST00000374469.1_Missense_Mutation_p.F3138I|SVEP1_ENST00000297826.5_Missense_Mutation_p.F1087I	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3161	Sushi 29. {ECO:0000255|PROSITE- ProRule:PRU00302}.		F -> I (in dbSNP:rs3739451). {ECO:0000269|PubMed:17974005}.		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						TGACAGGTGAATGTATCTGTA	0.393													A|||	543	0.108427	0.0091	0.1888	5008	,	,		20390	0.0714		0.1839	False		,,,				2504	0.1462				p.F3161I		Atlas-SNP	.											.	SVEP1	326	.	0			c.T9481A						PASS	.	A	ILE/PHE	139,3631		4,131,1750	257.0	246.0	249.0		9481	1.6	1.0	9	dbSNP_107	249	1588,6642		155,1278,2682	yes	missense	SVEP1	NM_153366.3	21	159,1409,4432	TT,TA,AA		19.2953,3.687,14.3917	benign	3161/3572	113166792	1727,10273	1885	4115	6000	SO:0001583	missense	79987	exon39			AGGTGAATGTATC	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.9481T>A	9.37:g.113166792A>T	ENSP00000384917:p.Phe3161Ile	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	228	125	0.548246	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	247	0.1130952380952381	9	0.018292682926829267	64	0.17679558011049723	46	0.08041958041958042	128	0.16886543535620052	A	9.735	1.163258	0.21538	0.03687	0.192953	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.60424	0.19;0.19;0.19	5.76	1.62	0.23740	Complement control module (2);Sushi/SCR/CCP (3);	0.564293	0.19600	N	0.110409	T	0.00039	0.0001	N	0.02539	-0.55	0.09310	P	0.99999872883	B	0.12630	0.006	B	0.15870	0.014	T	0.12319	-1.0552	9	0.09843	T	0.71	.	3.8013	0.08760	0.6201:0.1051:0.0677:0.2071	rs3739451;rs17733833;rs56603622;rs3739451	3161	Q4LDE5	SVEP1_HUMAN	I	3161;3138;1087	ENSP00000384917:F3161I;ENSP00000363593:F3138I;ENSP00000297826:F1087I	ENSP00000297826:F1087I	F	-	1	0	SVEP1	112206613	0.993000	0.37304	1.000000	0.80357	0.693000	0.40251	1.663000	0.37429	0.447000	0.26695	-0.326000	0.08463	TTC	A|0.878;T|0.122	0.122	strong		0.393	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
LEPREL1	55214	hgsc.bcm.edu	37	3	189712010	189712010	+	Silent	SNP	G	G	A	rs1719600	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:189712010G>A	ENST00000319332.5	-	3	893	c.696C>T	c.(694-696)caC>caT	p.H232H	LEPREL1_ENST00000427335.2_Silent_p.H51H	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	232					collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	CTTGTTCGAAGTGCCTGATAG	0.398													G|||	809	0.161542	0.0545	0.1571	5008	,	,		15915	0.1577		0.2763	False		,,,				2504	0.1953				p.H232H		Atlas-SNP	.											.	LEPREL1	95	.	0			c.C696T						PASS	.	G	,	382,4024	188.5+/-214.9	17,348,1838	87.0	85.0	86.0		153,696	2.0	1.0	3	dbSNP_89	86	2238,6362	378.8+/-339.0	290,1658,2352	no	coding-synonymous,coding-synonymous	LEPREL1	NM_001134418.1,NM_018192.3	,	307,2006,4190	AA,AG,GG		26.0233,8.67,20.1445	,	51/528,232/709	189712010	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	55214	exon3			TTCGAAGTGCCTG		CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 2"""	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.696C>T	3.37:g.189712010G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_018192	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Silent	SNP	ENST00000319332.5	37	CCDS3294.1																																																																																			G|0.812;A|0.188	0.188	strong		0.398	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192	
SLC36A3	285641	hgsc.bcm.edu	37	5	150666933	150666933	+	Silent	SNP	C	C	A	rs375396	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150666933C>A	ENST00000335230.3	-	6	993	c.582G>T	c.(580-582)ctG>ctT	p.L194L	SLC36A3_ENST00000377713.3_Silent_p.L235L	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	194						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)			GCAGGATTATCAGCATGTAGA	0.527													C|||	1267	0.252995	0.1997	0.1455	5008	,	,		20331	0.4474		0.1809	False		,,,				2504	0.2751				p.L235L		Atlas-SNP	.											.	SLC36A3	54	.	0			c.G705T						PASS	.	C	,	822,3584	327.5+/-300.1	85,652,1466	168.0	156.0	160.0		705,582	-2.0	0.1	5	dbSNP_80	160	1566,7034	294.0+/-301.7	149,1268,2883	no	coding-synonymous,coding-synonymous	SLC36A3	NM_001145017.1,NM_181774.3	,	234,1920,4349	AA,AC,CC		18.2093,18.6564,18.3608	,	235/512,194/471	150666933	2388,10618	2203	4300	6503	SO:0001819	synonymous_variant	285641	exon7			GATTATCAGCATG	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.582G>T	5.37:g.150666933C>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	199	107	0.537688	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	37	CCDS4314.1																																																																																			C|0.776;A|0.224	0.224	strong		0.527	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
GAS2L2	246176	hgsc.bcm.edu	37	17	34072555	34072555	+	Missense_Mutation	SNP	G	G	A	rs3744374	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:34072555G>A	ENST00000254466.6	-	6	1988	c.1961C>T	c.(1960-1962)gCc>gTc	p.A654V	GAS2L2_ENST00000587565.1_Missense_Mutation_p.A638V	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	654			A -> V (in dbSNP:rs3744374).		cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)	p.A654V(2)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTCTTGGATGGCTTTGTCATA	0.627													A|||	1011	0.201877	0.3714	0.1297	5008	,	,		18244	0.127		0.2068	False		,,,				2504	0.0961				p.A654V		Atlas-SNP	.											GAS2L2,NS,carcinoma,0,1	GAS2L2	94	1	2	Substitution - Missense(2)	prostate(2)	c.C1961T						PASS	.	A	VAL/ALA	1418,2988	678.6+/-403.6	226,966,1011	80.0	93.0	89.0		1961	4.6	1.0	17	dbSNP_107	89	2112,6488	709.5+/-405.7	268,1576,2456	yes	missense	GAS2L2	NM_139285.3	64	494,2542,3467	AA,AG,GG		24.5581,32.1834,27.1413	benign	654/881	34072555	3530,9476	2203	4300	6503	SO:0001583	missense	246176	exon6			TGGATGGCTTTGT	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1961C>T	17.37:g.34072555G>A	ENSP00000254466:p.Ala654Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	478	0.21886446886446886	173	0.3516260162601626	60	0.16574585635359115	87	0.1520979020979021	158	0.20844327176781002	A	0.227	-1.024236	0.02061	0.321834	0.245581	ENSG00000132139	ENST00000254466	T	0.07800	3.16	4.58	4.58	0.56647	.	0.000000	0.51477	N	0.000087	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45731	-0.9241	9	0.02654	T	1	-21.9719	6.1261	0.20180	0.8016:0.0:0.1984:0.0	rs3744374;rs61222146;rs3744374	654	Q8NHY3	GA2L2_HUMAN	V	654	ENSP00000254466:A654V	ENSP00000254466:A654V	A	-	2	0	GAS2L2	31096668	0.998000	0.40836	1.000000	0.80357	0.273000	0.26683	1.310000	0.33551	0.807000	0.34208	-0.817000	0.03123	GCC	G|0.753;A|0.247	0.247	strong		0.627	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
HYOU1	10525	hgsc.bcm.edu	37	11	118925935	118925935	+	Silent	SNP	G	G	A	rs511134	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:118925935G>A	ENST00000404233.3	-	5	505	c.381C>T	c.(379-381)ttC>ttT	p.F127F	HYOU1_ENST00000543287.1_Silent_p.F40F|HYOU1_ENST00000525859.1_Silent_p.F127F|HYOU1_ENST00000529972.1_Silent_p.F127F	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	127					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		TCTGTGGGTCGAAAGTCAGCT	0.582													G|||	232	0.0463259	0.1104	0.0216	5008	,	,		20549	0.0089		0.0089	False		,,,				2504	0.0542				p.F127F		Atlas-SNP	.											.	HYOU1	88	.	0			c.C381T						PASS	.	G	,	367,4033	188.8+/-215.1	20,327,1853	118.0	113.0	114.0		381,381	-1.2	0.6	11	dbSNP_83	114	104,8486	56.8+/-118.0	2,100,4193	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	22,427,6046	AA,AG,GG		1.2107,8.3409,3.6259	,	127/1000,127/1000	118925935	471,12519	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon5			TGGGTCGAAAGTC	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.381C>T	11.37:g.118925935G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	37	CCDS8408.1																																																																																			G|0.962;A|0.038	0.038	strong		0.582	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
MTCL1	23255	hgsc.bcm.edu	37	18	8798185	8798185	+	Missense_Mutation	SNP	G	G	A	rs12386117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:8798185G>A	ENST00000306329.11	+	8	3289	c.3289G>A	c.(3289-3291)Ggc>Agc	p.G1097S	SOGA2_ENST00000518815.1_Missense_Mutation_p.G93S|SOGA2_ENST00000400050.3_Missense_Mutation_p.G737S|SOGA2_ENST00000306285.7_Missense_Mutation_p.G93S|SOGA2_ENST00000517570.1_Missense_Mutation_p.G737S|SOGA2_ENST00000359865.3_Missense_Mutation_p.G778S																							CAGTGACCGAGGCTGTGGCTT	0.647													G|||	375	0.0748802	0.0567	0.0865	5008	,	,		18114	0.0228		0.1421	False		,,,				2504	0.0757				p.G778S		Atlas-SNP	.											.	.	.	.	0			c.G2332A						PASS	.	G	SER/GLY	247,4159	139.6+/-175.2	4,239,1960	69.0	57.0	61.0		2332	4.5	0.2	18	dbSNP_120	61	1247,7353	242.5+/-272.5	94,1059,3147	yes	missense	CCDC165	NM_015210.3	56	98,1298,5107	AA,AG,GG		14.5,5.606,11.487	benign	778/1587	8798185	1494,11512	2203	4300	6503	SO:0001583	missense	23255	exon10			GACCGAGGCTGTG																												ENST00000306329.11:c.3289G>A	18.37:g.8798185G>A	ENSP00000305027:p.Gly1097Ser	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	223	105	0.470852	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		180	0.08241758241758242	23	0.046747967479674794	33	0.09116022099447514	13	0.022727272727272728	111	0.14643799472295516	G	17.56	3.420396	0.62622	0.05606	0.145	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.39	4.51	0.55191	.	0.116848	0.39544	N	0.001333	T	0.00300	0.0009	N	0.17082	0.46	0.43652	P	0.003939000000000026	B;B	0.27351	0.024;0.176	B;B	0.21917	0.016;0.037	T	0.07829	-1.0752	9	0.13470	T	0.59	-29.5545	11.5355	0.50634	0.0845:0.0:0.9155:0.0	rs12386117;rs52826794;rs12386117	1088;778	Q9Y4B5;Q9Y4B5-3	CC165_HUMAN;.	S	799;737;778;737;93	ENSP00000429556:G737S;ENSP00000352927:G778S;ENSP00000382924:G737S;ENSP00000303670:G93S	ENSP00000303670:G93S	G	+	1	0	CCDC165	8788185	0.857000	0.29778	0.163000	0.22734	0.254000	0.26022	1.961000	0.40432	1.404000	0.46819	0.555000	0.69702	GGC	G|0.897;A|0.103	0.103	strong		0.647	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
TGFBI	7045	hgsc.bcm.edu	37	5	135392426	135392426	+	Silent	SNP	T	T	C	rs4669	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:135392426T>C	ENST00000442011.2	+	12	1781	c.1620T>C	c.(1618-1620)ttT>ttC	p.F540F	TGFBI_ENST00000508076.1_5'Flank|TGFBI_ENST00000305126.8_Silent_p.F540F	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	540	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082}.		F -> S (in CDL3A). {ECO:0000269|PubMed:15790870}.|Missing (in CDRB). {ECO:0000269|PubMed:10660331, ECO:0000269|PubMed:11923233}.		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)			ACACAGTCTTTGCTCCCACAA	0.498													C|||	2106	0.420527	0.6687	0.3703	5008	,	,		17729	0.3433		0.2584	False		,,,				2504	0.3671				p.F540F		Atlas-SNP	.											.	TGFBI	76	.	0			c.T1620C						PASS	.	C		2356,1582		707,942,320	78.0	82.0	81.0		1620	-2.7	0.9	5	dbSNP_52	81	2249,6075		315,1619,2228	no	coding-synonymous	TGFBI	NM_000358.2		1022,2561,2548	CC,CT,TT		27.0183,40.1727,37.555		540/684	135392426	4605,7657	1969	4162	6131	SO:0001819	synonymous_variant	7045	exon12			AGTCTTTGCTCCC	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.1620T>C	5.37:g.135392426T>C		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	226	125	0.553097	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1	852	0.3901098901098901	328	0.6666666666666666	128	0.35359116022099446	195	0.3409090909090909	201	0.26517150395778366	C	9.636	1.137809	0.21123	0.598273	0.270183	ENSG00000120708	ENST00000514554	.	.	.	5.82	-2.69	0.06022	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.28522	-1.0041	3	.	.	.	-1.5181	14.5145	0.67809	0.0:0.3811:0.0:0.6189	rs4669;rs1054164;rs2228406;rs3173019;rs7727187;rs17403539;rs17849263;rs17849891;rs56414978;rs59886758;rs4669	.	.	.	R	258	.	.	C	+	1	0	TGFBI	135420325	0.441000	0.25626	0.868000	0.34077	0.823000	0.46562	-0.359000	0.07632	-1.131000	0.02910	-1.551000	0.00897	TGC	T|0.599;C|0.401	0.401	strong		0.498	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
METTL11B	149281	hgsc.bcm.edu	37	1	170135669	170135669	+	Silent	SNP	C	C	T	rs6427234	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:170135669C>T	ENST00000439373.2	+	3	464	c.357C>T	c.(355-357)tgC>tgT	p.C119C	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	119						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						GAACAGACTGCGCCTTGGACT	0.542													C|||	1458	0.291134	0.5076	0.2421	5008	,	,		16699	0.1349		0.2724	False		,,,				2504	0.2137				p.C119C		Atlas-SNP	.											.	METTL11B	18	.	0			c.C357T						PASS	.	C		657,727		159,339,194	85.0	80.0	82.0		357	-7.7	0.7	1	dbSNP_116	82	885,2297		133,619,839	no	coding-synonymous	METTL11B	NM_001136107.1		292,958,1033	TT,TC,CC		27.8127,47.4711,33.7714		119/284	170135669	1542,3024	692	1591	2283	SO:0001819	synonymous_variant	149281	exon3			AGACTGCGCCTTG	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.357C>T	1.37:g.170135669C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			C|0.725;T|0.275	0.275	strong		0.542	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
KDR	3791	hgsc.bcm.edu	37	4	55972946	55972946	+	Missense_Mutation	SNP	A	A	G	rs34231037	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:55972946A>G	ENST00000263923.4	-	11	1739	c.1444T>C	c.(1444-1446)Tgt>Cgt	p.C482R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	482	Ig-like C2-type 5.		C -> R (in HCI susceptibility; expression of FLT1 in hemangioma endothelial cells is markedly reduced and KDR activity is increased compared to controls; low FLT1 expression in hemangioma cells is caused by reduced activity of a pathway involving ITGB1, ANTXR1, KDR and NFATC2IP; the mutation predicts to result in loss-of-function and disruption of the normal association of these molecules; dbSNP:rs34231037). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:18931684}.		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)	CATTCTTCACAAGGGTATGGG	0.333			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			A|||	45	0.00898562	0.0015	0.0144	5008	,	,		18156	0.0		0.0308	False		,,,				2504	0.002				p.C482R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,middle_lobe,carcinoma,+2,1	KDR	307	1	0			c.T1444C						PASS	.	A	ARG/CYS	23,4383	31.7+/-61.6	0,23,2180	81.0	85.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1444	5.7	0.9	4	dbSNP_126	83	242,8358	97.2+/-158.9	4,234,4062	yes	missense	KDR	NM_002253.2	180	4,257,6242	GG,GA,AA		2.814,0.522,2.0375	probably-damaging	482/1357	55972946	265,12741	2203	4300	6503	SO:0001583	missense	3791	exon11			CTTCACAAGGGTA	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.1444T>C	4.37:g.55972946A>G	ENSP00000263923:p.Cys482Arg	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	224	100	0.446429	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	A	13.84	2.356951	0.41801	0.00522	0.02814	ENSG00000128052	ENST00000263923	T	0.76839	-1.05	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.75436	0.3849	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82382	-0.0485	10	0.40728	T	0.16	.	15.905	0.79419	1.0:0.0:0.0:0.0	rs34231037	482;482	P35968-2;P35968	.;VGFR2_HUMAN	R	482	ENSP00000263923:C482R	ENSP00000263923:C482R	C	-	1	0	KDR	55667703	1.000000	0.71417	0.927000	0.36925	0.088000	0.18126	6.349000	0.73013	2.150000	0.67090	0.533000	0.62120	TGT	A|0.980;G|0.020	0.020	strong		0.333	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673015	7673015	+	Silent	SNP	G	G	A	rs5864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7673015G>A	ENST00000299492.4	+	23	2764	c.2376G>A	c.(2374-2376)gaG>gaA	p.E792E	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000530181.1_Silent_p.E649E|PPFIBP2_ENST00000528883.1_Silent_p.E680E|PPFIBP2_ENST00000533792.1_Silent_p.E634E	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	68	0	0		WXS	Illumina HiSeq	Phase_I	74	27	0.364865	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	
C5	727	hgsc.bcm.edu	37	9	123725926	123725926	+	Missense_Mutation	SNP	T	T	G	rs17612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123725926T>G	ENST00000223642.1	-	34	4340	c.4311A>C	c.(4309-4311)gaA>gaC	p.E1437D		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1437			E -> D (in dbSNP:rs17612). {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)	CTTTTAAGTCTTCTTCATTTG	0.353													T|||	177	0.0353435	0.0083	0.0375	5008	,	,		16581	0.002		0.0596	False		,,,				2504	0.0798				p.E1437D		Atlas-SNP	.											.	C5	124	.	0			c.A4311C						PASS	.	T	ASP/GLU	101,4305	80.4+/-118.8	0,101,2102	72.0	67.0	68.0		4311	-2.9	0.8	9	dbSNP_63	68	600,8000	159.5+/-212.8	32,536,3732	yes	missense	C5	NM_001735.2	45	32,637,5834	GG,GT,TT		6.9767,2.2923,5.3898	benign	1437/1677	123725926	701,12305	2203	4300	6503	SO:0001583	missense	727	exon34			TAAGTCTTCTTCA	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.4311A>C	9.37:g.123725926T>G	ENSP00000223642:p.Glu1437Asp	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	243	127	0.522634	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	64	0.029304029304029304	6	0.012195121951219513	14	0.03867403314917127	0	0.0	44	0.05804749340369393	T	12.35	1.911353	0.33721	0.022923	0.069767	ENSG00000106804	ENST00000223642	T	0.28895	1.59	5.33	-2.86	0.05717	Alpha-macroglobulin, receptor-binding (3);	0.217109	0.46758	N	0.000271	T	0.01061	0.0035	L	0.28694	0.88	0.35098	D	0.764931	B	0.09022	0.002	B	0.17098	0.017	T	0.23619	-1.0183	10	0.19147	T	0.46	.	5.7421	0.18100	0.4801:0.0817:0.0:0.4381	rs17612;rs16910239;rs17612	1437	P01031	CO5_HUMAN	D	1437	ENSP00000223642:E1437D	ENSP00000223642:E1437D	E	-	3	2	C5	122765747	0.951000	0.32395	0.775000	0.31657	0.886000	0.51366	-0.254000	0.08781	-0.719000	0.04942	-0.302000	0.09304	GAA	T|0.954;G|0.046	0.046	strong		0.353	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
WDR18	57418	hgsc.bcm.edu	37	19	984533	984533	+	Silent	SNP	T	T	C	rs2301810	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:984533T>C	ENST00000251289.5	+	1	203	c.180T>C	c.(178-180)aaT>aaC	p.N60N	WDR18_ENST00000591997.1_Intron|WDR18_ENST00000587001.2_Silent_p.N60N	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	60					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGCAAGAATTACATCAGCG	0.711													.|||	2246	0.448482	0.4667	0.438	5008	,	,		11366	0.3899		0.5577	False		,,,				2504	0.3793				p.N60N		Atlas-SNP	.											.	WDR18	20	.	0			c.T180C						PASS	.	C		1857,2351		456,945,703	7.0	9.0	9.0		180	3.3	1.0	19	dbSNP_100	9	4066,4176		1101,1864,1156	no	coding-synonymous	WDR18	NM_024100.3		1557,2809,1859	CC,CT,TT		49.3327,44.1302,47.5743		60/433	984533	5923,6527	2104	4121	6225	SO:0001819	synonymous_variant	57418	exon1			CAAGAATTACATC		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.180T>C	19.37:g.984533T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			T|0.552;C|0.448	0.448	strong		0.711	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
ESF1	51575	hgsc.bcm.edu	37	20	13695607	13695607	+	Missense_Mutation	SNP	T	T	G	rs34414644	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:13695607T>G	ENST00000202816.1	-	14	2577	c.2470A>C	c.(2470-2472)Att>Ctt	p.I824L		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	824	Lys-rich.		I -> L (in dbSNP:rs34414644).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						GCAGGATCAATGGACTTCCTT	0.358													T|||	368	0.0734824	0.0045	0.1455	5008	,	,		15043	0.0694		0.1123	False		,,,				2504	0.0798				p.I824L		Atlas-SNP	.											.	ESF1	77	.	0			c.A2470C						PASS	.	T	LEU/ILE	125,4281	92.5+/-131.2	1,123,2079	165.0	151.0	156.0		2470	4.9	1.0	20	dbSNP_126	156	1074,7526	225.1+/-261.3	75,924,3301	yes	missense	ESF1	NM_016649.3	5	76,1047,5380	GG,GT,TT		12.4884,2.837,9.2188	benign	824/852	13695607	1199,11807	2203	4300	6503	SO:0001583	missense	51575	exon14			GATCAATGGACTT		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 6"""	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.2470A>C	20.37:g.13695607T>G	ENSP00000202816:p.Ile824Leu	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Missense_Mutation	SNP	ENST00000202816.1	37	CCDS13117.1	169	0.07738095238095238	4	0.008130081300813009	48	0.13259668508287292	30	0.05244755244755245	87	0.11477572559366754	T	10.73	1.432380	0.25813	0.02837	0.124884	ENSG00000089048	ENST00000202816	T	0.52526	0.66	6.05	4.95	0.65309	.	0.307141	0.34067	N	0.004282	T	0.00384	0.0012	L	0.44542	1.39	0.42677	P	0.006461999999999968	B	0.06786	0.001	B	0.06405	0.002	T	0.09618	-1.0666	9	0.27785	T	0.31	0.0172	7.6251	0.28208	0.1258:0.0675:0.0:0.8067	rs34414644	824	Q9H501	ESF1_HUMAN	L	824	ENSP00000202816:I824L	ENSP00000202816:I824L	I	-	1	0	ESF1	13643607	0.823000	0.29233	0.997000	0.53966	0.986000	0.74619	2.142000	0.42177	1.123000	0.41961	0.528000	0.53228	ATT	T|0.915;G|0.085	0.085	strong		0.358	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649	
PKD1L1	168507	hgsc.bcm.edu	37	7	47971575	47971575	+	Silent	SNP	A	A	G	rs885337	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:47971575A>G	ENST00000289672.2	-	5	527	c.477T>C	c.(475-477)tgT>tgC	p.C159C		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	159					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						TCCCAGTAGCACACAGCCGCC	0.512													A|||	2398	0.478834	0.4584	0.5231	5008	,	,		16993	0.5149		0.5219	False		,,,				2504	0.3937				p.C159C		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T477C						PASS	.	A		2059,2347	569.1+/-382.5	492,1075,636	78.0	89.0	85.0		477	0.7	0.0	7	dbSNP_86	85	4356,4244	582.0+/-391.3	1094,2168,1038	no	coding-synonymous	PKD1L1	NM_138295.3		1586,3243,1674	GG,GA,AA		49.3488,46.7317,49.3234		159/2850	47971575	6415,6591	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon5			AGTAGCACACAGC	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.477T>C	7.37:g.47971575A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			A|0.509;G|0.491	0.491	strong		0.512	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
RGS9BP	388531	hgsc.bcm.edu	37	19	33167208	33167208	+	Silent	SNP	C	C	G	rs3826926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33167208C>G	ENST00000334176.3	+	1	896	c.39C>G	c.(37-39)ctC>ctG	p.L13L	ANKRD27_ENST00000587352.1_5'Flank|ANKRD27_ENST00000306065.4_5'Flank	NM_207391.2	NP_997274.2	Q6ZS82	R9BP_HUMAN	regulator of G protein signaling 9 binding protein	13					detection of light stimulus involved in visual perception (GO:0050908)|negative regulation of signal transduction (GO:0009968)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	integral component of membrane (GO:0016021)				central_nervous_system(1)|lung(2)	3	Esophageal squamous(110;0.137)					TGGACGGGCTCAACAAGACGA	0.711													C|||	368	0.0734824	0.0113	0.036	5008	,	,		13221	0.2063		0.0537	False		,,,				2504	0.0675				p.L13L		Atlas-SNP	.											.	RGS9BP	9	.	0			c.C39G						PASS	.	C		79,4277		0,79,2099	37.0	29.0	31.0		39	2.3	1.0	19	dbSNP_107	31	328,8198		6,316,3941	no	coding-synonymous	RGS9BP	NM_207391.2		6,395,6040	GG,GC,CC		3.8471,1.8136,3.1594		13/236	33167208	407,12475	2178	4263	6441	SO:0001819	synonymous_variant	388531	exon1			CGGGCTCAACAAG	AW302149	CCDS12424.1	19q13.11	2008-02-05	2007-08-14			ENSG00000186326			30304	protein-coding gene	gene with protein product		607814	"""regulator of G protein signalling 9 binding protein"""			12119397, 8889548	Standard	NM_207391		Approved	FLJ45744, PERRS, R9AP, RGS9	uc002ntp.1	Q6ZS82		ENST00000334176.3:c.39C>G	19.37:g.33167208C>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_207391	Q6ZVJ6	Silent	SNP	ENST00000334176.3	37	CCDS12424.1																																																																																			C|0.953;G|0.047	0.047	strong		0.711	RGS9BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450337.1	NM_207391	
DNAH17	8632	hgsc.bcm.edu	37	17	76522785	76522785	+	Missense_Mutation	SNP	C	C	T	rs61744544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:76522785C>T	ENST00000585328.1	-	24	3774	c.3650G>A	c.(3649-3651)cGc>cAc	p.R1217H	DNAH17_ENST00000389840.5_Missense_Mutation_p.R1220H	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)			CGGGGCCTCGCGCCTGAACCT	0.587													.|||	463	0.0924521	0.0136	0.1614	5008	,	,		14576	0.0804		0.1948	False		,,,				2504	0.0573				p.R1220H		Atlas-SNP	.											DNAH17,NS,carcinoma,-1,1	DNAH17	347	1	0			c.G3659A						scavenged	.	C	HIS/ARG	121,3805		1,119,1843	46.0	50.0	49.0		3659	-7.9	0.0	17	dbSNP_129	49	1456,6830		127,1202,2814	yes	missense	DNAH17	NM_173628.3	29	128,1321,4657	TT,TC,CC		17.5718,3.082,12.9135		1220/4463	76522785	1577,10635	1963	4143	6106	SO:0001583	missense	8632	exon24			GCCTCGCGCCTGA	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.3650G>A	17.37:g.76522785C>T	ENSP00000465516:p.Arg1217His	Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		256	0.11721611721611722	9	0.018292682926829267	58	0.16022099447513813	53	0.09265734265734266	136	0.17941952506596306	C	4.522	0.096799	0.08681	0.03082	0.175718	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.23348	1.91	4.37	-7.87	0.01183	.	.	.	.	.	T	0.00039	0.0001	N	0.25485	0.75	0.80722	P	0.0	.	.	.	.	.	.	T	0.31998	-0.9923	6	0.52906	T	0.07	.	8.2143	0.31503	0.1717:0.2213:0.0:0.607	.	.	.	.	H	1217;1220	ENSP00000374490:R1220H	ENSP00000300671:R1217H	R	-	2	0	DNAH17	74034380	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.782000	0.00772	-1.574000	0.01657	-1.351000	0.01236	CGC	C|0.872;T|0.128	0.128	strong		0.587	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
OBSCN	84033	hgsc.bcm.edu	37	1	228548197	228548197	+	Intron	SNP	G	G	A	rs10158354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228548197G>A	ENST00000422127.1	+	80	18705				OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Missense_Mutation_p.R3654H|OBSCN_ENST00000284548.11_Missense_Mutation_p.R6535H|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)				CCTGAGCCCCGTGGGGCGTCA	0.711													G|||	740	0.147764	0.0832	0.0764	5008	,	,		17345	0.3284		0.0984	False		,,,				2504	0.1503				p.R6535H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G19604A						PASS	.	G	,HIS/ARG	386,3526		18,350,1588	15.0	19.0	18.0		,19604	-5.6	0.0	1	dbSNP_119	18	710,7576		29,652,3462	yes	intron,missense	OBSCN	NM_001098623.1,NM_052843.2	,29	47,1002,5050	AA,AG,GG		8.5687,9.8671,8.9851	,	,6535/6621	228548197	1096,11102	1956	4143	6099	SO:0001627	intron_variant	84033	exon81			AGCCCCGTGGGGC	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.18662-2080G>A	1.37:g.228548197G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_052843	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	46	0.09349593495934959	35	0.09668508287292818	190	0.3321678321678322	75	0.09894459102902374	G	17.43	3.387211	0.61956	0.098671	0.085687	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.56776	0.44;0.58	3.31	-5.62	0.02481	.	.	.	.	.	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	0.30966	-0.9960	8	0.42905	T	0.14	.	5.8246	0.18546	0.6394:0.163:0.1059:0.0917	rs10158354	6535	Q5VST9-3	.	H	6535;3654	ENSP00000284548:R6535H;ENSP00000355670:R3654H	ENSP00000284548:R6535H	R	+	2	0	OBSCN	226614820	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.165000	0.03132	-1.292000	0.02366	-0.194000	0.12790	CGT	G|0.847;A|0.153	0.153	strong		0.711	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CLEC3B	7123	hgsc.bcm.edu	37	3	45077123	45077123	+	Missense_Mutation	SNP	G	G	A	rs13963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:45077123G>A	ENST00000296130.4	+	3	496	c.316G>A	c.(316-318)Ggc>Agc	p.G106S	RNU5B-3P_ENST00000516601.1_RNA|CLEC3B_ENST00000428034.1_Missense_Mutation_p.G64S|CLEC3B_ENST00000490386.1_3'UTR	NM_003278.2	NP_003269.2	P05452	TETN_HUMAN	C-type lectin domain family 3, member B	106	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		G -> S (in dbSNP:rs13963). {ECO:0000269|PubMed:1354271, ECO:0000269|PubMed:1511740, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3427041, ECO:0000269|Ref.3}.		bone mineralization (GO:0030282)|cellular response to organic substance (GO:0071310)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ossification (GO:0001503)|positive regulation of plasminogen activation (GO:0010756)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)|kringle domain binding (GO:0036143)			endometrium(1)|lung(3)	4				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Tenecteplase(DB00031)	GGGCACCCTGGGCACCCCTCA	0.637													G|||	2822	0.563498	0.4002	0.5144	5008	,	,		15918	0.8591		0.3817	False		,,,				2504	0.7014				p.G106S	GBM(139;1487 3263 30871)	Atlas-SNP	.											.	CLEC3B	15	.	0			c.G316A						PASS	.	G	SER/GLY	1708,2698	511.2+/-367.7	331,1046,826	47.0	46.0	46.0		316	-0.1	1.0	3	dbSNP_52	46	3484,5116	508.9+/-377.2	690,2104,1506	yes	missense	CLEC3B	NM_003278.2	56	1021,3150,2332	AA,AG,GG		40.5116,38.7653,39.92	benign	106/203	45077123	5192,7814	2203	4300	6503	SO:0001583	missense	7123	exon3			ACCCTGGGCACCC		CCDS2726.1	3p22-p21.3	2010-04-27	2005-02-09	2005-02-09	ENSG00000163815	ENSG00000163815		"""C-type lectin domain containing"""	11891	protein-coding gene	gene with protein product		187520	"""tetranectin (plasminogen binding protein)"""	TNA			Standard	NM_003278		Approved	TN	uc003cok.4	P05452	OTTHUMG00000133087	ENST00000296130.4:c.316G>A	3.37:g.45077123G>A	ENSP00000296130:p.Gly106Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_003278	Q6FGX6	Missense_Mutation	SNP	ENST00000296130.4	37	CCDS2726.1	1177	0.5389194139194139	199	0.40447154471544716	178	0.49171270718232046	499	0.8723776223776224	301	0.3970976253298153	G	9.397	1.076946	0.20227	0.387653	0.405116	ENSG00000163815	ENST00000296130;ENST00000428034	T;T	0.18174	2.23;2.23	4.53	-0.0541	0.13815	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.324435	0.36854	N	0.002366	T	0.00012	0.0000	N	0.03224	-0.385	0.31816	P	0.626606	B	0.24186	0.099	B	0.29353	0.101	T	0.06770	-1.0808	9	0.27082	T	0.32	-15.8475	8.7078	0.34365	0.6061:0.0:0.3939:0.0	rs13963;rs3188726;rs17077143;rs17850716;rs13963	106	P05452	TETN_HUMAN	S	106;64	ENSP00000296130:G106S;ENSP00000396013:G64S	ENSP00000296130:G106S	G	+	1	0	CLEC3B	45052127	1.000000	0.71417	0.996000	0.52242	0.395000	0.30598	1.497000	0.35649	0.121000	0.18284	-0.258000	0.10820	GGC	G|0.539;A|0.461	0.461	strong		0.637	CLEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256745.1	NM_003278	
RBAK	57786	hgsc.bcm.edu	37	7	5104275	5104275	+	Silent	SNP	G	G	A	rs12674330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:5104275G>A	ENST00000353796.3	+	6	1512	c.1188G>A	c.(1186-1188)acG>acA	p.T396T	RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Silent_p.T396T	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	396					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)		GAACTCACACGGGAGAGAAGC	0.463													A|||	890	0.177716	0.0446	0.1499	5008	,	,		20023	0.372		0.1272	False		,,,				2504	0.229				p.T396T		Atlas-SNP	.											.	RBAK	82	.	0			c.G1188A						PASS	.	A	,,	287,4119	799.6+/-415.5	6,275,1922	80.0	81.0	80.0		1188,,1188	-4.3	0.9	7	dbSNP_120	80	981,7619	773.5+/-407.7	53,875,3372	no	coding-synonymous,intron,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	59,1150,5294	AA,AG,GG		11.407,6.5138,9.7493	,,	396/715,,396/715	5104275	1268,11738	2203	4300	6503	SO:0001819	synonymous_variant	57786	exon6			TCACACGGGAGAG	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.1188G>A	7.37:g.5104275G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			G|0.868;A|0.132	0.132	strong		0.463	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
CHD6	84181	hgsc.bcm.edu	37	20	40049450	40049450	+	Missense_Mutation	SNP	T	T	A	rs140143834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:40049450T>A	ENST00000373233.3	-	31	6002	c.5825A>T	c.(5824-5826)cAc>cTc	p.H1942L		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1942					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCTCTCCATGTGTTTGCAGTG	0.478													T|||	13	0.00259585	0.0008	0.0029	5008	,	,		19525	0.0		0.007	False		,,,				2504	0.0031				p.H1942L		Atlas-SNP	.											.	CHD6	312	.	0			c.A5825T						PASS	.	T	LEU/HIS	3,4403	6.2+/-15.9	0,3,2200	138.0	131.0	134.0		5825	3.6	1.0	20	dbSNP_134	134	59,8541	37.8+/-93.5	0,59,4241	yes	missense	CHD6	NM_032221.3	99	0,62,6441	AA,AT,TT		0.686,0.0681,0.4767	benign	1942/2716	40049450	62,12944	2203	4300	6503	SO:0001583	missense	84181	exon31			TCCATGTGTTTGC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.5825A>T	20.37:g.40049450T>A	ENSP00000362330:p.His1942Leu	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	263	136	0.51711	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	12.05	1.822032	0.32237	6.81E-4	0.00686	ENSG00000124177	ENST00000373233	D	0.85339	-1.97	5.86	3.56	0.40772	.	0.195101	0.36101	N	0.002783	T	0.72293	0.3442	L	0.51422	1.61	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.67952	-0.5537	10	0.26408	T	0.33	-16.7152	8.1319	0.31033	0.1166:0.0:0.1688:0.7146	.	1942	Q8TD26	CHD6_HUMAN	L	1942	ENSP00000362330:H1942L	ENSP00000362330:H1942L	H	-	2	0	CHD6	39482864	0.810000	0.29049	0.998000	0.56505	0.808000	0.45660	1.583000	0.36579	1.005000	0.39183	0.533000	0.62120	CAC	T|0.995;A|0.005	0.005	strong		0.478	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
DOC2B	8447	hgsc.bcm.edu	37	17	6157	6157	+	Silent	SNP	A	A	G	rs2294076	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:6157A>G	ENST00000343572.7	-	6	933	c.777T>C	c.(775-777)acT>acC	p.T259T	AC108004.5_ENST00000583926.1_RNA	NM_003585.3	NP_003576	Q14184	DOC2B_HUMAN	double C2-like domains, beta	259	Mediates interaction with STXBP3. {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						ACTTGTCTTCAGTCTTGTCCA	0.637													G|||	3682	0.735224	0.5613	0.8055	5008	,	,		18034	0.8591		0.7326	False		,,,				2504	0.7955				p.T259T		Atlas-SNP	.											.	DOC2B	6	.	0			c.T777C						PASS	.	G		840,544		255,330,107	65.0	68.0	67.0		777	-9.0	0.1	17	dbSNP_100	67	2346,836		866,614,111	no	coding-synonymous	DOC2B	NM_003585.3		1121,944,218	GG,GA,AA		26.2728,39.3064,30.2234		259/413	6157	3186,1380	692	1591	2283	SO:0001819	synonymous_variant	8447	exon6			GTCTTCAGTCTTG	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.777T>C	17.37:g.6157A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_003585		Silent	SNP	ENST00000343572.7	37																																																																																				A|0.249;G|0.751	0.751	strong		0.637	DOC2B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335122.3	NM_003585	
EBI3	10148	hgsc.bcm.edu	37	19	4236996	4236996	+	Missense_Mutation	SNP	G	G	A	rs4740	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	64	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	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		
PIGQ	9091	hgsc.bcm.edu	37	16	632283	632283	+	Intron	SNP	G	G	A	rs7187227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:632283G>A	ENST00000026218.5	+	10	1619				PIGQ_ENST00000321878.5_Missense_Mutation_p.G523S|PIGQ_ENST00000409527.2_Missense_Mutation_p.G523S	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q						C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GCACGAGGCCGGCAGGCCCCT	0.692													G|||	696	0.138978	0.1377	0.0793	5008	,	,		17264	0.0248		0.1799	False		,,,				2504	0.2587				p.G523S		Atlas-SNP	.											.	PIGQ	43	.	0			c.G1567A						PASS	.	G	SER/GLY,	675,3717		50,575,1571	25.0	26.0	26.0		1567,	5.1	1.0	16	dbSNP_116	26	1560,7032		144,1272,2880	yes	missense,intron	PIGQ	NM_004204.3,NM_148920.1	56,	194,1847,4451	AA,AG,GG		18.1564,15.3689,17.2135	,	523/582,	632283	2235,10749	2196	4296	6492	SO:0001627	intron_variant	9091	exon10			GAGGCCGGCAGGC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.1532-600G>A	16.37:g.632283G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	143	72	0.503497	NM_004204	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	268	0.1227106227106227	73	0.1483739837398374	32	0.08839779005524862	18	0.03146853146853147	145	0.19129287598944592	G	22.4	4.284826	0.80803	0.153689	0.181564	ENSG00000007541	ENST00000409527;ENST00000321878;ENST00000540241	T;T	0.44482	0.92;0.92	5.08	5.08	0.68730	.	.	.	.	.	T	0.00178	0.0005	M	0.73598	2.24	0.09310	P	1.0	D	0.89917	1.0	D	0.76575	0.988	T	0.08743	-1.0707	8	0.10636	T	0.68	.	17.4349	0.87548	0.0:0.0:1.0:0.0	rs7187227	523	Q9BRB3-2	.	S	523;523;81	ENSP00000386760:G523S;ENSP00000326674:G523S	ENSP00000326674:G523S	G	+	1	0	PIGQ	572284	1.000000	0.71417	0.995000	0.50966	0.430000	0.31655	5.884000	0.69729	2.361000	0.80049	0.561000	0.74099	GGC	G|0.853;A|0.147	0.147	strong		0.692	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
APBA3	9546	hgsc.bcm.edu	37	19	3752601	3752601	+	Missense_Mutation	SNP	G	G	A	rs147130540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3752601G>A	ENST00000316757.3	-	8	1500	c.1300C>T	c.(1300-1302)Cgc>Tgc	p.R434C	AC005954.4_ENST00000586503.1_RNA|AC005954.3_ENST00000591962.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	434	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCCCGAGCGCTCAGCAGGC	0.751													G|||	57	0.0113818	0.0083	0.0288	5008	,	,		13216	0.0		0.0199	False		,,,				2504	0.0061				p.R434C		Atlas-SNP	.											.	APBA3	28	.	0			c.C1300T						PASS	.	G	CYS/ARG	29,4221		0,29,2096	6.0	9.0	8.0		1300	4.2	0.9	19	dbSNP_134	8	160,8140		1,158,3991	yes	missense	APBA3	NM_004886.3	180	1,187,6087	AA,AG,GG		1.9277,0.6824,1.506	probably-damaging	434/576	3752601	189,12361	2125	4150	6275	SO:0001583	missense	9546	exon8			CCGAGCGCTCAGC	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.1300C>T	19.37:g.3752601G>A	ENSP00000315136:p.Arg434Cys	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	12	9	0.75	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	28	0.01282051282051282	6	0.012195121951219513	8	0.022099447513812154	0	0.0	14	0.018469656992084433	G	14.60	2.583092	0.46006	0.006824	0.019277	ENSG00000011132	ENST00000316757	T	0.29655	1.56	4.21	4.21	0.49690	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000001	T	0.49660	0.1570	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.72030	-0.4413	10	0.87932	D	0	.	12.3996	0.55405	0.0:0.0:0.8316:0.1684	.	434	O96018	APBA3_HUMAN	C	434	ENSP00000315136:R434C	ENSP00000315136:R434C	R	-	1	0	APBA3	3703601	1.000000	0.71417	0.911000	0.35937	0.297000	0.27493	1.807000	0.38902	1.894000	0.54839	0.462000	0.41574	CGC	G|0.987;A|0.013	0.013	strong		0.751	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
CFI	3426	hgsc.bcm.edu	37	4	110681505	110681505	+	Silent	SNP	C	C	T	rs2298749	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:110681505C>T	ENST00000394634.2	-	6	1011	c.804G>A	c.(802-804)tcG>tcA	p.S268S	CFI_ENST00000394635.3_Silent_p.S268S|CFI_ENST00000512148.1_Silent_p.S268S	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	268	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)		TGCAAACACCCGATTTGCAAT	0.428													C|||	1563	0.312101	0.357	0.4395	5008	,	,		19434	0.3095		0.2455	False		,,,				2504	0.2321				p.S268S		Atlas-SNP	.											.	CFI	59	.	0			c.G804A						PASS	.	C		1631,2775	501.2+/-364.9	314,1003,886	143.0	129.0	134.0		804	-2.0	0.9	4	dbSNP_100	134	2195,6405	374.3+/-337.3	293,1609,2398	no	coding-synonymous	CFI	NM_000204.3		607,2612,3284	TT,TC,CC		25.5233,37.0177,29.4172		268/584	110681505	3826,9180	2203	4300	6503	SO:0001819	synonymous_variant	3426	exon6			AACACCCGATTTG	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.804G>A	4.37:g.110681505C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	151	60	0.397351	NM_000204	O60442	Silent	SNP	ENST00000394634.2	37	CCDS34049.1																																																																																			C|0.702;T|0.298	0.298	strong		0.428	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
RASA1	5921	hgsc.bcm.edu	37	5	86564564	86564564	+	Missense_Mutation	SNP	C	C	T	rs111840875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:86564564C>T	ENST00000274376.6	+	1	860	c.296C>T	c.(295-297)gCt>gTt	p.A99V	RASA1_ENST00000506290.1_5'Flank|RASA1_ENST00000456692.2_5'Flank|RASA1_ENST00000512763.1_5'Flank	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	99					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)	p.A99_A106delAAGVAGAA(1)		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)		gctggtgctgctgctggcgtg	0.647													C|||	63	0.0125799	0.003	0.0245	5008	,	,		14161	0.0		0.0368	False		,,,				2504	0.0051				p.A99V		Atlas-SNP	.											.	RASA1	213	.	1	Deletion - In frame(1)	large_intestine(1)	c.C296T						PASS	.	C	VAL/ALA	35,4371	40.0+/-72.8	0,35,2168	48.0	36.0	40.0		296	0.6	0.1	5	dbSNP_132	40	246,8354	96.1+/-157.9	0,246,4054	yes	missense	RASA1	NM_002890.2	64	0,281,6222	TT,TC,CC		2.8605,0.7944,2.1605	benign	99/1048	86564564	281,12725	2203	4300	6503	SO:0001583	missense	5921	exon1			GTGCTGCTGCTGG		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.296C>T	5.37:g.86564564C>T	ENSP00000274376:p.Ala99Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_002890	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	36	0.016483516483516484	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	23	0.030343007915567283	C	3.718	-0.058129	0.07317	0.007944	0.028605	ENSG00000145715	ENST00000274376;ENST00000534133	T	0.74209	-0.82	1.6	0.623	0.17654	.	2.236220	0.02643	N	0.105591	T	0.25158	0.0611	N	0.08118	0	0.80722	D	1	P;B	0.51933	0.949;0.334	B;B	0.34346	0.18;0.014	T	0.40739	-0.9547	10	0.36615	T	0.2	.	4.8392	0.13481	0.3611:0.6389:0.0:0.0	.	132;99	Q59GK3;P20936	.;RASA1_HUMAN	V	99;132	ENSP00000274376:A99V	ENSP00000274376:A99V	A	+	2	0	RASA1	86600320	0.999000	0.42202	0.103000	0.21229	0.047000	0.14425	2.605000	0.46283	0.192000	0.20272	0.655000	0.94253	GCT	C|0.982;T|0.018	0.018	strong		0.647	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890	
TRRAP	8295	hgsc.bcm.edu	37	7	98506441	98506441	+	Silent	SNP	C	C	T	rs35310331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:98506441C>T	ENST00000359863.4	+	14	1415	c.1206C>T	c.(1204-1206)ttC>ttT	p.F402F	TRRAP_ENST00000355540.3_Silent_p.F402F|TRRAP_ENST00000446306.3_Silent_p.F402F	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	402					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)			TCCAGCTCTTCGCCAAGAACA	0.652													C|||	791	0.157947	0.497	0.0591	5008	,	,		18525	0.0		0.0547	False		,,,				2504	0.0389				p.F402F		Atlas-SNP	.											.	TRRAP	863	.	0			c.C1206T						PASS	.	C		1893,2513	529.2+/-372.6	397,1099,707	82.0	54.0	64.0		1206	-2.7	1.0	7	dbSNP_126	64	407,8193	124.6+/-183.3	8,391,3901	no	coding-synonymous	TRRAP	NM_003496.3		405,1490,4608	TT,TC,CC		4.7326,42.9641,17.6841		402/3831	98506441	2300,10706	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon14			GCTCTTCGCCAAG	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.1206C>T	7.37:g.98506441C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	312	0.14285714285714285	249	0.5060975609756098	25	0.06906077348066299	0	0.0	38	0.05013192612137203	C	10.23	1.292117	0.23564	0.429641	0.047326	ENSG00000196367	ENST00000456197	.	.	.	5.84	-2.67	0.06059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42137	-0.9469	3	.	.	.	.	11.7464	0.51821	0.0:0.3465:0.0:0.6535	rs35310331	.	.	.	L	117	.	.	S	+	2	0	TRRAP	98344377	0.356000	0.24930	0.971000	0.41717	0.971000	0.66376	-0.336000	0.07863	-0.736000	0.04831	-1.192000	0.01694	TCG	C|0.831;T|0.169	0.169	strong		0.652	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
ZDHHC23	254887	hgsc.bcm.edu	37	3	113673125	113673125	+	Missense_Mutation	SNP	A	A	G	rs11921691	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:113673125A>G	ENST00000330212.3	+	3	1039	c.740A>G	c.(739-741)aAg>aGg	p.K247R	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.K241R	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	247			K -> R (in dbSNP:rs11921691). {ECO:0000269|Ref.2}.		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						GGCTCTTCCAAGATGCCAGCT	0.592													G|||	2992	0.597444	0.646	0.5346	5008	,	,		17824	0.6696		0.5646	False		,,,				2504	0.5358				p.K247R		Atlas-SNP	.											ZDHHC23,NS,carcinoma,-1,1	ZDHHC23	38	1	0			c.A740G						PASS	.	G	ARG/LYS	2687,1719	510.3+/-367.5	823,1041,339	60.0	59.0	59.0		740	2.2	0.0	3	dbSNP_120	59	4617,3983	546.9+/-385.1	1231,2155,914	yes	missense	ZDHHC23	NM_173570.3	26	2054,3196,1253	GG,GA,AA		46.314,39.015,43.8413	benign	247/410	113673125	7304,5702	2203	4300	6503	SO:0001583	missense	254887	exon3			CTTCCAAGATGCC	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.740A>G	3.37:g.113673125A>G	ENSP00000330485:p.Lys247Arg	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_173570	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	37	CCDS33827.1	1325	0.6066849816849816	319	0.6483739837398373	192	0.5303867403314917	376	0.6573426573426573	438	0.5778364116094987	G	0.036	-1.308369	0.01342	0.60985	0.53686	ENSG00000184307	ENST00000330212;ENST00000498275	T;T	0.25250	1.81;1.81	5.11	2.19	0.27852	.	0.693518	0.15317	N	0.268754	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	0.31420	-0.9944	9	0.15499	T	0.54	-8.3726	10.1295	0.42669	0.3368:0.0:0.6632:0.0	rs11921691;rs58737175;rs11921691	247	Q8IYP9	ZDH23_HUMAN	R	247;241	ENSP00000330485:K247R;ENSP00000417840:K241R	ENSP00000330485:K247R	K	+	2	0	ZDHHC23	115155815	0.020000	0.18652	0.000000	0.03702	0.052000	0.14988	1.792000	0.38754	0.309000	0.22966	-0.215000	0.12644	AAG	A|0.415;G|0.585	0.585	strong		0.592	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570	
MIA2	117153	hgsc.bcm.edu	37	14	39716201	39716201	+	Missense_Mutation	SNP	A	A	G	rs11845046	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:39716201A>G	ENST00000280082.3	+	4	622	c.423A>G	c.(421-423)atA>atG	p.I141M	RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.I141M|MIA2_ENST00000556784.1_Missense_Mutation_p.I140M	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	141					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)		GTGAAAATATATATCCTTATG	0.284													A|||	1193	0.238219	0.1407	0.183	5008	,	,		19920	0.502		0.2127	False		,,,				2504	0.1636				p.I141M		Atlas-SNP	.											.	MIA2	82	.	0			c.A423G						PASS	.	A	MET/ILE	733,3653		69,595,1529	33.0	37.0	35.0		423	-1.4	0.0	14	dbSNP_120	35	1787,6795		158,1471,2662	yes	missense	MIA2	NM_054024.3	10	227,2066,4191	GG,GA,AA		20.8227,16.7123,19.4324	benign	141/655	39716201	2520,10448	2193	4291	6484	SO:0001583	missense	117153	exon4			AAATATATATCCT	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.423A>G	14.37:g.39716201A>G	ENSP00000280082:p.Ile141Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_054024	A1L4H0|Q9H6C1	Missense_Mutation	SNP	ENST00000280082.3	37	CCDS9672.1	577	0.2641941391941392	59	0.11991869918699187	74	0.20441988950276244	292	0.5104895104895105	152	0.20052770448548812	A	2.767	-0.256608	0.05829	0.167123	0.208227	ENSG00000150526;ENSG00000150526;ENSG00000258941	ENST00000280082;ENST00000556784;ENST00000553728	T;T;T	0.45276	0.9;0.92;3.26	5.64	-1.41	0.08941	.	0.727822	0.12041	N	0.505098	T	0.00012	0.0000	N	0.21448	0.665	0.80722	P	0.0	B;B	0.16396	0.01;0.017	B;B	0.10450	0.002;0.005	T	0.48293	-0.9048	8	.	.	.	-0.5151	3.1326	0.06429	0.6104:0.1108:0.1708:0.108	rs11845046;rs11845046	141;141	Q96PC5;Q96PC5-2	MIA2_HUMAN;.	M	141;140;141	ENSP00000280082:I141M;ENSP00000451934:I140M;ENSP00000452252:I141M	.	I	+	3	3	MIA2;RP11-407N17.3	38785952	0.000000	0.05858	0.019000	0.16419	0.059000	0.15707	0.264000	0.18497	0.079000	0.16929	0.533000	0.62120	ATA	A|0.770;G|0.230	0.230	strong		0.284	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024	
EGFL7	51162	hgsc.bcm.edu	37	9	139564668	139564668	+	Missense_Mutation	SNP	G	G	A	rs2297538	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139564668G>A	ENST00000371699.1	+	7	1368	c.457G>A	c.(457-459)Gtc>Atc	p.V153I	MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000406555.3_Missense_Mutation_p.V153I|EGFL7_ENST00000308874.7_Missense_Mutation_p.V153I|EGFL7_ENST00000371698.3_Missense_Mutation_p.V153I|EGFL7_ENST00000492002.1_3'UTR			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	84	0	0		WXS	Illumina HiSeq	Phase_I	75	26	0.346667	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	
IRX4	50805	hgsc.bcm.edu	37	5	1880891	1880891	+	Missense_Mutation	SNP	C	C	T	rs2232376	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:1880891C>T	ENST00000505790.1	-	4	811	c.355G>A	c.(355-357)Gct>Act	p.A119T	IRX4_ENST00000513692.1_Missense_Mutation_p.A119T|IRX4_ENST00000231357.2_Missense_Mutation_p.A119T|IRX4_ENST00000505938.1_5'UTR	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	64	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	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	
MUC2	4583	hgsc.bcm.edu	37	11	1088835	1088835	+	Missense_Mutation	SNP	C	C	T	rs41389046	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1088835C>T	ENST00000441003.2	+	26	3647	c.3620C>T	c.(3619-3621)aCc>aTc	p.T1207I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1207I	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1207					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACCGAGGAGACCTGCAAGTCC	0.572													T|||	326	0.0650958	0.053	0.0591	5008	,	,		23089	0.0556		0.0974	False		,,,				2504	0.0624				p.T1207I		Atlas-SNP	.											MUC2_ENST00000441003,colon,carcinoma,0,2	MUC2	614	2	0			c.C3620T						PASS	.	T	ILE/THR	227,3961		5,217,1872	51.0	53.0	52.0		3620	-7.2	0.0	11	dbSNP_127	52	782,7632		36,710,3461	yes	missense	MUC2	NM_002457.2	89	41,927,5333	TT,TC,CC		9.294,5.4202,8.0067	benign	1207/2813	1088835	1009,11593	2094	4207	6301	SO:0001583	missense	4583	exon26			AGGAGACCTGCAA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3620C>T	11.37:g.1088835C>T	ENSP00000415183:p.Thr1207Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		136	0.06227106227106227	21	0.042682926829268296	18	0.049723756906077346	28	0.04895104895104895	69	0.09102902374670185	T	4.811	0.150695	0.09185	0.054202	0.09294	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13196	2.67;2.61	3.61	-7.21	0.01490	.	8.859210	0.01114	N	0.005658	T	0.00178	0.0005	N	0.00742	-1.23	0.58432	P	2.9999999999752447E-6	B	0.14805	0.011	B	0.15870	0.014	T	0.38735	-0.9647	9	0.39692	T	0.17	.	8.0296	0.30457	0.5745:0.2881:0.0:0.1374	rs41389046;rs61732138	1207	E7EUV1	.	I	1207	ENSP00000415183:T1207I;ENSP00000351956:T1207I	ENSP00000351956:T1207I	T	+	2	0	MUC2	1078835	0.002000	0.14202	0.000000	0.03702	0.068000	0.16541	-0.083000	0.11286	-3.281000	0.00197	-0.847000	0.03039	ACC	C|0.932;T|0.068	0.068	strong		0.572	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
COL22A1	169044	hgsc.bcm.edu	37	8	139712355	139712355	+	Splice_Site	SNP	G	G	A	rs77613350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:139712355G>A	ENST00000303045.6	-	32	3038	c.2592C>T	c.(2590-2592)ccC>ccT	p.P864P	COL22A1_ENST00000435777.1_Splice_Site_p.P864P|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	864	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TACTACTTACGGGCATCCGTG	0.552										HNSCC(7;0.00092)			G|||	168	0.0335463	0.0787	0.0187	5008	,	,		17017	0.0278		0.0189	False		,,,				2504	0.0041				p.P864P		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2592T						PASS	.	G		268,4138	151.4+/-185.3	5,258,1940	80.0	69.0	73.0		2592	-8.3	0.0	8	dbSNP_131	73	138,8462	68.0+/-130.5	1,136,4163	yes	coding-synonymous-near-splice	COL22A1	NM_152888.1		6,394,6103	AA,AG,GG		1.6047,6.0826,3.1216		864/1627	139712355	406,12600	2203	4300	6503	SO:0001630	splice_region_variant	169044	exon32			ACTTACGGGCATC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2592+1C>T	8.37:g.139712355G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			G|0.967;A|0.033	0.033	strong		0.552	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Silent
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500224	90500224	+	Silent	SNP	C	C	T	rs58932350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90500224C>T	ENST00000325643.5	+	4	888	c.822C>T	c.(820-822)ccC>ccT	p.P274P		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	274	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAACATGCCCCGTCCCCCAGA	0.622													.|||	514	0.102636	0.267	0.0418	5008	,	,		17017	0.0347		0.0636	False		,,,				2504	0.0337				p.P274P		Atlas-SNP	.											.	.	.	.	0			c.C822T						PASS	.	C		926,3480		90,746,1367	48.0	51.0	50.0		822	-3.8	0.0	9	dbSNP_129	50	412,8188		7,398,3895	no	coding-synonymous	C9orf79	NM_178828.4		97,1144,5262	TT,TC,CC		4.7907,21.0168,10.2876		274/1446	90500224	1338,11668	2203	4300	6503	SO:0001819	synonymous_variant	286234	exon4			ATGCCCCGTCCCC	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.822C>T	9.37:g.90500224C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																			C|0.902;T|0.098	0.098	strong		0.622	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
BAAT	570	hgsc.bcm.edu	37	9	104130469	104130469	+	Missense_Mutation	SNP	C	C	G	rs41281027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:104130469C>G	ENST00000395051.3	-	2	672	c.602G>C	c.(601-603)cGc>cCc	p.R201P	BAAT_ENST00000259407.2_Missense_Mutation_p.R201P			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	201					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	TTCTGGTTTGCGGGGCAGGTC	0.498													G|||	777	0.155152	0.236	0.1383	5008	,	,		12055	0.0456		0.1571	False		,,,				2504	0.1687				p.R201P		Atlas-SNP	.											BAAT,bladder,carcinoma,-1,1	BAAT	52	1	0			c.G602C						scavenged	.	G	PRO/ARG,PRO/ARG	957,3449	730.6+/-410.2	104,749,1350	74.0	80.0	78.0		602,602	-3.1	0.0	9	dbSNP_127	78	1250,7350	760.2+/-407.6	90,1070,3140	yes	missense,missense	BAAT	NM_001127610.1,NM_001701.3	103,103	194,1819,4490	GG,GC,CC		14.5349,21.7204,16.9691	benign,benign	201/419,201/419	104130469	2207,10799	2203	4300	6503	SO:0001583	missense	570	exon3			GGTTTGCGGGGCA	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"""glycine N-choloyltransferase"""	602938	"""bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)"", ""bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"""				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.602G>C	9.37:g.104130469C>G	ENSP00000378491:p.Arg201Pro	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	121	46	0.380165	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	37	CCDS6752.1	314	0.14377289377289376	118	0.23983739837398374	53	0.1464088397790055	27	0.0472027972027972	116	0.15303430079155672	G	5.108	0.205558	0.09704	0.217204	0.145349	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.45276	0.9;0.9	4.47	-3.11	0.05299	.	3.070920	0.00995	N	0.003597	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16158	-1.0412	9	0.42905	T	0.14	7.5868	0.7619	0.01008	0.2513:0.3284:0.1798:0.2405	rs41281027;rs61755097	201	Q14032	BAAT_HUMAN	P	201	ENSP00000259407:R201P;ENSP00000378491:R201P	ENSP00000259407:R201P	R	-	2	0	BAAT	103170290	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.429000	0.02437	-0.719000	0.04942	-0.216000	0.12614	CGC	C|0.839;G|0.161	0.161	strong		0.498	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1		
DDR1	780	hgsc.bcm.edu	37	6	30857072	30857072	+	Silent	SNP	G	G	C	rs2229933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30857072G>C	ENST00000324771.8	+	6	830	c.282G>C	c.(280-282)ctG>ctC	p.L94L	DDR1_ENST00000452441.1_Silent_p.L94L|DDR1_ENST00000418800.2_Silent_p.L94L|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000376569.3_Silent_p.L94L|DDR1_ENST00000513240.1_Silent_p.L94L|DDR1_ENST00000376575.3_Silent_p.L94L|DDR1_ENST00000454612.2_Silent_p.L94L|DDR1_ENST00000361741.4_5'Flank|DDR1_ENST00000376568.3_Silent_p.L94L|DDR1_ENST00000376567.2_Silent_p.L94L|DDR1_ENST00000508312.1_Silent_p.L112L|DDR1_ENST00000446312.1_Silent_p.L94L|DDR1_ENST00000376570.4_Silent_p.L94L			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	94	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.			L -> V (in Ref. 2; AAA02866 and 5; AAC50917). {ECO:0000305}.	branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	TACAACGACTGCACCTGGTGG	0.667													G|||	2080	0.415335	0.2746	0.4294	5008	,	,		16904	0.6121		0.2227	False		,,,				2504	0.591				p.L112L		Atlas-SNP	.											.	DDR1	213	.	0			c.G336C						PASS	.	G	,,,,,	785,2237		104,577,830	111.0	112.0	111.0		282,282,336,282,282,282	2.3	1.0	6	dbSNP_98	111	967,4449		87,793,1828	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,,,,,	191,1370,2658	CC,CG,GG		17.8545,25.9762,20.7632	,,,,,	94/509,94/768,112/895,94/877,94/914,94/920	30857072	1752,6686	1511	2708	4219	SO:0001819	synonymous_variant	780	exon4			ACGACTGCACCTG	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.282G>C	6.37:g.30857072G>C		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	37	CCDS34385.1	766	0.3507326007326007	125	0.2540650406504065	144	0.39779005524861877	310	0.541958041958042	187	0.24670184696569922	G	9.040	0.989395	0.18966	0.259762	0.178545	ENSG00000204580	ENST00000424544	.	.	.	4.81	2.33	0.28932	.	.	.	.	.	T	0.13798	0.0334	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16600	-1.0397	3	.	.	.	.	2.6727	0.05071	0.3107:0.0:0.4746:0.2147	rs2229933;rs2229933	.	.	.	P	78	.	.	A	+	1	0	DDR1	30965051	0.996000	0.38824	0.995000	0.50966	0.911000	0.54048	0.384000	0.20668	0.882000	0.36016	0.305000	0.20034	GCA	G|0.733;C|0.267	0.267	strong		0.667	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
DNAH14	127602	hgsc.bcm.edu	37	1	225534219	225534219	+	Missense_Mutation	SNP	T	T	C	rs7527925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225534219T>C	ENST00000445597.2	+	49	8471	c.8471T>C	c.(8470-8472)gTa>gCa	p.V2824A	DNAH14_ENST00000439375.2_Missense_Mutation_p.V3627A|DNAH14_ENST00000430092.1_Missense_Mutation_p.V3627A			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2824					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CTTTGCACTGTAATCATGCAA	0.323													C|||	2650	0.529153	0.6407	0.4697	5008	,	,		17450	0.5089		0.4046	False		,,,				2504	0.5695				p.V3627A		Atlas-SNP	.											.	DNAH14	300	.	0			c.T10880C						PASS	.	C	ALA/VAL	842,542		268,306,118	70.0	60.0	63.0		10880	3.5	0.2	1	dbSNP_116	63	1404,1770		323,758,506	yes	missense	DNAH14	NM_001373.1	64	591,1064,624	CC,CT,TT		44.2344,39.1618,49.276	benign	3627/4516	225534219	2246,2312	692	1587	2279	SO:0001583	missense	127602	exon69			GCACTGTAATCAT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8471T>C	1.37:g.225534219T>C	ENSP00000409472:p.Val2824Ala	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	206	101	0.490291	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	2.312	-0.357714	0.05138	0.608382	0.442344	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.50001	0.76;0.76;0.76	5.48	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.45086	-0.9285	7	0.15066	T	0.55	.	3.7279	0.08481	0.1327:0.5895:0.1289:0.1488	rs7527925;rs52797267;rs56543759;rs61045802;rs7527925	3627	Q0VDD8-4	.	A	2824;3627;3627	ENSP00000409472:V2824A;ENSP00000414402:V3627A;ENSP00000392061:V3627A	ENSP00000414402:V3627A	V	+	2	0	DNAH14	223600842	0.000000	0.05858	0.155000	0.22561	0.949000	0.60115	0.067000	0.14510	0.662000	0.31006	-0.294000	0.09567	GTA	T|0.500;C|0.500	0.500	strong		0.323	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PSMC5	5705	hgsc.bcm.edu	37	17	61908556	61908556	+	Silent	SNP	C	C	T	rs13030	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:61908556C>T	ENST00000310144.6	+	8	1148	c.840C>T	c.(838-840)ctC>ctT	p.L280L	PSMC5_ENST00000375812.4_Silent_p.L272L|PSMC5_ENST00000580864.1_Silent_p.L272L|PSMC5_ENST00000581882.1_Silent_p.L272L|FTSJ3_ENST00000580295.1_5'Flank	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	280	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TCAACCAGCTCGACGGCTTTG	0.602													C|||	1986	0.396565	0.1884	0.4467	5008	,	,		18688	0.505		0.327	False		,,,				2504	0.6022				p.L280L		Atlas-SNP	.											.	PSMC5	41	.	0			c.C840T						PASS	.	C	,	916,3490	346.2+/-308.9	104,708,1391	98.0	102.0	100.0		816,840	2.6	1.0	17	dbSNP_52	100	2770,5830	434.2+/-357.7	457,1856,1987	yes	coding-synonymous,coding-synonymous	PSMC5	NM_001199163.1,NM_002805.5	,	561,2564,3378	TT,TC,CC		32.2093,20.7898,28.3408	,	272/399,280/407	61908556	3686,9320	2203	4300	6503	SO:0001819	synonymous_variant	5705	exon8			CCAGCTCGACGGC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.840C>T	17.37:g.61908556C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	37	CCDS11645.1																																																																																			C|0.689;T|0.311	0.311	strong		0.602	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
DNAH17	8632	hgsc.bcm.edu	37	17	76528591	76528591	+	Silent	SNP	C	C	T	rs11868065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	94	0	0		WXS	Illumina HiSeq	Phase_I	127	124	0.976378	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	
NEDD8	4738	hgsc.bcm.edu	37	14	24687414	24687414	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24687414C>T	ENST00000250495.5	-	3	260	c.74G>A	c.(73-75)cGa>cAa	p.R25Q	NEDD8-MDP1_ENST00000604306.1_5'UTR|MDP1_ENST00000396833.2_5'Flank|NEDD8-MDP1_ENST00000534348.1_Missense_Mutation_p.R25Q|MDP1_ENST00000532557.1_5'Flank|MDP1_ENST00000288087.7_5'Flank|AL136419.6_ENST00000565988.1_RNA|NEDD8_ENST00000524927.1_Missense_Mutation_p.R25Q	NM_006156.2	NP_006147.1	Q15843	NEDD8_HUMAN	neural precursor cell expressed, developmentally down-regulated 8	25					anatomical structure morphogenesis (GO:0009653)|cellular protein modification process (GO:0006464)|protein localization (GO:0008104)|protein neddylation (GO:0045116)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to organic cyclic compound (GO:0014070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.R25Q(2)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5				GBM - Glioblastoma multiforme(265;0.0186)		CTCCTTGATTCGCTCCACCTT	0.517																																					p.R25Q		Atlas-SNP	.											NEDD8,rectum,carcinoma,0,2	.	.	2	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G74A						scavenged	.						118.0	103.0	108.0					14																	24687414		2203	4300	6503	SO:0001583	missense	100528064	exon3			TTGATTCGCTCCA	D23662	CCDS9621.1	14q11.2	2008-08-13			ENSG00000129559	ENSG00000129559			7732	protein-coding gene	gene with protein product		603171				9353319	Standard	NM_006156		Approved	Nedd-8		Q15843	OTTHUMG00000029325	ENST00000250495.5:c.74G>A	14.37:g.24687414C>T	ENSP00000250495:p.Arg25Gln	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	169	3	0.0177515	NM_001199823	Q3SXN8|Q6LES6	Missense_Mutation	SNP	ENST00000250495.5	37	CCDS9621.1	.	.	.	.	.	.	.	.	.	.	C	32	5.179410	0.94846	.	.	ENSG00000255526;ENSG00000129559;ENSG00000129559	ENST00000534348;ENST00000250495;ENST00000524927	T;T;T	0.71222	-0.55;-0.55;-0.55	5.15	5.15	0.70609	Ubiquitin supergroup (1);Ubiquitin (2);	0.068063	0.56097	N	0.000028	T	0.57330	0.2046	N	0.16862	0.45	0.80722	D	1	D	0.55605	0.972	B	0.40410	0.328	T	0.67106	-0.5754	10	0.87932	D	0	-5.2715	17.5536	0.87884	0.0:1.0:0.0:0.0	.	25	Q15843	NEDD8_HUMAN	Q	25	ENSP00000431482:R25Q;ENSP00000250495:R25Q;ENSP00000448192:R25Q	ENSP00000250495:R25Q	R	-	2	0	NEDD8-MDP1;NEDD8	23757254	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.780000	0.62382	2.675000	0.91044	0.655000	0.94253	CGA	.	.	none		0.517	NEDD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073146.2	NM_006156	
CYFIP1	23191	hgsc.bcm.edu	37	15	22969232	22969232	+	Missense_Mutation	SNP	G	G	A	rs7170637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:22969232G>A	ENST00000313077.7	+	22	2583	c.2458G>A	c.(2458-2460)Ggc>Agc	p.G820S	CYFIP1_ENST00000435939.2_Missense_Mutation_p.G389S|CYFIP1_ENST00000560848.1_Missense_Mutation_p.G820S	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GACGCTGGACGGCTTCGACGC	0.607													A|||	1331	0.265775	0.6906	0.1484	5008	,	,		20818	0.004		0.1769	False		,,,				2504	0.136				p.G820S		Atlas-SNP	.											CYFIP1_ENST00000435939,colon,carcinoma,0,2	CYFIP1	159	2	0			c.G2458A						PASS	.	A	SER/GLY,SER/GLY	2625,1781	527.9+/-372.3	787,1051,365	137.0	101.0	113.0		1165,2458	5.4	1.0	15	dbSNP_116	113	1407,7193	753.6+/-407.5	124,1159,3017	yes	missense,missense	CYFIP1	NM_001033028.1,NM_014608.2	56,56	911,2210,3382	AA,AG,GG		16.3605,40.4222,31.0011	benign,benign	389/823,820/1254	22969232	4032,8974	2203	4300	6503	SO:0001583	missense	23191	exon22			CTGGACGGCTTCG	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2458G>A	15.37:g.22969232G>A	ENSP00000324549:p.Gly820Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	37	CCDS10009.1	532	0.24358974358974358	340	0.6910569105691057	51	0.1408839779005525	3	0.005244755244755245	138	0.1820580474934037	A	9.988	1.229904	0.22542	0.595778	0.163605	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.20332	2.08;2.08	5.41	5.41	0.78517	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00210	-1.845	0.41978	P	0.009217999999999948	B;B;B	0.13145	0.002;0.007;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.33701	-0.9858	9	0.08381	T	0.77	-23.3927	11.3522	0.49594	0.9287:0.0:0.0713:0.0	rs7170637;rs17844900;rs17857620;rs7170637	848;389;820	E7EQ04;Q7L576-2;Q7L576	.;.;CYFP1_HUMAN	S	820;848;389	ENSP00000324549:G820S;ENSP00000405956:G389S	ENSP00000324549:G820S	G	+	1	0	CYFIP1	20520673	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	6.190000	0.72057	0.901000	0.36495	-0.361000	0.07541	GGC	G|0.704;A|0.296	0.296	strong		0.607	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
NBPF10	100132406	hgsc.bcm.edu	37	1	145323667	145323667	+	Missense_Mutation	SNP	C	C	G	rs199626421		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:145323667C>G	ENST00000342960.5	+	27	3539	c.3504C>G	c.(3502-3504)gaC>gaG	p.D1168E	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	755						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.D1168E(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TTAAAAAGGACGAAGAAGAGG	0.468																																					p.D1168E		Atlas-SNP	.											NBPF10,NS,carcinoma,0,6	NBPF10	221	6	1	Substitution - Missense(1)	kidney(1)	c.C3504G						scavenged	.																																			SO:0001583	missense	100132406	exon27			AAAGGACGAAGAA	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.3504C>G	1.37:g.145323667C>G	ENSP00000345684:p.Asp1168Glu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	48	7	0.145833	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	8.960	0.970347	0.18659	.	.	ENSG00000163386	ENST00000342960	T	0.03272	3.99	.	.	.	.	.	.	.	.	T	0.01905	0.0060	L	0.60455	1.87	0.09310	N	1	.	.	.	.	.	.	T	0.41716	-0.9493	5	0.42905	T	0.14	.	.	.	.	.	.	.	.	E	1168	ENSP00000345684:D1168E	ENSP00000345684:D1168E	D	+	3	2	NBPF10	144035024	0.003000	0.15002	0.002000	0.10522	0.088000	0.18126	0.035000	0.13797	-0.430000	0.07318	0.152000	0.16155	GAC	.	.	weak		0.468	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
BPIFB4	149954	hgsc.bcm.edu	37	20	31676804	31676804	+	Missense_Mutation	SNP	A	A	C	rs2889732	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31676804A>C	ENST00000375483.3	+	6	959	c.959A>C	c.(958-960)aAc>aCc	p.N320T		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	320			N -> T (in dbSNP:rs2889732).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										AATTTAGTGAACCGAGTCCTG	0.597													A|||	2762	0.551518	0.5703	0.4971	5008	,	,		19286	0.753		0.3917	False		,,,				2504	0.5215				p.N320T		Atlas-SNP	.											.	.	.	.	0			c.A959C						PASS	.	A	THR/ASN	2292,2114	602.2+/-389.9	616,1060,527	165.0	153.0	157.0		959	5.0	1.0	20	dbSNP_101	157	3188,5412	481.9+/-370.8	604,1980,1716	yes	missense	BPIFB4	NM_182519.2	65	1220,3040,2243	CC,CA,AA		37.0698,47.98,42.1344	possibly-damaging	320/615	31676804	5480,7526	2203	4300	6503	SO:0001583	missense	149954	exon6			TAGTGAACCGAGT	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.959A>C	20.37:g.31676804A>C	ENSP00000364632:p.Asn320Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	1202	0.5503663003663004	297	0.6036585365853658	170	0.4696132596685083	435	0.7604895104895105	300	0.39577836411609496	A	21.1	4.101996	0.76983	0.5202	0.370698	ENSG00000186191	ENST00000375483	T	0.04917	3.53	5.01	5.01	0.66863	.	0.248711	0.36066	N	0.002803	T	0.00012	0.0000	N	0.14661	0.345	0.32313	P	0.563458	D	0.57257	0.979	P	0.51615	0.675	T	0.00008	-1.2485	9	0.29301	T	0.29	-15.4391	11.1066	0.48207	1.0:0.0:0.0:0.0	rs2889732;rs52822767;rs61707423;rs2889732	320	P59827	BPIB4_HUMAN	T	320	ENSP00000364632:N320T	ENSP00000364632:N320T	N	+	2	0	BPIFB4	31140465	0.991000	0.36638	1.000000	0.80357	0.935000	0.57460	3.261000	0.51530	1.887000	0.54652	0.482000	0.46254	AAC	A|0.522;C|0.478	0.478	strong		0.597	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
KIAA1467	57613	hgsc.bcm.edu	37	12	13208552	13208552	+	Silent	SNP	C	C	T	rs4763924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:13208552C>T	ENST00000197268.8	+	2	225	c.105C>T	c.(103-105)gaC>gaT	p.D35D		NM_020853.1	NP_065904.1	A2RU67	K1467_HUMAN	KIAA1467	35						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(4)	36		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		AGAGCGAAGACGATCTGGTGC	0.512													C|||	1642	0.327875	0.3903	0.2752	5008	,	,		20666	0.4901		0.17	False		,,,				2504	0.2761				p.D35D		Atlas-SNP	.											.	KIAA1467	78	.	0			c.C105T						PASS	.	C		1557,2849	490.8+/-361.9	270,1017,916	80.0	80.0	80.0		105	-2.3	0.9	12	dbSNP_111	80	1223,7377	247.2+/-275.4	106,1011,3183	no	coding-synonymous	KIAA1467	NM_020853.1		376,2028,4099	TT,TC,CC		14.2209,35.3382,21.3748		35/623	13208552	2780,10226	2203	4300	6503	SO:0001819	synonymous_variant	57613	exon2			CGAAGACGATCTG	AB040900	CCDS31750.1	12p13.1	2006-01-23				ENSG00000084444			29288	protein-coding gene	gene with protein product						10819331	Standard	XM_005253450		Approved		uc001rbi.3	A2RU67		ENST00000197268.8:c.105C>T	12.37:g.13208552C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_020853	Q49AF2|Q5CZ81|Q6ZUV7|Q9P261	Silent	SNP	ENST00000197268.8	37	CCDS31750.1																																																																																			C|0.738;T|0.262	0.262	strong		0.512	KIAA1467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401007.1	NM_020853	
TRIM65	201292	hgsc.bcm.edu	37	17	73888427	73888427	+	Missense_Mutation	SNP	A	A	C	rs7222757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73888427A>C	ENST00000269383.3	-	3	730	c.665T>G	c.(664-666)gTc>gGc	p.V222G		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	222			V -> G (in dbSNP:rs7222757). {ECO:0000269|PubMed:15489334}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTCCAAATGGACCCGCAGCCG	0.647													C|||	2044	0.408147	0.7859	0.2709	5008	,	,		16251	0.2212		0.2972	False		,,,				2504	0.3016				p.V222G		Atlas-SNP	.											.	TRIM65	23	.	0			c.T665G						PASS	.	C	GLY/VAL	3126,1276		1135,856,210	23.0	28.0	26.0		665	0.9	0.1	17	dbSNP_116	26	2529,6069		385,1759,2155	no	missense	TRIM65	NM_173547.2	109	1520,2615,2365	CC,CA,AA		29.4138,28.9868,43.5	benign	222/518	73888427	5655,7345	2201	4299	6500	SO:0001583	missense	201292	exon3			AAATGGACCCGCA	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.665T>G	17.37:g.73888427A>C	ENSP00000269383:p.Val222Gly	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	37	CCDS11732.1	842|842	0.38553113553113555|0.38553113553113555	374|374	0.7601626016260162|0.7601626016260162	109|109	0.3011049723756906|0.3011049723756906	147|147	0.256993006993007|0.256993006993007	212|212	0.2796833773087071|0.2796833773087071	C|C	0.013|0.013	-1.613393|-1.613393	0.00835|0.00835	0.710132|0.710132	0.294138|0.294138	ENSG00000141569|ENSG00000141569	ENST00000543309|ENST00000269383	.|T	.|0.55588	.|0.51	4.23|4.23	0.864|0.864	0.19068|0.19068	.|.	.|0.902753	.|0.09382	.|N	.|0.809767	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.50171|0.50171	P|P	1.4999999999998348E-4|1.4999999999998348E-4	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.35301|0.35301	-0.9794|-0.9794	4|9	.|0.22706	.|T	.|0.39	.|.	2.6845|2.6845	0.05103|0.05103	0.218:0.3051:0.0:0.4769|0.218:0.3051:0.0:0.4769	rs7222757;rs61169735|rs7222757;rs61169735	.|222	.|Q6PJ69	.|TRI65_HUMAN	A|G	96|222	.|ENSP00000269383:V222G	.|ENSP00000269383:V222G	S|V	-|-	1|2	0|0	TRIM65|TRIM65	71400022|71400022	0.000000|0.000000	0.05858|0.05858	0.128000|0.128000	0.21923|0.21923	0.003000|0.003000	0.03518|0.03518	-1.241000|-1.241000	0.02911|0.02911	0.101000|0.101000	0.17610|0.17610	-0.358000|-0.358000	0.07595|0.07595	TCC|GTC	A|0.572;C|0.428	0.428	strong		0.647	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
MAP9	79884	hgsc.bcm.edu	37	4	156289900	156289900	+	Silent	SNP	C	C	T	rs3733390	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:156289900C>T	ENST00000311277.4	-	5	809	c.546G>A	c.(544-546)ttG>ttA	p.L182L	AC097467.2_ENST00000597831.1_RNA|MAP9_ENST00000379248.2_Silent_p.L109L|AC097467.2_ENST00000596165.1_RNA|AC097467.2_ENST00000598890.1_RNA|MAP9_ENST00000515654.1_Silent_p.L182L|AC097467.2_ENST00000600928.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	182					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TTTTCTTTTTCAACATACTCC	0.388													C|||	1848	0.36901	0.1649	0.3963	5008	,	,		18797	0.6419		0.3549	False		,,,				2504	0.3589				p.L182L		Atlas-SNP	.											.	MAP9	79	.	0			c.G546A						PASS	.	C		805,3601	320.4+/-296.6	58,689,1456	157.0	144.0	148.0		546	-1.9	0.1	4	dbSNP_107	148	2785,5815	439.7+/-359.3	457,1871,1972	no	coding-synonymous	MAP9	NM_001039580.1		515,2560,3428	TT,TC,CC		32.3837,18.2705,27.6026		182/648	156289900	3590,9416	2203	4300	6503	SO:0001819	synonymous_variant	79884	exon5			CTTTTTCAACATA	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.546G>A	4.37:g.156289900C>T		Somatic	470	0	0		WXS	Illumina HiSeq	Phase_I	475	215	0.452632	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Silent	SNP	ENST00000311277.4	37	CCDS35493.1																																																																																			C|0.687;T|0.313	0.313	strong		0.388	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
PCSK4	54760	hgsc.bcm.edu	37	19	1487059	1487059	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1487059G>T	ENST00000300954.5	-	8	922	c.861C>A	c.(859-861)cgC>cgA	p.R287R	PCSK4_ENST00000587784.1_5'Flank|CTB-25B13.6_ENST00000585643.1_RNA	NM_017573.3	NP_060043.2			proprotein convertase subtilisin/kexin type 4											cervix(2)|endometrium(2)|kidney(1)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCCCGCCGCGGCCCTGGG	0.697																																					p.R287R		Atlas-SNP	.											.	PCSK4	44	.	0			c.C861A						PASS	.						28.0	29.0	29.0					19																	1487059		2199	4296	6495	SO:0001819	synonymous_variant	54760	exon8			CCCGCCGCGGCCC	AK057235	CCDS12069.2	19p13.3	2008-02-05			ENSG00000115257	ENSG00000115257			8746	protein-coding gene	gene with protein product		600487				7782070	Standard	XM_005259586		Approved	PC4, SPC5, DKFZp434B217, MGC34749	uc002ltb.1	Q6UW60	OTTHUMG00000128541	ENST00000300954.5:c.861C>A	19.37:g.1487059G>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	21	15	0.714286	NM_017573		Silent	SNP	ENST00000300954.5	37	CCDS12069.2																																																																																			.	.	none		0.697	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573	
C1orf127	148345	hgsc.bcm.edu	37	1	11008497	11008497	+	Silent	SNP	G	G	C	rs1281017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	127	0	0		WXS	Illumina HiSeq	Phase_I	179	89	0.497207	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	
CCDC38	120935	hgsc.bcm.edu	37	12	96266039	96266039	+	Missense_Mutation	SNP	C	C	T	rs75483222	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:96266039C>T	ENST00000344280.3	-	14	2035	c.1478G>A	c.(1477-1479)cGg>cAg	p.R493Q	SNRPF_ENST00000552085.1_Intron|SNRPF_ENST00000553192.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	493										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTACTTTTGCCGCCATTCTTT	0.393													C|||	10	0.00199681	0.0076	0.0	5008	,	,		18605	0.0		0.0	False		,,,				2504	0.0				p.R493Q		Atlas-SNP	.											CCDC38,NS,carcinoma,-1,1	CCDC38	45	1	0			c.G1478A						scavenged	.	C	GLN/ARG	32,4374	37.6+/-69.7	0,32,2171	223.0	202.0	209.0		1478	5.6	1.0	12	dbSNP_131	209	0,8600		0,0,4300	yes	missense	CCDC38	NM_182496.2	43	0,32,6471	TT,TC,CC		0.0,0.7263,0.246	probably-damaging	493/564	96266039	32,12974	2203	4300	6503	SO:0001583	missense	120935	exon14			TTTTGCCGCCATT	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.1478G>A	12.37:g.96266039C>T	ENSP00000345470:p.Arg493Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	184	6	0.0326087	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	28.7	4.939045	0.92526	0.007263	0.0	ENSG00000165972	ENST00000344280	T	0.63255	-0.03	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.76062	0.3935	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.80686	-0.1272	10	0.72032	D	0.01	-14.7893	18.8133	0.92068	0.0:1.0:0.0:0.0	.	493	Q502W7	CCD38_HUMAN	Q	493	ENSP00000345470:R493Q	ENSP00000345470:R493Q	R	-	2	0	CCDC38	94790170	0.998000	0.40836	1.000000	0.80357	0.882000	0.50991	4.039000	0.57325	2.812000	0.96745	0.555000	0.69702	CGG	C|0.997;T|0.003	0.003	strong		0.393	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
MAN2A1	4124	hgsc.bcm.edu	37	5	109110537	109110537	+	Silent	SNP	T	T	A	rs6894260	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:109110537T>A	ENST00000261483.4	+	8	2297	c.1245T>A	c.(1243-1245)cgT>cgA	p.R415R		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	415					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AGCTTTTTCGTACCAAAGTTC	0.363													T|||	1683	0.336062	0.5552	0.3314	5008	,	,		14466	0.2609		0.3489	False		,,,				2504	0.1074				p.R415R		Atlas-SNP	.											MAN2A1,extremity,malignant_melanoma,+2,1	MAN2A1	136	1	0			c.T1245A						PASS	.	T		2462,1942	621.9+/-393.8	701,1060,441	77.0	76.0	76.0		1245	-3.9	0.5	5	dbSNP_116	76	2914,5686	454.3+/-363.5	522,1870,1908	no	coding-synonymous	MAN2A1	NM_002372.2		1223,2930,2349	AA,AT,TT		33.8837,44.0963,41.3411		415/1145	109110537	5376,7628	2202	4300	6502	SO:0001819	synonymous_variant	4124	exon8			TTTTCGTACCAAA		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.1245T>A	5.37:g.109110537T>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_002372	Q16767	Silent	SNP	ENST00000261483.4	37	CCDS34209.1																																																																																			A|0.390;N|0.000	0.390	strong		0.363	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
ZNF746	155061	hgsc.bcm.edu	37	7	149191460	149191460	+	Silent	SNP	G	G	A	rs112293204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:149191460G>A	ENST00000340622.3	-	2	439	c.159C>T	c.(157-159)gcC>gcT	p.A53A	ZNF746_ENST00000458143.2_Silent_p.A53A|ZNF746_ENST00000461958.2_Silent_p.A53A			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	53					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)			CGAACTCCACGGCTGTCTTCT	0.622													.|||	1742	0.347843	0.2648	0.3329	5008	,	,		18600	0.5079		0.2734	False		,,,				2504	0.3824				p.A53A		Atlas-SNP	.											.	ZNF746	68	.	0			c.C159T						PASS	.	G	,	1095,3311		118,859,1226	63.0	67.0	66.0		159,159	-2.7	0.0	7	dbSNP_132	66	2519,6077		385,1749,2164	no	coding-synonymous,coding-synonymous	ZNF746	NM_001163474.1,NM_152557.4	,	503,2608,3390	AA,AG,GG		29.3043,24.8525,27.7957	,	53/646,53/645	149191460	3614,9388	2203	4298	6501	SO:0001819	synonymous_variant	155061	exon2			CTCCACGGCTGTC	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.159C>T	7.37:g.149191460G>A		Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	270	141	0.522222	NM_001163474	A8K6Z9|Q6ZRF9	Silent	SNP	ENST00000340622.3	37	CCDS5897.1																																																																																			G|0.714;A|0.286	0.286	strong		0.622	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
SMPD2	6610	hgsc.bcm.edu	37	6	109762332	109762332	+	Missense_Mutation	SNP	C	C	T	rs1048197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:109762332C>T	ENST00000258052.3	+	1	367	c.8C>T	c.(7-9)cCc>cTc	p.P3L	PPIL6_ENST00000424445.2_5'UTR|PPIL6_ENST00000521072.2_5'UTR|PPIL6_ENST00000440797.2_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	80	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	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		
OR51I2	390064	hgsc.bcm.edu	37	11	5475505	5475505	+	Missense_Mutation	SNP	C	C	T	rs75620804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5475505C>T	ENST00000341449.2	+	1	868	c.787C>T	c.(787-789)Cgc>Tgc	p.R263C	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	263			R -> H (in dbSNP:rs11037502).		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)		CACAGTGCACCGCTTTGGGAA	0.483													C|||	38	0.00758786	0.0	0.0101	5008	,	,		22942	0.001		0.0239	False		,,,				2504	0.0061				p.R263C		Atlas-SNP	.											.	OR51I2	76	.	0			c.C787T						PASS	.	C	CYS/ARG	18,4384	25.3+/-52.1	0,18,2183	221.0	187.0	198.0		787	4.7	1.0	11	dbSNP_131	198	242,8352	96.6+/-158.3	2,238,4057	yes	missense	OR51I2	NM_001004754.2	180	2,256,6240	TT,TC,CC		2.8159,0.4089,2.0006	probably-damaging	263/313	5475505	260,12736	2201	4297	6498	SO:0001583	missense	390064	exon1			GTGCACCGCTTTG	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.787C>T	11.37:g.5475505C>T	ENSP00000341987:p.Arg263Cys	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	229	113	0.49345	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	30	0.013736263736263736	0	0.0	7	0.019337016574585635	1	0.0017482517482517483	22	0.029023746701846966	C	11.07	1.529354	0.27387	0.004089	0.028159	ENSG00000187918	ENST00000341449	T	0.37411	1.2	5.58	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.096182	0.46758	N	0.000280	T	0.38054	0.1026	M	0.91354	3.2	0.40176	D	0.977235	D	0.89917	1.0	D	0.87578	0.998	T	0.61520	-0.7046	10	0.72032	D	0.01	.	5.4856	0.16747	0.1603:0.6806:0.0:0.1591	.	263	Q9H344	O51I2_HUMAN	C	263	ENSP00000341987:R263C	ENSP00000341987:R263C	R	+	1	0	OR51I2	5432081	0.002000	0.14202	0.985000	0.45067	0.048000	0.14542	0.094000	0.15107	1.610000	0.50200	-0.126000	0.14955	CGC	C|0.983;T|0.017	0.017	strong		0.483	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
NAB1	4664	hgsc.bcm.edu	37	2	191550283	191550283	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:191550283A>T	ENST00000337386.5	+	8	1638	c.1177A>T	c.(1177-1179)Agg>Tgg	p.R393W	NAB1_ENST00000409641.1_Missense_Mutation_p.R392W|AC006460.2_ENST00000411949.1_RNA|NAB1_ENST00000545490.1_Missense_Mutation_p.R133W|AC006460.2_ENST00000421437.1_RNA|AC006460.2_ENST00000428032.1_RNA|NAB1_ENST00000357215.5_Missense_Mutation_p.R364W|NAB1_ENST00000409581.1_Missense_Mutation_p.R393W	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	393					endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			TGCCGAGAGGAGGTTGTCTGC	0.478																																					p.R393W		Atlas-SNP	.											NAB1,colon,carcinoma,-1,1	NAB1	31	1	0			c.A1177T						scavenged	.						74.0	69.0	70.0					2																	191550283		2203	4300	6503	SO:0001583	missense	4664	exon8			GAGAGGAGGTTGT		CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"""EGR1 binding protein 1"""	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.1177A>T	2.37:g.191550283A>T	ENSP00000336894:p.Arg393Trp	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	218	3	0.0137615	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	37	CCDS2307.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.50|13.50	2.255892|2.255892	0.39896|0.39896	.|.	.|.	ENSG00000138386|ENSG00000138386	ENST00000434473|ENST00000409581;ENST00000337386;ENST00000357215;ENST00000409641;ENST00000545490	.|.	.|.	.|.	5.28|5.28	1.4|1.4	0.22301|0.22301	.|Nab1, C-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.51534|0.51534	0.1680|0.1680	N|N	0.24115|0.24115	0.695|0.695	0.45295|0.45295	D|D	0.998293|0.998293	.|D;D;D	.|0.69078	.|0.99;0.997;0.997	.|P;D;D	.|0.65573	.|0.852;0.936;0.936	T|T	0.50415|0.50415	-0.8831|-0.8831	5|9	.|0.62326	.|D	.|0.03	-20.3431|-20.3431	8.1945|8.1945	0.31387|0.31387	0.3457:0.5327:0.0:0.1216|0.3457:0.5327:0.0:0.1216	.|.	.|364;392;393	.|F8W8J7;B8ZZS2;Q13506	.|.;.;NAB1_HUMAN	V|W	145|393;393;364;392;133	.|.	.|ENSP00000336894:R393W	E|R	+|+	2|1	0|2	NAB1|NAB1	191258528|191258528	0.983000|0.983000	0.35010|0.35010	0.798000|0.798000	0.32154|0.32154	0.037000|0.037000	0.13140|0.13140	1.748000|1.748000	0.38308|0.38308	0.419000|0.419000	0.25927|0.25927	0.533000|0.533000	0.62120|0.62120	GAG|AGG	.	.	none		0.478	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966	
UBC	7316	hgsc.bcm.edu	37	12	125397435	125397435	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:125397435G>A	ENST00000536769.1	-	1	2459	c.883C>T	c.(883-885)Ctg>Ttg	p.L295L	UBC_ENST00000538617.1_Intron|UBC_ENST00000536661.1_5'Flank|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000546120.1_Silent_p.L219L|UBC_ENST00000339647.5_Silent_p.L295L			P0CG48	UBC_HUMAN	ubiquitin C	295	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)			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)		ACCAGGTGCAGGGTAGACTCT	0.547																																					p.L295L		Atlas-SNP	.											UBC,NS,carcinoma,0,1	UBC	79	1	0			c.C883T						scavenged	.						71.0	65.0	67.0					12																	125397435		2202	4284	6486	SO:0001819	synonymous_variant	7316	exon2			GGTGCAGGGTAGA		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		ENST00000536769.1:c.883C>T	12.37:g.125397435G>A		Somatic	314	1	0.00318471		WXS	Illumina HiSeq	Phase_I	294	6	0.0204082	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	37	CCDS9260.1																																																																																			.	.	none		0.547	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009	
MUC16	94025	hgsc.bcm.edu	37	19	8999453	8999453	+	Silent	SNP	C	C	T	rs11085765	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8999453C>T	ENST00000397910.4	-	56	40925	c.40722G>A	c.(40720-40722)ctG>ctA	p.L13574L	MUC16_ENST00000380951.5_Silent_p.L215L	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13576	SEA 10. {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						TGCTGTGGGTCAGCTGGCTCA	0.567													C|||	2997	0.598442	0.3812	0.7219	5008	,	,		19925	0.6062		0.7177	False		,,,				2504	0.6738				p.L13574L		Atlas-SNP	.											.	MUC16	4315	.	0			c.G40722A						PASS	.	C		1771,2329		291,1189,570	221.0	186.0	197.0		40722	2.4	0.6	19	dbSNP_120	197	5520,2878		1639,2242,318	no	coding-synonymous	MUC16	NM_024690.2		1930,3431,888	TT,TC,CC		34.2701,43.1951,41.6627		13574/14508	8999453	7291,5207	2050	4199	6249	SO:0001819	synonymous_variant	94025	exon56			GTGGGTCAGCTGG	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.40722G>A	19.37:g.8999453C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	255	181	0.709804	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.353;T|0.647	0.647	strong		0.567	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10574813	10574813	+	Missense_Mutation	SNP	G	G	A	rs9931441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10574813G>A	ENST00000396560.2	+	11	1854	c.1627G>A	c.(1627-1629)Gca>Aca	p.A543T	ATF7IP2_ENST00000543967.1_Missense_Mutation_p.A87T|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.M520I|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.M520I|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.A543T	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	543			A -> T (in dbSNP:rs9931441).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						GGCACAAAATGCAGTCCAGGT	0.413													G|||	507	0.101238	0.1921	0.0216	5008	,	,		16525	0.126		0.0219	False		,,,				2504	0.091				p.A543T		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.G1627A						PASS	.	G	THR/ALA	774,3620	313.8+/-293.3	71,632,1494	96.0	97.0	97.0		1627	0.4	0.1	16	dbSNP_119	97	205,8395	88.1+/-150.5	4,197,4099	yes	missense	ATF7IP2	NM_024997.2	58	75,829,5593	AA,AG,GG		2.3837,17.6149,7.5342	possibly-damaging	543/683	10574813	979,12015	2197	4300	6497	SO:0001583	missense	80063	exon11			CAAAATGCAGTCC	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.1627G>A	16.37:g.10574813G>A	ENSP00000379808:p.Ala543Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	186|186	0.08516483516483517|0.08516483516483517	100|100	0.2032520325203252|0.2032520325203252	12|12	0.03314917127071823|0.03314917127071823	66|66	0.11538461538461539|0.11538461538461539	8|8	0.010554089709762533|0.010554089709762533	G|G	2.931|2.931	-0.221130|-0.221130	0.06061|0.06061	0.176149|0.176149	0.023837|0.023837	ENSG00000166669|ENSG00000166669	ENST00000543967;ENST00000396560;ENST00000356427|ENST00000396559;ENST00000324570	T;T;T|.	0.23147|.	1.92;1.93;1.93|.	4.7|4.7	0.447|0.447	0.16608|0.16608	.|.	1.168940|.	0.06352|.	N|.	0.710075|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	P|P	0.0|0.0	P|B	0.47910|0.10296	0.902|0.003	P|B	0.46659|0.09377	0.523|0.004	T|T	0.13683|0.13683	-1.0500|-1.0500	9|7	0.49607|0.87932	T|D	0.09|0	-1.4743|-1.4743	2.7285|2.7285	0.05220|0.05220	0.2951:0.0:0.4373:0.2676|0.2951:0.0:0.4373:0.2676	rs9931441;rs52793507;rs9931441|rs9931441;rs52793507;rs9931441	543|520	Q5U623|Q5U623-2	MCAF2_HUMAN|.	T|I	87;543;543|520	ENSP00000446119:A87T;ENSP00000379808:A543T;ENSP00000348799:A543T|.	ENSP00000348799:A543T|ENSP00000322811:M520I	A|M	+|+	1|3	0|0	ATF7IP2|ATF7IP2	10482314|10482314	0.990000|0.990000	0.36364|0.36364	0.071000|0.071000	0.20095|0.20095	0.024000|0.024000	0.10985|0.10985	0.595000|0.595000	0.24029|0.24029	0.348000|0.348000	0.23949|0.23949	0.563000|0.563000	0.77884|0.77884	GCA|ATG	G|0.914;A|0.086	0.086	strong		0.413	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
MAST2	23139	hgsc.bcm.edu	37	1	46500251	46500251	+	Missense_Mutation	SNP	G	G	A	rs33931638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46500251G>A	ENST00000361297.2	+	29	4193	c.3910G>A	c.(3910-3912)Gtg>Atg	p.V1304M	MAST2_ENST00000372009.2_Intron	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)					CAGCTCCAGCGTGCCCAGTTC	0.602													g|||	122	0.024361	0.0038	0.0461	5008	,	,		16069	0.001		0.0795	False		,,,				2504	0.0041				p.V1304M		Atlas-SNP	.											.	MAST2	136	.	0			c.G3910A						PASS	.		MET/VAL	68,4184		0,68,2058	48.0	56.0	53.0		3910	4.2	1.0	1	dbSNP_126	53	645,7829		19,607,3611	yes	missense	MAST2	NM_015112.2	21	19,675,5669	AA,AG,GG		7.6115,1.5992,5.6027	probably-damaging	1304/1799	46500251	713,12013	2126	4237	6363	SO:0001583	missense	23139	exon29			TCCAGCGTGCCCA	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.3910G>A	1.37:g.46500251G>A	ENSP00000354671:p.Val1304Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	211	99	0.469194	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	74	0.03388278388278388	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	51	0.06728232189973615	g	18.85	3.712308	0.68730	0.015992	0.076115	ENSG00000086015	ENST00000361297	T	0.34472	1.36	4.22	4.22	0.49857	.	0.222787	0.37012	N	0.002287	T	0.02767	0.0083	L	0.55481	1.735	0.80722	D	1	P	0.52170	0.951	P	0.46362	0.514	T	0.01202	-1.1420	10	0.46703	T	0.11	-1.3935	17.1505	0.86776	0.0:0.0:1.0:0.0	rs33931638	1304	Q6P0Q8	MAST2_HUMAN	M	1304	ENSP00000354671:V1304M	ENSP00000354671:V1304M	V	+	1	0	MAST2	46272838	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.535000	0.67173	2.339000	0.79563	0.558000	0.71614	GTG	G|0.951;A|0.049	0.049	strong		0.602	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
IL34	146433	hgsc.bcm.edu	37	16	70694000	70694000	+	Nonsense_Mutation	SNP	C	C	A	rs4985556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70694000C>A	ENST00000288098.2	+	6	1022	c.639C>A	c.(637-639)taC>taA	p.Y213*	IL34_ENST00000566361.1_Nonsense_Mutation_p.Y188*|IL34_ENST00000429149.2_Nonsense_Mutation_p.Y213*|FLJ00418_ENST00000597002.1_5'Flank	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	213					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						CCCAGCTGTACCCTCCGCCCC	0.657													C|||	300	0.0599042	0.0053	0.0375	5008	,	,		13120	0.0665		0.1044	False		,,,				2504	0.0971				p.Y213X		Atlas-SNP	.											.	IL34	26	.	0			c.C639A						PASS	.	C	stop/TYR,stop/TYR,stop/TYR	105,4291	81.4+/-119.9	1,103,2094	74.0	83.0	80.0		636,639,639	0.4	0.1	16	dbSNP_111	80	1018,7582	215.9+/-255.1	60,898,3342	yes	stop-gained,stop-gained,stop-gained	IL34	NM_001172771.1,NM_001172772.1,NM_152456.2	,,	61,1001,5436	AA,AC,CC		11.8372,2.3885,8.6411	,,	212/242,213/243,213/243	70694000	1123,11873	2198	4300	6498	SO:0001587	stop_gained	146433	exon7			GCTGTACCCTCCG	BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368		"""Interleukins and interleukin receptors"""	28529	protein-coding gene	gene with protein product		612081	"""chromosome 16 open reading frame 77"""	C16orf77		18467591	Standard	NM_152456		Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.639C>A	16.37:g.70694000C>A	ENSP00000288098:p.Tyr213*	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	221	110	0.497738	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Nonsense_Mutation	SNP	ENST00000288098.2	37	CCDS10895.1	122	0.055860805860805864	2	0.0040650406504065045	14	0.03867403314917127	26	0.045454545454545456	80	0.10554089709762533	C	22.0	4.233060	0.79688	0.023885	0.118372	ENSG00000157368	ENST00000429149;ENST00000288098	.	.	.	4.8	0.394	0.16299	.	1.242800	0.05737	N	0.600667	.	.	.	.	.	.	0.42010	D	0.99093	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.5745	4.6997	0.12822	0.0:0.5589:0.158:0.2831	rs4985556;rs58625464;rs4985556	.	.	.	X	213	.	ENSP00000288098:Y213X	Y	+	3	2	IL34	69251501	0.001000	0.12720	0.072000	0.20136	0.013000	0.08279	0.237000	0.17985	0.082000	0.17018	-0.463000	0.05309	TAC	C|0.927;A|0.073	0.073	strong		0.657	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456	
ERICH1	157697	hgsc.bcm.edu	37	8	623593	623593	+	Silent	SNP	G	G	A	rs55783038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:623593G>A	ENST00000262109.7	-	4	836	c.759C>T	c.(757-759)gcC>gcT	p.A253A	ERICH1_ENST00000522706.1_Silent_p.A159A|ERICH1_ENST00000518277.1_5'Flank	NM_207332.1	NP_997215.1	Q86X53	ERIC1_HUMAN	glutamate-rich 1	253	Glu-rich.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)	20		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		CTTCCTCACTGGCGTCCGCAC	0.632													G|||	989	0.197484	0.0371	0.2435	5008	,	,		17962	0.0675		0.4066	False		,,,				2504	0.3006				p.A253A		Atlas-SNP	.											.	ERICH1	50	.	0			c.C759T						PASS	.	G		398,4008	197.7+/-221.8	17,364,1822	109.0	102.0	104.0		759	0.1	0.0	8	dbSNP_129	104	3438,5162	505.0+/-376.3	677,2084,1539	no	coding-synonymous	ERICH1	NM_207332.1		694,2448,3361	AA,AG,GG		39.9767,9.0331,29.4941		253/444	623593	3836,9170	2203	4300	6503	SO:0001819	synonymous_variant	157697	exon4			CTCACTGGCGTCC		CCDS5955.1	8p23.3	2005-09-01			ENSG00000104714	ENSG00000104714			27234	protein-coding gene	gene with protein product							Standard	NM_207332		Approved		uc003wph.3	Q86X53	OTTHUMG00000129163	ENST00000262109.7:c.759C>T	8.37:g.623593G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_207332	A8K2J9|Q9P063	Silent	SNP	ENST00000262109.7	37	CCDS5955.1	462	0.21153846153846154	12	0.024390243902439025	116	0.32044198895027626	35	0.06118881118881119	299	0.3944591029023747	G	3.781	-0.045708	0.07452	0.090331	0.399767	ENSG00000104714	ENST00000522893	.	.	.	1.05	0.0893	0.14458	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44620	-0.9316	3	.	.	.	.	1.7477	0.02965	0.2453:0.0:0.4267:0.3279	rs55783038;rs61743224	.	.	.	L	22	.	.	P	-	2	0	ERICH1	613593	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.004000	0.13106	0.005000	0.14708	0.543000	0.68304	CCA	G|0.717;A|0.283	0.283	strong		0.632	ERICH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251228.3	NM_207332	
DPY19L2	283417	hgsc.bcm.edu	37	12	63954304	63954304	+	Silent	SNP	T	T	C	rs1054891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:63954304T>C	ENST00000324472.4	-	22	2448	c.2265A>G	c.(2263-2265)ttA>ttG	p.L755L	DPY19L2_ENST00000413230.2_Silent_p.L202L	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	755					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		AGTTAACCTTTAATACTCTGT	0.418													N|||	2174	0.434105	0.7057	0.4568	5008	,	,		16369	0.2857		0.4245	False		,,,				2504	0.2137				p.L755L		Atlas-SNP	.											DPY19L2,colon,carcinoma,0,1	DPY19L2	97	1	0			c.A2265G						PASS	.	C		2776,1630	500.0+/-364.6	884,1008,311	85.0	80.0	82.0		2265	-1.3	0.3	12	dbSNP_86	82	3491,5109	633.6+/-398.7	694,2103,1503	no	coding-synonymous	DPY19L2	NM_173812.4		1578,3111,1814	CC,CT,TT		40.593,36.995,48.1855		755/759	63954304	6267,6739	2203	4300	6503	SO:0001819	synonymous_variant	283417	exon22			AACCTTTAATACT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.2265A>G	12.37:g.63954304T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	158	69	0.436709	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	37	CCDS31851.1																																																																																			T|0.532;C|0.468	0.468	strong		0.418	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
PMS2	5395	hgsc.bcm.edu	37	7	6043386	6043386	+	Silent	SNP	G	G	A	rs12532895	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:6043386G>A	ENST00000265849.7	-	4	393	c.288C>T	c.(286-288)gcC>gcT	p.A96A	PMS2_ENST00000382321.4_Silent_p.A96A|Y_RNA_ENST00000365120.1_RNA|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Silent_p.A96A|PMS2_ENST00000441476.2_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	96					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		GAGTTAGGTCGGCAAACTCTT	0.403			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				g|||	569	0.113618	0.0113	0.0504	5008	,	,		16647	0.3284		0.0338	False		,,,				2504	0.1575				p.A96A		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.C288T						PASS	.	G		54,2794		0,54,1370	55.0	63.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	288	-1.1	1.0	7	dbSNP_120	60	136,4768		0,136,2316	no	coding-synonymous	PMS2	NM_000535.5		0,190,3686	AA,AG,GG		2.7732,1.8961,2.451		96/863	6043386	190,7562	1424	2452	3876	SO:0001819	synonymous_variant	5395	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TAGGTCGGCAAAC		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.288C>T	7.37:g.6043386G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																			G|0.942;A|0.058	0.058	strong		0.403	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
PRSS55	203074	hgsc.bcm.edu	37	8	10390452	10390452	+	Missense_Mutation	SNP	C	C	T	rs4406360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10390452C>T	ENST00000328655.3	+	4	675	c.635C>T	c.(634-636)gCg>gTg	p.A212V	PRSS55_ENST00000522210.1_Missense_Mutation_p.A212V|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	212	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> V (in dbSNP:rs4406360). {ECO:0000269|PubMed:12975309}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						CTGATGAAAGCGCCAATGGTC	0.478													C|||	1709	0.341254	0.2224	0.3329	5008	,	,		20467	0.4266		0.334	False		,,,				2504	0.4274				p.A212V		Atlas-SNP	.											.	PRSS55	67	.	0			c.C635T						PASS	.	C	VAL/ALA,VAL/ALA	1085,3321	393.3+/-328.8	113,859,1231	115.0	107.0	110.0		635,635	-4.1	0.6	8	dbSNP_111	110	2962,5638	460.7+/-365.2	476,2010,1814	yes	missense,missense	PRSS55	NM_001197020.1,NM_198464.3	64,64	589,2869,3045	TT,TC,CC		34.4419,24.6255,31.1164	benign,benign	212/277,212/353	10390452	4047,8959	2203	4300	6503	SO:0001583	missense	203074	exon4			TGAAAGCGCCAAT	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.635C>T	8.37:g.10390452C>T	ENSP00000333003:p.Ala212Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_001197020	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	749	0.34294871794871795	126	0.25609756097560976	128	0.35359116022099446	232	0.40559440559440557	263	0.3469656992084433	C	7.360	0.624582	0.14193	0.246255	0.344419	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.92446	-3.04;-3.04	5.27	-4.08	0.03963	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.552989	0.13570	N	0.378158	T	0.00012	0.0000	N	0.05280	-0.08	0.80722	P	0.0	B	0.24651	0.108	B	0.16289	0.015	T	0.14200	-1.0481	9	0.20519	T	0.43	.	7.1514	0.25612	0.0:0.4539:0.1334:0.4127	rs4406360;rs61420274;rs4406360	212	Q6UWB4	PRS55_HUMAN	V	212	ENSP00000333003:A212V;ENSP00000430459:A212V	ENSP00000333003:A212V	A	+	2	0	PRSS55	10427862	0.002000	0.14202	0.642000	0.29436	0.005000	0.04900	-0.579000	0.05834	-0.461000	0.06993	-0.218000	0.12543	GCG	C|0.668;T|0.332	0.332	strong		0.478	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
SFI1	9814	hgsc.bcm.edu	37	22	31998612	31998612	+	Missense_Mutation	SNP	G	G	A	rs2006771	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31998612G>A	ENST00000400288.2	+	17	1751	c.1646G>A	c.(1645-1647)cGa>cAa	p.R549Q	SFI1_ENST00000414585.1_Missense_Mutation_p.R396Q|SFI1_ENST00000443326.1_Missense_Mutation_p.R467Q|SFI1_ENST00000400289.1_Missense_Mutation_p.R467Q|SFI1_ENST00000432498.1_Missense_Mutation_p.R518Q|SFI1_ENST00000443011.1_Missense_Mutation_p.R396Q|SFI1_ENST00000540643.1_Missense_Mutation_p.R494Q	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	182	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	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	
KCNK16	83795	hgsc.bcm.edu	37	6	39290200	39290200	+	Silent	SNP	C	C	T	rs3734619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:39290200C>T	ENST00000373229.5	-	1	130	c.117G>A	c.(115-117)gcG>gcA	p.A39A	KCNK16_ENST00000373227.4_Silent_p.A39A|KCNK16_ENST00000425054.2_Silent_p.A39A|KCNK16_ENST00000437525.2_Silent_p.A39A|KCNK16_ENST00000507712.1_5'UTR	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	39					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)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						ACTGAGCCTCCGCCTGCCTCT	0.617													C|||	1934	0.386182	0.5386	0.4049	5008	,	,		19138	0.3681		0.3628	False		,,,				2504	0.2096				p.A39A		Atlas-SNP	.											KCNK16_ENST00000425054,NS,carcinoma,-1,2	KCNK16	59	2	0			c.G117A						PASS	.	C	,,,	2177,2229	578.1+/-384.6	552,1073,578	46.0	40.0	42.0		117,117,117,117	-11.8	0.1	6	dbSNP_107	42	3304,5296	486.2+/-371.8	638,2028,1634	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNK16	NM_001135105.1,NM_001135106.1,NM_001135107.1,NM_032115.3	,,,	1190,3101,2212	TT,TC,CC		38.4186,49.4099,42.1421	,,,	39/323,39/295,39/263,39/310	39290200	5481,7525	2203	4300	6503	SO:0001819	synonymous_variant	83795	exon1			AGCCTCCGCCTGC	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.117G>A	6.37:g.39290200C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Silent	SNP	ENST00000373229.5	37	CCDS4843.1																																																																																			C|0.591;T|0.409	0.409	strong		0.617	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	T	C	rs200214744|rs565505867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39274291T>C	ENST00000391413.2	-	1	315	c.277A>G	c.(277-279)Atg>Gtg	p.M93V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	93	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.M93V(4)		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)			TGGCAGCACATAGACTGGCAG	0.662																																					p.M93V		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,12	KRTAP4-11	94	12	4	Substitution - Missense(4)	endometrium(3)|kidney(1)	c.A277G						scavenged	.						6.0	10.0	8.0					17																	39274291		651	1556	2207	SO:0001583	missense	653240	exon1			AGCACATAGACTG	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.277A>G	17.37:g.39274291T>C	ENSP00000375232:p.Met93Val	Somatic	75	7	0.0933333		WXS	Illumina HiSeq	Phase_I	94	9	0.0957447	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.073	-1.199029	0.01581	.	.	ENSG00000212721	ENST00000391413	T	0.00580	6.43	4.25	-4.9	0.03094	.	.	.	.	.	T	0.00109	0.0003	N	0.00040	-2.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	9	0.02654	T	1	.	0.4739	0.00536	0.3479:0.2455:0.1203:0.2863	.	93	Q9BYQ6	KR411_HUMAN	V	93	ENSP00000375232:M93V	ENSP00000375232:M93V	M	-	1	0	KRTAP4-11	36527817	.	.	0.012000	0.15200	0.010000	0.07245	.	.	-1.319000	0.02286	-1.132000	0.01976	ATG	.	.	weak		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
PIK3C2G	5288	hgsc.bcm.edu	37	12	18719972	18719972	+	Missense_Mutation	SNP	T	T	G	rs12099555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:18719972T>G	ENST00000266497.5	+	27	3907	c.3869T>G	c.(3868-3870)gTa>gGa	p.V1290G	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.V1331G|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.V1290G			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1290	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		V -> G (in dbSNP:rs12099555).		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)				ATATTAAATGTATCACATGAA	0.289													G|||	438	0.0874601	0.2943	0.036	5008	,	,		16621	0.0		0.0229	False		,,,				2504	0.001				p.V1290G		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T3869G						PASS	.	G	GLY/VAL	924,2712		118,688,1012	76.0	74.0	75.0		3869	4.2	0.7	12	dbSNP_120	75	143,7987		4,135,3926	yes	missense	PIK3C2G	NM_004570.4	109	122,823,4938	GG,GT,TT		1.7589,25.4125,9.0685	benign	1290/1446	18719972	1067,10699	1818	4065	5883	SO:0001583	missense	5288	exon28			TAAATGTATCACA	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.3869T>G	12.37:g.18719972T>G	ENSP00000266497:p.Val1290Gly	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	164	0.07509157509157509	135	0.27439024390243905	12	0.03314917127071823	0	0.0	17	0.022427440633245383	G	0.026	-1.369431	0.01225	0.254125	0.017589	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.39056	1.1;1.1;1.1	4.18	4.18	0.49190	Phox homologous domain (5);	0.274240	0.29424	N	0.012196	T	0.00012	0.0000	N	0.01048	-1.04	0.32557	P	0.531612	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25257	-1.0137	9	0.10111	T	0.7	-12.3348	11.8575	0.52446	0.0:0.0:0.8243:0.1756	rs12099555;rs60425948;rs12099555	1330;1331;1290	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	G	1290;1290;1331	ENSP00000404845:V1290G;ENSP00000266497:V1290G;ENSP00000445381:V1331G	ENSP00000266497:V1290G	V	+	2	0	PIK3C2G	18611239	1.000000	0.71417	0.661000	0.29709	0.096000	0.18686	2.898000	0.48672	1.370000	0.46153	-0.121000	0.15023	GTA	T|0.912;G|0.088	0.088	strong		0.289	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
CCDC82	79780	hgsc.bcm.edu	37	11	96116444	96116444	+	Missense_Mutation	SNP	T	T	C	rs10831519	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:96116444T>C	ENST00000278520.5	-	4	1408	c.980A>G	c.(979-981)cAg>cGg	p.Q327R	CCDC82_ENST00000423339.2_Missense_Mutation_p.Q327R|CCDC82_ENST00000542662.1_Missense_Mutation_p.Q327R			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	327			Q -> R (in dbSNP:rs10831519). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		AAGAGAATTCTGTTTTACTAA	0.284													T|||	1132	0.226038	0.2035	0.2262	5008	,	,		15318	0.3095		0.2217	False		,,,				2504	0.1748				p.Q327R		Atlas-SNP	.											CCDC82,NS,carcinoma,+1,1	CCDC82	63	1	0			c.A980G						PASS	.	T	ARG/GLN	972,3402	359.6+/-314.9	101,770,1316	93.0	87.0	89.0		980	3.0	1.0	11	dbSNP_120	89	1712,6876	305.6+/-307.5	175,1362,2757	yes	missense	CCDC82	NM_024725.3	43	276,2132,4073	CC,CT,TT		19.9348,22.2222,20.7067	benign	327/545	96116444	2684,10278	2187	4294	6481	SO:0001583	missense	79780	exon5			GAATTCTGTTTTA	AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231			26282	protein-coding gene	gene with protein product						12477932	Standard	NM_024725		Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000278520.5:c.980A>G	11.37:g.96116444T>C	ENSP00000278520:p.Gln327Arg	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	139	77	0.553957	NM_024725	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	Missense_Mutation	SNP	ENST00000278520.5	37	CCDS8307.1	536	0.2454212454212454	104	0.21138211382113822	83	0.2292817679558011	189	0.3304195804195804	160	0.21108179419525067	T	8.051	0.766048	0.15983	0.222222	0.199348	ENSG00000149231	ENST00000278520;ENST00000542662;ENST00000423339	T;T;T	0.43294	0.95;0.95;0.95	5.63	2.99	0.34606	.	0.845200	0.10567	N	0.659556	T	0.00012	0.0000	L	0.27053	0.805	0.40637	P	0.018086999999999964	B;B	0.24186	0.099;0.001	B;B	0.22386	0.039;0.004	T	0.40572	-0.9556	9	0.21014	T	0.42	-0.8729	8.4617	0.32931	0.0:0.1849:0.0:0.8151	rs10831519;rs17853200;rs52832292;rs59975070;rs10831519	327;327	Q8N4S0-2;Q8N4S0	.;CCD82_HUMAN	R	327	ENSP00000278520:Q327R;ENSP00000444010:Q327R;ENSP00000397156:Q327R	ENSP00000278520:Q327R	Q	-	2	0	CCDC82	95756092	0.999000	0.42202	0.999000	0.59377	0.989000	0.77384	0.740000	0.26188	0.966000	0.38159	0.472000	0.43445	CAG	T|0.781;C|0.219	0.219	strong		0.284	CCDC82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395542.2	NM_024725	
VENTX	27287	hgsc.bcm.edu	37	10	135053710	135053710	+	Missense_Mutation	SNP	C	C	A	rs74164127	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:135053710C>A	ENST00000325980.9	+	3	1188	c.677C>A	c.(676-678)gCg>gAg	p.A226E		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	226					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)		CAGCCTCTGGCGTCCCACCCC	0.687													C|||	514	0.102636	0.1172	0.1354	5008	,	,		8381	0.0823		0.0586	False		,,,				2504	0.1258				p.A226E		Atlas-SNP	.											VENTX,striated_muscle,rhabdoid_tumour,-1,1	VENTX	24	1	0			c.C677A						PASS	.	C	GLU/ALA	477,3871		26,425,1723	10.0	12.0	11.0		677	-2.2	0.0	10	dbSNP_130	11	524,7962		21,482,3740	no	missense	VENTX	NM_014468.2	107	47,907,5463	AA,AC,CC		6.1749,10.9706,7.7996	benign	226/259	135053710	1001,11833	2174	4243	6417	SO:0001583	missense	27287	exon3			CTCTGGCGTCCCA	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.677C>A	10.37:g.135053710C>A	ENSP00000357556:p.Ala226Glu	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	197	0.0902014652014652	63	0.12804878048780488	46	0.1270718232044199	47	0.08216783216783216	41	0.05408970976253298	C	8.100	0.776378	0.16051	0.109706	0.061749	ENSG00000151650	ENST00000325980	D	0.90620	-2.7	2.3	-2.19	0.07015	.	2.090010	0.03032	U	0.152181	T	0.03477	0.0100	N	0.14661	0.345	0.80722	P	0.0	P	0.42584	0.784	B	0.38106	0.265	T	0.54255	-0.8321	9	0.30854	T	0.27	.	6.4789	0.22051	0.0:0.4188:0.0:0.5812	.	226	O95231	VENTX_HUMAN	E	226	ENSP00000357556:A226E	ENSP00000357556:A226E	A	+	2	0	VENTX	134903700	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.040000	0.13905	-0.591000	0.05859	-0.417000	0.06048	GCG	C|0.917;A|0.083	0.083	strong		0.687	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
CCT3	7203	hgsc.bcm.edu	37	1	156290656	156290656	+	Missense_Mutation	SNP	T	T	C	rs11548200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156290656T>C	ENST00000295688.3	-	7	863	c.583A>G	c.(583-585)Ata>Gta	p.I195V	CCT3_ENST00000472765.2_Missense_Mutation_p.I150V|CCT3_ENST00000368261.3_Missense_Mutation_p.I150V|CCT3_ENST00000368259.2_Missense_Mutation_p.I157V	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	195					'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)					TATTTTTTTATGTCAATCTCT	0.398													T|||	104	0.0207668	0.0015	0.0403	5008	,	,		23838	0.002		0.0537	False		,,,				2504	0.0184				p.I195V		Atlas-SNP	.											.	CCT3	61	.	0			c.A583G						PASS	.	T	VAL/ILE,VAL/ILE	58,4348	56.8+/-93.2	0,58,2145	253.0	243.0	246.0		469,583	5.9	1.0	1	dbSNP_120	246	493,8107	142.0+/-198.3	19,455,3826	yes	missense,missense	CCT3	NM_001008800.2,NM_005998.4	29,29	19,513,5971	CC,CT,TT		5.7326,1.3164,4.2365	possibly-damaging,possibly-damaging	157/508,195/546	156290656	551,12455	2203	4300	6503	SO:0001583	missense	7203	exon7			TTTTTATGTCAAT	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.583A>G	1.37:g.156290656T>C	ENSP00000295688:p.Ile195Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	174	73	0.41954	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	37	CCDS1140.2	65	0.02976190476190476	0	0.0	18	0.049723756906077346	1	0.0017482517482517483	46	0.06068601583113457	T	22.1	4.250744	0.80135	0.013164	0.057326	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765;ENST00000413555;ENST00000496684;ENST00000533194;ENST00000446905	T;T;T;T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04;-1.04;-1.04;0.4	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.80539	0.4642	L	0.49571	1.57	0.58432	D	0.999994	B;D;B	0.63880	0.078;0.993;0.153	B;D;B	0.85130	0.019;0.997;0.111	T	0.81320	-0.0986	10	0.44086	T	0.13	-18.4868	12.7903	0.57530	0.0:0.0:0.0:1.0	rs11548200	157;194;195	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	V	195;157;150;150;219;194;116;181	ENSP00000295688:I195V;ENSP00000357242:I157V;ENSP00000357244:I150V;ENSP00000431543:I150V;ENSP00000413308:I219V;ENSP00000434232:I194V;ENSP00000434481:I116V;ENSP00000388799:I181V	ENSP00000295688:I195V	I	-	1	0	CCT3	154557280	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	7.697000	0.84279	2.274000	0.75844	0.519000	0.50382	ATA	T|0.961;C|0.039	0.039	strong		0.398	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998	
NCKAP5	344148	hgsc.bcm.edu	37	2	133542014	133542014	+	Silent	SNP	T	T	C	rs12616282	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133542014T>C	ENST00000409261.1	-	14	2743	c.2370A>G	c.(2368-2370)gcA>gcG	p.A790A	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Silent_p.A790A|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	790										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						TGCCCATGGGTGCCGAAGACC	0.458													c|||	3548	0.708466	0.8328	0.67	5008	,	,		18099	0.8681		0.507	False		,,,				2504	0.6104				p.A790A		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A2370G						PASS	.	C	,	3005,761		1211,583,89	133.0	134.0	134.0		2370,	-0.4	0.0	2	dbSNP_120	134	4348,3894		1139,2070,912	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	2350,2653,1001	CC,CT,TT		47.2458,20.2071,38.7658	,	790/1910,	133542014	7353,4655	1883	4121	6004	SO:0001819	synonymous_variant	344148	exon14			CATGGGTGCCGAA	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.2370A>G	2.37:g.133542014T>C		Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	185	184	0.994595	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			T|0.335;C|0.665	0.665	strong		0.458	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415200	105415200	+	Silent	SNP	G	G	C	rs10145566	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105415200G>C	ENST00000333244.5	-	7	6707	c.6588C>G	c.(6586-6588)ctC>ctG	p.L2196L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2196						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)			CAGTGGTCTTGAGGTCCCCCT	0.637													.|||	1452	0.289936	0.1483	0.3213	5008	,	,		17263	0.1359		0.4891	False		,,,				2504	0.4131				p.L2196L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C6588G						PASS	.	G		553,3361		51,451,1455	123.0	103.0	110.0		6588	0.3	0.0	14	dbSNP_119	110	3961,4283		1006,1949,1167	no	coding-synonymous	AHNAK2	NM_138420.2		1057,2400,2622	CC,CG,GG		48.0471,14.1288,37.1278		2196/5796	105415200	4514,7644	1957	4122	6079	SO:0001819	synonymous_variant	113146	exon7			GGTCTTGAGGTCC	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.6588C>G	14.37:g.105415200G>C		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.680;C|0.320	0.320	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
RBM19	9904	hgsc.bcm.edu	37	12	114377877	114377877	+	Missense_Mutation	SNP	T	T	C	rs2290789	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:114377877T>C	ENST00000545145.2	-	15	1904	c.1826A>G	c.(1825-1827)cAt>cGt	p.H609R	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.H609R|RBM19_ENST00000392561.3_Missense_Mutation_p.H609R	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	609	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		H -> R (in dbSNP:rs2290789). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCTGCCAAAATGGCCGAAGGT	0.642													C|||	996	0.198882	0.3464	0.0764	5008	,	,		17496	0.1885		0.1133	False		,,,				2504	0.1851				p.H609R		Atlas-SNP	.											.	RBM19	117	.	0			c.A1826G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS	1442,2964	676.6+/-403.3	255,932,1016	63.0	69.0	67.0		1826,1826,1826	0.2	0.0	12	dbSNP_100	67	886,7714	776.2+/-407.7	38,810,3452	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	29,29,29	293,1742,4468	CC,CT,TT		10.3023,32.7281,17.8994	benign,benign,benign	609/961,609/961,609/961	114377877	2328,10678	2203	4300	6503	SO:0001583	missense	9904	exon15			CCAAAATGGCCGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1826A>G	12.37:g.114377877T>C	ENSP00000442053:p.His609Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	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	
ZNF440	126070	hgsc.bcm.edu	37	19	11943713	11943713	+	Silent	SNP	G	G	A	rs56167415	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11943713G>A	ENST00000304060.5	+	4	1886	c.1722G>A	c.(1720-1722)agG>agA	p.R574R		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	574					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TGCATGTAAGGAATGTGGGAA	0.453													g|||	338	0.067492	0.0083	0.1023	5008	,	,		22084	0.0		0.2048	False		,,,				2504	0.0511				p.R574R		Atlas-SNP	.											.	ZNF440	56	.	0			c.G1722A						PASS	.	G		174,4206	102.1+/-140.7	2,170,2018	66.0	65.0	65.0		1722	-1.6	0.0	19	dbSNP_129	65	1845,6735	313.5+/-311.4	184,1477,2629	no	coding-synonymous	ZNF440	NM_152357.2		186,1647,4647	AA,AG,GG		21.5035,3.9726,15.5787		574/596	11943713	2019,10941	2190	4290	6480	SO:0001819	synonymous_variant	126070	exon4			TGTAAGGAATGTG	AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295		"""Zinc fingers, C2H2-type"", ""-"""	20874	protein-coding gene	gene with protein product							Standard	NM_152357		Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.1722G>A	19.37:g.11943713G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_152357	Q8N1R9	Silent	SNP	ENST00000304060.5	37	CCDS42503.1																																																																																			G|0.863;A|0.137	0.137	strong		0.453	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
TIAM1	7074	hgsc.bcm.edu	37	21	32638549	32638549	+	Missense_Mutation	SNP	C	C	A	rs386817934|rs2070417	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:32638549C>A	ENST00000286827.3	-	5	1211	c.740G>T	c.(739-741)gGg>gTg	p.G247V	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.G247V	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	247			G -> R (in dbSNP:rs2070418).|G -> V (in dbSNP:rs2070417).	G -> M (in Ref. 1; AAA98443). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CCCCGGCCCCCCGTTTGCTGT	0.532													C|||	1069	0.213458	0.0159	0.2594	5008	,	,		16243	0.4107		0.1133	False		,,,				2504	0.3476				p.G247V		Atlas-SNP	.											.	TIAM1	522	.	0			c.G740T						PASS	.	C	VAL/GLY	145,4261	86.3+/-125.0	6,133,2064	69.0	73.0	72.0		740	4.4	1.0	21	dbSNP_96	72	711,7889	137.1+/-194.1	38,635,3627	yes	missense	TIAM1	NM_003253.2	109	44,768,5691	AA,AC,CC		8.2674,3.291,6.5816	probably-damaging	247/1592	32638549	856,12150	2203	4300	6503	SO:0001583	missense	7074	exon5			GGCCCCCCGTTTG		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.740G>T	21.37:g.32638549C>A	ENSP00000286827:p.Gly247Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	353	0.16163003663003664	7	0.014227642276422764	80	0.22099447513812154	196	0.34265734265734266	70	0.09234828496042216	C	16.56	3.156271	0.57259	0.03291	0.082674	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.41065	1.03;1.01	5.4	4.45	0.53987	.	0.367039	0.30869	N	0.008718	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	0.999999663474	B;B;B	0.30281	0.275;0.18;0.18	B;B;B	0.30646	0.118;0.055;0.055	T	0.33803	-0.9854	9	0.52906	T	0.07	.	14.725	0.69339	0.0:0.9206:0.0:0.0794	rs2070417;rs59059207;rs2070417	247;247;247	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	V	247;88;247	ENSP00000286827:G247V;ENSP00000441570:G247V	ENSP00000286827:G247V	G	-	2	0	TIAM1	31560420	0.938000	0.31826	1.000000	0.80357	0.994000	0.84299	4.159000	0.58157	2.803000	0.96430	0.585000	0.79938	GGG	C|0.874;A|0.119	0.119	strong		0.532	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
CORT	1325	hgsc.bcm.edu	37	1	10511534	10511534	+	Missense_Mutation	SNP	G	G	T	rs201163116		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10511534G>T	ENST00000377049.3	+	2	705	c.200G>T	c.(199-201)gGa>gTa	p.G67V	CORT_ENST00000320498.4_Missense_Mutation_p.G117V|APITD1_ENST00000602296.1_3'UTR|APITD1-CORT_ENST00000465026.1_3'UTR|APITD1-CORT_ENST00000400900.2_Missense_Mutation_p.G126V|APITD1_ENST00000602787.1_Missense_Mutation_p.G126V|APITD1-CORT_ENST00000470413.2_3'UTR	NM_001302.4	NP_001293.3	O00230	CORT_HUMAN	cortistatin	67					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)	G-protein coupled receptor binding (GO:0001664)|neuropeptide hormone activity (GO:0005184)			breast(1)|endometrium(1)|stomach(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-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)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0487)		CCCCTCATAGGAGAGGAAGCC	0.627																																					p.G126V		Atlas-SNP	.											.	.	.	.	0			c.G377T						PASS	.						26.0	32.0	30.0					1																	10511534		2200	4298	6498	SO:0001583	missense	100526739	exon5			TCATAGGAGAGGA	AF013252	CCDS117.1, CCDS117.2	1p36.22	2013-02-25			ENSG00000241563	ENSG00000241563		"""Endogenous ligands"""	2257	protein-coding gene	gene with protein product	"""prepro-cortistatin"""	602784				9205124	Standard	NM_001302		Approved	MGC32686		O00230	OTTHUMG00000001906	ENST00000377049.3:c.200G>T	1.37:g.10511534G>T	ENSP00000366248:p.Gly67Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	191	82	0.429319	NM_198544	Q5T6G0|Q6UX11	Missense_Mutation	SNP	ENST00000377049.3	37	CCDS117.2	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173907	0.57692	.	.	ENSG00000175279;ENSG00000251503;ENSG00000241563;ENSG00000241563	ENST00000556104;ENST00000400900;ENST00000377049;ENST00000320498	.	.	.	5.39	2.33	0.28932	.	0.777718	0.12758	N	0.441634	T	0.24586	0.0596	L	0.50333	1.59	0.09310	N	0.999994	P;B	0.37781	0.608;0.019	B;B	0.31290	0.127;0.015	T	0.13098	-1.0522	9	0.23302	T	0.38	-15.679	4.4404	0.11572	0.0813:0.2856:0.4862:0.1469	.	67;126	O00230;Q8N2Z9-2	CORT_HUMAN;.	V	126;126;67;117	.	ENSP00000383692:G126V	G	+	2	0	APITD1-CORT;APITD1;CORT	10434121	0.005000	0.15991	0.006000	0.13384	0.188000	0.23474	0.349000	0.20055	0.196000	0.20367	0.591000	0.81541	GGA	G|0.999;T|0.001	0.001	weak		0.627	CORT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005410.3	NM_001302	
ADRA1A	148	hgsc.bcm.edu	37	8	26628028	26628028	+	Missense_Mutation	SNP	A	A	G	rs1048101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:26628028A>G	ENST00000519229.1	-	2	1045	c.1039T>C	c.(1039-1041)Tgc>Cgc	p.C347R	ADRA1A_ENST00000380573.3_Missense_Mutation_p.C347R|ADRA1A_ENST00000354550.4_Missense_Mutation_p.C347R|ADRA1A_ENST00000380582.3_Missense_Mutation_p.C347R|ADRA1A_ENST00000276393.4_Missense_Mutation_p.C347R|ADRA1A_ENST00000380587.1_Intron|ADRA1A_ENST00000380586.1_Missense_Mutation_p.C347R|ADRA1A_ENST00000380581.2_Intron			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	310					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	TGCTTTCTGCAGAGACACTGG	0.547													G|||	3246	0.648163	0.7844	0.4928	5008	,	,		17261	0.8929		0.4334	False		,,,				2504	0.5429				p.C347R		Atlas-SNP	.											.	ADRA1A	337	.	0			c.T1039C	GRCh37	CM064954	ADRA1A	M	rs1048101	PASS	.	G	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	3258,1148	406.6+/-333.9	1199,860,144	152.0	155.0	154.0		1039,1039,1039,1039	5.8	1.0	8	dbSNP_86	154	3831,4769	611.7+/-395.9	833,2165,1302	yes	missense,missense,missense,missense	ADRA1A	NM_000680.2,NM_033302.2,NM_033303.3,NM_033304.2	180,180,180,180	2032,3025,1446	GG,GA,AA		44.5465,26.0554,45.4944	benign,benign,benign,benign	347/467,347/430,347/476,347/456	26628028	7089,5917	2203	4300	6503	SO:0001583	missense	148	exon2			TTCTGCAGAGACA	L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"""GPCR / Class A : Adrenoceptors : alpha"""	277	protein-coding gene	gene with protein product		104221	"""adrenergic, alpha-1A-, receptor"""	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.1039T>C	8.37:g.26628028A>G	ENSP00000430793:p.Cys347Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	90	0.978261	NM_033303	Q9NPY0	Missense_Mutation	SNP	ENST00000519229.1	37		1397	0.6396520146520146	381	0.774390243902439	178	0.49171270718232046	506	0.8846153846153846	332	0.43799472295514513	G	6.452	0.451582	0.12223	0.739446	0.445465	ENSG00000120907	ENST00000380586;ENST00000380582;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573	T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4	5.83	5.83	0.93111	.	0.069666	0.53938	N	0.000059	T	0.00012	0.0000	N	0.00823	-1.155	0.19945	P	0.9999494131	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	0.35674	-0.9779	9	0.05959	T	0.93	.	14.8702	0.70450	0.0692:0.0:0.9308:0.0	rs1048101;rs3188081;rs3729633;rs17425094;rs52806290;rs57898697;rs1048101	347;347;347;347	P35348;P35348-4;P35348-3;B0ZBD3	ADA1A_HUMAN;.;.;.	R	347	ENSP00000369960:C347R;ENSP00000369956:C347R;ENSP00000430793:C347R;ENSP00000346557:C347R;ENSP00000276393:C347R;ENSP00000369947:C347R	ENSP00000276393:C347R	C	-	1	0	ADRA1A	26683945	0.631000	0.27164	0.995000	0.50966	0.875000	0.50365	2.915000	0.48805	1.498000	0.48600	-0.119000	0.15052	TGC	T|0.003;G|0.595	0.595	strong		0.547	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303	
GDF15	9518	hgsc.bcm.edu	37	19	18499238	18499238	+	Silent	SNP	G	G	T	rs1804826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18499238G>T	ENST00000252809.3	+	2	452	c.420G>T	c.(418-420)ccG>ccT	p.P140P	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	140					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						TGACACGACCGCTGCGGCGTC	0.716											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1323	0.264177	0.1611	0.3573	5008	,	,		13438	0.4276		0.2475	False		,,,				2504	0.1861				p.P140P		Atlas-SNP	.											.	GDF15	31	.	0			c.G420T						PASS	.	G		677,3579		70,537,1521	10.0	12.0	12.0		420	-0.5	0.0	19	dbSNP_89	12	1879,6511		245,1389,2561	no	coding-synonymous	GDF15	NM_004864.2		315,1926,4082	TT,TG,GG		22.3957,15.907,20.2119		140/309	18499238	2556,10090	2128	4195	6323	SO:0001819	synonymous_variant	9518	exon2			ACGACCGCTGCGG	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.420G>T	19.37:g.18499238G>T		Somatic	20	0	0	726	WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																			G|0.737;T|0.263	0.263	strong		0.716	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864	
WWP2	11060	hgsc.bcm.edu	37	16	69970329	69970329	+	Silent	SNP	A	A	G	rs1983016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:69970329A>G	ENST00000359154.2	+	19	2192	c.2091A>G	c.(2089-2091)acA>acG	p.T697T	WWP2_ENST00000448661.1_Silent_p.T697T|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000356003.2_Silent_p.T697T|WWP2_ENST00000568684.1_Silent_p.T258T|WWP2_ENST00000542271.1_Silent_p.T581T	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	697	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						TCCGGGTCACAGAGGAGAACA	0.592													g|||	4234	0.845447	0.907	0.7565	5008	,	,		18658	0.9663		0.7515	False		,,,				2504	0.7975				p.T697T		Atlas-SNP	.											WWP2,NS,carcinoma,0,2	WWP2	88	2	0			c.A2091G						PASS	.		,	3794,602	265.0+/-266.4	1633,528,37	78.0	70.0	73.0		2091,774	-11.1	0.0	16	dbSNP_92	73	6405,2195	375.3+/-337.7	2394,1617,289	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	4027,2145,326	GG,GA,AA		25.5233,13.6943,21.522	,	697/871,258/432	69970329	10199,2797	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon19			GGTCACAGAGGAG	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.2091A>G	16.37:g.69970329A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			A|0.193;G|0.807	0.807	strong		0.592	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
IL2RB	3560	hgsc.bcm.edu	37	22	37531436	37531436	+	Silent	SNP	G	G	A	rs228953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37531436G>A	ENST00000216223.5	-	8	948	c.750C>T	c.(748-750)ggC>ggT	p.G250G	AL022314.1_ENST00000516333.1_RNA	NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	250					cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	CCCCGCTGAGGCCCACGAGGA	0.577													G|||	2059	0.411142	0.413	0.428	5008	,	,		13117	0.3929		0.4235	False		,,,				2504	0.4029				p.G250G		Atlas-SNP	.											.	IL2RB	44	.	0			c.C750T						PASS	.	G		1790,2616	527.1+/-372.1	358,1074,771	108.0	107.0	107.0		750	2.9	0.1	22	dbSNP_79	107	3715,4885	530.6+/-381.8	806,2103,1391	no	coding-synonymous	IL2RB	NM_000878.2		1164,3177,2162	AA,AG,GG		43.1977,40.6264,42.3266		250/552	37531436	5505,7501	2203	4300	6503	SO:0001819	synonymous_variant	3560	exon8			GCTGAGGCCCACG	M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"""Interleukins and interleukin receptors"", ""CD molecules"""	6009	protein-coding gene	gene with protein product		146710	"""interleukin 15 receptor, beta"""	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.750C>T	22.37:g.37531436G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	74	0.973684	NM_000878	B2R765	Silent	SNP	ENST00000216223.5	37	CCDS13942.1	919	0.4207875457875458	186	0.3780487804878049	156	0.430939226519337	258	0.45104895104895104	319	0.420844327176781	G	4.119	0.020364	0.08006	0.406264	0.431977	ENSG00000100385	ENST00000447922	.	.	.	3.96	2.94	0.34122	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.199999999996649E-5	.	.	.	.	.	.	T	0.49986	-0.8880	3	.	.	.	-7.8657	6.7992	0.23742	0.1273:0.0:0.8727:0.0	rs228953;rs2228142;rs17845770;rs17858730;rs228953	.	.	.	S	5	.	.	P	-	1	0	IL2RB	35861382	0.000000	0.05858	0.062000	0.19696	0.005000	0.04900	0.230000	0.17852	2.211000	0.71520	0.549000	0.68633	CCT	G|0.585;A|0.415	0.415	strong		0.577	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1		
COL9A3	1299	hgsc.bcm.edu	37	20	61460124	61460124	+	Silent	SNP	G	G	A	rs2249903	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61460124G>A	ENST00000343916.3	+	18	912	c.909G>A	c.(907-909)ccG>ccA	p.P303P		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	303	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					AGGGCATGCCGGGCAAGGACG	0.682													G|||	422	0.0842652	0.0363	0.1167	5008	,	,		19021	0.0308		0.1889	False		,,,				2504	0.0736				p.P303P		Atlas-SNP	.											COL9A3,right_lower_lobe,carcinoma,+1,1	COL9A3	70	1	0			c.G909A						scavenged	.	G		276,4126	150.3+/-184.3	11,254,1936	51.0	47.0	48.0		909	-7.8	1.0	20	dbSNP_100	48	1507,7091	281.8+/-295.3	135,1237,2927	no	coding-synonymous	COL9A3	NM_001853.3		146,1491,4863	AA,AG,GG		17.5273,6.2699,13.7154		303/685	61460124	1783,11217	2201	4299	6500	SO:0001819	synonymous_variant	1299	exon18			CATGCCGGGCAAG	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.909G>A	20.37:g.61460124G>A		Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_001853	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			G|0.833;A|0.167	0.167	strong		0.682	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
STKLD1	169436	hgsc.bcm.edu	37	9	136268038	136268038	+	Silent	SNP	C	C	T	rs3124748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136268038C>T	ENST00000371957.3	+	14	1478	c.1371C>T	c.(1369-1371)aaC>aaT	p.N457N	C9orf96_ENST00000371955.1_Intron	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		457							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AGCTGCAGAACGCTGGGCTGC	0.647													C|||	2221	0.44349	0.3926	0.4928	5008	,	,		18663	0.4643		0.4334	False		,,,				2504	0.4663				p.N457N		Atlas-SNP	.											.	C9orf96	77	.	0			c.C1371T						PASS	.	C		1773,2625		368,1037,794	34.0	31.0	32.0		1371	-1.3	0.1	9	dbSNP_103	32	3808,4786		858,2092,1347	no	coding-synonymous	C9orf96	NM_153710.3		1226,3129,2141	TT,TC,CC		44.31,40.3138,42.9572		457/681	136268038	5581,7411	2199	4297	6496	SO:0001819	synonymous_variant	169436	exon14			GCAGAACGCTGGG																												ENST00000371957.3:c.1371C>T	9.37:g.136268038C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	213	108	0.507042	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	37	CCDS35169.1																																																																																			C|0.588;T|0.412	0.412	strong		0.647	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
OR2T8	343172	hgsc.bcm.edu	37	1	248084631	248084631	+	Silent	SNP	A	A	C	rs28689982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248084631A>C	ENST00000319968.4	+	1	312	c.312A>C	c.(310-312)acA>acC	p.T104T		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(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)			TCCTCCCCACACTGGGTGGTG	0.592													A|||	3299	0.658746	0.6717	0.732	5008	,	,		7269	0.5536		0.7903	False		,,,				2504	0.5624				p.T104T		Atlas-SNP	.											OR2T8,colon,carcinoma,+2,1	OR2T8	67	1	0			c.A312C						scavenged	.						7.0	2.0	4.0					1																	248084631		1581	2935	4516	SO:0001819	synonymous_variant	343172	exon1			CCCCACACTGGGT		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.312A>C	1.37:g.248084631A>C		Somatic	102	11	0.107843		WXS	Illumina HiSeq	Phase_I	115	98	0.852174	NM_001005522		Silent	SNP	ENST00000319968.4	37	CCDS31100.1																																																																																			C|1.000;|0.000	1.000	weak		0.592	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
CCDC94	55702	hgsc.bcm.edu	37	19	4251069	4251069	+	Silent	SNP	T	T	C	rs1045750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	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	
SP2	6668	hgsc.bcm.edu	37	17	46002744	46002744	+	Silent	SNP	G	G	T	rs1130932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:46002744G>T	ENST00000376741.4	+	6	1715	c.1578G>T	c.(1576-1578)gtG>gtT	p.V526V	AC003665.1_ENST00000411573.2_RNA|AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000433001.1_RNA|AC003665.1_ENST00000451140.2_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	526					cardiovascular system development (GO:0072358)|embryonic organ development (GO:0048568)|fibroblast proliferation (GO:0048144)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)	p.V526V(1)		endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						AGAAGCACGTGTGCCACATCC	0.592													G|||	2518	0.502796	0.3805	0.4697	5008	,	,		22979	0.7708		0.4583	False		,,,				2504	0.4611				p.V526V		Atlas-SNP	.											SP2,colon,carcinoma,0,2	SP2	38	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G1578T						PASS	.	G		1758,2648	521.1+/-370.4	355,1048,800	122.0	106.0	112.0		1578	5.0	1.0	17	dbSNP_86	112	3721,4879	530.3+/-381.8	807,2107,1386	no	coding-synonymous	SP2	NM_003110.5		1162,3155,2186	TT,TG,GG		43.2674,39.9001,42.1267		526/614	46002744	5479,7527	2203	4300	6503	SO:0001819	synonymous_variant	6668	exon6			GCACGTGTGCCAC		CCDS11521.2	17q21.3-q22	2013-01-08			ENSG00000167182	ENSG00000167182		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11207	protein-coding gene	gene with protein product		601801				1341900, 9730617	Standard	NM_003110		Approved	KIAA0048	uc002imk.3	Q02086	OTTHUMG00000150196	ENST00000376741.4:c.1578G>T	17.37:g.46002744G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_003110	A6NK74	Silent	SNP	ENST00000376741.4	37	CCDS11521.2																																																																																			G|0.537;T|0.463	0.463	strong		0.592	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
UBE2F	140739	hgsc.bcm.edu	37	2	238903399	238903399	+	Silent	SNP	G	G	A	rs12615308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238903399G>A	ENST00000272930.4	+	4	356	c.162G>A	c.(160-162)gtG>gtA	p.V54V	UBE2F_ENST00000409633.1_Silent_p.V54V|UBE2F_ENST00000414443.1_Intron|UBE2F_ENST00000409332.1_Intron|UBE2F-SCLY_ENST00000449191.1_Silent_p.V54V|UBE2F_ENST00000409953.1_Silent_p.V30V	NM_001278305.1|NM_080678.2	NP_001265234.1|NP_542409.1	Q969M7	UBE2F_HUMAN	ubiquitin-conjugating enzyme E2F (putative)	54					protein neddylation (GO:0045116)		ATP binding (GO:0005524)|NEDD8 ligase activity (GO:0019788)			endometrium(1)|large_intestine(1)	2		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;6.7e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|Kidney(56;3.53e-09)|KIRC - Kidney renal clear cell carcinoma(57;9.79e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000136)|Lung(119;0.0126)|LUSC - Lung squamous cell carcinoma(224;0.0301)		CATGTAAAGTGCATTTTCCTG	0.383													G|||	516	0.103035	0.0091	0.1052	5008	,	,		20580	0.1429		0.1471	False		,,,				2504	0.1421				p.V54V		Atlas-SNP	.											.	UBE2F	11	.	0			c.G162A						PASS	.	G		135,4271	97.1+/-135.8	0,135,2068	197.0	160.0	173.0		162	3.7	1.0	2	dbSNP_120	173	1216,7384	246.1+/-274.7	85,1046,3169	no	coding-synonymous	UBE2F	NM_080678.2		85,1181,5237	AA,AG,GG		14.1395,3.064,10.3875		54/186	238903399	1351,11655	2203	4300	6503	SO:0001819	synonymous_variant	140739	exon4			TAAAGTGCATTTT	BC010549	CCDS2523.1, CCDS63175.1, CCDS63176.1, CCDS63177.1	2q37.3	2008-02-05	2005-12-15		ENSG00000184182	ENSG00000184182		"""Ubiquitin-conjugating enzymes E2"""	12480	protein-coding gene	gene with protein product	"""NEDD8 conjugating enzyme"""					12477932	Standard	NM_080678		Approved	NCE2	uc031rrz.1	Q969M7	OTTHUMG00000133341	ENST00000272930.4:c.162G>A	2.37:g.238903399G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_080678	A8K1Z8|B4DDT9|B4DFI1|B4DMK3|B4DZU2|B8ZZG2|C9J212|H9KVB9	Silent	SNP	ENST00000272930.4	37	CCDS2523.1																																																																																			G|0.885;A|0.115	0.115	strong		0.383	UBE2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257171.2	NM_080678	
OR4Q3	441669	hgsc.bcm.edu	37	14	20215989	20215989	+	Missense_Mutation	SNP	A	A	G	rs17210864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20215989A>G	ENST00000331723.1	+	1	403	c.403A>G	c.(403-405)Aca>Gca	p.T135A		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	135			T -> A (in dbSNP:rs17210864).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GCGCTACCTTACAGTCATGAA	0.493													A|||	549	0.109625	0.0885	0.0764	5008	,	,		30995	0.0079		0.1481	False		,,,				2504	0.227				p.T135A		Atlas-SNP	.											.	OR4Q3	117	.	0			c.A403G						PASS	.		ALA/THR	475,3931		8,459,1736	121.0	123.0	122.0		403	3.2	0.1	14	dbSNP_123	122	1437,7163		36,1365,2899	no	missense	OR4Q3	NM_172194.1	58	44,1824,4635	GG,GA,AA		16.7093,10.7808,14.7009	benign	135/314	20215989	1912,11094	2203	4300	6503	SO:0001583	missense	441669	exon1			TACCTTACAGTCA	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.403A>G	14.37:g.20215989A>G	ENSP00000330049:p.Thr135Ala	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	180	70	0.388889	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	37	CCDS32020.1	187	0.08562271062271062	31	0.06300813008130081	33	0.09116022099447514	5	0.008741258741258742	118	0.15567282321899736	.	4.346	0.063601	0.08388	0.107808	0.167093	ENSG00000182652	ENST00000331723	T	0.00388	7.59	4.36	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.359276	0.19822	U	0.105292	T	0.00012	0.0000	N	0.25332	0.735	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.51426	-0.8707	10	0.59425	D	0.04	.	4.5362	0.12032	0.6998:0.1965:0.1037:0.0	rs17210864;rs52817214;rs17210864	135	Q8NH05	OR4Q3_HUMAN	A	135	ENSP00000330049:T135A	ENSP00000330049:T135A	T	+	1	0	OR4Q3	19285829	0.000000	0.05858	0.108000	0.21378	0.045000	0.14185	-0.357000	0.07651	0.707000	0.31934	0.333000	0.21579	ACA	A|0.904;G|0.096	0.096	strong		0.493	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
MYH4	4622	hgsc.bcm.edu	37	17	10355371	10355371	+	Missense_Mutation	SNP	C	C	T	rs11651295	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10355371C>T	ENST00000255381.2	-	27	3735	c.3625G>A	c.(3625-3627)Gag>Aag	p.E1209K	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1209			E -> K (in dbSNP:rs11651295). {ECO:0000269|PubMed:10388558}.		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)			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						TCAATCTGCTCCCCAAGCTCA	0.542													C|||	2544	0.507987	0.3011	0.4841	5008	,	,		18293	0.8631		0.334	False		,,,				2504	0.6176				p.E1209K		Atlas-SNP	.											.	MYH4	349	.	0			c.G3625A						PASS	.	C	LYS/GLU	1391,3015	458.6+/-352.0	222,947,1034	105.0	85.0	92.0		3625	5.5	1.0	17	dbSNP_120	92	3130,5470	476.6+/-369.4	595,1940,1765	yes	missense	MYH4	NM_017533.2	56	817,2887,2799	TT,TC,CC		36.3953,31.5706,34.7609	probably-damaging	1209/1940	10355371	4521,8485	2203	4300	6503	SO:0001583	missense	4622	exon27			TCTGCTCCCCAAG		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.3625G>A	17.37:g.10355371C>T	ENSP00000255381:p.Glu1209Lys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	168	75	0.446429	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1069	0.48946886446886445	147	0.29878048780487804	170	0.4696132596685083	498	0.8706293706293706	254	0.33509234828496043	C	34	5.299995	0.95574	0.315706	0.363953	ENSG00000141048	ENST00000255381	T	0.80480	-1.38	5.51	5.51	0.81932	Myosin tail (1);	0.000000	0.37577	U	0.002023	T	0.00012	0.0000	H	0.94847	3.59	0.09310	P	0.999999800477	D	0.58970	0.984	D	0.63113	0.911	T	0.48525	-0.9028	9	0.87932	D	0	.	19.7768	0.96398	0.0:1.0:0.0:0.0	rs11651295;rs52799277;rs58579935;rs11651295	1209	Q9Y623	MYH4_HUMAN	K	1209	ENSP00000255381:E1209K	ENSP00000255381:E1209K	E	-	1	0	MYH4	10296096	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	7.722000	0.84778	2.745000	0.94114	0.655000	0.94253	GAG	C|0.616;T|0.384	0.384	strong		0.542	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
MUC2	4583	hgsc.bcm.edu	37	11	1104123	1104123	+	Silent	SNP	C	C	T	rs12270802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1104123C>T	ENST00000441003.2	+	49	8341	c.8314C>T	c.(8314-8316)Ctg>Ttg	p.L2772L		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5134					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.L2772L(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TGAGGTGGTCCTGAGCTGCCC	0.672													C|||	778	0.155351	0.4039	0.072	5008	,	,		14321	0.0357		0.0934	False		,,,				2504	0.0654				p.L2768L		Atlas-SNP	.											MUC2_ENST00000441003,NS,lymphoid_neoplasm,0,1	MUC2	614	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C8302T						scavenged	.	C		1294,2806		202,890,958	14.0	20.0	18.0		8299	1.6	0.0	11	dbSNP_120	18	690,7674		27,636,3519	no	coding-synonymous	MUC2	NM_002457.2		229,1526,4477	TT,TC,CC		8.2496,31.561,15.9178		2767/2813	1104123	1984,10480	2050	4182	6232	SO:0001819	synonymous_variant	4583	exon50			GTGGTCCTGAGCT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8314C>T	11.37:g.1104123C>T		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	111	69	0.621622	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.894;T|0.106	0.106	strong		0.672	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF222	7673	hgsc.bcm.edu	37	19	44536397	44536397	+	Silent	SNP	T	T	C	rs151037918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44536397T>C	ENST00000187879.8	+	4	732	c.570T>C	c.(568-570)acT>acC	p.T190T	ZNF222_ENST00000391960.3_Silent_p.T230T|ZNF223_ENST00000591793.1_Intron	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	190					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(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GTCTGCAAACTCATCAAAGAG	0.428													T|||	12	0.00239617	0.0008	0.0029	5008	,	,		21542	0.0		0.008	False		,,,				2504	0.001				p.T230T		Atlas-SNP	.											.	ZNF222	90	.	0			c.T690C						PASS	.	T	,	9,4397	15.5+/-35.6	0,9,2194	135.0	138.0	137.0		690,570	0.3	0.0	19	dbSNP_134	137	59,8541	36.9+/-92.0	0,59,4241	no	coding-synonymous,coding-synonymous	ZNF222	NM_001129996.1,NM_013360.2	,	0,68,6435	CC,CT,TT		0.686,0.2043,0.5228	,	230/492,190/452	44536397	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	7673	exon4			GCAAACTCATCAA	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"""Zinc fingers, C2H2-type"", ""-"""	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.570T>C	19.37:g.44536397T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Silent	SNP	ENST00000187879.8	37	CCDS33045.1																																																																																			T|0.996;C|0.004	0.004	strong		0.428	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2		
PLEKHH1	57475	hgsc.bcm.edu	37	14	68029313	68029313	+	Missense_Mutation	SNP	G	G	A	rs2236235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:68029313G>A	ENST00000329153.5	+	7	1097	c.965G>A	c.(964-966)cGg>cAg	p.R322Q		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	322			R -> Q (in dbSNP:rs2236235).			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)		GGCACCCCGCGGGACAGCATC	0.632													G|||	867	0.173123	0.0136	0.1758	5008	,	,		18193	0.2887		0.2207	False		,,,				2504	0.2188				p.R322Q		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G965A						PASS	.	G	GLN/ARG	154,3814		4,146,1834	21.0	24.0	23.0		965	2.3	0.0	14	dbSNP_98	23	1779,6509		180,1419,2545	yes	missense	PLEKHH1	NM_020715.2	43	184,1565,4379	AA,AG,GG		21.4648,3.881,15.7719	probably-damaging	322/1365	68029313	1933,10323	1984	4144	6128	SO:0001583	missense	57475	exon7			CCCCGCGGGACAG	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.965G>A	14.37:g.68029313G>A	ENSP00000330278:p.Arg322Gln	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	404	0.184981684981685	6	0.012195121951219513	62	0.1712707182320442	170	0.2972027972027972	166	0.21899736147757257	G	8.718	0.913728	0.17907	0.03881	0.214648	ENSG00000054690	ENST00000329153	T	0.22134	1.97	5.08	2.26	0.28386	.	0.279487	0.38548	N	0.001647	T	0.00012	0.0000	M	0.64997	1.995	0.09310	P	0.99999495267	B	0.16166	0.016	B	0.09377	0.004	T	0.41998	-0.9477	9	0.18710	T	0.47	.	8.094	0.30818	0.2591:0.0:0.7409:0.0	rs2236235;rs17782308;rs59522386;rs2236235	322	Q9ULM0	PKHH1_HUMAN	Q	322	ENSP00000330278:R322Q	ENSP00000330278:R322Q	R	+	2	0	PLEKHH1	67099066	0.997000	0.39634	0.016000	0.15963	0.052000	0.14988	2.565000	0.45939	0.310000	0.22990	0.491000	0.48974	CGG	G|0.809;N|0.000	.	strong		0.632	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
TWF2	11344	hgsc.bcm.edu	37	3	52264907	52264907	+	Silent	SNP	T	T	C	rs352143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:52264907T>C	ENST00000305533.5	-	6	831	c.588A>G	c.(586-588)aaA>aaG	p.K196K	TLR9_ENST00000494383.1_Missense_Mutation_p.N57D|TLR9_ENST00000597542.1_5'UTR|TWF2_ENST00000499914.2_Silent_p.K196K	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	196	ADF-H 2. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		AGTTGACCATTTTCTGCTTGA	0.597													C|||	1016	0.202875	0.4244	0.1671	5008	,	,		21314	0.0357		0.1909	False		,,,				2504	0.1135				p.K196K		Atlas-SNP	.											.	TWF2	33	.	0			c.A588G						PASS	.	C		1514,2890	657.1+/-400.2	261,992,949	87.0	84.0	85.0		588	3.9	0.4	3	dbSNP_79	85	1736,6864	721.9+/-406.4	174,1388,2738	no	coding-synonymous	TWF2	NM_007284.3		435,2380,3687	CC,CT,TT		20.186,34.3778,24.9923		196/350	52264907	3250,9754	2202	4300	6502	SO:0001819	synonymous_variant	11344	exon6			GACCATTTTCTGC	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"""protein tyrosine kinase 9-like (A6-related protein)"", ""PTK9L protein tyrosine kinase 9-like (A6-related protein)"", ""twinfilin, actin-binding protein, homolog 2 (Drosophila)"""	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.588A>G	3.37:g.52264907T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_007284	Q9Y3F5	Silent	SNP	ENST00000305533.5	37	CCDS2849.1	419	0.19184981684981686	192	0.3902439024390244	67	0.1850828729281768	21	0.03671328671328671	139	0.18337730870712401	C	3.859	-0.030265	0.07543	0.343778	0.20186	ENSG00000173366	ENST00000494383	.	.	.	4.74	3.86	0.44501	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999168762	.	.	.	.	.	.	T	0.38650	-0.9651	3	.	.	.	.	10.7667	0.46297	0.0:0.8434:0.0:0.1566	rs352143;rs17844842;rs17857554;rs17858381;rs57276328;rs352143	.	.	.	D	57	.	.	N	-	1	0	RP11-330H6.5	52239947	0.071000	0.21146	0.409000	0.26459	0.360000	0.29518	0.533000	0.23082	0.431000	0.26258	-0.374000	0.07098	AAT	T|0.768;G|0.002	.	strong		0.597	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2		
CCDC74B	91409	hgsc.bcm.edu	37	2	130898813	130898813	+	Missense_Mutation	SNP	G	G	A	rs142452531	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:130898813G>A	ENST00000310463.6	-	4	738	c.601C>T	c.(601-603)Ccc>Tcc	p.P201S	CCDC74B_ENST00000409943.3_Missense_Mutation_p.P135S|CCDC74B_ENST00000392984.3_Missense_Mutation_p.P303S|CCDC74B_ENST00000409128.1_Missense_Mutation_p.P177S|MED15P9_ENST00000427638.1_RNA	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	201										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					GCCTTCTGGGGGACGTCAGCT	0.592																																					p.P201S		Atlas-SNP	.											CCDC74B,NS,carcinoma,+2,2	CCDC74B	27	2	0			c.C601T						scavenged	.						165.0	115.0	132.0					2																	130898813		2201	4264	6465	SO:0001583	missense	91409	exon4			TCTGGGGGACGTC		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.601C>T	2.37:g.130898813G>A	ENSP00000308873:p.Pro201Ser	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	177	24	0.135593	NM_207310	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	37	CCDS2155.1	114	0.0521978021978022	3	0.006097560975609756	31	0.0856353591160221	5	0.008741258741258742	75	0.09894459102902374	.	0.008	-1.866645	0.00547	.	.	ENSG00000152076	ENST00000409943;ENST00000310463;ENST00000392984;ENST00000409488;ENST00000409128	T;T;T;T	0.44881	1.9;1.93;1.87;0.91	2.39	1.48	0.22813	.	0.638174	0.12247	U	0.485969	T	0.00875	0.0029	M	0.62723	1.935	0.09310	N	1	P;B;B	0.50710	0.938;0.009;0.264	B;B;B	0.38156	0.266;0.015;0.05	T	0.02560	-1.1141	10	0.30854	T	0.27	-0.2433	4.9656	0.14089	0.1864:0.0:0.8136:0.0	.	303;135;201	E7ESC5;Q96LY2-2;Q96LY2	.;.;CC74B_HUMAN	S	135;201;303;139;177	ENSP00000386294:P135S;ENSP00000308873:P201S;ENSP00000376710:P303S;ENSP00000386644:P177S	ENSP00000308873:P201S	P	-	1	0	CCDC74B	130615283	0.000000	0.05858	0.044000	0.18714	0.014000	0.08584	0.104000	0.15313	0.333000	0.23563	0.298000	0.19748	CCC	G|0.700;A|0.300	0.300	strong		0.592	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310	
D2HGDH	728294	hgsc.bcm.edu	37	2	242690745	242690745	+	Missense_Mutation	SNP	C	C	T	rs1105273	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242690745C>T	ENST00000321264.4	+	8	1291	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	D2HGDH_ENST00000486953.1_Intron|D2HGDH_ENST00000403782.1_Missense_Mutation_p.A227V	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	361			A -> V (in dbSNP:rs1105273).		2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		CTGGAGCACGCGCTGGGCTCC	0.617													C|||	1078	0.215256	0.2882	0.3271	5008	,	,		19217	0.2242		0.1133	False		,,,				2504	0.1329				p.A361V		Atlas-SNP	.											D2HGDH,NS,carcinoma,-1,1	D2HGDH	39	1	0			c.C1082T						PASS	.	T	VAL/ALA	1168,3238	408.0+/-334.4	153,862,1188	54.0	51.0	52.0		1082	-7.9	0.0	2	dbSNP_86	52	912,7680	201.8+/-245.2	50,812,3434	yes	missense	D2HGDH	NM_152783.3	64	203,1674,4622	TT,TC,CC		10.6145,26.5093,16.0025	benign	361/522	242690745	2080,10918	2203	4296	6499	SO:0001583	missense	728294	exon8			AGCACGCGCTGGG	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.1082C>T	2.37:g.242690745C>T	ENSP00000315351:p.Ala361Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	468	0.21428571428571427	134	0.27235772357723576	111	0.30662983425414364	132	0.23076923076923078	91	0.12005277044854881	c	0.048	-1.258655	0.01445	0.265093	0.106145	ENSG00000180902	ENST00000321264;ENST00000403782;ENST00000454048	T;T;T	0.78595	-1.19;-1.19;-1.01	5.1	-7.9	0.01169	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.602385	0.16472	N	0.212932	T	0.00012	0.0000	N	0.20845	0.615	0.27582	P	0.9495508	B	0.13145	0.007	B	0.14023	0.01	T	0.12091	-1.0561	9	0.02654	T	1	-0.5439	16.7058	0.85371	0.0:0.3272:0.0:0.6728	rs1105273	361	Q8N465	D2HDH_HUMAN	V	361;227;62	ENSP00000315351:A361V;ENSP00000384723:A227V;ENSP00000404596:A62V	ENSP00000315351:A361V	A	+	2	0	D2HGDH	242339418	0.045000	0.20229	0.000000	0.03702	0.026000	0.11368	0.251000	0.18257	-1.680000	0.01450	-0.974000	0.02594	GCG	C|0.817;T|0.183	0.183	strong		0.617	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
ABCB5	340273	hgsc.bcm.edu	37	7	20691047	20691047	+	Missense_Mutation	SNP	T	T	C	rs34603556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20691047T>C	ENST00000404938.2	+	13	1989	c.1337T>C	c.(1336-1338)aTg>aCg	p.M446T	ABCB5_ENST00000258738.6_Start_Codon_SNP_p.M1T|ABCB5_ENST00000406935.1_Start_Codon_SNP_p.M1T|ABCB5_ENST00000443026.2_Start_Codon_SNP_p.M1T|ABCB5_ENST00000477094.1_3'UTR	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	446	ABC transporter 1. {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						TGGCAGATCATGGTGGATGAG	0.403													C|||	509	0.101637	0.0287	0.0937	5008	,	,		20900	0.0397		0.2068	False		,,,				2504	0.1616				p.M446T		Atlas-SNP	.											.	ABCB5	357	.	0			c.T1337C						PASS	.	C	THR/MET,THR/MET,THR/MET,THR/MET	265,4141	802.3+/-415.7	11,243,1949	133.0	117.0	122.0		1337,2,2,2	0.4	0.0	7	dbSNP_126	122	1749,6851	735.6+/-407.0	194,1361,2745	yes	missense,missense,missense,missense	ABCB5	NM_001163941.1,NM_001163942.1,NM_001163993.1,NM_178559.5	81,81,81,81	205,1604,4694	CC,CT,TT		20.3372,6.0145,15.4852	benign,benign,benign,benign	446/1258,1/132,1/127,1/813	20691047	2014,10992	2203	4300	6503	SO:0001583	missense	340273	exon13			AGATCATGGTGGA	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.1337T>C	7.37:g.20691047T>C	ENSP00000384881:p.Met446Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	228	0.1043956043956044	13	0.026422764227642278	34	0.09392265193370165	22	0.038461538461538464	159	0.20976253298153033	C	3.745	-0.052773	0.07362	0.060145	0.203372	ENSG00000004846	ENST00000404938;ENST00000443026;ENST00000406935;ENST00000258738	D;D;D;D	0.92911	-3.13;-2.83;-2.82;-2.09	4.2	0.375	0.16188	.	0.273866	0.16105	U	0.229369	T	0.00412	0.0013	.	.	.	0.09310	P	1.0	B;B;B;B	0.27853	0.146;0.0;0.0;0.191	B;B;B;B	0.31191	0.119;0.0;0.0;0.125	T	0.35895	-0.9770	8	0.87932	D	0	.	9.2879	0.37769	0.0:0.6146:0.0:0.3854	rs34603556;rs58341346	1;446;1;1	B5MD19;A7BKA4;Q2M3G0;Q2M3G0-2	.;.;ABCB5_HUMAN;.	T	446;1;1;1	ENSP00000384881:M446T;ENSP00000406730:M1T;ENSP00000383899:M1T;ENSP00000258738:M1T	ENSP00000258738:M1T	M	+	2	0	ABCB5	20657572	0.006000	0.16342	0.042000	0.18584	0.016000	0.09150	0.188000	0.17018	-0.134000	0.11516	-0.930000	0.02707	ATG	T|0.866;C|0.134	0.134	strong		0.403	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
SPECC1	92521	hgsc.bcm.edu	37	17	20013802	20013802	+	Silent	SNP	G	G	A	rs3764436	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:20013802G>A	ENST00000261503.5	+	3	261	c.210G>A	c.(208-210)gtG>gtA	p.V70V	SPECC1_ENST00000395527.4_Silent_p.V70V|SPECC1_ENST00000395529.3_Silent_p.V70V|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	70					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)		CATCGGGGGTGGTTCGCCTGA	0.627													G|||	545	0.108826	0.0787	0.1369	5008	,	,		16233	0.0962		0.1223	False		,,,				2504	0.1288				p.V70V		Atlas-SNP	.											.	SPECC1	100	.	0			c.G210A						PASS	.	G	,	387,4019	191.6+/-217.2	19,349,1835	43.0	45.0	45.0		210,210	-9.5	0.0	17	dbSNP_107	45	1148,7452	234.9+/-267.6	85,978,3237	no	coding-synonymous,coding-synonymous	SPECC1	NM_001033553.2,NM_152904.4	,	104,1327,5072	AA,AG,GG		13.3488,8.7835,11.8022	,	70/1069,70/791	20013802	1535,11471	2203	4300	6503	SO:0001819	synonymous_variant	92521	exon3			GGGGGTGGTTCGC	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.210G>A	17.37:g.20013802G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	247	112	0.453441	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																			G|0.892;A|0.108	0.108	strong		0.627	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
HOXD12	3238	hgsc.bcm.edu	37	2	176965086	176965086	+	Missense_Mutation	SNP	G	G	A	rs35817516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:176965086G>A	ENST00000406506.2	+	1	629	c.557G>A	c.(556-558)cGa>cAa	p.R186Q	HOXD12_ENST00000404162.2_Missense_Mutation_p.R186Q			P35452	HXD12_HUMAN	homeobox D12	186			R -> Q (in dbSNP:rs35817516).		embryonic digit morphogenesis (GO:0042733)|pattern specification process (GO:0007389)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(7)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		TCTTGCCTGCGACCTTCACTG	0.662													G|||	344	0.0686901	0.0106	0.2176	5008	,	,		14242	0.006		0.1223	False		,,,				2504	0.0511				p.R186Q		Atlas-SNP	.											.	HOXD12	25	.	0			c.G557A						PASS	.	G	GLN/ARG	110,3442		1,108,1667	12.0	14.0	13.0		557	4.6	1.0	2	dbSNP_126	13	912,6792		41,830,2981	yes	missense	HOXD12	NM_021193.3	43	42,938,4648	AA,AG,GG		11.838,3.0968,9.0796	benign	186/271	176965086	1022,10234	1776	3852	5628	SO:0001583	missense	3238	exon1			GCCTGCGACCTTC		CCDS46456.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170178	ENSG00000170178		"""Homeoboxes / ANTP class : HOXL subclass"""	5135	protein-coding gene	gene with protein product		142988	"""homeo box D12"""	HOX4H		1675198, 1973146	Standard	NM_021193		Approved		uc010zev.1	P35452	OTTHUMG00000150358	ENST00000406506.2:c.557G>A	2.37:g.176965086G>A	ENSP00000385586:p.Arg186Gln	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	188	82	0.43617	NM_021193	B5MCP0|Q0VAD7|Q0VAD8|Q9NS03	Missense_Mutation	SNP	ENST00000406506.2	37	CCDS46456.1	159	0.07280219780219781	5	0.01016260162601626	65	0.17955801104972377	2	0.0034965034965034965	87	0.11477572559366754	G	16.01	3.000424	0.54147	0.030968	0.11838	ENSG00000170178	ENST00000406506;ENST00000404162	D	0.95588	-3.75	5.46	4.58	0.56647	Homeodomain-like (1);	0.057159	0.64402	D	0.000002	T	0.01765	0.0056	L	0.55103	1.725	0.28197	P	0.9275293	P;P	0.37500	0.597;0.51	B;B	0.23018	0.043;0.025	T	0.47736	-0.9094	9	0.35671	T	0.21	.	12.8047	0.57607	0.0759:0.0:0.9241:0.0	rs35817516;rs62188664;rs35817516	186;186	B5MCD3;P35452	.;HXD12_HUMAN	Q	186	ENSP00000385586:R186Q	ENSP00000385132:R186Q	R	+	2	0	HOXD12	176673332	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.452000	0.66638	1.305000	0.44909	0.655000	0.94253	CGA	G|0.928;A|0.072	0.072	strong		0.662	HOXD12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359253.2	NM_021193	
DLGAP5	9787	hgsc.bcm.edu	37	14	55618524	55618524	+	Missense_Mutation	SNP	C	C	G	rs35954941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:55618524C>G	ENST00000247191.2	-	17	2473	c.2257G>C	c.(2257-2259)Gaa>Caa	p.E753Q	DLGAP5_ENST00000395425.2_Missense_Mutation_p.E753Q	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	753			E -> Q (in dbSNP:rs35954941).		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						GAATTCAGTTCCATTCCTTCC	0.358													C|||	66	0.0131789	0.0265	0.0086	5008	,	,		16533	0.0		0.0089	False		,,,				2504	0.0164				p.E753Q		Atlas-SNP	.											.	DLGAP5	84	.	0			c.G2257C						PASS	.	C	GLN/GLU,GLN/GLU	88,4316	73.1+/-111.1	1,86,2115	121.0	111.0	115.0		2257,2257	2.6	0.6	14	dbSNP_126	115	88,8508	49.8+/-109.6	1,86,4211	yes	missense,missense	DLGAP5	NM_001146015.1,NM_014750.4	29,29	2,172,6326	GG,GC,CC		1.0237,1.9982,1.3538	possibly-damaging,possibly-damaging	753/843,753/847	55618524	176,12824	2202	4298	6500	SO:0001583	missense	9787	exon17			TCAGTTCCATTCC	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.2257G>C	14.37:g.55618524C>G	ENSP00000247191:p.Glu753Gln	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	196	88	0.44898	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	27	0.012362637362637362	15	0.03048780487804878	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	12.71	2.019702	0.35606	0.019982	0.010237	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.32023	1.47;1.47	4.46	2.58	0.30949	.	3.240000	0.00837	N	0.001708	T	0.19725	0.0474	L	0.29908	0.895	0.22378	N	0.999159	D;D	0.67145	0.996;0.991	P;P	0.59115	0.852;0.755	T	0.30563	-0.9974	10	0.54805	T	0.06	.	10.5055	0.44832	0.0:0.8307:0.0:0.1693	rs35954941	753;753	A8MTM6;Q15398	.;DLGP5_HUMAN	Q	753	ENSP00000378815:E753Q;ENSP00000247191:E753Q	ENSP00000247191:E753Q	E	-	1	0	DLGAP5	54688277	0.902000	0.30710	0.566000	0.28421	0.209000	0.24338	1.088000	0.30877	0.564000	0.29238	0.655000	0.94253	GAA	C|0.986;G|0.014	0.014	strong		0.358	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
FAM86B2	653333	hgsc.bcm.edu	37	8	12285250	12285250	+	Missense_Mutation	SNP	G	G	A	rs199873615	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:12285250G>A	ENST00000262365.4	-	7	807	c.808C>T	c.(808-810)Cgg>Tgg	p.R270W	FAM86B2_ENST00000309608.5_Missense_Mutation_p.P147L|FAM86B2_ENST00000351291.4_Missense_Mutation_p.R236W|FAM86B2_ENST00000393715.3_Missense_Mutation_p.R42W	NM_001137610.1	NP_001131082.1	P0C5J1	F86B2_HUMAN	family with sequence similarity 86, member B2	270										endometrium(1)|kidney(2)	3						TTGTGCTCCCGGCAGGCAGCC	0.607													g|||	517	0.103235	0.0121	0.1081	5008	,	,		11073	0.2252		0.1213	False		,,,				2504	0.0787				p.R270W		Atlas-SNP	.											FAM86B2_ENST00000393715,brain,glioma,0,3	FAM86B2	19	3	0			c.C808T						scavenged	.																																			SO:0001583	missense	653333	exon7			GCTCCCGGCAGGC		CCDS59092.1	8p23.1	2011-07-01			ENSG00000145002	ENSG00000145002			32222	protein-coding gene	gene with protein product							Standard	NM_001137610		Approved		uc003wvt.4	P0C5J1	OTTHUMG00000165462	ENST00000262365.4:c.808C>T	8.37:g.12285250G>A	ENSP00000262365:p.Arg270Trp	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_001137610		Missense_Mutation	SNP	ENST00000262365.4	37	CCDS59092.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	12.29|12.29	1.894306|1.894306	0.33442|0.33442	.|.	.|.	ENSG00000145002|ENSG00000145002	ENST00000309608;ENST00000532480|ENST00000393715;ENST00000262365;ENST00000351291;ENST00000527331	T;T|T;T;T;T	0.26373|0.26810	2.12;1.74|1.71;3.26;3.26;3.26	1.82|1.82	0.604|0.604	0.17547|0.17547	.|.	35.965900|.	0.00520|.	U|.	0.000195|.	T|T	0.24353|0.24353	0.0590|0.0590	M|M	0.65498|0.65498	2.005|2.005	0.09310|0.09310	N|N	1|1	.|B	.|0.16396	.|0.017	.|B	.|0.18561	.|0.022	T|T	0.27839|0.27839	-1.0062|-1.0062	8|9	0.87932|0.49607	D|T	0|0.09	.|.	5.3222|5.3222	0.15887|0.15887	0.0:0.0:0.468:0.532|0.0:0.0:0.468:0.532	.|.	.|270	.|P0C5J1	.|F86B2_HUMAN	L|W	147|42;270;236;236	ENSP00000311330:P147L;ENSP00000436338:P147L|ENSP00000377318:R42W;ENSP00000262365:R270W;ENSP00000283479:R236W;ENSP00000432491:R236W	ENSP00000311330:P147L|ENSP00000262365:R270W	P|R	-|-	2|1	0|2	FAM86B2|FAM86B2	12329621|12329621	0.701000|0.701000	0.27806|0.27806	0.012000|0.012000	0.15200|0.15200	0.020000|0.020000	0.10135|0.10135	0.558000|0.558000	0.23469|0.23469	0.945000|0.945000	0.37605|0.37605	0.162000|0.162000	0.16502|0.16502	CCG|CGG	G|0.834;A|0.166	0.166	strong		0.607	FAM86B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_928336	
LRP8	7804	hgsc.bcm.edu	37	1	53712727	53712727	+	Splice_Site	SNP	C	C	T	rs5174	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:53712727C>T	ENST00000306052.6	-	19	2956	c.2855G>A	c.(2854-2856)cGa>cAa	p.R952Q	LRP8_ENST00000354412.3_Splice_Site_p.R689Q|LRP8_ENST00000465675.1_Splice_Site_p.R446Q|LRP8_ENST00000371454.2_Splice_Site_p.R893Q|RP5-1024G6.8_ENST00000602943.1_lincRNA|LRP8_ENST00000347547.2_Splice_Site_p.R782Q	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	952			R -> Q (associated with susceptibility to myocardial infarction type 1; increases activation of MAPK14 by oxidized low density lipoprotein; dbSNP:rs5174). {ECO:0000269|PubMed:12399018, ECO:0000269|PubMed:17847002}.		ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						TAATGCCACTCGCTGGGGAGA	0.423													C|||	723	0.144369	0.0166	0.1772	5008	,	,		19833	0.0327		0.3956	False		,,,				2504	0.1503				p.R952Q		Atlas-SNP	.											.	LRP8	58	.	0			c.G2855A	GRCh37	CM074332	LRP8	M	rs5174	PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	365,4041	187.1+/-213.8	21,323,1859	111.0	97.0	102.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2678,2855,2066,2345	5.4	1.0	1	dbSNP_52	102	3401,5199	502.2+/-375.6	679,2043,1578	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	LRP8	NM_001018054.2,NM_004631.4,NM_017522.4,NM_033300.3	43,43,43,43	700,2366,3437	TT,TC,CC		39.5465,8.2842,28.9559	probably-damaging,probably-damaging,probably-damaging,probably-damaging	893/905,952/964,689/701,782/794	53712727	3766,9240	2203	4300	6503	SO:0001630	splice_region_variant	7804	exon19			GCCACTCGCTGGG	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"""Low density lipoprotein receptors"""	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.2854-1G>A	1.37:g.53712727C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	401	0.18360805860805862	15	0.03048780487804878	68	0.1878453038674033	19	0.033216783216783216	299	0.3944591029023747	C	29.9	5.045892	0.93685	0.082842	0.395465	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000465675;ENST00000354412;ENST00000347547	D;D;D;D;D	0.94000	-2.9;-2.82;-3.33;-2.75;-2.86	5.43	5.43	0.79202	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.99999806194	D;D;P;D;D	0.89917	1.0;0.999;0.832;0.999;0.968	D;D;B;D;P	0.83275	0.996;0.99;0.096;0.978;0.49	T	0.00114	-1.2041	8	0.56958	D	0.05	.	17.4324	0.87543	0.0:1.0:0.0:0.0	rs5174;rs17192669;rs52836108;rs58848179;rs5174	689;782;893;952;446	Q14114-2;Q14114-4;Q14114-3;Q14114;E9PP15	.;.;.;LRP8_HUMAN;.	Q	952;893;446;689;782	ENSP00000303634:R952Q;ENSP00000360509:R893Q;ENSP00000437009:R446Q;ENSP00000346391:R689Q;ENSP00000334522:R782Q	ENSP00000303634:R952Q	R	-	2	0	LRP8	53485315	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.102000	0.77005	2.550000	0.86006	0.563000	0.77884	CGA	C|0.764;T|0.236	0.236	strong		0.423	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631	Missense_Mutation
CABIN1	23523	hgsc.bcm.edu	37	22	24564477	24564477	+	Silent	SNP	C	C	T	rs17854875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:24564477C>T	ENST00000398319.2	+	33	6130	c.5745C>T	c.(5743-5745)gcC>gcT	p.A1915A	CABIN1_ENST00000485008.1_3'UTR|CABIN1_ENST00000337989.7_Silent_p.A340A|CABIN1_ENST00000263119.5_Silent_p.A1915A|CABIN1_ENST00000405822.2_Silent_p.A1836A	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1915					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TTGGGGCTGCCGCCCAGAGAC	0.602													C|||	361	0.0720847	0.0038	0.0375	5008	,	,		21063	0.1677		0.1213	False		,,,				2504	0.0399				p.A1915A		Atlas-SNP	.											.	CABIN1	153	.	0			c.C5745T						PASS	.	C	,,	77,4275		1,75,2100	54.0	41.0	45.0		5745,5595,5745	-10.6	0.1	22	dbSNP_123	45	763,7771		39,685,3543	no	coding-synonymous,coding-synonymous,coding-synonymous	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	,,	40,760,5643	TT,TC,CC		8.9407,1.7693,6.5187	,,	1915/2221,1865/2171,1915/2221	24564477	840,12046	2176	4267	6443	SO:0001819	synonymous_variant	23523	exon33			GGCTGCCGCCCAG	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.5745C>T	22.37:g.24564477C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	75	0.6	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Silent	SNP	ENST00000398319.2	37	CCDS13823.1	216	0.0989010989010989	2	0.0040650406504065045	17	0.04696132596685083	102	0.17832167832167833	95	0.12532981530343007	C	8.143	0.785733	0.16189	0.017693	0.089407	ENSG00000099991	ENST00000403176	.	.	.	5.28	-10.6	0.00265	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999865869	.	.	.	.	.	.	T	0.10405	-1.0631	4	0.30854	T	0.27	.	10.3646	0.44015	0.2388:0.5416:0.0:0.2196	rs17854875;rs17854875	.	.	.	L	340	.	ENSP00000384729:P340L	P	+	2	0	CABIN1	22894477	0.014000	0.17966	0.052000	0.19188	0.927000	0.56198	-1.153000	0.03169	-2.333000	0.00631	-1.096000	0.02151	CCG	C|0.918;T|0.082	0.082	strong		0.602	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
ESYT3	83850	hgsc.bcm.edu	37	3	138191232	138191232	+	Missense_Mutation	SNP	G	G	A	rs10935282	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:138191232G>A	ENST00000389567.4	+	18	1954	c.1768G>A	c.(1768-1770)Ggg>Agg	p.G590R		NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	590			G -> R (in dbSNP:rs10935282).		lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						ACGAGAGCTGGGGAGCCCATA	0.542													G|||	1893	0.377995	0.0514	0.5447	5008	,	,		17433	0.5347		0.4374	False		,,,				2504	0.4785				p.G590R		Atlas-SNP	.											.	ESYT3	64	.	0			c.G1768A						PASS	.	G	ARG/GLY	430,3538		27,376,1581	103.0	107.0	106.0		1768	4.4	1.0	3	dbSNP_120	106	3713,4613		856,2001,1306	yes	missense	ESYT3	NM_031913.3	125	883,2377,2887	AA,AG,GG		44.5952,10.8367,33.6994	possibly-damaging	590/887	138191232	4143,8151	1984	4163	6147	SO:0001583	missense	83850	exon18			GAGCTGGGGAGCC	AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"""Synaptotagmins"""	24295	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member C"""	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.1768G>A	3.37:g.138191232G>A	ENSP00000374218:p.Gly590Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	851	0.38965201465201466	34	0.06910569105691057	160	0.4419889502762431	326	0.5699300699300699	331	0.4366754617414248	G	10.11	1.261640	0.23051	0.108367	0.445952	ENSG00000158220	ENST00000389567	T	0.70749	-0.51	4.45	4.45	0.53987	C2 calcium/lipid-binding domain, CaLB (1);	0.369897	0.21839	N	0.068343	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	B	0.28636	0.218	B	0.21546	0.035	T	0.42120	-0.9470	9	0.15499	T	0.54	-2.9836	14.6169	0.68556	0.0:0.0:1.0:0.0	rs10935282;rs58020269;rs10935282	590	A0FGR9	ESYT3_HUMAN	R	590	ENSP00000374218:G590R	ENSP00000374218:G590R	G	+	1	0	ESYT3	139673922	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.950000	0.40323	2.304000	0.77564	0.462000	0.41574	GGG	G|0.622;A|0.378	0.378	strong		0.542	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913	
ZNF30	90075	hgsc.bcm.edu	37	19	35434448	35434448	+	Missense_Mutation	SNP	A	A	G	rs62122088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:35434448A>G	ENST00000601142.1	+	5	815	c.578A>G	c.(577-579)aAg>aGg	p.K193R	ZNF30_ENST00000426813.2_Missense_Mutation_p.K112R|ZNF30_ENST00000303586.7_Missense_Mutation_p.K194R|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000439785.1_Missense_Mutation_p.K194R			P17039	ZNF30_HUMAN	zinc finger protein 30	193				K -> R (in Ref. 2; CAE45802). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		GCCTTTGTTAAGCATGGGAGA	0.398													A|||	427	0.0852636	0.0628	0.0403	5008	,	,		19724	0.0635		0.1551	False		,,,				2504	0.0982				p.K194R		Atlas-SNP	.											.	ZNF30	44	.	0			c.A581G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	309,3769		11,287,1741	39.0	42.0	41.0		581,581,578	-0.0	0.0	19	dbSNP_129	41	1266,7172		91,1084,3044	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	26,26,26	102,1371,4785	GG,GA,AA		15.0036,7.5772,12.5839	benign,benign,benign	194/625,194/625,193/624	35434448	1575,10941	2039	4219	6258	SO:0001583	missense	90075	exon5			TTGTTAAGCATGG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.578A>G	19.37:g.35434448A>G	ENSP00000469954:p.Lys193Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	198	0.09065934065934066	30	0.06097560975609756	18	0.049723756906077346	30	0.05244755244755245	120	0.158311345646438	A	0.019	-1.464275	0.01053	0.075772	0.150036	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813	T;T	0.13657	2.57;2.57	2.4	-0.0256	0.13934	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04373	-0.215	0.80722	P	0.0	B;B	0.15473	0.005;0.013	B;B	0.13407	0.009;0.007	T	0.44651	-0.9314	8	0.10377	T	0.69	.	2.7105	0.05174	0.5563:0.2742:0.1695:0.0	rs62122088	194;193	P17039-2;P17039	.;ZNF30_HUMAN	R	194;193;112	ENSP00000403441:K194R;ENSP00000416457:K112R	ENSP00000303889:K193R	K	+	2	0	ZNF30	40126288	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.896000	0.00706	-0.220000	0.09988	-0.487000	0.04747	AAG	A|0.892;G|0.108	0.108	strong		0.398	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
CEACAM7	1087	hgsc.bcm.edu	37	19	42190859	42190859	+	Missense_Mutation	SNP	A	A	T	rs8102488	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:42190859A>T	ENST00000006724.3	-	2	559	c.358T>A	c.(358-360)Ttc>Atc	p.F120I	CEACAM7_ENST00000602225.1_Missense_Mutation_p.F120I|CEACAM7_ENST00000338196.4_Missense_Mutation_p.F120I|CEACAM7_ENST00000599715.1_5'UTR|CEACAM7_ENST00000401731.1_Missense_Mutation_p.F120I	NM_006890.3	NP_008821.1	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 7	120	Ig-like V-type.		F -> I (in dbSNP:rs8102488). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.			anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		AGGGTATAGAATCCTGCGTCA	0.458													T|||	2971	0.593251	0.8389	0.513	5008	,	,		19283	0.5109		0.4543	False		,,,				2504	0.546				p.F120I		Atlas-SNP	.											.	CEACAM7	33	.	0			c.T358A						PASS	.	T	ILE/PHE	3445,961	362.9+/-316.3	1344,757,102	183.0	180.0	181.0		358	-3.4	0.0	19	dbSNP_116	181	3981,4619	601.3+/-394.3	942,2097,1261	yes	missense	CEACAM7	NM_006890.3	21	2286,2854,1363	TT,TA,AA		46.2907,21.8112,42.9033	benign	120/266	42190859	7426,5580	2203	4300	6503	SO:0001583	missense	1087	exon2			TATAGAATCCTGC	X98311	CCDS12583.1	19q13.2	2013-01-29			ENSG00000007306	ENSG00000007306		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1819	protein-coding gene	gene with protein product	"""carcinoembryonic antigen gene family member 2"""			CGM2		7806520, 9135022	Standard	XM_005278379		Approved	CEA	uc002ori.1	Q14002	OTTHUMG00000151063	ENST00000006724.3:c.358T>A	19.37:g.42190859A>T	ENSP00000006724:p.Phe120Ile	Somatic	409	0	0		WXS	Illumina HiSeq	Phase_I	485	235	0.484536	NM_006890	A8K848|O15148|O15149|Q0VAC1|Q13983|Q9UPJ2	Missense_Mutation	SNP	ENST00000006724.3	37	CCDS12583.1	1247	0.5709706959706959	404	0.8211382113821138	191	0.5276243093922652	302	0.527972027972028	350	0.46174142480211083	T	1.095	-0.662917	0.03454	0.781888	0.462907	ENSG00000007306	ENST00000006724;ENST00000412062;ENST00000401731;ENST00000338196	T;T;T	0.62232	0.04;0.04;0.04	1.68	-3.36	0.04913	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.004	T	0.39603	-0.9606	8	0.21014	T	0.42	.	3.9709	0.09452	0.5366:0.2689:0.0:0.1944	rs8102488;rs56638435;rs61559620;rs8102488	120;120	Q14002-2;Q14002	.;CEAM7_HUMAN	I	120;99;120;120	ENSP00000006724:F120I;ENSP00000385932:F120I;ENSP00000343286:F120I	ENSP00000006724:F120I	F	-	1	0	CEACAM7	46882699	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.387000	0.00488	-3.597000	0.00135	-3.062000	0.00068	TTC	A|0.427;N|0.000	.	strong		0.458	CEACAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321145.1	NM_006890	
GATA2	2624	hgsc.bcm.edu	37	3	128204951	128204951	+	Missense_Mutation	SNP	C	C	T	rs2335052	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:128204951C>T	ENST00000341105.2	-	3	821	c.490G>A	c.(490-492)Gcc>Acc	p.A164T	GATA2_ENST00000487848.1_Missense_Mutation_p.A164T|GATA2_ENST00000430265.2_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	111	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	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	
KIAA1462	57608	hgsc.bcm.edu	37	10	30317073	30317073	+	Silent	SNP	G	G	A	rs9337951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:30317073G>A	ENST00000375377.1	-	3	2105	c.2004C>T	c.(2002-2004)caC>caT	p.H668H		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	668					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						GCTTTGTAAGGTGGATGAAAC	0.498													G|||	751	0.14996	0.0234	0.2565	5008	,	,		20536	0.0228		0.3489	False		,,,				2504	0.1718				p.H668H		Atlas-SNP	.											.	KIAA1462	162	.	0			c.C2004T						PASS	.	G		263,3625		15,233,1696	152.0	142.0	145.0		2004	1.1	0.0	10	dbSNP_120	145	2797,5513		469,1859,1827	no	coding-synonymous	KIAA1462	NM_020848.2		484,2092,3523	AA,AG,GG		33.6582,6.7644,25.0861		668/1360	30317073	3060,9138	1944	4155	6099	SO:0001819	synonymous_variant	57608	exon3			TGTAAGGTGGATG	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.2004C>T	10.37:g.30317073G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	211	87	0.412322	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			G|0.815;A|0.185	0.185	strong		0.498	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
RBBP6	5930	hgsc.bcm.edu	37	16	24582299	24582299	+	Silent	SNP	C	C	G	rs7196736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:24582299C>G	ENST00000319715.4	+	18	4344	c.3912C>G	c.(3910-3912)acC>acG	p.T1304T	RBBP6_ENST00000348022.2_Silent_p.T1270T|RBBP6_ENST00000381039.3_Silent_p.T464T	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1304					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		ATGACAATACCGCGCCAGCTG	0.393													G|||	641	0.127995	0.149	0.1585	5008	,	,		16201	0.0149		0.1402	False		,,,				2504	0.182				p.T1304T		Atlas-SNP	.											RBBP6,NS,adenocarcinoma,+2,1	RBBP6	158	1	0			c.C3912G						PASS	.	G	,	712,3682	755.0+/-412.5	57,598,1542	55.0	53.0	54.0		3912,3810	-3.1	0.5	16	dbSNP_116	54	1472,7128	747.2+/-407.3	128,1216,2956	no	coding-synonymous,coding-synonymous	RBBP6	NM_006910.4,NM_018703.3	,	185,1814,4498	GG,GC,CC		17.1163,16.2039,16.8078	,	1304/1793,1270/1759	24582299	2184,10810	2197	4300	6497	SO:0001819	synonymous_variant	5930	exon18			CAATACCGCGCCA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3912C>G	16.37:g.24582299C>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	173	80	0.462428	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																			C|0.848;G|0.152	0.152	strong		0.393	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
GRM8	2918	hgsc.bcm.edu	37	7	126544178	126544178	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:126544178C>T	ENST00000339582.2	-	5	1674	c.866G>A	c.(865-867)aGg>aAg	p.R289K	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000444921.2_Missense_Mutation_p.R289K|GRM8_ENST00000358373.3_Missense_Mutation_p.R289K|GRM8_ENST00000405249.1_Missense_Mutation_p.R289K			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	289					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)				TTCCAATATCCTCCTACAGGA	0.348										HNSCC(24;0.065)																											p.R289K		Atlas-SNP	.											GRM8_ENST00000405249,NS,malignant_melanoma,+1,4	GRM8	377	4	0			c.G866A						scavenged	.						82.0	77.0	79.0					7																	126544178		2203	4300	6503	SO:0001583	missense	2918	exon4			AATATCCTCCTAC		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.866G>A	7.37:g.126544178C>T	ENSP00000344173:p.Arg289Lys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	126	3	0.0238095	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.677268	0.47886	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249;ENST00000457830	D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66	5.27	5.27	0.74061	Extracellular ligand-binding receptor (1);	0.065861	0.64402	D	0.000009	T	0.77143	0.4087	L	0.31578	0.945	0.58432	D	0.999999	B;B;B	0.17038	0.017;0.02;0.016	B;B;B	0.24155	0.051;0.006;0.034	T	0.71451	-0.4589	10	0.35671	T	0.21	.	17.9065	0.88919	0.0:1.0:0.0:0.0	.	289;289;289	O00222-3;O00222-2;O00222	.;.;GRM8_HUMAN	K	289	ENSP00000344173:R289K;ENSP00000409790:R289K;ENSP00000351142:R289K;ENSP00000385731:R289K;ENSP00000415522:R289K	ENSP00000344173:R289K	R	-	2	0	GRM8	126331414	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.720000	0.84759	2.467000	0.83353	0.508000	0.49915	AGG	.	.	none		0.348	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
SNAI3	333929	hgsc.bcm.edu	37	16	88747799	88747799	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88747799C>T	ENST00000332281.5	-	2	486	c.400G>A	c.(400-402)Ggg>Agg	p.G134R	SNAI3-AS1_ENST00000563261.1_RNA	NM_178310.3	NP_840101.1	Q3KNW1	SNAI3_HUMAN	snail family zinc finger 3	134					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	copper ion binding (GO:0005507)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G134R(1)		NS(1)|central_nervous_system(1)|kidney(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(80;0.048)		TCCGGAGCCCCGTGCCGGTCT	0.667																																					p.G134R	Colon(27;366 710 19748 23199 27567)	Atlas-SNP	.											SNAI3,NS,malignant_melanoma,0,1	SNAI3	23	1	1	Substitution - Missense(1)	NS(1)	c.G400A						scavenged	.						45.0	56.0	52.0					16																	88747799		2198	4299	6497	SO:0001583	missense	333929	exon2			GAGCCCCGTGCCG	BC041461	CCDS32505.1	16q24.3	2013-05-23	2013-05-23			ENSG00000185669		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	18411	protein-coding gene	gene with protein product		612741	"""zinc finger protein 293"", ""snail homolog 3 (Drosophila)"""	ZNF293		12579345	Standard	NM_178310		Approved	SMUC, Zfp293	uc002flj.3	Q3KNW1		ENST00000332281.5:c.400G>A	16.37:g.88747799C>T	ENSP00000327968:p.Gly134Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	3	0.0267857	NM_178310	Q86SU5	Missense_Mutation	SNP	ENST00000332281.5	37	CCDS32505.1	.	.	.	.	.	.	.	.	.	.	C	4.889	0.165211	0.09339	.	.	ENSG00000185669	ENST00000332281	T	0.06449	3.3	4.64	-2.91	0.05631	.	2.065270	0.01995	N	0.045808	T	0.03959	0.0111	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41413	-0.9510	10	0.33940	T	0.23	0.982	8.5383	0.33377	0.0:0.3365:0.1238:0.5397	.	134	Q3KNW1	SNAI3_HUMAN	R	134	ENSP00000327968:G134R	ENSP00000327968:G134R	G	-	1	0	SNAI3	87275300	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.196000	0.09532	-0.792000	0.04480	-1.579000	0.00862	GGG	.	.	none		0.667	SNAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422582.1		
KIAA1755	85449	hgsc.bcm.edu	37	20	36869741	36869741	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36869741G>A	ENST00000279024.4	-	3	1063	c.792C>T	c.(790-792)gaC>gaT	p.D264D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	264										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)				TGACCACCTCGTCCATCCTGA	0.572																																					p.D264D		Atlas-SNP	.											KIAA1755,NS,malignant_melanoma,-2,2	KIAA1755	145	2	0			c.C792T						scavenged	.						138.0	122.0	127.0					20																	36869741		2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			CACCTCGTCCATC	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.792C>T	20.37:g.36869741G>A		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	185	89	0.481081	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			.	.	none		0.572	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
MTUS1	57509	hgsc.bcm.edu	37	8	17541957	17541957	+	Silent	SNP	C	C	T	rs74754090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:17541957C>T	ENST00000262102.6	-	7	2942	c.2718G>A	c.(2716-2718)acG>acA	p.T906T	MTUS1_ENST00000519263.1_Silent_p.T852T|MTUS1_ENST00000544260.1_Silent_p.T51T|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000297488.6_Silent_p.T72T|MTUS1_ENST00000381869.3_Silent_p.T852T|MIR548V_ENST00000584165.1_RNA|MTUS1_ENST00000381861.3_Silent_p.T153T	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	906					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)		TTTTATATTGCGTCAATTCAA	0.443													C|||	418	0.0834665	0.0469	0.111	5008	,	,		20121	0.0982		0.005	False		,,,				2504	0.1789				p.T906T		Atlas-SNP	.											.	MTUS1	144	.	0			c.G2718A						PASS	.	C	,,,,	159,3719		3,153,1783	261.0	253.0	255.0		2718,2556,459,153,216	-2.7	0.4	8	dbSNP_132	255	70,8218		0,70,4074	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	,,,,	3,223,5857	TT,TC,CC		0.8446,4.1001,1.8823	,,,,	906/1271,852/1217,153/518,51/416,72/437	17541957	229,11937	1939	4144	6083	SO:0001819	synonymous_variant	57509	exon7			ATATTGCGTCAAT	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.2718G>A	8.37:g.17541957C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			C|0.967;T|0.033	0.033	strong		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
SNRNP48	154007	hgsc.bcm.edu	37	6	7590624	7590624	+	Missense_Mutation	SNP	C	C	T	rs2757594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:7590624C>T	ENST00000342415.5	+	1	193	c.134C>T	c.(133-135)cCc>cTc	p.P45L		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	45			P -> L (in dbSNP:rs2757594). {ECO:0000269|PubMed:15489334}.		mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						AGTCTGGATCCCGGGGAAGAG	0.687													C|||	1070	0.213658	0.1415	0.2435	5008	,	,		12876	0.0744		0.3817	False		,,,				2504	0.2607				p.P45L		Atlas-SNP	.											.	SNRNP48	32	.	0			c.C134T						PASS	.	C	LEU/PRO	702,3610		72,558,1526	11.0	13.0	13.0		134	2.3	0.7	6	dbSNP_100	13	3045,5415		579,1887,1764	yes	missense	SNRNP48	NM_152551.3	98	651,2445,3290	TT,TC,CC		35.9929,16.2801,29.3376	benign	45/340	7590624	3747,9025	2156	4230	6386	SO:0001583	missense	154007	exon1			TGGATCCCGGGGA	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"""U11/U12 snRNP 48K"""		"""chromosome 6 open reading frame 151"""	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.134C>T	6.37:g.7590624C>T	ENSP00000339834:p.Pro45Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Missense_Mutation	SNP	ENST00000342415.5	37	CCDS4502.1	507	0.23214285714285715	77	0.1565040650406504	103	0.2845303867403315	36	0.06293706293706294	291	0.3839050131926121	C	15.96	2.985607	0.53934	0.162801	0.359929	ENSG00000168566	ENST00000342415;ENST00000397475	T	0.30182	1.54	5.16	2.33	0.28932	.	0.471174	0.19972	N	0.101950	T	0.06325	0.0163	N	0.19112	0.55	0.28431	P	0.9172821	B	0.02656	0.0	B	0.06405	0.002	T	0.24584	-1.0156	9	0.33940	T	0.23	-0.0562	5.8231	0.18538	0.0:0.6621:0.1573:0.1807	rs2757594;rs17397753;rs52799491;rs59594751;rs2757594	45	Q6IEG0	SNR48_HUMAN	L	45	ENSP00000339834:P45L	ENSP00000339834:P45L	P	+	2	0	SNRNP48	7535623	0.012000	0.17670	0.748000	0.31131	0.993000	0.82548	0.390000	0.20768	0.545000	0.28902	0.563000	0.77884	CCC	C|0.778;T|0.222	0.222	strong		0.687	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551	
HLA-A	3105	hgsc.bcm.edu	37	6	29910698	29910698	+	Missense_Mutation	SNP	G	G	A	rs1059449	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29910698G>A	ENST00000396634.1	+	4	579	c.238G>A	c.(238-240)Ggg>Agg	p.G80R	HLA-A_ENST00000376809.5_Missense_Mutation_p.G80R|HLA-A_ENST00000376806.5_Missense_Mutation_p.G80R|HLA-A_ENST00000376802.2_Missense_Mutation_p.G80R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	80	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGAGCAGGAGGGGCCGGAGTA	0.657									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	405	0.0808706	0.1528	0.0908	5008	,	,		12494	0.0506		0.0537	False		,,,				2504	0.0358				p.G80R		Atlas-SNP	.											.	HLA-A	89	.	0			c.G238A						PASS	.	G	ARG/GLY	609,3797		44,521,1638	59.0	63.0	62.0		238	2.8	0.0	6	dbSNP_86	62	423,8177		21,381,3898	no	missense	HLA-A	NM_002116.7	125	65,902,5536	AA,AG,GG		4.9186,13.8221,7.9348	possibly-damaging	80/366	29910698	1032,11974	2203	4300	6503	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CAGGAGGGGCCGG	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.238G>A	6.37:g.29910698G>A	ENSP00000379873:p.Gly80Arg	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	242	130	0.53719	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	236	0.10805860805860806	98	0.1991869918699187	46	0.1270718232044199	50	0.08741258741258741	42	0.055408970976253295	.	14.97	2.695089	0.48202	0.138221	0.049186	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00912	5.55;5.55;5.55;5.55	3.72	2.81	0.32909	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	.	.	.	.	T	0.03348	0.0097	H	0.96833	3.89	0.80722	P	0.0	B;P;P;P	0.51351	0.004;0.822;0.944;0.805	B;P;P;P	0.58013	0.046;0.782;0.782;0.831	T	0.01800	-1.1271	8	0.87932	D	0	.	9.1894	0.37189	0.0:0.2232:0.7768:0.0	rs1059449;rs2230985;rs3200129;rs16895981;rs41550018	80;80;80;80	P13746;Q5SRN7;Q5SRN5;P04439	1A11_HUMAN;.;.;1A03_HUMAN	R	80	ENSP00000379873:G80R;ENSP00000366002:G80R;ENSP00000366005:G80R;ENSP00000365998:G80R	ENSP00000348012:G80R	G	+	1	0	HLA-A	30018677	0.001000	0.12720	0.012000	0.15200	0.204000	0.24138	0.539000	0.23175	0.889000	0.36185	0.478000	0.44815	GGG	G|0.915;A|0.085	0.085	strong		0.657	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
RFX7	64864	hgsc.bcm.edu	37	15	56387142	56387142	+	Silent	SNP	G	G	A	rs34361729	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:56387142G>A	ENST00000559447.2	-	9	2764	c.2493C>T	c.(2491-2493)caC>caT	p.H831H	RFX7_ENST00000423270.1_Silent_p.H928H|RFX7_ENST00000422057.1_Silent_p.H831H|RFX7_ENST00000317318.6_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	86	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	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	
PCDHGA7	56108	hgsc.bcm.edu	37	5	140763339	140763339	+	Missense_Mutation	SNP	G	G	A	rs187406135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140763339G>A	ENST00000518325.1	+	1	873	c.873G>A	c.(871-873)atG>atA	p.M291I	PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	291	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(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)			TTCCAAAGATGTTTCATCTGA	0.413													.|||	2	0.000399361	0.0	0.0029	5008	,	,		22196	0.0		0.0	False		,,,				2504	0.0				p.M291I		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.G873A						PASS	.						56.0	56.0	56.0					5																	140763339		1866	4110	5976	SO:0001583	missense	56108	exon1			AAAGATGTTTCAT	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.873G>A	5.37:g.140763339G>A	ENSP00000430024:p.Met291Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	103	41	0.398058	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	0.004	-2.295701	0.00245	.	.	ENSG00000253537	ENST00000518325	T	0.51574	0.7	5.15	-3.98	0.04082	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.12646	0.0307	N	0.01048	-1.04	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.25363	-1.0134	9	0.13108	T	0.6	.	2.6961	0.05135	0.189:0.2096:0.4053:0.1961	.	291;291	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	I	291	ENSP00000430024:M291I	ENSP00000430024:M291I	M	+	3	0	PCDHGA7	140743523	0.000000	0.05858	0.081000	0.20488	0.030000	0.12068	-1.451000	0.02387	-0.495000	0.06659	-0.302000	0.09304	ATG	G|1.000;A|0.000	0.000	strong		0.413	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
LMO7	4008	hgsc.bcm.edu	37	13	76395620	76395620	+	Missense_Mutation	SNP	C	C	T	rs9593132	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:76395620C>T	ENST00000321797.8	+	12	2537	c.1816C>T	c.(1816-1818)Cgt>Tgt	p.R606C	LMO7_ENST00000377534.3_Missense_Mutation_p.R891C|LMO7_ENST00000357063.3_Missense_Mutation_p.R891C|LMO7_ENST00000526202.1_Missense_Mutation_p.R456C|LMO7_ENST00000465261.2_Missense_Mutation_p.R606C|LMO7_ENST00000341547.4_Missense_Mutation_p.R557C			Q8WWI1	LMO7_HUMAN	LIM domain 7	891					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R891S(1)|p.R606S(1)|p.R557S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		GGAATCAACTCGTGTTTCAGC	0.468													C|||	417	0.0832668	0.0628	0.0937	5008	,	,		20167	0.121		0.0517	False		,,,				2504	0.0971				p.R606C		Atlas-SNP	.											.	LMO7	334	.	3	Substitution - Missense(3)	lung(3)	c.C1816T						PASS	.	C	CYS/ARG,CYS/ARG	249,4157	145.0+/-179.8	4,241,1958	103.0	98.0	99.0		1669,1816	5.0	1.0	13	dbSNP_119	99	391,8209	126.3+/-184.8	10,371,3919	yes	missense,missense	LMO7	NM_005358.5,NM_015842.2	180,180	14,612,5877	TT,TC,CC		4.5465,5.6514,4.9208	probably-damaging,probably-damaging	557/1350,606/1386	76395620	640,12366	2203	4300	6503	SO:0001583	missense	4008	exon11			TCAACTCGTGTTT	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.1816C>T	13.37:g.76395620C>T	ENSP00000317802:p.Arg606Cys	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	203	98	0.482759	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		169|169	0.07738095238095238|0.07738095238095238	29|29	0.05894308943089431|0.05894308943089431	31|31	0.0856353591160221|0.0856353591160221	68|68	0.11888111888111888|0.11888111888111888	41|41	0.05408970976253298|0.05408970976253298	C|C	25.6|25.6	4.654163|4.654163	0.88056|0.88056	0.056514|0.056514	0.045465|0.045465	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000447038	T;T;T;T;T;T;T|.	0.55052|.	0.54;0.54;0.54;0.54;0.54;0.54;0.54|.	5.91|5.91	5.01|5.01	0.66863|0.66863	.|.	0.336411|.	0.31233|.	N|.	0.008008|.	T|T	0.03390|0.03390	0.0098|0.0098	M|M	0.76002|0.76002	2.32|2.32	0.19775|0.19775	P|P	0.9999524132|0.9999524132	D;D;D;D;D|.	0.89917|.	0.999;1.0;1.0;0.999;1.0|.	P;P;D;P;D|.	0.79784|.	0.72;0.897;0.988;0.72;0.993|.	T|T	0.35500|0.35500	-0.9786|-0.9786	9|4	0.72032|.	D|.	0.01|.	-8.1547|-8.1547	15.8911|15.8911	0.79299|0.79299	0.136:0.864:0.0:0.0|0.136:0.864:0.0:0.0	rs9593132;rs52821804;rs60587323;rs9593132|rs9593132;rs52821804;rs60587323;rs9593132	456;557;891;606;839|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	C|L	557;891;891;505;606;456;606|514	ENSP00000342112:R557C;ENSP00000349571:R891C;ENSP00000366757:R891C;ENSP00000366719:R505C;ENSP00000317802:R606C;ENSP00000431129:R456C;ENSP00000433352:R606C|.	ENSP00000317802:R606C|.	R|S	+|+	1|2	0|0	LMO7|LMO7	75293621|75293621	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.939000|0.939000	0.58152|0.58152	3.903000|3.903000	0.56318|0.56318	2.791000|2.791000	0.96007|0.96007	0.650000|0.650000	0.86243|0.86243	CGT|TCG	C|0.935;T|0.065	0.065	strong		0.468	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
DHX33	56919	hgsc.bcm.edu	37	17	5347788	5347788	+	Missense_Mutation	SNP	G	G	A	rs75426953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5347788G>A	ENST00000225296.3	-	12	2061	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	DHX33_ENST00000433302.3_Missense_Mutation_p.R397C	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	621					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						AGGCAGCGGCGGACACTCTCC	0.607													G|||	35	0.00698882	0.0008	0.0086	5008	,	,		19061	0.001		0.0239	False		,,,				2504	0.0031				p.R621C		Atlas-SNP	.											DHX33,NS,carcinoma,0,1	DHX33	41	1	0			c.C1861T						PASS	.	G	CYS/ARG,CYS/ARG	24,4382	30.8+/-60.4	1,22,2180	74.0	69.0	70.0		1342,1861	4.6	1.0	17	dbSNP_131	70	203,8397	88.4+/-150.7	2,199,4099	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	180,180	3,221,6279	AA,AG,GG		2.3605,0.5447,1.7453	probably-damaging,probably-damaging	448/535,621/708	5347788	227,12779	2203	4300	6503	SO:0001583	missense	56919	exon12			AGCGGCGGACACT	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.1861C>T	17.37:g.5347788G>A	ENSP00000225296:p.Arg621Cys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	17	0.022427440633245383	G	25.8	4.678553	0.88542	0.005447	0.023605	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.02890	4.12;4.12	4.59	4.59	0.56863	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	M	0.85373	2.75	0.80722	D	1	D;P	0.89917	1.0;0.626	D;B	0.81914	0.995;0.287	T	0.00235	-1.1892	10	0.66056	D	0.02	.	16.9197	0.86161	0.0:0.0:1.0:0.0	.	397;621	Q05BE5;Q9H6R0	.;DHX33_HUMAN	C	621;397	ENSP00000225296:R621C;ENSP00000413779:R397C	ENSP00000225296:R621C	R	-	1	0	DHX33	5288512	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.073000	0.93992	2.548000	0.85928	0.561000	0.74099	CGC	A|0.014;C|0.000;G|0.986	0.014	strong		0.607	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45555829	45555829	+	Silent	SNP	T	T	C	rs7231151	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:45555829T>C	ENST00000588982.1	-	4	2163	c.1662A>G	c.(1660-1662)acA>acG	p.T554T	ZBTB7C_ENST00000332053.2_Silent_p.T554T|ZBTB7C_ENST00000590800.1_Silent_p.T554T|ZBTB7C_ENST00000535628.2_Silent_p.T554T|ZBTB7C_ENST00000586438.1_Silent_p.T554T			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	554							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						GCTTCATCTGTGTCTCCTCGA	0.721													C|||	2061	0.411542	0.562	0.366	5008	,	,		9999	0.4673		0.2594	False		,,,				2504	0.3395				p.T554T		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.A1662G						PASS	.	C		2040,2344		497,1046,649	12.0	12.0	12.0		1662	0.5	1.0	18	dbSNP_116	12	2358,6186		325,1708,2239	no	coding-synonymous	ZBTB7C	NM_001039360.2		822,2754,2888	CC,CT,TT		27.5983,46.5328,34.0192		554/620	45555829	4398,8530	2192	4272	6464	SO:0001819	synonymous_variant	201501	exon3			CATCTGTGTCTCC	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.1662A>G	18.37:g.45555829T>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			T|0.652;C|0.348	0.348	strong		0.721	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
DAOA	267012	hgsc.bcm.edu	37	13	106142235	106142235	+	Intron	SNP	C	C	T	rs778294	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:106142235C>T	ENST00000375936.3	+	4	327				DAOA_ENST00000329625.5_Intron|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						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)					caactgagaccggatctcctt	0.498													c|||	1087	0.217053	0.2405	0.2507	5008	,	,		17670	0.1081		0.2763	False		,,,				2504	0.2127				p.T61T		Atlas-SNP	.											.	DAOA	26	.	0			c.C183T						PASS	.	T	,,	957,3427	319.3+/-296.1	117,723,1352	78.0	84.0	82.0		183,,	-4.4	0.0	13	dbSNP_86	82	2447,6137	391.3+/-343.6	344,1759,2189	no	coding-synonymous,intron,intron	DAOA	NM_001161812.1,NM_001161814.1,NM_172370.3	,,	461,2482,3541	TT,TC,CC		28.5065,21.8294,26.2492	,,	61/126,,	106142235	3404,9564	2192	4292	6484	SO:0001627	intron_variant	267012	exon4			TGAGACCGGATCT	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.282-15C>T	13.37:g.106142235C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001161812	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Silent	SNP	ENST00000375936.3	37	CCDS41905.1																																																																																			C|0.763;T|0.237	0.237	strong		0.498	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370	
OR2D3	120775	hgsc.bcm.edu	37	11	6942695	6942695	+	Missense_Mutation	SNP	C	C	T	rs12806437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	281	0	0		WXS	Illumina HiSeq	Phase_I	270	144	0.533333	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	
ASAP2	8853	hgsc.bcm.edu	37	2	9514917	9514917	+	Silent	SNP	C	C	T	rs33930824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:9514917C>T	ENST00000281419.3	+	17	1930	c.1590C>T	c.(1588-1590)taC>taT	p.Y530Y	ASAP2_ENST00000315273.4_Silent_p.Y530Y	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	530	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						CAGCCAAGTACATCGAGAGGA	0.502													C|||	662	0.132188	0.0295	0.1513	5008	,	,		19184	0.001		0.2594	False		,,,				2504	0.2618				p.Y530Y		Atlas-SNP	.											.	ASAP2	91	.	0			c.C1590T						PASS	.	C	,	302,4104	163.6+/-195.4	9,284,1910	106.0	99.0	102.0		1590,1590	2.5	1.0	2	dbSNP_126	102	2204,6396	375.5+/-337.8	288,1628,2384	no	coding-synonymous,coding-synonymous	ASAP2	NM_001135191.1,NM_003887.2	,	297,1912,4294	TT,TC,CC		25.6279,6.8543,19.268	,	530/962,530/1007	9514917	2506,10500	2203	4300	6503	SO:0001819	synonymous_variant	8853	exon17			CAAGTACATCGAG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1590C>T	2.37:g.9514917C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_001135191	D6W4Y8	Silent	SNP	ENST00000281419.3	37	CCDS1661.1																																																																																			C|0.825;T|0.175	0.175	strong		0.502	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887	
OR1S2	219958	hgsc.bcm.edu	37	11	57971201	57971201	+	Silent	SNP	G	G	A	rs11229280	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57971201G>A	ENST00000302592.6	-	1	452	c.453C>T	c.(451-453)gcC>gcT	p.A151A		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A151A(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGCCGAACCTGGCCCGCATGA	0.478													G|||	2575	0.514177	0.2806	0.4971	5008	,	,		22031	0.7927		0.4245	False		,,,				2504	0.6472				p.A151A		Atlas-SNP	.											OR1S2,NS,carcinoma,-2,3	OR1S2	119	3	1	Substitution - coding silent(1)	stomach(1)	c.C453T						PASS	.	G		1327,3075	446.5+/-348.0	200,927,1074	165.0	156.0	159.0		453	-1.2	0.0	11	dbSNP_120	159	3639,4953	524.0+/-380.4	784,2071,1441	no	coding-synonymous	OR1S2	NM_001004459.1		984,2998,2515	AA,AG,GG		42.3534,30.1454,38.2176		151/326	57971201	4966,8028	2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			GAACCTGGCCCGC	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.453C>T	11.37:g.57971201G>A		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	251	104	0.414343	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.585;A|0.415	0.415	strong		0.478	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
ADRA1D	146	hgsc.bcm.edu	37	20	4228735	4228735	+	Silent	SNP	C	C	T	rs35105284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:4228735C>T	ENST00000379453.4	-	1	986	c.870G>A	c.(868-870)gcG>gcA	p.A290A		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	290					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	GCTTGACGCCCGCCTCGAGGC	0.716													c|||	1026	0.204872	0.1679	0.317	5008	,	,		12525	0.0546		0.2753	False		,,,				2504	0.2577				p.A290A		Atlas-SNP	.											.	ADRA1D	36	.	0			c.G870A						PASS	.			748,3524		84,580,1472	13.0	11.0	12.0		870	-2.3	1.0	20	dbSNP_126	12	2056,6376		285,1486,2445	no	coding-synonymous	ADRA1D	NM_000678.3		369,2066,3917	TT,TC,CC		24.3833,17.5094,22.0718		290/573	4228735	2804,9900	2136	4216	6352	SO:0001819	synonymous_variant	146	exon1			GACGCCCGCCTCG	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"""GPCR / Class A : Adrenoceptors : alpha"""	280	protein-coding gene	gene with protein product		104219	"""adrenergic, alpha-1D-, receptor"""			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.870G>A	20.37:g.4228735C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	19	12	0.631579	NM_000678	Q9NPY0	Silent	SNP	ENST00000379453.4	37	CCDS13079.1																																																																																			C|0.787;T|0.213	0.213	strong		0.716	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678	
PSKH2	85481	hgsc.bcm.edu	37	8	87060927	87060927	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87060927G>A	ENST00000276616.2	-	3	996	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	308	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						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)			GCTGACATGCGATGACCAGCC	0.478																																					p.R308C		Atlas-SNP	.											PSKH2,caecum,carcinoma,+1,2	PSKH2	79	2	0			c.C922T						PASS	.						75.0	82.0	80.0					8																	87060927		2203	4300	6503	SO:0001583	missense	85481	exon3			ACATGCGATGACC	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.922C>T	8.37:g.87060927G>A	ENSP00000276616:p.Arg308Cys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178342	0.78564	.	.	ENSG00000147613	ENST00000276616	T	0.80738	-1.41	4.94	4.05	0.47172	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.92938	0.7753	H	0.98646	4.29	0.46260	D	0.998955	D	0.89917	1.0	D	0.97110	1.0	D	0.93418	0.6774	9	0.87932	D	0	.	10.2011	0.43084	0.1009:0.0:0.8991:0.0	.	308	Q96QS6	KPSH2_HUMAN	C	308	ENSP00000276616:R308C	ENSP00000276616:R308C	R	-	1	0	PSKH2	87130043	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.946000	0.56644	1.034000	0.39945	0.555000	0.69702	CGC	.	.	none		0.478	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
USP15	9958	hgsc.bcm.edu	37	12	62696599	62696599	+	Silent	SNP	C	C	T	rs11174420	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:62696599C>T	ENST00000280377.5	+	3	304	c.246C>T	c.(244-246)caC>caT	p.H82H	USP15_ENST00000312635.6_Silent_p.H82H|USP15_ENST00000550632.1_3'UTR|USP15_ENST00000393654.3_Silent_p.H82H|USP15_ENST00000353364.3_Silent_p.H82H	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	82	DUSP. {ECO:0000255|PROSITE- ProRule:PRU00613}.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TTAAGGAACACCTTATTGATG	0.363													T|||	1595	0.31849	0.4849	0.2392	5008	,	,		16503	0.1528		0.3082	False		,,,				2504	0.3313				p.H82H	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.C246T						PASS	.	T		2023,2383	611.5+/-391.8	469,1085,649	141.0	137.0	138.0		246	2.1	1.0	12	dbSNP_120	138	2637,5963	686.7+/-404.1	399,1839,2062	no	coding-synonymous	USP15	NM_006313.1		868,2924,2711	TT,TC,CC		30.6628,45.9147,35.8296		82/953	62696599	4660,8346	2203	4300	6503	SO:0001819	synonymous_variant	9958	exon3			GGAACACCTTATT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.246C>T	12.37:g.62696599C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	CCDS58251.1	647	0.29624542124542125	235	0.47764227642276424	95	0.26243093922651933	96	0.16783216783216784	221	0.29155672823219	T	9.131	1.011384	0.19277	0.459147	0.306628	ENSG00000135655	ENST00000549237	.	.	.	5.72	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48080	-0.9066	3	.	.	.	-16.2145	9.3407	0.38079	0.0:0.2693:0.0:0.7307	rs11174420;rs61396060;rs11174420	.	.	.	I	78	.	.	T	+	2	0	USP15	60982866	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	1.279000	0.33191	-0.090000	0.12462	-0.381000	0.06696	ACC	C|0.662;T|0.338	0.338	strong		0.363	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
IQCE	23288	hgsc.bcm.edu	37	7	2644519	2644519	+	Missense_Mutation	SNP	C	C	T	rs2293404	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2644519C>T	ENST00000402050.2	+	19	1821	c.1637C>T	c.(1636-1638)gCt>gTt	p.A546V	IQCE_ENST00000404984.1_Missense_Mutation_p.A495V|IQCE_ENST00000438376.2_Missense_Mutation_p.A530V|IQCE_ENST00000325979.7_Missense_Mutation_p.A481V	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	546	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.		A -> V (in dbSNP:rs2293404).			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)		TGACAGGCGGCTGTGGTGCTT	0.642													C|||	2062	0.411741	0.3956	0.4625	5008	,	,		18690	0.495		0.326	False		,,,				2504	0.3998				p.A546V		Atlas-SNP	.											IQCE,NS,carcinoma,0,1	IQCE	66	1	0			c.C1637T						PASS	.	C	VAL/ALA,VAL/ALA	1489,2673		282,925,874	43.0	49.0	47.0		1589,1637	4.9	0.0	7	dbSNP_100	47	2309,6123		307,1695,2214	yes	missense,missense	IQCE	NM_001100390.1,NM_152558.3	64,64	589,2620,3088	TT,TC,CC		27.3838,35.7761,30.1572	benign,benign	530/680,546/696	2644519	3798,8796	2081	4216	6297	SO:0001583	missense	23288	exon19			AGGCGGCTGTGGT	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.1637C>T	7.37:g.2644519C>T	ENSP00000385597:p.Ala546Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	878	0.40201465201465203	187	0.3800813008130081	144	0.39779005524861877	298	0.5209790209790209	249	0.32849604221635886	C	7.940	0.742568	0.15642	0.357761	0.273838	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979;ENST00000423196	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	4.9	4.9	0.64082	.	0.472269	0.21142	N	0.079466	T	0.00012	0.0000	L	0.46741	1.465	0.58432	P	1.0000000000287557E-6	B;B;P;P	0.38745	0.187;0.187;0.645;0.592	B;B;B;B	0.40444	0.19;0.176;0.329;0.221	T	0.51585	-0.8687	9	0.39692	T	0.17	-6.2302	13.6658	0.62393	0.0:1.0:0.0:0.0	rs2293404;rs52800467;rs61534484;rs2293404	481;530;546;530	B4DXN1;B4DDX4;Q6IPM2;Q6IPM2-4	.;.;IQCE_HUMAN;.	V	546;495;530;481;126	ENSP00000385597:A546V;ENSP00000385945:A495V;ENSP00000396178:A530V;ENSP00000313772:A481V;ENSP00000405982:A126V	ENSP00000313772:A481V	A	+	2	0	IQCE	2611045	0.889000	0.30405	0.031000	0.17742	0.630000	0.37929	2.567000	0.45956	2.286000	0.76751	0.650000	0.86243	GCT	C|0.622;T|0.378	0.378	strong		0.642	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
PWP1	11137	hgsc.bcm.edu	37	12	108096769	108096769	+	Missense_Mutation	SNP	G	G	C	rs11547907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:108096769G>C	ENST00000412830.3	+	9	1032	c.864G>C	c.(862-864)ttG>ttC	p.L288F	PWP1_ENST00000541166.1_Missense_Mutation_p.L226F	NM_007062.1	NP_008993.1	Q13610	PWP1_HUMAN	PWP1 homolog (S. cerevisiae)	288			L -> F (in dbSNP:rs11547907).		transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|endometrium(4)|kidney(1)|large_intestine(8)|lung(6)|urinary_tract(1)	23						ATATGTCCTTGGGGAAACCAG	0.403													G|||	226	0.0451278	0.0098	0.0245	5008	,	,		17751	0.0774		0.0348	False		,,,				2504	0.0849				p.L288F		Atlas-SNP	.											.	PWP1	43	.	0			c.G864C						PASS	.	G	PHE/LEU	84,4322	72.0+/-110.0	2,80,2121	121.0	111.0	114.0		864	4.8	1.0	12	dbSNP_120	114	340,8260	117.6+/-177.1	5,330,3965	yes	missense	PWP1	NM_007062.1	22	7,410,6086	CC,CG,GG		3.9535,1.9065,3.26	benign	288/502	108096769	424,12582	2203	4300	6503	SO:0001583	missense	11137	exon9			GTCCTTGGGGAAA	BC000067	CCDS9114.1	12q23.3	2013-06-10				ENSG00000136045		"""WD repeat domain containing"""	17015	protein-coding gene	gene with protein product	"""endonuclein"""					7828893, 11850830	Standard	NM_007062		Approved	IEF-SSP-9502	uc001tmo.1	Q13610	OTTHUMG00000169913	ENST00000412830.3:c.864G>C	12.37:g.108096769G>C	ENSP00000387365:p.Leu288Phe	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_007062	A8K3R6|Q7Z3X9	Missense_Mutation	SNP	ENST00000412830.3	37	CCDS9114.1	87	0.03983516483516483	11	0.022357723577235773	11	0.03038674033149171	37	0.06468531468531469	28	0.036939313984168866	G	14.02	2.410319	0.42715	0.019065	0.039535	ENSG00000136045	ENST00000412830;ENST00000258531;ENST00000541166	T;T	0.29142	1.58;2.23	5.71	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.543212	0.20171	N	0.097733	T	0.02418	0.0074	L	0.27053	0.805	0.29613	N	0.846797	B	0.17667	0.023	B	0.25140	0.058	T	0.04767	-1.0928	10	0.56958	D	0.05	.	8.9358	0.35700	0.2248:0.0:0.7752:0.0	rs11547907;rs52791867;rs11547907	288	Q13610	PWP1_HUMAN	F	288;288;226	ENSP00000387365:L288F;ENSP00000445249:L226F	ENSP00000258531:L288F	L	+	3	2	PWP1	106620899	1.000000	0.71417	0.991000	0.47740	0.961000	0.63080	2.422000	0.44696	1.422000	0.47177	-0.140000	0.14226	TTG	G|0.964;C|0.036	0.036	strong		0.403	PWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406539.1	NM_007062	
CTAGE5	4253	hgsc.bcm.edu	37	14	39818076	39818076	+	Missense_Mutation	SNP	A	A	G	rs61742363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:39818076A>G	ENST00000280083.3	+	23	2457	c.2143A>G	c.(2143-2145)Aga>Gga	p.R715G	CTAGE5_ENST00000557038.1_Missense_Mutation_p.R635G|CTAGE5_ENST00000341749.3_Missense_Mutation_p.R703G|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.R686G|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.R1250G|CTAGE5_ENST00000556148.1_Missense_Mutation_p.R640G|CTAGE5_ENST00000553352.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000348007.3_Missense_Mutation_p.R672G|CTAGE5_ENST00000553383.1_3'UTR|CTAGE5_ENST00000396165.4_Missense_Mutation_p.R686G|CTAGE5_ENST00000341502.5_Missense_Mutation_p.R715G|CTAGE5_ENST00000396158.2_Missense_Mutation_p.R720G			O15320	CTGE5_HUMAN	CTAGE family, member 5	715	Pro-rich.				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)		ATTCTTGAGAAGAGGACCTCC	0.532													A|||	27	0.00539137	0.0	0.0173	5008	,	,		14299	0.0		0.0149	False		,,,				2504	0.0				p.R720G		Atlas-SNP	.											.	CTAGE5	75	.	0			c.A2158G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	16,4390	22.3+/-47.3	0,16,2187	125.0	130.0	129.0		2143,2107,2014,2056	3.1	1.0	14	dbSNP_129	129	156,8444	73.5+/-136.2	0,156,4144	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	125,125,125,125	0,172,6331	GG,GA,AA		1.814,0.3631,1.3225	probably-damaging,probably-damaging,probably-damaging,probably-damaging	715/805,703/793,672/762,686/776	39818076	172,12834	2203	4300	6503	SO:0001583	missense	4253	exon23			TTGAGAAGAGGAC	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.2143A>G	14.37:g.39818076A>G	ENSP00000280083:p.Arg715Gly	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	169	98	0.579882	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	22	0.010073260073260074	0	0.0	8	0.022099447513812154	0	0.0	14	0.018469656992084433	A	14.78	2.638501	0.47153	0.003631	0.01814	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.4;2.37;2.36;2.91;2.63;2.64;2.36;3.17;2.36	5.64	3.12	0.35913	.	0.000000	0.37623	N	0.002009	T	0.12178	0.0296	M	0.83312	2.635	0.29744	N	0.83689	B;B;B;B;B	0.28713	0.22;0.181;0.22;0.181;0.22	B;B;B;B;B	0.29267	0.1;0.074;0.1;0.074;0.1	T	0.06588	-1.0818	9	.	.	.	.	11.6343	0.51194	0.6083:0.3917:0.0:0.0	rs61742363	720;672;715;643;703	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	G	1250;703;635;686;715;720;715;640;672;686	ENSP00000452252:R1250G;ENSP00000343897:R703G;ENSP00000450869:R635G;ENSP00000379468:R686G;ENSP00000339286:R715G;ENSP00000379462:R720G;ENSP00000280083:R715G;ENSP00000452562:R640G;ENSP00000343912:R672G;ENSP00000450449:R686G	.	R	+	1	2	CTAGE5;RP11-407N17.3	38887827	1.000000	0.71417	0.992000	0.48379	0.895000	0.52256	0.816000	0.27267	0.940000	0.37473	0.533000	0.62120	AGA	A|0.988;G|0.012	0.012	strong		0.532	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
CNRIP1	25927	hgsc.bcm.edu	37	2	68546374	68546374	+	Silent	SNP	T	T	C	rs4671898	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:68546374T>C	ENST00000263655.3	-	1	764	c.159A>G	c.(157-159)aaA>aaG	p.K53K	CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409862.1_Silent_p.K53K|CNRIP1_ENST00000409559.3_Silent_p.K53K	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	53										kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						GCGTGCTGGGTTTAATCTTCA	0.647													C|||	2068	0.412939	0.5386	0.487	5008	,	,		14600	0.1558		0.4553	False		,,,				2504	0.4121				p.K53K		Atlas-SNP	.											CNRIP1_ENST00000409559,colon,carcinoma,0,6	CNRIP1	45	6	0			c.A159G						PASS	.	C	,	2011,2171		516,979,596	53.0	44.0	47.0		159,159	4.7	1.0	2	dbSNP_111	47	3616,4482		877,1862,1310	no	coding-synonymous,coding-synonymous	CNRIP1	NM_001111101.1,NM_015463.2	,	1393,2841,1906	CC,CT,TT		44.653,48.087,45.8225	,	53/129,53/165	68546374	5627,6653	2091	4049	6140	SO:0001819	synonymous_variant	25927	exon1			GCTGGGTTTAATC	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.159A>G	2.37:g.68546374T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001111101	B2R4D0|Q49AN4|Q9UFZ0	Silent	SNP	ENST00000263655.3	37	CCDS1886.1																																																																																			C|0.424;N|0.000	0.424	strong		0.647	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463	
TTYH2	94015	hgsc.bcm.edu	37	17	72240168	72240168	+	Missense_Mutation	SNP	G	G	A	rs35682745	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72240168G>A	ENST00000269346.4	+	6	858	c.784G>A	c.(784-786)Gct>Act	p.A262T	TTYH2_ENST00000534346.1_3'UTR|TTYH2_ENST00000529107.1_Missense_Mutation_p.A241T	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	262			A -> T (in dbSNP:rs35682745). {ECO:0000269|PubMed:15489334}.			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						ATCCCTGGCCGCTGATGGCTC	0.652													G|||	545	0.108826	0.0847	0.1556	5008	,	,		13730	0.0486		0.1511	False		,,,				2504	0.1268				p.A262T		Atlas-SNP	.											TTYH2,colon,carcinoma,-1,1	TTYH2	63	1	0			c.G784A						PASS	.	G	THR/ALA	513,3893	232.0+/-245.7	34,445,1724	69.0	64.0	66.0		784	3.2	0.0	17	dbSNP_126	66	1327,7273	260.6+/-283.4	108,1111,3081	yes	missense	TTYH2	NM_032646.5	58	142,1556,4805	AA,AG,GG		15.4302,11.6432,14.1473	benign	262/535	72240168	1840,11166	2203	4300	6503	SO:0001583	missense	94015	exon6			CTGGCCGCTGATG		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.784G>A	17.37:g.72240168G>A	ENSP00000269346:p.Ala262Thr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	230	0.10531135531135531	39	0.07926829268292683	50	0.13812154696132597	25	0.043706293706293704	116	0.15303430079155672	G	15.05	2.716813	0.48622	0.116432	0.154302	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.12255	2.7;2.7	5.21	3.16	0.36331	.	0.292448	0.37261	N	0.002167	T	0.00109	0.0003	M	0.78223	2.4	0.20489	P	0.999897314	B;B	0.17667	0.023;0.009	B;B	0.15484	0.01;0.013	T	0.04153	-1.0973	9	0.46703	T	0.11	-4.1565	8.8593	0.35247	0.1856:0.0:0.8144:0.0	rs35682745;rs62065674	241;262	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	T	262;241	ENSP00000269346:A262T;ENSP00000433089:A241T	ENSP00000269346:A262T	A	+	1	0	TTYH2	69751763	0.860000	0.29831	0.028000	0.17463	0.195000	0.23768	4.109000	0.57824	0.536000	0.28733	-0.493000	0.04662	GCT	G|0.877;A|0.123	0.123	strong		0.652	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
EMR1	2015	hgsc.bcm.edu	37	19	6904137	6904137	+	Missense_Mutation	SNP	C	C	T	rs370094	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6904137C>T	ENST00000312053.4	+	8	930	c.893C>T	c.(892-894)gCa>gTa	p.A298V	EMR1_ENST00000381404.4_Missense_Mutation_p.A246V|EMR1_ENST00000250572.8_Missense_Mutation_p.A298V|EMR1_ENST00000381407.5_Missense_Mutation_p.A157V|EMR1_ENST00000450315.3_Intron	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	132	0	0		WXS	Illumina HiSeq	Phase_I	148	82	0.554054	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		
CSMD1	64478	hgsc.bcm.edu	37	8	3351195	3351195	+	Silent	SNP	C	C	A	rs56109797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:3351195C>A	ENST00000520002.1	-	12	1956	c.1401G>T	c.(1399-1401)ctG>ctT	p.L467L	CSMD1_ENST00000537824.1_Silent_p.L466L|CSMD1_ENST00000602723.1_Silent_p.L467L|CSMD1_ENST00000400186.3_Silent_p.L467L|CSMD1_ENST00000542608.1_Silent_p.L466L|CSMD1_ENST00000602557.1_Silent_p.L467L|CSMD1_ENST00000539096.1_Silent_p.L466L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	467	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CACCAACCGTCAGGGTGTCAT	0.498													C|||	463	0.0924521	0.0454	0.0533	5008	,	,		17218	0.1954		0.0716	False		,,,				2504	0.0992				p.L466L		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G1398T						PASS	.	C		214,4150	119.2+/-156.9	6,202,1974	81.0	86.0	84.0		1398	-11.0	0.1	8	dbSNP_129	84	685,7911	164.2+/-216.6	32,621,3645	no	coding-synonymous	CSMD1	NM_033225.5		38,823,5619	AA,AC,CC		7.9688,4.9038,6.9367		466/3565	3351195	899,12061	2182	4298	6480	SO:0001819	synonymous_variant	64478	exon11			AACCGTCAGGGTG			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.1401G>T	8.37:g.3351195C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37																																																																																				C|0.922;A|0.078	0.078	strong		0.498	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
OR2J3	442186	hgsc.bcm.edu	37	6	29080344	29080344	+	Missense_Mutation	SNP	G	G	A	rs3749977	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29080344G>A	ENST00000377169.1	+	1	677	c.677G>A	c.(676-678)cGa>cAa	p.R226Q		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	226			R -> Q (in allele 6M1-3*02; decreased response to C3HEX; dbSNP:rs3749977). {ECO:0000269|PubMed:22714804, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						GCCATCGTCCGAGCTATACTG	0.458													G|||	1861	0.371605	0.6021	0.2752	5008	,	,		22524	0.252		0.2286	False		,,,				2504	0.3988				p.R226Q		Atlas-SNP	.											.	OR2J3	53	.	0			c.G677A						PASS	.	G	GLN/ARG	1332,1250		337,658,296	110.0	118.0	116.0		677	-4.1	0.0	6	dbSNP_107	116	1194,3948		151,892,1528	yes	missense	OR2J3	NM_001005216.2	43	488,1550,1824	AA,AG,GG		23.2205,48.4121,32.7033	benign	226/312	29080344	2526,5198	1291	2571	3862	SO:0001583	missense	442186	exon1			TCGTCCGAGCTAT		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.677G>A	6.37:g.29080344G>A	ENSP00000366374:p.Arg226Gln	Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	370	175	0.472973	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	704	0.32234432234432236	305	0.6199186991869918	95	0.26243093922651933	133	0.23251748251748253	171	0.22559366754617413	G	0.012	-1.666039	0.00765	0.515879	0.232205	ENSG00000204701	ENST00000377169	T	0.39406	1.08	2.78	-4.13	0.03904	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.08403	0.0209	L	0.31294	0.92	0.80722	P	0.0	B	0.12630	0.006	B	0.15870	0.014	T	0.32981	-0.9886	8	0.12766	T	0.61	.	8.1363	0.31056	0.1874:0.1869:0.6257:0.0	rs3749977;rs6923417;rs3749977	226	O76001	OR2J3_HUMAN	Q	226	ENSP00000366374:R226Q	ENSP00000366374:R226Q	R	+	2	0	OR2J3	29188323	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-3.580000	0.00424	-1.536000	0.01738	-0.602000	0.04101	CGA	G|0.651;A|0.349	0.349	strong		0.458	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
OR2D3	120775	hgsc.bcm.edu	37	11	6942726	6942726	+	Missense_Mutation	SNP	G	G	C	rs10839659	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6942726G>C	ENST00000317834.3	+	1	522	c.494G>C	c.(493-495)tGg>tCg	p.W165S		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	165			W -> S (in dbSNP:rs10839659).			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)		TTCAGGTCCTGGGCCAGTGGG	0.493													G|||	1313	0.262181	0.0545	0.3199	5008	,	,		19557	0.3363		0.3827	False		,,,				2504	0.3016				p.W165S		Atlas-SNP	.											.	OR2D3	51	.	0			c.G494C						PASS	.	G	SER/TRP	454,3948	215.8+/-234.7	30,394,1777	133.0	113.0	120.0		494	5.2	1.0	11	dbSNP_120	120	3214,5378	485.7+/-371.7	603,2008,1685	yes	missense	OR2D3	NM_001004684.1	177	633,2402,3462	CC,CG,GG		37.4069,10.3135,28.2284	probably-damaging	165/331	6942726	3668,9326	2201	4296	6497	SO:0001583	missense	120775	exon1			GGTCCTGGGCCAG	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.494G>C	11.37:g.6942726G>C	ENSP00000320560:p.Trp165Ser	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	284	119	0.419014	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	619	0.2834249084249084	38	0.07723577235772358	114	0.3149171270718232	186	0.32517482517482516	281	0.370712401055409	G	19.45	3.829810	0.71258	0.103135	0.374069	ENSG00000178358	ENST00000317834	T	0.59502	0.26	5.17	5.17	0.71159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41938	D	0.000794	T	0.00012	0.0000	H	0.96777	3.88	0.09310	P	0.9999999920009	D	0.89917	1.0	D	0.91635	0.999	T	0.04153	-1.0973	9	0.87932	D	0	-22.9266	16.5766	0.84681	0.0:0.0:1.0:0.0	rs10839659;rs17275979;rs52822521;rs10839659	165	Q8NGH3	OR2D3_HUMAN	S	165	ENSP00000320560:W165S	ENSP00000320560:W165S	W	+	2	0	OR2D3	6899302	0.006000	0.16342	1.000000	0.80357	0.848000	0.48234	0.714000	0.25808	2.865000	0.98341	0.655000	0.94253	TGG	G|0.707;C|0.292	0.292	strong		0.493	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
NMRAL1	57407	hgsc.bcm.edu	37	16	4519439	4519439	+	Missense_Mutation	SNP	G	G	A	rs11557236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4519439G>A	ENST00000574733.1	-	3	797	c.68C>T	c.(67-69)aCa>aTa	p.T23I	NMRAL1_ENST00000574425.1_Missense_Mutation_p.T23I|NMRAL1_ENST00000283429.6_Missense_Mutation_p.T23I|NMRAL1_ENST00000572391.1_Intron|NMRAL1_ENST00000404295.3_Missense_Mutation_p.T23I			Q9HBL8	NMRL1_HUMAN	NmrA-like family domain containing 1	23			T -> I (in dbSNP:rs11557236).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|prostate(2)|stomach(1)	15						TTCCAGGAGTGTGCGGGCCAC	0.562													G|||	161	0.0321486	0.0098	0.0663	5008	,	,		17285	0.0		0.0835	False		,,,				2504	0.0184				p.T23I		Atlas-SNP	.											.	NMRAL1	31	.	0			c.C68T						PASS	.	G	ILE/THR	86,4308	71.4+/-109.4	2,82,2113	206.0	189.0	195.0		68	5.4	0.3	16	dbSNP_120	195	718,7882	175.5+/-225.5	29,660,3611	yes	missense	NMRAL1	NM_020677.3	89	31,742,5724	AA,AG,GG		8.3488,1.9572,6.1875	possibly-damaging	23/300	4519439	804,12190	2197	4300	6497	SO:0001583	missense	57407	exon3			AGGAGTGTGCGGG	AF225419	CCDS10516.1	16p13.3	2013-10-11			ENSG00000153406	ENSG00000153406		"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	24987	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 48A, member 1"""					19027726	Standard	NM_020677		Approved	FLJ25918, HSCARG, SDR48A1	uc002cwo.3	Q9HBL8	OTTHUMG00000129468	ENST00000574733.1:c.68C>T	16.37:g.4519439G>A	ENSP00000458762:p.Thr23Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_020677		Missense_Mutation	SNP	ENST00000574733.1	37	CCDS10516.1	94	0.04304029304029304	6	0.012195121951219513	26	0.0718232044198895	0	0.0	62	0.08179419525065963	G	17.66	3.443806	0.63067	0.019572	0.083488	ENSG00000153406	ENST00000283429;ENST00000404295	T;T	0.40476	1.03;1.03	5.37	5.37	0.77165	NAD(P)-binding domain (1);NmrA-like (1);	0.288644	0.32161	N	0.006492	T	0.02455	0.0075	L	0.47716	1.5	0.26852	N	0.968138	P	0.44006	0.824	B	0.39590	0.304	T	0.01561	-1.1324	10	0.44086	T	0.13	-2.5522	16.2746	0.82638	0.0:0.0:1.0:0.0	rs11557236;rs11557236	23	Q9HBL8	NMRL1_HUMAN	I	23	ENSP00000283429:T23I;ENSP00000383962:T23I	ENSP00000283429:T23I	T	-	2	0	NMRAL1	4459440	0.914000	0.31030	0.296000	0.24974	0.952000	0.60782	6.079000	0.71291	2.534000	0.85438	0.561000	0.74099	ACA	G|0.939;A|0.061	0.061	strong		0.562	NMRAL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438579.1	NM_020677	
PRR32	100130613	hgsc.bcm.edu	37	X	125955428	125955428	+	Silent	SNP	G	G	A	rs2269777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:125955428G>A	ENST00000371125.3	+	2	887	c.807G>A	c.(805-807)ccG>ccA	p.P269P		NM_001122716.1	NP_001116188.1	B1ATL7	PRR32_HUMAN		269	Pro-rich.																CTCCTCCTCCGATATTTGGTC	0.483													G|||	1178	0.312053	0.0386	0.2363	3775	,	,		14648	0.3601		0.3827	False		,,,				2504	0.2198				p.P269P		Atlas-SNP	.											.	.	.	.	0			c.G807A						PASS	.	G		121,1088		6,85,24,426,151	356.0	235.0	272.0		807	-7.9	0.0	X	dbSNP_100	272	1227,1164		216,397,398,187,393	no	coding-synonymous	CXorf64	NM_001122716.1		222,482,422,613,544	AA,AG,A,GG,G		48.6826,10.0083,37.4444		269/299	125955428	1348,2252	692	1591	2283	SO:0001819	synonymous_variant	100130613	exon2			TCCTCCGATATTT																												ENST00000371125.3:c.807G>A	X.37:g.125955428G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001122716		Silent	SNP	ENST00000371125.3	37	CCDS48163.1																																																																																			G|0.667;0|0.006	.	strong		0.483	CXorf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058188.1		
FLG	2312	hgsc.bcm.edu	37	1	152276660	152276660	+	Missense_Mutation	SNP	G	G	C	rs7540123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276660G>C	ENST00000368799.1	-	3	10737	c.10702C>G	c.(10702-10704)Cag>Gag	p.Q3568E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3568	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACTGCTCCTGAGCAGATCCA	0.572									Ichthyosis				G|||	1035	0.206669	0.2133	0.1916	5008	,	,		17873	0.3403		0.0696	False		,,,				2504	0.2117				p.Q3568E		Atlas-SNP	.											FLG,NS,carcinoma,+2,1	FLG	900	1	0			c.C10702G						scavenged	.						149.0	201.0	183.0					1																	152276660		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCCTGAGCAGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10702C>G	1.37:g.152276660G>C	ENSP00000357789:p.Gln3568Glu	Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	297	37	0.124579	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	
MEF2A	4205	hgsc.bcm.edu	37	15	100252805	100252805	+	Silent	SNP	G	G	T	rs325400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:100252805G>T	ENST00000557785.1	+	11	1672	c.1323G>T	c.(1321-1323)ggG>ggT	p.G441G	MEF2A_ENST00000557942.1_Silent_p.G449G|MEF2A_ENST00000354410.5_Silent_p.G443G|MEF2A_ENST00000449277.2_Silent_p.G373G|MEF2A_ENST00000338042.6_Silent_p.G450G|MEF2A_ENST00000558812.1_Silent_p.G381G|MEF2A_ENST00000453228.2_Silent_p.G441G	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	451	Gln/Pro-rich.		Missing (loss of nuclear localization; 66% decrease in transcription activation; loss of synergistic activation by MEF2A and GATA1 through a dominant-negative mechanism).		apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|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 regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|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)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			AGGAAATGGGGCGCTCCCCTG	0.652													G|||	1749	0.349241	0.121	0.4078	5008	,	,		11092	0.2976		0.5139	False		,,,				2504	0.5				p.G443G		Atlas-SNP	.											.	MEF2A	138	.	0			c.G1329T						PASS	.	G	,,,,	628,3094		76,476,1309	14.0	16.0	16.0		1323,1143,1119,1323,1329	-1.3	1.0	15	dbSNP_79	16	3848,3940		1054,1740,1100	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MEF2A	NM_001130926.1,NM_001130927.1,NM_001130928.1,NM_001171894.1,NM_005587.2	,,,,	1130,2216,2409	TT,TG,GG		49.4093,16.8726,38.8879	,,,,	441/498,381/438,373/430,441/498,443/500	100252805	4476,7034	1861	3894	5755	SO:0001819	synonymous_variant	4205	exon11			AATGGGGCGCTCC		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1323G>T	15.37:g.100252805G>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																			G|0.641;T|0.359	0.359	strong		0.652	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
ZNF135	7694	hgsc.bcm.edu	37	19	58578578	58578578	+	Silent	SNP	C	C	T	rs2229375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58578578C>T	ENST00000313434.5	+	5	827	c.726C>T	c.(724-726)taC>taT	p.Y242Y	ZNF135_ENST00000439855.2_Silent_p.Y242Y|ZNF135_ENST00000401053.4_Silent_p.Y266Y|ZNF135_ENST00000511556.1_Silent_p.Y254Y|ZNF135_ENST00000506786.1_Silent_p.Y200Y|ZNF135_ENST00000359978.6_Silent_p.Y254Y|RN7SL526P_ENST00000469492.2_RNA	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	242					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)		AGAGACCTTACGAATGTCACG	0.478													C|||	1837	0.366813	0.3548	0.4798	5008	,	,		20709	0.2103		0.4105	False		,,,				2504	0.4192				p.Y266Y		Atlas-SNP	.											.	ZNF135	159	.	0			c.C798T						PASS	.	C	,,,	1488,2918	474.8+/-357.1	252,984,967	135.0	127.0	130.0		,762,762,798	-7.1	0.0	19	dbSNP_98	130	3459,5141	505.6+/-376.4	685,2089,1526	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous	ZNF135	NM_001164529.1,NM_001164530.1,NM_003436.3,NM_007134.1	,,,	937,3073,2493	TT,TC,CC		40.2209,33.7721,38.0363	,,,	,254/391,254/671,266/683	58578578	4947,8059	2203	4300	6503	SO:0001819	synonymous_variant	7694	exon4			ACCTTACGAATGT	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.726C>T	19.37:g.58578578C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Silent	SNP	ENST00000313434.5	37		784	0.358974358974359	178	0.3617886178861789	163	0.45027624309392267	138	0.24125874125874125	305	0.4023746701846966	C	0.011	-1.709594	0.00712	0.337721	0.402209	ENSG00000176293	ENST00000391699	.	.	.	3.52	-7.05	0.01573	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.26950	-1.0088	3	.	.	.	.	8.0246	0.30430	0.0:0.3306:0.1105:0.5589	rs2229375;rs3745125;rs17307311;rs60749458;rs2229375	.	.	.	M	260	.	.	T	+	2	0	ZNF135	63270390	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.161000	0.01278	-2.190000	0.00757	-1.012000	0.02466	ACG	C|0.659;T|0.341	0.341	strong		0.478	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
RALGDS	5900	hgsc.bcm.edu	37	9	135983504	135983504	+	Silent	SNP	T	T	C	rs2285375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:135983504T>C	ENST00000372050.3	-	6	1089	c.1068A>G	c.(1066-1068)gcA>gcG	p.A356A	RALGDS_ENST00000372047.3_Silent_p.A344A|RALGDS_ENST00000542690.1_Silent_p.A427A|RALGDS_ENST00000372062.3_Silent_p.A327A|RALGDS_ENST00000393157.3_Silent_p.A355A|RALGDS_ENST00000393160.3_Silent_p.A301A|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	356					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)		ATGGAACTGGTGCTGGAGCTG	0.572			T	CIITA	"""PMBL, Hodgkin Lymphona, """								C|||	1447	0.288938	0.4796	0.353	5008	,	,		20807	0.1577		0.2972	False		,,,				2504	0.1125				p.A356A	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.A1068G						PASS	.	C	,	1927,2479	624.1+/-394.3	418,1091,694	75.0	76.0	76.0		903,1068	-3.2	0.0	9	dbSNP_100	76	2628,5972	686.4+/-404.1	399,1830,2071	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	817,2921,2765	CC,CT,TT		30.5581,43.7358,35.0223	,	301/860,356/915	135983504	4555,8451	2203	4300	6503	SO:0001819	synonymous_variant	5900	exon6			AACTGGTGCTGGA	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.1068A>G	9.37:g.135983504T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	106	39	0.367925	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			T|0.669;C|0.331	0.331	strong		0.572	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
GALK2	2585	hgsc.bcm.edu	37	15	49620200	49620200	+	Silent	SNP	C	C	T	rs1055254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:49620200C>T	ENST00000560031.1	+	10	1528	c.1221C>T	c.(1219-1221)tgC>tgT	p.C407C	GALK2_ENST00000543495.1_3'UTR|GALK2_ENST00000396509.2_Silent_p.C383C|GALK2_ENST00000544523.1_Silent_p.C383C|GALK2_ENST00000327171.3_Silent_p.C396C|GALK2_ENST00000559454.1_Silent_p.C383C			Q01415	GALK2_HUMAN	galactokinase 2	407					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		GGGGAGGCTGCACAGTATCAA	0.458													C|||	1012	0.202077	0.2428	0.1873	5008	,	,		17677	0.0466		0.2575	False		,,,				2504	0.2607				p.C407C		Atlas-SNP	.											.	GALK2	78	.	0			c.C1221T						PASS	.	C	,	1090,3302	393.5+/-328.9	140,810,1246	99.0	99.0	99.0		1188,1221	2.6	1.0	15	dbSNP_86	99	1905,6685	339.4+/-323.1	215,1475,2605	no	coding-synonymous,coding-synonymous	GALK2	NM_001001556.1,NM_002044.2	,	355,2285,3851	TT,TC,CC		22.1769,24.8179,23.0704	,	396/448,407/459	49620200	2995,9987	2196	4295	6491	SO:0001819	synonymous_variant	2585	exon10			AGGCTGCACAGTA		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.1221C>T	15.37:g.49620200C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	103	38	0.368932	NM_002044	Q7Z4Q4	Silent	SNP	ENST00000560031.1	37	CCDS42034.1																																																																																			C|0.783;T|0.217	0.217	strong		0.458	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1		
EPPK1	83481	hgsc.bcm.edu	37	8	144946252	144946252	+	Silent	SNP	C	C	T	rs11136330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144946252C>T	ENST00000525985.1	-	2	1241	c.1170G>A	c.(1168-1170)ctG>ctA	p.L390L				P58107	EPIPL_HUMAN	epiplakin 1	390						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)			GCCGCAGTGCCAGTGGCCTGT	0.692													C|||	2548	0.508786	0.4266	0.6657	5008	,	,		15586	0.2778		0.673	False		,,,				2504	0.5777				p.L390L		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	1	0			c.G1170A						scavenged	.	C		1969,1833		584,801,516	4.0	6.0	5.0		1170	2.1	0.6	8	dbSNP_120	5	5499,2537		2009,1481,528	no	coding-synonymous	EPPK1	NM_031308.1		2593,2282,1044	TT,TC,CC		31.5704,48.2115,36.915		390/2420	144946252	7468,4370	1901	4018	5919	SO:0001819	synonymous_variant	83481	exon1			CAGTGCCAGTGGC	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.1170G>A	8.37:g.144946252C>T		Somatic	52	1	0.0192308		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.474;T|0.526	0.526	strong		0.692	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
CD300E	342510	hgsc.bcm.edu	37	17	72610089	72610089	+	Missense_Mutation	SNP	C	C	T	rs1878061	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72610089C>T	ENST00000328630.3	-	3	512	c.472G>A	c.(472-474)Ggg>Agg	p.G158R	CD300E_ENST00000392619.1_Missense_Mutation_p.G185R|CD300E_ENST00000426295.2_Missense_Mutation_p.G199R			Q496F6	CLM2_HUMAN	CD300e molecule	158			G -> R (in dbSNP:rs1878061). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G158R(1)		breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						AACACCTCCCCGGTGCTGAGG	0.607													C|||	1102	0.220048	0.0953	0.2622	5008	,	,		17883	0.0794		0.4135	False		,,,				2504	0.3047				p.G158R		Atlas-SNP	.											CD300E,NS,carcinoma,0,1	CD300E	70	1	1	Substitution - Missense(1)	stomach(1)	c.G472A						PASS	.	C	ARG/GLY	695,3711	290.4+/-280.9	53,589,1561	114.0	92.0	100.0		472	-5.8	0.0	17	dbSNP_92	100	3457,5143	505.1+/-376.3	719,2019,1562	yes	missense	CD300E	NM_181449.2	125	772,2608,3123	TT,TC,CC		40.1977,15.7739,31.9237	possibly-damaging	158/206	72610089	4152,8854	2203	4300	6503	SO:0001583	missense	342510	exon3			CCTCCCCGGTGCT	BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	28874	protein-coding gene	gene with protein product		609801	"""CD300 antigen like family member E"", ""CD300e antigen"""	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.472G>A	17.37:g.72610089C>T	ENSP00000329942:p.Gly158Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_181449	B4DNS1|Q7Z7I3	Missense_Mutation	SNP	ENST00000328630.3	37	CCDS11702.1	519	0.23763736263736263	51	0.10365853658536585	110	0.30386740331491713	45	0.07867132867132867	313	0.4129287598944591	C	0.198	-1.047342	0.01981	0.157739	0.401977	ENSG00000186407	ENST00000392619;ENST00000426295;ENST00000328630	T;T;T	0.03607	3.88;3.87;3.91	2.88	-5.75	0.02384	.	4.595650	0.00674	U	0.000640	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.44659	0.84	B	0.33568	0.166	T	0.50381	-0.8835	9	0.16896	T	0.51	.	2.733	0.05232	0.112:0.1222:0.3353:0.4304	rs1878061;rs17555132;rs52818238;rs58718257;rs1878061	158	Q496F6	CLM2_HUMAN	R	185;199;158	ENSP00000376395:G185R;ENSP00000416642:G199R;ENSP00000329942:G158R	ENSP00000329942:G158R	G	-	1	0	CD300E	70121684	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.366000	0.01078	-2.914000	0.00307	-0.474000	0.04947	GGG	C|0.728;N|0.000	.	strong		0.607	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449	
CATSPERG	57828	hgsc.bcm.edu	37	19	38827960	38827960	+	Missense_Mutation	SNP	T	T	C	rs2302182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38827960T>C	ENST00000409235.3	+	2	201	c.86T>C	c.(85-87)cTc>cCc	p.L29P	CATSPERG_ENST00000410018.1_Missense_Mutation_p.L29P|CATSPERG_ENST00000215069.4_Missense_Mutation_p.L45P	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	29			L -> P (in dbSNP:rs2302182). {ECO:0000269|PubMed:17974005}.		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						CTGGCAGTGCTCCTGGCGTCG	0.622													t|||	751	0.14996	0.0348	0.2378	5008	,	,		16010	0.1339		0.1849	False		,,,				2504	0.2239				p.L29P		Atlas-SNP	.											.	CATSPERG	121	.	0			c.T86C						PASS	.		PRO/LEU	94,1290		4,86,602	132.0	118.0	122.0		86	3.3	0.0	19	dbSNP_100	122	494,2688		39,416,1136	yes	missense	CATSPERG	NM_021185.4	98	43,502,1738	CC,CT,TT		15.5248,6.7919,12.8778	probably-damaging	29/1160	38827960	588,3978	692	1591	2283	SO:0001583	missense	57828	exon2			CAGTGCTCCTGGC	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.86T>C	19.37:g.38827960T>C	ENSP00000386962:p.Leu29Pro	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	331	0.15155677655677655	17	0.034552845528455285	87	0.24033149171270718	85	0.1486013986013986	142	0.18733509234828497	t	14.33	2.502586	0.44455	0.067919	0.155248	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	3.3	3.3	0.37823	.	0.000000	0.32736	N	0.005711	T	0.00039	0.0001	L	0.56769	1.78	0.45427	P	0.001595000000000013	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.05289	-1.0894	9	0.59425	D	0.04	-9.8134	8.3357	0.32213	0.0:0.0:0.0:1.0	rs2302182;rs52832791;rs2302182	29;29	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	P	29;29;29;45	ENSP00000387057:L29P;ENSP00000386962:L29P;ENSP00000386950:L29P;ENSP00000215069:L45P	ENSP00000215069:L45P	L	+	2	0	CATSPERG	43519800	0.190000	0.23276	0.025000	0.17156	0.004000	0.04260	1.135000	0.31454	1.760000	0.52011	0.370000	0.22315	CTC	T|0.855;C|0.145	0.145	strong		0.622	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
HS3ST6	64711	hgsc.bcm.edu	37	16	1962046	1962046	+	Missense_Mutation	SNP	C	C	T	rs386787777|rs1742399	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1962046C>T	ENST00000293937.3	-	2	573	c.574G>A	c.(574-576)Gcc>Acc	p.A192T	HS3ST6_ENST00000454677.2_Missense_Mutation_p.A209T|HS3ST6_ENST00000443547.1_Missense_Mutation_p.A161T			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	192				A -> T (in Ref. 1). {ECO:0000305}.	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						AGCGTCTGGGCGTAGTCGGAG	0.726													c|||	2004	0.40016	0.2345	0.3386	5008	,	,		13827	0.4931		0.3837	False		,,,				2504	0.589				p.A161T		Atlas-SNP	.											.	HS3ST6	26	.	0			c.G481A						PASS	.	T	THR/ALA	964,3418		115,734,1342	17.0	21.0	20.0		481	3.7	0.5	16	dbSNP_89	20	2937,5655		544,1849,1903	no	missense	HS3ST6	NM_001009606.2	58	659,2583,3245	TT,TC,CC		34.183,21.9991,30.0678	benign	161/312	1962046	3901,9073	2191	4296	6487	SO:0001583	missense	64711	exon2			TCTGGGCGTAGTC			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.574G>A	16.37:g.1962046C>T	ENSP00000293937:p.Ala192Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_001009606	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	37		783	0.3585164835164835	100	0.2032520325203252	109	0.3011049723756906	287	0.5017482517482518	287	0.3786279683377309	c	6.931	0.541419	0.13250	0.219991	0.34183	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	D;D	0.81579	-1.51;-1.51	4.83	3.65	0.41850	Sulfotransferase domain (1);	0.103832	0.64402	D	0.000003	T	0.00012	0.0000	N	0.00382	-1.575	0.33610	P	0.39651000000000003	B	0.23442	0.085	B	0.17098	0.017	T	0.41928	-0.9481	9	0.02654	T	1	.	6.299	0.21101	0.0:0.7313:0.0:0.2687	rs1742399;rs1742399	192	Q96QI5	HS3S6_HUMAN	T	192;161;231	ENSP00000293937:A192T;ENSP00000390354:A161T	ENSP00000293937:A192T	A	-	1	0	HS3ST6	1902047	1.000000	0.71417	0.456000	0.27044	0.919000	0.55068	3.317000	0.51968	2.248000	0.74166	0.500000	0.49745	GCC	C|0.646;T|0.354	0.354	strong		0.726	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
TNK1	8711	hgsc.bcm.edu	37	17	7290695	7290695	+	Splice_Site	SNP	A	A	G	rs7220814	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7290695A>G	ENST00000576812.1	+	10	1781		c.e10-1		TNK1_ENST00000570896.1_Splice_Site|TNK1_ENST00000311668.2_Splice_Site	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				CCTCTCCGACAGAGACAGAAA	0.567													.|||	387	0.0772764	0.003	0.1542	5008	,	,		15933	0.1786		0.0686	False		,,,				2504	0.0276				.		Atlas-SNP	.											.	TNK1	31	.	0			c.1413-2A>G						PASS	.	A		58,3836		0,58,1889	36.0	38.0	37.0			3.9	0.9	17	dbSNP_116	37	487,7795		19,449,3673	yes	splice-3	TNK1	NM_003985.3		19,507,5562	GG,GA,AA		5.8802,1.4895,4.476			7290695	545,11631	1947	4141	6088	SO:0001630	splice_region_variant	8711	exon10			TCCGACAGAGACA	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.1413-1A>G	17.37:g.7290695A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_001251902		Splice_Site	SNP	ENST00000576812.1	37	CCDS58510.1	218	0.09981684981684982	5	0.01016260162601626	36	0.09944751381215469	122	0.21328671328671328	55	0.07255936675461741	A	11.81	1.750202	0.30955	0.014895	0.058802	ENSG00000174292	ENST00000311668	.	.	.	3.93	3.93	0.45458	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.472	0.38849	1.0:0.0:0.0:0.0	rs7220814;rs7220814	.	.	.	.	-1	.	.	.	+	.	.	TNK1	7231419	0.980000	0.34600	0.944000	0.38274	0.054000	0.15201	3.792000	0.55476	2.026000	0.59711	0.379000	0.24179	.	A|0.902;G|0.098	0.098	strong		0.567	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	Intron
ACSS1	84532	hgsc.bcm.edu	37	20	25000734	25000734	+	Silent	SNP	G	G	A	rs6115003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:25000734G>A	ENST00000323482.4	-	7	1237	c.1158C>T	c.(1156-1158)ggC>ggT	p.G386G	ACSS1_ENST00000542618.1_Silent_p.G265G|ACSS1_ENST00000537502.1_Silent_p.G303G|ACSS1_ENST00000432802.2_Silent_p.G386G	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	386					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)	CCGTTGGGGCGCCATAGAACT	0.552													G|||	546	0.109026	0.2262	0.0793	5008	,	,		18028	0.003		0.0984	False		,,,				2504	0.092				p.G386G		Atlas-SNP	.											.	ACSS1	46	.	0			c.C1158T						PASS	.	G		889,3517	344.1+/-307.9	80,729,1394	202.0	176.0	185.0		1158	-11.4	0.0	20	dbSNP_114	185	881,7719	199.6+/-243.6	51,779,3470	no	coding-synonymous	ACSS1	NM_032501.2		131,1508,4864	AA,AG,GG		10.2442,20.177,13.6091		386/690	25000734	1770,11236	2203	4300	6503	SO:0001819	synonymous_variant	84532	exon7			TGGGGCGCCATAG		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.1158C>T	20.37:g.25000734G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			G|0.872;A|0.128	0.128	strong		0.552	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
UGDH	7358	hgsc.bcm.edu	37	4	39510264	39510264	+	Silent	SNP	A	A	G	rs1129052	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:39510264A>G	ENST00000316423.6	-	7	1170	c.828T>C	c.(826-828)tgT>tgC	p.C276C	UGDH_ENST00000515398.1_5'Flank|UGDH_ENST00000501493.2_Silent_p.C209C|UGDH_ENST00000507089.1_Silent_p.C179C|UGDH_ENST00000506179.1_Silent_p.C276C	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	61	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	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	
TYW1	55253	hgsc.bcm.edu	37	7	66648157	66648157	+	Silent	SNP	C	C	T	rs4145350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	95	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	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	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500193	90500193	+	Missense_Mutation	SNP	C	C	G	rs59256416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90500193C>G	ENST00000325643.5	+	4	857	c.791C>G	c.(790-792)gCt>gGt	p.A264G		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	264	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCCAGCCTGGCTGGACTTCAG	0.622													.|||	622	0.124201	0.3464	0.0461	5008	,	,		17766	0.0347		0.0636	False		,,,				2504	0.0337				p.A264G		Atlas-SNP	.											.	.	.	.	0			c.C791G						PASS	.	C	GLY/ALA	1265,3141		176,913,1114	61.0	64.0	63.0		791	-3.4	0.0	9	dbSNP_129	63	417,8183		7,403,3890	no	missense	C9orf79	NM_178828.4	60	183,1316,5004	GG,GC,CC		4.8488,28.7108,12.9325	possibly-damaging	264/1446	90500193	1682,11324	2203	4300	6503	SO:0001583	missense	286234	exon4			GCCTGGCTGGACT	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.791C>G	9.37:g.90500193C>G	ENSP00000322640:p.Ala264Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	254	0.1163003663003663	164	0.3333333333333333	20	0.055248618784530384	19	0.033216783216783216	51	0.06728232189973615	.	4.145	0.025191	0.08054	0.287108	0.048488	ENSG00000177992	ENST00000325643	T	0.03524	3.9	1.7	-3.39	0.04868	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.36171	0.541	B	0.34301	0.179	T	0.43556	-0.9384	8	0.18710	T	0.47	.	3.7701	0.08637	0.1731:0.2979:0.0:0.529	rs59256416	264	Q6ZUB1	CI079_HUMAN	G	264	ENSP00000322640:A264G	ENSP00000322640:A264G	A	+	2	0	C9orf79	89690013	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	-0.872000	0.04219	-1.792000	0.01259	-1.517000	0.00937	GCT	C|0.881;G|0.119	0.119	strong		0.622	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
HFM1	164045	hgsc.bcm.edu	37	1	91782031	91782031	+	Missense_Mutation	SNP	T	T	C	rs11584478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:91782031T>C	ENST00000370425.3	-	26	2913	c.2815A>G	c.(2815-2817)Ata>Gta	p.I939V	HFM1_ENST00000370424.3_Missense_Mutation_p.I618V|HFM1_ENST00000294696.5_Missense_Mutation_p.I171V|HFM1_ENST00000462405.1_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	939	SEC63.		I -> V (in dbSNP:rs11584478).		resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GACAATGTTATACCTGTGGAA	0.239													T|||	626	0.125	0.1233	0.1571	5008	,	,		12671	0.005		0.2346	False		,,,				2504	0.1155				p.I939V		Atlas-SNP	.											.	HFM1	188	.	0			c.A2815G						PASS	.	T	VAL/ILE	616,3788	261.9+/-264.6	38,540,1624	73.0	76.0	75.0		2815	1.3	1.0	1	dbSNP_120	75	2199,6389	372.1+/-336.5	275,1649,2370	yes	missense	HFM1	NM_001017975.3	29	313,2189,3994	CC,CT,TT		25.6055,13.9873,21.6672	benign	939/1436	91782031	2815,10177	2202	4294	6496	SO:0001583	missense	164045	exon26			ATGTTATACCTGT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2815A>G	1.37:g.91782031T>C	ENSP00000359454:p.Ile939Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	294	0.1346153846153846	53	0.10772357723577236	63	0.17403314917127072	2	0.0034965034965034965	176	0.23218997361477572	T	4.108	0.018200	0.07959	0.139873	0.256055	ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	T;T;T	0.60040	0.22;0.22;0.22	5.07	1.31	0.21738	Sec63 domain (2);	0.276343	0.34906	N	0.003594	T	0.11707	0.0285	N	0.04203	-0.255	0.37949	P	0.06741399999999997	B;B;B	0.14012	0.001;0.009;0.009	B;B;B	0.15484	0.007;0.013;0.013	T	0.14755	-1.0461	9	0.20519	T	0.43	.	6.864	0.24082	0.0:0.6073:0.0:0.3927	rs11584478;rs17556195;rs52804592;rs59939430;rs11584478	618;150;939	A6NGI5;B1B0B5;A2PYH4	.;.;HFM1_HUMAN	V	939;171;618;623	ENSP00000359454:I939V;ENSP00000294696:I171V;ENSP00000359453:I618V	ENSP00000294696:I171V	I	-	1	0	HFM1	91554619	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.352000	0.44080	0.254000	0.21573	0.455000	0.32223	ATA	T|0.824;C|0.176	0.176	strong		0.239	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
SPTBN2	6712	hgsc.bcm.edu	37	11	66458980	66458980	+	Silent	SNP	G	G	A	rs623022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66458980G>A	ENST00000533211.1	-	27	5671	c.5340C>T	c.(5338-5340)aaC>aaT	p.N1780N	SPTBN2_ENST00000529997.1_Silent_p.N1780N|SPTBN2_ENST00000309996.2_Silent_p.N1780N			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1780					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CCCAGGCCTCGTTGAGACTGT	0.677													G|||	316	0.063099	0.003	0.0533	5008	,	,		17128	0.1329		0.0557	False		,,,				2504	0.0869				p.N1780N		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C5340T						PASS	.	G		46,4354	45.3+/-79.5	0,46,2154	53.0	42.0	46.0		5340	-2.7	1.0	11	dbSNP_83	46	427,8163	129.3+/-187.4	13,401,3881	no	coding-synonymous	SPTBN2	NM_006946.2		13,447,6035	AA,AG,GG		4.9709,1.0455,3.6413		1780/2391	66458980	473,12517	2200	4295	6495	SO:0001819	synonymous_variant	6712	exon26			GGCCTCGTTGAGA	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.5340C>T	11.37:g.66458980G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			G|0.952;A|0.048	0.048	strong		0.677	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
TMEM63A	9725	hgsc.bcm.edu	37	1	226041438	226041438	+	Silent	SNP	C	C	T	rs2292556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226041438C>T	ENST00000366835.3	-	19	1959	c.1689G>A	c.(1687-1689)tcG>tcA	p.S563S		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	563					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)					CGATGAAGGCCGAGGCGATGA	0.597													C|||	344	0.0686901	0.0045	0.0735	5008	,	,		20098	0.1567		0.0497	False		,,,				2504	0.0808				p.S563S		Atlas-SNP	.											TMEM63A,NS,carcinoma,0,1	TMEM63A	75	1	0			c.G1689A						PASS	.	C		43,4363	43.1+/-76.7	0,43,2160	53.0	40.0	45.0		1689	-4.4	1.0	1	dbSNP_100	45	349,8249	110.2+/-170.6	3,343,3953	no	coding-synonymous	TMEM63A	NM_014698.2		3,386,6113	TT,TC,CC		4.0591,0.9759,3.0145		563/808	226041438	392,12612	2203	4299	6502	SO:0001819	synonymous_variant	9725	exon19			GAAGGCCGAGGCG		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.1689G>A	1.37:g.226041438C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			C|0.960;T|0.040	0.040	strong		0.597	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
ZNF71	58491	hgsc.bcm.edu	37	19	57133921	57133921	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57133921C>T	ENST00000328070.6	+	3	1500	c.1266C>T	c.(1264-1266)agC>agT	p.S422S		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	422					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.S422S(1)		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)		TCAGCCAGAGCGCCTACCTCA	0.642																																					p.S422S		Atlas-SNP	.											ZNF71,NS,carcinoma,0,1	ZNF71	69	1	1	Substitution - coding silent(1)	lung(1)	c.C1266T						scavenged	.						82.0	69.0	73.0					19																	57133921		2203	4300	6503	SO:0001819	synonymous_variant	58491	exon3			CCAGAGCGCCTAC	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.1266C>T	19.37:g.57133921C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	142	2	0.0140845	NM_021216	Q15919|Q9UC09|Q9UQD3	Silent	SNP	ENST00000328070.6	37	CCDS12947.1																																																																																			.	.	none		0.642	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216	
MAN2A2	4122	hgsc.bcm.edu	37	15	91452595	91452595	+	Missense_Mutation	SNP	A	A	G	rs2106673	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:91452595A>G	ENST00000559717.1	+	9	1694	c.1235A>G	c.(1234-1236)cAg>cGg	p.Q412R	MAN2A2_ENST00000360468.3_Missense_Mutation_p.Q412R|MAN2A2_ENST00000431652.2_5'UTR|MAN2A2_ENST00000430376.2_5'Flank			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	412			Q -> R (in dbSNP:rs2106673).		cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			AAGAAGTCCCAGCTGTTCCGA	0.552													G|||	2562	0.511581	0.3275	0.6066	5008	,	,		17237	0.9673		0.2833	False		,,,				2504	0.4581				p.Q412R		Atlas-SNP	.											.	MAN2A2	99	.	0			c.A1235G						PASS	.	G	ARG/GLN	1401,2995	685.4+/-404.6	218,965,1015	72.0	67.0	69.0		1235	2.4	1.0	15	dbSNP_96	69	2592,6004	689.0+/-404.3	380,1832,2086	yes	missense	MAN2A2	NM_006122.2	43	598,2797,3101	GG,GA,AA		30.1536,31.8699,30.7343	benign	412/1151	91452595	3993,8999	2198	4298	6496	SO:0001583	missense	4122	exon8			AGTCCCAGCTGTT	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.1235A>G	15.37:g.91452595A>G	ENSP00000452948:p.Gln412Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	37	CCDS32332.1	1119	0.5123626373626373	155	0.3150406504065041	200	0.5524861878453039	556	0.972027972027972	208	0.27440633245382584	G	11.69	1.713975	0.30413	0.318699	0.301536	ENSG00000196547	ENST00000360468	T	0.74002	-0.8	5.74	2.42	0.29668	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.273076	0.38959	N	0.001506	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999949408	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33445	-0.9868	9	0.15499	T	0.54	-25.785	8.1177	0.30953	0.5043:0.0:0.4957:0.0	rs2106673;rs52827682;rs56746832;rs2106673	82;412;412	B4DIK4;P49641-1;P49641	.;.;MA2A2_HUMAN	R	412	ENSP00000353655:Q412R	ENSP00000353655:Q412R	Q	+	2	0	MAN2A2	89253599	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	3.686000	0.54685	0.394000	0.25230	-0.222000	0.12452	CAG	A|0.596;G|0.404	0.404	strong		0.552	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122	
TMEM99	147184	hgsc.bcm.edu	37	17	38991100	38991100	+	Missense_Mutation	SNP	A	A	G	rs199620244		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38991100A>G	ENST00000301665.3	+	3	636	c.332A>G	c.(331-333)aAc>aGc	p.N111S		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	111						integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				CTCTTCAACAACTGGACTGGA	0.502																																					p.N111S		Atlas-SNP	.											.	TMEM99	21	.	0			c.A332G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,3846		0,0,1923	141.0	139.0	140.0		332,332,332	-0.5	0.0	17		140	3,8281		0,3,4139	yes	missense,missense,missense	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	46,46,46	0,3,6062	GG,GA,AA		0.0362,0.0,0.0247	benign,benign,benign	111/259,111/259,111/259	38991100	3,12127	1923	4142	6065	SO:0001583	missense	147184	exon3			TCAACAACTGGAC	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	ENST00000301665.3:c.332A>G	17.37:g.38991100A>G	ENSP00000301665:p.Asn111Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_001195386	B4DQ34|Q96BP9	Missense_Mutation	SNP	ENST00000301665.3	37	CCDS42319.1	.	.	.	.	.	.	.	.	.	.	A	2.048	-0.418367	0.04766	0.0	3.62E-4	ENSG00000167920	ENST00000436612;ENST00000301665	T;T	0.27402	1.67;1.67	0.235	-0.47	0.12131	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.09310	N	1	B	0.19073	0.033	B	0.15870	0.014	T	0.21280	-1.0250	8	0.87932	D	0	.	.	.	.	.	111	Q8N816	TMM99_HUMAN	S	111	ENSP00000390036:N111S;ENSP00000301665:N111S	ENSP00000301665:N111S	N	+	2	0	TMEM99	36244626	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-1.620000	0.02046	-0.738000	0.04817	-0.736000	0.03550	AAC	.	.	weak		0.502	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77353973	77353973	+	Missense_Mutation	SNP	G	G	T	rs9930984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:77353973G>T	ENST00000282849.5	-	16	2723	c.2305C>A	c.(2305-2307)Ctc>Atc	p.L769I		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	769	Spacer.		L -> I (in dbSNP:rs9930984). {ECO:0000269|PubMed:15489334}.		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GCTGGAATGAGGACCACCGGA	0.488													T|||	3180	0.634984	0.7731	0.6268	5008	,	,		16886	0.8681		0.3648	False		,,,				2504	0.4918				p.L769I		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.C2305A						PASS	.	T	ILE/LEU	3290,1106	395.1+/-329.5	1247,796,155	47.0	53.0	51.0		2305	2.1	0.0	16	dbSNP_119	51	3395,5205	638.9+/-399.4	683,2029,1588	yes	missense	ADAMTS18	NM_199355.2	5	1930,2825,1743	TT,TG,GG		39.4767,25.1592,48.5611	benign	769/1222	77353973	6685,6311	2198	4300	6498	SO:0001583	missense	170692	exon16			GAATGAGGACCAC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2305C>A	16.37:g.77353973G>T	ENSP00000282849:p.Leu769Ile	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	1348	0.6172161172161172	368	0.7479674796747967	207	0.5718232044198895	493	0.8618881118881119	280	0.36939313984168864	T	0.356	-0.942285	0.02322	0.748408	0.394767	ENSG00000140873	ENST00000282849	T	0.51574	0.7	5.54	2.08	0.27032	ADAM-TS Spacer 1 (1);	1.032820	0.07672	N	0.935568	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.001	T	0.33497	-0.9866	9	0.46703	T	0.11	.	5.8572	0.18727	0.0:0.2071:0.1293:0.6636	rs9930984;rs17855795;rs52810859;rs59142387;rs9930984	769;769	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	I	769	ENSP00000282849:L769I	ENSP00000282849:L769I	L	-	1	0	ADAMTS18	75911474	0.998000	0.40836	0.004000	0.12327	0.076000	0.17211	2.540000	0.45727	-0.130000	0.11599	-1.221000	0.01599	CTC	G|0.434;T|0.566	0.566	strong		0.488	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
OR13G1	441933	hgsc.bcm.edu	37	1	247835950	247835950	+	Missense_Mutation	SNP	T	T	C	rs1151640	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:247835950T>C	ENST00000359688.2	-	1	415	c.394A>G	c.(394-396)Att>Gtt	p.I132V	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	132			I -> V (in dbSNP:rs1151640).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGTTCATAATAGTACTGTAA	0.468													T|||	2033	0.40595	0.1286	0.5937	5008	,	,		22510	0.6032		0.4195	False		,,,				2504	0.4305				p.I132V		Atlas-SNP	.											OR13G1,colon,carcinoma,0,1	OR13G1	78	1	0			c.A394G	GRCh37	CM053366	OR13G1	M	rs1151640	PASS	.	T	VAL/ILE	739,3667	305.5+/-289.0	58,623,1522	101.0	84.0	90.0		394	-3.4	0.0	1	dbSNP_87	90	3654,4946	525.3+/-380.7	772,2110,1418	yes	missense	OR13G1	NM_001005487.1	29	830,2733,2940	CC,CT,TT		42.4884,16.7726,33.7767	benign	132/308	247835950	4393,8613	2203	4300	6503	SO:0001583	missense	441933	exon1			TCATAATAGTACT	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.394A>G	1.37:g.247835950T>C	ENSP00000352717:p.Ile132Val	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	123	48	0.390244	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	960	0.43956043956043955	65	0.13211382113821138	204	0.56353591160221	372	0.6503496503496503	319	0.420844327176781	T	3.452	-0.111750	0.06881	0.167726	0.424884	ENSG00000197437	ENST00000359688	T	0.00695	5.83	4.2	-3.4	0.04853	GPCR, rhodopsin-like superfamily (1);	0.680368	0.12654	N	0.450235	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.07404	-1.0774	9	0.17832	T	0.49	-11.8146	5.9215	0.19084	0.0:0.1648:0.4093:0.4259	rs1151640;rs52796519;rs57652947;rs1151640	132	Q8NGZ3	O13G1_HUMAN	V	132	ENSP00000352717:I132V	ENSP00000352717:I132V	I	-	1	0	OR13G1	245902573	0.000000	0.05858	0.000000	0.03702	0.101000	0.19017	-0.022000	0.12480	-0.755000	0.04709	0.460000	0.39030	ATT	T|0.630;C|0.370	0.370	strong		0.468	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
GPC1	2817	hgsc.bcm.edu	37	2	241404499	241404499	+	Silent	SNP	C	C	T	rs2228327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241404499C>T	ENST00000264039.2	+	7	1388	c.1140C>T	c.(1138-1140)tcC>tcT	p.S380S		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	380					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)		CACAGGTCTCCGAAGCCAAGG	0.672													C|||	1239	0.247404	0.3139	0.2392	5008	,	,		15390	0.0893		0.3161	False		,,,				2504	0.2556				p.S380S		Atlas-SNP	.											GPC1,NS,carcinoma,0,1	GPC1	32	1	0			c.C1140T						PASS	.	C		1443,2929		246,951,989	18.0	22.0	20.0		1140	-8.5	0.6	2	dbSNP_98	20	2543,6043		375,1793,2125	no	coding-synonymous	GPC1	NM_002081.2		621,2744,3114	TT,TC,CC		29.618,33.0055,30.7609		380/559	241404499	3986,8972	2186	4293	6479	SO:0001819	synonymous_variant	2817	exon7			GGTCTCCGAAGCC	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.1140C>T	2.37:g.241404499C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	557	0.25503663003663	163	0.3313008130081301	97	0.26795580110497236	62	0.10839160839160839	235	0.3100263852242744	C	1.912	-0.450581	0.04572	0.330055	0.29618	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	4.27	-8.54	0.00912	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999417036	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.8275	1.6277	0.02726	0.1486:0.3681:0.1724:0.3108	rs2228327;rs11689371;rs17854676;rs2228327	.	.	.	X	420;132	.	.	R	+	1	2	GPC1	241053172	0.000000	0.05858	0.650000	0.29550	0.281000	0.26958	-6.390000	0.00068	-2.785000	0.00359	-1.366000	0.01203	CGA	C|0.727;T|0.273	0.273	strong		0.672	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
DCTN4	51164	hgsc.bcm.edu	37	5	150097883	150097883	+	Missense_Mutation	SNP	G	G	C	rs11954652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150097883G>C	ENST00000447998.2	-	11	1141	c.1026C>G	c.(1024-1026)ttC>ttG	p.F342L	DCTN4_ENST00000446090.2_Missense_Mutation_p.F349L|DCTN4_ENST00000424236.1_Missense_Mutation_p.F285L	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	104	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	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		
SMCO4	56935	hgsc.bcm.edu	37	11	93212254	93212254	+	Silent	SNP	C	C	T	rs2658797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:93212254C>T	ENST00000298966.2	-	3	487	c.102G>A	c.(100-102)gtG>gtA	p.V34V	SMCO4_ENST00000527149.1_Silent_p.V34V|SMCO4_ENST00000525141.1_Silent_p.V34V	NM_020179.2	NP_064564.1	Q9NRQ5	SMCO4_HUMAN	single-pass membrane protein with coiled-coil domains 4	34						integral component of membrane (GO:0016021)											GCGTGGGCAGCACCACTGTAG	0.642													C|||	3502	0.699281	0.6172	0.7219	5008	,	,		14999	0.9435		0.504	False		,,,				2504	0.7434				p.V34V		Atlas-SNP	.											.	.	.	.	0			c.G102A						PASS	.	C		2766,1636	660.5+/-400.7	879,1008,314	104.0	88.0	93.0		102	5.0	1.0	11	dbSNP_100	93	4236,4360	572.7+/-389.8	1057,2122,1119	no	coding-synonymous	C11orf75	NM_020179.2		1936,3130,1433	TT,TC,CC		49.2787,37.1649,46.1302		34/60	93212254	7002,5996	2201	4298	6499	SO:0001819	synonymous_variant	0	exon3			GGGCAGCACCACT	BC031564	CCDS8292.1	11q21	2013-03-11	2013-03-11	2013-03-11	ENSG00000166002	ENSG00000166002			24810	protein-coding gene	gene with protein product		609477	"""chromosome 11 open reading frame 75"""	C11orf75		10863097	Standard	NM_020179		Approved	FN5	uc001pds.4	Q9NRQ5	OTTHUMG00000167442	ENST00000298966.2:c.102G>A	11.37:g.93212254C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_020179		Silent	SNP	ENST00000298966.2	37	CCDS8292.1																																																																																			C|0.421;T|0.579	0.579	strong		0.642	SMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394630.1	NM_020179	
WDR24	84219	hgsc.bcm.edu	37	16	737269	737269	+	Silent	SNP	C	C	T	rs17850290	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:737269C>T	ENST00000248142.6	-	7	1196	c.1197G>A	c.(1195-1197)acG>acA	p.T399T	JMJD8_ENST00000293882.4_5'Flank|JMJD8_ENST00000609261.1_5'Flank|JMJD8_ENST00000454700.1_5'Flank|JMJD8_ENST00000562111.1_5'Flank|JMJD8_ENST00000562824.1_5'Flank|LA16c-313D11.12_ENST00000566927.1_RNA|WDR24_ENST00000293883.4_Silent_p.T269T|JMJD8_ENST00000412368.2_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	399										breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				TCATGGAGCACGTGGCCAGGT	0.622													C|||	438	0.0874601	0.0053	0.0706	5008	,	,		16745	0.002		0.1461	False		,,,				2504	0.2382				p.T269T		Atlas-SNP	.											.	WDR24	111	.	0			c.G807A						PASS	.	C		146,4252	98.5+/-137.1	4,138,2057	40.0	42.0	41.0		807	-8.6	0.2	16	dbSNP_123	41	1397,7199	264.6+/-285.7	106,1185,3007	no	coding-synonymous	WDR24	NM_032259.2		110,1323,5064	TT,TC,CC		16.2517,3.3197,11.8747		269/791	737269	1543,11451	2199	4298	6497	SO:0001819	synonymous_variant	84219	exon3			GGAGCACGTGGCC	AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580		"""WD repeat domain containing"""	20852	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 21"""	C16orf21		11230166	Standard	NM_032259		Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000248142.6:c.1197G>A	16.37:g.737269C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Silent	SNP	ENST00000248142.6	37																																																																																				C|0.902;T|0.098	0.098	strong		0.622	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259	
TM4SF4	7104	hgsc.bcm.edu	37	3	149193684	149193684	+	Silent	SNP	T	T	C	rs1802837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:149193684T>C	ENST00000305354.4	+	2	1153	c.249T>C	c.(247-249)tgT>tgC	p.C83C		NM_004617.3	NP_004608.1	P48230	T4S4_HUMAN	transmembrane 4 L six family member 4	83					tissue regeneration (GO:0042246)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			ACGAGGGCTGTGGGAAGCGAT	0.562													C|||	1147	0.229034	0.23	0.3026	5008	,	,		17580	0.0704		0.3966	False		,,,				2504	0.1667				p.C83C		Atlas-SNP	.											.	TM4SF4	27	.	0			c.T249C						PASS	.	C		1069,3067		156,757,1155	54.0	59.0	57.0		249	-9.1	0.6	3	dbSNP_89	57	3568,4848		761,2046,1401	no	coding-synonymous	TM4SF4	NM_004617.3		917,2803,2556	CC,CT,TT		42.3954,25.8462,36.9423		83/203	149193684	4637,7915	2068	4208	6276	SO:0001819	synonymous_variant	7104	exon2			GGGCTGTGGGAAG		CCDS46932.1	3q25	2005-03-21	2005-03-21		ENSG00000169903	ENSG00000169903			11856	protein-coding gene	gene with protein product		606567	"""transmembrane 4 superfamily member 4"""			7665614	Standard	NM_004617		Approved	il-TMP	uc003exd.2	P48230	OTTHUMG00000159619	ENST00000305354.4:c.249T>C	3.37:g.149193684T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	243	118	0.485597	NM_004617	B2RDA4	Silent	SNP	ENST00000305354.4	37	CCDS46932.1																																																																																			C|0.263;N|0.000	0.263	strong		0.562	TM4SF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356528.1		
LATS1	9113	hgsc.bcm.edu	37	6	150005250	150005250	+	Silent	SNP	A	A	G	rs56246065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:150005250A>G	ENST00000543571.1	-	4	1522	c.975T>C	c.(973-975)gtT>gtC	p.V325V	LATS1_ENST00000392273.3_Silent_p.V325V|LATS1_ENST00000253339.5_Silent_p.V325V|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		GTTGTCTGCCAACAGGAACAG	0.473													A|||	36	0.0071885	0.0008	0.0101	5008	,	,		22471	0.0		0.0239	False		,,,				2504	0.0041				p.V325V		Atlas-SNP	.											.	LATS1	241	.	0			c.T975C						PASS	.	A		16,4390	23.3+/-48.9	0,16,2187	156.0	150.0	152.0		975	1.5	1.0	6	dbSNP_129	152	203,8397	87.1+/-149.5	1,201,4098	no	coding-synonymous	LATS1	NM_004690.2		1,217,6285	GG,GA,AA		2.3605,0.3631,1.6838		325/1131	150005250	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	9113	exon4			TCTGCCAACAGGA	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.975T>C	6.37:g.150005250A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	182	93	0.510989	NM_001270519		Silent	SNP	ENST00000543571.1	37	CCDS34551.1																																																																																			A|0.986;G|0.014	0.014	strong		0.473	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
FKRP	79147	hgsc.bcm.edu	37	19	47258842	47258842	+	Silent	SNP	C	C	T	rs2287717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	116	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	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	
FAM161B	145483	hgsc.bcm.edu	37	14	74413129	74413129	+	Silent	SNP	C	C	G	rs7146634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74413129C>G	ENST00000534936.1	-	2	339	c.234G>C	c.(232-234)ggG>ggC	p.G78G	FAM161B_ENST00000286544.3_Silent_p.G141G			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	78										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						GACACCATCTCCCTTTCTGCT	0.478													G|||	1301	0.259784	0.3003	0.3429	5008	,	,		20403	0.0506		0.4056	False		,,,				2504	0.2117				p.G141G		Atlas-SNP	.											.	FAM161B	67	.	0			c.G423C						PASS	.	G		1345,3061	694.1+/-405.8	198,949,1056	197.0	188.0	191.0		423	-0.5	0.0	14	dbSNP_116	191	3561,5039	628.9+/-398.2	730,2101,1469	no	coding-synonymous	FAM161B	NM_152445.2		928,3050,2525	GG,GC,CC		41.407,30.5266,37.7211		141/711	74413129	4906,8100	2203	4300	6503	SO:0001819	synonymous_variant	145483	exon2			CCATCTCCCTTTC	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 44"""	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.234G>C	14.37:g.74413129C>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	NM_152445	B7Z882|J3KNA2	Silent	SNP	ENST00000534936.1	37																																																																																				C|0.648;G|0.352	0.352	strong		0.478	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
REXO1	57455	hgsc.bcm.edu	37	19	1819125	1819125	+	Missense_Mutation	SNP	T	T	C	rs2396359	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1819125T>C	ENST00000170168.4	-	8	2750	c.2656A>G	c.(2656-2658)Agt>Ggt	p.S886G	MIR1909_ENST00000411312.1_RNA|CTB-31O20.4_ENST00000593201.1_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	115	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	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	
OR51L1	119682	hgsc.bcm.edu	37	11	5021055	5021055	+	Missense_Mutation	SNP	C	C	G	rs61734126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5021055C>G	ENST00000321543.1	+	1	843	c.843C>G	c.(841-843)atC>atG	p.I281M		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	281						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)		TGGCAGACATCTACCTTCTTC	0.468													C|||	411	0.0820687	0.0265	0.0793	5008	,	,		20764	0.1577		0.0964	False		,,,				2504	0.0665				p.I281M		Atlas-SNP	.											.	OR51L1	60	.	0			c.C843G						PASS	.	C	MET/ILE	167,4235	109.1+/-147.4	6,155,2040	172.0	148.0	156.0		843	0.8	1.0	11	dbSNP_129	156	858,7738	195.8+/-240.9	42,774,3482	yes	missense	OR51L1	NM_001004755.1	10	48,929,5522	GG,GC,CC		9.9814,3.7937,7.8858	benign	281/316	5021055	1025,11973	2201	4298	6499	SO:0001583	missense	119682	exon1			AGACATCTACCTT	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.843C>G	11.37:g.5021055C>G	ENSP00000322156:p.Ile281Met	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	159	88	0.553459	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	37	CCDS31369.1	211	0.09661172161172162	12	0.024390243902439025	27	0.07458563535911603	91	0.1590909090909091	81	0.10686015831134564	C	12.37	1.916529	0.33815	0.037937	0.099814	ENSG00000176798	ENST00000321543	T	0.00076	8.76	5.43	0.795	0.18643	GPCR, rhodopsin-like superfamily (1);	0.298674	0.21981	N	0.066304	T	0.00012	0.0000	L	0.39245	1.2	0.42659	P	0.0065269999999999495	B	0.31274	0.317	B	0.42030	0.373	T	0.13602	-1.0503	9	0.42905	T	0.14	.	4.7531	0.13070	0.1543:0.5622:0.0:0.2836	rs61734126	281	Q8NGJ5	O51L1_HUMAN	M	281	ENSP00000322156:I281M	ENSP00000322156:I281M	I	+	3	3	OR51L1	4977631	0.001000	0.12720	0.993000	0.49108	0.849000	0.48306	-0.201000	0.09464	-0.026000	0.13895	0.650000	0.86243	ATC	C|0.918;G|0.082	0.082	strong		0.468	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
ATP10D	57205	hgsc.bcm.edu	37	4	47578971	47578971	+	Missense_Mutation	SNP	G	G	A	rs16851681	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:47578971G>A	ENST00000273859.3	+	19	3817	c.3548G>A	c.(3547-3549)aGa>aAa	p.R1183K		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1183			R -> K (in dbSNP:rs16851681).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						GAACTTTACAGAAGTGGTCAG	0.428													A|||	1412	0.281949	0.3707	0.3487	5008	,	,		20469	0.2004		0.2575	False		,,,				2504	0.2239				p.R1183K		Atlas-SNP	.											.	ATP10D	168	.	0			c.G3548A						PASS	.	A	LYS/ARG	1516,2890	674.8+/-403.0	244,1028,931	95.0	88.0	90.0		3548	-6.0	0.0	4	dbSNP_123	90	2003,6597	722.2+/-406.4	232,1539,2529	yes	missense	ATP10D	NM_020453.3	26	476,2567,3460	AA,AG,GG		23.2907,34.4076,27.0567	benign	1183/1427	47578971	3519,9487	2203	4300	6503	SO:0001583	missense	57205	exon19			TTTACAGAAGTGG	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.3548G>A	4.37:g.47578971G>A	ENSP00000273859:p.Arg1183Lys	Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	277	148	0.534296	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	657	0.3008241758241758	198	0.4024390243902439	134	0.3701657458563536	123	0.21503496503496503	202	0.26649076517150394	A	0.090	-1.169224	0.01660	0.344076	0.232907	ENSG00000145246	ENST00000273859	T	0.75154	-0.91	5.21	-5.96	0.02234	.	0.669752	0.15504	N	0.258904	T	0.00012	0.0000	N	0.05441	-0.05	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13229	-1.0517	9	0.02654	T	1	-2.1125	2.5327	0.04707	0.2771:0.1853:0.3696:0.168	rs16851681;rs52806274;rs61423063;rs16851681	1183	Q9P241	AT10D_HUMAN	K	1183	ENSP00000273859:R1183K	ENSP00000273859:R1183K	R	+	2	0	ATP10D	47273728	0.000000	0.05858	0.029000	0.17559	0.460000	0.32559	-0.312000	0.08113	-1.293000	0.02362	-1.322000	0.01289	AGA	G|0.728;A|0.272	0.272	strong		0.428	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
SPATA5	166378	hgsc.bcm.edu	37	4	123949389	123949389	+	Missense_Mutation	SNP	G	G	C	rs35343500	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123949389G>C	ENST00000274008.4	+	11	1987	c.1918G>C	c.(1918-1920)Gaa>Caa	p.E640Q	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	640					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						ACTGAAGTTGGAACAGGCTGT	0.428													G|||	309	0.0617013	0.062	0.0418	5008	,	,		16432	0.0089		0.0129	False		,,,				2504	0.18				p.E640Q		Atlas-SNP	.											.	SPATA5	62	.	0			c.G1918C						PASS	.	G	GLN/GLU	263,4143	149.5+/-183.7	10,243,1950	143.0	144.0	144.0		1918	3.2	1.0	4	dbSNP_126	144	149,8451	73.5+/-136.2	2,145,4153	yes	missense	SPATA5	NM_145207.2	29	12,388,6103	CC,CG,GG		1.7326,5.9691,3.1678	benign	640/894	123949389	412,12594	2203	4300	6503	SO:0001583	missense	166378	exon11			AAGTTGGAACAGG	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"""ATPases / AAA-type"""	18119	protein-coding gene	gene with protein product	"""ATPase family gene 2 homolog (S. cerevisiae)"""	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1918G>C	4.37:g.123949389G>C	ENSP00000274008:p.Glu640Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Missense_Mutation	SNP	ENST00000274008.4	37	CCDS3730.1	53	0.024267399267399268	32	0.06504065040650407	14	0.03867403314917127	2	0.0034965034965034965	5	0.006596306068601583	G	10.20	1.284131	0.23392	0.059691	0.017326	ENSG00000145375	ENST00000274008	D	0.94897	-3.55	5.8	3.23	0.37069	.	0.164734	0.52532	D	0.000077	T	0.26448	0.0646	N	0.01091	-1.02	0.21527	N	0.999653	B;B	0.10296	0.001;0.003	B;B	0.09377	0.002;0.004	T	0.57294	-0.7836	10	0.07482	T	0.82	-12.3529	8.5429	0.33404	0.8023:0.1299:0.0678:0.0	rs35343500;rs61732389	640;640	Q8NB90;Q8NB90-3	SPAT5_HUMAN;.	Q	640	ENSP00000274008:E640Q	ENSP00000274008:E640Q	E	+	1	0	SPATA5	124168839	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	3.072000	0.50049	1.006000	0.39211	-0.383000	0.06682	GAA	G|0.967;C|0.033	0.033	strong		0.428	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207	
OR5W2	390148	hgsc.bcm.edu	37	11	55681566	55681566	+	Missense_Mutation	SNP	G	G	A	rs61749302	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	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	
FLG	2312	hgsc.bcm.edu	37	1	152283236	152283236	+	Missense_Mutation	SNP	T	T	C	rs11581433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152283236T>C	ENST00000368799.1	-	3	4161	c.4126A>G	c.(4126-4128)Aga>Gga	p.R1376G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1376	Ser-rich.		R -> G (in dbSNP:rs11581433).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGCTTGTCTGTGCCCAATG	0.532									Ichthyosis				C|||	1718	0.343051	0.1218	0.4236	5008	,	,		21937	0.6062		0.171	False		,,,				2504	0.4908				p.R1376G		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A4126G						PASS	.	C	GLY/ARG	607,3799	768.9+/-413.6	43,521,1639	411.0	383.0	392.0		4126	-4.5	0.0	1	dbSNP_120	392	1436,7160	750.9+/-407.4	123,1190,2985	no	missense	FLG	NM_002016.1	125	166,1711,4624	CC,CT,TT		16.7054,13.7767,15.713	benign	1376/4062	152283236	2043,10959	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTTGTCTGTGCCC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4126A>G	1.37:g.152283236T>C	ENSP00000357789:p.Arg1376Gly	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	177	76	0.429379	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	588	0.2692307692307692	51	0.10365853658536585	109	0.3011049723756906	317	0.5541958041958042	111	0.14643799472295516	C	6.987	0.552125	0.13374	0.137767	0.167054	ENSG00000143631	ENST00000368799	T	0.02032	4.49	4.29	-4.46	0.03536	.	.	.	.	.	T	0.00178	0.0005	N	0.00642	-1.3	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39663	-0.9603	8	0.02654	T	1	.	8.0818	0.30750	0.0:0.1976:0.1306:0.6718	rs11581433	1376	P20930	FILA_HUMAN	G	1376	ENSP00000357789:R1376G	ENSP00000357789:R1376G	R	-	1	2	FLG	150549860	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.374000	0.01072	-0.955000	0.03636	-0.949000	0.02662	AGA	T|0.807;C|0.193	0.193	strong		0.532	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
BEND3	57673	hgsc.bcm.edu	37	6	107391213	107391213	+	Silent	SNP	C	C	T	rs3814072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:107391213C>T	ENST00000369042.1	-	4	1372	c.1182G>A	c.(1180-1182)acG>acA	p.T394T	BEND3_ENST00000429433.2_Silent_p.T394T			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	394	BEN 2. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						TGAGGTCCTGCGTGTCCACCA	0.632													c|||	344	0.0686901	0.0598	0.0764	5008	,	,		18142	0.0585		0.0934	False		,,,				2504	0.0603				p.T394T		Atlas-SNP	.											.	BEND3	70	.	0			c.G1182A						PASS	.	C		322,4084	170.9+/-201.2	11,300,1892	72.0	72.0	72.0		1182	-1.3	1.0	6	dbSNP_107	72	719,7881	176.0+/-226.0	32,655,3613	no	coding-synonymous	BEND3	NM_001080450.2		43,955,5505	TT,TC,CC		8.3605,7.3082,8.004		394/829	107391213	1041,11965	2203	4300	6503	SO:0001819	synonymous_variant	57673	exon5			GTCCTGCGTGTCC	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"""BEN domain containing"""	23040	protein-coding gene	gene with protein product			"""KIAA1553"""	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1182G>A	6.37:g.107391213C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_001080450	A2RRH2|Q9HCL9	Silent	SNP	ENST00000369042.1	37	CCDS34507.1																																																																																			C|0.925;T|0.075	0.075	strong		0.632	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
ATP8A1	10396	hgsc.bcm.edu	37	4	42576646	42576646	+	Missense_Mutation	SNP	C	C	T	rs61755862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	198	0	0		WXS	Illumina HiSeq	Phase_I	218	110	0.504587	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	
MUSK	4593	hgsc.bcm.edu	37	9	113538122	113538122	+	Missense_Mutation	SNP	G	G	A	rs2274419	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:113538122G>A	ENST00000374448.4	+	10	1373	c.1239G>A	c.(1237-1239)atG>atA	p.M413I	MUSK_ENST00000416899.2_Missense_Mutation_p.M413I|MUSK_ENST00000189978.5_Missense_Mutation_p.M413I|MUSK_ENST00000374438.1_Missense_Mutation_p.G5R	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	413	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		M -> I (in dbSNP:rs2274419). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						GGCTGGTAATGGAAGAGAAGA	0.468													G|||	503	0.100439	0.0045	0.0389	5008	,	,		17692	0.1895		0.1252	False		,,,				2504	0.1564				p.M413I		Atlas-SNP	.											.	MUSK	112	.	0			c.G1239A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET	83,3709		0,83,1813	84.0	85.0	85.0		1005,975,1239	1.1	0.9	9	dbSNP_100	85	1094,7152		73,948,3102	yes	missense,missense,missense	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	10,10,10	73,1031,4915	AA,AG,GG		13.267,2.1888,9.7774	benign,benign,benign	335/784,325/774,413/870	113538122	1177,10861	1896	4123	6019	SO:0001583	missense	4593	exon9			GGTAATGGAAGAG	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.1239G>A	9.37:g.113538122G>A	ENSP00000363571:p.Met413Ile	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	219	100	0.456621	NM_005592	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	224|224	0.10256410256410256|0.10256410256410256	3|3	0.006097560975609756|0.006097560975609756	14|14	0.03867403314917127|0.03867403314917127	119|119	0.20804195804195805|0.20804195804195805	88|88	0.11609498680738786|0.11609498680738786	G|G	5.688|5.688	0.311434|0.311434	0.10789|0.10789	0.021888|0.021888	0.13267|0.13267	ENSG00000030304|ENSG00000030304	ENST00000374441;ENST00000374438|ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	D|T	0.84442|0.71817	-1.85|-0.6	5.43|5.43	1.08|1.08	0.20341|0.20341	.|Frizzled domain (2);	.|0.533746	.|0.23008	.|N	.|0.052987	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.04229|0.04229	-1.0967|-1.0967	6|9	0.87932|0.10377	D|T	0|0.69	.|.	7.3856|7.3856	0.26880|0.26880	0.2043:0.139:0.6568:0.0|0.2043:0.139:0.6568:0.0	rs2274419;rs52816297;rs56547888;rs59906813;rs2274419|rs2274419;rs52816297;rs56547888;rs59906813;rs2274419	.|413	.|O15146	.|MUSK_HUMAN	R|I	5|419;413;413;335;335;419	ENSP00000363561:G5R|ENSP00000363571:M413I	ENSP00000363561:G5R|ENSP00000189978:M419I	G|M	+|+	1|3	0|0	MUSK|MUSK	112577943|112577943	1.000000|1.000000	0.71417|0.71417	0.924000|0.924000	0.36721|0.36721	0.605000|0.605000	0.37080|0.37080	0.809000|0.809000	0.27168|0.27168	0.259000|0.259000	0.21709|0.21709	0.655000|0.655000	0.94253|0.94253	GGA|ATG	G|0.885;A|0.115	0.115	strong		0.468	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PMM2	5373	hgsc.bcm.edu	37	16	8906914	8906914	+	Missense_Mutation	SNP	A	A	C	rs34258285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:8906914A>C	ENST00000268261.4	+	7	656	c.590A>C	c.(589-591)gAa>gCa	p.E197A	PMM2_ENST00000566983.1_Missense_Mutation_p.E170A|PMM2_ENST00000539622.1_Missense_Mutation_p.E114A|PMM2_ENST00000537352.1_Missense_Mutation_p.E72A|PMM2_ENST00000569958.1_Missense_Mutation_p.E106A	NM_000303.2	NP_000294.1	O15305	PMM2_HUMAN	phosphomannomutase 2	197			E -> A (in CDG1A; dbSNP:rs34258285). {ECO:0000269|PubMed:11058895, ECO:0000269|PubMed:15844218}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|mannose biosynthetic process (GO:0019307)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	phosphomannomutase activity (GO:0004615)			breast(3)|cervix(1)|endometrium(2)|large_intestine(1)|ovary(1)|skin(1)	9						CGACATGTGGAAAATGACGGT	0.463													A|||	45	0.00898562	0.0015	0.0216	5008	,	,		21288	0.0		0.0249	False		,,,				2504	0.0031				p.E197A	Esophageal Squamous(154;1308 1842 2827 29799 42829)	Atlas-SNP	.											.	PMM2	25	.	0			c.A590C	GRCh37	CM002843	PMM2	M	rs34258285	PASS	.	A	ALA/GLU	21,4373	28.1+/-56.4	0,21,2176	148.0	131.0	137.0		590	4.9	0.9	16	dbSNP_126	137	219,8381	92.1+/-154.2	6,207,4087	yes	missense	PMM2	NM_000303.2	107	6,228,6263	CC,CA,AA		2.5465,0.4779,1.847	benign	197/247	8906914	240,12754	2197	4300	6497	SO:0001583	missense	5373	exon7			ATGTGGAAAATGA	BC008310	CCDS10536.1	16p13	2012-09-06			ENSG00000140650	ENSG00000140650	5.3.1.8		9115	protein-coding gene	gene with protein product	"""phosphomannose isomerase 1"""	601785		CDG1		9140401	Standard	NM_000303		Approved	CDGS, CDG1a, PMI, PMI1	uc002czf.4	O15305	OTTHUMG00000129697	ENST00000268261.4:c.590A>C	16.37:g.8906914A>C	ENSP00000268261:p.Glu197Ala	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	131	56	0.427481	NM_000303	A8K672|B7Z6R0|D3DUF3	Missense_Mutation	SNP	ENST00000268261.4	37	CCDS10536.1	28	0.01282051282051282	0	0.0	10	0.027624309392265192	0	0.0	18	0.023746701846965697	A	9.835	1.189414	0.21954	0.004779	0.025465	ENSG00000140650	ENST00000268261;ENST00000539622;ENST00000537352	D;D;D	0.98474	-4.95;-4.95;-4.95	4.89	4.89	0.63831	HAD-like domain (2);	0.049443	0.85682	D	0.000000	D	0.90113	0.6911	L	0.52364	1.645	0.58432	D	0.999991	B;B;B	0.16603	0.018;0.0;0.002	B;B;B	0.19148	0.021;0.008;0.024	D	0.89308	0.3631	10	0.18710	T	0.47	.	10.2623	0.43434	0.8343:0.1657:0.0:0.0	rs34258285	50;114;197	B7Z922;F5H0W0;O15305	.;.;PMM2_HUMAN	A	197;114;72	ENSP00000268261:E197A;ENSP00000445879:E114A;ENSP00000438359:E72A	ENSP00000268261:E197A	E	+	2	0	PMM2	8814415	0.971000	0.33674	0.909000	0.35828	0.101000	0.19017	2.489000	0.45285	1.839000	0.53478	0.533000	0.62120	GAA	A|0.984;C|0.016	0.016	strong		0.463	PMM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251904.1	NM_000303	
RBAK	57786	hgsc.bcm.edu	37	7	5105208	5105208	+	Silent	SNP	C	C	T	rs36026500	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:5105208C>T	ENST00000353796.3	+	6	2445	c.2121C>T	c.(2119-2121)aaC>aaT	p.N707N	RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Silent_p.N707N	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	707	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		GAAATATGAACGTACTTGATG	0.368													C|||	890	0.177716	0.0446	0.1499	5008	,	,		18480	0.373		0.1262	False		,,,				2504	0.229				p.N707N		Atlas-SNP	.											.	RBAK	82	.	0			c.C2121T						PASS	.	C	,,	267,4081		2,263,1909	51.0	57.0	55.0		2121,,2121	-5.0	0.0	7	dbSNP_126	55	954,7624		52,850,3387	no	coding-synonymous,intron,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	54,1113,5296	TT,TC,CC		11.1215,6.1408,9.4461	,,	707/715,,707/715	5105208	1221,11705	2174	4289	6463	SO:0001819	synonymous_variant	57786	exon6			TATGAACGTACTT	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.2121C>T	7.37:g.5105208C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			C|0.872;T|0.128	0.128	strong		0.368	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
PSMD13	5719	hgsc.bcm.edu	37	11	237087	237087	+	Missense_Mutation	SNP	A	A	G	rs1045288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:237087A>G	ENST00000532097.1	+	1	542	c.38A>G	c.(37-39)aAc>aGc	p.N13S	SIRT3_ENST00000529382.1_5'Flank|SIRT3_ENST00000532956.1_5'Flank|SIRT3_ENST00000382743.4_5'Flank|PSMD13_ENST00000431206.2_Missense_Mutation_p.N13S|SIRT3_ENST00000524564.1_5'Flank|SIRT3_ENST00000525319.1_5'Flank|SIRT3_ENST00000528702.1_5'Flank|PSMD13_ENST00000352303.5_Missense_Mutation_p.N13S	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	13			N -> S (in dbSNP:rs1045288). {ECO:0000269|PubMed:10225435, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17323924, ECO:0000269|Ref.2, ECO:0000269|Ref.4, ECO:0000269|Ref.7}.		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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		CAGAGCCAGAACTCCGGGCCC	0.667													G|||	4092	0.817093	0.8918	0.83	5008	,	,		14994	0.8075		0.7316	False		,,,				2504	0.8047				p.N13S		Atlas-SNP	.											.	PSMD13	53	.	0			c.A38G						PASS	.	G	SER/ASN,SER/ASN	3892,514	227.5+/-242.7	1719,454,30	27.0	33.0	31.0		38,38	4.1	1.0	11	dbSNP_86	31	6398,2202	366.0+/-334.1	2378,1642,280	yes	missense,missense	PSMD13	NM_002817.3,NM_175932.2	46,46	4097,2096,310	GG,GA,AA		25.6047,11.6659,20.8827	benign,benign	13/377,13/379	237087	10290,2716	2203	4300	6503	SO:0001583	missense	5719	exon1			GCCAGAACTCCGG	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.38A>G	11.37:g.237087A>G	ENSP00000436186:p.Asn13Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	1746	0.7994505494505495	437	0.8882113821138211	293	0.8093922651933702	464	0.8111888111888111	552	0.7282321899736148	G	4.622	0.115571	0.08831	0.883341	0.743953	ENSG00000185627	ENST00000532097;ENST00000431206;ENST00000528906;ENST00000352303	T;T;T;T	0.16457	2.34;2.36;2.56;2.35	5.0	4.08	0.47627	.	0.082589	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01096	-1.015	0.45502	P	0.001534999999999953	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.34825	-0.9813	9	0.02654	T	1	.	9.8872	0.41268	0.1696:0.0:0.8304:0.0	rs1045288;rs3168345;rs17844885;rs17857602;rs17857647;rs57507796;rs1045288	13;13	Q9UNM6-2;Q9UNM6	.;PSD13_HUMAN	S	13	ENSP00000436186:N13S;ENSP00000396937:N13S;ENSP00000433364:N13S;ENSP00000333811:N13S	ENSP00000333811:N13S	N	+	2	0	PSMD13	227087	1.000000	0.71417	1.000000	0.80357	0.344000	0.29017	3.321000	0.51999	1.093000	0.41377	-0.226000	0.12346	AAC	A|0.201;G|0.799	0.799	strong		0.667	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
TCEB3C	162699	hgsc.bcm.edu	37	18	44555147	44555147	+	Missense_Mutation	SNP	T	T	G	rs139717358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:44555147T>G	ENST00000330682.2	-	1	1302	c.1067A>C	c.(1066-1068)gAa>gCa	p.E356A	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_145653.3	NP_663628.2	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide 3C (elongin A3)	356	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(16)|skin(2)	30						GGGGACCCCTTCCACGTCGCC	0.647																																					p.E356A		Atlas-SNP	.											TCEB3C,NS,carcinoma,0,1	TCEB3C	49	1	0			c.A1067C						scavenged	.	T	,ALA/GLU	71,3171		0,71,1550	233.0	223.0	226.0		,1067	-1.6	0.0	18	dbSNP_134	226	595,6065		0,595,2735	no	intron,missense	KATNAL2,TCEB3C	NM_031303.2,NM_145653.3	,107	0,666,4285	GG,GT,TT		8.9339,2.19,6.7259	,benign	,356/547	44555147	666,9236	1621	3330	4951	SO:0001583	missense	162699	exon1			ACCCCTTCCACGT	AB076840	CCDS11931.1	18q21.1	2008-08-13			ENSG00000183791	ENSG00000183791			24617	protein-coding gene	gene with protein product	"""elongin A3"""					11932239, 11994304	Standard	NM_145653		Approved	HsT829, TCEB3L2	uc010xdb.2	Q8NG57	OTTHUMG00000132651	ENST00000330682.2:c.1067A>C	18.37:g.44555147T>G	ENSP00000328232:p.Glu356Ala	Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	399	124	0.310777	NM_145653		Missense_Mutation	SNP	ENST00000330682.2	37	CCDS11931.1	.	.	.	.	.	.	.	.	.	.	t	5.286	0.238258	0.10023	0.0219	0.089339	ENSG00000183791	ENST00000330682	T	0.29397	1.57	1.6	-1.61	0.08399	.	0.408249	0.20310	N	0.094854	T	0.00580	0.0019	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.10382	-1.0632	10	0.62326	D	0.03	-1.0576	6.2705	0.20951	0.0:0.6512:0.0:0.3488	.	356	Q8NG57	ELOA3_HUMAN	A	356	ENSP00000328232:E356A	ENSP00000328232:E356A	E	-	2	0	TCEB3C	42809145	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.045000	0.12003	-0.528000	0.06366	-1.744000	0.00683	GAA	T|0.924;G|0.076	0.076	strong		0.647	TCEB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255902.1	NM_145653	
GPR31	2853	hgsc.bcm.edu	37	6	167571266	167571266	+	Silent	SNP	A	A	T	rs4569938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:167571266A>T	ENST00000366834.1	-	1	551	c.54T>A	c.(52-54)ggT>ggA	p.G18G		NM_005299.2	NP_005290.2	O00270	GPR31_HUMAN	G protein-coupled receptor 31	18					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)			NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		CCAGCAAGACACCCACAGCTG	0.657													A|||	148	0.0295527	0.0234	0.0504	5008	,	,		18007	0.0		0.0666	False		,,,				2504	0.0153				p.G18G		Atlas-SNP	.											.	GPR31	44	.	0			c.T54A						PASS	.	A		105,4285		1,103,2091	23.0	20.0	21.0		54	1.8	0.0	6	dbSNP_111	21	567,8013		22,523,3745	no	coding-synonymous	GPR31	NM_005299.2		23,626,5836	TT,TA,AA		6.6084,2.3918,5.1812		18/320	167571266	672,12298	2195	4290	6485	SO:0001819	synonymous_variant	2853	exon1			CAAGACACCCACA	U65402	CCDS5299.1	6q27	2012-08-21				ENSG00000120436		"""GPCR / Class A : Orphans"""	4486	protein-coding gene	gene with protein product	"""hydroxyeicosatetraenoic (HETE) acid receptor 1"", ""12-(S)-HETE acid receptor"""	602043				9205127, 21712392	Standard	NM_005299		Approved	HETER1, 12-HETER	uc011egq.2	O00270		ENST00000366834.1:c.54T>A	6.37:g.167571266A>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_005299	B0M0K2|Q4VBL3|Q9NQ20	Silent	SNP	ENST00000366834.1	37	CCDS5299.1																																																																																			A|0.955;T|0.045	0.045	strong		0.657	GPR31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043111.1	NM_005299	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411971	105411971	+	Missense_Mutation	SNP	T	T	C	rs28737397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105411971T>C	ENST00000333244.5	-	7	9936	c.9817A>G	c.(9817-9819)Agc>Ggc	p.S3273G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3273						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)			ACCTCCATGCTGGGCTGAGAC	0.632													.|||	1310	0.261581	0.1369	0.3069	5008	,	,		15097	0.0843		0.4851	False		,,,				2504	0.3507				p.S3273G		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A9817G						PASS	.	C	GLY/SER	34,3684		2,30,1827	104.0	79.0	87.0		9817	1.5	0.1	14	dbSNP_125	87	457,6761		37,383,3189	no	missense	AHNAK2	NM_138420.2	56	39,413,5016	CC,CT,TT		6.3314,0.9145,4.4898	benign	3273/5796	105411971	491,10445	1859	3609	5468	SO:0001583	missense	113146	exon7			CCATGCTGGGCTG	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.9817A>G	14.37:g.105411971T>C	ENSP00000353114:p.Ser3273Gly	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	222	0.10164835164835165	21	0.042682926829268296	49	0.13535911602209943	8	0.013986013986013986	144	0.18997361477572558	N	2.209	-0.381113	0.05000	0.009145	0.063314	ENSG00000185567	ENST00000333244	T	0.00682	5.86	3.87	1.45	0.22620	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.20261	0.043	B	0.20184	0.028	T	0.33497	-0.9866	8	0.22706	T	0.39	.	6.2963	0.21087	0.0:0.2172:0.0:0.7828	rs28737397	3273	Q8IVF2	AHNK2_HUMAN	G	3273	ENSP00000353114:S3273G	ENSP00000353114:S3273G	S	-	1	0	AHNAK2	104483016	0.007000	0.16637	0.102000	0.21198	0.005000	0.04900	0.903000	0.28475	0.023000	0.15187	-0.502000	0.04539	AGC	T|0.898;C|0.102	0.102	strong		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CILP2	148113	hgsc.bcm.edu	37	19	19654189	19654189	+	Silent	SNP	G	G	A	rs45556231	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19654189G>A	ENST00000291495.5	+	7	1195	c.1110G>A	c.(1108-1110)tcG>tcA	p.S370S	CILP2_ENST00000586018.1_Silent_p.S376S	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	370	Ig-like C2-type.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.S370S(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCGTGCGCTCGGGCACTGCCC	0.647													G|||	593	0.118411	0.1634	0.1167	5008	,	,		14555	0.0		0.166	False		,,,				2504	0.1319				p.S370S		Atlas-SNP	.											CILP2,NS,carcinoma,0,1	CILP2	84	1	1	Substitution - coding silent(1)	prostate(1)	c.G1110A						scavenged	.	G		716,3690		51,614,1538	43.0	43.0	43.0		1110	-8.9	0.0	19	dbSNP_127	43	1420,7178		113,1194,2992	no	coding-synonymous	CILP2	NM_153221.2		164,1808,4530	AA,AG,GG		16.5155,16.2506,16.4257		370/1157	19654189	2136,10868	2203	4299	6502	SO:0001819	synonymous_variant	148113	exon7			GCGCTCGGGCACT	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1110G>A	19.37:g.19654189G>A		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	176	70	0.397727	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			G|0.842;A|0.158	0.158	strong		0.647	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
PPOX	5498	hgsc.bcm.edu	37	1	161139738	161139738	+	Missense_Mutation	SNP	G	G	A	rs36013429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161139738G>A	ENST00000367999.4	+	9	1177	c.911G>A	c.(910-912)cGt>cAt	p.R304H	PPOX_ENST00000544598.1_Intron|PPOX_ENST00000352210.5_Missense_Mutation_p.R304H|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_3'UTR|B4GALT3_ENST00000470882.1_5'Flank	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	304			R -> H (in dbSNP:rs36013429). {ECO:0000269|PubMed:10486317, ECO:0000269|PubMed:8806618, ECO:0000269|PubMed:8852667}.		heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			CCTCTGGCTCGTGCCCTGAGT	0.567													G|||	245	0.0489217	0.003	0.0519	5008	,	,		19244	0.0675		0.0626	False		,,,				2504	0.0757				p.R304H		Atlas-SNP	.											.	PPOX	34	.	0			c.G911A						PASS	.	G	HIS/ARG,HIS/ARG	52,4354	52.3+/-87.9	1,50,2152	73.0	66.0	68.0		911,911	-9.8	0.0	1	dbSNP_126	68	540,8060	150.3+/-205.2	20,500,3780	yes	missense,missense	PPOX	NM_000309.3,NM_001122764.1	29,29	21,550,5932	AA,AG,GG		6.2791,1.1802,4.5517	benign,benign	304/478,304/478	161139738	592,12414	2203	4300	6503	SO:0001583	missense	5498	exon9			TGGCTCGTGCCCT	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"""variegate porphyria"""	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.911G>A	1.37:g.161139738G>A	ENSP00000356978:p.Arg304His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	NM_000309	D3DVG0|Q5VTW8	Missense_Mutation	SNP	ENST00000367999.4	37	CCDS1221.1	104|104	0.047619047619047616|0.047619047619047616	4|4	0.008130081300813009|0.008130081300813009	15|15	0.04143646408839779|0.04143646408839779	36|36	0.06293706293706294|0.06293706293706294	49|49	0.06464379947229551|0.06464379947229551	G|G	12.54|12.54	1.968895|1.968895	0.34754|0.34754	0.011802|0.011802	0.062791|0.062791	ENSG00000143224|ENSG00000143224	ENST00000352210;ENST00000367999;ENST00000435935|ENST00000537829	D;D|.	0.93133|.	-3.17;-3.17|.	5.43|5.43	-9.75|-9.75	0.00506|0.00506	Amine oxidase (1);|.	1.060600|.	0.07188|.	N|.	0.855199|.	T|T	0.19485|0.19485	0.0468|0.0468	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	N|N	1|1	B;B;B|.	0.13594|.	0.008;0.006;0.0|.	B;B;B|.	0.12837|.	0.008;0.001;0.0|.	T|T	0.27905|0.27905	-1.0060|-1.0060	10|5	0.41790|.	T|.	0.15|.	-0.0081|-0.0081	11.3476|11.3476	0.49569|0.49569	0.7146:0.095:0.1904:0.0|0.7146:0.095:0.1904:0.0	rs36013429;rs36013429|rs36013429;rs36013429	271;142;304|.	B4DY76;B3KT30;P50336|.	.;.;PPOX_HUMAN|.	H|M	304;304;271|27	ENSP00000343943:R304H;ENSP00000356978:R304H|.	ENSP00000343943:R304H|.	R|V	+|+	2|1	0|0	PPOX|PPOX	159406362|159406362	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.944000|0.944000	0.59088|0.59088	-0.448000|-0.448000	0.06820|0.06820	-1.827000|-1.827000	0.01204|0.01204	-0.142000|-0.142000	0.14014|0.14014	CGT|GTG	G|0.955;A|0.045	0.045	strong		0.567	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309	
AARS	16	hgsc.bcm.edu	37	16	70303580	70303580	+	Silent	SNP	G	G	A	rs2070203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70303580G>A	ENST00000261772.8	-	7	1046	c.903C>T	c.(901-903)caC>caT	p.H301H		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		TGGTCCGAGCGTGGTCAGCCA	0.587													G|||	2130	0.425319	0.438	0.4078	5008	,	,		18233	0.4256		0.5338	False		,,,				2504	0.3088				p.H301H		Atlas-SNP	.											.	AARS	62	.	0			c.C903T	GRCh37	CM995271	AARS	M	rs2070203	PASS	.	G		2071,2325	570.7+/-382.9	465,1141,592	200.0	167.0	178.0		903	-11.3	0.1	16	dbSNP_96	178	4307,4293	578.3+/-390.7	1084,2139,1077	yes	coding-synonymous	AARS	NM_001605.2		1549,3280,1669	AA,AG,GG		49.9186,47.111,49.0766		301/969	70303580	6378,6618	2198	4300	6498	SO:0001819	synonymous_variant	16	exon7			CCGAGCGTGGTCA	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	20	protein-coding gene	gene with protein product	"""alanine tRNA ligase 1, cytoplasmic"""	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.903C>T	16.37:g.70303580G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001605		Silent	SNP	ENST00000261772.8	37	CCDS32474.1																																																																																			G|0.526;A|0.474	0.474	strong		0.587	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605	
HLA-A	3105	hgsc.bcm.edu	37	6	29910335	29910335	+	Missense_Mutation	SNP	C	C	T	rs200058378		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29910335C>T	ENST00000396634.1	+	3	346	c.5C>T	c.(4-6)gCc>gTc	p.A2V	HLA-A_ENST00000376809.5_Missense_Mutation_p.A2V|HLA-A_ENST00000376806.5_Missense_Mutation_p.A2V|HLA-A_ENST00000376802.2_Missense_Mutation_p.A2V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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						CCGAGGATGGCCGTCATGGCG	0.672									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.A2V		Atlas-SNP	.											HLA-A,NS,carcinoma,-1,1	HLA-A	89	1	0			c.C5T						scavenged	.						36.0	38.0	37.0					6																	29910335		2201	4296	6497	SO:0001583	missense	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGATGGCCGTCAT	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.5C>T	6.37:g.29910335C>T	ENSP00000379873:p.Ala2Val	Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	183	7	0.0382514	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.183	0.794292	0.16327	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00662	5.94;5.93;5.94;5.94	2.6	-4.04	0.04010	.	.	.	.	.	T	0.00552	0.0018	L	0.27053	0.805	0.09310	N	1	D;B;D;B	0.76494	0.999;0.003;0.997;0.001	D;B;D;B	0.75484	0.986;0.014;0.986;0.014	T	0.50065	-0.8871	9	0.56958	D	0.05	.	4.6272	0.12484	0.4071:0.1733:0.4196:0.0	.	2;2;2;2	Q5SRN7;P16188;Q5SRN5;P04439	.;1A30_HUMAN;.;1A03_HUMAN	V	2	ENSP00000379873:A2V;ENSP00000366002:A2V;ENSP00000366005:A2V;ENSP00000365998:A2V	ENSP00000348012:A2V	A	+	2	0	HLA-A	30018314	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.890000	0.01613	-0.952000	0.03649	-0.531000	0.04308	GCC	C|0.999;T|0.001	0.001	weak		0.672	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CIDEC	63924	hgsc.bcm.edu	37	3	9918811	9918811	+	Missense_Mutation	SNP	G	G	A	rs61742367	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:9918811G>A	ENST00000336832.2	-	3	285	c.146C>T	c.(145-147)aCg>aTg	p.T49M	CIDEC_ENST00000430427.1_Missense_Mutation_p.T49M|CIDEC_ENST00000455015.1_Intron|CIDEC_ENST00000383817.1_Missense_Mutation_p.T49M|CIDEC_ENST00000423850.1_Intron|CIDEC_ENST00000443115.1_Missense_Mutation_p.T49M	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	49	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				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)					TCGATCCGCCGTGCTTACGCG	0.652													G|||	65	0.0129792	0.0	0.0331	5008	,	,		19217	0.0		0.0338	False		,,,				2504	0.0082				p.T62M		Atlas-SNP	.											CIDEC,NS,adenoma,0,2	CIDEC	22	2	0			c.C185T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	27,4287		0,27,2130	41.0	33.0	36.0		146,146,185,146	-0.5	0.0	3	dbSNP_129	36	260,8188		2,256,3966	yes	missense,missense,missense,missense	CIDEC	NM_001199551.1,NM_001199552.1,NM_001199623.1,NM_022094.3	81,81,81,81	2,283,6096	AA,AG,GG		3.0777,0.6259,2.2489	probably-damaging,probably-damaging,probably-damaging,probably-damaging	49/249,49/239,62/252,49/239	9918811	287,12475	2157	4224	6381	SO:0001583	missense	63924	exon3			TCCGCCGTGCTTA		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.146C>T	3.37:g.9918811G>A	ENSP00000338642:p.Thr49Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Missense_Mutation	SNP	ENST00000336832.2	37	CCDS2587.1	36	0.016483516483516484	0	0.0	12	0.03314917127071823	0	0.0	24	0.0316622691292876	G	13.34	2.209001	0.39003	0.006259	0.030777	ENSG00000187288	ENST00000336832;ENST00000383817;ENST00000430427;ENST00000443115	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.3	-0.542	0.11854	Caspase-activated nuclease CIDE-N (3);	0.196863	0.50627	D	0.000110	T	0.26376	0.0644	M	0.62723	1.935	0.26980	N	0.965374	D;D;D	0.76494	0.999;0.998;0.999	P;P;P	0.60886	0.862;0.828;0.88	T	0.32295	-0.9912	10	0.87932	D	0	-6.4291	7.9027	0.29744	0.0:0.3571:0.2248:0.4181	.	49;49;49	Q96AQ7-3;Q96AQ7;C9JMN7	.;CIDEC_HUMAN;.	M	49	ENSP00000338642:T49M;ENSP00000373328:T49M;ENSP00000408631:T49M;ENSP00000411356:T49M	ENSP00000338642:T49M	T	-	2	0	CIDEC	9893811	0.730000	0.28100	0.029000	0.17559	0.172000	0.22775	0.989000	0.29629	-0.246000	0.09611	0.650000	0.86243	ACG	G|0.982;A|0.018	0.018	strong		0.652	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
TEKT5	146279	hgsc.bcm.edu	37	16	10769958	10769958	+	Missense_Mutation	SNP	T	T	C	rs2719710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10769958T>C	ENST00000283025.2	-	5	1015	c.944A>G	c.(943-945)cAg>cGg	p.Q315R		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	315			Q -> R (in dbSNP:rs2719710).			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						CTCCCGCAGCTGGATGGAGTT	0.562													C|||	3176	0.634185	0.6944	0.6009	5008	,	,		21094	0.8135		0.3588	False		,,,				2504	0.6748				p.Q315R		Atlas-SNP	.											.	TEKT5	66	.	0			c.A944G						PASS	.	C	ARG/GLN	2872,1522	482.4+/-359.4	936,1000,261	127.0	109.0	115.0		944	2.7	1.0	16	dbSNP_100	115	3382,5218	641.8+/-399.7	664,2054,1582	yes	missense	TEKT5	NM_144674.1	43	1600,3054,1843	CC,CT,TT		39.3256,34.6381,48.1299	benign	315/486	10769958	6254,6740	2197	4300	6497	SO:0001583	missense	146279	exon5			CGCAGCTGGATGG		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.944A>G	16.37:g.10769958T>C	ENSP00000283025:p.Gln315Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	1277	0.5847069597069597	330	0.6707317073170732	193	0.5331491712707183	467	0.8164335664335665	287	0.3786279683377309	C	10.05	1.245159	0.22796	0.653619	0.393256	ENSG00000153060	ENST00000283025	T	0.02525	4.26	4.68	2.67	0.31697	.	0.145954	0.33691	N	0.004648	T	0.00012	0.0000	N	0.04373	-0.215	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.04191	-1.0970	9	0.19147	T	0.46	-30.7844	6.4945	0.22133	0.0:0.5605:0.0:0.4395	rs2719710;rs3803673;rs60988360;rs2719710	315	Q96M29	TEKT5_HUMAN	R	315	ENSP00000283025:Q315R	ENSP00000283025:Q315R	Q	-	2	0	TEKT5	10677459	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	1.681000	0.37618	0.521000	0.28445	-0.213000	0.12676	CAG	T|0.469;C|0.531	0.531	strong		0.562	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
LRRTM1	347730	hgsc.bcm.edu	37	2	80530062	80530062	+	Missense_Mutation	SNP	T	T	C	rs76300062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:80530062T>C	ENST00000295057.3	-	2	1539	c.883A>G	c.(883-885)Atc>Gtc	p.I295V	CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000466387.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.I295V|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000402739.4_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	295					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						CGGGGCTCGATGTAGGTGAGG	0.622										HNSCC(69;0.2)			T|||	115	0.0229633	0.0061	0.0144	5008	,	,		18209	0.0397		0.0358	False		,,,				2504	0.0215				p.I295V		Atlas-SNP	.											.	LRRTM1	251	.	0			c.A883G						PASS	.	T	,,VAL/ILE	37,4369	41.6+/-74.8	0,37,2166	57.0	57.0	57.0		,,883	-8.1	0.3	2	dbSNP_131	57	193,8407	84.8+/-147.2	0,193,4107	yes	intron,intron,missense	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,29	0,230,6273	CC,CT,TT		2.2442,0.8398,1.7684	,,benign	,,295/523	80530062	230,12776	2203	4300	6503	SO:0001583	missense	347730	exon2			GCTCGATGTAGGT	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.883A>G	2.37:g.80530062T>C	ENSP00000295057:p.Ile295Val	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	231	118	0.510823	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	64	0.029304029304029304	2	0.0040650406504065045	9	0.024861878453038673	25	0.043706293706293704	28	0.036939313984168866	T	0.873	-0.731247	0.03135	0.008398	0.022442	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.62498	0.02;0.02	5.26	-8.12	0.01078	.	0.308918	0.30901	N	0.008659	T	0.09949	0.0244	N	0.16602	0.42	0.36834	D	0.88705	B	0.06786	0.001	B	0.10450	0.005	T	0.12372	-1.0550	9	.	.	.	.	11.4996	0.50430	0.0:0.5628:0.1164:0.3207	.	295	Q86UE6	LRRT1_HUMAN	V	295	ENSP00000295057:I295V;ENSP00000386646:I295V	.	I	-	1	0	LRRTM1	80383573	0.984000	0.35163	0.299000	0.25016	0.957000	0.61999	0.178000	0.16820	-2.019000	0.00942	-0.899000	0.02877	ATC	T|0.979;C|0.021	0.021	strong		0.622	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
COLEC11	78989	hgsc.bcm.edu	37	2	3691548	3691548	+	Missense_Mutation	SNP	A	A	G	rs7567833	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:3691548A>G	ENST00000349077.4	+	7	759	c.656A>G	c.(655-657)cAc>cGc	p.H219R	COLEC11_ENST00000382062.2_Missense_Mutation_p.H195R|COLEC11_ENST00000402922.1_Missense_Mutation_p.H169R|COLEC11_ENST00000402794.1_Missense_Mutation_p.H169R|COLEC11_ENST00000236693.7_Missense_Mutation_p.H216R|COLEC11_ENST00000418971.2_Missense_Mutation_p.H233R|COLEC11_ENST00000404205.1_Missense_Mutation_p.H145R|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000403096.3_Missense_Mutation_p.H193R	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	112	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	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	
MAP4K3	8491	hgsc.bcm.edu	37	2	39494378	39494378	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:39494378C>T	ENST00000263881.3	-	27	2308	c.1984G>A	c.(1984-1986)Gta>Ata	p.V662I	MAP4K3_ENST00000341681.5_Missense_Mutation_p.V641I|MAP4K3_ENST00000437545.1_Missense_Mutation_p.V578I|MAP4K3_ENST00000536018.1_Missense_Mutation_p.V215I	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	662	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				TTTGCTGATACAGAAAATTTC	0.348																																					p.V662I		Atlas-SNP	.											MAP4K3,right_lower_lobe,carcinoma,0,1	MAP4K3	109	1	0			c.G1984A						scavenged	.						109.0	110.0	110.0					2																	39494378		2203	4300	6503	SO:0001583	missense	8491	exon27			CTGATACAGAAAA	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1984G>A	2.37:g.39494378C>T	ENSP00000263881:p.Val662Ile	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	3	0.0422535	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.371764	0.61624	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681;ENST00000536018	T;T;T;T	0.04862	3.54;3.54;3.54;3.54	5.42	5.42	0.78866	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.10680	0.0261	L	0.33485	1.01	0.58432	D	0.999997	P;P	0.39903	0.694;0.624	P;P	0.46718	0.452;0.525	T	0.32214	-0.9915	10	0.21540	T	0.41	.	19.6002	0.95559	0.0:1.0:0.0:0.0	.	641;662	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	I	662;578;641;215	ENSP00000263881:V662I;ENSP00000416958:V578I;ENSP00000345434:V641I;ENSP00000440580:V215I	ENSP00000263881:V662I	V	-	1	0	MAP4K3	39347882	0.999000	0.42202	1.000000	0.80357	0.983000	0.72400	3.286000	0.51724	2.691000	0.91804	0.655000	0.94253	GTA	.	.	none		0.348	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
R3HDM1	23518	hgsc.bcm.edu	37	2	136393658	136393658	+	Splice_Site	SNP	A	A	G	rs961360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:136393658A>G	ENST00000264160.4	+	11	1178	c.808A>G	c.(808-810)Atg>Gtg	p.M270V	R3HDM1_ENST00000409478.1_Splice_Site_p.M226V|R3HDM1_ENST00000410054.1_Splice_Site_p.M214V|R3HDM1_ENST00000329971.3_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	123	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	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
CACNA1I	8911	hgsc.bcm.edu	37	22	39966856	39966856	+	Silent	SNP	C	C	T	rs3747178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39966856C>T	ENST00000402142.3	+	1	99	c.99C>T	c.(97-99)tcC>tcT	p.S33S	CACNA1I_ENST00000401624.1_Silent_p.S33S|CACNA1I_ENST00000404898.1_Silent_p.S33S|CACNA1I_ENST00000336649.4_Silent_p.S33S|CACNA1I_ENST00000400164.3_Silent_p.S33S|CACNA1I_ENST00000407673.1_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	145	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	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	
F5	2153	hgsc.bcm.edu	37	1	169526019	169526019	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:169526019C>T	ENST00000367797.3	-	6	1018	c.817G>A	c.(817-819)Ggc>Agc	p.G273S	F5_ENST00000367796.3_Missense_Mutation_p.G273S|F5_ENST00000546081.1_Missense_Mutation_p.G136S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	273	F5/8 type A 1.|Plastocyanin-like 2.				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)	AGGACCTGGCCGTTGAAATGA	0.507																																					p.G273S		Atlas-SNP	.											F5,colon,carcinoma,0,1	F5	301	1	0			c.G817A						PASS	.						139.0	112.0	121.0					1																	169526019		2203	4300	6503	SO:0001583	missense	2153	exon6			CCTGGCCGTTGAA	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.817G>A	1.37:g.169526019C>T	ENSP00000356771:p.Gly273Ser	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	208	95	0.456731	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	36	5.703228	0.96812	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.99894	-7.58;-7.58;-7.58	6.07	6.07	0.98685	Cupredoxin (2);	0.090272	0.85682	D	0.000000	D	0.99921	0.9963	M	0.90369	3.11	0.44018	D	0.996733	D	0.89917	1.0	D	0.91635	0.999	D	0.96555	0.9411	9	0.87932	D	0	-22.8868	20.6439	0.99570	0.0:1.0:0.0:0.0	.	273	P12259	FA5_HUMAN	S	273;273;136	ENSP00000356771:G273S;ENSP00000356770:G273S;ENSP00000439664:G136S	ENSP00000356770:G273S	G	-	1	0	F5	167792643	1.000000	0.71417	0.983000	0.44433	0.973000	0.67179	7.456000	0.80751	2.890000	0.99128	0.650000	0.86243	GGC	.	.	none		0.507	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ZSWIM4	65249	hgsc.bcm.edu	37	19	13919757	13919757	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:13919757T>C	ENST00000254323.2	+	4	1009	c.820T>C	c.(820-822)Tac>Cac	p.Y274H	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	274							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)			CAATGGCGGCTACTACGGGGC	0.701																																					p.Y274H		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.T820C						PASS	.						18.0	18.0	18.0					19																	13919757		2184	4276	6460	SO:0001583	missense	65249	exon4			GGCGGCTACTACG	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.820T>C	19.37:g.13919757T>C	ENSP00000254323:p.Tyr274His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	77	4	0.0519481	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527572	0.44969	.	.	ENSG00000132003	ENST00000254323	T	0.41400	1.0	4.07	3.03	0.35002	.	0.129202	0.33895	N	0.004453	T	0.38108	0.1028	M	0.68593	2.085	0.80722	D	1	B	0.02656	0.0	B	0.10450	0.005	T	0.20438	-1.0275	10	0.51188	T	0.08	-0.0495	6.9161	0.24361	0.0:0.1211:0.0:0.8789	.	274	Q9H7M6	ZSWM4_HUMAN	H	274	ENSP00000254323:Y274H	ENSP00000254323:Y274H	Y	+	1	0	ZSWIM4	13780757	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	4.760000	0.62235	0.456000	0.26937	0.155000	0.16302	TAC	.	.	none		0.701	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
PCMTD2	55251	hgsc.bcm.edu	37	20	62896665	62896665	+	Silent	SNP	G	G	A	rs17878941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62896665G>A	ENST00000308824.6	+	4	592	c.465G>A	c.(463-465)ccG>ccA	p.P155P	PCMTD2_ENST00000609372.1_Intron|PCMTD2_ENST00000299468.7_Silent_p.P155P|PCMTD2_ENST00000369758.4_Silent_p.P155P	NM_018257.2	NP_060727.2	Q9NV79	PCMD2_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	155						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(9)|upper_aerodigestive_tract(1)	17	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					AGATTTCTCCGGATTGTTCTC	0.433													G|||	545	0.108826	0.1172	0.1124	5008	,	,		20094	0.0754		0.162	False		,,,				2504	0.0746				p.P155P		Atlas-SNP	.											.	PCMTD2	35	.	0			c.G465A						PASS	.	G	,	410,3996		24,362,1817	136.0	129.0	131.0		465,465	-1.0	0.2	20	dbSNP_124	131	1338,7262		110,1118,3072	no	coding-synonymous,coding-synonymous	PCMTD2	NM_001104925.1,NM_018257.2	,	134,1480,4889	AA,AG,GG		15.5581,9.3055,13.44	,	155/335,155/362	62896665	1748,11258	2203	4300	6503	SO:0001819	synonymous_variant	55251	exon4			TTCTCCGGATTGT	AK001745	CCDS13559.1, CCDS46631.1	20q13.33	2012-10-02	2005-10-06	2005-10-06	ENSG00000203880	ENSG00000203880			15882	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 36"""	C20orf36			Standard	NM_018257		Approved	FLJ10883	uc002yil.4	Q9NV79	OTTHUMG00000033029	ENST00000308824.6:c.465G>A	20.37:g.62896665G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	170	70	0.411765	NM_001104925	E1P5H3|Q8IW60|Q9H4K2	Silent	SNP	ENST00000308824.6	37	CCDS13559.1																																																																																			G|0.867;A|0.133	0.133	strong		0.433	PCMTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080301.1	NM_018257	
EMID1	129080	hgsc.bcm.edu	37	22	29630337	29630337	+	Splice_Site	SNP	G	G	A	rs3950176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:29630337G>A	ENST00000404820.3	+	12	1200	c.1073G>A	c.(1072-1074)cGg>cAg	p.R358Q	EMID1_ENST00000404755.3_Splice_Site_p.R337Q|EMID1_ENST00000334018.6_Splice_Site_p.R358Q			Q96A84	EMID1_HUMAN	EMI domain containing 1	356	Collagen-like.					collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)|skin(3)	12						GCTGGGCAGCGGGTAAGTGTT	0.607													G|||	724	0.144569	0.1974	0.0605	5008	,	,		19383	0.2302		0.1044	False		,,,				2504	0.0859				p.R358Q		Atlas-SNP	.											.	EMID1	33	.	0			c.G1073A						PASS	.	G	GLN/ARG	837,3569	324.2+/-298.5	82,673,1448	93.0	71.0	78.0		1073	-2.8	0.9	22	dbSNP_108	78	940,7660	203.0+/-246.1	50,840,3410	yes	missense-near-splice	EMID1	NM_133455.2	43	132,1513,4858	AA,AG,GG		10.9302,18.9968,13.6629	benign	358/444	29630337	1777,11229	2203	4300	6503	SO:0001630	splice_region_variant	129080	exon12			GGCAGCGGGTAAG	AJ416090	CCDS33630.1	22q12.2	2009-08-04			ENSG00000186998	ENSG00000186998		"""EMI domain containing"""	18036	protein-coding gene	gene with protein product	"""emilin and multimerin-domain containing protein 1"", ""putative emu1"""	608926				12221002	Standard	NM_001267895		Approved	EMU1, hEmu1, EMI5	uc003aem.4	Q96A84	OTTHUMG00000151013	ENST00000404820.3:c.1074+1G>A	22.37:g.29630337G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	37	0.381443	NM_133455	B0QYK6|Q6ICG1|Q86SS7	Missense_Mutation	SNP	ENST00000404820.3	37		355|355	0.16254578754578755|0.16254578754578755	100|100	0.2032520325203252|0.2032520325203252	26|26	0.0718232044198895|0.0718232044198895	143|143	0.25|0.25	86|86	0.11345646437994723|0.11345646437994723	G|G	12.74|12.74	2.028660|2.028660	0.35797|0.35797	0.189968|0.189968	0.109302|0.109302	ENSG00000186998|ENSG00000186998	ENST00000433143|ENST00000334018;ENST00000404755;ENST00000404820	.|D;T;D	.|0.90788	.|-2.73;2.32;-2.73	4.43|4.43	-2.76|-2.76	0.05896|0.05896	.|.	.|0.777093	.|0.11137	.|N	.|0.595736	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.12569|0.12569	0.235|0.235	0.49687|0.49687	P|P	1.8399999999996197E-4|1.8399999999996197E-4	.|B;B;B;B	.|0.19200	.|0.015;0.016;0.034;0.012	.|B;B;B;B	.|0.12156	.|0.007;0.004;0.007;0.004	T|T	0.03394|0.03394	-1.1041|-1.1041	4|9	.|0.11182	.|T	.|0.66	-1.0737|-1.0737	5.4627|5.4627	0.16626|0.16626	0.315:0.2571:0.4278:0.0|0.315:0.2571:0.4278:0.0	rs3950176;rs60629999;rs3950176|rs3950176;rs60629999;rs3950176	.|337;358;356;358	.|B0QYK4;B0QYK5;Q96A84;Q96A84-3	.|.;.;EMID1_HUMAN;.	R|Q	221|358;337;358	.|ENSP00000335481:R358Q;ENSP00000385414:R337Q;ENSP00000384452:R358Q	.|ENSP00000335481:R358Q	G|R	+|+	1|2	0|0	EMID1|EMID1	27960337|27960337	0.564000|0.564000	0.26602|0.26602	0.932000|0.932000	0.37286|0.37286	0.853000|0.853000	0.48598|0.48598	-0.446000|-0.446000	0.06837|0.06837	-1.014000|-1.014000	0.03379|0.03379	-0.797000|-0.797000	0.03246|0.03246	GGG|CGG	G|0.849;A|0.151	0.151	strong		0.607	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455	Missense_Mutation
TRPC6	7225	hgsc.bcm.edu	37	11	101323770	101323770	+	Silent	SNP	C	C	T	rs12805398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:101323770C>T	ENST00000344327.3	-	13	3136	c.2712G>A	c.(2710-2712)caG>caA	p.Q904Q	TRPC6_ENST00000360497.4_Silent_p.Q849Q|TRPC6_ENST00000532133.1_Silent_p.Q826Q|TRPC6_ENST00000348423.4_Silent_p.Q788Q	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	904					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)		CTTCTGTATTCTGAGATTTTT	0.378													C|||	375	0.0748802	0.0068	0.0677	5008	,	,		17040	0.0724		0.1501	False		,,,				2504	0.0971				p.Q904Q	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											.	TRPC6	132	.	0			c.G2712A						PASS	.	C		119,4287	90.6+/-129.3	3,113,2087	169.0	166.0	167.0		2712	3.8	1.0	11	dbSNP_121	167	1142,7458	234.0+/-267.1	74,994,3232	no	coding-synonymous	TRPC6	NM_004621.5		77,1107,5319	TT,TC,CC		13.2791,2.7009,9.6955		904/932	101323770	1261,11745	2203	4300	6503	SO:0001819	synonymous_variant	7225	exon13			TGTATTCTGAGAT	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.2712G>A	11.37:g.101323770C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	215	100	0.465116	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Silent	SNP	ENST00000344327.3	37	CCDS8311.1																																																																																			C|0.909;T|0.091	0.091	strong		0.378	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621	
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743249	22743249	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:22743249T>A	ENST00000560659.2	+	8	1484	c.1484T>A	c.(1483-1485)aTg>aAg	p.M495K	GOLGA6L1_ENST00000316397.3_Missense_Mutation_p.M545K			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	538										NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						caggaggagatgatgcaggaa	0.552																																					p.M545K		Atlas-SNP	.											GOLGA6L1,caecum,carcinoma,0,1	GOLGA6L1	20	1	0			c.T1634A						scavenged	.																																			SO:0001583	missense	283767	exon8			AGGAGATGATGCA	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.1484T>A	15.37:g.22743249T>A	ENSP00000452626:p.Met495Lys	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	36	3	0.0833333	NM_001001413		Missense_Mutation	SNP	ENST00000560659.2	37		.	.	.	.	.	.	.	.	.	.	.	0.004	-2.347201	0.00219	.	.	ENSG00000197414	ENST00000316397	T	0.07688	3.17	.	.	.	.	.	.	.	.	T	0.01976	0.0062	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.37197	-0.9716	5	0.02654	T	1	.	1.3913	0.02251	0.3258:0.0:0.3254:0.3488	.	.	.	.	K	545	ENSP00000320207:M545K	ENSP00000320207:M545K	M	+	2	0	GOLGA6L1	20294613	0.232000	0.23762	0.009000	0.14445	0.009000	0.06853	-1.148000	0.03185	-1.878000	0.01128	-2.010000	0.00438	ATG	.	.	none		0.552	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
TRIM66	9866	hgsc.bcm.edu	37	11	8646763	8646763	+	Missense_Mutation	SNP	G	G	C	rs7935453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8646763G>C	ENST00000299550.6	-	11	2082	c.1888C>G	c.(1888-1890)Ctg>Gtg	p.L630V	TRIM66_ENST00000402157.2_Missense_Mutation_p.L628V	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	630						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						ATGATGCTCAGCGAGGTGGAG	0.572													C|||	1552	0.309904	0.2746	0.2608	5008	,	,		21059	0.3621		0.2505	False		,,,				2504	0.3998				p.L630V		Atlas-SNP	.											.	TRIM66	45	.	0			c.C1888G						PASS	.						9.0	9.0	9.0					11																	8646763		692	1590	2282	SO:0001583	missense	9866	exon11			TGCTCAGCGAGGT	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.1888C>G	11.37:g.8646763G>C	ENSP00000299550:p.Leu630Val	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		613	0.2806776556776557	124	0.25203252032520324	104	0.287292817679558	192	0.3356643356643357	193	0.2546174142480211	C	0.011	-1.692612	0.00731	.	.	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.63417	-0.04;-0.02	5.72	2.82	0.32997	.	0.126710	0.36002	N	0.002849	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.33007	-0.9885	9	0.10902	T	0.67	-4.491	3.4232	0.07401	0.1293:0.4771:0.251:0.1426	rs7935453;rs52800221;rs7935453	630	O15016	TRI66_HUMAN	V	630;628	ENSP00000299550:L630V;ENSP00000384876:L628V	ENSP00000299550:L630V	L	-	1	2	TRIM66	8603339	0.198000	0.23374	0.384000	0.26145	0.519000	0.34347	0.427000	0.21379	0.356000	0.24157	-0.120000	0.15030	CTG	G|0.719;C|0.281	0.281	strong		0.572	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319399	21319399	+	Missense_Mutation	SNP	A	A	G	rs4985866	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:21319399A>G	ENST00000583088.1	+	3	1640	c.745A>G	c.(745-747)Atc>Gtc	p.I249V	KCNJ12_ENST00000331718.5_Missense_Mutation_p.I249V	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	249			I -> V (in dbSNP:rs4985866).		muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GCTGGACCAGATCGACATCGA	0.622										Prostate(3;0.18)																											p.I249V		Atlas-SNP	.											KCNJ12,NS,neuroblastoma,0,1	.	.	1	0			c.A745G						scavenged	.	A	VAL/ILE	964,3442		0,964,1239	127.0	92.0	104.0		745	4.3	1.0	17	dbSNP_111	104	2315,6285		0,2315,1985	yes	missense	KCNJ12	NM_021012.4	29	0,3279,3224	GG,GA,AA		26.9186,21.8793,25.2114	benign	249/434	21319399	3279,9727	2203	4300	6503	SO:0001583	missense	100134444	exon3			GACCAGATCGACA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.745A>G	17.37:g.21319399A>G	ENSP00000463778:p.Ile249Val	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	205	38	0.185366	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	816	0.37362637362637363	160	0.3252032520325203	129	0.356353591160221	276	0.4825174825174825	251	0.3311345646437995	A	6.561	0.471839	0.12461	0.218793	0.269186	ENSG00000184185	ENST00000331718	D	0.91180	-2.8	5.43	4.33	0.51752	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.052254	0.85682	D	0.000000	T	0.00012	0.0000	N	0.05124	-0.11	0.23735	P	0.99698559	B	0.06786	0.001	B	0.04013	0.001	T	0.24548	-1.0157	9	0.14656	T	0.56	.	12.5199	0.56054	0.8604:0.1396:0.0:0.0	rs4985866;rs4985866	249	Q14500	IRK12_HUMAN	V	249	ENSP00000328150:I249V	ENSP00000328150:I249V	I	+	1	0	KCNJ12	21259992	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	5.809000	0.69172	0.873000	0.35799	0.533000	0.62120	ATC	A|0.625;G|0.375	0.375	strong		0.622	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
CASP10	843	hgsc.bcm.edu	37	2	202050677	202050677	+	Silent	SNP	A	A	G	rs3900115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202050677A>G	ENST00000272879.5	+	2	361	c.177A>G	c.(175-177)tcA>tcG	p.S59S	CASP10_ENST00000313728.7_Silent_p.S59S|CASP10_ENST00000360132.3_Silent_p.S59S|CASP10_ENST00000448480.1_Silent_p.S59S|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000286186.6_Silent_p.S59S|CASP10_ENST00000346817.5_Silent_p.S59S|CASP10_ENST00000374650.3_Silent_p.S59S	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	59	DED 1. {ECO:0000255|PROSITE- ProRule:PRU00065}.				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						GCTCAGCCTCAGATGTTTTTG	0.483													G|||	1974	0.394169	0.4887	0.402	5008	,	,		19843	0.2192		0.5119	False		,,,				2504	0.32				p.S59S		Atlas-SNP	.											.	CASP10	95	.	0			c.A177G						PASS	.	G	,,,,,	2154,2252	595.7+/-388.5	521,1112,570	56.0	55.0	55.0		177,177,177,177,177,177	-5.2	0.0	2	dbSNP_108	55	4481,4119	563.6+/-388.2	1158,2165,977	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASP10	NM_001206524.1,NM_001206542.1,NM_001230.4,NM_032974.4,NM_032976.3,NM_032977.3	,,,,,	1679,3277,1547	GG,GA,AA		47.8953,48.8879,48.9851	,,,,,	59/456,59/479,59/480,59/522,59/274,59/523	202050677	6635,6371	2203	4300	6503	SO:0001819	synonymous_variant	843	exon2			AGCCTCAGATGTT	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.177A>G	2.37:g.202050677A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_032976	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Silent	SNP	ENST00000272879.5	37	CCDS2338.1																																																																																			A|0.545;G|0.455	0.455	strong		0.483	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977	
GSDMA	284110	hgsc.bcm.edu	37	17	38122686	38122686	+	Missense_Mutation	SNP	G	G	A	rs7212944	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38122686G>A	ENST00000301659.4	+	3	506	c.388G>A	c.(388-390)Gag>Aag	p.E130K		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	130			E -> K (in dbSNP:rs7212944). {ECO:0000269|PubMed:17471240}.		apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						GACCGTGCAGGAGAGGTGAGA	0.617													G|||	1595	0.31849	0.3389	0.2795	5008	,	,		16891	0.38		0.331	False		,,,				2504	0.2423				p.E130K		Atlas-SNP	.											.	GSDMA	26	.	0			c.G388A						PASS	.	G	LYS/GLU	1364,2680		232,900,890	72.0	81.0	78.0		388	3.0	0.4	17	dbSNP_116	78	2755,5607		443,1869,1869	yes	missense	GSDMA	NM_178171.4	56	675,2769,2759	AA,AG,GG		32.9467,33.729,33.2017	benign	130/446	38122686	4119,8287	2022	4181	6203	SO:0001583	missense	284110	exon3			GTGCAGGAGAGGT	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.388G>A	17.37:g.38122686G>A	ENSP00000301659:p.Glu130Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	767	0.35119047619047616	181	0.3678861788617886	103	0.2845303867403315	230	0.4020979020979021	253	0.3337730870712401	G	9.682	1.149475	0.21288	0.33729	0.329467	ENSG00000167914	ENST00000301659	T	0.21031	2.03	4.97	2.99	0.34606	.	1.021790	0.07809	N	0.957779	T	0.00012	0.0000	N	0.10782	0.045	0.46279	P	0.0010320000000000329	B	0.19583	0.037	B	0.25614	0.062	T	0.47169	-0.9138	9	0.08599	T	0.76	-11.5077	7.4073	0.26998	0.1956:0.0:0.8044:0.0	rs7212944;rs12950665;rs59929480	130	Q96QA5	GSDMA_HUMAN	K	130	ENSP00000301659:E130K	ENSP00000301659:E130K	E	+	1	0	GSDMA	35376212	1.000000	0.71417	0.418000	0.26571	0.493000	0.33554	2.671000	0.46842	0.692000	0.31613	0.563000	0.77884	GAG	G|0.646;A|0.354	0.354	strong		0.617	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
LRRC18	474354	hgsc.bcm.edu	37	10	50121454	50121454	+	Silent	SNP	G	G	A	rs41302987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50121454G>A	ENST00000374160.3	-	1	823	c.747C>T	c.(745-747)gaC>gaT	p.D249D	RP11-523O18.7_ENST00000430438.1_RNA|LRRC18_ENST00000298124.3_Silent_p.D249D|WDFY4_ENST00000325239.5_Intron|WDFY4_ENST00000413659.2_Intron	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	249						cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						CTTCCCAGGAGTCCTTGGCCA	0.547													G|||	140	0.0279553	0.0159	0.0375	5008	,	,		20260	0.001		0.0696	False		,,,				2504	0.0225				p.D249D		Atlas-SNP	.											.	LRRC18	52	.	0			c.C747T						PASS	.	G	,	141,4265	100.3+/-138.9	3,135,2065	185.0	187.0	187.0		747,	-11.9	0.0	10	dbSNP_127	187	508,8092	144.5+/-200.4	10,488,3802	no	coding-synonymous,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	,	13,623,5867	AA,AG,GG		5.907,3.2002,4.99	,	249/262,	50121454	649,12357	2203	4300	6503	SO:0001819	synonymous_variant	474354	exon1			CCAGGAGTCCTTG	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.747C>T	10.37:g.50121454G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	201	94	0.467662	NM_001006939	Q6UY02	Silent	SNP	ENST00000374160.3	37	CCDS31197.1																																																																																			G|0.956;A|0.044	0.044	strong		0.547	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
INMT	11185	hgsc.bcm.edu	37	7	30795331	30795331	+	Missense_Mutation	SNP	A	A	G	rs2302340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:30795331A>G	ENST00000013222.5	+	3	672	c.656A>G	c.(655-657)gAg>gGg	p.E219G	INMT_ENST00000484180.1_3'UTR|INMT_ENST00000409539.1_Missense_Mutation_p.E218G|INMT-FAM188B_ENST00000458257.1_Intron	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	219			E -> G (in dbSNP:rs2302340). {ECO:0000269|PubMed:10552930, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)	p.E219G(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						CTGGAGAAAGAGGAGGTGGAG	0.587													A|||	1649	0.329273	0.059	0.5086	5008	,	,		20038	0.5476		0.4294	False		,,,				2504	0.2393				p.E219G		Atlas-SNP	.											INMT,NS,carcinoma,0,1	INMT	38	1	1	Substitution - Missense(1)	stomach(1)	c.A656G						PASS	.	A	GLY/GLU,GLY/GLU	553,3853	247.8+/-255.9	34,485,1684	109.0	102.0	104.0		653,656	3.7	1.0	7	dbSNP_100	104	3577,5023	517.9+/-379.1	768,2041,1491	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	98,98	802,2526,3175	GG,GA,AA		41.593,12.5511,31.7546	possibly-damaging,possibly-damaging	218/263,219/264	30795331	4130,8876	2203	4300	6503	SO:0001583	missense	11185	exon3			AGAAAGAGGAGGT		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.656A>G	7.37:g.30795331A>G	ENSP00000013222:p.Glu219Gly	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	857	0.3923992673992674	41	0.08333333333333333	178	0.49171270718232046	314	0.548951048951049	324	0.42744063324538256	A	16.68	3.190717	0.58017	0.125511	0.41593	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.11495	2.77;2.77	3.67	3.67	0.42095	.	0.170656	0.37530	N	0.002047	T	0.00012	0.0000	M	0.73598	2.24	0.25776	P	0.9847839	D;D	0.54964	0.969;0.969	P;P	0.58873	0.847;0.847	T	0.45411	-0.9263	9	0.52906	T	0.07	-16.1597	10.6007	0.45365	1.0:0.0:0.0:0.0	rs2302340;rs52838184;rs56784180;rs2302340	218;219	B8ZZ69;O95050	.;INMT_HUMAN	G	219;218	ENSP00000013222:E219G;ENSP00000386961:E218G	ENSP00000013222:E219G	E	+	2	0	INMT	30761856	0.986000	0.35501	0.998000	0.56505	0.625000	0.37756	3.452000	0.52971	1.635000	0.50512	0.459000	0.35465	GAG	A|0.661;G|0.339	0.339	strong		0.587	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
PM20D1	148811	hgsc.bcm.edu	37	1	205812912	205812912	+	Missense_Mutation	SNP	A	A	G	rs7518979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205812912A>G	ENST00000367136.4	-	6	754	c.710T>C	c.(709-711)aTt>aCt	p.I237T	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	237			I -> T (in dbSNP:rs7518979). {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)			TGAGACTGCAATCCTGTAGAA	0.493													A|||	1275	0.254593	0.3691	0.1398	5008	,	,		18869	0.3829		0.169	False		,,,				2504	0.137				p.I237T		Atlas-SNP	.											.	PM20D1	56	.	0			c.T710C						PASS	.	A	THR/ILE	1466,2940	471.7+/-356.1	234,998,971	93.0	87.0	89.0		710	4.9	0.0	1	dbSNP_116	89	1248,7352	250.0+/-277.0	85,1078,3137	yes	missense	PM20D1	NM_152491.4	89	319,2076,4108	GG,GA,AA		14.5116,33.2728,20.8673	possibly-damaging	237/503	205812912	2714,10292	2203	4300	6503	SO:0001583	missense	148811	exon6			ACTGCAATCCTGT		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.710T>C	1.37:g.205812912A>G	ENSP00000356104:p.Ile237Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	581	0.266025641025641	193	0.39227642276422764	45	0.12430939226519337	218	0.3811188811188811	125	0.16490765171503957	A	12.48	1.950833	0.34471	0.332728	0.145116	ENSG00000162877	ENST00000367136	T	0.09911	2.93	6.06	4.92	0.64577	.	0.242071	0.49305	D	0.000152	T	0.00012	0.0000	M	0.89287	3.02	0.32399	P	0.5521769999999999	D	0.67145	0.996	D	0.70716	0.97	T	0.35798	-0.9774	9	0.52906	T	0.07	.	13.2167	0.59865	0.867:0.133:0.0:0.0	rs7518979;rs52830461;rs7518979	237	Q6GTS8	P20D1_HUMAN	T	237	ENSP00000356104:I237T	ENSP00000356104:I237T	I	-	2	0	PM20D1	204079535	0.999000	0.42202	0.009000	0.14445	0.017000	0.09413	6.988000	0.76212	1.085000	0.41206	0.533000	0.62120	ATT	A|0.764;G|0.236	0.236	strong		0.493	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
NUDT18	79873	hgsc.bcm.edu	37	8	21965113	21965113	+	Missense_Mutation	SNP	T	T	C	rs3739435	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:21965113T>C	ENST00000309188.6	-	5	788	c.670A>G	c.(670-672)Atg>Gtg	p.M224V	NUDT18_ENST00000521807.2_3'UTR|NUDT18_ENST00000522405.1_Missense_Mutation_p.M147V	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	70	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	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	
HIPK2	28996	hgsc.bcm.edu	37	7	139415943	139415943	+	Silent	SNP	G	G	A	rs4074826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:139415943G>A	ENST00000406875.3	-	2	985	c.891C>T	c.(889-891)ccC>ccT	p.P297P	HIPK2_ENST00000428878.2_Silent_p.P297P|HIPK2_ENST00000342645.6_Silent_p.P297P	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	297	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					TGTATTTGAGGGGCAAGGGGC	0.483													G|||	597	0.119209	0.1051	0.1729	5008	,	,		23447	0.1081		0.164	False		,,,				2504	0.0654				p.P297P		Atlas-SNP	.											.	HIPK2	192	.	0			c.C891T						PASS	.	G	,	394,2742		24,346,1198	148.0	134.0	138.0		891,891	4.4	1.0	7	dbSNP_108	138	1164,6000		80,1004,2498	no	coding-synonymous,coding-synonymous	HIPK2	NM_001113239.2.dup,NM_022740.4.dup	,	104,1350,3696	AA,AG,GG		16.2479,12.5638,15.1262	,	297/368,297/368	139415943	1558,8742	1568	3582	5150	SO:0001819	synonymous_variant	28996	exon2			TTTGAGGGGCAAG	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.891C>T	7.37:g.139415943G>A		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	240	123	0.5125	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	37																																																																																				G|0.847;A|0.153	0.153	strong		0.483	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
FBXO30	84085	hgsc.bcm.edu	37	6	146125793	146125793	+	Missense_Mutation	SNP	A	A	T	rs3811102	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:146125793A>T	ENST00000237281.4	-	2	1915	c.1749T>A	c.(1747-1749)caT>caA	p.H583Q		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	583			H -> Q (in dbSNP:rs3811102). {ECO:0000269|Ref.3}.				ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		ATGACCTCAAATGGCGGTCAT	0.418																																					p.H583Q		Atlas-SNP	.											.	FBXO30	56	.	0			c.T1749A						PASS	.	A	GLN/HIS	960,3446	362.6+/-316.2	110,740,1353	99.0	86.0	91.0		1749	0.4	0.9	6	dbSNP_107	91	3546,5052	515.7+/-378.7	724,2098,1477	yes	missense	FBXO30	NM_032145.4	24	834,2838,2830	TT,TA,AA		41.2421,21.7885,34.6509	probably-damaging	583/746	146125793	4506,8498	2203	4299	6502	SO:0001583	missense	84085	exon2			CCTCAAATGGCGG	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"""F-boxes /  ""other"""""	15600	protein-coding gene	gene with protein product		609101	"""F-box only protein, helicase, 18"""				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.1749T>A	6.37:g.146125793A>T	ENSP00000237281:p.His583Gln	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_032145	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	37	CCDS5208.1	654	0.29945054945054944	106	0.21544715447154472	89	0.24585635359116023	149	0.26048951048951047	310	0.40897097625329815	A	9.123	1.009522	0.19277	0.217885	0.412421	ENSG00000118496	ENST00000237281	T	0.17213	2.29	5.73	0.452	0.16634	.	0.135004	0.64402	N	0.000002	T	0.03520	0.0101	L	0.29908	0.895	0.23030	P	0.99840109	B	0.06786	0.001	B	0.12156	0.007	T	0.35375	-0.9791	9	0.46703	T	0.11	-7.8808	5.4721	0.16676	0.5341:0.2505:0.2154:0.0	rs3811102;rs17822232;rs3811102	583	Q8TB52	FBX30_HUMAN	Q	583	ENSP00000237281:H583Q	ENSP00000237281:H583Q	H	-	3	2	FBXO30	146167486	0.953000	0.32496	0.912000	0.35992	0.957000	0.61999	0.282000	0.18829	-0.138000	0.11434	0.533000	0.62120	CAT	A|0.672;T|0.328	0.328	strong		0.418	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2		
POU5F1B	5462	hgsc.bcm.edu	37	8	128428638	128428638	+	Missense_Mutation	SNP	G	G	A	rs6998061	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:128428638G>A	ENST00000465342.2	+	2	1684	c.527G>A	c.(526-528)gGg>gAg	p.G176E	CASC8_ENST00000502082.1_RNA|CASC8_ENST00000501396.1_RNA|POU5F1B_ENST00000391675.1_Missense_Mutation_p.G176E|CASC8_ENST00000523825.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	176	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.		G -> E (in dbSNP:rs6998061). {ECO:0000269|PubMed:21341266}.		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						GTTCTATTTGGGAAGGTGTTC	0.532													g|||	1870	0.373403	0.1172	0.3991	5008	,	,		17368	0.5565		0.4314	False		,,,				2504	0.453				p.G176E		Atlas-SNP	.											.	POU5F1B	32	.	0			c.G527A	GRCh37	CM073275	POU5F1B	M	rs6998061	PASS	.	G	GLU/GLY	198,1186		14,170,508	77.0	88.0	85.0		527	1.1	1.0	8	dbSNP_116	85	1316,1866		261,794,536	no	missense	POU5F1B	NM_001159542.1	98	275,964,1044	AA,AG,GG		41.3576,14.3064,33.1581	probably-damaging	176/360	128428638	1514,3052	692	1591	2283	SO:0001583	missense	5462	exon1			TATTTGGGAAGGT	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.527G>A	8.37:g.128428638G>A	ENSP00000419298:p.Gly176Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	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	894	0.40934065934065933	74	0.15040650406504066	136	0.3756906077348066	336	0.5874125874125874	348	0.45910290237467016	G	21.1	4.092755	0.76756	0.143064	0.413576	ENSG00000212993	ENST00000465342;ENST00000391675	D;D	0.82803	-1.65;-1.65	1.14	1.14	0.20703	POU-specific (3);Lambda repressor-like, DNA-binding (2);	0.000000	0.50627	D	0.000108	T	0.00012	0.0000	M	0.79258	2.445	0.09310	P	0.999999568388	P	0.46457	0.878	P	0.54706	0.759	T	0.43925	-0.9361	9	0.56958	D	0.05	.	8.3083	0.32055	0.0:0.0:1.0:0.0	rs6998061;rs60145230	176	Q06416	P5F1B_HUMAN	E	176	ENSP00000419298:G176E;ENSP00000375557:G176E	ENSP00000375557:G176E	G	+	2	0	POU5F1B	128497820	1.000000	0.71417	0.997000	0.53966	0.578000	0.36192	4.714000	0.61902	0.968000	0.38212	0.134000	0.15878	GGG	.	.	weak		0.532	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
SPZ1	84654	hgsc.bcm.edu	37	5	79617039	79617039	+	Silent	SNP	A	A	G	rs374023153		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79617039A>G	ENST00000296739.4	+	1	1250	c.1005A>G	c.(1003-1005)gtA>gtG	p.V335V		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	335					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		AGCAGAGAGTAGAGATTCTCA	0.423													A|||	1	0.000199681	0.0	0.0014	5008	,	,		19001	0.0		0.0	False		,,,				2504	0.0				p.V335V		Atlas-SNP	.											.	SPZ1	60	.	0			c.A1005G						PASS	.	A		0,3766		0,0,1883	112.0	106.0	108.0		1005	-6.3	0.0	5		108	3,8245		0,3,4121	no	coding-synonymous	SPZ1	NM_032567.3		0,3,6004	GG,GA,AA		0.0364,0.0,0.025		335/431	79617039	3,12011	1883	4124	6007	SO:0001819	synonymous_variant	84654	exon1			GAGAGTAGAGATT		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.1005A>G	5.37:g.79617039A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Silent	SNP	ENST00000296739.4	37	CCDS43336.1																																																																																			.	.	weak		0.423	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
FGG	2266	hgsc.bcm.edu	37	4	155533035	155533035	+	Missense_Mutation	SNP	G	G	C	rs148685782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155533035G>C	ENST00000336098.3	-	4	361	c.323C>G	c.(322-324)gCt>gGt	p.A108G	FGG_ENST00000404648.3_Missense_Mutation_p.A108G|FGG_ENST00000407946.1_Missense_Mutation_p.A108G|FGG_ENST00000405164.1_Missense_Mutation_p.A108G	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	108					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CTTCAAAGTAGCAGCGTCTAT	0.294													G|||	8	0.00159744	0.0	0.0	5008	,	,		16621	0.0		0.006	False		,,,				2504	0.002				p.A108G		Atlas-SNP	.											.	FGG	71	.	0			c.C323G	GRCh37	CM000383	FGG	M	rs148685782	PASS	.	G	GLY/ALA,GLY/ALA	4,4398	8.1+/-20.4	0,4,2197	74.0	75.0	75.0		323,323	5.1	0.7	4	dbSNP_134	75	30,8564	21.0+/-64.5	0,30,4267	yes	missense,missense	FGG	NM_000509.4,NM_021870.2	60,60	0,34,6464	CC,CG,GG		0.3491,0.0909,0.2616	benign,benign	108/438,108/454	155533035	34,12962	2201	4297	6498	SO:0001583	missense	2266	exon4			AAAGTAGCAGCGT		CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3694	protein-coding gene	gene with protein product		134850	"""fibrinogen, gamma polypeptide"""				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.323C>G	4.37:g.155533035G>C	ENSP00000336829:p.Ala108Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_000509	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Missense_Mutation	SNP	ENST00000336098.3	37	CCDS3788.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	11.32	1.605287	0.28623	9.09E-4	0.003491	ENSG00000171557	ENST00000404648;ENST00000405164;ENST00000336098;ENST00000407946;ENST00000443553;ENST00000393846	D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	6.02	5.07	0.68467	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	0.481885	0.23983	N	0.042648	T	0.69513	0.3119	M	0.69463	2.115	0.25585	N	0.986755	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.08055	0.002;0.003;0.003;0.001	T	0.56378	-0.7989	10	0.25751	T	0.34	.	2.5551	0.04758	0.2099:0.0:0.5124:0.2777	.	108;108;108;108	C9JC84;P02679;C9JEU5;P02679-2	.;FIBG_HUMAN;.;.	G	108;108;108;108;5;5	ENSP00000384860:A108G;ENSP00000384101:A108G;ENSP00000336829:A108G;ENSP00000384552:A108G;ENSP00000407562:A5G;ENSP00000377429:A5G	ENSP00000336829:A108G	A	-	2	0	FGG	155752485	0.594000	0.26849	0.681000	0.30009	0.005000	0.04900	2.105000	0.41825	2.857000	0.98124	0.650000	0.86243	GCT	G|0.998;C|0.002	0.002	strong		0.294	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870	
SETMAR	6419	hgsc.bcm.edu	37	3	4358476	4358476	+	Missense_Mutation	SNP	C	C	T	rs115195721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:4358476C>T	ENST00000358065.4	+	3	1668	c.1601C>T	c.(1600-1602)aCt>aTt	p.T534I	SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000425863.1_Missense_Mutation_p.T395I	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	534	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)		gtcatggtcactatttggtgg	0.463								Chromatin Structure					C|||	43	0.00858626	0.0008	0.0144	5008	,	,		19453	0.0		0.0258	False		,,,				2504	0.0061				p.T534I		Atlas-SNP	.											SETMAR,NS,carcinoma,0,1	SETMAR	30	1	0			c.C1601T						PASS	.	C	ILE/THR	13,3159		0,13,1573	9.0	6.0	7.0		1601	0.2	0.8	3	dbSNP_132	7	122,5474		0,122,2676	no	missense	SETMAR	NM_006515.3	89	0,135,4249	TT,TC,CC		2.1801,0.4098,1.5397	possibly-damaging	534/685	4358476	135,8633	1586	2798	4384	SO:0001583	missense	6419	exon3			TGGTCACTATTTG	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.1601C>T	3.37:g.4358476C>T	ENSP00000373354:p.Thr534Ile	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	31	8	0.258065	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	20	0.009157509157509158	0	0.0	8	0.022099447513812154	0	0.0	12	0.0158311345646438	C	11.57	1.678774	0.29783	0.004098	0.021801	ENSG00000170364	ENST00000358065;ENST00000425863	D;T	0.94931	-3.56;0.57	0.235	0.235	0.15431	.	.	.	.	.	D	0.90820	0.7117	M	0.65975	2.015	0.20926	N	0.999826	P;P;P;D	0.52996	0.908;0.898;0.91;0.957	P;P;P;P	0.56648	0.796;0.775;0.803;0.803	D	0.84476	0.0602	8	0.56958	D	0.05	.	.	.	.	.	278;395;521;279	B4DND2;E7EN68;Q53H47;Q96H41	.;.;SETMR_HUMAN;.	I	534;395	ENSP00000373354:T534I;ENSP00000403145:T395I	ENSP00000373354:T534I	T	+	2	0	SETMAR	4333476	0.851000	0.29673	0.754000	0.31244	0.760000	0.43138	0.305000	0.19254	0.308000	0.22923	0.313000	0.20887	ACT	C|0.991;T|0.009	0.009	strong		0.463	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
HSPD1	3329	hgsc.bcm.edu	37	2	198363504	198363504	+	Silent	SNP	A	A	G	rs1050347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:198363504A>G	ENST00000388968.3	-	2	336	c.69T>C	c.(67-69)acT>acC	p.T23T	HSPE1_ENST00000409468.1_5'Flank|HSPE1-MOB4_ENST00000604458.1_5'Flank|HSPE1_ENST00000233893.5_5'Flank|HSPD1_ENST00000345042.2_Silent_p.T23T|HSPD1_ENST00000544407.1_Silent_p.T23T|HSPE1_ENST00000409729.1_5'Flank	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	23					'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)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			CATAAGCCCGAGTGAGATGAG	0.502													A|||	792	0.158147	0.1029	0.1744	5008	,	,		17688	0.2282		0.2117	False		,,,				2504	0.0941				p.T23T		Atlas-SNP	.											.	HSPD1	68	.	0			c.T69C						PASS	.	A	,	492,3914		25,442,1736	57.0	57.0	57.0		69,69	2.4	1.0	2	dbSNP_86	57	1646,6954		104,1438,2758	no	coding-synonymous,coding-synonymous	HSPD1	NM_002156.4,NM_199440.1	,	129,1880,4494	GG,GA,AA		19.1395,11.1666,16.4386	,	23/574,23/574	198363504	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	3329	exon2			AGCCCGAGTGAGA	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.69T>C	2.37:g.198363504A>G		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	295	132	0.447458	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Silent	SNP	ENST00000388968.3	37	CCDS33357.1																																																																																			A|0.813;G|0.187	0.187	strong		0.502	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
FLG	2312	hgsc.bcm.edu	37	1	152285413	152285413	+	Missense_Mutation	SNP	T	T	C	rs111791016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152285413T>C	ENST00000368799.1	-	3	1984	c.1949A>G	c.(1948-1950)cAg>cGg	p.Q650R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	650	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	0.552									Ichthyosis				-|||	12	0.00239617	0.0076	0.0029	5008	,	,		20273	0.0		0.0	False		,,,				2504	0.0				p.Q650R		Atlas-SNP	.											FLG,NS,carcinoma,-1,1	FLG	900	1	0			c.A1949G						scavenged	.						228.0	237.0	234.0					1																	152285413		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.1949A>G	1.37:g.152285413T>C	ENSP00000357789:p.Gln650Arg	Somatic	448	0	0		WXS	Illumina HiSeq	Phase_I	458	6	0.0131004	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	t	3.485	-0.105032	0.06967	.	.	ENSG00000143631	ENST00000368799	T	0.01647	4.71	3.46	-4.62	0.03370	.	.	.	.	.	T	0.00271	0.0008	N	0.02802	-0.49	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.37934	-0.9684	9	0.11182	T	0.66	.	11.2819	0.49199	0.0:0.4927:0.0:0.5073	.	650	P20930	FILA_HUMAN	R	650	ENSP00000357789:Q650R	ENSP00000357789:Q650R	Q	-	2	0	FLG	150552037	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.603000	0.05674	-1.436000	0.01970	-2.175000	0.00321	CAG	T|0.995;C|0.005	0.005	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TPRX1	284355	hgsc.bcm.edu	37	19	48305651	48305651	+	Missense_Mutation	SNP	G	G	A	rs62130758	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	47	0	0		WXS	Illumina HiSeq	Phase_I	25	21	0.84	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	
COL27A1	85301	hgsc.bcm.edu	37	9	116973273	116973273	+	Silent	SNP	C	C	T	rs34350265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:116973273C>T	ENST00000356083.3	+	12	2725	c.2334C>T	c.(2332-2334)ggC>ggT	p.G778G	MIR455_ENST00000384993.1_RNA	NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	778	Collagen-like 3.|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						GCCTGCCTGGCGTTCCTGGCA	0.647													C|||	425	0.0848642	0.1407	0.062	5008	,	,		18001	0.0565		0.0875	False		,,,				2504	0.0521				p.G778G		Atlas-SNP	.											.	COL27A1	200	.	0			c.C2334T						PASS	.	C		523,3883	238.7+/-250.0	30,463,1710	101.0	89.0	93.0		2334	-1.8	0.8	9	dbSNP_126	93	736,7864	178.9+/-228.2	27,682,3591	no	coding-synonymous	COL27A1	NM_032888.2		57,1145,5301	TT,TC,CC		8.5581,11.8702,9.6801		778/1861	116973273	1259,11747	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon12			GCCTGGCGTTCCT	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.2334C>T	9.37:g.116973273C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			C|0.906;T|0.094	0.094	strong		0.647	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
DFNB31	25861	hgsc.bcm.edu	37	9	117166311	117166311	+	Silent	SNP	G	G	A	rs34963246	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:117166311G>A	ENST00000362057.3	-	10	2451	c.2283C>T	c.(2281-2283)agC>agT	p.S761S	DFNB31_ENST00000374059.3_Silent_p.S410S|DFNB31_ENST00000265134.6_Silent_p.S378S	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	761					inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CACTGTCCTCGCTTAGAGTCT	0.622													G|||	463	0.0924521	0.1921	0.147	5008	,	,		19778	0.001		0.0905	False		,,,				2504	0.0153				p.S761S		Atlas-SNP	.											.	DFNB31	100	.	0			c.C2283T						PASS	.	G	,,	849,3557	329.9+/-301.2	82,685,1436	58.0	53.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1134,2280,2283	-4.2	0.3	9	dbSNP_126	55	755,7845	179.9+/-228.9	31,693,3576	no	coding-synonymous,coding-synonymous,coding-synonymous	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	,,	113,1378,5012	AA,AG,GG		8.7791,19.2692,12.3328	,,	378/525,760/907,761/908	117166311	1604,11402	2203	4300	6503	SO:0001819	synonymous_variant	25861	exon10			GTCCTCGCTTAGA	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.2283C>T	9.37:g.117166311G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_015404	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Silent	SNP	ENST00000362057.3	37	CCDS6806.1																																																																																			A|0.112;G|0.887;T|0.000	0.112	strong		0.622	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077765	19077765	+	Missense_Mutation	SNP	T	T	C	rs10833049	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	62	0	0		WXS	Illumina HiSeq	Phase_I	91	58	0.637363	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	
GDF15	9518	hgsc.bcm.edu	37	19	18497024	18497024	+	Missense_Mutation	SNP	G	G	C	rs1059519	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18497024G>C	ENST00000252809.3	+	1	57	c.25G>C	c.(25-27)Gtg>Ctg	p.V9L	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	9			V -> L (in dbSNP:rs1059519). {ECO:0000269|PubMed:9326641, ECO:0000269|PubMed:9348093, ECO:0000269|PubMed:9593718, ECO:0000269|Ref.5}.		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)	p.V9L(1)		kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						ACTCAGGACGGTGAATGGCTC	0.647													C|||	3566	0.712061	0.8215	0.7017	5008	,	,		13295	0.6835		0.675	False		,,,				2504	0.6391				p.V9L		Atlas-SNP	.											GDF15,hand,carcinoma,0,1	GDF15	31	1	1	Substitution - Missense(1)	skin(1)	c.G25C						PASS	.	C	LEU/VAL	3467,939	354.4+/-312.6	1367,733,103	50.0	52.0	51.0		25	-1.7	0.0	19	dbSNP_86	51	5670,2930	455.5+/-363.8	1867,1936,497	yes	missense	GDF15	NM_004864.2	32	3234,2669,600	CC,CG,GG		34.0698,21.3118,29.7478	benign	9/309	18497024	9137,3869	2203	4300	6503	SO:0001583	missense	9518	exon1			AGGACGGTGAATG	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.25G>C	19.37:g.18497024G>C	ENSP00000252809:p.Val9Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	64	0.492308	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Missense_Mutation	SNP	ENST00000252809.3	37	CCDS12376.1	1580	0.7234432234432234	402	0.8170731707317073	262	0.7237569060773481	397	0.6940559440559441	519	0.6846965699208444	C	1.154	-0.645698	0.03531	0.786882	0.659302	ENSG00000130513	ENST00000252809	D	0.81908	-1.55	3.56	-1.7	0.08159	.	2.072990	0.03063	N	0.156134	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	0.40289	-0.9571	9	0.24483	T	0.36	1.3119	1.2396	0.01960	0.1628:0.3099:0.3193:0.2079	rs1059519;rs3170464;rs3746178;rs17526133;rs17655460;rs61009832;rs1059519	9	Q99988	GDF15_HUMAN	L	9	ENSP00000252809:V9L	ENSP00000252809:V9L	V	+	1	0	GDF15	18358024	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.408000	0.07169	-0.515000	0.06479	-0.647000	0.03941	GTG	G|0.292;C|0.708	0.708	strong		0.647	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864	
STK32B	55351	hgsc.bcm.edu	37	4	5170126	5170126	+	Missense_Mutation	SNP	G	G	A	rs200882867		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:5170126G>A	ENST00000282908.5	+	3	631	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	STK32B_ENST00000512636.1_Missense_Mutation_p.R23Q|STK32B_ENST00000510398.1_Missense_Mutation_p.R23Q	NM_018401.1	NP_060871.1			serine/threonine kinase 32B									p.R70L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						AATGTTTTCCGGGAGCTGCAG	0.537																																					p.R70Q		Atlas-SNP	.											STK32B,colon,carcinoma,+1,2	STK32B	87	2	1	Substitution - Missense(1)	lung(1)	c.G209A						scavenged	.	G	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	99.0	89.0	92.0		209	5.0	1.0	4		92	0,8600		0,0,4300	yes	missense	STK32B	NM_018401.1	43	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	70/415	5170126	2,13004	2203	4300	6503	SO:0001583	missense	55351	exon3			TTTTCCGGGAGCT	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.209G>A	4.37:g.5170126G>A	ENSP00000282908:p.Arg70Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	187	2	0.0106952	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	37	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193978	0.58017	4.54E-4	0.0	ENSG00000152953	ENST00000282908;ENST00000512636;ENST00000510398	T;T;T	0.27890	1.64;1.64;1.64	5.03	5.03	0.67393	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38897	U	0.001526	T	0.41994	0.1183	L	0.31207	0.915	0.49130	D	0.999759	D	0.76494	0.999	D	0.65323	0.934	T	0.15464	-1.0436	10	0.32370	T	0.25	.	17.3654	0.87362	0.0:0.0:1.0:0.0	.	70	Q9NY57	ST32B_HUMAN	Q	70;23;23	ENSP00000282908:R70Q;ENSP00000423209:R23Q;ENSP00000420984:R23Q	ENSP00000282908:R70Q	R	+	2	0	STK32B	5221027	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	3.550000	0.53691	2.331000	0.79229	0.655000	0.94253	CGG	.	.	weak		0.537	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
TMEM176B	28959	hgsc.bcm.edu	37	7	150493495	150493495	+	Missense_Mutation	SNP	G	G	A	rs11546671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150493495G>A	ENST00000447204.2	-	2	535	c.163C>T	c.(163-165)Cct>Tct	p.P55S	TMEM176B_ENST00000326442.5_Missense_Mutation_p.P55S|TMEM176B_ENST00000450753.2_Missense_Mutation_p.P55S|TMEM176B_ENST00000429904.2_Missense_Mutation_p.P55S|TMEM176B_ENST00000492607.1_Missense_Mutation_p.P55S|TMEM176B_ENST00000434545.1_Missense_Mutation_p.P55S	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	55			P -> S (in dbSNP:rs11546671). {ECO:0000269|PubMed:9922225}.		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)		GCTGTGGAAGGCACAGTGTCC	0.537													G|||	66	0.0131789	0.0023	0.0317	5008	,	,		16243	0.0		0.0348	False		,,,				2504	0.0061				p.P55S		Atlas-SNP	.											.	TMEM176B	36	.	0			c.C163T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	39,4367	43.1+/-76.7	0,39,2164	73.0	70.0	71.0		163,163,163,163	0.7	0.0	7	dbSNP_120	71	369,8231	122.0+/-181.0	7,355,3938	yes	missense,missense,missense,missense	TMEM176B	NM_001101311.1,NM_001101312.1,NM_001101314.1,NM_014020.3	74,74,74,74	7,394,6102	AA,AG,GG		4.2907,0.8852,3.137	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	55/271,55/271,55/234,55/271	150493495	408,12598	2203	4300	6503	SO:0001583	missense	28959	exon2			TGGAAGGCACAGT	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.163C>T	7.37:g.150493495G>A	ENSP00000410269:p.Pro55Ser	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	47	0.02152014652014652	3	0.006097560975609756	17	0.04696132596685083	0	0.0	27	0.03562005277044855	G	12.68	2.012058	0.35511	0.008852	0.042907	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.08282	3.25;3.25;3.25;3.25;3.25;3.11	3.82	0.672	0.17935	.	3.130830	0.01716	N	0.028014	T	0.02533	0.0077	L	0.45581	1.43	0.09310	N	1	D;D	0.89917	1.0;0.959	D;P	0.74348	0.983;0.556	T	0.41928	-0.9481	10	0.09084	T	0.74	-2.2578	3.3595	0.07181	0.252:0.2217:0.5263:0.0	rs11546671;rs52825959;rs11546671	55;55	E9PAV4;Q3YBM2	.;T176B_HUMAN	S	55	ENSP00000419258:P55S;ENSP00000318409:P55S;ENSP00000410269:P55S;ENSP00000413531:P55S;ENSP00000397810:P55S;ENSP00000404831:P55S	ENSP00000318409:P55S	P	-	1	0	TMEM176B	150124428	0.019000	0.18553	0.001000	0.08648	0.017000	0.09413	0.824000	0.27379	0.368000	0.24481	0.467000	0.42956	CCT	G|0.973;A|0.027	0.027	strong		0.537	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137565	32137565	+	Missense_Mutation	SNP	G	G	A	rs1057994	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32137565G>A	ENST00000312561.4	+	4	4090	c.3676G>A	c.(3676-3678)Gtc>Atc	p.V1226I	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1226			V -> I (in dbSNP:rs1057994).														TGATAGAGATGTCACTGTTGT	0.383													G|||	680	0.135783	0.0688	0.1254	5008	,	,		20750	0.0833		0.1859	False		,,,				2504	0.2362				p.V1226I		Atlas-SNP	.											.	.	.	.	0			c.G3676A						PASS	.	G	ILE/VAL	349,4057	178.3+/-207.1	12,325,1866	77.0	77.0	77.0		3676	-2.9	0.0	12	dbSNP_86	77	1725,6875	313.8+/-311.5	167,1391,2742	yes	missense	C12orf35	NM_018169.3	29	179,1716,4608	AA,AG,GG		20.0581,7.921,15.9465	benign	1226/1748	32137565	2074,10932	2203	4300	6503	SO:0001583	missense	55196	exon4			AGAGATGTCACTG	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.3676G>A	12.37:g.32137565G>A	ENSP00000310338:p.Val1226Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	281	0.12866300366300365	40	0.08130081300813008	47	0.1298342541436464	57	0.09965034965034965	137	0.18073878627968337	G	0.278	-0.988559	0.02162	0.07921	0.200581	ENSG00000174718	ENST00000312561	T	0.12039	2.72	5.01	-2.92	0.05615	.	1.194850	0.06254	N	0.692682	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.17038	0.02	B	0.15484	0.013	T	0.45862	-0.9232	8	.	.	.	.	1.7735	0.03016	0.4028:0.1323:0.3312:0.1337	rs1057994;rs3198567;rs3759298;rs17511296;rs59161433;rs1057994	1226	Q9HCM1	CL035_HUMAN	I	1226	ENSP00000310338:V1226I	.	V	+	1	0	C12orf35	32028832	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.029000	0.12329	-0.459000	0.07013	-0.251000	0.11542	GTC	G|0.852;A|0.148	0.148	strong		0.383	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
TEP1	7011	hgsc.bcm.edu	37	14	20871973	20871973	+	Missense_Mutation	SNP	T	T	C	rs2228035	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20871973T>C	ENST00000262715.5	-	6	1143	c.1103A>G	c.(1102-1104)aAa>aGa	p.K368R	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	368	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.		K -> R (in dbSNP:rs2228035).		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)		CTGGGCAAATTTGTCCGTCAT	0.587													T|||	273	0.0545128	0.0068	0.1009	5008	,	,		17018	0.0456		0.0487	False		,,,				2504	0.1012				p.K368R		Atlas-SNP	.											.	TEP1	224	.	0			c.A1103G						PASS	.	T	ARG/LYS	60,4346	58.1+/-94.6	0,60,2143	110.0	113.0	112.0		1103	5.7	1.0	14	dbSNP_98	112	453,8147	135.7+/-192.9	12,429,3859	yes	missense	TEP1	NM_007110.4	26	12,489,6002	CC,CT,TT		5.2674,1.3618,3.9443	probably-damaging	368/2628	20871973	513,12493	2203	4300	6503	SO:0001583	missense	7011	exon6			GCAAATTTGTCCG		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.1103A>G	14.37:g.20871973T>C	ENSP00000262715:p.Lys368Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	113	0.051739926739926737	4	0.008130081300813009	34	0.09392265193370165	34	0.05944055944055944	41	0.05408970976253298	T	33	5.239026	0.95240	0.013618	0.052674	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.14391	2.51	5.69	5.69	0.88448	TROVE (2);	0.000000	0.85682	D	0.000000	T	0.01835	0.0058	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00154	-1.1981	10	0.44086	T	0.13	-16.3016	14.9467	0.71039	0.0:0.0:0.0:1.0	rs2228035;rs2297611;rs17211404;rs2228035	368	Q99973	TEP1_HUMAN	R	368	ENSP00000262715:K368R	ENSP00000262715:K368R	K	-	2	0	TEP1	19941813	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.242000	0.72376	2.163000	0.67991	0.533000	0.62120	AAA	T|0.952;C|0.048	0.048	strong		0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
MOV10L1	54456	hgsc.bcm.edu	37	22	50558946	50558946	+	Silent	SNP	A	A	G	rs71316583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50558946A>G	ENST00000262794.5	+	10	1553	c.1470A>G	c.(1468-1470)caA>caG	p.Q490Q	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.Q490Q|MOV10L1_ENST00000395858.3_Silent_p.Q490Q|MOV10L1_ENST00000540615.1_Silent_p.Q470Q	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	490					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CAAGACGACAACTTCCAAGTT	0.353													A|||	123	0.0245607	0.003	0.0389	5008	,	,		21643	0.0		0.0696	False		,,,				2504	0.0225				p.Q490Q		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A1470G						PASS	.	A	,,	55,4351	54.2+/-90.2	2,51,2150	101.0	102.0	102.0		1470,1410,1470	-6.0	0.9	22	dbSNP_130	102	592,8008	158.3+/-211.8	17,558,3725	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	19,609,5875	GG,GA,AA		6.8837,1.2483,4.9746	,,	490/1166,470/1166,490/1212	50558946	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon10			ACGACAACTTCCA	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1470A>G	22.37:g.50558946A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			A|0.954;G|0.046	0.046	strong		0.353	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
TSSC4	10078	hgsc.bcm.edu	37	11	2424647	2424647	+	Missense_Mutation	SNP	G	G	A	rs2234281	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:2424647G>A	ENST00000333256.6	+	3	1227	c.784G>A	c.(784-786)Ggg>Agg	p.G262R	AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000380992.1_Intron|TSSC4_ENST00000451491.2_Missense_Mutation_p.G262R|TSSC4_ENST00000380996.5_Missense_Mutation_p.G198R|TSSC4_ENST00000467308.1_Intron			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	262			G -> R (in dbSNP:rs2234281).							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)		CCATCTGGCCGGGCCCGGGAG	0.697													G|||	432	0.086262	0.2602	0.0274	5008	,	,		15026	0.0258		0.0119	False		,,,				2504	0.0317				p.G262R		Atlas-SNP	.											.	TSSC4	19	.	0			c.G784A						PASS	.	G	ARG/GLY	917,3453		96,725,1364	21.0	24.0	23.0		784	-4.9	0.0	11	dbSNP_98	23	85,8503		0,85,4209	yes	missense	TSSC4	NM_005706.2	125	96,810,5573	AA,AG,GG		0.9898,20.984,7.7327	benign	262/330	2424647	1002,11956	2185	4294	6479	SO:0001583	missense	10078	exon2			CTGGCCGGGCCCG	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.784G>A	11.37:g.2424647G>A	ENSP00000331087:p.Gly262Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	161	86	0.534162	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	37	CCDS7735.1	152	0.0695970695970696	125	0.2540650406504065	10	0.027624309392265192	11	0.019230769230769232	6	0.0079155672823219	G	3.750	-0.051815	0.07362	0.20984	0.009898	ENSG00000184281	ENST00000380996;ENST00000333256;ENST00000440813;ENST00000451491	T;T;T;T	0.28666	2.2;2.45;1.6;2.45	2.98	-4.9	0.03094	.	0.680164	0.12101	N	0.499559	T	0.00012	0.0000	N	0.25890	0.77	0.80722	P	0.0	B;B	0.15719	0.006;0.014	B;B	0.08055	0.003;0.003	T	0.35919	-0.9769	9	0.06757	T	0.87	-5.5467	6.2699	0.20949	0.543:0.0:0.331:0.126	rs2234281	262;198	Q9Y5U2;Q9Y5U2-2	TSSC4_HUMAN;.	R	198;262;198;262	ENSP00000370384:G198R;ENSP00000331087:G262R;ENSP00000416937:G198R;ENSP00000411224:G262R	ENSP00000331087:G262R	G	+	1	0	TSSC4	2381223	0.000000	0.05858	0.001000	0.08648	0.652000	0.38707	0.201000	0.17276	-0.835000	0.04234	-0.672000	0.03802	GGG	G|0.920;A|0.080	0.080	strong		0.697	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706	
EXPH5	23086	hgsc.bcm.edu	37	11	108464209	108464209	+	Missense_Mutation	SNP	T	T	C	rs2640738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:108464209T>C	ENST00000265843.4	-	1	165	c.55A>G	c.(55-57)Agg>Ggg	p.R19G	EXPH5_ENST00000525344.1_Missense_Mutation_p.R12G	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	19	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.		R -> G (in dbSNP:rs2640738). {ECO:0000269|PubMed:12062444, ECO:0000269|PubMed:15489334}.		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)	p.R19G(1)		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)		AGGATCTTCCTGGCCTCTTCG	0.473													T|||	1944	0.388179	0.2012	0.562	5008	,	,		15778	0.3839		0.495	False		,,,				2504	0.4121				p.R19G		Atlas-SNP	.											EXPH5,NS,carcinoma,0,1	EXPH5	193	1	1	Substitution - Missense(1)	stomach(1)	c.A55G						PASS	.	T	GLY/ARG	1112,3290	399.9+/-331.4	133,846,1222	119.0	114.0	116.0		55	2.8	1.0	11	dbSNP_100	116	4097,4499	561.8+/-387.8	983,2131,1184	yes	missense	EXPH5	NM_015065.2	125	1116,2977,2406	CC,CT,TT		47.6617,25.2612,40.0754	probably-damaging	19/1990	108464209	5209,7789	2201	4298	6499	SO:0001583	missense	23086	exon1			TCTTCCTGGCCTC		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.55A>G	11.37:g.108464209T>C	ENSP00000265843:p.Arg19Gly	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	918	0.42032967032967034	112	0.22764227642276422	187	0.5165745856353591	247	0.4318181818181818	372	0.49076517150395776	T	18.98	3.737521	0.69304	0.252612	0.476617	ENSG00000110723	ENST00000265843;ENST00000525344	T;T	0.02525	4.26;4.26	5.22	2.85	0.33270	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);	0.136337	0.34067	N	0.004291	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	0.9999999999588944	D	0.71674	0.998	D	0.66979	0.948	T	0.44967	-0.9293	9	0.66056	D	0.02	-1.2952	5.9861	0.19434	0.1571:0.0:0.3257:0.5172	rs2640738;rs52828943;rs60556820;rs2640738	19	Q8NEV8	EXPH5_HUMAN	G	19;12	ENSP00000265843:R19G;ENSP00000432546:R12G	ENSP00000265843:R19G	R	-	1	2	EXPH5	107969419	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	0.817000	0.27281	0.298000	0.22638	0.379000	0.24179	AGG	T|0.609;C|0.391	0.391	strong		0.473	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
PHLDB3	653583	hgsc.bcm.edu	37	19	43990795	43990795	+	Missense_Mutation	SNP	G	G	A	rs117243018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43990795G>A	ENST00000292140.5	-	12	1754	c.1394C>T	c.(1393-1395)gCc>gTc	p.A465V		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	465							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				CTCCGCCATGGCCTGCTGCAG	0.657													G|||	49	0.00978435	0.0008	0.0072	5008	,	,		14217	0.0		0.0308	False		,,,				2504	0.0123				p.A465V		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1394T						PASS	.	G	VAL/ALA	21,4051		0,21,2015	26.0	29.0	28.0		1394	4.0	1.0	19	dbSNP_132	28	261,8097		4,253,3922	yes	missense	PHLDB3	NM_198850.3	64	4,274,5937	AA,AG,GG		3.1228,0.5157,2.2687	probably-damaging	465/641	43990795	282,12148	2036	4179	6215	SO:0001583	missense	653583	exon12			GCCATGGCCTGCT		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1394C>T	19.37:g.43990795G>A	ENSP00000292140:p.Ala465Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	32	0.014652014652014652	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	26	0.03430079155672823	G	16.53	3.149195	0.57151	0.005157	0.031228	ENSG00000176531	ENST00000292140	T	0.56941	0.43	4.01	4.01	0.46588	.	0.000000	0.44285	U	0.000478	T	0.18002	0.0432	L	0.29908	0.895	0.58432	D	0.999992	B;B	0.30793	0.295;0.131	B;B	0.26310	0.068;0.027	T	0.34079	-0.9843	10	0.72032	D	0.01	.	14.0682	0.64844	0.0:0.0:1.0:0.0	.	169;465	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	V	465	ENSP00000292140:A465V	ENSP00000292140:A465V	A	-	2	0	PHLDB3	48682635	1.000000	0.71417	0.981000	0.43875	0.819000	0.46315	6.294000	0.72738	2.252000	0.74401	0.465000	0.42564	GCC	G|0.984;A|0.016	0.016	strong		0.657	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
VWF	7450	hgsc.bcm.edu	37	12	6172138	6172138	+	Silent	SNP	G	G	A	rs377198574		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6172138G>A	ENST00000261405.5	-	13	1769	c.1515C>T	c.(1513-1515)cgC>cgT	p.R505R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	505	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GCAGCCTCCCGCGGCCATCCC	0.632											OREG0021618	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R505R		Atlas-SNP	.											.	VWF	338	.	0			c.C1515T						PASS	.	G		0,4406		0,0,2203	49.0	40.0	43.0		1515	-10.4	0.2	12		43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VWF	NM_000552.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		505/2814	6172138	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon13			CCTCCCGCGGCCA		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.1515C>T	12.37:g.6172138G>A		Somatic	48	0	0	632	WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			.	.	weak		0.632	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
PRPF8	10594	hgsc.bcm.edu	37	17	1565211	1565211	+	Silent	SNP	T	T	C	rs118000367	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1565211T>C	ENST00000572621.1	-	24	4276	c.4011A>G	c.(4009-4011)caA>caG	p.Q1337Q	PRPF8_ENST00000304992.6_Silent_p.Q1337Q			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1337	Linker.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		TGAGGTCGGATTGGGGGATGA	0.498													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		20374	0.0		0.0249	False		,,,				2504	0.002				p.Q1337Q		Atlas-SNP	.											.	PRPF8	169	.	0			c.A4011G						PASS	.	T		29,4377	35.2+/-66.4	0,29,2174	91.0	79.0	83.0		4011	3.5	1.0	17	dbSNP_132	83	227,8373	93.8+/-155.7	3,221,4076	no	coding-synonymous	PRPF8	NM_006445.3		3,250,6250	CC,CT,TT		2.6395,0.6582,1.9683		1337/2336	1565211	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	10594	exon25			GTCGGATTGGGGG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.4011A>G	17.37:g.1565211T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_006445	O14547|O75965	Silent	SNP	ENST00000572621.1	37	CCDS11010.1																																																																																			T|0.983;C|0.017	0.017	strong		0.498	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
PSAPL1	768239	hgsc.bcm.edu	37	4	7435486	7435486	+	Missense_Mutation	SNP	G	G	T	rs61738677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:7435486G>T	ENST00000319098.4	-	1	1214	c.1121C>A	c.(1120-1122)gCa>gAa	p.A374E	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)	374					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						ATCATGGACTGCCCGGGCCCG	0.622													G|||	384	0.0766773	0.0129	0.1037	5008	,	,		20007	0.0734		0.1342	False		,,,				2504	0.0879				p.A374E		Atlas-SNP	.											.	PSAPL1	51	.	0			c.C1121A						PASS	.	G	GLU/ALA,	112,4106		1,110,1998	77.0	82.0	80.0		1121,	-0.5	0.0	4	dbSNP_129	80	1157,7275		76,1005,3135	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	107,	77,1115,5133	TT,TG,GG		13.7215,2.6553,10.0316	benign,	374/522,	7435486	1269,11381	2109	4216	6325	SO:0001583	missense	768239	exon1			TGGACTGCCCGGG	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.1121C>A	4.37:g.7435486G>T	ENSP00000317445:p.Ala374Glu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	69	67	0.971014	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	183	0.08379120879120878	8	0.016260162601626018	44	0.12154696132596685	33	0.057692307692307696	98	0.12928759894459102	G	8.527	0.870137	0.17322	0.026553	0.137215	ENSG00000178597	ENST00000319098	T	0.67171	-0.25	3.8	-0.503	0.12000	.	0.966691	0.08446	N	0.944753	T	0.00300	0.0009	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.06338	-1.0832	9	0.09338	T	0.73	-5.5767	5.0721	0.14611	0.1119:0.0:0.3044:0.5836	rs61738677	374	Q6NUJ1	SAPL1_HUMAN	E	374	ENSP00000317445:A374E	ENSP00000317445:A374E	A	-	2	0	PSAPL1	7486387	0.021000	0.18746	0.001000	0.08648	0.002000	0.02628	0.718000	0.25866	-0.011000	0.14247	-0.397000	0.06425	GCA	G|0.900;T|0.100	0.100	strong		0.622	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
FLG	2312	hgsc.bcm.edu	37	1	152279729	152279729	+	Missense_Mutation	SNP	C	C	T	rs3126072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152279729C>T	ENST00000368799.1	-	3	7668	c.7633G>A	c.(7633-7635)Gga>Aga	p.G2545R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2545	Ser-rich.		G -> R (in dbSNP:rs3126072).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCGAGTGTCCAGAGCTGTCG	0.577									Ichthyosis				T|||	2378	0.47484	0.5658	0.451	5008	,	,		19229	0.6548		0.173	False		,,,				2504	0.4939				p.G2545R		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.G7633A						PASS	.	T	ARG/GLY	2198,2202	581.0+/-385.3	593,1012,595	204.0	228.0	220.0		7633	0.8	0.0	1	dbSNP_103	220	1457,7143	750.7+/-407.4	126,1205,2969	no	missense	FLG	NM_002016.1	125	719,2217,3564	TT,TC,CC		16.9419,49.9545,28.1154	benign	2545/4062	152279729	3655,9345	2200	4300	6500	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTGTCCAGAGCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7633G>A	1.37:g.152279729C>T	ENSP00000357789:p.Gly2545Arg	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	302	165	0.546358	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	
MAPT	4137	hgsc.bcm.edu	37	17	44073889	44073889	+	Silent	SNP	A	A	G	rs1052553	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44073889A>G	ENST00000571987.1	+	9	1632	c.1632A>G	c.(1630-1632)gcA>gcG	p.A544A	MAPT_ENST00000347967.5_Silent_p.A133A|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000576518.1_Silent_p.A158A|MAPT_ENST00000351559.5_Silent_p.A227A|MAPT_ENST00000334239.8_Silent_p.A169A|MAPT_ENST00000431008.3_Silent_p.A227A|MAPT_ENST00000344290.5_Silent_p.A562A|MAPT_ENST00000420682.2_Silent_p.A198A|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000340799.5_Silent_p.A198A|MAPT_ENST00000415613.2_Silent_p.A562A|MAPT_ENST00000574436.1_Silent_p.A227A|MAPT_ENST00000446361.3_Silent_p.A169A|MAPT_ENST00000262410.5_Silent_p.A544A|MAPT_ENST00000535772.1_Silent_p.A227A			P10636	TAU_HUMAN	microtubule-associated protein tau	544					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	AGAAGGTGGCAGTGGTCCGTA	0.682													G|||	442	0.0882588	0.0219	0.1571	5008	,	,		11254	0.001		0.2416	False		,,,				2504	0.0613				p.A562A		Atlas-SNP	.											MAPT_ENST00000344290,NS,carcinoma,0,2	MAPT	135	2	0			c.A1686G						PASS	.	G	,,,,,,,	231,4175	776.6+/-414.2	6,219,1978	24.0	25.0	24.0		1686,594,594,681,681,507,1632,507	-11.2	0.4	17	dbSNP_86	24	1901,6699	699.3+/-405.1	215,1471,2614	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,	221,1690,4592	GG,GA,AA		22.1047,5.2429,16.3924	,,,,,,,	562/777,198/413,198/382,227/411,227/442,169/384,544/759,169/353	44073889	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	4137	exon11			GGTGGCAGTGGTC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1632A>G	17.37:g.44073889A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			A|0.865;G|0.135	0.135	strong		0.682	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5209210	5209210	+	Missense_Mutation	SNP	G	G	A	rs16875054	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:5209210G>A	ENST00000274181.7	+	10	1594	c.1456G>A	c.(1456-1458)Gct>Act	p.A486T	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.A486T	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	486	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.		A -> T (in dbSNP:rs16875054).		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						TTTCAGCACCGCTCAAGCTAT	0.423													G|||	280	0.0559105	0.0038	0.1124	5008	,	,		17709	0.124		0.0358	False		,,,				2504	0.0368				p.A486T		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.G1456A						PASS	.	G	THR/ALA	32,3734		0,32,1851	173.0	170.0	171.0		1456	4.8	0.1	5	dbSNP_123	171	297,7933		4,289,3822	yes	missense	ADAMTS16	NM_139056.2	58	4,321,5673	AA,AG,GG		3.6087,0.8497,2.7426	benign	486/1225	5209210	329,11667	1883	4115	5998	SO:0001583	missense	170690	exon10			AGCACCGCTCAAG	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.1456G>A	5.37:g.5209210G>A	ENSP00000274181:p.Ala486Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	166	83	0.5	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	152	0.0695970695970696	5	0.01016260162601626	38	0.10497237569060773	80	0.13986013986013987	29	0.03825857519788918	G	12.42	1.931187	0.34096	0.008497	0.036087	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.03607	3.87;3.87	5.62	4.75	0.60458	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.061490	0.64402	N	0.000005	T	0.00039	0.0001	L	0.31664	0.95	0.18873	P	0.9999845094	D;B;P	0.53312	0.959;0.326;0.638	P;B;B	0.48795	0.59;0.134;0.212	T	0.50882	-0.8775	9	0.62326	D	0.03	.	13.4377	0.61094	0.076:0.0:0.924:0.0	rs16875054;rs16875054	486;486;486	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	T	486	ENSP00000274181:A486T;ENSP00000421631:A486T	ENSP00000274181:A486T	A	+	1	0	ADAMTS16	5262210	0.998000	0.40836	0.147000	0.22382	0.009000	0.06853	2.662000	0.46766	1.385000	0.46445	0.650000	0.86243	GCT	G|0.938;A|0.062	0.062	strong		0.423	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
SIRPG	55423	hgsc.bcm.edu	37	20	1610894	1610894	+	Silent	SNP	G	G	A	rs3746721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:1610894G>A	ENST00000303415.3	-	5	1204	c.1140C>T	c.(1138-1140)taC>taT	p.Y380Y	SIRPG_ENST00000381583.2_Silent_p.Y269Y|SIRPG_ENST00000344103.4_Silent_p.Y163Y|SIRPG_ENST00000381580.1_Silent_p.Y347Y|SIRPG_ENST00000216927.4_Silent_p.Y269Y|SIRPG_ENST00000478145.2_5'UTR	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	380					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						TCCAGGGGACGTAGATGGGGC	0.582													g|||	1724	0.344249	0.1014	0.268	5008	,	,		18842	0.625		0.2594	False		,,,				2504	0.5245				p.Y380Y		Atlas-SNP	.											SIRPG,NS,carcinoma,0,1	SIRPG	61	1	0			c.C1140T						PASS	.	G	,,	502,3902		26,450,1726	63.0	50.0	54.0		807,1140,489	-4.2	0.0	20	dbSNP_107	54	2159,6433		279,1601,2416	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	305,2051,4142	AA,AG,GG		25.128,11.3987,20.4755	,,	269/277,380/388,163/171	1610894	2661,10335	2202	4296	6498	SO:0001819	synonymous_variant	55423	exon5			GGGGACGTAGATG	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.1140C>T	20.37:g.1610894G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			G|0.742;A|0.258	0.258	strong		0.582	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
FAM150B	285016	hgsc.bcm.edu	37	2	287646	287646	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:287646G>T	ENST00000403610.4	-	2	530	c.190C>A	c.(190-192)Cgg>Agg	p.R64R	AC079779.4_ENST00000427831.1_RNA|FAM150B_ENST00000405290.1_5'Flank|FAM150B_ENST00000401503.1_5'Flank|FAM150B_ENST00000344414.5_5'Flank	NM_001002919.2	NP_001002919.2	Q6UX46	F150B_HUMAN	family with sequence similarity 150, member B	64						extracellular region (GO:0005576)				breast(1)|kidney(2)	3	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.00091)|Epithelial(75;0.00656)|OV - Ovarian serous cystadenocarcinoma(76;0.00954)|GBM - Glioblastoma multiforme(21;0.128)		GCGCAGTCCCGCCCGAGGAGC	0.776																																					p.R64R		Atlas-SNP	.											.	FAM150B	12	.	0			c.C190A						PASS	.						1.0	1.0	1.0					2																	287646		772	1574	2346	SO:0001819	synonymous_variant	285016	exon2			AGTCCCGCCCGAG		CCDS46218.1	2p25.3	2008-05-02			ENSG00000189292	ENSG00000189292			27683	protein-coding gene	gene with protein product							Standard	NM_001002919		Approved		uc002qwi.4	Q6UX46	OTTHUMG00000151366	ENST00000403610.4:c.190C>A	2.37:g.287646G>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001002919	B5MC76	Silent	SNP	ENST00000403610.4	37	CCDS46218.1																																																																																			.	.	none		0.776	FAM150B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322394.2	NM_001002919	
MYO1E	4643	hgsc.bcm.edu	37	15	59517011	59517011	+	Silent	SNP	G	G	A	rs373337685		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:59517011G>A	ENST00000288235.4	-	8	1053	c.654C>T	c.(652-654)ggC>ggT	p.G218G	MYO1E_ENST00000558814.1_5'UTR	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	218	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		CTGCAGAGGCGCCCTCGATGA	0.537																																					p.G218G		Atlas-SNP	.											.	MYO1E	99	.	0			c.C654T						PASS	.	G		0,4380		0,0,2190	93.0	73.0	80.0		654	-5.0	1.0	15		80	3,8577	3.0+/-9.4	0,3,4287	no	coding-synonymous	MYO1E	NM_004998.2		0,3,6477	AA,AG,GG		0.035,0.0,0.0231		218/1109	59517011	3,12957	2190	4290	6480	SO:0001819	synonymous_variant	4643	exon8			AGAGGCGCCCTCG	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"""Myosins / Myosin superfamily : Class I"""	7599	protein-coding gene	gene with protein product	"""myosin-IC"""	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.654C>T	15.37:g.59517011G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			.	.	weak		0.537	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998	
ABCA13	154664	hgsc.bcm.edu	37	7	48313510	48313510	+	Missense_Mutation	SNP	A	A	G	rs17547830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:48313510A>G	ENST00000435803.1	+	17	4271	c.4247A>G	c.(4246-4248)cAt>cGt	p.H1416R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1416				H -> R (in Ref. 1; AAP13576). {ECO:0000305}.	transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCACAAGGTCATCTTCAAAAT	0.303													A|||	938	0.1873	0.1566	0.2032	5008	,	,		17417	0.0129		0.3917	False		,,,				2504	0.1871				p.H1416R		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A4247G						PASS	.	A	ARG/HIS	671,2947		69,533,1207	39.0	36.0	37.0		4247	-7.5	0.0	7	dbSNP_123	37	2865,5253		499,1867,1693	yes	missense	ABCA13	NM_152701.3	29	568,2400,2900	GG,GA,AA		35.2919,18.5462,30.1295	benign	1416/5059	48313510	3536,8200	1809	4059	5868	SO:0001583	missense	154664	exon17			AAGGTCATCTTCA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4247A>G	7.37:g.48313510A>G	ENSP00000411096:p.His1416Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	477	0.2184065934065934	85	0.17276422764227642	80	0.22099447513812154	5	0.008741258741258742	307	0.4050131926121372	A	3.082	-0.188874	0.06299	0.185462	0.352919	ENSG00000179869	ENST00000435803	D	0.85088	-1.94	5.04	-7.5	0.01351	.	0.720289	0.12327	N	0.478767	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.19192	-1.0313	8	.	.	.	.	2.3723	0.04333	0.2845:0.3312:0.2764:0.1079	rs17547830;rs52821200;rs58931054;rs17547830	1416	Q86UQ4	ABCAD_HUMAN	R	1416	ENSP00000411096:H1416R	.	H	+	2	0	ABCA13	48284056	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.100000	0.10990	-1.571000	0.01663	-0.464000	0.05259	CAT	A|0.781;G|0.219	0.219	strong		0.303	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
GTPBP2	54676	hgsc.bcm.edu	37	6	43590408	43590408	+	Silent	SNP	G	G	A	rs16896609	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43590408G>A	ENST00000307126.5	-	10	1428	c.1429C>T	c.(1429-1431)Ctg>Ttg	p.L477L	GTPBP2_ENST00000307114.7_Silent_p.L389L|GTPBP2_ENST00000476510.1_5'UTR	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	97	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	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		
SBF1	6305	hgsc.bcm.edu	37	22	50895020	50895020	+	Silent	SNP	C	C	T	rs5771001	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50895020C>T	ENST00000390679.3	-	29	4093	c.3909G>A	c.(3907-3909)gcG>gcA	p.A1303A	SBF1_ENST00000380817.3_Silent_p.A1329A|SBF1_ENST00000476293.1_5'UTR|SBF1_ENST00000348911.6_Silent_p.A1304A			O95248	MTMR5_HUMAN	SET binding factor 1	1303	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GTGGGGCCAGCGCGTCTCTGC	0.677													C|||	1549	0.309305	0.0832	0.3718	5008	,	,		9483	0.7133		0.2256	False		,,,				2504	0.2403				p.A1329A		Atlas-SNP	.											.	SBF1	211	.	0			c.G3987A						PASS	.	C		369,3573		21,327,1623	7.0	9.0	9.0		3987	0.8	0.0	22	dbSNP_114	9	1571,6675		160,1251,2712	no	coding-synonymous	SBF1	NM_002972.2		181,1578,4335	TT,TC,CC		19.0517,9.3607,15.9173		1329/1894	50895020	1940,10248	1971	4123	6094	SO:0001819	synonymous_variant	6305	exon30			GGCCAGCGCGTCT	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.3909G>A	22.37:g.50895020C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				C|0.661;T|0.339	0.339	strong		0.677	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
CACTIN	58509	hgsc.bcm.edu	37	19	3611972	3611972	+	Silent	SNP	G	G	A	rs2158935	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3611972G>A	ENST00000429344.2	-	10	2278	c.2226C>T	c.(2224-2226)aaC>aaT	p.N742N	CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000221899.3_Silent_p.N674N|CACTIN_ENST00000248420.5_Silent_p.N742N	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	742					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)										GGAAGATGCCGTTGGCAAACT	0.637													G|||	2169	0.433107	0.3033	0.6066	5008	,	,		18889	0.3313		0.5805	False		,,,				2504	0.4387				p.N742N		Atlas-SNP	.											.	.	.	.	0			c.C2226T						PASS	.	G	,	1459,2595		245,969,813	62.0	72.0	69.0		2226,2226	-3.2	1.0	19	dbSNP_96	69	4755,3579		1343,2069,755	no	coding-synonymous,coding-synonymous	C19orf29	NM_001080543.1,NM_021231.1	,	1588,3038,1568	AA,AG,GG		42.9446,35.9891,49.8386	,	742/759,742/759	3611972	6214,6174	2027	4167	6194	SO:0001819	synonymous_variant	58509	exon10			GATGCCGTTGGCA	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.2226C>T	19.37:g.3611972G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Silent	SNP	ENST00000429344.2	37	CCDS45920.1	1005	0.46016483516483514	155	0.3150406504065041	220	0.6077348066298343	189	0.3304195804195804	441	0.5817941952506597	G	13.87	2.366515	0.41902	0.359891	0.570554	ENSG00000226800	ENST00000447295	.	.	.	4.3	-3.21	0.05140	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999882838	.	.	.	.	.	.	T	0.43556	-0.9384	4	0.09338	T	0.73	.	6.3668	0.21459	0.6301:0.1558:0.2141:0.0	rs2158935;rs58676824;rs2158935	.	.	.	I	82	.	ENSP00000412459:V82I	V	+	1	0	C19orf29OS	3562972	0.043000	0.20138	0.988000	0.46212	0.980000	0.70556	-0.748000	0.04818	-0.334000	0.08463	0.637000	0.83480	GTT	G|0.545;A|0.455	0.455	strong		0.637	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
CCDC30	728621	hgsc.bcm.edu	37	1	43108188	43108188	+	Silent	SNP	G	G	A	rs12036818	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:43108188G>A	ENST00000340612.4	+	11	1683	c.1683G>A	c.(1681-1683)ctG>ctA	p.L561L	CCDC30_ENST00000390640.4_Silent_p.L350L|CCDC30_ENST00000507855.1_Silent_p.L350L|CCDC30_ENST00000428554.2_Silent_p.L561L|CCDC30_ENST00000342022.4_Silent_p.L561L			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	561						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						ATGATACCCTGCTTCTAGAAA	0.423													G|||	725	0.144768	0.0234	0.085	5008	,	,		15146	0.3105		0.1133	False		,,,				2504	0.2127				p.L561L		Atlas-SNP	.											.	CCDC30	78	.	0			c.G1683A						PASS	.	G		187,4219	118.8+/-156.5	3,181,2019	150.0	149.0	149.0		1683	-0.8	0.9	1	dbSNP_120	149	913,7687	203.2+/-246.3	63,787,3450	no	coding-synonymous	CCDC30	NM_001080850.2		66,968,5469	AA,AG,GG		10.6163,4.2442,8.4576		561/784	43108188	1100,11906	2203	4300	6503	SO:0001819	synonymous_variant	728621	exon12			TACCCTGCTTCTA	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"""prefoldin 6-like"""					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1683G>A	1.37:g.43108188G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	194	102	0.525773	NM_001080850	Q14F06|Q5VVM5	Silent	SNP	ENST00000340612.4	37	CCDS30690.1																																																																																			G|0.891;A|0.109	0.109	strong		0.423	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030	
PLEKHS1	79949	hgsc.bcm.edu	37	10	115535599	115535599	+	Silent	SNP	T	T	C	rs3750901	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:115535599T>C	ENST00000369310.3	+	10	1567	c.1005T>C	c.(1003-1005)gcT>gcC	p.A335A	PLEKHS1_ENST00000369309.1_Silent_p.A169A|PLEKHS1_ENST00000361048.1_Silent_p.A355A|PLEKHS1_ENST00000354462.3_Silent_p.A85A|PLEKHS1_ENST00000369312.4_Silent_p.A253A	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	349																	ACTATCTTGCTCTCACAGAAG	0.403													T|||	1050	0.209665	0.1089	0.1787	5008	,	,		20109	0.3482		0.1799	False		,,,				2504	0.2556				p.A355A		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.T1065C						PASS	.	T	,,,	525,3881	240.3+/-251.1	35,455,1713	143.0	131.0	135.0		759,759,1065,1005	2.1	0.1	10	dbSNP_107	135	1612,6988	300.1+/-304.8	169,1274,2857	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4,NM_182601.1	,,,	204,1729,4570	CC,CT,TT		18.7442,11.9156,16.4309	,,,	253/367,253/367,355/364,335/466	115535599	2137,10869	2203	4300	6503	SO:0001819	synonymous_variant	79949	exon11			TCTTGCTCTCACA	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.1005T>C	10.37:g.115535599T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	183	89	0.486339	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Silent	SNP	ENST00000369310.3	37	CCDS53580.1	444	0.2032967032967033	66	0.13414634146341464	59	0.16298342541436464	194	0.33916083916083917	125	0.16490765171503957	T	6.850	0.526097	0.13066	0.119156	0.187442	ENSG00000148735	ENST00000448805	.	.	.	6.04	2.07	0.26955	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39482	-0.9612	3	.	.	.	-2.3292	6.1375	0.20241	0.2257:0.0:0.1415:0.6328	rs3750901;rs17774572;rs60109172;rs3750901	.	.	.	P	66	.	.	S	+	1	0	C10orf81	115525589	0.036000	0.19791	0.051000	0.19133	0.684000	0.39900	0.317000	0.19487	1.087000	0.41251	-0.466000	0.05196	TCT	T|0.813;C|0.187	0.187	strong		0.403	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
KIAA1244	57221	hgsc.bcm.edu	37	6	138628515	138628515	+	Silent	SNP	G	G	T	rs61752335	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:138628515G>T	ENST00000251691.4	+	23	4120	c.3954G>T	c.(3952-3954)ctG>ctT	p.L1318L		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)		AGGAGTACCTGGTTGGTGACT	0.433													G|||	46	0.0091853	0.0242	0.0115	5008	,	,		21044	0.0		0.005	False		,,,				2504	0.001				p.L1318L		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G3954T						PASS	.	G		83,4323	72.0+/-110.0	1,81,2121	183.0	182.0	182.0		3954	1.9	1.0	6	dbSNP_129	182	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous	KIAA1244	NM_020340.4		1,125,6377	TT,TG,GG		0.5116,1.8838,0.9765		1318/2178	138628515	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	57221	exon23			GTACCTGGTTGGT	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.3954G>T	6.37:g.138628515G>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																			G|0.992;T|0.008	0.008	strong		0.433	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
TMEM132A	54972	hgsc.bcm.edu	37	11	60703777	60703777	+	Missense_Mutation	SNP	G	G	A	rs55920775	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60703777G>A	ENST00000453848.2	+	11	2628	c.2470G>A	c.(2470-2472)Gaa>Aaa	p.E824K	TMEM132A_ENST00000005286.4_Missense_Mutation_p.E825K			Q24JP5	T132A_HUMAN	transmembrane protein 132A	824	Binds to HSPA5/GRP78. {ECO:0000250}.|Confers cellular localization similar to full-length form. {ECO:0000250}.|Glu-rich.			E -> K (in Ref. 2; BAB14613). {ECO:0000305}.		endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GGAGGAGACCGAAGCCAGgga	0.627													G|||	1558	0.311102	0.0356	0.3084	5008	,	,		17175	0.6349		0.2137	False		,,,				2504	0.4519				p.E825K		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G2473A						PASS	.	G	LYS/GLU,LYS/GLU	300,4106	163.6+/-195.4	12,276,1915	125.0	112.0	117.0		2473,2470	2.1	0.0	11	dbSNP_129	117	1921,6677	339.9+/-323.4	220,1481,2598	yes	missense,missense	TMEM132A	NM_017870.3,NM_178031.2	56,56	232,1757,4513	AA,AG,GG		22.3424,6.8089,17.0794	probably-damaging,probably-damaging	825/1025,824/1024	60703777	2221,10783	2203	4299	6502	SO:0001583	missense	54972	exon11			GAGACCGAAGCCA	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.2470G>A	11.37:g.60703777G>A	ENSP00000405823:p.Glu824Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	648	0.2967032967032967	18	0.036585365853658534	94	0.2596685082872928	365	0.6381118881118881	171	0.22559366754617413	G	0.054	-1.242138	0.01481	0.068089	0.223424	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	T;T	0.13657	2.57;2.57	4.98	2.07	0.26955	.	0.442730	0.20424	N	0.092620	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.28808	-1.0032	9	0.87932	D	0	-2.7396	10.687	0.45850	0.2361:0.0:0.7639:0.0	rs55920775;rs59948488	824;825	Q24JP5;Q24JP5-2	T132A_HUMAN;.	K	575;824;825	ENSP00000405823:E824K;ENSP00000005286:E825K	ENSP00000005286:E825K	E	+	1	0	TMEM132A	60460353	0.006000	0.16342	0.000000	0.03702	0.006000	0.05464	0.954000	0.29175	0.003000	0.14656	-1.134000	0.01955	GAA	G|0.795;A|0.205	0.205	strong		0.627	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
MACF1	23499	hgsc.bcm.edu	37	1	39835817	39835817	+	Missense_Mutation	SNP	A	A	G	rs2296172	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:39835817A>G	ENST00000372915.3	+	50	13156	c.13069A>G	c.(13069-13071)Atg>Gtg	p.M4357V	MACF1_ENST00000545844.1_Missense_Mutation_p.M2290V|MACF1_ENST00000539005.1_Missense_Mutation_p.M2290V|MACF1_ENST00000289893.4_Missense_Mutation_p.M2792V|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000567887.1_Missense_Mutation_p.M4389V|MACF1_ENST00000361689.2_Missense_Mutation_p.M2290V|MACF1_ENST00000564288.1_Missense_Mutation_p.M4352V|MACF1_ENST00000317713.7_Missense_Mutation_p.M2290V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4357			M -> V (in dbSNP:rs2296172). {ECO:0000269|PubMed:10559237}.		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GGAAACTTCTATGAGTGCTAA	0.433													A|||	592	0.118211	0.0121	0.2046	5008	,	,		20675	0.1587		0.1948	False		,,,				2504	0.0798				p.M2290V		Atlas-SNP	.											.	MACF1	909	.	0			c.A6868G						PASS	.	A	VAL/MET,VAL/MET	194,4212	122.1+/-159.5	1,192,2010	69.0	68.0	68.0		6868,8374	0.3	1.0	1	dbSNP_100	68	1919,6681	339.9+/-323.4	231,1457,2612	yes	missense,missense	MACF1	NM_012090.4,NM_033044.3	21,21	232,1649,4622	GG,GA,AA		22.314,4.4031,16.2463	benign,benign	2290/5431,2792/5939	39835817	2113,10893	2203	4300	6503	SO:0001583	missense	23499	exon47			ACTTCTATGAGTG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.13069A>G	1.37:g.39835817A>G	ENSP00000362006:p.Met4357Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		320|320	0.14652014652014653|0.14652014652014653	8|8	0.016260162601626018|0.016260162601626018	76|76	0.20994475138121546|0.20994475138121546	89|89	0.1555944055944056|0.1555944055944056	147|147	0.19393139841688653|0.19393139841688653	A|A	1.600|1.600	-0.526671|-0.526671	0.04141|0.04141	0.044031|0.044031	0.22314|0.22314	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.59364|.	0.3;0.33;0.3;0.27;0.4;1.43|.	5.37|5.37	0.348|0.348	0.16026|0.16026	.|.	0.777656|.	0.11516|.	N|.	0.556259|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	P|P	0.9999999709851|0.9999999709851	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.06405|.	0.002;0.001;0.001;0.002|.	T|T	0.37934|0.37934	-0.9684|-0.9684	9|4	0.06099|.	T|.	0.92|.	.|.	0.2216|0.2216	0.00168|0.00168	0.2976:0.2744:0.1754:0.2526|0.2976:0.2744:0.1754:0.2526	rs2296172;rs57700239;rs2296172|rs2296172;rs57700239;rs2296172	4357;2290;2290;2255|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	V|C	2290;4357;2290;2290;2290;2792|1423	ENSP00000439537:M2290V;ENSP00000362006:M4357V;ENSP00000354573:M2290V;ENSP00000313438:M2290V;ENSP00000444364:M2290V;ENSP00000289893:M2792V|.	ENSP00000289893:M2792V|.	M|Y	+|+	1|2	0|0	MACF1|MACF1	39608404|39608404	0.850000|0.850000	0.29656|0.29656	0.996000|0.996000	0.52242|0.52242	0.949000|0.949000	0.60115|0.60115	0.193000|0.193000	0.17116|0.17116	0.021000|0.021000	0.15133|0.15133	0.533000|0.533000	0.62120|0.62120	ATG|TAT	A|0.855;G|0.145	0.145	strong		0.433	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
APOL1	8542	hgsc.bcm.edu	37	22	36661646	36661646	+	Missense_Mutation	SNP	G	G	A	rs136176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36661646G>A	ENST00000397278.3	+	6	993	c.764G>A	c.(763-765)aGg>aAg	p.R255K	APOL1_ENST00000397279.4_Missense_Mutation_p.R255K|APOL1_ENST00000426053.1_Missense_Mutation_p.R237K|APOL1_ENST00000319136.4_Missense_Mutation_p.R271K|APOL1_ENST00000422706.1_Missense_Mutation_p.R255K|APOL1_ENST00000347595.7_Missense_Mutation_p.R134K	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	255			R -> K (in dbSNP:rs136176). {ECO:0000269|PubMed:11290834, ECO:0000269|PubMed:11944986, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9325276}.		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						AAGGAGGTGAGGGAGTTTTTG	0.498													a|||	4320	0.86262	0.9826	0.8847	5008	,	,		23243	0.7976		0.7813	False		,,,				2504	0.8354				p.R271K		Atlas-SNP	.											.	APOL1	35	.	0			c.G812A						PASS	.	A	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	4181,225	134.1+/-170.4	1984,213,6	117.0	109.0	111.0		764,710,764,812	-6.2	0.0	22	dbSNP_78	111	6861,1739	315.7+/-312.4	2728,1405,167	yes	missense,missense,missense,missense	APOL1	NM_001136540.1,NM_001136541.1,NM_003661.3,NM_145343.2	26,26,26,26	4712,1618,173	AA,AG,GG		20.2209,5.1067,15.1007	benign,benign,benign,benign	255/399,237/381,255/399,271/415	36661646	11042,1964	2203	4300	6503	SO:0001583	missense	8542	exon7			AGGTGAGGGAGTT	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.764G>A	22.37:g.36661646G>A	ENSP00000380448:p.Arg255Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_145343	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Missense_Mutation	SNP	ENST00000397278.3	37	CCDS13926.1	1839	0.842032967032967	475	0.9654471544715447	310	0.856353591160221	464	0.8111888111888111	590	0.7783641160949868	a	0.015	-1.560631	0.00910	0.948933	0.797791	ENSG00000100342	ENST00000397278;ENST00000422706;ENST00000426053;ENST00000319136;ENST00000347595;ENST00000397279	T;T;T;T;T;T	0.03035	4.07;4.07;4.07;4.07;4.07;4.07	3.12	-6.25	0.02039	.	5.050130	0.00649	N	0.000540	T	0.00012	0.0000	N	0.00275	-1.725	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	0.48536	-0.9027	9	0.02654	T	1	.	0.6239	0.00783	0.2996:0.3145:0.2127:0.1731	rs136176;rs17732959;rs52819634;rs59096597;rs136176	237;255;271	E9PF24;O14791;O14791-2	.;APOL1_HUMAN;.	K	255;255;237;271;134;255	ENSP00000380448:R255K;ENSP00000411507:R255K;ENSP00000388477:R237K;ENSP00000317674:R271K;ENSP00000216178:R134K;ENSP00000380449:R255K	ENSP00000317674:R271K	R	+	2	0	APOL1	34991592	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.569000	0.00214	-3.648000	0.00126	-1.140000	0.01884	AGG	G|0.154;A|0.846	0.846	strong		0.498	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343	
FLG	2312	hgsc.bcm.edu	37	1	152279841	152279841	+	Missense_Mutation	SNP	G	G	C	rs3126074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152279841G>C	ENST00000368799.1	-	3	7556	c.7521C>G	c.(7519-7521)caC>caG	p.H2507Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2507	Ser-rich.		H -> Q (in dbSNP:rs3126074).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGATCCTGAGTGCCCATGGG	0.552									Ichthyosis				C|||	2315	0.46226	0.5189	0.451	5008	,	,		20836	0.6548		0.172	False		,,,				2504	0.4939				p.H2507Q		Atlas-SNP	.											.	FLG	900	.	0			c.C7521G						PASS	.	C	GLN/HIS	2053,2353	607.9+/-391.1	471,1111,621	342.0	327.0	332.0		7521	-4.9	0.0	1	dbSNP_103	332	1456,7144	750.9+/-407.4	126,1204,2970	no	missense	FLG	NM_002016.1	24	597,2315,3591	CC,CG,GG		16.9302,46.5956,26.9799	benign	2507/4062	152279841	3509,9497	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCCTGAGTGCCCA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7521C>G	1.37:g.152279841G>C	ENSP00000357789:p.His2507Gln	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	336	169	0.502976	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	
C1orf111	284680	hgsc.bcm.edu	37	1	162344102	162344102	+	Silent	SNP	C	C	T	rs2282397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:162344102C>T	ENST00000367935.5	-	3	601	c.522G>A	c.(520-522)agG>agA	p.R174R	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	174										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			CTGGGTGCCACCTGGAAGCCA	0.587													C|||	1705	0.340455	0.1634	0.4222	5008	,	,		19892	0.5089		0.3817	False		,,,				2504	0.3057				p.R174R		Atlas-SNP	.											.	C1orf111	26	.	0			c.G522A						PASS	.	C		965,3441	363.6+/-316.6	114,737,1352	188.0	180.0	183.0		522	4.2	0.7	1	dbSNP_100	183	3228,5372	485.5+/-371.6	604,2020,1676	no	coding-synonymous	C1orf111	NM_182581.3		718,2757,3028	TT,TC,CC		37.5349,21.902,32.239		174/262	162344102	4193,8813	2203	4300	6503	SO:0001819	synonymous_variant	284680	exon3			GTGCCACCTGGAA	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.522G>A	1.37:g.162344102C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	152	78	0.513158	NM_182581	Q6X961|Q8NEC3	Silent	SNP	ENST00000367935.5	37	CCDS1238.1																																																																																			C|0.672;T|0.328	0.328	strong		0.587	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581	
ABCB5	340273	hgsc.bcm.edu	37	7	20683204	20683204	+	Silent	SNP	G	G	T	rs7349983	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20683204G>T	ENST00000404938.2	+	7	1279	c.627G>T	c.(625-627)gtG>gtT	p.V209V		NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	209	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						TCACCCTAGTGACTCTATCCA	0.448													G|||	225	0.0449281	0.0083	0.0576	5008	,	,		21028	0.0		0.1441	False		,,,				2504	0.0297				p.V209V		Atlas-SNP	.											.	ABCB5	357	.	0			c.G627T						PASS	.	G		89,3047		2,85,1481	150.0	128.0	134.0		627	1.9	1.0	7	dbSNP_116	134	957,6207		72,813,2697	no	coding-synonymous	ABCB5	NM_001163941.1		74,898,4178	TT,TG,GG		13.3585,2.838,10.1553		209/1258	20683204	1046,9254	1568	3582	5150	SO:0001819	synonymous_variant	340273	exon7			CCTAGTGACTCTA	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.627G>T	7.37:g.20683204G>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	205	88	0.429268	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			G|0.928;T|0.072	0.072	strong		0.448	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
DDX20	11218	hgsc.bcm.edu	37	1	112308972	112308972	+	Silent	SNP	G	G	A	rs197413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	103	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	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	
LGALS9	3965	hgsc.bcm.edu	37	17	25970642	25970642	+	Missense_Mutation	SNP	A	A	T	rs361498	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:25970642A>T	ENST00000395473.2	+	5	2004	c.536A>T	c.(535-537)cAa>cTa	p.Q179L	LGALS9_ENST00000310394.5_Intron|LGALS9_ENST00000302228.5_Intron|LGALS9_ENST00000413914.2_Missense_Mutation_p.Q122L|LGALS9_ENST00000313648.6_Intron	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	179					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)		GGGCGCAGACAAAAAGTGAGT	0.627													A|||	309	0.0617013	0.0121	0.0965	5008	,	,		17794	0.0		0.1998	False		,,,				2504	0.0256				p.Q179L	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.A536T						PASS	.	A	,LEU/GLN	180,4226		2,176,2025	20.0	20.0	20.0		,536	-0.1	0.0	17	dbSNP_79	20	1755,6819		190,1375,2722	no	intron,missense	LGALS9	NM_002308.3,NM_009587.2	,113	192,1551,4747	TT,TA,AA		20.4689,4.0853,14.9076	,benign	,179/356	25970642	1935,11045	2203	4287	6490	SO:0001583	missense	3965	exon5			GCAGACAAAAAGT	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.536A>T	17.37:g.25970642A>T	ENSP00000378856:p.Gln179Leu	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	459	219	0.477124	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	222	0.10164835164835165	14	0.028455284552845527	40	0.11049723756906077	4	0.006993006993006993	164	0.21635883905013192	A	12.31	1.899332	0.33535	0.040853	0.204689	ENSG00000168961	ENST00000395473;ENST00000413914	T;T	0.14893	3.89;2.47	3.53	-0.0973	0.13633	.	0.488214	0.17273	N	0.180295	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.21905	0.062;0.017	B;B	0.18871	0.023;0.004	T	0.45963	-0.9225	9	0.10902	T	0.67	.	9.0558	0.36405	0.6141:0.3859:0.0:0.0	rs361498;rs17399029	122;179	B4DWP7;O00182	.;LEG9_HUMAN	L	179;122	ENSP00000378856:Q179L;ENSP00000393695:Q122L	ENSP00000378856:Q179L	Q	+	2	0	LGALS9	22994769	0.000000	0.05858	0.022000	0.16811	0.614000	0.37383	-0.053000	0.11846	-0.054000	0.13266	-0.262000	0.10625	CAA	A|0.874;T|0.126	0.126	strong		0.627	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587	
EPB41L2	2037	hgsc.bcm.edu	37	6	131190838	131190838	+	Silent	SNP	G	G	A	rs17059736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:131190838G>A	ENST00000337057.3	-	15	2653	c.2472C>T	c.(2470-2472)ccC>ccT	p.P824P	EPB41L2_ENST00000531410.1_Intron|EPB41L2_ENST00000527411.1_Silent_p.P754P|EPB41L2_ENST00000528282.1_Intron|EPB41L2_ENST00000525271.1_Intron|EPB41L2_ENST00000525193.1_Intron|EPB41L2_ENST00000368128.2_Silent_p.P824P|EPB41L2_ENST00000529208.1_Silent_p.P754P|EPB41L2_ENST00000392427.3_Intron|EPB41L2_ENST00000530757.1_Intron|EPB41L2_ENST00000527659.1_Intron|EPB41L2_ENST00000524581.1_Silent_p.P202P|EPB41L2_ENST00000530481.1_Intron|EPB41L2_ENST00000445890.2_Intron	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	824					cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		TCTTCTCTCCGGGTATCTTTT	0.507													G|||	799	0.159545	0.2489	0.2104	5008	,	,		19065	0.0873		0.1262	False		,,,				2504	0.1115				p.P824P		Atlas-SNP	.											.	EPB41L2	96	.	0			c.C2472T						PASS	.	G	,,,,	1149,3257	408.4+/-334.6	155,839,1209	266.0	248.0	254.0		,,,,2472	-0.6	0.6	6	dbSNP_123	254	988,7612	212.5+/-252.8	51,886,3363	no	intron,intron,intron,intron,coding-synonymous	EPB41L2	NM_001135554.1,NM_001135555.2,NM_001199388.1,NM_001199389.1,NM_001431.3	,,,,	206,1725,4572	AA,AG,GG		11.4884,26.0781,16.4309	,,,,	,,,,824/1006	131190838	2137,10869	2203	4300	6503	SO:0001819	synonymous_variant	2037	exon15			CTCTCCGGGTATC	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.2472C>T	6.37:g.131190838G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	238	103	0.432773	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Silent	SNP	ENST00000337057.3	37	CCDS5141.1	336	0.15384615384615385	110	0.22357723577235772	71	0.19613259668508287	61	0.10664335664335664	94	0.12401055408970976	G	0.169	-1.073530	0.01918	0.260781	0.114884	ENSG00000079819	ENST00000456097	.	.	.	5.71	-0.641	0.11490	.	.	.	.	.	T	0.31389	0.0795	.	.	.	0.09310	P	0.9999999765644	.	.	.	.	.	.	T	0.18053	-1.0349	3	.	.	.	.	10.824	0.46620	0.5978:0.0:0.4022:0.0	rs17059736;rs17059736	.	.	.	W	367	.	.	R	-	1	2	EPB41L2	131232531	0.003000	0.15002	0.625000	0.29200	0.157000	0.22087	-0.125000	0.10579	-0.095000	0.12351	-1.587000	0.00848	CGG	G|0.841;A|0.159	0.159	strong		0.507	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3		
MUC6	4588	hgsc.bcm.edu	37	11	1029320	1029320	+	Missense_Mutation	SNP	C	C	T	rs11604757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1029320C>T	ENST00000421673.2	-	10	1233	c.1183G>A	c.(1183-1185)Gga>Aga	p.G395R		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	395					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCAGTGTCCGGGGCACGGC	0.687													c|||	212	0.0423323	0.0129	0.0793	5008	,	,		13984	0.0		0.1203	False		,,,				2504	0.0194				p.G395R		Atlas-SNP	.											.	MUC6	408	.	0			c.G1183A						PASS	.	C	ARG/GLY	87,4123		0,87,2018	16.0	17.0	17.0		1183	2.7	0.0	11	dbSNP_120	17	985,7415		58,869,3273	yes	missense	MUC6	NM_005961.2	125	58,956,5291	TT,TC,CC		11.7262,2.0665,8.5012	possibly-damaging	395/2440	1029320	1072,11538	2105	4200	6305	SO:0001583	missense	4588	exon10			AGTGTCCGGGGCA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.1183G>A	11.37:g.1029320C>T	ENSP00000406861:p.Gly395Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	130	0.05952380952380952	8	0.016260162601626018	32	0.08839779005524862	0	0.0	90	0.11873350923482849	C	16.24	3.067774	0.55539	0.020665	0.117262	ENSG00000184956	ENST00000421673	T	0.64085	-0.08	4.56	2.68	0.31781	von Willebrand factor, type D domain (1);	1.027660	0.07899	N	0.972423	T	0.01156	0.0038	M	0.69358	2.11	0.33001	P	0.47379499999999997	P	0.44659	0.84	B	0.30495	0.116	T	0.10683	-1.0619	9	0.54805	T	0.06	.	9.5498	0.39304	0.0:0.7562:0.1607:0.0831	rs11604757;rs59572872;rs11604757	395	Q6W4X9	MUC6_HUMAN	R	395	ENSP00000406861:G395R	ENSP00000406861:G395R	G	-	1	0	MUC6	1019320	0.091000	0.21658	0.004000	0.12327	0.162000	0.22319	1.681000	0.37618	0.489000	0.27749	0.313000	0.20887	GGA	C|0.945;T|0.055	0.055	strong		0.687	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ZNF668	79759	hgsc.bcm.edu	37	16	31072909	31072909	+	Missense_Mutation	SNP	G	G	A	rs8046978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31072909G>A	ENST00000538906.1	-	3	2124	c.1340C>T	c.(1339-1341)gCa>gTa	p.A447V	ZNF668_ENST00000394983.2_Missense_Mutation_p.A447V|ZNF668_ENST00000535577.1_Missense_Mutation_p.A447V|ZNF668_ENST00000539836.3_Missense_Mutation_p.A470V|ZNF668_ENST00000300849.4_Missense_Mutation_p.A447V|ZNF668_ENST00000426488.2_Missense_Mutation_p.A470V|ZNF668_ENST00000417110.2_Missense_Mutation_p.A33T	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	447			A -> V (in dbSNP:rs8046978).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CGCCCCTGCTGCCGGGGCGGC	0.711													G|||	472	0.0942492	0.0386	0.1383	5008	,	,		13492	0.003		0.2336	False		,,,				2504	0.089				p.A470V	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C1409T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	257,4127		6,245,1941	32.0	39.0	37.0		1340,1409,1340,1340	-1.8	0.0	16	dbSNP_116	37	1956,6638		208,1540,2549	no	missense,missense,missense,missense	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	64,64,64,64	214,1785,4490	AA,AG,GG		22.7601,5.8622,17.0519	benign,benign,benign,benign	447/620,470/643,447/620,447/620	31072909	2213,10765	2192	4297	6489	SO:0001583	missense	79759	exon4			CCTGCTGCCGGGG		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1340C>T	16.37:g.31072909G>A	ENSP00000440149:p.Ala447Val	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	28	17	0.607143	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	37	CCDS10701.1	265|265	0.12133699633699634|0.12133699633699634	31|31	0.06300813008130081|0.06300813008130081	58|58	0.16022099447513813|0.16022099447513813	0|0	0.0|0.0	176|176	0.23218997361477572|0.23218997361477572	G|G	7.430|7.430	0.638493|0.638493	0.14386|0.14386	0.058622|0.058622	0.227601|0.227601	ENSG00000232748|ENSG00000167394	ENST00000417110|ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	.|T;T;T;T;T	.|0.07444	.|3.19;3.2;3.2;3.2;3.2	4.63|4.63	-1.8|-1.8	0.07907|0.07907	.|.	0.914317|0.914317	0.08993|0.08993	N|N	0.864087|0.864087	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.47886|0.47886	-0.9082|-0.9082	6|9	0.87932|0.87932	D|D	0|0	-1.2257|-1.2257	4.0535|4.0535	0.09806|0.09806	0.1021:0.4895:0.2577:0.1507|0.1021:0.4895:0.2577:0.1507	rs8046978;rs8046978|rs8046978;rs8046978	.|447	.|Q96K58	.|ZN668_HUMAN	T|V	33|470;447;447;447;447	.|ENSP00000442573:A470V;ENSP00000441349:A447V;ENSP00000440149:A447V;ENSP00000378434:A447V;ENSP00000300849:A447V	ENSP00000391989:A33T|ENSP00000300849:A447V	A|A	+|-	1|2	0|0	AC135050.1|ZNF668	30980410|30980410	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.410000|0.410000	0.31052|0.31052	-0.300000|-0.300000	0.08243|0.08243	-0.091000|-0.091000	0.12440|0.12440	0.462000|0.462000	0.41574|0.41574	GCC|GCA	G|0.851;A|0.149	0.149	strong		0.711	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
DOCK8	81704	hgsc.bcm.edu	37	9	334337	334337	+	Missense_Mutation	SNP	A	A	G	rs10970979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:334337A>G	ENST00000453981.1	+	11	1350	c.1238A>G	c.(1237-1239)aAt>aGt	p.N413S	DOCK8_ENST00000432829.2_Missense_Mutation_p.N345S|DOCK8_ENST00000469391.1_Missense_Mutation_p.N345S			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	413			N -> S (in dbSNP:rs10970979). {ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		AGCTTCTTCAATGTCTCCACC	0.512													A|||	1000	0.199681	0.2073	0.2061	5008	,	,		18913	0.0377		0.2724	False		,,,				2504	0.2771				p.N413S		Atlas-SNP	.											.	DOCK8	401	.	0			c.A1238G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	1009,3397	375.4+/-321.6	121,767,1315	106.0	102.0	103.0		1034,1034,1238	2.3	0.9	9	dbSNP_120	103	2659,5941	428.2+/-355.8	395,1869,2036	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	46,46,46	516,2636,3351	GG,GA,AA		30.9186,22.9006,28.2024	benign,benign,benign	345/2000,345/2032,413/2100	334337	3668,9338	2203	4300	6503	SO:0001583	missense	81704	exon11			TCTTCAATGTCTC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1238A>G	9.37:g.334337A>G	ENSP00000408464:p.Asn413Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	158	78	0.493671	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	414	0.18956043956043955	99	0.20121951219512196	87	0.24033149171270718	18	0.03146853146853147	210	0.2770448548812665	A	8.178	0.793247	0.16327	0.229006	0.309186	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.30981	1.51;1.51;1.51	5.87	2.28	0.28536	.	0.351259	0.33772	N	0.004578	T	0.00012	0.0000	N	0.02775	-0.495	0.26695	P	0.9712807999999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	8.7127	0.34393	0.654:0.0:0.346:0.0	rs10970979;rs17846376;rs17859413;rs60522712;rs10970979	345;413	E9PH09;Q8NF50	.;DOCK8_HUMAN	S	413;413;345;345	ENSP00000408464:N413S;ENSP00000394888:N345S;ENSP00000419438:N345S	ENSP00000287364:N413S	N	+	2	0	DOCK8	324337	0.005000	0.15991	0.918000	0.36340	0.928000	0.56348	0.417000	0.21214	0.559000	0.29153	0.533000	0.62120	AAT	A|0.758;G|0.242	0.242	strong		0.512	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
APBA2	321	hgsc.bcm.edu	37	15	29346590	29346590	+	Missense_Mutation	SNP	C	C	T	rs148760039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29346590C>T	ENST00000558402.1	+	5	1102	c.503C>T	c.(502-504)cCg>cTg	p.P168L	APBA2_ENST00000411764.1_Missense_Mutation_p.P168L|APBA2_ENST00000558259.1_Missense_Mutation_p.P168L|APBA2_ENST00000558330.1_Missense_Mutation_p.P168L|APBA2_ENST00000561069.1_Missense_Mutation_p.P168L			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	168					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)		CTGCCCATTCCGGAGGATGAG	0.657													C|||	17	0.00339457	0.0	0.0	5008	,	,		18595	0.0169		0.0	False		,,,				2504	0.0				p.P168L		Atlas-SNP	.											APBA2,caecum,carcinoma,0,2	APBA2	132	2	0			c.C503T						PASS	.	C	LEU/PRO,LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	39.0	39.0	39.0		503,503	2.0	0.0	15	dbSNP_134	39	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	APBA2	NM_001130414.1,NM_005503.3	98,98	0,5,6498	TT,TC,CC		0.0349,0.0454,0.0384	benign,benign	168/738,168/750	29346590	5,13001	2203	4300	6503	SO:0001583	missense	321	exon3			CCATTCCGGAGGA	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.503C>T	15.37:g.29346590C>T	ENSP00000453293:p.Pro168Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	140	52	0.371429	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	11	0.005036630036630037	0	0.0	0	0.0	11	0.019230769230769232	0	0.0	C	5.373	0.254155	0.10185	4.54E-4	3.49E-4	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.04406	3.63	5.35	2.04	0.26737	.	0.382752	0.26048	N	0.026653	T	0.01592	0.0051	L	0.33137	0.985	0.09310	N	0.999998	B;B;B	0.13594	0.008;0.006;0.006	B;B;B	0.09377	0.004;0.003;0.003	T	0.43097	-0.9412	10	0.26408	T	0.33	.	5.3898	0.16237	0.0:0.4708:0.0:0.5292	.	168;168;168	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	L	168	ENSP00000409312:P168L	ENSP00000219865:P168L	P	+	2	0	APBA2	27133882	0.047000	0.20315	0.001000	0.08648	0.010000	0.07245	1.314000	0.33597	0.628000	0.30357	-0.142000	0.14014	CCG	C|0.998;T|0.002	0.002	strong		0.657	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
MYOM3	127294	hgsc.bcm.edu	37	1	24409191	24409191	+	Missense_Mutation	SNP	C	C	T	rs4320729	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24409191C>T	ENST00000374434.3	-	17	2146	c.1984G>A	c.(1984-1986)Ggg>Agg	p.G662R	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Missense_Mutation_p.G662R|MYOM3_ENST00000330966.7_Missense_Mutation_p.G663R|MYOM3_ENST00000475306.1_5'UTR|RP11-293P20.4_ENST00000429191.1_RNA	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	662	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> R (in dbSNP:rs4320729). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GTCCTCAGCCCGGGAACTGTA	0.537													C|||	1286	0.256789	0.0159	0.3213	5008	,	,		20504	0.4266		0.4364	False		,,,				2504	0.1769				p.G662R		Atlas-SNP	.											.	MYOM3	131	.	0			c.G1984A						PASS	.	C	ARG/GLY	335,3707		19,297,1705	54.0	57.0	56.0		1984	5.4	0.9	1	dbSNP_111	56	3520,4872		728,2064,1404	yes	missense	MYOM3	NM_152372.3	125	747,2361,3109	TT,TC,CC		41.9447,8.288,31.0037	probably-damaging	662/1438	24409191	3855,8579	2021	4196	6217	SO:0001583	missense	127294	exon17			TCAGCCCGGGAAC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.1984G>A	1.37:g.24409191C>T	ENSP00000363557:p.Gly662Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	706	0.3232600732600733	10	0.02032520325203252	108	0.2983425414364641	248	0.43356643356643354	340	0.44854881266490765	C	18.80	3.701981	0.68501	0.08288	0.419447	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.61980	0.06;0.06;0.06	5.41	5.41	0.78517	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.104378	0.64402	D	0.000003	T	0.00012	0.0000	M	0.78801	2.425	0.21782	P	0.999544475	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.21314	-1.0249	9	0.62326	D	0.03	.	19.1966	0.93691	0.0:1.0:0.0:0.0	rs4320729;rs52799837;rs57980115;rs4320729	662;662	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	R	662;663;662	ENSP00000363557:G662R;ENSP00000332670:G663R;ENSP00000328415:G662R	ENSP00000328415:G662R	G	-	1	0	MYOM3	24281778	1.000000	0.71417	0.922000	0.36590	0.308000	0.27856	5.783000	0.68982	2.546000	0.85860	0.557000	0.71058	GGG	C|0.679;T|0.321	0.321	strong		0.537	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
ARMC6	93436	hgsc.bcm.edu	37	19	19164983	19164983	+	Silent	SNP	C	C	T	rs142816550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19164983C>T	ENST00000535612.1	+	6	1308	c.876C>T	c.(874-876)atC>atT	p.I292I	ARMC6_ENST00000546344.1_Silent_p.I199I|ARMC6_ENST00000392336.3_Silent_p.I292I|ARMC6_ENST00000269932.6_Silent_p.I267I|ARMC6_ENST00000392335.2_Silent_p.I267I	NM_001199196.1	NP_001186125.1	Q6NXE6	ARMC6_HUMAN	armadillo repeat containing 6	292					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|prostate(1)	14			OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)			ACCCTGGCATCCTGAGCGAGC	0.637											OREG0025376	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	40	0.00798722	0.0008	0.0072	5008	,	,		16120	0.0		0.0328	False		,,,				2504	0.001				p.I292I		Atlas-SNP	.											.	ARMC6	56	.	0			c.C876T						PASS	.	C	,	17,4389	24.3+/-50.5	0,17,2186	95.0	85.0	88.0		876,801	1.1	0.5	19	dbSNP_134	88	168,8432	77.5+/-140.1	5,158,4137	no	coding-synonymous,coding-synonymous	ARMC6	NM_001199196.1,NM_033415.3	,	5,175,6323	TT,TC,CC		1.9535,0.3858,1.4224	,	292/502,267/477	19164983	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	93436	exon6			TGGCATCCTGAGC	BX648486	CCDS32965.1, CCDS56089.1	19p13	2013-02-14				ENSG00000105676		"""Armadillo repeat containing"""	25049	protein-coding gene	gene with protein product						12477932	Standard	NM_033415		Approved	MGC19595	uc002nlc.3	Q6NXE6		ENST00000535612.1:c.876C>T	19.37:g.19164983C>T		Somatic	102	0	0	731	WXS	Illumina HiSeq	Phase_I	131	69	0.526718	NM_001199196	B4DI98|O94999|Q9BTH5	Silent	SNP	ENST00000535612.1	37	CCDS56089.1																																																																																			C|0.985;T|0.015	0.015	strong		0.637	ARMC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403226.1	NM_033415	
GPATCH1	55094	hgsc.bcm.edu	37	19	33605300	33605300	+	Missense_Mutation	SNP	A	A	G	rs10416265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	94	0	0		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	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	
NKX1-2	390010	hgsc.bcm.edu	37	10	126136112	126136112	+	Silent	SNP	A	A	G	rs7075981|rs386748536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:126136112A>G	ENST00000451024.3	-	2	1059	c.819T>C	c.(817-819)aaT>aaC	p.N273N	NKX1-2_ENST00000440536.2_Silent_p.N295N|RP13-238F13.3_ENST00000604581.1_RNA|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						scavenged	.	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	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	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	
EMR1	2015	hgsc.bcm.edu	37	19	6897464	6897464	+	Missense_Mutation	SNP	C	C	G	rs330880	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6897464C>G	ENST00000312053.4	+	5	457	c.420C>G	c.(418-420)agC>agG	p.S140R	EMR1_ENST00000381404.4_Missense_Mutation_p.S88R|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000250572.8_Missense_Mutation_p.S140R|EMR1_ENST00000381407.5_Intron|EMR1_ENST00000450315.3_Splice_Site|AC020895.1_ENST00000580648.1_RNA	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	216	0	0		WXS	Illumina HiSeq	Phase_I	250	109	0.436	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		
ANXA13	312	hgsc.bcm.edu	37	8	124710664	124710664	+	Missense_Mutation	SNP	C	C	T	rs6995099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:124710664C>T	ENST00000419625.1	-	4	394	c.322G>A	c.(322-324)Gtc>Atc	p.V108I	ANXA13_ENST00000262219.6_Missense_Mutation_p.V149I	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	108			V -> I (in dbSNP:rs6995099).		cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			TCAATGAGGACGGACTCATCT	0.597													C|||	257	0.0513179	0.0643	0.062	5008	,	,		19912	0.005		0.0845	False		,,,				2504	0.0399				p.V149I		Atlas-SNP	.											.	ANXA13	38	.	0			c.G445A						PASS	.	C	ILE/VAL,ILE/VAL	313,4093	170.1+/-200.6	14,285,1904	108.0	98.0	102.0		445,322	-2.2	0.0	8	dbSNP_116	102	640,7960	163.6+/-216.1	20,600,3680	yes	missense,missense	ANXA13	NM_001003954.1,NM_004306.2	29,29	34,885,5584	TT,TC,CC		7.4419,7.1039,7.3274	benign,benign	149/358,108/317	124710664	953,12053	2203	4300	6503	SO:0001583	missense	312	exon5			TGAGGACGGACTC	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.322G>A	8.37:g.124710664C>T	ENSP00000390809:p.Val108Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_001003954	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	37	CCDS47917.1	129	0.059065934065934064	39	0.07926829268292683	24	0.06629834254143646	1	0.0017482517482517483	65	0.08575197889182058	C	13.11	2.138053	0.37728	0.071039	0.074419	ENSG00000104537	ENST00000262219;ENST00000419625;ENST00000520519	T;T;T	0.03635	3.86;3.86;3.86	5.67	-2.2	0.06994	Annexin repeat, conserved site (1);	0.422095	0.27956	N	0.017164	T	0.00144	0.0004	M	0.63208	1.945	0.53005	P	3.100000000000325E-5	P;P	0.37731	0.607;0.553	B;B	0.33690	0.168;0.105	T	0.34625	-0.9821	9	0.48119	T	0.1	.	0.8559	0.01182	0.2909:0.2147:0.2937:0.2007	rs6995099;rs52822457;rs59748842;rs6995099	108;149	P27216;P27216-2	ANX13_HUMAN;.	I	149;108;79	ENSP00000262219:V149I;ENSP00000390809:V108I;ENSP00000429358:V79I	ENSP00000262219:V149I	V	-	1	0	ANXA13	124779845	0.021000	0.18746	0.014000	0.15608	0.633000	0.38033	0.327000	0.19663	-0.417000	0.07461	-0.291000	0.09656	GTC	C|0.936;T|0.064	0.064	strong		0.597	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77359919	77359919	+	Missense_Mutation	SNP	A	A	T	rs11640912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:77359919A>T	ENST00000282849.5	-	13	2294	c.1876T>A	c.(1876-1878)Tta>Ata	p.L626I		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	626	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		L -> I (in dbSNP:rs11640912). {ECO:0000269|PubMed:11867212, ECO:0000269|PubMed:15489334}.		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GGACAGAATAAGCCACCATAC	0.368													T|||	2201	0.439497	0.146	0.5562	5008	,	,		19296	0.8681		0.3618	False		,,,				2504	0.3916				p.L626I		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.T1876A						PASS	.	T	ILE/LEU	905,3491	739.6+/-411.1	96,713,1389	70.0	64.0	66.0		1876	4.8	1.0	16	dbSNP_120	66	3239,5361	649.3+/-400.6	615,2009,1676	yes	missense	ADAMTS18	NM_199355.2	5	711,2722,3065	TT,TA,AA		37.6628,20.5869,31.8867	benign	626/1222	77359919	4144,8852	2198	4300	6498	SO:0001583	missense	170692	exon13			AGAATAAGCCACC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.1876T>A	16.37:g.77359919A>T	ENSP00000282849:p.Leu626Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	1037	0.4748168498168498	72	0.14634146341463414	195	0.5386740331491713	494	0.8636363636363636	276	0.3641160949868074	T	16.49	3.137533	0.56936	0.205869	0.376628	ENSG00000140873	ENST00000282849	T	0.03553	3.89	5.98	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.33624	1.015	0.80722	P	0.0	B;B	0.15930	0.015;0.007	B;B	0.11329	0.006;0.005	T	0.12218	-1.0556	9	0.87932	D	0	.	8.6403	0.33972	0.1282:0.0:0.1344:0.7373	rs11640912;rs17855796;rs52810617;rs11640912	626;626	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	I	626	ENSP00000282849:L626I	ENSP00000282849:L626I	L	-	1	2	ADAMTS18	75917420	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	4.234000	0.58658	1.087000	0.41251	-0.265000	0.10407	TTA	A|0.625;T|0.375	0.375	strong		0.368	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
SYK	6850	hgsc.bcm.edu	37	9	93641175	93641175	+	Silent	SNP	C	C	T	rs2306041	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:93641175C>T	ENST00000375754.4	+	11	1669	c.1521C>T	c.(1519-1521)taC>taT	p.Y507Y	SYK_ENST00000375747.1_Silent_p.Y484Y|SYK_ENST00000375751.4_Silent_p.Y484Y|SYK_ENST00000375746.1_Silent_p.Y507Y	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	507	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CCCAACATTACGCCAAGATCA	0.438			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	993	0.198283	0.2179	0.366	5008	,	,		20099	0.2321		0.1362	False		,,,				2504	0.0818				p.Y507Y		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.C1521T						PASS	.	C	,,,	968,3438	365.4+/-317.4	102,764,1337	181.0	158.0	166.0		1452,1521,1452,1521	-3.4	1.0	9	dbSNP_100	166	1215,7385	245.3+/-274.2	88,1039,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	190,1803,4510	TT,TC,CC		14.1279,21.97,16.7846	,,,	484/613,507/636,484/613,507/636	93641175	2183,10823	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon11			ACATTACGCCAAG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1521C>T	9.37:g.93641175C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			C|0.822;T|0.178	0.178	strong		0.438	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Intron	SNP	C	C	T	rs10258429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Intron|EGFR_ENST00000344576.2_Silent_p.H656H|EGFR_ENST00000455089.1_Intron	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	160	0	0		WXS	Illumina HiSeq	Phase_I	189	93	0.492063	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	
KIRREL2	84063	hgsc.bcm.edu	37	19	36351935	36351935	+	Silent	SNP	G	G	T	rs35854130	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36351935G>T	ENST00000360202.5	+	8	1251	c.1053G>T	c.(1051-1053)gcG>gcT	p.A351A	KIRREL2_ENST00000347900.6_Silent_p.A301A|KIRREL2_ENST00000262625.7_Silent_p.A351A|KIRREL2_ENST00000592409.1_Silent_p.A351A|NPHS1_ENST00000591817.1_Intron	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	351	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)			GCGGTGGCGCGCAGGTACAGC	0.677													G|||	895	0.178714	0.2042	0.1527	5008	,	,		15275	0.0139		0.2296	False		,,,				2504	0.2802				p.A351A		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G1053T						PASS	.	G	,,	915,3469		114,687,1391	12.0	14.0	13.0		1053,903,1053	-4.8	0.2	19	dbSNP_126	13	1946,6610		222,1502,2554	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	336,2189,3945	TT,TG,GG		22.7443,20.8714,22.1097	,,	351/634,301/584,351/709	36351935	2861,10079	2192	4278	6470	SO:0001819	synonymous_variant	84063	exon8			TGGCGCGCAGGTA	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.1053G>T	19.37:g.36351935G>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			G|0.811;T|0.189	0.189	strong		0.677	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
GJA4	2701	hgsc.bcm.edu	37	1	35259946	35259946	+	Silent	SNP	G	G	A	rs1764389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	185	0	0		WXS	Illumina HiSeq	Phase_I	207	116	0.560386	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	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254257	39254257	+	Missense_Mutation	SNP	G	G	T	rs142487897	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254257G>T	ENST00000333822.4	-	1	136	c.80C>A	c.(79-81)cCc>cAc	p.P27H		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	27	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						ACAGCAGCTGGGGCAGCAGCA	0.622													G|||	80	0.0159744	0.0008	0.0202	5008	,	,		17365	0.0		0.0447	False		,,,				2504	0.0204				p.P27H		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C80A						PASS	.						24.0	26.0	25.0					17																	39254257		692	1591	2283	SO:0001583	missense	728224	exon1			CAGCTGGGGCAGC	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.80C>A	17.37:g.39254257G>T	ENSP00000328444:p.Pro27His	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	40	0.018315018315018316	0	0.0	6	0.016574585635359115	0	0.0	34	0.044854881266490766	.	9.023	0.985453	0.18889	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.02177	4.41	3.56	3.56	0.40772	.	.	.	.	.	T	0.01061	0.0035	M	0.84948	2.725	0.30521	N	0.768452	P	0.34724	0.465	B	0.27608	0.081	T	0.01276	-1.1398	9	0.87932	D	0	.	13.0464	0.58928	0.0:0.0:1.0:0.0	.	27	Q9BYQ9	KRA48_HUMAN	H	27	ENSP00000328444:P27H	ENSP00000414561:P27H	P	-	2	0	KRTAP4-8	36507783	0.911000	0.30947	0.809000	0.32408	0.118000	0.20060	2.211000	0.42825	1.697000	0.51169	0.393000	0.25936	CCC	G|0.982;T|0.018	0.018	strong		0.622	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
IQSEC2	23096	hgsc.bcm.edu	37	X	53263764	53263764	+	Silent	SNP	C	C	T	rs184087864		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	80	0	0		WXS	Illumina HiSeq	Phase_I	103	96	0.932039	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	
CTSE	1510	hgsc.bcm.edu	37	1	206328803	206328803	+	Silent	SNP	T	T	C	rs41302235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:206328803T>C	ENST00000358184.2	+	7	988	c.870T>C	c.(868-870)ccT>ccC	p.P290P	CTSE_ENST00000361052.3_Silent_p.P295P|CTSE_ENST00000360218.2_Intron|CTSE_ENST00000432969.2_Intron	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	295					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			TCACTGGCCCTTCCGACAAGA	0.607													t|||	924	0.184505	0.3911	0.1671	5008	,	,		18519	0.0169		0.2107	False		,,,				2504	0.0634				p.P290P		Atlas-SNP	.											.	CTSE	72	.	0			c.T870C						PASS	.	T	,	1701,2705	513.1+/-368.2	355,991,857	82.0	76.0	78.0		870,	-2.3	0.1	1	dbSNP_127	78	1611,6989	298.2+/-303.8	147,1317,2836	no	coding-synonymous,intron	CTSE	NM_001910.3,NM_148964.2	,	502,2308,3693	CC,CT,TT		18.7326,38.6064,25.4652	,	290/397,	206328803	3312,9694	2203	4300	6503	SO:0001819	synonymous_variant	1510	exon7			TGGCCCTTCCGAC	BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"""Cathepsins"""	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.870T>C	1.37:g.206328803T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	188	186	0.989362	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Silent	SNP	ENST00000358184.2	37	CCDS1462.1																																																																																			T|0.768;C|0.232	0.232	strong		0.607	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910	
KRT37	8688	hgsc.bcm.edu	37	17	39580660	39580660	+	Missense_Mutation	SNP	T	T	C	rs9916724	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39580660T>C	ENST00000225550.3	-	1	115	c.116A>G	c.(115-117)aAt>aGt	p.N39S	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	39	Head.		N -> S (in dbSNP:rs9916724).			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)				GGAGGCAGCATTGGCCTCTGC	0.622													T|||	1960	0.391374	0.1846	0.3415	5008	,	,		20684	0.4067		0.4592	False		,,,				2504	0.6207				p.N39S		Atlas-SNP	.											.	KRT37	61	.	0			c.A116G						PASS	.	T	SER/ASN	983,3423		111,761,1331	52.0	53.0	53.0		116	2.9	0.0	17	dbSNP_119	53	4170,4430		1019,2132,1149	yes	missense	KRT37	NM_003770.4	46	1130,2893,2480	CC,CT,TT		48.4884,22.3105,39.6202	benign	39/450	39580660	5153,7853	2203	4300	6503	SO:0001583	missense	8688	exon1			GCAGCATTGGCCT	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.116A>G	17.37:g.39580660T>C	ENSP00000225550:p.Asn39Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	812	0.3717948717948718	101	0.20528455284552846	145	0.4005524861878453	227	0.3968531468531469	339	0.4472295514511873	.	5.186	0.219886	0.09863	0.223105	0.484884	ENSG00000108417	ENST00000225550	T	0.81247	-1.47	2.94	2.94	0.34122	.	0.677290	0.12593	N	0.455396	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	0.35919	-0.9769	9	0.10377	T	0.69	.	6.4153	0.21714	0.0:0.1301:0.0:0.8699	rs9916724;rs59188249	39	O76014	KRT37_HUMAN	S	39	ENSP00000225550:N39S	ENSP00000225550:N39S	N	-	2	0	KRT37	36834186	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.252000	0.08806	1.127000	0.42034	0.383000	0.25322	AAT	T|0.619;C|0.381	0.381	strong		0.622	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
TEP1	7011	hgsc.bcm.edu	37	14	20876253	20876253	+	Missense_Mutation	SNP	A	A	G	rs1760897	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	184	184	1	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	
SLC22A23	63027	hgsc.bcm.edu	37	6	3284097	3284097	+	Silent	SNP	C	C	T	rs142838841	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3284097C>T	ENST00000406686.3	-	9	1691	c.1692G>A	c.(1690-1692)ccG>ccA	p.P564P	SLC22A23_ENST00000436008.2_Silent_p.P572P|SLC22A23_ENST00000380302.4_Silent_p.P283P|PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000490273.1_Silent_p.P283P	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	564					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				TTATCACCGTCGGGGTGATCT	0.587													c|||	4	0.000798722	0.0	0.0	5008	,	,		19259	0.0		0.004	False		,,,				2504	0.0				p.P564P		Atlas-SNP	.											.	SLC22A23	89	.	0			c.G1692A						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	74.0	67.0	69.0		1692,849	0.3	0.9	6	dbSNP_134	69	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous,coding-synonymous	SLC22A23	NM_015482.1,NM_021945.5	,	0,43,6460	TT,TC,CC		0.4535,0.0908,0.3306	,	564/687,283/406	3284097	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	63027	exon9			CACCGTCGGGGTG	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"""Solute carriers"""	21106	protein-coding gene	gene with protein product		611697	"""chromosome 6 open reading frame 85"""	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1692G>A	6.37:g.3284097C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Silent	SNP	ENST00000406686.3	37	CCDS47363.1																																																																																			C|0.997;T|0.003	0.003	strong		0.587	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945	
POF1B	79983	hgsc.bcm.edu	37	X	84563194	84563194	+	Missense_Mutation	SNP	C	C	T	rs75398746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:84563194C>T	ENST00000262753.4	-	10	1131	c.986G>A	c.(985-987)cGa>cAa	p.R329Q	POF1B_ENST00000373145.3_Missense_Mutation_p.R329Q	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	329			R -> Q (in POF2B; disrupts binding to nonmuscle actin filaments; abolishes tight junction localization; altered ciliogenesis and cystogenesis; dbSNP:rs75398746). {ECO:0000269|PubMed:15459172, ECO:0000269|PubMed:16773570}.			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						CAGCACTAGTCGGAGTGACTT	0.343													C|||	11	0.00291391	0.0045	0.0058	3775	,	,		11719	0.0		0.001	False		,,,				2504	0.0				p.R329Q		Atlas-SNP	.											.	POF1B	77	.	0			c.G986A	GRCh37	CM066591	POF1B	M	rs75398746	PASS	.	C	GLN/ARG	26,3809		0,23,3,1609,568	93.0	80.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	986	5.0	0.7	X	dbSNP_131	84	17,6711		0,12,5,2416,1867	yes	missense	POF1B	NM_024921.3	43	0,35,8,4025,2435	TT,TC,T,CC,C		0.2527,0.678,0.4071	probably-damaging	329/590	84563194	43,10520	2203	4300	6503	SO:0001583	missense	79983	exon10			ACTAGTCGGAGTG	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.986G>A	X.37:g.84563194C>T	ENSP00000262753:p.Arg329Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	6	0.003616636528028933	1	0.0020408163265306124	3	0.008333333333333333	0	0.0	0	0.0	C	16.37	3.102992	0.56183	0.00678	0.002527	ENSG00000124429	ENST00000262753;ENST00000373145	T;T	0.16073	2.37;2.37	5.86	5.0	0.66597	.	0.101855	0.64402	N	0.000003	T	0.12347	0.0300	L	0.58101	1.795	0.29902	A	0.175686	B;B	0.32968	0.392;0.392	B;B	0.19946	0.027;0.027	T	0.16424	-1.0403	9	0.72032	D	0.01	-4.9537	12.8282	0.57731	0.0:0.9187:0.0:0.0813	.	329;329	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	Q	329	ENSP00000262753:R329Q;ENSP00000362238:R329Q	ENSP00000262753:R329Q	R	-	2	0	POF1B	84449850	0.934000	0.31675	0.671000	0.29857	0.941000	0.58515	2.969000	0.49232	1.236000	0.43740	0.600000	0.82982	CGA	C|0.996;T|0.004	0.004	strong		0.343	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921	
PAK4	10298	hgsc.bcm.edu	37	19	39663757	39663757	+	Missense_Mutation	SNP	G	G	A	rs56099436	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39663757G>A	ENST00000593690.1	+	5	831	c.404G>A	c.(403-405)cGa>cAa	p.R135Q	PAK4_ENST00000599386.1_Intron|PAK4_ENST00000358301.3_Missense_Mutation_p.R135Q|PAK4_ENST00000599470.1_Intron|PAK4_ENST00000321944.4_Intron|PAK4_ENST00000360442.3_Missense_Mutation_p.R135Q|PAK4_ENST00000435673.2_Missense_Mutation_p.R135Q	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	135	Linker.		R -> Q (in dbSNP:rs56099436). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			GCAGGCAGCCGAGGCCGGTTC	0.736													g|||	34	0.00678914	0.0008	0.0115	5008	,	,		10680	0.0		0.0189	False		,,,				2504	0.0061				p.R135Q		Atlas-SNP	.											.	PAK4	40	.	0			c.G404A						PASS	.		GLN/ARG,GLN/ARG,,,GLN/ARG	13,3671		0,13,1829	3.0	4.0	4.0		404,404,,,404	1.7	0.0	19	dbSNP_129	4	147,7075		0,147,3464	no	missense,missense,intron,intron,missense	PAK4	NM_001014831.2,NM_001014832.1,NM_001014834.2,NM_001014835.1,NM_005884.3	43,43,,,43	0,160,5293	AA,AG,GG		2.0354,0.3529,1.4671	possibly-damaging,possibly-damaging,,,possibly-damaging	135/592,135/592,,,135/592	39663757	160,10746	1842	3611	5453	SO:0001583	missense	10298	exon3			GCAGCCGAGGCCG	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"""p21(CDKN1A)-activated kinase 4"""			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.404G>A	19.37:g.39663757G>A	ENSP00000469413:p.Arg135Gln	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	25	0.011446886446886446	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	0.017	-1.510561	0.00984	0.003529	0.020354	ENSG00000130669	ENST00000358301;ENST00000435673;ENST00000360442	T;T;T	0.71103	-0.54;-0.54;-0.54	3.9	1.73	0.24493	.	1.445110	0.04338	N	0.353591	T	0.32734	0.0839	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21075	-1.0256	10	0.12430	T	0.62	.	7.4578	0.27276	0.3592:0.0:0.6408:0.0	rs56099436	135	O96013	PAK4_HUMAN	Q	135	ENSP00000351049:R135Q;ENSP00000392753:R135Q;ENSP00000353625:R135Q	ENSP00000351049:R135Q	R	+	2	0	PAK4	44355597	0.000000	0.05858	0.026000	0.17262	0.011000	0.07611	0.293000	0.19029	-0.014000	0.14175	-1.157000	0.01802	CGA	G|0.989;A|0.011	0.011	strong		0.736	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1		
AQP7	364	hgsc.bcm.edu	37	9	33385815	33385815	+	Missense_Mutation	SNP	T	T	C	rs62542745		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33385815T>C	ENST00000537089.1	-	6	617	c.299A>G	c.(298-300)cAg>cGg	p.Q100R	AQP7_ENST00000377425.4_Missense_Mutation_p.Q135R|AQP7_ENST00000539936.1_Missense_Mutation_p.Q192R|AQP7_ENST00000541274.1_Silent_p.P60P			O14520	AQP7_HUMAN	aquaporin 7	192					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)		GTTGTTCTCCTGGTCCGTGAT	0.612																																					p.Q192R		Atlas-SNP	.											AQP7,NS,carcinoma,0,1	AQP7	58	1	0			c.A575G						scavenged	.						123.0	107.0	113.0					9																	33385815		2203	4300	6503	SO:0001583	missense	364	exon7			TTCTCCTGGTCCG	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.299A>G	9.37:g.33385815T>C	ENSP00000441619:p.Gln100Arg	Somatic	81	4	0.0493827		WXS	Illumina HiSeq	Phase_I	84	8	0.0952381	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		.	.	.	.	.	.	.	.	.	.	t	2.177	-0.388519	0.04932	.	.	ENSG00000165269	ENST00000537089;ENST00000379507;ENST00000447660;ENST00000297988;ENST00000377425;ENST00000439678;ENST00000379506;ENST00000539936;ENST00000379503	D;D;D;D;D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93;-1.93	5.02	3.85	0.44370	Aquaporin-like (2);	0.260173	0.44483	D	0.000447	T	0.69360	0.3102	N	0.20483	0.58	0.09310	N	1	B;B;B;B	0.14012	0.001;0.001;0.001;0.009	B;B;B;B	0.17098	0.006;0.006;0.01;0.017	T	0.51260	-0.8728	10	0.13853	T	0.58	-14.4887	4.9508	0.14013	0.0:0.0932:0.1892:0.7176	rs62542745	191;192;135;192	Q5T5M0;B7Z4U2;Q6P5T0;O14520	.;.;.;AQP7_HUMAN	R	100;191;60;192;135;100;191;192;128	ENSP00000441619:Q100R;ENSP00000368821:Q191R;ENSP00000412868:Q60R;ENSP00000297988:Q192R;ENSP00000396111:Q135R;ENSP00000410138:Q100R;ENSP00000368820:Q191R;ENSP00000439534:Q192R;ENSP00000368817:Q128R	ENSP00000297988:Q192R	Q	-	2	0	AQP7	33375815	0.007000	0.16637	0.339000	0.25562	0.162000	0.22319	0.341000	0.19909	0.903000	0.36546	0.524000	0.50904	CAG	.	.	weak		0.612	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170	
FER1L5	90342	hgsc.bcm.edu	37	2	97359364	97359364	+	RNA	SNP	A	A	G	rs61750875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97359364A>G	ENST00000457909.1	+	0	1873							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						ACGAGAACCCACAGGACACCA	0.602													G|||	1051	0.209864	0.5053	0.0793	5008	,	,		18966	0.1984		0.0775	False		,,,				2504	0.0511				p.P1165P		Atlas-SNP	.											.	FER1L5	113	.	0			c.A3495G						PASS	.	G		574,810		115,344,233	75.0	87.0	83.0		3495	0.4	0.9	2	dbSNP_129	83	244,2938		11,222,1358	no	coding-synonymous	FER1L5	NM_001113382.1		126,566,1591	GG,GA,AA		7.6681,41.474,17.915		1165/2094	97359364	818,3748	692	1591	2283			90342	exon31			GAACCCACAGGAC	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"""fer-1-like 5 (C. elegans)"""				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		2.37:g.97359364A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_001113382	Q17RH2|Q6ZU24	Silent	SNP	ENST00000457909.1	37																																																																																				A|0.802;G|0.198	0.198	strong		0.602	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400	
RRP7A	27341	hgsc.bcm.edu	37	22	42910769	42910769	+	Silent	SNP	G	G	A	rs4822146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:42910769G>A	ENST00000323013.6	-	5	492	c.477C>T	c.(475-477)taC>taT	p.Y159Y	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	159							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y159Y(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						CAGAGTCTGCGTAGTCACTGA	0.622													G|||	383	0.0764776	0.0582	0.1772	5008	,	,		20886	0.004		0.1461	False		,,,				2504	0.0327				p.Y159Y		Atlas-SNP	.											RRP7A,NS,carcinoma,0,1	RRP7A	25	1	1	Substitution - coding silent(1)	prostate(1)	c.C477T						PASS	.	G		362,4036	158.9+/-191.5	33,296,1870	44.0	47.0	46.0		477	1.5	0.6	22	dbSNP_111	46	1171,7427	220.5+/-258.2	85,1001,3213	no	coding-synonymous	RRP7A	NM_015703.4		118,1297,5083	AA,AG,GG		13.6194,8.231,11.7959		159/281	42910769	1533,11463	2199	4299	6498	SO:0001819	synonymous_variant	27341	exon5			GTCTGCGTAGTCA	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.477C>T	22.37:g.42910769G>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	339	114	0.336283	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Silent	SNP	ENST00000323013.6	37	CCDS14036.1																																																																																			G|0.898;A|0.102	0.102	strong		0.622	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
DNAH14	127602	hgsc.bcm.edu	37	1	225534348	225534348	+	Missense_Mutation	SNP	G	G	A	rs7535953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225534348G>A	ENST00000445597.2	+	49	8600	c.8600G>A	c.(8599-8601)aGa>aAa	p.R2867K	DNAH14_ENST00000439375.2_Missense_Mutation_p.R3670K|DNAH14_ENST00000430092.1_Missense_Mutation_p.R3670K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2867					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TCCCAGTCTAGACTTACTAGT	0.338													G|||	2650	0.529153	0.6407	0.4697	5008	,	,		17939	0.5089		0.4046	False		,,,				2504	0.5695				p.R3670K		Atlas-SNP	.											.	DNAH14	300	.	0			c.G11009A						PASS	.						48.0	44.0	45.0					1																	225534348		692	1585	2277	SO:0001583	missense	127602	exon69			AGTCTAGACTTAC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8600G>A	1.37:g.225534348G>A	ENSP00000409472:p.Arg2867Lys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	148	64	0.432432	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	G	1.991	-0.431729	0.04669	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.39997	1.05;1.05;1.05	4.94	-3.81	0.04294	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.40213	-0.9575	7	0.02654	T	1	.	6.7277	0.23365	0.6059:0.0:0.272:0.1221	rs7535953;rs17522510;rs52812222;rs58063527;rs7535953	3670	Q0VDD8-4	.	K	2867;3670;3670	ENSP00000409472:R2867K;ENSP00000414402:R3670K;ENSP00000392061:R3670K	ENSP00000414402:R3670K	R	+	2	0	DNAH14	223600971	0.000000	0.05858	0.000000	0.03702	0.463000	0.32649	-0.207000	0.09384	-0.823000	0.04301	-0.357000	0.07601	AGA	G|0.499;A|0.501	0.501	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
NCOA4	8031	hgsc.bcm.edu	37	10	51568378	51568378	+	Intron	SNP	T	T	G	rs10761581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:51568378T>G	ENST00000374087.4	+	1	70				NCOA4_ENST00000498586.1_Intron|NCOA4_ENST00000452682.1_Missense_Mutation_p.F8V|NCOA4_ENST00000438493.1_Missense_Mutation_p.F8V|NCOA4_ENST00000430396.2_Intron|NCOA4_ENST00000414907.2_Intron	NM_001145263.1	NP_001138735.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4						androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)	p.F8V(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						GTTGACCACTTTTGCTCTAGC	0.418			T	RET	papillary thyroid								g|||	2302	0.459665	0.3222	0.3228	5008	,	,		16941	0.5119		0.4433	False		,,,				2504	0.7055				p.F8V		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	NCOA4_ENST00000452682,NS,carcinoma,0,1	NCOA4	58	1	1	Substitution - Missense(1)	stomach(1)	c.T22G						PASS	.	G	VAL/PHE,VAL/PHE,	492,892		87,318,287	94.0	87.0	89.0		22,22,	0.9	0.0	10	dbSNP_120	89	1396,1786		306,784,501	yes	missense,missense,intron	NCOA4	NM_001145260.1,NM_001145261.1,NM_001145263.1	50,50,	393,1102,788	GG,GT,TT		43.8718,35.5491,41.3491	benign,benign,	8/651,8/631,	51568378	1888,2678	692	1591	2283	SO:0001627	intron_variant	8031	exon2			ACCACTTTTGCTC	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"""RET-activating gene ELE1"""	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000374087.4:c.-15+3082T>G	10.37:g.51568378T>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000374087.4	37	CCDS7237.1	895	0.4097985347985348	146	0.2967479674796748	119	0.3287292817679558	301	0.5262237762237763	329	0.4340369393139842	G	0.006	-2.037693	0.00402	0.355491	0.438718	ENSG00000138293	ENST00000438493;ENST00000452682	T;T	0.12465	2.71;2.68	2.02	0.858	0.19030	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45352	-0.9267	7	0.02654	T	1	.	6.7255	0.23355	0.0:0.0:0.2523:0.7477	rs10761581;rs17720176;rs10761581	8	E9PAV7	.	V	8	ENSP00000405146:F8V;ENSP00000395465:F8V	ENSP00000405146:F8V	F	+	1	0	NCOA4	51238384	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.060000	0.11712	-0.120000	0.11809	-1.509000	0.00949	TTT	T|0.572;G|0.428	0.428	strong		0.418	NCOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048050.1	NM_005437	
ITGA2	3673	hgsc.bcm.edu	37	5	52347369	52347369	+	Silent	SNP	C	C	T	rs1126643	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:52347369C>T	ENST00000296585.5	+	7	902	c.759C>T	c.(757-759)ttC>ttT	p.F253F		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	253	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				CAAACACATTCGGAGCAATTC	0.328													C|||	1691	0.33766	0.2806	0.4424	5008	,	,		16165	0.2827		0.4026	False		,,,				2504	0.3303				p.F253F		Atlas-SNP	.											.	ITGA2	211	.	0			c.C759T	GRCh37	CM993453	ITGA2	M	rs1126643	PASS	.	C		1343,3063	448.1+/-348.6	209,925,1069	108.0	105.0	106.0		759	4.9	1.0	5	dbSNP_86	106	3414,5186	503.8+/-376.0	651,2112,1537	no	coding-synonymous	ITGA2	NM_002203.3		860,3037,2606	TT,TC,CC		39.6977,30.4812,36.5754		253/1182	52347369	4757,8249	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon7			CACATTCGGAGCA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.759C>T	5.37:g.52347369C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			C|0.629;T|0.371	0.371	strong		0.328	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
VPS13C	54832	hgsc.bcm.edu	37	15	62299603	62299603	+	Silent	SNP	T	T	G	rs9635356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:62299603T>G	ENST00000261517.5	-	15	1267	c.1194A>C	c.(1192-1194)atA>atC	p.I398I	VPS13C_ENST00000249837.3_Silent_p.I355I|VPS13C_ENST00000395898.3_Silent_p.I355I|VPS13C_ENST00000395896.4_Silent_p.I398I	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						TGTGCTTTTTTATGTTACTCC	0.318													T|||	545	0.108826	0.0484	0.2017	5008	,	,		17674	0.2063		0.0268	False		,,,				2504	0.1084				p.I398I		Atlas-SNP	.											.	VPS13C	506	.	0			c.A1194C						PASS	.	T	,,,	259,4145	146.1+/-180.8	8,243,1951	193.0	179.0	184.0		1194,1065,1065,1194	4.3	1.0	15	dbSNP_119	184	192,8404	82.9+/-145.4	2,188,4108	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	,,,	10,431,6059	GG,GT,TT		2.2336,5.881,3.4692	,,,	398/3629,355/3711,355/3586,398/3754	62299603	451,12549	2202	4298	6500	SO:0001819	synonymous_variant	54832	exon15			CTTTTTTATGTTA	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.1194A>C	15.37:g.62299603T>G		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	193	89	0.46114	NM_020821		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																			T|0.950;G|0.050	0.050	strong		0.318	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
DHX33	56919	hgsc.bcm.edu	37	17	5354204	5354204	+	Missense_Mutation	SNP	G	G	C	rs11653658	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5354204G>C	ENST00000225296.3	-	9	1647	c.1447C>G	c.(1447-1449)Cat>Gat	p.H483D	DHX33_ENST00000433302.3_Missense_Mutation_p.H259D	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	483			H -> D (in dbSNP:rs11653658).		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						TCATCCTTATGTTCAAGAGCA	0.428													G|||	234	0.0467252	0.0711	0.0389	5008	,	,		19648	0.002		0.0875	False		,,,				2504	0.0235				p.H483D		Atlas-SNP	.											.	DHX33	41	.	0			c.C1447G						PASS	.	G	ASP/HIS,ASP/HIS	356,4050	184.7+/-212.0	12,332,1859	174.0	163.0	167.0		928,1447	4.9	0.8	17	dbSNP_120	167	617,7983	162.2+/-214.9	26,565,3709	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	81,81	38,897,5568	CC,CG,GG		7.1744,8.0799,7.4812	benign,benign	310/535,483/708	5354204	973,12033	2203	4300	6503	SO:0001583	missense	56919	exon9			CCTTATGTTCAAG	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.1447C>G	17.37:g.5354204G>C	ENSP00000225296:p.His483Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	107	0.04899267399267399	24	0.04878048780487805	18	0.049723756906077346	2	0.0034965034965034965	63	0.08311345646437995	G	12.89	2.072280	0.36566	0.080799	0.071744	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.01947	4.54;4.54	5.85	4.87	0.63330	Helicase-associated domain (2);	0.559496	0.19884	N	0.103892	T	0.00073	0.0002	N	0.00135	-2.02	0.22156	N	0.999328	B;B	0.29378	0.243;0.001	B;B	0.34489	0.184;0.0	T	0.49781	-0.8903	10	0.87932	D	0	.	13.2079	0.59807	0.0:0.0:0.7104:0.2896	rs11653658;rs11653658	259;483	Q05BE5;Q9H6R0	.;DHX33_HUMAN	D	483;259	ENSP00000225296:H483D;ENSP00000413779:H259D	ENSP00000225296:H483D	H	-	1	0	DHX33	5294928	0.943000	0.32029	0.797000	0.32132	0.964000	0.63967	3.676000	0.54612	1.461000	0.47929	-0.182000	0.12963	CAT	G|0.935;C|0.065	0.065	strong		0.428	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
MLXIP	22877	hgsc.bcm.edu	37	12	122623000	122623000	+	Silent	SNP	T	T	C	rs4758686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:122623000T>C	ENST00000319080.7	+	14	2418	c.2286T>C	c.(2284-2286)acT>acC	p.T762T	MLXIP_ENST00000538698.1_Silent_p.T369T					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		TGCAGAAGACTGTGGAGTACA	0.627													C|||	2734	0.545927	0.5454	0.6081	5008	,	,		20432	0.4931		0.5596	False		,,,				2504	0.5429				p.T762T	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.T2286C						PASS	.	C		2371,1989		662,1047,471	47.0	52.0	50.0		1876	-9.1	0.7	12	dbSNP_111	50	4397,4161		1138,2121,1020	no	coding-synonymous	MLXIP	NM_014938.3		1800,3168,1491	CC,CT,TT		48.6212,45.6193,47.608		762/920	122623000	6768,6150	2180	4279	6459	SO:0001819	synonymous_variant	22877	exon14			GAAGACTGTGGAG	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.2286T>C	12.37:g.122623000T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_014938		Silent	SNP	ENST00000319080.7	37		1178	0.5393772893772893	256	0.5203252032520326	208	0.574585635359116	290	0.506993006993007	424	0.5593667546174143	C	9.339	1.062615	0.19987	0.543807	0.513788	ENSG00000175727	ENST00000542417	.	.	.	5.03	-9.09	0.00717	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999966	.	.	.	.	.	.	T	0.38779	-0.9645	3	.	.	.	-27.2568	4.0873	0.09953	0.5082:0.0964:0.2638:0.1316	rs4758686;rs17563695;rs57585600	.	.	.	P	98	.	.	L	+	2	0	MLXIP	121188953	0.000000	0.05858	0.659000	0.29680	0.920000	0.55202	-2.579000	0.00907	-1.934000	0.01051	-2.078000	0.00380	CTG	T|0.472;C|0.528	0.528	strong		0.627	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
UMODL1	89766	hgsc.bcm.edu	37	21	43531008	43531008	+	Missense_Mutation	SNP	T	T	C	rs220126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43531008T>C	ENST00000408910.2	+	11	1676	c.1676T>C	c.(1675-1677)aTg>aCg	p.M559T	UMODL1_ENST00000400427.1_Missense_Mutation_p.M487T|UMODL1_ENST00000400424.2_Missense_Mutation_p.M487T|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000408989.2_Missense_Mutation_p.M559T	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	559			M -> T (in dbSNP:rs220126). {ECO:0000269|PubMed:15194491, ECO:0000269|PubMed:16026467}.		adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GTGAGCCCCATGGGCGGTGGA	0.632													C|||	3847	0.768171	0.5817	0.8516	5008	,	,		15312	0.8909		0.8042	False		,,,				2504	0.7975				p.M559T	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T1676C						PASS	.	C	THR/MET,THR/MET,THR/MET,THR/MET	2745,1387		923,899,244	22.0	28.0	26.0		1676,1460,1460,1676	1.9	0.0	21	dbSNP_79	26	6724,1690		2705,1314,188	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	81,81,81,81	3628,2213,432	CC,CT,TT		20.0856,33.5673,24.5257	benign,benign,benign,benign	559/1319,487/1375,487/1247,559/1447	43531008	9469,3077	2066	4207	6273	SO:0001583	missense	89766	exon11			GCCCCATGGGCGG		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.1676T>C	21.37:g.43531008T>C	ENSP00000386147:p.Met559Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	1709	0.7825091575091575	284	0.5772357723577236	302	0.8342541436464088	503	0.8793706293706294	620	0.8179419525065963	C	0.005	-2.142517	0.00332	0.664327	0.799144	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.70045	-0.45;-0.44;-0.45;-0.44	3.7	1.88	0.25563	.	0.642001	0.12970	N	0.424186	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	0.38373	-0.9664	9	0.02654	T	1	-0.9973	6.4164	0.21719	0.0:0.704:0.0:0.296	rs220126;rs57829620	559;559	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	T	487;487;559;559	ENSP00000383279:M487T;ENSP00000383276:M487T;ENSP00000386126:M559T;ENSP00000386147:M559T	ENSP00000383276:M487T	M	+	2	0	UMODL1	42404077	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.208000	0.09371	0.188000	0.20168	-0.119000	0.15052	ATG	T|0.215;C|0.785	0.785	strong		0.632	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
OR52N1	79473	hgsc.bcm.edu	37	11	5809230	5809230	+	Silent	SNP	G	G	A	rs12794769	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5809230G>A	ENST00000317078.1	-	1	816	c.817C>T	c.(817-819)Cta>Tta	p.L273L	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	273						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(15)|prostate(2)|skin(3)	31		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		TGTATGTGTAGAGGAATGGTG	0.458													G|||	817	0.163139	0.034	0.1455	5008	,	,		12548	0.2927		0.1471	False		,,,				2504	0.2331				p.L273L		Atlas-SNP	.											.	OR52N1	70	.	0			c.C817T						PASS	.	G		262,3992		60,142,1925	157.0	145.0	149.0		817	2.8	0.9	11	dbSNP_121	149	1217,6963		280,657,3153	no	coding-synonymous	OR52N1	NM_001001913.1		340,799,5078	AA,AG,GG		14.8778,6.1589,11.8948		273/321	5809230	1479,10955	2127	4090	6217	SO:0001819	synonymous_variant	79473	exon1			TGTGTAGAGGAAT	AB065538	CCDS31398.1	11p15.4	2012-08-09			ENSG00000181001	ENSG00000181001		"""GPCR / Class A : Olfactory receptors"""	14853	protein-coding gene	gene with protein product							Standard	NM_001001913		Approved		uc010qzo.2	Q8NH53	OTTHUMG00000168800	ENST00000317078.1:c.817C>T	11.37:g.5809230G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001001913	Q6IFF6	Silent	SNP	ENST00000317078.1	37	CCDS31398.1																																																																																			G|0.828;A|0.172	0.172	strong		0.458	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
ABHD15	116236	hgsc.bcm.edu	37	17	27889986	27889986	+	Missense_Mutation	SNP	T	T	C	rs542939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:27889986T>C	ENST00000307201.4	-	2	1170	c.1000A>G	c.(1000-1002)Acc>Gcc	p.T334A	RP11-68I3.2_ENST00000581474.1_RNA	NM_198147.2	NP_937790.2	Q6UXT9	ABH15_HUMAN	abhydrolase domain containing 15	334			T -> A (in dbSNP:rs542939). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	10						TCCCAGTAGGTATCCCAGCTG	0.602													T|||	3846	0.767971	0.8109	0.6585	5008	,	,		18388	0.8998		0.6531	False		,,,				2504	0.7699				p.T334A		Atlas-SNP	.											.	ABHD15	18	.	0			c.A1000G						PASS	.	T	ALA/THR	3388,1018	725.8+/-409.7	1293,802,108	68.0	62.0	64.0		1000	2.6	1.0	17	dbSNP_83	64	5642,2958	666.5+/-402.4	1840,1962,498	yes	missense	ABHD15	NM_198147.2	58	3133,2764,606	CC,CT,TT		34.3953,23.1049,30.5705	benign	334/469	27889986	9030,3976	2203	4300	6503	SO:0001583	missense	116236	exon2			AGTAGGTATCCCA	AK056717	CCDS32602.1	17q11.2	2009-11-20			ENSG00000168792	ENSG00000168792		"""Abhydrolase domain containing"""	26971	protein-coding gene	gene with protein product						12975309	Standard	NM_198147		Approved		uc002hed.2	Q6UXT9		ENST00000307201.4:c.1000A>G	17.37:g.27889986T>C	ENSP00000302657:p.Thr334Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_198147	Q96EC5	Missense_Mutation	SNP	ENST00000307201.4	37	CCDS32602.1	1665	0.7623626373626373	395	0.8028455284552846	243	0.6712707182320442	520	0.9090909090909091	507	0.6688654353562006	T	9.089	1.001241	0.19121	0.768951	0.656047	ENSG00000168792	ENST00000307201	T	0.10763	2.84	5.92	2.57	0.30868	.	0.492803	0.21005	N	0.081795	T	0.00012	0.0000	N	0.02916	-0.46	0.44539	P	0.0025020000000000042	B	0.19935	0.04	B	0.20184	0.028	T	0.09952	-1.0651	9	0.23891	T	0.37	-10.5565	7.8137	0.29247	0.0:0.3108:0.0:0.6892	rs542939;rs3809794;rs52828212;rs59993345;rs542939	334	Q6UXT9	ABH15_HUMAN	A	334	ENSP00000302657:T334A	ENSP00000302657:T334A	T	-	1	0	ABHD15	24914112	0.040000	0.19996	0.994000	0.49952	0.997000	0.91878	0.092000	0.15066	0.510000	0.28216	0.533000	0.62120	ACC	T|0.268;C|0.732	0.732	strong		0.602	ABHD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447796.2	NM_198147	
SGCG	6445	hgsc.bcm.edu	37	13	23824783	23824783	+	Silent	SNP	T	T	G	rs1800351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	79	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	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	
WDR4	10785	hgsc.bcm.edu	37	21	44273858	44273858	+	Missense_Mutation	SNP	G	G	A	rs15736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44273858G>A	ENST00000398208.2	-	9	855	c.796C>T	c.(796-798)Cct>Tct	p.P266S	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Missense_Mutation_p.P266S	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)		TAGACCACAGGAGTGCTTGCC	0.622													G|||	1720	0.34345	0.6543	0.232	5008	,	,		18571	0.0744		0.3767	False		,,,				2504	0.2454				p.P266S		Atlas-SNP	.											.	WDR4	35	.	0			c.C796T						PASS	.	G	SER/PRO,SER/PRO	2681,1675		865,951,362	20.0	17.0	18.0		796,796	4.5	0.1	21	dbSNP_52	18	3341,5193		705,1931,1631	yes	missense,missense	WDR4	NM_018669.4,NM_033661.3	74,74	1570,2882,1993	AA,AG,GG		39.1493,38.4527,46.7184	benign,benign	266/413,266/413	44273858	6022,6868	2178	4267	6445	SO:0001583	missense	10785	exon9			CCACAGGAGTGCT	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.796C>T	21.37:g.44273858G>A	ENSP00000381266:p.Pro266Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	18	0.642857	NM_018669		Missense_Mutation	SNP	ENST00000398208.2	37	CCDS13691.1	760	0.34798534798534797	329	0.6686991869918699	92	0.2541436464088398	46	0.08041958041958042	293	0.3865435356200528	G	11.05	1.525330	0.27299	0.615473	0.391493	ENSG00000160193	ENST00000330317;ENST00000398208	T;T	0.26957	1.7;1.7	4.52	4.52	0.55395	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.230781	0.36234	N	0.002702	T	0.00012	0.0000	M	0.71581	2.175	0.23351	P	0.99785247	P;B	0.40431	0.717;0.314	B;B	0.41271	0.352;0.106	T	0.25328	-1.0135	9	0.18710	T	0.47	-17.5226	14.5336	0.67944	0.0:0.0:1.0:0.0	rs15736;rs7282594;rs16994761;rs17344018;rs17844881;rs17857598;rs52837379;rs57453345;rs15736	265;266	P57081-2;P57081	.;WDR4_HUMAN	S	266	ENSP00000328671:P266S;ENSP00000381266:P266S	ENSP00000328671:P266S	P	-	1	0	WDR4	43146927	1.000000	0.71417	0.134000	0.22075	0.274000	0.26718	4.410000	0.59774	2.227000	0.72691	0.609000	0.83330	CCT	G|0.581;A|0.419	0.419	strong		0.622	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
SOHLH2	54937	hgsc.bcm.edu	37	13	36744800	36744800	+	Silent	SNP	G	G	A	rs2296967	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:36744800G>A	ENST00000379881.3	-	10	1213	c.1125C>T	c.(1123-1125)taC>taT	p.Y375Y	CCDC169-SOHLH2_ENST00000511166.1_Silent_p.Y452Y|SOHLH2_ENST00000554962.1_Silent_p.Y452Y	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	375					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Y375Y(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		CAGTTGCATCGTAGGAAGGGG	0.448													G|||	374	0.0746805	0.003	0.085	5008	,	,		19637	0.0794		0.1014	False		,,,				2504	0.1319				p.Y452Y		Atlas-SNP	.											SOHLH2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1356T						PASS	.	G	,	114,4292	87.8+/-126.4	0,114,2089	161.0	147.0	152.0		1356,1125	1.0	0.0	13	dbSNP_100	152	1028,7572	218.1+/-256.6	62,904,3334	no	coding-synonymous,coding-synonymous	SOHLH2,CCDC169-SOHLH2	NM_001198910.1,NM_017826.2	,	62,1018,5423	AA,AG,GG		11.9535,2.5874,8.7806	,	452/503,375/426	36744800	1142,11864	2203	4300	6503	SO:0001819	synonymous_variant	100526761	exon15			TGCATCGTAGGAA	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.1125C>T	13.37:g.36744800G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	183	89	0.486339	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	37	CCDS9355.1																																																																																			G|0.916;A|0.084	0.084	strong		0.448	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
ZNF202	7753	hgsc.bcm.edu	37	11	123599897	123599897	+	Silent	SNP	G	G	A	rs11825443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123599897G>A	ENST00000529691.1	-	4	858	c.639C>T	c.(637-639)gaC>gaT	p.D213D	ZNF202_ENST00000336139.4_Silent_p.D213D|ZNF202_ENST00000530393.1_Silent_p.D213D			O95125	ZN202_HUMAN	zinc finger protein 202	213					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)		CTGCAGGAAGGTCTGGGTCCT	0.502													G|||	130	0.0259585	0.0953	0.0058	5008	,	,		19804	0.0		0.0	False		,,,				2504	0.0				p.D213D		Atlas-SNP	.											.	ZNF202	72	.	0			c.C639T						PASS	.	G		351,4053	181.5+/-209.5	12,327,1863	72.0	65.0	67.0		639	0.8	0.9	11	dbSNP_120	67	0,8598		0,0,4299	no	coding-synonymous	ZNF202	NM_003455.2		12,327,6162	AA,AG,GG		0.0,7.97,2.6996		213/649	123599897	351,12651	2202	4299	6501	SO:0001819	synonymous_variant	7753	exon6			AGGAAGGTCTGGG	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.639C>T	11.37:g.123599897G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	37	CCDS8443.1																																																																																			G|0.965;A|0.035	0.035	strong		0.502	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
LINGO1	84894	hgsc.bcm.edu	37	15	77907658	77907658	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:77907658C>T	ENST00000355300.6	-	2	765	c.591G>A	c.(589-591)acG>acA	p.T197T	LINGO1_ENST00000561030.1_Silent_p.T191T	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	197					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						ATTTCTCCAGCGTCAGCTGCT	0.602																																					p.T197T		Atlas-SNP	.											.	LINGO1	76	.	0			c.G591A						PASS	.						111.0	119.0	117.0					15																	77907658		2175	4274	6449	SO:0001819	synonymous_variant	84894	exon2			CTCCAGCGTCAGC	AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"""Immunoglobulin superfamily / I-set domain containing"""	21205	protein-coding gene	gene with protein product		609791	"""leucine rich repeat neuronal 6A"""	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.591G>A	15.37:g.77907658C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			.	.	none		0.602	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
C1QTNF6	114904	hgsc.bcm.edu	37	22	37581422	37581422	+	Missense_Mutation	SNP	G	G	C	rs229526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37581422G>C	ENST00000337843.2	-	2	200	c.125C>G	c.(124-126)cCt>cGt	p.P42R	C1QTNF6_ENST00000397110.2_Missense_Mutation_p.P42R|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000255836.6_5'Flank|C1QTNF6_ENST00000470655.1_5'UTR	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	23					protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						CTCCACCATAGGGATCTCACA	0.612													G|||	947	0.189097	0.2769	0.1369	5008	,	,		18321	0.1071		0.2068	False		,,,				2504	0.1738				p.P42R		Atlas-SNP	.											.	C1QTNF6	32	.	0			c.C125G						PASS	.	G	ARG/PRO,ARG/PRO	1169,3237	404.6+/-333.2	155,859,1189	40.0	40.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	125,125	4.5	0.2	22	dbSNP_79	40	1919,6681	338.1+/-322.6	217,1485,2598	yes	missense,missense	C1QTNF6	NM_031910.3,NM_182486.1	103,103	372,2344,3787	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.314,26.532,23.7429	probably-damaging,probably-damaging	42/279,42/279	37581422	3088,9918	2203	4300	6503	SO:0001583	missense	114904	exon2			ACCATAGGGATCT	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.125C>G	22.37:g.37581422G>C	ENSP00000338812:p.Pro42Arg	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_182486	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	394	0.1804029304029304	136	0.2764227642276423	58	0.16022099447513813	55	0.09615384615384616	145	0.19129287598944592	G	11.16	1.557493	0.27827	0.26532	0.22314	ENSG00000133466	ENST00000397110;ENST00000337843	T;T	0.39406	1.08;1.08	4.49	4.49	0.54785	.	0.162471	0.41097	D	0.000960	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	0.9999999999995662	P;P	0.49090	0.919;0.718	P;B	0.45506	0.483;0.387	T	0.12243	-1.0555	9	0.44086	T	0.13	.	15.3686	0.74545	0.0:0.0:1.0:0.0	rs229526;rs17812735;rs52834593;rs59914011;rs229526	42;23	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	R	42	ENSP00000380299:P42R;ENSP00000338812:P42R	ENSP00000338812:P42R	P	-	2	0	C1QTNF6	35911368	1.000000	0.71417	0.229000	0.23960	0.004000	0.04260	3.883000	0.56168	2.039000	0.60335	0.491000	0.48974	CCT	G|0.791;C|0.208	0.208	strong		0.612	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486	
OGFOD3	79701	hgsc.bcm.edu	37	17	80352303	80352303	+	Intron	SNP	G	G	A	rs62079523	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80352303G>A	ENST00000313056.5	-	9	975				OGFOD3_ENST00000578287.1_5'Flank|OGFOD3_ENST00000329197.5_Missense_Mutation_p.P314S	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3							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)										CCCCTCTCGGGCGGGTGGTGA	0.547													-|||	938	0.1873	0.1543	0.1974	5008	,	,		18469	0.003		0.325	False		,,,				2504	0.273				p.P314S		Atlas-SNP	.											.	.	.	.	0			c.C940T						PASS	.	G	,SER/PRO	845,3561	334.7+/-303.5	85,675,1443	160.0	148.0	152.0		,940	-0.6	0.0	17	dbSNP_129	152	2997,5603	464.6+/-366.3	533,1931,1836	yes	intron,missense	C17orf101	NM_024648.2,NM_175902.4	,74	618,2606,3279	AA,AG,GG		34.8488,19.1784,29.5402	,	,314/332	80352303	3842,9164	2203	4300	6503	SO:0001627	intron_variant	79701	exon9			TCTCGGGCGGGTG	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.824-1893C>T	17.37:g.80352303G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Missense_Mutation	SNP	ENST00000313056.5	37	CCDS11811.1	406	0.1858974358974359	80	0.16260162601626016	77	0.212707182320442	1	0.0017482517482517483	248	0.32717678100263853	G	7.804	0.714279	0.15306	0.191784	0.348488	ENSG00000181396	ENST00000329197	T	0.33438	1.41	0.894	-0.635	0.11512	.	0.154371	0.43747	D	0.000533	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.38800	0.648	B	0.31290	0.127	T	0.44802	-0.9304	8	0.59425	D	0.04	.	3.6609	0.08238	0.0:0.0:0.5663:0.4337	rs62079523	314	Q6PK18-2	.	S	314	ENSP00000330075:P314S	ENSP00000330075:P314S	P	-	1	0	C17orf101	77945592	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.380000	0.07427	-0.123000	0.11745	0.420000	0.28162	CCC	G|0.728;A|0.272	0.272	strong		0.547	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
PSMG4	389362	hgsc.bcm.edu	37	6	3264527	3264527	+	Intron	SNP	T	T	C	rs200271803|rs4959789	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3264527T>C	ENST00000438998.2	+	2	379				PSMG4_ENST00000380306.4_Intron|PSMG4_ENST00000419065.2_Missense_Mutation_p.L112P|PSMG4_ENST00000380305.4_Intron|PSMG4_ENST00000451246.2_Intron|PSMG4_ENST00000473000.2_3'UTR	NM_001128591.1	NP_001122063.1	Q5JS54	PSMG4_HUMAN	proteasome (prosome, macropain) assembly chaperone 4											endometrium(1)	1						TGCTCCACTCTTCCCACACCC	0.597													C|||	3091	0.617212	0.3033	0.7651	5008	,	,		23626	0.6647		0.8429	False		,,,				2504	0.6554				p.L112P		Atlas-SNP	.											PSMG4_ENST00000419065,colon,carcinoma,0,4	PSMG4	23	4	0			c.T335C						PASS	.						202.0	156.0	170.0					6																	3264527		692	1591	2283	SO:0001627	intron_variant	389362	exon3			CCACTCTTCCCAC		CCDS47360.1, CCDS47361.1, CCDS47362.1	6p25.2	2010-06-23	2008-02-25	2008-02-25	ENSG00000180822	ENSG00000180822			21108	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 86"""	C6orf86		17707236	Standard	NM_001128591		Approved	PAC4	uc010jnl.1	Q5JS54	OTTHUMG00000014142	ENST00000438998.2:c.250+534T>C	6.37:g.3264527T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_001128592	C9J2F8|F8WBZ2|Q5JS53|Q5JS56	Missense_Mutation	SNP	ENST00000438998.2	37	CCDS47361.1	1170	0.5357142857142857	141	0.2865853658536585	227	0.6270718232044199	311	0.5437062937062938	491	0.6477572559366754	C	2.996	-0.207044	0.06180	.	.	ENSG00000180822	ENST00000419065	.	.	.	3.38	0.507	0.16967	.	.	.	.	.	T	0.07188	0.0182	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22977	-1.0201	7	0.87932	D	0	.	2.7921	0.05391	0.203:0.4434:0.0:0.3536	rs4959789	112	C9J2F8	.	P	112	.	ENSP00000392353:L112P	L	+	2	0	PSMG4	3209526	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.672000	0.05244	-0.132000	0.11557	-1.212000	0.01626	CTT	T|0.464;C|0.536	0.536	strong		0.597	PSMG4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039678.2		
COL5A3	50509	hgsc.bcm.edu	37	19	10089262	10089262	+	Silent	SNP	G	G	A	rs12610207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10089262G>A	ENST00000264828.3	-	41	3091	c.3006C>T	c.(3004-3006)ccC>ccT	p.P1002P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1002	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.V1003fs*9(1)		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)			TGGCCCCCACGGGCCCTGGGG	0.542													g|||	3249	0.648762	0.9539	0.4798	5008	,	,		16038	0.5466		0.5229	False		,,,				2504	0.591				p.P1002P		Atlas-SNP	.											.	COL5A3	243	.	1	Insertion - Frameshift(1)	upper_aerodigestive_tract(1)	c.C3006T						PASS	.			3890,516	765.1+/-413.3	1729,432,42	33.0	30.0	31.0		3006	-3.6	0.0	19	dbSNP_120	31	4717,3883	588.4+/-392.4	1303,2111,886	no	coding-synonymous	COL5A3	NM_015719.3		3032,2543,928	AA,AG,GG		45.1512,11.7113,33.8229		1002/1746	10089262	8607,4399	2203	4300	6503	SO:0001819	synonymous_variant	50509	exon41			CCCCACGGGCCCT	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.3006C>T	19.37:g.10089262G>A		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	273	138	0.505495	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			G|0.342;A|0.658	0.658	strong		0.542	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
NEDD4	4734	hgsc.bcm.edu	37	15	56207811	56207811	+	Missense_Mutation	SNP	T	T	G	rs62043855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:56207811T>G	ENST00000508342.1	-	1	1518	c.1219A>C	c.(1219-1221)Aat>Cat	p.N407H	NEDD4_ENST00000435532.3_Intron|NEDD4_ENST00000338963.2_Missense_Mutation_p.N407H|NEDD4_ENST00000506154.1_Missense_Mutation_p.N407H	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	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	203	107	0.527094	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	
HIF3A	64344	hgsc.bcm.edu	37	19	46823702	46823702	+	Missense_Mutation	SNP	A	A	G	rs3764609	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46823702A>G	ENST00000377670.4	+	9	1059	c.1028A>G	c.(1027-1029)cAg>cGg	p.Q343R	HIF3A_ENST00000420102.2_Missense_Mutation_p.Q292R|HIF3A_ENST00000600383.1_Missense_Mutation_p.Q274R|HIF3A_ENST00000339613.2_Missense_Mutation_p.Q287R|HIF3A_ENST00000472815.1_Missense_Mutation_p.Q274R|HIF3A_ENST00000244303.6_Missense_Mutation_p.Q274R|HIF3A_ENST00000300862.3_Missense_Mutation_p.Q341R|AC007193.10_ENST00000596807.1_RNA	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	343			Q -> R (in dbSNP:rs3764609). {ECO:0000269|PubMed:15489334}.		cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		TACCCCAGCCAGGTGGAAGAG	0.597													G|||	1131	0.225839	0.0408	0.2824	5008	,	,		16275	0.3988		0.1809	False		,,,				2504	0.3037				p.Q343R		Atlas-SNP	.											HIF3A_ENST00000377670,brain,glioma,0,2	HIF3A	154	2	0			c.A1028G						scavenged	.	G	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	319,4087	795.8+/-415.3	12,295,1896	75.0	71.0	72.0		821,1022,1028,821	2.7	1.0	19	dbSNP_107	72	1601,6999	742.1+/-407.2	162,1277,2861	yes	missense,missense,missense,missense	HIF3A	NM_022462.4,NM_152794.3,NM_152795.3,NM_152796.2	43,43,43,43	174,1572,4757	GG,GA,AA		18.6163,7.2401,14.7624	benign,benign,benign,benign	274/601,341/668,343/670,274/451	46823702	1920,11086	2203	4300	6503	SO:0001583	missense	64344	exon9			CCAGCCAGGTGGA	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1028A>G	19.37:g.46823702A>G	ENSP00000366898:p.Gln343Arg	Somatic	48	2	0.0416667		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	37	CCDS12681.2	508	0.2326007326007326	20	0.04065040650406504	88	0.2430939226519337	254	0.44405594405594406	146	0.19261213720316622	G	11.06	1.528818	0.27387	0.072401	0.186163	ENSG00000124440	ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	4.85	2.68	0.31781	.	0.167273	0.28815	N	0.014058	T	0.00012	0.0000	N	0.01576	-0.805	0.58432	P	9.000000000036756E-6	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.46748	-0.9169	9	0.30078	T	0.28	.	5.1771	0.15141	0.1682:0.0:0.6716:0.1603	rs3764609;rs52805117;rs59819378;rs3764609	292;274;341;287;343;343	F5H884;B4DNA2;Q9Y2N7-2;A8MPQ1;Q9Y2N7;B0M185	.;.;.;.;HIF3A_HUMAN;.	R	343;343;274;287;287;341;292	ENSP00000366898:Q343R;ENSP00000244303:Q274R;ENSP00000341877:Q287R;ENSP00000300862:Q341R;ENSP00000407771:Q292R	ENSP00000244302:Q343R	Q	+	2	0	HIF3A	51515542	0.987000	0.35691	0.980000	0.43619	0.385000	0.30292	0.545000	0.23268	0.208000	0.20626	-0.930000	0.02707	CAG	A|0.820;G|0.180	0.180	strong		0.597	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
SLC35G6	643664	hgsc.bcm.edu	37	17	7386173	7386173	+	Silent	SNP	G	G	T	rs181183603		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7386173G>T	ENST00000412468.2	+	2	985	c.870G>T	c.(868-870)gtG>gtT	p.V290V	POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank|ZBTB4_ENST00000311403.4_Intron	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	290	EamA 2.					integral component of membrane (GO:0016021)											ATTCCGAGGTGGTGGTGGCCC	0.587																																					p.V290V		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,+1,1	.	.	1	0			c.G870T						scavenged	.						193.0	180.0	185.0					17																	7386173		2203	4300	6503	SO:0001819	synonymous_variant	643664	exon2			CGAGGTGGTGGTG		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.870G>T	17.37:g.7386173G>T		Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	401	6	0.0149626	NM_001102614		Silent	SNP	ENST00000412468.2	37	CCDS45603.1																																																																																			.	.	weak		0.587	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
MOV10L1	54456	hgsc.bcm.edu	37	22	50582550	50582550	+	Silent	SNP	C	C	A	rs2272836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50582550C>A	ENST00000262794.5	+	18	2466	c.2383C>A	c.(2383-2385)Cgg>Agg	p.R795R	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.R795R|MOV10L1_ENST00000395858.3_Silent_p.R795R|MOV10L1_ENST00000540615.1_Silent_p.R775R|MOV10L1_ENST00000395852.1_5'Flank	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	795					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GCCGGACAGTCGGATTTTAGT	0.557													C|||	1140	0.227636	0.1316	0.3674	5008	,	,		22800	0.2431		0.167	False		,,,				2504	0.3047				p.R795R		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C2383A						PASS	.	C	,,	683,3723	288.9+/-280.1	55,573,1575	273.0	227.0	243.0		2383,2323,2383	4.8	0.7	22	dbSNP_100	243	1568,7032	295.1+/-302.2	141,1286,2873	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	196,1859,4448	AA,AC,CC		18.2326,15.5016,17.3074	,,	795/1166,775/1166,795/1212	50582550	2251,10755	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon18			GACAGTCGGATTT	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2383C>A	22.37:g.50582550C>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	244	124	0.508197	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.812;A|0.188	0.188	strong		0.557	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232564297	232564297	+	Missense_Mutation	SNP	T	T	A	rs3210731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:232564297T>A	ENST00000366630.1	-	16	4628	c.4270A>T	c.(4270-4272)Atg>Ttg	p.M1424L	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.M498L|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.M1424L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1424			M -> L (in dbSNP:rs3210731).		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)				ATGACATCCATCTCACTATAC	0.388													T|||	470	0.0938498	0.0371	0.1801	5008	,	,		18168	0.003		0.1909	False		,,,				2504	0.1033				p.M1424L		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.A4270T						PASS	.	T	LEU/MET	262,3590		8,246,1672	76.0	69.0	71.0		4270	2.2	1.0	1	dbSNP_105	71	1592,6702		137,1318,2692	yes	missense	SIPA1L2	NM_020808.3	15	145,1564,4364	AA,AT,TT		19.1946,6.8017,15.2643	benign	1424/1723	232564297	1854,10292	1926	4147	6073	SO:0001583	missense	57568	exon15			CATCCATCTCACT	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.4270A>T	1.37:g.232564297T>A	ENSP00000355589:p.Met1424Leu	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	228	111	0.486842	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	223	0.1021062271062271	22	0.044715447154471545	65	0.17955801104972377	0	0.0	136	0.17941952506596306	T	11.79	1.743600	0.30865	0.068017	0.191946	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.28666	1.6;1.6;1.6	5.86	2.18	0.27775	.	0.562852	0.20407	N	0.092929	T	0.00039	0.0001	N	0.22421	0.69	0.42286	P	0.007882999999999973	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30357	-0.9981	9	0.24483	T	0.36	-10.3789	2.2509	0.04043	0.1274:0.1339:0.1335:0.6052	rs3210731;rs7516919;rs17178860;rs17414777;rs52797543;rs7516919	1424;498	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	L	1424;1424;498	ENSP00000355589:M1424L;ENSP00000262861:M1424L;ENSP00000309102:M498L	ENSP00000262861:M1424L	M	-	1	0	SIPA1L2	230630920	0.624000	0.27102	0.962000	0.40283	0.789000	0.44602	0.529000	0.23019	0.114000	0.18032	0.533000	0.62120	ATG	T|0.624;A|0.376	0.376	strong		0.388	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
KDM4C	23081	hgsc.bcm.edu	37	9	7170006	7170006	+	Intron	SNP	G	G	A	rs7022348	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:7170006G>A	ENST00000381309.3	+	21	3559				KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.S1037N|KDM4C_ENST00000428870.2_Intron	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C						histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						TCTAAAAAAAGCCAATGCAAC	0.398													G|||	667	0.133187	0.1876	0.1369	5008	,	,		19592	0.001		0.2366	False		,,,				2504	0.0869				p.S1037N		Atlas-SNP	.											.	KDM4C	186	.	0			c.G3110A						PASS	.	G	ASN/SER,	232,1152		24,184,484	50.0	44.0	46.0		3110,	0.9	0.0	9	dbSNP_116	46	728,2454		83,562,946	yes	missense,intron	KDM4C	NM_001146694.1,NM_015061.3	46,	107,746,1430	AA,AG,GG		22.8787,16.763,21.025	,	1037/1048,	7170006	960,3606	692	1591	2283	SO:0001627	intron_variant	23081	exon21			AAAAAAGCCAATG	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2994+116G>A	9.37:g.7170006G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	316	0.1446886446886447	87	0.17682926829268292	56	0.15469613259668508	0	0.0	173	0.22823218997361477	G	11.29	1.595464	0.28445	0.16763	0.228787	ENSG00000107077	ENST00000381306	T	0.16196	2.36	4.15	0.896	0.19253	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50171	P	1.4300000000000423E-4	B	0.06786	0.001	B	0.09377	0.004	T	0.45556	-0.9253	6	.	.	.	.	6.7317	0.23387	0.3685:0.0:0.6315:0.0	rs7022348;rs7022348	1037	Q9H3R0-2	.	N	1037	ENSP00000370707:S1037N	.	S	+	2	0	KDM4C	7160006	0.000000	0.05858	0.011000	0.14972	0.016000	0.09150	-0.100000	0.10990	0.173000	0.19788	0.467000	0.42956	AGC	G|0.846;A|0.154	0.154	strong		0.398	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
TPSD1	23430	hgsc.bcm.edu	37	16	1306973	1306973	+	Missense_Mutation	SNP	A	A	G	rs79313952		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306973A>G	ENST00000211076.3	+	3	578	c.430A>G	c.(430-432)Atc>Gtc	p.I144V	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.I137V	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	144	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CTCCAGCCACATCCACACGGT	0.642																																					p.I144V		Atlas-SNP	.											TPSD1,NS,NS,0,1	TPSD1	47	1	0			c.A430G						PASS	.						49.0	47.0	47.0					16																	1306973		2198	4299	6497	SO:0001583	missense	23430	exon3			AGCCACATCCACA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.430A>G	16.37:g.1306973A>G	ENSP00000211076:p.Ile144Val	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	529	180	0.340265	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	761	0.3484432234432234	140	0.2845528455284553	110	0.30386740331491713	250	0.4370629370629371	261	0.34432717678100266	a	0.001	-2.882799	0.00061	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.85702	-2.02;-2.02	2.55	-5.1	0.02911	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.756136	0.11242	N	0.584558	T	0.00012	0.0000	N	0.04043	-0.29	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.13407	0.009;0.009	T	0.23404	-1.0189	9	0.02654	T	1	.	0.0994	0.00046	0.3174:0.1569:0.211:0.3148	.	128;144	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	V	137;144	ENSP00000380668:I137V;ENSP00000211076:I144V	ENSP00000211076:I144V	I	+	1	0	TPSD1	1246974	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-1.101000	0.03336	-1.132000	0.02907	-1.639000	0.00775	ATC	A|0.652;G|0.348	0.348	strong		0.642	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
FMN2	56776	hgsc.bcm.edu	37	1	240370952	240370952	+	Missense_Mutation	SNP	C	C	T	rs201741828	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240370952C>T	ENST00000319653.9	+	5	3070	c.2840C>T	c.(2839-2841)cCt>cTt	p.P947L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	947	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCTCCGCCCCCTCTACCCGGA	0.692																																					p.P947L		Atlas-SNP	.											FMN2,NS,carcinoma,+1,2	FMN2	451	2	0			c.C2840T						PASS	.						25.0	30.0	29.0					1																	240370952		2201	4295	6496	SO:0001583	missense	56776	exon5			CGCCCCCTCTACC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2840C>T	1.37:g.240370952C>T	ENSP00000318884:p.Pro947Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	127	12	0.0944882	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	C	10.92	1.486864	0.26686	.	.	ENSG00000155816	ENST00000319653	T	0.57436	0.4	4.22	3.31	0.37934	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.64843	0.2635	M	0.78456	2.415	0.80722	D	1	D	0.60575	0.988	P	0.59761	0.863	T	0.65421	-0.6172	8	.	.	.	.	7.9072	0.29769	0.0:0.7888:0.0:0.2112	.	947	Q9NZ56	FMN2_HUMAN	L	947	ENSP00000318884:P947L	.	P	+	2	0	FMN2	238437575	0.192000	0.23301	0.105000	0.21289	0.009000	0.06853	1.683000	0.37638	1.135000	0.42183	-0.361000	0.07541	CCT	C|0.986;G|0.000;T|0.014	0.014	strong		0.692	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
OR5L1	219437	hgsc.bcm.edu	37	11	55579102	55579102	+	Missense_Mutation	SNP	C	C	T	rs34961497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	199	0	0		WXS	Illumina HiSeq	Phase_I	227	100	0.440529	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	
FAM71F1	84691	hgsc.bcm.edu	37	7	128359133	128359133	+	Missense_Mutation	SNP	C	C	T	rs6949056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128359133C>T	ENST00000315184.5	+	3	736	c.683C>T	c.(682-684)tCg>tTg	p.S228L	FAM71F1_ENST00000469348.1_3'UTR|FAM71F1_ENST00000485070.1_Missense_Mutation_p.S129L	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	228			S -> L (in dbSNP:rs6949056).							NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						TCAGGAGATTCGAAGGTAAGT	0.527													C|||	1258	0.251198	0.1604	0.2651	5008	,	,		15529	0.4077		0.2376	False		,,,				2504	0.2168				p.S228L		Atlas-SNP	.											.	FAM71F1	42	.	0			c.C683T						PASS	.	C	LEU/SER	698,3708	293.0+/-282.3	51,596,1556	93.0	86.0	88.0		683	2.8	0.0	7	dbSNP_116	88	1978,6622	344.9+/-325.5	233,1512,2555	yes	missense	FAM71F1	NM_032599.2	145	284,2108,4111	TT,TC,CC		23.0,15.842,20.5751	benign	228/345	128359133	2676,10330	2203	4300	6503	SO:0001583	missense	84691	exon3			GAGATTCGAAGGT	AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member A"""	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.683C>T	7.37:g.128359133C>T	ENSP00000326652:p.Ser228Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_032599	Q8IY75|Q8NA48	Missense_Mutation	SNP	ENST00000315184.5	37	CCDS5804.1	576	0.26373626373626374	91	0.18495934959349594	90	0.24861878453038674	213	0.3723776223776224	182	0.24010554089709762	C	13.48	2.248810	0.39797	0.15842	0.23	ENSG00000135248	ENST00000485070;ENST00000315184;ENST00000466842	T;T;T	0.25085	1.82;3.2;1.88	4.69	2.82	0.32997	.	1.292180	0.05116	N	0.489775	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P;P;P;P;D	0.59357	0.918;0.863;0.733;0.772;0.985	B;B;B;B;B	0.40702	0.288;0.176;0.187;0.122;0.338	T	0.39781	-0.9597	9	0.46703	T	0.11	-0.2479	5.5328	0.16995	0.1967:0.7013:0.0:0.102	rs6949056;rs52814344;rs59123459;rs6949056	120;228;228;228;129	B4DY15;F8WC62;Q96KD3-2;Q96KD3;Q8NA48	.;.;.;F71F1_HUMAN;.	L	129;228;84	ENSP00000418192:S129L;ENSP00000326652:S228L;ENSP00000417930:S84L	ENSP00000326652:S228L	S	+	2	0	FAM71F1	128146369	0.001000	0.12720	0.005000	0.12908	0.129000	0.20672	0.676000	0.25247	0.666000	0.31087	0.591000	0.81541	TCG	C|0.765;N|0.000	.	strong		0.527	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599	
ZNF214	7761	hgsc.bcm.edu	37	11	7022360	7022360	+	Missense_Mutation	SNP	A	A	C	rs2239734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7022360A>C	ENST00000278314.4	-	3	869	c.554T>G	c.(553-555)aTa>aGa	p.I185R	ZNF214_ENST00000531083.1_5'Flank|ZNF214_ENST00000536068.1_Missense_Mutation_p.I185R	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	185			I -> R (in dbSNP:rs2239734).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		ATGCTGAACTATGAGCTTCTG	0.433													A|||	522	0.104233	0.0378	0.1542	5008	,	,		18495	0.128		0.1083	False		,,,				2504	0.1299				p.I185R	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.T554G						PASS	.	A	ARG/ILE	262,4138	146.1+/-180.8	6,250,1944	105.0	105.0	105.0		554	3.1	0.9	11	dbSNP_98	105	843,7745	192.7+/-238.6	44,755,3495	yes	missense	ZNF214	NM_013249.2	97	50,1005,5439	CC,CA,AA		9.816,5.9545,8.5079	possibly-damaging	185/607	7022360	1105,11883	2200	4294	6494	SO:0001583	missense	7761	exon3			TGAACTATGAGCT	AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.554T>G	11.37:g.7022360A>C	ENSP00000278314:p.Ile185Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_013249	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	37	CCDS31418.1	241	0.11034798534798534	13	0.026422764227642278	56	0.15469613259668508	89	0.1555944055944056	83	0.10949868073878628	A	6.532	0.466409	0.12402	0.059545	0.09816	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.08008	3.14;3.14	4.29	3.12	0.35913	.	0.444056	0.19246	N	0.119042	T	0.00012	0.0000	N	0.08118	0	0.58432	P	4.000000000004E-6	B	0.09022	0.002	B	0.04013	0.001	T	0.43556	-0.9384	9	0.25106	T	0.35	.	7.7734	0.29021	0.7869:0.2131:0.0:0.0	rs2239734;rs17278329;rs52798655;rs57682570;rs2239734	185	Q9UL59	ZN214_HUMAN	R	185	ENSP00000278314:I185R;ENSP00000445373:I185R	ENSP00000278314:I185R	I	-	2	0	ZNF214	6978936	0.000000	0.05858	0.916000	0.36221	0.940000	0.58332	0.082000	0.14847	0.759000	0.33084	0.533000	0.62120	ATA	A|0.909;C|0.091	0.091	strong		0.433	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
SPATC1L	84221	hgsc.bcm.edu	37	21	47581949	47581949	+	Missense_Mutation	SNP	C	C	T	rs113146399	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47581949C>T	ENST00000291672.5	-	4	1638	c.577G>A	c.(577-579)Gcg>Acg	p.A193T	SPATC1L_ENST00000330205.6_Missense_Mutation_p.A39T	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	193																	ACCACGCGCGCGTCCTTCTCG	0.697													C|||	202	0.0403355	0.0106	0.0504	5008	,	,		12184	0.0139		0.0954	False		,,,				2504	0.044				p.A193T		Atlas-SNP	.											.	.	.	.	0			c.G577A						PASS	.	C	THR/ALA,THR/ALA	71,4299		0,71,2114	22.0	19.0	20.0		577,115	2.2	0.9	21	dbSNP_132	20	729,7835		22,685,3575	yes	missense,missense	C21orf56	NM_001142854.1,NM_032261.4	58,58	22,756,5689	TT,TC,CC		8.5124,1.6247,6.1852	benign,benign	193/341,39/187	47581949	800,12134	2185	4282	6467	SO:0001583	missense	84221	exon4			CGCGCGCGTCCTT	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.577G>A	21.37:g.47581949C>T	ENSP00000291672:p.Ala193Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	109	0.04990842490842491	6	0.012195121951219513	23	0.06353591160220995	8	0.013986013986013986	72	0.09498680738786279	C	14.99	2.700515	0.48307	0.016247	0.085124	ENSG00000160284	ENST00000330205;ENST00000291672	T;T	0.41400	1.0;1.61	4.1	2.24	0.28232	.	0.295993	0.24231	N	0.040356	T	0.00666	0.0022	N	0.08118	0	0.09310	N	0.999998	B	0.26935	0.164	B	0.17433	0.018	T	0.07462	-1.0771	10	0.38643	T	0.18	-23.1208	6.861	0.24067	0.0:0.7752:0.0:0.2248	.	193	Q9H0A9	CU056_HUMAN	T	39;193	ENSP00000333869:A39T;ENSP00000291672:A193T	ENSP00000291672:A193T	A	-	1	0	C21orf56	46406377	0.001000	0.12720	0.902000	0.35471	0.941000	0.58515	0.477000	0.22196	0.720000	0.32209	0.655000	0.94253	GCG	C|0.944;T|0.056	0.056	strong		0.697	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
STOML1	9399	hgsc.bcm.edu	37	15	74277795	74277795	+	Silent	SNP	T	T	C	rs10851866	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:74277795T>C	ENST00000316900.5	-	5	778	c.654A>G	c.(652-654)gcA>gcG	p.A218A	STOML1_ENST00000316911.6_Silent_p.A168A|STOML1_ENST00000561656.1_Silent_p.A131A|STOML1_ENST00000359750.4_Silent_p.A218A|STOML1_ENST00000541638.1_Silent_p.A176A|STOML1_ENST00000564777.1_Silent_p.A168A	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	218						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CGGCCTCCACTGCCAGCTCCA	0.612													C|||	3436	0.686102	0.8449	0.598	5008	,	,		18179	0.6379		0.6421	False		,,,				2504	0.6288				p.A218A		Atlas-SNP	.											.	STOML1	22	.	0			c.A654G						PASS	.	C		3577,787		1478,621,83	18.0	15.0	16.0		654	-10.4	0.0	15	dbSNP_120	16	5430,3134		1744,1942,596	no	coding-synonymous	STOML1	NM_004809.3		3222,2563,679	CC,CT,TT		36.595,18.0339,30.3295		218/399	74277795	9007,3921	2182	4282	6464	SO:0001819	synonymous_variant	9399	exon5			CTCCACTGCCAGC	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"""stomatin-like 1"", ""stomatin (EBP72)-like 1"""	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.654A>G	15.37:g.74277795T>C		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Silent	SNP	ENST00000316900.5	37	CCDS10254.1																																																																																			T|0.294;C|0.706	0.706	strong		0.612	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809	
SCML4	256380	hgsc.bcm.edu	37	6	108029109	108029109	+	Silent	SNP	T	T	C	rs3734754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	104	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	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	
POSTN	10631	hgsc.bcm.edu	37	13	38156538	38156538	+	Missense_Mutation	SNP	C	C	T	rs117103342	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:38156538C>T	ENST00000379747.4	-	10	1474	c.1357G>A	c.(1357-1359)Gga>Aga	p.G453R	POSTN_ENST00000379749.4_Missense_Mutation_p.G453R|POSTN_ENST00000541179.1_Missense_Mutation_p.G453R|POSTN_ENST00000379742.4_Missense_Mutation_p.G453R|POSTN_ENST00000379743.4_Missense_Mutation_p.G453R|POSTN_ENST00000541481.1_Missense_Mutation_p.G453R	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	453	FAS1 3. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TGTTTGCCTCCGATGGTTTCC	0.373													C|||	17	0.00339457	0.0	0.0101	5008	,	,		17409	0.0		0.0089	False		,,,				2504	0.001				p.G453R		Atlas-SNP	.											.	POSTN	161	.	0			c.G1357A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	4,4402	9.9+/-24.2	0,4,2199	155.0	149.0	151.0		1357,1357,1357,1357	6.1	1.0	13	dbSNP_132	151	77,8523	45.8+/-104.6	1,75,4224	yes	missense,missense,missense,missense	POSTN	NM_001135934.1,NM_001135935.1,NM_001135936.1,NM_006475.2	125,125,125,125	1,79,6423	TT,TC,CC		0.8953,0.0908,0.6228	probably-damaging,probably-damaging,probably-damaging,probably-damaging	453/780,453/782,453/752,453/837	38156538	81,12925	2203	4300	6503	SO:0001583	missense	10631	exon10			TGCCTCCGATGGT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1357G>A	13.37:g.38156538C>T	ENSP00000369071:p.Gly453Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	23.8	4.459234	0.84317	9.08E-4	0.008953	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	6.07	6.07	0.98685	FAS1 domain (5);	0.154285	0.56097	D	0.000022	T	0.79215	0.4408	M	0.61703	1.905	0.47476	D	0.999438	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;0.999;0.951;0.995	T	0.78788	-0.2067	10	0.42905	T	0.14	-22.8572	20.6593	0.99626	0.0:1.0:0.0:0.0	.	453;453;453;453;453;453;453	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	R	453	ENSP00000437959:G453R;ENSP00000369073:G453R;ENSP00000369071:G453R;ENSP00000369067:G453R;ENSP00000369066:G453R;ENSP00000437953:G453R	ENSP00000369066:G453R	G	-	1	0	POSTN	37054538	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	5.590000	0.67530	2.885000	0.99019	0.655000	0.94253	GGA	C|0.994;T|0.006	0.006	strong		0.373	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
ZNF780B	163131	hgsc.bcm.edu	37	19	40540812	40540812	+	Missense_Mutation	SNP	G	G	A	rs115484124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40540812G>A	ENST00000434248.1	-	5	2019	c.1954C>T	c.(1954-1956)Cgt>Tgt	p.R652C	ZNF780B_ENST00000221355.6_Missense_Mutation_p.R504C	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	652					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TTTGAGACACGATTAAAGGAC	0.403													g|||	156	0.0311502	0.0666	0.0101	5008	,	,		22218	0.0069		0.0089	False		,,,				2504	0.046				p.R652C		Atlas-SNP	.											ZNF780B_ENST00000434248,NS,carcinoma,+1,2	ZNF780B	143	2	0			c.C1954T						PASS	.	G	CYS/ARG	266,4134	138.8+/-174.5	5,256,1939	169.0	182.0	178.0		1954	-1.2	0.0	19	dbSNP_132	178	57,8543	35.9+/-90.5	1,55,4244	no	missense	ZNF780B	NM_001005851.2	180	6,311,6183	AA,AG,GG		0.6628,6.0455,2.4846	benign	652/834	40540812	323,12677	2200	4300	6500	SO:0001583	missense	163131	exon5			AGACACGATTAAA	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.1954C>T	19.37:g.40540812G>A	ENSP00000391641:p.Arg652Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	52	0.023809523809523808	34	0.06910569105691057	6	0.016574585635359115	5	0.008741258741258742	7	0.009234828496042216	g	8.444	0.851485	0.17034	0.060455	0.006628	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.16073	2.37;2.37	2.56	-1.21	0.09524	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00695	0.0023	N	0.25957	0.775	0.09310	N	1	B	0.14012	0.009	B	0.06405	0.002	T	0.33214	-0.9877	9	0.33141	T	0.24	.	6.8154	0.23826	0.3924:0.0:0.6076:0.0	.	652	Q9Y6R6	Z780B_HUMAN	C	652;504	ENSP00000391641:R652C;ENSP00000221355:R504C	ENSP00000221355:R504C	R	-	1	0	ZNF780B	45232652	0.000000	0.05858	0.001000	0.08648	0.172000	0.22775	-1.463000	0.02361	-0.088000	0.12506	-0.448000	0.05591	CGT	G|0.979;A|0.021	0.021	strong		0.403	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
NASP	4678	hgsc.bcm.edu	37	1	46073697	46073697	+	Missense_Mutation	SNP	C	C	A	rs200497808	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46073697C>A	ENST00000350030.3	+	6	1201	c.1114C>A	c.(1114-1116)Cca>Aca	p.P372T	NASP_ENST00000402363.3_Missense_Mutation_p.P374T|NASP_ENST00000351223.3_Intron|NASP_ENST00000537798.1_Missense_Mutation_p.P308T|NASP_ENST00000372052.4_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	372	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)	p.P374T(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					GCAGGAGGCTCCAGTTCTCCC	0.507													C|||	5	0.000998403	0.0008	0.0014	5008	,	,		19634	0.001		0.0	False		,,,				2504	0.002				p.P372T		Atlas-SNP	.											NASP,NS,carcinoma,0,3	NASP	77	3	1	Substitution - Missense(1)	skin(1)	c.C1114A						scavenged	.						111.0	118.0	116.0					1																	46073697		2203	4300	6503	SO:0001583	missense	4678	exon6			GAGGCTCCAGTTC	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.1114C>A	1.37:g.46073697C>A	ENSP00000255120:p.Pro372Thr	Somatic	301	6	0.0199336		WXS	Illumina HiSeq	Phase_I	353	10	0.0283286	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	37	CCDS524.1	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.230947	0.00023	.	.	ENSG00000132780	ENST00000537798;ENST00000402363;ENST00000341288;ENST00000350030	D;D;D	0.94376	-3.41;-3.41;-3.41	5.27	3.01	0.34805	.	1.088120	0.06802	N	0.788899	T	0.79161	0.4399	N	0.01352	-0.895	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	0.70346	-0.4897	9	.	.	.	-0.0398	5.0466	0.14487	0.7192:0.1889:0.0919:0.0	.	308;372;272;372;374	F5H3J2;Q53H03;B4DS57;P49321;P49321-3	.;.;.;NASP_HUMAN;.	T	308;374;272;372	ENSP00000438871:P308T;ENSP00000384529:P374T;ENSP00000255120:P372T	.	P	+	1	0	NASP	45846284	0.000000	0.05858	0.001000	0.08648	0.171000	0.22731	-0.472000	0.06623	1.129000	0.42072	-0.265000	0.10407	CCA	C|0.985;A|0.015	0.015	strong		0.507	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
TANC2	26115	hgsc.bcm.edu	37	17	61315272	61315272	+	Silent	SNP	G	G	A	rs2460111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:61315272G>A	ENST00000424789.2	+	6	649	c.645G>A	c.(643-645)caG>caA	p.Q215Q	AC037445.1_ENST00000581421.1_RNA|TANC2_ENST00000389520.4_Silent_p.Q215Q	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	215					in utero embryonic development (GO:0001701)			p.Q215Q(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						AACCTTGGCAGTCTCAAAAAT	0.393													A|||	2677	0.534545	0.9281	0.4827	5008	,	,		17601	0.1667		0.4911	False		,,,				2504	0.4632				p.Q215Q		Atlas-SNP	.											TANC2_ENST00000389520,NS,lymphoid_neoplasm,0,2	TANC2	266	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.G645A						PASS	.	A		3152,522		1371,410,56	47.0	45.0	46.0		645	0.8	1.0	17	dbSNP_100	46	4195,3997		1083,2029,984	no	coding-synonymous	TANC2	NM_025185.3		2454,2439,1040	AA,AG,GG		48.7915,14.2079,38.0836		215/1991	61315272	7347,4519	1837	4096	5933	SO:0001819	synonymous_variant	26115	exon6			TTGGCAGTCTCAA	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30212	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.645G>A	17.37:g.61315272G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Silent	SNP	ENST00000424789.2	37	CCDS45754.1																																																																																			G|0.463;A|0.537	0.537	strong		0.393	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1		
LYSMD3	116068	hgsc.bcm.edu	37	5	89820984	89820984	+	Silent	SNP	T	T	C	rs10069050	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:89820984T>C	ENST00000315948.6	-	2	267	c.123A>G	c.(121-123)gaA>gaG	p.E41E	LYSMD3_ENST00000509384.1_Silent_p.E41E|LYSMD3_ENST00000500869.2_Silent_p.E41E	NM_198273.1	NP_938014.1	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain containing 3	41						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(2)|prostate(1)|urinary_tract(1)	7		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		TGGATCGAAGTTCATACACTT	0.378													C|||	3068	0.61262	0.7678	0.428	5008	,	,		17152	0.6081		0.5408	False		,,,				2504	0.6125				p.E41E		Atlas-SNP	.											.	LYSMD3	25	.	0			c.A123G						PASS	.	C		2727,1049		983,761,144	151.0	137.0	141.0		123	1.7	1.0	5	dbSNP_119	141	4636,3612		1309,2018,797	no	coding-synonymous	LYSMD3	NM_198273.1		2292,2779,941	CC,CT,TT		43.7924,27.7807,38.7641		41/307	89820984	7363,4661	1888	4124	6012	SO:0001819	synonymous_variant	116068	exon2			TCGAAGTTCATAC	BX537972	CCDS43338.1, CCDS68911.1	5q14.3	2010-12-09			ENSG00000176018	ENSG00000176018			26969	protein-coding gene	gene with protein product							Standard	NM_001286812		Approved	FLJ13542	uc003kjr.3	Q7Z3D4	OTTHUMG00000162667	ENST00000315948.6:c.123A>G	5.37:g.89820984T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	NM_198273	Q5H9U0|Q6PEK0|Q9NTE9	Silent	SNP	ENST00000315948.6	37	CCDS43338.1																																																																																			T|0.410;C|0.590	0.590	strong		0.378	LYSMD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369987.2	XM_371760	
PCTP	58488	hgsc.bcm.edu	37	17	53844742	53844742	+	Missense_Mutation	SNP	G	G	A	rs112454522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:53844742G>A	ENST00000268896.5	+	2	313	c.188G>A	c.(187-189)tGc>tAc	p.C63Y	PCTP_ENST00000325214.6_5'UTR|PCTP_ENST00000576183.1_Missense_Mutation_p.C63Y|PCTP_ENST00000573500.1_Missense_Mutation_p.C63Y	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	63	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			CTGGAGGACTGCTCACCAACT	0.383													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18999	0.0		0.0089	False		,,,				2504	0.0				p.C63Y		Atlas-SNP	.											.	PCTP	17	.	0			c.G188A						PASS	.	G	,TYR/CYS	7,4399	12.9+/-30.5	0,7,2196	138.0	125.0	129.0		,188	5.6	0.1	17	dbSNP_132	129	84,8516	48.5+/-108.0	1,82,4217	yes	utr-5,missense	PCTP	NM_001102402.2,NM_021213.3	,194	1,89,6413	AA,AG,GG		0.9767,0.1589,0.6997	,probably-damaging	,63/215	53844742	91,12915	2203	4300	6503	SO:0001583	missense	58488	exon2			AGGACTGCTCACC	AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"""StAR-related lipid transfer (START) domain containing"""	8752	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 2"""	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.188G>A	17.37:g.53844742G>A	ENSP00000268896:p.Cys63Tyr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_021213	Q9BSC9|Q9UIT3|Q9UKW7	Missense_Mutation	SNP	ENST00000268896.5	37	CCDS11588.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	25.3	4.628072	0.87560	0.001589	0.009767	ENSG00000141179	ENST00000268896;ENST00000325214	T	0.42131	0.98	5.64	5.64	0.86602	Lipid-binding START (3);START-like domain (1);	0.111691	0.64402	D	0.000007	T	0.56202	0.1969	M	0.77820	2.39	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.66497	0.944;0.944	T	0.63712	-0.6575	10	0.56958	D	0.05	-12.5478	15.2077	0.73192	0.0:0.0:1.0:0.0	.	63;63	Q549N3;Q9UKL6	.;PPCT_HUMAN	Y	63;42	ENSP00000268896:C63Y	ENSP00000268896:C63Y	C	+	2	0	PCTP	51199741	1.000000	0.71417	0.093000	0.20910	0.500000	0.33767	6.637000	0.74304	2.642000	0.89623	0.650000	0.86243	TGC	G|0.993;A|0.007	0.007	strong		0.383	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107423188	107423188	+	Silent	SNP	G	G	A	rs1470591	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:107423188G>A	ENST00000409382.3	-	6	2146	c.1536C>T	c.(1534-1536)ccC>ccT	p.P512P	ST6GAL2_ENST00000361686.4_Silent_p.P512P	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	512					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						CCTGGAAGCCGGGAAGAACCA	0.542													G|||	1094	0.21845	0.1823	0.3285	5008	,	,		18730	0.0377		0.4533	False		,,,				2504	0.1339				p.P512P		Atlas-SNP	.											ST6GAL2,NS,carcinoma,-1,1	ST6GAL2	159	1	0			c.C1536T						scavenged	.	G	,	990,3416	370.8+/-319.7	101,788,1314	112.0	101.0	105.0		1536,1536	-11.6	0.0	2	dbSNP_88	105	3968,4632	551.5+/-385.9	900,2168,1232	no	coding-synonymous,coding-synonymous	ST6GAL2	NM_001142351.1,NM_032528.2	,	1001,2956,2546	AA,AG,GG		46.1395,22.4694,38.1209	,	512/530,512/530	107423188	4958,8048	2203	4300	6503	SO:0001819	synonymous_variant	84620	exon6			GAAGCCGGGAAGA	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.1536C>T	2.37:g.107423188G>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	37	CCDS2073.1	568	0.2600732600732601	91	0.18495934959349594	119	0.3287292817679558	16	0.027972027972027972	342	0.45118733509234826	G	0.016	-1.537599	0.00942	0.224694	0.461395	ENSG00000144057	ENST00000361803	.	.	.	5.8	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999995177	.	.	.	.	.	.	T	0.08554	-1.0716	3	.	.	.	-32.3354	5.7615	0.18203	0.1271:0.0587:0.471:0.3432	rs1470591;rs3796113;rs17629922;rs1470591	.	.	.	W	78	.	.	R	-	1	2	ST6GAL2	106789620	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-5.699000	0.00104	-5.603000	0.00012	-5.073000	0.00001	CGG	G|0.679;A|0.321	0.321	strong		0.542	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
PTGIR	5739	hgsc.bcm.edu	37	19	47124714	47124714	+	Silent	SNP	T	T	G	rs2229129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47124714T>G	ENST00000291294.2	-	3	1117	c.984A>C	c.(982-984)tcA>tcC	p.S328S	PTGIR_ENST00000598865.1_Silent_p.S116S|PTGIR_ENST00000597185.1_Silent_p.S57S|PTGIR_ENST00000594275.1_Silent_p.S85S	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	328					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)	CCCTCCTCCCTGAGGCGAGCT	0.677													t|||	2088	0.416933	0.4387	0.3833	5008	,	,		18163	0.3819		0.3867	False		,,,				2504	0.4785				p.S328S		Atlas-SNP	.											PTGIR,NS,carcinoma,0,1	PTGIR	31	1	0			c.A984C						PASS	.	A		1906,2498		416,1074,712	34.0	39.0	37.0		984	-9.1	0.0	19	dbSNP_98	37	3378,5222		675,2028,1597	yes	coding-synonymous	PTGIR	NM_000960.3		1091,3102,2309	GG,GT,TT		39.2791,43.2788,40.6337		328/387	47124714	5284,7720	2202	4300	6502	SO:0001819	synonymous_variant	5739	exon3			CCTCCCTGAGGCG		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.984A>C	19.37:g.47124714T>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_000960		Silent	SNP	ENST00000291294.2	37	CCDS12686.1																																																																																			T|0.599;G|0.401	0.401	strong		0.677	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
ZNF287	57336	hgsc.bcm.edu	37	17	16469879	16469879	+	Missense_Mutation	SNP	T	T	C	rs149325980		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16469879T>C	ENST00000395824.1	-	3	1078	c.461A>G	c.(460-462)cAt>cGt	p.H154R	ZNF287_ENST00000395825.3_Missense_Mutation_p.H154R|ZNF287_ENST00000461555.1_5'Flank			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	147					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		CTGGAAAGCATGTTTTCCTCT	0.438																																					p.H154R		Atlas-SNP	.											.	ZNF287	60	.	0			c.A461G						PASS	.						170.0	167.0	168.0					17																	16469879		2203	4300	6503	SO:0001583	missense	57336	exon3			AAAGCATGTTTTC	AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.461A>G	17.37:g.16469879T>C	ENSP00000379168:p.His154Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	154	85	0.551948	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	T	5.385	0.256302	0.10185	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.04809	3.55;3.55	4.18	-2.2	0.06994	Transcription regulator SCAN (1);	1.448190	0.04304	N	0.347863	T	0.02533	0.0077	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45556	-0.9253	10	0.15952	T	0.53	.	5.8246	0.18546	0.0:0.189:0.5011:0.3099	.	147	Q9HBT7	ZN287_HUMAN	R	154	ENSP00000379169:H154R;ENSP00000379168:H154R	ENSP00000379168:H154R	H	-	2	0	ZNF287	16410604	0.001000	0.12720	0.026000	0.17262	0.849000	0.48306	-0.217000	0.09253	-0.462000	0.06984	-0.290000	0.09829	CAT	T|1.000;A|0.000	.	alt		0.438	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1		
HAGH	3029	hgsc.bcm.edu	37	16	1869940	1869940	+	Silent	SNP	G	G	A	rs146440574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1869940G>A	ENST00000397356.3	-	4	796	c.390C>T	c.(388-390)atC>atT	p.I130I	HAGH_ENST00000397353.2_Silent_p.I82I|HAGH_ENST00000455446.2_Silent_p.I130I|HAGH_ENST00000566709.1_Silent_p.I82I	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	130					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)	TCAGGGCCCCGATACGGTCGT	0.612													G|||	6	0.00119808	0.003	0.0014	5008	,	,		15540	0.0		0.0	False		,,,				2504	0.001				p.I130I	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C390T						PASS	.	G	,	19,4379	25.3+/-52.1	0,19,2180	126.0	99.0	108.0		246,390	-10.0	0.6	16	dbSNP_134	108	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	0,22,6477	AA,AG,GG		0.0349,0.432,0.1693	,	82/261,130/309	1869940	22,12976	2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			GGCCCCGATACGG	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.390C>T	16.37:g.1869940G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.999;A|0.001	0.001	strong		0.612	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326	
SLC7A9	11136	hgsc.bcm.edu	37	19	33353061	33353061	+	Missense_Mutation	SNP	G	G	T	rs1007160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33353061G>T	ENST00000023064.4	-	6	858	c.667C>A	c.(667-669)Ctg>Atg	p.L223M	SLC7A9_ENST00000587772.1_Missense_Mutation_p.L223M|SLC7A9_ENST00000590341.1_Missense_Mutation_p.L223M|RN7SKP22_ENST00000365097.1_RNA	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	223			L -> M (in dbSNP:rs1007160). {ECO:0000269|PubMed:12371955}.		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)	TAAAACGCCAGGCTGATGGCT	0.532													G|||	1393	0.278155	0.3033	0.1772	5008	,	,		17292	0.3046		0.3668	False		,,,				2504	0.1973				p.L223M	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.C667A						PASS	.	G	MET/LEU,MET/LEU	1380,3026	454.9+/-350.8	214,952,1037	104.0	100.0	101.0		667,667	4.1	1.0	19	dbSNP_86	101	2908,5692	455.0+/-363.7	476,1956,1868	yes	missense,missense	SLC7A9	NM_001126335.1,NM_014270.4	15,15	690,2908,2905	TT,TG,GG		33.814,31.3209,32.9694	possibly-damaging,possibly-damaging	223/488,223/488	33353061	4288,8718	2203	4300	6503	SO:0001583	missense	11136	exon6			ACGCCAGGCTGAT	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.667C>A	19.37:g.33353061G>T	ENSP00000023064:p.Leu223Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_001243036	B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	37	CCDS12425.1	659	0.3017399267399267	142	0.2886178861788618	69	0.19060773480662985	164	0.2867132867132867	284	0.37467018469656993	G	12.92	2.081948	0.36758	0.313209	0.33814	ENSG00000021488	ENST00000023064	D	0.91011	-2.77	5.12	4.07	0.47477	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.73753	2.245	0.20873	P	0.999834507	P	0.42123	0.771	P	0.48334	0.574	T	0.00275	-1.1856	9	0.52906	T	0.07	.	7.8546	0.29474	0.2315:0.0:0.7685:0.0	rs1007160;rs52805941;rs59199560;rs1007160	223	P82251	BAT1_HUMAN	M	223	ENSP00000023064:L223M	ENSP00000023064:L223M	L	-	1	2	SLC7A9	38044901	0.977000	0.34250	0.970000	0.41538	0.430000	0.31655	1.765000	0.38481	2.553000	0.86117	0.561000	0.74099	CTG	G|0.697;T|0.303	0.303	strong		0.532	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
PSG8	440533	hgsc.bcm.edu	37	19	43269704	43269704	+	Silent	SNP	T	T	C	rs71337226|rs34129574|rs62112127	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43269704T>C	ENST00000306511.4	-	1	127	c.30A>G	c.(28-30)acA>acG	p.T10T	PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Silent_p.T10T|PSG8_ENST00000406636.3_Silent_p.T10T	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	25	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	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		
CCDC30	728621	hgsc.bcm.edu	37	1	43047057	43047057	+	Silent	SNP	A	A	G	rs12037518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:43047057A>G	ENST00000340612.4	+	7	1092	c.1092A>G	c.(1090-1092)gaA>gaG	p.E364E	CCDC30_ENST00000390640.4_Silent_p.E153E|CCDC30_ENST00000507855.1_Silent_p.E153E|CCDC30_ENST00000428554.2_Silent_p.E364E|CCDC30_ENST00000342022.4_Silent_p.E364E			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	364						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						GGAAATTAGAACATGCTCATA	0.348													A|||	1397	0.278954	0.1702	0.1499	5008	,	,		18052	0.4395		0.1879	False		,,,				2504	0.4458				p.E364E		Atlas-SNP	.											.	CCDC30	78	.	0			c.A1092G						PASS	.	A		792,3614	317.7+/-295.3	72,648,1483	89.0	93.0	92.0		1092	2.0	0.8	1	dbSNP_120	92	1708,6892	311.8+/-310.5	177,1354,2769	no	coding-synonymous	CCDC30	NM_001080850.2		249,2002,4252	GG,GA,AA		19.8605,17.9755,19.2219		364/784	43047057	2500,10506	2203	4300	6503	SO:0001819	synonymous_variant	728621	exon8			ATTAGAACATGCT	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"""prefoldin 6-like"""					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1092A>G	1.37:g.43047057A>G		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	322	171	0.531056	NM_001080850	Q14F06|Q5VVM5	Silent	SNP	ENST00000340612.4	37	CCDS30690.1																																																																																			A|0.811;G|0.189	0.189	strong		0.348	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030	
TACC2	10579	hgsc.bcm.edu	37	10	123842498	123842498	+	Silent	SNP	T	T	A	rs41288000	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123842498T>A	ENST00000369005.1	+	4	823	c.483T>A	c.(481-483)tcT>tcA	p.S161S	TACC2_ENST00000334433.3_Silent_p.S161S|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.S161S|TACC2_ENST00000453444.2_Silent_p.S161S|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.S161S	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	161					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)				GGGACAGCTCTACTCCATACC	0.582													T|||	40	0.00798722	0.0015	0.013	5008	,	,		17987	0.0		0.0258	False		,,,				2504	0.0031				p.S161S		Atlas-SNP	.											.	TACC2	271	.	0			c.T483A						PASS	.	T	,	7,4399	14.3+/-33.2	0,7,2196	34.0	34.0	34.0		,483	-2.7	0.0	10	dbSNP_127	34	126,8474	63.1+/-125.2	2,122,4176	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	2,129,6372	AA,AT,TT		1.4651,0.1589,1.0226	,	,161/2949	123842498	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			CAGCTCTACTCCA	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.483T>A	10.37:g.123842498T>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1	22	0.010073260073260074	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	16	0.021108179419525065	T	6.333	0.429621	0.11987	0.001589	0.014651	ENSG00000138162	ENST00000491540	.	.	.	4.05	-2.67	0.06059	.	.	.	.	.	T	0.11750	0.0286	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24440	-1.0160	4	.	.	.	1.9864	5.2291	0.15412	0.0:0.4425:0.1818:0.3757	rs41288000	.	.	.	N	175	.	.	Y	+	1	0	TACC2	123832488	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	0.181000	0.16880	-0.817000	0.04335	-0.379000	0.06801	TAC	T|0.987;A|0.013	0.013	strong		0.582	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
NAALADL2	254827	hgsc.bcm.edu	37	3	174814909	174814909	+	Missense_Mutation	SNP	G	G	A	rs150099163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:174814909G>A	ENST00000454872.1	+	2	501	c.373G>A	c.(373-375)Gtc>Atc	p.V125I	NAALADL2-AS3_ENST00000453180.1_RNA|NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	125						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		CTTTTGCCACGTCTTAAAAAT	0.388													G|||	13	0.00259585	0.0015	0.0014	5008	,	,		19658	0.0		0.001	False		,,,				2504	0.0092				p.V125I		Atlas-SNP	.											.	NAALADL2	86	.	0			c.G373A						PASS	.	G	ILE/VAL	6,3674		0,6,1834	99.0	101.0	100.0		373	0.7	0.8	3	dbSNP_134	100	35,8155		0,35,4060	yes	missense	NAALADL2	NM_207015.2	29	0,41,5894	AA,AG,GG		0.4274,0.163,0.3454	benign	125/796	174814909	41,11829	1840	4095	5935	SO:0001583	missense	254827	exon2			TGCCACGTCTTAA		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.373G>A	3.37:g.174814909G>A	ENSP00000404705:p.Val125Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.166	-0.171159	0.06421	0.00163	0.004274	ENSG00000177694	ENST00000434257;ENST00000454872	T;T	0.32272	1.55;1.46	5.72	0.72	0.18214	.	0.429836	0.19810	N	0.105542	T	0.10252	0.0251	N	0.08118	0	0.22858	N	0.998641	B;B	0.12630	0.006;0.0	B;B	0.04013	0.001;0.0	T	0.29852	-0.9998	10	0.07030	T	0.85	-6.3989	3.5335	0.07785	0.4399:0.3354:0.0925:0.1322	.	108;125	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	I	108;125	ENSP00000409858:V108I;ENSP00000404705:V125I	ENSP00000409858:V108I	V	+	1	0	NAALADL2	176297603	0.674000	0.27549	0.843000	0.33291	0.120000	0.20174	0.117000	0.15583	0.122000	0.18314	-0.134000	0.14843	GTC	G|0.998;A|0.002	0.002	strong		0.388	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464736	39464736	+	Missense_Mutation	SNP	C	C	G	rs2074284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	102	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	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	
VDR	7421	hgsc.bcm.edu	37	12	48272895	48272895	+	Start_Codon_SNP	SNP	A	A	G	rs2228570	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:48272895A>G	ENST00000395324.2	-	3	270	c.2T>C	c.(1-3)aTg>aCg	p.M1T	VDR_ENST00000549336.1_Start_Codon_SNP_p.M1T|VDR_ENST00000550325.1_Missense_Mutation_p.M51T|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	42	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	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
ZNF441	126068	hgsc.bcm.edu	37	19	11892255	11892255	+	Missense_Mutation	SNP	G	G	C	rs146452126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11892255G>C	ENST00000357901.4	+	4	1718	c.1616G>C	c.(1615-1617)gGc>gCc	p.G539A	ZNF441_ENST00000454339.2_Missense_Mutation_p.G472A	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	539					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGTGGGAAAGGCTTCAGGTCT	0.418													g|||	14	0.00279553	0.0008	0.0043	5008	,	,		21526	0.0		0.0089	False		,,,				2504	0.001				p.G539A		Atlas-SNP	.											.	ZNF441	123	.	0			c.G1616C						PASS	.	C	ALA/GLY	10,4396		0,10,2193	50.0	51.0	50.0		1616	-2.4	0.0	19	dbSNP_134	50	94,8506		0,94,4206	yes	missense	ZNF441	NM_152355.2	60	0,104,6399	CC,CG,GG		1.093,0.227,0.7996	benign	539/694	11892255	104,12902	2203	4300	6503	SO:0001583	missense	126068	exon4			GGAAAGGCTTCAG	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"""Zinc fingers, C2H2-type"", ""-"""	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.1616G>C	19.37:g.11892255G>C	ENSP00000350576:p.Gly539Ala	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	43	15	0.348837	NM_152355		Missense_Mutation	SNP	ENST00000357901.4	37	CCDS12266.2	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	-	0.006	-2.083379	0.00371	0.00227	0.01093	ENSG00000197044	ENST00000409902;ENST00000357901;ENST00000454339	T;T	0.15834	2.39;2.39	1.22	-2.44	0.06502	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02267	0.0070	N	0.01267	-0.92	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33317	-0.9873	9	0.02654	T	1	.	2.2937	0.04144	0.1554:0.3856:0.321:0.138	.	539	Q8N8Z8	ZN441_HUMAN	A	495;539;472	ENSP00000350576:G539A;ENSP00000403738:G472A	ENSP00000350576:G539A	G	+	2	0	ZNF441	11753255	0.000000	0.05858	0.002000	0.10522	0.726000	0.41606	-0.649000	0.05384	-0.884000	0.03976	-2.128000	0.00344	GGC	G|0.994;C|0.006	0.006	strong		0.418	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355	
DEK	7913	hgsc.bcm.edu	37	6	18258286	18258286	+	Silent	SNP	C	C	T	rs144486575	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:18258286C>T	ENST00000397239.3	-	4	702	c.255G>A	c.(253-255)ggG>ggA	p.G85G	DEK_ENST00000244776.7_Silent_p.G51G	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	85					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)			AAAGTTTCTGCCCCTTTCCTG	0.308			T	NUP214	AML																																p.G85G		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.G255A						PASS	.	C	,	2,4402	4.2+/-10.8	0,2,2200	59.0	58.0	58.0		153,255	-7.4	0.6	6	dbSNP_134	58	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	0,6,6495	TT,TC,CC		0.0465,0.0454,0.0461	,	51/342,85/376	18258286	6,12996	2202	4299	6501	SO:0001819	synonymous_variant	7913	exon4			TTTCTGCCCCTTT	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.255G>A	6.37:g.18258286C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			C|0.999;T|0.001	0.001	strong		0.308	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
ODAM	54959	hgsc.bcm.edu	37	4	71062308	71062308	+	Silent	SNP	C	C	A	rs61747755	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71062308C>A	ENST00000396094.2	+	1	96	c.48C>A	c.(46-48)gcC>gcA	p.A16A		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	16					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						CATTGTCAGCCCCAGTAAGTG	0.313													C|||	463	0.0924521	0.0061	0.1009	5008	,	,		16276	0.0079		0.1342	False		,,,				2504	0.2474				p.A16A		Atlas-SNP	.											.	ODAM	38	.	0			c.C48A						PASS	.	C		116,3510		3,110,1700	73.0	68.0	69.0		48	1.5	1.0	4	dbSNP_129	69	1189,6985		86,1017,2984	no	coding-synonymous	ODAM	NM_017855.3		89,1127,4684	AA,AC,CC		14.5461,3.1991,11.0593		16/280	71062308	1305,10495	1813	4087	5900	SO:0001819	synonymous_variant	54959	exon1			GTCAGCCCCAGTA	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.48C>A	4.37:g.71062308C>A		Somatic	436	0	0		WXS	Illumina HiSeq	Phase_I	376	160	0.425532	NM_017855	Q8WWE5|Q9NWZ9	Silent	SNP	ENST00000396094.2	37	CCDS3536.2																																																																																			C|0.906;A|0.094	0.094	strong		0.313	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855	
SEZ6L	23544	hgsc.bcm.edu	37	22	26695077	26695077	+	Missense_Mutation	SNP	G	G	T	rs663048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26695077G>T	ENST00000248933.6	+	5	1385	c.1290G>T	c.(1288-1290)atG>atT	p.M430I	SEZ6L_ENST00000529632.2_Missense_Mutation_p.M430I|SEZ6L_ENST00000403121.1_Missense_Mutation_p.M203I|SEZ6L_ENST00000343706.4_Missense_Mutation_p.M430I|SEZ6L_ENST00000404234.3_Missense_Mutation_p.M430I|SEZ6L_ENST00000360929.3_Missense_Mutation_p.M430I|SEZ6L_ENST00000402979.1_Missense_Mutation_p.M203I			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	430	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		M -> I (in dbSNP:rs663048). {ECO:0000269|PubMed:15489334}.		adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				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						GCGCTAAGATGCTGACATGCA	0.612													G|||	941	0.187899	0.3472	0.1484	5008	,	,		16674	0.0704		0.2376	False		,,,				2504	0.0706				p.M430I		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G1290T						PASS	.	G	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	1387,3019	452.8+/-350.1	225,937,1041	36.0	31.0	33.0		1290,1290,1290,1290,1290,1290	0.2	0.9	22	dbSNP_83	33	2002,6598	345.5+/-325.8	232,1538,2530	yes	missense,missense,missense,missense,missense,missense	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	10,10,10,10,10,10	457,2475,3571	TT,TG,GG		23.2791,31.4798,26.0572	benign,benign,benign,benign,benign,benign	430/1024,430/1014,430/1012,430/950,430/949,430/1025	26695077	3389,9617	2203	4300	6503	SO:0001583	missense	23544	exon5			TAAGATGCTGACA	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.1290G>T	22.37:g.26695077G>T	ENSP00000248933:p.Met430Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	453	0.20741758241758243	164	0.3333333333333333	63	0.17403314917127072	35	0.06118881118881119	191	0.2519788918205805	G	6.142	0.394361	0.11638	0.314798	0.232791	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	4.55	0.149	0.14863	Complement control module (2);Sushi/SCR/CCP (3);	0.396321	0.21795	N	0.069001	T	0.00012	0.0000	N	0.00729	-1.24	0.18873	P	0.9999801283	B;B;B;B;B;B	0.21753	0.007;0.014;0.06;0.0;0.03;0.017	B;B;B;B;B;B	0.24006	0.006;0.013;0.03;0.002;0.05;0.05	T	0.37220	-0.9715	9	0.25751	T	0.34	.	4.5191	0.11950	0.3064:0.0:0.549:0.1445	rs663048;rs57212145;rs663048	430;203;430;430;430;430	B7ZLJ8;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	I	430;430;430;430;430;203;203	ENSP00000384772:M430I;ENSP00000437037:M430I;ENSP00000354185:M430I;ENSP00000248933:M430I;ENSP00000342661:M430I;ENSP00000384838:M203I;ENSP00000384733:M203I	ENSP00000248933:M430I	M	+	3	0	SEZ6L	25025077	0.079000	0.21365	0.869000	0.34112	0.737000	0.42083	0.352000	0.20113	-0.041000	0.13558	-0.291000	0.09656	ATG	G|0.765;T|0.235	0.235	strong		0.612	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
NDUFAF7	55471	hgsc.bcm.edu	37	2	37459326	37459326	+	Missense_Mutation	SNP	C	C	T	rs146409773		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:37459326C>T	ENST00000002125.4	+	2	173	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W	NDUFAF7_ENST00000483999.1_Intron|CEBPZ_ENST00000234170.5_5'Flank|NDUFAF7_ENST00000336237.6_Missense_Mutation_p.R45W	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	45					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)										GCCGATGCTGCGGCATCTTAT	0.483																																					p.R45W		Atlas-SNP	.											.	.	.	.	0			c.C133T						PASS	.	C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	110.0	103.0	105.0		133,133	3.7	1.0	2	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C2orf56	NM_001083946.1,NM_144736.4	101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	45/344,45/442	37459326	2,13004	2203	4300	6503	SO:0001583	missense	55471	exon2			ATGCTGCGGCATC		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.133C>T	2.37:g.37459326C>T	ENSP00000002125:p.Arg45Trp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_001083946	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.887012	0.72410	2.27E-4	1.16E-4	ENSG00000003509	ENST00000002125;ENST00000336237;ENST00000416653;ENST00000439218;ENST00000432075	T;T	0.76448	-1.02;-1.02	5.51	3.7	0.42460	.	0.339095	0.29631	N	0.011611	D	0.88392	0.6424	M	0.86864	2.845	0.21499	N	0.999661	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.68765	0.929;0.913;0.96;0.929	T	0.82281	-0.0535	10	0.87932	D	0	-12.9679	13.9833	0.64317	0.5203:0.4797:0.0:0.0	.	45;45;45;45	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	W	45;45;3;3;3	ENSP00000002125:R45W;ENSP00000337431:R45W	ENSP00000002125:R45W	R	+	1	2	C2orf56	37312830	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.134000	0.31442	0.677000	0.31305	-0.270000	0.10280	CGG	C|1.000;T|0.000	0.000	weak		0.483	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736	
KCNN3	3782	hgsc.bcm.edu	37	1	154842243	154842243	+	Silent	SNP	A	A	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154842243A>C	ENST00000271915.4	-	1	513	c.198T>G	c.(196-198)ctT>ctG	p.L66L	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	66	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgctgaagctgcggag	0.701																																					p.L66L		Atlas-SNP	.											KCNN3,NS,carcinoma,0,3	KCNN3	141	3	0			c.T198G						scavenged	.						6.0	4.0	5.0					1																	154842243		1926	3811	5737	SO:0001819	synonymous_variant	3782	exon1			CTGCTGAAGCTGC	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.198T>G	1.37:g.154842243A>C		Somatic	25	4	0.16		WXS	Illumina HiSeq	Phase_I	42	6	0.142857	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																			.	.	none		0.701	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
EPHA3	2042	hgsc.bcm.edu	37	3	89521664	89521664	+	Missense_Mutation	SNP	G	G	A	rs17801309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:89521664G>A	ENST00000336596.2	+	16	2966	c.2741G>A	c.(2740-2742)cGc>cAc	p.R914H	EPHA3_ENST00000494014.1_Missense_Mutation_p.R914H	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	914	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.		R -> H (in dbSNP:rs17801309). {ECO:0000269|PubMed:17344846}.		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)		ACTACCTTCCGCACAACAGGT	0.468										TSP Lung(6;0.00050)			G|||	275	0.0549121	0.0091	0.062	5008	,	,		18757	0.0804		0.0875	False		,,,				2504	0.0521				p.R914H		Atlas-SNP	.											.	EPHA3	501	.	0			c.G2741A						PASS	.	G	HIS/ARG	78,4328	68.1+/-105.8	0,78,2125	179.0	168.0	172.0		2741	2.9	1.0	3	dbSNP_123	172	804,7796	188.1+/-235.2	36,732,3532	yes	missense	EPHA3	NM_005233.5	29	36,810,5657	AA,AG,GG		9.3488,1.7703,6.7815	benign	914/984	89521664	882,12124	2203	4300	6503	SO:0001583	missense	2042	exon16			CCTTCCGCACAAC	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.2741G>A	3.37:g.89521664G>A	ENSP00000337451:p.Arg914His	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	174	85	0.488506	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	142	0.06501831501831502	7	0.014227642276422764	26	0.0718232044198895	45	0.07867132867132867	64	0.08443271767810026	G	14.24	2.476980	0.44044	0.017703	0.093488	ENSG00000044524	ENST00000336596;ENST00000494014	D;T	0.84223	-1.82;-0.72	5.73	2.91	0.33838	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.328872	0.37012	N	0.002289	T	0.09818	0.0241	N	0.25485	0.75	0.43766	P	0.003719000000000028	B	0.14012	0.009	B	0.10450	0.005	T	0.50065	-0.8871	8	.	.	.	.	8.8084	0.34952	0.2944:0.0:0.7056:0.0	rs17801309;rs17801309	914	P29320	EPHA3_HUMAN	H	914	ENSP00000337451:R914H;ENSP00000419190:R914H	.	R	+	2	0	EPHA3	89604354	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.430000	0.34914	0.744000	0.32741	0.655000	0.94253	CGC	G|0.933;A|0.067	0.067	strong		0.468	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
KRT84	3890	hgsc.bcm.edu	37	12	52777439	52777439	+	Silent	SNP	A	A	G	rs1614888	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	132	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	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	
CEP55	55165	hgsc.bcm.edu	37	10	95276742	95276742	+	Missense_Mutation	SNP	G	G	C	rs41308663	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:95276742G>C	ENST00000371485.3	+	6	1034	c.730G>C	c.(730-732)Gca>Cca	p.A244P		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	244					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)		p.A244P(1)		kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				CTTGGCAAGTGCAAAAAAAGA	0.333													G|||	453	0.0904553	0.0635	0.1369	5008	,	,		19502	0.1905		0.0378	False		,,,				2504	0.045				p.A244P		Atlas-SNP	.											CEP55,NS,carcinoma,0,1	CEP55	35	1	1	Substitution - Missense(1)	stomach(1)	c.G730C						PASS	.	G	PRO/ALA,PRO/ALA	262,4144	147.6+/-182.1	7,248,1948	68.0	68.0	68.0		730,730	4.8	1.0	10	dbSNP_127	68	256,8344	99.5+/-161.0	5,246,4049	yes	missense,missense	CEP55	NM_001127182.1,NM_018131.4	27,27	12,494,5997	CC,CG,GG		2.9767,5.9464,3.9828	probably-damaging,probably-damaging	244/465,244/465	95276742	518,12488	2203	4300	6503	SO:0001583	missense	55165	exon6			GCAAGTGCAAAAA	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.730G>C	10.37:g.95276742G>C	ENSP00000360540:p.Ala244Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	37	CCDS7428.1	191	0.08745421245421245	38	0.07723577235772358	33	0.09116022099447514	93	0.16258741258741258	27	0.03562005277044855	G	23.4	4.416670	0.83449	0.059464	0.029767	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.24151	1.87	5.74	4.83	0.62350	.	0.399738	0.29348	N	0.012404	T	0.00210	0.0006	L	0.50333	1.59	0.26198	P	0.9794814	D	0.71674	0.998	P	0.62014	0.897	T	0.00512	-1.1696	9	0.59425	D	0.04	-15.3059	15.0411	0.71791	0.0691:0.0:0.9309:0.0	rs41308663;rs62642533	244	Q53EZ4	CEP55_HUMAN	P	244	ENSP00000360540:A244P	ENSP00000351102:A244P	A	+	1	0	CEP55	95266732	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.516000	0.53436	2.710000	0.92621	0.561000	0.74099	GCA	G|0.948;C|0.052	0.052	strong		0.333	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
MGEA5	10724	hgsc.bcm.edu	37	10	103577629	103577629	+	Missense_Mutation	SNP	C	C	T	rs35402016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103577629C>T	ENST00000361464.3	-	1	546	c.151G>A	c.(151-153)Gcc>Acc	p.A51T	MGEA5_ENST00000419011.2_Missense_Mutation_p.A51T|MGEA5_ENST00000439817.1_Missense_Mutation_p.A51T|MGEA5_ENST00000357797.5_Missense_Mutation_p.A51T|MGEA5_ENST00000370094.3_Missense_Mutation_p.A51T|KCNIP2-AS1_ENST00000412353.1_RNA	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	51					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		GCAGCCCCGGCCACCGCCGCT	0.721													C|||	10	0.00199681	0.0	0.0014	5008	,	,		11090	0.0		0.006	False		,,,				2504	0.0031				p.A51T		Atlas-SNP	.											.	MGEA5	53	.	0			c.G151A						PASS	.	C	THR/ALA,THR/ALA	2,3740		0,2,1869	6.0	7.0	6.0		151,151	1.8	0.2	10	dbSNP_126	6	38,7546		0,38,3754	no	missense,missense	MGEA5	NM_001142434.1,NM_012215.3	58,58	0,40,5623	TT,TC,CC		0.5011,0.0534,0.3532	benign,benign	51/864,51/917	103577629	40,11286	1871	3792	5663	SO:0001583	missense	10724	exon1			CCCCGGCCACCGC	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"""nuclear cytoplasmic O-GlcNAcase and acetyltransferase"""	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.151G>A	10.37:g.103577629C>T	ENSP00000354850:p.Ala51Thr	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_001142434	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Missense_Mutation	SNP	ENST00000361464.3	37	CCDS7520.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	10.90	1.481501	0.26598	5.34E-4	0.005011	ENSG00000198408	ENST00000439817;ENST00000361464;ENST00000357797;ENST00000370094;ENST00000419011	T;T;T;T;T	0.47869	1.49;1.5;1.5;1.49;0.83	4.71	1.76	0.24704	.	0.766530	0.11933	N	0.515498	T	0.18173	0.0436	N	0.14661	0.345	0.21020	N	0.999804	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.06405	0.0;0.001;0.002;0.0	T	0.22417	-1.0217	10	0.13853	T	0.58	-0.0165	5.4435	0.16521	0.0:0.5247:0.1481:0.3272	rs35402016	51;51;51;51	E9PGF9;O60502-2;O60502-3;O60502	.;.;.;NCOAT_HUMAN	T	51	ENSP00000409973:A51T;ENSP00000354850:A51T;ENSP00000350445:A51T;ENSP00000359112:A51T;ENSP00000407081:A51T	ENSP00000350445:A51T	A	-	1	0	MGEA5	103567619	0.070000	0.21116	0.189000	0.23252	0.328000	0.28507	-0.171000	0.09883	0.141000	0.18875	0.561000	0.74099	GCC	C|0.996;T|0.004	0.004	strong		0.721	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97933601	97933601	+	Silent	SNP	C	C	T	rs1045916	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97933601C>T	ENST00000005260.8	-	12	1544	c.1329G>A	c.(1327-1329)ttG>ttA	p.L443L		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	443					filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			CCCCCATGGACAAGCATTCCA	0.577													C|||	2783	0.555711	0.3253	0.6787	5008	,	,		18035	0.6915		0.7485	False		,,,				2504	0.4417				p.L443L		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.G1329A						PASS	.	C		1705,2701	512.7+/-368.2	340,1025,838	84.0	72.0	76.0		1329	3.9	0.0	7	dbSNP_86	76	6389,2211	710.1+/-405.8	2367,1655,278	no	coding-synonymous	BAIAP2L1	NM_018842.4		2707,2680,1116	TT,TC,CC		25.7093,38.6972,37.7672		443/512	97933601	8094,4912	2203	4300	6503	SO:0001819	synonymous_variant	55971	exon12			CATGGACAAGCAT	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1329G>A	7.37:g.97933601C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			C|0.383;T|0.617	0.617	strong		0.577	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
RHCE	6006	hgsc.bcm.edu	37	1	25747230	25747230	+	Missense_Mutation	SNP	G	G	C	rs586178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:25747230G>C	ENST00000294413.7	-	1	106	c.48C>G	c.(46-48)tgC>tgG	p.C16W	RHCE_ENST00000495048.1_5'UTR|RHCE_ENST00000346452.4_Missense_Mutation_p.C16W|RHCE_ENST00000413854.1_Missense_Mutation_p.C16W|RHCE_ENST00000425135.1_Missense_Mutation_p.C16W|RHCE_ENST00000243186.6_Missense_Mutation_p.C16W|RHCE_ENST00000349438.4_Missense_Mutation_p.C16W|RHCE_ENST00000455194.1_Missense_Mutation_p.C16W|RHCE_ENST00000340849.4_Missense_Mutation_p.C16W|RHCE_ENST00000349320.3_Intron	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	16			W -> C (associated with altered expression of E antigen). {ECO:0000269|PubMed:11380456, ECO:0000269|PubMed:11902138, ECO:0000269|PubMed:12393640, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16710414, ECO:0000269|Ref.10, ECO:0000269|Ref.12, ECO:0000269|Ref.13, ECO:0000269|Ref.8, ECO:0000269|Ref.9}.			integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			endometrium(8)|large_intestine(6)|lung(3)	17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		GTGTTAGGGCGCAGAGGGGCA	0.562													G|||	1998	0.398962	0.4781	0.4481	5008	,	,		14410	0.2202		0.5268	False		,,,				2504	0.3098				p.C16W		Atlas-SNP	.											RHCE,NS,carcinoma,0,1	RHCE	36	1	0			c.C48G	GRCh37	CM011810	RHCE	M	rs586178	scavenged	.						62.0	53.0	56.0					1																	25747230		2187	4274	6461	SO:0001583	missense	6006	exon1			TAGGGCGCAGAGG	BC075081	CCDS30634.1, CCDS30635.1, CCDS30636.1, CCDS30637.1	1p36.11	2014-09-17	2006-02-23		ENSG00000188672	ENSG00000188672		"""CD molecules"", ""Blood group antigens"""	10008	protein-coding gene	gene with protein product		111700	"""Rhesus blood group, CcEe antigens"""	RH		8220426	Standard	NM_138618		Approved	CD240CE	uc001bkf.3	P18577	OTTHUMG00000007650	ENST00000294413.7:c.48C>G	1.37:g.25747230G>C	ENSP00000294413:p.Cys16Trp	Somatic	214	2	0.00934579		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_138617	A7DW68|B7UDF3|B7UDF4|B7UDF5|B7UDF6|B7UDF7|B7UDF8|B7UDF9|B7UDG0|B7UDG1|B7UDG2|B7UDG3|Q02163|Q02164|Q02165|Q16160|Q2MJW0|Q2VC86|Q3LTM6|Q6AZX5|Q6J2U3|Q7RU06|Q8IZT2|Q8IZT3|Q8IZT4|Q8IZT5|Q9UD13|Q9UD14|Q9UD15|Q9UD16|Q9UD73|Q9UD74|Q9UEC2|Q9UEC3|Q9UPN0	Missense_Mutation	SNP	ENST00000294413.7	37	CCDS30635.1	745	0.3411172161172161	154	0.3130081300813008	129	0.356353591160221	124	0.21678321678321677	338	0.44591029023746703	G	0.004	-2.251843	0.00268	.	.	ENSG00000188672	ENST00000413854;ENST00000539650;ENST00000455194;ENST00000243186;ENST00000425135;ENST00000340849;ENST00000346452;ENST00000294413;ENST00000447203;ENST00000349438	T;T;T;T;T;T;T;T	0.23552	2.22;1.96;2.22;2.17;1.9;2.47;2.26;1.91	3.68	0.628	0.17681	.	0.827403	0.10882	N	0.623683	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.11329	0.006;0.004;0.0	T	0.48736	-0.9009	8	0.18710	T	0.47	1.3849	3.0722	0.06235	0.1659:0.3324:0.3995:0.1021	.	16;16;16	E7EQ47;Q5VSJ7;Q5VSJ8	.;.;.	W	16	ENSP00000415417:C16W;ENSP00000416275:C16W;ENSP00000243186:C16W;ENSP00000392809:C16W;ENSP00000345084:C16W;ENSP00000344485:C16W;ENSP00000294413:C16W;ENSP00000334570:C16W	ENSP00000243186:C16W	C	-	3	2	RHCE	25619817	0.000000	0.05858	0.006000	0.13384	0.017000	0.09413	-0.784000	0.04633	0.136000	0.18733	-0.384000	0.06662	TGC	C|0.343;G|0.657	0.343	strong		0.562	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485	
ZNF83	55769	hgsc.bcm.edu	37	19	53116940	53116940	+	Missense_Mutation	SNP	T	T	A	rs75857698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53116940T>A	ENST00000597597.1	-	2	3131	c.878A>T	c.(877-879)gAg>gTg	p.E293V	ZNF83_ENST00000391789.4_Intron|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Missense_Mutation_p.E293V|ZNF83_ENST00000301096.3_Missense_Mutation_p.E293V|ZNF83_ENST00000544146.1_Missense_Mutation_p.E293V|ZNF83_ENST00000545872.1_Missense_Mutation_p.E293V|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Missense_Mutation_p.E293V			P51522	ZNF83_HUMAN	zinc finger protein 83	293					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		CTTGCCACACTCATTACATTT	0.408													T|||	1368	0.273163	0.1641	0.4294	5008	,	,		2446	0.499		0.2137	False		,,,				2504	0.138				p.E293V		Atlas-SNP	.											.	ZNF83	73	.	0			c.A878T						PASS	.						84.0	84.0	84.0					19																	53116940		2201	4300	6501	SO:0001583	missense	55769	exon3			CCACACTCATTAC	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.878A>T	19.37:g.53116940T>A	ENSP00000472619:p.Glu293Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	21	0.318182	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	290	0.13278388278388278	19	0.03861788617886179	64	0.17679558011049723	135	0.23601398601398602	72	0.09498680738786279	t	5.390	0.257247	0.10239	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000545872;ENST00000541777	T;T;T;T;T	0.05580	3.42;3.42;3.42;3.42;3.42	1.63	-0.789	0.10935	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.05280	-0.08	0.09310	N	0.999996	B	0.10296	0.003	B	0.12837	0.008	T	0.49428	-0.8941	9	0.46703	T	0.11	.	6.1439	0.20275	0.4016:0.0:0.0:0.5984	.	293	P51522	ZNF83_HUMAN	V	293	ENSP00000445993:E293V;ENSP00000301096:E293V;ENSP00000445470:E293V;ENSP00000440713:E293V;ENSP00000439681:E293V	ENSP00000301096:E293V	E	-	2	0	ZNF83	57808752	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.740000	0.04861	-0.327000	0.08551	-0.820000	0.03113	GAG	T|0.867;A|0.133	0.133	strong		0.408	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
OR1S1	219959	hgsc.bcm.edu	37	11	57983162	57983162	+	Missense_Mutation	SNP	A	A	G	rs7103026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57983162A>G	ENST00000309433.6	+	1	946	c.946A>G	c.(946-948)Aag>Gag	p.K316E		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K316E(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TGCCCTGAGAAAGCTCATCAA	0.423													A|||	689	0.13758	0.0772	0.2205	5008	,	,		19269	0.0635		0.2386	False		,,,				2504	0.1329				p.K316E		Atlas-SNP	.											OR1S1,NS,carcinoma,0,2	OR1S1	139	2	1	Substitution - Missense(1)	prostate(1)	c.A946G						PASS	.	A	GLU/LYS	475,3927	224.6+/-240.7	28,419,1754	139.0	139.0	139.0		946	3.2	0.0	11	dbSNP_116	139	2223,6363	375.4+/-337.8	294,1635,2364	no	missense	OR1S1	NM_001004458.1	56	322,2054,4118	GG,GA,AA		25.891,10.7905,20.773	possibly-damaging	316/326	57983162	2698,10290	2201	4293	6494	SO:0001583	missense	219959	exon1			CTGAGAAAGCTCA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.946A>G	11.37:g.57983162A>G	ENSP00000311688:p.Lys316Glu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	97	62	0.639175	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	334	0.15293040293040294	32	0.06504065040650407	75	0.20718232044198895	47	0.08216783216783216	180	0.23746701846965698	A	8.760	0.923264	0.18056	0.107905	0.25891	ENSG00000172774	ENST00000309433	T	0.40476	1.03	3.23	3.23	0.37069	.	0.251674	0.27778	N	0.017891	T	0.00012	0.0000	M	0.76838	2.35	0.80722	P	0.0	P	0.44627	0.839	B	0.36719	0.231	T	0.14559	-1.0468	9	0.66056	D	0.02	.	10.883	0.46951	1.0:0.0:0.0:0.0	rs7103026	316	Q8NH92	OR1S1_HUMAN	E	316	ENSP00000311688:K316E	ENSP00000311688:K316E	K	+	1	0	OR1S1	57739738	0.007000	0.16637	0.011000	0.14972	0.479000	0.33129	2.259000	0.43259	1.345000	0.45676	0.392000	0.25879	AAG	A|0.817;G|0.183	0.183	strong		0.423	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
GPR146	115330	hgsc.bcm.edu	37	7	1097394	1097394	+	Silent	SNP	T	T	C	rs11767527	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1097394T>C	ENST00000397095.1	+	2	466	c.243T>C	c.(241-243)ccT>ccC	p.P81P	C7orf50_ENST00000357429.6_Intron|GPR146_ENST00000297468.3_Silent_p.P81P|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron|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	65	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	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	
KIAA0753	9851	hgsc.bcm.edu	37	17	6524298	6524298	+	Missense_Mutation	SNP	T	T	A	rs9889363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:6524298T>A	ENST00000361413.3	-	7	1483	c.1125A>T	c.(1123-1125)gaA>gaT	p.E375D	KIAA0753_ENST00000572370.1_Missense_Mutation_p.E76D|KIAA0753_ENST00000542606.1_Missense_Mutation_p.E76D|KIAA0753_ENST00000589033.1_5'Flank	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	375			E -> D (in dbSNP:rs9889363).|E -> G (in dbSNP:rs17794522).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		ACAGTTTCTTTTCCAGGAGAG	0.373													T|||	1542	0.307907	0.1581	0.4006	5008	,	,		15891	0.3562		0.3489	False		,,,				2504	0.3528				p.E375D		Atlas-SNP	.											.	KIAA0753	63	.	0			c.A1125T						PASS	.	T	ASP/GLU	734,2898		74,586,1156	62.0	60.0	60.0		1125	3.8	1.0	17	dbSNP_119	60	3078,5082		548,1982,1550	yes	missense	KIAA0753	NM_014804.2	45	622,2568,2706	AA,AT,TT		37.7206,20.2093,32.327	probably-damaging	375/968	6524298	3812,7980	1816	4080	5896	SO:0001583	missense	9851	exon7			TTTCTTTTCCAGG		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1125A>T	17.37:g.6524298T>A	ENSP00000355250:p.Glu375Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	669	0.30631868131868134	83	0.16869918699186992	154	0.425414364640884	178	0.3111888111888112	254	0.33509234828496043	T	24.0	4.484199	0.84854	0.202093	0.377206	ENSG00000198920	ENST00000361413;ENST00000542606	D;D	0.86956	-2.19;-2.19	4.92	3.84	0.44239	.	0.429523	0.27901	N	0.017391	T	0.00012	0.0000	M	0.76574	2.34	0.09310	P	0.9999999999992082	D	0.76494	0.999	D	0.80764	0.994	T	0.01074	-1.1460	9	0.62326	D	0.03	-12.5411	7.6264	0.28214	0.0:0.099:0.0:0.901	rs9889363;rs17804307;rs9889363	375	Q2KHM9	K0753_HUMAN	D	375;76	ENSP00000355250:E375D;ENSP00000444634:E76D	ENSP00000355250:E375D	E	-	3	2	KIAA0753	6465022	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.810000	0.27183	0.991000	0.38814	0.377000	0.23210	GAA	T|0.697;A|0.303	0.303	strong		0.373	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
TTK	7272	hgsc.bcm.edu	37	6	80741243	80741243	+	Silent	SNP	A	A	T	rs1801465	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:80741243A>T	ENST00000369798.2	+	14	1692	c.1581A>T	c.(1579-1581)atA>atT	p.I527I	TTK_ENST00000230510.3_Silent_p.I526I|TTK_ENST00000509894.1_Silent_p.I526I	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	527	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		TTTATTCCATATTAAAGCAGA	0.239													A|||	427	0.0852636	0.0265	0.1037	5008	,	,		12616	0.0109		0.1481	False		,,,				2504	0.1636				p.I527I		Atlas-SNP	.											.	TTK	199	.	0			c.A1581T						PASS	.	A	,	220,4180	115.4+/-153.4	8,204,1988	49.0	53.0	51.0		1578,1581	2.9	1.0	6	dbSNP_89	51	1473,7121	269.4+/-288.4	120,1233,2944	no	coding-synonymous,coding-synonymous	TTK	NM_001166691.1,NM_003318.4	,	128,1437,4932	TT,TA,AA		17.1399,5.0,13.0291	,	526/857,527/858	80741243	1693,11301	2200	4297	6497	SO:0001819	synonymous_variant	7272	exon14			TTCCATATTAAAG		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.1581A>T	6.37:g.80741243A>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Silent	SNP	ENST00000369798.2	37	CCDS4993.1																																																																																			A|0.883;T|0.117	0.117	strong		0.239	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		
SLC9A3R2	9351	hgsc.bcm.edu	37	16	2079665	2079665	+	Missense_Mutation	SNP	G	G	A	rs55864883		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2079665G>A	ENST00000424542.2	+	2	434	c.296G>A	c.(295-297)cGg>cAg	p.R99Q	SLC9A3R2_ENST00000432365.2_Missense_Mutation_p.R99Q|SLC9A3R2_ENST00000563587.1_5'UTR	NM_001130012.2|NM_004785.5	NP_001123484.1|NP_004776.3	Q15599	NHRF2_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 2	99					negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|protein complex assembly (GO:0006461)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatase binding (GO:0019902)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)	2						CTCCGCCGGCGGCAGCTGACC	0.682																																					p.R99Q	Ovarian(69;105 1552 17724 23473)	Atlas-SNP	.											.	SLC9A3R2	24	.	0			c.G296A						PASS	.	G	GLN/ARG,GLN/ARG	1,4107		0,1,2053	27.0	38.0	34.0		296,296	3.7	1.0	16	dbSNP_129	34	8,8288		0,8,4140	no	missense,missense	SLC9A3R2	NM_001130012.1,NM_004785.4	43,43	0,9,6193	AA,AG,GG		0.0964,0.0243,0.0726	possibly-damaging,possibly-damaging	99/338,99/327	2079665	9,12395	2054	4148	6202	SO:0001583	missense	9351	exon2			GCCGGCGGCAGCT	AF004900	CCDS45382.1, CCDS45383.1, CCDS58407.1	16p13.3	2014-09-04	2012-03-22		ENSG00000065054	ENSG00000065054			11076	protein-coding gene	gene with protein product		606553	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2"""			9054412, 9671706	Standard	NM_001130012		Approved	SIP-1, TKA-1, NHERF-2, E3KARP	uc002coi.3	Q15599	OTTHUMG00000176956	ENST00000424542.2:c.296G>A	16.37:g.2079665G>A	ENSP00000408005:p.Arg99Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_004785	D3DU84|D3DU85|H3BSV6|O00272|O00556|Q3KQY7	Missense_Mutation	SNP	ENST00000424542.2	37	CCDS45382.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801819	0.50315	2.43E-4	9.64E-4	ENSG00000065054	ENST00000424542;ENST00000432365	T;T	0.20463	2.09;2.07	4.8	3.74	0.42951	PDZ/DHR/GLGF (1);	0.398384	0.22670	N	0.057068	T	0.12646	0.0307	N	0.22421	0.69	0.80722	D	1	B;P	0.49862	0.146;0.929	B;B	0.41619	0.012;0.361	T	0.07065	-1.0792	10	0.11794	T	0.64	-7.4822	11.2924	0.49258	0.0:0.0:0.7611:0.2389	rs55864883;rs62617116	99;99	D3DU85;Q15599	.;NHRF2_HUMAN	Q	99	ENSP00000408005:R99Q;ENSP00000402857:R99Q	ENSP00000408005:R99Q	R	+	2	0	SLC9A3R2	2019666	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.942000	0.40243	2.215000	0.71742	0.561000	0.74099	CGG	.	.	weak		0.682	SLC9A3R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434448.1		
AASDH	132949	hgsc.bcm.edu	37	4	57219613	57219613	+	Silent	SNP	C	C	T	rs17086696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:57219613C>T	ENST00000205214.6	-	9	1713	c.1533G>A	c.(1531-1533)ccG>ccA	p.P511P	AASDH_ENST00000502617.1_Silent_p.P511P|AASDH_ENST00000434343.2_Silent_p.P26P|AASDH_ENST00000513376.1_Silent_p.P411P|AASDH_ENST00000451613.1_Silent_p.P511P|AASDH_ENST00000602986.1_Silent_p.P358P|AASDH_ENST00000510762.1_5'Flank	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	511					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CAAGCTCATCCGGGACTGCAT	0.338													C|||	1138	0.227236	0.2224	0.3804	5008	,	,		17420	0.2192		0.1302	False		,,,				2504	0.2331				p.P511P		Atlas-SNP	.											.	AASDH	101	.	0			c.G1533A						PASS	.	C		950,3456	359.9+/-315.0	103,744,1356	83.0	82.0	82.0		1533	-11.4	0.2	4	dbSNP_123	82	1096,7504	227.8+/-263.0	70,956,3274	no	coding-synonymous	AASDH	NM_181806.2		173,1700,4630	TT,TC,CC		12.7442,21.5615,15.7312		511/1099	57219613	2046,10960	2203	4300	6503	SO:0001819	synonymous_variant	132949	exon9			CTCATCCGGGACT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1533G>A	4.37:g.57219613C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	141	60	0.425532	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	37	CCDS3504.1																																																																																			C|0.825;T|0.175	0.175	strong		0.338	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274426	39274426	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39274426T>A	ENST00000391413.2	-	1	180	c.142A>T	c.(142-144)Agc>Tgc	p.S48C		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	48	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)			CTGCAGCAGCTGGACACACAG	0.672																																					p.S48C		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,+2,4	KRTAP4-11	94	4	0			c.A142T						scavenged	.						12.0	16.0	15.0					17																	39274426		688	1589	2277	SO:0001583	missense	653240	exon1			AGCAGCTGGACAC	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.142A>T	17.37:g.39274426T>A	ENSP00000375232:p.Ser48Cys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	108	3	0.0277778	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	13.54	2.267594	0.40095	.	.	ENSG00000212721	ENST00000391413	T	0.01963	4.53	3.91	1.56	0.23342	.	0.663392	0.11138	U	0.595595	T	0.04998	0.0134	M	0.84773	2.715	0.31757	N	0.633906	B	0.29481	0.245	B	0.28232	0.087	T	0.02244	-1.1189	10	0.62326	D	0.03	.	7.3302	0.26577	0.3502:0.0:0.0:0.6498	.	48	Q9BYQ6	KR411_HUMAN	C	48	ENSP00000375232:S48C	ENSP00000375232:S48C	S	-	1	0	KRTAP4-11	36527952	0.035000	0.19736	0.900000	0.35374	0.093000	0.18481	-0.330000	0.07925	0.082000	0.17018	0.496000	0.49642	AGC	.	.	none		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
CLEC18C	283971	hgsc.bcm.edu	37	16	70211380	70211380	+	Silent	SNP	G	G	A	rs3869429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70211380G>A	ENST00000569347.2	+	3	707	c.453G>A	c.(451-453)acG>acA	p.T151T	CLEC18C_ENST00000314151.8_Silent_p.T151T|CLEC18C_ENST00000536907.2_Silent_p.T151T|CLEC18C_ENST00000541793.2_Silent_p.T151T|CLEC18C_ENST00000561612.1_Intron	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	151	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|large_intestine(6)|lung(1)	10						CCCACTACACGCAGGTGAGTG	0.582																																					p.T151T		Atlas-SNP	.											CLEC18C,NS,carcinoma,+1,1	CLEC18C	15	1	0			c.G453A						scavenged	.						12.0	10.0	11.0					16																	70211380		2077	4023	6100	SO:0001819	synonymous_variant	283971	exon3			CTACACGCAGGTG	AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.453G>A	16.37:g.70211380G>A		Somatic	409	0	0		WXS	Illumina HiSeq	Phase_I	301	65	0.215947	NM_173619	Q8IUW8	Silent	SNP	ENST00000569347.2	37	CCDS32473.1																																																																																			.	.	weak		0.582	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
ZNF469	84627	hgsc.bcm.edu	37	16	88504850	88504850	+	Missense_Mutation	SNP	G	G	C	rs1105066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	57	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	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	
KIF3B	9371	hgsc.bcm.edu	37	20	30915461	30915461	+	Silent	SNP	T	T	C	rs1129012	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:30915461T>C	ENST00000375712.3	+	7	2132	c.1965T>C	c.(1963-1965)taT>taC	p.Y655Y	KIF3B_ENST00000418717.2_Silent_p.Y281Y	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	655	Globular.				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)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)	p.Y655Y(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AGGCCCGATATAGGGTGAGAA	0.468													T|||	1011	0.201877	0.3313	0.1441	5008	,	,		17700	0.2222		0.1859	False		,,,				2504	0.0634				p.Y655Y		Atlas-SNP	.											KIF3B,NS,carcinoma,0,1	KIF3B	75	1	1	Substitution - coding silent(1)	stomach(1)	c.T1965C						PASS	.	T		1346,3060	448.3+/-348.6	204,938,1061	93.0	81.0	85.0		1965	-4.2	0.4	20	dbSNP_86	85	1471,7129	281.7+/-295.2	136,1199,2965	no	coding-synonymous	KIF3B	NM_004798.3		340,2137,4026	CC,CT,TT		17.1047,30.5493,21.6592		655/748	30915461	2817,10189	2203	4300	6503	SO:0001819	synonymous_variant	9371	exon7			CCGATATAGGGTG	AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"""Kinesins"""	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.1965T>C	20.37:g.30915461T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_004798	B2RMP4|B4DSR5|E1P5M5	Silent	SNP	ENST00000375712.3	37	CCDS13200.1																																																																																			A|0.000;C|0.216;G|0.000;T|0.784	0.216	strong		0.468	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1	NM_004798	
SP110	3431	hgsc.bcm.edu	37	2	231077112	231077112	+	Missense_Mutation	SNP	G	G	A	rs28930679	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:231077112G>A	ENST00000358662.4	-	5	695	c.617C>T	c.(616-618)gCg>gTg	p.A206V	SP110_ENST00000392048.3_Missense_Mutation_p.A206V|SP110_ENST00000540870.1_Missense_Mutation_p.A212V|SP110_ENST00000338556.3_5'UTR|SP110_ENST00000486146.2_5'UTR|SP110_ENST00000258382.5_Missense_Mutation_p.A206V|SP110_ENST00000258381.6_Missense_Mutation_p.A206V	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	206			A -> V (in dbSNP:rs28930679). {ECO:0000269|PubMed:16816019}.		regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		GTCTTCTTCCGCATTCATTTT	0.468													G|||	797	0.159145	0.1165	0.2133	5008	,	,		21939	0.0873		0.2724	False		,,,				2504	0.136				p.A212V		Atlas-SNP	.											.	SP110	105	.	0			c.C635T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	623,3783	268.9+/-268.7	42,539,1622	220.0	172.0	188.0		635,617,617,617	-0.2	0.0	2	dbSNP_125	188	2177,6423	371.6+/-336.3	284,1609,2407	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	64,64,64,64	326,2148,4029	AA,AG,GG		25.314,14.1398,21.5285	benign,benign,benign,benign	212/556,206/690,206/550,206/714	231077112	2800,10206	2203	4300	6503	SO:0001583	missense	3431	exon6			TCTTCCGCATTCA	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.617C>T	2.37:g.231077112G>A	ENSP00000351488:p.Ala206Val	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	188	186	0.989362	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	371	0.16987179487179488	52	0.10569105691056911	71	0.19613259668508287	44	0.07692307692307693	204	0.2691292875989446	G	9.635	1.137510	0.21123	0.141398	0.25314	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000409815;ENST00000455674	T;T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01;3.01	3.63	-0.151	0.13411	.	2.041240	0.02374	N	0.078122	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.27700	0.083;0.186;0.117;0.001	B;B;B;B	0.18263	0.021;0.021;0.009;0.0	T	0.42515	-0.9447	9	0.31617	T	0.26	.	4.5859	0.12282	0.0:0.1096:0.3972:0.4932	rs28930679	206;212;206;206	G5E9C0;F5H1M1;Q9HB58;Q9HB58-6	.;.;SP110_HUMAN;.	V	206;206;206;206;212;206;160	ENSP00000258381:A206V;ENSP00000351488:A206V;ENSP00000375902:A206V;ENSP00000258382:A206V;ENSP00000439558:A212V;ENSP00000387172:A206V;ENSP00000393992:A160V	ENSP00000258381:A206V	A	-	2	0	SP110	230785356	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.085000	0.11250	-0.031000	0.13781	-0.386000	0.06593	GCG	G|0.797;A|0.203	0.203	strong		0.468	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
AOAH	313	hgsc.bcm.edu	37	7	36763688	36763688	+	Silent	SNP	C	C	T	rs2228411	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	49	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	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	
BPIFB3	359710	hgsc.bcm.edu	37	20	31652292	31652292	+	Missense_Mutation	SNP	G	G	A	rs4911290	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31652292G>A	ENST00000375494.3	+	7	682	c.682G>A	c.(682-684)Gtg>Atg	p.V228M		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	228	Leu-rich.		V -> M (in dbSNP:rs4911290).		innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCTTGGGTCCGTGGAATTCTC	0.557													G|||	2454	0.490016	0.3464	0.4755	5008	,	,		18488	0.756		0.3867	False		,,,				2504	0.5266				p.V228M		Atlas-SNP	.											.	.	.	.	0			c.G682A						PASS	.	G	MET/VAL	1447,2959	470.2+/-355.7	245,957,1001	97.0	77.0	84.0		682	2.6	0.8	20	dbSNP_111	84	3141,5459	478.1+/-369.8	585,1971,1744	yes	missense	BPIFB3	NM_182658.1	21	830,2928,2745	AA,AG,GG		36.5233,32.8416,35.276	benign	228/477	31652292	4588,8418	2203	4300	6503	SO:0001583	missense	359710	exon7			GGGTCCGTGGAAT	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.682G>A	20.37:g.31652292G>A	ENSP00000364643:p.Val228Met	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	145	63	0.434483	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	1061	0.4858058608058608	178	0.3617886178861789	161	0.4447513812154696	430	0.7517482517482518	292	0.38522427440633245	G	8.111	0.778703	0.16120	0.328416	0.365233	ENSG00000186190	ENST00000375494	T	0.06687	3.27	4.58	2.63	0.31362	.	0.282354	0.24960	N	0.034221	T	0.00012	0.0000	M	0.70275	2.135	0.45035	P	0.001943000000000028	P	0.34837	0.472	B	0.34385	0.181	T	0.02339	-1.1174	9	0.87932	D	0	-12.5412	13.1368	0.59413	0.0:0.1717:0.8283:0.0	rs4911290;rs52793725;rs58138039;rs4911290	228	P59826	BPIB3_HUMAN	M	228	ENSP00000364643:V228M	ENSP00000364643:V228M	V	+	1	0	BPIFB3	31115953	0.921000	0.31238	0.833000	0.33012	0.052000	0.14988	1.284000	0.33249	0.569000	0.29329	-0.853000	0.03031	GTG	G|0.588;A|0.412	0.412	strong		0.557	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
SLC13A2	9058	hgsc.bcm.edu	37	17	26817537	26817537	+	Silent	SNP	G	G	A	rs11568466	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:26817537G>A	ENST00000314669.5	+	3	717	c.297G>A	c.(295-297)gcG>gcA	p.A99A	SLC13A2_ENST00000444914.3_Silent_p.A148A|SLC13A2_ENST00000545060.1_Silent_p.A56A|SLC13A2_ENST00000537681.1_Silent_p.A28A	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	99					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	TGGCCATCGCGGTGGAACACT	0.622													G|||	770	0.153754	0.1679	0.1628	5008	,	,		18210	0.0446		0.2137	False		,,,				2504	0.1789				p.A148A		Atlas-SNP	.											.	SLC13A2	125	.	0			c.G444A						PASS	.	G	,,	702,3704	292.4+/-282.0	71,560,1572	137.0	110.0	119.0		444,168,297	-11.2	0.0	17	dbSNP_126	119	1809,6791	325.6+/-317.0	177,1455,2668	yes	coding-synonymous,coding-synonymous,coding-synonymous	SLC13A2	NM_001145975.1,NM_001145976.1,NM_003984.3	,,	248,2015,4240	AA,AG,GG		21.0349,15.9328,19.3065	,,	148/642,56/550,99/593	26817537	2511,10495	2203	4300	6503	SO:0001819	synonymous_variant	9058	exon3			CATCGCGGTGGAA	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"""Solute carriers"""	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.297G>A	17.37:g.26817537G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Silent	SNP	ENST00000314669.5	37	CCDS11231.1																																																																																			G|0.830;C|0.000;A|0.170	0.170	strong		0.622	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984	
IL1R2	7850	hgsc.bcm.edu	37	2	102641015	102641015	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102641015T>C	ENST00000332549.3	+	7	1001	c.772T>C	c.(772-774)Tgt>Cgt	p.C258R	IL1R2_ENST00000485335.1_3'UTR|IL1R2_ENST00000393414.2_Missense_Mutation_p.C258R|IL1R2_ENST00000441002.1_Missense_Mutation_p.C258R	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	258	Ig-like C2-type 3.				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						GACAATCCCGTGTAAGGTGTT	0.602																																					p.C258R	Pancreas(106;189 1628 2302 5133 12295)	Atlas-SNP	.											IL1R2,colon,carcinoma,-2,1	IL1R2	58	1	0			c.T772C						scavenged	.						79.0	79.0	79.0					2																	102641015		2203	4300	6503	SO:0001583	missense	7850	exon7			ATCCCGTGTAAGG	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.772T>C	2.37:g.102641015T>C	ENSP00000330959:p.Cys258Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	183	3	0.0163934	NM_001261419	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	37	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	T	19.17	3.775695	0.70107	.	.	ENSG00000115590	ENST00000332549;ENST00000393414;ENST00000441002	D;D;D	0.86097	-2.07;-2.07;-2.07	5.87	5.87	0.94306	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.91415	0.7291	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92207	0.5773	10	0.87932	D	0	.	13.8038	0.63218	0.0:0.0:0.0:1.0	.	258	P27930	IL1R2_HUMAN	R	258	ENSP00000330959:C258R;ENSP00000377066:C258R;ENSP00000414611:C258R	ENSP00000330959:C258R	C	+	1	0	IL1R2	102007447	0.999000	0.42202	0.990000	0.47175	0.759000	0.43091	4.529000	0.60588	2.248000	0.74166	0.533000	0.62120	TGT	.	.	none		0.602	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633	
NPSR1	387129	hgsc.bcm.edu	37	7	34851393	34851393	+	Silent	SNP	C	C	G	rs9655357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:34851393C>G	ENST00000360581.1	+	4	524	c.396C>G	c.(394-396)ctC>ctG	p.L132L	NPSR1_ENST00000531252.1_Silent_p.L121L|NPSR1_ENST00000381542.1_Intron|NPSR1_ENST00000359791.1_Silent_p.L132L|NPSR1_ENST00000381539.3_Silent_p.L132L	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	132						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	TTGTGCTGCTCTACGCCTCTA	0.473													C|||	744	0.148562	0.0113	0.1556	5008	,	,		20300	0.3165		0.2068	False		,,,				2504	0.0961				p.L132L		Atlas-SNP	.											NPSR1_ENST00000359791,NS,carcinoma,+2,2	NPSR1	134	2	0			c.C396G						scavenged	.	C	,	201,4205	125.3+/-162.5	6,189,2008	250.0	187.0	208.0		396,396	1.1	1.0	7	dbSNP_119	208	1589,7011	296.7+/-303.1	140,1309,2851	no	coding-synonymous,coding-synonymous	NPSR1	NM_207172.1,NM_207173.1	,	146,1498,4859	GG,GC,CC		18.4767,4.562,13.7629	,	132/372,132/378	34851393	1790,11216	2203	4300	6503	SO:0001819	synonymous_variant	387129	exon4			GCTGCTCTACGCC	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.396C>G	7.37:g.34851393C>G		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	119	40	0.336134	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Silent	SNP	ENST00000360581.1	37	CCDS5444.1																																																																																			C|0.847;G|0.153	0.153	strong		0.473	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
ATP13A4	84239	hgsc.bcm.edu	37	3	193183817	193183817	+	Silent	SNP	A	A	G	rs3796181	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:193183817A>G	ENST00000342695.4	-	11	1591	c.1269T>C	c.(1267-1269)agT>agC	p.S423S	ATP13A4_ENST00000295548.3_Silent_p.S423S|ATP13A4_ENST00000392443.3_Intron	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	423						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		AGCTTACCCCACTAAGCACAT	0.423													G|||	2775	0.554113	0.6838	0.5288	5008	,	,		16612	0.5387		0.4503	False		,,,				2504	0.5194				p.S423S		Atlas-SNP	.											.	ATP13A4	154	.	0			c.T1269C						PASS	.	G		2811,1595	496.0+/-363.4	883,1045,275	169.0	152.0	158.0		1269	-2.9	0.9	3	dbSNP_107	158	3828,4772	611.5+/-395.8	876,2076,1348	no	coding-synonymous	ATP13A4	NM_032279.2		1759,3121,1623	GG,GA,AA		44.5116,36.2006,48.9543		423/1197	193183817	6639,6367	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon11			TACCCCACTAAGC	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.1269T>C	3.37:g.193183817A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			A|0.474;G|0.526	0.526	strong		0.423	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
TMEM51	55092	hgsc.bcm.edu	37	1	15546077	15546077	+	Silent	SNP	G	G	A	rs3753313	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15546077G>A	ENST00000428417.1	+	3	1046	c.600G>A	c.(598-600)ccG>ccA	p.P200P	TMEM51_ENST00000376014.3_Silent_p.P200P|TMEM51_ENST00000400796.3_Silent_p.P200P|TMEM51_ENST00000376008.2_Silent_p.P200P|TMEM51_ENST00000434578.2_3'UTR	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	200						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		GACTGAAACCGCTGAAAGTTC	0.532													G|||	1023	0.204273	0.0741	0.2003	5008	,	,		17895	0.0754		0.3499	False		,,,				2504	0.3661				p.P200P		Atlas-SNP	.											TMEM51,NS,lymphoid_neoplasm,+1,1	TMEM51	28	1	0			c.G600A						PASS	.	G	,,,	535,3871	242.1+/-252.3	29,477,1697	70.0	81.0	77.0		600,600,600,600	-8.2	0.6	1	dbSNP_107	77	3040,5560	468.0+/-367.2	566,1908,1826	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM51	NM_001136216.1,NM_001136217.1,NM_001136218.1,NM_018022.2	,,,	595,2385,3523	AA,AG,GG		35.3488,12.1425,27.4873	,,,	200/254,200/254,200/254,200/254	15546077	3575,9431	2203	4300	6503	SO:0001819	synonymous_variant	55092	exon3			GAAACCGCTGAAA	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 72"""	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.600G>A	1.37:g.15546077G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_018022	A8K819	Silent	SNP	ENST00000428417.1	37	CCDS154.1																																																																																			G|0.767;A|0.233	0.233	strong		0.532	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022	
EPHX1	2052	hgsc.bcm.edu	37	1	226027659	226027659	+	Silent	SNP	C	C	T	rs2292568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226027659C>T	ENST00000366837.4	+	6	1048	c.852C>T	c.(850-852)ccC>ccT	p.P284P	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Silent_p.P284P	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	284					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)					TGCTGTACCCCGTCAAGGAGA	0.557													C|||	378	0.0754792	0.0227	0.0749	5008	,	,		18608	0.1538		0.0487	False		,,,				2504	0.0941				p.P284P		Atlas-SNP	.											.	EPHX1	57	.	0			c.C852T						PASS	.	C	,	106,4300	84.4+/-122.9	0,106,2097	169.0	147.0	154.0		852,852	-3.3	0.0	1	dbSNP_100	154	350,8250	118.3+/-177.8	3,344,3953	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	3,450,6050	TT,TC,CC		4.0698,2.4058,3.5061	,	284/456,284/456	226027659	456,12550	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon6			GTACCCCGTCAAG	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.852C>T	1.37:g.226027659C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			C|0.950;N|0.001	.	strong		0.557	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
SLC9C1	285335	hgsc.bcm.edu	37	3	111898387	111898387	+	Silent	SNP	A	A	G	rs74367861	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:111898387A>G	ENST00000305815.5	-	23	3162	c.2910T>C	c.(2908-2910)acT>acC	p.T970T	SLC9C1_ENST00000487372.1_Silent_p.T922T	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	970					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)	p.T970T(1)									CCTCCACTACAGTTTTGCAGG	0.323													A|||	625	0.1248	0.1195	0.0922	5008	,	,		15663	0.2133		0.0815	False		,,,				2504	0.1084				p.T970T		Atlas-SNP	.											SLC9A10,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	pancreas(1)	c.T2910C						PASS	.	A		538,3868	240.6+/-251.3	30,478,1695	92.0	98.0	96.0		2910	3.4	1.0	3	dbSNP_131	96	702,7898	173.0+/-223.6	34,634,3632	no	coding-synonymous	SLC9A10	NM_183061.1		64,1112,5327	GG,GA,AA		8.1628,12.2106,9.5341		970/1178	111898387	1240,11766	2203	4300	6503	SO:0001819	synonymous_variant	285335	exon23			CACTACAGTTTTG	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2910T>C	3.37:g.111898387A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_183061	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	37	CCDS33817.1																																																																																			A|0.902;G|0.098	0.098	strong		0.323	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
TAF10	6881	hgsc.bcm.edu	37	11	6636106	6636106	+	5'Flank	SNP	T	T	A	rs1128396	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6636106T>A	ENST00000299424.4	-	0	0				TPP1_ENST00000299427.6_Silent_p.G514G|TPP1_ENST00000533371.1_Silent_p.G271G|TAF10_ENST00000531760.1_5'Flank|TPP1_ENST00000534644.1_5'Flank	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa						chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATCAAAGAGTCCTGCCCCAT	0.537													T|||	1158	0.23123	0.23	0.2075	5008	,	,		18533	0.3512		0.161	False		,,,				2504	0.1984				p.G514G		Atlas-SNP	.											.	TPP1	71	.	0			c.A1542T						PASS	.	T		978,3424	367.1+/-318.1	111,756,1334	244.0	266.0	259.0		1542	3.8	1.0	11	dbSNP_86	259	1431,7161	275.0+/-291.5	129,1173,2994	no	coding-synonymous	TPP1	NM_000391.3		240,1929,4328	AA,AT,TT		16.655,22.2172,18.5393		514/564	6636106	2409,10585	2201	4296	6497	SO:0001631	upstream_gene_variant	1200	exon12			AAAGAGTCCTGCC	U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"""	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402		11.37:g.6636106T>A	Exception_encountered	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_000391	O00703|Q13175|Q6FH13	Silent	SNP	ENST00000299424.4	37	CCDS7769.1																																																																																			T|0.785;A|0.215	0.215	strong		0.537	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284	
PLB1	151056	hgsc.bcm.edu	37	2	28821613	28821613	+	Silent	SNP	C	C	T	rs35746006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:28821613C>T	ENST00000327757.5	+	35	2504	c.2460C>T	c.(2458-2460)ccC>ccT	p.P820P	PLB1_ENST00000422425.2_Silent_p.P809P	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	820	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)					AAGCTGTTCCCGGAGCAAAGG	0.537													C|||	187	0.0373403	0.0061	0.062	5008	,	,		23140	0.0		0.1034	False		,,,				2504	0.0327				p.P820P		Atlas-SNP	.											PLB1_ENST00000422425,rectum,carcinoma,0,2	PLB1	255	2	0			c.C2460T						PASS	.	C	,	90,4316	74.1+/-112.3	1,88,2114	126.0	117.0	120.0		2427,2460	-3.0	1.0	2	dbSNP_126	120	912,7688	203.4+/-246.4	44,824,3432	no	coding-synonymous,coding-synonymous	PLB1	NM_001170585.1,NM_153021.4	,	45,912,5546	TT,TC,CC		10.6047,2.0427,7.7041	,	809/1448,820/1459	28821613	1002,12004	2203	4300	6503	SO:0001819	synonymous_variant	151056	exon35			TGTTCCCGGAGCA		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.2460C>T	2.37:g.28821613C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	125	0.05723443223443223	7	0.014227642276422764	32	0.08839779005524862	0	0.0	86	0.11345646437994723	C	6.397	0.441408	0.12164	0.020427	0.106047	ENSG00000163803	ENST00000404858	T	0.23147	1.92	5.84	-3.04	0.05412	.	0.176611	0.40908	D	0.000982	T	0.00328	0.0010	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.07501	-1.0769	6	0.54805	T	0.06	-7.3789	1.0688	0.01616	0.1433:0.2178:0.1962:0.4428	rs35746006;rs61745135	.	.	.	L	808	ENSP00000384187:P808L	ENSP00000384187:P808L	P	+	2	0	PLB1	28675117	0.014000	0.17966	0.980000	0.43619	0.589000	0.36550	-1.888000	0.01616	-0.131000	0.11578	-1.434000	0.01081	CCG	C|0.931;T|0.069	0.069	strong		0.537	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
KIAA1755	85449	hgsc.bcm.edu	37	20	36850940	36850940	+	Silent	SNP	G	G	C	rs41310010	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36850940G>C	ENST00000279024.4	-	10	2599	c.2328C>G	c.(2326-2328)ccC>ccG	p.P776P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	776										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)				CCAGTAGGCCGGGGTCCCTCA	0.657											OREG0025921	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	546	0.109026	0.1649	0.0461	5008	,	,		18609	0.0992		0.0696	False		,,,				2504	0.1288				p.P776P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C2328G						PASS	.	C		680,3726	759.2+/-412.9	65,550,1588	50.0	47.0	48.0		2328	-9.9	0.5	20	dbSNP_127	48	582,8018	790.4+/-407.6	23,536,3741	no	coding-synonymous	KIAA1755	NM_001029864.1		88,1086,5329	CC,CG,GG		6.7674,15.4335,9.7032		776/1201	36850940	1262,11744	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon10			TAGGCCGGGGTCC	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.2328C>G	20.37:g.36850940G>C		Somatic	38	0	0	866	WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.891;C|0.109	0.109	strong		0.657	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
RPH3AL	9501	hgsc.bcm.edu	37	17	171137	171137	+	Silent	SNP	C	C	A	rs78269977	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:171137C>A	ENST00000331302.7	-	4	454	c.147G>T	c.(145-147)ccG>ccT	p.P49P	RPH3AL_ENST00000536489.2_Silent_p.P49P|RP11-1260E13.1_ENST00000570501.1_RNA|RPH3AL_ENST00000576001.1_5'Flank|RPH3AL_ENST00000323434.8_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	82	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	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	
POTEE	445582	hgsc.bcm.edu	37	2	131976353	131976353	+	Silent	SNP	C	C	T	rs62177516		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:131976353C>T	ENST00000356920.5	+	1	472	c.378C>T	c.(376-378)agC>agT	p.S126S	PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron|POTEE_ENST00000358087.5_Silent_p.S126S	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	126					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											ACGATGACAGCGCCTTCATGG	0.597																																					p.S126S		Atlas-SNP	.											POTE2_HUMAN,right_upper_lobe,carcinoma,+1,2	.	.	2	0			c.C378T						scavenged	.						107.0	111.0	110.0					2																	131976353		2203	4300	6503	SO:0001819	synonymous_variant	445582	exon1			TGACAGCGCCTTC	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.378C>T	2.37:g.131976353C>T		Somatic	378	1	0.0026455		WXS	Illumina HiSeq	Phase_I	445	59	0.132584	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	ENST00000356920.5	37	CCDS46414.1																																																																																			C|0.500;T|0.500	0.500	weak		0.597	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
COL6A3	1293	hgsc.bcm.edu	37	2	238283605	238283605	+	Silent	SNP	G	G	A	rs12622093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238283605G>A	ENST00000295550.4	-	8	3581	c.3129C>T	c.(3127-3129)ggC>ggT	p.G1043G	COL6A3_ENST00000347401.3_Silent_p.G842G|COL6A3_ENST00000353578.4_Silent_p.G837G|COL6A3_ENST00000392004.3_Silent_p.G837G|COL6A3_ENST00000392003.2_Silent_p.G636G|COL6A3_ENST00000346358.4_Silent_p.G843G|COL6A3_ENST00000472056.1_Silent_p.G436G|COL6A3_ENST00000409809.1_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	44	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	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	
HDHD1	8226	hgsc.bcm.edu	37	X	7023678	7023678	+	Missense_Mutation	SNP	G	G	A	rs1131197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:7023678G>A	ENST00000381077.5	-	2	339	c.263C>T	c.(262-264)aCg>aTg	p.T88M	HDHD1_ENST00000498474.2_5'UTR|HDHD1_ENST00000540122.1_Missense_Mutation_p.T88M|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	127	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	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	
CNOT4	4850	hgsc.bcm.edu	37	7	135123060	135123060	+	Missense_Mutation	SNP	G	G	C	rs17480616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:135123060G>C	ENST00000315544.5	-	2	299	c.20C>G	c.(19-21)gCg>gGg	p.A7G	CNOT4_ENST00000423368.2_Missense_Mutation_p.A7G|CNOT4_ENST00000451834.1_Missense_Mutation_p.A7G|CNOT4_ENST00000428680.2_Missense_Mutation_p.A7G|CNOT4_ENST00000361528.4_Missense_Mutation_p.A7G|CNOT4_ENST00000414802.1_Missense_Mutation_p.A7G|CNOT4_ENST00000356162.4_Missense_Mutation_p.A7G|CNOT4_ENST00000541284.1_Missense_Mutation_p.A7G	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	7			A -> G (in dbSNP:rs17480616). {ECO:0000269|Ref.3}.		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)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						GTCTTCCTTCGCATCAGGACT	0.433													G|||	37	0.00738818	0.0023	0.0173	5008	,	,		17128	0.0		0.0209	False		,,,				2504	0.001				p.A7G	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.C20G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	17,3759		0,17,1871	67.0	63.0	65.0		20,20,20,20,20,20	1.5	1.0	7	dbSNP_123	65	228,7992		4,220,3886	yes	missense,missense,missense,missense,missense,missense	CNOT4	NM_001008225.2,NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,NM_013316.3	60,60,60,60,60,60	4,237,5757	CC,CG,GG		2.7737,0.4502,2.0423	benign,benign,benign,benign,benign,benign	7/573,7/643,7/576,7/711,7/714,7/640	135123060	245,11751	1888	4110	5998	SO:0001583	missense	4850	exon2			TCCTTCGCATCAG	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.20C>G	7.37:g.135123060G>C	ENSP00000326731:p.Ala7Gly	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	27	0.012362637362637362	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	14	0.018469656992084433	G	12.53	1.964625	0.34659	0.004502	0.027737	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;D;D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08	5.87	1.55	0.23275	Zinc finger, RING/FYVE/PHD-type (1);	0.373548	0.33938	N	0.004417	T	0.50103	0.1596	N	0.14661	0.345	0.21290	N	0.999735	B;B;B;P;B;B	0.34997	0.211;0.315;0.405;0.479;0.019;0.019	B;B;B;B;B;B	0.31946	0.071;0.138;0.102;0.119;0.022;0.022	T	0.54063	-0.8349	10	0.32370	T	0.25	0.5143	9.3711	0.38254	0.4834:0.0:0.5166:0.0	rs17480616;rs52814664;rs17480616	7;7;7;7;7;7	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	G	7	ENSP00000445508:A7G;ENSP00000388491:A7G;ENSP00000406777:A7G;ENSP00000354673:A7G;ENSP00000416532:A7G;ENSP00000348485:A7G;ENSP00000399108:A7G;ENSP00000326731:A7G	ENSP00000262563:A7G	A	-	2	0	CNOT4	134773600	0.999000	0.42202	0.976000	0.42696	0.929000	0.56500	1.442000	0.35046	-0.007000	0.14345	0.655000	0.94253	GCG	G|0.983;C|0.017	0.017	strong		0.433	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
FSTL5	56884	hgsc.bcm.edu	37	4	162841653	162841653	+	Silent	SNP	G	G	A	rs359502	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:162841653G>A	ENST00000306100.5	-	4	748	c.312C>T	c.(310-312)gaC>gaT	p.D104D	FSTL5_ENST00000427802.2_Silent_p.D103D|FSTL5_ENST00000536695.1_Silent_p.D103D|FSTL5_ENST00000379164.4_Silent_p.D103D	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	104	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		AGAATTCTCCGTCAGATCCAC	0.438													A|||	502	0.10024	0.2481	0.0447	5008	,	,		16702	0.0298		0.006	False		,,,				2504	0.1094				p.D104D		Atlas-SNP	.											.	FSTL5	207	.	0			c.C312T						PASS	.	A	,,	844,3562	746.3+/-411.7	82,680,1441	128.0	116.0	120.0		309,309,312	0.3	1.0	4	dbSNP_79	120	49,8551	816.6+/-406.9	0,49,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	,,	82,729,5692	AA,AG,GG		0.5698,19.1557,6.8661	,,	103/847,103/838,104/848	162841653	893,12113	2203	4300	6503	SO:0001819	synonymous_variant	56884	exon4			TTCTCCGTCAGAT	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.312C>T	4.37:g.162841653G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	238	116	0.487395	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			G|0.914;A|0.086	0.086	strong		0.438	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
IL1R1	3554	hgsc.bcm.edu	37	2	102792875	102792875	+	Silent	SNP	A	A	C	rs3917320	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102792875A>C	ENST00000410023.1	+	12	1684	c.1366A>C	c.(1366-1368)Aga>Cga	p.R456R	IL1R1_ENST00000233946.3_Silent_p.R456R|IL1R1_ENST00000424272.1_3'UTR|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000409929.1_Silent_p.R425R			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	456	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				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)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	CATTTTAGTCAGAGAAACATC	0.368													A|||	232	0.0463259	0.1089	0.0418	5008	,	,		20122	0.0		0.0537	False		,,,				2504	0.0051				p.R456R		Atlas-SNP	.											.	IL1R1	52	.	0			c.A1366C						PASS	.	A		376,4030	191.2+/-216.9	18,340,1845	60.0	61.0	61.0		1366	-1.0	0.3	2	dbSNP_108	61	444,8156	134.3+/-191.7	12,420,3868	no	coding-synonymous	IL1R1	NM_000877.2		30,760,5713	CC,CA,AA		5.1628,8.5338,6.3048		456/570	102792875	820,12186	2203	4300	6503	SO:0001819	synonymous_variant	3554	exon11			TTAGTCAGAGAAA	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.1366A>C	2.37:g.102792875A>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	37	0.324561	NM_000877	Q587I7	Silent	SNP	ENST00000410023.1	37	CCDS2055.1																																																																																			A|0.943;C|0.057	0.057	strong		0.368	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
CRYBB2	1415	hgsc.bcm.edu	37	22	25627604	25627604	+	Silent	SNP	G	G	A	rs8140949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	146	0	0		WXS	Illumina HiSeq	Phase_I	143	57	0.398601	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	
DENND2C	163259	hgsc.bcm.edu	37	1	115130353	115130353	+	Silent	SNP	C	C	T	rs61000990	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:115130353C>T	ENST00000393274.1	-	19	3277	c.2652G>A	c.(2650-2652)cgG>cgA	p.R884R	DENND2C_ENST00000393277.1_Silent_p.R772R|DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393276.3_Silent_p.R827R	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	884					positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCCACTTTTCCGAAGCTCTC	0.393													C|||	271	0.0541134	0.0545	0.0519	5008	,	,		16954	0.0139		0.0507	False		,,,				2504	0.1002				p.R884R		Atlas-SNP	.											.	DENND2C	105	.	0			c.G2652A						PASS	.	C		191,4215	113.3+/-151.4	4,183,2016	50.0	50.0	50.0		2481	1.6	1.0	1	dbSNP_129	50	425,8175	123.4+/-182.3	18,389,3893	no	coding-synonymous	DENND2C	NM_198459.3		22,572,5909	TT,TC,CC		4.9419,4.335,4.7363		827/872	115130353	616,12390	2203	4300	6503	SO:0001819	synonymous_variant	163259	exon19			ACTTTTCCGAAGC		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.2652G>A	1.37:g.115130353C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Silent	SNP	ENST00000393274.1	37	CCDS58018.1																																																																																			C|0.949;T|0.051	0.051	strong		0.393	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
CIT	11113	hgsc.bcm.edu	37	12	120260706	120260706	+	Silent	SNP	G	G	A	rs145804827		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120260706G>A	ENST00000261833.7	-	9	1081	c.1029C>T	c.(1027-1029)tgC>tgT	p.C343C	CIT_ENST00000392521.2_Silent_p.C343C	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	343	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		CTTTCTGGCCGCACAACAAGC	0.388													A|||	1	0.000199681	0.0	0.0	5008	,	,		17060	0.0		0.001	False		,,,				2504	0.0				p.C343C		Atlas-SNP	.											.	CIT	535	.	0			c.C1029T						PASS	.	A	,	1,4405	826.1+/-416.6	0,1,2202	100.0	94.0	96.0		1029,1029	4.6	1.0	12	dbSNP_134	96	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	,	343/2070,343/2028	120260706	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon9			CTGGCCGCACAAC	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.1029C>T	12.37:g.120260706G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.388	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
LRIT2	340745	hgsc.bcm.edu	37	10	85981801	85981801	+	Missense_Mutation	SNP	T	T	G	rs6585847	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85981801T>G	ENST00000372113.4	-	3	1533	c.1528A>C	c.(1528-1530)Acc>Ccc	p.T510P	LRIT2_ENST00000538192.1_Missense_Mutation_p.T520P	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	510			T -> P (in dbSNP:rs6585847).			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						GCTGCAGGGGTGCAGCTGGGG	0.627													G|||	2780	0.555112	0.8192	0.5346	5008	,	,		18652	0.4107		0.4662	False		,,,				2504	0.453				p.T510P		Atlas-SNP	.											LRIT2,colon,carcinoma,0,3	LRIT2	81	3	0			c.A1528C						PASS	.	G	PRO/THR	3294,1108		1273,748,180	55.0	62.0	60.0		1528	5.1	0.1	10	dbSNP_116	60	3909,4689		934,2041,1324	yes	missense	LRIT2	NM_001017924.2	38	2207,2789,1504	GG,GT,TT		45.4641,25.1704,44.5923	benign	510/551	85981801	7203,5797	2201	4299	6500	SO:0001583	missense	340745	exon3			CAGGGGTGCAGCT		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.1528A>C	10.37:g.85981801T>G	ENSP00000361185:p.Thr510Pro	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	115	46	0.4	NM_001017924	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	1173	0.5370879120879121	410	0.8333333333333334	189	0.5220994475138122	219	0.38286713286713286	355	0.4683377308707124	G	2.589	-0.295668	0.05532	0.748296	0.454641	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.10099	2.91;2.91	5.06	5.06	0.68205	.	0.677483	0.14615	N	0.308798	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	0.28235	-1.0050	9	0.02654	T	1	.	11.3765	0.49730	0.0:0.0:0.8184:0.1816	rs6585847;rs57540747	520;510	B7ZME6;A6NDA9	.;LRIT2_HUMAN	P	510;520	ENSP00000361185:T510P;ENSP00000438264:T520P	ENSP00000361185:T510P	T	-	1	0	LRIT2	85971781	0.039000	0.19947	0.109000	0.21407	0.030000	0.12068	1.715000	0.37971	1.288000	0.44600	-0.121000	0.15023	ACC	T|0.443;G|0.557	0.557	strong		0.627	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
HPS1	3257	hgsc.bcm.edu	37	10	100190920	100190920	+	Silent	SNP	G	G	A	rs1801287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:100190920G>A	ENST00000325103.6	-	7	869	c.636C>T	c.(634-636)ctC>ctT	p.L212L	HPS1_ENST00000467246.1_5'UTR|MIR4685_ENST00000578185.1_RNA|HPS1_ENST00000338546.5_Silent_p.L212L|HPS1_ENST00000361490.4_Silent_p.L212L	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	212					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGGAGTGCACGAGCAGGAAGG	0.622									Hermansky-Pudlak syndrome				G|||	1417	0.282947	0.1369	0.2911	5008	,	,		20397	0.3442		0.2952	False		,,,				2504	0.3988				p.L212L		Atlas-SNP	.											HPS1,NS,carcinoma,0,1	HPS1	65	1	0			c.C636T						PASS	.	G	,	592,3814	258.9+/-262.7	45,502,1656	64.0	56.0	59.0		636,636	-10.6	0.2	10	dbSNP_89	59	2515,6085	408.7+/-349.6	385,1745,2170	no	coding-synonymous,coding-synonymous	HPS1	NM_000195.3,NM_182639.2	,	430,2247,3826	AA,AG,GG		29.2442,13.4362,23.889	,	212/701,212/325	100190920	3107,9899	2203	4300	6503	SO:0001819	synonymous_variant	3257	exon7	Familial Cancer Database	HPS, HPS1-8	GTGCACGAGCAGG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.636C>T	10.37:g.100190920G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1	601	0.2751831501831502	68	0.13821138211382114	104	0.287292817679558	202	0.3531468531468531	227	0.2994722955145119	G	7.097	0.573403	0.13623	0.134362	0.292442	ENSG00000107521	ENST00000414009	.	.	.	5.3	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999561151	.	.	.	.	.	.	T	0.12218	-1.0556	3	.	.	.	.	8.2338	0.31614	0.3875:0.4577:0.0859:0.0689	rs1801287;rs17535258;rs1801287	.	.	.	C	80	.	.	R	-	1	0	HPS1	100180910	0.000000	0.05858	0.235000	0.24058	0.788000	0.44548	-1.746000	0.01829	-2.442000	0.00549	-2.005000	0.00442	CGT	G|0.745;A|0.255	0.255	strong		0.622	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
UGT3A2	167127	hgsc.bcm.edu	37	5	36037933	36037933	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:36037933C>T	ENST00000282507.3	-	6	1362	c.1261G>A	c.(1261-1263)Gct>Act	p.A421T	UGT3A2_ENST00000545528.1_Missense_Mutation_p.A119T|UGT3A2_ENST00000513300.1_Missense_Mutation_p.A387T|UGT3A2_ENST00000504954.1_5'Flank	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	421					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)			ATCTTAAGAGCCAATGTCTCT	0.438																																					p.A421T		Atlas-SNP	.											.	UGT3A2	117	.	0			c.G1261A						PASS	.						174.0	160.0	165.0					5																	36037933		2203	4300	6503	SO:0001583	missense	167127	exon6			TAAGAGCCAATGT		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.1261G>A	5.37:g.36037933C>T	ENSP00000282507:p.Ala421Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	C	8.741	0.918940	0.17982	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.63580	-0.05;-0.05;3.2	3.18	0.239	0.15484	.	0.283721	0.27802	U	0.017798	T	0.48677	0.1513	L	0.42581	1.335	0.09310	N	1	B;B	0.26400	0.009;0.148	B;B	0.31191	0.024;0.125	T	0.36939	-0.9727	10	0.37606	T	0.19	.	6.4334	0.21809	0.3166:0.5888:0.0:0.0946	.	387;421	E9PFK7;Q3SY77	.;UD3A2_HUMAN	T	421;387;119	ENSP00000282507:A421T;ENSP00000427404:A387T;ENSP00000445367:A119T	ENSP00000282507:A421T	A	-	1	0	UGT3A2	36073690	0.000000	0.05858	0.014000	0.15608	0.623000	0.37688	-0.069000	0.11542	0.018000	0.15052	0.563000	0.77884	GCT	.	.	none		0.438	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914	
ADRB2	154	hgsc.bcm.edu	37	5	148207447	148207447	+	Silent	SNP	G	G	C	rs1042719	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:148207447G>C	ENST00000305988.4	+	1	1292	c.1053G>C	c.(1051-1053)ggG>ggC	p.G351G		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	351					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	AGGCCTATGGGAATGGCTACT	0.522													G|||	1874	0.374201	0.3533	0.3516	5008	,	,		18458	0.4772		0.2793	False		,,,				2504	0.41				p.G351G		Atlas-SNP	.											.	ADRB2	42	.	0			c.G1053C						PASS	.	G		1554,2852	486.7+/-360.7	281,992,930	55.0	57.0	56.0		1053	3.9	1.0	5	dbSNP_86	56	2468,6132	407.0+/-349.0	350,1768,2182	no	coding-synonymous	ADRB2	NM_000024.5		631,2760,3112	CC,CG,GG		28.6977,35.2701,30.9242		351/414	148207447	4022,8984	2203	4300	6503	SO:0001819	synonymous_variant	154	exon1			CTATGGGAATGGC	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.1053G>C	5.37:g.148207447G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																			G|0.668;C|0.332	0.332	strong		0.522	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
CCDC102B	79839	hgsc.bcm.edu	37	18	66513615	66513615	+	Missense_Mutation	SNP	A	A	G	rs2187094	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:66513615A>G	ENST00000360242.5	+	4	1010	c.893A>G	c.(892-894)aAg>aGg	p.K298R	CCDC102B_ENST00000584156.1_Missense_Mutation_p.K298R|CCDC102B_ENST00000358653.5_Splice_Site_p.E312E|CCDC102B_ENST00000577772.1_3'UTR|CCDC102B_ENST00000319445.6_Missense_Mutation_p.K298R	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	298			K -> R (in dbSNP:rs2187094). {ECO:0000269|PubMed:17974005}.					p.K298R(1)		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)				TGGAAGTGGAAGTATGAAGAA	0.358													A|||	1842	0.367812	0.0703	0.4467	5008	,	,		12915	0.6438		0.4006	False		,,,				2504	0.3957				p.K298R		Atlas-SNP	.											CCDC102B,NS,carcinoma,0,2	CCDC102B	92	2	1	Substitution - Missense(1)	stomach(1)	c.A893G						PASS	.	A	ARG/LYS,ARG/LYS	561,3845	245.3+/-254.3	37,487,1679	70.0	70.0	70.0		893,893	4.4	1.0	18	dbSNP_96	70	3289,5311	486.0+/-371.8	639,2011,1650	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	26,26	676,2498,3329	GG,GA,AA		38.2442,12.7326,29.6017	benign,benign	298/514,298/514	66513615	3850,9156	2203	4300	6503	SO:0001583	missense	79839	exon6			AGTGGAAGTATGA	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.893A>G	18.37:g.66513615A>G	ENSP00000353377:p.Lys298Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	168	96	0.571429	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	850	0.3891941391941392	37	0.07520325203252033	156	0.430939226519337	359	0.6276223776223776	298	0.39313984168865435	A	8.901	0.956416	0.18507	0.127326	0.382442	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.15256	2.44;2.44	5.56	4.4	0.53042	.	0.000000	0.64402	D	0.000011	T	0.00012	0.0000	L	0.37697	1.125	0.09310	P	1.0	P	0.47034	0.889	B	0.42827	0.399	T	0.11155	-1.0599	9	0.18710	T	0.47	-26.3717	9.5041	0.39035	0.9196:0.0:0.0804:0.0	rs2187094;rs52829798;rs58141486;rs2187094	298	Q68D86	C102B_HUMAN	R	298	ENSP00000316237:K298R;ENSP00000353377:K298R	ENSP00000316237:K298R	K	+	2	0	CCDC102B	64664595	1.000000	0.71417	0.998000	0.56505	0.313000	0.28021	2.635000	0.46537	1.043000	0.40175	0.528000	0.53228	AAG	A|0.674;G|0.326	0.326	strong		0.358	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
LYST	1130	hgsc.bcm.edu	37	1	235972867	235972867	+	Silent	SNP	T	T	C	rs1063128	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	62	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	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		
HYDIN	54768	hgsc.bcm.edu	37	16	71025245	71025245	+	Silent	SNP	C	C	T	rs1774516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71025245C>T	ENST00000393567.2	-	25	3990	c.3840G>A	c.(3838-3840)acG>acA	p.T1280T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1280					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)				TGGAAGCTTTCGTTTTTCTTA	0.463																																					p.T1280T		Atlas-SNP	.											LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	0			c.G3840A						scavenged	.						130.0	119.0	122.0					16																	71025245		1909	4145	6054	SO:0001819	synonymous_variant	54768	exon25			AGCTTTCGTTTTT	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.3840G>A	16.37:g.71025245C>T		Somatic	145	11	0.0758621		WXS	Illumina HiSeq	Phase_I	183	14	0.0765027	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
LOXL4	84171	hgsc.bcm.edu	37	10	100020880	100020880	+	Missense_Mutation	SNP	C	C	T	rs33995374	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:100020880C>T	ENST00000260702.3	-	4	611	c.461G>A	c.(460-462)cGg>cAg	p.R154Q		NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	154			R -> Q (in dbSNP:rs33995374).			extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		CTCCAGCCGCCGGCCCTGCGG	0.657													C|||	450	0.0898562	0.0303	0.085	5008	,	,		16945	0.1062		0.1332	False		,,,				2504	0.1125				p.R154Q		Atlas-SNP	.											.	LOXL4	60	.	0			c.G461A						PASS	.	C	GLN/ARG	256,4148		9,238,1955	38.0	35.0	36.0		461	-3.5	1.0	10	dbSNP_126	36	1219,7375		96,1027,3174	yes	missense	LOXL4	NM_032211.6	43	105,1265,5129	TT,TC,CC		14.1843,5.8129,11.3479	benign	154/757	100020880	1475,11523	2202	4297	6499	SO:0001583	missense	84171	exon4			AGCCGCCGGCCCT	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.461G>A	10.37:g.100020880C>T	ENSP00000260702:p.Arg154Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	37	CCDS7473.1	207	0.09478021978021978	14	0.028455284552845527	36	0.09944751381215469	57	0.09965034965034965	100	0.13192612137203166	C	6.951	0.545293	0.13312	0.058129	0.141843	ENSG00000138131	ENST00000260702	T	0.47177	0.85	5.43	-3.54	0.04653	Speract/scavenger receptor-related (1);	0.437295	0.19564	N	0.111255	T	0.00144	0.0004	N	0.19112	0.55	0.47994	P	4.330000000000167E-4	B	0.13145	0.007	B	0.04013	0.001	T	0.14090	-1.0485	9	0.14252	T	0.57	.	4.6645	0.12659	0.1146:0.2095:0.1023:0.5736	rs33995374	154	Q96JB6	LOXL4_HUMAN	Q	154	ENSP00000260702:R154Q	ENSP00000260702:R154Q	R	-	2	0	LOXL4	100010870	0.024000	0.19004	0.958000	0.39756	0.456000	0.32438	-1.163000	0.03138	-0.556000	0.06134	-0.812000	0.03155	CGG	C|0.888;T|0.112	0.112	strong		0.657	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
FAM175B	23172	hgsc.bcm.edu	37	10	126515249	126515249	+	Missense_Mutation	SNP	G	G	A	rs140695652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:126515249G>A	ENST00000298492.5	+	5	398	c.353G>A	c.(352-354)cGc>cAc	p.R118H		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	118					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						CAGCTCACCCGCATCCTCGGC	0.498													G|||	2	0.000399361	0.0	0.0014	5008	,	,		20576	0.0		0.001	False		,,,				2504	0.0				p.R118H		Atlas-SNP	.											.	FAM175B	39	.	0			c.G353A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	195.0	173.0	180.0		353	3.8	1.0	10	dbSNP_134	180	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FAM175B	NM_032182.3	29	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	benign	118/416	126515249	6,13000	2203	4300	6503	SO:0001583	missense	23172	exon5			TCACCCGCATCCT	D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"""Abraxas brother"""	611144	"""KIAA0157"""	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.353G>A	10.37:g.126515249G>A	ENSP00000298492:p.Arg118His	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_032182	B4DKR2|Q96H11	Missense_Mutation	SNP	ENST00000298492.5	37	CCDS31308.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	14.64	2.596729	0.46318	2.27E-4	5.81E-4	ENSG00000165660	ENST00000298492	T	0.43294	0.95	5.82	3.76	0.43208	.	0.413144	0.28459	N	0.015269	T	0.21267	0.0512	N	0.11560	0.145	0.35051	D	0.760609	B	0.12630	0.006	B	0.08055	0.003	T	0.13629	-1.0502	10	0.40728	T	0.16	-9.0446	6.6535	0.22975	0.3087:0.0:0.6913:0.0	.	118	Q15018	F175B_HUMAN	H	118	ENSP00000298492:R118H	ENSP00000298492:R118H	R	+	2	0	FAM175B	126505239	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	4.660000	0.61511	1.470000	0.48102	0.557000	0.71058	CGC	G|1.000;A|0.000	0.000	strong		0.498	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182	
DDX27	55661	hgsc.bcm.edu	37	20	47841660	47841660	+	Missense_Mutation	SNP	G	G	T	rs11553387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	195	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	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		
FASN	2194	hgsc.bcm.edu	37	17	80037253	80037253	+	Missense_Mutation	SNP	C	C	T	rs149224679		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80037253C>T	ENST00000306749.2	-	42	7596	c.7378G>A	c.(7378-7380)Gcg>Acg	p.A2460T	FASN_ENST00000579758.1_5'UTR	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2460	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			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)	TTGTAGTCCGCGCCCAGGTCC	0.662													.|||	1	0.000199681	0.0	0.0	5008	,	,		13195	0.0		0.001	False		,,,				2504	0.0				p.A2460T	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											FASN,colon,carcinoma,+1,1	FASN	154	1	0			c.G7378A						PASS	.	C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	67.0	62.0	63.0		7378	2.3	1.0	17	dbSNP_134	63	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FASN	NM_004104.4	58	0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538	possibly-damaging	2460/2512	80037253	7,12999	2203	4300	6503	SO:0001583	missense	2194	exon42			AGTCCGCGCCCAG	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.7378G>A	17.37:g.80037253C>T	ENSP00000304592:p.Ala2460Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	2.912	-0.225212	0.06022	4.54E-4	5.81E-4	ENSG00000169710	ENST00000306749	T	0.26223	1.75	4.46	2.28	0.28536	Thioesterase (1);	0.598725	0.16037	N	0.232575	T	0.17152	0.0412	L	0.54323	1.7	0.09310	N	1	P	0.35600	0.511	B	0.24701	0.055	T	0.11867	-1.0570	10	0.19590	T	0.45	-25.5473	6.4869	0.22093	0.0:0.6284:0.1613:0.2103	.	2460	P49327	FAS_HUMAN	T	2460	ENSP00000304592:A2460T	ENSP00000304592:A2460T	A	-	1	0	FASN	77630542	0.003000	0.15002	0.997000	0.53966	0.114000	0.19823	1.776000	0.38594	1.077000	0.40990	-0.304000	0.09214	GCG	C|1.000;T|0.000	0.000	strong		0.662	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
GIMAP8	155038	hgsc.bcm.edu	37	7	150171710	150171710	+	Silent	SNP	T	T	C	rs60114833	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150171710T>C	ENST00000307271.3	+	4	1867	c.1293T>C	c.(1291-1293)tgT>tgC	p.C431C		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	431	AIG1-type G 2.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		ACAAGCATTGTGTTTTCAGAG	0.343													T|||	1301	0.259784	0.1097	0.2233	5008	,	,		15551	0.4187		0.3698	False		,,,				2504	0.2117				p.C431C		Atlas-SNP	.											.	GIMAP8	136	.	0			c.T1293C						PASS	.	T		697,3709	291.3+/-281.4	59,579,1565	67.0	71.0	70.0		1293	-3.3	0.0	7	dbSNP_129	70	3020,5580	463.4+/-366.0	550,1920,1830	no	coding-synonymous	GIMAP8	NM_175571.2		609,2499,3395	CC,CT,TT		35.1163,15.8193,28.5791		431/666	150171710	3717,9289	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon4			GCATTGTGTTTTC	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1293T>C	7.37:g.150171710T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	57	39	0.684211	NM_175571		Silent	SNP	ENST00000307271.3	37	CCDS34777.1																																																																																			T|0.704;C|0.296	0.296	strong		0.343	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
TARBP1	6894	hgsc.bcm.edu	37	1	234529540	234529540	+	Silent	SNP	G	G	A	rs1134756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	190	0	0		WXS	Illumina HiSeq	Phase_I	169	58	0.343195	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	
PSCA	8000	hgsc.bcm.edu	37	8	143763531	143763531	+	Nonsense_Mutation	SNP	G	G	A	rs138377917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:143763531G>A	ENST00000301258.4	+	3	409	c.326G>A	c.(325-327)tGg>tAg	p.W109*		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	118						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CTGCTGCTCTGGGGACCCGGC	0.706													G|||	38	0.00758786	0.0008	0.013	5008	,	,		14034	0.0		0.0258	False		,,,				2504	0.002				p.W109X		Atlas-SNP	.											PSCA,rectum,carcinoma,0,1	PSCA	9	1	0			c.G326A						PASS	.	G	stop/TRP	29,4163		1,27,2068	19.0	22.0	21.0		326	3.2	1.0	8	dbSNP_134	21	287,8139		7,273,3933	yes	stop-gained	PSCA	NM_005672.4		8,300,6001	AA,AG,GG		3.4061,0.6918,2.5044		109/115	143763531	316,12302	2096	4213	6309	SO:0001587	stop_gained	8000	exon3			TGCTCTGGGGACC	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.326G>A	8.37:g.143763531G>A	ENSP00000301258:p.Trp109*	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_005672	Q6UW92	Nonsense_Mutation	SNP	ENST00000301258.4	37	CCDS47925.2	27	0.012362637362637362	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	19	0.025065963060686015	G	17.42	3.384145	0.61845	0.006918	0.034061	ENSG00000167653	ENST00000301258	.	.	.	3.21	3.21	0.36854	.	0.705245	0.11876	N	0.520920	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1903	0.43021	0.0:0.0:1.0:0.0	.	.	.	.	X	118	.	ENSP00000301258:W118X	W	+	2	0	PSCA	143760533	0.999000	0.42202	0.953000	0.39169	0.012000	0.07955	1.837000	0.39201	2.096000	0.63516	0.563000	0.77884	TGG	G|0.988;A|0.012	0.012	strong		0.706	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
SCFD1	23256	hgsc.bcm.edu	37	14	31099738	31099738	+	Missense_Mutation	SNP	A	A	G	rs229150	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:31099738A>G	ENST00000458591.2	+	3	415	c.188A>G	c.(187-189)aAg>aGg	p.K63R	SCFD1_ENST00000421551.3_Intron|SCFD1_ENST00000396629.2_Intron|SCFD1_ENST00000541123.1_5'UTR|SCFD1_ENST00000544052.2_5'UTR	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	63			K -> R (in dbSNP:rs229150). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		CTATCTGTGAAGGAGCTAAGA	0.323													A|||	2893	0.577676	0.7935	0.5029	5008	,	,		17065	0.7103		0.3608	False		,,,				2504	0.4254				p.K63R		Atlas-SNP	.											SCFD1,NS,carcinoma,0,1	SCFD1	43	1	0			c.A188G						PASS	.	A	ARG/LYS,	3123,1283	699.6+/-406.5	1127,869,207	152.0	159.0	157.0		188,	5.6	1.0	14	dbSNP_79	157	2940,5658	457.1+/-364.2	506,1928,1865	yes	missense,utr-5	SCFD1	NM_016106.2,NM_182835.1	26,	1633,2797,2072	GG,GA,AA		34.194,29.1194,46.6241	benign,	63/643,	31099738	6063,6941	2203	4299	6502	SO:0001583	missense	23256	exon3			CTGTGAAGGAGCT	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 163"""	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.188A>G	14.37:g.31099738A>G	ENSP00000390783:p.Lys63Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	78	49	0.628205	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	CCDS9639.1	1221	0.5590659340659341	388	0.7886178861788617	169	0.46685082872928174	405	0.708041958041958	259	0.341688654353562	A	15.51	2.853519	0.51270	0.708806	0.34194	ENSG00000092108	ENST00000458591;ENST00000557076	T;T	0.29917	1.55;1.55	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.49126	1.545	0.09310	P	1.0	B	0.17667	0.023	B	0.32928	0.155	T	0.25676	-1.0125	9	0.42905	T	0.14	-17.8222	15.7861	0.78304	1.0:0.0:0.0:0.0	rs229150;rs230378;rs17362188;rs17851559;rs52794734;rs60052190;rs229150	63	Q8WVM8	SCFD1_HUMAN	R	63;38	ENSP00000390783:K63R;ENSP00000450755:K38R	ENSP00000309417:K71R	K	+	2	0	SCFD1	30169489	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.719000	0.91436	2.129000	0.65627	0.528000	0.53228	AAG	G|0.519;N|0.000	0.519	strong		0.323	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835	
MPRIP	23164	hgsc.bcm.edu	37	17	17062065	17062065	+	Missense_Mutation	SNP	C	C	G	rs138508481	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:17062065C>G	ENST00000341712.4	+	14	1795	c.1795C>G	c.(1795-1797)Ctc>Gtc	p.L599V	MPRIP_ENST00000395804.3_Missense_Mutation_p.L599V|MPRIP_ENST00000395811.5_Missense_Mutation_p.L599V|MPRIP_ENST00000444976.1_Missense_Mutation_p.L561V			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	599	Interaction with RHOA.					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						CTTCGGGATGCTCGACGCCAC	0.692													C|||	7	0.00139776	0.0008	0.0	5008	,	,		15711	0.0		0.005	False		,,,				2504	0.001				p.L599V		Atlas-SNP	.											.	MPRIP	87	.	0			c.C1795G						PASS	.	C	VAL/LEU,VAL/LEU	0,4402		0,0,2201	29.0	33.0	32.0		1795,1795	4.1	0.4	17	dbSNP_134	32	20,8562		0,20,4271	no	missense,missense	MPRIP	NM_015134.3,NM_201274.3	32,32	0,20,6472	GG,GC,CC		0.233,0.0,0.154	,	599/1039,599/1026	17062065	20,12964	2201	4291	6492	SO:0001583	missense	23164	exon14			GGGATGCTCGACG	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.1795C>G	17.37:g.17062065C>G	ENSP00000342379:p.Leu599Val	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	37	CCDS32578.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	C|C	3.840|3.840	-0.034057|-0.034057	0.07543|0.07543	0.0|0.0	0.00233|0.00233	ENSG00000133030|ENSG00000133030	ENST00000423885|ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	.|T;T;T;T	.|0.19105	.|2.17;2.49;2.47;2.47	5.1|5.1	4.07|4.07	0.47477|0.47477	.|.	.|.	.|.	.|.	.|.	T|T	0.06508|0.06508	0.0167|0.0167	N|N	0.16478|0.16478	0.41|0.41	0.09310|0.09310	N|N	1|1	.|B;B	.|0.09022	.|0.002;0.0	.|B;B	.|0.10450	.|0.005;0.001	T|T	0.43572|0.43572	-0.9383|-0.9383	5|9	.|0.02654	.|T	.|1	.|.	4.5008|4.5008	0.11863|0.11863	0.2295:0.5676:0.1148:0.0881|0.2295:0.5676:0.1148:0.0881	.|.	.|599;599	.|Q6WCQ1-2;Q6WCQ1	.|.;MPRIP_HUMAN	W|V	85|561;599;599;599	.|ENSP00000400189:L561V;ENSP00000379156:L599V;ENSP00000379149:L599V;ENSP00000342379:L599V	.|ENSP00000342379:L599V	C|L	+|+	3|1	2|0	MPRIP|MPRIP	17002790|17002790	0.000000|0.000000	0.05858|0.05858	0.393000|0.393000	0.26258|0.26258	0.462000|0.462000	0.32619|0.32619	-0.018000|-0.018000	0.12568|0.12568	2.373000|2.373000	0.80994|0.80994	0.313000|0.313000	0.20887|0.20887	TGC|CTC	C|0.998;G|0.002	0.002	strong		0.692	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
C3orf33	285315	hgsc.bcm.edu	37	3	155485302	155485302	+	Missense_Mutation	SNP	C	C	T	rs358733	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:155485302C>T	ENST00000340171.2	-	4	577	c.479G>A	c.(478-480)aGt>aAt	p.S160N	C3orf33_ENST00000534941.1_Missense_Mutation_p.S117N			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	160			S -> N (in dbSNP:rs358733). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		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)			GCTTACCTTACTCACCAGAAG	0.333													T|||	4212	0.841054	0.8343	0.8516	5008	,	,		15550	0.9117		0.7714	False		,,,				2504	0.8415				p.S117N		Atlas-SNP	.											.	C3orf33	18	.	0			c.G350A						PASS	.	T	ASN/SER	3038,640		1255,528,56	139.0	99.0	111.0		350	4.1	1.0	3	dbSNP_79	111	6390,1796		2487,1416,190	yes	missense	C3orf33	NM_173657.1	46	3742,1944,246	TT,TC,CC		21.9399,17.4008,20.5327	benign	117/252	155485302	9428,2436	1839	4093	5932	SO:0001583	missense	285315	exon5			ACCTTACTCACCA	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.479G>A	3.37:g.155485302C>T	ENSP00000342512:p.Ser160Asn	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_173657	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Missense_Mutation	SNP	ENST00000340171.2	37		1818	0.8324175824175825	413	0.8394308943089431	301	0.8314917127071824	531	0.9283216783216783	573	0.7559366754617414	T	1.068	-0.670850	0.03403	0.825992	0.780601	ENSG00000174928	ENST00000534941;ENST00000340171;ENST00000537385	T;T	0.21361	2.01;2.01	5.28	4.05	0.47172	Staphylococcal nuclease (SNase-like) (1);	0.306370	0.35466	N	0.003188	T	0.00012	0.0000	N	0.00419	-1.52	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34030	-0.9845	9	0.02654	T	1	-6.2449	7.1394	0.25548	0.0:0.079:0.1469:0.7742	rs358733;rs17205103;rs17846330;rs17855926;rs17859361;rs60478260;rs358733	160	Q6P1S2	CC033_HUMAN	N	117;160;160	ENSP00000445446:S117N;ENSP00000342512:S160N	ENSP00000342512:S160N	S	-	2	0	C3orf33	156967996	1.000000	0.71417	0.998000	0.56505	0.528000	0.34623	2.956000	0.49129	0.847000	0.35167	-0.332000	0.08345	AGT	C|0.161;T|0.839	0.839	strong		0.333	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657	
FLG	2312	hgsc.bcm.edu	37	1	152281008	152281008	+	Silent	SNP	A	A	G	rs7512554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281008A>G	ENST00000368799.1	-	3	6389	c.6354T>C	c.(6352-6354)caT>caC	p.H2118H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2118	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTGATCATAATGGGATCCTT	0.572									Ichthyosis				-|||	1641	0.327676	0.3843	0.3357	5008	,	,		29299	0.4355		0.1282	False		,,,				2504	0.3395				p.H2118H		Atlas-SNP	.											.	FLG	900	.	0			c.T6354C						PASS	.	G		1446,2960		0,1446,757	349.0	263.0	292.0		6354	-0.6	0.0	1	dbSNP_116	292	1083,7517		0,1083,3217	no	coding-synonymous	FLG	NM_002016.1		0,2529,3974	GG,GA,AA		12.593,32.8189,19.4449		2118/4062	152281008	2529,10477	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATCATAATGGGAT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6354T>C	1.37:g.152281008A>G		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	541	174	0.321627	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	
KANSL1	284058	hgsc.bcm.edu	37	17	44249096	44249096	+	Silent	SNP	A	A	C	rs571568457	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44249096A>C	ENST00000262419.6	-	2	884	c.414T>G	c.(412-414)ctT>ctG	p.L138L	KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.L138L|KANSL1_ENST00000572904.1_Silent_p.L138L|KANSL1_ENST00000575318.1_Silent_p.L138L|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000432791.1_Silent_p.L138L	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	138					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TCATGGTTCTAAGATTTTCTA	0.428													A|||	364	0.0726837	0.0113	0.1398	5008	,	,		24050	0.001		0.1998	False		,,,				2504	0.0511				p.L138L		Atlas-SNP	.											.	.	.	.	0			c.T414G						PASS	.	A	,,	169,4237		0,169,2034	140.0	201.0	180.0		414,414,414	0.8	1.0	17	dbSNP_123	180	1588,7012		0,1588,2712	yes	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	0,1757,4746	CC,CA,AA		18.4651,3.8357,13.5091	,,	138/1105,138/1106,138/1106	44249096	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			GGTTCTAAGATTT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.414T>G	17.37:g.44249096A>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	69	22	0.318841	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.888;C|0.112	0.112	strong		0.428	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
CEP41	95681	hgsc.bcm.edu	37	7	130038814	130038814	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:130038814T>C	ENST00000223208.5	-	11	1310	c.1040A>G	c.(1039-1041)aAt>aGt	p.N347S	CEP41_ENST00000541543.1_Missense_Mutation_p.N259S|CEP41_ENST00000343969.5_Missense_Mutation_p.N275S	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	347					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)											ACCTGGCAGATTCTGAGCGCT	0.582																																					p.N347S		Atlas-SNP	.											.	.	.	.	0			c.A1040G						PASS	.						104.0	120.0	115.0					7																	130038814		2203	4300	6503	SO:0001583	missense	95681	exon11			GGCAGATTCTGAG	AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"""testis specific, 14"""	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.1040A>G	7.37:g.130038814T>C	ENSP00000223208:p.Asn347Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	89	49	0.550562	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	T	0.124	-1.121417	0.01785	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969	D;D;D	0.88586	-2.27;-2.08;-2.4	4.97	-6.65	0.01795	.	0.854162	0.10676	N	0.646990	T	0.67306	0.2879	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.61647	-0.7020	10	0.08599	T	0.76	-0.4038	8.3272	0.32165	0.0:0.5135:0.2736:0.2129	.	259;275;347	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	S	347;259;275	ENSP00000223208:N347S;ENSP00000445888:N259S;ENSP00000342738:N275S	ENSP00000223208:N347S	N	-	2	0	TSGA14	129826050	0.807000	0.29009	0.020000	0.16555	0.048000	0.14542	-0.534000	0.06150	-0.868000	0.04058	-0.250000	0.11733	AAT	.	.	none		0.582	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718	
ROS1	6098	hgsc.bcm.edu	37	6	117725578	117725578	+	Silent	SNP	T	T	A	rs2243378	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:117725578T>A	ENST00000368508.3	-	5	501	c.303A>T	c.(301-303)ctA>ctT	p.L101L	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Silent_p.L110L	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	94	0	0		WXS	Illumina HiSeq	Phase_I	82	82	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		
VPS13B	157680	hgsc.bcm.edu	37	8	100865836	100865836	+	Missense_Mutation	SNP	G	G	A	rs6468694	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:100865836G>A	ENST00000358544.2	+	56	10405	c.10294G>A	c.(10294-10296)Ggg>Agg	p.G3432R	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.G3407R	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3432			G -> R (in dbSNP:rs6468694).		protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TCCCCTCCCTGGGGAAGAGCC	0.522													G|||	556	0.111022	0.1112	0.111	5008	,	,		17263	0.1171		0.1312	False		,,,				2504	0.0838				p.G3432R	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G10294A						PASS	.	G	ARG/GLY,ARG/GLY	474,3932	223.3+/-239.8	32,410,1761	63.0	60.0	61.0		10294,10219	2.3	0.6	8	dbSNP_116	61	1082,7518	227.8+/-263.0	57,968,3275	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	125,125	89,1378,5036	AA,AG,GG		12.5814,10.7581,11.9637	possibly-damaging,possibly-damaging	3432/4023,3407/3998	100865836	1556,11450	2203	4300	6503	SO:0001583	missense	157680	exon56			CTCCCTGGGGAAG	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.10294G>A	8.37:g.100865836G>A	ENSP00000351346:p.Gly3432Arg	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	229	115	0.502183	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	287	0.13141025641025642	63	0.12804878048780488	51	0.1408839779005525	77	0.1346153846153846	96	0.1266490765171504	G	1.681	-0.506533	0.04231	0.107581	0.125814	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.68624	-0.34;-0.34	5.43	2.35	0.29111	.	0.703847	0.13406	N	0.390207	T	0.00496	0.0016	L	0.46157	1.445	0.58432	P	4.000000000004E-6	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.07158	-1.0787	9	0.10636	T	0.68	.	4.5219	0.11962	0.091:0.3788:0.4168:0.1134	rs6468694;rs52794107;rs56921051;rs6468694	3407;3432	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	R	3407;3432	ENSP00000349685:G3407R;ENSP00000351346:G3432R	ENSP00000349685:G3407R	G	+	1	0	VPS13B	100935012	0.067000	0.21026	0.638000	0.29380	0.321000	0.28281	1.287000	0.33284	1.271000	0.44313	-0.143000	0.13931	GGG	G|0.876;A|0.124	0.124	strong		0.522	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
RBBP7	5931	hgsc.bcm.edu	37	X	16887655	16887655	+	Intron	SNP	C	C	T	rs67984110		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:16887655C>T	ENST00000380087.2	-	2	377				RBBP7_ENST00000380084.4_Missense_Mutation_p.R37H|RBBP7_ENST00000404022.1_Intron			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7						cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)			biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					AGGGGCTGCGCGACCCAGTCG	0.572													C|||	989	0.261987	0.1157	0.1556	3775	,	,		10610	0.0437		0.3201	False		,,,				2504	0.3701				p.R37H		Atlas-SNP	.											.	RBBP7	58	.	0			c.G110A						PASS	.																																			SO:0001627	intron_variant	5931	exon1			GCTGCGCGACCCA	U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"""WD repeat domain containing"""	9890	protein-coding gene	gene with protein product	"""G1/S transition control protein-binding protein RbAp46"", ""retinoblastoma-binding protein 7"", ""retinoblastoma-binding protein RbAp46"", ""histone acetyltransferase type B subunit 2"", ""retinoblastoma-binding protein p46"""	300825	"""retinoblastoma-binding protein 7"""			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.17-312G>A	X.37:g.16887655C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001198719	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	37	CCDS14179.1	383	0.23086196503918022	43	0.09347826086956522	41	0.12654320987654322	10	0.017793594306049824	165	0.2796610169491525	C	15.32	2.798641	0.50208	.	.	ENSG00000102054	ENST00000380084	T	0.74106	-0.81	3.88	3.88	0.44766	.	0.540328	0.16034	N	0.232734	T	0.00012	0.0000	.	.	.	0.23978	P	0.996286	P	0.47841	0.901	B	0.26864	0.074	T	0.10200	-1.0640	8	0.59425	D	0.04	-11.0168	10.2474	0.43350	0.0:1.0:0.0:0.0	.	37	Q5JP00	.	H	37	ENSP00000369424:R37H	ENSP00000369424:R37H	R	-	2	0	RBBP7	16797576	0.004000	0.15560	0.250000	0.24296	0.009000	0.06853	1.149000	0.31626	2.173000	0.68751	0.594000	0.82650	CGC	C|0.769;T|0.231	0.231	strong		0.572	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893	
ZNF653	115950	hgsc.bcm.edu	37	19	11598483	11598483	+	Silent	SNP	T	T	C	rs311805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	195	0	0		WXS	Illumina HiSeq	Phase_I	196	89	0.454082	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	
ZNF23	7571	hgsc.bcm.edu	37	16	71487206	71487206	+	Missense_Mutation	SNP	T	T	C	rs2070832	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71487206T>C	ENST00000393539.2	-	5	895	c.82A>G	c.(82-84)Agt>Ggt	p.S28G	ZNF23_ENST00000497160.1_Missense_Mutation_p.S28G|ZNF23_ENST00000564528.1_5'UTR|ZNF23_ENST00000357254.4_Missense_Mutation_p.S28G|ZNF23_ENST00000358700.2_Missense_Mutation_p.S28G|ZNF23_ENST00000428724.2_5'UTR|ZNF23_ENST00000417828.1_Missense_Mutation_p.S28G|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000539742.1_Intron	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	28	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		S -> G (in dbSNP:rs2070832).		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.S28G(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		CCCAGCTCACTTCCTCCCTCC	0.512													C|||	3338	0.666534	0.9743	0.5346	5008	,	,		19096	0.2887		0.6978	False		,,,				2504	0.7014				p.S28G		Atlas-SNP	.											ZNF23,NS,carcinoma,0,1	ZNF23	65	1	1	Substitution - Missense(1)	stomach(1)	c.A82G						scavenged	.	C	GLY/SER	4070,326	164.4+/-196.0	1890,290,18	36.0	32.0	33.0		82	0.6	1.0	16	dbSNP_96	33	5971,2629	407.0+/-349.0	2087,1797,416	yes	missense	ZNF23	NM_145911.1	56	3977,2087,434	CC,CT,TT		30.5698,7.4158,22.7378	benign	28/644	71487206	10041,2955	2198	4300	6498	SO:0001583	missense	7571	exon5			GCTCACTTCCTCC	X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"""Zinc fingers, C2H2-type"""	13023	protein-coding gene	gene with protein product		194527	"""zinc finger protein 359"""	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.82A>G	16.37:g.71487206T>C	ENSP00000377171:p.Ser28Gly	Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	NM_145911	Q8NDP5|Q96IT3|Q9UG42	Missense_Mutation	SNP	ENST00000393539.2	37	CCDS10900.1	1380	0.6318681318681318	463	0.9410569105691057	218	0.6022099447513812	173	0.30244755244755245	526	0.6939313984168866	C	7.744	0.701872	0.15172	0.925842	0.694302	ENSG00000167377	ENST00000393539;ENST00000357254;ENST00000417828	T;T;T	0.28069	1.63;1.63;1.63	4.75	0.548	0.17208	Krueppel-associated box (2);	0.758722	0.10982	N	0.612574	T	0.00012	0.0000	N	0.05031	-0.125	0.09310	P	0.9999999875883	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18999	-1.0319	9	0.27082	T	0.32	-0.148	8.8389	0.35129	0.0:0.578:0.0:0.422	rs2070832;rs52807057;rs61511212;rs2070832	28;28	B3KR55;P17027	.;ZNF23_HUMAN	G	28	ENSP00000377171:S28G;ENSP00000349796:S28G;ENSP00000395712:S28G	ENSP00000349796:S28G	S	-	1	0	ZNF23	70044707	0.000000	0.05858	0.985000	0.45067	0.357000	0.29423	0.120000	0.15647	0.035000	0.15519	-0.898000	0.02899	AGT	T|0.279;C|0.721	0.721	strong		0.512	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911	
PPP1CC	5501	hgsc.bcm.edu	37	12	111160003	111160003	+	Silent	SNP	G	G	A	rs1973505	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:111160003G>A	ENST00000335007.5	-	6	1009	c.819C>T	c.(817-819)tgC>tgT	p.C273C	PPP1CC_ENST00000546933.1_Silent_p.C282C|PPP1CC_ENST00000551676.1_3'UTR|PPP1CC_ENST00000340766.5_Silent_p.C273C|PPP1CC_ENST00000550991.1_Silent_p.C273C	NM_002710.3	NP_002701.1	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma isozyme	273		Inhibition by microcystin toxin binding.			cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|large_intestine(2)|lung(3)	6						CAAACTCTCCGCAATAATTGG	0.368													A|||	1176	0.234824	0.5303	0.121	5008	,	,		19020	0.0635		0.164	False		,,,				2504	0.1656				p.C273C		Atlas-SNP	.											.	PPP1CC	22	.	0			c.C819T						PASS	.	A		2158,2248	595.9+/-388.5	534,1090,579	109.0	104.0	105.0		819	4.6	1.0	12	dbSNP_92	105	1182,7418	764.6+/-407.6	84,1014,3202	no	coding-synonymous	PPP1CC	NM_002710.3		618,2104,3781	AA,AG,GG		13.7442,48.9787,25.6805		273/324	111160003	3340,9666	2203	4300	6503	SO:0001819	synonymous_variant	5501	exon6			CTCTCCGCAATAA		CCDS9150.1, CCDS58279.1	12q24.1-q24.2	2013-01-17	2010-03-05		ENSG00000186298	ENSG00000186298	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9283	protein-coding gene	gene with protein product		176914	"""protein phosphatase 1, catalytic subunit, gamma isoform"""				Standard	NM_002710		Approved	PP1C, PP1gamma	uc021rdx.1	P36873	OTTHUMG00000169531	ENST00000335007.5:c.819C>T	12.37:g.111160003G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	151	89	0.589404	NM_002710		Silent	SNP	ENST00000335007.5	37	CCDS9150.1																																																																																			G|0.770;A|0.230	0.230	strong		0.368	PPP1CC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404659.1		
NFASC	23114	hgsc.bcm.edu	37	1	204945934	204945934	+	Silent	SNP	A	A	G	rs6657372	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204945934A>G	ENST00000403080.1	+	16	2129	c.1842A>G	c.(1840-1842)ccA>ccG	p.P614P	NFASC_ENST00000401399.1_Intron|NFASC_ENST00000367172.4_Intron|NFASC_ENST00000367170.4_Intron|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000360049.4_Intron|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000539706.1_Intron|NFASC_ENST00000513543.1_Intron|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000367171.4_Intron|NFASC_ENST00000339876.6_Intron|NFASC_ENST00000338586.6_Intron|NFASC_ENST00000338515.6_Intron	NM_001005389.1|NM_001160333.1	NP_001005389.2|NP_001153805.1	O94856	NFASC_HUMAN	neurofascin	140					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)			GTAACTGCCCATGCTCACCCT	0.667													C|||	461	0.0920527	0.2057	0.0648	5008	,	,		18061	0.0089		0.0706	False		,,,				2504	0.0654				p.P614P		Atlas-SNP	.											.	NFASC	396	.	0			c.A1842G						PASS	.	C	,,,,,	957,3449		103,751,1349	124.0	101.0	109.0		,1842,,,1824,	2.1	0.0	1	dbSNP_116	109	967,7633		61,845,3394	no	intron,coding-synonymous,intron,intron,coding-synonymous,intron	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	,,,,,	164,1596,4743	GG,GA,AA		11.2442,21.7204,14.7932	,,,,,	,614/620,,,608/614,	204945934	1924,11082	2203	4300	6503	SO:0001819	synonymous_variant	23114	exon16			CTGCCCATGCTCA	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	ENST00000403080.1:c.1842A>G	1.37:g.204945934A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_001005389	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000403080.1	37	CCDS53461.1																																																																																			A|0.899;G|0.101	0.101	strong		0.667	NFASC-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131234.1	NM_001005388	
MUC4	4585	hgsc.bcm.edu	37	3	195506499	195506499	+	Silent	SNP	G	G	A	rs542643120	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195506499G>A	ENST00000463781.3	-	2	12411	c.11952C>T	c.(11950-11952)ccC>ccT	p.P3984P	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.P3984P	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.P3984P(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)		TGACAGGAAGGGGGGTGGCGT	0.592													.|||	1079	0.215455	0.2126	0.183	5008	,	,		8207	0.0952		0.338	False		,,,				2504	0.2403				p.P3984P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	stomach(1)	c.C11952T						scavenged	.						10.0	7.0	8.0					3																	195506499		443	903	1346	SO:0001819	synonymous_variant	4585	exon2			AGGAAGGGGGGTG	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.11952C>T	3.37:g.195506499G>A		Somatic	9	9	1		WXS	Illumina HiSeq	Phase_I	14	13	0.928571	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	
FLG	2312	hgsc.bcm.edu	37	1	152280347	152280347	+	Missense_Mutation	SNP	C	C	T	rs139476473	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280347C>T	ENST00000368799.1	-	3	7050	c.7015G>A	c.(7015-7017)Gac>Aac	p.D2339N	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2339	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.D2339N(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGAGCTGTCTGCTGACTGC	0.557									Ichthyosis																												p.D2339N		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	1	Substitution - Missense(1)	stomach(1)	c.G7015A						scavenged	.	C	ASN/ASP	81,4309		0,81,2114	193.0	265.0	240.0		7015	4.1	0.1	1	dbSNP_134	240	282,8314		22,238,4038	no	missense	FLG	NM_002016.1	23	22,319,6152	TT,TC,CC		3.2806,1.8451,2.7953	probably-damaging	2339/4062	152280347	363,12623	2195	4298	6493	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGCTGTCTGCTGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7015G>A	1.37:g.152280347C>T	ENSP00000357789:p.Asp2339Asn	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	263	65	0.247148	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	432	0.1978021978021978	6	0.012195121951219513	90	0.24861878453038674	245	0.42832167832167833	91	0.12005277044854881	C	13.82	2.350104	0.41599	0.018451	0.032806	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.08008	3.14	4.12	4.12	0.48240	.	.	.	.	.	T	0.14570	0.0352	M	0.62723	1.935	0.80722	P	0.0	D	0.69078	0.997	D	0.66196	0.942	T	0.00619	-1.1641	8	0.66056	D	0.02	.	12.0996	0.53776	0.0:1.0:0.0:0.0	.	2339	P20930	FILA_HUMAN	N	2339;249	ENSP00000357789:D2339N	ENSP00000271820:D249N	D	-	1	0	FLG	150546971	0.223000	0.23663	0.097000	0.21041	0.004000	0.04260	1.691000	0.37721	2.287000	0.76781	0.430000	0.28490	GAC	.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CIT	11113	hgsc.bcm.edu	37	12	120189888	120189888	+	Silent	SNP	T	T	C	rs904654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120189888T>C	ENST00000261833.7	-	22	2797	c.2745A>G	c.(2743-2745)acA>acG	p.T915T	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Silent_p.T957T	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	915					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)		CAGCTTCTGCTGTGGTCTCTT	0.607													T|||	2697	0.538538	0.4682	0.634	5008	,	,		18524	0.5665		0.499	False		,,,				2504	0.5777				p.T957T		Atlas-SNP	.											.	CIT	535	.	0			c.A2871G						PASS	.	T	,	2035,2371	565.5+/-381.7	478,1079,646	68.0	61.0	64.0		2871,2745	-10.8	0.0	12	dbSNP_86	64	4309,4291	577.3+/-390.5	1063,2183,1054	yes	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	1541,3262,1700	CC,CT,TT		49.8953,46.187,48.7775	,	957/2070,915/2028	120189888	6344,6662	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon23			TTCTGCTGTGGTC	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.2745A>G	12.37:g.120189888T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	120	49	0.408333	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	1134	0.5192307692307693	217	0.4410569105691057	232	0.6408839779005525	306	0.534965034965035	379	0.5	T	9.141	1.013878	0.19277	0.46187	0.501047	ENSG00000122966	ENST00000392520	.	.	.	5.38	-10.8	0.00216	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999961	.	.	.	.	.	.	T	0.37384	-0.9708	3	.	.	.	.	2.0898	0.03654	0.2771:0.2271:0.3515:0.1443	rs904654;rs58144994;rs904654	.	.	.	R	543	.	.	Q	-	2	0	CIT	118674271	0.000000	0.05858	0.027000	0.17364	0.950000	0.60333	-5.023000	0.00159	-2.162000	0.00784	0.454000	0.30748	CAG	T|0.506;C|0.494	0.494	strong		0.607	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
ZNF326	284695	hgsc.bcm.edu	37	1	90482944	90482944	+	Missense_Mutation	SNP	A	A	G	rs200399673		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:90482944A>G	ENST00000340281.4	+	8	1138	c.995A>G	c.(994-996)gAa>gGa	p.E332G	ZNF326_ENST00000370447.3_Missense_Mutation_p.E243G|ZNF326_ENST00000455342.2_Missense_Mutation_p.E126G	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	332					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)		CTGCATCTGGAAAGTTCTTCA	0.284																																					p.E332G		Atlas-SNP	.											.	ZNF326	60	.	0			c.A995G						PASS	.	A	GLY/GLU	0,4402		0,0,2201	61.0	62.0	62.0		995	5.5	1.0	1		62	2,8584		0,2,4291	yes	missense	ZNF326	NM_182976.2	98	0,2,6492	GG,GA,AA		0.0233,0.0,0.0154	benign	332/583	90482944	2,12986	2201	4293	6494	SO:0001583	missense	284695	exon8			ATCTGGAAAGTTC	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.995A>G	1.37:g.90482944A>G	ENSP00000340796:p.Glu332Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	13.17	2.156916	0.38119	0.0	2.33E-4	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.46063	0.88;0.88;0.88	5.48	5.48	0.80851	Zinc finger, C2H2-like (1);	0.187115	0.46758	D	0.000280	T	0.17152	0.0412	L	0.29908	0.895	0.33497	D	0.589491	P;B	0.39094	0.659;0.449	B;B	0.36567	0.228;0.191	T	0.11108	-1.0601	10	0.41790	T	0.15	-16.081	11.5747	0.50854	0.8508:0.1492:0.0:0.0	.	332;332	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	G	332;332;243;126	ENSP00000340796:E332G;ENSP00000359476:E243G;ENSP00000403470:E126G	ENSP00000340796:E332G	E	+	2	0	ZNF326	90255532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.363000	0.52321	2.082000	0.62665	0.529000	0.55759	GAA	A|0.999;G|0.001	0.001	weak		0.284	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
GNB5	10681	hgsc.bcm.edu	37	15	52433397	52433397	+	Silent	SNP	C	C	T	rs17612637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52433397C>T	ENST00000261837.7	-	7	632	c.567G>A	c.(565-567)aaG>aaA	p.K189K	CTD-2184D3.7_ENST00000557898.1_RNA|GNB5_ENST00000559348.1_5'Flank|GNB5_ENST00000396335.4_Intron|GNB5_ENST00000358784.7_Silent_p.K147K|CTD-2184D3.7_ENST00000560613.1_RNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	189					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)		TAGCAACAGACTTCTTTTTGG	0.473													C|||	82	0.0163738	0.0008	0.0389	5008	,	,		18151	0.0		0.0368	False		,,,				2504	0.0174				p.K189K		Atlas-SNP	.											.	GNB5	28	.	0			c.G567A						PASS	.	C	,	35,4355	39.2+/-71.8	1,33,2161	166.0	150.0	155.0		441,567	5.3	1.0	15	dbSNP_123	155	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,342,6141	TT,TC,CC		3.6921,0.7973,2.7127	,	147/354,189/396	52433397	352,12624	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon7			AACAGACTTCTTT	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.567G>A	15.37:g.52433397C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;G|0.000;T|0.027	0.027	strong		0.473	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
MT-ND4	4538	hgsc.bcm.edu	37	M	11920	11920	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrM:11920C>T	ENST00000361381.2	+	1	1161	c.1161C>T	c.(1159-1161)tcC>tcT	p.S387S	MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	387					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						ACCACGTTCTCCTGATCAAAT	0.458																																					p.S387S		Atlas-SNP	.											.	.	.	.	0			c.C1161T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			GTTCTCCTGATCA			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.1161C>T	M.37:g.11920C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	8	8	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	
RNF157	114804	hgsc.bcm.edu	37	17	74208466	74208466	+	Silent	SNP	A	A	G	rs61760884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74208466A>G	ENST00000269391.6	-	2	318	c.186T>C	c.(184-186)ttT>ttC	p.F62F	RNF157_ENST00000592271.1_Silent_p.F62F|RNF157_ENST00000319945.6_Silent_p.F62F	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	62							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)			TGTTCCCCAGAAAGTTCAGAT	0.413													A|||	11	0.00219649	0.0	0.0014	5008	,	,		19125	0.0		0.0099	False		,,,				2504	0.0				p.F62F	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.T186C						PASS	.	A		5,4401	9.9+/-24.2	0,5,2198	123.0	116.0	119.0		186	-2.6	1.0	17	dbSNP_129	119	51,8549	33.3+/-86.6	0,51,4249	no	coding-synonymous	RNF157	NM_052916.2		0,56,6447	GG,GA,AA		0.593,0.1135,0.4306		62/680	74208466	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	114804	exon2			CCCCAGAAAGTTC	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.186T>C	17.37:g.74208466A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	192	83	0.432292	NM_052916	Q8NB72|Q96N56	Silent	SNP	ENST00000269391.6	37	CCDS32740.1																																																																																			A|0.996;G|0.004	0.004	strong		0.413	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732	
AFF2	2334	hgsc.bcm.edu	37	X	148035200	148035200	+	Silent	SNP	G	G	A	rs12011040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:148035200G>A	ENST00000370460.2	+	10	1967	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	AFF2_ENST00000286437.5_Silent_p.S137S|AFF2_ENST00000370457.5_Silent_p.S463S|AFF2_ENST00000342251.3_Silent_p.S463S	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	183	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	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	
CR1L	1379	hgsc.bcm.edu	37	1	207890866	207890866	+	Missense_Mutation	SNP	T	T	C	rs2796257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:207890866T>C	ENST00000508064.2	+	11	1532	c.1472T>C	c.(1471-1473)cTt>cCt	p.L491P		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	491	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.		L -> P (in dbSNP:rs2796257).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GGAACTCCCCTTGGAGATATT	0.453													t|||	1347	0.26897	0.1362	0.5115	5008	,	,		18096	0.1171		0.4344	False		,,,				2504	0.2628				p.L491P		Atlas-SNP	.											.	CR1L	97	.	0			c.T1472C						PASS	.	T	PRO/LEU	640,3070		49,542,1264	116.0	106.0	109.0		1472	-0.9	0.0	1	dbSNP_100	109	3543,4643		742,2059,1292	no	missense	CR1L	NM_175710.1	98	791,2601,2556	CC,CT,TT		43.2812,17.2507,35.1631	possibly-damaging	491/570	207890866	4183,7713	1855	4093	5948	SO:0001583	missense	1379	exon11			CTCCCCTTGGAGA	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1472T>C	1.37:g.207890866T>C	ENSP00000421736:p.Leu491Pro	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	277	146	0.527076	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	664	0.304029304029304	75	0.1524390243902439	178	0.49171270718232046	80	0.13986013986013987	331	0.4366754617414248	.	9.255	1.041822	0.19748	0.172507	0.432812	ENSG00000197721	ENST00000508064	T	0.23754	1.89	3.01	-0.852	0.10713	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.58925	1.835	0.80722	P	0.0	P	0.48230	0.907	P	0.56865	0.808	T	0.43523	-0.9386	8	0.33141	T	0.24	.	2.8399	0.05526	0.0:0.3307:0.2605:0.4088	rs2796257;rs12735951	491	Q2VPA4	CR1L_HUMAN	P	491	ENSP00000421736:L491P	ENSP00000421736:L491P	L	+	2	0	CR1L	205957489	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	0.293000	0.19029	-0.041000	0.13558	0.254000	0.18369	CTT	T|0.675;C|0.325	0.325	strong		0.453	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
SMAD7	4092	hgsc.bcm.edu	37	18	46468946	46468946	+	Intron	SNP	G	G	A	rs3764482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:46468946G>A	ENST00000262158.2	-	3	954				SMAD7_ENST00000589634.1_Intron|SMAD7_ENST00000591805.1_Intron|SMAD7_ENST00000585986.1_Intron	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7						adherens junction assembly (GO:0034333)|artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|cellular protein complex localization (GO:0034629)|cellular response to transforming growth factor beta stimulus (GO:0071560)|gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|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 peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by competitive promoter binding (GO:0010944)|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 ubiquitin-protein transferase activity (GO:0051444)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of cardiac muscle contraction (GO:0055117)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|response to laminar fluid shear stress (GO:0034616)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activin binding (GO:0048185)|beta-catenin binding (GO:0008013)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|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 transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	10	Colorectal(1;0.0518)					GAAAAGGGGAGAGAAAGAAAT	0.463													G|||	440	0.0878594	0.0159	0.1297	5008	,	,		20399	0.0665		0.1978	False		,,,				2504	0.0644				p.S28F		Atlas-SNP	.											.	SMAD7	22	.	0			c.C83T						PASS	.	G	,,PHE/SER,	177,4229	113.3+/-151.4	5,167,2031	56.0	62.0	60.0		,,83,	2.4	0.0	18	dbSNP_107	60	1653,6947	301.2+/-305.3	161,1331,2808	yes	intron,intron,missense,intron	SMAD7	NM_001190821.1,NM_001190822.1,NM_001190823.1,NM_005904.3	,,155,	166,1498,4839	AA,AG,GG		19.2209,4.0172,14.0704	,,,	,,28/239,	46468946	1830,11176	2203	4300	6503	SO:0001627	intron_variant	4092	exon1			AGGGGAGAGAAAG	AF010193	CCDS11936.1, CCDS54186.1, CCDS59317.1	18q21.1	2006-11-06	2006-11-06	2004-05-26	ENSG00000101665	ENSG00000101665		"""SMADs"""	6773	protein-coding gene	gene with protein product		602932	"""MAD, mothers against decapentaplegic homolog 7 (Drosophila)"", ""SMAD, mothers against DPP homolog 7 (Drosophila)"""	MADH8, MADH7		9256479, 9730599	Standard	NM_005904		Approved		uc002ldg.3	O15105	OTTHUMG00000132655	ENST00000262158.2:c.668-21C>T	18.37:g.46468946G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001190823	B7Z773|K7EQ10|O14740|Q6DK23	Missense_Mutation	SNP	ENST00000262158.2	37	CCDS11936.1																																																																																			G|0.884;A|0.116	0.116	strong		0.463	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	NM_005904	
SLC9A8	23315	hgsc.bcm.edu	37	20	48466166	48466166	+	Silent	SNP	G	G	A	rs6012755	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:48466166G>A	ENST00000361573.2	+	6	525	c.483G>A	c.(481-483)ggG>ggA	p.G161G	SLC9A8_ENST00000417961.1_Silent_p.G161G|SLC9A8_ENST00000541138.1_5'UTR|SLC9A8_ENST00000539601.1_5'UTR			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	161					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)			CTGTTTTTGGGACGGCAATCT	0.383													G|||	716	0.142971	0.4251	0.0778	5008	,	,		21110	0.0		0.0616	False		,,,				2504	0.0389				p.G161G		Atlas-SNP	.											.	SLC9A8	63	.	0			c.G483A						PASS	.	G		1487,2919	476.3+/-357.6	242,1003,958	168.0	163.0	165.0		483	-3.5	1.0	20	dbSNP_114	165	592,8008	156.4+/-210.3	24,544,3732	no	coding-synonymous	SLC9A8	NM_015266.1		266,1547,4690	AA,AG,GG		6.8837,33.7494,15.9849		161/582	48466166	2079,10927	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon6			TTTTGGGACGGCA	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.483G>A	20.37:g.48466166G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	235	102	0.434043	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			G|0.845;A|0.155	0.155	strong		0.383	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524	
CNNM2	54805	hgsc.bcm.edu	37	10	104836853	104836853	+	Silent	SNP	C	C	T	rs35647154	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:104836853C>T	ENST00000369878.4	+	8	2732	c.2544C>T	c.(2542-2544)gaC>gaT	p.D848D	CNNM2_ENST00000433628.2_Silent_p.D826D	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	848					magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GGTTGCCAGACGAGACAGCCA	0.552													C|||	139	0.0277556	0.0106	0.0461	5008	,	,		17827	0.001		0.0795	False		,,,				2504	0.0123				p.D848D		Atlas-SNP	.											.	CNNM2	119	.	0			c.C2544T						PASS	.	C	,	98,4154		1,96,2029	97.0	104.0	102.0		2544,2478	-9.7	0.2	10	dbSNP_126	102	584,7862		21,542,3660	no	coding-synonymous,coding-synonymous	CNNM2	NM_017649.3,NM_199076.1	,	22,638,5689	TT,TC,CC		6.9145,2.3048,5.3709	,	848/876,826/854	104836853	682,12016	2126	4223	6349	SO:0001819	synonymous_variant	54805	exon8			GCCAGACGAGACA	AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"""cyclin M2"""	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.2544C>T	10.37:g.104836853C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_017649	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	37	CCDS44474.1																																																																																			C|0.952;T|0.048	0.048	strong		0.552	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649	
EMR1	2015	hgsc.bcm.edu	37	19	6901891	6901891	+	Missense_Mutation	SNP	G	G	A	rs897738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6901891G>A	ENST00000312053.4	+	6	557	c.520G>A	c.(520-522)Gat>Aat	p.D174N	EMR1_ENST00000381404.4_Missense_Mutation_p.D122N|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000250572.8_Missense_Mutation_p.D174N|EMR1_ENST00000381407.5_Intron|EMR1_ENST00000450315.3_Intron	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	145	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	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		
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201951	32201951	+	RNA	SNP	A	A	G	rs9982775	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	139	0	0		WXS	Illumina HiSeq	Phase_I	188	187	0.994681	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	
PCDH15	65217	hgsc.bcm.edu	37	10	55955444	55955444	+	Splice_Site	SNP	T	T	G	rs4935502	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:55955444T>G	ENST00000320301.6	-	11	1698	c.1304A>C	c.(1303-1305)gAt>gCt	p.D435A	PCDH15_ENST00000373955.1_Splice_Site_p.D435A|PCDH15_ENST00000395446.1_Splice_Site_p.D435A|PCDH15_ENST00000373957.3_Splice_Site_p.D413A|PCDH15_ENST00000409834.1_Splice_Site_p.D39A|PCDH15_ENST00000437009.1_Splice_Site_p.D435A|PCDH15_ENST00000361849.3_Splice_Site_p.D435A|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395432.2_Splice_Site_p.D398A|PCDH15_ENST00000395433.1_Splice_Site_p.D413A|PCDH15_ENST00000395438.1_Splice_Site_p.D435A|PCDH15_ENST00000373965.2_Splice_Site_p.D435A|PCDH15_ENST00000395430.1_Splice_Site_p.D435A|PCDH15_ENST00000395445.1_Splice_Site_p.D435A|PCDH15_ENST00000395440.1_Splice_Site_p.D435A|PCDH15_ENST00000414778.1_Splice_Site_p.D440A	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	435	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		D -> A (in dbSNP:rs4935502). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:22815625}.		equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTAACTTACATCTTCTATGTC	0.373										HNSCC(58;0.16)			T|||	1729	0.345248	0.1346	0.2536	5008	,	,		16771	0.8413		0.1312	False		,,,				2504	0.4039				p.D440A		Atlas-SNP	.											PCDH15_ENST00000417177,colon,carcinoma,-1,12	PCDH15	1715	12	0			c.A1319C						PASS	.	T	ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP	579,3827	256.4+/-261.2	30,519,1654	84.0	79.0	81.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1319,1304,1304,1304,1193,1238,1319,1304,1319,1304,1238,1304	5.1	1.0	10	dbSNP_111	81	1133,7467	234.0+/-267.1	89,955,3256	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	126,126,126,126,126,126,126,126,126,126,126,126	119,1474,4910	GG,GT,TT		13.1744,13.1412,13.1632	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	440/1963,435/1958,435/1887,435/1953,398/1916,413/1936,440/1791,435/1540,440/1683,435/1678,413/1933,435/1956	55955444	1712,11294	2203	4300	6503	SO:0001630	splice_region_variant	65217	exon12			CTTACATCTTCTA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1305+1A>C	10.37:g.55955444T>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	736	0.336996336996337	60	0.12195121951219512	89	0.24585635359116023	493	0.8618881118881119	94	0.12401055408970976	T	16.49	3.137493	0.56936	0.131412	0.131744	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58797	0.41;0.69;0.69;0.4;0.35;0.69;0.31;0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.07	5.07	0.68467	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.26555	P	0.9738414	D;D;P;B;D;D;D;P;P;P;P;P;P;P;P	0.64830	0.986;0.975;0.884;0.234;0.994;0.975;0.986;0.866;0.779;0.948;0.727;0.866;0.837;0.866;0.949	D;P;P;B;P;P;D;P;B;P;P;P;B;P;P	0.63033	0.91;0.871;0.719;0.29;0.9;0.871;0.91;0.507;0.392;0.576;0.507;0.507;0.287;0.507;0.796	T	0.12167	-1.0558	8	0.52906	T	0.07	.	14.4836	0.67599	0.0:0.0:0.0:1.0	rs4935502;rs52792713;rs58556608;rs4935502	413;435;435;440;435;398;435;435;435;435;435;440;435;413;435	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	A	435;440;435;435;39;435;435;435;398;435;413;413;435;435;440;435;435	ENSP00000363076:D435A;ENSP00000410304:D440A;ENSP00000378826:D435A;ENSP00000386693:D39A;ENSP00000378832:D435A;ENSP00000378833:D435A;ENSP00000378827:D435A;ENSP00000378820:D398A;ENSP00000354950:D435A;ENSP00000378821:D413A;ENSP00000363068:D413A;ENSP00000322604:D435A;ENSP00000378818:D435A;ENSP00000412628:D435A;ENSP00000363066:D435A	ENSP00000322604:D435A	D	-	2	0	PCDH15	55625450	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	8.008000	0.88588	1.918000	0.55548	0.482000	0.46254	GAT	G|0.226;N|0.000	0.226	strong		0.373	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	Missense_Mutation
ZWINT	11130	hgsc.bcm.edu	37	10	58118630	58118630	+	Missense_Mutation	SNP	T	T	C	rs2241666	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:58118630T>C	ENST00000373944.3	-	6	597	c.559A>G	c.(559-561)Agg>Ggg	p.R187G	ZWINT_ENST00000361148.6_Intron|ZWINT_ENST00000318387.2_Missense_Mutation_p.R67G|ZWINT_ENST00000395405.1_Missense_Mutation_p.R187G|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	154	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	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		
GPR98	84059	hgsc.bcm.edu	37	5	90151620	90151620	+	Missense_Mutation	SNP	C	C	A	rs201254386		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:90151620C>A	ENST00000405460.2	+	82	17753	c.17657C>A	c.(17656-17658)gCc>gAc	p.A5886D	GPR98_ENST00000425867.2_Missense_Mutation_p.A1547D	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5886	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				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)		GTGGAATGTGCCTGTTCACAC	0.413																																					p.A5886D		Atlas-SNP	.											.	GPR98	605	.	0			c.C17657A						PASS	.	C	ASP/ALA	0,3922		0,0,1961	292.0	273.0	279.0		17657	5.5	1.0	5		279	2,8298		0,2,4148	yes	missense	GPR98	NM_032119.3	126	0,2,6109	AA,AC,CC		0.0241,0.0,0.0164	benign	5886/6307	90151620	2,12220	1961	4150	6111	SO:0001583	missense	84059	exon82			AATGTGCCTGTTC	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.17657C>A	5.37:g.90151620C>A	ENSP00000384582:p.Ala5886Asp	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	226	96	0.424779	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039679	0.93630	0.0	2.41E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.69306	-0.39;-0.39	5.5	5.5	0.81552	GPS domain (3);	0.000000	0.85682	D	0.000000	T	0.81955	0.4932	M	0.76574	2.34	0.80722	D	1	D;D;D	0.71674	0.975;0.998;0.968	P;D;P	0.71656	0.776;0.974;0.667	T	0.81193	-0.1044	9	.	.	.	.	19.7578	0.96301	0.0:1.0:0.0:0.0	.	1547;5886;1547	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	D	5886;5886;1547	ENSP00000384582:A5886D;ENSP00000392618:A1547D	.	A	+	2	0	GPR98	90187376	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.083000	0.76859	2.746000	0.94184	0.591000	0.81541	GCC	.	.	weak		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
HLA-A	3105	hgsc.bcm.edu	37	6	29910703	29910703	+	Silent	SNP	G	G	T	rs41541222	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29910703G>T	ENST00000396634.1	+	4	584	c.243G>T	c.(241-243)ccG>ccT	p.P81P	HLA-A_ENST00000376809.5_Silent_p.P81P|HLA-A_ENST00000376806.5_Silent_p.P81P|HLA-A_ENST00000376802.2_Silent_p.P81P			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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)|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						AGGAGGGGCCGGAGTATTGGG	0.667									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|||	405	0.0808706	0.1528	0.0908	5008	,	,		12237	0.0506		0.0537	False		,,,				2504	0.0358				p.P81P		Atlas-SNP	.											HLA-A,colon,carcinoma,+1,1	HLA-A	89	1	0			c.G243T						PASS	.	G		615,3791		46,523,1634	65.0	69.0	68.0		243	-4.8	0.0	6	dbSNP_127	68	427,8173		22,383,3895	no	coding-synonymous	HLA-A	NM_002116.7		68,906,5529	TT,TG,GG		4.9651,13.9582,8.0117		81/366	29910703	1042,11964	2203	4300	6503	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGGGCCGGAGTAT	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.243G>T	6.37:g.29910703G>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	245	138	0.563265	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.915;T|0.085	0.085	strong		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CEL	1056	hgsc.bcm.edu	37	9	135945997	135945997	+	Missense_Mutation	SNP	C	C	T	rs201677850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:135945997C>T	ENST00000372080.4	+	10	1461	c.1445C>T	c.(1444-1446)aCa>aTa	p.T482I	CEL_ENST00000351304.7_Intron	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	479					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CAAGACAGGACAGTCTCTAAG	0.607																																					p.T482I		Atlas-SNP	.											CEL,NS,carcinoma,+1,1	CEL	71	1	0			c.C1445T						PASS	.						83.0	95.0	91.0					9																	135945997		2003	4163	6166	SO:0001583	missense	1056	exon10			ACAGGACAGTCTC	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1445C>T	9.37:g.135945997C>T	ENSP00000361151:p.Thr482Ile	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	237	20	0.0843882	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395574	0.62177	.	.	ENSG00000170835	ENST00000372080;ENST00000303626	T	0.67171	-0.25	5.69	5.69	0.88448	Carboxylesterase, type B (1);	0.296062	0.38058	N	0.001840	T	0.57344	0.2047	N	0.13327	0.33	0.80722	D	1	D	0.54397	0.966	P	0.50352	0.638	T	0.55386	-0.8149	10	0.26408	T	0.33	.	13.7707	0.63023	0.1534:0.8466:0.0:0.0	.	479	P19835	CEL_HUMAN	I	482;481	ENSP00000361151:T482I	ENSP00000304021:T481I	T	+	2	0	CEL	134935818	0.940000	0.31905	0.109000	0.21407	0.603000	0.37013	2.046000	0.41260	2.698000	0.92095	0.472000	0.43445	ACA	C|0.998;T|0.002	0.002	strong		0.607	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
ENTPD7	57089	hgsc.bcm.edu	37	10	101445591	101445591	+	Silent	SNP	A	A	C	rs3740078	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:101445591A>C	ENST00000370489.4	+	6	769	c.591A>C	c.(589-591)ccA>ccC	p.P197P		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	197						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		AAGATTTACCACTGGAGTTTG	0.443													A|||	1260	0.251597	0.233	0.2277	5008	,	,		18818	0.2956		0.3082	False		,,,				2504	0.1902				p.P197P		Atlas-SNP	.											.	ENTPD7	44	.	0			c.A591C						PASS	.	A		1020,3386	379.0+/-323.1	114,792,1297	127.0	119.0	121.0		591	-11.0	0.2	10	dbSNP_107	121	2571,6029	419.2+/-353.0	391,1789,2120	no	coding-synonymous	ENTPD7	NM_020354.3		505,2581,3417	CC,CA,AA		29.8953,23.1502,27.6103		197/605	101445591	3591,9415	2203	4300	6503	SO:0001819	synonymous_variant	57089	exon6			TTTACCACTGGAG	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.591A>C	10.37:g.101445591A>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_020354	B2RB83|B3KP21|D3DR64	Silent	SNP	ENST00000370489.4	37	CCDS7480.1																																																																																			A|0.734;C|0.266	0.266	strong		0.443	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
PBXIP1	57326	hgsc.bcm.edu	37	1	154917551	154917551	+	Silent	SNP	C	C	T	rs79526479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154917551C>T	ENST00000368463.3	-	11	2216	c.2145G>A	c.(2143-2145)gcG>gcA	p.A715A	PBXIP1_ENST00000542459.1_Silent_p.A560A|PBXIP1_ENST00000539880.1_Silent_p.A542A|PBXIP1_ENST00000368465.1_Silent_p.A686A|PBXIP1_ENST00000498553.1_5'Flank	NM_020524.2	NP_065385.2	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein 1	715					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)	cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(6)|lung(13)|prostate(1)|urinary_tract(1)	24	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCCTGGGCCCCGCAGCTCTTG	0.632													C|||	56	0.0111821	0.0015	0.0259	5008	,	,		17402	0.0		0.0199	False		,,,				2504	0.0164				p.A715A		Atlas-SNP	.											.	PBXIP1	59	.	0			c.G2145A						PASS	.	C		39,4367	41.6+/-74.8	0,39,2164	113.0	99.0	104.0		2145	-2.7	0.0	1	dbSNP_132	104	264,8336	102.3+/-163.5	6,252,4042	no	coding-synonymous	PBXIP1	NM_020524.2		6,291,6206	TT,TC,CC		3.0698,0.8852,2.3297		715/732	154917551	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	57326	exon11			GGGCCCCGCAGCT	AF221521	CCDS1074.1	1q22	2008-02-05	2007-01-30		ENSG00000163346	ENSG00000163346			21199	protein-coding gene	gene with protein product			"""pre-B-cell leukemia transcription factor interacting protein 1"""			7505766, 10825160	Standard	NM_020524		Approved	HPIP	uc001ffr.3	Q96AQ6	OTTHUMG00000037369	ENST00000368463.3:c.2145G>A	1.37:g.154917551C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_020524	Q5T174|Q5T176|Q9H8X6|Q9HA02|Q9HD85	Silent	SNP	ENST00000368463.3	37	CCDS1074.1																																																																																			C|0.979;G|0.000;T|0.021	0.021	strong		0.632	PBXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090943.1	NM_020524	
CCDC129	223075	hgsc.bcm.edu	37	7	31682601	31682601	+	Silent	SNP	T	T	C	rs38396	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:31682601T>C	ENST00000407970.3	+	11	1655	c.1617T>C	c.(1615-1617)caT>caC	p.H539H	CCDC129_ENST00000319386.3_Silent_p.H391H|CCDC129_ENST00000451887.2_Silent_p.H565H|CCDC129_ENST00000409210.1_Silent_p.H447H	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	539										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AAGACAGCCATCTGTGGCAGC	0.552													T|||	682	0.136182	0.0182	0.1556	5008	,	,		20135	0.1806		0.2177	False		,,,				2504	0.1524				p.H565H		Atlas-SNP	.											.	CCDC129	127	.	0			c.T1695C						PASS	.	T		222,4184	132.9+/-169.3	9,204,1990	141.0	135.0	137.0		1617	-10.0	0.0	7	dbSNP_76	137	1730,6870	315.1+/-312.1	183,1364,2753	no	coding-synonymous	CCDC129	NM_194300.2		192,1568,4743	CC,CT,TT		20.1163,5.0386,15.0085		539/1045	31682601	1952,11054	2203	4300	6503	SO:0001819	synonymous_variant	223075	exon11			CAGCCATCTGTGG	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1617T>C	7.37:g.31682601T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	130	51	0.392308	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			T|0.862;C|0.138	0.138	strong		0.552	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
SLC25A39	51629	hgsc.bcm.edu	37	17	42398052	42398052	+	Missense_Mutation	SNP	A	A	G	rs2011951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42398052A>G	ENST00000377095.5	-	9	858	c.739T>C	c.(739-741)Ttc>Ctc	p.F247L	SLC25A39_ENST00000225308.8_Missense_Mutation_p.F239L|SLC25A39_ENST00000586016.1_Missense_Mutation_p.F115L|SLC25A39_ENST00000590194.1_Missense_Mutation_p.F239L|SLC25A39_ENST00000537904.2_Missense_Mutation_p.F224L	NM_001143780.1	NP_001137252.1	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39	247			F -> L (in dbSNP:rs2011951). {ECO:0000269|PubMed:11139402, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5, ECO:0000269|Ref.7}.		heme biosynthetic process (GO:0006783)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TTCGGCCTGAACCCATTGAGC	0.602													G|||	3411	0.68111	0.7791	0.5764	5008	,	,		18046	0.9266		0.4036	False		,,,				2504	0.6554				p.F247L		Atlas-SNP	.											.	SLC25A39	24	.	0			c.T739C						PASS	.	G	LEU/PHE,LEU/PHE	3223,1183	415.2+/-337.1	1198,827,178	114.0	121.0	118.0		739,715	0.7	0.0	17	dbSNP_92	118	3331,5269	644.4+/-400.0	638,2055,1607	yes	missense,missense	SLC25A39	NM_001143780.1,NM_016016.2	22,22	1836,2882,1785	GG,GA,AA		38.7326,26.8498,49.6079	benign,benign	247/360,239/352	42398052	6554,6452	2203	4300	6503	SO:0001583	missense	51629	exon9			GCCTGAACCCATT	BC096819	CCDS11482.1, CCDS45700.1	17q12	2013-05-22			ENSG00000013306	ENSG00000013306		"""Solute carriers"""	24279	protein-coding gene	gene with protein product		610820				16949250	Standard	NM_001143780		Approved	FLJ22407, CGI-69	uc002ign.2	Q9BZJ4	OTTHUMG00000132628	ENST00000377095.5:c.739T>C	17.37:g.42398052A>G	ENSP00000366299:p.Phe247Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_001143780	A8JZZ2|D3DX51|D3DX54|Q4V9M1|Q9P182|Q9UF66|Q9Y379	Missense_Mutation	SNP	ENST00000377095.5	37	CCDS45700.1	1421	0.6506410256410257	377	0.766260162601626	206	0.569060773480663	525	0.9178321678321678	313	0.4129287598944591	G	2.061	-0.415327	0.04766	0.731502	0.387326	ENSG00000013306	ENST00000225308;ENST00000377095;ENST00000537904	T;T;T	0.79247	-1.25;-1.1;-1.22	5.18	0.7	0.18099	Mitochondrial carrier domain (2);	2.312390	0.01561	N	0.020130	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	0.37384	-0.9708	9	0.09084	T	0.74	-5.109	5.6686	0.17709	0.3855:0.0:0.4808:0.1337	rs2011951;rs3200280;rs17424083;rs17856304;rs57988364;rs2011951	224;247;239	B4DFG5;Q9BZJ4;Q9BZJ4-2	.;S2539_HUMAN;.	L	239;247;224	ENSP00000225308:F239L;ENSP00000366299:F247L;ENSP00000444540:F224L	ENSP00000225308:F239L	F	-	1	0	SLC25A39	39753578	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	0.161000	0.16481	0.094000	0.17404	-0.119000	0.15052	TTC	A|0.426;G|0.574	0.574	strong		0.602	SLC25A39-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457745.1	NM_016016	
SARDH	1757	hgsc.bcm.edu	37	9	136561367	136561367	+	Silent	SNP	G	G	A	rs2502740	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136561367G>A	ENST00000371872.4	-	14	2042	c.1785C>T	c.(1783-1785)tcC>tcT	p.S595S	SARDH_ENST00000371868.1_Silent_p.S23S|SARDH_ENST00000422262.2_Silent_p.S427S|SARDH_ENST00000439388.1_Silent_p.S595S	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	595					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		TGACATCTGCGGAGAAGAGCC	0.617																																					p.S595S		Atlas-SNP	.											SARDH,NS,carcinoma,0,1	SARDH	112	1	0			c.C1785T						PASS	.	A	,	656,3750	276.0+/-272.9	77,502,1624	61.0	56.0	58.0		1785,1785	-10.0	0.0	9	dbSNP_100	58	2932,5668	458.5+/-364.6	508,1916,1876	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	585,2418,3500	AA,AG,GG		34.093,14.8888,27.5873	,	595/919,595/919	136561367	3588,9418	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon14			ATCTGCGGAGAAG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1785C>T	9.37:g.136561367G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.744;A|0.256	0.256	strong		0.617	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
ESRRG	2104	hgsc.bcm.edu	37	1	216692669	216692669	+	Silent	SNP	C	C	T	rs945453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:216692669C>T	ENST00000408911.3	-	6	1110	c.957G>A	c.(955-957)tcG>tcA	p.S319S	ESRRG_ENST00000463665.1_Silent_p.S257S|ESRRG_ENST00000493603.1_Silent_p.S296S|ESRRG_ENST00000487276.1_Silent_p.S296S|ESRRG_ENST00000361395.2_Silent_p.S296S|ESRRG_ENST00000360012.3_Silent_p.S296S|ESRRG_ENST00000359162.2_Silent_p.S296S|ESRRG_ENST00000391890.3_Silent_p.S303S|ESRRG_ENST00000361525.3_Silent_p.S296S|ESRRG_ENST00000493748.1_Silent_p.S296S|ESRRG_ENST00000366937.1_Silent_p.S331S|ESRRG_ENST00000366940.2_Silent_p.S296S|ESRRG_ENST00000366938.2_Silent_p.S296S	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	319					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)	CATCCTCAAACGAAAGAGACC	0.473													C|||	3168	0.632588	0.733	0.6354	5008	,	,		15698	0.7381		0.4344	False		,,,				2504	0.59				p.S331S		Atlas-SNP	.											.	ESRRG	111	.	0			c.G993A						PASS	.	C	,,,	2915,1491	676.3+/-403.2	956,1003,244	89.0	86.0	87.0		888,957,888,888	-11.0	0.5	1	dbSNP_86	87	3563,5037	516.1+/-378.7	742,2079,1479	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRRG	NM_001134285.2,NM_001438.3,NM_206594.2,NM_206595.2	,,,	1698,3082,1723	TT,TC,CC		41.4302,33.8402,49.8078	,,,	296/436,319/459,296/436,296/436	216692669	6478,6528	2203	4300	6503	SO:0001819	synonymous_variant	2104	exon7			CTCAAACGAAAGA	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.957G>A	1.37:g.216692669C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Silent	SNP	ENST00000408911.3	37	CCDS41468.1																																																																																			C|0.442;T|0.558	0.558	strong		0.473	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595	
PSG3	5671	hgsc.bcm.edu	37	19	43243218	43243218	+	Silent	SNP	A	A	G	rs34721205|rs12185497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	223	0	0		WXS	Illumina HiSeq	Phase_I	221	91	0.411765	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	
PCNXL4	64430	hgsc.bcm.edu	37	14	60585131	60585131	+	Missense_Mutation	SNP	A	A	G	rs308998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:60585131A>G	ENST00000406854.1	+	7	2217	c.1663A>G	c.(1663-1665)Aaa>Gaa	p.K555E	PCNXL4_ENST00000317623.4_Missense_Mutation_p.K321E|PCNXL4_ENST00000535349.1_5'Flank|PCNXL4_ENST00000406949.1_Missense_Mutation_p.K321E|PCNXL4_ENST00000404681.2_Missense_Mutation_p.K555E			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	555				EK -> QE (in Ref. 2; CAH56141). {ECO:0000305}.		integral component of membrane (GO:0016021)											ATGGACAGAGAAAAAACAACG	0.368													A|||	1708	0.341054	0.5794	0.1398	5008	,	,		18327	0.3462		0.1183	False		,,,				2504	0.3855				p.K321E		Atlas-SNP	.											.	.	.	.	0			c.A961G						PASS	.	A	GLU/LYS	2099,2213		511,1077,568	97.0	96.0	96.0		961	4.9	1.0	14	dbSNP_79	96	1072,7478		73,926,3276	yes	missense	C14orf135	NM_022495.5	56	584,2003,3844	GG,GA,AA		12.538,48.6781,24.654	benign	321/939	60585131	3171,9691	2156	4275	6431	SO:0001583	missense	64430	exon6			ACAGAGAAAAAAC	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.1663A>G	14.37:g.60585131A>G	ENSP00000384801:p.Lys555Glu	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	282	156	0.553191	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		602	0.27564102564102566	269	0.5467479674796748	56	0.15469613259668508	197	0.34440559440559443	80	0.10554089709762533	A	17.38	3.374655	0.61735	0.486781	0.12538	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	T;T;T;T	0.27890	1.74;1.74;1.64;1.74	6.07	4.93	0.64822	.	.	.	.	.	T	0.00012	0.0000	M	0.78637	2.42	0.09310	P	1.0	B;B	0.15930	0.015;0.005	B;B	0.14578	0.011;0.01	T	0.40590	-0.9555	8	0.21540	T	0.41	.	12.334	0.55056	0.9343:0.0:0.0657:0.0	rs308998;rs308998	555;321	Q63HM2;B5MC47	CN135_HUMAN;.	E	321;555;321;555	ENSP00000317396:K321E;ENSP00000384801:K555E;ENSP00000385201:K321E;ENSP00000385713:K555E	ENSP00000317396:K321E	K	+	1	0	C14orf135	59654884	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	5.726000	0.68515	1.116000	0.41820	-0.280000	0.10049	AAA	A|0.702;G|0.298	0.298	strong		0.368	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
CDHR1	92211	hgsc.bcm.edu	37	10	85972043	85972043	+	Silent	SNP	A	A	G	rs10749482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85972043A>G	ENST00000372117.3	+	15	1765	c.1662A>G	c.(1660-1662)gaA>gaG	p.E554E	CDHR1_ENST00000332904.3_Silent_p.E554E|CDHR1_ENST00000440770.2_Silent_p.E258E	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	554	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGGACATGGAAGGCAAGTACA	0.542													G|||	2149	0.429113	0.7542	0.3876	5008	,	,		20639	0.2619		0.2853	False		,,,				2504	0.3395				p.E554E		Atlas-SNP	.											.	CDHR1	122	.	0			c.A1662G						PASS	.	G	,	2938,1468	472.6+/-356.4	990,958,255	172.0	152.0	159.0		1662,1662	0.6	1.0	10	dbSNP_120	159	2503,6097	694.5+/-404.7	376,1751,2173	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	1366,2709,2428	GG,GA,AA		29.1047,33.3182,41.8345	,	554/746,554/860	85972043	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	92211	exon15			CATGGAAGGCAAG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1662A>G	10.37:g.85972043A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			A|0.585;G|0.415	0.415	strong		0.542	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
GALNT2	2590	hgsc.bcm.edu	37	1	230384937	230384937	+	Silent	SNP	T	T	C	rs3748006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:230384937T>C	ENST00000366672.4	+	9	897	c.825T>C	c.(823-825)gaT>gaC	p.D275D	GALNT2_ENST00000541865.1_Silent_p.D185D|GALNT2_ENST00000543760.1_Silent_p.D237D	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	275					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)				CAGGTTTTGATTGGAACTTGG	0.502													T|||	1270	0.253594	0.1906	0.3458	5008	,	,		16095	0.5992		0.0547	False		,,,				2504	0.1217				p.D275D		Atlas-SNP	.											.	GALNT2	83	.	0			c.T825C						PASS	.	T		754,3652	309.1+/-290.9	71,612,1520	95.0	99.0	97.0		825	-3.5	1.0	1	dbSNP_107	97	430,8170	132.3+/-190.0	11,408,3881	no	coding-synonymous	GALNT2	NM_004481.3		82,1020,5401	CC,CT,TT		5.0,17.113,9.1035		275/572	230384937	1184,11822	2203	4300	6503	SO:0001819	synonymous_variant	2590	exon9			TTTTGATTGGAAC	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.825T>C	1.37:g.230384937T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	222	120	0.540541	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Silent	SNP	ENST00000366672.4	37	CCDS1582.1																																																																																			T|0.822;C|0.178	0.178	strong		0.502	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
RIN3	79890	hgsc.bcm.edu	37	14	93118038	93118038	+	Missense_Mutation	SNP	A	A	G	rs3829947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:93118038A>G	ENST00000216487.7	+	6	803	c.644A>G	c.(643-645)cAt>cGt	p.H215R	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	215			H -> L (in dbSNP:rs3829947).|H -> P (in dbSNP:rs3829947).|H -> R (in dbSNP:rs3829947).		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)				CCCACAGCCCATGACGCAAAC	0.592													A|||	2216	0.442492	0.4561	0.451	5008	,	,		9678	0.2748		0.5815	False		,,,				2504	0.4479				p.H215R		Atlas-SNP	.											.	RIN3	81	.	0			c.A644G						PASS	.	A	ARG/HIS	2011,2395	561.1+/-380.6	462,1087,654	89.0	88.0	88.0		644	-5.5	0.0	14	dbSNP_107	88	4902,3698	620.5+/-397.1	1373,2156,771	yes	missense	RIN3	NM_024832.3	29	1835,3243,1425	GG,GA,AA		43.0,45.6423,46.8476	benign	215/986	93118038	6913,6093	2203	4300	6503	SO:0001583	missense	79890	exon6			CAGCCCATGACGC	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.644A>G	14.37:g.93118038A>G	ENSP00000216487:p.His215Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	160	65	0.40625	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	948	0.4340659340659341	223	0.4532520325203252	162	0.44751381215469616	136	0.23776223776223776	427	0.5633245382585752	A	14.79	2.642037	0.47153	0.456423	0.57	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.21932	1.98	5.28	-5.52	0.02560	.	1.972690	0.02771	N	0.119728	T	0.00012	0.0000	N	0.11560	0.145	0.32136	P	0.5861620000000001	B	0.02656	0.0	B	0.04013	0.001	T	0.43909	-0.9362	9	0.07325	T	0.83	-0.4206	2.511	0.04657	0.4579:0.194:0.2534:0.0947	rs3829947;rs57313910;rs3829947	215	Q8TB24	RIN3_HUMAN	R	215	ENSP00000216487:H215R	ENSP00000216487:H215R	H	+	2	0	RIN3	92187791	0.000000	0.05858	0.000000	0.03702	0.954000	0.61252	-0.197000	0.09518	-0.914000	0.03827	0.260000	0.18958	CAT	G|0.492;A|0.508	0.492	strong		0.592	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
PLEKHM2	23207	hgsc.bcm.edu	37	1	16044401	16044401	+	Silent	SNP	G	G	A	rs16851970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16044401G>A	ENST00000375799.3	+	4	518	c.291G>A	c.(289-291)ctG>ctA	p.L97L	PLEKHM2_ENST00000375793.2_Silent_p.L97L	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	97	Interaction with KIF5B.|RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GTGCCTGGCTGTACCTGGCCC	0.547													G|||	932	0.186102	0.3676	0.1527	5008	,	,		21735	0.0337		0.1889	False		,,,				2504	0.1186				p.L97L		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.G291A						PASS	.	G		1185,2735		177,831,952	62.0	64.0	63.0		291	2.0	1.0	1	dbSNP_123	63	1573,6729		144,1285,2722	no	coding-synonymous	PLEKHM2	NM_015164.2		321,2116,3674	AA,AG,GG		18.9472,30.2296,22.5659		97/1020	16044401	2758,9464	1960	4151	6111	SO:0001819	synonymous_variant	23207	exon4			CTGGCTGTACCTG	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.291G>A	1.37:g.16044401G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																			G|0.797;A|0.203	0.203	strong		0.547	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
IFNA8	3445	hgsc.bcm.edu	37	9	21409439	21409439	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21409439C>T	ENST00000380205.1	+	1	294	c.264C>T	c.(262-264)ttC>ttT	p.F88F		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	88					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(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		AGCAGACCTTCAACCTCTTCA	0.473																																					p.F88F		Atlas-SNP	.											.	IFNA8	19	.	0			c.C264T						PASS	.						102.0	95.0	98.0					9																	21409439		2203	4300	6503	SO:0001819	synonymous_variant	3445	exon1			GACCTTCAACCTC		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"""Interferons"""	5429	protein-coding gene	gene with protein product	"""interferon alpha-B''"", ""interferon alpha type 201"""	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.264C>T	9.37:g.21409439C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	205	81	0.395122	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Silent	SNP	ENST00000380205.1	37	CCDS6507.1																																																																																			.	.	none		0.473	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170	
TNFSF15	9966	hgsc.bcm.edu	37	9	117552885	117552885	+	Silent	SNP	T	T	C	rs3810936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:117552885T>C	ENST00000374045.4	-	4	716	c.603A>G	c.(601-603)gtA>gtG	p.V201V	TNFSF15_ENST00000374044.1_Silent_p.V124V|AL390240.1_ENST00000408807.1_RNA	NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	201					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						CTACTTCGCATACAGACTTGG	0.532													C|||	3561	0.711062	0.913	0.6988	5008	,	,		19447	0.5069		0.675	False		,,,				2504	0.6943				p.V201V		Atlas-SNP	.											.	TNFSF15	23	.	0			c.A603G						PASS	.	C	,	3891,515	235.5+/-248.0	1716,459,28	189.0	151.0	164.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	426,603	4.0	1.0	9	dbSNP_107	164	5899,2701	433.1+/-357.3	2007,1885,408	yes	coding-synonymous,coding-synonymous	TNFSF15	NM_001204344.1,NM_005118.3	,	3723,2344,436	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	31.407,11.6886,24.727	,	142/193,201/252	117552885	9790,3216	2203	4300	6503	SO:0001819	synonymous_variant	9966	exon4			TTCGCATACAGAC	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.603A>G	9.37:g.117552885T>C		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	266	265	0.996241	NM_005118	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Silent	SNP	ENST00000374045.4	37	CCDS6809.1																																																																																			T|0.266;C|0.734	0.734	strong		0.532	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118	
SNAPC4	6621	hgsc.bcm.edu	37	9	139275204	139275204	+	Silent	SNP	A	A	C	rs3812570	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139275204A>C	ENST00000298532.2	-	19	2855	c.2487T>G	c.(2485-2487)gtT>gtG	p.V829V		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)		GCAGAAGATGAACTGGTGGGT	0.662													C|||	2064	0.412141	0.3858	0.6066	5008	,	,		17164	0.3214		0.4165	False		,,,				2504	0.3988				p.V829V		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T2487G						PASS	.			1679,2719	634.7+/-396.3	323,1033,843	53.0	46.0	48.0		2487	-4.0	0.0	9	dbSNP_107	48	3805,4789	598.1+/-393.9	845,2115,1337	no	coding-synonymous	SNAPC4	NM_003086.2		1168,3148,2180	CC,CA,AA		44.2751,38.1764,42.2106		829/1470	139275204	5484,7508	2199	4297	6496	SO:0001819	synonymous_variant	6621	exon19			AAGATGAACTGGT	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.2487T>G	9.37:g.139275204A>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.591;C|0.409	0.409	strong		0.662	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
ERCC6	2074	hgsc.bcm.edu	37	10	50740600	50740600	+	Silent	SNP	C	C	T	rs4253013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50740600C>T	ENST00000355832.5	-	2	489	c.411G>A	c.(409-411)ctG>ctA	p.L137L	ERCC6-PGBD3_ENST00000447839.2_Silent_p.L137L|ERCC6-PGBD3_ENST00000515869.1_Silent_p.L137L|PGBD3_ENST00000603152.1_Silent_p.L137L	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	137					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGAGGTCATCCAGGACCGACC	0.522								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	880	0.175719	0.118	0.2089	5008	,	,		23800	0.4107		0.0666	False		,,,				2504	0.1002				p.R137R		Atlas-SNP	.											.	ERCC6	162	.	0			c.A411A						PASS	.	C		473,3933	222.6+/-239.4	29,415,1759	116.0	92.0	100.0		411	3.7	1.0	10	dbSNP_111	100	552,8048	151.0+/-205.8	16,520,3764	no	coding-synonymous	ERCC6	NM_000124.2		45,935,5523	TT,TC,CC		6.4186,10.7354,7.881		137/1494	50740600	1025,11981	2203	4300	6503	SO:0001819	synonymous_variant	2074	exon2			GTCATCCAGGACC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.411G>A	10.37:g.50740600C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			C|0.878;T|0.122	0.122	strong		0.522	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
IRG1	730249	hgsc.bcm.edu	37	13	77531492	77531492	+	Missense_Mutation	SNP	G	G	A	rs61741168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:77531492G>A	ENST00000377462.1	+	5	880	c.818G>A	c.(817-819)cGt>cAt	p.R273H	IRG1_ENST00000449753.1_Missense_Mutation_p.R273H	NM_001258406.1	NP_001245335.1	A6NK06	IRG1_HUMAN	immunoresponsive 1 homolog (mouse)	273					cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to progesterone stimulus (GO:0071393)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of type I interferon production (GO:0032480)|positive regulation of antimicrobial humoral response (GO:0002760)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|propionate catabolic process (GO:0019543)|tolerance induction to lipopolysaccharide (GO:0072573)	mitochondrion (GO:0005739)	2-methylcitrate dehydratase activity (GO:0047547)|aconitate decarboxylase activity (GO:0047613)										GCCTTTAAGCGTTTTCCTGCA	0.512													G|||	32	0.00638978	0.0227	0.0029	5008	,	,		22983	0.0		0.0	False		,,,				2504	0.0				p.R269H		Atlas-SNP	.											.	IRG1	1	.	0			c.G806A						PASS	.																																			SO:0001583	missense	730249	exon4			TTAAGCGTTTTCC		CCDS58299.1	13q22.3	2013-04-29			ENSG00000102794	ENSG00000102794			33904	protein-coding gene	gene with protein product		615275				23610393	Standard	NM_001258406		Approved		uc031qmi.1	A6NK06	OTTHUMG00000017098	ENST00000377462.1:c.818G>A	13.37:g.77531492G>A	ENSP00000366682:p.Arg273His	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	246	119	0.48374	NM_001258406		Missense_Mutation	SNP	ENST00000377462.1	37	CCDS58299.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	16.59	3.166481	0.57476	.	.	ENSG00000102794	ENST00000377462;ENST00000449753	.	.	.	5.78	4.04	0.47022	.	0.292392	0.44688	D	0.000434	T	0.58366	0.2117	M	0.72894	2.215	0.32992	D	0.525088	.	.	.	.	.	.	T	0.68318	-0.5440	7	0.15952	T	0.53	0.102	16.9717	0.86302	0.0:0.0:0.8491:0.1509	rs61741168	.	.	.	H	273	.	ENSP00000366682:R273H	R	+	2	0	IRG1	76429493	1.000000	0.71417	0.959000	0.39883	0.431000	0.31685	4.522000	0.60539	0.785000	0.33685	0.563000	0.77884	CGT	G|0.997;A|0.003	0.003	strong		0.512	IRG1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045311.1	XM_001133269	
IMPDH1	3614	hgsc.bcm.edu	37	7	128034629	128034629	+	Silent	SNP	C	C	T	rs2228075	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128034629C>T	ENST00000480861.1	-	12	1382	c.1305G>A	c.(1303-1305)gcG>gcA	p.A435A	IMPDH1_ENST00000496200.1_Silent_p.A415A|IMPDH1_ENST00000343214.4_Silent_p.A415A|IMPDH1_ENST00000470772.1_Silent_p.A439A|IMPDH1_ENST00000354269.5_Silent_p.A515A|IMPDH1_ENST00000348127.6_Silent_p.A489A|IMPDH1_ENST00000378717.4_Silent_p.A456A|IMPDH1_ENST00000338791.6_Silent_p.A525A|IMPDH1_ENST00000419067.2_Silent_p.A492A	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						AGACACCCTGCGCGATCTTCA	0.587													C|||	1390	0.277556	0.2239	0.2651	5008	,	,		19268	0.3839		0.2724	False		,,,				2504	0.2546				p.A525A		Atlas-SNP	.											.	IMPDH1	38	.	0			c.G1575A						PASS	.	C	,,,,,,	893,3513	347.2+/-309.4	97,699,1407	75.0	73.0	74.0		1575,1545,1320,1305,1245,1476,1467	-10.4	0.1	7	dbSNP_98	74	2232,6368	378.1+/-338.8	298,1636,2366	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IMPDH1	NM_000883.3,NM_001102605.1,NM_001142573.1,NM_001142574.1,NM_001142575.1,NM_001142576.1,NM_183243.2	,,,,,,	395,2335,3773	TT,TC,CC		25.9535,20.2678,24.0274	,,,,,,	525/600,515/590,440/515,435/510,415/490,492/567,489/564	128034629	3125,9881	2203	4300	6503	SO:0001819	synonymous_variant	3614	exon15			ACCCTGCGCGATC		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"""retinitis pigmentosa 10 (autosomal dominant)"", ""IMP (inosine monophosphate) dehydrogenase 1"""	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.1305G>A	7.37:g.128034629C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_000883		Silent	SNP	ENST00000480861.1	37	CCDS55161.1																																																																																			T|0.249;G|0.000;C|0.750	0.249	strong		0.587	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883	
PRDM10	56980	hgsc.bcm.edu	37	11	129785594	129785594	+	Silent	SNP	G	G	A	rs3734073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:129785594G>A	ENST00000360871.3	-	16	2718	c.2487C>T	c.(2485-2487)ccC>ccT	p.P829P	PRDM10_ENST00000358825.5_Silent_p.P833P|PRDM10_ENST00000423662.2_Silent_p.P747P|PRDM10_ENST00000304538.6_Silent_p.P743P|PRDM10_ENST00000526082.1_Silent_p.P747P|PRDM10_ENST00000528746.1_Silent_p.P803P	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	833					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		GACAGCAGACGGGAGGGGTGG	0.597													G|||	1149	0.229433	0.1218	0.2896	5008	,	,		16915	0.1567		0.3231	False		,,,				2504	0.3108				p.P833P		Atlas-SNP	.											PRDM10,colon,carcinoma,0,1	PRDM10	120	1	0			c.C2499T						PASS	.	G	,,,	726,3676	300.7+/-286.5	64,598,1539	104.0	101.0	102.0		2499,2487,2241,2229	-7.1	0.7	11	dbSNP_107	102	2773,5821	441.1+/-359.7	439,1895,1963	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	503,2493,3502	AA,AG,GG		32.2667,16.4925,26.9237	,,,	833/1161,829/1157,747/1062,743/1024	129785594	3499,9497	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon17			GCAGACGGGAGGG	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.2487C>T	11.37:g.129785594G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			G|0.729;A|0.271	0.271	strong		0.597	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
ZFYVE1	53349	hgsc.bcm.edu	37	14	73440864	73440864	+	Silent	SNP	C	C	T	rs12931	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:73440864C>T	ENST00000556143.1	-	11	2745	c.2025G>A	c.(2023-2025)acG>acA	p.T675T	ZFYVE1_ENST00000555072.1_Silent_p.T260T|ZFYVE1_ENST00000554145.1_5'Flank|ZFYVE1_ENST00000553891.1_Silent_p.T675T|ZFYVE1_ENST00000318876.5_Silent_p.T661T|ZFYVE1_ENST00000394207.2_Silent_p.T260T	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	675					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		GAGCAATGAGCGTTCCACCTT	0.537													T|||	2400	0.479233	0.5877	0.4049	5008	,	,		20915	0.371		0.4781	False		,,,				2504	0.498				p.T675T		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.G2025A						PASS	.	T	,	2386,2020	562.1+/-380.9	628,1130,445	157.0	121.0	133.0		2025,780	-9.5	0.2	14	dbSNP_52	133	4175,4425	586.6+/-392.1	1029,2117,1154	yes	coding-synonymous,coding-synonymous	ZFYVE1	NM_021260.2,NM_178441.1	,	1657,3247,1599	TT,TC,CC		48.5465,45.8466,49.5541	,	675/778,260/363	73440864	6561,6445	2203	4300	6503	SO:0001819	synonymous_variant	53349	exon11			AATGAGCGTTCCA	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.2025G>A	14.37:g.73440864C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																			C|0.501;T|0.499	0.499	strong		0.537	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
PCDHA9	9752	hgsc.bcm.edu	37	5	140228413	140228413	+	Missense_Mutation	SNP	C	C	A	rs17844323	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140228413C>A	ENST00000532602.1	+	1	1366	c.333C>A	c.(331-333)gaC>gaA	p.D111E	PCDHA9_ENST00000378122.3_Missense_Mutation_p.D111E|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	111	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(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)			TGATCGTAGACAGGCCGCTGC	0.547													.|||	1014	0.202476	0.0272	0.2954	5008	,	,		15362	0.1339		0.3012	False		,,,				2504	0.3425				p.D111E	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											PCDHA9_ENST00000532602,bladder,carcinoma,+2,2	PCDHA9	373	2	0			c.C333A						scavenged	.	C	GLU/ASP,,,,,,,,,,,GLU/ASP	36,4310		9,18,2146	111.0	87.0	95.0		333,,,,,,,,,,,333	1.1	0.7	5	dbSNP_123	95	891,7347		303,285,3531	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	45,,,,,,,,,,,45	312,303,5677	AA,AC,CC		10.8157,0.8283,7.3665	,,,,,,,,,,,	111/843,,,,,,,,,,,111/951	140228413	927,11657	2173	4119	6292	SO:0001583	missense	9752	exon1			CGTAGACAGGCCG	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.333C>A	5.37:g.140228413C>A	ENSP00000436042:p.Asp111Glu	Somatic	271	3	0.0110701		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	393	0.17994505494505494	19	0.03861788617886179	113	0.31215469613259667	63	0.11013986013986014	198	0.2612137203166227	C	9.157	1.017662	0.19355	0.008283	0.108157	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.21031	2.03;2.03	4.13	1.1	0.20463	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.275715	0.18390	N	0.142694	T	0.00012	0.0000	N	0.11341	0.13	0.51767	P	6.099999999997774E-5	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.44298	-0.9337	9	0.54805	T	0.06	.	8.9368	0.35704	0.0:0.3062:0.5482:0.1455	rs17844323	111;111	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	E	111	ENSP00000436042:D111E;ENSP00000367362:D111E	ENSP00000367362:D111E	D	+	3	2	PCDHA9	140208597	0.000000	0.05858	0.746000	0.31095	0.806000	0.45545	-2.220000	0.01217	0.080000	0.16959	-0.274000	0.10170	GAC	C|0.819;A|0.181	0.181	strong		0.547	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
MED11	400569	hgsc.bcm.edu	37	17	4638737	4638737	+	IGR	SNP	A	A	G	rs1050998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4638737A>G	ENST00000293777.5	+	0	833				CXCL16_ENST00000574412.1_Missense_Mutation_p.I142T|CXCL16_ENST00000293778.6_Missense_Mutation_p.I142T|CXCL16_ENST00000576153.1_5'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.I142T(1)		lung(2)|ovary(2)	4						GGCCTGAGAAATTGGGGGGCT	0.547													A|||	2320	0.463259	0.2958	0.4813	5008	,	,		15653	0.5883		0.4394	False		,,,				2504	0.5726				p.I142T		Atlas-SNP	.											CXCL16_ENST00000293778,NS,carcinoma,0,1	CXCL16	30	1	1	Substitution - Missense(1)	stomach(1)	c.T425C						PASS	.	A	THR/ILE,THR/ILE	1377,3029	442.7+/-346.8	219,939,1045	40.0	46.0	44.0		425,425	-10.8	0.0	17	dbSNP_86	44	3757,4843	524.7+/-380.6	837,2083,1380	yes	missense,missense	CXCL16	NM_022059.2,NM_001100812.1	89,89	1056,3022,2425	GG,GA,AA		43.686,31.2528,39.4741	benign,benign	142/274,142/274	4638737	5134,7872	2203	4300	6503	SO:0001628	intergenic_variant	58191	exon4			TGAGAAATTGGGG	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638737A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_022059	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	CCDS32533.1	988	0.4523809523809524	149	0.30284552845528456	162	0.44751381215469616	342	0.5979020979020979	335	0.4419525065963061	A	7.511	0.654588	0.14580	0.312528	0.43686	ENSG00000161921	ENST00000293778	T	0.37058	1.22	5.39	-10.8	0.00216	.	1.751720	0.03251	N	0.181791	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.31641	-0.9936	9	0.20519	T	0.43	-0.0524	11.7582	0.51888	0.1525:0.3809:0.4666:0.0	rs1050998;rs3191367;rs17824101;rs17846369;rs17859405;rs52827810;rs57321128;rs1050998	123	Q9H2A7	CXL16_HUMAN	T	142	ENSP00000293778:I142T	ENSP00000293778:I142T	I	-	2	0	CXCL16	4585486	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.475000	0.06599	-2.302000	0.00657	-1.759000	0.00671	ATT	G|0.428;N|0.001	0.428	strong		0.547	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2415801	2415801	+	Silent	SNP	G	G	A	rs61732208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2415801G>A	ENST00000332578.3	+	10	1605	c.1605G>A	c.(1603-1605)ggG>ggA	p.G535G		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	535	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGTGGTGGGGGACCGCTGGC	0.701													G|||	729	0.145567	0.2005	0.0706	5008	,	,		16110	0.2341		0.0437	False		,,,				2504	0.138				p.G535G		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G1605A						PASS	.	G		876,3530	328.8+/-300.7	98,680,1425	42.0	49.0	47.0		1605	-7.6	0.3	19	dbSNP_129	47	378,8220	120.6+/-179.8	4,370,3925	no	coding-synonymous	TMPRSS9	NM_182973.1		102,1050,5350	AA,AG,GG		4.3964,19.882,9.6432		535/1060	2415801	1254,11750	2203	4299	6502	SO:0001819	synonymous_variant	360200	exon10			GGTGGGGGACCGC	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.1605G>A	19.37:g.2415801G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			G|0.892;A|0.108	0.108	strong		0.701	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
COL14A1	7373	hgsc.bcm.edu	37	8	121215991	121215991	+	Silent	SNP	T	T	C	rs2305600	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:121215991T>C	ENST00000297848.3	+	9	1191	c.921T>C	c.(919-921)tcT>tcC	p.S307S	COL14A1_ENST00000247781.3_Silent_p.S212S|COL14A1_ENST00000537875.1_Silent_p.S307S|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.S307S	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)			AGATCGCCTCTGAACCAGACA	0.483													C|||	3197	0.638379	0.8041	0.5937	5008	,	,		15320	0.6736		0.4612	False		,,,				2504	0.592				p.S307S		Atlas-SNP	.											.	COL14A1	292	.	0			c.T921C						PASS	.	C		3285,1121	402.6+/-332.4	1245,795,163	138.0	119.0	125.0		921	-10.2	0.0	8	dbSNP_100	125	4107,4493	591.9+/-392.9	995,2117,1188	no	coding-synonymous	COL14A1	NM_021110.1		2240,2912,1351	CC,CT,TT		47.7558,25.4426,43.1647		307/1797	121215991	7392,5614	2203	4300	6503	SO:0001819	synonymous_variant	7373	exon9			CGCCTCTGAACCA		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.921T>C	8.37:g.121215991T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_021110		Silent	SNP	ENST00000297848.3	37	CCDS34938.1	1330	0.6089743589743589	391	0.7947154471544715	217	0.5994475138121547	383	0.6695804195804196	339	0.4472295514511873	C	0.415	-0.911146	0.02434	0.745574	0.477558	ENSG00000187955	ENST00000523142	.	.	.	5.09	-10.2	0.00374	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999999988	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.3649	0.16107	0.1156:0.3145:0.365:0.2048	rs2305600;rs60185002;rs2305600	.	.	.	R	64	.	.	X	+	1	0	COL14A1	121285172	0.000000	0.05858	0.001000	0.08648	0.222000	0.24845	-6.194000	0.00076	-7.555000	0.00001	-3.839000	0.00018	TGA	T|0.409;C|0.591	0.591	strong		0.483	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
MINK1	50488	hgsc.bcm.edu	37	17	4797305	4797305	+	Missense_Mutation	SNP	G	G	A	rs2302319	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4797305G>A	ENST00000355280.6	+	22	2783	c.2587G>A	c.(2587-2589)Gtc>Atc	p.V863I	MINK1_ENST00000347992.7_Missense_Mutation_p.V834I|MINK1_ENST00000453408.3_Missense_Mutation_p.V843I	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						TACAGACAGCGTCAGCACCAT	0.657													G|||	1045	0.208666	0.0076	0.0764	5008	,	,		17031	0.5069		0.1024	False		,,,				2504	0.3763				p.V863I		Atlas-SNP	.											.	MINK1	110	.	0			c.G2587A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	67,4037		1,65,1986	27.0	31.0	30.0		2527,2476,2587,2500	3.2	1.0	17	dbSNP_100	30	632,7756		24,584,3586	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	29,29,29,29	25,649,5572	AA,AG,GG		7.5346,1.6326,5.5956	benign,benign,benign,benign	843/1313,826/1296,863/1333,834/1304	4797305	699,11793	2052	4194	6246	SO:0001583	missense	50488	exon22			GACAGCGTCAGCA	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2587G>A	17.37:g.4797305G>A	ENSP00000347427:p.Val863Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_153827		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	391	0.17902930402930403	6	0.012195121951219513	30	0.08287292817679558	276	0.4825174825174825	79	0.10422163588390501	G	14.06	2.423731	0.43020	0.016326	0.075346	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.75154	-0.91;-0.91;-0.91	5.24	3.22	0.36961	.	0.144593	0.44902	D	0.000414	T	0.00012	0.0000	M	0.70275	2.135	0.29795	P	0.832938	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	0.37056	-0.9722	9	0.59425	D	0.04	.	10.3147	0.43729	0.1658:0.0:0.8342:0.0	rs2302319;rs59653681;rs2302319	826;843;863;834	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	I	863;843;834	ENSP00000347427:V863I;ENSP00000406487:V843I;ENSP00000269296:V834I	ENSP00000269296:V834I	V	+	1	0	MINK1	4738081	0.991000	0.36638	0.989000	0.46669	0.946000	0.59487	2.046000	0.41260	1.446000	0.47643	-0.137000	0.14449	GTC	G|0.828;A|0.172	0.172	strong		0.657	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296675	39296675	+	Missense_Mutation	SNP	C	C	T	rs147498528	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39296675C>T	ENST00000345847.4	-	1	64	c.65G>A	c.(64-66)cGc>cAc	p.R22H		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	22	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GCAGCTGGGGCGGCAGCAGGT	0.632													C|||	10	0.00199681	0.0076	0.0	5008	,	,		17854	0.0		0.0	False		,,,				2504	0.0				p.R22H		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,+1,2	KRTAP4-6	46	2	0			c.G65A						PASS	.																																			SO:0001583	missense	81871	exon1			CTGGGGCGGCAGC	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.65G>A	17.37:g.39296675C>T	ENSP00000328270:p.Arg22His	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	.	7.766	0.706433	0.15239	.	.	ENSG00000198090	ENST00000345847	T	0.01430	4.9	4.15	-5.03	0.02973	.	3.358020	0.01113	U	0.005612	T	0.02119	0.0066	M	0.71296	2.17	0.09310	N	1	.	.	.	.	.	.	T	0.33828	-0.9853	8	0.41790	T	0.15	.	6.0155	0.19601	0.1242:0.3795:0.0:0.4963	.	.	.	.	H	22	ENSP00000328270:R22H	ENSP00000328270:R22H	R	-	2	0	KRTAP4-6	36550201	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-1.428000	0.02439	-1.147000	0.02851	-0.265000	0.10407	CGC	C|0.997;T|0.003	0.003	strong		0.632	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
NACC2	138151	hgsc.bcm.edu	37	9	138905136	138905136	+	Silent	SNP	C	C	T	rs2280486	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	177	0	0		WXS	Illumina HiSeq	Phase_I	178	91	0.511236	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	
KRT84	3890	hgsc.bcm.edu	37	12	52777513	52777513	+	Missense_Mutation	SNP	T	T	C	rs2245203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	175	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	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	
OR2AE1	81392	hgsc.bcm.edu	37	7	99473858	99473858	+	Missense_Mutation	SNP	G	G	C	rs17161997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	93	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	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		
EPHB4	2050	hgsc.bcm.edu	37	7	100420155	100420155	+	Silent	SNP	A	A	G	rs56173078	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100420155A>G	ENST00000358173.3	-	4	1014	c.546T>C	c.(544-546)ggT>ggC	p.G182G	RN7SL750P_ENST00000582814.1_RNA|EPHB4_ENST00000360620.3_Silent_p.G182G|EPHB4_ENST00000477446.1_5'UTR	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	182	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCATGCAGGCACCCTGGTCCT	0.632													A|||	444	0.0886581	0.1354	0.0735	5008	,	,		15670	0.0248		0.0905	False		,,,				2504	0.1002				p.G182G	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.T546C						PASS	.	A		560,3846	246.5+/-255.1	34,492,1677	53.0	54.0	53.0		546	-11.3	0.5	7	dbSNP_129	53	730,7870	173.3+/-223.8	26,678,3596	no	coding-synonymous	EPHB4	NM_004444.4		60,1170,5273	GG,GA,AA		8.4884,12.7099,9.9185		182/988	100420155	1290,11716	2203	4300	6503	SO:0001819	synonymous_variant	2050	exon4			GCAGGCACCCTGG	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3395	protein-coding gene	gene with protein product		600011	"""EphB4"""	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.546T>C	7.37:g.100420155A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	138	67	0.485507	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	37	CCDS5706.1																																																																																			A|0.905;G|0.095	0.095	strong		0.632	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
WDPCP	51057	hgsc.bcm.edu	37	2	63631515	63631515	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:63631515C>T	ENST00000272321.7	-	10	1630	c.1103G>A	c.(1102-1104)cGt>cAt	p.R368H	WDPCP_ENST00000409199.1_Missense_Mutation_p.R176H|WDPCP_ENST00000409562.3_Missense_Mutation_p.R368H|WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409120.1_Missense_Mutation_p.R176H|WDPCP_ENST00000398544.3_Missense_Mutation_p.R209H	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	368					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						AGTCACTCTACGGTGAGTTTC	0.458																																					p.R368H		Atlas-SNP	.											WDPCP,NS,carcinoma,0,1	WDPCP	79	1	0			c.G1103A						scavenged	.						104.0	98.0	100.0					2																	63631515		1909	4131	6040	SO:0001583	missense	51057	exon10			ACTCTACGGTGAG		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"""chromosome 2 open reading frame 86"""	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.1103G>A	2.37:g.63631515C>T	ENSP00000272321:p.Arg368His	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	179	3	0.0167598	NM_015910	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.631157	0.28978	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544;ENST00000409562	T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65	5.4	3.54	0.40534	WD40/YVTN repeat-like-containing domain (1);	0.259771	0.38058	N	0.001825	T	0.63212	0.2492	M	0.71581	2.175	0.09310	N	0.999998	D;B;D;D	0.89917	1.0;0.03;0.999;1.0	D;B;D;D	0.66979	0.921;0.011;0.948;0.917	T	0.56025	-0.8047	10	0.62326	D	0.03	-2.447	10.5865	0.45286	0.0:0.7769:0.0:0.2231	.	176;368;368;209	E9PFG9;O95876-2;O95876;O95876-3	.;.;FRITZ_HUMAN;.	H	368;176;176;209;368	ENSP00000272321:R368H;ENSP00000386592:R176H;ENSP00000386769:R176H;ENSP00000381552:R209H;ENSP00000387222:R368H	ENSP00000272321:R368H	R	-	2	0	WDPCP	63485019	0.921000	0.31238	0.548000	0.28192	0.048000	0.14542	1.872000	0.39549	0.713000	0.32060	0.591000	0.81541	CGT	.	.	none		0.458	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910	
USP25	29761	hgsc.bcm.edu	37	21	17172112	17172112	+	Silent	SNP	C	C	T	rs145029756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:17172112C>T	ENST00000285679.6	+	6	961	c.592C>T	c.(592-594)Ctg>Ttg	p.L198L	USP25_ENST00000285681.2_Silent_p.L198L|USP25_ENST00000547201.1_3'UTR|USP25_ENST00000400183.2_Silent_p.L198L|USP25_ENST00000351097.5_Silent_p.L198L	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	198	USP.				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		AAGATTAGTTCTGAATTACAA	0.289													C|||	2	0.000399361	0.0	0.0	5008	,	,		16107	0.0		0.002	False		,,,				2504	0.0				p.L198L		Atlas-SNP	.											.	USP25	156	.	0			c.C592T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	90.0	89.0	89.0		592	2.2	1.0	21	dbSNP_134	89	28,8558	17.9+/-57.8	0,28,4265	no	coding-synonymous	USP25	NM_013396.3		0,31,6465	TT,TC,CC		0.3261,0.0681,0.2386		198/1056	17172112	31,12961	2203	4293	6496	SO:0001819	synonymous_variant	29761	exon6			TTAGTTCTGAATT	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.592C>T	21.37:g.17172112C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	178	87	0.488764	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	37	CCDS33515.1																																																																																			C|0.998;T|0.002	0.002	strong		0.289	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
USP6	9098	hgsc.bcm.edu	37	17	5042894	5042894	+	Missense_Mutation	SNP	T	T	C	rs8073787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5042894T>C	ENST00000574788.1	+	22	3653	c.1423T>C	c.(1423-1425)Tgg>Cgg	p.W475R	USP6_ENST00000332776.4_Missense_Mutation_p.W475R|USP6_ENST00000250066.6_Missense_Mutation_p.W475R|USP6_ENST00000304328.5_Missense_Mutation_p.W158R			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	475			W -> R (in dbSNP:rs8073787). {ECO:0000269|PubMed:1565468}.		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						TGATTTTGAATGGAGCTGCTG	0.587			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								T|||	3881	0.77496	0.8805	0.5735	5008	,	,		18430	0.9087		0.5626	False		,,,				2504	0.8558				p.W475R		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6_ENST00000250066,NS,carcinoma,-1,2	USP6	213	2	0			c.T1423C						PASS	.	T	ARG/TRP	3571,835	741.1+/-411.2	1441,689,73	46.0	52.0	50.0		1423	-0.5	0.0	17	dbSNP_116	50	4723,3877	605.6+/-395.0	1312,2099,889	yes	missense	USP6	NM_004505.2	101	2753,2788,962	CC,CT,TT		45.0814,18.9514,36.2294	benign	475/1407	5042894	8294,4712	2203	4300	6503	SO:0001583	missense	9098	exon14			TTTGAATGGAGCT	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.1423T>C	17.37:g.5042894T>C	ENSP00000460380:p.Trp475Arg	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	1584	0.7252747252747253	425	0.8638211382113821	205	0.5662983425414365	523	0.9143356643356644	431	0.5686015831134564	T	4.806	0.149914	0.09185	0.810486	0.549186	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.13089	2.62;3.11;2.7	0.266	-0.532	0.11890	.	0.115600	0.85682	D	0.000000	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.003;0.006	B;B	0.04013	0.001;0.001	T	0.09997	-1.0649	8	0.19147	T	0.46	.	.	.	.	rs8073787;rs52828858;rs59236784;rs8073787	158;475	P35125-2;P35125	.;UBP6_HUMAN	R	475;475;158	ENSP00000328010:W475R;ENSP00000250066:W475R;ENSP00000305473:W158R	ENSP00000250066:W475R	W	+	1	0	USP6	4983618	0.074000	0.21230	0.001000	0.08648	0.001000	0.01503	-0.049000	0.11924	-1.209000	0.02631	-1.203000	0.01651	TGG	T|0.322;C|0.678	0.678	strong		0.587	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
MYT1	4661	hgsc.bcm.edu	37	20	62850358	62850358	+	Silent	SNP	C	C	T	rs41279348	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62850358C>T	ENST00000328439.1	+	12	2305	c.1941C>T	c.(1939-1941)ctC>ctT	p.L647L	MYT1_ENST00000536311.1_Silent_p.L674L|MYT1_ENST00000360149.4_Silent_p.L349L	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)					CTGAGAACCTCAGCACGAAGC	0.592													C|||	398	0.0794728	0.0234	0.0821	5008	,	,		19551	0.0685		0.1282	False		,,,				2504	0.1145				p.L647L	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.C1941T						PASS	.	C		197,4209	123.7+/-161.0	5,187,2011	60.0	48.0	52.0		1941	5.3	1.0	20	dbSNP_127	52	1115,7485	229.6+/-264.2	72,971,3257	no	coding-synonymous	MYT1	NM_004535.2		77,1158,5268	TT,TC,CC		12.9651,4.4712,10.0877		647/1122	62850358	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	4661	exon12			GAACCTCAGCACG	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.1941C>T	20.37:g.62850358C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	37	CCDS13558.1																																																																																			C|0.907;T|0.093	0.093	strong		0.592	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
KLHL40	131377	hgsc.bcm.edu	37	3	42728144	42728144	+	Missense_Mutation	SNP	A	A	G	rs6805421	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42728144A>G	ENST00000287777.4	+	1	1134	c.1034A>G	c.(1033-1035)aAc>aGc	p.N345S		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	345			N -> S (in dbSNP:rs6805421). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)		p.N345S(1)									TCCCTCTCCAACCAGGTCCCC	0.557													A|||	3118	0.622604	0.3638	0.5922	5008	,	,		20403	0.8343		0.672	False		,,,				2504	0.7249				p.N345S		Atlas-SNP	.											KBTBD5,colon,carcinoma,0,2	.	.	2	1	Substitution - Missense(1)	stomach(1)	c.A1034G						PASS	.	A	SER/ASN	1828,2578	535.8+/-374.3	385,1058,760	86.0	76.0	79.0		1034	3.2	1.0	3	dbSNP_116	79	5454,3146	656.0+/-401.3	1730,1994,576	yes	missense	KBTBD5	NM_152393.2	46	2115,3052,1336	GG,GA,AA		36.5814,41.4889,44.0105	benign	345/622	42728144	7282,5724	2203	4300	6503	SO:0001583	missense	131377	exon1			TCTCCAACCAGGT	AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"""Kelch-like"", ""BTB/POZ domain containing"""	30372	protein-coding gene	gene with protein product	"""sarcosynapsin"", ""nemaline myopathy type 8"""	615340	"""kelch repeat and BTB (POZ) domain containing 5"", ""kelch-like 40 (Drosophila)"""	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.1034A>G	3.37:g.42728144A>G	ENSP00000287777:p.Asn345Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_152393	Q86SI1|Q96MR2	Missense_Mutation	SNP	ENST00000287777.4	37	CCDS2703.1	1409	0.6451465201465202	211	0.42886178861788615	229	0.6325966850828729	460	0.8041958041958042	509	0.6715039577836411	A	6.854	0.526858	0.13066	0.414889	0.634186	ENSG00000157119	ENST00000287777;ENST00000452129	T	0.66099	-0.19	5.08	3.24	0.37175	Kelch-type beta propeller (1);	0.201582	0.52532	D	0.000072	T	0.00012	0.0000	N	0.02539	-0.55	0.46631	P	8.700000000000374E-4	B	0.09022	0.002	B	0.04013	0.001	T	0.40059	-0.9583	9	0.07325	T	0.83	.	11.0302	0.47767	0.1611:0.7139:0.125:0.0	rs6805421;rs6805421	345	Q2TBA0	KBTB5_HUMAN	S	345;90	ENSP00000287777:N345S	ENSP00000287777:N345S	N	+	2	0	KBTBD5	42703148	0.915000	0.31059	0.993000	0.49108	0.996000	0.88848	1.917000	0.39996	0.518000	0.28383	-0.280000	0.10049	AAC	A|0.408;G|0.592	0.592	strong		0.557	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393	
ATP8B2	57198	hgsc.bcm.edu	37	1	154316434	154316434	+	Silent	SNP	C	C	T	rs2274988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154316434C>T	ENST00000368489.3	+	18	1923	c.1923C>T	c.(1921-1923)taC>taT	p.Y641Y		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	627					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)			AAGAGTACTACGAGGAGTGGG	0.602													C|||	983	0.196286	0.2549	0.1657	5008	,	,		18937	0.125		0.2525	False		,,,				2504	0.1544				p.Y641Y		Atlas-SNP	.											ATP8B2,colon,carcinoma,0,1	ATP8B2	158	1	0			c.C1923T						PASS	.	C		987,3419	363.6+/-316.6	118,751,1334	46.0	47.0	47.0		1923	-2.8	0.0	1	dbSNP_100	47	2129,6471	358.9+/-331.3	282,1565,2453	no	coding-synonymous	ATP8B2	NM_020452.3		400,2316,3787	TT,TC,CC		24.7558,22.4013,23.9582		641/1224	154316434	3116,9890	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon18			GTACTACGAGGAG	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.1923C>T	1.37:g.154316434C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368489.3	37	CCDS1066.1																																																																																			C|0.774;T|0.226	0.226	strong		0.602	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	
LBP	3929	hgsc.bcm.edu	37	20	36982754	36982754	+	Missense_Mutation	SNP	G	G	A	rs36015492	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36982754G>A	ENST00000217407.2	+	4	600	c.439G>A	c.(439-441)Gag>Aag	p.E147K		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	147			E -> K (in dbSNP:rs36015492).		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)				GTTGGGCAGCGAGTCCTCCGG	0.572													G|||	36	0.0071885	0.0015	0.0101	5008	,	,		17794	0.0		0.0159	False		,,,				2504	0.0112				p.E147K		Atlas-SNP	.											.	LBP	60	.	0			c.G439A						PASS	.	G	LYS/GLU	13,4393	20.2+/-43.8	0,13,2190	86.0	72.0	77.0		439	4.8	0.2	20	dbSNP_126	77	122,8478	63.5+/-125.6	1,120,4179	yes	missense	LBP	NM_004139.2	56	1,133,6369	AA,AG,GG		1.4186,0.2951,1.038	possibly-damaging	147/482	36982754	135,12871	2203	4300	6503	SO:0001583	missense	3929	exon4			GGCAGCGAGTCCT		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.439G>A	20.37:g.36982754G>A	ENSP00000217407:p.Glu147Lys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	87	47	0.54023	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	15	0.006868131868131868	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	8	0.010554089709762533	G	16.78	3.217753	0.58560	0.002951	0.014186	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.04502	3.61	4.77	4.77	0.60923	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.464529	0.21044	N	0.081102	T	0.05686	0.0149	L	0.60455	1.87	0.09310	N	0.999997	P	0.47484	0.896	B	0.42959	0.403	T	0.12066	-1.0562	10	0.72032	D	0.01	-10.5021	13.4963	0.61428	0.0:0.0:1.0:0.0	rs36015492	147	P18428	LBP_HUMAN	K	147	ENSP00000217407:E147K	ENSP00000217407:E147K	E	+	1	0	LBP	36416168	0.974000	0.33945	0.241000	0.24154	0.385000	0.30292	4.595000	0.61048	2.648000	0.89879	0.561000	0.74099	GAG	G|0.988;A|0.012	0.012	strong		0.572	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
TRPV2	51393	hgsc.bcm.edu	37	17	16326005	16326005	+	Silent	SNP	A	A	C	rs1129235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16326005A>C	ENST00000338560.7	+	4	826	c.427A>C	c.(427-429)Agg>Cgg	p.R143R	TRPV2_ENST00000577397.1_5'UTR	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	143	Required for interaction with SLC50A1. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GCAGATCGACAGGGACTCTGG	0.557													C|||	1861	0.371605	0.5938	0.366	5008	,	,		20463	0.2302		0.3867	False		,,,				2504	0.2055				p.R143R		Atlas-SNP	.											.	TRPV2	74	.	0			c.A427C						PASS	.	C		2362,2044	561.1+/-380.6	643,1076,484	73.0	60.0	64.0		427	-2.9	0.0	17	dbSNP_86	64	3361,5239	636.2+/-399.1	648,2065,1587	no	coding-synonymous	TRPV2	NM_016113.4		1291,3141,2071	CC,CA,AA		39.0814,46.3913,44.0028		143/765	16326005	5723,7283	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon4			ATCGACAGGGACT	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.427A>C	17.37:g.16326005A>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1	867	0.39697802197802196	285	0.5792682926829268	148	0.4088397790055249	147	0.256993006993007	287	0.3786279683377309	C	8.991	0.977622	0.18812	0.536087	0.390814	ENSG00000187688	ENST00000455666	.	.	.	5.24	-2.87	0.05700	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40404	P	0.020321000000000033	.	.	.	.	.	.	T	0.37056	-0.9722	3	.	.	.	-11.1604	14.0002	0.64429	0.6578:0.2566:0.0856:0.0	rs1129235;rs3186911;rs16959673;rs58276834;rs1129235	.	.	.	P	100	.	.	Q	+	2	0	TRPV2	16266730	0.001000	0.12720	0.005000	0.12908	0.899000	0.52679	-0.477000	0.06583	-0.859000	0.04105	-0.121000	0.15023	CAG	A|0.578;C|0.422	0.422	strong		0.557	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
MUC2	4583	hgsc.bcm.edu	37	11	1092910	1092910	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1092910G>A	ENST00000441003.2	+	30	4756	c.4729G>A	c.(4729-4731)Ggc>Agc	p.G1577S	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.G1578S|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.G1577S(1)|p.G1578S(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aacacccaccggcacacagac	0.637																																					p.G1577S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,6	MUC2	614	6	2	Substitution - Missense(2)	prostate(2)	c.G4729A						scavenged	.						85.0	125.0	111.0					11																	1092910		1937	3603	5540	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.4729G>A	11.37:g.1092910G>A	ENSP00000415183:p.Gly1577Ser	Somatic	65	5	0.0769231		WXS	Illumina HiSeq	Phase_I	89	9	0.101124	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	g	2.787	-0.252217	0.05829	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11169	2.8;2.9	1.49	-2.97	0.05530	.	1.221530	0.07178	U	0.853623	T	0.04092	0.0114	.	.	.	0.09310	N	1	B	0.24882	0.113	B	0.11329	0.006	T	0.37798	-0.9690	9	0.07175	T	0.84	.	4.8921	0.13731	0.6336:0.1684:0.198:0.0	.	1577	E7EUV1	.	S	1577;1578	ENSP00000415183:G1577S;ENSP00000351956:G1578S	ENSP00000351956:G1578S	G	+	1	0	MUC2	1082910	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.266000	0.02842	-2.620000	0.00440	-1.713000	0.00713	GGC	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CACNA1S	779	hgsc.bcm.edu	37	1	201047111	201047111	+	Silent	SNP	A	A	G	rs9427714	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201047111A>G	ENST00000362061.3	-	11	1741	c.1515T>C	c.(1513-1515)tgT>tgC	p.C505C	CACNA1S_ENST00000367338.3_Silent_p.C505C	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	505					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGATACCGCTACACACCACGA	0.572													G|||	636	0.126997	0.028	0.2032	5008	,	,		19464	0.001		0.34	False		,,,				2504	0.1176				p.C505C		Atlas-SNP	.											.	CACNA1S	249	.	0			c.T1515C						PASS	.	G		346,4060	794.9+/-415.3	18,310,1875	116.0	92.0	100.0		1515	4.8	1.0	1	dbSNP_119	100	3252,5348	648.8+/-400.5	652,1948,1700	no	coding-synonymous	CACNA1S	NM_000069.2		670,2258,3575	GG,GA,AA		37.814,7.8529,27.6642		505/1874	201047111	3598,9408	2203	4300	6503	SO:0001819	synonymous_variant	779	exon11			ACCGCTACACACC	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1515T>C	1.37:g.201047111A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	200	89	0.445	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			A|0.768;G|0.232	0.232	strong		0.572	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
EPRS	2058	hgsc.bcm.edu	37	1	220156704	220156704	+	Missense_Mutation	SNP	T	T	C	rs5030752	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:220156704T>C	ENST00000366923.3	-	22	3396	c.3127A>G	c.(3127-3129)Ata>Gta	p.I1043V		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1043	Proline--tRNA ligase.		I -> V (in dbSNP:rs5030752). {ECO:0000269|PubMed:17974005}.		cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)	p.I1043V(1)		breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	CAGCCACTTATGTCATGGTAT	0.363													C|||	328	0.0654952	0.0756	0.0389	5008	,	,		17830	0.0536		0.0944	False		,,,				2504	0.0532				p.I1043V		Atlas-SNP	.											EPRS,NS,carcinoma,0,1	EPRS	140	1	1	Substitution - Missense(1)	stomach(1)	c.A3127G						PASS	.	C	VAL/ILE	320,4086	796.1+/-415.3	12,296,1895	55.0	57.0	57.0		3127	4.6	1.0	1	dbSNP_113	57	673,7927	788.6+/-407.6	29,615,3656	yes	missense	EPRS	NM_004446.2	29	41,911,5551	CC,CT,TT		7.8256,7.2628,7.6349	benign	1043/1513	220156704	993,12013	2203	4300	6503	SO:0001583	missense	2058	exon22			CACTTATGTCATG	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3127A>G	1.37:g.220156704T>C	ENSP00000355890:p.Ile1043Val	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	37	CCDS31027.1	146	0.06684981684981685	35	0.07113821138211382	18	0.049723756906077346	25	0.043706293706293704	68	0.08970976253298153	C	4.410	0.075691	0.08485	0.072628	0.078256	ENSG00000136628	ENST00000366923	T	0.26810	1.71	5.47	4.56	0.56223	.	0.000000	0.85682	N	0.000000	T	0.00271	0.0008	N	0.00599	-1.345	0.50467	P	1.2999999999996348E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.27054	-1.0085	9	0.02654	T	1	-12.0557	12.1012	0.53785	0.0:0.861:0.0:0.139	rs5030752;rs5030752	1043	P07814	SYEP_HUMAN	V	1043	ENSP00000355890:I1043V	ENSP00000355890:I1043V	I	-	1	0	EPRS	218223327	1.000000	0.71417	0.998000	0.56505	0.706000	0.40770	5.884000	0.69729	0.714000	0.32081	-0.726000	0.03593	ATA	T|0.929;C|0.071	0.071	strong		0.363	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	
ZWILCH	55055	hgsc.bcm.edu	37	15	66821250	66821250	+	Missense_Mutation	SNP	A	A	G	rs11071896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:66821250A>G	ENST00000307897.5	+	11	1410	c.1030A>G	c.(1030-1032)Agt>Ggt	p.S344G	ZWILCH_ENST00000565627.1_Missense_Mutation_p.S230G|ZWILCH_ENST00000535141.2_Missense_Mutation_p.S230G|ZWILCH_ENST00000446801.2_Missense_Mutation_p.S230G	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	344			S -> G (in dbSNP:rs11071896).		mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						CAAAGTTCGGAGTGATCTTGA	0.378													A|||	910	0.181709	0.0325	0.1585	5008	,	,		18579	0.1825		0.2535	False		,,,				2504	0.3252				p.S344G		Atlas-SNP	.											.	ZWILCH	46	.	0			c.A1030G						PASS	.	A	GLY/SER	321,4081	173.7+/-203.5	12,297,1892	121.0	110.0	113.0		1030	3.2	0.0	15	dbSNP_120	113	2191,6407	373.7+/-337.1	267,1657,2375	yes	missense	ZWILCH	NM_017975.3	56	279,1954,4267	GG,GA,AA		25.4827,7.2921,19.3231	benign	344/592	66821250	2512,10488	2201	4299	6500	SO:0001583	missense	55055	exon11			GTTCGGAGTGATC	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"""Zwilch, kinetochore associated, homolog (Drosophila)"""			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.1030A>G	15.37:g.66821250A>G	ENSP00000311429:p.Ser344Gly	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	177	74	0.418079	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	37	CCDS10219.1	348	0.15934065934065933	8	0.016260162601626018	75	0.20718232044198895	75	0.13111888111888112	190	0.25065963060686014	A	8.607	0.888157	0.17540	0.072921	0.254827	ENSG00000174442	ENST00000307897;ENST00000446801;ENST00000535141	T;T;T	0.38887	1.11;1.11;1.11	5.26	3.19	0.36642	.	0.149273	0.64402	N	0.000011	T	0.00012	0.0000	N	0.00082	-2.215	0.40739	P	0.01719000000000004	B	0.02656	0.0	B	0.01281	0.0	T	0.36261	-0.9755	9	0.02654	T	1	-4.1282	8.9379	0.35711	0.0848:0.0:0.7718:0.1434	rs11071896;rs52805664;rs59123612;rs11071896	344	Q9H900	ZWILC_HUMAN	G	344;230;230	ENSP00000311429:S344G;ENSP00000402217:S230G;ENSP00000437749:S230G	ENSP00000311429:S344G	S	+	1	0	ZWILCH	64608304	1.000000	0.71417	0.029000	0.17559	0.464000	0.32679	4.667000	0.61561	0.566000	0.29273	0.374000	0.22700	AGT	A|0.818;G|0.182	0.182	strong		0.378	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975	
CDKL2	8999	hgsc.bcm.edu	37	4	76551010	76551010	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:76551010G>A	ENST00000429927.2	-	2	866	c.163C>T	c.(163-165)Cta>Tta	p.L55L	CDKL2_ENST00000307465.4_Silent_p.L55L	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	55	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CTCACCTTTAGTAACTTGATT	0.284																																					p.L55L		Atlas-SNP	.											CDKL2,colon,carcinoma,+1,1	CDKL2	58	1	0			c.C163T						scavenged	.						135.0	126.0	129.0					4																	76551010		2202	4300	6502	SO:0001819	synonymous_variant	8999	exon2			CCTTTAGTAACTT	U35146	CCDS3570.1	4q21.21	2011-11-04			ENSG00000138769	ENSG00000138769		"""Cyclin-dependent kinases"""	1782	protein-coding gene	gene with protein product		603442				9000130	Standard	NM_003948		Approved	P56, KKIAMRE	uc003hiq.3	Q92772	OTTHUMG00000130103	ENST00000429927.2:c.163C>T	4.37:g.76551010G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	109	4	0.0366972	NM_003948	B2R695	Silent	SNP	ENST00000429927.2	37	CCDS3570.1																																																																																			.	.	none		0.284	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948	
SREBF2	6721	hgsc.bcm.edu	37	22	42276742	42276742	+	Missense_Mutation	SNP	G	G	C	rs2228314	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	173	0	0		WXS	Illumina HiSeq	Phase_I	203	98	0.482759	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	
FOXO3	2309	hgsc.bcm.edu	37	6	108882570	108882570	+	Silent	SNP	C	C	T	rs11757217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	31	0	0		WXS	Illumina HiSeq	Phase_I	59	18	0.305085	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		
WDR62	284403	hgsc.bcm.edu	37	19	36593915	36593915	+	Missense_Mutation	SNP	T	T	G	rs61741470	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36593915T>G	ENST00000270301.7	+	28	3386	c.3386T>G	c.(3385-3387)aTg>aGg	p.M1129R	WDR62_ENST00000401500.2_Missense_Mutation_p.M1134R			O43379	WDR62_HUMAN	WD repeat domain 62	1129					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)			GTCAAGCTCATGGACCGAGGC	0.632													T|||	275	0.0549121	0.0159	0.036	5008	,	,		19098	0.1062		0.0358	False		,,,				2504	0.0879				p.M1134R		Atlas-SNP	.											.	WDR62	102	.	0			c.T3401G						PASS	.	T	ARG/MET,ARG/MET	112,4294	83.4+/-121.9	0,112,2091	50.0	50.0	50.0		3401,3386	-5.3	0.0	19	dbSNP_129	50	337,8263	112.5+/-172.7	4,329,3967	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	91,91	4,441,6058	GG,GT,TT		3.9186,2.542,3.4523	benign,benign	1134/1524,1129/1519	36593915	449,12557	2203	4300	6503	SO:0001583	missense	284403	exon28			AGCTCATGGACCG	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.3386T>G	19.37:g.36593915T>G	ENSP00000270301:p.Met1129Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	99	0.04532967032967033	9	0.018292682926829267	16	0.04419889502762431	45	0.07867132867132867	29	0.03825857519788918	T	6.810	0.518486	0.13005	0.02542	0.039186	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.44482	1.0;0.92	4.68	-5.29	0.02747	.	2.109050	0.01890	N	0.038466	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B;B	0.17852	0.024;0.014	B;B	0.23150	0.044;0.019	T	0.12915	-1.0529	10	0.11794	T	0.64	2.1238	11.0584	0.47933	0.0:0.3636:0.0:0.6364	rs61741470	1134;1129	O43379-4;O43379	.;WDR62_HUMAN	R	1134;1129	ENSP00000384792:M1134R;ENSP00000270301:M1129R	ENSP00000270301:M1129R	M	+	2	0	WDR62	41285755	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-1.463000	0.02361	-0.706000	0.05028	-0.182000	0.12963	ATG	T|0.959;G|0.041	0.041	strong		0.632	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
CEACAM18	729767	hgsc.bcm.edu	37	19	51986547	51986547	+	Missense_Mutation	SNP	A	A	G	rs10426247	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51986547A>G	ENST00000396477.4	+	4	971	c.950A>G	c.(949-951)cAt>cGt	p.H317R	CEACAM18_ENST00000451626.1_Missense_Mutation_p.H378R	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	317										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAGGCCCCCCATGAGTGCAGC	0.612													a|||	888	0.177316	0.1278	0.1686	5008	,	,		20149	0.1429		0.2445	False		,,,				2504	0.2168				p.H378R		Atlas-SNP	.											CEACAM18_ENST00000451626,colon,carcinoma,0,1	CEACAM18	96	1	0			c.A1133G						PASS	.	A	ARG/HIS	556,3676		35,486,1595	56.0	58.0	57.0		1133	1.5	0.0	19	dbSNP_119	57	2006,6466		222,1562,2452	no	missense	CEACAM18	NM_001080405.1	29	257,2048,4047	GG,GA,AA		23.678,13.138,20.1669	benign	378/399	51986547	2562,10142	2116	4236	6352	SO:0001583	missense	729767	exon5			CCCCCCATGAGTG			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.950A>G	19.37:g.51986547A>G	ENSP00000379738:p.His317Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		368	0.1684981684981685	55	0.11178861788617886	69	0.19060773480662985	74	0.12937062937062938	170	0.22427440633245382	.	0.006	-2.020692	0.00418	0.13138	0.23678	ENSG00000213822	ENST00000451626;ENST00000451086	T	0.04706	3.57	2.53	1.48	0.22813	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46898	-0.9158	7	.	.	.	.	5.6185	0.17444	0.1594:0.0:0.8406:0.0	rs10426247	378	A8MTB9	CEA18_HUMAN	R	378;317	ENSP00000402203:H378R	.	H	+	2	0	CEACAM18	56678359	0.032000	0.19561	0.036000	0.18154	0.008000	0.06430	0.395000	0.20850	0.670000	0.31165	-0.413000	0.06143	CAT	A|0.816;G|0.184	0.184	strong		0.612	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
NT5C2	22978	hgsc.bcm.edu	37	10	104849468	104849468	+	Silent	SNP	G	G	A	rs3740387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:104849468G>A	ENST00000404739.3	-	17	1670	c.1647C>T	c.(1645-1647)gaC>gaT	p.D549D	CNNM2_ENST00000369878.4_3'UTR|NT5C2_ENST00000369857.4_5'UTR|NT5C2_ENST00000423468.2_Silent_p.D520D|NT5C2_ENST00000343289.5_Silent_p.D549D			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	549	Asp/Glu-rich (acidic).				cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	catcatcttcgtcATGGCAGT	0.498													A|||	2114	0.422125	0.3442	0.4135	5008	,	,		18060	0.499		0.4135	False		,,,				2504	0.4632				p.D549D		Atlas-SNP	.											.	NT5C2	41	.	0			c.C1647T						PASS	.	A	,	1652,2754	659.5+/-400.6	318,1016,869	97.0	87.0	90.0		1647,1647	2.3	1.0	10	dbSNP_107	90	3509,5091	633.3+/-398.7	701,2107,1492	no	coding-synonymous,coding-synonymous	NT5C2	NM_001134373.1,NM_012229.3	,	1019,3123,2361	AA,AG,GG		40.8023,37.4943,39.6817	,	549/562,549/562	104849468	5161,7845	2203	4300	6503	SO:0001819	synonymous_variant	22978	exon19			ATCTTCGTCATGG	D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"""purine 5' nucleotidase"""	600417	"""5'-nucleotidase (purine), cytosolic type B"""	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.1647C>T	10.37:g.104849468G>A		Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	283	126	0.44523	NM_012229	B7Z382|D3DR91|Q5JUV5	Silent	SNP	ENST00000404739.3	37	CCDS7544.1																																																																																			G|0.600;A|0.400	0.400	strong		0.498	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462926	37462926	+	Silent	SNP	G	G	A	rs2235321	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37462926G>A	ENST00000346753.3	-	17	2333	c.2217C>T	c.(2215-2217)taC>taT	p.Y739Y	TMPRSS6_ENST00000381792.2_Silent_p.Y752Y|TMPRSS6_ENST00000406856.1_Silent_p.Y752Y|TMPRSS6_ENST00000406725.1_Silent_p.Y730Y	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	739	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.Y739Y(1)		breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GCGTCACCTGGTAGCGATAGA	0.607													G|||	1783	0.35603	0.41	0.2118	5008	,	,		20113	0.4087		0.4245	False		,,,				2504	0.2607				p.Y739Y		Atlas-SNP	.											TMPRSS6,NS,carcinoma,0,1	TMPRSS6	99	1	1	Substitution - coding silent(1)	stomach(1)	c.C2217T						PASS	.	G		1850,2556	536.1+/-374.4	378,1094,731	133.0	98.0	110.0		2217	3.7	1.0	22	dbSNP_98	110	3223,5377	485.3+/-371.6	616,1991,1693	yes	coding-synonymous	TMPRSS6	NM_153609.2		994,3085,2424	AA,AG,GG		37.4767,41.9882,39.0051		739/812	37462926	5073,7933	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon17			CACCTGGTAGCGA	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.2217C>T	22.37:g.37462926G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	180	110	0.611111	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			G|0.622;A|0.377	0.377	strong		0.607	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
SLCO3A1	28232	hgsc.bcm.edu	37	15	92638193	92638193	+	Silent	SNP	G	G	A	rs2286355	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:92638193G>A	ENST00000318445.6	+	3	943	c.729G>A	c.(727-729)gcG>gcA	p.A243A	SLCO3A1_ENST00000424469.2_Silent_p.A243A	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	243					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)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	ACGTGGATGCGGTCTTCATTG	0.468													G|||	1608	0.321086	0.112	0.4265	5008	,	,		19588	0.4087		0.3738	False		,,,				2504	0.3845				p.A243A		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.G729A						PASS	.	G	,	631,3765	272.8+/-271.0	48,535,1615	152.0	140.0	144.0		729,729	-11.7	0.4	15	dbSNP_100	144	3318,5278	493.8+/-373.7	617,2084,1597	no	coding-synonymous,coding-synonymous	SLCO3A1	NM_001145044.1,NM_013272.3	,	665,2619,3212	AA,AG,GG		38.5993,14.354,30.3956	,	243/693,243/711	92638193	3949,9043	2198	4298	6496	SO:0001819	synonymous_variant	28232	exon3			GGATGCGGTCTTC	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"""Solute carriers"""	10952	protein-coding gene	gene with protein product		612435	"""solute carrier family 21 (organic anion transporter), member 11"""	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.729G>A	15.37:g.92638193G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	199	87	0.437186	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Silent	SNP	ENST00000318445.6	37	CCDS10371.1																																																																																			G|0.684;N|0.000	.	strong		0.468	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80923536	80923536	+	Silent	SNP	C	C	T	rs4986144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	60	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	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	
MUC16	94025	hgsc.bcm.edu	37	19	9048035	9048035	+	Missense_Mutation	SNP	G	G	C	rs10417358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9048035G>C	ENST00000397910.4	-	5	33799	c.33596C>G	c.(33595-33597)gCt>gGt	p.A11199G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11201	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGGGAGACAGCTAAAGTTGG	0.453													G|||	949	0.189497	0.1982	0.1988	5008	,	,		24115	0.0258		0.2823	False		,,,				2504	0.2444				p.A11199G		Atlas-SNP	.											.	MUC16	4315	.	0			c.C33596G						PASS	.		GLY/ALA	753,3155		71,611,1272	60.0	53.0	55.0		33596	1.4	0.0	19	dbSNP_119	55	2512,5794		398,1716,2039	yes	missense	MUC16	NM_024690.2	60	469,2327,3311	CC,CG,GG		30.2432,19.2682,26.7316	possibly-damaging	11199/14508	9048035	3265,8949	1954	4153	6107	SO:0001583	missense	94025	exon5			GAGACAGCTAAAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33596C>G	19.37:g.9048035G>C	ENSP00000381008:p.Ala11199Gly	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	408	0.18681318681318682	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	218	0.287598944591029	g	9.969	1.225012	0.22457	0.192682	0.302432	ENSG00000181143	ENST00000397910	T	0.02763	4.17	2.54	1.44	0.22558	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	.	.	.	P	0.34977	0.478	B	0.41236	0.351	T	0.51529	-0.8694	8	0.87932	D	0	.	5.6913	0.17831	0.1608:0.0:0.8392:0.0	rs10417358;rs52819888;rs10417358	11199	B5ME49	.	G	11199	ENSP00000381008:A11199G	ENSP00000381008:A11199G	A	-	2	0	MUC16	8909035	0.002000	0.14202	0.001000	0.08648	0.590000	0.36582	0.657000	0.24963	0.586000	0.29626	0.306000	0.20318	GCT	G|0.780;C|0.220	0.220	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRUNE2	158471	hgsc.bcm.edu	37	9	79323952	79323952	+	Missense_Mutation	SNP	C	C	T	rs377620126		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79323952C>T	ENST00000376718.3	-	8	3361	c.3238G>A	c.(3238-3240)Gac>Aac	p.D1080N	PRUNE2_ENST00000428286.1_Missense_Mutation_p.D721N	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1080					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						CTGGGGTCGTCGTAACTGGAC	0.512																																					p.D1080N		Atlas-SNP	.											PRUNE2_ENST00000376718,NS,carcinoma,+2,1	PRUNE2	331	1	0			c.G3238A						scavenged	.	C	ASN/ASP	1,3135		0,1,1567	261.0	223.0	234.0		3238	5.0	0.9	9		234	0,7164		0,0,3582	no	missense	PRUNE2	NM_015225.2	23	0,1,5149	TT,TC,CC		0.0,0.0319,0.0097	probably-damaging	1080/3089	79323952	1,10299	1568	3582	5150	SO:0001583	missense	158471	exon8			GGTCGTCGTAACT	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.3238G>A	9.37:g.79323952C>T	ENSP00000365908:p.Asp1080Asn	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	368	4	0.0108696	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.9|21.9	4.221286|4.221286	0.79464|0.79464	3.19E-4|3.19E-4	0.0|0.0	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.57107|.	0.42;0.43|.	5.94|5.94	5.04|5.04	0.67666|0.67666	.|.	0.318759|.	0.27134|.	N|.	0.020767|.	T|T	0.52693|0.52693	0.1750|0.1750	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	P|.	0.56788|.	0.806|.	T|T	0.49173|0.49173	-0.8967|-0.8967	10|5	0.87932|.	D|.	0|.	-6.6734|-6.6734	11.3444|11.3444	0.49552|0.49552	0.0:0.8558:0.0:0.1442|0.0:0.8558:0.0:0.1442	.|.	1080|.	Q8WUY3|.	PRUN2_HUMAN|.	N|Q	1080;721;1079|401	ENSP00000365908:D1080N;ENSP00000397425:D721N|.	ENSP00000365908:D1080N|.	D|R	-|-	1|2	0|0	PRUNE2|PRUNE2	78513772|78513772	1.000000|1.000000	0.71417|0.71417	0.919000|0.919000	0.36401|0.36401	0.958000|0.958000	0.62258|0.62258	1.925000|1.925000	0.40074|0.40074	1.517000|1.517000	0.48917|0.48917	0.561000|0.561000	0.74099|0.74099	GAC|CGA	.	.	weak		0.512	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
FMN2	56776	hgsc.bcm.edu	37	1	240256781	240256781	+	Missense_Mutation	SNP	G	G	A	rs142335257		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240256781G>A	ENST00000319653.9	+	1	1602	c.1372G>A	c.(1372-1374)Gcc>Acc	p.A458T		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	458					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)			GTCCAGAACTGCCCTGGCCTC	0.706													G|||	1	0.000199681	0.0	0.0	5008	,	,		10887	0.0		0.001	False		,,,				2504	0.0				p.A458T		Atlas-SNP	.											.	FMN2	451	.	0			c.G1372A						PASS	.	G	THR/ALA	0,4386		0,0,2193	25.0	31.0	29.0		1372	1.4	0.0	1	dbSNP_134	29	8,8546		0,8,4269	yes	missense	FMN2	NM_020066.4	58	0,8,6462	AA,AG,GG		0.0935,0.0,0.0618	benign	458/1723	240256781	8,12932	2193	4277	6470	SO:0001583	missense	56776	exon1			AGAACTGCCCTGG	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.1372G>A	1.37:g.240256781G>A	ENSP00000318884:p.Ala458Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	34	22	0.647059	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	10.15	1.270343	0.23221	0.0	9.35E-4	ENSG00000155816	ENST00000319653	T	0.80214	-1.35	4.61	1.41	0.22369	.	0.629084	0.14102	N	0.341281	T	0.57666	0.2069	N	0.12182	0.205	0.09310	N	0.999998	B	0.17038	0.02	B	0.12156	0.007	T	0.38286	-0.9668	10	0.18710	T	0.47	.	3.6747	0.08287	0.2369:0.2099:0.5532:0.0	.	458	Q9NZ56	FMN2_HUMAN	T	458	ENSP00000318884:A458T	ENSP00000318884:A458T	A	+	1	0	FMN2	238323404	0.000000	0.05858	0.001000	0.08648	0.656000	0.38851	-0.020000	0.12525	0.531000	0.28639	0.563000	0.77884	GCC	G|0.999;A|0.001	0.001	strong		0.706	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
MRPL36	64979	hgsc.bcm.edu	37	5	1799001	1799001	+	Missense_Mutation	SNP	T	T	G	rs114776273	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:1799001T>G	ENST00000508987.1	-	2	185	c.49A>C	c.(49-51)Agt>Cgt	p.S17R	NDUFS6_ENST00000274137.5_5'Flank|MRPL36_ENST00000505818.1_Missense_Mutation_p.S17R|NDUFS6_ENST00000469176.1_5'Flank|MRPL36_ENST00000505059.2_Missense_Mutation_p.S17R|MRPL36_ENST00000382647.7_Missense_Mutation_p.S17R			Q9P0J6	RM36_HUMAN	mitochondrial ribosomal protein L36	17					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	structural constituent of ribosome (GO:0003735)			breast(1)|lung(2)	3				GBM - Glioblastoma multiforme(108;0.241)		GTGTGACGACTGAGATAGAGC	0.507													T|||	32	0.00638978	0.0008	0.0072	5008	,	,		20418	0.002		0.0229	False		,,,				2504	0.001				p.S17R		Atlas-SNP	.											.	MRPL36	5	.	0			c.A49C						PASS	.	T	ARG/SER	17,4389	25.3+/-52.1	0,17,2186	75.0	84.0	81.0		49	1.1	0.0	5	dbSNP_132	81	181,8419	79.8+/-142.4	0,181,4119	no	missense	MRPL36	NM_032479.3	110	0,198,6305	GG,GT,TT		2.1047,0.3858,1.5224	possibly-damaging	17/104	1799001	198,12808	2203	4300	6503	SO:0001583	missense	64979	exon2			GACGACTGAGATA	AB049654	CCDS3865.1	5p15.3	2012-09-13			ENSG00000171421	ENSG00000171421		"""Mitochondrial ribosomal proteins / large subunits"""	14490	protein-coding gene	gene with protein product	"""putative BRCA1-interacting protein"", ""39S ribosomal protein L36, mitochondrial"""	611842				11543634	Standard	NM_032479		Approved	BRIP1, RPMJ, L36mt, PRPL36, MRP-L36	uc003jcx.4	Q9P0J6	OTTHUMG00000090373	ENST00000508987.1:c.49A>C	5.37:g.1799001T>G	ENSP00000423399:p.Ser17Arg	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	281	129	0.459075	NM_032479	A4UCS0|B2R4Z2|Q3SWV6|Q9UKL7	Missense_Mutation	SNP	ENST00000508987.1	37	CCDS3865.1	27	0.012362637362637362	1	0.0020325203252032522	5	0.013812154696132596	2	0.0034965034965034965	19	0.025065963060686015	T	14.86	2.661939	0.47572	0.003858	0.021047	ENSG00000171421	ENST00000505818;ENST00000382647;ENST00000505059;ENST00000508987;ENST00000510999	.	.	.	3.62	1.06	0.20224	.	0.702565	0.12527	N	0.461179	T	0.10680	0.0261	L	0.32530	0.975	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.17107	-1.0380	9	0.66056	D	0.02	-3.5236	4.37	0.11242	0.0:0.1123:0.2015:0.6862	.	17	Q9P0J6	RM36_HUMAN	R	17	.	ENSP00000372093:S17R	S	-	1	0	MRPL36	1852001	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	0.011000	0.13264	-0.052000	0.13311	0.397000	0.26171	AGT	T|0.988;G|0.012	0.012	strong		0.507	MRPL36-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365908.2	NM_032479	
ZNF347	84671	hgsc.bcm.edu	37	19	53644417	53644417	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53644417C>T	ENST00000334197.7	-	5	1732	c.1664G>A	c.(1663-1665)aGc>aAc	p.S555N	ZNF347_ENST00000601469.2_Missense_Mutation_p.S556N|ZNF347_ENST00000452676.2_Missense_Mutation_p.S556N|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	555					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.S555N(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		GGTAGTTAGGCTTGAATACAC	0.413																																					p.S556N	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											ZNF347,NS,carcinoma,0,1	ZNF347	87	1	1	Substitution - Missense(1)	endometrium(1)	c.G1667A						scavenged	.						166.0	159.0	162.0					19																	53644417		2203	4300	6503	SO:0001583	missense	84671	exon5			GTTAGGCTTGAAT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"""Zinc fingers, C2H2-type"", ""-"""	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.1664G>A	19.37:g.53644417C>T	ENSP00000334146:p.Ser555Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	104	3	0.0288462	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	37	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	0.418	-0.909912	0.02434	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.15718	2.4;2.4	3.01	-6.02	0.02192	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05410	0.0143	N	0.05414	-0.055	0.09310	N	1	B;B	0.18013	0.008;0.025	B;B	0.19666	0.014;0.026	T	0.37009	-0.9724	9	0.02654	T	1	.	6.3395	0.21314	0.0:0.359:0.2214:0.4196	.	556;555	G5E9N4;Q96SE7	.;ZN347_HUMAN	N	555;556	ENSP00000334146:S555N;ENSP00000405218:S556N	ENSP00000334146:S555N	S	-	2	0	ZNF347	58336229	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-14.724000	0.00000	-1.917000	0.01074	-0.176000	0.13171	AGC	.	.	none		0.413	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584	
PAPOLB	56903	hgsc.bcm.edu	37	7	4900095	4900095	+	Silent	SNP	A	A	G	rs1553960	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:4900095A>G	ENST00000404991.1	-	1	1530	c.1344T>C	c.(1342-1344)aaT>aaC	p.N448N	RADIL_ENST00000399583.3_Intron|RADIL_ENST00000536091.1_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	209	0	0		WXS	Illumina HiSeq	Phase_I	240	238	0.991667	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	
ZGRF1	55345	hgsc.bcm.edu	37	4	113539969	113539969	+	Missense_Mutation	SNP	T	T	C	rs7696816	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:113539969T>C	ENST00000505019.1	-	6	1354	c.1229A>G	c.(1228-1230)aAt>aGt	p.N410S	C4orf21_ENST00000445203.2_Missense_Mutation_p.N379S|C4orf21_ENST00000309071.5_Missense_Mutation_p.N410S	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		410			N -> S (in dbSNP:rs7696816).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		ACTGCTTTCATTGAATGAAGG	0.333													T|||	2092	0.417732	0.3003	0.5086	5008	,	,		20068	0.4117		0.4284	False		,,,				2504	0.5072				p.N410S		Atlas-SNP	.											.	C4orf21	223	.	0			c.A1229G						PASS	.	T	SER/ASN	1433,2973	455.5+/-351.0	234,965,1004	89.0	89.0	89.0		1229	-0.2	0.0	4	dbSNP_116	89	3647,4953	521.4+/-379.9	755,2137,1408	yes	missense	C4orf21	NM_018392.4	46	989,3102,2412	CC,CT,TT		42.407,32.5238,39.0589	benign	410/2105	113539969	5080,7926	2203	4300	6503	SO:0001583	missense	55345	exon6			CTTTCATTGAATG																												ENST00000505019.1:c.1229A>G	4.37:g.113539969T>C	ENSP00000424737:p.Asn410Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		905	0.4143772893772894	153	0.31097560975609756	181	0.5	245	0.42832167832167833	326	0.43007915567282323	T	0.008	-1.932518	0.00488	0.325238	0.42407	ENSG00000138658	ENST00000505019;ENST00000309071;ENST00000445203	T;T;T	0.81163	-1.46;2.03;1.62	5.05	-0.147	0.13428	.	1.081160	0.07099	N	0.840098	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30592	-0.9973	9	0.02654	T	1	1.4592	1.4742	0.02422	0.1541:0.4062:0.2096:0.2301	rs7696816;rs52796218;rs56876657;rs7696816	410;410	Q86YA3;G5EA02	CD021_HUMAN;.	S	410;410;379	ENSP00000424737:N410S;ENSP00000309095:N410S;ENSP00000390505:N379S	ENSP00000309095:N410S	N	-	2	0	C4orf21	113759418	0.000000	0.05858	0.011000	0.14972	0.022000	0.10575	-1.654000	0.01984	0.149000	0.19098	-1.022000	0.02435	AAT	T|0.598;C|0.402	0.402	strong		0.333	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
C3orf30	152405	hgsc.bcm.edu	37	3	118865970	118865970	+	Missense_Mutation	SNP	G	G	A	rs4077930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:118865970G>A	ENST00000295622.1	+	1	974	c.934G>A	c.(934-936)Ggc>Agc	p.G312S	IGSF11_ENST00000425327.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000354673.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	312			G -> S (in dbSNP:rs4077930).							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)		CCAAGTGTACGGCCAAGCCAC	0.498													G|||	1064	0.21246	0.2579	0.1873	5008	,	,		12582	0.0794		0.17	False		,,,				2504	0.3497				p.G312S		Atlas-SNP	.											.	C3orf30	64	.	0			c.G934A						PASS	.	G	SER/GLY	1082,3324	392.1+/-328.4	130,822,1251	85.0	73.0	77.0		934	0.8	0.0	3	dbSNP_108	77	1388,7212	268.2+/-287.7	121,1146,3033	yes	missense	C3orf30	NM_152539.2	56	251,1968,4284	AA,AG,GG		16.1395,24.5574,18.9912	benign	312/537	118865970	2470,10536	2203	4300	6503	SO:0001583	missense	152405	exon1			GTGTACGGCCAAG	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.934G>A	3.37:g.118865970G>A	ENSP00000295622:p.Gly312Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	346|346	0.15842490842490842|0.15842490842490842	130|130	0.26422764227642276|0.26422764227642276	59|59	0.16298342541436464|0.16298342541436464	32|32	0.055944055944055944|0.055944055944055944	125|125	0.16490765171503957|0.16490765171503957	G|G	9.369|9.369	1.069912|1.069912	0.20147|0.20147	0.245574|0.245574	0.161395|0.161395	ENSG00000163424|ENSG00000163424	ENST00000295622;ENST00000470341|ENST00000460150;ENST00000473121;ENST00000492792	T|.	0.10860|.	2.83|.	2.72|2.72	0.781|0.781	0.18561|0.18561	.|.	2.285220|.	0.01726|.	N|.	0.028592|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	P|P	0.0|0.0	B;P|.	0.46656|.	0.079;0.882|.	B;B|.	0.39935|.	0.005;0.314|.	T|T	0.23119|0.23119	-1.0197|-1.0197	9|4	0.11182|.	T|.	0.66|.	-0.8248|-0.8248	2.9986|2.9986	0.06007|0.06007	0.1542:0.0:0.5771:0.2687|0.1542:0.0:0.5771:0.2687	rs4077930;rs52836987;rs59901526;rs4077930|rs4077930;rs52836987;rs59901526;rs4077930	312;312|.	E9PFE5;Q96M34|.	.;CC030_HUMAN|.	S|Q	312|275;104;46	ENSP00000295622:G312S|.	ENSP00000295622:G312S|.	G|R	+|+	1|2	0|0	C3orf30|C3orf30	120348660|120348660	0.010000|0.010000	0.17322|0.17322	0.001000|0.001000	0.08648|0.08648	0.047000|0.047000	0.14425|0.14425	1.464000|1.464000	0.35288|0.35288	0.201000|0.201000	0.20466|0.20466	0.467000|0.467000	0.42956|0.42956	GGC|CGG	G|0.818;A|0.182	0.182	strong		0.498	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
STAT2	6773	hgsc.bcm.edu	37	12	56740682	56740682	+	Missense_Mutation	SNP	C	C	G	rs2066807	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56740682C>G	ENST00000314128.4	-	20	1805	c.1782G>C	c.(1780-1782)atG>atC	p.M594I	STAT2_ENST00000557235.1_Missense_Mutation_p.M590I|STAT2_ENST00000556539.1_5'UTR			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	594	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		M -> I (in dbSNP:rs2066807). {ECO:0000269|Ref.3}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						AGGTGCCAGACATGGTCTTCT	0.597													G|||	163	0.0325479	0.0015	0.0562	5008	,	,		17682	0.0357		0.0666	False		,,,				2504	0.0194				p.M594I		Atlas-SNP	.											.	STAT2	70	.	0			c.G1782C						PASS	.	G	ILE/MET,ILE/MET	44,4362	822.2+/-416.4	1,42,2160	101.0	80.0	87.0		1782,1770	-3.2	0.0	12	dbSNP_94	87	539,8061	795.2+/-407.5	22,495,3783	yes	missense,missense	STAT2	NM_005419.3,NM_198332.1	10,10	23,537,5943	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	6.2674,0.9986,4.4825	benign,benign	594/852,590/848	56740682	583,12423	2203	4300	6503	SO:0001583	missense	6773	exon20			GCCAGACATGGTC	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1782G>C	12.37:g.56740682C>G	ENSP00000315768:p.Met594Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	174	85	0.488506	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	102	0.046703296703296704	3	0.006097560975609756	22	0.06077348066298342	23	0.04020979020979021	54	0.0712401055408971	G	1.160	-0.643974	0.03531	0.009986	0.062674	ENSG00000170581	ENST00000314128;ENST00000557235	D;D	0.96365	-3.99;-3.99	5.76	-3.19	0.05171	SH2 motif (4);	1.258400	0.05235	N	0.511045	T	0.47060	0.1425	N	0.01352	-0.895	0.25534	N	0.98725	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.63603	-0.6600	10	0.34782	T	0.22	1.5197	18.0076	0.89214	0.0:0.6583:0.1875:0.1542	rs2066807;rs52819760;rs2066807	590;594	G3V2M6;P52630	.;STAT2_HUMAN	I	594;590	ENSP00000315768:M594I;ENSP00000450751:M590I	ENSP00000315768:M594I	M	-	3	0	STAT2	55026949	0.000000	0.05858	0.024000	0.17045	0.096000	0.18686	-1.914000	0.01579	-0.687000	0.05162	-1.068000	0.02270	ATG	C|0.958;G|0.042	0.042	strong		0.597	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	
ANO10	55129	hgsc.bcm.edu	37	3	43602803	43602803	+	Missense_Mutation	SNP	C	C	T	rs3772165	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:43602803C>T	ENST00000292246.3	-	9	1555	c.1385G>A	c.(1384-1386)cGg>cAg	p.R462Q	ANO10_ENST00000451430.2_Missense_Mutation_p.R351Q|ANO10_ENST00000350459.4_Missense_Mutation_p.R272Q|ANO10_ENST00000414522.2_Missense_Mutation_p.R462Q|ANO10_ENST00000396091.3_Missense_Mutation_p.R396Q	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	462			R -> Q (in dbSNP:rs3772165). {ECO:0000269|PubMed:14702039}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						CCTCTTCACCCGCACACCATG	0.423													C|||	3321	0.663139	0.4463	0.7334	5008	,	,		16590	0.8849		0.5785	False		,,,				2504	0.7648				p.R462Q		Atlas-SNP	.											.	ANO10	70	.	0			c.G1385A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	2193,2213	586.4+/-386.5	547,1099,557	128.0	120.0	123.0		1385,1187,1052,815,1385	-5.4	0.0	3	dbSNP_107	123	5050,3550	630.8+/-398.4	1511,2028,761	yes	missense,missense,missense,missense,missense	ANO10	NM_001204831.1,NM_001204832.1,NM_001204833.1,NM_001204834.1,NM_018075.3	43,43,43,43,43	2058,3127,1318	TT,TC,CC		41.2791,49.773,44.3103	benign,benign,benign,benign,benign	462/628,396/595,351/550,272/471,462/661	43602803	7243,5763	2203	4300	6503	SO:0001583	missense	55129	exon9			TTCACCCGCACAC	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25519	protein-coding gene	gene with protein product		613726	"""transmembrane protein 16K"""	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.1385G>A	3.37:g.43602803C>T	ENSP00000292246:p.Arg462Gln	Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_018075	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Missense_Mutation	SNP	ENST00000292246.3	37	CCDS2710.2	1428	0.6538461538461539	208	0.42276422764227645	257	0.7099447513812155	515	0.9003496503496503	448	0.5910290237467019	C	13.89	2.371895	0.42003	0.49773	0.587209	ENSG00000160746	ENST00000292246;ENST00000350459;ENST00000396091;ENST00000414522;ENST00000451430	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	5.42	-5.43	0.02632	.	0.506358	0.22536	N	0.058784	T	0.00012	0.0000	L	0.43152	1.355	0.48040	P	4.290000000000127E-4	B;B;P;B;B	0.38420	0.007;0.003;0.63;0.007;0.001	B;B;B;B;B	0.26864	0.009;0.007;0.074;0.009;0.003	T	0.30090	-0.9990	9	0.27082	T	0.32	.	16.2443	0.82434	0.0:0.5744:0.0:0.4255	rs3772165;rs52793486;rs3772165	351;462;272;396;462	Q9NW15-4;C9JHS1;Q9NW15-2;Q9NW15-3;Q9NW15	.;.;.;.;ANO10_HUMAN	Q	462;272;396;462;351	ENSP00000292246:R462Q;ENSP00000327767:R272Q;ENSP00000379398:R396Q;ENSP00000396990:R462Q;ENSP00000394119:R351Q	ENSP00000292246:R462Q	R	-	2	0	ANO10	43577807	0.011000	0.17503	0.017000	0.16124	0.982000	0.71751	-0.139000	0.10358	-0.909000	0.03852	-0.484000	0.04775	CGG	C|0.413;T|0.587	0.587	strong		0.423	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075	
BNIPL	149428	hgsc.bcm.edu	37	1	151015868	151015868	+	Missense_Mutation	SNP	G	G	A	rs12068365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:151015868G>A	ENST00000368931.3	+	6	833	c.677G>A	c.(676-678)aGc>aAc	p.S226N	BNIPL_ENST00000295294.7_Missense_Mutation_p.S144N	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	226	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		S -> N (in dbSNP:rs12068365).		apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CTACCCAGAAGCAGCATCCCC	0.463													G|||	292	0.0583067	0.146	0.036	5008	,	,		22151	0.0		0.0656	False		,,,				2504	0.0082				p.S226N		Atlas-SNP	.											.	BNIPL	45	.	0			c.G677A						PASS	.	G	ASN/SER,ASN/SER	690,3716	290.4+/-280.9	59,572,1572	266.0	230.0	242.0		431,677	4.4	1.0	1	dbSNP_120	242	709,7891	174.5+/-224.7	29,651,3620	yes	missense,missense	BNIPL	NM_001159642.1,NM_138278.3	46,46	88,1223,5192	AA,AG,GG		8.2442,15.6605,10.7566	benign,benign	144/276,226/358	151015868	1399,11607	2203	4300	6503	SO:0001583	missense	149428	exon6			CCAGAAGCAGCAT	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.677G>A	1.37:g.151015868G>A	ENSP00000357927:p.Ser226Asn	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	354	182	0.514124	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	37	CCDS978.2	140	0.0641025641025641	72	0.14634146341463414	13	0.03591160220994475	0	0.0	55	0.07255936675461741	G	16.96	3.267359	0.59540	0.156605	0.082442	ENSG00000163141	ENST00000368931;ENST00000361277;ENST00000295294	T;T;T	0.25749	1.78;1.78;1.78	5.3	4.36	0.52297	Cellular retinaldehyde-binding/triple function, C-terminal (3);	0.189199	0.56097	D	0.000028	T	0.06188	0.0160	N	0.16166	0.38	0.36735	P	0.11808600000000002	P	0.40578	0.722	B	0.41466	0.358	T	0.21930	-1.0231	9	0.27082	T	0.32	.	7.1673	0.25698	0.0912:0.1752:0.7336:0.0	rs12068365;rs52815988;rs59638468;rs12068365	226	Q7Z465	BNIPL_HUMAN	N	226;224;144	ENSP00000357927:S226N;ENSP00000355333:S224N;ENSP00000295294:S144N	ENSP00000295294:S144N	S	+	2	0	BNIPL	149282492	1.000000	0.71417	0.999000	0.59377	0.753000	0.42808	3.521000	0.53472	1.160000	0.42584	0.462000	0.41574	AGC	G|0.904;A|0.096	0.096	strong		0.463	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279	
MYH9	4627	hgsc.bcm.edu	37	22	36684980	36684980	+	Silent	SNP	G	G	A	rs11549907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36684980G>A	ENST00000216181.5	-	33	4793	c.4563C>T	c.(4561-4563)caC>caT	p.H1521H	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1521					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TCTCCAGCTCGTGGACCTGAG	0.627			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				G|||	203	0.0405351	0.062	0.1383	5008	,	,		17692	0.0		0.0199	False		,,,				2504	0.0051				p.H1521H		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.C4563T						PASS	.	G		267,4139	150.3+/-184.3	8,251,1944	59.0	57.0	58.0		4563	-10.5	0.3	22	dbSNP_120	58	109,8491	59.5+/-121.1	1,107,4192	no	coding-synonymous	MYH9	NM_002473.4		9,358,6136	AA,AG,GG		1.2674,6.0599,2.891		1521/1961	36684980	376,12630	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon33	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CAGCTCGTGGACC		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.4563C>T	22.37:g.36684980G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			G|0.970;A|0.030	0.030	strong		0.627	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
UPK3B	80761	hgsc.bcm.edu	37	7	76140315	76140315	+	Missense_Mutation	SNP	G	G	A	rs144609046	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:76140315G>A	ENST00000257632.5	+	1	474	c.346G>A	c.(346-348)Gat>Aat	p.D116N	UPK3B_ENST00000419923.2_Missense_Mutation_p.D116N|UPK3B_ENST00000443097.2_Missense_Mutation_p.D61N|UPK3B_ENST00000334348.3_Missense_Mutation_p.D61N|UPK3B_ENST00000448265.3_Missense_Mutation_p.D116N|UPK3B_ENST00000394849.1_Missense_Mutation_p.D61N			Q9BT76	UPK3B_HUMAN	uroplakin 3B	116					negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				CTGTGTCTTCGATGGGCTTGC	0.632													.|||	3	0.000599042	0.0	0.0	5008	,	,		18847	0.0		0.001	False		,,,				2504	0.002				p.D116N		Atlas-SNP	.											.	UPK3B	15	.	0			c.G346A						PASS	.	G	ASN/ASP,ASN/ASP	0,4310		0,0,2155	9.0	8.0	9.0		346,181	3.0	0.2	7	dbSNP_134	9	10,8410		0,10,4200	no	missense,missense	UPK3B	NM_030570.2,NM_182684.1	23,23	0,10,6355	AA,AG,GG		0.1188,0.0,0.0786	possibly-damaging,possibly-damaging	116/321,61/277	76140315	10,12720	2155	4210	6365	SO:0001583	missense	80761	exon1			GTCTTCGATGGGC	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"""uroplakin IIIb"""	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.346G>A	7.37:g.76140315G>A	ENSP00000257632:p.Asp116Asn	Somatic	649	1	0.00154083		WXS	Illumina HiSeq	Phase_I	535	226	0.42243	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	37	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	12.85	2.061280	0.36373	0.0	0.001188	ENSG00000243566	ENST00000334348;ENST00000419923;ENST00000448265;ENST00000443097;ENST00000257632;ENST00000394849	T;T;T;T;T;T	0.58358	0.34;1.28;1.28;0.34;1.28;1.29	4.93	2.99	0.34606	.	0.412335	0.23849	N	0.043977	T	0.48554	0.1506	N	0.17474	0.49	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.991	D;P;P	0.63381	0.914;0.9;0.539	T	0.22941	-1.0202	10	0.46703	T	0.11	-8.2617	7.7594	0.28944	0.0919:0.0:0.7447:0.1633	.	61;116;61	Q9BT76-2;Q9BT76;A6NHH5	.;UPK3B_HUMAN;.	N	61;116;116;61;116;61	ENSP00000334938:D61N;ENSP00000441602:D116N;ENSP00000441284:D116N;ENSP00000444585:D61N;ENSP00000257632:D116N;ENSP00000378319:D61N	ENSP00000257632:D116N	D	+	1	0	UPK3B	75978251	0.037000	0.19845	0.162000	0.22713	0.010000	0.07245	0.841000	0.27613	2.281000	0.76405	0.400000	0.26472	GAT	G|0.999;A|0.001	0.001	strong		0.632	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570	
PTPRH	5794	hgsc.bcm.edu	37	19	55697279	55697279	+	Missense_Mutation	SNP	C	C	T	rs61734259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55697279C>T	ENST00000376350.3	-	17	2874	c.2852G>A	c.(2851-2853)gGt>gAt	p.G951D	PTPRH_ENST00000263434.5_Missense_Mutation_p.G773D	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	951	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.			G -> D (in Ref. 4; AAI11716). {ECO:0000305}.	apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CACTTCCTCACCTACCAGGGT	0.627													C|||	294	0.0587061	0.0908	0.0706	5008	,	,		18169	0.0		0.0954	False		,,,				2504	0.0297				p.G951D		Atlas-SNP	.											.	PTPRH	139	.	0			c.G2852A						PASS	.	C	ASP/GLY,ASP/GLY	447,3959	214.5+/-233.7	23,401,1779	111.0	95.0	100.0		2318,2852	0.2	0.0	19	dbSNP_129	100	902,7698	201.7+/-245.1	54,794,3452	yes	missense,missense	PTPRH	NM_001161440.1,NM_002842.3	94,94	77,1195,5231	TT,TC,CC		10.4884,10.1453,10.3721	benign,benign	773/938,951/1116	55697279	1349,11657	2203	4300	6503	SO:0001583	missense	5794	exon17			TCCTCACCTACCA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2852G>A	19.37:g.55697279C>T	ENSP00000365528:p.Gly951Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	145	0.06639194139194139	45	0.09146341463414634	33	0.09116022099447514	0	0.0	67	0.08839050131926121	C	1.107	-0.659372	0.03454	0.101453	0.104884	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.10382	2.88;2.88	5.21	0.241	0.15494	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.602793	0.13898	N	0.355126	T	0.00178	0.0005	N	0.16201	0.385	0.09310	N	1	B;B	0.18461	0.015;0.028	B;B	0.22386	0.027;0.039	T	0.46555	-0.9183	10	0.19590	T	0.45	.	6.2007	0.20575	0.0:0.397:0.4261:0.1769	.	773;951	C9JCH2;Q9HD43	.;PTPRH_HUMAN	D	951;773	ENSP00000365528:G951D;ENSP00000263434:G773D	ENSP00000263434:G773D	G	-	2	0	PTPRH	60389091	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-0.107000	0.10873	0.288000	0.22398	0.650000	0.86243	GGT	C|0.912;T|0.088	0.088	strong		0.627	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
CCDC13	152206	hgsc.bcm.edu	37	3	42781276	42781276	+	Silent	SNP	G	G	T	rs62246603	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42781276G>T	ENST00000310232.6	-	9	1097	c.1014C>A	c.(1012-1014)ctC>ctA	p.L338L	CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	338										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GCTCTCTCTGGAGGACATCCC	0.522													G|||	997	0.199081	0.1362	0.1686	5008	,	,		19669	0.1597		0.2674	False		,,,				2504	0.2761				p.L338L		Atlas-SNP	.											.	CCDC13	71	.	0			c.C1014A						PASS	.	G		692,3714	293.0+/-282.3	53,586,1564	147.0	127.0	134.0		1014	-1.7	0.8	3	dbSNP_129	134	2339,6261	392.8+/-344.1	302,1735,2263	no	coding-synonymous	CCDC13	NM_144719.3		355,2321,3827	TT,TG,GG		27.1977,15.7059,23.3046		338/716	42781276	3031,9975	2203	4300	6503	SO:0001819	synonymous_variant	152206	exon9			TCTCTGGAGGACA	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1014C>A	3.37:g.42781276G>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	177	77	0.435028	NM_144719		Silent	SNP	ENST00000310232.6	37	CCDS2705.1																																																																																			G|0.778;T|0.222	0.222	strong		0.522	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
OR51B5	282763	hgsc.bcm.edu	37	11	5364522	5364522	+	Missense_Mutation	SNP	G	G	T	rs57273781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364522G>T	ENST00000300773.2	-	1	287	c.233C>A	c.(232-234)aCg>aAg	p.T78K	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	78			T -> K (in dbSNP:rs57273781).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCCAGCACCGTGGGCATTGT	0.542													G|||	487	0.0972444	0.3048	0.0476	5008	,	,		18344	0.0		0.0457	False		,,,				2504	0.0051				p.T78K		Atlas-SNP	.											OR51B5,NS,malignant_melanoma,+1,2	OR51B5	60	2	0			c.C233A						PASS	.	G	LYS/THR	1219,3183	416.7+/-337.7	164,891,1146	44.0	46.0	45.0		233	3.9	0.3	11	dbSNP_129	45	445,8149	132.5+/-190.1	13,419,3865	yes	missense	OR51B5	NM_001005567.2	78	177,1310,5011	TT,TG,GG		5.178,27.692,12.8039	probably-damaging	78/313	5364522	1664,11332	2201	4297	6498	SO:0001583	missense	282763	exon5			AGCACCGTGGGCA	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.233C>A	11.37:g.5364522G>T	ENSP00000300773:p.Thr78Lys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	188	0.08608058608058608	135	0.27439024390243905	20	0.055248618784530384	0	0.0	33	0.04353562005277045	G	17.13	3.311894	0.60414	0.27692	0.05178	ENSG00000242180	ENST00000300773	T	0.01538	4.79	4.76	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	D	0.000713	T	0.00012	0.0000	L	0.27944	0.81	0.58432	P	1.0000000000287557E-6	D	0.67145	0.996	P	0.57846	0.828	T	0.61720	-0.7005	9	0.52906	T	0.07	.	11.866	0.52493	0.0855:0.0:0.9145:0.0	rs57273781;rs61738468	78	Q9H339	O51B5_HUMAN	K	78	ENSP00000300773:T78K	ENSP00000300773:T78K	T	-	2	0	OR51B5	5321098	0.000000	0.05858	0.313000	0.25210	0.802000	0.45316	0.385000	0.20685	1.255000	0.44051	0.650000	0.86243	ACG	G|0.889;T|0.111	0.111	strong		0.542	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
DNMBP	23268	hgsc.bcm.edu	37	10	101657880	101657880	+	Silent	SNP	G	G	A	rs7919323	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:101657880G>A	ENST00000324109.4	-	9	2974	c.2883C>T	c.(2881-2883)aaC>aaT	p.N961N	DNMBP_ENST00000543621.1_Silent_p.N207N|DNMBP_ENST00000540316.1_De_novo_Start_OutOfFrame|DNMBP_ENST00000342239.3_Silent_p.N961N	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	961	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TAATGTTAACGTTGATTTCCT	0.433													G|||	1375	0.274561	0.1589	0.3256	5008	,	,		17198	0.2183		0.3946	False		,,,				2504	0.3292				p.N961N		Atlas-SNP	.											.	DNMBP	173	.	0			c.C2883T						PASS	.			890,3516	345.4+/-308.5	84,722,1397	130.0	114.0	119.0		2883	-4.9	0.9	10	dbSNP_116	119	3322,5278	495.3+/-374.0	654,2014,1632	no	coding-synonymous	DNMBP	NM_015221.2		738,2736,3029	AA,AG,GG		38.6279,20.1997,32.3851		961/1578	101657880	4212,8794	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon9			GTTAACGTTGATT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.2883C>T	10.37:g.101657880G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	146	142	0.972603	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			G|0.689;A|0.311	0.311	strong		0.433	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
MYH13	8735	hgsc.bcm.edu	37	17	10261086	10261086	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10261086G>A	ENST00000418404.3	-	7	867	c.704C>T	c.(703-705)gCc>gTc	p.A235V	MYH13_ENST00000252172.4_Missense_Mutation_p.A235V			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	235	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CACAGTCTTGGCATTTCCAAA	0.453																																					p.A235V		Atlas-SNP	.											.	MYH13	533	.	0			c.C704T						PASS	.						99.0	107.0	105.0					17																	10261086		2180	4296	6476	SO:0001583	missense	8735	exon8			GTCTTGGCATTTC	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.704C>T	17.37:g.10261086G>A	ENSP00000404570:p.Ala235Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.001634	0.93227	.	.	ENSG00000006788	ENST00000252172	D	0.83914	-1.78	3.94	3.94	0.45596	Myosin head, motor domain (3);	.	.	.	.	D	0.94810	0.8324	H	0.99249	4.485	0.53005	D	0.999965	D	0.67145	0.996	D	0.69142	0.962	D	0.97360	0.9969	9	0.87932	D	0	.	16.5222	0.84320	0.0:0.0:1.0:0.0	.	235	Q9UKX3	MYH13_HUMAN	V	235	ENSP00000252172:A235V	ENSP00000252172:A235V	A	-	2	0	MYH13	10201811	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.450000	0.97607	2.200000	0.70718	0.467000	0.42956	GCC	.	.	none		0.453	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	
GRHL1	29841	hgsc.bcm.edu	37	2	10101468	10101468	+	Missense_Mutation	SNP	A	A	G	rs16867256	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:10101468A>G	ENST00000324907.9	+	4	708	c.572A>G	c.(571-573)aAt>aGt	p.N191S	GRHL1_ENST00000405379.2_Missense_Mutation_p.N191S|GRHL1_ENST00000324883.5_Missense_Mutation_p.I28V	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	191			N -> S (in dbSNP:rs16867256). {ECO:0000269|PubMed:15489334}.		cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		CGGAATCTCAATACTGACCAG	0.542													G|||	883	0.176318	0.438	0.1052	5008	,	,		18383	0.0119		0.1461	False		,,,				2504	0.0736				p.N191S		Atlas-SNP	.											.	GRHL1	95	.	0			c.A572G						PASS	.	G	SER/ASN	1597,2809	664.3+/-401.3	279,1039,885	121.0	118.0	119.0		572	-8.9	0.0	2	dbSNP_123	119	1160,7440	765.5+/-407.6	74,1012,3214	yes	missense	GRHL1	NM_198182.2	46	353,2051,4099	GG,GA,AA		13.4884,36.246,21.1979	benign	191/619	10101468	2757,10249	2203	4300	6503	SO:0001583	missense	29841	exon4			ATCTCAATACTGA	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"""transcription factor CP2-like 2"""	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.572A>G	2.37:g.10101468A>G	ENSP00000324693:p.Asn191Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	37	CCDS33144.2	339|339	0.15521978021978022|0.15521978021978022	195|195	0.39634146341463417|0.39634146341463417	36|36	0.09944751381215469|0.09944751381215469	4|4	0.006993006993006993|0.006993006993006993	104|104	0.13720316622691292|0.13720316622691292	G|G	0.388|0.388	-0.924831|-0.924831	0.02377|0.02377	0.36246|0.36246	0.134884|0.134884	ENSG00000134317|ENSG00000134317	ENST00000324883|ENST00000405379;ENST00000324907	T|T;T	0.16743|0.11169	2.32|2.8;2.8	5.5|5.5	-8.89|-8.89	0.00785|0.00785	.|.	.|0.571760	.|0.20829	.|N	.|0.084921	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.40887|0.40887	-0.9539|-0.9539	8|9	0.07482|0.15952	T|T	0.82|0.53	.|.	10.4728|10.4728	0.44646|0.44646	0.3294:0.2381:0.4325:0.0|0.3294:0.2381:0.4325:0.0	rs16867256;rs52810082;rs16867256|rs16867256;rs52810082;rs16867256	28|191	Q9NZI5-2|Q9NZI5	.|GRHL1_HUMAN	V|S	28|191	ENSP00000324494:I28V|ENSP00000384209:N191S;ENSP00000324693:N191S	ENSP00000324494:I28V|ENSP00000324693:N191S	I|N	+|+	1|2	0|0	GRHL1|GRHL1	10018919|10018919	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.440000|0.440000	0.31957|0.31957	-0.411000|-0.411000	0.07142|0.07142	-2.729000|-2.729000	0.00385|0.00385	-1.945000|-1.945000	0.00491|0.00491	ATA|AAT	A|0.801;G|0.199	0.199	strong		0.542	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552	
DNAH17	8632	hgsc.bcm.edu	37	17	76528790	76528790	+	Missense_Mutation	SNP	A	A	G	rs11651537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:76528790A>G	ENST00000585328.1	-	20	3003	c.2879T>C	c.(2878-2880)aTa>aCa	p.I960T	DNAH17_ENST00000389840.5_Missense_Mutation_p.I963T|RN7SL454P_ENST00000492744.2_RNA	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	71	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	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	
FMN2	56776	hgsc.bcm.edu	37	1	240370629	240370629	+	Silent	SNP	C	C	G	rs10926166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	97	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	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	
TPSD1	23430	hgsc.bcm.edu	37	16	1306642	1306642	+	Missense_Mutation	SNP	C	C	T	rs61739908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306642C>T	ENST00000211076.3	+	2	356	c.208C>T	c.(208-210)Ctc>Ttc	p.L70F	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.L63F	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	70	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)				CGGGGGCTCCCTCATCCACCC	0.687													-|||	390	0.0778754	0.0212	0.1383	5008	,	,		17204	0.0		0.1918	False		,,,				2504	0.0746				p.L70F		Atlas-SNP	.											.	TPSD1	47	.	0			c.C208T						PASS	.	C	PHE/LEU	184,4214		3,178,2018	54.0	65.0	61.0		208	2.0	1.0	16	dbSNP_129	61	1661,6939		148,1365,2787	no	missense	TPSD1	NM_012217.2	22	151,1543,4805	TT,TC,CC		19.314,4.1837,14.1945	probably-damaging	70/243	1306642	1845,11153	2199	4300	6499	SO:0001583	missense	23430	exon2			GGCTCCCTCATCC	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.208C>T	16.37:g.1306642C>T	ENSP00000211076:p.Leu70Phe	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	197	87	0.441624	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	197	0.0902014652014652	8	0.016260162601626018	56	0.15469613259668508	0	0.0	133	0.17546174142480211	-	11.87	1.766589	0.31228	0.041837	0.19314	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.90732	-2.72;-2.72	3.0	1.96	0.26148	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.43110	D	0.000606	T	0.02267	0.0070	M	0.90369	3.11	0.27973	P	0.9363324	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.52253	-0.8600	9	0.87932	D	0	.	5.3213	0.15883	0.235:0.5352:0.2298:0.0	rs61739908	63;70	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	F	63;70	ENSP00000380668:L63F;ENSP00000211076:L70F	ENSP00000211076:L70F	L	+	1	0	TPSD1	1246643	0.974000	0.33945	0.995000	0.50966	0.156000	0.22039	3.403000	0.52615	0.499000	0.27970	0.185000	0.17295	CTC	C|0.872;T|0.128	0.128	strong		0.687	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
ZNF669	79862	hgsc.bcm.edu	37	1	247267274	247267274	+	Missense_Mutation	SNP	C	C	A	rs4925692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:247267274C>A	ENST00000343381.6	-	1	400	c.228G>T	c.(226-228)gaG>gaT	p.E76D	ZNF669_ENST00000448299.2_Intron|ZNF669_ENST00000366500.1_Intron|ZNF669_ENST00000358785.4_Missense_Mutation_p.E76D|ZNF669_ENST00000366501.1_Intron	NM_024804.2	NP_079080.2	Q96BR6	ZN669_HUMAN	zinc finger protein 669	76			E -> D (in dbSNP:rs4925692). {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)|endometrium(3)|kidney(4)|large_intestine(2)|lung(6)	17	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CCCGACAGGGCTCCGGCCGGC	0.711													C|||	1260	0.251597	0.1172	0.2925	5008	,	,		12776	0.123		0.332	False		,,,				2504	0.454				p.E76D		Atlas-SNP	.											.	ZNF669	46	.	0			c.G228T						PASS	.	C	,ASP/GLU	605,3555		61,483,1536	7.0	10.0	9.0		,228	0.3	0.1	1	dbSNP_111	9	2506,5700		406,1694,2003	yes	intron,missense	ZNF669	NM_001142572.1,NM_024804.2	,45	467,2177,3539	AA,AC,CC		30.5386,14.5433,25.1577	,benign	,76/465	247267274	3111,9255	2080	4103	6183	SO:0001583	missense	79862	exon1			ACAGGGCTCCGGC		CCDS31088.1, CCDS44345.1	1q44	2013-01-08			ENSG00000188295	ENSG00000188295		"""Zinc fingers, C2H2-type"", ""-"""	25736	protein-coding gene	gene with protein product						12477932	Standard	NM_024804		Approved	FLJ12606	uc001ice.2	Q96BR6	OTTHUMG00000040869	ENST00000343381.6:c.228G>T	1.37:g.247267274C>A	ENSP00000342818:p.Glu76Asp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_024804	B3KP94|Q5VT39|Q9H9Q6	Missense_Mutation	SNP	ENST00000343381.6	37	CCDS31088.1	484	0.2216117216117216	58	0.11788617886178862	109	0.3011049723756906	69	0.12062937062937062	248	0.32717678100263853	C	15.19	2.758708	0.49468	0.145433	0.305386	ENSG00000188295	ENST00000358785;ENST00000343381;ENST00000476158	T;T;T	0.05925	4.79;3.37;4.75	0.342	0.342	0.15996	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.47511	P	5.560000000000009E-4	P	0.46578	0.88	P	0.50270	0.636	T	0.44174	-0.9345	8	0.17832	T	0.49	.	2.7626	0.05311	0.0:0.5869:0.0:0.4131	rs4925692;rs17855457;rs4925692	76	Q96BR6	ZN669_HUMAN	D	76	ENSP00000351636:E76D;ENSP00000342818:E76D;ENSP00000429550:E76D	ENSP00000342818:E76D	E	-	3	2	ZNF669	245333897	0.005000	0.15991	0.066000	0.19879	0.068000	0.16541	-1.229000	0.02945	0.392000	0.25172	0.397000	0.26171	GAG	C|0.780;A|0.220	0.220	strong		0.711	ZNF669-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000098394.4	NM_024804	
CCSER1	401145	hgsc.bcm.edu	37	4	91230579	91230579	+	Missense_Mutation	SNP	G	G	A	rs12647859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:91230579G>A	ENST00000509176.1	+	2	1432	c.1144G>A	c.(1144-1146)Ggt>Agt	p.G382S	CCSER1_ENST00000432775.2_Missense_Mutation_p.G382S|CCSER1_ENST00000333691.8_Missense_Mutation_p.G382S	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	382			G -> S (in dbSNP:rs12647859).														GTTACAAAATGGTGAAACAAT	0.398													G|||	875	0.17472	0.2405	0.0576	5008	,	,		19313	0.3026		0.1054	False		,,,				2504	0.1084				p.G382S		Atlas-SNP	.											.	.	.	.	0			c.G1144A						PASS	.	G	SER/GLY,SER/GLY	754,2938		71,612,1163	118.0	113.0	114.0		1144,1144	4.1	0.9	4	dbSNP_120	114	788,7398		41,706,3346	yes	missense,missense	FAM190A	NM_001145065.1,NM_207491.2	56,56	112,1318,4509	AA,AG,GG		9.6262,20.4225,12.982	possibly-damaging,possibly-damaging	382/901,382/678	91230579	1542,10336	1846	4093	5939	SO:0001583	missense	401145	exon2			CAAAATGGTGAAA		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.1144G>A	4.37:g.91230579G>A	ENSP00000425040:p.Gly382Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	383	0.17536630036630035	115	0.23373983739837398	19	0.052486187845303865	167	0.291958041958042	82	0.10817941952506596	G	7.428	0.638111	0.14386	0.204225	0.096262	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.47177	1.37;0.85;1.37	4.96	4.12	0.48240	.	0.190995	0.42548	D	0.000699	T	0.00012	0.0000	L	0.36672	1.1	0.39962	P	0.025329000000000046	B;B;B	0.26081	0.141;0.068;0.01	B;B;B	0.26202	0.067;0.019;0.035	T	0.28202	-1.0051	9	0.19147	T	0.46	-14.3215	11.3264	0.49450	0.1638:0.0:0.8362:0.0	rs12647859;rs52811484;rs57934044;rs12647859	382;382;382	Q9C0I3-2;Q9C0I3;E7EUW0	.;F190A_HUMAN;.	S	382	ENSP00000425040:G382S;ENSP00000389283:G382S;ENSP00000329482:G382S	ENSP00000329482:G382S	G	+	1	0	FAM190A	91449602	0.984000	0.35163	0.944000	0.38274	0.146000	0.21551	1.934000	0.40163	1.420000	0.47138	-0.198000	0.12761	GGT	G|0.822;A|0.178	0.178	strong		0.398	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
PPL	5493	hgsc.bcm.edu	37	16	4934777	4934777	+	Silent	SNP	C	C	T	rs61744951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4934777C>T	ENST00000345988.2	-	22	3968	c.3879G>A	c.(3877-3879)caG>caA	p.Q1293Q	PPL_ENST00000590782.2_Silent_p.Q1291Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1293					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						GGAGGATCTCCTGGACCACCT	0.507													C|||	286	0.0571086	0.1135	0.0317	5008	,	,		18685	0.006		0.0775	False		,,,				2504	0.0307				p.Q1293Q		Atlas-SNP	.											.	PPL	168	.	0			c.G3879A						PASS	.	C		499,3895	230.4+/-244.6	17,465,1715	170.0	169.0	169.0		3879	2.2	1.0	16	dbSNP_129	169	657,7943	166.1+/-218.1	29,599,3672	no	coding-synonymous	PPL	NM_002705.4		46,1064,5387	TT,TC,CC		7.6395,11.3564,8.8964		1293/1757	4934777	1156,11838	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			GATCTCCTGGACC	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.3879G>A	16.37:g.4934777C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	161	82	0.509317	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			C|0.918;T|0.082	0.082	strong		0.507	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
MUC2	4583	hgsc.bcm.edu	37	11	1075850	1075850	+	Silent	SNP	G	G	A	rs11825969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	74	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	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	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149008467	149008467	+	Missense_Mutation	SNP	C	C	A	rs3733662	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149008467C>A	ENST00000333677.6	+	12	1919	c.1756C>A	c.(1756-1758)Ccc>Acc	p.P586T		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	586			P -> T (in dbSNP:rs3733662).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GAACAAAGACCCCCGATGTCT	0.602													C|||	803	0.160343	0.0189	0.1412	5008	,	,		17591	0.3333		0.1501	False		,,,				2504	0.1973				p.P586T		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.C1756A						PASS	.	C	THR/PRO	154,3812		0,154,1829	49.0	54.0	52.0		1756	2.9	0.0	5	dbSNP_107	52	1277,7041		87,1103,2969	yes	missense	ARHGEF37	NM_001001669.2	38	87,1257,4798	AA,AC,CC		15.3522,3.883,11.6493	benign	586/676	149008467	1431,10853	1983	4159	6142	SO:0001583	missense	389337	exon12			AAAGACCCCCGAT	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1756C>A	5.37:g.149008467C>A	ENSP00000328083:p.Pro586Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	364	0.16666666666666666	9	0.018292682926829267	59	0.16298342541436464	179	0.3129370629370629	117	0.15435356200527706	C	5.285	0.237941	0.10023	0.03883	0.153522	ENSG00000183111	ENST00000333677	T	0.55052	0.54	5.4	2.86	0.33363	.	0.980252	0.08377	N	0.955147	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.34551	-0.9824	9	0.22706	T	0.39	-0.6438	3.7967	0.08743	0.2349:0.1019:0.0:0.6632	rs3733662;rs58657387;rs3733662	586	A1IGU5	ARH37_HUMAN	T	586	ENSP00000328083:P586T	ENSP00000328083:P586T	P	+	1	0	ARHGEF37	148988660	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.583000	0.23849	0.267000	0.21916	-0.339000	0.08088	CCC	C|0.839;A|0.161	0.161	strong		0.602	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
CILP2	148113	hgsc.bcm.edu	37	19	19654117	19654117	+	Silent	SNP	G	G	C	rs7252453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	153	0	0		WXS	Illumina HiSeq	Phase_I	165	88	0.533333	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	
DDX60	55601	hgsc.bcm.edu	37	4	169146815	169146815	+	Missense_Mutation	SNP	C	C	T	rs146255632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:169146815C>T	ENST00000393743.3	-	34	4837	c.4546G>A	c.(4546-4548)Gat>Aat	p.D1516N		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1516					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TCAGGGAGATCATCAAGGAAC	0.353																																					p.D1516N		Atlas-SNP	.											.	DDX60	304	.	0			c.G4546A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	79.0	81.0	80.0		4546	5.0	0.5	4	dbSNP_134	80	14,8584	10.5+/-38.8	0,14,4285	yes	missense	DDX60	NM_017631.5	23	0,14,6488	TT,TC,CC		0.1628,0.0,0.1077	probably-damaging	1516/1713	169146815	14,12990	2203	4299	6502	SO:0001583	missense	55601	exon34			GGAGATCATCAAG	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.4546G>A	4.37:g.169146815C>T	ENSP00000377344:p.Asp1516Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.89|15.89	2.966660|2.966660	0.53507|0.53507	0.0|0.0	0.001628|0.001628	ENSG00000137628|ENSG00000137628	ENST00000393743|ENST00000511317	T|.	0.18810|.	2.19|.	5.82|5.82	4.97|4.97	0.65823|0.65823	.|.	0.190110|.	0.37012|.	N|.	0.002284|.	T|T	0.64136|0.64136	0.2571|0.2571	M|M	0.80982|0.80982	2.52|2.52	0.26026|0.26026	N|N	0.981803|0.981803	D|.	0.56287|.	0.975|.	P|.	0.50754|.	0.649|.	T|T	0.58847|0.58847	-0.7564|-0.7564	10|5	0.35671|.	T|.	0.21|.	.|.	14.3138|14.3138	0.66434|0.66434	0.0:0.9259:0.0:0.0741|0.0:0.9259:0.0:0.0741	.|.	1516|.	Q8IY21|.	DDX60_HUMAN|.	N|I	1516|8	ENSP00000377344:D1516N|.	ENSP00000377344:D1516N|.	D|M	-|-	1|3	0|0	DDX60|DDX60	169383390|169383390	0.995000|0.995000	0.38212|0.38212	0.540000|0.540000	0.28089|0.28089	0.111000|0.111000	0.19643|0.19643	2.338000|2.338000	0.43957|0.43957	2.755000|2.755000	0.94549|0.94549	0.563000|0.563000	0.77884|0.77884	GAT|ATG	C|0.999;T|0.001	0.001	strong		0.353	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
SYNE2	23224	hgsc.bcm.edu	37	14	64612845	64612845	+	Silent	SNP	C	C	T	rs11629287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64612845C>T	ENST00000344113.4	+	84	15755	c.15543C>T	c.(15541-15543)atC>atT	p.I5181I	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.I1815I|SYNE2_ENST00000358025.3_Silent_p.I5181I|SYNE2_ENST00000394768.2_Silent_p.I1566I|SYNE2_ENST00000554584.1_Silent_p.I5098I|SYNE2_ENST00000357395.3_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	206	2	0.00970874		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	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	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501609	90501609	+	Missense_Mutation	SNP	C	C	T	rs34791830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90501609C>T	ENST00000325643.5	+	4	2273	c.2207C>T	c.(2206-2208)gCa>gTa	p.A736V		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	736			A -> V (in dbSNP:rs34791830).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GACAAGGAGGCAGAAGGTGAC	0.547													.|||	388	0.077476	0.2322	0.036	5008	,	,		19140	0.0		0.0497	False		,,,				2504	0.0061				p.A736V		Atlas-SNP	.											.	.	.	.	0			c.C2207T						PASS	.	C	VAL/ALA	805,3601	316.3+/-294.6	62,681,1460	56.0	55.0	55.0		2207	0.1	0.0	9	dbSNP_126	55	376,8224	120.8+/-180.0	5,366,3929	yes	missense	C9orf79	NM_178828.4	64	67,1047,5389	TT,TC,CC		4.3721,18.2705,9.0804	probably-damaging	736/1446	90501609	1181,11825	2203	4300	6503	SO:0001583	missense	286234	exon4			AGGAGGCAGAAGG	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.2207C>T	9.37:g.90501609C>T	ENSP00000322640:p.Ala736Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	67	0.656863	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	167	0.07646520146520147	111	0.22560975609756098	16	0.04419889502762431	0	0.0	40	0.052770448548812667	c	10.99	1.508556	0.27036	0.182705	0.043721	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.06768	3.26	2.43	0.0982	0.14497	.	2.788200	0.01610	N	0.022504	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;P	0.50819	0.311;0.939	B;P	0.45406	0.159;0.479	T	0.29088	-1.0023	9	0.39692	T	0.17	.	4.7011	0.12827	0.0:0.6028:0.0:0.3972	rs34791830	736;388	Q6ZUB1;Q8NA33	CI079_HUMAN;.	V	736;388	ENSP00000322640:A736V	ENSP00000322640:A736V	A	+	2	0	C9orf79	89691429	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.604000	0.05667	0.022000	0.15160	0.557000	0.71058	GCA	C|0.916;T|0.084	0.084	strong		0.547	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
GSN	2934	hgsc.bcm.edu	37	9	124088908	124088908	+	Missense_Mutation	SNP	C	C	G	rs77681311	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:124088908C>G	ENST00000373818.4	+	12	1757	c.1688C>G	c.(1687-1689)aCc>aGc	p.T563S	GSN_ENST00000545652.1_Missense_Mutation_p.T520S|GSN_ENST00000373823.3_Missense_Mutation_p.T512S|GSN_ENST00000373806.1_5'UTR|GSN_ENST00000341272.2_Missense_Mutation_p.T512S|GSN_ENST00000412819.1_Missense_Mutation_p.T512S|GSN_ENST00000394353.2_Missense_Mutation_p.T523S|GSN_ENST00000436847.1_Missense_Mutation_p.T523S|GSN_ENST00000373807.1_Missense_Mutation_p.T294S|GSN_ENST00000373808.2_Missense_Mutation_p.T512S|GSN_ENST00000449733.1_Missense_Mutation_p.T512S	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	563	Actin-binding, Ca-sensitive. {ECO:0000255}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						CCTGCCAGCACCCGCCTCTTC	0.642													C|||	119	0.023762	0.0265	0.0202	5008	,	,		17479	0.0		0.0308	False		,,,				2504	0.0399				p.T563S		Atlas-SNP	.											.	GSN	81	.	0			c.C1688G						PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	141,4261		3,135,2063	17.0	18.0	18.0		1688,1535,1535,1535,1535,1568,1568,1535	4.2	1.0	9	dbSNP_131	18	270,8320		5,260,4030	no	missense,missense,missense,missense,missense,missense,missense,missense	GSN	NM_000177.4,NM_001127662.1,NM_001127663.1,NM_001127664.1,NM_001127665.1,NM_001127666.1,NM_001127667.1,NM_198252.2	58,58,58,58,58,58,58,58	8,395,6093	GG,GC,CC		3.1432,3.2031,3.1635	benign,benign,benign,benign,benign,benign,benign,benign	563/783,512/732,512/732,512/732,512/732,523/743,523/743,512/732	124088908	411,12581	2201	4295	6496	SO:0001583	missense	2934	exon12			CCAGCACCCGCCT	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.1688C>G	9.37:g.124088908C>G	ENSP00000362924:p.Thr563Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	37	CCDS6828.1	45	0.020604395604395604	12	0.024390243902439025	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	16.12	3.032917	0.54790	0.032031	0.031432	ENSG00000148180	ENST00000373823;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818;ENST00000373807	T;T;T;T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89	5.13	4.22	0.49857	.	0.154614	0.64402	D	0.000019	T	0.14184	0.0343	M	0.86953	2.85	0.42695	D	0.993598	B;P;B;B;B	0.34826	0.42;0.471;0.043;0.009;0.087	B;B;B;B;B	0.36534	0.227;0.149;0.069;0.021;0.086	T	0.04427	-1.0952	10	0.40728	T	0.16	-23.1495	9.5322	0.39200	0.0:0.8376:0.0:0.1624	.	536;520;523;294;563	B7Z9A0;F5H1A8;B7Z373;Q5T0H9;P06396	.;.;.;.;GELS_HUMAN	S	512;523;523;512;512;512;512;496;486;520;563;294	ENSP00000362929:T512S;ENSP00000411293:T523S;ENSP00000377882:T523S;ENSP00000409358:T512S;ENSP00000416586:T512S;ENSP00000340888:T512S;ENSP00000362914:T512S;ENSP00000445823:T520S;ENSP00000362924:T563S;ENSP00000362913:T294S	ENSP00000340888:T512S	T	+	2	0	GSN	123128729	0.990000	0.36364	0.970000	0.41538	0.966000	0.64601	2.987000	0.49378	1.119000	0.41883	0.655000	0.94253	ACC	C|0.969;G|0.031	0.031	strong		0.642	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516871	173516871	+	Missense_Mutation	SNP	G	G	C	rs16846206	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:173516871G>C	ENST00000367714.3	-	13	1936	c.1514C>G	c.(1513-1515)gCt>gGt	p.A505G	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Missense_Mutation_p.A403G	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	505			A -> G (in dbSNP:rs16846206).		sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										CTCCATTAAAGCTTCATCTGT	0.348													G|||	1676	0.334665	0.1293	0.3256	5008	,	,		18034	0.6448		0.2107	False		,,,				2504	0.4264				p.A505G		Atlas-SNP	.											.	.	.	.	0			c.C1514G						PASS	.	G	GLY/ALA	584,3822	256.7+/-261.4	38,508,1657	158.0	142.0	147.0		1514	-0.2	1.0	1	dbSNP_123	147	1771,6829	319.3+/-314.1	183,1405,2712	yes	missense	SLC9A11	NM_178527.3	60	221,1913,4369	CC,CG,GG		20.593,13.2547,18.107	benign	505/1125	173516871	2355,10651	2203	4300	6503	SO:0001583	missense	284525	exon13			ATTAAAGCTTCAT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1514C>G	1.37:g.173516871G>C	ENSP00000356687:p.Ala505Gly	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	700	0.32051282051282054	69	0.1402439024390244	112	0.30939226519337015	355	0.6206293706293706	164	0.21635883905013192	G	10.10	1.258637	0.23051	0.132547	0.20593	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.25414	1.8;1.8	5.5	-0.206	0.13193	.	0.673556	0.13000	N	0.421735	T	0.03053	0.0090	N	0.08118	0	0.46241	P	0.0010580000000000034	B	0.27068	0.167	B	0.21360	0.034	T	0.42068	-0.9473	9	0.30854	T	0.27	-6.9082	4.5975	0.12336	0.3998:0.0:0.0905:0.5097	rs16846206;rs52835556;rs61192359;rs16846206	505	Q5TAH2	S9A11_HUMAN	G	505;403	ENSP00000356687:A505G;ENSP00000445437:A403G	ENSP00000356687:A505G	A	-	2	0	SLC9A11	171783494	0.999000	0.42202	0.997000	0.53966	0.401000	0.30781	0.324000	0.19610	0.035000	0.15519	-0.440000	0.05779	GCT	G|0.763;C|0.237	0.237	strong		0.348	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
SLC9C1	285335	hgsc.bcm.edu	37	3	111918215	111918215	+	Missense_Mutation	SNP	C	C	T	rs386664658|rs28516377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:111918215C>T	ENST00000305815.5	-	20	2728	c.2476G>A	c.(2476-2478)Ggc>Agc	p.G826S	SLC9C1_ENST00000487372.1_Missense_Mutation_p.G778S	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	826			G -> S (in dbSNP:rs28516377). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CCTTTTAAGCCAAAAGCCTTA	0.308													T|||	1682	0.335863	0.3699	0.4049	5008	,	,		17248	0.3393		0.2376	False		,,,				2504	0.3384				p.G826S		Atlas-SNP	.											SLC9A10,NS,carcinoma,0,1	.	.	1	0			c.G2476A						PASS	.	T	SER/GLY	1595,2807	650.4+/-399.0	307,981,913	75.0	82.0	80.0		2476	-3.0	0.0	3	dbSNP_125	80	2317,6279	697.4+/-404.9	321,1675,2302	yes	missense	SLC9A10	NM_183061.1	56	628,2656,3215	TT,TC,CC		26.9544,36.2335,30.0969	benign	826/1178	111918215	3912,9086	2201	4298	6499	SO:0001583	missense	285335	exon20			TTAAGCCAAAAGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2476G>A	3.37:g.111918215C>T	ENSP00000306627:p.Gly826Ser	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	540	0.24725274725274726	114	0.23170731707317074	121	0.3342541436464088	160	0.27972027972027974	145	0.19129287598944592	T	0.024	-1.394455	0.01175	0.362335	0.269544	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.76060	-0.98;-0.99	5.55	-3.0	0.05480	.	1.049680	0.07428	N	0.895123	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.29716	0.004;0.255	B;B	0.24394	0.006;0.053	T	0.05683	-1.0870	9	0.15952	T	0.53	.	8.7266	0.34474	0.0:0.4304:0.1116:0.458	rs28516377	778;826	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	S	826;778	ENSP00000306627:G826S;ENSP00000420688:G778S	ENSP00000306627:G826S	G	-	1	0	SLC9A10	113400905	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.009000	0.13219	-0.760000	0.04677	-3.067000	0.00067	GGC	C|0.725;T|0.275	0.275	strong		0.308	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
PCNT	5116	hgsc.bcm.edu	37	21	47773177	47773177	+	Missense_Mutation	SNP	C	C	T	rs2249060	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47773177C>T	ENST00000359568.5	+	10	1723	c.1616C>T	c.(1615-1617)aCc>aTc	p.T539I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	539	Glu-rich.		T -> I (in dbSNP:rs2249060).		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)					GAAGACCTAACCCTGTTACAG	0.488													C|||	798	0.159345	0.1059	0.183	5008	,	,		19818	0.1944		0.1272	False		,,,				2504	0.2117				p.T539I		Atlas-SNP	.											.	PCNT	283	.	0			c.C1616T						PASS	.	C	ILE/THR	460,3946	218.1+/-236.3	27,406,1770	78.0	85.0	83.0		1616	1.4	0.0	21	dbSNP_100	83	1070,7530	225.0+/-261.2	67,936,3297	yes	missense	PCNT	NM_006031.5	89	94,1342,5067	TT,TC,CC		12.4419,10.4403,11.7638	possibly-damaging	539/3337	47773177	1530,11476	2203	4300	6503	SO:0001583	missense	5116	exon10			ACCTAACCCTGTT	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.1616C>T	21.37:g.47773177C>T	ENSP00000352572:p.Thr539Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	318	0.14560439560439561	51	0.10365853658536585	50	0.13812154696132597	117	0.20454545454545456	100	0.13192612137203166	C	3.165	-0.171228	0.06421	0.104403	0.124419	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01560	4.77	4.84	1.4	0.22301	.	.	.	.	.	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	B;B	0.28783	0.222;0.142	B;B	0.27500	0.08;0.037	T	0.47433	-0.9118	8	0.37606	T	0.19	.	3.6814	0.08312	0.2572:0.5264:0.1169:0.0995	rs2249060;rs17297784;rs52808599;rs57443527;rs2249060	421;539	O95613-2;O95613	.;PCNT_HUMAN	I	539;526	ENSP00000352572:T539I	ENSP00000338675:T526I	T	+	2	0	PCNT	46597605	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.178000	0.16820	0.377000	0.24735	0.563000	0.77884	ACC	C|0.866;T|0.134	0.134	strong		0.488	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
EFS	10278	hgsc.bcm.edu	37	14	23830042	23830042	+	Splice_Site	SNP	T	T	C	rs2231798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23830042T>C	ENST00000216733.3	-	2	626	c.19A>G	c.(19-21)Acc>Gcc	p.T7A	EFS_ENST00000429593.2_Intron|EFS_ENST00000351354.3_Intron	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	7	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		T -> A (in dbSNP:rs2231798).		cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		GCCAGCTGGGTCTGGTTGGGG	0.637													C|||	2282	0.455671	0.8759	0.2478	5008	,	,		16776	0.3046		0.2763	False		,,,				2504	0.3753				p.T7A		Atlas-SNP	.											.	EFS	37	.	0			c.A19G						PASS	.	C	ALA/THR,	3380,1010		1320,740,135	15.0	18.0	17.0		19,	5.0	1.0	14	dbSNP_98	17	2555,6017		413,1729,2144	yes	missense-near-splice,intron	EFS	NM_005864.2,NM_032459.1	58,	1733,2469,2279	CC,CT,TT		29.8063,23.0068,45.7877	benign,	7/562,	23830042	5935,7027	2195	4286	6481	SO:0001630	splice_region_variant	10278	exon2			GCTGGGTCTGGTT	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.19-1A>G	14.37:g.23830042T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	37	CCDS9595.1	930	0.4258241758241758	426	0.8658536585365854	111	0.30662983425414364	186	0.32517482517482516	207	0.27308707124010556	C	5.796	0.331223	0.10956	0.769932	0.298063	ENSG00000100842	ENST00000216733	T	0.55760	0.5	4.99	4.99	0.66335	Src homology-3 domain (2);	0.124031	0.53938	N	0.000051	T	0.00012	0.0000	N	0.21545	0.675	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27331	-1.0077	9	0.11794	T	0.64	-12.5983	11.7333	0.51750	0.0:0.9141:0.0:0.0859	rs2231798;rs57406640;rs2231798	7	O43281	EFS_HUMAN	A	7	ENSP00000216733:T7A	ENSP00000216733:T7A	T	-	1	0	EFS	22899882	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	1.376000	0.34306	1.496000	0.48567	-0.213000	0.12676	ACC	T|0.564;C|0.436	0.436	strong		0.637	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		Missense_Mutation
INADL	10207	hgsc.bcm.edu	37	1	62579823	62579823	+	Silent	SNP	G	G	A	rs1475563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:62579823G>A	ENST00000371158.2	+	35	4674	c.4560G>A	c.(4558-4560)gaG>gaA	p.E1520E	INADL_ENST00000316485.6_Silent_p.E1550E|INADL_ENST00000543708.1_Silent_p.E334E|INADL_ENST00000545929.1_Silent_p.E165E	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1520	PDZ 8. {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						ATAGAGATGAGGCACACTACC	0.567													G|||	3050	0.609026	0.4206	0.7161	5008	,	,		16626	0.754		0.66	False		,,,				2504	0.5859				p.E1520E		Atlas-SNP	.											.	INADL	179	.	0			c.G4560A						PASS	.	G		2062,2344	568.4+/-382.4	473,1116,614	82.0	78.0	80.0		4560	0.5	0.0	1	dbSNP_88	80	6007,2593	688.6+/-404.3	2086,1835,379	no	coding-synonymous	INADL	NM_176877.2		2559,2951,993	AA,AG,GG		30.1512,46.7998,37.9594		1520/1802	62579823	8069,4937	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon35			AGATGAGGCACAC	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.4560G>A	1.37:g.62579823G>A		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	251	123	0.49004	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			G|0.370;N|0.000	.	strong		0.567	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
UBA6	55236	hgsc.bcm.edu	37	4	68562365	68562365	+	Silent	SNP	A	A	G	rs17572160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:68562365A>G	ENST00000322244.5	-	2	191	c.132T>C	c.(130-132)taT>taC	p.Y44Y	UBA6_ENST00000420827.2_Silent_p.Y44Y	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	44					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						ATTCTTACCTATACAATGCAT	0.303													G|||	925	0.184704	0.1906	0.2277	5008	,	,		15105	0.1746		0.2575	False		,,,				2504	0.0818				p.Y44Y		Atlas-SNP	.											.	UBA6	98	.	0			c.T132C						PASS	.	G		863,3541	743.2+/-411.4	86,691,1425	88.0	85.0	86.0		132	1.1	1.0	4	dbSNP_123	86	2212,6378	707.8+/-405.6	291,1630,2374	no	coding-synonymous	UBA6	NM_018227.5		377,2321,3799	GG,GA,AA		25.7509,19.5958,23.6648		44/1053	68562365	3075,9919	2202	4295	6497	SO:0001819	synonymous_variant	55236	exon2			TTACCTATACAAT	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.132T>C	4.37:g.68562365A>G		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	368	177	0.480978	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	37	CCDS3516.1																																																																																			A|0.778;G|0.222	0.222	strong		0.303	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	
PCDH15	65217	hgsc.bcm.edu	37	10	55755491	55755491	+	Missense_Mutation	SNP	C	C	T	rs2135720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:55755491C>T	ENST00000320301.6	-	21	3180	c.2786G>A	c.(2785-2787)cGa>cAa	p.R929Q	PCDH15_ENST00000373955.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.R540Q|PCDH15_ENST00000437009.1_Missense_Mutation_p.R858Q|PCDH15_ENST00000361849.3_Missense_Mutation_p.R929Q|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.R892Q|PCDH15_ENST00000395433.1_Missense_Mutation_p.R907Q|PCDH15_ENST00000395438.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000373965.2_Missense_Mutation_p.R936Q|PCDH15_ENST00000395430.1_Missense_Mutation_p.R929Q|PCDH15_ENST00000395445.1_Missense_Mutation_p.R936Q|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.R934Q	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	99	0	0		WXS	Illumina HiSeq	Phase_I	101	42	0.415842	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	
NANS	54187	hgsc.bcm.edu	37	9	100823135	100823135	+	Missense_Mutation	SNP	G	G	C	rs1058446	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100823135G>C	ENST00000210444.5	+	2	274	c.204G>C	c.(202-204)gaG>gaC	p.E68D		NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	68			E -> D (in dbSNP:rs1058446). {ECO:0000269|PubMed:15489334}.		lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				AAGCCTTGGAGAGGCCATACA	0.502													G|||	963	0.192292	0.2224	0.2622	5008	,	,		18731	0.2004		0.2207	False		,,,				2504	0.0644				p.E68D		Atlas-SNP	.											.	NANS	24	.	0			c.G204C						PASS	.	G	ASP/GLU	937,3469	357.4+/-313.9	105,727,1371	182.0	180.0	181.0		204	3.0	1.0	9	dbSNP_86	181	2075,6525	359.9+/-331.7	269,1537,2494	yes	missense	NANS	NM_018946.3	45	374,2264,3865	CC,CG,GG		24.1279,21.2665,23.1585	benign	68/360	100823135	3012,9994	2203	4300	6503	SO:0001583	missense	54187	exon2			CTTGGAGAGGCCA	AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"""sialic acid synthase"""	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.204G>C	9.37:g.100823135G>C	ENSP00000210444:p.Glu68Asp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_018946	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Missense_Mutation	SNP	ENST00000210444.5	37	CCDS6733.1	498	0.22802197802197802	120	0.24390243902439024	88	0.2430939226519337	125	0.21853146853146854	165	0.21767810026385223	G	12.90	2.077207	0.36662	0.212665	0.241279	ENSG00000095380	ENST00000210444	T	0.43294	0.95	5.73	2.95	0.34219	Aldolase-type TIM barrel (1);N-acetylneuraminic acid synthase, N-terminal (1);	0.043833	0.85682	D	0.000000	T	0.00012	0.0000	N	0.02751	-0.505	0.22754	P	0.99877242	B	0.02656	0.0	B	0.11329	0.006	T	0.29150	-1.0021	9	0.27082	T	0.32	-17.3272	9.6941	0.40147	0.2239:0.0:0.7761:0.0	rs1058446;rs3199071;rs17858509;rs52795099;rs1058446	68	Q9NR45	SIAS_HUMAN	D	68	ENSP00000210444:E68D	ENSP00000210444:E68D	E	+	3	2	NANS	99862956	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.315000	0.43752	0.470000	0.27294	0.655000	0.94253	GAG	G|0.775;C|0.225	0.225	strong		0.502	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417102	105417102	+	Silent	SNP	T	T	C	rs2248966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	235	234	0.995745	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417285	105417285	+	Silent	SNP	C	C	T	rs76453246	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105417285C>T	ENST00000333244.5	-	7	4622	c.4503G>A	c.(4501-4503)ccG>ccA	p.P1501P	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)			CCCCGAACGACGGCATCTTGA	0.607													.|||	331	0.0660942	0.0333	0.0836	5008	,	,		14865	0.003		0.162	False		,,,				2504	0.0644				p.P1501P		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,-1,1	AHNAK2	719	1	0			c.G4503A						scavenged	.	G		179,3707		37,105,1801	193.0	134.0	153.0		4503	-8.1	0.1	14	dbSNP_131	153	1343,6733		343,657,3038	no	coding-synonymous	AHNAK2	NM_138420.2		380,762,4839	TT,TC,CC		16.6295,4.6063,12.7236		1501/5796	105417285	1522,10440	1943	4038	5981	SO:0001819	synonymous_variant	113146	exon7			GAACGACGGCATC	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.4503G>A	14.37:g.105417285C>T		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	69	25	0.362319	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.948;T|0.052	0.052	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SNAP47	116841	hgsc.bcm.edu	37	1	227935444	227935444	+	Missense_Mutation	SNP	A	A	G	rs2236359	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:227935444A>G	ENST00000366759.4	+	2	556	c.142A>G	c.(142-144)Agg>Ggg	p.R48G	SNAP47_ENST00000366760.1_Intron|SNAP47_ENST00000315781.5_Missense_Mutation_p.R48G|SNAP47-AS1_ENST00000413347.2_RNA	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	48			R -> G (in dbSNP:rs2236359).		long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						ACAGATGAGCAGGGATGTCTG	0.572													A|||	2100	0.419329	0.4826	0.4928	5008	,	,		20212	0.3651		0.3996	False		,,,				2504	0.3579				p.R48G		Atlas-SNP	.											.	SNAP47	42	.	0			c.A142G						PASS	.	A	GLY/ARG	1937,2469	549.3+/-377.7	427,1083,693	83.0	67.0	72.0		142	1.7	0.6	1	dbSNP_98	72	3550,5050	515.5+/-378.6	722,2106,1472	yes	missense	SNAP47	NM_053052.3	125	1149,3189,2165	GG,GA,AA		41.2791,43.9628,42.1882	benign	48/465	227935444	5487,7519	2203	4300	6503	SO:0001583	missense	116841	exon2			ATGAGCAGGGATG	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 142"""	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.142A>G	1.37:g.227935444A>G	ENSP00000355721:p.Arg48Gly	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	286	129	0.451049	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	918|918	0.42032967032967034|0.42032967032967034	231|231	0.4695121951219512|0.4695121951219512	168|168	0.46408839779005523|0.46408839779005523	214|214	0.3741258741258741|0.3741258741258741	305|305	0.4023746701846966|0.4023746701846966	A|A	6.376|6.376	0.437453|0.437453	0.12104|0.12104	0.439628|0.439628	0.412791|0.412791	ENSG00000143740|ENSG00000143740	ENST00000426344|ENST00000366759;ENST00000315781	.|T;T	.|0.16897	.|2.31;2.31	4.08|4.08	1.67|1.67	0.24075|0.24075	.|.	.|0.767945	.|0.12787	.|N	.|0.439145	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38838|0.38838	1.175|1.175	0.40237|0.40237	P|P	0.022087999999999997|0.022087999999999997	.|B;B	.|0.06786	.|0.001;0.001	.|B;B	.|0.06405	.|0.002;0.002	T|T	0.44390|0.44390	-0.9331|-0.9331	4|9	.|0.35671	.|T	.|0.21	-14.59|-14.59	4.557|4.557	0.12141|0.12141	0.7309:0.0:0.0991:0.17|0.7309:0.0:0.0991:0.17	rs2236359;rs3183672;rs17555295;rs52818129;rs61005345;rs2236359|rs2236359;rs3183672;rs17555295;rs52818129;rs61005345;rs2236359	.|48;48	.|Q5SQN1;Q5SQN1-2	.|SNP47_HUMAN;.	R|G	39|48	.|ENSP00000355721:R48G;ENSP00000314157:R48G	.|ENSP00000314157:R48G	Q|R	+|+	2|1	0|2	SNAP47|SNAP47	226002067|226002067	1.000000|1.000000	0.71417|0.71417	0.568000|0.568000	0.28447|0.28447	0.240000|0.240000	0.25518|0.25518	2.485000|2.485000	0.45250|0.45250	0.139000|0.139000	0.18822|0.18822	0.482000|0.482000	0.46254|0.46254	CAG|AGG	A|0.578;G|0.422	0.422	strong		0.572	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052	
SH3GLB2	56904	hgsc.bcm.edu	37	9	131771505	131771505	+	Silent	SNP	C	C	T	rs1129098	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:131771505C>T	ENST00000372564.3	-	10	1105	c.960G>A	c.(958-960)ccG>ccA	p.P320P	SH3GLB2_ENST00000372559.1_Silent_p.P320P|SH3GLB2_ENST00000372554.4_Silent_p.P329P|SH3GLB2_ENST00000417224.1_Silent_p.P325P|SH3GLB2_ENST00000416629.1_Silent_p.P299P	NM_020145.2	NP_064530.1	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	320						cytoplasm (GO:0005737)				NS(1)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)	12						AGGCCTCCCCCGGAGGGGCCA	0.697													C|||	1281	0.255791	0.0885	0.3991	5008	,	,		13246	0.1696		0.4135	False		,,,				2504	0.3067				p.P320P		Atlas-SNP	.											.	SH3GLB2	32	.	0			c.G960A						PASS	.	C		514,3880		35,444,1718	12.0	14.0	13.0		960	-9.2	0.0	9	dbSNP_86	13	3084,5506		580,1924,1791	no	coding-synonymous	SH3GLB2	NM_020145.2		615,2368,3509	TT,TC,CC		35.9022,11.6978,27.711		320/396	131771505	3598,9386	2197	4295	6492	SO:0001819	synonymous_variant	56904	exon10			CTCCCCCGGAGGG	AF257319	CCDS6916.1, CCDS69680.1	9q34	2008-02-05	2001-12-04		ENSG00000148341	ENSG00000148341			10834	protein-coding gene	gene with protein product		609288	"""SH3-domain, GRB2-like, endophilin B2"""			11161816	Standard	NM_020145		Approved	KIAA1848	uc004bwv.3	Q9NR46	OTTHUMG00000020769	ENST00000372564.3:c.960G>A	9.37:g.131771505C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	80	76	0.95	NM_020145	A6NC47|A8MPS4|Q8WY61|Q96JH9	Silent	SNP	ENST00000372564.3	37	CCDS6916.1																																																																																			C|0.726;T|0.274	0.274	strong		0.697	SH3GLB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054535.2		
RBM10	8241	hgsc.bcm.edu	37	X	47041666	47041666	+	Missense_Mutation	SNP	G	G	C	rs79693964	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:47041666G>C	ENST00000377604.3	+	17	2633	c.1891G>C	c.(1891-1893)Gca>Cca	p.A631P	RBM10_ENST00000329236.7_Missense_Mutation_p.A553P|RBM10_ENST00000345781.6_Missense_Mutation_p.A554P	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	631					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						GGAGACAGGGGCACCCTCGAA	0.587													G|||	39	0.0103311	0.0008	0.0058	3775	,	,		15264	0.0		0.0318	False		,,,				2504	0.002				p.A696P	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G2086C						PASS	.	G	PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	9,3826		0,8,1,1624,570	115.0	107.0	110.0		1660,1888,2086,1891,1657	4.8	1.0	X	dbSNP_131	110	137,6591		1,104,31,2323,1841	yes	missense,missense,missense,missense,missense	RBM10	NM_001204466.1,NM_001204467.1,NM_001204468.1,NM_005676.4,NM_152856.2	27,27,27,27,27	1,112,32,3947,2411	CC,CG,C,GG,G		2.0363,0.2347,1.3822	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	554/854,630/930,696/996,631/931,553/853	47041666	146,10417	2203	4300	6503	SO:0001583	missense	8241	exon17			ACAGGGGCACCCT	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.1891G>C	X.37:g.47041666G>C	ENSP00000366829:p.Ala631Pro	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	31	0.018685955394816153	0	0.0	2	0.005555555555555556	0	0.0	21	0.028225806451612902	G	10.31	1.314486	0.23908	0.002347	0.020363	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.19532	2.8;2.14;2.41	4.85	4.85	0.62838	.	0.154569	0.40222	N	0.001150	T	0.07234	0.0183	L	0.54323	1.7	0.26178	P	0.9797689	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.08055	0.003;0.001;0.002;0.001;0.001	T	0.11203	-1.0597	9	0.23302	T	0.38	-12.2348	12.6848	0.56942	0.0:0.0:1.0:0.0	.	554;696;630;553;631	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	P	631;553;554	ENSP00000366829:A631P;ENSP00000328848:A553P;ENSP00000329659:A554P	ENSP00000328848:A553P	A	+	1	0	RBM10	46926610	0.992000	0.36948	0.956000	0.39512	0.703000	0.40648	2.086000	0.41643	2.137000	0.66172	0.436000	0.28706	GCA	G|0.984;C|0.016	0.016	strong		0.587	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
NUP107	57122	hgsc.bcm.edu	37	12	69090684	69090684	+	Silent	SNP	A	A	G	rs35054844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:69090684A>G	ENST00000229179.4	+	6	866	c.534A>G	c.(532-534)gaA>gaG	p.E178E	NUP107_ENST00000378905.2_Silent_p.E27E|NUP107_ENST00000539906.1_Silent_p.E149E	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	178					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			AAGAGTATGAAAACATCTGTG	0.353													A|||	154	0.0307508	0.0507	0.0403	5008	,	,		19586	0.001		0.0229	False		,,,				2504	0.0358				p.E178E		Atlas-SNP	.											NUP107,NS,carcinoma,+2,1	NUP107	88	1	0			c.A534G						PASS	.	A		178,4228	116.3+/-154.2	3,172,2028	115.0	106.0	109.0		534	1.9	1.0	12	dbSNP_126	109	194,8406	85.3+/-147.7	3,188,4109	no	coding-synonymous	NUP107	NM_020401.2		6,360,6137	GG,GA,AA		2.2558,4.0399,2.8602		178/926	69090684	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon6			GTATGAAAACATC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.534A>G	12.37:g.69090684A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			A|0.975;G|0.025	0.025	strong		0.353	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
CCDC60	160777	hgsc.bcm.edu	37	12	119866533	119866533	+	Missense_Mutation	SNP	A	A	G	rs1064319	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:119866533A>G	ENST00000327554.2	+	2	601	c.136A>G	c.(136-138)Ata>Gta	p.I46V	CCDC60_ENST00000536742.1_Missense_Mutation_p.I46V|CCDC60_ENST00000539847.1_Missense_Mutation_p.I46V|RP11-768F21.1_ENST00000509470.2_lincRNA|CCDC60_ENST00000546345.1_3'UTR	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	46			I -> V (in dbSNP:rs1064319).							endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GGACAAGGAAATAATAAACCT	0.438													A|||	1268	0.253195	0.2194	0.245	5008	,	,		22575	0.2788		0.326	False		,,,				2504	0.2035				p.I46V		Atlas-SNP	.											CCDC60,NS,carcinoma,0,1	CCDC60	84	1	0			c.A136G						PASS	.	A	VAL/ILE	971,3435	357.9+/-314.1	124,723,1356	79.0	69.0	72.0		136	0.9	0.0	12	dbSNP_86	72	2863,5737	435.0+/-357.9	479,1905,1916	yes	missense	CCDC60	NM_178499.3	29	603,2628,3272	GG,GA,AA		33.2907,22.0381,29.4787	probably-damaging	46/551	119866533	3834,9172	2203	4300	6503	SO:0001583	missense	160777	exon2			AAGGAAATAATAA	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.136A>G	12.37:g.119866533A>G	ENSP00000333374:p.Ile46Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	600	0.27472527472527475	105	0.21341463414634146	99	0.27348066298342544	150	0.26223776223776224	246	0.3245382585751979	A	11.70	1.717191	0.30413	0.220381	0.332907	ENSG00000183273	ENST00000536742;ENST00000327554;ENST00000539847	T;T;T	0.58797	0.51;1.85;0.31	4.54	0.905	0.19307	.	0.502010	0.18504	N	0.139250	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.12630	0.006	B	0.14578	0.011	T	0.29458	-1.0011	8	.	.	.	-11.3508	6.5238	0.22289	0.7105:0.0:0.2895:0.0	rs1064319;rs3742048;rs17627026;rs60254996;rs1064319	46	Q8IWA6	CCD60_HUMAN	V	46	ENSP00000445505:I46V;ENSP00000333374:I46V;ENSP00000443403:I46V	.	I	+	1	0	CCDC60	118350916	0.623000	0.27094	0.044000	0.18714	0.858000	0.48976	0.868000	0.27982	0.151000	0.19162	-0.256000	0.11100	ATA	A|0.720;G|0.280	0.280	strong		0.438	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
TRH	7200	hgsc.bcm.edu	37	3	129694681	129694681	+	Missense_Mutation	SNP	C	C	G	rs5658	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	170	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	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	
APBA3	9546	hgsc.bcm.edu	37	19	3754020	3754020	+	Silent	SNP	G	G	C	rs61731066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3754020G>C	ENST00000316757.3	-	5	1046	c.846C>G	c.(844-846)tcC>tcG	p.S282S	AC005954.4_ENST00000586503.1_RNA|AC005954.3_ENST00000591962.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	282	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCGTACCTGGGAGTCCGCTG	0.706													G|||	86	0.0171725	0.0091	0.036	5008	,	,		12207	0.0		0.0308	False		,,,				2504	0.0184				p.S282S		Atlas-SNP	.											.	APBA3	28	.	0			c.C846G						PASS	.	G		41,4365	35.2+/-66.4	0,41,2162	27.0	25.0	26.0		846	1.7	1.0	19	dbSNP_129	26	286,8314	97.2+/-158.9	4,278,4018	no	coding-synonymous	APBA3	NM_004886.3		4,319,6180	CC,CG,GG		3.3256,0.9305,2.5142		282/576	3754020	327,12679	2203	4300	6503	SO:0001819	synonymous_variant	9546	exon5			TACCTGGGAGTCC	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.846C>G	19.37:g.3754020G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.968;C|0.032	0.032	strong		0.706	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
MED11	400569	hgsc.bcm.edu	37	17	4638563	4638563	+	IGR	SNP	G	G	A	rs2277680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4638563G>A	ENST00000293777.5	+	0	833				RP11-314A20.5_ENST00000570493.2_RNA|CXCL16_ENST00000574412.1_Missense_Mutation_p.A200V|CXCL16_ENST00000293778.6_Missense_Mutation_p.A200V|CXCL16_ENST00000576153.1_5'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						CTCAGGCCCAGCTGCCAGACT	0.602													A|||	2311	0.461462	0.2958	0.4813	5008	,	,		17949	0.5804		0.4394	False		,,,				2504	0.5716				p.A200V		Atlas-SNP	.											.	CXCL16	30	.	0			c.C599T	GRCh37	CM057933	CXCL16	M	rs2277680	PASS	.	A	VAL/ALA,VAL/ALA	1377,3029	689.7+/-405.2	217,943,1043	63.0	58.0	59.0		599,599	-2.6	0.0	17	dbSNP_100	59	3756,4844	616.2+/-396.5	835,2086,1379	yes	missense,missense	CXCL16	NM_001100812.1,NM_022059.2	64,64	1052,3029,2422	AA,AG,GG		43.6744,31.2528,39.4664	possibly-damaging,possibly-damaging	200/274,200/274	4638563	5133,7873	2203	4300	6503	SO:0001628	intergenic_variant	58191	exon4			GGCCCAGCTGCCA	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638563G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	185	96	0.518919	NM_022059	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	CCDS32533.1	986	0.45146520146520147	149	0.30284552845528456	162	0.44751381215469616	340	0.5944055944055944	335	0.4419525065963061	A	7.358	0.624211	0.14193	0.312528	0.436744	ENSG00000161921	ENST00000293778	T	0.37058	1.22	5.31	-2.64	0.06114	.	1.206380	0.05967	N	0.641717	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.45205	-0.9277	9	0.19147	T	0.46	-0.9058	13.3114	0.60382	0.2755:0.0:0.7245:0.0	rs2277680;rs17824095;rs17857293;rs52830669;rs58179207;rs2277680	181	Q9H2A7	CXL16_HUMAN	V	200	ENSP00000293778:A200V	ENSP00000293778:A200V	A	-	2	0	CXCL16	4585312	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.819000	0.04462	-0.477000	0.06832	-1.214000	0.01621	GCT	G|0.576;A|0.424	0.424	strong		0.602	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
SMIM24	284422	hgsc.bcm.edu	37	19	3474941	3474941	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3474941T>G	ENST00000215531.4	-	4	371	c.293A>C	c.(292-294)aAg>aCg	p.K98T	C19orf77_ENST00000591708.1_Missense_Mutation_p.K28T|C19orf77_ENST00000587847.1_Missense_Mutation_p.K28T	NM_001136503.1	NP_001129975.1	O75264	SIM24_HUMAN		98						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											ctttttctccttcttcctctt	0.463																																					p.K98T		Atlas-SNP	.											.	C19orf77	6	.	0			c.A293C						PASS	.						137.0	120.0	125.0					19																	3474941		692	1591	2283	SO:0001583	missense	284422	exon4			TTCTCCTTCTTCC																												ENST00000215531.4:c.293A>C	19.37:g.3474941T>G	ENSP00000215531:p.Lys98Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	77	0.534722	NM_001136503	B9EJF4|Q9P059	Missense_Mutation	SNP	ENST00000215531.4	37	CCDS45915.1	.	.	.	.	.	.	.	.	.	.	T	1.844	-0.466592	0.04476	.	.	ENSG00000095932	ENST00000215531	.	.	.	1.97	0.911	0.19343	.	.	.	.	.	T	0.26195	0.0639	N	0.14661	0.345	0.09310	N	1	P	0.39665	0.682	P	0.48030	0.564	T	0.15636	-1.0430	8	0.48119	T	0.1	.	3.8581	0.08984	0.0:0.197:0.0:0.803	.	98	O75264	CS077_HUMAN	T	98	.	ENSP00000215531:K98T	K	-	2	0	C19orf77	3425941	0.002000	0.14202	0.001000	0.08648	0.227000	0.25037	0.318000	0.19504	0.214000	0.20742	0.402000	0.26972	AAG	.	.	none		0.463	C19orf77-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452929.1		
TSC1	7248	hgsc.bcm.edu	37	9	135771795	135771795	+	Missense_Mutation	SNP	C	C	T	rs118203753		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:135771795C>T	ENST00000298552.3	-	23	3543	c.3322G>A	c.(3322-3324)Ggc>Agc	p.G1108S	TSC1_ENST00000440111.2_Missense_Mutation_p.G1108S|TSC1_ENST00000545250.1_Missense_Mutation_p.G1057S	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	1108			G -> S. {ECO:0000269|PubMed:9924605}.		activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CTGGTCATGCCGTCCTCATCA	0.527			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.G1108S		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	TSC1,right_lower_lobe,carcinoma,0,1	TSC1	167	1	1	Unknown(1)	bone(1)	c.G3322A						scavenged	.						142.0	115.0	124.0					9																	135771795		2203	4300	6503	SO:0001583	missense	7248	exon23	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCATGCCGTCCTC	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.3322G>A	9.37:g.135771795C>T	ENSP00000298552:p.Gly1108Ser	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	230	3	0.0130435	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	37	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	C	3.568	-0.088245	0.07097	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	T;T;T	0.80566	-1.39;-1.39;-1.2	5.59	-3.58	0.04597	.	0.606437	0.18127	N	0.150854	T	0.57344	0.2047	N	0.21448	0.665	0.25410	N	0.98836	B;B	0.13594	0.008;0.005	B;B	0.06405	0.002;0.001	T	0.49781	-0.8903	10	0.07175	T	0.84	-1.1024	7.1624	0.25671	0.108:0.3919:0.0:0.5001	.	1057;1108	B7Z897;Q92574	.;TSC1_HUMAN	S	1108;1108;1057	ENSP00000298552:G1108S;ENSP00000394524:G1108S;ENSP00000444017:G1057S	ENSP00000298552:G1108S	G	-	1	0	TSC1	134761616	0.032000	0.19561	0.063000	0.19743	0.635000	0.38103	-1.008000	0.03663	-0.718000	0.04949	0.563000	0.77884	GGC	.	.	weak		0.527	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
PLA2G4F	255189	hgsc.bcm.edu	37	15	42439444	42439444	+	Missense_Mutation	SNP	C	C	T	rs111633028	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:42439444C>T	ENST00000382396.4	-	13	1383	c.1297G>A	c.(1297-1299)Gct>Act	p.A433T	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.A435T			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	433	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)		GTGGACAAAGCTCCCATCTTA	0.627													C|||	260	0.0519169	0.0038	0.049	5008	,	,		17887	0.002		0.0616	False		,,,				2504	0.1605				p.A433T		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.G1297A						PASS	.	C	THR/ALA	64,4342	58.7+/-95.3	1,62,2140	71.0	64.0	66.0		1297	2.4	0.1	15	dbSNP_132	66	544,8054	150.6+/-205.5	19,506,3774	yes	missense	PLA2G4F	NM_213600.3	58	20,568,5914	TT,TC,CC		6.3271,1.4526,4.6755	benign	433/850	42439444	608,12396	2203	4299	6502	SO:0001583	missense	255189	exon13			ACAAAGCTCCCAT		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.1297G>A	15.37:g.42439444C>T	ENSP00000371833:p.Ala433Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	61	0.027930402930402932	1	0.0020325203252032522	16	0.04419889502762431	1	0.0017482517482517483	43	0.05672823218997362	C	15.43	2.830823	0.50845	0.014526	0.063271	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.04551	3.6;3.6	5.35	2.39	0.29439	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.166691	0.40908	D	0.000995	T	0.01029	0.0034	M	0.71206	2.165	0.19300	N	0.999974	P;P	0.47484	0.896;0.896	P;P	0.53224	0.721;0.721	T	0.11616	-1.0580	10	0.26408	T	0.33	-0.4356	7.0883	0.25270	0.1406:0.7074:0.0:0.152	.	220;433	A2RRC4;Q68DD2	.;PA24F_HUMAN	T	429;435;433;433	ENSP00000380442:A435T;ENSP00000371833:A433T	ENSP00000290497:A429T	A	-	1	0	PLA2G4F	40226736	0.107000	0.21998	0.129000	0.21949	0.266000	0.26442	1.450000	0.35134	0.724000	0.32296	0.561000	0.74099	GCT	C|0.956;T|0.044	0.044	strong		0.627	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
TTC16	158248	hgsc.bcm.edu	37	9	130489743	130489743	+	Splice_Site	SNP	A	A	G	rs13298768	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130489743A>G	ENST00000373289.3	+	12	1843	c.1763A>G	c.(1762-1764)gAg>gGg	p.E588G	PTRH1_ENST00000429848.1_5'Flank|PTRH1_ENST00000419060.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	588			E -> G (in dbSNP:rs13298768). {ECO:0000269|PubMed:15489334}.							central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						gagaaaaaagaggTAAGTGGA	0.607													A|||	1698	0.339058	0.2171	0.4625	5008	,	,		19083	0.245		0.499	False		,,,				2504	0.3487				p.E588G		Atlas-SNP	.											.	TTC16	55	.	0			c.A1763G						PASS	.	A	GLY/GLU	1125,3207		186,753,1227	7.0	8.0	7.0		1763	1.7	0.5	9	dbSNP_121	7	3722,4792		873,1976,1408	yes	missense-near-splice	TTC16	NM_144965.1	98	1059,2729,2635	GG,GA,AA		43.7162,25.9695,37.7316	benign	588/874	130489743	4847,7999	2166	4257	6423	SO:0001630	splice_region_variant	158248	exon12			AAAAAGAGGTAAG	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1764+1A>G	9.37:g.130489743A>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	37	CCDS6875.1	838	0.3836996336996337	132	0.2682926829268293	173	0.47790055248618785	151	0.263986013986014	382	0.503957783641161	A	10.94	1.491729	0.26774	0.259695	0.437162	ENSG00000167094	ENST00000373289;ENST00000373288	T	0.17213	2.29	4.07	1.73	0.24493	.	1.745110	0.02966	N	0.143856	T	0.00012	0.0000	N	0.24115	0.695	0.19575	P	0.9999695627	B;P	0.35077	0.006;0.483	B;B	0.24974	0.003;0.057	T	0.45891	-0.9230	9	0.62326	D	0.03	-2.2453	5.5863	0.17277	0.776:0.0:0.224:0.0	rs13298768;rs17856925;rs57133291;rs13298768	575;588	B4DZ42;Q8NEE8	.;TTC16_HUMAN	G	588;366	ENSP00000362386:E588G	ENSP00000362385:E366G	E	+	2	0	TTC16	129529564	0.972000	0.33761	0.476000	0.27291	0.034000	0.12701	2.120000	0.41968	0.372000	0.24591	0.459000	0.35465	GAG	A|0.638;G|0.362	0.362	strong		0.607	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	Missense_Mutation
COG6	57511	hgsc.bcm.edu	37	13	40229891	40229891	+	Missense_Mutation	SNP	G	G	A	rs3812882	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	40	0	0		WXS	Illumina HiSeq	Phase_I	74	45	0.608108	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		
ACOX2	8309	hgsc.bcm.edu	37	3	58494661	58494661	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58494661G>A	ENST00000302819.5	-	14	2233	c.1942C>T	c.(1942-1944)Cgc>Tgc	p.R648C	ACOX2_ENST00000481527.1_5'UTR|ACOX2_ENST00000459701.2_Missense_Mutation_p.R634C	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	648					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)		TGGAACAGGCGTTCGTAGACG	0.433																																					p.R648C		Atlas-SNP	.											.	ACOX2	53	.	0			c.C1942T						PASS	.						130.0	114.0	119.0					3																	58494661		2203	4300	6503	SO:0001583	missense	8309	exon14			ACAGGCGTTCGTA	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.1942C>T	3.37:g.58494661G>A	ENSP00000307697:p.Arg648Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	37	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885004	0.72410	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.47528	0.84;0.84	5.43	4.52	0.55395	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.198277	0.34959	N	0.003549	T	0.71022	0.3291	M	0.87682	2.9	0.48571	D	0.999672	D	0.89917	1.0	D	0.79784	0.993	T	0.76408	-0.2970	10	0.87932	D	0	-16.8637	13.3882	0.60807	0.0:0.0:0.7178:0.2822	.	648	Q99424	ACOX2_HUMAN	C	634;648	ENSP00000418562:R634C;ENSP00000307697:R648C	ENSP00000307697:R648C	R	-	1	0	ACOX2	58469701	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.978000	0.49305	2.583000	0.87209	0.579000	0.79373	CGC	.	.	none		0.433	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
IRGC	56269	hgsc.bcm.edu	37	19	44223145	44223145	+	Silent	SNP	C	C	T	rs34439296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44223145C>T	ENST00000244314.5	+	2	634	c.435C>T	c.(433-435)tgC>tgT	p.C145C		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	145	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)				CCCGCCGCTGCGGGGCCGTCG	0.652													C|||	258	0.0515176	0.0242	0.0548	5008	,	,		15818	0.001		0.1272	False		,,,				2504	0.0603				p.C145C	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											IRGC,NS,carcinoma,+1,1	IRGC	67	1	0			c.C435T						PASS	.	C		160,4046		4,152,1947	12.0	12.0	12.0		435	-0.3	0.0	19	dbSNP_126	12	901,7403		48,805,3299	no	coding-synonymous	IRGC	NM_019612.3		52,957,5246	TT,TC,CC		10.8502,3.8041,8.4812		145/464	44223145	1061,11449	2103	4152	6255	SO:0001819	synonymous_variant	56269	exon2			CCGCTGCGGGGCC	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.435C>T	19.37:g.44223145C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_019612	Q05BR8	Silent	SNP	ENST00000244314.5	37	CCDS12629.1																																																																																			C|0.927;T|0.073	0.073	strong		0.652	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612	
B4GALNT4	338707	hgsc.bcm.edu	37	11	372157	372157	+	Missense_Mutation	SNP	C	C	T	rs34063493	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	94	93	0.989362	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	
BRD2	6046	hgsc.bcm.edu	37	6	32942302	32942302	+	Silent	SNP	G	G	A	rs516535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32942302G>A	ENST00000374825.4	+	3	1794	c.93G>A	c.(91-93)aaG>aaA	p.K31K	BRD2_ENST00000449085.2_5'UTR|BRD2_ENST00000443797.2_5'UTR|BRD2_ENST00000395289.2_Silent_p.K31K|BRD2_ENST00000374831.4_Silent_p.K31K|BRD2_ENST00000395287.1_Silent_p.K31K|XXbac-BPG181M17.6_ENST00000580587.1_RNA	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	31					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CACCAGGGAAGAGGATTCGAA	0.572													A|||	3051	0.609225	0.7927	0.5389	5008	,	,		18019	0.504		0.5954	False		,,,				2504	0.5337				p.K31K		Atlas-SNP	.											.	BRD2	70	.	0			c.G93A						PASS	.	A	,,,	3427,979	365.4+/-317.4	1338,751,114	94.0	96.0	95.0		93,93,,93	2.9	1.0	6	dbSNP_83	95	5125,3475	508.7+/-377.1	1544,2037,719	yes	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	2882,2788,833	AA,AG,GG		40.407,22.2197,34.2457	,,,	31/802,31/837,,31/802	32942302	8552,4454	2203	4300	6503	SO:0001819	synonymous_variant	6046	exon3			AGGGAAGAGGATT	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.93G>A	6.37:g.32942302G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	122	50	0.409836	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	1336	0.6117216117216118	404	0.8211382113821138	193	0.5331491712707183	280	0.48951048951048953	459	0.6055408970976254	A	8.816	0.936314	0.18206	0.777803	0.59593	ENSG00000204256	ENST00000456339;ENST00000449025	.	.	.	5.26	2.9	0.33743	.	.	.	.	.	T	0.25901	0.0631	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.08086	-1.0739	3	.	.	.	-16.5361	7.4925	0.27471	0.7191:0.0:0.2809:0.0	rs516535;rs3189384;rs3752527;rs17584137;rs58877819;rs516535	.	.	.	K	33;37	.	.	R	+	2	0	BRD2	33050280	0.991000	0.36638	1.000000	0.80357	0.804000	0.45430	0.394000	0.20834	0.474000	0.27392	-0.268000	0.10319	AGA	G|0.363;A|0.637	0.637	strong		0.572	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
ASB2	51676	hgsc.bcm.edu	37	14	94417531	94417531	+	Missense_Mutation	SNP	T	T	C	rs11555542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:94417531T>C	ENST00000315988.4	-	4	1038	c.550A>G	c.(550-552)Aac>Gac	p.N184D	ASB2_ENST00000555019.1_Missense_Mutation_p.N232D|ASB2_ENST00000556337.1_Intron|MIR4506_ENST00000584693.1_RNA	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	184					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CAGCGGTGGTTGGTGTCTGCA	0.632													T|||	104	0.0207668	0.0023	0.0605	5008	,	,		19972	0.001		0.0567	False		,,,				2504	0.001				p.N232D		Atlas-SNP	.											.	ASB2	71	.	0			c.A694G						PASS	.	T	ASP/ASN,ASP/ASN	50,4356	50.9+/-86.3	0,50,2153	76.0	63.0	67.0		694,550	5.6	1.0	14	dbSNP_120	67	469,8131	139.0+/-195.8	10,449,3841	yes	missense,missense	ASB2	NM_001202429.1,NM_016150.4	23,23	10,499,5994	CC,CT,TT		5.4535,1.1348,3.9905	possibly-damaging,possibly-damaging	232/636,184/588	94417531	519,12487	2203	4300	6503	SO:0001583	missense	51676	exon6			GGTGGTTGGTGTC	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.550A>G	14.37:g.94417531T>C	ENSP00000320675:p.Asn184Asp	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	67	0.030677655677655676	2	0.0040650406504065045	25	0.06906077348066299	1	0.0017482517482517483	39	0.051451187335092345	T	27.5	4.840814	0.91197	0.011348	0.054535	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507;ENST00000556062	T;T;T;T	0.73789	-0.5;-0.5;-0.5;-0.78	5.62	5.62	0.85841	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	N	0.25201	0.72	0.54753	D	0.999986	P;D;P	0.76494	0.922;0.999;0.922	P;D;P	0.83275	0.841;0.996;0.677	T	0.60742	-0.7203	10	0.30078	T	0.28	-2.7607	15.8384	0.78818	0.0:0.0:0.0:1.0	rs11555542;rs11555542	200;232;184	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	D	232;200;184;130;130;78	ENSP00000451575:N232D;ENSP00000320675:N184D;ENSP00000450940:N130D;ENSP00000451694:N78D	ENSP00000320675:N184D	N	-	1	0	ASB2	93487284	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.258000	0.72487	2.137000	0.66172	0.459000	0.35465	AAC	T|0.964;C|0.036	0.036	strong		0.632	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
THEMIS2	9473	hgsc.bcm.edu	37	1	28209362	28209362	+	Silent	SNP	T	T	C	rs3766399	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:28209362T>C	ENST00000373921.3	+	4	1531	c.1527T>C	c.(1525-1527)gtT>gtC	p.V509V	THEMIS2_ENST00000328928.7_Silent_p.V380V|THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	509	CABIT 2.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACCTGACTGTTGTGAAGGCCA	0.567													C|||	2376	0.474441	0.1566	0.5086	5008	,	,		18222	0.504		0.6322	False		,,,				2504	0.6871				p.V509V		Atlas-SNP	.											.	.	.	.	0			c.T1527C						PASS	.	C	,,	1078,2992		131,816,1088	108.0	100.0	103.0		,1527,	-10.0	0.3	1	dbSNP_107	103	5434,2908		1784,1866,521	no	intron,coding-synonymous,intron	C1orf38	NM_001039477.1,NM_001105556.1,NM_004848.2	,,	1915,2682,1609	CC,CT,TT		34.8597,26.4865,47.5346	,,	,509/644,	28209362	6512,5900	2035	4171	6206	SO:0001819	synonymous_variant	9473	exon4			GACTGTTGTGAAG	AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"""induced by contact to basement membrane 1"""		"""chromosome 1 open reading frame 38"""	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.1527T>C	1.37:g.28209362T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_001105556	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Silent	SNP	ENST00000373921.3	37	CCDS41290.1	1035	0.4739010989010989	87	0.17682926829268292	192	0.5303867403314917	280	0.48951048951048953	476	0.6279683377308707	C	0.080	-1.185382	0.01620	0.264865	0.651403	ENSG00000130775	ENST00000456990	.	.	.	4.98	-9.96	0.00443	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999792943	.	.	.	.	.	.	T	0.05435	-1.0885	3	.	.	.	-13.5242	11.8762	0.52548	0.0:0.2266:0.3523:0.421	rs3766399	.	.	.	S	257	.	.	L	+	2	0	C1orf38	28081949	0.000000	0.05858	0.284000	0.24805	0.030000	0.12068	-3.595000	0.00420	-2.370000	0.00602	-3.133000	0.00060	TTG	T|0.468;C|0.532	0.532	strong		0.567	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848	
DIP2A	23181	hgsc.bcm.edu	37	21	47969793	47969793	+	Silent	SNP	C	C	T	rs17302700	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47969793C>T	ENST00000417564.2	+	22	2653	c.2632C>T	c.(2632-2634)Ctg>Ttg	p.L878L	DIP2A_ENST00000427143.2_Silent_p.L814L|DIP2A_ENST00000457905.3_Silent_p.L878L|DIP2A_ENST00000318711.7_Silent_p.L879L|DIP2A_ENST00000400274.1_Silent_p.L874L			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	878					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)		GAGCCGTGTGCTGCAGGTGGG	0.657													C|||	199	0.0397364	0.0091	0.0591	5008	,	,		13747	0.0149		0.0815	False		,,,				2504	0.0501				p.L878L		Atlas-SNP	.											.	DIP2A	332	.	0			c.C2632T						PASS	.	C	,,,	77,4325	60.5+/-97.4	0,77,2124	60.0	69.0	66.0		2440,2620,2632,2632	3.9	1.0	21	dbSNP_123	66	717,7883	173.7+/-224.2	28,661,3611	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146116.1,NM_015151.3,NM_206889.2	,,,	28,738,5735	TT,TC,CC		8.3372,1.7492,6.1068	,,,	814/1111,874/1568,878/1572,878/890	47969793	794,12208	2201	4300	6501	SO:0001819	synonymous_variant	23181	exon22			CGTGTGCTGCAGG	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.2632C>T	21.37:g.47969793C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_206889	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			C|0.949;T|0.051	0.051	strong		0.657	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
IL7R	3575	hgsc.bcm.edu	37	5	35876449	35876449	+	Missense_Mutation	SNP	C	C	T	rs2229232	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:35876449C>T	ENST00000303115.3	+	8	1370	c.1241C>T	c.(1240-1242)aCg>aTg	p.T414M	IL7R_ENST00000343305.4_3'UTR	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	414			T -> M (in dbSNP:rs2229232).		B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			ACAAACAGCACGCTGCCCCCT	0.517			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						C|||	69	0.013778	0.0008	0.0043	5008	,	,		19505	0.0278		0.002	False		,,,				2504	0.0358				p.T414M		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	IL7R,NS,carcinoma,-1,1	IL7R	200	1	0			c.C1241T						PASS	.	C	MET/THR	4,4402	8.1+/-20.4	0,4,2199	95.0	83.0	87.0		1241	-1.1	0.0	5	dbSNP_98	87	47,8553	30.1+/-81.4	0,47,4253	yes	missense	IL7R	NM_002185.2	81	0,51,6452	TT,TC,CC		0.5465,0.0908,0.3921	possibly-damaging	414/460	35876449	51,12955	2203	4300	6503	SO:0001583	missense	3575	exon8			ACAGCACGCTGCC	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.1241C>T	5.37:g.35876449C>T	ENSP00000306157:p.Thr414Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	26	0.011904761904761904	0	0.0	1	0.0027624309392265192	23	0.04020979020979021	2	0.002638522427440633	C	9.529	1.110228	0.20714	9.08E-4	0.005465	ENSG00000168685	ENST00000303115;ENST00000505875	T;T	0.36340	1.78;1.26	5.6	-1.06	0.10002	.	1.447760	0.03498	N	0.217605	T	0.11153	0.0272	L	0.54323	1.7	0.09310	N	0.999999	D	0.60160	0.987	P	0.47470	0.548	T	0.14448	-1.0472	10	0.52906	T	0.07	-13.3475	3.1654	0.06534	0.2999:0.3346:0.0:0.3655	rs2229232;rs2229232	414	P16871	IL7RA_HUMAN	M	414;180	ENSP00000306157:T414M;ENSP00000420923:T180M	ENSP00000306157:T414M	T	+	2	0	IL7R	35912206	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.672000	0.05244	-0.218000	0.10018	-0.345000	0.07892	ACG	C|0.989;T|0.011	0.011	strong		0.517	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
FLG	2312	hgsc.bcm.edu	37	1	152280170	152280170	+	Missense_Mutation	SNP	C	C	G	rs71625201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280170C>G	ENST00000368799.1	-	3	7227	c.7192G>C	c.(7192-7194)Gag>Cag	p.E2398Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2398	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGTGTGGACTCTTGGTGGCTC	0.587									Ichthyosis				C|||	1655	0.330471	0.1135	0.4092	5008	,	,		20923	0.5665		0.169	False		,,,				2504	0.4908				p.E2398Q		Atlas-SNP	.											.	FLG	900	.	0			c.G7192C						PASS	.	C	GLN/GLU	584,3820	250.6+/-257.6	42,500,1660	70.0	74.0	72.0		7192	-3.5	0.0	1	dbSNP_130	72	1418,7138	262.7+/-284.6	121,1176,2981	no	missense	FLG	NM_002016.1	29	163,1676,4641	GG,GC,CC		16.5732,13.2607,15.4475	benign	2398/4062	152280170	2002,10958	2202	4278	6480	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGACTCTTGGTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7192G>C	1.37:g.152280170C>G	ENSP00000357789:p.Glu2398Gln	Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	344	137	0.398256	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	602	0.27564102564102566	64	0.13008130081300814	116	0.32044198895027626	294	0.513986013986014	128	0.16886543535620052	C	10.08	1.253118	0.22965	0.132607	0.165732	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01787	4.64	3.76	-3.46	0.04767	.	.	.	.	.	T	0.00815	0.0027	M	0.78223	2.4	0.80722	P	0.0	B	0.20052	0.041	B	0.13407	0.009	T	0.39522	-0.9610	8	0.33141	T	0.24	.	4.314	0.10984	0.0:0.2844:0.322:0.3937	.	2398	P20930	FILA_HUMAN	Q	2398;308	ENSP00000357789:E2398Q	ENSP00000271820:E308Q	E	-	1	0	FLG	150546794	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.310000	0.02725	-0.408000	0.07565	-0.494000	0.04653	GAG	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PGR	5241	hgsc.bcm.edu	37	11	100998623	100998623	+	Silent	SNP	G	G	A	rs1379130	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:100998623G>A	ENST00000325455.5	-	1	2632	c.1179C>T	c.(1177-1179)ggC>ggT	p.G393G	PGR_ENST00000263463.5_Silent_p.G393G|PGR_ENST00000534013.1_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	393	Modulating, Pro-Rich.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	AGGCCTCCGCGCCTTCCTCCT	0.697													G|||	720	0.14377	0.034	0.2406	5008	,	,		10133	0.006		0.3211	False		,,,				2504	0.183				p.G393G	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C1179T						PASS	.	G	,	359,3637		37,285,1676	8.0	11.0	10.0		1179,687	1.5	1.0	11	dbSNP_88	10	2558,5530		453,1652,1939	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	490,1937,3615	AA,AG,GG		31.6271,8.984,24.1394	,	393/934,229/770	100998623	2917,9167	1998	4044	6042	SO:0001819	synonymous_variant	5241	exon1			CTCCGCGCCTTCC	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1179C>T	11.37:g.100998623G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			G|0.842;A|0.158	0.158	strong		0.697	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
DACT1	51339	hgsc.bcm.edu	37	14	59112677	59112677	+	Missense_Mutation	SNP	G	G	A	rs34015825	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:59112677G>A	ENST00000335867.4	+	4	1360	c.1336G>A	c.(1336-1338)Gac>Aac	p.D446N	DACT1_ENST00000395153.3_Missense_Mutation_p.D409N|DACT1_ENST00000556859.1_Missense_Mutation_p.D165N|DACT1_ENST00000541264.2_Missense_Mutation_p.D165N			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	446			D -> N (in dbSNP:rs34015825).		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						CGCTGCCTCCGACCTTCAGAG	0.602													G|||	165	0.0329473	0.0287	0.0375	5008	,	,		14404	0.003		0.0606	False		,,,				2504	0.0378				p.D446N		Atlas-SNP	.											.	DACT1	119	.	0			c.G1336A						PASS	.	G	ASN/ASP,ASN/ASP	138,4268	93.4+/-132.2	2,134,2067	41.0	47.0	45.0		1225,1336	5.3	0.3	14	dbSNP_126	45	469,8131	132.3+/-190.0	9,451,3840	yes	missense,missense	DACT1	NM_001079520.1,NM_016651.5	23,23	11,585,5907	AA,AG,GG		5.4535,3.1321,4.6671	benign,benign	409/800,446/837	59112677	607,12399	2203	4300	6503	SO:0001583	missense	51339	exon4			GCCTCCGACCTTC	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.1336G>A	14.37:g.59112677G>A	ENSP00000337439:p.Asp446Asn	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	78	0.03571428571428571	19	0.03861788617886179	16	0.04419889502762431	1	0.0017482517482517483	42	0.055408970976253295	G	15.69	2.909382	0.52439	0.031321	0.054535	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.35	5.35	0.76521	.	0.172795	0.49916	D	0.000130	T	0.02807	0.0084	N	0.08118	0	0.38547	D	0.949373	P;P	0.46277	0.846;0.875	B;B	0.36030	0.123;0.216	T	0.09122	-1.0689	10	0.56958	D	0.05	-10.3889	19.0563	0.93067	0.0:0.0:1.0:0.0	rs34015825	409;446	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	N	165;165;409;446;165	ENSP00000451598:D165N;ENSP00000378581:D165N;ENSP00000378582:D409N;ENSP00000337439:D446N;ENSP00000442850:D165N	ENSP00000337439:D446N	D	+	1	0	DACT1	58182430	1.000000	0.71417	0.348000	0.25681	0.454000	0.32378	4.669000	0.61575	2.519000	0.84933	0.563000	0.77884	GAC	G|0.957;A|0.043	0.043	strong		0.602	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
CDT1	81620	hgsc.bcm.edu	37	16	88872229	88872229	+	Missense_Mutation	SNP	A	A	G	rs480727	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	87	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	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	
ATP11A	23250	hgsc.bcm.edu	37	13	113536132	113536132	+	3'UTR	SNP	T	T	C	rs1290177	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:113536132T>C	ENST00000487903.1	+	0	3508				ATP11A_ENST00000375630.2_Silent_p.N1110N|ATP11A_ENST00000375645.3_Intron			P98196	AT11A_HUMAN	ATPase, class VI, type 11A						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)				CTCAGCAGAATGGGTGCGCAC	0.622													T|||	2829	0.564896	0.5802	0.5101	5008	,	,		18472	0.6359		0.497	False		,,,				2504	0.5798				p.N1110N		Atlas-SNP	.											.	ATP11A	225	.	0			c.T3330C						PASS	.	T	,	2520,1886	627.3+/-394.9	734,1052,417	65.0	65.0	65.0		,3330	-5.1	0.0	13	dbSNP_87	65	4480,4120	590.0+/-392.6	1160,2160,980	no	intron,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	1894,3212,1397	CC,CT,TT		47.907,42.8053,46.1787	,	,1110/1192	113536132	7000,6006	2203	4300	6503	SO:0001624	3_prime_UTR_variant	23250	exon29			GCAGAATGGGTGC	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.*15T>C	13.37:g.113536132T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1																																																																																			C|0.553;N|0.000	0.553	strong		0.622	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
NUF2	83540	hgsc.bcm.edu	37	1	163297322	163297322	+	Silent	SNP	A	A	C	rs16852612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:163297322A>C	ENST00000271452.3	+	3	447	c.168A>C	c.(166-168)gtA>gtC	p.V56V	NUF2_ENST00000490881.1_3'UTR|NUF2_ENST00000524800.1_Silent_p.V56V|NUF2_ENST00000367900.3_Silent_p.V56V	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	56	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					TACAAATAGTATATGGAATTC	0.353													A|||	391	0.0780751	0.0408	0.1441	5008	,	,		17943	0.0238		0.1769	False		,,,				2504	0.0358				p.V56V		Atlas-SNP	.											.	NUF2	138	.	0			c.A168C						PASS	.	A	,	238,4168	139.2+/-174.8	7,224,1972	173.0	174.0	174.0		168,168	-8.7	0.1	1	dbSNP_123	174	1443,7157	276.9+/-292.6	125,1193,2982	no	coding-synonymous,coding-synonymous	NUF2	NM_031423.3,NM_145697.2	,	132,1417,4954	CC,CA,AA		16.7791,5.4017,12.9248	,	56/465,56/465	163297322	1681,11325	2203	4300	6503	SO:0001819	synonymous_variant	83540	exon3			AATAGTATATGGA	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.168A>C	1.37:g.163297322A>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	177	84	0.474576	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Silent	SNP	ENST00000271452.3	37	CCDS1245.1																																																																																			A|0.888;C|0.112	0.112	strong		0.353	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	
LAMB3	3914	hgsc.bcm.edu	37	1	209811886	209811886	+	Silent	SNP	T	T	G	rs2076356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:209811886T>G	ENST00000356082.4	-	4	425	c.291A>C	c.(289-291)tcA>tcC	p.S97S	LAMB3_ENST00000391911.1_Silent_p.S97S|LAMB3_ENST00000367030.3_Silent_p.S97S	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	97	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.S97S(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CACCATTCTGTGACTGCCACC	0.532													T|||	2166	0.432508	0.3517	0.4582	5008	,	,		18725	0.2847		0.6412	False		,,,				2504	0.4611				p.S97S		Atlas-SNP	.											LAMB3,NS,carcinoma,0,1	LAMB3	136	1	1	Substitution - coding silent(1)	stomach(1)	c.A291C						PASS	.	T	,,	1917,2489	547.6+/-377.3	408,1101,694	96.0	75.0	82.0		291,291,291	-7.7	0.9	1	dbSNP_96	82	5556,3044	661.4+/-401.9	1792,1972,536	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	2200,3073,1230	GG,GT,TT		35.3953,43.5089,42.5419	,,	97/1173,97/1173,97/1173	209811886	7473,5533	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon4			ATTCTGTGACTGC	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.291A>C	1.37:g.209811886T>G		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			T|0.476;G|0.524	0.524	strong		0.532	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
NID1	4811	hgsc.bcm.edu	37	1	236175327	236175327	+	Missense_Mutation	SNP	C	C	A	rs3738531	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:236175327C>A	ENST00000264187.6	-	12	2503	c.2421G>T	c.(2419-2421)caG>caT	p.Q807H	NID1_ENST00000366595.3_Intron	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	807	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		Q -> H (in dbSNP:rs3738531). {ECO:0000269|Ref.6}.		basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	ATCGGCTTGGCTGGCATTCAT	0.498													C|||	974	0.194489	0.1104	0.3127	5008	,	,		14781	0.2589		0.0885	False		,,,				2504	0.2669				p.Q807H		Atlas-SNP	.											.	NID1	196	.	0			c.G2421T						PASS	.	C	HIS/GLN	485,3921	225.9+/-241.6	28,429,1746	101.0	83.0	89.0		2421	3.6	1.0	1	dbSNP_107	89	846,7754	192.8+/-238.7	40,766,3494	yes	missense	NID1	NM_002508.2	24	68,1195,5240	AA,AC,CC		9.8372,11.0077,10.2337	possibly-damaging	807/1248	236175327	1331,11675	2203	4300	6503	SO:0001583	missense	4811	exon12			GCTTGGCTGGCAT	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2421G>T	1.37:g.236175327C>A	ENSP00000264187:p.Gln807His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	351	0.16071428571428573	57	0.11585365853658537	84	0.23204419889502761	151	0.263986013986014	59	0.07783641160949868	C	16.29	3.081801	0.55861	0.110077	0.098372	ENSG00000116962	ENST00000264187	D	0.83837	-1.77	5.77	3.58	0.41010	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.048578	0.85682	D	0.000000	T	0.00039	0.0001	L	0.38175	1.15	0.09310	P	1.0	P	0.52463	0.953	P	0.61874	0.895	T	0.01617	-1.1311	9	0.46703	T	0.11	.	9.7286	0.40348	0.0:0.7536:0.0:0.2464	rs3738531;rs52819661;rs3738531	807	P14543	NID1_HUMAN	H	807	ENSP00000264187:Q807H	ENSP00000264187:Q807H	Q	-	3	2	NID1	234241950	0.990000	0.36364	0.952000	0.39060	0.916000	0.54674	1.145000	0.31577	1.425000	0.47237	0.650000	0.86243	CAG	C|0.874;A|0.126	0.126	strong		0.498	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
KIRREL3	84623	hgsc.bcm.edu	37	11	126294661	126294661	+	Silent	SNP	G	G	A	rs34844660	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126294661G>A	ENST00000525144.2	-	17	2400	c.2151C>T	c.(2149-2151)agC>agT	p.S717S	KIRREL3_ENST00000529097.2_Silent_p.S705S|KIRREL3_ENST00000416561.2_Silent_p.S184S	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	112	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	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	
METTL11B	149281	hgsc.bcm.edu	37	1	170135760	170135760	+	Missense_Mutation	SNP	T	T	C	rs6427235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:170135760T>C	ENST00000439373.2	+	3	555	c.448T>C	c.(448-450)Tcc>Ccc	p.S150P	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	150			S -> P (in dbSNP:rs6427235).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						TATGATGGAATCCTTTCTCCT	0.517													T|||	1459	0.291334	0.5076	0.2435	5008	,	,		18050	0.1349		0.2724	False		,,,				2504	0.2137				p.S150P		Atlas-SNP	.											.	METTL11B	18	.	0			c.T448C						PASS	.	T	PRO/SER	657,727		159,339,194	116.0	107.0	110.0		448	-1.3	0.6	1	dbSNP_116	110	885,2297		133,619,839	yes	missense	METTL11B	NM_001136107.1	74	292,958,1033	CC,CT,TT		27.8127,47.4711,33.7714	benign	150/284	170135760	1542,3024	692	1591	2283	SO:0001583	missense	149281	exon3			ATGGAATCCTTTC	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.448T>C	1.37:g.170135760T>C	ENSP00000408058:p.Ser150Pro	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	164	72	0.439024	NM_001136107	B2RXI0	Missense_Mutation	SNP	ENST00000439373.2	37	CCDS44275.1	610	0.2793040293040293	227	0.4613821138211382	93	0.2569060773480663	70	0.12237762237762238	220	0.29023746701846964	T	10.56	1.383329	0.25031	0.474711	0.278127	ENSG00000203740	ENST00000439373	T	0.22539	1.95	5.25	-1.26	0.09376	.	0.478630	0.25096	N	0.033178	T	0.01940	0.0061	N	0.02697	-0.525	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.44421	-0.9329	9	0.28530	T	0.3	-0.9035	5.4805	0.16721	0.2123:0.435:0.0:0.3527	rs6427235	150	Q5VVY1	NTM1B_HUMAN	P	150	ENSP00000408058:S150P	ENSP00000408058:S150P	S	+	1	0	METTL11B	168402384	0.799000	0.28903	0.609000	0.28983	0.989000	0.77384	0.422000	0.21296	0.078000	0.16900	0.533000	0.62120	TCC	T|0.719;C|0.281	0.281	strong		0.517	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
ANK1	286	hgsc.bcm.edu	37	8	41563685	41563685	+	Silent	SNP	G	G	A	rs1137177	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:41563685G>A	ENST00000347528.4	-	18	2156	c.2073C>T	c.(2071-2073)ggC>ggT	p.G691G	ANK1_ENST00000352337.4_Silent_p.G691G|ANK1_ENST00000289734.7_Silent_p.G691G|ANK1_ENST00000379758.2_Silent_p.G691G|ANK1_ENST00000396942.1_Silent_p.G691G|ANK1_ENST00000265709.8_Silent_p.G724G|ANK1_ENST00000396945.1_Silent_p.G691G	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	691	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CCACCATGACGCCGTGTTTGA	0.542													G|||	906	0.180911	0.0159	0.2954	5008	,	,		17858	0.0794		0.2823	False		,,,				2504	0.3231				p.G724G		Atlas-SNP	.											.	ANK1	497	.	0			c.C2172T						PASS	.	G	,,,,	250,4156	145.4+/-180.2	7,236,1960	82.0	73.0	76.0		2073,2172,2073,2073,2073	-10.6	0.0	8	dbSNP_86	76	2304,6296	387.5+/-342.2	320,1664,2316	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	327,1900,4276	AA,AG,GG		26.7907,5.6741,19.6371	,,,,	691/1881,724/1898,691/1857,691/1882,691/1720	41563685	2554,10452	2203	4300	6503	SO:0001819	synonymous_variant	286	exon18			CATGACGCCGTGT	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2073C>T	8.37:g.41563685G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	369	0.16895604395604397	11	0.022357723577235773	100	0.27624309392265195	37	0.06468531468531469	221	0.29155672823219	G	0.494	-0.874159	0.02550	0.056741	0.267907	ENSG00000029534	ENST00000520299	.	.	.	5.32	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999952	.	.	.	.	.	.	T	0.17228	-1.0376	3	.	.	.	.	1.3955	0.02260	0.2645:0.2406:0.3132:0.1818	rs1137177;rs2304878;rs3200981;rs17424473;rs17602822;rs1137177	.	.	.	C	5	.	.	R	-	1	0	ANK1	41682842	0.002000	0.14202	0.002000	0.10522	0.035000	0.12851	-1.576000	0.02129	-3.094000	0.00246	-1.075000	0.02238	CGT	G|0.832;N|0.000	.	strong		0.542	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
OR2F2	135948	hgsc.bcm.edu	37	7	143632984	143632984	+	Missense_Mutation	SNP	G	G	A	rs61740239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:143632984G>A	ENST00000408955.2	+	1	726	c.659G>A	c.(658-660)cGg>cAg	p.R220Q		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					TCCTACATCCGGATCATCTCC	0.527													g|||	149	0.0297524	0.0234	0.0202	5008	,	,		21654	0.0288		0.0408	False		,,,				2504	0.0348				p.R220Q		Atlas-SNP	.											.	OR2F2	63	.	0			c.G659A						PASS	.	A	GLN/ARG	126,4280	93.0+/-131.7	2,122,2079	170.0	155.0	160.0		659	-7.0	0.0	7	dbSNP_129	160	300,8300	109.0+/-169.6	7,286,4007	yes	missense	OR2F2	NM_001004685.1	43	9,408,6086	AA,AG,GG		3.4884,2.8597,3.2754	benign	220/318	143632984	426,12580	2203	4300	6503	SO:0001583	missense	135948	exon1			ACATCCGGATCAT		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"""GPCR / Class A : Olfactory receptors"""	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.659G>A	7.37:g.143632984G>A	ENSP00000386222:p.Arg220Gln	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	257	123	0.478599	NM_001004685	A4D2G0|Q6IFP8	Missense_Mutation	SNP	ENST00000408955.2	37	CCDS43666.1	64	0.029304029304029304	9	0.018292682926829267	10	0.027624309392265192	15	0.026223776223776224	30	0.0395778364116095	g	0.052	-1.246956	0.01481	0.028597	0.034884	ENSG00000221910	ENST00000408955	T	0.00031	8.89	3.61	-7.02	0.01589	GPCR, rhodopsin-like superfamily (1);	1.058040	0.07431	N	0.895644	T	0.00039	0.0001	L	0.35854	1.095	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.03268	-1.1054	10	0.25106	T	0.35	-0.3632	8.2488	0.31704	0.3675:0.0:0.5166:0.116	rs61740239	220	O95006	OR2F2_HUMAN	Q	220	ENSP00000386222:R220Q	ENSP00000386222:R220Q	R	+	2	0	OR2F2	143263917	0.000000	0.05858	0.003000	0.11579	0.061000	0.15899	-1.199000	0.03032	-1.909000	0.01085	-2.879000	0.00098	CGG	G|0.965;A|0.035	0.035	strong		0.527	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1		
MUC16	94025	hgsc.bcm.edu	37	19	9060125	9060125	+	Silent	SNP	G	G	A	rs12972088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9060125G>A	ENST00000397910.4	-	3	27524	c.27321C>T	c.(27319-27321)caC>caT	p.H9107H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9109	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATGCAGTTGAGTGGGTCCCTG	0.483													G|||	1053	0.210264	0.2595	0.2118	5008	,	,		23165	0.0099		0.3121	False		,,,				2504	0.2444				p.H9107H		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27321T						PASS	.	G		945,2921		98,749,1086	126.0	116.0	119.0		27321	-3.1	0.0	19	dbSNP_121	119	2804,5482		499,1806,1838	no	coding-synonymous	MUC16	NM_024690.2		597,2555,2924	AA,AG,GG		33.8402,24.4439,30.8509		9107/14508	9060125	3749,8403	1933	4143	6076	SO:0001819	synonymous_variant	94025	exon3			AGTTGAGTGGGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27321C>T	19.37:g.9060125G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	156	79	0.50641	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.760;A|0.240	0.240	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KALRN	8997	hgsc.bcm.edu	37	3	124196094	124196094	+	Silent	SNP	A	A	T	rs2289843	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:124196094A>T	ENST00000240874.3	+	27	4255	c.4098A>T	c.(4096-4098)gcA>gcT	p.A1366A	KALRN_ENST00000460856.1_Silent_p.A1357A|KALRN_ENST00000360013.3_Silent_p.A1366A	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1366	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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.A1366A(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						CTTTTTAGGCAGACAAATTTC	0.423													A|||	988	0.197284	0.0159	0.2421	5008	,	,		19682	0.498		0.1292	False		,,,				2504	0.1708				p.A1366A		Atlas-SNP	.											KALRN_ENST00000360013,NS,carcinoma,0,2	KALRN	556	2	2	Substitution - coding silent(2)	stomach(2)	c.A4098T						PASS	.	A	,	161,4245	107.3+/-145.7	2,157,2044	131.0	126.0	128.0		4098,4098	2.8	1.0	3	dbSNP_100	128	941,7659	205.6+/-248.0	52,837,3411	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	54,994,5455	TT,TA,AA		10.9419,3.6541,8.473	,	1366/2987,1366/1664	124196094	1102,11904	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon27			TTAGGCAGACAAA	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.4098A>T	3.37:g.124196094A>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	56	0.4375	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	473	0.21657509157509158	11	0.022357723577235773	73	0.20165745856353592	285	0.4982517482517482	104	0.13720316622691292	A	12.22	1.872263	0.33069	0.036541	0.109419	ENSG00000160145	ENST00000354186	.	.	.	5.22	2.82	0.32997	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48043	-0.9069	3	.	.	.	.	4.4483	0.11609	0.4962:0.3335:0.1703:0.0	rs2289843;rs60272149;rs2289843	.	.	.	L	1335	.	.	Q	+	2	0	KALRN	125678784	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	0.657000	0.24963	0.435000	0.26365	0.533000	0.62120	CAG	A|0.862;T|0.138	0.138	strong		0.423	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
KCNK6	9424	hgsc.bcm.edu	37	19	38817486	38817486	+	Silent	SNP	T	T	C	rs3745951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38817486T>C	ENST00000263372.3	+	2	683	c.576T>C	c.(574-576)ttT>ttC	p.F192F		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	192					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	CTGTGATCTTTGCCCACCTCG	0.652													C|||	896	0.178914	0.0673	0.2507	5008	,	,		16393	0.1518		0.2217	False		,,,				2504	0.2628				p.F192F		Atlas-SNP	.											.	KCNK6	37	.	0			c.T576C						PASS	.	C		389,4017	791.1+/-415.1	28,333,1842	144.0	138.0	140.0		576	-3.4	0.0	19	dbSNP_107	140	1603,6997	742.8+/-407.2	149,1305,2846	no	coding-synonymous	KCNK6	NM_004823.1		177,1638,4688	CC,CT,TT		18.6395,8.8289,15.316		192/314	38817486	1992,11014	2203	4300	6503	SO:0001819	synonymous_variant	9424	exon2			GATCTTTGCCCAC	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.576T>C	19.37:g.38817486T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_004823	Q9HB47	Silent	SNP	ENST00000263372.3	37	CCDS12513.1																																																																																			T|0.836;C|0.164	0.164	strong		0.652	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
FHAD1	114827	hgsc.bcm.edu	37	1	15708557	15708557	+	Silent	SNP	G	G	A	rs35816204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15708557G>A	ENST00000375998.4	+	29	3990	c.3990G>A	c.(3988-3990)tcG>tcA	p.S1330S	FHAD1_ENST00000358897.4_Silent_p.S1330S|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Silent_p.S583S|FHAD1_ENST00000375999.3_Silent_p.S1330S|FHAD1_ENST00000417793.1_Silent_p.S1294S			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1330										skin(1)|stomach(1)	2						TGTACCAGTCGCAGGTGGCAA	0.542													G|||	64	0.0127796	0.0015	0.0173	5008	,	,		21738	0.0		0.0437	False		,,,				2504	0.0061				p.S1330S		Atlas-SNP	.											.	FHAD1	78	.	0			c.G3990A						PASS	.	G		7,1377		0,7,685	70.0	72.0	71.0		3990	-6.5	0.7	1	dbSNP_126	71	102,3080		1,100,1490	no	coding-synonymous	FHAD1	NM_052929.1		1,107,2175	AA,AG,GG		3.2055,0.5058,2.3872		1330/1413	15708557	109,4457	692	1591	2283	SO:0001819	synonymous_variant	114827	exon30			CCAGTCGCAGGTG	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.3990G>A	1.37:g.15708557G>A		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	318	147	0.462264	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37		49	0.022435897435897436	6	0.012195121951219513	10	0.027624309392265192	0	0.0	33	0.04353562005277045	G	4.900	0.167197	0.09339	0.005058	0.032055	ENSG00000142621	ENST00000444385	.	.	.	5.95	-6.47	0.01902	.	.	.	.	.	T	0.18383	0.0441	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46034	-0.9220	4	.	.	.	-10.4491	8.2849	0.31922	0.2893:0.2408:0.4699:0.0	rs35816204	.	.	.	H	649	.	.	R	+	2	0	FHAD1	15581144	0.000000	0.05858	0.746000	0.31095	0.416000	0.31233	-2.185000	0.01252	-1.616000	0.01572	-1.224000	0.01588	CGC	G|0.975;A|0.025	0.025	strong		0.542	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
PPFIA4	8497	hgsc.bcm.edu	37	1	203028371	203028371	+	Missense_Mutation	SNP	G	G	T	rs61732315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:203028371G>T	ENST00000447715.2	+	25	2848	c.2407G>T	c.(2407-2409)Gca>Tca	p.A803S	PPFIA4_ENST00000599966.1_Missense_Mutation_p.A319S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.A319S|PPFIA4_ENST00000414050.2_Missense_Mutation_p.A532S|PPFIA4_ENST00000367240.2_Missense_Mutation_p.A804S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.A319S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	803				A -> S (in Ref. 3; AAI44263). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						GGGGACCCAGGCAGAGAAGGA	0.602													G|||	610	0.121805	0.0129	0.1196	5008	,	,		18586	0.1577		0.1759	False		,,,				2504	0.1779				p.A319S		Atlas-SNP	.											.	PPFIA4	139	.	0			c.G955T						PASS	.	G	SER/ALA	150,3658		5,140,1759	18.0	20.0	19.0		955	4.8	1.0	1	dbSNP_129	19	1379,6841		122,1135,2853	yes	missense	PPFIA4	NM_015053.1	99	127,1275,4612	TT,TG,GG		16.7762,3.9391,12.712	possibly-damaging	319/702	203028371	1529,10499	1904	4110	6014	SO:0001583	missense	8497	exon7			ACCCAGGCAGAGA	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2407G>T	1.37:g.203028371G>T	ENSP00000402576:p.Ala803Ser	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	251	123	0.49004	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		257	0.11767399267399267	11	0.022357723577235773	37	0.10220994475138122	68	0.11888111888111888	141	0.18601583113456466	G	19.80	3.894080	0.72639	0.039391	0.167762	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.25085	2.17;1.85;1.82;1.84;1.82	4.83	4.83	0.62350	.	0.000000	0.45126	D	0.000395	T	0.00073	0.0002	M	0.66939	2.045	0.09310	P	0.999999060264	B;B;P;P	0.48089	0.011;0.011;0.905;0.665	B;B;P;P	0.57720	0.01;0.054;0.826;0.563	T	0.02417	-1.1162	9	0.48119	T	0.1	-10.7022	11.5666	0.50809	0.0813:0.0:0.9187:0.0	rs61732315	803;14;319;319	B1N949;B3KN22;O75335-2;O75335	.;.;.;LIPA4_HUMAN	S	804;803;319;532;319	ENSP00000356209:A804S;ENSP00000402576:A803S;ENSP00000295706:A319S;ENSP00000400379:A532S;ENSP00000272198:A319S	ENSP00000272198:A319S	A	+	1	0	PPFIA4	201294994	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.834000	0.86773	2.495000	0.84180	0.462000	0.41574	GCA	G|0.878;T|0.122	0.122	strong		0.602	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111611076	111611076	+	Silent	SNP	A	A	G	rs12521830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:111611076A>G	ENST00000261486.5	-	4	558	c.282T>C	c.(280-282)ttT>ttC	p.F94F		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	94	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		ATTTAATACCAAAATACAAAG	0.264													A|||	1616	0.322684	0.4077	0.3545	5008	,	,		17567	0.3413		0.337	False		,,,				2504	0.1513				p.F94F		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.T282C						PASS	.	A		1431,2089		312,807,641	48.0	54.0	52.0		282	4.4	1.0	5	dbSNP_120	52	2837,5193		528,1781,1706	no	coding-synonymous	EPB41L4A	NM_022140.3		840,2588,2347	GG,GA,AA		35.33,40.6534,36.9524		94/687	111611076	4268,7282	1760	4015	5775	SO:0001819	synonymous_variant	64097	exon4			AATACCAAAATAC	AB030240	CCDS43350.1	5q21.3	2008-02-05			ENSG00000129595	ENSG00000129595			13278	protein-coding gene	gene with protein product		612141				10874211	Standard	XM_005272043		Approved	NBL4	uc003kpv.1	Q9HCS5	OTTHUMG00000162902	ENST00000261486.5:c.282T>C	5.37:g.111611076A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	146	144	0.986301	NM_022140	A4FUI6	Silent	SNP	ENST00000261486.5	37	CCDS43350.1																																																																																			A|0.639;G|0.361	0.361	strong		0.264	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		
DNAH7	56171	hgsc.bcm.edu	37	2	196922836	196922836	+	Missense_Mutation	SNP	T	T	A	rs72917299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:196922836T>A	ENST00000312428.6	-	2	120	c.20A>T	c.(19-21)aAa>aTa	p.K7I	DNAH7_ENST00000410072.1_Missense_Mutation_p.K7I	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	7	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GCTGGCCGATTTATCCTGTAT	0.313													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		16097	0.0		0.0129	False		,,,				2504	0.0				p.K7I		Atlas-SNP	.											.	DNAH7	512	.	0			c.A20T						PASS	.	T	ILE/LYS	10,3592		0,10,1791	181.0	174.0	176.0		20	4.3	0.9	2	dbSNP_130	176	108,8028		1,106,3961	yes	missense	DNAH7	NM_018897.2	102	1,116,5752	AA,AT,TT		1.3274,0.2776,1.0053	possibly-damaging	7/4025	196922836	118,11620	1801	4068	5869	SO:0001583	missense	56171	exon2			GCCGATTTATCCT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.20A>T	2.37:g.196922836T>A	ENSP00000311273:p.Lys7Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	10	0.013192612137203167	T	13.85	2.361068	0.41801	0.002776	0.013274	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23754	1.89;2.52	4.29	4.29	0.51040	.	.	.	.	.	T	0.26919	0.0659	N	0.22421	0.69	0.31255	N	0.693556	D	0.65815	0.995	D	0.75484	0.986	T	0.19712	-1.0297	9	0.87932	D	0	.	10.1288	0.42665	0.0:0.0:0.0:1.0	.	7	Q8WXX0	DYH7_HUMAN	I	7	ENSP00000311273:K7I;ENSP00000386260:K7I	ENSP00000311273:K7I	K	-	2	0	DNAH7	196631081	0.996000	0.38824	0.876000	0.34364	0.572000	0.35998	3.399000	0.52586	2.155000	0.67459	0.460000	0.39030	AAA	T|0.991;A|0.009	0.009	strong		0.313	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
OR52J3	119679	hgsc.bcm.edu	37	11	5068297	5068297	+	Missense_Mutation	SNP	G	G	A	rs58664826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5068297G>A	ENST00000380370.1	+	1	542	c.542G>A	c.(541-543)tGt>tAt	p.C181Y		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|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)		CATTCCTACTGTGAGCACATG	0.423													G|||	504	0.100639	0.0242	0.2767	5008	,	,		23123	0.0863		0.1372	False		,,,				2504	0.0562				p.C181Y		Atlas-SNP	.											.	OR52J3	77	.	0			c.G542A						PASS	.	G	TYR/CYS	164,4238	109.5+/-147.8	2,160,2039	198.0	169.0	179.0		542	4.2	1.0	11	dbSNP_129	179	1059,7537	224.4+/-260.8	66,927,3305	yes	missense	OR52J3	NM_001001916.2	194	68,1087,5344	AA,AG,GG		12.3197,3.7256,9.4091	probably-damaging	181/312	5068297	1223,11775	2201	4298	6499	SO:0001583	missense	119679	exon1			CCTACTGTGAGCA	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.542G>A	11.37:g.5068297G>A	ENSP00000369728:p.Cys181Tyr	Somatic	337	1	0.00296736		WXS	Illumina HiSeq	Phase_I	365	177	0.484931	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	250	0.11446886446886446	11	0.022357723577235773	78	0.2154696132596685	62	0.10839160839160839	99	0.13060686015831136	G	19.90	3.912644	0.72983	0.037256	0.123197	ENSG00000205495	ENST00000380370	T	0.61980	0.06	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000088	T	0.00210	0.0006	M	0.94101	3.495	0.21290	P	0.999736777	D	0.89917	1.0	D	0.97110	1.0	T	0.09618	-1.0666	9	0.87932	D	0	.	15.2669	0.73669	0.0:0.0:1.0:0.0	rs58664826;rs61729561	181	Q8NH60	O52J3_HUMAN	Y	181	ENSP00000369728:C181Y	ENSP00000369728:C181Y	C	+	2	0	OR52J3	5024873	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.316000	0.79007	2.143000	0.66587	0.655000	0.94253	TGT	G|0.894;A|0.106	0.106	strong		0.423	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
PDZD7	79955	hgsc.bcm.edu	37	10	102783354	102783354	+	Silent	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:102783354C>G	ENST00000370215.3	-	4	606	c.381G>C	c.(379-381)ctG>ctC	p.L127L	PDZD7_ENST00000470414.1_Silent_p.L127L	NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	127	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		CCCCCACGCACAGGCCAGCCC	0.652																																					p.L127L		Atlas-SNP	.											.	PDZD7	101	.	0			c.G381C						PASS	.						63.0	54.0	57.0					10																	102783354		2203	4300	6503	SO:0001819	synonymous_variant	79955	exon4			CACGCACAGGCCA	AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.381G>C	10.37:g.102783354C>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001195263	D5FJ77|Q8N321	Silent	SNP	ENST00000370215.3	37	CCDS31269.1																																																																																			.	.	none		0.652	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895	
YIF1B	90522	hgsc.bcm.edu	37	19	38798086	38798086	+	Silent	SNP	T	T	C	rs3178327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38798086T>C	ENST00000339413.6	-	7	816	c.771A>G	c.(769-771)gtA>gtG	p.V257V	YIF1B_ENST00000392124.3_Silent_p.V226V|YIF1B_ENST00000329420.8_Silent_p.V242V|YIF1B_ENST00000591755.1_Silent_p.V254V|YIF1B_ENST00000592246.1_Silent_p.V191V|YIF1B_ENST00000337679.8_Silent_p.V254V|YIF1B_ENST00000587361.1_5'Flank|YIF1B_ENST00000591784.1_Silent_p.V226V|YIF1B_ENST00000592694.1_Silent_p.V226V	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	257						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAAAGATGGCTACGCAGCACC	0.622													C|||	1876	0.374601	0.1581	0.4712	5008	,	,		17154	0.5823		0.326	False		,,,				2504	0.4346				p.V257V		Atlas-SNP	.											YIF1B_ENST00000339413,NS,carcinoma,-2,3	YIF1B	47	3	0			c.A771G						PASS	.	C	,,,,,,	819,3587	744.1+/-411.5	72,675,1456	84.0	74.0	77.0		726,771,762,720,678,762,678	2.3	0.4	19	dbSNP_105	77	2373,6227	699.3+/-405.1	316,1741,2243	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YIF1B	NM_001039671.2,NM_001039672.2,NM_001039673.2,NM_001145461.1,NM_001145462.1,NM_001145463.1,NM_033557.3	,,,,,,	388,2416,3699	CC,CT,TT		27.593,18.5883,24.5425	,,,,,,	242/300,257/315,254/312,240/298,226/284,254/292,226/284	38798086	3192,9814	2203	4300	6503	SO:0001819	synonymous_variant	90522	exon7			GATGGCTACGCAG	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.771A>G	19.37:g.38798086T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	100	56	0.56	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Silent	SNP	ENST00000339413.6	37	CCDS33010.1																																																																																			T|0.699;C|0.301	0.301	strong		0.622	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557	
VWDE	221806	hgsc.bcm.edu	37	7	12410362	12410362	+	Silent	SNP	C	C	T	rs1072557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	189	0	0		WXS	Illumina HiSeq	Phase_I	173	90	0.520231	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	
POLR1D	51082	hgsc.bcm.edu	37	13	28239970	28239970	+	Silent	SNP	G	G	A	rs14105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28239970G>A	ENST00000399697.3	+	3	367	c.249G>A	c.(247-249)ccG>ccA	p.P83P	POLR1D_ENST00000465887.1_3'UTR	NM_001206559.1|NM_152705.2	NP_001193488.1|NP_689918.1	Q9Y2S0	RPAC2_HUMAN	polymerase (RNA) I polypeptide D, 16kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.P83P(1)		endometrium(1)|large_intestine(1)|lung(4)|stomach(2)	8		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0758)|OV - Ovarian serous cystadenocarcinoma(117;0.1)|Epithelial(112;0.213)		AAGAAAACCCGAAGAAACACA	0.507													g|||	1862	0.371805	0.2042	0.5706	5008	,	,		16564	0.3363		0.4115	False		,,,				2504	0.453				p.P83P		Atlas-SNP	.											POLR1D,NS,carcinoma,0,1	POLR1D	31	1	1	Substitution - coding silent(1)	stomach(1)	c.G249A						scavenged	.	A	,	961,3445	362.4+/-316.1	110,741,1352	112.0	114.0	113.0		165,249	-10.2	0.0	13	dbSNP_52	113	3712,4888	529.7+/-381.6	791,2130,1379	no	coding-synonymous,coding-synonymous	POLR1D	NM_001206559.1,NM_152705.2	,	901,2871,2731	AA,AG,GG		43.1628,21.8112,35.9296	,	55/95,83/123	28239970	4673,8333	2203	4300	6503	SO:0001819	synonymous_variant	51082	exon3			AAACCCGAAGAAA	AF077044, BC018528	CCDS9324.1, CCDS9325.1, CCDS73555.1	13q12.2	2013-01-21			ENSG00000186184	ENSG00000186184		"""RNA polymerase subunits"""	20422	protein-coding gene	gene with protein product		613715				11042152, 12391170	Standard	NM_015972		Approved	RPAC2, RPA16, RPO1-3, RPA9, MGC9850	uc001urp.3	Q9Y2S0	OTTHUMG00000016635	ENST00000399697.3:c.249G>A	13.37:g.28239970G>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_152705	Q5TBX2|Q96BR3	Silent	SNP	ENST00000399697.3	37	CCDS9324.1																																																																																			G|0.646;A|0.354	0.354	strong		0.507	POLR1D-004	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044306.1	NM_015972, NM_152705	
ZNF492	57615	hgsc.bcm.edu	37	19	22847084	22847084	+	Missense_Mutation	SNP	G	G	T	rs139985933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	398	1	0.00251256		WXS	Illumina HiSeq	Phase_I	410	169	0.412195	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	
FLG	2312	hgsc.bcm.edu	37	1	152276871	152276871	+	Silent	SNP	A	A	G	rs3126066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276871A>G	ENST00000368799.1	-	3	10526	c.10491T>C	c.(10489-10491)gaT>gaC	p.D3497D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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	302	0	0		WXS	Illumina HiSeq	Phase_I	306	157	0.513072	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	
DAAM1	23002	hgsc.bcm.edu	37	14	59789892	59789892	+	Silent	SNP	G	G	T	rs17096074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:59789892G>T	ENST00000395125.1	+	5	746	c.723G>T	c.(721-723)ctG>ctT	p.L241L	DAAM1_ENST00000351081.1_Silent_p.L241L|DAAM1_ENST00000360909.3_Silent_p.L241L	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	241	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AGAAGGTTCTGCAGGCCATGC	0.552													G|||	147	0.029353	0.0053	0.0375	5008	,	,		18273	0.0109		0.0865	False		,,,				2504	0.0164				p.L241L		Atlas-SNP	.											DAAM1,NS,carcinoma,+2,1	DAAM1	95	1	0			c.G723T						PASS	.	G		67,4339	64.1+/-101.4	0,67,2136	26.0	26.0	26.0		723	5.1	1.0	14	dbSNP_123	26	784,7816	180.3+/-229.3	32,720,3548	no	coding-synonymous	DAAM1	NM_014992.1		32,787,5684	TT,TG,GG		9.1163,1.5207,6.5431		241/1079	59789892	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon6			GGTTCTGCAGGCC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.723G>T	14.37:g.59789892G>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	133	74	0.556391	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	
CD69	969	hgsc.bcm.edu	37	12	9906179	9906179	+	Silent	SNP	G	G	A	rs11052883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:9906179G>A	ENST00000228434.3	-	5	578	c.498C>T	c.(496-498)aaC>aaT	p.N166N		NM_001781.2	NP_001772.1	Q07108	CD69_HUMAN	CD69 molecule	166	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular response to drug (GO:0035690)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						ACCCTGTAACGTTGAACCTGT	0.358													G|||	63	0.0125799	0.0015	0.0303	5008	,	,		18994	0.0		0.0348	False		,,,				2504	0.0051				p.N166N		Atlas-SNP	.											CD69,NS,carcinoma,-1,1	CD69	23	1	0			c.C498T						PASS	.	G		41,4365	43.8+/-77.6	0,41,2162	43.0	43.0	43.0		498	5.1	0.8	12	dbSNP_120	43	414,8186	129.7+/-187.7	8,398,3894	yes	coding-synonymous	CD69	NM_001781.2		8,439,6056	AA,AG,GG		4.814,0.9305,3.4984		166/200	9906179	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	969	exon5			TGTAACGTTGAAC	Z22576	CCDS8604.1	12p13	2011-08-30	2006-03-28		ENSG00000110848	ENSG00000110848		"""C-type lectin domain containing"", ""CD molecules"""	1694	protein-coding gene	gene with protein product		107273	"""CD69 antigen (p60, early T-cell activation antigen)"""			1612643	Standard	NM_001781		Approved	CLEC2C	uc001qwk.3	Q07108	OTTHUMG00000168481	ENST00000228434.3:c.498C>T	12.37:g.9906179G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_001781		Silent	SNP	ENST00000228434.3	37	CCDS8604.1																																																																																			G|0.970;A|0.030	0.030	strong		0.358	CD69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399876.1		
HSPA1L	3305	hgsc.bcm.edu	37	6	31778529	31778529	+	Silent	SNP	C	C	T	rs2075799	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	119	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	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		
MDM1	56890	hgsc.bcm.edu	37	12	68709892	68709892	+	Missense_Mutation	SNP	C	C	T	rs17224810	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:68709892C>T	ENST00000303145.7	-	8	1233	c.1147G>A	c.(1147-1149)Gtt>Att	p.V383I	MDM1_ENST00000411698.2_Missense_Mutation_p.V348I|MDM1_ENST00000540418.1_Missense_Mutation_p.V103I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	383			V -> I (in dbSNP:rs17224810).		retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		TTGCTACTAACGGTTCCTTCT	0.408													C|||	687	0.137181	0.059	0.3098	5008	,	,		19331	0.1131		0.1859	False		,,,				2504	0.0951				p.V383I		Atlas-SNP	.											MDM1,caecum,carcinoma,+1,1	MDM1	74	1	0			c.G1147A						PASS	.	C	ILE/VAL,ILE/VAL	396,4010	197.1+/-221.3	19,358,1826	86.0	80.0	82.0		1042,1147	-6.2	0.0	12	dbSNP_123	82	1678,6922	307.6+/-308.5	189,1300,2811	yes	missense,missense	MDM1	NM_001205028.1,NM_017440.4	29,29	208,1658,4637	TT,TC,CC		19.5116,8.9877,15.9465	benign,benign	348/680,383/715	68709892	2074,10932	2203	4300	6503	SO:0001583	missense	56890	exon8			TACTAACGGTTCC	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"""Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"""			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1147G>A	12.37:g.68709892C>T	ENSP00000302537:p.Val383Ile	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	122	120	0.983607	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	320	0.14652014652014653	26	0.052845528455284556	94	0.2596685082872928	66	0.11538461538461539	134	0.17678100263852242	C	0.004	-2.246298	0.00271	0.089877	0.195116	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.19105	2.17;2.17;2.17	5.77	-6.15	0.02105	.	0.637167	0.15333	N	0.267906	T	0.00012	0.0000	N	0.04203	-0.255	0.34656	P	0.27787300000000004	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.41413	-0.9510	8	.	.	.	-2.47	15.5588	0.76223	0.0:0.5298:0.0:0.4702	rs17224810;rs52820856;rs56563436;rs56944808;rs17224810	348;383	E7EPQ3;Q8TC05	.;MDM1_HUMAN	I	103;383;348	ENSP00000443815:V103I;ENSP00000302537:V383I;ENSP00000391006:V348I	.	V	-	1	0	MDM1	66996159	0.310000	0.24527	0.043000	0.18650	0.010000	0.07245	-0.243000	0.08915	-1.379000	0.02118	-2.048000	0.00412	GTT	C|0.857;T|0.143	0.143	strong		0.408	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
CD81	975	hgsc.bcm.edu	37	11	2417935	2417935	+	Silent	SNP	T	T	C	rs2229751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:2417935T>C	ENST00000263645.5	+	7	895	c.639T>C	c.(637-639)gcT>gcC	p.A213A	CD81_ENST00000492627.1_Silent_p.A142A|CD81_ENST00000381036.3_Silent_p.A251A|CD81_ENST00000526072.1_Silent_p.A142A|CD81_ENST00000481687.1_Silent_p.A219A	NM_004356.3	NP_004347.1	P60033	CD81_HUMAN	CD81 molecule	213					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of 1-phosphatidylinositol 4-kinase activity (GO:0043128)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization (GO:0008104)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of immune response (GO:0050776)|viral entry into host cell (GO:0046718)	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)|vesicle (GO:0031982)	MHC class II protein complex binding (GO:0023026)			endometrium(1)|lung(3)|skin(1)	5		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;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)		TCGTGGTCGCTGTGATCATGG	0.672													C|||	611	0.122005	0.3797	0.0389	5008	,	,		14509	0.0317		0.0149	False		,,,				2504	0.0358				p.A213A		Atlas-SNP	.											.	CD81	11	.	0			c.T639C						PASS	.	C		1440,2964	676.0+/-403.2	234,972,996	70.0	69.0	69.0		639	-6.8	0.9	11	dbSNP_98	69	96,8502	812.8+/-407.0	0,96,4203	no	coding-synonymous	CD81	NM_004356.3		234,1068,5199	CC,CT,TT		1.1165,32.6975,11.8136		213/237	2417935	1536,11466	2202	4299	6501	SO:0001819	synonymous_variant	975	exon7			GGTCGCTGTGATC		CCDS7734.1, CCDS73240.1	11p15.5	2014-09-17	2006-03-28		ENSG00000110651	ENSG00000110651		"""CD molecules"", ""Tetraspanins"""	1701	protein-coding gene	gene with protein product		186845	"""CD81 antigen (target of antiproliferative antibody 1)"""	TAPA1		1650385	Standard	XM_005253260		Approved	TAPA-1, TSPAN28	uc001lwf.1	P60033	OTTHUMG00000009892	ENST00000263645.5:c.639T>C	11.37:g.2417935T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_004356	P18582|Q5U0J6	Silent	SNP	ENST00000263645.5	37	CCDS7734.1	214	0.09798534798534798	181	0.3678861788617886	14	0.03867403314917127	13	0.022727272727272728	6	0.0079155672823219	C	9.923	1.212674	0.22289	0.326975	0.011165	ENSG00000110651	ENST00000464784	.	.	.	3.39	-6.79	0.01715	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21782	P	0.99954863	.	.	.	.	.	.	T	0.39583	-0.9607	3	.	.	.	.	2.2106	0.03946	0.2049:0.4112:0.1113:0.2725	rs2229751;rs12275019;rs2229751	.	.	.	P	198	.	.	L	+	2	0	CD81	2374511	0.000000	0.05858	0.860000	0.33809	0.896000	0.52359	-3.414000	0.00479	-2.053000	0.00901	-0.355000	0.07637	CTG	T|0.890;C|0.110	0.110	strong		0.672	CD81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027357.4	NM_004356	
ARSG	22901	hgsc.bcm.edu	37	17	66364691	66364691	+	Missense_Mutation	SNP	C	C	G	rs1558876	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:66364691C>G	ENST00000448504.2	+	7	1503	c.707C>G	c.(706-708)aCc>aGc	p.T236S	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Missense_Mutation_p.T72S	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	236			T -> S (in dbSNP:rs1558876).		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)			TGTTTCAGCACCAGCGGGAGG	0.597													C|||	1382	0.275958	0.1914	0.3934	5008	,	,		18964	0.126		0.4076	False		,,,				2504	0.3262				p.T236S		Atlas-SNP	.											.	ARSG	55	.	0			c.C707G						PASS	.	C	SER/THR	984,3422	363.6+/-316.6	121,742,1340	62.0	62.0	62.0		707	4.2	1.0	17	dbSNP_88	62	3769,4831	530.3+/-381.8	834,2101,1365	yes	missense	ARSG	NM_014960.3	58	955,2843,2705	GG,GC,CC		43.8256,22.3332,36.5447	benign	236/526	66364691	4753,8253	2203	4300	6503	SO:0001583	missense	22901	exon7			TCAGCACCAGCGG	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.707C>G	17.37:g.66364691C>G	ENSP00000407193:p.Thr236Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	624	0.2857142857142857	92	0.18699186991869918	137	0.3784530386740331	80	0.13986013986013987	315	0.4155672823218997	C	3.051	-0.195352	0.06259	0.223332	0.438256	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.26	4.24	0.50183	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.713760	0.13649	N	0.372438	T	0.00012	0.0000	N	0.16478	0.41	0.44492	P	0.002569999999999961	B	0.18166	0.026	B	0.18871	0.023	T	0.37126	-0.9719	8	0.38643	T	0.18	.	12.9999	0.58670	0.2038:0.7962:0.0:0.0	rs1558876;rs3826352;rs17739339;rs52794112;rs58616018;rs1558876	236	Q96EG1	ARSG_HUMAN	S	236;135	.	ENSP00000407193:T135S	T	+	2	0	ARSG	63876286	0.184000	0.23200	0.962000	0.40283	0.373000	0.29922	2.123000	0.41996	2.733000	0.93635	0.655000	0.94253	ACC	C|0.673;G|0.327	0.327	strong		0.597	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
CLCA4	22802	hgsc.bcm.edu	37	1	87045902	87045902	+	Silent	SNP	A	A	T	rs1932809|rs4001061|rs77067122|rs56040873|rs574759485|rs368263974	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:87045902A>T	ENST00000370563.3	+	14	2676	c.2634A>T	c.(2632-2634)acA>acT	p.T878T	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	878			Missing. {ECO:0000269|PubMed:10437792, 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)		TTGAtcctacacctactccta	0.348														35	0.00698882	0.0234	0.0014	5008	,	,		16699	0.002		0.001	False		,,,				2504	0.0				p.T878T		Atlas-SNP	.											.	CLCA4	131	.	0			c.A2634T						PASS	.	A		815,2361		278,259,1051	73.0	63.0	66.0		2634	-1.3	0.0	1	dbSNP_92	66	2425,4057		1007,411,1823	no	coding-synonymous	CLCA4	NM_012128.3		1285,670,2874	TT,TA,AA		37.4113,25.6612,33.5473		878/920	87045902	3240,6418	1588	3241	4829	SO:0001819	synonymous_variant	22802	exon14			TCCTACACCTACT	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.2634A>T	1.37:g.87045902A>T		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	82	79	0.963415	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Silent	SNP	ENST00000370563.3	37	CCDS41355.1																																																																																			A|0.601;T|0.399	0.399	strong		0.348	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
OR5P2	120065	hgsc.bcm.edu	37	11	7818190	7818190	+	Silent	SNP	C	C	T	rs73406607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7818190C>T	ENST00000329434.2	-	1	330	c.300G>A	c.(298-300)gcG>gcA	p.A100A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAAAGAAAGCCGCTGAACCAA	0.483													C|||	1185	0.236621	0.348	0.2911	5008	,	,		18298	0.128		0.2763	False		,,,				2504	0.1186				p.A100A		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	0			c.G300A						PASS	.	C		1370,2838		401,568,1135	98.0	116.0	110.0		300	-7.1	0.0	11	dbSNP_130	110	2424,6160		392,1640,2260	no	coding-synonymous	OR5P2	NM_153444.1		793,2208,3395	TT,TC,CC		28.2386,32.557,29.6592		100/323	7818190	3794,8998	2104	4292	6396	SO:0001819	synonymous_variant	120065	exon1			GAAAGCCGCTGAA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.300G>A	11.37:g.7818190C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			C|0.738;T|0.262	0.262	strong		0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
OR5I1	10798	hgsc.bcm.edu	37	11	55703728	55703728	+	Missense_Mutation	SNP	A	A	G	rs4367963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	138	66	0.478261	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	
LRRN2	10446	hgsc.bcm.edu	37	1	204587047	204587047	+	Missense_Mutation	SNP	G	G	A	rs11588857	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204587047G>A	ENST00000367175.1	-	1	4286	c.2074C>T	c.(2074-2076)Cca>Tca	p.P692S	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367176.3_Missense_Mutation_p.P692S|LRRN2_ENST00000367177.3_Missense_Mutation_p.P692S			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	692			P -> S (in dbSNP:rs11588857).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TTCCTCCCTGGATTCCAGGGC	0.587													G|||	923	0.184305	0.0575	0.0922	5008	,	,		8413	0.3075		0.2237	False		,,,				2504	0.2536				p.P692S		Atlas-SNP	.											.	LRRN2	81	.	0			c.C2074T						PASS	.	G	SER/PRO,SER/PRO	357,4049	183.6+/-211.2	16,325,1862	92.0	98.0	96.0		2074,2074	5.2	1.0	1	dbSNP_120	96	1832,6768	326.2+/-317.3	182,1468,2650	yes	missense,missense	LRRN2	NM_006338.2,NM_201630.1	74,74	198,1793,4512	AA,AG,GG		21.3023,8.1026,16.8307	possibly-damaging,possibly-damaging	692/714,692/714	204587047	2189,10817	2203	4300	6503	SO:0001583	missense	10446	exon3			TCCCTGGATTCCA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.2074C>T	1.37:g.204587047G>A	ENSP00000356143:p.Pro692Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	418	0.19139194139194138	38	0.07723577235772358	39	0.10773480662983426	172	0.3006993006993007	169	0.22295514511873352	G	16.07	3.018815	0.54576	0.081026	0.213023	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.58358	0.34;0.34;0.34	5.16	5.16	0.70880	.	0.206931	0.24115	N	0.041409	T	0.00012	0.0000	N	0.08118	0	0.30449	P	0.775467	B	0.20671	0.047	B	0.19391	0.025	T	0.15549	-1.0433	9	0.10636	T	0.68	.	11.3325	0.49484	0.0854:0.0:0.9146:0.0	rs11588857;rs57344872;rs11588857	692	O75325	LRRN2_HUMAN	S	692	ENSP00000356144:P692S;ENSP00000356145:P692S;ENSP00000356143:P692S	ENSP00000356143:P692S	P	-	1	0	LRRN2	202853670	0.999000	0.42202	0.996000	0.52242	0.824000	0.46624	3.223000	0.51231	2.688000	0.91661	0.561000	0.74099	CCA	G|0.827;A|0.173	0.173	strong		0.587	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
IGFBP7	3490	hgsc.bcm.edu	37	4	57907014	57907014	+	Silent	SNP	C	C	T	rs35855328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:57907014C>T	ENST00000295666.4	-	2	594	c.561G>A	c.(559-561)ccG>ccA	p.P187P	IGFBP7_ENST00000512512.1_5'UTR|IGFBP7_ENST00000537922.1_Silent_p.P187P	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	187	Ig-like C2-type.				cell adhesion (GO:0007155)|cellular response to hormone stimulus (GO:0032870)|embryo implantation (GO:0007566)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|regulation of steroid biosynthetic process (GO:0050810)|response to cortisol (GO:0051414)|response to heat (GO:0009408)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GGACAGGTGTCGGGATTCCGA	0.527													C|||	18	0.00359425	0.0015	0.0058	5008	,	,		18916	0.0		0.0089	False		,,,				2504	0.0031				p.P187P		Atlas-SNP	.											IGFBP7,NS,malignant_melanoma,-2,1	IGFBP7	22	1	0			c.G561A						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	88.0	74.0	79.0		561	-4.2	0.9	4	dbSNP_126	79	105,8495	57.9+/-119.4	1,103,4196	no	coding-synonymous	IGFBP7	NM_001553.1		1,110,6392	TT,TC,CC		1.2209,0.1589,0.8611		187/283	57907014	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	3490	exon2			AGGTGTCGGGATT	S75725	CCDS3512.1	4q12	2013-01-11			ENSG00000163453	ENSG00000163453		"""Immunoglobulin superfamily / I-set domain containing"""	5476	protein-coding gene	gene with protein product		602867				7694637, 7980422	Standard	NM_001553		Approved	MAC25, IGFBP-7, PSF, FSTL2	uc003hcn.3	Q16270	OTTHUMG00000128772	ENST00000295666.4:c.561G>A	4.37:g.57907014C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_001553	B4E1N2|B7Z9W7|Q07822|Q53YE6|Q9UCA8	Silent	SNP	ENST00000295666.4	37	CCDS3512.1																																																																																			C|0.992;T|0.008	0.008	strong		0.527	IGFBP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250693.1		
TRAF3	7187	hgsc.bcm.edu	37	14	103342049	103342049	+	Missense_Mutation	SNP	T	T	C	rs1131877	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:103342049T>C	ENST00000560371.1	+	4	603	c.386T>C	c.(385-387)aTg>aCg	p.M129T	TRAF3_ENST00000351691.5_Missense_Mutation_p.M129T|TRAF3_ENST00000392745.2_Missense_Mutation_p.M129T|TRAF3_ENST00000347662.4_Missense_Mutation_p.M129T|TRAF3_ENST00000539721.1_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	61	0	0		WXS	Illumina HiSeq	Phase_I	57	21	0.368421	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	
PAPL	390928	hgsc.bcm.edu	37	19	39592138	39592138	+	Silent	SNP	C	C	T	rs1313617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39592138C>T	ENST00000331256.5	+	11	1348	c.1074C>T	c.(1072-1074)acC>acT	p.T358T	PAPL_ENST00000594229.1_Missense_Mutation_p.P317L	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		358						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										TGCCCTACACCAACCCGCGAG	0.582													C|||	1136	0.226837	0.3359	0.1671	5008	,	,		16890	0.1488		0.2018	False		,,,				2504	0.228				p.T358T		Atlas-SNP	.											.	.	.	.	0			c.C1074T						PASS	.	C		1424,2982	462.3+/-353.2	231,962,1010	60.0	52.0	55.0		1074	4.2	1.0	19	dbSNP_87	55	1798,6802	319.9+/-314.4	180,1438,2682	no	coding-synonymous	PAPL	NM_001004318.2		411,2400,3692	TT,TC,CC		20.907,32.3196,24.7732		358/439	39592138	3222,9784	2203	4300	6503	SO:0001819	synonymous_variant	0	exon11			CTACACCAACCCG																												ENST00000331256.5:c.1074C>T	19.37:g.39592138C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			C|0.765;T|0.235	0.235	strong		0.582	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
FGB	2244	hgsc.bcm.edu	37	4	155488821	155488821	+	Silent	SNP	C	C	T	rs6056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155488821C>T	ENST00000302068.4	+	4	630	c.567C>T	c.(565-567)agC>agT	p.S189S	FGB_ENST00000509493.1_5'UTR|FGB_ENST00000502545.1_3'UTR	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	189					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CTGTGAATAGCAATATCCCAA	0.343													T|||	768	0.153355	0.0756	0.1499	5008	,	,		18198	0.2242		0.1998	False		,,,				2504	0.1401				p.S189S	NSCLC(106;1133 1613 21870 46110 52656)	Atlas-SNP	.											.	FGB	71	.	0			c.C567T						PASS	.	T	,	390,4016	790.2+/-415.0	12,366,1825	109.0	105.0	106.0	http://www.ncbi.nlm.nih.gov/pubmed?term	390,567	1.9	0.0	4	dbSNP_52	106	1643,6957	741.5+/-407.2	177,1289,2834	yes	coding-synonymous,coding-synonymous	FGB	NM_001184741.1,NM_005141.4	,	189,1655,4659	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	19.1047,8.8516,15.6312	,	130/433,189/492	155488821	2033,10973	2203	4300	6503	SO:0001819	synonymous_variant	2244	exon4			GAATAGCAATATC		CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3662	protein-coding gene	gene with protein product		134830	"""fibrinogen, B beta polypeptide"""				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.567C>T	4.37:g.155488821C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	187	65	0.347594	NM_005141	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Silent	SNP	ENST00000302068.4	37	CCDS3786.1																																																																																			C|0.841;T|0.159	0.159	strong		0.343	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141	
ARIH2	10425	hgsc.bcm.edu	37	3	48965078	48965078	+	Missense_Mutation	SNP	A	A	C	rs34221642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:48965078A>C	ENST00000356401.4	+	3	426	c.87A>C	c.(85-87)gaA>gaC	p.E29D	ARIH2_ENST00000490095.1_Intron|ARIH2_ENST00000449376.1_Missense_Mutation_p.E29D	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	29	Asp/Glu-rich (acidic).|Poly-Glu.		E -> D (in dbSNP:rs34221642).		developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		aagaagaagaagaCGACCCTG	0.517													T|||	69	0.013778	0.0008	0.0216	5008	,	,		18640	0.001		0.0408	False		,,,				2504	0.0112				p.E29D		Atlas-SNP	.											.	ARIH2	32	.	0			c.A87C						PASS	.	T	ASP/GLU	50,4356		1,48,2154	55.0	59.0	58.0		87	-10.5	0.0	3	dbSNP_126	58	460,8140		16,428,3856	yes	missense	ARIH2	NM_006321.2	45	17,476,6010	CC,CA,AA		5.3488,1.1348,3.9213	benign	29/494	48965078	510,12496	2203	4300	6503	SO:0001583	missense	10425	exon3			AGAAGAAGACGAC	AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"""all-trans retinoic acid inducible RING finger"""	605615	"""ariadne (Drosophila) homolog 2"", ""ariadne homolog 2 (Drosophila)"""			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.87A>C	3.37:g.48965078A>C	ENSP00000348769:p.Glu29Asp	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	41	0.376147	NM_006321	Q9HBZ6|Q9UEM9	Missense_Mutation	SNP	ENST00000356401.4	37	CCDS2780.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	1	0.0017482517482517483	24	0.0316622691292876	T	0.001	-3.878292	0.00003	0.011348	0.053488	ENSG00000177479	ENST00000452882;ENST00000430423;ENST00000356401;ENST00000449376;ENST00000420814;ENST00000449729;ENST00000433170;ENST00000444790	T;T;D;D;T;T;T	0.82255	1.56;1.57;-1.59;-1.59;1.56;1.66;1.64	5.24	-10.5	0.00291	.	0.259935	0.37261	N	0.002171	T	0.09379	0.0231	N	0.00926	-1.1	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.001;0.002;0.0	T	0.48525	-0.9028	10	0.05620	T	0.96	.	6.7821	0.23652	0.2314:0.0824:0.0635:0.6226	rs34221642	36;29;29;29	B3KMG5;C9JBC5;F8WCS4;O95376	.;.;.;ARI2_HUMAN	D	29;29;29;29;29;29;29;28	ENSP00000395560:E29D;ENSP00000399788:E29D;ENSP00000348769:E29D;ENSP00000403222:E29D;ENSP00000397225:E29D;ENSP00000404838:E29D;ENSP00000406063:E29D	ENSP00000348769:E29D	E	+	3	2	ARIH2	48940082	0.000000	0.05858	0.002000	0.10522	0.071000	0.16799	-3.341000	0.00505	-4.564000	0.00042	-2.192000	0.00311	GAA	A|0.970;C|0.030	0.030	strong		0.517	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321	
EMC1	23065	hgsc.bcm.edu	37	1	19565344	19565344	+	Missense_Mutation	SNP	C	C	G	rs709683	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19565344C>G	ENST00000477853.1	-	10	1076	c.1034G>C	c.(1033-1035)aGt>aCt	p.S345T	EMC1_ENST00000375208.3_Missense_Mutation_p.S323T|RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375199.3_Missense_Mutation_p.S344T	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	104	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	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	
GRIN1	2902	hgsc.bcm.edu	37	9	140051238	140051238	+	Silent	SNP	A	A	G	rs6293	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140051238A>G	ENST00000371561.3	+	5	1886	c.789A>G	c.(787-789)ccA>ccG	p.P263P	GRIN1_ENST00000350902.5_Silent_p.P263P|GRIN1_ENST00000315048.3_Silent_p.P263P|GRIN1_ENST00000371553.3_Silent_p.P284P|GRIN1_ENST00000371560.3_Silent_p.P284P|GRIN1_ENST00000371559.4_Silent_p.P263P|GRIN1_ENST00000371555.4_Silent_p.P284P|GRIN1_ENST00000371546.4_Silent_p.P284P|GRIN1_ENST00000371550.4_Silent_p.P263P|GRIN1_ENST00000471122.1_3'UTR	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	263					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|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 density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTACGCCCCAGACGGTGAGT	0.687													G|||	705	0.140775	0.0287	0.2032	5008	,	,		12489	0.002		0.337	False		,,,				2504	0.1892				p.P284P	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											GRIN1,NS,carcinoma,0,2	GRIN1	51	2	0			c.A852G						scavenged	.	G	,,,,	285,4099		15,255,1922	20.0	21.0	21.0		789,852,852,789,789	-5.6	0.9	9	dbSNP_52	21	2706,5866		442,1822,2022	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRIN1	NM_000832.6,NM_001185090.1,NM_001185091.1,NM_007327.3,NM_021569.3	,,,,	457,2077,3944	GG,GA,AA		31.5679,6.5009,23.0858	,,,,	263/886,284/944,284/907,263/939,263/902	140051238	2991,9965	2192	4286	6478	SO:0001819	synonymous_variant	2902	exon6			CGCCCCAGACGGT		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4584	protein-coding gene	gene with protein product		138249	"""N-methyl-D-aspartate receptor subunit NR1"""	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.789A>G	9.37:g.140051238A>G		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Silent	SNP	ENST00000371561.3	37	CCDS7031.1																																																																																			A|0.831;G|0.169	0.169	strong		0.687	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327	
GALNT18	374378	hgsc.bcm.edu	37	11	11292700	11292700	+	Silent	SNP	G	G	C	rs10831567	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	56	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	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	
PDAP1	11333	hgsc.bcm.edu	37	7	98997955	98997955	+	Silent	SNP	G	G	A	rs148987199		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:98997955G>A	ENST00000350498.3	-	4	586	c.306C>T	c.(304-306)gaC>gaT	p.D102D	PDAP1_ENST00000496335.1_5'Flank	NM_014891.6	NP_055706.1	Q13442	HAP28_HUMAN	PDGFA associated protein 1	102					cell proliferation (GO:0008283)|signal transduction (GO:0007165)		poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)|prostate(1)|skin(1)	9	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)			CCTTTGGCCCGTCCAGATCCA	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		20454	0.0		0.001	False		,,,				2504	0.0				p.D102D		Atlas-SNP	.											.	PDAP1	17	.	0			c.C306T						PASS	.	G		0,4406		0,0,2203	168.0	123.0	138.0		306	-10.5	0.8	7	dbSNP_134	138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDAP1	NM_014891.6		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		102/182	98997955	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11333	exon4			TGGCCCGTCCAGA	U41745	CCDS5662.1	7q	2008-07-18			ENSG00000106244	ENSG00000106244			14634	protein-coding gene	gene with protein product	"""PDGF associated protein"""	607075				8780057	Standard	NM_014891		Approved	PAP1, PAP, HASPP28	uc003uqe.3	Q13442	OTTHUMG00000154629	ENST00000350498.3:c.306C>T	7.37:g.98997955G>A		Somatic	394	1	0.00253807		WXS	Illumina HiSeq	Phase_I	369	175	0.474255	NM_014891	D6W5S5|Q92906	Silent	SNP	ENST00000350498.3	37	CCDS5662.1																																																																																			G|1.000;A|0.000	0.000	strong		0.552	PDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336388.2	NM_014891	
DSG3	1830	hgsc.bcm.edu	37	18	29055635	29055635	+	Silent	SNP	C	C	T	rs117661169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:29055635C>T	ENST00000257189.4	+	16	2495	c.2412C>T	c.(2410-2412)gaC>gaT	p.D804D		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	804					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CGGAGGAAGACGATGGCCAGG	0.418													C|||	92	0.0183706	0.0015	0.0202	5008	,	,		19856	0.0		0.0298	False		,,,				2504	0.047				p.D804D		Atlas-SNP	.											.	DSG3	172	.	0			c.C2412T						PASS	.	C		24,4382	32.6+/-62.9	0,24,2179	120.0	115.0	117.0		2412	-10.6	0.0	18	dbSNP_132	117	288,8312	107.8+/-168.5	2,284,4014	no	coding-synonymous	DSG3	NM_001944.2		2,308,6193	TT,TC,CC		3.3488,0.5447,2.3989		804/1000	29055635	312,12694	2203	4300	6503	SO:0001819	synonymous_variant	1830	exon16			GGAAGACGATGGC	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2412C>T	18.37:g.29055635C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	37	CCDS11898.1																																																																																			C|0.976;T|0.024	0.024	strong		0.418	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
FAT1	2195	hgsc.bcm.edu	37	4	187517758	187517758	+	Silent	SNP	G	G	A	rs3822060	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187517758G>A	ENST00000441802.2	-	25	13145	c.12936C>T	c.(12934-12936)ccC>ccT	p.P4312P	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4312					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGTTTGAAGGGGGTGGGGGAG	0.547										HNSCC(5;0.00058)			G|||	278	0.0555112	0.0023	0.1066	5008	,	,		15389	0.1538		0.0348	False		,,,				2504	0.0112				p.P4312P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C12936T						PASS	.	G		31,4093		0,31,2031	42.0	47.0	45.0		12936	-10.7	0.0	4	dbSNP_107	45	253,8155		3,247,3954	no	coding-synonymous	FAT1	NM_005245.3		3,278,5985	AA,AG,GG		3.009,0.7517,2.2662		4312/4589	187517758	284,12248	2062	4204	6266	SO:0001819	synonymous_variant	2195	exon25			TGAAGGGGGTGGG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12936C>T	4.37:g.187517758G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1	157	0.07188644688644688	2	0.0040650406504065045	23	0.06353591160220995	101	0.17657342657342656	31	0.040897097625329816	G	0.015	-1.543438	0.00934	0.007517	0.03009	ENSG00000083857	ENST00000512772	.	.	.	5.37	-10.7	0.00240	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999743339	.	.	.	.	.	.	T	0.56165	-0.8024	5	0.07325	T	0.83	.	9.8232	0.40896	0.1357:0.4098:0.3872:0.0672	rs3822060	.	.	.	S	80	.	ENSP00000424157:P80S	P	-	1	0	FAT1	187754752	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.133000	0.01308	-6.898000	0.00002	-3.755000	0.00021	CCC	G|0.938;A|0.062	0.062	strong		0.547	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TGS1	96764	hgsc.bcm.edu	37	8	56711713	56711713	+	Missense_Mutation	SNP	A	A	G	rs10109493	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:56711713A>G	ENST00000260129.5	+	8	2260	c.1783A>G	c.(1783-1785)Act>Gct	p.T595A		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	595			T -> A (in dbSNP:rs10109493).		7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CTTGCTAGCAACTGTTCCAGA	0.433													A|||	575	0.114816	0.171	0.1167	5008	,	,		19247	0.0099		0.1103	False		,,,				2504	0.1503				p.T595A	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.A1783G						PASS	.	A	ALA/THR	730,3676	301.8+/-287.1	60,610,1533	79.0	77.0	78.0		1783	-7.3	0.0	8	dbSNP_119	78	925,7675	205.1+/-247.6	48,829,3423	yes	missense	TGS1	NM_024831.6	58	108,1439,4956	GG,GA,AA		10.7558,16.5683,12.7249	benign	595/854	56711713	1655,11351	2203	4300	6503	SO:0001583	missense	96764	exon8			CTAGCAACTGTTC	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.1783A>G	8.37:g.56711713A>G	ENSP00000260129:p.Thr595Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	219	0.10027472527472528	92	0.18699186991869918	42	0.11602209944751381	0	0.0	85	0.11213720316622691	A	3.946	-0.013212	0.07727	0.165683	0.107558	ENSG00000137574	ENST00000260129	T	0.09073	3.02	5.94	-7.35	0.01422	.	1.979650	0.02270	N	0.068340	T	0.00012	0.0000	N	0.02830	-0.485	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38351	-0.9665	9	0.05959	T	0.93	0.0049	5.9341	0.19154	0.3639:0.0:0.3806:0.2556	rs10109493;rs57840550;rs10109493	595;595	B2RBJ7;Q96RS0	.;TGS1_HUMAN	A	595	ENSP00000260129:T595A	ENSP00000260129:T595A	T	+	1	0	TGS1	56874267	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.427000	0.06999	-1.389000	0.02090	-0.263000	0.10527	ACT	A|0.876;G|0.124	0.124	strong		0.433	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
GJD4	219770	hgsc.bcm.edu	37	10	35896700	35896700	+	Missense_Mutation	SNP	C	C	T	rs76906304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:35896700C>T	ENST00000321660.1	+	2	417	c.259C>T	c.(259-261)Ctc>Ttc	p.L87F	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	87					cell communication (GO:0007154)|regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014717)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GTGCGTCCTCCTCCCCTCCGC	0.706													C|||	33	0.00658946	0.0	0.013	5008	,	,		11126	0.0		0.0119	False		,,,				2504	0.0123				p.L87F		Atlas-SNP	.											GJD4,NS,carcinoma,0,1	GJD4	38	1	0			c.C259T						PASS	.	C	PHE/LEU	16,4390	21.2+/-45.6	0,16,2187	148.0	122.0	131.0		259	4.3	0.1	10	dbSNP_131	131	148,8452	70.7+/-133.2	1,146,4153	yes	missense	GJD4	NM_153368.2	22	1,162,6340	TT,TC,CC		1.7209,0.3631,1.261	probably-damaging	87/371	35896700	164,12842	2203	4300	6503	SO:0001583	missense	219770	exon2			GTCCTCCTCCCCT	AJ414564	CCDS7191.1	10p11.22	2007-11-27			ENSG00000177291	ENSG00000177291		"""Ion channels / Gap junction proteins (connexins)"""	23296	protein-coding gene	gene with protein product	"""connexin 40.1"""	611922				12477932	Standard	NM_153368		Approved	CX40.1, FLJ90023	uc001iyy.1	Q96KN9	OTTHUMG00000017957	ENST00000321660.1:c.259C>T	10.37:g.35896700C>T	ENSP00000315070:p.Leu87Phe	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_153368	Q8N2R7	Missense_Mutation	SNP	ENST00000321660.1	37	CCDS7191.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	15.31	2.795160	0.50208	0.003631	0.017209	ENSG00000177291	ENST00000321660	D	0.99129	-5.46	6.11	4.27	0.50696	Connexin, N-terminal (1);	0.215706	0.41938	N	0.000797	D	0.97228	0.9094	L	0.56769	1.78	0.51233	D	0.999916	D	0.52996	0.957	P	0.55087	0.768	D	0.93664	0.6984	10	0.62326	D	0.03	.	13.6296	0.62188	0.0:0.8795:0.0:0.1205	.	87	Q96KN9	CXD4_HUMAN	F	87	ENSP00000315070:L87F	ENSP00000315070:L87F	L	+	1	0	GJD4	35936706	0.680000	0.27605	0.144000	0.22314	0.036000	0.12997	1.246000	0.32803	0.916000	0.36871	0.655000	0.94253	CTC	C|0.989;T|0.011	0.011	strong		0.706	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368	
GNB3	2784	hgsc.bcm.edu	37	12	6954875	6954875	+	Silent	SNP	C	C	T	rs5443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6954875C>T	ENST00000229264.3	+	10	1230	c.825C>T	c.(823-825)tcC>tcT	p.S275S	CDCA3_ENST00000422785.3_3'UTR|GNB3_ENST00000435982.2_Silent_p.S274S|CDCA3_ENST00000604599.1_5'UTR	NM_002075.2	NP_002066.1	P16520	GBB3_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 3	275					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|signal transducer activity (GO:0004871)	p.S275S(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|stomach(1)	20						GCATCACGTCCGTGGCCTTCT	0.602													C|||	2465	0.492212	0.8192	0.379	5008	,	,		-128	0.503		0.3072	False		,,,				2504	0.3098				p.S275S		Atlas-SNP	.											GNB3,bladder,carcinoma,+1,2	GNB3	36	2	1	Substitution - coding silent(1)	stomach(1)	c.C825T	GRCh37	CS983412	GNB3	S	rs5443	PASS	.	C		3183,1223	707.5+/-407.5	1137,909,157	179.0	167.0	171.0		825	-9.2	0.0	12	dbSNP_52	171	2667,5933	429.2+/-356.1	436,1795,2069	no	coding-synonymous	GNB3	NM_002075.2		1573,2704,2226	TT,TC,CC		31.0116,27.7576,44.9792		275/341	6954875	5850,7156	2203	4300	6503	SO:0001819	synonymous_variant	2784	exon10			CACGTCCGTGGCC		CCDS8564.1, CCDS73427.1	12p13	2013-01-10			ENSG00000111664	ENSG00000111664		"""WD repeat domain containing"""	4400	protein-coding gene	gene with protein product		139130				11770079, 16600389	Standard	XM_005253680		Approved		uc001qrd.3	P16520	OTTHUMG00000168517	ENST00000229264.3:c.825C>T	12.37:g.6954875C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_002075	Q96B71|Q9BQC0	Silent	SNP	ENST00000229264.3	37	CCDS8564.1																																																																																			C|0.542;T|0.458	0.458	strong		0.602	GNB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400006.1	NM_002075	
MUC16	94025	hgsc.bcm.edu	37	19	9003618	9003618	+	Missense_Mutation	SNP	C	C	T	rs11085776	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9003618C>T	ENST00000397910.4	-	49	40225	c.40022G>A	c.(40021-40023)cGt>cAt	p.R13341H	MUC16_ENST00000380951.5_5'Flank	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13343	SEA 9. {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						GCCAGGGCGACGCATGTCCTC	0.552													c|||	3105	0.620008	0.4599	0.7291	5008	,	,		18301	0.6071		0.7177	False		,,,				2504	0.6718				p.R13341H		Atlas-SNP	.											.	MUC16	4315	.	0			c.G40022A						PASS	.	G	HIS/ARG	2239,1833		607,1025,404	247.0	204.0	218.0		40022	-6.5	0.0	19	dbSNP_120	218	6214,2160		2322,1570,295	yes	missense	MUC16	NM_024690.2	29	2929,2595,699	TT,TC,CC		25.7941,45.0147,32.0826	benign	13341/14508	9003618	8453,3993	2036	4187	6223	SO:0001583	missense	94025	exon49			GGGCGACGCATGT	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.40022G>A	19.37:g.9003618C>T	ENSP00000381008:p.Arg13341His	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	1414|1414	0.6474358974358975|0.6474358974358975	245|245	0.49796747967479676|0.49796747967479676	261|261	0.7209944751381215|0.7209944751381215	383|383	0.6695804195804196|0.6695804195804196	525|525	0.6926121372031663|0.6926121372031663	.|.	4.257|4.257	0.046692|0.046692	0.08243|0.08243	0.549853|0.549853	0.742059|0.742059	ENSG00000181143|ENSG00000181143	ENST00000397910|ENST00000542240	T|.	0.29397|.	1.57|.	3.24|3.24	-6.47|-6.47	0.01902|0.01902	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	.|.	.|.	.|.	B|.	0.28971|.	0.229|.	B|.	0.23150|.	0.044|.	T|T	0.03619|0.03619	-1.1019|-1.1019	7|3	0.87932|.	D|.	0|.	2.498|2.498	10.8862|10.8862	0.46968|0.46968	0.0:0.7904:0.0996:0.11|0.0:0.7904:0.0996:0.11	rs11085776;rs57696817|rs11085776;rs57696817	13341|.	B5ME49|.	.|.	H|I	13341|181	ENSP00000381008:R13341H|.	ENSP00000381008:R13341H|.	R|V	-|-	2|1	0|0	MUC16|MUC16	8864618|8864618	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-4.861000|-4.861000	0.00177|0.00177	-2.840000|-2.840000	0.00335|0.00335	-4.955000|-4.955000	0.00002|0.00002	CGT|GTC	C|0.352;T|0.648	0.648	strong		0.552	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PIP5K1B	8395	hgsc.bcm.edu	37	9	71549847	71549847	+	Missense_Mutation	SNP	G	G	A	rs55897616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:71549847G>A	ENST00000265382.3	+	13	1548	c.1243G>A	c.(1243-1245)Gcc>Acc	p.A415T	RNU6-820P_ENST00000384273.1_RNA|PIP5K1B_ENST00000541509.1_Missense_Mutation_p.A415T	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	415			A -> T (in dbSNP:rs55897616). {ECO:0000269|PubMed:9177790}.		phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			breast(1)|large_intestine(2)|stomach(1)	4				Lung(182;0.133)		CAATTCAATCGCCGCCCTAAA	0.418													G|||	114	0.0227636	0.0008	0.0403	5008	,	,		12650	0.0		0.0706	False		,,,				2504	0.0143				p.A415T		Atlas-SNP	.											.	PIP5K1B	40	.	0			c.G1243A						PASS	.	G	THR/ALA	57,4349	55.5+/-91.7	0,57,2146	75.0	71.0	72.0		1243	5.4	0.2	9	dbSNP_129	72	624,7976	163.0+/-215.7	19,586,3695	yes	missense	PIP5K1B	NM_003558.2	58	19,643,5841	AA,AG,GG		7.2558,1.2937,5.236	benign	415/541	71549847	681,12325	2203	4300	6503	SO:0001583	missense	8395	exon13			TCAATCGCCGCCC	U78579	CCDS6624.1, CCDS65063.1	9q13	2008-02-05			ENSG00000107242	ENSG00000107242			8995	protein-coding gene	gene with protein product		602745				9177790, 8841185	Standard	NM_003558		Approved	STM7, MSS4	uc004agu.4	O14986	OTTHUMG00000019976	ENST00000265382.3:c.1243G>A	9.37:g.71549847G>A	ENSP00000265382:p.Ala415Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_003558	A8K9L9|B4DIG7|P78518|P78519|Q5T5K6|Q5T5K8|Q5T5K9|Q5VZ00|Q7KYT5|Q8NHQ5|Q92749	Missense_Mutation	SNP	ENST00000265382.3	37	CCDS6624.1	66	0.03021978021978022	0	0.0	13	0.03591160220994475	0	0.0	53	0.06992084432717678	G	6.527	0.465542	0.12402	0.012937	0.072558	ENSG00000107242	ENST00000541509;ENST00000377290;ENST00000265382;ENST00000419747	T;T	0.26067	1.77;1.76	5.37	5.37	0.77165	.	0.350833	0.34314	N	0.004069	T	0.00754	0.0025	N	0.04636	-0.2	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.21827	-1.0234	10	0.10902	T	0.67	-12.36	11.4928	0.50391	0.0899:0.0:0.9101:0.0	rs55897616;rs61752952	415	O14986	PI51B_HUMAN	T	415;415;415;362	ENSP00000438082:A415T;ENSP00000265382:A415T	ENSP00000265382:A415T	A	+	1	0	PIP5K1B	70739667	0.063000	0.20901	0.159000	0.22649	0.100000	0.18952	1.332000	0.33805	2.670000	0.90874	0.655000	0.94253	GCC	G|0.955;A|0.045	0.045	strong		0.418	PIP5K1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052561.2	NM_003558	
RRN3	54700	hgsc.bcm.edu	37	16	15166809	15166809	+	Silent	SNP	A	A	G	rs72774849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:15166809A>G	ENST00000198767.6	-	12	1209	c.1126T>C	c.(1126-1128)Ttg>Ctg	p.L376L	RRN3_ENST00000429751.2_Silent_p.L346L|RRN3_ENST00000327307.7_Silent_p.L343L|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000540462.1_Silent_p.L194L|RRN3_ENST00000563559.1_Silent_p.L376L	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	376					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						TTACTCACCAATTTGAAACTA	0.383													.|||	22	0.00439297	0.0008	0.0043	5008	,	,		17623	0.0		0.0159	False		,,,				2504	0.002				p.L376L		Atlas-SNP	.											.	RRN3	36	.	0			c.T1126C						PASS	.	A		8,4386		0,8,2189	107.0	93.0	98.0		1126	-0.7	0.9	16	dbSNP_130	98	154,8446		1,152,4147	no	coding-synonymous	RRN3	NM_018427.3		1,160,6336	GG,GA,AA		1.7907,0.1821,1.2467		376/652	15166809	162,12832	2197	4300	6497	SO:0001819	synonymous_variant	54700	exon12			TCACCAATTTGAA	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.1126T>C	16.37:g.15166809A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Silent	SNP	ENST00000198767.6	37	CCDS10559.1																																																																																			A|0.987;G|0.013	0.013	strong		0.383	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	
CCDC85A	114800	hgsc.bcm.edu	37	2	56420296	56420296	+	Missense_Mutation	SNP	C	C	T	rs75743618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:56420296C>T	ENST00000407595.2	+	2	1463	c.961C>T	c.(961-963)Cgg>Tgg	p.R321W	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	321	His-rich.									breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CCAGAAGCACCGGTCAGGGAG	0.652													C|||	411	0.0820687	0.0257	0.0504	5008	,	,		17336	0.1677		0.0736	False		,,,				2504	0.1012				p.R321W		Atlas-SNP	.											.	CCDC85A	70	.	0			c.C961T						PASS	.	C	TRP/ARG	100,3968		1,98,1935	58.0	69.0	65.0		961	3.0	1.0	2	dbSNP_131	65	554,7810		19,516,3647	yes	missense	CCDC85A	NM_001080433.1	101	20,614,5582	TT,TC,CC		6.6236,2.4582,5.2606	probably-damaging	321/554	56420296	654,11778	2034	4182	6216	SO:0001583	missense	114800	exon2			AAGCACCGGTCAG	AB067499	CCDS46290.1	2p16.1	2006-03-29			ENSG00000055813	ENSG00000055813			29400	protein-coding gene	gene with protein product						11572484	Standard	NM_001080433		Approved	KIAA1912	uc002rzn.3	Q96PX6	OTTHUMG00000152033	ENST00000407595.2:c.961C>T	2.37:g.56420296C>T	ENSP00000384040:p.Arg321Trp	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_001080433		Missense_Mutation	SNP	ENST00000407595.2	37	CCDS46290.1	188	0.08608058608058608	17	0.034552845528455285	24	0.06629834254143646	95	0.1660839160839161	52	0.06860158311345646	C	16.61	3.169980	0.57584	0.024582	0.066236	ENSG00000055813	ENST00000407595	T	0.53423	0.62	5.35	2.99	0.34606	.	0.052544	0.85682	D	0.000000	T	0.00328	0.0010	L	0.61218	1.895	0.09310	P	0.9999999999999978	D	0.89917	1.0	D	0.72075	0.976	T	0.13176	-1.0519	9	0.87932	D	0	-12.8112	13.3766	0.60743	0.4838:0.5162:0.0:0.0	.	321	Q96PX6	CC85A_HUMAN	W	321	ENSP00000384040:R321W	ENSP00000384040:R321W	R	+	1	2	CCDC85A	56273800	1.000000	0.71417	0.998000	0.56505	0.888000	0.51559	2.138000	0.42140	0.321000	0.23259	0.591000	0.81541	CGG	C|0.918;T|0.082	0.082	strong		0.652	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1		
RRP12	23223	hgsc.bcm.edu	37	10	99160152	99160152	+	Silent	SNP	A	A	G	rs1048442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99160152A>G	ENST00000370992.4	-	2	390	c.279T>C	c.(277-279)ggT>ggC	p.G93G	RRP12_ENST00000315563.6_Silent_p.G93G|RRP12_ENST00000414986.1_Silent_p.G93G|RP11-452K12.7_ENST00000422848.1_RNA	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	93						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TCAGGAAGGTACCCGAGGACT	0.597													G|||	2006	0.400559	0.5378	0.3444	5008	,	,		18936	0.3125		0.336	False		,,,				2504	0.4121				p.G93G		Atlas-SNP	.											.	RRP12	97	.	0			c.T279C						PASS	.	G	,	2190,2216	589.6+/-387.2	554,1082,567	127.0	123.0	125.0		279,279	1.5	0.1	10	dbSNP_86	125	2722,5878	681.7+/-403.7	430,1862,2008	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	984,2944,2575	GG,GA,AA		31.6512,49.7049,37.7672	,	93/1237,93/1298	99160152	4912,8094	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon2			GAAGGTACCCGAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.279T>C	10.37:g.99160152A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_001145114	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			A|0.622;G|0.378	0.378	strong		0.597	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
INTS10	55174	hgsc.bcm.edu	37	8	19677915	19677915	+	Silent	SNP	G	G	A	rs7822495	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:19677915G>A	ENST00000397977.3	+	4	725	c.327G>A	c.(325-327)cgG>cgA	p.R109R	INTS10_ENST00000521758.1_Intron	NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	109					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TTCCTGGTCGGGTCCAGTGTG	0.423													G|||	1221	0.24381	0.2784	0.2781	5008	,	,		19987	0.2927		0.169	False		,,,				2504	0.1994				p.R109R		Atlas-SNP	.											.	INTS10	46	.	0			c.G327A						PASS	.	G		978,2756		129,720,1018	135.0	128.0	130.0		327	-5.2	0.7	8	dbSNP_116	130	1465,6735		144,1177,2779	no	coding-synonymous	INTS10	NM_018142.2		273,1897,3797	AA,AG,GG		17.8659,26.1918,20.4709		109/711	19677915	2443,9491	1867	4100	5967	SO:0001819	synonymous_variant	55174	exon4			TGGTCGGGTCCAG	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"""chromosome 8 open reading frame 35"""	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.327G>A	8.37:g.19677915G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Silent	SNP	ENST00000397977.3	37	CCDS6011.2																																																																																			G|0.763;A|0.237	0.237	strong		0.423	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142	
BRAF	673	hgsc.bcm.edu	37	7	140449150	140449150	+	Silent	SNP	T	T	C	rs9648696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	167	0	0		WXS	Illumina HiSeq	Phase_I	138	65	0.471014	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	
ALS2CR11	151254	hgsc.bcm.edu	37	2	202436684	202436684	+	Silent	SNP	T	T	A	rs55872838	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202436684T>A	ENST00000286195.3	-	8	857	c.813A>T	c.(811-813)ccA>ccT	p.P271P	ALS2CR11_ENST00000439802.1_Silent_p.P271P|ALS2CR11_ENST00000439140.1_Silent_p.P271P|ALS2CR11_ENST00000450242.1_Silent_p.P271P	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	271										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						CTGTTCTTTCTGGAGGTGGTG	0.353													T|||	209	0.0417332	0.0915	0.0476	5008	,	,		19354	0.0		0.0477	False		,,,				2504	0.0072				p.P271P		Atlas-SNP	.											.	ALS2CR11	194	.	0			c.A813T						PASS	.	T	,,,	324,4082	172.3+/-202.3	14,296,1893	127.0	120.0	123.0		813,813,813,813	0.4	1.0	2	dbSNP_129	123	462,8138	137.1+/-194.1	14,434,3852	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ALS2CR11	NM_001168216.1,NM_001168217.1,NM_001168221.1,NM_152525.5	,,,	28,730,5745	AA,AT,TT		5.3721,7.3536,6.0434	,,,	271/396,271/551,271/1821,271/624	202436684	786,12220	2203	4300	6503	SO:0001819	synonymous_variant	151254	exon8			TCTTTCTGGAGGT	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.813A>T	2.37:g.202436684T>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_001168217	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Silent	SNP	ENST00000286195.3	37	CCDS2349.1																																																																																			T|0.948;A|0.052	0.052	strong		0.353	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525	
MTTP	4547	hgsc.bcm.edu	37	4	100518247	100518247	+	Silent	SNP	C	C	A	rs17029213	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100518247C>A	ENST00000265517.5	+	8	1136	c.933C>A	c.(931-933)acC>acA	p.T311T	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Silent_p.T311T|MTTP_ENST00000511045.1_Silent_p.T338T			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	311	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				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)	GGCGGTCCACCAGGAAATACC	0.512													C|||	354	0.0706869	0.1876	0.036	5008	,	,		17475	0.0		0.0437	False		,,,				2504	0.0378				p.T311T		Atlas-SNP	.											.	MTTP	127	.	0			c.C933A						PASS	.	C		684,3722	287.8+/-279.5	63,558,1582	98.0	98.0	98.0		933	2.5	0.9	4	dbSNP_123	98	338,8262	116.5+/-176.2	5,328,3967	no	coding-synonymous	MTTP	NM_000253.2		68,886,5549	AA,AC,CC		3.9302,15.5243,7.8579		311/895	100518247	1022,11984	2203	4300	6503	SO:0001819	synonymous_variant	4547	exon9			GTCCACCAGGAAA		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.933C>A	4.37:g.100518247C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_000253	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	37	CCDS3651.1																																																																																			C|0.933;A|0.067	0.067	strong		0.512	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
EPHA1	2041	hgsc.bcm.edu	37	7	143092269	143092269	+	Missense_Mutation	SNP	G	G	A	rs34372369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:143092269G>A	ENST00000275815.3	-	13	2176	c.2090C>T	c.(2089-2091)cCg>cTg	p.P697L		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	697	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> L (in dbSNP:rs34372369). {ECO:0000269|PubMed:17344846}.		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)				GATCATGATCGGCTTTCCTGA	0.552													G|||	157	0.0313498	0.0023	0.0389	5008	,	,		21134	0.003		0.0527	False		,,,				2504	0.0726				p.P697L		Atlas-SNP	.											.	EPHA1	193	.	0			c.C2090T						PASS	.	G	LEU/PRO	47,4359	49.6+/-84.7	1,45,2157	172.0	152.0	159.0		2090	4.8	1.0	7	dbSNP_126	159	493,8107	142.5+/-198.7	10,473,3817	yes	missense	EPHA1	NM_005232.4	98	11,518,5974	AA,AG,GG		5.7326,1.0667,4.1519	probably-damaging	697/977	143092269	540,12466	2203	4300	6503	SO:0001583	missense	2041	exon13			ATGATCGGCTTTC	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.2090C>T	7.37:g.143092269G>A	ENSP00000275815:p.Pro697Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	57	0.0260989010989011	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	39	0.051451187335092345	G	18.09	3.546466	0.65198	0.010667	0.057326	ENSG00000146904	ENST00000275815	D	0.84146	-1.81	4.83	4.83	0.62350	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000010	T	0.62792	0.2457	M	0.84433	2.695	0.80722	D	1	D	0.71674	0.998	P	0.55999	0.789	T	0.80453	-0.1376	10	0.87932	D	0	.	15.602	0.76631	0.0:0.1374:0.8626:0.0	rs34372369;rs34372369	697	P21709	EPHA1_HUMAN	L	697	ENSP00000275815:P697L	ENSP00000275815:P697L	P	-	2	0	EPHA1	142802391	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	1.858000	0.39408	2.669000	0.90835	0.655000	0.94253	CCG	G|0.961;A|0.039	0.039	strong		0.552	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
ATP2A3	489	hgsc.bcm.edu	37	17	3845927	3845927	+	Silent	SNP	A	A	G	rs17846889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3845927A>G	ENST00000352011.3	-	12	1572	c.1518T>C	c.(1516-1518)acT>acC	p.T506T	ATP2A3_ENST00000309890.7_Silent_p.T506T|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000397043.3_Silent_p.T506T|ATP2A3_ENST00000359983.3_Silent_p.T506T|ATP2A3_ENST00000397041.3_Silent_p.T506T|ATP2A3_ENST00000397035.3_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	34	0	0		WXS	Illumina HiSeq	Phase_I	34	34	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	
SCN10A	6336	hgsc.bcm.edu	37	3	38768334	38768334	+	Silent	SNP	T	T	C	rs7374804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:38768334T>C	ENST00000449082.2	-	16	2849	c.2850A>G	c.(2848-2850)aaA>aaG	p.K950K		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	950					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K950K(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AGAGTGGGAGTTTCACCACCA	0.607													T|||	681	0.135982	0.1051	0.1037	5008	,	,		20020	0.2599		0.0636	False		,,,				2504	0.1472				p.K950K		Atlas-SNP	.											SCN10A,NS,carcinoma,0,1	SCN10A	359	1	1	Substitution - coding silent(1)	stomach(1)	c.A2850G						scavenged	.	T		362,4044	186.0+/-213.0	17,328,1858	68.0	70.0	69.0		2850	-5.9	0.3	3	dbSNP_116	69	557,8043	151.9+/-206.6	17,523,3760	no	coding-synonymous	SCN10A	NM_006514.2		34,851,5618	CC,CT,TT		6.4767,8.2161,7.066		950/1957	38768334	919,12087	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon16			TGGGAGTTTCACC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.2850A>G	3.37:g.38768334T>C		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	155	79	0.509677	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			T|0.913;C|0.087	0.087	strong		0.607	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
PRUNE2	158471	hgsc.bcm.edu	37	9	79324955	79324955	+	Missense_Mutation	SNP	C	C	T	rs11145017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79324955C>T	ENST00000376718.3	-	8	2358	c.2235G>A	c.(2233-2235)atG>atA	p.M745I	PRUNE2_ENST00000428286.1_Missense_Mutation_p.M386I	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	745					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						GTGACTTCTCCATGGGCAGGT	0.488													C|||	1189	0.23742	0.2103	0.1599	5008	,	,		18877	0.4643		0.1551	False		,,,				2504	0.18				p.M745I		Atlas-SNP	.											.	PRUNE2	331	.	0			c.G2235A						PASS	.	C	ILE/MET	627,2509		49,529,990	58.0	53.0	55.0		2235	-1.0	0.0	9	dbSNP_120	55	882,6282		50,782,2750	yes	missense	PRUNE2	NM_015225.2	10	99,1311,3740	TT,TC,CC		12.3116,19.9936,14.6505	benign	745/3089	79324955	1509,8791	1568	3582	5150	SO:0001583	missense	158471	exon8			CTTCTCCATGGGC	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.2235G>A	9.37:g.79324955C>T	ENSP00000365908:p.Met745Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	164	72	0.439024	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	559|559	0.25595238095238093|0.25595238095238093	109|109	0.22154471544715448|0.22154471544715448	51|51	0.1408839779005525|0.1408839779005525	284|284	0.4965034965034965|0.4965034965034965	115|115	0.1517150395778364|0.1517150395778364	C|C	0.007|0.007	-1.952972|-1.952972	0.00470|0.00470	0.199936|0.199936	0.123116|0.123116	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.41065	.|1.01;1.01	5.85|5.85	-0.966|-0.966	0.10320|0.10320	.|.	.|0.879152	.|0.09764	.|N	.|0.758826	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.22926|0.22926	P|P	0.99855568|0.99855568	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.48927|0.48927	-0.8991|-0.8991	4|9	.|0.21014	.|T	.|0.42	0.0478|0.0478	7.2488|7.2488	0.26138|0.26138	0.3842:0.1308:0.0:0.485|0.3842:0.1308:0.0:0.485	rs11145017;rs17786899;rs52806352;rs59241784;rs11145017|rs11145017;rs17786899;rs52806352;rs59241784;rs11145017	.|745	.|Q8WUY3	.|PRUN2_HUMAN	R|I	67|745;386;744	.|ENSP00000365908:M745I;ENSP00000397425:M386I	.|ENSP00000365908:M745I	G|M	-|-	1|3	0|0	PRUNE2|PRUNE2	78514775|78514775	0.084000|0.084000	0.21492|0.21492	0.016000|0.016000	0.15963|0.15963	0.003000|0.003000	0.03518|0.03518	0.401000|0.401000	0.20948|0.20948	-0.419000|-0.419000	0.07439|0.07439	-0.253000|-0.253000	0.11424|0.11424	GGA|ATG	C|0.743;N|0.000	.	strong		0.488	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
ORC2	4999	hgsc.bcm.edu	37	2	201785837	201785837	+	Silent	SNP	G	G	A	rs2307362	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:201785837G>A	ENST00000234296.2	-	14	1422	c.1173C>T	c.(1171-1173)ctC>ctT	p.L391L		NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	391					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						AATTGTGGATGAGAAGGAAGA	0.363													G|||	960	0.191693	0.4486	0.147	5008	,	,		16745	0.0139		0.1928	False		,,,				2504	0.0583				p.L391L		Atlas-SNP	.											.	ORC2	48	.	0			c.C1173T						PASS	.	G		1639,2767	502.2+/-365.2	305,1029,869	75.0	72.0	73.0		1173	-2.0	1.0	2	dbSNP_100	73	1469,7131	279.9+/-294.2	110,1249,2941	no	coding-synonymous	ORC2	NM_006190.4		415,2278,3810	AA,AG,GG		17.0814,37.1993,23.8967		391/578	201785837	3108,9898	2203	4300	6503	SO:0001819	synonymous_variant	4999	exon14			GTGGATGAGAAGG		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"""origin recognition complex, subunit 2 (yeast homolog)-like"", ""origin recognition complex, subunit 2-like (yeast)"", ""origin recognition complex, subunit 2 homolog (yeast)"""	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1173C>T	2.37:g.201785837G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_006190	Q13204|Q53TX5	Silent	SNP	ENST00000234296.2	37	CCDS2334.1																																																																																			G|0.783;A|0.217	0.217	strong		0.363	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190	
PSMD13	5719	hgsc.bcm.edu	37	11	244129	244129	+	Intron	SNP	C	C	T	rs7116130	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244129C>T	ENST00000532097.1	+	4	713				PSMD13_ENST00000431206.2_Missense_Mutation_p.R62W|PSMD13_ENST00000352303.5_Intron	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13						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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TGATGCTCGGCGGTGCTCAAA	0.413													T|||	4083	0.815296	0.8918	0.83	5008	,	,		15555	0.8036		0.7306	False		,,,				2504	0.8006				p.R62W		Atlas-SNP	.											.	PSMD13	53	.	0			c.C184T						PASS	.	T	,TRP/ARG	3843,561	235.2+/-247.8	1713,417,72	54.0	60.0	58.0		,184	0.1	0.0	11	dbSNP_116	58	6261,2335	373.8+/-337.2	2364,1533,401	yes	intron,missense	PSMD13	NM_002817.3,NM_175932.2	,101	4077,1950,473	TT,TC,CC		27.1638,12.7384,22.2769	,	,62/379	244129	10104,2896	2202	4298	6500	SO:0001627	intron_variant	5719	exon2			GCTCGGCGGTGCT	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.210-32C>T	11.37:g.244129C>T		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	1756	0.8040293040293041	440	0.8943089430894309	295	0.8149171270718232	469	0.8199300699300699	552	0.7282321899736148	T	11.22	1.574193	0.28092	0.872616	0.728362	ENSG00000185627	ENST00000431206	T	0.18016	2.24	5.52	0.0511	0.14296	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10894	-1.0610	6	.	.	.	.	6.1341	0.20221	0.0:0.1466:0.3857:0.4677	rs7116130;rs17155624;rs60616643;rs7116130	62	Q9UNM6-2	.	W	62	ENSP00000396937:R62W	.	R	+	1	2	PSMD13	234129	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.163000	0.16520	-0.105000	0.12132	-0.360000	0.07572	CGG	C|0.202;T|0.798	0.798	strong		0.413	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
SYNE2	23224	hgsc.bcm.edu	37	14	64596823	64596823	+	Missense_Mutation	SNP	C	C	A	rs75568433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64596823C>A	ENST00000344113.4	+	76	14409	c.14197C>A	c.(14197-14199)Cct>Act	p.P4733T	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.P1367T|SYNE2_ENST00000358025.3_Missense_Mutation_p.P4733T|SYNE2_ENST00000394768.2_Missense_Mutation_p.P1118T|SYNE2_ENST00000554584.1_Missense_Mutation_p.P4650T|SYNE2_ENST00000357395.3_Missense_Mutation_p.P1118T	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4733				P -> S (in Ref. 2; AAL33802 and 3). {ECO:0000305}.	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)		ACTCAGCAGCCCTTTCGTCAC	0.473													C|||	14	0.00279553	0.0	0.0029	5008	,	,		21176	0.0		0.0109	False		,,,				2504	0.001				p.P4733T		Atlas-SNP	.											.	SYNE2	577	.	0			c.C14197A						PASS	.	C	THR/PRO,THR/PRO	6,4400	11.4+/-27.6	0,6,2197	101.0	88.0	92.0		14197,14197	5.8	1.0	14	dbSNP_131	92	170,8430	79.5+/-142.1	3,164,4133	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	38,38	3,170,6330	AA,AC,CC		1.9767,0.1362,1.3532	probably-damaging,probably-damaging	4733/6886,4733/6908	64596823	176,12830	2203	4300	6503	SO:0001583	missense	23224	exon76			AGCAGCCCTTTCG	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.14197C>A	14.37:g.64596823C>A	ENSP00000341781:p.Pro4733Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	138	70	0.507246	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	8.851	0.944568	0.18356	0.001362	0.019767	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.56275	0.81;4.12;0.8;0.47;4.17;4.12	5.82	5.82	0.92795	.	0.000000	0.53938	D	0.000043	T	0.53158	0.1779	M	0.63428	1.95	0.80722	D	1	D;D;D	0.76494	0.964;0.979;0.999	P;P;D	0.71414	0.839;0.766;0.973	T	0.59327	-0.7475	10	0.35671	T	0.21	.	15.5498	0.76141	0.0:0.8625:0.1375:0.0	.	1118;4733;4733	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	T	4733;1118;4733;4650;4650;1367;1118	ENSP00000350719:P4733T;ENSP00000349969:P1118T;ENSP00000341781:P4733T;ENSP00000452570:P4650T;ENSP00000450831:P1367T;ENSP00000378249:P1118T	ENSP00000261678:P4650T	P	+	1	0	SYNE2	63666576	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	1.707000	0.37888	2.757000	0.94681	0.655000	0.94253	CCT	C|0.990;A|0.010	0.010	strong		0.473	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
TNIP2	79155	hgsc.bcm.edu	37	4	2744087	2744087	+	Missense_Mutation	SNP	G	G	A	rs2269495	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2744087G>A	ENST00000315423.7	-	6	1273	c.1187C>T	c.(1186-1188)gCc>gTc	p.A396V	TNIP2_ENST00000503235.1_Missense_Mutation_p.A313V|TNIP2_ENST00000510267.1_Missense_Mutation_p.A289V|TNIP2_ENST00000505186.1_5'UTR	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)		GCCTCTCTGGGCCGCGCCAGG	0.667													G|||	1717	0.342851	0.0651	0.5663	5008	,	,		16508	0.3879		0.4165	False		,,,				2504	0.4376				p.A396V		Atlas-SNP	.											TNIP2,NS,carcinoma,0,1	TNIP2	28	1	0			c.C1187T						PASS	.	G	VAL/ALA,VAL/ALA	628,3778	265.0+/-266.4	47,534,1622	31.0	34.0	33.0		866,1187	2.0	0.0	4	dbSNP_100	33	3674,4926	513.9+/-378.3	792,2090,1418	no	missense,missense	TNIP2	NM_001161527.1,NM_024309.3	64,64	839,2624,3040	AA,AG,GG		42.7209,14.2533,33.077	benign,benign	289/323,396/430	2744087	4302,8704	2203	4300	6503	SO:0001583	missense	79155	exon6			CTCTGGGCCGCGC	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.1187C>T	4.37:g.2744087G>A	ENSP00000321203:p.Ala396Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	162	89	0.549383	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	37	CCDS3362.1	795	0.364010989010989	42	0.08536585365853659	189	0.5220994475138122	232	0.40559440559440557	332	0.43799472295514513	G	17.98	3.520625	0.64747	0.142533	0.427209	ENSG00000168884	ENST00000510267;ENST00000315423;ENST00000503235	T;T;T	0.38722	1.12;1.12;1.12	5.11	1.99	0.26369	.	0.969853	0.08459	N	0.942635	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	P;P	0.38078	0.617;0.483	B;B	0.33960	0.173;0.163	T	0.45396	-0.9264	9	0.54805	T	0.06	-3.312	12.8156	0.57663	0.0:0.0:0.4836:0.5164	rs2269495;rs17849661;rs2269495	313;396	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	V	289;396;313	ENSP00000427613:A289V;ENSP00000321203:A396V;ENSP00000426314:A313V	ENSP00000321203:A396V	A	-	2	0	TNIP2	2713885	0.002000	0.14202	0.001000	0.08648	0.006000	0.05464	0.476000	0.22180	0.536000	0.28733	0.561000	0.74099	GCC	G|0.671;N|0.001	.	strong		0.667	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309	
ARL2	402	hgsc.bcm.edu	37	11	64789222	64789222	+	Silent	SNP	C	C	T	rs61736632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:64789222C>T	ENST00000246747.4	+	5	545	c.450C>T	c.(448-450)caC>caT	p.H150H	ARL2_ENST00000533729.1_Silent_p.H123H|RP11-399J13.3_ENST00000301886.3_Intron|ARL2_ENST00000529384.1_Silent_p.H150H	NM_001667.3	NP_001658.2	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	150					cell cycle (GO:0007049)|centrosome organization (GO:0051297)|GTP catabolic process (GO:0006184)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of GTPase activity (GO:0034260)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of microtubule polymerization (GO:0031116)|regulation of microtubule polymerization (GO:0031113)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)|tubulin complex assembly (GO:0007021)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|GTPase inhibitor activity (GO:0005095)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	5						TCCGCAGCCACCACTGGTGCA	0.642													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		17847	0.0		0.0129	False		,,,				2504	0.002				p.H150H		Atlas-SNP	.											.	ARL2	11	.	0			c.C450T						PASS	.	C	,	10,4392	16.8+/-37.8	0,10,2191	47.0	40.0	42.0		369,450	4.5	1.0	11	dbSNP_129	42	112,8482	58.7+/-120.3	0,112,4185	no	coding-synonymous,coding-synonymous	ARL2	NM_001199745.1,NM_001667.3	,	0,122,6376	TT,TC,CC		1.3032,0.2272,0.9388	,	123/158,150/185	64789222	122,12874	2201	4297	6498	SO:0001819	synonymous_variant	402	exon5			CAGCCACCACTGG	AF493888	CCDS8088.1, CCDS55770.1	11q13	2014-05-09			ENSG00000213465	ENSG00000213465		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	693	protein-coding gene	gene with protein product		601175				8415637, 9253601	Standard	NM_001667		Approved	ARFL2	uc001och.4	P36404	OTTHUMG00000165728	ENST00000246747.4:c.450C>T	11.37:g.64789222C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_001667	G3V184|Q9BUK8	Silent	SNP	ENST00000246747.4	37	CCDS8088.1																																																																																			C|0.992;T|0.008	0.008	strong		0.642	ARL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385963.1	NM_001667	
MTTP	4547	hgsc.bcm.edu	37	4	100532602	100532602	+	Missense_Mutation	SNP	G	G	A	rs113337987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100532602G>A	ENST00000265517.5	+	14	2184	c.1981G>A	c.(1981-1983)Ggt>Agt	p.G661S	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.G661S|MTTP_ENST00000511045.1_Missense_Mutation_p.G688S			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	661					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)	TGGTCTTCACGGTAGCCAGGT	0.413													G|||	49	0.00978435	0.0	0.036	5008	,	,		19260	0.001		0.0209	False		,,,				2504	0.002				p.G661S		Atlas-SNP	.											MTTP,caecum,carcinoma,0,1	MTTP	127	1	0			c.G1981A						PASS	.	G	SER/GLY	26,4380	31.7+/-61.6	0,26,2177	144.0	132.0	136.0		1981	3.7	0.0	4	dbSNP_132	136	305,8295	110.0+/-170.5	11,283,4006	yes	missense	MTTP	NM_000253.2	56	11,309,6183	AA,AG,GG		3.5465,0.5901,2.545	benign	661/895	100532602	331,12675	2203	4300	6503	SO:0001583	missense	4547	exon15			CTTCACGGTAGCC		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.1981G>A	4.37:g.100532602G>A	ENSP00000265517:p.Gly661Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	64	0.615385	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	38	0.0173992673992674	0	0.0	22	0.06077348066298342	0	0.0	16	0.021108179419525065	G	7.432	0.639007	0.14386	0.005901	0.035465	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.60299	0.2;0.21;0.21	5.62	3.68	0.42216	.	0.320705	0.36703	N	0.002460	T	0.07503	0.0189	L	0.34521	1.04	0.34748	D	0.731457	B;B	0.17852	0.024;0.008	B;B	0.09377	0.003;0.004	T	0.21895	-1.0232	10	0.36615	T	0.2	-11.0583	11.7253	0.51706	0.1287:0.0:0.8713:0.0	.	688;661	E9PBP6;P55157	.;MTP_HUMAN	S	688;661;661	ENSP00000427679:G688S;ENSP00000400821:G661S;ENSP00000265517:G661S	ENSP00000265517:G661S	G	+	1	0	MTTP	100751625	1.000000	0.71417	0.004000	0.12327	0.011000	0.07611	4.409000	0.59768	0.533000	0.28675	0.655000	0.94253	GGT	G|0.970;A|0.030	0.030	strong		0.413	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
ETAA1	54465	hgsc.bcm.edu	37	2	67632125	67632125	+	Missense_Mutation	SNP	C	C	T	rs3770655	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:67632125C>T	ENST00000272342.5	+	5	2441	c.2311C>T	c.(2311-2313)Cca>Tca	p.P771S	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	771			P -> S (in dbSNP:rs3770655). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.P771S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						ATTGGTTCTTCCAGGAAGTTC	0.318													T|||	3735	0.745807	0.916	0.7233	5008	,	,		20216	0.5685		0.7316	False		,,,				2504	0.729				p.P771S		Atlas-SNP	.											ETAA1,NS,carcinoma,-1,2	ETAA1	88	2	1	Substitution - Missense(1)	stomach(1)	c.C2311T						scavenged	.	T	SER/PRO	3929,475	214.1+/-233.5	1752,425,25	45.0	47.0	46.0		2311	-8.3	0.0	2	dbSNP_107	46	6160,2438	398.3+/-346.1	2220,1720,359	yes	missense	ETAA1	NM_019002.3	74	3972,2145,384	TT,TC,CC		28.3554,10.7856,22.4042	benign	771/927	67632125	10089,2913	2202	4299	6501	SO:0001583	missense	54465	exon5			GTTCTTCCAGGAA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.2311C>T	2.37:g.67632125C>T	ENSP00000272342:p.Pro771Ser	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	1596	0.7307692307692307	451	0.9166666666666666	267	0.7375690607734806	325	0.5681818181818182	553	0.7295514511873351	T	0.330	-0.956856	0.02267	0.892144	0.716446	ENSG00000143971	ENST00000272342	T	0.15834	2.39	5.83	-8.29	0.01009	.	1.402030	0.04371	N	0.359154	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	9	0.05833	T	0.94	5.3941	0.9202	0.01313	0.4421:0.1547:0.1612:0.2421	rs3770655;rs52826099;rs60544664;rs3770655	771	Q9NY74	ETAA1_HUMAN	S	771	ENSP00000272342:P771S	ENSP00000272342:P771S	P	+	1	0	ETAA1	67485629	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.232000	0.09055	-1.968000	0.01006	-2.541000	0.00179	CCA	C|0.244;T|0.756	0.756	strong		0.318	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
OR1S1	219959	hgsc.bcm.edu	37	11	57982763	57982763	+	Missense_Mutation	SNP	A	A	G	rs1993088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57982763A>G	ENST00000309433.6	+	1	547	c.547A>G	c.(547-549)Aac>Gac	p.N183D		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	183			N -> D (in dbSNP:rs1993088).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N183D(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GCTCTTCTGTAACCACAACAC	0.463																																					p.N183D		Atlas-SNP	.											OR1S1,NS,carcinoma,0,2	OR1S1	139	2	1	Substitution - Missense(1)	stomach(1)	c.A547G						PASS	.	A	ASP/ASN	839,3563		197,445,1559	211.0	172.0	185.0		547	-1.1	0.0	11	dbSNP_92	185	2540,6040		772,996,2522	no	missense	OR1S1	NM_001004458.1	23	969,1441,4081	GG,GA,AA		29.6037,19.0595,26.0283	benign	183/326	57982763	3379,9603	2201	4290	6491	SO:0001583	missense	219959	exon1			TTCTGTAACCACA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.547A>G	11.37:g.57982763A>G	ENSP00000311688:p.Asn183Asp	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	194	51	0.262887	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	962	0.44047619047619047	111	0.22560975609756098	174	0.48066298342541436	408	0.7132867132867133	269	0.3548812664907652	A	0.009	-1.849961	0.00563	0.190595	0.296037	ENSG00000172774	ENST00000309433	T	0.00241	8.46	3.45	-1.1	0.09872	GPCR, rhodopsin-like superfamily (1);	0.551977	0.16162	N	0.226699	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38286	-0.9668	9	0.37606	T	0.19	.	5.0446	0.14477	0.2795:0.278:0.4425:0.0	rs1993088	183	Q8NH92	OR1S1_HUMAN	D	183	ENSP00000311688:N183D	ENSP00000311688:N183D	N	+	1	0	OR1S1	57739339	0.000000	0.05858	0.017000	0.16124	0.033000	0.12548	0.105000	0.15333	-0.506000	0.06558	-1.305000	0.01319	AAC	A|0.671;G|0.329	0.329	strong		0.463	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
HSPBAP1	79663	hgsc.bcm.edu	37	3	122474121	122474121	+	Missense_Mutation	SNP	G	G	C	rs61756481	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:122474121G>C	ENST00000306103.2	-	5	870	c.727C>G	c.(727-729)Ctg>Gtg	p.L243V	HSPBAP1_ENST00000465044.1_5'UTR|HSPBAP1_ENST00000383659.1_3'UTR	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	243	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		CCTGGGCTCAGTGTAACCGCA	0.448													G|||	134	0.0267572	0.0106	0.0533	5008	,	,		18520	0.0		0.0706	False		,,,				2504	0.0123				p.L243V		Atlas-SNP	.											.	HSPBAP1	32	.	0			c.C727G						PASS	.	G	VAL/LEU	96,4310	79.3+/-117.8	1,94,2108	104.0	91.0	95.0		727	3.4	0.3	3	dbSNP_129	95	658,7942	167.0+/-218.8	33,592,3675	yes	missense	HSPBAP1	NM_024610.5	32	34,686,5783	CC,CG,GG		7.6512,2.1788,5.7973	probably-damaging	243/489	122474121	754,12252	2203	4300	6503	SO:0001583	missense	79663	exon5			GGCTCAGTGTAAC	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"""HSPB (heat shock 27kD) associated protein 1"""			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.727C>G	3.37:g.122474121G>C	ENSP00000302562:p.Leu243Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	37	CCDS3017.1	71	0.03250915750915751	6	0.012195121951219513	20	0.055248618784530384	0	0.0	45	0.059366754617414245	G	16.87	3.242889	0.58995	0.021788	0.076512	ENSG00000169087	ENST00000306103	T	0.35605	1.3	5.24	3.42	0.39159	Cupin, JmjC-type (1);Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.341374	0.30820	N	0.008816	T	0.04907	0.0132	M	0.64260	1.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00577	-1.1662	10	0.45353	T	0.12	.	8.884	0.35392	0.2331:0.0:0.7669:0.0	rs61756481	243	Q96EW2	HBAP1_HUMAN	V	243	ENSP00000302562:L243V	ENSP00000302562:L243V	L	-	1	2	HSPBAP1	123956811	1.000000	0.71417	0.347000	0.25668	0.865000	0.49528	3.707000	0.54838	0.586000	0.29626	0.580000	0.79431	CTG	G|0.952;C|0.048	0.048	strong		0.448	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610	
MAPT	4137	hgsc.bcm.edu	37	17	44071294	44071294	+	Intron	SNP	T	T	C	rs62063845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44071294T>C	ENST00000571987.1	+	8	1507				MAPT_ENST00000347967.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Silent_p.T504T|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Silent_p.T504T|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000535772.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau						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)	TTTAAGCGACTAAGCAAGTCC	0.557													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		18596	0.001		0.2406	False		,,,				2504	0.0613				p.T504T		Atlas-SNP	.											.	MAPT	135	.	0			c.T1512C						PASS	.	C	,,,,,,,	154,2966		6,142,1412	50.0	46.0	47.0		1512,,,,,,,	0.6	1.0	17	dbSNP_129	47	1577,5579		183,1211,2184	no	coding-synonymous,intron,intron,intron,intron,intron,intron,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	,,,,,,,	189,1353,3596	CC,CT,TT		22.0375,4.9359,16.8451	,,,,,,,	504/777,,,,,,,	44071294	1731,8545	1560	3578	5138	SO:0001627	intron_variant	4137	exon10			AGCGACTAAGCAA	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.1507+2342T>C	17.37:g.44071294T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			T|0.860;C|0.140	0.140	strong		0.557	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501500	90501500	+	Missense_Mutation	SNP	G	G	A	rs34017995	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90501500G>A	ENST00000325643.5	+	4	2164	c.2098G>A	c.(2098-2100)Gga>Aga	p.G700R		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	700			G -> R (in dbSNP:rs34017995).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAGGAGCTCCGGAAGGTTCTC	0.597													.|||	388	0.077476	0.2322	0.036	5008	,	,		18362	0.0		0.0497	False		,,,				2504	0.0061				p.G700R		Atlas-SNP	.											.	.	.	.	0			c.G2098A						PASS	.	G	ARG/GLY	803,3603	304.4+/-288.4	64,675,1464	53.0	67.0	62.0		2098	-1.1	0.0	9	dbSNP_126	62	374,8224	120.1+/-179.3	5,364,3930	yes	missense	C9orf79	NM_178828.4	125	69,1039,5394	AA,AG,GG		4.3498,18.2251,9.0511	benign	700/1446	90501500	1177,11827	2203	4299	6502	SO:0001583	missense	286234	exon4			AGCTCCGGAAGGT	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.2098G>A	9.37:g.90501500G>A	ENSP00000322640:p.Gly700Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	43	0.632353	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	166	0.076007326007326	111	0.22560975609756098	16	0.04419889502762431	0	0.0	39	0.051451187335092345	g	0.083	-1.180499	0.01633	0.182251	0.043498	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.06933	3.24	2.36	-1.14	0.09741	.	3.218580	0.01220	N	0.008098	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B;B	0.28178	0.202;0.09	B;B	0.15870	0.012;0.014	T	0.39800	-0.9596	9	0.09084	T	0.74	.	5.4249	0.16419	0.5651:0.0:0.4349:0.0	rs34017995	700;352	Q6ZUB1;Q8NA33	CI079_HUMAN;.	R	700;352	ENSP00000322640:G700R	ENSP00000322640:G700R	G	+	1	0	C9orf79	89691320	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	-0.316000	0.08071	-0.284000	0.09102	0.557000	0.71058	GGA	G|0.919;A|0.081	0.081	strong		0.597	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
EIF2A	83939	hgsc.bcm.edu	37	3	150280445	150280445	+	Missense_Mutation	SNP	C	C	G	rs1132979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:150280445C>G	ENST00000460851.1	+	4	399	c.290C>G	c.(289-291)aCt>aGt	p.T97S	SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000273435.5_Missense_Mutation_p.T92S|EIF2A_ENST00000406576.3_Missense_Mutation_p.T97S|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	35	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	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	
NPEPPS	9520	hgsc.bcm.edu	37	17	45669359	45669359	+	Missense_Mutation	SNP	T	T	G	rs200616431		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45669359T>G	ENST00000322157.4	+	11	1535	c.1298T>G	c.(1297-1299)tTt>tGt	p.F433C	NPEPPS_ENST00000530173.1_Missense_Mutation_p.F429C|NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000544660.1_Missense_Mutation_p.F353C	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	433					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.F433C(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						GATGAGATATTTGATGCTATA	0.383																																					p.F433C		Atlas-SNP	.											NPEPPS,mouth,carcinoma,0,1	NPEPPS	59	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.T1298G						PASS	.						123.0	78.0	93.0					17																	45669359		2020	4149	6169	SO:0001583	missense	9520	exon11			AGATATTTGATGC	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1298T>G	17.37:g.45669359T>G	ENSP00000320324:p.Phe433Cys	Somatic	693	0	0		WXS	Illumina HiSeq	Phase_I	765	221	0.288889	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.519381	0.85495	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000539572;ENST00000544660;ENST00000527964;ENST00000527360	T;T;T;T;T	0.09911	2.93;2.93;2.93;2.93;2.93	5.51	5.51	0.81932	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.54532	0.1864	H	0.99435	4.565	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.76427	-0.2963	10	0.87932	D	0	.	15.6257	0.76855	0.0:0.0:0.0:1.0	.	433;429;433	A6NEC2;E9PLK3;P55786	PSAL_HUMAN;.;PSA_HUMAN	C	429;433;420;353;116;130	ENSP00000433287:F429C;ENSP00000320324:F433C;ENSP00000442461:F353C;ENSP00000435639:F116C;ENSP00000435966:F130C	ENSP00000320324:F433C	F	+	2	0	NPEPPS	43024358	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.850000	0.86915	2.099000	0.63709	0.528000	0.53228	TTT	T|1.000;|0.000	.	weak		0.383	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
THAP8	199745	hgsc.bcm.edu	37	19	36530428	36530428	+	Missense_Mutation	SNP	G	G	A	rs34250145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36530428G>A	ENST00000292894.1	-	3	1013	c.469C>T	c.(469-471)Cct>Tct	p.P157S	THAP8_ENST00000538849.1_Missense_Mutation_p.P12S|AC002116.7_ENST00000586962.1_RNA|THAP8_ENST00000524106.1_5'Flank	NM_152658.2	NP_689871.1	Q8NA92	THAP8_HUMAN	THAP domain containing 8	157			P -> S (in dbSNP:rs34250145). {ECO:0000269|PubMed:15489334}.				DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GACCGCTCAGGAGTTGGCGCA	0.692													g|||	446	0.0890575	0.0318	0.2622	5008	,	,		15842	0.0367		0.0964	False		,,,				2504	0.09				p.P157S		Atlas-SNP	.											.	THAP8	11	.	0			c.C469T						PASS	.	G	SER/PRO	169,4231		2,165,2033	15.0	15.0	15.0		469	-0.7	0.0	19	dbSNP_126	15	824,7764		27,770,3497	yes	missense	THAP8	NM_152658.2	74	29,935,5530	AA,AG,GG		9.5948,3.8409,7.6455	possibly-damaging	157/275	36530428	993,11995	2200	4294	6494	SO:0001583	missense	199745	exon3			GCTCAGGAGTTGG	AK057453	CCDS33000.1	19q13.13	2013-01-25			ENSG00000161277	ENSG00000161277		"""THAP (C2CH-type zinc finger) domain containing"""	23191	protein-coding gene	gene with protein product		612536				12575992	Standard	NM_152658		Approved	FLJ32891	uc002oda.1	Q8NA92	OTTHUMG00000048138	ENST00000292894.1:c.469C>T	19.37:g.36530428G>A	ENSP00000292894:p.Pro157Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_152658	Q0P5Z7|Q96M21	Missense_Mutation	SNP	ENST00000292894.1	37	CCDS33000.1	189	0.08653846153846154	23	0.046747967479674794	77	0.212707182320442	16	0.027972027972027972	73	0.09630606860158311	g	11.30	1.596797	0.28445	0.038409	0.095948	ENSG00000161277	ENST00000292894;ENST00000392182;ENST00000538849	D;T	0.90069	-2.61;1.82	4.54	-0.702	0.11265	.	1.768490	0.05563	U	0.569616	T	0.00210	0.0006	L	0.27053	0.805	0.80722	P	0.0	B	0.18461	0.028	B	0.15052	0.012	T	0.10177	-1.0641	9	0.09338	T	0.73	-13.0061	6.1343	0.20223	0.186:0.2854:0.5286:0.0	rs34250145;rs34250145	157	Q8NA92	THAP8_HUMAN	S	157;157;12	ENSP00000292894:P157S;ENSP00000445493:P12S	ENSP00000292894:P157S	P	-	1	0	THAP8	41222268	0.000000	0.05858	0.005000	0.12908	0.007000	0.05969	-0.644000	0.05415	0.093000	0.17368	0.552000	0.68991	CCT	G|0.931;A|0.069	0.069	strong		0.692	THAP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379036.1	NM_152658	
KLHL8	57563	hgsc.bcm.edu	37	4	88116518	88116518	+	Silent	SNP	A	A	G	rs74604071	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88116518A>G	ENST00000273963.5	-	2	515	c.174T>C	c.(172-174)ctT>ctC	p.L58L	KLHL8_ENST00000425278.2_Silent_p.L58L|KLHL8_ENST00000545252.1_5'UTR|KLHL8_ENST00000512111.1_Silent_p.L58L|KLHL8_ENST00000498875.2_Silent_p.L58L	NM_020803.3	NP_065854.3	Q9P2G9	KLHL8_HUMAN	kelch-like family member 8	58					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)		p.L58L(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		CATAAAATCGAAGAAGAGAAC	0.363													A|||	527	0.105232	0.0688	0.0504	5008	,	,		18625	0.2163		0.0388	False		,,,				2504	0.1472				p.L58L		Atlas-SNP	.											KLHL8,NS,carcinoma,0,1	KLHL8	51	1	1	Substitution - coding silent(1)	stomach(1)	c.T174C						PASS	.	A		255,4151	145.7+/-180.5	10,235,1958	96.0	97.0	97.0		174	-6.6	0.1	4	dbSNP_131	97	222,8378	92.1+/-154.2	4,214,4082	no	coding-synonymous	KLHL8	NM_020803.3		14,449,6040	GG,GA,AA		2.5814,5.7876,3.6675		58/621	88116518	477,12529	2203	4300	6503	SO:0001819	synonymous_variant	57563	exon2			AAATCGAAGAAGA	AB037799	CCDS3617.1, CCDS75163.1	4q21.3	2013-01-30	2013-01-30		ENSG00000145332	ENSG00000145332		"""Kelch-like"", ""BTB/POZ domain containing"""	18644	protein-coding gene	gene with protein product		611967	"""kelch-like 8 (Drosophila)"""				Standard	XM_005263153		Approved	KIAA1378	uc003hql.1	Q9P2G9	OTTHUMG00000130593	ENST00000273963.5:c.174T>C	4.37:g.88116518A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	159	68	0.427673	NM_020803	Q53XA3|Q6N018	Silent	SNP	ENST00000273963.5	37	CCDS3617.1																																																																																			A|0.944;G|0.056	0.056	strong		0.363	KLHL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253040.1		
FLI1	2313	hgsc.bcm.edu	37	11	128675292	128675292	+	Silent	SNP	T	T	A	rs7113191	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000534087.2_Silent_p.A196A|FLI1_ENST00000281428.8_Silent_p.A163A|FLI1_ENST00000525560.1_Silent_p.A36A	NM_001271010.1|NM_002017.4	NP_001257939.1|NP_002008.2	Q01543	FLI1_HUMAN	Fli-1 proto-oncogene, ETS transcription factor	229					blood circulation (GO:0008015)|cell differentiation (GO:0030154)|hemostasis (GO:0007599)|megakaryocyte development (GO:0035855)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/FLI1(2569)	NS(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(2)	31	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		GAAGAGGAGCTTGGGGCAATA	0.398			T	EWSR1	Ewing sarcoma								t|||	877	0.17512	0.2579	0.1254	5008	,	,		21079	0.1706		0.1093	False		,,,				2504	0.1708				p.A229A		Atlas-SNP	.		Dom	yes		11	11q24	2313	Friend leukemia virus integration 1		M	.	FLI1	72	.	0			c.T687A						PASS	.	A	,	916,2778		125,666,1056	77.0	76.0	76.0		588,687	-0.8	0.6	11	dbSNP_116	76	890,7286		47,796,3245	no	coding-synonymous,coding-synonymous	FLI1	NM_001167681.2,NM_002017.3	,	172,1462,4301	AA,AT,TT		10.8855,24.797,15.2148	,	196/420,229/453	128675292	1806,10064	1847	4088	5935	SO:0001819	synonymous_variant	2313	exon6			AGGAGCTTGGGGC	M98833	CCDS44768.1, CCDS53725.1, CCDS59230.1, CCDS59231.1	11q24.1-q24.3	2014-09-17	2013-08-07		ENSG00000151702	ENSG00000151702			3749	protein-coding gene	gene with protein product		193067	"""Friend leukemia virus integration 1"""			1765382	Standard	NM_001167681		Approved	SIC-1, EWSR2	uc010sbu.2	Q01543	OTTHUMG00000165792	ENST00000527786.2:c.687T>A	11.37:g.128675292T>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	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	
SIK1	150094	hgsc.bcm.edu	37	21	44846016	44846016	+	Missense_Mutation	SNP	C	C	T	rs3746951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44846016C>T	ENST00000270162.6	-	2	175	c.43G>A	c.(43-45)Ggt>Agt	p.G15S		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	15			G -> S (in dbSNP:rs3746951). {ECO:0000269|PubMed:17344846}.		cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	TGGCCCTGACCCTGGCCCGCG	0.692													C|||	834	0.166534	0.0129	0.2925	5008	,	,		11980	0.2153		0.2684	False		,,,				2504	0.1299				p.G15S		Atlas-SNP	.											.	SIK1	65	.	0			c.G43A						PASS	.	C	SER/GLY	212,4172		8,196,1988	15.0	17.0	16.0		43	2.4	0.5	21	dbSNP_107	16	2211,6371		269,1673,2349	yes	missense	SIK1	NM_173354.3	56	277,1869,4337	TT,TC,CC		25.7632,4.8358,18.6873	benign	15/784	44846016	2423,10543	2192	4291	6483	SO:0001583	missense	150094	exon2			CCTGACCCTGGCC	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.43G>A	21.37:g.44846016C>T	ENSP00000270162:p.Gly15Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	435	0.19917582417582416	11	0.022357723577235773	95	0.26243093922651933	122	0.21328671328671328	207	0.27308707124010556	C	9.340	1.062697	0.19987	0.048358	0.257632	ENSG00000142178	ENST00000270162	T	0.70869	-0.52	3.5	2.39	0.29439	Protein kinase-like domain (1);	0.506824	0.20703	N	0.087231	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.06607	-1.0817	9	0.09084	T	0.74	.	5.0217	0.14365	0.0:0.6186:0.0:0.3814	rs3746951;rs3746951	15	P57059	SIK1_HUMAN	S	15	ENSP00000270162:G15S	ENSP00000270162:G15S	G	-	1	0	SIK1	43670444	0.800000	0.28916	0.467000	0.27180	0.405000	0.30901	1.484000	0.35508	1.506000	0.48736	0.405000	0.27470	GGT	C|0.827;T|0.173	0.173	strong		0.692	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
ALK	238	hgsc.bcm.edu	37	2	29497967	29497967	+	Missense_Mutation	SNP	G	G	A	rs35228363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:29497967G>A	ENST00000389048.3	-	11	2945	c.2039C>T	c.(2038-2040)aCa>aTa	p.T680I	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	680			T -> I (in dbSNP:rs35228363). {ECO:0000269|PubMed:17344846}.		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)	ACCCTTACCTGTAGGGTCAAA	0.463			"""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|||	50	0.00998403	0.0	0.0288	5008	,	,		19632	0.001		0.0268	False		,,,				2504	0.002				p.T680I		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C2039T						PASS	.	G	ILE/THR	23,4383	29.0+/-57.7	0,23,2180	91.0	92.0	91.0		2039	5.2	1.0	2	dbSNP_126	91	250,8350	99.0+/-160.6	4,242,4054	yes	missense	ALK	NM_004304.4	89	4,265,6234	AA,AG,GG		2.907,0.522,2.099	benign	680/1621	29497967	273,12733	2203	4300	6503	SO:0001583	missense	238	exon11	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TTACCTGTAGGGT	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.2039C>T	2.37:g.29497967G>A	ENSP00000373700:p.Thr680Ile	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	224	113	0.504464	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	21	0.009615384615384616	0	0.0	9	0.024861878453038673	0	0.0	12	0.0158311345646438	G	14.36	2.511497	0.44660	0.00522	0.02907	ENSG00000171094	ENST00000389048	T	0.78246	-1.16	5.21	5.21	0.72293	.	0.304589	0.23175	U	0.051094	T	0.49677	0.1571	L	0.53249	1.67	0.80722	D	1	B	0.22983	0.078	B	0.15484	0.013	T	0.60905	-0.7170	9	.	.	.	.	14.2919	0.66284	0.0:0.0:1.0:0.0	rs35228363;rs61730441	680	Q9UM73	ALK_HUMAN	I	680	ENSP00000373700:T680I	.	T	-	2	0	ALK	29351471	1.000000	0.71417	1.000000	0.80357	0.443000	0.32047	4.489000	0.60309	2.433000	0.82419	0.561000	0.74099	ACA	G|0.984;A|0.016	0.016	strong		0.463	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
TMTC4	84899	hgsc.bcm.edu	37	13	101287340	101287340	+	Missense_Mutation	SNP	C	C	T	rs946837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:101287340C>T	ENST00000376234.3	-	10	1444	c.1255G>A	c.(1255-1257)Gtt>Att	p.V419I	TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000342624.5_Missense_Mutation_p.V438I|TMTC4_ENST00000328767.5_Missense_Mutation_p.V308I	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	419			V -> I (in dbSNP:rs946837).			integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CAGTACCCAACGCTGGGGAGG	0.532													.|||	1950	0.389377	0.3805	0.245	5008	,	,		18621	0.6052		0.3022	False		,,,				2504	0.3712				p.V438I		Atlas-SNP	.											TMTC4,caecum,carcinoma,0,1	TMTC4	103	1	0			c.G1312A						scavenged	.	C	ILE/VAL,ILE/VAL	1575,2831	491.7+/-362.2	274,1027,902	79.0	73.0	75.0		1255,1312	2.4	0.0	13	dbSNP_86	75	2561,6039	416.8+/-352.2	387,1787,2126	yes	missense,missense	TMTC4	NM_001079669.1,NM_032813.2	29,29	661,2814,3028	TT,TC,CC		29.7791,35.7467,31.8007	benign,benign	419/742,438/761	101287340	4136,8870	2203	4300	6503	SO:0001583	missense	84899	exon11			ACCCAACGCTGGG		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1255G>A	13.37:g.101287340C>T	ENSP00000365408:p.Val419Ile	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	837	0.38324175824175827	200	0.4065040650406504	82	0.2265193370165746	330	0.5769230769230769	225	0.29683377308707126	C	0.773	-0.765192	0.02996	0.357467	0.297791	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.51071	0.72;0.72;0.72	5.5	2.4	0.29515	.	0.364899	0.31415	N	0.007686	T	0.00012	0.0000	N	0.17723	0.515	0.80722	P	0.0	B;B;B;B	0.12013	0.002;0.001;0.0;0.005	B;B;B;B	0.12837	0.005;0.008;0.002;0.002	T	0.45145	-0.9281	9	0.10377	T	0.69	.	8.9018	0.35499	0.0:0.6428:0.0:0.3572	rs946837;rs17613595;rs52804855;rs61344452;rs946837	308;419;419;438	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	I	419;438;308	ENSP00000365408:V419I;ENSP00000343871:V438I;ENSP00000365409:V308I	ENSP00000365409:V308I	V	-	1	0	TMTC4	100085341	0.022000	0.18835	0.004000	0.12327	0.099000	0.18886	1.160000	0.31761	0.697000	0.31718	-0.251000	0.11542	GTT	C|0.645;N|0.001	.	strong		0.532	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21196424	21196424	+	Missense_Mutation	SNP	T	T	A	rs11045676	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21196424T>A	ENST00000421593.2	+	6	743	c.743T>A	c.(742-744)tTt>tAt	p.F248Y	LST3_ENST00000540229.1_Intron|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.F295Y|LST3_ENST00000381541.3_Missense_Mutation_p.F295Y|SLCO1B3_ENST00000553473.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GTTTCACTATTTTTGCATGTG	0.299													T|||	359	0.0716853	0.0083	0.1354	5008	,	,		17505	0.003		0.1879	False		,,,				2504	0.0634				p.F248Y		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.T743A						PASS	.	T	TYR/PHE	178,4216		8,162,2027	71.0	72.0	72.0		743	-0.2	0.0	12	dbSNP_120	72	1709,6885		173,1363,2761	yes	missense	SLCO1B7	NM_001009562.4	22	181,1525,4788	AA,AT,TT		19.886,4.051,14.5288		248/641	21196424	1887,11101	2197	4297	6494	SO:0001583	missense	338821	exon6			CACTATTTTTGCA	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.743T>A	12.37:g.21196424T>A	ENSP00000394168:p.Phe248Tyr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	197	0.0902014652014652	6	0.012195121951219513	48	0.13259668508287292	1	0.0017482517482517483	142	0.18733509234828497	.	6.090	0.384882	0.11524	0.04051	0.19886	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.38401	1.14;1.14;1.14	3.17	-0.223	0.13118	.	3.846580	0.00397	N	0.000059	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.30709	0.291;0.078	B;B	0.25884	0.064;0.025	T	0.16988	-1.0384	9	0.62326	D	0.03	.	2.4823	0.04590	0.2331:0.4843:0.0:0.2825	rs11045676;rs52823168	248;295	G3V0H7;F5H094	.;.	Y	295;295;248	ENSP00000370952:F295Y;ENSP00000452013:F295Y;ENSP00000394168:F248Y	ENSP00000370952:F295Y	F	+	2	0	SLCO1B7;RP11-545J16.1	21087691	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	0.207000	0.17395	0.144000	0.18951	-0.756000	0.03474	TTT	T|0.895;A|0.105	0.105	strong		0.299	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
PCNT	5116	hgsc.bcm.edu	37	21	47856916	47856916	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47856916C>T	ENST00000359568.5	+	40	9128	c.9021C>T	c.(9019-9021)tcC>tcT	p.S3007S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3007	Interaction with NEK2.				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)					GGACGTCATCCAATGAGAAAG	0.498																																					p.S3007S		Atlas-SNP	.											.	PCNT	283	.	0			c.C9021T						PASS	.						111.0	94.0	100.0					21																	47856916		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon40			GTCATCCAATGAG	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.9021C>T	21.37:g.47856916C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	77	4	0.0519481	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			.	.	none		0.498	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
PRRC2B	84726	hgsc.bcm.edu	37	9	134340174	134340174	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134340174C>T	ENST00000357304.4	+	11	1484	c.1429C>T	c.(1429-1431)Cgg>Tgg	p.R477W	PRRC2B_ENST00000405995.1_Missense_Mutation_p.R477W|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.R477W	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	477							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						CAGCATGTTCCGGCAACAGTC	0.582																																					p.R477W		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C1429T						PASS	.						30.0	32.0	32.0					9																	134340174		2030	4175	6205	SO:0001583	missense	84726	exon11			ATGTTCCGGCAAC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.1429C>T	9.37:g.134340174C>T	ENSP00000349856:p.Arg477Trp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.806464	0.70682	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550;ENST00000422467	T;T;T;T	0.26373	4.12;4.46;4.12;1.74	5.61	3.64	0.41730	.	0.000000	0.39210	U	0.001428	T	0.45478	0.1344	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.45991	-0.9223	10	0.66056	D	0.02	-3.5568	13.2394	0.59987	0.3749:0.6251:0.0:0.0	.	477	Q5JSZ5	PRC2B_HUMAN	W	477;477;477;17	ENSP00000384606:R477W;ENSP00000349856:R477W;ENSP00000398853:R477W;ENSP00000391063:R17W	ENSP00000349856:R477W	R	+	1	2	PRRC2B	133329995	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.986000	0.40677	1.355000	0.45865	0.655000	0.94253	CGG	.	.	none		0.582	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
NAA25	80018	hgsc.bcm.edu	37	12	112471090	112471090	+	Missense_Mutation	SNP	G	G	T	rs12298022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	97	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	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	
ZMYND12	84217	hgsc.bcm.edu	37	1	42915727	42915727	+	Silent	SNP	C	C	G	rs12047095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:42915727C>G	ENST00000372565.3	-	2	383	c.114G>C	c.(112-114)ggG>ggC	p.G38G	ZMYND12_ENST00000433602.2_5'UTR	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	38						intracellular (GO:0005622)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GATGTACCACCCCACTGACAA	0.443													C|||	1418	0.283147	0.1778	0.1571	5008	,	,		22131	0.4355		0.1879	False		,,,				2504	0.456				p.G38G		Atlas-SNP	.											.	ZMYND12	35	.	0			c.G114C						PASS	.	C	,	827,3579	328.0+/-300.3	81,665,1457	140.0	125.0	130.0		,114	1.9	0.6	1	dbSNP_120	130	1698,6902	310.9+/-310.1	176,1346,2778	no	utr-5,coding-synonymous	ZMYND12	NM_001146192.1,NM_032257.4	,	257,2011,4235	GG,GC,CC		19.7442,18.7699,19.4141	,	,38/366	42915727	2525,10481	2203	4300	6503	SO:0001819	synonymous_variant	84217	exon2			TACCACCCCACTG	AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"""Zinc fingers, MYND-type"""	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.114G>C	1.37:g.42915727C>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_032257	Q5VUS6|Q8TC87|Q96M51	Silent	SNP	ENST00000372565.3	37	CCDS467.1																																																																																			C|0.791;G|0.209	0.209	strong		0.443	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257	
DLC1	10395	hgsc.bcm.edu	37	8	12952293	12952293	+	Silent	SNP	C	C	T	rs658856	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:12952293C>T	ENST00000276297.4	-	12	3910	c.3501G>A	c.(3499-3501)tcG>tcA	p.S1167S	DLC1_ENST00000510318.1_5'UTR|DLC1_ENST00000520226.1_Silent_p.S656S|DLC1_ENST00000358919.2_Silent_p.S730S|DLC1_ENST00000512044.2_Silent_p.S764S	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	112	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	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	
MYEOV2	150678	hgsc.bcm.edu	37	2	241066325	241066325	+	Silent	SNP	A	A	C	rs12614632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241066325A>C	ENST00000307266.3	-	5	413	c.414T>G	c.(412-414)gcT>gcG	p.A138A		NM_138336.1	NP_612209.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	0										breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		CTCTGTCCAAAGCTGCCACTT	0.552													A|||	1081	0.215855	0.0817	0.196	5008	,	,		17504	0.4563		0.2058	False		,,,				2504	0.1738				p.A138A		Atlas-SNP	.											.	MYEOV2	20	.	0			c.T414G						PASS	.	A		396,4010	190.9+/-216.7	17,362,1824	74.0	84.0	81.0		414	0.8	0.0	2	dbSNP_120	81	1563,7035	285.4+/-297.1	134,1295,2870	no	coding-synonymous	MYEOV2	NM_138336.1		151,1657,4694	CC,CA,AA		18.1786,8.9877,15.0646		138/253	241066325	1959,11045	2203	4299	6502	SO:0001819	synonymous_variant	150678	exon5			GTCCAAAGCTGCC	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000307266.3:c.414T>G	2.37:g.241066325A>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_138336	Q8N110	Silent	SNP	ENST00000307266.3	37	CCDS2532.1																																																																																			A|0.814;C|0.186	0.186	strong		0.552	MYEOV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257182.2	NM_138336	
MYO1D	4642	hgsc.bcm.edu	37	17	31048141	31048141	+	Missense_Mutation	SNP	G	G	A	rs375202047		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:31048141G>A	ENST00000318217.5	-	15	2117	c.1813C>T	c.(1813-1815)Cgc>Tgc	p.R605C	MYO1D_ENST00000579584.1_Missense_Mutation_p.R605C|MYO1D_ENST00000394649.4_Missense_Mutation_p.R517C	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	605	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			TGCCGGCAGCGTTCATCATCA	0.428																																					p.R605C		Atlas-SNP	.											.	MYO1D	93	.	0			c.C1813T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	164.0	172.0	169.0		1813	4.3	1.0	17		169	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYO1D	NM_015194.1	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	605/1007	31048141	1,13005	2203	4300	6503	SO:0001583	missense	4642	exon15			GGCAGCGTTCATC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.1813C>T	17.37:g.31048141G>A	ENSP00000324527:p.Arg605Cys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	162	84	0.518519	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.620942	0.87460	0.0	1.16E-4	ENSG00000176658	ENST00000318217	D	0.87179	-2.22	5.33	4.32	0.51571	Myosin head, motor domain (2);	0.000000	0.33834	U	0.004520	D	0.93294	0.7863	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	D	0.93324	0.6695	10	0.72032	D	0.01	.	11.2797	0.49186	0.0:0.0:0.7002:0.2998	.	516;605	Q7Z3N6;O94832	.;MYO1D_HUMAN	C	605	ENSP00000324527:R605C	ENSP00000324527:R605C	R	-	1	0	MYO1D	28072254	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	6.347000	0.73004	2.781000	0.95711	0.650000	0.86243	CGC	.	.	weak		0.428	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
ABHD16B	140701	hgsc.bcm.edu	37	20	62492922	62492922	+	Missense_Mutation	SNP	T	T	A	rs2281534	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62492922T>A	ENST00000369916.3	+	1	357	c.29T>A	c.(28-30)cTg>cAg	p.L10Q	C20ORF135_ENST00000601296.1_Missense_Mutation_p.Q99L	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	10			L -> Q (in dbSNP:rs2281534).				hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						GTGAAGGCGCTGGTGCGCGTG	0.677													T|||	329	0.0656949	0.0136	0.0548	5008	,	,		11583	0.129		0.0706	False		,,,				2504	0.0736				p.L10Q		Atlas-SNP	.											.	ABHD16B	22	.	0			c.T29A						PASS	.	T	GLN/LEU	73,4309		0,73,2118	25.0	16.0	19.0		29	3.8	1.0	20	dbSNP_100	19	598,7952		8,582,3685	yes	missense	ABHD16B	NM_080622.3	113	8,655,5803	AA,AT,TT		6.9942,1.6659,5.1887	probably-damaging	10/470	62492922	671,12261	2191	4275	6466	SO:0001583	missense	140701	exon1			AGGCGCTGGTGCG		CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"""Abhydrolase domain containing"""	16128	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 135"""	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.29T>A	20.37:g.62492922T>A	ENSP00000358932:p.Leu10Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_080622		Missense_Mutation	SNP	ENST00000369916.3	37	CCDS13539.1	154	0.07051282051282051	8	0.016260162601626018	20	0.055248618784530384	72	0.1258741258741259	54	0.0712401055408971	T	19.21	3.784167	0.70222	0.016659	0.069942	ENSG00000183260	ENST00000369916	T	0.54866	0.55	3.77	3.77	0.43336	.	0.612694	0.15192	U	0.275503	T	0.01454	0.0047	M	0.76727	2.345	0.35373	P	0.21074700000000002	D	0.76494	0.999	P	0.61800	0.894	T	0.46317	-0.9200	9	0.87932	D	0	-8.8752	10.7261	0.46068	0.0:0.0:0.0:1.0	rs2281534	10	Q9H3Z7	ABHGB_HUMAN	Q	10	ENSP00000358932:L10Q	ENSP00000358932:L10Q	L	+	2	0	ABHD16B	61963366	0.986000	0.35501	0.987000	0.45799	0.990000	0.78478	4.022000	0.57203	1.476000	0.48215	0.533000	0.62120	CTG	T|0.942;A|0.058	0.058	strong		0.677	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1		
AFF3	3899	hgsc.bcm.edu	37	2	100623130	100623130	+	Silent	SNP	G	G	A	rs34506074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:100623130G>A	ENST00000409236.2	-	5	949	c.837C>T	c.(835-837)gcC>gcT	p.A279A	AFF3_ENST00000317233.4_Silent_p.A279A|AFF3_ENST00000356421.2_Silent_p.A304A|AFF3_ENST00000409579.1_Silent_p.A304A			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	279					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						TGGAGAGCTTGGCCTTGGCTC	0.542													G|||	166	0.033147	0.093	0.0173	5008	,	,		18440	0.0		0.0149	False		,,,				2504	0.0164				p.A304A		Atlas-SNP	.											.	AFF3	164	.	0			c.C912T						PASS	.	G	,	318,4088	166.9+/-198.0	18,282,1903	53.0	57.0	56.0		912,837	4.5	1.0	2	dbSNP_126	56	112,8488	58.7+/-120.3	0,112,4188	no	coding-synonymous,coding-synonymous	AFF3	NM_001025108.1,NM_002285.2	,	18,394,6091	AA,AG,GG		1.3023,7.2174,3.3062	,	304/1252,279/1227	100623130	430,12576	2203	4300	6503	SO:0001819	synonymous_variant	3899	exon6			GAGCTTGGCCTTG	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.837C>T	2.37:g.100623130G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																			G|0.965;A|0.035	0.035	strong		0.542	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72503344	72503344	+	Silent	SNP	G	G	A	rs10999502	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:72503344G>A	ENST00000373207.1	+	13	1965	c.1965G>A	c.(1963-1965)acG>acA	p.T655T	ADAMTS14_ENST00000373208.1_Silent_p.T658T	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	655	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CGGCGGACACGGGGGACGTGG	0.622													G|||	1560	0.311502	0.1641	0.2089	5008	,	,		19688	0.5387		0.2167	False		,,,				2504	0.4468				p.T658T		Atlas-SNP	.											ADAMTS14,NS,adenoma,0,1	ADAMTS14	148	1	0			c.G1974A						PASS	.	G	,	760,3646	308.0+/-290.3	51,658,1494	95.0	76.0	82.0		1965,1974	-10.0	0.4	10	dbSNP_120	82	1824,6776	328.1+/-318.2	192,1440,2668	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	243,2098,4162	AA,AG,GG		21.2093,17.2492,19.8678	,	655/1224,658/1227	72503344	2584,10422	2203	4300	6503	SO:0001819	synonymous_variant	140766	exon13			GGACACGGGGGAC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1965G>A	10.37:g.72503344G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	155	87	0.56129	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			G|0.768;A|0.232	0.232	strong		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
UBXN11	91544	hgsc.bcm.edu	37	1	26608896	26608896	+	Missense_Mutation	SNP	C	C	G	rs367932248|rs72872911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26608896C>G	ENST00000374222.1	-	16	1921	c.1457G>C	c.(1456-1458)tGt>tCt	p.C486S	UBXN11_ENST00000357089.4_Missense_Mutation_p.C453S|UBXN11_ENST00000314675.7_Missense_Mutation_p.C366S|UBXN11_ENST00000374217.2_Missense_Mutation_p.C453S|UBXN11_ENST00000374221.3_Missense_Mutation_p.C486S|UBXN11_ENST00000374223.1_Missense_Mutation_p.C243S			Q5T124	UBX11_HUMAN	UBX domain protein 11	486	Pro-rich.		C -> CPGPGPGPS. {ECO:0000269|PubMed:15498874}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggaccgggacagggaccagg	0.721																																					p.C486S		Atlas-SNP	.											UBXN11,colon,carcinoma,0,2	UBXN11	54	2	0			c.G1457C						PASS	.	C	SER/CYS,SER/CYS,SER/CYS	921,2795		132,657,1069	52.0	64.0	60.0		1457,1358,1097	-0.6	0.0	1	dbSNP_130	60	768,7372		37,694,3339	yes	missense,missense,missense	UBXN11	NM_183008.2,NM_145345.2,NM_001077262.1	112,112,112	169,1351,4408	GG,GC,CC		9.4349,24.7847,14.246	benign,benign,benign	486/521,453/488,366/401	26608896	1689,10167	1858	4070	5928	SO:0001583	missense	91544	exon16			CCGGGACAGGGAC	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.1457G>C	1.37:g.26608896C>G	ENSP00000363339:p.Cys486Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	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	356	0.163003663003663	139	0.28252032520325204	61	0.1685082872928177	83	0.1451048951048951	73	0.09630606860158311	C	0.430	-0.903960	0.02453	0.247847	0.094349	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.15139	2.45;2.45;2.72;2.72;2.72;2.72	1.54	-0.618	0.11576	.	11.973500	0.00901	U	0.002346	T	0.00012	0.0000	N	0.08118	0	0.58432	P	4.000000000004E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.35151	-0.9800	9	0.06891	T	0.86	.	3.807	0.08782	0.0:0.4965:0.0:0.5035	.	453;448;366;486	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	366;243;453;486;486;453	ENSP00000324721:C366S;ENSP00000363340:C243S;ENSP00000349601:C453S;ENSP00000363338:C486S;ENSP00000363339:C486S;ENSP00000363334:C453S	ENSP00000324721:C366S	C	-	2	0	UBXN11	26481483	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.279000	0.02807	-0.021000	0.14009	0.462000	0.41574	TGT	C|0.849;G|0.151	0.151	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
LPA	4018	hgsc.bcm.edu	37	6	161007538	161007538	+	Missense_Mutation	SNP	G	G	C	rs7765803	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	132	0	0		WXS	Illumina HiSeq	Phase_I	112	43	0.383929	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	
SLC27A5	10998	hgsc.bcm.edu	37	19	59009949	59009949	+	Missense_Mutation	SNP	G	G	C	rs145618122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:59009949G>C	ENST00000263093.2	-	10	2115	c.2006C>G	c.(2005-2007)gCc>gGc	p.A669G	SLC27A5_ENST00000594786.1_Missense_Mutation_p.A74G|SLC27A5_ENST00000601355.1_Missense_Mutation_p.A585G|SLC27A5_ENST00000599700.1_5'UTR	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	669					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)		GAAGGACTGGGCCCGGTTGTC	0.582													G|||	22	0.00439297	0.0015	0.0043	5008	,	,		18662	0.0		0.008	False		,,,				2504	0.0092				p.A669G		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C2006G						PASS	.	G	GLY/ALA	2,4404	4.2+/-10.8	0,2,2201	124.0	106.0	112.0		2006	2.5	0.0	19	dbSNP_134	112	78,8522	42.2+/-99.7	0,78,4222	yes	missense	SLC27A5	NM_012254.2	60	0,80,6423	CC,CG,GG		0.907,0.0454,0.6151	benign	669/691	59009949	80,12926	2203	4300	6503	SO:0001583	missense	10998	exon10			GACTGGGCCCGGT	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.2006C>G	19.37:g.59009949G>C	ENSP00000263093:p.Ala669Gly	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	11	0.005036630036630037	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	7.891	0.732413	0.15507	4.54E-4	0.00907	ENSG00000083807	ENST00000263093	T	0.53423	0.62	4.85	2.51	0.30379	.	0.370857	0.28130	N	0.016500	T	0.22742	0.0549	N	0.25245	0.725	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.12426	-1.0548	10	0.27082	T	0.32	-8.9846	9.675	0.40034	0.0:0.0:0.6228:0.3772	.	669	Q9Y2P5	S27A5_HUMAN	G	669	ENSP00000263093:A669G	ENSP00000263093:A669G	A	-	2	0	SLC27A5	63701761	0.000000	0.05858	0.005000	0.12908	0.392000	0.30506	0.058000	0.14301	1.137000	0.42214	0.655000	0.94253	GCC	G|0.992;C|0.008	0.008	strong		0.582	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
EXOSC6	118460	hgsc.bcm.edu	37	16	70287177	70287177	+	5'Flank	SNP	A	A	G	rs4081753	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70287177A>G	ENST00000435634.1	-	0	0				AARS_ENST00000564359.1_5'Flank|AARS_ENST00000261772.8_Silent_p.V905V	NM_058219.2	NP_478126.1	Q5RKV6	EXOS6_HUMAN	exosome component 6						DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										TGACCTGGGGAACTTGACACA	0.532											OREG0023912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	4413	0.88119	0.9894	0.7795	5008	,	,		21337	0.9663		0.7972	False		,,,				2504	0.8057				p.V905V		Atlas-SNP	.											AARS,NS,carcinoma,0,1	AARS	62	1	0			c.T2715C						PASS	.	G		4210,186		2016,178,4	108.0	89.0	95.0		2715	-1.1	0.9	16	dbSNP_108	95	6826,1774		2702,1422,176	no	coding-synonymous	AARS	NM_001605.2		4718,1600,180	GG,GA,AA		20.6279,4.2311,15.0816		905/969	70287177	11036,1960	2198	4300	6498	SO:0001631	upstream_gene_variant	16	exon20			CTGGGGAACTTGA	BC052252	CCDS10887.1	16q22.1	2008-02-05			ENSG00000223496	ENSG00000223496			19055	protein-coding gene	gene with protein product	"""Mtr3 (mRNA transport regulator 3)-homolog (yeast)"""	606490				11719186, 12419256	Standard	NM_058219		Approved	MTR3, hMtr3p, Mtr3p, EAP4, p11	uc002eym.1	Q5RKV6	OTTHUMG00000137578		16.37:g.70287177A>G	Exception_encountered	Somatic	171	1	0.00584795	1121	WXS	Illumina HiSeq	Phase_I	166	166	1	NM_001605		Silent	SNP	ENST00000435634.1	37	CCDS10887.1																																																																																			A|0.137;C|0.000;G|0.863	0.863	strong		0.532	EXOSC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268966.1	NM_058219	
EBLN2	55096	hgsc.bcm.edu	37	3	73111368	73111368	+	Missense_Mutation	SNP	T	T	C	rs2231924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:73111368T>C	ENST00000533473.1	+	1	559	c.136T>C	c.(136-138)Tcc>Ccc	p.S46P	PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	46										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						GAACCAATTTTCCACAATGTC	0.418													C|||	2637	0.526558	0.6188	0.3689	5008	,	,		17712	0.4514		0.508	False		,,,				2504	0.6104				p.S46P		Atlas-SNP	.											.	EBLN2	18	.	0			c.T136C						PASS	.	C	PRO/SER,	2389,1425		746,897,264	38.0	36.0	37.0		136,	-0.5	0.0	3	dbSNP_98	37	4205,4035		1078,2049,993	yes	missense,intron	EBLN2,PPP4R2	NM_018029.3,NM_174907.2	74,	1824,2946,1257	CC,CT,TT		48.9684,37.3623,45.2962	benign,	46/273,	73111368	6594,5460	1907	4120	6027	SO:0001583	missense	55096	exon1			CAATTTTCCACAA		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 2"""	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.136T>C	3.37:g.73111368T>C	ENSP00000432104:p.Ser46Pro	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	154	152	0.987013	NM_018029	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	1073	0.4913003663003663	301	0.6117886178861789	143	0.39502762430939226	249	0.4353146853146853	380	0.5013192612137203	C	0.507	-0.868432	0.02590	0.626377	0.510316	ENSG00000255423	ENST00000533473	.	.	.	0.587	-0.462	0.12168	.	.	.	.	.	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	0.41752	-0.9491	6	0.18710	T	0.47	.	.	.	.	rs2231924;rs3732439;rs52803163;rs2231924	46	Q6P2I7	EBLN2_HUMAN	P	46	.	ENSP00000432104:S46P	S	+	1	0	EBLN2	73194058	0.005000	0.15991	0.003000	0.11579	0.006000	0.05464	-1.034000	0.03567	-1.023000	0.03342	-0.684000	0.03749	TCC	T|0.501;C|0.499	0.499	strong		0.418	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029	
TBXAS1	6916	hgsc.bcm.edu	37	7	139717523	139717523	+	Missense_Mutation	SNP	G	G	T	rs561266357|rs149988492	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:139717523G>T	ENST00000336425.5	+	16	1806	c.1417G>T	c.(1417-1419)Ggg>Tgg	p.G473W	TBXAS1_ENST00000425687.1_Missense_Mutation_p.G406W|TBXAS1_ENST00000436047.2_Missense_Mutation_p.G474W|TBXAS1_ENST00000263552.6_Missense_Mutation_p.G474W|TBXAS1_ENST00000411653.1_Intron|TBXAS1_ENST00000416849.2_Missense_Mutation_p.G520W|TBXAS1_ENST00000448866.1_Missense_Mutation_p.G473W|TBXAS1_ENST00000414508.2_Intron|TBXAS1_ENST00000458722.1_Missense_Mutation_p.G519W			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	473					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)	CCTGCCCTTCGGGGCCGGCCC	0.682																																					p.G520W		Atlas-SNP	.											.	TBXAS1	121	.	0			c.G1558T						PASS	.	G	TRP/GLY,TRP/GLY,TRP/GLY,TRP/GLY,	1,4405	2.1+/-5.4	0,1,2202	41.0	46.0	44.0		1420,1420,1558,1216,	4.7	0.3	7	dbSNP_134	44	0,8598		0,0,4299	no	missense,missense,missense,missense,intron	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	184,184,184,184,	0,1,6501	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,	474/535,474/535,520/581,406/467,	139717523	1,13003	2203	4299	6502	SO:0001583	missense	6916	exon13			CCCTTCGGGGCCG	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.1417G>T	7.37:g.139717523G>T	ENSP00000338087:p.Gly473Trp	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	324	182	0.561728	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		.	.	.	.	.	.	.	.	.	.	G	22.0	4.228603	0.79576	2.27E-4	0.0	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000448866;ENST00000458722	T;T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36	4.69	4.69	0.59074	Cytochrome P450, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93242	0.7847	H	0.97291	3.975	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.95589	0.8653	10	0.87932	D	0	.	15.4076	0.74890	0.0:0.0:1.0:0.0	.	454;520;406;474;473	B4DVP1;E7EP08;E7ESB5;Q53F23;P24557	.;.;.;.;THAS_HUMAN	W	406;474;473;520;474;473;519	ENSP00000388736:G406W;ENSP00000263552:G474W;ENSP00000338087:G473W;ENSP00000389414:G520W;ENSP00000392361:G474W;ENSP00000402536:G473W;ENSP00000411274:G519W	ENSP00000263552:G474W	G	+	1	0	TBXAS1	139363992	1.000000	0.71417	0.334000	0.25495	0.882000	0.50991	6.773000	0.75006	2.162000	0.67917	0.561000	0.74099	GGG	G|1.000;T|0.000	0.000	strong		0.682	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
DNAH14	127602	hgsc.bcm.edu	37	1	225533931	225533931	+	Missense_Mutation	SNP	A	A	G	rs17522489	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225533931A>G	ENST00000445597.2	+	48	8258	c.8258A>G	c.(8257-8259)cAa>cGa	p.Q2753R	DNAH14_ENST00000439375.2_Missense_Mutation_p.Q3556R|DNAH14_ENST00000430092.1_Missense_Mutation_p.Q3556R			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2753					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						AGCAAAGAACAAGAACATAGT	0.348													A|||	698	0.139377	0.0325	0.1182	5008	,	,		17247	0.1389		0.1571	False		,,,				2504	0.2812				p.Q3556R		Atlas-SNP	.											.	DNAH14	300	.	0			c.A10667G						PASS	.	A	ARG/GLN	52,1332		1,50,641	55.0	46.0	49.0		10667	5.4	0.0	1	dbSNP_123	49	520,2662		53,414,1124	yes	missense	DNAH14	NM_001373.1	43	54,464,1765	GG,GA,AA		16.3419,3.7572,12.5274	probably-damaging	3556/4516	225533931	572,3994	692	1591	2283	SO:0001583	missense	127602	exon68			AAGAACAAGAACA	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.8258A>G	1.37:g.225533931A>G	ENSP00000409472:p.Gln2753Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		267	0.12225274725274725	17	0.034552845528455285	48	0.13259668508287292	72	0.1258741258741259	130	0.17150395778364116	A	7.092	0.572263	0.13623	0.037572	0.163419	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.57107	0.42;1.51;1.51	5.45	5.45	0.79879	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	0.999999999524782	P	0.38677	0.642	B	0.38458	0.274	T	0.10543	-1.0625	7	0.23302	T	0.38	.	13.0181	0.58771	1.0:0.0:0.0:0.0	rs17522489;rs52821134;rs17522489	3556	Q0VDD8-4	.	R	2753;3556;3556	ENSP00000409472:Q2753R;ENSP00000414402:Q3556R;ENSP00000392061:Q3556R	ENSP00000414402:Q3556R	Q	+	2	0	DNAH14	223600554	0.000000	0.05858	0.019000	0.16419	0.680000	0.39746	0.710000	0.25748	2.055000	0.61198	0.416000	0.27883	CAA	A|0.887;G|0.113	0.113	strong		0.348	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
RPH3AL	9501	hgsc.bcm.edu	37	17	96910	96910	+	Missense_Mutation	SNP	C	C	T	rs376959240		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:96910C>T	ENST00000331302.7	-	7	912	c.605G>A	c.(604-606)cGa>cAa	p.R202Q	RPH3AL_ENST00000536489.2_Missense_Mutation_p.R173Q|RPH3AL_ENST00000576001.1_5'UTR|RPH3AL_ENST00000323434.8_Missense_Mutation_p.R173Q	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	202					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)		ACCTCTTCCTCGGGCCCACGT	0.632													c|||	1	0.000199681	0.0	0.0	5008	,	,		17004	0.001		0.0	False		,,,				2504	0.0				p.R202Q		Atlas-SNP	.											.	RPH3AL	18	.	0			c.G605A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	98.0	91.0	93.0		605,518,518,605	5.1	1.0	17		93	0,8600		0,0,4300	no	missense,missense,missense,missense	RPH3AL	NM_001190411.1,NM_001190412.1,NM_001190413.1,NM_006987.3	43,43,43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	202/316,173/287,173/287,202/316	96910	1,13005	2203	4300	6503	SO:0001583	missense	9501	exon7			CTTCCTCGGGCCC		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.605G>A	17.37:g.96910C>T	ENSP00000328977:p.Arg202Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_006987	D3DTG7|Q9BSB3	Missense_Mutation	SNP	ENST00000331302.7	37	CCDS10994.1	.	.	.	.	.	.	.	.	.	.	c	18.68	3.676535	0.67928	2.27E-4	0.0	ENSG00000181031	ENST00000323434;ENST00000331302;ENST00000536489	.	.	.	5.06	5.06	0.68205	.	0.114746	0.35235	N	0.003345	T	0.62011	0.2393	M	0.77103	2.36	0.22710	N	0.998827	D;D;D	0.76494	0.981;0.999;0.999	P;D;P	0.64237	0.551;0.923;0.849	T	0.55786	-0.8086	9	0.21540	T	0.41	-5.7361	9.6113	0.39665	0.0:0.9048:0.0:0.0952	.	173;173;202	A8K7D5;Q9UNE2-2;Q9UNE2	.;.;RPH3L_HUMAN	Q	202;173;173	.	ENSP00000319210:R202Q	R	-	2	0	RPH3AL	96910	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	2.084000	0.41625	2.378000	0.81104	0.544000	0.68410	CGA	.	.	weak		0.632	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987	
OR2L8	391190	hgsc.bcm.edu	37	1	248112627	248112627	+	Silent	SNP	T	T	C	rs4925787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248112627T>C	ENST00000357191.3	+	1	468	c.468T>C	c.(466-468)tgT>tgC	p.C156C	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	156						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)			TCAATGCTTGTGCTCACACTG	0.463													T|||	2063	0.411941	0.0893	0.549	5008	,	,		22525	0.4385		0.6103	False		,,,				2504	0.5194				p.C156C		Atlas-SNP	.											.	OR2L8	92	.	0			c.T468C						PASS	.	T	,	826,3580		53,720,1430	228.0	168.0	188.0		468,	1.8	1.0	1	dbSNP_111	188	5178,3422		1425,2328,547	no	coding-synonymous,intron	OR2L13,OR2L8	NM_001001963.1,NM_175911.2	,	1478,3048,1977	CC,CT,TT		39.7907,18.7472,46.1633	,	156/313,	248112627	6004,7002	2203	4300	6503	SO:0001819	synonymous_variant	391190	exon1			TGCTTGTGCTCAC	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.468T>C	1.37:g.248112627T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	203	201	0.990148	NM_001001963	Q6IF03	Silent	SNP	ENST00000357191.3	37	CCDS31101.1																																																																																			C|1.000;|0.000	1.000	weak		0.463	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
MYO7B	4648	hgsc.bcm.edu	37	2	128321770	128321770	+	Missense_Mutation	SNP	G	G	A	rs2404991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:128321770G>A	ENST00000409816.2	+	2	93	c.61G>A	c.(61-63)Ggc>Agc	p.G21S	MYO7B_ENST00000389524.4_Missense_Mutation_p.G21S|MYO7B_ENST00000428314.1_Missense_Mutation_p.G21S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	21			G -> S (in dbSNP:rs2404991).			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)		CCACAAGACCGGCGTGGCCAT	0.612													G|||	1980	0.395367	0.1392	0.5807	5008	,	,		20314	0.5526		0.4801	False		,,,				2504	0.3609				p.G21S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G61A						PASS	.	G	SER/GLY	773,3267		85,603,1332	53.0	66.0	62.0		61	-0.3	0.0	2	dbSNP_100	62	4180,4166		1054,2072,1047	yes	missense	MYO7B	NM_001080527.1	56	1139,2675,2379	AA,AG,GG		49.9161,19.1337,39.9887	benign	21/2117	128321770	4953,7433	2020	4173	6193	SO:0001583	missense	4648	exon3			AAGACCGGCGTGG		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.61G>A	2.37:g.128321770G>A	ENSP00000386461:p.Gly21Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	989	0.45283882783882784	82	0.16666666666666666	206	0.569060773480663	316	0.5524475524475524	385	0.5079155672823219	G	6.991	0.552909	0.13374	0.191337	0.500839	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86956	-2.19;-2.19;-2.19	5.48	-0.284	0.12870	.	1.356880	0.04746	N	0.423624	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18310	0.027	B	0.12156	0.007	T	0.19614	-1.0300	9	0.07030	T	0.85	.	10.5274	0.44957	0.7558:0.0:0.2442:0.0	rs2404991;rs17261901;rs57174242	21	Q6PIF6	MYO7B_HUMAN	S	21	ENSP00000374175:G21S;ENSP00000415090:G21S;ENSP00000386461:G21S	ENSP00000374175:G21S	G	+	1	0	MYO7B	128038240	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	0.446000	0.21694	0.001000	0.14605	0.563000	0.77884	GGC	G|0.541;A|0.458	0.458	strong		0.612	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
MAGEA11	4110	hgsc.bcm.edu	37	X	148798223	148798223	+	Silent	SNP	T	T	C	rs2233050	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:148798223T>C	ENST00000355220.5	+	5	1179	c.1077T>C	c.(1075-1077)ctT>ctC	p.L359L	MAGEA11_ENST00000333104.4_Silent_p.L330L	NM_005366.4	NP_005357.2	P43364	MAGAB_HUMAN	melanoma antigen family A, 11	359	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	9	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					AGAGGCTCCTTACCCAAAATT	0.567													-|||	1917	0.507815	0.6543	0.4914	3775	,	,		15281	0.1776		0.3946	False		,,,				2504	0.138				p.L359L		Atlas-SNP	.											.	MAGEA11	86	.	0			c.T1077C						PASS	.	C	,	3095,740		1059,506,471,67,100	129.0	134.0	132.0		990,1077	-0.1	0.0	X	dbSNP_98	132	3249,3479		585,1168,911,675,961	no	coding-synonymous,coding-synonymous	MAGEA11	NM_001011544.1,NM_005366.4	,	1644,1674,1382,742,1061	CC,CT,C,TT,T		48.2907,19.296,39.9413	,	330/401,359/430	148798223	6344,4219	2203	4300	6503	SO:0001819	synonymous_variant	4110	exon5			GCTCCTTACCCAA		CCDS48180.1	Xq28	2009-03-13			ENSG00000185247	ENSG00000185247			6798	protein-coding gene	gene with protein product	"""MAGE-11 antigen"", ""melanoma-associated antigen 11"", ""cancer/testis antigen family 1, member 11"""	300344		MAGE11		8575766	Standard	NM_001011544		Approved	MAGE-11, MAGEA-11, MGC10511, CT1.11	uc004fdq.3	P43364	OTTHUMG00000022633	ENST00000355220.5:c.1077T>C	X.37:g.148798223T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_005366	Q5ETU4|Q6ZRZ5	Silent	SNP	ENST00000355220.5	37	CCDS48180.1																																																																																			T|0.400;C|0.600	0.600	strong		0.567	MAGEA11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058725.4	NM_005366	
MUC5B	727897	hgsc.bcm.edu	37	11	1265987	1265987	+	Missense_Mutation	SNP	C	C	G	rs3021158	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1265987C>G	ENST00000529681.1	+	31	7935	c.7877C>G	c.(7876-7878)aCg>aGg	p.T2626R	MUC5B_ENST00000447027.1_Missense_Mutation_p.T2629R|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2626	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)		p.T2605R(1)		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)		AGCCCAGGGACGGCACGCACG	0.652													c|||	583	0.116414	0.0915	0.2147	5008	,	,		18972	0.0526		0.1302	False		,,,				2504	0.1319				p.T2626R		Atlas-SNP	.											MUC5AC,brain,glioma,0,1	MUC5B	473	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C7877G						scavenged	.	C	ARG/THR	357,3869		17,323,1773	138.0	169.0	159.0		7877	0.1	0.0	11	dbSNP_101	159	1041,7425		66,909,3258	no	missense	MUC5B	NM_002458.2	71	83,1232,5031	GG,GC,CC		12.2962,8.4477,11.0148	probably-damaging	2626/5763	1265987	1398,11294	2113	4233	6346	SO:0001583	missense	727897	exon31			CAGGGACGGCACG	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.7877C>G	11.37:g.1265987C>G	ENSP00000436812:p.Thr2626Arg	Somatic	235	2	0.00851064		WXS	Illumina HiSeq	Phase_I	299	152	0.508361	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	259	0.11858974358974358	39	0.07926829268292683	71	0.19613259668508287	43	0.07517482517482517	106	0.13984168865435356	c	3.340	-0.134883	0.06711	0.084477	0.122962	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000537836	T;T	0.19938	2.11;2.29	1.19	0.116	0.14647	.	.	.	.	.	T	0.00039	0.0001	M	0.63843	1.955	0.80722	P	0.0	D;D	0.64830	0.994;0.994	P;P	0.60682	0.878;0.878	T	0.08289	-1.0729	8	0.87932	D	0	.	6.8768	0.24151	0.0:0.8162:0.0:0.1838	.	3264;2629	A7Y9J9;E9PBJ0	.;.	R	2626;2629;2598;2641;167	ENSP00000436812:T2626R;ENSP00000415793:T2629R	ENSP00000343037:T2598R	T	+	2	0	MUC5B	1222563	0.307000	0.24500	0.000000	0.03702	0.007000	0.05969	0.522000	0.22909	0.036000	0.15547	0.205000	0.17691	ACG	C|0.873;G|0.127	0.127	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CCDC38	120935	hgsc.bcm.edu	37	12	96288860	96288860	+	Missense_Mutation	SNP	T	T	C	rs10859974	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:96288860T>C	ENST00000344280.3	-	8	1236	c.679A>G	c.(679-681)Atg>Gtg	p.M227V	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	227			M -> V (in dbSNP:rs10859974).							breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTTGGAGACATTTGCAGCAGA	0.333													T|||	1228	0.245208	0.2738	0.1282	5008	,	,		13669	0.4236		0.1988	False		,,,				2504	0.1534				p.M227V		Atlas-SNP	.											.	CCDC38	45	.	0			c.A679G						PASS	.	T	VAL/MET	1194,3208	417.2+/-337.8	166,862,1173	211.0	204.0	206.0		679	-1.6	1.0	12	dbSNP_120	206	1489,7109	283.3+/-296.1	124,1241,2934	yes	missense	CCDC38	NM_182496.2	21	290,2103,4107	CC,CT,TT		17.318,27.124,20.6385	benign	227/564	96288860	2683,10317	2201	4299	6500	SO:0001583	missense	120935	exon8			GAGACATTTGCAG	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.679A>G	12.37:g.96288860T>C	ENSP00000345470:p.Met227Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	118	71	0.601695	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	550	0.2518315018315018	122	0.24796747967479674	41	0.1132596685082873	224	0.3916083916083916	163	0.21503957783641162	T	7.320	0.616850	0.14129	0.27124	0.17318	ENSG00000165972	ENST00000344280	T	0.09073	3.02	5.23	-1.62	0.08372	.	0.164203	0.40385	N	0.001117	T	0.00012	0.0000	N	0.00841	-1.15	0.09310	P	0.999999986606	B	0.02656	0.0	B	0.01281	0.0	T	0.47058	-0.9146	9	0.32370	T	0.25	-8.8723	0.3596	0.00362	0.3028:0.1429:0.2707:0.2835	rs10859974;rs56430645;rs59112589;rs10859974	227	Q502W7	CCD38_HUMAN	V	227	ENSP00000345470:M227V	ENSP00000345470:M227V	M	-	1	0	CCDC38	94812991	0.738000	0.28186	0.987000	0.45799	0.355000	0.29361	-0.095000	0.11077	-0.122000	0.11766	-0.536000	0.04276	ATG	T|0.772;C|0.228	0.228	strong		0.333	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
HIST1H2BA	255626	hgsc.bcm.edu	37	6	25727517	25727517	+	Silent	SNP	G	G	A	rs9358872	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25727517G>A	ENST00000274764.2	+	1	381	c.381G>A	c.(379-381)aaG>aaA	p.K127K	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	127					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)	2						CCAGCTCCAAGTAAGCCTGCT	0.478													A|||	1738	0.347045	0.0976	0.4366	5008	,	,		19317	0.6825		0.2922	False		,,,				2504	0.3313				p.K127K		Atlas-SNP	.											.	HIST1H2BA	25	.	0			c.G381A						PASS	.	A		605,3801	769.6+/-413.7	47,511,1645	260.0	188.0	212.0		381	1.5	0.1	6	dbSNP_119	212	2390,6210	700.4+/-405.1	338,1714,2248	no	coding-synonymous	HIST1H2BA	NM_170610.2		385,2225,3893	AA,AG,GG		27.7907,13.7313,23.0278		127/128	25727517	2995,10011	2203	4300	6503	SO:0001819	synonymous_variant	255626	exon1			CTCCAAGTAAGCC	AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"""Histones / Replication-dependent"""	18730	protein-coding gene	gene with protein product		609904	"""H2B histone family, member U, (testis-specific)"", ""histone 1, H2ba"""			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.381G>A	6.37:g.25727517G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_170610	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Silent	SNP	ENST00000274764.2	37	CCDS4563.1																																																																																			G|0.713;A|0.287	0.287	strong		0.478	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610	
TRPA1	8989	hgsc.bcm.edu	37	8	72966002	72966002	+	Silent	SNP	G	G	A	rs3735943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:72966002G>A	ENST00000262209.4	-	13	1837	c.1630C>T	c.(1630-1632)Ctg>Ttg	p.L544L	RP11-383H13.1_ENST00000457356.4_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	544					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	TCTTCATCCAGGCGATCTGTG	0.468													G|||	2907	0.580471	0.5091	0.6671	5008	,	,		18636	0.6905		0.4791	False		,,,				2504	0.6063				p.L544L		Atlas-SNP	.											.	TRPA1	256	.	0			c.C1630T						PASS	.	G		2248,2158	591.8+/-387.6	588,1072,543	82.0	68.0	73.0		1630	3.2	0.2	8	dbSNP_107	73	4234,4366	569.4+/-389.2	1053,2128,1119	no	coding-synonymous	TRPA1	NM_007332.2		1641,3200,1662	AA,AG,GG		49.2326,48.9787,49.8385		544/1120	72966002	6482,6524	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon13			CATCCAGGCGATC	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1630C>T	8.37:g.72966002G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			G|0.483;A|0.517	0.517	strong		0.468	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
INADL	10207	hgsc.bcm.edu	37	1	62483599	62483599	+	Silent	SNP	G	G	A	rs34726576	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:62483599G>A	ENST00000371158.2	+	29	4053	c.3939G>A	c.(3937-3939)aaG>aaA	p.K1313K	INADL_ENST00000316485.6_Silent_p.K1313K|INADL_ENST00000543708.1_Silent_p.K97K|INADL_ENST00000545929.1_Intron	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1313	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CCCCATCAAAGGTCAAGCTGG	0.363													G|||	537	0.107228	0.0424	0.147	5008	,	,		16837	0.002		0.2416	False		,,,				2504	0.137				p.K1313K		Atlas-SNP	.											.	INADL	179	.	0			c.G3939A						PASS	.	G		298,4108	164.7+/-196.3	10,278,1915	151.0	137.0	142.0		3939	-1.0	0.2	1	dbSNP_126	142	2210,6390	375.7+/-337.9	278,1654,2368	no	coding-synonymous	INADL	NM_176877.2		288,1932,4283	AA,AG,GG		25.6977,6.7635,19.2834		1313/1802	62483599	2508,10498	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon29			ATCAAAGGTCAAG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3939G>A	1.37:g.62483599G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			G|0.818;A|0.182	0.182	strong		0.363	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
HTT	3064	hgsc.bcm.edu	37	4	3148653	3148653	+	Missense_Mutation	SNP	T	T	G	rs1143646	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:3148653T>G	ENST00000355072.5	+	25	3418	c.3273T>G	c.(3271-3273)atT>atG	p.I1091M		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1091			I -> M (in dbSNP:rs1143646).		anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ATGCTTTGATTTTGGCCGGAA	0.502													T|||	112	0.0223642	0.0023	0.0231	5008	,	,		19236	0.0		0.0487	False		,,,				2504	0.045				p.I1091M		Atlas-SNP	.											.	HTT	221	.	0			c.T3273G						PASS	.	T	MET/ILE	35,3891		0,35,1928	351.0	350.0	351.0		3273	-4.2	0.0	4	dbSNP_86	351	403,7927		11,381,3773	yes	missense	HTT	NM_002111.6	10	11,416,5701	GG,GT,TT		4.8379,0.8915,3.5738	benign	1091/3143	3148653	438,11818	1963	4165	6128	SO:0001583	missense	3064	exon25			TTTGATTTTGGCC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.3273T>G	4.37:g.3148653T>G	ENSP00000347184:p.Ile1091Met	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	204	94	0.460784	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	50	0.022893772893772892	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	41	0.05408970976253298	T	13.78	2.338654	0.41398	0.008915	0.048379	ENSG00000197386	ENST00000355072	T	0.64803	-0.12	4.68	-4.18	0.03846	Armadillo-type fold (1);	0.398024	0.28057	N	0.016777	T	0.08223	0.0205	L	0.40543	1.245	0.25629	N	0.986323	P	0.35208	0.49	B	0.32624	0.149	T	0.07947	-1.0746	10	0.33940	T	0.23	.	2.2434	0.04025	0.2123:0.3798:0.1117:0.2962	rs1143646;rs3025846;rs17362442;rs17781557;rs17781557	1091	P42858	HD_HUMAN	M	1091	ENSP00000347184:I1091M	ENSP00000347184:I1091M	I	+	3	3	HTT	3118451	0.381000	0.25140	0.023000	0.16930	0.993000	0.82548	-0.425000	0.07017	-0.600000	0.05790	0.460000	0.39030	ATT	T|0.968;G|0.032	0.032	strong		0.502	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
NREP	9315	hgsc.bcm.edu	37	5	111066697	111066697	+	Missense_Mutation	SNP	T	T	C	rs11559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:111066697T>C	ENST00000379671.3	-	5	392	c.128A>G	c.(127-129)gAg>gGg	p.E43G	NREP_ENST00000447165.2_Missense_Mutation_p.E43G|NREP_ENST00000395634.3_Missense_Mutation_p.E87G|NREP_ENST00000508870.1_Missense_Mutation_p.E43G|NREP_ENST00000507742.1_5'UTR|NREP_ENST00000509025.1_Intron|NREP_ENST00000455559.2_Missense_Mutation_p.E43G|NREP_ENST00000419114.2_Missense_Mutation_p.E43G|NREP_ENST00000446294.2_Missense_Mutation_p.E43G|NREP_ENST00000257435.7_Missense_Mutation_p.E43G|STARD4-AS1_ENST00000513221.1_RNA|NREP_ENST00000509427.1_Missense_Mutation_p.E43G|NREP_ENST00000450761.2_Missense_Mutation_p.E43G|STARD4-AS1_ENST00000500779.2_RNA|NREP_ENST00000509979.1_3'UTR|NREP_ENST00000453526.2_Missense_Mutation_p.E43G|NREP_ENST00000515855.1_3'UTR	NM_001142478.1	NP_001135950.1	Q16612	NREP_HUMAN	neuronal regeneration related protein	43			E -> G (in dbSNP:rs11559).		axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											AGCGTTTGTCTCATCGTTCTT	0.478													T|||	345	0.0688898	0.0151	0.036	5008	,	,		17682	0.2123		0.0427	False		,,,				2504	0.044				p.E87G		Atlas-SNP	.											C5orf13_ENST00000395634,brain,glioma,0,2	.	.	2	0			c.A260G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	133,4271	96.7+/-135.4	3,127,2072	173.0	142.0	153.0		230,260,128,128,128,128,128,128,128,128,128	0.3	0.0	5	dbSNP_52	153	477,8123	140.3+/-196.8	10,457,3833	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	C5orf13	NM_001142474.1,NM_001142475.1,NM_001142476.1,NM_001142477.1,NM_001142478.1,NM_001142479.1,NM_001142480.1,NM_001142481.1,NM_001142482.1,NM_001142483.1,NM_004772.2	98,98,98,98,98,98,98,98,98,98,98	13,584,5905	CC,CT,TT		5.5465,3.02,4.6909	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	77/103,87/113,43/69,43/69,43/69,43/69,43/69,43/69,43/69,43/69,43/69	111066697	610,12394	2202	4300	6502	SO:0001583	missense	9315	exon4			TTTGTCTCATCGT	AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986			16834	protein-coding gene	gene with protein product	"""neuronal protein 3.1"""	607332	"""chromosome 5 open reading frame 13"", ""neuronal regeneration related protein homolog (rat)"""	C5orf13		8261136, 10981724, 15485502	Standard	NM_004772		Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000379671.3:c.128A>G	5.37:g.111066697T>C	ENSP00000368993:p.Glu43Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001142475	B2RDN8|B7Z5D2|D3DSZ8	Missense_Mutation	SNP	ENST00000379671.3	37	CCDS4105.1	182	0.08333333333333333	8	0.016260162601626018	14	0.03867403314917127	129	0.22552447552447552	31	0.040897097625329816	T	1.341	-0.594183	0.03771	0.0302	0.055465	ENSG00000134986	ENST00000379671;ENST00000257435;ENST00000447165;ENST00000446294;ENST00000395634;ENST00000450761;ENST00000419114;ENST00000509427;ENST00000453526;ENST00000455559;ENST00000508870;ENST00000513100	T;T;T;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;0.6;0.6;0.6	5.81	0.269	0.15631	.	0.487688	0.20424	N	0.092601	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.15141	0.012;0.012;0.004	B;B;B	0.16722	0.016;0.016;0.011	T	0.10291	-1.0636	8	0.39692	T	0.17	-0.6214	3.0237	0.06084	0.1154:0.1293:0.1203:0.635	rs11559;rs3797721	43;87;43	D6RIC9;B7Z5D2;Q16612	.;.;NP311_HUMAN	G	43;43;43;43;87;43;43;43;43;43;43;43	ENSP00000368993:E43G;ENSP00000257435:E43G;ENSP00000408839:E43G;ENSP00000402965:E43G;ENSP00000378996:E87G;ENSP00000416617:E43G;ENSP00000399766:E43G;ENSP00000422630:E43G;ENSP00000403383:E43G;ENSP00000392559:E43G;ENSP00000427149:E43G;ENSP00000427476:E43G	ENSP00000257435:E43G	E	-	2	0	C5orf13	111094596	0.431000	0.25546	0.001000	0.08648	0.019000	0.09904	2.033000	0.41136	0.101000	0.17610	-0.327000	0.08410	GAG	T|0.940;C|0.060	0.060	strong		0.478	NREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250722.1	NM_004772	
ADRB2	154	hgsc.bcm.edu	37	5	148206646	148206646	+	Silent	SNP	G	G	A	rs113509650|rs1042717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:148206646G>A	ENST00000305988.4	+	1	491	c.252G>A	c.(250-252)ctG>ctA	p.L84L		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	84					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)	TCATGGGCCTGGCAGTGGTGC	0.522													G|||	1576	0.314696	0.3404	0.2997	5008	,	,		19280	0.3641		0.1988	False		,,,				2504	0.3589				p.L84L		Atlas-SNP	.											.	ADRB2	42	.	0			c.G252A						PASS	.	G		1442,2964	468.5+/-355.1	242,958,1003	89.0	84.0	85.0		252	1.8	1.0	5	dbSNP_86	85	1702,6898	312.6+/-310.9	162,1378,2760	no	coding-synonymous	ADRB2	NM_000024.5		404,2336,3763	AA,AG,GG		19.7907,32.7281,24.1735		84/414	148206646	3144,9862	2203	4300	6503	SO:0001819	synonymous_variant	154	exon1			GGGCCTGGCAGTG	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.252G>A	5.37:g.148206646G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	178	93	0.522472	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																			G|0.772;A|0.228	0.228	strong		0.522	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
TFG	10342	hgsc.bcm.edu	37	3	100467018	100467018	+	Silent	SNP	T	T	C	rs11353	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:100467018T>C	ENST00000240851.4	+	8	1186	c.846T>C	c.(844-846)ccT>ccC	p.P282P	TFG_ENST00000476228.1_Silent_p.P278P|TFG_ENST00000481203.1_3'UTR|TFG_ENST00000490574.1_Silent_p.P282P|TFG_ENST00000418917.2_Silent_p.P278P	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	282					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						AGACTGGACCTCAACAACCTC	0.448			T	"""NTRK1, ALK"""	"""papillary thyroid, ALCL, NSCLC"""								C|||	3571	0.713059	0.646	0.8055	5008	,	,		19679	0.6518		0.6412	False		,,,				2504	0.8753				p.P282P		Atlas-SNP	.		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"""E, L"""	.	TFG	42	.	0			c.T846C						PASS	.	C	,,,	2872,1534		946,980,277	82.0	83.0	82.0		846,846,834,846	4.8	1.0	3	dbSNP_52	82	5648,2952		1851,1946,503	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TFG	NM_001007565.2,NM_001195478.1,NM_001195479.1,NM_006070.5	,,,	2797,2926,780	CC,CT,TT		34.3256,34.8162,34.4918	,,,	282/401,282/401,278/397,282/401	100467018	8520,4486	2203	4300	6503	SO:0001819	synonymous_variant	10342	exon8			TGGACCTCAACAA	BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.846T>C	3.37:g.100467018T>C		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	304	139	0.457237	NM_006070	D3DN49|G5E9V1|Q15656|Q969I2	Silent	SNP	ENST00000240851.4	37	CCDS2939.1	1442	0.6602564102564102	309	0.6280487804878049	292	0.8066298342541437	355	0.6206293706293706	486	0.6411609498680739	C	4.324	0.059524	0.08339	0.651838	0.656744	ENSG00000114354	ENST00000443578	.	.	.	5.64	4.77	0.60923	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999999	.	.	.	.	.	.	T	0.20806	-1.0264	3	.	.	.	-1.4612	5.7931	0.18371	0.0:0.592:0.132:0.276	rs11353;rs1059445;rs3200128;rs6441516;rs57273775;rs6441516	.	.	.	P	278	.	.	L	+	2	0	TFG	101949708	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	1.055000	0.30467	0.953000	0.37825	-0.128000	0.14901	CTC	T|0.339;C|0.661	0.661	strong		0.448	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412363	105412363	+	Missense_Mutation	SNP	T	T	C	rs201377363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105412363T>C	ENST00000333244.5	-	7	9544	c.9425A>G	c.(9424-9426)aAg>aGg	p.K3142R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3142						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.K3142R(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)			CATTTTGAACTTGCTGTCTTT	0.592																																					p.K3142R		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,NS,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	NS(1)	c.A9425G						scavenged	.						181.0	139.0	152.0					14																	105412363		1912	4076	5988	SO:0001583	missense	113146	exon7			TTGAACTTGCTGT	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.9425A>G	14.37:g.105412363T>C	ENSP00000353114:p.Lys3142Arg	Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	11.62	1.694140	0.30052	.	.	ENSG00000185567	ENST00000333244	T	0.00882	5.58	3.45	3.45	0.39498	.	.	.	.	.	T	0.05502	0.0145	M	0.85462	2.755	0.23620	N	0.997271	D	0.71674	0.998	D	0.78314	0.991	T	0.12372	-1.0550	9	0.54805	T	0.06	.	9.5748	0.39450	0.0:0.0:0.1761:0.8239	.	3142	Q8IVF2	AHNK2_HUMAN	R	3142	ENSP00000353114:K3142R	ENSP00000353114:K3142R	K	-	2	0	AHNAK2	104483408	0.794000	0.28838	0.977000	0.42913	0.041000	0.13682	3.435000	0.52849	1.195000	0.43115	0.260000	0.18958	AAG	T|0.760;C|0.240	0.240	strong		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CSF1R	1436	hgsc.bcm.edu	37	5	149457678	149457678	+	Silent	SNP	G	G	A	rs2228422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149457678G>A	ENST00000286301.3	-	5	1017	c.726C>T	c.(724-726)acC>acT	p.T242T	CSF1R_ENST00000543093.1_Silent_p.T242T	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	242	Ig-like C2-type 3.				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)	p.T242T(1)		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)	GACTGACCTTGGTGTTGTTGT	0.572													G|||	1940	0.38738	0.2799	0.366	5008	,	,		20014	0.2113		0.5457	False		,,,				2504	0.5665				p.T242T		Atlas-SNP	.											CSF1R_ENST00000286301,NS,carcinoma,0,1	CSF1R	250	1	1	Substitution - coding silent(1)	stomach(1)	c.C726T						scavenged	.	G		1388,3018	457.5+/-351.6	220,948,1035	224.0	186.0	199.0		726	-0.9	1.0	5	dbSNP_98	199	4864,3736	618.2+/-396.8	1391,2082,827	no	coding-synonymous	CSF1R	NM_005211.3		1611,3030,1862	AA,AG,GG		43.4419,31.5025,48.0701		242/973	149457678	6252,6754	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon5			GACCTTGGTGTTG	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.726C>T	5.37:g.149457678G>A		Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	195	80	0.410256	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			G|0.561;A|0.439	0.439	strong		0.572	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
FAM178B	51252	hgsc.bcm.edu	37	2	97638311	97638311	+	Missense_Mutation	SNP	G	G	A	rs146972264	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97638311G>A	ENST00000417561.3	-	6	549	c.550C>T	c.(550-552)Ccc>Tcc	p.P184S	FAM178B_ENST00000490605.2_Missense_Mutation_p.P36S|FAM178B_ENST00000327896.3_Missense_Mutation_p.P4S			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	184										large_intestine(1)|ovary(1)	2						GTCTCCTGGGGCCCAGCCATC	0.577													G|||	111	0.0221645	0.0015	0.0591	5008	,	,		18707	0.001		0.0278	False		,,,				2504	0.0399				p.P36S		Atlas-SNP	.											.	FAM178B	35	.	0			c.C106T						PASS	.	G	SER/PRO	8,1376		0,8,684	28.0	31.0	30.0		106	0.9	0.4	2	dbSNP_134	30	106,3076		2,102,1487	yes	missense	FAM178B	NM_001122646.2	74	2,110,2171	AA,AG,GG		3.3312,0.578,2.4967	benign	36/680	97638311	114,4452	692	1591	2283	SO:0001583	missense	51252	exon2			CCTGGGGCCCAGC	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.550C>T	2.37:g.97638311G>A	ENSP00000413245:p.Pro184Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	37		38	0.0173992673992674	0	0.0	15	0.04143646408839779	0	0.0	23	0.030343007915567283	G	5.500	0.277266	0.10403	0.00578	0.033312	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000490605	T;T;T	0.46451	0.87;0.97;0.94	3.71	0.901	0.19284	.	.	.	.	.	T	0.04497	0.0123	N	0.08118	0	0.09310	N	0.999999	.	.	.	.	.	.	T	0.12837	-1.0532	7	0.36615	T	0.2	.	3.2231	0.06723	0.2255:0.0:0.5676:0.207	.	.	.	.	S	184;4;36	ENSP00000413245:P184S;ENSP00000333553:P4S;ENSP00000429896:P36S	ENSP00000333553:P4S	P	-	1	0	FAM178B	97002038	0.013000	0.17824	0.355000	0.25773	0.146000	0.21551	-0.209000	0.09358	0.176000	0.19873	0.655000	0.94253	CCC	G|0.983;A|0.017	0.017	strong		0.577	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
CLSTN3	9746	hgsc.bcm.edu	37	12	7287956	7287956	+	Silent	SNP	C	C	T	rs34933247	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:7287956C>T	ENST00000266546.6	+	4	867	c.417C>T	c.(415-417)aaC>aaT	p.N139N	CLSTN3_ENST00000537408.1_Silent_p.N151N	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	139	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						ACGATGTGAACGAGTTTGCCC	0.547													C|||	592	0.118211	0.0847	0.049	5008	,	,		-128	0.124		0.0676	False		,,,				2504	0.2587				p.N139N		Atlas-SNP	.											.	CLSTN3	84	.	0			c.C417T						PASS	.	C		407,3999	200.4+/-223.7	21,365,1817	220.0	130.0	160.0		417	-8.4	0.6	12	dbSNP_126	160	722,7878	176.2+/-226.1	24,674,3602	no	coding-synonymous	CLSTN3	NM_014718.3		45,1039,5419	TT,TC,CC		8.3953,9.2374,8.6806		139/957	7287956	1129,11877	2203	4300	6503	SO:0001819	synonymous_variant	9746	exon4			TGTGAACGAGTTT	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.417C>T	12.37:g.7287956C>T		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	251	132	0.525896	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Silent	SNP	ENST00000266546.6	37	CCDS8575.1																																																																																			C|0.917;T|0.083	0.083	strong		0.547	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197173	39197173	+	Silent	SNP	A	A	G	rs144980478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39197173A>G	ENST00000306271.4	-	1	540	c.477T>C	c.(475-477)tgT>tgC	p.C159C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	159						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)			AGGACTGTCCACAGTAGGATG	0.617													a|||	10	0.00199681	0.0	0.0029	5008	,	,		17718	0.0		0.008	False		,,,				2504	0.0				p.C159C		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.T477C						PASS	.	A		5,4099		0,5,2047	31.0	35.0	34.0		477	4.1	1.0	17	dbSNP_134	34	34,8330		0,34,4148	no	coding-synonymous	KRTAP1-1	NM_030967.2		0,39,6195	GG,GA,AA		0.4065,0.1218,0.3128		159/178	39197173	39,12429	2052	4182	6234	SO:0001819	synonymous_variant	81851	exon1			CTGTCCACAGTAG	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.477T>C	17.37:g.39197173A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	180	96	0.533333	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			A|0.996;G|0.004	0.004	strong		0.617	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
FLG	2312	hgsc.bcm.edu	37	1	152283975	152283975	+	Silent	SNP	A	A	G	rs66831674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152283975A>G	ENST00000368799.1	-	3	3422	c.3387T>C	c.(3385-3387)tcT>tcC	p.S1129S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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	319	0	0		WXS	Illumina HiSeq	Phase_I	314	137	0.436306	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	
MAGEA1	4100	hgsc.bcm.edu	37	X	152482198	152482198	+	Silent	SNP	G	G	A	rs2233045	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:152482198G>A	ENST00000356661.5	-	3	1031	c.813C>T	c.(811-813)ctC>ctT	p.L271L		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	271	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGTTTCAGCGAGGGCCCTTG	0.537													t|||	427	0.113113	0.0257	0.0519	3775	,	,		15459	0.1131		0.0905	False		,,,				2504	0.1554				p.L271L		Atlas-SNP	.											.	MAGEA1	57	.	0			c.C813T						PASS	.	G		162,3673		1,145,15,1486,556	126.0	120.0	122.0		813	-2.5	0.1	X	dbSNP_98	122	972,5756		44,617,267,1767,1605	no	coding-synonymous	MAGEA1	NM_004988.4		45,762,282,3253,2161	AA,AG,A,GG,G		14.4471,4.2243,10.7356		271/310	152482198	1134,9429	2203	4300	6503	SO:0001819	synonymous_variant	4100	exon3			TTCAGCGAGGGCC		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.813C>T	X.37:g.152482198G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_004988	B2RC81|O00346	Silent	SNP	ENST00000356661.5	37	CCDS14720.1																																																																																			G|0.660;T|0.028	.	strong		0.537	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
BAAT	570	hgsc.bcm.edu	37	9	104133278	104133278	+	Missense_Mutation	SNP	C	C	T	rs144591246	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:104133278C>T	ENST00000395051.3	-	1	479	c.409G>A	c.(409-411)Gtc>Atc	p.V137I	BAAT_ENST00000259407.2_Missense_Mutation_p.V137I			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	137					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	ATTCGTGTGACACCAGGTGCC	0.448													C|||	2	0.000399361	0.0	0.0	5008	,	,		18281	0.0		0.002	False		,,,				2504	0.0				p.V137I		Atlas-SNP	.											.	BAAT	52	.	0			c.G409A						PASS	.	C	ILE/VAL,ILE/VAL	0,4406		0,0,2203	90.0	87.0	88.0		409,409	2.7	0.9	9	dbSNP_134	88	33,8567	22.2+/-67.0	1,31,4268	yes	missense,missense	BAAT	NM_001127610.1,NM_001701.3	29,29	1,31,6471	TT,TC,CC		0.3837,0.0,0.2537	probably-damaging,probably-damaging	137/419,137/419	104133278	33,12973	2203	4300	6503	SO:0001583	missense	570	exon2			GTGTGACACCAGG	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"""glycine N-choloyltransferase"""	602938	"""bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)"", ""bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"""				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.409G>A	9.37:g.104133278C>T	ENSP00000378491:p.Val137Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	37	CCDS6752.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.58	3.162696	0.57368	0.0	0.003837	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.78246	-1.16;-1.16	4.51	2.67	0.31697	Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (1);	0.323194	0.25450	N	0.030588	D	0.84202	0.5420	M	0.83118	2.625	0.35375	D	0.789388	D	0.58620	0.983	P	0.58077	0.832	D	0.86424	0.1756	10	0.54805	T	0.06	-11.2209	8.7563	0.34648	0.0:0.8138:0.0:0.1862	.	137	Q14032	BAAT_HUMAN	I	137	ENSP00000259407:V137I;ENSP00000378491:V137I	ENSP00000259407:V137I	V	-	1	0	BAAT	103173099	0.103000	0.21917	0.939000	0.37840	0.935000	0.57460	0.942000	0.29017	0.521000	0.28445	0.655000	0.94253	GTC	C|0.998;T|0.002	0.002	strong		0.448	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1		
COL18A1	80781	hgsc.bcm.edu	37	21	46909426	46909426	+	Silent	SNP	G	G	A	rs61731167	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46909426G>A	ENST00000359759.4	+	18	3216	c.3195G>A	c.(3193-3195)ccG>ccA	p.P1065P	COL18A1_ENST00000400337.2_Silent_p.P650P|COL18A1_ENST00000355480.5_Silent_p.P830P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1065	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTGGGCTGCCGGGGGCGAAGG	0.701													g|||	230	0.0459265	0.0219	0.0288	5008	,	,		11637	0.005		0.0755	False		,,,				2504	0.1022				p.P830P		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2490A						PASS	.	A	,	94,3850		1,92,1879	14.0	18.0	16.0		2490,1950	-7.5	0.0	21	dbSNP_129	16	458,7796		9,440,3678	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	10,532,5557	AA,AG,GG		5.5488,2.3834,4.5253	,	830/1520,650/1340	46909426	552,11646	1972	4127	6099	SO:0001819	synonymous_variant	80781	exon18			GCTGCCGGGGGCG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3195G>A	21.37:g.46909426G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				G|0.956;A|0.044	0.044	strong		0.701	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
TRIM21	6737	hgsc.bcm.edu	37	11	4411241	4411241	+	Silent	SNP	C	C	T	rs926101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4411241C>T	ENST00000254436.7	-	2	511	c.399G>A	c.(397-399)caG>caA	p.Q133Q	TRIM21_ENST00000543625.1_Silent_p.Q133Q	NM_003141.3	NP_003132.2	P19474	RO52_HUMAN	tripartite motif containing 21	133					cell cycle (GO:0007049)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein deubiquitination (GO:0090086)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral entry into host cell (GO:0046598)|protein autoubiquitination (GO:0051865)|protein destabilization (GO:0031648)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)	16		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		CCTGGTACTCCTGTGCAGCCT	0.557													C|||	1054	0.210463	0.1921	0.1254	5008	,	,		19787	0.2837		0.1233	False		,,,				2504	0.3098				p.Q133Q		Atlas-SNP	.											.	TRIM21	45	.	0			c.G399A						PASS	.	C		646,3316		47,552,1382	43.0	45.0	44.0		399	2.1	1.0	11	dbSNP_86	44	1036,7308		77,882,3213	no	coding-synonymous	TRIM21	NM_003141.3		124,1434,4595	TT,TC,CC		12.4161,16.3049,13.6681		133/476	4411241	1682,10624	1981	4172	6153	SO:0001819	synonymous_variant	6737	exon2			GTACTCCTGTGCA	AF391283	CCDS44525.1	11p15.5-p15.3	2014-02-14	2011-01-25	2004-11-26		ENSG00000132109		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	11312	protein-coding gene	gene with protein product		109092	"""Sjogren syndrome antigen A1 (52kDa, ribonucleoprotein autoantigen SS-A/Ro)"", ""tripartite motif-containing 21"""	SSA1		8094596	Standard	NM_003141		Approved	RNF81, RO52, Ro/SSA	uc001lyy.1	P19474		ENST00000254436.7:c.399G>A	11.37:g.4411241C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_003141	Q5XPV5|Q96RF8	Silent	SNP	ENST00000254436.7	37	CCDS44525.1																																																																																			C|0.811;T|0.189	0.189	strong		0.557	TRIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385842.1	NM_003141	
TACC1	6867	hgsc.bcm.edu	37	8	38677932	38677932	+	Silent	SNP	A	A	G	rs2013586	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:38677932A>G	ENST00000317827.4	+	3	1549	c.1170A>G	c.(1168-1170)gaA>gaG	p.E390E	TACC1_ENST00000520611.1_5'Flank|TACC1_ENST00000519416.1_Silent_p.E195E|TACC1_ENST00000379931.3_Silent_p.E390E|TACC1_ENST00000518415.1_Silent_p.E345E|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000520615.1_Silent_p.E195E|TACC1_ENST00000520340.1_Silent_p.E354E|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000443286.2_Silent_p.E406E|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000520973.1_Silent_p.E195E	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	390	Interaction with YEATS4.|SPAZ 2.				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)		p.E390E(1)		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)			GTCAGTGGGAAAGCCCCAGCT	0.547													A|||	1257	0.250998	0.112	0.2594	5008	,	,		17274	0.2688		0.3887	False		,,,				2504	0.273				p.E390E		Atlas-SNP	.											TACC1_ENST00000317827,NS,carcinoma,0,1	TACC1	98	1	1	Substitution - coding silent(1)	stomach(1)	c.A1170G						PASS	.	A	,,	690,3716	288.9+/-280.1	39,612,1552	112.0	114.0	113.0		,585,1170	-7.8	0.0	8	dbSNP_92	113	3562,5038	517.0+/-379.0	754,2054,1492	no	intron,coding-synonymous,coding-synonymous	TACC1	NM_001122824.1,NM_001146216.2,NM_006283.2	,,	793,2666,3044	GG,GA,AA		41.4186,15.6605,32.6926	,,	,195/611,390/806	38677932	4252,8754	2203	4300	6503	SO:0001819	synonymous_variant	6867	exon3			GTGGGAAAGCCCC	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.1170A>G	8.37:g.38677932A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Silent	SNP	ENST00000317827.4	37	CCDS6109.1	608	0.2783882783882784	59	0.11991869918699187	94	0.2596685082872928	154	0.2692307692307692	301	0.3970976253298153	A	5.770	0.326458	0.10900	0.156605	0.414186	ENSG00000147526	ENST00000521866;ENST00000518809	.	.	.	5.4	-7.82	0.01205	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47341	P	6.059999999999954E-4	.	.	.	.	.	.	T	0.34030	-0.9845	3	.	.	.	0.0051	5.4787	0.16710	0.1022:0.4703:0.1079:0.3196	rs2013586;rs3739249;rs17514141;rs17854120;rs58803062;rs2013586	.	.	.	R	165;28	.	.	K	+	2	0	TACC1	38797089	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.316000	0.02710	-1.870000	0.01139	-0.890000	0.02929	AAA	A|0.696;G|0.304	0.304	strong		0.547	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283	
ZNF808	388558	hgsc.bcm.edu	37	19	53056953	53056953	+	Missense_Mutation	SNP	G	G	A	rs329965	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53056953G>A	ENST00000359798.4	+	5	964	c.784G>A	c.(784-786)Gat>Aat	p.D262N		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	262			D -> N (in dbSNP:rs329965).		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)		ATATAAATGTGATGTATGTGG	0.393													G|||	1088	0.217252	0.1831	0.2983	5008	,	,		22090	0.0754		0.3022	False		,,,				2504	0.2648				p.D262N		Atlas-SNP	.											.	ZNF808	81	.	0			c.G784A						PASS	.	G	ASN/ASP	855,3551		79,697,1427	158.0	157.0	158.0		784	-1.5	0.0	19	dbSNP_79	158	2468,6132		351,1766,2183	no	missense	ZNF808	NM_001039886.3	23	430,2463,3610	AA,AG,GG		28.6977,19.4054,25.5497	possibly-damaging	262/904	53056953	3323,9683	2203	4300	6503	SO:0001583	missense	388558	exon5			AAATGTGATGTAT	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.784G>A	19.37:g.53056953G>A	ENSP00000352846:p.Asp262Asn	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	155	68	0.43871	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	465	0.2129120879120879	91	0.18495934959349594	109	0.3011049723756906	37	0.06468531468531469	228	0.3007915567282322	.	9.422	1.083267	0.20309	0.194054	0.286977	ENSG00000198482	ENST00000359798	T	0.07567	3.18	1.57	-1.46	0.08800	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28458	0.855	0.58432	P	5.000000000032756E-6	P	0.39022	0.655	P	0.47786	0.557	T	0.16660	-1.0395	8	0.02654	T	1	.	2.604	0.04873	0.3051:0.0:0.3404:0.3545	rs329965;rs489728;rs1300305	262	Q8N4W9	ZN808_HUMAN	N	262	ENSP00000352846:D262N	ENSP00000352846:D262N	D	+	1	0	ZNF808	57748765	0.000000	0.05858	0.023000	0.16930	0.168000	0.22595	-2.115000	0.01328	-0.660000	0.05352	0.305000	0.20034	GAT	G|0.792;A|0.208	0.208	strong		0.393	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886	
DENND1A	57706	hgsc.bcm.edu	37	9	126144441	126144441	+	Missense_Mutation	SNP	G	G	A	rs200503663		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:126144441G>A	ENST00000373624.2	-	22	2501	c.2300C>T	c.(2299-2301)cCg>cTg	p.P767L	DENND1A_ENST00000542603.1_Missense_Mutation_p.P552L|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Missense_Mutation_p.P778L	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	767	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						AGGGCTGAGCGGCTGGAGCAG	0.701																																					p.P767L		Atlas-SNP	.											DENND1A,colon,carcinoma,-1,1	DENND1A	112	1	0			c.C2300T						PASS	.	G	LEU/PRO	0,4364		0,0,2182	11.0	16.0	15.0		2300	4.8	0.9	9		15	1,8551		0,1,4275	yes	missense	DENND1A	NM_020946.1	98	0,1,6457	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	767/1010	126144441	1,12915	2182	4276	6458	SO:0001583	missense	57706	exon22			CTGAGCGGCTGGA	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.2300C>T	9.37:g.126144441G>A	ENSP00000362727:p.Pro767Leu	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.267066	0.59540	0.0	1.17E-4	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219	T;T;T	0.28895	2.99;1.59;2.9	4.83	4.83	0.62350	.	0.133128	0.51477	D	0.000095	T	0.47358	0.1441	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.993;0.979	P;P;P;P	0.56398	0.742;0.797;0.557;0.481	T	0.49466	-0.8937	10	0.56958	D	0.05	-7.2386	16.1301	0.81422	0.0:0.0:1.0:0.0	.	778;768;767;630	Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4	.;.;DEN1A_HUMAN;.	L	767;552;778	ENSP00000362727:P767L;ENSP00000437457:P552L;ENSP00000377766:P778L	ENSP00000362727:P767L	P	-	2	0	DENND1A	125184262	1.000000	0.71417	0.906000	0.35671	0.485000	0.33311	6.349000	0.73013	2.224000	0.72417	0.557000	0.71058	CCG	.	.	weak		0.701	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
COL6A5	256076	hgsc.bcm.edu	37	3	130129322	130129322	+	Missense_Mutation	SNP	G	G	C	rs35886424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:130129322G>C	ENST00000432398.2	+	20	5110	c.4616G>C	c.(4615-4617)aGt>aCt	p.S1539T	COL6A5_ENST00000265379.6_Missense_Mutation_p.S1539T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1539	Triple-helical region.				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						TAGGGTAGAAGTGGACAGAAA	0.388													C|||	549	0.109625	0.0953	0.1037	5008	,	,		18486	0.1081		0.1123	False		,,,				2504	0.1319				p.S1539T		Atlas-SNP	.											.	COL6A5	205	.	0			c.G4616C						PASS	.	C	THR/SER	143,1241		8,127,557	114.0	90.0	97.0		4616	4.8	0.6	3	dbSNP_126	97	431,2751		27,377,1187	yes	missense	COL6A5	NM_153264.5	58	35,504,1744	CC,CG,GG		13.5449,10.3324,12.5712	benign	1539/2527	130129322	574,3992	692	1591	2283	SO:0001583	missense	256076	exon20			GTAGAAGTGGACA	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.4616G>C	3.37:g.130129322G>C	ENSP00000390895:p.Ser1539Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		241	0.11034798534798534	40	0.08130081300813008	44	0.12154696132596685	69	0.12062937062937062	88	0.11609498680738786	C	4.952	0.176814	0.09443	0.103324	0.135449	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.93604	-3.2;-3.25	5.73	4.84	0.62591	.	.	.	.	.	T	0.02230	0.0069	N	0.01091	-1.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.54173	-0.8333	8	0.23302	T	0.38	.	12.913	0.58190	0.0:0.5405:0.4595:0.0	rs35886424	1539	A8TX70-2	.	T	1539	ENSP00000390895:S1539T;ENSP00000265379:S1539T	ENSP00000265379:S1539T	S	+	2	0	COL6A5	131612012	0.049000	0.20398	0.606000	0.28943	0.230000	0.25150	1.005000	0.29834	1.445000	0.47624	-0.127000	0.14921	AGT	G|0.888;C|0.112	0.112	strong		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
MUC4	4585	hgsc.bcm.edu	37	3	195506014	195506014	+	Missense_Mutation	SNP	G	G	A	rs200152370		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195506014G>A	ENST00000463781.3	-	2	12896	c.12437C>T	c.(12436-12438)cCt>cTt	p.P4146L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4146L	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)		GATGGTGACAGGAAGAGGCGT	0.587																																					p.P4146L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12437T						PASS	.						35.0	20.0	25.0					3																	195506014		647	1559	2206	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.12437C>T	3.37:g.195506014G>A	ENSP00000417498:p.Pro4146Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	135	19	0.140741	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	4.464	0.086057	0.08583	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.39056	1.42;1.1	.	.	.	.	.	.	.	.	T	0.39279	0.1072	N	0.19112	0.55	0.09310	N	1	D	0.64830	0.994	P	0.62885	0.908	T	0.23940	-1.0174	7	.	.	.	.	5.8679	0.18786	8.0E-4:0.0:0.9992:0.0	.	4018	E7ESK3	.	L	4146	ENSP00000417498:P4146L;ENSP00000420243:P4146L	.	P	-	2	0	MUC4	196990793	0.001000	0.12720	0.016000	0.15963	0.017000	0.09413	0.709000	0.25734	0.088000	0.17205	0.089000	0.15464	CCT	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134207	32134207	+	Missense_Mutation	SNP	C	C	A	rs2388981	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32134207C>A	ENST00000312561.4	+	4	732	c.318C>A	c.(316-318)caC>caA	p.H106Q	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	106			H -> Q (in dbSNP:rs2388981).														AACTAACTCACAATTTGCAGA	0.393													C|||	680	0.135783	0.0681	0.1254	5008	,	,		23821	0.0843		0.1859	False		,,,				2504	0.2362				p.H106Q		Atlas-SNP	.											.	.	.	.	0			c.C318A						PASS	.	C	GLN/HIS	350,4056	180.5+/-208.7	12,326,1865	86.0	80.0	82.0		318	-11.2	0.0	12	dbSNP_100	82	1726,6874	313.9+/-311.6	168,1390,2742	yes	missense	C12orf35	NM_018169.3	24	180,1716,4607	AA,AC,CC		20.0698,7.9437,15.9619	benign	106/1748	32134207	2076,10930	2203	4300	6503	SO:0001583	missense	55196	exon4			AACTCACAATTTG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.318C>A	12.37:g.32134207C>A	ENSP00000310338:p.His106Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	65	0.448276	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	282	0.12912087912087913	40	0.08130081300813008	47	0.1298342541436464	58	0.10139860139860139	137	0.18073878627968337	C	8.274	0.814058	0.16537	0.079437	0.200698	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.06933	3.24;3.24	5.59	-11.2	0.00127	.	0.459276	0.20637	N	0.088474	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.21586	-1.0241	8	.	.	.	.	3.0339	0.06116	0.2278:0.1376:0.1066:0.528	rs2388981;rs17511064;rs2388981	106	Q9HCM1	CL035_HUMAN	Q	106	ENSP00000310338:H106Q;ENSP00000370442:H106Q	.	H	+	3	2	C12orf35	32025474	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.821000	0.00749	-2.883000	0.00318	-1.734000	0.00692	CAC	C|0.850;A|0.150	0.150	strong		0.393	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
LGR5	8549	hgsc.bcm.edu	37	12	71977787	71977787	+	Missense_Mutation	SNP	T	T	C	rs17109924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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|RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000536515.1_Missense_Mutation_p.V594A			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	148	0	0		WXS	Illumina HiSeq	Phase_I	171	86	0.502924	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	
MUC4	4585	hgsc.bcm.edu	37	3	195506482	195506482	+	Missense_Mutation	SNP	G	G	T	rs113936020	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195506482G>T	ENST00000463781.3	-	2	12428	c.11969C>A	c.(11968-11970)aCt>aAt	p.T3990N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3990N	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)		TACTGAGGAAGTGTCGGTGAC	0.592																																					p.T3990N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.C11969A						scavenged	.						10.0	7.0	8.0					3																	195506482		623	1357	1980	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.11969C>A	3.37:g.195506482G>T	ENSP00000417498:p.Thr3990Asn	Somatic	12	4	0.333333		WXS	Illumina HiSeq	Phase_I	19	4	0.210526	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	0.405	-0.916416	0.02415	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.37;1.46	0.481	0.481	0.16809	.	0.562686	0.09843	U	0.748557	T	0.35913	0.0948	N	0.14661	0.345	0.09310	N	1	D	0.57257	0.979	D	0.68192	0.956	T	0.29852	-0.9998	9	.	.	.	.	6.8687	0.24108	1.0E-4:0.0:0.9999:0.0	.	3862	E7ESK3	.	N	3990	ENSP00000417498:T3990N;ENSP00000420243:T3990N	.	T	-	2	0	MUC4	196991261	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.001000	0.12947	0.537000	0.28751	0.064000	0.15345	ACT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PADI3	51702	hgsc.bcm.edu	37	1	17601165	17601165	+	Silent	SNP	C	C	T	rs11585357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17601165C>T	ENST00000375460.3	+	11	1231	c.1191C>T	c.(1189-1191)cgC>cgT	p.R397R		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	397					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	GGGAACCACGCGACAGGTCTG	0.597											OREG0013148	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	304	0.0607029	0.0121	0.0994	5008	,	,		17565	0.001		0.1759	False		,,,				2504	0.0419				p.R397R		Atlas-SNP	.											PADI3,colon,carcinoma,+2,1	PADI3	81	1	0			c.C1191T						PASS	.	C		130,4276	94.4+/-133.1	1,128,2074	65.0	63.0	64.0		1191	-6.9	0.0	1	dbSNP_120	64	1309,7291	259.0+/-282.4	106,1097,3097	no	coding-synonymous	PADI3	NM_016233.2		107,1225,5171	TT,TC,CC		15.2209,2.9505,11.0641		397/665	17601165	1439,11567	2203	4300	6503	SO:0001819	synonymous_variant	51702	exon11			ACCACGCGACAGG	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"""Peptidyl arginine deiminases"""	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1191C>T	1.37:g.17601165C>T		Somatic	108	0	0	719	WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_016233	Q58EY7|Q70SX5	Silent	SNP	ENST00000375460.3	37	CCDS179.1																																																																																			C|0.902;T|0.098	0.098	strong		0.597	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1		
LSG1	55341	hgsc.bcm.edu	37	3	194387300	194387300	+	Splice_Site	SNP	C	C	T	rs1675943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:194387300C>T	ENST00000265245.5	-	3	542	c.228G>A	c.(226-228)gaG>gaA	p.E76E	AC046143.1_ENST00000408791.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	76					GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		TATTAAGTTTCTCTGTTCAAA	0.358													C|||	2129	0.42512	0.2587	0.4481	5008	,	,		17143	0.4405		0.5348	False		,,,				2504	0.5051				p.E76E		Atlas-SNP	.											.	LSG1	38	.	0			c.G228A						PASS	.	C		1332,3074	415.2+/-337.1	212,908,1083	54.0	55.0	54.0		228	3.5	1.0	3	dbSNP_89	54	4540,4060	571.5+/-389.6	1223,2094,983	yes	coding-synonymous-near-splice	LSG1	NM_018385.2		1435,3002,2066	TT,TC,CC		47.2093,30.2315,45.1484		76/659	194387300	5872,7134	2203	4300	6503	SO:0001630	splice_region_variant	55341	exon3			AAGTTTCTCTGTT		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"""large subunit GTPase 1 homolog (S. cerevisiae)"""			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.227-1G>A	3.37:g.194387300C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1																																																																																			C|0.573;T|0.427	0.427	strong		0.358	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	Silent
TUBG2	27175	hgsc.bcm.edu	37	17	40818353	40818353	+	Silent	SNP	C	C	T	rs523338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40818353C>T	ENST00000251412.7	+	10	1208	c.1009C>T	c.(1009-1011)Ctg>Ttg	p.L337L	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	337					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)	p.L337L(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		CCACAAGAGCCTGCAGAGGAT	0.672																																					p.L337L		Atlas-SNP	.											TUBG2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	TUBG2	43	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C1009T						scavenged	.						46.0	48.0	47.0					17																	40818353		2203	4300	6503	SO:0001819	synonymous_variant	27175	exon10			AAGAGCCTGCAGA	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.1009C>T	17.37:g.40818353C>T		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	347	41	0.118156	NM_016437	A6NDI4|Q32NB2	Silent	SNP	ENST00000251412.7	37	CCDS32658.1																																																																																			C|0.801;T|0.199	0.199	strong		0.672	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
SDHAF1	644096	hgsc.bcm.edu	37	19	36486509	36486509	+	Silent	SNP	C	C	G	rs76336581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36486509C>G	ENST00000378887.2	+	1	420	c.333C>G	c.(331-333)cgC>cgG	p.R111R		NM_001042631.2	NP_001036096			succinate dehydrogenase complex assembly factor 1																		CGGAGACCCGCCCCGACGGAC	0.721													G|||	234	0.0467252	0.0582	0.0562	5008	,	,		14200	0.0109		0.0517	False		,,,				2504	0.0562				p.R111R		Atlas-SNP	.											.	.	.	.	0			c.C333G						PASS	.	G		134,3692		1,132,1780	3.0	4.0	4.0		333	-2.9	0.0	19	dbSNP_132	4	249,7165		3,243,3461	no	coding-synonymous	SDHAF1	NM_001042631.2		4,375,5241	GG,GC,CC		3.3585,3.5024,3.4075		111/116	36486509	383,10857	1913	3707	5620	SO:0001819	synonymous_variant	644096	exon1			GACCCGCCCCGAC		CCDS32999.1	19q13.12	2014-06-05			ENSG00000205138	ENSG00000205138		"""Mitochondrial respiratory chain complex assembly factors"", ""LYR motif containing"""	33867	protein-coding gene	gene with protein product	"""LYR motif containing 8"""	612848				19465911	Standard	NM_001042631		Approved	LYRM8	uc002ocp.3	A6NFY7		ENST00000378887.2:c.333C>G	19.37:g.36486509C>G		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_001042631		Silent	SNP	ENST00000378887.2	37	CCDS32999.1																																																																																			C|0.958;G|0.042	0.042	strong		0.721	SDHAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457409.2	NM_001042631	
STARD3	10948	hgsc.bcm.edu	37	17	37818561	37818561	+	Silent	SNP	T	T	C	rs2941513	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:37818561T>C	ENST00000336308.5	+	14	1415	c.1197T>C	c.(1195-1197)gtT>gtC	p.V399V	TCAP_ENST00000309889.2_5'Flank|STARD3_ENST00000544210.2_Silent_p.V399V|STARD3_ENST00000394250.4_Silent_p.V381V|STARD3_ENST00000580611.1_Silent_p.V373V	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	399	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			ACCCCCGTGTTTGCACCTTTG	0.572													C|||	151	0.0301518	0.0643	0.0274	5008	,	,		16051	0.0		0.0437	False		,,,				2504	0.0031				p.V399V		Atlas-SNP	.											.	STARD3	33	.	0			c.T1197C						PASS	.	C	,,	292,4114	798.0+/-415.4	16,260,1927	54.0	54.0	54.0		1197,1143,1197	-0.2	0.9	17	dbSNP_101	54	484,8116	796.9+/-407.5	18,448,3834	yes	coding-synonymous,coding-synonymous,coding-synonymous	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	,,	34,708,5761	CC,CT,TT		5.6279,6.6273,5.9665	,,	399/446,381/428,399/446	37818561	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	10948	exon14			CCGTGTTTGCACC		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.1197T>C	17.37:g.37818561T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Silent	SNP	ENST00000336308.5	37	CCDS11341.1																																																																																			T|0.953;C|0.047	0.047	strong		0.572	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		
ZNF789	285989	hgsc.bcm.edu	37	7	99081730	99081730	+	Missense_Mutation	SNP	A	A	G	rs6962772	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99081730A>G	ENST00000331410.5	+	4	499	c.229A>G	c.(229-231)Act>Gct	p.T77A	ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000494186.1_3'UTR|ZNF789_ENST00000448667.1_Missense_Mutation_p.T70A	NM_213603.2	NP_998768.2	Q5FWF6	ZN789_HUMAN	zinc finger protein 789	77	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		T -> A (in dbSNP:rs6962772). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)	11	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TCTACCGAGAACTGGGAATAG	0.527													G|||	2321	0.463458	0.9372	0.2839	5008	,	,		19277	0.3393		0.165	False		,,,				2504	0.3855				p.T77A		Atlas-SNP	.											.	ZNF789	33	.	0			c.A229G						PASS	.	G	ALA/THR	3483,923	354.6+/-312.7	1372,739,92	127.0	125.0	126.0		229	-2.8	0.0	7	dbSNP_116	126	1238,7362	762.4+/-407.6	102,1034,3164	yes	missense	ZNF789	NM_213603.2	58	1474,1773,3256	GG,GA,AA		14.3953,20.9487,36.2986	benign	77/426	99081730	4721,8285	2203	4300	6503	SO:0001583	missense	285989	exon4			CCGAGAACTGGGA	AK093141	CCDS34693.1, CCDS34694.1	7q22.1	2013-01-08			ENSG00000198556	ENSG00000198556		"""Zinc fingers, C2H2-type"", ""-"""	27801	protein-coding gene	gene with protein product						12477932	Standard	XM_005250281		Approved		uc003uqq.1	Q5FWF6	OTTHUMG00000154601	ENST00000331410.5:c.229A>G	7.37:g.99081730A>G	ENSP00000331927:p.Thr77Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	NM_213603	A4D282|A6NH61|Q6ZMZ9	Missense_Mutation	SNP	ENST00000331410.5	37	CCDS34693.1	876	0.4010989010989011	447	0.9085365853658537	112	0.30939226519337015	191	0.3339160839160839	126	0.1662269129287599	G	0.984	-0.696284	0.03279	0.790513	0.143953	ENSG00000198556	ENST00000331410;ENST00000448667	T;T	0.04917	3.53;5.48	4.15	-2.85	0.05734	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.30939	P	0.7259880000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.30297	-0.9983	8	0.07644	T	0.81	.	0.9601	0.01393	0.4435:0.1255:0.1777:0.2534	rs6962772;rs10358546;rs56621679;rs60618959;rs6962772	77	Q5FWF6	ZN789_HUMAN	A	77;70	ENSP00000331927:T77A;ENSP00000405206:T70A	ENSP00000331927:T77A	T	+	1	0	ZNF789	98919666	0.000000	0.05858	0.007000	0.13788	0.922000	0.55478	-0.578000	0.05841	-0.645000	0.05458	-0.119000	0.15052	ACT	A|0.607;G|0.393	0.393	strong		0.527	ZNF789-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336266.1	NM_213603	
WDFY4	57705	hgsc.bcm.edu	37	10	49998824	49998824	+	Silent	SNP	C	C	T	rs10857644	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.						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	180	0	0		WXS	Illumina HiSeq	Phase_I	169	75	0.443787	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	
CCDC114	93233	hgsc.bcm.edu	37	19	48806015	48806015	+	Silent	SNP	C	C	T	rs34540645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48806015C>T	ENST00000315396.7	-	10	1747	c.1065G>A	c.(1063-1065)tcG>tcA	p.S355S		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	355					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)		GCTCAGCCTCCGAGTGCACCT	0.642													c|||	130	0.0259585	0.0015	0.0432	5008	,	,		19810	0.0		0.0845	False		,,,				2504	0.0133				p.S355S		Atlas-SNP	.											.	CCDC114	100	.	0			c.G1065A						PASS	.			98,4308	77.3+/-115.6	1,96,2106	82.0	76.0	78.0		1065	-6.7	0.0	19	dbSNP_126	78	866,7734	193.9+/-239.5	40,786,3474	no	coding-synonymous	CCDC114	NM_144577.3		41,882,5580	TT,TC,CC		10.0698,2.2242,7.412		355/671	48806015	964,12042	2203	4300	6503	SO:0001819	synonymous_variant	93233	exon10			AGCCTCCGAGTGC	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.1065G>A	19.37:g.48806015C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Silent	SNP	ENST00000315396.7	37	CCDS12714.2																																																																																			C|0.935;T|0.065	0.065	strong		0.642	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
VWDE	221806	hgsc.bcm.edu	37	7	12409535	12409535	+	Silent	SNP	A	A	G	rs3801366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	160	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	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	
WHAMM	123720	hgsc.bcm.edu	37	15	83502066	83502066	+	Missense_Mutation	SNP	C	C	G	rs386785864|rs11259954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:83502066C>G	ENST00000286760.4	+	10	2307	c.2208C>G	c.(2206-2208)caC>caG	p.H736Q		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	736	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.		H -> P (in dbSNP:rs11259953).|H -> Q (in dbSNP:rs11259954).		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						GCCCTCCCCACGCCTCAATCA	0.537													C|||	676	0.134984	0.1256	0.1902	5008	,	,		18665	0.1935		0.1203	False		,,,				2504	0.0634				p.H736Q		Atlas-SNP	.											.	WHAMM	63	.	0			c.C2208G						PASS	.	C	GLN/HIS	4,3998		2,0,1999	58.0	58.0	58.0		2208	-10.6	0.0	15	dbSNP_120	58	3,8325		0,3,4161	yes	missense	WHAMM	NM_001080435.1	24	2,3,6160	GG,GC,CC		0.036,0.1,0.0568	benign	736/810	83502066	7,12323	2001	4164	6165	SO:0001583	missense	123720	exon10			TCCCCACGCCTCA	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.2208C>G	15.37:g.83502066C>G	ENSP00000286760:p.His736Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	265	0.12133699633699634	46	0.09349593495934959	50	0.13812154696132597	95	0.1660839160839161	74	0.09762532981530343	C	8.855	0.945433	0.18356	0.001	3.6E-4	ENSG00000156232	ENST00000286760	T	0.28666	1.6	5.57	-10.6	0.00265	.	1.175250	0.06034	N	0.653556	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	B	0.28400	0.21	B	0.22753	0.041	T	0.08289	-1.0729	9	0.14656	T	0.56	.	2.7903	0.05386	0.2348:0.2633:0.0722:0.4297	rs11259954;rs60545449;rs11259954	736	Q8TF30	WHAMM_HUMAN	Q	736	ENSP00000286760:H736Q	ENSP00000286760:H736Q	H	+	3	2	WHAMM	81299120	0.000000	0.05858	0.000000	0.03702	0.272000	0.26649	-1.690000	0.01922	-1.720000	0.01380	-0.319000	0.08680	CAC	C|0.877;G|0.123	0.123	strong		0.537	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
PRX	57716	hgsc.bcm.edu	37	19	40901496	40901496	+	Missense_Mutation	SNP	T	T	C	rs268673	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40901496T>C	ENST00000324001.7	-	7	3033	c.2763A>G	c.(2761-2763)atA>atG	p.I921M	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	921			I -> M (in dbSNP:rs268673). {ECO:0000269|PubMed:11133365}.		axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTTTTGTCTCTATCATCTCCA	0.577													C|||	1486	0.296725	0.3071	0.3833	5008	,	,		18355	0.1885		0.3767	False		,,,				2504	0.2505				p.I921M		Atlas-SNP	.											.	PRX	151	.	0			c.A2763G						PASS	.	C	,MET/ILE	1428,2978	683.5+/-404.3	254,920,1029	75.0	86.0	82.0		,2763	-5.4	0.0	19	dbSNP_79	82	3336,5264	642.8+/-399.9	633,2070,1597	yes	utr-3,missense	PRX	NM_020956.2,NM_181882.2	,10	887,2990,2626	CC,CT,TT		38.7907,32.4103,36.6292	,benign	,921/1462	40901496	4764,8242	2203	4300	6503	SO:0001583	missense	57716	exon7			TGTCTCTATCATC	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.2763A>G	19.37:g.40901496T>C	ENSP00000326018:p.Ile921Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	683	0.31272893772893773	153	0.31097560975609756	158	0.43646408839779005	93	0.16258741258741258	279	0.36807387862796836	C	1.471	-0.559849	0.03967	0.324103	0.387907	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.03094	4.05	5.2	-5.36	0.02689	.	2.289120	0.01899	N	0.039096	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999480482	B	0.02656	0.0	B	0.01281	0.0	T	0.46428	-0.9192	9	0.29301	T	0.29	7.6947	8.8913	0.35434	0.1258:0.2674:0.0:0.6068	rs268673;rs60675249;rs268673	921	Q9BXM0	PRAX_HUMAN	M	921	ENSP00000326018:I921M	ENSP00000326018:I921M	I	-	3	3	PRX	45593336	0.000000	0.05858	0.003000	0.11579	0.076000	0.17211	-2.763000	0.00784	-0.939000	0.03709	-0.215000	0.12644	ATA	T|0.669;C|0.331	0.331	strong		0.577	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
CD200	4345	hgsc.bcm.edu	37	3	112066562	112066562	+	Silent	SNP	G	G	A	rs1050572	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:112066562G>A	ENST00000315711.8	+	4	636	c.579G>A	c.(577-579)acG>acA	p.T193T	CD200_ENST00000383681.3_Silent_p.T119T|CD200_ENST00000473539.1_Silent_p.T218T	NM_005944.5	NP_005935.4	P41217	OX2G_HUMAN	CD200 molecule	193	Ig-like C2-type.				regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.T218T(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				ATGGGACCACGTCTGTTACCA	0.557													G|||	1072	0.214058	0.3132	0.0677	5008	,	,		729	0.255		0.0746	False		,,,				2504	0.2853				p.T218T		Atlas-SNP	.											CD200,NS,carcinoma,0,1	CD200	33	1	1	Substitution - coding silent(1)	stomach(1)	c.G654A						PASS	.	G	,	1219,3187	424.0+/-340.3	151,917,1135	128.0	125.0	126.0		654,579	-9.3	0.4	3	dbSNP_86	126	657,7943	166.4+/-218.3	24,609,3667	no	coding-synonymous,coding-synonymous	CD200	NM_001004196.2,NM_005944.5	,	175,1526,4802	AA,AG,GG		7.6395,27.6668,14.4241	,	218/295,193/270	112066562	1876,11130	2203	4300	6503	SO:0001819	synonymous_variant	4345	exon5			GACCACGTCTGTT		CCDS2965.1, CCDS33818.1	3q13.2	2013-09-20	2006-03-28	2004-09-01	ENSG00000091972	ENSG00000091972		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7203	protein-coding gene	gene with protein product		155970	"""antigen identified by monoclonal antibody MRC OX-2"", ""CD200 antigen"""	MOX1, MOX2			Standard	XM_005247482		Approved	MRC, OX-2	uc003dyw.3	P41217	OTTHUMG00000159248	ENST00000315711.8:c.579G>A	3.37:g.112066562G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_001004196	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Silent	SNP	ENST00000315711.8	37	CCDS2965.1																																																																																			G|0.836;A|0.164	0.164	strong		0.557	CD200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354078.1		
PCED1B	91523	hgsc.bcm.edu	37	12	47629368	47629368	+	Silent	SNP	G	G	T	rs2244818	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:47629368G>T	ENST00000546455.1	+	4	1253	c.522G>T	c.(520-522)ggG>ggT	p.G174G	RP11-493L12.3_ENST00000547748.1_RNA|PCED1B_ENST00000432328.1_Silent_p.G174G			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	25	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	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	
PIK3IP1	113791	hgsc.bcm.edu	37	22	31679110	31679110	+	Missense_Mutation	SNP	G	G	C	rs2040533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31679110G>C	ENST00000215912.5	-	6	935	c.752C>G	c.(751-753)aCc>aGc	p.T251S	PIK3IP1_ENST00000441972.1_3'UTR|PIK3IP1_ENST00000487265.2_Missense_Mutation_p.T172S	NM_052880.4	NP_443112.2	Q96FE7	P3IP1_HUMAN	phosphoinositide-3-kinase interacting protein 1	251			T -> S (in dbSNP:rs2040533). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase catalytic subunit binding (GO:0036313)			large_intestine(2)|lung(1)|ovary(1)	4						AAGGGGGGTGGTGCCCTCCTG	0.642													C|||	4232	0.845048	0.9856	0.7478	5008	,	,		17270	0.876		0.7266	False		,,,				2504	0.8139				p.T251S		Atlas-SNP	.											.	PIK3IP1	20	.	0			c.C752G						PASS	.	C	,SER/THR	4164,242	141.1+/-176.5	1970,224,9	53.0	40.0	45.0		,752	1.3	0.5	22	dbSNP_94	45	6233,2367	390.0+/-343.1	2259,1715,326	yes	utr-3,missense	PIK3IP1	NM_001135911.1,NM_052880.4	,58	4229,1939,335	CC,CG,GG		27.5233,5.4925,20.06	,benign	,251/264	31679110	10397,2609	2203	4300	6503	SO:0001583	missense	113791	exon6			GGGGTGGTGCCCT	BC011049	CCDS13893.1, CCDS46690.1	22q12.2	2007-04-13			ENSG00000100100	ENSG00000100100			24942	protein-coding gene	gene with protein product						12477932	Standard	NM_052880		Approved	HGFL, MGC17330	uc003akm.3	Q96FE7	OTTHUMG00000151256	ENST00000215912.5:c.752C>G	22.37:g.31679110G>C	ENSP00000215912:p.Thr251Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_052880	B4DRR9|D1MEI0|O00318|Q49A94|Q86YW2|Q8NCJ9	Missense_Mutation	SNP	ENST00000215912.5	37	CCDS13893.1	1797	0.8228021978021978	484	0.983739837398374	275	0.7596685082872928	498	0.8706293706293706	540	0.712401055408971	C	0.005	-2.192325	0.00302	0.945075	0.724767	ENSG00000100100	ENST00000215912;ENST00000416925;ENST00000487265	T;T	0.42131	0.98;0.98	5.67	1.32	0.21799	.	0.557605	0.22422	N	0.060270	T	0.00012	0.0000	N	0.00289	-1.7	0.43902	P	0.0034610000000000474	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34104	-0.9842	9	0.02654	T	1	-11.371	2.2271	0.03987	0.1251:0.4863:0.1217:0.267	rs2040533;rs17760782;rs17845282;rs17858115;rs59901552;rs2040533	172;251	D1MEI0;Q96FE7	.;P3IP1_HUMAN	S	251;229;172	ENSP00000215912:T251S;ENSP00000441361:T172S	ENSP00000215912:T251S	T	-	2	0	PIK3IP1	30009110	0.006000	0.16342	0.473000	0.27253	0.033000	0.12548	0.236000	0.17967	0.357000	0.24183	-0.978000	0.02582	ACC	G|0.183;C|0.817	0.817	strong		0.642	PIK3IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321939.1	NM_052880	
PRUNE2	158471	hgsc.bcm.edu	37	9	79325297	79325297	+	Silent	SNP	T	T	G	rs11145018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79325297T>G	ENST00000376718.3	-	8	2016	c.1893A>C	c.(1891-1893)acA>acC	p.T631T	PRUNE2_ENST00000428286.1_Silent_p.T272T	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	631					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						TCATATCTTCTGTATAGAGTG	0.488													T|||	1192	0.238019	0.2126	0.1599	5008	,	,		18192	0.4643		0.1551	False		,,,				2504	0.18				p.T631T		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A1893C						PASS	.	T		628,2508		50,528,990	113.0	101.0	104.0		1893	4.6	0.7	9	dbSNP_120	104	882,6282		50,782,2750	no	coding-synonymous	PRUNE2	NM_015225.2		100,1310,3740	GG,GT,TT		12.3116,20.0255,14.6602		631/3089	79325297	1510,8790	1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			ATCTTCTGTATAG	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.1893A>C	9.37:g.79325297T>G		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	279	135	0.483871	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1																																																																																			T|0.748;G|0.252	0.252	strong		0.488	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
CATSPER4	378807	hgsc.bcm.edu	37	1	26524520	26524520	+	Silent	SNP	G	G	A	rs61776651	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26524520G>A	ENST00000456354.2	+	5	697	c.630G>A	c.(628-630)tcG>tcA	p.S210S		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	210					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTGCAGTCGGTGCCTGACA	0.637													G|||	180	0.0359425	0.0045	0.0389	5008	,	,		16368	0.0		0.1292	False		,,,				2504	0.0174				p.S210S		Atlas-SNP	.											.	CATSPER4	59	.	0			c.G630A						PASS	.	G		120,4286	88.7+/-127.4	3,114,2086	179.0	162.0	168.0		630	-4.7	1.0	1	dbSNP_129	168	1102,7498	229.7+/-264.3	78,946,3276	no	coding-synonymous	CATSPER4	NM_198137.1		81,1060,5362	AA,AG,GG		12.814,2.7236,9.3957		210/473	26524520	1222,11784	2203	4300	6503	SO:0001819	synonymous_variant	378807	exon5			GCAGTCGGTGCCT	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.630G>A	1.37:g.26524520G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_198137	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																			G|0.917;A|0.083	0.083	strong		0.637	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
TMEM136	219902	hgsc.bcm.edu	37	11	120198093	120198093	+	Intron	SNP	G	G	A	rs1893261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:120198093G>A	ENST00000375095.2	+	2	240				TMEM136_ENST00000529187.1_Silent_p.Q3Q|TMEM136_ENST00000531346.1_Intron|TMEM136_ENST00000314475.2_Silent_p.Q3Q	NM_001198671.1|NM_001198672.1|NM_001198673.1|NM_001198674.1|NM_001198675.1	NP_001185600.1|NP_001185601.1|NP_001185602.1|NP_001185603.1|NP_001185604.1	Q6ZRR5	TM136_HUMAN	transmembrane protein 136							integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|ovary(1)	4		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)		AAATGACCCAGTGCTGTTTTC	0.383													A|||	1994	0.398163	0.4493	0.3372	5008	,	,		20706	0.2897		0.3777	False		,,,				2504	0.5051				p.Q3Q		Atlas-SNP	.											.	TMEM136	35	.	0			c.G9A						PASS	.	A	,,,,,,	1933,2473	623.4+/-394.1	424,1085,694	157.0	150.0	152.0		9,,,,,,9	-10.7	0.0	11	dbSNP_92	152	3252,5346	649.0+/-400.6	600,2052,1647	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	TMEM136	NM_001198670.1,NM_001198671.1,NM_001198672.1,NM_001198673.1,NM_001198674.1,NM_001198675.1,NM_174926.2	,,,,,,	1024,3137,2341	AA,AG,GG		37.8227,43.872,39.8723	,,,,,,	3/268,,,,,,3/149	120198093	5185,7819	2203	4299	6502	SO:0001627	intron_variant	219902	exon2			GACCCAGTGCTGT	BC015232	CCDS8432.1, CCDS55792.1, CCDS55793.1	11q23.3	2006-11-24				ENSG00000181264			28280	protein-coding gene	gene with protein product						12477932	Standard	NM_174926		Approved	MGC17839	uc001pxj.3	Q6ZRR5		ENST00000375095.2:c.-1-57G>A	11.37:g.120198093G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	207	92	0.444444	NM_001198670	B4DGQ4|B4E230|Q8IZ79	Silent	SNP	ENST00000375095.2	37	CCDS55793.1																																																																																			G|0.611;A|0.389	0.389	strong		0.383	TMEM136-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388045.1	NM_174926	
FCGR3A	2214	hgsc.bcm.edu	37	1	161599571	161599571	+	Intron	SNP	T	T	C	rs2290834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161599571T>C	ENST00000540048.1	-	2	94				FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.I106V|FCGR3B_ENST00000531221.1_Missense_Mutation_p.I142V|FCGR3B_ENST00000367964.2_Missense_Mutation_p.I106V			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AACTCACCGATATGGACTTCT	0.478																																					p.I142V		Atlas-SNP	.											FCGR3B,NS,carcinoma,+2,1	FCGR3B	35	1	0			c.A424G						scavenged	.						24.0	26.0	25.0					1																	161599571		2124	4279	6403	SO:0001627	intron_variant	2215	exon3			CACCGATATGGAC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+586A>G	1.37:g.161599571T>C		Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	233	54	0.23176	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	1.794|1.794	-0.478839|-0.478839	0.04414|0.04414	.|.	.|.	ENSG00000162747|ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221;ENST00000534776|ENST00000421702	T;T;T;T|.	0.02787|.	4.91;4.91;5.01;4.16|.	2.79|2.79	-5.57|-5.57	0.02521|0.02521	.|.	4.037030|.	0.00559|.	N|.	0.000262|.	T|T	0.02727|0.02727	0.0082|0.0082	N|N	0.04508|0.04508	-0.205|-0.205	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.16660|0.16660	-1.0395|-1.0395	9|4	0.20046|.	T|.	0.44|.	.|.	3.2984|3.2984	0.06974|0.06974	0.1208:0.478:0.2427:0.1584|0.1208:0.478:0.2427:0.1584	.|.	106|.	O75015|.	FCG3B_HUMAN|.	V|C	106;106;142;89|126	ENSP00000356941:I106V;ENSP00000294800:I106V;ENSP00000433642:I142V;ENSP00000437084:I89V|.	ENSP00000294800:I106V|.	I|Y	-|-	1|2	0|0	FCGR3B|FCGR3B	159866195|159866195	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	-7.325000|-7.325000	0.00039|0.00039	-3.260000|-3.260000	0.00202|0.00202	0.319000|0.319000	0.21371|0.21371	ATC|TAT	.	.	weak		0.478	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
MTRR	4552	hgsc.bcm.edu	37	5	7892933	7892933	+	Silent	SNP	A	A	G	rs35890938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7892933A>G	ENST00000264668.2	+	11	1575	c.1545A>G	c.(1543-1545)gtA>gtG	p.V515V	MTRR_ENST00000440940.2_Silent_p.V488V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	515	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GGAAGGGAGTATGTACAGGCT	0.473													G|||	40	0.00798722	0.0015	0.0245	5008	,	,		18051	0.0		0.0189	False		,,,				2504	0.002				p.V515V		Atlas-SNP	.											.	MTRR	74	.	0			c.A1545G						PASS	.	G	,	46,4360	822.1+/-416.4	0,46,2157	150.0	129.0	136.0		1464,1545	0.7	0.5	5	dbSNP_126	136	207,8393	810.1+/-407.1	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	GG,GA,AA		2.407,1.044,1.9453	,	488/699,515/726	7892933	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			GGGAGTATGTACA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1545A>G	5.37:g.7892933A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
MYO3B	140469	hgsc.bcm.edu	37	2	171242761	171242761	+	Silent	SNP	G	G	A	rs17497636	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:171242761G>A	ENST00000408978.4	+	13	1496	c.1353G>A	c.(1351-1353)caG>caA	p.Q451Q	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.Q451Q|MYO3B_ENST00000334231.6_Silent_p.Q460Q	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	451	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TGATTGTTCAGCATTTGACTT	0.433													G|||	569	0.113618	0.0461	0.0965	5008	,	,		20758	0.0794		0.162	False		,,,				2504	0.2025				p.Q451Q		Atlas-SNP	.											.	MYO3B	320	.	0			c.G1353A						PASS	.	G	,,	227,3659		8,211,1724	128.0	125.0	126.0		1353,1353,1353	1.1	1.0	2	dbSNP_123	126	1424,6866		112,1200,2833	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	120,1411,4557	AA,AG,GG		17.1773,5.8415,13.5595	,,	451/1315,451/1276,451/1342	171242761	1651,10525	1943	4145	6088	SO:0001819	synonymous_variant	140469	exon13			TGTTCAGCATTTG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1353G>A	2.37:g.171242761G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	235	116	0.493617	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																			G|0.891;A|0.109	0.109	strong		0.433	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967680	49967680	+	Silent	SNP	G	G	A	rs2293009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49967680G>A	ENST00000293350.4	+	11	1501	c.1338G>A	c.(1336-1338)caG>caA	p.Q446Q	ALDH16A1_ENST00000433981.2_Silent_p.Q281Q|CTD-3148I10.9_ENST00000599536.1_Missense_Mutation_p.R36K|ALDH16A1_ENST00000540132.1_Silent_p.Q283Q|ALDH16A1_ENST00000455361.2_Silent_p.Q395Q	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	446						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)		ACAGGCTCCAGGTGGGCACTG	0.652													G|||	1560	0.311502	0.1256	0.2219	5008	,	,		13775	0.3363		0.4165	False		,,,				2504	0.4928				p.Q446Q		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1338A						PASS	.	G	,	755,3649		78,599,1525	21.0	24.0	23.0		1185,1338	2.5	0.7	19	dbSNP_100	23	3526,5074		724,2078,1498	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	802,2677,3023	AA,AG,GG		41.0,17.1435,32.9206	,	395/752,446/803	49967680	4281,8723	2202	4300	6502	SO:0001819	synonymous_variant	126133	exon11			GCTCCAGGTGGGC	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.1338G>A	19.37:g.49967680G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	105	40	0.380952	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			G|0.712;A|0.288	0.288	strong		0.652	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
KIR2DL3	3804	hgsc.bcm.edu	37	19	55263898	55263898	+	Missense_Mutation	SNP	G	G	A	rs1049267	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55263898G>A	ENST00000342376.3	+	8	984	c.953G>A	c.(952-954)cGc>cAc	p.R318H	KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL3_ENST00000434419.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	318			R -> H (in dbSNP:rs1049267). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8662091, ECO:0000269|PubMed:9059894, ECO:0000269|PubMed:9430221}.		immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		AAAATCACTCGCCCTTCTCAG	0.498													.|||	1314	0.26238	0.2958	0.2133	5008	,	,		14495	0.1319		0.4135	False		,,,				2504	0.2311				p.R318H		Atlas-SNP	.											KIR2DL3,NS,carcinoma,0,2	KIR2DL3	68	2	0			c.G953A						PASS	.	G	HIS/ARG	1268,2832		409,450,1191	172.0	190.0	184.0		953	-1.8	0.0	19	dbSNP_86	184	3466,4526		1194,1078,1724	no	missense	KIR2DL3	NM_015868.2	29	1603,1528,2915	AA,AG,GG		43.3684,30.9268,39.1499		318/342	55263898	4734,7358	2050	3996	6046	SO:0001583	missense	3804	exon8			TCACTCGCCCTTC	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.953G>A	19.37:g.55263898G>A	ENSP00000342215:p.Arg318His	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	128	123	0.960938	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	37	CCDS33107.1	621	0.28434065934065933	137	0.2784552845528455	96	0.26519337016574585	69	0.12062937062937062	319	0.420844327176781	g	4.003	-0.002093	0.07819	0.309268	0.433684	ENSG00000243772	ENST00000342376	T	0.00464	7.24	0.909	-1.82	0.07857	.	.	.	.	.	T	0.00012	0.0000	M	0.80028	2.48	0.80722	P	0.0	D;B;B	0.53151	0.958;0.006;0.006	P;B;B	0.48488	0.579;0.002;0.002	T	0.34428	-0.9829	8	0.42905	T	0.14	.	8.3911	0.32528	0.0:0.6188:0.3812:0.0	rs1049267;rs3189371;rs11671789;rs16985912;rs17845997;rs17858981;rs17859525	220;318;318	P43628-2;P43628;E3NZD8	.;KI2L3_HUMAN;.	H	318	ENSP00000342215:R318H	ENSP00000342215:R318H	R	+	2	0	KIR2DL3	59955710	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.002000	0.12924	-2.805000	0.00350	-2.747000	0.00125	CGC	.	.	weak		0.498	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1		
TKT	7086	hgsc.bcm.edu	37	3	53264485	53264485	+	Silent	SNP	A	A	G	rs1131728	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:53264485A>G	ENST00000462138.1	-	8	1183	c.1095T>C	c.(1093-1095)gcT>gcC	p.A365A	TKT_ENST00000296289.6_Silent_p.A318A|TKT_ENST00000423525.2_Silent_p.A365A|TKT_ENST00000423516.1_Silent_p.A373A|TKT_ENST00000461139.1_5'UTR			P29401	TKT_HUMAN	transketolase	365					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		TGTTCTGCTCAGCAATGTAGC	0.602													G|||	886	0.176917	0.1203	0.1427	5008	,	,		18973	0.1567		0.169	False		,,,				2504	0.3067				p.A373A	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.T1119C						PASS	.	G	,	668,3738	764.0+/-413.3	55,558,1590	109.0	103.0	105.0		1095,1095	-11.6	0.0	3	dbSNP_86	105	1661,6939	740.6+/-407.1	161,1339,2800	no	coding-synonymous,coding-synonymous	TKT	NM_001064.3,NM_001135055.2	,	216,1897,4390	GG,GA,AA		19.314,15.1611,17.9071	,	365/624,365/624	53264485	2329,10677	2203	4300	6503	SO:0001819	synonymous_variant	7086	exon9			CTGCTCAGCAATG		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"""Wernicke-Korsakoff syndrome"""	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.1095T>C	3.37:g.53264485A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	37	CCDS2871.1																																																																																			T|0.159;G|0.140;C|0.026;A|0.674	0.140	strong		0.602	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
C5orf58	133874	hgsc.bcm.edu	37	5	169661994	169661994	+	Missense_Mutation	SNP	G	G	C	rs957998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:169661994G>C	ENST00000521850.1	+	2	1766	c.77G>C	c.(76-78)cGt>cCt	p.R26P	C5orf58_ENST00000593851.1_Missense_Mutation_p.R26P|C5orf58_ENST00000517575.1_3'UTR			C9J3I9	CE058_HUMAN	chromosome 5 open reading frame 58	26										large_intestine(1)|lung(4)|urinary_tract(1)	6						GGTAAGAAGCGTGTTACTGAT	0.254																																					p.R26P		Atlas-SNP	.											.	C5orf58	13	.	0			c.G77C						PASS	.	G	PRO/ARG	1740,1854		450,840,507	48.0	45.0	46.0		77	3.5	0.0	5	dbSNP_86	46	4070,4038		1024,2022,1008	yes	missense	C5orf58	NM_001102609.1	103	1474,2862,1515	CC,CG,GG		49.8027,48.414,49.6496	benign	26/103	169661994	5810,5892	1797	4054	5851	SO:0001583	missense	133874	exon3			AGAAGCGTGTTAC	BC030767	CCDS47338.1	5q35.1	2009-09-30			ENSG00000234511	ENSG00000234511			37272	protein-coding gene	gene with protein product							Standard	NM_001102609		Approved		uc010jjn.3	C9J3I9	OTTHUMG00000163122	ENST00000521850.1:c.77G>C	5.37:g.169661994G>C	ENSP00000428956:p.Arg26Pro	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	166	70	0.421687	NM_001102609		Missense_Mutation	SNP	ENST00000521850.1	37	CCDS47338.1	1168	0.5347985347985348	238	0.483739837398374	217	0.5994475138121547	318	0.5559440559440559	395	0.521108179419525	G	0.246	-1.010296	0.02095	0.48414	0.501973	ENSG00000234511	ENST00000521850	.	.	.	5.87	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.43540	-0.9385	7	0.34782	T	0.22	.	7.9123	0.29798	0.836:0.0:0.164:0.0	rs957998;rs3761751;rs59509559;rs957998	26	C9J3I9	CE058_HUMAN	P	26	.	ENSP00000428956:R26P	R	+	2	0	C5orf58	169594572	0.725000	0.28048	0.002000	0.10522	0.004000	0.04260	1.242000	0.32755	0.584000	0.29591	-0.302000	0.09304	CGT	G|0.480;C|0.520	0.520	strong		0.254	C5orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371739.1	NM_001102609	
HAUS6	54801	hgsc.bcm.edu	37	9	19063108	19063108	+	Silent	SNP	T	T	C	rs13302748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:19063108T>C	ENST00000380502.3	-	14	1994	c.1527A>G	c.(1525-1527)ttA>ttG	p.L509L	HAUS6_ENST00000380496.1_Silent_p.L373L|SCARNA8_ENST00000515924.1_RNA	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	509					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						CAACATCTGATAATGGAGAAT	0.358													T|||	1763	0.352037	0.1702	0.4035	5008	,	,		19022	0.38		0.4493	False		,,,				2504	0.4325				p.L509L		Atlas-SNP	.											.	HAUS6	66	.	0			c.A1527G						PASS	.	T		888,3518	341.2+/-306.6	104,680,1419	105.0	96.0	99.0		1527	2.0	0.0	9	dbSNP_121	99	3911,4685	544.6+/-384.6	883,2145,1270	no	coding-synonymous	HAUS6	NM_017645.3		987,2825,2689	CC,CT,TT		45.4979,20.1543,36.9097		509/956	19063108	4799,8203	2203	4298	6501	SO:0001819	synonymous_variant	54801	exon14			ATCTGATAATGGA	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.1527A>G	9.37:g.19063108T>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	174	81	0.465517	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			T|0.703;C|0.297	0.297	strong		0.358	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
COL21A1	81578	hgsc.bcm.edu	37	6	56033094	56033094	+	Splice_Site	SNP	G	G	A	rs35471617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:56033094G>A	ENST00000244728.5	-	6	1425	c.1028C>T	c.(1027-1029)aCg>aTg	p.T343M	COL21A1_ENST00000535941.1_Splice_Site_p.T343M|COL21A1_ENST00000370819.1_Splice_Site_p.T343M	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	343	Laminin G-like.		T -> M (in dbSNP:rs35471617). {ECO:0000269|PubMed:14702039}.		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)			ATCAAACAACGTCTACAAAAA	0.348													G|||	363	0.072484	0.0045	0.1095	5008	,	,		18138	0.0863		0.0865	False		,,,				2504	0.1094				p.T343M		Atlas-SNP	.											COL21A1_ENST00000244728,caecum,carcinoma,+1,2	COL21A1	201	2	0			c.C1028T						PASS	.	G	MET/THR	61,3587		0,61,1763	44.0	39.0	41.0		1028	2.4	0.9	6	dbSNP_126	41	585,7579		19,547,3516	yes	missense-near-splice	COL21A1	NM_030820.3	81	19,608,5279	AA,AG,GG		7.1656,1.6721,5.469	possibly-damaging	343/958	56033094	646,11166	1824	4082	5906	SO:0001630	splice_region_variant	81578	exon6			AACAACGTCTACA	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.1027-1C>T	6.37:g.56033094G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	49	33	0.673469	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	163	0.07463369963369963	5	0.01016260162601626	34	0.09392265193370165	57	0.09965034965034965	67	0.08839050131926121	G	7.044	0.563114	0.13498	0.016721	0.071656	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	T;T;T	0.02280	4.36;4.36;4.36	5.35	2.41	0.29592	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	0.425748	0.21461	N	0.074164	T	0.02047	0.0064	L	0.47716	1.5	0.09310	P	0.99999999539863	D;D	0.76494	0.999;0.995	P;P	0.61003	0.882;0.533	T	0.48068	-0.9067	9	0.54805	T	0.06	.	4.3099	0.10965	0.2124:0.0:0.4653:0.3223	rs35471617	343;343	Q96P44-3;Q96P44	.;COLA1_HUMAN	M	343	ENSP00000244728:T343M;ENSP00000359855:T343M;ENSP00000444384:T343M	ENSP00000244728:T343M	T	-	2	0	COL21A1	56141053	0.952000	0.32445	0.885000	0.34714	0.138000	0.21146	0.256000	0.18351	0.150000	0.19136	0.655000	0.94253	ACG	G|0.927;A|0.073	0.073	strong		0.348	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		Missense_Mutation
CPA4	51200	hgsc.bcm.edu	37	7	129938598	129938598	+	Missense_Mutation	SNP	G	G	T	rs34587586	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:129938598G>T	ENST00000222482.4	+	2	109	c.81G>T	c.(79-81)ttG>ttT	p.L27F	CPA4_ENST00000493259.1_Intron|CPA4_ENST00000445470.2_Missense_Mutation_p.L27F	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	27			L -> F (in dbSNP:rs34587586).		histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					ACCAAGTTTTGAGGATTAATG	0.428													T|||	1783	0.35603	0.3253	0.3458	5008	,	,		20606	0.3581		0.3877	False		,,,				2504	0.3701				p.L27F		Atlas-SNP	.											.	CPA4	47	.	0			c.G81T						PASS	.	T	PHE/LEU,PHE/LEU	1486,2920	676.9+/-403.3	252,982,969	126.0	125.0	125.0		81,81	4.5	1.0	7	dbSNP_126	125	3453,5147	636.4+/-399.1	715,2023,1562	yes	missense,missense	CPA4	NM_001163446.1,NM_016352.3	22,22	967,3005,2531	TT,TG,GG		40.1512,33.7267,37.9748	benign,benign	27/389,27/422	129938598	4939,8067	2203	4300	6503	SO:0001583	missense	51200	exon2			AGTTTTGAGGATT	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.81G>T	7.37:g.129938598G>T	ENSP00000222482:p.Leu27Phe	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	210	101	0.480952	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	793	0.3630952380952381	159	0.3231707317073171	141	0.38950276243093923	213	0.3723776223776224	280	0.36939313984168864	T	7.318	0.616383	0.14129	0.337267	0.401512	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000492072;ENST00000473956	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.61	4.47	0.54385	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.227453	0.39146	N	0.001446	T	0.00012	0.0000	N	0.20483	0.58	0.42641	P	0.006581999999999977	B;B	0.13594	0.008;0.002	B;B	0.36186	0.219;0.023	T	0.48906	-0.8993	9	0.12103	T	0.63	.	5.3961	0.16271	0.0:0.0931:0.1772:0.7297	rs34587586	27;27	B7Z576;Q9UI42	.;CBPA4_HUMAN	F	27	ENSP00000412947:L27F;ENSP00000222482:L27F;ENSP00000417255:L27F;ENSP00000418392:L27F	ENSP00000222482:L27F	L	+	3	2	CPA4	129725834	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.604000	0.24164	0.512000	0.28257	-0.525000	0.04345	TTG	G|0.630;T|0.370	0.370	strong		0.428	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
FER1L6	654463	hgsc.bcm.edu	37	8	124987478	124987478	+	Silent	SNP	T	T	C	rs7465584	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:124987478T>C	ENST00000522917.1	+	8	821	c.615T>C	c.(613-615)agT>agC	p.S205S	FER1L6_ENST00000399018.1_Silent_p.S205S	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	205						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)			GTGACATCAGTGTCATGGGAA	0.502													C|||	1984	0.396166	0.3971	0.3602	5008	,	,		19869	0.4405		0.4871	False		,,,				2504	0.2812				p.S205S		Atlas-SNP	.											.	FER1L6	268	.	0			c.T615C						PASS	.	C		1716,2238		377,962,638	137.0	131.0	133.0		615	-10.1	0.0	8	dbSNP_116	133	3865,4451		912,2041,1205	yes	coding-synonymous	FER1L6	NM_001039112.2		1289,3003,1843	CC,CT,TT		46.4767,43.3991,45.4849		205/1858	124987478	5581,6689	1977	4158	6135	SO:0001819	synonymous_variant	654463	exon8			CATCAGTGTCATG	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.615T>C	8.37:g.124987478T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	195	194	0.994872	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			C|0.427;N|0.000	0.427	strong		0.502	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
HCN2	610	hgsc.bcm.edu	37	19	613898	613898	+	Silent	SNP	T	T	C	rs1054786	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:613898T>C	ENST00000251287.2	+	7	1925	c.1872T>C	c.(1870-1872)gcT>gcC	p.A624A	AC005559.2_ENST00000591847.1_RNA	NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	624					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			endometrium(5)|lung(4)	9		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGTGCGGGCTGACACCTACT	0.706													c|||	4115	0.821685	0.9796	0.7349	5008	,	,		4851	0.8958		0.5865	False		,,,				2504	0.8354				p.A624A	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.T1872C						PASS	.	C		4024,366		1851,322,22	28.0	29.0	28.0		1872	-7.7	0.6	19	dbSNP_86	28	4945,3649		1422,2101,774	no	coding-synonymous	HCN2	NM_001194.3		3273,2423,796	CC,CT,TT		42.4599,8.3371,30.9227		624/890	613898	8969,4015	2195	4297	6492	SO:0001819	synonymous_variant	610	exon7			GCGGGCTGACACC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.1872T>C	19.37:g.613898T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			T|0.274;C|0.726	0.726	strong		0.706	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
PKP1	5317	hgsc.bcm.edu	37	1	201252866	201252866	+	Silent	SNP	C	C	T	rs2268147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201252866C>T	ENST00000352845.3	+	1	36	c.36C>T	c.(34-36)taC>taT	p.Y12Y	PKP1_ENST00000367324.3_Silent_p.Y12Y|PKP1_ENST00000263946.3_Silent_p.Y12Y			Q13835	PKP1_HUMAN	plakophilin 1	12					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						CCTTGGCGTACGAATGCTTCC	0.657													C|||	903	0.180312	0.3828	0.1052	5008	,	,		17870	0.0873		0.0716	False		,,,				2504	0.1677				p.Y12Y		Atlas-SNP	.											.	PKP1	127	.	0			c.C36T						PASS	.	C	,	1508,2898	477.9+/-358.1	266,976,961	83.0	64.0	70.0		36,36	2.8	1.0	1	dbSNP_100	70	750,7850	180.5+/-229.4	36,678,3586	no	coding-synonymous,coding-synonymous	PKP1	NM_000299.3,NM_001005337.2	,	302,1654,4547	TT,TC,CC		8.7209,34.2261,17.3612	,	12/748,12/727	201252866	2258,10748	2203	4300	6503	SO:0001819	synonymous_variant	5317	exon1			GGCGTACGAATGC	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.36C>T	1.37:g.201252866C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_001005337	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																			C|0.839;T|0.161	0.161	strong		0.657	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
HEXB	3074	hgsc.bcm.edu	37	5	73985215	73985215	+	Missense_Mutation	SNP	A	A	G	rs11556045	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73985215A>G	ENST00000261416.7	+	2	479	c.362A>G	c.(361-363)aAa>aGa	p.K121R	HEXB_ENST00000511181.1_5'UTR	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	121			K -> R (in dbSNP:rs11556045).		astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.K121R(1)		endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		TTCCAGGCTAAAACCCAGGTT	0.383													G|||	1115	0.222644	0.2693	0.2421	5008	,	,		20059	0.1667		0.1809	False		,,,				2504	0.2464				p.K121R	Melanoma(66;841 1270 13391 18706 27225)	Atlas-SNP	.											HEXB,NS,carcinoma,0,1	HEXB	34	1	1	Substitution - Missense(1)	stomach(1)	c.A362G						PASS	.	G	ARG/LYS	1141,3265	716.3+/-408.6	153,835,1215	175.0	174.0	174.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	362	-7.6	0.0	5	dbSNP_120	174	1452,7148	751.3+/-407.4	142,1168,2990	yes	missense	HEXB	NM_000521.3	26	295,2003,4205	GG,GA,AA		16.8837,25.8965,19.937	benign	121/557	73985215	2593,10413	2203	4300	6503	SO:0001583	missense	3074	exon2			AGGCTAAAACCCA	M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.362A>G	5.37:g.73985215A>G	ENSP00000261416:p.Lys121Arg	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	140	79	0.564286	NM_000521		Missense_Mutation	SNP	ENST00000261416.7	37	CCDS4022.1	453	0.20741758241758243	136	0.2764227642276423	83	0.2292817679558011	96	0.16783216783216784	138	0.1820580474934037	G	3.616	-0.078595	0.07141	0.258965	0.168837	ENSG00000049860	ENST00000261416	D	0.88664	-2.41	5.83	-7.58	0.01313	Acetylhexosaminidase, subunit a/b (1);	1.785790	0.02227	N	0.064526	T	0.00012	0.0000	N	0.16708	0.43	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48525	-0.9028	9	0.12103	T	0.63	2.2681	11.1512	0.48460	0.4827:0.2908:0.2265:0.0	rs11556045;rs56932933;rs11556045	121	P07686	HEXB_HUMAN	R	121	ENSP00000261416:K121R	ENSP00000261416:K121R	K	+	2	0	HEXB	74020971	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.913000	0.04042	-3.763000	0.00110	-3.424000	0.00037	AAA	A|0.792;G|0.208	0.208	strong		0.383	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50660137	50660137	+	Missense_Mutation	SNP	G	G	A	rs34455105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50660137G>A	ENST00000248846.5	-	16	2755	c.2651C>T	c.(2650-2652)gCg>gTg	p.A884V	TUBGCP6_ENST00000439308.2_Missense_Mutation_p.A884V|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	884			A -> V (in dbSNP:rs34455105).		G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GGCCCCCTCCGCCTGCTGCAG	0.672													G|||	132	0.0263578	0.0053	0.0432	5008	,	,		16222	0.0		0.0696	False		,,,				2504	0.0256				p.A884V		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.C2651T						PASS	.	G	VAL/ALA	56,4348	52.3+/-87.9	0,56,2146	35.0	37.0	36.0		2651	-1.6	0.0	22	dbSNP_126	36	560,8038	147.3+/-202.7	14,532,3753	yes	missense	TUBGCP6	NM_020461.3	64	14,588,5899	AA,AG,GG		6.5131,1.2716,4.7377	benign	884/1820	50660137	616,12386	2202	4299	6501	SO:0001583	missense	85378	exon16			CCCTCCGCCTGCT	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.2651C>T	22.37:g.50660137G>A	ENSP00000248846:p.Ala884Val	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	188	86	0.457447	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	75	0.034340659340659344	3	0.006097560975609756	18	0.049723756906077346	1	0.0017482517482517483	53	0.06992084432717678	G	7.374	0.627376	0.14257	0.012716	0.065131	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.12465	3.08;2.68	2.35	-1.64	0.08318	.	3.676470	0.00974	N	0.003295	T	0.00496	0.0016	N	0.04880	-0.145	0.09310	N	1	B;B	0.21309	0.054;0.054	B;B	0.21546	0.035;0.023	T	0.29058	-1.0024	10	0.33141	T	0.24	.	3.8471	0.08939	0.3208:0.2085:0.4707:0.0	rs34455105	876;884	B2RWN4;Q96RT7	.;GCP6_HUMAN	V	884	ENSP00000248846:A884V;ENSP00000397387:A884V	ENSP00000248846:A884V	A	-	2	0	TUBGCP6	49002264	0.000000	0.05858	0.008000	0.14137	0.004000	0.04260	-0.232000	0.09055	-0.160000	0.11002	-1.099000	0.02127	GCG	G|0.956;A|0.044	0.044	strong		0.672	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
BFSP1	631	hgsc.bcm.edu	37	20	17474791	17474791	+	Silent	SNP	G	G	A	rs6080717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:17474791G>A	ENST00000377873.3	-	8	1965	c.1926C>T	c.(1924-1926)acC>acT	p.T642T	BFSP1_ENST00000377868.2_Silent_p.T517T|BFSP1_ENST00000536626.1_Silent_p.T503T|BFSP1_ENST00000544874.1_Silent_p.T503T	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	642	Tail.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.T642T(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CGATCACAGCGGTTTCTTCAT	0.448													G|||	1031	0.205871	0.2315	0.2205	5008	,	,		20785	0.0665		0.2962	False		,,,				2504	0.2117				p.T642T		Atlas-SNP	.											BFSP1,NS,carcinoma,0,1	BFSP1	55	1	1	Substitution - coding silent(1)	stomach(1)	c.C1926T						PASS	.	G	,	1112,3294	401.3+/-331.9	155,802,1246	140.0	145.0	143.0		1551,1926	-10.1	0.0	20	dbSNP_114	143	2484,6116	408.0+/-349.4	353,1778,2169	no	coding-synonymous,coding-synonymous	BFSP1	NM_001161705.1,NM_001195.3	,	508,2580,3415	AA,AG,GG		28.8837,25.2383,27.6488	,	517/541,642/666	17474791	3596,9410	2203	4300	6503	SO:0001819	synonymous_variant	631	exon8			CACAGCGGTTTCT	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.1926C>T	20.37:g.17474791G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	237	114	0.481013	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Silent	SNP	ENST00000377873.3	37	CCDS13126.1																																																																																			G|0.761;A|0.239	0.239	strong		0.448	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626820	43626820	+	Missense_Mutation	SNP	G	G	C	rs138779714	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:43626820G>C	ENST00000332857.6	-	4	1895	c.1867C>G	c.(1867-1869)Cgg>Ggg	p.R623G	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	623					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GATTCGTCCCGAAGCTGCATC	0.542													G|||	1620	0.323482	0.0764	0.5303	5008	,	,		10590	0.2411		0.4334	False		,,,				2504	0.4826				p.R623G		Atlas-SNP	.											FAM75A6,NS,carcinoma,0,2	.	.	2	0			c.C1867G						scavenged	.						2.0	2.0	2.0					9																	43626820		38	330	368	SO:0001583	missense	389730	exon4			CGTCCCGAAGCTG		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.1867C>G	9.37:g.43626820G>C	ENSP00000329825:p.Arg623Gly	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	51	34	0.666667	NM_001145196		Missense_Mutation	SNP	ENST00000332857.6	37	CCDS47973.1	524	0.23992673992673993	19	0.03861788617886179	149	0.4116022099447514	95	0.1660839160839161	261	0.34432717678100266	G	6.183	0.401995	0.11696	.	.	ENSG00000185775	ENST00000332857	T	0.06687	3.27	2.97	2.06	0.26882	.	0.721119	0.12036	N	0.505462	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.45629	-0.9248	9	0.52906	T	0.07	-2.4748	6.1646	0.20384	0.1491:0.0:0.8509:0.0	.	623	Q5VVP1	F75A6_HUMAN	G	623	ENSP00000329825:R623G	ENSP00000329825:R623G	R	-	1	2	FAM75A6	43566816	0.028000	0.19301	0.001000	0.08648	0.001000	0.01503	0.853000	0.27777	0.610000	0.30035	-0.559000	0.04183	CGG	G|0.760;C|0.240	0.240	strong		0.542	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
RABEP1	9135	hgsc.bcm.edu	37	17	5284698	5284698	+	Silent	SNP	A	A	G	rs1143206	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5284698A>G	ENST00000546142.2	+	17	2572	c.2385A>G	c.(2383-2385)caA>caG	p.Q795Q	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000408982.2_Silent_p.Q762Q|RABEP1_ENST00000262477.6_Silent_p.Q795Q|RABEP1_ENST00000537505.1_Silent_p.Q752Q|RABEP1_ENST00000341923.6_Silent_p.Q762Q			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	63	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	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	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254037	39254037	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254037G>A	ENST00000333822.4	-	1	356	c.300C>T	c.(298-300)tgC>tgT	p.C100C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	100	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						agctggggcggcagcagctgg	0.662																																					p.C100C		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	0			c.C300T						scavenged	.						6.0	9.0	8.0					17																	39254037		676	1553	2229	SO:0001819	synonymous_variant	728224	exon1			GGGGCGGCAGCAG	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.300C>T	17.37:g.39254037G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	87	20	0.229885	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			.	.	none		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
SH3BGR	6450	hgsc.bcm.edu	37	21	40871810	40871810	+	Missense_Mutation	SNP	T	T	C	rs9974333	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:40871810T>C	ENST00000333634.4	+	4	641	c.563T>C	c.(562-564)gTg>gCg	p.V188A	SH3BGR_ENST00000380637.3_Missense_Mutation_p.V77A|SH3BGR_ENST00000380631.1_Missense_Mutation_p.V77A|SH3BGR_ENST00000458295.1_Intron|SH3BGR_ENST00000380634.1_Missense_Mutation_p.V77A	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	188	Glu-rich (acidic).		V -> A (in dbSNP:rs9974333). {ECO:0000269|PubMed:15489334}.		positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		AGTGAAGATGTGGGCAACCTC	0.468													C|||	2759	0.550919	0.4334	0.6124	5008	,	,		20218	0.6905		0.5288	False		,,,				2504	0.545				p.V188A		Atlas-SNP	.											SH3BGR,NS,carcinoma,-1,2	SH3BGR	29	2	0			c.T563C						PASS	.	C	ALA/VAL,ALA/VAL	1983,2423		447,1089,667	124.0	114.0	117.0		230,563	-1.8	0.0	21	dbSNP_119	117	4599,4001		1239,2121,940	yes	missense,missense	SH3BGR	NM_001001713.1,NM_007341.2	64,64	1686,3210,1607	CC,CT,TT		46.5233,45.0068,49.3926	benign,benign	77/129,188/240	40871810	6582,6424	2203	4300	6503	SO:0001583	missense	6450	exon4			AAGATGTGGGCAA		CCDS13666.1, CCDS33560.1	21q22.3	2014-02-19	2014-02-19		ENSG00000185437	ENSG00000185437			10822	protein-coding gene	gene with protein product	"""21-glutamic acid-rich protein"""	602230	"""SH3 domain binding glutamic acid-rich protein"""			9050928	Standard	NM_007341		Approved	21-GARP	uc002yya.3	P55822	OTTHUMG00000074113	ENST00000333634.4:c.563T>C	21.37:g.40871810T>C	ENSP00000332513:p.Val188Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	NM_007341	A6ND59|D3DSI2|Q9BRB8	Missense_Mutation	SNP	ENST00000333634.4	37	CCDS13666.1	1189	0.5444139194139194	194	0.3943089430894309	210	0.580110497237569	390	0.6818181818181818	395	0.521108179419525	.	2.530	-0.308722	0.05458	0.450068	0.534767	ENSG00000185437	ENST00000380637;ENST00000380634;ENST00000440288;ENST00000380631;ENST00000333634;ENST00000423596;ENST00000447939	T;T;T;T;T;T;T	0.56275	1.03;1.03;1.06;1.03;1.98;0.8;0.47	4.96	-1.76	0.08006	.	1.400190	0.03918	N	0.282949	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	0.43940	-0.9360	9	0.02654	T	1	.	0.4012	0.00426	0.2399:0.2441:0.2734:0.2426	rs9974333;rs11575940;rs52803258;rs61401446;rs9974333	188	P55822	SH3BG_HUMAN	A	77;77;77;77;188;30;21	ENSP00000370011:V77A;ENSP00000370008:V77A;ENSP00000401572:V77A;ENSP00000370005:V77A;ENSP00000332513:V188A;ENSP00000413981:V30A;ENSP00000403115:V21A	ENSP00000332513:V188A	V	+	2	0	SH3BGR	39793680	0.000000	0.05858	0.006000	0.13384	0.035000	0.12851	-1.098000	0.03346	-0.467000	0.06932	-0.231000	0.12243	GTG	T|0.476;C|0.524	0.524	strong		0.468	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341	
CASZ1	54897	hgsc.bcm.edu	37	1	10725498	10725498	+	Silent	SNP	G	G	A	rs284322	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10725498G>A	ENST00000377022.3	-	5	464	c.147C>T	c.(145-147)gaC>gaT	p.D49D	CASZ1_ENST00000478728.2_5'UTR|CASZ1_ENST00000344008.5_Silent_p.D49D	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	49					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GGGAGCCGGCGTCAGCTCGCT	0.706													G|||	899	0.179513	0.2216	0.1412	5008	,	,		14988	0.1498		0.169	False		,,,				2504	0.1912				p.D49D		Atlas-SNP	.											.	CASZ1	150	.	0			c.C147T						PASS	.	G	,	700,3600		59,582,1509	23.0	28.0	27.0		147,147	2.5	0.9	1	dbSNP_79	27	1293,7179		89,1115,3032	no	coding-synonymous,coding-synonymous	CASZ1	NM_001079843.1,NM_017766.3	,	148,1697,4541	AA,AG,GG		15.262,16.2791,15.6044	,	49/1760,49/1167	10725498	1993,10779	2150	4236	6386	SO:0001819	synonymous_variant	54897	exon5			GCCGGCGTCAGCT	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.147C>T	1.37:g.10725498G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			G|0.817;A|0.183	0.183	strong		0.706	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
RCN2	5955	hgsc.bcm.edu	37	15	77241542	77241542	+	Silent	SNP	T	T	C	rs15939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:77241542T>C	ENST00000394885.3	+	7	1156	c.933T>C	c.(931-933)taT>taC	p.Y311Y	RCN2_ENST00000320963.5_Silent_p.Y329Y|RCN2_ENST00000394883.3_Silent_p.Y210Y	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	311						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						ATGATGACTATTTCTATCATG	0.393													T|||	249	0.0497204	0.0045	0.0706	5008	,	,		14638	0.0		0.1272	False		,,,				2504	0.0675				p.Y329Y		Atlas-SNP	.											.	RCN2	16	.	0			c.T987C						PASS	.	T		106,4286	82.9+/-121.4	1,104,2091	98.0	98.0	98.0		933	-3.5	1.0	15	dbSNP_52	98	948,7640	207.9+/-249.5	41,866,3387	no	coding-synonymous	RCN2	NM_002902.2		42,970,5478	CC,CT,TT		11.0387,2.4135,8.1202		311/318	77241542	1054,11926	2196	4294	6490	SO:0001819	synonymous_variant	5955	exon8			TGACTATTTCTAT	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"""EF-hand domain containing"""	9935	protein-coding gene	gene with protein product	"""Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"""	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.933T>C	15.37:g.77241542T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_001271837	A8MTG6|F8WCY5|Q53XN8	Silent	SNP	ENST00000394885.3	37	CCDS10291.1																																																																																			T|0.927;C|0.073	0.073	strong		0.393	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902	
KIAA0922	23240	hgsc.bcm.edu	37	4	154553973	154553973	+	Silent	SNP	G	G	A	rs35897141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:154553973G>A	ENST00000409663.3	+	32	4360	c.4308G>A	c.(4306-4308)tcG>tcA	p.S1436S	KIAA0922_ENST00000440693.1_Silent_p.S1353S|KIAA0922_ENST00000409959.3_Silent_p.S1437S	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1436						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)				TTCAGGAGTCGGCCCCGGTTC	0.512													G|||	81	0.0161741	0.0053	0.0259	5008	,	,		19375	0.0		0.0408	False		,,,				2504	0.0153				p.S1437S		Atlas-SNP	.											.	KIAA0922	214	.	0			c.G4311A						PASS	.	G	,	55,4351	53.6+/-89.4	0,55,2148	132.0	103.0	113.0		4311,4308	-10.2	0.0	4	dbSNP_126	113	599,8001	158.8+/-212.2	23,553,3724	no	coding-synonymous,coding-synonymous	KIAA0922	NM_001131007.1,NM_015196.3	,	23,608,5872	AA,AG,GG		6.9651,1.2483,5.0284	,	1437/1611,1436/1610	154553973	654,12352	2203	4300	6503	SO:0001819	synonymous_variant	23240	exon32			GGAGTCGGCCCCG	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.4308G>A	4.37:g.154553973G>A		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	228	119	0.52193	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			G|0.960;A|0.040	0.040	strong		0.512	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
ABCB1	5243	hgsc.bcm.edu	37	7	87138645	87138645	+	Silent	SNP	A	A	G	rs1045642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:87138645A>G	ENST00000265724.3	-	27	3852	c.3435T>C	c.(3433-3435)atT>atC	p.I1145I	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Silent_p.I1081I	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	1145	ABC transporter 2. {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)	CTGCCCTCACAATCTCTTCCT	0.527													G|||	3029	0.604832	0.8502	0.572	5008	,	,		20497	0.6022		0.4821	False		,,,				2504	0.4254				p.I1145I		Atlas-SNP	.											.	ABCB1	263	.	0			c.T3435C	GRCh37	CM000496	ABCB1	M	rs1045642	PASS	.	G		3403,1003	375.9+/-321.8	1308,787,108	178.0	156.0	163.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3435	-6.8	0.0	7	dbSNP_86	163	4097,4503	591.8+/-392.9	966,2165,1169	no	coding-synonymous	ABCB1	NM_000927.4		2274,2952,1277	GG,GA,AA		47.6395,22.7644,42.3343		1145/1281	87138645	7500,5506	2203	4300	6503	SO:0001819	synonymous_variant	5243	exon27			CCTCACAATCTCT	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.3435T>C	7.37:g.87138645A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_000927	A8K294|B5AK60|Q12755|Q14812	Silent	SNP	ENST00000265724.3	37	CCDS5608.1																																																																																			T|0.007;G|0.591;C|0.006;A|0.396	0.591	strong		0.527	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
DSPP	1834	hgsc.bcm.edu	37	4	88537294	88537294	+	Silent	SNP	T	T	C	rs111216206		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537294T>C	ENST00000282478.7	+	4	3513	c.3480T>C	c.(3478-3480)agT>agC	p.S1160S	DSPP_ENST00000399271.1_Silent_p.S1160S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1160	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)		gcgacagcagtgacagcagcg	0.567																																					p.S1160S		Atlas-SNP	.											.	DSPP	174	.	0			c.T3480C						PASS	.						43.0	58.0	53.0					4																	88537294		1580	2849	4429	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.3480T>C	4.37:g.88537294T>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	177	17	0.0960452	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	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189125	11189125	+	Silent	SNP	C	C	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11189125C>A	ENST00000382435.4	+	1	729	c.510C>A	c.(508-510)atC>atA	p.I170I		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	170	EamA 1.					integral component of membrane (GO:0016021)											TAGGACTAATCATCATTCTGG	0.597																																					p.I170I		Atlas-SNP	.											AMAC1L2,NS,carcinoma,+1,1	.	.	1	0			c.C510A						PASS	.						180.0	173.0	176.0					8																	11189125		2203	4300	6503	SO:0001819	synonymous_variant	83650	exon1			ACTAATCATCATT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.510C>A	8.37:g.11189125C>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	166	14	0.0843373	NM_054028	A2RRL6	Silent	SNP	ENST00000382435.4	37	CCDS5980.1																																																																																			.	.	none		0.597	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
SGSM2	9905	hgsc.bcm.edu	37	17	2266812	2266812	+	Silent	SNP	T	T	C	rs2003968	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2266812T>C	ENST00000426855.2	+	7	901	c.726T>C	c.(724-726)tgT>tgC	p.C242C	SGSM2_ENST00000574563.1_Silent_p.C242C|SGSM2_ENST00000268989.3_Silent_p.C242C	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	242					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		TGGCTGCCTGTGCCCGCGAGT	0.642													C|||	2836	0.566294	0.5431	0.3444	5008	,	,		16364	0.7639		0.4314	False		,,,				2504	0.6902				p.C242C		Atlas-SNP	.											SGSM2,rectum,carcinoma,0,1	SGSM2	60	1	0			c.T726C						PASS	.	C	,	2372,2034		640,1092,471	25.0	28.0	27.0		726,726	-11.5	0.1	17	dbSNP_92	27	3921,4677		893,2135,1271	yes	coding-synonymous,coding-synonymous	SGSM2	NM_001098509.1,NM_014853.2	,	1533,3227,1742	CC,CT,TT		45.6036,46.1643,48.3928	,	242/1007,242/1052	2266812	6293,6711	2203	4299	6502	SO:0001819	synonymous_variant	9905	exon7			TGCCTGTGCCCGC	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.726T>C	17.37:g.2266812T>C		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_001098509	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	37	CCDS45570.1																																																																																			C|0.502;T|0.498	0.502	strong		0.642	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410183	105410183	+	Missense_Mutation	SNP	T	T	C	rs10438246	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	208	207	0.995192	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	
TOP2B	7155	hgsc.bcm.edu	37	3	25679738	25679738	+	Silent	SNP	T	T	C	rs60422476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	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			
TNIK	23043	hgsc.bcm.edu	37	3	170802910	170802910	+	Missense_Mutation	SNP	C	C	T	rs17857452	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:170802910C>T	ENST00000436636.2	-	25	3339	c.2995G>A	c.(2995-2997)Gca>Aca	p.A999T	TNIK_ENST00000341852.6_Missense_Mutation_p.A915T|TNIK_ENST00000460047.1_Missense_Mutation_p.A936T|TNIK_ENST00000475336.1_Missense_Mutation_p.A907T|TNIK_ENST00000369326.5_Missense_Mutation_p.A977T|TNIK_ENST00000470834.1_Missense_Mutation_p.A962T|TNIK_ENST00000538048.1_Missense_Mutation_p.A951T|TNIK_ENST00000284483.8_Missense_Mutation_p.A991T|TNIK_ENST00000488470.1_Missense_Mutation_p.A944T|TNIK_ENST00000357327.5_Missense_Mutation_p.A970T	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	999	Mediates interaction with NEDD4.		A -> T (in dbSNP:rs17857452). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			TGCTTACCTGCGGCTGATGAT	0.483													c|||	202	0.0403355	0.0045	0.0634	5008	,	,		17196	0.0		0.0934	False		,,,				2504	0.0593				p.A999T		Atlas-SNP	.											.	TNIK	313	.	0			c.G2995A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	53,3761		0,53,1854	58.0	59.0	59.0		2971,2908,2884,2830,2806,2743,2719,2995	0.1	0.0	3	dbSNP_123	59	721,7523		28,665,3429	yes	missense,missense,missense,missense,missense,missense,missense,missense	TNIK	NM_001161560.1,NM_001161561.1,NM_001161562.1,NM_001161563.1,NM_001161564.1,NM_001161565.1,NM_001161566.1,NM_015028.2	58,58,58,58,58,58,58,58	28,718,5283	TT,TC,CC		8.7458,1.3896,6.419	benign,benign,benign,benign,benign,benign,benign,benign	991/1353,970/1332,962/1324,944/1306,936/1298,915/1277,907/1269,999/1361	170802910	774,11284	1907	4122	6029	SO:0001583	missense	23043	exon25			TACCTGCGGCTGA	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2995G>A	3.37:g.170802910C>T	ENSP00000399511:p.Ala999Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	97	0.044413919413919416	4	0.008130081300813009	24	0.06629834254143646	0	0.0	69	0.09102902374670185	c	0.015	-1.562875	0.00903	0.013896	0.087458	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.72394	-0.64;-0.63;-0.63;-0.64;-0.64;-0.64;-0.65;-0.64;-0.64;-0.65	5.37	0.144	0.14824	.	0.582061	0.19613	N	0.110097	T	0.03053	0.0090	L	0.35723	1.085	0.53688	P	2.8000000000028002E-5	B;B;B;B;B;B;B;B	0.24651	0.001;0.006;0.0;0.001;0.108;0.013;0.0;0.066	B;B;B;B;B;B;B;B	0.22753	0.001;0.01;0.001;0.001;0.041;0.005;0.001;0.018	T	0.19386	-1.0307	9	0.07482	T	0.82	.	8.3344	0.32206	0.0:0.3338:0.0:0.6662	rs17857452;rs17857452	907;962;936;915;991;970;944;999	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	T	999;977;951;915;991;907;970;936;944;962	ENSP00000399511:A999T;ENSP00000358332:A977T;ENSP00000443278:A951T;ENSP00000345352:A915T;ENSP00000284483:A991T;ENSP00000418156:A907T;ENSP00000349880:A970T;ENSP00000418916:A936T;ENSP00000418378:A944T;ENSP00000419990:A962T	ENSP00000284483:A991T	A	-	1	0	TNIK	172285604	0.048000	0.20356	0.047000	0.18901	0.005000	0.04900	0.181000	0.16880	0.104000	0.17725	-0.970000	0.02610	GCA	C|0.934;G|0.013;T|0.052	0.052	strong		0.483	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
STRC	161497	hgsc.bcm.edu	37	15	43900153	43900153	+	Silent	SNP	C	C	T	rs62018890	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43900153C>T	ENST00000450892.2	-	18	3779	c.3702G>A	c.(3700-3702)gaG>gaA	p.E1234E	STRC_ENST00000541030.1_Silent_p.E461E	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1234					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)		TCCGCTGTAGCTCTGCCCAGA	0.562													C|||	643	0.128395	0.205	0.0908	5008	,	,		20208	0.001		0.1859	False		,,,				2504	0.1237				p.E1234E		Atlas-SNP	.											.	STRC	58	.	0			c.G3702A						PASS	.	C		696,3642		116,464,1589	103.0	115.0	111.0		3702	-2.5	1.0	15	dbSNP_134	111	1557,7033		143,1271,2881	no	coding-synonymous	STRC	NM_153700.2		259,1735,4470	TT,TC,CC		18.1257,16.0443,17.4273		1234/1776	43900153	2253,10675	2169	4295	6464	SO:0001819	synonymous_variant	161497	exon18			CTGTAGCTCTGCC	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.3702G>A	15.37:g.43900153C>T		Somatic	480	2	0.00416667		WXS	Illumina HiSeq	Phase_I	516	239	0.463178	NM_153700		Silent	SNP	ENST00000450892.2	37	CCDS10098.1																																																																																			C|0.500;T|0.500	0.500	weak		0.562	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
TPSB2	64499	hgsc.bcm.edu	37	16	1279710	1279710	+	RNA	SNP	G	G	A	rs200630968	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1279710G>A	ENST00000339687.6	-	0	112				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				CCCCAACGATGCCCACTCGCT	0.706																																					p.G30G		Atlas-SNP	.											.	TPSB2	8	.	0			c.C90T						PASS	.						27.0	34.0	32.0					16																	1279710		2182	4297	6479			64499	exon3			AACGATGCCCACT	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.1279710G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	86	58	0.674419	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Silent	SNP	ENST00000339687.6	37																																																																																				G|0.872;A|0.128	0.128	strong		0.706	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
SP9	100131390	hgsc.bcm.edu	37	2	175201299	175201299	+	Silent	SNP	C	C	G	rs62174227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:175201299C>G	ENST00000394967.2	+	2	633	c.486C>G	c.(484-486)ggC>ggG	p.G162G	AC018470.1_ENST00000595354.1_Missense_Mutation_p.A285P	NM_001145250.1	NP_001138722.1	P0CG40	SP9_HUMAN	Sp9 transcription factor	162					embryonic limb morphogenesis (GO:0030326)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(1)	1						ACAAGTCGGGCTTCCATTCGA	0.687													c|||	1604	0.320288	0.1036	0.4409	5008	,	,		12721	0.6478		0.2137	False		,,,				2504	0.2996				p.G162G		Atlas-SNP	.											.	SP9	15	.	0			c.C486G						PASS	.						6.0	9.0	8.0					2																	175201299		678	1565	2243	SO:0001819	synonymous_variant	100131390	exon2			GTCGGGCTTCCAT		CCDS46453.1	2q31.1	2013-01-08	2012-12-07		ENSG00000217236	ENSG00000217236		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	30690	protein-coding gene	gene with protein product	"""zinc finger protein 990"""		"""Sp9 transcription factor homolog (mouse)"""				Standard	NM_001145250		Approved	ZNF990	uc010zem.1	P0CG40	OTTHUMG00000150371	ENST00000394967.2:c.486C>G	2.37:g.175201299C>G		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_001145250		Silent	SNP	ENST00000394967.2	37	CCDS46453.1																																																																																			C|0.661;G|0.339	0.339	strong		0.687	SP9-001	NOVEL	not_organism_supported|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317878.1	NM_001145250	
ASPM	259266	hgsc.bcm.edu	37	1	197070707	197070707	+	Silent	SNP	G	G	A	rs41308365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:197070707G>A	ENST00000367409.4	-	18	7930	c.7674C>T	c.(7672-7674)atC>atT	p.I2558I	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2558	IQ 27. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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						TTTGTATTACGATAGAAGCTT	0.333													G|||	1073	0.214257	0.0431	0.2277	5008	,	,		18864	0.1637		0.4105	False		,,,				2504	0.2863				p.I2558I		Atlas-SNP	.											.	ASPM	444	.	0			c.C7674T						PASS	.	G	,	462,3944	214.1+/-233.5	27,408,1768	68.0	60.0	63.0		,7674	3.3	0.0	1	dbSNP_127	63	3721,4875	521.6+/-379.9	811,2099,1388	no	intron,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	838,2507,3156	AA,AG,GG		43.2876,10.4857,32.172	,	,2558/3478	197070707	4183,8819	2203	4298	6501	SO:0001819	synonymous_variant	259266	exon18			TATTACGATAGAA	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.7674C>T	1.37:g.197070707G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			A|0.300;G|0.700;T|0.000	0.300	strong		0.333	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
SCAF4	57466	hgsc.bcm.edu	37	21	33074608	33074608	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:33074608C>T	ENST00000286835.7	-	5	788	c.406G>A	c.(406-408)Gcg>Acg	p.A136T	SCAF4_ENST00000399804.1_Missense_Mutation_p.A136T|SCAF4_ENST00000434667.3_Missense_Mutation_p.A121T	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	136	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CTGGTTCCCGCTGCCATGTCC	0.393																																					p.A136T		Atlas-SNP	.											SCAF4,NS,carcinoma,+2,1	SCAF4	142	1	0			c.G406A						scavenged	.						155.0	132.0	140.0					21																	33074608		2203	4300	6503	SO:0001583	missense	57466	exon5			TTCCCGCTGCCAT	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.406G>A	21.37:g.33074608C>T	ENSP00000286835:p.Ala136Thr	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	297	3	0.010101	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	37	CCDS33537.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.485884	0.84854	.	.	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.43688	0.94;0.94;0.94	5.69	5.69	0.88448	ENTH/VHS (2);RNA polymerase II, large subunit, CTD (2);	0.122954	0.53938	D	0.000045	T	0.53384	0.1793	L	0.31294	0.92	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.99;0.99;0.996;0.99	T	0.38001	-0.9681	10	0.18276	T	0.48	-18.3783	19.8097	0.96542	0.0:1.0:0.0:0.0	.	121;136;136;136	C9JLZ0;Q0P607;O95104-2;O95104	.;.;.;SFR15_HUMAN	T	121;136;136	ENSP00000402377:A121T;ENSP00000286835:A136T;ENSP00000382703:A136T	ENSP00000286835:A136T	A	-	1	0	SCAF4	31996479	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	5.964000	0.70379	2.685000	0.91497	0.484000	0.47621	GCG	.	.	none		0.393	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
MST1L	11223	hgsc.bcm.edu	37	1	17084078	17084078	+	RNA	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17084078G>A	ENST00000455405.2	-	0	634							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										ACATGTCCTCGGTGCTTGATG	0.602																																					p.R615X		Atlas-SNP	.											Q13209_HUMAN,NS,haematopoietic_neoplasm,0,1	.	.	1	0			c.C1843T						scavenged	.																																					11223	exon14			GTCCTCGGTGCTT	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.17084078G>A		Somatic	1222	1	0.000818331		WXS	Illumina HiSeq	Phase_I	1404	117	0.0833333	NM_001271733	B7WPB1|Q13209	Nonsense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	18.45	3.625708	0.66901	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.000000	0.34777	N	0.003682	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.089	0.09960	0.0:1.0E-4:0.3481:0.6518	.	.	.	.	X	615;641	.	ENSP00000439273:R615X	R	-	1	2	MST1P9	16956665	0.991000	0.36638	0.124000	0.21820	0.000000	0.00434	1.469000	0.35343	-0.879000	0.04002	0.000000	0.15137	CGA	.	.	none		0.602	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
UMODL1	89766	hgsc.bcm.edu	37	21	43522349	43522349	+	Silent	SNP	T	T	C	rs220109	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43522349T>C	ENST00000408910.2	+	8	1260	c.1260T>C	c.(1258-1260)agT>agC	p.S420S	UMODL1_ENST00000400427.1_Silent_p.S348S|UMODL1_ENST00000400424.2_Silent_p.S348S|C21orf128_ENST00000329015.2_3'UTR|UMODL1_ENST00000408989.2_Silent_p.S420S	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	420	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						ACCGCAGCAGTGTGGAGTACC	0.438													C|||	2716	0.542332	0.4516	0.6484	5008	,	,		20187	0.5813		0.5358	False		,,,				2504	0.5562				p.S420S	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T1260C						PASS	.	C	,,,	1858,1970		454,950,510	90.0	89.0	89.0		1260,1044,1044,1260	1.1	0.1	21	dbSNP_79	89	4490,3774		1235,2020,877	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	1689,2970,1387	CC,CT,TT		45.668,48.5371,47.5025	,,,	420/1319,348/1375,348/1247,420/1447	43522349	6348,5744	1914	4132	6046	SO:0001819	synonymous_variant	89766	exon8			CAGCAGTGTGGAG		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1260T>C	21.37:g.43522349T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			T|0.458;C|0.542	0.542	strong		0.438	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
AFG3L2	10939	hgsc.bcm.edu	37	18	12348285	12348285	+	Silent	SNP	T	T	C	rs11553521	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:12348285T>C	ENST00000269143.3	-	13	1881	c.1650A>G	c.(1648-1650)gaA>gaG	p.E550E		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	550					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)	p.E550E(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	CAATCACTCGTTCAATTGCCT	0.413													C|||	3555	0.709864	0.7421	0.5937	5008	,	,		21505	0.6151		0.7674	False		,,,				2504	0.7873				p.E550E		Atlas-SNP	.											AFG3L2,NS,carcinoma,0,1	AFG3L2	60	1	1	Substitution - coding silent(1)	stomach(1)	c.A1650G						PASS	.	C		3400,1006	376.3+/-322.0	1316,768,119	133.0	104.0	114.0		1650	-1.5	1.0	18	dbSNP_120	114	6735,1865	333.1+/-320.4	2637,1461,202	no	coding-synonymous	AFG3L2	NM_006796.2		3953,2229,321	CC,CT,TT		21.686,22.8325,22.0744		550/798	12348285	10135,2871	2203	4300	6503	SO:0001819	synonymous_variant	10939	exon13			CACTCGTTCAATT	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"""ATPases / AAA-type"""	315	protein-coding gene	gene with protein product		604581	"""AFG3 (ATPase family gene 3, yeast)-like 2"", ""spinocerebellar ataxia 28"", ""AFG3 ATPase family gene 3-like 2 (yeast)"", ""AFG3 ATPase family gene 3-like 2 (S. cerevisiae)"", ""AFG3 ATPase family member 3-like 2 (S. cerevisiae)"""	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.1650A>G	18.37:g.12348285T>C		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_006796	Q6P1L0	Silent	SNP	ENST00000269143.3	37	CCDS11859.1																																																																																			T|0.239;C|0.761	0.761	strong		0.413	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796	
CINP	51550	hgsc.bcm.edu	37	14	102814945	102814945	+	Silent	SNP	G	G	A	rs7012	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:102814945G>A	ENST00000216756.6	-	5	628	c.588C>T	c.(586-588)agC>agT	p.S196S	CINP_ENST00000541568.2_3'UTR|CINP_ENST00000536961.2_Silent_p.S211S|CINP_ENST00000560326.1_5'Flank	NM_032630.2	NP_116019.1	Q9BW66	CINP_HUMAN	cyclin-dependent kinase 2 interacting protein	196				S -> R (in Ref. 6; BU174070). {ECO:0000305}.|SDSR -> NDNK (in Ref. 1; AAF44747/ AAF44748). {ECO:0000305}.	cell cycle (GO:0007049)|cell division (GO:0051301)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	nucleus (GO:0005634)				large_intestine(2)|lung(2)	4						GATGCAGCCTGCTGTCGCTCT	0.642													G|||	1322	0.263978	0.0666	0.2478	5008	,	,		19248	0.4861		0.332	False		,,,				2504	0.2434				p.S211S		Atlas-SNP	.											.	CINP	17	.	0			c.C633T						PASS	.	G	,,	490,3916	228.5+/-243.3	27,436,1740	63.0	45.0	51.0		633,,588	4.0	0.5	14	dbSNP_52	51	2690,5910	428.0+/-355.8	422,1846,2032	no	coding-synonymous,utr-3,coding-synonymous	CINP	NM_001177611.1,NM_001177612.1,NM_032630.2	,,	449,2282,3772	AA,AG,GG		31.2791,11.1212,24.4503	,,	211/228,,196/213	102814945	3180,9826	2203	4300	6503	SO:0001819	synonymous_variant	51550	exon5			CAGCCTGCTGTCG	AK056112, AF228148, AF228149	CCDS9972.1	14q32.33	2010-02-17			ENSG00000100865	ENSG00000100865			23789	protein-coding gene	gene with protein product		613362				16082200	Standard	NM_032630		Approved	MGC849	uc021sea.1	Q9BW66		ENST00000216756.6:c.588C>T	14.37:g.102814945G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_001177611	F5H7P3|F5H8A7|Q9NPF9	Silent	SNP	ENST00000216756.6	37	CCDS9972.1																																																																																			G|0.737;A|0.263	0.263	strong		0.642	CINP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415055.1	NM_032630	
SCUBE1	80274	hgsc.bcm.edu	37	22	43618695	43618695	+	Missense_Mutation	SNP	C	C	A	rs148458324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:43618695C>A	ENST00000360835.4	-	12	1507	c.1381G>T	c.(1381-1383)Gcg>Tcg	p.A461S		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	461					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)				TTCTGCAGCGCCTTGCCCTGC	0.657													C|||	13	0.00259585	0.0	0.0072	5008	,	,		18680	0.0		0.008	False		,,,				2504	0.0				p.A461S		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G1381T						PASS	.	C	SER/ALA	6,4392	9.9+/-24.2	0,6,2193	52.0	40.0	44.0		1381	-1.2	0.0	22	dbSNP_134	44	96,8502	51.9+/-112.3	2,92,4205	yes	missense	SCUBE1	NM_173050.3	99	2,98,6398	AA,AC,CC		1.1165,0.1364,0.7849	benign	461/989	43618695	102,12894	2199	4299	6498	SO:0001583	missense	80274	exon12			GCAGCGCCTTGCC		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.1381G>T	22.37:g.43618695C>A	ENSP00000354080:p.Ala461Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	82	49	0.597561	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	0.029	-1.348806	0.01266	0.001364	0.011165	ENSG00000159307	ENST00000360835	D	0.84873	-1.91	5.16	-1.2	0.09554	.	0.847688	0.11048	N	0.605376	T	0.49949	0.1587	N	0.02391	-0.57	0.54753	D	0.999981	B	0.02656	0.0	B	0.04013	0.001	T	0.48692	-0.9013	10	0.07030	T	0.85	.	6.1713	0.20418	0.2337:0.4632:0.0:0.3031	.	461	Q8IWY4	SCUB1_HUMAN	S	461	ENSP00000354080:A461S	ENSP00000354080:A461S	A	-	1	0	SCUBE1	41948639	0.001000	0.12720	0.034000	0.17996	0.045000	0.14185	-0.867000	0.04241	-0.138000	0.11434	-0.302000	0.09304	GCG	C|0.994;A|0.006	0.006	strong		0.657	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
MUC5B	727897	hgsc.bcm.edu	37	11	1272039	1272039	+	Silent	SNP	G	G	A	rs2943513	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1272039G>A	ENST00000529681.1	+	31	13987	c.13929G>A	c.(13927-13929)ccG>ccA	p.P4643P	MUC5B_ENST00000447027.1_Silent_p.P4646P|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4643	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)		cctccatcccggggaccaccc	0.622													G|||	315	0.0628994	0.0159	0.1081	5008	,	,		18162	0.0466		0.0815	False		,,,				2504	0.092				p.P4643P		Atlas-SNP	.											.	MUC5B	473	.	0			c.G13929A						PASS	.	G		72,4164		1,70,2047	119.0	147.0	138.0		13929	-3.1	0.0	11	dbSNP_101	138	605,7817		23,559,3629	no	coding-synonymous	MUC5B	NM_002458.2		24,629,5676	AA,AG,GG		7.1836,1.6997,5.3484		4643/5763	1272039	677,11981	2118	4211	6329	SO:0001819	synonymous_variant	727897	exon31			CATCCCGGGGACC	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.13929G>A	11.37:g.1272039G>A		Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	480	219	0.45625	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2	152	0.0695970695970696	12	0.024390243902439025	37	0.10220994475138122	40	0.06993006993006994	63	0.08311345646437995	-	2.435	-0.329842	0.05314	0.016997	0.071836	ENSG00000117983	ENST00000535652	.	.	.	1.53	-3.06	0.05379	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.06807	-1.0806	4	0.21014	T	0.42	.	1.4009	0.02270	0.4051:0.1958:0.2746:0.1246	rs2943513	.	.	.	R	418	.	ENSP00000439776:G418R	G	+	1	0	MUC5B	1228615	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	-8.200000	0.00023	-3.526000	0.00147	-1.109000	0.02080	GGG	G|0.925;A|0.075	0.075	strong		0.622	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
FICD	11153	hgsc.bcm.edu	37	12	108912621	108912621	+	Missense_Mutation	SNP	C	C	A	rs146316463		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:108912621C>A	ENST00000552695.1	+	3	981	c.746C>A	c.(745-747)aCc>aAc	p.T249N	FICD_ENST00000361549.2_3'UTR	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	249					negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733)			NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2)	15						ATCCTGGAGACCCGCTACGCC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		22220	0.0		0.001	False		,,,				2504	0.0				p.T249N		Atlas-SNP	.											.	FICD	35	.	0			c.C746A						PASS	.	C	ASN/THR	0,4406		0,0,2203	108.0	81.0	90.0		746	6.1	1.0	12	dbSNP_134	90	3,8597	3.7+/-12.6	0,3,4297	yes	missense	FICD	NM_007076.2	65	0,3,6500	AA,AC,CC		0.0349,0.0,0.0231	possibly-damaging	249/459	108912621	3,13003	2203	4300	6503	SO:0001583	missense	11153	exon3			TGGAGACCCGCTA	AF049611	CCDS9116.1	12q24.1	2007-12-05				ENSG00000198855			18416	protein-coding gene	gene with protein product	"""huntingtin interacting protein 13"", ""fic S-phase protein cell division homolog (E. coli)"""					9700202	Standard	NM_007076		Approved	HYPE, HIP13	uc001tmx.1	Q9BVA6		ENST00000552695.1:c.746C>A	12.37:g.108912621C>A	ENSP00000446479:p.Thr249Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	134	76	0.567164	NM_007076	O75406	Missense_Mutation	SNP	ENST00000552695.1	37	CCDS9116.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.8	4.461591	0.84317	0.0	3.49E-4	ENSG00000198855	ENST00000552695	.	.	.	6.07	6.07	0.98685	Filamentation induced by cAMP/death on curing-related (1);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	L	0.31926	0.97	0.80722	D	1	D	0.56035	0.974	P	0.51701	0.677	T	0.46610	-0.9179	9	0.11485	T	0.65	-9.4005	20.6439	0.99570	0.0:1.0:0.0:0.0	.	249	Q9BVA6	FICD_HUMAN	N	249	.	ENSP00000446479:T249N	T	+	2	0	FICD	107436751	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.884000	0.98904	0.655000	0.94253	ACC	C|0.999;A|0.001	0.001	strong		0.582	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076	
CCDC37	348807	hgsc.bcm.edu	37	3	126137558	126137558	+	Silent	SNP	C	C	T	rs4679242|rs386665601	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:126137558C>T	ENST00000352312.1	+	7	690	c.591C>T	c.(589-591)gcC>gcT	p.A197A	CCDC37_ENST00000393425.1_Silent_p.A198A|CCDC37_ENST00000505024.1_Silent_p.A198A	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	197										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)		AGAAGGACGCCGCCTTGTTCG	0.652													C|||	1248	0.249201	0.3623	0.2666	5008	,	,		14683	0.1339		0.1869	False		,,,				2504	0.2669				p.A197A		Atlas-SNP	.											.	CCDC37	69	.	0			c.C591T						PASS	.	C		1565,2827		278,1009,909	47.0	51.0	50.0		591	-5.7	0.0	3	dbSNP_111	50	1826,6770		204,1418,2676	no	coding-synonymous	CCDC37	NM_182628.2		482,2427,3585	TT,TC,CC		21.2424,35.633,26.1087		197/612	126137558	3391,9597	2196	4298	6494	SO:0001819	synonymous_variant	348807	exon7			GGACGCCGCCTTG	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.591C>T	3.37:g.126137558C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			C|0.760;T|0.240	0.240	strong		0.652	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
MLLT4	4301	hgsc.bcm.edu	37	6	168352105	168352105	+	Silent	SNP	G	G	A	rs2076664	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168352105G>A	ENST00000447894.2	+	29	4050	c.4050G>A	c.(4048-4050)ccG>ccA	p.P1350P	MLLT4_ENST00000366806.2_Silent_p.P1350P|MLLT4_ENST00000392112.1_Silent_p.P1333P|MLLT4_ENST00000351017.4_Silent_p.P1357P|MLLT4_ENST00000400822.3_Silent_p.P1349P|MLLT4_ENST00000344191.4_Silent_p.P1350P|MLLT4_ENST00000392108.3_Silent_p.P1350P			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1350	Pro-rich.				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)		CAGCCATACCGGCCACCCCTG	0.602			T	MLL	AL								G|||	621	0.124002	0.152	0.1124	5008	,	,		10848	0.0595		0.1899	False		,,,				2504	0.093				p.P1350P		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	MLLT4,NS,carcinoma,+1,1	MLLT4	351	1	0			c.G4050A						PASS	.	G	,	632,3756		45,542,1607	46.0	64.0	58.0		4050,3999	-1.2	0.0	6	dbSNP_96	58	1419,7155		116,1187,2984	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	161,1729,4591	AA,AG,GG		16.55,14.4029,15.8232	,	1350/1652,1333/1744	168352105	2051,10911	2194	4287	6481	SO:0001819	synonymous_variant	4301	exon29			CATACCGGCCACC	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.4050G>A	6.37:g.168352105G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	82	30	0.365854	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				G|0.852;A|0.148	0.148	strong		0.602	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
GALC	2581	hgsc.bcm.edu	37	14	88414211	88414211	+	Silent	SNP	G	G	A	rs398076	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:88414211G>A	ENST00000261304.2	-	13	1456	c.1350C>T	c.(1348-1350)agC>agT	p.S450S	GALC_ENST00000393569.2_Silent_p.S424S|GALC_ENST00000544807.2_Silent_p.S394S|GALC_ENST00000393568.4_Silent_p.S427S	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	450					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AACTGCCATCGCTGTCAAGGA	0.458													G|||	1836	0.366613	0.4387	0.33	5008	,	,		17166	0.2302		0.4105	False		,,,				2504	0.3906				p.S450S		Atlas-SNP	.											.	GALC	48	.	0			c.C1350T						PASS	.	G	,,	1755,2369		398,959,705	73.0	75.0	74.0		1350,1281,1272	-2.8	0.0	14	dbSNP_80	74	3357,5039		672,2013,1513	no	coding-synonymous,coding-synonymous,coding-synonymous	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	,,	1070,2972,2218	AA,AG,GG		39.9833,42.5558,40.8307	,,	450/686,427/663,424/660	88414211	5112,7408	2062	4198	6260	SO:0001819	synonymous_variant	2581	exon13			GCCATCGCTGTCA	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"""Krabbe disease"""	606890	"""galactosylceramidase (Krabbe disease)"""				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1350C>T	14.37:g.88414211G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Silent	SNP	ENST00000261304.2	37	CCDS9878.2																																																																																			G|0.650;A|0.350	0.350	strong		0.458	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
PIGZ	80235	hgsc.bcm.edu	37	3	196674518	196674518	+	Missense_Mutation	SNP	A	A	G	rs1147238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:196674518A>G	ENST00000412723.1	-	3	1396	c.1250T>C	c.(1249-1251)gTc>gCc	p.V417A		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	417			V -> A (in dbSNP:rs1147238).		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)		GTTGAAGAGGACCACAGTGCC	0.642													A|||	912	0.182109	0.4554	0.1052	5008	,	,		19269	0.0		0.1511	False		,,,				2504	0.0869				p.V417A		Atlas-SNP	.											.	PIGZ	34	.	0			c.T1250C						PASS	.	A	ALA/VAL	1748,2656	514.2+/-368.6	336,1076,790	45.0	46.0	46.0		1250	2.6	1.0	3	dbSNP_87	46	1146,7454	233.5+/-266.7	74,998,3228	yes	missense	PIGZ	NM_025163.2	64	410,2074,4018	GG,GA,AA		13.3256,39.6912,22.2547	benign	417/580	196674518	2894,10110	2202	4300	6502	SO:0001583	missense	80235	exon3			AAGAGGACCACAG	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.1250T>C	3.37:g.196674518A>G	ENSP00000413405:p.Val417Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	37	CCDS3324.1	368	0.1684981684981685	210	0.4268292682926829	41	0.1132596685082873	0	0.0	117	0.15435356200527706	A	5.516	0.280073	0.10458	0.396912	0.133256	ENSG00000119227	ENST00000412723	T	0.65178	-0.14	5.0	2.58	0.30949	.	0.821696	0.10487	N	0.668835	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.999999999068829	B	0.13145	0.007	B	0.17433	0.018	T	0.34279	-0.9835	9	0.56958	D	0.05	-10.7564	9.341	0.38080	0.8429:0.0:0.1571:0.0	rs1147238;rs1147238	417	Q86VD9	PIGZ_HUMAN	A	417	ENSP00000413405:V417A	ENSP00000413405:V417A	V	-	2	0	PIGZ	198158915	0.943000	0.32029	0.983000	0.44433	0.175000	0.22909	2.683000	0.46943	0.872000	0.35775	0.459000	0.35465	GTC	A|0.789;G|0.211	0.211	strong		0.642	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
LY6G6F	259215	hgsc.bcm.edu	37	6	31675501	31675501	+	Missense_Mutation	SNP	G	G	A	rs9267547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31675501G>A	ENST00000375832.4	+	2	341	c.319G>A	c.(319-321)Gct>Act	p.A107T	MEGT1_ENST00000503322.1_Missense_Mutation_p.A107T|XXbac-BPG32J3.20_ENST00000461287.1_Intron|LY6G6F_ENST00000556581.1_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	144	0	0		WXS	Illumina HiSeq	Phase_I	181	181	1	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	
RHBG	57127	hgsc.bcm.edu	37	1	156347834	156347834	+	Missense_Mutation	SNP	T	T	A	rs11586833	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156347834T>A	ENST00000368249.1	+	3	466	c.428T>A	c.(427-429)gTc>gAc	p.V143D	RHBG_ENST00000451864.2_Missense_Mutation_p.V74D|RHBG_ENST00000255013.3_Missense_Mutation_p.V74D|RHBG_ENST00000537040.1_Intron|RHBG_ENST00000400992.2_Missense_Mutation_p.V74D|RHBG_ENST00000368246.2_Missense_Mutation_p.V143D	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	168	2	0.0119048		WXS	Illumina HiSeq	Phase_I	175	95	0.542857	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	
KDM3B	51780	hgsc.bcm.edu	37	5	137708434	137708434	+	Silent	SNP	C	C	T	rs4835678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	215	0	0		WXS	Illumina HiSeq	Phase_I	167	76	0.45509	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	
ZNF335	63925	hgsc.bcm.edu	37	20	44578961	44578961	+	Silent	SNP	A	A	G	rs3746503	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:44578961A>G	ENST00000322927.2	-	22	3484	c.3384T>C	c.(3382-3384)ccT>ccC	p.P1128P	ZNF335_ENST00000426788.1_Silent_p.P973P	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1128					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TCCTCCCATCAGGACTGTGCA	0.587													A|||	783	0.15635	0.0855	0.072	5008	,	,		17543	0.3294		0.0954	False		,,,				2504	0.1963				p.P1128P		Atlas-SNP	.											.	ZNF335	115	.	0			c.T3384C						PASS	.	A		262,4144	148.0+/-182.4	6,250,1947	93.0	97.0	96.0		3384	-7.5	0.2	20	dbSNP_107	96	939,7661	206.9+/-248.8	49,841,3410	no	coding-synonymous	ZNF335	NM_022095.3		55,1091,5357	GG,GA,AA		10.9186,5.9464,9.2342		1128/1343	44578961	1201,11805	2203	4300	6503	SO:0001819	synonymous_variant	63925	exon22			CCCATCAGGACTG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3384T>C	20.37:g.44578961A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	181	77	0.425414	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																			A|0.879;G|0.121	0.121	strong		0.587	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
UBXN11	91544	hgsc.bcm.edu	37	1	26608866	26608866	+	Missense_Mutation	SNP	C	C	G	rs188535926		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26608866C>G	ENST00000374222.1	-	16	1951	c.1487G>C	c.(1486-1488)gGt>gCt	p.G496A	UBXN11_ENST00000357089.4_Missense_Mutation_p.G463A|UBXN11_ENST00000314675.7_Missense_Mutation_p.G376A|UBXN11_ENST00000374217.2_Missense_Mutation_p.G463A|UBXN11_ENST00000374221.3_Missense_Mutation_p.G496A|UBXN11_ENST00000374223.1_Missense_Mutation_p.G253A			Q5T124	UBX11_HUMAN	UBX domain protein 11	496	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			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						gggaccgggaccgggactggg	0.721																																					p.G496A		Atlas-SNP	.											UBXN11,colon,carcinoma,-1,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1487C						PASS	.						25.0	29.0	28.0					1																	26608866		1767	4017	5784	SO:0001583	missense	91544	exon16			CCGGGACCGGGAC	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.1487G>C	1.37:g.26608866C>G	ENSP00000363339:p.Gly496Ala	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	8	0.228571	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	20	0.009157509157509158	6	0.012195121951219513	1	0.0027624309392265192	5	0.008741258741258742	8	0.010554089709762533	C	2.556	-0.303022	0.05495	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.21932	1.98;2.16;2.48;2.34;2.34;2.48	.	.	.	.	.	.	.	.	T	0.06325	0.0163	N	0.08118	0	0.58432	P	2.9999999999752447E-6	P;P;P;P	0.49961	0.93;0.93;0.93;0.886	B;B;B;B	0.40444	0.329;0.329;0.329;0.176	T	0.15292	-1.0442	7	0.45353	T	0.12	.	5.6498	0.17610	0.0:0.6576:0.3424:0.0	.	463;458;376;496	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	A	376;253;463;496;496;463	ENSP00000324721:G376A;ENSP00000363340:G253A;ENSP00000349601:G463A;ENSP00000363338:G496A;ENSP00000363339:G496A;ENSP00000363334:G463A	ENSP00000324721:G376A	G	-	2	0	UBXN11	26481453	0.000000	0.05858	0.127000	0.21898	0.134000	0.20937	-0.138000	0.10374	0.392000	0.25172	0.391000	0.25812	GGT	C|0.991;G|0.009	0.009	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
B4GALNT3	283358	hgsc.bcm.edu	37	12	667726	667726	+	Missense_Mutation	SNP	G	G	C	rs61730392	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:667726G>C	ENST00000266383.5	+	18	2673	c.2660G>C	c.(2659-2661)gGa>gCa	p.G887A		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	887					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TTCCCAGCTGGAGTCATCGAT	0.602													G|||	16	0.00319489	0.0	0.0086	5008	,	,		18909	0.001		0.006	False		,,,				2504	0.0031				p.G887A		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G2660C						PASS	.	G	ALA/GLY	6,4400	11.4+/-27.6	0,6,2197	186.0	148.0	161.0		2660	4.8	0.2	12	dbSNP_129	161	56,8544	35.9+/-90.5	0,56,4244	yes	missense	B4GALNT3	NM_173593.3	60	0,62,6441	CC,CG,GG		0.6512,0.1362,0.4767	possibly-damaging	887/999	667726	62,12944	2203	4300	6503	SO:0001583	missense	283358	exon18			CAGCTGGAGTCAT	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.2660G>C	12.37:g.667726G>C	ENSP00000266383:p.Gly887Ala	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	11	0.005036630036630037	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	4	0.005277044854881266	G	6.874	0.530673	0.13127	0.001362	0.006512	ENSG00000139044	ENST00000266383	T	0.37235	1.21	4.85	4.85	0.62838	.	0.450561	0.23498	N	0.047531	T	0.22513	0.0543	L	0.55103	1.725	0.23406	N	0.997748	B	0.23806	0.091	B	0.30716	0.119	T	0.21280	-1.0250	10	0.49607	T	0.09	-16.6496	14.0123	0.64505	0.0:0.1514:0.8486:0.0	rs61730392	887	Q6L9W6	B4GN3_HUMAN	A	887	ENSP00000266383:G887A	ENSP00000266383:G887A	G	+	2	0	B4GALNT3	537987	0.997000	0.39634	0.245000	0.24217	0.374000	0.29953	2.734000	0.47368	2.385000	0.81259	0.462000	0.41574	GGA	G|0.996;C|0.004	0.004	strong		0.602	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
FCGBP	8857	hgsc.bcm.edu	37	19	40363926	40363926	+	Missense_Mutation	SNP	C	C	G	rs3746013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	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	
NRIP1	8204	hgsc.bcm.edu	37	21	16339172	16339172	+	Missense_Mutation	SNP	G	G	C	rs2229742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:16339172G>C	ENST00000400202.1	-	3	2054	c.1342C>G	c.(1342-1344)Cga>Gga	p.R448G	NRIP1_ENST00000318948.4_Missense_Mutation_p.R448G|NRIP1_ENST00000400199.1_Missense_Mutation_p.R448G|AF127577.10_ENST00000446301.1_RNA			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	448	Repression domain 2.|Required for targeting to small nuclear foci.		R -> G (common polymorphism; dbSNP:rs2229742). {ECO:0000269|PubMed:16131398, ECO:0000269|PubMed:7641693}.		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)		TTTTCAGTTCGGTGTTTGCAA	0.388													G|||	194	0.038738	0.0038	0.0562	5008	,	,		20737	0.0		0.0984	False		,,,				2504	0.0521				p.R448G		Atlas-SNP	.											NRIP1,NS,carcinoma,+1,1	NRIP1	103	1	0			c.C1342G	GRCh37	CM067440	NRIP1	M	rs2229742	PASS	.	G	GLY/ARG	79,4327	69.2+/-107.0	0,79,2124	138.0	130.0	132.0		1342	5.2	1.0	21	dbSNP_98	132	898,7702	201.6+/-245.0	41,816,3443	yes	missense	NRIP1	NM_003489.3	125	41,895,5567	CC,CG,GG		10.4419,1.793,7.5119	probably-damaging	448/1159	16339172	977,12029	2203	4300	6503	SO:0001583	missense	8204	exon4			CAGTTCGGTGTTT	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.1342C>G	21.37:g.16339172G>C	ENSP00000383063:p.Arg448Gly	Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	310	150	0.483871	NM_003489	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	101	0.04624542124542125	3	0.006097560975609756	22	0.06077348066298342	0	0.0	76	0.10026385224274406	G	15.32	2.799433	0.50208	0.01793	0.104419	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.19938	2.11;2.11;2.11	6.06	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.01287	0.0042	L	0.58101	1.795	0.50039	D	0.999844	D	0.76494	0.999	D	0.69479	0.964	T	0.00030	-1.2288	10	0.48119	T	0.1	0.5295	14.5149	0.67811	0.0:0.0:0.6522:0.3478	rs2229742;rs17208772;rs52814411;rs2229742	448	P48552	NRIP1_HUMAN	G	448	ENSP00000383060:R448G;ENSP00000383063:R448G;ENSP00000327213:R448G	ENSP00000327213:R448G	R	-	1	2	NRIP1	15261043	1.000000	0.71417	0.990000	0.47175	0.976000	0.68499	2.239000	0.43079	1.494000	0.48533	0.650000	0.86243	CGA	G|0.929;C|0.071	0.071	strong		0.388	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
IQCF6	440956	hgsc.bcm.edu	37	3	51812952	51812952	+	Missense_Mutation	SNP	C	C	T	rs11130296|rs35586812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:51812952C>T	ENST00000398780.3	-	1	57	c.11G>A	c.(10-12)cGg>cAg	p.R4Q		NM_001143833.3	NP_001137305.2	A8MYZ5	IQCF6_HUMAN	IQ motif containing F6	4										breast(1)	1						CAGTAACGTCCGGCGCACCAT	0.547													C|||	663	0.132388	0.0098	0.1787	5008	,	,		20767	0.0764		0.2873	False		,,,				2504	0.1636				p.R4Q		Atlas-SNP	.											.	IQCF6	2	.	0			c.G11A						PASS	.	C	GLN/ARG	64,1320		0,64,628	19.0	17.0	18.0		11	1.8	0.8	3	dbSNP_120	18	853,2329		111,631,849	yes	missense	IQCF6	NM_001143833.3	43	111,695,1477	TT,TC,CC		26.807,4.6243,20.0832	probably-damaging	4/108	51812952	917,3649	692	1591	2283	SO:0001583	missense	440956	exon2			AACGTCCGGCGCA		CCDS54590.1	3p21.1	2008-10-16			ENSG00000214686	ENSG00000214686			35158	protein-coding gene	gene with protein product							Standard	NM_001143833		Approved		uc021wyv.1	A8MYZ5		ENST00000398780.3:c.11G>A	3.37:g.51812952C>T	ENSP00000381760:p.Arg4Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001143833		Missense_Mutation	SNP	ENST00000398780.3	37	CCDS54590.1	355	0.16254578754578755	5	0.01016260162601626	70	0.19337016574585636	53	0.09265734265734266	227	0.2994722955145119	C	15.40	2.822346	0.50739	0.046243	0.26807	ENSG00000214686	ENST00000398780	T	0.57595	0.39	4.9	1.79	0.24919	.	.	.	.	.	T	0.00012	0.0000	M	0.66939	2.045	0.43267	P	0.004781999999999953	B	0.02656	0.0	B	0.06405	0.002	T	0.09596	-1.0667	8	0.66056	D	0.02	-28.0976	6.1264	0.20182	0.0:0.6293:0.0:0.3707	rs11130296;rs60424990;rs11130296	27	A8MYZ5	IQCF6_HUMAN	Q	4	ENSP00000381760:R4Q	ENSP00000381760:R4Q	R	-	2	0	IQCF6	51787992	0.081000	0.21417	0.777000	0.31699	0.943000	0.58893	0.131000	0.15870	0.156000	0.19299	0.655000	0.94253	CGG	C|0.837;T|0.163	0.163	strong		0.547	IQCF6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496643	
NDUFA7	4701	hgsc.bcm.edu	37	19	8376431	8376431	+	Silent	SNP	G	G	A	rs561	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8376431G>A	ENST00000301457.2	-	4	337	c.300C>T	c.(298-300)ccC>ccT	p.P100P	NDUFA7_ENST00000598884.1_Silent_p.P100P	NM_005001.3	NP_004992.2	O95182	NDUA7_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa	100					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)	5						ACCTCTTTATGGGAGGAGCTG	0.557													G|||	692	0.138179	0.0303	0.2666	5008	,	,		16617	0.2083		0.1859	False		,,,				2504	0.0716				p.P100P		Atlas-SNP	.											.	NDUFA7	11	.	0			c.C300T						PASS	.	G		227,3867		6,215,1826	88.0	95.0	92.0		300	-1.1	0.6	19	dbSNP_36	92	1592,6782		153,1286,2748	no	coding-synonymous	NDUFA7	NM_005001.3		159,1501,4574	AA,AG,GG		19.0112,5.5447,14.5893		100/114	8376431	1819,10649	2047	4187	6234	SO:0001819	synonymous_variant	4701	exon4			CTTTATGGGAGGA	AF050637	CCDS42492.1	19p13.2	2013-05-14	2002-08-29		ENSG00000267855	ENSG00000267855		"""Mitochondrial respiratory chain complex / Complex I"""	7691	protein-coding gene	gene with protein product	"""complex I B14.5a subunit"""	602139	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (14.5kD, B14.5a)"""			9763676	Standard	NM_005001		Approved	B14.5a	uc002mjm.2	O95182	OTTHUMG00000182459	ENST00000301457.2:c.300C>T	19.37:g.8376431G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_005001		Silent	SNP	ENST00000301457.2	37	CCDS42492.1																																																																																			G|0.844;A|0.156	0.156	strong		0.557	NDUFA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461373.1	NM_005001	
OR51L1	119682	hgsc.bcm.edu	37	11	5020832	5020832	+	Missense_Mutation	SNP	C	C	T	rs10768450	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5020832C>T	ENST00000321543.1	+	1	620	c.620C>T	c.(619-621)gCc>gTc	p.A207V		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	207			A -> V (in dbSNP:rs10768450).			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)		GTAGTCATTGCCACACTAGGT	0.428													C|||	1155	0.230631	0.3011	0.1599	5008	,	,		25398	0.0694		0.3131	False		,,,				2504	0.2669				p.A207V		Atlas-SNP	.											.	OR51L1	60	.	0			c.C620T						PASS	.	C	VAL/ALA	1371,3031	455.5+/-351.0	199,973,1029	247.0	212.0	224.0		620	-4.7	0.0	11	dbSNP_120	224	2566,6030	418.5+/-352.8	383,1800,2115	yes	missense	OR51L1	NM_001004755.1	64	582,2773,3144	TT,TC,CC		29.8511,31.1449,30.2893	benign	207/316	5020832	3937,9061	2201	4298	6499	SO:0001583	missense	119682	exon1			TCATTGCCACACT	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.620C>T	11.37:g.5020832C>T	ENSP00000322156:p.Ala207Val	Somatic	315	1	0.0031746		WXS	Illumina HiSeq	Phase_I	344	134	0.389535	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	37	CCDS31369.1	491	0.22481684981684982	143	0.29065040650406504	66	0.18232044198895028	41	0.07167832167832168	241	0.3179419525065963	C	0.005	-2.140741	0.00332	0.311449	0.298511	ENSG00000176798	ENST00000321543	T	0.34859	1.34	5.18	-4.71	0.03279	GPCR, rhodopsin-like superfamily (1);	1.479880	0.04460	N	0.374160	T	0.00012	0.0000	L	0.35341	1.055	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.42899	-0.9424	9	0.02654	T	1	.	13.7055	0.62636	0.0:0.3172:0.0:0.6828	rs10768450;rs57593930;rs10768450	207	Q8NGJ5	O51L1_HUMAN	V	207	ENSP00000322156:A207V	ENSP00000322156:A207V	A	+	2	0	OR51L1	4977408	0.000000	0.05858	0.012000	0.15200	0.379000	0.30106	-3.800000	0.00363	-0.798000	0.04444	-0.259000	0.10710	GCC	C|0.721;T|0.279	0.279	strong		0.428	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
RIC3	79608	hgsc.bcm.edu	37	11	8159857	8159857	+	Missense_Mutation	SNP	C	C	T	rs55990541	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8159857C>T	ENST00000309737.6	-	3	388	c.389G>A	c.(388-390)tGc>tAc	p.C130Y	RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000425599.2_Missense_Mutation_p.C130Y|RIC3_ENST00000539720.1_Missense_Mutation_p.C81Y|RIC3_ENST00000343202.4_Missense_Mutation_p.C130Y|RIC3_ENST00000335425.7_Intron			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	130			C -> Y (in dbSNP:rs55990541).		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)		GGCAGTATAGCATTTCCCATC	0.453													C|||	402	0.0802716	0.0809	0.0807	5008	,	,		15995	0.0605		0.0656	False		,,,				2504	0.1145				p.C130Y		Atlas-SNP	.											.	RIC3	42	.	0			c.G389A						PASS	.	C	,TYR/CYS,TYR/CYS,TYR/CYS	321,4081	171.6+/-201.8	17,287,1897	278.0	268.0	271.0		,389,389,389	2.7	1.0	11	dbSNP_129	271	546,8046	150.0+/-205.0	18,510,3768	yes	intron,missense,missense,missense	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	,194,194,194	35,797,5665	TT,TC,CC		6.3547,7.2921,6.6723	,probably-damaging,probably-damaging,probably-damaging	,130/370,130/289,130/369	8159857	867,12127	2201	4296	6497	SO:0001583	missense	79608	exon3			GTATAGCATTTCC		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.389G>A	11.37:g.8159857C>T	ENSP00000308820:p.Cys130Tyr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	51	0.41129	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	151	0.06913919413919414	37	0.07520325203252033	28	0.07734806629834254	36	0.06293706293706294	50	0.06596306068601583	C	1.252	-0.618180	0.03663	0.072921	0.063547	ENSG00000166405	ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.78	2.7	0.31948	.	0.483461	0.23039	N	0.052629	T	0.00845	0.0028	L	0.37897	1.145	0.54753	D	0.999986	B;B;B;B	0.25169	0.024;0.119;0.041;0.041	B;B;B;B	0.26202	0.015;0.067;0.018;0.018	T	0.05007	-1.0912	10	0.02654	T	1	.	6.8312	0.23911	0.1263:0.6612:0.1382:0.0743	rs55990541	130;130;130;130	B7Z1U4;B0B1U0;Q7Z5B4;Q7Z5B4-5	.;.;RIC3_HUMAN;.	Y	130;130;130;81;130;130	ENSP00000344904:C130Y;ENSP00000308820:C130Y;ENSP00000443871:C81Y;ENSP00000395320:C130Y;ENSP00000431658:C130Y	ENSP00000308820:C130Y	C	-	2	0	RIC3	8116433	0.948000	0.32251	0.998000	0.56505	0.975000	0.68041	0.513000	0.22770	1.416000	0.47057	0.609000	0.83330	TGC	C|0.934;T|0.066	0.066	strong		0.453	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
ENOSF1	55556	hgsc.bcm.edu	37	18	691266	691266	+	Missense_Mutation	SNP	A	A	G	rs2612086	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:691266A>G	ENST00000251101.7	-	6	522	c.434T>C	c.(433-435)aTg>aCg	p.M145T	ENOSF1_ENST00000340116.7_Missense_Mutation_p.M166T|ENOSF1_ENST00000580982.1_Intron|ENOSF1_ENST00000383578.3_Missense_Mutation_p.M63T|ENOSF1_ENST00000539164.1_3'UTR	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	145			M -> T (in dbSNP:rs2612086). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8493092, ECO:0000269|PubMed:8764108, ECO:0000269|Ref.5}.		cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						GGATACCAGCATCCTGGGATC	0.428													G|||	1280	0.255591	0.2927	0.3516	5008	,	,		19176	0.0942		0.3469	False		,,,				2504	0.2096				p.M166T		Atlas-SNP	.											.	ENOSF1	44	.	0			c.T497C						PASS	.	G	THR/MET,THR/MET,THR/MET	1346,3060	689.8+/-405.2	214,918,1071	63.0	60.0	61.0		188,434,497	-1.3	0.1	18	dbSNP_100	61	3088,5512	656.7+/-401.4	547,1994,1759	yes	missense,missense,missense	ENOSF1	NM_001126123.3,NM_017512.5,NM_202758.3	81,81,81	761,2912,2830	GG,GA,AA		35.907,30.5493,34.092	benign,benign,benign	63/362,145/444,166/451	691266	4434,8572	2203	4300	6503	SO:0001583	missense	55556	exon6			ACCAGCATCCTGG	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.434T>C	18.37:g.691266A>G	ENSP00000251101:p.Met145Thr	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Missense_Mutation	SNP	ENST00000251101.7	37	CCDS11822.1	573	0.2623626373626374	150	0.3048780487804878	122	0.3370165745856354	47	0.08216783216783216	254	0.33509234828496043	G	8.524	0.869414	0.17322	0.305493	0.35907	ENSG00000132199	ENST00000383578;ENST00000251101;ENST00000340116	T;T;T	0.28069	1.63;2.03;2.04	5.37	-1.31	0.09230	.	0.326617	0.37012	N	0.002281	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.999999425105	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.46105	-0.9215	9	0.44086	T	0.13	.	4.7042	0.12841	0.3927:0.0:0.2228:0.3845	rs2612086;rs11555884;rs60754709;rs2612086	166;190;145;63	A6NMP3;Q6ZS08;Q7L5Y1;Q7L5Y1-2	.;.;ENOF1_HUMAN;.	T	63;145;166	ENSP00000373072:M63T;ENSP00000251101:M145T;ENSP00000345974:M166T	ENSP00000251101:M145T	M	-	2	0	ENOSF1	681266	0.336000	0.24757	0.055000	0.19348	0.852000	0.48524	-0.106000	0.10890	-0.377000	0.07930	-0.724000	0.03597	ATG	T|0.005;G|0.301	0.301	strong		0.428	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
SPTB	6710	hgsc.bcm.edu	37	14	65245962	65245962	+	Silent	SNP	A	A	G	rs1741487	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:65245962A>G	ENST00000389721.5	-	21	4508	c.4476T>C	c.(4474-4476)ctT>ctC	p.L1492L	SPTB_ENST00000556626.1_Silent_p.L1492L|SPTB_ENST00000389722.3_Silent_p.L1492L|SPTB_ENST00000542895.1_Silent_p.L1492L|SPTB_ENST00000389720.3_Silent_p.L1492L	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1492					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CCTCCACCCAAAGCTGCAGAG	0.567													G|||	2063	0.411941	0.7012	0.1657	5008	,	,		14583	0.3532		0.2445	False		,,,				2504	0.4284				p.L1492L		Atlas-SNP	.											.	SPTB	378	.	0			c.T4476C						PASS	.	G	,	2662,1744	502.4+/-365.2	813,1036,354	55.0	59.0	58.0		4476,4476	3.4	1.0	14	dbSNP_89	58	2045,6555	710.4+/-405.8	250,1545,2505	yes	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1063,2581,2859	GG,GA,AA		23.7791,39.5824,36.191	,	1492/2138,1492/2329	65245962	4707,8299	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon21			CACCCAAAGCTGC		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4476T>C	14.37:g.65245962A>G		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			A|0.635;G|0.365	0.365	strong		0.567	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
ZNF746	155061	hgsc.bcm.edu	37	7	149190046	149190046	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:149190046G>A	ENST00000340622.3	-	4	704	c.424C>T	c.(424-426)Ccc>Tcc	p.P142S	ZNF746_ENST00000458143.2_Missense_Mutation_p.P142S|ZNF746_ENST00000461958.2_Missense_Mutation_p.P142S			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	142	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			AGGACCTCGGGCTTGGAGATG	0.552																																					p.P142S		Atlas-SNP	.											ZNF746,NS,neuroblastoma,0,1	ZNF746	68	1	0			c.C424T						scavenged	.						75.0	64.0	68.0					7																	149190046		2203	4300	6503	SO:0001583	missense	155061	exon4			CCTCGGGCTTGGA	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.424C>T	7.37:g.149190046G>A	ENSP00000345140:p.Pro142Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	176	10	0.0568182	NM_001163474	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	37	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	.	17.07	3.295226	0.60086	.	.	ENSG00000181220	ENST00000340622;ENST00000458143;ENST00000461958	T;T	0.00966	5.49;5.49	5.33	5.33	0.75918	Krueppel-associated box (3);	0.000000	0.45361	D	0.000365	T	0.04137	0.0115	L	0.52573	1.65	0.41412	D	0.987746	B;D	0.89917	0.357;1.0	B;D	0.80764	0.413;0.994	T	0.48340	-0.9044	10	0.87932	D	0	-17.1738	16.5039	0.84264	0.0:0.0:1.0:0.0	.	142;142	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	S	142;142;129	ENSP00000345140:P142S;ENSP00000395007:P142S	ENSP00000345140:P142S	P	-	1	0	ZNF746	148820979	0.984000	0.35163	1.000000	0.80357	0.998000	0.95712	2.158000	0.42329	2.497000	0.84241	0.609000	0.83330	CCC	.	.	none		0.552	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386732	56386732	+	Missense_Mutation	SNP	C	C	T	rs61741210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56386732C>T	ENST00000343736.4	-	22	4064	c.3901G>A	c.(3901-3903)Gac>Aac	p.D1301N	BZRAP1_ENST00000268893.6_Missense_Mutation_p.D1241N|BZRAP1_ENST00000355701.3_Missense_Mutation_p.D1301N			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1301						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)					CAAAAGGGGTCGGGCTGGGAC	0.577													C|||	78	0.0155751	0.0008	0.013	5008	,	,		18724	0.0		0.0328	False		,,,				2504	0.0358				p.D1301N		Atlas-SNP	.											.	BZRAP1	287	.	0			c.G3901A						PASS	.	C	ASN/ASP,ASN/ASP	25,4379	30.8+/-60.4	0,25,2177	39.0	39.0	39.0		3901,3721	5.6	0.9	17	dbSNP_129	39	223,8377	86.9+/-149.2	3,217,4080	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	23,23	3,242,6257	TT,TC,CC		2.593,0.5677,1.9071	benign,benign	1301/1858,1241/1798	56386732	248,12756	2202	4300	6502	SO:0001583	missense	9256	exon22			AGGGGTCGGGCTG	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.3901G>A	17.37:g.56386732C>T	ENSP00000345824:p.Asp1301Asn	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	32	0.014652014652014652	0	0.0	4	0.011049723756906077	0	0.0	28	0.036939313984168866	C	14.65	2.599495	0.46318	0.005677	0.02593	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	D;D;D	0.87491	-2.26;-2.26;-2.26	5.59	5.59	0.84812	.	0.222124	0.39146	N	0.001447	T	0.60495	0.2273	L	0.59436	1.845	0.26084	N	0.981058	P;B;B	0.51240	0.943;0.014;0.004	B;B;B	0.40825	0.341;0.012;0.001	T	0.70193	-0.4939	10	0.15952	T	0.53	.	16.3282	0.82996	0.0:1.0:0.0:0.0	rs61741210	1301;1241;1301	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	N	1301;1301;1241	ENSP00000347929:D1301N;ENSP00000345824:D1301N;ENSP00000268893:D1241N	ENSP00000268893:D1241N	D	-	1	0	BZRAP1	53741731	0.081000	0.21417	0.906000	0.35671	0.818000	0.46254	2.225000	0.42954	2.643000	0.89663	0.655000	0.94253	GAC	C|0.982;T|0.018	0.018	strong		0.577	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
ARFGAP2	84364	hgsc.bcm.edu	37	11	47185680	47185680	+	IGR	SNP	G	G	A	rs11039114	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47185680G>A	ENST00000524782.1	-	0	2976				ARFGAP2_ENST00000395449.3_5'Flank|C11orf49_ENST00000378618.2_Silent_p.Q286Q	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2						protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						CCTCACGGCAGCACAGAGCCA	0.607													G|||	776	0.154952	0.0174	0.1254	5008	,	,		17888	0.0744		0.2276	False		,,,				2504	0.3701				p.Q286Q		Atlas-SNP	.											.	C11orf49	41	.	0			c.G858A						PASS	.	G		211,4191	129.4+/-166.1	6,199,1996	57.0	56.0	56.0		858	5.3	1.0	11	dbSNP_120	56	1916,6682	339.0+/-323.0	196,1524,2579	no	coding-synonymous	C11orf49	NM_001003678.1		202,1723,4575	AA,AG,GG		22.2843,4.7933,16.3615		286/327	47185680	2127,10873	2201	4299	6500	SO:0001628	intergenic_variant	79096	exon9			ACGGCAGCACAGA	AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"""ADP-ribosylation factor GTPase activating proteins"""	13504	protein-coding gene	gene with protein product		606908	"""zinc finger protein 289, ID1 regulated"""	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773		11.37:g.47185680G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_001003678	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Silent	SNP	ENST00000524782.1	37	CCDS7926.1																																																																																			G|0.847;A|0.153	0.153	strong		0.607	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389	
XAGE3	170626	hgsc.bcm.edu	37	X	52891653	52891653	+	Silent	SNP	C	C	T	rs73206488		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:52891653C>T	ENST00000346279.3	-	5	400	c.330G>A	c.(328-330)caG>caA	p.Q110Q	XAGE3_ENST00000375491.3_Silent_p.Q110Q	NM_133179.2	NP_573440.1	Q8WTP9	XAGE3_HUMAN	X antigen family, member 3	110								p.Q110Q(1)		kidney(1)|large_intestine(1)|lung(2)	4						TCATTTAAACCTGTGGTTGCC	0.338																																					p.Q110Q		Atlas-SNP	.											.	XAGE3	8	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G330A						PASS	.																																			SO:0001819	synonymous_variant	170626	exon5			TTAAACCTGTGGT	BG354572	CCDS14347.1	Xp11.22	2010-09-27	2004-06-07	2005-01-27	ENSG00000171402	ENSG00000171402			14618	protein-coding gene	gene with protein product	"""cancer/testis antigen family 12, member 3a"", ""cancer/testis antigen family 12, member 3b"""	300740	"""placenta-specific 6; G antigen, family D, 4"""	PLAC6, GAGED4			Standard	NM_133179		Approved	XAGE-3, pp9012, CT12.3a, CT12.3b	uc004dre.3	Q8WTP9	OTTHUMG00000021587	ENST00000346279.3:c.330G>A	X.37:g.52891653C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	209	96	0.45933	NM_133179	Q5JS82|Q8WYS9	Silent	SNP	ENST00000346279.3	37	CCDS14347.1																																																																																			C|0.500;T|0.500	0.500	strong		0.338	XAGE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056686.1	NM_133179	
PRRC2B	84726	hgsc.bcm.edu	37	9	134351343	134351343	+	Missense_Mutation	SNP	C	C	T	rs11243403	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134351343C>T	ENST00000357304.4	+	15	3882	c.3827C>T	c.(3826-3828)gCg>gTg	p.A1276V	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1276				A -> V (in Ref. 5; CAH18678). {ECO:0000305}.			poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GACAGCCGCGCGGAGGACAAG	0.572											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1681	0.335663	0.3707	0.3228	5008	,	,		17060	0.1161		0.5586	False		,,,				2504	0.2945				p.A1276V		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C3827T						PASS	.	C	VAL/ALA	1653,2295		349,955,670	43.0	49.0	47.0		3827	0.8	0.0	9	dbSNP_120	47	4883,3429		1416,2051,689	yes	missense	PRRC2B	NM_013318.3	64	1765,3006,1359	TT,TC,CC		41.2536,41.8693,46.6884	benign	1276/2230	134351343	6536,5724	1974	4156	6130	SO:0001583	missense	84726	exon15			GCCGCGCGGAGGA	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.3827C>T	9.37:g.134351343C>T	ENSP00000349856:p.Ala1276Val	Somatic	59	0	0	1610	WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	789	0.36126373626373626	176	0.35772357723577236	135	0.3729281767955801	63	0.11013986013986014	415	0.5474934036939314	C	1.360	-0.588965	0.03799	0.418693	0.587464	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.01871	4.59	5.66	0.799	0.18667	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.54753	P	1.399999999995849E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04128	-1.0975	8	0.29301	T	0.29	.	5.3177	0.15864	0.0:0.3088:0.1429:0.5483	rs11243403;rs60709203;rs11243403	9;1276	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	V	1276;572	ENSP00000349856:A1276V	ENSP00000349856:A1276V	A	+	2	0	PRRC2B	133341164	0.020000	0.18652	0.003000	0.11579	0.019000	0.09904	0.735000	0.26115	-0.091000	0.12440	-0.302000	0.09304	GCG	C|0.636;T|0.364	0.364	strong		0.572	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
VSIG10	54621	hgsc.bcm.edu	37	12	118520170	118520170	+	Silent	SNP	G	G	A	rs7488309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	119	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	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	
MRPS24	64951	hgsc.bcm.edu	37	7	43906513	43906513	+	Missense_Mutation	SNP	A	A	G	rs670573	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:43906513A>G	ENST00000317534.5	-	4	350	c.289T>C	c.(289-291)Tgg>Cgg	p.W97R	MRPS24_ENST00000467084.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_3'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	97			W -> R (in dbSNP:rs670573).		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						AAGGTACCCCACATGAACTTG	0.552													A|||	492	0.0982428	0.1445	0.0865	5008	,	,		17920	0.1379		0.0865	False		,,,				2504	0.0153				p.W97R		Atlas-SNP	.											.	MRPS24	9	.	0			c.T289C						PASS	.	A	,ARG/TRP	541,3865	244.3+/-253.7	32,477,1694	73.0	67.0	69.0		,289	-5.2	0.6	7	dbSNP_83	69	614,7986	160.7+/-213.8	23,568,3709	yes	utr-3,missense	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	,101	55,1045,5403	GG,GA,AA		7.1395,12.2787,8.8805	,benign	,97/168	43906513	1155,11851	2203	4300	6503	SO:0001583	missense	64951	exon4			TACCCCACATGAA	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.289T>C	7.37:g.43906513A>G	ENSP00000318158:p.Trp97Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_032014	A4D1U9|P82668|Q96Q23|Q9P047	Missense_Mutation	SNP	ENST00000317534.5	37	CCDS5473.1	280	0.1282051282051282	91	0.18495934959349594	33	0.09116022099447514	94	0.16433566433566432	62	0.08179419525065963	A	9.445	1.089135	0.20390	0.122787	0.071395	ENSG00000062582	ENST00000317534	T	0.39056	1.1	5.24	-5.21	0.02815	.	0.555420	0.19142	N	0.121667	T	0.00039	0.0001	N	0.01352	-0.895	0.46222	P	0.0010639999999999539	B	0.14438	0.01	B	0.18871	0.023	T	0.24440	-1.0160	9	0.25106	T	0.35	.	4.527	0.11986	0.3699:0.0:0.2779:0.3522	rs670573;rs1058812;rs3199453;rs3735265;rs11549686;rs52789329;rs58986208;rs670573	97	Q96EL2	RT24_HUMAN	R	97	ENSP00000318158:W97R	ENSP00000318158:W97R	W	-	1	0	MRPS24	43873038	0.990000	0.36364	0.587000	0.28692	0.609000	0.37215	0.834000	0.27518	-0.925000	0.03775	-0.242000	0.12053	TGG	T|0.000;G|0.102;N|0.000;A|0.898	0.102	strong		0.552	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014	
CD300A	11314	hgsc.bcm.edu	37	17	72469958	72469958	+	Silent	SNP	A	A	G	rs1127737	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72469958A>G	ENST00000360141.3	+	2	612	c.324A>G	c.(322-324)ccA>ccG	p.P108P	CD300A_ENST00000361933.3_Intron|CD300A_ENST00000577511.1_5'UTR|CD300A_ENST00000310828.5_Intron|CD300A_ENST00000392625.3_Intron	NM_001256841.1|NM_007261.3	NP_001243770.1|NP_009192.2	Q9UGN4	CLM8_HUMAN	CD300a molecule	108	Ig-like V-type.				cell adhesion (GO:0007155)|immune system process (GO:0002376)|negative regulation of activation of JAK2 kinase activity (GO:1902569)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of eosinophil activation (GO:1902567)|negative regulation of eosinophil migration (GO:2000417)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell activation involved in immune response (GO:0033007)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of neutrophil activation (GO:1902564)|negative regulation of NK T cell activation (GO:0051134)|negative regulation of phagocytosis, engulfment (GO:0060101)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|regulation of T cell receptor signaling pathway (GO:0050856)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)|signaling receptor activity (GO:0038023)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(4)|urinary_tract(1)	16						TGGATACACCATGGCTCCGAG	0.567													a|||	3441	0.687101	0.9614	0.6657	5008	,	,		17609	0.7212		0.4483	False		,,,				2504	0.5419				p.P108P		Atlas-SNP	.											.	CD300A	40	.	0			c.A324G						PASS	.	G		3914,492	781.4+/-414.5	1743,428,32	122.0	132.0	128.0		324	-6.8	0.0	17	dbSNP_86	128	3721,4879	530.4+/-381.8	802,2117,1381	no	coding-synonymous	CD300A	NM_007261.2		2545,2545,1413	GG,GA,AA		43.2674,11.1666,41.2963		108/300	72469958	7635,5371	2203	4300	6503	SO:0001819	synonymous_variant	11314	exon2			TACACCATGGCTC	BC032352	CCDS32720.1, CCDS58590.1	17q25.2	2013-01-11	2006-03-28		ENSG00000167851	ENSG00000167851		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19319	protein-coding gene	gene with protein product		606790	"""CD300a antigen"""			9701027, 10746781	Standard	NM_007261		Approved	Irp60, CMRF35H, CMRF-35-H9, IRC1, IRC2, IGSF12	uc002jkv.4	Q9UGN4	OTTHUMG00000067612	ENST00000360141.3:c.324A>G	17.37:g.72469958A>G		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	259	259	1	NM_007261	A8MW96|O95100|Q9HD97|Q9P0F3|Q9UBK4|Q9UMS9|Q9UMT0	Silent	SNP	ENST00000360141.3	37	CCDS32720.1																																																																																			A|0.418;G|0.582	0.582	strong		0.567	CD300A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145091.1	NM_007261	
IQCB1	9657	hgsc.bcm.edu	37	3	121500699	121500699	+	Missense_Mutation	SNP	C	C	T	rs17849995	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:121500699C>T	ENST00000310864.6	-	13	1515	c.1301G>A	c.(1300-1302)tGc>tAc	p.C434Y	IQCB1_ENST00000349820.6_Missense_Mutation_p.C301Y	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	434	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.		C -> Y (in dbSNP:rs17849995). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TTTCTTACGGCACTTCGCTAG	0.403													C|||	1516	0.302716	0.2413	0.5043	5008	,	,		19245	0.1647		0.2495	False		,,,				2504	0.4397				p.C434Y		Atlas-SNP	.											.	IQCB1	50	.	0			c.G1301A						PASS	.	C	TYR/CYS,TYR/CYS	1026,3380	380.2+/-323.6	119,788,1296	113.0	109.0	110.0		1301,902	3.7	1.0	3	dbSNP_123	110	2057,6543	356.9+/-330.5	235,1587,2478	yes	missense,missense	IQCB1	NM_001023570.2,NM_001023571.2	194,194	354,2375,3774	TT,TC,CC		23.9186,23.2864,23.7044	possibly-damaging,possibly-damaging	434/599,301/466	121500699	3083,9923	2203	4300	6503	SO:0001583	missense	9657	exon13			TTACGGCACTTCG	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"""nephrocystin-5"""	609237	"""IQ calmodulin-binding motif containing 1"""			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1301G>A	3.37:g.121500699C>T	ENSP00000311505:p.Cys434Tyr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	SNP	ENST00000310864.6	37	CCDS33837.1	571	0.26144688644688646	130	0.26422764227642276	169	0.46685082872928174	77	0.1346153846153846	195	0.25725593667546176	C	5.418	0.262198	0.10239	0.232864	0.239186	ENSG00000173226	ENST00000310864;ENST00000349820	T;T	0.71461	-0.57;-0.57	4.61	3.74	0.42951	.	0.105267	0.64402	D	0.000003	T	0.00012	0.0000	L	0.36672	1.1	0.33126	P	0.45759000000000005	P;D	0.64830	0.826;0.994	B;P	0.59703	0.191;0.862	T	0.40136	-0.9579	9	0.02654	T	1	0.2067	8.7599	0.34667	0.0:0.8971:0.0:0.1029	rs17849995	434;301	Q15051;Q15051-2	IQCB1_HUMAN;.	Y	434;301	ENSP00000311505:C434Y;ENSP00000323756:C301Y	ENSP00000311505:C434Y	C	-	2	0	IQCB1	122983389	0.946000	0.32159	0.998000	0.56505	0.043000	0.13939	2.801000	0.47908	1.298000	0.44778	0.591000	0.81541	TGC	C|0.759;T|0.241	0.241	strong		0.403	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642	
MRPL11	65003	hgsc.bcm.edu	37	11	66206169	66206169	+	Silent	SNP	C	C	T	rs11110	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66206169C>T	ENST00000310999.7	-	1	150	c.57G>A	c.(55-57)gtG>gtA	p.V19V	MRPL11_ENST00000430466.2_Intron|MRPL11_ENST00000329819.4_Silent_p.V19V|MRPL11_ENST00000524576.1_Intron	NM_016050.3	NP_057134.1	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11	19					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|prostate(1)	7						TCGCCCGGATCACACCGCCGA	0.721													C|||	1158	0.23123	0.2254	0.2003	5008	,	,		14099	0.2798		0.3002	False		,,,				2504	0.1401				p.V19V		Atlas-SNP	.											.	MRPL11	25	.	0			c.G57A						PASS	.	C	,,	870,3286		105,660,1313	9.0	12.0	11.0		57,,57	1.6	1.0	11	dbSNP_52	11	2320,6066		337,1646,2210	no	coding-synonymous,intron,coding-synonymous	MRPL11	NM_016050.3,NM_170738.2,NM_170739.2	,,	442,2306,3523	TT,TC,CC		27.6652,20.9336,25.4345	,,	19/193,,19/182	66206169	3190,9352	2078	4193	6271	SO:0001819	synonymous_variant	65003	exon1			CCGGATCACACCG	AB051338	CCDS8139.1, CCDS8140.1, CCDS44655.1	11q13.2	2012-11-14			ENSG00000174547	ENSG00000174547		"""Mitochondrial ribosomal proteins / large subunits"""	14042	protein-coding gene	gene with protein product		611826					Standard	XR_247672		Approved		uc001ohz.4	Q9Y3B7	OTTHUMG00000167097	ENST00000310999.7:c.57G>A	11.37:g.66206169C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_170739	A6NLT0|A8K219|Q32P46|Q96Q73	Silent	SNP	ENST00000310999.7	37	CCDS8139.1																																																																																			C|0.735;T|0.265	0.265	strong		0.721	MRPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393098.2	NM_016050	
GIMAP5	55340	hgsc.bcm.edu	37	7	150439500	150439500	+	Silent	SNP	C	C	T	rs759011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	72	36	0.5	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	
PSMD8	5714	hgsc.bcm.edu	37	19	38872778	38872778	+	Silent	SNP	C	C	T	rs1131182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38872778C>T	ENST00000215071.4	+	6	891	c.825C>T	c.(823-825)atC>atT	p.I275I	GGN_ENST00000591809.1_5'Flank|PSMD8_ENST00000602911.1_Silent_p.I212I|PSMD8_ENST00000592035.1_Silent_p.I108I	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	275					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(1)	6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGGGTGCATCGAGAAGGCCT	0.542													C|||	318	0.0634984	0.0053	0.1657	5008	,	,		19668	0.0437		0.1014	False		,,,				2504	0.0511				p.I275I		Atlas-SNP	.											.	PSMD8	31	.	0			c.C825T						PASS	.	C		54,2600		0,54,1273	73.0	56.0	62.0		825	-5.0	0.9	19	dbSNP_86	62	419,4199		18,383,1908	no	coding-synonymous	PSMD8	NM_002812.4		18,437,3181	TT,TC,CC		9.0732,2.0347,6.5044		275/351	38872778	473,6799	1327	2309	3636	SO:0001819	synonymous_variant	5714	exon6			GTGCATCGAGAAG	D38047	CCDS12515.2	19q13.2	2009-05-07			ENSG00000099341	ENSG00000099341		"""Proteasome (prosome, macropain) subunits"""	9566	protein-coding gene	gene with protein product						7621825	Standard	NM_002812		Approved	S14, Nin1p, p31, HIP6, HYPF, Rpn12	uc002oii.4	P48556	OTTHUMG00000150691	ENST00000215071.4:c.825C>T	19.37:g.38872778C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_002812	B4DX18|Q6P1L7	Silent	SNP	ENST00000215071.4	37	CCDS12515.2																																																																																			C|0.918;T|0.082	0.082	strong		0.542	PSMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319627.1	NM_002812	
PSIP1	11168	hgsc.bcm.edu	37	9	15486870	15486870	+	Silent	SNP	A	A	G	rs2821529	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:15486870A>G	ENST00000380733.4	-	5	691	c.348T>C	c.(346-348)agT>agC	p.S116S	PSIP1_ENST00000397519.2_Silent_p.S116S|PSIP1_ENST00000380715.1_Silent_p.S116S|PSIP1_ENST00000380716.4_Silent_p.S116S|PSIP1_ENST00000380738.4_Silent_p.S116S			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	116					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		CCTTTGAAACACTAGTTTCCT	0.323													A|||	339	0.0676917	0.171	0.0476	5008	,	,		16515	0.005		0.0507	False		,,,				2504	0.0245				p.S116S		Atlas-SNP	.											.	PSIP1	93	.	0			c.T348C						PASS	.	A	,,	629,3777	273.1+/-271.2	43,543,1617	152.0	139.0	143.0		348,348,348	4.0	1.0	9	dbSNP_100	143	419,8179	131.2+/-189.0	10,399,3890	no	coding-synonymous,coding-synonymous,coding-synonymous	PSIP1	NM_001128217.1,NM_021144.3,NM_033222.3	,,	53,942,5507	GG,GA,AA		4.8732,14.276,8.0591	,,	116/531,116/334,116/531	15486870	1048,11956	2203	4299	6502	SO:0001819	synonymous_variant	11168	exon4			TGAAACACTAGTT	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"""PC4 and SFRS1 interacting protein 2"""	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.348T>C	9.37:g.15486870A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	133	54	0.406015	NM_021144	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Silent	SNP	ENST00000380733.4	37	CCDS6479.1																																																																																			T|0.000;G|0.078;A|0.922	0.078	strong		0.323	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222	
ABHD16A	7920	hgsc.bcm.edu	37	6	31655438	31655438	+	Silent	SNP	G	G	A	rs10573	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31655438G>A	ENST00000395952.3	-	18	1689	c.1527C>T	c.(1525-1527)ccC>ccT	p.P509P	ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000375842.4_Silent_p.P290P|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000440843.2_Silent_p.P476P	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	509						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						AGGGGAAGTCGGGCCCGTGTT	0.587													G|||	507	0.101238	0.1589	0.0576	5008	,	,		19102	0.0714		0.0726	False		,,,				2504	0.1145				p.P509P		Atlas-SNP	.											.	ABHD16A	34	.	0			c.C1527T						PASS	.	G	,	415,2599		28,359,1120	48.0	52.0	50.0		1428,1527	-2.0	1.0	6	dbSNP_52	50	398,5018		15,368,2325	no	coding-synonymous,coding-synonymous	ABHD16A	NM_001177515.1,NM_021160.2	,	43,727,3445	AA,AG,GG		7.3486,13.7691,9.6441	,	476/526,509/559	31655438	813,7617	1507	2708	4215	SO:0001819	synonymous_variant	7920	exon18			GAAGTCGGGCCCG	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"""Abhydrolase domain containing"""	13921	protein-coding gene	gene with protein product		142620	"""HLA-B associated transcript 5"""	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.1527C>T	6.37:g.31655438G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Silent	SNP	ENST00000395952.3	37	CCDS4713.1																																																																																			G|0.901;A|0.099	0.099	strong		0.587	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4		
ERICH6B	220081	hgsc.bcm.edu	37	13	46115731	46115731	+	Missense_Mutation	SNP	C	C	A	rs1536207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46115731C>A	ENST00000298738.2	-	15	2121	c.1957G>T	c.(1957-1959)Gtc>Ttc	p.V653F	FAM194B_ENST00000504261.1_Intron	NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		653			V -> F (in dbSNP:rs1536207).							breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						CCCAGAAGGACCCGGATCTTC	0.507													C|||	1845	0.368411	0.1626	0.3631	5008	,	,		18039	0.5645		0.3608	False		,,,				2504	0.456				p.V653F		Atlas-SNP	.											.	FAM194B	42	.	0			c.G1957T						PASS	.						170.0	160.0	163.0					13																	46115731		692	1591	2283	SO:0001583	missense	220081	exon15			GAAGGACCCGGAT																												ENST00000298738.2:c.1957G>T	13.37:g.46115731C>A	ENSP00000298738:p.Val653Phe	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_182542	Q96MB5	Missense_Mutation	SNP	ENST00000298738.2	37	CCDS45045.1	827	0.37866300366300365	97	0.19715447154471544	133	0.3674033149171271	329	0.5751748251748252	268	0.35356200527704484	C	12.56	1.974839	0.34848	.	.	ENSG00000165837	ENST00000298738	T	0.11930	2.73	4.89	-4.76	0.03229	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	D	0.57899	0.981	P	0.54026	0.74	T	0.32322	-0.9911	8	0.87932	D	0	-4.4035	12.9301	0.58282	0.0:0.7089:0.0:0.2911	rs1536207;rs61562259;rs1536207	653	Q5W0A0	F194B_HUMAN	F	653	ENSP00000298738:V653F	ENSP00000298738:V653F	V	-	1	0	FAM194B	45013732	0.002000	0.14202	0.334000	0.25495	0.122000	0.20287	-0.714000	0.05002	-0.620000	0.05641	-0.904000	0.02843	GTC	C|0.626;A|0.374	0.374	strong		0.507	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
PRRC2C	23215	hgsc.bcm.edu	37	1	171526910	171526910	+	Missense_Mutation	SNP	G	G	A	rs57486971|rs12025905	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171526910G>A	ENST00000338920.4	+	19	5890	c.5653G>A	c.(5653-5655)Gcc>Acc	p.A1885T	PRRC2C_ENST00000367742.3_Missense_Mutation_p.A1887T|PRRC2C_ENST00000426496.2_Missense_Mutation_p.A1885T|PRRC2C_ENST00000392078.3_Missense_Mutation_p.A1887T	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1885	Ala-rich.		A -> T (in dbSNP:rs12025905).		hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										ttccccagctgccccagtcAT	0.607													G|||	592	0.118211	0.1097	0.1427	5008	,	,		13028	0.1637		0.1233	False		,,,				2504	0.0603				p.A1885T		Atlas-SNP	.											.	.	.	.	0			c.G5653A						PASS	.	G	THR/ALA	389,3135		20,349,1393	49.0	39.0	42.0		5653	3.1	0.0	1	dbSNP_120	42	943,5705		57,829,2438	yes	missense	PRRC2C	NM_015172.3	58	77,1178,3831	AA,AG,GG		14.1847,11.0386,13.0948	benign	1885/2818	171526910	1332,8840	1762	3324	5086	SO:0001583	missense	23215	exon19			CCAGCTGCCCCAG	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.5653G>A	1.37:g.171526910G>A	ENSP00000343629:p.Ala1885Thr	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	260	251	0.965385	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	315	0.14423076923076922	69	0.1402439024390244	56	0.15469613259668508	96	0.16783216783216784	94	0.12401055408970976	G	10.40	1.339351	0.24339	0.110386	0.141847	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.01998	4.52;4.51;4.52;4.52	4.04	3.1	0.35709	.	.	.	.	.	T	0.00552	0.0018	N	0.08118	0	0.80722	P	0.0	B	0.25609	0.13	B	0.19391	0.025	T	0.49153	-0.8969	8	0.33141	T	0.24	.	9.8145	0.40844	0.0:0.2087:0.7913:0.0	rs12025905;rs12025905	1885	Q9Y520-4	.	T	1887;1839;1885;1887;1885;1642	ENSP00000375928:A1887T;ENSP00000410219:A1885T;ENSP00000356716:A1887T;ENSP00000343629:A1885T	ENSP00000343629:A1885T	A	+	1	0	PRRC2C	169793534	0.002000	0.14202	0.002000	0.10522	0.160000	0.22226	-0.015000	0.12634	1.256000	0.44068	0.549000	0.68633	GCC	G|0.862;A|0.138	0.138	strong		0.607	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
CDKN2B	1030	hgsc.bcm.edu	37	9	22006147	22006147	+	Missense_Mutation	SNP	C	C	T	rs148421170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:22006147C>T	ENST00000276925.6	-	2	665	c.256G>A	c.(256-258)Gat>Aat	p.D86N	CDKN2B-AS1_ENST00000584351.1_RNA|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B-AS1_ENST00000584637.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000584816.1_RNA|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA|CDKN2B-AS1_ENST00000577551.1_RNA|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2B-AS1_ENST00000581051.1_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000582072.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B_ENST00000380142.4_3'UTR|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000582301.1_RNA	NM_004936.3|NM_078487.2	NP_004927.2|NP_511042.1	P42772	CDN2B_HUMAN	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	86					aging (GO:0007568)|cell cycle arrest (GO:0007050)|cellular response to extracellular stimulus (GO:0031668)|cellular response to nutrient (GO:0031670)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|liver development (GO:0001889)|megakaryocyte differentiation (GO:0030219)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of epithelial cell differentiation (GO:0030858)|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 cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to cytokine (GO:0034097)|response to organic cyclic compound (GO:0014070)|spleen development (GO:0048536)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0(1)|p.0?(1)		lung(2)	2		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;1.31e-280)|Lung NSC(2;2.28e-131)|all_lung(2;2.11e-123)|Glioma(2;5.66e-57)|all_neural(2;3.05e-50)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;8.01e-33)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00369)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;3.29e-71)|Epithelial(2;9.08e-60)|LUSC - Lung squamous cell carcinoma(2;5.8e-46)|LUAD - Lung adenocarcinoma(2;1.43e-25)|BRCA - Breast invasive adenocarcinoma(2;5.37e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;6.92e-07)|KIRC - Kidney renal clear cell carcinoma(2;8.63e-07)|OV - Ovarian serous cystadenocarcinoma(39;0.014)|COAD - Colon adenocarcinoma(8;0.143)		CGGGCAGCATCATGCACCGGT	0.716													C|||	2	0.000399361	0.0	0.0	5008	,	,		14208	0.0		0.002	False		,,,				2504	0.0				p.D86N		Atlas-SNP	.											.	CDKN2B	12	.	2	Whole gene deletion(2)	lung(2)	c.G256A						PASS	.	C	ASN/ASP,	1,4381		0,1,2190	19.0	23.0	22.0		256,	4.8	1.0	9	dbSNP_134	22	26,8552		0,26,4263	no	missense,utr-3	CDKN2B	NM_004936.3,NM_078487.2	23,	0,27,6453	TT,TC,CC		0.3031,0.0228,0.2083	probably-damaging,	86/139,	22006147	27,12933	2191	4289	6480	SO:0001583	missense	1030	exon2			CAGCATCATGCAC	AB060808	CCDS6512.1, CCDS6513.1	9p21	2008-07-21			ENSG00000147883	ENSG00000147883			1788	protein-coding gene	gene with protein product		600431				8078588	Standard	NM_004936		Approved	P15, MTS2, INK4B, TP15, CDK4I, p15INK4b	uc003zpo.3	P42772	OTTHUMG00000019691	ENST00000276925.6:c.256G>A	9.37:g.22006147C>T	ENSP00000276925:p.Asp86Asn	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_004936	O15125|Q6FI09	Missense_Mutation	SNP	ENST00000276925.6	37	CCDS6512.1	.	.	.	.	.	.	.	.	.	.	C	33	5.278680	0.95459	2.28E-4	0.003031	ENSG00000147883	ENST00000276925	D	0.93906	-3.31	4.78	4.78	0.61160	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.93893	0.8046	L	0.28400	0.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93080	0.6490	10	0.35671	T	0.21	-31.5885	15.3443	0.74324	0.0:1.0:0.0:0.0	.	86	P42772	CDN2B_HUMAN	N	86	ENSP00000276925:D86N	ENSP00000276925:D86N	D	-	1	0	CDKN2B	21996147	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.857000	0.62939	2.472000	0.83506	0.655000	0.94253	GAT	C|0.998;T|0.002	0.002	strong		0.716	CDKN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051932.2	NM_004936	
AMELX	265	hgsc.bcm.edu	37	X	11316742	11316742	+	Silent	SNP	C	C	T	rs2106416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:11316742C>T	ENST00000380714.3	+	5	287	c.219C>T	c.(217-219)caC>caT	p.H73H	ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000380732.3_Intron|AMELX_ENST00000348912.4_Silent_p.H57H|AMELX_ENST00000380712.3_Silent_p.H87H|ARHGAP6_ENST00000337414.4_Intron|ARHGAP6_ENST00000413512.3_Intron|ARHGAP6_ENST00000380736.1_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	73					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						CCCAACAGCACCCCCCGACTC	0.597													C|||	622	0.164768	0.2133	0.0865	3775	,	,		11178	0.0149		0.168	False		,,,				2504	0.0982				p.H87H		Atlas-SNP	.											.	AMELX	31	.	0			c.C261T						PASS	.	C	,,,,	1114,2721		134,679,167,819,404	140.0	121.0	128.0		219,,,261,171	-3.8	0.9	X	dbSNP_96	128	1475,5253		94,850,437,1484,1435	no	coding-synonymous,intron,intron,coding-synonymous,coding-synonymous	AMELX,ARHGAP6	NM_001142.2,NM_006125.2,NM_013427.2,NM_182680.1,NM_182681.1	,,,,	228,1529,604,2303,1839	TT,TC,T,CC,C		21.9233,29.0482,24.5101	,,,,	73/192,,,87/206,57/176	11316742	2589,7974	2203	4300	6503	SO:0001819	synonymous_variant	265	exon6			ACAGCACCCCCCG		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"""amelogenesis imperfecta 1"""	300391	"""amelogenin (X chromosome, amelogenesis imperfecta 1)"""	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.219C>T	X.37:g.11316742C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_182680	Q96NW6|Q9UCA7	Silent	SNP	ENST00000380714.3	37	CCDS14144.1																																																																																			C|0.765;T|0.235	0.235	strong		0.597	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142	
ETFDH	2110	hgsc.bcm.edu	37	4	159629589	159629589	+	Silent	SNP	T	T	C	rs141180629		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:159629589T>C	ENST00000511912.1	+	13	2096	c.1764T>C	c.(1762-1764)caT>caC	p.H588H	ETFDH_ENST00000307738.5_Silent_p.H541H	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	588	4Fe-4S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00711}.				cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		ACTGTGTACATTGTAAAACAT	0.358													T|||	1	0.000199681	0.0	0.0	5008	,	,		17185	0.0		0.001	False		,,,				2504	0.0				p.H588H		Atlas-SNP	.											.	ETFDH	57	.	0			c.T1764C						PASS	.						116.0	114.0	114.0					4																	159629589		2203	4300	6503	SO:0001819	synonymous_variant	2110	exon13			TGTACATTGTAAA	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.1764T>C	4.37:g.159629589T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_004453	B4E3R9|J3KND9|Q7Z347	Silent	SNP	ENST00000511912.1	37	CCDS3800.1																																																																																			T|1.000;C|0.000	0.000	strong		0.358	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2		
USP6	9098	hgsc.bcm.edu	37	17	5044794	5044794	+	Splice_Site	SNP	G	G	A	rs2304449	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5044794G>A	ENST00000574788.1	+	23	3803	c.1573G>A	c.(1573-1575)Gtt>Att	p.V525I	USP6_ENST00000332776.4_Splice_Site_p.V525I|USP6_ENST00000250066.6_Splice_Site_p.V525I|USP6_ENST00000304328.5_Splice_Site_p.V208I			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	525			V -> I (in dbSNP:rs2304449).		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						TAGACAAAAGGGTAAGTCTCC	0.299			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								G|||	360	0.071885	0.0393	0.0403	5008	,	,		15669	0.1468		0.0557	False		,,,				2504	0.0777				p.V525I		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.G1573A						PASS	.	G	ILE/VAL	242,4164	136.9+/-172.8	12,218,1973	72.0	69.0	70.0		1573	2.6	1.0	17	dbSNP_100	70	505,8085	139.4+/-196.0	30,445,3820	yes	missense-near-splice	USP6	NM_004505.2	29	42,663,5793	AA,AG,GG		5.8789,5.4925,5.7479	possibly-damaging	525/1407	5044794	747,12249	2203	4295	6498	SO:0001630	splice_region_variant	9098	exon15			CAAAAGGGTAAGT	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.1573+1G>A	17.37:g.5044794G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	243	111	0.45679	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	155	0.07097069597069597	21	0.042682926829268296	14	0.03867403314917127	73	0.12762237762237763	47	0.06200527704485488	G	6.586	0.476412	0.12521	0.054925	0.058789	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.13778	2.56;2.99;2.59	2.63	2.63	0.31362	.	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	N	0.14661	0.345	0.19575	P	0.9999656806	P;B	0.40431	0.717;0.204	B;B	0.38264	0.269;0.033	T	0.44003	-0.9356	9	0.19147	T	0.46	.	11.0154	0.47685	0.0:0.0:1.0:0.0	rs2304449;rs52796621;rs2304449	208;525	P35125-2;P35125	.;UBP6_HUMAN	I	525;525;208	ENSP00000328010:V525I;ENSP00000250066:V525I;ENSP00000305473:V208I	ENSP00000250066:V525I	V	+	1	0	USP6	4985518	1.000000	0.71417	0.998000	0.56505	0.200000	0.23975	9.169000	0.94788	1.470000	0.48102	0.194000	0.17425	GTT	G|0.940;A|0.060	0.060	strong		0.299	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	Missense_Mutation
E2F4	1874	hgsc.bcm.edu	37	16	67234197	67234197	+	IGR	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:67234197T>C	ENST00000379378.3	+	0	2096				ELMO3_ENST00000571638.1_3'UTR|ELMO3_ENST00000360833.1_Missense_Mutation_p.F152L|ELMO3_ENST00000477898.1_Missense_Mutation_p.F3L|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000393997.2_Missense_Mutation_p.F169L	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)		GGACATGATCTTTGCCAGGGA	0.602																																					p.F169L		Atlas-SNP	.											.	ELMO3	41	.	0			c.T505C						PASS	.						49.0	52.0	51.0					16																	67234197		2067	4182	6249	SO:0001628	intergenic_variant	79767	exon5			ATGATCTTTGCCA	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.67234197T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	5	0.0413223	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795457	0.90453	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.43688	0.94;0.94	5.2	5.2	0.72013	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.66056	0.2751	M	0.80616	2.505	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.997;0.995;0.99	T	0.71523	-0.4567	10	0.87932	D	0	-9.902	13.9039	0.63821	0.0:0.0:0.0:1.0	.	116;152;169	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	L	152;169	ENSP00000354077:F152L;ENSP00000377566:F169L	ENSP00000354077:F152L	F	+	1	0	ELMO3	65791698	1.000000	0.71417	1.000000	0.80357	0.546000	0.35178	7.179000	0.77665	1.971000	0.57363	0.379000	0.24179	TTT	.	.	none		0.602	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
KLF14	136259	hgsc.bcm.edu	37	7	130418525	130418525	+	Silent	SNP	G	G	A	rs76603546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:130418525G>A	ENST00000310992.4	-	1	363	c.336C>T	c.(334-336)tcC>tcT	p.S112S		NM_138693.2	NP_619638.2	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	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)			large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(18;0.0435)					CGGAGAAGCCGGACGAGGCGC	0.746													G|||	1930	0.385383	0.1067	0.4697	5008	,	,		9011	0.5397		0.498	False		,,,				2504	0.4274				p.S112S		Atlas-SNP	.											.	KLF14	15	.	0			c.C336T						PASS	.	G		729,3497		105,519,1489	6.0	10.0	8.0		336	-6.1	0.0	7	dbSNP_131	8	3856,4508		998,1860,1324	no	coding-synonymous	KLF14	NM_138693.2		1103,2379,2813	AA,AG,GG		46.1023,17.2504,36.4178		112/324	130418525	4585,8005	2113	4182	6295	SO:0001819	synonymous_variant	136259	exon1			GAAGCCGGACGAG	AF490374	CCDS5825.1	7q32.3	2014-05-06			ENSG00000174595	ENSG00000266265		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	23025	protein-coding gene	gene with protein product		609393				17480121	Standard	NM_138693		Approved	BTEB5	uc003vqk.2	Q8TD94	OTTHUMG00000188298	ENST00000310992.4:c.336C>T	7.37:g.130418525G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_138693	Q19A42|Q19A43	Silent	SNP	ENST00000310992.4	37	CCDS5825.1																																																																																			G|0.582;A|0.418	0.418	strong		0.746	KLF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338013.1	NM_138693	
F11	2160	hgsc.bcm.edu	37	4	187201211	187201211	+	Silent	SNP	A	A	G	rs5974	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187201211A>G	ENST00000403665.2	+	8	1153	c.801A>G	c.(799-801)acA>acG	p.T267T	F11_ENST00000264692.4_Silent_p.T215T	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	267	Apple 3. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	TGCCCAGTACACGCATTAAAA	0.388													A|||	837	0.167133	0.2579	0.1398	5008	,	,		19090	0.0387		0.163	False		,,,				2504	0.2004				p.T267T		Atlas-SNP	.											F11,colon,carcinoma,+1,1	F11	65	1	0			c.A801G						PASS	.	A		949,3457	358.6+/-314.5	113,723,1367	80.0	80.0	80.0		801	-5.1	0.3	4	dbSNP_52	80	1214,7386	244.3+/-273.6	89,1036,3175	no	coding-synonymous	F11	NM_000128.3		202,1759,4542	GG,GA,AA		14.1163,21.5388,16.6308		267/626	187201211	2163,10843	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon8			CAGTACACGCATT	M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"""plasma thromboplastin antecedent"""	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.801A>G	4.37:g.187201211A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1	317	0.14514652014652016	114	0.23170731707317074	61	0.1685082872928177	22	0.038461538461538464	120	0.158311345646438	A	1.280	-0.610683	0.03690	0.215388	0.141163	ENSG00000088926	ENST00000452239	.	.	.	5.63	-5.12	0.02893	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.999999999950489E-6	.	.	.	.	.	.	T	0.31251	-0.9950	3	.	.	.	.	4.8271	0.13421	0.6382:0.1749:0.0636:0.1234	rs5974;rs56560313;rs60184336;rs5974	.	.	.	R	83	.	.	H	+	2	0	F11	187438205	0.000000	0.05858	0.252000	0.24328	0.167000	0.22549	-0.992000	0.03724	-0.481000	0.06792	0.524000	0.50904	CAC	A|0.837;G|0.163	0.163	strong		0.388	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4		
PHF2	5253	hgsc.bcm.edu	37	9	96407953	96407953	+	Silent	SNP	G	G	A	rs35505758	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96407953G>A	ENST00000359246.4	+	4	709	c.342G>A	c.(340-342)acG>acA	p.T114T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	114					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		GTCAGCTCACGCTGGGCTACA	0.642													G|||	88	0.0175719	0.0227	0.0058	5008	,	,		19930	0.0139		0.0268	False		,,,				2504	0.0133				p.T114T		Atlas-SNP	.											.	PHF2	113	.	0			c.G342A						PASS	.	G		95,4311	78.8+/-117.2	1,93,2109	87.0	80.0	82.0		342	-9.2	0.0	9	dbSNP_126	82	166,8434	77.5+/-140.1	3,160,4137	no	coding-synonymous	PHF2	NM_005392.3		4,253,6246	AA,AG,GG		1.9302,2.1562,2.0068		114/1097	96407953	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon4			GCTCACGCTGGGC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.342G>A	9.37:g.96407953G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			G|0.980;A|0.020	0.020	strong		0.642	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
ATP8B3	148229	hgsc.bcm.edu	37	19	1811603	1811603	+	Missense_Mutation	SNP	C	C	T	rs7250872	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1811603C>T	ENST00000310127.6	-	2	371	c.133G>A	c.(133-135)Gga>Aga	p.G45R	ATP8B3_ENST00000539485.1_Missense_Mutation_p.G45R|ATP8B3_ENST00000525591.1_5'UTR|ATP8B3_ENST00000526092.2_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	66	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	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	
ACAA2	10449	hgsc.bcm.edu	37	18	47318626	47318626	+	Missense_Mutation	SNP	T	T	C	rs11549285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:47318626T>C	ENST00000285093.10	-	6	1124	c.649A>G	c.(649-651)Atg>Gtg	p.M217V	ACAA2_ENST00000589432.1_Missense_Mutation_p.M162V|ACAA2_ENST00000587994.1_Missense_Mutation_p.M214V	NM_006111.2	NP_006102.2	P42765	THIM_HUMAN	acetyl-CoA acyltransferase 2	217			M -> V (in dbSNP:rs11549285).		cellular response to hypoxia (GO:0071456)|cholesterol biosynthetic process (GO:0006695)|fatty acid metabolic process (GO:0006631)|negative regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902109)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	acetyl-CoA C-acyltransferase activity (GO:0003988)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(7)|ovary(1)	10						TCTACCTGCATTGTCTGTTTT	0.423													T|||	300	0.0599042	0.0015	0.0375	5008	,	,		16355	0.1885		0.0268	False		,,,				2504	0.0562				p.M217V		Atlas-SNP	.											.	ACAA2	29	.	0			c.A649G						PASS	.	T	VAL/MET	13,4393	17.9+/-39.9	0,13,2190	172.0	144.0	153.0		649	1.8	0.7	18	dbSNP_120	153	191,8409	84.5+/-147.0	6,179,4115	yes	missense	ACAA2	NM_006111.2	21	6,192,6305	CC,CT,TT		2.2209,0.2951,1.5685	benign	217/398	47318626	204,12802	2203	4300	6503	SO:0001583	missense	10449	exon6			CCTGCATTGTCTG	D16294	CCDS11939.1	18q21	2010-04-30	2010-04-30		ENSG00000167315	ENSG00000167315	2.3.1.16		83	protein-coding gene	gene with protein product	"""mitochondrial 3-oxoacyl-Coenzyme A thiolase"""	604770	"""acetyl-Coenzyme A acyltransferase 2"""			8241273	Standard	NM_006111		Approved	DSAEC	uc002ldw.4	P42765	OTTHUMG00000132667	ENST00000285093.10:c.649A>G	18.37:g.47318626T>C	ENSP00000285093:p.Met217Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	170	93	0.547059	NM_006111	Q9BUT6	Missense_Mutation	SNP	ENST00000285093.10	37	CCDS11939.1	126	0.057692307692307696	2	0.0040650406504065045	14	0.03867403314917127	91	0.1590909090909091	19	0.025065963060686015	T	2.008	-0.427751	0.04701	0.002951	0.022209	ENSG00000167315	ENST00000285093	D	0.87334	-2.24	5.49	1.75	0.24633	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.104157	0.85682	N	0.000000	T	0.00440	0.0014	N	0.01464	-0.85	0.20074	P	0.999936946	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.05550	-1.0878	9	0.15499	T	0.54	-15.6312	9.3216	0.37968	0.0:0.2745:0.0:0.7255	rs11549285;rs52835379;rs11549285	217;217	B2RB23;P42765	.;THIM_HUMAN	V	217	ENSP00000285093:M217V	ENSP00000285093:M217V	M	-	1	0	ACAA2	45572624	0.963000	0.33076	0.699000	0.30290	0.306000	0.27790	1.674000	0.37544	0.063000	0.16370	-0.269000	0.10298	ATG	T|0.970;C|0.030	0.030	strong		0.423	ACAA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255921.2	NM_006111	
C5	727	hgsc.bcm.edu	37	9	123780005	123780005	+	Silent	SNP	G	G	A	rs25681	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123780005G>A	ENST00000223642.1	-	13	1661	c.1632C>T	c.(1630-1632)taC>taT	p.Y544Y		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	544					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)	CTGTGACGATGTAATAGACCA	0.398													G|||	2032	0.405751	0.0295	0.5	5008	,	,		18022	0.5724		0.4592	False		,,,				2504	0.6207				p.Y544Y		Atlas-SNP	.											C5,colon,carcinoma,0,1	C5	124	1	0			c.C1632T						PASS	.	G		394,4012	195.7+/-220.2	24,346,1833	118.0	113.0	115.0		1632	4.2	1.0	9	dbSNP_72	115	3827,4773	540.0+/-383.7	886,2055,1359	no	coding-synonymous	C5	NM_001735.2		910,2401,3192	AA,AG,GG		44.5,8.9424,32.4543		544/1677	123780005	4221,8785	2203	4300	6503	SO:0001819	synonymous_variant	727	exon13			GACGATGTAATAG	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.1632C>T	9.37:g.123780005G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			G|0.644;A|0.356	0.356	strong		0.398	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807781	18807781	+	Silent	SNP	C	C	T	rs35013594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:18807781C>T	ENST00000400664.1	+	1	358	c.306C>T	c.(304-306)ggC>ggT	p.G102G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	102						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCAAGAGGCCCCTATGTCC	0.652													C|||	445	0.0888578	0.1021	0.1239	5008	,	,		17088	0.0377		0.1233	False		,,,				2504	0.0634				p.G102G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C306T						PASS	.	C		309,3613		11,287,1663	18.0	21.0	20.0		306	-5.4	0.0	1	dbSNP_126	20	1028,7288		66,896,3196	no	coding-synonymous	KLHDC7A	NM_152375.2		77,1183,4859	TT,TC,CC		12.3617,7.8786,10.925		102/778	18807781	1337,10901	1961	4158	6119	SO:0001819	synonymous_variant	127707	exon1			AAGAGGCCCCTAT	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.306C>T	1.37:g.18807781C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			C|0.899;T|0.101	0.101	strong		0.652	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
NEK2	4751	hgsc.bcm.edu	37	1	211846876	211846876	+	Silent	SNP	A	A	G	rs701929	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:211846876A>G	ENST00000366999.4	-	3	642	c.504T>C	c.(502-504)caT>caC	p.H168H	RP11-122M14.1_ENST00000415202.1_RNA|NEK2_ENST00000462283.1_5'Flank|NEK2_ENST00000540251.1_Silent_p.H125H|NEK2_ENST00000366998.3_Silent_p.H168H	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	168	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		AACTCGTGTCATGGTTTAATA	0.368													G|||	3020	0.603035	0.5454	0.6671	5008	,	,		19471	0.7252		0.4732	False		,,,				2504	0.6431				p.H168H		Atlas-SNP	.											.	NEK2	49	.	0			c.T504C						PASS	.	G	,,	2353,2053	566.7+/-382.0	640,1073,490	86.0	88.0	87.0		504,504,504	-10.5	0.2	1	dbSNP_86	87	4169,4431	586.8+/-392.1	1022,2125,1153	no	coding-synonymous,coding-synonymous,coding-synonymous	NEK2	NM_001204182.1,NM_001204183.1,NM_002497.3	,,	1662,3198,1643	GG,GA,AA		48.4767,46.5956,49.8539	,,	168/389,168/385,168/446	211846876	6522,6484	2203	4300	6503	SO:0001819	synonymous_variant	4751	exon3			CGTGTCATGGTTT	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"""HsPK 21"", ""protein phosphatase 1, regulatory subunit 111"""	604043	"""NIMA (never in mitosis gene a)-related kinase 2"""			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.504T>C	1.37:g.211846876A>G		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	180	76	0.422222	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Silent	SNP	ENST00000366999.4	37	CCDS1500.1																																																																																			A|0.463;G|0.537	0.537	strong		0.368	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
MFF	56947	hgsc.bcm.edu	37	2	228197238	228197238	+	Silent	SNP	G	G	A	rs11557342	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228197238G>A	ENST00000353339.3	+	5	804	c.363G>A	c.(361-363)acG>acA	p.T121T	MFF_ENST00000354503.6_Silent_p.T95T|MFF_ENST00000409616.1_Silent_p.T95T|MFF_ENST00000392059.1_Silent_p.T121T|MFF_ENST00000409565.1_Silent_p.T95T|MFF_ENST00000476924.1_3'UTR|MFF_ENST00000304593.9_Silent_p.T95T|MFF_ENST00000349901.7_Silent_p.T95T|MFF_ENST00000337110.7_Silent_p.T95T|MFF_ENST00000524634.1_De_novo_Start_InFrame	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	121					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)	p.T121T(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						GTGTACTTACGCTGAGTGAAA	0.393													G|||	446	0.0890575	0.0741	0.1081	5008	,	,		17428	0.1022		0.0716	False		,,,				2504	0.1002				p.T121T		Atlas-SNP	.											MFF,NS,carcinoma,0,1	MFF	48	1	1	Substitution - coding silent(1)	stomach(1)	c.G363A						scavenged	.	G		328,4078	171.6+/-201.8	4,320,1879	259.0	254.0	256.0		363	-10.2	0.5	2	dbSNP_120	256	749,7851	179.6+/-228.7	30,689,3581	no	coding-synonymous	MFF	NM_020194.4		34,1009,5460	AA,AG,GG		8.7093,7.4444,8.2808		121/343	228197238	1077,11929	2203	4300	6503	SO:0001819	synonymous_variant	56947	exon5			ACTTACGCTGAGT	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.363G>A	2.37:g.228197238G>A		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	225	99	0.44	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Silent	SNP	ENST00000353339.3	37	CCDS2465.1																																																																																			G|0.922;A|0.078	0.078	strong		0.393	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
TPSB2	64499	hgsc.bcm.edu	37	16	1279584	1279584	+	RNA	SNP	T	T	C	rs111992451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1279584T>C	ENST00000339687.6	-	0	238				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				CGCAGTGCGCTGCGGTCAGCA	0.701													T|||	2385	0.476238	0.3986	0.3862	5008	,	,		6594	0.6617		0.4622	False		,,,				2504	0.4683				p.A72A		Atlas-SNP	.											.	TPSB2	8	.	0			c.A216G						PASS	.						17.0	23.0	21.0					16																	1279584		2126	4277	6403			64499	exon3			GTGCGCTGCGGTC	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.1279584T>C		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	70	67	0.957143	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Silent	SNP	ENST00000339687.6	37																																																																																				C|1.000;|0.000	1.000	weak		0.701	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
COL4A3	1285	hgsc.bcm.edu	37	2	228131752	228131752	+	Silent	SNP	G	G	A	rs34019152	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228131752G>A	ENST00000396578.3	+	23	1614	c.1452G>A	c.(1450-1452)ggG>ggA	p.G484G	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	484	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)		ATATCCCAGGGCCTCCCGGTC	0.463													G|||	527	0.105232	0.0454	0.1787	5008	,	,		16826	0.1577		0.0686	False		,,,				2504	0.1176				p.G484G		Atlas-SNP	.											.	COL4A3	293	.	0			c.G1452A						PASS	.	G		176,3554		4,168,1693	66.0	66.0	66.0		1452	-2.1	0.1	2	dbSNP_126	66	636,7560		21,594,3483	no	coding-synonymous	COL4A3	NM_000091.4		25,762,5176	AA,AG,GG		7.7599,4.7185,6.8087		484/1671	228131752	812,11114	1865	4098	5963	SO:0001819	synonymous_variant	1285	exon23			CCCAGGGCCTCCC		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.1452G>A	2.37:g.228131752G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	37	CCDS42829.1																																																																																			G|0.905;A|0.095	0.095	strong		0.463	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
OR51B5	282763	hgsc.bcm.edu	37	11	5364476	5364476	+	Silent	SNP	C	C	T	rs61738485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364476C>T	ENST00000300773.2	-	1	333	c.279G>A	c.(277-279)gcG>gcA	p.A93A	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	93					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAGCAGGCCGCACTTCCAA	0.562													T|||	491	0.0980431	0.3071	0.049	5008	,	,		18817	0.0		0.0457	False		,,,				2504	0.0051				p.A93A		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.G279A						PASS	.	T		1240,3162	701.9+/-406.8	168,904,1129	43.0	42.0	42.0		279	-8.9	0.0	11	dbSNP_129	42	455,8139	796.1+/-407.5	13,429,3855	no	coding-synonymous	OR51B5	NM_001005567.2		181,1333,4984	TT,TC,CC		5.2944,28.169,13.0425		93/313	5364476	1695,11301	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			GCAGGCCGCACTT	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.279G>A	11.37:g.5364476C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			C|0.885;T|0.115	0.115	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
OLFML1	283298	hgsc.bcm.edu	37	11	7507182	7507182	+	Missense_Mutation	SNP	A	A	G	rs118163706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7507182A>G	ENST00000329293.3	+	1	470	c.76A>G	c.(76-78)Acc>Gcc	p.T26A	CTD-2516F10.2_ENST00000530201.1_RNA|OLFML1_ENST00000530135.1_Missense_Mutation_p.T26A|OLFML1_ENST00000528758.1_Missense_Mutation_p.T26A	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	26						extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GCCGCAGTGTACCCAGGACCC	0.547													G|||	80	0.0159744	0.0053	0.0115	5008	,	,		18910	0.0		0.0517	False		,,,				2504	0.0133				p.T26A		Atlas-SNP	.											.	OLFML1	54	.	0			c.A76G						PASS	.	G	ALA/THR	71,4331	819.6+/-416.4	1,69,2131	129.0	116.0	120.0		76	5.6	0.8	11	dbSNP_132	120	593,7999	792.1+/-407.5	16,561,3719	yes	missense	OLFML1	NM_198474.3	58	17,630,5850	GG,GA,AA		6.9018,1.6129,5.1101	benign	26/403	7507182	664,12330	2201	4296	6497	SO:0001583	missense	283298	exon1			CAGTGTACCCAGG	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.76A>G	11.37:g.7507182A>G	ENSP00000332511:p.Thr26Ala	Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	205	132	0.643902	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	37	CCDS7779.1	49	0.022435897435897436	3	0.006097560975609756	6	0.016574585635359115	0	0.0	40	0.052770448548812667	G	5.656	0.305689	0.10733	0.016129	0.069018	ENSG00000183801	ENST00000530135;ENST00000329293;ENST00000534244;ENST00000528758	D;D	0.86627	-2.15;-2.15	5.59	5.59	0.84812	.	0.272836	0.35096	N	0.003445	T	0.08179	0.0204	N	0.00146	-1.995	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39121	-0.9629	10	0.02654	T	1	.	10.7027	0.45937	0.0878:0.0:0.9122:0.0	.	26;26	Q6UWY5;Q5HYE3	OLFL1_HUMAN;.	A	26	ENSP00000433455:T26A;ENSP00000332511:T26A	ENSP00000332511:T26A	T	+	1	0	OLFML1	7463758	0.836000	0.29430	0.814000	0.32528	0.621000	0.37620	1.491000	0.35583	1.377000	0.46286	-0.186000	0.12905	ACC	A|0.959;G|0.041	0.041	strong		0.547	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474	
PRR27	401137	hgsc.bcm.edu	37	4	71024466	71024466	+	Missense_Mutation	SNP	C	C	T	rs201012961		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024466C>T	ENST00000344526.5	+	3	686	c.497C>T	c.(496-498)gCt>gTt	p.A166V	C4orf40_ENST00000502294.1_Missense_Mutation_p.A166V|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		166	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)		p.A166V(1)		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						CCTGTTGGAGCTGAGCCTGCT	0.632																																					p.A166V		Atlas-SNP	.											.	C4orf40	19	.	1	Substitution - Missense(1)	lung(1)	c.C497T						PASS	.						30.0	30.0	30.0					4																	71024466		2203	4298	6501	SO:0001583	missense	401137	exon3			TTGGAGCTGAGCC																												ENST00000344526.5:c.497C>T	4.37:g.71024466C>T	ENSP00000343172:p.Ala166Val	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	113	26	0.230089	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.250256	0.22880	.	.	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.33654	1.4;1.4	4.45	-4.02	0.04034	.	.	.	.	.	T	0.14874	0.0359	N	0.14661	0.345	0.09310	N	1	B	0.28713	0.22	B	0.22880	0.042	T	0.14952	-1.0454	9	0.45353	T	0.12	-4.1741	1.4635	0.02401	0.1179:0.3066:0.2443:0.3312	.	166	Q6MZM9	CD040_HUMAN	V	166	ENSP00000426249:A166V;ENSP00000343172:A166V	ENSP00000343172:A166V	A	+	2	0	C4orf40	71059055	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-1.976000	0.01497	-0.789000	0.04498	0.609000	0.83330	GCT	C|0.999;T|0.001	0.001	weak		0.632	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
OXER1	165140	hgsc.bcm.edu	37	2	42990101	42990101	+	Missense_Mutation	SNP	G	G	C	rs2278586	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:42990101G>C	ENST00000378661.2	-	1	1300	c.1219C>G	c.(1219-1221)Ctg>Gtg	p.L407V		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	407			L -> V (in dbSNP:rs2278586). {ECO:0000269|PubMed:12606753}.		G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						TGCACTTTCAGCTTCCCTATG	0.687													.|||	1677	0.334864	0.2042	0.2363	5008	,	,		20163	0.5952		0.2406	False		,,,				2504	0.41				p.L407V		Atlas-SNP	.											OXER1,brain,glioma,0,1	OXER1	33	1	0			c.C1219G						PASS	.	G	VAL/LEU	1012,3394	371.5+/-320.0	114,784,1305	61.0	61.0	61.0		1219	2.9	0.0	2	dbSNP_100	61	1807,6793	322.8+/-315.7	191,1425,2684	yes	missense	OXER1	NM_148962.4	32	305,2209,3989	CC,CG,GG		21.0116,22.9687,21.6746	possibly-damaging	407/424	42990101	2819,10187	2203	4300	6503	SO:0001583	missense	165140	exon1			CTTTCAGCTTCCC	AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"""GPCR / Class A : Leukotriene receptors"""	24884	protein-coding gene	gene with protein product	"""5-oxo-ETE acid G-protein-coupled receptor 1"""					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.1219C>G	2.37:g.42990101G>C	ENSP00000367930:p.Leu407Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_148962	Q86WP7|Q8NGW4	Missense_Mutation	SNP	ENST00000378661.2	37	CCDS1810.1	718	0.32875457875457875	99	0.20121951219512196	83	0.2292817679558011	359	0.6276223776223776	177	0.23350923482849603	G	13.36	2.214215	0.39102	0.229687	0.210116	ENSG00000162881	ENST00000378661	T	0.63096	-0.02	3.93	2.94	0.34122	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.17038	0.02	B	0.12837	0.008	T	0.44847	-0.9301	8	0.17369	T	0.5	.	12.0117	0.53291	0.0:0.2206:0.7794:0.0	rs2278586;rs56603157;rs60919568;rs2278586	407	Q8TDS5	OXER1_HUMAN	V	407	ENSP00000367930:L407V	ENSP00000367930:L407V	L	-	1	2	OXER1	42843605	0.000000	0.05858	0.012000	0.15200	0.035000	0.12851	-0.036000	0.12185	0.936000	0.37367	0.655000	0.94253	CTG	G|0.738;C|0.261	0.261	strong		0.687	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962	
PRDM9	56979	hgsc.bcm.edu	37	5	23527724	23527724	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:23527724A>G	ENST00000296682.3	+	11	2709	c.2527A>G	c.(2527-2529)Aat>Gat	p.N843D		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	843					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.N843D(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGCTTTCGCAATAAGTCACA	0.587										HNSCC(3;0.000094)																											p.N843D		Atlas-SNP	.											PRDM9,trunk,malignant_melanoma,0,2	PRDM9	344	2	2	Substitution - Missense(2)	skin(2)	c.A2527G						scavenged	.						66.0	76.0	72.0					5																	23527724		2183	4295	6478	SO:0001583	missense	56979	exon11			TTTCGCAATAAGT	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2527A>G	5.37:g.23527724A>G	ENSP00000296682:p.Asn843Asp	Somatic	145	5	0.0344828		WXS	Illumina HiSeq	Phase_I	167	6	0.0359281	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.847213	0.00067	.	.	ENSG00000164256	ENST00000296682	T	0.07444	3.19	2.67	-5.34	0.02705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02848	0.0085	N	0.04355	-0.22	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.30208	-0.9986	9	0.32370	T	0.25	.	1.9842	0.03433	0.2035:0.1472:0.4036:0.2457	.	843	Q9NQV7	PRDM9_HUMAN	D	843	ENSP00000296682:N843D	ENSP00000296682:N843D	N	+	1	0	PRDM9	23563481	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-14.808000	0.00000	-5.282000	0.00017	-3.452000	0.00036	AAT	.	.	none		0.587	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
FAT2	2196	hgsc.bcm.edu	37	5	150908813	150908813	+	Missense_Mutation	SNP	G	G	A	rs2304024	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150908813G>A	ENST00000261800.5	-	14	9964	c.9952C>T	c.(9952-9954)Cgg>Tgg	p.R3318W		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3318	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> Q (in dbSNP:rs7718054).|R -> W (in dbSNP:rs2304024).		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)			AATTGGGGCCGGTGTTCATTG	0.527													G|||	484	0.0966454	0.0083	0.1571	5008	,	,		21748	0.125		0.1938	False		,,,				2504	0.044				p.R3318W		Atlas-SNP	.											.	FAT2	465	.	0			c.C9952T						PASS	.	G	TRP/ARG	161,4245	107.3+/-145.7	6,149,2048	144.0	137.0	139.0		9952	3.9	1.0	5	dbSNP_100	139	1815,6785	328.0+/-318.1	201,1413,2686	yes	missense	FAT2	NM_001447.2	101	207,1562,4734	AA,AG,GG		21.1047,3.6541,15.193	probably-damaging	3318/4350	150908813	1976,11030	2203	4300	6503	SO:0001583	missense	2196	exon14			GGGGCCGGTGTTC	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.9952C>T	5.37:g.150908813G>A	ENSP00000261800:p.Arg3318Trp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	288|288	0.13186813186813187|0.13186813186813187	6|6	0.012195121951219513|0.012195121951219513	65|65	0.17955801104972377|0.17955801104972377	81|81	0.14160839160839161|0.14160839160839161	136|136	0.17941952506596306|0.17941952506596306	G|G	17.07|17.07	3.295417|3.295417	0.60086|0.60086	0.036541|0.036541	0.211047|0.211047	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.61392	.|0.11	5.78|5.78	3.9|3.9	0.45041|0.45041	.|Cadherin (3);Cadherin-like (1);	.|1.332910	.|0.04805	.|N	.|0.434197	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.61036|0.61036	1.89|1.89	0.39169|0.39169	P|P	0.03744499999999995|0.03744499999999995	.|D;D	.|0.62365	.|0.991;0.989	.|P;B	.|0.46452	.|0.517;0.409	T|T	0.04153|0.04153	-1.0973|-1.0973	4|9	.|0.87932	.|D	.|0	.|.	6.7277|6.7277	0.23365|0.23365	0.1644:0.2384:0.5973:0.0|0.1644:0.2384:0.5973:0.0	rs2304024;rs17404244;rs52798374;rs2304024|rs2304024;rs17404244;rs52798374;rs2304024	.|3318;509	.|Q9NYQ8;E9PDJ8	.|FAT2_HUMAN;.	L|W	176|3318	.|ENSP00000261800:R3318W	.|ENSP00000261800:R3318W	P|R	-|-	2|1	0|2	FAT2|FAT2	150889006|150889006	0.204000|0.204000	0.23447|0.23447	0.977000|0.977000	0.42913|0.42913	0.589000|0.589000	0.36550|0.36550	0.780000|0.780000	0.26760|0.26760	1.450000|1.450000	0.47717|0.47717	-0.170000|-0.170000	0.13304|0.13304	CCG|CGG	G|0.858;N|0.001	.	strong		0.527	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
RRP7A	27341	hgsc.bcm.edu	37	22	42912097	42912097	+	Missense_Mutation	SNP	C	C	T	rs11553441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:42912097C>T	ENST00000323013.6	-	3	277	c.262G>A	c.(262-264)Gta>Ata	p.V88I		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	88	RRM.		V -> I (in dbSNP:rs11553441).				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						TGCAACTCTACAGACTGGACG	0.627													C|||	381	0.0760783	0.0567	0.1772	5008	,	,		19105	0.003		0.1461	False		,,,				2504	0.0337				p.V88I		Atlas-SNP	.											.	RRP7A	25	.	0			c.G262A						PASS	.	C	ILE/VAL	342,4064	174.1+/-203.8	13,316,1874	53.0	50.0	51.0		262	2.9	0.1	22	dbSNP_120	51	1182,7418	238.1+/-269.7	92,998,3210	yes	missense	RRP7A	NM_015703.4	29	105,1314,5084	TT,TC,CC		13.7442,7.7621,11.7177	benign	88/281	42912097	1524,11482	2203	4300	6503	SO:0001583	missense	27341	exon3			ACTCTACAGACTG	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.262G>A	22.37:g.42912097C>T	ENSP00000321449:p.Val88Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	37	CCDS14036.1	204	0.09340659340659341	25	0.0508130081300813	71	0.19613259668508287	1	0.0017482517482517483	107	0.14116094986807387	C	9.919	1.211667	0.22289	0.077621	0.137442	ENSG00000189306	ENST00000323013	T	0.18502	2.21	3.93	2.9	0.33743	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.65320	2	0.09310	P	0.9999962723	P	0.51057	0.941	B	0.42030	0.373	T	0.28618	-1.0038	9	0.45353	T	0.12	-21.505	12.1146	0.53858	0.0:0.9124:0.0:0.0876	rs11553441;rs11553441	88	Q9Y3A4	RRP7A_HUMAN	I	88	ENSP00000321449:V88I	ENSP00000321449:V88I	V	-	1	0	RRP7A	41242041	0.994000	0.37717	0.050000	0.19076	0.004000	0.04260	3.845000	0.55880	0.946000	0.37632	-0.346000	0.07831	GTA	C|0.893;T|0.107	0.107	strong		0.627	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
FAM135B	51059	hgsc.bcm.edu	37	8	139164192	139164192	+	Silent	SNP	G	G	A	rs3750306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:139164192G>A	ENST00000395297.1	-	13	2696	c.2526C>T	c.(2524-2526)ccC>ccT	p.P842P		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	842										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)			CTATGTATCCGGGGCCCTGCT	0.512										HNSCC(54;0.14)			G|||	1862	0.371805	0.1815	0.4207	5008	,	,		19302	0.5298		0.3757	False		,,,				2504	0.4274				p.P842P		Atlas-SNP	.											.	FAM135B	423	.	0			c.C2526T						PASS	.	G		973,3433	365.6+/-317.5	115,743,1345	92.0	81.0	85.0		2526	-10.9	0.0	8	dbSNP_107	85	3009,5591	465.1+/-366.4	542,1925,1833	no	coding-synonymous	FAM135B	NM_015912.3		657,2668,3178	AA,AG,GG		34.9884,22.0835,30.6166		842/1407	139164192	3982,9024	2203	4300	6503	SO:0001819	synonymous_variant	51059	exon13			GTATCCGGGGCCC	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.2526C>T	8.37:g.139164192G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			G|0.665;A|0.335	0.335	strong		0.512	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
OLFM4	10562	hgsc.bcm.edu	37	13	53608632	53608632	+	Silent	SNP	C	C	T	rs2298231	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:53608632C>T	ENST00000219022.2	+	2	432	c.354C>T	c.(352-354)tcC>tcT	p.S118S		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	118					cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		AAGAACTTTCCAAAGTAAGCA	0.358													T|||	2831	0.565296	0.4168	0.6225	5008	,	,		19452	0.7242		0.501	False		,,,				2504	0.6278				p.S118S		Atlas-SNP	.											.	OLFM4	94	.	0			c.C354T						PASS	.	T		1919,2487	625.9+/-394.6	395,1129,679	44.0	39.0	40.0		354	3.0	1.0	13	dbSNP_100	40	4200,4400	581.9+/-391.3	1079,2042,1179	no	coding-synonymous	OLFM4	NM_006418.4		1474,3171,1858	TT,TC,CC		48.8372,43.5542,47.0475		118/511	53608632	6119,6887	2203	4300	6503	SO:0001819	synonymous_variant	10562	exon2			ACTTTCCAAAGTA	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.354C>T	13.37:g.53608632C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_006418	O95362|Q5VWG0|Q86T22	Silent	SNP	ENST00000219022.2	37	CCDS9440.1																																																																																			C|0.494;T|0.506	0.506	strong		0.358	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418	
MUC2	4583	hgsc.bcm.edu	37	11	1093393	1093393	+	Missense_Mutation	SNP	G	G	A	rs199525790		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093393G>A	ENST00000441003.2	+	30	5239	c.5212G>A	c.(5212-5214)Ggc>Agc	p.G1738S	MUC2_ENST00000333592.6_Missense_Mutation_p.G26S|MUC2_ENST00000359061.5_Missense_Mutation_p.G1705S|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aacacccaccggcacacagac	0.647																																					p.G1738S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G5212A						scavenged	.						167.0	217.0	200.0					11																	1093393		1999	3870	5869	SO:0001583	missense	4583	exon30			CCCACCGGCACAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5212G>A	11.37:g.1093393G>A	ENSP00000415183:p.Gly1738Ser	Somatic	78	2	0.025641		WXS	Illumina HiSeq	Phase_I	93	6	0.0645161	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	0.322	-0.961495	0.02249	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.16743	3.21;3.25;2.32	0.677	-1.35	0.09114	.	381.381000	0.01358	N	0.012136	T	0.08537	0.0212	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21861	-1.0233	9	0.12430	T	0.62	.	4.7623	0.13113	0.7467:0.0:0.2533:0.0	.	1738	E7EUV1	.	S	1738;1705;26	ENSP00000415183:G1738S;ENSP00000351956:G1705S;ENSP00000331373:G26S	ENSP00000331373:G26S	G	+	1	0	MUC2	1083393	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.042000	0.13949	-0.796000	0.04456	-1.112000	0.02068	GGC	.	.	weak		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
MST1L	11223	hgsc.bcm.edu	37	1	17083778	17083778	+	RNA	SNP	C	C	T	rs28455793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17083778C>T	ENST00000455405.2	-	0	810							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CAGAGACACGCGTGAAGACGG	0.542																																					p.T673T		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	0			c.G2019A						scavenged	.																																					11223	exon15			GACACGCGTGAAG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17083778C>T		Somatic	356	8	0.0224719		WXS	Illumina HiSeq	Phase_I	318	121	0.380503	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				C|0.312;T|0.688	0.688	strong		0.542	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
GEMIN4	50628	hgsc.bcm.edu	37	17	648186	648186	+	Missense_Mutation	SNP	G	G	A	rs7813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:648186G>A	ENST00000319004.5	-	2	3215	c.3097C>T	c.(3097-3099)Cgc>Tgc	p.R1033C	GEMIN4_ENST00000576778.1_Missense_Mutation_p.R1022C	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	1033			R -> C (in dbSNP:rs7813).		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)		TTTAAGAAGCGCTGCTCGTGT	0.562													G|||	3541	0.707069	0.8782	0.6398	5008	,	,		20723	0.7232		0.5905	False		,,,				2504	0.6268				p.R1033C		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C3097T	GRCh37	CM086125	GEMIN4	M	rs7813	PASS	.	G	CYS/ARG	3317,651		1388,541,55	53.0	53.0	53.0		3097	5.7	1.0	17	dbSNP_52	53	4676,3632		1322,2032,800	yes	missense	GEMIN4	NM_015721.2	180	2710,2573,855	AA,AG,GG		43.7169,16.4062,34.8892	probably-damaging	1033/1059	648186	7993,4283	1984	4154	6138	SO:0001583	missense	50628	exon2			AGAAGCGCTGCTC	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.3097C>T	17.37:g.648186G>A	ENSP00000321706:p.Arg1033Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	1503	0.6881868131868132	427	0.8678861788617886	220	0.6077348066298343	407	0.7115384615384616	449	0.5923482849604221	G	17.37	3.372854	0.61624	0.835938	0.562831	ENSG00000179409	ENST00000319004	T	0.06933	3.24	5.71	5.71	0.89125	.	0.101917	0.64402	D	0.000003	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	D	0.65815	0.995	P	0.46825	0.528	T	0.00752	-1.1581	9	0.72032	D	0.01	-12.3701	18.8558	0.92251	0.0:0.0:1.0:0.0	rs7813;rs3169636;rs3744739;rs52814935;rs57042701;rs7813	1033	P57678	GEMI4_HUMAN	C	1033	ENSP00000321706:R1033C	ENSP00000321706:R1033C	R	-	1	0	GEMIN4	594936	1.000000	0.71417	1.000000	0.80357	0.380000	0.30137	7.130000	0.77235	2.709000	0.92574	0.655000	0.94253	CGC	G|0.315;A|0.685	0.685	strong		0.562	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036505	33036505	+	Silent	SNP	G	G	C	rs1042434	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33036505G>C	ENST00000419277.1	-	5	834	c.705C>G	c.(703-705)gtC>gtG	p.V235V	HLA-DPA1_ENST00000428995.1_Silent_p.V235V|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	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	187	0	0		WXS	Illumina HiSeq	Phase_I	198	64	0.323232	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	
IGFLR1	79713	hgsc.bcm.edu	37	19	36230767	36230767	+	Missense_Mutation	SNP	A	A	G	rs34562867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36230767A>G	ENST00000592537.1	-	4	665	c.565T>C	c.(565-567)Tgg>Cgg	p.W189R	IGFLR1_ENST00000588992.1_Intron|KMT2B_ENST00000607650.1_RNA|IGFLR1_ENST00000344990.3_Intron|IGFLR1_ENST00000592889.1_Intron|IGFLR1_ENST00000246532.1_Missense_Mutation_p.W189R|AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000587101.1_5'UTR			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	189			W -> R (in dbSNP:rs34562867).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						TCCTTGGGCCAGCAGAGATGC	0.617													a|||	512	0.102236	0.087	0.1037	5008	,	,		17881	0.0883		0.1163	False		,,,				2504	0.1217				p.W189R		Atlas-SNP	.											.	IGFLR1	28	.	0			c.T565C						PASS	.	G	ARG/TRP	382,4024	192.3+/-217.7	11,360,1832	84.0	85.0	85.0		565	-6.9	0.0	19	dbSNP_126	85	808,7792	188.0+/-235.1	32,744,3524	yes	missense	IGFLR1	NM_024660.2	101	43,1104,5356	GG,GA,AA		9.3953,8.67,9.1496	benign	189/356	36230767	1190,11816	2203	4300	6503	SO:0001583	missense	79713	exon4			TGGGCCAGCAGAG	AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 4"", ""transmembrane protein 149"""	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.565T>C	19.37:g.36230767A>G	ENSP00000466181:p.Trp189Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_024660	Q8N5X0	Missense_Mutation	SNP	ENST00000592537.1	37	CCDS12472.1	222	0.10164835164835165	48	0.0975609756097561	37	0.10220994475138122	48	0.08391608391608392	89	0.11741424802110818	a	1.272	-0.612700	0.03690	0.0867	0.093953	ENSG00000126246	ENST00000246532	T	0.43688	0.94	4.86	-6.94	0.01633	.	1.644740	0.03371	N	0.198957	T	0.00210	0.0006	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07501	-1.0769	9	0.06365	T	0.9	0.0469	3.4203	0.07391	0.5219:0.1111:0.2544:0.1126	rs34562867;rs61644838	189	Q9H665	IGFR1_HUMAN	R	189	ENSP00000246532:W189R	ENSP00000246532:W189R	W	-	1	0	IGFLR1	40922607	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.954000	0.03873	-1.998000	0.00968	-2.826000	0.00107	TGG	T|0.000;G|0.091;A|0.909	0.091	strong		0.617	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660	
WDFY4	57705	hgsc.bcm.edu	37	10	50183042	50183042	+	Missense_Mutation	SNP	G	G	A	rs61733240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50183042G>A	ENST00000325239.5	+	57	9091	c.9064G>A	c.(9064-9066)Gcc>Acc	p.A3022T	RP11-523O18.5_ENST00000428825.4_RNA|WDFY4_ENST00000465910.1_3'UTR|WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	3022						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						CCGCCTGCCCGCCCATCGGGA	0.607													A|||	598	0.119409	0.2496	0.1239	5008	,	,		19367	0.006		0.0706	False		,,,				2504	0.1074				p.A3022T		Atlas-SNP	.											.	WDFY4	205	.	0			c.G9064A						PASS	.	A	THR/ALA	331,1053		41,249,402	60.0	65.0	64.0		9064	-1.2	0.0	10	dbSNP_129	64	202,2980		5,192,1394	yes	missense	WDFY4	NM_020945.1	58	46,441,1796	AA,AG,GG		6.3482,23.9162,11.6732	benign	3022/3185	50183042	533,4033	692	1591	2283	SO:0001583	missense	57705	exon58			CTGCCCGCCCATC	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.9064G>A	10.37:g.50183042G>A	ENSP00000320563:p.Ala3022Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	147	66	0.44898	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	215|215	0.09844322344322344|0.09844322344322344	120|120	0.24390243902439024|0.24390243902439024	43|43	0.11878453038674033|0.11878453038674033	4|4	0.006993006993006993|0.006993006993006993	48|48	0.0633245382585752|0.0633245382585752	A|A	8.330|8.330	0.826276|0.826276	0.16749|0.16749	0.239162|0.239162	0.063482|0.063482	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239;ENST00000544136|ENST00000312002	T|.	0.29142|.	1.58|.	5.61|5.61	-1.18|-1.18	0.09617|0.09617	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.590841|.	0.17291|.	N|.	0.179628|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38531|0.38531	1.155|1.155	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B|.	0.23591|.	0.013;0.088|.	B;B|.	0.10450|.	0.003;0.005|.	T|T	0.24977|0.24977	-1.0145|-1.0145	8|4	.|.	.|.	.|.	.|.	8.4404|8.4404	0.32812|0.32812	0.3567:0.0985:0.5448:0.0|0.3567:0.0985:0.5448:0.0	rs61733240|rs61733240	485;3022|.	B4DWY9;Q6ZS81|.	.;WDFY4_HUMAN|.	T|H	3022;3022;485|2112	ENSP00000320563:A3022T|.	.|.	A|R	+|+	1|2	0|0	WDFY4|WDFY4	49853048|49853048	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.003000|0.003000	0.03518|0.03518	0.572000|0.572000	0.23684|0.23684	-0.654000|-0.654000	0.05394|0.05394	-0.834000|-0.834000	0.03071|0.03071	GCC|CGC	G|0.901;A|0.099	0.099	strong		0.607	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
KLK2	3817	hgsc.bcm.edu	37	19	51381777	51381777	+	Missense_Mutation	SNP	C	C	T	rs198977	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51381777C>T	ENST00000325321.3	+	5	973	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W	KLK2_ENST00000391810.2_Missense_Mutation_p.R148W|KLK2_ENST00000358049.4_3'UTR			P20151	KLK2_HUMAN	kallikrein-related peptidase 2	250	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> W (in dbSNP:rs198977).		extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)		KLK2/ETV1(3)|KLK2/ETV4(2)	large_intestine(3)|lung(6)|ovary(1)|skin(1)	11		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.00871)		GGTGCATTACCGGAAGTGGAT	0.532			T	ETV4	prostate								C|||	1411	0.281749	0.4667	0.2752	5008	,	,		19114	0.1657		0.2833	False		,,,				2504	0.1544				p.R250W		Atlas-SNP	.		Dom	yes		19	19q13.41	3817	kallikrein-related peptidase 2		E	.	KLK2	66	.	0			c.C748T						PASS	.	C	,TRP/ARG	1879,2527	542.0+/-375.9	402,1075,726	206.0	191.0	196.0		,748	-7.1	0.0	19	dbSNP_79	196	2124,6476	364.7+/-333.6	272,1580,2448	yes	utr-3,missense	KLK2	NM_001002231.1,NM_005551.3	,101	674,2655,3174	TT,TC,CC		24.6977,42.6464,30.7781	,benign	,250/262	51381777	4003,9003	2203	4300	6503	SO:0001583	missense	3817	exon5			CATTACCGGAAGT	M18157	CCDS12808.1, CCDS42597.1, CCDS58675.1	19q13.33	2008-02-05	2006-10-27				3.4.21.35	"""Kallikreins"""	6363	protein-coding gene	gene with protein product		147960	"""kallikrein 2, prostatic"""			2468530, 16800724, 16800723	Standard	NM_005551		Approved		uc002ptv.3	P20151		ENST00000325321.3:c.748C>T	19.37:g.51381777C>T	ENSP00000313581:p.Arg250Trp	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_005551	B4DU93|B4DUB0|F5H8L3|Q15946|Q9UJZ9	Missense_Mutation	SNP	ENST00000325321.3	37	CCDS12808.1	632	0.2893772893772894	216	0.43902439024390244	102	0.281767955801105	108	0.1888111888111888	206	0.2717678100263852	C	9.421	1.083044	0.20309	0.426464	0.246977	ENSG00000167751	ENST00000325321;ENST00000391810	D;D	0.89050	-2.46;-2.46	3.54	-7.07	0.01563	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	4.259990	0.00732	N	0.000949	T	0.00012	0.0000	M	0.78916	2.43	0.80722	P	0.0	P;B	0.43477	0.808;0.235	B;B	0.26202	0.067;0.029	T	0.48502	-0.9030	9	0.56958	D	0.05	.	5.4122	0.16354	0.2251:0.1641:0.5237:0.0871	rs198977;rs3170124;rs57089040;rs198977	233;250	B4DU77;P20151	.;KLK2_HUMAN	W	250;148	ENSP00000313581:R250W;ENSP00000375686:R148W	ENSP00000313581:R250W	R	+	1	2	KLK2	56073589	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.634000	0.00108	-1.997000	0.00969	-0.217000	0.12591	CGG	C|0.708;T|0.292	0.292	strong		0.532	KLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464438.3	NM_005551.3	
MUC5B	727897	hgsc.bcm.edu	37	11	1266561	1266561	+	Silent	SNP	G	G	A	rs200970694	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1266561G>A	ENST00000529681.1	+	31	8509	c.8451G>A	c.(8449-8451)agG>agA	p.R2817R	MUC5B_ENST00000447027.1_Silent_p.R2820R|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2817	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)		CTAGCAGCAGGACCACCGAGT	0.682																																					p.R2817R		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.G8451A						scavenged	.						27.0	43.0	38.0					11																	1266561		1927	4011	5938	SO:0001819	synonymous_variant	727897	exon31			CAGCAGGACCACC	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.8451G>A	11.37:g.1266561G>A		Somatic	423	1	0.00236407		WXS	Illumina HiSeq	Phase_I	277	32	0.115523	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.989;A|0.011	0.011	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ANKLE2	23141	hgsc.bcm.edu	37	12	133331537	133331537	+	Missense_Mutation	SNP	G	G	A	rs1132375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:133331537G>A	ENST00000357997.5	-	2	453	c.364C>T	c.(364-366)Cac>Tac	p.H122Y	ANKLE2_ENST00000337516.5_Missense_Mutation_p.H122Y|ANKLE2_ENST00000539605.1_Missense_Mutation_p.H60Y	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	122			H -> Y (in dbSNP:rs1132375). {ECO:0000269|PubMed:15489334}.		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)		GCCTCATGGTGGTAGAAAGAA	0.463													G|||	1304	0.260383	0.087	0.2147	5008	,	,		18879	0.2421		0.4105	False		,,,				2504	0.3916				p.H122Y		Atlas-SNP	.											.	ANKLE2	76	.	0			c.C364T						PASS	.	G	TYR/HIS	487,3359		31,425,1467	66.0	66.0	66.0		364	3.2	0.0	12	dbSNP_86	66	3186,5088		592,2002,1543	yes	missense	ANKLE2	NM_015114.1	83	623,2427,3010	AA,AG,GG		38.5062,12.6625,30.3053	possibly-damaging	122/939	133331537	3673,8447	1923	4137	6060	SO:0001583	missense	23141	exon2			CATGGTGGTAGAA	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.364C>T	12.37:g.133331537G>A	ENSP00000350686:p.His122Tyr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	582	0.2664835164835165	54	0.10975609756097561	86	0.23756906077348067	128	0.22377622377622378	314	0.41424802110817943	G	10.64	1.407405	0.25378	0.126625	0.385062	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516	T;T;T	0.30981	1.94;1.93;1.51	5.18	3.23	0.37069	.	1.485960	0.03980	N	0.293112	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;P	0.44090	0.826;0.557	B;B	0.37480	0.251;0.132	T	0.38090	-0.9677	9	0.44086	T	0.13	-15.757	6.2722	0.20961	0.1782:0.3137:0.5081:0.0	rs1132375;rs3087780;rs3193087;rs52794671;rs56476922;rs60870365;rs1132375	122;122	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	Y	60;122;122	ENSP00000446268:H60Y;ENSP00000350686:H122Y;ENSP00000337651:H122Y	ENSP00000337651:H122Y	H	-	1	0	ANKLE2	131841610	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	0.656000	0.24948	1.193000	0.43086	0.650000	0.86243	CAC	G|0.716;A|0.284	0.284	strong		0.463	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
PIEZO1	9780	hgsc.bcm.edu	37	16	88779739	88779739	+	IGR	SNP	A	A	G	rs11549837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88779739A>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Missense_Mutation_p.M166V|CTU2_ENST00000453996.2_Missense_Mutation_p.M253V|CTU2_ENST00000567949.1_Missense_Mutation_p.M324V|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.M253V	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	82	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105405942	105405942	+	Silent	SNP	G	G	A	rs28454709	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	72	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	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	
DUSP27	92235	hgsc.bcm.edu	37	1	167096931	167096931	+	Missense_Mutation	SNP	A	A	C	rs267746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:167096931A>C	ENST00000361200.2	+	6	2729	c.2563A>C	c.(2563-2565)Aaa>Caa	p.K855Q	DUSP27_ENST00000271385.5_Missense_Mutation_p.K855Q|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.K855Q			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	855			K -> Q (in dbSNP:rs267746). {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						GTCTGAGTACAAAATGGAAAA	0.498													A|||	1016	0.202875	0.4138	0.1398	5008	,	,		22916	0.127		0.16	False		,,,				2504	0.0849				p.K855Q		Atlas-SNP	.											.	DUSP27	235	.	0			c.A2563C						PASS	.	A	GLN/LYS	1654,2752	503.5+/-365.6	319,1016,868	70.0	62.0	64.0		2563	3.0	1.0	1	dbSNP_79	64	1479,7121	281.4+/-295.0	128,1223,2949	yes	missense	DUSP27	NM_001080426.1	53	447,2239,3817	CC,CA,AA		17.1977,37.5397,24.0889	benign	855/1159	167096931	3133,9873	2203	4300	6503	SO:0001583	missense	92235	exon5			GAGTACAAAATGG	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.2563A>C	1.37:g.167096931A>C	ENSP00000354483:p.Lys855Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	434	0.1987179487179487	200	0.4065040650406504	53	0.1464088397790055	73	0.12762237762237763	108	0.1424802110817942	A	1.366	-0.587281	0.03799	0.375397	0.171977	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03242	4.0;4.0;4.0	5.47	2.98	0.34508	.	0.225631	0.36482	N	0.002580	T	0.01156	0.0038	L	0.39898	1.24	0.35006	P	0.24358400000000002	B	0.19706	0.038	B	0.13407	0.009	T	0.40289	-0.9571	9	0.09843	T	0.71	-21.8314	12.2843	0.54783	0.4647:0.5353:0.0:0.0	rs267746;rs59992554;rs267746	855	Q5VZP5	DUS27_HUMAN	Q	855	ENSP00000354483:K855Q;ENSP00000271385:K855Q;ENSP00000404874:K855Q	ENSP00000271385:K855Q	K	+	1	0	DUSP27	165363555	0.999000	0.42202	0.985000	0.45067	0.162000	0.22319	2.360000	0.44151	0.873000	0.35799	-0.485000	0.04761	AAA	A|0.780;C|0.220	0.220	strong		0.498	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
KANSL1	284058	hgsc.bcm.edu	37	17	44159849	44159849	+	Silent	SNP	T	T	C	rs17576165	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44159849T>C	ENST00000262419.6	-	4	1961	c.1491A>G	c.(1489-1491)ccA>ccG	p.P497P	KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.P497P|KANSL1_ENST00000572904.1_Silent_p.P497P|KANSL1_ENST00000575318.1_Silent_p.P497P|KANSL1_ENST00000432791.1_Silent_p.P497P	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	497					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CAGAACTAAGTGGAAGAAATA	0.428													C|||	432	0.086262	0.0151	0.1571	5008	,	,		20419	0.001		0.2406	False		,,,				2504	0.0613				p.P497P		Atlas-SNP	.											.	.	.	.	0			c.A1491G						PASS	.	C	,,	202,4204	807.5+/-415.9	5,192,2006	87.0	86.0	87.0		1491,1491,1491	-0.7	1.0	17	dbSNP_123	87	1928,6672	726.3+/-406.6	220,1488,2592	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	225,1680,4598	CC,CT,TT		22.4186,4.5847,16.3771	,,	497/1105,497/1106,497/1106	44159849	2130,10876	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon4			ACTAAGTGGAAGA	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.1491A>G	17.37:g.44159849T>C		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			T|0.854;C|0.146	0.146	strong		0.428	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
RBM33	155435	hgsc.bcm.edu	37	7	155531080	155531080	+	Missense_Mutation	SNP	A	A	G	rs3735576	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	73	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	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	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037579	33037579	+	Missense_Mutation	SNP	A	A	T	rs2308912|rs36013091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	167	0	0		WXS	Illumina HiSeq	Phase_I	134	48	0.358209	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	
CCDC38	120935	hgsc.bcm.edu	37	12	96312686	96312686	+	Missense_Mutation	SNP	C	C	A	rs12368787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:96312686C>A	ENST00000344280.3	-	3	663	c.106G>T	c.(106-108)Gtc>Ttc	p.V36F	CCDC38_ENST00000549752.1_5'Flank	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	36			V -> F (in dbSNP:rs12368787).							breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTTTCTTTGACAAGAAAGAGA	0.318													A|||	335	0.066893	0.0401	0.0749	5008	,	,		21521	0.0278		0.1372	False		,,,				2504	0.0654				p.V36F		Atlas-SNP	.											.	CCDC38	45	.	0			c.G106T						PASS	.	A	PHE/VAL	213,4191	806.9+/-415.9	4,205,1993	156.0	148.0	150.0		106	4.8	1.0	12	dbSNP_120	150	1070,7530	769.8+/-407.6	67,936,3297	yes	missense	CCDC38	NM_182496.2	50	71,1141,5290	AA,AC,CC		12.4419,4.8365,9.8662	benign	36/564	96312686	1283,11721	2202	4300	6502	SO:0001583	missense	120935	exon3			CTTTGACAAGAAA	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.106G>T	12.37:g.96312686C>A	ENSP00000345470:p.Val36Phe	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	134	55	0.410448	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	159	0.07280219780219781	24	0.04878048780487805	25	0.06906077348066299	10	0.017482517482517484	100	0.13192612137203166	A	3.234	-0.156872	0.06544	0.048365	0.124419	ENSG00000165972	ENST00000344280	T	0.26957	1.7	4.85	4.85	0.62838	.	0.267312	0.34777	N	0.003681	T	0.00073	0.0002	N	0.01168	-0.975	0.09310	P	0.9999999999622513	B	0.02656	0.0	B	0.01281	0.0	T	0.24476	-1.0159	9	0.12430	T	0.62	-4.2424	8.8974	0.35472	0.811:0.189:0.0:0.0	rs12368787;rs52827128;rs61694415;rs12368787	36	Q502W7	CCD38_HUMAN	F	36	ENSP00000345470:V36F	ENSP00000345470:V36F	V	-	1	0	CCDC38	94836817	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	2.491000	0.45303	0.983000	0.38602	-0.363000	0.07495	GTC	C|0.915;A|0.085	0.085	strong		0.318	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
ZNF236	7776	hgsc.bcm.edu	37	18	74672741	74672741	+	Silent	SNP	C	C	T	rs72987221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:74672741C>T	ENST00000253159.8	+	30	5541	c.5343C>T	c.(5341-5343)gcC>gcT	p.A1781A	ZNF236_ENST00000320610.9_Silent_p.A1783A	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1781					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)		ACAAGTGTGCCTACTGCGTCA	0.582													C|||	290	0.0579073	0.0477	0.036	5008	,	,		19084	0.0248		0.0497	False		,,,				2504	0.1299				p.A1781A		Atlas-SNP	.											.	ZNF236	325	.	0			c.C5343T						PASS	.	C		171,4011		1,169,1921	57.0	61.0	60.0		5343	-0.0	0.0	18	dbSNP_130	60	367,8115		5,357,3879	no	coding-synonymous	ZNF236	NM_007345.3		6,526,5800	TT,TC,CC		4.3268,4.089,4.2483		1781/1846	74672741	538,12126	2091	4241	6332	SO:0001819	synonymous_variant	7776	exon30			GTGTGCCTACTGC	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.5343C>T	18.37:g.74672741C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			C|0.955;T|0.045	0.045	strong		0.582	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
BMPER	168667	hgsc.bcm.edu	37	7	34085921	34085921	+	Missense_Mutation	SNP	G	G	A	rs74734392	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:34085921G>A	ENST00000297161.2	+	8	954	c.580G>A	c.(580-582)Ggc>Agc	p.G194S	BMPER_ENST00000426693.1_Missense_Mutation_p.G194S|BMPER_ENST00000494786.1_3'UTR	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	194	VWFC 3. {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						TTCTTAGGGAGGCAGGACACA	0.443													G|||	123	0.0245607	0.0136	0.0029	5008	,	,		19634	0.0893		0.008	False		,,,				2504	0.0051				p.G194S		Atlas-SNP	.											.	BMPER	131	.	0			c.G580A						PASS	.	G	SER/GLY	34,4372	39.2+/-71.8	0,34,2169	126.0	116.0	119.0		580	5.8	1.0	7	dbSNP_131	119	20,8580	14.0+/-48.4	0,20,4280	yes	missense	BMPER	NM_133468.3	56	0,54,6449	AA,AG,GG		0.2326,0.7717,0.4152	probably-damaging	194/686	34085921	54,12952	2203	4300	6503	SO:0001583	missense	168667	exon8			TAGGGAGGCAGGA		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.580G>A	7.37:g.34085921G>A	ENSP00000297161:p.Gly194Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	102	60	0.588235	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	37	CCDS5442.1	83	0.038003663003663	11	0.022357723577235773	1	0.0027624309392265192	63	0.11013986013986014	8	0.010554089709762533	G	31	5.060906	0.93846	0.007717	0.002326	ENSG00000164619	ENST00000297161;ENST00000426693	T;T	0.72835	-0.69;-0.69	5.78	5.78	0.91487	von Willebrand factor, type C (4);	0.000000	0.85682	D	0.000000	T	0.12050	0.0293	M	0.79926	2.475	0.09310	P	0.999999999282912	D	0.89917	1.0	D	0.77004	0.989	T	0.57854	-0.7739	9	0.46703	T	0.11	.	19.6126	0.95616	0.0:0.0:1.0:0.0	.	194	Q8N8U9	BMPER_HUMAN	S	194	ENSP00000297161:G194S;ENSP00000393950:G194S	ENSP00000297161:G194S	G	+	1	0	BMPER	34052446	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.290000	0.89925	2.730000	0.93505	0.650000	0.86243	GGC	G|0.987;A|0.013	0.013	strong		0.443	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
EIF4E	1977	hgsc.bcm.edu	37	4	99808254	99808254	+	Silent	SNP	G	G	A	rs62323192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:99808254G>A	ENST00000450253.2	-	5	1899	c.375C>T	c.(373-375)gaC>gaT	p.D125D	EIF4E_ENST00000505992.1_Silent_p.D125D|EIF4E_ENST00000280892.6_Silent_p.D145D|EIF4E_ENST00000504432.1_Silent_p.D153D	NM_001968.3	NP_001959.1	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	125					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of mitotic cell cycle (GO:0045931)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|mRNA cap binding complex (GO:0005845)|RISC complex (GO:0016442)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation initiation factor activity (GO:0003743)	p.D125D(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		AGCGATCGAGGTCACTTCGTC	0.383													G|||	548	0.109425	0.0144	0.1455	5008	,	,		21025	0.001		0.2734	False		,,,				2504	0.1554				p.D145D		Atlas-SNP	.											EIF4E,NS,carcinoma,0,1	EIF4E	18	1	1	Substitution - coding silent(1)	prostate(1)	c.C435T						PASS	.	G	,,	230,4176	136.1+/-172.1	7,216,1980	239.0	207.0	218.0		435,375,375	4.1	1.0	4	dbSNP_129	218	2472,6128	406.4+/-348.8	344,1784,2172	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4E	NM_001130678.1,NM_001130679.1,NM_001968.3	,,	351,2000,4152	AA,AG,GG		28.7442,5.2202,20.775	,,	145/238,125/249,125/218	99808254	2702,10304	2203	4300	6503	SO:0001819	synonymous_variant	1977	exon5			ATCGAGGTCACTT	M15353	CCDS34031.1, CCDS47109.1, CCDS54779.1	4q21-q25	2008-02-05			ENSG00000151247	ENSG00000151247			3287	protein-coding gene	gene with protein product		133440		EIF4EL1, EIF4F		9330633, 1916814	Standard	NM_001968		Approved	EIF4E1	uc011cea.1	P06730	OTTHUMG00000161090	ENST00000450253.2:c.375C>T	4.37:g.99808254G>A		Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	264	120	0.454545	NM_001130678	B7Z6V1|D6RCQ6|Q96E95	Silent	SNP	ENST00000450253.2	37	CCDS34031.1	271	0.12408424908424909	9	0.018292682926829267	54	0.14917127071823205	1	0.0017482517482517483	207	0.27308707124010556	G	10.27	1.303728	0.23736	0.052202	0.287442	ENSG00000151247	ENST00000511644	.	.	.	5.85	4.14	0.48551	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16129	-1.0413	3	.	.	.	-16.6535	9.8967	0.41322	0.2072:0.0:0.7928:0.0	rs62323192	.	.	.	S	122	.	.	P	-	1	0	EIF4E	100027277	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.700000	0.61803	0.823000	0.34589	0.557000	0.71058	CCT	G|0.819;A|0.181	0.181	strong		0.383	EIF4E-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363739.1	NM_001968	
DNAH5	1767	hgsc.bcm.edu	37	5	13867949	13867949	+	Silent	SNP	T	T	C	rs146191243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:13867949T>C	ENST00000265104.4	-	25	4091	c.3987A>G	c.(3985-3987)aaA>aaG	p.K1329K	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1329	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)					TAATAAGCTCTTTCTTGAAAC	0.453									Kartagener syndrome				T|||	16	0.00319489	0.0	0.0058	5008	,	,		17132	0.0		0.008	False		,,,				2504	0.0041				p.K1329K		Atlas-SNP	.											.	DNAH5	868	.	0			c.A3987G						PASS	.	T		12,4394	19.1+/-41.9	1,10,2192	131.0	124.0	126.0		3987	-0.1	1.0	5	dbSNP_134	126	158,8442	74.5+/-137.1	0,158,4142	no	coding-synonymous	DNAH5	NM_001369.2		1,168,6334	CC,CT,TT		1.8372,0.2724,1.3071		1329/4625	13867949	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon25	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AAGCTCTTTCTTG	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.3987A>G	5.37:g.13867949T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	174	96	0.551724	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.990;C|0.010	0.010	strong		0.453	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
FUK	197258	hgsc.bcm.edu	37	16	70506907	70506907	+	Silent	SNP	T	T	C	rs7192865	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70506907T>C	ENST00000288078.6	+	15	1660	c.1428T>C	c.(1426-1428)ccT>ccC	p.P476P	FUK_ENST00000378912.2_Silent_p.P508P|FUK_ENST00000571514.1_5'UTR	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	476						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)	p.P476P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				TGTGGGACCCTGAGACGCTGC	0.647													C|||	2895	0.578075	0.7821	0.5764	5008	,	,		15962	0.6607		0.498	False		,,,				2504	0.3006				p.P476P		Atlas-SNP	.											FUK,NS,carcinoma,0,1	FUK	72	1	1	Substitution - coding silent(1)	prostate(1)	c.T1428C						PASS	.	C		3008,986		1159,690,148	11.0	16.0	15.0		1428	-2.7	0.9	16	dbSNP_116	15	4055,4293		1019,2017,1138	no	coding-synonymous	FUK	NM_145059.2		2178,2707,1286	CC,CT,TT		48.5745,24.687,42.7726		476/1085	70506907	7063,5279	1997	4174	6171	SO:0001819	synonymous_variant	197258	exon15			GGACCCTGAGACG		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.1428T>C	16.37:g.70506907T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	113	112	0.99115	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Silent	SNP	ENST00000288078.6	37	CCDS10891.2																																																																																			T|0.402;C|0.598	0.598	strong		0.647	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
MRPL23	6150	hgsc.bcm.edu	37	11	1977552	1977552	+	Missense_Mutation	SNP	G	G	A	rs12812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1977552G>A	ENST00000397298.3	+	5	449	c.364G>A	c.(364-366)Gct>Act	p.A122T	MRPL23_ENST00000381514.3_Intron|MRPL23_ENST00000381519.1_Missense_Mutation_p.A122T|MRPL23_ENST00000397294.3_Intron|MRPL23_ENST00000397297.3_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	39	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	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	
GNAZ	2781	hgsc.bcm.edu	37	22	23438191	23438191	+	Silent	SNP	C	C	T	rs1805058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:23438191C>T	ENST00000248996.4	+	2	975	c.309C>T	c.(307-309)gaC>gaT	p.D103D	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	103					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|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)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)	p.D103D(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		GCGCCTACGACGCTGTGCAGC	0.667													c|||	1222	0.24401	0.1286	0.3516	5008	,	,		16223	0.3601		0.2495	False		,,,				2504	0.1984				p.D103D		Atlas-SNP	.											GNAZ,NS,carcinoma,0,2	GNAZ	45	2	1	Substitution - coding silent(1)	prostate(1)	c.C309T						PASS	.	T	,	671,3735	281.1+/-275.7	46,579,1578	87.0	94.0	92.0		309,	-9.2	0.1	22	dbSNP_89	92	2257,6341	377.7+/-338.6	304,1649,2346	no	coding-synonymous,intron	GNAZ,RTDR1	NM_002073.2,NM_014433.2	,	350,2228,3924	TT,TC,CC		26.2503,15.2292,22.5161	,	103/356,	23438191	2928,10076	2203	4299	6502	SO:0001819	synonymous_variant	2781	exon2			CTACGACGCTGTG		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.309C>T	22.37:g.23438191C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	27	0.72973	NM_002073	B2R6C1|Q4QRJ6	Silent	SNP	ENST00000248996.4	37	CCDS13804.1																																																																																			C|0.762;T|0.238	0.238	strong		0.667	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073	
TTLL6	284076	hgsc.bcm.edu	37	17	46878625	46878625	+	Silent	SNP	A	A	G	rs17634167	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:46878625A>G	ENST00000393382.3	-	5	744	c.603T>C	c.(601-603)ctT>ctC	p.L201L		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						ACTCAGCAGGAAGACACCAGG	0.542													A|||	280	0.0559105	0.0295	0.0648	5008	,	,		18470	0.0446		0.1213	False		,,,				2504	0.0297				p.L201L		Atlas-SNP	.											.	TTLL6	113	.	0			c.T603C						PASS	.	A		63,1321		0,63,629	90.0	95.0	94.0		603	-1.1	1.0	17	dbSNP_123	94	437,2745		33,371,1187	no	coding-synonymous	TTLL6	NM_001130918.1		33,434,1816	GG,GA,AA		13.7335,4.552,10.9505		201/892	46878625	500,4066	692	1591	2283	SO:0001819	synonymous_variant	284076	exon5			AGCAGGAAGACAC	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.603T>C	17.37:g.46878625A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_001130918		Silent	SNP	ENST00000393382.3	37	CCDS45724.1																																																																																			A|0.923;G|0.077	0.077	strong		0.542	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
SPATA16	83893	hgsc.bcm.edu	37	3	172835290	172835290	+	Missense_Mutation	SNP	C	C	T	rs1515441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	301	0	0		WXS	Illumina HiSeq	Phase_I	283	142	0.501767	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	
LEPR	3953	hgsc.bcm.edu	37	1	66036441	66036441	+	Missense_Mutation	SNP	A	A	G	rs1137100	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:66036441A>G	ENST00000349533.6	+	4	511	c.326A>G	c.(325-327)aAg>aGg	p.K109R	LEPR_ENST00000406510.3_5'UTR|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371060.3_Missense_Mutation_p.K109R|snoU13_ENST00000459362.1_RNA|LEPR_ENST00000371059.3_Missense_Mutation_p.K109R|LEPR_ENST00000344610.8_Missense_Mutation_p.K109R|LEPR_ENST00000371058.1_Missense_Mutation_p.K109R	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		ATTGAAGGAAAGACATTTGTT	0.318													A|||	1604	0.320288	0.1528	0.2378	5008	,	,		18463	0.8046		0.2704	False		,,,				2504	0.1575				p.K109R		Atlas-SNP	.											.	LEPR	284	.	0			c.A326G	GRCh37	CM032948	LEPR	M	rs1137100	PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	762,3644	301.0+/-286.6	58,646,1499	65.0	66.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	326,326,326,326,326,326	4.6	0.9	1	dbSNP_86	65	2273,6327	377.6+/-338.6	304,1665,2331	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	26,26,26,26,26,26	362,2311,3830	GG,GA,AA		26.4302,17.2946,23.3354	benign,benign,benign,benign,benign,benign	109/897,109/959,109/959,109/907,109/897,109/1166	66036441	3035,9971	2203	4300	6503	SO:0001583	missense	3953	exon4			AAGGAAAGACATT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.326A>G	1.37:g.66036441A>G	ENSP00000330393:p.Lys109Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	841	0.3850732600732601	63	0.12804878048780488	96	0.26519337016574585	464	0.8111888111888111	218	0.287598944591029	A	11.95	1.792657	0.31685	0.172946	0.264302	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.59906	0.27;0.26;0.29;0.23;0.27	5.69	4.55	0.56014	.	0.204186	0.43260	D	0.000583	T	0.50188	0.1601	L	0.53249	1.67	0.09310	P	0.999999999901199	D;B;B;D	0.61697	0.971;0.077;0.204;0.99	P;B;B;P	0.59056	0.725;0.021;0.084;0.851	T	0.50206	-0.8855	9	0.20519	T	0.43	-5.8543	8.8143	0.34987	0.9121:0.0:0.0879:0.0	rs1137100;rs1805092;rs3200841;rs3790430;rs17127718;rs17356583;rs17434225;rs59932898;rs1137100	109;109;109;109	P48357-4;P48357;P48357-2;P48357-3	.;LEPR_HUMAN;.;.	R	109	ENSP00000340884:K109R;ENSP00000330393:K109R;ENSP00000360099:K109R;ENSP00000360098:K109R;ENSP00000360097:K109R	ENSP00000340884:K109R	K	+	2	0	LEPR	65809029	0.986000	0.35501	0.871000	0.34182	0.808000	0.45660	2.343000	0.44001	2.167000	0.68274	0.455000	0.32223	AAG	A|0.705;G|0.295	0.295	strong		0.318	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465389	39465389	+	Silent	SNP	T	T	A	rs12451604	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	106	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	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	
LRBA	987	hgsc.bcm.edu	37	4	151388906	151388906	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:151388906T>C	ENST00000357115.3	-	45	6975	c.6732A>G	c.(6730-6732)ccA>ccG	p.P2244P	LRBA_ENST00000510413.1_Silent_p.P2233P|LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000535741.1_Silent_p.P2233P|LRBA_ENST00000507224.1_Silent_p.P2233P	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2244	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AAGGAAACACTGGATACTGAT	0.323																																					p.P2244P		Atlas-SNP	.											.	LRBA	253	.	0			c.A6732G						PASS	.						117.0	110.0	113.0					4																	151388906		2203	4297	6500	SO:0001819	synonymous_variant	987	exon45			AAACACTGGATAC	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.6732A>G	4.37:g.151388906T>C		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	241	101	0.419087	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.283943	0.23392	.	.	ENSG00000198589	ENST00000509835	.	.	.	4.98	-2.12	0.07165	.	.	.	.	.	T	0.51143	0.1657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47129	-0.9141	4	.	.	.	.	7.1251	0.25467	0.4743:0.0795:0.0:0.4462	.	.	.	.	R	886	.	.	Q	-	2	0	LRBA	151608356	0.547000	0.26465	0.999000	0.59377	0.998000	0.95712	-0.270000	0.08584	-0.014000	0.14175	0.477000	0.44152	CAG	.	.	none		0.323	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
EGLN1	54583	hgsc.bcm.edu	37	1	231557164	231557164	+	Missense_Mutation	SNP	C	C	G	rs61750991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:231557164C>G	ENST00000366641.3	-	1	3626	c.471G>C	c.(469-471)caG>caC	p.Q157H	EGLN1_ENST00000476717.1_5'Flank	NM_022051.2	NP_071334.1			egl-9 family hypoxia-inducible factor 1											breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	16		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)				TCGCCTTCTCCTGGAACAGCG	0.766													C|||	33	0.00658946	0.0	0.0029	5008	,	,		9987	0.001		0.0268	False		,,,				2504	0.0031				p.Q157H		Atlas-SNP	.											.	EGLN1	38	.	0			c.G471C						PASS	.	C	HIS/GLN	17,3709		0,17,1846	6.0	6.0	6.0		471	-2.4	0.0	1	dbSNP_129	6	157,7197		2,153,3522	yes	missense	EGLN1	NM_022051.2	24	2,170,5368	GG,GC,CC		2.1349,0.4563,1.5704	possibly-damaging	157/427	231557164	174,10906	1863	3677	5540	SO:0001583	missense	54583	exon1			CTTCTCCTGGAAC	AJ310543	CCDS1595.1	1q42.1	2013-08-21	2013-08-21	2001-08-24	ENSG00000135766	ENSG00000135766		"""Zinc fingers, MYND-type"""	1232	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 2"""	606425	"""EGL nine (C.elegans) homolog 1"", ""egl nine homolog 1 (C. elegans)"""	C1orf12		11056053	Standard	NM_022051		Approved	SM-20, PHD2, ZMYND6, HIFPH2	uc001huv.2	Q9GZT9	OTTHUMG00000038027	ENST00000366641.3:c.471G>C	1.37:g.231557164C>G	ENSP00000355601:p.Gln157His	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	13	11	0.846154	NM_022051		Missense_Mutation	SNP	ENST00000366641.3	37	CCDS1595.1	27	0.012362637362637362	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	14.92	2.680157	0.47886	0.004563	0.021349	ENSG00000135766	ENST00000366641	D	0.86164	-2.08	4.06	-2.39	0.06602	.	.	.	.	.	T	0.49201	0.1543	N	0.14661	0.345	0.09310	N	1	B	0.30664	0.289	B	0.28916	0.096	T	0.53788	-0.8389	9	0.38643	T	0.18	0.2922	5.8621	0.18754	0.1263:0.41:0.3885:0.0752	rs61750991	157	Q9GZT9	EGLN1_HUMAN	H	157	ENSP00000355601:Q157H	ENSP00000355601:Q157H	Q	-	3	2	EGLN1	229623787	0.007000	0.16637	0.000000	0.03702	0.015000	0.08874	0.147000	0.16202	-0.278000	0.09180	0.557000	0.71058	CAG	C|0.988;G|0.012	0.012	strong		0.766	EGLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092879.1	NM_022051	
POU2F3	25833	hgsc.bcm.edu	37	11	120175749	120175749	+	Missense_Mutation	SNP	A	A	G	rs7110845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:120175749A>G	ENST00000543440.2	+	7	605	c.455A>G	c.(454-456)cAc>cGc	p.H152R	POU2F3_ENST00000260264.4_Missense_Mutation_p.H154R	NM_014352.3	NP_055167.2	Q9UKI9	PO2F3_HUMAN	POU class 2 homeobox 3	152			H -> R (in dbSNP:rs7110845). {ECO:0000269|PubMed:10473598, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|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)|sequence-specific DNA binding (GO:0043565)			large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)	17		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)		GCATTTGGGCACCCTGGGCTG	0.463													G|||	4158	0.830272	0.9682	0.7104	5008	,	,		15168	0.9405		0.5567	False		,,,				2504	0.8967				p.H154R		Atlas-SNP	.											POU2F3,NS,carcinoma,+1,1	POU2F3	44	1	0			c.A461G						PASS	.	G	ARG/HIS	3928,478	223.3+/-239.8	1761,406,36	60.0	65.0	63.0		455	6.2	1.0	11	dbSNP_116	63	4949,3649	524.7+/-380.6	1404,2141,754	yes	missense	POU2F3	NM_014352.3	29	3165,2547,790	GG,GA,AA		42.4401,10.8488,31.7364	benign	152/437	120175749	8877,4127	2203	4299	6502	SO:0001583	missense	25833	exon7			TTGGGCACCCTGG	AF133895	CCDS8431.1, CCDS58190.1	11q23.3	2011-06-20	2007-07-13		ENSG00000137709	ENSG00000137709		"""Homeoboxes / POU class"""	19864	protein-coding gene	gene with protein product		607394	"""POU domain class 2, transcription factor 3"""			10473598	Standard	NM_014352		Approved	OCT11, PLA-1, Skn-1a, Epoc-1	uc021qrk.1	Q9UKI9	OTTHUMG00000166140	ENST00000543440.2:c.455A>G	11.37:g.120175749A>G	ENSP00000441687:p.His152Arg	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	129	125	0.968992	NM_001244682	A8K7H8|B4DY07|F5GWW6|Q3MIY3|Q9UKR7|Q9Y504	Missense_Mutation	SNP	ENST00000543440.2	37	CCDS8431.1	1663	0.7614468864468864	469	0.9532520325203252	236	0.6519337016574586	535	0.9353146853146853	423	0.558047493403694	G	8.445	0.851801	0.17034	0.891512	0.575599	ENSG00000137709	ENST00000543440;ENST00000260264;ENST00000533620	D;D;D	0.82619	-1.52;-1.51;-1.63	6.17	6.17	0.99709	.	0.100339	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00621	-1.32	0.49130	P	2.48000000000026E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43940	-0.9360	9	0.02654	T	1	.	15.8587	0.79005	0.0644:0.0:0.9356:0.0	rs7110845;rs52834965;rs58648072;rs7110845	106;152	E9PIN6;Q9UKI9	.;PO2F3_HUMAN	R	154;152;106	ENSP00000441687:H154R;ENSP00000260264:H152R;ENSP00000435738:H106R	ENSP00000260264:H152R	H	+	2	0	POU2F3	119680959	1.000000	0.71417	0.996000	0.52242	0.789000	0.44602	7.551000	0.82182	1.644000	0.50603	-0.119000	0.15052	CAC	A|0.260;G|0.740	0.740	strong		0.463	POU2F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388039.2		
TAS2R14	50840	hgsc.bcm.edu	37	12	11091693	11091693	+	Silent	SNP	T	T	A	rs7138535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:11091693T>A	ENST00000537503.1	-	1	169	c.114A>T	c.(112-114)ggA>ggT	p.G38G	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_023922.1	NP_076411.1	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	38					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)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	8						AGATCTTTCTTCCCTTGACCC	0.378													T|||	1117	0.223043	0.2337	0.2911	5008	,	,		20154	0.2073		0.2147	False		,,,				2504	0.1851				p.G38G		Atlas-SNP	.											.	TAS2R14	26	.	0			c.A114T						PASS	.	T		984,3422	364.6+/-317.1	116,752,1335	68.0	67.0	67.0		114	-1.9	0.0	12	dbSNP_116	67	2072,6528	352.1+/-328.5	259,1554,2487	no	coding-synonymous	TAS2R14	NM_023922.1		375,2306,3822	AA,AT,TT		24.093,22.3332,23.4968		38/318	11091693	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	50840	exon1			CTTTCTTCCCTTG	AF227138	CCDS8637.1	12p13	2012-08-22			ENSG00000212127	ENSG00000212127		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14920	protein-coding gene	gene with protein product		604790				10761934, 10766242	Standard	NM_023922		Approved	T2R14, TRB1	uc010shi.2	Q9NYV8	OTTHUMG00000162720	ENST00000537503.1:c.114A>T	12.37:g.11091693T>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	71	46	0.647887	NM_023922	Q645X3	Silent	SNP	ENST00000537503.1	37	CCDS8637.1																																																																																			T|0.766;A|0.234	0.234	strong		0.378	TAS2R14-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370194.4	NM_023922	
ITGB8	3696	hgsc.bcm.edu	37	7	20421490	20421490	+	Silent	SNP	T	T	C	rs2230398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20421490T>C	ENST00000222573.4	+	6	1626	c.942T>C	c.(940-942)taT>taC	p.Y314Y	ITGB8_ENST00000537992.1_Silent_p.Y179Y	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	314	VWFA.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)	p.Y314Y(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						ACAACGTCTATGTCAAATCGA	0.398													C|||	1687	0.336861	0.3336	0.2579	5008	,	,		17840	0.4097		0.4493	False		,,,				2504	0.2065				p.Y314Y		Atlas-SNP	.											ITGB8_ENST00000222573,NS,carcinoma,0,1	ITGB8	159	1	1	Substitution - coding silent(1)	stomach(1)	c.T942C						PASS	.	C		1589,2817	666.0+/-401.6	289,1011,903	133.0	115.0	121.0		942	-0.4	0.9	7	dbSNP_116	121	3733,4867	618.2+/-396.8	804,2125,1371	no	coding-synonymous	ITGB8	NM_002214.2		1093,3136,2274	CC,CT,TT		43.407,36.0645,40.9196		314/770	20421490	5322,7684	2203	4300	6503	SO:0001819	synonymous_variant	3696	exon6			CGTCTATGTCAAA		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.942T>C	7.37:g.20421490T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_002214	A4D133|B4DHD4	Silent	SNP	ENST00000222573.4	37	CCDS5370.1																																																																																			A|0.000;C|0.395;G|0.000;T|0.605	0.395	strong		0.398	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	
TTYH2	94015	hgsc.bcm.edu	37	17	72233559	72233559	+	Missense_Mutation	SNP	G	G	A	rs62621376	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72233559G>A	ENST00000269346.4	+	4	615	c.541G>A	c.(541-543)Gtt>Att	p.V181I	TTYH2_ENST00000529107.1_Missense_Mutation_p.V160I	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	181				V -> I (in Ref. 1; AAL16784 and 2; BAC03579). {ECO:0000305}.		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						GGCGGGCAGCGTTGTTGTTCA	0.592													G|||	1112	0.222045	0.3517	0.1455	5008	,	,		16521	0.0298		0.2147	False		,,,				2504	0.3067				p.V181I		Atlas-SNP	.											.	TTYH2	63	.	0			c.G541A						PASS	.	G	ILE/VAL	1447,2959	469.2+/-355.4	231,985,987	81.0	74.0	76.0		541	-2.0	0.0	17	dbSNP_129	76	2040,6560	356.4+/-330.3	259,1522,2519	yes	missense	TTYH2	NM_032646.5	29	490,2507,3506	AA,AG,GG		23.7209,32.8416,26.8107	benign	181/535	72233559	3487,9519	2203	4300	6503	SO:0001583	missense	94015	exon4			GGCAGCGTTGTTG		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.541G>A	17.37:g.72233559G>A	ENSP00000269346:p.Val181Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	105	37	0.352381	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	420	0.19230769230769232	175	0.3556910569105691	50	0.13812154696132597	19	0.033216783216783216	176	0.23218997361477572	G	2.510	-0.313099	0.05422	0.328416	0.237209	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.10960	2.82;2.82	5.52	-2.01	0.07410	.	0.321536	0.33772	N	0.004572	T	0.00012	0.0000	N	0.04043	-0.29	0.09310	P	0.9999999999999724	B;B	0.30021	0.087;0.265	B;B	0.27262	0.028;0.078	T	0.46596	-0.9180	9	0.15066	T	0.55	-26.4556	11.549	0.50711	0.6651:0.0:0.3349:0.0	rs62621376	160;181	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	I	181;160	ENSP00000269346:V181I;ENSP00000433089:V160I	ENSP00000269346:V181I	V	+	1	0	TTYH2	69745154	0.667000	0.27484	0.001000	0.08648	0.001000	0.01503	1.290000	0.33319	-0.453000	0.07076	-1.110000	0.02074	GTT	G|0.751;A|0.249	0.249	strong		0.592	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
LAMC1	3915	hgsc.bcm.edu	37	1	182993025	182993025	+	Silent	SNP	C	C	T	rs10911194	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:182993025C>T	ENST00000258341.4	+	1	431	c.174C>T	c.(172-174)gcC>gcT	p.A58A		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	58	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TCAACGCCGCCTTCAACGTGA	0.697													C|||	2602	0.519569	0.3192	0.611	5008	,	,		11827	0.628		0.5338	False		,,,				2504	0.5992				p.A58A		Atlas-SNP	.											.	LAMC1	176	.	0			c.C174T						PASS	.	C		1571,2835	469.6+/-355.5	304,963,936	32.0	34.0	33.0		174	4.2	1.0	1	dbSNP_120	33	4679,3921	588.7+/-392.4	1223,2233,844	no	coding-synonymous	LAMC1	NM_002293.3		1527,3196,1780	TT,TC,CC		45.593,35.6559,48.0547		58/1610	182993025	6250,6756	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon1			CGCCGCCTTCAAC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.174C>T	1.37:g.182993025C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			C|0.512;T|0.488	0.488	strong		0.697	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
CD8A	925	hgsc.bcm.edu	37	2	87017662	87017662	+	Silent	SNP	G	G	T	rs2229239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:87017662G>T	ENST00000409511.2	-	5	1222	c.192C>A	c.(190-192)gcC>gcA	p.A64A	CD8A_ENST00000456996.2_Silent_p.A64A|CD8A_ENST00000283635.3_Silent_p.A64A|CD8A_ENST00000352580.3_Silent_p.A64A|CD8A_ENST00000538832.1_Silent_p.A105A|CD8A_ENST00000409781.1_Silent_p.A64A	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	64	Ig-like V-type.				antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	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)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						TGGGACTGGCGGCGGCGCCGC	0.672													G|||	183	0.0365415	0.0696	0.0288	5008	,	,		10342	0.0		0.0626	False		,,,				2504	0.0082				p.A64A		Atlas-SNP	.											.	CD8A	28	.	0			c.C192A						PASS	.	G	,,	346,4056		17,312,1872	38.0	47.0	44.0		192,192,192	1.7	0.0	2	dbSNP_98	44	647,7947		25,597,3675	no	coding-synonymous,coding-synonymous,coding-synonymous	CD8A	NM_001145873.1,NM_001768.6,NM_171827.3	,,	42,909,5547	TT,TG,GG		7.5285,7.8601,7.6408	,,	64/236,64/236,64/199	87017662	993,12003	2201	4297	6498	SO:0001819	synonymous_variant	925	exon5			ACTGGCGGCGGCG		CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1706	protein-coding gene	gene with protein product		186910	"""CD8 antigen, alpha polypeptide (p32)"", ""T-cell surface glycoprotein CD8 alpha chain"""	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.192C>A	2.37:g.87017662G>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_001145873	B4DT80|D6W5M8|Q13970|Q4ZG17	Silent	SNP	ENST00000409511.2	37	CCDS1992.1																																																																																			G|0.932;T|0.068	0.068	strong		0.672	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768	
AP3D1	8943	hgsc.bcm.edu	37	19	2138654	2138654	+	Silent	SNP	T	T	G	rs25672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2138654T>G	ENST00000345016.5	-	2	387	c.156A>C	c.(154-156)atA>atC	p.I52I	AP3D1_ENST00000356926.4_Silent_p.I52I|AP3D1_ENST00000350812.6_Silent_p.I52I|AP3D1_ENST00000355272.6_Silent_p.I52I	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	52					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)		CCTTCACCGCTATGTTGTCCT	0.522													G|||	1184	0.236422	0.1127	0.2911	5008	,	,		21431	0.1994		0.4453	False		,,,				2504	0.1881				p.I52I		Atlas-SNP	.											.	AP3D1	81	.	0			c.A156C						PASS	.	G	,	708,3638		83,542,1548	150.0	152.0	151.0		156,156	-3.4	0.6	19	dbSNP_72	151	3636,4882		782,2072,1405	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	865,2614,2953	GG,GT,TT		42.6861,16.2908,33.7687	,	52/1113,52/1154	2138654	4344,8520	2173	4259	6432	SO:0001819	synonymous_variant	8943	exon2			CACCGCTATGTTG	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.156A>C	19.37:g.2138654T>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			T|0.695;G|0.304;N|0.000;A|0.000	0.304	strong		0.522	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
CD22	933	hgsc.bcm.edu	37	19	35836530	35836530	+	Missense_Mutation	SNP	G	G	A	rs10406069	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:35836530G>A	ENST00000085219.5	+	12	2300	c.2234G>A	c.(2233-2235)gGc>gAc	p.G745D	CD22_ENST00000419549.2_Missense_Mutation_p.G573D|CD22_ENST00000594250.1_Missense_Mutation_p.G568D|CD22_ENST00000270311.6_Intron|MIR5196_ENST00000578146.1_RNA|CD22_ENST00000536635.2_Missense_Mutation_p.G657D|CD22_ENST00000341773.6_Missense_Mutation_p.G568D|CD22_ENST00000544992.2_Intron	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	745			G -> D (in dbSNP:rs10406069). {ECO:0000269|PubMed:10079291}.		cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CTCTCTGAAGGCCCCCACTCC	0.577													G|||	625	0.1248	0.0514	0.1311	5008	,	,		17429	0.2153		0.1849	False		,,,				2504	0.0644				p.G745D	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.G2234A						PASS	.	G	ASP/GLY,,ASP/GLY,ASP/GLY	314,4092	168.3+/-199.2	12,290,1901	106.0	86.0	92.0		1970,,1703,2234	-1.4	0.0	19	dbSNP_119	92	1781,6819	323.2+/-315.9	193,1395,2712	yes	missense,intron,missense,missense	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	94,,94,94	205,1685,4613	AA,AG,GG		20.7093,7.1266,16.108	benign,,benign,benign	657/760,,568/671,745/848	35836530	2095,10911	2203	4300	6503	SO:0001583	missense	933	exon12			CTGAAGGCCCCCA	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.2234G>A	19.37:g.35836530G>A	ENSP00000085219:p.Gly745Asp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_001771	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	37	CCDS12457.1	315	0.14423076923076922	14	0.028455284552845527	51	0.1408839779005525	111	0.19405594405594406	139	0.18337730870712401	G	11.00	1.510191	0.27036	0.071266	0.207093	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000419549	T;T;T;T	0.56444	0.97;0.55;0.46;1.08	4.68	-1.39	0.08997	.	0.819353	0.10554	N	0.661060	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.30664	0.289;0.021;0.034;0.082	B;B;B;B	0.26517	0.07;0.016;0.01;0.039	T	0.11421	-1.0588	9	0.49607	T	0.09	.	4.9823	0.14172	0.2281:0.4116:0.3603:0.0	rs10406069;rs58427269;rs10406069	573;657;745;568	Q32M46;F5H7U3;P20273;P20273-2	.;.;CD22_HUMAN;.	D	745;657;568;573	ENSP00000085219:G745D;ENSP00000442279:G657D;ENSP00000339349:G568D;ENSP00000403822:G573D	ENSP00000085219:G745D	G	+	2	0	CD22	40528370	0.002000	0.14202	0.011000	0.14972	0.087000	0.18053	-0.119000	0.10676	0.100000	0.17581	0.462000	0.41574	GGC	G|0.855;A|0.145	0.145	strong		0.577	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
KRT77	374454	hgsc.bcm.edu	37	12	53086645	53086645	+	Missense_Mutation	SNP	G	G	A	rs3782489	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53086645G>A	ENST00000341809.3	-	6	1128	c.1100C>T	c.(1099-1101)aCg>aTg	p.T367M	RP11-641A6.3_ENST00000547533.1_RNA|KRT77_ENST00000537195.1_Missense_Mutation_p.T134M	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	367	Coil 2.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						TCTCCCTGCCGTGATCTGGAG	0.587													G|||	1900	0.379393	0.4584	0.3703	5008	,	,		20084	0.245		0.3499	False		,,,				2504	0.4479				p.T367M		Atlas-SNP	.											.	KRT77	58	.	0			c.C1100T						PASS	.	G	MET/THR	1850,2554		392,1066,744	145.0	105.0	118.0		1100	1.4	0.0	12	dbSNP_107	118	3151,5391		728,1695,1848	yes	missense	KRT77	NM_175078.2	81	1120,2761,2592	AA,AG,GG		36.8883,42.0073,38.6297	probably-damaging	367/579	53086645	5001,7945	2202	4271	6473	SO:0001583	missense	374454	exon6			CCTGCCGTGATCT	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.1100C>T	12.37:g.53086645G>A	ENSP00000342710:p.Thr367Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	209	209	1	NM_175078	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	729	0.33379120879120877	211	0.42886178861788615	119	0.3287292817679558	128	0.22377622377622378	271	0.3575197889182058	G	16.26	3.073422	0.55646	0.420073	0.368883	ENSG00000189182	ENST00000341809;ENST00000537195	D;D	0.89196	-2.48;-1.64	3.44	1.41	0.22369	Filament (1);	.	.	.	.	T	0.00012	0.0000	M	0.92367	3.3	0.80722	P	0.0	D	0.76494	0.999	D	0.69479	0.964	T	0.00010	-1.2454	8	0.72032	D	0.01	.	8.8356	0.35111	0.2067:0.0:0.7933:0.0	rs3782489;rs58781522;rs3782489	367	Q7Z794	K2C1B_HUMAN	M	367;134	ENSP00000342710:T367M;ENSP00000440803:T134M	ENSP00000342710:T367M	T	-	2	0	KRT77	51372912	0.002000	0.14202	0.000000	0.03702	0.359000	0.29487	1.188000	0.32102	0.371000	0.24564	0.456000	0.33151	ACG	G|0.631;A|0.369	0.369	strong		0.587	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
TGFBR3	7049	hgsc.bcm.edu	37	1	92185657	92185657	+	Silent	SNP	C	C	T	rs1805112	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:92185657C>T	ENST00000525962.1	-	8	1267	c.1206G>A	c.(1204-1206)ccG>ccA	p.P402P	TGFBR3_ENST00000370399.2_Silent_p.P401P|TGFBR3_ENST00000212355.4_Silent_p.P402P			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	402					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)		GGAAAGGAAACGGAAGGCCTC	0.577													G|||	2034	0.40615	0.2814	0.2824	5008	,	,		18343	0.5308		0.4592	False		,,,				2504	0.4796				p.P402P		Atlas-SNP	.											TGFBR3,bladder,carcinoma,-1,1	TGFBR3	103	1	0			c.G1206A						PASS	.	G	,,	1398,3008		213,972,1018	61.0	63.0	63.0		1203,1203,1206	0.2	1.0	1	dbSNP_89	63	3566,5034		754,2058,1488	no	coding-synonymous,coding-synonymous,coding-synonymous	TGFBR3	NM_001195683.1,NM_001195684.1,NM_003243.4	,,	967,3030,2506	TT,TC,CC		41.4651,31.7295,38.167	,,	401/851,401/851,402/852	92185657	4964,8042	2203	4300	6503	SO:0001819	synonymous_variant	7049	exon9			AGGAAACGGAAGG	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.1206G>A	1.37:g.92185657C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_003243	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Silent	SNP	ENST00000525962.1	37	CCDS30770.1																																																																																			C|0.620;T|0.380	0.380	strong		0.577	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243	
ZNF407	55628	hgsc.bcm.edu	37	18	72344553	72344553	+	Silent	SNP	G	G	A	rs7227391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:72344553G>A	ENST00000299687.5	+	1	1578	c.1578G>A	c.(1576-1578)acG>acA	p.T526T	ZNF407_ENST00000582337.1_Silent_p.T526T|ZNF407_ENST00000577538.1_Silent_p.T526T|ZNF407_ENST00000309902.6_Silent_p.T526T	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	526					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GCTCTCAGACGTTGTGTGCTT	0.542													G|||	341	0.0680911	0.112	0.0663	5008	,	,		19719	0.003		0.1064	False		,,,				2504	0.0378				p.T526T		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1578A						PASS	.	G	,,	401,3607		17,367,1620	138.0	147.0	144.0		1578,1578,1578	3.0	0.0	18	dbSNP_116	144	1159,7179		87,985,3097	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	104,1352,4717	AA,AG,GG		13.9002,10.005,12.6357	,,	526/1816,526/1661,526/2249	72344553	1560,10786	2004	4169	6173	SO:0001819	synonymous_variant	55628	exon1			TCAGACGTTGTGT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1578G>A	18.37:g.72344553G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	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	
CACNA1H	8912	hgsc.bcm.edu	37	16	1272655	1272655	+	IGR	SNP	C	C	T	rs117769620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1272655C>T	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.G170R	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TCCTCACCTCCCTCCCGCGTA	0.667													c|||	13	0.00259585	0.0	0.0014	5008	,	,		15592	0.0		0.0109	False		,,,				2504	0.001				p.G170R		Atlas-SNP	.											.	TPSG1	19	.	0			c.G508A						PASS	.		ARG/GLY	3,4389	6.2+/-15.9	0,3,2193	70.0	87.0	81.0		508	2.5	0.8	16	dbSNP_132	81	56,8540	32.8+/-85.7	0,56,4242	yes	missense	TPSG1	NM_012467.3	125	0,59,6435	TT,TC,CC		0.6515,0.0683,0.4543	possibly-damaging	170/322	1272655	59,12929	2196	4298	6494	SO:0001628	intergenic_variant	25823	exon4			CACCTCCCTCCCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180			16.37:g.1272655C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	c	13.73	2.323926	0.41096	6.83E-4	0.006515	ENSG00000116176	ENST00000234798	D	0.93763	-3.28	3.47	2.48	0.30137	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.90123	0.6914	L	0.58101	1.795	0.39248	D	0.963972	D	0.52996	0.957	P	0.52031	0.688	D	0.87282	0.2293	9	0.25751	T	0.34	.	9.1608	0.37021	0.0:0.8827:0.0:0.1173	.	170	Q9NRR2	TRYG1_HUMAN	R	170	ENSP00000234798:G170R	ENSP00000234798:G170R	G	-	1	0	TPSG1	1212656	0.119000	0.22226	0.814000	0.32528	0.083000	0.17756	0.758000	0.26447	0.518000	0.28383	0.556000	0.70494	GGA	C|0.995;T|0.005	0.005	strong		0.667	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
NDUFS2	4720	hgsc.bcm.edu	37	1	161183516	161183516	+	Silent	SNP	C	C	T	rs1136207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161183516C>T	ENST00000367993.3	+	13	1738	c.1290C>T	c.(1288-1290)gcC>gcT	p.A430A	FCER1G_ENST00000289902.1_5'Flank|FCER1G_ENST00000367992.3_5'Flank|NDUFS2_ENST00000465923.1_3'UTR|NDUFS2_ENST00000392179.4_Silent_p.A430A	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	430					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	CTGGTTTTGCCCATCTGGTAA	0.468													C|||	792	0.158147	0.0348	0.2291	5008	,	,		20562	0.3562		0.1392	False		,,,				2504	0.09				p.A430A		Atlas-SNP	.											.	NDUFS2	33	.	0			c.C1290T						PASS	.	C	,	223,4183	132.9+/-169.3	6,211,1986	110.0	104.0	106.0		1290,1290	1.5	1.0	1	dbSNP_86	106	1155,7445	237.1+/-269.0	74,1007,3219	no	coding-synonymous,coding-synonymous	NDUFS2	NM_001166159.1,NM_004550.4	,	80,1218,5205	TT,TC,CC		13.4302,5.0613,10.5951	,	430/458,430/464	161183516	1378,11628	2203	4300	6503	SO:0001819	synonymous_variant	4720	exon12			TTTTGCCCATCTG	BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7708	protein-coding gene	gene with protein product	"""complex I 49kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"""	602985	"""NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"""			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.1290C>T	1.37:g.161183516C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	NM_001166159	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Silent	SNP	ENST00000367993.3	37	CCDS1224.1																																																																																			C|0.862;T|0.138	0.138	strong		0.468	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360144	71360144	+	Missense_Mutation	SNP	A	A	C	rs10199088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71360144A>C	ENST00000244230.2	+	2	558	c.206A>C	c.(205-207)gAa>gCa	p.E69A	MPHOSPH10_ENST00000468427.1_3'UTR|MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.E69A|MCEE_ENST00000244217.5_5'Flank	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	69			E -> A (in dbSNP:rs10199088).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						CTTGTGATAGAAAATTTTGAT	0.318													C|||	1784	0.35623	0.4259	0.4049	5008	,	,		19377	0.2738		0.2982	False		,,,				2504	0.3722				p.E69A		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.A206C						PASS	.	C	ALA/GLU	1656,2750	625.0+/-394.4	301,1054,848	37.0	39.0	38.0		206	-3.0	0.0	2	dbSNP_119	38	2571,6029	666.7+/-402.4	405,1761,2134	no	missense	MPHOSPH10	NM_005791.2	107	706,2815,2982	CC,CA,AA		29.8953,37.5851,32.5004	benign	69/682	71360144	4227,8779	2203	4300	6503	SO:0001583	missense	10199	exon2			TGATAGAAAATTT	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.206A>C	2.37:g.71360144A>C	ENSP00000244230:p.Glu69Ala	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	171	92	0.538012	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	754	0.34523809523809523	215	0.4369918699186992	140	0.3867403314917127	180	0.3146853146853147	219	0.28891820580474936	C	9.061	0.994481	0.19043	0.375851	0.298953	ENSG00000124383	ENST00000244230	T	0.12039	2.72	4.47	-3.03	0.05429	.	0.648090	0.16397	N	0.216201	T	0.00012	0.0000	M	0.62088	1.915	0.58432	P	2.9999999999752447E-6	B	0.16166	0.016	B	0.12837	0.008	T	0.43491	-0.9388	9	0.46703	T	0.11	.	6.9292	0.24432	0.4658:0.385:0.1492:0.0	rs10199088;rs52833288;rs10199088	69	O00566	MPP10_HUMAN	A	69	ENSP00000244230:E69A	ENSP00000244230:E69A	E	+	2	0	MPHOSPH10	71213652	0.994000	0.37717	0.000000	0.03702	0.561000	0.35649	3.299000	0.51826	-1.020000	0.03354	-1.558000	0.00888	GAA	A|0.666;C|0.334	0.334	strong		0.318	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
ZNF658	26149	hgsc.bcm.edu	37	9	40772563	40772563	+	Silent	SNP	G	G	A	rs62561229	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:40772563G>A	ENST00000602553.1	-	5	3006	c.2712C>T	c.(2710-2712)cgC>cgT	p.R904R	ZNF658_ENST00000377626.3_Silent_p.R904R|ZNF658_ENST00000441795.1_Intron			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	904					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TCTCCCCTGAGCGAGTTCTAA	0.453													G|||	913	0.182308	0.2776	0.1167	5008	,	,		18539	0.1964		0.1789	False		,,,				2504	0.089				p.R904R		Atlas-SNP	.											ZNF658,NS,carcinoma,-1,1	ZNF658	100	1	0			c.C2712T						scavenged	.	G		1147,3255	406.0+/-333.7	121,905,1175	78.0	77.0	78.0		2712	-1.4	0.0	9	dbSNP_131	78	1305,7257	258.4+/-282.1	94,1117,3070	no	coding-synonymous	ZNF658	NM_033160.5		215,2022,4245	AA,AG,GG		15.2418,26.0563,18.9139		904/1060	40772563	2452,10512	2201	4281	6482	SO:0001819	synonymous_variant	26149	exon5			CCCTGAGCGAGTT	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.2712C>T	9.37:g.40772563G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	192	112	0.583333	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Silent	SNP	ENST00000602553.1	37	CCDS35023.1																																																																																			G|0.814;A|0.186	0.186	strong		0.453	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
PCDH8	5100	hgsc.bcm.edu	37	13	53422553	53422553	+	Missense_Mutation	SNP	A	A	G	rs3742301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:53422553A>G	ENST00000377942.3	-	1	222	c.19T>C	c.(19-21)Tgg>Cgg	p.W7R	PCDH8_ENST00000338862.4_Missense_Mutation_p.W7R	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	7			W -> R (in dbSNP:rs3742301). {ECO:0000269|PubMed:12884975}.		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)		GGGCTGCCCCAACGCCTCACA	0.592													A|||	1425	0.284545	0.1876	0.2579	5008	,	,		16382	0.5119		0.2048	False		,,,				2504	0.2822				p.W7R	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.T19C						PASS	.	A	ARG/TRP,ARG/TRP	881,3523		103,675,1424	36.0	35.0	35.0		19,19	-0.2	0.5	13	dbSNP_107	35	1620,6978		145,1330,2824	yes	missense,missense	PCDH8	NM_002590.3,NM_032949.2	101,101	248,2005,4248	GG,GA,AA		18.8416,20.0045,19.2355	benign,benign	7/1071,7/974	53422553	2501,10501	2202	4299	6501	SO:0001583	missense	5100	exon1			TGCCCCAACGCCT	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.19T>C	13.37:g.53422553A>G	ENSP00000367177:p.Trp7Arg	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	6	0.352941	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	37	CCDS9438.1	608	0.2783882783882784	89	0.18089430894308944	64	0.17679558011049723	293	0.5122377622377622	162	0.21372031662269128	A	5.090	0.202283	0.09652	0.200045	0.188416	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.51817	0.72;0.69	5.3	-0.221	0.13126	.	0.164261	0.28841	N	0.013964	T	0.00012	0.0000	N	0.08118	0	0.51012	P	9.40000000000385E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46176	-0.9210	9	0.25751	T	0.34	.	2.1402	0.03772	0.3347:0.3898:0.0967:0.1789	rs3742301;rs3742301	7;7	O95206-2;O95206	.;PCDH8_HUMAN	R	7	ENSP00000367177:W7R;ENSP00000341350:W7R	ENSP00000341350:W7R	W	-	1	0	PCDH8	52320554	0.032000	0.19561	0.455000	0.27031	0.390000	0.30446	0.115000	0.15540	-0.415000	0.07484	0.460000	0.39030	TGG	A|0.769;G|0.231	0.231	strong		0.592	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590	
CPT1C	126129	hgsc.bcm.edu	37	19	50209653	50209653	+	Silent	SNP	C	C	T	rs12978911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50209653C>T	ENST00000392518.4	+	12	1698	c.1326C>T	c.(1324-1326)gcC>gcT	p.A442A	CPT1C_ENST00000354199.5_Silent_p.A442A|CPT1C_ENST00000323446.5_Silent_p.A442A|CPT1C_ENST00000405931.2_Silent_p.A431A|CPT1C_ENST00000598293.1_Silent_p.A442A	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	442					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		CTCTGCTGGCCGGCCGGGGCC	0.642													c|||	351	0.0700879	0.0461	0.0922	5008	,	,		14081	0.001		0.1889	False		,,,				2504	0.0358				p.A442A		Atlas-SNP	.											.	CPT1C	93	.	0			c.C1326T						PASS	.	C	,,,	280,4096		13,254,1921	11.0	13.0	13.0		1293,1326,1326,1326	-8.4	0.1	19	dbSNP_121	13	1380,7174		122,1136,3019	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	,,,	135,1390,4940	TT,TC,CC		16.1328,6.3985,12.8384	,,,	431/793,442/804,442/804,442/804	50209653	1660,11270	2188	4277	6465	SO:0001819	synonymous_variant	126129	exon12			GCTGGCCGGCCGG	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.1326C>T	19.37:g.50209653C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Silent	SNP	ENST00000392518.4	37	CCDS12779.1																																																																																			C|0.898;T|0.102	0.102	strong		0.642	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359	
FAM167A	83648	hgsc.bcm.edu	37	8	11301601	11301601	+	Missense_Mutation	SNP	G	G	C	rs3021512	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11301601G>C	ENST00000528897.1	-	2	939	c.320C>G	c.(319-321)aCt>aGt	p.T107S	FAM167A_ENST00000284486.4_Missense_Mutation_p.T107S|FAM167A_ENST00000534308.1_Missense_Mutation_p.T107S|FAM167A_ENST00000531564.1_5'Flank			Q96KS9	F167A_HUMAN	family with sequence similarity 167, member A	107			T -> S (in dbSNP:rs3021512). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.							breast(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)	9						CAGCTTGCCAGTGGACAGGGG	0.627													G|||	394	0.0786741	0.034	0.1124	5008	,	,		15628	0.0		0.2107	False		,,,				2504	0.0603				p.T107S		Atlas-SNP	.											.	FAM167A	21	.	0			c.C320G						PASS	.	G	SER/THR	236,3916		7,222,1847	50.0	55.0	53.0		320	2.5	0.0	8	dbSNP_101	53	1710,6754		177,1356,2699	yes	missense	FAM167A	NM_053279.2	58	184,1578,4546	CC,CG,GG		20.2032,5.684,15.4249	benign	107/215	11301601	1946,10670	2076	4232	6308	SO:0001583	missense	83648	exon2			TTGCCAGTGGACA		CCDS5981.1	8p23-p22	2010-08-27	2008-06-11	2008-06-11	ENSG00000154319	ENSG00000154319			15549	protein-coding gene	gene with protein product		610085	"""chromosome 8 open reading frame 13"""	C8orf13			Standard	NM_053279		Approved		uc003wtw.2	Q96KS9	OTTHUMG00000129361	ENST00000528897.1:c.320C>G	8.37:g.11301601G>C	ENSP00000436655:p.Thr107Ser	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	210	87	0.414286	NM_053279	A8K3T9|Q3SXY1|Q3SXY3|Q8N3M3|Q9NSR0	Missense_Mutation	SNP	ENST00000528897.1	37	CCDS5981.1	233	0.10668498168498168	18	0.036585365853658534	48	0.13259668508287292	0	0.0	167	0.22031662269129287	G	3.552	-0.091530	0.07053	0.05684	0.202032	ENSG00000154319	ENST00000284486;ENST00000534308;ENST00000528897	T;T;T	0.06933	3.24;3.24;3.24	5.42	2.55	0.30701	.	1.544380	0.03516	N	0.220302	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39165	-0.9627	9	0.05620	T	0.96	0.7646	7.0385	0.25006	0.1488:0.0:0.7113:0.1399	rs3021512	107	Q96KS9	F167A_HUMAN	S	107	ENSP00000284486:T107S;ENSP00000432232:T107S;ENSP00000436655:T107S	ENSP00000284486:T107S	T	-	2	0	FAM167A	11339011	0.993000	0.37304	0.000000	0.03702	0.004000	0.04260	3.705000	0.54823	0.661000	0.30985	0.655000	0.94253	ACT	G|0.854;C|0.146	0.146	strong		0.627	FAM167A-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000383901.1		
ENOSF1	55556	hgsc.bcm.edu	37	18	712568	712568	+	Missense_Mutation	SNP	G	G	A	rs3786349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:712568G>A	ENST00000251101.7	-	1	108	c.20C>T	c.(19-21)tCc>tTc	p.S7F	ENOSF1_ENST00000340116.7_5'Flank|ENOSF1_ENST00000580982.1_Missense_Mutation_p.S7F|ENOSF1_ENST00000383578.3_5'UTR|ENOSF1_ENST00000539164.1_Missense_Mutation_p.S7F	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	11	0	0		WXS	Illumina HiSeq	Phase_I	6	5	0.833333	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	
FRAS1	80144	hgsc.bcm.edu	37	4	79385719	79385719	+	Silent	SNP	G	G	A	rs6851427	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79385719G>A	ENST00000264895.6	+	49	7451	c.7011G>A	c.(7009-7011)gcG>gcA	p.A2337A		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2337					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AGCTTAAGGCGGTGGATGCTG	0.542													G|||	1490	0.297524	0.1422	0.4409	5008	,	,		20735	0.3194		0.3618	False		,,,				2504	0.317				p.A2337A		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7011A						PASS	.	G		735,3483		64,607,1438	103.0	99.0	101.0		7011	-11.0	0.0	4	dbSNP_116	101	3199,5261		581,2037,1612	no	coding-synonymous	FRAS1	NM_025074.6		645,2644,3050	AA,AG,GG		37.8132,17.4253,31.0301		2337/4013	79385719	3934,8744	2109	4230	6339	SO:0001819	synonymous_variant	80144	exon49			TAAGGCGGTGGAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7011G>A	4.37:g.79385719G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	700	0.32051282051282054	85	0.17276422764227642	155	0.4281767955801105	180	0.3146853146853147	280	0.36939313984168864	G	0.089	-1.170149	0.01660	0.174253	0.378132	ENSG00000138759	ENST00000512123	.	.	.	5.49	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999981	.	.	.	.	.	.	T	0.12477	-1.0546	3	.	.	.	.	5.2213	0.15370	0.5169:0.2383:0.0704:0.1744	rs6851427;rs6851427	.	.	.	S	566	.	.	G	+	1	0	FRAS1	79604743	0.000000	0.05858	0.029000	0.17559	0.016000	0.09150	-2.249000	0.01188	-3.583000	0.00137	-0.137000	0.14449	GGT	G|0.682;A|0.318	0.318	strong		0.542	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPTA1	6708	hgsc.bcm.edu	37	1	158592847	158592847	+	Missense_Mutation	SNP	G	G	A	rs78394850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592847G>A	ENST00000368147.4	-	43	6226	c.6046C>T	c.(6046-6048)Cgc>Tgc	p.R2016C		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2016					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)					TGTTCCCAGCGCTTCAGCAGA	0.478													G|||	272	0.0543131	0.1407	0.0317	5008	,	,		16998	0.0		0.0239	False		,,,				2504	0.0409				p.R2016C		Atlas-SNP	.											SPTA1,colon,carcinoma,+1,3	SPTA1	720	3	0			c.C6046T						PASS	.	G	CYS/ARG	541,3327		26,489,1419	237.0	236.0	236.0		6046	4.8	0.6	1	dbSNP_132	236	131,8137		2,127,4005	yes	missense	SPTA1	NM_003126.2	180	28,616,5424	AA,AG,GG		1.5844,13.9866,5.5372	probably-damaging	2016/2420	158592847	672,11464	1934	4134	6068	SO:0001583	missense	6708	exon43			CCCAGCGCTTCAG	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.6046C>T	1.37:g.158592847G>A	ENSP00000357129:p.Arg2016Cys	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	204	86	0.421569	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	103	0.04716117216117216	75	0.1524390243902439	11	0.03038674033149171	0	0.0	17	0.022427440633245383	G	17.61	3.432615	0.62844	0.139866	0.015844	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.41758	0.99;0.99	4.78	4.78	0.61160	.	.	.	.	.	T	0.60728	0.2291	M	0.79693	2.465	0.58432	D	0.999993	D	0.89917	1.0	D	0.83275	0.996	T	0.64918	-0.6294	9	0.56958	D	0.05	.	16.5446	0.84426	0.0:0.0:1.0:0.0	.	2016	P02549	SPTA1_HUMAN	C	2016;2013	ENSP00000357130:R2016C;ENSP00000357129:R2013C	ENSP00000357129:R2013C	R	-	1	0	SPTA1	156859471	1.000000	0.71417	0.631000	0.29282	0.015000	0.08874	8.964000	0.93389	2.481000	0.83766	0.655000	0.94253	CGC	G|0.959;A|0.041	0.041	strong		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
LILRB4	11006	hgsc.bcm.edu	37	19	55177358	55177358	+	Missense_Mutation	SNP	C	C	T	rs200475774		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55177358C>T	ENST00000391736.1	+	9	1165	c.850C>T	c.(850-852)Cgt>Tgt	p.R284C	LILRB4_ENST00000391733.3_Missense_Mutation_p.R284C|LILRB4_ENST00000391734.3_Missense_Mutation_p.R284C|LILRB4_ENST00000270452.2_Missense_Mutation_p.R284C|LILRB4_ENST00000430952.2_Missense_Mutation_p.R284C	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	284					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)		ccAACACTGGCGTCAGGGAAA	0.592																																					p.R284C		Atlas-SNP	.											LILRB4,NS,carcinoma,0,2	LILRB4	86	2	0			c.C850T						PASS	.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	138.0	92.0	108.0		850,850	-0.5	0.0	19		108	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	180,180	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	284/448,284/449	55177358	4,13002	2203	4300	6503	SO:0001583	missense	11006	exon7			CACTGGCGTCAGG	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.850C>T	19.37:g.55177358C>T	ENSP00000375616:p.Arg284Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	C	6.615	0.481950	0.12581	0.0	4.65E-4	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00490	7.1;7.1;7.1;7.03;7.12;7.03	1.86	-0.498	0.12019	.	.	.	.	.	T	0.00356	0.0011	L	0.43701	1.375	0.09310	N	1	D;D;P;P;B	0.62365	0.991;0.978;0.954;0.875;0.017	B;B;B;P;B	0.44561	0.446;0.265;0.335;0.453;0.002	T	0.50734	-0.8793	9	0.49607	T	0.09	.	2.8633	0.05593	0.0:0.4992:0.3032:0.1976	.	284;283;284;284;284	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	C	284;284;284;284;284;283	ENSP00000375616:R284C;ENSP00000270452:R284C;ENSP00000408995:R284C;ENSP00000375614:R284C;ENSP00000375613:R284C;ENSP00000401962:R283C	ENSP00000270452:R284C	R	+	1	0	LILRB4	59869170	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.104000	0.03326	-0.054000	0.13266	0.407000	0.27541	CGT	C|0.999;T|0.001	0.001	weak		0.592	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
BOD1L1	259282	hgsc.bcm.edu	37	4	13604418	13604418	+	Missense_Mutation	SNP	G	G	C	rs17745712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:13604418G>C	ENST00000040738.5	-	10	4241	c.4106C>G	c.(4105-4107)gCt>gGt	p.A1369G		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1369			A -> G (in dbSNP:rs17745712).			nucleus (GO:0005634)	DNA binding (GO:0003677)										AGCCTGGTGAGCTTCTGGAAT	0.413													C|||	695	0.138778	0.1619	0.2133	5008	,	,		22483	0.003		0.1501	False		,,,				2504	0.183				p.A1369G		Atlas-SNP	.											.	.	.	.	0			c.C4106G						PASS	.	C	GLY/ALA	715,3691	757.3+/-412.7	48,619,1536	152.0	151.0	151.0		4106	2.2	0.1	4	dbSNP_123	151	1296,7304	757.8+/-407.5	86,1124,3090	yes	missense	BOD1L	NM_148894.2	60	134,1743,4626	CC,CG,GG		15.0698,16.2279,15.4621	benign	1369/3052	13604418	2011,10995	2203	4300	6503	SO:0001583	missense	259282	exon10			TGGTGAGCTTCTG	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.4106C>G	4.37:g.13604418G>C	ENSP00000040738:p.Ala1369Gly	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	212	126	0.59434	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	269	0.12316849816849818	85	0.17276422764227642	73	0.20165745856353592	0	0.0	111	0.14643799472295516	C	0.007	-2.002897	0.00431	0.162279	0.150698	ENSG00000038219	ENST00000040738	T	0.07021	3.23	5.55	2.24	0.28232	.	0.628007	0.14931	N	0.290053	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46105	-0.9215	9	0.08381	T	0.77	-0.6927	5.4252	0.16421	0.0:0.4686:0.2543:0.2772	rs17745712;rs52797471;rs17745712	1369	Q8NFC6	BOD1L_HUMAN	G	1369	ENSP00000040738:A1369G	ENSP00000040738:A1369G	A	-	2	0	BOD1L	13213516	0.001000	0.12720	0.083000	0.20561	0.056000	0.15407	-0.124000	0.10595	-0.107000	0.12088	-0.120000	0.15030	GCT	G|0.848;C|0.152	0.152	strong		0.413	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
PCNT	5116	hgsc.bcm.edu	37	21	47808679	47808679	+	Missense_Mutation	SNP	C	C	T	rs7279204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47808679C>T	ENST00000359568.5	+	18	3594	c.3487C>T	c.(3487-3489)Cgc>Tgc	p.R1163C	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1163			R -> C (in dbSNP:rs7279204).		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)					GGACGCCCTGCGCAGGCTGCT	0.677													C|||	762	0.152157	0.0711	0.1816	5008	,	,		16098	0.1984		0.1312	False		,,,				2504	0.2147				p.R1163C		Atlas-SNP	.											PCNT,face,carcinoma,-1,1	PCNT	283	1	0			c.C3487T						PASS	.	C	CYS/ARG	288,4118	152.9+/-186.6	13,262,1928	55.0	57.0	56.0		3487	-3.1	0.1	21	dbSNP_116	56	1110,7490	226.8+/-262.4	71,968,3261	yes	missense	PCNT	NM_006031.5	180	84,1230,5189	TT,TC,CC		12.907,6.5365,10.7489	probably-damaging	1163/3337	47808679	1398,11608	2203	4300	6503	SO:0001583	missense	5116	exon18			GCCCTGCGCAGGC	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.3487C>T	21.37:g.47808679C>T	ENSP00000352572:p.Arg1163Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	303	0.13873626373626374	36	0.07317073170731707	49	0.13535911602209943	114	0.1993006993006993	104	0.13720316622691292	C	12.00	1.806265	0.31961	0.065365	0.12907	ENSG00000160299	ENST00000359568	T	0.01685	4.69	4.57	-3.08	0.05347	.	0.246216	0.19223	N	0.119601	T	0.00012	0.0000	M	0.62723	1.935	0.58432	P	1.0000000000287557E-6	D;D	0.89917	1.0;1.0	D;D	0.83275	0.981;0.996	T	0.04128	-1.0975	9	0.72032	D	0.01	.	15.9319	0.79668	0.2121:0.7879:0.0:0.0	rs7279204	1045;1163	O95613-2;O95613	.;PCNT_HUMAN	C	1163	ENSP00000352572:R1163C	ENSP00000352572:R1163C	R	+	1	0	PCNT	46633107	0.095000	0.21747	0.091000	0.20842	0.071000	0.16799	0.207000	0.17395	-0.233000	0.09797	-0.274000	0.10170	CGC	C|0.883;T|0.117	0.117	strong		0.677	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
TRAK2	66008	hgsc.bcm.edu	37	2	202264156	202264156	+	Missense_Mutation	SNP	C	C	T	rs13022344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202264156C>T	ENST00000332624.3	-	5	852	c.424G>A	c.(424-426)Gtc>Atc	p.V142I	TRAK2_ENST00000430254.1_Missense_Mutation_p.V142I	NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	142	HAP1 N-terminal.		V -> I (in dbSNP:rs13022344). {ECO:0000269|PubMed:11161814, ECO:0000269|PubMed:14702039}.		protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						TCAGATAAGACATGGTTCCGC	0.408													C|||	2701	0.539337	0.3495	0.5634	5008	,	,		20096	0.4911		0.663	False		,,,				2504	0.7014				p.V142I		Atlas-SNP	.											.	TRAK2	62	.	0			c.G424A	GRCh37	CM072094	TRAK2	M	rs13022344	PASS	.	C	ILE/VAL	1648,2758	505.9+/-366.3	303,1042,858	113.0	107.0	109.0		424	5.2	1.0	2	dbSNP_121	109	5787,2813	676.2+/-403.3	1935,1917,448	yes	missense	TRAK2	NM_015049.2	29	2238,2959,1306	TT,TC,CC		32.7093,37.4035,42.8341	benign	142/915	202264156	7435,5571	2203	4300	6503	SO:0001583	missense	66008	exon5			ATAAGACATGGTT	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.424G>A	2.37:g.202264156C>T	ENSP00000328875:p.Val142Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	37	CCDS2347.1	1148	0.5256410256410257	166	0.33739837398373984	200	0.5524861878453039	272	0.4755244755244755	510	0.6728232189973615	C	12.84	2.058989	0.36373	0.374035	0.672907	ENSG00000115993	ENST00000332624;ENST00000542292;ENST00000430254	T;T	0.18810	2.19;2.19	6.07	5.2	0.72013	.	0.333863	0.28624	N	0.014683	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.9999999999240134	B;B	0.10296	0.0;0.003	B;B	0.12837	0.001;0.008	T	0.33111	-0.9881	9	0.34782	T	0.22	.	6.0626	0.19846	0.0:0.6364:0.1501:0.2135	rs13022344;rs17854051;rs17854102;rs17859473;rs52798654;rs57001181;rs13022344	142;142	E7EV21;O60296	.;TRAK2_HUMAN	I	142;48;142	ENSP00000328875:V142I;ENSP00000409333:V142I	ENSP00000328875:V142I	V	-	1	0	TRAK2	201972401	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.282000	0.43461	1.580000	0.49851	-0.150000	0.13652	GTC	C|0.463;T|0.537	0.537	strong		0.408	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
MMS19	64210	hgsc.bcm.edu	37	10	99220707	99220707	+	Missense_Mutation	SNP	C	C	T	rs3740526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99220707C>T	ENST00000438925.2	-	24	2704	c.2369G>A	c.(2368-2370)gGc>gAc	p.G790D	MMS19_ENST00000355839.6_Missense_Mutation_p.G747D|MMS19_ENST00000370782.2_Missense_Mutation_p.G790D|MMS19_ENST00000327238.10_Missense_Mutation_p.G692D|MMS19_ENST00000327277.7_3'UTR	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	790			G -> D (in dbSNP:rs3740526). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)	p.G790D(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		GGGCCCAGAGCCCAGGCCAGC	0.498								Direct reversal of damage					C|||	1653	0.330072	0.1793	0.4063	5008	,	,		18602	0.375		0.4503	False		,,,				2504	0.3098				p.G790D		Atlas-SNP	.											MMS19,NS,carcinoma,0,1	MMS19	36	1	1	Substitution - Missense(1)	stomach(1)	c.G2369A						PASS	.	C	ASP/GLY	889,3513		81,727,1393	33.0	32.0	32.0		2369	3.6	0.6	10	dbSNP_107	32	3552,5030		740,2072,1479	yes	missense	MMS19	NM_022362.4	94	821,2799,2872	TT,TC,CC		41.389,20.1954,34.2036	benign	790/1031	99220707	4441,8543	2201	4291	6492	SO:0001583	missense	64210	exon24			CCAGAGCCCAGGC	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.2369G>A	10.37:g.99220707C>T	ENSP00000412698:p.Gly790Asp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	37	CCDS7464.1	819|819	0.375|0.375	96|96	0.1951219512195122|0.1951219512195122	157|157	0.43370165745856354|0.43370165745856354	220|220	0.38461538461538464|0.38461538461538464	346|346	0.45646437994722955|0.45646437994722955	C|C	12.25|12.25	1.880974|1.880974	0.33255|0.33255	0.201954|0.201954	0.41389|0.41389	ENSG00000155229|ENSG00000155229	ENST00000434538|ENST00000438925;ENST00000370782;ENST00000327238;ENST00000422291;ENST00000355839	.|T;T;T;T	.|0.64991	.|1.62;1.62;-0.13;1.62	5.66|5.66	3.64|3.64	0.41730|0.41730	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.491931	.|0.23435	.|N	.|0.048216	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B;B;B;B	.|0.24426	.|0.103;0.061;0.0;0.054	.|B;B;B;B	.|0.23419	.|0.029;0.046;0.004;0.013	T|T	0.43750|0.43750	-0.9372|-0.9372	4|9	.|0.12430	.|T	.|0.62	.|.	4.9046|4.9046	0.13791|0.13791	0.1374:0.4075:0.3757:0.0794|0.1374:0.4075:0.3757:0.0794	rs3740526;rs52816448;rs57965173;rs3740526|rs3740526;rs52816448;rs57965173;rs3740526	.|692;747;790;747	.|Q96T76-5;F8W9Y2;Q96T76;B4E2I3	.|.;.;MMS19_HUMAN;.	T|D	365|790;790;692;769;747	.|ENSP00000412698:G790D;ENSP00000359818:G790D;ENSP00000320059:G692D;ENSP00000348097:G747D	.|ENSP00000320059:G692D	A|G	-|-	1|2	0|0	MMS19|MMS19	99210697|99210697	0.656000|0.656000	0.27385|0.27385	0.647000|0.647000	0.29507|0.29507	0.947000|0.947000	0.59692|0.59692	1.234000|1.234000	0.32660|0.32660	1.336000|1.336000	0.45506|0.45506	0.484000|0.484000	0.47621|0.47621	GCT|GGC	C|0.642;T|0.358	0.358	strong		0.498	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
DHRS4	10901	hgsc.bcm.edu	37	14	24424367	24424367	+	Silent	SNP	G	G	A	rs12147221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24424367G>A	ENST00000313250.5	+	2	455	c.252G>A	c.(250-252)acG>acA	p.T84T	DHRS4_ENST00000558263.1_Silent_p.T84T|DHRS4_ENST00000543741.2_Silent_p.T84T|DHRS4_ENST00000421831.1_Silent_p.T66T|DHRS4_ENST00000382761.3_Silent_p.T66T|DHRS4_ENST00000397074.3_Silent_p.T84T|DHRS4_ENST00000397075.3_Silent_p.T84T|DHRS4_ENST00000558581.1_Silent_p.T84T|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000308178.8_Silent_p.T66T|DHRS4_ENST00000559632.1_Silent_p.T84T|DHRS4_ENST00000397073.2_Silent_p.T66T	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	84					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	TGAGCGTGACGGGCACCGTGT	0.682													.|||	1006	0.200879	0.5998	0.1095	5008	,	,		15536	0.0099		0.0785	False		,,,				2504	0.0491				p.T84T		Atlas-SNP	.											.	DHRS4	22	.	0			c.G252A						PASS	.	G		2291,2115		588,1115,500	37.0	41.0	39.0		252	-6.6	0.3	14	dbSNP_120	39	612,7988		6,600,3694	no	coding-synonymous	DHRS4	NM_021004.2		594,1715,4194	AA,AG,GG		7.1163,48.0027,22.3205		84/279	24424367	2903,10103	2203	4300	6503	SO:0001819	synonymous_variant	10901	exon2			CGTGACGGGCACC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.252G>A	14.37:g.24424367G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	218	129	0.591743	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		
GRID1	2894	hgsc.bcm.edu	37	10	87484382	87484382	+	Missense_Mutation	SNP	C	C	T	rs2306265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:87484382C>T	ENST00000327946.7	-	11	1670	c.1585G>A	c.(1585-1587)Gtt>Att	p.V529I	GRID1_ENST00000536331.1_Missense_Mutation_p.V100I	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	529			V -> I (in dbSNP:rs2306265).		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)	p.V529I(1)		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						AAGTCCACAACGCTCTCCCTC	0.498										Multiple Myeloma(13;0.14)			C|||	116	0.0231629	0.0015	0.0058	5008	,	,		19080	0.0506		0.0199	False		,,,				2504	0.0399				p.V529I		Atlas-SNP	.											GRID1,NS,carcinoma,0,1	GRID1	204	1	1	Substitution - Missense(1)	stomach(1)	c.G1585A						PASS	.	C	ILE/VAL	26,4380	30.8+/-60.4	1,24,2178	74.0	69.0	71.0		1585	5.8	1.0	10	dbSNP_100	71	171,8429	78.4+/-141.0	0,171,4129	yes	missense	GRID1	NM_017551.2	29	1,195,6307	TT,TC,CC		1.9884,0.5901,1.5147	probably-damaging	529/1010	87484382	197,12809	2203	4300	6503	SO:0001583	missense	2894	exon11			CCACAACGCTCTC	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.1585G>A	10.37:g.87484382C>T	ENSP00000330148:p.Val529Ile	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	53	0.024267399267399268	1	0.0020325203252032522	2	0.0055248618784530384	33	0.057692307692307696	17	0.022427440633245383	C	32	5.164570	0.94727	0.005901	0.019884	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.28255	1.62;1.62	5.83	5.83	0.93111	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.12987	0.0315	M	0.73217	2.22	0.80722	D	1	D	0.67145	0.996	D	0.71414	0.973	T	0.20338	-1.0278	10	0.87932	D	0	.	19.0851	0.93200	0.0:1.0:0.0:0.0	rs2306265;rs52801325;rs2306265	529	Q9ULK0	GRID1_HUMAN	I	529;100	ENSP00000330148:V529I;ENSP00000444455:V100I	ENSP00000330148:V529I	V	-	1	0	GRID1	87474362	1.000000	0.71417	0.998000	0.56505	0.907000	0.53573	7.747000	0.85070	2.741000	0.93983	0.650000	0.86243	GTT	C|0.981;T|0.019	0.019	strong		0.498	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
XYLT1	64131	hgsc.bcm.edu	37	16	17353202	17353202	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:17353202G>A	ENST00000261381.6	-	3	640	c.556C>T	c.(556-558)Ccg>Tcg	p.P186S		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	186					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						TGTCTACTCGGTGGCTTCTTC	0.527																																					p.P186S		Atlas-SNP	.											XYLT1,right_lower_lobe,carcinoma,0,1	XYLT1	147	1	0			c.C556T						scavenged	.						132.0	130.0	131.0					16																	17353202		2197	4300	6497	SO:0001583	missense	64131	exon3			TACTCGGTGGCTT	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.556C>T	16.37:g.17353202G>A	ENSP00000261381:p.Pro186Ser	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	262	4	0.0152672	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	G	4.191	0.034206	0.08101	.	.	ENSG00000103489	ENST00000261381	T	0.03831	3.79	5.43	4.46	0.54185	.	0.425465	0.28312	N	0.015802	T	0.03263	0.0095	N	0.08118	0	0.19575	N	0.999962	B	0.20887	0.049	B	0.19666	0.026	T	0.43261	-0.9402	10	0.28530	T	0.3	-7.6306	13.808	0.63246	0.0:0.2928:0.7072:0.0	.	186	Q86Y38	XYLT1_HUMAN	S	186	ENSP00000261381:P186S	ENSP00000261381:P186S	P	-	1	0	XYLT1	17260703	0.178000	0.23122	0.115000	0.21578	0.796000	0.44982	2.548000	0.45794	1.269000	0.44280	0.655000	0.94253	CCG	.	.	none		0.527	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
P2RY14	9934	hgsc.bcm.edu	37	3	150931811	150931811	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:150931811G>A	ENST00000309170.3	-	3	606	c.294C>T	c.(292-294)gcC>gcT	p.A98A	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|P2RY14_ENST00000424796.2_Silent_p.A98A	NM_001081455.1|NM_014879.3	NP_001074924.1|NP_055694.3	Q15391	P2Y14_HUMAN	purinergic receptor P2Y, G-protein coupled, 14	98					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)	p.A98A(1)		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)			AGAAGAGCACGGCAGAGACCC	0.458																																					p.A98A		Atlas-SNP	.											P2RY14,NS,carcinoma,0,1	P2RY14	50	1	1	Substitution - coding silent(1)	endometrium(1)	c.C294T						scavenged	.						84.0	71.0	75.0					3																	150931811		2203	4300	6503	SO:0001819	synonymous_variant	9934	exon3			GAGCACGGCAGAG	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.294C>T	3.37:g.150931811G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	138	3	0.0217391	NM_014879	Q8IYT7	Silent	SNP	ENST00000309170.3	37	CCDS3156.1																																																																																			.	.	none		0.458	P2RY14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357789.1	NM_014879	
KLHL2	11275	hgsc.bcm.edu	37	4	166231868	166231868	+	Silent	SNP	A	A	G	rs28678193	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:166231868A>G	ENST00000226725.6	+	10	1462	c.1203A>G	c.(1201-1203)ttA>ttG	p.L401L	KLHL2_ENST00000506761.1_Silent_p.L235L|KLHL2_ENST00000509028.1_3'UTR|KLHL2_ENST00000538127.1_Silent_p.L313L|KLHL2_ENST00000421009.2_Silent_p.L304L|KLHL2_ENST00000514860.1_Silent_p.L405L	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	401					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)		TAAATGGATTATTATACGCTG	0.428													G|||	1631	0.325679	0.3964	0.2795	5008	,	,		18007	0.2956		0.4453	False		,,,				2504	0.1708				p.L405L		Atlas-SNP	.											.	KLHL2	42	.	0			c.A1215G						PASS	.	G	,,	1782,2624	642.5+/-397.7	382,1018,803	254.0	261.0	259.0		1215,939,1203	4.9	0.0	4	dbSNP_125	259	3714,4886	619.7+/-397.0	801,2112,1387	no	coding-synonymous,coding-synonymous,coding-synonymous	KLHL2	NM_001161521.1,NM_001161522.1,NM_007246.3	,,	1183,3130,2190	GG,GA,AA		43.186,40.4448,42.2574	,,	405/598,313/506,401/594	166231868	5496,7510	2203	4300	6503	SO:0001819	synonymous_variant	11275	exon10			TGGATTATTATAC	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.1203A>G	4.37:g.166231868A>G		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	242	133	0.549587	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Silent	SNP	ENST00000226725.6	37	CCDS34094.1																																																																																			A|0.593;G|0.407	0.407	strong		0.428	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1		
CSMD1	64478	hgsc.bcm.edu	37	8	3200877	3200877	+	Silent	SNP	C	C	T	rs2161752	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:3200877C>T	ENST00000520002.1	-	24	4128	c.3573G>A	c.(3571-3573)ctG>ctA	p.L1191L	CSMD1_ENST00000537824.1_Silent_p.L1190L|CSMD1_ENST00000602723.1_Silent_p.L1191L|CSMD1_ENST00000400186.3_Silent_p.L1191L|CSMD1_ENST00000542608.1_Silent_p.L1190L|CSMD1_ENST00000602557.1_Silent_p.L1191L|CSMD1_ENST00000539096.1_Silent_p.L1190L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1191	CUB 7. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACTCTAGCCACAGGTGATTGG	0.423													C|||	628	0.125399	0.1256	0.1182	5008	,	,		17006	0.1081		0.172	False		,,,				2504	0.1002				p.L1190L		Atlas-SNP	.											CSMD1_ENST00000537824,colon,carcinoma,0,4	CSMD1	1469	4	0			c.G3570A						PASS	.	C		508,3368		43,422,1473	167.0	170.0	169.0		3570	5.0	1.0	8	dbSNP_96	169	1458,6816		130,1198,2809	no	coding-synonymous	CSMD1	NM_033225.5		173,1620,4282	TT,TC,CC		17.6215,13.1063,16.1811		1190/3565	3200877	1966,10184	1938	4137	6075	SO:0001819	synonymous_variant	64478	exon23			TAGCCACAGGTGA			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.3573G>A	8.37:g.3200877C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	223	93	0.41704	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		317	0.14514652014652016	79	0.16056910569105692	48	0.13259668508287292	66	0.11538461538461539	124	0.16358839050131926	C	8.521	0.868721	0.17322	0.131063	0.176215	ENSG00000183117	ENST00000335551	.	.	.	5.86	4.99	0.66335	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14504	-1.0470	3	.	.	.	.	9.3779	0.38295	0.0:0.7882:0.0:0.2118	rs2161752;rs59686879;rs2161752	.	.	.	M	671	.	.	V	-	1	0	CSMD1	3188284	0.996000	0.38824	1.000000	0.80357	0.751000	0.42716	0.482000	0.22276	1.626000	0.50381	0.650000	0.86243	GTG	C|0.853;T|0.147	0.147	strong		0.423	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
WDR18	57418	hgsc.bcm.edu	37	19	984554	984554	+	Silent	SNP	C	C	G	rs4806884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:984554C>G	ENST00000251289.5	+	1	224	c.201C>G	c.(199-201)ctC>ctG	p.L67L	WDR18_ENST00000591997.1_Intron|WDR18_ENST00000587001.2_Silent_p.L67L	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	67					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTGGGAGCTCCAGCGGAAGG	0.711													.|||	1837	0.366813	0.3283	0.4092	5008	,	,		11315	0.2768		0.5567	False		,,,				2504	0.2863				p.L67L		Atlas-SNP	.											.	WDR18	20	.	0			c.C201G						PASS	.	G		1233,2751		232,769,991	5.0	7.0	7.0		201	-1.1	1.0	19	dbSNP_111	7	3627,4195		956,1715,1240	no	coding-synonymous	WDR18	NM_024100.3		1188,2484,2231	GG,GC,CC		46.3692,30.9488,41.1655		67/433	984554	4860,6946	1992	3911	5903	SO:0001819	synonymous_variant	57418	exon1			GGAGCTCCAGCGG		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.201C>G	19.37:g.984554C>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	13	4	0.307692	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			C|0.614;G|0.386	0.386	strong		0.711	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
PROSER3	148137	hgsc.bcm.edu	37	19	36258842	36258842	+	Missense_Mutation	SNP	G	G	C	rs231217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36258842G>C	ENST00000544099.1	+	9	1158	c.1095G>C	c.(1093-1095)aaG>aaC	p.K365N	AC002398.13_ENST00000589397.1_RNA|C19orf55_ENST00000396908.4_Missense_Mutation_p.K365N			Q2NL68	PRSR3_HUMAN		365			K -> N (in dbSNP:rs231217).							cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	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)			CCACAGTCAAGGCCTCGCCGC	0.716													G|||	510	0.101837	0.0915	0.1009	5008	,	,		12837	0.0744		0.1203	False		,,,				2504	0.1258				p.K365N		Atlas-SNP	.											.	C19orf55	39	.	0			c.G1095C						PASS	.	G	ASN/LYS	402,3532		21,360,1586	16.0	19.0	18.0		1095	0.6	0.0	19	dbSNP_79	18	865,7435		38,789,3323	yes	missense	C19orf55	NM_001039887.2	94	59,1149,4909	CC,CG,GG		10.4217,10.2186,10.3564	probably-damaging	365/481	36258842	1267,10967	1967	4150	6117	SO:0001583	missense	148137	exon9			AGTCAAGGCCTCG																												ENST00000544099.1:c.1095G>C	19.37:g.36258842G>C	ENSP00000467267:p.Lys365Asn	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	37		216	0.0989010989010989	45	0.09146341463414634	37	0.10220994475138122	38	0.06643356643356643	96	0.1266490765171504	G	10.46	1.357114	0.24598	0.102186	0.104217	ENSG00000167595	ENST00000396908	T	0.33865	1.39	2.8	0.609	0.17575	.	.	.	.	.	T	0.00271	0.0008	L	0.50333	1.59	0.80722	P	0.0	B	0.32160	0.358	B	0.32864	0.154	T	0.10405	-1.0631	8	0.29301	T	0.29	0.5901	4.6861	0.12758	0.3155:0.0:0.6845:0.0	rs231217;rs59022087	365	E5RFB9	.	N	365	ENSP00000380116:K365N	ENSP00000380116:K365N	K	+	3	2	C19orf55	40950682	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.184000	0.16939	0.239000	0.21243	0.467000	0.42956	AAG	G|0.901;C|0.099	0.099	strong		0.716	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		
PPL	5493	hgsc.bcm.edu	37	16	4933939	4933939	+	Missense_Mutation	SNP	G	G	C	rs2037912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4933939G>C	ENST00000345988.2	-	22	4806	c.4717C>G	c.(4717-4719)Caa>Gaa	p.Q1573E	PPL_ENST00000590782.2_Missense_Mutation_p.Q1571E	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1573			Q -> E (in dbSNP:rs2037912). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581, ECO:0000269|Ref.5}.		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						TGCAGGTTTTGCCTCTCCAGC	0.537													G|||	2017	0.402756	0.0303	0.4712	5008	,	,		20646	0.6518		0.5318	False		,,,				2504	0.4683				p.Q1573E		Atlas-SNP	.											.	PPL	168	.	0			c.C4717G						PASS	.	G	GLU/GLN	513,3881	233.6+/-246.7	36,441,1720	110.0	110.0	110.0		4717	5.8	1.0	16	dbSNP_94	110	4748,3852	609.1+/-395.5	1310,2128,862	yes	missense	PPL	NM_002705.4	29	1346,2569,2582	CC,CG,GG		44.7907,11.675,40.4879	possibly-damaging	1573/1757	4933939	5261,7733	2197	4300	6497	SO:0001583	missense	5493	exon22			GGTTTTGCCTCTC	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.4717C>G	16.37:g.4933939G>C	ENSP00000340510:p.Gln1573Glu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	185	87	0.47027	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	972	0.44505494505494503	20	0.04065040650406504	166	0.4585635359116022	376	0.6573426573426573	410	0.5408970976253298	G	17.76	3.469610	0.63625	0.11675	0.552093	ENSG00000118898	ENST00000345988	T	0.45276	0.9	5.83	5.83	0.93111	.	0.066791	0.64402	D	0.000009	T	0.00012	0.0000	M	0.70595	2.14	0.09310	P	0.99999843917	D	0.64830	0.994	D	0.72338	0.977	T	0.27938	-1.0059	9	0.02654	T	1	.	20.1184	0.97949	0.0:0.0:1.0:0.0	rs2037912;rs52812562;rs2037912	1573	O60437	PEPL_HUMAN	E	1573	ENSP00000340510:Q1573E	ENSP00000340510:Q1573E	Q	-	1	0	PPL	4873940	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	9.428000	0.97476	2.769000	0.95229	0.655000	0.94253	CAA	G|0.581;C|0.419	0.419	strong		0.537	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
SNRPD3	6634	hgsc.bcm.edu	37	22	24964128	24964128	+	Silent	SNP	T	T	C	rs4597	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:24964128T>C	ENST00000215829.3	+	3	890	c.303T>C	c.(301-303)gcT>gcC	p.A101A	SNRPD3_ENST00000402849.1_Silent_p.A101A	NM_001278656.1|NM_004175.3	NP_001265585.1|NP_004166.1	P62318	SMD3_HUMAN	small nuclear ribonucleoprotein D3 polypeptide 18kDa	101	Arg/Lys-rich (basic).				gene expression (GO:0010467)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	enzyme binding (GO:0019899)|histone pre-mRNA DCP binding (GO:0071208)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6						GAAAAGCTGCTATTCTCAAGG	0.458													T|||	3414	0.681709	0.4191	0.7925	5008	,	,		18115	0.8522		0.8539	False		,,,				2504	0.6053				p.A101A		Atlas-SNP	.											.	SNRPD3	12	.	0			c.T303C						PASS	.	T		2215,2191	578.1+/-384.6	570,1075,558	53.0	50.0	51.0		303	-3.2	1.0	22	dbSNP_52	51	7170,1430	728.9+/-406.7	3023,1124,153	no	coding-synonymous	SNRPD3	NM_004175.3		3593,2199,711	CC,CT,TT		16.6279,49.7276,27.841		101/127	24964128	9385,3621	2203	4300	6503	SO:0001819	synonymous_variant	6634	exon3			AGCTGCTATTCTC	U15009	CCDS13828.1	22q11.23	2011-10-11	2002-08-29		ENSG00000100028	ENSG00000100028			11160	protein-coding gene	gene with protein product		601062	"""small nuclear ribonucleoprotein D3 polypeptide (18kD)"""			1701240, 7527560	Standard	NM_004175		Approved	SMD3, Sm-D3	uc003aam.1	P62318	OTTHUMG00000150727	ENST00000215829.3:c.303T>C	22.37:g.24964128T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_004175	B4DJP7|B5BU13|P43331	Silent	SNP	ENST00000215829.3	37	CCDS13828.1																																																																																			A|0.000;C|0.725;T|0.275	0.725	strong		0.458	SNRPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319813.1	NM_004175	
MAST2	23139	hgsc.bcm.edu	37	1	46493460	46493460	+	Missense_Mutation	SNP	T	T	G	rs1707336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46493460T>G	ENST00000361297.2	+	17	2260	c.1977T>G	c.(1975-1977)atT>atG	p.I659M	MAST2_ENST00000372009.2_Missense_Mutation_p.I589M	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					TGTCCAAAATTGGCCTCATGA	0.438													T|||	2430	0.485224	0.4259	0.4827	5008	,	,		21616	0.6607		0.4463	False		,,,				2504	0.4264				p.I659M		Atlas-SNP	.											.	MAST2	136	.	0			c.T1977G						PASS	.	T	MET/ILE	1588,2230		341,906,662	116.0	112.0	113.0		1977	-0.6	1.0	1	dbSNP_89	113	3613,4673		806,2001,1336	yes	missense	MAST2	NM_015112.2	10	1147,2907,1998	GG,GT,TT		43.6037,41.5925,42.9693	benign	659/1799	46493460	5201,6903	1909	4143	6052	SO:0001583	missense	23139	exon17			CAAAATTGGCCTC	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.1977T>G	1.37:g.46493460T>G	ENSP00000354671:p.Ile659Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	1011	0.46291208791208793	196	0.3983739837398374	170	0.4696132596685083	343	0.5996503496503497	302	0.39841688654353563	T	12.25	1.881032	0.33255	0.415925	0.436037	ENSG00000086015	ENST00000361297;ENST00000372009;ENST00000432341;ENST00000372008	T;T;T	0.65364	-0.15;-0.15;-0.15	5.41	-0.618	0.11576	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.21545	0.675	0.20307	P	0.9999129408	D;B;D;B	0.89917	0.988;0.12;1.0;0.379	D;B;D;P	0.91635	0.977;0.068;0.999;0.45	T	0.39440	-0.9614	9	0.02654	T	1	-11.8172	5.7492	0.18138	0.1423:0.203:0.0:0.6546	rs1707336;rs17402588;rs17845481;rs17858361;rs61064119;rs1707336	589;333;589;659	Q6P0Q8-2;E7EWL1;E7ERL6;Q6P0Q8	.;.;.;MAST2_HUMAN	M	659;589;333;544	ENSP00000354671:I659M;ENSP00000361079:I589M;ENSP00000361078:I544M	ENSP00000354671:I659M	I	+	3	3	MAST2	46266047	0.264000	0.24093	1.000000	0.80357	0.937000	0.57800	-0.392000	0.07314	0.093000	0.17368	0.459000	0.35465	ATT	G|0.474;N|0.000	0.474	strong		0.438	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
HNF1A	6927	hgsc.bcm.edu	37	12	121416622	121416622	+	Silent	SNP	C	C	G	rs1169289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:121416622C>G	ENST00000257555.6	+	1	277	c.51C>G	c.(49-51)ctC>ctG	p.L17L	HNF1A-AS1_ENST00000537361.1_RNA|HNF1A_ENST00000402929.1_Silent_p.L17L|HNF1A_ENST00000400024.2_Silent_p.L17L|HNF1A_ENST00000538626.1_Silent_p.L17L|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000544413.1_Silent_p.L17L|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000541395.1_Silent_p.L17L			P20823	HNF1A_HUMAN	HNF1 homeobox A	17	Dimerization.				glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.?(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGGCCCTGCTCGAGTCAGGGC	0.687									Hepatic Adenoma, Familial Clustering of				C|||	2146	0.428514	0.3169	0.438	5008	,	,		11818	0.3819		0.4692	False		,,,				2504	0.5787				p.L17L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	1	Unknown(1)	endometrium(1)	c.C51G						PASS	.	C		1508,2894		278,952,971	24.0	29.0	27.0		51	-3.7	0.9	12	dbSNP_87	27	3915,4673		915,2085,1294	no	coding-synonymous	HNF1A	NM_000545.5		1193,3037,2265	GG,GC,CC		45.5869,34.2572,41.7475		17/632	121416622	5423,7567	2201	4294	6495	SO:0001819	synonymous_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCTGCTCGAGTCA	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.51C>G	12.37:g.121416622C>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.405;C|0.595	0.405	strong		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
CHDH	55349	hgsc.bcm.edu	37	3	53857676	53857676	+	Silent	SNP	C	C	T	rs17053532	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	14	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	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	
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219695	28219695	+	Missense_Mutation	SNP	G	G	A	rs62638680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	65	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	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	
DEF6	50619	hgsc.bcm.edu	37	6	35280252	35280252	+	Silent	SNP	G	G	A	rs142511424		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35280252G>A	ENST00000316637.5	+	4	602	c.597G>A	c.(595-597)cgG>cgA	p.R199R	DEF6_ENST00000542066.1_Intron	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	199						cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						GCGTGGGCCGGGACACCCTCA	0.652																																					p.R199R		Atlas-SNP	.											DEF6,right_lower_lobe,carcinoma,+2,1	DEF6	36	1	0			c.G597A						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	33.0	39.0	37.0		597	-1.5	1.0	6	dbSNP_134	37	0,8600		0,0,4300	no	coding-synonymous	DEF6	NM_022047.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		199/632	35280252	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	50619	exon4			GGGCCGGGACACC	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"""Pleckstrin homology (PH) domain containing"""	2760	protein-coding gene	gene with protein product	"""SWAP-70-like adaptor protein of T cells"""	610094	"""differentially expressed in FDCP (mouse homolog) 6"""			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.597G>A	6.37:g.35280252G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	124	3	0.0241935	NM_022047	Q86VF4	Silent	SNP	ENST00000316637.5	37	CCDS4802.1	.	.	.	.	.	.	.	.	.	.	G	8.814	0.936008	0.18206	2.27E-4	0.0	ENSG00000023892	ENST00000444278	.	.	.	5.52	-1.48	0.08745	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.51767	D	0.999931	.	.	.	.	.	.	T	0.32534	-0.9903	4	.	.	.	-29.405	0.6609	0.00842	0.2917:0.1972:0.3159:0.1952	.	.	.	.	R	108	.	.	G	+	1	0	DEF6	35388230	0.995000	0.38212	0.976000	0.42696	0.995000	0.86356	0.487000	0.22356	-0.124000	0.11724	-0.137000	0.14449	GGA	G|1.000;A|0.000	0.000	weak		0.652	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047	
ZNF780A	284323	hgsc.bcm.edu	37	19	40580426	40580426	+	Silent	SNP	A	A	G	rs399405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40580426A>G	ENST00000595687.2	-	6	2132	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000455521.1_Silent_p.S642S|ZNF780A_ENST00000594395.1_Silent_p.S642S|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000450241.2_Silent_p.S607S|ZNF780A_ENST00000340963.5_Silent_p.S641S	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	190	0	0		WXS	Illumina HiSeq	Phase_I	199	90	0.452261	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	
AIM1	202	hgsc.bcm.edu	37	6	106967185	106967185	+	Missense_Mutation	SNP	A	A	C	rs1159148	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:106967185A>C	ENST00000369066.3	+	2	1365	c.878A>C	c.(877-879)cAa>cCa	p.Q293P		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)		ATTCGAGGCCAAAGGAATACT	0.428													C|||	1034	0.20647	0.1974	0.1945	5008	,	,		19009	0.0536		0.2366	False		,,,				2504	0.3538				p.Q293P		Atlas-SNP	.											.	AIM1	161	.	0			c.A878C						PASS	.	C	PRO/GLN	925,3481	733.5+/-410.5	84,757,1362	55.0	55.0	55.0		878	2.6	0.0	6	dbSNP_87	55	2232,6368	704.2+/-405.4	297,1638,2365	yes	missense	AIM1	NM_001624.2	76	381,2395,3727	CC,CA,AA		25.9535,20.9941,24.2734	benign	293/1724	106967185	3157,9849	2203	4300	6503	SO:0001583	missense	202	exon2			GAGGCCAAAGGAA	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.878A>C	6.37:g.106967185A>C	ENSP00000358062:p.Gln293Pro	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	373	0.1707875457875458	98	0.1991869918699187	73	0.20165745856353592	27	0.0472027972027972	175	0.23087071240105542	C	2.681	-0.275346	0.05679	0.209941	0.259535	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71103	-0.54	5.73	2.58	0.30949	.	1.852350	0.03052	N	0.154645	T	0.22820	0.0551	N	0.02011	-0.69	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.03184	-1.1063	9	0.25106	T	0.35	.	8.426	0.32729	0.1137:0.6849:0.0:0.2014	rs1159148;rs17495353;rs56550327;rs58077185;rs1159148	293	Q9Y4K1	AIM1_HUMAN	P	701;293	ENSP00000358062:Q293P	ENSP00000285105:Q701P	Q	+	2	0	AIM1	107073878	0.001000	0.12720	0.000000	0.03702	0.018000	0.09664	1.127000	0.31357	0.381000	0.24851	-0.121000	0.15023	CAA	A|0.787;C|0.213	0.213	strong		0.428	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
KCNQ3	3786	hgsc.bcm.edu	37	8	133192449	133192449	+	Silent	SNP	A	A	G	rs41272387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133192449A>G	ENST00000388996.4	-	4	1152	c.732T>C	c.(730-732)ggT>ggC	p.G244G	KCNQ3_ENST00000519445.1_Silent_p.G244G|KCNQ3_ENST00000521134.1_Silent_p.G124G	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	244					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TCCAGGTGCCACCTCTCCGGT	0.602													G|||	121	0.0241613	0.003	0.0303	5008	,	,		19755	0.0		0.0835	False		,,,				2504	0.0123				p.G244G		Atlas-SNP	.											.	KCNQ3	164	.	0			c.T732C						PASS	.	G	,	64,4342	820.1+/-416.4	0,64,2139	84.0	75.0	78.0		372,732	-5.8	0.9	8	dbSNP_127	78	606,7994	791.9+/-407.5	27,552,3721	no	coding-synonymous,coding-synonymous	KCNQ3	NM_001204824.1,NM_004519.3	,	27,616,5860	GG,GA,AA		7.0465,1.4526,5.1515	,	124/753,244/873	133192449	670,12336	2203	4300	6503	SO:0001819	synonymous_variant	3786	exon4			GGTGCCACCTCTC	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.732T>C	8.37:g.133192449A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																			A|0.951;G|0.049	0.049	strong		0.602	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
NFRKB	4798	hgsc.bcm.edu	37	11	129754668	129754668	+	Silent	SNP	T	T	C	rs2303662	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:129754668T>C	ENST00000446488.3	-	6	817	c.714A>G	c.(712-714)acA>acG	p.T238T	NFRKB_ENST00000304521.5_Silent_p.T238T|NFRKB_ENST00000524746.1_Silent_p.T238T|NFRKB_ENST00000524794.1_Silent_p.T263T	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	238					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)		TGGTTGAAAGTGTGGGCACCA	0.517													T|||	844	0.16853	0.174	0.111	5008	,	,		16465	0.0565		0.1859	False		,,,				2504	0.2996				p.T263T		Atlas-SNP	.											.	NFRKB	101	.	0			c.A789G						PASS	.	T	,	761,3641	306.3+/-289.4	66,629,1506	69.0	76.0	74.0		714,789	-3.7	1.0	11	dbSNP_100	74	1381,7213	266.5+/-286.8	102,1177,3018	no	coding-synonymous,coding-synonymous	NFRKB	NM_001143835.1,NM_006165.3	,	168,1806,4524	CC,CT,TT		16.0694,17.2876,16.482	,	238/1300,263/1325	129754668	2142,10854	2201	4297	6498	SO:0001819	synonymous_variant	4798	exon5			TGAAAGTGTGGGC		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.714A>G	11.37:g.129754668T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																			T|0.849;C|0.151	0.151	strong		0.517	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
ZNF423	23090	hgsc.bcm.edu	37	16	49672520	49672520	+	Silent	SNP	A	A	G	rs3803665	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:49672520A>G	ENST00000561648.1	-	4	596	c.543T>C	c.(541-543)cgT>cgC	p.R181R	ZNF423_ENST00000567169.1_Silent_p.R64R|ZNF423_ENST00000262383.2_Silent_p.R181R|ZNF423_ENST00000563137.2_Silent_p.R121R|ZNF423_ENST00000562871.1_Silent_p.R121R|ZNF423_ENST00000562520.1_Silent_p.R121R|ZNF423_ENST00000535559.1_Silent_p.R64R	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	181					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|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)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				TGTGCCGGTCACGGCTCCTCT	0.582													G|||	2898	0.578674	0.9115	0.4597	5008	,	,		19203	0.4603		0.4254	False		,,,				2504	0.4928				p.R181R		Atlas-SNP	.											.	ZNF423	463	.	0			c.T543C						PASS	.	G		3731,665	280.2+/-275.2	1592,547,59	49.0	44.0	46.0		543	-2.0	1.0	16	dbSNP_107	46	3677,4923	619.8+/-397.0	799,2079,1422	no	coding-synonymous	ZNF423	NM_015069.2		2391,2626,1481	GG,GA,AA		42.7558,15.1274,42.9978		181/1285	49672520	7408,5588	2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			CCGGTCACGGCTC	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.543T>C	16.37:g.49672520A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	37	CCDS32445.1																																																																																			A|0.440;G|0.560	0.560	strong		0.582	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
SPAG5	10615	hgsc.bcm.edu	37	17	26919894	26919894	+	Missense_Mutation	SNP	C	C	T	rs34977204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:26919894C>T	ENST00000321765.5	-	3	700	c.368G>A	c.(367-369)gGc>gAc	p.G123D		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	123					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CATATAATTGCCCAGTGGGTC	0.453													C|||	23	0.00459265	0.0008	0.0144	5008	,	,		20736	0.0		0.0119	False		,,,				2504	0.0				p.G123D		Atlas-SNP	.											.	SPAG5	92	.	0			c.G368A						PASS	.	C	ASP/GLY	9,4397	15.5+/-35.6	0,9,2194	180.0	170.0	173.0		368	2.2	0.0	17	dbSNP_126	173	52,8548	34.3+/-88.2	0,52,4248	yes	missense	SPAG5	NM_006461.3	94	0,61,6442	TT,TC,CC		0.6047,0.2043,0.469	benign	123/1194	26919894	61,12945	2203	4300	6503	SO:0001583	missense	10615	exon3			TAATTGCCCAGTG	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.368G>A	17.37:g.26919894C>T	ENSP00000323300:p.Gly123Asp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	12	0.005494505494505495	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	5	0.006596306068601583	C	1.295	-0.606509	0.03717	0.002043	0.006047	ENSG00000076382	ENST00000321765	T	0.19250	2.16	5.76	2.17	0.27698	.	0.812758	0.11135	N	0.595928	T	0.01421	0.0046	N	0.00119	-2.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40117	-0.9580	10	0.02654	T	1	0.0508	3.8674	0.09022	0.154:0.1682:0.0:0.6778	rs34977204;rs34977204	123	Q96R06	SPAG5_HUMAN	D	123	ENSP00000323300:G123D	ENSP00000323300:G123D	G	-	2	0	SPAG5	23944021	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.442000	0.21628	0.431000	0.26258	-0.294000	0.09567	GGC	C|0.994;T|0.006	0.006	strong		0.453	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
LCP2	3937	hgsc.bcm.edu	37	5	169685163	169685163	+	Silent	SNP	C	C	T	rs315717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:169685163C>T	ENST00000046794.5	-	16	1593	c.978G>A	c.(976-978)caG>caA	p.Q326Q	LCP2_ENST00000521416.1_Silent_p.Q121Q	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	326					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		GCAAAGGTCTCTGATGCACTG	0.493													T|||	2781	0.555312	0.6762	0.5865	5008	,	,		19183	0.5675		0.4712	False		,,,				2504	0.4438				p.Q326Q		Atlas-SNP	.											.	LCP2	133	.	0			c.G978A						PASS	.	T		2494,1374		820,854,260	166.0	164.0	165.0		978	-11.4	0.0	5	dbSNP_79	165	4023,4259		962,2099,1080	yes	coding-synonymous	LCP2	NM_005565.3		1782,2953,1340	TT,TC,CC		48.5752,35.5222,46.3621		326/534	169685163	6517,5633	1934	4141	6075	SO:0001819	synonymous_variant	3937	exon16			AGGTCTCTGATGC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.978G>A	5.37:g.169685163C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_005565	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	37	CCDS47339.1																																																																																			C|0.429;T|0.571	0.571	strong		0.493	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
SYNE2	23224	hgsc.bcm.edu	37	14	64580061	64580061	+	Silent	SNP	C	C	T	rs114604397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64580061C>T	ENST00000344113.4	+	66	12824	c.12612C>T	c.(12610-12612)ggC>ggT	p.G4204G	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.G838G|SYNE2_ENST00000358025.3_Silent_p.G4204G|SYNE2_ENST00000394768.2_Silent_p.G589G|SYNE2_ENST00000554584.1_Silent_p.G4219G|SYNE2_ENST00000357395.3_Silent_p.G589G	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4204					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)		TCTCTTAGGGCACCACACCTC	0.522													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18493	0.0		0.0	False		,,,				2504	0.0				p.G4204G		Atlas-SNP	.											.	SYNE2	577	.	0			c.C12612T						PASS	.	C	,	75,4331	67.0+/-104.6	1,73,2129	54.0	55.0	55.0		12612,12612	2.3	1.0	14	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	1,73,6429	TT,TC,CC		0.0,1.7022,0.5767	,	4204/6886,4204/6908	64580061	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon66			TTAGGGCACCACA	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.12612C>T	14.37:g.64580061C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.993;T|0.007	0.007	strong		0.522	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
OR51G2	81282	hgsc.bcm.edu	37	11	4936613	4936613	+	Missense_Mutation	SNP	G	G	T	rs16907312	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4936613G>T	ENST00000322013.3	-	1	309	c.281C>A	c.(280-282)gCa>gAa	p.A94E	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	94			A -> E (in dbSNP:rs16907312).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A94E(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		AATTTCTCGTGCTCCAACCCA	0.507													G|||	965	0.192692	0.3366	0.1009	5008	,	,		21623	0.0526		0.1233	False		,,,				2504	0.2791				p.A94E		Atlas-SNP	.											OR51G2,NS,carcinoma,0,1	OR51G2	70	1	1	Substitution - Missense(1)	stomach(1)	c.C281A						PASS	.	G	GLU/ALA	1155,3247	408.9+/-334.8	161,833,1207	90.0	81.0	84.0		281	3.7	0.0	11	dbSNP_123	84	1081,7515	225.5+/-261.6	87,907,3304	yes	missense	OR51G2	NM_001005238.1	107	248,1740,4511	TT,TG,GG		12.5756,26.2381,17.2026	possibly-damaging	94/315	4936613	2236,10762	2201	4298	6499	SO:0001583	missense	81282	exon1			TCTCGTGCTCCAA	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"""GPCR / Class A : Olfactory receptors"""	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.281C>A	11.37:g.4936613G>T	ENSP00000322593:p.Ala94Glu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	299	0.13690476190476192	138	0.2804878048780488	42	0.11602209944751381	35	0.06118881118881119	84	0.11081794195250659	G	5.610	0.297375	0.10622	0.262381	0.125756	ENSG00000176893	ENST00000322013	T	0.02944	4.1	5.58	3.73	0.42828	GPCR, rhodopsin-like superfamily (1);	1.020540	0.07833	N	0.961665	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P	0.37914	0.611	B	0.29353	0.101	T	0.47484	-0.9114	9	0.56958	D	0.05	.	10.8956	0.47021	0.1512:0.0:0.8488:0.0	rs16907312;rs61577190;rs16907312	94	Q8NGK0	O51G2_HUMAN	E	94	ENSP00000322593:A94E	ENSP00000322593:A94E	A	-	2	0	OR51G2	4893189	0.000000	0.05858	0.020000	0.16555	0.016000	0.09150	-0.688000	0.05150	0.922000	0.37019	0.655000	0.94253	GCA	G|0.831;T|0.169	0.169	strong		0.507	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238	
ABHD8	79575	hgsc.bcm.edu	37	19	17412366	17412366	+	Silent	SNP	G	G	A	rs11086066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17412366G>A	ENST00000247706.3	-	2	299	c.60C>T	c.(58-60)gcC>gcT	p.A20A	MRPL34_ENST00000594999.1_5'Flank|MRPL34_ENST00000595444.1_Intron|MRPL34_ENST00000600434.1_Intron	NM_024527.4	NP_078803.4	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	20							hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	9						GTGGCCCCACGGCGTTGGGGG	0.652													G|||	1187	0.237021	0.1286	0.2277	5008	,	,		15353	0.1319		0.325	False		,,,				2504	0.408				p.A20A	Ovarian(156;1368 2543 15275 41187)	Atlas-SNP	.											.	ABHD8	26	.	0			c.C60T						PASS	.	G		707,3643		62,583,1530	23.0	25.0	24.0		60	-10.5	0.7	19	dbSNP_120	24	2448,6010		382,1684,2163	no	coding-synonymous	ABHD8	NM_024527.4		444,2267,3693	AA,AG,GG		28.943,16.2529,24.633		20/440	17412366	3155,9653	2175	4229	6404	SO:0001819	synonymous_variant	79575	exon2			CCCCACGGCGTTG	AK021805	CCDS12355.1	19p13.12	2010-12-09			ENSG00000127220	ENSG00000127220		"""Abhydrolase domain containing"""	23759	protein-coding gene	gene with protein product						12477932	Standard	NM_024527		Approved	FLJ11743, MGC14280, MGC2512	uc002ngb.4	Q96I13		ENST00000247706.3:c.60C>T	19.37:g.17412366G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_024527	Q9HAE9	Silent	SNP	ENST00000247706.3	37	CCDS12355.1																																																																																			G|0.784;A|0.216	0.216	strong		0.652	ABHD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462937.1	NM_024527	
FES	2242	hgsc.bcm.edu	37	15	91428290	91428290	+	Silent	SNP	C	C	T	rs11539637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:91428290C>T	ENST00000328850.3	+	2	157	c.15C>T	c.(13-15)tcC>tcT	p.S5S	FES_ENST00000450438.2_Silent_p.S5S|FES_ENST00000394300.3_Silent_p.S5S|FES_ENST00000444422.2_Silent_p.S5S|FES_ENST00000414248.2_Silent_p.S5S|FES_ENST00000394302.1_Silent_p.S5S	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	5	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.|Important for interaction with membranes containing phosphoinositides.				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)			GCTTCTCTTCCGAGCTGTGCA	0.632													C|||	2942	0.58746	0.382	0.7277	5008	,	,		19330	0.8065		0.5258	False		,,,				2504	0.6033				p.S5S		Atlas-SNP	.											.	FES	102	.	0			c.C15T						PASS	.	C	,,,	1859,2537	529.5+/-372.7	378,1103,717	106.0	119.0	115.0		15,15,15,15	-9.8	0.0	15	dbSNP_120	115	4555,4041	593.3+/-393.1	1210,2135,953	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FES	NM_001143783.1,NM_001143784.1,NM_001143785.1,NM_002005.3	,,,	1588,3238,1670	TT,TC,CC		47.0102,42.2884,49.3688	,,,	5/765,5/753,5/695,5/823	91428290	6414,6578	2198	4298	6496	SO:0001819	synonymous_variant	2242	exon1			CTCTTCCGAGCTG	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.15C>T	15.37:g.91428290C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_001143783	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																			C|0.473;T|0.527	0.527	strong		0.632	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005	
CHST13	166012	hgsc.bcm.edu	37	3	126261345	126261345	+	Missense_Mutation	SNP	G	G	A	rs1056522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:126261345G>A	ENST00000319340.2	+	3	1000	c.950G>A	c.(949-951)cGg>cAg	p.R317Q		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	317			R -> Q (in dbSNP:rs1056522). {ECO:0000269|PubMed:15489334}.		carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		TTCTACCAGCGGCGCCTCTTC	0.687													G|||	1612	0.321885	0.4622	0.3444	5008	,	,		9648	0.2569		0.2992	False		,,,				2504	0.2065				p.R317Q		Atlas-SNP	.											.	CHST13	21	.	0			c.G950A						PASS	.	G	GLN/ARG	1519,2051		338,843,604	11.0	11.0	11.0		950	2.0	1.0	3	dbSNP_86	11	2065,5231		339,1387,1922	yes	missense	CHST13	NM_152889.2	43	677,2230,2526	AA,AG,GG		28.3032,42.549,32.9836	probably-damaging	317/342	126261345	3584,7282	1785	3648	5433	SO:0001583	missense	166012	exon3			ACCAGCGGCGCCT	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"""Sulfotransferases, membrane-bound"""	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.950G>A	3.37:g.126261345G>A	ENSP00000317404:p.Arg317Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_152889	Q3SYA3|Q3SYA5	Missense_Mutation	SNP	ENST00000319340.2	37	CCDS3039.1	738	0.33791208791208793	232	0.4715447154471545	126	0.34806629834254144	151	0.263986013986014	229	0.3021108179419525	G	7.729	0.698807	0.15106	0.42549	0.283032	ENSG00000180767	ENST00000319340	T	0.72942	-0.7	3.89	1.96	0.26148	.	0.134719	0.44688	U	0.000428	T	0.00012	0.0000	L	0.41824	1.3	0.09310	P	0.99999902818	B	0.28419	0.211	B	0.28011	0.085	T	0.45041	-0.9288	9	0.26408	T	0.33	-22.0086	7.5408	0.27737	0.2353:0.0:0.7647:0.0	rs1056522;rs3172309;rs59933474;rs1056522	317	Q8NET6	CHSTD_HUMAN	Q	317	ENSP00000317404:R317Q	ENSP00000317404:R317Q	R	+	2	0	CHST13	127744035	1.000000	0.71417	0.995000	0.50966	0.060000	0.15804	1.832000	0.39151	0.102000	0.17638	0.313000	0.20887	CGG	G|0.655;A|0.345	0.345	strong		0.687	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552717	43552717	+	Silent	SNP	G	G	C	rs147243132	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	309	0	0		WXS	Illumina HiSeq	Phase_I	276	259	0.938406	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	
GRIK2	2898	hgsc.bcm.edu	37	6	102503317	102503317	+	Silent	SNP	G	G	A	rs2227283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:102503317G>A	ENST00000421544.1	+	15	2914	c.2424G>A	c.(2422-2424)gaG>gaA	p.E808E	GRIK2_ENST00000369137.3_Silent_p.E732E|GRIK2_ENST00000369138.1_Silent_p.E808E|GRIK2_ENST00000413795.1_Silent_p.E808E|GRIK2_ENST00000369134.4_Silent_p.E759E|GRIK2_ENST00000318991.6_Silent_p.E808E	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	808					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CAGAAGAGGAGAGCAAAGAGG	0.493													G|||	1640	0.327476	0.2375	0.4107	5008	,	,		14836	0.3601		0.4414	False		,,,				2504	0.2393				p.E808E		Atlas-SNP	.											.	GRIK2	487	.	0			c.G2424A						PASS	.	G	,,	1237,3169	424.9+/-340.6	172,893,1138	110.0	114.0	113.0		2424,2424,2424	0.9	1.0	6	dbSNP_98	113	3789,4811	536.8+/-383.1	847,2095,1358	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIK2	NM_001166247.1,NM_021956.4,NM_175768.3	,,	1019,2988,2496	AA,AG,GG		44.0581,28.0754,38.6437	,,	808/893,808/909,808/870	102503317	5026,7980	2203	4300	6503	SO:0001819	synonymous_variant	2898	exon15			AGAGGAGAGCAAA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2424G>A	6.37:g.102503317G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																			A|0.381;C|0.006	0.381	strong		0.493	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
FHAD1	114827	hgsc.bcm.edu	37	1	15616139	15616139	+	Missense_Mutation	SNP	G	G	A	rs486557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15616139G>A	ENST00000375998.4	+	3	545	c.545G>A	c.(544-546)cGc>cAc	p.R182H	FHAD1_ENST00000358897.4_Missense_Mutation_p.R182H|FHAD1_ENST00000375999.3_Missense_Mutation_p.R182H|FHAD1_ENST00000417793.1_Missense_Mutation_p.R182H			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	182										skin(1)|stomach(1)	2						GACGACGCCCGCAAGCCACCC	0.612													G|||	1042	0.208067	0.2073	0.2089	5008	,	,		16676	0.0417		0.326	False		,,,				2504	0.2587				p.R182H		Atlas-SNP	.											.	FHAD1	78	.	0			c.G545A						PASS	.						28.0	36.0	34.0					1																	15616139		692	1591	2283	SO:0001583	missense	114827	exon4			ACGCCCGCAAGCC	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.545G>A	1.37:g.15616139G>A	ENSP00000365166:p.Arg182His	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		473	0.21657509157509158	110	0.22357723577235772	100	0.27624309392265195	22	0.038461538461538464	241	0.3179419525065963	G	5.490	0.275364	0.10403	.	.	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998	T;T;T;T	0.46819	0.88;0.87;0.86;0.88	3.77	-7.54	0.01332	.	1.620530	0.04279	N	0.343560	T	0.00012	0.0000	N	0.02539	-0.55	0.50313	P	1.36000000000025E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.17228	-1.0376	9	0.36615	T	0.2	-1.7323	12.0544	0.53527	0.1394:0.6827:0.178:0.0	rs486557;rs3765352;rs52797627;rs60426766;rs486557	182	B1AJZ9	FHAD1_HUMAN	H	182	ENSP00000351770:R182H;ENSP00000407615:R182H;ENSP00000365167:R182H;ENSP00000365166:R182H	ENSP00000351770:R182H	R	+	2	0	FHAD1	15488726	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.847000	0.04331	-1.849000	0.01171	-1.154000	0.01816	CGC	G|0.777;A|0.223	0.223	strong		0.612	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
CLTCL1	8218	hgsc.bcm.edu	37	22	19197896	19197896	+	Silent	SNP	T	T	C	rs698423	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:19197896T>C	ENST00000263200.10	-	20	3261	c.3189A>G	c.(3187-3189)gcA>gcG	p.A1063A	CLTCL1_ENST00000353891.5_Silent_p.A1063A|CLTCL1_ENST00000442042.2_5'Flank|CLTCL1_ENST00000427926.1_Silent_p.A1063A	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1063	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)					CCTCATACAGTGCGCTGCTGA	0.552			T	?	ALCL								C|||	4247	0.848043	0.9652	0.7767	5008	,	,		19950	0.9365		0.6272	False		,,,				2504	0.8763				p.A1063A		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.A3189G						PASS	.	C	,	3844,356		1765,314,21	94.0	95.0	95.0		3189,3189	-5.9	0.0	22	dbSNP_86	95	5417,3041		1713,1991,525	no	coding-synonymous,coding-synonymous	CLTCL1	NM_001835.3,NM_007098.3	,	3478,2305,546	CC,CT,TT		35.9541,8.4762,26.8368	,	1063/1584,1063/1641	19197896	9261,3397	2100	4229	6329	SO:0001819	synonymous_variant	8218	exon20			ATACAGTGCGCTG		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.3189A>G	22.37:g.19197896T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			T|0.225;C|0.775	0.775	strong		0.552	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
NLRP13	126204	hgsc.bcm.edu	37	19	56416409	56416409	+	Silent	SNP	G	G	A	rs28506091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56416409G>A	ENST00000342929.3	-	8	2516	c.2517C>T	c.(2515-2517)caC>caT	p.H839H	NLRP13_ENST00000588751.1_Silent_p.H839H	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	839							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		ATCGAGTTACGTGTTGGATGC	0.537													G|||	257	0.0513179	0.0741	0.0735	5008	,	,		16374	0.0		0.0954	False		,,,				2504	0.0123				p.H839H		Atlas-SNP	.											.	NLRP13	220	.	0			c.C2517T						PASS	.	G		357,4049	184.7+/-212.0	15,327,1861	157.0	119.0	132.0		2517	-4.6	0.0	19	dbSNP_125	132	735,7865	177.6+/-227.2	26,683,3591	no	coding-synonymous	NLRP13	NM_176810.2		41,1010,5452	AA,AG,GG		8.5465,8.1026,8.3961		839/1044	56416409	1092,11914	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon8			AGTTACGTGTTGG	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2517C>T	19.37:g.56416409G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.922;A|0.078	0.078	strong		0.537	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
SYK	6850	hgsc.bcm.edu	37	9	93641199	93641199	+	Silent	SNP	T	T	C	rs2306040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:93641199T>C	ENST00000375754.4	+	11	1693	c.1545T>C	c.(1543-1545)ctT>ctC	p.L515L	SYK_ENST00000375747.1_Silent_p.L492L|SYK_ENST00000375751.4_Silent_p.L492L|SYK_ENST00000375746.1_Silent_p.L515L	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	515	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						ATTTCGGACTTTCCAAAGCAC	0.408			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								T|||	655	0.130791	0.0628	0.3084	5008	,	,		20561	0.2321		0.0636	False		,,,				2504	0.0613				p.L515L		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.T1545C						PASS	.	T	,,,	311,4095	166.2+/-197.5	16,279,1908	141.0	127.0	132.0		1476,1545,1476,1545	2.7	1.0	9	dbSNP_100	132	555,8045	150.3+/-205.2	13,529,3758	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	29,808,5666	CC,CT,TT		6.4535,7.0586,6.6585	,,,	492/613,515/636,492/613,515/636	93641199	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon11			CGGACTTTCCAAA	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.1545T>C	9.37:g.93641199T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			T|0.908;C|0.092	0.092	strong		0.408	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
MCM3AP	8888	hgsc.bcm.edu	37	21	47703649	47703649	+	Silent	SNP	G	G	A	rs11702450	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47703649G>A	ENST00000397708.1	-	3	1577	c.1323C>T	c.(1321-1323)aaC>aaT	p.N441N	YBEY_ENST00000397701.4_5'Flank|YBEY_ENST00000329319.3_5'Flank|MCM3AP_ENST00000291688.1_Silent_p.N441N|YBEY_ENST00000397692.1_5'Flank|YBEY_ENST00000339195.6_5'Flank|YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000397694.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	441	DNA primase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					AGTCAGGGATGTTCTTGCACT	0.517													G|||	1355	0.270567	0.2005	0.232	5008	,	,		19290	0.1558		0.4125	False		,,,				2504	0.365				p.N441N		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C1323T						PASS	.	G		952,3454	360.4+/-315.2	94,764,1345	141.0	125.0	131.0		1323	2.5	1.0	21	dbSNP_120	131	3378,5222	501.6+/-375.5	668,2042,1590	no	coding-synonymous	MCM3AP	NM_003906.3		762,2806,2935	AA,AG,GG		39.2791,21.6069,33.2923		441/1981	47703649	4330,8676	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon2			AGGGATGTTCTTG	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.1323C>T	21.37:g.47703649G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			G|0.699;A|0.301	0.301	strong		0.517	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
USH1C	10083	hgsc.bcm.edu	37	11	17531146	17531146	+	Intron	SNP	G	G	A	rs17776775	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:17531146G>A	ENST00000318024.4	-	16	1393				USH1C_ENST00000529563.1_Intron|USH1C_ENST00000527020.1_Intron|USH1C_ENST00000005226.7_Silent_p.A590A|USH1C_ENST00000527720.1_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						GAGAGGATGAGGCGCTCACAT	0.672													G|||	345	0.0688898	0.0076	0.0389	5008	,	,		7889	0.0397		0.0527	False		,,,				2504	0.2198				p.A590A		Atlas-SNP	.											.	USH1C	157	.	0			c.C1770T						PASS	.	G	,	77,4311		2,73,2119	11.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,1770	4.6	0.6	11	dbSNP_123	13	396,8166		10,376,3895	no	intron,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	12,449,6014	AA,AG,GG		4.6251,1.7548,3.6525	,	,590/900	17531146	473,12477	2194	4281	6475	SO:0001627	intron_variant	10083	exon18			GGATGAGGCGCTC	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.1285-7619C>T	11.37:g.17531146G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			A|0.048;G|0.952	0.048	strong		0.672	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
NOLC1	9221	hgsc.bcm.edu	37	10	103920475	103920475	+	Missense_Mutation	SNP	T	T	C	rs1049455	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103920475T>C	ENST00000605788.1	+	10	1601	c.1366T>C	c.(1366-1368)Tct>Cct	p.S456P	NOLC1_ENST00000603742.1_Missense_Mutation_p.S175P|NOLC1_ENST00000488254.2_Missense_Mutation_p.S457P|NOLC1_ENST00000405356.1_Missense_Mutation_p.S466P	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	456	11 X 12 AA approximate repeats of an acidic serine cluster.		S -> P (in dbSNP:rs1049455). {ECO:0000269|PubMed:7584026}.		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)		AGCAGCTCTATCTCTGCCTGC	0.557													C|||	916	0.182907	0.5477	0.1052	5008	,	,		20309	0.001		0.0815	False		,,,				2504	0.0368				p.S456P		Atlas-SNP	.											.	NOLC1	61	.	0			c.T1366C						PASS	.	C	PRO/SER	2015,2389	604.0+/-390.2	459,1097,646	59.0	58.0	58.0		1366	-0.5	0.0	10	dbSNP_86	58	729,7871	775.3+/-407.7	33,663,3604	yes	missense	NOLC1	NM_004741.3	74	492,1760,4250	CC,CT,TT		8.4767,45.7539,21.1012	benign	456/700	103920475	2744,10260	2202	4300	6502	SO:0001583	missense	9221	exon10			GCTCTATCTCTGC	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.1366T>C	10.37:g.103920475T>C	ENSP00000474710:p.Ser456Pro	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	37	CCDS7530.1	355	0.16254578754578755	241	0.4898373983739837	44	0.12154696132596685	0	0.0	70	0.09234828496042216	C	2.603	-0.292553	0.05568	0.457539	0.084767	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.49720	0.77	5.94	-0.492	0.12041	.	0.538227	0.18818	N	0.130321	T	0.00012	0.0000	L	0.31526	0.94	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	0.47923	-0.9079	9	0.22109	T	0.4	0.0149	5.2759	0.15649	0.0:0.3173:0.2697:0.413	rs1049455;rs3189626;rs1049455	457;466;456	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	P	466;456	ENSP00000385410:S466P	ENSP00000359024:S456P	S	+	1	0	NOLC1	103910465	0.000000	0.05858	0.005000	0.12908	0.016000	0.09150	-0.550000	0.06034	-0.348000	0.08286	-1.073000	0.02249	TCT	T|0.797;C|0.203	0.203	strong		0.557	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2422177	2422177	+	Missense_Mutation	SNP	G	G	A	rs735911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2422177G>A	ENST00000332578.3	+	13	2378	c.2378G>A	c.(2377-2379)aGc>aAc	p.S793N		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	793			S -> N (in dbSNP:rs735911). {ECO:0000269|PubMed:14702039}.		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)		TCTGCCGTGAGCACCACTGCT	0.667													G|||	631	0.125998	0.1316	0.0634	5008	,	,		15988	0.2361		0.0398	False		,,,				2504	0.138				p.S793N		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G2378A						PASS	.	G	ASN/SER	554,3852	249.0+/-256.6	45,464,1694	85.0	91.0	89.0		2378	-1.8	0.0	19	dbSNP_86	89	374,8226	122.2+/-181.2	3,368,3929	yes	missense	TMPRSS9	NM_182973.1	46	48,832,5623	AA,AG,GG		4.3488,12.5738,7.1352	benign	793/1060	2422177	928,12078	2203	4300	6503	SO:0001583	missense	360200	exon13			CCGTGAGCACCAC	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.2378G>A	19.37:g.2422177G>A	ENSP00000330264:p.Ser793Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	283	0.1295787545787546	62	0.12601626016260162	31	0.0856353591160221	156	0.2727272727272727	34	0.044854881266490766	G	6.930	0.541281	0.13250	0.125738	0.043488	ENSG00000178297	ENST00000332578	D	0.88124	-2.34	3.6	-1.81	0.07882	.	0.521109	0.17635	N	0.167240	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.26195	0.144	B	0.20577	0.03	T	0.03231	-1.1058	9	0.17832	T	0.49	.	4.2769	0.10813	0.0986:0.4641:0.2968:0.1405	rs735911;rs61033695;rs735911	793	Q7Z410	TMPS9_HUMAN	N	793	ENSP00000330264:S793N	ENSP00000330264:S793N	S	+	2	0	TMPRSS9	2373177	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.096000	0.11059	-0.330000	0.08514	-0.448000	0.05591	AGC	G|0.896;A|0.104	0.104	strong		0.667	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
MAN1B1	11253	hgsc.bcm.edu	37	9	140002995	140002995	+	Silent	SNP	C	C	T	rs118117962	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140002995C>T	ENST00000371589.4	+	13	2125	c.2052C>T	c.(2050-2052)taC>taT	p.Y684Y	MAN1B1_ENST00000474902.1_Silent_p.Y387Y|MAN1B1_ENST00000540391.1_3'UTR	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	684					cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|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 quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.Y684Y(1)		autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		TGGATGCCTACGTGTTCAACA	0.592													C|||	81	0.0161741	0.0015	0.0331	5008	,	,		18114	0.0		0.0368	False		,,,				2504	0.0194				p.Y684Y		Atlas-SNP	.											MAN1B1,NS,carcinoma,0,1	MAN1B1	40	1	1	Substitution - coding silent(1)	ovary(1)	c.C2052T						PASS	.	C		39,4367	43.1+/-76.7	0,39,2164	202.0	199.0	200.0		2052	-7.6	0.1	9	dbSNP_132	200	400,8200	127.5+/-185.8	10,380,3910	no	coding-synonymous	MAN1B1	NM_016219.3		10,419,6074	TT,TC,CC		4.6512,0.8852,3.3754		684/700	140002995	439,12567	2203	4300	6503	SO:0001819	synonymous_variant	11253	exon13			TGCCTACGTGTTC	AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239			6823	protein-coding gene	gene with protein product	"""endoplasmic reticulum alpha-mannosidase 1"", ""alpha 1,2-mannosidase"", ""endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1"", ""ER alpha 1,2-mannosidase"", ""Man9GlcNAc2-specific processing alpha-mannosidase"""	604346				10409699, 10521544	Standard	NM_016219		Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.2052C>T	9.37:g.140002995C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	156	71	0.455128	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Silent	SNP	ENST00000371589.4	37	CCDS7029.1	46|46	0.021062271062271064|0.021062271062271064	1|1	0.0020325203252032522|0.0020325203252032522	16|16	0.04419889502762431|0.04419889502762431	0|0	0.0|0.0	29|29	0.03825857519788918|0.03825857519788918	C|C	9.288|9.288	1.049890|1.049890	0.19827|0.19827	0.008852|0.008852	0.046512|0.046512	ENSG00000177239|ENSG00000177239	ENST00000550113|ENST00000475449	.|.	.|.	.|.	5.44|5.44	-7.55|-7.55	0.01327|0.01327	.|.	.|.	.|.	.|.	.|.	T|T	0.24928|0.24928	0.0605|0.0605	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.65853|0.65853	-0.6067|-0.6067	4|4	.|.	.|.	.|.	.|.	17.6248|17.6248	0.88091|0.88091	0.0119:0.794:0.0:0.194|0.0119:0.794:0.0:0.194	.|.	.|.	.|.	.|.	C|M	109|110	.|.	.|.	R|T	+|+	1|2	0|0	MAN1B1|MAN1B1	139122816|139122816	0.001000|0.001000	0.12720|0.12720	0.058000|0.058000	0.19502|0.19502	0.156000|0.156000	0.22039|0.22039	-1.774000|-1.774000	0.01784|0.01784	-1.344000|-1.344000	0.02216|0.02216	-1.036000|-1.036000	0.02392|0.02392	CGT|ACG	C|0.968;T|0.032	0.032	strong		0.592	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219	
RASGRF2	5924	hgsc.bcm.edu	37	5	80382675	80382675	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:80382675C>T	ENST00000265080.4	+	9	1360	c.1293C>T	c.(1291-1293)agC>agT	p.S431S	RASGRF2_ENST00000502677.1_3'UTR	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	431					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)		ATGAAGTCAGCGACACTGAAA	0.468																																					p.S431S		Atlas-SNP	.											.	RASGRF2	165	.	0			c.C1293T						PASS	.						146.0	123.0	131.0					5																	80382675		2203	4300	6503	SO:0001819	synonymous_variant	5924	exon9			AGTCAGCGACACT	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.1293C>T	5.37:g.80382675C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_006909	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	37	CCDS4052.1																																																																																			.	.	none		0.468	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
SHROOM2	357	hgsc.bcm.edu	37	X	9914947	9914947	+	Missense_Mutation	SNP	G	G	C	rs2073942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:9914947G>C	ENST00000380913.3	+	10	4911	c.4821G>C	c.(4819-4821)ttG>ttC	p.L1607F	SHROOM2_ENST00000418909.2_Missense_Mutation_p.L442F	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	1607	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.		L -> F (in dbSNP:rs2073942).		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)				AGTGCTTATTGGACAGCCTTC	0.567													C|||	1751	0.463841	0.5787	0.3429	3775	,	,		12496	0.4276		0.1819	False		,,,				2504	0.137				p.L1607F		Atlas-SNP	.											.	SHROOM2	139	.	0			c.G4821C						PASS	.	C	PHE/LEU	2631,1199		774,690,393,168,173	27.0	22.0	24.0		4821	-9.4	0.0	X	dbSNP_96	24	1645,5081		165,878,437,1385,1433	yes	missense	SHROOM2	NM_001649.2	22	939,1568,830,1553,1606	CC,CG,C,GG,G		24.4573,31.3055,40.5078	benign	1607/1617	9914947	4276,6280	2198	4298	6496	SO:0001583	missense	357	exon10			CTTATTGGACAGC	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.4821G>C	X.37:g.9914947G>C	ENSP00000370299:p.Leu1607Phe	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	37	CCDS14135.1	831	0.5009041591320073	219	0.6801242236024845	84	0.28378378378378377	180	0.47368421052631576	83	0.12691131498470948	C	8.484	0.860544	0.17178	0.686945	0.244573	ENSG00000146950	ENST00000380913;ENST00000418909	T;T	0.30714	1.52;1.52	4.69	-9.37	0.00626	Apx/shroom, ASD2 (2);	1.014080	0.07897	N	0.972089	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.23655	-1.0182	9	0.31617	T	0.26	-3.6589	11.2952	0.49274	0.0:0.4623:0.2526:0.2851	rs2073942;rs17255327;rs2073942	1607	Q13796	SHRM2_HUMAN	F	1607;442	ENSP00000370299:L1607F;ENSP00000415229:L442F	ENSP00000370299:L1607F	L	+	3	2	SHROOM2	9874947	0.000000	0.05858	0.003000	0.11579	0.729000	0.41735	-3.530000	0.00440	-2.894000	0.00314	-2.367000	0.00236	TTG	0|0.003;C|0.476	0.476	strong		0.567	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
FSCB	84075	hgsc.bcm.edu	37	14	44974189	44974189	+	Missense_Mutation	SNP	C	C	A	rs11621923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:44974189C>A	ENST00000340446.4	-	1	2293	c.2002G>T	c.(2002-2004)Gct>Tct	p.A668S	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	668	Ala-rich.					sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TGAACTTCAGCGGGGGCCTCC	0.617																																					p.A668S		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.G2002T						PASS	.						10.0	12.0	11.0					14																	44974189		2171	4287	6458	SO:0001583	missense	84075	exon1			CTTCAGCGGGGGC	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.2002G>T	14.37:g.44974189C>A	ENSP00000344579:p.Ala668Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	50	0.78125	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	839	0.3841575091575092	172	0.34959349593495936	128	0.35359116022099446	225	0.39335664335664333	314	0.41424802110817943	C	8.835	0.940852	0.18281	.	.	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.12039	2.72	4.24	-8.48	0.00935	.	.	.	.	.	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	B	0.25105	0.118	B	0.24155	0.051	T	0.44982	-0.9292	8	0.14656	T	0.56	-0.0478	4.397	0.11367	0.4313:0.2556:0.2435:0.0696	rs11621923	668	Q5H9T9	FSCB_HUMAN	S	668;561	ENSP00000344579:A668S	ENSP00000344579:A668S	A	-	1	0	FSCB	44043939	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-1.504000	0.02275	-1.989000	0.00979	-0.719000	0.03609	GCT	C|0.624;A|0.376	0.376	strong		0.617	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
ITGA1	3672	hgsc.bcm.edu	37	5	52229745	52229745	+	Missense_Mutation	SNP	T	T	G	rs12520591	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:52229745T>G	ENST00000282588.6	+	23	3341	c.2883T>G	c.(2881-2883)atT>atG	p.I961M	CTD-2175A23.1_ENST00000505701.1_RNA|CTD-2175A23.1_ENST00000503559.1_RNA	NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	961			I -> M (in dbSNP:rs12520591).		activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				AATACCACATTTCAATTGCTG	0.289													T|||	484	0.0966454	0.0182	0.2709	5008	,	,		10481	0.1548		0.0606	False		,,,				2504	0.0562				p.I961M		Atlas-SNP	.											.	ITGA1	112	.	0			c.T2883G						PASS	.	T	MET/ILE	137,4255	87.3+/-125.9	0,137,2059	41.0	45.0	44.0		2883	5.8	1.0	5	dbSNP_120	44	540,8018	144.5+/-200.4	16,508,3755	yes	missense	ITGA1	NM_181501.1	10	16,645,5814	GG,GT,TT		6.3099,3.1193,5.2278	probably-damaging	961/1180	52229745	677,12273	2196	4279	6475	SO:0001583	missense	3672	exon23			CCACATTTCAATT	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"""CD molecules"", ""Integrins"""	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.2883T>G	5.37:g.52229745T>G	ENSP00000282588:p.Ile961Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	37	CCDS3955.1	219	0.10027472527472528	12	0.024390243902439025	70	0.19337016574585636	90	0.15734265734265734	47	0.06200527704485488	T	19.56	3.850523	0.71719	0.031193	0.063099	ENSG00000213949	ENST00000282588	T	0.47528	0.84	5.77	5.77	0.91146	Integrin alpha-2 (1);	0.369480	0.30538	N	0.009420	T	0.00109	0.0003	L	0.34521	1.04	0.26804	P	0.9691364	P	0.48407	0.91	P	0.55161	0.77	T	0.05068	-1.0908	9	0.39692	T	0.17	.	12.482	0.55850	0.0:0.0:0.0:1.0	rs12520591;rs52813026;rs12520591	961	P56199	ITA1_HUMAN	M	961	ENSP00000282588:I961M	ENSP00000282588:I961M	I	+	3	3	ITGA1	52265502	1.000000	0.71417	0.997000	0.53966	0.871000	0.50021	2.323000	0.43823	2.194000	0.70268	0.528000	0.53228	ATT	T|0.931;G|0.069	0.069	strong		0.289	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501	
TTC28	23331	hgsc.bcm.edu	37	22	28378688	28378688	+	Missense_Mutation	SNP	C	C	G	rs9613558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:28378688C>G	ENST00000397906.2	-	23	7108	c.6967G>C	c.(6967-6969)Gct>Cct	p.A2323P	TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000430525.1_RNA|TTC28-AS1_ENST00000425112.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000454996.1_RNA|TTC28-AS1_ENST00000435348.1_RNA|TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000419253.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	2323	Ser-rich.				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						TAGGAGAGAGCTGGGGAGGGT	0.562													C|||	202	0.0403355	0.0023	0.1398	5008	,	,		17180	0.0		0.0755	False		,,,				2504	0.0266				p.A2323P		Atlas-SNP	.											.	TTC28	84	.	0			c.G6967C						PASS	.	C	PRO/ALA	19,1365		0,19,673	66.0	61.0	63.0		6967	5.1	0.4	22	dbSNP_119	63	180,3002		4,172,1415	yes	missense	TTC28	NM_001145418.1	27	4,191,2088	GG,GC,CC		5.6568,1.3728,4.3583	probably-damaging	2323/2482	28378688	199,4367	692	1591	2283	SO:0001583	missense	23331	exon23			AGAGAGCTGGGGA	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.6967G>C	22.37:g.28378688C>G	ENSP00000381003:p.Ala2323Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Missense_Mutation	SNP	ENST00000397906.2	37	CCDS46678.1	113	0.051739926739926737	2	0.0040650406504065045	47	0.1298342541436464	0	0.0	64	0.08443271767810026	C	21.6	4.173535	0.78452	0.013728	0.056568	ENSG00000100154	ENST00000397906	D	0.91792	-2.91	5.09	5.09	0.68999	.	0.064020	0.64402	D	0.000009	T	0.17619	0.0423	L	0.34521	1.04	0.58432	D	0.999999	D	0.89917	1.0	D	0.69307	0.963	T	0.66160	-0.5993	10	0.72032	D	0.01	-13.7889	17.8705	0.88810	0.0:1.0:0.0:0.0	rs9613558	2323	Q96AY4	TTC28_HUMAN	P	2323	ENSP00000381003:A2323P	ENSP00000381003:A2323P	A	-	1	0	TTC28	26708688	1.000000	0.71417	0.376000	0.26042	0.962000	0.63368	4.518000	0.60510	2.539000	0.85634	0.655000	0.94253	GCT	C|0.927;G|0.073	0.073	strong		0.562	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
SRPK1	6732	hgsc.bcm.edu	37	6	35803103	35803103	+	Missense_Mutation	SNP	C	C	T	rs35124200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35803103C>T	ENST00000373825.2	-	16	2231	c.1946G>A	c.(1945-1947)cGg>cAg	p.R649Q	SRPK1_ENST00000373822.1_Missense_Mutation_p.R541Q|SRPK1_ENST00000423325.2_Missense_Mutation_p.R633Q					SRSF protein kinase 1											endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						CCAAGGGTGCCGGAGACACTC	0.562													C|||	15	0.00299521	0.0008	0.0043	5008	,	,		17497	0.002		0.006	False		,,,				2504	0.0031				p.R649Q	NSCLC(31;67 978 16289 24856 26454)	Atlas-SNP	.											.	SRPK1	61	.	0			c.G1946A						PASS	.	C	GLN/ARG	11,4087		0,11,2038	48.0	56.0	54.0		1946	4.8	1.0	6	dbSNP_126	54	98,8296		1,96,4100	yes	missense	SRPK1	NM_003137.4	43	1,107,6138	TT,TC,CC		1.1675,0.2684,0.8726	benign	649/656	35803103	109,12383	2049	4197	6246	SO:0001583	missense	6732	exon16			GGGTGCCGGAGAC	U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"""SR protein kinase 1"", ""serine/arginine-rich splicing factor kinase 1"""	601939	"""SFRS protein kinase 1"""			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1946G>A	6.37:g.35803103C>T	ENSP00000362931:p.Arg649Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	NM_003137		Missense_Mutation	SNP	ENST00000373825.2	37	CCDS47415.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	2	0.0034965034965034965	4	0.005277044854881266	C	10.84	1.464011	0.26335	0.002684	0.011675	ENSG00000096063	ENST00000373825;ENST00000361690;ENST00000423325;ENST00000373822	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.64	4.77	0.60923	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.10252	0.0251	N	0.01146	-0.985	0.50039	D	0.999849	P;B	0.45240	0.854;0.093	B;B	0.32393	0.145;0.007	T	0.22800	-1.0206	9	0.08179	T	0.78	-5.1123	10.6703	0.45755	0.0:0.8541:0.0:0.1459	rs35124200	633;649	B4DS61;Q96SB4	.;SRPK1_HUMAN	Q	649;665;633;541	ENSP00000362931:R649Q;ENSP00000354674:R665Q;ENSP00000391069:R633Q;ENSP00000362928:R541Q	ENSP00000354674:R665Q	R	-	2	0	SRPK1	35911081	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.142000	0.42177	1.381000	0.46364	0.655000	0.94253	CGG	C|0.996;T|0.004	0.004	strong		0.562	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137	
MS4A14	84689	hgsc.bcm.edu	37	11	60182970	60182970	+	Missense_Mutation	SNP	A	A	T	rs7131283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60182970A>T	ENST00000300187.6	+	5	806	c.529A>T	c.(529-531)Aat>Tat	p.N177Y	MS4A14_ENST00000531787.1_Missense_Mutation_p.N65Y|MS4A14_ENST00000395005.2_Missense_Mutation_p.N160Y|MS4A14_ENST00000531783.1_Missense_Mutation_p.N210Y|MS4A14_ENST00000395001.1_3'UTR	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	177			N -> Y (in dbSNP:rs7131283). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			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						CCCAGAAGAAAATGATCAATT	0.358													A|||	2894	0.577875	0.5492	0.6902	5008	,	,		18916	0.4097		0.7018	False		,,,				2504	0.5828				p.N210Y		Atlas-SNP	.											.	MS4A14	120	.	0			c.A628T						PASS	.	A	TYR/ASN,TYR/ASN	2352,2054	606.6+/-390.8	623,1106,474	128.0	125.0	126.0		478,529	0.1	0.0	11	dbSNP_116	126	5976,2624	686.5+/-404.1	2071,1834,395	yes	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	143,143	2694,2940,869	TT,TA,AA		30.5116,46.6182,35.968	probably-damaging,probably-damaging	160/663,177/680	60182970	8328,4678	2203	4300	6503	SO:0001583	missense	84689	exon6			GAAGAAAATGATC	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.529A>T	11.37:g.60182970A>T	ENSP00000300187:p.Asn177Tyr	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	177	82	0.463277	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	1310	0.5998168498168498	272	0.5528455284552846	247	0.6823204419889503	264	0.46153846153846156	527	0.6952506596306068	A	13.06	2.125193	0.37533	0.533818	0.694884	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.12879	4.33;4.33;4.33;2.64	3.73	0.0768	0.14405	.	.	.	.	.	T	0.00012	0.0000	M	0.64997	1.995	0.58432	P	6.999999999979245E-6	D;D	0.69078	0.996;0.997	D;D	0.68353	0.947;0.957	T	0.41197	-0.9522	8	0.62326	D	0.03	-7.6972	3.2744	0.06893	0.5593:0.2118:0.2289:0.0	rs7131283;rs52794552;rs57607368;rs7131283	160;177	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	Y	65;177;160;210	ENSP00000437222:N65Y;ENSP00000300187:N177Y;ENSP00000378453:N160Y;ENSP00000433761:N210Y	ENSP00000300187:N177Y	N	+	1	0	MS4A14	59939546	0.700000	0.27796	0.022000	0.16811	0.009000	0.06853	0.397000	0.20883	-0.006000	0.14370	-0.263000	0.10527	AAT	A|0.376;T|0.624	0.624	strong		0.358	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
PSMB9	5698	hgsc.bcm.edu	37	6	32826233	32826233	+	Silent	SNP	A	A	G	rs20547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32826233A>G	ENST00000374859.2	+	5	552	c.483A>G	c.(481-483)gcA>gcG	p.A161A	PSMB9_ENST00000453265.2_Silent_p.A117A|PSMB9_ENST00000395330.1_Silent_p.A138A	NM_002800.4	NP_002791.1	P28065	PSB9_HUMAN	proteasome (prosome, macropain) subunit, beta type, 9	161					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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			large_intestine(4)|lung(4)|skin(1)	9					Carfilzomib(DB08889)	TGGATGCAGCATATAAGCCAG	0.542													A|||	503	0.100439	0.0189	0.1095	5008	,	,		19445	0.2093		0.0338	False		,,,				2504	0.1605				p.A161A		Atlas-SNP	.											PSMB9_ENST00000453265,NS,carcinoma,+2,2	PSMB9	16	2	0			c.A483G						PASS	.	A		65,2957		0,65,1446	76.0	82.0	80.0		483	-9.7	0.1	6	dbSNP_67	80	196,5220		1,194,2513	no	coding-synonymous	PSMB9	NM_002800.4		1,259,3959	GG,GA,AA		3.6189,2.1509,3.0932		161/220	32826233	261,8177	1511	2708	4219	SO:0001819	synonymous_variant	5698	exon5			TGCAGCATATAAG		CCDS4759.1	6p21.3	2013-03-27	2013-03-27		ENSG00000240065	ENSG00000240065		"""Proteasome (prosome, macropain) subunits"""	9546	protein-coding gene	gene with protein product		177045	"""proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)"", ""large multifunctional peptidase 2"""	LMP2		1922385, 1529427	Standard	NM_002800		Approved	RING12, beta1i, PSMB6i	uc003sga.3	P28065	OTTHUMG00000031287	ENST00000374859.2:c.483A>G	6.37:g.32826233A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_002800	B0V0T1|Q16523|Q5JNW4	Silent	SNP	ENST00000374859.2	37	CCDS4759.1																																																																																			A|0.938;G|0.062	0.062	strong		0.542	PSMB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076624.5	NM_002800	
DPYSL2	1808	hgsc.bcm.edu	37	8	26441477	26441477	+	Silent	SNP	G	G	A	rs11786691	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:26441477G>A	ENST00000311151.5	+	3	703	c.291G>A	c.(289-291)ctG>ctA	p.L97L	DPYSL2_ENST00000521913.1_Silent_p.L61L|DPYSL2_ENST00000523027.1_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	102	0	0		WXS	Illumina HiSeq	Phase_I	97	56	0.57732	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	
HOXB13	10481	hgsc.bcm.edu	37	17	46805443	46805443	+	Silent	SNP	A	A	G	rs9900627	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:46805443A>G	ENST00000290295.7	-	1	1097	c.513T>C	c.(511-513)tcT>tcC	p.S171S	PRAC2_ENST00000422730.2_RNA	NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	171					angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						CGAGAGCCCAAGACTGGTAAC	0.562													G|||	607	0.121206	0.0983	0.2075	5008	,	,		18987	0.1835		0.1064	False		,,,				2504	0.0419				p.S171S		Atlas-SNP	.											.	HOXB13	28	.	0			c.T513C						PASS	.	G		473,3933	782.9+/-414.6	30,413,1760	77.0	73.0	74.0		513	-0.7	1.0	17	dbSNP_119	74	826,7774	781.5+/-407.6	46,734,3520	no	coding-synonymous	HOXB13	NM_006361.5		76,1147,5280	GG,GA,AA		9.6047,10.7354,9.9877		171/285	46805443	1299,11707	2203	4300	6503	SO:0001819	synonymous_variant	10481	exon1			AGCCCAAGACTGG	U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184		"""Homeoboxes / ANTP class : HOXL subclass"""	5112	protein-coding gene	gene with protein product		604607	"""homeo box B13"""			8756292, 9665387	Standard	NM_006361		Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.513T>C	17.37:g.46805443A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_006361	B2R878|Q96QM4|Q99810	Silent	SNP	ENST00000290295.7	37	CCDS11536.1																																																																																			A|0.892;G|0.108	0.108	strong		0.562	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358087.3	NM_006361	
TSHZ3	57616	hgsc.bcm.edu	37	19	31770477	31770477	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:31770477G>A	ENST00000240587.4	-	2	549	c.222C>T	c.(220-222)agC>agT	p.S74S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	74					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)	p.S74S(1)		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)					TGTGTGACTCGCTGTCCATTT	0.592																																					p.S74S		Atlas-SNP	.											TSHZ3_ENST00000240587,colon,carcinoma,0,1	TSHZ3	549	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C222T						scavenged	.						55.0	54.0	54.0					19																	31770477		1982	4150	6132	SO:0001819	synonymous_variant	57616	exon2			TGACTCGCTGTCC	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.222C>T	19.37:g.31770477G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	2	0.0149254	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			.	.	none		0.592	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
ERMP1	79956	hgsc.bcm.edu	37	9	5805741	5805741	+	Silent	SNP	C	C	T	rs35643913	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:5805741C>T	ENST00000339450.5	-	9	1682	c.1593G>A	c.(1591-1593)tcG>tcA	p.S531S	ERMP1_ENST00000543230.1_Silent_p.S109S|ERMP1_ENST00000381506.3_Silent_p.S307S|ERMP1_ENST00000214893.5_5'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	531						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		GGACAAACAGCGAAATGTCAA	0.423													C|||	35	0.00698882	0.0	0.0029	5008	,	,		18923	0.0		0.006	False		,,,				2504	0.0276				p.S531S		Atlas-SNP	.											.	ERMP1	63	.	0			c.G1593A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	90.0	81.0	84.0		1593	-1.9	0.5	9	dbSNP_126	84	67,8533	40.3+/-97.0	0,67,4233	no	coding-synonymous	ERMP1	NM_024896.2		0,72,6431	TT,TC,CC		0.7791,0.1135,0.5536		531/905	5805741	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	79956	exon9			AAACAGCGAAATG	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.1593G>A	9.37:g.5805741C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Silent	SNP	ENST00000339450.5	37	CCDS34983.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
FPR1	2357	hgsc.bcm.edu	37	19	52249947	52249947	+	Missense_Mutation	SNP	C	C	G	rs2070745	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	scavenged	.	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	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	148	74	0.5	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	
C2orf54	79919	hgsc.bcm.edu	37	2	241828012	241828012	+	Silent	SNP	T	T	C	rs6708304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241828012T>C	ENST00000388934.4	-	4	1106	c.948A>G	c.(946-948)gaA>gaG	p.E316E	C2orf54_ENST00000307486.8_Silent_p.E167E|C2orf54_ENST00000402775.2_Silent_p.E148E	NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	316										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		CGCCCTGCAGTTCTGCCCAGT	0.697													C|||	2843	0.567692	0.8192	0.366	5008	,	,		9793	0.5278		0.5219	False		,,,				2504	0.4591				p.E316E		Atlas-SNP	.											C2orf54,colon,carcinoma,0,1	C2orf54	14	1	0			c.A948G						PASS	.	C	,	3233,979		1276,681,149	10.0	14.0	13.0		948,444	1.1	0.9	2	dbSNP_116	13	4211,4237		1104,2003,1117	no	coding-synonymous,coding-synonymous	C2orf54	NM_001085437.1,NM_024861.2	,	2380,2684,1266	CC,CT,TT		49.8461,23.2431,41.2006	,	316/448,148/280	241828012	7444,5216	2106	4224	6330	SO:0001819	synonymous_variant	79919	exon4			CTGCAGTTCTGCC	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.948A>G	2.37:g.241828012T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	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	
CES1	1066	hgsc.bcm.edu	37	16	55862712	55862712	+	Missense_Mutation	SNP	C	C	T	rs2307240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:55862712C>T	ENST00000361503.4	-	2	354	c.224G>A	c.(223-225)aGc>aAc	p.S75N	CES1_ENST00000422046.2_Missense_Mutation_p.S75N|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Missense_Mutation_p.S76N			P23141	EST1_HUMAN	carboxylesterase 1	75			S -> N (in dbSNP:rs2307240).	S -> A (in Ref. 14; AA sequence). {ECO:0000305}.	epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CTTCACAAAGCTCCATGGTTC	0.542													.|||	252	0.0503195	0.0356	0.0231	5008	,	,		31596	0.0437		0.0606	False		,,,				2504	0.0859				p.S76N	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.G227A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	199,4197		0,199,1999	111.0	110.0	110.0		224,227,224	-9.0	0.1	16	dbSNP_100	110	454,8146		0,454,3846	yes	missense,missense,missense	CES1	NM_001025194.1,NM_001025195.1,NM_001266.4	46,46,46	0,653,5845	TT,TC,CC		5.2791,4.5268,5.0246	benign,benign,benign	75/568,76/569,75/567	55862712	653,12343	2198	4300	6498	SO:0001583	missense	1066	exon2			ACAAAGCTCCATG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.224G>A	16.37:g.55862712C>T	ENSP00000355193:p.Ser75Asn	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	125	36	0.288	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	98	0.04487179487179487	18	0.036585365853658534	10	0.027624309392265192	25	0.043706293706293704	45	0.059366754617414245	.	5.134	0.210398	0.09757	0.045268	0.052791	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.09723	3.13;3.13;2.95	4.48	-8.96	0.00761	Carboxylesterase, type B (1);	1.157410	0.06501	N	0.736348	T	0.00695	0.0023	L	0.34521	1.04	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.001	B;B;B	0.12837	0.008;0.008;0.005	T	0.31024	-0.9958	10	0.35671	T	0.21	.	8.6444	0.33996	0.0:0.2843:0.149:0.5667	rs2307240;rs52810343;rs2307240	75;75;76	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	N	76;75;75	ENSP00000353720:S76N;ENSP00000355193:S75N;ENSP00000390492:S75N	ENSP00000353720:S76N	S	-	2	0	CES1	54420213	0.000000	0.05858	0.103000	0.21229	0.008000	0.06430	-0.082000	0.11304	-2.439000	0.00551	-0.515000	0.04445	AGC	C|0.956;T|0.044	0.044	strong		0.542	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
FLG	2312	hgsc.bcm.edu	37	1	152277345	152277345	+	Silent	SNP	C	C	T	rs2065956	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152277345C>T	ENST00000368799.1	-	3	10052	c.10017G>A	c.(10015-10017)caG>caA	p.Q3339Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3339	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TATCACTGGCCTGACTACCAC	0.572									Ichthyosis				C|||	1440	0.28754	0.0113	0.3905	5008	,	,		19931	0.5823		0.1421	False		,,,				2504	0.4335				p.Q3339Q		Atlas-SNP	.											.	FLG	900	.	0			c.G10017A						PASS	.	C		161,4245	107.8+/-146.2	2,157,2044	382.0	376.0	378.0		10017	0.7	0.0	1	dbSNP_94	378	1244,7356	248.6+/-276.2	102,1040,3158	no	coding-synonymous	FLG	NM_002016.1		104,1197,5202	TT,TC,CC		14.4651,3.6541,10.8027		3339/4062	152277345	1405,11601	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACTGGCCTGACTA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10017G>A	1.37:g.152277345C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	224	110	0.491071	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			C|0.843;T|0.157	0.157	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
NUP153	9972	hgsc.bcm.edu	37	6	17688798	17688798	+	Silent	SNP	G	G	A	rs1065057	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:17688798G>A	ENST00000262077.2	-	2	162	c.163C>T	c.(163-165)Cta>Tta	p.L55L	NUP153_ENST00000537253.1_Silent_p.L55L	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	55					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)			TATCTTTGTAGCCACCCTGGC	0.383													G|||	1362	0.271965	0.0431	0.3184	5008	,	,		19289	0.2431		0.4006	False		,,,				2504	0.4458				p.L55L		Atlas-SNP	.											.	NUP153	116	.	0			c.C163T						PASS	.	G		408,3998	200.4+/-223.7	21,366,1816	137.0	130.0	132.0		163	3.0	1.0	6	dbSNP_120	132	3044,5556	468.3+/-367.3	542,1960,1798	no	coding-synonymous	NUP153	NM_005124.2		563,2326,3614	AA,AG,GG		35.3953,9.2601,26.5416		55/1476	17688798	3452,9554	2203	4300	6503	SO:0001819	synonymous_variant	9972	exon2			TTTGTAGCCACCC	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.163C>T	6.37:g.17688798G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	64	0.547009	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Silent	SNP	ENST00000262077.2	37	CCDS4541.1																																																																																			G|0.720;C|0.000;N|0.000;A|0.279	0.279	strong		0.383	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
KRT23	25984	hgsc.bcm.edu	37	17	39084504	39084504	+	Missense_Mutation	SNP	T	T	C	rs9257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	135	0	0		WXS	Illumina HiSeq	Phase_I	166	79	0.475904	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		
IKBKAP	8518	hgsc.bcm.edu	37	9	111660851	111660851	+	Missense_Mutation	SNP	C	C	T	rs2230792	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111660851C>T	ENST00000374647.5	-	22	2601	c.2294G>A	c.(2293-2295)gGa>gAa	p.G765E	IKBKAP_ENST00000537196.1_Missense_Mutation_p.G416E	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	765			G -> E (in dbSNP:rs2230792).		chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TTCCACATTTCCAAGAAACAC	0.294													T|||	1448	0.289137	0.4493	0.2493	5008	,	,		19511	0.2589		0.1998	False		,,,				2504	0.2239				p.G765E		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G2294A						PASS	.	T	GLU/GLY	1820,2578	625.1+/-394.5	384,1052,763	68.0	71.0	70.0		2294	4.1	1.0	9	dbSNP_98	70	1566,7032	740.3+/-407.1	143,1280,2876	yes	missense	IKBKAP	NM_003640.3	98	527,2332,3639	TT,TC,CC		18.2135,41.3824,26.0542	benign	765/1333	111660851	3386,9610	2199	4299	6498	SO:0001583	missense	8518	exon22			ACATTTCCAAGAA	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2294G>A	9.37:g.111660851C>T	ENSP00000363779:p.Gly765Glu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	605	0.27701465201465203	208	0.42276422764227645	97	0.26795580110497236	157	0.2744755244755245	143	0.18865435356200527	T	0.014	-1.591131	0.00864	0.413824	0.182135	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.23950	1.88;1.88	5.21	4.05	0.47172	.	0.107189	0.64402	N	0.000006	T	0.00012	0.0000	N	0.00028	-2.63	0.50813	P	1.0399999999999299E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	9	0.02654	T	1	-6.7461	6.8594	0.24058	0.0:0.0809:0.1511:0.768	rs2230792;rs2275629;rs10979601;rs11554113;rs16913664;rs52832678;rs60459262;rs10979601	765	O95163	ELP1_HUMAN	E	765;416	ENSP00000363779:G765E;ENSP00000439367:G416E	ENSP00000363779:G765E	G	-	2	0	IKBKAP	110700672	1.000000	0.71417	0.996000	0.52242	0.120000	0.20174	2.915000	0.48805	0.368000	0.24481	-1.179000	0.01719	GGA	T|0.207;G|0.122;C|0.615;A|0.056	0.207	strong		0.294	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1252369	1252369	+	Missense_Mutation	SNP	C	C	T	rs61734410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1252369C>T	ENST00000348261.5	+	9	2167	c.1919C>T	c.(1918-1920)cCg>cTg	p.P640L	CACNA1H_ENST00000358590.4_Missense_Mutation_p.P640L|CACNA1H_ENST00000565831.1_Missense_Mutation_p.P640L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	640			P -> L (in dbSNP:rs61734410). {ECO:0000269|PubMed:12891677, ECO:0000269|Ref.7}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GCCGGTGGACCGCCAGGCACC	0.687													C|||	2203	0.439896	0.2368	0.4683	5008	,	,		14593	0.8383		0.3002	False		,,,				2504	0.4274				p.P640L		Atlas-SNP	.											CACNA1H_ENST00000358590,bladder,carcinoma,-1,2	CACNA1H	317	2	0			c.C1919T						PASS	.	C	LEU/PRO,LEU/PRO	747,3103		83,581,1261	5.0	7.0	7.0		1919,1919	2.6	0.0	16	dbSNP_129	7	1905,6109		242,1421,2344	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	98,98	325,2002,3605	TT,TC,CC		23.7709,19.4026,22.3533	benign,benign	640/2348,640/2354	1252369	2652,9212	1925	4007	5932	SO:0001583	missense	8912	exon9			GTGGACCGCCAGG	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.1919C>T	16.37:g.1252369C>T	ENSP00000334198:p.Pro640Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	977	0.44734432234432236	106	0.21544715447154472	149	0.4116022099447514	487	0.8513986013986014	235	0.3100263852242744	C	10.68	1.417079	0.25552	0.194026	0.237709	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96265	-3.96;-3.9	3.55	2.56	0.30785	.	2509.280000	0.00166	N	0.000000	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P;B	0.36378	0.55;0.216	B;B	0.25614	0.062;0.019	T	0.49303	-0.8954	9	0.37606	T	0.19	.	9.4648	0.38806	0.3835:0.6165:0.0:0.0	rs61734410	640;640	O95180-2;O95180	.;CAC1H_HUMAN	L	640	ENSP00000334198:P640L;ENSP00000351401:P640L	ENSP00000334198:P640L	P	+	2	0	CACNA1H	1192370	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	1.293000	0.33353	0.650000	0.30769	0.563000	0.77884	CCG	C|0.556;T|0.444	0.444	strong		0.687	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ZNF230	7773	hgsc.bcm.edu	37	19	44515514	44515514	+	Missense_Mutation	SNP	C	C	A	rs12753	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44515514C>A	ENST00000429154.2	+	5	1551	c.1323C>A	c.(1321-1323)gaC>gaA	p.D441E		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	441			D -> E (in dbSNP:rs12753).		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.D441E(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				AACAAGGAGACCACAATGGAG	0.398													C|||	1104	0.220447	0.2738	0.2925	5008	,	,		16585	0.256		0.1789	False		,,,				2504	0.1033				p.D441E	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											ZNF230,NS,carcinoma,0,2	ZNF230	44	2	1	Substitution - Missense(1)	stomach(1)	c.C1323A						PASS	.	C	GLU/ASP	1076,3330	356.6+/-313.6	123,830,1250	54.0	59.0	57.0		1323	-5.1	0.0	19	dbSNP_52	57	1363,7235	249.7+/-276.9	96,1171,3032	yes	missense	ZNF230	NM_006300.3	45	219,2001,4282	AA,AC,CC		15.8525,24.4212,18.7558	benign	441/475	44515514	2439,10565	2203	4299	6502	SO:0001583	missense	7773	exon5			AGGAGACCACAAT	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.1323C>A	19.37:g.44515514C>A	ENSP00000409318:p.Asp441Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	474	0.21703296703296704	130	0.26422764227642276	104	0.287292817679558	122	0.21328671328671328	118	0.15567282321899736	C	12.74	2.028758	0.35797	0.244212	0.158525	ENSG00000159882	ENST00000429154	T	0.14766	2.48	2.55	-5.09	0.02920	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.33469	P	0.41407000000000005	P	0.36789	0.57	B	0.29524	0.103	T	0.40720	-0.9548	8	0.87932	D	0	.	4.3319	0.11067	0.1352:0.3704:0.3957:0.0987	rs12753;rs3201816;rs16978609;rs52823461;rs12753	441	Q9UIE0	ZN230_HUMAN	E	441	ENSP00000409318:D441E	ENSP00000409318:D441E	D	+	3	2	ZNF230	49207354	0.000000	0.05858	0.000000	0.03702	0.485000	0.33311	-1.548000	0.02184	-1.102000	0.03023	0.205000	0.17691	GAC	C|0.807;A|0.193	0.193	strong		0.398	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		
TMCO6	55374	hgsc.bcm.edu	37	5	140021482	140021482	+	Silent	SNP	C	C	T	rs11554680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140021482C>T	ENST00000394671.3	+	4	443	c.342C>T	c.(340-342)gtC>gtT	p.V114V	NDUFA2_ENST00000510680.1_Intron|TMCO6_ENST00000252100.6_Silent_p.V114V|TMCO6_ENST00000537378.1_Intron|TMCO6_ENST00000511410.1_3'UTR	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	114					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCCTGGTCGGGCTCCTGA	0.637													C|||	1194	0.238419	0.1891	0.2248	5008	,	,		18076	0.2966		0.2455	False		,,,				2504	0.2474				p.V114V		Atlas-SNP	.											TMCO6,NS,carcinoma,+1,1	TMCO6	30	1	0			c.C342T						PASS	.	C		708,3390		72,564,1413	34.0	38.0	37.0		342	-8.4	0.9	5	dbSNP_120	37	2006,6370		247,1512,2429	no	coding-synonymous	TMCO6	NM_018502.3		319,2076,3842	TT,TC,CC		23.9494,17.2767,21.7573		114/494	140021482	2714,9760	2049	4188	6237	SO:0001819	synonymous_variant	55374	exon4			CCTGGTCGGGCTC	BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	ENST00000394671.3:c.342C>T	5.37:g.140021482C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_018502	Q9BUU0|Q9P198	Silent	SNP	ENST00000394671.3	37	CCDS4233.2																																																																																			C|0.757;T|0.243	0.243	strong		0.637	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502	
PRDM2	7799	hgsc.bcm.edu	37	1	14105298	14105298	+	Silent	SNP	G	G	A	rs1203678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:14105298G>A	ENST00000235372.7	+	8	1864	c.1008G>A	c.(1006-1008)gaG>gaA	p.E336E	PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000343137.4_Silent_p.E135E|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000413440.1_Silent_p.E135E|PRDM2_ENST00000311066.5_Silent_p.E336E	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	336				EV -> DL (in Ref. 6; AAA87023). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		ACTGCTCAGAGGTAACACCTG	0.398													G|||	1584	0.316294	0.2012	0.5389	5008	,	,		20390	0.373		0.3101	False		,,,				2504	0.2618				p.E336E		Atlas-SNP	.											.	PRDM2	147	.	0			c.G1008A						PASS	.	G	,,,	1073,3333	388.6+/-327.0	130,813,1260	98.0	95.0	96.0		405,,1008,1008	-0.2	0.0	1	dbSNP_87	96	2964,5636	460.9+/-365.3	475,2014,1811	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	,,,	605,2827,3071	AA,AG,GG		34.4651,24.3532,31.0395	,,,	135/1482,,336/1719,336/1683	14105298	4037,8969	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			CTCAGAGGTAACA	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.1008G>A	1.37:g.14105298G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																			G|0.681;N|0.000	.	strong		0.398	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
NEDD4	4734	hgsc.bcm.edu	37	15	56207983	56207983	+	Silent	SNP	C	C	T	rs7174459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:56207983C>T	ENST00000508342.1	-	1	1346	c.1047G>A	c.(1045-1047)tcG>tcA	p.S349S	NEDD4_ENST00000435532.3_Intron|NEDD4_ENST00000338963.2_Silent_p.S349S|NEDD4_ENST00000506154.1_Silent_p.S349S	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	349					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)		TCTTCTGTAACGAGCCCTTCC	0.418													C|||	901	0.179912	0.1044	0.3386	5008	,	,		19211	0.1032		0.2694	False		,,,				2504	0.1564				p.S349S		Atlas-SNP	.											.	NEDD4	167	.	0			c.G1047A						PASS	.	C	,	596,3782		39,518,1632	56.0	58.0	58.0		,1047	-9.6	0.0	15	dbSNP_116	58	2435,6145		353,1729,2208	no	intron,coding-synonymous	NEDD4	NM_006154.2,NM_198400.2	,	392,2247,3840	TT,TC,CC		28.38,13.6135,23.391	,	,349/1248	56207983	3031,9927	2189	4290	6479	SO:0001819	synonymous_variant	4734	exon1			CTGTAACGAGCCC	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.1047G>A	15.37:g.56207983C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000508342.1	37																																																																																				C|0.791;T|0.209	0.209	strong		0.418	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
COL4A2	1284	hgsc.bcm.edu	37	13	111082772	111082772	+	Missense_Mutation	SNP	G	G	T	rs62621885	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:111082772G>T	ENST00000360467.5	+	9	880	c.574G>T	c.(574-576)Gtc>Ttc	p.V192F	COL4A2_ENST00000462309.1_3'UTR	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	192	Triple-helical region.		V -> F (polymorphism that does not affect COL4A2 and COL4A1 secretion; dbSNP:rs62621885). {ECO:0000269|PubMed:21527998, ECO:0000269|PubMed:22209247}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GCCTGGATTGGTCGGTTTCCA	0.348													G|||	45	0.00898562	0.0015	0.0346	5008	,	,		15447	0.001		0.004	False		,,,				2504	0.0143				p.V192F		Atlas-SNP	.											.	COL4A2	178	.	0			c.G574T						PASS	.	G	PHE/VAL	4,3604		0,4,1800	86.0	84.0	85.0		574	3.1	0.0	13	dbSNP_129	85	63,8073		1,61,4006	yes	missense	COL4A2	NM_001846.2	50	1,65,5806	TT,TG,GG		0.7743,0.1109,0.5705	possibly-damaging	192/1713	111082772	67,11677	1804	4068	5872	SO:0001583	missense	1284	exon9			GGATTGGTCGGTT	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.574G>T	13.37:g.111082772G>T	ENSP00000353654:p.Val192Phe	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	45	0.428571	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	17	0.007783882783882784	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	3	0.00395778364116095	G	8.517	0.867871	0.17250	0.001109	0.007743	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93604	-3.25	5.19	3.1	0.35709	.	0.413978	0.20322	N	0.094616	T	0.69305	0.3096	L	0.41492	1.28	0.09310	N	1	P	0.44946	0.846	B	0.41236	0.351	T	0.73920	-0.3830	10	0.59425	D	0.04	.	6.4174	0.21723	0.3306:0.0:0.6694:0.0	rs62621885	192	P08572	CO4A2_HUMAN	F	192	ENSP00000353654:V192F	ENSP00000257309:V192F	V	+	1	0	COL4A2	109880773	0.007000	0.16637	0.024000	0.17045	0.483000	0.33249	0.542000	0.23222	1.170000	0.42753	0.650000	0.86243	GTC	G|0.991;T|0.009	0.009	strong		0.348	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
COL28A1	340267	hgsc.bcm.edu	37	7	7514235	7514235	+	Missense_Mutation	SNP	C	C	G	rs6952195	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	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	
HOXA1	3198	hgsc.bcm.edu	37	7	27135319	27135319	+	Silent	SNP	G	G	A	rs2074398		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:27135319G>A	ENST00000343060.4	-	1	274	c.213C>T	c.(211-213)caC>caT	p.H71H	HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOXA1_ENST00000355633.5_Silent_p.H71H|HOTAIRM1_ENST00000425358.2_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	71	Poly-His.				abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ggtggcgatggtggtggtggt	0.642											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.H71H		Atlas-SNP	.											.	HOXA1	64	.	0			c.C213T						PASS	.						37.0	40.0	39.0					7																	27135319		2203	4300	6503	SO:0001819	synonymous_variant	3198	exon1			GCGATGGTGGTGG		CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.213C>T	7.37:g.27135319G>A		Somatic	42	0	0	792	WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_153620	A4D184|B2R8U7|O43363	Silent	SNP	ENST00000343060.4	37	CCDS5401.1																																																																																			.	.	weak		0.642	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
KRT77	374454	hgsc.bcm.edu	37	12	53091566	53091566	+	Missense_Mutation	SNP	C	C	A	rs1567759	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53091566C>A	ENST00000341809.3	-	2	686	c.658G>T	c.(658-660)Ggt>Tgt	p.G220C	RP11-641A6.3_ENST00000547533.1_RNA|KRT77_ENST00000537195.1_5'UTR	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	220	Coil 1B.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CGCAGGTCACCGATGTAGTTC	0.562													C|||	2036	0.40655	0.4811	0.4121	5008	,	,		20180	0.246		0.4026	False		,,,				2504	0.4714				p.G220C		Atlas-SNP	.											KRT77,colon,carcinoma,0,1	KRT77	58	1	0			c.G658T						PASS	.	C	CYS/GLY	1988,2418	557.0+/-379.6	437,1114,652	222.0	215.0	217.0		658	-2.0	0.0	12	dbSNP_88	217	3625,4975	522.6+/-380.1	764,2097,1439	yes	missense	KRT77	NM_175078.2	159	1201,3211,2091	AA,AC,CC		42.1512,45.1203,43.157	probably-damaging	220/579	53091566	5613,7393	2203	4300	6503	SO:0001583	missense	374454	exon2			GGTCACCGATGTA	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.658G>T	12.37:g.53091566C>A	ENSP00000342710:p.Gly220Cys	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	NM_175078	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	800	0.3663003663003663	226	0.45934959349593496	137	0.3784530386740331	127	0.22202797202797203	310	0.40897097625329815	C	13.82	2.350744	0.41599	0.451203	0.421512	ENSG00000189182	ENST00000341809	D	0.88818	-2.43	4.4	-2.05	0.07321	Filament (1);	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.39443	P	0.03272200000000003	D	0.76494	0.999	D	0.72075	0.976	T	0.14144	-1.0483	8	0.56958	D	0.05	.	7.0738	0.25193	0.0:0.4467:0.1351:0.4182	rs1567759;rs52816334;rs58131065;rs1567759	220	Q7Z794	K2C1B_HUMAN	C	220	ENSP00000342710:G220C	ENSP00000342710:G220C	G	-	1	0	KRT77	51377833	0.000000	0.05858	0.010000	0.14722	0.000000	0.00434	-1.970000	0.01504	-0.220000	0.09988	-1.240000	0.01540	GGT	C|0.593;A|0.407	0.407	strong		0.562	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
NCOA7	135112	hgsc.bcm.edu	37	6	126210395	126210395	+	Missense_Mutation	SNP	T	T	G	rs6919947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:126210395T>G	ENST00000368357.3	+	10	1547	c.1195T>G	c.(1195-1197)Tct>Gct	p.S399A	NCOA7_ENST00000229634.9_Missense_Mutation_p.S284A|NCOA7_ENST00000392477.2_Missense_Mutation_p.S399A	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	399			S -> A (in dbSNP:rs6919947). {ECO:0000269|PubMed:11971969, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		CGACACTTCTTCTGCATTTGA	0.433													G|||	2396	0.478435	0.4024	0.4899	5008	,	,		20109	0.5903		0.5189	False		,,,				2504	0.4162				p.S399A		Atlas-SNP	.											.	NCOA7	92	.	0			c.T1195G						PASS	.	G	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	1895,2511	610.6+/-391.6	411,1073,719	57.0	60.0	59.0		1162,1195,1195,850,1195	-7.8	0.0	6	dbSNP_116	59	4329,4271	571.1+/-389.5	1092,2145,1063	yes	missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_181782.4	99,99,99,99,99	1503,3218,1782	GG,GT,TT		49.6628,43.0095,47.8548	benign,benign,benign,benign,benign	388/932,399/943,399/943,284/828,399/943	126210395	6224,6782	2203	4300	6503	SO:0001583	missense	135112	exon10			ACTTCTTCTGCAT	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.1195T>G	6.37:g.126210395T>G	ENSP00000357341:p.Ser399Ala	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	1134	0.5192307692307693	198	0.4024390243902439	184	0.5082872928176796	357	0.6241258741258742	395	0.521108179419525	G	0.005	-2.154608	0.00325	0.430095	0.503372	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.29397	2.81;2.81;2.81;1.57	4.63	-7.76	0.01232	.	1.855050	0.02104	N	0.054209	T	0.01661	0.0053	N	0.01874	-0.695	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.09207	-1.0685	9	0.02654	T	1	0.7746	3.8292	0.08867	0.5446:0.0911:0.0925:0.2718	rs6919947;rs13217790;rs17807774;rs59024241;rs6919947	388;388;399	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	A	399;399;284;197	ENSP00000357341:S399A;ENSP00000376269:S399A;ENSP00000229634:S284A;ENSP00000389186:S197A	ENSP00000229634:S284A	S	+	1	0	NCOA7	126252088	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.657000	0.05335	-2.239000	0.00711	-1.084000	0.02203	TCT	T|0.507;G|0.493	0.493	strong		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
GXYLT1	283464	hgsc.bcm.edu	37	12	42491379	42491379	+	Silent	SNP	T	T	A	rs139072942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:42491379T>A	ENST00000398675.3	-	7	1258	c.1026A>T	c.(1024-1026)cgA>cgT	p.R342R	GXYLT1_ENST00000280876.6_Silent_p.R311R	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	342					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						AATGATCTGGTCGATAATTCC	0.368													T|||	16	0.00319489	0.0	0.0072	5008	,	,		18036	0.0		0.008	False		,,,				2504	0.0031				p.R342R		Atlas-SNP	.											Q8IXV1_HUMAN,NS,carcinoma,-1,2	GXYLT1	47	2	0			c.A1026T						PASS	.	T	,	2,3706		0,2,1852	134.0	127.0	129.0		933,1026	-7.5	0.9	12	dbSNP_134	129	67,8127		2,63,4032	no	coding-synonymous,coding-synonymous	GXYLT1	NM_001099650.1,NM_173601.1	,	2,65,5884	AA,AT,TT		0.8177,0.0539,0.5797	,	311/410,342/441	42491379	69,11833	1854	4097	5951	SO:0001819	synonymous_variant	283464	exon7			ATCTGGTCGATAA	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.1026A>T	12.37:g.42491379T>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Silent	SNP	ENST00000398675.3	37	CCDS41772.1																																																																																			T|0.994;A|0.006	0.006	strong		0.368	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726772	32726772	+	Silent	SNP	G	G	A	rs200147031		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32726772G>A	ENST00000437316.2	-	3	564	c.501C>T	c.(499-501)gcC>gcT	p.A167A	HLA-DQB2_ENST00000435145.2_Silent_p.A167A|HLA-DQB2_ENST00000411527.1_Silent_p.A167A			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	171	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						ACACAACACCGGCTGTCTCCT	0.547																																					p.A167A		Atlas-SNP	.											HLA-DQB2,NS,carcinoma,-2,4	HLA-DQB2	22	4	0			c.C501T						PASS	.																																			SO:0001819	synonymous_variant	3120	exon3			AACACCGGCTGTC	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.501C>T	6.37:g.32726772G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	195	33	0.169231	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Silent	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	G	1.934	-0.445141	0.04604	.	.	ENSG00000232629	ENST00000427449	.	.	.	3.43	-4.55	0.03441	.	.	.	.	.	T	0.10035	0.0246	.	.	.	0.28648	N	0.906781	.	.	.	.	.	.	T	0.28459	-1.0043	4	.	.	.	.	4.9433	0.13976	0.3541:0.3084:0.3376:0.0	.	.	.	.	L	166	.	.	P	-	2	0	HLA-DQB2	32834750	0.000000	0.05858	0.601000	0.28877	0.295000	0.27426	-1.774000	0.01784	-0.898000	0.03906	-0.339000	0.08088	CCG	.	.	weak		0.547	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
DDX19A	55308	hgsc.bcm.edu	37	16	70395387	70395387	+	Silent	SNP	C	C	T	rs1134074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70395387C>T	ENST00000302243.7	+	5	523	c.360C>T	c.(358-360)aaC>aaT	p.N120N	DDX19A_ENST00000562509.1_3'UTR|DDX19A_ENST00000417604.2_Intron|RP11-529K1.3_ENST00000567706.1_Intron|DDX19A_ENST00000443119.2_Silent_p.N30N	NM_018332.3	NP_060802.1	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A	120	N-terminal lobe. {ECO:0000250}.				mRNA transport (GO:0051028)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|urinary_tract(1)	11		Ovarian(137;0.221)				TACAAGAGAACGCATTACCCA	0.498													C|||	1130	0.225639	0.0234	0.3184	5008	,	,		19485	0.3036		0.3996	False		,,,				2504	0.1738				p.N120N		Atlas-SNP	.											.	DDX19A	39	.	0			c.C360T						PASS	.	C		368,4028	188.1+/-214.6	18,332,1848	145.0	112.0	123.0		360	-9.3	0.0	16	dbSNP_86	123	3273,5327	491.2+/-373.0	623,2027,1650	no	coding-synonymous	DDX19A	NM_018332.3		641,2359,3498	TT,TC,CC		38.0581,8.3712,28.0163		120/479	70395387	3641,9355	2198	4300	6498	SO:0001819	synonymous_variant	55308	exon5			AGAGAACGCATTA	AF183422	CCDS10889.1	16q22.1	2012-02-23	2012-02-23	2005-07-13	ENSG00000168872	ENSG00000168872		"""DEAD-boxes"""	25628	protein-coding gene	gene with protein product			"""DEAD (Asp-Glu-Ala-As) box polypeptide 19-like"""	DDX19L		12477932	Standard	NM_018332		Approved	FLJ11126		Q9NUU7	OTTHUMG00000137579	ENST00000302243.7:c.360C>T	16.37:g.70395387C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	NM_018332	B2RPL0|B4DRZ7|Q53FM0	Silent	SNP	ENST00000302243.7	37	CCDS10889.1																																																																																			C|0.732;T|0.268	0.268	strong		0.498	DDX19A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268967.2	NM_018332	
PCSK5	5125	hgsc.bcm.edu	37	9	78938043	78938043	+	Missense_Mutation	SNP	G	G	A	rs2495207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	107	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	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			
MVB12B	89853	hgsc.bcm.edu	37	9	129143435	129143435	+	Silent	SNP	A	A	G	rs2286889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:129143435A>G	ENST00000361171.3	+	3	378	c.297A>G	c.(295-297)tcA>tcG	p.S99S	MVB12B_ENST00000545391.1_Silent_p.S99S|MVB12B_ENST00000436593.3_Silent_p.S84S|MVB12B_ENST00000535766.1_Silent_p.S92S	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	99	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										TCACAAGATCATTTTCCAAAG	0.403													A|||	649	0.129593	0.0053	0.1427	5008	,	,		21125	0.2639		0.1113	False		,,,				2504	0.1687				p.S99S		Atlas-SNP	.											.	.	.	.	0			c.A297G						PASS	.	A	,	99,4307	79.3+/-117.8	2,95,2106	104.0	96.0	99.0		297,297	1.5	1.0	9	dbSNP_100	99	956,7644	209.1+/-250.4	52,852,3396	no	coding-synonymous,coding-synonymous	FAM125B	NM_001011703.2,NM_033446.2	,	54,947,5502	GG,GA,AA		11.1163,2.2469,8.1116	,	99/222,99/320	129143435	1055,11951	2203	4300	6503	SO:0001819	synonymous_variant	89853	exon3			AAGATCATTTTCC	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 28"", ""family with sequence similarity 125, member B"""	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.297A>G	9.37:g.129143435A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_001011703	Q8N6S7	Silent	SNP	ENST00000361171.3	37	CCDS35142.1																																																																																			A|0.895;G|0.105	0.105	strong		0.403	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525	
NDNF	79625	hgsc.bcm.edu	37	4	121958691	121958691	+	Silent	SNP	T	T	C	rs3733559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:121958691T>C	ENST00000379692.4	-	4	961	c.435A>G	c.(433-435)ttA>ttG	p.L145L	NDNF_ENST00000506900.1_5'UTR	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	145					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						CCAACTGATATAAACCGGATG	0.408													T|||	1127	0.22504	0.0998	0.3357	5008	,	,		19003	0.2351		0.2038	False		,,,				2504	0.3272				p.L145L		Atlas-SNP	.											NDNF,colon,carcinoma,-2,1	NDNF	72	1	0			c.A435G						PASS	.	T		445,3451		28,389,1531	139.0	133.0	135.0		435	-8.0	0.0	4	dbSNP_107	135	1732,6590		179,1374,2608	no	coding-synonymous	NDNF	NM_024574.3		207,1763,4139	CC,CT,TT		20.8123,11.422,17.818		145/569	121958691	2177,10041	1948	4161	6109	SO:0001819	synonymous_variant	79625	exon4			CTGATATAAACCG	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.435A>G	4.37:g.121958691T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	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	
C1orf177	163747	hgsc.bcm.edu	37	1	55307501	55307501	+	Silent	SNP	A	A	G	rs41297871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	75	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	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	
NCOA4	8031	hgsc.bcm.edu	37	10	51582894	51582894	+	Silent	SNP	C	C	T	rs41306524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:51582894C>T	ENST00000443446.1	+	7	898	c.669C>T	c.(667-669)gaC>gaT	p.D223D	NCOA4_ENST00000498586.1_3'UTR|NCOA4_ENST00000452682.1_Silent_p.D239D|NCOA4_ENST00000344348.6_Silent_p.D223D|NCOA4_ENST00000438493.1_Silent_p.D239D|NCOA4_ENST00000374082.1_Silent_p.D223D|NCOA4_ENST00000430396.2_Silent_p.D123D|NCOA4_ENST00000374087.4_Silent_p.D223D|NCOA4_ENST00000414907.2_Silent_p.D57D	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	223					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						CCAGCACCGACCCCCAGGACT	0.498			T	RET	papillary thyroid								.|||	394	0.0786741	0.056	0.0706	5008	,	,		15427	0.0694		0.1272	False		,,,				2504	0.0746				p.D239D		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4	58	.	0			c.C717T						PASS	.	C	,,,,	317,4089	170.1+/-200.6	12,293,1898	82.0	74.0	76.0		717,717,669,669,669	0.9	0.9	10	dbSNP_127	76	917,7683	204.1+/-246.9	52,813,3435	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA4	NM_001145260.1,NM_001145261.1,NM_001145262.1,NM_001145263.1,NM_005437.3	,,,,	64,1106,5333	TT,TC,CC		10.6628,7.1947,9.4879	,,,,	239/651,239/631,223/615,223/615,223/615	51582894	1234,11772	2203	4300	6503	SO:0001819	synonymous_variant	8031	exon8			CACCGACCCCCAG	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"""RET-activating gene ELE1"""	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.669C>T	10.37:g.51582894C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Silent	SNP	ENST00000443446.1	37	CCDS7237.1	203	0.09294871794871795	34	0.06910569105691057	34	0.09392265193370165	42	0.07342657342657342	93	0.12269129287598944	C	0.728	-0.781039	0.02929	0.071947	0.106628	ENSG00000138293	ENST00000431200	.	.	.	5.93	0.901	0.19284	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.09310	P	0.9999999600709	.	.	.	.	.	.	T	0.12192	-1.0557	3	.	.	.	-6.5159	6.0322	0.19686	0.1171:0.5529:0.0:0.33	rs41306524;rs61749176	.	.	.	S	139	.	.	P	+	1	0	NCOA4	51252900	0.339000	0.24784	0.905000	0.35620	0.024000	0.10985	0.207000	0.17395	-0.088000	0.12506	-0.136000	0.14681	CCC	C|0.904;T|0.096	0.096	strong		0.498	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437	
ZNF512B	57473	hgsc.bcm.edu	37	20	62591460	62591460	+	Silent	SNP	G	G	A	rs45570933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62591460G>A	ENST00000450537.1	-	17	2520	c.2460C>T	c.(2458-2460)ccC>ccT	p.P820P	ZNF512B_ENST00000217130.3_Silent_p.P820P|ZNF512B_ENST00000369888.1_Silent_p.P820P			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	820					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					TCCTGTGTTTGGGAGGTGGGT	0.567													G|||	102	0.0203674	0.0038	0.036	5008	,	,		18765	0.0		0.0606	False		,,,				2504	0.0112				p.P820P		Atlas-SNP	.											.	ZNF512B	72	.	0			c.C2460T						PASS	.	G		65,4339	59.3+/-96.0	0,65,2137	83.0	90.0	88.0		2460	3.9	0.3	20	dbSNP_127	88	606,7994	158.6+/-212.1	23,560,3717	no	coding-synonymous	ZNF512B	NM_020713.1		23,625,5854	AA,AG,GG		7.0465,1.4759,5.16		820/893	62591460	671,12333	2202	4300	6502	SO:0001819	synonymous_variant	57473	exon17			GTGTTTGGGAGGT	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.2460C>T	20.37:g.62591460G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_020713	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			G|0.955;A|0.045	0.045	strong		0.567	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
NOTCH3	4854	hgsc.bcm.edu	37	19	15298031	15298031	+	Silent	SNP	C	C	T	rs79926127	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15298031C>T	ENST00000263388.2	-	11	1800	c.1725G>A	c.(1723-1725)acG>acA	p.T575T		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	575	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			AGCGTGTGCCCGTGTAGCCAG	0.647													C|||	19	0.00379393	0.0	0.0115	5008	,	,		15230	0.001		0.006	False		,,,				2504	0.0041				p.T575T		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G1725A						PASS	.	C		8,4398	11.4+/-27.6	0,8,2195	57.0	49.0	52.0		1725	-9.0	0.7	19	dbSNP_131	52	101,8499	52.7+/-113.3	1,99,4200	no	coding-synonymous	NOTCH3	NM_000435.2		1,107,6395	TT,TC,CC		1.1744,0.1816,0.8381		575/2322	15298031	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	4854	exon11			TGTGCCCGTGTAG	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.1725G>A	19.37:g.15298031C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	187	88	0.470588	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	CCDS12326.1																																																																																			T|0.007;C|0.993	0.007	strong		0.647	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
GTF2H4	2968	hgsc.bcm.edu	37	6	30881103	30881103	+	Silent	SNP	C	C	A	rs1132408	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30881103C>A	ENST00000259895.4	+	13	1378	c.1155C>A	c.(1153-1155)ccC>ccA	p.P385P	VARS2_ENST00000321897.5_5'Flank|VARS2_ENST00000416670.2_5'Flank|GTF2H4_ENST00000376316.2_Silent_p.P385P|VARS2_ENST00000541562.1_5'Flank|VARS2_ENST00000542001.1_5'Flank	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	385					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|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)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						TGCTGCCCCCCACCATCACCG	0.577								Nucleotide excision repair (NER)					C|||	69	0.013778	0.0166	0.0072	5008	,	,		16179	0.0149		0.0179	False		,,,				2504	0.0092				p.P385P		Atlas-SNP	.											.	GTF2H4	38	.	0			c.C1155A						PASS	.	C		92,2930		0,92,1419	77.0	87.0	83.0		1155	4.7	1.0	6	dbSNP_86	83	85,5331		0,85,2623	no	coding-synonymous	GTF2H4	NM_001517.4		0,177,4042	AA,AC,CC		1.5694,3.0443,2.0977		385/463	30881103	177,8261	1511	2708	4219	SO:0001819	synonymous_variant	2968	exon13			GCCCCCCACCATC	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	4658	protein-coding gene	gene with protein product		601760	"""general transcription factor IIH, polypeptide 4 (52kD subunit)"""			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.1155C>A	6.37:g.30881103C>A		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	220	218	0.990909	NM_001517	B4DTJ5|Q76KU4	Silent	SNP	ENST00000259895.4	37	CCDS34386.1																																																																																			C|0.980;A|0.020	0.020	strong		0.577	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517	
ZNF215	7762	hgsc.bcm.edu	37	11	6953858	6953858	+	Missense_Mutation	SNP	A	A	G	rs11041108	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6953858A>G	ENST00000278319.5	+	3	943	c.355A>G	c.(355-357)Atg>Gtg	p.M119V	ZNF215_ENST00000414517.2_Missense_Mutation_p.M119V|ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000529903.1_Missense_Mutation_p.M119V	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	119	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.		M -> V (in dbSNP:rs11041108).		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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		CAGTAAAGATATGGTGACCCT	0.378													A|||	1301	0.259784	0.0393	0.3026	5008	,	,		20131	0.37		0.3658	False		,,,				2504	0.3047				p.M119V		Atlas-SNP	.											.	ZNF215	72	.	0			c.A355G						PASS	.	A	VAL/MET	401,4001	192.3+/-217.7	27,347,1827	58.0	61.0	60.0		355	2.2	0.9	11	dbSNP_120	60	3115,5477	473.0+/-368.5	559,1997,1740	yes	missense	ZNF215	NM_013250.2	21	586,2344,3567	GG,GA,AA		36.2547,9.1095,27.0586	benign	119/518	6953858	3516,9478	2201	4296	6497	SO:0001583	missense	7762	exon3			AAAGATATGGTGA	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.355A>G	11.37:g.6953858A>G	ENSP00000278319:p.Met119Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	599	0.2742673992673993	23	0.046747967479674794	103	0.2845303867403315	203	0.3548951048951049	270	0.3562005277044855	A	0	-2.754117	0.00085	0.091095	0.362547	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.04502	3.61;3.61;3.61	4.14	2.17	0.27698	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.516931	0.14835	N	0.295605	T	0.00012	0.0000	N	0.00017	-2.845	0.45762	P	0.0013450000000000406	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.42949	-0.9421	9	0.02654	T	1	-3.9644	6.3178	0.21200	0.2259:0.0:0.7741:0.0	rs11041108;rs52821111;rs58656969;rs11041108	119;119;119	B4DYW9;Q96C84;Q9UL58	.;.;ZN215_HUMAN	V	119	ENSP00000278319:M119V;ENSP00000393202:M119V;ENSP00000432306:M119V	ENSP00000278319:M119V	M	+	1	0	ZNF215	6910434	0.981000	0.34729	0.871000	0.34182	0.052000	0.14988	1.693000	0.37742	0.678000	0.31325	-0.177000	0.13119	ATG	A|0.721;G|0.279	0.279	strong		0.378	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73072354	73072354	+	Missense_Mutation	SNP	T	T	C	rs7714670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73072354T>C	ENST00000426542.2	+	5	693	c.673T>C	c.(673-675)Tgg>Cgg	p.W225R	ARHGEF28_ENST00000437974.1_Missense_Mutation_p.W225R|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.W225R|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.W225R|CTC-575I10.1_ENST00000506717.1_RNA|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.W225R|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.W225R			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	225			W -> R (in dbSNP:rs7714670).		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)										TCAGGGCAGATGGTCCCCAAG	0.527													T|||	1855	0.370407	0.3381	0.366	5008	,	,		15351	0.3194		0.4573	False		,,,				2504	0.3804				p.W225R		Atlas-SNP	.											NP_001073948_1,NS,carcinoma,0,2	.	.	2	0			c.T673C						PASS	.	T	ARG/TRP,ARG/TRP	1467,2625		261,945,840	68.0	72.0	71.0		673,673	0.8	0.0	5	dbSNP_116	71	3811,4619		902,2007,1306	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	101,101	1163,2952,2146	CC,CT,TT		45.2076,35.8504,42.1498	benign,benign	225/1732,225/1706	73072354	5278,7244	2046	4215	6261	SO:0001583	missense	64283	exon6			GGCAGATGGTCCC		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.673T>C	5.37:g.73072354T>C	ENSP00000412175:p.Trp225Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	154	78	0.506494	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	822	0.37637362637362637	166	0.33739837398373984	135	0.3729281767955801	170	0.2972027972027972	351	0.4630606860158311	T	0.005	-2.170811	0.00315	0.358504	0.452076	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542	T;T;T;T;T;T	0.08102	3.38;3.38;3.38;3.13;3.38;3.38	5.15	0.823	0.18812	.	.	.	.	.	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	0.42103	-0.9471	8	0.06365	T	0.9	.	4.5007	0.11863	0.1502:0.5769:0.0:0.2729	rs7714670;rs17634387;rs58192310;rs7714670	225;225;225;225	Q8N1W1;E9PC75;Q8N1W1-2;Q8N1W1-4	RGNEF_HUMAN;.;.;.	R	225	ENSP00000296794:W225R;ENSP00000441913:W225R;ENSP00000441436:W225R;ENSP00000287898:W225R;ENSP00000411459:W225R;ENSP00000412175:W225R	ENSP00000287898:W225R	W	+	1	0	RP11-428C6.1	73108110	0.000000	0.05858	0.000000	0.03702	0.253000	0.25986	0.228000	0.17814	0.151000	0.19162	-1.140000	0.01884	TGG	C|0.364;N|0.001	0.364	strong		0.527	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
GALNT9	50614	hgsc.bcm.edu	37	12	132688115	132688115	+	Missense_Mutation	SNP	C	C	T	rs11246991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:132688115C>T	ENST00000328957.8	-	7	1197	c.1198G>A	c.(1198-1200)Gcc>Acc	p.A400T	GALNT9_ENST00000541995.1_Missense_Mutation_p.A34T|GALNT9_ENST00000535228.1_Missense_Mutation_p.A151T|GALNT9_ENST00000397325.2_Missense_Mutation_p.A34T	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	400					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)		ACCTCGGCGGCGCGCAGGGCG	0.642													c|||	259	0.0517173	0.0068	0.0965	5008	,	,		16204	0.0		0.1491	False		,,,				2504	0.0337				p.A400T	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											GALNT9_ENST00000535228,NS,carcinoma,+2,3	GALNT9	74	3	0			c.G1198A						PASS	.	C	THR/ALA,THR/ALA	130,4230		0,130,2050	72.0	85.0	81.0		121,100	3.0	0.5	12	dbSNP_120	81	1212,7332		88,1036,3148	yes	missense,missense	GALNT9	NM_001122636.1.dup,NM_021808.3	58,58	88,1166,5198	TT,TC,CC		14.1854,2.9817,10.3999	possibly-damaging,possibly-damaging	41/245,34/238	132688115	1342,11562	2180	4272	6452	SO:0001583	missense	50614	exon7			CGGCGGCGCGCAG	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.1198G>A	12.37:g.132688115C>T	ENSP00000329846:p.Ala400Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Missense_Mutation	SNP	ENST00000328957.8	37		150|150	0.06868131868131869|0.06868131868131869	3|3	0.006097560975609756|0.006097560975609756	38|38	0.10497237569060773|0.10497237569060773	0|0	0.0|0.0	109|109	0.1437994722955145|0.1437994722955145	c|c	22.5|22.5	4.303589|4.303589	0.81136|0.81136	0.029817|0.029817	0.141854|0.141854	ENSG00000182870|ENSG00000182870	ENST00000397325;ENST00000328957;ENST00000535228;ENST00000541995;ENST00000538356;ENST00000542942|ENST00000411988	T;T;T;T;T;T|T	0.65732|0.70986	-0.17;-0.17;-0.17;-0.17;-0.17;1.3|-0.53	3.87|3.87	2.97|2.97	0.34412|0.34412	.|.	0.101944|.	0.64402|.	N|.	0.000003|.	T|T	0.00637|0.00637	0.0021|0.0021	N|N	0.11154|0.11154	0.105|0.105	0.09310|0.09310	P|P	0.9999978708|0.9999978708	D;P;P|.	0.67145|.	0.996;0.95;0.95|.	P;B;B|.	0.55545|.	0.778;0.368;0.439|.	T|T	0.37244|0.37244	-0.9714|-0.9714	9|6	0.46703|0.87932	T|D	0.11|0	.|.	11.2217|11.2217	0.48860|0.48860	0.0:0.9078:0.0:0.0922|0.0:0.9078:0.0:0.0922	rs11246991;rs59928391;rs11246991|rs11246991;rs59928391;rs11246991	151;400;257|.	B3KNR7;Q9HCQ5;B3KP58|.	.;GALT9_HUMAN;.|.	T|H	34;400;151;34;34;34|172	ENSP00000380488:A34T;ENSP00000329846:A400T;ENSP00000439745:A151T;ENSP00000440544:A34T;ENSP00000444709:A34T;ENSP00000438221:A34T|ENSP00000394446:R172H	ENSP00000329846:A400T|ENSP00000394446:R172H	A|R	-|-	1|2	0|0	GALNT9|GALNT9	131254068|131254068	1.000000|1.000000	0.71417|0.71417	0.483000|0.483000	0.27378|0.27378	0.880000|0.880000	0.50808|0.50808	5.780000|5.780000	0.68956|0.68956	0.726000|0.726000	0.32339|0.32339	0.448000|0.448000	0.29417|0.29417	GCC|CGC	C|0.918;T|0.082	0.082	strong		0.642	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
TMEM161A	54929	hgsc.bcm.edu	37	19	19230868	19230868	+	Silent	SNP	A	A	G	rs756791	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19230868A>G	ENST00000162044.9	-	12	1375	c.1311T>C	c.(1309-1311)gcT>gcC	p.A437A	TMEM161A_ENST00000450333.2_Silent_p.A334A|TMEM161A_ENST00000587583.2_Silent_p.A412A	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	437					cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			GGCCACCCAGAGCCCCGGCAA	0.667													G|||	4395	0.877596	0.8911	0.8804	5008	,	,		14894	0.9206		0.8459	False		,,,				2504	0.8456				p.A437A		Atlas-SNP	.											.	TMEM161A	37	.	0			c.T1311C						PASS	.	G		3815,567		1668,479,44	18.0	20.0	19.0		1311	2.4	0.5	19	dbSNP_86	19	7135,1441		2979,1177,132	no	coding-synonymous	TMEM161A	NM_017814.1		4647,1656,176	GG,GA,AA		16.8027,12.9393,15.4962		437/480	19230868	10950,2008	2191	4288	6479	SO:0001819	synonymous_variant	54929	exon12			ACCCAGAGCCCCG	BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545			26020	protein-coding gene	gene with protein product						12975309	Standard	NM_017814		Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.1311T>C	19.37:g.19230868A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	177	79	0.446328	NM_017814	B3KUE0|G5E9M6|Q7L2Y1	Silent	SNP	ENST00000162044.9	37	CCDS12393.1																																																																																			A|0.145;G|0.855	0.855	strong		0.667	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460089.2	NM_017814	
CEP63	80254	hgsc.bcm.edu	37	3	134225969	134225969	+	Silent	SNP	T	T	C	rs9827878	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:134225969T>C	ENST00000337090.3	+	3	236	c.63T>C	c.(61-63)tgT>tgC	p.C21C	CEP63_ENST00000354446.3_Silent_p.C21C|CEP63_ENST00000504013.1_3'UTR|CEP63_ENST00000383229.3_Silent_p.C21C|CEP63_ENST00000332047.5_Silent_p.C21C|CEP63_ENST00000513612.2_Silent_p.C21C|CEP63_ENST00000606977.1_Silent_p.C21C			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	21					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TGACATCTTGTGAAGCAGAAC	0.348													T|||	861	0.171925	0.1415	0.1153	5008	,	,		14824	0.2183		0.17	False		,,,				2504	0.2076				p.C21C		Atlas-SNP	.											.	CEP63	56	.	0			c.T63C						PASS	.	T	,,,	551,3855	246.8+/-255.3	34,483,1686	97.0	98.0	98.0		63,63,63,63	4.5	1.0	3	dbSNP_119	98	1342,7258	262.3+/-284.3	108,1126,3066	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CEP63	NM_001042383.1,NM_001042384.1,NM_001042400.1,NM_025180.3	,,,	142,1609,4752	CC,CT,TT		15.6047,12.5057,14.5548	,,,	21/496,21/476,21/542,21/704	134225969	1893,11113	2203	4300	6503	SO:0001819	synonymous_variant	80254	exon3			ATCTTGTGAAGCA	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.63T>C	3.37:g.134225969T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Silent	SNP	ENST00000337090.3	37	CCDS3086.1																																																																																			T|0.841;C|0.159	0.159	strong		0.348	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418275	105418275	+	Silent	SNP	T	T	C	rs2819441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	224	0	0		WXS	Illumina HiSeq	Phase_I	147	57	0.387755	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	
DPY19L2	283417	hgsc.bcm.edu	37	12	63954300	63954300	+	Missense_Mutation	SNP	C	C	T	rs12314553	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:63954300C>T	ENST00000324472.4	-	22	2452	c.2269G>A	c.(2269-2271)Gtt>Att	p.V757I	DPY19L2_ENST00000413230.2_Missense_Mutation_p.V204I	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	757			V -> I (in dbSNP:rs12314553).		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)		TCTCAGTTAACCTTTAATACT	0.408													c|||	672	0.134185	0.2466	0.1239	5008	,	,		16421	0.0099		0.172	False		,,,				2504	0.0787				p.V757I		Atlas-SNP	.											.	DPY19L2	97	.	0			c.G2269A						PASS	.	C	ILE/VAL	1016,3390	374.6+/-321.3	105,806,1292	86.0	81.0	82.0		2269	2.1	0.4	12	dbSNP_120	82	1320,7280	259.7+/-282.8	101,1118,3081	yes	missense	DPY19L2	NM_173812.4	29	206,1924,4373	TT,TC,CC		15.3488,23.0595,17.9609	benign	757/759	63954300	2336,10670	2203	4300	6503	SO:0001583	missense	283417	exon22			AGTTAACCTTTAA		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.2269G>A	12.37:g.63954300C>T	ENSP00000315988:p.Val757Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	156	68	0.435897	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	310	0.14194139194139194	129	0.2621951219512195	50	0.13812154696132597	6	0.01048951048951049	125	0.16490765171503957	C	12.42	1.934130	0.34096	0.230595	0.153488	ENSG00000177990	ENST00000324472;ENST00000413230	T;T	0.55588	0.51;0.51	3.0	2.07	0.26955	.	0.063133	0.64402	D	0.000007	T	0.00012	0.0000	L	0.35414	1.06	0.32875	P	0.490194	B	0.31581	0.329	B	0.40375	0.327	T	0.21621	-1.0240	8	.	.	.	.	5.5277	0.16967	0.0:0.8213:0.0:0.1787	rs12314553	757	Q6NUT2	D19L2_HUMAN	I	757;204	ENSP00000315988:V757I;ENSP00000439794:V204I	.	V	-	1	0	DPY19L2	62240567	1.000000	0.71417	0.389000	0.26208	0.194000	0.23727	2.462000	0.45049	0.345000	0.23873	0.162000	0.16502	GTT	C|0.836;T|0.164	0.164	strong		0.408	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
DSPP	1834	hgsc.bcm.edu	37	4	88536886	88536886	+	Silent	SNP	C	C	T	rs111205182		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88536886C>T	ENST00000282478.7	+	4	3105	c.3072C>T	c.(3070-3072)agC>agT	p.S1024S	DSPP_ENST00000399271.1_Silent_p.S1024S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1024	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)		gcagcaatagcagtgacagca	0.517																																					p.S1024S		Atlas-SNP	.											DSPP,NS,carcinoma,0,3	DSPP	174	3	0			c.C3072T						PASS	.						44.0	40.0	41.0					4																	88536886		1516	2409	3925	SO:0001819	synonymous_variant	1834	exon5			CAATAGCAGTGAC	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.3072C>T	4.37:g.88536886C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	149	22	0.147651	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.517	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ITGA10	8515	hgsc.bcm.edu	37	1	145533175	145533175	+	Silent	SNP	T	T	C	rs11590105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:145533175T>C	ENST00000369304.3	+	11	1445	c.1270T>C	c.(1270-1272)Ttg>Ctg	p.L424L	ITGA10_ENST00000538811.1_Silent_p.L293L|ITGA10_ENST00000539363.1_Silent_p.L281L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	424					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCCCCCTGCATTGCAGAACCA	0.582													T|||	1001	0.19988	0.062	0.3458	5008	,	,		16859	0.1617		0.3559	False		,,,				2504	0.1616				p.L424L		Atlas-SNP	.											.	ITGA10	131	.	0			c.T1270C						PASS	.	T		500,3906	230.4+/-244.6	32,436,1735	48.0	43.0	45.0		1270	-5.7	0.0	1	dbSNP_120	45	3015,5585	463.6+/-366.0	549,1917,1834	no	coding-synonymous	ITGA10	NM_003637.3		581,2353,3569	CC,CT,TT		35.0581,11.3482,27.026		424/1168	145533175	3515,9491	2203	4300	6503	SO:0001819	synonymous_variant	8515	exon11			CCTGCATTGCAGA	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.1270T>C	1.37:g.145533175T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Silent	SNP	ENST00000369304.3	37	CCDS918.1																																																																																			T|0.762;C|0.238	0.238	strong		0.582	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
CEMIP	57214	hgsc.bcm.edu	37	15	81212521	81212521	+	Silent	SNP	T	T	C	rs2271160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:81212521T>C	ENST00000394685.3	+	15	2303	c.1884T>C	c.(1882-1884)tgT>tgC	p.C628C	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Silent_p.C628C|KIAA1199_ENST00000220244.3_Silent_p.C628C			Q8WUJ3	CEMIP_HUMAN		628					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)	p.C628C(1)		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						TTGACCACTGTCTTGGCCTCC	0.557													T|||	885	0.176717	0.1399	0.1354	5008	,	,		20777	0.2669		0.1342	False		,,,				2504	0.2065				p.C628C		Atlas-SNP	.											KIAA1199,NS,carcinoma,0,1	KIAA1199	118	1	1	Substitution - coding silent(1)	stomach(1)	c.T1884C						PASS	.	T		610,3796	268.3+/-268.4	41,528,1634	188.0	126.0	147.0		1884	-3.3	0.7	15	dbSNP_100	147	1181,7419	240.6+/-271.2	86,1009,3205	no	coding-synonymous	KIAA1199	NM_018689.1		127,1537,4839	CC,CT,TT		13.7326,13.8448,13.7706		628/1362	81212521	1791,11215	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon14			CCACTGTCTTGGC																												ENST00000394685.3:c.1884T>C	15.37:g.81212521T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			T|0.844;C|0.156	0.156	strong		0.557	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
ST6GAL2	84620	hgsc.bcm.edu	37	2	107423395	107423395	+	Silent	SNP	T	T	G	rs1470590	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:107423395T>G	ENST00000409382.3	-	6	1939	c.1329A>C	c.(1327-1329)atA>atC	p.I443I	ST6GAL2_ENST00000361686.4_Silent_p.I443I	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	443					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						TGGACATCATTATGAGGATTC	0.488													G|||	2049	0.409145	0.4546	0.4654	5008	,	,		18331	0.1726		0.6113	False		,,,				2504	0.3436				p.I443I		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.A1329C						PASS	.	G	,	2113,2293	598.5+/-389.1	497,1119,587	46.0	42.0	43.0		1329,1329	2.8	1.0	2	dbSNP_88	43	5062,3538	513.7+/-378.2	1473,2116,711	no	coding-synonymous,coding-synonymous	ST6GAL2	NM_001142351.1,NM_032528.2	,	1970,3235,1298	GG,GT,TT		41.1395,47.9573,44.8332	,	443/530,443/530	107423395	7175,5831	2203	4300	6503	SO:0001819	synonymous_variant	84620	exon6			CATCATTATGAGG	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.1329A>C	2.37:g.107423395T>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	37	CCDS2073.1	932	0.4267399267399267	207	0.42073170731707316	173	0.47790055248618785	89	0.1555944055944056	463	0.6108179419525066	G	10.29	1.310325	0.23821	0.479573	0.588605	ENSG00000144057	ENST00000361803	.	.	.	5.56	2.8	0.32819	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.44421	-0.9329	3	.	.	.	-12.1283	4.4342	0.11542	0.1359:0.1246:0.6101:0.1294	rs1470590;rs3796112;rs17629939;rs59094752;rs1470590	.	.	.	H	9	.	.	N	-	1	0	ST6GAL2	106789827	1.000000	0.71417	0.991000	0.47740	0.980000	0.70556	1.535000	0.36061	0.062000	0.16340	-0.121000	0.15023	AAT	T|0.514;G|0.486	0.486	strong		0.488	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
PAN2	9924	hgsc.bcm.edu	37	12	56718422	56718422	+	Silent	SNP	T	T	C	rs11171803	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56718422T>C	ENST00000425394.2	-	11	2047	c.1671A>G	c.(1669-1671)gcA>gcG	p.A557A	PAN2_ENST00000440411.3_Silent_p.A557A|PAN2_ENST00000257931.5_Silent_p.A557A|PAN2_ENST00000548043.1_Silent_p.A557A	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	CCAGCTCACATGCCAGACAGA	0.498													T|||	158	0.0315495	0.0015	0.0519	5008	,	,		22053	0.0347		0.0656	False		,,,				2504	0.0194				p.A557A		Atlas-SNP	.											.	PAN2	107	.	0			c.A1671G						PASS	.	T	,,	44,4362	46.0+/-80.4	1,42,2160	76.0	70.0	72.0		1671,1671,1671	-10.4	0.9	12	dbSNP_120	72	537,8063	148.9+/-204.1	22,493,3785	no	coding-synonymous,coding-synonymous,coding-synonymous	PAN2	NM_001127460.2,NM_001166279.1,NM_014871.4	,,	23,535,5945	CC,CT,TT		6.2442,0.9986,4.4672	,,	557/1203,557/1202,557/1199	56718422	581,12425	2203	4300	6503	SO:0001819	synonymous_variant	9924	exon11			CTCACATGCCAGA	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"""Ubiquitin-specific peptidases"""	20074	protein-coding gene	gene with protein product	"""PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"""		"""ubiquitin specific protease 52"", ""ubiquitin specific peptidase 52"", ""PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1671A>G	12.37:g.56718422T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	188	100	0.531915	NM_014871		Silent	SNP	ENST00000425394.2	37	CCDS44922.1																																																																																			T|0.960;C|0.040	0.040	strong		0.498	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871	
IL1R1	3554	hgsc.bcm.edu	37	2	102791086	102791086	+	Missense_Mutation	SNP	C	C	T	rs28362304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102791086C>T	ENST00000410023.1	+	10	1349	c.1031C>T	c.(1030-1032)aCg>aTg	p.T344M	IL1R1_ENST00000233946.3_Missense_Mutation_p.T344M|IL1R1_ENST00000409288.1_Missense_Mutation_p.T344M|IL1R1_ENST00000424272.1_Missense_Mutation_p.T344M|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000409329.1_Missense_Mutation_p.T344M|IL1R1_ENST00000409929.1_Missense_Mutation_p.T344M			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	344			T -> M (in dbSNP:rs28362304).		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)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	ATATGTGTCACGTTGACAGTC	0.313													C|||	228	0.0455272	0.0083	0.0072	5008	,	,		17379	0.0714		0.006	False		,,,				2504	0.137				p.T344M		Atlas-SNP	.											.	IL1R1	52	.	0			c.C1031T						PASS	.	C	MET/THR	49,4355	50.2+/-85.5	0,49,2153	185.0	167.0	173.0		1031	-3.8	0.0	2	dbSNP_125	173	43,8551	28.5+/-78.6	0,43,4254	yes	missense	IL1R1	NM_000877.2	81	0,92,6407	TT,TC,CC		0.5003,1.1126,0.7078	benign	344/570	102791086	92,12906	2202	4297	6499	SO:0001583	missense	3554	exon9			GTGTCACGTTGAC	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.1031C>T	2.37:g.102791086C>T	ENSP00000386380:p.Thr344Met	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	92	34	0.369565	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	37	CCDS2055.1	50	0.022893772893772892	2	0.0040650406504065045	3	0.008287292817679558	40	0.06993006993006994	5	0.006596306068601583	C	9.085	1.000223	0.19121	0.011126	0.005003	ENSG00000115594	ENST00000409929;ENST00000424272;ENST00000409329;ENST00000428279;ENST00000409288;ENST00000410023;ENST00000233946	T;T;T;T;T;T;T	0.05447	4.36;3.75;3.75;3.44;3.75;4.38;4.38	5.57	-3.75	0.04372	.	1.033190	0.07574	N	0.919117	T	0.00328	0.0010	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.13145	0.003;0.002;0.007	B;B;B	0.09377	0.001;0.002;0.004	T	0.42882	-0.9425	10	0.37606	T	0.19	.	14.2823	0.66221	0.0:0.7461:0.0:0.2539	rs28362304;rs28362304	344;344;344	B8ZZW4;P14778;B8ZZ73	.;IL1R1_HUMAN;.	M	344;344;344;200;344;344;344	ENSP00000386776:T344M;ENSP00000415366:T344M;ENSP00000387131:T344M;ENSP00000410461:T200M;ENSP00000386478:T344M;ENSP00000386380:T344M;ENSP00000233946:T344M	ENSP00000233946:T344M	T	+	2	0	IL1R1	102157518	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.517000	0.22832	-0.397000	0.07691	-0.982000	0.02568	ACG	C|0.985;T|0.015	0.015	strong		0.313	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
RPTOR	57521	hgsc.bcm.edu	37	17	78936339	78936339	+	Silent	SNP	G	G	A	rs17848671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78936339G>A	ENST00000306801.3	+	32	4133	c.3771G>A	c.(3769-3771)acG>acA	p.T1257T	RPTOR_ENST00000544334.2_Silent_p.T1099T|RPTOR_ENST00000575542.1_3'UTR|CTD-2561B21.3_ENST00000571591.1_RNA	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1257					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						AGGGGCTGACGGCCCTGGACA	0.632													G|||	3	0.000599042	0.0	0.0029	5008	,	,		17401	0.001		0.0	False		,,,				2504	0.0				p.T1257T		Atlas-SNP	.											.	RPTOR	122	.	0			c.G3771A						PASS	.						95.0	83.0	87.0					17																	78936339		2203	4300	6503	SO:0001819	synonymous_variant	57521	exon32			GCTGACGGCCCTG		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.3771G>A	17.37:g.78936339G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			G|0.999;A|0.001	0.001	strong		0.632	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
DNAH8	1769	hgsc.bcm.edu	37	6	38980081	38980081	+	Missense_Mutation	SNP	A	A	G	rs10484847	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:38980081A>G	ENST00000359357.3	+	88	13065	c.12811A>G	c.(12811-12813)Ata>Gta	p.I4271V	DNAH8_ENST00000441566.1_Missense_Mutation_p.I4235V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4271			I -> V (in dbSNP:rs10484847). {ECO:0000269|PubMed:12297094}.		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AGTCATTTCAATACTCCGCAG	0.358													A|||	533	0.10643	0.1188	0.1225	5008	,	,		20665	0.002		0.1769	False		,,,				2504	0.1135				p.I4488V		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,-1,2	DNAH8	1239	2	0			c.A13462G						PASS	.	A	VAL/ILE	642,3764	273.7+/-271.5	45,552,1606	157.0	145.0	149.0		13462	2.5	0.1	6	dbSNP_119	149	1549,7051	291.5+/-300.3	136,1277,2887	yes	missense	DNAH8	NM_001206927.1	29	181,1829,4493	GG,GA,AA		18.0116,14.571,16.8461	benign	4488/4708	38980081	2191,10815	2203	4300	6503	SO:0001583	missense	1769	exon90			ATTTCAATACTCC	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.12811A>G	6.37:g.38980081A>G	ENSP00000352312:p.Ile4271Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		243	0.11126373626373626	61	0.12398373983739837	51	0.1408839779005525	2	0.0034965034965034965	129	0.17018469656992086	A	7.940	0.742626	0.15642	0.14571	0.180116	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.08102	3.13;3.13;3.13	6.16	2.45	0.29901	Dynein heavy chain (1);	0.554802	0.19449	N	0.113988	T	0.00815	0.0027	N	0.02736	-0.51	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48175	-0.9058	9	0.27785	T	0.31	.	1.9397	0.03344	0.5499:0.1244:0.206:0.1197	rs10484847;rs17422343;rs52803138;rs57264205;rs10484847	4271	Q96JB1	DYH8_HUMAN	V	4476;4271;4235	ENSP00000333363:I4476V;ENSP00000352312:I4271V;ENSP00000402294:I4235V	ENSP00000333363:I4476V	I	+	1	0	DNAH8	39088059	0.013000	0.17824	0.079000	0.20413	0.978000	0.69477	0.402000	0.20965	0.187000	0.20147	0.528000	0.53228	ATA	A|0.890;G|0.110	0.110	strong		0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
CDHR4	389118	hgsc.bcm.edu	37	3	49831032	49831032	+	Missense_Mutation	SNP	A	A	G	rs115485248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49831032A>G	ENST00000412678.2	-	12	1615	c.1607T>C	c.(1606-1608)aTt>aCt	p.I536T	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	536	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(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						CTCGATGGTAATGGTACAGGA	0.488													A|||	3	0.000599042	0.0	0.0	5008	,	,		22546	0.0		0.003	False		,,,				2504	0.0				p.I536T		Atlas-SNP	.											.	CDHR4	37	.	0			c.T1607C						PASS	.	A	THR/ILE	0,1384		0,0,692	186.0	175.0	178.0		1607	5.7	1.0	3	dbSNP_132	178	9,3173		0,9,1582	yes	missense	CDHR4	NM_001007540.2	89	0,9,2274	GG,GA,AA		0.2828,0.0,0.1971	probably-damaging	536/789	49831032	9,4557	692	1591	2283	SO:0001583	missense	389118	exon12			ATGGTAATGGTAC		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1607T>C	3.37:g.49831032A>G	ENSP00000391409:p.Ile536Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	37	CCDS46829.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	17.57	3.423523	0.62733	0.0	0.002828	ENSG00000187492	ENST00000412678	T	0.43688	0.94	5.67	5.67	0.87782	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.66396	0.2785	M	0.84511	2.7	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	T	0.72253	-0.4347	9	0.87932	D	0	.	12.3323	0.55046	1.0:0.0:0.0:0.0	.	536	A6H8M9	CDHR4_HUMAN	T	536	ENSP00000391409:I536T	ENSP00000391409:I536T	I	-	2	0	CDHR4	49806036	0.899000	0.30636	0.997000	0.53966	0.981000	0.71138	4.401000	0.59716	2.170000	0.68504	0.529000	0.55759	ATT	A|0.999;G|0.001	0.001	strong		0.488	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
RBM4B	83759	hgsc.bcm.edu	37	11	66436255	66436255	+	Missense_Mutation	SNP	C	C	T	rs149014922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66436255C>T	ENST00000525754.1	-	2	1588	c.920G>A	c.(919-921)cGt>cAt	p.R307H	RBM4B_ENST00000310046.4_Missense_Mutation_p.R307H|RBM4B_ENST00000531969.1_Intron|RBM4B_ENST00000529195.2_5'UTR|RP11-658F2.8_ENST00000548810.1_RNA|RP11-658F2.8_ENST00000550837.1_RNA			Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	307	Interaction with TNPO3. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|entrainment of circadian clock by photoperiod (GO:0043153)|mRNA processing (GO:0006397)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)|urinary_tract(2)	10						TGCAGCACGACGCAGTGGGCT	0.567													C|||	4	0.000798722	0.0008	0.0043	5008	,	,		18986	0.0		0.0	False		,,,				2504	0.0				p.R307H		Atlas-SNP	.											RBM4B,NS,carcinoma,-1,1	RBM4B	27	1	0			c.G920A						scavenged	.						58.0	56.0	57.0					11																	66436255		2200	4295	6495	SO:0001583	missense	83759	exon3			GCACGACGCAGTG	AK095158	CCDS8149.1, CCDS66144.1	11q13	2013-02-12	2006-01-25	2006-01-25				"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	28842	protein-coding gene	gene with protein product			"""RNA binding motif protein 30"""	RBM30		12477932	Standard	XR_247213		Approved	MGC10871, ZCCHC15, RBM4L, ZCRB3B, ZCCHC21B	uc001ojb.3	Q9BQ04		ENST00000525754.1:c.920G>A	11.37:g.66436255C>T	ENSP00000433071:p.Arg307His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	128	3	0.0234375	NM_031492	B3KT83	Missense_Mutation	SNP	ENST00000525754.1	37	CCDS8149.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.82	3.704686	0.68615	.	.	ENSG00000173914	ENST00000525754;ENST00000310046	T;T	0.30981	1.51;1.51	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.37433	0.1003	M	0.69823	2.125	0.80722	D	1	B	0.27068	0.167	B	0.17098	0.017	T	0.07712	-1.0758	10	0.41790	T	0.15	.	19.6313	0.95704	0.0:1.0:0.0:0.0	.	307	Q9BQ04	RBM4B_HUMAN	H	307	ENSP00000433071:R307H;ENSP00000310471:R307H	ENSP00000310471:R307H	R	-	2	0	RBM4B	66192831	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	3.789000	0.55454	2.937000	0.99478	0.650000	0.86243	CGT	C|1.000;T|0.000	0.000	strong		0.567	RBM4B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393851.1	NM_031492	
KIAA1551	55196	hgsc.bcm.edu	37	12	32137447	32137447	+	Silent	SNP	C	C	T	rs3759300	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32137447C>T	ENST00000312561.4	+	4	3972	c.3558C>T	c.(3556-3558)ccC>ccT	p.P1186P	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1186																	AAGGAGTACCCCAGTGTCAGT	0.448													C|||	620	0.123802	0.0106	0.0879	5008	,	,		20430	0.2321		0.1382	False		,,,				2504	0.1759				p.P1186P		Atlas-SNP	.											.	.	.	.	0			c.C3558T						PASS	.	C		133,4273	95.7+/-134.4	0,133,2070	134.0	127.0	130.0		3558	1.4	0.2	12	dbSNP_107	130	1204,7396	243.5+/-273.1	83,1038,3179	no	coding-synonymous	C12orf35	NM_018169.3		83,1171,5249	TT,TC,CC		14.0,3.0186,10.2799		1186/1748	32137447	1337,11669	2203	4300	6503	SO:0001819	synonymous_variant	55196	exon4			AGTACCCCAGTGT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3558C>T	12.37:g.32137447C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			C|0.883;T|0.117	0.117	strong		0.448	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
KMT2D	8085	hgsc.bcm.edu	37	12	49445028	49445028	+	Missense_Mutation	SNP	G	G	A	rs75226229	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:49445028G>A	ENST00000301067.7	-	10	2437	c.2438C>T	c.(2437-2439)cCg>cTg	p.P813L		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	813	Pro-rich.		P -> L (in dbSNP:rs75226229). {ECO:0000269|PubMed:21280141}.	Missing (in Ref. 1; AAC51734). {ECO:0000305}.	chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGACAGGTGCGGCTCCTCAGT	0.647													G|||	80	0.0159744	0.0023	0.0274	5008	,	,		15268	0.0		0.0487	False		,,,				2504	0.0092				p.P813L		Atlas-SNP	.											.	MLL2	1173	.	0			c.C2438T						PASS	.	G	LEU/PRO	45,3979		0,45,1967	36.0	40.0	38.0		2438	-1.4	0.0	12	dbSNP_132	38	424,7814		15,394,3710	yes	missense	MLL2	NM_003482.3	98	15,439,5677	AA,AG,GG		5.1469,1.1183,3.8248	probably-damaging	813/5538	49445028	469,11793	2012	4119	6131	SO:0001583	missense	8085	exon10			AGGTGCGGCTCCT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.2438C>T	12.37:g.49445028G>A	ENSP00000301067:p.Pro813Leu	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	56	0.02564102564102564	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	43	0.05672823218997362	G	5.855	0.341913	0.11069	0.011183	0.051469	ENSG00000167548	ENST00000301067	T	0.33216	1.42	3.68	-1.4	0.08968	.	.	.	.	.	T	0.01189	0.0039	N	0.02539	-0.55	0.21386	N	0.999707	B	0.02656	0.0	B	0.01281	0.0	T	0.22730	-1.0208	9	0.87932	D	0	.	8.578	0.33609	0.6006:0.0:0.3994:0.0	.	813	O14686	MLL2_HUMAN	L	813	ENSP00000301067:P813L	ENSP00000301067:P813L	P	-	2	0	MLL2	47731295	0.000000	0.05858	0.028000	0.17463	0.009000	0.06853	-0.587000	0.05780	-0.301000	0.08882	-0.972000	0.02603	CCG	G|0.971;A|0.029	0.029	strong		0.647	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
TLR10	81793	hgsc.bcm.edu	37	4	38775040	38775040	+	Silent	SNP	A	A	G	rs10776483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:38775040A>G	ENST00000308973.4	-	4	2777	c.2172T>C	c.(2170-2172)caT>caC	p.H724H	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Silent_p.H724H|TLR10_ENST00000506111.1_Silent_p.H724H|TLR10_ENST00000361424.2_Silent_p.H724H	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	724	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				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						TAAGAATTATATGATCAGAAT	0.388													A|||	1496	0.298722	0.2126	0.3184	5008	,	,		19051	0.4325		0.2495	False		,,,				2504	0.3139				p.H724H		Atlas-SNP	.											.	TLR10	87	.	0			c.T2172C						PASS	.	A	,,,,	981,3425	352.6+/-311.8	101,779,1323	91.0	96.0	94.0		2172,2172,2172,2130,2172	-2.2	0.0	4	dbSNP_120	94	1746,6854	315.3+/-312.2	187,1372,2741	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	,,,,	288,2151,4064	GG,GA,AA		20.3023,22.2651,20.9672	,,,,	724/812,724/812,724/812,710/798,724/812	38775040	2727,10279	2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			AATTATATGATCA	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.2172T>C	4.37:g.38775040A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			A|0.738;G|0.262	0.262	strong		0.388	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
TH	7054	hgsc.bcm.edu	37	11	2190951	2190951	+	Missense_Mutation	SNP	C	C	T	rs6356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000333684.5_Missense_Mutation_p.V85M|TH_ENST00000352909.3_Missense_Mutation_p.V81M	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	133	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	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	
FREM2	341640	hgsc.bcm.edu	37	13	39264690	39264690	+	Missense_Mutation	SNP	T	T	C	rs2496425	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	scavenged	.	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	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	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	
OR5D14	219436	hgsc.bcm.edu	37	11	55563602	55563602	+	Missense_Mutation	SNP	G	G	A	rs68042892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	294	0	0		WXS	Illumina HiSeq	Phase_I	258	129	0.5	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	
KCNN3	3782	hgsc.bcm.edu	37	1	154842244	154842244	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154842244A>T	ENST00000271915.4	-	1	512	c.197T>A	c.(196-198)cTt>cAt	p.L66H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	66	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	ctgctgctgaagctgcggagg	0.701																																					p.L66H		Atlas-SNP	.											KCNN3,NS,carcinoma,+1,3	KCNN3	141	3	0			c.T197A						scavenged	.																																			SO:0001583	missense	3782	exon1			TGCTGAAGCTGCG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.197T>A	1.37:g.154842244A>T	ENSP00000271915:p.Leu66His	Somatic	25	4	0.16		WXS	Illumina HiSeq	Phase_I	42	6	0.142857	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	a	9.986	1.229557	0.22542	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.58060	0.36	4.47	-1.06	0.10002	.	2.530250	0.01603	N	0.022141	T	0.17152	0.0412	N	0.08118	0	0.35103	D	0.765442	.	.	.	.	.	.	T	0.03807	-1.1002	8	0.72032	D	0.01	-1.1381	4.5154	0.11932	0.5982:0.0:0.2622:0.1396	.	.	.	.	H	66;161	ENSP00000271915:L66H	ENSP00000271915:L66H	L	-	2	0	KCNN3	153108868	0.001000	0.12720	0.839000	0.33178	0.980000	0.70556	0.019000	0.13444	0.013000	0.14918	0.460000	0.39030	CTT	.	.	none		0.701	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
PIGN	23556	hgsc.bcm.edu	37	18	59810563	59810563	+	Silent	SNP	A	A	G	rs34227891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	205	0	0		WXS	Illumina HiSeq	Phase_I	205	112	0.546341	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	
RSPO3	84870	hgsc.bcm.edu	37	6	127476516	127476516	+	Silent	SNP	G	G	A	rs1892172	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:127476516G>A	ENST00000356698.4	+	4	1156	c.567G>A	c.(565-567)ctG>ctA	p.L189L	RSPO3_ENST00000368317.3_Silent_p.L189L	NM_032784.3	NP_116173.2	Q9BXY4	RSPO3_HUMAN	R-spondin 3	189	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)	extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		PTPRK/RSPO3(10)	breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17				GBM - Glioblastoma multiforme(226;0.0555)		AGGGTAACCTGTGTCCCCCAA	0.438													g|||	2668	0.532748	0.5983	0.5231	5008	,	,		20533	0.494		0.5	False		,,,				2504	0.5245				p.L189L		Atlas-SNP	.											RSPO3,rectum,carcinoma,0,1	RSPO3	32	1	0			c.G567A						PASS	.	A		2614,1792	641.7+/-397.5	789,1036,378	110.0	99.0	103.0		567	4.6	1.0	6	dbSNP_92	103	4583,4017	597.8+/-393.8	1220,2143,937	yes	coding-synonymous	RSPO3	NM_032784.3		2009,3179,1315	AA,AG,GG		46.7093,40.6718,44.664		189/273	127476516	7197,5809	2203	4300	6503	SO:0001819	synonymous_variant	84870	exon4			TAACCTGTGTCCC	BC022367	CCDS5135.1	6q22.33	2013-02-28	2011-06-29	2005-08-08	ENSG00000146374	ENSG00000146374		"""Endogenous ligands"""	20866	protein-coding gene	gene with protein product		610574	"""thrombospondin, type I, domain containing 2"", ""R-spondin 3 homolog (Xenopus laevis)"""	THSD2		10842357, 15469841	Standard	NM_032784		Approved	FLJ14440	uc003qar.3	Q9BXY4	OTTHUMG00000015521	ENST00000356698.4:c.567G>A	6.37:g.127476516G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	163	81	0.496933	NM_032784	B2RC27|Q5VTV4|Q96K87	Silent	SNP	ENST00000356698.4	37	CCDS5135.1																																																																																			G|0.455;A|0.545	0.545	strong		0.438	RSPO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042111.1	NM_032784	
CLCA1	1179	hgsc.bcm.edu	37	1	86965419	86965419	+	Silent	SNP	T	T	C	rs1882753	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:86965419T>C	ENST00000234701.3	+	15	2787	c.2436T>C	c.(2434-2436)acT>acC	p.T812T	CLCA1_ENST00000394711.1_Silent_p.T812T			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	812					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		TGAATACTACTGCTCTCATCC	0.343													T|||	1766	0.352636	0.2837	0.2291	5008	,	,		18120	0.5446		0.2604	False		,,,				2504	0.4305				p.T812T		Atlas-SNP	.											.	CLCA1	109	.	0			c.T2436C						PASS	.	T		1173,3231	395.6+/-329.7	162,849,1191	89.0	92.0	91.0		2436	-4.7	0.0	1	dbSNP_92	91	2238,6362	375.2+/-337.7	316,1606,2378	no	coding-synonymous	CLCA1	NM_001285.3		478,2455,3569	CC,CT,TT		26.0233,26.6349,26.2304		812/915	86965419	3411,9593	2202	4300	6502	SO:0001819	synonymous_variant	1179	exon14			TACTACTGCTCTC		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"""chloride channel, calcium activated, family member 1"", ""chloride channel regulator 1"""			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.2436T>C	1.37:g.86965419T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	37	CCDS709.1																																																																																			T|0.690;C|0.310	0.310	strong		0.343	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
PTGS1	5742	hgsc.bcm.edu	37	9	125143792	125143792	+	Silent	SNP	C	C	A	rs5788	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125143792C>A	ENST00000362012.2	+	6	644	c.639C>A	c.(637-639)ggC>ggA	p.G213G	PTGS1_ENST00000223423.4_Silent_p.G213G|PTGS1_ENST00000373698.5_Silent_p.G104G|PTGS1_ENST00000540753.1_Silent_p.G188G	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	213					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.G213G(1)		large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	AAACTTCTGGCAAGATGGGTC	0.542													C|||	1356	0.270767	0.6876	0.2406	5008	,	,		19091	0.0407		0.1402	False		,,,				2504	0.1002				p.G213G		Atlas-SNP	.											PTGS1,NS,carcinoma,0,1	PTGS1	84	1	1	Substitution - coding silent(1)	stomach(1)	c.C639A						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	218	0	0		WXS	Illumina HiSeq	Phase_I	189	88	0.465608	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		
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253956	39253956	+	Silent	SNP	G	G	A	rs139720993	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39253956G>A	ENST00000333822.4	-	1	437	c.381C>T	c.(379-381)ccC>ccT	p.P127P		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	127	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.P127P(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						tgctgcagctggggcggcagc	0.677													G|||	1899	0.379193	0.4198	0.3934	5008	,	,		14956	0.2292		0.4553	False		,,,				2504	0.3906				p.P127P		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	1	Substitution - coding silent(1)	kidney(1)	c.C381T						scavenged	.						3.0	5.0	4.0					17																	39253956		591	1415	2006	SO:0001819	synonymous_variant	728224	exon1			GCAGCTGGGGCGG	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.381C>T	17.37:g.39253956G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	65	18	0.276923	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			G|0.500;A|0.500	0.500	strong		0.677	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
PNO1	56902	hgsc.bcm.edu	37	2	68388823	68388823	+	Silent	SNP	A	A	G	rs1137930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:68388823A>G	ENST00000263657.2	+	3	457	c.366A>G	c.(364-366)aaA>aaG	p.K122K	RP11-474G23.1_ENST00000406334.3_Intron	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	122						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						AGACTTGTAAAGAAACCAAGG	0.348													A|||	1702	0.339856	0.0809	0.353	5008	,	,		19239	0.4881		0.327	False		,,,				2504	0.5409				p.K122K	NSCLC(83;642 1410 13044 32832 40058)	Atlas-SNP	.											.	PNO1	17	.	0			c.A366G						PASS	.	A		562,3844	247.2+/-255.5	36,490,1677	100.0	103.0	102.0		366	3.4	1.0	2	dbSNP_86	102	2618,5982	420.3+/-353.3	402,1814,2084	yes	coding-synonymous	PNO1	NM_020143.2		438,2304,3761	GG,GA,AA		30.4419,12.7553,24.4503		122/253	68388823	3180,9826	2203	4300	6503	SO:0001819	synonymous_variant	56902	exon3			TTGTAAAGAAACC	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.366A>G	2.37:g.68388823A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_020143	A8K6Q0|Q53G13|Q8WVB8	Silent	SNP	ENST00000263657.2	37	CCDS1885.1																																																																																			A|0.731;G|0.269	0.269	strong		0.348	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143	
SP2	6668	hgsc.bcm.edu	37	17	45994154	45994154	+	Silent	SNP	G	G	A	rs2229358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45994154G>A	ENST00000376741.4	+	3	854	c.717G>A	c.(715-717)ccG>ccA	p.P239P	AC003665.1_ENST00000411573.2_RNA|AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000433001.1_RNA|AC003665.1_ENST00000451140.2_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	239					cardiovascular system development (GO:0072358)|embryonic organ development (GO:0048568)|fibroblast proliferation (GO:0048144)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						CCCCAACCCCGCTGTCTAAGA	0.607													G|||	2473	0.49381	0.3457	0.4625	5008	,	,		17625	0.7748		0.4602	False		,,,				2504	0.4611				p.P239P		Atlas-SNP	.											.	SP2	38	.	0			c.G717A						PASS	.	G		1622,2784	498.8+/-364.2	303,1016,884	82.0	87.0	85.0		717	-10.8	0.0	17	dbSNP_98	85	3732,4868	531.3+/-382.0	811,2110,1379	no	coding-synonymous	SP2	NM_003110.5		1114,3126,2263	AA,AG,GG		43.3953,36.8134,41.1656		239/614	45994154	5354,7652	2203	4300	6503	SO:0001819	synonymous_variant	6668	exon3			AACCCCGCTGTCT		CCDS11521.2	17q21.3-q22	2013-01-08			ENSG00000167182	ENSG00000167182		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11207	protein-coding gene	gene with protein product		601801				1341900, 9730617	Standard	NM_003110		Approved	KIAA0048	uc002imk.3	Q02086	OTTHUMG00000150196	ENST00000376741.4:c.717G>A	17.37:g.45994154G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_003110	A6NK74	Silent	SNP	ENST00000376741.4	37	CCDS11521.2																																																																																			G|0.545;A|0.455	0.455	strong		0.607	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
PSG8	440533	hgsc.bcm.edu	37	19	43269699	43269699	+	Missense_Mutation	SNP	C	C	T	rs71337226|rs7260508	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43269699C>T	ENST00000306511.4	-	1	132	c.35G>A	c.(34-36)cGc>cAc	p.R12H	PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.R12H|PSG8_ENST00000406636.3_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	22	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	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		
APOL5	80831	hgsc.bcm.edu	37	22	36122380	36122380	+	Missense_Mutation	SNP	T	T	A	rs41283201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36122380T>A	ENST00000249044.2	+	3	265	c.265T>A	c.(265-267)Tcc>Acc	p.S89T		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	89					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						TGACAAAGATTCCATGCCAGA	0.393													T|||	190	0.0379393	0.0794	0.0231	5008	,	,		23061	0.0		0.0268	False		,,,				2504	0.0429				p.S89T		Atlas-SNP	.											.	APOL5	45	.	0			c.T265A						PASS	.	T	THR/SER	243,4163	142.3+/-177.5	6,231,1966	106.0	95.0	99.0		265	-2.6	0.0	22	dbSNP_127	99	217,8383	90.6+/-152.8	6,205,4089	yes	missense	APOL5	NM_030642.1	58	12,436,6055	AA,AT,TT		2.5233,5.5152,3.5368	possibly-damaging	89/434	36122380	460,12546	2203	4300	6503	SO:0001583	missense	80831	exon3			AAAGATTCCATGC	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.265T>A	22.37:g.36122380T>A	ENSP00000249044:p.Ser89Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	36	0.36	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	37	CCDS13920.1	72	0.03296703296703297	49	0.09959349593495935	7	0.019337016574585635	0	0.0	16	0.021108179419525065	T	10.93	1.489505	0.26686	0.055152	0.025233	ENSG00000128313	ENST00000249044	T	0.03272	3.99	2.77	-2.59	0.06209	.	5.536730	0.01072	N	0.004824	T	0.00073	0.0002	N	0.08118	0	0.09310	N	1	B	0.24618	0.107	B	0.23716	0.048	T	0.42716	-0.9435	10	0.18276	T	0.48	.	3.4069	0.07344	0.2328:0.5108:0.0:0.2565	rs41283201;rs61731696	89	Q9BWW9	APOL5_HUMAN	T	89	ENSP00000249044:S89T	ENSP00000249044:S89T	S	+	1	0	APOL5	34452326	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.445000	0.06845	-0.396000	0.07703	-0.654000	0.03906	TCC	T|0.964;A|0.036	0.036	strong		0.393	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
CENPF	1063	hgsc.bcm.edu	37	1	214820299	214820299	+	Silent	SNP	A	A	G	rs3748698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214820299A>G	ENST00000366955.3	+	13	7554	c.7386A>G	c.(7384-7386)gaA>gaG	p.E2462E		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2558	2 X 177 AA tandem repeats.				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)		ATGACCAAGAAGCCTGTAAGG	0.418													G|||	532	0.10623	0.1089	0.1066	5008	,	,		16506	0.1151		0.0507	False		,,,				2504	0.1503				p.E2462E	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A7386G						PASS	.	G		425,3981	774.4+/-414.0	20,385,1798	71.0	83.0	79.0		7386	-4.1	0.0	1	dbSNP_107	79	461,8139	795.5+/-407.5	12,437,3851	no	coding-synonymous	CENPF	NM_016343.3		32,822,5649	GG,GA,AA		5.3605,9.6459,6.8122		2462/3115	214820299	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	1063	exon13			CCAAGAAGCCTGT	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.7386A>G	1.37:g.214820299A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			A|0.916;G|0.084	0.084	strong		0.418	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
GSTO1	9446	hgsc.bcm.edu	37	10	106022789	106022789	+	Missense_Mutation	SNP	C	C	A	rs4925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:106022789C>A	ENST00000369713.5	+	4	613	c.419C>A	c.(418-420)gCt>gAt	p.A140D	GSTO1_ENST00000539281.1_Missense_Mutation_p.A112D|GSTO1_ENST00000493946.1_3'UTR|GSTO1_ENST00000369710.4_Intron	NM_004832.2	NP_004823.1	P78417	GSTO1_HUMAN	glutathione S-transferase omega 1	140	GST C-terminal.		A -> D (in allele GSTO1*C; no effect on protein stability; dbSNP:rs4925). {ECO:0000269|PubMed:12618591, ECO:0000269|PubMed:12928150}.		cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014810)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)	p.A140D(1)		large_intestine(1)|lung(1)|stomach(1)	3		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)|Vitamin E(DB00163)	GAAGACTATGCTGGCCTAAAA	0.353													C|||	888	0.177316	0.0696	0.2075	5008	,	,		18895	0.13		0.337	False		,,,				2504	0.1861				p.A140D		Atlas-SNP	.											GSTO1,NS,carcinoma,0,1	GSTO1	14	1	1	Substitution - Missense(1)	stomach(1)	c.C419A	GRCh37	CM061795	GSTO1	M	rs4925	PASS	.	C	,ASP/ALA,ASP/ALA	481,3925	226.2+/-241.8	25,431,1747	88.0	85.0	86.0		,335,419	3.9	0.0	10	dbSNP_52	86	2665,5935	427.8+/-355.7	415,1835,2050	yes	intron,missense,missense	GSTO1	NM_001191002.1,NM_001191003.1,NM_004832.2	,126,126	440,2266,3797	AA,AC,CC		30.9884,10.9169,24.1888	,benign,benign	,112/214,140/242	106022789	3146,9860	2203	4300	6503	SO:0001583	missense	9446	exon4			ACTATGCTGGCCT	AF212303	CCDS7555.1, CCDS53572.1, CCDS53573.1	10q25.1	2012-06-21			ENSG00000148834	ENSG00000148834	2.5.1.18, 1.8.5.1, 1.20.4.2	"""Glutathione S-transferases / Soluble"""	13312	protein-coding gene	gene with protein product		605482				10783391, 12618591	Standard	NM_004832		Approved	GSTTLp28, P28	uc001kya.3	P78417	OTTHUMG00000019001	ENST00000369713.5:c.419C>A	10.37:g.106022789C>A	ENSP00000358727:p.Ala140Asp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_004832	D3DRA3|F5H7H0|Q5TA03|Q7Z3T2	Missense_Mutation	SNP	ENST00000369713.5	37	CCDS7555.1	459	0.21016483516483517	32	0.06504065040650407	87	0.24033149171270718	86	0.15034965034965034	254	0.33509234828496043	C	13.32	2.201635	0.38905	0.109169	0.309884	ENSG00000148834	ENST00000539281;ENST00000369713;ENST00000445155	T;T;T	0.13196	2.61;2.61;2.61	4.83	3.93	0.45458	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.523772	0.23569	N	0.046768	T	0.00012	0.0000	N	0.02158	-0.66	0.50467	P	1.2500000000004174E-4	B	0.29136	0.234	B	0.29716	0.106	T	0.48103	-0.9064	9	0.25106	T	0.35	-0.2439	11.8844	0.52594	0.0:0.915:0.0:0.085	rs4925;rs3184686;rs3740467;rs17825384;rs17880534;rs56435924;rs56733715;rs4925	140	P78417	GSTO1_HUMAN	D	112;140;112	ENSP00000441488:A112D;ENSP00000358727:A140D;ENSP00000406708:A112D	ENSP00000358727:A140D	A	+	2	0	GSTO1	106012779	0.016000	0.18221	0.046000	0.18839	0.099000	0.18886	0.831000	0.27476	1.389000	0.46526	0.655000	0.94253	GCT	C|0.778;A|0.222	0.222	strong		0.353	GSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050193.1	NM_004832	
CENPO	79172	hgsc.bcm.edu	37	2	25022598	25022598	+	Missense_Mutation	SNP	A	A	G	rs1550116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:25022598A>G	ENST00000380834.2	+	3	526	c.101A>G	c.(100-102)cAg>cGg	p.Q34R	CENPO_ENST00000260662.1_Missense_Mutation_p.Q34R|CENPO_ENST00000473706.1_Missense_Mutation_p.Q28R			Q9BU64	CENPO_HUMAN	centromere protein O	34			Q -> R (in dbSNP:rs1550116). {ECO:0000269|PubMed:14702039}.		CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TCCCGTAAACAGTCTGAAGAG	0.498													A|||	663	0.132388	0.1097	0.1138	5008	,	,		19092	0.2063		0.1461	False		,,,				2504	0.0859				p.Q34R		Atlas-SNP	.											.	CENPO	18	.	0			c.A101G						PASS	.	A	ARG/GLN,ARG/GLN	486,3920	226.5+/-242.0	21,444,1738	89.0	99.0	96.0		83,101	-3.6	0.0	2	dbSNP_88	96	1275,7325	252.5+/-278.5	85,1105,3110	yes	missense,missense	CENPO	NM_001199803.1,NM_024322.2	43,43	106,1549,4848	GG,GA,AA		14.8256,11.0304,13.5399	benign,benign	28/295,34/301	25022598	1761,11245	2203	4300	6503	SO:0001583	missense	79172	exon3			GTAAACAGTCTGA	AK027859	CCDS1714.1, CCDS56113.1	2p23.3	2013-11-05			ENSG00000138092	ENSG00000138092			28152	protein-coding gene	gene with protein product		611504				16622420, 16622419	Standard	NM_024322		Approved	MGC11266, CENP-O	uc002rfp.2	Q9BU64	OTTHUMG00000125525	ENST00000380834.2:c.101A>G	2.37:g.25022598A>G	ENSP00000370214:p.Gln34Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_024322	B2RDC0|D6W536|Q53T55|Q96JV3	Missense_Mutation	SNP	ENST00000380834.2	37	CCDS1714.1	332	0.152014652014652	47	0.09552845528455285	54	0.14917127071823205	123	0.21503496503496503	108	0.1424802110817942	A	2.705	-0.270191	0.05716	0.110304	0.148256	ENSG00000138092	ENST00000380834;ENST00000473706;ENST00000260662	T;T;T	0.44482	0.92;0.95;0.92	4.75	-3.63	0.04529	.	0.848021	0.10091	N	0.717152	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	0.26503	-1.0101	9	0.44086	T	0.13	-23.6971	6.5348	0.22346	0.4062:0.1499:0.4439:0.0	rs1550116;rs52799040;rs61143613;rs1550116	28;34	Q9BU64-2;Q9BU64	.;CENPO_HUMAN	R	34;28;34	ENSP00000370214:Q34R;ENSP00000417787:Q28R;ENSP00000260662:Q34R	ENSP00000260662:Q34R	Q	+	2	0	CENPO	24876102	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	0.288000	0.18939	-0.951000	0.03654	-0.792000	0.03331	CAG	A|0.859;G|0.141	0.141	strong		0.498	CENPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246856.2	NM_024322	
TRPM5	29850	hgsc.bcm.edu	37	11	2439767	2439767	+	Missense_Mutation	SNP	T	T	C	rs886277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:2439767T>C	ENST00000155858.6	-	5	712	c.704A>G	c.(703-705)aAc>aGc	p.N235S	TRPM5_ENST00000533060.1_Missense_Mutation_p.N235S|TRPM5_ENST00000452833.1_Missense_Mutation_p.N237S|TRPM5_ENST00000528453.1_Missense_Mutation_p.N235S	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	158	0	0		WXS	Illumina HiSeq	Phase_I	225	102	0.453333	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	
SERTAD1	29950	hgsc.bcm.edu	37	19	40929363	40929363	+	Missense_Mutation	SNP	T	T	C	rs268687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40929363T>C	ENST00000357949.4	-	2	249	c.91A>G	c.(91-93)Aca>Gca	p.T31A		NM_013376.3	NP_037508.2	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	31			T -> A (in dbSNP:rs268687). {ECO:0000269|PubMed:10580009, ECO:0000269|PubMed:11331592, ECO:0000269|Ref.3}.		positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription, DNA-templated (GO:0006351)					endometrium(2)|lung(1)|prostate(1)|skin(1)	5			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCCACCGCTGTGTGGCCAGGA	0.632													C|||	2714	0.541933	0.8797	0.4914	5008	,	,		14942	0.2411		0.503	False		,,,				2504	0.4714				p.T31A		Atlas-SNP	.											.	SERTAD1	18	.	0			c.A91G						PASS	.	C	ALA/THR	3613,759		1517,579,90	26.0	30.0	29.0		91	1.5	0.1	19	dbSNP_79	29	4441,4127		1193,2055,1036	yes	missense	SERTAD1	NM_013376.3	58	2710,2634,1126	CC,CT,TT		48.1676,17.3605,37.7589	benign	31/237	40929363	8054,4886	2186	4284	6470	SO:0001583	missense	29950	exon2			CCGCTGTGTGGCC	AF117959	CCDS12557.1	19q13.1-q13.2	2008-02-05				ENSG00000197019			17932	protein-coding gene	gene with protein product	"""CDK4-binding protein p34SEI"", ""transcriptional regulator interacting with the PHD-bromodomain 1"""					6434876, 10580009	Standard	NM_013376		Approved	SEI1, TRIP-Br1	uc002ont.4	Q9UHV2		ENST00000357949.4:c.91A>G	19.37:g.40929363T>C	ENSP00000350633:p.Thr31Ala	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	91	32	0.351648	NM_013376	Q9BUE7	Missense_Mutation	SNP	ENST00000357949.4	37	CCDS12557.1	1113	0.5096153846153846	411	0.8353658536585366	199	0.5497237569060773	129	0.22552447552447552	374	0.49340369393139843	C	0.011	-1.731682	0.00687	0.826395	0.518324	ENSG00000197019	ENST00000357949	T	0.42900	0.96	5.0	1.5	0.22942	.	0.180459	0.37761	N	0.001944	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	0.33059	-0.9883	9	0.08179	T	0.78	-5.4715	3.7036	0.08391	0.0896:0.1253:0.4702:0.3149	rs268687;rs17670026;rs268687	31	Q9UHV2	SRTD1_HUMAN	A	31	ENSP00000350633:T31A	ENSP00000350633:T31A	T	-	1	0	SERTAD1	45621203	0.923000	0.31300	0.074000	0.20217	0.048000	0.14542	0.243000	0.18106	0.173000	0.19788	-1.157000	0.01802	ACA	T|0.444;C|0.556	0.556	strong		0.632	SERTAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462571.1	NM_013376	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412005	105412005	+	Silent	SNP	A	A	G	rs28564728	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	166	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	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	
HJURP	55355	hgsc.bcm.edu	37	2	234749354	234749354	+	Missense_Mutation	SNP	G	G	A	rs12582	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:234749354G>A	ENST00000411486.2	-	8	2137	c.2072C>T	c.(2071-2073)tCc>tTc	p.S691F	HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000432087.1_Missense_Mutation_p.S637F|HJURP_ENST00000441687.1_Missense_Mutation_p.S606F	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	691			S -> F (in dbSNP:rs12582). {ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		CTGGCGTCCGGAGCCCTGGGG	0.597													G|||	793	0.158347	0.2005	0.121	5008	,	,		18776	0.2837		0.0885	False		,,,				2504	0.0706				p.S691F		Atlas-SNP	.											.	HJURP	72	.	0			c.C2072T						PASS	.	G	PHE/SER	692,3714	290.7+/-281.1	53,586,1564	83.0	86.0	85.0		2072	-3.1	0.0	2	dbSNP_52	85	827,7773	190.3+/-236.8	40,747,3513	yes	missense	HJURP	NM_018410.3	155	93,1333,5077	AA,AG,GG		9.6163,15.7059,11.6792	probably-damaging	691/749	234749354	1519,11487	2203	4300	6503	SO:0001583	missense	55355	exon8			CGTCCGGAGCCCT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.2072C>T	2.37:g.234749354G>A	ENSP00000414109:p.Ser691Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	397	0.18177655677655677	97	0.19715447154471544	39	0.10773480662983426	188	0.32867132867132864	73	0.09630606860158311	G	10.41	1.342731	0.24339	0.157059	0.096163	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687	T;T;T	0.08546	3.08;3.08;3.08	4.19	-3.06	0.05379	.	0.946932	0.08763	N	0.897402	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B;B	0.31318	0.319;0.141;0.213	B;B;B	0.21917	0.037;0.037;0.028	T	0.47156	-0.9139	9	0.10111	T	0.7	0.0	6.2783	0.20993	0.0:0.288:0.152:0.56	rs12582;rs3172174;rs3821239;rs52802639;rs57951043;rs12582	606;637;691	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	F	691;637;606	ENSP00000414109:S691F;ENSP00000407208:S637F;ENSP00000401944:S606F	ENSP00000414109:S691F	S	-	2	0	HJURP	234414093	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.031000	0.03578	-0.734000	0.04843	-0.344000	0.07964	TCC	G|0.846;A|0.154	0.154	strong		0.597	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
GPN2	54707	hgsc.bcm.edu	37	1	27210721	27210721	+	Missense_Mutation	SNP	T	T	C	rs3170660	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	120	0	0		WXS	Illumina HiSeq	Phase_I	110	110	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	
TICAM1	148022	hgsc.bcm.edu	37	19	4816719	4816719	+	Silent	SNP	G	G	A	rs2292151	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4816719G>A	ENST00000248244.5	-	2	1900	c.1671C>T	c.(1669-1671)gaC>gaT	p.D557D		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	557	Sufficient to induce apoptosis.				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)		TCCGCTCACCGTCCAGGTGTT	0.622													G|||	1390	0.277556	0.1573	0.33	5008	,	,		16459	0.4345		0.2694	False		,,,				2504	0.2495				p.D557D		Atlas-SNP	.											.	TICAM1	69	.	0			c.C1671T						PASS	.	G		776,3630	315.8+/-294.3	62,652,1489	79.0	58.0	65.0		1671	-4.2	0.0	19	dbSNP_100	65	2064,6536	357.3+/-330.7	257,1550,2493	no	coding-synonymous	TICAM1	NM_182919.2		319,2202,3982	AA,AG,GG		24.0,17.6123,21.8361		557/713	4816719	2840,10166	2203	4300	6503	SO:0001819	synonymous_variant	148022	exon2			CTCACCGTCCAGG	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.1671C>T	19.37:g.4816719G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_182919	B3Y691|O75532|Q86XP8|Q96GA0	Silent	SNP	ENST00000248244.5	37	CCDS12136.1																																																																																			G|0.743;A|0.257	0.257	strong		0.622	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261	
MYO1G	64005	hgsc.bcm.edu	37	7	45009325	45009325	+	Silent	SNP	G	G	A	rs3735484	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:45009325G>A	ENST00000258787.7	-	11	1618	c.1482C>T	c.(1480-1482)caC>caT	p.H494H		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	494	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						TGTAGTGTAGGTGATGGCGGT	0.662													G|||	2092	0.417732	0.3169	0.3732	5008	,	,		16832	0.6081		0.4085	False		,,,				2504	0.3988				p.H494H		Atlas-SNP	.											.	MYO1G	86	.	0			c.C1482T						PASS	.	G		1422,2984	448.8+/-348.8	234,954,1015	91.0	91.0	91.0		1482	2.3	0.9	7	dbSNP_107	91	3550,5046	497.4+/-374.5	718,2114,1466	no	coding-synonymous	MYO1G	NM_033054.2		952,3068,2481	AA,AG,GG		41.2983,32.2742,38.2403		494/1019	45009325	4972,8030	2203	4298	6501	SO:0001819	synonymous_variant	64005	exon11			GTGTAGGTGATGG	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.1482C>T	7.37:g.45009325G>A		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Silent	SNP	ENST00000258787.7	37	CCDS34629.1																																																																																			G|0.608;A|0.392	0.392	strong		0.662	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
NRK	203447	hgsc.bcm.edu	37	X	105193709	105193709	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:105193709A>G	ENST00000243300.9	+	27	4799	c.4496A>G	c.(4495-4497)gAc>gGc	p.D1499G	NRK_ENST00000428173.2_Missense_Mutation_p.D1500G|NRK_ENST00000540278.1_Missense_Mutation_p.D80G	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1499	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				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						ATGTGGAAAGACATACCATCT	0.383										HNSCC(51;0.14)																											p.D1499G		Atlas-SNP	.											.	NRK	321	.	0			c.A4496G						PASS	.						70.0	59.0	62.0					X																	105193709		1868	4085	5953	SO:0001583	missense	203447	exon27			GGAAAGACATACC	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.4496A>G	X.37:g.105193709A>G	ENSP00000434830:p.Asp1499Gly	Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	A	18.18	3.567047	0.65651	.	.	ENSG00000123572	ENST00000243300;ENST00000428173;ENST00000540278	T;T;T	0.03982	3.74;3.74;3.74	5.96	5.96	0.96718	Citron-like (2);	0.000000	0.47093	D	0.000252	T	0.10895	0.0266	L	0.36672	1.1	0.39530	D	0.968642	P;P	0.49447	0.674;0.924	P;P	0.55785	0.457;0.784	T	0.02505	-1.1149	10	0.87932	D	0	.	12.9799	0.58557	1.0:0.0:0.0:0.0	.	80;1499	B7Z1I7;Q7Z2Y5	.;NRK_HUMAN	G	1499;1500;80	ENSP00000434830:D1499G;ENSP00000438378:D1500G;ENSP00000438148:D80G	ENSP00000434830:D1499G	D	+	2	0	NRK	105080365	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	6.778000	0.75043	2.002000	0.58637	0.486000	0.48141	GAC	.	.	none		0.383	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
WHAMM	123720	hgsc.bcm.edu	37	15	83502065	83502065	+	Missense_Mutation	SNP	A	A	C	rs386785864|rs11259953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:83502065A>C	ENST00000286760.4	+	10	2306	c.2207A>C	c.(2206-2208)cAc>cCc	p.H736P		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	736	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.		H -> P (in dbSNP:rs11259953).|H -> Q (in dbSNP:rs11259954).		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						CGCCCTCCCCACGCCTCAATC	0.542													A|||	678	0.135383	0.1256	0.1916	5008	,	,		18610	0.1944		0.1203	False		,,,				2504	0.0634				p.H736P		Atlas-SNP	.											.	WHAMM	63	.	0			c.A2207C						PASS	.	A	PRO/HIS	20,3982		8,4,1989	58.0	59.0	59.0		2207	1.5	0.1	15	dbSNP_120	59	21,8307		5,11,4148	no	missense	WHAMM	NM_001080435.1	77	13,15,6137	CC,CA,AA		0.2522,0.4998,0.3325	benign	736/810	83502065	41,12289	2001	4164	6165	SO:0001583	missense	123720	exon10			CTCCCCACGCCTC	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.2207A>C	15.37:g.83502065A>C	ENSP00000286760:p.His736Pro	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	271	0.12408424908424909	48	0.0975609756097561	50	0.13812154696132597	97	0.16958041958041958	76	0.10026385224274406	A	9.969	1.224994	0.22457	0.004998	0.002522	ENSG00000156232	ENST00000286760	T	0.28255	1.62	5.57	1.54	0.23209	.	1.175250	0.06034	N	0.653556	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	B	0.31790	0.34	B	0.25140	0.058	T	0.23190	-1.0195	9	0.26408	T	0.33	.	8.6421	0.33983	0.4993:0.0:0.5007:0.0	rs11259953;rs60987975	736	Q8TF30	WHAMM_HUMAN	P	736	ENSP00000286760:H736P	ENSP00000286760:H736P	H	+	2	0	WHAMM	81299119	0.000000	0.05858	0.127000	0.21898	0.266000	0.26442	-0.146000	0.10250	0.291000	0.22468	-0.479000	0.04858	CAC	A|0.879;C|0.121	0.121	strong		0.542	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
GPR50	9248	hgsc.bcm.edu	37	X	150349871	150349871	+	Missense_Mutation	SNP	A	A	G	rs13440581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:150349871A>G	ENST00000218316.3	+	2	1885	c.1816A>G	c.(1816-1818)Att>Gtt	p.I606V	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	606	Pro-rich.		I -> V (higher fasting circulating triglyceride levels; dbSNP:rs13440581). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					TGTCGTGGTTATTGATGTTGA	0.478													A|||	1032	0.273377	0.18	0.196	3775	,	,		17863	0.0129		0.4443	False		,,,				2504	0.2025				p.I606V		Atlas-SNP	.											.	GPR50	195	.	0			c.A1816G						PASS	.	A	VAL/ILE	996,2675		130,591,145,829,426	123.0	122.0	122.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1816	2.1	0.0	X	dbSNP_121	122	3870,2763		797,1197,1079,408,750	yes	missense	GPR50	NM_004224.3	29	927,1788,1224,1237,1176	GG,GA,G,AA,A		41.6554,27.1316,47.2244	benign	606/618	150349871	4866,5438	2121	4231	6352	SO:0001583	missense	9248	exon2			GTGGTTATTGATG	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1816A>G	X.37:g.150349871A>G	ENSP00000218316:p.Ile606Val	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	516	0.31103074141048825	75	0.16968325791855204	53	0.17434210526315788	4	0.007017543859649123	225	0.41058394160583944	A	6.036	0.375080	0.11409	0.271316	0.583446	ENSG00000102195	ENST00000218316	T	0.70282	-0.47	3.33	2.13	0.27403	.	0.209202	0.24136	N	0.041201	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.14438	0.01	B	0.06405	0.002	T	0.43081	-0.9413	9	0.51188	T	0.08	-4.0928	4.235	0.10621	0.8259:0.0:0.1741:0.0	rs13440581	606	Q13585	MTR1L_HUMAN	V	606	ENSP00000218316:I606V	ENSP00000218316:I606V	I	+	1	0	GPR50	150100529	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-1.224000	0.02959	0.493000	0.27837	0.430000	0.28490	ATT	A|0.687;G|0.313	0.313	strong		0.478	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
TTN	7273	hgsc.bcm.edu	37	2	179558366	179558366	+	Missense_Mutation	SNP	T	T	C	rs2042995	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179558366T>C	ENST00000591111.1	-	117	30837	c.30613A>G	c.(30613-30615)Att>Gtt	p.I10205V	TTN_ENST00000589042.1_Missense_Mutation_p.I10522V|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I9278V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.			I -> V (in Ref. 3; CAD12456 and 9; AAP80791). {ECO:0000305}.	adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTTGGAAATGGCAACGTGA	0.308													C|||	2393	0.477835	0.5877	0.4193	5008	,	,		17705	0.5685		0.2455	False		,,,				2504	0.5164				p.I10522V		Atlas-SNP	.											.	TTN	18412	.	0			c.A31564G						PASS	.	C	,VAL/ILE,,	2003,1581		579,845,368	60.0	62.0	61.0		,27832,,	5.8	1.0	2	dbSNP_94	61	1858,6270		194,1470,2400	yes	intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,29,,	773,2315,2768	CC,CT,TT		22.8593,44.1127,32.9662	,benign,,	,9278/33424,,	179558366	3861,7851	1792	4064	5856	SO:0001583	missense	7273	exon119			TGGAAATGGCAAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30613A>G	2.37:g.179558366T>C	ENSP00000465570:p.Ile10205Val	Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	302	136	0.450331	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		910	0.4166666666666667	287	0.5833333333333334	133	0.3674033149171271	306	0.534965034965035	184	0.24274406332453827	C	0.877	-0.730053	0.03135	0.558873	0.228593	ENSG00000155657	ENST00000342992;ENST00000414766;ENST00000473181	T	0.60548	0.18	5.85	5.85	0.93711	.	.	.	.	.	T	0.00012	0.0000	N	0.00960	-1.095	0.09310	P	0.9999999999343484	.	.	.	.	.	.	T	0.29027	-1.0025	6	0.87932	D	0	.	9.3114	0.37908	0.0:0.8379:0.0:0.1621	rs2042995;rs56726642;rs2042995	.	.	.	V	9278;400;32	ENSP00000343764:I9278V	ENSP00000343764:I9278V	I	-	1	0	TTN	179266611	0.947000	0.32204	1.000000	0.80357	0.933000	0.57130	1.140000	0.31516	1.498000	0.48600	-0.128000	0.14901	ATT	T|0.582;C|0.418	0.418	strong		0.308	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OVOL2	58495	hgsc.bcm.edu	37	20	18022362	18022362	+	Silent	SNP	G	G	T	rs6111803	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:18022362G>T	ENST00000278780.6	-	3	569	c.327C>A	c.(325-327)acC>acA	p.T109T	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	109					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						ACGTGCCTGTGGTGAACTGGG	0.627													G|||	202	0.0403355	0.0726	0.0173	5008	,	,		15700	0.004		0.0636	False		,,,				2504	0.0266				p.T109T		Atlas-SNP	.											.	OVOL2	18	.	0			c.C327A						PASS	.	G		316,4090	169.4+/-200.1	11,294,1898	54.0	42.0	46.0		327	0.9	1.0	20	dbSNP_114	46	594,8006	156.1+/-210.0	23,548,3729	no	coding-synonymous	OVOL2	NM_021220.2		34,842,5627	TT,TG,GG		6.907,7.172,6.9968		109/276	18022362	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	58495	exon3			GCCTGTGGTGAAC	AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"""Zinc fingers, C2H2-type"""	15804	protein-coding gene	gene with protein product			"""zinc finger protein 339"", ""ovo-like 2 (Drosophila)"""	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.327C>A	20.37:g.18022362G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_021220	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Silent	SNP	ENST00000278780.6	37	CCDS13132.1																																																																																			G|0.945;T|0.055	0.055	strong		0.627	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220	
MTRR	4552	hgsc.bcm.edu	37	5	7897061	7897061	+	Silent	SNP	T	T	C	rs6874544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7897061T>C	ENST00000264668.2	+	13	1872	c.1842T>C	c.(1840-1842)taT>taC	p.Y614Y	MTRR_ENST00000440940.2_Silent_p.Y587Y	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	614					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ATAGGGATTATCTATTCAGGT	0.368													T|||	40	0.00798722	0.0015	0.0245	5008	,	,		18320	0.0		0.0189	False		,,,				2504	0.002				p.Y614Y		Atlas-SNP	.											.	MTRR	74	.	0			c.T1842C						PASS	.	T	,	46,4360	48.2+/-83.0	0,46,2157	56.0	59.0	58.0		1761,1842	-3.0	0.0	5	dbSNP_116	58	207,8393	88.1+/-150.5	2,203,4095	yes	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	CC,CT,TT		2.407,1.044,1.9453	,	587/699,614/726	7897061	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon13			GGATTATCTATTC	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1842T>C	5.37:g.7897061T>C		Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	292	132	0.452055	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			T|0.981;C|0.019	0.019	strong		0.368	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
DHX29	54505	hgsc.bcm.edu	37	5	54557283	54557283	+	Silent	SNP	G	G	A	rs1052132	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54557283G>A	ENST00000251636.5	-	25	4021	c.3873C>T	c.(3871-3873)acC>acT	p.T1291T	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	1291						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				CTGGAAAAGGGGTTATTAGGG	0.368													G|||	75	0.014976	0.0015	0.0331	5008	,	,		15111	0.0		0.0338	False		,,,				2504	0.0164				p.T1291T		Atlas-SNP	.											.	DHX29	116	.	0			c.C3873T						PASS	.	G		28,4378	33.5+/-64.1	0,28,2175	97.0	101.0	100.0		3873	-2.2	0.9	5	dbSNP_86	100	433,8167	132.0+/-189.7	10,413,3877	no	coding-synonymous	DHX29	NM_019030.2		10,441,6052	AA,AG,GG		5.0349,0.6355,3.5445		1291/1370	54557283	461,12545	2203	4300	6503	SO:0001819	synonymous_variant	54505	exon25			AAAAGGGGTTATT	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"""DEAH-boxes"""	15815	protein-coding gene	gene with protein product		612720	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"""	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.3873C>T	5.37:g.54557283G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Silent	SNP	ENST00000251636.5	37	CCDS34158.1																																																																																			G|0.965;A|0.035	0.035	strong		0.368	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030	
UBN2	254048	hgsc.bcm.edu	37	7	138946316	138946316	+	Silent	SNP	C	C	T	rs377072849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:138946316C>T	ENST00000473989.3	+	6	1224	c.1224C>T	c.(1222-1224)ttC>ttT	p.F408F	UBN2_ENST00000288561.8_Silent_p.F325F	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	408						extracellular space (GO:0005615)|nucleus (GO:0005634)		p.F325F(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						ATTTTGACTTCGACAGATTAC	0.483													C|||	4	0.000798722	0.003	0.0	5008	,	,		18634	0.0		0.0	False		,,,				2504	0.0				p.F408F		Atlas-SNP	.											UBN2,NS,carcinoma,0,2	UBN2	90	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C1224T						scavenged	.	C		7,3835		0,7,1914	103.0	100.0	101.0		1224	1.0	1.0	7		101	0,8260		0,0,4130	no	coding-synonymous	UBN2	NM_173569.3		0,7,6044	TT,TC,CC		0.0,0.1822,0.0578		408/1348	138946316	7,12095	1921	4130	6051	SO:0001819	synonymous_variant	254048	exon6			TGACTTCGACAGA	AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.1224C>T	7.37:g.138946316C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_173569	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Silent	SNP	ENST00000473989.3	37	CCDS43655.2	.	.	.	.	.	.	.	.	.	.	C	8.677	0.904259	0.17760	0.001822	0.0	ENSG00000157741	ENST00000483726	.	.	.	6.08	0.967	0.19674	.	.	.	.	.	T	0.58018	0.2093	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50423	-0.8830	4	.	.	.	-7.0076	10.016	0.42014	0.0:0.0612:0.2169:0.7219	.	.	.	.	L	177	.	.	S	+	2	0	UBN2	138596856	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	0.810000	0.27183	-0.060000	0.13132	-2.282000	0.00269	TCG	.	.	weak		0.483	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569	
PPOX	5498	hgsc.bcm.edu	37	1	161138933	161138933	+	Missense_Mutation	SNP	C	C	G	rs12735723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161138933C>G	ENST00000367999.4	+	7	1033	c.767C>G	c.(766-768)cCg>cGg	p.P256R	PPOX_ENST00000544598.1_Intron|PPOX_ENST00000352210.5_Missense_Mutation_p.P256R|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_3'UTR|B4GALT3_ENST00000470882.1_5'Flank	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	256			P -> R (found in patients with the homozygous variant of variegate porphyria; unknown pathological significance; reported as a polymorphism in some Western European populations; the variant results in reduction of activity in a prokariotyc expression system but has normal activity when expressed in an eukaryotic system; dbSNP:rs12735723). {ECO:0000269|PubMed:10486317, ECO:0000269|PubMed:11286631}.		heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AGAGGCCAGCCGGTCTGTGGG	0.577													C|||	14	0.00279553	0.0	0.0014	5008	,	,		18263	0.0		0.0119	False		,,,				2504	0.001				p.P256R		Atlas-SNP	.											.	PPOX	34	.	0			c.C767G	GRCh37	CM011458	PPOX	M	rs12735723	PASS	.	C	ARG/PRO,ARG/PRO	5,4401	9.9+/-24.2	0,5,2198	51.0	54.0	53.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	767,767	5.6	1.0	1	dbSNP_121	53	85,8513	48.1+/-107.5	1,83,4215	yes	missense,missense	PPOX	NM_000309.3,NM_001122764.1	103,103	1,88,6413	GG,GC,CC		0.9886,0.1135,0.6921	possibly-damaging,possibly-damaging	256/478,256/478	161138933	90,12914	2203	4299	6502	SO:0001583	missense	5498	exon7			GCCAGCCGGTCTG	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"""variegate porphyria"""	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.767C>G	1.37:g.161138933C>G	ENSP00000356978:p.Pro256Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_000309	D3DVG0|Q5VTW8	Missense_Mutation	SNP	ENST00000367999.4	37	CCDS1221.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	C|C	12.99|12.99	2.102051|2.102051	0.37048|0.37048	0.001135|0.001135	0.009886|0.009886	ENSG00000143224|ENSG00000143224	ENST00000352210;ENST00000367999;ENST00000435935|ENST00000537523	D;D|.	0.91686|.	-2.89;-2.89|.	5.57|5.57	5.57|5.57	0.84162|0.84162	Amine oxidase (1);|.	0.177644|.	0.49305|.	D|.	0.000148|.	T|T	0.50939|0.50939	0.1645|0.1645	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	A|A	1|1	B;D;P|.	0.57899|.	0.105;0.981;0.788|.	B;P;B|.	0.51895|.	0.173;0.683;0.444|.	T|T	0.45454|0.45454	-0.9260|-0.9260	9|4	0.14656|.	T|.	0.56|.	-20.6534|-20.6534	18.3212|18.3212	0.90239|0.90239	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs12735723;rs52807980;rs12735723|rs12735723;rs52807980;rs12735723	223;94;256|.	B4DY76;B3KT30;P50336|.	.;.;PPOX_HUMAN|.	R|G	256;256;223|69	ENSP00000343943:P256R;ENSP00000356978:P256R|.	ENSP00000343943:P256R|.	P|R	+|+	2|1	0|2	PPOX|PPOX	159405557|159405557	0.642000|0.642000	0.27260|0.27260	0.956000|0.956000	0.39512|0.39512	0.739000|0.739000	0.42172|0.42172	2.295000|2.295000	0.43576|0.43576	2.602000|2.602000	0.87976|0.87976	0.655000|0.655000	0.94253|0.94253	CCG|CGG	C|0.994;G|0.006	0.006	strong		0.577	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309	
TTN	7273	hgsc.bcm.edu	37	2	179451420	179451420	+	Missense_Mutation	SNP	G	G	A	rs2042996	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179451420G>A	ENST00000591111.1	-	258	59509	c.59285C>T	c.(59284-59286)aCt>aTt	p.T19762I	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T21403I|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T12463I|TTN_ENST00000460472.2_Missense_Mutation_p.T12338I|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T12530I|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T18835I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19762	Fibronectin type-III 43. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> I. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTGTAACTAGTGATGTAGCC	0.468													A|||	2542	0.507588	0.5582	0.4078	5008	,	,		19158	0.7212		0.2485	False		,,,				2504	0.5562				p.T21403I		Atlas-SNP	.											.	TTN	18412	.	0			c.C64208T						PASS	.	A	ILE/THR,ILE/THR,ILE/THR,ILE/THR	2009,1945		527,955,495	184.0	180.0	181.0		37589,37388,56504,37013	6.1	0.9	2	dbSNP_94	181	1837,6525		187,1463,2531	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	714,2418,3026	AA,AG,GG		21.9684,49.1907,31.2277	benign,benign,benign,benign	12530/27119,12463/27052,18835/33424,12338/26927	179451420	3846,8470	1977	4181	6158	SO:0001583	missense	7273	exon308			TAACTAGTGATGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.59285C>T	2.37:g.179451420G>A	ENSP00000465570:p.Thr19762Ile	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		977	0.44734432234432236	274	0.556910569105691	130	0.35911602209944754	390	0.6818181818181818	183	0.24142480211081793	A	15.37	2.813873	0.50527	0.508093	0.219684	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.07	6.07	0.98685	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00004	-3.385	0.50039	P	1.5100000000001224E-4	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.48031	-0.9070	8	0.87932	D	0	.	12.3663	0.55230	0.9347:0.0:0.0653:0.0	rs2042996;rs52829581;rs2042996	12338;12463;12530;19762	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	18835;12338;12530;12463;12336	ENSP00000343764:T18835I;ENSP00000434586:T12338I;ENSP00000340554:T12530I;ENSP00000352154:T12463I	ENSP00000340554:T12530I	T	-	2	0	TTN	179159666	1.000000	0.71417	0.901000	0.35422	0.836000	0.47400	7.476000	0.81055	1.120000	0.41904	-0.254000	0.11334	ACT	G|0.553;N|0.000	.	strong		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SKA3	221150	hgsc.bcm.edu	37	13	21735998	21735998	+	Missense_Mutation	SNP	T	T	C	rs17345690	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:21735998T>C	ENST00000314759.5	-	5	884	c.760A>G	c.(760-762)Aca>Gca	p.T254A	SKA3_ENST00000400018.3_Missense_Mutation_p.T254A	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	254			T -> A (in dbSNP:rs17345690). {ECO:0000269|PubMed:15489334}.		chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)		p.T254A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CTGGATTCTGTATCTATGGCC	0.368													T|||	491	0.0980431	0.0666	0.0735	5008	,	,		16660	0.0972		0.1362	False		,,,				2504	0.1196				p.T254A		Atlas-SNP	.											SKA3,NS,carcinoma,0,1	SKA3	76	1	1	Substitution - Missense(1)	stomach(1)	c.A760G						PASS	.	T	ALA/THR,ALA/THR	343,4063	178.0+/-206.8	13,317,1873	134.0	136.0	135.0		760,760	1.3	0.0	13	dbSNP_123	135	1184,7416	239.0+/-270.3	71,1042,3187	yes	missense,missense	SKA3	NM_001166017.1,NM_145061.5	58,58	84,1359,5060	CC,CT,TT		13.7674,7.7848,11.7407	benign,benign	254/389,254/413	21735998	1527,11479	2203	4300	6503	SO:0001583	missense	221150	exon5			ATTCTGTATCTAT	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.760A>G	13.37:g.21735998T>C	ENSP00000319417:p.Thr254Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	249	0.11401098901098901	46	0.09349593495934959	30	0.08287292817679558	60	0.1048951048951049	113	0.14907651715039577	T	11.04	1.523280	0.27299	0.077848	0.137674	ENSG00000165480	ENST00000314759;ENST00000400018	T;T	0.22945	1.93;1.93	4.99	1.32	0.21799	.	0.796448	0.11947	N	0.514052	T	0.00073	0.0002	L	0.56769	1.78	0.80722	P	0.0	B;B	0.20671	0.017;0.047	B;B	0.17979	0.02;0.02	T	0.31586	-0.9938	9	0.02654	T	1	-1.4902	1.4913	0.02457	0.1775:0.0953:0.1855:0.5418	rs17345690;rs17851040;rs52826626;rs17345690	254;254	Q8IX90-3;Q8IX90	.;SKA3_HUMAN	A	254	ENSP00000319417:T254A;ENSP00000382896:T254A	ENSP00000319417:T254A	T	-	1	0	SKA3	20633998	0.001000	0.12720	0.030000	0.17652	0.059000	0.15707	0.091000	0.15046	0.436000	0.26393	0.482000	0.46254	ACA	T|0.886;C|0.114	0.114	strong		0.368	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
COLEC11	78989	hgsc.bcm.edu	37	2	3685163	3685163	+	Silent	SNP	T	T	C	rs34347618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:3685163T>C	ENST00000349077.4	+	4	346	c.243T>C	c.(241-243)cgT>cgC	p.R81R	COLEC11_ENST00000382062.2_Intron|COLEC11_ENST00000402922.1_Intron|COLEC11_ENST00000402794.1_Silent_p.R31R|COLEC11_ENST00000236693.7_Silent_p.R78R|COLEC11_ENST00000418971.2_Silent_p.R95R|COLEC11_ENST00000404205.1_Intron|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000403096.3_Silent_p.R55R	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	81	Collagen-like.				developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		GTGTGGGTCGTCATGGAAAAA	0.512													C|||	277	0.0553115	0.0605	0.0418	5008	,	,		21109	0.0228		0.0249	False		,,,				2504	0.1227				p.R95R		Atlas-SNP	.											COLEC11_ENST00000418971,colon,carcinoma,+1,4	COLEC11	93	4	0			c.T285C						PASS	.	C	,	257,4149	803.1+/-415.7	8,241,1954	293.0	228.0	250.0		243,234	2.0	1.0	2	dbSNP_126	250	277,8323	807.2+/-407.2	6,265,4029	no	coding-synonymous,coding-synonymous	COLEC11	NM_024027.3,NM_199235.1	,	14,506,5983	CC,CT,TT		3.2209,5.833,4.1058	,	81/272,78/269	3685163	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	78989	exon5			GGGTCGTCATGGA	BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.243T>C	2.37:g.3685163T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	145	60	0.413793	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	37	CCDS1649.1																																																																																			T|0.961;C|0.039	0.039	strong		0.512	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027	
MTRR	4552	hgsc.bcm.edu	37	5	7878179	7878179	+	Missense_Mutation	SNP	C	C	T	rs1532268	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7878179C>T	ENST00000264668.2	+	5	635	c.605C>T	c.(604-606)tCg>tTg	p.S202L	MTRR_ENST00000440940.2_Missense_Mutation_p.S175L|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	202	Hinge.		S -> L (in dbSNP:rs1532268). {ECO:0000269|PubMed:10564814, ECO:0000269|PubMed:9501215}.		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)	CCTGCATCCTCGAGGACAGAC	0.498													c|||	1352	0.269968	0.2708	0.2147	5008	,	,		17846	0.129		0.336	False		,,,				2504	0.3855				p.S202L		Atlas-SNP	.											.	MTRR	74	.	0			c.C605T	GRCh37	CM025887	MTRR	M	rs1532268	PASS	.	T	LEU/SER,LEU/SER	1172,3234	413.9+/-336.6	161,850,1192	70.0	66.0	67.0		524,605	-10.6	0.0	5	dbSNP_88	67	3097,5503	473.5+/-368.6	579,1939,1782	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	145,145	740,2789,2974	TT,TC,CC		36.0116,26.6001,32.8233	benign,benign	175/699,202/726	7878179	4269,8737	2203	4300	6503	SO:0001583	missense	4552	exon5			CATCCTCGAGGAC	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.605C>T	5.37:g.7878179C>T	ENSP00000264668:p.Ser202Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	556	0.25457875457875456	151	0.30691056910569103	85	0.23480662983425415	59	0.10314685314685315	261	0.34432717678100266	c	9.011	0.982408	0.18889	0.266001	0.360116	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.02280	4.36;4.37	5.29	-10.6	0.00265	.	2.922120	0.00738	N	0.000983	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	0.47711	-0.9096	9	0.28530	T	0.3	2.493	3.722	0.08460	0.1847:0.4312:0.1038:0.2804	rs1532268;rs58799540;rs1532268	202	Q9UBK8	MTRR_HUMAN	L	202;175	ENSP00000264668:S202L;ENSP00000402510:S175L	ENSP00000264668:S202L	S	+	2	0	MTRR	7931179	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.590000	0.02102	-2.652000	0.00423	-1.594000	0.00841	TCG	C|0.704;T|0.296	0.296	strong		0.498	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
ANO8	57719	hgsc.bcm.edu	37	19	17435887	17435887	+	Silent	SNP	C	C	T	rs56286266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17435887C>T	ENST00000159087.4	-	17	3128	c.2970G>A	c.(2968-2970)tcG>tcA	p.S990S		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	990					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						TGGCCCCTGACGAGAGGAATT	0.672													C|||	1233	0.246206	0.1293	0.2406	5008	,	,		15681	0.1429		0.34	False		,,,				2504	0.4182				p.S990S		Atlas-SNP	.											.	ANO8	67	.	0			c.G2970A						PASS	.	C		778,3628	302.7+/-287.5	73,632,1498	80.0	88.0	85.0		2970	-7.7	0.0	19	dbSNP_129	85	2754,5846	415.2+/-351.7	466,1822,2012	no	coding-synonymous	ANO8	NM_020959.2		539,2454,3510	TT,TC,CC		32.0233,17.6577,27.1567		990/1233	17435887	3532,9474	2203	4300	6503	SO:0001819	synonymous_variant	57719	exon17			CCCTGACGAGAGG	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.2970G>A	19.37:g.17435887C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	37	CCDS32949.1																																																																																			C|0.746;T|0.254	0.254	strong		0.672	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815662	23815662	+	Missense_Mutation	SNP	C	C	T	rs8192678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:23815662C>T	ENST00000264867.2	-	8	1563	c.1444G>A	c.(1444-1446)Ggt>Agt	p.G482S	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	482	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.		G -> S (in dbSNP:rs8192678). {ECO:0000269|PubMed:10643692}.		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)				CTCAGTTCACCGGTCTTGTCT	0.463													T|||	1331	0.265775	0.0454	0.2565	5008	,	,		19910	0.4425		0.3608	False		,,,				2504	0.2904				p.G482S	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.G1444A	GRCh37	CM013959	PPARGC1A	M	rs8192678	PASS	.	T	SER/GLY	455,3951	785.2+/-414.7	22,411,1770	129.0	118.0	122.0		1444	6.0	1.0	4	dbSNP_117	122	2988,5612	666.0+/-402.3	484,2020,1796	yes	missense	PPARGC1A	NM_013261.3	56	506,2431,3566	TT,TC,CC		34.7442,10.3268,26.4724	benign	482/799	23815662	3443,9563	2203	4300	6503	SO:0001583	missense	10891	exon8			GTTCACCGGTCTT	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.1444G>A	4.37:g.23815662C>T	ENSP00000264867:p.Gly482Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	37	CCDS3429.1	635	0.2907509157509158	23	0.046747967479674794	84	0.23204419889502761	256	0.44755244755244755	272	0.35883905013192613	T	3.141	-0.176377	0.06380	0.103268	0.347442	ENSG00000109819	ENST00000264867	T	0.20200	2.09	6.02	6.02	0.97574	.	0.241030	0.49305	N	0.000156	T	0.00012	0.0000	N	0.01576	-0.805	0.09310	P	1.0	B	0.21225	0.053	B	0.09377	0.004	T	0.42716	-0.9435	9	0.02654	T	1	-1.3449	10.8867	0.46971	0.0:0.1297:0.0:0.8703	rs8192678;rs17847358;rs52829424;rs56570248;rs56707915;rs8192678	482	Q9UBK2	PRGC1_HUMAN	S	482	ENSP00000264867:G482S	ENSP00000264867:G482S	G	-	1	0	PPARGC1A	23424760	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.170000	0.42443	1.099000	0.41499	-0.269000	0.10298	GGT	C|0.724;T|0.276	0.276	strong		0.463	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
TRAF4	9618	hgsc.bcm.edu	37	17	27075423	27075423	+	Silent	SNP	C	C	T	rs2070265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:27075423C>T	ENST00000262395.5	+	5	735	c.606C>T	c.(604-606)ttC>ttT	p.F202F	AC010761.9_ENST00000577325.1_RNA|AC010761.10_ENST00000579468.1_RNA|TRAF4_ENST00000262396.6_Intron|TRAF4_ENST00000444415.3_Silent_p.F202F	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	202					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			CTAAGGAGTTCGTCTTTGACA	0.582													C|||	1049	0.209465	0.1415	0.2363	5008	,	,		21283	0.1786		0.1938	False		,,,				2504	0.3303				p.F202F		Atlas-SNP	.											.	TRAF4	20	.	0			c.C606T						PASS	.	C		662,3744	277.2+/-273.6	63,536,1604	78.0	60.0	66.0		606	-5.5	0.9	17	dbSNP_96	66	1695,6905	304.9+/-307.2	167,1361,2772	no	coding-synonymous	TRAF4	NM_004295.3		230,1897,4376	TT,TC,CC		19.7093,15.025,18.1224		202/471	27075423	2357,10649	2203	4300	6503	SO:0001819	synonymous_variant	9618	exon5			GGAGTTCGTCTTT	X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"""RING-type (C3HC4) zinc fingers"""	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.606C>T	17.37:g.27075423C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_004295	O75615|Q14848|Q2KJU4|Q2PJN8	Silent	SNP	ENST00000262395.5	37	CCDS11243.1																																																																																			C|0.813;T|0.187	0.187	strong		0.582	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255944.2	NM_145751	
ZNF83	55769	hgsc.bcm.edu	37	19	53116949	53116949	+	Missense_Mutation	SNP	T	T	C	rs113015820|rs560464978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53116949T>C	ENST00000597597.1	-	2	3122	c.869A>G	c.(868-870)aAa>aGa	p.K290R	ZNF83_ENST00000391789.4_Intron|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Missense_Mutation_p.K290R|ZNF83_ENST00000301096.3_Missense_Mutation_p.K290R|ZNF83_ENST00000544146.1_Missense_Mutation_p.K290R|ZNF83_ENST00000545872.1_Missense_Mutation_p.K290R|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Missense_Mutation_p.K290R			P51522	ZNF83_HUMAN	zinc finger protein 83	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		CTCATTACATTTGTAAGGTTT	0.408																																					p.K290R		Atlas-SNP	.											ZNF83,NS,carcinoma,0,1	ZNF83	73	1	0			c.A869G						PASS	.						82.0	80.0	81.0					19																	53116949		2201	4300	6501	SO:0001583	missense	55769	exon3			TTACATTTGTAAG	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.869A>G	19.37:g.53116949T>C	ENSP00000472619:p.Lys290Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	62	16	0.258065	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	257	0.11767399267399267	18	0.036585365853658534	47	0.1298342541436464	126	0.2202797202797203	66	0.0870712401055409	t	12.57	1.977557	0.34848	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000545872;ENST00000541777	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	1.63	1.63	0.23807	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.13003	0.285	0.80722	P	0.0	B	0.33777	0.425	B	0.28638	0.092	T	0.38845	-0.9642	8	0.54805	T	0.06	.	5.8046	0.18432	0.0:0.0:0.273:0.727	.	290	P51522	ZNF83_HUMAN	R	290	ENSP00000445993:K290R;ENSP00000301096:K290R;ENSP00000445470:K290R;ENSP00000440713:K290R;ENSP00000439681:K290R	ENSP00000301096:K290R	K	-	2	0	ZNF83	57808761	0.000000	0.05858	0.005000	0.12908	0.038000	0.13279	-0.230000	0.09083	0.989000	0.38761	0.332000	0.21555	AAA	T|0.882;C|0.118	0.118	strong		0.408	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
ASB6	140459	hgsc.bcm.edu	37	9	132400480	132400480	+	Silent	SNP	G	G	A	rs3739851	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:132400480G>A	ENST00000277458.4	-	6	1020	c.855C>T	c.(853-855)gcC>gcT	p.A285A	ASB6_ENST00000450050.2_Silent_p.A206A|ASB6_ENST00000277459.4_3'UTR|RP11-483H20.4_ENST00000455074.1_RNA	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	285					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				AGTTGTAGGCGGCTCCGGACT	0.612													G|||	2311	0.461462	0.3238	0.4899	5008	,	,		19853	0.5129		0.5567	False		,,,				2504	0.4765				p.A285A		Atlas-SNP	.											.	ASB6	31	.	0			c.C855T						PASS	.	G	,,	1622,2784	498.9+/-364.3	297,1028,878	53.0	50.0	51.0		768,855,	-9.3	0.1	9	dbSNP_107	51	5248,3352	643.3+/-399.9	1600,2048,652	no	coding-synonymous,coding-synonymous,utr-3	ASB6	NM_001202403.1,NM_017873.3,NM_177999.2	,,	1897,3076,1530	AA,AG,GG		38.9767,36.8134,47.1782	,,	256/393,285/422,	132400480	6870,6136	2203	4300	6503	SO:0001819	synonymous_variant	140459	exon6			GTAGGCGGCTCCG		CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"""Ankyrin repeat domain containing"""	17181	protein-coding gene	gene with protein product		615051	"""ankyrin repeat and SOCS box-containing 6"""				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.855C>T	9.37:g.132400480G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_017873	Q5SZB7|Q9BV15	Silent	SNP	ENST00000277458.4	37	CCDS6924.1																																																																																			G|0.503;A|0.497	0.497	strong		0.612	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873	
CACNA2D1	781	hgsc.bcm.edu	37	7	81667468	81667468	+	Silent	SNP	C	C	T	rs2229952	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:81667468C>T	ENST00000356253.5	-	11	1218	c.963G>A	c.(961-963)gcG>gcA	p.A321A	CACNA2D1_ENST00000356860.3_Silent_p.A321A			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	321	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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.A321A(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)	TATTATTCACCGCGTCTTTCA	0.343													C|||	97	0.019369	0.0015	0.0144	5008	,	,		16047	0.0		0.0577	False		,,,				2504	0.0276				p.A321A		Atlas-SNP	.											CACNA2D1,colon,carcinoma,-1,1	CACNA2D1	191	1	1	Substitution - coding silent(1)	lung(1)	c.G963A						PASS	.	C		39,4367	43.1+/-76.7	0,39,2164	154.0	151.0	152.0		963	-9.5	1.0	7	dbSNP_130	152	385,8215	125.1+/-183.8	10,365,3925	no	coding-synonymous	CACNA2D1	NM_000722.2		10,404,6089	TT,TC,CC		4.4767,0.8852,3.26		321/1092	81667468	424,12582	2203	4300	6503	SO:0001819	synonymous_variant	781	exon11			ATTCACCGCGTCT	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.963G>A	7.37:g.81667468C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37																																																																																				C|0.968;T|0.032	0.032	strong		0.343	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
LRRTM1	347730	hgsc.bcm.edu	37	2	80529956	80529956	+	Missense_Mutation	SNP	T	T	C	rs6733871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:80529956T>C	ENST00000295057.3	-	2	1645	c.989A>G	c.(988-990)aAc>aGc	p.N330S	CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000466387.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.N330S|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000402739.4_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	330	LRRCT.		N -> S (in dbSNP:rs6733871). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						CTGGAAGTTGTTGAGCCACGA	0.642										HNSCC(69;0.2)			C|||	1840	0.367412	0.5076	0.3213	5008	,	,		19987	0.4831		0.1839	False		,,,				2504	0.2802				p.N330S		Atlas-SNP	.											.	LRRTM1	251	.	0			c.A989G						PASS	.	C	,,SER/ASN	1982,2424	604.8+/-390.4	471,1040,692	34.0	32.0	32.0		,,989	3.5	1.0	2	dbSNP_116	32	1535,7065	732.0+/-406.8	137,1261,2902	yes	intron,intron,missense	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,46	608,2301,3594	CC,CT,TT		17.8488,44.9841,27.0414	,,benign	,,330/523	80529956	3517,9489	2203	4300	6503	SO:0001583	missense	347730	exon2			AAGTTGTTGAGCC	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.989A>G	2.37:g.80529956T>C	ENSP00000295057:p.Asn330Ser	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	801	0.36675824175824173	238	0.483739837398374	103	0.2845303867403315	317	0.5541958041958042	143	0.18865435356200527	C	3.194	-0.165220	0.06461	0.449841	0.178488	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.39406	1.08;1.08	5.26	3.46	0.39613	.	0.048240	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00237	-1.79	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45454	-0.9260	8	.	.	.	.	10.5735	0.45214	0.0:0.7891:0.0:0.2109	rs6733871;rs17846373;rs17859410;rs58032559;rs6733871	330	Q86UE6	LRRT1_HUMAN	S	330	ENSP00000295057:N330S;ENSP00000386646:N330S	.	N	-	2	0	LRRTM1	80383467	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	2.149000	0.42244	0.219000	0.20840	-0.766000	0.03442	AAC	C|0.316;N|0.000	0.316	strong		0.642	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
LRFN2	57497	hgsc.bcm.edu	37	6	40400288	40400288	+	Missense_Mutation	SNP	C	C	T	rs61731040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:40400288C>T	ENST00000338305.6	-	2	1107	c.565G>A	c.(565-567)Gcc>Acc	p.A189T		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	189						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					GTGCCCTCGGCGATGTGATCC	0.622													C|||	371	0.0740815	0.1135	0.1196	5008	,	,		17438	0.001		0.1203	False		,,,				2504	0.0164				p.A189T		Atlas-SNP	.											.	LRFN2	133	.	0			c.G565A						PASS	.	C	THR/ALA	471,3935	223.6+/-240.1	18,435,1750	84.0	86.0	86.0		565	4.9	1.0	6	dbSNP_129	86	1166,7434	239.4+/-270.5	65,1036,3199	yes	missense	LRFN2	NM_020737.1	58	83,1471,4949	TT,TC,CC		13.5581,10.69,12.5865	benign	189/790	40400288	1637,11369	2203	4300	6503	SO:0001583	missense	57497	exon2			CCTCGGCGATGTG	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.565G>A	6.37:g.40400288C>T	ENSP00000345985:p.Ala189Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	37	CCDS34443.1	200	0.09157509157509157	54	0.10975609756097561	47	0.1298342541436464	1	0.0017482517482517483	98	0.12928759894459102	C	12.19	1.864037	0.32884	0.1069	0.135581	ENSG00000156564	ENST00000338305	T	0.57107	0.42	5.76	4.89	0.63831	.	0.199765	0.53938	D	0.000054	T	0.13884	0.0336	N	0.04705	-0.18	0.36592	P	0.125865	B	0.23937	0.094	B	0.21708	0.036	T	0.05632	-1.0873	9	0.40728	T	0.16	.	8.1605	0.31196	0.0:0.7667:0.0:0.2333	rs61731040	189	Q9ULH4	LRFN2_HUMAN	T	189	ENSP00000345985:A189T	ENSP00000345985:A189T	A	-	1	0	LRFN2	40508266	0.286000	0.24305	0.995000	0.50966	0.894000	0.52154	0.871000	0.28023	1.455000	0.47813	0.655000	0.94253	GCC	C|0.890;T|0.110	0.110	strong		0.622	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
BMP1	649	hgsc.bcm.edu	37	8	22067022	22067022	+	Silent	SNP	C	C	A	rs77242743	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:22067022C>A	ENST00000306385.5	+	19	3310	c.2640C>A	c.(2638-2640)ggC>ggA	p.G880G	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	880	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		CCCAGTTTGGCGACAACAACT	0.617													C|||	176	0.0351438	0.003	0.0605	5008	,	,		18109	0.0198		0.0895	False		,,,				2504	0.0204				p.G880G		Atlas-SNP	.											.	BMP1	131	.	0			c.C2640A						PASS	.	C		112,4294	85.8+/-124.5	1,110,2092	260.0	204.0	223.0		2640	-9.5	0.2	8	dbSNP_132	223	989,7611	214.2+/-253.9	52,885,3363	no	coding-synonymous	BMP1	NM_006129.4		53,995,5455	AA,AC,CC		11.5,2.542,8.4653		880/987	22067022	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	649	exon19			GTTTGGCGACAAC		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.2640C>A	8.37:g.22067022C>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			C|0.929;A|0.071	0.071	strong		0.617	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
KRT76	51350	hgsc.bcm.edu	37	12	53171001	53171001	+	Silent	SNP	G	G	A	rs11170272	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53171001G>A	ENST00000332411.2	-	1	128	c.75C>T	c.(73-75)tcC>tcT	p.S25S		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	25	Head.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGCTGCTGCCGGAGACCACAG	0.607													g|||	235	0.0469249	0.0121	0.0562	5008	,	,		16759	0.002		0.1123	False		,,,				2504	0.0665				p.S25S		Atlas-SNP	.											.	KRT76	72	.	0			c.C75T						PASS	.	A		108,4298	83.4+/-121.9	1,106,2096	45.0	55.0	51.0		75	-8.6	0.0	12	dbSNP_120	51	1097,7503	227.9+/-263.1	82,933,3285	no	coding-synonymous	KRT76	NM_015848.4		83,1039,5381	AA,AG,GG		12.7558,2.4512,9.265		25/639	53171001	1205,11801	2203	4300	6503	SO:0001819	synonymous_variant	51350	exon1			GCTGCCGGAGACC	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.75C>T	12.37:g.53171001G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_015848	B4DRR3|Q7Z795	Silent	SNP	ENST00000332411.2	37	CCDS8838.1																																																																																			G|0.916;A|0.084	0.084	strong		0.607	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
HFM1	164045	hgsc.bcm.edu	37	1	91859801	91859801	+	Missense_Mutation	SNP	A	A	G	rs11165778	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:91859801A>G	ENST00000370425.3	-	4	441	c.343T>C	c.(343-345)Tca>Cca	p.S115P	HFM1_ENST00000370424.3_Intron|HFM1_ENST00000294696.5_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	115			S -> P (in dbSNP:rs11165778). {ECO:0000269|PubMed:17286053}.		resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GCAATATGTGATAAGTCATTA	0.333													A|||	685	0.136781	0.1649	0.1585	5008	,	,		15059	0.005		0.2356	False		,,,				2504	0.1176				p.S115P		Atlas-SNP	.											.	HFM1	188	.	0			c.T343C						PASS	.	A	PRO/SER	776,3630	313.6+/-293.2	56,664,1483	108.0	101.0	103.0		343	-2.8	0.1	1	dbSNP_120	103	2219,6379	376.6+/-338.2	284,1651,2364	yes	missense	HFM1	NM_001017975.3	74	340,2315,3847	GG,GA,AA		25.8083,17.6123,23.0314	benign	115/1436	91859801	2995,10009	2203	4299	6502	SO:0001583	missense	164045	exon4			TATGTGATAAGTC	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.343T>C	1.37:g.91859801A>G	ENSP00000359454:p.Ser115Pro	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	231	99	0.428571	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	313	0.1433150183150183	72	0.14634146341463414	63	0.17403314917127072	2	0.0034965034965034965	176	0.23218997361477572	A	0.947	-0.707603	0.03230	0.176123	0.258083	ENSG00000162669	ENST00000370425;ENST00000541820;ENST00000427444;ENST00000455133	T;T;T	0.59502	0.26;1.33;1.37	4.28	-2.82	0.05787	.	.	.	.	.	T	0.15652	0.0377	N	0.12746	0.255	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12993	-1.0526	8	0.30854	T	0.27	.	9.8673	0.41152	0.3613:0.0:0.6387:0.0	rs11165778;rs58165672;rs11165778	115;115	B7ZM16;A2PYH4	.;HFM1_HUMAN	P	115;148;73;115	ENSP00000359454:S115P;ENSP00000388900:S73P;ENSP00000409827:S115P	ENSP00000359454:S115P	S	-	1	0	HFM1	91632389	0.000000	0.05858	0.089000	0.20774	0.069000	0.16628	-0.443000	0.06862	-0.377000	0.07930	-0.326000	0.08463	TCA	A|0.808;G|0.192	0.192	strong		0.333	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
DSC3	1825	hgsc.bcm.edu	37	18	28611061	28611061	+	Missense_Mutation	SNP	A	A	T	rs276937	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	110	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	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	
MYPN	84665	hgsc.bcm.edu	37	10	69926325	69926325	+	Silent	SNP	C	C	T	rs2673793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:69926325C>T	ENST00000358913.5	+	10	2363	c.1875C>T	c.(1873-1875)ccC>ccT	p.P625P	MYPN_ENST00000540630.1_Silent_p.P625P|MYPN_ENST00000354393.2_Silent_p.P350P	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	625					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						AGACCAGGCCCGATTCTTTCC	0.557													C|||	790	0.157748	0.1362	0.2767	5008	,	,		16669	0.0962		0.1759	False		,,,				2504	0.1472				p.P625P		Atlas-SNP	.											.	MYPN	189	.	0			c.C1875T						PASS	.	C		636,3770	272.8+/-271.0	42,552,1609	74.0	67.0	70.0		1875	-7.2	0.0	10	dbSNP_100	70	1605,6995	298.5+/-303.9	171,1263,2866	no	coding-synonymous	MYPN	NM_032578.2		213,1815,4475	TT,TC,CC		18.6628,14.4349,17.2305		625/1321	69926325	2241,10765	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon10			CAGGCCCGATTCT	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1875C>T	10.37:g.69926325C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	131	76	0.580153	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			C|0.825;T|0.175	0.175	strong		0.557	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
SLC22A8	9376	hgsc.bcm.edu	37	11	62766431	62766431	+	Silent	SNP	A	A	T	rs2276299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:62766431A>T	ENST00000336232.2	-	5	858	c.723T>A	c.(721-723)acT>acA	p.T241T	SLC22A8_ENST00000535878.1_Silent_p.T118T|SLC22A8_ENST00000311438.8_Silent_p.T241T|SLC22A8_ENST00000430500.2_Silent_p.T241T|SLC22A8_ENST00000542795.1_5'UTR|SLC22A8_ENST00000545207.1_Silent_p.T150T	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	241					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GAATGGACACAGTTAACTGCA	0.572													A|||	932	0.186102	0.0371	0.3516	5008	,	,		22117	0.2718		0.1809	False		,,,				2504	0.1871				p.T241T		Atlas-SNP	.											.	SLC22A8	60	.	0			c.T723A						PASS	.	A	,,,	272,4130	151.8+/-185.6	11,250,1940	120.0	110.0	113.0		723,450,354,723	-3.0	0.0	11	dbSNP_100	113	1469,7127	279.5+/-294.0	120,1229,2949	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC22A8	NM_001184732.1,NM_001184733.1,NM_001184736.1,NM_004254.3	,,,	131,1479,4889	TT,TA,AA		17.0893,6.179,13.3944	,,,	241/543,150/452,118/420,241/543	62766431	1741,11257	2201	4298	6499	SO:0001819	synonymous_variant	9376	exon5			GGACACAGTTAAC	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"""Solute carriers"""	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.723T>A	11.37:g.62766431A>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Silent	SNP	ENST00000336232.2	37	CCDS8042.1																																																																																			A|0.839;T|0.161	0.161	strong		0.572	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254	
ABCB8	11194	hgsc.bcm.edu	37	7	150742408	150742408	+	Missense_Mutation	SNP	G	G	T	rs59397762	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150742408G>T	ENST00000297504.6	+	17	2246	c.2180G>T	c.(2179-2181)gGc>gTc	p.G727V	ASIC3_ENST00000357922.4_5'Flank|ABCB8_ENST00000542328.1_Missense_Mutation_p.G622V|ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000358849.4_Missense_Mutation_p.G710V|ABCB8_ENST00000498578.1_Missense_Mutation_p.G685V			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	727					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)	AAGCCAGAAGGCCCCAGGAGC	0.657													G|||	137	0.0273562	0.0121	0.0418	5008	,	,		16050	0.0198		0.0596	False		,,,				2504	0.0123				p.G710V		Atlas-SNP	.											.	ABCB8	65	.	0			c.G2129T						PASS	.	G	VAL/GLY	78,4328	67.0+/-104.6	0,78,2125	43.0	41.0	42.0		2129	-0.8	0.0	7	dbSNP_129	42	503,8097	142.8+/-198.9	12,479,3809	yes	missense	ABCB8	NM_007188.3	109	12,557,5934	TT,TG,GG		5.8488,1.7703,4.4672	benign	710/719	150742408	581,12425	2203	4300	6503	SO:0001583	missense	11194	exon16			CAGAAGGCCCCAG	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.2180G>T	7.37:g.150742408G>T	ENSP00000297504:p.Gly727Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		91	0.041666666666666664	10	0.02032520325203252	19	0.052486187845303865	10	0.017482517482517484	52	0.06860158311345646	g	12.05	1.821361	0.32237	0.017703	0.058488	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578	D;D;D;D	0.90069	-2.56;-2.57;-2.48;-2.61	4.4	-0.765	0.11023	.	0.614119	0.13996	N	0.348451	T	0.14743	0.0356	N	0.08118	0	0.09310	N	1	B;B;P;B	0.42039	0.0;0.0;0.769;0.0	B;B;B;B	0.34346	0.001;0.0;0.18;0.001	T	0.53662	-0.8407	10	0.30854	T	0.27	-5.2056	1.1317	0.01746	0.228:0.1665:0.4356:0.1699	rs59397762;rs61741007	622;685;727;710	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2	.;.;ABCB8_HUMAN;.	V	710;693;727;622;685	ENSP00000351717:G710V;ENSP00000297504:G727V;ENSP00000438776:G622V;ENSP00000418271:G685V	ENSP00000297504:G727V	G	+	2	0	ABCB8	150373341	0.027000	0.19231	0.000000	0.03702	0.016000	0.09150	0.216000	0.17585	-0.271000	0.09272	0.457000	0.33378	GGC	G|0.963;T|0.037	0.037	strong		0.657	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
OLFM3	118427	hgsc.bcm.edu	37	1	102296279	102296279	+	Silent	SNP	T	T	C	rs10493973	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:102296279T>C	ENST00000338858.5	-	3	380	c.381A>G	c.(379-381)aaA>aaG	p.K127K	OLFM3_ENST00000536598.1_Silent_p.K32K|OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000370103.4_Silent_p.K107K|OLFM3_ENST00000359814.3_Silent_p.K127K			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	158	0	0		WXS	Illumina HiSeq	Phase_I	163	79	0.484663	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		
ZNRF4	148066	hgsc.bcm.edu	37	19	5456450	5456450	+	Silent	SNP	T	T	C	rs8111108	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5456450T>C	ENST00000222033.4	+	1	1025	c.948T>C	c.(946-948)taT>taC	p.Y316Y		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	316						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		TGGATGAGTATGAGGAGGGCG	0.632													C|||	3529	0.704673	0.7458	0.5865	5008	,	,		18522	0.8581		0.5785	False		,,,				2504	0.7045				p.Y316Y		Atlas-SNP	.											.	ZNRF4	59	.	0			c.T948C						PASS	.	C		3091,1161		1131,829,166	95.0	108.0	104.0		948	-2.1	0.3	19	dbSNP_116	104	4774,3704		1360,2054,825	no	coding-synonymous	ZNRF4	NM_181710.3		2491,2883,991	CC,CT,TT		43.6895,27.3048,38.2168		316/430	5456450	7865,4865	2126	4239	6365	SO:0001819	synonymous_variant	148066	exon1			TGAGTATGAGGAG	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.948T>C	19.37:g.5456450T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_181710	A8K886|O75866	Silent	SNP	ENST00000222033.4	37	CCDS42475.1																																																																																			T|0.315;C|0.685	0.685	strong		0.632	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189601	11189601	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11189601G>T	ENST00000382435.4	+	1	1205	c.986G>T	c.(985-987)aGc>aTc	p.S329I		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	329						integral component of membrane (GO:0016021)											CGGAACCTCAGCTGTGAGAGG	0.517																																					p.S329I		Atlas-SNP	.											AMAC1L2,NS,carcinoma,-1,1	.	.	1	0			c.G986T						scavenged	.						67.0	68.0	68.0					8																	11189601		2203	4300	6503	SO:0001583	missense	83650	exon1			ACCTCAGCTGTGA	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.986G>T	8.37:g.11189601G>T	ENSP00000371872:p.Ser329Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	166	9	0.0542169	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	g	0.299	-0.974907	0.02215	.	.	ENSG00000177710	ENST00000382435	T	0.28666	1.6	.	.	.	.	0.000000	0.52532	D	0.000061	T	0.22244	0.0536	L	0.54323	1.7	0.26188	N	0.979621	B	0.02656	0.0	B	0.06405	0.002	T	0.18241	-1.0343	8	0.22706	T	0.39	-1.3917	.	.	.	.	329	Q96KT7	S35G5_HUMAN	I	329	ENSP00000371872:S329I	ENSP00000371872:S329I	S	+	2	0	SLC35G5	11227011	0.173000	0.23056	0.298000	0.25002	0.299000	0.27559	0.335000	0.19806	0.064000	0.16427	0.064000	0.15345	AGC	.	.	none		0.517	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
KNDC1	85442	hgsc.bcm.edu	37	10	134997480	134997480	+	Silent	SNP	C	C	T	rs57510763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:134997480C>T	ENST00000304613.3	+	5	633	c.612C>T	c.(610-612)ttC>ttT	p.F204F	KNDC1_ENST00000368571.2_Silent_p.F139F|KNDC1_ENST00000368572.2_Silent_p.F204F			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	204	KIND 1. {ECO:0000255|PROSITE- ProRule:PRU00709}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TCGAGTCCTTCGGAGCGCTGC	0.577													c|||	2101	0.419529	0.118	0.3876	5008	,	,		20472	0.5843		0.4384	False		,,,				2504	0.6605				p.F204F		Atlas-SNP	.											.	KNDC1	155	.	0			c.C612T						PASS	.			737,3669	300.4+/-286.3	62,613,1528	156.0	130.0	139.0		612	-1.1	1.0	10	dbSNP_129	139	4027,4573	555.7+/-386.7	951,2125,1224	no	coding-synonymous	KNDC1	NM_152643.6		1013,2738,2752	TT,TC,CC		46.8256,16.7272,36.6292		204/1750	134997480	4764,8242	2203	4300	6503	SO:0001819	synonymous_variant	85442	exon5			GTCCTTCGGAGCG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.612C>T	10.37:g.134997480C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	CCDS7674.1																																																																																			C|0.611;T|0.389	0.389	strong		0.577	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
MYH4	4622	hgsc.bcm.edu	37	17	10363410	10363410	+	Silent	SNP	A	A	G	rs3744561	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10363410A>G	ENST00000255381.2	-	14	1385	c.1275T>C	c.(1273-1275)aaT>aaC	p.N425N	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	425	Myosin motor.				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)			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						CACCCACTGCATTGTACACCT	0.448													A|||	2682	0.535543	0.3442	0.5245	5008	,	,		19217	0.8601		0.3708	False		,,,				2504	0.637				p.N425N		Atlas-SNP	.											.	MYH4	349	.	0			c.T1275C						PASS	.	A		1585,2821	494.3+/-362.9	281,1023,899	182.0	169.0	174.0		1275	-2.7	0.0	17	dbSNP_107	174	3590,5010	520.1+/-379.6	761,2068,1471	no	coding-synonymous	MYH4	NM_017533.2		1042,3091,2370	GG,GA,AA		41.7442,35.9737,39.7893		425/1940	10363410	5175,7831	2203	4300	6503	SO:0001819	synonymous_variant	4622	exon14			CACTGCATTGTAC		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.1275T>C	17.37:g.10363410A>G		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	212	93	0.438679	NM_017533		Silent	SNP	ENST00000255381.2	37	CCDS11154.1																																																																																			A|0.575;G|0.425	0.425	strong		0.448	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
GPR146	115330	hgsc.bcm.edu	37	7	1097895	1097895	+	Silent	SNP	A	A	G	rs61910751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1097895A>G	ENST00000397095.1	+	2	967	c.744A>G	c.(742-744)ccA>ccG	p.P248P	C7orf50_ENST00000357429.6_Intron|GPR146_ENST00000297468.3_Silent_p.P248P|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron|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	23	0	0		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	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	
RADIL	55698	hgsc.bcm.edu	37	7	4874420	4874420	+	Missense_Mutation	SNP	G	G	C	rs2292498	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:4874420G>C	ENST00000399583.3	-	4	1421	c.1234C>G	c.(1234-1236)Cac>Gac	p.H412D	RADIL_ENST00000538469.1_Missense_Mutation_p.H172D|RADIL_ENST00000536091.1_Missense_Mutation_p.H412D	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	412			H -> D (in dbSNP:rs2292498). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TCCTCCAGGTGGGGCTCAAAC	0.716													G|||	1259	0.251398	0.0401	0.2853	5008	,	,		9176	0.3294		0.2873	False		,,,				2504	0.3957				p.H412D		Atlas-SNP	.											.	RADIL	110	.	0			c.C1234G						PASS	.	G	ASP/HIS	299,3725		19,261,1732	12.0	15.0	14.0		1234	2.6	0.0	7	dbSNP_100	14	2520,5808		397,1726,2041	yes	missense	RADIL	NM_018059.4	81	416,1987,3773	CC,CG,GG		30.2594,7.4304,22.8222	benign	412/1076	4874420	2819,9533	2012	4164	6176	SO:0001583	missense	55698	exon4			CCAGGTGGGGCTC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.1234C>G	7.37:g.4874420G>C	ENSP00000382492:p.His412Asp	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	526	0.24084249084249085	22	0.044715447154471545	94	0.2596685082872928	195	0.3409090909090909	215	0.2836411609498681	-	0.008	-1.905182	0.00512	0.074304	0.302594	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000536091;ENST00000538469	T;T;T	0.21031	3.45;2.03;3.37	4.45	2.56	0.30785	.	1.666850	0.02995	N	0.147315	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43261	-0.9402	9	0.11794	T	0.64	-5.6915	8.1854	0.31335	0.1638:0.6284:0.2079:0.0	rs2292498;rs2292498	412	Q96JH8	RADIL_HUMAN	D	412;383;146;412;172	ENSP00000382492:H412D;ENSP00000442533:H412D;ENSP00000442966:H172D	ENSP00000320946:H383D	H	-	1	0	RADIL	4840946	0.095000	0.21747	0.004000	0.12327	0.011000	0.07611	1.196000	0.32198	0.291000	0.22468	-0.218000	0.12543	CAC	G|0.754;C|0.246	0.246	strong		0.716	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
FCRLA	84824	hgsc.bcm.edu	37	1	161680617	161680617	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161680617G>A	ENST00000236938.6	+	2	440	c.198G>A	c.(196-198)gaG>gaA	p.E66E	FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000367950.1_Silent_p.E26E|FCRLA_ENST00000367959.2_Silent_p.E72E|FCRLA_ENST00000367949.2_Silent_p.E66E|FCRLA_ENST00000367957.2_Intron|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000309691.6_Silent_p.E49E|FCRLA_ENST00000294796.4_Intron|FCRLA_ENST00000546024.1_Silent_p.E66E|FCRLA_ENST00000540521.1_Intron|FCRLA_ENST00000367953.3_Silent_p.E55E|FCRLA_ENST00000540926.1_Silent_p.E55E|FCRLA_ENST00000349527.4_Silent_p.E49E	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	49					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)			GCCACACGGAGGATGACTTGA	0.557																																					p.E72E		Atlas-SNP	.											.	FCRLA	101	.	0			c.G216A						PASS	.						108.0	81.0	90.0					1																	161680617		2203	4300	6503	SO:0001819	synonymous_variant	84824	exon3			CACGGAGGATGAC	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.198G>A	1.37:g.161680617G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Silent	SNP	ENST00000236938.6	37	CCDS30926.1																																																																																			.	.	none		0.557	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
PRR12	57479	hgsc.bcm.edu	37	19	50097784	50097784	+	Silent	SNP	T	T	C	rs10414643	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	71	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	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	
FLG	2312	hgsc.bcm.edu	37	1	152282267	152282267	+	Missense_Mutation	SNP	G	G	A	rs12405278	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152282267G>A	ENST00000368799.1	-	3	5130	c.5095C>T	c.(5095-5097)Cgc>Tgc	p.R1699C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1699	Ser-rich.		R -> C (in dbSNP:rs12405278).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTTGTCTGCGCCCAGTGCCT	0.572									Ichthyosis				g|||	1441	0.28774	0.0121	0.3905	5008	,	,		20090	0.5843		0.1421	False		,,,				2504	0.4315				p.R1699C		Atlas-SNP	.											FLG,colon,carcinoma,+1,1	FLG	900	1	0			c.C5095T						PASS	.	C	CYS/ARG	161,4245	108.2+/-146.6	2,157,2044	256.0	259.0	258.0		5095	1.8	0.0	1	dbSNP_120	258	1240,7360	249.0+/-276.5	97,1046,3157	yes	missense	FLG	NM_002016.1	180	99,1203,5201	AA,AG,GG		14.4186,3.6541,10.772	probably-damaging	1699/4062	152282267	1401,11605	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCTGCGCCCAGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5095C>T	1.37:g.152282267G>A	ENSP00000357789:p.Arg1699Cys	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	212	100	0.471698	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	573	0.2623626373626374	9	0.018292682926829267	118	0.3259668508287293	335	0.5856643356643356	111	0.14643799472295516	g	3.096	-0.185843	0.06340	0.036541	0.144186	ENSG00000143631	ENST00000368799	T	0.04275	3.66	2.69	1.76	0.24704	.	.	.	.	.	T	0.05823	0.0152	L	0.54323	1.7	0.80722	P	0.0	D	0.76494	0.999	D	0.63192	0.912	T	0.21484	-1.0244	8	0.54805	T	0.06	.	7.611	0.28131	0.0:0.2659:0.7341:0.0	rs56401605;rs58569216	1699	P20930	FILA_HUMAN	C	1699	ENSP00000357789:R1699C	ENSP00000357789:R1699C	R	-	1	0	FLG	150548891	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.137000	0.15995	0.482000	0.27582	-0.672000	0.03802	CGC	G|0.811;A|0.189	0.189	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC16	94025	hgsc.bcm.edu	37	19	9047305	9047305	+	Silent	SNP	G	G	A	rs10415818	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9047305G>A	ENST00000397910.4	-	5	34529	c.34326C>T	c.(34324-34326)caC>caT	p.H11442H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11444	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGAACTTGTGTGTGTCTCAG	0.478													G|||	918	0.183307	0.177	0.1945	5008	,	,		23374	0.0258		0.2823	False		,,,				2504	0.2444				p.H11442H		Atlas-SNP	.											.	MUC16	4315	.	0			c.C34326T						PASS	.			696,3340		57,582,1379	187.0	188.0	187.0		34326	-6.2	0.0	19	dbSNP_119	187	2515,5805		401,1713,2046	no	coding-synonymous	MUC16	NM_024690.2		458,2295,3425	AA,AG,GG		30.2284,17.2448,25.9874		11442/14508	9047305	3211,9145	2018	4160	6178	SO:0001819	synonymous_variant	94025	exon5			ACTTGTGTGTGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34326C>T	19.37:g.9047305G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.797;A|0.203	0.203	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR5L2	26338	hgsc.bcm.edu	37	11	55595017	55595017	+	Missense_Mutation	SNP	G	G	T	rs117277709|rs34954823|rs386753700	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	130	0	0		WXS	Illumina HiSeq	Phase_I	119	29	0.243697	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	
PJA2	9867	hgsc.bcm.edu	37	5	108713982	108713982	+	Silent	SNP	T	T	C	rs12523186	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:108713982T>C	ENST00000361189.2	-	4	1445	c.1206A>G	c.(1204-1206)gcA>gcG	p.A402A	PJA2_ENST00000361557.3_Silent_p.A402A|PJA2_ENST00000511624.1_5'Flank	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	402					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		CTTGCCTTCCTGCTGTGGCTC	0.408													T|||	1628	0.32508	0.0643	0.4726	5008	,	,		20694	0.0565		0.5915	False		,,,				2504	0.5757				p.A402A		Atlas-SNP	.											.	PJA2	53	.	0			c.A1206G						PASS	.	T		690,3714	286.9+/-279.0	54,582,1566	204.0	179.0	187.0		1206	-2.2	0.3	5	dbSNP_120	187	5097,3503	632.8+/-398.7	1517,2063,720	no	coding-synonymous	PJA2	NM_014819.4		1571,2645,2286	CC,CT,TT		40.7326,15.6676,44.5017		402/709	108713982	5787,7217	2202	4300	6502	SO:0001819	synonymous_variant	9867	exon4			CCTTCCTGCTGTG	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.1206A>G	5.37:g.108713982T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	246	244	0.99187	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Silent	SNP	ENST00000361189.2	37	CCDS4099.1																																																																																			T|0.606;C|0.394	0.394	strong		0.408	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
LDLR	3949	hgsc.bcm.edu	37	19	11222300	11222300	+	Missense_Mutation	SNP	G	G	A	rs11669576	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11222300G>A	ENST00000558518.1	+	8	1358	c.1171G>A	c.(1171-1173)Gcc>Acc	p.A391T	LDLR_ENST00000455727.2_Missense_Mutation_p.A223T|LDLR_ENST00000558013.1_Missense_Mutation_p.A391T|LDLR_ENST00000557933.1_Missense_Mutation_p.A391T|LDLR_ENST00000535915.1_Missense_Mutation_p.A350T|LDLR_ENST00000545707.1_Missense_Mutation_p.A264T	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	27	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	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		
OR51F1	256892	hgsc.bcm.edu	37	11	4790857	4790857	+	Silent	SNP	A	A	G	rs11033797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790857A>G	ENST00000380383.1	-	1	311	c.312T>C	c.(310-312)taT>taC	p.Y104Y	OR51F1_ENST00000343430.3_Silent_p.Y97Y|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	104						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)		CAATGCAGCTATATAGACTGA	0.448													A|||	1080	0.215655	0.4569	0.2017	5008	,	,		22329	0.0		0.2704	False		,,,				2504	0.0654				p.Y97Y		Atlas-SNP	.											.	OR51F1	60	.	0			c.T291C						PASS	.	A		1968,2434	554.2+/-379.0	445,1078,678	77.0	74.0	75.0		291	2.6	0.0	11	dbSNP_120	75	2178,6418	371.0+/-336.1	290,1598,2410	no	coding-synonymous	OR51F1	NM_001004752.1		735,2676,3088	GG,GA,AA		25.3374,44.707,31.8972		97/313	4790857	4146,8852	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			GCAGCTATATAGA	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.312T>C	11.37:g.4790857A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.713;G|0.287	0.287	strong		0.448	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
PTCD3	55037	hgsc.bcm.edu	37	2	86352925	86352925	+	Silent	SNP	A	A	G	rs139474497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:86352925A>G	ENST00000254630.7	+	12	939	c.873A>G	c.(871-873)gtA>gtG	p.V291V	PTCD3_ENST00000409277.3_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	291					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						CAGCTGATGTATACACATTTA	0.338													A|||	28	0.00559105	0.0	0.0086	5008	,	,		20926	0.0		0.0219	False		,,,				2504	0.0				p.V291V		Atlas-SNP	.											.	PTCD3	51	.	0			c.A873G						PASS	.	A		6,4400	11.4+/-27.6	0,6,2197	44.0	49.0	47.0		873	-11.5	0.0	2	dbSNP_134	47	127,8473	64.6+/-126.8	1,125,4174	no	coding-synonymous	PTCD3	NM_017952.5		1,131,6371	GG,GA,AA		1.4767,0.1362,1.0226		291/690	86352925	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	55037	exon12			TGATGTATACACA		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.873A>G	2.37:g.86352925A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Silent	SNP	ENST00000254630.7	37	CCDS33235.1																																																																																			A|0.991;G|0.009	0.009	strong		0.338	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952	
BOK	666	hgsc.bcm.edu	37	2	242501765	242501765	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242501765G>A	ENST00000318407.3	+	3	525	c.223G>A	c.(223-225)Gat>Aat	p.D75N		NM_032515.4	NP_115904.1	Q9UMX3	BOK_HUMAN	BCL2-related ovarian killer	75					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell proliferation (GO:0008283)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|neuron apoptotic process (GO:0051402)|oligodendrocyte differentiation (GO:0048709)|positive regulation of apoptotic process (GO:0043065)|positive regulation of execution phase of apoptosis (GO:1900119)	cytoplasm (GO:0005737)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)	5		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;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)		CCACACAGGCGATGAGCTGGA	0.647																																					p.D75N		Atlas-SNP	.											.	BOK	16	.	0			c.G223A						PASS	.						84.0	66.0	72.0					2																	242501765		2203	4300	6503	SO:0001583	missense	666	exon3			ACAGGCGATGAGC	AF174487	CCDS2550.1	2q37.3	2008-05-22			ENSG00000176720	ENSG00000176720			1087	protein-coding gene	gene with protein product		605404				9356461, 11034351, 15102863	Standard	NM_032515		Approved	BCL2L9, BOKL, MGC4631	uc002wbq.3	Q9UMX3	OTTHUMG00000133411	ENST00000318407.3:c.223G>A	2.37:g.242501765G>A	ENSP00000314132:p.Asp75Asn	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_032515		Missense_Mutation	SNP	ENST00000318407.3	37	CCDS2550.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087479	0.94100	.	.	ENSG00000176720	ENST00000318407	T	0.55588	0.51	4.97	4.97	0.65823	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.116231	0.56097	D	0.000026	T	0.74222	0.3688	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.78360	-0.2234	10	0.62326	D	0.03	-17.3648	18.2203	0.89899	0.0:0.0:1.0:0.0	.	75	Q9UMX3	BOK_HUMAN	N	75	ENSP00000314132:D75N	ENSP00000314132:D75N	D	+	1	0	BOK	242150438	1.000000	0.71417	0.978000	0.43139	0.758000	0.43043	9.034000	0.93747	2.283000	0.76528	0.655000	0.94253	GAT	.	.	none		0.647	BOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257268.2	NM_032515	
UGT2B28	54490	hgsc.bcm.edu	37	4	70146804	70146804	+	Missense_Mutation	SNP	G	G	C	rs148987832	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70146804G>C	ENST00000335568.5	+	1	588	c.586G>C	c.(586-588)Gtt>Ctt	p.V196L	UGT2B28_ENST00000511240.1_Missense_Mutation_p.V196L	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	196					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.V196L(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						CTACATACCTGTTGTTATGTC	0.383													-|||	540	0.107827	0.0794	0.1066	5008	,	,		15023	0.001		0.1998	False		,,,				2504	0.1626				p.V196L		Atlas-SNP	.											UGT2B28,NS,carcinoma,0,1	UGT2B28	101	1	1	Substitution - Missense(1)	pancreas(1)	c.G586C						PASS	.	A	LEU/VAL,LEU/VAL	456,3602		118,220,1691	82.0	85.0	84.0		586,586	-3.0	0.0	4	dbSNP_134	84	1636,6830		327,982,2924	no	missense,missense	UGT2B28	NM_001207004.1,NM_053039.1	32,32	445,1202,4615	CC,CG,GG		19.3244,11.2371,16.7039	benign,benign	196/336,196/530	70146804	2092,10432	2029	4233	6262	SO:0001583	missense	54490	exon1			ATACCTGTTGTTA	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.586G>C	4.37:g.70146804G>C	ENSP00000334276:p.Val196Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	231	112	0.484848	NM_053039	B5BUM0|Q9BY62|Q9BY63	Missense_Mutation	SNP	ENST00000335568.5	37	CCDS3528.1	232	0.10622710622710622	34	0.06910569105691057	47	0.1298342541436464	6	0.01048951048951049	145	0.19129287598944592	-	5.967	0.362313	0.11296	0.112371	0.193244	ENSG00000135226	ENST00000335568;ENST00000511240	T;T	0.60171	0.21;0.21	2.18	-2.99	0.05497	.	10.250200	0.01475	U	0.016449	T	0.00109	0.0003	L	0.58101	1.795	0.80722	P	0.0	B;B	0.23185	0.081;0.005	B;B	0.33750	0.169;0.031	T	0.07385	-1.0775	9	0.10111	T	0.7	.	7.3598	0.26739	0.4534:0.0:0.5466:0.0	.	196;196	Q9BY64-2;Q9BY64	.;UDB28_HUMAN	L	196	ENSP00000334276:V196L;ENSP00000427399:V196L	ENSP00000334276:V196L	V	+	1	0	UGT2B28	70181393	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.213000	0.17521	-1.067000	0.03160	-1.139000	0.01908	GTT	.	.	weak		0.383	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
FBXO34	55030	hgsc.bcm.edu	37	14	55818275	55818275	+	Silent	SNP	A	A	G	rs35342573	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:55818275A>G	ENST00000313833.4	+	2	1412	c.1167A>G	c.(1165-1167)ttA>ttG	p.L389L	FBXO34_ENST00000440021.1_Silent_p.L389L	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	389										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GTGCAGAGTTAGAGCCGGGTT	0.507													A|||	63	0.0125799	0.025	0.0086	5008	,	,		20089	0.0		0.008	False		,,,				2504	0.0164				p.L389L		Atlas-SNP	.											.	FBXO34	61	.	0			c.A1167G						PASS	.	A	,	77,4329	67.0+/-104.6	0,77,2126	116.0	101.0	106.0		1167,1167	-3.0	0.0	14	dbSNP_126	106	88,8512	50.2+/-110.2	1,86,4213	no	coding-synonymous,coding-synonymous	FBXO34	NM_017943.3,NM_152231.1	,	1,163,6339	GG,GA,AA		1.0233,1.7476,1.2686	,	389/712,389/712	55818275	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	55030	exon2			AGAGTTAGAGCCG	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.1167A>G	14.37:g.55818275A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	159	90	0.566038	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																			A|0.987;G|0.013	0.013	strong		0.507	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092624	1092624	+	Silent	SNP	C	C	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1092624C>A	ENST00000441003.2	+	30	4470	c.4443C>A	c.(4441-4443)acC>acA	p.T1481T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1482T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4216	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gccctccaaccaccactccca	0.627																																					p.T1481T		Atlas-SNP	.											MUC2_ENST00000441003,extremity,malignant_melanoma,+2,2	MUC2	614	2	0			c.C4443A						scavenged	.						223.0	336.0	297.0					11																	1092624		1558	2939	4497	SO:0001819	synonymous_variant	4583	exon30			TCCAACCACCACT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4443C>A	11.37:g.1092624C>A		Somatic	251	4	0.0159363		WXS	Illumina HiSeq	Phase_I	235	19	0.0808511	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ADCY9	115	hgsc.bcm.edu	37	16	4164364	4164364	+	Silent	SNP	C	C	T	rs2230738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4164364C>T	ENST00000294016.3	-	2	1618	c.1080G>A	c.(1078-1080)agG>agA	p.R360R		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	360					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						AGGTGGCATGCCTCTTGACAG	0.468													C|||	1624	0.324281	0.0234	0.3199	5008	,	,		20673	0.6111		0.2575	False		,,,				2504	0.5072				p.R360R		Atlas-SNP	.											.	ADCY9	151	.	0			c.G1080A						PASS	.	C		236,4158	138.8+/-174.5	11,214,1972	168.0	158.0	162.0		1080	3.0	1.0	16	dbSNP_98	162	2198,6402	374.2+/-337.3	285,1628,2387	no	coding-synonymous	ADCY9	NM_001116.3		296,1842,4359	TT,TC,CC		25.5581,5.371,18.7317		360/1354	4164364	2434,10560	2197	4300	6497	SO:0001819	synonymous_variant	115	exon2			GGCATGCCTCTTG	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.1080G>A	16.37:g.4164364C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	111	45	0.405405	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			C|0.761;T|0.239	0.239	strong		0.468	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
TARBP1	6894	hgsc.bcm.edu	37	1	234529552	234529552	+	Silent	SNP	C	C	T	rs2175594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	177	0	0		WXS	Illumina HiSeq	Phase_I	152	53	0.348684	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	
COL4A2	1284	hgsc.bcm.edu	37	13	111121620	111121620	+	Missense_Mutation	SNP	C	C	T	rs9583500	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:111121620C>T	ENST00000360467.5	+	28	2458	c.2152C>T	c.(2152-2154)Ccc>Tcc	p.P718S		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	718	Triple-helical region.		P -> S (polymorphism that does not affect COL4A2 and COL4A1 secretion; dbSNP:rs9583500). {ECO:0000269|PubMed:21527998, ECO:0000269|PubMed:22209247}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			AGGACCAGGGCCCAGGGGCTT	0.602													C|||	956	0.190895	0.3578	0.2176	5008	,	,		16522	0.0208		0.2167	False		,,,				2504	0.0951				p.P718S		Atlas-SNP	.											.	COL4A2	178	.	0			c.C2152T						PASS	.	C	SER/PRO	1150,2674		161,828,923	65.0	64.0	64.0		2152	5.6	1.0	13	dbSNP_119	64	1637,6601		154,1329,2636	yes	missense	COL4A2	NM_001846.2	74	315,2157,3559	TT,TC,CC		19.8713,30.0732,23.1056	probably-damaging	718/1713	111121620	2787,9275	1912	4119	6031	SO:0001583	missense	1284	exon28			CCAGGGCCCAGGG	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.2152C>T	13.37:g.111121620C>T	ENSP00000353654:p.Pro718Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	154	58	0.376623	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	418	0.19139194139194138	160	0.3252032520325203	83	0.2292817679558011	12	0.02097902097902098	163	0.21503957783641162	C	0.613	-0.824320	0.02755	0.300732	0.198713	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.94793	-3.52	5.57	5.57	0.84162	.	0.136981	0.33327	N	0.005022	T	0.00012	0.0000	M	0.66297	2.02	0.42507	P	0.007041999999999993	B	0.28400	0.21	B	0.28991	0.097	T	0.31971	-0.9924	9	0.08599	T	0.76	.	9.8067	0.40797	0.0:0.8463:0.0:0.1537	rs9583500;rs52830583;rs57845568;rs9583500	718	P08572	CO4A2_HUMAN	S	718	ENSP00000353654:P718S	ENSP00000257309:P718S	P	+	1	0	COL4A2	109919621	0.938000	0.31826	0.972000	0.41901	0.002000	0.02628	1.281000	0.33214	2.618000	0.88619	0.563000	0.77884	CCC	C|0.812;T|0.188	0.188	strong		0.602	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
KIAA1109	84162	hgsc.bcm.edu	37	4	123150286	123150286	+	Missense_Mutation	SNP	T	T	C	rs6848868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123150286T>C	ENST00000264501.4	+	25	3306	c.2933T>C	c.(2932-2934)aTt>aCt	p.I978T	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Missense_Mutation_p.I978T|KIAA1109_ENST00000388738.3_Missense_Mutation_p.I978T			Q2LD37	K1109_HUMAN	KIAA1109	978			I -> T (in dbSNP:rs6848868).		regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTGAGTTGTATTCCTGGGCCT	0.313													T|||	175	0.0349441	0.0295	0.0677	5008	,	,		16397	0.0		0.0835	False		,,,				2504	0.0051				p.I978T		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T2933C						PASS	.	T	THR/ILE	146,3546		2,142,1702	198.0	181.0	186.0		2933	5.3	1.0	4	dbSNP_116	186	746,7442		34,678,3382	yes	missense	KIAA1109	NM_015312.3	89	36,820,5084	CC,CT,TT		9.1109,3.9545,7.5084	benign	978/5006	123150286	892,10988	1846	4094	5940	SO:0001583	missense	84162	exon23			GTTGTATTCCTGG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2933T>C	4.37:g.123150286T>C	ENSP00000264501:p.Ile978Thr	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	108	0.04945054945054945	18	0.036585365853658534	29	0.08011049723756906	0	0.0	61	0.08047493403693931	T	10.64	1.407193	0.25378	0.039545	0.091109	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637;ENST00000449251	T;T;T;T	0.49139	0.79;0.79;0.79;0.81	5.33	5.33	0.75918	.	1.589940	0.04402	N	0.364430	T	0.01320	0.0043	N	0.14661	0.345	0.32948	P	0.48066	B	0.12013	0.005	B	0.14023	0.01	T	0.06917	-1.0800	9	0.22706	T	0.39	.	8.009	0.30342	0.1341:0.0:0.1399:0.726	rs6848868;rs6848868	978	Q2LD37	K1109_HUMAN	T	978;978;978;143	ENSP00000264501:I978T;ENSP00000373390:I978T;ENSP00000389925:I978T;ENSP00000413018:I143T	ENSP00000264501:I978T	I	+	2	0	KIAA1109	123369736	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.210000	0.65214	2.131000	0.65755	0.459000	0.35465	ATT	T|0.937;C|0.063	0.063	strong		0.313	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
MOXD1	26002	hgsc.bcm.edu	37	6	132722527	132722527	+	Silent	SNP	G	G	A	rs77906164	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:132722527G>A	ENST00000367963.3	-	1	157	c.39C>T	c.(37-39)ctC>ctT	p.L13L	MOXD1_ENST00000392401.3_Silent_p.L13L	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	13						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		CCGTCCCGGGGAGCAGCCCCC	0.746													G|||	486	0.0970447	0.034	0.1037	5008	,	,		7906	0.002		0.2097	False		,,,				2504	0.1595				p.L13L		Atlas-SNP	.											.	MOXD1	136	.	0			c.C39T						PASS	.	G		227,3493		9,209,1642	3.0	4.0	4.0		39	1.3	1.0	6	dbSNP_131	4	1403,6167		112,1179,2494	no	coding-synonymous	MOXD1	NM_015529.2		121,1388,4136	AA,AG,GG		18.5337,6.1022,14.4376		13/614	132722527	1630,9660	1860	3785	5645	SO:0001819	synonymous_variant	26002	exon1			CCCGGGGAGCAGC	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.39C>T	6.37:g.132722527G>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_015529	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Silent	SNP	ENST00000367963.3	37	CCDS5152.2																																																																																			G|0.888;A|0.112	0.112	strong		0.746	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529	
CPXM2	119587	hgsc.bcm.edu	37	10	125528048	125528048	+	Silent	SNP	G	G	A	rs1219725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	18	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	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	
STAP1	26228	hgsc.bcm.edu	37	4	68447040	68447040	+	Silent	SNP	C	C	T	rs11556615	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:68447040C>T	ENST00000265404.2	+	5	463	c.381C>T	c.(379-381)aaC>aaT	p.N127N	STAP1_ENST00000396225.1_Silent_p.N127N	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	127					intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						TTCCCCAAAACGTGTCACTCC	0.423													T|||	631	0.125998	0.1135	0.1628	5008	,	,		20180	0.005		0.2475	False		,,,				2504	0.1166				p.N127N		Atlas-SNP	.											.	STAP1	46	.	0			c.C381T						PASS	.	T		624,3782	768.4+/-413.6	47,530,1626	131.0	123.0	126.0		381	-2.2	0.7	4	dbSNP_120	126	2294,6306	705.6+/-405.5	282,1730,2288	no	coding-synonymous	STAP1	NM_012108.2		329,2260,3914	TT,TC,CC		26.6744,14.1625,22.4358		127/296	68447040	2918,10088	2203	4300	6503	SO:0001819	synonymous_variant	26228	exon5			CCAAAACGTGTCA	AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"""SH2 domain containing"""	24133	protein-coding gene	gene with protein product	"""BCR downstream signaling 1"""	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.381C>T	4.37:g.68447040C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_012108	B2R980	Silent	SNP	ENST00000265404.2	37	CCDS3515.1																																																																																			T|0.162;G|0.138;C|0.673;A|0.027	0.162	strong		0.423	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1	NM_012108	
PSMG4	389362	hgsc.bcm.edu	37	6	3264487	3264487	+	Intron	SNP	T	T	C	rs4959786	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3264487T>C	ENST00000438998.2	+	2	379				PSMG4_ENST00000380306.4_Intron|PSMG4_ENST00000419065.2_Missense_Mutation_p.W99R|PSMG4_ENST00000380305.4_Intron|PSMG4_ENST00000451246.2_Intron|PSMG4_ENST00000473000.2_3'UTR	NM_001128591.1	NP_001122063.1	Q5JS54	PSMG4_HUMAN	proteasome (prosome, macropain) assembly chaperone 4											endometrium(1)	1						TGGCGTAGAGTGGGGATTAAG	0.582													C|||	3085	0.616014	0.2988	0.7651	5008	,	,		24518	0.6647		0.8429	False		,,,				2504	0.6554				p.W99R		Atlas-SNP	.											.	PSMG4	23	.	0			c.T295C						PASS	.	C	,ARG/TRP	519,865		94,331,267	253.0	195.0	212.0		,295	0.6	0.0	6	dbSNP_111	212	2557,625		1019,519,53	yes	intron,missense	PSMG4	NM_001128591.1,NM_001128592.1	,101	1113,850,320	CC,CT,TT		19.6417,37.5,32.6325	,benign	,99/163	3264487	3076,1490	692	1591	2283	SO:0001627	intron_variant	389362	exon3			GTAGAGTGGGGAT		CCDS47360.1, CCDS47361.1, CCDS47362.1	6p25.2	2010-06-23	2008-02-25	2008-02-25	ENSG00000180822	ENSG00000180822			21108	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 86"""	C6orf86		17707236	Standard	NM_001128591		Approved	PAC4	uc010jnl.1	Q5JS54	OTTHUMG00000014142	ENST00000438998.2:c.250+494T>C	6.37:g.3264487T>C		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_001128592	C9J2F8|F8WBZ2|Q5JS53|Q5JS56	Missense_Mutation	SNP	ENST00000438998.2	37	CCDS47361.1	1445	0.6616300366300366	159	0.3231707317073171	276	0.7624309392265194	369	0.6451048951048951	641	0.8456464379947229	C	0.006	-2.089720	0.00367	0.375	0.803583	ENSG00000180822	ENST00000419065	.	.	.	3.06	0.595	0.17490	.	.	.	.	.	T	0.07999	0.0200	N	0.08118	0	0.80722	P	0.0	B	0.17852	0.024	B	0.26969	0.075	T	0.33624	-0.9861	7	0.27785	T	0.31	.	6.8245	0.23874	0.0:0.2343:0.0:0.7657	rs4959786;rs4959786	99	C9J2F8	.	R	99	.	ENSP00000392353:W99R	W	+	1	0	PSMG4	3209486	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.297000	0.02759	-0.142000	0.11354	-2.444000	0.00210	TGG	A|0.000;C|0.620;T|0.380	0.620	strong		0.582	PSMG4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039678.2		
ATP2A3	489	hgsc.bcm.edu	37	17	3848013	3848013	+	Silent	SNP	A	A	C	rs1800911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3848013A>C	ENST00000352011.3	-	10	1326	c.1272T>G	c.(1270-1272)gcT>gcG	p.A424A	ATP2A3_ENST00000309890.7_Silent_p.A424A|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000397043.3_Silent_p.A424A|ATP2A3_ENST00000359983.3_Silent_p.A424A|ATP2A3_ENST00000397041.3_Silent_p.A424A|ATP2A3_ENST00000397035.3_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	129	0	0		WXS	Illumina HiSeq	Phase_I	107	107	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	
LLGL2	3993	hgsc.bcm.edu	37	17	73569211	73569211	+	Silent	SNP	C	C	T	rs376055189		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73569211C>T	ENST00000392550.3	+	20	2694	c.2577C>T	c.(2575-2577)taC>taT	p.Y859Y	LLGL2_ENST00000577200.1_Silent_p.Y859Y|LLGL2_ENST00000167462.5_Silent_p.Y859Y	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	859					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)			CCGAGGACTACGGGGAGCACC	0.662																																					p.Y859Y		Atlas-SNP	.											.	LLGL2	155	.	0			c.C2577T						PASS	.	C	,	1,4405		0,1,2202	59.0	50.0	53.0		2577,2577	-6.2	0.8	17		53	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	LLGL2	NM_001031803.1,NM_004524.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	859/1021,859/1016	73569211	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3993	exon20			GGACTACGGGGAG	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.2577C>T	17.37:g.73569211C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	179	81	0.452514	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			.	.	weak		0.662	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
MUC2	4583	hgsc.bcm.edu	37	11	1087972	1087972	+	Silent	SNP	C	C	T	rs10902088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1087972C>T	ENST00000441003.2	+	25	3474	c.3447C>T	c.(3445-3447)aaC>aaT	p.N1149N	MUC2_ENST00000359061.5_Silent_p.N1149N	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1149					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GGACCATCAACGGCATCCACT	0.622													C|||	1641	0.327676	0.3759	0.3631	5008	,	,		15887	0.3899		0.2167	False		,,,				2504	0.2873				p.N1149N		Atlas-SNP	.											.	MUC2	614	.	0			c.C3447T						PASS	.			1440,2836		247,946,945	56.0	61.0	60.0		3447	-2.9	0.0	11	dbSNP_120	60	1693,6791		174,1345,2723	no	coding-synonymous	MUC2	NM_002457.2		421,2291,3668	TT,TC,CC		19.9552,33.6763,24.5533		1149/2813	1087972	3133,9627	2138	4242	6380	SO:0001819	synonymous_variant	4583	exon25			CATCAACGGCATC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3447C>T	11.37:g.1087972C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.712;T|0.288	0.288	strong		0.622	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
KRT72	140807	hgsc.bcm.edu	37	12	52981442	52981442	+	Missense_Mutation	SNP	C	C	A	rs11170183	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52981442C>A	ENST00000537672.2	-	7	1293	c.1283G>T	c.(1282-1284)cGc>cTc	p.R428L	KRT72_ENST00000293745.2_Missense_Mutation_p.R428L|KRT72_ENST00000398066.3_Missense_Mutation_p.R240L|KRT72_ENST00000354310.4_Missense_Mutation_p.R386L	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	428	Coil 2.|Rod.		R -> L (in dbSNP:rs11170183). {ECO:0000269|PubMed:14702039}.			extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R428H(1)		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)		CAGCAGCTTGCGGTAGGTGGC	0.607													C|||	892	0.178115	0.0968	0.1527	5008	,	,		18427	0.0655		0.2416	False		,,,				2504	0.3569				p.R428L		Atlas-SNP	.											KRT72,caecum,carcinoma,0,2	KRT72	70	2	1	Substitution - Missense(1)	large_intestine(1)	c.G1283T						PASS	.	C	LEU/ARG,LEU/ARG,LEU/ARG	609,3797	267.1+/-267.6	46,517,1640	105.0	96.0	99.0		1283,1157,1283	4.0	1.0	12	dbSNP_120	99	2201,6399	375.7+/-337.9	277,1647,2376	no	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	102,102,102	323,2164,4016	AA,AC,CC		25.593,13.8221,21.6054	benign,benign,benign	428/512,386/470,428/512	52981442	2810,10196	2203	4300	6503	SO:0001583	missense	140807	exon7			AGCTTGCGGTAGG	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.1283G>T	12.37:g.52981442C>A	ENSP00000441160:p.Arg428Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	336	0.15384615384615385	52	0.10569105691056911	50	0.13812154696132597	39	0.06818181818181818	195	0.25725593667546176	C	18.06	3.539200	0.65085	0.138221	0.25593	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51	4.92	4.03	0.46877	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.44483	D	0.000445	T	0.00412	0.0013	H	0.99764	4.76	0.28550	P	0.9116638	B	0.18610	0.029	B	0.27076	0.076	T	0.48536	-0.9027	9	0.87932	D	0	.	14.1097	0.65113	0.0:0.926:0.0:0.074	rs11170183;rs52806663;rs11170183	428	Q14CN4	K2C72_HUMAN	L	428;428;386;240	ENSP00000441160:R428L;ENSP00000293745:R428L;ENSP00000346269:R386L;ENSP00000446151:R240L	ENSP00000293745:R428L	R	-	2	0	KRT72	51267709	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	4.630000	0.61297	1.383000	0.46405	0.650000	0.86243	CGC	C|0.804;A|0.196	0.196	strong		0.607	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
ARPC1B	10095	hgsc.bcm.edu	37	7	98984399	98984399	+	Silent	SNP	C	C	T	rs4765	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:98984399C>T	ENST00000451682.1	+	5	465	c.156C>T	c.(154-156)aaC>aaT	p.N52N	ARPC1B_ENST00000252725.5_Silent_p.N52N|ARPC1A_ENST00000432884.2_3'UTR|ARPC1B_ENST00000474880.1_3'UTR			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	52					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)			AGGAGCACAACGGGCAGGTGA	0.582													C|||	1159	0.23143	0.6974	0.1066	5008	,	,		20395	0.004		0.0825	False		,,,				2504	0.0777				p.N52N		Atlas-SNP	.											.	ARPC1B	41	.	0			c.C156T						PASS	.	C		2601,1805	639.7+/-397.2	766,1069,368	127.0	115.0	119.0		156	-5.5	0.7	7	dbSNP_52	119	502,8098	142.3+/-198.5	20,462,3818	no	coding-synonymous	ARPC1B	NM_005720.3		786,1531,4186	TT,TC,CC		5.8372,40.9669,23.8582		52/373	98984399	3103,9903	2203	4300	6503	SO:0001819	synonymous_variant	10095	exon3			GCACAACGGGCAG	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.156C>T	7.37:g.98984399C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	21	0.318182	NM_005720	Q9BU00	Silent	SNP	ENST00000451682.1	37	CCDS5661.1																																																																																			C|0.757;T|0.243	0.243	strong		0.582	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720	
AKR7A3	22977	hgsc.bcm.edu	37	1	19610598	19610598	+	Silent	SNP	A	A	G	rs116050237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19610598A>G	ENST00000361640.4	-	6	1266	c.726T>C	c.(724-726)ttT>ttC	p.F242F		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	242					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)		CAATGCCCTCAAAGTGGTGCT	0.652													G|||	155	0.0309505	0.0	0.0202	5008	,	,		16844	0.0476		0.0288	False		,,,				2504	0.0654				p.F242F		Atlas-SNP	.											.	AKR7A3	30	.	0			c.T726C						PASS	.	G		49,4349		2,45,2152	45.0	46.0	46.0		726	0.9	0.9	1	dbSNP_132	46	335,8265		10,315,3975	no	coding-synonymous	AKR7A3	NM_012067.2		12,360,6127	GG,GA,AA		3.8953,1.1141,2.9543		242/332	19610598	384,12614	2199	4300	6499	SO:0001819	synonymous_variant	22977	exon6			GCCCTCAAAGTGG	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.726T>C	1.37:g.19610598A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Silent	SNP	ENST00000361640.4	37	CCDS193.1																																																																																			A|0.973;G|0.027	0.027	strong		0.652	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
ZBTB42	100128927	hgsc.bcm.edu	37	14	105268104	105268104	+	Silent	SNP	G	G	A	rs10141867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105268104G>A	ENST00000342537.7	+	1	855	c.570G>A	c.(568-570)ctG>ctA	p.L190L	ZBTB42_ENST00000555360.1_Silent_p.L190L	NM_001137601.1	NP_001131073.1	B2RXF5	ZBT42_HUMAN	zinc finger and BTB domain containing 42	190	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CCCTGGACCTGTCGTTGAAGT	0.677													G|||	1092	0.218051	0.3064	0.2406	5008	,	,		17283	0.1022		0.2684	False		,,,				2504	0.1503				p.L190L		Atlas-SNP	.											ZBTB42_ENST00000342537,NS,carcinoma,0,2	ZBTB42	10	2	0			c.G570A						PASS	.	G		427,957		76,275,341	18.0	24.0	23.0		570	3.4	1.0	14	dbSNP_119	23	880,2288		123,634,827	no	coding-synonymous	ZBTB42	NM_001137601.1		199,909,1168	AA,AG,GG		27.7778,30.8526,28.7127		190/423	105268104	1307,3245	692	1584	2276	SO:0001819	synonymous_variant	100128927	exon2			GGACCTGTCGTTG	AX721091	CCDS45174.1	14q32.33	2013-01-09				ENSG00000179627		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	32550	protein-coding gene	gene with protein product		613915					Standard	NM_001137601		Approved	ZNF925	uc001ypp.3	B2RXF5		ENST00000342537.7:c.570G>A	14.37:g.105268104G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_001137601	B7ZW21	Silent	SNP	ENST00000342537.7	37	CCDS45174.1																																																																																			G|0.771;A|0.229	0.229	strong		0.677	ZBTB42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410372.1		
NEIL3	55247	hgsc.bcm.edu	37	4	178231152	178231152	+	Silent	SNP	C	C	A	rs10013040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:178231152C>A	ENST00000264596.3	+	1	163	c.45C>A	c.(43-45)cgC>cgA	p.R15R		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	15					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AGAAGATTCGCGCGCGGGTGC	0.677								Base excision repair (BER), DNA glycosylases					C|||	848	0.169329	0.1384	0.1744	5008	,	,		12488	0.1369		0.2177	False		,,,				2504	0.1912				p.R15R		Atlas-SNP	.											.	NEIL3	89	.	0			c.C45A						PASS	.	C		641,3763	266.2+/-267.1	43,555,1604	30.0	33.0	32.0		45	-1.0	0.6	4	dbSNP_119	32	1936,6664	333.4+/-320.5	196,1544,2560	no	coding-synonymous	NEIL3	NM_018248.2		239,2099,4164	AA,AC,CC		22.5116,14.555,19.817		15/606	178231152	2577,10427	2202	4300	6502	SO:0001819	synonymous_variant	55247	exon1			GATTCGCGCGCGG	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.45C>A	4.37:g.178231152C>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																			C|0.815;A|0.184	0.184	strong		0.677	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
EFR3A	23167	hgsc.bcm.edu	37	8	132999936	132999936	+	Silent	SNP	A	A	G	rs2270875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:132999936A>G	ENST00000254624.5	+	18	2277	c.2052A>G	c.(2050-2052)gtA>gtG	p.V684V	EFR3A_ENST00000334503.4_Silent_p.V684V|EFR3A_ENST00000519656.1_Silent_p.V648V	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	684						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.V684V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTCCGTATGTACCACAAGTAA	0.353													A|||	662	0.132188	0.034	0.1513	5008	,	,		15583	0.1587		0.1064	False		,,,				2504	0.2505				p.V684V		Atlas-SNP	.											EFR3A,rectum,carcinoma,0,2	EFR3A	96	2	1	Substitution - coding silent(1)	stomach(1)	c.A2052G						PASS	.	A		198,4204	115.4+/-153.4	6,186,2009	93.0	76.0	81.0		2052	-6.3	0.8	8	dbSNP_100	81	1013,7583	201.3+/-244.8	55,903,3340	no	coding-synonymous	EFR3A	NM_015137.4		61,1089,5349	GG,GA,AA		11.7846,4.498,9.3168		684/822	132999936	1211,11787	2201	4298	6499	SO:0001819	synonymous_variant	23167	exon18			GTATGTACCACAA	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.2052A>G	8.37:g.132999936A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	37	CCDS34942.2																																																																																			A|0.899;G|0.101	0.101	strong		0.353	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	
BCL10	8915	hgsc.bcm.edu	37	1	85733328	85733328	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:85733328A>G	ENST00000370580.1	-	3	1421	c.684T>C	c.(682-684)cgT>cgC	p.R228R		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	228					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)			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)		GTGAAACAGTACGTGATCTTA	0.363			T	IGH@	MALT																																p.R228R	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.T684C						PASS	.						62.0	65.0	64.0					1																	85733328		2203	4300	6503	SO:0001819	synonymous_variant	8915	exon3			AACAGTACGTGAT	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.684T>C	1.37:g.85733328A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	4	0.0597015	NM_003921	Q5VUF1	Silent	SNP	ENST00000370580.1	37	CCDS704.1																																																																																			.	.	none		0.363	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
CDC25B	994	hgsc.bcm.edu	37	20	3783764	3783764	+	Silent	SNP	C	C	T	rs2228464	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3783764C>T	ENST00000245960.5	+	13	1964	c.1267C>T	c.(1267-1269)Cta>Tta	p.L423L	CDC25B_ENST00000340833.4_Silent_p.L382L|CDC25B_ENST00000379598.5_Silent_p.L332L|CDC25B_ENST00000439880.2_Silent_p.L409L|CDC25B_ENST00000344256.6_Silent_p.L359L|CDC25B_ENST00000467519.1_3'UTR	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	423					female meiosis I (GO:0007144)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|oocyte maturation (GO:0001556)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein kinase activity (GO:0045860)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(1)	18						GATGGTGGCCCTATTGACGGG	0.552													C|||	145	0.0289537	0.0061	0.0331	5008	,	,		21658	0.005		0.0795	False		,,,				2504	0.0297				p.L423L		Atlas-SNP	.											.	CDC25B	76	.	0			c.C1267T						PASS	.	C	,,	77,4329	68.1+/-105.8	2,73,2128	81.0	70.0	73.0		1225,1144,1267	1.5	1.0	20	dbSNP_98	73	598,8002	157.5+/-211.1	19,560,3721	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC25B	NM_004358.3,NM_021872.2,NM_021873.2	,,	21,633,5849	TT,TC,CC		6.9535,1.7476,5.1899	,,	409/567,382/540,423/581	3783764	675,12331	2203	4300	6503	SO:0001819	synonymous_variant	994	exon13			GTGGCCCTATTGA		CCDS13065.1, CCDS13066.1, CCDS13067.1, CCDS74700.1, CCDS74701.1	20p13	2013-01-17	2013-01-17		ENSG00000101224	ENSG00000101224		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"""	1726	protein-coding gene	gene with protein product		116949	"""cell division cycle 25B"", ""cell division cycle 25 homolog B (S. cerevisiae)"", ""cell division cycle 25 homolog B (S. pombe)"""			1836978	Standard	NM_021873		Approved		uc002wjn.3	P30305	OTTHUMG00000031764	ENST00000245960.5:c.1267C>T	20.37:g.3783764C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_021873	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	Silent	SNP	ENST00000245960.5	37	CCDS13067.1																																																																																			C|0.955;T|0.045	0.045	strong		0.552	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077779.2	NM_021874	
DOC2B	8447	hgsc.bcm.edu	37	17	6115	6115	+	Silent	SNP	G	G	C	rs61739713	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:6115G>C	ENST00000343572.7	-	6	975	c.819C>G	c.(817-819)tcC>tcG	p.S273S	AC108004.5_ENST00000583926.1_RNA	NM_003585.3	NP_003576	Q14184	DOC2B_HUMAN	double C2-like domains, beta	273	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Mediates interaction with STXBP3. {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						TGTACTTGAGGGAGATGAGGA	0.632													G|||	3628	0.724441	0.5212	0.804	5008	,	,		18786	0.8591		0.7326	False		,,,				2504	0.7955				p.S273S		Atlas-SNP	.											.	DOC2B	6	.	0			c.C819G						PASS	.	G		796,588		227,342,123	87.0	97.0	94.0		819	1.5	1.0	17	dbSNP_129	94	2343,839		864,615,112	no	coding-synonymous	DOC2B	NM_003585.3		1091,957,235	CC,CG,GG		26.3671,42.4855,31.2527		273/413	6115	3139,1427	692	1591	2283	SO:0001819	synonymous_variant	8447	exon6			CTTGAGGGAGATG	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.819C>G	17.37:g.6115G>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_003585		Silent	SNP	ENST00000343572.7	37																																																																																				T|0.000;G|0.259;C|0.741	0.741	strong		0.632	DOC2B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335122.3	NM_003585	
PTPRH	5794	hgsc.bcm.edu	37	19	55710074	55710074	+	Missense_Mutation	SNP	G	G	A	rs16986309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55710074G>A	ENST00000376350.3	-	8	1649	c.1627C>T	c.(1627-1629)Ctc>Ttc	p.L543F	PTPRH_ENST00000263434.5_Missense_Mutation_p.L365F|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	543	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.		L -> F (in dbSNP:rs16986309).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CAGACGGTGAGGTGGTACAGG	0.572													G|||	464	0.0926518	0.1278	0.1095	5008	,	,		19650	0.0099		0.1213	False		,,,				2504	0.089				p.L543F		Atlas-SNP	.											.	PTPRH	139	.	0			c.C1627T						PASS	.	G	PHE/LEU,PHE/LEU	595,3811	260.7+/-263.8	41,513,1649	163.0	132.0	142.0		1093,1627	-0.3	0.0	19	dbSNP_123	142	996,7604	214.6+/-254.2	57,882,3361	yes	missense,missense	PTPRH	NM_001161440.1,NM_002842.3	22,22	98,1395,5010	AA,AG,GG		11.5814,13.5043,12.2328	benign,benign	365/938,543/1116	55710074	1591,11415	2203	4300	6503	SO:0001583	missense	5794	exon8			CGGTGAGGTGGTA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1627C>T	19.37:g.55710074G>A	ENSP00000365528:p.Leu543Phe	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	224	0.10256410256410256	75	0.1524390243902439	50	0.13812154696132597	0	0.0	99	0.13060686015831136	G	0.093	-1.164239	0.01673	0.135043	0.115814	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.52754	0.65;0.65	2.27	-0.302	0.12796	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00109	0.0003	N	0.05124	-0.11	0.80722	P	0.0	B;B;B	0.12630	0.006;0.005;0.004	B;B;B	0.17433	0.018;0.01;0.004	T	0.20207	-1.0282	8	0.12766	T	0.61	.	1.6305	0.02732	0.4856:0.0:0.2259:0.2886	rs16986309;rs52822550;rs58326738;rs16986309	365;365;543	C9JCH2;Q9HD43-2;Q9HD43	.;.;PTPRH_HUMAN	F	543;365	ENSP00000365528:L543F;ENSP00000263434:L365F	ENSP00000263434:L365F	L	-	1	0	PTPRH	60401886	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	0.009000	0.13219	-0.107000	0.12088	0.561000	0.74099	CTC	G|0.884;A|0.116	0.116	strong		0.572	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
PSKH2	85481	hgsc.bcm.edu	37	8	87076520	87076520	+	Missense_Mutation	SNP	C	C	A	rs6998760	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87076520C>A	ENST00000276616.2	-	2	600	c.526G>T	c.(526-528)Gcg>Tcg	p.A176S	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> S (in dbSNP:rs6998760). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A176S(1)		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)			ATCTGCAGCGCATGCAAATAC	0.438													C|||	1481	0.295727	0.0885	0.2911	5008	,	,		19925	0.4415		0.3698	False		,,,				2504	0.3528				p.A176S		Atlas-SNP	.											PSKH2,NS,carcinoma,0,1	PSKH2	79	1	1	Substitution - Missense(1)	stomach(1)	c.G526T						PASS	.	C	SER/ALA	521,3885	236.1+/-248.4	35,451,1717	67.0	71.0	69.0		526	-3.3	0.0	8	dbSNP_116	69	3101,5499	473.3+/-368.6	554,1993,1753	yes	missense	PSKH2	NM_033126.1	99	589,2444,3470	AA,AC,CC		36.0581,11.8248,27.8487	benign	176/386	87076520	3622,9384	2203	4300	6503	SO:0001583	missense	85481	exon2			GCAGCGCATGCAA	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.526G>T	8.37:g.87076520C>A	ENSP00000276616:p.Ala176Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	713	0.32646520146520147	48	0.0975609756097561	114	0.3149171270718232	271	0.4737762237762238	280	0.36939313984168864	C	0.004	-2.272117	0.00257	0.118248	0.360581	ENSG00000147613	ENST00000276616	T	0.35421	1.31	5.69	-3.35	0.04928	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	0.01779	-0.725	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.44174	-0.9345	8	0.02654	T	1	.	12.4195	0.55512	0.0:0.3184:0.0:0.6816	rs6998760;rs52821427;rs58447935;rs6998760	176	Q96QS6	KPSH2_HUMAN	S	176	ENSP00000276616:A176S	ENSP00000276616:A176S	A	-	1	0	PSKH2	87145636	0.357000	0.24938	0.000000	0.03702	0.005000	0.04900	0.430000	0.21428	-0.517000	0.06461	-1.910000	0.00522	GCG	C|0.705;A|0.295	0.295	strong		0.438	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
HPS3	84343	hgsc.bcm.edu	37	3	148863151	148863151	+	Silent	SNP	A	A	G	rs11718908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148863151A>G	ENST00000296051.2	+	5	1121	c.981A>G	c.(979-981)acA>acG	p.T327T	HPS3_ENST00000460120.1_Silent_p.T162T	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	327					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)			GTTCTCTTACATCTGATGGAA	0.348									Hermansky-Pudlak syndrome				G|||	1390	0.277556	0.4546	0.2363	5008	,	,		18776	0.1706		0.1998	False		,,,				2504	0.2577				p.T327T		Atlas-SNP	.											HPS3,NS,carcinoma,+1,1	HPS3	104	1	0			c.A981G						PASS	.	G		1887,2519	621.7+/-393.8	406,1075,722	91.0	97.0	95.0		981	1.1	0.0	3	dbSNP_120	95	1849,6751	729.2+/-406.7	186,1477,2637	no	coding-synonymous	HPS3	NM_032383.3		592,2552,3359	GG,GA,AA		21.5,42.828,28.7252		327/1005	148863151	3736,9270	2203	4300	6503	SO:0001819	synonymous_variant	84343	exon5	Familial Cancer Database	HPS, HPS1-8	TCTTACATCTGAT	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.981A>G	3.37:g.148863151A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1																																																																																			A|0.725;G|0.275	0.275	strong		0.348	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
Unknown	0	hgsc.bcm.edu	37	1	144619346	144619346	+	IGR	SNP	G	G	A	rs4649563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:144619346G>A								RP11-640M9.2 (13455 upstream) : NBPF9 (192397 downstream)																							TGTATTTATAGAAAATGACGA	0.423													.|||	2809	0.560903	0.2436	0.6196	5008	,	,		25951	0.7986		0.5288	False		,,,				2504	0.7362				.		Atlas-SNP	.											.	NBPF9	88	.	0			c.492-1G>A						PASS	.																																			SO:0001628	intergenic_variant	400818	exon5			TTTATAGAAAATG																													1.37:g.144619346G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	40	13	0.325	NM_001037675		Splice_Site	SNP		37																																																																																				G|0.580;A|0.420	0.420	strong	0	0.423								
FMN2	56776	hgsc.bcm.edu	37	1	240370934	240370934	+	Missense_Mutation	SNP	G	G	C	rs71170718|rs4997328|rs562038978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240370934G>C	ENST00000319653.9	+	5	3052	c.2822G>C	c.(2821-2823)gGa>gCa	p.G941A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	941	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCCGGAGCGGGAATACCTCCT	0.706													G|||	1385	0.276558	0.3616	0.1902	5008	,	,		7542	0.3115		0.2276	False		,,,				2504	0.2372				p.G941A		Atlas-SNP	.											FMN2,NS,carcinoma,0,3	FMN2	451	3	0			c.G2822C						PASS	.						25.0	31.0	29.0					1																	240370934		2135	4205	6340	SO:0001583	missense	56776	exon5			GAGCGGGAATACC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2822G>C	1.37:g.240370934G>C	ENSP00000318884:p.Gly941Ala	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	142	28	0.197183	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	510	0.23351648351648352	149	0.30284552845528456	59	0.16298342541436464	154	0.2692307692307692	148	0.19525065963060687	G	6.179	0.401283	0.11696	.	.	ENSG00000155816	ENST00000319653	T	0.51574	0.7	3.52	2.6	0.31112	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.28291	0.206	B	0.31869	0.137	T	0.28618	-1.0038	7	.	.	.	.	8.7591	0.34663	0.0:0.2724:0.5786:0.149	rs4997328	941	Q9NZ56	FMN2_HUMAN	A	941	ENSP00000318884:G941A	.	G	+	2	0	FMN2	238437557	0.024000	0.19004	0.019000	0.16419	0.001000	0.01503	0.529000	0.23019	1.071000	0.40834	-0.415000	0.06103	GGA	G|0.781;C|0.219	0.219	strong		0.706	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
ZNF845	91664	hgsc.bcm.edu	37	19	53848779	53848779	+	Silent	SNP	T	T	C	rs75887836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53848779T>C	ENST00000595091.1	+	4	255	c.36T>C	c.(34-36)gaT>gaC	p.D12D	ZNF845_ENST00000458035.1_Silent_p.D12D			Q96IR2	ZN845_HUMAN	zinc finger protein 845	12	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						CATTCAGGGATGTGGCCATAG	0.443													.|||	673	0.134385	0.1536	0.0893	5008	,	,		18186	0.1617		0.1083	False		,,,				2504	0.1391				p.D12D		Atlas-SNP	.											.	ZNF845	101	.	0			c.T36C						PASS	.	C		194,1190		11,172,509	87.0	83.0	84.0		36	-0.7	0.8	19	dbSNP_131	84	316,2866		22,272,1297	no	coding-synonymous	ZNF845	NM_138374.1		33,444,1806	CC,CT,TT		9.9309,14.0173,11.1695		12/971	53848779	510,4056	692	1591	2283	SO:0001819	synonymous_variant	91664	exon3			CAGGGATGTGGCC	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.36T>C	19.37:g.53848779T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			T|0.880;C|0.120	0.120	strong		0.443	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
HERC6	55008	hgsc.bcm.edu	37	4	89300241	89300241	+	Silent	SNP	C	C	A	rs61978650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:89300241C>A	ENST00000264346.7	+	1	227	c.168C>A	c.(166-168)ggC>ggA	p.G56G	HERC6_ENST00000273960.3_Silent_p.G56G|HERC6_ENST00000380265.5_Silent_p.G56G	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	56					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		GTCAGCTGGGCCGCAGGGGCG	0.721													C|||	518	0.103435	0.0938	0.1297	5008	,	,		12109	0.0357		0.1799	False		,,,				2504	0.089				p.G56G		Atlas-SNP	.											.	HERC6	104	.	0			c.C168A						PASS	.						3.0	4.0	3.0					4																	89300241		1638	3675	5313	SO:0001819	synonymous_variant	55008	exon1			GCTGGGCCGCAGG	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.168C>A	4.37:g.89300241C>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	24	17	0.708333	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Silent	SNP	ENST00000264346.7	37	CCDS47098.1	266	0.12179487179487179	55	0.11178861788617886	53	0.1464088397790055	17	0.02972027972027972	141	0.18601583113456466	C	4.468	0.086782	0.08583	.	.	ENSG00000138642	ENST00000502870	.	.	.	3.8	1.98	0.26296	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999903432	.	.	.	.	.	.	T	0.06917	-1.0800	3	.	.	.	.	12.2098	0.54373	0.0:0.6693:0.3307:0.0	rs61978650	.	.	.	D	9	.	.	A	+	2	0	HERC6	89519265	0.957000	0.32711	0.630000	0.29268	0.289000	0.27227	1.715000	0.37971	0.244000	0.21351	0.313000	0.20887	GCC	C|0.875;A|0.125	0.125	strong		0.721	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
MUC2	4583	hgsc.bcm.edu	37	11	1081074	1081074	+	Splice_Site	SNP	T	T	C	rs41411848	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1081074T>C	ENST00000441003.2	+	11	1397	c.1370T>C	c.(1369-1371)gTg>gCg	p.V457A	MUC2_ENST00000359061.5_Splice_Site_p.V457A	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	457	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TCCCTGCAGGTGGTGGTCTTC	0.657													T|||	1816	0.36262	0.4206	0.366	5008	,	,		16156	0.372		0.2207	False		,,,				2504	0.4182				p.V457A		Atlas-SNP	.											.	MUC2	614	.	0			c.T1370C						PASS	.	T	ALA/VAL	1534,2400		311,912,744	39.0	45.0	43.0		1370	2.2	1.0	11	dbSNP_127	43	1706,6598		183,1340,2629	no	missense-near-splice	MUC2	NM_002457.2	64	494,2252,3373	CC,CT,TT		20.5443,38.9934,26.4749	benign	457/2813	1081074	3240,8998	1967	4152	6119	SO:0001630	splice_region_variant	4583	exon11			TGCAGGTGGTGGT	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.1369-1T>C	11.37:g.1081074T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		678	0.31043956043956045	185	0.37601626016260165	108	0.2983425414364641	222	0.3881118881118881	163	0.21503957783641162	T	8.556	0.876751	0.17395	0.389934	0.205443	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.65549	-0.16;-0.16	3.43	2.25	0.28309	.	0.231656	0.26470	U	0.024184	T	0.00012	0.0000	.	.	.	0.34554	P	0.28835500000000003	B	0.33379	0.41	B	0.41174	0.349	T	0.40156	-0.9578	8	0.39692	T	0.17	.	7.978	0.30166	0.0:0.1046:0.0:0.8954	rs41411848;rs61738283	457	E7EUV1	.	A	457	ENSP00000415183:V457A;ENSP00000351956:V457A	ENSP00000351956:V457A	V	+	2	0	MUC2	1071074	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	2.109000	0.41863	1.441000	0.47550	0.358000	0.22013	GTG	T|0.714;C|0.286	0.286	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Missense_Mutation
ZNF462	58499	hgsc.bcm.edu	37	9	109689752	109689752	+	Missense_Mutation	SNP	C	C	T	rs3814541	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:109689752C>T	ENST00000277225.5	+	3	3848	c.3559C>T	c.(3559-3561)Cct>Tct	p.P1187S	ZNF462_ENST00000441147.2_Missense_Mutation_p.P32S|ZNF462_ENST00000457913.1_Missense_Mutation_p.P1187S			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1187			P -> S (in dbSNP:rs3814541).		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						AGATGGCCCTCCTGTGGAGAA	0.552													C|||	519	0.103634	0.0151	0.0908	5008	,	,		12475	0.0794		0.162	False		,,,				2504	0.1973				p.P1187S		Atlas-SNP	.											.	ZNF462	322	.	0			c.C3559T						PASS	.	C	SER/PRO	134,4272	96.2+/-134.9	2,130,2071	201.0	204.0	203.0		3559	5.4	1.0	9	dbSNP_107	203	1253,7347	251.2+/-277.8	79,1095,3126	yes	missense	ZNF462	NM_021224.4	74	81,1225,5197	TT,TC,CC		14.5698,3.0413,10.6643	possibly-damaging	1187/2507	109689752	1387,11619	2203	4300	6503	SO:0001583	missense	58499	exon3			GGCCCTCCTGTGG	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.3559C>T	9.37:g.109689752C>T	ENSP00000277225:p.Pro1187Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	228	0.1043956043956044	9	0.018292682926829267	41	0.1132596685082873	45	0.07867132867132867	133	0.17546174142480211	C	10.38	1.335080	0.24253	0.030413	0.145698	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.05649	3.41;3.85;3.78;3.93	5.37	5.37	0.77165	.	0.224101	0.47852	D	0.000218	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	1.0	B;B	0.21905	0.062;0.004	B;B	0.23419	0.046;0.002	T	0.29701	-1.0003	9	0.42905	T	0.14	.	13.4114	0.60944	0.0:0.9246:0.0:0.0754	rs3814541;rs59869283;rs3814541	1187;1187	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	S	1187;1187;70;32	ENSP00000277225:P1187S;ENSP00000414570:P1187S;ENSP00000363818:P70S;ENSP00000397306:P32S	ENSP00000277225:P1187S	P	+	1	0	ZNF462	108729573	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	3.028000	0.49705	2.513000	0.84729	0.561000	0.74099	CCT	C|0.898;T|0.102	0.102	strong		0.552	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
ZMYM4	9202	hgsc.bcm.edu	37	1	35847032	35847032	+	Missense_Mutation	SNP	G	G	A	rs34924462	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:35847032G>A	ENST00000314607.6	+	8	1434	c.1354G>A	c.(1354-1356)Gtt>Att	p.V452I	ZMYM4_ENST00000373297.2_Missense_Mutation_p.V452I	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	452			V -> I (in dbSNP:rs34924462). {ECO:0000269|PubMed:9455477}.		cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GAAGAATGCTGTTGTAAGTTA	0.353													G|||	48	0.00958466	0.0015	0.0187	5008	,	,		21566	0.0		0.0268	False		,,,				2504	0.0061				p.V452I		Atlas-SNP	.											.	ZMYM4	143	.	0			c.G1354A						PASS	.	G	ILE/VAL	37,4369	41.6+/-74.8	0,37,2166	80.0	71.0	74.0		1354	5.3	1.0	1	dbSNP_126	74	299,8301	109.2+/-169.8	5,289,4006	yes	missense	ZMYM4	NM_005095.2	29	5,326,6172	AA,AG,GG		3.4767,0.8398,2.5834	possibly-damaging	452/1549	35847032	336,12670	2203	4300	6503	SO:0001583	missense	9202	exon8			AATGCTGTTGTAA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.1354G>A	1.37:g.35847032G>A	ENSP00000322915:p.Val452Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	31|31	0.014194139194139194|0.014194139194139194	0|0	0.0|0.0	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	23|23	0.030343007915567283|0.030343007915567283	G|G	27.9|27.9	4.870837|4.870837	0.91587|0.91587	0.008398|0.008398	0.034767|0.034767	ENSG00000146463|ENSG00000146463	ENST00000457946|ENST00000314607;ENST00000373297	.|T;T	.|0.24350	.|1.95;1.86	5.31|5.31	5.31|5.31	0.75309|0.75309	.|TRASH (1);	.|0.133540	.|0.50627	.|D	.|0.000107	T|T	0.07773|0.07773	0.0195|0.0195	N|N	0.22421|0.22421	0.69|0.69	0.22500|0.22500	N|N	0.999041|0.999041	.|B	.|0.19200	.|0.034	.|B	.|0.24394	.|0.053	T|T	0.06250|0.06250	-1.0837|-1.0837	5|10	.|0.33940	.|T	.|0.23	-7.3083|-7.3083	18.9703|18.9703	0.92712|0.92712	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs34924462;rs61750998|rs34924462;rs61750998	.|452	.|Q5VZL5	.|ZMYM4_HUMAN	Y|I	200|452	.|ENSP00000322915:V452I;ENSP00000362394:V452I	.|ENSP00000322915:V452I	C|V	+|+	2|1	0|0	ZMYM4|ZMYM4	35619619|35619619	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	4.554000|4.554000	0.60760|0.60760	2.487000|2.487000	0.83934|0.83934	0.591000|0.591000	0.81541|0.81541	TGT|GTT	G|0.979;A|0.021	0.021	strong		0.353	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	
ZADH2	284273	hgsc.bcm.edu	37	18	72914280	72914280	+	Silent	SNP	G	G	A	rs7230037	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:72914280G>A	ENST00000322342.3	-	2	514	c.225C>T	c.(223-225)aaC>aaT	p.N75N	ZADH2_ENST00000537114.2_De_novo_Start_OutOfFrame	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	75						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		TGTCAGATGCGTTAACACCAA	0.428													G|||	1490	0.297524	0.056	0.3948	5008	,	,		20046	0.4563		0.4493	False		,,,				2504	0.2352				p.N75N		Atlas-SNP	.											.	ZADH2	25	.	0			c.C225T						PASS	.	G		560,3846	250.3+/-257.4	49,462,1692	68.0	65.0	66.0		225	-7.8	0.1	18	dbSNP_116	66	3514,5086	513.9+/-378.3	717,2080,1503	no	coding-synonymous	ZADH2	NM_175907.4		766,2542,3195	AA,AG,GG		40.8605,12.7099,31.324		75/378	72914280	4074,8932	2203	4300	6503	SO:0001819	synonymous_variant	284273	exon2			AGATGCGTTAACA	BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.225C>T	18.37:g.72914280G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_175907	A8KA15|B4DZ91	Silent	SNP	ENST00000322342.3	37	CCDS12008.1																																																																																			G|0.687;A|0.313	0.313	strong		0.428	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907	
TIGD2	166815	hgsc.bcm.edu	37	4	90035549	90035549	+	Missense_Mutation	SNP	A	A	G	rs2280099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:90035549A>G	ENST00000317005.2	+	1	1582	c.1424A>G	c.(1423-1425)cAt>cGt	p.H475R	RP11-84C13.1_ENST00000603357.1_lincRNA|FAM13A_ENST00000502459.1_5'Flank	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	475			H -> R (in dbSNP:rs2280099).			nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		CCAGAGAAGCATATTAGCCAT	0.423													A|||	611	0.122005	0.0121	0.1066	5008	,	,		18799	0.1647		0.1918	False		,,,				2504	0.1656				p.H475R		Atlas-SNP	.											.	TIGD2	36	.	0			c.A1424G						PASS	.	A	ARG/HIS	191,4215	119.6+/-157.3	6,179,2018	52.0	52.0	52.0		1424	3.3	1.0	4	dbSNP_100	52	1522,7078	281.8+/-295.3	137,1248,2915	yes	missense	TIGD2	NM_145715.2	29	143,1427,4933	GG,GA,AA		17.6977,4.335,13.1708	probably-damaging	475/526	90035549	1713,11293	2203	4300	6503	SO:0001583	missense	166815	exon1			AGAAGCATATTAG	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.1424A>G	4.37:g.90035549A>G	ENSP00000317170:p.His475Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	132	76	0.575758	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	37	CCDS3633.1	274	0.12545787545787546	7	0.014227642276422764	38	0.10497237569060773	96	0.16783216783216784	133	0.17546174142480211	A	13.12	2.141726	0.37825	0.04335	0.176977	ENSG00000180346	ENST00000317005	T	0.22539	1.95	4.49	3.28	0.37604	.	0.479025	0.17418	N	0.174951	T	0.00039	0.0001	L	0.50333	1.59	0.37050	P	0.10244699999999995	D	0.53462	0.96	P	0.51701	0.677	T	0.10428	-1.0630	9	0.10377	T	0.69	-1.9981	7.153	0.25622	0.801:0.0:0.0:0.199	rs2280099;rs17821016;rs58960369;rs2280099	475	Q4W5G0	TIGD2_HUMAN	R	475	ENSP00000317170:H475R	ENSP00000317170:H475R	H	+	2	0	TIGD2	90254572	0.886000	0.30341	1.000000	0.80357	0.942000	0.58702	0.941000	0.29005	0.729000	0.32403	0.383000	0.25322	CAT	G|0.132;N|0.000	0.132	strong		0.423	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715	
RICTOR	253260	hgsc.bcm.edu	37	5	38953634	38953634	+	Missense_Mutation	SNP	G	G	A	rs146765449	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:38953634G>A	ENST00000357387.3	-	28	2749	c.2719C>T	c.(2719-2721)Cgt>Tgt	p.R907C	RICTOR_ENST00000296782.5_Missense_Mutation_p.R907C|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)					CGAACATTACGACAGAGTTCT	0.284													G|||	4	0.000798722	0.0	0.0	5008	,	,		10912	0.0		0.002	False		,,,				2504	0.002				p.R907C		Atlas-SNP	.											.	RICTOR	182	.	0			c.C2719T						PASS	.	G	CYS/ARG	3,4397	6.2+/-15.9	0,3,2197	95.0	104.0	101.0		2719	3.2	1.0	5	dbSNP_134	101	36,8552	23.4+/-69.3	0,36,4258	yes	missense	RICTOR	NM_152756.3	180	0,39,6455	AA,AG,GG		0.4192,0.0682,0.3003	possibly-damaging	907/1709	38953634	39,12949	2200	4294	6494	SO:0001583	missense	253260	exon28			CATTACGACAGAG		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.2719C>T	5.37:g.38953634G>A	ENSP00000349959:p.Arg907Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.11	2.140773	0.37825	6.82E-4	0.004192	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.66638	-0.22;-0.22	5.38	3.2	0.36748	Armadillo-type fold (1);	0.216053	0.49916	D	0.000125	T	0.46908	0.1417	N	0.14661	0.345	0.30574	N	0.763163	P;P	0.48764	0.915;0.608	P;B	0.45138	0.471;0.123	T	0.53989	-0.8360	10	0.87932	D	0	-0.1339	3.4177	0.07381	0.3517:0.2231:0.4252:0.0	.	907;907	Q6R327;Q6R327-3	RICTR_HUMAN;.	C	907	ENSP00000349959:R907C;ENSP00000296782:R907C	ENSP00000296782:R907C	R	-	1	0	RICTOR	38989391	1.000000	0.71417	0.973000	0.42090	0.822000	0.46500	5.393000	0.66279	1.392000	0.46585	0.591000	0.81541	CGT	G|0.997;A|0.003	0.003	strong		0.284	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
FCGR1B	2210	hgsc.bcm.edu	37	1	120930088	120930088	+	Missense_Mutation	SNP	C	C	T	rs148290064	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:120930088C>T	ENST00000369384.4	-	4	555	c.513G>A	c.(511-513)atG>atA	p.M171I	FCGR1B_ENST00000369383.4_Missense_Mutation_p.M79I|RP11-439A17.10_ENST00000426275.1_RNA|FCGR1B_ENST00000472543.1_5'UTR|RP11-439A17.9_ENST00000457996.1_RNA	NM_001017986.3	NP_001017986.1	Q92637	FCGRB_HUMAN	Fc fragment of IgG, high affinity Ib, receptor (CD64)	171	Ig-like C2-type 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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|Fc receptor signaling pathway (GO:0038093)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	immunoglobulin receptor activity (GO:0019763)			breast(1)|endometrium(1)|lung(2)	4	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)	Intravenous Immunoglobulin(DB00028)	GATGCTTTCCCATGCCTGAGC	0.433													C|||	18	0.00359425	0.0	0.0086	5008	,	,		22223	0.0		0.005	False		,,,				2504	0.0072				p.M171I		Atlas-SNP	.											.	FCGR1B	14	.	0			c.G513A						PASS	.	C	ILE/MET,ILE/MET	10,4396	16.8+/-37.8	0,10,2193	135.0	119.0	124.0		237,513	1.2	0.0	1	dbSNP_134	124	65,8535	39.8+/-96.3	0,65,4235	no	missense,missense	FCGR1B	NM_001004340.2,NM_001017986.2	10,10	0,75,6428	TT,TC,CC		0.7558,0.227,0.5767	benign,benign	79/189,171/281	120930088	75,12931	2203	4300	6503	SO:0001583	missense	2210	exon4			CTTTCCCATGCCT		CCDS72844.1, CCDS72845.1, CCDS72846.1	1p11.2	2013-01-11	2005-02-02		ENSG00000198019	ENSG00000198019		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3614	protein-coding gene	gene with protein product		601502	"""Fc fragment of IgG, high affinity Ib, receptor for (CD64)"""			8697799, 9763663	Standard	NM_001017986		Approved	CD64b	uc001eip.3	Q92637	OTTHUMG00000040903	ENST00000369384.4:c.513G>A	1.37:g.120930088C>T	ENSP00000358391:p.Met171Ile	Somatic	812	0	0		WXS	Illumina HiSeq	Phase_I	827	378	0.457074	NM_001017986	Q7KZ13|Q92638	Missense_Mutation	SNP	ENST00000369384.4	37	CCDS30821.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	C|C	0.017|0.017	-1.503314|-1.503314	0.00992|0.00992	0.00227|0.00227	0.007558|0.007558	ENSG00000198019|ENSG00000198019	ENST00000369178|ENST00000369384;ENST00000369383	.|T;T	.|0.08807	.|3.05;3.05	2.16|2.16	1.23|1.23	0.21249|0.21249	.|Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.|1.731270	.|0.03034	.|N	.|0.152573	T|T	0.01156|0.01156	0.0038|0.0038	N|N	0.04724|0.04724	-0.175|-0.175	0.09310|0.09310	N|N	1|1	.|B;B;B;P	.|0.35174	.|0.168;0.001;0.183;0.488	.|B;B;B;B	.|0.34385	.|0.06;0.001;0.019;0.181	T|T	0.39461|0.39461	-0.9613|-0.9613	5|10	.|0.19147	.|T	.|0.46	.|.	4.6833|4.6833	0.12745|0.12745	0.0:0.8106:0.0:0.1894|0.0:0.8106:0.0:0.1894	.|.	.|171;171;79;171	.|P12314-2;Q92637-2;Q92637-3;Q92637	.|.;.;.;FCGRB_HUMAN	R|I	156|171;79	.|ENSP00000358391:M171I;ENSP00000358390:M79I	.|ENSP00000358390:M79I	G|M	-|-	1|3	0|0	FCGR1B|FCGR1B	120731611|120731611	0.000000|0.000000	0.05858|0.05858	0.004000|0.004000	0.12327|0.12327	0.149000|0.149000	0.21700|0.21700	-0.477000|-0.477000	0.06583|0.06583	0.489000|0.489000	0.27749|0.27749	0.184000|0.184000	0.17185|0.17185	GGG|ATG	C|0.994;T|0.006	0.006	strong		0.433	FCGR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098241.1		
KIAA1549L	25758	hgsc.bcm.edu	37	11	33604885	33604885	+	Splice_Site	SNP	C	C	T	rs2273117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:33604885C>T	ENST00000321505.4	+	10	3693	c.3513C>T	c.(3511-3513)ccC>ccT	p.P1171P	KIAA1549L_ENST00000389726.3_Splice_Site_p.P1177P|KIAA1549L_ENST00000265654.5_Splice_Site_p.P1177P			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1171						integral component of membrane (GO:0016021)											TTCCCACAGCCGTGGTGAAGA	0.577													C|||	973	0.194289	0.0764	0.2378	5008	,	,		20548	0.3591		0.2197	False		,,,				2504	0.1268				p.P1171P		Atlas-SNP	.											.	.	.	.	0			c.C3513T						PASS	.	C		374,3764		16,342,1711	32.0	35.0	34.0		3513	-2.6	1.0	11	dbSNP_100	34	1961,6495		225,1511,2492	yes	coding-synonymous-near-splice	C11orf41	NM_012194.2		241,1853,4203	TT,TC,CC		23.1906,9.0382,18.5406		1171/1850	33604885	2335,10259	2069	4228	6297	SO:0001630	splice_region_variant	25758	exon10			CACAGCCGTGGTG	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.3512-1C>T	11.37:g.33604885C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	492	0.22527472527472528	36	0.07317073170731707	80	0.22099447513812154	206	0.36013986013986016	170	0.22427440633245382	C	10.63	1.402903	0.25291	0.090382	0.231906	ENSG00000110427	ENST00000526400	.	.	.	5.57	-2.59	0.06209	.	0.049055	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.34551	-0.9824	5	0.87932	D	0	.	9.6103	0.39659	0.0:0.1407:0.1313:0.728	rs2273117;rs2273117	.	.	.	L	569	.	ENSP00000433481:P569L	P	+	2	0	C11orf41	33561461	0.953000	0.32496	0.994000	0.49952	0.963000	0.63663	0.040000	0.13905	-0.235000	0.09767	0.561000	0.74099	CCG	C|0.789;T|0.211	0.211	strong		0.577	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	Silent
SAP30BP	29115	hgsc.bcm.edu	37	17	73702135	73702135	+	Silent	SNP	G	G	A	rs56144802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73702135G>A	ENST00000584667.1	+	10	965	c.708G>A	c.(706-708)acG>acA	p.T236T	SAP30BP_ENST00000355423.3_Silent_p.T220T	NM_013260.6	NP_037392.1			SAP30 binding protein											kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)	17	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ccaacgccacgtccaccacca	0.577													G|||	118	0.0235623	0.003	0.0331	5008	,	,		17530	0.0		0.0378	False		,,,				2504	0.0542				p.T236T		Atlas-SNP	.											.	SAP30BP	30	.	0			c.G708A						PASS	.	G		38,4368	41.6+/-74.8	0,38,2165	133.0	83.0	100.0		708	-11.6	0.0	17	dbSNP_129	100	409,8191	126.2+/-184.7	13,383,3904	no	coding-synonymous	SAP30BP	NM_013260.6		13,421,6069	AA,AG,GG		4.7558,0.8625,3.4369		236/309	73702135	447,12559	2203	4300	6503	SO:0001819	synonymous_variant	29115	exon10			CGCCACGTCCACC	AY082382	CCDS11726.1	17q25.1	2006-01-05				ENSG00000161526			30785	protein-coding gene	gene with protein product		610218				15496587	Standard	NM_013260		Approved	HCNGP, HTRG, HTRP	uc002jpe.3	Q9UHR5		ENST00000584667.1:c.708G>A	17.37:g.73702135G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	25	8	0.32	NM_013260		Silent	SNP	ENST00000584667.1	37	CCDS11726.1																																																																																			G|0.972;A|0.028	0.028	strong		0.577	SAP30BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448227.1	NM_013260	
ZNF728	388523	hgsc.bcm.edu	37	19	23158720	23158720	+	Silent	SNP	A	A	T	rs1836017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:23158720A>T	ENST00000594710.1	-	4	1564	c.1419T>A	c.(1417-1419)atT>atA	p.I473I		NM_001267716.1	NP_001254645.1	P0DKX0	ZN728_HUMAN	zinc finger protein 728	473					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										CTCCAGCATGAATTGCCTTAT	0.388													.|||	558	0.111422	0.09	0.0764	5008	,	,		22676	0.1369		0.1093	False		,,,				2504	0.1411				p.I473I		Atlas-SNP	.											.	.	.	.	0			c.T1419A						PASS	.																																			SO:0001819	synonymous_variant	388523	exon4			AGCATGAATTGCC	BC128130	CCDS59370.1	19p12	2014-02-14			ENSG00000269067	ENSG00000269067		"""Zinc fingers, C2H2-type"", ""-"""	32463	protein-coding gene	gene with protein product							Standard	NM_001267716		Approved		uc002nqz.2	P0DKX0	OTTHUMG00000183124	ENST00000594710.1:c.1419T>A	19.37:g.23158720A>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_001267716		Silent	SNP	ENST00000594710.1	37	CCDS59370.1																																																																																			A|0.887;T|0.113	0.113	strong		0.388	ZNF728-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465176.1	NM_001267716	
C9orf84	158401	hgsc.bcm.edu	37	9	114476748	114476748	+	Missense_Mutation	SNP	T	T	A	rs11791445	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114476748T>A	ENST00000318737.4	-	15	2328	c.2200A>T	c.(2200-2202)Atg>Ttg	p.M734L	C9orf84_ENST00000394777.4_Missense_Mutation_p.M660L|C9orf84_ENST00000374287.3_Missense_Mutation_p.M734L|C9orf84_ENST00000394779.3_Missense_Mutation_p.M695L	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	734			M -> L (in dbSNP:rs11791445).							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						TGACTTTGCATCCAACTTAGT	0.338													T|||	718	0.143371	0.1422	0.196	5008	,	,		18121	0.0268		0.2286	False		,,,				2504	0.1401				p.M734L		Atlas-SNP	.											C9orf84_ENST00000374287,NS,adenoma,0,2	C9orf84	207	2	0			c.A2200T						PASS	.	T	LEU/MET,LEU/MET	769,3635	311.9+/-292.3	67,635,1500	186.0	171.0	176.0		2083,2200	2.9	1.0	9	dbSNP_120	176	1991,6609	348.2+/-326.9	227,1537,2536	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	15,15	294,2172,4036	AA,AT,TT		23.1512,17.4614,21.2242	benign,benign	695/1406,734/1445	114476748	2760,10244	2202	4300	6502	SO:0001583	missense	158401	exon15			TTTGCATCCAACT	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.2200A>T	9.37:g.114476748T>A	ENSP00000322108:p.Met734Leu	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	229	111	0.484716	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	331	0.15155677655677655	72	0.14634146341463414	69	0.19060773480662985	15	0.026223776223776224	175	0.23087071240105542	T	12.51	1.959296	0.34565	0.174614	0.231512	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.03860	3.78;3.78;3.79;3.79	5.63	2.93	0.34026	.	0.269718	0.28006	N	0.016970	T	0.00012	0.0000	N	0.12746	0.255	0.44129	P	0.003082000000000029	B;B;B	0.18461	0.028;0.028;0.028	B;B;B	0.16722	0.016;0.016;0.016	T	0.49244	-0.8960	9	0.23891	T	0.37	-7.6893	7.4418	0.27187	0.0:0.1267:0.1384:0.7349	rs11791445;rs17271275;rs11791445	660;734;695	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	L	695;660;348;734;734	ENSP00000378259:M695L;ENSP00000378257:M660L;ENSP00000363405:M734L;ENSP00000322108:M734L	ENSP00000322108:M734L	M	-	1	0	C9orf84	113516569	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.577000	0.23758	0.955000	0.37878	0.533000	0.62120	ATG	T|0.809;A|0.191	0.191	strong		0.338	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
MAP3K11	4296	hgsc.bcm.edu	37	11	65373249	65373249	+	Missense_Mutation	SNP	G	G	T	rs145297254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:65373249G>T	ENST00000530153.1	-	8	1564	c.1043C>A	c.(1042-1044)aCa>aAa	p.T348K	MAP3K11_ENST00000532507.1_Missense_Mutation_p.T21K|MAP3K11_ENST00000309100.3_Missense_Mutation_p.T605K|MAP3K11_ENST00000534432.1_5'UTR					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						TGCTGGGGGTGTGGAAGGAGA	0.602																																					p.T605K		Atlas-SNP	.											.	MAP3K11	67	.	0			c.C1814A						PASS	.	G	LYS/THR	0,4402		0,0,2201	58.0	51.0	54.0		1814	4.1	1.0	11	dbSNP_134	54	6,8588	5.0+/-18.6	0,6,4291	yes	missense	MAP3K11	NM_002419.3	78	0,6,6492	TT,TG,GG		0.0698,0.0,0.0462	probably-damaging	605/848	65373249	6,12990	2201	4297	6498	SO:0001583	missense	4296	exon8			GGGGGTGTGGAAG		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.1043C>A	11.37:g.65373249G>T	ENSP00000433886:p.Thr348Lys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_002419		Missense_Mutation	SNP	ENST00000530153.1	37		.	.	.	.	.	.	.	.	.	.	G	20.3	3.969099	0.74131	0.0	6.98E-4	ENSG00000173327	ENST00000309100;ENST00000532507;ENST00000530153	T;T	0.73681	-0.67;-0.77	5.04	4.12	0.48240	.	0.292498	0.28312	N	0.015805	T	0.65228	0.2671	L	0.29908	0.895	0.35129	D	0.767737	P;D	0.54207	0.911;0.965	P;P	0.48704	0.587;0.456	T	0.67616	-0.5625	10	0.19147	T	0.46	.	9.1853	0.37168	0.0976:0.0:0.9024:0.0	.	112;605	B3KQY4;Q16584	.;M3K11_HUMAN	K	605;21;348	ENSP00000309597:T605K;ENSP00000433886:T348K	ENSP00000309597:T605K	T	-	2	0	MAP3K11	65129825	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	1.629000	0.37071	1.354000	0.45846	0.655000	0.94253	ACA	G|0.999;T|0.001	0.001	strong		0.602	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		
ZNF276	92822	hgsc.bcm.edu	37	16	89799950	89799950	+	Silent	SNP	C	C	T	rs17177891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89799950C>T	ENST00000443381.2	+	8	1438	c.1341C>T	c.(1339-1341)ggC>ggT	p.G447G	ZNF276_ENST00000568064.1_Silent_p.G355G|ZNF276_ENST00000289816.5_Silent_p.G372G|ZNF276_ENST00000446326.2_Silent_p.G233G	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	447					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)		TGTACCGAGGCGCTGACGGCA	0.627													C|||	364	0.0726837	0.0068	0.0187	5008	,	,		17139	0.2579		0.0656	False		,,,				2504	0.0164				p.G447G		Atlas-SNP	.											ZNF276_ENST00000443381,colon,carcinoma,0,2	ZNF276	70	2	0			c.C1341T						PASS	.	C	,	91,4303	73.1+/-111.1	0,91,2106	89.0	81.0	84.0		1341,1116	-6.2	0.2	16	dbSNP_123	84	696,7904	169.9+/-221.1	27,642,3631	no	coding-synonymous,coding-synonymous	ZNF276	NM_001113525.1,NM_152287.3	,	27,733,5737	TT,TC,CC		8.093,2.071,6.0566	,	447/615,372/540	89799950	787,12207	2197	4300	6497	SO:0001819	synonymous_variant	92822	exon8			CCGAGGCGCTGAC	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.1341C>T	16.37:g.89799950C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	208	88	0.423077	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Silent	SNP	ENST00000443381.2	37	CCDS45554.1																																																																																			C|0.932;T|0.068	0.068	strong		0.627	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
EXOC2	55770	hgsc.bcm.edu	37	6	592566	592566	+	Silent	SNP	C	C	T	rs62385137		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:592566C>T	ENST00000230449.4	-	11	1230	c.1095G>A	c.(1093-1095)gcG>gcA	p.A365A	EXOC2_ENST00000448181.3_Intron	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	365					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GGTCACCAGACGCATGAAGGT	0.448																																					p.A365A		Atlas-SNP	.											EXOC2,colon,carcinoma,-1,1	EXOC2	81	1	0			c.G1095A						PASS	.	G		0,4406		0,0,2203	110.0	94.0	99.0		1095	-11.2	0.0	6	dbSNP_129	99	2,8598		0,2,4298	no	coding-synonymous	EXOC2	NM_018303.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		365/925	592566	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	55770	exon11			ACCAGACGCATGA	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1095G>A	6.37:g.592566C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Silent	SNP	ENST00000230449.4	37	CCDS34327.1																																																																																			C|1.000;T|0.000	0.000	weak		0.448	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
WDR83OS	51398	hgsc.bcm.edu	37	19	12780179	12780179	+	Silent	SNP	G	G	A	rs62108388	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12780179G>A	ENST00000596731.1	-	1	1991	c.39C>T	c.(37-39)aaC>aaT	p.N13N	MAN2B1_ENST00000456935.2_5'Flank|WDR83_ENST00000418543.3_Intron|WDR83OS_ENST00000222190.5_Silent_p.N13N|WDR83_ENST00000242796.4_5'Flank|MAN2B1_ENST00000221363.4_5'Flank|CTD-2192J16.24_ENST00000597961.1_Silent_p.N11N|WDR83OS_ENST00000600694.1_5'Flank	NM_016145.3	NP_057229.1	Q9Y284	ASTER_HUMAN	WD repeat domain 83 opposite strand	13						integral component of membrane (GO:0016021)											TCAGCACTTTGTTCGGCCTCC	0.637													G|||	95	0.0189696	0.003	0.0303	5008	,	,		15943	0.0		0.0646	False		,,,				2504	0.0051				p.N13N		Atlas-SNP	.											.	.	.	.	0			c.C39T						PASS	.	G	,	88,4316		3,82,2117	68.0	55.0	60.0		,39	5.7	1.0	19	dbSNP_129	60	570,8030		13,544,3743	no	intron,coding-synonymous	C19orf56,WDR83	NM_001099737.2,NM_016145.3	,	16,626,5860	AA,AG,GG		6.6279,1.9982,5.06	,	,13/107	12780179	658,12346	2202	4300	6502	SO:0001819	synonymous_variant	51398	exon1			CACTTTGTTCGGC	AF151898	CCDS12274.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000105583	ENSG00000105583			30203	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 56"""	C19orf56		10810093	Standard	NM_016145		Approved	PTD008	uc002mud.2	Q9Y284		ENST00000596731.1:c.39C>T	19.37:g.12780179G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_016145	B2R4T8|Q9BVI3	Silent	SNP	ENST00000596731.1	37	CCDS12274.1																																																																																			G|0.956;A|0.044	0.044	strong		0.637	WDR83OS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462702.1	NM_016145	
MUC4	4585	hgsc.bcm.edu	37	3	195511316	195511316	+	Missense_Mutation	SNP	A	A	T	rs79528160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195511316A>T	ENST00000463781.3	-	2	7594	c.7135T>A	c.(7135-7137)Tca>Aca	p.S2379T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S2379T	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.S2379T(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)		GTGTGACCTGAGGATGCTGAG	0.587													.|||	31	0.0061901	0.0121	0.0043	5008	,	,		14857	0.002		0.0089	False		,,,				2504	0.001				p.S2379T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.T7135A						scavenged	.																																			SO:0001583	missense	4585	exon2			GACCTGAGGATGC	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.7135T>A	3.37:g.195511316A>T	ENSP00000417498:p.Ser2379Thr	Somatic	315	3	0.00952381		WXS	Illumina HiSeq	Phase_I	329	21	0.0638298	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	2.169	-0.390229	0.04932	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.39;1.37	.	.	.	.	.	.	.	.	T	0.09862	0.0242	N	0.02539	-0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.17561	-1.0365	7	.	.	.	.	1.439	0.02350	0.32:0.2722:0.0:0.4078	.	2379	E7ESK3	.	T	2379	ENSP00000417498:S2379T;ENSP00000420243:S2379T	.	S	-	1	0	MUC4	196995711	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-2.388000	0.01059	-2.322000	0.00640	-2.525000	0.00183	TCA	A|0.500;T|0.500	0.500	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386118	56386118	+	Silent	SNP	A	A	G	rs2680689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	G	,	1294,3082		192,910,1086	19.0	21.0	20.0		4515,4335	-9.7	0.2	17	dbSNP_100	20	2545,6013		413,1719,2147	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	605,2629,3233	GG,GA,AA		29.7383,29.5704,29.6815	,	1505/1858,1445/1798	56386118	3839,9095	2188	4279	6467	SO:0001819	synonymous_variant	9256	exon22			CTGCTCATCCTCC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4515T>C	17.37:g.56386118A>G		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	100	54	0.54	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	
SLC7A9	11136	hgsc.bcm.edu	37	19	33355055	33355055	+	Missense_Mutation	SNP	A	A	G	rs12150889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33355055A>G	ENST00000023064.4	-	4	616	c.425T>C	c.(424-426)gTg>gCg	p.V142A	SLC7A9_ENST00000587772.1_Missense_Mutation_p.V142A|SLC7A9_ENST00000590341.1_Missense_Mutation_p.V142A|RN7SKP22_ENST00000365097.1_RNA	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	142			V -> A (in dbSNP:rs12150889).		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)	CTTGCAGCCCACATAGAAGGG	0.587													G|||	1533	0.30611	0.3926	0.196	5008	,	,		19907	0.3036		0.3757	False		,,,				2504	0.1984				p.V142A	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.T425C						PASS	.	G	ALA/VAL,ALA/VAL	1660,2746	657.6+/-400.3	328,1004,871	98.0	77.0	84.0		425,425	1.3	0.0	19	dbSNP_120	84	2985,5615	665.4+/-402.3	500,1985,1815	yes	missense,missense	SLC7A9	NM_001126335.1,NM_014270.4	64,64	828,2989,2686	GG,GA,AA		34.7093,37.6759,35.7143	benign,benign	142/488,142/488	33355055	4645,8361	2203	4300	6503	SO:0001583	missense	11136	exon4			CAGCCCACATAGA	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.425T>C	19.37:g.33355055A>G	ENSP00000023064:p.Val142Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_001243036	B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	37	CCDS12425.1	710	0.3250915750915751	183	0.3719512195121951	76	0.20994475138121546	163	0.28496503496503495	288	0.37994722955145116	G	11.30	1.599231	0.28534	0.376759	0.347093	ENSG00000021488	ENST00000023064	D	0.89746	-2.56	4.97	1.28	0.21552	Amino acid permease domain (1);	0.585084	0.19718	N	0.107646	T	0.00012	0.0000	N	0.05259	-0.085	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17837	-1.0356	9	0.46703	T	0.11	.	10.5362	0.45004	0.1887:0.0994:0.712:0.0	rs12150889;rs58557565;rs12150889	142	P82251	BAT1_HUMAN	A	142	ENSP00000023064:V142A	ENSP00000023064:V142A	V	-	2	0	SLC7A9	38046895	0.989000	0.36119	0.001000	0.08648	0.000000	0.00434	3.365000	0.52335	-0.010000	0.14271	-2.888000	0.00096	GTG	A|0.667;G|0.333	0.333	strong		0.587	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
FAM83F	113828	hgsc.bcm.edu	37	22	40417820	40417820	+	Missense_Mutation	SNP	A	A	G	rs5995794	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	40	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	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	
CASP2	835	hgsc.bcm.edu	37	7	142988726	142988726	+	Silent	SNP	G	G	A	rs4647288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142988726G>A	ENST00000310447.5	+	2	409	c.168G>A	c.(166-168)ttG>ttA	p.L56L	CASP2_ENST00000392925.2_Silent_p.L56L|CASP2_ENST00000493642.1_3'UTR|RN7SL535P_ENST00000479087.2_RNA	NM_032982.3|NM_032983.3	NP_116764.2|NP_116765.2	P42575	CASP2_HUMAN	caspase 2, apoptosis-related cysteine peptidase	56	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|ectopic germ cell programmed cell death (GO:0035234)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|luteolysis (GO:0001554)|neural retina development (GO:0003407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron apoptotic process (GO:0043525)|protein processing (GO:0016485)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(164;0.059)					TGAGCGAATTGTTAGAACATC	0.448													G|||	58	0.0115815	0.0008	0.0202	5008	,	,		17867	0.0		0.0328	False		,,,				2504	0.0102				p.L56L		Atlas-SNP	.											.	CASP2	55	.	0			c.G168A						PASS	.	G	,,	35,4371	40.8+/-73.8	0,35,2168	189.0	191.0	190.0		75,168,168	2.8	1.0	7	dbSNP_111	190	272,8328	103.8+/-164.8	4,264,4032	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP2	NM_001224.4,NM_032982.3,NM_032983.3	,,	4,299,6200	AA,AG,GG		3.1628,0.7944,2.3604	,,	25/313,56/453,56/109	142988726	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	835	exon2			CGAATTGTTAGAA	AK096245, BC002427, BM998653, BX537669, CB988674, U13021	CCDS5879.1, CCDS47733.1	7q34-q35	2014-01-20	2008-08-01		ENSG00000106144	ENSG00000106144		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1503	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 57"""	600639	"""neural precursor cell expressed, developmentally down-regulated 2"""	NEDD2		7789948, 8780721	Standard	NM_032982		Approved	ICH1, PPP1R57, MGC2181	uc003wco.3	P42575	OTTHUMG00000023641	ENST00000310447.5:c.168G>A	7.37:g.142988726G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	NM_032982	A8K5F9|D3DXD6|E9PDN0|P42576|Q59F21|Q7KZL6|Q86UJ3|Q9BUP7|Q9BZK9|Q9BZL0	Silent	SNP	ENST00000310447.5	37	CCDS5879.1																																																																																			G|0.981;A|0.019	0.019	strong		0.448	CASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059962.3	NM_032982	
EFCAB2	84288	hgsc.bcm.edu	37	1	245245402	245245402	+	Silent	SNP	C	C	T	rs10927387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:245245402C>T	ENST00000366522.2	+	5	750	c.609C>T	c.(607-609)ccC>ccT	p.P203P	EFCAB2_ENST00000366523.1_Silent_p.P67P|EFCAB2_ENST00000447569.2_Silent_p.P67P|EFCAB2_ENST00000487845.1_3'UTR			Q5VUJ9	EFCB2_HUMAN	EF-hand calcium binding domain 2	203							calcium ion binding (GO:0005509)	p.P67P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|stomach(2)	13	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			AAGAAGAACCCACTGGATACA	0.353													C|||	1449	0.289337	0.2489	0.2853	5008	,	,		22027	0.1935		0.4453	False		,,,				2504	0.2853				p.P67P		Atlas-SNP	.											EFCAB2,NS,carcinoma,0,1	EFCAB2	19	1	1	Substitution - coding silent(1)	stomach(1)	c.C201T						PASS	.	C	,	1111,3295	394.9+/-329.4	145,821,1237	101.0	96.0	97.0		201,201	2.6	1.0	1	dbSNP_120	97	3394,5206	502.2+/-375.6	647,2100,1553	no	coding-synonymous,coding-synonymous	EFCAB2	NM_001143943.1,NM_032328.3	,	792,2921,2790	TT,TC,CC		39.4651,25.2156,34.6379	,	67/134,67/163	245245402	4505,8501	2203	4300	6503	SO:0001819	synonymous_variant	84288	exon4			AGAACCCACTGGA	AB209286	CCDS31082.1, CCDS44341.1	1q44	2014-07-18			ENSG00000203666	ENSG00000203666		"""EF-hand domain containing"""	28166	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 8"""					23427265	Standard	NM_032328		Approved	MGC12458, DRC8, CFAP200	uc001ibc.2	Q5VUJ9	OTTHUMG00000040474	ENST00000366522.2:c.609C>T	1.37:g.245245402C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_001143943	B4DZE9|Q59G23|Q9BS36	Silent	SNP	ENST00000366522.2	37		694|694	0.31776556776556775|0.31776556776556775	135|135	0.27439024390243905|0.27439024390243905	113|113	0.31215469613259667|0.31215469613259667	123|123	0.21503496503496503|0.21503496503496503	323|323	0.4261213720316623|0.4261213720316623	C|C	9.619|9.619	1.133382|1.133382	0.21041|0.21041	0.252156|0.252156	0.394651|0.394651	ENSG00000203666|ENSG00000203666	ENST00000366521|ENST00000551317;ENST00000425550	.|T;T	.|0.80393	.|-1.24;-1.37	5.61|5.61	2.57|2.57	0.30868|0.30868	.|.	.|0.390107	.|0.23325	.|N	.|0.049410	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999979|0.9999999999999979	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.25984|0.25984	-1.0116|-1.0116	3|6	.|0.87932	.|D	.|0	.|.	3.9513|3.9513	0.09371|0.09371	0.1661:0.5755:0.0:0.2584|0.1661:0.5755:0.0:0.2584	rs10927387;rs60076946;rs10927387|rs10927387;rs60076946;rs10927387	.|.	.|.	.|.	Y|L	126|59	.|ENSP00000447807:P59L;ENSP00000405269:P59L	.|ENSP00000405269:P59L	H|P	+|+	1|2	0|0	EFCAB2|EFCAB2	243312025|243312025	0.842000|0.842000	0.29525|0.29525	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	-0.343000|-0.343000	0.07791|0.07791	0.722000|0.722000	0.32252|0.32252	0.557000|0.557000	0.71058|0.71058	CAC|CCA	C|0.661;T|0.339	0.339	strong		0.353	EFCAB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000097407.2		
GAS7	8522	hgsc.bcm.edu	37	17	9846521	9846521	+	Silent	SNP	G	G	C	rs17339499	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:9846521G>C	ENST00000432992.2	-	7	808	c.648C>G	c.(646-648)acC>acG	p.T216T	GAS7_ENST00000396115.2_Intron|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000323816.4_Silent_p.T156T|GAS7_ENST00000578655.1_5'Flank|GAS7_ENST00000583882.1_Intron|GAS7_ENST00000585266.1_Silent_p.T156T|GAS7_ENST00000542249.1_Silent_p.T152T|GAS7_ENST00000437099.2_Silent_p.T152T|GAS7_ENST00000579158.1_Silent_p.T152T|GAS7_ENST00000580865.1_Silent_p.T76T	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	216	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						ACCCAGCCACGGTGCCGTTGC	0.532			T	MLL	AML*								A|||	692	0.138179	0.1263	0.1758	5008	,	,		20203	0.005		0.2286	False		,,,				2504	0.1718				p.T216T		Atlas-SNP	.		Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7	113	.	0			c.C648G						PASS	.	A	,,,	707,3699		58,591,1554	165.0	149.0	154.0		456,228,468,648	-10.7	0.0	17	dbSNP_123	154	1971,6629		214,1543,2543	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GAS7	NM_001130831.1,NM_003644.2,NM_201432.1,NM_201433.1	,,,	272,2134,4097	CC,CG,GG		22.9186,16.0463,20.5905	,,,	152/413,76/337,156/417,216/477	9846521	2678,10328	2203	4300	6503	SO:0001819	synonymous_variant	8522	exon7			AGCCACGGTGCCG	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.648C>G	17.37:g.9846521G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_201433	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Silent	SNP	ENST00000432992.2	37	CCDS11152.1																																																																																			G|0.811;C|0.189	0.189	strong		0.532	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433	
DOCK8	81704	hgsc.bcm.edu	37	9	312134	312134	+	Missense_Mutation	SNP	G	G	A	rs11789099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:312134G>A	ENST00000453981.1	+	6	821	c.709G>A	c.(709-711)Gag>Aag	p.E237K	DOCK8_ENST00000432829.2_Missense_Mutation_p.E169K|DOCK8_ENST00000469391.1_Missense_Mutation_p.E169K			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	237			E -> K (in dbSNP:rs11789099).		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)		TAGGCAGGCCGAGCTCTTTGC	0.547													G|||	88	0.0175719	0.003	0.0159	5008	,	,		18669	0.001		0.0229	False		,,,				2504	0.0501				p.E237K		Atlas-SNP	.											.	DOCK8	401	.	0			c.G709A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	36,4370	41.6+/-74.8	0,36,2167	50.0	48.0	49.0		505,505,709	5.6	0.9	9	dbSNP_120	49	283,8317	106.0+/-166.9	8,267,4025	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	56,56,56	8,303,6192	AA,AG,GG		3.2907,0.8171,2.4527	possibly-damaging,possibly-damaging,possibly-damaging	169/2000,169/2032,237/2100	312134	319,12687	2203	4300	6503	SO:0001583	missense	81704	exon6			CAGGCCGAGCTCT	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.709G>A	9.37:g.312134G>A	ENSP00000408464:p.Glu237Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	128	69	0.539062	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	25	0.011446886446886446	4	0.008130081300813009	4	0.011049723756906077	0	0.0	17	0.022427440633245383	G	17.97	3.518485	0.64634	0.008171	0.032907	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.17528	2.27;2.27;2.27	5.57	5.57	0.84162	.	0.054729	0.64402	D	0.000001	T	0.12050	0.0293	L	0.36672	1.1	0.58432	D	0.999999	P;D;P	0.89917	0.782;1.0;0.782	B;D;B	0.75020	0.155;0.985;0.155	T	0.01512	-1.1336	10	0.09843	T	0.71	.	19.5358	0.95253	0.0:0.0:1.0:0.0	rs11789099;rs52813468;rs11789099	169;237;237	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	K	237;237;169;169	ENSP00000408464:E237K;ENSP00000394888:E169K;ENSP00000419438:E169K	ENSP00000287364:E237K	E	+	1	0	DOCK8	302134	1.000000	0.71417	0.926000	0.36857	0.957000	0.61999	7.602000	0.82796	2.627000	0.88993	0.467000	0.42956	GAG	G|0.978;A|0.022	0.022	strong		0.547	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
RRP36	88745	hgsc.bcm.edu	37	6	42995211	42995211	+	Silent	SNP	A	A	G	rs1138141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42995211A>G	ENST00000244496.5	+	6	649	c.639A>G	c.(637-639)aaA>aaG	p.K213K		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	213					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						ACTTCCTGAAAAAATGTGAGT	0.572													G|||	1566	0.3127	0.5953	0.2378	5008	,	,		16765	0.2123		0.1233	False		,,,				2504	0.2822				p.K213K		Atlas-SNP	.											.	RRP36	20	.	0			c.A639G						PASS	.	G		2388,2018	549.6+/-377.8	646,1096,461	64.0	63.0	64.0		639	5.3	1.0	6	dbSNP_86	64	1116,7484	754.9+/-407.5	70,976,3254	no	coding-synonymous	RRP36	NM_033112.2		716,2072,3715	GG,GA,AA		12.9767,45.8012,26.9414		213/260	42995211	3504,9502	2203	4300	6503	SO:0001819	synonymous_variant	88745	exon6			CCTGAAAAAATGT	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.639A>G	6.37:g.42995211A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	158	83	0.525316	NM_033112	Q9BRF6|Q9P0C8	Silent	SNP	ENST00000244496.5	37	CCDS34453.1																																																																																			A|0.725;G|0.275	0.275	strong		0.572	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
ARSG	22901	hgsc.bcm.edu	37	17	66364749	66364749	+	Silent	SNP	T	T	C	rs1558877	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	77	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	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	
MAP2	4133	hgsc.bcm.edu	37	2	210557380	210557380	+	Silent	SNP	C	C	T	rs6720659	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	70	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	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	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5239921	5239921	+	Silent	SNP	C	C	T	rs11742341	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:5239921C>T	ENST00000274181.7	+	16	2544	c.2406C>T	c.(2404-2406)acC>acT	p.T802T		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	802	Spacer.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						GGCACTGGACCGTGGACTGGC	0.527													C|||	574	0.114617	0.0061	0.111	5008	,	,		17373	0.0764		0.1928	False		,,,				2504	0.2229				p.T802T		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C2406T						PASS	.	C		126,3638		1,124,1757	106.0	101.0	103.0		2406	-11.1	0.3	5	dbSNP_120	103	1609,6609		163,1283,2663	no	coding-synonymous	ADAMTS16	NM_139056.2		164,1407,4420	TT,TC,CC		19.579,3.3475,14.4801		802/1225	5239921	1735,10247	1882	4109	5991	SO:0001819	synonymous_variant	170690	exon16			CTGGACCGTGGAC	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17108	protein-coding gene	gene with protein product		607510	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"""			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.2406C>T	5.37:g.5239921C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	CCDS43299.1																																																																																			C|0.865;T|0.135	0.135	strong		0.527	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
KLK11	11012	hgsc.bcm.edu	37	19	51527364	51527364	+	Missense_Mutation	SNP	G	G	A	rs1048328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51527364G>A	ENST00000594768.1	-	4	681	c.496C>T	c.(496-498)Cgc>Tgc	p.R166C	KLK11_ENST00000594458.1_5'Flank|KLK11_ENST00000319720.7_Missense_Mutation_p.R134C|KLK11_ENST00000600362.1_Intron|KLK11_ENST00000453757.3_Missense_Mutation_p.R134C|KLK11_ENST00000391804.3_Missense_Mutation_p.R159C	NM_144947.1	NP_659196.1	Q9UBX7	KLK11_HUMAN	kallikrein-related peptidase 11	166	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> C (in dbSNP:rs1048328).			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		GTGACACAGCGTGAGGAGAGG	0.632													G|||	135	0.0269569	0.0023	0.0504	5008	,	,		19656	0.0		0.0905	False		,,,				2504	0.0061				p.R166C		Atlas-SNP	.											.	KLK11	28	.	0			c.C496T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	54,4352	54.2+/-90.2	0,54,2149	64.0	40.0	48.0		400,475,400,496	2.1	0.0	19	dbSNP_86	48	749,7851	177.2+/-226.9	35,679,3586	yes	missense,missense,missense,missense	KLK11	NM_001136032.2,NM_001167605.1,NM_006853.2,NM_144947.1	180,180,180,180	35,733,5735	AA,AG,GG		8.7093,1.2256,6.1741	probably-damaging,probably-damaging,probably-damaging,probably-damaging	134/251,159/276,134/251,166/283	51527364	803,12203	2203	4300	6503	SO:0001583	missense	11012	exon4			CACAGCGTGAGGA	AB012917	CCDS12818.1, CCDS12819.1, CCDS54297.1	19q13.33	2011-09-07	2006-10-27			ENSG00000167757		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6359	protein-coding gene	gene with protein product		604434	"""kallikrein 11"""	PRSS20		9765601, 10662548, 16800724, 16800723	Standard	NM_006853		Approved	TLSP	uc002pvb.2	Q9UBX7		ENST00000594768.1:c.496C>T	19.37:g.51527364G>A	ENSP00000473047:p.Arg166Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_144947	O75837|Q0WXX5|Q8IXD7|Q9NS65	Missense_Mutation	SNP	ENST00000594768.1	37	CCDS12818.1	98	0.04487179487179487	1	0.0020325203252032522	25	0.06906077348066299	0	0.0	72	0.09498680738786279	g	11.44	1.639326	0.29157	0.012256	0.087093	ENSG00000167757	ENST00000391804;ENST00000319720;ENST00000453757;ENST00000319756	D;D;D	0.89196	-2.48;-2.48;-2.48	4.42	2.13	0.27403	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.402480	0.04907	N	0.452435	T	0.42245	0.1194	M	0.80422	2.495	0.09310	N	1	D;D	0.57899	0.981;0.981	P;P	0.52386	0.697;0.697	T	0.63532	-0.6616	10	0.87932	D	0	.	7.2704	0.26254	0.0:0.1635:0.5003:0.3362	rs1048328;rs3170130;rs52799296;rs61476730;rs1048328	166;159	Q9UBX7;Q8IXD7	KLK11_HUMAN;.	C	159;134;134;166	ENSP00000375680:R159C;ENSP00000324269:R134C;ENSP00000413958:R134C	ENSP00000324269:R134C	R	-	1	0	KLK11	56219176	0.000000	0.05858	0.017000	0.16124	0.382000	0.30200	-2.107000	0.01337	1.062000	0.40625	-0.475000	0.04921	CGC	G|0.951;A|0.049	0.049	strong		0.632	KLK11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464314.2	NM_006853	
MUC4	4585	hgsc.bcm.edu	37	3	195513590	195513590	+	Missense_Mutation	SNP	C	C	T	rs74192533		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195513590C>T	ENST00000463781.3	-	2	5320	c.4861G>A	c.(4861-4863)Gac>Aac	p.D1621N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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	539	15	0.0278293		WXS	Illumina HiSeq	Phase_I	574	25	0.043554	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	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33385953	33385953	+	5'Flank	SNP	A	A	G	rs1705003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33385953A>G	ENST00000418600.2	+	0	0				CUTA_ENST00000374496.3_5'Flank|CUTA_ENST00000488478.1_5'Flank|CUTA_ENST00000494751.1_5'Flank|CUTA_ENST00000374500.5_Missense_Mutation_p.S4P|CUTA_ENST00000440279.3_5'Flank|CUTA_ENST00000492510.1_5'UTR|SYNGAP1_ENST00000293748.5_5'Flank|CUTA_ENST00000607266.1_5'Flank|CUTA_ENST00000488034.1_5'Flank	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1						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						GCCAATCCCGACCCTATCATG	0.582													G|||	678	0.135383	0.2474	0.121	5008	,	,		18836	0.0407		0.1421	False		,,,				2504	0.0849				p.S4P		Atlas-SNP	.											CUTA_ENST00000374500,colon,carcinoma,0,1	CUTA	5	1	0			c.T10C						PASS	.	G	,,,,PRO/SER	1089,3317	720.0+/-409.0	130,829,1244	59.0	65.0	63.0		,,,,10	3.6	0.0	6	dbSNP_89	63	1408,7192	752.1+/-407.4	129,1150,3021	yes	utr-5,utr-5,utr-5,utr-5,missense	CUTA	NM_001014837.1,NM_001014838.1,NM_001014840.1,NM_015921.2,NM_001014433.2	,,,,74	259,1979,4265	GG,GA,AA		16.3721,24.7163,19.1988	,,,,benign	,,,,4/199	33385953	2497,10509	2203	4300	6503	SO:0001631	upstream_gene_variant	51596	exon1			ATCCCGACCCTAT	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		6.37:g.33385953A>G	Exception_encountered	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_001014433	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	296	0.13553113553113552	121	0.2459349593495935	48	0.13259668508287292	24	0.04195804195804196	103	0.1358839050131926	G	1.350	-0.591552	0.03799	0.247163	0.163721	ENSG00000112514	ENST00000374500	.	.	.	4.46	3.59	0.41128	.	3.045880	0.01062	N	0.004663	T	0.10035	0.0246	.	.	.	0.47862	P	4.6400000000001995E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.11494	-1.0585	7	0.18710	T	0.47	11.9437	6.5376	0.22363	0.0986:0.1811:0.7203:0.0	rs1705003;rs1705003	4	O60888-2	.	P	4	.	ENSP00000363624:S4P	S	-	1	0	CUTA	33493931	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	0.462000	0.21956	0.635000	0.30488	-0.213000	0.12676	TCG	A|0.825;G|0.175	0.175	strong		0.582	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
PVRIG	79037	hgsc.bcm.edu	37	7	99817878	99817878	+	Missense_Mutation	SNP	C	C	T	rs141119008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99817878C>T	ENST00000317271.2	+	3	623	c.260C>T	c.(259-261)aCg>aTg	p.T87M	GATS_ENST00000543273.1_RNA|GATS_ENST00000436886.2_Intron|AC005071.1_ENST00000410550.1_RNA	NM_024070.3	NP_076975.2	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin domain containing	87						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)	11	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGGGGACCACGCTGGCTGTG	0.657													C|||	27	0.00539137	0.0	0.0043	5008	,	,		16534	0.001		0.0099	False		,,,				2504	0.0133				p.T87M		Atlas-SNP	.											.	PVRIG	20	.	0			c.C260T						PASS	.	C	MET/THR,	9,4381		0,9,2186	14.0	15.0	14.0		260,	-5.6	0.0	7	dbSNP_134	14	64,8512		0,64,4224	no	missense,intron	PVRIG,GATS	NM_024070.3,NM_178831.6	81,	0,73,6410	TT,TC,CC		0.7463,0.205,0.563	benign,	87/327,	99817878	73,12893	2195	4288	6483	SO:0001583	missense	79037	exon3			GGACCACGCTGGC	BC001129	CCDS5690.1	7q22.1	2013-06-26			ENSG00000213413	ENSG00000213413			32190	protein-coding gene	gene with protein product						16926269	Standard	NM_024070		Approved	MGC2463, C7orf15	uc003uuf.1	Q6DKI7	OTTHUMG00000156798	ENST00000317271.2:c.260C>T	7.37:g.99817878C>T	ENSP00000316675:p.Thr87Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_024070	D6W5U9|Q9BVK3	Missense_Mutation	SNP	ENST00000317271.2	37	CCDS5690.1	10	0.004578754578754579	0	0.0	0	0.0	1	0.0017482517482517483	9	0.011873350923482849	c	3.683	-0.065201	0.07273	0.00205	0.007463	ENSG00000213413	ENST00000317271	T	0.46819	0.86	2.78	-5.57	0.02521	.	.	.	.	.	T	0.15782	0.0380	N	0.14661	0.345	0.09310	N	1	B	0.33748	0.423	B	0.31495	0.131	T	0.11446	-1.0587	9	0.62326	D	0.03	.	1.9805	0.03425	0.3123:0.3941:0.162:0.1317	.	87	Q6DKI7	PVRIG_HUMAN	M	87	ENSP00000316675:T87M	ENSP00000316675:T87M	T	+	2	0	PVRIG	99655814	0.000000	0.05858	0.011000	0.14972	0.389000	0.30415	-4.471000	0.00229	-1.950000	0.01030	-1.395000	0.01148	ACG	C|0.995;T|0.005	0.005	strong		0.657	PVRIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345870.2	NM_024070	
WDR93	56964	hgsc.bcm.edu	37	15	90245174	90245174	+	Missense_Mutation	SNP	T	T	A	rs4287542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90245174T>A	ENST00000268130.7	+	2	298	c.197T>A	c.(196-198)cTt>cAt	p.L66H	RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Missense_Mutation_p.L66H|WDR93_ENST00000558000.1_Missense_Mutation_p.L66H	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	66			L -> H (in dbSNP:rs4287542).		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)			CTGGTGAACCTTCTGTTTGAC	0.502													T|||	1963	0.391973	0.5061	0.3617	5008	,	,		20048	0.2063		0.4026	False		,,,				2504	0.4397				p.L66H		Atlas-SNP	.											.	WDR93	63	.	0			c.T197A						PASS	.	T	HIS/LEU	2141,2259	581.7+/-385.4	529,1083,588	88.0	78.0	82.0		197	0.1	0.0	15	dbSNP_111	82	3848,4750	541.6+/-384.0	846,2156,1297	yes	missense	WDR93	NM_020212.1	99	1375,3239,1885	AA,AT,TT		44.7546,48.6591,46.0763	benign	66/687	90245174	5989,7009	2200	4299	6499	SO:0001583	missense	56964	exon2			TGAACCTTCTGTT		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.197T>A	15.37:g.90245174T>A	ENSP00000268130:p.Leu66His	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	787	0.36034798534798534	218	0.44308943089430897	141	0.38950276243093923	124	0.21678321678321677	304	0.40105540897097625	T	1.654	-0.513158	0.04200	0.486591	0.447546	ENSG00000140527	ENST00000268130	T	0.22134	1.97	5.59	0.0743	0.14394	.	0.586451	0.15989	N	0.234922	T	0.00012	0.0000	N	0.12746	0.255	0.58432	P	4.000000000004E-6	B;B;B	0.20261	0.01;0.043;0.01	B;B;B	0.18561	0.01;0.022;0.01	T	0.45352	-0.9267	9	0.13470	T	0.59	-1.9233	1.6993	0.02869	0.4348:0.0838:0.1407:0.3407	rs4287542;rs57513749;rs4287542	66;66;66	Q6P2C0-2;B4E3E2;Q6P2C0	.;.;WDR93_HUMAN	H	66	ENSP00000268130:L66H	ENSP00000268130:L66H	L	+	2	0	WDR93	88046178	0.011000	0.17503	0.008000	0.14137	0.289000	0.27227	-0.054000	0.11826	0.039000	0.15632	0.528000	0.53228	CTT	T|0.574;A|0.426	0.426	strong		0.502	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
FLG	2312	hgsc.bcm.edu	37	1	152276772	152276772	+	Missense_Mutation	SNP	C	C	A	rs72697000	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276772C>A	ENST00000368799.1	-	3	10625	c.10590G>T	c.(10588-10590)agG>agT	p.R3530S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3530	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCTGCTTGTCCTGGGCCCCG	0.577									Ichthyosis				C|||	1455	0.290535	0.0113	0.3919	5008	,	,		18815	0.5853		0.1421	False		,,,				2504	0.4448				p.R3530S		Atlas-SNP	.											.	FLG	900	.	0			c.G10590T						PASS	.	C	SER/ARG	161,4245	108.2+/-146.6	2,157,2044	192.0	199.0	196.0		10590	-3.0	0.0	1	dbSNP_130	196	1264,7336	251.9+/-278.2	121,1022,3157	yes	missense	FLG	NM_002016.1	110	123,1179,5201	AA,AC,CC		14.6977,3.6541,10.9565	probably-damaging	3530/4062	152276772	1425,11581	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTTGTCCTGGGC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10590G>T	1.37:g.152276772C>A	ENSP00000357789:p.Arg3530Ser	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	340	158	0.464706	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	587	0.26877289377289376	9	0.018292682926829267	119	0.3287292817679558	347	0.6066433566433567	112	0.14775725593667546	C	10.62	1.400937	0.25291	0.036541	0.146977	ENSG00000143631	ENST00000368799	T	0.04406	3.63	3.63	-2.97	0.05530	.	.	.	.	.	T	0.04770	0.0129	M	0.76574	2.34	0.80722	P	0.0	D	0.71674	0.998	D	0.87578	0.998	T	0.26360	-1.0105	8	0.10377	T	0.69	.	4.3032	0.10933	0.1524:0.4281:0.0:0.4194	.	3530	P20930	FILA_HUMAN	S	3530	ENSP00000357789:R3530S	ENSP00000357789:R3530S	R	-	3	2	FLG	150543396	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.006000	0.00160	-0.437000	0.07243	-0.552000	0.04208	AGG	C|0.842;A|0.158	0.158	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ENC1	8507	hgsc.bcm.edu	37	5	73930751	73930751	+	Silent	SNP	C	C	T	rs300239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73930751C>T	ENST00000302351.4	-	2	2690	c.1560G>A	c.(1558-1560)aaG>aaA	p.K520K	ENC1_ENST00000510316.1_Silent_p.K447K|ENC1_ENST00000509284.1_5'Flank|ENC1_ENST00000537006.1_Silent_p.K520K	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	520				YTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDV TAKRMSCHAVASGNKLYVVGGYFGIQRCKTLDCYDPTLDVW NSITTVPYSLIPTAFVSTWKHLPS -> IHSQASCPGGTQD FLLWGVIQNFSACFCL (in Ref. 1; AAC39532). {ECO:0000305}.	multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		CATCTCCCACCTTGGTCCACT	0.488													C|||	3094	0.617812	0.5287	0.7464	5008	,	,		20019	0.6181		0.6948	False		,,,				2504	0.5675				p.K520K		Atlas-SNP	.											.	ENC1	56	.	0			c.G1560A						PASS	.	C		2421,1985	616.7+/-392.8	656,1109,438	93.0	92.0	92.0		1560	2.9	1.0	5	dbSNP_79	92	5628,2972	667.1+/-402.4	1853,1922,525	no	coding-synonymous	ENC1	NM_003633.2		2509,3031,963	TT,TC,CC		34.5581,45.0522,38.1132		520/590	73930751	8049,4957	2203	4300	6503	SO:0001819	synonymous_variant	8507	exon2			TCCCACCTTGGTC	AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"""Kelch-like"", ""BTB/POZ domain containing"""	3345	protein-coding gene	gene with protein product	"""kelch-like family member 37"""	605173	"""ectodermal-neural cortex 1 (with BTB-like domain)"""	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1560G>A	5.37:g.73930751C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Silent	SNP	ENST00000302351.4	37	CCDS4021.1																																																																																			C|0.367;G|0.000;T|0.633	0.633	strong		0.488	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633	
PRSS58	136541	hgsc.bcm.edu	37	7	141952110	141952110	+	Silent	SNP	G	G	A	rs1052406	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:141952110G>A	ENST00000552471.1	-	5	976	c.657C>T	c.(655-657)gcC>gcT	p.A219A	PRSS58_ENST00000547058.2_Silent_p.A219A			Q8IYP2	PRS58_HUMAN	protease, serine, 58	219	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						TGCCAACATCGGCTCTCAAAA	0.428													G|||	1030	0.205671	0.2088	0.2277	5008	,	,		17409	0.0089		0.3469	False		,,,				2504	0.2434				p.A219A		Atlas-SNP	.											.	PRSS58	41	.	0			c.C657T						PASS	.	G		1072,3334	390.7+/-327.8	121,830,1252	61.0	66.0	64.0		657	-4.1	1.0	7	dbSNP_86	64	3212,5388	484.6+/-371.4	603,2006,1691	no	coding-synonymous	PRSS58	NM_001001317.3		724,2836,2943	AA,AG,GG		37.3488,24.3305,32.9386		219/242	141952110	4284,8722	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon6			AACATCGGCTCTC		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"""Serine peptidases / Serine peptidases"""	39125	protein-coding gene	gene with protein product	"""trypsin X3"""						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.657C>T	7.37:g.141952110G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			G|0.709;A|0.291	0.291	strong		0.428	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317	
C1QTNF2	114898	hgsc.bcm.edu	37	5	159776637	159776637	+	Silent	SNP	C	C	T	rs10053189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:159776637C>T	ENST00000393975.3	-	3	534	c.531G>A	c.(529-531)aaG>aaA	p.K177K		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	132	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				activation of MAPK activity (GO:0000187)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(2)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	13	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)			CTGGCTCCCCCTTCTTGCCCT	0.692													c|||	1696	0.338658	0.2133	0.4063	5008	,	,		18204	0.3284		0.4781	False		,,,				2504	0.3272				p.K177K		Atlas-SNP	.											.	C1QTNF2	33	.	0			c.G531A						PASS	.	T		1099,3307	375.1+/-321.5	144,811,1248	96.0	106.0	103.0		531	1.8	1.0	5	dbSNP_119	103	4016,4584	538.4+/-383.4	956,2104,1240	no	coding-synonymous	C1QTNF2	NM_031908.4		1100,2915,2488	TT,TC,CC		46.6977,24.9433,39.328		177/331	159776637	5115,7891	2203	4300	6503	SO:0001819	synonymous_variant	114898	exon3			CTCCCCCTTCTTG	AF329836	CCDS4351.2	5q33.3	2008-05-15			ENSG00000145861	ENSG00000145861			14325	protein-coding gene	gene with protein product							Standard	XM_005265815		Approved	CTRP2	uc003lyd.3	Q9BXJ5	OTTHUMG00000130323	ENST00000393975.3:c.531G>A	5.37:g.159776637C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_031908		Silent	SNP	ENST00000393975.3	37	CCDS4351.2																																																																																			C|0.626;T|0.374	0.374	strong		0.692	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2		
TTC28	23331	hgsc.bcm.edu	37	22	28378384	28378384	+	Missense_Mutation	SNP	G	G	C	rs41278845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:28378384G>C	ENST00000397906.2	-	23	7412	c.7271C>G	c.(7270-7272)gCt>gGt	p.A2424G	TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000430525.1_RNA|TTC28-AS1_ENST00000425112.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000454996.1_RNA|TTC28-AS1_ENST00000435348.1_RNA|TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000419253.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	2424					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						TTTCGGTGGAGCTCCGTCATG	0.642													G|||	79	0.0157748	0.0015	0.0259	5008	,	,		14166	0.0		0.0517	False		,,,				2504	0.0072				p.A2424G		Atlas-SNP	.											.	TTC28	84	.	0			c.C7271G						PASS	.	G	GLY/ALA	12,1372		0,12,680	65.0	70.0	68.0		7271	0.2	0.0	22	dbSNP_127	68	192,2990		7,178,1406	yes	missense	TTC28	NM_001145418.1	60	7,190,2086	CC,CG,GG		6.0339,0.8671,4.4678	benign	2424/2482	28378384	204,4362	692	1591	2283	SO:0001583	missense	23331	exon23			GGTGGAGCTCCGT	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.7271C>G	22.37:g.28378384G>C	ENSP00000381003:p.Ala2424Gly	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Missense_Mutation	SNP	ENST00000397906.2	37	CCDS46678.1	49	0.022435897435897436	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	41	0.05408970976253298	G	0.807	-0.753278	0.03041	0.008671	0.060339	ENSG00000100154	ENST00000397906	D	0.87966	-2.32	4.99	0.179	0.15063	.	0.888191	0.09809	N	0.752972	T	0.26882	0.0658	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38993	-0.9635	10	0.31617	T	0.26	-0.1023	5.7923	0.18367	0.2533:0.1378:0.6089:0.0	rs41278845;rs61744145	2424	Q96AY4	TTC28_HUMAN	G	2424	ENSP00000381003:A2424G	ENSP00000381003:A2424G	A	-	2	0	TTC28	26708384	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.282000	0.18829	-0.066000	0.12998	0.655000	0.94253	GCT	G|0.947;C|0.053	0.053	strong		0.642	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
KIF1A	547	hgsc.bcm.edu	37	2	241713646	241713646	+	Silent	SNP	A	A	G	rs1063353	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	139	0	0		WXS	Illumina HiSeq	Phase_I	203	116	0.571429	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	
LSP1	4046	hgsc.bcm.edu	37	11	1874404	1874404	+	Silent	SNP	C	C	T	rs2089910	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1874404C>T	ENST00000311604.3	+	1	205	c.30C>T	c.(28-30)gcC>gcT	p.A10A		NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	10					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		ACCCGGGTGCCGAGGAGCGGG	0.657													C|||	1462	0.291933	0.2799	0.2795	5008	,	,		13920	0.4623		0.2654	False		,,,				2504	0.1687				p.A10A		Atlas-SNP	.											LSP1_ENST00000311604,rectum,carcinoma,0,1	LSP1	59	1	0			c.C30T						PASS	.	C		1155,3241	375.1+/-321.5	150,855,1193	65.0	65.0	65.0		30	-5.1	0.0	11	dbSNP_96	65	1971,6619	325.8+/-317.1	236,1499,2560	no	coding-synonymous	LSP1	NM_002339.2		386,2354,3753	TT,TC,CC		22.9453,26.2739,24.0721		10/340	1874404	3126,9860	2198	4295	6493	SO:0001819	synonymous_variant	4046	exon1			GGGTGCCGAGGAG	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.30C>T	11.37:g.1874404C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_002339	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Silent	SNP	ENST00000311604.3	37	CCDS31334.1																																																																																			C|0.721;T|0.279	0.279	strong		0.657	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
RPL27A	6157	hgsc.bcm.edu	37	11	8706406	8706406	+	Silent	SNP	T	T	G	rs4670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8706406T>G	ENST00000314138.6	+	4	688	c.285T>G	c.(283-285)acT>acG	p.T95T	RPL27A_ENST00000524496.1_Silent_p.T38T|RPL27A_ENST00000532359.1_Silent_p.T60T|SNORA3_ENST00000364113.1_RNA|RPL27A_ENST00000530022.1_Silent_p.T38T|RPL27A_ENST00000531978.1_Silent_p.T95T|SNORA45_ENST00000391305.1_RNA|RPL27A_ENST00000526562.1_Silent_p.T38T|RPL27A_ENST00000530913.1_Silent_p.T38T	NM_000990.4	NP_000981.1	P46776	RL27A_HUMAN	ribosomal protein L27a	95					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAAACAAGACTGGGGCTGCTC	0.438													T|||	676	0.134984	0.2617	0.1009	5008	,	,		20797	0.0635		0.0646	False		,,,				2504	0.1339				p.T95T		Atlas-SNP	.											.	RPL27A	5	.	0			c.T285G						PASS	.	T		924,3478	352.3+/-311.7	107,710,1384	154.0	160.0	158.0		285	-10.0	0.3	11	dbSNP_52	158	736,7856	178.3+/-227.7	33,670,3593	no	coding-synonymous	RPL27A	NM_000990.4		140,1380,4977	GG,GT,TT		8.5661,20.9905,12.7751		95/149	8706406	1660,11334	2201	4296	6497	SO:0001819	synonymous_variant	6157	exon4			CAAGACTGGGGCT	U14968	CCDS7790.1	11p15	2011-04-06				ENSG00000166441		"""L ribosomal proteins"""	10329	protein-coding gene	gene with protein product		603637				7772601, 9582194	Standard	NM_000990		Approved	L27A	uc001mgs.4	P46776		ENST00000314138.6:c.285T>G	11.37:g.8706406T>G		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	169	74	0.43787	NM_000990	B2R4B3	Silent	SNP	ENST00000314138.6	37	CCDS7790.1																																																																																			T|0.877;G|0.123	0.123	strong		0.438	RPL27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386506.1	NM_000990	
C17orf82	388407	hgsc.bcm.edu	37	17	59489893	59489893	+	Missense_Mutation	SNP	T	T	C	rs200497494|rs9907379	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:59489893T>C	ENST00000335108.2	+	1	782	c.557T>C	c.(556-558)cTc>cCc	p.L186P	RP11-332H18.4_ENST00000592009.1_RNA	NM_203425.1	NP_982249	Q86X59	CQ082_HUMAN	chromosome 17 open reading frame 82	186			L -> P (in dbSNP:rs9907379). {ECO:0000269|PubMed:15489334}.							cervix(1)|lung(1)	2						CGGCAACTCCTCACAGGTCCA	0.731													C|||	3623	0.723442	0.7769	0.6571	5008	,	,		12512	0.7004		0.8002	False		,,,				2504	0.6431				p.L186P		Atlas-SNP	.											C17orf82_ENST00000335108,NS,carcinoma,0,2	C17orf82	16	2	0			c.T557C						scavenged	.	C	PRO/LEU	3143,775		1281,581,97	4.0	6.0	5.0		557	0.9	0.1	17	dbSNP_119	5	6355,1647		2560,1235,206	no	missense	C17orf82	NM_203425.1	98	3841,1816,303	CC,CT,TT		20.5824,19.7805,20.3188	benign	186/252	59489893	9498,2422	1959	4001	5960	SO:0001583	missense	388407	exon1			AACTCCTCACAGG	BC046200	CCDS11628.1	17q23.2	2012-10-23			ENSG00000187013	ENSG00000187013			32699	protein-coding gene	gene with protein product							Standard	NM_203425		Approved		uc002izh.1	Q86X59	OTTHUMG00000180077	ENST00000335108.2:c.557T>C	17.37:g.59489893T>C	ENSP00000335229:p.Leu186Pro	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_203425		Missense_Mutation	SNP	ENST00000335108.2	37	CCDS11628.1	1628	0.7454212454212454	382	0.7764227642276422	236	0.6519337016574586	399	0.6975524475524476	611	0.8060686015831134	C	8.991	0.977736	0.18812	0.802195	0.794176	ENSG00000187013	ENST00000335108	T	0.58210	0.35	4.29	0.931	0.19460	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.40031	P	0.024463000000000013	B	0.02656	0.0	B	0.01281	0.0	T	0.21109	-1.0255	8	0.39692	T	0.17	.	1.8756	0.03217	0.1483:0.381:0.2903:0.1804	rs9907379;rs17846388;rs17859430;rs57634035;rs9907379	186	Q86X59	CQ082_HUMAN	P	186	ENSP00000335229:L186P	ENSP00000335229:L186P	L	+	2	0	C17orf82	56844675	0.009000	0.17119	0.119000	0.21687	0.106000	0.19336	0.032000	0.13732	-0.103000	0.12175	-0.380000	0.06706	CTC	T|0.261;C|0.739	0.739	strong		0.731	C17orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449646.1	NM_203425	
LNPEP	4012	hgsc.bcm.edu	37	5	96315320	96315320	+	Missense_Mutation	SNP	C	C	G	rs61752351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:96315320C>G	ENST00000231368.5	+	2	1190	c.498C>G	c.(496-498)atC>atG	p.I166M	LNPEP_ENST00000395770.3_Missense_Mutation_p.I152M	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	166					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		GGGCACAGATCAGGCTTCCCA	0.458													C|||	33	0.00658946	0.0008	0.0115	5008	,	,		21134	0.0		0.0209	False		,,,				2504	0.0031				p.I166M		Atlas-SNP	.											.	LNPEP	80	.	0			c.C498G						PASS	.	C	MET/ILE,MET/ILE	19,4387	26.2+/-53.5	0,19,2184	94.0	92.0	93.0		498,456	-1.4	0.2	5	dbSNP_129	93	168,8432	78.9+/-141.6	2,164,4134	yes	missense,missense	LNPEP	NM_005575.2,NM_175920.3	10,10	2,183,6318	GG,GC,CC		1.9535,0.4312,1.4378	benign,benign	166/1026,152/1012	96315320	187,12819	2203	4300	6503	SO:0001583	missense	4012	exon2			ACAGATCAGGCTT	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"""cystinyl aminopeptidase"", ""placental leucine aminopeptidase"""	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.498C>G	5.37:g.96315320C>G	ENSP00000231368:p.Ile166Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	23	0.010531135531135532	0	0.0	5	0.013812154696132596	0	0.0	18	0.023746701846965697	C	0.007	-1.961172	0.00465	0.004312	0.019535	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.04275	3.66;3.66	5.78	-1.36	0.09085	.	1.298990	0.04688	N	0.413675	T	0.01222	0.0040	N	0.08118	0	0.09310	N	0.999999	B	0.06786	0.001	B	0.17098	0.017	T	0.45833	-0.9234	10	0.25751	T	0.34	.	3.8746	0.09051	0.1147:0.1325:0.4957:0.2571	rs61752351	166	Q9UIQ6	LCAP_HUMAN	M	166;152	ENSP00000231368:I166M;ENSP00000379117:I152M	ENSP00000231368:I166M	I	+	3	3	LNPEP	96341076	0.048000	0.20356	0.200000	0.23457	0.089000	0.18198	-0.030000	0.12308	0.047000	0.15862	-0.226000	0.12346	ATC	C|0.986;G|0.014	0.014	strong		0.458	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575	
MAST1	22983	hgsc.bcm.edu	37	19	12958697	12958697	+	Silent	SNP	T	T	C	rs2290688	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12958697T>C	ENST00000251472.4	+	7	639	c.600T>C	c.(598-600)ttT>ttC	p.F200F	MAST1_ENST00000591495.1_Silent_p.F196F	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						TGCGCGACTTTACCCGCGCCT	0.692											OREG0025277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2516	0.502396	0.6664	0.3473	5008	,	,		16382	0.621		0.2893	False		,,,				2504	0.4877				p.F200F		Atlas-SNP	.											MAST1_ENST00000251472,NS,carcinoma,0,2	MAST1	214	2	0			c.T600C						PASS	.	C		2717,1689	490.8+/-361.9	853,1011,339	40.0	35.0	36.0		600	1.1	1.0	19	dbSNP_100	36	2297,6301	679.6+/-403.6	283,1731,2285	no	coding-synonymous	MAST1	NM_014975.2		1136,2742,2624	CC,CT,TT		26.7155,38.3341,38.5574		200/1571	12958697	5014,7990	2203	4299	6502	SO:0001819	synonymous_variant	22983	exon7			CGACTTTACCCGC	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.600T>C	19.37:g.12958697T>C		Somatic	95	0	0	683	WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_014975		Silent	SNP	ENST00000251472.4	37	CCDS32921.1																																																																																			T|0.575;C|0.425	0.425	strong		0.692	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975	
LAX1	54900	hgsc.bcm.edu	37	1	203743653	203743653	+	Silent	SNP	C	C	T	rs3766748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:203743653C>T	ENST00000442561.2	+	5	1431	c.1041C>T	c.(1039-1041)gaC>gaT	p.D347D	LAX1_ENST00000367215.1_3'UTR|LAX1_ENST00000367217.5_Silent_p.D331D	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	347					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			ATTATGCAGACTTTCAGCCAT	0.453													C|||	1428	0.285144	0.289	0.1628	5008	,	,		24361	0.2321		0.331	False		,,,				2504	0.3742				p.D347D		Atlas-SNP	.											.	LAX1	48	.	0			c.C1041T						PASS	.	C	,	1294,3112	438.0+/-345.2	171,952,1080	125.0	120.0	122.0		993,1041	1.0	0.0	1	dbSNP_107	122	2800,5800	442.1+/-360.0	465,1870,1965	no	coding-synonymous,coding-synonymous	LAX1	NM_001136190.1,NM_017773.3	,	636,2822,3045	TT,TC,CC		32.5581,29.369,31.4778	,	331/383,347/399	203743653	4094,8912	2203	4300	6503	SO:0001819	synonymous_variant	54900	exon5			TGCAGACTTTCAG	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"""LAT-like membrane associated protein"", ""linker for activation of x cells"""					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.1041C>T	1.37:g.203743653C>T		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Silent	SNP	ENST00000442561.2	37	CCDS1441.2																																																																																			C|0.699;T|0.301	0.301	strong		0.453	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773	
OR2W5	441932	hgsc.bcm.edu	37	1	247654498	247654498	+	RNA	SNP	G	G	A	rs61070846	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:247654498G>A	ENST00000522351.1	+	0	129							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)			GGCCTGGACTGGAGAAAATTC	0.488													g|||	647	0.129193	0.1483	0.2176	5008	,	,		18871	0.0288		0.1909	False		,,,				2504	0.0808				p.L23L		Atlas-SNP	.											.	OR2W5	97	.	0			c.G69A						PASS	.	A		647,3759	277.5+/-273.7	41,565,1597	164.0	149.0	154.0		69	-3.0	0.0	1	dbSNP_129	154	1810,6790	326.0+/-317.2	186,1438,2676	no	coding-synonymous	OR2W5	NM_001004698.2		227,2003,4273	AA,AG,GG		21.0465,14.6845,18.8913		23/321	247654498	2457,10549	2203	4300	6503			441932	exon1			TGGACTGGAGAAA			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.247654498G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	264	124	0.469697	NM_001004698	B9EH85	Silent	SNP	ENST00000522351.1	37																																																																																				G|0.820;A|0.180	0.180	strong		0.488	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
ANAPC2	29882	hgsc.bcm.edu	37	9	140079522	140079522	+	Silent	SNP	G	G	A	rs11549106	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140079522G>A	ENST00000323927.2	-	4	895	c.891C>T	c.(889-891)gtC>gtT	p.V297V		NM_013366.3	NP_037498.1	Q9UJX6	ANC2_HUMAN	anaphase promoting complex subunit 2	297					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.000858)		CGAGCCAGCCGACCACCCGCT	0.697													G|||	927	0.185104	0.1657	0.1268	5008	,	,		14730	0.0417		0.2425	False		,,,				2504	0.3415				p.V297V		Atlas-SNP	.											.	ANAPC2	57	.	0			c.C891T						PASS	.	G		648,3478		70,508,1485	14.0	12.0	13.0		891	-6.3	1.0	9	dbSNP_120	13	1925,6183		246,1433,2375	no	coding-synonymous	ANAPC2	NM_013366.3		316,1941,3860	AA,AG,GG		23.742,15.7053,21.0316		297/823	140079522	2573,9661	2063	4054	6117	SO:0001819	synonymous_variant	29882	exon4			CCAGCCGACCACC	AB037827	CCDS7033.1	9q34.3	2011-06-15			ENSG00000176248	ENSG00000176248		"""Anaphase promoting complex subunits"""	19989	protein-coding gene	gene with protein product		606946				11739784	Standard	NM_013366		Approved	APC2, KIAA1406	uc004clr.1	Q9UJX6	OTTHUMG00000020983	ENST00000323927.2:c.891C>T	9.37:g.140079522G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_013366	Q5VSG1|Q96DG5|Q96GG4|Q9P2E1	Silent	SNP	ENST00000323927.2	37	CCDS7033.1																																																																																			G|0.814;A|0.186	0.186	strong		0.697	ANAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055315.1	NM_013366	
GABPB2	126626	hgsc.bcm.edu	37	1	151062957	151062957	+	Missense_Mutation	SNP	G	G	A	rs11204774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:151062957G>A	ENST00000368918.3	+	3	515	c.184G>A	c.(184-186)Gtt>Att	p.V62I	GABPB2_ENST00000368917.1_Missense_Mutation_p.V62I|GABPB2_ENST00000368916.1_Missense_Mutation_p.V62I	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	62			V -> I (in dbSNP:rs11204774).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		TCGAGCAGGTGTTAGCAGGGA	0.507													G|||	275	0.0549121	0.1339	0.0346	5008	,	,		18969	0.0		0.0656	False		,,,				2504	0.0082				p.V62I		Atlas-SNP	.											.	GABPB2	41	.	0			c.G184A						PASS	.	G	ILE/VAL	665,3741	283.4+/-277.1	52,561,1590	122.0	108.0	112.0		184	5.5	0.9	1	dbSNP_120	112	705,7895	173.9+/-224.3	28,649,3623	yes	missense	GABPB2	NM_144618.2	29	80,1210,5213	AA,AG,GG		8.1977,15.0931,10.5336	benign	62/449	151062957	1370,11636	2203	4300	6503	SO:0001583	missense	126626	exon3			GCAGGTGTTAGCA		CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458		"""Ankyrin repeat domain containing"""	28441	protein-coding gene	gene with protein product						7958862	Standard	NM_144618		Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.184G>A	1.37:g.151062957G>A	ENSP00000357914:p.Val62Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_144618	B1AVJ8|D3DV14|Q8NAR5	Missense_Mutation	SNP	ENST00000368918.3	37	CCDS983.1	128	0.05860805860805861	61	0.12398373983739837	12	0.03314917127071823	0	0.0	55	0.07255936675461741	G	19.61	3.860454	0.71834	0.150931	0.081977	ENSG00000143458	ENST00000368918;ENST00000368917;ENST00000446567;ENST00000368916	T;T;T	0.40225	1.04;1.04;1.04	5.46	5.46	0.80206	Ankyrin repeat-containing domain (3);	0.056829	0.64402	D	0.000001	T	0.40956	0.1138	N	0.21583	0.68	0.18873	P	0.9999867038	P;P	0.48764	0.915;0.558	D;B	0.64877	0.93;0.154	T	0.11275	-1.0594	9	0.32370	T	0.25	-11.65	18.0974	0.89494	0.0:0.0:1.0:0.0	rs11204774;rs59365643;rs11204774	78;62	B4DXA3;Q8TAK5	.;GABP2_HUMAN	I	62;62;78;62	ENSP00000357914:V62I;ENSP00000357913:V62I;ENSP00000357912:V62I	ENSP00000357912:V62I	V	+	1	0	GABPB2	149329581	1.000000	0.71417	0.908000	0.35775	0.984000	0.73092	9.368000	0.97152	2.861000	0.98227	0.650000	0.86243	GTT	G|0.910;A|0.090	0.090	strong		0.507	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033700.2	NM_144618	
SOWAHC	65124	hgsc.bcm.edu	37	2	110373197	110373197	+	Silent	SNP	G	G	A	rs1560884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:110373197G>A	ENST00000356454.3	+	1	1287	c.1131G>A	c.(1129-1131)aaG>aaA	p.K377K	SEPT10_ENST00000397714.2_5'Flank|SEPT10_ENST00000356688.4_5'Flank|SEPT10_ENST00000334001.6_5'Flank|SEPT10_ENST00000437928.1_5'Flank|SEPT10_ENST00000545389.1_5'Flank|SEPT10_ENST00000397712.2_5'Flank|SEPT10_ENST00000415095.1_5'Flank	NM_023016.3	NP_075392.2	Q53LP3	SWAHC_HUMAN	sosondowah ankyrin repeat domain family member C	377																	GTGGGAAAAAGGCCTCCCAGT	0.657													G|||	1623	0.324081	0.2526	0.4697	5008	,	,		16294	0.3929		0.2575	False		,,,				2504	0.3149				p.K377K		Atlas-SNP	.											.	.	.	.	0			c.G1131A						PASS	.	G		1206,3200	388.6+/-327.0	156,894,1153	48.0	55.0	53.0		1131	1.6	0.1	2	dbSNP_88	53	2121,6479	341.3+/-324.0	258,1605,2437	no	coding-synonymous	ANKRD57	NM_023016.3		414,2499,3590	AA,AG,GG		24.6628,27.3718,25.5805		377/526	110373197	3327,9679	2203	4300	6503	SO:0001819	synonymous_variant	65124	exon1			GAAAAAGGCCTCC	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.1131G>A	2.37:g.110373197G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_023016	Q8NE15|Q9H6U1	Silent	SNP	ENST00000356454.3	37	CCDS33270.1																																																																																			G|0.728;A|0.272	0.272	strong		0.657	SOWAHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330168.1	NM_023016	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383215	41383215	+	Silent	SNP	G	G	C	rs2302986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41383215G>C	ENST00000301146.4	-	7	1582	c.1041C>G	c.(1039-1041)acC>acG	p.T347T	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Silent_p.T296T	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)			AGGGCATCTTGGTCCGGTCCT	0.532													.|||	563	0.11242	0.0325	0.1455	5008	,	,		17595	0.1796		0.1044	False		,,,				2504	0.136				p.T347T		Atlas-SNP	.											.	CYP2A7	71	.	0			c.C1041G						PASS	.	G	,	207,4199	129.4+/-166.1	8,191,2004	111.0	92.0	99.0		1041,888	0.9	0.4	19	dbSNP_100	99	963,7633	210.5+/-251.4	75,813,3410	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	83,1004,5414	CC,CG,GG		11.2029,4.6981,8.9986	,	347/495,296/444	41383215	1170,11832	2203	4298	6501	SO:0001819	synonymous_variant	1549	exon7			CATCTTGGTCCGG	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.1041C>G	19.37:g.41383215G>C		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	319	148	0.46395	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			G|0.904;C|0.096	0.096	strong		0.532	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377094	168377094	+	lincRNA	SNP	G	G	A	rs75642682|rs9364375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168377094G>A	ENST00000538528.1	-	0	525																											TGCAGTGTGGGGGGAGGAGAA	0.627																																					p.P80L		Atlas-SNP	.											.	.	.	.	0			c.C239T						PASS	.						4.0	6.0	5.0					6																	168377094		639	1519	2158			0	exon1			GTGTGGGGGGAGG																													6.37:g.168377094G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	200	25	0.125	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				G|0.500;A|0.500	0.500	weak		0.627	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
STAB1	23166	hgsc.bcm.edu	37	3	52540773	52540773	+	Silent	SNP	T	T	C	rs1010553	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:52540773T>C	ENST00000321725.6	+	18	1972	c.1896T>C	c.(1894-1896)ggT>ggC	p.G632G		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	632	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CCGCCAATGGTGTGATCCACA	0.667													C|||	3199	0.638778	0.8601	0.4265	5008	,	,		18395	0.5446		0.4682	False		,,,				2504	0.7628				p.G632G		Atlas-SNP	.											STAB1,trunk,malignant_melanoma,+1,1	STAB1	178	1	0			c.T1896C						scavenged	.	C		3617,789	311.1+/-291.9	1492,633,78	63.0	58.0	60.0		1896	-9.9	0.1	3	dbSNP_86	60	4119,4479	585.3+/-391.9	1009,2101,1189	no	coding-synonymous	STAB1	NM_015136.2		2501,2734,1267	CC,CT,TT		47.9065,17.9074,40.5106		632/2571	52540773	7736,5268	2203	4299	6502	SO:0001819	synonymous_variant	23166	exon18			CAATGGTGTGATC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.1896T>C	3.37:g.52540773T>C		Somatic	147	2	0.0136054		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			T|0.407;C|0.593	0.593	strong		0.667	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
SEMA3A	10371	hgsc.bcm.edu	37	7	83634713	83634713	+	Silent	SNP	A	A	G	rs7804122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:83634713A>G	ENST00000265362.4	-	11	1616	c.1302T>C	c.(1300-1302)atT>atC	p.I434I	SEMA3A_ENST00000436949.1_Silent_p.I434I	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	434	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						GGTCTACGACAATTTGTGTAA	0.368													A|||	1128	0.22524	0.2678	0.1729	5008	,	,		15936	0.1548		0.2058	False		,,,				2504	0.2975				p.I434I		Atlas-SNP	.											SEMA3A,colon,carcinoma,0,1	SEMA3A	121	1	0			c.T1302C						PASS	.	A		1158,3248	408.4+/-334.6	161,836,1206	195.0	175.0	182.0		1302	-0.1	1.0	7	dbSNP_116	182	1894,6706	332.4+/-320.1	221,1452,2627	no	coding-synonymous	SEMA3A	NM_006080.2		382,2288,3833	GG,GA,AA		22.0233,26.2823,23.4661		434/772	83634713	3052,9954	2203	4300	6503	SO:0001819	synonymous_variant	10371	exon11			TACGACAATTTGT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1302T>C	7.37:g.83634713A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_006080		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			A|0.771;G|0.229	0.229	strong		0.368	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	
NCOR1	9611	hgsc.bcm.edu	37	17	16005030	16005030	+	Missense_Mutation	SNP	T	T	C	rs150909544		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16005030T>C	ENST00000268712.3	-	20	2481	c.2224A>G	c.(2224-2226)Act>Gct	p.T742A	NCOR1_ENST00000395851.1_Missense_Mutation_p.T758A|NCOR1_ENST00000395848.1_Missense_Mutation_p.T649A|NCOR1_ENST00000583226.1_5'Flank|RNU6-314P_ENST00000516574.1_RNA	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	742					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)		CCTCGAGAAGTAGCATTTTCA	0.483													T|||	1	0.000199681	0.0008	0.0	5008	,	,		21166	0.0		0.0	False		,,,				2504	0.0				p.T758A		Atlas-SNP	.											.	NCOR1	240	.	0			c.A2272G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	1,4405	2.1+/-5.4	0,1,2202	93.0	88.0	90.0		1945,2272,2224	-10.8	0.0	17	dbSNP_134	90	0,8600		0,0,4300	no	missense,missense,missense	NCOR1	NM_001190438.1,NM_001190440.1,NM_006311.3	58,58,58	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,benign	649/915,758/2338,742/2441	16005030	1,13005	2203	4300	6503	SO:0001583	missense	9611	exon19			GAGAAGTAGCATT	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.2224A>G	17.37:g.16005030T>C	ENSP00000268712:p.Thr742Ala	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	7.122	0.578209	0.13686	2.27E-4	0.0	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395848	T;T;T	0.27402	3.47;1.67;1.67	5.77	-10.8	0.00216	.	0.521213	0.24063	N	0.041899	T	0.08313	0.0207	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.25187	-1.0139	10	0.27082	T	0.32	0.119	4.1227	0.10112	0.1739:0.4619:0.1847:0.1796	.	649;742;758	E9PGV6;O75376;O75376-2	.;NCOR1_HUMAN;.	A	742;758;649;649	ENSP00000268712:T742A;ENSP00000379192:T758A;ENSP00000379189:T649A	ENSP00000268712:T742A	T	-	1	0	NCOR1	15945755	0.008000	0.16893	0.027000	0.17364	0.990000	0.78478	-0.887000	0.04152	-1.821000	0.01213	-0.290000	0.09829	ACT	T|1.000;C|0.000	0.000	weak		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
RBM19	9904	hgsc.bcm.edu	37	12	114395651	114395651	+	Missense_Mutation	SNP	T	T	C	rs10850256	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:114395651T>C	ENST00000545145.2	-	6	854	c.776A>G	c.(775-777)aAg>aGg	p.K259R	RBM19_ENST00000261741.5_Missense_Mutation_p.K259R|RBM19_ENST00000392561.3_Missense_Mutation_p.K259R	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	259				K -> R (in Ref. 1; BAA31657 and 6; AAH06137/AAH04289). {ECO:0000305}.	multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCCTGCACCCTTGCTGTCTCT	0.592													T|||	1069	0.213458	0.407	0.0821	5008	,	,		17914	0.1806		0.1143	False		,,,				2504	0.181				p.K259R		Atlas-SNP	.											.	RBM19	117	.	0			c.A776G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	1678,2728	509.1+/-367.1	339,1000,864	156.0	138.0	144.0		776,776,776	-6.1	0.0	12	dbSNP_120	144	886,7714	198.7+/-243.0	38,810,3452	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	26,26,26	377,1810,4316	CC,CT,TT		10.3023,38.0844,19.714	benign,benign,benign	259/961,259/961,259/961	114395651	2564,10442	2203	4300	6503	SO:0001583	missense	9904	exon6			GCACCCTTGCTGT	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.776A>G	12.37:g.114395651T>C	ENSP00000442053:p.Lys259Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	142	59	0.415493	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	378	0.17307692307692307	165	0.3353658536585366	29	0.08011049723756906	98	0.17132867132867133	86	0.11345646437994723	T	7.544	0.661283	0.14645	0.380844	0.103023	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05649	3.41;3.41;3.41	4.51	-6.07	0.02158	Nucleotide-binding, alpha-beta plait (1);	4.525770	0.00710	N	0.000820	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47249	-0.9132	9	0.20519	T	0.43	0.3269	7.0053	0.24833	0.0:0.3222:0.3793:0.2985	rs10850256;rs17850047;rs17857776;rs10850256	259	Q9Y4C8	RBM19_HUMAN	R	259	ENSP00000442053:K259R;ENSP00000376344:K259R;ENSP00000261741:K259R	ENSP00000261741:K259R	K	-	2	0	RBM19	112880034	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.091000	0.11146	-1.269000	0.02436	-1.074000	0.02243	AAG	T|0.808;C|0.192	0.192	strong		0.592	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
PHLDB2	90102	hgsc.bcm.edu	37	3	111688578	111688578	+	Silent	SNP	C	C	T	rs774854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:111688578C>T	ENST00000431670.2	+	16	3768	c.3357C>T	c.(3355-3357)gaC>gaT	p.D1119D	PHLDB2_ENST00000495180.1_Silent_p.D610D|PHLDB2_ENST00000393923.3_Silent_p.D1103D|PHLDB2_ENST00000481953.1_Silent_p.D1076D|PHLDB2_ENST00000412622.1_Silent_p.D1076D|PHLDB2_ENST00000393925.3_Silent_p.D1119D	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	1119						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						GGAAGGAAGACTTTGATTTGC	0.448													C|||	911	0.181909	0.289	0.1311	5008	,	,		16544	0.0655		0.1551	False		,,,				2504	0.2209				p.D1119D		Atlas-SNP	.											.	PHLDB2	449	.	0			c.C3357T						PASS	.	C	,,,	1210,3196	419.1+/-338.5	158,894,1151	81.0	84.0	83.0		3309,3357,3357,3228	3.8	1.0	3	dbSNP_86	83	1610,6990	297.1+/-303.3	155,1300,2845	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PHLDB2	NM_001134437.1,NM_001134438.1,NM_001134439.1,NM_145753.2	,,,	313,2194,3996	TT,TC,CC		18.7209,27.4626,21.6823	,,,	1103/1238,1119/1254,1119/1254,1076/1211	111688578	2820,10186	2203	4300	6503	SO:0001819	synonymous_variant	90102	exon16			GGAAGACTTTGAT		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.3357C>T	3.37:g.111688578C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Silent	SNP	ENST00000431670.2	37	CCDS46886.1																																																																																			C|0.808;T|0.192	0.192	strong		0.448	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753	
CER1	9350	hgsc.bcm.edu	37	9	14722616	14722616	+	Missense_Mutation	SNP	G	G	A	rs10115703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:14722616G>A	ENST00000380911.3	-	1	99	c.55C>T	c.(55-57)Cgg>Tgg	p.R19W		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	19			R -> W (in dbSNP:rs10115703). {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)		TCCTGGTGCCGTGTGGTCTTT	0.532													G|||	457	0.091254	0.1089	0.1282	5008	,	,		17449	0.0179		0.0815	False		,,,				2504	0.1268				p.R19W		Atlas-SNP	.											CER1,NS,carcinoma,+2,1	CER1	41	1	0			c.C55T	GRCh37	CM067359	CER1	M	rs10115703	PASS	.	G	TRP/ARG	418,3988	204.8+/-226.9	17,384,1802	80.0	81.0	80.0		55	-11.8	0.0	9	dbSNP_119	80	713,7887	174.9+/-225.1	26,661,3613	yes	missense	CER1	NM_005454.2	101	43,1045,5415	AA,AG,GG		8.2907,9.4871,8.696	possibly-damaging	19/268	14722616	1131,11875	2203	4300	6503	SO:0001583	missense	9350	exon1			GGTGCCGTGTGGT	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.55C>T	9.37:g.14722616G>A	ENSP00000370297:p.Arg19Trp	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Missense_Mutation	SNP	ENST00000380911.3	37	CCDS6476.1	182	0.08333333333333333	68	0.13821138211382114	51	0.1408839779005525	5	0.008741258741258742	58	0.07651715039577836	G	3.846	-0.032878	0.07543	0.094871	0.082907	ENSG00000147869	ENST00000380911	T	0.18016	2.24	5.92	-11.8	0.00035	.	2.511830	0.01028	N	0.004089	T	0.00073	0.0002	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.25012	-1.0144	9	0.62326	D	0.03	3.5839	0.9882	0.01451	0.3205:0.1387:0.1372:0.4035	rs10115703;rs60750353;rs10115703	19	O95813	CER1_HUMAN	W	19	ENSP00000370297:R19W	ENSP00000370297:R19W	R	-	1	2	CER1	14712616	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.422000	0.00476	-4.349000	0.00055	-0.895000	0.02911	CGG	G|0.912;A|0.088	0.088	strong		0.532	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454	
OBSCN	84033	hgsc.bcm.edu	37	1	228467072	228467072	+	Silent	SNP	C	C	G	rs185248802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228467072C>G	ENST00000422127.1	+	27	7367	c.7323C>G	c.(7321-7323)acC>acG	p.T2441T	OBSCN_ENST00000359599.6_Silent_p.T1288T|OBSCN_ENST00000570156.2_Silent_p.T2870T|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.T2441T|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2441					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)				TGCGGCGGACCTGCTCCACCA	0.697													C|||	15	0.00299521	0.0008	0.0014	5008	,	,		15002	0.0		0.0119	False		,,,				2504	0.001				p.T2870T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C8610G						PASS	.	C	,	8,4214		0,8,2103	40.0	48.0	45.0		7323,7323	2.7	1.0	1		45	85,8337		0,85,4126	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,93,6229	GG,GC,CC		1.0093,0.1895,0.7355	,	2441/7969,2441/6621	228467072	93,12551	2111	4211	6322	SO:0001819	synonymous_variant	84033	exon32			GCGGACCTGCTCC	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.7323C>G	1.37:g.228467072C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	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|0.989;G|0.011	0.011	strong		0.697	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MUC16	94025	hgsc.bcm.edu	37	19	9005674	9005674	+	Silent	SNP	G	G	A	rs4804091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9005674G>A	ENST00000397910.4	-	46	39935	c.39732C>T	c.(39730-39732)gaC>gaT	p.D13244D	MUC16_ENST00000380951.5_5'Flank	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13246	SEA 8. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGATTTTGGGGTCAGGGCGGT	0.582													N|||	1104	0.220447	0.1528	0.2939	5008	,	,		18886	0.2212		0.2793	False		,,,				2504	0.1984				p.D13244D		Atlas-SNP	.											.	MUC16	4315	.	0			c.C39732T						PASS	.	A		796,3300		77,642,1329	98.0	93.0	95.0		39732	-0.4	0.0	19	dbSNP_111	95	2503,5855		346,1811,2022	no	coding-synonymous	MUC16	NM_024690.2		423,2453,3351	AA,AG,GG		29.9474,19.4336,26.4895		13244/14508	9005674	3299,9155	2048	4179	6227	SO:0001819	synonymous_variant	94025	exon46			TTTGGGGTCAGGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.39732C>T	19.37:g.9005674G>A		Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	506	0.2316849816849817	62	0.12601626016260162	102	0.281767955801105	141	0.2465034965034965	201	0.26517150395778366	.	2.958	-0.215194	0.06101	0.194336	0.299474	ENSG00000181143	ENST00000542240	.	.	.	3.31	-0.436	0.12275	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.38499	-0.9658	3	.	.	.	-15.3585	3.311	0.07016	0.2474:0.0:0.5502:0.2024	rs4804091	.	.	.	I	84	.	.	T	-	2	0	MUC16	8866674	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.480000	0.06559	-0.105000	0.12132	-0.372000	0.07161	ACC	G|0.754;A|0.246	0.246	strong		0.582	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRR12	57479	hgsc.bcm.edu	37	19	50100484	50100484	+	Silent	SNP	G	G	A	rs77535345	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50100484G>A	ENST00000418929.2	+	4	2904	c.2892G>A	c.(2890-2892)aaG>aaA	p.K964K		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							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)		ACTACGGCAAGGCCGGGCCAC	0.682													G|||	271	0.0541134	0.0514	0.0288	5008	,	,		11669	0.006		0.0467	False		,,,				2504	0.1329				p.K964K		Atlas-SNP	.											.	PRR12	157	.	0			c.G2892A						PASS	.	G		219,3661		9,201,1730	5.0	7.0	6.0		2892	3.8	1.0	19	dbSNP_132	6	398,7748		4,390,3679	no	coding-synonymous	PRR12	NM_020719.1		13,591,5409	AA,AG,GG		4.8858,5.6443,5.1306		964/2037	50100484	617,11409	1940	4073	6013	SO:0001819	synonymous_variant	57479	exon4			CGGCAAGGCCGGG	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.2892G>A	19.37:g.50100484G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_020719	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																			G|0.963;A|0.037	0.037	strong		0.682	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
NEK4	6787	hgsc.bcm.edu	37	3	52780205	52780205	+	Missense_Mutation	SNP	A	A	G	rs34986855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:52780205A>G	ENST00000233027.5	-	10	1901	c.1699T>C	c.(1699-1701)Ttt>Ctt	p.F567L	NEK4_ENST00000535191.1_Missense_Mutation_p.F478L|NEK4_ENST00000383721.4_Missense_Mutation_p.F521L	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	567			F -> L (in dbSNP:rs34986855). {ECO:0000269|PubMed:17344846}.		mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		GAAGGCAAAAATCGAGGAGGC	0.418													A|||	66	0.0131789	0.0023	0.0115	5008	,	,		19175	0.001		0.0348	False		,,,				2504	0.0194				p.F567L		Atlas-SNP	.											.	NEK4	51	.	0			c.T1699C						PASS	.	A	LEU/PHE,LEU/PHE	29,4377	32.6+/-62.9	0,29,2174	120.0	117.0	118.0		1432,1699	2.3	0.0	3	dbSNP_126	118	304,8296	101.0+/-162.3	3,298,3999	yes	missense,missense	NEK4	NM_001193533.1,NM_003157.4	22,22	3,327,6173	GG,GA,AA		3.5349,0.6582,2.5604	benign,benign	478/753,567/842	52780205	333,12673	2203	4300	6503	SO:0001583	missense	6787	exon10			GCAAAAATCGAGG	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.1699T>C	3.37:g.52780205A>G	ENSP00000233027:p.Phe567Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	37	CCDS2863.1	30	0.013736263736263736	3	0.006097560975609756	3	0.008287292817679558	1	0.0017482517482517483	23	0.030343007915567283	A	0.004	-2.301416	0.00243	0.006582	0.035349	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.70164	2.35;2.35;-0.46;2.35	5.05	2.3	0.28687	.	0.682217	0.12893	N	0.430387	T	0.04634	0.0126	N	0.00162	-1.95	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	0.28235	-1.0050	10	0.02654	T	1	.	3.4221	0.07397	0.0844:0.1486:0.4628:0.3042	rs34986855	478;521;567	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	L	567;478;521;478	ENSP00000233027:F567L;ENSP00000437703:F478L;ENSP00000373227:F521L;ENSP00000419666:F478L	ENSP00000233027:F567L	F	-	1	0	NEK4	52755245	0.002000	0.14202	0.028000	0.17463	0.004000	0.04260	0.941000	0.29005	0.188000	0.20168	-2.559000	0.00174	TTT	A|0.975;G|0.025	0.025	strong		0.418	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
ZIM2	23619	hgsc.bcm.edu	37	19	57286688	57286688	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57286688G>A	ENST00000391708.3	-	12	1494	c.952C>T	c.(952-954)Ccc>Tcc	p.P318S	ZIM2_ENST00000601070.1_Missense_Mutation_p.P318S|AC006115.3_ENST00000597946.1_RNA|ZIM2_ENST00000599935.1_Missense_Mutation_p.P318S|AC006115.3_ENST00000595954.1_RNA|ZIM2_ENST00000593711.1_Missense_Mutation_p.P318S|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000221722.5_Missense_Mutation_p.P318S	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	318					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)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		GCTGACTGGGGACTCGTACAT	0.448																																					p.P318S		Atlas-SNP	.											ZIM2,NS,malignant_melanoma,+1,1	ZIM2	511	1	0			c.C952T						PASS	.						136.0	126.0	130.0					19																	57286688		2203	4300	6503	SO:0001583	missense	23619	exon11			ACTGGGGACTCGT	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"""Zinc fingers, C2H2-type"""	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.952C>T	19.37:g.57286688G>A	ENSP00000375589:p.Pro318Ser	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	310	149	0.480645	NM_015363	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	37	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	G	5.759	0.324523	0.10900	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.05081	3.5;3.5	3.89	-0.711	0.11230	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	.	.	.	B	0.23058	0.079	B	0.18263	0.021	T	0.39354	-0.9618	8	0.87932	D	0	.	3.4921	0.07641	0.3462:0.1968:0.4569:0.0	.	318	Q9NZV7	ZIM2_HUMAN	S	318	ENSP00000375589:P318S;ENSP00000221722:P318S	ENSP00000221722:P318S	P	-	1	0	ZIM2	61978500	.	.	0.000000	0.03702	0.211000	0.24417	.	.	-0.024000	0.13941	0.655000	0.94253	CCC	.	.	none		0.448	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2		
PACS2	23241	hgsc.bcm.edu	37	14	105858022	105858022	+	Missense_Mutation	SNP	C	C	T	rs147461490	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105858022C>T	ENST00000325438.8	+	21	2633	c.2129C>T	c.(2128-2130)cCg>cTg	p.P710L	PACS2_ENST00000458164.2_Missense_Mutation_p.P725L|PACS2_ENST00000547217.1_Missense_Mutation_p.P680L|PACS2_ENST00000551801.1_5'UTR|PACS2_ENST00000447393.1_Missense_Mutation_p.P714L|PACS2_ENST00000551743.1_Missense_Mutation_p.P224L|PACS2_ENST00000430725.2_Missense_Mutation_p.P635L			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	710					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		TCCACCCCGCCGTCCGCATCT	0.716													C|||	84	0.0167732	0.0008	0.0447	5008	,	,		13167	0.0		0.0388	False		,,,				2504	0.0133				p.P725L		Atlas-SNP	.											PACS2,caecum,carcinoma,-1,4	PACS2	75	4	0			c.C2174T						PASS	.	C	LEU/PRO,LEU/PRO	55,4331		0,55,2138	20.0	21.0	21.0		2141,2129	3.1	0.8	14	dbSNP_134	21	439,8153		10,419,3867	no	missense,missense	PACS2	NM_001100913.2,NM_015197.3	98,98	10,474,6005	TT,TC,CC		5.1094,1.254,3.8064	possibly-damaging,possibly-damaging	714/894,710/890	105858022	494,12484	2193	4296	6489	SO:0001583	missense	23241	exon22			CCCCGCCGTCCGC	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"""phosphofurin acidic cluster sorting protein 1-like"""	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.2129C>T	14.37:g.105858022C>T	ENSP00000321834:p.Pro710Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	35	0.660377	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Missense_Mutation	SNP	ENST00000325438.8	37	CCDS32168.1	49	0.022435897435897436	3	0.006097560975609756	19	0.052486187845303865	0	0.0	27	0.03562005277044855	C	15.13	2.741116	0.49151	0.01254	0.051094	ENSG00000179364	ENST00000430725;ENST00000325438;ENST00000458164;ENST00000447393;ENST00000547217;ENST00000551743	T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61	4.97	3.08	0.35506	.	0.126903	0.53938	D	0.000048	T	0.18593	0.0446	L	0.47190	1.495	0.80722	D	1	D;D;B;D	0.89917	0.958;0.989;0.144;1.0	B;P;B;D	0.91635	0.36;0.512;0.028;0.999	T	0.20840	-1.0263	10	0.54805	T	0.06	-13.6782	9.0338	0.36275	0.0:0.7676:0.1489:0.0836	.	714;725;710;711	E9PB38;Q86VP3-2;Q86VP3;Q86VP3-3	.;.;PACS2_HUMAN;.	L	635;710;725;714;680;224	ENSP00000393524:P635L;ENSP00000321834:P710L;ENSP00000399732:P725L;ENSP00000393559:P714L;ENSP00000449525:P680L;ENSP00000449254:P224L	ENSP00000321834:P710L	P	+	2	0	PACS2	104929067	1.000000	0.71417	0.751000	0.31187	0.292000	0.27327	5.588000	0.67517	0.459000	0.27016	0.462000	0.41574	CCG	C|0.965;T|0.035	0.035	strong		0.716	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
GPR56	9289	hgsc.bcm.edu	37	16	57689385	57689385	+	Missense_Mutation	SNP	C	C	G	rs1801257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57689385C>G	ENST00000388812.4	+	6	1283	c.843C>G	c.(841-843)agC>agG	p.S281R	GPR56_ENST00000540164.2_Missense_Mutation_p.S281R|GPR56_ENST00000544297.1_Missense_Mutation_p.S106R|GPR56_ENST00000379694.4_Missense_Mutation_p.S111R|GPR56_ENST00000567835.1_Missense_Mutation_p.S281R|GPR56_ENST00000562558.1_Missense_Mutation_p.S281R|GPR56_ENST00000568908.1_Missense_Mutation_p.S281R|GPR56_ENST00000568909.1_Missense_Mutation_p.S281R|GPR56_ENST00000538815.1_Missense_Mutation_p.S281R|GPR56_ENST00000562631.1_Missense_Mutation_p.S281R|GPR56_ENST00000379696.3_Missense_Mutation_p.S281R|GPR56_ENST00000456916.1_Missense_Mutation_p.S281R|GPR56_ENST00000388813.5_Missense_Mutation_p.S281R			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	281			S -> R (in dbSNP:rs1801257). {ECO:0000269|PubMed:10049584, ECO:0000269|PubMed:10100861, ECO:0000269|PubMed:14702039}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						AAGGCCGGAGCGGGGAGGCTG	0.597													A|||	3610	0.720847	0.8918	0.7075	5008	,	,		17295	0.8591		0.497	False		,,,				2504	0.5869				p.S286R		Atlas-SNP	.											GPR56,NS,carcinoma,0,1	GPR56	44	1	0			c.C858G						scavenged	.	A	ARG/SER,ARG/SER,ARG/SER,ARG/SER,ARG/SER,ARG/SER,ARG/SER,ARG/SER	3624,772		1490,644,64	52.0	56.0	54.0		843,843,843,858,843,843,843,843	-6.2	0.0	16	dbSNP_89	54	4241,4359		1069,2103,1128	yes	missense,missense,missense,missense,missense,missense,missense,missense	GPR56	NM_001145770.1,NM_001145771.1,NM_001145772.1,NM_001145773.1,NM_001145774.1,NM_005682.5,NM_201524.2,NM_201525.2	110,110,110,110,110,110,110,110	2559,2747,1192	GG,GC,CC		49.314,17.5614,39.4814	benign,benign,benign,benign,benign,benign,benign,benign	281/688,281/694,281/688,286/693,281/688,281/694,281/688,281/688	57689385	7865,5131	2198	4300	6498	SO:0001583	missense	9289	exon6			CCGGAGCGGGGAG	AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.843C>G	16.37:g.57689385C>G	ENSP00000373464:p.Ser281Arg	Somatic	48	1	0.0208333		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001145773	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	ENST00000388812.4	37	CCDS32460.1	1519	0.6955128205128205	431	0.8760162601626016	239	0.6602209944751382	488	0.8531468531468531	361	0.4762532981530343	A	0.001	-3.941006	0.00003	0.824386	0.49314	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.38887	1.11;1.12;1.11;1.12;1.11;1.9;1.29;1.12	5.04	-6.2	0.02072	.	0.303615	0.27214	N	0.020386	T	0.00012	0.0000	N	0.00074	-2.255	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	0.34700	-0.9818	9	0.05525	T	0.97	.	8.5178	0.33257	0.5243:0.2233:0.2524:0.0	rs1801257;rs1801257	106;286;281;281;111	F5H144;B4DR54;Q9Y653-2;Q9Y653;E7ENB2	.;.;.;GPR56_HUMAN;.	R	281;281;281;281;281;106;111;281	ENSP00000373465:S281R;ENSP00000373464:S281R;ENSP00000444415:S281R;ENSP00000398034:S281R;ENSP00000444911:S281R;ENSP00000438006:S106R;ENSP00000369016:S111R;ENSP00000369018:S281R	ENSP00000369016:S111R	S	+	3	2	GPR56	56246886	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.550000	0.02180	-1.221000	0.02591	-1.212000	0.01626	AGC	C|0.364;G|0.636;T|0.000	0.636	strong		0.597	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3		
SALL4	57167	hgsc.bcm.edu	37	20	50408377	50408377	+	Silent	SNP	G	G	C	rs61737139	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:50408377G>C	ENST00000217086.4	-	2	756	c.645C>G	c.(643-645)ctC>ctG	p.L215L	SALL4_ENST00000395997.3_Silent_p.L215L|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	215					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						AGATCTGCTCGAGGACCCACG	0.642													G|||	58	0.0115815	0.0008	0.0115	5008	,	,		18825	0.0		0.0219	False		,,,				2504	0.0276				p.L215L		Atlas-SNP	.											.	SALL4	168	.	0			c.C645G						PASS	.	G		20,4386	26.2+/-53.5	0,20,2183	63.0	64.0	64.0		645	-9.1	0.9	20	dbSNP_129	64	272,8328	97.9+/-159.5	3,266,4031	no	coding-synonymous	SALL4	NM_020436.3		3,286,6214	CC,CG,GG		3.1628,0.4539,2.2451		215/1054	50408377	292,12714	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			CTGCTCGAGGACC	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.645C>G	20.37:g.50408377G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			G|0.974;C|0.026	0.026	strong		0.642	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
C3orf22	152065	hgsc.bcm.edu	37	3	126268918	126268918	+	Silent	SNP	G	G	A	rs869463	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:126268918G>A	ENST00000318225.2	-	4	597	c.219C>T	c.(217-219)ctC>ctT	p.L73L		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	73										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		CTGGAGCCCCGAGCCTAGAGA	0.607													G|||	873	0.174321	0.0356	0.2695	5008	,	,		17005	0.255		0.2485	False		,,,				2504	0.135				p.L73L		Atlas-SNP	.											.	C3orf22	17	.	0			c.C219T						PASS	.	G		355,4051	182.9+/-210.6	13,329,1861	75.0	65.0	69.0		219	-1.6	0.0	3	dbSNP_86	69	2056,6544	356.3+/-330.2	241,1574,2485	no	coding-synonymous	C3orf22	NM_152533.1		254,1903,4346	AA,AG,GG		23.907,8.0572,18.5376		73/142	126268918	2411,10595	2203	4300	6503	SO:0001819	synonymous_variant	152065	exon4			AGCCCCGAGCCTA		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.219C>T	3.37:g.126268918G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_152533	B3KUS9	Silent	SNP	ENST00000318225.2	37	CCDS3040.1																																																																																			G|0.805;A|0.195	0.195	strong		0.607	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
TTI1	9675	hgsc.bcm.edu	37	20	36641522	36641522	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36641522C>T	ENST00000373448.2	-	3	935	c.697G>A	c.(697-699)Gta>Ata	p.V233I	TTI1_ENST00000449821.1_Missense_Mutation_p.V233I|TTI1_ENST00000373447.3_Missense_Mutation_p.V233I|TTI1_ENST00000487362.1_Intron	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	233					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)		p.V233I(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						AGGGAAGATACGACAATGCTG	0.428																																					p.V233I		Atlas-SNP	.											TTI1,rectum,carcinoma,0,1	TTI1	104	1	1	Substitution - Missense(1)	large_intestine(1)	c.G697A						scavenged	.						157.0	154.0	155.0					20																	36641522		2203	4300	6503	SO:0001583	missense	9675	exon3			AAGATACGACAAT	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"""smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	614425	"""KIAA0406"", ""Tel2 interacting protein 1 homolog (S. pombe)"""	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.697G>A	20.37:g.36641522C>T	ENSP00000362547:p.Val233Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	137	5	0.0364963	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	C	0.900	-0.722465	0.03182	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.15139	2.45;2.45;2.45	5.45	3.38	0.38709	Armadillo-like helical (1);Armadillo-type fold (1);	0.302894	0.36409	N	0.002618	T	0.11707	0.0285	L	0.38175	1.15	0.09310	N	1	B	0.19331	0.035	B	0.15052	0.012	T	0.15578	-1.0432	10	0.33141	T	0.24	-27.6647	6.4202	0.21740	0.1648:0.6876:0.0:0.1476	.	233	O43156	TTI1_HUMAN	I	233	ENSP00000362547:V233I;ENSP00000362546:V233I;ENSP00000407270:V233I	ENSP00000362546:V233I	V	-	1	0	TTI1	36074936	0.420000	0.25457	0.013000	0.15412	0.755000	0.42902	1.413000	0.34725	1.517000	0.48917	-0.188000	0.12872	GTA	.	.	none		0.428	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657	
STON1	11037	hgsc.bcm.edu	37	2	48808152	48808152	+	Missense_Mutation	SNP	G	G	C	rs940389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48808152G>C	ENST00000406226.1	+	3	575	c.380G>C	c.(379-381)aGa>aCa	p.R127T	STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.R127T|STON1_ENST00000309835.3_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.R127T|STON1_ENST00000404752.1_Missense_Mutation_p.R127T	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	127			R -> T (in dbSNP:rs940389).		endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTGCCTACCAGACCAACATGT	0.463													G|||	1781	0.355631	0.3079	0.3271	5008	,	,		22141	0.3919		0.341	False		,,,				2504	0.4182				p.R127T		Atlas-SNP	.											.	STON1	100	.	0			c.G380C						PASS	.	G	THR/ARG,THR/ARG,THR/ARG,THR/ARG,THR/ARG	1400,3006	458.0+/-351.8	227,946,1030	110.0	106.0	108.0		380,380,380,380,380	2.8	0.0	2	dbSNP_86	108	2852,5748	448.7+/-361.9	492,1868,1940	yes	missense,missense,missense,missense,missense	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	71,71,71,71,71	719,2814,2970	CC,CG,GG		33.1628,31.7749,32.6926	benign,benign,benign,benign,benign	127/1159,127/1136,127/736,127/736,127/1183	48808152	4252,8754	2203	4300	6503	SO:0001583	missense	11037	exon3			CTACCAGACCAAC	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.380G>C	2.37:g.48808152G>C	ENSP00000384615:p.Arg127Thr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	37	CCDS1841.1	768	0.3516483516483517	153	0.31097560975609756	105	0.2900552486187845	239	0.4178321678321678	271	0.3575197889182058	G	1.930	-0.446092	0.04604	0.317749	0.331628	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.10005	2.92;2.92;2.92;2.92;2.92;2.92;2.92;3.09	5.24	2.83	0.33086	.	0.643344	0.17146	N	0.185261	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.27625	0.183;0.0;0.039	B;B;B	0.28011	0.085;0.0;0.034	T	0.47368	-0.9123	9	0.33141	T	0.24	.	7.6523	0.28354	0.7847:0.141:0.0743:0.0	rs940389;rs3749141;rs52795264;rs940389	127;127;127	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	T	127	ENSP00000385273:R127T;ENSP00000384615:R127T;ENSP00000310969:R127T;ENSP00000385499:R127T;ENSP00000385701:R127T;ENSP00000378236:R127T;ENSP00000311493:R127T;ENSP00000378234:R127T	ENSP00000310969:R127T	R	+	2	0	STON1-GTF2A1L;STON1	48661656	0.015000	0.18098	0.002000	0.10522	0.002000	0.02628	0.909000	0.28558	0.517000	0.28361	-0.302000	0.09304	AGA	G|0.659;C|0.341	0.341	strong		0.463	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
OR5P2	120065	hgsc.bcm.edu	37	11	7817852	7817852	+	Missense_Mutation	SNP	C	C	G	rs76615008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7817852C>G	ENST00000329434.2	-	1	668	c.638G>C	c.(637-639)tGc>tCc	p.C213S	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATAGATGTAGCAGACGGCTAT	0.493													G|||	1185	0.236621	0.3472	0.2911	5008	,	,		18597	0.128		0.2763	False		,,,				2504	0.1196				p.C213S		Atlas-SNP	.											.	OR5P2	68	.	0			c.G638C						PASS	.	G	SER/CYS	1372,2840		401,570,1135	99.0	103.0	102.0		638	5.5	1.0	11	dbSNP_131	102	2424,6160		393,1638,2261	no	missense	OR5P2	NM_153444.1	112	794,2208,3396	GG,GC,CC		28.2386,32.5736,29.6655	benign	213/323	7817852	3796,9000	2106	4292	6398	SO:0001583	missense	120065	exon1			ATGTAGCAGACGG	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.638G>C	11.37:g.7817852C>G	ENSP00000331823:p.Cys213Ser	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	G	1.419	-0.573385	0.03882	0.325736	0.282386	ENSG00000183303	ENST00000329434	T	0.35048	1.33	5.5	5.5	0.81552	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00000	-3.99	0.48975	P	2.609999999999557E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.48514	-0.9029	9	0.02654	T	1	-60.4257	14.3625	0.66782	0.0:0.1489:0.8511:0.0	.	213	Q8WZ92	OR5P2_HUMAN	S	213	ENSP00000331823:C213S	ENSP00000331823:C213S	C	-	2	0	OR5P2	7774428	1.000000	0.71417	0.985000	0.45067	0.597000	0.36814	3.226000	0.51254	1.580000	0.49851	-0.225000	0.12378	TGC	C|0.738;G|0.262	0.262	strong		0.493	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
OR9G1	390174	hgsc.bcm.edu	37	11	56467945	56467945	+	Missense_Mutation	SNP	G	G	T	rs36184181|rs397849604	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56467945G>T	ENST00000312153.1	+	1	82	c.82G>T	c.(82-84)Gtg>Ttg	p.V28L		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GGGCCTCTTCGTGGTGTTCCT	0.502													G|||	4	0.000798722	0.0	0.0	5008	,	,		18770	0.001		0.0	False		,,,				2504	0.0031				p.V28L		Atlas-SNP	.											.	.	.	.	0			c.G82T						PASS	.	G	LEU/VAL	497,3905		0,497,1704	164.0	141.0	149.0		82	2.6	0.0	11	dbSNP_126	149	2528,6064		0,2528,1768	yes	missense	OR9G1	NM_001005213.1	32	0,3025,3472	TT,TG,GG		29.4227,11.2903,23.28	benign	28/306	56467945	3025,9969	2201	4296	6497	SO:0001583	missense	504191	exon1			CTCTTCGTGGTGT	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.82G>T	11.37:g.56467945G>T	ENSP00000309012:p.Val28Leu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	184	38	0.206522	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	773	0.35393772893772896	65	0.13211382113821138	162	0.44751381215469616	244	0.42657342657342656	302	0.39841688654353563	G	0.022	-1.408655	0.01155	0.112903	0.294227	ENSG00000174914	ENST00000312153	T	0.00448	7.38	4.52	2.63	0.31362	.	0.289314	0.24649	N	0.036723	T	0.00012	0.0000	N	0.11789	0.175	0.09310	N	1	B	0.14012	0.009	B	0.19148	0.024	T	0.31916	-0.9926	10	0.07482	T	0.82	-9.336	9.4573	0.38762	0.2451:0.0:0.7549:0.0	rs36184181	28	Q8NH87	OR9G1_HUMAN	L	28	ENSP00000309012:V28L	ENSP00000309012:V28L	V	+	1	0	OR9G1	56224521	0.000000	0.05858	0.006000	0.13384	0.011000	0.07611	-0.943000	0.03917	0.621000	0.30232	0.573000	0.79308	GTG	G|0.646;T|0.354	0.354	strong		0.502	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
SCTR	6344	hgsc.bcm.edu	37	2	120194680	120194680	+	IGR	SNP	C	C	G	rs72833259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:120194680C>G	ENST00000019103.5	-	0	1865				TMEM37_ENST00000306406.4_Silent_p.A79A|TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Silent_p.A91A	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)	TGGGCCAGGCCCATGTGCCCG	0.667													C|||	71	0.0141773	0.003	0.0144	5008	,	,		14497	0.001		0.0209	False		,,,				2504	0.0358				p.A79A		Atlas-SNP	.											.	TMEM37	40	.	0			c.C237G						PASS	.	C		21,4383	28.1+/-56.4	0,21,2181	50.0	53.0	52.0		237	1.8	0.0	2	dbSNP_130	52	234,8366	95.2+/-157.0	2,230,4068	no	coding-synonymous	TMEM37	NM_183240.2		2,251,6249	GG,GC,CC		2.7209,0.4768,1.9609		79/191	120194680	255,12749	2202	4300	6502	SO:0001628	intergenic_variant	140738	exon2			CCAGGCCCATGTG		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.120194680C>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	42	27	0.642857	NM_183240	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	37	CCDS2127.1																																																																																			C|0.983;G|0.017	0.017	strong		0.667	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
DPYD	1806	hgsc.bcm.edu	37	1	98157291	98157291	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:98157291C>T	ENST00000370192.3	-	7	844	c.744G>A	c.(742-744)atG>atA	p.M248I	DPYD_ENST00000474241.1_5'UTR|DPYD_ENST00000423006.2_3'UTR	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	248					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	CAAGGTCCTTCATTAGCTCAA	0.373																																					p.M248I		Atlas-SNP	.											DPYD,NS,carcinoma,-1,1	DPYD	219	1	0			c.G744A						scavenged	.						106.0	106.0	106.0					1																	98157291		2203	4300	6503	SO:0001583	missense	1806	exon7			GTCCTTCATTAGC	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.744G>A	1.37:g.98157291C>T	ENSP00000359211:p.Met248Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.781147	0.49891	.	.	ENSG00000188641	ENST00000370192	D	0.94417	-3.42	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.86744	0.6006	L	0.28740	0.885	0.80722	D	1	B	0.18741	0.03	B	0.15870	0.014	T	0.82481	-0.0436	10	0.24483	T	0.36	-22.6226	18.7184	0.91685	0.0:1.0:0.0:0.0	.	248	Q12882	DPYD_HUMAN	I	248	ENSP00000359211:M248I	ENSP00000359211:M248I	M	-	3	0	DPYD	97929879	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.705000	0.68355	2.497000	0.84241	0.460000	0.39030	ATG	.	.	none		0.373	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
DIDO1	11083	hgsc.bcm.edu	37	20	61528271	61528271	+	Missense_Mutation	SNP	C	C	T	rs1883847	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61528271C>T	ENST00000266070.4	-	7	1991	c.1666G>A	c.(1666-1668)Gcg>Acg	p.A556T	DIDO1_ENST00000395335.2_Missense_Mutation_p.A556T|DIDO1_ENST00000395343.1_Missense_Mutation_p.A556T|DIDO1_ENST00000395340.1_Missense_Mutation_p.A556T	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	556			A -> T (in dbSNP:rs1883847). {ECO:0000269|PubMed:16127461}.		apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A556T(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					TTGCCCACCGCGGAGCCTGGA	0.562													C|||	1399	0.279353	0.3026	0.3112	5008	,	,		17584	0.3323		0.1948	False		,,,				2504	0.2577				p.A556T	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,0,1	DIDO1	321	1	1	Substitution - Missense(1)	stomach(1)	c.G1666A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	1135,3271	396.0+/-329.9	149,837,1217	35.0	37.0	36.0		1666,1666,1666,1666	-8.2	0.0	20	dbSNP_92	36	1838,6762	318.6+/-313.7	205,1428,2667	yes	missense,missense,missense,missense	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	58,58,58,58	354,2265,3884	TT,TC,CC		21.3721,25.7603,22.8587	benign,benign,benign,benign	556/2241,556/1190,556/2241,556/1190	61528271	2973,10033	2203	4300	6503	SO:0001583	missense	11083	exon7			CCACCGCGGAGCC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1666G>A	20.37:g.61528271C>T	ENSP00000266070:p.Ala556Thr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	161	71	0.440994	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	560	0.2564102564102564	136	0.2764227642276423	112	0.30939226519337015	178	0.3111888111888112	134	0.17678100263852242	C	10.19	1.281329	0.23392	0.257603	0.213721	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.12672	3.04;3.04;2.66;2.66	5.71	-8.25	0.01025	.	1.786570	0.03882	N	0.277200	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B	0.15930	0.014;0.015	B;B	0.08055	0.003;0.003	T	0.44937	-0.9295	9	0.06757	T	0.87	0.9897	12.6879	0.56958	0.1107:0.5888:0.0:0.3005	rs1883847;rs57309326;rs1883847	556;556	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	T	556	ENSP00000266070:A556T;ENSP00000378752:A556T;ENSP00000378749:A556T;ENSP00000378744:A556T	ENSP00000266070:A556T	A	-	1	0	DIDO1	60998716	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.603000	0.02077	-1.541000	0.01727	-0.222000	0.12452	GCG	C|0.752;T|0.248	0.248	strong		0.562	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
PTGR1	22949	hgsc.bcm.edu	37	9	114359624	114359624	+	Missense_Mutation	SNP	C	C	A	rs1053959	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114359624C>A	ENST00000407693.2	-	2	341	c.79G>T	c.(79-81)Gct>Tct	p.A27S	PTGR1_ENST00000238248.3_5'UTR|PTGR1_ENST00000309195.5_Missense_Mutation_p.A27S|PTGR1_ENST00000538962.1_Missense_Mutation_p.A27S	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	27			A -> S (in dbSNP:rs1053959). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						GGGAGCTCAGCTGTCTTCAAC	0.413													C|||	2994	0.597843	0.5492	0.5836	5008	,	,		22278	0.6587		0.5696	False		,,,				2504	0.6401				p.A27S	Ovarian(200;132 2151 7551 19220 46064)	Atlas-SNP	.											.	PTGR1	23	.	0			c.G79T						PASS	.	C	SER/ALA,SER/ALA,SER/ALA	2471,1935	620.5+/-393.6	705,1061,437	111.0	100.0	104.0		79,79,79	-0.4	0.0	9	dbSNP_86	104	5173,3427	637.2+/-399.2	1574,2025,701	yes	missense,missense,missense	PTGR1	NM_001146108.1,NM_001146109.1,NM_012212.3	99,99,99	2279,3086,1138	AA,AC,CC		39.8488,43.9174,41.2271	benign,benign,benign	27/330,27/302,27/330	114359624	7644,5362	2203	4300	6503	SO:0001583	missense	22949	exon2			GCTCAGCTGTCTT	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"""zinc binding alcohol dehydrogenase domain containing 3"""	601274	"""leukotriene B4 12-hydroxydehydrogenase"""	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.79G>T	9.37:g.114359624C>A	ENSP00000385763:p.Ala27Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Missense_Mutation	SNP	ENST00000407693.2	37	CCDS6779.1	1279	0.5856227106227107	286	0.5813008130081301	213	0.5883977900552486	341	0.5961538461538461	439	0.579155672823219	C	9.694	1.152557	0.21371	0.560826	0.601512	ENSG00000106853	ENST00000538962;ENST00000309195;ENST00000407693;ENST00000333580;ENST00000422125;ENST00000374313;ENST00000374308	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	4.63	-0.431	0.12295	GroES-like (1);	0.644240	0.16715	N	0.202489	T	0.00012	0.0000	N	0.20328	0.56	0.58432	P	1.0000000000287557E-6	B;B	0.16802	0.019;0.004	B;B	0.20577	0.03;0.007	T	0.44097	-0.9350	9	0.10636	T	0.68	0.4782	8.6856	0.34236	0.0:0.5206:0.0:0.4794	rs1053959;rs3178286;rs3194516;rs12553022;rs16916236;rs17846129;rs17859135;rs58734827	27;27	F5GY50;Q14914	.;PTGR1_HUMAN	S	27	ENSP00000440281:A27S;ENSP00000311572:A27S;ENSP00000385763:A27S;ENSP00000395965:A27S	ENSP00000311572:A27S	A	-	1	0	PTGR1	113399445	0.001000	0.12720	0.038000	0.18304	0.955000	0.61496	0.091000	0.15046	-0.078000	0.12730	0.462000	0.41574	GCT	C|0.410;A|0.590	0.590	strong		0.413	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2		
GPR158	57512	hgsc.bcm.edu	37	10	25888180	25888180	+	Missense_Mutation	SNP	A	A	G	rs10828833	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:25888180A>G	ENST00000376351.3	+	11	3984	c.3625A>G	c.(3625-3627)Atc>Gtc	p.I1209V	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1209			I -> V (in dbSNP:rs10828833).		protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GAAAGAAGAGATCTGGGATAG	0.438													G|||	3323	0.663538	0.9652	0.5144	5008	,	,		18834	0.7579		0.3956	False		,,,				2504	0.5399				p.I1209V		Atlas-SNP	.											GPR158,right_upper_lobe,carcinoma,-2,1	GPR158	255	1	0			c.A3625G						PASS	.	G	VAL/ILE	3819,587		1656,507,40	43.0	51.0	48.0		3625	3.1	0.1	10	dbSNP_120	48	3647,4951		764,2119,1416	yes	missense	GPR158	NM_020752.2	29	2420,2626,1456	GG,GA,AA		42.4168,13.3227,42.5869	benign	1209/1216	25888180	7466,5538	2203	4299	6502	SO:0001583	missense	57512	exon11			GAAGAGATCTGGG	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3625A>G	10.37:g.25888180A>G	ENSP00000365529:p.Ile1209Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	45	27	0.6	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	1407	0.6442307692307693	467	0.9491869918699187	199	0.5497237569060773	432	0.7552447552447552	309	0.4076517150395778	G	0.009	-1.856044	0.00558	0.866773	0.424168	ENSG00000151025	ENST00000376351	T	0.59083	0.29	5.92	3.1	0.35709	.	1.738420	0.03741	N	0.255005	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	0.40079	-0.9582	9	0.02654	T	1	.	10.728	0.46079	0.2544:0.0:0.7456:0.0	rs10828833;rs17639060;rs52832343;rs58605179;rs10828833	1209	Q5T848	GP158_HUMAN	V	1209	ENSP00000365529:I1209V	ENSP00000365529:I1209V	I	+	1	0	GPR158	25928186	0.991000	0.36638	0.145000	0.22337	0.573000	0.36030	2.214000	0.42853	0.136000	0.18733	-0.119000	0.15052	ATC	A|0.388;G|0.612	0.612	strong		0.438	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
EML2	24139	hgsc.bcm.edu	37	19	46133256	46133256	+	Missense_Mutation	SNP	G	G	A	rs7252175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46133256G>A	ENST00000245925.3	-	7	609	c.559C>T	c.(559-561)Ctc>Ttc	p.L187F	EML2_ENST00000589876.1_Missense_Mutation_p.L187F|EML2_ENST00000536630.1_Missense_Mutation_p.L334F|EML2_ENST00000586902.1_5'UTR|EML2_ENST00000587152.1_Missense_Mutation_p.L388F	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	187	Tandem atypical propeller in EMLs. {ECO:0000250}.		L -> F (in dbSNP:rs7252175).		negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CACACCGAGAGCATGTGATCA	0.572													G|||	647	0.129193	0.1626	0.1297	5008	,	,		16961	0.1032		0.1083	False		,,,				2504	0.1319				p.L388F		Atlas-SNP	.											EML2,colon,carcinoma,+2,1	EML2	64	1	0			c.C1162T						PASS	.		PHE/LEU,PHE/LEU,PHE/LEU	674,3732	284.6+/-277.7	64,546,1593	195.0	125.0	149.0		1162,1000,559	4.7	1.0	19	dbSNP_116	149	1141,7459	234.0+/-267.1	81,979,3240	yes	missense,missense,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	22,22,22	145,1525,4833	AA,AG,GG		13.2674,15.2973,13.9551	probably-damaging,probably-damaging,probably-damaging	388/851,334/797,187/650	46133256	1815,11191	2203	4300	6503	SO:0001583	missense	24139	exon10			CCGAGAGCATGTG	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.559C>T	19.37:g.46133256G>A	ENSP00000245925:p.Leu187Phe	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	273	0.125	94	0.1910569105691057	48	0.13259668508287292	53	0.09265734265734266	78	0.10290237467018469	G	17.13	3.311155	0.60414	0.152973	0.132674	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.50277	0.75;0.75;4.77	4.74	4.74	0.60224	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.00328	0.0010	M	0.93197	3.39	0.09310	P	0.99999586405	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.999;0.999	T	0.25813	-1.0121	9	0.87932	D	0	-21.5047	15.2691	0.73686	0.0:0.0:1.0:0.0	rs7252175;rs59814666;rs7252175	187;353;334;345;187	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	F	334;187;388;345	ENSP00000442365:L334F;ENSP00000245925:L187F;ENSP00000382503:L345F	ENSP00000245925:L187F	L	-	1	0	EML2	50825096	1.000000	0.71417	0.983000	0.44433	0.792000	0.44763	4.183000	0.58317	2.491000	0.84063	0.305000	0.20034	CTC	G|0.857;A|0.143	0.143	strong		0.572	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
CCAR1	55749	hgsc.bcm.edu	37	10	70549579	70549579	+	Silent	SNP	G	G	A	rs11594683	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:70549579G>A	ENST00000265872.6	+	24	3419	c.3300G>A	c.(3298-3300)tcG>tcA	p.S1100S	CCAR1_ENST00000543719.1_Silent_p.S1085S|CCAR1_ENST00000535016.1_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	182	0	0		WXS	Illumina HiSeq	Phase_I	205	95	0.463415	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	
TMEM120B	144404	hgsc.bcm.edu	37	12	122209423	122209423	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:122209423G>A	ENST00000449592.2	+	8	748	c.647G>A	c.(646-648)cGc>cAc	p.R216H	TMEM120B_ENST00000540377.1_Intron	NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	216						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)		CAGAAGTTTCGCAACCAGTTC	0.488																																					p.R216H		Atlas-SNP	.											TMEM120B_ENST00000449592,NS,carcinoma,+1,2	TMEM120B	43	2	0			c.G647A						scavenged	.						206.0	183.0	190.0					12																	122209423		1867	4107	5974	SO:0001583	missense	144404	exon8			AGTTTCGCAACCA	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.647G>A	12.37:g.122209423G>A	ENSP00000404991:p.Arg216His	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	224	3	0.0133929	NM_001080825	A0PK01|B3KX33	Missense_Mutation	SNP	ENST00000449592.2	37	CCDS41852.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.491867	0.64074	.	.	ENSG00000188735	ENST00000449592;ENST00000541467	T;T	0.35789	1.29;1.29	5.43	4.51	0.55191	.	0.049151	0.85682	D	0.000000	T	0.68851	0.3046	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.78099	-0.2336	10	0.62326	D	0.03	-27.3826	14.8539	0.70319	0.0:0.1451:0.8549:0.0	.	216	A0PK00	T120B_HUMAN	H	216;195	ENSP00000404991:R216H;ENSP00000442105:R195H	ENSP00000345152:R216H	R	+	2	0	TMEM120B	120693806	1.000000	0.71417	0.803000	0.32268	0.229000	0.25112	9.608000	0.98331	1.241000	0.43820	0.514000	0.50259	CGC	.	.	none		0.488	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402158.1	NM_001080825	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255506	25255506	+	Silent	SNP	C	C	T	rs11642611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:25255506C>T	ENST00000328086.7	-	6	2384	c.1581G>A	c.(1579-1581)aaG>aaA	p.K527K		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	527					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)		ACAATTTGCTCTTCCGATGAC	0.498													C|||	1672	0.333866	0.4713	0.3026	5008	,	,		18387	0.3294		0.2107	False		,,,				2504	0.3016				p.K527K		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.G1581A						PASS	.	C		1983,2411	548.5+/-377.6	450,1083,664	68.0	68.0	68.0		1581	2.3	1.0	16	dbSNP_120	68	1784,6816	316.7+/-312.9	181,1422,2697	no	coding-synonymous	ZKSCAN2	NM_001012981.4		631,2505,3361	TT,TC,CC		20.7442,45.1297,28.9903		527/968	25255506	3767,9227	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon6			TTTGCTCTTCCGA	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.1581G>A	16.37:g.25255506C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			C|0.698;T|0.302	0.302	strong		0.498	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
WNK2	65268	hgsc.bcm.edu	37	9	96052295	96052295	+	Silent	SNP	C	C	G	rs4744216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96052295C>G	ENST00000297954.4	+	21	5013	c.5013C>G	c.(5011-5013)gcC>gcG	p.A1671A	WNK2_ENST00000427277.2_Silent_p.A1246A|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Silent_p.A1283A|WNK2_ENST00000395477.2_Silent_p.A1634A	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1671					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CTCGAGGGGCCGTGATGGAGC	0.557													C|||	508	0.101438	0.0567	0.1931	5008	,	,		18250	0.0794		0.165	False		,,,				2504	0.0542				p.A1634A		Atlas-SNP	.											.	WNK2	277	.	0			c.C4902G						PASS	.	C		287,4111		8,271,1920	56.0	43.0	47.0		4902	-7.8	0.0	9	dbSNP_111	47	1109,7465		87,935,3265	no	coding-synonymous	WNK2	NM_006648.3		95,1206,5185	GG,GC,CC		12.9345,6.5257,10.7616		1634/2218	96052295	1396,11576	2199	4287	6486	SO:0001819	synonymous_variant	65268	exon20			AGGGGCCGTGATG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.5013C>G	9.37:g.96052295C>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		285|285	0.1304945054945055|0.1304945054945055	35|35	0.07113821138211382|0.07113821138211382	66|66	0.18232044198895028|0.18232044198895028	60|60	0.1048951048951049|0.1048951048951049	124|124	0.16358839050131926|0.16358839050131926	C|C	4.351|4.351	0.064678|0.064678	0.08388|0.08388	0.065257|0.065257	0.129345|0.129345	ENSG00000165238|ENSG00000165238	ENST00000432730;ENST00000448251;ENST00000453718|ENST00000411624	.|.	.|.	.|.	3.88|3.88	-7.75|-7.75	0.01236|0.01236	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.58432|0.58432	P|P	9.000000000036756E-6|9.000000000036756E-6	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.14172|0.14172	-1.0482|-1.0482	3|3	.|.	.|.	.|.	.|.	4.9979|4.9979	0.14249|0.14249	0.0956:0.5305:0.1214:0.2525|0.0956:0.5305:0.1214:0.2525	rs4744216;rs17342460;rs59448703|rs4744216;rs17342460;rs59448703	.|.	.|.	.|.	R|G	1630;431;157|1238	.|.	.|.	P|R	+|+	2|1	0|0	WNK2|WNK2	95092116|95092116	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.063000|0.063000	0.16089|0.16089	-2.141000|-2.141000	0.01300|0.01300	-2.184000|-2.184000	0.00762|0.00762	-1.267000|-1.267000	0.01435|0.01435	CCG|CGT	C|0.887;G|0.112	0.112	strong		0.557	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
SEZ6L	23544	hgsc.bcm.edu	37	22	26693026	26693026	+	Missense_Mutation	SNP	C	C	A	rs146559583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26693026C>A	ENST00000248933.6	+	4	1237	c.1142C>A	c.(1141-1143)aCc>aAc	p.T381N	SEZ6L_ENST00000529632.2_Missense_Mutation_p.T381N|SEZ6L_ENST00000403121.1_Missense_Mutation_p.T154N|SEZ6L_ENST00000343706.4_Missense_Mutation_p.T381N|SEZ6L_ENST00000404234.3_Missense_Mutation_p.T381N|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T381N|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T154N			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	381	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				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						GGCCTTGGGACCTTCCAGCTT	0.542																																					p.T381N		Atlas-SNP	.											.	SEZ6L	174	.	0			c.C1142A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR	0,4406		0,0,2203	41.0	37.0	38.0		1142,1142,1142,1142,1142,1142	1.7	0.9	22	dbSNP_134	38	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense,missense,missense,missense	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	65,65,65,65,65,65	0,6,6497	AA,AC,CC		0.0698,0.0,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	381/1024,381/1014,381/1012,381/950,381/949,381/1025	26693026	6,13000	2203	4300	6503	SO:0001583	missense	23544	exon4			TTGGGACCTTCCA	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.1142C>A	22.37:g.26693026C>A	ENSP00000248933:p.Thr381Asn	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088478	0.36855	0.0	6.98E-4	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24;2.24;2.24	5.13	1.7	0.24286	CUB (5);	0.214517	0.31071	N	0.008302	T	0.16128	0.0388	L	0.55481	1.735	0.80722	D	1	B;B;B;B;B;B;B	0.23990	0.033;0.075;0.016;0.061;0.095;0.034;0.044	B;B;B;B;B;B;B	0.24848	0.03;0.056;0.016;0.033;0.038;0.022;0.056	T	0.05468	-1.0883	10	0.34782	T	0.22	.	10.0647	0.42297	0.2781:0.5879:0.134:0.0	.	381;381;154;381;381;381;381	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	N	381;381;381;381;381;154;154	ENSP00000384772:T381N;ENSP00000437037:T381N;ENSP00000354185:T381N;ENSP00000248933:T381N;ENSP00000342661:T381N;ENSP00000384838:T154N;ENSP00000384733:T154N	ENSP00000248933:T381N	T	+	2	0	SEZ6L	25023026	0.954000	0.32549	0.916000	0.36221	0.995000	0.86356	1.759000	0.38420	0.139000	0.18822	0.561000	0.74099	ACC	C|1.000;A|0.000	0.000	strong		0.542	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
CSE1L	1434	hgsc.bcm.edu	37	20	47685320	47685320	+	Silent	SNP	G	G	C	rs2227946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:47685320G>C	ENST00000262982.2	+	7	759	c.636G>C	c.(634-636)ctG>ctC	p.L212L	CSE1L_ENST00000396192.3_Silent_p.L212L|CSE1L_ENST00000542325.1_Intron	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	212					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TTTCTTCCCTGATCCTGATCT	0.358													G|||	746	0.148962	0.2186	0.1844	5008	,	,		17604	0.0407		0.2107	False		,,,				2504	0.0777				p.L212L		Atlas-SNP	.											.	CSE1L	83	.	0			c.G636C						PASS	.	G		938,3468	357.4+/-313.9	99,740,1364	181.0	153.0	162.0		636	2.4	1.0	20	dbSNP_98	162	2133,6467	367.5+/-334.7	250,1633,2417	yes	coding-synonymous	CSE1L	NM_001316.2		349,2373,3781	CC,CG,GG		24.8023,21.2892,23.6122		212/972	47685320	3071,9935	2203	4300	6503	SO:0001819	synonymous_variant	1434	exon7			TTCCCTGATCCTG	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"""Exportins"""	2431	protein-coding gene	gene with protein product	"""cellular apoptosis susceptibility"""	601342	"""chromosome segregation 1 (yeast homolog)-like"""			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.636G>C	20.37:g.47685320G>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	269	136	0.505576	NM_001256135	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	37	CCDS13412.1																																																																																			G|0.784;C|0.216	0.216	strong		0.358	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316	
SIAE	54414	hgsc.bcm.edu	37	11	124506967	124506967	+	Silent	SNP	C	C	T	rs7941327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124506967C>T	ENST00000263593.3	-	10	1624	c.1452G>A	c.(1450-1452)acG>acA	p.T484T	RNA5SP352_ENST00000363408.1_RNA|SIAE_ENST00000545756.1_Silent_p.T449T			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	171	0	0		WXS	Illumina HiSeq	Phase_I	177	84	0.474576	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	
GPR39	2863	hgsc.bcm.edu	37	2	133174999	133174999	+	Silent	SNP	A	A	G	rs2241763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133174999A>G	ENST00000329321.3	+	1	853	c.384A>G	c.(382-384)acA>acG	p.T128T		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	128					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACGTGCTGACACTCAGCTTTG	0.582													G|||	1947	0.388778	0.5825	0.3444	5008	,	,		21679	0.2321		0.327	False		,,,				2504	0.3834				p.T128T		Atlas-SNP	.											.	GPR39	60	.	0			c.A384G						PASS	.	G		2351,2055	566.7+/-382.0	618,1115,470	121.0	106.0	111.0		384	-0.9	1.0	2	dbSNP_98	111	2814,5786	676.3+/-403.3	478,1858,1964	no	coding-synonymous	GPR39	NM_001508.2		1096,2973,2434	GG,GA,AA		32.7209,46.6409,39.7124		128/454	133174999	5165,7841	2203	4300	6503	SO:0001819	synonymous_variant	2863	exon1			GCTGACACTCAGC	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.384A>G	2.37:g.133174999A>G		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	177	73	0.412429	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	37	CCDS2170.1																																																																																			A|0.608;G|0.392	0.392	strong		0.582	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
FMR1NB	158521	hgsc.bcm.edu	37	X	147088249	147088249	+	Missense_Mutation	SNP	C	C	T	rs764631	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	38	0	0		WXS	Illumina HiSeq	Phase_I	49	47	0.959184	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	
RTL1	388015	hgsc.bcm.edu	37	14	101349764	101349764	+	Silent	SNP	C	C	T	rs34163305|rs369221263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:101349764C>T	ENST00000534062.1	-	1	1420	c.1362G>A	c.(1360-1362)ccG>ccA	p.P454P	MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	454					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						GCTGTGGGTACGGCTTCTCGT	0.612													C|||	470	0.0938498	0.0136	0.1412	5008	,	,		15877	0.003		0.2296	False		,,,				2504	0.1227				p.P454P		Atlas-SNP	.											.	RTL1	120	.	0			c.G1362A						PASS	.	C		64,1320		3,58,631	28.0	31.0	30.0		1362	-3.8	0.3	14	dbSNP_126	30	797,2385		113,571,907	no	coding-synonymous	RTL1	NM_001134888.2		116,629,1538	TT,TC,CC		25.0471,4.6243,18.8568		454/1359	101349764	861,3705	692	1591	2283	SO:0001819	synonymous_variant	388015	exon1			TGGGTACGGCTTC		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.1362G>A	14.37:g.101349764C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001134888	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																			C|0.883;T|0.117	0.117	strong		0.612	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
BMPER	168667	hgsc.bcm.edu	37	7	34125420	34125420	+	Silent	SNP	G	G	T	rs77064045	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:34125420G>T	ENST00000297161.2	+	14	1835	c.1461G>T	c.(1459-1461)ccG>ccT	p.P487P	BMPER_ENST00000426693.1_Silent_p.P487P	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	487	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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						TGGCTGCGCCGCATCTCAAGG	0.443													G|||	948	0.189297	0.1573	0.2089	5008	,	,		21922	0.1002		0.3141	False		,,,				2504	0.182				p.P487P		Atlas-SNP	.											BMPER,left_upper_lobe,carcinoma,+2,1	BMPER	131	1	0			c.G1461T						PASS	.	G		760,3646	310.2+/-291.5	82,596,1525	114.0	101.0	105.0		1461	-11.6	0.6	7	dbSNP_131	105	2456,6144	405.4+/-348.5	360,1736,2204	no	coding-synonymous	BMPER	NM_133468.3		442,2332,3729	TT,TG,GG		28.5581,17.2492,24.727		487/686	34125420	3216,9790	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon14			TGCGCCGCATCTC		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.1461G>T	7.37:g.34125420G>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1																																																																																			G|0.769;T|0.231	0.231	strong		0.443	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
MUC2	4583	hgsc.bcm.edu	37	11	1101649	1101649	+	Silent	SNP	T	T	C	rs7480563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1101649T>C	ENST00000441003.2	+	42	7689	c.7662T>C	c.(7660-7662)ccT>ccC	p.P2554P		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4916					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)	GGTGCTGTCCTTTCTACTGGT	0.627													C|||	3492	0.697284	0.6808	0.6196	5008	,	,		15474	0.9931		0.5219	False		,,,				2504	0.6503				p.P2550P		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.T7650C						PASS	.	C		2577,1589		802,973,308	93.0	103.0	100.0		7647	-5.3	0.0	11	dbSNP_116	100	4354,4066		1136,2082,992	no	coding-synonymous	MUC2	NM_002457.2		1938,3055,1300	CC,CT,TT		48.2898,38.1421,44.9309		2549/2813	1101649	6931,5655	2083	4210	6293	SO:0001819	synonymous_variant	4583	exon43			CTGTCCTTTCTAC	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.7662T>C	11.37:g.1101649T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.346;C|0.654	0.654	strong		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
LRRC19	64922	hgsc.bcm.edu	37	9	26995787	26995787	+	Missense_Mutation	SNP	G	G	A	rs41272237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:26995787G>A	ENST00000380055.5	-	5	955	c.845C>T	c.(844-846)aCg>aTg	p.T282M	IFT74_ENST00000380062.5_Intron|LRRC19_ENST00000482770.1_5'UTR|IFT74_ENST00000443698.1_Intron|IFT74_ENST00000433700.1_Intron|IFT74_ENST00000429045.2_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	282						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)	6		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		AAGTGAAGTCGTCAGTACAGT	0.373													G|||	275	0.0549121	0.0303	0.0317	5008	,	,		17735	0.0288		0.0537	False		,,,				2504	0.1329				p.T282M		Atlas-SNP	.											.	LRRC19	24	.	0			c.C845T						PASS	.	G	,,,MET/THR,	160,4246	108.6+/-147.0	5,150,2048	80.0	73.0	75.0		,,,845,	3.5	0.0	9	dbSNP_127	75	486,8114	142.3+/-198.5	11,464,3825	yes	intron,intron,intron,missense,intron	LRRC19,IFT74	NM_001099222.1,NM_001099223.1,NM_001099224.1,NM_022901.2,NM_025103.2	,,,81,	16,614,5873	AA,AG,GG		5.6512,3.6314,4.9669	,,,benign,	,,,282/371,	26995787	646,12360	2203	4300	6503	SO:0001583	missense	64922	exon5			GAAGTCGTCAGTA	AK024955	CCDS6518.1	9p21.1	2008-02-05			ENSG00000184434	ENSG00000184434			23379	protein-coding gene	gene with protein product							Standard	NM_022901		Approved	FLJ21302	uc003zqh.3	Q9H756	OTTHUMG00000019710	ENST00000380055.5:c.845C>T	9.37:g.26995787G>A	ENSP00000369395:p.Thr282Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_022901	A0AV00|B9EG91	Missense_Mutation	SNP	ENST00000380055.5	37	CCDS6518.1	86	0.039377289377289376	9	0.018292682926829267	15	0.04143646408839779	17	0.02972027972027972	45	0.059366754617414245	G	1.352	-0.591147	0.03799	0.036314	0.056512	ENSG00000184434	ENST00000380055	T	0.50548	0.74	4.72	3.5	0.40072	.	1.132640	0.06444	N	0.726486	T	0.02119	0.0066	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07712	-1.0758	10	0.33141	T	0.24	1.5351	7.1144	0.25409	0.7251:0.1893:0.0855:0.0	rs41272237	282	Q9H756	LRC19_HUMAN	M	282	ENSP00000369395:T282M	ENSP00000369395:T282M	T	-	2	0	LRRC19	26985787	0.000000	0.05858	0.013000	0.15412	0.210000	0.24377	0.285000	0.18883	0.934000	0.37316	-0.438000	0.05819	ACG	G|0.949;A|0.051	0.051	strong		0.373	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2	NM_022901	
ZNF83	55769	hgsc.bcm.edu	37	19	53117017	53117017	+	Silent	SNP	T	T	G	rs7248435	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53117017T>G	ENST00000597597.1	-	2	3054	c.801A>C	c.(799-801)ggA>ggC	p.G267G	ZNF83_ENST00000391789.4_Silent_p.G267G|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Silent_p.G267G|ZNF83_ENST00000301096.3_Silent_p.G267G|ZNF83_ENST00000544146.1_Silent_p.G267G|ZNF83_ENST00000545872.1_Silent_p.G267G|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Silent_p.G267G			P51522	ZNF83_HUMAN	zinc finger protein 83	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		GGAAGACCTTTCCACATACAT	0.403													T|||	1368	0.273163	0.1649	0.4323	5008	,	,		17989	0.497		0.2137	False		,,,				2504	0.137				p.G267G		Atlas-SNP	.											.	ZNF83	73	.	0			c.A801C						PASS	.	T	,,,,,,,,	384,4022		38,308,1857	84.0	78.0	80.0		801,801,801,801,801,801,801,801,801	0.5	0.1	19	dbSNP_116	80	907,7693		116,675,3509	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF83	NM_001105549.1,NM_001105550.1,NM_001105551.1,NM_001105552.1,NM_001105553.1,NM_001105554.1,NM_001242531.1,NM_001242538.1,NM_018300.3	,,,,,,,,	154,983,5366	GG,GT,TT		10.5465,8.7154,9.9262	,,,,,,,,	267/517,267/517,267/517,267/517,267/489,267/489,267/489,267/489,267/517	53117017	1291,11715	2203	4300	6503	SO:0001819	synonymous_variant	55769	exon3			GACCTTTCCACAT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.801A>C	19.37:g.53117017T>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	44	11	0.25	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	37	CCDS12854.1	.	.	.	.	.	.	.	.	.	.	-	0.039	-1.293052	0.01375	0.087154	0.105465	ENSG00000167766	ENST00000434535	.	.	.	1.64	0.536	0.17138	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999998759	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.1646	0.10300	0.0:0.2128:0.3331:0.4541	rs7248435;rs7248435	.	.	.	.	-1	.	.	.	-	.	.	ZNF83	57808829	0.000000	0.05858	0.070000	0.20053	0.008000	0.06430	-3.515000	0.00445	0.214000	0.20742	-0.811000	0.03165	.	T|0.881;G|0.119	0.119	strong		0.403	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
TCEB3	6924	hgsc.bcm.edu	37	1	24077451	24077451	+	Missense_Mutation	SNP	C	C	T	rs2235541	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24077451C>T	ENST00000418390.2	+	4	705	c.434C>T	c.(433-435)aCg>aTg	p.T145M	TCEB3_ENST00000609199.1_Missense_Mutation_p.T119M	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	145			T -> M (in dbSNP:rs2235541).		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)		TGGAAAGCCACGGGGAGCCGA	0.552													C|||	404	0.0806709	0.0038	0.1095	5008	,	,		17089	0.0883		0.0905	False		,,,				2504	0.1462				p.T145M		Atlas-SNP	.											TCEB3,NS,carcinoma,-1,1	TCEB3	61	1	0			c.C434T						scavenged	.	C	MET/THR	84,4322	70.3+/-108.2	2,80,2121	49.0	55.0	53.0		434	5.7	0.3	1	dbSNP_98	53	807,7793	187.4+/-234.7	30,747,3523	yes	missense	TCEB3	NM_003198.2	81	32,827,5644	TT,TC,CC		9.3837,1.9065,6.8507	benign	145/799	24077451	891,12115	2203	4300	6503	SO:0001583	missense	6924	exon4			AAGCCACGGGGAG	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.434C>T	1.37:g.24077451C>T	ENSP00000395574:p.Thr145Met	Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_003198	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	37	CCDS239.2	153	0.07005494505494506	4	0.008130081300813009	31	0.0856353591160221	61	0.10664335664335664	57	0.07519788918205805	C	14.92	2.678199	0.47886	0.019065	0.093837	ENSG00000011007	ENST00000418390	T	0.07216	3.21	5.74	5.74	0.90152	.	0.192513	0.37437	N	0.002093	T	0.00144	0.0004	N	0.08118	0	0.38839	P	0.04397399999999996	D	0.54772	0.968	B	0.38156	0.266	T	0.48559	-0.9025	9	0.59425	D	0.04	-8.3454	19.9357	0.97140	0.0:1.0:0.0:0.0	rs2235541;rs2235541	145	Q14241	ELOA1_HUMAN	M	145	ENSP00000395574:T145M	ENSP00000395574:T145M	T	+	2	0	TCEB3	23950038	0.995000	0.38212	0.276000	0.24689	0.525000	0.34531	5.333000	0.65917	2.715000	0.92844	0.655000	0.94253	ACG	C|0.932;T|0.068	0.068	strong		0.552	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
ATP1A1	476	hgsc.bcm.edu	37	1	116937809	116937809	+	Missense_Mutation	SNP	A	A	G	rs77217304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:116937809A>G	ENST00000295598.5	+	13	1990	c.1738A>G	c.(1738-1740)Atc>Gtc	p.I580V	ATP1A1_ENST00000369496.4_Missense_Mutation_p.I549V|ATP1A1_ENST00000537345.1_Missense_Mutation_p.I580V	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	580					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GAATTTCCCTATCGATAATCT	0.512													A|||	46	0.0091853	0.003	0.0202	5008	,	,		17691	0.0		0.0239	False		,,,				2504	0.0041				p.I580V		Atlas-SNP	.											.	ATP1A1	87	.	0			c.A1738G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	27,4379	33.5+/-64.1	0,27,2176	203.0	185.0	191.0		1738,1738,1645	-2.7	0.0	1	dbSNP_131	191	276,8324	105.0+/-166.0	6,264,4030	yes	missense,missense,missense	ATP1A1	NM_000701.7,NM_001160233.1,NM_001160234.1	29,29,29	6,291,6206	GG,GA,AA		3.2093,0.6128,2.3297	benign,benign,benign	580/1024,580/1024,549/993	116937809	303,12703	2203	4300	6503	SO:0001583	missense	476	exon13			TTCCCTATCGATA	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1738A>G	1.37:g.116937809A>G	ENSP00000295598:p.Ile580Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	189	84	0.444444	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	33	0.01510989010989011	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	21	0.027704485488126648	A	3.882	-0.025753	0.07589	0.006128	0.032093	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	T;T;T	0.75938	-0.98;-0.98;-0.98	4.54	-2.67	0.06059	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.461301	0.25178	N	0.032547	T	0.22742	0.0549	N	0.11927	0.2	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34875	-0.9811	10	0.14252	T	0.57	.	5.1931	0.15220	0.3627:0.2485:0.3888:0.0	.	580;580	F5H3A1;P05023	.;AT1A1_HUMAN	V	580;580;579;549	ENSP00000295598:I580V;ENSP00000445306:I580V;ENSP00000358508:I549V	ENSP00000295598:I580V	I	+	1	0	ATP1A1	116739332	0.035000	0.19736	0.002000	0.10522	0.442000	0.32017	0.865000	0.27940	-0.556000	0.06134	-0.177000	0.13119	ATC	A|0.977;G|0.023	0.023	strong		0.512	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178540975	178540975	+	Missense_Mutation	SNP	G	G	A	rs1054480	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:178540975G>A	ENST00000251582.7	-	22	3630	c.3529C>T	c.(3529-3531)Ccc>Tcc	p.P1177S		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1177			P -> S (in dbSNP:rs1054480).		collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		ATTAGGTTGGGTGGCTGGACT	0.498													G|||	1321	0.263778	0.0401	0.3833	5008	,	,		18793	0.3105		0.2952	False		,,,				2504	0.4008				p.P1177S		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C3529T						PASS	.	G	SER/PRO	357,4049	183.6+/-211.2	14,329,1860	219.0	212.0	215.0		3529	5.1	1.0	5	dbSNP_86	215	2527,6073	414.0+/-351.3	386,1755,2159	yes	missense	ADAMTS2	NM_014244.4	74	400,2084,4019	AA,AG,GG		29.3837,8.1026,22.1744	possibly-damaging	1177/1212	178540975	2884,10122	2203	4300	6503	SO:0001583	missense	9509	exon22			GGTTGGGTGGCTG	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3529C>T	5.37:g.178540975G>A	ENSP00000251582:p.Pro1177Ser	Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	380	184	0.484211	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	551	0.2522893772893773	26	0.052845528455284556	123	0.3397790055248619	176	0.3076923076923077	226	0.29815303430079154	G	10.57	1.386031	0.25031	0.081026	0.293837	ENSG00000087116	ENST00000251582	T	0.58210	0.35	5.05	5.05	0.67936	.	0.126916	0.34676	N	0.003764	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	1.0	P	0.38922	0.651	B	0.27887	0.084	T	0.37753	-0.9692	9	0.14252	T	0.57	.	17.3941	0.87440	0.0:0.0:1.0:0.0	rs1054480;rs3195011;rs17603677;rs52799825;rs58744885;rs1054480	1177	O95450	ATS2_HUMAN	S	1177	ENSP00000251582:P1177S	ENSP00000251582:P1177S	P	-	1	0	ADAMTS2	178473581	1.000000	0.71417	0.973000	0.42090	0.192000	0.23643	3.893000	0.56243	2.308000	0.77769	0.561000	0.74099	CCC	G|0.764;N|0.000	.	strong		0.498	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
RYR3	6263	hgsc.bcm.edu	37	15	34137200	34137200	+	Silent	SNP	T	T	G	rs41279228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:34137200T>G	ENST00000389232.4	+	93	13504	c.13434T>G	c.(13432-13434)cgT>cgG	p.R4478R	RYR3_ENST00000415757.3_Silent_p.R4473R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4478					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)		CAACCCTGCGTGCCCTGGCCA	0.498													G|||	551	0.110024	0.1097	0.1412	5008	,	,		19803	0.0069		0.2078	False		,,,				2504	0.0941				p.R4478R		Atlas-SNP	.											RYR3,brain,glioma,0,1	RYR3	760	1	0			c.T13434G						PASS	.	G		467,3611		28,411,1600	141.0	139.0	140.0		13434	2.3	1.0	15	dbSNP_127	140	1788,6612		176,1436,2588	no	coding-synonymous	RYR3	NM_001036.3		204,1847,4188	GG,GT,TT		21.2857,11.4517,18.0718		4478/4871	34137200	2255,10223	2039	4200	6239	SO:0001819	synonymous_variant	6263	exon93			CCTGCGTGCCCTG		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.13434T>G	15.37:g.34137200T>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	153	85	0.555556	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			T|0.854;G|0.146	0.146	strong		0.498	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
SEC16A	9919	hgsc.bcm.edu	37	9	139371786	139371786	+	Silent	SNP	A	A	C	rs6560632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139371786A>C	ENST00000313050.7	-	1	355	c.282T>G	c.(280-282)gtT>gtG	p.V94V	SEC16A_ENST00000371706.3_5'Flank|SEC16A_ENST00000290037.6_5'Flank|SEC16A_ENST00000431893.2_5'Flank	NM_014866.1	NP_055681.1	O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	0					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)		GTGTGTGAGGAACAAGCAAAC	0.587													C|||	1909	0.38119	0.4266	0.6124	5008	,	,		19570	0.2153		0.4105	False		,,,				2504	0.2965				p.V94V		Atlas-SNP	.											.	SEC16A	249	.	0			c.T282G						PASS	.	C		1609,2377		332,945,716	74.0	78.0	77.0		282	1.1	0.0	9	dbSNP_116	77	3719,4601		818,2083,1259	no	coding-synonymous	SEC16A	NM_014866.1		1150,3028,1975	CC,CA,AA		44.6995,40.3663,43.296		94/2358	139371786	5328,6978	1993	4160	6153	SO:0001819	synonymous_variant	9919	exon3			GTGAGGAACAAGC	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	ENST00000313050.7:c.282T>G	9.37:g.139371786A>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000313050.7	37	CCDS55351.1																																																																																			A|0.601;C|0.399	0.399	strong		0.587	SEC16A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088459	
MYCT1	80177	hgsc.bcm.edu	37	6	153043035	153043035	+	Missense_Mutation	SNP	G	G	A	rs17710008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:153043035G>A	ENST00000367245.5	+	2	363	c.355G>A	c.(355-357)Ggc>Agc	p.G119S	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	119			G -> S (in dbSNP:rs17710008).			nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		TTACACCCACGGCCTCAACAG	0.522													G|||	550	0.109824	0.0098	0.2392	5008	,	,		16013	0.0893		0.159	False		,,,				2504	0.1237				p.G119S		Atlas-SNP	.											.	MYCT1	48	.	0			c.G355A						PASS	.	G	SER/GLY	183,4223	119.2+/-156.9	3,177,2023	126.0	120.0	122.0		355	3.8	1.0	6	dbSNP_123	122	1435,7165	275.8+/-292.0	112,1211,2977	yes	missense	MYCT1	NM_025107.2	56	115,1388,5000	AA,AG,GG		16.686,4.1534,12.4404	benign	119/236	153043035	1618,11388	2203	4300	6503	SO:0001583	missense	80177	exon2			ACCCACGGCCTCA	AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.355G>A	6.37:g.153043035G>A	ENSP00000356214:p.Gly119Ser	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	192	105	0.546875	NM_025107	Q8N396|Q8TBE8|Q9H763	Missense_Mutation	SNP	ENST00000367245.5	37	CCDS5239.1	282	0.12912087912087913	12	0.024390243902439025	86	0.23756906077348067	62	0.10839160839160839	122	0.16094986807387862	G	11.15	1.552847	0.27739	0.041534	0.16686	ENSG00000120279	ENST00000367245	T	0.28895	1.59	5.78	3.77	0.43336	.	0.440979	0.24652	N	0.036711	T	0.04588	0.0125	N	0.13043	0.29	0.09310	P	0.99999877397	B	0.31817	0.341	B	0.20384	0.029	T	0.27971	-1.0058	9	0.10377	T	0.69	-16.9903	8.1426	0.31093	0.1779:0.0:0.6906:0.1315	rs17710008;rs52810941;rs17710008	119	Q8N699	MYCT1_HUMAN	S	119	ENSP00000356214:G119S	ENSP00000356214:G119S	G	+	1	0	MYCT1	153084728	0.329000	0.24696	0.967000	0.41034	0.954000	0.61252	0.603000	0.24149	1.451000	0.47736	0.579000	0.79373	GGC	G|0.882;A|0.118	0.118	strong		0.522	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107	
NCKAP5	344148	hgsc.bcm.edu	37	2	133541107	133541107	+	Missense_Mutation	SNP	T	T	A	rs16841277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133541107T>A	ENST00000409261.1	-	14	3650	c.3277A>T	c.(3277-3279)Aat>Tat	p.N1093Y	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.N1093Y|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1093	Ser-rich.		N -> Y (in dbSNP:rs16841277).							NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GCGCTATCATTCAATTGTCCT	0.502													T|||	894	0.178514	0.0446	0.1888	5008	,	,		17828	0.251		0.2256	False		,,,				2504	0.229				p.N1093Y		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A3277T						PASS	.	T	TYR/ASN,	280,3714		13,254,1730	256.0	267.0	263.0		3277,	3.0	0.0	2	dbSNP_123	263	1972,6352		218,1536,2408	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	143,	231,1790,4138	AA,AT,TT		23.6905,7.0105,18.2822	benign,	1093/1910,	133541107	2252,10066	1997	4162	6159	SO:0001583	missense	344148	exon14			TATCATTCAATTG	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.3277A>T	2.37:g.133541107T>A	ENSP00000387128:p.Asn1093Tyr	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	263	139	0.528517	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	421	0.19276556776556777	29	0.05894308943089431	60	0.16574585635359115	152	0.26573426573426573	180	0.23746701846965698	T	11.70	1.718039	0.30503	0.070105	0.236905	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.11821	2.74;2.74	5.41	3.01	0.34805	.	0.789167	0.10545	U	0.662156	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	4.000000000004E-6	D	0.54964	0.969	P	0.47827	0.558	T	0.47394	-0.9121	9	0.66056	D	0.02	.	8.714	0.34401	0.0:0.1506:0.0:0.8494	rs16841277;rs16841277	1093	O14513	NCKP5_HUMAN	Y	1093	ENSP00000387128:N1093Y;ENSP00000380603:N1093Y	ENSP00000380603:N1093Y	N	-	1	0	NCKAP5	133257577	0.000000	0.05858	0.007000	0.13788	0.127000	0.20565	0.514000	0.22786	1.086000	0.41228	0.533000	0.62120	AAT	T|0.780;A|0.220	0.220	strong		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
OR6S1	341799	hgsc.bcm.edu	37	14	21109385	21109385	+	Missense_Mutation	SNP	C	C	T	rs11622969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21109385C>T	ENST00000320704.3	-	1	465	c.466G>A	c.(466-468)Gtc>Atc	p.V156I		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	156			V -> I (in dbSNP:rs11622969).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		AGCACAGGGACGAGTCCCCCC	0.612													C|||	2246	0.448482	0.4887	0.5375	5008	,	,		20938	0.252		0.5219	False		,,,				2504	0.4581				p.V156I		Atlas-SNP	.											.	OR6S1	49	.	0			c.G466A						PASS	.	C	ILE/VAL	2247,2159	591.6+/-387.6	552,1143,508	81.0	66.0	71.0		466	-0.8	0.7	14	dbSNP_120	71	4680,3920	602.9+/-394.6	1273,2134,893	yes	missense	OR6S1	NM_001001968.1	29	1825,3277,1401	TT,TC,CC		45.5814,49.0014,46.74	benign	156/332	21109385	6927,6079	2203	4300	6503	SO:0001583	missense	341799	exon1			CAGGGACGAGTCC	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.466G>A	14.37:g.21109385C>T	ENSP00000313110:p.Val156Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	997	0.4565018315018315	229	0.4654471544715447	212	0.585635359116022	158	0.2762237762237762	398	0.525065963060686	C	4.909	0.168995	0.09339	0.509986	0.544186	ENSG00000181803	ENST00000320704	T	0.37584	1.19	5.76	-0.768	0.11013	GPCR, rhodopsin-like superfamily (1);	0.502259	0.16827	N	0.197918	T	0.00012	0.0000	N	0.10629	0.01	0.80722	P	0.0	B	0.23854	0.092	B	0.20184	0.028	T	0.40572	-0.9556	9	0.54805	T	0.06	-4.6747	2.6503	0.04996	0.1442:0.4007:0.2291:0.226	rs11622969;rs52800855;rs60154084;rs11622969	156	Q8NH40	OR6S1_HUMAN	I	156	ENSP00000313110:V156I	ENSP00000313110:V156I	V	-	1	0	OR6S1	20179225	0.000000	0.05858	0.698000	0.30274	0.050000	0.14768	-1.513000	0.02256	-0.153000	0.11137	-1.114000	0.02060	GTC	C|0.498;T|0.502	0.502	strong		0.612	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
ZBTB37	84614	hgsc.bcm.edu	37	1	173839907	173839907	+	Silent	SNP	C	C	T	rs36119794	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:173839907C>T	ENST00000367701.5	+	2	735	c.544C>T	c.(544-546)Ctg>Ttg	p.L182L	ZBTB37_ENST00000427304.1_Silent_p.L182L|ZBTB37_ENST00000367704.1_Silent_p.L182L|ZBTB37_ENST00000432989.1_Silent_p.L182L|ZBTB37_ENST00000367702.1_Silent_p.L182L			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	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)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						TAGTGCTGTGCTGGATATCAG	0.527													C|||	144	0.028754	0.0045	0.0418	5008	,	,		18954	0.0		0.0755	False		,,,				2504	0.0337				p.L182L		Atlas-SNP	.											.	ZBTB37	38	.	0			c.C544T						PASS	.	C	,	62,4344	58.7+/-95.3	0,62,2141	58.0	59.0	59.0		544,544	1.9	1.0	1	dbSNP_126	59	710,7890	173.7+/-224.2	23,664,3613	no	coding-synonymous,coding-synonymous	ZBTB37	NM_001122770.1,NM_032522.3	,	23,726,5754	TT,TC,CC		8.2558,1.4072,5.9357	,	182/504,182/362	173839907	772,12234	2203	4300	6503	SO:0001819	synonymous_variant	84614	exon3			GCTGTGCTGGATA	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.544C>T	1.37:g.173839907C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	50	0.60241	NM_032522	Q5TC80|Q96M87|Q9BQ88	Silent	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			C|0.948;T|0.052	0.052	strong		0.527	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522	
ZNF638	27332	hgsc.bcm.edu	37	2	71650236	71650236	+	Missense_Mutation	SNP	T	T	C	rs79157966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71650236T>C	ENST00000409544.1	+	22	4222	c.3592T>C	c.(3592-3594)Tgt>Cgt	p.C1198R	ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000264447.4_Missense_Mutation_p.C1198R|ZNF638_ENST00000409407.1_Missense_Mutation_p.C138R	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1198	Glu-rich.				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						TGCCGAGGAGTGTGCTTTAAA	0.408													T|||	9	0.00179712	0.0	0.0014	5008	,	,		19971	0.0		0.008	False		,,,				2504	0.0				p.C1198R		Atlas-SNP	.											.	ZNF638	179	.	0			c.T3592C						PASS	.	T	ARG/CYS,ARG/CYS	4,4402	8.1+/-20.4	0,4,2199	96.0	96.0	96.0		3592,3592	4.4	1.0	2	dbSNP_131	96	74,8526	44.5+/-102.8	0,74,4226	yes	missense,missense	ZNF638	NM_001014972.1,NM_014497.3	180,180	0,78,6425	CC,CT,TT		0.8605,0.0908,0.5997	benign,benign	1198/1979,1198/1979	71650236	78,12928	2203	4300	6503	SO:0001583	missense	27332	exon22			GAGGAGTGTGCTT	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.3592T>C	2.37:g.71650236T>C	ENSP00000386433:p.Cys1198Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	9.920	1.211800	0.22289	9.08E-4	0.008605	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.30182	1.54;1.54;1.82	5.55	4.36	0.52297	.	0.556954	0.16511	N	0.211226	T	0.12305	0.0299	N	0.24115	0.695	0.80722	D	1	B;B;B	0.29432	0.244;0.144;0.089	B;B;B	0.21151	0.032;0.033;0.032	T	0.05209	-1.0899	10	0.15499	T	0.54	-1.0544	8.8782	0.35358	0.1665:0.0:0.0:0.8335	.	1198;1198;1198	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	R	777;1198;1198;138;138	ENSP00000264447:C1198R;ENSP00000386433:C1198R;ENSP00000386813:C138R	ENSP00000264447:C1198R	C	+	1	0	ZNF638	71503744	0.997000	0.39634	0.998000	0.56505	0.476000	0.33039	1.649000	0.37281	0.991000	0.38814	0.533000	0.62120	TGT	T|0.994;C|0.006	0.006	strong		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
KRT38	8687	hgsc.bcm.edu	37	17	39595484	39595484	+	Nonsense_Mutation	SNP	G	G	A	rs148768443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39595484G>A	ENST00000246646.3	-	3	702	c.703C>T	c.(703-705)Cag>Tag	p.Q235*		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	235	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.Q235*(2)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				AGGGAGAGCTGCTCCTCCTTC	0.667																																					p.Q235X		Atlas-SNP	.											KRT38,NS,carcinoma,0,7	KRT38	63	7	2	Substitution - Nonsense(2)	breast(1)|central_nervous_system(1)	c.C703T						PASS	.						58.0	53.0	54.0					17																	39595484		2203	4298	6501	SO:0001587	stop_gained	8687	exon3			AGAGCTGCTCCTC	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6456	protein-coding gene	gene with protein product		604542	"""keratin, hair, acidic, 8"""	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.703C>T	17.37:g.39595484G>A	ENSP00000246646:p.Gln235*	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	110	21	0.190909	NM_006771	A2RRM5|Q6A164	Nonsense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.158641	0.57368	.	.	ENSG00000171360	ENST00000246646	.	.	.	4.31	1.01	0.19927	.	0.526305	0.15723	N	0.247837	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	8.0787	0.30731	0.0815:0.0:0.5477:0.3708	.	.	.	.	X	235	.	ENSP00000246646:Q235X	Q	-	1	0	KRT38	36849010	0.779000	0.28652	0.994000	0.49952	0.627000	0.37826	0.894000	0.28350	1.013000	0.39391	0.484000	0.47621	CAG	G|0.975;A|0.025	0.025	strong		0.667	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
KRT81	3887	hgsc.bcm.edu	37	12	52681080	52681080	+	Silent	SNP	G	G	A	rs4761784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52681080G>A	ENST00000327741.5	-	7	1121	c.1053C>T	c.(1051-1053)gcC>gcT	p.A351A	KRT86_ENST00000544024.1_Intron|KRT86_ENST00000423955.2_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	351	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTCAGACTGGGCCACCGCGG	0.607													.|||	1476	0.294728	0.1082	0.3386	5008	,	,		18323	0.4296		0.332	False		,,,				2504	0.3384				p.A351A		Atlas-SNP	.											.	KRT81	46	.	0			c.C1053T						PASS	.	G		607,3799		60,487,1656	25.0	28.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1053	1.0	0.7	12	dbSNP_111	27	2649,5951		396,1857,2047	no	coding-synonymous	KRT81	NM_002281.3		456,2344,3703	AA,AG,GG		30.8023,13.7767,25.0346		351/506	52681080	3256,9750	2203	4300	6503	SO:0001819	synonymous_variant	3887	exon7			AGACTGGGCCACC	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.1053C>T	12.37:g.52681080G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	37	CCDS31805.1																																																																																			G|0.744;A|0.256	0.256	strong		0.607	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
COL5A3	50509	hgsc.bcm.edu	37	19	10079093	10079093	+	Missense_Mutation	SNP	C	C	T	rs3815746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10079093C>T	ENST00000264828.3	-	59	4367	c.4282G>A	c.(4282-4284)Gtg>Atg	p.V1428M		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1428	Triple-helical region.		V -> M (in dbSNP:rs3815746).		axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			GGTCCCTGCACGCCTGGCAAC	0.587													C|||	900	0.179712	0.1838	0.1383	5008	,	,		16730	0.2222		0.2048	False		,,,				2504	0.1339				p.V1428M		Atlas-SNP	.											.	COL5A3	243	.	0			c.G4282A						PASS	.	C	MET/VAL	840,3566	331.5+/-302.0	80,680,1443	109.0	124.0	119.0		4282	1.7	1.0	19	dbSNP_107	119	1917,6683	336.3+/-321.8	206,1505,2589	yes	missense	COL5A3	NM_015719.3	21	286,2185,4032	TT,TC,CC		22.2907,19.0649,21.1979	benign	1428/1746	10079093	2757,10249	2203	4300	6503	SO:0001583	missense	50509	exon59			CCTGCACGCCTGG	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.4282G>A	19.37:g.10079093C>T	ENSP00000264828:p.Val1428Met	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	462	0.21153846153846154	102	0.2073170731707317	57	0.1574585635359116	143	0.25	160	0.21108179419525067	C	5.488	0.275036	0.10403	0.190649	0.222907	ENSG00000080573	ENST00000264828	D	0.93604	-3.25	3.92	1.72	0.24424	.	0.205140	0.33401	N	0.004946	T	0.00073	0.0002	N	0.16368	0.405	0.44117	P	0.0031079999999999997	B	0.15930	0.015	B	0.09377	0.004	T	0.10800	-1.0614	9	0.33141	T	0.24	.	6.1598	0.20358	0.0:0.6715:0.0:0.3285	rs3815746;rs57414063;rs3815746	1428	P25940	CO5A3_HUMAN	M	1428	ENSP00000264828:V1428M	ENSP00000264828:V1428M	V	-	1	0	COL5A3	9940093	0.000000	0.05858	0.994000	0.49952	0.020000	0.10135	-0.266000	0.08631	0.861000	0.35504	-0.216000	0.12614	GTG	C|0.783;T|0.216	0.216	strong		0.587	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
MUC17	140453	hgsc.bcm.edu	37	7	100679366	100679366	+	Missense_Mutation	SNP	A	A	G	rs74209688	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100679366A>G	ENST00000306151.4	+	3	4733	c.4669A>G	c.(4669-4671)Act>Gct	p.T1557A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1557	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.T1557A(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)					ATCTCCTACAACTGCTGACGG	0.493																																					p.T1557A		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	1	1	Substitution - Missense(1)	stomach(1)	c.A4669G						PASS	.	A	ALA/THR	348,4058	180.1+/-208.5	15,318,1870	261.0	243.0	249.0		4669	-1.3	0.0	7	dbSNP_130	249	2280,6320	385.7+/-341.6	299,1682,2319	no	missense	MUC17	NM_001040105.1	58	314,2000,4189	GG,GA,AA		26.5116,7.8983,20.2061	possibly-damaging	1557/4494	100679366	2628,10378	2203	4300	6503	SO:0001583	missense	140453	exon3			CCTACAACTGCTG	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.4669A>G	7.37:g.100679366A>G	ENSP00000302716:p.Thr1557Ala	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	538	0.24633699633699635	23	0.046747967479674794	76	0.20994475138121546	230	0.4020979020979021	209	0.2757255936675462	A	2.243	-0.373277	0.05034	0.078983	0.265116	ENSG00000169876	ENST00000306151	T	0.01981	4.52	0.922	-1.27	0.09347	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.40476	0.718	B	0.32805	0.153	T	0.22765	-1.0207	8	0.07030	T	0.85	.	3.075	0.06243	0.5662:0.0:0.0:0.4338	.	1557	Q685J3	MUC17_HUMAN	A	1557	ENSP00000302716:T1557A	ENSP00000302716:T1557A	T	+	1	0	MUC17	100466086	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	0.057000	0.14279	-0.205000	0.10219	0.102000	0.15555	ACT	A|0.784;G|0.216	0.216	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
AKAP13	11214	hgsc.bcm.edu	37	15	86284342	86284342	+	Silent	SNP	C	C	T	rs16943792	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:86284342C>T	ENST00000394518.2	+	35	7769	c.7674C>T	c.(7672-7674)ctC>ctT	p.L2558L	AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000361243.2_Silent_p.L2562L|AKAP13_ENST00000394510.2_Silent_p.L803L|RP11-158M2.3_ENST00000558375.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2558	Interaction with ESR1.				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						AGAGGGCGCTCACTCGCAGCT	0.637													C|||	1185	0.236621	0.1483	0.2493	5008	,	,		16124	0.3234		0.2048	False		,,,				2504	0.2904				p.L2562L	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											AKAP13_ENST00000394518,NS,carcinoma,0,2	AKAP13	394	2	0			c.C7686T						PASS	.	C	,,	669,3735	283.4+/-277.1	59,551,1592	46.0	46.0	46.0		7686,7674,2409	-0.7	0.0	15	dbSNP_123	46	1641,6957	301.7+/-305.6	169,1303,2827	no	coding-synonymous,coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3,NM_144767.3	,,	228,1854,4419	TT,TC,CC		19.0858,15.1907,17.7665	,,	2562/2818,2558/2814,803/1059	86284342	2310,10692	2202	4299	6501	SO:0001819	synonymous_variant	11214	exon35			GGCGCTCACTCGC	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.7674C>T	15.37:g.86284342C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	211	97	0.459716	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																			C|0.809;T|0.191	0.191	strong		0.637	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
CERS3	204219	hgsc.bcm.edu	37	15	101042043	101042043	+	Silent	SNP	C	C	T	rs77089459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:101042043C>T	ENST00000394113.1	-	5	702	c.12G>A	c.(10-12)acG>acA	p.T4T	CERS3_ENST00000538112.2_Silent_p.T4T|CERS3_ENST00000560944.1_Intron|CERS3_ENST00000284382.4_Silent_p.T4T			Q8IU89	CERS3_HUMAN	ceramide synthase 3	4					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)										ATTCTTTAAACGTCCAAAACA	0.393													C|||	107	0.0213658	0.003	0.0331	5008	,	,		21339	0.001		0.0577	False		,,,				2504	0.0215				p.T4T		Atlas-SNP	.											.	.	.	.	0			c.G12A						PASS	.	C		46,4360	47.5+/-82.1	1,44,2158	81.0	75.0	77.0		12	-6.4	0.0	15	dbSNP_132	77	609,7991	160.3+/-213.4	27,555,3718	no	coding-synonymous	CERS3	NM_178842.3		28,599,5876	TT,TC,CC		7.0814,1.044,5.0361		4/384	101042043	655,12351	2203	4300	6503	SO:0001819	synonymous_variant	204219	exon4			TTTAAACGTCCAA		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.12G>A	15.37:g.101042043C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_178842	Q8NE64|Q8NEN6	Silent	SNP	ENST00000394113.1	37	CCDS10384.1																																																																																			C|0.959;T|0.041	0.041	strong		0.393	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39497404	39497404	+	Missense_Mutation	SNP	G	G	C	rs139297	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39497404G>C	ENST00000401756.1	+	3	389	c.313G>C	c.(313-315)Ggc>Cgc	p.G105R	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.G105R|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.G105R|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.G105R	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	105			G -> R (in allele A3H-Var; haplotype 2; allele presenting a higher expression and which is more effective in retrotransposons and HIV-1 restriction; increases protein stability and exhibits a cytoplasmic localization; dbSNP:rs139297). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					TCTGAACCTGGGCATCTTCGC	0.612													C|||	2628	0.52476	0.8752	0.3833	5008	,	,		4666	0.3155		0.4642	False		,,,				2504	0.4294				p.G105R		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G313C						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3573,833		1455,663,85	91.0	67.0	75.0		313,313,313,313	-4.6	0.0	22	dbSNP_78	75	3964,4636		887,2190,1223	yes	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	125,125,125,125	2342,2853,1308	CC,CG,GG		46.093,18.906,42.0498	benign,benign,benign,benign	105/183,105/201,105/155,105/184	39497404	7537,5469	2203	4300	6503	SO:0001583	missense	164668	exon3			AACCTGGGCATCT	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.313G>C	22.37:g.39497404G>C	ENSP00000385741:p.Gly105Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	1088	0.4981684981684982	427	0.8678861788617886	127	0.35082872928176795	172	0.3006993006993007	362	0.47757255936675463	.	0.023	-1.398362	0.01175	0.81094	0.46093	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	3.33	-4.63	0.03359	.	.	.	.	.	T	0.00012	0.0000	N	0.00030	-2.605	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38112	-0.9676	8	0.02654	T	1	-0.0266	7.6083	0.28115	0.5538:0.2197:0.2266:0.0	rs139297;rs52798787;rs61578228;rs139297	105	B7TQM3	.	R	105	ENSP00000216123:G105R;ENSP00000411754:G105R;ENSP00000393520:G105R;ENSP00000385741:G105R	ENSP00000216123:G105R	G	+	1	0	APOBEC3H	37827350	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	-1.028000	0.03589	-1.275000	0.02417	-0.365000	0.07479	GGC	G|0.456;C|0.544	0.544	strong		0.612	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
ERN1	2081	hgsc.bcm.edu	37	17	62132160	62132160	+	Silent	SNP	C	C	T	rs55653398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62132160C>T	ENST00000433197.3	-	14	1796	c.1701G>A	c.(1699-1701)ggG>ggA	p.G567G		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						AGGAAATTTTCCCAACTATCA	0.488													C|||	59	0.0117812	0.0015	0.0072	5008	,	,		21939	0.0		0.0169	False		,,,				2504	0.0358				p.G567G		Atlas-SNP	.											.	ERN1	102	.	0			c.G1701A						PASS	.	C		15,4003		0,15,1994	52.0	53.0	53.0		1701	1.1	0.9	17	dbSNP_129	53	191,8155		4,183,3986	no	coding-synonymous	ERN1	NM_001433.3		4,198,5980	TT,TC,CC		2.2885,0.3733,1.6661		567/978	62132160	206,12158	2009	4173	6182	SO:0001819	synonymous_variant	2081	exon14			AATTTTCCCAACT	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.1701G>A	17.37:g.62132160C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			C|0.988;T|0.012	0.012	strong		0.488	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
KBTBD12	166348	hgsc.bcm.edu	37	3	127703085	127703085	+	Silent	SNP	G	G	A	rs13100951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:127703085G>A	ENST00000405109.1	+	6	2303	c.1836G>A	c.(1834-1836)ccG>ccA	p.P612P	KBTBD12_ENST00000343941.4_Silent_p.P187P|KBTBD12_ENST00000407609.3_Silent_p.P219P|KBTBD12_ENST00000492025.1_3'UTR|KBTBD12_ENST00000405256.1_Silent_p.P612P			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	612										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TCATCCCCCCGCCTTCAGATT	0.537													G|||	1097	0.21905	0.1241	0.2983	5008	,	,		20696	0.2887		0.2614	False		,,,				2504	0.1759				p.P612P		Atlas-SNP	.											.	KBTBD12	41	.	0			c.G1836A						PASS	.	G		655,3751	278.1+/-274.1	54,547,1602	97.0	90.0	93.0		1836	-9.4	0.3	3	dbSNP_121	93	2157,6443	369.1+/-335.3	290,1577,2433	no	coding-synonymous	KBTBD12	NM_207335.2		344,2124,4035	AA,AG,GG		25.0814,14.8661,21.6208		612/624	127703085	2812,10194	2203	4300	6503	SO:0001819	synonymous_variant	166348	exon5			CCCCCCGCCTTCA		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.1836G>A	3.37:g.127703085G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	131	54	0.412214	NM_207335	B5MCC6|Q6ZRK1	Silent	SNP	ENST00000405109.1	37	CCDS33848.2																																																																																			G|0.771;A|0.229	0.229	strong		0.537	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
MTMR6	9107	hgsc.bcm.edu	37	13	25831928	25831928	+	Silent	SNP	C	C	T	rs186466011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25831928C>T	ENST00000381801.5	-	8	1676	c.915G>A	c.(913-915)tcG>tcA	p.S305S	MTMR6_ENST00000540661.1_Silent_p.S305S|MTMR6_ENST00000482345.1_5'Flank	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	305	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GAAGCCATCCCGAGCTCTCCA	0.383													C|||	2	0.000399361	0.0	0.0014	5008	,	,		16484	0.0		0.001	False		,,,				2504	0.0				p.S305S		Atlas-SNP	.											.	MTMR6	75	.	0			c.G915A						PASS	.	C		0,4406		0,0,2203	70.0	75.0	74.0		915	-5.6	0.3	13		74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTMR6	NM_004685.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		305/622	25831928	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9107	exon8			CCATCCCGAGCTC	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.915G>A	13.37:g.25831928C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Silent	SNP	ENST00000381801.5	37	CCDS9313.1																																																																																			C|1.000;T|0.000	0.000	strong		0.383	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685	
EFHB	151651	hgsc.bcm.edu	37	3	19962044	19962044	+	Missense_Mutation	SNP	G	G	A	rs13078867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:19962044G>A	ENST00000295824.9	-	2	966	c.805C>T	c.(805-807)Cca>Tca	p.P269S	EFHB_ENST00000498089.1_5'UTR|EFHB_ENST00000344838.4_Missense_Mutation_p.P139S	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	269			P -> S (in dbSNP:rs13078867).				calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TAACCAACTGGAATAACTTTT	0.373													G|||	956	0.190895	0.0734	0.1758	5008	,	,		16758	0.2143		0.2495	False		,,,				2504	0.2761				p.P269S		Atlas-SNP	.											.	EFHB	186	.	0			c.C805T						PASS	.	G	SER/PRO	433,3973	211.5+/-231.7	22,389,1792	80.0	81.0	81.0		805	4.9	0.1	3	dbSNP_121	81	2224,6376	377.8+/-338.7	280,1664,2356	yes	missense	EFHB	NM_144715.3	74	302,2053,4148	AA,AG,GG		25.8605,9.8275,20.429	probably-damaging	269/834	19962044	2657,10349	2203	4300	6503	SO:0001583	missense	151651	exon2			CAACTGGAATAAC	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.805C>T	3.37:g.19962044G>A	ENSP00000295824:p.Pro269Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	51	16	0.313726	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	426	0.19505494505494506	44	0.08943089430894309	63	0.17403314917127072	121	0.21153846153846154	198	0.2612137203166227	G	17.37	3.373042	0.61624	0.098275	0.258605	ENSG00000163576	ENST00000295824;ENST00000344838;ENST00000389256	T;T;T	0.26957	1.7;1.8;2.0	5.75	4.88	0.63580	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	M	0.72894	2.215	0.37975	P	0.06657100000000005	P;P	0.46142	0.873;0.675	P;B	0.47673	0.554;0.32	T	0.19712	-1.0297	8	.	.	.	-12.5966	12.1223	0.53897	0.0804:0.0:0.9196:0.0	rs13078867;rs52802880;rs58072698;rs13078867	139;269	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	S	269;139;269	ENSP00000295824:P269S;ENSP00000342263:P139S;ENSP00000373908:P269S	.	P	-	1	0	EFHB	19937048	1.000000	0.71417	0.055000	0.19348	0.929000	0.56500	4.533000	0.60615	1.438000	0.47492	0.655000	0.94253	CCA	G|0.804;A|0.196	0.196	strong		0.373	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
RALGAPA2	57186	hgsc.bcm.edu	37	20	20493222	20493222	+	Silent	SNP	G	G	A	rs35039408	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:20493222G>A	ENST00000202677.7	-	32	4798	c.4791C>T	c.(4789-4791)ccC>ccT	p.P1597P		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1597					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.P1597P(3)		endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						AGGGTCCTCGGGGCTCCACTG	0.458													G|||	1355	0.270567	0.0295	0.4395	5008	,	,		18071	0.2163		0.4195	False		,,,				2504	0.3793				p.P1597P		Atlas-SNP	.											RALGAPA2_ENST00000202677,NS,carcinoma,0,3	RALGAPA2	274	3	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.C4791T						PASS	.	G		345,3435		16,313,1561	55.0	55.0	55.0		4791	-1.7	0.9	20	dbSNP_126	55	3405,4817		696,2013,1402	no	coding-synonymous	RALGAPA2	NM_020343.3		712,2326,2963	AA,AG,GG		41.4133,9.127,31.2448		1597/1874	20493222	3750,8252	1890	4111	6001	SO:0001819	synonymous_variant	57186	exon32			TCCTCGGGGCTCC	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4791C>T	20.37:g.20493222G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Silent	SNP	ENST00000202677.7	37	CCDS46584.1	609	0.27884615384615385	22	0.044715447154471545	151	0.4171270718232044	122	0.21328671328671328	314	0.41424802110817943	G	8.371	0.835272	0.16820	0.09127	0.414133	ENSG00000188559	ENST00000430436;ENST00000427175	D;D	0.94184	-3.37;-3.37	5.97	-1.68	0.08212	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999810333	.	.	.	.	.	.	T	0.02238	-1.1190	6	0.62326	D	0.03	.	5.9471	0.19225	0.1225:0.0744:0.498:0.305	rs35039408;rs61739707	.	.	.	L	1414;8	ENSP00000400085:P1414L;ENSP00000388695:P8L	ENSP00000388695:P8L	P	-	2	0	RALGAPA2	20441222	0.002000	0.14202	0.914000	0.36105	0.978000	0.69477	-1.513000	0.02256	-0.136000	0.11475	0.561000	0.74099	CCC	G|0.683;A|0.317	0.317	strong		0.458	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
TRIO	7204	hgsc.bcm.edu	37	5	14498727	14498727	+	Silent	SNP	G	G	A	rs26107	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:14498727G>A	ENST00000344204.4	+	53	8334	c.8310G>A	c.(8308-8310)tcG>tcA	p.S2770S	TRIO_ENST00000537187.1_Silent_p.S2594S|TRIO_ENST00000344135.5_Silent_p.S269S	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2770	Ig-like C2-type.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CAGCCTCATCGTCGGCCAGCC	0.577													G|||	560	0.111821	0.0537	0.2089	5008	,	,		22675	0.13		0.0934	False		,,,				2504	0.1217				p.S2770S		Atlas-SNP	.											.	TRIO	305	.	0			c.G8310A						PASS	.	G		242,4164	139.2+/-174.8	5,232,1966	188.0	158.0	168.0		8310	-10.6	0.0	5	dbSNP_76	168	1034,7566	221.0+/-258.6	77,880,3343	no	coding-synonymous	TRIO	NM_007118.2		82,1112,5309	AA,AG,GG		12.0233,5.4925,9.8109		2770/3098	14498727	1276,11730	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon53			CTCATCGTCGGCC	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.8310G>A	5.37:g.14498727G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			G|0.894;N|0.000	.	strong		0.577	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
OR14C36	127066	hgsc.bcm.edu	37	1	248512749	248512749	+	Missense_Mutation	SNP	G	G	A	rs28377739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248512749G>A	ENST00000317861.1	+	1	673	c.673G>A	c.(673-675)Ggg>Agg	p.G225R		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	225			G -> R (in dbSNP:rs28377739).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						GACCGTGCTCGGGTTTCCAAG	0.498													a|||	2306	0.460463	0.3601	0.4885	5008	,	,		19309	0.4315		0.5239	False		,,,				2504	0.5409				p.G225R		Atlas-SNP	.											OR14C36,NS,adenoma,0,1	OR14C36	113	1	0			c.G673A						PASS	.	A	ARG/GLY	1764,2642	643.9+/-397.9	352,1060,791	191.0	146.0	161.0		673	1.2	0.0	1	dbSNP_125	161	4894,3706	530.1+/-381.7	1390,2114,796	yes	missense	OR14C36	NM_001001918.1	125	1742,3174,1587	AA,AG,GG		43.093,40.0363,48.8082	benign	225/313	248512749	6658,6348	2203	4300	6503	SO:0001583	missense	127066	exon1			GTGCTCGGGTTTC	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.673G>A	1.37:g.248512749G>A	ENSP00000324534:p.Gly225Arg	Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	386	178	0.46114	NM_001001918	Q6IEZ6	Missense_Mutation	SNP	ENST00000317861.1	37	CCDS31112.1	1006	0.4606227106227106	169	0.3434959349593496	179	0.494475138121547	253	0.4423076923076923	405	0.5343007915567283	A	0.005	-2.203520	0.00296	0.400363	0.56907	ENSG00000177174	ENST00000317861	T	0.00019	9.06	3.91	1.2	0.21068	GPCR, rhodopsin-like superfamily (1);	0.422559	0.19555	N	0.111462	T	0.00012	0.0000	N	0.00227	-1.8	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.37776	-0.9691	9	0.02654	T	1	.	6.3589	0.21417	0.6176:0.2982:0.0841:0.0	rs28377739	225	Q8NHC7	O14CZ_HUMAN	R	225	ENSP00000324534:G225R	ENSP00000324534:G225R	G	+	1	0	OR14C36	246579372	0.000000	0.05858	0.035000	0.18076	0.144000	0.21451	0.145000	0.16157	0.101000	0.17610	-1.086000	0.02197	GGG	G|0.502;A|0.498	0.498	strong		0.498	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918	
COL2A1	1280	hgsc.bcm.edu	37	12	48398080	48398080	+	Missense_Mutation	SNP	T	T	A	rs3803183	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:48398080T>A	ENST00000380518.3	-	1	189	c.25A>T	c.(25-27)Acg>Tcg	p.T9S	COL2A1_ENST00000337299.6_Missense_Mutation_p.T9S|RP1-228P16.3_ENST00000552958.1_lincRNA	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	9			T -> S (in dbSNP:rs3803183). {ECO:0000269|PubMed:18272325, ECO:0000269|PubMed:2081599, ECO:0000269|PubMed:2587267, ECO:0000269|PubMed:2714801, ECO:0000269|PubMed:2803268, ECO:0000269|PubMed:8948452}.		axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	AGCACCAGCGTCTGGGGAGCC	0.721													T|||	3432	0.685304	0.643	0.6254	5008	,	,		12607	0.5685		0.836	False		,,,				2504	0.7505				p.T9S		Atlas-SNP	.											.	COL2A1	368	.	0			c.A25T						PASS	.	T	SER/THR,SER/THR	2615,1185		910,795,195	26.0	24.0	25.0		25,25	2.9	1.0	12	dbSNP_107	25	6023,1123		2549,925,99	yes	missense,missense	COL2A1	NM_033150.2,NM_001844.4	58,58	3459,1720,294	AA,AT,TT		15.7151,31.1842,21.0853	benign,benign	9/1419,9/1488	48398080	8638,2308	1900	3573	5473	SO:0001583	missense	1280	exon1			CCAGCGTCTGGGG	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.25A>T	12.37:g.48398080T>A	ENSP00000369889:p.Thr9Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_033150	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	37	CCDS41778.1	1517	0.6945970695970696	324	0.6585365853658537	229	0.6325966850828729	328	0.5734265734265734	636	0.8390501319261213	T	13.97	2.394909	0.42512	0.688158	0.842849	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.89270	-2.49;-2.43	4.2	2.88	0.33553	.	0.135928	0.47093	N	0.000260	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	0.04013	0.001;0.0	T	0.41980	-0.9478	9	0.06365	T	0.9	.	7.296	0.26393	0.265:0.0:0.0:0.735	rs3803183;rs57829293	9;9	P02458-1;P02458	.;CO2A1_HUMAN	S	9	ENSP00000369889:T9S;ENSP00000338213:T9S	ENSP00000338213:T9S	T	-	1	0	COL2A1	46684347	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	1.888000	0.39708	0.486000	0.27676	0.533000	0.62120	ACG	T|0.277;A|0.723	0.723	strong		0.721	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
KRT20	54474	hgsc.bcm.edu	37	17	39041052	39041052	+	Missense_Mutation	SNP	C	C	T	rs7212483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39041052C>T	ENST00000167588.3	-	1	427	c.386G>A	c.(385-387)aGt>aAt	p.S129N		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	129	Coil 1B.|Rod.		S -> N (in dbSNP:rs7212483). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				TCTCACCTGACTTCGCAGCTC	0.438													T|||	611	0.122005	0.2413	0.1326	5008	,	,		19700	0.0149		0.1014	False		,,,				2504	0.0849				p.S129N		Atlas-SNP	.											.	KRT20	38	.	0			c.G386A						PASS	.	T	ASN/SER	952,3454	734.6+/-410.6	105,742,1356	86.0	84.0	85.0		386	3.3	0.0	17	dbSNP_116	85	728,7872	786.4+/-407.6	32,664,3604	yes	missense	KRT20	NM_019010.2	46	137,1406,4960	TT,TC,CC		8.4651,21.6069,12.9171	benign	129/425	39041052	1680,11326	2203	4300	6503	SO:0001583	missense	54474	exon1			ACCTGACTTCGCA	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.386G>A	17.37:g.39041052C>T	ENSP00000167588:p.Ser129Asn	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	135	58	0.42963	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	37	CCDS11379.1	257	0.11767399267399267	115	0.23373983739837398	45	0.12430939226519337	11	0.019230769230769232	86	0.11345646437994723	T	0.378	-0.930229	0.02359	0.216069	0.084651	ENSG00000171431	ENST00000167588	D	0.88741	-2.42	5.5	3.27	0.37495	Filament (1);	1.029950	0.07689	N	0.938459	T	0.00073	0.0002	N	0.02315	-0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.04495	-1.0947	9	0.02654	T	1	.	9.8179	0.40865	0.0:0.34:0.0:0.66	rs7212483;rs52812133;rs61023437;rs7212483	129	P35900	K1C20_HUMAN	N	129	ENSP00000167588:S129N	ENSP00000167588:S129N	S	-	2	0	KRT20	36294578	0.000000	0.05858	0.031000	0.17742	0.060000	0.15804	-0.373000	0.07494	0.390000	0.25115	-0.254000	0.11334	AGT	C|0.874;T|0.126	0.126	strong		0.438	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
FANCM	57697	hgsc.bcm.edu	37	14	45665434	45665434	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:45665434A>G	ENST00000267430.5	+	21	5485	c.5400A>G	c.(5398-5400)ccA>ccG	p.P1800P	FANCM_ENST00000542564.2_Silent_p.P1774P	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1800	Interaction with FAAP24 and EME1.				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						AGTCAAGACCACATTTAGCTG	0.433								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.P1800P		Atlas-SNP	.											.	FANCM	225	.	0			c.A5400G						PASS	.						137.0	134.0	135.0					14																	45665434		2203	4300	6503	SO:0001819	synonymous_variant	57697	exon21	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGACCACATTTA	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.5400A>G	14.37:g.45665434A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Silent	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	6.666	0.491392	0.12702	.	.	ENSG00000187790	ENST00000554809	.	.	.	5.39	1.43	0.22495	.	.	.	.	.	T	0.26195	0.0639	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24119	-1.0169	4	.	.	.	.	5.1811	0.15160	0.6463:0.0:0.0786:0.2751	.	.	.	.	A	768	.	.	T	+	1	0	FANCM	44735184	0.000000	0.05858	0.040000	0.18447	0.278000	0.26855	0.476000	0.22180	-0.008000	0.14320	0.460000	0.39030	ACA	.	.	none		0.433	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
HEPH	9843	hgsc.bcm.edu	37	X	65427124	65427124	+	Silent	SNP	A	A	G	rs809363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65427124A>G	ENST00000343002.2	+	13	3043	c.2379A>G	c.(2377-2379)acA>acG	p.T793T	HEPH_ENST00000519389.1_Silent_p.T847T|HEPH_ENST00000441993.2_Silent_p.T796T|HEPH_ENST00000336279.5_Silent_p.T526T|HEPH_ENST00000419594.1_Silent_p.T604T|HEPH_ENST00000374727.3_Silent_p.T796T			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	65	0	0		WXS	Illumina HiSeq	Phase_I	71	71	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	
FLG	2312	hgsc.bcm.edu	37	1	152284549	152284549	+	Missense_Mutation	SNP	G	G	C	rs141646551	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152284549G>C	ENST00000368799.1	-	3	2848	c.2813C>G	c.(2812-2814)aCa>aGa	p.T938R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	938	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.T938R(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCGCCTGCTTGTCCTGGACCC	0.572									Ichthyosis				-|||	170	0.0339457	0.0	0.0403	5008	,	,		21979	0.0754		0.007	False		,,,				2504	0.0603				p.T938R		Atlas-SNP	.											FLG,rectum,NS,0,1	FLG	900	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2813G						scavenged	.						325.0	297.0	306.0					1																	152284549		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGCTTGTCCTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2813C>G	1.37:g.152284549G>C	ENSP00000357789:p.Thr938Arg	Somatic	355	1	0.0028169		WXS	Illumina HiSeq	Phase_I	427	28	0.0655738	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	5.712	0.315925	0.10789	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.04083	3.71	3.85	0.458	0.16670	.	.	.	.	.	T	0.01124	0.0037	L	0.38531	1.155	0.09310	N	1	B	0.14805	0.011	B	0.23018	0.043	T	0.48163	-0.9059	9	0.30854	T	0.27	.	2.2232	0.03978	0.119:0.1996:0.4931:0.1882	.	938	P20930	FILA_HUMAN	R	938;145	ENSP00000357789:T938R	ENSP00000357789:T938R	T	-	2	0	FLG	150551173	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.641000	0.02007	0.119000	0.18210	0.473000	0.43528	ACA	G|0.989;C|0.011	0.011	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
KLHL26	55295	hgsc.bcm.edu	37	19	18779113	18779113	+	Silent	SNP	C	C	T	rs17852385	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18779113C>T	ENST00000300976.4	+	3	996	c.906C>T	c.(904-906)acC>acT	p.T302T	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	302										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTCCGCGCACCGCCGTGCGCT	0.657													C|||	81	0.0161741	0.003	0.0288	5008	,	,		16478	0.0		0.0477	False		,,,				2504	0.0092				p.T302T		Atlas-SNP	.											.	KLHL26	43	.	0			c.C906T						PASS	.	C		39,4351		0,39,2156	42.0	44.0	43.0		906	-10.1	0.0	19	dbSNP_123	43	461,8099		12,437,3831	no	coding-synonymous	KLHL26	NM_018316.1		12,476,5987	TT,TC,CC		5.3855,0.8884,3.861		302/616	18779113	500,12450	2195	4280	6475	SO:0001819	synonymous_variant	55295	exon3			GCGCACCGCCGTG		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.906C>T	19.37:g.18779113C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	37	25	0.675676	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.969;T|0.031	0.031	strong		0.657	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
SMCO2	341346	hgsc.bcm.edu	37	12	27648710	27648710	+	Missense_Mutation	SNP	C	C	T	rs3751223	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:27648710C>T	ENST00000535986.1	+	7	755	c.755C>T	c.(754-756)aCg>aTg	p.T252M	SMCO2_ENST00000298876.4_Missense_Mutation_p.T202M|SMCO2_ENST00000416383.1_Missense_Mutation_p.T252M|SMCO2_ENST00000538647.1_3'UTR			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	252						integral component of membrane (GO:0016021)											GAAATAGATACGGAAGAGATG	0.502													C|||	795	0.158746	0.1354	0.1138	5008	,	,		16511	0.2758		0.0457	False		,,,				2504	0.2178				p.T252M		Atlas-SNP	.											.	.	.	.	0			c.C755T						PASS	.	C	MET/THR	148,1216		17,114,551	83.0	77.0	79.0		755	-4.9	0.0	12	dbSNP_107	79	174,3006		5,164,1421	yes	missense	C12orf70	NM_001145010.1	81	22,278,1972	TT,TC,CC		5.4717,10.8504,7.0863	benign	252/344	27648710	322,4222	682	1590	2272	SO:0001583	missense	0	exon8			TAGATACGGAAGA		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.755C>T	12.37:g.27648710C>T	ENSP00000441688:p.Thr252Met	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_001145010		Missense_Mutation	SNP	ENST00000535986.1	37	CCDS44852.1	303	0.13873626373626374	75	0.1524390243902439	37	0.10220994475138122	156	0.2727272727272727	35	0.04617414248021108	C	0.009	-1.815579	0.00600	0.108504	0.054717	ENSG00000165935	ENST00000298876;ENST00000416383;ENST00000535986	.	.	.	2.9	-4.91	0.03085	.	2.373830	0.01721	N	0.028263	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.25950	-1.0117	8	0.21014	T	0.42	5.4188	4.633	0.12511	0.0:0.3447:0.3463:0.309	rs3751223;rs17657996;rs59005772;rs3751223	252	A6NFE2	CL070_HUMAN	M	202;252;252	.	ENSP00000298876:T202M	T	+	2	0	C12orf70	27539977	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.208000	0.03005	-1.089000	0.03073	-2.030000	0.00424	ACG	C|0.859;T|0.141	0.141	strong		0.502	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
DNAH17	8632	hgsc.bcm.edu	37	17	76472768	76472768	+	Silent	SNP	G	G	A	rs7405830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	195	0	0		WXS	Illumina HiSeq	Phase_I	239	113	0.472803	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	
TRIM77	390231	hgsc.bcm.edu	37	11	89447375	89447375	+	Missense_Mutation	SNP	C	C	T	rs17221124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:89447375C>T	ENST00000398290.3	+	3	523	c.523C>T	c.(523-525)Cgg>Tgg	p.R175W		NM_001146162.1	NP_001139634.1	I1YAP6	TRI77_HUMAN	tripartite motif containing 77	175						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										TATAAATTTGCGGAGCATGAT	0.373													C|||	140	0.0279553	0.003	0.0461	5008	,	,		17103	0.0		0.0915	False		,,,				2504	0.0123				p.R175W		Atlas-SNP	.											.	.	.	.	0			c.C523T						PASS	.	C	TRP/ARG	31,1353		1,29,662	69.0	58.0	61.0		523	0.9	0.0	11	dbSNP_123	61	315,2867		14,287,1290	yes	missense	TRIM77P	NM_001146162.1	101	15,316,1952	TT,TC,CC		9.8994,2.2399,7.5777		175/451	89447375	346,4220	692	1591	2283	SO:0001583	missense	390231	exon3			AATTTGCGGAGCA		CCDS60929.1	11q14.3	2014-02-17	2013-01-14	2013-01-14	ENSG00000214414	ENSG00000214414		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	34228	protein-coding gene	gene with protein product			"""tripartite motif-containing 77"", ""tripartite motif containing 77, pseudogene"""	TRIM77P			Standard	NM_001146162		Approved		uc010rtw.2	I1YAP6	OTTHUMG00000167624	ENST00000398290.3:c.523C>T	11.37:g.89447375C>T	ENSP00000474003:p.Arg175Trp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_001146162		Missense_Mutation	SNP	ENST00000398290.3	37																																																																																				C|0.957;T|0.043	0.043	strong		0.373	TRIM77-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146162	
SACS	26278	hgsc.bcm.edu	37	13	23909162	23909162	+	Silent	SNP	A	A	G	rs9552929	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:23909162A>G	ENST00000382292.3	-	9	9126	c.8853T>C	c.(8851-8853)gtT>gtC	p.V2951V	SACS_ENST00000402364.1_Silent_p.V2201V|SACS_ENST00000382298.3_Silent_p.V2951V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2951					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)		TGTCCTTTACAACATGAATAG	0.353													A|||	1298	0.259185	0.056	0.3617	5008	,	,		20798	0.3145		0.2783	False		,,,				2504	0.3845				p.V2951V		Atlas-SNP	.											.	SACS	871	.	0			c.T8853C						PASS	.	A		427,3979	207.8+/-229.1	21,385,1797	98.0	99.0	99.0		8853	-11.3	0.6	13	dbSNP_119	99	2236,6364	378.4+/-338.9	292,1652,2356	no	coding-synonymous	SACS	NM_014363.4		313,2037,4153	GG,GA,AA		26.0,9.6913,20.4752		2951/4580	23909162	2663,10343	2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			CTTTACAACATGA	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.8853T>C	13.37:g.23909162A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			A|0.767;G|0.233	0.233	strong		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
PRSS33	260429	hgsc.bcm.edu	37	16	2834711	2834711	+	Silent	SNP	G	G	A	rs45570838	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2834711G>A	ENST00000293851.5	-	6	936	c.777C>T	c.(775-777)aaC>aaT	p.N259N	PRSS33_ENST00000570702.1_Silent_p.N259N|PRSS33_ENST00000576886.1_3'UTR	NM_152891.2	NP_690851.2	Q8NF86	PRS33_HUMAN	protease, serine, 33	259	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			prostate(1)	1						CCCCTGGACGGTTGGGCAGGG	0.637													G|||	190	0.0379393	0.003	0.0562	5008	,	,		16160	0.001		0.1302	False		,,,				2504	0.0153				p.N259N	NSCLC(194;489 2153 16702 19171 27758)	Atlas-SNP	.											PRSS33,NS,carcinoma,0,1	PRSS33	7	1	0			c.C777T						scavenged	.			96,4036		0,96,1970	25.0	30.0	29.0		777	4.7	1.0	16	dbSNP_127	29	1099,7329		70,959,3185	no	coding-synonymous	PRSS33	NM_152891.2		70,1055,5155	AA,AG,GG		13.0399,2.3233,9.5143		259/281	2834711	1195,11365	2066	4214	6280	SO:0001819	synonymous_variant	260429	exon6			TGGACGGTTGGGC	AF536382	CCDS42110.1	16p13.3	2014-09-04			ENSG00000103355	ENSG00000103355		"""Serine peptidases / Serine peptidases"""	30405	protein-coding gene	gene with protein product		613797				12795636	Standard	NM_152891		Approved	EOS	uc002cro.1	Q8NF86	OTTHUMG00000177360	ENST00000293851.5:c.777C>T	16.37:g.2834711G>A		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_152891	A6NNQ3|Q8N171	Silent	SNP	ENST00000293851.5	37	CCDS42110.1																																																																																			G|0.934;A|0.066	0.066	strong		0.637	PRSS33-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436446.1	NM_152891	
HIST1H2BA	255626	hgsc.bcm.edu	37	6	25727334	25727334	+	Silent	SNP	C	C	T	rs4712961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25727334C>T	ENST00000274764.2	+	1	198	c.198C>T	c.(196-198)tcC>tcT	p.S66S	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	66					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)	2						TTATGAATTCCTTCGTCACTG	0.468													C|||	1738	0.347045	0.0976	0.4366	5008	,	,		21573	0.6825		0.2922	False		,,,				2504	0.3313				p.S66S		Atlas-SNP	.											.	HIST1H2BA	25	.	0			c.C198T						PASS	.	C		605,3801	265.3+/-266.6	47,511,1645	401.0	304.0	337.0		198	-5.9	0.0	6	dbSNP_111	337	2391,6209	398.2+/-346.0	339,1713,2248	no	coding-synonymous	HIST1H2BA	NM_170610.2		386,2224,3893	TT,TC,CC		27.8023,13.7313,23.0355		66/128	25727334	2996,10010	2203	4300	6503	SO:0001819	synonymous_variant	255626	exon1			GAATTCCTTCGTC	AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"""Histones / Replication-dependent"""	18730	protein-coding gene	gene with protein product		609904	"""H2B histone family, member U, (testis-specific)"", ""histone 1, H2ba"""			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.198C>T	6.37:g.25727334C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_170610	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Silent	SNP	ENST00000274764.2	37	CCDS4563.1																																																																																			C|0.679;T|0.321	0.321	strong		0.468	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610	
PCSK9	255738	hgsc.bcm.edu	37	1	55505564	55505564	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:55505564G>T	ENST00000302118.5	+	1	344	c.54G>T	c.(52-54)ctG>ctT	p.L18L	PCSK9_ENST00000452118.2_Silent_p.L18L|PCSK9_ENST00000543384.1_5'Flank	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	18					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						tgctgctgctgctgctgctgc	0.706																																					p.L18L	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.G54T						PASS	.						11.0	11.0	11.0					1																	55505564		2128	4166	6294	SO:0001819	synonymous_variant	255738	exon1			GCTGCTGCTGCTG	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.54G>T	1.37:g.55505564G>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	84	57	0.678571	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	37	CCDS603.1																																																																																			.	.	none		0.706	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
OPLAH	26873	hgsc.bcm.edu	37	8	145113241	145113241	+	Missense_Mutation	SNP	T	T	G	rs3935209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145113241T>G	ENST00000426825.1	-	7	931	c.850A>C	c.(850-852)Agt>Cgt	p.S284R	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	284			S -> R (in dbSNP:rs3935209).		glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGCACAGCACTGGAGCCGCTG	0.687													G|||	1014	0.202476	0.5998	0.0893	5008	,	,		15381	0.003		0.0984	False		,,,				2504	0.0583				p.S284R		Atlas-SNP	.											OPLAH,NS,carcinoma,0,1	OPLAH	78	1	0			c.A850C						PASS	.	G	ARG/SER	1818,2076		465,888,594	6.0	9.0	8.0		850	2.9	1.0	8	dbSNP_108	8	604,7624		25,554,3535	yes	missense	OPLAH	NM_017570.3	110	490,1442,4129	GG,GT,TT		7.3408,46.6872,19.9802	benign	284/1289	145113241	2422,9700	1947	4114	6061	SO:0001583	missense	26873	exon7			CAGCACTGGAGCC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.850A>C	8.37:g.145113241T>G	ENSP00000475943:p.Ser284Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		421	0.19276556776556777	297	0.6036585365853658	37	0.10220994475138122	13	0.022727272727272728	74	0.09762532981530343	G	11.48	1.649903	0.29336	0.466872	0.073408	ENSG00000178814	ENST00000426825	.	.	.	3.95	2.94	0.34122	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.19575	N	0.999967	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44421	-0.9329	7	0.02654	T	1	.	11.4387	0.50083	0.0:0.0:0.6654:0.3346	rs3935209;rs3935209	284;284	A7E261;O14841	.;OPLA_HUMAN	R	284	.	ENSP00000412071:S284R	S	-	1	0	OPLAH	145185229	0.940000	0.31905	0.981000	0.43875	0.538000	0.34931	0.568000	0.23623	0.652000	0.30806	-0.352000	0.07741	AGT	T|0.812;G|0.188	0.188	strong		0.687	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
LGMN	5641	hgsc.bcm.edu	37	14	93172903	93172903	+	Silent	SNP	C	C	T	rs143184687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:93172903C>T	ENST00000393218.2	-	13	1453	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	LGMN_ENST00000555699.1_Intron|LGMN_ENST00000334869.4_Silent_p.P372P|LGMN_ENST00000557434.1_Intron	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	372					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		GCCCCGTGAGCGGGGCTCTCT	0.647													C|||	31	0.0061901	0.0008	0.0072	5008	,	,		17490	0.0		0.0229	False		,,,				2504	0.002				p.P372P		Atlas-SNP	.											.	LGMN	28	.	0			c.G1116A						PASS	.	C	,	18,4388	23.3+/-48.9	0,18,2185	45.0	46.0	46.0		1116,1116	-1.2	0.0	14	dbSNP_134	46	216,8384	92.1+/-154.2	0,216,4084	no	coding-synonymous,coding-synonymous	LGMN	NM_001008530.2,NM_005606.6	,	0,234,6269	TT,TC,CC		2.5116,0.4085,1.7992	,	372/434,372/434	93172903	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	5641	exon12			CGTGAGCGGGGCT	D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"""protease, cysteine, 1 (legumain)"""	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1116G>A	14.37:g.93172903C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_005606	O00123|Q86TV2|Q86TV3|Q9BTY1	Silent	SNP	ENST00000393218.2	37	CCDS9904.1																																																																																			C|0.984;T|0.016	0.016	strong		0.647	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606	
PSPH	5723	hgsc.bcm.edu	37	7	56088825	56088825	+	Missense_Mutation	SNP	T	T	A	rs74445297	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	209	0	0		WXS	Illumina HiSeq	Phase_I	214	30	0.140187	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	
MCTP2	55784	hgsc.bcm.edu	37	15	94841691	94841691	+	Missense_Mutation	SNP	G	G	A	rs61737195	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:94841691G>A	ENST00000357742.4	+	1	197	c.197G>A	c.(196-198)cGg>cAg	p.R66Q	MCTP2_ENST00000451018.3_Missense_Mutation_p.R66Q|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000543482.1_Missense_Mutation_p.R66Q	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	66					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)			CCAGAGGGCCGGCCTTACTCC	0.607													G|||	864	0.172524	0.0643	0.2133	5008	,	,		14378	0.2579		0.1402	False		,,,				2504	0.2352				p.R66Q		Atlas-SNP	.											MCTP2,colon,carcinoma,+1,1	MCTP2	122	1	0			c.G197A						PASS	.	G	GLN/ARG,GLN/ARG	350,4044	180.8+/-209.0	18,314,1865	52.0	57.0	55.0		197,197	0.1	0.1	15	dbSNP_129	55	964,7632	209.6+/-250.7	55,854,3389	yes	missense,missense	MCTP2	NM_001159643.1,NM_018349.3	43,43	73,1168,5254	AA,AG,GG		11.2145,7.9654,10.1155	benign,benign	66/824,66/879	94841691	1314,11676	2197	4298	6495	SO:0001583	missense	55784	exon1			AGGGCCGGCCTTA	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.197G>A	15.37:g.94841691G>A	ENSP00000350377:p.Arg66Gln	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	26	0.619048	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	340	0.15567765567765568	22	0.044715447154471545	70	0.19337016574585636	138	0.24125874125874125	110	0.14511873350923482	G	14.58	2.576502	0.45902	0.079654	0.112145	ENSG00000140563	ENST00000543482;ENST00000556363;ENST00000451018;ENST00000357742	T;T;T	0.69561	-0.41;-0.19;-0.04	4.52	0.129	0.14739	.	0.649782	0.13110	N	0.413018	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	6.999999999979245E-6	P;P;B;P;P	0.40250	0.709;0.709;0.357;0.585;0.709	B;B;B;B;B	0.27500	0.05;0.05;0.036;0.023;0.08	T	0.06770	-1.0808	9	0.15952	T	0.53	.	0.8754	0.01223	0.372:0.2116:0.2715:0.1449	rs61737195	66;66;66;66;66	F5H415;Q6DN12-2;Q6DN12;B7Z6H2;G3V2J2	.;.;MCTP2_HUMAN;.;.	Q	66	ENSP00000438521:R66Q;ENSP00000395109:R66Q;ENSP00000350377:R66Q	ENSP00000350377:R66Q	R	+	2	0	MCTP2	92642695	0.000000	0.05858	0.095000	0.20976	0.650000	0.38633	0.048000	0.14078	0.165000	0.19558	0.563000	0.77884	CGG	G|0.880;A|0.120	0.120	strong		0.607	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
TPCN2	219931	hgsc.bcm.edu	37	11	68851466	68851466	+	Silent	SNP	G	G	T	rs896973	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:68851466G>T	ENST00000294309.3	+	19	1844	c.1743G>T	c.(1741-1743)gcG>gcT	p.A581A	TPCN2_ENST00000442692.2_3'UTR|MIR3164_ENST00000581178.1_RNA|TPCN2_ENST00000542467.1_Intron	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	581					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			ACATGCGTGCGTTTGGCGGGA	0.667													G|||	1670	0.333466	0.357	0.3285	5008	,	,		17038	0.2867		0.4831	False		,,,				2504	0.1994				p.A581A		Atlas-SNP	.											.	TPCN2	63	.	0			c.G1743T						PASS	.	G		1688,2712	510.6+/-367.6	325,1038,837	194.0	146.0	162.0		1743	-7.5	0.2	11	dbSNP_86	162	4281,4307	574.0+/-390.0	1034,2213,1047	no	coding-synonymous	TPCN2	NM_139075.3		1359,3251,1884	TT,TG,GG		49.8486,38.3636,45.9578		581/753	68851466	5969,7019	2200	4294	6494	SO:0001819	synonymous_variant	219931	exon19			GCGTGCGTTTGGC	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1743G>T	11.37:g.68851466G>T		Somatic	326	1	0.00306748		WXS	Illumina HiSeq	Phase_I	302	301	0.996689	NM_139075	Q9NT82	Silent	SNP	ENST00000294309.3	37	CCDS8189.1																																																																																			G|0.583;T|0.417	0.417	strong		0.667	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
C19orf57	79173	hgsc.bcm.edu	37	19	14000196	14000196	+	Missense_Mutation	SNP	G	G	T	rs61732721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14000196G>T	ENST00000586783.1	-	5	1472	c.1473C>A	c.(1471-1473)gaC>gaA	p.D491E	C19orf57_ENST00000454313.1_Missense_Mutation_p.D491E|C19orf57_ENST00000346736.2_Missense_Mutation_p.D491E|C19orf57_ENST00000591586.1_Intron			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	491				D -> E (in Ref. 2; AAI19720). {ECO:0000305}.	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)			CCTGGAGAGGGTCGTCTGCTA	0.617													G|||	11	0.00219649	0.0	0.0029	5008	,	,		17053	0.0		0.008	False		,,,				2504	0.001				p.D491E		Atlas-SNP	.											.	C19orf57	34	.	0			c.C1473A						PASS	.	G	GLU/ASP	7,4399	12.9+/-30.5	0,7,2196	66.0	72.0	70.0		1473	1.3	0.0	19	dbSNP_129	70	85,8515	48.1+/-107.5	0,85,4215	yes	missense	C19orf57	NM_024323.3	45	0,92,6411	TT,TG,GG		0.9884,0.1589,0.7074	benign	491/638	14000196	92,12914	2203	4300	6503	SO:0001583	missense	79173	exon6			GAGAGGGTCGTCT	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.1473C>A	19.37:g.14000196G>T	ENSP00000465822:p.Asp491Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	12.21	1.868899	0.32977	0.001589	0.009884	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.52057	0.68;0.68	4.73	1.32	0.21799	.	1.305730	0.05407	N	0.541685	T	0.25382	0.0617	N	0.19112	0.55	0.09310	N	1	B;B	0.15473	0.013;0.013	B;B	0.21917	0.025;0.037	T	0.26121	-1.0112	10	0.41790	T	0.15	-2.8432	5.2907	0.15725	0.3744:0.0:0.6256:0.0	.	491;491	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	E	491	ENSP00000404382:D491E;ENSP00000254336:D491E	ENSP00000254336:D491E	D	-	3	2	C19orf57	13861196	0.007000	0.16637	0.003000	0.11579	0.014000	0.08584	0.845000	0.27668	0.599000	0.29845	0.637000	0.83480	GAC	G|0.996;T|0.004	0.004	strong		0.617	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
TNN	63923	hgsc.bcm.edu	37	1	175092674	175092674	+	Missense_Mutation	SNP	C	C	T	rs2285215	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:175092674C>T	ENST00000239462.4	+	12	2902	c.2789C>T	c.(2788-2790)cCg>cTg	p.P930L		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	930	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.		P -> L (in dbSNP:rs2285215).		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)		p.P930L(1)		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)		AGGGAGGTTCCGGTGGGGAAG	0.617													C|||	2996	0.598243	0.6203	0.6671	5008	,	,		17437	0.4921		0.6421	False		,,,				2504	0.5838				p.P930L		Atlas-SNP	.											TNN,colon,carcinoma,0,3	TNN	297	3	1	Substitution - Missense(1)	stomach(1)	c.C2789T						PASS	.	C	LEU/PRO	2669,1737	647.4+/-398.5	798,1073,332	96.0	81.0	86.0		2789	3.1	0.0	1	dbSNP_100	86	5434,3166	655.1+/-401.2	1732,1970,598	no	missense	TNN	NM_022093.1	98	2530,3043,930	TT,TC,CC		36.814,39.4235,37.698	possibly-damaging	930/1300	175092674	8103,4903	2203	4300	6503	SO:0001583	missense	63923	exon12			AGGTTCCGGTGGG	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.2789C>T	1.37:g.175092674C>T	ENSP00000239462:p.Pro930Leu	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	213	213	1	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	1334	0.6108058608058609	315	0.6402439024390244	243	0.6712707182320442	282	0.493006993006993	494	0.6517150395778364	C	14.27	2.485302	0.44147	0.605765	0.63186	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.56444	0.46	4.98	3.1	0.35709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.350805	0.30028	N	0.010594	T	0.00012	0.0000	M	0.75150	2.29	0.80722	P	0.0	D	0.55800	0.973	P	0.52598	0.703	T	0.47535	-0.9110	9	0.21540	T	0.41	.	5.8964	0.18941	0.1521:0.6823:0.0:0.1655	rs2285215;rs2285215	930	Q9UQP3	TENN_HUMAN	L	930;753	ENSP00000239462:P930L	ENSP00000239462:P930L	P	+	2	0	TNN	173359297	0.002000	0.14202	0.001000	0.08648	0.668000	0.39293	1.703000	0.37846	0.605000	0.29947	0.462000	0.41574	CCG	C|0.379;T|0.621	0.621	strong		0.617	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
LMAN1L	79748	hgsc.bcm.edu	37	15	75117912	75117912	+	Missense_Mutation	SNP	G	G	T	rs79217743	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:75117912G>T	ENST00000309664.5	+	14	1686	c.1547G>T	c.(1546-1548)aGg>aTg	p.R516M	RP11-414J4.2_ENST00000564823.1_RNA|LMAN1L_ENST00000379709.3_Missense_Mutation_p.R504M|CPLX3_ENST00000395018.4_5'Flank	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	516						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						GGGATTCTGAGGAGGCAGCCT	0.627													G|||	381	0.0760783	0.0204	0.1225	5008	,	,		17145	0.002		0.159	False		,,,				2504	0.1094				p.R516M		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G1547T						PASS	.	G	MET/ARG	148,4246	103.0+/-141.5	1,146,2050	69.0	72.0	71.0		1547	3.9	1.0	15	dbSNP_131	71	1175,7415	233.9+/-267.0	89,997,3209	yes	missense	LMAN1L	NM_021819.2	91	90,1143,5259	TT,TG,GG		13.6787,3.3682,10.1895	probably-damaging	516/527	75117912	1323,11661	2197	4295	6492	SO:0001583	missense	79748	exon14			TTCTGAGGAGGCA	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.1547G>T	15.37:g.75117912G>T	ENSP00000310431:p.Arg516Met	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	181	0.08287545787545787	9	0.018292682926829267	48	0.13259668508287292	1	0.0017482517482517483	123	0.16226912928759896	G	10.41	1.341989	0.24339	0.033682	0.136787	ENSG00000140506	ENST00000309664;ENST00000379709	T;T	0.55413	0.59;0.52	3.93	3.93	0.45458	.	0.283692	0.24949	N	0.034308	T	0.00440	0.0014	L	0.46157	1.445	0.29696	P	0.840516	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.995	T	0.17379	-1.0371	9	0.87932	D	0	.	11.7673	0.51939	0.0:0.0:1.0:0.0	.	504;516	Q9HAT1-3;Q9HAT1	.;LMA1L_HUMAN	M	516;504	ENSP00000310431:R516M;ENSP00000369031:R504M	ENSP00000310431:R516M	R	+	2	0	LMAN1L	72904965	1.000000	0.71417	0.974000	0.42286	0.010000	0.07245	4.171000	0.58236	2.486000	0.83907	0.561000	0.74099	AGG	G|0.903;T|0.097	0.097	strong		0.627	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
TJP3	27134	hgsc.bcm.edu	37	19	3731985	3731985	+	Silent	SNP	G	G	A	rs1879040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3731985G>A	ENST00000541714.2	+	6	1128	c.666G>A	c.(664-666)tcG>tcA	p.S222S	TJP3_ENST00000262968.9_Silent_p.S241S|TJP3_ENST00000589378.1_Silent_p.S231S|TJP3_ENST00000587686.1_Silent_p.S241S|TJP3_ENST00000382008.3_Silent_p.S222S|TJP3_ENST00000539908.2_Silent_p.S186S	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	222	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)		p.S241S(1)		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)		TTACAGATTCGGGCCTGGCTG	0.592													g|||	1644	0.328275	0.2179	0.4179	5008	,	,		16720	0.2768		0.3459	False		,,,				2504	0.4489				p.S231S		Atlas-SNP	.											TJP3,colon,carcinoma,0,2	TJP3	79	2	1	Substitution - coding silent(1)	stomach(1)	c.G693A						PASS	.	A		1168,3238	409.5+/-335.0	147,874,1182	50.0	45.0	46.0		723	-5.4	0.2	19	dbSNP_92	46	3001,5599	462.4+/-365.7	548,1905,1847	no	coding-synonymous	TJP3	NM_014428.1		695,2779,3029	AA,AG,GG		34.8953,26.5093,32.0544		241/953	3731985	4169,8837	2203	4300	6503	SO:0001819	synonymous_variant	27134	exon6			AGATTCGGGCCTG	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.666G>A	19.37:g.3731985G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	53	18	0.339623	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			G|0.686;A|0.314	0.314	strong		0.592	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
ITLN2	142683	hgsc.bcm.edu	37	1	160922421	160922421	+	Missense_Mutation	SNP	T	T	G	rs145457015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160922421T>G	ENST00000368029.3	-	3	239	c.182A>C	c.(181-183)cAt>cCt	p.H61P	ITLN2_ENST00000494442.1_5'Flank|RP11-544M22.1_ENST00000356006.3_RNA	NM_080878.2	NP_543154.1	Q8WWU7	ITLN2_HUMAN	intelectin 2	61	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	19	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			ACCTGCACTATGGCAGCGTTC	0.483													T|||	44	0.00878594	0.0	0.0029	5008	,	,		21066	0.0		0.0	False		,,,				2504	0.0429				p.H61P		Atlas-SNP	.											.	ITLN2	35	.	0			c.A182C						PASS	.	T	PRO/HIS	5,4401	9.9+/-24.2	0,5,2198	101.0	95.0	97.0		182	-7.9	0.0	1	dbSNP_134	97	17,8583	11.9+/-42.8	0,17,4283	yes	missense	ITLN2	NM_080878.2	77	0,22,6481	GG,GT,TT		0.1977,0.1135,0.1692	benign	61/326	160922421	22,12984	2203	4300	6503	SO:0001583	missense	142683	exon3			GCACTATGGCAGC	AY065973	CCDS1212.1	1q22-q23.5	2013-02-06			ENSG00000158764	ENSG00000158764		"""Fibrinogen C domain containing"""	20599	protein-coding gene	gene with protein product		609874				11181563	Standard	NM_080878		Approved	HL-2	uc001fxd.3	Q8WWU7	OTTHUMG00000028605	ENST00000368029.3:c.182A>C	1.37:g.160922421T>G	ENSP00000357008:p.His61Pro	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_080878	Q17RR2|Q5VYI0	Missense_Mutation	SNP	ENST00000368029.3	37	CCDS1212.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	3.839	-0.034106	0.07543	0.001135	0.001977	ENSG00000158764	ENST00000368029	D	0.91631	-2.88	3.95	-7.9	0.01169	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.289890	0.06467	N	0.730523	T	0.52549	0.1741	N	0.02181	-0.65	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.004	T	0.57189	-0.7854	10	0.13470	T	0.59	0.3882	10.3753	0.44079	0.0:0.1869:0.1496:0.6635	.	60;61	A6NI51;Q8WWU7	.;ITLN2_HUMAN	P	61	ENSP00000357008:H61P	ENSP00000357008:H61P	H	-	2	0	ITLN2	159189045	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.326000	0.00070	-2.805000	0.00350	-0.396000	0.06452	CAT	T|0.999;G|0.001	0.001	strong		0.483	ITLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071465.1	NM_080878	
CLNK	116449	hgsc.bcm.edu	37	4	10586571	10586571	+	Missense_Mutation	SNP	G	G	A	rs61759824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:10586571G>A	ENST00000226951.6	-	4	331	c.92C>T	c.(91-93)cCt>cTt	p.P31L	CLNK_ENST00000507719.1_5'UTR|CLNK_ENST00000442825.2_5'UTR	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	31					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						ATTGATGCGAGGCCATGACCT	0.507													G|||	130	0.0259585	0.0091	0.0389	5008	,	,		16233	0.0		0.0567	False		,,,				2504	0.0348				p.P31L	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.C92T						PASS	.	G	LEU/PRO	48,4018		1,46,1986	98.0	106.0	103.0		92	3.9	0.8	4	dbSNP_129	103	515,7829		15,485,3672	yes	missense	CLNK	NM_052964.2	98	16,531,5658	AA,AG,GG		6.1721,1.1805,4.5367	probably-damaging	31/429	10586571	563,11847	2033	4172	6205	SO:0001583	missense	116449	exon4			ATGCGAGGCCATG	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"""SH2 domain containing"""	17438	protein-coding gene	gene with protein product	"""mast cell immunoreceptor signal transducer"""	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.92C>T	4.37:g.10586571G>A	ENSP00000226951:p.Pro31Leu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	65	0.02976190476190476	7	0.014227642276422764	12	0.03314917127071823	0	0.0	46	0.06068601583113457	G	10.66	1.412027	0.25465	0.011805	0.061721	ENSG00000109684	ENST00000226951;ENST00000429087	T	0.26660	1.72	4.79	3.94	0.45596	.	0.000000	0.44902	D	0.000411	T	0.03477	0.0100	L	0.29908	0.895	0.80722	D	1	D	0.60160	0.987	P	0.55011	0.766	T	0.00389	-1.1770	10	0.87932	D	0	-2.6544	10.4696	0.44629	0.0:0.0:0.8061:0.1939	rs61759824	31	Q7Z7G1	CLNK_HUMAN	L	31	ENSP00000226951:P31L	ENSP00000226951:P31L	P	-	2	0	CLNK	10195669	0.974000	0.33945	0.843000	0.33291	0.044000	0.14063	1.881000	0.39638	1.357000	0.45904	0.563000	0.77884	CCT	G|0.967;A|0.033	0.033	strong		0.507	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964	
GLIPR1	11010	hgsc.bcm.edu	37	12	75884254	75884254	+	Silent	SNP	C	C	T	rs28932170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:75884254C>T	ENST00000266659.3	+	3	690	c.489C>T	c.(487-489)gaC>gaT	p.D163D	RP11-585P4.5_ENST00000547326.1_RNA	NM_006851.2	NP_006842.2	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1	163	SCP.		D -> E (in dbSNP:rs28932170).		cellular lipid metabolic process (GO:0044255)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	14						CTGGCTTTGACGCTCTTTCCA	0.443													C|||	251	0.0501198	0.0015	0.0648	5008	,	,		11657	0.0		0.0895	False		,,,				2504	0.1166				p.D163D		Atlas-SNP	.											.	GLIPR1	33	.	0			c.C489T						PASS	.	C		82,4324	69.2+/-107.0	0,82,2121	93.0	91.0	92.0		489	-10.4	0.0	12	dbSNP_125	92	764,7836	182.5+/-230.9	37,690,3573	no	coding-synonymous	GLIPR1	NM_006851.2		37,772,5694	TT,TC,CC		8.8837,1.8611,6.5047		163/267	75884254	846,12160	2203	4300	6503	SO:0001819	synonymous_variant	11010	exon3			CTTTGACGCTCTT	U16307	CCDS9011.1	12q14.1	2008-08-15	2008-08-15			ENSG00000139278			17001	protein-coding gene	gene with protein product		602692	"""GLI pathogenesis-related 1 (glioma)"""			7607567, 8973356	Standard	NM_006851		Approved	RTVP1, GliPR	uc001sxs.3	P48060	OTTHUMG00000169757	ENST00000266659.3:c.489C>T	12.37:g.75884254C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_006851	A7YET6|F8VUC2|Q15409|Q969K2	Silent	SNP	ENST00000266659.3	37	CCDS9011.1	92	0.04212454212454213	1	0.0020325203252032522	29	0.08011049723756906	0	0.0	62	0.08179419525065963	C	8.595	0.885384	0.17540	0.018611	0.088837	ENSG00000139278	ENST00000456650;ENST00000550491	T	0.13420	2.59	5.22	-10.4	0.00318	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.34502	-0.9826	8	0.66056	D	0.02	.	5.5295	0.16976	0.2208:0.505:0.1203:0.1539	rs28932170;rs28932170	187	F6VVE8	.	M	187;46	ENSP00000391144:T187M	ENSP00000391144:T187M	T	+	2	0	GLIPR1	74170521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.521000	0.00951	-2.785000	0.00359	-2.269000	0.00276	ACG	T|0.059;C|0.941	0.059	strong		0.443	GLIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405722.1	NM_006851	
PUS7	54517	hgsc.bcm.edu	37	7	105148683	105148683	+	Missense_Mutation	SNP	A	A	G	rs139058270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:105148683A>G	ENST00000356362.2	-	2	491	c.277T>C	c.(277-279)Tgc>Cgc	p.C93R	PUS7_ENST00000469408.1_Missense_Mutation_p.C93R	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	93					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						TCCTCCTCGCACTCCTCTGAA	0.493													A|||	8	0.00159744	0.0008	0.0014	5008	,	,		17461	0.0		0.006	False		,,,				2504	0.0				p.C93R	Colon(138;2387 3051 17860)	Atlas-SNP	.											.	PUS7	59	.	0			c.T277C						PASS	.	A	ARG/CYS	6,4400	11.4+/-27.6	0,6,2197	212.0	178.0	190.0		277	4.7	0.1	7	dbSNP_134	190	61,8539	38.3+/-94.2	0,61,4239	yes	missense	PUS7	NM_019042.3	180	0,67,6436	GG,GA,AA		0.7093,0.1362,0.5151	benign	93/662	105148683	67,12939	2203	4300	6503	SO:0001583	missense	54517	exon2			CCTCGCACTCCTC	AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"""pseudouridylate synthase 7 homolog (S. cerevisiae)"""			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.277T>C	7.37:g.105148683A>G	ENSP00000348722:p.Cys93Arg	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	244	112	0.459016	NM_019042	Q75MG4|Q9NX19	Missense_Mutation	SNP	ENST00000356362.2	37	CCDS34725.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	A	1.729	-0.494708	0.04322	0.001362	0.007093	ENSG00000091127	ENST00000356362;ENST00000544995;ENST00000469408	T;T	0.39592	1.07;1.07	5.58	4.69	0.59074	.	0.706924	0.14641	N	0.307220	T	0.15089	0.0364	N	0.08118	0	0.29644	N	0.844509	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.16424	-1.0403	10	0.16420	T	0.52	-6.8005	8.3068	0.32047	0.1631:0.759:0.0:0.0779	.	93;93	B3KY42;Q96PZ0	.;PUS7_HUMAN	R	93	ENSP00000348722:C93R;ENSP00000417402:C93R	ENSP00000348722:C93R	C	-	1	0	PUS7	104935919	0.000000	0.05858	0.097000	0.21041	0.261000	0.26267	0.758000	0.26447	1.326000	0.45319	-0.648000	0.03929	TGC	A|0.995;G|0.005	0.005	strong		0.493	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042	
KANK1	23189	hgsc.bcm.edu	37	9	712599	712599	+	Silent	SNP	C	C	T	rs11789987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:712599C>T	ENST00000382303.1	+	7	2485	c.1833C>T	c.(1831-1833)aaC>aaT	p.N611N	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Silent_p.N453N|KANK1_ENST00000382297.2_Silent_p.N611N	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	611					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)		AGTCTGTGAACGACCTCACAC	0.502													C|||	1267	0.252995	0.0923	0.2262	5008	,	,		24150	0.126		0.4105	False		,,,				2504	0.4581				p.N611N		Atlas-SNP	.											KANK1_ENST00000382303,colon,carcinoma,0,2	KANK1	231	2	0			c.C1833T						scavenged	.	C	,	606,3800	263.8+/-265.7	50,506,1647	173.0	148.0	157.0		1833,1359	-7.5	0.1	9	dbSNP_120	157	3458,5142	508.6+/-377.1	678,2102,1520	no	coding-synonymous,coding-synonymous	KANK1	NM_015158.2,NM_153186.3	,	728,2608,3167	TT,TC,CC		40.2093,13.754,31.2471	,	611/1353,453/1195	712599	4064,8942	2203	4300	6503	SO:0001819	synonymous_variant	23189	exon7			TGTGAACGACCTC	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.1833C>T	9.37:g.712599C>T		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			C|0.719;T|0.281	0.281	strong		0.502	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
TNC	3371	hgsc.bcm.edu	37	9	117846580	117846580	+	Missense_Mutation	SNP	T	T	C	rs1061494	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000537320.1_Missense_Mutation_p.Q680R|TNC_ENST00000542877.1_Missense_Mutation_p.Q680R|TNC_ENST00000341037.4_Missense_Mutation_p.Q680R|TNC_ENST00000340094.3_Missense_Mutation_p.Q680R|TNC_ENST00000423613.2_Missense_Mutation_p.Q680R|TNC_ENST00000345230.3_Missense_Mutation_p.Q680R|TNC_ENST00000346706.3_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	84	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	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	
BOK	666	hgsc.bcm.edu	37	2	242501828	242501828	+	Silent	SNP	C	C	T	rs145137590	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242501828C>T	ENST00000318407.3	+	3	588	c.286C>T	c.(286-288)Ctg>Ttg	p.L96L		NM_032515.4	NP_115904.1	Q9UMX3	BOK_HUMAN	BCL2-related ovarian killer	96					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell proliferation (GO:0008283)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|neuron apoptotic process (GO:0051402)|oligodendrocyte differentiation (GO:0048709)|positive regulation of apoptotic process (GO:0043065)|positive regulation of execution phase of apoptosis (GO:1900119)	cytoplasm (GO:0005737)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.L96L(1)		large_intestine(1)|lung(3)|ovary(1)	5		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;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)		GCACATCTCCCTGCAGTCTGA	0.637													C|||	11	0.00219649	0.0008	0.0029	5008	,	,		19434	0.0		0.008	False		,,,				2504	0.0				p.L96L		Atlas-SNP	.											BOK,NS,carcinoma,0,1	BOK	16	1	1	Substitution - coding silent(1)	lung(1)	c.C286T						PASS	.	C		12,4390	16.8+/-37.8	0,12,2189	116.0	85.0	95.0		286	5.0	1.0	2	dbSNP_134	95	75,8525	43.1+/-100.9	2,71,4227	no	coding-synonymous	BOK	NM_032515.4		2,83,6416	TT,TC,CC		0.8721,0.2726,0.6691		96/213	242501828	87,12915	2201	4300	6501	SO:0001819	synonymous_variant	666	exon3			ATCTCCCTGCAGT	AF174487	CCDS2550.1	2q37.3	2008-05-22			ENSG00000176720	ENSG00000176720			1087	protein-coding gene	gene with protein product		605404				9356461, 11034351, 15102863	Standard	NM_032515		Approved	BCL2L9, BOKL, MGC4631	uc002wbq.3	Q9UMX3	OTTHUMG00000133411	ENST00000318407.3:c.286C>T	2.37:g.242501828C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_032515		Silent	SNP	ENST00000318407.3	37	CCDS2550.1																																																																																			C|0.995;T|0.005	0.005	strong		0.637	BOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257268.2	NM_032515	
TDRD10	126668	hgsc.bcm.edu	37	1	154516477	154516477	+	Missense_Mutation	SNP	G	G	A	rs12750774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154516477G>A	ENST00000368480.3	+	9	627	c.542G>A	c.(541-543)cGa>cAa	p.R181Q	TDRD10_ENST00000479937.1_3'UTR|TDRD10_ENST00000368482.4_Missense_Mutation_p.R181Q			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	181			R -> Q (in dbSNP:rs12750774).				nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R181Q(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GAATGCTTCCGAGACCTGAGC	0.602													G|||	658	0.13139	0.0144	0.2522	5008	,	,		20020	0.0308		0.3082	False		,,,				2504	0.1258				p.R181Q		Atlas-SNP	.											TDRD10,NS,carcinoma,+1,3	TDRD10	48	3	1	Substitution - Missense(1)	stomach(1)	c.G542A						PASS	.	G	GLN/ARG,GLN/ARG	270,4136	152.2+/-185.9	13,244,1946	159.0	140.0	147.0		542,542	-1.6	0.0	1	dbSNP_121	147	2637,5963	426.1+/-355.2	425,1787,2088	yes	missense,missense	TDRD10	NM_001098475.1,NM_182499.3	43,43	438,2031,4034	AA,AG,GG		30.6628,6.128,22.3512	benign,benign	181/367,181/352	154516477	2907,10099	2203	4300	6503	SO:0001583	missense	126668	exon9			GCTTCCGAGACCT	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"""Tudor domain containing"", ""RNA binding motif (RRM) containing"""	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.542G>A	1.37:g.154516477G>A	ENSP00000357465:p.Arg181Gln	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	135	75	0.555556	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	37	CCDS41406.1	352	0.16117216117216118	10	0.02032520325203252	84	0.23204419889502761	23	0.04020979020979021	235	0.3100263852242744	G	3.590	-0.083717	0.07141	0.06128	0.306628	ENSG00000163239	ENST00000368482;ENST00000368480	T;T	0.22539	1.97;1.95	4.07	-1.63	0.08345	.	0.697753	0.11381	N	0.569811	T	0.03434	0.0099	N	0.17082	0.46	0.80722	P	0.0	B;B	0.30686	0.29;0.078	B;B	0.17979	0.015;0.02	T	0.36114	-0.9761	9	0.49607	T	0.09	0.0401	8.5311	0.33335	0.2944:0.0:0.7056:0.0	rs12750774;rs12750774	181;181	Q5VZ19;Q5VZ19-2	TDR10_HUMAN;.	Q	181	ENSP00000357467:R181Q;ENSP00000357465:R181Q	ENSP00000357465:R181Q	R	+	2	0	TDRD10	152783101	0.015000	0.18098	0.002000	0.10522	0.036000	0.12997	-0.475000	0.06599	-0.453000	0.07076	-0.391000	0.06502	CGA	G|0.809;A|0.191	0.191	strong		0.602	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499	
POM121	9883	hgsc.bcm.edu	37	7	72409197	72409197	+	Silent	SNP	G	G	A	rs112174498	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:72409197G>A	ENST00000434423.2	+	6	1344	c.1344G>A	c.(1342-1344)ccG>ccA	p.P448P	POM121_ENST00000446813.1_Silent_p.P183P|POM121_ENST00000358357.3_Silent_p.P183P|POM121_ENST00000257622.4_Silent_p.P183P|POM121_ENST00000395270.1_Silent_p.P183P			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	448	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CCCAGACACCGGAGAGGCCAG	0.547													.|||	59	0.0117812	0.0015	0.0072	5008	,	,		18704	0.0		0.0427	False		,,,				2504	0.0092				p.P183P		Atlas-SNP	.											.	POM121	131	.	0			c.G549A						PASS	.	G		31,4375	38.4+/-70.7	0,31,2172	119.0	130.0	126.0		549	-2.1	1.0	7	dbSNP_132	126	277,8323	105.0+/-166.0	3,271,4026	no	coding-synonymous	POM121	NM_172020.2		3,302,6198	AA,AG,GG		3.2209,0.7036,2.3681		183/985	72409197	308,12698	2203	4300	6503	SO:0001819	synonymous_variant	9883	exon6			GACACCGGAGAGG	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.1344G>A	7.37:g.72409197G>A		Somatic	445	1	0.00224719		WXS	Illumina HiSeq	Phase_I	462	239	0.517316	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000434423.2	37																																																																																				G|0.977;A|0.023	0.023	strong		0.547	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
CLGN	1047	hgsc.bcm.edu	37	4	141320081	141320081	+	Missense_Mutation	SNP	G	G	A	rs114046582	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:141320081G>A	ENST00000325617.5	-	8	1248	c.808C>T	c.(808-810)Ccc>Tcc	p.P270S	CLGN_ENST00000414773.1_Missense_Mutation_p.P270S|CLGN_ENST00000537281.1_Missense_Mutation_p.P270S	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	270					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)					TTATCATTGGGATCTTCAATT	0.403													G|||	62	0.0123802	0.0015	0.0317	5008	,	,		13813	0.0		0.0338	False		,,,				2504	0.0041				p.P270S		Atlas-SNP	.											.	CLGN	76	.	0			c.C808T						PASS	.	G	SER/PRO,SER/PRO	17,4389	24.3+/-50.5	0,17,2186	182.0	177.0	179.0		808,808	4.9	0.9	4	dbSNP_132	179	201,8399	87.1+/-149.5	5,191,4104	yes	missense,missense	CLGN	NM_001130675.1,NM_004362.2	74,74	5,208,6290	AA,AG,GG		2.3372,0.3858,1.6761	probably-damaging,probably-damaging	270/611,270/611	141320081	218,12788	2203	4300	6503	SO:0001583	missense	1047	exon9			CATTGGGATCTTC	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.808C>T	4.37:g.141320081G>A	ENSP00000326699:p.Pro270Ser	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	223	101	0.452915	NM_001130675	B3KS90|B4DXV8|D3DNY8	Missense_Mutation	SNP	ENST00000325617.5	37	CCDS3751.1	36	0.016483516483516484	0	0.0	12	0.03314917127071823	0	0.0	24	0.0316622691292876	G	15.37	2.812019	0.50527	0.003858	0.023372	ENSG00000153132	ENST00000325617;ENST00000414773;ENST00000537281;ENST00000545667	T;T;T	0.69561	-0.41;-0.41;-0.41	5.74	4.89	0.63831	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Calreticulin/calnexin, P (1);	0.095290	0.85682	N	0.000000	T	0.54854	0.1884	M	0.91768	3.24	0.80722	D	1	B	0.29378	0.243	B	0.32289	0.143	T	0.73190	-0.4061	10	0.87932	D	0	-2.8189	16.7709	0.85537	0.0:0.1292:0.8708:0.0	.	270	O14967	CLGN_HUMAN	S	270;270;270;187	ENSP00000326699:P270S;ENSP00000392782:P270S;ENSP00000439381:P270S	ENSP00000326699:P270S	P	-	1	0	CLGN	141539531	1.000000	0.71417	0.921000	0.36526	0.565000	0.35776	7.938000	0.87678	1.398000	0.46701	0.637000	0.83480	CCC	G|0.981;A|0.019	0.019	strong		0.403	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	
ANLN	54443	hgsc.bcm.edu	37	7	36459076	36459076	+	Silent	SNP	G	G	A	rs17213431	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:36459076G>A	ENST00000265748.2	+	10	2078	c.1857G>A	c.(1855-1857)gtG>gtA	p.V619V	ANLN_ENST00000396068.2_Silent_p.V582V	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	619	Interaction with F-actin.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						CAGTTGGTGTGGTAAGTCCAG	0.418													G|||	357	0.0712859	0.0045	0.0677	5008	,	,		20963	0.0337		0.1382	False		,,,				2504	0.1339				p.V619V		Atlas-SNP	.											.	ANLN	101	.	0			c.G1857A						PASS	.	G		143,4263	99.8+/-138.5	7,129,2067	90.0	83.0	85.0		1857	1.0	0.4	7	dbSNP_123	85	1135,7465	234.9+/-267.6	60,1015,3225	no	coding-synonymous	ANLN	NM_018685.2		67,1144,5292	AA,AG,GG		13.1977,3.2456,9.8262		619/1125	36459076	1278,11728	2203	4300	6503	SO:0001819	synonymous_variant	54443	exon10			TGGTGTGGTAAGT	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"""Pleckstrin homology (PH) domain containing"""	14082	protein-coding gene	gene with protein product			"""anillin (Drosophila Scraps homolog), actin binding protein"", ""anillin, actin binding protein (scraps homolog, Drosophila)"""			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.1857G>A	7.37:g.36459076G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	37	CCDS5447.1																																																																																			G|0.916;A|0.084	0.084	strong		0.418	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
COG3	83548	hgsc.bcm.edu	37	13	46099171	46099171	+	Missense_Mutation	SNP	C	C	T	rs144497765		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46099171C>T	ENST00000349995.5	+	20	2327	c.2215C>T	c.(2215-2217)Cct>Tct	p.P739S		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	739					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		CTCACAGCAGCCTTGGGCACA	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		18679	0.0		0.001	False		,,,				2504	0.0				p.P739S	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C2215T						PASS	.	C	SER/PRO	2,4404	4.2+/-10.8	0,2,2201	93.0	87.0	89.0		2215	5.2	1.0	13	dbSNP_134	89	9,8591	7.1+/-27.0	0,9,4291	yes	missense	COG3	NM_031431.3	74	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	benign	739/829	46099171	11,12995	2203	4300	6503	SO:0001583	missense	83548	exon20			CAGCAGCCTTGGG	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.2215C>T	13.37:g.46099171C>T	ENSP00000258654:p.Pro739Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	37	CCDS9398.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.16	2.750401	0.49257	4.54E-4	0.001047	ENSG00000136152	ENST00000349995	T	0.54071	0.59	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.62720	0.2451	M	0.64997	1.995	0.80722	D	1	B;D	0.60575	0.264;0.988	B;P	0.54815	0.074;0.761	T	0.58352	-0.7651	10	0.20046	T	0.44	-11.7744	17.7148	0.88333	0.0:1.0:0.0:0.0	.	576;739	B4E2F3;Q96JB2	.;COG3_HUMAN	S	739	ENSP00000258654:P739S	ENSP00000258654:P739S	P	+	1	0	COG3	44997172	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.666000	0.83877	2.426000	0.82243	0.655000	0.94253	CCT	C|0.999;T|0.001	0.001	strong		0.388	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
COL4A3	1285	hgsc.bcm.edu	37	2	228131169	228131169	+	Missense_Mutation	SNP	A	A	G	rs11677877	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228131169A>G	ENST00000396578.3	+	22	1514	c.1352A>G	c.(1351-1353)cAc>cGc	p.H451R	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	451	Triple-helical region.		H -> R (in dbSNP:rs11677877). {ECO:0000269|PubMed:11134255}.		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)		CCTGGAGATCACGGACTGCCA	0.398													G|||	558	0.111422	0.0666	0.183	5008	,	,		17815	0.1577		0.0686	False		,,,				2504	0.1176				p.H451R		Atlas-SNP	.											COL4A3_ENST00000328380,caecum,carcinoma,-1,2	COL4A3	293	2	0			c.A1352G	GRCh37	CM085146	COL4A3	M	rs11677877	PASS	.	G	ARG/HIS	245,3437		10,225,1606	72.0	70.0	71.0		1352	-4.1	0.0	2	dbSNP_120	71	628,7562		21,586,3488	yes	missense	COL4A3	NM_000091.4	29	31,811,5094	GG,GA,AA		7.6679,6.654,7.3534	benign	451/1671	228131169	873,10999	1841	4095	5936	SO:0001583	missense	1285	exon22			GAGATCACGGACT		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.1352A>G	2.37:g.228131169A>G	ENSP00000379823:p.His451Arg	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	231	126	0.545455	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	221	0.10119047619047619	25	0.0508130081300813	60	0.16574585635359115	87	0.1520979020979021	49	0.06464379947229551	G	5.410	0.260736	0.10239	0.06654	0.076679	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.96619	-4.07	5.69	-4.09	0.03951	.	1.358520	0.04708	N	0.417004	T	0.00784	0.0026	N	0.00313	-1.665	0.80722	P	0.0	B;B;B;B	0.26258	0.015;0.043;0.043;0.145	B;B;B;B	0.29267	0.019;0.012;0.019;0.1	T	0.63545	-0.6613	9	0.06891	T	0.86	.	4.1959	0.10443	0.5232:0.1033:0.2691:0.1045	rs11677877;rs56438970;rs11677877	451;451;451;451	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	R	451	ENSP00000379823:H451R	ENSP00000323334:H451R	H	+	2	0	COL4A3	227839413	0.000000	0.05858	0.000000	0.03702	0.127000	0.20565	-0.285000	0.08410	-1.113000	0.02981	-1.595000	0.00837	CAC	A|0.908;G|0.092	0.092	strong		0.398	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
CFHR3	10878	hgsc.bcm.edu	37	1	196757392	196757392	+	Silent	SNP	C	C	T	rs400344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:196757392C>T	ENST00000367425.4	+	4	569	c.477C>T	c.(475-477)tcC>tcT	p.S159S	CFHR3_ENST00000391985.3_Intron|CFHR3_ENST00000471440.2_Silent_p.S159S	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	159	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						GATTCATTTCCGAATCTTCCT	0.254													-|||	3252	0.649361	0.646	0.6657	5008	,	,		9863	0.9484		0.501	False		,,,				2504	0.4867				p.S159S		Atlas-SNP	.											CFHR3,NS,carcinoma,0,1	CFHR3	52	1	0			c.C477T						PASS	.						9.0	15.0	13.0					1																	196757392		1478	3842	5320	SO:0001819	synonymous_variant	10878	exon4			CATTTCCGAATCT	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"""Complement system"""	16980	protein-coding gene	gene with protein product	"""complement factor H related 3"""	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.477C>T	1.37:g.196757392C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_021023	B4DPR0|Q9UJ16	Silent	SNP	ENST00000367425.4	37	CCDS30958.1																																																																																			C|0.379;T|0.621	0.621	strong		0.254	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023	
DSG1	1828	hgsc.bcm.edu	37	18	28934681	28934681	+	Missense_Mutation	SNP	A	A	T	rs3752095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000581452.1_RNA|DSG1_ENST00000462981.2_Missense_Mutation_p.Y200F|RP11-534N16.1_ENST00000578477.1_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	180	0	0		WXS	Illumina HiSeq	Phase_I	215	102	0.474419	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	
COL4A1	1282	hgsc.bcm.edu	37	13	110827574	110827574	+	Silent	SNP	T	T	A	rs874203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:110827574T>A	ENST00000375820.4	-	37	3310	c.3189A>T	c.(3187-3189)cgA>cgT	p.R1063R		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1063	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)			CCTTTTCACCTCGCAGCCCTG	0.567													A|||	1592	0.317891	0.2549	0.3501	5008	,	,		22228	0.2788		0.3668	False		,,,				2504	0.3701				p.R1063R		Atlas-SNP	.											COL4A1_ENST00000375815,NS,carcinoma,-1,2	COL4A1	372	2	0			c.A3189T						PASS	.	A		1251,3155	703.5+/-407.0	181,889,1133	150.0	115.0	127.0		3189	-6.8	0.1	13	dbSNP_86	127	3118,5482	658.0+/-401.5	568,1982,1750	no	coding-synonymous	COL4A1	NM_001845.4		749,2871,2883	AA,AT,TT		36.2558,28.3931,33.5922		1063/1670	110827574	4369,8637	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon37			TTCACCTCGCAGC	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.3189A>T	13.37:g.110827574T>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			T|0.665;A|0.335	0.335	strong		0.567	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
CSMD1	64478	hgsc.bcm.edu	37	8	2807783	2807783	+	Silent	SNP	G	G	A	rs35043129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:2807783G>A	ENST00000520002.1	-	68	10842	c.10287C>T	c.(10285-10287)ttC>ttT	p.F3429F	CSMD1_ENST00000537824.1_Silent_p.F3428F|CSMD1_ENST00000602723.1_Silent_p.F3252F|CSMD1_ENST00000400186.3_Silent_p.F3252F|CSMD1_ENST00000542608.1_Silent_p.F3251F|CSMD1_ENST00000602557.1_Silent_p.F3429F			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3429						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)		TGTCATTTTCGAACTTGCTTA	0.428													G|||	776	0.154952	0.2345	0.1311	5008	,	,		18125	0.1319		0.1511	False		,,,				2504	0.092				p.F3428F		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C10284T						PASS	.	G		751,2953		82,587,1183	173.0	172.0	172.0		10284	-0.1	1.0	8	dbSNP_126	172	1018,7164		72,874,3145	no	coding-synonymous	CSMD1	NM_033225.5		154,1461,4328	AA,AG,GG		12.4419,20.2754,14.8831		3428/3565	2807783	1769,10117	1852	4091	5943	SO:0001819	synonymous_variant	64478	exon67			ATTTTCGAACTTG			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.10287C>T	8.37:g.2807783G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		372	0.17032967032967034	132	0.2682926829268293	41	0.1132596685082873	87	0.1520979020979021	112	0.14775725593667546	G	6.388	0.439751	0.12104	0.202754	0.124419	ENSG00000183117	ENST00000335551	.	.	.	5.14	-0.13	0.13498	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999783068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0882	0.42432	0.6522:0.0:0.3478:0.0	rs35043129;rs56930695	.	.	.	X	2831	.	.	R	-	1	2	CSMD1	2795190	0.999000	0.42202	0.999000	0.59377	0.694000	0.40290	0.880000	0.28159	0.007000	0.14760	-1.062000	0.02293	CGA	G|0.836;A|0.164	0.164	strong		0.428	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SHANK3	85358	hgsc.bcm.edu	37	22	51153371	51153371	+	Missense_Mutation	SNP	G	G	A	rs61729471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:51153371G>A	ENST00000414786.2	+	19	2346	c.2119G>A	c.(2119-2121)Gcc>Acc	p.A707T	SHANK3_ENST00000445220.2_Missense_Mutation_p.A723T|SHANK3_ENST00000262795.3_Missense_Mutation_p.A737T			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	721					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GCTGGCAGCCGCCGCAGAGCC	0.662													G|||	127	0.0253594	0.0	0.0274	5008	,	,		14931	0.003		0.0268	False		,,,				2504	0.0798				p.A707T		Atlas-SNP	.											.	SHANK3	96	.	0			c.G2119A						PASS	.	G	THR/ALA	31,4295		0,31,2132	11.0	14.0	13.0		2209	4.1	0.2	22	dbSNP_129	13	274,8220		7,260,3980	yes	missense	SHANK3	NM_001080420.1	58	7,291,6112	AA,AG,GG		3.2258,0.7166,2.3791	possibly-damaging	737/1748	51153371	305,12515	2163	4247	6410	SO:0001583	missense	85358	exon19			GCAGCCGCCGCAG	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.2119G>A	22.37:g.51153371G>A	ENSP00000464552:p.Ala707Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		26	0.011904761904761904	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	18	0.023746701846965697	G	14.08	2.427407	0.43122	0.007166	0.032258	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.39229	1.09;1.12	4.06	4.06	0.47325	.	.	.	.	.	T	0.10809	0.0264	L	0.47190	1.495	0.09310	N	0.999996	P;P	0.50710	0.739;0.938	B;B	0.29353	0.041;0.101	T	0.18840	-1.0324	9	0.62326	D	0.03	.	9.0818	0.36556	0.0:0.0:0.7811:0.2189	rs61729471	722;737	Q9BYB0;F2Z3L0	SHAN3_HUMAN;.	T	737;723	ENSP00000442518:A737T;ENSP00000446078:A723T	ENSP00000442518:A737T	A	+	1	0	SHANK3	49500237	1.000000	0.71417	0.169000	0.22859	0.821000	0.46438	3.411000	0.52672	2.102000	0.63906	0.511000	0.50034	GCC	G|0.988;A|0.012	0.012	strong		0.662	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923934	43923934	+	Silent	SNP	T	T	C	rs11079725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43923934T>C	ENST00000329196.5	+	1	1679	c.1662T>C	c.(1660-1662)gaT>gaC	p.D554D	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	554						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										GCGCAGCAGATGCCCACACAG	0.597													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		17960	0.001		0.2396	False		,,,				2504	0.0613				p.D554D		Atlas-SNP	.											.	.	.	.	0			c.T1662C						PASS	.	C		201,4205	806.3+/-415.8	5,191,2007	49.0	48.0	48.0		1662	-9.4	0.0	17	dbSNP_120	48	1926,6674	725.4+/-406.5	221,1484,2595	no	coding-synonymous	IMP5	NM_175882.2		226,1675,4602	CC,CT,TT		22.3953,4.562,16.354		554/685	43923934	2127,10879	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			AGCAGATGCCCAC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1662T>C	17.37:g.43923934T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			T|0.854;C|0.146	0.146	strong		0.597	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
GALNT2	2590	hgsc.bcm.edu	37	1	230415148	230415148	+	Missense_Mutation	SNP	G	G	A	rs2273970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:230415148G>A	ENST00000366672.4	+	16	1732	c.1660G>A	c.(1660-1662)Gtg>Atg	p.V554M	GALNT2_ENST00000485438.1_3'UTR|RP5-956O18.3_ENST00000414640.1_RNA|GALNT2_ENST00000543760.1_Missense_Mutation_p.V516M	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	554	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		V -> M (in dbSNP:rs2273970). {ECO:0000269|PubMed:14702039}.		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)				AAGCGTGGAGGTGTGTGGCCC	0.642													G|||	568	0.113419	0.0121	0.1427	5008	,	,		17031	0.3115		0.0437	False		,,,				2504	0.0971				p.V554M		Atlas-SNP	.											.	GALNT2	83	.	0			c.G1660A						PASS	.	G	MET/VAL	107,4299	83.9+/-122.4	1,105,2097	67.0	61.0	63.0		1660	5.4	1.0	1	dbSNP_100	63	438,8162	134.1+/-191.5	9,420,3871	yes	missense	GALNT2	NM_004481.3	21	10,525,5968	AA,AG,GG		5.093,2.4285,4.1904	benign	554/572	230415148	545,12461	2203	4300	6503	SO:0001583	missense	2590	exon16			GTGGAGGTGTGTG	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.1660G>A	1.37:g.230415148G>A	ENSP00000355632:p.Val554Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	266	0.12179487179487179	5	0.01016260162601626	43	0.11878453038674033	188	0.32867132867132864	30	0.0395778364116095	G	13.33	2.206082	0.39003	0.024285	0.05093	ENSG00000143641	ENST00000543760;ENST00000366672	T;T	0.27256	1.68;1.68	5.45	5.45	0.79879	Ricin B-related lectin (1);Ricin B lectin (3);	0.117117	0.56097	D	0.000024	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	1.0	P;B	0.41910	0.764;0.219	B;B	0.37508	0.252;0.104	T	0.46359	-0.9197	9	0.49607	T	0.09	.	13.0282	0.58827	0.0837:0.0:0.9163:0.0	rs2273970;rs58228348;rs2273970	554;516	Q10471;G3V1S6	GALT2_HUMAN;.	M	516;554	ENSP00000445017:V516M;ENSP00000355632:V554M	ENSP00000355632:V554M	V	+	1	0	GALNT2	228481771	1.000000	0.71417	1.000000	0.80357	0.231000	0.25187	7.905000	0.87416	2.576000	0.86940	0.491000	0.48974	GTG	G|0.925;A|0.075	0.075	strong		0.642	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
KRT33A	3883	hgsc.bcm.edu	37	17	39503163	39503163	+	Missense_Mutation	SNP	G	G	A	rs12937519	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	108	101	0.935185	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	
MGLL	11343	hgsc.bcm.edu	37	3	127413881	127413881	+	Silent	SNP	T	T	C	rs4881	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:127413881T>C	ENST00000434178.2	-	7	1619	c.723A>G	c.(721-723)ctA>ctG	p.L241L	MGLL_ENST00000476682.1_5'UTR|MGLL_ENST00000265052.5_Silent_p.L251L|MGLL_ENST00000453507.2_Silent_p.L221L|MGLL_ENST00000398101.3_Silent_p.L215L|MGLL_ENST00000398104.1_Silent_p.L241L			Q99685	MGLL_HUMAN	monoglyceride lipase	241					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						TGCTGTCACATAGGCGATCGG	0.622													C|||	503	0.100439	0.1974	0.0778	5008	,	,		17787	0.0129		0.0944	False		,,,				2504	0.0818				p.L251L		Atlas-SNP	.											.	MGLL	19	.	0			c.A753G						PASS	.	C	,	652,3480		50,552,1464	50.0	57.0	55.0		723,753	-0.9	1.0	3	dbSNP_52	55	783,7603		42,699,3452	no	coding-synonymous,coding-synonymous	MGLL	NM_001003794.1,NM_007283.5	,	92,1251,4916	CC,CT,TT		9.337,15.7793,11.4635	,	241/304,251/314	127413881	1435,11083	2066	4193	6259	SO:0001819	synonymous_variant	11343	exon7			GTCACATAGGCGA	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.723A>G	3.37:g.127413881T>C		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	251	111	0.442231	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	37	CCDS43148.1	199	0.09111721611721611	87	0.17682926829268292	35	0.09668508287292818	7	0.012237762237762238	70	0.09234828496042216	C	11.08	1.534009	0.27387	0.157793	0.09337	ENSG00000074416	ENST00000496306	.	.	.	5.02	-0.899	0.10547	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999997122	.	.	.	.	.	.	T	0.21759	-1.0236	3	.	.	.	-7.5383	5.3013	0.15780	0.2029:0.3099:0.4138:0.0734	rs4881;rs2070258;rs3183250;rs4881	.	.	.	C	147	.	.	Y	-	2	0	MGLL	128896571	0.944000	0.32072	0.975000	0.42487	0.991000	0.79684	-0.074000	0.11450	-0.464000	0.06963	-0.186000	0.12905	TAT	T|0.903;C|0.097	0.097	strong		0.622	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
HRNR	388697	hgsc.bcm.edu	37	1	152189038	152189038	+	Silent	SNP	A	A	G	rs145118416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152189038A>G	ENST00000368801.2	-	3	5142	c.5067T>C	c.(5065-5067)taT>taC	p.Y1689Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1689					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGCTGACCATAGCGGGAAG	0.617																																					p.Y1689Y		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.T5067C						scavenged	.	A		321,2979		2,317,1331	67.0	73.0	71.0		5067	-0.7	0.0	1	dbSNP_134	71	363,6063		1,361,2851	no	coding-synonymous	HRNR	NM_001009931.1		3,678,4182	GG,GA,AA		5.6489,9.7273,7.0327		1689/2851	152189038	684,9042	1650	3213	4863	SO:0001819	synonymous_variant	388697	exon3			CTGACCATAGCGG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5067T>C	1.37:g.152189038A>G		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	268	30	0.11194	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			A|0.968;G|0.032	0.032	strong		0.617	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
CPVL	54504	hgsc.bcm.edu	37	7	29111950	29111950	+	Silent	SNP	A	A	G	rs62442642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:29111950A>G	ENST00000409850.1	-	12	1345	c.699T>C	c.(697-699)atT>atC	p.I233I	CPVL_ENST00000265394.5_Silent_p.I233I|CPVL_ENST00000396276.3_Silent_p.I233I			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	233						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						CTCCAATAGCAATTCCGTTCA	0.438													A|||	15	0.00299521	0.0015	0.0058	5008	,	,		20173	0.001		0.007	False		,,,				2504	0.001				p.I233I		Atlas-SNP	.											.	CPVL	60	.	0			c.T699C						PASS	.	A	,	9,4397	15.5+/-35.6	0,9,2194	154.0	129.0	138.0		699,699	-3.6	0.9	7	dbSNP_129	138	58,8542	36.4+/-91.3	0,58,4242	no	coding-synonymous,coding-synonymous	CPVL	NM_019029.2,NM_031311.3	,	0,67,6436	GG,GA,AA		0.6744,0.2043,0.5151	,	233/477,233/477	29111950	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	54504	exon8			AATAGCAATTCCG	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.699T>C	7.37:g.29111950A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	37	CCDS5419.1																																																																																			A|0.995;G|0.005	0.005	strong		0.438	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
TEKT4	150483	hgsc.bcm.edu	37	2	95537330	95537330	+	Silent	SNP	G	G	A	rs140196891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:95537330G>A	ENST00000295201.4	+	1	143	c.6G>A	c.(4-6)gcG>gcA	p.A2A	TEKT4_ENST00000427593.2_Silent_p.A2A|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	2					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						GCACCATGGCGCAGACAGTGC	0.697													.|||	17	0.00339457	0.0015	0.0043	5008	,	,		17151	0.0		0.007	False		,,,				2504	0.0051				p.A2A		Atlas-SNP	.											.	TEKT4	72	.	0			c.G6A						PASS	.	G		5,4261		0,5,2128	9.0	10.0	10.0		6	0.6	0.3	2	dbSNP_134	10	48,8290		0,48,4121	no	coding-synonymous	TEKT4	NM_144705.2		0,53,6249	AA,AG,GG		0.5757,0.1172,0.4205		2/436	95537330	53,12551	2133	4169	6302	SO:0001819	synonymous_variant	150483	exon1			CATGGCGCAGACA	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.6G>A	2.37:g.95537330G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			G|0.995;A|0.005	0.005	strong		0.697	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
AHNAK2	113146	hgsc.bcm.edu	37	14	105406372	105406372	+	Missense_Mutation	SNP	C	C	T	rs61421370	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105406372C>T	ENST00000333244.5	-	7	15535	c.15416G>A	c.(15415-15417)gGg>gAg	p.G5139E	AHNAK2_ENST00000557457.1_Missense_Mutation_p.G137E	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5139			G -> E (in dbSNP:rs61421370).			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)			TGGGACATCCCCGAGCCCACA	0.582													C|||	1468	0.293131	0.2398	0.317	5008	,	,		20449	0.0843		0.4821	False		,,,				2504	0.3691				p.G5139E		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-1,2	AHNAK2	719	2	0			c.G15416A						PASS	.	C	GLU/GLY	1179,2901		174,831,1035	65.0	72.0	70.0		15416	-1.8	0.0	14	dbSNP_129	70	4131,4239		1028,2075,1082	yes	missense	AHNAK2	NM_138420.2	98	1202,2906,2117	TT,TC,CC		49.3548,28.8971,42.6506	benign	5139/5796	105406372	5310,7140	2040	4185	6225	SO:0001583	missense	113146	exon7			ACATCCCCGAGCC	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.15416G>A	14.37:g.105406372C>T	ENSP00000353114:p.Gly5139Glu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	60	0.967742	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	689	0.31547619047619047	153	0.31097560975609756	125	0.3453038674033149	36	0.06293706293706294	375	0.4947229551451187	C	8.613	0.889475	0.17540	0.288971	0.493548	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.02763	4.17;4.29	3.7	-1.83	0.07833	.	1.260240	0.06340	U	0.707893	T	0.00012	0.0000	M	0.68593	2.085	0.80722	P	0.0	B	0.29432	0.244	B	0.25759	0.063	T	0.48198	-0.9056	9	0.02654	T	1	.	0.4206	0.00455	0.1865:0.2688:0.1835:0.3612	rs61421370;rs61996030	5139	Q8IVF2	AHNK2_HUMAN	E	137;5139	ENSP00000450998:G137E;ENSP00000353114:G5139E	ENSP00000353114:G5139E	G	-	2	0	AHNAK2	104477417	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.063000	0.01388	-0.309000	0.08779	0.462000	0.41574	GGG	C|0.639;T|0.361	0.361	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DUSP19	142679	hgsc.bcm.edu	37	2	183951888	183951888	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:183951888T>C	ENST00000354221.4	+	3	569	c.394T>C	c.(394-396)Tgt>Cgt	p.C132R	DUSP19_ENST00000469344.1_3'UTR|DUSP19_ENST00000342619.6_Intron|AC064871.3_ENST00000444562.1_RNA	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	132					inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						TTTTCCAGAATGTTTTGAATT	0.343																																					p.C132R		Atlas-SNP	.											.	DUSP19	41	.	0			c.T394C						PASS	.						93.0	92.0	92.0					2																	183951888		2202	4299	6501	SO:0001583	missense	142679	exon3			CCAGAATGTTTTG	AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.394T>C	2.37:g.183951888T>C	ENSP00000346160:p.Cys132Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_080876	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	t	19.13	3.768014	0.69878	.	.	ENSG00000162999	ENST00000354221	T	0.60424	0.19	5.37	4.18	0.49190	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.082767	0.85682	D	0.000000	T	0.81432	0.4821	H	0.95079	3.62	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.85083	0.0947	10	0.72032	D	0.01	.	11.6994	0.51562	0.1327:0.0:0.0:0.8673	.	132	Q8WTR2	DUS19_HUMAN	R	132	ENSP00000346160:C132R	ENSP00000346160:C132R	C	+	1	0	DUSP19	183660133	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.113000	0.77095	0.934000	0.37316	0.520000	0.50463	TGT	.	.	none		0.343	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1		
RRP12	23223	hgsc.bcm.edu	37	10	99116903	99116903	+	Missense_Mutation	SNP	C	C	T	rs1048445	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99116903C>T	ENST00000370992.4	-	34	3953	c.3842G>A	c.(3841-3843)cGg>cAg	p.R1281Q	RRP12_ENST00000315563.6_Missense_Mutation_p.R1181Q|RRP12_ENST00000536831.1_Missense_Mutation_p.R999Q|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000414986.1_Missense_Mutation_p.R1220Q	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1281			R -> Q (in dbSNP:rs1048445). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GGAACCTCGCCGGGCAGCCTT	0.612													C|||	1419	0.283347	0.1762	0.2853	5008	,	,		20496	0.3075		0.2813	False		,,,				2504	0.4039				p.R1281Q		Atlas-SNP	.											.	RRP12	97	.	0			c.G3842A						PASS	.	C	GLN/ARG,GLN/ARG	769,3637	314.1+/-293.5	70,629,1504	91.0	86.0	88.0		3659,3842	3.1	1.0	10	dbSNP_86	88	2304,6296	387.6+/-342.3	309,1686,2305	yes	missense,missense	RRP12	NM_001145114.1,NM_015179.3	43,43	379,2315,3809	TT,TC,CC		26.7907,17.4535,23.6276	benign,benign	1220/1237,1281/1298	99116903	3073,9933	2203	4300	6503	SO:0001583	missense	23223	exon34			CCTCGCCGGGCAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3842G>A	10.37:g.99116903C>T	ENSP00000360031:p.Arg1281Gln	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	570	0.260989010989011	88	0.17886178861788618	106	0.292817679558011	162	0.28321678321678323	214	0.28232189973614774	C	11.11	1.542652	0.27563	0.174535	0.267907	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.29917	1.56;1.55;1.56;1.55	5.4	3.1	0.35709	.	0.323342	0.34002	N	0.004349	T	0.00012	0.0000	N	0.00729	-1.24	0.35557	P	0.195639	B;B;B;B	0.15473	0.001;0.001;0.013;0.0	B;B;B;B	0.08055	0.001;0.002;0.003;0.0	T	0.41520	-0.9504	9	0.16420	T	0.52	-8.9726	10.3808	0.44110	0.0:0.1009:0.0:0.8991	rs1048445;rs3188453;rs17504948;rs17844956;rs17857696;rs60604007;rs1048445	1220;1181;999;1281	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	Q	1281;1181;1220;999	ENSP00000360031:R1281Q;ENSP00000324315:R1181Q;ENSP00000414863:R1220Q;ENSP00000446184:R999Q	ENSP00000324315:R1181Q	R	-	2	0	RRP12	99106893	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.901000	0.48695	0.374000	0.24650	-0.258000	0.10820	CGG	C|0.753;T|0.247	0.247	strong		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
RGSL1	353299	hgsc.bcm.edu	37	1	182443014	182443014	+	Missense_Mutation	SNP	G	G	C	rs647224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:182443014G>C	ENST00000294854.8	+	6	788	c.768G>C	c.(766-768)tgG>tgC	p.W256C	RGSL1_ENST00000542961.1_Missense_Mutation_p.W291C	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1	256			W -> C (in dbSNP:rs647224).		termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)		p.W291C(1)		central_nervous_system(2)|skin(4)	6						GGAAGATGTGGCAATTGGTAG	0.493													G|||	617	0.123203	0.1089	0.1412	5008	,	,		23260	0.246		0.0567	False		,,,				2504	0.0716				p.W256C	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Atlas-SNP	.											RGSL2,NS,carcinoma,0,1	RGSL1	111	1	1	Substitution - Missense(1)	stomach(1)	c.G768C						PASS	.	G	CYS/TRP	148,1236		10,128,554	156.0	145.0	148.0		768	5.1	1.0	1	dbSNP_83	148	170,3012		7,156,1428	yes	missense	RGSL1	NM_001137669.1	215	17,284,1982	CC,CG,GG		5.3426,10.6936,6.9645	probably-damaging	256/1077	182443014	318,4248	692	1591	2283	SO:0001583	missense	353299	exon6			GATGTGGCAATTG	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.768G>C	1.37:g.182443014G>C	ENSP00000457748:p.Trp256Cys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	146	70	0.479452	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Missense_Mutation	SNP	ENST00000294854.8	37	CCDS58049.1																																																																																			G|0.871;C|0.129	0.129	strong		0.493	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	
MUC16	94025	hgsc.bcm.edu	37	19	9049396	9049396	+	Silent	SNP	C	C	G	rs10425044	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9049396C>G	ENST00000397910.4	-	5	32438	c.32235G>C	c.(32233-32235)ggG>ggC	p.G10745G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10747	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTGTCTGTCCCAGAACTAG	0.478													C|||	939	0.1875	0.1566	0.2637	5008	,	,		22460	0.0258		0.2823	False		,,,				2504	0.2444				p.G10745G		Atlas-SNP	.											.	MUC16	4315	.	0			c.G32235C						PASS	.			624,3188		47,530,1329	173.0	156.0	161.0		32235	-1.9	0.0	19	dbSNP_119	161	2503,5737		402,1699,2019	no	coding-synonymous	MUC16	NM_024690.2		449,2229,3348	GG,GC,CC		30.3762,16.3694,25.9459		10745/14508	9049396	3127,8925	1906	4120	6026	SO:0001819	synonymous_variant	94025	exon5			GTCTGTCCCAGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32235G>C	19.37:g.9049396C>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	178	83	0.466292	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.781;G|0.219	0.219	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CACHD1	57685	hgsc.bcm.edu	37	1	65147002	65147002	+	Silent	SNP	C	C	T	rs3828064	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:65147002C>T	ENST00000371073.2	+	25	3468	c.3468C>T	c.(3466-3468)caC>caT	p.H1156H	CACHD1_ENST00000290039.5_Silent_p.H1105H|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1156					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						ACGACAGCCACGAAGACAGAG	0.418													C|||	639	0.127596	0.1815	0.0879	5008	,	,		17472	0.1935		0.0457	False		,,,				2504	0.0992				p.H1105H		Atlas-SNP	.											.	CACHD1	125	.	0			c.C3315T						PASS	.	C		721,3685	298.7+/-285.4	51,619,1533	129.0	120.0	123.0		3315	-3.0	0.9	1	dbSNP_107	123	396,8204	126.5+/-185.0	12,372,3916	no	coding-synonymous	CACHD1	NM_020925.2		63,991,5449	TT,TC,CC		4.6047,16.364,8.5883		1105/1224	65147002	1117,11889	2203	4300	6503	SO:0001819	synonymous_variant	57685	exon25			CAGCCACGAAGAC	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3468C>T	1.37:g.65147002C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	180	87	0.483333	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																				C|0.900;T|0.100	0.100	strong		0.418	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523636	42523636	+	Splice_Site	SNP	C	C	A	rs1135831|rs3915951		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:42523636C>A	ENST00000360608.5	-	7	1100	c.986G>T	c.(985-987)cGc>cTc	p.R329L	NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|CYP2D6_ENST00000389970.3_Splice_Site_p.R329L|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Splice_Site_p.R278L|NDUFA6-AS1_ENST00000439129.1_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	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	154	17	0.11039	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
OR52J3	119679	hgsc.bcm.edu	37	11	5068431	5068431	+	Missense_Mutation	SNP	G	G	A	rs17350764	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5068431G>A	ENST00000380370.1	+	1	676	c.676G>A	c.(676-678)Gtc>Atc	p.V226I		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	226			V -> I (in dbSNP:rs17350764).			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)		TCTCCGTGCTGTCTTCCGCCT	0.443													G|||	1114	0.222444	0.2519	0.3372	5008	,	,		21888	0.1081		0.1829	False		,,,				2504	0.2597				p.V226I		Atlas-SNP	.											OR52J3,right_upper_lobe,carcinoma,-2,1	OR52J3	77	1	0			c.G676A						PASS	.	G	ILE/VAL	1079,3323	392.8+/-328.6	139,801,1261	338.0	302.0	314.0		676	3.3	0.9	11	dbSNP_123	314	1605,6991	298.6+/-304.0	159,1287,2852	yes	missense	OR52J3	NM_001001916.2	29	298,2088,4113	AA,AG,GG		18.6715,24.5116,20.6493	probably-damaging	226/312	5068431	2684,10314	2201	4298	6499	SO:0001583	missense	119679	exon1			CGTGCTGTCTTCC	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.676G>A	11.37:g.5068431G>A	ENSP00000369728:p.Val226Ile	Somatic	366	1	0.00273224		WXS	Illumina HiSeq	Phase_I	394	200	0.507614	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	431	0.19734432234432234	124	0.25203252032520324	104	0.287292817679558	71	0.12412587412587413	132	0.1741424802110818	G	12.36	1.915057	0.33815	0.245116	0.186715	ENSG00000205495	ENST00000380370	T	0.00224	8.51	4.19	3.28	0.37604	GPCR, rhodopsin-like superfamily (1);	0.163104	0.28393	N	0.015504	T	0.00012	0.0000	M	0.69463	2.115	0.80722	P	0.0	D	0.57899	0.981	P	0.61070	0.883	T	0.52335	-0.8589	9	0.66056	D	0.02	.	7.7255	0.28757	0.1939:0.0:0.8061:0.0	rs17350764;rs57530495;rs17350764	226	Q8NH60	O52J3_HUMAN	I	226	ENSP00000369728:V226I	ENSP00000369728:V226I	V	+	1	0	OR52J3	5025007	0.109000	0.22037	0.924000	0.36721	0.042000	0.13812	0.668000	0.25127	0.970000	0.38263	-0.126000	0.14955	GTC	G|0.792;A|0.208	0.208	strong		0.443	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
LSAMP	4045	hgsc.bcm.edu	37	3	115571364	115571364	+	Silent	SNP	C	C	T	rs3821560	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:115571364C>T	ENST00000490035.2	-	4	1114	c.615G>A	c.(613-615)tcG>tcA	p.S205S	LSAMP_ENST00000539563.1_Silent_p.S202S|LSAMP_ENST00000498645.1_5'UTR	NM_002338.3	NP_002329.2	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	205	Ig-like C2-type 2.				cell adhesion (GO:0007155)|locomotory exploration behavior (GO:0035641)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.S205S(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(4)|lung(14)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		TGACATCCGCCGAGGAGACCT	0.532													C|||	665	0.132788	0.0303	0.304	5008	,	,		18611	0.1756		0.0855	False		,,,				2504	0.1544				p.S205S		Atlas-SNP	.											LSAMP,NS,carcinoma,0,1	LSAMP	62	1	1	Substitution - coding silent(1)	stomach(1)	c.G615A						scavenged	.	C		172,4234	112.1+/-150.2	0,172,2031	149.0	126.0	133.0		615	-6.5	0.3	3	dbSNP_107	133	664,7936	168.0+/-219.6	28,608,3664	no	coding-synonymous	LSAMP	NM_002338.3		28,780,5695	TT,TC,CC		7.7209,3.9038,6.4278		205/339	115571364	836,12170	2203	4300	6503	SO:0001819	synonymous_variant	4045	exon4			ATCCGCCGAGGAG	U41901	CCDS2982.1	3q13.2-q21	2013-01-11			ENSG00000185565	ENSG00000185565		"""Immunoglobulin superfamily / I-set domain containing"""	6705	protein-coding gene	gene with protein product	"""IgLON family member 3"""	603241				9615236	Standard	NM_002338		Approved	LAMP, IGLON3	uc003ebs.3	Q13449	OTTHUMG00000159308	ENST00000490035.2:c.615G>A	3.37:g.115571364C>T		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	159	76	0.477987	NM_002338	Q8IV49	Silent	SNP	ENST00000490035.2	37	CCDS2982.1																																																																																			C|0.912;T|0.088	0.088	strong		0.532	LSAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354495.4	NM_002338	
OR52M1	119772	hgsc.bcm.edu	37	11	4567185	4567185	+	Silent	SNP	T	T	C	rs12295898	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4567185T>C	ENST00000360213.1	+	1	765	c.765T>C	c.(763-765)taT>taC	p.Y255Y		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	255						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)		TGATCTTTTATGTTCCCATTG	0.512													T|||	183	0.0365415	0.0045	0.0807	5008	,	,		20913	0.0		0.0944	False		,,,				2504	0.0266				p.Y255Y		Atlas-SNP	.											.	OR52M1	53	.	0			c.T765C						PASS	.	T		81,4321	67.0+/-104.6	2,77,2122	287.0	245.0	259.0		765	2.6	1.0	11	dbSNP_120	259	898,7698	202.1+/-245.5	49,800,3449	no	coding-synonymous	OR52M1	NM_001004137.1		51,877,5571	CC,CT,TT		10.4467,1.8401,7.5319		255/318	4567185	979,12019	2201	4298	6499	SO:0001819	synonymous_variant	119772	exon1			CTTTTATGTTCCC	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.765T>C	11.37:g.4567185T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	236	107	0.45339	NM_001004137		Silent	SNP	ENST00000360213.1	37	CCDS31353.1																																																																																			T|0.933;C|0.067	0.067	strong		0.512	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
DOK6	220164	hgsc.bcm.edu	37	18	67266681	67266681	+	Missense_Mutation	SNP	C	C	T	rs140434706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:67266681C>T	ENST00000382713.5	+	3	426	c.236C>T	c.(235-237)gCg>gTg	p.A79V	RP11-465I4.2_ENST00000583991.1_RNA	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	79	PH.									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)				AAGAAGCATGCGGTGGCAATC	0.398													C|||	3	0.000599042	0.0	0.0014	5008	,	,		21209	0.0		0.002	False		,,,				2504	0.0				p.A79V		Atlas-SNP	.											.	DOK6	56	.	0			c.C236T						PASS	.	C	VAL/ALA	3,4403	6.2+/-15.9	0,3,2200	96.0	78.0	84.0		236	5.9	1.0	18	dbSNP_134	84	24,8576	16.6+/-54.9	0,24,4276	yes	missense	DOK6	NM_152721.5	64	0,27,6476	TT,TC,CC		0.2791,0.0681,0.2076	probably-damaging	79/332	67266681	27,12979	2203	4300	6503	SO:0001583	missense	220164	exon3			AGCATGCGGTGGC	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.236C>T	18.37:g.67266681C>T	ENSP00000372160:p.Ala79Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_152721	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Missense_Mutation	SNP	ENST00000382713.5	37	CCDS32841.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	25.6	4.652559	0.88056	6.81E-4	0.002791	ENSG00000206052	ENST00000382713	T	0.74737	-0.87	5.91	5.91	0.95273	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.111009	0.64402	D	0.000009	D	0.84306	0.5443	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79024	-0.1972	10	0.20046	T	0.44	-0.5669	19.2865	0.94077	0.0:1.0:0.0:0.0	.	79	Q6PKX4	DOK6_HUMAN	V	79	ENSP00000372160:A79V	ENSP00000372160:A79V	A	+	2	0	DOK6	65417661	1.000000	0.71417	0.968000	0.41197	0.416000	0.31233	7.786000	0.85741	2.802000	0.96397	0.655000	0.94253	GCG	C|0.998;T|0.002	0.002	strong		0.398	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721	
SVIL	6840	hgsc.bcm.edu	37	10	29770551	29770551	+	Missense_Mutation	SNP	A	A	G	rs11007612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:29770551A>G	ENST00000355867.4	-	28	5814	c.5062T>C	c.(5062-5064)Tcg>Ccg	p.S1688P	PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.S602P|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000375400.3_Missense_Mutation_p.S1262P|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000538146.1_Missense_Mutation_p.S480P|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000375398.2_Missense_Mutation_p.S1688P	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1688			S -> P (in dbSNP:rs11007612).		cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TTCTCATTCGATCTCTTCAGT	0.517													G|||	253	0.0505192	0.0371	0.0533	5008	,	,		16228	0.001		0.1362	False		,,,				2504	0.0297				p.S1688P		Atlas-SNP	.											SVIL,NS,carcinoma,+1,1	SVIL	226	1	0			c.T5062C						PASS	.	G	PRO/SER,PRO/SER	223,4183	806.3+/-415.8	0,223,1980	197.0	218.0	211.0		3784,5062	3.3	0.1	10	dbSNP_120	211	1131,7469	767.0+/-407.6	81,969,3250	yes	missense,missense	SVIL	NM_003174.3,NM_021738.2	74,74	81,1192,5230	GG,GA,AA		13.1512,5.0613,10.4106	benign,benign	1262/1789,1688/2215	29770551	1354,11652	2203	4300	6503	SO:0001583	missense	6840	exon28			CATTCGATCTCTT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5062T>C	10.37:g.29770551A>G	ENSP00000348128:p.Ser1688Pro	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	188	92	0.489362	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	148	0.06776556776556776	17	0.034552845528455285	25	0.06906077348066299	0	0.0	106	0.13984168865435356	G	0.022	-1.418037	0.01136	0.050613	0.131512	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	4.27	3.35	0.38373	.	0.168540	0.52532	N	0.000062	T	0.00039	0.0001	N	0.02916	-0.46	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.0;0.002;0.0	T	0.38200	-0.9672	9	0.09338	T	0.73	-6.3887	9.3137	0.37921	0.0814:0.1543:0.7642:0.0	rs11007612;rs17756635;rs52797377;rs11007612	602;480;1262;1688	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	P	1262;1688;1688;602;642;480	ENSP00000364549:S1262P;ENSP00000364547:S1688P;ENSP00000348128:S1688P;ENSP00000445472:S602P;ENSP00000440343:S480P	ENSP00000348128:S1688P	S	-	1	0	SVIL	29810557	1.000000	0.71417	0.112000	0.21494	0.161000	0.22273	4.520000	0.60524	0.440000	0.26502	-0.215000	0.12644	TCG	A|0.915;G|0.085	0.085	strong		0.517	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
IFT74	80173	hgsc.bcm.edu	37	9	27009100	27009100	+	Missense_Mutation	SNP	T	T	C	rs17694549	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:27009100T>C	ENST00000443698.1	+	9	841	c.670T>C	c.(670-672)Ttt>Ctt	p.F224L	IFT74_ENST00000380062.5_Missense_Mutation_p.F224L|IFT74_ENST00000433700.1_Missense_Mutation_p.F224L|IFT74_ENST00000429045.2_Missense_Mutation_p.F224L	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	224			F -> L (in dbSNP:rs17694549). {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)		AAATATGTCTTTTGAAAACCA	0.343													C|||	371	0.0740815	0.1006	0.0346	5008	,	,		17761	0.0278		0.0547	False		,,,				2504	0.1339				p.F224L		Atlas-SNP	.											.	IFT74	46	.	0			c.T670C						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE	387,3299		21,345,1477	94.0	90.0	91.0		670,670,670,670	3.8	1.0	9	dbSNP_123	91	460,7720		12,436,3642	yes	missense,missense,missense,missense	IFT74	NM_001099222.1,NM_001099223.1,NM_001099224.1,NM_025103.2	22,22,22,22	33,781,5119	CC,CT,TT		5.6235,10.4992,7.138	benign,benign,benign,benign	224/601,224/601,224/373,224/601	27009100	847,11019	1843	4090	5933	SO:0001583	missense	80173	exon9			ATGTCTTTTGAAA	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.670T>C	9.37:g.27009100T>C	ENSP00000404122:p.Phe224Leu	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	237	117	0.493671	NM_001099222	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Missense_Mutation	SNP	ENST00000443698.1	37	CCDS43793.1	105	0.04807692307692308	29	0.05894308943089431	16	0.04419889502762431	14	0.024475524475524476	46	0.06068601583113457	C	14.10	2.434757	0.43224	0.104992	0.056235	ENSG00000096872	ENST00000433700;ENST00000443698;ENST00000380062;ENST00000544022;ENST00000429045	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.67	3.79	0.43588	.	0.612906	0.17074	N	0.188042	T	0.00384	0.0012	N	0.14661	0.345	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.25328	-1.0135	10	0.27082	T	0.32	-0.0904	2.8142	0.05451	0.1324:0.4752:0.2402:0.1522	rs17694549;rs52818293;rs17694549	224;224	Q96LB3;Q96LB3-2	IFT74_HUMAN;.	L	224	ENSP00000389224:F224L;ENSP00000404122:F224L;ENSP00000369402:F224L;ENSP00000393907:F224L	ENSP00000369402:F224L	F	+	1	0	IFT74	26999100	0.345000	0.24835	0.994000	0.49952	0.951000	0.60555	0.362000	0.20284	0.326000	0.23384	-0.227000	0.12334	TTT	T|0.943;C|0.057	0.057	strong		0.343	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103	
RNF133	168433	hgsc.bcm.edu	37	7	122338664	122338664	+	Silent	SNP	T	T	C	rs373664210		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:122338664T>C	ENST00000340112.2	-	1	546	c.309A>G	c.(307-309)gcA>gcG	p.A103A	CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000449022.2_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	103	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						GTTCAATAAGTGCAAGCCAGG	0.458																																					p.A103A	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.A309G						PASS	.	T	,,,	0,4406		0,0,2203	155.0	165.0	162.0		,,,309	-5.2	0.7	7		162	2,8596	2.2+/-6.3	0,2,4297	no	intron,intron,intron,coding-synonymous	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,	0,2,6500	CC,CT,TT		0.0233,0.0,0.0154	,,,	,,,103/377	122338664	2,13002	2203	4299	6502	SO:0001819	synonymous_variant	168433	exon1			AATAAGTGCAAGC	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"""RING-type (C3HC4) zinc fingers"""	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.309A>G	7.37:g.122338664T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	153	69	0.45098	NM_139175	A4D0W2|Q8N7G7	Silent	SNP	ENST00000340112.2	37	CCDS5784.1																																																																																			.	.	weak		0.458	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175	
CCDC74B	91409	hgsc.bcm.edu	37	2	130897218	130897218	+	Silent	SNP	T	T	C	rs13006246	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:130897218T>C	ENST00000310463.6	-	8	1190	c.1053A>G	c.(1051-1053)gcA>gcG	p.A351A	CCDC74B_ENST00000409943.3_Silent_p.A285A|CCDC74B_ENST00000392984.3_Silent_p.A453A|MED15P9_ENST00000427638.1_RNA	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	351										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					TCTGCTTCAGTGCGGGCAGGA	0.632													.|||	549	0.109625	0.025	0.1873	5008	,	,		16457	0.0288		0.2863	False		,,,				2504	0.0706				p.A351A		Atlas-SNP	.											.	CCDC74B	27	.	0			c.A1053G						PASS	.	T		293,4109		9,275,1917	40.0	36.0	37.0		1053	-9.4	0.0	2	dbSNP_121	37	2250,6348		287,1676,2336	no	coding-synonymous	CCDC74B	NM_207310.1		296,1951,4253	CC,CT,TT		26.1689,6.6561,19.5615		351/381	130897218	2543,10457	2201	4299	6500	SO:0001819	synonymous_variant	91409	exon8			CTTCAGTGCGGGC		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.1053A>G	2.37:g.130897218T>C		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	279	133	0.476703	NM_207310	Q6NW18	Silent	SNP	ENST00000310463.6	37	CCDS2155.1	305	0.13965201465201466	16	0.032520325203252036	80	0.22099447513812154	21	0.03671328671328671	188	0.24802110817941952	.	0.207	-1.039639	0.02013	0.066561	0.261689	ENSG00000152076	ENST00000409488	.	.	.	4.68	-9.37	0.00626	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999467645	.	.	.	.	.	.	T	0.16837	-1.0389	4	0.87932	D	0	.	2.0144	0.03495	0.1495:0.3335:0.2059:0.3111	rs13006246	.	.	.	R	245	.	ENSP00000386250:H245R	H	-	2	0	CCDC74B	130613688	0.408000	0.25360	0.005000	0.12908	0.007000	0.05969	-1.147000	0.03188	-3.106000	0.00243	-2.385000	0.00230	CAC	T|0.826;C|0.174	0.174	strong		0.632	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310	
TJP2	9414	hgsc.bcm.edu	37	9	71864319	71864319	+	Missense_Mutation	SNP	G	G	A	rs150494393		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:71864319G>A	ENST00000377245.4	+	20	3117	c.2909G>A	c.(2908-2910)cGa>cAa	p.R970Q	TJP2_ENST00000453658.2_Intron|TJP2_ENST00000535702.1_Intron|TJP2_ENST00000539225.1_Missense_Mutation_p.R1001Q|TJP2_ENST00000348208.4_Intron	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	970					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						CCAGAGCCACGAGCTCAGATG	0.542																																					p.R1001Q		Atlas-SNP	.											TJP2,caecum,carcinoma,0,1	TJP2	120	1	0			c.G3002A						PASS	.	G	,,GLN/ARG,,GLN/ARG,	0,4406		0,0,2203	40.0	33.0	35.0		,,3002,,2909,	3.0	1.0	9	dbSNP_134	35	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,missense,utr-3,missense,intron	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,43,,43,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,probably-damaging,,probably-damaging,	,,1001/1222,,970/1191,	71864319	2,13004	2203	4300	6503	SO:0001583	missense	9414	exon20			AGCCACGAGCTCA	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.2909G>A	9.37:g.71864319G>A	ENSP00000366453:p.Arg970Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	70	0.679612	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390626	0.62066	0.0	2.33E-4	ENSG00000119139	ENST00000377245;ENST00000539225	T;T	0.09350	2.99;3.03	5.82	2.96	0.34315	.	0.136502	0.47093	N	0.000255	T	0.17152	0.0412	L	0.53249	1.67	0.80722	D	1	D;D	0.67145	0.996;0.985	P;P	0.55871	0.786;0.638	T	0.07424	-1.0773	10	0.16896	T	0.51	.	9.3062	0.37876	0.1309:0.1201:0.749:0.0	.	1001;970	F5H301;Q9UDY2	.;ZO2_HUMAN	Q	970;1001	ENSP00000366453:R970Q;ENSP00000438262:R1001Q	ENSP00000366453:R970Q	R	+	2	0	TJP2	71054139	1.000000	0.71417	0.968000	0.41197	0.993000	0.82548	1.825000	0.39081	0.363000	0.24346	0.563000	0.77884	CGA	G|1.000;A|0.000	0.000	weak		0.542	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
CABP5	56344	hgsc.bcm.edu	37	19	48543923	48543923	+	Silent	SNP	C	C	A	rs12982629	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	119	0	0		WXS	Illumina HiSeq	Phase_I	157	72	0.458599	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	
KIAA1024	23251	hgsc.bcm.edu	37	15	79750256	79750256	+	Silent	SNP	A	A	G	rs3750002	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79750256A>G	ENST00000305428.3	+	2	1842	c.1767A>G	c.(1765-1767)gaA>gaG	p.E589E		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	589						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						ACCACTCGGAAGAAGAGCTGA	0.542													A|||	435	0.086861	0.003	0.0187	5008	,	,		21374	0.3065		0.0537	False		,,,				2504	0.0562				p.E589E		Atlas-SNP	.											.	KIAA1024	146	.	0			c.A1767G						PASS	.	A		55,4337	52.9+/-88.7	3,49,2144	72.0	68.0	70.0		1767	0.0	1.0	15	dbSNP_107	70	462,8124	136.0+/-193.2	16,430,3847	no	coding-synonymous	KIAA1024	NM_015206.2		19,479,5991	GG,GA,AA		5.3809,1.2523,3.9837		589/917	79750256	517,12461	2196	4293	6489	SO:0001819	synonymous_variant	23251	exon2			CTCGGAAGAAGAG	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.1767A>G	15.37:g.79750256A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_015206	A7MD43	Silent	SNP	ENST00000305428.3	37	CCDS32306.1																																																																																			A|0.931;G|0.069	0.069	strong		0.542	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
KANK3	256949	hgsc.bcm.edu	37	19	8399272	8399272	+	Silent	SNP	G	G	A	rs8106699	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	103	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	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	
ZBTB32	27033	hgsc.bcm.edu	37	19	36206050	36206050	+	Missense_Mutation	SNP	A	A	C	rs2227278	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36206050A>C	ENST00000392197.2	+	3	840	c.522A>C	c.(520-522)agA>agC	p.R174S	ZBTB32_ENST00000262630.3_Missense_Mutation_p.R174S|KMT2B_ENST00000222270.7_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000341701.1_5'Flank			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	174			R -> S (in dbSNP:rs2227278).		DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CAAGAGGCAGACCCGAGATGG	0.572													C|||	522	0.104233	0.087	0.1023	5008	,	,		18987	0.0903		0.1243	False		,,,				2504	0.1227				p.R174S		Atlas-SNP	.											.	ZBTB32	33	.	0			c.A522C						PASS	.	C	SER/ARG	383,4023	782.5+/-414.6	12,359,1832	43.0	44.0	44.0		522	-4.8	0.0	19	dbSNP_98	44	849,7751	774.3+/-407.7	40,769,3491	yes	missense	ZBTB32	NM_014383.1	110	52,1128,5323	CC,CA,AA		9.8721,8.6927,9.4726	benign	174/488	36206050	1232,11774	2203	4300	6503	SO:0001583	missense	27033	exon2			AGGCAGACCCGAG	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16763	protein-coding gene	gene with protein product	"""repressor of GATA"""	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.522A>C	19.37:g.36206050A>C	ENSP00000376035:p.Arg174Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	37	CCDS12471.1	229	0.10485347985347986	47	0.09552845528455285	37	0.10220994475138122	48	0.08391608391608392	97	0.1279683377308707	C	0.012	-1.666134	0.00765	0.086927	0.098721	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.07567	3.18;3.18	5.2	-4.76	0.03229	.	0.490294	0.19235	N	0.119307	T	0.00039	0.0001	N	0.04880	-0.145	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39941	-0.9589	9	0.11182	T	0.66	0.4559	0.9884	0.01451	0.2298:0.2038:0.338:0.2284	rs2227278;rs52799862;rs57776358;rs2227278	174	Q9Y2Y4	ZBT32_HUMAN	S	174	ENSP00000262630:R174S;ENSP00000376035:R174S	ENSP00000262630:R174S	R	+	3	2	ZBTB32	40897890	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.760000	0.04756	-0.286000	0.09076	-0.121000	0.15023	AGA	A|0.905;C|0.095	0.095	strong		0.572	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383	
BTC	685	hgsc.bcm.edu	37	4	75675841	75675841	+	Missense_Mutation	SNP	A	A	T	rs11938093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:75675841A>T	ENST00000395743.3	-	4	730	c.370T>A	c.(370-372)Ttg>Atg	p.L124M		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	124			L -> M (in dbSNP:rs11938093). {ECO:0000269|PubMed:15489334}.		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 apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			ACTGCTATCAAACAAATCACC	0.358													A|||	1001	0.19988	0.2428	0.2003	5008	,	,		16216	0.0407		0.2555	False		,,,				2504	0.2485				p.L124M		Atlas-SNP	.											.	BTC	23	.	0			c.T370A						PASS	.	A	MET/LEU	1191,3215	415.4+/-337.2	152,887,1164	188.0	198.0	195.0		370	2.9	1.0	4	dbSNP_120	195	2282,6318	383.8+/-340.9	296,1690,2314	yes	missense	BTC	NM_001729.2	15	448,2577,3478	TT,TA,AA		26.5349,27.0313,26.7031	probably-damaging	124/179	75675841	3473,9533	2203	4300	6503	SO:0001583	missense	685	exon4			CTATCAAACAAAT	S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.370T>A	4.37:g.75675841A>T	ENSP00000379092:p.Leu124Met	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	256	110	0.429688	NM_001729	Q96F48	Missense_Mutation	SNP	ENST00000395743.3	37	CCDS3566.1	392	0.1794871794871795	115	0.23373983739837398	81	0.22375690607734808	13	0.022727272727272728	183	0.24142480211081793	A	16.81	3.224906	0.58668	0.270313	0.265349	ENSG00000174808	ENST00000395743	T	0.15139	2.45	5.32	2.94	0.34122	.	0.163209	0.44285	D	0.000462	T	0.00012	0.0000	L	0.27053	0.805	0.35815	P	0.17586800000000002	D	0.76494	0.999	D	0.74023	0.982	T	0.26950	-1.0088	9	0.54805	T	0.06	-3.2024	5.9362	0.19167	0.7332:0.0:0.2668:0.0	rs11938093;rs17845298;rs17858133;rs52824759;rs11938093	124	P35070	BTC_HUMAN	M	124	ENSP00000379092:L124M	ENSP00000379092:L124M	L	-	1	2	BTC	75894865	0.974000	0.33945	1.000000	0.80357	0.723000	0.41478	0.064000	0.14437	1.101000	0.41535	0.460000	0.39030	TTG	A|0.755;T|0.245	0.245	strong		0.358	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1		
ARSF	416	hgsc.bcm.edu	37	X	3030403	3030403	+	Missense_Mutation	SNP	C	C	T	rs1052638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:3030403C>T	ENST00000381127.1	+	11	1800	c.1579C>T	c.(1579-1581)Cat>Tat	p.H527Y	ARSF_ENST00000359361.2_Missense_Mutation_p.H527Y|ARSF_ENST00000537104.1_Missense_Mutation_p.H527Y	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	527			H -> Y (in dbSNP:rs1052638). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9192838}.		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)				AGAGCCCCTCCATGATTTTGT	0.547													c|||	203	0.0537748	0.0408	0.062	3775	,	,		13694	0.0149		0.0577	False		,,,				2504	0.0337				p.H527Y		Atlas-SNP	.											.	ARSF	97	.	0			c.C1579T						PASS	.	C	TYR/HIS,TYR/HIS,TYR/HIS	280,3555		8,224,40,1400,531	92.0	81.0	85.0		1579,1579,1579	1.3	0.0	X	dbSNP_86	85	571,6157		23,376,149,2029,1723	yes	missense,missense,missense	ARSF	NM_001201538.1,NM_001201539.1,NM_004042.4	83,83,83	31,600,189,3429,2254	TT,TC,T,CC,C		8.4869,7.3012,8.0564	benign,benign,benign	527/591,527/591,527/591	3030403	851,9712	2203	4300	6503	SO:0001583	missense	416	exon11			CCCCTCCATGATT	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.1579C>T	X.37:g.3030403C>T	ENSP00000370519:p.His527Tyr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	63	0.969231	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	104	0.06268836648583484	11	0.023206751054852322	15	0.04335260115606936	4	0.007042253521126761	37	0.05124653739612189	C	0.047	-1.263794	0.01433	0.073012	0.084869	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.87179	-2.22;-2.22;-2.22	2.52	1.27	0.21489	Alkaline-phosphatase-like, core domain (1);	0.431913	0.23241	N	0.050352	T	0.06096	0.0158	N	0.00841	-1.15	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.44034	-0.9354	9	0.02654	T	1	.	6.6931	0.23183	0.0:0.1342:0.0:0.8658	rs1052638;rs3193092;rs17851997;rs1052638	527	P54793	ARSF_HUMAN	Y	527	ENSP00000370519:H527Y;ENSP00000445594:H527Y;ENSP00000352319:H527Y	ENSP00000352319:H527Y	H	+	1	0	ARSF	3040403	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	1.021000	0.30040	-0.001000	0.14495	-0.467000	0.05162	CAT	C|0.930;T|0.070	0.070	strong		0.547	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
FAT1	2195	hgsc.bcm.edu	37	4	187549428	187549428	+	Missense_Mutation	SNP	C	C	T	rs2304867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187549428C>T	ENST00000441802.2	-	9	4899	c.4690G>A	c.(4690-4692)Gct>Act	p.A1564T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1564	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in dbSNP:rs2304867).		actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TAGGAGGAAGCGGTGAACCAC	0.502										HNSCC(5;0.00058)			C|||	346	0.0690895	0.003	0.1499	5008	,	,		18441	0.1825		0.0338	False		,,,				2504	0.0204				p.A1564T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,colon,carcinoma,0,2	FAT1	500	2	0			c.G4690A						scavenged	.	C	THR/ALA	41,4153		0,41,2056	51.0	54.0	53.0		4690	3.1	1.0	4	dbSNP_100	53	255,8217		4,247,3985	yes	missense	FAT1	NM_005245.3	58	4,288,6041	TT,TC,CC		3.0099,0.9776,2.337	benign	1564/4589	187549428	296,12370	2097	4236	6333	SO:0001583	missense	2195	exon9			AGGAAGCGGTGAA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.4690G>A	4.37:g.187549428C>T	ENSP00000406229:p.Ala1564Thr	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	191	0.08745421245421245	3	0.006097560975609756	40	0.11049723756906077	117	0.20454545454545456	31	0.040897097625329816	C	14.75	2.629927	0.46944	0.009776	0.030099	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01821	4.62	5.49	3.09	0.35607	Cadherin (2);Cadherin-like (1);	0.170756	0.64402	D	0.000004	T	0.00012	0.0000	L	0.31371	0.925	0.32901	P	0.48679300000000003	B	0.26547	0.152	B	0.18561	0.022	T	0.50558	-0.8814	9	0.22109	T	0.4	.	7.3645	0.26766	0.1287:0.0695:0.0:0.8018	rs2304867;rs17692527;rs52820211;rs61327668;rs2304867	1564	Q14517	FAT1_HUMAN	T	1564;1563	ENSP00000406229:A1564T	ENSP00000260147:A1563T	A	-	1	0	FAT1	187786422	0.993000	0.37304	0.998000	0.56505	0.760000	0.43138	2.569000	0.45973	0.530000	0.28619	-1.093000	0.02169	GCT	C|0.922;T|0.078	0.078	strong		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ELMOD3	84173	hgsc.bcm.edu	37	2	85595818	85595818	+	Missense_Mutation	SNP	C	C	T	rs955592	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:85595818C>T	ENST00000409890.2	+	7	876	c.209C>T	c.(208-210)aCa>aTa	p.T70I	RN7SL113P_ENST00000497900.2_RNA|ELMOD3_ENST00000393852.4_Missense_Mutation_p.T70I|ELMOD3_ENST00000315658.7_Missense_Mutation_p.T70I|ELMOD3_ENST00000409013.3_Missense_Mutation_p.T70I|ELMOD3_ENST00000409344.3_Missense_Mutation_p.T70I|Y_RNA_ENST00000365512.1_RNA|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000428955.2_Missense_Mutation_p.T70I			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	70			T -> I (in dbSNP:rs955592).		phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						GTTGTGAGTACAGAGGTGGTC	0.552													C|||	158	0.0315495	0.0219	0.036	5008	,	,		18926	0.0099		0.0547	False		,,,				2504	0.0399				p.T70I		Atlas-SNP	.											.	ELMOD3	53	.	0			c.C209T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR,ILE/THR	140,4266	97.1+/-135.8	2,136,2065	131.0	110.0	117.0		209,209,209,209	2.2	0.1	2	dbSNP_86	117	616,7984	160.5+/-213.6	21,574,3705	yes	missense,missense,missense,missense	ELMOD3	NM_001135021.1,NM_001135022.1,NM_001135023.1,NM_032213.4	89,89,89,89	23,710,5770	TT,TC,CC		7.1628,3.1775,5.8127	benign,benign,benign,benign	70/382,70/382,70/382,70/392	85595818	756,12250	2203	4300	6503	SO:0001583	missense	84173	exon7			TGAGTACAGAGGT	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"""RNA binding motif (RRM) containing"""	26158	protein-coding gene	gene with protein product		615427	"""RNA binding motif protein 29"", ""RNA binding motif and ELMO/CED-12 domain 1"", ""deafness, autosomal recessive 88"""	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.209C>T	2.37:g.85595818C>T	ENSP00000386304:p.Thr70Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Missense_Mutation	SNP	ENST00000409890.2	37	CCDS46352.1	74	0.03388278388278388	14	0.028455284552845527	15	0.04143646408839779	3	0.005244755244755245	42	0.055408970976253295	C	11.80	1.747127	0.30955	0.031775	0.071628	ENSG00000115459	ENST00000409331;ENST00000409013;ENST00000409890;ENST00000409344;ENST00000393852;ENST00000428955;ENST00000315658;ENST00000418268	T;T;T;T;T;T;T;T	0.31510	1.56;1.54;1.54;1.54;1.54;1.53;1.49;1.53	5.08	2.22	0.28083	.	1.501900	0.03555	N	0.226185	T	0.02012	0.0063	L	0.40543	1.245	0.09310	N	1	B;B	0.20671	0.02;0.047	B;B	0.18871	0.023;0.01	T	0.11891	-1.0569	10	0.45353	T	0.12	1.7855	5.1075	0.14793	0.1642:0.6568:0.0:0.1789	rs955592;rs17735041;rs57387558;rs955592	70;70	Q96FG2-6;Q96FG2	.;ELMD3_HUMAN	I	70	ENSP00000386257:T70I;ENSP00000387139:T70I;ENSP00000386304:T70I;ENSP00000386248:T70I;ENSP00000377434:T70I;ENSP00000412692:T70I;ENSP00000318264:T70I;ENSP00000393443:T70I	ENSP00000318264:T70I	T	+	2	0	ELMOD3	85449329	0.000000	0.05858	0.125000	0.21846	0.769000	0.43574	0.327000	0.19663	0.705000	0.31890	0.455000	0.32223	ACA	C|0.951;T|0.049	0.049	strong		0.552	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213	
CER1	9350	hgsc.bcm.edu	37	9	14720357	14720357	+	Missense_Mutation	SNP	C	C	T	rs7036635	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:14720357C>T	ENST00000380911.3	-	2	579	c.535G>A	c.(535-537)Gta>Ata	p.V179I		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	179	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.		V -> I (in dbSNP:rs7036635). {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)		TGAACAACTACTTTTTCACAG	0.423													C|||	520	0.103834	0.1543	0.1326	5008	,	,		21572	0.0179		0.0805	False		,,,				2504	0.1278				p.V179I		Atlas-SNP	.											.	CER1	41	.	0			c.G535A						PASS	.	C	ILE/VAL	585,3821	253.7+/-259.5	37,511,1655	66.0	58.0	61.0		535	3.6	1.0	9	dbSNP_116	61	732,7868	173.2+/-223.7	49,634,3617	no	missense	CER1	NM_005454.2	29	86,1145,5272	TT,TC,CC		8.5116,13.2773,10.1261	probably-damaging	179/268	14720357	1317,11689	2203	4300	6503	SO:0001583	missense	9350	exon2			CAACTACTTTTTC	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.535G>A	9.37:g.14720357C>T	ENSP00000370297:p.Val179Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Missense_Mutation	SNP	ENST00000380911.3	37	CCDS6476.1	202	0.0924908424908425	87	0.17682926829268292	51	0.1408839779005525	5	0.008741258741258742	59	0.07783641160949868	C	15.85	2.954042	0.53293	0.132773	0.085116	ENSG00000147869	ENST00000380911	T	0.32515	1.45	5.52	3.56	0.40772	DAN (1);Cystine knot, C-terminal (2);	0.104382	0.42420	D	0.000720	T	0.00073	0.0002	M	0.64676	1.99	0.26192	P	0.9795724	B	0.31413	0.322	B	0.32980	0.156	T	0.09335	-1.0679	9	0.49607	T	0.09	-5.196	7.1118	0.25395	0.0:0.6051:0.2487:0.1462	rs7036635;rs61296156	179	O95813	CER1_HUMAN	I	179	ENSP00000370297:V179I	ENSP00000370297:V179I	V	-	1	0	CER1	14710357	0.793000	0.28825	0.963000	0.40424	0.677000	0.39632	0.737000	0.26144	1.470000	0.48102	0.655000	0.94253	GTA	A|0.005;C|0.899;T|0.096	0.096	strong		0.423	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454	
MAMDC4	158056	hgsc.bcm.edu	37	9	139748690	139748690	+	Missense_Mutation	SNP	A	A	G	rs151266186	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139748690A>G	ENST00000317446.2	+	7	748	c.698A>G	c.(697-699)cAc>cGc	p.H233R	MAMDC4_ENST00000445819.1_Missense_Mutation_p.H233R|MAMDC4_ENST00000485732.1_3'UTR	NM_206920.2	NP_996803.2			MAM domain containing 4											breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CCCCCGGGACACCACCACTGC	0.657													A|||	2	0.000399361	0.0	0.0	5008	,	,		13727	0.0		0.002	False		,,,				2504	0.0				p.H233R		Atlas-SNP	.											.	MAMDC4	117	.	0			c.A698G						PASS	.	A	ARG/HIS	1,4379		0,1,2189	24.0	26.0	25.0		698	4.3	0.0	9	dbSNP_134	25	14,8574		0,14,4280	yes	missense	MAMDC4	NM_206920.2	29	0,15,6469	GG,GA,AA		0.163,0.0228,0.1157	probably-damaging	233/1138	139748690	15,12953	2190	4294	6484	SO:0001583	missense	158056	exon7			CGGGACACCACCA	AL834531	CCDS7010.1	9q34.3	2013-10-21			ENSG00000177943	ENSG00000177943			24083	protein-coding gene	gene with protein product	"""apical early endosomal glycoprotein precursor"", ""endotubin"""					7829488	Standard	NM_206920		Approved	AEGP, DKFZp434M1411	uc004cjs.3	Q6UXC1	OTTHUMG00000020951	ENST00000317446.2:c.698A>G	9.37:g.139748690A>G	ENSP00000319388:p.His233Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	95	34	0.357895	NM_206920		Missense_Mutation	SNP	ENST00000317446.2	37	CCDS7010.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	.	8.328	0.825771	0.16749	2.28E-4	0.00163	ENSG00000177943	ENST00000317446;ENST00000445819	D;D	0.95272	-3.66;-3.66	4.34	4.34	0.51931	.	0.426385	0.21311	N	0.076630	D	0.91236	0.7238	L	0.48935	1.535	0.09310	N	1	B	0.28636	0.218	B	0.31101	0.124	T	0.82218	-0.0566	10	0.25106	T	0.35	-8.7896	12.4851	0.55868	1.0:0.0:0.0:0.0	.	233	Q6UXC1-2	.	R	233	ENSP00000319388:H233R;ENSP00000411339:H233R	ENSP00000319388:H233R	H	+	2	0	MAMDC4	138868511	0.004000	0.15560	0.013000	0.15412	0.461000	0.32589	1.047000	0.30367	1.818000	0.53035	0.459000	0.35465	CAC	A|0.999;G|0.001	0.001	strong		0.657	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920	
RYR1	6261	hgsc.bcm.edu	37	19	39008003	39008003	+	Silent	SNP	G	G	A	rs2304151	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39008003G>A	ENST00000359596.3	+	66	9690	c.9690G>A	c.(9688-9690)ctG>ctA	p.L3230L	RYR1_ENST00000360985.3_Silent_p.L3230L|RYR1_ENST00000355481.4_Silent_p.L3230L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3230					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)	CCCCAGTCCTGGGGCTCCCCA	0.632													G|||	453	0.0904553	0.0227	0.0461	5008	,	,		12385	0.1329		0.0865	False		,,,				2504	0.1738				p.L3230L		Atlas-SNP	.											.	RYR1	708	.	0			c.G9690A						PASS	.	G	,	136,4270	91.6+/-130.3	3,130,2070	30.0	34.0	32.0		9690,9690	2.8	1.0	19	dbSNP_100	32	571,8029	149.4+/-204.5	13,545,3742	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	16,675,5812	AA,AG,GG		6.6395,3.0867,5.436	,	3230/5039,3230/5034	39008003	707,12299	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon66			AGTCCTGGGGCTC	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.9690G>A	19.37:g.39008003G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			G|0.938;A|0.062	0.062	strong		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
CDHR2	54825	hgsc.bcm.edu	37	5	175998246	175998246	+	Silent	SNP	T	T	C	rs17078320	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	98	0	0		WXS	Illumina HiSeq	Phase_I	81	32	0.395062	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	
OR2A5	393046	hgsc.bcm.edu	37	7	143748257	143748257	+	Missense_Mutation	SNP	G	G	A	rs6464574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:143748257G>A	ENST00000408906.2	+	1	797	c.763G>A	c.(763-765)Gcc>Acc	p.A255T		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	255			A -> T (in dbSNP:rs6464574).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A255T(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CTTTGGCAGCGCCATTGTCAT	0.587													.|||	1198	0.239217	0.3533	0.2493	5008	,	,		19374	0.0079		0.2873	False		,,,				2504	0.2669				p.A255T		Atlas-SNP	.											OR2A5,NS,carcinoma,0,1	OR2A5	78	1	1	Substitution - Missense(1)	lung(1)	c.G763A						scavenged	.	G	THR/ALA	1296,2754		229,838,958	95.0	95.0	95.0		763	5.4	1.0	7	dbSNP_116	95	2613,5763		401,1811,1976	no	missense	OR2A5	NM_012365.1	58	630,2649,2934	AA,AG,GG		31.1963,32.0,31.4582	benign	255/312	143748257	3909,8517	2025	4188	6213	SO:0001583	missense	393046	exon1			GGCAGCGCCATTG	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"""GPCR / Class A : Olfactory receptors"""	8232	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 5"""	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.763G>A	7.37:g.143748257G>A	ENSP00000386208:p.Ala255Thr	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	444	0.2032967032967033	146	0.2967479674796748	94	0.2596685082872928	0	0.0	204	0.2691292875989446	G	17.51	3.407798	0.62399	0.32	0.311963	ENSG00000221836	ENST00000408906	T	0.00169	8.63	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31872	U	0.006933	T	0.00012	0.0000	L	0.41356	1.27	0.43110	P	0.005184999999999995	D	0.65815	0.995	P	0.53006	0.715	T	0.67469	-0.5663	9	0.72032	D	0.01	.	11.5247	0.50573	0.0:0.0:0.8216:0.1784	rs6464574	255	Q96R48	OR2A5_HUMAN	T	255	ENSP00000386208:A255T	ENSP00000386208:A255T	A	+	1	0	OR2A5	143379190	0.001000	0.12720	0.986000	0.45419	0.966000	0.64601	1.051000	0.30417	2.797000	0.96272	0.650000	0.86243	GCC	G|0.752;A|0.248	0.248	strong		0.587	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
PTPRB	5787	hgsc.bcm.edu	37	12	70963619	70963619	+	Missense_Mutation	SNP	G	G	A	rs2304821	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:70963619G>A	ENST00000261266.5	-	12	2845	c.2816C>T	c.(2815-2817)aCg>aTg	p.T939M	PTPRB_ENST00000538708.1_Missense_Mutation_p.T939M|PTPRB_ENST00000451516.2_Missense_Mutation_p.T849M|PTPRB_ENST00000550857.1_Missense_Mutation_p.T849M|PTPRB_ENST00000551525.1_Missense_Mutation_p.T1156M|PTPRB_ENST00000550358.1_Missense_Mutation_p.T1069M|PTPRB_ENST00000334414.6_Missense_Mutation_p.T1157M	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	939	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> M (in dbSNP:rs2304821).		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)			TGCCGACACCGTGTAGGAATC	0.517													G|||	343	0.0684904	0.0847	0.0663	5008	,	,		18306	0.0337		0.0915	False		,,,				2504	0.0603				p.T1157M		Atlas-SNP	.											.	PTPRB	676	.	0			c.C3470T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	301,3759		8,285,1737	87.0	86.0	87.0		3470,2546,2816,2816	-2.7	0.0	12	dbSNP_100	87	793,7567		43,707,3430	yes	missense,missense,missense,missense	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	81,81,81,81	51,992,5167	AA,AG,GG		9.4856,7.4138,8.8084	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1157/2216,849/1908,939/1908,939/1998	70963619	1094,11326	2030	4180	6210	SO:0001583	missense	5787	exon14			GACACCGTGTAGG	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.2816C>T	12.37:g.70963619G>A	ENSP00000261266:p.Thr939Met	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	238	117	0.491597	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	141	0.06456043956043957	34	0.06910569105691057	22	0.06077348066298342	16	0.027972027972027972	69	0.09102902374670185	G	11.71	1.718953	0.30503	0.074138	0.094856	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35	5.3	-2.7	0.06004	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.774615	0.12361	N	0.475680	T	0.01287	0.0042	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B;B;P	0.37276	0.098;0.05;0.028;0.144;0.446;0.12;0.589	B;B;B;B;B;B;B	0.32624	0.092;0.092;0.067;0.063;0.092;0.149;0.099	T	0.02352	-1.1172	10	0.44086	T	0.13	.	3.8671	0.09021	0.3453:0.0:0.4019:0.2528	rs2304821;rs52833376;rs60373517;rs2304821	849;939;1036;1156;1157;939;1069	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	M	1157;849;1069;939;849;939;1156;1036	ENSP00000334928:T1157M;ENSP00000393028:T849M;ENSP00000448058:T1069M;ENSP00000438927:T939M;ENSP00000447302:T849M;ENSP00000261266:T939M;ENSP00000448349:T1156M;ENSP00000446982:T1036M	ENSP00000261266:T939M	T	-	2	0	PTPRB	69249886	0.229000	0.23729	0.001000	0.08648	0.843000	0.47879	0.583000	0.23849	-0.321000	0.08627	-0.271000	0.10264	ACG	G|0.934;A|0.066	0.066	strong		0.517	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254247	39254247	+	Nonsense_Mutation	SNP	A	A	T	rs137943557	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254247A>T	ENST00000333822.4	-	1	146	c.90T>A	c.(88-90)tgT>tgA	p.C30*		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	30	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						AGGTGGTCTGACAGCAGCTGG	0.632													A|||	80	0.0159744	0.0008	0.0202	5008	,	,		16884	0.0		0.0447	False		,,,				2504	0.0204				p.C30X		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.T90A						PASS	.	A	stop/CYS	11,1373		0,11,681	23.0	25.0	25.0		90	-1.6	0.2	17	dbSNP_134	25	141,3041		4,133,1454	no	stop-gained	KRTAP4-8	NM_031960.2		4,144,2135	TT,TA,AA		4.4312,0.7948,3.329		30/186	39254247	152,4414	692	1591	2283	SO:0001587	stop_gained	728224	exon1			GGTCTGACAGCAG	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.90T>A	17.37:g.39254247A>T	ENSP00000328444:p.Cys30*	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	130	63	0.484615	NM_031960	A8MSH3	Nonsense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	40	0.018315018315018316	0	0.0	6	0.016574585635359115	0	0.0	34	0.044854881266490766	.	12.05	1.821859	0.32237	0.007948	0.044312	ENSG00000204880	ENST00000333822;ENST00000332991	.	.	.	3.56	-1.56	0.08532	.	0.122142	0.37348	U	0.002137	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.7326	0.18049	0.3:0.1451:0.5549:0.0	.	.	.	.	X	30	.	ENSP00000414561:C30X	C	-	3	2	KRTAP4-8	36507773	0.004000	0.15560	0.165000	0.22776	0.234000	0.25298	-0.095000	0.11077	-0.555000	0.06142	-1.744000	0.00683	TGT	A|0.982;T|0.018	0.018	strong		0.632	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
KNG1	3827	hgsc.bcm.edu	37	3	186460110	186460110	+	Missense_Mutation	SNP	G	G	C	rs5030087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:186460110G>C	ENST00000265023.4	+	10	2137	c.1925G>C	c.(1924-1926)gGc>gCc	p.G642A	KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_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	42	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	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	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994841	45994841	+	Nonstop_Mutation	SNP	A	A	C	rs7276273	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45994841A>C	ENST00000400374.3	+	1	1236	c.1206A>C	c.(1204-1206)tgA>tgC	p.*402C	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	0						keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CCCTCCTCTGACGCCCCGTGT	0.716													.|||	442	0.0882588	0.2496	0.0591	5008	,	,		15650	0.001		0.0189	False		,,,				2504	0.0521				p.X402C		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.A1206C						PASS	.	C	,CYS/stop	879,3505		84,711,1397	30.0	38.0	35.0		,1206	4.4	1.0	21	dbSNP_116	35	91,8447		1,89,4179	no	intron,stop-lost	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,	85,800,5576	CC,CA,AA		1.0658,20.0502,7.5066	,	,402/402	45994841	970,11952	2192	4269	6461	SO:0001578	stop_lost	386672	exon1			CCTCTGACGCCCC	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.1206A>C	21.37:g.45994841A>C	ENSP00000383225:p.*402Cysext*10	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	151	0.06913919413919414	118	0.23983739837398374	21	0.058011049723756904	2	0.0034965034965034965	10	0.013192612137203167	c	5.415	0.261711	0.10239	0.200502	0.010658	ENSG00000215454	ENST00000400374;ENST00000334871	.	.	.	4.38	4.38	0.52667	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.8727	0.18812	0.1932:0.7078:0.0:0.099	rs7276273	.	.	.	C	402;198	.	.	X	+	3	0	KRTAP10-4	44819269	0.420000	0.25457	0.962000	0.40283	0.048000	0.14542	-0.586000	0.05787	0.962000	0.38057	-0.224000	0.12420	TGA	A|0.948;C|0.052	0.052	strong		0.716	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
FLG	2312	hgsc.bcm.edu	37	1	152277168	152277168	+	Silent	SNP	A	A	G	rs3091276	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152277168A>G	ENST00000368799.1	-	3	10229	c.10194T>C	c.(10192-10194)tcT>tcC	p.S3398S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3398	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	0.612									Ichthyosis				G|||	2372	0.473642	0.5567	0.4539	5008	,	,		18388	0.6587		0.173	False		,,,				2504	0.4939				p.S3398S		Atlas-SNP	.											.	FLG	900	.	0			c.T10194C						PASS	.	G		2149,2257	583.6+/-385.9	541,1067,595	157.0	188.0	177.0		10194	-6.1	0.0	1	dbSNP_103	177	1267,7329	753.3+/-407.4	124,1019,3155	no	coding-synonymous	FLG	NM_002016.1		665,2086,3750	GG,GA,AA		14.7394,48.7744,26.2729		3398/4062	152277168	3416,9586	2203	4298	6501	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.10194T>C	1.37:g.152277168A>G		Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	318	143	0.449686	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			.	.	weak		0.612	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TANC1	85461	hgsc.bcm.edu	37	2	160028693	160028693	+	Missense_Mutation	SNP	T	T	G	rs113262393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160028693T>G	ENST00000263635.6	+	11	1650	c.1413T>G	c.(1411-1413)agT>agG	p.S471R	TANC1_ENST00000454300.1_Missense_Mutation_p.S365R	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	471					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						CTTCCACAAGTGCTTCCAGCA	0.448													T|||	50	0.00998403	0.0008	0.0072	5008	,	,		18666	0.001		0.005	False		,,,				2504	0.0389				p.S471R		Atlas-SNP	.											.	TANC1	157	.	0			c.T1413G						PASS	.	T	ARG/SER,ARG/SER	10,3798		0,10,1894	108.0	108.0	108.0		1389,1413	1.9	0.1	2	dbSNP_132	108	91,8181		1,89,4046	yes	missense,missense	TANC1	NM_001145909.1,NM_033394.2	110,110	1,99,5940	GG,GT,TT		1.1001,0.2626,0.8361	possibly-damaging,possibly-damaging	463/1391,471/1862	160028693	101,11979	1904	4136	6040	SO:0001583	missense	85461	exon11			CACAAGTGCTTCC	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.1413T>G	2.37:g.160028693T>G	ENSP00000263635:p.Ser471Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	141	79	0.560284	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	4	0.005277044854881266	T	14.19	2.460386	0.43736	0.002626	0.011001	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.20738	2.05;2.05	5.66	1.93	0.25924	.	0.269514	0.47455	D	0.000229	T	0.13030	0.0316	L	0.50333	1.59	0.58432	D	0.99999	B;P;B	0.35656	0.38;0.514;0.238	B;B;B	0.35607	0.102;0.206;0.167	T	0.02751	-1.1115	10	0.36615	T	0.2	.	9.2772	0.37707	0.0:0.2094:0.0:0.7906	.	463;365;471	B9EK39;Q9C0D5-2;Q9C0D5	.;.;TANC1_HUMAN	R	365;471	ENSP00000396339:S365R;ENSP00000263635:S471R	ENSP00000263635:S471R	S	+	3	2	TANC1	159736939	1.000000	0.71417	0.055000	0.19348	0.036000	0.12997	2.065000	0.41442	0.091000	0.17302	-0.326000	0.08463	AGT	T|0.993;G|0.007	0.007	strong		0.448	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
CENPF	1063	hgsc.bcm.edu	37	1	214819044	214819044	+	Missense_Mutation	SNP	C	C	T	rs7533166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214819044C>T	ENST00000366955.3	+	13	6299	c.6131C>T	c.(6130-6132)tCa>tTa	p.S2044L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2140					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)	p.S2044*(1)		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)		GAAAAGGACTCACAGGCACTG	0.428													C|||	192	0.0383387	0.1082	0.0115	5008	,	,		20872	0.001		0.0139	False		,,,				2504	0.0266				p.S2044L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	1	Substitution - Nonsense(1)	lung(1)	c.C6131T						PASS	.	C	LEU/SER	404,4002	194.7+/-219.5	20,364,1819	68.0	72.0	71.0		6131	3.6	0.3	1	dbSNP_116	71	126,8474	62.8+/-124.8	1,124,4175	yes	missense	CENPF	NM_016343.3	145	21,488,5994	TT,TC,CC		1.4651,9.1693,4.075	benign	2044/3115	214819044	530,12476	2203	4300	6503	SO:0001583	missense	1063	exon13			AGGACTCACAGGC	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.6131C>T	1.37:g.214819044C>T	ENSP00000355922:p.Ser2044Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	74	0.03388278388278388	61	0.12398373983739837	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	14.17	2.456003	0.43634	0.091693	0.014651	ENSG00000117724	ENST00000366955	T	0.03242	4.0	5.45	3.57	0.40892	.	0.278256	0.19506	N	0.112638	T	0.00073	0.0002	M	0.63428	1.95	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.48559	-0.9025	10	0.10111	T	0.7	.	7.8558	0.29480	0.0:0.6987:0.0:0.3013	rs7533166;rs52791225;rs7533166	2140	P49454	CENPF_HUMAN	L	2044	ENSP00000355922:S2044L	ENSP00000355922:S2044L	S	+	2	0	CENPF	212885667	0.024000	0.19004	0.328000	0.25416	0.973000	0.67179	0.156000	0.16382	1.293000	0.44690	0.603000	0.83216	TCA	C|0.958;T|0.042	0.042	strong		0.428	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
RNF165	494470	hgsc.bcm.edu	37	18	44015315	44015315	+	Silent	SNP	A	A	G	rs139779598	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:44015315A>G	ENST00000269439.7	+	3	492	c.441A>G	c.(439-441)caA>caG	p.Q147Q	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	147							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		ACTTCGGCCAACTGCAGACAC	0.642													A|||	30	0.00599042	0.0008	0.0159	5008	,	,		17217	0.0		0.0159	False		,,,				2504	0.002				p.Q147Q		Atlas-SNP	.											.	RNF165	34	.	0			c.A441G						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	63.0	54.0	57.0		441	5.7	1.0	18	dbSNP_134	57	93,8507	52.3+/-112.8	0,93,4207	no	coding-synonymous	RNF165	NM_152470.2		0,102,6401	GG,GA,AA		1.0814,0.2043,0.7843		147/347	44015315	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	494470	exon3			CGGCCAACTGCAG	BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"""RING-type (C3HC4) zinc fingers"""	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.441A>G	18.37:g.44015315A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_152470	B3KVD1	Silent	SNP	ENST00000269439.7	37	CCDS32823.1																																																																																			A|0.992;G|0.008	0.008	strong		0.642	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470	
MUC5B	727897	hgsc.bcm.edu	37	11	1264890	1264890	+	Silent	SNP	A	A	G	rs12286473	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1264890A>G	ENST00000529681.1	+	31	6838	c.6780A>G	c.(6778-6780)agA>agG	p.R2260R	MUC5B_ENST00000447027.1_Silent_p.R2263R|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2260	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CTAGCAGCAGAACCACCGAGT	0.657													g|||	489	0.0976438	0.0446	0.0922	5008	,	,		16843	0.0208		0.1779	False		,,,				2504	0.1697				p.R2260R		Atlas-SNP	.											.	MUC5B	473	.	0			c.A6780G						PASS	.	G		113,4227		13,87,2070	156.0	182.0	173.0		6780	-3.4	0.0	11	dbSNP_120	173	955,7541		138,679,3431	no	coding-synonymous	MUC5B	NM_002458.2		151,766,5501	GG,GA,AA		11.2406,2.6037,8.3203		2260/5763	1264890	1068,11768	2170	4248	6418	SO:0001819	synonymous_variant	727897	exon31			CAGCAGAACCACC	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.6780A>G	11.37:g.1264890A>G		Somatic	421	1	0.0023753		WXS	Illumina HiSeq	Phase_I	619	223	0.360258	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			A|0.906;G|0.094	0.094	strong		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
AKNAD1	254268	hgsc.bcm.edu	37	1	109394564	109394564	+	Silent	SNP	T	T	C	rs17030016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109394564T>C	ENST00000370001.3	-	2	991	c.723A>G	c.(721-723)gcA>gcG	p.A241A	AKNAD1_ENST00000369994.1_Silent_p.A241A|AKNAD1_ENST00000357393.4_Intron|AKNAD1_ENST00000369995.3_Silent_p.A241A	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	95	0	0		WXS	Illumina HiSeq	Phase_I	126	75	0.595238	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	
NCKAP5	344148	hgsc.bcm.edu	37	2	133541575	133541575	+	Missense_Mutation	SNP	C	C	T	rs12611515	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133541575C>T	ENST00000409261.1	-	14	3182	c.2809G>A	c.(2809-2811)Gtc>Atc	p.V937I	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.V937I|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	937			V -> I (in dbSNP:rs12611515).							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						AGCAGGGAGACGGACCTGCCT	0.617													c|||	1867	0.372804	0.4554	0.3141	5008	,	,		15512	0.497		0.2952	False		,,,				2504	0.2546				p.V937I		Atlas-SNP	.											NCKAP5,NS,carcinoma,0,2	NCKAP5	322	2	0			c.G2809A						PASS	.	C	ILE/VAL,	1698,2154		418,862,646	16.0	18.0	18.0		2809,	3.4	0.9	2	dbSNP_120	18	2375,5867		371,1633,2117	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	29,	789,2495,2763	TT,TC,CC		28.8158,44.081,33.6779	possibly-damaging,	937/1910,	133541575	4073,8021	1926	4121	6047	SO:0001583	missense	344148	exon14			GGGAGACGGACCT	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.2809G>A	2.37:g.133541575C>T	ENSP00000387128:p.Val937Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	844	0.38644688644688646	218	0.44308943089430897	118	0.3259668508287293	296	0.5174825174825175	212	0.2796833773087071	c	3.753	-0.051168	0.07407	0.44081	0.288158	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10960	2.82;2.82	5.18	3.36	0.38483	.	0.794876	0.10109	U	0.714992	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	0.9999999999528724	B	0.10296	0.003	B	0.08055	0.003	T	0.42103	-0.9471	9	0.32370	T	0.25	.	3.5614	0.07884	0.2085:0.5653:0.0:0.2261	rs12611515;rs52798675;rs57514357;rs12611515	937	O14513	NCKP5_HUMAN	I	937	ENSP00000387128:V937I;ENSP00000380603:V937I	ENSP00000380603:V937I	V	-	1	0	NCKAP5	133258045	1.000000	0.71417	0.934000	0.37439	0.077000	0.17291	2.178000	0.42519	0.753000	0.32945	-0.148000	0.13756	GTC	C|0.618;T|0.382	0.382	strong		0.617	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
MEGF6	1953	hgsc.bcm.edu	37	1	3512008	3512008	+	Silent	SNP	G	G	T	rs112138743	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3512008G>T	ENST00000356575.4	-	3	496	c.270C>A	c.(268-270)acC>acA	p.T90T		NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	90	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					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)		TGTAGTAGACGGTTCTAGAAA	0.622													g|||	15	0.00299521	0.0008	0.0086	5008	,	,		15701	0.0		0.006	False		,,,				2504	0.002				p.T90T	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C270A						PASS	.			6,4060		0,6,2027	36.0	42.0	40.0		270	-0.8	0.4	1	dbSNP_132	40	95,8275		2,91,4092	no	coding-synonymous	MEGF6	NM_001409.3		2,97,6119	TT,TG,GG		1.135,0.1476,0.8122		90/1542	3512008	101,12335	2033	4185	6218	SO:0001819	synonymous_variant	1953	exon3			GTAGACGGTTCTA	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.270C>A	1.37:g.3512008G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1																																																																																			G|0.993;T|0.007	0.007	strong		0.622	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
CTSE	1510	hgsc.bcm.edu	37	1	206327510	206327510	+	Silent	SNP	T	T	C	rs61742539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:206327510T>C	ENST00000358184.2	+	6	817	c.699T>C	c.(697-699)ttT>ttC	p.F233F	CTSE_ENST00000468617.1_3'UTR|CTSE_ENST00000361052.3_Silent_p.F238F|CTSE_ENST00000360218.2_Silent_p.F233F|CTSE_ENST00000432969.2_Silent_p.F158F	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	238					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			AGCTGATTTTTGGAGGCTACG	0.527													c|||	879	0.175519	0.3744	0.1628	5008	,	,		19775	0.0169		0.2038	False		,,,				2504	0.0501				p.F233F		Atlas-SNP	.											.	CTSE	72	.	0			c.T699C						PASS	.	C	,	1617,2789	662.4+/-401.0	302,1013,888	171.0	173.0	172.0		699,699	-6.6	0.5	1	dbSNP_129	172	1568,7032	745.1+/-407.3	144,1280,2876	no	coding-synonymous,coding-synonymous	CTSE	NM_001910.3,NM_148964.2	,	446,2293,3764	CC,CT,TT		18.2326,36.7,24.4887	,	233/397,233/364	206327510	3185,9821	2203	4300	6503	SO:0001819	synonymous_variant	1510	exon6			GATTTTTGGAGGC	BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"""Cathepsins"""	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.699T>C	1.37:g.206327510T>C		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Silent	SNP	ENST00000358184.2	37	CCDS1462.1																																																																																			T|0.778;C|0.222	0.222	strong		0.527	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910	
HHLA2	11148	hgsc.bcm.edu	37	3	108081277	108081277	+	Missense_Mutation	SNP	C	C	A	rs6779094	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:108081277C>A	ENST00000357759.5	+	7	1506	c.1092C>A	c.(1090-1092)agC>agA	p.S364R	HHLA2_ENST00000467761.1_Missense_Mutation_p.S364R|HHLA2_ENST00000491820.1_Missense_Mutation_p.S364R|HHLA2_ENST00000467562.1_Missense_Mutation_p.S300R|HHLA2_ENST00000489514.2_Missense_Mutation_p.S364R	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	364			S -> R (in dbSNP:rs6779094).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						TGATTTGGAGCGTAAAATGTT	0.413													A|||	546	0.109026	0.0809	0.1571	5008	,	,		17658	0.001		0.2336	False		,,,				2504	0.0961				p.S364R		Atlas-SNP	.											.	HHLA2	95	.	0			c.C1092A						PASS	.	A	ARG/SER	456,3216		30,396,1410	111.0	99.0	103.0		1092	-8.0	0.0	3	dbSNP_116	103	1906,6284		237,1432,2426	yes	missense	HHLA2	NM_007072.2	110	267,1828,3836	AA,AC,CC		23.2723,12.4183,19.9123	possibly-damaging	364/415	108081277	2362,9500	1836	4095	5931	SO:0001583	missense	11148	exon7			TTGGAGCGTAAAA	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1092C>A	3.37:g.108081277C>A	ENSP00000350402:p.Ser364Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	299|299	0.13690476190476192|0.13690476190476192	44|44	0.08943089430894309|0.08943089430894309	66|66	0.18232044198895028|0.18232044198895028	0|0	0.0|0.0	189|189	0.24934036939313983|0.24934036939313983	A|A	0.596|0.596	-0.830853|-0.830853	0.02713|0.02713	0.124183|0.124183	0.232723|0.232723	ENSG00000114455|ENSG00000114455	ENST00000482099|ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514	.|T;T;T;T;T	.|0.10382	.|5.08;2.88;5.05;5.05;5.05	3.98|3.98	-7.96|-7.96	0.01144|0.01144	.|.	.|8.316520	.|0.00166	.|N	.|0.000010	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.30851|0.30851	-0.9964|-0.9964	4|9	.|0.72032	.|D	.|0.01	-18.4602|-18.4602	5.9093|5.9093	0.19018|0.19018	0.1377:0.0963:0.5385:0.2274|0.1377:0.0963:0.5385:0.2274	rs6779094;rs17242385;rs52829163;rs59044069;rs6779094|rs6779094;rs17242385;rs52829163;rs59044069;rs6779094	.|300;364;364	.|B4DKN2;C9J7D0;Q9UM44	.|.;.;HHLA2_HUMAN	S|R	267|364;300;364;364;364	.|ENSP00000418284:S364R;ENSP00000418345:S300R;ENSP00000350402:S364R;ENSP00000419207:S364R;ENSP00000417856:S364R	.|ENSP00000350402:S364R	R|S	+|+	1|3	0|2	HHLA2|HHLA2	109563967|109563967	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.012000|0.012000	0.07955|0.07955	-2.044000|-2.044000	0.01411|0.01411	-3.721000|-3.721000	0.00115|0.00115	-1.066000|-1.066000	0.02275|0.02275	CGT|AGC	C|0.868;A|0.132	0.132	strong		0.413	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
GPR146	115330	hgsc.bcm.edu	37	7	1097183	1097183	+	Missense_Mutation	SNP	G	G	A	rs11761941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1097183G>A	ENST00000397095.1	+	2	255	c.32G>A	c.(31-33)gGg>gAg	p.G11E	C7orf50_ENST00000357429.6_Intron|GPR146_ENST00000297468.3_Missense_Mutation_p.G11E|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron|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	141	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	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	
FKTN	2218	hgsc.bcm.edu	37	9	108397495	108397495	+	Missense_Mutation	SNP	A	A	G	rs41313301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:108397495A>G	ENST00000223528.2	+	10	1460	c.1336A>G	c.(1336-1338)Aat>Gat	p.N446D	FKTN_ENST00000602661.1_Missense_Mutation_p.N446D|FKTN_ENST00000448551.2_Intron|FKTN_ENST00000540160.1_3'UTR|FKTN_ENST00000357998.5_Intron	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	446			N -> D (in dbSNP:rs41313301). {ECO:0000269|PubMed:14627679}.		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						TGTGCAACCCAATGGAATCTG	0.428													A|||	26	0.00519169	0.0015	0.0043	5008	,	,		20826	0.0		0.008	False		,,,				2504	0.0133				p.N446D		Atlas-SNP	.											.	FKTN	47	.	0			c.A1336G						PASS	.	A	ASP/ASN,,ASP/ASN	9,4397	15.5+/-35.6	0,9,2194	156.0	142.0	146.0		1336,,1336	6.0	1.0	9	dbSNP_127	146	107,8493	57.5+/-118.9	1,105,4194	yes	missense,intron,missense	FKTN	NM_001079802.1,NM_001198963.1,NM_006731.2	23,,23	1,114,6388	GG,GA,AA		1.2442,0.2043,0.8919	probably-damaging,,probably-damaging	446/462,,446/462	108397495	116,12890	2203	4300	6503	SO:0001583	missense	2218	exon10			CAACCCAATGGAA		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.1336A>G	9.37:g.108397495A>G	ENSP00000223528:p.Asn446Asp	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	195	98	0.502564	NM_006731	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Missense_Mutation	SNP	ENST00000223528.2	37	CCDS6766.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	A	31	5.088104	0.94100	0.002043	0.012442	ENSG00000106692	ENST00000223528	T	0.46451	0.87	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.60650	0.2285	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.69907	-0.5018	10	0.66056	D	0.02	-12.2047	15.7697	0.78157	1.0:0.0:0.0:0.0	rs41313301	446	O75072	FKTN_HUMAN	D	446	ENSP00000223528:N446D	ENSP00000223528:N446D	N	+	1	0	FKTN	107437316	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.901000	0.92560	2.317000	0.78254	0.460000	0.39030	AAT	A|0.992;G|0.008	0.008	strong		0.428	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731	
WIPF1	7456	hgsc.bcm.edu	37	2	175436496	175436496	+	Missense_Mutation	SNP	G	G	A	rs149434153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:175436496G>A	ENST00000392547.2	-	5	1136	c.1037C>T	c.(1036-1038)cCc>cTc	p.P346L	WIPF1_ENST00000409891.1_Missense_Mutation_p.P346L|AC018890.6_ENST00000412835.1_RNA|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409415.3_Missense_Mutation_p.P346L|WIPF1_ENST00000272746.5_Missense_Mutation_p.P346L|WIPF1_ENST00000359761.3_Missense_Mutation_p.P346L|WIPF1_ENST00000392546.2_Missense_Mutation_p.P346L|WIPF1_ENST00000467149.1_5'Flank	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	346	Pro-rich.				actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						AGGTAACGGGGGCGTGGACGA	0.652													G|||	2	0.000399361	0.0	0.0	5008	,	,		15243	0.0		0.002	False		,,,				2504	0.0				p.P346L		Atlas-SNP	.											.	WIPF1	88	.	0			c.C1037T						PASS	.	G	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	57.0	58.0	58.0		1037,1037	5.0	0.6	2	dbSNP_134	58	21,8579	15.3+/-51.7	0,21,4279	yes	missense,missense	WIPF1	NM_001077269.1,NM_003387.4	98,98	0,22,6481	AA,AG,GG		0.2442,0.0227,0.1692	benign,benign	346/504,346/504	175436496	22,12984	2203	4300	6503	SO:0001583	missense	7456	exon5			AACGGGGGCGTGG	AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"""Wiskott-Aldrich syndrome protein interacting protein"""	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1037C>T	2.37:g.175436496G>A	ENSP00000376330:p.Pro346Leu	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_003387	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	ENST00000392547.2	37	CCDS2260.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.07	2.127895	0.37533	2.27E-4	0.002442	ENSG00000115935	ENST00000392547;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891;ENST00000409415	T;T;T;T;T;T	0.55930	1.36;1.36;1.36;1.36;0.7;0.49	5.03	5.03	0.67393	.	0.262379	0.36591	N	0.002509	T	0.72763	0.3501	M	0.77103	2.36	0.80722	D	1	D;D;D;D	0.69078	0.997;0.997;0.997;0.995	D;D;D;P	0.65987	0.94;0.928;0.94;0.873	T	0.77172	-0.2685	10	0.72032	D	0.01	.	17.9584	0.89076	0.0:0.0:1.0:0.0	.	346;346;346;346	O43516-3;E9PB87;O43516-2;O43516	.;.;.;WIPF1_HUMAN	L	346	ENSP00000376330:P346L;ENSP00000272746:P346L;ENSP00000352802:P346L;ENSP00000376329:P346L;ENSP00000386431:P346L;ENSP00000387150:P346L	ENSP00000272746:P346L	P	-	2	0	WIPF1	175144742	1.000000	0.71417	0.569000	0.28460	0.030000	0.12068	4.451000	0.60047	2.345000	0.79718	0.536000	0.68110	CCC	G|0.999;A|0.001	0.001	strong		0.652	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387	
GPLD1	2822	hgsc.bcm.edu	37	6	24437458	24437458	+	Missense_Mutation	SNP	T	T	C	rs1042303	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:24437458T>C	ENST00000230036.1	-	21	2190	c.2080A>G	c.(2080-2082)Atg>Gtg	p.M694V		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	694			M -> V (in dbSNP:rs1042303). {ECO:0000269|PubMed:11072085}.		cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						AGTGCGTACATGCGAGTGGCT	0.577													T|||	1533	0.30611	0.2549	0.3386	5008	,	,		20191	0.253		0.4364	False		,,,				2504	0.273				p.M694V		Atlas-SNP	.											.	GPLD1	91	.	0			c.A2080G						PASS	.	T	VAL/MET	1259,3147	432.0+/-343.1	201,857,1145	137.0	109.0	119.0		2080	0.9	0.1	6	dbSNP_86	119	3979,4621	552.9+/-386.2	915,2149,1236	yes	missense	GPLD1	NM_001503.2	21	1116,3006,2381	CC,CT,TT		46.2674,28.5747,40.2737	benign	694/841	24437458	5238,7768	2203	4300	6503	SO:0001583	missense	2822	exon21			CGTACATGCGAGT	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.2080A>G	6.37:g.24437458T>C	ENSP00000230036:p.Met694Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	715	0.3273809523809524	137	0.2784552845528455	125	0.3453038674033149	130	0.22727272727272727	323	0.4261213720316623	T	3.704	-0.060886	0.07317	0.285747	0.462674	ENSG00000112293	ENST00000230036	T	0.65364	-0.15	4.69	0.898	0.19264	.	0.307417	0.33346	N	0.005014	T	0.18130	0.0435	L	0.28014	0.82	0.24258	P	0.99529279	B	0.02656	0.0	B	0.04013	0.001	T	0.09015	-1.0694	9	0.12103	T	0.63	-21.3146	4.8618	0.13588	0.0:0.2324:0.153:0.6146	rs1042303;rs3181758;rs17306368;rs60071487	694	P80108	PHLD_HUMAN	V	694	ENSP00000230036:M694V	ENSP00000230036:M694V	M	-	1	0	GPLD1	24545437	0.633000	0.27181	0.141000	0.22245	0.010000	0.07245	0.711000	0.25764	0.068000	0.16574	0.460000	0.39030	ATG	T|0.628;C|0.372	0.372	strong		0.577	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
SFRP2	6423	hgsc.bcm.edu	37	4	154709910	154709910	+	Silent	SNP	G	G	A	rs4076441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:154709910G>A	ENST00000274063.4	-	1	362	c.78C>T	c.(76-78)ttC>ttT	p.F26F		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	26					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)				GGCCAAAGAGGAAGAGCCCGC	0.672													G|||	178	0.0355431	0.1006	0.0331	5008	,	,		14258	0.0		0.0179	False		,,,				2504	0.0041				p.F26F		Atlas-SNP	.											.	SFRP2	45	.	0			c.C78T						PASS	.	G		428,3974		25,378,1798	21.0	25.0	24.0		78	2.5	1.0	4	dbSNP_108	24	80,8496		1,78,4209	no	coding-synonymous	SFRP2	NM_003013.2		26,456,6007	AA,AG,GG		0.9328,9.7229,3.9143		26/296	154709910	508,12470	2201	4288	6489	SO:0001819	synonymous_variant	6423	exon1			AAAGAGGAAGAGC	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.78C>T	4.37:g.154709910G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_003013	B3KQR2|O14778|Q9HAP5	Silent	SNP	ENST00000274063.4	37	CCDS34082.1																																																																																			G|0.966;A|0.034	0.034	strong		0.672	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1		
COL11A2	1302	hgsc.bcm.edu	37	6	33136310	33136310	+	Missense_Mutation	SNP	G	G	T	rs2229784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33136310G>T	ENST00000374708.4	-	52	3946	c.3688C>A	c.(3688-3690)Cca>Aca	p.P1230T	COL11A2_ENST00000374713.1_Missense_Mutation_p.P1269T|COL11A2_ENST00000341947.2_Missense_Mutation_p.P1316T|COL11A2_ENST00000395197.1_Missense_Mutation_p.P1256T|COL11A2_ENST00000357486.1_Missense_Mutation_p.P1295T|COL11A2_ENST00000374714.1_Missense_Mutation_p.P1290T|COL11A2_ENST00000361917.1_Missense_Mutation_p.P1209T|COL11A2_ENST00000374712.1_Missense_Mutation_p.P1235T|COL11A2_ENST00000477772.1_Intron	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1316	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TTTCCAAGTGGCCCTGGGGGT	0.632													G|||	288	0.057508	0.0908	0.0403	5008	,	,		15707	0.0883		0.0308	False		,,,				2504	0.0204				p.P1316T	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.C3946A						PASS	.	G	THR/PRO,THR/PRO,THR/PRO	194,2828		6,182,1323	55.0	50.0	52.0		3625,3946,3688	3.4	1.0	6	dbSNP_98	52	168,5250		2,164,2543	yes	missense,missense,missense	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	38,38,38	8,346,3866	TT,TG,GG		3.1008,6.4196,4.2891	probably-damaging,probably-damaging,probably-damaging	1209/1630,1316/1737,1230/1651	33136310	362,8078	1511	2709	4220	SO:0001583	missense	1302	exon54			CAAGTGGCCCTGG	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.3688C>A	6.37:g.33136310G>T	ENSP00000363840:p.Pro1230Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	37	CCDS43452.1	117	0.05357142857142857	35	0.07113821138211382	13	0.03591160220994475	52	0.09090909090909091	17	0.022427440633245383	G	15.27	2.785207	0.49997	0.064196	0.031008	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.96856	-3.2;-4.15;-4.15;-4.15;-4.15;-3.2;-4.15;-4.15	4.25	3.38	0.38709	.	0.066730	0.64402	N	0.000010	D	0.95781	0.8627	M	0.64404	1.975	0.58432	D	0.999998	D;D;D	0.58268	0.982;0.982;0.97	P;P;P	0.60236	0.871;0.871;0.746	D	0.95434	0.8519	10	0.72032	D	0.01	.	9.8222	0.40889	0.1015:0.0:0.8985:0.0	rs2229784;rs2272904;rs45631887;rs59414740;rs2229784	1209;1230;1316	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	T	1230;1316;1295;1290;1269;1256;1235;1209	ENSP00000363840:P1230T;ENSP00000339915:P1316T;ENSP00000350079:P1295T;ENSP00000363846:P1290T;ENSP00000363845:P1269T;ENSP00000378623:P1256T;ENSP00000363844:P1235T;ENSP00000355123:P1209T	ENSP00000339915:P1316T	P	-	1	0	COL11A2	33244288	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.325000	0.79124	1.008000	0.39264	0.551000	0.68910	CCA	G|0.947;T|0.053	0.053	strong		0.632	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
PLEKHG2	64857	hgsc.bcm.edu	37	19	39907036	39907036	+	Silent	SNP	C	C	T	rs2277743	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39907036C>T	ENST00000409794.3	+	5	1378	c.528C>T	c.(526-528)gcC>gcT	p.A176A	PLEKHG2_ENST00000378550.1_Silent_p.A176A|PLEKHG2_ENST00000425673.1_Silent_p.A176A|PLEKHG2_ENST00000458508.2_Silent_p.A117A|PLEKHG2_ENST00000409797.2_Silent_p.A176A	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	176	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGGGTATTGCCGAGTGCTTCG	0.657													C|||	883	0.176318	0.2163	0.1974	5008	,	,		13310	0.0387		0.1859	False		,,,				2504	0.2393				p.A176A		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C528T						PASS	.	C		977,3429	355.4+/-313.0	113,751,1339	62.0	71.0	68.0		528	-4.2	1.0	19	dbSNP_100	68	1533,7067	280.8+/-294.7	135,1263,2902	no	coding-synonymous	PLEKHG2	NM_022835.2		248,2014,4241	TT,TC,CC		17.8256,22.1743,19.2988		176/1387	39907036	2510,10496	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon5			TATTGCCGAGTGC	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.528C>T	19.37:g.39907036C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	22	0.366667	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	359	0.16437728937728938	114	0.23170731707317074	86	0.23756906077348067	14	0.024475524475524476	145	0.19129287598944592	C	10.86	1.469971	0.26423	0.221743	0.178256	ENSG00000090924	ENST00000205135	.	.	.	4.68	-4.25	0.03766	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999842	.	.	.	.	.	.	T	0.35226	-0.9797	3	.	.	.	.	2.0945	0.03665	0.1055:0.2325:0.2962:0.3659	rs2277743;rs17206567;rs60635542;rs2277743	.	.	.	L	73	.	.	P	+	2	0	PLEKHG2	44598876	0.000000	0.05858	0.959000	0.39883	0.945000	0.59286	-6.192000	0.00076	-0.551000	0.06175	0.491000	0.48974	CCG	C|0.826;T|0.174	0.174	strong		0.657	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
ST3GAL4	6484	hgsc.bcm.edu	37	11	126277216	126277216	+	Silent	SNP	C	C	T	rs2230278	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126277216C>T	ENST00000526727.1	+	4	626	c.252C>T	c.(250-252)taC>taT	p.Y84Y	ST3GAL4_ENST00000532243.1_Silent_p.Y83Y|ST3GAL4_ENST00000227495.6_Silent_p.Y80Y|ST3GAL4_ENST00000356132.4_Silent_p.Y90Y|ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000530591.1_Silent_p.Y80Y|ST3GAL4_ENST00000449406.2_Silent_p.Y73Y|ST3GAL4_ENST00000534457.1_Silent_p.Y79Y|ST3GAL4_ENST00000534083.1_Silent_p.Y84Y|ST3GAL4_ENST00000392669.2_Silent_p.Y84Y|ST3GAL4_ENST00000444328.2_Silent_p.Y84Y			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	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	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	
PIGM	93183	hgsc.bcm.edu	37	1	160000435	160000435	+	Missense_Mutation	SNP	A	A	T	rs12409352	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160000435A>T	ENST00000368090.2	-	1	1348	c.1095T>A	c.(1093-1095)ttT>ttA	p.F365L		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	365			F -> L (in dbSNP:rs12409352).		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)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CCTGCCCTATAAACCATAACA	0.438													A|||	341	0.0680911	0.0091	0.1182	5008	,	,		21320	0.0357		0.1292	False		,,,				2504	0.0828				p.F365L		Atlas-SNP	.											.	PIGM	27	.	0			c.T1095A						PASS	.	A	LEU/PHE	155,4251	106.0+/-144.5	5,145,2053	134.0	143.0	140.0		1095	-0.8	0.1	1	dbSNP_120	140	1528,7072	289.2+/-299.1	138,1252,2910	yes	missense	PIGM	NM_145167.2	22	143,1397,4963	TT,TA,AA		17.7674,3.5179,12.9402	possibly-damaging	365/424	160000435	1683,11323	2203	4300	6503	SO:0001583	missense	93183	exon1			CCCTATAAACCAT	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	18858	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 1"", ""DPM:GlcN-(acyl-)PI mannosyltransferase"", ""dol-P-Man dependent GPI mannosyltransferase"""	610273	"""phosphatidylinositol glycan, class M"""			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.1095T>A	1.37:g.160000435A>T	ENSP00000357069:p.Phe365Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_145167		Missense_Mutation	SNP	ENST00000368090.2	37	CCDS1192.1	184	0.08424908424908426	10	0.02032520325203252	44	0.12154696132596685	28	0.04895104895104895	102	0.1345646437994723	A	11.34	1.609087	0.28623	0.035179	0.177674	ENSG00000143315	ENST00000368090	T	0.38722	1.12	5.4	-0.827	0.10802	.	0.058196	0.64402	D	0.000001	T	0.11196	0.0273	N	0.25647	0.755	0.29209	P	0.87474	B	0.24618	0.107	B	0.27262	0.078	T	0.20505	-1.0273	8	.	.	.	-21.1888	10.5406	0.45031	0.3832:0.0:0.6168:0.0	rs12409352;rs12409352	365	Q9H3S5	PIGM_HUMAN	L	365	ENSP00000357069:F365L	.	F	-	3	2	PIGM	158267059	0.000000	0.05858	0.067000	0.19924	0.986000	0.74619	-0.710000	0.05024	-0.155000	0.11098	0.379000	0.24179	TTT	A|0.892;T|0.108	0.108	strong		0.438	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167	
FANCA	2175	hgsc.bcm.edu	37	16	89815152	89815152	+	Missense_Mutation	SNP	G	G	A	rs17233497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89815152G>A	ENST00000389301.3	-	33	3293	c.3263C>T	c.(3262-3264)tCt>tTt	p.S1088F	FANCA_ENST00000568369.1_Missense_Mutation_p.S1088F	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1088			S -> F (in FA; dbSNP:rs17233497). {ECO:0000269|PubMed:10094191, ECO:0000269|PubMed:18987736}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GCAGAGGACAGACGAAGGCAG	0.587			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	117	0.0233626	0.0038	0.0187	5008	,	,		21735	0.0218		0.0646	False		,,,				2504	0.0123				p.S1088F		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,lymph_node,lymphoid_neoplasm,0,1	FANCA	99	1	0			c.C3263T	GRCh37	CM992318	FANCA	M	rs17233497	PASS	.	G	PHE/SER	73,4323	62.9+/-100.1	0,73,2125	80.0	59.0	66.0		3263	3.7	0.0	16	dbSNP_123	66	697,7903	172.7+/-223.4	27,643,3630	yes	missense	FANCA	NM_000135.2	155	27,716,5755	AA,AG,GG		8.1047,1.6606,5.9249	possibly-damaging	1088/1456	89815152	770,12226	2198	4300	6498	SO:0001583	missense	2175	exon33	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGGACAGACGAAG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3263C>T	16.37:g.89815152G>A	ENSP00000373952:p.Ser1088Phe	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	73	0.033424908424908424	3	0.006097560975609756	9	0.024861878453038673	11	0.019230769230769232	50	0.06596306068601583	G	14.27	2.484066	0.44147	0.016606	0.081047	ENSG00000187741	ENST00000389301;ENST00000305699	D	0.85955	-2.05	4.63	3.68	0.42216	.	0.363675	0.24115	N	0.041417	T	0.32556	0.0833	M	0.72118	2.19	0.21020	N	0.999803	P;P;P	0.50272	0.906;0.933;0.933	P;B;B	0.49665	0.618;0.401;0.401	T	0.58589	-0.7610	10	0.66056	D	0.02	-6.0479	8.8363	0.35115	0.1022:0.0:0.8978:0.0	rs17233497;rs17233497	65;1088;1088	B7Z6Y4;B4DRI7;O15360	.;.;FANCA_HUMAN	F	1088;65	ENSP00000373952:S1088F	ENSP00000306281:S65F	S	-	2	0	FANCA	88342653	0.024000	0.19004	0.003000	0.11579	0.202000	0.24057	2.054000	0.41335	1.329000	0.45376	0.462000	0.41574	TCT	G|0.954;A|0.046	0.046	strong		0.587	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
OR52B6	340980	hgsc.bcm.edu	37	11	5602275	5602275	+	Missense_Mutation	SNP	A	A	G	rs1077126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	192	0	0		WXS	Illumina HiSeq	Phase_I	239	111	0.464435	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	
TULP3	7289	hgsc.bcm.edu	37	12	3047365	3047365	+	Missense_Mutation	SNP	G	G	C	rs34246393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:3047365G>C	ENST00000448120.2	+	10	1160	c.1109G>C	c.(1108-1110)aGt>aCt	p.S370T	TULP3_ENST00000397132.2_Missense_Mutation_p.S370T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	370					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			GTCTGGAACAGTGACACTCAG	0.507													g|||	2	0.000399361	0.0008	0.0	5008	,	,		19047	0.0		0.001	False		,,,				2504	0.0				p.S370T		Atlas-SNP	.											.	TULP3	45	.	0			c.G1109C						PASS	.		THR/SER,THR/SER	4,4402	8.1+/-20.4	0,4,2199	127.0	118.0	121.0		1109,1109	2.8	0.2	12	dbSNP_126	121	24,8576	17.3+/-56.4	0,24,4276	yes	missense,missense	TULP3	NM_001160408.1,NM_003324.4	58,58	0,28,6475	CC,CG,GG		0.2791,0.0908,0.2153	benign,benign	370/502,370/443	3047365	28,12978	2203	4300	6503	SO:0001583	missense	7289	exon10			GGAACAGTGACAC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1109G>C	12.37:g.3047365G>C	ENSP00000410051:p.Ser370Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	g|g	13.39|13.39	2.224334|2.224334	0.39300|0.39300	9.08E-4|9.08E-4	0.002791|0.002791	ENSG00000078246|ENSG00000078246	ENST00000541678;ENST00000538704|ENST00000228245;ENST00000544943;ENST00000542730;ENST00000448120;ENST00000397132	.|D;D;D	.|0.85088	.|-1.94;-1.94;-1.94	5.2|5.2	2.83|2.83	0.33086|0.33086	.|Tubby, C-terminal (4);	.|0.196879	.|0.52532	.|D	.|0.000064	T|T	0.72843|0.72843	0.3511|0.3511	N|N	0.19112|0.19112	0.55|0.55	0.22918|0.22918	N|N	0.998569|0.998569	.|B;B;P	.|0.44946	.|0.126;0.249;0.846	.|B;B;B	.|0.41135	.|0.247;0.348;0.333	T|T	0.65911|0.65911	-0.6053|-0.6053	5|10	.|0.87932	.|D	.|0	-2.0951|-2.0951	6.7817|6.7817	0.23650|0.23650	0.766:0.1528:0.0812:0.0|0.766:0.1528:0.0812:0.0	rs34246393|rs34246393	.|194;370;370	.|B7Z1E7;O75386;F8WBZ9	.|.;TULP3_HUMAN;.	H|T	46;35|370;97;194;370;370	.|ENSP00000442631:S97T;ENSP00000410051:S370T;ENSP00000380321:S370T	.|ENSP00000228245:S370T	Q|S	+|+	3|2	2|0	TULP3|TULP3	2917626|2917626	1.000000|1.000000	0.71417|0.71417	0.175000|0.175000	0.22980|0.22980	0.619000|0.619000	0.37552|0.37552	7.521000|7.521000	0.81832|0.81832	0.302000|0.302000	0.22762|0.22762	-1.075000|-1.075000	0.02238|0.02238	CAG|AGT	G|0.998;C|0.002	0.002	strong		0.507	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
PSMD13	5719	hgsc.bcm.edu	37	11	244171	244171	+	Silent	SNP	T	T	C	rs1128321	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244171T>C	ENST00000532097.1	+	4	724	c.220T>C	c.(220-222)Ttg>Ctg	p.L74L	PSMD13_ENST00000431206.2_Silent_p.L76L|PSMD13_ENST00000352303.5_Silent_p.L74L	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	74					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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		GGTGAACCCTTTGTCCCTCGT	0.418													T|||	4082	0.815096	0.8918	0.83	5008	,	,		16592	0.8026		0.7306	False		,,,				2504	0.8006				p.L76L		Atlas-SNP	.											.	PSMD13	53	.	0			c.T226C						PASS	.	T	,	3846,560	758.4+/-412.8	1713,420,70	56.0	61.0	59.0		220,226	-5.0	1.0	11	dbSNP_86	59	6307,2293	693.8+/-404.7	2372,1563,365	no	coding-synonymous,coding-synonymous	PSMD13	NM_002817.3,NM_175932.2	,	4085,1983,435	CC,CT,TT		26.6628,12.7099,21.936	,	74/377,76/379	244171	10153,2853	2203	4300	6503	SO:0001819	synonymous_variant	5719	exon2			AACCCTTTGTCCC	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.220T>C	11.37:g.244171T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Silent	SNP	ENST00000532097.1	37	CCDS7692.1																																																																																			T|0.201;C|0.799	0.799	strong		0.418	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
MUC2	4583	hgsc.bcm.edu	37	11	1090343	1090343	+	Silent	SNP	T	T	C	rs12221966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1090343T>C	ENST00000441003.2	+	27	3666	c.3639T>C	c.(3637-3639)tgT>tgC	p.C1213C	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1213					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCAGCGTGTGTACCAACTCCT	0.647													C|||	422	0.0842652	0.0537	0.0893	5008	,	,		17608	0.0685		0.1163	False		,,,				2504	0.1053				p.C1213C		Atlas-SNP	.											.	MUC2	614	.	0			c.T3639C						PASS	.			298,4082		12,274,1904	64.0	73.0	70.0		3639	0.3	0.0	11	dbSNP_120	70	945,7609		47,851,3379	no	coding-synonymous	MUC2	NM_002457.2		59,1125,5283	CC,CT,TT		11.0475,6.8037,9.6103		1213/2813	1090343	1243,11691	2190	4277	6467	SO:0001819	synonymous_variant	4583	exon27			CGTGTGTACCAAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3639T>C	11.37:g.1090343T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	128	45	0.351562	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.916;C|0.084	0.084	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
MUC17	140453	hgsc.bcm.edu	37	7	100681359	100681359	+	Missense_Mutation	SNP	C	C	G	rs11979706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100681359C>G	ENST00000306151.4	+	3	6726	c.6662C>G	c.(6661-6663)cCa>cGa	p.P2221R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2221	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)					GGAAGCACTCCATTCACAAGT	0.507													C|||	3362	0.671326	0.6293	0.4553	5008	,	,		26662	0.8393		0.6163	False		,,,				2504	0.7648				p.P2221R		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	1	0			c.C6662G						scavenged	.						351.0	345.0	347.0					7																	100681359		2203	4300	6503	SO:0001583	missense	140453	exon3			GCACTCCATTCAC	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.6662C>G	7.37:g.100681359C>G	ENSP00000302716:p.Pro2221Arg	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	1428	0.6538461538461539	307	0.6239837398373984	182	0.5027624309392266	468	0.8181818181818182	471	0.6213720316622692	C	3.549	-0.092113	0.07053	.	.	ENSG00000169876	ENST00000306151	T	0.03272	3.99	1.11	1.11	0.20524	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D	0.59357	0.985	P	0.46885	0.53	T	0.02075	-1.1218	8	0.23891	T	0.37	.	7.7662	0.28980	0.0:1.0:0.0:0.0	rs60369600	2221	Q685J3	MUC17_HUMAN	R	2221	ENSP00000302716:P2221R	ENSP00000302716:P2221R	P	+	2	0	MUC17	100468079	0.000000	0.05858	0.024000	0.17045	0.024000	0.10985	-0.228000	0.09114	0.551000	0.29008	0.134000	0.15878	CCA	C|0.379;G|0.621	0.621	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
NNT	23530	hgsc.bcm.edu	37	5	43609343	43609343	+	Silent	SNP	C	C	T	rs10057103	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:43609343C>T	ENST00000264663.5	+	2	267	c.46C>T	c.(46-48)Cta>Tta	p.L16L	NNT_ENST00000512996.2_Intron|NNT_ENST00000344920.4_Silent_p.L16L	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	16					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)	p.L16L(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					CTCGTGTCCTCTACTTAGCAA	0.428													T|||	2797	0.558506	0.9433	0.451	5008	,	,		17105	0.2014		0.5885	False		,,,				2504	0.4519				p.L16L		Atlas-SNP	.											NNT,NS,carcinoma,0,1	NNT	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C46T						PASS	.	T	,	3869,537	243.4+/-253.1	1705,459,39	134.0	138.0	137.0		46,46	3.2	0.8	5	dbSNP_119	137	4907,3693	527.8+/-381.2	1383,2141,776	no	coding-synonymous,coding-synonymous	NNT	NM_012343.3,NM_182977.2	,	3088,2600,815	TT,TC,CC		42.9419,12.1879,32.5235	,	16/1087,16/1087	43609343	8776,4230	2203	4300	6503	SO:0001819	synonymous_variant	23530	exon2			TGTCCTCTACTTA	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.46C>T	5.37:g.43609343C>T		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	151	149	0.986755	NM_182977	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	37	CCDS3949.1																																																																																			C|0.373;T|0.627	0.627	strong		0.428	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
MYT1L	23040	hgsc.bcm.edu	37	2	1926488	1926488	+	Silent	SNP	C	C	T	rs13399855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:1926488C>T	ENST00000399161.2	-	10	1800	c.1053G>A	c.(1051-1053)ccG>ccA	p.P351P	MYT1L_ENST00000428368.2_Silent_p.P351P	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	351					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TGTTCTGCTGCGGATTCCTCT	0.577													C|||	125	0.0249601	0.025	0.0101	5008	,	,		20452	0.001		0.0755	False		,,,				2504	0.0082				p.P351P		Atlas-SNP	.											MYT1L,NS,carcinoma,-1,1	MYT1L	241	1	0			c.G1053A						PASS	.	C		116,4122		3,110,2006	47.0	52.0	50.0		1053	-2.6	0.0	2	dbSNP_121	50	466,8008		17,432,3788	no	coding-synonymous	MYT1L	NM_015025.2		20,542,5794	TT,TC,CC		5.4992,2.7371,4.5784		351/1185	1926488	582,12130	2119	4237	6356	SO:0001819	synonymous_variant	23040	exon10			CTGCTGCGGATTC	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.1053G>A	2.37:g.1926488C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	199	104	0.522613	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				C|0.961;T|0.039	0.039	strong		0.577	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
ATG9A	79065	hgsc.bcm.edu	37	2	220088468	220088468	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220088468A>G	ENST00000409618.1	-	10	1877	c.1438T>C	c.(1438-1440)Ttg>Ctg	p.L480L	AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000409422.1_Silent_p.L419L|ATG9A_ENST00000396761.2_Silent_p.L480L|ATG9A_ENST00000361242.4_Silent_p.L480L			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	480					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGGCTCAGCAACTCTTCCAAA	0.577																																					p.L480L		Atlas-SNP	.											.	ATG9A	50	.	0			c.T1438C						PASS	.						57.0	66.0	63.0					2																	220088468		2035	4206	6241	SO:0001819	synonymous_variant	79065	exon10			TCAGCAACTCTTC	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1438T>C	2.37:g.220088468A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Silent	SNP	ENST00000409618.1	37	CCDS42820.1																																																																																			.	.	none		0.577	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085	
CACNA1E	777	hgsc.bcm.edu	37	1	181548341	181548341	+	Silent	SNP	A	A	G	rs17443123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:181548341A>G	ENST00000367573.2	+	5	750	c.750A>G	c.(748-750)gcA>gcG	p.A250A	CACNA1E_ENST00000360108.3_Silent_p.A250A|CACNA1E_ENST00000367570.1_Silent_p.A250A|CACNA1E_ENST00000526775.1_Silent_p.A250A|CACNA1E_ENST00000358338.5_Silent_p.A201A|CACNA1E_ENST00000357570.5_Silent_p.A201A|CACNA1E_ENST00000367567.4_5'UTR	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	250					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TACATCGAGCATGCTTCATGA	0.468													A|||	321	0.0640974	0.0204	0.0937	5008	,	,		22040	0.0079		0.1491	False		,,,				2504	0.0726				p.A250A		Atlas-SNP	.											CACNA1E,NS,carcinoma,+2,1	CACNA1E	778	1	0			c.A750G						PASS	.	A	,,	148,3768		4,140,1814	332.0	306.0	315.0		750,750,750	-6.0	1.0	1	dbSNP_123	315	1191,7147		75,1041,3053	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	,,	79,1181,4867	GG,GA,AA		14.284,3.7794,10.927	,,	250/2271,250/2314,250/2252	181548341	1339,10915	1958	4169	6127	SO:0001819	synonymous_variant	777	exon5			TCGAGCATGCTTC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.750A>G	1.37:g.181548341A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	174	92	0.528736	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			A|0.910;G|0.090	0.090	strong		0.468	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
NWD1	284434	hgsc.bcm.edu	37	19	16899865	16899865	+	Missense_Mutation	SNP	A	A	G	rs2608738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:16899865A>G	ENST00000552788.1	+	11	2804	c.2804A>G	c.(2803-2805)cAc>cGc	p.H935R	NWD1_ENST00000549814.1_Missense_Mutation_p.H935R|NWD1_ENST00000524140.2_Missense_Mutation_p.H935R|NWD1_ENST00000339803.6_Missense_Mutation_p.H800R|NWD1_ENST00000523826.1_Missense_Mutation_p.H729R|NWD1_ENST00000379808.3_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	102	0	0		WXS	Illumina HiSeq	Phase_I	117	43	0.367521	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	
TPSD1	23430	hgsc.bcm.edu	37	16	1307050	1307050	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1307050C>T	ENST00000211076.3	+	3	655	c.507C>T	c.(505-507)gaC>gaT	p.D169D	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.D162D	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	169	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)				GCTGGGGCGACGTGGACAATA	0.677																																					p.D169D		Atlas-SNP	.											.	TPSD1	47	.	0			c.C507T						PASS	.						24.0	24.0	24.0					16																	1307050		2198	4297	6495	SO:0001819	synonymous_variant	23430	exon3			GGGCGACGTGGAC	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.507C>T	16.37:g.1307050C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	202	39	0.193069	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			.	.	none		0.677	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
TMTC4	84899	hgsc.bcm.edu	37	13	101315269	101315269	+	Silent	SNP	C	C	T	rs201804960	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:101315269C>T	ENST00000376234.3	-	4	633	c.444G>A	c.(442-444)gcG>gcA	p.A148A	TMTC4_ENST00000342624.5_Silent_p.A167A|TMTC4_ENST00000328767.5_Intron	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	148						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCAGCAGGGACGCCCTGGGGG	0.602													T|||	19	0.00379393	0.0	0.0043	5008	,	,		17444	0.0		0.006	False		,,,				2504	0.0102				p.A167A		Atlas-SNP	.											TMTC4,bladder,carcinoma,-1,5	TMTC4	103	5	0			c.G501A						PASS	.	C	,	3,4297		0,3,2147	55.0	64.0	61.0		444,501	-10.9	0.0	13		61	31,8503		0,31,4236	no	coding-synonymous,coding-synonymous	TMTC4	NM_001079669.1,NM_032813.2	,	0,34,6383	TT,TC,CC		0.3633,0.0698,0.2649	,	148/742,167/761	101315269	34,12800	2150	4267	6417	SO:0001819	synonymous_variant	84899	exon5			CAGGGACGCCCTG		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.444G>A	13.37:g.101315269C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			C|0.996;T|0.004	0.004	strong		0.602	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
MOCS1	4337	hgsc.bcm.edu	37	6	39881102	39881102	+	Missense_Mutation	SNP	A	A	T	rs7762875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:39881102A>T	ENST00000340692.5	-	6	719	c.716T>A	c.(715-717)cTc>cAc	p.L239H	MOCS1_ENST00000308559.7_Missense_Mutation_p.L239H|MOCS1_ENST00000373175.4_Missense_Mutation_p.L210H|MOCS1_ENST00000373186.4_Missense_Mutation_p.L239H|MOCS1_ENST00000373195.3_Missense_Mutation_p.L152H|MOCS1_ENST00000373188.2_Missense_Mutation_p.L239H|MOCS1_ENST00000425303.2_Missense_Mutation_p.L239H|MOCS1_ENST00000432280.2_Missense_Mutation_p.L210H			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	239	Molybdenum cofactor biosynthesis protein A.			L -> H (in Ref. 2; AAB87523). {ECO:0000305}.	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)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					ATCCAGGGGGAGGCCCTCAGT	0.582													A|||	127	0.0253594	0.0038	0.0317	5008	,	,		19663	0.0		0.0885	False		,,,				2504	0.0112				p.L239H	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.T716A						PASS	.	A	HIS/LEU,HIS/LEU	69,4337	63.5+/-100.7	1,67,2135	105.0	92.0	97.0		716,716	4.7	1.0	6	dbSNP_116	97	846,7754	194.4+/-239.8	33,780,3487	yes	missense,missense	MOCS1	NM_001075098.3,NM_005943.5	99,99	34,847,5622	TT,TA,AA		9.8372,1.566,7.0352	possibly-damaging,possibly-damaging	239/386,239/386	39881102	915,12091	2203	4300	6503	SO:0001583	missense	4337	exon5			AGGGGGAGGCCCT	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.716T>A	6.37:g.39881102A>T	ENSP00000344794:p.Leu239His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	37		80	0.03663003663003663	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	68	0.08970976253298153	A	12.73	2.024995	0.35701	0.01566	0.098372	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	4.68	4.68	0.58851	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);	0.143616	0.47455	D	0.000232	T	0.14098	0.0341	N	0.05592	-0.015	0.36950	D	0.892828	B;P;B;B;P	0.47034	0.442;0.889;0.315;0.442;0.811	B;P;B;B;P	0.47376	0.092;0.545;0.042;0.092;0.545	T	0.03840	-1.0999	9	.	.	.	-20.4487	8.3884	0.32514	0.6999:0.0:0.0:0.3001	rs7762875	239;239;239;239;239	Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;.;MOCS1_HUMAN;.;.	H	239;239;210;239;152;239;239;210	ENSP00000362282:L239H;ENSP00000309843:L239H;ENSP00000362270:L210H;ENSP00000362284:L239H;ENSP00000362291:L152H;ENSP00000344794:L239H;ENSP00000416478:L239H;ENSP00000410809:L210H	.	L	-	2	0	MOCS1	39989080	1.000000	0.71417	0.977000	0.42913	0.097000	0.18754	4.363000	0.59473	1.760000	0.52011	0.533000	0.62120	CTC	A|0.942;T|0.058	0.058	strong		0.582	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943	
MUC16	94025	hgsc.bcm.edu	37	19	9001833	9001833	+	Missense_Mutation	SNP	A	A	G	rs386806621|rs12976122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9001833A>G	ENST00000397910.4	-	53	40618	c.40415T>C	c.(40414-40416)aTg>aCg	p.M13472T	MUC16_ENST00000380951.5_Missense_Mutation_p.M113T	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13474					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						GTACTCACTCATGGGTCCAGA	0.443													-|||	2996	0.598243	0.3812	0.7219	5008	,	,		22164	0.6062		0.7177	False		,,,				2504	0.6728				p.M13472T		Atlas-SNP	.											.	MUC16	4315	.	0			c.T40415C						PASS	.		THR/MET	1875,2115		453,969,573	83.0	80.0	81.0		40415	-0.1	0.0	19	dbSNP_121	81	6109,2221		2299,1511,355	yes	missense	MUC16	NM_024690.2	81	2752,2480,928	GG,GA,AA		26.6627,46.9925,35.1948	benign	13472/14508	9001833	7984,4336	1995	4165	6160	SO:0001583	missense	94025	exon53			TCACTCATGGGTC	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.40415T>C	19.37:g.9001833A>G	ENSP00000381008:p.Met13472Thr	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	1378|1378	0.6309523809523809|0.6309523809523809	210|210	0.4268292682926829|0.4268292682926829	258|258	0.712707182320442|0.712707182320442	382|382	0.6678321678321678|0.6678321678321678	528|528	0.6965699208443272|0.6965699208443272	.|.	0.021|0.021	-1.423077|-1.423077	0.01126|0.01126	0.469925|0.469925	0.733373|0.733373	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.31769|.	1.48;2.05|.	1.04|1.04	-0.0904|-0.0904	0.13665|0.13665	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	.|.	.|.	.|.	B|.	0.22851|.	0.076|.	B|.	0.26202|.	0.067|.	T|.	0.30851|.	-0.9964|.	7|.	0.02654|.	T|.	1|.	.|.	3.9375|3.9375	0.09311|0.09311	0.5095:0.0:0.4905:0.0|0.5095:0.0:0.4905:0.0	rs12976122|rs12976122	13472|.	B5ME49|.	.|.	T|R	13472;113|312	ENSP00000381008:M13472T;ENSP00000370338:M113T|.	ENSP00000370338:M113T|.	M|X	-|-	2|1	0|0	MUC16|MUC16	8862833|8862833	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.056000|0.056000	0.15407|0.15407	-0.127000|-0.127000	0.10547|0.10547	-0.397000|-0.397000	0.07691|0.07691	-0.830000|-0.830000	0.03078|0.03078	ATG|TGA	A|0.353;G|0.647	0.647	strong		0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ANPEP	290	hgsc.bcm.edu	37	15	90335534	90335534	+	Silent	SNP	G	G	A	rs25652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90335534G>A	ENST00000300060.6	-	18	2698	c.2385C>T	c.(2383-2385)acC>acT	p.T795T		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	795	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	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)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	TGCAGTAGACGGTGGACCGCA	0.642													G|||	1263	0.252196	0.27	0.2075	5008	,	,		17265	0.1766		0.2584	False		,,,				2504	0.3313				p.T795T	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C2385T						PASS	.	G		1120,3280	402.2+/-332.3	147,826,1227	121.0	126.0	124.0		2385	-5.8	0.3	15	dbSNP_72	124	2288,6310	385.2+/-341.4	271,1746,2282	no	coding-synonymous	ANPEP	NM_001150.2		418,2572,3509	AA,AG,GG		26.6108,25.4545,26.2194		795/968	90335534	3408,9590	2200	4299	6499	SO:0001819	synonymous_variant	290	exon18			GTAGACGGTGGAC	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2385C>T	15.37:g.90335534G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	211	91	0.43128	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																			T|0.000;G|0.749;A|0.251	0.251	strong		0.642	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
THNSL1	79896	hgsc.bcm.edu	37	10	25313254	25313254	+	Missense_Mutation	SNP	C	C	A	rs41279892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:25313254C>A	ENST00000524413.1	+	3	1449	c.1102C>A	c.(1102-1104)Cca>Aca	p.P368T	THNSL1_ENST00000376356.4_Missense_Mutation_p.P368T			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	368						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)	CTGTATCCCACCAAGTTGCAA	0.383													C|||	51	0.0101837	0.0023	0.0187	5008	,	,		19468	0.0		0.0258	False		,,,				2504	0.0092				p.P368T		Atlas-SNP	.											.	THNSL1	70	.	0			c.C1102A						PASS	.	C	THR/PRO	19,4387	25.3+/-52.1	0,19,2184	93.0	91.0	92.0		1102	3.9	0.3	10	dbSNP_127	92	198,8402	86.9+/-149.2	0,198,4102	yes	missense	THNSL1	NM_024838.4	38	0,217,6286	AA,AC,CC		2.3023,0.4312,1.6685	benign	368/744	25313254	217,12789	2203	4300	6503	SO:0001583	missense	79896	exon3			ATCCCACCAAGTT	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.1102C>A	10.37:g.25313254C>A	ENSP00000434887:p.Pro368Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	96	42	0.4375	NM_024838	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	18	0.023746701846965697	C	2.420	-0.333296	0.05278	0.004312	0.023023	ENSG00000185875	ENST00000524413;ENST00000376356	T;T	0.10860	2.83;2.83	5.71	3.88	0.44766	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.324845	0.30269	N	0.010010	T	0.02304	0.0071	N	0.25789	0.76	0.09310	N	1	B	0.19445	0.036	B	0.21546	0.035	T	0.29366	-1.0014	10	0.72032	D	0.01	-24.6105	6.0648	0.19858	0.2421:0.6037:0.0:0.1541	rs41279892	368	Q8IYQ7	THNS1_HUMAN	T	368	ENSP00000434887:P368T;ENSP00000365534:P368T	ENSP00000365534:P368T	P	+	1	0	THNSL1	25353260	0.056000	0.20664	0.287000	0.24848	0.804000	0.45430	3.083000	0.50136	0.783000	0.33636	-0.143000	0.13931	CCA	C|0.984;A|0.016	0.016	strong		0.383	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
TMCO6	55374	hgsc.bcm.edu	37	5	140023238	140023238	+	Missense_Mutation	SNP	C	C	G	rs17208187	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140023238C>G	ENST00000394671.3	+	8	997	c.896C>G	c.(895-897)aCc>aGc	p.T299S	NDUFA2_ENST00000510680.1_Intron|TMCO6_ENST00000252100.6_Missense_Mutation_p.T305S|TMCO6_ENST00000537378.1_Missense_Mutation_p.T59S	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	299			T -> S (in dbSNP:rs17208187). {ECO:0000269|PubMed:15489334}.		protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCAGAAAACCGAGGATGCA	0.527													C|||	1037	0.207069	0.0605	0.2176	5008	,	,		19225	0.3016		0.2545	False		,,,				2504	0.2515				p.T299S		Atlas-SNP	.											.	TMCO6	30	.	0			c.C896G						PASS	.	C	SER/THR	320,3632		13,294,1669	140.0	142.0	142.0		896	2.4	0.3	5	dbSNP_123	142	2002,6328		248,1506,2411	yes	missense	TMCO6	NM_018502.3	58	261,1800,4080	GG,GC,CC		24.0336,8.0972,18.9057	benign	299/494	140023238	2322,9960	1976	4165	6141	SO:0001583	missense	55374	exon8			AGAAAACCGAGGA	BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	ENST00000394671.3:c.896C>G	5.37:g.140023238C>G	ENSP00000378166:p.Thr299Ser	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	168	87	0.517857	NM_018502	Q9BUU0|Q9P198	Missense_Mutation	SNP	ENST00000394671.3	37	CCDS4233.2	495	0.22664835164835165	34	0.06910569105691057	90	0.24861878453038674	166	0.2902097902097902	205	0.2704485488126649	C	0.007	-1.937287	0.00484	0.080972	0.240336	ENSG00000113119	ENST00000394671;ENST00000537378;ENST00000252100	T;T;T	0.41065	2.32;1.01;2.3	5.12	2.37	0.29283	Armadillo-like helical (1);Armadillo-type fold (1);	0.592775	0.17865	N	0.159399	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.39292	-0.9621	9	0.27785	T	0.31	-0.4379	6.1096	0.20094	0.0:0.6376:0.1383:0.2241	rs17208187;rs17849552;rs56597340;rs58706596;rs17208187	305;299	Q96DC7-2;Q96DC7	.;TMCO6_HUMAN	S	299;59;305	ENSP00000378166:T299S;ENSP00000444474:T59S;ENSP00000252100:T305S	ENSP00000252100:T305S	T	+	2	0	TMCO6	140003422	0.080000	0.21391	0.341000	0.25589	0.183000	0.23260	0.397000	0.20883	0.328000	0.23435	0.561000	0.74099	ACC	C|0.780;G|0.220	0.220	strong		0.527	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502	
NPEPL1	79716	hgsc.bcm.edu	37	20	57289017	57289017	+	Silent	SNP	C	C	T	rs35104993	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:57289017C>T	ENST00000356091.6	+	10	1458	c.1170C>T	c.(1168-1170)agC>agT	p.S390S	NPEPL1_ENST00000525967.1_Silent_p.S362S|NPEPL1_ENST00000525817.1_Silent_p.S342S|STX16-NPEPL1_ENST00000530122.1_3'UTR|RP11-261P9.4_ENST00000530479.1_RNA	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	390						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TCACCAACAGCGCTGAGTGGG	0.667													C|||	393	0.0784744	0.0847	0.0749	5008	,	,		15687	0.006		0.0924	False		,,,				2504	0.1329				p.S390S		Atlas-SNP	.											NPEPL1,rectum,carcinoma,0,1	NPEPL1	36	1	0			c.C1170T						PASS	.	C	,,	279,3447		5,269,1589	13.0	20.0	18.0		1086,1026,1170	-2.9	1.0	20	dbSNP_126	18	656,6926		26,604,3161	no	coding-synonymous,coding-synonymous,coding-synonymous	NPEPL1	NM_001204872.1,NM_001204873.1,NM_024663.3	,,	31,873,4750	TT,TC,CC		8.6521,7.4879,8.2685	,,	362/496,342/476,390/524	57289017	935,10373	1863	3791	5654	SO:0001819	synonymous_variant	79716	exon10			CAACAGCGCTGAG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.1170C>T	20.37:g.57289017C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																			C|0.938;T|0.062	0.062	strong		0.667	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
OR4C16	219428	hgsc.bcm.edu	37	11	55339676	55339676	+	Missense_Mutation	SNP	G	G	T	rs12800642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:55339676G>T	ENST00000314634.3	+	1	73	c.73G>T	c.(73-75)Gtg>Ttg	p.V25L		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	25			V -> L (in dbSNP:rs12800642).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				GAAGAAAATAGTGTTTGTTAT	0.393													g|||	869	0.173522	0.1188	0.2378	5008	,	,		18312	0.1528		0.2117	False		,,,				2504	0.184				p.V25L		Atlas-SNP	.											.	OR4C16	104	.	0			c.G73T						PASS	.	G	LEU/VAL	593,3809	260.7+/-263.8	40,513,1648	163.0	152.0	155.0		73	-2.1	0.0	11	dbSNP_121	155	1890,6702	337.3+/-322.2	226,1438,2632	yes	missense	OR4C16	NM_001004701.2	32	266,1951,4280	TT,TG,GG		21.9972,13.4711,19.1088	benign	25/311	55339676	2483,10511	2201	4296	6497	SO:0001583	missense	219428	exon1			AAAATAGTGTTTG	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.73G>T	11.37:g.55339676G>T	ENSP00000324913:p.Val25Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	143	80	0.559441	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	380	0.17399267399267399	36	0.07317073170731707	84	0.23204419889502761	94	0.16433566433566432	166	0.21899736147757257	G	9.773	1.173101	0.21704	0.134711	0.219972	ENSG00000181935	ENST00000314634	T	0.00682	5.86	4.98	-2.08	0.07254	.	0.595988	0.15457	N	0.261315	T	0.00012	0.0000	N	0.02192	-0.645	0.80722	P	0.0	B	0.14012	0.009	B	0.16722	0.016	T	0.34229	-0.9837	9	0.02654	T	1	.	1.1987	0.01880	0.2607:0.2863:0.3151:0.1378	rs12800642;rs52798686;rs58232726;rs12800642	25	Q8NGL9	OR4CG_HUMAN	L	25	ENSP00000324913:V25L	ENSP00000324913:V25L	V	+	1	0	OR4C16	55096252	0.000000	0.05858	0.000000	0.03702	0.680000	0.39746	-1.171000	0.03115	-0.203000	0.10251	0.549000	0.68633	GTG	G|0.817;T|0.183	0.183	strong		0.393	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
ERAP1	51752	hgsc.bcm.edu	37	5	96116808	96116808	+	Silent	SNP	G	G	A	rs17481856	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:96116808G>A	ENST00000443439.2	-	17	2608	c.2542C>T	c.(2542-2544)Ctg>Ttg	p.L848L	ERAP1_ENST00000514604.1_5'Flank|ERAP1_ENST00000296754.3_Silent_p.L848L	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	848					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TGCCAGGCCAGTGGGTATCCT	0.398													A|||	299	0.0597045	0.0053	0.1138	5008	,	,		17033	0.0		0.1382	False		,,,				2504	0.0757				p.L848L		Atlas-SNP	.											.	ERAP1	59	.	0			c.C2542T						PASS	.	A	,,	103,4303	816.5+/-416.3	0,103,2100	99.0	105.0	103.0		2542,2542,2542	-5.5	0.0	5	dbSNP_123	103	1169,7431	764.7+/-407.6	63,1043,3194	no	coding-synonymous,coding-synonymous,coding-synonymous	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	,,	63,1146,5294	AA,AG,GG		13.593,2.3377,9.7801	,,	848/942,848/942,848/949	96116808	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	51752	exon17			AGGCCAGTGGGTA	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2542C>T	5.37:g.96116808G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			G|0.917;A|0.083	0.083	strong		0.398	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
BIRC6	57448	hgsc.bcm.edu	37	2	32690189	32690189	+	Silent	SNP	A	A	G	rs35682129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:32690189A>G	ENST00000421745.2	+	26	5447	c.5313A>G	c.(5311-5313)caA>caG	p.Q1771Q		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1771					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATTTTCTTCAACCTCCGCCTC	0.343													A|||	340	0.0678914	0.0076	0.0879	5008	,	,		13221	0.1498		0.0765	False		,,,				2504	0.0419				p.Q1771Q	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,caecum,carcinoma,0,11	BIRC6	838	11	0			c.A5313G						scavenged	.	A		88,4318	70.9+/-108.8	0,88,2115	57.0	57.0	57.0		5313	-7.2	0.7	2	dbSNP_126	57	664,7934	162.3+/-215.1	22,620,3657	no	coding-synonymous	BIRC6	NM_016252.3		22,708,5772	GG,GA,AA		7.7227,1.9973,5.7828		1771/4858	32690189	752,12252	2203	4299	6502	SO:0001819	synonymous_variant	57448	exon26			TCTTCAACCTCCG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5313A>G	2.37:g.32690189A>G		Somatic	209	2	0.00956938		WXS	Illumina HiSeq	Phase_I	260	127	0.488462	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			A|0.932;G|0.068	0.068	strong		0.343	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
ERP27	121506	hgsc.bcm.edu	37	12	15068620	15068620	+	Splice_Site	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:15068620T>A	ENST00000266397.2	-	6	1150	c.577A>T	c.(577-579)Att>Ttt	p.I193F	ERP27_ENST00000544881.1_5'UTR|ERP27_ENST00000540097.1_Splice_Site_p.I92F	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	193						endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						ATAAAGAGAATCTGCAGTTGG	0.388																																					p.I193F		Atlas-SNP	.											.	ERP27	37	.	0			c.A577T						PASS	.						52.0	52.0	52.0					12																	15068620		2203	4300	6503	SO:0001630	splice_region_variant	121506	exon6			AGAGAATCTGCAG	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.577-1A>T	12.37:g.15068620T>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_152321		Missense_Mutation	SNP	ENST00000266397.2	37	CCDS8670.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.679429	0.29783	.	.	ENSG00000139055	ENST00000266397;ENST00000540097	T;T	0.33654	1.4;1.4	4.79	1.17	0.20885	Thioredoxin-like fold (1);	0.393229	0.28109	N	0.016563	T	0.26268	0.0641	L	0.46741	1.465	0.42936	D	0.99433	B	0.22983	0.078	B	0.18871	0.023	T	0.05402	-1.0887	10	0.41790	T	0.15	-22.2204	6.2103	0.20626	0.0:0.3251:0.0:0.6749	.	193	Q96DN0	ERP27_HUMAN	F	193;92	ENSP00000266397:I193F;ENSP00000440573:I92F	ENSP00000266397:I193F	I	-	1	0	ERP27	14959887	0.999000	0.42202	0.998000	0.56505	0.833000	0.47200	0.155000	0.16362	0.200000	0.20447	-0.290000	0.09829	ATT	.	.	none		0.388	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	Missense_Mutation
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104280	26104280	+	Silent	SNP	T	T	C	rs2229768	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	91	0	0		WXS	Illumina HiSeq	Phase_I	107	61	0.570093	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	
PI4KA	5297	hgsc.bcm.edu	37	22	21066897	21066897	+	Silent	SNP	G	G	A	rs1135929	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21066897G>A	ENST00000572273.1	-	50	5735	c.5505C>T	c.(5503-5505)tgC>tgT	p.C1835C	PI4KA_ENST00000255882.6_Silent_p.C1893C|PI4KA_ENST00000414196.3_Silent_p.C645C			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1835	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.C1835C(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CGATCACCCCGCACTAGGAGG	0.652													g|||	2170	0.433307	0.5083	0.4683	5008	,	,		12263	0.4752		0.3976	False		,,,				2504	0.3006				p.C1893C	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,2	PI4KA	313	2	2	Substitution - coding silent(2)	stomach(2)	c.C5679T						scavenged	.						20.0	24.0	23.0					22																	21066897		2111	4203	6314	SO:0001819	synonymous_variant	5297	exon50			CACCCCGCACTAG	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5505C>T	22.37:g.21066897G>A		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	165	142	0.860606	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|1.000;|0.000	1.000	weak		0.652	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
POP7	10248	hgsc.bcm.edu	37	7	100304864	100304864	+	Silent	SNP	C	C	A	rs11559028	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100304864C>A	ENST00000303151.4	+	2	673	c.411C>A	c.(409-411)gtC>gtA	p.V137V		NM_005837.2	NP_005828.2	O75817	POP7_HUMAN	processing of precursor 7, ribonuclease P/MRP subunit (S. cerevisiae)	137					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ribonuclease P activity (GO:0004526)			endometrium(2)|kidney(1)|ovary(1)	4	Lung NSC(181;0.041)|all_lung(186;0.0581)					TCTTCAGGGTCACACCCAAGT	0.542													C|||	150	0.0299521	0.0038	0.036	5008	,	,		18413	0.0		0.0636	False		,,,				2504	0.0573				p.V137V		Atlas-SNP	.											.	POP7	8	.	0			c.C411A						PASS	.	C		41,4365	43.8+/-77.6	0,41,2162	66.0	68.0	67.0		411	-0.1	0.9	7	dbSNP_120	67	419,8181	129.8+/-187.9	10,399,3891	no	coding-synonymous	POP7	NM_005837.2		10,440,6053	AA,AC,CC		4.8721,0.9305,3.5368		137/141	100304864	460,12546	2203	4300	6503	SO:0001819	synonymous_variant	10248	exon2			CAGGGTCACACCC	U94316	CCDS5704.1	7q22	2012-05-21	2007-06-26		ENSG00000172336	ENSG00000172336			19949	protein-coding gene	gene with protein product	"""ribonuclease P protein subunit p20"""	606113	"""processing of precursor 7, ribonuclease P subunit (S. cerevisiae)"""			9630247	Standard	NM_005837		Approved	RPP20, RPP2	uc003uwh.4	O75817	OTTHUMG00000044311	ENST00000303151.4:c.411C>A	7.37:g.100304864C>A		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	280	127	0.453571	NM_005837	A4D2E0|Q9BV74	Silent	SNP	ENST00000303151.4	37	CCDS5704.1																																																																																			A|0.035;C|0.965;G|0.000	0.035	strong		0.542	POP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103070.1	NM_005837	
GRM1	2911	hgsc.bcm.edu	37	6	146755560	146755560	+	Silent	SNP	T	T	G	rs1047006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:146755560T>G	ENST00000282753.1	+	8	3448	c.3213T>G	c.(3211-3213)ccT>ccG	p.P1071P	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000361719.2_Silent_p.P1071P|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1071	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)		CCCCGCCACCTCCGCAGCACC	0.682													t|||	998	0.199281	0.0499	0.2925	5008	,	,		14141	0.0843		0.4165	False		,,,				2504	0.2301				p.P1071P		Atlas-SNP	.											GRM1,colon,carcinoma,0,2	GRM1	419	2	0			c.T3213G						PASS	.	T	,	492,3896		30,432,1732	28.0	33.0	31.0		3213,	-11.4	0.0	6	dbSNP_86	31	3341,5243		672,1997,1623	no	coding-synonymous,utr-3	GRM1	NM_000838.3,NM_001114329.1	,	702,2429,3355	GG,GT,TT		38.9212,11.2124,29.5483	,	1071/1195,	146755560	3833,9139	2194	4292	6486	SO:0001819	synonymous_variant	2911	exon9			GCCACCTCCGCAG	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.3213T>G	6.37:g.146755560T>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																			T|0.746;G|0.254	0.254	strong		0.682	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
CLEC18A	348174	hgsc.bcm.edu	37	16	69988463	69988463	+	Missense_Mutation	SNP	C	C	G	rs78531533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:69988463C>G	ENST00000288040.6	+	3	630	c.443C>G	c.(442-444)aCc>aGc	p.T148S	CLEC18A_ENST00000393701.2_Missense_Mutation_p.T148S|CLEC18A_ENST00000449317.2_Missense_Mutation_p.T148S|CLEC18A_ENST00000568461.1_Missense_Mutation_p.T148S	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	148	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						GCCACCTGCACCCACTACACG	0.602																																					p.T148S		Atlas-SNP	.											CLEC18A,NS,carcinoid-endocrine_tumour,0,1	CLEC18A	9	1	0			c.C443G						PASS	.						22.0	21.0	21.0					16																	69988463		2198	4297	6495	SO:0001583	missense	348174	exon4			CCTGCACCCACTA	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.443C>G	16.37:g.69988463C>G	ENSP00000288040:p.Thr148Ser	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	362	43	0.118785	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	37	CCDS10886.1	.	.	.	.	.	.	.	.	.	.	.	8.343	0.829050	0.16749	.	.	ENSG00000157322	ENST00000393701;ENST00000539957;ENST00000545150;ENST00000449317;ENST00000288040	T;T;T	0.07688	3.17;3.17;3.17	1.97	1.97	0.26223	CAP domain (3);	0.557277	0.19650	N	0.109248	T	0.03959	0.0111	N	0.12502	0.225	0.21782	N	0.999542	B;B;B	0.27068	0.005;0.003;0.167	B;B;B	0.24394	0.02;0.008;0.053	T	0.43734	-0.9373	9	.	.	.	.	7.5137	0.27587	0.0:1.0:0.0:0.0	.	148;148;148	B4DPF2;A5D8T8;F8W692	.;CL18A_HUMAN;.	S	148;148;145;148;148	ENSP00000377304:T148S;ENSP00000413990:T148S;ENSP00000288040:T148S	.	T	+	2	0	CLEC18A	68545964	0.596000	0.26866	0.995000	0.50966	0.088000	0.18126	1.195000	0.32186	1.424000	0.47217	0.184000	0.17185	ACC	C|0.997;G|0.003	0.003	strong		0.602	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
ZNF687	57592	hgsc.bcm.edu	37	1	151259043	151259043	+	Silent	SNP	C	C	T	rs2298265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:151259043C>T	ENST00000368879.2	+	2	374	c.276C>T	c.(274-276)ccC>ccT	p.P92P		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	92					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CTGTGTGTCCCGAGCAGTCTG	0.607													c|||	510	0.101837	0.115	0.1412	5008	,	,		19268	0.0615		0.1282	False		,,,				2504	0.0706				p.P92P		Atlas-SNP	.											.	ZNF687	94	.	0			c.C276T						PASS	.	C		513,3893	235.5+/-248.0	28,457,1718	52.0	56.0	55.0		276	-8.6	0.9	1	dbSNP_100	55	1026,7574	218.1+/-256.6	55,916,3329	no	coding-synonymous	ZNF687	NM_020832.1		83,1373,5047	TT,TC,CC		11.9302,11.6432,11.833		92/1238	151259043	1539,11467	2203	4300	6503	SO:0001819	synonymous_variant	57592	exon2			GTGTCCCGAGCAG		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.276C>T	1.37:g.151259043C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	37																																																																																				C|0.892;T|0.108	0.108	strong		0.607	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832	
IGLL1	3543	hgsc.bcm.edu	37	22	23915610	23915610	+	Missense_Mutation	SNP	A	A	T	rs111903752	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:23915610A>T	ENST00000330377.2	-	3	602	c.485T>A	c.(484-486)aTg>aAg	p.M162K	AP000345.2_ENST00000454863.1_RNA|AP000345.2_ENST00000458318.1_RNA|IGLL1_ENST00000249053.3_3'UTR	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	162	C region (By similarity to lambda light- chain).|Ig-like C1-type.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.M162K(1)		kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						GGGCGTGGTCATCTCCACGCC	0.577													a|||	192	0.0383387	0.0711	0.0259	5008	,	,		18776	0.0188		0.0388	False		,,,				2504	0.0225				p.M162K		Atlas-SNP	.											IGLL1,extremity,malignant_melanoma,0,1	IGLL1	27	1	1	Substitution - Missense(1)	skin(1)	c.T485A						PASS	.	A	LYS/MET,	288,4118		6,276,1921	125.0	111.0	116.0		485,	1.4	0.0	22	dbSNP_132	116	252,8348		5,242,4053	no	missense,utr-3	IGLL1	NM_020070.2,NM_152855.1	95,	11,518,5974	TT,TA,AA		2.9302,6.5365,4.1519	benign,	162/214,	23915610	540,12466	2203	4300	6503	SO:0001583	missense	3543	exon3			GTGGTCATCTCCA	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.485T>A	22.37:g.23915610A>T	ENSP00000329312:p.Met162Lys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	213	124	0.58216	NM_020070	Q0P681	Missense_Mutation	SNP	ENST00000330377.2	37	CCDS13809.1	98	0.04487179487179487	46	0.09349593495934959	13	0.03591160220994475	11	0.019230769230769232	28	0.036939313984168866	-	3.289	-0.145450	0.06627	0.065365	0.029302	ENSG00000128322	ENST00000330377;ENST00000438703	T;T	0.02446	4.29;4.29	2.45	1.36	0.22044	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.338611	0.25047	N	0.033550	T	0.00109	0.0003	N	0.12182	0.205	0.22066	N	0.999384	B	0.06786	0.001	B	0.17722	0.019	T	0.49143	-0.8970	10	0.87932	D	0	.	9.2804	0.37725	0.1454:0.0:0.8546:0.0	.	162	P15814	IGLL1_HUMAN	K	162;163	ENSP00000329312:M162K;ENSP00000403391:M163K	ENSP00000329312:M162K	M	-	2	0	IGLL1	22245610	1.000000	0.71417	0.011000	0.14972	0.002000	0.02628	2.268000	0.43338	-0.018000	0.14079	-1.782000	0.00648	ATG	A|0.959;T|0.041	0.041	strong		0.577	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5240002	5240002	+	Silent	SNP	C	C	A	rs11742370	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:5240002C>A	ENST00000274181.7	+	16	2625	c.2487C>A	c.(2485-2487)atC>atA	p.I829I		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	829	Spacer.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AGAACTTAATCGCTACTGGAC	0.512													C|||	568	0.113419	0.0053	0.1081	5008	,	,		16010	0.0734		0.1938	False		,,,				2504	0.2219				p.I829I		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C2487A						PASS	.	C		117,3623		1,115,1754	95.0	92.0	93.0		2487	0.2	0.1	5	dbSNP_120	93	1579,6649		163,1253,2698	no	coding-synonymous	ADAMTS16	NM_139056.2		164,1368,4452	AA,AC,CC		19.1906,3.1283,14.1711		829/1225	5240002	1696,10272	1870	4114	5984	SO:0001819	synonymous_variant	170690	exon16			CTTAATCGCTACT	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.2487C>A	5.37:g.5240002C>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_139056	C6G490|Q8IVE2	Silent	SNP	ENST00000274181.7	37	CCDS43299.1																																																																																			A|0.136;C|0.864;T|0.000	0.136	strong		0.512	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
HTR6	3362	hgsc.bcm.edu	37	1	19992513	19992513	+	Silent	SNP	C	C	T	rs1805054	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19992513C>T	ENST00000289753.1	+	1	734	c.267C>T	c.(265-267)taC>taT	p.Y89Y		NM_000871.1	NP_000862.1	P50406	5HT6R_HUMAN	5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled	89					brain development (GO:0007420)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|long-term synaptic potentiation (GO:0060291)|negative regulation of acetylcholine secretion, neurotransmission (GO:0014058)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|synaptic transmission (GO:0007268)	cilium (GO:0005929)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)|serotonin receptor activity (GO:0004993)			endometrium(1)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Mianserin(DB06148)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Quetiapine(DB01224)|Sertindole(DB06144)|Ziprasidone(DB00246)	ACGCGCTGTACGGGCGCTGGG	0.657													C|||	864	0.172524	0.202	0.1167	5008	,	,		14788	0.2123		0.1163	False		,,,				2504	0.1892				p.Y89Y	Esophageal Squamous(168;1879 2619 6848 21062)	Atlas-SNP	.											.	HTR6	38	.	0			c.C267T	GRCh37	CM994739	HTR6	M	rs1805054	PASS	.	C		838,3566	324.2+/-298.5	78,682,1442	43.0	42.0	42.0		267	1.2	1.0	1	dbSNP_89	42	1141,7455	231.2+/-265.3	79,983,3236	no	coding-synonymous	HTR6	NM_000871.1		157,1665,4678	TT,TC,CC		13.2736,19.0282,15.2231		89/441	19992513	1979,11021	2202	4298	6500	SO:0001819	synonymous_variant	3362	exon1			GCTGTACGGGCGC	L41147	CCDS197.1	1p36-p35	2012-08-08	2012-02-03		ENSG00000158748	ENSG00000158748		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5301	protein-coding gene	gene with protein product		601109	"""5-hydroxytryptamine (serotonin) receptor 6"""			8522988	Standard	NM_000871		Approved	5-HT6, 5-HT6R	uc001bcl.3	P50406	OTTHUMG00000002713	ENST00000289753.1:c.267C>T	1.37:g.19992513C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	90	58	0.644444	NM_000871	Q13640|Q5TGZ1	Silent	SNP	ENST00000289753.1	37	CCDS197.1																																																																																			C|0.839;T|0.161	0.161	strong		0.657	HTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007704.1	NM_000871	
APOL1	8542	hgsc.bcm.edu	37	22	36661536	36661536	+	Silent	SNP	C	C	A	rs136174	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36661536C>A	ENST00000397278.3	+	6	883	c.654C>A	c.(652-654)gcC>gcA	p.A218A	APOL1_ENST00000397279.4_Silent_p.A218A|APOL1_ENST00000440669.2_3'UTR|APOL1_ENST00000426053.1_Silent_p.A200A|APOL1_ENST00000319136.4_Silent_p.A234A|APOL1_ENST00000422706.1_Silent_p.A218A|APOL1_ENST00000347595.7_Silent_p.A97A	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	218					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						GAATCACAGCCGCTTTGACCG	0.557													c|||	4328	0.864217	0.9781	0.8862	5008	,	,		20559	0.7976		0.7813	False		,,,				2504	0.8487				p.A234A		Atlas-SNP	.											.	APOL1	35	.	0			c.C702A						PASS	.	T	,,,	4154,252	803.3+/-415.7	1959,236,8	105.0	102.0	103.0		654,600,654,702	-0.1	0.0	22	dbSNP_78	103	6859,1741	736.3+/-407.0	2727,1405,168	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APOL1	NM_001136540.1,NM_001136541.1,NM_003661.3,NM_145343.2	,,,	4686,1641,176	AA,AC,CC		20.2442,5.7195,15.3237	,,,	218/399,200/381,218/399,234/415	36661536	11013,1993	2203	4300	6503	SO:0001819	synonymous_variant	8542	exon7			CACAGCCGCTTTG	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.654C>A	22.37:g.36661536C>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	109	62	0.568807	NM_145343	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Silent	SNP	ENST00000397278.3	37	CCDS13926.1																																																																																			C|0.154;A|0.846	0.846	strong		0.557	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343	
SCTR	6344	hgsc.bcm.edu	37	2	120194674	120194674	+	IGR	SNP	C	C	T	rs72833258	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:120194674C>T	ENST00000019103.5	-	0	1865				TMEM37_ENST00000306406.4_Silent_p.G77G|TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Silent_p.G89G	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)	GAGACCTGGGCCAGGCCCATG	0.657													C|||	72	0.014377	0.003	0.0144	5008	,	,		14624	0.001		0.0209	False		,,,				2504	0.0368				p.G77G		Atlas-SNP	.											.	TMEM37	40	.	0			c.C231T						PASS	.	C		21,4383	28.1+/-56.4	0,21,2181	50.0	53.0	52.0		231	-4.2	0.1	2	dbSNP_130	52	232,8366	94.2+/-156.2	2,228,4069	no	coding-synonymous	TMEM37	NM_183240.2		2,249,6250	TT,TC,CC		2.6983,0.4768,1.9459		77/191	120194674	253,12749	2202	4299	6501	SO:0001628	intergenic_variant	140738	exon2			CCTGGGCCAGGCC		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.120194674C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	44	28	0.636364	NM_183240	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	37	CCDS2127.1																																																																																			C|0.983;T|0.017	0.017	strong		0.657	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
BTC	685	hgsc.bcm.edu	37	4	75719517	75719517	+	Missense_Mutation	SNP	A	A	C	rs28549760	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:75719517A>C	ENST00000395743.3	-	1	379	c.19T>G	c.(19-21)Tgc>Ggc	p.C7G		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	7			C -> G (in dbSNP:rs28549760).		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 apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			GCGCCGCTGCACCGGGCGGCC	0.711													C|||	1256	0.250799	0.528	0.1931	5008	,	,		11677	0.0526		0.1252	False		,,,				2504	0.2505				p.C7G		Atlas-SNP	.											BTC,NS,carcinoma,0,1	BTC	23	1	0			c.T19G	GRCh37	CM051015	BTC	M	rs28549760	PASS	.	C	GLY/CYS	1222,2206		223,776,715	3.0	4.0	4.0		19	2.0	0.2	4	dbSNP_125	4	707,5837		52,603,2617	no	missense	BTC	NM_001729.2	159	275,1379,3332	CC,CA,AA		10.8038,35.6476,19.3442	possibly-damaging	7/179	75719517	1929,8043	1714	3272	4986	SO:0001583	missense	685	exon1			CGCTGCACCGGGC	S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.19T>G	4.37:g.75719517A>C	ENSP00000379092:p.Cys7Gly	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_001729	Q96F48	Missense_Mutation	SNP	ENST00000395743.3	37	CCDS3566.1	423	0.1936813186813187	234	0.47560975609756095	68	0.1878453038674033	27	0.0472027972027972	94	0.12401055408970976	C	0.003	-2.407671	0.00193	0.356476	0.108038	ENSG00000174808	ENST00000395743	T	0.08546	3.08	2.87	2.0	0.26442	.	1.854280	0.02912	N	0.136898	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	0.46148	-0.9212	9	0.02654	T	1	-10.1459	5.4134	0.16360	0.2346:0.5378:0.2276:0.0	rs28549760	7	P35070	BTC_HUMAN	G	7	ENSP00000379092:C7G	ENSP00000379092:C7G	C	-	1	0	BTC	75938541	0.143000	0.22626	0.175000	0.22980	0.197000	0.23852	0.419000	0.21247	0.244000	0.21351	-0.358000	0.07595	TGC	A|0.802;C|0.198	0.198	strong		0.711	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1		
KANK1	23189	hgsc.bcm.edu	37	9	712060	712060	+	Missense_Mutation	SNP	G	G	C	rs4465020	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:712060G>C	ENST00000382303.1	+	7	1946	c.1294G>C	c.(1294-1296)Gag>Cag	p.E432Q	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Missense_Mutation_p.E274Q|KANK1_ENST00000382297.2_Missense_Mutation_p.E432Q	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	432	Interaction with KIF21A.		E -> Q (in dbSNP:rs4465020). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.E274Q(2)|p.E432Q(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GACACTTGTTGAGATGAGAAA	0.522													G|||	1178	0.235224	0.0303	0.2176	5008	,	,		21322	0.123		0.4066	False		,,,				2504	0.4642				p.E432Q		Atlas-SNP	.											KANK1_ENST00000382303,NS,carcinoma,0,2	KANK1	231	2	3	Substitution - Missense(3)	prostate(3)	c.G1294C						PASS	.	G	GLN/GLU,GLN/GLU	353,4053	182.2+/-210.1	15,323,1865	113.0	98.0	103.0		1294,820	4.8	0.1	9	dbSNP_111	103	3393,5207	502.5+/-375.7	648,2097,1555	yes	missense,missense	KANK1	NM_015158.2,NM_153186.3	29,29	663,2420,3420	CC,CG,GG		39.4535,8.0118,28.8021	benign,benign	432/1353,274/1195	712060	3746,9260	2203	4300	6503	SO:0001583	missense	23189	exon7			CTTGTTGAGATGA	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.1294G>C	9.37:g.712060G>C	ENSP00000371740:p.Glu432Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	481	0.22023809523809523	25	0.0508130081300813	84	0.23204419889502761	60	0.1048951048951049	312	0.41160949868073876	G	2.483	-0.319282	0.05386	0.080118	0.394535	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.47177	0.85;0.85;0.92	5.73	4.81	0.61882	.	0.418748	0.20444	N	0.092235	T	0.00012	0.0000	L	0.49126	1.545	0.52501	P	4.700000000001925E-5	B;B	0.32203	0.36;0.36	B;B	0.28465	0.09;0.09	T	0.42949	-0.9421	9	0.22706	T	0.39	-3.643	9.3954	0.38399	0.0731:0.2712:0.6557:0.0	rs4465020;rs17853758;rs17853807;rs52805693	432;432	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	432;432;432;274	ENSP00000371740:E432Q;ENSP00000371734:E432Q;ENSP00000371730:E274Q	ENSP00000346479:E432Q	E	+	1	0	KANK1	702060	0.546000	0.26457	0.120000	0.21714	0.005000	0.04900	2.053000	0.41326	2.721000	0.93114	0.655000	0.94253	GAG	G|0.734;C|0.266	0.266	strong		0.522	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
SHISA4	149345	hgsc.bcm.edu	37	1	201860626	201860626	+	Missense_Mutation	SNP	A	A	G	rs2250377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201860626A>G	ENST00000362011.6	+	4	764	c.477A>G	c.(475-477)atA>atG	p.I159M	RP11-307B6.3_ENST00000414927.1_RNA|SHISA4_ENST00000464117.1_3'UTR	NM_198149.2	NP_937792.2	Q96DD7	SHSA4_HUMAN	shisa family member 4	159	Pro-rich.		I -> M (in dbSNP:rs2250377). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				kidney(1)|lung(4)	5						CTGGCTTCATATACCCACCTA	0.587													G|||	3928	0.784345	0.8041	0.7767	5008	,	,		16314	0.8978		0.6988	False		,,,				2504	0.7342				p.I159M		Atlas-SNP	.											.	SHISA4	9	.	0			c.A477G						PASS	.	G	MET/ILE	3471,935	359.1+/-314.7	1352,767,84	112.0	114.0	114.0		477	5.5	1.0	1	dbSNP_100	114	5872,2728	436.7+/-358.4	1994,1884,422	yes	missense	SHISA4	NM_198149.2	10	3346,2651,506	GG,GA,AA		31.7209,21.2211,28.1639	benign	159/198	201860626	9343,3663	2203	4300	6503	SO:0001583	missense	149345	exon4			CTTCATATACCCA	AY358589	CCDS1416.1	1q32.1	2013-07-31	2013-07-31	2008-04-01	ENSG00000198892	ENSG00000198892		"""Shisa homologs"""	27139	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 40"", ""transmembrane protein 58"", ""shisa homolog 4 (Xenopus laevis)"""	C1orf40, TMEM58		12975309	Standard	NR_030775		Approved	hShisa4	uc001gxa.3	Q96DD7	OTTHUMG00000035807	ENST00000362011.6:c.477A>G	1.37:g.201860626A>G	ENSP00000355064:p.Ile159Met	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_198149	B4DFI0|B7ZAJ7|Q5VUU1|Q6P711|Q6UWY7	Missense_Mutation	SNP	ENST00000362011.6	37	CCDS1416.1	1661	0.7605311355311355	365	0.741869918699187	272	0.7513812154696132	507	0.8863636363636364	517	0.6820580474934037	G	8.231	0.804709	0.16467	0.787789	0.682791	ENSG00000198892	ENST00000362011	T	0.42513	0.97	5.46	5.46	0.80206	.	0.385153	0.30686	N	0.009082	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	0.22800	-1.0206	9	0.21540	T	0.41	-26.174	12.2783	0.54749	0.0831:0.0:0.9169:0.0	rs2250377;rs61313306;rs2250377	159	Q96DD7	SHSA4_HUMAN	M	159	ENSP00000355064:I159M	ENSP00000355064:I159M	I	+	3	3	SHISA4	200127249	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	1.845000	0.39279	1.314000	0.45095	-0.215000	0.12644	ATA	A|0.254;G|0.746	0.746	strong		0.587	SHISA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087096.1	NM_198149	
PALB2	79728	hgsc.bcm.edu	37	16	23635348	23635348	+	Missense_Mutation	SNP	A	A	C	rs45478192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:23635348A>C	ENST00000261584.4	-	8	2968	c.2816T>G	c.(2815-2817)tTg>tGg	p.L939W	CTD-2196E14.3_ENST00000561764.1_RNA	NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	939	Interaction with RAD51, BRCA2 and POLH.|Required for interaction with POLH and POLH DNA synthesis stimulation.		L -> W (may be associated with breast cancer susceptibility; reduces interaction with BRCA2, RAD51 and XRCC3; decreases double-stranded DNA break- initiated homologous recombination; increases sensitivity to IR; dbSNP:rs45478192). {ECO:0000269|PubMed:21618343}.		DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		TCTGATTTCCAAATTTCCCAA	0.378			"""F, N, Mis"""			"""Wilms tumor, medulloblastoma, AML ,breast"""		Involved in tolerance or repair of DNA crosslinks					A|||	4	0.000798722	0.0008	0.0014	5008	,	,		17096	0.0		0.002	False		,,,				2504	0.0				p.L939W		Atlas-SNP	.	yes	Rec		"""Fanconi anaemia N, breast cancer susceptibility """	16	16p12.1	79728	partner and localizer of BRCA2		"""L, O, E"""	.	PALB2	108	.	0			c.T2816G						PASS	.	A	TRP/LEU	0,4394		0,0,2197	101.0	94.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2816	5.8	1.0	16	dbSNP_127	96	20,8580	15.3+/-51.7	0,20,4280	yes	missense	PALB2	NM_024675.3	61	0,20,6477	CC,CA,AA		0.2326,0.0,0.1539	probably-damaging	939/1187	23635348	20,12974	2197	4300	6497	SO:0001583	missense	79728	exon8			ATTTCCAAATTTC		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"""Fanconi anemia, complementation groups"""	26144	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group N"""	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.2816T>G	16.37:g.23635348A>C	ENSP00000261584:p.Leu939Trp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	119	43	0.361345	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	20.9	4.060595	0.76074	0.0	0.002326	ENSG00000083093	ENST00000261584	T	0.28666	1.6	5.81	5.81	0.92471	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000005	T	0.56171	0.1967	M	0.77103	2.36	0.45914	D	0.998756	D	0.89917	1.0	D	0.97110	1.0	T	0.60994	-0.7152	10	0.87932	D	0	-7.0825	12.557	0.56258	1.0:0.0:0.0:0.0	rs45478192;rs61755167	939	Q86YC2	PALB2_HUMAN	W	939	ENSP00000261584:L939W	ENSP00000261584:L939W	L	-	2	0	PALB2	23542849	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.166000	0.64965	2.230000	0.72887	0.528000	0.53228	TTG	A|0.999;C|0.001	0.001	strong		0.378	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675	
DHX32	55760	hgsc.bcm.edu	37	10	127530325	127530325	+	Silent	SNP	T	T	C	rs3208565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:127530325T>C	ENST00000284690.3	-	7	2020	c.1530A>G	c.(1528-1530)gcA>gcG	p.A510A	BCCIP_ENST00000368759.5_Intron|DHX32_ENST00000284688.6_Silent_p.A429A|BCCIP_ENST00000299130.3_3'UTR|AL360176.1_ENST00000401153.1_RNA|BCCIP_ENST00000429863.2_3'UTR|DHX32_ENST00000368721.1_Silent_p.A134A	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	510						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.A510A(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTACCATGGCTGCGATTGTTA	0.368													C|||	2274	0.454073	0.5961	0.3487	5008	,	,		18241	0.3234		0.4443	False		,,,				2504	0.4816				p.A510A		Atlas-SNP	.											DHX32,NS,carcinoma,0,1	DHX32	67	1	1	Substitution - coding silent(1)	stomach(1)	c.A1530G						PASS	.	C	,,	2532,1874	542.2+/-376.0	738,1056,409	73.0	69.0	70.0		,1530,	-0.5	1.0	10	dbSNP_105	70	3952,4648	602.5+/-394.5	917,2118,1265	no	intron,coding-synonymous,utr-3	DHX32,BCCIP	NM_016567.3,NM_018180.2,NM_078469.2	,,	1655,3174,1674	CC,CT,TT		45.9535,42.5329,49.8539	,,	,510/744,	127530325	6484,6522	2203	4300	6503	SO:0001819	synonymous_variant	55760	exon7			CATGGCTGCGATT		CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876		"""DEAH-boxes"""	16717	protein-coding gene	gene with protein product		607960	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32"""	DDX32			Standard	NM_018180		Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.1530A>G	10.37:g.127530325T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	127	52	0.409449	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Silent	SNP	ENST00000284690.3	37	CCDS7652.1																																																																																			T|0.521;C|0.479	0.479	strong		0.368	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180	
PIEZO1	9780	hgsc.bcm.edu	37	16	88787673	88787673	+	Missense_Mutation	SNP	G	G	A	rs35159887	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88787673G>A	ENST00000301015.9	-	39	5815	c.5569C>T	c.(5569-5571)Ccc>Tcc	p.P1857S	RP5-1142A6.9_ENST00000564984.1_RNA|PIEZO1_ENST00000327397.7_5'Flank	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1857					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						TCCACTTGGGGTTCTGGGGTC	0.652													G|||	832	0.166134	0.0144	0.1787	5008	,	,		17762	0.0764		0.3072	False		,,,				2504	0.3098				p.P1857S		Atlas-SNP	.											PIEZO1,NS,carcinoma,0,1	PIEZO1	79	1	0			c.C5569T						PASS	.	G	SER/PRO	84,1300		3,78,611	58.0	57.0	57.0		5569	-0.4	0.0	16	dbSNP_126	57	1069,2109		167,735,687	yes	missense	PIEZO1	NM_001142864.2	74	170,813,1298	AA,AG,GG		33.6375,6.0694,25.274	benign	1857/2522	88787673	1153,3409	692	1589	2281	SO:0001583	missense	9780	exon39			CTTGGGGTTCTGG	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.5569C>T	16.37:g.88787673G>A	ENSP00000301015:p.Pro1857Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	359|359	0.16437728937728938|0.16437728937728938	13|13	0.026422764227642278|0.026422764227642278	81|81	0.22375690607734808|0.22375690607734808	39|39	0.06818181818181818|0.06818181818181818	226|226	0.29815303430079154|0.29815303430079154	G|G	6.191|6.191	0.403423|0.403423	0.11754|0.11754	0.060694|0.060694	0.336375|0.336375	ENSG00000103335|ENSG00000103335	ENST00000301015|ENST00000451779	T|.	0.71579|.	-0.58|.	4.48|4.48	-0.409|-0.409	0.12378|0.12378	.|.	1.563880|.	0.04107|.	N|.	0.313931|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.42965|0.42965	-0.9420|-0.9420	9|4	0.08837|.	T|.	0.75|.	-3.4232|-3.4232	7.7829|7.7829	0.29074|0.29074	0.1446:0.3574:0.498:0.0|0.1446:0.3574:0.498:0.0	rs35159887|rs35159887	1857|.	Q92508|.	PIEZ1_HUMAN|.	S|I	1857|1802	ENSP00000301015:P1857S|.	ENSP00000301015:P1857S|.	P|T	-|-	1|2	0|0	FAM38A|FAM38A	87315174|87315174	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.292000|0.292000	0.27327|0.27327	-0.123000|-0.123000	0.10611|0.10611	0.077000|0.077000	0.16863|0.16863	0.448000|0.448000	0.29417|0.29417	CCC|ACC	G|0.825;A|0.175	0.175	strong		0.652	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
COL20A1	57642	hgsc.bcm.edu	37	20	61944193	61944193	+	Silent	SNP	T	T	C	rs4809530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61944193T>C	ENST00000358894.6	+	16	2083	c.1983T>C	c.(1981-1983)gaT>gaC	p.D661D	COL20A1_ENST00000326996.6_Silent_p.D661D|COL20A1_ENST00000422202.1_Silent_p.D668D|COL20A1_ENST00000435874.1_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	151	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	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	
TENM4	26011	hgsc.bcm.edu	37	11	78381156	78381156	+	Silent	SNP	G	G	A	rs139879711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:78381156G>A	ENST00000278550.7	-	32	6696	c.6234C>T	c.(6232-6234)aaC>aaT	p.N2078N		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2078					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)										CAAAACGGGCGTTGACCATGC	0.537													G|||	17	0.00339457	0.0008	0.0014	5008	,	,		22662	0.0		0.0119	False		,,,				2504	0.0031				p.N2078N		Atlas-SNP	.											ODZ4_ENST00000278550,NS,carcinoma,0,2	.	.	2	0			c.C6234T						PASS	.	G		8,4190		0,8,2091	79.0	84.0	82.0		6234	-9.9	0.6	11	dbSNP_134	82	79,8339		0,79,4130	no	coding-synonymous	ODZ4	NM_001098816.2		0,87,6221	AA,AG,GG		0.9385,0.1906,0.6896		2078/2770	78381156	87,12529	2099	4209	6308	SO:0001819	synonymous_variant	26011	exon32			ACGGGCGTTGACC	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.6234C>T	11.37:g.78381156G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	221	120	0.542986	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			G|0.996;A|0.004	0.004	strong		0.537	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
COASY	80347	hgsc.bcm.edu	37	17	40714804	40714804	+	Missense_Mutation	SNP	C	C	A	rs615942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40714804C>A	ENST00000393818.2	+	1	620	c.164C>A	c.(163-165)tCc>tAc	p.S55Y	COASY_ENST00000420359.1_Missense_Mutation_p.S55Y|COASY_ENST00000421097.2_Missense_Mutation_p.S55Y|COASY_ENST00000590958.1_Missense_Mutation_p.S84Y|COASY_ENST00000449624.1_Intron|RP11-400F19.8_ENST00000585572.1_RNA	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	55			S -> Y (in dbSNP:rs615942). {ECO:0000269|PubMed:11923312, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		cell death (GO:0008219)|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)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CAGCCCCAGTCCAGCCCCGTG	0.627													C|||	2539	0.506989	0.4289	0.487	5008	,	,		16531	0.4524		0.5239	False		,,,				2504	0.6656				p.S84Y		Atlas-SNP	.											COASY,colon,carcinoma,0,1	COASY	45	1	0			c.C251A						scavenged	.	C	TYR/SER,TYR/SER,,TYR/SER,TYR/SER	1897,2505		400,1097,704	48.0	59.0	55.0		164,164,,251,164	5.7	1.0	17	dbSNP_83	55	4667,3929		1289,2089,920	yes	missense,missense,intron,missense,missense	COASY	NM_001042529.1,NM_001042530.1,NM_001042531.1,NM_001042532.2,NM_025233.5	144,144,,144,144	1689,3186,1624	AA,AC,CC		45.7073,43.094,49.4999	benign,benign,,benign,benign	55/565,55/565,,84/594,55/565	40714804	6564,6434	2201	4298	6499	SO:0001583	missense	80347	exon3			CCCAGTCCAGCCC	AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"""Coenzyme A synthase"""			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.164C>A	17.37:g.40714804C>A	ENSP00000377406:p.Ser55Tyr	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_001042532	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Missense_Mutation	SNP	ENST00000393818.2	37	CCDS11429.1	1035	0.4739010989010989	222	0.45121951219512196	158	0.43646408839779005	256	0.44755244755244755	399	0.5263852242744064	C	19.53	3.845183	0.71603	0.43094	0.542927	ENSG00000068120	ENST00000421097;ENST00000420359;ENST00000393818;ENST00000426807	T;T	0.32515	1.45;1.45	5.69	5.69	0.88448	.	0.237138	0.43919	D	0.000516	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	1.0	P;P	0.51351	0.944;0.802	P;B	0.51135	0.66;0.176	T	0.48490	-0.9031	9	0.72032	D	0.01	-2.8551	17.2983	0.87175	0.0:1.0:0.0:0.0	rs615942;rs3198732;rs17738735;rs57211394;rs615942	84;55	Q13057-2;Q13057	.;COASY_HUMAN	Y	84;55;55;55	ENSP00000413338:S55Y;ENSP00000377406:S55Y	ENSP00000377406:S55Y	S	+	2	0	COASY	37968330	1.000000	0.71417	0.993000	0.49108	0.942000	0.58702	5.153000	0.64888	2.693000	0.91896	0.561000	0.74099	TCC	C|0.512;A|0.488	0.488	strong		0.627	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233	
HINT3	135114	hgsc.bcm.edu	37	6	126278230	126278230	+	Missense_Mutation	SNP	G	G	C	rs2295005	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:126278230G>C	ENST00000229633.5	+	1	304	c.107G>C	c.(106-108)gGc>gCc	p.G36A		NM_138571.4	NP_612638.3	Q9NQE9	HINT3_HUMAN	histidine triad nucleotide binding protein 3	36			G -> A (2.5-fold increase in affinity for indolepropinoic acyl-adenylate and cytosine; 2-fold decrease in hypoxanthine affinity; nearly no change in affinity for adenine, guanine and uracil; dbSNP:rs2295005). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17870088, ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(1)|lung(1)|stomach(1)	4				UCEC - Uterine corpus endometrioid carcinoma (4;0.153)|GBM - Glioblastoma multiforme(226;0.0321)		GAAGCCGCTGGCAAGTCACCA	0.672											OREG0017649	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3479	0.694688	0.6944	0.6844	5008	,	,		14861	0.9534		0.495	False		,,,				2504	0.6411				p.G36A		Atlas-SNP	.											HINT3,NS,carcinoma,0,1	HINT3	14	1	0			c.G107C						PASS	.	C	ALA/GLY	2578,1154		926,726,214	26.0	20.0	22.0		107	4.5	0.0	6	dbSNP_100	22	3795,3485		1052,1691,897	yes	missense	HINT3	NM_138571.4	60	1978,2417,1111	CC,CG,GG		47.8709,30.9218,42.1268	benign	36/183	126278230	6373,4639	1866	3640	5506	SO:0001583	missense	135114	exon1			CCGCTGGCAAGTC	AK057688	CCDS5133.1	6q22.33	2007-12-04			ENSG00000111911	ENSG00000111911			18468	protein-coding gene	gene with protein product		609998				11805111	Standard	NM_138571		Approved	FLJ33126	uc003qal.4	Q9NQE9	OTTHUMG00000015514	ENST00000229633.5:c.107G>C	6.37:g.126278230G>C	ENSP00000229633:p.Gly36Ala	Somatic	68	0	0	1548	WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_138571	B3KQ91|Q8N0Y9	Missense_Mutation	SNP	ENST00000229633.5	37	CCDS5133.1	1538	0.7042124542124543	372	0.7560975609756098	243	0.6712707182320442	545	0.9527972027972028	378	0.49868073878627966	C	3.977	-0.007271	0.07773	0.690782	0.521291	ENSG00000111911	ENST00000229633	D	0.90844	-2.74	4.51	4.51	0.55191	Histidine triad-like motif (1);	1.657570	0.03007	N	0.148899	T	0.55893	0.1949	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48714	-0.9011	9	0.02654	T	1	-18.9857	11.9951	0.53196	0.0:0.8247:0.1753:0.0	rs2295005;rs17292865;rs52818664;rs2295005	36	Q9NQE9	HINT3_HUMAN	A	36	ENSP00000229633:G36A	ENSP00000229633:G36A	G	+	2	0	HINT3	126319923	0.001000	0.12720	0.016000	0.15963	0.016000	0.09150	0.449000	0.21744	1.129000	0.42072	-0.371000	0.07208	GGC	G|0.358;C|0.642	0.642	strong		0.672	HINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042090.1	NM_138571	
CCDC88C	440193	hgsc.bcm.edu	37	14	91760522	91760522	+	Silent	SNP	C	C	T	rs12891713	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:91760522C>T	ENST00000389857.6	-	23	4193	c.4107G>A	c.(4105-4107)caG>caA	p.Q1369Q		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1369					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)				CTTACATGTACTGCTTCTGCT	0.567													C|||	1015	0.202676	0.4856	0.1412	5008	,	,		21614	0.0843		0.1193	False		,,,				2504	0.0716				p.Q1369Q		Atlas-SNP	.											.	CCDC88C	192	.	0			c.G4107A						PASS	.	C		1763,2535		364,1035,750	260.0	275.0	270.0		4107	3.1	1.0	14	dbSNP_121	270	948,7556		64,820,3368	no	coding-synonymous	CCDC88C	NM_001080414.3		428,1855,4118	TT,TC,CC		11.1477,41.0191,21.1764		1369/2029	91760522	2711,10091	2149	4252	6401	SO:0001819	synonymous_variant	440193	exon23			CATGTACTGCTTC		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.4107G>A	14.37:g.91760522C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	190	78	0.410526	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.823;T|0.177	0.177	strong		0.567	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
CASZ1	54897	hgsc.bcm.edu	37	1	10709441	10709441	+	Silent	SNP	C	C	T	rs284299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10709441C>T	ENST00000377022.3	-	14	3251	c.2934G>A	c.(2932-2934)gcG>gcA	p.A978A	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Silent_p.A978A	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	978					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GGCTCCCCTCCGCTTCCGCCT	0.647													C|||	1567	0.312899	0.5416	0.1427	5008	,	,		16270	0.2321		0.1839	False		,,,				2504	0.3405				p.A978A		Atlas-SNP	.											CASZ1,NS,carcinoma,0,1	CASZ1	150	1	0			c.G2934A						PASS	.	C	,	1958,2436		448,1062,687	20.0	23.0	22.0		2934,2934	-9.6	0.0	1	dbSNP_79	22	1520,7080		140,1240,2920	no	coding-synonymous,coding-synonymous	CASZ1	NM_001079843.1,NM_017766.3	,	588,2302,3607	TT,TC,CC		17.6744,44.5608,26.7662	,	978/1760,978/1167	10709441	3478,9516	2197	4300	6497	SO:0001819	synonymous_variant	54897	exon14			CCCCTCCGCTTCC	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2934G>A	1.37:g.10709441C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			T|0.279;C|0.721	0.279	strong		0.647	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
CATSPER2	117155	hgsc.bcm.edu	37	15	43928340	43928340	+	Missense_Mutation	SNP	C	C	G	rs146701338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43928340C>G	ENST00000321596.5	-	8	1119	c.920G>C	c.(919-921)tGg>tCg	p.W307S	CATSPER2_ENST00000355438.2_Missense_Mutation_p.W307S|RNU6-610P_ENST00000384264.1_RNA|CATSPER2_ENST00000354127.4_Missense_Mutation_p.W307S|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000396879.1_Missense_Mutation_p.W307S|CATSPER2_ENST00000381761.1_Missense_Mutation_p.W313S			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	307					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		AGGCACCTTCCAGACGTCCTG	0.443													.|||	6	0.00119808	0.0	0.0	5008	,	,		20134	0.0		0.004	False		,,,				2504	0.002				p.W307S		Atlas-SNP	.											.	CATSPER2	49	.	0			c.G920C						PASS	.	C	SER/TRP,SER/TRP	4,4390		0,4,2193	27.0	27.0	27.0		920,920	4.8	1.0	15	dbSNP_134	27	33,8511		0,33,4239	no	missense,missense	CATSPER2	NM_054020.2,NM_172095.1	177,177	0,37,6432	GG,GC,CC		0.3862,0.091,0.286	probably-damaging,probably-damaging	307/529,307/531	43928340	37,12901	2197	4272	6469	SO:0001583	missense	117155	exon8			ACCTTCCAGACGT	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"""Voltage-gated ion channels / Cation channels, sperm associated"""	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.920G>C	15.37:g.43928340C>G	ENSP00000321463:p.Trp307Ser	Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	459	192	0.418301	NM_054020	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	8.365	0.834073	0.16820	9.1E-4	0.003862	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438	D;D;D;D;D	0.97161	-4.27;-4.27;-4.27;-4.27;-4.27	4.81	4.81	0.61882	Ion transport (1);	0.472448	0.20479	N	0.091522	D	0.96386	0.8821	L	0.54323	1.7	0.53688	D	0.999972	D;D	0.71674	0.997;0.998	D;D	0.71184	0.953;0.972	D	0.94092	0.7354	10	0.26408	T	0.33	.	13.2328	0.59953	0.0:1.0:0.0:0.0	.	313;307	F8W9H2;Q96P56	.;CTSR2_HUMAN	S	307;307;313;307;307;307	ENSP00000380088:W307S;ENSP00000371180:W313S;ENSP00000321463:W307S;ENSP00000339137:W307S;ENSP00000347613:W307S	ENSP00000299989:W307S	W	-	2	0	CATSPER2	41715632	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	4.485000	0.60279	2.488000	0.83962	0.655000	0.94253	TGG	C|0.997;G|0.003	0.003	strong		0.443	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020	
ABCC8	6833	hgsc.bcm.edu	37	11	17419279	17419279	+	Silent	SNP	C	C	T	rs1799859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	57	0	0		WXS	Illumina HiSeq	Phase_I	61	61	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	
SACS	26278	hgsc.bcm.edu	37	13	23907909	23907909	+	Missense_Mutation	SNP	A	A	G	rs17078605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:23907909A>G	ENST00000382292.3	-	9	10379	c.10106T>C	c.(10105-10107)gTc>gCc	p.V3369A	SACS_ENST00000402364.1_Missense_Mutation_p.V2619A|SACS_ENST00000382298.3_Missense_Mutation_p.V3369A			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3369			V -> A (in dbSNP:rs17078605). {ECO:0000269|PubMed:10655055}.		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)		TGAAGTTTGGACCATATAATG	0.353													A|||	1297	0.258986	0.0552	0.3617	5008	,	,		19598	0.3145		0.2783	False		,,,				2504	0.3845				p.V3369A		Atlas-SNP	.											.	SACS	871	.	0			c.T10106C						PASS	.	A	ALA/VAL	424,3982	204.5+/-226.7	20,384,1799	75.0	73.0	74.0		10106	5.9	1.0	13	dbSNP_123	74	2236,6362	376.1+/-338.0	291,1654,2354	yes	missense	SACS	NM_014363.4	64	311,2038,4153	GG,GA,AA		26.006,9.6232,20.4552	possibly-damaging	3369/4580	23907909	2660,10344	2203	4299	6502	SO:0001583	missense	26278	exon10			GTTTGGACCATAT	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.10106T>C	13.37:g.23907909A>G	ENSP00000371729:p.Val3369Ala	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	142	62	0.43662	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	585	0.26785714285714285	33	0.06707317073170732	129	0.356353591160221	208	0.36363636363636365	215	0.2836411609498681	A	16.35	3.099588	0.56183	0.096232	0.26006	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88046	-2.19;-2.33;-2.19	5.94	5.94	0.96194	.	0.059335	0.64402	D	0.000002	T	0.00012	0.0000	N	0.19112	0.55	0.27915	P	0.9384827	P	0.41313	0.745	B	0.37480	0.251	T	0.02676	-1.1125	9	0.45353	T	0.12	.	16.3979	0.83621	1.0:0.0:0.0:0.0	rs17078605;rs52795397;rs17078605	3369	Q9NZJ4	SACS_HUMAN	A	3369;2619;3369	ENSP00000371729:V3369A;ENSP00000385844:V2619A;ENSP00000371735:V3369A	ENSP00000371729:V3369A	V	-	2	0	SACS	22805909	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	9.339000	0.96797	2.279000	0.76181	0.459000	0.35465	GTC	A|0.769;G|0.231	0.231	strong		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
FERMT1	55612	hgsc.bcm.edu	37	20	6088265	6088265	+	Missense_Mutation	SNP	G	G	A	rs62200482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:6088265G>A	ENST00000217289.4	-	6	1551	c.763C>T	c.(763-765)Cgc>Tgc	p.R255C	FERMT1_ENST00000536936.1_De_novo_Start_OutOfFrame	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	255	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ATAAGGGAGCGTGAGGAGTCT	0.333													G|||	256	0.0511182	0.003	0.0418	5008	,	,		16905	0.0804		0.0875	False		,,,				2504	0.0552				p.R255C		Atlas-SNP	.											.	FERMT1	106	.	0			c.C763T						PASS	.	G	CYS/ARG	86,4320	70.3+/-108.2	2,82,2119	55.0	54.0	55.0		763	4.5	0.8	20	dbSNP_129	55	743,7857	179.9+/-228.9	25,693,3582	yes	missense	FERMT1	NM_017671.4	180	27,775,5701	AA,AG,GG		8.6395,1.9519,6.374	probably-damaging	255/678	6088265	829,12177	2203	4300	6503	SO:0001583	missense	55612	exon6			GGGAGCGTGAGGA	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.763C>T	20.37:g.6088265G>A	ENSP00000217289:p.Arg255Cys	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	203	107	0.527094	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Missense_Mutation	SNP	ENST00000217289.4	37	CCDS13098.1	124	0.056776556776556776	3	0.006097560975609756	14	0.03867403314917127	45	0.07867132867132867	62	0.08179419525065963	G	16.82	3.229469	0.58777	0.019519	0.086395	ENSG00000101311	ENST00000217289;ENST00000339538	T	0.78126	-1.15	5.5	4.54	0.55810	FERM, N-terminal (1);Band 4.1 domain (1);	0.050080	0.85682	D	0.000000	T	0.29684	0.0741	M	0.83384	2.64	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.97110	0.993;1.0	T	0.72711	-0.4211	9	0.87932	D	0	-9.0744	13.859	0.63548	0.0:0.0:0.7233:0.2767	rs62200482	255;255	Q9BQL6-4;Q9BQL6	.;FERM1_HUMAN	C	255	ENSP00000217289:R255C	ENSP00000217289:R255C	R	-	1	0	FERMT1	6036265	1.000000	0.71417	0.803000	0.32268	0.360000	0.29518	4.367000	0.59498	1.438000	0.47492	0.650000	0.86243	CGC	G|0.936;A|0.064	0.064	strong		0.333	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
IGFN1	91156	hgsc.bcm.edu	37	1	201193964	201193964	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201193964G>C	ENST00000335211.4	+	21	10578	c.10448G>C	c.(10447-10449)gGg>gCg	p.G3483A	RP11-567E21.3_ENST00000453155.1_RNA|IGFN1_ENST00000295591.8_Intron	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1026						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACCCTGCAGGGGAAGGAGGTT	0.602																																					p.G3483A		Atlas-SNP	.											IGFN1_ENST00000335211,NS,carcinoma,+1,2	IGFN1	220	2	0			c.G10448C						PASS	.						68.0	54.0	59.0					1																	201193964		2203	4300	6503	SO:0001583	missense	91156	exon21			TGCAGGGGAAGGA	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.10448G>C	1.37:g.201193964G>C	ENSP00000334714:p.Gly3483Ala	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355022	0.61293	.	.	ENSG00000163395	ENST00000335211	T	0.81247	-1.47	4.11	3.16	0.36331	.	0.071084	0.56097	N	0.000031	D	0.89619	0.6767	M	0.86343	2.81	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90409	0.4408	10	0.87932	D	0	.	11.9403	0.52896	0.0:0.1757:0.8242:0.0	.	3483	F8WAI1	.	A	3483	ENSP00000334714:G3483A	ENSP00000334714:G3483A	G	+	2	0	IGFN1	199460587	1.000000	0.71417	0.112000	0.21494	0.893000	0.52053	5.952000	0.70282	0.878000	0.35920	0.491000	0.48974	GGG	.	.	none		0.602	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
PLCXD1	55344	hgsc.bcm.edu	37	X	200939	200939	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:200939C>T	ENST00000381657.2	+	2	599	c.85C>T	c.(85-87)Ccc>Tcc	p.P29S	PLCXD1_ENST00000484611.2_3'UTR|PLCXD1_ENST00000381663.3_Missense_Mutation_p.P29S|PLCXD1_ENST00000399012.1_Missense_Mutation_p.P29S	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	29					lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	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)				GGCACTGTGTCCCCGGCTCTG	0.652													c|||	7	0.00139776	0.0008	0.0058	5008	,	,		15888	0.0		0.002	False		,,,				2504	0.0				p.P29S		Atlas-SNP	.											.	PLCXD1	18	.	0			c.C85T						PASS	.		SER/PRO	7,4399		0,7,2196	131.0	118.0	123.0		85	2.0	0.4	X	dbSNP_134	123	74,8518		0,74,4222	no	missense	PLCXD1	NM_018390.3	74	0,81,6418	TT,TC,CC		0.8613,0.1589,0.6232	benign	29/324	200939	81,12917	2203	4296	6499	SO:0001583	missense	55344	exon2			CTGTGTCCCCGGC	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"""Pseudoautosomal regions / PAR1"""	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.85C>T	X.37:g.200939C>T	ENSP00000371073:p.Pro29Ser	Somatic	376	1	0.00265957		WXS	Illumina HiSeq	Phase_I	343	169	0.492711	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	37	CCDS14103.1	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	.	0.110	-1.139616	0.01728	0.001589	0.008613	ENSG00000182378	ENST00000399012;ENST00000430923;ENST00000445062;ENST00000381657;ENST00000429181;ENST00000381663;ENST00000443019;ENST00000415337;ENST00000447472;ENST00000448477	.	.	.	1.98	1.98	0.26296	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.820267	0.11258	U	0.582867	T	0.10208	0.0250	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.27262	-1.0079	8	0.05721	T	0.95	.	7.6567	0.28379	0.0:1.0:0.0:0.0	.	29	Q9NUJ7	PLCX1_HUMAN	S	29	.	ENSP00000371073:P29S	P	+	1	0	PLCXD1	140939	0.000000	0.05858	0.388000	0.26195	0.309000	0.27889	-0.301000	0.08232	0.793000	0.33875	0.449000	0.29647	CCC	C|0.995;T|0.005	0.005	strong		0.652	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390	
CYP2A7	1549	hgsc.bcm.edu	37	19	41386147	41386147	+	Missense_Mutation	SNP	C	C	T	rs143990356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41386147C>T	ENST00000301146.4	-	4	1037	c.496G>A	c.(496-498)Gcc>Acc	p.A166T	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.A115T	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	166						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)			TCGATATTGGCGCCTGCGGGT	0.537													.|||	19	0.00379393	0.0	0.0	5008	,	,		14656	0.0		0.002	False		,,,				2504	0.0174				p.A166T		Atlas-SNP	.											.	CYP2A7	71	.	0			c.G496A						PASS	.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	109.0	98.0	102.0		496,343	1.1	0.0	19	dbSNP_134	102	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	CYP2A7	NM_000764.2,NM_030589.2	58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	166/495,115/444	41386147	2,13004	2203	4300	6503	SO:0001583	missense	1549	exon4			TATTGGCGCCTGC	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.496G>A	19.37:g.41386147C>T	ENSP00000301146:p.Ala166Thr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	210	90	0.428571	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	9.362	1.068261	0.20067	0.0	2.33E-4	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.69175	-0.38;-0.38	2.2	1.11	0.20524	.	1.028510	0.07730	U	0.945117	T	0.46678	0.1405	N	0.13299	0.325	0.09310	N	1	B;B;B	0.24368	0.055;0.102;0.053	B;B;B	0.18263	0.015;0.021;0.015	T	0.34354	-0.9832	10	0.45353	T	0.12	.	6.2876	0.21041	0.0:0.8373:0.0:0.1627	.	166;115;166	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	T	166;115	ENSP00000301146:A166T;ENSP00000291764:A115T	ENSP00000291764:A115T	A	-	1	0	CYP2A7	46077987	0.005000	0.15991	0.003000	0.11579	0.148000	0.21650	0.229000	0.17833	0.248000	0.21435	0.187000	0.17357	GCC	C|1.000;T|0.000	0.000	strong		0.537	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
IPO8	10526	hgsc.bcm.edu	37	12	30823971	30823971	+	Silent	SNP	A	A	G	rs1054426	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:30823971A>G	ENST00000256079.4	-	9	1307	c.969T>C	c.(967-969)ctT>ctC	p.L323L	IPO8_ENST00000544829.1_Silent_p.L118L	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	323					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					ATGCTTGCTGAAGAACACGGG	0.378													G|||	2474	0.49401	0.702	0.2911	5008	,	,		13803	0.4484		0.5089	False		,,,				2504	0.3885				p.L323L		Atlas-SNP	.											.	IPO8	105	.	0			c.T969C						PASS	.	G	,	2902,1504	477.0+/-357.8	951,1000,252	154.0	158.0	157.0		354,969	0.4	1.0	12	dbSNP_86	157	4449,4151	564.8+/-388.4	1146,2157,997	no	coding-synonymous,coding-synonymous	IPO8	NM_001190995.1,NM_006390.3	,	2097,3157,1249	GG,GA,AA		48.2674,34.1353,43.4799	,	118/833,323/1038	30823971	7351,5655	2203	4300	6503	SO:0001819	synonymous_variant	10526	exon9			TTGCTGAAGAACA	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"""Importins"""	9853	protein-coding gene	gene with protein product		605600	"""RAN binding protein 8"""	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.969T>C	12.37:g.30823971A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	172	63	0.366279	NM_006390	B7Z7M3	Silent	SNP	ENST00000256079.4	37	CCDS8719.1																																																																																			A|0.447;G|0.553	0.553	strong		0.378	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390	
LY6G6C	80740	hgsc.bcm.edu	37	6	31691657	31691657	+	5'Flank	SNP	G	G	A	rs453098	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31691657G>A	ENST00000375819.2	-	0	0				LY6G6C_ENST00000495859.1_5'Flank|C6orf25_ENST00000375809.3_Silent_p.G101G|C6orf25_ENST00000375810.4_Silent_p.G101G|C6orf25_ENST00000480039.1_Silent_p.G101G|C6orf25_ENST00000375805.2_Silent_p.G101G	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						TGAGCGCGGGGGACTCGGGCA	0.677													G|||	677	0.135184	0.3116	0.0764	5008	,	,		14592	0.0407		0.0755	False		,,,				2504	0.0971				p.G101G		Atlas-SNP	.											C6orf25_ENST00000375806,NS,carcinoma,0,4	C6orf25	52	4	0			c.G303A						PASS	.	G	,,,,,	1122,3270		143,836,1217	56.0	68.0	64.0		303,303,303,303,303,303	2.9	0.9	6	dbSNP_80	64	574,8000		21,532,3734	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C6orf25	NM_025260.3,NM_138272.2,NM_138273.2,NM_138274.2,NM_138275.2,NM_138277.2	,,,,,	164,1368,4951	AA,AG,GG		6.6947,25.5464,13.0804	,,,,,	101/238,101/242,101/218,101/194,101/198,101/223	31691657	1696,11270	2196	4287	6483	SO:0001631	upstream_gene_variant	80739	exon2			CGCGGGGGACTCG		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.31691657G>A	Exception_encountered	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_138277	Q5SRS8|Q8IY94	Silent	SNP	ENST00000375819.2	37	CCDS4714.1																																																																																			G|0.882;A|0.118	0.118	strong		0.677	LY6G6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076530.2		
RPTOR	57521	hgsc.bcm.edu	37	17	78935197	78935197	+	Silent	SNP	C	C	T	rs9899178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78935197C>T	ENST00000306801.3	+	31	3971	c.3609C>T	c.(3607-3609)cgC>cgT	p.R1203R	RPTOR_ENST00000544334.2_Silent_p.R1045R|RPTOR_ENST00000575542.1_3'UTR|CTD-2561B21.3_ENST00000571591.1_RNA	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1203					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						CCTACAGCCGCGTCATGACGT	0.672													C|||	1550	0.309505	0.0862	0.3415	5008	,	,		15561	0.5546		0.3479	False		,,,				2504	0.2965				p.R1203R		Atlas-SNP	.											.	RPTOR	122	.	0			c.C3609T						PASS	.	C	,	512,3812		39,434,1689	69.0	41.0	50.0		3135,3609	-3.8	1.0	17	dbSNP_119	50	2659,5691		428,1803,1944	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	467,2237,3633	TT,TC,CC		31.8443,11.8409,25.0197	,	1045/1178,1203/1336	78935197	3171,9503	2162	4175	6337	SO:0001819	synonymous_variant	57521	exon31			CAGCCGCGTCATG		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.3609C>T	17.37:g.78935197C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.703;T|0.297	0.297	strong		0.672	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
SH2D3A	10045	hgsc.bcm.edu	37	19	6763718	6763718	+	Silent	SNP	A	A	G	rs2305805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6763718A>G	ENST00000245908.6	-	2	311	c.42T>C	c.(40-42)ccT>ccC	p.P14P	SH2D3A_ENST00000437152.3_Missense_Mutation_p.L9P|SH2D3A_ENST00000599563.1_5'Flank	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	64	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	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	
KANK3	256949	hgsc.bcm.edu	37	19	8398006	8398006	+	Missense_Mutation	SNP	C	C	T	rs7249069	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8398006C>T	ENST00000593649.1	-	7	1893	c.1828G>A	c.(1828-1830)Gaa>Aaa	p.E610K	KANK3_ENST00000330915.3_Missense_Mutation_p.E610K			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	610										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						GCCAGCAGTTCGGGTCCCAGG	0.682													C|||	268	0.0535144	0.0053	0.072	5008	,	,		9281	0.0317		0.0875	False		,,,				2504	0.093				p.E610K		Atlas-SNP	.											.	KANK3	35	.	0			c.G1828A						PASS	.	C	LYS/GLU	92,4314	72.0+/-110.0	3,86,2114	32.0	29.0	30.0		1828	2.5	0.7	19	dbSNP_116	30	699,7901	168.6+/-220.1	37,625,3638	yes	missense	KANK3	NM_198471.2	56	40,711,5752	TT,TC,CC		8.1279,2.0881,6.0818	probably-damaging	610/822	8398006	791,12215	2203	4300	6503	SO:0001583	missense	256949	exon7			GCAGTTCGGGTCC	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.1828G>A	19.37:g.8398006C>T	ENSP00000470728:p.Glu610Lys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	172	94	0.546512	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	Missense_Mutation	SNP	ENST00000593649.1	37		125	0.05723443223443223	7	0.014227642276422764	37	0.10220994475138122	15	0.026223776223776224	66	0.0870712401055409	C	17.74	3.462825	0.63513	0.020881	0.081279	ENSG00000186994	ENST00000330915;ENST00000381056	T	0.27104	1.69	4.79	2.53	0.30540	.	.	.	.	.	T	0.00440	0.0014	N	0.17764	0.52	0.80722	P	0.0	D	0.63046	0.992	P	0.47744	0.556	T	0.06679	-1.0813	8	0.14252	T	0.57	-14.4279	9.3675	0.38234	0.0:0.7723:0.1446:0.0831	rs7249069	610	Q6NY19-2	.	K	610;154	ENSP00000328923:E610K	ENSP00000328923:E610K	E	-	1	0	KANK3	8304006	0.022000	0.18835	0.725000	0.30721	0.658000	0.38924	1.704000	0.37857	1.187000	0.43000	0.448000	0.29417	GAA	C|0.939;T|0.061	0.061	strong		0.682	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
FZD10	11211	hgsc.bcm.edu	37	12	130648576	130648576	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:130648576G>T	ENST00000229030.4	+	1	1573	c.1089G>T	c.(1087-1089)gcG>gcT	p.A363A	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_Missense_Mutation_p.G331C			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	363					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)	p.A363A(1)		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)		CCATCCCGGCGGTGAAGACCA	0.667																																					p.A363A		Atlas-SNP	.											FZD10,NS,carcinoma,0,1	FZD10	95	1	1	Substitution - coding silent(1)	prostate(1)	c.G1089T						PASS	.						55.0	52.0	53.0					12																	130648576		2203	4300	6503	SO:0001819	synonymous_variant	11211	exon1			CCCGGCGGTGAAG	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.1089G>T	12.37:g.130648576G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_007197		Silent	SNP	ENST00000229030.4	37	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	G	9.518	1.107438	0.20714	.	.	ENSG00000111432	ENST00000539839	.	.	.	5.1	-2.97	0.05530	.	.	.	.	.	T	0.69214	0.3086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73575	-0.3939	5	0.87932	D	0	.	12.6005	0.56494	0.0:0.2627:0.5494:0.1879	.	.	.	.	C	331	.	ENSP00000438460:G331C	G	+	1	0	FZD10	129214529	0.004000	0.15560	0.985000	0.45067	0.997000	0.91878	-1.256000	0.02869	-0.391000	0.07763	0.561000	0.74099	GGT	.	.	none		0.667	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PSG1	5669	hgsc.bcm.edu	37	19	43382402	43382402	+	Silent	SNP	G	G	A	rs17423717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43382402G>A	ENST00000436291.2	-	2	209	c.93C>T	c.(91-93)ccC>ccT	p.P31P	PSG1_ENST00000595124.1_Silent_p.P31P|PSG1_ENST00000244296.2_Silent_p.P31P|PSG1_ENST00000595356.1_Silent_p.P31P|PSG1_ENST00000312439.6_Silent_p.P31P|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000403380.3_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	247	0	0		WXS	Illumina HiSeq	Phase_I	246	8	0.0325203	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		
GLT1D1	144423	hgsc.bcm.edu	37	12	129360498	129360498	+	Silent	SNP	G	G	A	rs482401	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:129360498G>A	ENST00000442111.2	+	2	196	c.108G>A	c.(106-108)aaG>aaA	p.K36K	GLT1D1_ENST00000281703.6_Silent_p.K36K|GLT1D1_ENST00000542193.1_5'UTR|GLT1D1_ENST00000537468.1_Silent_p.K25K			Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	36					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)		GCGTTTTGAAGGATGCCTTTG	0.478													A|||	1704	0.340256	0.4803	0.304	5008	,	,		16962	0.2361		0.2256	False		,,,				2504	0.4018				p.K36K		Atlas-SNP	.											.	GLT1D1	48	.	0			c.G108A						PASS	.	A		1921,2485	625.8+/-394.6	405,1111,687	158.0	159.0	159.0		108	4.4	1.0	12	dbSNP_83	159	1699,6901	738.4+/-407.1	185,1329,2786	no	coding-synonymous	GLT1D1	NM_144669.1		590,2440,3473	AA,AG,GG		19.7558,43.5996,27.8333		36/267	129360498	3620,9386	2203	4300	6503	SO:0001819	synonymous_variant	144423	exon2			TTTGAAGGATGCC		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.108G>A	12.37:g.129360498G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	150	69	0.46	NM_144669	Q86XG8	Silent	SNP	ENST00000442111.2	37																																																																																				G|0.706;A|0.294	0.294	strong		0.478	GLT1D1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000399740.1	NM_144669	
TNPO3	23534	hgsc.bcm.edu	37	7	128607384	128607384	+	Silent	SNP	G	G	A	rs8043	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128607384G>A	ENST00000265388.5	-	21	2804	c.2661C>T	c.(2659-2661)gcC>gcT	p.A887A	TNPO3_ENST00000393245.1_Silent_p.A921A|TNPO3_ENST00000471234.1_Silent_p.A823A|TNPO3_ENST00000471166.1_Silent_p.A921A|TNPO3_ENST00000482320.1_Silent_p.A821A			Q9Y5L0	TNPO3_HUMAN	transportin 3	887					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TCACTGTGACGGCTCCCACGG	0.438													G|||	2388	0.476837	0.5061	0.366	5008	,	,		19398	0.4425		0.5318	False		,,,				2504	0.4949				p.A887A	Pancreas(147;583 2585 39696 52331)	Atlas-SNP	.											.	TNPO3	148	.	0			c.C2661T						PASS	.	G	,	2198,2208	588.0+/-386.8	545,1108,550	170.0	146.0	154.0		2469,2661	-7.2	0.9	7	dbSNP_52	154	4443,4157	588.3+/-392.3	1124,2195,981	no	coding-synonymous,coding-synonymous	TNPO3	NM_001191028.2,NM_012470.3	,	1669,3303,1531	AA,AG,GG		48.3372,49.8865,48.939	,	823/860,887/924	128607384	6641,6365	2203	4300	6503	SO:0001819	synonymous_variant	23534	exon21			TGTGACGGCTCCC	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"""Importins"""	17103	protein-coding gene	gene with protein product	"""importin 12"""	610032	"""limb girdle muscular dystrophy 1F (autosomal dominant)"""	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.2661C>T	7.37:g.128607384G>A		Somatic	227	2	0.00881057		WXS	Illumina HiSeq	Phase_I	205	205	1	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Silent	SNP	ENST00000265388.5	37	CCDS5809.1																																																																																			G|0.504;N|0.000	.	strong		0.438	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470	
OR52N1	79473	hgsc.bcm.edu	37	11	5809990	5809990	+	Silent	SNP	G	G	A	rs11039038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5809990G>A	ENST00000317078.1	-	1	56	c.57C>T	c.(55-57)atC>atT	p.I19I	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(15)|prostate(2)|skin(3)	31		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		CCAAACCAGGGATGCCATTTA	0.428													G|||	486	0.0970447	0.0113	0.0735	5008	,	,		22917	0.2232		0.0746	False		,,,				2504	0.1227				p.I19I		Atlas-SNP	.											.	OR52N1	70	.	0			c.C57T						PASS	.	G		102,4300	77.8+/-116.1	2,98,2101	80.0	73.0	76.0		57	-1.8	1.0	11	dbSNP_120	76	743,7849	173.5+/-223.9	34,675,3587	no	coding-synonymous	OR52N1	NM_001001913.1		36,773,5688	AA,AG,GG		8.6476,2.3171,6.503		19/321	5809990	845,12149	2201	4296	6497	SO:0001819	synonymous_variant	79473	exon1			ACCAGGGATGCCA	AB065538	CCDS31398.1	11p15.4	2012-08-09			ENSG00000181001	ENSG00000181001		"""GPCR / Class A : Olfactory receptors"""	14853	protein-coding gene	gene with protein product							Standard	NM_001001913		Approved		uc010qzo.2	Q8NH53	OTTHUMG00000168800	ENST00000317078.1:c.57C>T	11.37:g.5809990G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_001001913	Q6IFF6	Silent	SNP	ENST00000317078.1	37	CCDS31398.1																																																																																			G|0.916;A|0.084	0.084	strong		0.428	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
AS3MT	57412	hgsc.bcm.edu	37	10	104638723	104638723	+	Missense_Mutation	SNP	T	T	C	rs11191439	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:104638723T>C	ENST00000369880.3	+	9	937	c.860T>C	c.(859-861)aTg>aCg	p.M287T	C10orf32-ASMT_ENST00000299353.6_3'UTR	NM_020682.3	NP_065733.2	Q9HBK9	AS3MT_HUMAN	arsenite methyltransferase	287			M -> T (common polymorphism; frequency in African-Americans 0.108 and Caucasian- Americans 0.100; enzyme activity is 350% of wild-type; dbSNP:rs11191439). {ECO:0000269|PubMed:16407288, ECO:0000269|PubMed:18334919}.		arsonoacetate metabolic process (GO:0018872)|toxin metabolic process (GO:0009404)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	arsenite methyltransferase activity (GO:0030791)|methylarsonite methyltransferase activity (GO:0030792)			large_intestine(1)|lung(6)	7		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)		AAAGAACTAATGTTTGATGCC	0.368													T|||	386	0.0770767	0.0938	0.1009	5008	,	,		20509	0.0218		0.1133	False		,,,				2504	0.0573				p.M287T		Atlas-SNP	.											.	AS3MT	17	.	0			c.T860C	GRCh37	CM081161	AS3MT	M	rs11191439	PASS	.	T	THR/MET	434,3340		27,380,1480	132.0	121.0	124.0		860	2.9	0.1	10	dbSNP_120	124	843,7359		38,767,3296	yes	missense	AS3MT	NM_020682.3	81	65,1147,4776	CC,CT,TT		10.278,11.4997,10.663	benign	287/376	104638723	1277,10699	1887	4101	5988	SO:0001583	missense	57412	exon9			AACTAATGTTTGA	AF226730	CCDS41567.1	10q24.33	2014-05-09	2014-05-09		ENSG00000214435	ENSG00000214435	2.1.1.137		17452	protein-coding gene	gene with protein product		611806	"""arsenic (+3 oxidation state) methyltransferase"""			11790780	Standard	NM_020682		Approved	CYT19	uc001kwk.3	Q9HBK9	OTTHUMG00000018972	ENST00000369880.3:c.860T>C	10.37:g.104638723T>C	ENSP00000358896:p.Met287Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_020682	A6NP79|Q0VDK3|Q0VDK4|Q5PZ02	Missense_Mutation	SNP	ENST00000369880.3	37	CCDS41567.1	179	0.08195970695970696	48	0.0975609756097561	31	0.0856353591160221	14	0.024475524475524476	86	0.11345646437994723	T	0.012	-1.669566	0.00758	0.114997	0.10278	ENSG00000214435	ENST00000369880	T	0.21932	1.98	5.4	2.9	0.33743	.	0.531595	0.19599	N	0.110423	T	0.00144	0.0004	N	0.04508	-0.205	0.24058	P	0.996029	B;B;B	0.13594	0.008;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.0	T	0.31696	-0.9934	9	0.14252	T	0.57	-1.7851	5.5404	0.17036	0.2478:0.0856:0.0:0.6667	rs11191439;rs17725209;rs17884200;rs17885947;rs11191439	287;287;287	Q0VDK3;Q9HBK9;Q0VDK4	.;AS3MT_HUMAN;.	T	287	ENSP00000358896:M287T	ENSP00000358896:M287T	M	+	2	0	AS3MT	104628713	1.000000	0.71417	0.113000	0.21522	0.025000	0.11179	2.096000	0.41738	0.977000	0.38444	-0.441000	0.05720	ATG	T|0.914;C|0.086	0.086	strong		0.368	AS3MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050107.1	NM_020682	
CDH4	1002	hgsc.bcm.edu	37	20	60503350	60503350	+	Missense_Mutation	SNP	A	A	G	rs6142884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:60503350A>G	ENST00000360469.5	+	12	1962	c.1874A>G	c.(1873-1875)aAg>aGg	p.K625R	CDH4_ENST00000543233.1_Missense_Mutation_p.K551R	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	625	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		K -> R (in dbSNP:rs6142884). {ECO:0000269|PubMed:2059658, ECO:0000269|PubMed:7982033}.		adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ATCTGCGAGAAGCCCAACCTG	0.642													A|||	2841	0.567292	0.2504	0.5793	5008	,	,		19647	0.8413		0.5239	False		,,,				2504	0.7495				p.K625R		Atlas-SNP	.											.	CDH4	172	.	0			c.A1874G						PASS	.	A	ARG/LYS	1393,3013	457.3+/-351.6	248,897,1058	114.0	117.0	116.0		1874	-2.0	0.4	20	dbSNP_114	116	4434,4166	583.4+/-391.6	1136,2162,1002	yes	missense	CDH4	NM_001794.2	26	1384,3059,2060	GG,GA,AA		48.4419,31.616,44.8024	benign	625/917	60503350	5827,7179	2203	4300	6503	SO:0001583	missense	1002	exon12			GCGAGAAGCCCAA	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1874A>G	20.37:g.60503350A>G	ENSP00000353656:p.Lys625Arg	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	1220	0.5586080586080586	126	0.25609756097560976	206	0.569060773480663	488	0.8531468531468531	400	0.5277044854881267	A	0.007	-1.998776	0.00435	0.31616	0.515581	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.60548	0.18;0.18	4.56	-2.0	0.07433	Cadherin (1);Cadherin-like (1);	0.263746	0.34338	N	0.004045	T	0.00012	0.0000	N	0.01152	-0.98	0.46336	P	0.0010069999999999801	B	0.02656	0.0	B	0.04013	0.001	T	0.36915	-0.9728	8	.	.	.	.	12.4864	0.55874	0.423:0.0:0.577:0.0	rs6142884;rs8120066;rs58243163;rs6142884	625	P55283	CADH4_HUMAN	R	625;533;551	ENSP00000353656:K625R;ENSP00000443301:K551R	.	K	+	2	0	CDH4	59936745	0.994000	0.37717	0.432000	0.26747	0.022000	0.10575	0.395000	0.20850	-0.818000	0.04329	-0.464000	0.05259	AAG	A|0.508;G|0.492	0.492	strong		0.642	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
NUP98	4928	hgsc.bcm.edu	37	11	3733899	3733899	+	Silent	SNP	C	C	T	rs35803045	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:3733899C>T	ENST00000324932.7	-	20	3057	c.2637G>A	c.(2635-2637)ccG>ccA	p.P879P	NUP98_ENST00000359171.4_Silent_p.P879P|RNU6-1143P_ENST00000516125.1_RNA|NUP98_ENST00000397007.4_Silent_p.P896P|NUP98_ENST00000397004.4_Silent_p.P879P|NUP98_ENST00000355260.3_Silent_p.P879P	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	896	Peptidase S59. {ECO:0000255|PROSITE- ProRule:PRU00765}.				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)		TAGTTTTAGACGGATGCTCCT	0.458			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML								c|||	126	0.0251597	0.0023	0.0476	5008	,	,		16969	0.001		0.0746	False		,,,				2504	0.0143				p.P896P		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.G2688A						PASS	.	C	,,,	72,4330	63.5+/-100.7	0,72,2129	160.0	149.0	153.0		2688,2637,2637,2637	0.4	1.0	11	dbSNP_126	153	632,7964	162.3+/-215.1	33,566,3699	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NUP98	NM_005387.5,NM_016320.4,NM_139131.3,NM_139132.3	,,,	33,638,5828	TT,TC,CC		7.3523,1.6356,5.4162	,,,	896/938,879/1801,879/921,879/1727	3733899	704,12294	2201	4298	6499	SO:0001819	synonymous_variant	4928	exon20			TTTAGACGGATGC	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.2637G>A	11.37:g.3733899C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	37	CCDS7746.1																																																																																			C|0.946;T|0.054	0.054	strong		0.458	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
OR5K2	402135	hgsc.bcm.edu	37	3	98217178	98217178	+	Nonsense_Mutation	SNP	T	T	A	rs55639376	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:98217178T>A	ENST00000427338.1	+	1	731	c.654T>A	c.(652-654)taT>taA	p.Y218*	CLDND1_ENST00000502288.1_Intron	NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TAATATCTTATCTCTATATTC	0.368													T|||	620	0.123802	0.1422	0.1412	5008	,	,		19030	0.0526		0.16	False		,,,				2504	0.1227				p.Y218X		Atlas-SNP	.											.	OR5K2	56	.	0			c.T654A						PASS	.	T	stop/TYR	596,3810	260.7+/-263.8	42,512,1649	132.0	131.0	131.0		654	-2.8	0.0	3	dbSNP_129	131	1581,7017	293.4+/-301.3	156,1269,2874	no	stop-gained	OR5K2	NM_001004737.1		198,1781,4523	AA,AT,TT		18.388,13.527,16.741		218/317	98217178	2177,10827	2203	4299	6502	SO:0001587	stop_gained	402135	exon1			ATCTTATCTCTAT	AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"""GPCR / Class A : Olfactory receptors"""	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.654T>A	3.37:g.98217178T>A	ENSP00000393889:p.Tyr218*	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	233	128	0.549356	NM_001004737	B2RN70|Q6IF47	Nonsense_Mutation	SNP	ENST00000427338.1	37	CCDS33804.1	278	0.12728937728937728	66	0.13414634146341464	62	0.1712707182320442	39	0.06818181818181818	111	0.14643799472295516	T	10.46	1.356721	0.24598	0.13527	0.18388	ENSG00000231861	ENST00000427338	.	.	.	2.82	-2.78	0.05859	.	0.000000	0.38959	N	0.001505	.	.	.	.	.	.	0.39546	P	0.031106999999999996	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.3632	9.4431	0.38681	0.0:0.6126:0.0:0.3874	rs55639376;rs61750892	.	.	.	X	218	.	ENSP00000393889:Y218X	Y	+	3	2	OR5K2	99699868	0.000000	0.05858	0.002000	0.10522	0.203000	0.24098	-2.229000	0.01208	-0.629000	0.05575	0.260000	0.18958	TAT	T|0.847;A|0.153	0.153	strong		0.368	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2		
CD5	921	hgsc.bcm.edu	37	11	60886913	60886913	+	Missense_Mutation	SNP	C	C	T	rs2241002	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60886913C>T	ENST00000347785.3	+	5	837	c.671C>T	c.(670-672)cCa>cTa	p.P224L		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	224	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		P -> L (in dbSNP:rs2241002). {ECO:0000269|PubMed:14702039}.		apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		GCCCAAGACCCAGGGGAGCCA	0.562													C|||	861	0.171925	0.3064	0.1369	5008	,	,		19463	0.0625		0.1491	False		,,,				2504	0.1513				p.P224L		Atlas-SNP	.											.	CD5	52	.	0			c.C671T						PASS	.	C	LEU/PRO	1223,3183	422.1+/-339.6	171,881,1151	59.0	59.0	59.0		671	1.3	0.0	11	dbSNP_98	59	1505,7093	283.2+/-296.0	136,1233,2930	yes	missense	CD5	NM_014207.3	98	307,2114,4081	TT,TC,CC		17.5041,27.7576,20.9782	probably-damaging	224/496	60886913	2728,10276	2203	4299	6502	SO:0001583	missense	921	exon5			AAGACCCAGGGGA	X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"""CD molecules"""	1685	protein-coding gene	gene with protein product		153340	"""CD5 antigen (p56-62)"""	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.671C>T	11.37:g.60886913C>T	ENSP00000342681:p.Pro224Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_014207	A0N0P4|A8K9I3	Missense_Mutation	SNP	ENST00000347785.3	37	CCDS8000.1	348	0.15934065934065933	168	0.34146341463414637	56	0.15469613259668508	32	0.055944055944055944	92	0.12137203166226913	C	10.38	1.333753	0.24167	0.277576	0.175041	ENSG00000110448	ENST00000347785	T	0.29917	1.55	4.3	1.32	0.21799	Speract/scavenger receptor (1);	0.275244	0.25456	N	0.030547	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	2.9999999999752447E-6	B	0.15473	0.013	B	0.08055	0.003	T	0.41052	-0.9530	9	0.46703	T	0.11	-2.5347	6.9155	0.24357	0.0:0.6873:0.0:0.3127	rs2241002;rs2241002	224	P06127	CD5_HUMAN	L	224	ENSP00000342681:P224L	ENSP00000342681:P224L	P	+	2	0	CD5	60643489	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.782000	0.26788	0.294000	0.22547	-0.908000	0.02827	CCA	C|0.799;T|0.201	0.201	strong		0.562	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207	
TTN	7273	hgsc.bcm.edu	37	2	179659912	179659912	+	Missense_Mutation	SNP	G	G	A	rs16866538	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000359218.5_Missense_Mutation_p.R328C|TTN_ENST00000460472.2_Missense_Mutation_p.R328C|TTN_ENST00000342175.6_Missense_Mutation_p.R328C|TTN_ENST00000342992.6_Missense_Mutation_p.R328C|TTN_ENST00000360870.5_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	82	0	0		WXS	Illumina HiSeq	Phase_I	84	42	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		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	
ATXN3L	92552	hgsc.bcm.edu	37	X	13337115	13337115	+	Silent	SNP	C	C	T	rs17322143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:13337115C>T	ENST00000380622.2	-	1	1403	c.939G>A	c.(937-939)agG>agA	p.R313R	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	313					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TTGTTGTTGGCCTTTCGTGTA	0.438													C|||	311	0.0823841	0.0038	0.0778	3775	,	,		14913	0.0427		0.0755	False		,,,				2504	0.136				p.R313R		Atlas-SNP	.											.	ATXN3L	64	.	0			c.G939A						PASS	.	C		56,2571		0,47,9,1012,500	188.0	152.0	163.0		939	-1.6	0.0	X	dbSNP_123	163	598,4900		17,389,175,1510,1491	no	coding-synonymous	ATXN3L	NM_001135995.1		17,436,184,2522,1991	TT,TC,T,CC,C		10.8767,2.1317,8.0492		313/356	13337115	654,7471	1568	3582	5150	SO:0001819	synonymous_variant	92552	exon1			TGTTGGCCTTTCG		CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.939G>A	X.37:g.13337115C>T		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	115	113	0.982609	NM_001135995	B2RNY8	Silent	SNP	ENST00000380622.2	37	CCDS48080.1																																																																																			C|0.905;0|0.032	.	strong		0.438	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995	
SENP7	57337	hgsc.bcm.edu	37	3	101080694	101080694	+	Silent	SNP	T	T	C	rs7616677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:101080694T>C	ENST00000394095.2	-	11	1541	c.1488A>G	c.(1486-1488)gaA>gaG	p.E496E	SENP7_ENST00000394094.2_Silent_p.E431E|SENP7_ENST00000348610.3_Silent_p.E463E|SENP7_ENST00000314261.7_Silent_p.E430E|SENP7_ENST00000358203.3_Silent_p.E332E|SENP7_ENST00000394091.1_Silent_p.E332E	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	496						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						ATGGGCATAATTCAGATGACA	0.284													T|||	2142	0.427716	0.348	0.5533	5008	,	,		15942	0.4901		0.4115	False		,,,				2504	0.3988				p.E496E		Atlas-SNP	.											.	SENP7	170	.	0			c.A1488G						PASS	.	T	,	1400,3002	434.1+/-343.8	229,942,1030	56.0	57.0	57.0		1293,1488	1.8	1.0	3	dbSNP_116	57	3450,5104	498.2+/-374.7	701,2048,1528	no	coding-synonymous,coding-synonymous	SENP7	NM_001077203.1,NM_020654.3	,	930,2990,2558	CC,CT,TT		40.332,31.8037,37.4344	,	431/986,496/1051	101080694	4850,8106	2201	4277	6478	SO:0001819	synonymous_variant	57337	exon11			GCATAATTCAGAT		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.1488A>G	3.37:g.101080694T>C		Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																			T|0.604;C|0.396	0.396	strong		0.284	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201866	32201866	+	RNA	SNP	A	A	G	rs9982755	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	196	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	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	
DCLK1	9201	hgsc.bcm.edu	37	13	36686138	36686138	+	Silent	SNP	T	T	C	rs3748308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:36686138T>C	ENST00000360631.3	-	3	802	c.591A>G	c.(589-591)ccA>ccG	p.P197P	DCLK1_ENST00000255448.4_Silent_p.P197P|DCLK1_ENST00000379892.4_Silent_p.P197P			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	197	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				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)		CAGCTTTCCGTGGCTTCACGC	0.532													C|||	1107	0.221046	0.2436	0.219	5008	,	,		17955	0.1548		0.2137	False		,,,				2504	0.2679				p.P197P		Atlas-SNP	.											.	DCLK1	350	.	0			c.A591G						PASS	.	C		1148,3258	714.5+/-408.4	161,826,1216	177.0	156.0	163.0		591	-8.9	0.8	13	dbSNP_107	163	2152,6448	714.5+/-406.0	269,1614,2417	no	coding-synonymous	DCLK1	NM_004734.4		430,2440,3633	CC,CT,TT		25.0233,26.0554,25.3729		197/730	36686138	3300,9706	2203	4300	6503	SO:0001819	synonymous_variant	9201	exon3			TTTCCGTGGCTTC	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.591A>G	13.37:g.36686138T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																				T|0.765;C|0.235	0.235	strong		0.532	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
OR10H5	284433	hgsc.bcm.edu	37	19	15905661	15905661	+	Missense_Mutation	SNP	C	C	A	rs67455341	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	170	0	0		WXS	Illumina HiSeq	Phase_I	229	107	0.467249	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		
FCGBP	8857	hgsc.bcm.edu	37	19	40363020	40363020	+	Missense_Mutation	SNP	G	G	A	rs741143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40363020G>A	ENST00000221347.6	-	32	15057	c.15050C>T	c.(15049-15051)gCg>gTg	p.A5017V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5017	VWFD 12. {ECO:0000255|PROSITE- ProRule:PRU00580}.		A -> V (in dbSNP:rs741143). {ECO:0000269|PubMed:9182547}.			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)			GGAGCCGGGCGCCCGCCATGC	0.652													G|||	1380	0.275559	0.1868	0.1571	5008	,	,		14056	0.5367		0.1988	False		,,,				2504	0.2894				p.A5017V		Atlas-SNP	.											FCGBP,NS,carcinoma,-1,1	FCGBP	416	1	0			c.C15050T						PASS	.	G	VAL/ALA	854,3550		89,676,1437	15.0	19.0	18.0		15050	-1.2	0.0	19	dbSNP_86	18	1820,6778		205,1410,2684	yes	missense	FCGBP	NM_003890.2	64	294,2086,4121	AA,AG,GG		21.1677,19.3915,20.5661	benign	5017/5406	40363020	2674,10328	2202	4299	6501	SO:0001583	missense	8857	exon32			CCGGGCGCCCGCC	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.15050C>T	19.37:g.40363020G>A	ENSP00000221347:p.Ala5017Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	51	41	0.803922	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	618	0.28296703296703296	88	0.17886178861788618	62	0.1712707182320442	316	0.5524475524475524	152	0.20052770448548812	G	2.898	-0.228255	0.06022	0.193915	0.211677	ENSG00000090920	ENST00000221347	T	0.14022	2.54	4.9	-1.24	0.09435	von Willebrand factor, type D domain (1);	0.202030	0.29638	U	0.011593	T	0.00012	0.0000	N	0.02751	-0.505	0.80722	P	0.0	P	0.38729	0.644	B	0.37304	0.246	T	0.25572	-1.0128	9	0.02654	T	1	.	4.4927	0.11820	0.4089:0.0:0.444:0.1471	rs741143;rs1053685;rs741143	5017	Q9Y6R7	FCGBP_HUMAN	V	5017	ENSP00000221347:A5017V	ENSP00000221347:A5017V	A	-	2	0	FCGBP	45054860	0.000000	0.05858	0.029000	0.17559	0.467000	0.32768	-0.017000	0.12590	0.005000	0.14708	0.313000	0.20887	GCG	G|0.749;A|0.251	0.251	strong		0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ARHGDIB	397	hgsc.bcm.edu	37	12	15095558	15095558	+	Silent	SNP	C	C	G	rs4703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000541644.1_Silent_p.A168A|ARHGDIB_ENST00000539131.1_5'UTR	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	71	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	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	
SLBP	7884	hgsc.bcm.edu	37	4	1701317	1701317	+	Silent	SNP	G	G	A	rs2247341	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:1701317G>A	ENST00000489418.1	-	5	819	c.453C>T	c.(451-453)taC>taT	p.Y151Y	SLBP_ENST00000318386.4_Silent_p.Y158Y|SLBP_ENST00000488267.1_Silent_p.Y116Y|SLBP_ENST00000429429.2_Silent_p.Y112Y	NM_006527.2	NP_006518.1	Q14493	SLBP_HUMAN	stem-loop binding protein	151	RNA-binding.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA transport (GO:0051028)|nuclear cell cycle DNA replication (GO:0033260)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	histone pre-mRNA DCP binding (GO:0071208)|histone pre-mRNA stem-loop binding (GO:0071207)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(2)	5		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.0055)			TATAACGATCGTAGGCAATTG	0.433													G|||	1951	0.389577	0.1263	0.366	5008	,	,		19279	0.6935		0.332	False		,,,				2504	0.5082				p.Y151Y		Atlas-SNP	.											.	SLBP	12	.	0			c.C453T						PASS	.	G		795,3611	321.3+/-297.0	89,617,1497	170.0	157.0	161.0		453	-6.9	1.0	4	dbSNP_100	161	2953,5647	459.5+/-364.9	512,1929,1859	yes	coding-synonymous	SLBP	NM_006527.2		601,2546,3356	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.3372,18.0436,28.8175		151/271	1701317	3748,9258	2203	4300	6503	SO:0001819	synonymous_variant	7884	exon5			ACGATCGTAGGCA	Z71188	CCDS3350.1	4p16.3	2008-02-11	2008-02-11		ENSG00000163950	ENSG00000163950			10904	protein-coding gene	gene with protein product	"""histone binding protein"""	602422	"""stem-loop (histone) binding protein"""			9049306, 1338771	Standard	NM_006527		Approved	HBP	uc003gdi.1	Q14493	OTTHUMG00000089349	ENST00000489418.1:c.453C>T	4.37:g.1701317G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	250	129	0.516	NM_006527	B3KRJ5	Silent	SNP	ENST00000489418.1	37	CCDS3350.1	850|850	0.3891941391941392|0.3891941391941392	63|63	0.12804878048780488|0.12804878048780488	132|132	0.36464088397790057|0.36464088397790057	392|392	0.6853146853146853|0.6853146853146853	263|263	0.3469656992084433|0.3469656992084433	G|G	10.10|10.10	1.257050|1.257050	0.22965|0.22965	0.180436|0.180436	0.343372|0.343372	ENSG00000163950|ENSG00000163950	ENST00000480936|ENST00000483348	.|.	.|.	.|.	5.19|5.19	-6.91|-6.91	0.01649|0.01649	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.10019	.|-1.0648	.|3	.|.	.|.	.|.	-11.6628|-11.6628	15.2628|15.2628	0.73637|0.73637	0.9153:0.0:0.0847:0.0|0.9153:0.0:0.0847:0.0	rs2247341;rs56570242;rs60784822;rs2247341|rs2247341;rs56570242;rs60784822;rs2247341	.|.	.|.	.|.	X|M	159|106	.|.	.|.	R|T	-|-	1|2	2|0	SLBP|SLBP	1671115|1671115	0.401000|0.401000	0.25303|0.25303	0.964000|0.964000	0.40570|0.40570	0.992000|0.992000	0.81027|0.81027	-0.109000|-0.109000	0.10840|0.10840	-0.982000|-0.982000	0.03515|0.03515	-0.322000|-0.322000	0.08575|0.08575	CGA|ACG	G|0.647;T|0.001	.	strong		0.433	SLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203176.1	NM_006527	
KCTD8	386617	hgsc.bcm.edu	37	4	44176960	44176960	+	Silent	SNP	T	T	C	rs13143747	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:44176960T>C	ENST00000360029.3	-	2	1552	c.1269A>G	c.(1267-1269)acA>acG	p.T423T		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	423					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)				central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						TGGACAGATTTGTTTCCCGGG	0.403										HNSCC(17;0.042)			T|||	198	0.0395367	0.0045	0.0389	5008	,	,		19523	0.0		0.0984	False		,,,				2504	0.0675				p.T423T		Atlas-SNP	.											KCTD8,NS,carcinoma,-1,1	KCTD8	96	1	0			c.A1269G						PASS	.	T		92,4314	74.7+/-112.8	1,90,2112	209.0	219.0	215.0		1269	-4.7	1.0	4	dbSNP_121	215	970,7630	211.0+/-251.7	59,852,3389	no	coding-synonymous	KCTD8	NM_198353.2		60,942,5501	CC,CT,TT		11.2791,2.0881,8.1655		423/474	44176960	1062,11944	2203	4300	6503	SO:0001819	synonymous_variant	386617	exon2			CAGATTTGTTTCC	AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 8"""				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.1269A>G	4.37:g.44176960T>C		Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	246	127	0.51626	NM_198353	A2RU39	Silent	SNP	ENST00000360029.3	37	CCDS3467.1																																																																																			T|0.929;C|0.071	0.071	strong		0.403	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1		
OR4A47	403253	hgsc.bcm.edu	37	11	48511050	48511050	+	Missense_Mutation	SNP	T	T	C	rs76991989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:48511050T>C	ENST00000446524.1	+	1	782	c.706T>C	c.(706-708)Tca>Cca	p.S236P		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	236						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						AAAAGCCCTCTCAACCTGCAG	0.428													T|||	41	0.0081869	0.0015	0.0086	5008	,	,		18021	0.0		0.0268	False		,,,				2504	0.0061				p.S236P		Atlas-SNP	.											OR4A47,bladder,carcinoma,-1,1	OR4A47	72	1	0			c.T706C						PASS	.	T	PRO/SER	23,4379		0,23,2178	148.0	144.0	145.0		706	2.4	0.1	11	dbSNP_131	145	217,8379		3,211,4084	yes	missense	OR4A47	NM_001005512.2	74	3,234,6262	CC,CT,TT		2.5244,0.5225,1.8464	benign	236/310	48511050	240,12758	2201	4298	6499	SO:0001583	missense	403253	exon1			GCCCTCTCAACCT	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.706T>C	11.37:g.48511050T>C	ENSP00000412752:p.Ser236Pro	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	N	11.71	1.719811	0.30503	0.005225	0.025244	ENSG00000237388	ENST00000446524	T	0.00309	8.16	4.59	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.553031	0.16377	N	0.217096	T	0.00300	0.0009	H	0.98407	4.225	0.09310	N	0.999997	D	0.53462	0.96	P	0.54965	0.765	T	0.40098	-0.9581	10	0.87932	D	0	.	5.4392	0.16498	0.0:0.2998:0.0:0.7002	.	236	Q6IF82	O4A47_HUMAN	P	236	ENSP00000412752:S236P	ENSP00000412752:S236P	S	+	1	0	OR4A47	48467626	0.000000	0.05858	0.139000	0.22197	0.222000	0.24845	0.081000	0.14823	0.225000	0.20959	0.172000	0.16884	TCA	T|0.981;C|0.019	0.019	strong		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512	
C5orf60	285679	hgsc.bcm.edu	37	5	179071836	179071836	+	Silent	SNP	C	C	T	rs4990391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:179071836C>T	ENST00000448248.2	-	1	211	c.186G>A	c.(184-186)ccG>ccA	p.P62P	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	62						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GCACTGAGGACGGCTCCCTGG	0.532													-|||	717	0.143171	0.171	0.0951	5008	,	,		22464	0.0546		0.2256	False		,,,				2504	0.1462				p.P62P		Atlas-SNP	.											C5orf60,colon,carcinoma,0,1	C5orf60	24	1	0			c.G186A						scavenged	.						64.0	60.0	62.0					5																	179071836		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			TGAGGACGGCTCC	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.186G>A	5.37:g.179071836C>T		Somatic	110	3	0.0272727		WXS	Illumina HiSeq	Phase_I	183	52	0.284153	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			C|0.848;T|0.152	0.152	strong		0.532	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
MUC16	94025	hgsc.bcm.edu	37	19	9072296	9072296	+	Silent	SNP	G	G	T	rs7254970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9072296G>T	ENST00000397910.4	-	3	15353	c.15150C>A	c.(15148-15150)acC>acA	p.T5050T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5052	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGAAGGTGTGGTCATTGCAG	0.468													G|||	844	0.16853	0.171	0.1844	5008	,	,		20301	0.0089		0.2634	False		,,,				2504	0.2209				p.T5050T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C15150A						PASS	.			664,3246		60,544,1351	91.0	86.0	88.0		15150	0.5	0.0	19	dbSNP_116	88	2428,5862		370,1688,2087	no	coding-synonymous	MUC16	NM_024690.2		430,2232,3438	TT,TG,GG		29.2883,16.9821,25.3443		5050/14508	9072296	3092,9108	1955	4145	6100	SO:0001819	synonymous_variant	94025	exon3			AGGTGTGGTCATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15150C>A	19.37:g.9072296G>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.815;T|0.185	0.185	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LRRC45	201255	hgsc.bcm.edu	37	17	79986156	79986156	+	Missense_Mutation	SNP	C	C	T	rs72861736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79986156C>T	ENST00000306688.3	+	10	1436	c.1094C>T	c.(1093-1095)gCc>gTc	p.A365V		NM_144999.2	NP_659436.1	Q96CN5	LRC45_HUMAN	leucine rich repeat containing 45	365						centrosome (GO:0005813)				lung(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	5	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)			TTGTCTGCTGCCAATGAAAAG	0.627													C|||	188	0.0375399	0.0356	0.0418	5008	,	,		17173	0.003		0.0855	False		,,,				2504	0.0235				p.A365V		Atlas-SNP	.											LRRC45,NS,carcinoma,0,1	LRRC45	22	1	0			c.C1094T						PASS	.	C	VAL/ALA	242,4100		11,220,1940	30.0	28.0	29.0		1094	3.5	0.6	17	dbSNP_130	29	868,7714		42,784,3465	yes	missense	LRRC45	NM_144999.2	64	53,1004,5405	TT,TC,CC		10.1142,5.5735,8.5887	benign	365/671	79986156	1110,11814	2171	4291	6462	SO:0001583	missense	201255	exon10			CTGCTGCCAATGA	BC014109	CCDS11797.1	17q25.3	2005-08-09				ENSG00000169683			28302	protein-coding gene	gene with protein product						12477932	Standard	NM_144999		Approved	MGC20806	uc002kde.3	Q96CN5		ENST00000306688.3:c.1094C>T	17.37:g.79986156C>T	ENSP00000306760:p.Ala365Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	59	0.440298	NM_144999		Missense_Mutation	SNP	ENST00000306688.3	37	CCDS11797.1	102	0.046703296703296704	13	0.026422764227642278	19	0.052486187845303865	0	0.0	70	0.09234828496042216	C	12.19	1.863901	0.32884	0.055735	0.101142	ENSG00000169683	ENST00000306688	T	0.45668	0.89	4.45	3.47	0.39725	.	0.633338	0.15766	N	0.245678	T	0.00936	0.0031	L	0.56769	1.78	0.80722	P	0.0	B	0.31680	0.335	B	0.22386	0.039	T	0.07868	-1.0750	8	.	.	.	-3.2521	8.7456	0.34585	0.1692:0.6672:0.1636:0.0	.	365	Q96CN5	LRC45_HUMAN	V	365	ENSP00000306760:A365V	.	A	+	2	0	LRRC45	77579445	0.000000	0.05858	0.604000	0.28916	0.853000	0.48598	0.731000	0.26058	0.836000	0.34901	0.561000	0.74099	GCC	C|0.935;T|0.065	0.065	strong		0.627	LRRC45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442058.1	NM_144999	
TCOF1	6949	hgsc.bcm.edu	37	5	149772280	149772280	+	Missense_Mutation	SNP	C	C	G	rs1136103	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149772280C>G	ENST00000504761.2	+	22	3527	c.3527C>G	c.(3526-3528)cCc>cGc	p.P1176R	TCOF1_ENST00000513346.1_Missense_Mutation_p.P1176R|TCOF1_ENST00000323668.7_Missense_Mutation_p.P1099R|TCOF1_ENST00000445265.2_Missense_Mutation_p.P1100R|TCOF1_ENST00000439160.2_Missense_Mutation_p.P1139R|TCOF1_ENST00000377797.3_Missense_Mutation_p.P1177R|TCOF1_ENST00000451292.1_Missense_Mutation_p.P1213R			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1176			P -> R (in dbSNP:rs1136103).		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)			GGTCCCACCCCCTCCAGGACA	0.642													C|||	408	0.0814696	0.0076	0.1282	5008	,	,		17532	0.001		0.2396	False		,,,				2504	0.0685				p.P1176R		Atlas-SNP	.											.	TCOF1	154	.	0			c.C3527G						PASS	.	C	ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO	201,4205	124.9+/-162.1	5,191,2007	51.0	47.0	48.0		3296,3527,3416,3299,3413	2.6	0.0	5	dbSNP_86	48	2018,6582	347.8+/-326.7	215,1588,2497	yes	missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	103,103,103,103,103	220,1779,4504	GG,GC,CC		23.4651,4.562,17.0614	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1099/1412,1176/1489,1139/1452,1100/1413,1138/1451	149772280	2219,10787	2203	4300	6503	SO:0001583	missense	6949	exon22			CCACCCCCTCCAG		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.3527C>G	5.37:g.149772280C>G	ENSP00000421655:p.Pro1176Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	236	0.10805860805860806	7	0.014227642276422764	42	0.11602209944751381	0	0.0	187	0.24670184696569922	C	17.94	3.512605	0.64522	0.04562	0.234651	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.28	2.57	0.30868	.	0.629309	0.13283	N	0.399585	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D;P;D;D;P	0.69078	0.971;0.95;0.971;0.997;0.95	P;P;P;P;P	0.60886	0.839;0.776;0.839;0.88;0.776	T	0.07986	-1.0744	9	0.56958	D	0.05	-0.2445	7.322	0.26533	0.0:0.7321:0.0:0.2679	rs1136103;rs3199234;rs17420522;rs52811168	1139;1099;1138;1176;1100	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	R	1213;1177;1100;1099;1139;1138;1176;1176	ENSP00000400939:P1213R;ENSP00000367028:P1177R;ENSP00000409944:P1100R;ENSP00000325223:P1099R;ENSP00000406888:P1139R;ENSP00000390717:P1138R;ENSP00000421655:P1176R;ENSP00000427484:P1176R	ENSP00000325223:P1099R	P	+	2	0	TCOF1	149752473	0.001000	0.12720	0.000000	0.03702	0.647000	0.38526	0.723000	0.25939	0.246000	0.21394	0.561000	0.74099	CCC	C|0.855;G|0.145	0.145	strong		0.642	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
ZFP28	140612	hgsc.bcm.edu	37	19	57050515	57050515	+	Missense_Mutation	SNP	C	C	G	rs7258088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57050515C>G	ENST00000301318.3	+	1	199	c.128C>G	c.(127-129)gCc>gGc	p.A43G	AC005498.3_ENST00000593218.1_lincRNA|ZFP28_ENST00000594386.1_3'UTR|ZFP28_ENST00000591844.1_Missense_Mutation_p.A43G	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	43					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)		GCCCTCCCTGCCCGGGGAAGG	0.721													C|||	2108	0.420927	0.4607	0.3573	5008	,	,		8452	0.625		0.2654	False		,,,				2504	0.362				p.A43G	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											ZFP28,NS,carcinoma,0,3	ZFP28	99	3	0			c.C128G						PASS	.	C	GLY/ALA	1471,2575		277,917,829	6.0	7.0	7.0		128	-1.5	0.0	19	dbSNP_116	7	1824,6286		227,1370,2458	no	missense	ZFP28	NM_020828.1	60	504,2287,3287	GG,GC,CC		22.4908,36.3569,27.106	benign	43/869	57050515	3295,8861	2023	4055	6078	SO:0001583	missense	140612	exon1			TCCCTGCCCGGGG		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.128C>G	19.37:g.57050515C>G	ENSP00000301318:p.Ala43Gly	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	893	0.4088827838827839	214	0.4349593495934959	126	0.34806629834254144	358	0.6258741258741258	195	0.25725593667546176	C	11.01	1.514162	0.27123	0.363569	0.224908	ENSG00000196867	ENST00000301318	T	0.05649	3.41	2.51	-1.5	0.08691	.	0.611150	0.12404	N	0.471850	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.17852	0.0;0.024	B;B	0.12837	0.002;0.008	T	0.19224	-1.0312	9	0.17369	T	0.5	.	5.6932	0.17841	0.209:0.3812:0.4099:0.0	rs7258088	43;43	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	G	43	ENSP00000301318:A43G	ENSP00000301318:A43G	A	+	2	0	ZFP28	61742327	0.002000	0.14202	0.013000	0.15412	0.663000	0.39108	0.096000	0.15147	-0.198000	0.10333	-0.502000	0.04539	GCC	C|0.610;G|0.390	0.390	strong		0.721	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
CDHR1	92211	hgsc.bcm.edu	37	10	85974236	85974236	+	Silent	SNP	T	T	C	rs3814213	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85974236T>C	ENST00000372117.3	+	17	2542	c.2439T>C	c.(2437-2439)acT>acC	p.T813T	CDHR1_ENST00000332904.3_Intron|CDHR1_ENST00000440770.2_Silent_p.T517T	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	813	Pro-rich.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CCGTGCCTACTGTCTCTGGCT	0.622													t|||	2873	0.573682	0.829	0.5692	5008	,	,		12883	0.4107		0.5189	False		,,,				2504	0.456				p.T813T		Atlas-SNP	.											.	CDHR1	122	.	0			c.T2439C						PASS	.	A	,	3375,1031	725.8+/-409.7	1300,775,128	76.0	85.0	82.0		,2439	-11.2	0.0	10	dbSNP_107	82	4492,4108	590.3+/-392.6	1180,2132,988	no	intron,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	2480,2907,1116	CC,CT,TT		47.7674,23.3999,39.5125	,	,813/860	85974236	7867,5139	2203	4300	6503	SO:0001819	synonymous_variant	92211	exon17			GCCTACTGTCTCT	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.2439T>C	10.37:g.85974236T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	17	0.34	NM_033100	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			T|0.409;C|0.591	0.591	strong		0.622	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
COL6A1	1291	hgsc.bcm.edu	37	21	47423509	47423509	+	Missense_Mutation	SNP	C	C	T	rs71336107|rs13051496	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47423509C>T	ENST00000361866.3	+	35	2783	c.2669C>T	c.(2668-2670)tCg>tTg	p.S890L	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	890	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		S -> L (in dbSNP:rs13051496). {ECO:0000269|PubMed:15689448, ECO:0000269|PubMed:16130093}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GAGCGGGCGTCGCTGCAGTTC	0.677													C|||	545	0.108826	0.0424	0.1196	5008	,	,		14971	0.0615		0.2604	False		,,,				2504	0.0838				p.S890L		Atlas-SNP	.											COL6A1,NS,carcinoma,0,1	COL6A1	101	1	0			c.C2669T						PASS	.	C	LEU/SER	246,4160		9,228,1966	29.0	30.0	29.0		2669	4.0	0.0	21	dbSNP_121	29	1859,6739		209,1441,2649	yes	missense	COL6A1	NM_001848.2	145	218,1669,4615	TT,TC,CC		21.6213,5.5833,16.1873	possibly-damaging	890/1029	47423509	2105,10899	2203	4299	6502	SO:0001583	missense	1291	exon35			GGGCGTCGCTGCA	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2669C>T	21.37:g.47423509C>T	ENSP00000355180:p.Ser890Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	95	59	0.621053	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	326	0.14926739926739926	32	0.06504065040650407	49	0.13535911602209943	41	0.07167832167832168	204	0.2691292875989446	C	10.83	1.462082	0.26248	0.055833	0.216213	ENSG00000142156	ENST00000361866	T	0.79352	-1.26	4.94	4.03	0.46877	von Willebrand factor, type A (3);	0.392531	0.22699	N	0.056720	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.25441	0.126	B	0.22753	0.041	T	0.05068	-1.0908	9	0.30854	T	0.27	-11.2045	11.892	0.52635	0.4862:0.5138:0.0:0.0	rs13051496	890	P12109	CO6A1_HUMAN	L	890	ENSP00000355180:S890L	ENSP00000355180:S890L	S	+	2	0	COL6A1	46247937	0.996000	0.38824	0.003000	0.11579	0.134000	0.20937	3.945000	0.56637	1.035000	0.39972	0.530000	0.56133	TCG	C|0.849;T|0.151	0.151	strong		0.677	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
RAPGEF2	9693	hgsc.bcm.edu	37	4	160277276	160277276	+	Silent	SNP	C	C	T	rs1135004	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:160277276C>T	ENST00000264431.4	+	23	4859	c.4440C>T	c.(4438-4440)ccC>ccT	p.P1480P		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1480					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)			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)		GCCTCGCCCCCTATCAGTCCC	0.527													C|||	1753	0.35004	0.2352	0.5519	5008	,	,		15707	0.0982		0.5497	False		,,,				2504	0.4162				p.P1480P		Atlas-SNP	.											.	RAPGEF2	171	.	0			c.C4440T						PASS	.	C		1050,2994		127,796,1099	38.0	40.0	39.0		4440	1.9	0.1	4	dbSNP_86	39	4833,3503		1415,2003,750	no	coding-synonymous	RAPGEF2	NM_014247.2		1542,2799,1849	TT,TC,CC		42.0226,25.9644,47.5202		1480/1500	160277276	5883,6497	2022	4168	6190	SO:0001819	synonymous_variant	9693	exon23			CGCCCCCTATCAG	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.4440C>T	4.37:g.160277276C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_014247	D3DP27	Silent	SNP	ENST00000264431.4	37	CCDS43277.1																																																																																			C|0.575;T|0.425	0.425	strong		0.527	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999753	45999753	+	Missense_Mutation	SNP	C	C	G	rs464424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45999753C>G	ENST00000400372.1	-	1	728	c.703G>C	c.(703-705)Gtg>Ctg	p.V235L	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	235	22 X 5 AA repeats of C-C-X(3).		V -> L (in dbSNP:rs464424). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GAGATGGGCACGCAGCAGGCG	0.711													.|||	589	0.117612	0.0923	0.0634	5008	,	,		18363	0.2024		0.0626	False		,,,				2504	0.1595				p.V235L		Atlas-SNP	.											.	KRTAP10-5	43	.	0			c.G703C						PASS	.	C	,LEU/VAL	417,3989	194.7+/-219.5	20,377,1806	51.0	61.0	58.0		,703	1.7	0.0	21	dbSNP_80	58	430,8168	129.5+/-187.6	15,400,3884	no	intron,missense	TSPEAR,KRTAP10-5	NM_144991.2,NM_198694.2	,32	35,777,5690	GG,GC,CC		5.0012,9.4644,6.5134	,probably-damaging	,235/272	45999753	847,12157	2203	4299	6502	SO:0001583	missense	386680	exon1			TGGGCACGCAGCA	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.703G>C	21.37:g.45999753C>G	ENSP00000383223:p.Val235Leu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	226	0.10347985347985347	40	0.08130081300813008	24	0.06629834254143646	122	0.21328671328671328	40	0.052770448548812667	c	9.845	1.192015	0.21954	0.094644	0.050012	ENSG00000241123	ENST00000400372	T	0.00753	5.74	3.59	1.68	0.24146	.	.	.	.	.	T	0.00012	0.0000	M	0.80616	2.505	0.80722	P	0.0	D	0.56287	0.975	D	0.63597	0.916	T	0.44892	-0.9298	8	0.66056	D	0.02	.	6.6908	0.23169	0.0:0.7117:0.1807:0.1076	rs464424	235	P60370	KR105_HUMAN	L	235	ENSP00000383223:V235L	ENSP00000383223:V235L	V	-	1	0	KRTAP10-5	44824181	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-0.031000	0.12287	0.290000	0.22444	-0.384000	0.06662	GTG	C|0.913;G|0.087	0.087	strong		0.711	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
OR2V2	285659	hgsc.bcm.edu	37	5	180582604	180582604	+	Missense_Mutation	SNP	A	A	G	rs2546423	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180582604A>G	ENST00000328275.1	+	1	662	c.662A>G	c.(661-663)cAc>cGc	p.H221R		NM_206880.1	NP_996763.1	Q96R30	OR2V2_HUMAN	olfactory receptor, family 2, subfamily V, member 2	221			H -> R (in dbSNP:rs2546423). {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)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(89;8.26e-06)|all_epithelial(37;1.02e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.0103)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0652)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCTATGCTCACATTCTAGGG	0.532													N|||	3289	0.656749	0.8086	0.7507	5008	,	,		23223	0.5665		0.5417	False		,,,				2504	0.5961				p.H221R		Atlas-SNP	.											.	OR2V2	56	.	0			c.A662G						PASS	.	G	ARG/HIS	3431,975		1336,759,108	227.0	219.0	222.0		662	0.5	0.0	5	dbSNP_100	222	4588,4012		1215,2158,927	yes	missense	OR2V2	NM_206880.1	29	2551,2917,1035	GG,GA,AA		46.6512,22.1289,38.3438	benign	221/316	180582604	8019,4987	2203	4300	6503	SO:0001583	missense	285659	exon1			ATGCTCACATTCT	AL161615	CCDS4461.1	5q35.3	2012-08-09			ENSG00000182613	ENSG00000182613		"""GPCR / Class A : Olfactory receptors"""	15341	protein-coding gene	gene with protein product				OR2V3			Standard	NM_206880		Approved	OST713	uc011dhj.2	Q96R30	OTTHUMG00000130933	ENST00000328275.1:c.662A>G	5.37:g.180582604A>G	ENSP00000332185:p.His221Arg	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	320	152	0.475	NM_206880	Q6IFL6|Q8NGV1	Missense_Mutation	SNP	ENST00000328275.1	37	CCDS4461.1	1393	0.6378205128205128	395	0.8028455284552846	253	0.6988950276243094	342	0.5979020979020979	403	0.5316622691292876	.	0.001	-3.354548	0.00016	0.778711	0.533488	ENSG00000182613	ENST00000328275	T	0.00063	8.78	3.48	0.494	0.16884	GPCR, rhodopsin-like superfamily (1);	0.683829	0.12135	N	0.496393	T	0.00012	0.0000	N	0.05467	-0.045	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.43278	-0.9401	9	0.07325	T	0.83	.	7.5328	0.27693	0.4699:0.0:0.5301:0.0	rs2546423;rs17617281;rs52805044;rs60483447;rs2546423	221	Q96R30	OR2V2_HUMAN	R	221	ENSP00000332185:H221R	ENSP00000332185:H221R	H	+	2	0	OR2V2	180515210	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-3.065000	0.00621	-0.030000	0.13804	-0.684000	0.03749	CAC	A|0.376;G|0.624	0.624	strong		0.532	OR2V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253529.1		
ALPK2	115701	hgsc.bcm.edu	37	18	56246682	56246682	+	Silent	SNP	T	T	G	rs114432784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:56246682T>G	ENST00000361673.3	-	4	1539	c.1326A>C	c.(1324-1326)tcA>tcC	p.S442S	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	442						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						GTTCTGTCACTGAAGACGTTC	0.517											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	168	0.0335463	0.0242	0.0173	5008	,	,		19742	0.0923		0.0109	False		,,,				2504	0.0204				p.S442S		Atlas-SNP	.											.	ALPK2	487	.	0			c.A1326C						PASS	.	T		85,4321	72.5+/-110.5	0,85,2118	114.0	114.0	114.0		1326	-4.3	0.0	18	dbSNP_132	114	64,8536	39.3+/-95.6	0,64,4236	no	coding-synonymous	ALPK2	NM_052947.3		0,149,6354	GG,GT,TT		0.7442,1.9292,1.1456		442/2171	56246682	149,12857	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon4			TGTCACTGAAGAC	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.1326A>C	18.37:g.56246682T>G		Somatic	162	0	0	1014	WXS	Illumina HiSeq	Phase_I	135	73	0.540741	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			T|0.981;G|0.019	0.019	strong		0.517	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
MED27	9442	hgsc.bcm.edu	37	9	134955076	134955076	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134955076A>G	ENST00000292035.5	-	1	219	c.156T>C	c.(154-156)ttT>ttC	p.F52F	MED27_ENST00000474263.1_Silent_p.F52F|MED27_ENST00000357028.2_Silent_p.F52F|RP11-32B11.2_ENST00000444872.2_RNA	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	52					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.F52F(3)		breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	18		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		AGTGCGCAATAAAGGCCTTCT	0.647																																					p.F52F	Colon(41;784 923 6932 42329 52483)	Atlas-SNP	.											MED27,NS,carcinoma,0,3	MED27	37	3	3	Substitution - coding silent(3)	endometrium(2)|kidney(1)	c.T156C						scavenged	.						79.0	81.0	80.0					9																	134955076		2203	4300	6503	SO:0001819	synonymous_variant	9442	exon1			CGCAATAAAGGCC	AF104252	CCDS6945.1, CCDS59153.1, CCDS69689.1	9q34.13	2008-02-05	2007-07-30	2007-07-30	ENSG00000160563	ENSG00000160563			2377	protein-coding gene	gene with protein product		605044	"""cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa"""	CRSP8		9989412	Standard	NM_004269		Approved	TRAP37, CRSP34	uc004cbe.2	Q6P2C8	OTTHUMG00000020833	ENST00000292035.5:c.156T>C	9.37:g.134955076A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	160	7	0.04375	NM_001253881	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Silent	SNP	ENST00000292035.5	37	CCDS6945.1																																																																																			.	.	none		0.647	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269	
DNMBP	23268	hgsc.bcm.edu	37	10	101639877	101639877	+	Missense_Mutation	SNP	A	A	C	rs11190305	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:101639877A>C	ENST00000324109.4	-	16	4330	c.4239T>G	c.(4237-4239)tgT>tgG	p.C1413W	DNMBP_ENST00000543621.1_Missense_Mutation_p.C659W|DNMBP_ENST00000540316.1_Missense_Mutation_p.C349W|DNMBP_ENST00000342239.3_Missense_Mutation_p.C1437W	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1413	Ser-rich.		C -> W (in dbSNP:rs11190305). {ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TTCCTTGGTCACATTCTTTTG	0.542													A|||	1388	0.277157	0.1437	0.3329	5008	,	,		19778	0.244		0.3917	False		,,,				2504	0.3344				p.C1413W		Atlas-SNP	.											.	DNMBP	173	.	0			c.T4239G						PASS	.		TRP/CYS	827,3579	328.5+/-300.6	82,663,1458	194.0	191.0	192.0		4239	0.6	0.0	10	dbSNP_120	192	3271,5329	490.7+/-372.9	638,1995,1667	yes	missense	DNMBP	NM_015221.2	215	720,2658,3125	CC,CA,AA		38.0349,18.7699,31.5085	benign	1413/1578	101639877	4098,8908	2203	4300	6503	SO:0001583	missense	23268	exon16			TTGGTCACATTCT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.4239T>G	10.37:g.101639877A>C	ENSP00000315659:p.Cys1413Trp	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	245	243	0.991837	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	630	0.28846153846153844	55	0.11178861788617886	133	0.3674033149171271	150	0.26223776223776224	292	0.38522427440633245	A	9.817	1.184720	0.21870	0.187699	0.380349	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000540316	T;T;T;T	0.34275	2.81;2.76;2.42;1.37	5.77	0.604	0.17547	.	2.318410	0.01492	N	0.017126	T	0.00012	0.0000	N	0.14661	0.345	0.44104	P	0.003125999999999962	B;P;B	0.37573	0.328;0.6;0.102	B;B;B	0.41202	0.094;0.35;0.078	T	0.28618	-1.0038	9	0.37606	T	0.19	11.0357	1.0338	0.01543	0.3826:0.2917:0.1845:0.1411	rs11190305;rs17495998;rs17846312;rs17859342;rs52793133;rs56919867;rs11190305	1413;659;1437	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	W	1437;1413;659;659;349	ENSP00000344914:C1437W;ENSP00000315659:C1413W;ENSP00000443657:C659W;ENSP00000443573:C349W	ENSP00000315659:C1413W	C	-	3	2	DNMBP	101629867	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	-0.874000	0.04210	-0.132000	0.11557	-0.366000	0.07423	TGT	A|0.708;C|0.292	0.292	strong		0.542	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
GABBR2	9568	hgsc.bcm.edu	37	9	101340316	101340316	+	Silent	SNP	T	T	C	rs3750344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	87	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	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		
SLX4IP	128710	hgsc.bcm.edu	37	20	10603750	10603750	+	Missense_Mutation	SNP	G	G	A	rs6077853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:10603750G>A	ENST00000334534.5	+	8	1130	c.950G>A	c.(949-951)cGa>cAa	p.R317Q		NM_001009608.1	NP_001009608.1	Q5VYV7	SLX4I_HUMAN	SLX4 interacting protein	317			R -> Q (in dbSNP:rs6077853).														GGAAGTGATCGATTAGTCCCG	0.463													G|||	328	0.0654952	0.0121	0.1066	5008	,	,		19050	0.004		0.1322	False		,,,				2504	0.1033				p.R317Q		Atlas-SNP	.											C20orf94,NS,carcinoma,+1,1	.	.	1	0			c.G950A						scavenged	.	G	GLN/ARG	126,4280	91.6+/-130.3	3,120,2080	86.0	97.0	93.0		950	-4.0	0.9	20	dbSNP_114	93	1361,7239	266.3+/-286.6	98,1165,3037	yes	missense	C20orf94	NM_001009608.1	43	101,1285,5117	AA,AG,GG		15.8256,2.8597,11.4332	benign	317/409	10603750	1487,11519	2203	4300	6503	SO:0001583	missense	128710	exon8			GTGATCGATTAGT	AL035456	CCDS33439.1	20p12	2012-10-30	2012-10-30	2012-10-30	ENSG00000149346	ENSG00000149346			16225	protein-coding gene	gene with protein product		615958	"""chromosome 20 open reading frame 94"""	C20orf94		19596235	Standard	XM_005260664		Approved	dJ1099D15.3	uc010zre.2	Q5VYV7	OTTHUMG00000031873	ENST00000334534.5:c.950G>A	20.37:g.10603750G>A	ENSP00000335557:p.Arg317Gln	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_001009608	Q05CG2|Q05CT9	Missense_Mutation	SNP	ENST00000334534.5	37	CCDS33439.1	149	0.06822344322344322	8	0.016260162601626018	38	0.10497237569060773	2	0.0034965034965034965	101	0.13324538258575197	G	13.21	2.169666	0.38315	0.028597	0.158256	ENSG00000149346	ENST00000334534	T	0.42513	0.97	6.16	-3.95	0.04118	.	1.653010	0.02928	N	0.138845	T	0.00073	0.0002	N	0.08118	0	0.49915	P	1.6300000000002424E-4	B	0.13594	0.008	B	0.06405	0.002	T	0.09662	-1.0664	9	0.21540	T	0.41	3.431	10.517	0.44896	0.665:0.1796:0.1554:0.0	rs6077853;rs17456471;rs52827887;rs6077853	317	Q5VYV7	CT094_HUMAN	Q	317	ENSP00000335557:R317Q	ENSP00000335557:R317Q	R	+	2	0	C20orf94	10551750	0.000000	0.05858	0.882000	0.34594	0.992000	0.81027	-1.462000	0.02364	-0.514000	0.06488	-0.145000	0.13849	CGA	G|0.904;A|0.096	0.096	strong		0.463	SLX4IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078000.3	NM_001009608	
SLC9A1	6548	hgsc.bcm.edu	37	1	27480757	27480757	+	Silent	SNP	A	A	G	rs34306208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:27480757A>G	ENST00000263980.3	-	1	644	c.69T>C	c.(67-69)gtT>gtC	p.V23V	SLC9A1_ENST00000374086.3_Silent_p.V23V|SLC9A1_ENST00000545949.1_5'UTR	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	23					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	CCACCAAAGCAACCACCACGA	0.597													G|||	1251	0.2498	0.2534	0.1902	5008	,	,		17269	0.1161		0.332	False		,,,				2504	0.3405				p.V23V		Atlas-SNP	.											.	SLC9A1	68	.	0			c.T69C						PASS	.	G		1195,3211	707.3+/-407.5	166,863,1174	86.0	74.0	78.0		69	-9.2	0.0	1	dbSNP_126	78	3056,5544	661.1+/-401.8	546,1964,1790	no	coding-synonymous	SLC9A1	NM_003047.3		712,2827,2964	GG,GA,AA		35.5349,27.1221,32.6849		23/816	27480757	4251,8755	2203	4300	6503	SO:0001819	synonymous_variant	6548	exon1			CAAAGCAACCACC	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"""Solute carriers"""	11071	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 143"""	107310	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 1"""	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.69T>C	1.37:g.27480757A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_003047	B1ALD6|D3DPL4|Q96EM2	Silent	SNP	ENST00000263980.3	37	CCDS295.1																																																																																			A|0.711;G|0.289	0.289	strong		0.597	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047	
GAS2L1	10634	hgsc.bcm.edu	37	22	29704627	29704627	+	Missense_Mutation	SNP	C	C	T	rs191844093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:29704627C>T	ENST00000406549.3	+	2	682	c.532C>T	c.(532-534)Cct>Tct	p.P178S	GAS2L1_ENST00000403764.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000471961.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000407854.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000341313.6_Missense_Mutation_p.P178S|GAS2L1_ENST00000360113.2_Missense_Mutation_p.P178S|GAS2L1_ENST00000407647.2_Missense_Mutation_p.P178S	NM_001278730.1	NP_001265659.1	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1	178					cell cycle arrest (GO:0007050)|cellular response to starvation (GO:0009267)|cellular response to thyroid hormone stimulus (GO:0097067)|microtubule bundle formation (GO:0001578)|negative regulation of cell growth (GO:0030308)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of gene expression (GO:0010629)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)|thyroid hormone receptor binding (GO:0046966)			endometrium(2)|lung(2)|prostate(1)	5						CCCCAACGCCCCTGCCGCTGG	0.726													C|||	10	0.00199681	0.0008	0.0072	5008	,	,		14057	0.0		0.004	False		,,,				2504	0.0				p.P178S		Atlas-SNP	.											.	GAS2L1	54	.	0			c.C532T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	1,4357		0,1,2178	10.0	14.0	13.0		532,532,532	3.8	0.1	22		13	45,8529		0,45,4242	yes	missense,missense,missense	GAS2L1	NM_006478.3,NM_152236.1,NM_152237.1	74,74,74	0,46,6420	TT,TC,CC		0.5248,0.0229,0.3557	probably-damaging,probably-damaging,probably-damaging	178/682,178/682,178/338	29704627	46,12886	2179	4287	6466	SO:0001583	missense	10634	exon2			AACGCCCCTGCCG	BC001782	CCDS63438.1, CCDS74840.1	22q12.2	2008-06-11			ENSG00000185340	ENSG00000185340			16955	protein-coding gene	gene with protein product		602128				8975699, 12584248, 1607387	Standard	NM_001278730		Approved	GAR22	uc003afc.1	Q99501	OTTHUMG00000151108	ENST00000406549.3:c.532C>T	22.37:g.29704627C>T	ENSP00000383995:p.Pro178Ser	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_152237	B5MCR7|Q53EN7|Q92640|Q9BUY9	Missense_Mutation	SNP	ENST00000406549.3	37		8	0.003663003663003663	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	11.65	1.700485	0.30142	2.29E-4	0.005248	ENSG00000185340	ENST00000407647;ENST00000333679;ENST00000406549;ENST00000360113;ENST00000341313;ENST00000403764;ENST00000471961;ENST00000407854	T;T;T;T;T;T;T	0.49139	0.79;0.87;0.91;0.92;0.79;0.79;0.79	4.85	3.81	0.43845	Calponin homology domain (1);	0.846890	0.10081	N	0.718392	T	0.24198	0.0586	L	0.29908	0.895	0.09310	N	0.999996	P;B;B;B	0.35527	0.507;0.113;0.03;0.03	B;B;B;B	0.28232	0.087;0.04;0.031;0.031	T	0.03259	-1.1055	10	0.08837	T	0.75	-16.2742	12.6928	0.56985	0.0:0.6044:0.3956:0.0	.	178;178;178;178	B5MCR7;E7EQM6;A0A5E8;Q99501	.;.;.;GA2L1_HUMAN	S	178	ENSP00000385554:P178S;ENSP00000383995:P178S;ENSP00000353229:P178S;ENSP00000344012:P178S;ENSP00000385358:P178S;ENSP00000450152:P178S;ENSP00000385023:P178S	ENSP00000332834:P178S	P	+	1	0	GAS2L1	28034627	0.007000	0.16637	0.093000	0.20910	0.064000	0.16182	1.674000	0.37544	1.014000	0.39417	0.491000	0.48974	CCT	C|0.996;T|0.004	0.004	strong		0.726	GAS2L1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321365.1	NM_006478	
GIN1	54826	hgsc.bcm.edu	37	5	102433409	102433409	+	Missense_Mutation	SNP	G	G	A	rs34813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:102433409G>A	ENST00000399004.2	-	5	810	c.716C>T	c.(715-717)aCg>aTg	p.T239M	GIN1_ENST00000508629.1_Intron	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	239	Integrase catalytic. {ECO:0000255|PROSITE-ProRule:PRU00457}.		T -> M (in dbSNP:rs34813). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)	p.T239M(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		TGTACTTTCCGTTGGGTTAAC	0.373													G|||	1190	0.23762	0.1271	0.2205	5008	,	,		16273	0.4494		0.2813	False		,,,				2504	0.136				p.T239M		Atlas-SNP	.											GIN1,NS,carcinoma,0,1	GIN1	53	1	1	Substitution - Missense(1)	stomach(1)	c.C716T						PASS	.	G	MET/THR	544,3234		36,472,1381	217.0	196.0	203.0		716	1.2	0.0	5	dbSNP_76	203	2479,5769		378,1723,2023	yes	missense	GIN1	NM_017676.2	81	414,2195,3404	AA,AG,GG		30.0558,14.3992,25.1372	possibly-damaging	239/523	102433409	3023,9003	1889	4124	6013	SO:0001583	missense	54826	exon5			CTTTCCGTTGGGT	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"""gypsy integrase 1"", ""Ty3/Gypsy integrase 1"""		"""zinc finger, H2C2 domain containing"""	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.716C>T	5.37:g.102433409G>A	ENSP00000381970:p.Thr239Met	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	37	CCDS43349.1	629	0.288003663003663	63	0.12804878048780488	90	0.24861878453038674	252	0.4405594405594406	224	0.2955145118733509	G	0.473	-0.883355	0.02530	0.143992	0.300558	ENSG00000145723	ENST00000399004	T	0.29917	1.55	5.66	1.24	0.21308	Integrase, catalytic core (1);Ribonuclease H-like (1);	1.067360	0.07311	N	0.875922	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.33904	0.431	B	0.27608	0.081	T	0.45205	-0.9277	9	0.56958	D	0.05	-2.2558	2.5043	0.04641	0.1495:0.1836:0.4628:0.2041	rs34813;rs1183588;rs52830528;rs57735832;rs34813	239	Q9NXP7	GIN1_HUMAN	M	239	ENSP00000381970:T239M	ENSP00000381970:T239M	T	-	2	0	GIN1	102461308	0.047000	0.20315	0.003000	0.11579	0.000000	0.00434	0.561000	0.23515	0.327000	0.23409	-0.813000	0.03139	ACG	G|0.705;A|0.295	0.295	strong		0.373	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676	
WDR17	116966	hgsc.bcm.edu	37	4	177098285	177098285	+	Missense_Mutation	SNP	G	G	A	rs17625943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:177098285G>A	ENST00000280190.4	+	29	3799	c.3643G>A	c.(3643-3645)Gct>Act	p.A1215T	WDR17_ENST00000508596.1_Missense_Mutation_p.A1176T|WDR17_ENST00000393643.2_Missense_Mutation_p.A1191T|WDR17_ENST00000507824.2_Missense_Mutation_p.A1190T			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1215			A -> T (in dbSNP:rs17625943). {ECO:0000269|PubMed:15489334}.							breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		TGCATGGAGAGCTTGCACACA	0.373													G|||	1305	0.260583	0.2519	0.4164	5008	,	,		15205	0.2569		0.2624	False		,,,				2504	0.1636				p.A1215T		Atlas-SNP	.											WDR17,rectum,carcinoma,-1,1	WDR17	198	1	0			c.G3643A						PASS	.	G	THR/ALA,THR/ALA	1062,3344	369.5+/-319.1	140,782,1281	61.0	62.0	61.0		3643,3526	4.1	1.0	4	dbSNP_123	61	2190,6408	368.6+/-335.1	282,1626,2391	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	58,58	422,2408,3672	AA,AG,GG		25.471,24.1035,25.0077	benign,benign	1215/1323,1176/1284	177098285	3252,9752	2203	4299	6502	SO:0001583	missense	116966	exon29			TGGAGAGCTTGCA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3643G>A	4.37:g.177098285G>A	ENSP00000280190:p.Ala1215Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	623|623	0.28525641025641024|0.28525641025641024	139|139	0.28252032520325204|0.28252032520325204	137|137	0.3784530386740331|0.3784530386740331	161|161	0.28146853146853146|0.28146853146853146	186|186	0.24538258575197888|0.24538258575197888	G|G	21.1|21.1	4.105116|4.105116	0.77096|0.77096	0.241035|0.241035	0.25471|0.25471	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.54479|.	0.57;0.57;0.57|.	5.94|5.94	4.11|4.11	0.48088|0.48088	.|.	0.192654|.	0.43579|.	D|.	0.000542|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.69823|0.69823	2.125|2.125	0.19775|0.19775	P|P	0.9999589415|0.9999589415	P;P;P|.	0.41910|.	0.764;0.764;0.764|.	B;B;B|.	0.39503|.	0.301;0.235;0.235|.	T|T	0.10451|0.10451	-1.0629|-1.0629	9|4	0.62326|.	D|.	0.03|.	-16.1407|-16.1407	14.9963|14.9963	0.71433|0.71433	0.0:0.0:0.7179:0.2821|0.0:0.0:0.7179:0.2821	rs17625943;rs52821017;rs17625943|rs17625943;rs52821017;rs17625943	1191;1176;1215|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	T|N	1176;1191;1215;1191|449	ENSP00000422763:A1176T;ENSP00000377258:A1191T;ENSP00000280190:A1215T|.	ENSP00000280190:A1215T|.	A|S	+|+	1|2	0|0	WDR17|WDR17	177335279|177335279	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	5.753000|5.753000	0.68736|0.68736	1.470000|1.470000	0.48102|0.48102	0.644000|0.644000	0.83932|0.83932	GCT|AGC	G|0.743;A|0.257	0.257	strong		0.373	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
FMN2	56776	hgsc.bcm.edu	37	1	240371112	240371112	+	Silent	SNP	G	G	T	rs71646889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371112G>T	ENST00000319653.9	+	5	3230	c.3000G>T	c.(2998-3000)ccG>ccT	p.P1000P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1000	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1143P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACCCCCTCCGCCCCCACTTC	0.716													G|||	1341	0.267772	0.357	0.1873	5008	,	,		4654	0.2927		0.2008	False		,,,				2504	0.2474				p.P1000P		Atlas-SNP	.											FMN2,NS,carcinoma,0,4	FMN2	451	4	1	Substitution - coding silent(1)	prostate(1)	c.G3000T						PASS	.						4.0	6.0	6.0					1																	240371112		1774	3850	5624	SO:0001819	synonymous_variant	56776	exon5			CCCTCCGCCCCCA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3000G>T	1.37:g.240371112G>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	115	28	0.243478	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.000;G|0.879;T|0.121	0.121	strong		0.716	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
C10orf105	414152	hgsc.bcm.edu	37	10	73492027	73492027	+	Intron	SNP	G	G	A	rs111033453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73492027G>A	ENST00000398786.2	-	1	97				CDH23_ENST00000224721.6_Silent_p.V1338V	NM_001168390.1	NP_001161862.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105							integral component of membrane (GO:0016021)											CTGAGATTGTGCGGGTCCAGG	0.562													G|||	5	0.000998403	0.0	0.0043	5008	,	,		21580	0.0		0.002	False		,,,				2504	0.0				p.V1333V		Atlas-SNP	.											.	CDH23	365	.	0			c.G3999A						PASS	.	G	,,	2,4110		0,2,2054	68.0	70.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,3999,3999	4.8	1.0	10	dbSNP_132	69	24,8384		0,24,4180	no	intron,coding-synonymous,coding-synonymous	CDH23,C10orf105	NM_001168390.1,NM_001171930.1,NM_022124.5	,,	0,26,6234	AA,AG,GG		0.2854,0.0486,0.2077	,,	,1333/1382,1333/3355	73492027	26,12494	2056	4204	6260	SO:0001627	intron_variant	64072	exon31			GATTGTGCGGGTC	AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427	ENST00000398786.2:c.4+5457C>T	10.37:g.73492027G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_022124		Silent	SNP	ENST00000398786.2	37	CCDS44430.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	C10orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048551.2	NM_001164375	
GLI3	2737	hgsc.bcm.edu	37	7	42088222	42088222	+	Missense_Mutation	SNP	T	T	C	rs846266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:42088222T>C	ENST00000395925.3	-	5	631	c.547A>G	c.(547-549)Act>Gct	p.T183A	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	183			T -> A (in dbSNP:rs846266). {ECO:0000269|PubMed:10441342, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2118997}.		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						GAAGCAGCAGTGGGGTTCCGG	0.532									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				C|||	3023	0.603634	0.8941	0.3833	5008	,	,		18454	0.5665		0.5755	False		,,,				2504	0.4346				p.T183A		Atlas-SNP	.											.	GLI3	312	.	0			c.A547G	GRCh37	CD050865	GLI3	D	rs846266	PASS	.	C	ALA/THR	3767,639	274.3+/-271.8	1612,543,48	123.0	128.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	547	3.2	0.7	7	dbSNP_86	126	4841,3759	535.1+/-382.7	1345,2151,804	yes	missense	GLI3	NM_000168.5	58	2957,2694,852	CC,CT,TT		43.7093,14.503,33.8152	benign	183/1581	42088222	8608,4398	2203	4300	6503	SO:0001583	missense	2737	exon5	Familial Cancer Database	;	CAGCAGTGGGGTT		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.547A>G	7.37:g.42088222T>C	ENSP00000379258:p.Thr183Ala	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	186	184	0.989247	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	1366	0.6254578754578755	445	0.9044715447154471	147	0.40607734806629836	334	0.583916083916084	440	0.5804749340369393	C	4.296	0.054227	0.08291	0.85497	0.562907	ENSG00000106571	ENST00000395925	T	0.35973	1.28	5.13	3.22	0.36961	.	0.165421	0.53938	N	0.000046	T	0.00012	0.0000	N	0.00483	-1.445	0.09310	P	0.9999999999999868	B	0.02656	0.0	B	0.01281	0.0	T	0.39165	-0.9627	9	0.02654	T	1	.	8.7561	0.34645	0.0:0.7359:0.0:0.2641	rs846266;rs957976;rs17721554;rs60657470;rs846266	183	P10071	GLI3_HUMAN	A	183	ENSP00000379258:T183A	ENSP00000379258:T183A	T	-	1	0	GLI3	42054747	0.994000	0.37717	0.666000	0.29783	0.865000	0.49528	3.147000	0.50639	0.225000	0.20959	-0.186000	0.12905	ACT	T|0.354;G|0.001	.	strong		0.532	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
SHC4	399694	hgsc.bcm.edu	37	15	49127134	49127134	+	Silent	SNP	G	G	A	rs1426199	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:49127134G>A	ENST00000332408.4	-	11	1997	c.1569C>T	c.(1567-1569)agC>agT	p.S523S	SHC4_ENST00000396535.3_Silent_p.S280S|SHC4_ENST00000537958.1_Silent_p.S237S	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	523	CH1.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		AGCATTCTTCGCTCCACAGCT	0.552													g|||	402	0.0802716	0.028	0.0692	5008	,	,		19061	0.0754		0.1133	False		,,,				2504	0.1299				p.S523S		Atlas-SNP	.											.	SHC4	70	.	0			c.C1569T						PASS	.	G		165,4229	111.2+/-149.4	3,159,2035	78.0	65.0	69.0		1569	-0.1	0.0	15	dbSNP_88	69	926,7664	205.4+/-247.8	58,810,3427	no	coding-synonymous	SHC4	NM_203349.3		61,969,5462	AA,AG,GG		10.78,3.7551,8.4026		523/631	49127134	1091,11893	2197	4295	6492	SO:0001819	synonymous_variant	399694	exon11			TTCTTCGCTCCAC	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"""SH2 domain containing"""	16743	protein-coding gene	gene with protein product	"""rai-like protein"""						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1569C>T	15.37:g.49127134G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_203349	Q6UXQ3|Q8IYW3	Silent	SNP	ENST00000332408.4	37	CCDS10130.1																																																																																			G|0.918;A|0.082	0.082	strong		0.552	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349	
GRAMD1C	54762	hgsc.bcm.edu	37	3	113655207	113655207	+	Silent	SNP	C	C	T	rs3765114	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:113655207C>T	ENST00000358160.4	+	14	2043	c.1551C>T	c.(1549-1551)aaC>aaT	p.N517N	GRAMD1C_ENST00000452134.2_Silent_p.N246N|GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000440446.2_Silent_p.N312N|GRAMD1C_ENST00000472026.1_Silent_p.N350N	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	517						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						GAACCTTCAACCGAACAGCAG	0.433													C|||	1152	0.230032	0.0371	0.3156	5008	,	,		16490	0.2679		0.328	False		,,,				2504	0.2904				p.N517N		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.C1551T						PASS	.	C	,	364,4042	185.3+/-212.5	19,326,1858	126.0	121.0	123.0		936,1551	5.0	1.0	3	dbSNP_107	123	2767,5833	439.2+/-359.1	427,1913,1960	no	coding-synonymous,coding-synonymous	GRAMD1C	NM_001172105.1,NM_017577.4	,	446,2239,3818	TT,TC,CC		32.1744,8.2615,24.0735	,	312/458,517/663	113655207	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	54762	exon14			CTTCAACCGAACA		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.1551C>T	3.37:g.113655207C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Silent	SNP	ENST00000358160.4	37	CCDS33826.1																																																																																			C|0.756;T|0.244	0.244	strong		0.433	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577	
ENTHD2	146705	hgsc.bcm.edu	37	17	79204447	79204447	+	Missense_Mutation	SNP	C	C	T	rs143572077		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79204447C>T	ENST00000300714.3	-	11	983	c.926G>A	c.(925-927)aGc>aAc	p.S309N	AC027601.1_ENST00000569559.1_RNA|ENTHD2_ENST00000374769.2_Missense_Mutation_p.S225N|AC027601.1_ENST00000575922.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	309						cytoplasmic vesicle (GO:0031410)											GAGGTCGCTGCTCCCCAGGGA	0.692											OREG0024811	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S309N		Atlas-SNP	.											.	.	.	.	0			c.G926A						PASS	.	C	ASN/SER	0,4406		0,0,2203	23.0	25.0	24.0		926	3.1	0.0	17	dbSNP_134	24	1,8597		0,1,4298	no	missense	C17orf56	NM_144679.2	46	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	309/526	79204447	1,13003	2203	4299	6502	SO:0001583	missense	146705	exon11			TCGCTGCTCCCCA	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.926G>A	17.37:g.79204447C>T	ENSP00000300714:p.Ser309Asn	Somatic	102	0	0	1189	WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_144679	Q6ZQU0|Q6ZSQ9	Missense_Mutation	SNP	ENST00000300714.3	37	CCDS11779.1	.	.	.	.	.	.	.	.	.	.	C	7.062	0.566626	0.13560	0.0	1.16E-4	ENSG00000167302	ENST00000300714;ENST00000374769	T;T	0.27720	1.65;1.65	5.17	3.13	0.36017	.	1.579650	0.03019	N	0.150445	T	0.24624	0.0597	L	0.29908	0.895	0.09310	N	1	P;P	0.41265	0.454;0.744	B;B	0.35813	0.105;0.211	T	0.24941	-1.0146	10	0.38643	T	0.18	-0.3904	8.4158	0.32670	0.0:0.7609:0.1556:0.0835	.	309;225	Q96N21;Q96N21-2	CQ056_HUMAN;.	N	309;225	ENSP00000300714:S309N;ENSP00000363901:S225N	ENSP00000300714:S309N	S	-	2	0	C17orf56	76819042	0.044000	0.20184	0.004000	0.12327	0.007000	0.05969	1.325000	0.33724	0.544000	0.28883	0.555000	0.69702	AGC	C|1.000;T|0.000	0.000	weak		0.692	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679	
HHLA1	10086	hgsc.bcm.edu	37	8	133108005	133108005	+	Silent	SNP	A	A	G	rs55906165	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133108005A>G	ENST00000414222.1	-	5	308	c.309T>C	c.(307-309)agT>agC	p.S103S	HHLA1_ENST00000434736.2_Silent_p.S139S	NM_001145095.1	NP_001138567.1	C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	103						extracellular region (GO:0005576)				endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						AGGAAGTGACACTCAGCAAGG	0.433													A|||	143	0.0285543	0.0015	0.0476	5008	,	,		16813	0.0		0.0865	False		,,,				2504	0.0215				p.S103S		Atlas-SNP	.											.	HHLA1	35	.	0			c.T309C						PASS	.	A		21,1363		0,21,671	104.0	101.0	102.0		309	-1.8	0.0	8	dbSNP_129	102	267,2915		11,245,1335	no	coding-synonymous	HHLA1	NM_001145095.1		11,266,2006	GG,GA,AA		8.3909,1.5173,6.3075		103/532	133108005	288,4278	692	1591	2283	SO:0001819	synonymous_variant	10086	exon5			AGTGACACTCAGC	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.309T>C	8.37:g.133108005A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_001145095		Silent	SNP	ENST00000414222.1	37																																																																																				A|0.947;G|0.053	0.053	strong		0.433	HHLA1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XR_017860	
DBNL	28988	hgsc.bcm.edu	37	7	44100497	44100497	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:44100497C>T	ENST00000448521.1	+	13	1373	c.1275C>T	c.(1273-1275)taC>taT	p.Y425Y	DBNL_ENST00000440166.1_Silent_p.Y322Y|DBNL_ENST00000468694.1_Silent_p.Y434Y|DBNL_ENST00000490734.2_Silent_p.Y331Y|DBNL_ENST00000452943.1_Silent_p.Y401Y|DBNL_ENST00000456905.1_Silent_p.Y377Y|DBNL_ENST00000494774.1_Silent_p.Y426Y|DBNL_ENST00000497184.1_3'UTR	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	425	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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.Y426Y(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						CTGCCAACTACGTGGAGCTCA	0.572																																					p.Y434Y	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											DBNL,colon,carcinoma,0,1	DBNL	26	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1302T						scavenged	.						131.0	103.0	112.0					7																	44100497		2203	4300	6503	SO:0001819	synonymous_variant	28988	exon13			CAACTACGTGGAG	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.1275C>T	7.37:g.44100497C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	101	2	0.019802	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Silent	SNP	ENST00000448521.1	37	CCDS34623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.690|9.690	1.151524|1.151524	0.21371|0.21371	.|.	.|.	ENSG00000136279|ENSG00000136279	ENST00000432854|ENST00000452661	.|.	.|.	.|.	5.4|5.4	-6.83|-6.83	0.01693|0.01693	.|.	.|.	.|.	.|.	.|.	T|T	0.63260|0.63260	0.2496|0.2496	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.66810|0.66810	-0.5829|-0.5829	4|4	.|.	.|.	.|.	-21.5864|-21.5864	16.458|16.458	0.84029|0.84029	0.0:0.3521:0.0:0.6479|0.0:0.3521:0.0:0.6479	.|.	.|.	.|.	.|.	C|M	354|133	.|.	.|.	R|T	+|+	1|2	0|0	DBNL|DBNL	44067022|44067022	0.275000|0.275000	0.24201|0.24201	0.762000|0.762000	0.31397|0.31397	0.987000|0.987000	0.75469|0.75469	-0.230000|-0.230000	0.09083|0.09083	-1.421000|-1.421000	0.02007|0.02007	-0.266000|-0.266000	0.10368|0.10368	CGT|ACG	.	.	none		0.572	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
AKAP12	9590	hgsc.bcm.edu	37	6	151671182	151671182	+	Silent	SNP	C	C	T	rs41289369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151671182C>T	ENST00000253332.1	+	3	1845	c.1656C>T	c.(1654-1656)gcC>gcT	p.A552A	AKAP12_ENST00000354675.6_Silent_p.A454A|AKAP12_ENST00000359755.5_Silent_p.A447A|AKAP12_ENST00000402676.2_Silent_p.A552A|snoU13_ENST00000458767.1_RNA			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	552	Involved in PKC-binding. {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)		AGGTTCCAGCCGATTCTCCGG	0.542													C|||	318	0.0634984	0.0378	0.1153	5008	,	,		18991	0.1379		0.0199	False		,,,				2504	0.0297				p.A552A	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.C1656T						PASS	.	C	,	159,4247	106.9+/-145.3	3,153,2047	41.0	45.0	44.0		1656,1362	-10.4	0.0	6	dbSNP_127	44	178,8422	81.2+/-143.8	3,172,4125	no	coding-synonymous,coding-synonymous	AKAP12	NM_005100.3,NM_144497.2	,	6,325,6172	TT,TC,CC		2.0698,3.6087,2.5911	,	552/1783,454/1685	151671182	337,12669	2203	4300	6503	SO:0001819	synonymous_variant	9590	exon4			TCCAGCCGATTCT	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.1656C>T	6.37:g.151671182C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Silent	SNP	ENST00000253332.1	37	CCDS5229.1																																																																																			C|0.962;T|0.038	0.038	strong		0.542	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
SORCS1	114815	hgsc.bcm.edu	37	10	108389111	108389111	+	Silent	SNP	A	A	G	rs3802553	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1262907	1262907	+	Silent	SNP	T	T	C	rs2037089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1262907T>C	ENST00000529681.1	+	31	4855	c.4797T>C	c.(4795-4797)agT>agC	p.S1599S	MUC5B_ENST00000447027.1_Silent_p.S1602S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1599	7 X Cys-rich subdomain repeats.				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)		TCTGCTGCAGTGACGACCACT	0.637													t|||	1025	0.204673	0.2685	0.2709	5008	,	,		15649	0.0615		0.2078	False		,,,				2504	0.2157				p.S1599S		Atlas-SNP	.											.	MUC5B	473	.	0			c.T4797C						PASS	.			1122,3124		151,820,1152	21.0	28.0	26.0		4797	-2.8	0.0	11	dbSNP_94	26	1595,6851		162,1271,2790	no	coding-synonymous	MUC5B	NM_002458.2		313,2091,3942	CC,CT,TT		18.8847,26.4249,21.4072		1599/5763	1262907	2717,9975	2123	4223	6346	SO:0001819	synonymous_variant	727897	exon31			CTGCAGTGACGAC	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.4797T>C	11.37:g.1262907T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			T|0.797;C|0.203	0.203	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CACNA1H	8912	hgsc.bcm.edu	37	16	1252441	1252441	+	Missense_Mutation	SNP	T	T	C	rs4984636	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1252441T>C	ENST00000348261.5	+	9	2239	c.1991T>C	c.(1990-1992)gTc>gCc	p.V664A	CACNA1H_ENST00000358590.4_Missense_Mutation_p.V664A|CACNA1H_ENST00000565831.1_Missense_Mutation_p.V664A	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	664			V -> A (in dbSNP:rs4984636). {ECO:0000269|PubMed:11751928, ECO:0000269|PubMed:12891677, ECO:0000269|PubMed:9670923}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CCGCATGTGGTCGGGGAGCAT	0.682													T|||	530	0.105831	0.0091	0.1744	5008	,	,		16513	0.002		0.2863	False		,,,				2504	0.1094				p.V664A		Atlas-SNP	.											CACNA1H_ENST00000358590,rectum,carcinoma,0,2	CACNA1H	317	2	0			c.T1991C						PASS	.	T	ALA/VAL,ALA/VAL	178,3466		11,156,1655	4.0	5.0	5.0		1991,1991	4.5	0.2	16	dbSNP_111	5	1823,5663		248,1327,2168	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	64,64	259,1483,3823	CC,CT,TT		24.3521,4.8847,17.9784	possibly-damaging,possibly-damaging	664/2348,664/2354	1252441	2001,9129	1822	3743	5565	SO:0001583	missense	8912	exon9			ATGTGGTCGGGGA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1991T>C	16.37:g.1252441T>C	ENSP00000334198:p.Val664Ala	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	17	7	0.411765	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	287	0.13141025641025642	8	0.016260162601626018	63	0.17403314917127072	1	0.0017482517482517483	215	0.2836411609498681	T	17.49	3.403103	0.62288	0.048847	0.243521	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96619	-4.07;-4.01	4.47	4.47	0.54385	.	157.429000	0.00166	N	0.000000	T	0.00178	0.0005	L	0.50333	1.59	0.36796	P	0.11489499999999997	P;D	0.53151	0.571;0.958	B;P	0.46026	0.288;0.501	T	0.54669	-0.8259	9	0.51188	T	0.08	.	13.0686	0.59048	0.0:0.0:0.0:1.0	rs4984636;rs57010276;rs4984636	664;664	O95180-2;O95180	.;CAC1H_HUMAN	A	664	ENSP00000334198:V664A;ENSP00000351401:V664A	ENSP00000334198:V664A	V	+	2	0	CACNA1H	1192442	1.000000	0.71417	0.174000	0.22961	0.858000	0.48976	4.766000	0.62279	1.864000	0.54056	0.533000	0.62120	GTC	T|0.874;C|0.126	0.126	strong		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39908574	39908574	+	Silent	SNP	C	C	T	rs35466645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39908574C>T	ENST00000409794.3	+	9	1762	c.912C>T	c.(910-912)acC>acT	p.T304T	PLEKHG2_ENST00000378550.1_Silent_p.T304T|PLEKHG2_ENST00000425673.1_Silent_p.T304T|PLEKHG2_ENST00000458508.2_Silent_p.T245T|PLEKHG2_ENST00000409797.2_Silent_p.T304T	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	304					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GTGGCTGGACCGGACCAGAGC	0.692													C|||	788	0.157348	0.1762	0.1844	5008	,	,		10187	0.0367		0.1769	False		,,,				2504	0.2168				p.T304T		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C912T						PASS	.	C		677,3487		50,577,1455	16.0	21.0	20.0		912	-9.3	0.4	19	dbSNP_126	20	1233,6895		85,1063,2916	no	coding-synonymous	PLEKHG2	NM_022835.2		135,1640,4371	TT,TC,CC		15.1698,16.2584,15.5386		304/1387	39908574	1910,10382	2082	4064	6146	SO:0001819	synonymous_variant	64857	exon9			CTGGACCGGACCA	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.912C>T	19.37:g.39908574C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	333	0.15247252747252749	97	0.19715447154471544	83	0.2292817679558011	14	0.024475524475524476	139	0.18337730870712401	C	1.970	-0.436763	0.04636	0.162584	0.151698	ENSG00000090924	ENST00000205135	.	.	.	4.66	-9.32	0.00643	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999992221	.	.	.	.	.	.	T	0.10245	-1.0638	3	.	.	.	.	12.7222	0.57147	0.0:0.6049:0.2787:0.1164	rs35466645;rs62119735	.	.	.	L	201	.	.	P	+	2	0	PLEKHG2	44600414	0.012000	0.17670	0.371000	0.25978	0.271000	0.26615	-1.138000	0.03216	-2.668000	0.00415	-2.717000	0.00132	CCG	C|0.847;T|0.153	0.153	strong		0.692	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
VN1R1	57191	hgsc.bcm.edu	37	19	57967049	57967049	+	Missense_Mutation	SNP	G	G	T	rs61744949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57967049G>T	ENST00000321039.3	-	1	805	c.806C>A	c.(805-807)gCc>gAc	p.A269D	AC004076.9_ENST00000415705.3_5'UTR|AC004076.9_ENST00000596831.1_Missense_Mutation_p.P107T	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	269			A -> D (in allele VN1R1*3; dbSNP:rs61744949). {ECO:0000269|PubMed:10973240, ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		TGTGGCTCTGGCTTCCTGGGA	0.488													G|||	2070	0.413339	0.3109	0.451	5008	,	,		18776	0.5913		0.2783	False		,,,				2504	0.4806				p.A269D		Atlas-SNP	.											.	VN1R1	48	.	0			c.C806A						PASS	.	G	ASP/ALA	1342,3064	450.2+/-349.3	188,966,1049	126.0	88.0	101.0		806	-0.9	0.0	19	dbSNP_129	101	2454,6146	404.0+/-348.0	330,1794,2176	yes	missense	VN1R1	NM_020633.3	126	518,2760,3225	TT,TG,GG		28.5349,30.4585,29.1865	possibly-damaging	269/354	57967049	3796,9210	2203	4300	6503	SO:0001583	missense	57191	exon1			GCTCTGGCTTCCT	AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	13548	protein-coding gene	gene with protein product		605234	"""vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"""	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.806C>A	19.37:g.57967049G>T	ENSP00000322339:p.Ala269Asp	Somatic	325	1	0.00307692		WXS	Illumina HiSeq	Phase_I	289	287	0.99308	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	877	0.4015567765567766	149	0.30284552845528456	135	0.3729281767955801	368	0.6433566433566433	225	0.29683377308707126	G	10.04	1.242857	0.22796	0.304585	0.285349	ENSG00000178201	ENST00000321039	T	0.09255	3.0	4.17	-0.913	0.10500	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.25060	0.705	0.80722	P	0.0	B	0.25609	0.13	B	0.31016	0.123	T	0.24621	-1.0155	8	0.56958	D	0.05	.	4.0826	0.09932	0.3162:0.3379:0.3459:0.0	rs61744949	269	Q9GZP7	VN1R1_HUMAN	D	269	ENSP00000322339:A269D	ENSP00000322339:A269D	A	-	2	0	VN1R1	62658861	0.996000	0.38824	0.000000	0.03702	0.015000	0.08874	0.517000	0.22832	-0.140000	0.11394	0.650000	0.86243	GCC	G|0.675;T|0.325	0.325	strong		0.488	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633	
PRKCB	5579	hgsc.bcm.edu	37	16	24202458	24202458	+	Silent	SNP	C	C	T	rs3729904	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:24202458C>T	ENST00000321728.7	+	16	1945	c.1770C>T	c.(1768-1770)ggC>ggT	p.G590G	PRKCB_ENST00000303531.7_Silent_p.G590G	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	590	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	GACCTGAAGGCGAACGTGATA	0.428													C|||	1259	0.251398	0.3343	0.1974	5008	,	,		19955	0.0942		0.2535	False		,,,				2504	0.3374				p.G590G		Atlas-SNP	.											PRKCB_ENST00000321728,NS,carcinoma,+2,3	PRKCB	383	3	0			c.C1770T						PASS	.	C	,	1274,3120	437.4+/-345.0	179,916,1102	104.0	102.0	102.0		1770,1770	-10.5	0.9	16	dbSNP_107	102	2111,6489	363.5+/-333.2	265,1581,2454	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	444,2497,3556	TT,TC,CC		24.5465,28.9941,26.0505	,	590/674,590/672	24202458	3385,9609	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon16			TGAAGGCGAACGT	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1770C>T	16.37:g.24202458C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			C|0.765;T|0.235	0.235	strong		0.428	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
CYP2C19	1557	hgsc.bcm.edu	37	10	96534922	96534922	+	Missense_Mutation	SNP	G	G	C	rs17878459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:96534922G>C	ENST00000371321.3	+	2	358	c.276G>C	c.(274-276)gaG>gaC	p.E92D	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	92			E -> D (in dbSNP:rs17878459). {ECO:0000269|PubMed:9732415, ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|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)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	ATCTTGGAGAGGAGTTTTCTG	0.498													G|||	45	0.00898562	0.0038	0.0058	5008	,	,		19874	0.0		0.0358	False		,,,				2504	0.0				p.E92D		Atlas-SNP	.											.	CYP2C19	88	.	0			c.G276C	GRCh37	CM983292	CYP2C19	M	rs17878459	PASS	.	G	ASP/GLU	38,4368	43.1+/-76.7	0,38,2165	230.0	214.0	219.0		276	-5.0	0.3	10	dbSNP_124	219	262,8338	102.1+/-163.3	3,256,4041	no	missense	CYP2C19	NM_000769.1	45	3,294,6206	CC,CG,GG		3.0465,0.8625,2.3066	benign	92/491	96534922	300,12706	2203	4300	6503	SO:0001583	missense	1557	exon2			TGGAGAGGAGTTT	M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.276G>C	10.37:g.96534922G>C	ENSP00000360372:p.Glu92Asp	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	291	113	0.388316	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Missense_Mutation	SNP	ENST00000371321.3	37	CCDS7436.1	36	0.016483516483516484	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	32	0.04221635883905013	G	2.054	-0.416917	0.04766	0.008625	0.030465	ENSG00000165841	ENST00000371321	T	0.70282	-0.47	3.74	-4.98	0.03019	.	0.153153	0.41823	U	0.000818	T	0.15955	0.0384	N	0.21508	0.67	0.24617	N	0.993695	B	0.06786	0.001	B	0.10450	0.005	T	0.10590	-1.0623	10	0.23302	T	0.38	.	7.3624	0.26754	0.608:0.1274:0.2646:0.0	rs17878459;rs59510926	92	P33261	CP2CJ_HUMAN	D	92	ENSP00000360372:E92D	ENSP00000360372:E92D	E	+	3	2	CYP2C19	96524912	0.000000	0.05858	0.256000	0.24389	0.262000	0.26303	-2.760000	0.00786	-1.099000	0.03034	-0.491000	0.04670	GAG	C|0.018;G|0.982	0.018	strong		0.498	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
IFT81	28981	hgsc.bcm.edu	37	12	110566907	110566907	+	Missense_Mutation	SNP	A	A	G	rs34684319	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:110566907A>G	ENST00000242591.5	+	4	907	c.401A>G	c.(400-402)gAt>gGt	p.D134G	IFT81_ENST00000552912.1_Missense_Mutation_p.D134G|IFT81_ENST00000361948.4_Missense_Mutation_p.D134G	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	134					cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						TTTCTTCAGGATGAAACTGTG	0.348													A|||	86	0.0171725	0.0008	0.0173	5008	,	,		18581	0.001		0.0239	False		,,,				2504	0.0491				p.D134G		Atlas-SNP	.											.	IFT81	86	.	0			c.A401G						PASS	.	A	GLY/ASP,GLY/ASP,GLY/ASP	15,4391	21.2+/-45.6	0,15,2188	63.0	63.0	63.0		401,401,401	5.6	1.0	12	dbSNP_126	63	173,8427	79.2+/-141.9	2,169,4129	yes	missense,missense,missense	IFT81	NM_001143779.1,NM_014055.3,NM_031473.3	94,94,94	2,184,6317	GG,GA,AA		2.0116,0.3404,1.4455	probably-damaging,probably-damaging,probably-damaging	134/677,134/677,134/432	110566907	188,12818	2203	4300	6503	SO:0001583	missense	28981	exon4			TTCAGGATGAAAC	AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"""Intraflagellar transport homologs"""	14313	protein-coding gene	gene with protein product		605489	"""carnitine deficiency-associated, expressed in ventricle 1"", ""intraflagellar transport 81 homolog (Chlamydomonas)"""	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.401A>G	12.37:g.110566907A>G	ENSP00000242591:p.Asp134Gly	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	37	CCDS41831.1	30	0.013736263736263736	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	21	0.027704485488126648	A	24.5	4.535055	0.85812	0.003404	0.020116	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	T;T	0.75704	0.37;-0.96	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.75657	0.3879	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.995	D	0.85252	0.1045	10	0.87932	D	0	-22.477	15.6967	0.77506	1.0:0.0:0.0:0.0	rs34684319;rs61742786;rs34684319	134;134	Q8WYA0;Q8WYA0-3	IFT81_HUMAN;.	G	134	ENSP00000355372:D134G;ENSP00000446950:D134G	ENSP00000242591:D134G	D	+	2	0	IFT81	109051290	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.930000	0.92872	2.111000	0.64477	0.383000	0.25322	GAT	A|0.984;G|0.016	0.016	strong		0.348	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055	
EP400	57634	hgsc.bcm.edu	37	12	132547087	132547087	+	Silent	SNP	G	G	A	rs12366766	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:132547087G>A	ENST00000333577.4	+	48	8392	c.8283G>A	c.(8281-8283)caG>caA	p.Q2761Q	EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000389561.2_Silent_p.Q2725Q|EP400_ENST00000332482.4_Silent_p.Q2688Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2761	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.Q2724Q(16)|p.Q2725Q(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)		agcagcagcagcaacaacagc	0.562													G|||	37	0.00738818	0.0038	0.0072	5008	,	,		15585	0.002		0.0149	False		,,,				2504	0.0102				p.Q2725Q		Atlas-SNP	.											EP400,NS,carcinoma,0,20	EP400	370	20	17	Substitution - coding silent(17)	prostate(4)|kidney(4)|central_nervous_system(3)|lung(3)|endometrium(2)|urinary_tract(1)	c.G8175A						scavenged	.						28.0	31.0	30.0					12																	132547087		2199	4282	6481	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAACAA	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.8283G>A	12.37:g.132547087G>A		Somatic	97	2	0.0206186		WXS	Illumina HiSeq	Phase_I	109	15	0.137615	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				.	.	weak		0.562	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
CMBL	134147	hgsc.bcm.edu	37	5	10282333	10282333	+	Silent	SNP	A	A	G	rs115129340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:10282333A>G	ENST00000296658.3	-	5	954	c.534T>C	c.(532-534)aaT>aaC	p.N178N	CMBL_ENST00000510532.1_Intron	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	178						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						TCACAACATCATTTTCAGCAA	0.403													A|||	35	0.00698882	0.0	0.0173	5008	,	,		20290	0.0		0.0199	False		,,,				2504	0.0031				p.N178N		Atlas-SNP	.											.	CMBL	24	.	0			c.T534C						PASS	.	A		7,4399	15.5+/-35.6	0,7,2196	102.0	104.0	103.0		534	-5.9	0.5	5	dbSNP_132	103	108,8492	57.9+/-119.4	1,106,4193	no	coding-synonymous	CMBL	NM_138809.3		1,113,6389	GG,GA,AA		1.2558,0.1589,0.8842		178/246	10282333	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	134147	exon5			AACATCATTTTCA		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"""carboxymethylenebutenolidase-like (Pseudomonas)"""			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.534T>C	5.37:g.10282333A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	180	68	0.377778	NM_138809	D3DTC7|Q8TED6	Silent	SNP	ENST00000296658.3	37	CCDS3878.1																																																																																			A|0.990;G|0.010	0.010	strong		0.403	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809	
MED16	10025	hgsc.bcm.edu	37	19	868115	868115	+	Missense_Mutation	SNP	C	C	T	rs13090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:868115C>T	ENST00000589119.1	-	15	2619	c.2620G>A	c.(2620-2622)Gag>Aag	p.E874K	MED16_ENST00000325464.1_Missense_Mutation_p.E874K|MED16_ENST00000312090.6_3'UTR|MED16_ENST00000269814.4_3'UTR|MED16_ENST00000395808.3_3'UTR			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	874			E -> K (in dbSNP:rs13090).		androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGACGGTCCTCTGGATGCAGA	0.672													c|||	1201	0.239816	0.4334	0.2075	5008	,	,		14335	0.0327		0.2783	False		,,,				2504	0.1748				p.E874K		Atlas-SNP	.											MED16,NS,carcinoma,0,1	MED16	61	1	0			c.G2620A						PASS	.		LYS/GLU	1733,2661	500.3+/-364.7	341,1051,805	35.0	34.0	35.0		2620	-0.5	0.0	19	dbSNP_52	35	2419,6171	389.6+/-343.0	340,1739,2216	yes	missense	MED16	NM_005481.2	56	681,2790,3021	TT,TC,CC		28.1607,39.4401,31.9778	benign	874/878	868115	4152,8832	2197	4295	6492	SO:0001583	missense	10025	exon16			GGTCCTCTGGATG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2620G>A	19.37:g.868115C>T	ENSP00000464810:p.Glu874Lys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	CCDS12047.1	540	0.24725274725274726	225	0.4573170731707317	85	0.23480662983425415	21	0.03671328671328671	209	0.2757255936675462	c	7.534	0.659189	0.14645	0.394401	0.281607	ENSG00000175221	ENST00000325464	T	0.32988	1.43	0.652	-0.498	0.12019	.	7739.210000	0.00166	U	0.000003	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.13594	0.008	B	0.04013	0.001	T	0.46512	-0.9186	8	0.40728	T	0.16	.	.	.	.	rs13090;rs61664660;rs13090	874	Q9Y2X0	MED16_HUMAN	K	874	ENSP00000325612:E874K	ENSP00000325612:E874K	E	-	1	0	MED16	819115	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	-0.075000	0.11431	-0.185000	0.10550	0.457000	0.33378	GAG	C|0.702;T|0.298	0.298	strong		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
ZNF714	148206	hgsc.bcm.edu	37	19	21300284	21300284	+	Missense_Mutation	SNP	A	A	G	rs140003541	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:21300284A>G	ENST00000596143.1	+	5	1139	c.814A>G	c.(814-816)Act>Gct	p.T272A	ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	272					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						TTCAGCCCTTACTACACATAA	0.353													.|||	26	0.00519169	0.0015	0.0144	5008	,	,		21973	0.001		0.0099	False		,,,				2504	0.0031				p.T272A		Atlas-SNP	.											.	ZNF714	121	.	0			c.A814G						PASS	.	A	ALA/THR	16,4320		0,16,2152	28.0	30.0	29.0		814	-1.1	0.0	19	dbSNP_134	29	130,8424		1,128,4148	no	missense	ZNF714	NM_182515.3	58	1,144,6300	GG,GA,AA		1.5198,0.369,1.1327	possibly-damaging	272/555	21300284	146,12744	2168	4277	6445	SO:0001583	missense	148206	exon5			GCCCTTACTACAC	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.814A>G	19.37:g.21300284A>G	ENSP00000472368:p.Thr272Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	8	0.010554089709762533	.	8.090	0.774274	0.16051	0.00369	0.015198	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	-1.12	0.09808	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12817	0.0311	N	0.16602	0.42	0.09310	N	1	B;P;P	0.37423	0.019;0.578;0.594	B;B;P	0.44477	0.031;0.297;0.451	T	0.23691	-1.0181	8	0.41790	T	0.15	.	5.5708	0.17196	0.5925:0.4074:0.0:0.0	.	273;272;273	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	A	272	.	ENSP00000291770:T272A	T	+	1	0	ZNF714	21092124	0.000000	0.05858	0.015000	0.15790	0.015000	0.08874	-0.701000	0.05075	0.378000	0.24764	0.369000	0.22263	ACT	A|0.990;G|0.010	0.010	strong		0.353	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
MUC6	4588	hgsc.bcm.edu	37	11	1016849	1016849	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	1298	46	0.0354391		WXS	Illumina HiSeq	Phase_I	1063	51	0.0479774	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	
FERMT1	55612	hgsc.bcm.edu	37	20	6096632	6096632	+	Silent	SNP	G	G	A	rs1056141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:6096632G>A	ENST00000217289.4	-	3	999	c.211C>T	c.(211-213)Ctg>Ttg	p.L71L	FERMT1_ENST00000536936.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	71					cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						TGGGTTTTCAGAAGCCAGCAA	0.468													G|||	442	0.0882588	0.1339	0.0576	5008	,	,		20955	0.0794		0.0905	False		,,,				2504	0.0552				p.L71L		Atlas-SNP	.											.	FERMT1	106	.	0			c.C211T						PASS	.	G		594,3812	260.1+/-263.5	47,500,1656	50.0	51.0	51.0		211	5.5	1.0	20	dbSNP_86	51	816,7784	188.9+/-235.7	33,750,3517	no	coding-synonymous	FERMT1	NM_017671.4		80,1250,5173	AA,AG,GG		9.4884,13.4816,10.8412		71/678	6096632	1410,11596	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon3			TTTTCAGAAGCCA	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.211C>T	20.37:g.6096632G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	125	79	0.632	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			G|0.894;A|0.106	0.106	strong		0.468	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
BEST3	144453	hgsc.bcm.edu	37	12	70048829	70048829	+	Missense_Mutation	SNP	T	T	C	rs17106884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:70048829T>C	ENST00000330891.5	-	10	2091	c.1865A>G	c.(1864-1866)gAa>gGa	p.E622G	BEST3_ENST00000488961.1_Missense_Mutation_p.E409G|BEST3_ENST00000331471.4_Intron|BEST3_ENST00000553096.1_Missense_Mutation_p.E516G	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	622			E -> G (in dbSNP:rs17106884).		negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.E622G(1)		cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			TGAGGATGTTTCTGTGTCAAT	0.493													T|||	217	0.0433307	0.0893	0.0432	5008	,	,		19055	0.0099		0.0388	False		,,,				2504	0.0204				p.E622G		Atlas-SNP	.											BEST3_ENST00000330891,NS,carcinoma,0,1	BEST3	129	1	1	Substitution - Missense(1)	stomach(1)	c.A1865G						PASS	.	T	GLY/GLU,GLY/GLU	277,3509		8,261,1624	88.0	85.0	86.0		1865,1226	5.5	0.0	12	dbSNP_123	86	267,7983		6,255,3864	yes	missense,missense	BEST3	NM_032735.2,NM_152439.2	98,98	14,516,5488	CC,CT,TT		3.2364,7.3164,4.5198	benign,benign	622/669,409/456	70048829	544,11492	1893	4125	6018	SO:0001583	missense	144453	exon10			GATGTTTCTGTGT	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17105	protein-coding gene	gene with protein product		607337	"""vitelliform macular dystrophy 2-like 3"""	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.1865A>G	12.37:g.70048829T>C	ENSP00000332413:p.Glu622Gly	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000330891.5	37	CCDS8992.2	90	0.04120879120879121	38	0.07723577235772358	15	0.04143646408839779	8	0.013986013986013986	29	0.03825857519788918	T	14.57	2.575692	0.45902	0.073164	0.032364	ENSG00000127325	ENST00000488961;ENST00000330891;ENST00000553096	D;D;D	0.98135	-4.43;-4.74;-4.71	5.53	5.53	0.82687	.	0.451458	0.22531	N	0.058858	T	0.62356	0.2421	L	0.36672	1.1	0.23962	N	0.996331	B;B	0.12630	0.002;0.006	B;B	0.12156	0.002;0.007	T	0.76364	-0.2986	10	0.49607	T	0.09	-8.88	10.87	0.46877	0.0:0.0:0.1572:0.8428	rs17106884;rs17106884	622;409	Q8N1M1;B5MDI8	BEST3_HUMAN;.	G	409;622;516	ENSP00000433213:E409G;ENSP00000332413:E622G;ENSP00000449548:E516G	ENSP00000332413:E622G	E	-	2	0	BEST3	68335096	0.002000	0.14202	0.022000	0.16811	0.592000	0.36648	0.750000	0.26334	2.095000	0.63458	0.460000	0.39030	GAA	T|0.955;C|0.045	0.045	strong		0.493	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439	
CHPT1	56994	hgsc.bcm.edu	37	12	102108301	102108301	+	Silent	SNP	T	T	C	rs2066920	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102108301T>C	ENST00000229266.3	+	3	676	c.441T>C	c.(439-441)gcT>gcC	p.A147A	CHPT1_ENST00000550385.1_3'UTR|CHPT1_ENST00000549872.1_Silent_p.A147A	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	147					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CAGTGGGAGCTTCAATTGCCG	0.333													T|||	516	0.103035	0.0325	0.1614	5008	,	,		15157	0.1687		0.1143	False		,,,				2504	0.0777				p.A147A		Atlas-SNP	.											.	CHPT1	27	.	0			c.T441C						PASS	.	T		228,4178	135.3+/-171.4	8,212,1983	106.0	96.0	100.0		441	-3.0	0.8	12	dbSNP_94	100	1062,7538	223.4+/-260.2	67,928,3305	no	coding-synonymous	CHPT1	NM_020244.2		75,1140,5288	CC,CT,TT		12.3488,5.1748,9.9185		147/407	102108301	1290,11716	2203	4300	6503	SO:0001819	synonymous_variant	56994	exon3			GGGAGCTTCAATT		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"""phosphatidylcholine synthesizing enzyme"""					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.441T>C	12.37:g.102108301T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	207	99	0.478261	NM_020244	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Silent	SNP	ENST00000229266.3	37	CCDS9086.1																																																																																			C|0.107;T|0.893	0.107	strong		0.333	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244	
PASK	23178	hgsc.bcm.edu	37	2	242072357	242072357	+	Silent	SNP	G	G	A	rs34401965	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242072357G>A	ENST00000405260.1	-	9	2093	c.1395C>T	c.(1393-1395)acC>acT	p.T465T	PASK_ENST00000234040.4_Silent_p.T465T|PASK_ENST00000358649.4_Silent_p.T465T|PASK_ENST00000403638.3_Silent_p.T465T|PASK_ENST00000544142.1_Silent_p.T279T|PASK_ENST00000539818.1_Silent_p.T249T	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	465					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)		TCTGAGTCCCGGTGAAGATGT	0.562													G|||	383	0.0764776	0.056	0.0562	5008	,	,		20239	0.0169		0.0825	False		,,,				2504	0.1738				p.T465T		Atlas-SNP	.											.	PASK	230	.	0			c.C1395T						PASS	.	G		273,4133	154.0+/-187.5	13,247,1943	115.0	96.0	102.0		1395	-5.9	0.0	2	dbSNP_126	102	772,7828	184.3+/-232.3	36,700,3564	no	coding-synonymous	PASK	NM_015148.2		49,947,5507	AA,AG,GG		8.9767,6.1961,8.0348		465/1324	242072357	1045,11961	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon9			AGTCCCGGTGAAG	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.1395C>T	2.37:g.242072357G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			G|0.925;A|0.075	0.075	strong		0.562	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
TSC22D4	81628	hgsc.bcm.edu	37	7	100064719	100064719	+	Silent	SNP	A	A	G	rs7806537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100064719A>G	ENST00000300181.2	-	5	1805	c.1051T>C	c.(1051-1053)Ttg>Ctg	p.L351L	TSC22D4_ENST00000496728.1_Intron|C7orf61_ENST00000332375.3_5'Flank|TSC22D4_ENST00000393991.1_Silent_p.L112L	NM_030935.3	NP_112197.1	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	351	Leucine-zipper.				negative regulation of transcription, DNA-templated (GO:0045892)|response to osmotic stress (GO:0006970)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGCTCCGCCAATTCCCGGATC	0.692													G|||	1684	0.336262	0.4478	0.2651	5008	,	,		16634	0.0972		0.3956	False		,,,				2504	0.4213				p.L351L		Atlas-SNP	.											TSC22D4,NS,carcinoma,0,1	TSC22D4	28	1	0			c.T1051C						PASS	.	G		1922,2484	624.6+/-394.4	428,1066,709	50.0	51.0	51.0		1051	3.3	1.0	7	dbSNP_116	51	3333,5267	643.3+/-399.9	640,2053,1607	no	coding-synonymous	TSC22D4	NM_030935.3		1068,3119,2316	GG,GA,AA		38.7558,43.6223,40.4044		351/396	100064719	5255,7751	2203	4300	6503	SO:0001819	synonymous_variant	81628	exon5			CCGCCAATTCCCG	BC010406	CCDS5695.1	7p21-p15	2010-04-30			ENSG00000166925	ENSG00000166925			21696	protein-coding gene	gene with protein product		611914					Standard	NM_030935		Approved	THG-1, TILZ2	uc003uva.3	Q9Y3Q8	OTTHUMG00000150233	ENST00000300181.2:c.1051T>C	7.37:g.100064719A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	165	88	0.533333	NM_030935	A4D2C3|A8MWR6|D6W5V9	Silent	SNP	ENST00000300181.2	37	CCDS5695.1																																																																																			A|0.644;G|0.356	0.356	strong		0.692	TSC22D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316970.1	NM_030935	
KNG1	3827	hgsc.bcm.edu	37	3	186459927	186459927	+	Missense_Mutation	SNP	T	T	C	rs710446	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:186459927T>C	ENST00000265023.4	+	10	1954	c.1742T>C	c.(1741-1743)aTa>aCa	p.I581T	KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|KNG1_ENST00000287611.2_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	581			I -> T (in dbSNP:rs710446).		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)	p.I581T(1)		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)		CCAGCTCCCATACAGAGTGAT	0.448													C|||	2080	0.415335	0.5204	0.4654	5008	,	,		21496	0.2966		0.4175	False		,,,				2504	0.3579				p.I581T		Atlas-SNP	.											KNG1_ENST00000265023,NS,carcinoma,0,1	KNG1	129	1	1	Substitution - Missense(1)	stomach(1)	c.T1742C						PASS	.	C	,THR/ILE,	1968,1958		501,966,496	149.0	140.0	143.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,1742,	5.6	1.0	3	dbSNP_86	143	3422,4850		747,1928,1461	yes	intron,missense,intron	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,89,	1248,2894,1957	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	41.3685,49.8726,44.1876	,benign,	,581/645,	186459927	5390,6808	1963	4136	6099	SO:0001583	missense	3827	exon10			CTCCCATACAGAG		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.1742T>C	3.37:g.186459927T>C	ENSP00000265023:p.Ile581Thr	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	236	236	1	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	37	CCDS43183.1	916	0.4194139194139194	254	0.516260162601626	181	0.5	164	0.2867132867132867	317	0.4182058047493404	C	0.015	-1.546701	0.00926	0.501274	0.413685	ENSG00000113889	ENST00000265023	T	0.11712	2.75	5.61	5.61	0.85477	.	0.141093	0.33092	N	0.005282	T	0.00012	0.0000	N	0.00289	-1.7	0.09310	P	0.9999999999999405	B	0.02656	0.0	B	0.01281	0.0	T	0.34650	-0.9820	8	.	.	.	-7.9109	11.0572	0.47925	0.0:0.9148:0.0:0.0852	rs710446;rs1656898;rs52828577;rs59963046;rs710446	581	P01042	KNG1_HUMAN	T	581	ENSP00000265023:I581T	.	I	+	2	0	KNG1	187942621	0.667000	0.27484	0.974000	0.42286	0.026000	0.11368	1.999000	0.40806	1.546000	0.49388	-0.119000	0.15052	ATA	T|0.573;G|0.006	.	strong		0.448	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
RABGEF1	27342	hgsc.bcm.edu	37	7	66274184	66274184	+	Silent	SNP	G	G	A	rs61758774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:66274184G>A	ENST00000284957.5	+	9	1466	c.1389G>A	c.(1387-1389)ccG>ccA	p.P463P	GTF2IRD1P1_ENST00000457166.1_RNA|RABGEF1_ENST00000437078.2_Silent_p.P477P|KCTD7_ENST00000380828.2_Silent_p.P503P|RABGEF1_ENST00000484547.2_3'UTR|KCTD7_ENST00000510829.2_Silent_p.P463P|KCTD7_ENST00000451741.2_Silent_p.P463P|RABGEF1_ENST00000439720.2_Silent_p.P476P|RABGEF1_ENST00000450873.2_Silent_p.P463P			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	680	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						TTAAGCCTCCGAATCAACCGT	0.403													g|||	14	0.00279553	0.0008	0.0058	5008	,	,		21231	0.0		0.004	False		,,,				2504	0.0051				p.P463P		Atlas-SNP	.											.	RABGEF1	56	.	0			c.G1389A						PASS	.	G		8,4398	15.5+/-35.6	0,8,2195	71.0	70.0	70.0		1389	-5.5	0.1	7	dbSNP_129	70	74,8526	44.0+/-102.2	1,72,4227	no	coding-synonymous	RABGEF1	NM_014504.2		1,80,6422	AA,AG,GG		0.8605,0.1816,0.6305		463/492	66274184	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	27342	exon9			GCCTCCGAATCAA	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.1389G>A	7.37:g.66274184G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_014504	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Silent	SNP	ENST00000284957.5	37	CCDS5535.1																																																																																			G|0.995;A|0.005	0.005	strong		0.403	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504	
MYH4	4622	hgsc.bcm.edu	37	17	10348354	10348354	+	Missense_Mutation	SNP	T	T	C	rs2277649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10348354T>C	ENST00000255381.2	-	37	5515	c.5405A>G	c.(5404-5406)gAt>gGt	p.D1802G	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1802			D -> G (in dbSNP:rs2277649). {ECO:0000269|PubMed:10388558}.		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)			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						CTCAGCCTCATCCAGACGGAG	0.567													T|||	2278	0.454872	0.233	0.4755	5008	,	,		18937	0.8214		0.3181	False		,,,				2504	0.5031				p.D1802G		Atlas-SNP	.											.	MYH4	349	.	0			c.A5405G						PASS	.	T	GLY/ASP	1137,3269	405.8+/-333.6	141,855,1207	143.0	140.0	141.0		5405	5.5	0.9	17	dbSNP_100	141	3050,5550	469.9+/-367.7	536,1978,1786	no	missense	MYH4	NM_017533.2	94	677,2833,2993	CC,CT,TT		35.4651,25.8057,32.1928	possibly-damaging	1802/1940	10348354	4187,8819	2203	4300	6503	SO:0001583	missense	4622	exon37			GCCTCATCCAGAC		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.5405A>G	17.37:g.10348354T>C	ENSP00000255381:p.Asp1802Gly	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	214	96	0.448598	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	979	0.4482600732600733	106	0.21544715447154472	162	0.44751381215469616	473	0.8269230769230769	238	0.31398416886543534	T	19.34	3.809062	0.70797	0.258057	0.354651	ENSG00000141048	ENST00000255381	T	0.78481	-1.18	5.5	5.5	0.81552	Myosin tail (1);	0.000000	0.38605	U	0.001638	T	0.00012	0.0000	H	0.95079	3.62	0.09310	P	0.999999246958	D	0.63880	0.993	D	0.70487	0.969	T	0.47761	-0.9092	9	0.87932	D	0	.	15.8867	0.79255	0.0:0.0:0.0:1.0	rs2277649;rs61532457;rs2277649	1802	Q9Y623	MYH4_HUMAN	G	1802	ENSP00000255381:D1802G	ENSP00000255381:D1802G	D	-	2	0	MYH4	10289079	1.000000	0.71417	0.938000	0.37757	0.170000	0.22686	6.257000	0.72480	2.214000	0.71695	0.482000	0.46254	GAT	T|0.644;C|0.356	0.356	strong		0.567	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
C14orf39	317761	hgsc.bcm.edu	37	14	60932752	60932752	+	Missense_Mutation	SNP	G	G	A	rs12586711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:60932752G>A	ENST00000321731.3	-	11	1076	c.917C>T	c.(916-918)gCg>gTg	p.A306V		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	306				A -> V (in Ref. 1; BAC05253). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TGACTGCTTCGCAGAACTTTC	0.313													g|||	1079	0.215455	0.0393	0.121	5008	,	,		14149	0.5516		0.2197	False		,,,				2504	0.1697				p.A306V		Atlas-SNP	.											.	C14orf39	79	.	0			c.C917T						PASS	.	G	VAL/ALA	346,4056	178.0+/-206.8	13,320,1868	50.0	51.0	51.0		917	-1.9	0.0	14	dbSNP_120	51	1800,6794	318.0+/-313.5	181,1438,2678	yes	missense	C14orf39	NM_174978.2	64	194,1758,4546	AA,AG,GG		20.9448,7.8601,16.5128	benign	306/588	60932752	2146,10850	2201	4297	6498	SO:0001583	missense	317761	exon11			TGCTTCGCAGAAC	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.917C>T	14.37:g.60932752G>A	ENSP00000324920:p.Ala306Val	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	542	0.24816849816849818	15	0.03048780487804878	57	0.1574585635359116	302	0.527972027972028	168	0.22163588390501318	g	0.009	-1.801153	0.00611	0.078601	0.209448	ENSG00000179008	ENST00000321731	T	0.22134	1.97	5.68	-1.88	0.07713	.	1.276350	0.05272	N	0.517772	T	0.00012	0.0000	N	0.01267	-0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	9	0.13108	T	0.6	2.3088	10.289	0.43584	0.4884:0.0:0.5116:0.0	rs12586711;rs12586711	306	Q8N1H7	S6OS1_HUMAN	V	306	ENSP00000324920:A306V	ENSP00000324920:A306V	A	-	2	0	C14orf39	60002505	0.000000	0.05858	0.025000	0.17156	0.142000	0.21351	0.038000	0.13862	-0.110000	0.12022	-1.068000	0.02270	GCG	G|0.800;A|0.200	0.200	strong		0.313	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	
ANKRD35	148741	hgsc.bcm.edu	37	1	145561116	145561116	+	Silent	SNP	G	G	A	rs11578772	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:145561116G>A	ENST00000355594.4	+	10	891	c.804G>A	c.(802-804)caG>caA	p.Q268Q	ANKRD35_ENST00000544626.1_3'UTR	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	268										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTGAGCCCCAGGCAGGTTCTC	0.527													G|||	183	0.0365415	0.0023	0.0692	5008	,	,		19121	0.0		0.1133	False		,,,				2504	0.0184				p.Q268Q	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G804A						PASS	.	G		115,4291	81.4+/-119.9	5,105,2093	35.0	41.0	39.0		804	0.8	0.9	1	dbSNP_120	39	1073,7527	221.5+/-258.9	75,923,3302	no	coding-synonymous	ANKRD35	NM_144698.3		80,1028,5395	AA,AG,GG		12.4767,2.6101,9.1342		268/1002	145561116	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	148741	exon10			GCCCCAGGCAGGT	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.804G>A	1.37:g.145561116G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	37	CCDS919.1																																																																																			G|0.922;A|0.078	0.078	strong		0.527	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
OR10G8	219869	hgsc.bcm.edu	37	11	123901175	123901175	+	Silent	SNP	C	C	A	rs11825515	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123901175C>A	ENST00000431524.1	+	1	879	c.846C>A	c.(844-846)ctC>ctA	p.L282L		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L282L(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)		CGCCCCTTCTCAACCCTGTTG	0.498													C|||	367	0.0732827	0.1286	0.0202	5008	,	,		19804	0.0734		0.0308	False		,,,				2504	0.0798				p.L282L		Atlas-SNP	.											OR10G8,middle_lobe,carcinoma,+1,2	OR10G8	132	2	1	Substitution - coding silent(1)	stomach(1)	c.C846A						PASS	.	C		536,3866	243.1+/-252.9	31,474,1696	121.0	116.0	118.0		846	-0.1	0.9	11	dbSNP_120	118	267,8331	102.3+/-163.5	4,259,4036	no	coding-synonymous	OR10G8	NM_001004464.1		35,733,5732	AA,AC,CC		3.1054,12.1763,6.1769		282/312	123901175	803,12197	2201	4299	6500	SO:0001819	synonymous_variant	219869	exon1			CCTTCTCAACCCT	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.846C>A	11.37:g.123901175C>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	195	88	0.451282	NM_001004464	B2RNJ3|Q6IEV2	Silent	SNP	ENST00000431524.1	37	CCDS31704.1																																																																																			A|0.066;C|0.934;T|0.000	0.066	strong		0.498	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
TMCO3	55002	hgsc.bcm.edu	37	13	114154419	114154419	+	Silent	SNP	G	G	A	rs2260159	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:114154419G>A	ENST00000434316.2	+	4	1130	c.771G>A	c.(769-771)aaG>aaA	p.K257K	TMCO3_ENST00000474393.1_3'UTR|TMCO3_ENST00000375391.1_Silent_p.K257K	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	113	0	0		WXS	Illumina HiSeq	Phase_I	157	61	0.388535	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	
ZNF880	400713	hgsc.bcm.edu	37	19	52876385	52876385	+	Missense_Mutation	SNP	G	G	A	rs14048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:52876385G>A	ENST00000422689.2	+	2	49	c.34G>A	c.(34-36)Gtg>Atg	p.V12M	ZNF880_ENST00000344085.5_Missense_Mutation_p.V12M|ZNF880_ENST00000600321.1_Missense_Mutation_p.V12M|ZNF880_ENST00000424032.2_Missense_Mutation_p.V12M|ZNF880_ENST00000595099.1_3'UTR|ZNF880_ENST00000597976.1_Missense_Mutation_p.V12M	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	12	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						ATTCAGGGACGTGGCCATAGA	0.453													g|||	202	0.0403355	0.0061	0.0303	5008	,	,		15687	0.0		0.1163	False		,,,				2504	0.0573				p.V12M		Atlas-SNP	.											.	ZNF880	45	.	0			c.G34A						PASS	.	G	MET/VAL	33,1351		0,33,659	117.0	101.0	106.0		34	1.6	0.9	19	dbSNP_52	106	343,2839		17,309,1265	no	missense	ZNF880	NM_001145434.1	21	17,342,1924	AA,AG,GG		10.7794,2.3844,8.2348	probably-damaging	12/578	52876385	376,4190	692	1591	2283	SO:0001583	missense	400713	exon2			AGGGACGTGGCCA	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.34G>A	19.37:g.52876385G>A	ENSP00000406318:p.Val12Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	39	0.361111	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	109	0.04990842490842491	5	0.01016260162601626	14	0.03867403314917127	0	0.0	90	0.11873350923482849	g	9.241	1.038238	0.19669	0.023844	0.107794	ENSG00000221923	ENST00000424032;ENST00000344085;ENST00000422689	T;T;T	0.10382	2.88;2.88;2.88	1.61	1.61	0.23674	Krueppel-associated box (4);	.	.	.	.	T	0.00524	0.0017	H	0.95539	3.685	0.51012	P	9.199999999998099E-5	D	0.76494	0.999	P	0.59357	0.856	T	0.11275	-1.0594	8	0.66056	D	0.02	.	8.2474	0.31698	0.0:0.0:1.0:0.0	rs14048;rs1129900;rs3177668;rs3188205;rs11546948;rs17296839;rs17355912	12	Q6PDB4	ZN880_HUMAN	M	12	ENSP00000414470:V12M;ENSP00000343625:V12M;ENSP00000406318:V12M	ENSP00000343625:V12M	V	+	1	0	ZNF880	57568197	0.985000	0.35326	0.861000	0.33841	0.107000	0.19398	1.214000	0.32419	0.870000	0.35726	0.305000	0.20034	GTG	G|0.941;A|0.059	0.059	strong		0.453	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
APEH	327	hgsc.bcm.edu	37	3	49723784	49723784	+	IGR	SNP	C	C	A	rs9713651	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49723784C>A	ENST00000296456.5	+	0	3220				MST1_ENST00000383728.3_Silent_p.P251P|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000545762.1_3'UTR|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000449682.2_Silent_p.P326P	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)		GGTGCTGATGCGGGATTTGCG	0.647																																					p.P326P		Atlas-SNP	.											.	MST1	84	.	0			c.G978T						PASS	.	C		1307,3095		67,1173,961	22.0	21.0	22.0		978	-2.8	0.9	3	dbSNP_119	22	3605,4981		373,2859,1061	no	coding-synonymous	MST1	NM_020998.3		440,4032,2022	AA,AC,CC		41.987,29.691,37.8195		326/726	49723784	4912,8076	2201	4293	6494	SO:0001628	intergenic_variant	4485	exon8			CTGATGCGGGATT	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.49723784C>A		Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	243	152	0.625514	NM_020998	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1																																																																																			C|0.562;A|0.438	0.438	strong		0.647	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
CSMD3	114788	hgsc.bcm.edu	37	8	113364697	113364697	+	Missense_Mutation	SNP	T	T	C	rs139786530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:113364697T>C	ENST00000297405.5	-	39	6447	c.6203A>G	c.(6202-6204)tAt>tGt	p.Y2068C	CSMD3_ENST00000343508.3_Missense_Mutation_p.Y2028C|CSMD3_ENST00000455883.2_Missense_Mutation_p.Y1964C|CSMD3_ENST00000352409.3_Missense_Mutation_p.Y1998C	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2068	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Y2028C(1)|p.Y2068C(1)		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						TCCAACCATATATCTGTCTCC	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	3	0.000599042	0.0	0.0014	5008	,	,		16755	0.0		0.002	False		,,,				2504	0.0				p.Y2068C		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	2	2	Substitution - Missense(2)	lung(2)	c.A6203G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	2,4404	4.2+/-10.8	0,2,2201	110.0	103.0	105.0		5891,6203,6083	5.0	1.0	8	dbSNP_134	105	16,8582	11.2+/-40.8	0,16,4283	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	194,194,194	0,18,6484	CC,CT,TT		0.1861,0.0454,0.1384	probably-damaging,probably-damaging,probably-damaging	1964/3539,2068/3708,2028/3668	113364697	18,12986	2203	4299	6502	SO:0001583	missense	114788	exon39			ACCATATATCTGT	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.6203A>G	8.37:g.113364697T>C	ENSP00000297405:p.Tyr2068Cys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	141	48	0.340426	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	18.72	3.684011	0.68157	4.54E-4	0.001861	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44	4.96	4.96	0.65561	Complement control module (2);Sushi/SCR/CCP (3);	0.084638	0.49305	D	0.000151	D	0.85652	0.5746	M	0.93808	3.46	0.50467	D	0.999878	D;D;D	0.76494	0.999;0.996;0.999	D;D;D	0.72625	0.959;0.926;0.978	D	0.89488	0.3755	10	0.72032	D	0.01	.	15.0773	0.72087	0.0:0.0:0.0:1.0	.	1964;2068;2028	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	C	2028;2068;1338;1964;1998	ENSP00000345799:Y2028C;ENSP00000297405:Y2068C;ENSP00000341558:Y1338C;ENSP00000412263:Y1964C;ENSP00000343124:Y1998C	ENSP00000297405:Y2068C	Y	-	2	0	CSMD3	113433873	1.000000	0.71417	0.980000	0.43619	0.996000	0.88848	5.007000	0.63984	2.205000	0.71048	0.533000	0.62120	TAT	T|0.999;C|0.001	0.001	strong		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
FARSA	2193	hgsc.bcm.edu	37	19	13035722	13035722	+	Missense_Mutation	SNP	T	T	C	rs35087277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:13035722T>C	ENST00000314606.4	-	9	1040	c.1022A>G	c.(1021-1023)cAg>cGg	p.Q341R	FARSA_ENST00000423140.2_Missense_Mutation_p.Q310R|FARSA_ENST00000588025.1_Missense_Mutation_p.Q381R	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	341			Q -> R (in dbSNP:rs35087277).		gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	CCGCACCTTCTGGGCAAGGCG	0.627													T|||	38	0.00758786	0.0015	0.0043	5008	,	,		16893	0.0		0.0318	False		,,,				2504	0.001				p.Q341R		Atlas-SNP	.											.	FARSA	46	.	0			c.A1022G						PASS	.	T	ARG/GLN	29,4377	36.0+/-67.5	0,29,2174	82.0	86.0	85.0		1022	4.6	1.0	19	dbSNP_126	85	261,8339	100.1+/-161.6	3,255,4042	yes	missense	FARSA	NM_004461.2	43	3,284,6216	CC,CT,TT		3.0349,0.6582,2.2297	benign	341/509	13035722	290,12716	2203	4300	6503	SO:0001583	missense	2193	exon9			ACCTTCTGGGCAA	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	3592	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, alpha, cytoplasmic"""	602918	"""phenylalanine-tRNA synthetase-like"", ""phenylalanyl-tRNA synthetase-like, alpha subunit"""	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.1022A>G	19.37:g.13035722T>C	ENSP00000320309:p.Gln341Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Missense_Mutation	SNP	ENST00000314606.4	37	CCDS12287.1	30	0.013736263736263736	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	26	0.03430079155672823	T	12.52	1.962335	0.34659	0.006582	0.030349	ENSG00000179115	ENST00000314606;ENST00000423140	T;T	0.62941	-0.01;-0.01	5.56	4.55	0.56014	Aminoacyl-tRNA synthetase, class II (1);Phenylalanyl-tRNA synthetase (1);	0.177406	0.51477	N	0.000097	T	0.26955	0.0660	L	0.38953	1.18	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.14023	0.003;0.01;0.01	T	0.26608	-1.0098	10	0.48119	T	0.1	-9.325	10.5465	0.45062	0.0:0.0773:0.0:0.9227	rs35087277	310;341;341	B4E363;Q6IBR2;Q9Y285	.;.;SYFA_HUMAN	R	341;310	ENSP00000320309:Q341R;ENSP00000396548:Q310R	ENSP00000320309:Q341R	Q	-	2	0	FARSA	12896722	1.000000	0.71417	0.996000	0.52242	0.028000	0.11728	3.134000	0.50538	0.946000	0.37632	0.459000	0.35465	CAG	T|0.980;C|0.020	0.020	strong		0.627	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
ABCB1	5243	hgsc.bcm.edu	37	7	87160618	87160618	+	Missense_Mutation	SNP	A	A	C	rs2032582	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:87160618A>C	ENST00000265724.3	-	22	3094	c.2677T>G	c.(2677-2679)Tct>Gct	p.S893A	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Missense_Mutation_p.S829A	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	893	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		S -> A (common allele; associated with susceptibility to IBD13; has decreased enzyme activity; dbSNP:rs2032582). {ECO:0000269|PubMed:11240981, ECO:0000269|PubMed:11829140, ECO:0000269|PubMed:14610718, ECO:0000269|PubMed:1967175, ECO:0000269|PubMed:2876781, ECO:0000269|PubMed:9038218, ECO:0000269|PubMed:9473242, ECO:0000269|Ref.5}.|S -> T (rare allele; dbSNP:rs2032582). {ECO:0000269|PubMed:11240981, ECO:0000269|PubMed:11829140, ECO:0000269|PubMed:14610718}.		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)	ACCTTCCCAGAACCTTCTAGT	0.343													C|||	3090	0.617013	0.9796	0.572	5008	,	,		18212	0.4683		0.5726	False		,,,				2504	0.3579				p.S893A		Atlas-SNP	.											ABCB1,NS,carcinoma,+1,1	ABCB1	263	1	0			c.T2677G	GRCh37	CM033585|CM065955	ABCB1	M	rs2032582	PASS	.	C	ALA/SER	3930,476	222.6+/-239.4	1760,410,33	115.0	118.0	117.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2677	3.7	1.0	7	dbSNP_94	117	4889,3711	525.4+/-380.7	1432,2025,843	yes	missense	ABCB1	NM_000927.4	99	3192,2435,876	CC,CA,AA		43.1512,10.8034,32.1928	benign	893/1281	87160618	8819,4187	2203	4300	6503	SO:0001583	missense	5243	exon22			TCCCAGAACCTTC	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.2677T>G	7.37:g.87160618A>C	ENSP00000265724:p.Ser893Ala	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	1440	0.6593406593406593	478	0.9715447154471545	214	0.5911602209944752	317	0.5541958041958042	431	0.5686015831134564	C	5.057	0.196173	0.09599	0.891966	0.568488	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.87334	-2.24;-2.24	5.67	3.72	0.42706	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.218654	0.46442	N	0.000295	T	0.00012	0.0000	N	0.01152	-0.98	0.46654	P	8.569999999999967E-4	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.002	T	0.48536	-0.9027	9	0.02654	T	1	-8.4387	14.5627	0.68151	0.4865:0.5135:0.0:0.0	rs2032582;rs2229106;rs9641018;rs10228331;rs57135550;rs2032582	829;893	B5AK60;P08183	.;MDR1_HUMAN	A	674;893;829	ENSP00000265724:S893A;ENSP00000444095:S829A	ENSP00000265724:S893A	S	-	1	0	ABCB1	86998554	0.998000	0.40836	0.999000	0.59377	0.978000	0.69477	2.118000	0.41949	0.319000	0.23209	-0.187000	0.12897	TCT	T|0.004;G|0.002;C|0.656;A|0.337	0.656	strong		0.343	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
EXT1	2131	hgsc.bcm.edu	37	8	118819578	118819578	+	Silent	SNP	C	C	T	rs7837891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:118819578C>T	ENST00000378204.2	-	9	2567	c.1761G>A	c.(1759-1761)gaG>gaA	p.E587E		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	587					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|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 development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|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)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			CCACAATCCTCTCAGGGAAGC	0.502			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses				C|||	1695	0.338458	0.1634	0.549	5008	,	,		17366	0.38		0.4185	False		,,,				2504	0.3006				p.E587E		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.G1761A						PASS	.	C		935,3471	357.6+/-314.0	104,727,1372	73.0	65.0	68.0		1761	5.9	1.0	8	dbSNP_116	68	3631,4969	524.4+/-380.5	771,2089,1440	no	coding-synonymous	EXT1	NM_000127.2		875,2816,2812	TT,TC,CC		42.2209,21.2211,35.1069		587/747	118819578	4566,8440	2203	4300	6503	SO:0001819	synonymous_variant	2131	exon9	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	AATCCTCTCAGGG	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3512	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608177	"""Langer-Giedion syndrome chromosome region"", ""exostoses (multiple) 1"", ""exostosin 1"""	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1761G>A	8.37:g.118819578C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1																																																																																			C|0.659;T|0.341	0.341	strong		0.502	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
DOCK11	139818	hgsc.bcm.edu	37	X	117676909	117676909	+	Silent	SNP	A	A	G	rs17326744	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:117676909A>G	ENST00000276202.7	+	3	303	c.240A>G	c.(238-240)caA>caG	p.Q80Q	DOCK11_ENST00000276204.6_Silent_p.Q80Q	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	80	Interaction with activated CDC42. {ECO:0000250}.				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						TAGGTCGTCAACGCAGAACGG	0.403													A|||	151	0.04	0.0045	0.0303	3775	,	,		7882	0.001		0.1004	False		,,,				2504	0.0225				p.Q80Q		Atlas-SNP	.											.	DOCK11	185	.	0			c.A240G						PASS	.	A		49,3786		1,41,6,1590,565	106.0	99.0	102.0		240	-1.3	0.9	X	dbSNP_123	102	659,6069		18,428,195,1982,1677	no	coding-synonymous	DOCK11	NM_144658.3		19,469,201,3572,2242	GG,GA,G,AA,A		9.7949,1.2777,6.7026		80/2074	117676909	708,9855	2203	4300	6503	SO:0001819	synonymous_variant	139818	exon3			TCGTCAACGCAGA	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.240A>G	X.37:g.117676909A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			A|0.929;0|0.016	.	strong		0.403	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
GRIN3B	116444	hgsc.bcm.edu	37	19	1004844	1004844	+	Silent	SNP	T	T	C	rs4806909	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1004844T>C	ENST00000234389.3	+	3	1363	c.1344T>C	c.(1342-1344)ccT>ccC	p.P448P	AC004528.4_ENST00000588380.1_RNA|GRIN3B_ENST00000588335.1_3'UTR	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	448					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)	GCCTGGACCCTGGCACCAACG	0.652													N|||	1605	0.320487	0.4213	0.2421	5008	,	,		15607	0.1667		0.3847	False		,,,				2504	0.3323				p.P448P		Atlas-SNP	.											GRIN3B,rectum,carcinoma,0,1	GRIN3B	46	1	0			c.T1344C						PASS	.	C		1841,2565	616.7+/-392.8	383,1075,745	51.0	50.0	50.0		1344	-9.2	0.0	19	dbSNP_111	50	3312,5280	623.5+/-397.5	640,2032,1624	no	coding-synonymous	GRIN3B	NM_138690.1		1023,3107,2369	CC,CT,TT		38.5475,41.7839,39.6446		448/1044	1004844	5153,7845	2203	4296	6499	SO:0001819	synonymous_variant	116444	exon3			GGACCCTGGCACC		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.1344T>C	19.37:g.1004844T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			T|0.639;C|0.361	0.361	strong		0.652	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
TTN	7273	hgsc.bcm.edu	37	2	179606590	179606590	+	Silent	SNP	T	T	C	rs72648918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179606590T>C	ENST00000591111.1	-	46	10643	c.10419A>G	c.(10417-10419)caA>caG	p.Q3473Q	TTN_ENST00000589042.1_Silent_p.Q3790Q|TTN_ENST00000359218.5_Silent_p.Q3552Q|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000460472.2_Silent_p.Q3427Q|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Silent_p.Q3619Q|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000578746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13796					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)			TTTTAGATAATTGAAGTTCGG	0.338													T|||	3	0.000599042	0.0	0.0014	5008	,	,		14760	0.0		0.002	False		,,,				2504	0.0				p.Q3790Q		Atlas-SNP	.											.	TTN	18412	.	0			c.A11370G						PASS	.	T	,,,	0,3592		0,0,1796	41.0	37.0	39.0		10281,,10656,10857	-1.6	0.0	2	dbSNP_130	39	8,8112		1,6,4053	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	1,6,5849	CC,CT,TT		0.0985,0.0,0.0683	,,,	3427/26927,,3552/27052,3619/27119	179606590	8,11704	1796	4060	5856	SO:0001819	synonymous_variant	7273	exon48			AGATAATTGAAGT	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.10419A>G	2.37:g.179606590T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	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|0.999;C|0.001	0.001	strong		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SLC25A6	293	hgsc.bcm.edu	37	X	1508324	1508324	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:1508324G>A	ENST00000381401.5	-	2	1122	c.408C>T	c.(406-408)ttC>ttT	p.F136F	SLC25A6_ENST00000475167.1_5'UTR	NM_001636.3	NP_001627.2	P12236	ADT3_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6	136					active induction of host immune response by virus (GO:0046732)|ADP transport (GO:0015866)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|modulation by virus of host morphology or physiology (GO:0019048)|protein targeting to mitochondrion (GO:0006626)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP:ADP antiporter activity (GO:0005471)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|upper_aerodigestive_tract(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Clodronate(DB00720)	GGGTTCTGGCGAAATCCAGCG	0.652													g|||	1617	0.322883	0.4856	0.3256	5008	,	,		17263	0.1062		0.2724	False		,,,				2504	0.3763				p.F136F		Atlas-SNP	.											.	SLC25A6	27	.	0			c.C408T						PASS	.	G		1974,2432		461,1052,690	110.0	118.0	115.0		408	-1.4	0.4	X	dbSNP_134	115	2176,6416		278,1620,2398	no	coding-synonymous	SLC25A6	NM_001636.3		739,2672,3088	AA,AG,GG		25.3259,44.8025,31.928		136/299	1508324	4150,8848	2203	4296	6499	SO:0001819	synonymous_variant	293	exon2			TCTGGCGAAATCC	AY007135	CCDS14114.1	Xp22.32 and Yp11.3	2013-05-22			ENSG00000169100	ENSG00000169100		"""Pseudoautosomal regions / PAR1"", ""Solute carriers"""	10992	protein-coding gene	gene with protein product		300151, 403000		ANT3			Standard	NM_001636		Approved	ANT3Y, MGC17525	uc004cpt.3	P12236	OTTHUMG00000021058	ENST00000381401.5:c.408C>T	X.37:g.1508324G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	187	88	0.470588	NM_001636	Q96C49	Silent	SNP	ENST00000381401.5	37	CCDS14114.1																																																																																			G|0.691;A|0.309	0.309	strong		0.652	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636	
PDIA2	64714	hgsc.bcm.edu	37	16	334543	334543	+	Missense_Mutation	SNP	C	C	G	rs45614840	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:334543C>G	ENST00000219406.6	+	2	374	c.356C>G	c.(355-357)aCg>aGg	p.T119R	PDIA2_ENST00000404312.1_Missense_Mutation_p.T119R	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	119	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.		T -> R (in dbSNP:rs45614840).		cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GAGTACCCTACGCTCAAGTTC	0.677													c|||	240	0.0479233	0.0045	0.0749	5008	,	,		16618	0.0		0.1421	False		,,,				2504	0.0399				p.T119R		Atlas-SNP	.											.	PDIA2	51	.	0			c.C356G						PASS	.	C	ARG/THR	110,4208		2,106,2051	55.0	62.0	59.0		356	3.2	0.8	16	dbSNP_127	59	1147,7363		69,1009,3177	yes	missense	PDIA2	NM_006849.2	71	71,1115,5228	GG,GC,CC		13.4783,2.5475,9.7989	probably-damaging	119/526	334543	1257,11571	2159	4255	6414	SO:0001583	missense	64714	exon2			ACCCTACGCTCAA	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.356C>G	16.37:g.334543C>G	ENSP00000219406:p.Thr119Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	137|137	0.06272893772893773|0.06272893772893773	3|3	0.006097560975609756|0.006097560975609756	31|31	0.0856353591160221|0.0856353591160221	0|0	0.0|0.0	103|103	0.1358839050131926|0.1358839050131926	c|c	13.79|13.79	2.341804|2.341804	0.41498|0.41498	0.025475|0.025475	0.134783|0.134783	ENSG00000185615|ENSG00000185615	ENST00000456379|ENST00000219406;ENST00000455994;ENST00000404312	.|T;T	.|0.05258	.|3.47;3.47	4.14|4.14	3.17|3.17	0.36434|0.36434	.|Thioredoxin domain (1);Thioredoxin-like fold (3);	.|0.273073	.|0.32578	.|N	.|0.005912	T|T	0.00271|0.00271	0.0008|0.0008	H|H	0.95151|0.95151	3.63|3.63	0.24811|0.24811	P|P	0.99264751|0.99264751	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.13575|0.13575	-1.0504|-1.0504	4|9	.|0.87932	.|D	.|0	.|.	11.2461|11.2461	0.48998|0.48998	0.0:0.9043:0.0:0.0957|0.0:0.9043:0.0:0.0957	rs45614840|rs45614840	.|119	.|Q13087	.|PDIA2_HUMAN	G|R	116|119;88;119	.|ENSP00000219406:T119R;ENSP00000384410:T119R	.|ENSP00000219406:T119R	R|T	+|+	1|2	0|0	PDIA2|PDIA2	274544|274544	0.053000|0.053000	0.20554|0.20554	0.797000|0.797000	0.32132|0.32132	0.182000|0.182000	0.23217|0.23217	1.869000|1.869000	0.39519|0.39519	1.873000|1.873000	0.54277|0.54277	0.550000|0.550000	0.68814|0.68814	CGC|ACG	C|0.922;G|0.078	0.078	strong		0.677	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45221423	45221423	+	Silent	SNP	A	A	T	rs3209476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45221423A>T	ENST00000389774.2	+	8	780	c.639A>T	c.(637-639)ccA>ccT	p.P213P	PRR5-ARHGAP8_ENST00000352766.7_Silent_p.P392P|ARHGAP8_ENST00000356099.6_Silent_p.P182P|ARHGAP8_ENST00000389773.5_Silent_p.P304P|ARHGAP8_ENST00000336963.4_Silent_p.P182P|ARHGAP8_ENST00000517296.3_Silent_p.P392P|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.P313P	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	213					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)		CCAAGACACCACCGCCGCGGC	0.652													a|||	732	0.146166	0.1914	0.085	5008	,	,		13154	0.0099		0.1948	False		,,,				2504	0.2188				p.P304P		Atlas-SNP	.											PRR5-ARHGAP8,colon,carcinoma,+1,2	PRR5-ARHGAP8	53	2	0			c.A912T						scavenged	.	A	,,,	846,3558	315.2+/-294.0	65,716,1421	31.0	33.0	33.0		639,546,912,546	-8.8	0.0	22	dbSNP_105	33	1678,6920	290.7+/-299.9	164,1350,2785	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	229,2066,4206	TT,TA,AA		19.5162,19.2098,19.4124	,,,	213/465,182/306,304/556,182/434	45221423	2524,10478	2202	4299	6501	SO:0001819	synonymous_variant	553158	exon10			GACACCACCGCCG	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.639A>T	22.37:g.45221423A>T		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	172	78	0.453488	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	268	0.1227106227106227	92	0.18699186991869918	29	0.08011049723756906	1	0.0017482517482517483	146	0.19261213720316622	a	6.831	0.522414	0.13066	0.192098	0.195162	ENSG00000248405	ENST00000515632	.	.	.	4.39	-8.78	0.00824	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.33833	P	0.36955499999999997	.	.	.	.	.	.	T	0.17837	-1.0356	3	.	.	.	.	1.066	0.01611	0.3899:0.2635:0.1256:0.2211	rs3209476;rs17410467	.	.	.	L	236	.	.	H	+	2	0	PRR5-ARHGAP8	43600087	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-6.362000	0.00069	-2.852000	0.00330	-0.771000	0.03389	CAC	A|0.825;T|0.175	0.175	strong		0.652	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
LTF	4057	hgsc.bcm.edu	37	3	46501213	46501213	+	Missense_Mutation	SNP	T	T	C	rs1126478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:46501213T>C	ENST00000231751.4	-	2	435	c.140A>G	c.(139-141)aAa>aGa	p.K47R	LTF_ENST00000417439.1_Missense_Mutation_p.K47R|LTF_ENST00000426532.2_Missense_Mutation_p.K3R	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	47	Bactericidal and antifungal activity.|Interaction with lipopolysaccharide.|Involved in glycosaminoglycan binding.|Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.		K -> R (decreased antibacterial activity against Gram-positive bacteria; seems to reduce susceptibility to localized juvenile periodontitis; associated with increased plasma lactoferrin concentrations and possibly with susceptibility to coronary artery stenosis; dbSNP:rs1126478). {ECO:0000269|PubMed:11702692, ECO:0000269|PubMed:14573629, ECO:0000269|PubMed:22406253, 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)		GCCACGCACTTTTCTCATATT	0.562													C|||	3142	0.627396	0.9644	0.487	5008	,	,		17963	0.6498		0.3489	False		,,,				2504	0.5348				p.K47R		Atlas-SNP	.											.	LTF	98	.	0			c.A140G						PASS	.	C	ARG/LYS,ARG/LYS	3783,623	270.4+/-269.6	1637,509,57	149.0	133.0	139.0		8,140	-9.7	0.0	3	dbSNP_86	139	2720,5880	682.3+/-403.8	441,1838,2021	yes	missense,missense	LTF	NM_001199149.1,NM_002343.3	26,26	2078,2347,2078	CC,CT,TT		31.6279,14.1398,50.0	benign,benign	3/667,47/711	46501213	6503,6503	2203	4300	6503	SO:0001583	missense	4057	exon2			CGCACTTTTCTCA		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.140A>G	3.37:g.46501213T>C	ENSP00000231751:p.Lys47Arg	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	214	92	0.429907	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	1278	0.5851648351648352	472	0.959349593495935	169	0.46685082872928174	371	0.6486013986013986	266	0.35092348284960423	C	9.497	1.102132	0.20632	0.858602	0.316279	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496;ENST00000443743;ENST00000431944;ENST00000415180	T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32;1.32	4.83	-9.66	0.00534	.	0.832641	0.10628	N	0.652479	T	0.00012	0.0000	N	0.25380	0.74	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	0.10823	-1.0613	9	0.15952	T	0.53	-0.6452	6.3207	0.21217	0.0921:0.4621:0.0936:0.3522	rs1126478;rs3181525;rs17220161;rs52823440;rs60725703;rs1126478	47;34;47	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	R	47;3;47;34;47;58;3	ENSP00000231751:K47R;ENSP00000405719:K3R;ENSP00000405546:K47R;ENSP00000397427:K34R;ENSP00000395234:K58R;ENSP00000400254:K3R	ENSP00000231751:K47R	K	-	2	0	LTF	46476217	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.120000	0.01323	-2.970000	0.00286	-1.929000	0.00512	AAA	T|0.446;C|0.554	0.554	strong		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
KIAA1244	57221	hgsc.bcm.edu	37	6	138645228	138645228	+	Silent	SNP	G	G	A	rs3734301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	62	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	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	
LRPAP1	4043	hgsc.bcm.edu	37	4	3526645	3526645	+	Missense_Mutation	SNP	C	C	T	rs11549516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:3526645C>T	ENST00000500728.2	-	2	484	c.338G>A	c.(337-339)cGc>cAc	p.R113H	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	113					extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		ATTGAGGTTGCGTATGAGTCT	0.478													.|||	248	0.0495208	0.0461	0.0793	5008	,	,		21715	0.0337		0.0358	False		,,,				2504	0.0634				p.R113H		Atlas-SNP	.											LRPAP1,NS,carcinoma,-1,1	LRPAP1	29	1	0			c.G338A						PASS	.	C	HIS/ARG	161,4245	109.1+/-147.4	4,153,2046	331.0	333.0	332.0		338	1.8	0.0	4	dbSNP_120	332	299,8301	109.4+/-169.9	4,291,4005	yes	missense	LRPAP1	NM_002337.3	29	8,444,6051	TT,TC,CC		3.4767,3.6541,3.5368	benign	113/358	3526645	460,12546	2203	4300	6503	SO:0001583	missense	4043	exon2			AGGTTGCGTATGA		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"""low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"""	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.338G>A	4.37:g.3526645C>T	ENSP00000421922:p.Arg113His	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	177	77	0.435028	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Missense_Mutation	SNP	ENST00000500728.2	37	CCDS3371.1	86	0.039377289377289376	21	0.042682926829268296	23	0.06353591160220995	16	0.027972027972027972	26	0.03430079155672823	C	13.32	2.201919	0.38905	0.036541	0.034767	ENSG00000163956	ENST00000500728	T	0.51574	0.7	4.08	1.82	0.25136	Alpha-2-macroglobulin receptor-associated protein, domain 1 (3);	0.112824	0.64402	N	0.000007	T	0.05364	0.0142	L	0.51422	1.61	0.54753	D	0.999985	B	0.28713	0.22	B	0.30716	0.119	T	0.01899	-1.1251	10	0.38643	T	0.18	-26.787	6.8256	0.23880	0.0:0.7121:0.0:0.2879	rs11549516;rs17848283	113	P30533	AMRP_HUMAN	H	113	ENSP00000421922:R113H	ENSP00000421922:R113H	R	-	2	0	LRPAP1	3496443	1.000000	0.71417	0.011000	0.14972	0.026000	0.11368	2.865000	0.48412	0.268000	0.21939	0.655000	0.94253	CGC	C|0.964;T|0.036	0.036	strong		0.478	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
EFCAB13	124989	hgsc.bcm.edu	37	17	45468842	45468842	+	Missense_Mutation	SNP	A	A	T	rs72825679	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45468842A>T	ENST00000331493.2	+	15	2033	c.1622A>T	c.(1621-1623)gAt>gTt	p.D541V	EFCAB13_ENST00000517484.1_Missense_Mutation_p.D445V	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	541	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.D541V(1)									AAAATTAAAGATAAAAATGTG	0.289													A|||	447	0.0892572	0.0469	0.0893	5008	,	,		12383	0.1657		0.0537	False		,,,				2504	0.1043				p.D541V		Atlas-SNP	.											C17orf57,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A1622T						PASS	.	A	VAL/ASP,VAL/ASP	222,4184	131.8+/-168.3	7,208,1988	50.0	54.0	52.0		1334,1622	3.2	0.8	17	dbSNP_130	52	506,8090	141.9+/-198.1	18,470,3810	yes	missense,missense	C17orf57	NM_001195192.1,NM_152347.4	152,152	25,678,5798	TT,TA,AA		5.8865,5.0386,5.5991	probably-damaging,probably-damaging	445/785,541/974	45468842	728,12274	2203	4298	6501	SO:0001583	missense	124989	exon15			TTAAAGATAAAAA	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.1622A>T	17.37:g.45468842A>T	ENSP00000332111:p.Asp541Val	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	211	111	0.526066	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	193	0.08836996336996338	29	0.05894308943089431	25	0.06906077348066299	97	0.16958041958041958	42	0.055408970976253295	A	13.36	2.215371	0.39102	0.050386	0.058865	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176;ENST00000523842	T;T;T	0.69685	0.01;-0.42;0.51	3.2	3.2	0.36748	EF-hand-like domain (1);	0.650407	0.13990	N	0.348875	T	0.00580	0.0019	M	0.62723	1.935	0.22581	P	0.99896837	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.81914	0.994;0.995;0.984	T	0.35674	-0.9779	9	0.87932	D	0	-8.8716	8.1506	0.31139	1.0:0.0:0.0:0.0	.	493;541;445	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	V	541;445;493;67	ENSP00000332111:D541V;ENSP00000430048:D445V;ENSP00000429566:D67V	ENSP00000332111:D541V	D	+	2	0	C17orf57	42823841	1.000000	0.71417	0.826000	0.32828	0.473000	0.32948	2.948000	0.49066	1.671000	0.50874	0.383000	0.25322	GAT	A|0.931;T|0.069	0.069	strong		0.289	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
CDH17	1015	hgsc.bcm.edu	37	8	95143138	95143138	+	Silent	SNP	A	A	G	rs2513797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:95143138A>G	ENST00000027335.3	-	16	2374	c.2250T>C	c.(2248-2250)ggT>ggC	p.G750G	CDH17_ENST00000441892.2_Silent_p.G536G|CDH17_ENST00000450165.2_Silent_p.G750G	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	750	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			AGGGTGGCCGACCCCCATCAT	0.502													A|||	419	0.0836661	0.1339	0.1009	5008	,	,		18290	0.0		0.1153	False		,,,				2504	0.0573				p.G750G		Atlas-SNP	.											.	CDH17	119	.	0			c.T2250C						PASS	.	A	,	492,3914	230.1+/-244.4	32,428,1743	128.0	121.0	123.0		2250,2250	-11.7	0.0	8	dbSNP_100	123	1049,7551	222.4+/-259.5	71,907,3322	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	103,1335,5065	GG,GA,AA		12.1977,11.1666,11.8484	,	750/833,750/833	95143138	1541,11465	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon16			TGGCCGACCCCCA	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.2250T>C	8.37:g.95143138A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			A|0.892;G|0.108	0.108	strong		0.502	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
NPY4R	5540	hgsc.bcm.edu	37	10	47087501	47087501	+	Missense_Mutation	SNP	C	C	T	rs3824733	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:47087501C>T	ENST00000395716.1	+	2	803	c.718C>T	c.(718-720)Cgc>Tgc	p.R240C	NPY4R_ENST00000374312.1_Missense_Mutation_p.R240C			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	240			R -> C (in dbSNP:rs3824733). {ECO:0000269|Ref.6}.		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)										CATCTACCGGCGCCTGCAGAG	0.602																																					p.R240C		Atlas-SNP	.											PPYR1,rectum,carcinoma,-1,1	PPYR1	54	1	0			c.C718T						PASS	.	C	CYS/ARG	529,3877		0,529,1674	155.0	130.0	139.0		718	4.2	1.0	10	dbSNP_107	139	2450,6150		2,2446,1852	yes	missense	PPYR1	NM_005972.4	180	2,2975,3526	TT,TC,CC		28.4884,12.0064,22.9048	possibly-damaging	240/376	47087501	2979,10027	2203	4300	6503	SO:0001583	missense	5540	exon3			TACCGGCGCCTGC		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.718C>T	10.37:g.47087501C>T	ENSP00000379066:p.Arg240Cys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	113	69	0.610619	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	648	0.2967032967032967	45	0.09146341463414634	116	0.32044198895027626	269	0.47027972027972026	218	0.287598944591029	C	11.53	1.666627	0.29604	0.120064	0.284884	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.38240	1.15;1.15	5.12	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.116071	0.64402	D	0.000009	T	0.00012	0.0000	L	0.51422	1.61	0.80722	D	1	B	0.22346	0.068	B	0.28385	0.089	T	0.54153	-0.8336	10	0.37606	T	0.19	.	11.5752	0.50858	0.0:0.9121:0.0:0.0879	rs3824733	240	P50391	NPY4R_HUMAN	C	240	ENSP00000363431:R240C;ENSP00000379066:R240C	ENSP00000363431:R240C	R	+	1	0	PPYR1	46507507	1.000000	0.71417	0.967000	0.41034	0.627000	0.37826	4.530000	0.60595	1.307000	0.44944	0.609000	0.83330	CGC	C|0.702;T|0.298	0.298	strong		0.602	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
LARP4	113251	hgsc.bcm.edu	37	12	50848132	50848132	+	Missense_Mutation	SNP	T	T	A	rs17124706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:50848132T>A	ENST00000398473.2	+	10	1165	c.1053T>A	c.(1051-1053)ttT>ttA	p.F351L	LARP4_ENST00000522085.1_Missense_Mutation_p.F351L|LARP4_ENST00000347328.5_Missense_Mutation_p.F280L|LARP4_ENST00000429001.3_Missense_Mutation_p.F357L|LARP4_ENST00000293618.8_Missense_Mutation_p.F351L|LARP4_ENST00000518561.1_Missense_Mutation_p.F281L|LARP4_ENST00000518444.1_Missense_Mutation_p.F350L	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	351			F -> L (in dbSNP:rs17124706).		cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						TGAATGGCTTTAATTCGCCAG	0.348													T|||	214	0.0427316	0.003	0.0663	5008	,	,		16476	0.0179		0.0477	False		,,,				2504	0.1002				p.F351L		Atlas-SNP	.											.	LARP4	58	.	0			c.T1053A						PASS	.	T	LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE	29,3585		0,29,1778	98.0	86.0	90.0		840,1053,1053,1053,1050,840	3.8	1.0	12	dbSNP_123	90	418,7726		8,402,3662	yes	missense,missense,missense,missense,missense,missense	LARP4	NM_001170803.1,NM_001170804.1,NM_001170808.1,NM_052879.4,NM_199188.2,NM_199190.2	22,22,22,22,22,22	8,431,5440	AA,AT,TT		5.1326,0.8024,3.8017	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	280/583,351/446,351/654,351/725,350/724,280/654	50848132	447,11311	1807	4072	5879	SO:0001583	missense	113251	exon10			TGGCTTTAATTCG	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"""La ribonucleoprotein domain containing"""	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.1053T>A	12.37:g.50848132T>A	ENSP00000381490:p.Phe351Leu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	37	CCDS41782.1	68	0.031135531135531136	4	0.008130081300813009	18	0.049723756906077346	6	0.01048951048951049	40	0.052770448548812667	T	17.97	3.519403	0.64634	0.008024	0.051326	ENSG00000161813	ENST00000293618;ENST00000429001;ENST00000398473;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000518561;ENST00000520064;ENST00000347328	T;T;T;T;T;T;T	0.59906	1.43;1.43;1.43;1.43;1.43;1.43;0.23	3.85	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.30324	0.0761	M	0.66939	2.045	0.53005	D	0.999967	D;D;D;D;D;D	0.69078	0.997;0.985;0.996;0.987;0.99;0.984	D;P;D;P;D;P	0.73380	0.96;0.828;0.98;0.897;0.935;0.881	T	0.57653	-0.7774	10	0.56958	D	0.05	.	8.9613	0.35849	0.0:0.0928:0.0:0.9072	rs17124706;rs52832230;rs17124706	252;350;351;280;351;357	Q71RC2-2;Q71RC2-3;G3XAA8;G5E976;Q71RC2;Q71RC2-4	.;.;.;.;LARP4_HUMAN;.	L	351;357;351;351;351;350;281;252;280	ENSP00000293618:F351L;ENSP00000415464:F357L;ENSP00000381490:F351L;ENSP00000429781:F351L;ENSP00000429077:F350L;ENSP00000430851:F281L;ENSP00000340901:F280L	ENSP00000293618:F351L	F	+	3	2	LARP4	49134399	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.450000	0.44943	1.700000	0.51204	0.402000	0.26972	TTT	T|0.969;A|0.031	0.031	strong		0.348	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	
ICAM3	3385	hgsc.bcm.edu	37	19	10449358	10449358	+	Splice_Site	SNP	T	T	C	rs7258015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	141	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	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
ZNF492	57615	hgsc.bcm.edu	37	19	22848028	22848028	+	Missense_Mutation	SNP	G	G	C	rs3745115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	734	1	0.0013624		WXS	Illumina HiSeq	Phase_I	673	195	0.289747	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	
SMG1	23049	hgsc.bcm.edu	37	16	18839362	18839362	+	Silent	SNP	T	T	C	rs12445870	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:18839362T>C	ENST00000446231.2	-	55	10144	c.9732A>G	c.(9730-9732)gcA>gcG	p.A3244A	SMG1_ENST00000389467.3_Silent_p.A3245A			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3244					DNA repair (GO:0006281)|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)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CCTGAACTGTTGCAATAGAAG	0.438													T|||	1216	0.242812	0.1346	0.2997	5008	,	,		12614	0.1081		0.3926	False		,,,				2504	0.3333				p.A3244A		Atlas-SNP	.											.	SMG1	401	.	0			c.A9732G						PASS	.	T		675,3159		56,563,1298	66.0	67.0	67.0		9732	-0.1	1.0	16	dbSNP_120	67	3223,5013		653,1917,1548	no	coding-synonymous	SMG1	NM_015092.4		709,2480,2846	CC,CT,TT		39.1331,17.6056,32.2949		3244/3662	18839362	3898,8172	1917	4118	6035	SO:0001819	synonymous_variant	23049	exon55			AACTGTTGCAATA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.9732A>G	16.37:g.18839362T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	123	50	0.406504	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			T|0.764;C|0.236	0.236	strong		0.438	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
MUC16	94025	hgsc.bcm.edu	37	19	9047267	9047267	+	Missense_Mutation	SNP	C	C	T	rs10410169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9047267C>T	ENST00000397910.4	-	5	34567	c.34364G>A	c.(34363-34365)gGt>gAt	p.G11455D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11457	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTTTGATGCACCAGGGGAGAC	0.493													C|||	949	0.189497	0.1982	0.1988	5008	,	,		24195	0.0258		0.2823	False		,,,				2504	0.2444				p.G11455D		Atlas-SNP	.											.	MUC16	4315	.	0			c.G34364A						PASS	.		ASP/GLY	754,3276		70,614,1331	173.0	169.0	170.0		34364	0.9	0.0	19	dbSNP_119	170	2524,5826		402,1720,2053	yes	missense	MUC16	NM_024690.2	94	472,2334,3384	TT,TC,CC		30.2275,18.7097,26.4782	possibly-damaging	11455/14508	9047267	3278,9102	2015	4175	6190	SO:0001583	missense	94025	exon5			GATGCACCAGGGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34364G>A	19.37:g.9047267C>T	ENSP00000381008:p.Gly11455Asp	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	408	0.18681318681318682	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	218	0.287598944591029	c	7.617	0.676019	0.14841	0.187097	0.302275	ENSG00000181143	ENST00000397910	T	0.04862	3.54	3.05	0.877	0.19145	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	.	.	.	P	0.36086	0.536	B	0.39339	0.297	T	0.49234	-0.8961	8	0.87932	D	0	.	5.0244	0.14378	0.0:0.7109:0.0:0.2891	rs10410169;rs52822154;rs58775557;rs10410169	11455	B5ME49	.	D	11455	ENSP00000381008:G11455D	ENSP00000381008:G11455D	G	-	2	0	MUC16	8908267	0.000000	0.05858	0.001000	0.08648	0.182000	0.23217	-1.197000	0.03038	0.307000	0.22880	0.306000	0.20318	GGT	C|0.788;T|0.212	0.212	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NISCH	11188	hgsc.bcm.edu	37	3	52507782	52507782	+	Silent	SNP	G	G	A	rs56114678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:52507782G>A	ENST00000479054.1	+	8	774	c.702G>A	c.(700-702)ggG>ggA	p.G234G	NISCH_ENST00000420808.2_Silent_p.G234G|NISCH_ENST00000488380.1_Silent_p.G234G|NISCH_ENST00000345716.4_Silent_p.G234G			Q9Y2I1	NISCH_HUMAN	nischarin	234	Necessary for homooligomerization and targeting to endosomes.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	ACATCAGAGGGCTGGTCGCAT	0.522													G|||	83	0.0165735	0.0008	0.013	5008	,	,		21056	0.001		0.0517	False		,,,				2504	0.0204				p.G234G		Atlas-SNP	.											.	NISCH	97	.	0			c.G702A						PASS	.	G		46,4360	48.2+/-83.0	1,44,2158	94.0	76.0	82.0		702	-2.6	1.0	3	dbSNP_129	82	435,8165	133.6+/-191.1	9,417,3874	no	coding-synonymous	NISCH	NM_007184.3		10,461,6032	AA,AG,GG		5.0581,1.044,3.6983		234/1505	52507782	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	11188	exon7			CAGAGGGCTGGTC	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"""imidazoline receptor candidate"", ""I-1 receptor candidate protein"", ""imidazoline receptor antisera selected"""	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.702G>A	3.37:g.52507782G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	41	28	0.682927	NM_001276293	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	37	CCDS33767.1																																																																																			G|0.967;A|0.033	0.033	strong		0.522	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129946	175129946	+	Silent	SNP	C	C	T	rs386636937|rs542219168|rs71563271|rs2072035	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:175129946C>T	ENST00000423313.1	-	4	740	c.204G>A	c.(202-204)aaG>aaA	p.K68K	KIAA0040_ENST00000545251.2_Silent_p.K68K|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_Silent_p.K68K	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcttcttcttcttgt	0.498																																					p.K68K		Atlas-SNP	.											.	KIAA0040	2	.	0			c.G204A						PASS	.						82.0	69.0	73.0					1																	175129946		692	1591	2283	SO:0001819	synonymous_variant	9674	exon3			CTTCTTCTTCTTC	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.204G>A	1.37:g.175129946C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_001162895	A8K9H6|Q2NKQ0	Silent	SNP	ENST00000423313.1	37																																																																																				C|0.428;T|0.572	0.572	strong		0.498	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
YBX1	4904	hgsc.bcm.edu	37	1	43166630	43166630	+	Missense_Mutation	SNP	G	G	A	rs200741644		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:43166630G>A	ENST00000321358.7	+	7	1058	c.919G>A	c.(919-921)Gat>Aat	p.D307N		NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	307					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.D307N(1)		large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AAAAGCAGCCGATCCACCAGC	0.562																																					p.D307N		Atlas-SNP	.											YBX1,mouth,carcinoma,0,1	YBX1	49	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G919A						scavenged	.						56.0	58.0	57.0					1																	43166630		2203	4299	6502	SO:0001583	missense	4904	exon7			GCAGCCGATCCAC	BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"""nuclease sensitive element binding protein 1"""	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.919G>A	1.37:g.43166630G>A	ENSP00000361626:p.Asp307Asn	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	210	7	0.0333333	NM_004559	P16990|P16991|Q14972|Q15325|Q5FVF0	Missense_Mutation	SNP	ENST00000321358.7	37	CCDS470.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735579	0.69189	.	.	ENSG00000065978	ENST00000321358;ENST00000318612	T	0.31510	1.49	5.39	5.39	0.77823	.	0.236880	0.49916	N	0.000136	T	0.22044	0.0531	N	0.17379	0.485	0.54753	D	0.999989	B	0.25312	0.123	B	0.15052	0.012	T	0.04078	-1.0979	10	0.62326	D	0.03	-3.4519	16.6483	0.85182	0.0:0.0:1.0:0.0	.	307	P67809	YBOX1_HUMAN	N	307;297	ENSP00000361626:D307N	ENSP00000361621:D297N	D	+	1	0	YBX1	42939217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.018000	0.93657	2.505000	0.84491	0.557000	0.71058	GAT	G|0.998;A|0.002	0.002	weak		0.562	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559	
FLG	2312	hgsc.bcm.edu	37	1	152284823	152284823	+	Missense_Mutation	SNP	A	A	G	rs74129459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152284823A>G	ENST00000368799.1	-	3	2574	c.2539T>C	c.(2539-2541)Tca>Cca	p.S847P	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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						scavenged	.						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	315	1	0.0031746		WXS	Illumina HiSeq	Phase_I	280	6	0.0214286	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	
CENPF	1063	hgsc.bcm.edu	37	1	214818548	214818548	+	Missense_Mutation	SNP	C	C	T	rs61732022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214818548C>T	ENST00000366955.3	+	13	5803	c.5635C>T	c.(5635-5637)Cgt>Tgt	p.R1879C		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1975					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)		TAAATCATCACGTGAAGATAT	0.403													C|||	59	0.0117812	0.0113	0.0072	5008	,	,		19531	0.0		0.0129	False		,,,				2504	0.0266				p.R1879C	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.C5635T						PASS	.	C	CYS/ARG	73,4333	64.7+/-102.0	0,73,2130	54.0	53.0	53.0		5635	-3.9	0.0	1	dbSNP_129	53	123,8477	63.9+/-126.0	1,121,4178	yes	missense	CENPF	NM_016343.3	180	1,194,6308	TT,TC,CC		1.4302,1.6568,1.507	possibly-damaging	1879/3115	214818548	196,12810	2203	4300	6503	SO:0001583	missense	1063	exon13			TCATCACGTGAAG	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.5635C>T	1.37:g.214818548C>T	ENSP00000355922:p.Arg1879Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	20	0.009157509157509158	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	C	2.391	-0.339808	0.05243	0.016568	0.014302	ENSG00000117724	ENST00000366955	T	0.03181	4.02	5.26	-3.94	0.04130	.	1.696420	0.03816	N	0.266752	T	0.00724	0.0024	N	0.03608	-0.345	0.09310	N	1	P	0.48764	0.915	B	0.35312	0.2	T	0.37572	-0.9700	10	0.54805	T	0.06	.	3.8333	0.08883	0.2347:0.144:0.4665:0.1548	rs61732022	1975	P49454	CENPF_HUMAN	C	1879	ENSP00000355922:R1879C	ENSP00000355922:R1879C	R	+	1	0	CENPF	212885171	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-0.847000	0.04331	-0.631000	0.05560	-0.192000	0.12808	CGT	C|0.986;T|0.014	0.014	strong		0.403	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
SYNE2	23224	hgsc.bcm.edu	37	14	64637147	64637147	+	Silent	SNP	C	C	A	rs7161192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64637147C>A	ENST00000344113.4	+	94	17414	c.17202C>A	c.(17200-17202)ctC>ctA	p.L5734L	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.L2368L|SYNE2_ENST00000358025.3_Silent_p.L5734L|SYNE2_ENST00000394768.2_Silent_p.L2119L|SYNE2_ENST00000554584.1_Intron|SYNE2_ENST00000357395.3_Silent_p.L2119L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5734					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTTCAGCCTCTACCAAACCA	0.498													C|||	1832	0.365815	0.3464	0.3055	5008	,	,		20635	0.5526		0.335	False		,,,				2504	0.274				p.L5734L		Atlas-SNP	.											.	SYNE2	577	.	0			c.C17202A						PASS	.	C	,	1625,2781	499.1+/-364.3	318,989,896	77.0	54.0	62.0		17202,17202	3.6	0.7	14	dbSNP_116	62	2795,5805	440.8+/-359.6	455,1885,1960	yes	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	773,2874,2856	AA,AC,CC		32.5,36.8815,33.9843	,	5734/6886,5734/6908	64637147	4420,8586	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon94			CAGCCTCTACCAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.17202C>A	14.37:g.64637147C>A		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.628;A|0.372	0.372	strong		0.498	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
GDPGP1	390637	hgsc.bcm.edu	37	15	90784632	90784632	+	Missense_Mutation	SNP	G	G	T	rs144466387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90784632G>T	ENST00000558017.1	+	4	912	c.492G>T	c.(490-492)tgG>tgT	p.W164C	GDPGP1_ENST00000329600.6_Missense_Mutation_p.W164C	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	164					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)										CCCTGGAGTGGGGCCACGTGC	0.652													G|||	2	0.000399361	0.0	0.0014	5008	,	,		16490	0.0		0.001	False		,,,				2504	0.0				p.W164C		Atlas-SNP	.											.	.	.	.	0			c.G492T						PASS	.	G	CYS/TRP	0,4398		0,0,2199	49.0	53.0	52.0		492	3.9	1.0	15	dbSNP_134	52	13,8583	9.8+/-36.6	0,13,4285	yes	missense	C15orf58	NM_001013657.2	215	0,13,6484	TT,TG,GG		0.1512,0.0,0.1	probably-damaging	164/386	90784632	13,12981	2199	4298	6497	SO:0001583	missense	390637	exon4			GGAGTGGGGCCAC		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.492G>T	15.37:g.90784632G>T	ENSP00000452793:p.Trp164Cys	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	15.09	2.729619	0.48833	0.0	0.001512	ENSG00000183208	ENST00000329600	T	0.22539	1.95	5.85	3.93	0.45458	.	0.291899	0.33591	N	0.004747	T	0.35248	0.0925	M	0.67953	2.075	0.58432	D	0.999999	D	0.64830	0.994	P	0.58391	0.838	T	0.04053	-1.0981	10	0.38643	T	0.18	-6.2663	9.1104	0.36723	0.0:0.2636:0.4647:0.2716	.	164	Q6ZNW5	VTC2_HUMAN	C	164	ENSP00000368405:W164C	ENSP00000368405:W164C	W	+	3	0	C15orf58	88585636	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	2.143000	0.42187	0.776000	0.33473	-0.165000	0.13383	TGG	G|0.999;T|0.001	0.001	strong		0.652	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
ZNF57	126295	hgsc.bcm.edu	37	19	2917178	2917178	+	Missense_Mutation	SNP	G	G	A	rs61742111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917178G>A	ENST00000306908.5	+	4	707	c.559G>A	c.(559-561)Gga>Aga	p.G187R	ZNF57_ENST00000523428.1_Missense_Mutation_p.G155R|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	187					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		ACACAGTCACGGAAGAACTGA	0.498													G|||	131	0.0261581	0.0257	0.0288	5008	,	,		21208	0.001		0.0169	False		,,,				2504	0.0603				p.G187R	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G559A						PASS	.	G	ARG/GLY	95,4311	77.3+/-115.6	0,95,2108	109.0	81.0	90.0		559	-3.2	0.0	19	dbSNP_129	90	209,8391	88.9+/-151.2	4,201,4095	yes	missense	ZNF57	NM_173480.2	125	4,296,6203	AA,AG,GG		2.4302,2.1562,2.3374	benign	187/556	2917178	304,12702	2203	4300	6503	SO:0001583	missense	126295	exon4			AGTCACGGAAGAA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.559G>A	19.37:g.2917178G>A	ENSP00000303696:p.Gly187Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	41	0.018772893772893772	17	0.034552845528455285	13	0.03591160220994475	1	0.0017482517482517483	10	0.013192612137203167	G	11.69	1.714569	0.30413	0.021562	0.024302	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.14144	2.53;2.53	1.7	-3.23	0.05109	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00666	0.0022	N	0.00599	-1.345	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.39292	-0.9621	9	0.44086	T	0.13	.	3.5597	0.07877	0.3623:0.3552:0.2825:0.0	rs61742111	187	Q68EA5	ZNF57_HUMAN	R	187;189;155	ENSP00000303696:G187R;ENSP00000430223:G155R	ENSP00000303696:G187R	G	+	1	0	ZNF57	2868178	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	-0.336000	0.07863	-0.406000	0.07588	0.407000	0.27541	GGA	G|0.973;A|0.027	0.027	strong		0.498	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
TENM2	57451	hgsc.bcm.edu	37	5	167645888	167645888	+	Silent	SNP	T	T	C	rs1363560	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:167645888T>C	ENST00000518659.1	+	23	5031	c.4992T>C	c.(4990-4992)aaT>aaC	p.N1664N	TENM2_ENST00000520394.1_Silent_p.N1425N|TENM2_ENST00000519204.1_Silent_p.N1543N|TENM2_ENST00000403607.2_Silent_p.N1488N|TENM2_ENST00000545108.1_Silent_p.N1663N	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1664					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TGGGCACCAATGGAGGCCTCA	0.557													.|||	2052	0.409744	0.6422	0.2205	5008	,	,		20614	0.5942		0.2207	False		,,,				2504	0.2342				p.N1655N		Atlas-SNP	.											.	.	.	.	0			c.T4965C						PASS	.	T		2411,1783		709,993,395	147.0	153.0	151.0		4965	-9.2	0.0	5	dbSNP_88	151	1905,6525		229,1447,2539	no	coding-synonymous	ODZ2	NM_001122679.1		938,2440,2934	CC,CT,TT		22.5979,42.5131,34.1888		1655/2766	167645888	4316,8308	2097	4215	6312	SO:0001819	synonymous_variant	57451	exon23			CACCAATGGAGGC	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4992T>C	5.37:g.167645888T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	190	94	0.494737	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				T|0.589;C|0.411	0.411	strong		0.557	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
SDCBP2	27111	hgsc.bcm.edu	37	20	1293141	1293141	+	Missense_Mutation	SNP	C	C	T	rs35367003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:1293141C>T	ENST00000360779.3	-	7	745	c.572G>A	c.(571-573)cGg>cAg	p.R191Q	SDCBP2_ENST00000467129.1_5'Flank|SDCBP2_ENST00000381812.1_Missense_Mutation_p.R191Q|SDCBP2_ENST00000381808.3_Missense_Mutation_p.R106Q|SDCBP2_ENST00000339987.3_Missense_Mutation_p.R191Q	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	191			R -> Q (in a colorectal cancer sample; somatic mutation; dbSNP:rs35367003). {ECO:0000269|PubMed:16959974}.		intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R106Q(2)|p.R191Q(2)		endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						GGTGACAGTCCGCTGGAACGG	0.627													C|||	100	0.0199681	0.0	0.0159	5008	,	,		20985	0.0		0.0219	False		,,,				2504	0.0685				p.R191Q		Atlas-SNP	.											SDCBP2_ENST00000381812,colon,carcinoma,-1,13	SDCBP2	78	13	4	Substitution - Missense(4)	endometrium(3)|large_intestine(1)	c.G572A						scavenged	.	C	GLN/ARG,GLN/ARG,GLN/ARG	9,4397	15.5+/-35.6	0,9,2194	86.0	72.0	77.0		572,317,572	4.7	1.0	20	dbSNP_126	77	186,8414	84.0+/-146.5	2,182,4116	yes	missense,missense,missense	SDCBP2	NM_001199784.1,NM_015685.5,NM_080489.4	43,43,43	2,191,6310	TT,TC,CC		2.1628,0.2043,1.4993	probably-damaging,probably-damaging,probably-damaging	191/293,106/208,191/293	1293141	195,12811	2203	4300	6503	SO:0001583	missense	27111	exon7			ACAGTCCGCTGGA	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.572G>A	20.37:g.1293141C>T	ENSP00000354013:p.Arg191Gln	Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	37	CCDS42848.1	19	0.0086996336996337	0	0.0	9	0.024861878453038673	0	0.0	10	0.013192612137203167	c	33	5.245370	0.95272	0.002043	0.021628	ENSG00000125775	ENST00000381812;ENST00000381808;ENST00000360779;ENST00000339987	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	4.7	4.7	0.59300	PDZ/DHR/GLGF (2);	0.000000	0.85682	D	0.000000	T	0.33000	0.0848	M	0.86864	2.845	0.58432	D	0.999997	D	0.76494	0.999	P	0.60173	0.87	T	0.55134	-0.8188	10	0.87932	D	0	-22.2379	17.4325	0.87543	0.0:1.0:0.0:0.0	rs35367003	191	Q9H190	SDCB2_HUMAN	Q	191;106;191;191	ENSP00000371233:R191Q;ENSP00000371229:R106Q;ENSP00000354013:R191Q;ENSP00000342935:R191Q	ENSP00000342935:R191Q	R	-	2	0	SDCBP2	1241141	1.000000	0.71417	0.995000	0.50966	0.918000	0.54935	7.534000	0.82004	2.417000	0.82017	0.561000	0.74099	CGG	C|0.985;T|0.015	0.015	strong		0.627	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
ITGA4	3676	hgsc.bcm.edu	37	2	182399097	182399097	+	Splice_Site	SNP	T	T	C	rs7562325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:182399097T>C	ENST00000397033.2	+	26	3313	c.2883T>C	c.(2881-2883)caT>caC	p.H961H		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	961					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)	ATGTTGCGCATGTAAGATTAC	0.368													T|||	3290	0.656949	0.6452	0.6297	5008	,	,		19942	0.621		0.5457	False		,,,				2504	0.8436				p.H961H		Atlas-SNP	.											.	ITGA4	142	.	0			c.T2883C						PASS	.	T		2384,1312		759,866,223	68.0	61.0	63.0		2883	0.6	1.0	2	dbSNP_116	63	4793,3397		1426,1941,728	yes	coding-synonymous-near-splice	ITGA4	NM_000885.4		2185,2807,951	CC,CT,TT		41.4774,35.4978,39.618		961/1033	182399097	7177,4709	1848	4095	5943	SO:0001630	splice_region_variant	3676	exon26			TGCGCATGTAAGA		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.2883+1T>C	2.37:g.182399097T>C		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	37	CCDS42788.1																																																																																			T|0.385;C|0.615	0.615	strong		0.368	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		Silent
GPATCH1	55094	hgsc.bcm.edu	37	19	33602757	33602757	+	Silent	SNP	C	C	T	rs10420258	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33602757C>T	ENST00000170564.2	+	12	2027	c.1713C>T	c.(1711-1713)caC>caT	p.H571H		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	571					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)					GGTTCACTCACGCCAAGGAGG	0.552													C|||	1019	0.203474	0.1082	0.1254	5008	,	,		17067	0.3333		0.1382	False		,,,				2504	0.3211				p.H571H	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C1713T						PASS	.	C		481,3925	226.2+/-241.8	23,435,1745	116.0	97.0	103.0		1713	-4.7	0.4	19	dbSNP_119	103	1334,7266	262.1+/-284.2	97,1140,3063	no	coding-synonymous	GPATCH1	NM_018025.2		120,1575,4808	TT,TC,CC		15.5116,10.9169,13.9551		571/932	33602757	1815,11191	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon12			CACTCACGCCAAG	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.1713C>T	19.37:g.33602757C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.829;T|0.171	0.171	strong		0.552	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
FOCAD	54914	hgsc.bcm.edu	37	9	20885216	20885216	+	Missense_Mutation	SNP	C	C	T	rs187654100		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:20885216C>T	ENST00000380249.1	+	23	2976	c.2612C>T	c.(2611-2613)gCt>gTt	p.A871V	FOCAD_ENST00000605086.1_Missense_Mutation_p.A307V|FOCAD_ENST00000338382.6_Missense_Mutation_p.A871V	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	871						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ACTTCACTTGCTCTTGTACAT	0.368													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13975	0.0		0.0	False		,,,				2504	0.0				p.A871V		Atlas-SNP	.											.	.	.	.	0			c.C2612T						PASS	.						231.0	199.0	209.0					9																	20885216		2203	4300	6503	SO:0001583	missense	54914	exon23			CACTTGCTCTTGT	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.2612C>T	9.37:g.20885216C>T	ENSP00000369599:p.Ala871Val	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	260	128	0.492308	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.10	2.435384	0.43224	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.08370	3.1;3.1	5.3	5.3	0.74995	Armadillo-type fold (1);	0.224065	0.46145	D	0.000317	T	0.09686	0.0238	L	0.53249	1.67	0.53005	D	0.999965	P	0.43412	0.806	B	0.32393	0.145	T	0.21895	-1.0232	10	0.29301	T	0.29	-28.1342	19.3232	0.94250	0.0:1.0:0.0:0.0	.	871	Q5VW36	K1797_HUMAN	V	871	ENSP00000369599:A871V;ENSP00000344307:A871V	ENSP00000344307:A871V	A	+	2	0	KIAA1797	20875216	1.000000	0.71417	0.526000	0.27913	0.138000	0.21146	5.289000	0.65656	2.633000	0.89246	0.650000	0.86243	GCT	C|1.000;T|0.000	0.000	strong		0.368	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
MDH1B	130752	hgsc.bcm.edu	37	2	207615724	207615724	+	Missense_Mutation	SNP	C	C	T	rs61744963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:207615724C>T	ENST00000374412.3	-	6	1261	c.986G>A	c.(985-987)aGa>aAa	p.R329K	MDH1B_ENST00000392214.2_Intron|MDH1B_ENST00000449792.1_Missense_Mutation_p.R231K|MDH1B_ENST00000454776.2_Missense_Mutation_p.R329K	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	329					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		ACTCTCATATCTGTACACCCT	0.353													C|||	201	0.0401358	0.0522	0.0403	5008	,	,		15986	0.0585		0.0209	False		,,,				2504	0.0245				p.R329K	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.G986A						PASS	.	C	LYS/ARG	193,4213	120.8+/-158.4	4,185,2014	128.0	128.0	128.0		986	-0.1	0.0	2	dbSNP_129	128	234,8364	94.7+/-156.6	2,230,4067	yes	missense	MDH1B	NM_001039845.1	26	6,415,6081	TT,TC,CC		2.7216,4.3804,3.2836	benign	329/519	207615724	427,12577	2203	4299	6502	SO:0001583	missense	130752	exon6			TCATATCTGTACA		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.986G>A	2.37:g.207615724C>T	ENSP00000363533:p.Arg329Lys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	39	0.354545	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	88	0.040293040293040296	22	0.044715447154471545	15	0.04143646408839779	33	0.057692307692307696	18	0.023746701846965697	C	9.523	1.108701	0.20714	0.043804	0.027216	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.65916	-0.18;-0.18;-0.18	5.97	-0.139	0.13460	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.491701	0.25520	N	0.030104	T	0.05823	0.0152	L	0.28115	0.83	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.003;0.004	T	0.13575	-1.0504	10	0.05721	T	0.95	-2.1313	10.1918	0.43030	0.0:0.5215:0.0:0.4785	.	329;329	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	K	329;231;329	ENSP00000363533:R329K;ENSP00000416577:R231K;ENSP00000389916:R329K	ENSP00000363533:R329K	R	-	2	0	MDH1B	207323969	1.000000	0.71417	0.001000	0.08648	0.995000	0.86356	1.309000	0.33539	-0.079000	0.12707	0.655000	0.94253	AGA	C|0.964;T|0.036	0.036	strong		0.353	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318773	21318773	+	Missense_Mutation	SNP	G	G	A	rs3752034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:21318773G>A	ENST00000583088.1	+	3	1014	c.119G>A	c.(118-120)cGc>cAc	p.R40H	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R40H	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	40					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CACACGCGGCGCAGGTGCCGC	0.612										Prostate(3;0.18)			.|||	1734	0.346246	0.1505	0.366	5008	,	,		36495	0.4812		0.3559	False		,,,				2504	0.4479				p.R40H		Atlas-SNP	.											KCNJ12,NS,carcinoma,+1,1	.	.	1	0			c.G119A						PASS	.	G	HIS/ARG	626,3780		0,626,1577	122.0	91.0	101.0		119	5.3	1.0	17	dbSNP_107	101	2643,5957		0,2643,1657	yes	missense	KCNJ12	NM_021012.4	29	0,3269,3234	AA,AG,GG		30.7326,14.2079,25.1346	benign	40/434	21318773	3269,9737	2203	4300	6503	SO:0001583	missense	100134444	exon3			CGCGGCGCAGGTG	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.119G>A	17.37:g.21318773G>A	ENSP00000463778:p.Arg40His	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	168	33	0.196429	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	717	0.3282967032967033	78	0.15853658536585366	120	0.3314917127071823	270	0.47202797202797203	249	0.32849604221635886	G	17.23	3.337271	0.60963	0.142079	0.307326	ENSG00000184185	ENST00000331718	T	0.36699	1.24	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.175986	0.42964	N	0.000638	T	0.00012	0.0000	L	0.47716	1.5	0.53005	D	0.999968	B	0.20780	0.048	B	0.21546	0.035	T	0.50056	-0.8872	10	0.62326	D	0.03	.	19.026	0.92932	0.0:0.0:1.0:0.0	rs3752034;rs3752034	40	Q14500	IRK12_HUMAN	H	40	ENSP00000328150:R40H	ENSP00000328150:R40H	R	+	2	0	KCNJ12	21259366	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.619000	0.74219	2.506000	0.84524	0.591000	0.81541	CGC	G|0.744;A|0.256	0.256	strong		0.612	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
CELA2A	63036	hgsc.bcm.edu	37	1	15789297	15789297	+	Silent	SNP	A	A	C	rs3815787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15789297A>C	ENST00000359621.4	+	4	322	c.297A>C	c.(295-297)gcA>gcC	p.A99A		NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	99	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)	p.A99A(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						GCTCGCTGGCAGTCAGTGTCT	0.602													C|||	1997	0.398762	0.6762	0.3213	5008	,	,		15780	0.2321		0.3161	False		,,,				2504	0.3354				p.A99A		Atlas-SNP	.											CELA2A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CELA2A	32	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A297C						PASS	.	C		2681,1725	516.5+/-369.2	827,1027,349	98.0	104.0	102.0		297	-6.5	0.0	1	dbSNP_107	102	2851,5749	673.3+/-403.0	473,1905,1922	no	coding-synonymous	CELA2A	NM_033440.2		1300,2932,2271	CC,CA,AA		33.1512,39.1512,42.5342		99/270	15789297	5532,7474	2203	4300	6503	SO:0001819	synonymous_variant	63036	exon4			GCTGGCAGTCAGT		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"""elastase 2A"""	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.297A>C	1.37:g.15789297A>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	196	96	0.489796	NM_033440	B2R5I4|Q14243	Silent	SNP	ENST00000359621.4	37	CCDS157.1																																																																																			.	.	weak		0.602	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440	
SLCO3A1	28232	hgsc.bcm.edu	37	15	92647684	92647684	+	Missense_Mutation	SNP	A	A	C	rs72655652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:92647684A>C	ENST00000318445.6	+	4	1135	c.921A>C	c.(919-921)agA>agC	p.R307S	SLCO3A1_ENST00000555549.1_3'UTR|SLCO3A1_ENST00000424469.2_Missense_Mutation_p.R307S	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	307					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)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	TCTCCGAAAGAGAATACGAGA	0.592													A|||	35	0.00698882	0.0008	0.0058	5008	,	,		16771	0.0		0.0139	False		,,,				2504	0.0164				p.R307S		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.A921C						PASS	.	A	SER/ARG,SER/ARG	7,4389	15.5+/-35.6	0,7,2191	81.0	71.0	74.0		921,921	5.3	1.0	15	dbSNP_130	74	123,8473	64.2+/-126.4	2,119,4177	yes	missense,missense	SLCO3A1	NM_001145044.1,NM_013272.3	110,110	2,126,6368	CC,CA,AA		1.4309,0.1592,1.0006	benign,benign	307/693,307/711	92647684	130,12862	2198	4298	6496	SO:0001583	missense	28232	exon4			CGAAAGAGAATAC	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"""Solute carriers"""	10952	protein-coding gene	gene with protein product		612435	"""solute carrier family 21 (organic anion transporter), member 11"""	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.921A>C	15.37:g.92647684A>C	ENSP00000320634:p.Arg307Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	37	CCDS10371.1	14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	A	10.86	1.469546	0.26423	0.001592	0.014309	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000556649;ENST00000555549	T;T	0.38722	1.12;1.12	5.31	5.31	0.75309	Major facilitator superfamily domain, general substrate transporter (1);	0.648102	0.16571	N	0.208631	T	0.10680	0.0261	N	0.01640	-0.785	0.46203	D	0.998922	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.11329	0.001;0.001;0.006	T	0.13737	-1.0498	10	0.09084	T	0.74	.	8.0237	0.30425	0.8765:0.0:0.1235:0.0	.	249;307;307	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	S	307;307;100;26	ENSP00000320634:R307S;ENSP00000387846:R307S	ENSP00000320634:R307S	R	+	3	2	SLCO3A1	90448688	1.000000	0.71417	0.988000	0.46212	0.864000	0.49448	2.032000	0.41127	1.987000	0.57996	0.533000	0.62120	AGA	A|0.990;C|0.010	0.010	strong		0.592	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272	
MUC16	94025	hgsc.bcm.edu	37	19	9056930	9056930	+	Silent	SNP	T	T	G	rs918535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9056930T>G	ENST00000397910.4	-	3	30719	c.30516A>C	c.(30514-30516)acA>acC	p.T10172T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10174	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGACATGTTTGTCTTCCTAA	0.443													g|||	1218	0.243211	0.3525	0.2867	5008	,	,		22488	0.0258		0.2833	False		,,,				2504	0.2474				p.T10172T		Atlas-SNP	.											.	MUC16	4315	.	0			c.A30516C						PASS	.	G		1268,2662		217,834,914	122.0	121.0	121.0		30516	-6.6	0.0	19	dbSNP_86	121	2525,5781		402,1721,2030	no	coding-synonymous	MUC16	NM_024690.2		619,2555,2944	GG,GT,TT		30.3997,32.2646,30.9987		10172/14508	9056930	3793,8443	1965	4153	6118	SO:0001819	synonymous_variant	94025	exon3			CATGTTTGTCTTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30516A>C	19.37:g.9056930T>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.739;G|0.261	0.261	strong		0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GPAM	57678	hgsc.bcm.edu	37	10	113917085	113917085	+	Silent	SNP	T	T	A	rs2254537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:113917085T>A	ENST00000348367.4	-	19	2240	c.2043A>T	c.(2041-2043)ccA>ccT	p.P681P	GPAM_ENST00000369425.1_Silent_p.P681P|GPAM_ENST00000423155.1_Silent_p.P681P			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	681					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)		ACAAAGGTTCTGGAAGCTTCT	0.458													A|||	3794	0.757588	0.7837	0.6499	5008	,	,		21482	0.7589		0.6879	False		,,,				2504	0.8691				p.P681P	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.A2043T						PASS	.	A		3313,1093	395.1+/-329.5	1246,821,136	148.0	127.0	134.0		2043	-11.3	0.1	10	dbSNP_100	134	6067,2533	414.4+/-351.5	2150,1767,383	no	coding-synonymous	GPAM	NM_020918.4		3396,2588,519	AA,AT,TT		29.4535,24.8071,27.8794		681/829	113917085	9380,3626	2203	4300	6503	SO:0001819	synonymous_variant	57678	exon19			AGGTTCTGGAAGC	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.2043A>T	10.37:g.113917085T>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	181	95	0.524862	NM_001244949	Q5VW51|Q86TA3	Silent	SNP	ENST00000348367.4	37	CCDS7570.1																																																																																			T|0.286;A|0.714	0.714	strong		0.458	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
EFCAB5	374786	hgsc.bcm.edu	37	17	28381069	28381069	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28381069A>G	ENST00000394835.3	+	10	2289	c.2097A>G	c.(2095-2097)gaA>gaG	p.E699E	EFCAB5_ENST00000394832.2_Silent_p.E699E|EFCAB5_ENST00000536908.2_Silent_p.E643E|EFCAB5_ENST00000320856.5_Silent_p.E699E|EFCAB5_ENST00000541045.1_Silent_p.E356E|EFCAB5_ENST00000378738.3_Silent_p.E699E	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	699							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						CTCTACAGGAAAAGAGGTCTT	0.378																																					p.E699E		Atlas-SNP	.											.	EFCAB5	122	.	0			c.A2097G						PASS	.						33.0	31.0	32.0					17																	28381069		1831	4083	5914	SO:0001819	synonymous_variant	374786	exon10			ACAGGAAAAGAGG	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.2097A>G	17.37:g.28381069A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	222	112	0.504505	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			.	.	none		0.378	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
SPZ1	84654	hgsc.bcm.edu	37	5	79616400	79616400	+	Missense_Mutation	SNP	G	G	A	rs200562315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79616400G>A	ENST00000296739.4	+	1	611	c.366G>A	c.(364-366)atG>atA	p.M122I		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	122					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M122I(1)		endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		TCAATGAAATGTTATCAACAA	0.368																																					p.M122I		Atlas-SNP	.											SPZ1,trunk,malignant_melanoma,0,1	SPZ1	60	1	1	Substitution - Missense(1)	skin(1)	c.G366A						scavenged	.						49.0	44.0	45.0					5																	79616400		1799	4058	5857	SO:0001583	missense	84654	exon1			TGAAATGTTATCA		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.366G>A	5.37:g.79616400G>A	ENSP00000369611:p.Met122Ile	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	265	12	0.045283	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	G	8.567	0.879064	0.17395	.	.	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.39787	1.06;1.62	2.92	-2.42	0.06542	.	.	.	.	.	T	0.17238	0.0414	N	0.05078	-0.115	0.09310	N	1	B	0.20988	0.05	B	0.10450	0.005	T	0.15178	-1.0446	9	0.33940	T	0.23	.	4.398	0.11372	0.5786:0.0:0.2498:0.1716	.	122	Q9BXG8	SPZ1_HUMAN	I	122	ENSP00000426530:M122I;ENSP00000369611:M122I	ENSP00000369611:M122I	M	+	3	0	SPZ1	79652156	0.000000	0.05858	0.000000	0.03702	0.514000	0.34195	-1.754000	0.01816	-0.613000	0.05694	0.313000	0.20887	ATG	G|0.998;A|0.002	0.002	strong		0.368	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
PRUNE2	158471	hgsc.bcm.edu	37	9	79324439	79324439	+	Silent	SNP	A	A	G	rs12238013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79324439A>G	ENST00000376718.3	-	8	2874	c.2751T>C	c.(2749-2751)gaT>gaC	p.D917D	PRUNE2_ENST00000428286.1_Silent_p.D558D	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	917					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						GGTTCCAGGAATCTACCTTTT	0.398													A|||	1189	0.23742	0.2103	0.1599	5008	,	,		21577	0.4643		0.1551	False		,,,				2504	0.18				p.D917D		Atlas-SNP	.											PRUNE2_ENST00000376718,NS,carcinoma,0,1	PRUNE2	331	1	0			c.T2751C						scavenged	.	A		628,2508		50,528,990	230.0	215.0	219.0		2751	-2.7	1.0	9	dbSNP_120	219	882,6282		50,782,2750	no	coding-synonymous	PRUNE2	NM_015225.2		100,1310,3740	GG,GA,AA		12.3116,20.0255,14.6602		917/3089	79324439	1510,8790	1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			CCAGGAATCTACC	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.2751T>C	9.37:g.79324439A>G		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	198	85	0.429293	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	559	0.25595238095238093	109	0.22154471544715448	51	0.1408839779005525	284	0.4965034965034965	115	0.1517150395778364	A	0.044	-1.273443	0.01421	0.200255	0.123116	ENSG00000106772	ENST00000426088	.	.	.	5.83	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.41441	P	0.012071000000000054	.	.	.	.	.	.	T	0.47611	-0.9104	3	.	.	.	-23.2372	3.9591	0.09403	0.3405:0.1904:0.3791:0.09	rs12238013;rs17180830;rs59337370;rs12238013	.	.	.	L	239	.	.	F	-	1	0	PRUNE2	78514259	0.541000	0.26417	0.983000	0.44433	0.344000	0.29017	-0.311000	0.08124	-0.351000	0.08249	-0.379000	0.06801	TTC	A|0.747;G|0.253	0.253	strong		0.398	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
NEU2	4759	hgsc.bcm.edu	37	2	233899377	233899377	+	Silent	SNP	C	C	T	rs2233394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	247	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	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	
OR52N4	390072	hgsc.bcm.edu	37	11	5776788	5776788	+	Missense_Mutation	SNP	C	C	T	rs368392235		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5776788C>T	ENST00000317254.3	+	1	866	c.818C>T	c.(817-819)cCt>cTt	p.P273L	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	273						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(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		ATAATCCCCCCTTCTTGCCAC	0.448																																					p.P273L		Atlas-SNP	.											OR52N4,right_upper_lobe,carcinoma,0,1	OR52N4	55	1	0			c.C818T						scavenged	.						162.0	153.0	156.0					11																	5776788		1940	4162	6102	SO:0001583	missense	390072	exon1			TCCCCCCTTCTTG	AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"""GPCR / Class A : Olfactory receptors"""	15230	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily N, member 4"""				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	ENST00000317254.3:c.818C>T	11.37:g.5776788C>T	ENSP00000323224:p.Pro273Leu	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	254	3	0.011811	NM_001005175	B2RNP8|Q6IF77	Missense_Mutation	SNP	ENST00000317254.3	37	CCDS44528.1	.	.	.	.	.	.	.	.	.	.	C	0.033	-1.324358	0.01309	.	.	ENSG00000181074	ENST00000317254	T	0.00207	8.55	5.65	1.33	0.21861	GPCR, rhodopsin-like superfamily (1);	0.495299	0.15403	N	0.264190	T	0.00178	0.0005	L	0.61387	1.9	0.09310	N	1	B	0.02656	0.0	B	0.15052	0.012	T	0.28267	-1.0049	10	0.13470	T	0.59	.	4.8074	0.13326	0.2162:0.5407:0.0:0.243	.	273	Q8NGI2	O52N4_HUMAN	L	273	ENSP00000323224:P273L	ENSP00000323224:P273L	P	+	2	0	OR52N4	5733364	0.006000	0.16342	0.081000	0.20488	0.033000	0.12548	2.082000	0.41605	0.766000	0.33244	-0.147000	0.13772	CCT	.	.	alt		0.448	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175	
PRSS55	203074	hgsc.bcm.edu	37	8	10388826	10388826	+	Silent	SNP	G	G	A	rs4841367	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10388826G>A	ENST00000328655.3	+	3	409	c.369G>A	c.(367-369)gtG>gtA	p.V123V	PRSS55_ENST00000522210.1_Silent_p.V123V|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	123	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						TGAGTGTCGTGCTGGGGACCA	0.507													G|||	253	0.0505192	0.1142	0.0461	5008	,	,		19219	0.001		0.0636	False		,,,				2504	0.0051				p.V123V		Atlas-SNP	.											.	PRSS55	67	.	0			c.G369A						PASS	.	G	,	479,3927	224.3+/-240.5	26,427,1750	118.0	113.0	115.0		369,369	1.8	0.0	8	dbSNP_111	115	539,8061	148.6+/-203.8	13,513,3774	no	coding-synonymous,coding-synonymous	PRSS55	NM_001197020.1,NM_198464.3	,	39,940,5524	AA,AG,GG		6.2674,10.8715,7.8272	,	123/277,123/353	10388826	1018,11988	2203	4300	6503	SO:0001819	synonymous_variant	203074	exon3			TGTCGTGCTGGGG	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.369G>A	8.37:g.10388826G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001197020	E5RJX5	Silent	SNP	ENST00000328655.3	37	CCDS5976.1																																																																																			G|0.929;A|0.071	0.071	strong		0.507	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
ITGB2	3689	hgsc.bcm.edu	37	21	46313442	46313442	+	Silent	SNP	G	G	T	rs2230529	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46313442G>T	ENST00000397850.2	-	11	1553	c.1101C>A	c.(1099-1101)gtC>gtA	p.V367V	ITGB2_ENST00000355153.4_Silent_p.V367V|ITGB2_ENST00000302347.5_Silent_p.V367V|ITGB2_ENST00000397854.3_Silent_p.V310V|ITGB2_ENST00000397857.1_Silent_p.V367V|ITGB2_ENST00000397852.1_Silent_p.V367V			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	367					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	GATCCAGGAAGACCCTGGAGG	0.602													G|||	997	0.199081	0.2292	0.1542	5008	,	,		20095	0.0893		0.2505	False		,,,				2504	0.2505				p.V367V		Atlas-SNP	.											.	ITGB2	107	.	0			c.C1101A						PASS	.	G	,	963,3443	362.6+/-316.2	119,725,1359	148.0	131.0	137.0		1101,1101	3.7	1.0	21	dbSNP_98	137	2170,6430	371.4+/-336.2	270,1630,2400	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	389,2355,3759	TT,TG,GG		25.2326,21.8566,24.0889	,	367/770,367/770	46313442	3133,9873	2203	4300	6503	SO:0001819	synonymous_variant	3689	exon10			CAGGAAGACCCTG	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.1101C>A	21.37:g.46313442G>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	272	132	0.485294	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			G|0.775;T|0.225	0.225	strong		0.602	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
FRAS1	80144	hgsc.bcm.edu	37	4	79343111	79343111	+	Silent	SNP	G	G	A	rs78575519	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79343111G>A	ENST00000325942.6	+	34	5075	c.4635G>A	c.(4633-4635)ccG>ccA	p.P1545P	FRAS1_ENST00000264895.6_Silent_p.P1545P	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1545					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GCCCTCCCCCGGCAGCACCCC	0.572													G|||	496	0.0990415	0.0567	0.1599	5008	,	,		19452	0.001		0.2276	False		,,,				2504	0.0818				p.P1545P		Atlas-SNP	.											.	FRAS1	779	.	0			c.G4635A						PASS	.	G	,	396,3690		18,360,1665	127.0	140.0	136.0		4635,4635	-11.4	0.0	4	dbSNP_132	136	1945,6407		238,1469,2469	no	coding-synonymous,coding-synonymous	FRAS1	NM_001166133.1,NM_025074.6	,	256,1829,4134	AA,AG,GG		23.2878,9.6916,18.8214	,	1545/1977,1545/4013	79343111	2341,10097	2043	4176	6219	SO:0001819	synonymous_variant	80144	exon34			TCCCCCGGCAGCA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4635G>A	4.37:g.79343111G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	37	CCDS54772.1																																																																																			G|0.863;A|0.137	0.137	strong		0.572	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
GEM	2669	hgsc.bcm.edu	37	8	95272605	95272605	+	Missense_Mutation	SNP	G	G	C	rs2170363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:95272605G>C	ENST00000297596.2	-	2	391	c.127C>G	c.(127-129)Cgc>Ggc	p.R43G	GEM_ENST00000396194.2_Missense_Mutation_p.R43G	NM_005261.3	NP_005252.1	P55040	GEM_HUMAN	GTP binding protein overexpressed in skeletal muscle	43			R -> G (in dbSNP:rs2170363).		cell surface receptor signaling pathway (GO:0007166)|chromosome organization (GO:0051276)|immune response (GO:0006955)|metaphase plate congression (GO:0051310)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic side of plasma membrane (GO:0009898)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			TGGCGGTTGCGGTGGCTGTAC	0.607													G|||	565	0.112819	0.0923	0.0576	5008	,	,		15583	0.1438		0.1183	False		,,,				2504	0.1421				p.R43G	GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)	Atlas-SNP	.											GEM,colon,carcinoma,+1,1	GEM	40	1	0			c.C127G						PASS	.	G	GLY/ARG,GLY/ARG	463,3943		57,349,1797	76.0	74.0	75.0		127,127	5.3	0.0	8	dbSNP_96	75	1222,7378		104,1014,3182	yes	missense,missense	GEM	NM_005261.3,NM_181702.2	125,125	161,1363,4979	CC,CG,GG		14.2093,10.5084,12.9556	benign,benign	43/297,43/297	95272605	1685,11321	2203	4300	6503	SO:0001583	missense	2669	exon2			GGTTGCGGTGGCT		CCDS6261.1	8q13-q21	2014-05-09	2001-11-28		ENSG00000164949	ENSG00000164949			4234	protein-coding gene	gene with protein product	"""kinase-inducible Ras-like protein"""	600164	"""GTP-binding protein overexpressed in skeletal muscle"""			7912851, 11956230	Standard	NM_005261		Approved	KIR	uc003ygj.3	P55040	OTTHUMG00000164392	ENST00000297596.2:c.127C>G	8.37:g.95272605G>C	ENSP00000297596:p.Arg43Gly	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_181702	B2RA31	Missense_Mutation	SNP	ENST00000297596.2	37	CCDS6261.1	.	.	.	.	.	.	.	.	.	.	G	4.826	0.153596	0.09185	0.105084	0.142093	ENSG00000164949	ENST00000396194;ENST00000297596;ENST00000523433	T;T;T	0.64618	-0.11;-0.11;1.51	5.28	5.28	0.74379	.	0.771703	0.12758	N	0.441589	T	0.00637	0.0021	L	0.44542	1.39	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.21793	-1.0235	9	0.17369	T	0.5	.	18.9302	0.92561	0.0:0.0:1.0:0.0	rs2170363;rs3735859;rs3943139;rs17847125;rs52798968;rs2170363	43	P55040	GEM_HUMAN	G	43	ENSP00000379497:R43G;ENSP00000297596:R43G;ENSP00000428258:R43G	ENSP00000297596:R43G	R	-	1	0	GEM	95341781	0.995000	0.38212	0.013000	0.15412	0.059000	0.15707	7.430000	0.80321	2.469000	0.83416	0.655000	0.94253	CGC	A|0.009;C|0.090;G|0.902;N|0.000	0.090	strong		0.607	GEM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378566.1	NM_181702	
AP4E1	23431	hgsc.bcm.edu	37	15	51217361	51217361	+	Missense_Mutation	SNP	T	T	C	rs2306331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:51217361T>C	ENST00000261842.5	+	5	593	c.487T>C	c.(487-489)Tgc>Cgc	p.C163R	AP4E1_ENST00000560508.1_Missense_Mutation_p.C88R	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	163			C -> R (in dbSNP:rs2306331). {ECO:0000269|PubMed:11409905, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)		GATTTTCCCCTGCGAAATGAT	0.373													C|||	2208	0.440895	0.379	0.389	5008	,	,		18690	0.625		0.4662	False		,,,				2504	0.3456				p.C163R		Atlas-SNP	.											.	AP4E1	78	.	0			c.T487C						PASS	.	C	ARG/CYS	1745,2647	645.2+/-398.2	335,1075,786	128.0	113.0	118.0		487	5.5	1.0	15	dbSNP_100	118	3929,4659	604.0+/-394.7	910,2109,1275	yes	missense	AP4E1	NM_007347.3	180	1245,3184,2061	CC,CT,TT		45.7499,39.7313,43.7134	benign	163/1138	51217361	5674,7306	2196	4294	6490	SO:0001583	missense	23431	exon5			TTCCCCTGCGAAA	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.487T>C	15.37:g.51217361T>C	ENSP00000261842:p.Cys163Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	1044	0.47802197802197804	214	0.4349593495934959	137	0.3784530386740331	337	0.5891608391608392	356	0.46965699208443273	C	7.355	0.623751	0.14193	0.397313	0.457499	ENSG00000081014	ENST00000261842	T	0.11712	2.75	5.53	5.53	0.82687	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.165367	0.43416	N	0.000577	T	0.00012	0.0000	N	0.00321	-1.65	0.37602	P	0.079399	B	0.02656	0.0	B	0.01281	0.0	T	0.39563	-0.9608	9	0.02654	T	1	-0.0563	8.7491	0.34605	0.1486:0.7758:0.0:0.0756	rs2306331;rs17703100;rs52834083;rs59789697;rs2306331	163	Q9UPM8	AP4E1_HUMAN	R	163	ENSP00000261842:C163R	ENSP00000261842:C163R	C	+	1	0	AP4E1	49004653	1.000000	0.71417	0.998000	0.56505	0.689000	0.40095	3.863000	0.56016	1.348000	0.45733	-0.368000	0.07277	TGC	T|0.550;C|0.450	0.450	strong		0.373	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
ADCK5	203054	hgsc.bcm.edu	37	8	145603114	145603114	+	Missense_Mutation	SNP	A	A	C	rs6599528	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145603114A>C	ENST00000308860.6	+	2	95	c.51A>C	c.(49-51)agA>agC	p.R17S	ADCK5_ENST00000532190.1_Missense_Mutation_p.R17S|ADCK5_ENST00000526231.2_3'UTR	NM_174922.3	NP_777582.4	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	17			R -> S (in dbSNP:rs6599528). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	protein serine/threonine kinase activity (GO:0004674)	p.R17S(1)		endometrium(1)|lung(2)|prostate(2)|skin(1)|stomach(2)	8	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;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TGCTGCACAGAAGGCAGAAGC	0.602													C|||	3167	0.632388	0.8101	0.5648	5008	,	,		20220	0.6577		0.4314	False		,,,				2504	0.6207				p.R17S		Atlas-SNP	.											ADCK5,rectum,carcinoma,0,3	ADCK5	36	3	1	Substitution - Missense(1)	stomach(1)	c.A51C						PASS	.	C	SER/ARG	3290,1114	391.2+/-328.0	1218,854,130	64.0	54.0	57.0		51	3.7	0.0	8	dbSNP_116	57	3755,4845	613.8+/-396.1	826,2103,1371	yes	missense	ADCK5	NM_174922.3	110	2044,2957,1501	CC,CA,AA		43.6628,25.2952,45.8244	benign	17/581	145603114	7045,5959	2202	4300	6502	SO:0001583	missense	203054	exon2			GCACAGAAGGCAG	BC032402	CCDS34965.1, CCDS34965.2	8q24.3	2004-07-06			ENSG00000173137	ENSG00000173137			21738	protein-coding gene	gene with protein product							Standard	NM_174922		Approved	FLJ35454	uc003zch.3	Q3MIX3	OTTHUMG00000165190	ENST00000308860.6:c.51A>C	8.37:g.145603114A>C	ENSP00000310547:p.Arg17Ser	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	219	107	0.488584	NM_174922	B3KS46|Q5U4P1|Q6P2S4|Q8N5V3	Missense_Mutation	SNP	ENST00000308860.6	37	CCDS34965.1	1275	0.5837912087912088	387	0.7865853658536586	201	0.5552486187845304	369	0.6451048951048951	318	0.41952506596306066	C	0.157	-1.085760	0.01873	0.747048	0.436628	ENSG00000173137	ENST00000308860;ENST00000532190	T;T	0.74421	-0.84;0.92	4.55	3.68	0.42216	.	0.917523	0.09037	N	0.857810	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42582	-0.9443	9	0.07175	T	0.84	-5.5209	5.77	0.18247	0.1918:0.7078:0.0:0.1004	rs6599528;rs61015944;rs6599528	17	Q3MIX3	ADCK5_HUMAN	S	17	ENSP00000310547:R17S;ENSP00000435155:R17S	ENSP00000310547:R17S	R	+	3	2	ADCK5	145573922	0.127000	0.22367	0.001000	0.08648	0.279000	0.26890	2.275000	0.43399	0.389000	0.25086	-0.975000	0.02590	AGA	A|0.433;C|0.567	0.567	strong		0.602	ADCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382556.2	NM_174922	
PSAPL1	768239	hgsc.bcm.edu	37	4	7436239	7436239	+	Missense_Mutation	SNP	C	C	T	rs56402179	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:7436239C>T	ENST00000319098.4	-	1	461	c.368G>A	c.(367-369)cGt>cAt	p.R123H	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)	123	Saposin B-type 1. {ECO:0000255|PROSITE- ProRule:PRU00415}.				sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CGGGGCCCCACGGAGCATGCT	0.642													C|||	518	0.103435	0.0151	0.1282	5008	,	,		15529	0.0764		0.1909	False		,,,				2504	0.1431				p.R123H		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G368A						PASS	.	C	HIS/ARG,	160,3918		3,154,1882	21.0	22.0	22.0		368,	-2.8	0.0	4	dbSNP_129	22	1577,6775		145,1287,2744	no	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	29,	148,1441,4626	TT,TC,CC		18.8817,3.9235,13.9743	benign,	123/522,	7436239	1737,10693	2039	4176	6215	SO:0001583	missense	768239	exon1			GCCCCACGGAGCA	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.368G>A	4.37:g.7436239C>T	ENSP00000317445:p.Arg123His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	237	0.10851648351648352	10	0.02032520325203252	52	0.143646408839779	33	0.057692307692307696	142	0.18733509234828497	C	8.082	0.772668	0.16051	0.039235	0.188817	ENSG00000178597	ENST00000319098	D	0.84442	-1.85	3.21	-2.82	0.05787	Saposin-like (2);Saposin B (2);	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02132	-1.1208	8	0.41790	T	0.15	.	1.7598	0.02989	0.1384:0.4234:0.1367:0.3015	rs56402179;rs61734836	123	Q6NUJ1	SAPL1_HUMAN	H	123	ENSP00000317445:R123H	ENSP00000317445:R123H	R	-	2	0	PSAPL1	7487140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.605000	0.02074	-1.445000	0.01948	-2.630000	0.00154	CGT	C|0.882;T|0.118	0.118	strong		0.642	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
TTN	7273	hgsc.bcm.edu	37	2	179582327	179582327	+	Missense_Mutation	SNP	C	C	T	rs13390491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179582327C>T	ENST00000591111.1	-	85	24547	c.24323G>A	c.(24322-24324)aGc>aAc	p.S8108N	TTN_ENST00000589042.1_Missense_Mutation_p.S8425N|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.S7181N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12299	Ig-like 63.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCTATGTGGCTCTGGTCAGT	0.423													C|||	1221	0.24381	0.1936	0.183	5008	,	,		21045	0.4355		0.1571	False		,,,				2504	0.2464				p.S8425N		Atlas-SNP	.											.	TTN	18412	.	0			c.G25274A						PASS	.	C	,,,ASN/SER	613,3149		46,521,1314	76.0	78.0	77.0		,,,21542	5.5	1.0	2	dbSNP_121	77	1242,6996		96,1050,2973	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,46	142,1571,4287	TT,TC,CC		15.0765,16.2945,15.4583	,,,benign	,,,7181/33424	179582327	1855,10145	1881	4119	6000	SO:0001583	missense	7273	exon87			ATGTGGCTCTGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24323G>A	2.37:g.179582327C>T	ENSP00000465570:p.Ser8108Asn	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	263	135	0.513308	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		512	0.23443223443223443	98	0.1991869918699187	55	0.15193370165745856	243	0.42482517482517484	116	0.15303430079155672	C	8.404	0.842666	0.16963	0.162945	0.150765	ENSG00000155657	ENST00000342992	T	0.68903	-0.36	5.51	5.51	0.81932	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.61036	1.89	0.19945	P	0.999942837	B	0.26602	0.154	B	0.22753	0.041	T	0.31613	-0.9937	8	0.87932	D	0	.	10.3596	0.43984	0.0:0.7257:0.2009:0.0734	rs13390491;rs52812757;rs58114390;rs13390491	8108	Q8WZ42	TITIN_HUMAN	N	7181	ENSP00000343764:S7181N	ENSP00000343764:S7181N	S	-	2	0	TTN	179290572	0.357000	0.24938	1.000000	0.80357	0.939000	0.58152	0.935000	0.28924	2.738000	0.93877	0.655000	0.94253	AGC	C|0.774;T|0.226	0.226	strong		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MORC3	23515	hgsc.bcm.edu	37	21	37692589	37692589	+	Silent	SNP	A	A	T	rs2236433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:37692589A>T	ENST00000400485.1	+	1	103	c.27A>T	c.(25-27)atA>atT	p.I9I	MORC3_ENST00000487909.1_3'UTR|AP000692.10_ENST00000608391.1_RNA	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	9					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						CCCGCGGGATACGCCTCAGCG	0.736													A|||	1134	0.226438	0.0129	0.33	5008	,	,		9235	0.4871		0.1372	False		,,,				2504	0.2648				p.I9I		Atlas-SNP	.											.	MORC3	78	.	0			c.A27T						PASS	.	A		136,3520		5,126,1697	7.0	9.0	8.0		27	2.6	1.0	21	dbSNP_98	8	1112,6928		80,952,2988	no	coding-synonymous	MORC3	NM_015358.2		85,1078,4685	TT,TA,AA		13.8308,3.7199,10.6703		9/940	37692589	1248,10448	1828	4020	5848	SO:0001819	synonymous_variant	23515	exon1			CGGGATACGCCTC	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.27A>T	21.37:g.37692589A>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	37	CCDS42924.1																																																																																			A|0.762;T|0.238	0.238	strong		0.736	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
KRT37	8688	hgsc.bcm.edu	37	17	39577215	39577215	+	Missense_Mutation	SNP	G	G	A	rs8071814	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	59	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	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	
OR2A5	393046	hgsc.bcm.edu	37	7	143747870	143747870	+	Missense_Mutation	SNP	A	A	G	rs2961144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:143747870A>G	ENST00000408906.2	+	1	410	c.376A>G	c.(376-378)Atc>Gtc	p.I126V		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	126			I -> V (in dbSNP:rs2961144).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					GTACATGGCTATCTGCCACCC	0.498													A|||	1481	0.295727	0.5318	0.2695	5008	,	,		22246	0.0079		0.2903	False		,,,				2504	0.2975				p.I126V		Atlas-SNP	.											.	OR2A5	78	.	0			c.A376G						PASS	.	A	VAL/ILE	1970,2278		480,1010,634	181.0	185.0	183.0		376	5.2	1.0	7	dbSNP_101	183	2685,5801		428,1829,1986	yes	missense	OR2A5	NM_012365.1	29	908,2839,2620	GG,GA,AA		31.6403,46.3748,36.5557	possibly-damaging	126/312	143747870	4655,8079	2124	4243	6367	SO:0001583	missense	393046	exon1			ATGGCTATCTGCC	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"""GPCR / Class A : Olfactory receptors"""	8232	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 5"""	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.376A>G	7.37:g.143747870A>G	ENSP00000386208:p.Ile126Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	174	78	0.448276	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	538	0.24633699633699635	232	0.4715447154471545	101	0.27900552486187846	0	0.0	205	0.2704485488126649	A	13.91	2.378807	0.42207	0.463748	0.316403	ENSG00000221836	ENST00000408906	T	0.50813	0.73	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32563	U	0.005924	T	0.00012	0.0000	M	0.71296	2.17	0.27740	P	0.9445097	D	0.54207	0.965	P	0.51385	0.668	T	0.50980	-0.8763	9	0.15499	T	0.54	.	13.1424	0.59442	1.0:0.0:0.0:0.0	rs2961144;rs52833438;rs60301672;rs2961144	126	Q96R48	OR2A5_HUMAN	V	126	ENSP00000386208:I126V	ENSP00000386208:I126V	I	+	1	0	OR2A5	143378803	1.000000	0.71417	0.998000	0.56505	0.404000	0.30871	5.947000	0.70242	2.202000	0.70862	0.455000	0.32223	ATC	A|0.713;G|0.287	0.287	strong		0.498	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
TTN	7273	hgsc.bcm.edu	37	2	179398823	179398823	+	Silent	SNP	G	G	A	rs2857265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179398823G>A	ENST00000591111.1	-	308	97820	c.97596C>T	c.(97594-97596)ggC>ggT	p.G32532G	TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Silent_p.G34173G|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000359218.5_Silent_p.G25233G|TTN_ENST00000460472.2_Silent_p.G25108G|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.G25300G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.G31605G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000450692.2_RNA			Q8WZ42	TITIN_HUMAN	titin	32532	Ig-like 143.				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)			GCTGTCGGACGCCAAAGTACC	0.418													G|||	1162	0.232029	0.1483	0.1571	5008	,	,		23498	0.4514		0.1392	False		,,,				2504	0.2679				p.G34173G		Atlas-SNP	.											.	TTN	18412	.	0			c.C102519T						PASS	.	G	,,,	552,3352		40,472,1440	114.0	112.0	113.0		75324,94815,75699,75900	-10.3	0.8	2	dbSNP_100	113	1214,7072		92,1030,3021	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	132,1502,4461	AA,AG,GG		14.6512,14.1393,14.4873	,,,	25108/26927,31605/33424,25233/27052,25300/27119	179398823	1766,10424	1952	4143	6095	SO:0001819	synonymous_variant	7273	exon358			TCGGACGCCAAAG	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.97596C>T	2.37:g.179398823G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	143	71	0.496504	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|0.802;A|0.198	0.198	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RIT2	6014	hgsc.bcm.edu	37	18	40323497	40323497	+	Silent	SNP	G	G	T	rs1804730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:40323497G>T	ENST00000326695.5	-	5	786	c.615C>A	c.(613-615)ctC>ctA	p.L205L	RIT2_ENST00000590910.1_3'UTR|RIT2_ENST00000589109.1_3'UTR	NM_002930.2	NP_002921.1	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	205					neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AAGAACCTTTGAGCTTCTTCC	0.388													T|||	2954	0.589856	0.8215	0.6023	5008	,	,		17979	0.6984		0.3519	False		,,,				2504	0.4008				p.L205L		Atlas-SNP	.											.	RIT2	56	.	0			c.C615A						PASS	.	T		3291,1115	399.2+/-331.1	1246,799,158	139.0	145.0	143.0		615	1.5	1.0	18	dbSNP_89	143	3106,5494	657.9+/-401.5	577,1952,1771	no	coding-synonymous	RIT2	NM_002930.2		1823,2751,1929	TT,TG,GG		36.1163,25.3064,49.185		205/218	40323497	6397,6609	2203	4300	6503	SO:0001819	synonymous_variant	6014	exon5			ACCTTTGAGCTTC	BC018060	CCDS11921.1, CCDS62431.1	18q12.3	2014-05-09	2002-09-11	2002-09-13	ENSG00000152214	ENSG00000152214			10017	protein-coding gene	gene with protein product		609592	"""Ric (Drosophila)-like, expressed in neurons"""	RIN		8824319, 8918462	Standard	NM_002930		Approved	RIBA	uc002lav.4	Q99578	OTTHUMG00000132611	ENST00000326695.5:c.615C>A	18.37:g.40323497G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_002930	B2R9L1|O15295|Q8TD69|Q8WVF6|Q92964	Silent	SNP	ENST00000326695.5	37	CCDS11921.1																																																																																			G|0.455;T|0.545	0.545	strong		0.388	RIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255852.1	NM_002930	
FAM124B	79843	hgsc.bcm.edu	37	2	225244923	225244923	+	Silent	SNP	A	A	G	rs3738953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:225244923A>G	ENST00000409685.3	-	2	1000	c.735T>C	c.(733-735)gtT>gtC	p.V245V	FAM124B_ENST00000389874.3_3'UTR	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	245										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		GATTCAGCTGAACCTACAGGA	0.488													G|||	1156	0.230831	0.2542	0.1729	5008	,	,		19995	0.2798		0.169	False		,,,				2504	0.2536				p.V245V		Atlas-SNP	.											.	FAM124B	71	.	0			c.T735C						PASS	.	G	,	328,1056		32,264,396	34.0	36.0	35.0		735,	2.7	1.0	2	dbSNP_107	35	429,2753		31,367,1193	no	coding-synonymous,utr-3	FAM124B	NM_001122779.1,NM_024785.2	,	63,631,1589	GG,GA,AA		13.4821,23.6994,16.5791	,	245/456,	225244923	757,3809	692	1591	2283	SO:0001819	synonymous_variant	79843	exon2			CAGCTGAACCTAC	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.735T>C	2.37:g.225244923A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001122779	A6NNC7|Q8NBZ4|Q8TAV7	Silent	SNP	ENST00000409685.3	37	CCDS46527.1																																																																																			A|0.775;G|0.225	0.225	strong		0.488	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785	
PRDM16	63976	hgsc.bcm.edu	37	1	3319541	3319541	+	Missense_Mutation	SNP	G	G	A	rs141374404		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3319541G>A	ENST00000270722.5	+	6	912	c.863G>A	c.(862-864)cGg>cAg	p.R288Q	PRDM16_ENST00000511072.1_Missense_Mutation_p.R289Q|PRDM16_ENST00000442529.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.R289Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.R289Q|PRDM16_ENST00000441472.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378391.2_Missense_Mutation_p.R288Q			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	288					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)		GACTGCGAGCGGATGTTCCCC	0.657			T	EVI1	"""MDS, AML"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		15244	0.0		0.001	False		,,,				2504	0.0				p.R288Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.G863A						PASS	.						44.0	56.0	52.0					1																	3319541		2186	4274	6460	SO:0001583	missense	63976	exon6			GCGAGCGGATGTT	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.863G>A	1.37:g.3319541G>A	ENSP00000270722:p.Arg288Gln	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	266	115	0.432331	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.953	0.545736	0.13312	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18	4.32	3.39	0.38822	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.336202	0.19830	U	0.105113	T	0.09862	0.0242	L	0.29908	0.895	0.27992	N	0.935619	P;D;P;B	0.62365	0.85;0.991;0.636;0.39	B;P;B;B	0.49708	0.115;0.62;0.089;0.019	T	0.15607	-1.0431	10	0.21014	T	0.42	.	13.2179	0.59871	0.0:0.0:0.8395:0.1605	.	288;288;288;288	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	289;289;288;288;288;289;288;104;104;97	ENSP00000426975:R289Q;ENSP00000367651:R289Q;ENSP00000407968:R288Q;ENSP00000405253:R288Q;ENSP00000367643:R288Q;ENSP00000421400:R289Q;ENSP00000270722:R288Q;ENSP00000422504:R104Q;ENSP00000425796:R97Q	ENSP00000270722:R288Q	R	+	2	0	PRDM16	3309401	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	5.777000	0.68931	0.788000	0.33755	0.561000	0.74099	CGG	G|1.000;A|0.000	0.000	strong		0.657	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497904	32497904	+	Missense_Mutation	SNP	C	C	T	rs1141741|rs34716432	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32497904C>T	ENST00000374975.3	-	1	160	c.98G>A	c.(97-99)cGa>cAa	p.R33Q		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						GCACTTACGTCGGGTGTCCCC	0.532																																					p.R33Q		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G98A						PASS	.						101.0	103.0	102.0					6																	32497904		2203	4300	6503	SO:0001583	missense	3127	exon1			TTACGTCGGGTGT		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.98G>A	6.37:g.32497904C>T	ENSP00000364114:p.Arg33Gln	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	340	112	0.329412	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	9.244	1.039078	0.19669	.	.	ENSG00000198502	ENST00000374975	T	0.00272	8.36	4.54	-9.08	0.00720	MHC classes I/II-like antigen recognition protein (1);	2.794840	0.01443	N	0.015168	T	0.00039	0.0001	N	0.21240	0.645	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.32107	-0.9919	10	0.26408	T	0.33	.	0.8412	0.01150	0.2396:0.2134:0.3178:0.2292	rs34716432	33	Q30154	DRB5_HUMAN	Q	33	ENSP00000364114:R33Q	ENSP00000364114:R33Q	R	-	2	0	HLA-DRB5	32605882	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.275000	0.00530	-2.555000	0.00477	-0.462000	0.05337	CGA	C|0.873;T|0.127	0.127	strong		0.532	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ZNF285	26974	hgsc.bcm.edu	37	19	44892266	44892266	+	Splice_Site	SNP	T	T	C	rs200167944		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44892266T>C	ENST00000330997.4	-	4	207		c.e4-2		ZNF285_ENST00000591679.1_Splice_Site|ZNF285_ENST00000544719.2_Splice_Site|CTC-512J12.6_ENST00000588212.1_Intron	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	115	2	0.0173913		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	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
LRRC38	126755	hgsc.bcm.edu	37	1	13802437	13802437	+	Silent	SNP	G	G	A	rs3013106	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	167	0	0		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	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		
COL14A1	7373	hgsc.bcm.edu	37	8	121228679	121228679	+	Missense_Mutation	SNP	A	A	C	rs4870723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:121228679A>C	ENST00000297848.3	+	14	1957	c.1687A>C	c.(1687-1689)Aat>Cat	p.N563H	COL14A1_ENST00000247781.3_Missense_Mutation_p.N468H|COL14A1_ENST00000537875.1_3'UTR|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Missense_Mutation_p.N563H	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)			AAGACAGATCAATGGTTATCG	0.408													A|||	2955	0.590056	0.6286	0.5749	5008	,	,		17835	0.6687		0.4702	False		,,,				2504	0.591				p.N563H		Atlas-SNP	.											COL14A1,rectum,carcinoma,0,1	COL14A1	292	1	0			c.A1687C						PASS	.	A	HIS/ASN	2536,1870	632.1+/-395.8	757,1022,424	124.0	115.0	118.0		1687	2.8	0.0	8	dbSNP_111	118	4175,4425	567.4+/-388.8	1034,2107,1159	yes	missense	COL14A1	NM_021110.1	68	1791,3129,1583	CC,CA,AA		48.5465,42.4421,48.4007	benign	563/1797	121228679	6711,6295	2203	4300	6503	SO:0001583	missense	7373	exon14			CAGATCAATGGTT		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.1687A>C	8.37:g.121228679A>C	ENSP00000297848:p.Asn563His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	1247|1247	0.5709706959706959|0.5709706959706959	306|306	0.6219512195121951|0.6219512195121951	212|212	0.585635359116022|0.585635359116022	381|381	0.666083916083916|0.666083916083916	348|348	0.45910290237467016|0.45910290237467016	A|A	10.79|10.79	1.450389|1.450389	0.26074|0.26074	0.575579|0.575579	0.485465|0.485465	ENSG00000187955|ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620|ENST00000523142	T;T;T;T|.	0.57436|.	0.4;0.4;0.4;0.4|.	5.29|5.29	2.85|2.85	0.33270|0.33270	Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	1.232880|.	0.05311|.	N|.	0.524871|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25647|0.25647	0.755|0.755	0.51012|0.51012	P|P	9.499999999995623E-5|9.499999999995623E-5	P;B|.	0.35050|.	0.482;0.295|.	P;B|.	0.46172|.	0.506;0.298|.	T|T	0.37820|0.37820	-0.9689|-0.9689	9|4	0.56958|.	D|.	0.05|.	.|.	7.3206|7.3206	0.26526|0.26526	0.8012:0.0:0.0701:0.1287|0.8012:0.0:0.0701:0.1287	rs4870723;rs59507382;rs4870723|rs4870723;rs59507382;rs4870723	563;563|.	Q05707-2;Q05707|.	.;COEA1_HUMAN|.	H|P	563;563;468;376|319	ENSP00000311809:N563H;ENSP00000297848:N563H;ENSP00000247781:N468H;ENSP00000409461:N376H|.	ENSP00000247781:N468H|.	N|Q	+|+	1|2	0|0	COL14A1|COL14A1	121297860|121297860	0.244000|0.244000	0.23889|0.23889	0.010000|0.010000	0.14722|0.14722	0.003000|0.003000	0.03518|0.03518	3.215000|3.215000	0.51169|0.51169	0.435000|0.435000	0.26365|0.26365	0.533000|0.533000	0.62120|0.62120	AAT|CAA	A|0.456;C|0.544	0.544	strong		0.408	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
CENPE	1062	hgsc.bcm.edu	37	4	104102563	104102563	+	Silent	SNP	T	T	C	rs17217250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	364	0	0		WXS	Illumina HiSeq	Phase_I	362	191	0.527624	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			
OR51G1	79324	hgsc.bcm.edu	37	11	4945236	4945236	+	Missense_Mutation	SNP	T	T	C	rs35666095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4945236T>C	ENST00000321961.2	-	1	401	c.334A>G	c.(334-336)Atg>Gtg	p.M112V	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGACTCCATTGAAGACAAG	0.507													C|||	385	0.076877	0.0613	0.1527	5008	,	,		22605	0.0089		0.1083	False		,,,				2504	0.0818				p.M112V		Atlas-SNP	.											.	OR51G1	74	.	0			c.A334G						PASS	.	C	VAL/MET	276,4126	801.0+/-415.6	3,270,1928	100.0	93.0	95.0		334	-0.0	0.1	11	dbSNP_126	95	930,7666	776.4+/-407.7	61,808,3429	yes	missense	OR51G1	NM_001005237.1	21	64,1078,5357	CC,CT,TT		10.819,6.2699,9.2784	benign	112/322	4945236	1206,11792	2201	4298	6499	SO:0001583	missense	79324	exon1			ACTCCATTGAAGA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.334A>G	11.37:g.4945236T>C	ENSP00000322546:p.Met112Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	171	0.0782967032967033	34	0.06910569105691057	30	0.08287292817679558	5	0.008741258741258742	102	0.1345646437994723	C	0.005	-2.188683	0.00305	0.062699	0.10819	ENSG00000176879	ENST00000321961	T	0.02812	4.15	4.2	-0.00795	0.14007	GPCR, rhodopsin-like superfamily (1);	0.206562	0.23916	N	0.043292	T	0.00039	0.0001	L	0.47190	1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43621	-0.9380	9	0.30078	T	0.28	.	1.644	0.02758	0.1365:0.3161:0.1337:0.4136	rs35666095	112	Q8NGK1	O51G1_HUMAN	V	112	ENSP00000322546:M112V	ENSP00000322546:M112V	M	-	1	0	OR51G1	4901812	0.000000	0.05858	0.095000	0.20976	0.034000	0.12701	-1.074000	0.03427	-0.143000	0.11334	-0.996000	0.02517	ATG	T|0.912;C|0.088	0.088	strong		0.507	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
TRIM63	84676	hgsc.bcm.edu	37	1	26385003	26385003	+	Missense_Mutation	SNP	T	T	C	rs2275950	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26385003T>C	ENST00000374272.3	-	5	847	c.709A>G	c.(709-711)Aaa>Gaa	p.K237E	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	237			K -> E (in dbSNP:rs2275950). {ECO:0000269|PubMed:11243782, ECO:0000269|PubMed:15489334}.		cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K237E(1)		kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CTAAGCTTTTTCTCCTGCTCC	0.537													C|||	913	0.182308	0.267	0.1239	5008	,	,		20137	0.1706		0.2187	False		,,,				2504	0.0838				p.K237E		Atlas-SNP	.											TRIM63,NS,carcinoma,0,1	TRIM63	33	1	1	Substitution - Missense(1)	stomach(1)	c.A709G						PASS	.	C	GLU/LYS	1195,3211	710.2+/-407.8	175,845,1183	177.0	161.0	166.0		709	5.5	1.0	1	dbSNP_100	166	1862,6738	729.6+/-406.7	197,1468,2635	yes	missense	TRIM63	NM_032588.2	56	372,2313,3818	CC,CT,TT		21.6512,27.1221,23.5045	benign	237/354	26385003	3057,9949	2203	4300	6503	SO:0001583	missense	84676	exon5			GCTTTTTCTCCTG	AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	16007	protein-coding gene	gene with protein product	"""muscle-specific RING finger protein 1"", ""iris ring finger protein"", ""striated muscle RING zinc finger protein"""	606131	"""ring finger protein 28"", ""tripartite motif-containing 63"", ""tripartite motif containing 63"""	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.709A>G	1.37:g.26385003T>C	ENSP00000363390:p.Lys237Glu	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Missense_Mutation	SNP	ENST00000374272.3	37	CCDS273.1	434	0.1987179487179487	127	0.258130081300813	43	0.11878453038674033	100	0.17482517482517482	164	0.21635883905013192	C	7.836	0.720876	0.15372	0.271221	0.216512	ENSG00000158022	ENST00000374272	T	0.40756	1.02	5.5	5.5	0.81552	.	0.198167	0.52532	N	0.000069	T	0.00012	0.0000	N	0.00043	-2.47	0.48830	P	2.889999999999837E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	9	0.02654	T	1	.	14.2207	0.65826	0.0:0.9273:0.0:0.0727	rs2275950;rs52817885;rs60345068;rs2275950	237	Q969Q1	TRI63_HUMAN	E	237	ENSP00000363390:K237E	ENSP00000363390:K237E	K	-	1	0	TRIM63	26257590	0.957000	0.32711	1.000000	0.80357	0.788000	0.44548	2.222000	0.42926	1.336000	0.45506	-0.215000	0.12644	AAA	T|0.785;C|0.215	0.215	strong		0.537	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588	
FSTL4	23105	hgsc.bcm.edu	37	5	132535046	132535046	+	Missense_Mutation	SNP	G	G	A	rs3749817	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:132535046G>A	ENST00000265342.7	-	16	2519	c.2270C>T	c.(2269-2271)aCg>aTg	p.T757M	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	757			T -> M (in dbSNP:rs3749817). {ECO:0000269|PubMed:17974005}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			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)			GTCCGGCTCCGTGTGCAGAGC	0.582													G|||	1329	0.265375	0.062	0.4049	5008	,	,		19463	0.3948		0.2316	False		,,,				2504	0.3425				p.T757M		Atlas-SNP	.											.	FSTL4	74	.	0			c.C2270T						PASS	.	G	MET/THR	384,4022	193.0+/-218.2	12,360,1831	64.0	63.0	64.0		2270	-6.3	0.0	5	dbSNP_107	64	1863,6737	331.5+/-319.7	186,1491,2623	yes	missense	FSTL4	NM_015082.1	81	198,1851,4454	AA,AG,GG		21.6628,8.7154,17.2766	benign	757/843	132535046	2247,10759	2203	4300	6503	SO:0001583	missense	23105	exon16			GGCTCCGTGTGCA	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.2270C>T	5.37:g.132535046G>A	ENSP00000265342:p.Thr757Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_015082	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	37	CCDS34238.1	574	0.26282051282051283	30	0.06097560975609756	126	0.34806629834254144	246	0.43006993006993005	172	0.22691292875989447	G	2.282	-0.364594	0.05103	0.087154	0.216628	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.21734	1.99	4.76	-6.31	0.02001	WD40/YVTN repeat-like-containing domain (1);	1.045250	0.07416	N	0.893264	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.30584	0.014;0.286	B;B	0.18561	0.006;0.022	T	0.44802	-0.9304	9	0.45353	T	0.12	2.3158	2.6468	0.04986	0.4779:0.1994:0.2182:0.1044	rs3749817;rs60534030;rs3749817	757;406	Q6MZW2;B3KPF3	FSTL4_HUMAN;.	M	757;588	ENSP00000265342:T757M	ENSP00000265342:T757M	T	-	2	0	FSTL4	132562945	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.316000	0.19469	-1.355000	0.02186	-2.109000	0.00356	ACG	G|0.785;N|0.000	.	strong		0.582	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
DAPK1	1612	hgsc.bcm.edu	37	9	90321583	90321583	+	Silent	SNP	C	C	T	rs3118863	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90321583C>T	ENST00000408954.3	+	26	3932	c.3597C>T	c.(3595-3597)cgC>cgT	p.R1199R	DAPK1_ENST00000472284.1_Silent_p.R1199R|DAPK1_ENST00000469640.2_Silent_p.R1224R|DAPK1_ENST00000358077.5_Silent_p.R1199R|DAPK1_ENST00000491893.1_Silent_p.R1133R	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1199					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TCCAGGTCCGCGGCCTGGAGA	0.647									Chronic Lymphocytic Leukemia, Familial Clustering of				C|||	1786	0.356629	0.121	0.402	5008	,	,		18309	0.4107		0.4553	False		,,,				2504	0.4857				p.R1199R		Atlas-SNP	.											.	DAPK1	329	.	0			c.C3597T						PASS	.	C		777,3559		87,603,1478	29.0	34.0	32.0		3597	-6.1	0.3	9	dbSNP_103	32	3880,4652		862,2156,1248	no	coding-synonymous	DAPK1	NM_004938.2		949,2759,2726	TT,TC,CC		45.4759,17.9197,36.1906		1199/1431	90321583	4657,8211	2168	4266	6434	SO:0001819	synonymous_variant	1612	exon26	Familial Cancer Database	Familial CLL	GGTCCGCGGCCTG	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.3597C>T	9.37:g.90321583C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			C|0.642;T|0.358	0.358	strong		0.647	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
ZNF462	58499	hgsc.bcm.edu	37	9	109687403	109687403	+	Missense_Mutation	SNP	A	A	G	rs17723637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:109687403A>G	ENST00000277225.5	+	3	1499	c.1210A>G	c.(1210-1212)Atg>Gtg	p.M404V	ZNF462_ENST00000441147.2_5'Flank|ZNF462_ENST00000457913.1_Missense_Mutation_p.M404V			Q96JM2	ZN462_HUMAN	zinc finger protein 462	404			M -> V (in dbSNP:rs17723637).		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)	p.M404V(1)		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						TTTAAGTGCTATGGATCACCA	0.423													A|||	608	0.121406	0.0726	0.0994	5008	,	,		22153	0.0804		0.167	False		,,,				2504	0.1984				p.M404V		Atlas-SNP	.											ZNF462,NS,carcinoma,0,1	ZNF462	322	1	1	Substitution - Missense(1)	stomach(1)	c.A1210G						PASS	.	A	VAL/MET	352,4054	182.6+/-210.3	14,324,1865	107.0	101.0	103.0		1210	0.7	0.1	9	dbSNP_123	103	1260,7340	251.9+/-278.2	79,1102,3119	yes	missense	ZNF462	NM_021224.4	21	93,1426,4984	GG,GA,AA		14.6512,7.9891,12.3943	benign	404/2507	109687403	1612,11394	2203	4300	6503	SO:0001583	missense	58499	exon3			AGTGCTATGGATC	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.1210A>G	9.37:g.109687403A>G	ENSP00000277225:p.Met404Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	263	0.12042124542124542	36	0.07317073170731707	44	0.12154696132596685	46	0.08041958041958042	137	0.18073878627968337	A	10.33	1.320087	0.23994	0.079891	0.146512	ENSG00000148143	ENST00000277225;ENST00000457913	T;T	0.04917	3.53;3.97	5.87	0.684	0.18003	.	0.339451	0.40908	D	0.000989	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	1.0	B;B	0.09022	0.002;0.001	B;B	0.15870	0.014;0.006	T	0.48937	-0.8990	8	.	.	.	.	9.0012	0.36083	0.5125:0.3696:0.0:0.1179	rs17723637;rs52805606;rs17723637	404;404	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	V	404	ENSP00000277225:M404V;ENSP00000414570:M404V	.	M	+	1	0	ZNF462	108727224	0.563000	0.26594	0.088000	0.20740	0.747000	0.42532	1.389000	0.34453	-0.119000	0.11830	0.533000	0.62120	ATG	A|0.881;G|0.119	0.119	strong		0.423	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
DEPTOR	64798	hgsc.bcm.edu	37	8	121061879	121061879	+	Missense_Mutation	SNP	G	G	A	rs4871827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:121061879G>A	ENST00000286234.5	+	9	1296	c.1166G>A	c.(1165-1167)aGc>aAc	p.S389N	DEPTOR_ENST00000523492.1_Missense_Mutation_p.S288N	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	389	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.		S -> N (in dbSNP:rs4871827). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						CGGACCGTGAGCAATCTGATT	0.527													G|||	1500	0.299521	0.1241	0.4784	5008	,	,		16804	0.5526		0.331	False		,,,				2504	0.1166				p.S389N		Atlas-SNP	.											.	DEPTOR	41	.	0			c.G1166A						PASS	.	G	ASN/SER	657,3749	280.8+/-275.6	51,555,1597	180.0	155.0	164.0		1166	6.0	1.0	8	dbSNP_111	164	2726,5874	435.9+/-358.1	426,1874,2000	yes	missense	DEPTOR	NM_022783.2	46	477,2429,3597	AA,AG,GG		31.6977,14.9115,26.0111	possibly-damaging	389/410	121061879	3383,9623	2203	4300	6503	SO:0001583	missense	64798	exon9			CCGTGAGCAATCT		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.1166G>A	8.37:g.121061879G>A	ENSP00000286234:p.Ser389Asn	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	210	104	0.495238	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Missense_Mutation	SNP	ENST00000286234.5	37	CCDS6331.1	816	0.37362637362637363	65	0.13211382113821138	174	0.48066298342541436	326	0.5699300699300699	251	0.3311345646437995	G	17.16	3.319471	0.60524	0.149115	0.316977	ENSG00000155792	ENST00000523492;ENST00000286234	T;T	0.30182	1.54;1.54	6.01	6.01	0.97437	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.52011	1.625	0.09310	P	0.999999999649191	B;B	0.24721	0.11;0.013	B;B	0.21917	0.037;0.008	T	0.48559	-0.9025	9	0.52906	T	0.07	-33.6104	20.1162	0.97934	0.0:0.0:1.0:0.0	rs4871827;rs17850843;rs52808957;rs59755806;rs4871827	288;389	E7EV87;Q8TB45	.;DPTOR_HUMAN	N	288;389	ENSP00000430457:S288N;ENSP00000286234:S389N	ENSP00000286234:S389N	S	+	2	0	DEPTOR	121131060	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	8.997000	0.93544	2.861000	0.98227	0.650000	0.86243	AGC	G|0.693;A|0.307	0.307	strong		0.527	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
MYO10	4651	hgsc.bcm.edu	37	5	16794916	16794916	+	Silent	SNP	G	G	A	rs396514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:16794916G>A	ENST00000513610.1	-	4	760	c.306C>T	c.(304-306)tcC>tcT	p.S102S		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	102	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						AGGGGTTCACGGAGGCCAGGA	0.632													G|||	1312	0.261981	0.0219	0.3458	5008	,	,		15939	0.244		0.4304	False		,,,				2504	0.3722				p.S102S		Atlas-SNP	.											.	MYO10	198	.	0			c.C306T						PASS	.	G		377,3735		20,337,1699	24.0	29.0	27.0		306	-10.4	0.2	5	dbSNP_80	27	3602,4808		787,2028,1390	no	coding-synonymous	MYO10	NM_012334.2		807,2365,3089	AA,AG,GG		42.83,9.1683,31.7761		102/2059	16794916	3979,8543	2056	4205	6261	SO:0001819	synonymous_variant	4651	exon4			GTTCACGGAGGCC	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.306C>T	5.37:g.16794916G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.708;A|0.292	0.292	strong		0.632	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
DCSTAMP	81501	hgsc.bcm.edu	37	8	105360994	105360994	+	Missense_Mutation	SNP	C	C	A	rs61682032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:105360994C>A	ENST00000297581.2	+	2	263	c.214C>A	c.(214-216)Ctg>Atg	p.L72M	DCSTAMP_ENST00000517991.1_Missense_Mutation_p.L72M|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	72					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											GTGTGTTCTGCTGTGTTGCTC	0.522													C|||	179	0.0357428	0.0794	0.0144	5008	,	,		18689	0.0288		0.0189	False		,,,				2504	0.0164				p.L72M		Atlas-SNP	.											.	.	.	.	0			c.C214A						PASS	.	C	MET/LEU	252,4154	145.7+/-180.5	5,242,1956	129.0	117.0	121.0		214	4.1	0.8	8	dbSNP_129	121	73,8527	43.1+/-100.9	1,71,4228	yes	missense	TM7SF4	NM_030788.2	15	6,313,6184	AA,AC,CC		0.8488,5.7195,2.4988	probably-damaging	72/471	105360994	325,12681	2203	4300	6503	SO:0001583	missense	81501	exon2			GTTCTGCTGTGTT	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"""Dendritic cells (DC)-specific transmembrane protein"", ""IL-Four INDuced"""	605933	"""transmembrane 7 superfamily member 4"""	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.214C>A	8.37:g.105360994C>A	ENSP00000297581:p.Leu72Met	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	172	81	0.47093	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	68	0.031135531135531136	32	0.06504065040650407	5	0.013812154696132596	19	0.033216783216783216	12	0.0158311345646438	C	14.48	2.548417	0.45383	0.057195	0.008488	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.39229	1.09	5.84	4.05	0.47172	.	0.138356	0.49305	D	0.000154	T	0.08980	0.0222	M	0.64997	1.995	0.22779	N	0.998749	D	0.89917	1.0	D	0.79108	0.992	T	0.02437	-1.1159	9	.	.	.	-11.7717	8.7709	0.34731	0.0:0.7774:0.0:0.2226	rs61682032	72	Q9H295	TM7S4_HUMAN	M	72	ENSP00000297581:L72M	.	L	+	1	2	TM7SF4	105430170	.	.	0.761000	0.31378	0.580000	0.36256	.	.	1.496000	0.48567	0.655000	0.94253	CTG	C|0.973;A|0.027	0.027	strong		0.522	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
FBF1	85302	hgsc.bcm.edu	37	17	73914040	73914040	+	Silent	SNP	C	C	T	rs376546796		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73914040C>T	ENST00000586717.1	-	21	2589	c.2316G>A	c.(2314-2316)ggG>ggA	p.G772G	FBF1_ENST00000319129.5_Silent_p.G771G|FBF1_ENST00000389570.4_Silent_p.G772G			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	772					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						GCTGCCGGATCCCCAGCTCCC	0.677																																					p.G771G		Atlas-SNP	.											.	FBF1	48	.	0			c.G2313A						PASS	.	C		1,4061		0,1,2030	28.0	32.0	31.0		2313	-4.2	0.1	17		31	0,8382		0,0,4191	no	coding-synonymous	FBF1	NM_001080542.1		0,1,6221	TT,TC,CC		0.0,0.0246,0.0080		771/1134	73914040	1,12443	2031	4191	6222	SO:0001819	synonymous_variant	85302	exon21			CCGGATCCCCAGC	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.2316G>A	17.37:g.73914040C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	33	0.622642	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				.	.	weak		0.677	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
PM20D1	148811	hgsc.bcm.edu	37	1	205819104	205819104	+	Missense_Mutation	SNP	G	G	A	rs11540014	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205819104G>A	ENST00000367136.4	-	1	141	c.97C>T	c.(97-99)Cat>Tat	p.H33Y	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	33			H -> Y (in dbSNP:rs11540014). {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)			GCCCTTTGATGCTCCCCGCTC	0.602													G|||	806	0.160942	0.053	0.0605	5008	,	,		18337	0.4266		0.0974	False		,,,				2504	0.1697				p.H33Y		Atlas-SNP	.											.	PM20D1	56	.	0			c.C97T						PASS	.	G	TYR/HIS	266,4140	150.7+/-184.7	8,250,1945	85.0	86.0	85.0		97	-1.6	0.0	1	dbSNP_120	85	648,7952	165.9+/-218.0	20,608,3672	yes	missense	PM20D1	NM_152491.4	83	28,858,5617	AA,AG,GG		7.5349,6.0372,7.0275	benign	33/503	205819104	914,12092	2203	4300	6503	SO:0001583	missense	148811	exon1			TTTGATGCTCCCC		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.97C>T	1.37:g.205819104G>A	ENSP00000356104:p.His33Tyr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	184	84	0.456522	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	361	0.1652930402930403	23	0.046747967479674794	23	0.06353591160220995	241	0.42132867132867136	74	0.09762532981530343	G	1.008	-0.688948	0.03328	0.060372	0.075349	ENSG00000162877	ENST00000367136	T	0.06528	3.29	5.17	-1.59	0.08453	.	1.185250	0.05391	N	0.539060	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	0.45411	-0.9263	9	0.02654	T	1	.	0.572	0.00697	0.2463:0.1352:0.3419:0.2767	rs11540014;rs61022628;rs11540014	33	Q6GTS8	P20D1_HUMAN	Y	33	ENSP00000356104:H33Y	ENSP00000356104:H33Y	H	-	1	0	PM20D1	204085727	0.001000	0.12720	0.000000	0.03702	0.029000	0.11900	0.390000	0.20768	-0.492000	0.06687	0.655000	0.94253	CAT	G|0.889;A|0.111	0.111	strong		0.602	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036950	33036950	+	Silent	SNP	C	C	T	rs386699855|rs2308931	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33036950C>T	ENST00000419277.1	-	4	603	c.474G>A	c.(472-474)ctG>ctA	p.L158L	HLA-DPA1_ENST00000428995.1_Silent_p.L158L|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	158	Alpha-2.|Ig-like C1-type.		L -> P (in allele DPA1*02:01, allele DPA1*02:02 and allele DPA1*04:01; dbSNP:rs2308930).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CCTCAGTGACCAGCTCCCCGT	0.567													C|||	980	0.195687	0.239	0.2147	5008	,	,		18947	0.1319		0.1183	False		,,,				2504	0.2689				p.L158L		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G474A						PASS	.	C	,,	526,2492		50,426,1033	166.0	189.0	181.0		474,474,474	0.4	0.0	6	dbSNP_121	181	537,4879		26,485,2197	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	76,911,3230	TT,TC,CC		9.9151,17.4288,12.6037	,,	158/261,158/261,158/261	33036950	1063,7371	1509	2708	4217	SO:0001819	synonymous_variant	3113	exon3			AGTGACCAGCTCC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.474G>A	6.37:g.33036950C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	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	
PRR27	401137	hgsc.bcm.edu	37	4	71024467	71024467	+	Silent	SNP	T	T	G	rs201990073		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024467T>G	ENST00000344526.5	+	3	687	c.498T>G	c.(496-498)gcT>gcG	p.A166A	C4orf40_ENST00000502294.1_Silent_p.A166A|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		166	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)		p.A166V(1)		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						CTGTTGGAGCTGAGCCTGCTG	0.627																																					p.A166A		Atlas-SNP	.											.	C4orf40	19	.	1	Substitution - Missense(1)	lung(1)	c.T498G						PASS	.						30.0	31.0	30.0					4																	71024467		2203	4297	6500	SO:0001819	synonymous_variant	401137	exon3			TGGAGCTGAGCCT																												ENST00000344526.5:c.498T>G	4.37:g.71024467T>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	114	26	0.22807	NM_214711	A8MXP0|Q6MZR6	Silent	SNP	ENST00000344526.5	37	CCDS3535.1																																																																																			T|0.999;G|0.001	0.001	weak		0.627	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
ASIC2	40	hgsc.bcm.edu	37	17	32483270	32483270	+	Silent	SNP	C	C	G	rs2228989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:32483270C>G	ENST00000359872.6	-	1	1043	c.282G>C	c.(280-282)ctG>ctC	p.L94L		NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	94					central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)									Amiloride(DB00594)	GGAAGCCATTCAGGTTACAGA	0.577													G|||	1163	0.232228	0.0439	0.3573	5008	,	,		19977	0.3532		0.2008	False		,,,				2504	0.3057				p.L94L		Atlas-SNP	.											.	.	.	.	0			c.G282C						PASS	.	G		279,4085		6,267,1909	75.0	83.0	80.0		282	2.9	1.0	17	dbSNP_98	80	1632,6926		151,1330,2798	no	coding-synonymous	ACCN1	NM_001094.4		157,1597,4707	GG,GC,CC		19.0699,6.3932,14.7887		94/513	32483270	1911,11011	2182	4279	6461	SO:0001819	synonymous_variant	40	exon1			GCCATTCAGGTTA	AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	99	protein-coding gene	gene with protein product	"""degenerin"""	601784	"""amiloride-sensitive cation channel 1, neuronal"""	ACCN, ACCN1		8921408	Standard	NM_183377		Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.282G>C	17.37:g.32483270C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_001094	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Silent	SNP	ENST00000359872.6	37	CCDS42296.1																																																																																			C|0.782;G|0.218	0.218	strong		0.577	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094	
KIAA0195	9772	hgsc.bcm.edu	37	17	73492494	73492494	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73492494C>G	ENST00000314256.7	+	24	3579	c.3185C>G	c.(3184-3186)cCc>cGc	p.P1062R	KIAA0195_ENST00000375248.5_Missense_Mutation_p.P1072R|AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000579208.1_Missense_Mutation_p.P713R	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1062						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)			AACAGCCTGCCCTGTTCCCTG	0.617																																					p.P1062R		Atlas-SNP	.											.	KIAA0195	102	.	0			c.C3185G						PASS	.						57.0	54.0	55.0					17																	73492494		2203	4300	6503	SO:0001583	missense	9772	exon24			GCCTGCCCTGTTC		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.3185C>G	17.37:g.73492494C>G	ENSP00000313885:p.Pro1062Arg	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	199	100	0.502513	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.620105	0.46736	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.55760	0.5;0.5	5.54	5.54	0.83059	ATPase, P-type,  transmembrane domain (1);	0.253079	0.41500	D	0.000877	T	0.67674	0.2918	M	0.67397	2.05	0.53688	D	0.999973	B;P;P;B	0.39535	0.232;0.573;0.677;0.437	B;B;P;B	0.50970	0.077;0.219;0.655;0.109	T	0.68784	-0.5317	10	0.87932	D	0	-32.2942	19.8311	0.96636	0.0:1.0:0.0:0.0	.	1072;1072;1062;1062	B4DGC6;C9JL75;Q12767-2;Q12767	.;.;.;K0195_HUMAN	R	1062;1072	ENSP00000313885:P1062R;ENSP00000364397:P1072R	ENSP00000313885:P1062R	P	+	2	0	KIAA0195	71004089	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.656000	0.61483	2.768000	0.95171	0.561000	0.74099	CCC	.	.	none		0.617	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
DHRS4	10901	hgsc.bcm.edu	37	14	24423007	24423007	+	Missense_Mutation	SNP	G	G	A	rs17099455	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24423007G>A	ENST00000313250.5	+	1	213	c.10G>A	c.(10-12)Gcg>Acg	p.A4T	DHRS4_ENST00000558263.1_Missense_Mutation_p.A4T|DHRS4_ENST00000543741.2_Missense_Mutation_p.A4T|DHRS4_ENST00000421831.1_5'UTR|DHRS4_ENST00000382761.3_5'UTR|DHRS4_ENST00000397074.3_Missense_Mutation_p.A4T|DHRS4_ENST00000397075.3_Missense_Mutation_p.A4T|DHRS4_ENST00000558581.1_Missense_Mutation_p.A4T|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000308178.8_5'UTR|DHRS4_ENST00000559632.1_Missense_Mutation_p.A4T|DHRS4_ENST00000397073.2_5'UTR	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	4					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CATGCACAAGGCGGGGCTGCT	0.662													.|||	988	0.197284	0.6135	0.1023	5008	,	,		16663	0.0099		0.0517	False		,,,				2504	0.045				p.A4T		Atlas-SNP	.											.	DHRS4	22	.	0			c.G10A						PASS	.	A	THR/ALA	2359,2047		647,1065,491	49.0	54.0	52.0		10	1.8	0.0	14	dbSNP_123	52	456,8144		13,430,3857	yes	missense	DHRS4	NM_021004.2	58	660,1495,4348	AA,AG,GG		5.3023,46.4594,21.6439	benign	4/279	24423007	2815,10191	2203	4300	6503	SO:0001583	missense	10901	exon1			CACAAGGCGGGGC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.10G>A	14.37:g.24423007G>A	ENSP00000326219:p.Ala4Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	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		
CLEC12B	387837	hgsc.bcm.edu	37	12	10163375	10163375	+	Missense_Mutation	SNP	C	C	A	rs1359082	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:10163375C>A	ENST00000338896.5	+	1	145	c.17C>A	c.(16-18)aCc>aAc	p.T6N	CLEC12B_ENST00000396502.1_Missense_Mutation_p.T6N|CLEC1B_ENST00000428126.2_Intron	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	6			T -> N (in dbSNP:rs1359082). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						GAAGAAGTGACCTACGCGACA	0.403													C|||	1565	0.3125	0.3896	0.3775	5008	,	,		20689	0.1538		0.4245	False		,,,				2504	0.2106				p.T6N		Atlas-SNP	.											.	CLEC12B	25	.	0			c.C17A						PASS	.	C	ASN/THR,ASN/THR	1647,2759	495.3+/-363.2	309,1029,865	60.0	57.0	58.0		17,17	4.9	1.0	12	dbSNP_88	58	3306,5294	485.9+/-371.7	643,2020,1637	yes	missense,missense	CLEC12B	NM_001129998.1,NM_205852.2	65,65	952,3049,2502	AA,AC,CC		38.4419,37.3808,38.0824	probably-damaging,probably-damaging	6/277,6/233	10163375	4953,8053	2203	4300	6503	SO:0001583	missense	387837	exon1			AAGTGACCTACGC	AK128243	CCDS8610.1, CCDS44830.1	12p13.2	2010-08-17			ENSG00000256660	ENSG00000256660		"""C-type lectin domain containing"""	31966	protein-coding gene	gene with protein product						17562706	Standard	NM_205852		Approved		uc001qwz.2	Q2HXU8	OTTHUMG00000168397	ENST00000338896.5:c.17C>A	12.37:g.10163375C>A	ENSP00000344563:p.Thr6Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	70	23	0.328571	NM_001129998	Q6UWF2|Q6ZRG0	Missense_Mutation	SNP	ENST00000338896.5	37	CCDS44830.1	742	0.33974358974358976	192	0.3902439024390244	139	0.3839779005524862	84	0.14685314685314685	327	0.4313984168865435	C	18.07	3.542762	0.65198	0.373808	0.384419	ENSG00000256660	ENST00000396502;ENST00000338896	T;T	0.02158	4.42;4.73	4.88	4.88	0.63580	.	0.000000	0.56097	D	0.000029	T	0.00012	0.0000	M	0.69823	2.125	0.25333	P	0.9890114	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	T	0.52510	-0.8566	9	0.66056	D	0.02	.	14.2691	0.66140	0.0:1.0:0.0:0.0	rs1359082;rs60399276	6;6;6	Q2HXU8;Q2HXU8-2;F5H4H7	CL12B_HUMAN;.;.	N	6	ENSP00000379759:T6N;ENSP00000344563:T6N	ENSP00000344563:T6N	T	+	2	0	CLEC12B	10054642	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	1.818000	0.39012	2.652000	0.90054	0.561000	0.74099	ACC	C|0.642;A|0.358	0.358	strong		0.403	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2408495	2408495	+	Silent	SNP	T	T	G	rs62120713	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2408495T>G	ENST00000332578.3	+	7	882	c.882T>G	c.(880-882)gcT>gcG	p.A294A		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	294	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)		TTGACGTGGCTGTGCTGGAGC	0.662													G|||	710	0.141773	0.1831	0.0663	5008	,	,		8601	0.2361		0.0427	False		,,,				2504	0.1442				p.A294A		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.T882G						PASS	.	G		753,3653	752.7+/-412.3	72,609,1522	100.0	86.0	90.0		882	-1.3	0.8	19	dbSNP_129	90	378,8222	801.2+/-407.4	3,372,3925	no	coding-synonymous	TMPRSS9	NM_182973.1		75,981,5447	GG,GT,TT		4.3953,17.0903,8.696		294/1060	2408495	1131,11875	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon7			CGTGGCTGTGCTG	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.882T>G	19.37:g.2408495T>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			T|0.901;G|0.099	0.099	strong		0.662	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
SYT8	90019	hgsc.bcm.edu	37	11	1857207	1857207	+	Missense_Mutation	SNP	G	G	A	rs139074200		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1857207G>A	ENST00000381968.3	+	4	520	c.392G>A	c.(391-393)aGc>aAc	p.S131N	SYT8_ENST00000341958.3_Missense_Mutation_p.S117N|SYT8_ENST00000535046.1_Missense_Mutation_p.S269N|SYT8_ENST00000483280.1_3'UTR|SYT8_ENST00000436964.2_Missense_Mutation_p.S117N	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	131	C2 1. {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)		GACTTTGGAAGCCAGGAGGTG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15882	0.0		0.001	False		,,,				2504	0.0				p.S131N		Atlas-SNP	.											.	SYT8	29	.	0			c.G392A						PASS	.						43.0	48.0	46.0					11																	1857207		2202	4299	6501	SO:0001583	missense	90019	exon4			TTGGAAGCCAGGA	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.392G>A	11.37:g.1857207G>A	ENSP00000371394:p.Ser131Asn	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	4.933	0.173312	0.09391	.	.	ENSG00000149043	ENST00000436964;ENST00000535046;ENST00000381968;ENST00000341958	T;T;T;T	0.19669	2.13;2.13;3.08;3.08	3.01	0.926	0.19430	C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.12008	0.0292	L	0.28740	0.885	0.09310	N	0.999999	B;B;B	0.19583	0.037;0.031;0.031	B;B;B	0.15052	0.012;0.009;0.009	T	0.32587	-0.9901	9	0.26408	T	0.33	.	3.0174	0.06064	0.1045:0.3185:0.4148:0.1622	.	117;131;117	C9JSK3;Q8NBV8;A6NCR4	.;SYT8_HUMAN;.	N	117;269;131;117	ENSP00000414626:S117N;ENSP00000443325:S269N;ENSP00000371394:S131N;ENSP00000343691:S117N	ENSP00000343691:S117N	S	+	2	0	SYT8	1813783	0.003000	0.15002	0.654000	0.29608	0.166000	0.22503	0.440000	0.21592	0.108000	0.17862	0.305000	0.20034	AGC	G|1.000;A|0.000	0.000	strong		0.652	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
PLEKHA7	144100	hgsc.bcm.edu	37	11	16837788	16837788	+	Silent	SNP	G	G	A	rs217750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:16837788G>A	ENST00000355661.3	-	12	1900	c.1890C>T	c.(1888-1890)cgC>cgT	p.R630R	PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000531066.1_Silent_p.R630R|PLEKHA7_ENST00000448080.2_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	75	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	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	
CHRD	8646	hgsc.bcm.edu	37	3	184106493	184106493	+	Silent	SNP	T	T	G	rs2293606	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184106493T>G	ENST00000204604.1	+	21	2919	c.2673T>G	c.(2671-2673)ccT>ccG	p.P891P	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_Silent_p.P433P|CHRD_ENST00000450923.1_Silent_p.P891P|CHRD_ENST00000348986.3_Silent_p.P851P	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	891	VWFC 4. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)	p.P891P(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CAGTGCCCCCTTTTGGAGAGA	0.632													T|||	559	0.111621	0.1641	0.134	5008	,	,		18024	0.1062		0.0596	False		,,,				2504	0.0838				p.P891P		Atlas-SNP	.											CHRD,NS,carcinoma,0,1	CHRD	149	1	1	Substitution - coding silent(1)	breast(1)	c.T2673G						PASS	.	T		659,3747	279.9+/-275.1	56,547,1600	77.0	79.0	78.0		2673	1.1	1.0	3	dbSNP_100	78	450,8150	135.6+/-192.8	12,426,3862	no	coding-synonymous	CHRD	NM_003741.2		68,973,5462	GG,GT,TT		5.2326,14.9569,8.5268		891/956	184106493	1109,11897	2203	4300	6503	SO:0001819	synonymous_variant	8646	exon21			GCCCCCTTTTGGA	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.2673T>G	3.37:g.184106493T>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	37	CCDS3266.1																																																																																			T|0.904;G|0.096	0.096	strong		0.632	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037580	33037580	+	Missense_Mutation	SNP	T	T	G	rs36013091|rs2308911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33037580T>G	ENST00000419277.1	-	3	313	c.184A>C	c.(184-186)Atg>Ctg	p.M62L	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.M62L|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						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	135	47	0.348148	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	
OR6Q1	219952	hgsc.bcm.edu	37	11	57798723	57798723	+	Missense_Mutation	SNP	A	A	G	rs921135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57798723A>G	ENST00000302622.3	+	1	322	c.299A>G	c.(298-300)gAt>gGt	p.D100G	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	100				D -> G (in Ref. 1; BAC05958, 3; AAI51148 and 4; AAK95094). {ECO:0000305}.		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)				TCTTATGCTGATTGCCTATCC	0.478													G|||	2044	0.408147	0.3238	0.2651	5008	,	,		22105	0.6825		0.2913	False		,,,				2504	0.4611				p.D100G		Atlas-SNP	.											.	OR6Q1	58	.	0			c.A299G						PASS	.	G	GLY/ASP	1482,2920	677.5+/-403.4	247,988,966	173.0	163.0	166.0		299	3.8	1.0	11	dbSNP_86	166	2565,6027	690.1+/-404.4	395,1775,2126	yes	missense	OR6Q1	NM_001005186.2	94	642,2763,3092	GG,GA,AA		29.8534,33.6665,31.1451	benign	100/318	57798723	4047,8947	2201	4296	6497	SO:0001583	missense	219952	exon1			ATGCTGATTGCCT	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.299A>G	11.37:g.57798723A>G	ENSP00000307734:p.Asp100Gly	Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	402	162	0.402985	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	37	CCDS31541.1	840	0.38461538461538464	154	0.3130081300813008	96	0.26519337016574585	376	0.6573426573426573	214	0.28232189973614774	G	0.593	-0.832308	0.02713	0.336665	0.298534	ENSG00000172381	ENST00000302622	T	0.01172	5.23	4.76	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39210	N	0.001437	T	0.00012	0.0000	N	0.00080	-2.225	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16630	-1.0396	9	0.02654	T	1	.	7.9273	0.29883	0.0878:0.2843:0.6279:0.0	rs921135;rs52804731;rs57644368;rs921135	100	Q8NGQ2	OR6Q1_HUMAN	G	100	ENSP00000307734:D100G	ENSP00000307734:D100G	D	+	2	0	OR6Q1	57555299	0.027000	0.19231	0.992000	0.48379	0.888000	0.51559	0.808000	0.27154	1.036000	0.39998	-0.136000	0.14681	GAT	A|0.655;G|0.345	0.345	strong		0.478	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
NPHP4	261734	hgsc.bcm.edu	37	1	5965381	5965381	+	Silent	SNP	C	C	T	rs12120967	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:5965381C>T	ENST00000378156.4	-	15	2191	c.1926G>A	c.(1924-1926)gaG>gaA	p.E642E	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	642					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)		GTAGCACCATCTCGTTGCTTT	0.448													C|||	421	0.0840655	0.0083	0.1095	5008	,	,		22481	0.0823		0.1561	False		,,,				2504	0.0961				p.E642E		Atlas-SNP	.											.	NPHP4	119	.	0			c.G1926A						PASS	.	C		118,3862		4,110,1876	163.0	164.0	164.0		1926	-4.3	0.0	1	dbSNP_120	164	1466,6838		142,1182,2828	no	coding-synonymous	NPHP4	NM_015102.3		146,1292,4704	TT,TC,CC		17.6541,2.9648,12.8948		642/1427	5965381	1584,10700	1990	4152	6142	SO:0001819	synonymous_variant	261734	exon15			CACCATCTCGTTG	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.1926G>A	1.37:g.5965381C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	171	69	0.403509	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			C|0.908;T|0.092	0.092	strong		0.448	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
TEKT1	83659	hgsc.bcm.edu	37	17	6733672	6733672	+	Silent	SNP	T	T	C	rs8078571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	266	2	0.0075188		WXS	Illumina HiSeq	Phase_I	275	270	0.981818	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	
IQCH	64799	hgsc.bcm.edu	37	15	67692566	67692566	+	Missense_Mutation	SNP	T	T	C	rs35933176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:67692566T>C	ENST00000335894.4	+	14	2086	c.2020T>C	c.(2020-2022)Tac>Cac	p.Y674H	IQCH_ENST00000546225.1_Missense_Mutation_p.Y331H|IQCH_ENST00000358767.3_Missense_Mutation_p.Y410H|IQCH_ENST00000360277.4_Missense_Mutation_p.Y335H	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	674										NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		TATTCCTTCCTACCTAAAGTG	0.428													T|||	5	0.000998403	0.0	0.0	5008	,	,		19892	0.0		0.005	False		,,,				2504	0.0				p.Y674H		Atlas-SNP	.											.	IQCH	81	.	0			c.T2020C						PASS	.	T	HIS/TYR	0,4402		0,0,2201	143.0	134.0	137.0		2020	2.5	1.0	15	dbSNP_126	137	41,8557	27.4+/-76.7	0,41,4258	yes	missense	IQCH	NM_001031715.2	83	0,41,6459	CC,CT,TT		0.4769,0.0,0.3154	benign	674/1028	67692566	41,12959	2201	4299	6500	SO:0001583	missense	64799	exon14			CCTTCCTACCTAA	AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.2020T>C	15.37:g.67692566T>C	ENSP00000336861:p.Tyr674His	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	224	107	0.477679	NM_001031715	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	T	2.755	-0.259212	0.05791	0.0	0.004769	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.38722	1.12;1.13;1.15;1.12	5.43	2.45	0.29901	.	0.106121	0.64402	N	0.000006	T	0.06325	0.0163	N	0.00197	-1.87	0.27379	N	0.955461	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33929	-0.9849	10	0.07644	T	0.81	-22.218	9.1639	0.37038	0.0:0.734:0.0:0.266	rs35933176	331;335;674	Q86VS3-2;Q86VS3-4;Q86VS3	.;.;IQCH_HUMAN	H	410;331;674;335	ENSP00000351617:Y410H;ENSP00000444118:Y331H;ENSP00000336861:Y674H;ENSP00000353419:Y335H	ENSP00000336861:Y674H	Y	+	1	0	IQCH	65479620	0.957000	0.32711	0.983000	0.44433	0.741000	0.42261	2.152000	0.42272	0.224000	0.20940	-0.250000	0.11733	TAC	T|0.997;C|0.003	0.003	strong		0.428	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784	
CCND2	894	hgsc.bcm.edu	37	12	4388084	4388084	+	Splice_Site	SNP	C	C	G	rs3217805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4388084C>G	ENST00000261254.3	+	3	839	c.570C>G	c.(568-570)acC>acG	p.T190T	RP11-264F23.3_ENST00000539135.1_RNA|CCND2_ENST00000541542.1_3'UTR	NM_001759.3	NP_001750.1	P30279	CCND2_HUMAN	cyclin D2	190					cell cycle (GO:0007049)|cell division (GO:0051301)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of protein phosphorylation (GO:0001934)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)			TGTGTGCCACCGGTAAGATGA	0.552			T	IGL@	"""NHL,CLL"""								C|||	1101	0.219848	0.1679	0.2781	5008	,	,		18185	0.0833		0.3787	False		,,,				2504	0.226				p.T190T		Atlas-SNP	.		Dom	yes		12	12p13	894	cyclin D2		L	.	CCND2	50	.	0			c.C570G						PASS	.	C		866,3540	336.8+/-304.5	78,710,1415	45.0	40.0	41.0		570	-7.5	0.9	12	dbSNP_106	41	3378,5222	493.2+/-373.5	662,2054,1584	yes	coding-synonymous-near-splice	CCND2	NM_001759.3		740,2764,2999	GG,GC,CC		39.2791,19.655,32.6311		190/290	4388084	4244,8762	2203	4300	6503	SO:0001630	splice_region_variant	894	exon3			TGCCACCGGTAAG	AF518005	CCDS8524.1	12p13	2008-08-04			ENSG00000118971	ENSG00000118971			1583	protein-coding gene	gene with protein product	"""G1/S-specific cyclin D2"""	123833				1386335	Standard	NM_001759		Approved		uc001qmo.3	P30279	OTTHUMG00000168123	ENST00000261254.3:c.571+1C>G	12.37:g.4388084C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_001759	A8K531|Q13955|Q5U035	Silent	SNP	ENST00000261254.3	37	CCDS8524.1	552	0.25274725274725274	87	0.17682926829268292	111	0.30662983425414364	60	0.1048951048951049	294	0.38786279683377306	C	2.376	-0.343256	0.05243	0.19655	0.392791	ENSG00000118971	ENST00000536537	.	.	.	4.59	-7.54	0.01332	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43734	-0.9373	3	.	.	.	.	2.6573	0.05016	0.1809:0.1992:0.0922:0.5277	rs3217805;rs17772740;rs17845276;rs17858108;rs59857812;rs3217805	.	.	.	G	106	.	.	R	+	1	0	CCND2	4258345	0.492000	0.26027	0.945000	0.38365	0.375000	0.29983	-0.106000	0.10890	-1.038000	0.03279	-0.258000	0.10820	CGC	C|0.717;G|0.283	0.283	strong		0.552	CCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398287.1	NM_001759	Silent
OR5L1	219437	hgsc.bcm.edu	37	11	55579801	55579801	+	Missense_Mutation	SNP	T	T	C	rs12790505	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	127	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	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	
ABCB5	340273	hgsc.bcm.edu	37	7	20687181	20687181	+	Silent	SNP	C	C	T	rs2893006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:20687181C>T	ENST00000404938.2	+	10	1657	c.1005C>T	c.(1003-1005)agC>agT	p.S335S	ABCB5_ENST00000258738.6_5'UTR|ABCB5_ENST00000406935.1_5'UTR|ABCB5_ENST00000443026.2_5'UTR|ABCB5_ENST00000477094.1_3'UTR	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	335	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						TAATCCATAGCAGTTATTGCA	0.353													T|||	1099	0.219449	0.3986	0.1671	5008	,	,		18648	0.0407		0.2068	False		,,,				2504	0.2117				p.S335S		Atlas-SNP	.											.	ABCB5	357	.	0			c.C1005T						PASS	.	T	,,,	1189,1945		241,707,619	79.0	69.0	72.0		1005,,,	3.0	1.0	7	dbSNP_101	72	1478,5682		169,1140,2271	no	coding-synonymous,utr-5,utr-5,utr-5	ABCB5	NM_001163941.1,NM_001163942.1,NM_001163993.1,NM_178559.5	,,,	410,1847,2890	TT,TC,CC		20.6425,37.9387,25.9083	,,,	335/1258,,,	20687181	2667,7627	1567	3580	5147	SO:0001819	synonymous_variant	340273	exon10			CCATAGCAGTTAT	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.1005C>T	7.37:g.20687181C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			C|0.796;T|0.204	0.204	strong		0.353	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
MFSD6	54842	hgsc.bcm.edu	37	2	191364828	191364828	+	Missense_Mutation	SNP	C	C	T	rs149142084	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:191364828C>T	ENST00000392328.1	+	8	2584	c.2260C>T	c.(2260-2262)Cca>Tca	p.P754S	MFSD6_ENST00000281416.7_Missense_Mutation_p.P754S|MFSD6_ENST00000535751.1_Missense_Mutation_p.P216S	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	754					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						TAGAAACCAGCCATCCCCTGA	0.577													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		17915	0.0		0.008	False		,,,				2504	0.0031				p.P754S		Atlas-SNP	.											.	MFSD6	58	.	0			c.C2260T						PASS	.	C	SER/PRO	10,4396	16.8+/-37.8	0,10,2193	84.0	76.0	78.0		2260	4.2	0.9	2	dbSNP_134	78	73,8527	41.7+/-99.0	0,73,4227	yes	missense	MFSD6	NM_017694.3	74	0,83,6420	TT,TC,CC		0.8488,0.227,0.6382	benign	754/792	191364828	83,12923	2203	4300	6503	SO:0001583	missense	54842	exon8			AACCAGCCATCCC		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.2260C>T	2.37:g.191364828C>T	ENSP00000376141:p.Pro754Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	14.81	2.646173	0.47258	0.00227	0.008488	ENSG00000151690	ENST00000392328;ENST00000281416;ENST00000542423;ENST00000535751	T;T	0.30182	1.54;1.54	5.13	4.25	0.50352	.	0.273596	0.28236	N	0.016095	T	0.12561	0.0305	N	0.19112	0.55	0.31821	N	0.626035	B	0.12630	0.006	B	0.10450	0.005	T	0.15636	-1.0430	10	0.12430	T	0.62	-2.9407	10.4215	0.44352	0.0:0.9103:0.0:0.0897	.	754	Q6ZSS7	MFSD6_HUMAN	S	754;754;194;216	ENSP00000376141:P754S;ENSP00000281416:P754S	ENSP00000281416:P754S	P	+	1	0	MFSD6	191073073	1.000000	0.71417	0.898000	0.35279	0.850000	0.48378	1.967000	0.40491	1.385000	0.46445	0.655000	0.94253	CCA	C|0.994;T|0.006	0.006	strong		0.577	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
KIAA1551	55196	hgsc.bcm.edu	37	12	32137512	32137512	+	Missense_Mutation	SNP	C	C	G	rs3759299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32137512C>G	ENST00000312561.4	+	4	4037	c.3623C>G	c.(3622-3624)tCt>tGt	p.S1208C	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1208			S -> C (in dbSNP:rs3759299). {ECO:0000269|PubMed:14702039}.														GAGCAGTGTTCTCCTTTGGAT	0.413													C|||	879	0.175519	0.0477	0.1758	5008	,	,		20662	0.247		0.2366	False		,,,				2504	0.2117				p.S1208C		Atlas-SNP	.											.	.	.	.	0			c.C3623G						PASS	.	C	CYS/SER	357,4049	184.3+/-211.7	11,335,1857	102.0	99.0	100.0		3623	0.9	0.0	12	dbSNP_107	100	2229,6371	378.6+/-339.0	279,1671,2350	yes	missense	C12orf35	NM_018169.3	112	290,2006,4207	GG,GC,CC		25.9186,8.1026,19.8831	probably-damaging	1208/1748	32137512	2586,10420	2203	4300	6503	SO:0001583	missense	55196	exon4			AGTGTTCTCCTTT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3623C>G	12.37:g.32137512C>G	ENSP00000310338:p.Ser1208Cys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	64	0.615385	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	410	0.18772893772893773	26	0.052845528455284556	62	0.1712707182320442	137	0.2395104895104895	185	0.24406332453825857	C	13.40	2.226572	0.39300	0.081026	0.259186	ENSG00000174718	ENST00000312561	T	0.14640	2.49	4.05	0.933	0.19471	.	0.922951	0.08974	N	0.866898	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.20261	0.043	B	0.18871	0.023	T	0.43653	-0.9378	8	.	.	.	.	2.6973	0.05138	0.1883:0.5217:0.183:0.107	rs3759299;rs17511269;rs61122766;rs3759299	1208	Q9HCM1	CL035_HUMAN	C	1208	ENSP00000310338:S1208C	.	S	+	2	0	C12orf35	32028779	0.005000	0.15991	0.000000	0.03702	0.035000	0.12851	0.687000	0.25407	-0.022000	0.13986	-0.274000	0.10170	TCT	C|0.797;G|0.203	0.203	strong		0.413	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518336	161518336	+	Missense_Mutation	SNP	C	C	T	rs77144485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161518336C>T	ENST00000436743.1	-	4	348	c.194G>A	c.(193-195)aGc>aAc	p.S65N	FCGR3A_ENST00000443193.1_Missense_Mutation_p.S100N|FCGR3A_ENST00000540048.1_Missense_Mutation_p.S65N|FCGR3A_ENST00000476031.1_5'UTR|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000367969.3_Missense_Mutation_p.S101N	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)	65	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)	TGAGATGAGGCTCTCATTGTG	0.552																																					p.S101N		Atlas-SNP	.											.	FCGR3A	38	.	0			c.G302A						PASS	.						305.0	295.0	298.0					1																	161518336		2203	4300	6503	SO:0001583	missense	2214	exon3			ATGAGGCTCTCAT	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.194G>A	1.37:g.161518336C>T	ENSP00000416607:p.Ser65Asn	Somatic	614	0	0		WXS	Illumina HiSeq	Phase_I	682	164	0.240469	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	7.953|7.953	0.745268|0.745268	0.15710|0.15710	.|.	.|.	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336	.|T;T;T;T;T;T	.|0.12569	.|2.67;2.67;2.67;2.67;2.67;2.67	4.43|4.43	-8.86|-8.86	0.00795|0.00795	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|1.272100	.|0.05381	.|N	.|0.537252	T|T	0.02418|0.02418	0.0074|0.0074	L|L	0.41824|0.41824	1.3|1.3	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.26935	.|0.079;0.164;0.002	.|B;B;B	.|0.22386	.|0.029;0.039;0.006	T|T	0.18366|0.18366	-1.0339|-1.0339	5|10	.|0.21014	.|T	.|0.42	.|.	8.902|8.902	0.35501|0.35501	0.0:0.1449:0.3836:0.4715|0.0:0.1449:0.3836:0.4715	.|.	.|65;100;65	.|P08637;E9PG94;Q9UPY7	.|FCG3A_HUMAN;.;.	T|N	82|101;100;65;65;65;64	.|ENSP00000356946:S101N;ENSP00000392047:S100N;ENSP00000416607:S65N;ENSP00000356944:S65N;ENSP00000444971:S65N;ENSP00000396567:S64N	.|ENSP00000356944:S65N	A|S	-|-	1|2	0|0	FCGR3A|FCGR3A	159784960|159784960	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	-4.286000|-4.286000	0.00259|0.00259	-2.388000|-2.388000	0.00588|0.00588	-0.423000|-0.423000	0.05987|0.05987	GCC|AGC	C|0.950;T|0.050	0.050	strong		0.552	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
CNR2	1269	hgsc.bcm.edu	37	1	24201357	24201357	+	Silent	SNP	A	A	G	rs4649124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201357A>G	ENST00000374472.4	-	2	912	c.751T>C	c.(751-753)Ttg>Ctg	p.L251L	CNR2_ENST00000536471.1_Silent_p.L251L	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	251					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	AGCACAGCCAACACTAGCCCT	0.597													G|||	3272	0.653355	0.7943	0.6383	5008	,	,		21118	0.502		0.5875	False		,,,				2504	0.6973				p.L251L		Atlas-SNP	.											.	CNR2	78	.	0			c.T751C						PASS	.	G		3310,1096	396.0+/-329.9	1261,788,154	93.0	74.0	80.0		751	1.7	1.0	1	dbSNP_111	80	4935,3665	526.0+/-380.9	1402,2131,767	no	coding-synonymous	CNR2	NM_001841.2		2663,2919,921	GG,GA,AA		42.6163,24.8752,36.6062		251/361	24201357	8245,4761	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			CAGCCAACACTAG	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.751T>C	1.37:g.24201357A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	39	0.382353	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			A|0.358;G|0.642	0.642	strong		0.597	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
MIA3	375056	hgsc.bcm.edu	37	1	222802803	222802803	+	Silent	SNP	T	T	G	rs3748626	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:222802803T>G	ENST00000344922.5	+	4	2266	c.2241T>G	c.(2239-2241)ccT>ccG	p.P747P	MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Silent_p.P747P	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	747					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.P747P(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)		AAAAAAACCCTGGGAATCAGG	0.413													T|||	2541	0.507388	0.2504	0.5072	5008	,	,		19931	0.5823		0.7296	False		,,,				2504	0.5491				p.P747P		Atlas-SNP	.											MIA3,NS,carcinoma,0,1	MIA3	167	1	1	Substitution - coding silent(1)	stomach(1)	c.T2241G						PASS	.	T		1156,2516		182,792,862	70.0	64.0	66.0		2241	-2.5	0.0	1	dbSNP_107	66	5769,2393		2060,1649,372	no	coding-synonymous	MIA3	NM_198551.2		2242,2441,1234	GG,GT,TT		29.3188,31.4815,41.4822		747/1908	222802803	6925,4909	1836	4081	5917	SO:0001819	synonymous_variant	375056	exon4			AAACCCTGGGAAT		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.2241T>G	1.37:g.222802803T>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	37	CCDS41470.1	1221	0.5590659340659341	131	0.266260162601626	202	0.5580110497237569	338	0.5909090909090909	550	0.7255936675461742	T	4.887	0.164882	0.09287	0.314815	0.706812	ENSG00000154305	ENST00000354906	.	.	.	4.37	-2.45	0.06481	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34153	-0.9840	3	.	.	.	.	4.1199	0.10101	0.237:0.2982:0.0:0.4648	rs3748626	.	.	.	G	330	.	.	W	+	1	0	MIA3	220869426	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.162000	0.10012	-0.571000	0.06014	0.260000	0.18958	TGG	T|0.387;G|0.613	0.613	strong		0.413	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
FMN2	56776	hgsc.bcm.edu	37	1	240371469	240371469	+	Silent	SNP	C	C	T	rs199920451		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371469C>T	ENST00000319653.9	+	5	3587	c.3357C>T	c.(3355-3357)ccC>ccT	p.P1119P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1119	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1262P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGCATACCCCCTCCTCCCC	0.716																																					p.P1119P		Atlas-SNP	.											FMN2,NS,carcinoma,0,1	FMN2	451	1	1	Substitution - coding silent(1)	prostate(1)	c.C3357T						scavenged	.						8.0	10.0	9.0					1																	240371469		2095	4131	6226	SO:0001819	synonymous_variant	56776	exon5			CATACCCCCTCCT	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.3357C>T	1.37:g.240371469C>T		Somatic	92	2	0.0217391		WXS	Illumina HiSeq	Phase_I	96	11	0.114583	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.999;T|0.001	0.001	weak		0.716	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79089007	79089007	+	Silent	SNP	T	T	C	rs3743057	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79089007T>C	ENST00000388820.4	-	4	954	c.744A>G	c.(742-744)gtA>gtG	p.V248V	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	248	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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						CATCAGCTACTACCAGGGTCT	0.617													C|||	3969	0.792532	0.7534	0.8948	5008	,	,		15840	0.8631		0.7565	False		,,,				2504	0.7372				p.V248V		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A744G						PASS	.	C		3219,1173	413.7+/-336.6	1195,829,172	173.0	141.0	152.0		744	4.6	1.0	15	dbSNP_107	152	6475,2111	366.0+/-334.1	2454,1567,272	no	coding-synonymous	ADAMTS7	NM_014272.3		3649,2396,444	CC,CT,TT		24.5865,26.7077,25.3044		248/1687	79089007	9694,3284	2196	4293	6489	SO:0001819	synonymous_variant	11173	exon4			AGCTACTACCAGG	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.744A>G	15.37:g.79089007T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			T|0.234;C|0.766	0.766	strong		0.617	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124634	26124634	+	Silent	SNP	C	C	T	rs4645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26124634C>T	ENST00000602637.1	+	1	204	c.174C>T	c.(172-174)taC>taT	p.Y58Y	HIST1H2AC_ENST00000377791.2_Silent_p.Y58Y|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2BC_ENST00000396984.1_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	58						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						TGTTAGAGTACCTGACCGCCG	0.667													C|||	402	0.0802716	0.0076	0.1066	5008	,	,		16130	0.0139		0.2127	False		,,,				2504	0.092				p.Y58Y		Atlas-SNP	.											HIST1H2AC,NS,carcinoma,+1,1	HIST1H2AC	29	1	0			c.C174T						scavenged	.	C		208,4198		8,192,2003	53.0	54.0	54.0		174	3.0	1.0	6	dbSNP_52	54	1863,6737		201,1461,2638	no	coding-synonymous	HIST1H2AC	NM_003512.3		209,1653,4641	TT,TC,CC		21.6628,4.7208,15.9234		58/131	26124634	2071,10935	2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			AGAGTACCTGACC	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.174C>T	6.37:g.26124634C>T		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	165	75	0.454545	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			C|0.857;T|0.143	0.143	strong		0.667	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
KRT76	51350	hgsc.bcm.edu	37	12	53164848	53164848	+	Silent	SNP	G	G	A	rs7313832	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53164848G>A	ENST00000332411.2	-	7	1472	c.1419C>T	c.(1417-1419)aaC>aaT	p.N473N		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	473	Coil 2.|Rod.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CCAGCTTGACGTTCATCAGCT	0.577													G|||	2089	0.417133	0.3555	0.3991	5008	,	,		16564	0.3919		0.5855	False		,,,				2504	0.3661				p.N473N		Atlas-SNP	.											KRT76,NS,adenoma,0,1	KRT76	72	1	0			c.C1419T						PASS	.	G		1630,2776	502.0+/-365.1	303,1024,876	130.0	118.0	122.0		1419	-7.3	0.1	12	dbSNP_116	122	4790,3810	613.1+/-396.0	1335,2120,845	no	coding-synonymous	KRT76	NM_015848.4		1638,3144,1721	AA,AG,GG		44.3023,36.995,49.3618		473/639	53164848	6420,6586	2203	4300	6503	SO:0001819	synonymous_variant	51350	exon7			CTTGACGTTCATC	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.1419C>T	12.37:g.53164848G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_015848	B4DRR3|Q7Z795	Silent	SNP	ENST00000332411.2	37	CCDS8838.1																																																																																			G|0.510;A|0.490	0.490	strong		0.577	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
KDELC1	79070	hgsc.bcm.edu	37	13	103449202	103449202	+	Missense_Mutation	SNP	T	T	C	rs1047740	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103449202T>C	ENST00000376004.4	-	2	676	c.340A>G	c.(340-342)Att>Gtt	p.I114V	BIVM_ENST00000448849.2_5'Flank|KDELC1_ENST00000460338.1_5'UTR|BIVM_ENST00000257336.1_5'Flank|BIVM_ENST00000419638.1_5'Flank	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	114			I -> V (in dbSNP:rs1047740). {ECO:0000269|PubMed:15489334}.			endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TGGAATTTAATTTCCACCTTC	0.328													C|||	2091	0.417532	0.7269	0.2752	5008	,	,		14031	0.4821		0.2316	False		,,,				2504	0.2249				p.I114V		Atlas-SNP	.											.	KDELC1	66	.	0			c.A340G						PASS	.	C	VAL/ILE	2875,1531	483.3+/-359.7	923,1029,251	130.0	124.0	126.0		340	4.8	1.0	13	dbSNP_86	126	1892,6708	727.2+/-406.6	198,1496,2606	yes	missense	KDELC1	NM_024089.2	29	1121,2525,2857	CC,CT,TT		22.0,34.7481,36.6523	benign	114/503	103449202	4767,8239	2203	4300	6503	SO:0001583	missense	79070	exon2			ATTTAATTTCCAC	BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.340A>G	13.37:g.103449202T>C	ENSP00000365172:p.Ile114Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_024089	Q53HL3|Q9BVD2	Missense_Mutation	SNP	ENST00000376004.4	37	CCDS9504.1	939	0.42994505494505497	356	0.7235772357723578	101	0.27900552486187846	303	0.5297202797202797	179	0.23614775725593667	C	3.165	-0.171246	0.06421	0.652519	0.22	ENSG00000134901	ENST00000376004	D	0.81739	-1.53	5.69	4.85	0.62838	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.123413	0.56097	N	0.000036	T	0.00012	0.0000	N	0.00707	-1.245	0.43489	P	0.004274	B	0.02656	0.0	B	0.04013	0.001	T	0.43845	-0.9366	9	0.02654	T	1	.	10.0883	0.42432	0.0:0.7953:0.0:0.2047	rs1047740;rs3187754;rs17856043;rs52798404;rs58208195;rs1047740	114	Q6UW63	KDEL1_HUMAN	V	114	ENSP00000365172:I114V	ENSP00000365172:I114V	I	-	1	0	KDELC1	102247203	0.996000	0.38824	0.997000	0.53966	0.971000	0.66376	0.957000	0.29215	0.884000	0.36064	-0.119000	0.15052	ATT	T|0.602;C|0.398	0.398	strong		0.328	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1		
HEPH	9843	hgsc.bcm.edu	37	X	65427040	65427040	+	Silent	SNP	T	T	C	rs61746100|rs806607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65427040T>C	ENST00000343002.2	+	13	2959	c.2295T>C	c.(2293-2295)taT>taC	p.Y765Y	HEPH_ENST00000519389.1_Silent_p.Y819Y|HEPH_ENST00000441993.2_Silent_p.Y768Y|HEPH_ENST00000336279.5_Silent_p.Y498Y|HEPH_ENST00000419594.1_Silent_p.Y576Y|HEPH_ENST00000374727.3_Silent_p.Y768Y			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	82	0	0		WXS	Illumina HiSeq	Phase_I	79	79	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	
TACC2	10579	hgsc.bcm.edu	37	10	123844503	123844503	+	Missense_Mutation	SNP	C	C	T	rs10887063	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123844503C>T	ENST00000369005.1	+	4	2828	c.2488C>T	c.(2488-2490)Ctc>Ttc	p.L830F	TACC2_ENST00000334433.3_Missense_Mutation_p.L830F|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.L830F|TACC2_ENST00000453444.2_Missense_Mutation_p.L830F|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.L830F	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	830			L -> F (in dbSNP:rs10887063). {ECO:0000269|PubMed:12620397}.		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGAGAAGCATCTCCAGCCATC	0.557													C|||	922	0.184105	0.2882	0.17	5008	,	,		19229	0.0982		0.1829	False		,,,				2504	0.1431				p.L830F		Atlas-SNP	.											.	TACC2	271	.	0			c.C2488T						PASS	.	C	,PHE/LEU	1381,3025	455.7+/-351.1	210,961,1032	125.0	126.0	126.0		,2488	4.6	0.0	10	dbSNP_120	126	1595,7005	295.9+/-302.6	142,1311,2847	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,22	352,2272,3879	TT,TC,CC		18.5465,31.3436,22.8817	,benign	,830/2949	123844503	2976,10030	2203	4300	6503	SO:0001583	missense	10579	exon4			AAGCATCTCCAGC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.2488C>T	10.37:g.123844503C>T	ENSP00000358001:p.Leu830Phe	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	417	0.19093406593406592	141	0.2865853658536585	73	0.20165745856353592	68	0.11888111888111888	135	0.17810026385224276	C	14.53	2.561552	0.45590	0.313436	0.185465	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.04970	3.62;3.52;3.56;3.62;3.52	5.66	4.57	0.56435	.	0.260219	0.20581	N	0.089522	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P;P;P	0.47106	0.89;0.89;0.89	B;B;B	0.38954	0.286;0.286;0.286	T	0.54866	-0.8229	9	0.46703	T	0.11	-5.2727	12.3263	0.55013	0.0:0.9063:0.0:0.0937	rs10887063;rs52822997;rs10887063	830;830;830	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	F	830;830;830;830;830;820	ENSP00000358001:L830F;ENSP00000424467:L830F;ENSP00000427618:L830F;ENSP00000334280:L830F;ENSP00000395048:L830F	ENSP00000334280:L830F	L	+	1	0	TACC2	123834493	0.001000	0.12720	0.008000	0.14137	0.034000	0.12701	0.982000	0.29539	2.660000	0.90430	0.549000	0.68633	CTC	C|0.791;T|0.209	0.209	strong		0.557	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
MUC4	4585	hgsc.bcm.edu	37	3	195513812	195513812	+	Missense_Mutation	SNP	T	T	A	rs201142885	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195513812T>A	ENST00000463781.3	-	2	5098	c.4639A>T	c.(4639-4641)Aca>Tca	p.T1547S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1547S	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.M1535_T1550delMPLPVTSPSSASTGDT(4)|p.T1547S(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)		GTGTCACCTGTGGATGCTGAG	0.582																																					p.T1547S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|kidney(1)	c.A4639T						scavenged	.																																			SO:0001583	missense	4585	exon2			CACCTGTGGATGC	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.4639A>T	3.37:g.195513812T>A	ENSP00000417498:p.Thr1547Ser	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	114	7	0.0614035	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	.	.	.	.	.	.	.	.	.	.	-	6.021	0.372220	0.11409	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.48;1.46	0.844	-0.658	0.11428	.	.	.	.	.	T	0.22437	0.0541	N	0.19112	0.55	0.09310	N	1	P	0.46578	0.88	P	0.50270	0.636	T	0.13764	-1.0497	8	.	.	.	.	3.6421	0.08170	0.0:0.3306:0.0:0.6694	.	1547	E7ESK3	.	S	1547	ENSP00000417498:T1547S;ENSP00000420243:T1547S	.	T	-	1	0	MUC4	196998207	0.034000	0.19679	0.062000	0.19696	0.063000	0.16089	-0.041000	0.12084	0.077000	0.16863	0.076000	0.15429	ACA	T|0.976;A|0.023	0.023	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC6A12	6539	hgsc.bcm.edu	37	12	311949	311949	+	Silent	SNP	A	A	G	rs216250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:311949A>G	ENST00000428720.1	-	5	1190	c.447T>C	c.(445-447)acT>acC	p.T149T	SLC6A12_ENST00000424061.2_Silent_p.T149T|SLC6A12_ENST00000538272.1_5'UTR|SLC6A12_ENST00000397296.2_Silent_p.T149T|SLC6A12_ENST00000536824.1_Silent_p.T149T|RP11-283I3.2_ENST00000539568.1_RNA|SLC6A12_ENST00000359674.4_Silent_p.T149T	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	149					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			GCAGCTCAGAAGTGAAGGAGC	0.517													G|||	3085	0.616014	0.767	0.5908	5008	,	,		20019	0.6339		0.4632	False		,,,				2504	0.5685				p.T149T		Atlas-SNP	.											.	SLC6A12	60	.	0			c.T447C						PASS	.	G	,,,	3065,1341	447.9+/-348.5	1074,917,212	117.0	103.0	108.0		447,447,447,447	5.5	1.0	12	dbSNP_79	108	3811,4789	613.3+/-396.1	866,2079,1355	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC6A12	NM_001122847.2,NM_001122848.2,NM_001206931.1,NM_003044.4	,,,	1940,2996,1567	GG,GA,AA		44.314,30.4358,47.1321	,,,	149/615,149/615,149/615,149/615	311949	6876,6130	2203	4300	6503	SO:0001819	synonymous_variant	6539	exon5			CTCAGAAGTGAAG	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.447T>C	12.37:g.311949A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001122848	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	37	CCDS8501.1																																																																																			A|0.437;G|0.563	0.563	strong		0.517	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
CENPF	1063	hgsc.bcm.edu	37	1	214814125	214814125	+	Missense_Mutation	SNP	G	G	A	rs3795522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214814125G>A	ENST00000366955.3	+	12	2612	c.2444G>A	c.(2443-2445)cGt>cAt	p.R815H		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0			R -> H (in dbSNP:rs3795522).		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)		AGTGAATGTCGTTTAGAAGCA	0.393													A|||	526	0.105032	0.1006	0.1052	5008	,	,		20312	0.126		0.0507	False		,,,				2504	0.1452				p.R815H	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.G2444A						PASS	.	A	HIS/ARG	391,4009	721.6+/-409.2	15,361,1824	51.0	52.0	52.0		2444	-1.3	0.0	1	dbSNP_107	52	463,8135	783.8+/-407.6	11,441,3847	yes	missense	CENPF	NM_016343.3	29	26,802,5671	AA,AG,GG		5.385,8.8864,6.5702	benign	815/3115	214814125	854,12144	2200	4299	6499	SO:0001583	missense	1063	exon12			AATGTCGTTTAGA	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.2444G>A	1.37:g.214814125G>A	ENSP00000355922:p.Arg815His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	229	0.10485347985347986	63	0.12804878048780488	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	A	3.663	-0.069028	0.07228	0.088864	0.05385	ENSG00000117724	ENST00000366955	T	0.03181	4.02	5.59	-1.33	0.09172	.	1.124660	0.06903	N	0.806298	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.15719	0.014	B	0.08055	0.003	T	0.49082	-0.8976	8	0.25751	T	0.34	.	3.7733	0.08650	0.2005:0.4913:0.1937:0.1145	rs3795522;rs3795522	815	P49454	CENPF_HUMAN	H	815	ENSP00000355922:R815H	ENSP00000355922:R815H	R	+	2	0	CENPF	212880748	0.000000	0.05858	0.000000	0.03702	0.352000	0.29268	-0.794000	0.04584	-0.544000	0.06232	-0.308000	0.09152	CGT	G|0.917;A|0.083	0.083	strong		0.393	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
OR51T1	401665	hgsc.bcm.edu	37	11	4903219	4903219	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4903219C>T	ENST00000322049.1	+	1	90	c.90C>T	c.(88-90)tcC>tcT	p.S30S	OR51T1_ENST00000380378.1_Silent_p.S57S|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTGGATCTCCATTCCAGTCT	0.448																																					p.S57S		Atlas-SNP	.											.	OR51T1	92	.	0			c.C171T						PASS	.						208.0	170.0	183.0					11																	4903219		2201	4298	6499	SO:0001819	synonymous_variant	401665	exon1			GATCTCCATTCCA	BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"""GPCR / Class A : Olfactory receptors"""	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.90C>T	11.37:g.4903219C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	139	63	0.453237	NM_001004759	Q6IFH9	Silent	SNP	ENST00000322049.1	37																																																																																				.	.	none		0.448	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759	
ZFYVE16	9765	hgsc.bcm.edu	37	5	79741086	79741086	+	Silent	SNP	A	A	G	rs150392926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79741086A>G	ENST00000338008.5	+	6	2766	c.2586A>G	c.(2584-2586)ctA>ctG	p.L862L	ZFYVE16_ENST00000510158.1_Silent_p.L862L|ZFYVE16_ENST00000505560.1_Silent_p.L862L	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	862					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		TTCTAGGACTATGTTCCAAAG	0.318													a|||	10	0.00199681	0.0	0.0014	5008	,	,		18816	0.0		0.002	False		,,,				2504	0.0072				p.L862L	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.A2586G						PASS	.	G	,	0,4406		0,0,2203	112.0	108.0	109.0		2586,2586	-4.7	0.0	5	dbSNP_134	109	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	ZFYVE16	NM_001105251.1,NM_014733.3	,	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	,	862/1540,862/1540	79741086	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9765	exon7			AGGACTATGTTCC	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"""Zinc fingers, FYVE domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20756	protein-coding gene	gene with protein product	"""endofin"", ""protein phosphatase 1, regulatory subunit 69"""	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.2586A>G	5.37:g.79741086A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Silent	SNP	ENST00000338008.5	37	CCDS4050.1																																																																																			A|0.999;G|0.001	0.001	strong		0.318	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733	
OR4A5	81318	hgsc.bcm.edu	37	11	51412327	51412327	+	Missense_Mutation	SNP	T	T	A	rs56302591	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:51412327T>A	ENST00000319760.6	-	1	121	c.69A>T	c.(67-69)aaA>aaT	p.K23N		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	23			K -> N (in dbSNP:rs56302591).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CAAATAATGCTTTTTGCACAC	0.423													.|||	381	0.0760783	0.0401	0.0591	5008	,	,		19387	0.0853		0.1223	False		,,,				2504	0.0798				p.K23N		Atlas-SNP	.											.	OR4A5	116	.	0			c.A69T						PASS	.	T	ASN/LYS	213,4187		6,201,1993	45.0	43.0	44.0		69	0.8	0.0	11	dbSNP_129	44	1026,7566		58,910,3328	no	missense	OR4A5	NM_001005272.3	94	64,1111,5321	AA,AT,TT		11.9413,4.8409,9.5366	benign	23/316	51412327	1239,11753	2200	4296	6496	SO:0001583	missense	81318	exon1			TAATGCTTTTTGC	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.69A>T	11.37:g.51412327T>A	ENSP00000367664:p.Lys23Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	169	0.07738095238095238	16	0.032520325203252036	28	0.07734806629834254	34	0.05944055944055944	91	0.12005277044854881	.	3.543	-0.093218	0.07053	0.048409	0.119413	ENSG00000221840	ENST00000319760	T	0.00433	7.43	2.01	0.836	0.18891	.	0.291535	0.24630	N	0.036893	T	0.00012	0.0000	L	0.49699	1.58	0.80722	P	0.0	B	0.10296	0.003	B	0.17979	0.02	T	0.41215	-0.9521	9	0.54805	T	0.06	.	4.2576	0.10724	0.0:0.3576:0.0:0.6424	rs56302591	23	Q8NH83	OR4A5_HUMAN	N	23	ENSP00000367664:K23N	ENSP00000367664:K23N	K	-	3	2	OR4A5	51268903	0.000000	0.05858	0.019000	0.16419	0.216000	0.24613	-3.197000	0.00562	0.225000	0.20959	0.136000	0.15936	AAA	T|0.908;A|0.092	0.092	strong		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37678884	37678884	+	Missense_Mutation	SNP	C	C	G	rs17773251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:37678884C>G	ENST00000379800.3	-	1	919	c.510G>C	c.(508-510)agG>agC	p.R170S		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> S (in dbSNP:rs17773251). {ECO:0000269|PubMed:17344846}.		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)			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)		GTATGTGTTGCCTGGTCCTGT	0.448													C|||	373	0.0744808	0.0673	0.1037	5008	,	,		20071	0.0486		0.0954	False		,,,				2504	0.0685				p.R170S		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.G510C						PASS	.	C	SER/ARG	319,4087	171.6+/-201.8	18,283,1902	227.0	209.0	215.0		510	0.1	1.0	13	dbSNP_123	215	742,7858	179.0+/-228.3	28,686,3586	yes	missense	CSNK1A1L	NM_145203.5	110	46,969,5488	GG,GC,CC		8.6279,7.2401,8.1578	benign	170/338	37678884	1061,11945	2203	4300	6503	SO:0001583	missense	122011	exon1			GTGTTGCCTGGTC	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.510G>C	13.37:g.37678884C>G	ENSP00000369126:p.Arg170Ser	Somatic	418	0	0		WXS	Illumina HiSeq	Phase_I	452	189	0.418142	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	188	0.08608058608058608	35	0.07113821138211382	50	0.13812154696132597	31	0.05419580419580419	72	0.09498680738786279	C	9.579	1.123004	0.20959	0.072401	0.086279	ENSG00000180138	ENST00000379800	T	0.06218	3.33	1.04	0.126	0.14722	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.100359	0.64402	D	0.000002	T	0.00073	0.0002	M	0.63208	1.945	0.26327	P	0.9775763	P	0.41188	0.741	B	0.39935	0.314	T	0.24977	-1.0145	9	0.87932	D	0	.	5.3471	0.16016	0.0:0.7767:0.0:0.2233	rs17773251;rs17773251	170	Q8N752	KC1AL_HUMAN	S	170	ENSP00000369126:R170S	ENSP00000369126:R170S	R	-	3	2	CSNK1A1L	36576884	0.740000	0.28207	0.970000	0.41538	0.831000	0.47069	-0.282000	0.08445	0.014000	0.14944	-0.265000	0.10407	AGG	C|0.919;G|0.081	0.081	strong		0.448	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203	
TACC2	10579	hgsc.bcm.edu	37	10	123846485	123846485	+	Silent	SNP	A	A	G	rs4751871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123846485A>G	ENST00000369005.1	+	4	4810	c.4470A>G	c.(4468-4470)caA>caG	p.Q1490Q	TACC2_ENST00000334433.3_Silent_p.Q1490Q|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.Q1490Q|TACC2_ENST00000453444.2_Silent_p.Q1490Q|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.Q1490Q	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1490					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)				TGGCTCTGCAAGATCCAGCTT	0.597													G|||	1026	0.204872	0.3071	0.1844	5008	,	,		19551	0.1012		0.2117	False		,,,				2504	0.181				p.Q1490Q		Atlas-SNP	.											.	TACC2	271	.	0			c.A4470G						PASS	.	G	,	1515,2891	667.9+/-401.9	257,1001,945	48.0	45.0	46.0		,4470	3.0	0.2	10	dbSNP_111	46	1931,6669	721.9+/-406.4	215,1501,2584	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	472,2502,3529	GG,GA,AA		22.4535,34.3849,26.4955	,	,1490/2949	123846485	3446,9560	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			TCTGCAAGATCCA	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.4470A>G	10.37:g.123846485A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			A|0.762;G|0.238	0.238	strong		0.597	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
PTPLAD1	51495	hgsc.bcm.edu	37	15	65856653	65856653	+	Silent	SNP	G	G	A	rs11539008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:65856653G>A	ENST00000261875.5	+	7	799	c.633G>A	c.(631-633)acG>acA	p.T211T	PTPLAD1_ENST00000442729.2_Silent_p.T156T|PTPLAD1_ENST00000568793.1_Silent_p.T186T|PTPLAD1_ENST00000566074.1_Silent_p.T94T|PTPLAD1_ENST00000569894.1_Silent_p.T94T|PTPLAD1_ENST00000565299.1_Silent_p.T249T|PTPLAD1_ENST00000562901.1_Silent_p.T94T|PTPLAD1_ENST00000566511.1_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	134	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_016395	A0PJA1|B4DRF4|Q280Z3|Q6PD63|Q8IUI5|Q8NC86|Q8NCB1|Q96T12|Q9NQA7	Silent	SNP	ENST00000261875.5	37	CCDS45282.1																																																																																			G|0.872;A|0.128	0.128	strong		0.443	PTPLAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419739.1	NM_016395	
SCAI	286205	hgsc.bcm.edu	37	9	127818276	127818276	+	Missense_Mutation	SNP	C	C	T	rs589292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:127818276C>T	ENST00000336505.6	-	3	167	c.109G>A	c.(109-111)Gct>Act	p.A37T	SCAI_ENST00000373549.4_Missense_Mutation_p.A60T	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	37	Necessary to inhibit MKL1-induced SRF transcriptional activity. {ECO:0000250}.		A -> T (in dbSNP:rs589292).		negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TCTTTAAGAGCAAATTCAGTC	0.323													C|||	1160	0.231629	0.1339	0.2133	5008	,	,		16982	0.3065		0.3101	False		,,,				2504	0.2188				p.A60T		Atlas-SNP	.											.	SCAI	84	.	0			c.G178A						PASS	.	C	THR/ALA,THR/ALA	561,3071		47,467,1302	67.0	60.0	62.0		109,178	3.4	1.0	9	dbSNP_83	62	2493,5657		402,1689,1984	yes	missense,missense	SCAI	NM_001144877.2,NM_173690.4	58,58	449,2156,3286	TT,TC,CC		30.589,15.446,25.9209	possibly-damaging,possibly-damaging	37/607,60/630	127818276	3054,8728	1816	4075	5891	SO:0001583	missense	286205	exon4			TAAGAGCAAATTC	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.109G>A	9.37:g.127818276C>T	ENSP00000336756:p.Ala37Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Missense_Mutation	SNP	ENST00000336505.6	37	CCDS48017.1	545	0.24954212454212454	70	0.14227642276422764	84	0.23204419889502761	176	0.3076923076923077	215	0.2836411609498681	C	15.91	2.971661	0.53614	0.15446	0.30589	ENSG00000173611	ENST00000336505;ENST00000373549	T;T	0.47177	0.86;0.85	5.33	3.38	0.38709	.	0.147846	0.31784	N	0.007061	T	0.00012	0.0000	N	0.08118	0	0.43351	P	0.004585999999999979	B;B	0.27732	0.067;0.187	B;B	0.27715	0.025;0.082	T	0.31558	-0.9939	9	0.09084	T	0.74	-7.1051	9.353	0.38149	0.0:0.7741:0.1451:0.0808	rs589292;rs52797510;rs58484754;rs589292	37;60	Q8N9R8;Q8N9R8-2	SCAI_HUMAN;.	T	37;60	ENSP00000336756:A37T;ENSP00000362650:A60T	ENSP00000336756:A37T	A	-	1	0	SCAI	126858097	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.092000	0.30927	1.219000	0.43474	0.655000	0.94253	GCT	C|0.748;T|0.252	0.252	strong		0.323	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
ZNF792	126375	hgsc.bcm.edu	37	19	35449409	35449409	+	Silent	SNP	G	G	A	rs2651081	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	75	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	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	
ACSM1	116285	hgsc.bcm.edu	37	16	20648702	20648702	+	Silent	SNP	G	G	A	rs151328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:20648702G>A	ENST00000307493.4	-	8	1255	c.1188C>T	c.(1186-1188)taC>taT	p.Y396Y	ACSM1_ENST00000520010.1_Silent_p.Y396Y|ACSM1_ENST00000219151.4_Silent_p.Y15Y	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	396					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CCTGGACGTCGTAGGGTGGAG	0.542													G|||	1737	0.346845	0.5416	0.1916	5008	,	,		20252	0.3512		0.1799	False		,,,				2504	0.3609				p.Y396Y		Atlas-SNP	.											.	ACSM1	118	.	0			c.C1188T						PASS	.	G		2177,2225	586.1+/-386.4	540,1097,564	126.0	117.0	120.0		1188	-9.1	0.0	16	dbSNP_79	120	1726,6874	315.1+/-312.1	176,1374,2750	no	coding-synonymous	ACSM1	NM_052956.2		716,2471,3314	AA,AG,GG		20.0698,49.4548,30.0185		396/578	20648702	3903,9099	2201	4300	6501	SO:0001819	synonymous_variant	116285	exon8			GACGTCGTAGGGT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1188C>T	16.37:g.20648702G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1	674	0.3086080586080586	255	0.5182926829268293	73	0.20165745856353592	196	0.34265734265734266	150	0.19788918205804748	G	0.019	-1.451414	0.01080	0.494548	0.200698	ENSG00000166743	ENST00000524149	.	.	.	5.07	-9.12	0.00707	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.01920	-1.1247	3	.	.	.	.	17.3287	0.87257	0.8454:0.0:0.1546:0.0	rs151328;rs1262366;rs16970472;rs61455665;rs151328	.	.	.	M	102	.	.	T	-	2	0	ACSM1	20556203	0.000000	0.05858	0.015000	0.15790	0.014000	0.08584	-2.456000	0.01002	-1.806000	0.01237	-0.192000	0.12808	ACG	G|0.685;A|0.315	0.315	strong		0.542	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	
WDHD1	11169	hgsc.bcm.edu	37	14	55448409	55448409	+	Missense_Mutation	SNP	G	G	C	rs61741224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:55448409G>C	ENST00000360586.3	-	16	1977	c.1912C>G	c.(1912-1914)Cct>Gct	p.P638A	WDHD1_ENST00000420358.2_Missense_Mutation_p.P515A|WDHD1_ENST00000359167.4_Missense_Mutation_p.P156A|WDHD1_ENST00000421192.1_Missense_Mutation_p.P515A	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	638					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						ACGTAACAAGGGGTACCTAAA	0.368													G|||	144	0.028754	0.0023	0.036	5008	,	,		15265	0.0		0.1113	False		,,,				2504	0.0041				p.P638A		Atlas-SNP	.											.	WDHD1	82	.	0			c.C1912G						PASS	.	G	ALA/PRO,ALA/PRO	81,4325	69.8+/-107.6	3,75,2125	84.0	73.0	77.0		1543,1912	5.7	1.0	14	dbSNP_129	77	837,7763	192.7+/-238.6	36,765,3499	yes	missense,missense	WDHD1	NM_001008396.2,NM_007086.3	27,27	39,840,5624	CC,CG,GG		9.7326,1.8384,7.0583	probably-damaging,probably-damaging	515/1007,638/1130	55448409	918,12088	2203	4300	6503	SO:0001583	missense	11169	exon16			AACAAGGGGTACC	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"""WD repeat domain containing"""	23170	protein-coding gene	gene with protein product	"""CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"""	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.1912C>G	14.37:g.55448409G>C	ENSP00000353793:p.Pro638Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	101	0.04624542124542125	0	0.0	15	0.04143646408839779	0	0.0	86	0.11345646437994723	G	24.5	4.538803	0.85917	0.018384	0.097326	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.73363	-0.34;0.28;-0.74	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.17109	0.0411	M	0.89287	3.02	0.09310	P	0.99999999845594	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	T	0.63093	-0.6714	9	0.35671	T	0.21	-3.4145	19.9281	0.97110	0.0:0.0:1.0:0.0	rs61741224	156;638	F8W7P7;O75717	.;WDHD1_HUMAN	A	638;156;515	ENSP00000353793:P638A;ENSP00000352085:P156A;ENSP00000391049:P515A	ENSP00000352085:P156A	P	-	1	0	WDHD1	54518159	1.000000	0.71417	0.993000	0.49108	0.815000	0.46073	7.687000	0.84139	2.708000	0.92522	0.585000	0.79938	CCT	G|0.928;C|0.072	0.072	strong		0.368	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086	
LRP1	4035	hgsc.bcm.edu	37	12	57594908	57594908	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57594908C>T	ENST00000243077.3	+	65	10783	c.10317C>T	c.(10315-10317)tgC>tgT	p.C3439C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3439	LDL-receptor class A 23. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGGACAACTGCGGAGATGGGG	0.602																																					p.C3439C		Atlas-SNP	.											LRP1,NS,carcinoma,+2,2	LRP1	428	2	0			c.C10317T						scavenged	.						214.0	183.0	194.0					12																	57594908		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon65			CAACTGCGGAGAT	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.10317C>T	12.37:g.57594908C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	189	2	0.010582	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			.	.	none		0.602	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
MUC5B	727897	hgsc.bcm.edu	37	11	1263523	1263523	+	Missense_Mutation	SNP	G	G	A	rs1541314	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1263523G>A	ENST00000529681.1	+	31	5471	c.5413G>A	c.(5413-5415)Ggc>Agc	p.G1805S	MUC5B_ENST00000447027.1_Missense_Mutation_p.G1808S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1805	7 X Cys-rich subdomain repeats.|Thr-rich.		G -> S (in dbSNP:rs1541314). {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)		AGGGGTTGCAGGCGGGGACAT	0.582													g|||	328	0.0654952	0.0234	0.1095	5008	,	,		18135	0.0496		0.0815	False		,,,				2504	0.091				p.G1805S		Atlas-SNP	.											.	MUC5B	473	.	0			c.G5413A						PASS	.		SER/GLY	68,3940		0,68,1936	58.0	68.0	65.0		5413	1.1	0.0	11	dbSNP_88	65	596,7732		22,552,3590	yes	missense	MUC5B	NM_002458.2	56	22,620,5526	AA,AG,GG		7.1566,1.6966,5.3826	possibly-damaging	1805/5763	1263523	664,11672	2004	4164	6168	SO:0001583	missense	727897	exon31			GTTGCAGGCGGGG	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.5413G>A	11.37:g.1263523G>A	ENSP00000436812:p.Gly1805Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	154	67	0.435065	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	156	0.07142857142857142	12	0.024390243902439025	38	0.10497237569060773	43	0.07517482517482517	63	0.08311345646437995	g	13.68	2.308444	0.40895	0.016966	0.071566	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17370	2.28;2.28	4.32	1.15	0.20763	.	.	.	.	.	T	0.00637	0.0021	M	0.62154	1.92	0.80722	P	0.0	P;P	0.47034	0.817;0.889	B;P	0.50896	0.426;0.653	T	0.07385	-1.0775	8	0.87932	D	0	.	7.167	0.25695	0.1554:0.3933:0.4513:0.0	rs1541314;rs52836874;rs57142305;rs1541314	2498;1808	A7Y9J9;E9PBJ0	.;.	S	1805;1808;1806;1875	ENSP00000436812:G1805S;ENSP00000415793:G1808S	ENSP00000343037:G1806S	G	+	1	0	MUC5B	1220099	0.003000	0.15002	0.000000	0.03702	0.452000	0.32318	0.480000	0.22244	-0.043000	0.13513	0.306000	0.20318	GGC	G|0.928;A|0.072	0.072	strong		0.582	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MUC16	94025	hgsc.bcm.edu	37	19	9056941	9056941	+	Missense_Mutation	SNP	A	A	G	rs10410136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9056941A>G	ENST00000397910.4	-	3	30708	c.30505T>C	c.(30505-30507)Ttt>Ctt	p.F10169L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10171	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTTCCTAAATCCAGAAGTC	0.453													A|||	970	0.19369	0.1762	0.2666	5008	,	,		22681	0.0258		0.2823	False		,,,				2504	0.2474				p.F10169L		Atlas-SNP	.											.	MUC16	4315	.	0			c.T30505C						PASS	.	A	LEU/PHE	711,3201		59,593,1304	112.0	109.0	110.0		30505	-0.5	0.0	19	dbSNP_119	110	2507,5789		400,1707,2041	yes	missense	MUC16	NM_024690.2	22	459,2300,3345	GG,GA,AA		30.2194,18.1748,26.3598	benign	10169/14508	9056941	3218,8990	1956	4148	6104	SO:0001583	missense	94025	exon3			TCCTAAATCCAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30505T>C	19.37:g.9056941A>G	ENSP00000381008:p.Phe10169Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	61	0.580952	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	413	0.1891025641025641	91	0.18495934959349594	93	0.2569060773480663	11	0.019230769230769232	218	0.287598944591029	a	8.852	0.944925	0.18356	0.181748	0.302194	ENSG00000181143	ENST00000397910	T	0.02446	4.29	3.07	-0.497	0.12023	.	.	.	.	.	T	0.00012	0.0000	N	0.01168	-0.975	.	.	.	B	0.12630	0.006	B	0.06405	0.002	T	0.44877	-0.9299	8	0.87932	D	0	.	5.5872	0.17281	0.6046:0.0:0.3954:0.0	rs10410136;rs56575663;rs60219599;rs10410136	10169	B5ME49	.	L	10169	ENSP00000381008:F10169L	ENSP00000381008:F10169L	F	-	1	0	MUC16	8917941	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.150000	0.16263	-0.091000	0.12440	0.383000	0.25322	TTT	A|0.797;G|0.203	0.203	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ALG1	56052	hgsc.bcm.edu	37	16	5129756	5129756	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:5129756A>G	ENST00000262374.5	+	9	940	c.909A>G	c.(907-909)gaA>gaG	p.E303E	ALG1_ENST00000588623.1_Silent_p.E192E|ALG1_ENST00000544428.1_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	251	2	0.00796813		WXS	Illumina HiSeq	Phase_I	334	18	0.0538922	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	
SP2	6668	hgsc.bcm.edu	37	17	45994044	45994044	+	Silent	SNP	C	C	T	rs2228253	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45994044C>T	ENST00000376741.4	+	3	744	c.607C>T	c.(607-609)Ctg>Ttg	p.L203L	AC003665.1_ENST00000411573.2_RNA|AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000433001.1_RNA|AC003665.1_ENST00000451140.2_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	203					cardiovascular system development (GO:0072358)|embryonic organ development (GO:0048568)|fibroblast proliferation (GO:0048144)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						TGTGGTGAAGCTGACAGGTGG	0.627													T|||	2844	0.567891	0.615	0.4813	5008	,	,		17333	0.7748		0.4622	False		,,,				2504	0.4611				p.L203L		Atlas-SNP	.											.	SP2	38	.	0			c.C607T						PASS	.	T		2579,1827	534.7+/-374.0	741,1097,365	84.0	72.0	76.0		607	4.4	1.0	17	dbSNP_98	76	3754,4846	617.1+/-396.6	825,2104,1371	no	coding-synonymous	SP2	NM_003110.5		1566,3201,1736	TT,TC,CC		43.6512,41.4662,48.6929		203/614	45994044	6333,6673	2203	4300	6503	SO:0001819	synonymous_variant	6668	exon3			GTGAAGCTGACAG		CCDS11521.2	17q21.3-q22	2013-01-08			ENSG00000167182	ENSG00000167182		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11207	protein-coding gene	gene with protein product		601801				1341900, 9730617	Standard	NM_003110		Approved	KIAA0048	uc002imk.3	Q02086	OTTHUMG00000150196	ENST00000376741.4:c.607C>T	17.37:g.45994044C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_003110	A6NK74	Silent	SNP	ENST00000376741.4	37	CCDS11521.2																																																																																			C|0.479;T|0.521	0.521	strong		0.627	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
TIAM2	26230	hgsc.bcm.edu	37	6	155485554	155485554	+	Silent	SNP	G	G	A	rs1032141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:155485554G>A	ENST00000461783.3	+	10	3307	c.2034G>A	c.(2032-2034)caG>caA	p.Q678Q	TIAM2_ENST00000456877.2_5'UTR|TIAM2_ENST00000318981.5_Silent_p.Q678Q|TIAM2_ENST00000456144.1_Silent_p.Q678Q|TIAM2_ENST00000367174.2_Silent_p.Q30Q|TIAM2_ENST00000529824.2_Silent_p.Q678Q|TIAM2_ENST00000360366.4_Silent_p.Q678Q|TIAM2_ENST00000528391.2_5'UTR			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	678					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TTAAGATCCAGCAATGGGAGC	0.388													G|||	2860	0.571086	0.3608	0.7464	5008	,	,		17640	0.5605		0.6093	False		,,,				2504	0.7025				p.Q678Q		Atlas-SNP	.											.	TIAM2	161	.	0			c.G2034A						PASS	.	G		1926,2480	534.2+/-373.9	413,1100,690	50.0	55.0	53.0		2034	5.3	1.0	6	dbSNP_86	53	5351,3249	641.9+/-399.7	1657,2037,606	no	coding-synonymous	TIAM2	NM_012454.3		2070,3137,1296	AA,AG,GG		37.7791,43.7131,44.0489		678/1702	155485554	7277,5729	2203	4300	6503	SO:0001819	synonymous_variant	26230	exon7			GATCCAGCAATGG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2034G>A	6.37:g.155485554G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			G|0.435;A|0.565	0.565	strong		0.388	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
TCHH	7062	hgsc.bcm.edu	37	1	152079989	152079989	+	Missense_Mutation	SNP	T	T	G	rs1131471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152079989T>G	ENST00000368804.1	-	2	5703	c.5704A>C	c.(5704-5706)Aaa>Caa	p.K1902Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1902			K -> Q (in dbSNP:rs1131471). {ECO:0000269|PubMed:7685034}.		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)			TCTTGGGATTTTATCTCCCCG	0.582													g|||	2895	0.578075	0.5136	0.6484	5008	,	,		18437	0.5992		0.4016	False		,,,				2504	0.7751				p.K1902Q		Atlas-SNP	.											.	TCHH	275	.	0			c.A5704C						PASS	.		GLN/LYS	1823,2107		423,977,565	147.0	147.0	147.0		5704	1.3	0.0	1	dbSNP_86	147	3641,4641		801,2039,1301	yes	missense	TCHH	NM_007113.2	53	1224,3016,1866	GG,GT,TT		43.9628,46.3868,44.7429	possibly-damaging	1902/1944	152079989	5464,6748	1965	4141	6106	SO:0001583	missense	7062	exon3			GGGATTTTATCTC	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.5704A>C	1.37:g.152079989T>G	ENSP00000357794:p.Lys1902Gln	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	222	103	0.463964	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	1115	0.5105311355311355	256	0.5203252032520326	209	0.5773480662983426	332	0.5804195804195804	318	0.41952506596306066	g	0.050	-1.252895	0.01457	0.463868	0.439628	ENSG00000159450	ENST00000368804	T	0.05513	3.43	3.5	1.34	0.21922	.	.	.	.	.	T	0.00845	0.0028	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48927	-0.8991	8	0.20046	T	0.44	.	5.4353	0.16478	0.0:0.2059:0.391:0.4031	rs1131471;rs3191410;rs17647244;rs52826085;rs58290484;rs1131471	1902	Q07283	TRHY_HUMAN	Q	1902	ENSP00000357794:K1902Q	ENSP00000357794:K1902Q	K	-	1	0	TCHH	150346613	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.102000	0.03332	-0.365000	0.08076	-0.675000	0.03792	AAA	T|0.479;G|0.521	0.521	strong		0.582	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
SNED1	25992	hgsc.bcm.edu	37	2	242002263	242002263	+	Silent	SNP	C	C	T	rs3732228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242002263C>T	ENST00000310397.8	+	17	2313	c.2313C>T	c.(2311-2313)cgC>cgT	p.R771R	SNED1_ENST00000401884.1_Silent_p.R771R|SNED1_ENST00000342631.6_Silent_p.R771R|SNED1_ENST00000405547.3_Silent_p.R771R|AC005237.4_ENST00000458377.1_RNA	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	771	EGF-like 11; calcium-binding. {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)		GTCAGGACCGCGTTGCTGGGT	0.612													C|||	244	0.048722	0.0015	0.0202	5008	,	,		17995	0.1171		0.0417	False		,,,				2504	0.0695				p.R771R		Atlas-SNP	.											.	SNED1	76	.	0			c.C2313T						PASS	.	C		23,4035		1,21,2007	44.0	43.0	44.0		2313	-9.2	0.0	2	dbSNP_107	44	230,8136		3,224,3956	no	coding-synonymous	SNED1	NM_001080437.1		4,245,5963	TT,TC,CC		2.7492,0.5668,2.0364		771/1414	242002263	253,12171	2029	4183	6212	SO:0001819	synonymous_variant	25992	exon17			GGACCGCGTTGCT	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.2313C>T	2.37:g.242002263C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			C|0.950;T|0.050	0.050	strong		0.612	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
TIMP4	7079	hgsc.bcm.edu	37	3	12198336	12198336	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12198336C>G	ENST00000287814.4	-	3	846	c.336G>C	c.(334-336)aaG>aaC	p.K112N	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	112	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						AGAGATACTGCTTCTGGCTGT	0.433																																					p.K112N	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.G336C						PASS	.						122.0	111.0	115.0					3																	12198336		2203	4300	6503	SO:0001583	missense	7079	exon3			ATACTGCTTCTGG	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"""tissue inhibitor of metalloproteinase 4"""			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.336G>C	3.37:g.12198336C>G	ENSP00000287814:p.Lys112Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_003256	B2R7K6	Missense_Mutation	SNP	ENST00000287814.4	37	CCDS2608.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.819542	0.32145	.	.	ENSG00000157150	ENST00000287814	D	0.94184	-3.37	4.85	1.79	0.24919	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	0.246504	0.42172	D	0.000755	D	0.92391	0.7585	M	0.74467	2.265	0.43156	D	0.994932	P	0.43857	0.819	P	0.47402	0.546	D	0.89472	0.3744	10	0.56958	D	0.05	.	5.3067	0.15807	0.1289:0.5526:0.0:0.3185	.	112	Q99727	TIMP4_HUMAN	N	112	ENSP00000287814:K112N	ENSP00000287814:K112N	K	-	3	2	TIMP4	12173336	0.131000	0.22433	1.000000	0.80357	0.952000	0.60782	-0.631000	0.05496	0.541000	0.28827	-0.150000	0.13652	AAG	.	.	none		0.433	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629905	32629905	+	Missense_Mutation	SNP	T	T	C	rs2647032|rs386699586	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32629905T>C	ENST00000399082.3	-	2	274	c.230A>G	c.(229-231)gAt>gGt	p.D77G	XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.D167G|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.D167G|HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.D167G|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.D167G|HLA-DQB1_ENST00000460185.1_5'Flank			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	167	Beta-1.		E -> G (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:05, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:10, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:14, allele DQB1*03:15, allele DQB1*03:17, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*04:03, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05, allele DQB1*06:01, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:23, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; dbSNP:rs1049083). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CTCCTCCTGATCATTCCGAAA	0.557									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				T|||	507	0.101238	0.1528	0.098	5008	,	,		14276	0.0327		0.0984	False		,,,				2504	0.1074				p.D167G	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.A500G						PASS	.						39.0	40.0	40.0					6																	32629905		2173	4289	6462	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCCTGATCATTCC		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.230A>G	6.37:g.32629905T>C	ENSP00000382032:p.Asp77Gly	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	91	91	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		138	0.06318681318681318	40	0.08130081300813008	29	0.08011049723756906	18	0.03146853146853147	51	0.06728232189973615	.	3.251	-0.153354	0.06585	.	.	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.00529	6.78;6.78;6.78;6.78;6.78	4.52	-2.08	0.07254	.	0.506215	0.20122	N	0.098796	T	0.00039	0.0001	N	0.00042	-2.48	0.43965	P	0.0033570000000000544	B;B;B;B	0.11235	0.001;0.0;0.004;0.0	B;B;B;B	0.16722	0.016;0.009;0.015;0.009	T	0.03503	-1.1030	9	0.02654	T	1	.	11.2989	0.49294	0.0:0.7422:0.0:0.2578	rs2647032;rs3177750;rs9273983;rs28371191	167;132;167;167	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	G	77;167;167;167;167;103	ENSP00000382032:D77G;ENSP00000382029:D167G;ENSP00000364080:D167G;ENSP00000407332:D167G;ENSP00000382034:D167G	ENSP00000364080:D167G	D	-	2	0	HLA-DQB1	32737883	0.085000	0.21516	0.939000	0.37840	0.022000	0.10575	0.247000	0.18179	-0.317000	0.08677	0.260000	0.18958	GAT	T|0.925;C|0.075	0.075	strong		0.557	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
COL18A1	80781	hgsc.bcm.edu	37	21	46910210	46910210	+	Missense_Mutation	SNP	G	G	A	rs62000962	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46910210G>A	ENST00000359759.4	+	19	3247	c.3226G>A	c.(3226-3228)Gtc>Atc	p.V1076I	COL18A1_ENST00000400337.2_Missense_Mutation_p.V661I|COL18A1_ENST00000355480.5_Missense_Mutation_p.V841I			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1076	Triple-helical region 4 (COL4).		V -> I (in dbSNP:rs62000962). {ECO:0000269|PubMed:11606364, ECO:0000269|PubMed:14614989, ECO:0000269|PubMed:14695535, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9503365}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		AGCAGATGGAGTCCCCGGGTT	0.677													G|||	579	0.115615	0.1483	0.0821	5008	,	,		9232	0.0129		0.1322	False		,,,				2504	0.184				p.V841I		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2521A						PASS	.	G	ILE/VAL,ILE/VAL	564,3226		42,480,1373	17.0	21.0	20.0		2521,1981	-2.5	0.0	21	dbSNP_129	20	918,7298		47,824,3237	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	29,29	89,1304,4610	AA,AG,GG		11.1733,14.8813,12.3438	possibly-damaging,possibly-damaging	841/1520,661/1340	46910210	1482,10524	1895	4108	6003	SO:0001583	missense	80781	exon19			GATGGAGTCCCCG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3226G>A	21.37:g.46910210G>A	ENSP00000352798:p.Val1076Ile	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		220	0.10073260073260074	80	0.16260162601626016	32	0.08839779005524862	5	0.008741258741258742	103	0.1358839050131926	G	2.001	-0.429456	0.04701	0.148813	0.111733	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	D;D;D;D	0.93426	-3.2;-3.2;-3.2;-3.22	3.37	-2.52	0.06346	.	1.629170	0.03721	U	0.251925	T	0.01320	0.0043	N	0.03177	-0.4	0.80722	P	0.0	B;B;B	0.20780	0.048;0.016;0.016	B;B;B	0.19391	0.025;0.01;0.01	T	0.52366	-0.8585	9	0.16420	T	0.52	.	9.8421	0.41004	0.0934:0.5729:0.3337:0.0	rs62000962	1076;841;661	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	I	661;661;841;1076;1076;8	ENSP00000383191:V661I;ENSP00000347665:V841I;ENSP00000352798:V1076I;ENSP00000339118:V8I	ENSP00000339118:V8I	V	+	1	0	COL18A1	45734638	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.168000	0.09925	-0.562000	0.06086	0.460000	0.39030	GTC	G|0.896;A|0.104	0.104	strong		0.677	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
DNAJB8	165721	hgsc.bcm.edu	37	3	128182074	128182074	+	Silent	SNP	G	G	A	rs2981026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	170	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	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	
POTEM	641455	hgsc.bcm.edu	37	14	20020143	20020143	+	Silent	SNP	C	C	T	rs200891854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20020143C>T	ENST00000551509.1	-	1	129	c.78G>A	c.(76-78)aaG>aaA	p.K26K		NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	26										endometrium(4)|kidney(1)|lung(4)	9						GGCGGCACCACTTGCCCATCT	0.577																																					p.K26K		Atlas-SNP	.											POTEM_ENST00000551509,NS,carcinoma,0,2	POTEM	51	2	0			c.G78A						scavenged	.																																			SO:0001819	synonymous_variant	641455	exon1			GCACCACTTGCCC		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37096	protein-coding gene	gene with protein product	"""prostate-specific P704P"""					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.78G>A	14.37:g.20020143C>T		Somatic	459	1	0.00217865		WXS	Illumina HiSeq	Phase_I	492	209	0.424797	NM_001145442		Silent	SNP	ENST00000551509.1	37	CCDS45076.1																																																																																			C|0.986;T|0.014	0.014	strong		0.577	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442	
FAM83F	113828	hgsc.bcm.edu	37	22	40417780	40417780	+	Silent	SNP	C	C	T	rs5995793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	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	
FAM160A1	729830	hgsc.bcm.edu	37	4	152498625	152498625	+	Silent	SNP	C	C	T	rs17275536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:152498625C>T	ENST00000505231.1	+	3	288	c.129C>T	c.(127-129)caC>caT	p.H43H	FAM160A1_ENST00000435205.1_Silent_p.H43H|RN7SKP35_ENST00000517210.1_RNA			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	43										endometrium(2)|kidney(1)	3						TGGAGAAGCACGACCCCTTGA	0.418													T|||	1433	0.286142	0.2935	0.3184	5008	,	,		21202	0.1935		0.341	False		,,,				2504	0.2924				p.H43H		Atlas-SNP	.											.	FAM160A1	60	.	0			c.C129T						PASS	.	T		443,941		65,313,314	73.0	63.0	66.0		129	-7.7	0.5	4	dbSNP_123	66	1061,2121		159,743,689	no	coding-synonymous	FAM160A1	NM_001109977.1		224,1056,1003	TT,TC,CC		33.3438,32.0087,32.9391		43/1041	152498625	1504,3062	692	1591	2283	SO:0001819	synonymous_variant	729830	exon5			GAAGCACGACCCC		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.129C>T	4.37:g.152498625C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	NM_001109977	Q6ZUS2	Silent	SNP	ENST00000505231.1	37	CCDS47146.1																																																																																			C|0.718;T|0.282	0.282	strong		0.418	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
LRP1B	53353	hgsc.bcm.edu	37	2	141274576	141274576	+	Silent	SNP	T	T	C	rs4954672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:141274576T>C	ENST00000389484.3	-	50	9002	c.8031A>G	c.(8029-8031)caA>caG	p.Q2677Q		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2677					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)		TGTGTTTGTTTTGAACTGTGA	0.308										TSP Lung(27;0.18)			T|||	3217	0.642372	0.6921	0.7363	5008	,	,		15895	0.4167		0.7475	False		,,,				2504	0.6329				p.Q2677Q	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A8031G						PASS	.	T		3063,1341	689.0+/-405.1	1073,917,212	101.0	96.0	97.0		8031	5.2	1.0	2	dbSNP_111	97	6647,1953	722.4+/-406.4	2598,1451,251	no	coding-synonymous	LRP1B	NM_018557.2		3671,2368,463	CC,CT,TT		22.7093,30.4496,25.3307		2677/4600	141274576	9710,3294	2202	4300	6502	SO:0001819	synonymous_variant	53353	exon50			TTTGTTTTGAACT	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.8031A>G	2.37:g.141274576T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			T|0.290;C|0.710	0.710	strong		0.308	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
PRX	57716	hgsc.bcm.edu	37	19	40901614	40901614	+	Missense_Mutation	SNP	A	A	G	rs268671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40901614A>G	ENST00000324001.7	-	7	2915	c.2645T>C	c.(2644-2646)gTg>gCg	p.V882A	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	882			V -> A (in dbSNP:rs268671). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:11133365}.		axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGGGCCCTCCACCCGCTCTCC	0.627													G|||	2664	0.531949	0.8427	0.4784	5008	,	,		17084	0.2401		0.506	False		,,,				2504	0.4775				p.V882A		Atlas-SNP	.											.	PRX	151	.	0			c.T2645C						PASS	.	G	,ALA/VAL	3477,929	343.1+/-307.5	1384,709,110	38.0	46.0	43.0		,2645	2.7	0.0	19	dbSNP_79	43	4453,4147	555.8+/-386.7	1152,2149,999	yes	utr-3,missense	PRX	NM_020956.2,NM_181882.2	,64	2536,2858,1109	GG,GA,AA		48.2209,21.0849,39.0281	,benign	,882/1462	40901614	7930,5076	2203	4300	6503	SO:0001583	missense	57716	exon7			CCCTCCACCCGCT	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.2645T>C	19.37:g.40901614A>G	ENSP00000326018:p.Val882Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	75	28	0.373333	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	1082	0.49542124542124544	391	0.7947154471544715	193	0.5331491712707183	123	0.21503496503496503	375	0.4947229551451187	G	0.016	-1.538715	0.00942	0.789151	0.517791	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.01113	5.32	4.88	2.7	0.31948	.	0.563419	0.14794	N	0.298050	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.01360	-1.1375	9	0.17832	T	0.49	0.0625	7.2297	0.26036	0.1619:0.1377:0.7004:0.0	rs268671;rs3745204;rs52793723;rs60720056;rs268671	882	Q9BXM0	PRAX_HUMAN	A	882	ENSP00000326018:V882A	ENSP00000326018:V882A	V	-	2	0	PRX	45593454	0.346000	0.24844	0.033000	0.17914	0.004000	0.04260	2.680000	0.46918	0.119000	0.18210	-0.900000	0.02857	GTG	A|0.446;G|0.554	0.554	strong		0.627	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
ANKRD13A	88455	hgsc.bcm.edu	37	12	110456175	110456175	+	Silent	SNP	A	A	G	rs2302689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:110456175A>G	ENST00000261739.4	+	5	592	c.426A>G	c.(424-426)ccA>ccG	p.P142P	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	142						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						GAATATGCCCAAATGATGTCT	0.463													G|||	1560	0.311502	0.6717	0.183	5008	,	,		19584	0.1448		0.1769	False		,,,				2504	0.226				p.P142P		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.A426G						PASS	.	G		2675,1731	518.3+/-369.7	814,1047,342	103.0	98.0	100.0		426	-11.2	0.1	12	dbSNP_100	100	1375,7225	755.3+/-407.5	102,1171,3027	no	coding-synonymous	ANKRD13A	NM_033121.1		916,2218,3369	GG,GA,AA		15.9884,39.2873,31.1395		142/591	110456175	4050,8956	2203	4300	6503	SO:0001819	synonymous_variant	88455	exon5			ATGCCCAAATGAT	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"""Ankyrin repeat domain containing"""	21268	protein-coding gene	gene with protein product		615123	"""ankyrin repeat domain 13"""	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.426A>G	12.37:g.110456175A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	223	98	0.439462	NM_033121	O60736	Silent	SNP	ENST00000261739.4	37	CCDS9140.1																																																																																			A|0.706;G|0.294	0.294	strong		0.463	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411781	105411781	+	Missense_Mutation	SNP	G	G	A	rs10438247	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	205	0	0		WXS	Illumina HiSeq	Phase_I	209	208	0.995215	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	
ZBTB49	166793	hgsc.bcm.edu	37	4	4304522	4304522	+	Missense_Mutation	SNP	A	A	C	rs2920217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:4304522A>C	ENST00000337872.4	+	3	1080	c.959A>C	c.(958-960)tAc>tCc	p.Y320S	ZBTB49_ENST00000538529.1_5'UTR|ZBTB49_ENST00000355834.3_Missense_Mutation_p.Y320S	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	320			Y -> S (in dbSNP:rs2920217).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						TCACAGAAATACGCAGAGCAA	0.453													C|||	1015	0.202676	0.1036	0.2896	5008	,	,		21998	0.247		0.2694	False		,,,				2504	0.1605				p.Y320S		Atlas-SNP	.											.	ZBTB49	63	.	0			c.A959C						PASS	.	C	SER/TYR	743,3663	757.0+/-412.7	72,599,1532	71.0	71.0	71.0		959	-3.0	0.0	4	dbSNP_101	71	2462,6138	696.3+/-404.9	346,1770,2184	yes	missense	ZBTB49	NM_145291.3	144	418,2369,3716	CC,CA,AA		28.6279,16.8634,24.6425	benign	320/766	4304522	3205,9801	2203	4300	6503	SO:0001583	missense	166793	exon3			AGAAATACGCAGA	AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19883	protein-coding gene	gene with protein product			"""zinc finger protein 509"""	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.959A>C	4.37:g.4304522A>C	ENSP00000338807:p.Tyr320Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Missense_Mutation	SNP	ENST00000337872.4	37	CCDS3375.1	479|479	0.21932234432234432|0.21932234432234432	50|50	0.1016260162601626|0.1016260162601626	101|101	0.27900552486187846|0.27900552486187846	123|123	0.21503496503496503|0.21503496503496503	205|205	0.2704485488126649|0.2704485488126649	C|C	7.651|7.651	0.682838|0.682838	0.14907|0.14907	0.168634|0.168634	0.286279|0.286279	ENSG00000168826|ENSG00000168826	ENST00000504302|ENST00000355834;ENST00000337872	.|T;T	.|0.12255	.|2.7;3.06	5.57|5.57	-2.97|-2.97	0.05530|0.05530	.|.	.|1.034610	.|0.07647	.|N	.|0.931287	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00104|0.00104	-2.125|-2.125	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.44590|0.44590	-0.9318|-0.9318	4|9	.|0.18276	.|T	.|0.48	.|.	4.7855|4.7855	0.13223|0.13223	0.0952:0.3798:0.3715:0.1535|0.0952:0.3798:0.3715:0.1535	rs2920217;rs17644818;rs52807019;rs60931887;rs2920217|rs2920217;rs17644818;rs52807019;rs60931887;rs2920217	.|320;320	.|Q6ZSB9-2;Q6ZSB9	.|.;ZBT49_HUMAN	P|S	57|320	.|ENSP00000348091:Y320S;ENSP00000338807:Y320S	.|ENSP00000338807:Y320S	T|Y	+|+	1|2	0|0	ZBTB49|ZBTB49	4355423|4355423	0.050000|0.050000	0.20438|0.20438	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	0.668000|0.668000	0.25127|0.25127	-1.381000|-1.381000	0.02112|0.02112	-0.187000|-0.187000	0.12897|0.12897	ACG|TAC	A|0.779;C|0.221	0.221	strong		0.453	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291	
CUL9	23113	hgsc.bcm.edu	37	6	43184132	43184132	+	Missense_Mutation	SNP	A	A	C	rs2273709	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43184132A>C	ENST00000252050.4	+	31	6257	c.6173A>C	c.(6172-6174)cAc>cCc	p.H2058P	CUL9_ENST00000372647.2_Missense_Mutation_p.H2030P|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000354495.3_Missense_Mutation_p.H1948P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2058			H -> P (in dbSNP:rs2273709).	HQ -> PL (in Ref. 3; CAH18696). {ECO:0000305}.	microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CTGTGCGTACACCAGGCTCAG	0.632													C|||	2000	0.399361	0.7254	0.2233	5008	,	,		17713	0.4226		0.174	False		,,,				2504	0.2914				p.H2058P		Atlas-SNP	.											CUL9,colon,carcinoma,0,1	CUL9	248	1	0			c.A6173C						scavenged	.	C	PRO/HIS	2916,1490	473.1+/-356.6	970,976,257	70.0	66.0	67.0		6173	5.7	1.0	6	dbSNP_100	67	1803,6797	731.6+/-406.8	179,1445,2676	yes	missense	CUL9	NM_015089.2	77	1149,2421,2933	CC,CA,AA		20.9651,33.8175,36.2833	benign	2058/2518	43184132	4719,8287	2203	4300	6503	SO:0001583	missense	23113	exon31			GCGTACACCAGGC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.6173A>C	6.37:g.43184132A>C	ENSP00000252050:p.His2058Pro	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	809	0.37042124542124544	355	0.7215447154471545	84	0.23204419889502761	232	0.40559440559440557	138	0.1820580474934037	C	0.015	-1.547485	0.00926	0.661825	0.209651	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.03663	3.85;3.85;3.85	5.7	5.7	0.88788	.	0.058585	0.64402	N	0.000002	T	0.00328	0.0010	N	0.00289	-1.7	0.52099	P	5.299999999996974E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44452	-0.9327	9	0.02654	T	1	-18.3709	10.902	0.47058	0.2694:0.6127:0.1179:0.0	rs2273709;rs61442708;rs2273709	1948;2030;2058	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	P	2058;1948;2030	ENSP00000252050:H2058P;ENSP00000346490:H1948P;ENSP00000361730:H2030P	ENSP00000252050:H2058P	H	+	2	0	CUL9	43292110	0.995000	0.38212	0.998000	0.56505	0.076000	0.17211	2.797000	0.47877	1.430000	0.47334	-0.121000	0.15023	CAC	A|0.629;C|0.371	0.371	strong		0.632	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
CYP11B1	1584	hgsc.bcm.edu	37	8	143960597	143960597	+	Silent	SNP	G	G	A	rs5283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:143960597G>A	ENST00000292427.4	-	2	278	c.246C>T	c.(244-246)gaC>gaT	p.D82D	CYP11B1_ENST00000517471.1_Silent_p.D82D|CYP11B1_ENST00000377675.3_Silent_p.D127D	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	82					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)	CTCCTCCCAAGTCGTACCTGT	0.632									Familial Hyperaldosteronism type I				.|||	1516	0.302716	0.0356	0.4582	5008	,	,		19293	0.3115		0.4602	False		,,,				2504	0.3824				p.D82D		Atlas-SNP	.											.	CYP11B1	128	.	0			c.C246T						PASS	.	G	,	492,3914	228.1+/-243.1	37,418,1748	141.0	112.0	122.0		246,246	-2.1	0.0	8	dbSNP_52	122	3778,4822	536.4+/-383.0	822,2134,1344	no	coding-synonymous,coding-synonymous	CYP11B1	NM_000497.3,NM_001026213.1	,	859,2552,3092	AA,AG,GG		43.9302,11.1666,32.831	,	82/504,82/438	143960597	4270,8736	2203	4300	6503	SO:0001819	synonymous_variant	1584	exon2	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TCCCAAGTCGTAC	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.246C>T	8.37:g.143960597G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			G|0.668;A|0.332	0.332	strong		0.632	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
TM4SF19	116211	hgsc.bcm.edu	37	3	196054439	196054439	+	Missense_Mutation	SNP	T	T	G	rs6785339	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:196054439T>G	ENST00000273695.3	-	2	148	c.23A>C	c.(22-24)cAg>cCg	p.Q8P	TM4SF19_ENST00000454715.1_Missense_Mutation_p.Q8P|TM4SF19-AS1_ENST00000452051.1_RNA|TM4SF19_ENST00000442633.1_Missense_Mutation_p.Q8P|TM4SF19_ENST00000446879.1_Missense_Mutation_p.Q8P	NM_001204897.1|NM_138461.3	NP_001191826.1|NP_612470.2	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	8			Q -> P (in dbSNP:rs6785339). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(5)	12	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		TGAGCTTGCCTGCGTGCAGGG	0.602													G|||	3159	0.630791	0.4402	0.6009	5008	,	,		20050	0.871		0.5726	False		,,,				2504	0.7219				p.Q8P		Atlas-SNP	.											TM4SF19,NS,carcinoma,0,1	TM4SF19	21	1	0			c.A23C						PASS	.	G	PRO/GLN,PRO/GLN,PRO/GLN	2112,2294	599.9+/-389.4	524,1064,615	75.0	64.0	68.0		23,23,23	3.1	0.0	3	dbSNP_116	68	4958,3642	522.3+/-380.1	1419,2120,761	yes	missense,missense,missense	TM4SF19	NM_001204897.1,NM_001204898.1,NM_138461.3	76,76,76	1943,3184,1376	GG,GT,TT		42.3488,47.9346,45.6405	benign,benign,benign	8/243,8/184,8/210	196054439	7070,5936	2203	4300	6503	SO:0001583	missense	116211	exon2			CTTGCCTGCGTGC	BC013113	CCDS3316.1, CCDS56299.1	3q29	2005-08-09			ENSG00000145107	ENSG00000145107			25167	protein-coding gene	gene with protein product						12477932	Standard	NM_138461		Approved		uc021xjs.1	Q96DZ7	OTTHUMG00000155675	ENST00000273695.3:c.23A>C	3.37:g.196054439T>G	ENSP00000273695:p.Gln8Pro	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_001204897	B2RV20|E9PH22|Q336K7	Missense_Mutation	SNP	ENST00000273695.3	37	CCDS3316.1	1407	0.6442307692307693	237	0.4817073170731707	222	0.6132596685082873	504	0.8811188811188811	444	0.5857519788918206	G	10.19	1.282160	0.23392	0.479346	0.576512	ENSG00000145107	ENST00000446879;ENST00000454715;ENST00000273695	T;T;T	0.30714	1.88;1.52;1.53	5.58	3.1	0.35709	.	0.984540	0.08285	N	0.969300	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	0.23226	-1.0194	9	0.41790	T	0.15	0.2119	3.4069	0.07344	0.654:0.0:0.179:0.167	rs6785339;rs17856417;rs52827973;rs60135622;rs6785339	8;8;8	E9PH22;C9JCD5;Q96DZ7	.;.;T4S19_HUMAN	P	8	ENSP00000395280:Q8P;ENSP00000387728:Q8P;ENSP00000273695:Q8P	ENSP00000273695:Q8P	Q	-	2	0	TM4SF19	197538836	0.029000	0.19370	0.005000	0.12908	0.001000	0.01503	0.670000	0.25157	0.407000	0.25591	-1.094000	0.02160	CAG	T|0.414;G|0.586	0.586	strong		0.602	TM4SF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341174.1	NM_138461	
CEP350	9857	hgsc.bcm.edu	37	1	180080290	180080290	+	Silent	SNP	T	T	A	rs12126496	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:180080290T>A	ENST00000367607.3	+	38	9766	c.9348T>A	c.(9346-9348)ctT>ctA	p.L3116L	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	3116					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						GAATGCTACTTGTGTGACATC	0.463													T|||	211	0.0421326	0.0045	0.0476	5008	,	,		22888	0.0139		0.0984	False		,,,				2504	0.0603				p.L3116L		Atlas-SNP	.											.	CEP350	418	.	0			c.T9348A						PASS	.	T		104,4302	80.9+/-119.3	1,102,2100	92.0	77.0	83.0		9348	3.5	1.0	1	dbSNP_120	83	945,7655	207.7+/-249.4	70,805,3425	no	coding-synonymous	CEP350	NM_014810.4		71,907,5525	AA,AT,TT		10.9884,2.3604,8.0655		3116/3118	180080290	1049,11957	2203	4300	6503	SO:0001819	synonymous_variant	9857	exon38			GCTACTTGTGTGA	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.9348T>A	1.37:g.180080290T>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1	107	0.04899267399267399	4	0.008130081300813009	19	0.052486187845303865	2	0.0034965034965034965	82	0.10817941952506596	T	6.854	0.526772	0.13066	0.023604	0.109884	ENSG00000135837	ENST00000429851	.	.	.	5.9	3.47	0.39725	.	.	.	.	.	T	0.01695	0.0054	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00759	-1.1578	4	.	.	.	.	6.3592	0.21419	0.14:0.0739:0.0:0.7861	rs12126496;rs12126496	.	.	.	S	1291	.	.	C	+	1	0	CEP350	178346913	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.274000	0.33132	1.066000	0.40716	0.528000	0.53228	TGT	T|0.938;A|0.062	0.062	strong		0.463	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
CCR4	1233	hgsc.bcm.edu	37	3	32995928	32995928	+	Silent	SNP	C	C	T	rs2228428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:32995928C>T	ENST00000330953.5	+	2	1182	c.1014C>T	c.(1012-1014)taC>taT	p.Y338Y		NM_005508.4	NP_005499.1	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	338					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuron migration (GO:0001764)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of positive chemotaxis (GO:0050927)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)|tolerance induction (GO:0002507)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			NS(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)|stomach(1)	16						TCCAAATTTACTCTGCTGACA	0.463													C|||	735	0.146765	0.0356	0.2349	5008	,	,		19281	0.0208		0.3141	False		,,,				2504	0.1922				p.Y338Y		Atlas-SNP	.											.	CCR4	36	.	0			c.C1014T						PASS	.	C		348,4054	164.0+/-195.7	14,320,1867	52.0	52.0	52.0		1014	2.1	0.0	3	dbSNP_98	52	2713,5887	421.9+/-353.9	446,1821,2033	no	coding-synonymous	CCR4	NM_005508.4		460,2141,3900	TT,TC,CC		31.5465,7.9055,23.5425		338/361	32995928	3061,9941	2201	4300	6501	SO:0001819	synonymous_variant	1233	exon2			AATTTACTCTGCT	X85740	CCDS2656.1	3p24-p21.3	2012-08-08			ENSG00000183813	ENSG00000183813		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1605	protein-coding gene	gene with protein product		604836				7642634, 8884276	Standard	NM_005508		Approved	CC-CKR-4, CMKBR4, CKR4, k5-5, ChemR13, CD194	uc003cfg.1	P51679	OTTHUMG00000130752	ENST00000330953.5:c.1014C>T	3.37:g.32995928C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	231	97	0.419913	NM_005508	Q9ULY6|Q9ULY7	Silent	SNP	ENST00000330953.5	37	CCDS2656.1																																																																																			C|0.799;T|0.201	0.201	strong		0.463	CCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253252.2		
BMS1	9790	hgsc.bcm.edu	37	10	43318659	43318659	+	Nonsense_Mutation	SNP	C	C	T	rs200996070		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:43318659C>T	ENST00000374518.5	+	20	3289	c.3226C>T	c.(3226-3228)Cga>Tga	p.R1076*		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	1076					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GAAAGCACTCCGAGCTCCAGA	0.502																																					p.R1076X		Atlas-SNP	.											BMS1,caecum,carcinoma,0,2	BMS1	132	2	0			c.C3226T						scavenged	.						69.0	72.0	71.0					10																	43318659		2203	4300	6503	SO:0001587	stop_gained	9790	exon20			GCACTCCGAGCTC	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.3226C>T	10.37:g.43318659C>T	ENSP00000363642:p.Arg1076*	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	194	7	0.0360825	NM_014753	Q5QPT5|Q86XJ9	Nonsense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	C	40	8.399762	0.98794	.	.	ENSG00000165733	ENST00000374518	.	.	.	4.54	2.64	0.31445	.	0.161807	0.43747	D	0.000529	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	.	9.3986	0.38417	0.143:0.7805:0.0:0.0765	.	.	.	.	X	1076	.	ENSP00000363642:R1076X	R	+	1	2	BMS1	42638665	0.925000	0.31364	0.999000	0.59377	0.867000	0.49689	0.975000	0.29449	0.451000	0.26802	0.454000	0.30748	CGA	.	.	weak		0.502	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
PLEKHM2	23207	hgsc.bcm.edu	37	1	16056364	16056364	+	Silent	SNP	G	G	A	rs3817269	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16056364G>A	ENST00000375799.3	+	14	2375	c.2148G>A	c.(2146-2148)acG>acA	p.T716T	PLEKHM2_ENST00000375793.2_Silent_p.T696T|PLEKHM2_ENST00000477849.1_3'UTR|RP11-288I21.1_ENST00000453804.1_RNA	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	716					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GCATCCTGACGGATGCCACCA	0.527													G|||	1536	0.306709	0.711	0.2565	5008	,	,		7266	0.0437		0.2087	False		,,,				2504	0.1677				p.T716T		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.G2148A						PASS	.	G		2435,1507		754,927,290	68.0	71.0	70.0		2148	-10.9	0.7	1	dbSNP_107	70	1907,6413		224,1459,2477	no	coding-synonymous	PLEKHM2	NM_015164.2		978,2386,2767	AA,AG,GG		22.9207,38.2293,35.4102		716/1020	16056364	4342,7920	1971	4160	6131	SO:0001819	synonymous_variant	23207	exon14			CCTGACGGATGCC	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.2148G>A	1.37:g.16056364G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																			G|0.678;A|0.322	0.322	strong		0.527	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
TAS1R2	80834	hgsc.bcm.edu	37	1	19181015	19181015	+	Missense_Mutation	SNP	G	G	C	rs34447754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19181015G>C	ENST00000375371.3	-	3	970	c.949C>G	c.(949-951)Cgc>Ggc	p.R317G	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	317			R -> G (in dbSNP:rs34447754). {ECO:0000269|PubMed:11917125}.		detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	CCCAAGTGGCGCAGCTCCGTG	0.662													G|||	1193	0.238219	0.2602	0.2507	5008	,	,		19800	0.1032		0.3191	False		,,,				2504	0.2556				p.R317G		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C949G						PASS	.	G	GLY/ARG	1096,3310	394.9+/-329.4	130,836,1237	56.0	55.0	55.0		949	2.8	0.2	1	dbSNP_126	55	2795,5803	441.0+/-359.7	443,1909,1947	yes	missense	TAS1R2	NM_152232.2	125	573,2745,3184	CC,CG,GG		32.5076,24.8752,29.9216	benign	317/840	19181015	3891,9113	2203	4299	6502	SO:0001583	missense	80834	exon3			AGTGGCGCAGCTC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.949C>G	1.37:g.19181015G>C	ENSP00000364520:p.Arg317Gly	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	525	0.2403846153846154	124	0.25203252032520324	104	0.287292817679558	54	0.0944055944055944	243	0.32058047493403696	G	3.588	-0.084220	0.07097	0.248752	0.325076	ENSG00000179002	ENST00000375371	D	0.83419	-1.72	4.8	2.84	0.33178	Extracellular ligand-binding receptor (1);	1.158180	0.06535	N	0.742189	T	0.00012	0.0000	L	0.39245	1.2	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.04165	-1.0972	9	0.12103	T	0.63	.	10.6868	0.45848	0.0:0.0:0.4503:0.5497	rs34447754	317	Q8TE23	TS1R2_HUMAN	G	317	ENSP00000364520:R317G	ENSP00000364520:R317G	R	-	1	0	TAS1R2	19053602	0.249000	0.23941	0.156000	0.22583	0.115000	0.19883	0.582000	0.23834	0.556000	0.29098	0.561000	0.74099	CGC	G|0.720;C|0.280	0.280	strong		0.662	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
KTI12	112970	hgsc.bcm.edu	37	1	52498370	52498370	+	Silent	SNP	C	C	T	rs2809917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:52498370C>T	ENST00000371614.1	-	1	1118	c.1064G>A	c.(1063-1065)tGa>tAa	p.*355*	TXNDC12_ENST00000371626.4_Intron|RP11-91A18.4_ENST00000425802.1_RNA	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	0							ATP binding (GO:0005524)	p.*355*(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CTCCTCTGGTCAGTGCAGGCT	0.488													T|||	1102	0.220048	0.4092	0.1354	5008	,	,		20525	0.1786		0.0855	False		,,,				2504	0.2055				p.X355X		Atlas-SNP	.											KTI12,NS,carcinoma,0,1	KTI12	30	1	1	Substitution - coding silent(1)	stomach(1)	c.G1064A						PASS	.	T	,	1580,2826	652.5+/-399.4	302,976,925	46.0	50.0	48.0		,1064	0.9	0.1	1	dbSNP_100	48	971,7629	757.0+/-407.5	46,879,3375	no	intron,coding-synonymous	TXNDC12,KTI12	NM_015913.2,NM_138417.2	,	348,1855,4300	TT,TC,CC		11.2907,35.8602,19.614	,	,355/355	52498370	2551,10455	2203	4300	6503	SO:0001819	synonymous_variant	112970	exon1			TCTGGTCAGTGCA		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.1064G>A	1.37:g.52498370C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_138417		Silent	SNP	ENST00000371614.1	37	CCDS562.1																																																																																			C|0.799;T|0.201	0.201	strong		0.488	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417	
HIVEP2	3097	hgsc.bcm.edu	37	6	143090734	143090734	+	Silent	SNP	T	T	C	rs34530989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:143090734T>C	ENST00000367604.1	-	4	5781	c.5142A>G	c.(5140-5142)ggA>ggG	p.G1714G	HIVEP2_ENST00000012134.2_Silent_p.G1714G|HIVEP2_ENST00000367603.2_Silent_p.G1714G			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1714					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GCTTGCCGGTTCCAGGCCTAT	0.438													T|||	704	0.140575	0.0968	0.1124	5008	,	,		18652	0.0804		0.1968	False		,,,				2504	0.2239				p.G1714G	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.A5142G						PASS	.	T		375,3357		24,327,1515	117.0	107.0	110.0		5142	-1.1	0.2	6	dbSNP_126	110	1552,6686		140,1272,2707	no	coding-synonymous	HIVEP2	NM_006734.3		164,1599,4222	CC,CT,TT		18.8395,10.0482,16.0986		1714/2447	143090734	1927,10043	1866	4119	5985	SO:0001819	synonymous_variant	3097	exon5			GCCGGTTCCAGGC	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5142A>G	6.37:g.143090734T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	178	88	0.494382	NM_006734	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																			T|0.858;C|0.142	0.142	strong		0.438	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
TGOLN2	10618	hgsc.bcm.edu	37	2	85554080	85554080	+	Missense_Mutation	SNP	G	G	A	rs4247303	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:85554080G>A	ENST00000409232.3	-	2	836	c.775C>T	c.(775-777)Cgg>Tgg	p.R259W	TGOLN2_ENST00000377386.3_Missense_Mutation_p.R259W|TGOLN2_ENST00000444342.2_Missense_Mutation_p.R259W|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000398263.2_Intron|TGOLN2_ENST00000409015.1_Missense_Mutation_p.R259W			O43493	TGON2_HUMAN	trans-golgi network protein 2	259			R -> W (in dbSNP:rs4247303). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8907712, ECO:0000269|Ref.4, ECO:0000269|Ref.7}.			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											TGGTCTTTCCGGGAAGGCTGC	0.562													G|||	2903	0.579673	0.3419	0.6787	5008	,	,		18921	0.8671		0.4881	False		,,,				2504	0.6288				p.R259W		Atlas-SNP	.											TGOLN2_ENST00000377386,colon,carcinoma,0,1	TGOLN2	32	1	0			c.C775T						PASS	.	G	TRP/ARG,TRP/ARG,,TRP/ARG	1390,2502		244,902,800	82.0	81.0	81.0		775,775,,775	-3.7	0.0	2	dbSNP_111	81	4087,4191		1011,2065,1063	yes	missense,missense,intron,missense	TGOLN2	NM_001206840.1,NM_001206841.1,NM_001206844.1,NM_006464.3	101,101,,101	1255,2967,1863	AA,AG,GG		49.3718,35.7143,45.0041	probably-damaging,probably-damaging,,probably-damaging	259/481,259/454,,259/438	85554080	5477,6693	1946	4139	6085	SO:0001583	missense	10618	exon2			CTTTCCGGGAAGG	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"""trans-Golgi network protein (46, 48, 51kD isoforms)"""	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.775C>T	2.37:g.85554080G>A	ENSP00000386443:p.Arg259Trp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Missense_Mutation	SNP	ENST00000409232.3	37	CCDS56126.1	1255	0.5746336996336996	174	0.35365853658536583	228	0.6298342541436464	485	0.8479020979020979	368	0.48548812664907653	G	10.02	1.236273	0.22626	0.357143	0.493718	ENSG00000152291	ENST00000377386;ENST00000409232;ENST00000409015;ENST00000444342	T;T;T;T	0.10860	2.83;2.84;2.83;2.83	1.87	-3.74	0.04385	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.0000000000287557E-6	D;D;D	0.76494	0.999;0.999;0.997	P;P;P	0.58721	0.844;0.844;0.844	T	0.55903	-0.8067	8	0.72032	D	0.01	0.4595	0.9419	0.01357	0.4213:0.1167:0.2684:0.1936	rs4247303;rs17359940;rs59582594;rs4247303	259;259;259	O43493;O43493-5;O43493-2	TGON2_HUMAN;.;.	W	259	ENSP00000366603:R259W;ENSP00000386443:R259W;ENSP00000387035:R259W;ENSP00000391190:R259W	ENSP00000366603:R259W	R	-	1	2	TGOLN2	85407591	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.303000	0.01135	-3.248000	0.00205	-1.488000	0.00978	CGG	G|0.432;A|0.567	0.567	strong		0.562	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464	
PARP2	10038	hgsc.bcm.edu	37	14	20822331	20822331	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20822331A>C	ENST00000250416.5	+	8	754	c.727A>C	c.(727-729)Aag>Cag	p.K243Q	PARP2_ENST00000527915.1_Missense_Mutation_p.K243Q|PARP2_ENST00000429687.3_Missense_Mutation_p.K230Q	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	243	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		GGAGTTAATAAAGTTGATCTG	0.388								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.K243Q		Atlas-SNP	.											PARP2_ENST00000250416,NS,carcinoma,0,2	PARP2	92	2	0			c.A727C						PASS	.						130.0	125.0	127.0					14																	20822331		1866	4111	5977	SO:0001583	missense	10038	exon8			TTAATAAAGTTGA	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"""Poly (ADP-ribose) polymerases"""	272	protein-coding gene	gene with protein product		607725	"""ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2"", ""poly (ADP-ribose) polymerase family, member 2"""	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.727A>C	14.37:g.20822331A>C	ENSP00000250416:p.Lys243Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	161	70	0.434783	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Missense_Mutation	SNP	ENST00000250416.5	37	CCDS41910.1	.	.	.	.	.	.	.	.	.	.	A	9.194	1.026692	0.19512	.	.	ENSG00000129484	ENST00000429687;ENST00000250416;ENST00000527915	T;T;T	0.15718	2.4;2.4;2.4	4.97	1.27	0.21489	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.333967	0.32548	N	0.005946	T	0.09818	0.0241	N	0.25890	0.77	0.33351	D	0.571125	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.08493	-1.0719	10	0.41790	T	0.15	-3.5913	5.4142	0.16363	0.3821:0.4338:0.184:0.0	.	230;243	Q9UGN5-2;Q9UGN5	.;PARP2_HUMAN	Q	230;243;243	ENSP00000392972:K230Q;ENSP00000250416:K243Q;ENSP00000432283:K243Q	ENSP00000250416:K243Q	K	+	1	0	PARP2	19892171	0.812000	0.29077	0.992000	0.48379	0.704000	0.40688	0.898000	0.28404	0.424000	0.26061	0.477000	0.44152	AAG	.	.	none		0.388	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2		
SPTBN5	51332	hgsc.bcm.edu	37	15	42166500	42166500	+	Missense_Mutation	SNP	C	C	T	rs12593397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:42166500C>T	ENST00000320955.6	-	24	4906	c.4679G>A	c.(4678-4680)cGc>cAc	p.R1560H		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1560					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)		CTTGTGCTTGCGGTGAAGGCT	0.567													c|||	1979	0.395168	0.0439	0.5101	5008	,	,		18934	0.7034		0.4483	False		,,,				2504	0.4162				p.R1525H		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G4574A						PASS	.	C	HIS/ARG	450,3606		31,388,1609	111.0	110.0	111.0		4574	-5.2	0.0	15	dbSNP_120	111	3639,4709		790,2059,1325	yes	missense	SPTBN5	NM_016642.2	29	821,2447,2934	TT,TC,CC		43.5913,11.0947,32.9652	benign	1525/3640	42166500	4089,8315	2028	4174	6202	SO:0001583	missense	51332	exon24			TGCTTGCGGTGAA	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.4679G>A	15.37:g.42166500C>T	ENSP00000317790:p.Arg1560His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		974	0.445970695970696	24	0.04878048780487805	191	0.5276243093922652	406	0.7097902097902098	353	0.4656992084432718	.	6.946	0.544443	0.13312	0.110947	0.435913	ENSG00000137877	ENST00000320955	T	0.51817	0.69	4.91	-5.21	0.02815	.	1.413800	0.04962	N	0.462280	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39165	-0.9627	9	0.30854	T	0.27	.	4.544	0.12073	0.2365:0.3532:0.0:0.4104	rs12593397;rs17686044;rs61699871;rs12593397	1560	Q9NRC6	SPTN5_HUMAN	H	1560	ENSP00000317790:R1560H	ENSP00000317790:R1560H	R	-	2	0	SPTBN5	39953792	0.104000	0.21937	0.000000	0.03702	0.009000	0.06853	0.404000	0.20999	-0.897000	0.03910	-0.904000	0.02843	CGC	C|0.591;T|0.409	0.409	strong		0.567	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
FGB	2244	hgsc.bcm.edu	37	4	155491759	155491759	+	Missense_Mutation	SNP	G	G	A	rs4220	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155491759G>A	ENST00000302068.4	+	8	1496	c.1433G>A	c.(1432-1434)aGg>aAg	p.R478K	FGB_ENST00000509493.1_Missense_Mutation_p.R259K|FGB_ENST00000502545.1_3'UTR	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	478	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		R -> K (in Baltimore-2; dbSNP:rs4220). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:3194892, ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	TACTCAATGAGGAAGATGAGT	0.438													A|||	768	0.153355	0.0756	0.1499	5008	,	,		20179	0.2242		0.1998	False		,,,				2504	0.1401				p.R478K	NSCLC(106;1133 1613 21870 46110 52656)	Atlas-SNP	.											.	FGB	71	.	0			c.G1433A	GRCh37	CM080365	FGB	M	rs4220	PASS	.	A	LYS/ARG,LYS/ARG	390,4016	790.2+/-415.0	12,366,1825	188.0	170.0	176.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1256,1433	-3.0	0.2	4	dbSNP_36	176	1633,6967	742.0+/-407.2	175,1283,2842	yes	missense,missense	FGB	NM_001184741.1,NM_005141.4	26,26	187,1649,4667	AA,AG,GG		18.9884,8.8516,15.5544	benign,benign	419/433,478/492	155491759	2023,10983	2203	4300	6503	SO:0001583	missense	2244	exon8			CAATGAGGAAGAT		CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3662	protein-coding gene	gene with protein product		134830	"""fibrinogen, B beta polypeptide"""				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.1433G>A	4.37:g.155491759G>A	ENSP00000306099:p.Arg478Lys	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	291	112	0.38488	NM_005141	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Missense_Mutation	SNP	ENST00000302068.4	37	CCDS3786.1	378	0.17307692307692307	44	0.08943089430894309	72	0.19889502762430938	103	0.18006993006993008	159	0.20976253298153033	A	4.277	0.050543	0.08243	0.088516	0.189884	ENSG00000171564	ENST00000302068;ENST00000537843;ENST00000509493	T;T	0.78595	-1.19;-1.19	5.71	-2.97	0.05530	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.202388	0.56097	N	0.000037	T	0.00039	0.0001	N	0.00260	-1.75	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.09292	-1.0681	9	0.02654	T	1	.	7.4038	0.26979	0.5207:0.0:0.3763:0.103	rs4220;rs2227419;rs2303416;rs3183605;rs60022569;rs4220	461;478	B4E1D3;P02675	.;FIBB_HUMAN	K	478;461;259	ENSP00000306099:R478K;ENSP00000426757:R259K	ENSP00000306099:R478K	R	+	2	0	FGB	155711209	1.000000	0.71417	0.171000	0.22900	0.822000	0.46500	3.223000	0.51231	-1.030000	0.03312	-1.103000	0.02113	AGG	G|0.843;A|0.157	0.157	strong		0.438	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141	
RNF213	57674	hgsc.bcm.edu	37	17	78263514	78263514	+	Silent	SNP	G	G	A	rs17853713	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78263514G>A	ENST00000582970.1	+	6	1133	c.990G>A	c.(988-990)aaG>aaA	p.K330K	RNF213_ENST00000456466.1_Silent_p.K330K|RNF213_ENST00000319921.4_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						PASS	.	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	96	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	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	
PIEZO2	63895	hgsc.bcm.edu	37	18	10696227	10696227	+	Silent	SNP	C	C	T	rs2277860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:10696227C>T	ENST00000503781.3	-	43	6695	c.6696G>A	c.(6694-6696)ccG>ccA	p.P2232P	PIEZO2_ENST00000285141.4_Silent_p.P87P|PIEZO2_ENST00000538948.1_Silent_p.P189P|PIEZO2_ENST00000302079.6_Silent_p.P2232P|PIEZO2_ENST00000580640.1_Silent_p.P2257P	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2232					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TCACCAAAAACGGCCCCGGGA	0.522													C|||	1098	0.219249	0.1967	0.2133	5008	,	,		20401	0.1111		0.3569	False		,,,				2504	0.2239				p.P2232P		Atlas-SNP	.											.	.	.	.	0			c.G6696A						PASS	.	C		1040,3366	381.6+/-324.1	129,782,1292	65.0	65.0	65.0		6696	-11.1	0.0	18	dbSNP_100	65	3132,5468	477.0+/-369.5	602,1928,1770	no	coding-synonymous	PIEZO2	NM_022068.2		731,2710,3062	TT,TC,CC		36.4186,23.6042,32.0775		2232/2753	10696227	4172,8834	2203	4300	6503	SO:0001819	synonymous_variant	63895	exon43			CAAAAACGGCCCC	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6696G>A	18.37:g.10696227C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	117	65	0.555556	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Silent	SNP	ENST00000503781.3	37																																																																																				C|0.712;T|0.288	0.288	strong		0.522	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068	
CENPC	1060	hgsc.bcm.edu	37	4	68380070	68380070	+	Missense_Mutation	SNP	C	C	T	rs1056787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:68380070C>T	ENST00000273853.6	-	8	1416	c.1166G>A	c.(1165-1167)gGt>gAt	p.G389D		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	389			G -> D (in dbSNP:rs1056787). {ECO:0000269|PubMed:1339310}.		chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										TACTGTTTCACCTATCAAAGC	0.338													C|||	124	0.0247604	0.0045	0.0519	5008	,	,		18799	0.0		0.0755	False		,,,				2504	0.0061				p.G389D		Atlas-SNP	.											.	CENPC1	66	.	0			c.G1166A						PASS	.	C	ASP/GLY	66,3552		0,66,1743	79.0	66.0	70.0		1166	2.2	0.1	4	dbSNP_86	70	737,7421		25,687,3367	yes	missense	CENPC1	NM_001812.2	94	25,753,5110	TT,TC,CC		9.0341,1.8242,6.819	benign	389/944	68380070	803,10973	1809	4079	5888	SO:0001583	missense	1060	exon8			GTTTCACCTATCA	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"""centromere protein C 1"""	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.1166G>A	4.37:g.68380070C>T	ENSP00000273853:p.Gly389Asp	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	228	118	0.517544	NM_001812	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	37	CCDS47063.1	83	0.038003663003663	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	61	0.08047493403693931	C	3.004	-0.205492	0.06180	0.018242	0.090341	ENSG00000145241	ENST00000273853	.	.	.	4.63	2.17	0.27698	.	1.062250	0.07311	N	0.875940	T	0.00496	0.0016	N	0.04203	-0.255	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27088	-1.0084	8	0.02654	T	1	-1.2622	4.4653	0.11685	0.0:0.1071:0.1984:0.6945	rs1056787;rs3197406;rs17624860;rs52834666;rs60270492;rs1056787	389;389	Q8IW27;Q03188	.;CENPC_HUMAN	D	389	.	ENSP00000273853:G389D	G	-	2	0	CENPC1	68062665	0.331000	0.24713	0.056000	0.19401	0.083000	0.17756	0.306000	0.19279	0.370000	0.24538	-0.471000	0.05019	GGT	C|0.973;T|0.027	0.027	strong		0.338	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2		
DEFB114	245928	hgsc.bcm.edu	37	6	49931783	49931783	+	Silent	SNP	A	A	G	rs73737276	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:49931783A>G	ENST00000322066.3	-	1	35	c.36T>C	c.(34-36)taT>taC	p.Y12Y		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	12					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					TGAAGGTCACATAACACAGAA	0.294													A|||	333	0.0664936	0.0522	0.0692	5008	,	,		14819	0.0079		0.1282	False		,,,				2504	0.0808				p.Y12Y		Atlas-SNP	.											.	DEFB114	12	.	0			c.T36C						PASS	.	A		292,4112	159.6+/-192.1	9,274,1919	69.0	69.0	69.0		36	1.2	0.5	6	dbSNP_130	69	1103,7485	226.6+/-262.3	68,967,3259	no	coding-synonymous	DEFB114	NM_001037499.1		77,1241,5178	GG,GA,AA		12.8435,6.6303,10.7374		12/70	49931783	1395,11597	2202	4294	6496	SO:0001819	synonymous_variant	245928	exon1			GGTCACATAACAC	DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"""Defensins, beta"""	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.36T>C	6.37:g.49931783A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	NM_001037499	Q8NES9	Silent	SNP	ENST00000322066.3	37	CCDS34474.1																																																																																			A|0.899;G|0.101	0.101	strong		0.294	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499	
PRODH	5625	hgsc.bcm.edu	37	22	18912678	18912678	+	Missense_Mutation	SNP	A	A	G	rs386819653|rs4819756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:18912678A>G	ENST00000357068.6	-	4	818	c.553T>C	c.(553-555)Tgg>Cgg	p.W185R	PRODH_ENST00000420436.1_Missense_Mutation_p.W77R|PRODH_ENST00000334029.2_Missense_Mutation_p.W77R	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	185			R -> Q (no effect on enzymatic activity).|R -> W (moderate reduction of enzymatic activity; dbSNP:rs4819756).		4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	CCGAAGGCCCAGTGGGCCTGG	0.592													.|||	3911	0.78095	0.916	0.6715	5008	,	,		18594	0.9712		0.5567	False		,,,				2504	0.7106				p.W185R		Atlas-SNP	.											.	PRODH	42	.	0			c.T553C	GRCh37	CM057554	PRODH	M	rs4819756	PASS	.		ARG/TRP,ARG/TRP	3798,608		1646,506,51	104.0	104.0	104.0		229,553	2.9	0.2	22	dbSNP_111	104	4967,3633		1455,2057,788	yes	missense,missense	PRODH	NM_001195226.1,NM_016335.4	101,101	3101,2563,839	GG,GA,AA		42.2442,13.7994,32.608	probably-damaging,probably-damaging	77/493,185/601	18912678	8765,4241	2203	4300	6503	SO:0001583	missense	5625	exon5			AGGCCCAGTGGGC	AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	"""proline dehydrogenase (proline oxidase )"""			9385373, 10192398	Standard	NM_001195226		Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.553T>C	22.37:g.18912678A>G	ENSP00000349577:p.Trp185Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_016335	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	Missense_Mutation	SNP	ENST00000357068.6	37	CCDS13754.1	1621|1621	0.7422161172161172|0.7422161172161172	429|429	0.8719512195121951|0.8719512195121951	235|235	0.649171270718232|0.649171270718232	552|552	0.965034965034965|0.965034965034965	405|405	0.5343007915567283|0.5343007915567283	.|.	0.065|0.065	-1.215883|-1.215883	0.01542|0.01542	0.862006|0.862006	0.577558|0.577558	ENSG00000100033|ENSG00000100033	ENST00000457083|ENST00000357068;ENST00000438924;ENST00000450579	.|T;T	.|0.75260	.|-0.92;-0.92	5.03|5.03	2.88|2.88	0.33553|0.33553	.|.	.|0.520350	.|0.20347	.|N	.|0.094139	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.47476|0.47476	P|P	5.610000000000337E-4|5.610000000000337E-4	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.32402|0.32402	-0.9908|-0.9908	3|8	.|0.15952	.|T	.|0.53	0.0658|0.0658	6.4381|6.4381	0.21835|0.21835	0.1618:0.0:0.6925:0.1458|0.1618:0.0:0.6925:0.1458	rs4819756;rs58835750;rs4819756|rs4819756;rs58835750;rs4819756	.|77	.|E7EQL6	.|.	P|R	108|185;67;26	.|ENSP00000349577:W185R;ENSP00000396806:W26R	.|ENSP00000334726:W77R	L|W	-|-	2|1	0|0	PRODH|PRODH	17292678|17292678	0.975000|0.975000	0.34042|0.34042	0.234000|0.234000	0.24042|0.24042	0.007000|0.007000	0.05969|0.05969	3.683000|3.683000	0.54663|0.54663	0.250000|0.250000	0.21479|0.21479	-1.516000|-1.516000	0.00938|0.00938	CTG|TGG	A|0.284;G|0.716	0.716	strong		0.592	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316637.2	NM_016335	
PSMD13	5719	hgsc.bcm.edu	37	11	244115	244115	+	Intron	SNP	G	G	A	rs7128044	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244115G>A	ENST00000532097.1	+	3	713				PSMD13_ENST00000431206.2_Missense_Mutation_p.C57Y|PSMD13_ENST00000352303.5_Intron	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13						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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.C57Y(1)		NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		GAAAATGAGTGCATTGATGCT	0.408													A|||	4083	0.815296	0.8918	0.83	5008	,	,		15874	0.8036		0.7306	False		,,,				2504	0.8006				p.C57Y		Atlas-SNP	.											PSMD13_ENST00000431206,brain,glioma,0,3	PSMD13	53	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.G170A						PASS	.	A	,TYR/CYS	3844,562		1714,416,73	56.0	62.0	60.0		,170	-5.5	0.0	11	dbSNP_116	60	6210,2376		2359,1492,442	yes	intron,missense	PSMD13	NM_002817.3,NM_175932.2	,194	4073,1908,515	AA,AG,GG		27.673,12.7553,22.6139	,	,57/379	244115	10054,2938	2203	4293	6496	SO:0001627	intron_variant	5719	exon2			ATGAGTGCATTGA	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.209+40G>A	11.37:g.244115G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	1762	0.8067765567765568	440	0.8943089430894309	295	0.8149171270718232	471	0.8234265734265734	556	0.7335092348284961	A	4.120	0.020484	0.08006	0.872447	0.72327	ENSG00000185627	ENST00000431206	T	0.16457	2.34	5.94	-5.49	0.02584	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13442	-1.0509	6	.	.	.	.	8.4842	0.33061	0.1533:0.1719:0.5899:0.0848	rs7128044;rs61504449	57	Q9UNM6-2	.	Y	57	ENSP00000396937:C57Y	.	C	+	2	0	PSMD13	234115	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.479000	0.00983	-1.370000	0.02144	-0.360000	0.07572	TGC	G|0.224;A|0.776	0.776	strong		0.408	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
PRR27	401137	hgsc.bcm.edu	37	4	71024473	71024473	+	Silent	SNP	T	T	A	rs542201615		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024473T>A	ENST00000344526.5	+	3	693	c.504T>A	c.(502-504)ccT>ccA	p.P168P	C4orf40_ENST00000502294.1_Silent_p.P168P|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		168	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						GAGCTGAGCCTGCTGCAGAGG	0.627																																					p.P168P		Atlas-SNP	.											.	C4orf40	19	.	0			c.T504A						PASS	.																																			SO:0001819	synonymous_variant	401137	exon3			TGAGCCTGCTGCA																												ENST00000344526.5:c.504T>A	4.37:g.71024473T>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	125	20	0.16	NM_214711	A8MXP0|Q6MZR6	Silent	SNP	ENST00000344526.5	37	CCDS3535.1																																																																																			.	.	none		0.627	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
SETD4	54093	hgsc.bcm.edu	37	21	37410477	37410477	+	Missense_Mutation	SNP	T	T	C	rs2835239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:37410477T>C	ENST00000399215.1	-	9	2531	c.1159A>G	c.(1159-1161)Ata>Gta	p.I387V	SETD4_ENST00000332131.4_Missense_Mutation_p.I387V|SETD4_ENST00000399212.1_Missense_Mutation_p.I363V|AP000688.1_ENST00000600312.1_Intron|SETD4_ENST00000481477.1_5'UTR			Q9NVD3	SETD4_HUMAN	SET domain containing 4	387			I -> V (in dbSNP:rs2835239).	EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GTCTCTTCTATGAAATAATAG	0.348													T|||	128	0.0255591	0.0	0.036	5008	,	,		19033	0.002		0.0636	False		,,,				2504	0.0378				p.I387V		Atlas-SNP	.											.	SETD4	37	.	0			c.A1159G						PASS	.	T	VAL/ILE	56,4348	54.9+/-90.9	2,52,2148	164.0	159.0	161.0		1159	3.2	0.2	21	dbSNP_100	161	498,8102	144.3+/-200.2	8,482,3810	yes	missense	SETD4	NM_017438.3	29	10,534,5958	CC,CT,TT		5.7907,1.2716,4.2602	possibly-damaging	387/441	37410477	554,12450	2202	4300	6502	SO:0001583	missense	54093	exon10			CTTCTATGAAATA	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 27"", ""chromosome 21 open reading frame 18"""	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.1159A>G	21.37:g.37410477T>C	ENSP00000382163:p.Ile387Val	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	206	112	0.543689	NM_017438	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	CCDS13640.1	62	0.028388278388278388	0	0.0	13	0.03591160220994475	0	0.0	49	0.06464379947229551	T	14.91	2.676807	0.47886	0.012716	0.057907	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131	T;T;T	0.18016	2.24;2.24;2.24	5.79	3.22	0.36961	Rubisco LS methyltransferase, substrate-binding domain (1);	0.377760	0.30762	N	0.008935	T	0.02083	0.0065	M	0.70595	2.14	0.38358	D	0.94451	B;P	0.36789	0.27;0.57	B;B	0.41202	0.151;0.35	T	0.04294	-1.0962	10	0.24483	T	0.36	-25.5361	7.6719	0.28463	0.1314:0.0:0.2735:0.5951	rs2835239;rs17228507;rs52822224;rs59296148;rs2835239	363;387	Q9NVD3-3;Q9NVD3	.;SETD4_HUMAN	V	387;363;387	ENSP00000382163:I387V;ENSP00000382161:I363V;ENSP00000329189:I387V	ENSP00000329189:I387V	I	-	1	0	SETD4	36332347	0.986000	0.35501	0.209000	0.23619	0.729000	0.41735	0.337000	0.19841	0.970000	0.38263	0.459000	0.35465	ATA	T|0.963;C|0.037	0.037	strong		0.348	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	
ODAM	54959	hgsc.bcm.edu	37	4	71062426	71062426	+	Silent	SNP	C	C	T	rs17704351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	208	0	0		WXS	Illumina HiSeq	Phase_I	194	84	0.43299	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	
KAT2B	8850	hgsc.bcm.edu	37	3	20113830	20113830	+	Silent	SNP	G	G	A	rs3021408	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:20113830G>A	ENST00000263754.4	+	2	764	c.309G>A	c.(307-309)gaG>gaA	p.E103E	KAT2B_ENST00000426228.1_3'UTR	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	103					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						TTTAGGCCGAGGAGTCTTGTA	0.423													G|||	2336	0.466454	0.5234	0.4481	5008	,	,		17865	0.4137		0.4006	False		,,,				2504	0.5245				p.E103E		Atlas-SNP	.											.	KAT2B	73	.	0			c.G309A						PASS	.	G		2166,2240	583.1+/-385.7	521,1124,558	126.0	135.0	132.0		309	4.2	1.0	3	dbSNP_101	132	3184,5416	483.4+/-371.1	617,1950,1733	no	coding-synonymous	KAT2B	NM_003884.4		1138,3074,2291	AA,AG,GG		37.0233,49.1602,41.1349		103/833	20113830	5350,7656	2203	4300	6503	SO:0001819	synonymous_variant	8850	exon2			GGCCGAGGAGTCT	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"""Chromatin-modifying enzymes / K-acetyltransferases"""	8638	protein-coding gene	gene with protein product		602303	"""p300/CBP-associated factor"""	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.309G>A	3.37:g.20113830G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_003884	Q6NSK1	Silent	SNP	ENST00000263754.4	37	CCDS2634.1																																																																																			G|0.577;A|0.423	0.423	strong		0.423	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884	
RP1L1	94137	hgsc.bcm.edu	37	8	10466161	10466161	+	Missense_Mutation	SNP	C	C	T	rs79019225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10466161C>T	ENST00000382483.3	-	4	5670	c.5447G>A	c.(5446-5448)gGt>gAt	p.G1816D		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1896					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)		CGCAGCTTCACCCTGCAAGTT	0.617													C|||	151	0.0301518	0.0356	0.0144	5008	,	,		17632	0.002		0.0348	False		,,,				2504	0.0583				p.G1816D		Atlas-SNP	.											.	RP1L1	453	.	0			c.G5447A						PASS	.	C	ASP/GLY	140,4078		1,138,1970	170.0	192.0	185.0		5447	-2.6	0.0	8	dbSNP_131	185	334,8098		5,324,3887	yes	missense	RP1L1	NM_178857.5	94	6,462,5857	TT,TC,CC		3.9611,3.3191,3.747	benign	1816/2401	10466161	474,12176	2109	4216	6325	SO:0001583	missense	94137	exon4			GCTTCACCCTGCA	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.5447G>A	8.37:g.10466161C>T	ENSP00000371923:p.Gly1816Asp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	47	0.02152014652014652	15	0.03048780487804878	5	0.013812154696132596	2	0.0034965034965034965	25	0.032981530343007916	C	6.198	0.404781	0.11754	0.033191	0.039611	ENSG00000183638	ENST00000382483	T	0.19394	2.15	3.83	-2.56	0.06268	.	0.660471	0.11551	U	0.552790	T	0.01765	0.0056	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.38023	-0.9680	10	0.13108	T	0.6	0.2735	6.964	0.24613	0.0:0.2943:0.453:0.2527	.	1816	A6NKC6	.	D	1816	ENSP00000371923:G1816D	ENSP00000371923:G1816D	G	-	2	0	RP1L1	10503571	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-1.568000	0.02144	-0.964000	0.03595	-0.463000	0.05309	GGT	C|0.972;T|0.028	0.028	strong		0.617	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
GLB1L2	89944	hgsc.bcm.edu	37	11	134234269	134234269	+	Missense_Mutation	SNP	A	A	G	rs114723326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134234269A>G	ENST00000535456.2	+	8	969	c.781A>G	c.(781-783)Acc>Gcc	p.T261A	GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Missense_Mutation_p.T261A|GLB1L2_ENST00000389881.3_Missense_Mutation_p.T261A	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	261					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)		GCAGCTACTGACCACCTTTCT	0.557													A|||	117	0.0233626	0.0817	0.0086	5008	,	,		19623	0.0		0.003	False		,,,				2504	0.0				p.T261A		Atlas-SNP	.											.	GLB1L2	79	.	0			c.A781G						PASS	.	A	ALA/THR	254,4148	148.8+/-183.1	9,236,1956	286.0	251.0	263.0		781	4.0	0.0	11	dbSNP_132	263	6,8588	5.0+/-18.6	0,6,4291	yes	missense	GLB1L2	NM_138342.3	58	9,242,6247	GG,GA,AA		0.0698,5.7701,2.0006	benign	261/637	134234269	260,12736	2201	4297	6498	SO:0001583	missense	89944	exon8			CTACTGACCACCT		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.781A>G	11.37:g.134234269A>G	ENSP00000444628:p.Thr261Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Missense_Mutation	SNP	ENST00000535456.2	37	CCDS31724.1	40|40	0.018315018315018316|0.018315018315018316	38|38	0.07723577235772358|0.07723577235772358	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	A|A	5.513|5.513	0.279580|0.279580	0.10458|0.10458	0.057701|0.057701	6.98E-4|6.98E-4	ENSG00000149328|ENSG00000149328	ENST00000525089;ENST00000533324|ENST00000339772;ENST00000535456;ENST00000389881	.|D;D;D	.|0.97752	.|-4.52;-4.52;-4.52	3.97|3.97	3.97|3.97	0.46021|0.46021	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.599178	.|0.17894	.|N	.|0.158423	T|T	0.41789|0.41789	0.1174|0.1174	N|N	0.01649|0.01649	-0.78|-0.78	0.09310|0.09310	N|N	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.15052	.|0.012	T|T	0.67035|0.67035	-0.5772|-0.5772	5|10	.|0.12430	.|T	.|0.62	-7.5496|-7.5496	11.2062|11.2062	0.48771|0.48771	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|261	.|Q8IW92	.|GLBL2_HUMAN	G|A	199;88|261	.|ENSP00000344659:T261A;ENSP00000444628:T261A;ENSP00000374531:T261A	.|ENSP00000344659:T261A	D|T	+|+	2|1	0|0	GLB1L2|GLB1L2	133739479|133739479	0.002000|0.002000	0.14202|0.14202	0.022000|0.022000	0.16811|0.16811	0.050000|0.050000	0.14768|0.14768	1.637000|1.637000	0.37155|0.37155	2.026000|2.026000	0.59711|0.59711	0.533000|0.533000	0.62120|0.62120	GAC|ACC	A|0.981;G|0.019	0.019	strong		0.557	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
C12orf60	144608	hgsc.bcm.edu	37	12	14976553	14976553	+	Silent	SNP	G	G	C	rs17761825	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:14976553G>C	ENST00000330828.2	+	2	888	c.684G>C	c.(682-684)gcG>gcC	p.A228A	C12orf60_ENST00000527783.1_Intron	NM_175874.3	NP_787070.2	Q5U649	CL060_HUMAN	chromosome 12 open reading frame 60	228										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	9						TCCAAAAAGCGATAAAGACTA	0.363													C|||	526	0.105032	0.0545	0.1945	5008	,	,		18187	0.0317		0.1879	False		,,,				2504	0.1002				p.A228A		Atlas-SNP	.											.	C12orf60	31	.	0			c.G684C						PASS	.	C		289,4097		10,269,1914	40.0	40.0	40.0		684	2.5	0.0	12	dbSNP_123	40	1675,6909		169,1337,2786	no	coding-synonymous	C12orf60	NM_175874.3		179,1606,4700	CC,CG,GG		19.513,6.5891,15.1426		228/246	14976553	1964,11006	2193	4292	6485	SO:0001819	synonymous_variant	144608	exon2			AAAAGCGATAAAG	BC038836	CCDS8667.1	12p12.3	2012-08-16			ENSG00000182993	ENSG00000182993			28726	protein-coding gene	gene with protein product						12477932	Standard	NM_175874		Approved	MGC47869	uc001rcj.4	Q5U649	OTTHUMG00000167473	ENST00000330828.2:c.684G>C	12.37:g.14976553G>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_175874	A8K1M7|Q5XKK8|Q8IXY2	Silent	SNP	ENST00000330828.2	37	CCDS8667.1																																																																																			G|0.853;C|0.147	0.147	strong		0.363	C12orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394735.1	NM_175874	
DENND1C	79958	hgsc.bcm.edu	37	19	6468331	6468331	+	Missense_Mutation	SNP	T	T	C	rs62107586	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	227	0	0		WXS	Illumina HiSeq	Phase_I	181	181	1	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	
FAT1	2195	hgsc.bcm.edu	37	4	187541761	187541761	+	Silent	SNP	G	G	A	rs3733407	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187541761G>A	ENST00000441802.2	-	10	6188	c.5979C>T	c.(5977-5979)acC>acT	p.T1993T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1993	Cadherin 18. {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						TTTCGGCCTCGGTGGAATTCT	0.418										HNSCC(5;0.00058)			G|||	342	0.0682907	0.003	0.1499	5008	,	,		20962	0.1796		0.0338	False		,,,				2504	0.0194				p.T1993T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C5979T						PASS	.	G		39,3679		0,39,1820	220.0	220.0	220.0		5979	-10.5	0.0	4	dbSNP_107	220	252,7954		4,244,3855	no	coding-synonymous	FAT1	NM_005245.3		4,283,5675	AA,AG,GG		3.0709,1.049,2.4405		1993/4589	187541761	291,11633	1859	4103	5962	SO:0001819	synonymous_variant	2195	exon10			GGCCTCGGTGGAA	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.5979C>T	4.37:g.187541761G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	131	74	0.564885	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.921;A|0.079	0.079	strong		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
RAB8A	4218	hgsc.bcm.edu	37	19	16238279	16238279	+	Silent	SNP	C	C	T	rs1043308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	114	0	0		WXS	Illumina HiSeq	Phase_I	138	58	0.42029	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	
RAPSN	5913	hgsc.bcm.edu	37	11	47470345	47470345	+	Missense_Mutation	SNP	G	G	A	rs34312154	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47470345G>A	ENST00000298854.2	-	1	385	c.172C>T	c.(172-174)Cgc>Tgc	p.R58C	RAPSN_ENST00000529341.1_Missense_Mutation_p.R58C|RAPSN_ENST00000352508.3_Missense_Mutation_p.R58C|RAPSN_ENST00000524487.1_Missense_Mutation_p.R58C	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	58					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						TCCTTGTAGCGGCCCATCTCC	0.672													G|||	289	0.0577077	0.003	0.1023	5008	,	,		16716	0.005		0.1163	False		,,,				2504	0.0941				p.R58C		Atlas-SNP	.											.	RAPSN	27	.	0			c.C172T						PASS	.	G	CYS/ARG,CYS/ARG	99,4303	79.9+/-118.3	1,97,2103	97.0	92.0	94.0		172,172	5.4	1.0	11	dbSNP_126	94	918,7678	203.2+/-246.3	50,818,3430	yes	missense,missense	RAPSN	NM_005055.4,NM_032645.4	180,180	51,915,5533	AA,AG,GG		10.6794,2.249,7.8243	probably-damaging,probably-damaging	58/413,58/354	47470345	1017,11981	2201	4298	6499	SO:0001583	missense	5913	exon1			TGTAGCGGCCCAT		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.172C>T	11.37:g.47470345G>A	ENSP00000298854:p.Arg58Cys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_032645	Q8TDF3|Q9BTD9	Missense_Mutation	SNP	ENST00000298854.2	37	CCDS7936.1	138	0.06318681318681318	2	0.0040650406504065045	38	0.10497237569060773	5	0.008741258741258742	93	0.12269129287598944	G	26.8	4.776946	0.90195	0.02249	0.106794	ENSG00000165917	ENST00000298854;ENST00000352508;ENST00000524487;ENST00000529341	D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);Rapsyn, myristoylation/linker region, N-terminal (1);	0.046635	0.85682	D	0.000000	T	0.07773	0.0195	L	0.36672	1.1	0.09310	P	0.999993847	P;D;D	0.76494	0.477;0.998;0.999	B;P;P	0.59703	0.227;0.711;0.862	T	0.61491	-0.7052	9	0.59425	D	0.04	-47.9804	13.34	0.60538	0.0:0.0:0.7354:0.2646	rs34312154	58;58;58	E9PK11;Q13702-2;Q13702	.;.;RAPSN_HUMAN	C	58	ENSP00000298854:R58C;ENSP00000298853:R58C;ENSP00000435551:R58C;ENSP00000431732:R58C	ENSP00000298854:R58C	R	-	1	0	RAPSN	47426921	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.474000	0.66781	2.553000	0.86117	0.460000	0.39030	CGC	G|0.928;A|0.072	0.072	strong		0.672	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1		
SERHL2	253190	hgsc.bcm.edu	37	22	42970004	42970004	+	Silent	SNP	G	G	C	rs147451679	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:42970004G>C	ENST00000327678.5	+	12	990	c.888G>C	c.(886-888)gtG>gtC	p.V296V	SERHL2_ENST00000407614.4_Silent_p.V116V|SERHL2_ENST00000335879.5_Silent_p.V232V|RRP7B_ENST00000357802.2_RNA|SERHL2_ENST00000340239.4_3'UTR	NM_014509.3	NP_055324.2	Q9NQF3	SERHL_HUMAN	serine hydrolase-like 2	169							hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|lung(3)|skin(1)|stomach(1)	8						CCCAGCACGTGGCCAGTATCA	0.577																																					p.V296V		Atlas-SNP	.											SERHL2,NS,carcinoma,0,3	SERHL2	23	3	0			c.G888C						scavenged	.						132.0	116.0	121.0					22																	42970004		2203	4299	6502	SO:0001819	synonymous_variant	253190	exon12			GCACGTGGCCAGT		CCDS14037.1, CCDS63498.1	22q13	2005-08-09			ENSG00000183569	ENSG00000183569			29446	protein-coding gene	gene with protein product							Standard	NM_014509		Approved		uc003bcr.3	Q9H4I8	OTTHUMG00000150892	ENST00000327678.5:c.888G>C	22.37:g.42970004G>C		Somatic	398	0	0		WXS	Illumina HiSeq	Phase_I	611	72	0.11784	NM_014509	Q5JZ95|Q9UH21	Silent	SNP	ENST00000327678.5	37	CCDS14037.1																																																																																			G|0.998;C|0.002	0.002	strong		0.577	SERHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320454.1	NM_014509	
GPAM	57678	hgsc.bcm.edu	37	10	113920465	113920465	+	Silent	SNP	G	G	A	rs2277207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:113920465G>A	ENST00000348367.4	-	16	1853	c.1656C>T	c.(1654-1656)aaC>aaT	p.N552N	GPAM_ENST00000369425.1_Silent_p.N552N|GPAM_ENST00000423155.1_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	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	238	122	0.512605	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	
SHROOM3	57619	hgsc.bcm.edu	37	4	77675916	77675916	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77675916C>T	ENST00000296043.6	+	7	5233	c.4280C>T	c.(4279-4281)cCt>cTt	p.P1427L	RP11-359D14.2_ENST00000452412.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1427					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)			CAGTGGCCACCTCCTTCTCGA	0.592																																					p.P1427L		Atlas-SNP	.											SHROOM3,NS,carcinoma,+1,1	SHROOM3	134	1	0			c.C4280T						scavenged	.						57.0	48.0	51.0					4																	77675916		2203	4300	6503	SO:0001583	missense	57619	exon7			GGCCACCTCCTTC	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.4280C>T	4.37:g.77675916C>T	ENSP00000296043:p.Pro1427Leu	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	200	2	0.01	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	C	12.66	2.005454	0.35415	.	.	ENSG00000138771	ENST00000296043	T	0.22134	1.97	5.49	3.78	0.43462	.	0.699272	0.14116	N	0.340388	T	0.12987	0.0315	N	0.24115	0.695	0.09310	N	0.999997	B	0.06786	0.001	B	0.04013	0.001	T	0.31752	-0.9932	10	0.17832	T	0.49	-1.3662	8.6862	0.34238	0.0:0.7497:0.0:0.2503	.	1427	Q8TF72	SHRM3_HUMAN	L	1427	ENSP00000296043:P1427L	ENSP00000296043:P1427L	P	+	2	0	SHROOM3	77894940	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.622000	0.24433	0.884000	0.36064	0.655000	0.94253	CCT	.	.	none		0.592	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
SLC22A15	55356	hgsc.bcm.edu	37	1	116534852	116534852	+	Silent	SNP	C	C	T	rs4046190	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:116534852C>T	ENST00000369503.4	+	2	418	c.288C>T	c.(286-288)tcC>tcT	p.S96S	SLC22A15_ENST00000369502.1_Silent_p.S96S	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	96					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		GCTTCACCTCCATCGCCTCGG	0.478													C|||	2180	0.435304	0.1362	0.4827	5008	,	,		19432	0.4196		0.6441	False		,,,				2504	0.6074				p.S96S		Atlas-SNP	.											.	SLC22A15	65	.	0			c.C288T						PASS	.	C		810,3202		98,614,1294	27.0	27.0	27.0		288	3.3	1.0	1	dbSNP_108	27	5201,3149		1625,1951,599	no	coding-synonymous	SLC22A15	NM_018420.2		1723,2565,1893	TT,TC,CC		37.7126,20.1894,48.6248		96/548	116534852	6011,6351	2006	4175	6181	SO:0001819	synonymous_variant	55356	exon2			CACCTCCATCGCC	AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"""Solute carriers"""	20301	protein-coding gene	gene with protein product		608275	"""solute carrier family 22 (organic cation transporter), member 15"""			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.288C>T	1.37:g.116534852C>T		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Silent	SNP	ENST00000369503.4	37	CCDS44198.1																																																																																			C|0.564;T|0.436	0.436	strong		0.478	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420	
CEP164	22897	hgsc.bcm.edu	37	11	117267884	117267884	+	Missense_Mutation	SNP	A	A	G	rs573455	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:117267884A>G	ENST00000278935.3	+	27	3503	c.3356A>G	c.(3355-3357)cAg>cGg	p.Q1119R	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1119			Q -> R (in dbSNP:rs573455). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		TTCCTTGTGCAGCAGACACGC	0.617													G|||	2320	0.463259	0.5318	0.3386	5008	,	,		20013	0.381		0.5358	False		,,,				2504	0.4693				p.Q1122R		Atlas-SNP	.											.	CEP164	121	.	0			c.A3365G						PASS	.	G	ARG/GLN	2256,2146	581.7+/-385.4	566,1124,511	58.0	53.0	55.0		3356	-1.7	0.0	11	dbSNP_83	55	4681,3911	546.4+/-385.0	1291,2099,906	yes	missense	CEP164	NM_014956.4	43	1857,3223,1417	GG,GA,AA		45.5191,48.7506,46.6138	benign	1119/1461	117267884	6937,6057	2201	4296	6497	SO:0001583	missense	22897	exon26			TTGTGCAGCAGAC	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.3356A>G	11.37:g.117267884A>G	ENSP00000278935:p.Gln1119Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	1010	0.4624542124542125	248	0.5040650406504065	141	0.38950276243093923	219	0.38286713286713286	402	0.5303430079155673	G	0.004	-2.309267	0.00237	0.512494	0.544809	ENSG00000110274	ENST00000278935	T	0.18016	2.24	4.87	-1.69	0.08186	.	0.590552	0.14128	N	0.339568	T	0.00012	0.0000	N	0.03154	-0.405	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	0.41840	-0.9486	9	0.02654	T	1	-3.174	10.3014	0.43654	0.4933:0.0:0.5067:0.0	rs573455;rs3210734;rs17309657;rs52838154;rs59395518;rs573455	893;1119;1122	Q9NTH6;Q9UPV0;Q9UPV0-2	.;CE164_HUMAN;.	R	1119	ENSP00000278935:Q1119R	ENSP00000278935:Q1119R	Q	+	2	0	CEP164	116773094	0.000000	0.05858	0.006000	0.13384	0.032000	0.12392	-0.650000	0.05378	-0.916000	0.03818	-1.861000	0.00560	CAG	A|0.498;G|0.502	0.502	strong		0.617	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
PLG	5340	hgsc.bcm.edu	37	6	161132146	161132146	+	Silent	SNP	C	C	T	rs4757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	233	0	0		WXS	Illumina HiSeq	Phase_I	260	107	0.411538	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	
SYK	6850	hgsc.bcm.edu	37	9	93637015	93637015	+	Silent	SNP	C	C	T	rs2290890	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:93637015C>T	ENST00000375754.4	+	9	1213	c.1065C>T	c.(1063-1065)ccC>ccT	p.P355P	SYK_ENST00000375747.1_Silent_p.P332P|SYK_ENST00000375751.4_Silent_p.P332P|SYK_ENST00000375746.1_Silent_p.P355P	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	355	Interdomain B.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						ACGCGGACCCCGAGGAGATCA	0.562			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	981	0.195887	0.2088	0.366	5008	,	,		17794	0.2321		0.1362	False		,,,				2504	0.0818				p.P355P		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.C1065T						PASS	.	C	,,,	918,3488	352.6+/-311.8	90,738,1375	145.0	159.0	154.0		996,1065,996,1065	-8.3	0.4	9	dbSNP_100	154	1216,7384	245.4+/-274.3	88,1040,3172	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	178,1778,4547	TT,TC,CC		14.1395,20.8352,16.4078	,,,	332/613,355/636,332/613,355/636	93637015	2134,10872	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon9			GGACCCCGAGGAG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1065C>T	9.37:g.93637015C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			C|0.825;T|0.175	0.175	strong		0.562	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
CHFR	55743	hgsc.bcm.edu	37	12	133423662	133423662	+	Missense_Mutation	SNP	C	C	T	rs2306536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:133423662C>T	ENST00000432561.2	-	15	1811	c.1738G>A	c.(1738-1740)Gtg>Atg	p.V580M	CHFR_ENST00000443047.2_Missense_Mutation_p.V488M|CHFR_ENST00000315585.7_Missense_Mutation_p.V539M|CHFR_ENST00000266880.7_Missense_Mutation_p.V579M|CHFR_ENST00000537522.1_Missense_Mutation_p.V202M|CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000450056.2_Missense_Mutation_p.V568M|CHFR_ENST00000541341.1_Missense_Mutation_p.V7M			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	580			V -> M (common polymorphism; dbSNP:rs2306536). {ECO:0000269|PubMed:10935642, ECO:0000269|PubMed:11948416, ECO:0000269|PubMed:14702039}.		mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TGGAGAGCCACGAGGCTCTCG	0.507													C|||	1000	0.199681	0.2753	0.1427	5008	,	,		18582	0.0665		0.2058	False		,,,				2504	0.2689				p.V580M		Atlas-SNP	.											CHFR_ENST00000432561,colon,carcinoma,0,2	CHFR	83	2	0			c.G1738A	GRCh37	CM084783	CHFR	M	rs2306536	PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1238,3168	426.4+/-341.1	187,864,1152	133.0	138.0	137.0		1738,1735,1702,1462,1615	-2.6	0.0	12	dbSNP_100	137	1673,6927	308.2+/-308.8	160,1353,2787	yes	missense,missense,missense,missense,missense	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	21,21,21,21,21	347,2217,3939	TT,TC,CC		19.4535,28.098,22.382	benign,benign,benign,benign,benign	580/665,579/664,568/653,488/573,539/624	133423662	2911,10095	2203	4300	6503	SO:0001583	missense	55743	exon15			GAGCCACGAGGCT	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1738G>A	12.37:g.133423662C>T	ENSP00000392395:p.Val580Met	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Missense_Mutation	SNP	ENST00000432561.2	37	CCDS53849.1	364	0.16666666666666666	121	0.2459349593495935	55	0.15193370165745856	35	0.06118881118881119	153	0.20184696569920843	C	6.429	0.447239	0.12223	0.28098	0.194535	ENSG00000072609	ENST00000315585;ENST00000443047;ENST00000450056;ENST00000266880;ENST00000537522;ENST00000432561	T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52	5.64	-2.61	0.06171	.	0.724852	0.13465	N	0.385827	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B;B	0.24186	0.06;0.061;0.036;0.061;0.099	B;B;B;B;B	0.22601	0.04;0.03;0.013;0.03;0.04	T	0.38950	-0.9637	9	0.48119	T	0.1	-13.553	1.7815	0.03032	0.1432:0.2711:0.3167:0.269	rs2306536;rs3210617;rs52806127;rs60167259;rs2306536	488;579;580;568;539	Q96EP1-5;Q96EP1-4;Q96EP1;Q96EP1-2;Q96EP1-3	.;.;CHFR_HUMAN;.;.	M	539;488;568;579;202;580	ENSP00000320557:V539M;ENSP00000416431:V488M;ENSP00000398735:V568M;ENSP00000266880:V579M;ENSP00000442327:V202M;ENSP00000392395:V580M	ENSP00000266880:V579M	V	-	1	0	CHFR	131933735	0.035000	0.19736	0.012000	0.15200	0.117000	0.20001	0.255000	0.18333	-0.397000	0.07691	-0.258000	0.10820	GTG	C|0.795;T|0.205	0.205	strong		0.507	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
MAPT	4137	hgsc.bcm.edu	37	17	44067400	44067400	+	Missense_Mutation	SNP	T	T	C	rs10445337	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44067400T>C	ENST00000571987.1	+	7	1339	c.1339T>C	c.(1339-1341)Tcc>Ccc	p.S447P	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.S447P|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.S447P|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.S447P|MAPT_ENST00000535772.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	447			S -> P (in dbSNP:rs10445337). {ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TTCTGTCACTTCCCGAACTGG	0.532													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		17709	0.001		0.2406	False		,,,				2504	0.0613				p.S447P		Atlas-SNP	.											.	MAPT	135	.	0			c.T1339C						PASS	.	C	PRO/SER,,,,,,PRO/SER,	225,4181	804.2+/-415.7	6,213,1984	125.0	126.0	125.0		1339,,,,,,1339,	4.1	1.0	17	dbSNP_119	125	1917,6683	721.4+/-406.4	220,1477,2603	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	74,,,,,,74,	226,1690,4587	CC,CT,TT		22.2907,5.1067,16.4693	benign,,,,,,benign,	447/777,,,,,,447/759,	44067400	2142,10864	2203	4300	6503	SO:0001583	missense	4137	exon8			GTCACTTCCCGAA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1339T>C	17.37:g.44067400T>C	ENSP00000458742:p.Ser447Pro	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	4.363	0.066874	0.08388	0.051067	0.222907	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.22539	1.95;1.95;1.95	5.17	4.14	0.48551	.	0.000000	0.41396	N	0.000891	T	0.00012	0.0000	N	0.00436	-1.5	0.09310	P	0.9999999999986787	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37842	-0.9688	9	0.02654	T	1	-9.971	6.5764	0.22569	0.0:0.7842:0.0:0.2158	rs10445337;rs52822487;rs10445337	447;447	P10636-9;P10636	.;TAU_HUMAN	P	447	ENSP00000340820:S447P;ENSP00000262410:S447P;ENSP00000410838:S447P	ENSP00000262410:S447P	S	+	1	0	MAPT	41423237	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.033000	0.30191	1.427000	0.47276	-0.320000	0.08662	TCC	T|0.856;C|0.144	0.144	strong		0.532	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
TRIM48	79097	hgsc.bcm.edu	37	11	55029787	55029787	+	Splice_Site	SNP	G	G	A	rs12799381	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	165	0	0		WXS	Illumina HiSeq	Phase_I	147	66	0.44898	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
SYNE4	163183	hgsc.bcm.edu	37	19	36499173	36499173	+	Silent	SNP	C	C	T	rs2285424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36499173C>T	ENST00000324444.3	-	2	336	c.225G>A	c.(223-225)ccG>ccA	p.P75P	AC002116.8_ENST00000473572.2_RNA|ALKBH6_ENST00000495116.2_5'Flank|SYNE4_ENST00000340477.5_Silent_p.P75P	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	75					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											TTGACCATCTCGGGGGGTGAG	0.652													T|||	1616	0.322684	0.6112	0.4006	5008	,	,		16536	0.2153		0.159	False		,,,				2504	0.1564				p.P75P		Atlas-SNP	.											.	.	.	.	0			c.G225A						PASS	.	T		2041,1845		535,971,437	50.0	57.0	54.0		225	-2.1	0.0	19	dbSNP_100	54	1391,6881		108,1175,2853	no	coding-synonymous	C19orf46	NM_001039876.1		643,2146,3290	TT,TC,CC		16.8158,47.4781,28.2283		75/405	36499173	3432,8726	1943	4136	6079	SO:0001819	synonymous_variant	163183	exon2			CCATCTCGGGGGG	BC038360	CCDS42553.1	19q13.12	2014-01-28	2012-05-31	2012-05-31	ENSG00000181392	ENSG00000181392			26703	protein-coding gene	gene with protein product		615535	"""chromosome 19 open reading frame 46"", ""deafness, autosomal recessive 76"""	C19orf46, DFNB76		23348741	Standard	XM_005258597		Approved	FLJ36445, Nesprin-4, Nesp4	uc002ocq.1	Q8N205	OTTHUMG00000048135	ENST00000324444.3:c.225G>A	19.37:g.36499173C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_001039876	A8MRS0|A8MYE3|Q7Z7L3	Silent	SNP	ENST00000324444.3	37	CCDS42553.1	664	0.304029304029304	291	0.5914634146341463	114	0.3149171270718232	138	0.24125874125874125	121	0.15963060686015831	T	6.092	0.385312	0.11524	0.525219	0.168158	ENSG00000181392	ENST00000503121	.	.	.	4.22	-2.1	0.07210	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	9.99999999995449E-6	.	.	.	.	.	.	T	0.44997	-0.9291	3	.	.	.	-12.4381	7.6711	0.28460	0.0:0.1916:0.4832:0.3252	rs2285424;rs2285424	.	.	.	Q	63	.	.	R	-	2	0	C19orf46	41191013	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.306000	0.08178	-0.673000	0.05259	-1.006000	0.02489	CGA	C|0.707;T|0.293	0.293	strong		0.652	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876	
PSG1	5669	hgsc.bcm.edu	37	19	43373078	43373078	+	Missense_Mutation	SNP	C	C	G	rs143301512	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43373078C>G	ENST00000436291.2	-	4	934	c.818G>C	c.(817-819)tGg>tCg	p.W273S	PSG1_ENST00000595124.1_Missense_Mutation_p.W180S|PSG1_ENST00000244296.2_Missense_Mutation_p.W273S|PSG1_ENST00000595356.1_Missense_Mutation_p.W273S|PSG1_ENST00000312439.6_Missense_Mutation_p.W273S|PSG1_ENST00000403380.3_Missense_Mutation_p.W180S	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	273	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				ATTTAGCCACCAAATGTAGGT	0.473													.|||	158	0.0315495	0.0038	0.0576	5008	,	,		20871	0.0		0.0984	False		,,,				2504	0.0143				p.W273S		Atlas-SNP	.											.	PSG1	196	.	0			c.G818C						PASS	.	C	SER/TRP,SER/TRP,SER/TRP	57,2961		1,55,1453	67.0	75.0	72.0		818,818,818	1.5	0.0	19	dbSNP_134	72	503,4907		30,443,2232	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	177,177,177	31,498,3685	GG,GC,CC		9.2976,1.8887,6.6445	,,	273/420,273/418,273/427	43373078	560,7868	1509	2705	4214	SO:0001583	missense	5669	exon4			AGCCACCAAATGT		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.818G>C	19.37:g.43373078C>G	ENSP00000413041:p.Trp273Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	23	0.338235	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	107	0.04899267399267399	1	0.0020325203252032522	26	0.0718232044198895	1	0.0017482517482517483	79	0.10422163588390501	N	8.612	0.889433	0.17540	0.018887	0.092976	ENSG00000231924	ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	1.51	1.51	0.23008	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14700	0.0355	H	0.98426	4.23	0.80722	P	0.0	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.999;1.0;0.997;0.994	T	0.65557	-0.6139	8	0.51188	T	0.08	.	6.307	0.21145	0.0:1.0:0.0:0.0	.	273;180;273;180;273;145;273	P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;B4DTG5;P11464-2	.;.;PSG1_HUMAN;.;.;.;.	S	273;180;273;273	ENSP00000413041:W273S;ENSP00000385386:W180S;ENSP00000308970:W273S;ENSP00000244296:W273S	ENSP00000244296:W273S	W	-	2	0	PSG1	48064918	0.003000	0.15002	0.004000	0.12327	0.003000	0.03518	0.905000	0.28504	0.785000	0.33685	0.195000	0.17529	TGG	C|0.944;G|0.056	0.056	strong		0.473	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
DNASE2B	58511	hgsc.bcm.edu	37	1	84878228	84878228	+	Splice_Site	SNP	C	C	T	rs7511984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	44	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	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
C1QTNF9B	387911	hgsc.bcm.edu	37	13	24465537	24465537	+	Missense_Mutation	SNP	C	C	T	rs140860568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:24465537C>T	ENST00000382140.2	-	5	953	c.893G>A	c.(892-894)gGg>gAg	p.G298E	MIPEP_ENST00000469167.1_5'Flank|C1QTNF9B-AS1_ENST00000382133.4_RNA|MIPEP_ENST00000382172.3_5'Flank|C1QTNF9B-AS1_ENST00000435039.2_RNA|C1QTNF9B-AS1_ENST00000417034.1_RNA|C1QTNF9B_ENST00000556521.1_5'UTR|C1QTNF9B_ENST00000382137.3_Missense_Mutation_p.G298E|C1QTNF9B_ENST00000382145.1_3'UTR			B2RNN3	C1T9B_HUMAN	C1q and tumor necrosis factor related protein 9B	298	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(1)	6						CATCTCATCCCCGAGCTTCAG	0.512													C|||	50	0.00998403	0.0023	0.0187	5008	,	,		16761	0.0		0.0308	False		,,,				2504	0.0031				p.G298E		Atlas-SNP	.											.	C1QTNF9B	27	.	0			c.G893A						PASS	.	C	GLU/GLY,,	34,4310		6,22,2144	92.0	91.0	91.0		893,,	3.1	1.0	13	dbSNP_134	91	276,8220		29,218,4001	no	missense,utr-5,utr-5	C1QTNF9B,C1QTNF9B-AS1	NM_001007537.1,NM_001014442.2,NM_001135816.1	98,,	35,240,6145	TT,TC,CC		3.2486,0.7827,2.4143	probably-damaging,,	298/334,,	24465537	310,12530	2172	4248	6420	SO:0001583	missense	387911	exon3			TCATCCCCGAGCT	BC110413	CCDS31947.1	13q12.12	2011-05-08			ENSG00000205863	ENSG00000205863			34072	protein-coding gene	gene with protein product		614148				17544811	Standard	NM_001007537		Approved	CTRP9B	uc010tcv.1	B2RNN3	OTTHUMG00000016570	ENST00000382140.2:c.893G>A	13.37:g.24465537C>T	ENSP00000371575:p.Gly298Glu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	213	99	0.464789	NM_001007537	A2A3T6|B9EH31|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Missense_Mutation	SNP	ENST00000382140.2	37	CCDS31947.1	31	0.014194139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	20	0.026385224274406333	c	17.20	3.329762	0.60743	0.007827	0.032486	ENSG00000205863	ENST00000382137;ENST00000382140	D;D	0.82255	-1.59;-1.59	3.96	3.08	0.35506	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.100850	0.64402	D	0.000002	T	0.80401	0.4616	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85108	0.0961	10	0.49607	T	0.09	.	13.6179	0.62120	0.0:0.8431:0.1569:0.0	.	298	B2RNN3	C1T9B_HUMAN	E	298	ENSP00000371572:G298E;ENSP00000371575:G298E	ENSP00000371572:G298E	G	-	2	0	C1QTNF9B	23363537	1.000000	0.71417	0.954000	0.39281	0.593000	0.36681	5.940000	0.70187	0.762000	0.33152	0.456000	0.33151	GGG	C|0.980;T|0.020	0.020	strong		0.512	C1QTNF9B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044162.3	NM_001007537	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455971	5455971	+	Missense_Mutation	SNP	G	G	T	rs8103406	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5455971G>T	ENST00000222033.4	+	1	546	c.469G>T	c.(469-471)Gcc>Tcc	p.A157S		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	157	PA.		A -> S (in dbSNP:rs8103406).	AIV -> SIA (in Ref. 4; AAH17592). {ECO:0000305}.		cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		CTCTCTGGGCGCCATCGTGCT	0.682													G|||	2713	0.541733	0.3585	0.4971	5008	,	,		15533	0.753		0.5278	False		,,,				2504	0.6176				p.A157S		Atlas-SNP	.											.	ZNRF4	59	.	0			c.G469T						PASS	.	G	SER/ALA	1582,2672		336,910,881	27.0	31.0	30.0		469	-2.2	0.0	19	dbSNP_116	30	4185,4267		1076,2033,1117	no	missense	ZNRF4	NM_181710.3	99	1412,2943,1998	TT,TG,GG		49.5149,37.1885,45.388	benign	157/430	5455971	5767,6939	2127	4226	6353	SO:0001583	missense	148066	exon1			CTGGGCGCCATCG	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.469G>T	19.37:g.5455971G>T	ENSP00000222033:p.Ala157Ser	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	1225	0.5608974358974359	185	0.37601626016260165	200	0.5524861878453039	447	0.7814685314685315	393	0.5184696569920845	G	6.035	0.374881	0.11409	0.371885	0.495149	ENSG00000105428	ENST00000222033	T	0.05996	3.36	4.65	-2.19	0.07015	Protease-associated domain, PA (1);	0.532164	0.18743	U	0.132384	T	0.00012	0.0000	N	0.13327	0.33	0.80722	P	0.0	P	0.35527	0.507	B	0.40410	0.328	T	0.04140	-1.0974	9	0.20519	T	0.43	-12.463	8.1434	0.31097	0.0:0.1176:0.3591:0.5233	rs8103406;rs17205855;rs17845552;rs17858449;rs61351917;rs8103406	157	Q8WWF5	ZNRF4_HUMAN	S	157	ENSP00000222033:A157S	ENSP00000222033:A157S	A	+	1	0	ZNRF4	5406971	0.024000	0.19004	0.000000	0.03702	0.066000	0.16364	0.569000	0.23638	-0.062000	0.13088	0.491000	0.48974	GCC	G|0.460;T|0.540	0.540	strong		0.682	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
ZNF593	51042	hgsc.bcm.edu	37	1	26496651	26496651	+	Silent	SNP	T	T	C	rs7087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26496651T>C	ENST00000374266.5	+	1	290	c.177T>C	c.(175-177)ggT>ggC	p.G59G	RP11-96L14.7_ENST00000448923.1_RNA|RP11-96L14.7_ENST00000444682.1_RNA|RP11-96L14.7_ENST00000433939.1_RNA|ZNF593_ENST00000270812.5_Silent_p.G59G|RP11-96L14.7_ENST00000414762.1_RNA|RP11-96L14.7_ENST00000407889.2_RNA	NM_015871.4	NP_056955.2	O00488	ZN593_HUMAN	zinc finger protein 593	59					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			large_intestine(4)|prostate(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)		CAGGGGGCGGTCTGCACCGCT	0.706											OREG0013262	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2678	0.534744	0.6301	0.5504	5008	,	,		13465	0.6429		0.2992	False		,,,				2504	0.5256				p.G59G		Atlas-SNP	.											.	ZNF593	6	.	0			c.T177C						PASS	.	C		2355,1869		730,895,487	6.0	8.0	7.0		177	3.7	1.0	1	dbSNP_52	7	2256,6012		382,1492,2260	no	coding-synonymous	ZNF593	NM_015871.4		1112,2387,2747	CC,CT,TT		27.2859,44.2472,36.9116		59/135	26496651	4611,7881	2112	4134	6246	SO:0001819	synonymous_variant	51042	exon1			GGGCGGTCTGCAC	D45213	CCDS275.2	1p35.3	2012-10-05			ENSG00000142684	ENSG00000142684			30943	protein-coding gene	gene with protein product						9115366	Standard	NM_015871		Approved	ZT86	uc001bll.4	O00488	OTTHUMG00000007538	ENST00000374266.5:c.177T>C	1.37:g.26496651T>C		Somatic	10	0	0	787	WXS	Illumina HiSeq	Phase_I	11	6	0.545455	NM_015871	B2R4S0|Q5T2H7	Silent	SNP	ENST00000374266.5	37	CCDS275.2																																																																																			T|0.484;C|0.516	0.516	strong		0.706	ZNF593-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019842.2	NM_015871	
MTTP	4547	hgsc.bcm.edu	37	4	100521805	100521805	+	Missense_Mutation	SNP	A	A	C	rs17029215	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100521805A>C	ENST00000265517.5	+	9	1354	c.1151A>C	c.(1150-1152)gAc>gCc	p.D384A	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.D384A|MTTP_ENST00000511045.1_Missense_Mutation_p.D411A			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	384	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		D -> A (in dbSNP:rs17029215). {ECO:0000269|PubMed:8939939}.		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)	TTCAAAAGTGACAGCAGCATT	0.433													A|||	354	0.0706869	0.1876	0.036	5008	,	,		14436	0.0		0.0437	False		,,,				2504	0.0378				p.D384A		Atlas-SNP	.											.	MTTP	127	.	0			c.A1151C	GRCh37	CM057721	MTTP	M	rs17029215	PASS	.	A	ALA/ASP	683,3723	287.5+/-279.3	63,557,1583	108.0	107.0	107.0		1151	1.0	0.4	4	dbSNP_123	107	338,8262	116.6+/-176.3	5,328,3967	yes	missense	MTTP	NM_000253.2	126	68,885,5550	CC,CA,AA		3.9302,15.5016,7.8502	benign	384/895	100521805	1021,11985	2203	4300	6503	SO:0001583	missense	4547	exon10			AAAGTGACAGCAG		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.1151A>C	4.37:g.100521805A>C	ENSP00000265517:p.Asp384Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	109	0.04990842490842491	69	0.1402439024390244	10	0.027624309392265192	0	0.0	30	0.0395778364116095	A	3.302	-0.142690	0.06669	0.155016	0.039302	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.38077	1.16;1.16;1.16	4.86	0.96	0.19631	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2);	0.664814	0.16092	N	0.230019	T	0.00073	0.0002	L	0.29908	0.895	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.09377	0.004;0.002	T	0.21042	-1.0257	10	0.07030	T	0.85	-13.1503	5.1756	0.15133	0.4765:0.2925:0.2309:0.0	rs17029215;rs52803046;rs17029215	411;384	E9PBP6;P55157	.;MTP_HUMAN	A	411;384;384;384	ENSP00000427679:D411A;ENSP00000400821:D384A;ENSP00000265517:D384A	ENSP00000265517:D384A	D	+	2	0	MTTP	100740828	0.513000	0.26194	0.449000	0.26957	0.842000	0.47809	0.954000	0.29175	-0.062000	0.13088	0.533000	0.62120	GAC	A|0.929;C|0.071	0.071	strong		0.433	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
PATE1	160065	hgsc.bcm.edu	37	11	125617606	125617606	+	Missense_Mutation	SNP	G	G	A	rs537916	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:125617606G>A	ENST00000305738.5	+	4	148	c.136G>A	c.(136-138)Gtt>Att	p.V46I	PATE1_ENST00000437148.2_Missense_Mutation_p.V34I	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	46			V -> I (in dbSNP:rs537916).			extracellular region (GO:0005576)				large_intestine(1)|lung(5)	6						GATAGAAATTGTTCAGTGTAG	0.493													G|||	1373	0.274161	0.2073	0.2925	5008	,	,		21088	0.2282		0.334	False		,,,				2504	0.3374				p.V46I		Atlas-SNP	.											.	PATE1	21	.	0			c.G136A						PASS	.	G	ILE/VAL	1010,3392	374.9+/-321.4	128,754,1319	89.0	85.0	87.0		136	-6.2	0.0	11	dbSNP_83	87	3043,5555	468.7+/-367.4	533,1977,1789	yes	missense	PATE1	NM_138294.2	29	661,2731,3108	AA,AG,GG		35.392,22.9441,31.1769	benign	46/127	125617606	4053,8947	2201	4299	6500	SO:0001583	missense	160065	exon4			GAAATTGTTCAGT	AF462605	CCDS8464.1	11q24.2	2008-12-17				ENSG00000171053		"""PATE family"""	24664	protein-coding gene	gene with protein product	"""expressed in prostate and testis"""	606861				11880645, 15798027	Standard	NM_138294		Approved	PATE	uc001qct.3	Q8WXA2		ENST00000305738.5:c.136G>A	11.37:g.125617606G>A	ENSP00000307164:p.Val46Ile	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_138294	Q3KNX2	Missense_Mutation	SNP	ENST00000305738.5	37	CCDS8464.1	594	0.27197802197802196	99	0.20121951219512196	101	0.27900552486187846	139	0.243006993006993	255	0.33641160949868076	G	7.495	0.651394	0.14516	0.229441	0.35392	ENSG00000171053	ENST00000305738;ENST00000437148	T;T	0.27557	1.66;1.66	4.19	-6.17	0.02091	.	1.053100	0.07597	N	0.923050	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.12837	0.005;0.008	T	0.36578	-0.9742	9	0.26408	T	0.33	-0.0242	13.5369	0.61652	0.8035:0.0:0.1965:0.0	rs537916;rs1365079;rs58817293	34;46	Q8WXA2-2;Q8WXA2	.;PATE1_HUMAN	I	46;34	ENSP00000307164:V46I;ENSP00000396056:V34I	ENSP00000307164:V46I	V	+	1	0	PATE1	125122816	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	-1.626000	0.02035	-1.459000	0.01914	-0.140000	0.14226	GTT	G|0.697;A|0.303	0.303	strong		0.493	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386726.2	NM_138294	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416649	105416649	+	Silent	SNP	G	G	A	rs28593209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105416649G>A	ENST00000333244.5	-	7	5258	c.5139C>T	c.(5137-5139)gcC>gcT	p.A1713A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1713						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)			CCTCCAGGTCGGCGGAAGGGG	0.637													.|||	1387	0.276957	0.053	0.3674	5008	,	,		15025	0.0853		0.5398	False		,,,				2504	0.4427				p.A1713A		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	0			c.C5139T						PASS	.	A		503,3245		91,321,1462	103.0	122.0	116.0		5139	-6.8	0.0	14	dbSNP_125	116	4424,3718		1413,1598,1060	no	coding-synonymous	AHNAK2	NM_138420.2		1504,1919,2522	AA,AG,GG		45.6645,13.4205,41.4382		1713/5796	105416649	4927,6963	1874	4071	5945	SO:0001819	synonymous_variant	113146	exon7			CAGGTCGGCGGAA	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.5139C>T	14.37:g.105416649G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	235	235	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.650;A|0.350	0.350	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
C9orf84	158401	hgsc.bcm.edu	37	9	114490308	114490308	+	Missense_Mutation	SNP	T	T	C	rs7470491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114490308T>C	ENST00000318737.4	-	11	1375	c.1247A>G	c.(1246-1248)cAt>cGt	p.H416R	C9orf84_ENST00000394777.4_Missense_Mutation_p.H377R|C9orf84_ENST00000374287.3_Missense_Mutation_p.H416R|C9orf84_ENST00000394779.3_Missense_Mutation_p.H377R	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	416			H -> R (in dbSNP:rs7470491).							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						AGGTGAAGAATGACTTTTATG	0.333													t|||	4145	0.827676	0.7882	0.866	5008	,	,		19012	0.9266		0.7883	False		,,,				2504	0.7924				p.H416R		Atlas-SNP	.											.	C9orf84	207	.	0			c.A1247G						PASS	.	C	ARG/HIS,ARG/HIS	3535,871	736.9+/-410.8	1431,673,99	55.0	51.0	53.0		1130,1247	-3.1	0.0	9	dbSNP_116	53	6679,1917	722.8+/-406.4	2591,1497,210	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	29,29	4022,2170,309	CC,CT,TT		22.3011,19.7685,21.4429	benign,benign	377/1406,416/1445	114490308	10214,2788	2203	4298	6501	SO:0001583	missense	158401	exon11			GAAGAATGACTTT	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.1247A>G	9.37:g.114490308T>C	ENSP00000322108:p.His416Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	1839	0.842032967032967	400	0.8130081300813008	313	0.8646408839779005	526	0.9195804195804196	600	0.7915567282321899	t	0.004	-2.266479	0.00259	0.802315	0.776989	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.36	-3.13	0.05266	.	1.258710	0.05077	N	0.482765	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.24119	-1.0169	9	0.11794	T	0.64	6.0728	5.8347	0.18601	0.1277:0.4094:0.0:0.4629	rs7470491;rs17734330;rs57078232;rs7470491	377;416;377	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	R	377;377;30;416;416	ENSP00000378259:H377R;ENSP00000378257:H377R;ENSP00000363405:H416R;ENSP00000322108:H416R	ENSP00000322108:H416R	H	-	2	0	C9orf84	113530129	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.273000	0.08548	-0.440000	0.07211	-1.156000	0.01807	CAT	T|0.172;C|0.828	0.828	strong		0.333	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
MMEL1	79258	hgsc.bcm.edu	37	1	2560903	2560903	+	Silent	SNP	T	T	G	rs4648659	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:2560903T>G	ENST00000378412.3	-	2	182	c.21A>C	c.(19-21)ccA>ccC	p.P7P	MMEL1_ENST00000288709.6_5'UTR|MMEL1_ENST00000502556.1_Silent_p.P7P|MMEL1_ENST00000511099.1_5'Flank			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	7						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		CCATCCCCACTGGGCCTTCGG	0.721													-|||	2583	0.515775	0.4334	0.5519	5008	,	,		11780	0.4683		0.6909	False		,,,				2504	0.4703				p.P7P		Atlas-SNP	.											.	MMEL1	64	.	0			c.A21C						PASS	.	G		1843,1861		506,831,515	9.0	10.0	10.0		21	-6.5	0.0	1	dbSNP_111	10	5044,2006		1842,1360,323	no	coding-synonymous	MMEL1	NM_033467.3		2348,2191,838	GG,GT,TT		28.4539,49.757,35.9587		7/780	2560903	6887,3867	1852	3525	5377	SO:0001819	synonymous_variant	79258	exon2			CCCCACTGGGCCT	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.21A>C	1.37:g.2560903T>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2																																																																																			T|0.424;G|0.576	0.576	strong		0.721	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
TTN	7273	hgsc.bcm.edu	37	2	179427536	179427536	+	Missense_Mutation	SNP	T	T	C	rs3829746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179427536T>C	ENST00000591111.1	-	276	78624	c.78400A>G	c.(78400-78402)Ata>Gta	p.I26134V	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I27775V|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I18835V|TTN_ENST00000460472.2_Missense_Mutation_p.I18710V|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I18902V|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I25207V|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26134	Fibronectin type-III 90. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> V. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTTCTCTTATGGTCAAATTC	0.408													C|||	2546	0.508387	0.5658	0.4078	5008	,	,		21726	0.7153		0.2535	False		,,,				2504	0.5511				p.I27775V		Atlas-SNP	.											.	TTN	18412	.	0			c.A83323G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	2013,1773		546,921,426	64.0	58.0	60.0		56704,56503,75619,56128	5.2	1.0	2	dbSNP_107	60	1841,6417		193,1455,2481	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	739,2376,2907	CC,CT,TT		22.2935,46.8304,31.9993	benign,benign,benign,benign	18902/27119,18835/27052,25207/33424,18710/26927	179427536	3854,8190	1893	4129	6022	SO:0001583	missense	7273	exon326			CTCTTATGGTCAA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78400A>G	2.37:g.179427536T>C	ENSP00000465570:p.Ile26134Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		980	0.44871794871794873	281	0.5711382113821138	129	0.356353591160221	385	0.6730769230769231	185	0.24406332453825857	C	9.433	1.086053	0.20390	0.531696	0.222935	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	6.04	5.15	0.70609	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02275	-0.615	0.39703	P	0.028781999999999974	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.37314	-0.9711	8	0.87932	D	0	.	9.6301	0.39774	0.0:0.6833:0.0:0.3167	rs3829746;rs11565883;rs56750589;rs3829746	18710;18835;18902;26134	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	25207;18710;18902;18835;18708	ENSP00000343764:I25207V;ENSP00000434586:I18710V;ENSP00000340554:I18902V;ENSP00000352154:I18835V	ENSP00000340554:I18902V	I	-	1	0	TTN	179135782	0.155000	0.22806	0.994000	0.49952	0.900000	0.52787	0.683000	0.25349	0.883000	0.36040	-0.215000	0.12644	ATA	T|0.555;C|0.445	0.445	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LAMA3	3909	hgsc.bcm.edu	37	18	21494509	21494509	+	Missense_Mutation	SNP	C	C	T	rs147463397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:21494509C>T	ENST00000313654.9	+	57	7706	c.7465C>T	c.(7465-7467)Cgg>Tgg	p.R2489W	LAMA3_ENST00000399516.3_Missense_Mutation_p.R2433W|LAMA3_ENST00000587184.1_Missense_Mutation_p.R824W|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.R880W	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2489	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AGTTATGGATCGGGTGAAATT	0.488																																					p.R2489W		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7465T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	75.0	70.0	71.0		2638,7297,2470,7465	4.4	1.0	18	dbSNP_134	71	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	101,101,101,101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	880/1725,2433/3278,824/1669,2489/3334	21494509	3,13003	2203	4300	6503	SO:0001583	missense	3909	exon57			ATGGATCGGGTGA	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.7465C>T	18.37:g.21494509C>T	ENSP00000324532:p.Arg2489Trp	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206989	0.58343	0.0	3.49E-4	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.80566	-1.39;-1.39;-1.39	5.25	4.36	0.52297	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.88973	0.6583	M	0.73598	2.24	0.49915	D	0.999836	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.992;0.989	D	0.90115	0.4195	9	0.72032	D	0.01	.	15.1212	0.72443	0.1427:0.8573:0.0:0.0	.	824;880;2433;2489	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	W	2489;2433;880	ENSP00000324532:R2489W;ENSP00000382432:R2433W;ENSP00000269217:R880W	ENSP00000269217:R880W	R	+	1	2	LAMA3	19748507	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	2.974000	0.49272	1.179000	0.42884	0.561000	0.74099	CGG	C|1.000;T|0.000	0.000	strong		0.488	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
KRT10	3858	hgsc.bcm.edu	37	17	38978462	38978462	+	Missense_Mutation	SNP	C	C	T	rs77919366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38978462C>T	ENST00000269576.5	-	1	385	c.376G>A	c.(376-378)Ggc>Agc	p.G126S	TMEM99_ENST00000496847.1_Intron|TMEM99_ENST00000301665.3_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	126	Gly-rich.|Head.		G -> S (in dbSNP:rs77919366). {ECO:0000269|PubMed:7512983}.		cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)	p.G126S(1)		NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				cctccaaagccgcctccaCCA	0.557													C|||	665	0.132788	0.0703	0.1816	5008	,	,		11883	0.0377		0.2296	False		,,,				2504	0.181				p.G126S		Atlas-SNP	.											KRT10,NS,carcinoma,0,1	KRT10	56	1	1	Substitution - Missense(1)	prostate(1)	c.G376A						PASS	.	C	,,,SER/GLY	440,3964	209.8+/-230.5	29,382,1791	54.0	47.0	50.0		,,,376	-0.9	0.5	17	dbSNP_131	50	1968,6632	336.7+/-322.0	221,1526,2553	yes	intron,intron,intron,missense	KRT10,TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3,NM_000421.3	,,,56	250,1908,4344	TT,TC,CC		22.8837,9.9909,18.5174	,,,benign	,,,126/585	38978462	2408,10596	2202	4300	6502	SO:0001583	missense	3858	exon1			CAAAGCCGCCTCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.376G>A	17.37:g.38978462C>T	ENSP00000269576:p.Gly126Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	125	71	0.568	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	37	CCDS11377.1	302	0.1382783882783883	32	0.06504065040650407	71	0.19613259668508287	17	0.02972027972027972	182	0.24010554089709762	C	7.168	0.586981	0.13749	0.099909	0.228837	ENSG00000186395	ENST00000269576	D	0.82433	-1.61	0.445	-0.891	0.10573	.	0.536646	0.15796	N	0.244207	T	0.00039	0.0001	L	0.39898	1.24	0.58432	P	5.999999999950489E-6	B	0.17268	0.021	B	0.04013	0.001	T	0.02484	-1.1152	8	0.39692	T	0.17	.	.	.	.	.	126	P13645	K1C10_HUMAN	S	126	ENSP00000269576:G126S	ENSP00000269576:G126S	G	-	1	0	KRT10	36231988	0.002000	0.14202	0.500000	0.27589	0.782000	0.44232	0.081000	0.14823	-0.330000	0.08514	0.372000	0.22366	GGC	C|0.838;T|0.162	0.162	strong		0.557	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
COASY	80347	hgsc.bcm.edu	37	17	40716520	40716520	+	Silent	SNP	A	A	G	rs598126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40716520A>G	ENST00000393818.2	+	3	1428	c.972A>G	c.(970-972)acA>acG	p.T324T	MLX_ENST00000246912.4_5'Flank|MLX_ENST00000435881.2_5'Flank|MLX_ENST00000346833.4_5'Flank|COASY_ENST00000420359.1_Silent_p.T324T|COASY_ENST00000421097.2_Silent_p.T324T|COASY_ENST00000590958.1_Silent_p.T353T|COASY_ENST00000449624.1_Silent_p.T29T|RP11-400F19.8_ENST00000585572.1_RNA	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	324	Phosphopantetheine adenylyltransferase.				cell death (GO:0008219)|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)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		TCAGACATACAGAGAATGAAG	0.532													A|||	2527	0.504593	0.4198	0.487	5008	,	,		19784	0.4534		0.5229	False		,,,				2504	0.6656				p.T353T		Atlas-SNP	.											.	COASY	45	.	0			c.A1059G						PASS	.	A	,,,,	1861,2545	537.8+/-374.8	382,1097,724	69.0	70.0	70.0		972,972,87,1059,972	-7.1	0.0	17	dbSNP_83	70	4663,3937	603.4+/-394.7	1281,2101,918	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COASY	NM_001042529.1,NM_001042530.1,NM_001042531.1,NM_001042532.2,NM_025233.5	,,,,	1663,3198,1642	GG,GA,AA		45.7791,42.2379,49.8385	,,,,	324/565,324/565,29/270,353/594,324/565	40716520	6524,6482	2203	4300	6503	SO:0001819	synonymous_variant	80347	exon5			ACATACAGAGAAT	AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"""Coenzyme A synthase"""			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.972A>G	17.37:g.40716520A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_001042532	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Silent	SNP	ENST00000393818.2	37	CCDS11429.1																																																																																			A|0.515;G|0.485	0.485	strong		0.532	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233	
SLC35E4	339665	hgsc.bcm.edu	37	22	31032881	31032881	+	Silent	SNP	G	G	A	rs8136373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	42	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	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	
OR10T2	128360	hgsc.bcm.edu	37	1	158368964	158368964	+	Missense_Mutation	SNP	C	C	T	rs61818749	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158368964C>T	ENST00000334438.1	-	1	292	c.293G>A	c.(292-294)tGt>tAt	p.C98Y		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	98						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)					CTGGGTGGCACAGGCCATGAA	0.493													C|||	511	0.102037	0.003	0.0793	5008	,	,		21687	0.1369		0.1113	False		,,,				2504	0.2065				p.C98Y		Atlas-SNP	.											.	OR10T2	76	.	0			c.G293A						PASS	.	C	TYR/CYS	105,4301	82.4+/-120.9	1,103,2099	105.0	106.0	106.0		293	4.6	1.0	1	dbSNP_129	106	856,7744	195.2+/-240.5	45,766,3489	yes	missense	OR10T2	NM_001004475.1	194	46,869,5588	TT,TC,CC		9.9535,2.3831,7.3889	probably-damaging	98/315	158368964	961,12045	2203	4300	6503	SO:0001583	missense	128360	exon1			GTGGCACAGGCCA	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.293G>A	1.37:g.158368964C>T	ENSP00000334115:p.Cys98Tyr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	201	0.09203296703296704	4	0.008130081300813009	29	0.08011049723756906	95	0.1660839160839161	73	0.09630606860158311	C	16.33	3.093779	0.56075	0.023831	0.099535	ENSG00000186306	ENST00000334438	T	0.00547	6.66	4.56	4.56	0.56223	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42548	U	0.000691	T	0.02929	0.0087	H	0.97918	4.105	0.21627	P	0.999610839	D	0.89917	1.0	D	0.91635	0.999	T	0.02288	-1.1182	9	0.87932	D	0	.	16.2659	0.82579	0.0:1.0:0.0:0.0	rs61818749	98	Q8NGX3	O10T2_HUMAN	Y	98	ENSP00000334115:C98Y	ENSP00000334115:C98Y	C	-	2	0	OR10T2	156635588	1.000000	0.71417	1.000000	0.80357	0.326000	0.28443	7.166000	0.77553	2.355000	0.79922	0.650000	0.86243	TGT	C|0.918;T|0.082	0.082	strong		0.493	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
IKBKAP	8518	hgsc.bcm.edu	37	9	111663793	111663793	+	Silent	SNP	C	C	T	rs10979605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111663793C>T	ENST00000374647.5	-	18	2233	c.1926G>A	c.(1924-1926)acG>acA	p.T642T	IKBKAP_ENST00000537196.1_Silent_p.T293T	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	642					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						CTGCAAATGACGTGATATTTG	0.418													C|||	396	0.0790735	0.1755	0.0346	5008	,	,		19704	0.0		0.0915	False		,,,				2504	0.0491				p.T642T		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G1926A						PASS	.	C		654,3752	279.9+/-275.1	53,548,1602	129.0	109.0	116.0		1926	-6.5	0.9	9	dbSNP_120	116	702,7898	173.9+/-224.3	30,642,3628	no	coding-synonymous	IKBKAP	NM_003640.3		83,1190,5230	TT,TC,CC		8.1628,14.8434,10.426		642/1333	111663793	1356,11650	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon18			AAATGACGTGATA	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.1926G>A	9.37:g.111663793C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			C|0.909;T|0.091	0.091	strong		0.418	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
ADAM21	8747	hgsc.bcm.edu	37	14	70924697	70924697	+	Missense_Mutation	SNP	A	A	G	rs386778613|rs45545935	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.						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	145	0	0		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	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		
MYH15	22989	hgsc.bcm.edu	37	3	108117612	108117612	+	Missense_Mutation	SNP	G	G	A	rs76478083	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:108117612G>A	ENST00000273353.3	-	36	5121	c.5065C>T	c.(5065-5067)Cgc>Tgc	p.R1689C		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1689						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						AGAGAGTTGCGCCGCTCAGCC	0.542													G|||	17	0.00339457	0.0	0.0086	5008	,	,		18223	0.0		0.0089	False		,,,				2504	0.002				p.R1689C		Atlas-SNP	.											.	MYH15	223	.	0			c.C5065T						PASS	.	G	CYS/ARG	8,4152		0,8,2072	169.0	174.0	172.0		5065	-4.3	0.0	3	dbSNP_131	172	82,8358		0,82,4138	yes	missense	MYH15	NM_014981.1	180	0,90,6210	AA,AG,GG		0.9716,0.1923,0.7143	probably-damaging	1689/1947	108117612	90,12510	2080	4220	6300	SO:0001583	missense	22989	exon36			AGTTGCGCCGCTC	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.5065C>T	3.37:g.108117612G>A	ENSP00000273353:p.Arg1689Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	16.31	3.086630	0.55861	0.001923	0.009716	ENSG00000144821	ENST00000273353	D	0.83163	-1.69	5.5	-4.34	0.03666	Myosin tail (1);	.	.	.	.	D	0.87220	0.6123	M	0.91406	3.205	0.19575	N	0.999966	D	0.89917	1.0	D	0.77004	0.989	T	0.81176	-0.1052	9	0.87932	D	0	.	6.4453	0.21873	0.245:0.0:0.2714:0.4836	.	1689	Q9Y2K3	MYH15_HUMAN	C	1689	ENSP00000273353:R1689C	ENSP00000273353:R1689C	R	-	1	0	MYH15	109600302	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.354000	0.07681	-0.890000	0.03945	0.655000	0.94253	CGC	G|0.993;A|0.007	0.007	strong		0.542	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
NPAP1	23742	hgsc.bcm.edu	37	15	24922208	24922208	+	Silent	SNP	C	C	G	rs12905237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:24922208C>G	ENST00000329468.2	+	1	1668	c.1194C>G	c.(1192-1194)gcC>gcG	p.A398A		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	398	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)											CCCAGCCTGCCCCTTCTTTCT	0.527													C|||	615	0.122804	0.0787	0.0821	5008	,	,		17130	0.1528		0.17	False		,,,				2504	0.1319				p.A398A		Atlas-SNP	.											.	.	.	.	0			c.C1194G						PASS	.	C		401,4005		16,369,1818	69.0	70.0	70.0		1194	-0.1	0.0	15	dbSNP_121	70	1404,7196		115,1174,3011	no	coding-synonymous	C15orf2	NM_018958.2		131,1543,4829	GG,GC,CC		16.3256,9.1012,13.8782		398/1157	24922208	1805,11201	2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			GCCTGCCCCTTCT	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.1194C>G	15.37:g.24922208C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			C|0.867;G|0.133	0.133	strong		0.527	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744829	23744829	+	Silent	SNP	C	C	T	rs79723196|rs35076736|rs67447855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23744829C>T	ENST00000357460.5	-	2	1772	c.1608G>A	c.(1606-1608)gaG>gaA	p.E536E	HOMEZ_ENST00000431326.2_Silent_p.E538E|HOMEZ_ENST00000561013.1_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	109	0	0		WXS	Illumina HiSeq	Phase_I	105	14	0.133333	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	
OR5AR1	219493	hgsc.bcm.edu	37	11	56431834	56431834	+	Missense_Mutation	SNP	A	A	G	rs56067375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56431834A>G	ENST00000302969.2	+	1	697	c.673A>G	c.(673-675)Atc>Gtc	p.I225V		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	225			I -> V (in dbSNP:rs56067375).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I225V(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						CCTTGTTGCAATCATCAGAAT	0.468													A|||	270	0.0539137	0.0287	0.0159	5008	,	,		22087	0.0913		0.0547	False		,,,				2504	0.0757				p.I225V		Atlas-SNP	.											OR5AR1,NS,carcinoma,0,1	OR5AR1	68	1	1	Substitution - Missense(1)	stomach(1)	c.A673G						PASS	.	A	VAL/ILE	135,4267	96.2+/-134.9	1,133,2067	165.0	140.0	148.0		673	4.9	0.9	11	dbSNP_129	148	481,8111	140.8+/-197.2	13,455,3828	yes	missense	OR5AR1	NM_001004730.1	29	14,588,5895	GG,GA,AA		5.5982,3.0668,4.7406	benign	225/311	56431834	616,12378	2201	4296	6497	SO:0001583	missense	219493	exon1			GTTGCAATCATCA	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"""GPCR / Class A : Olfactory receptors"""	15260	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AR, member 1"""				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.673A>G	11.37:g.56431834A>G	ENSP00000302639:p.Ile225Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_001004730	Q6IF61	Missense_Mutation	SNP	ENST00000302969.2	37	CCDS31535.1	96	0.04395604395604396	12	0.024390243902439025	6	0.016574585635359115	41	0.07167832167832168	37	0.048812664907651716	A	9.001	0.980067	0.18812	0.030668	0.055982	ENSG00000172459	ENST00000302969	T	0.00024	8.98	4.91	4.91	0.64330	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000181	T	0.00012	0.0000	N	0.12502	0.225	0.26938	N	0.966306	B	0.24882	0.113	B	0.23574	0.047	T	0.10870	-1.0611	10	0.40728	T	0.16	.	8.2745	0.31864	0.9023:0.0:0.0977:0.0	rs56067375;rs61743856	225	Q8NGP9	O5AR1_HUMAN	V	225	ENSP00000302639:I225V	ENSP00000302639:I225V	I	+	1	0	OR5AR1	56188410	0.001000	0.12720	0.915000	0.36163	0.217000	0.24651	0.024000	0.13555	2.064000	0.61679	0.467000	0.42956	ATC	A|0.952;G|0.048	0.048	strong		0.468	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730	
FPR1	2357	hgsc.bcm.edu	37	19	52249702	52249702	+	Silent	SNP	G	G	T	rs2070746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	44	21	0.477273	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	
PXDNL	137902	hgsc.bcm.edu	37	8	52366200	52366200	+	Silent	SNP	G	G	A	rs6473599	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:52366200G>A	ENST00000356297.4	-	10	1228	c.1128C>T	c.(1126-1128)caC>caT	p.H376H	PXDNL_ENST00000543296.1_Silent_p.H376H	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	376	Ig-like C2-type 2.				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)				ACGTTGCCACGTGCCTGGATC	0.517													G|||	3736	0.746006	0.4841	0.9193	5008	,	,		16932	0.6915		0.9274	False		,,,				2504	0.8466				p.H376H		Atlas-SNP	.											.	PXDNL	414	.	0			c.C1128T						PASS	.	G		2474,1700		724,1026,337	130.0	130.0	130.0		1128	0.5	0.0	8	dbSNP_116	130	7911,497		3723,465,16	no	coding-synonymous	PXDNL	NM_144651.4		4447,1491,353	AA,AG,GG		5.911,40.7283,17.4615		376/1464	52366200	10385,2197	2087	4204	6291	SO:0001819	synonymous_variant	137902	exon10			TGCCACGTGCCTG		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.1128C>T	8.37:g.52366200G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	227	226	0.995595	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	37	CCDS47855.1																																																																																			G|0.234;A|0.764	0.764	strong		0.517	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
MBD3L2	125997	hgsc.bcm.edu	37	19	7051376	7051376	+	Missense_Mutation	SNP	G	G	A	rs200081225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7051376G>A	ENST00000381393.3	+	2	423	c.370G>A	c.(370-372)Ggt>Agt	p.G124S		NM_144614.3	NP_653215.2	Q8NHZ7	MB3L2_HUMAN	methyl-CpG binding domain protein 3-like 2	124				G -> S (in Ref. 1; AAM28154 and 3; BE502398). {ECO:0000305}.						endometrium(1)	1	all_hematologic(4;0.166)			Lung(535;0.179)		GGGGACGGCCGGTGAATCTCT	0.637													-|||	3194	0.63778	0.562	0.6931	5008	,	,		28287	0.6002		0.659	False		,,,				2504	0.7178				p.G124S		Atlas-SNP	.											MBD3L2,cerebellum,glioma,0,1	MBD3L2	2	1	0			c.G370A						scavenged	.						1.0	1.0	1.0					19																	7051376		536	1374	1910	SO:0001583	missense	125997	exon2			ACGGCCGGTGAAT	AF503919	CCDS42483.1	19p13.3	2011-01-31			ENSG00000230522	ENSG00000230522			18532	protein-coding gene	gene with protein product		607964					Standard	NM_144614		Approved		uc010dvf.1	Q8NHZ7		ENST00000381393.3:c.370G>A	19.37:g.7051376G>A	ENSP00000370800:p.Gly124Ser	Somatic	257	121	0.470817		WXS	Illumina HiSeq	Phase_I	180	37	0.205556	NM_144614		Missense_Mutation	SNP	ENST00000381393.3	37	CCDS42483.1	.	.	.	.	.	.	.	.	.	.	.	5.414	0.261475	0.10239	.	.	ENSG00000230522	ENST00000412046;ENST00000381393	.	.	.	0.791	-0.446	0.12238	.	.	.	.	.	T	0.23611	0.0571	L	0.54323	1.7	0.80722	P	0.0	P	0.51537	0.946	B	0.41088	0.347	T	0.33007	-0.9885	7	0.08837	T	0.75	-14.6112	3.2492	0.06808	0.3319:0.0:0.6681:0.0	.	124	Q8NHZ7	MB3L2_HUMAN	S	124	.	ENSP00000370800:G124S	G	+	1	0	MBD3L2	7002376	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.103000	0.15292	-0.088000	0.12506	0.448000	0.29417	GGT	.	.	weak		0.637	MBD3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458499.1	NM_144614	
RRP12	23223	hgsc.bcm.edu	37	10	99155984	99155984	+	Silent	SNP	G	G	A	rs3814553	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99155984G>A	ENST00000370992.4	-	3	555	c.444C>T	c.(442-444)ttC>ttT	p.F148F	RRP12_ENST00000315563.6_Silent_p.F148F|RRP12_ENST00000414986.1_Silent_p.F148F	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	148						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CCAGAGCAGCGAAGTACTCAG	0.572													G|||	2024	0.404153	0.5507	0.3429	5008	,	,		3638	0.3125		0.337	False		,,,				2504	0.4131				p.F148F		Atlas-SNP	.											.	RRP12	97	.	0			c.C444T						PASS	.	G	,	2174,2232	585.8+/-386.3	545,1084,574	141.0	119.0	127.0		444,444	3.7	1.0	10	dbSNP_107	127	2742,5858	437.3+/-358.6	438,1866,1996	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	983,2950,2570	AA,AG,GG		31.8837,49.3418,37.7979	,	148/1237,148/1298	99155984	4916,8090	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon3			AGCAGCGAAGTAC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.444C>T	10.37:g.99155984G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001145114	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.618;A|0.382	0.382	strong		0.572	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
PKM	5315	hgsc.bcm.edu	37	15	72502141	72502141	+	Silent	SNP	G	G	A	rs10514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:72502141G>A	ENST00000335181.5	-	5	541	c.438C>T	c.(436-438)aaC>aaT	p.N146N	PKM_ENST00000568883.1_Intron|PKM_ENST00000319622.6_Silent_p.N146N|PKM_ENST00000565184.1_Silent_p.N146N|PKM_ENST00000449901.2_Silent_p.N131N|PKM_ENST00000565154.1_Silent_p.N146N|PKM_ENST00000389093.3_Silent_p.N146N|PKM_ENST00000568459.1_Silent_p.N146N	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	146					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	CCATGTAGGCGTTATCCAGCG	0.522													G|||	178	0.0355431	0.0212	0.049	5008	,	,		17244	0.0		0.0865	False		,,,				2504	0.0297				p.N220N		Atlas-SNP	.											.	PKM	25	.	0			c.C660T						PASS	.	G	,,,,,,	153,4245	104.3+/-142.8	5,143,2051	237.0	200.0	213.0		660,216,393,453,438,438,438	-10.9	0.0	15	dbSNP_52	213	726,7868	176.0+/-226.0	25,676,3596	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PKM2	NM_001206796.1,NM_001206797.1,NM_001206798.1,NM_001206799.1,NM_002654.4,NM_182470.2,NM_182471.2	,,,,,,	30,819,5647	AA,AG,GG		8.4478,3.4789,6.7657	,,,,,,	220/606,72/458,131/517,151/537,146/532,146/532,146/532	72502141	879,12113	2199	4297	6496	SO:0001819	synonymous_variant	5315	exon6			GTAGGCGTTATCC	M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.438C>T	15.37:g.72502141G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	192	94	0.489583	NM_001206796	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Silent	SNP	ENST00000335181.5	37	CCDS32284.1																																																																																			G|0.939;A|0.061	0.061	strong		0.522	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1		
OAS3	4940	hgsc.bcm.edu	37	12	113401199	113401199	+	Silent	SNP	G	G	A	rs45603631	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:113401199G>A	ENST00000228928.7	+	10	2345	c.2166G>A	c.(2164-2166)gcG>gcA	p.A722A	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	722	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						AAGCAGCAGCGCTGGGGATGC	0.657													G|||	413	0.0824681	0.0643	0.0807	5008	,	,		17696	0.0089		0.1541	False		,,,				2504	0.1104				p.A722A		Atlas-SNP	.											.	OAS3	63	.	0			c.G2166A						PASS	.	G		270,3680		9,252,1714	15.0	18.0	17.0		2166	0.2	0.0	12	dbSNP_127	17	1094,7062		79,936,3063	no	coding-synonymous	OAS3	NM_006187.2		88,1188,4777	AA,AG,GG		13.4134,6.8354,11.2671		722/1088	113401199	1364,10742	1975	4078	6053	SO:0001819	synonymous_variant	4940	exon10			AGCAGCGCTGGGG	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.2166G>A	12.37:g.113401199G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			G|0.911;A|0.089	0.089	strong		0.657	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
SURF6	6838	hgsc.bcm.edu	37	9	136199503	136199503	+	Missense_Mutation	SNP	G	G	A	rs886090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136199503G>A	ENST00000372022.4	-	4	752	c.487C>T	c.(487-489)Cgg>Tgg	p.R163W	SURF6_ENST00000468290.1_5'UTR	NM_006753.4	NP_006744.2	O75683	SURF6_HUMAN	surfeit 6	163			R -> W (in dbSNP:rs886090).		ribosome biogenesis (GO:0042254)	granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	12				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)		TCTTTCGCCCGCAGCTCCTTT	0.687													G|||	1417	0.282947	0.0386	0.3501	5008	,	,		15157	0.3075		0.3569	False		,,,				2504	0.4642				p.R163W		Atlas-SNP	.											.	SURF6	32	.	0			c.C487T						PASS	.	G	TRP/ARG	372,4034	184.3+/-211.7	20,332,1851	106.0	109.0	108.0		487	1.0	0.1	9	dbSNP_86	108	3018,5582	457.2+/-364.3	543,1932,1825	yes	missense	SURF6	NM_006753.4	101	563,2264,3676	AA,AG,GG		35.093,8.443,26.0649	probably-damaging	163/362	136199503	3390,9616	2203	4300	6503	SO:0001583	missense	6838	exon4			TCGCCCGCAGCTC	AF186772	CCDS6962.1	9q33-q34	2010-07-06			ENSG00000148296	ENSG00000148296			11478	protein-coding gene	gene with protein product	"""surfeit locus protein 6"""	185642				9740673, 15629442	Standard	NM_006753		Approved	FLJ30322, RRP14	uc004cdb.4	O75683	OTTHUMG00000020871	ENST00000372022.4:c.487C>T	9.37:g.136199503G>A	ENSP00000361092:p.Arg163Trp	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_006753	Q5T8U1|Q9BRK9|Q9BTZ5|Q9UK24	Missense_Mutation	SNP	ENST00000372022.4	37	CCDS6962.1	590	0.27014652014652013	31	0.06300813008130081	122	0.3370165745856354	160	0.27972027972027974	277	0.3654353562005277	G	10.01	1.233467	0.22626	0.08443	0.35093	ENSG00000148296	ENST00000372022	T	0.15718	2.4	4.42	1.02	0.19986	.	0.655439	0.14812	N	0.296982	T	0.00012	0.0000	L	0.56769	1.78	0.46149	P	0.0011010000000000186	D	0.76494	0.999	D	0.63033	0.91	T	0.42241	-0.9463	9	0.66056	D	0.02	-1.4527	6.6473	0.22943	0.1205:0.0:0.4417:0.4377	rs886090;rs17293245;rs58674881;rs886090	163	O75683	SURF6_HUMAN	W	163	ENSP00000361092:R163W	ENSP00000361092:R163W	R	-	1	2	SURF6	135189324	0.028000	0.19301	0.112000	0.21494	0.571000	0.35966	0.524000	0.22940	0.029000	0.15352	0.467000	0.42956	CGG	G|0.745;A|0.255	0.255	strong		0.687	SURF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054905.1	NM_006753	
ACTG1	71	hgsc.bcm.edu	37	17	79478007	79478007	+	Silent	SNP	G	G	A	rs1135989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79478007G>A	ENST00000575842.1	-	4	1356	c.930C>T	c.(928-930)gcC>gcT	p.A310A	ACTG1_ENST00000331925.2_Silent_p.A310A|AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000573283.1_Silent_p.A310A|ACTG1_ENST00000575087.1_Silent_p.A310A			P63261	ACTG_HUMAN	actin, gamma 1	310					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			GCATCCTGTCGGCAATGCCCG	0.612													g|||	928	0.185304	0.1505	0.2522	5008	,	,		20969	0.005		0.3966	False		,,,				2504	0.1534				p.A310A		Atlas-SNP	.											.	ACTG1	55	.	0			c.C930T						PASS	.	G	,	852,3554	331.0+/-301.8	89,674,1440	67.0	64.0	65.0		930,930	-6.6	0.6	17	dbSNP_86	65	3263,5337	483.9+/-371.3	603,2057,1640	no	coding-synonymous,coding-synonymous	ACTG1	NM_001199954.1,NM_001614.3	,	692,2731,3080	AA,AG,GG		37.9419,19.3373,31.6392	,	310/376,310/376	79478007	4115,8891	2203	4300	6503	SO:0001819	synonymous_variant	71	exon5			CCTGTCGGCAATG		CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"""deafness, autosomal dominant 20; deafness, autosomal dominant 26"""	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.930C>T	17.37:g.79478007G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Silent	SNP	ENST00000575842.1	37	CCDS11782.1																																																																																			G|0.711;A|0.289	0.289	strong		0.612	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614	
IFNA10	3446	hgsc.bcm.edu	37	9	21206605	21206605	+	Missense_Mutation	SNP	C	C	G	rs28368148	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21206605C>G	ENST00000357374.2	-	1	537	c.492G>C	c.(490-492)tgG>tgC	p.W164C		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	164					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)		TGACAACCTCCCAGGCACAAG	0.428													c|||	23	0.00459265	0.0008	0.0058	5008	,	,		18519	0.0		0.0129	False		,,,				2504	0.0051				p.W164C		Atlas-SNP	.											.	IFNA10	29	.	0			c.G492C						PASS	.	C	CYS/TRP	8,4398		0,8,2195	250.0	255.0	253.0		492	3.8	1.0	9	dbSNP_125	253	119,8481		1,117,4182	no	missense	IFNA10	NM_002171.1	215	1,125,6377	GG,GC,CC		1.3837,0.1816,0.9765	probably-damaging	164/190	21206605	127,12879	2203	4300	6503	SO:0001583	missense	3446	exon1			AACCTCCCAGGCA		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.492G>C	9.37:g.21206605C>G	ENSP00000369566:p.Trp164Cys	Somatic	475	0	0		WXS	Illumina HiSeq	Phase_I	564	265	0.469858	NM_002171	Q5VV13	Missense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	13	0.005952380952380952	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	8	0.010554089709762533	-	15.33	2.801079	0.50315	0.001816	0.013837	ENSG00000186803	ENST00000357374	T	0.43294	0.95	3.75	3.75	0.43078	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.85682	D	0.000000	T	0.64472	0.2601	M	0.93678	3.445	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.77789	-0.2456	10	0.87932	D	0	.	12.9165	0.58209	0.0:1.0:0.0:0.0	rs28368148	164	P01566	IFN10_HUMAN	C	164	ENSP00000369566:W164C	ENSP00000369566:W164C	W	-	3	0	IFNA10	21196605	1.000000	0.71417	0.988000	0.46212	0.926000	0.56050	2.348000	0.44045	1.806000	0.52798	0.499000	0.49734	TGG	C|0.991;G|0.009	0.009	strong		0.428	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171	
PRR27	401137	hgsc.bcm.edu	37	4	71024481	71024481	+	Missense_Mutation	SNP	A	A	G	rs138334849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024481A>G	ENST00000344526.5	+	3	701	c.512A>G	c.(511-513)gAg>gGg	p.E171G	C4orf40_ENST00000502294.1_Missense_Mutation_p.E171G|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		171	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)		p.E171G(1)		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						CCTGCTGCAGAGGCACCTGTT	0.627																																					p.E171G		Atlas-SNP	.											C4orf40,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	C4orf40	19	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A512G						PASS	.						34.0	34.0	34.0					4																	71024481		2203	4295	6498	SO:0001583	missense	401137	exon3			CTGCAGAGGCACC																												ENST00000344526.5:c.512A>G	4.37:g.71024481A>G	ENSP00000343172:p.Glu171Gly	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	145	36	0.248276	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	.	.	.	.	.	.	.	.	.	.	A	8.738	0.918381	0.17982	.	.	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.32515	1.45;1.45	4.38	-8.76	0.00830	.	.	.	.	.	T	0.12135	0.0295	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.22695	-1.0209	9	0.22706	T	0.39	0.3609	5.0407	0.14458	0.5399:0.1242:0.2596:0.0763	.	171	Q6MZM9	CD040_HUMAN	G	171	ENSP00000426249:E171G;ENSP00000343172:E171G	ENSP00000343172:E171G	E	+	2	0	C4orf40	71059070	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-4.211000	0.00273	-1.601000	0.01601	-0.817000	0.03123	GAG	A|0.981;G|0.019	0.019	strong		0.627	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
MLIP	90523	hgsc.bcm.edu	37	6	53883843	53883843	+	Missense_Mutation	SNP	G	G	A	rs17625497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:53883843G>A	ENST00000274897.5	+	1	130	c.17G>A	c.(16-18)cGt>cAt	p.R6H	MLIP_ENST00000370877.2_Missense_Mutation_p.R6H|MLIP_ENST00000509997.1_Missense_Mutation_p.R6H|MLIP_ENST00000514921.1_Missense_Mutation_p.R6H	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	6	Interaction with LMNA.		R -> H (in dbSNP:rs17625497).			nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						CTTGAAAAGCGTGAAAAAAGA	0.353													G|||	987	0.197085	0.1702	0.3991	5008	,	,		18877	0.0575		0.2853	False		,,,				2504	0.1431				p.R6H		Atlas-SNP	.											.	MLIP	84	.	0			c.G17A						PASS	.	G	HIS/ARG	804,3602	314.9+/-293.9	66,672,1465	60.0	64.0	62.0		17	3.5	1.0	6	dbSNP_123	62	2418,6182	396.8+/-345.5	321,1776,2203	yes	missense	MLIP	NM_138569.2	29	387,2448,3668	AA,AG,GG		28.1163,18.2478,24.7732		6/459	53883843	3222,9784	2203	4300	6503	SO:0001583	missense	90523	exon1			AAAAGCGTGAAAA	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"""muscle-enriched A-type lamin interacting protein"""	614106	"""chromosome 6 open reading frame 142"""	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.17G>A	6.37:g.53883843G>A	ENSP00000274897:p.Arg6His	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	120	46	0.383333	NM_138569	B7Z2N0|D6RE05|Q96H08|Q96NF7	Missense_Mutation	SNP	ENST00000274897.5	37	CCDS4954.1	468	0.21428571428571427	72	0.14634146341463414	141	0.38950276243093923	41	0.07167832167832168	214	0.28232189973614774	G	4.650	0.120805	0.08881	0.182478	0.281163	ENSG00000146147	ENST00000274897;ENST00000514921;ENST00000370877;ENST00000509997	T;T;T;T	0.24538	2.21;1.86;1.85;1.86	5.9	3.46	0.39613	.	1.095070	0.06929	N	0.810852	T	0.01489	0.0048	N	0.00436	-1.5	0.09310	P	0.999999999963233	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43097	-0.9412	9	0.02654	T	1	-9.0E-4	7.5222	0.27635	0.8049:0.0:0.0689:0.1262	rs17625497;rs56485234;rs60544912;rs17625497	6;6	Q5VWP3;D6RE05	MLIP_HUMAN;.	H	6	ENSP00000274897:R6H;ENSP00000425142:R6H;ENSP00000359914:R6H;ENSP00000427584:R6H	ENSP00000274897:R6H	R	+	2	0	MLIP	53991802	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.751000	0.55165	0.454000	0.26884	-0.295000	0.09555	CGT	G|0.784;A|0.216	0.216	strong		0.353	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569	
PSMD13	5719	hgsc.bcm.edu	37	11	244108	244108	+	Intron	SNP	A	A	G	rs7107362|rs373900649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244108A>G	ENST00000532097.1	+	3	713				PSMD13_ENST00000431206.2_Missense_Mutation_p.N55D|PSMD13_ENST00000352303.5_Intron	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13						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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCACTTTGAAAATGAGTGCAT	0.403													A|||	4083	0.815296	0.8918	0.83	5008	,	,		16372	0.8036		0.7306	False		,,,				2504	0.8006				p.N55D		Atlas-SNP	.											.	PSMD13	53	.	0			c.A163G						PASS	.	A	,ASP/ASN	3795,611		1714,367,122	56.0	62.0	60.0		,163	-2.2	0.0	11	dbSNP_116	60	6111,2487		2367,1377,555	yes	intron,missense	PSMD13	NM_002817.3,NM_175932.2	,23	4081,1744,677	GG,GA,AA		28.9253,13.8675,23.8234	,	,55/379	244108	9906,3098	2203	4299	6502	SO:0001627	intron_variant	5719	exon2			TTTGAAAATGAGT	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.209+33A>G	11.37:g.244108A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	1762	0.8067765567765568	440	0.8943089430894309	295	0.8149171270718232	471	0.8234265734265734	556	0.7335092348284961	A	12.87	2.068678	0.36470	0.861325	0.710747	ENSG00000185627	ENST00000431206	T	0.16324	2.35	5.94	-2.23	0.06930	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.20780	0.048	B	0.20577	0.03	T	0.15321	-1.0441	6	.	.	.	.	2.2649	0.04076	0.2823:0.2604:0.34:0.1173	rs7107362;rs7107362	55	Q9UNM6-2	.	D	55	ENSP00000396937:N55D	.	N	+	1	0	PSMD13	234108	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.240000	0.08952	-0.079000	0.12707	0.460000	0.39030	AAT	A|0.215;G|0.785	0.785	strong		0.403	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
ROS1	6098	hgsc.bcm.edu	37	6	117622184	117622184	+	Missense_Mutation	SNP	G	G	C	rs619203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:117622184G>C	ENST00000368508.3	-	42	6884	c.6686C>G	c.(6685-6687)tCc>tGc	p.S2229C	RN7SKP51_ENST00000410781.1_RNA|RN7SKP18_ENST00000516005.1_RNA|ROS1_ENST00000368507.3_Missense_Mutation_p.S2223C	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2229			S -> C (in dbSNP:rs619203). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2352949}.		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)	p.S2229C(1)	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)		TTCATCTCTGGACTTATAAAT	0.368			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								C|||	698	0.139377	0.0386	0.1657	5008	,	,		16550	0.1587		0.2197	False		,,,				2504	0.1544				p.S2229C		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	ROS1_ENST00000368508,NS,carcinoma,0,1	ROS1	728	1	1	Substitution - Missense(1)	stomach(1)	c.C6686G	GRCh37	CM053397	ROS1	M	rs619203	scavenged	.	C	CYS/SER	327,4079	795.4+/-415.3	16,295,1892	82.0	82.0	82.0		6686	2.2	0.0	6	dbSNP_83	82	2234,6366	708.8+/-405.7	266,1702,2332	yes	missense	ROS1	NM_002944.2	112	282,1997,4224	CC,CG,GG		25.9767,7.4217,19.6909	benign	2229/2348	117622184	2561,10445	2203	4300	6503	SO:0001583	missense	6098	exon42			TCTCTGGACTTAT	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.6686C>G	6.37:g.117622184G>C	ENSP00000357494:p.Ser2229Cys	Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	87	34	0.390805	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	348	0.15934065934065933	21	0.042682926829268296	62	0.1712707182320442	87	0.1520979020979021	178	0.23482849604221637	C	1.417	-0.573990	0.03882	0.074217	0.259767	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.71579	-0.58;-0.58	5.02	2.24	0.28232	.	0.679781	0.14728	N	0.301935	T	0.15782	0.0380	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07770	-1.0755	9	0.32370	T	0.25	.	2.0926	0.03660	0.2841:0.4357:0.1249:0.1553	rs619203;rs17555622;rs52793578;rs619203	2229	P08922	ROS1_HUMAN	C	2229;2223	ENSP00000357494:S2229C;ENSP00000357493:S2223C	ENSP00000357493:S2223C	S	-	2	0	ROS1	117728877	0.000000	0.05858	0.001000	0.08648	0.793000	0.44817	-0.046000	0.11983	0.089000	0.17243	-0.120000	0.15030	TCC	G|0.818;C|0.182	0.182	strong		0.368	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
CLEC18A	348174	hgsc.bcm.edu	37	16	69996928	69996928	+	Missense_Mutation	SNP	G	G	A	rs201545424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:69996928G>A	ENST00000288040.6	+	11	1448	c.1261G>A	c.(1261-1263)Gac>Aac	p.D421N	CLEC18A_ENST00000393701.2_Missense_Mutation_p.D421N|CLEC18A_ENST00000449317.2_Missense_Mutation_p.D430N|CLEC18A_ENST00000568461.1_Missense_Mutation_p.D421N	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	478	0	0		WXS	Illumina HiSeq	Phase_I	424	53	0.125	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	
PLD2	5338	hgsc.bcm.edu	37	17	4712617	4712617	+	Missense_Mutation	SNP	C	C	T	rs2286672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4712617C>T	ENST00000263088.6	+	6	645	c.514C>T	c.(514-516)Cgt>Tgt	p.R172C	PLD2_ENST00000572940.1_Missense_Mutation_p.R172C|RP11-81A22.5_ENST00000571067.1_lincRNA	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	172	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		R -> C (in dbSNP:rs2286672). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9761774}.		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)	TTACCTCAACCGTCTCTTGAC	0.522													C|||	963	0.192292	0.0053	0.1037	5008	,	,		18128	0.4177		0.0855	False		,,,				2504	0.3855				p.R172C		Atlas-SNP	.											.	PLD2	138	.	0			c.C514T						PASS	.	C	CYS/ARG	80,4326	68.7+/-106.4	1,78,2124	105.0	102.0	103.0		514	4.1	1.0	17	dbSNP_100	103	636,7964	163.9+/-216.4	22,592,3686	yes	missense	PLD2	NM_002663.4	180	23,670,5810	TT,TC,CC		7.3953,1.8157,5.5052	benign	172/934	4712617	716,12290	2203	4300	6503	SO:0001583	missense	5338	exon6			CTCAACCGTCTCT	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.514C>T	17.37:g.4712617C>T	ENSP00000263088:p.Arg172Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	362	0.16575091575091574	6	0.012195121951219513	36	0.09944751381215469	248	0.43356643356643354	72	0.09498680738786279	C	13.19	2.161949	0.38217	0.018157	0.073953	ENSG00000129219	ENST00000263088	T	0.44482	0.92	5.1	4.14	0.48551	Phox homologous domain (5);	0.671775	0.16371	N	0.217313	T	0.00012	0.0000	L	0.40543	1.245	0.26703	P	0.9711236	B;B;B	0.12630	0.006;0.001;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.39231	-0.9624	9	0.56958	D	0.05	-10.7169	7.1432	0.25568	0.0:0.7373:0.1722:0.0905	rs2286672;rs11545162;rs17851268;rs58863422;rs2286672	29;172;172	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	C	172	ENSP00000263088:R172C	ENSP00000263088:R172C	R	+	1	0	PLD2	4659581	0.001000	0.12720	1.000000	0.80357	0.984000	0.73092	0.854000	0.27791	1.396000	0.46663	0.561000	0.74099	CGT	C|0.890;T|0.110	0.110	strong		0.522	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
EMILIN3	90187	hgsc.bcm.edu	37	20	39990614	39990614	+	Missense_Mutation	SNP	C	C	T	rs2235592	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:39990614C>T	ENST00000332312.3	-	4	1787	c.1595G>A	c.(1594-1596)aGc>aAc	p.S532N		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	532			S -> N (in dbSNP:rs2235592). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TGCCACGAGGCTGTCCAGGAT	0.647													T|||	1418	0.283147	0.3139	0.3012	5008	,	,		18066	0.4772		0.2127	False		,,,				2504	0.1012				p.S532N		Atlas-SNP	.											.	EMILIN3	63	.	0			c.G1595A						PASS	.	T	ASN/SER	1419,2987	678.0+/-403.5	227,965,1011	58.0	59.0	58.0		1595	0.3	1.0	20	dbSNP_98	58	1628,6970	736.7+/-407.0	165,1298,2836	yes	missense	EMILIN3	NM_052846.1	46	392,2263,3847	TT,TC,CC		18.9346,32.2061,23.4313	benign	532/767	39990614	3047,9957	2203	4299	6502	SO:0001583	missense	90187	exon4			ACGAGGCTGTCCA	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1595G>A	20.37:g.39990614C>T	ENSP00000332806:p.Ser532Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Missense_Mutation	SNP	ENST00000332312.3	37	CCDS13316.1	687	0.31456043956043955	143	0.29065040650406504	99	0.27348066298342544	274	0.479020979020979	171	0.22559366754617413	T	0.015	-1.566276	0.00903	0.322061	0.189346	ENSG00000183798	ENST00000332312	T	0.13778	2.56	4.56	0.312	0.15837	.	0.972341	0.08500	N	0.936658	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44892	-0.9298	8	.	.	.	-6.6365	2.2658	0.04078	0.1108:0.2638:0.3711:0.2543	rs2235592	532	Q9NT22	EMIL3_HUMAN	N	532	ENSP00000332806:S532N	.	S	-	2	0	EMILIN3	39424028	0.054000	0.20591	0.964000	0.40570	0.647000	0.38526	-0.098000	0.11024	-0.055000	0.13244	-0.361000	0.07541	AGC	C|0.743;T|0.257	0.257	strong		0.647	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
CPB1	1360	hgsc.bcm.edu	37	3	148562310	148562310	+	Missense_Mutation	SNP	G	G	A	rs1059502	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148562310G>A	ENST00000491148.1	+	8	956	c.622G>A	c.(622-624)Gac>Aac	p.D208N	CPB1_ENST00000282957.4_Missense_Mutation_p.D208N			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	208			D -> N (in dbSNP:rs1059502). {ECO:0000269|PubMed:9524066}.			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)			AGAGCTTCTCGACAAGTTAGA	0.413													G|||	1353	0.270168	0.3495	0.1412	5008	,	,		16749	0.2956		0.2048	False		,,,				2504	0.2955				p.D208N		Atlas-SNP	.											.	CPB1	74	.	0			c.G622A						PASS	.	G	ASN/ASP	1358,3048	452.4+/-350.0	197,964,1042	111.0	91.0	98.0		622	-2.8	0.0	3	dbSNP_86	98	1769,6831	320.3+/-314.5	169,1431,2700	yes	missense	CPB1	NM_001871.2	23	366,2395,3742	AA,AG,GG		20.5698,30.8216,24.0427	benign	208/418	148562310	3127,9879	2203	4300	6503	SO:0001583	missense	1360	exon7			CTTCTCGACAAGT	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.622G>A	3.37:g.148562310G>A	ENSP00000417222:p.Asp208Asn	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	164	162	0.987805	NM_001871	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	37	CCDS33874.1	518	0.23717948717948717	166	0.33739837398373984	52	0.143646408839779	139	0.243006993006993	161	0.21240105540897097	G	0.010	-1.761315	0.00657	0.308216	0.205698	ENSG00000153002	ENST00000491148;ENST00000282957;ENST00000468341	T;T;T	0.32515	1.45;1.45;1.45	5.78	-2.76	0.05896	Peptidase M14, carboxypeptidase A (2);	0.697197	0.15191	N	0.275529	T	0.00012	0.0000	N	0.25094	0.71	0.58432	P	1.999999999946489E-6	B	0.12013	0.005	B	0.14023	0.01	T	0.42616	-0.9441	9	0.07482	T	0.82	.	10.2126	0.43150	0.3714:0.0838:0.5448:0.0	rs1059502;rs3200197;rs56471857;rs60324209;rs1059502	208	P15086	CBPB1_HUMAN	N	208;208;174	ENSP00000417222:D208N;ENSP00000282957:D208N;ENSP00000419427:D174N	ENSP00000282957:D208N	D	+	1	0	CPB1	150045000	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.672000	0.05244	-0.671000	0.05274	-2.480000	0.00198	GAC	G|0.743;A|0.257	0.257	strong		0.413	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871	
TMEM132A	54972	hgsc.bcm.edu	37	11	60696399	60696399	+	Missense_Mutation	SNP	G	G	A	rs61751216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60696399G>A	ENST00000453848.2	+	4	991	c.833G>A	c.(832-834)cGg>cAg	p.R278Q	TMEM132A_ENST00000005286.4_Missense_Mutation_p.R278Q			Q24JP5	T132A_HUMAN	transmembrane protein 132A	278						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						CTCCTGCTTCGGCACAACTTC	0.637													G|||	50	0.00998403	0.003	0.013	5008	,	,		17378	0.0		0.0328	False		,,,				2504	0.0041				p.R278Q		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G833A						PASS	.	G	GLN/ARG,GLN/ARG	27,4375		0,27,2174	39.0	39.0	39.0		833,833	2.8	0.8	11	dbSNP_129	39	347,8245		9,329,3958	yes	missense,missense	TMEM132A	NM_017870.3,NM_178031.2	43,43	9,356,6132	AA,AG,GG		4.0386,0.6134,2.8783	possibly-damaging,possibly-damaging	278/1025,278/1024	60696399	374,12620	2201	4296	6497	SO:0001583	missense	54972	exon4			TGCTTCGGCACAA	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.833G>A	11.37:g.60696399G>A	ENSP00000405823:p.Arg278Gln	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_178031	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	34	0.015567765567765568	3	0.006097560975609756	6	0.016574585635359115	0	0.0	25	0.032981530343007916	G	16.23	3.064526	0.55432	0.006134	0.040386	ENSG00000006118	ENST00000544065;ENST00000453848;ENST00000005286	T;T;T	0.13538	2.7;2.58;2.58	4.66	2.77	0.32553	.	0.000000	0.43110	D	0.000618	T	0.03739	0.0106	L	0.47716	1.5	0.19575	N	0.999969	D;D;D	0.60575	0.988;0.976;0.976	P;P;P	0.50934	0.654;0.465;0.465	T	0.04281	-1.0963	10	0.87932	D	0	.	7.0037	0.24823	0.3377:0.0:0.6623:0.0	rs61751216	267;278;278	Q24JP5-3;Q24JP5;Q24JP5-2	.;T132A_HUMAN;.	Q	16;278;278	ENSP00000442754:R16Q;ENSP00000405823:R278Q;ENSP00000005286:R278Q	ENSP00000005286:R278Q	R	+	2	0	TMEM132A	60452975	0.001000	0.12720	0.809000	0.32408	0.955000	0.61496	0.300000	0.19156	0.521000	0.28445	0.484000	0.47621	CGG	G|0.976;A|0.024	0.024	strong		0.637	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
ZNF485	220992	hgsc.bcm.edu	37	10	44112763	44112763	+	Silent	SNP	C	C	G	rs7069748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:44112763C>G	ENST00000361807.3	+	5	1466	c.1272C>G	c.(1270-1272)gcC>gcG	p.A424A	ZNF485_ENST00000374437.2_Silent_p.A333A|ZNF485_ENST00000374435.3_Silent_p.A424A	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	424					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GAAGTTCAGCCCTTAAGCAAC	0.393													C|||	236	0.0471246	0.0393	0.0432	5008	,	,		19676	0.002		0.0696	False		,,,				2504	0.0838				p.A424A		Atlas-SNP	.											.	ZNF485	102	.	0			c.C1272G						PASS	.	C		235,4171	125.3+/-162.5	9,217,1977	39.0	43.0	41.0		1272	0.1	0.0	10	dbSNP_116	41	655,7945	161.1+/-214.1	32,591,3677	no	coding-synonymous	ZNF485	NM_145312.3		41,808,5654	GG,GC,CC		7.6163,5.3336,6.843		424/442	44112763	890,12116	2203	4300	6503	SO:0001819	synonymous_variant	220992	exon5			TTCAGCCCTTAAG	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.1272C>G	10.37:g.44112763C>G		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	37	CCDS7205.2																																																																																			C|0.938;G|0.062	0.062	strong		0.393	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
SIRPG	55423	hgsc.bcm.edu	37	20	1616137	1616137	+	Missense_Mutation	SNP	G	G	A	rs6034239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:1616137G>A	ENST00000303415.3	-	4	921	c.857C>T	c.(856-858)tCg>tTg	p.S286L	RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000381583.2_Intron|SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381580.1_Missense_Mutation_p.S253L|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000216927.4_Intron	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	286	Ig-like C1-type 2.		S -> L (in dbSNP:rs6034239). {ECO:0000269|PubMed:11185750}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						TCCATTCTCCGACCAGGTCAG	0.532													a|||	2983	0.595647	0.7625	0.4236	5008	,	,		21388	0.6369		0.4254	False		,,,				2504	0.6247				p.S286L		Atlas-SNP	.											.	SIRPG	61	.	0			c.C857T						PASS	.	A	,LEU/SER,	3201,1205		1155,891,157	176.0	149.0	158.0		,857,	1.6	1.0	20	dbSNP_114	158	3540,5060		754,2032,1514	yes	intron,missense,intron	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,145,	1909,2923,1671	AA,AG,GG		41.1628,27.3491,48.1701	,benign,	,286/388,	1616137	6741,6265	2203	4300	6503	SO:0001583	missense	55423	exon4			TTCTCCGACCAGG	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.857C>T	20.37:g.1616137G>A	ENSP00000305529:p.Ser286Leu	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	367	196	0.53406	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	1209	0.5535714285714286	377	0.766260162601626	164	0.4530386740331492	345	0.6031468531468531	323	0.4261213720316623	.	0.051	-1.249973	0.01469	0.726509	0.411628	ENSG00000089012	ENST00000381580;ENST00000303415	T;T	0.00574	6.47;6.47	1.6	1.6	0.23607	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.300419	0.23369	N	0.048925	T	0.00012	0.0000	N	0.00010	-3.025	0.09310	P	0.99999962275	B	0.02656	0.0	B	0.01281	0.0	T	0.16482	-1.0401	9	0.02654	T	1	.	3.5698	0.07913	0.7797:0.0:0.2203:0.0	rs6034239;rs6514586;rs6034239	286	Q9P1W8	SIRPG_HUMAN	L	253;286	ENSP00000370992:S253L;ENSP00000305529:S286L	ENSP00000305529:S286L	S	-	2	0	SIRPG	1564137	0.938000	0.31826	0.970000	0.41538	0.023000	0.10783	1.384000	0.34396	0.090000	0.17273	-1.298000	0.01336	TCG	G|0.459;A|0.541	0.541	strong		0.532	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
UGGT2	55757	hgsc.bcm.edu	37	13	96506633	96506633	+	Missense_Mutation	SNP	C	C	T	rs145358686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:96506633C>T	ENST00000376747.3	-	35	4175	c.4105G>A	c.(4105-4107)Gga>Aga	p.G1369R		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1369	Glucosyltransferase.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			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						AAACGATATCCATCCATTTCC	0.388													C|||	10	0.00199681	0.0008	0.0029	5008	,	,		17239	0.0		0.006	False		,,,				2504	0.001				p.G1369R		Atlas-SNP	.											.	UGGT2	127	.	0			c.G4105A						PASS	.	C	ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	111.0	106.0	108.0		4105	5.4	1.0	13	dbSNP_134	108	38,8562	25.7+/-73.6	0,38,4262	yes	missense	UGGT2	NM_020121.3	125	0,41,6462	TT,TC,CC		0.4419,0.0681,0.3152	probably-damaging	1369/1517	96506633	41,12965	2203	4300	6503	SO:0001583	missense	55757	exon35			GATATCCATCCAT	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.4105G>A	13.37:g.96506633C>T	ENSP00000365938:p.Gly1369Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	31	5.075920	0.94000	6.81E-4	0.004419	ENSG00000102595	ENST00000376747	T	0.42513	0.97	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.70159	0.3192	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82500	-0.0426	10	0.87932	D	0	-18.4057	19.0987	0.93265	0.0:1.0:0.0:0.0	.	1369	Q9NYU1	UGGG2_HUMAN	R	1369	ENSP00000365938:G1369R	ENSP00000365938:G1369R	G	-	1	0	UGGT2	95304634	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	7.487000	0.81328	2.512000	0.84698	0.591000	0.81541	GGA	C|0.997;T|0.003	0.003	strong		0.388	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
ITGA2	3673	hgsc.bcm.edu	37	5	52379277	52379277	+	Silent	SNP	C	C	T	rs2303122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:52379277C>T	ENST00000296585.5	+	27	3395	c.3252C>T	c.(3250-3252)ttC>ttT	p.F1084F		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	1084					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.F1084L(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				ACGGGACTTTCGCATCAGTAA	0.368													C|||	1662	0.331869	0.2806	0.4323	5008	,	,		19643	0.2946		0.3708	False		,,,				2504	0.3282				p.F1084F		Atlas-SNP	.											ITGA2,colon,carcinoma,0,1	ITGA2	211	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3252T						PASS	.	C		1316,3090	442.9+/-346.8	197,922,1084	103.0	96.0	98.0		3252	-2.5	1.0	5	dbSNP_100	98	3138,5462	477.9+/-369.8	554,2030,1716	no	coding-synonymous	ITGA2	NM_002203.3		751,2952,2800	TT,TC,CC		36.4884,29.8684,34.2457		1084/1182	52379277	4454,8552	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon27			GACTTTCGCATCA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.3252C>T	5.37:g.52379277C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			T|0.351;G|0.004	0.351	strong		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
PLB1	151056	hgsc.bcm.edu	37	2	28824793	28824793	+	Missense_Mutation	SNP	C	C	G	rs7601771	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:28824793C>G	ENST00000327757.5	+	38	2679	c.2635C>G	c.(2635-2637)Cac>Gac	p.H879D	PLB1_ENST00000422425.2_Missense_Mutation_p.H868D|PLB1_ENST00000541605.1_5'UTR	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	879	4 X 308-326 AA approximate repeats.		H -> D (in dbSNP:rs7601771).		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)					CAACTTTGTTCACCATCTCCG	0.537													G|||	3254	0.64976	0.6657	0.585	5008	,	,		17773	0.878		0.5765	False		,,,				2504	0.5143				p.H879D		Atlas-SNP	.											.	PLB1	255	.	0			c.C2635G						PASS	.	G	ASP/HIS,ASP/HIS	2870,1536	483.2+/-359.6	929,1012,262	145.0	129.0	134.0		2602,2635	1.5	0.0	2	dbSNP_116	134	4548,4052	558.5+/-387.2	1214,2120,966	yes	missense,missense	PLB1	NM_001170585.1,NM_153021.4	81,81	2143,3132,1228	GG,GC,CC		47.1163,34.8616,42.9648	benign,benign	868/1448,879/1459	28824793	7418,5588	2203	4300	6503	SO:0001583	missense	151056	exon38			TTTGTTCACCATC		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.2635C>G	2.37:g.28824793C>G	ENSP00000330442:p.His879Asp	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	1488|1488	0.6813186813186813|0.6813186813186813	347|347	0.7052845528455285|0.7052845528455285	214|214	0.5911602209944752|0.5911602209944752	485|485	0.8479020979020979|0.8479020979020979	442|442	0.58311345646438|0.58311345646438	G|G	0.004|0.004	-2.297355|-2.297355	0.00243|0.00243	0.651384|0.651384	0.528837|0.528837	ENSG00000163803|ENSG00000163803	ENST00000404858|ENST00000327757;ENST00000422425	.|T;T	.|0.10763	.|2.84;2.84	5.43|5.43	1.5|1.5	0.22942|0.22942	.|Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	.|1.582640	.|0.03350	.|N	.|0.196066	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00162|0.00162	-1.95|-1.95	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	0.35425|0.35425	-0.9789|-0.9789	4|9	.|0.12103	.|T	.|0.63	-2.0931|-2.0931	1.6046|1.6046	0.02681|0.02681	0.2233:0.2615:0.3807:0.1346|0.2233:0.2615:0.3807:0.1346	rs7601771;rs12999769;rs52803712;rs57054163;rs7601771|rs7601771;rs12999769;rs52803712;rs57054163;rs7601771	.|868;879	.|Q6P1J6-3;Q6P1J6	.|.;PLB1_HUMAN	L|D	866|879;868	.|ENSP00000330442:H879D;ENSP00000416440:H868D	.|ENSP00000330442:H879D	F|H	+|+	3|1	2|0	PLB1|PLB1	28678297|28678297	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.309000|-0.309000	0.08145|0.08145	-0.130000|-0.130000	0.11599|0.11599	-0.120000|-0.120000	0.15030|0.15030	TTC|CAC	C|0.383;G|0.617	0.617	strong		0.537	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
EFCAB6	64800	hgsc.bcm.edu	37	22	43936219	43936219	+	Missense_Mutation	SNP	C	C	T	rs61995890	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:43936219C>T	ENST00000262726.7	-	28	3920	c.3667G>A	c.(3667-3669)Gag>Aag	p.E1223K	EFCAB6_ENST00000461800.1_5'UTR|EFCAB6_ENST00000396231.2_Missense_Mutation_p.E1071K	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1223	EF-hand 14. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ACTGGCATCTCGTTCCAGAGT	0.567													C|||	493	0.0984425	0.0847	0.1066	5008	,	,		17636	0.0288		0.172	False		,,,				2504	0.1074				p.E1223K		Atlas-SNP	.											.	EFCAB6	177	.	0			c.G3667A						PASS	.	C	LYS/GLU,LYS/GLU	456,3950	218.1+/-236.3	22,412,1769	74.0	60.0	65.0		3667,3211	2.0	0.7	22	dbSNP_129	65	1444,7156	277.5+/-292.9	110,1224,2966	yes	missense,missense	EFCAB6	NM_022785.3,NM_198856.2	56,56	132,1636,4735	TT,TC,CC		16.7907,10.3495,14.6086	benign,benign	1223/1502,1071/1350	43936219	1900,11106	2203	4300	6503	SO:0001583	missense	64800	exon28			GCATCTCGTTCCA	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3667G>A	22.37:g.43936219C>T	ENSP00000262726:p.Glu1223Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	255	0.11675824175824176	57	0.11585365853658537	44	0.12154696132596685	19	0.033216783216783216	135	0.17810026385224276	C	11.66	1.704657	0.30232	0.103495	0.167907	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.80123	-1.34;-1.34	5.49	2.02	0.26589	EF-hand calcium-binding domain-containing protein 6 (1);EF-hand-like domain (1);	0.360922	0.26112	N	0.026268	T	0.00300	0.0009	L	0.43701	1.375	0.26526	P	0.9743357	B	0.19583	0.037	B	0.20955	0.032	T	0.05517	-1.0880	9	0.25751	T	0.34	-29.1738	5.0927	0.14718	0.0:0.4816:0.3178:0.2005	.	1223	Q5THR3	EFCB6_HUMAN	K	1071;1223	ENSP00000379533:E1071K;ENSP00000262726:E1223K	ENSP00000262726:E1223K	E	-	1	0	EFCAB6	42267552	0.269000	0.24143	0.687000	0.30102	0.981000	0.71138	0.472000	0.22116	0.787000	0.33731	0.650000	0.86243	GAG	C|0.860;T|0.140	0.140	strong		0.567	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
SPTBN5	51332	hgsc.bcm.edu	37	15	42159290	42159290	+	Missense_Mutation	SNP	C	C	T	rs2290553	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:42159290C>T	ENST00000320955.6	-	36	6574	c.6347G>A	c.(6346-6348)cGg>cAg	p.R2116Q	MIR4310_ENST00000582950.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2116					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)		CCGGGGGCGCCGGAGCGTCTT	0.736													c|||	711	0.141973	0.034	0.1671	5008	,	,		14161	0.0446		0.2833	False		,,,				2504	0.2249				p.R2081Q		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G6242A						PASS	.	C	GLN/ARG	191,3125		13,165,1480	3.0	4.0	4.0		6242	-4.3	0.0	15	dbSNP_100	4	1708,5692		230,1248,2222	no	missense	SPTBN5	NM_016642.2	43	243,1413,3702	TT,TC,CC		23.0811,5.76,17.7212	possibly-damaging	2081/3640	42159290	1899,8817	1658	3700	5358	SO:0001583	missense	51332	exon36			GGGCGCCGGAGCG	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.6347G>A	15.37:g.42159290C>T	ENSP00000317790:p.Arg2116Gln	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		308	0.14102564102564102	20	0.04065040650406504	61	0.1685082872928177	19	0.033216783216783216	208	0.27440633245382584	.	9.097	1.003238	0.19121	0.0576	0.230811	ENSG00000137877	ENST00000320955	T	0.47177	0.85	4.61	-4.26	0.03755	.	1.848070	0.02996	N	0.147432	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B	0.25743	0.133	B	0.17098	0.017	T	0.09292	-1.0681	9	0.14252	T	0.57	.	6.4787	0.22051	0.0:0.4092:0.1605:0.4303	rs2290553;rs17736981	2116	Q9NRC6	SPTN5_HUMAN	Q	2116	ENSP00000317790:R2116Q	ENSP00000317790:R2116Q	R	-	2	0	SPTBN5	39946582	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.487000	0.06505	-0.666000	0.05310	-0.389000	0.06534	CGG	C|0.858;T|0.142	0.142	strong		0.736	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
TTN	7273	hgsc.bcm.edu	37	2	179436020	179436020	+	Missense_Mutation	SNP	G	G	A	rs744426	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179436020G>A	ENST00000591111.1	-	276	70140	c.69916C>T	c.(69916-69918)Cgc>Tgc	p.R23306C	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R24947C|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R16007C|TTN_ENST00000460472.2_Missense_Mutation_p.R15882C|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R16074C|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R22379C|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23306	Fibronectin type-III 69. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> C. {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)			CTTTCCTTGCGTTCTAGATGA	0.428													G|||	1042	0.208067	0.0666	0.1455	5008	,	,		23224	0.4504		0.1372	False		,,,				2504	0.2669				p.R24947C		Atlas-SNP	.											TTN_ENST00000359218,brain,glioma,+1,10	TTN	18412	10	0			c.C74839T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	288,3574		10,268,1653	124.0	117.0	120.0		47644,67135,48019,48220	4.5	1.0	2	dbSNP_86	120	1195,7091		90,1015,3038	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	180,180,180,180	100,1283,4691	AA,AG,GG		14.4219,7.4573,12.2078	probably-damaging,probably-damaging,probably-damaging,probably-damaging	15882/26927,22379/33424,16007/27052,16074/27119	179436020	1483,10665	1931	4143	6074	SO:0001583	missense	7273	exon326			CCTTGCGTTCTAG	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.69916C>T	2.37:g.179436020G>A	ENSP00000465570:p.Arg23306Cys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	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		415	0.190018315018315	30	0.06097560975609756	42	0.11602209944751381	239	0.4178321678321678	104	0.13720316622691292	G	10.62	1.402466	0.25291	0.074573	0.144219	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.39	4.5	0.54988	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.63428	1.95	0.09310	P	0.99999816646	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	P;P;P;P	0.60609	0.877;0.877;0.877;0.877	T	0.34576	-0.9823	8	0.87932	D	0	.	13.6593	0.62357	0.0:0.0:0.7197:0.2803	rs744426;rs3731742;rs52810886;rs61022663;rs744426	15882;16007;16074;23306	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	22379;15882;16074;16007;15880	ENSP00000343764:R22379C;ENSP00000434586:R15882C;ENSP00000340554:R16074C;ENSP00000352154:R16007C	ENSP00000340554:R16074C	R	-	1	0	TTN	179144266	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.109000	0.50345	1.394000	0.46624	0.650000	0.86243	CGC	G|0.817;N|0.001	.	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DIP2C	22982	hgsc.bcm.edu	37	10	459940	459940	+	Silent	SNP	G	G	A	rs4881274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:459940G>A	ENST00000280886.6	-	8	1057	c.970C>T	c.(970-972)Ctg>Ttg	p.L324L	DIP2C_ENST00000381496.3_Silent_p.L217L	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	324						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CACCTCTGCAGTGCGGCCTCC	0.667													G|||	3139	0.626797	0.5772	0.6268	5008	,	,		15834	0.6915		0.5417	False		,,,				2504	0.7147				p.L324L		Atlas-SNP	.											.	DIP2C	195	.	0			c.C970T						PASS	.	G		2460,1946	622.4+/-393.9	691,1078,434	59.0	59.0	59.0		970	1.7	0.1	10	dbSNP_111	59	4653,3947	604.0+/-394.7	1260,2133,907	no	coding-synonymous	DIP2C	NM_014974.2		1951,3211,1341	AA,AG,GG		45.8953,44.167,45.3099		324/1557	459940	7113,5893	2203	4300	6503	SO:0001819	synonymous_variant	22982	exon8			TCTGCAGTGCGGC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.970C>T	10.37:g.459940G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																			G|0.440;A|0.560	0.560	strong		0.667	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291454	1291454	+	Missense_Mutation	SNP	G	G	A	rs201351744		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1291454G>A	ENST00000338844.3	+	4	286	c.253G>A	c.(253-255)Gcc>Acc	p.A85T	TPSAB1_ENST00000461509.2_Missense_Mutation_p.A92T	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	85	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> T (in dbSNP:rs1141968). {ECO:0000269|PubMed:10898108, ECO:0000269|PubMed:2677049, ECO:0000269|Ref.5}.		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				GGATCTGGCCGCCCTCAGGGT	0.667																																					p.A85T		Atlas-SNP	.											TPSAB1,NS,carcinoma,0,2	TPSAB1	24	2	0			c.G253A						scavenged	.						6.0	7.0	7.0					16																	1291454		2030	4042	6072	SO:0001583	missense	7177	exon4			CTGGCCGCCCTCA	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.253G>A	16.37:g.1291454G>A	ENSP00000343577:p.Ala85Thr	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	261	72	0.275862	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	.	.	.	.	.	.	.	.	.	.	g	1.250	-0.618741	0.03663	.	.	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.88975	-2.45;-2.45	2.93	-5.57	0.02521	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	2.192380	0.02106	N	0.054344	T	0.64204	0.2577	N	0.01146	-0.985	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.63475	-0.6629	10	0.12766	T	0.61	.	1.3572	0.02184	0.1257:0.3104:0.2064:0.3575	.	85	Q15661	TRYB1_HUMAN	T	85;92	ENSP00000343577:A85T;ENSP00000418247:A92T	ENSP00000343577:A85T	A	+	1	0	TPSAB1	1231455	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.166000	0.03129	-0.748000	0.04753	-0.346000	0.07831	GCC	.	.	weak		0.667	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
EVC	2121	hgsc.bcm.edu	37	4	5785442	5785442	+	Missense_Mutation	SNP	G	G	A	rs1383180	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:5785442G>A	ENST00000264956.6	+	12	1911	c.1727G>A	c.(1726-1728)cGg>cAg	p.R576Q	EVC_ENST00000382674.2_Missense_Mutation_p.R576Q	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	576			R -> Q (in dbSNP:rs1383180). {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)				AATCGCTTCCGGAGGCAGCAG	0.592													G|||	1510	0.301518	0.1793	0.4726	5008	,	,		19012	0.3254		0.3996	False		,,,				2504	0.2198				p.R576Q		Atlas-SNP	.											.	EVC	90	.	0			c.G1727A						PASS	.	G	GLN/ARG	871,3535	335.2+/-303.8	96,679,1428	39.0	39.0	39.0		1727	4.1	0.8	4	dbSNP_88	39	3135,5465	474.8+/-368.9	557,2021,1722	yes	missense	EVC	NM_153717.2	43	653,2700,3150	AA,AG,GG		36.4535,19.7685,30.8012	probably-damaging	576/993	5785442	4006,9000	2203	4300	6503	SO:0001583	missense	2121	exon12			GCTTCCGGAGGCA	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.1727G>A	4.37:g.5785442G>A	ENSP00000264956:p.Arg576Gln	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	172	84	0.488372	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	735	0.33653846153846156	93	0.18902439024390244	165	0.4558011049723757	173	0.30244755244755245	304	0.40105540897097625	G	16.90	3.248776	0.59103	0.197685	0.364535	ENSG00000072840	ENST00000264956;ENST00000382674	T;T	0.56275	0.47;0.47	4.94	4.1	0.47936	.	0.351137	0.26311	N	0.025114	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.9999999999999221	D	0.89917	1.0	D	0.81914	0.995	T	0.45220	-0.9276	9	0.44086	T	0.13	.	8.8367	0.35117	0.1044:0.0:0.8956:0.0	rs1383180;rs3774875;rs17691045;rs52795474;rs58525636;rs1383180	576	P57679	EVC_HUMAN	Q	576	ENSP00000264956:R576Q;ENSP00000372120:R576Q	ENSP00000264956:R576Q	R	+	2	0	EVC	5836343	1.000000	0.71417	0.841000	0.33234	0.393000	0.30537	4.544000	0.60691	1.085000	0.41206	0.557000	0.71058	CGG	G|0.687;T|0.001	.	strong		0.592	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
ZSWIM6	57688	hgsc.bcm.edu	37	5	60628411	60628411	+	Silent	SNP	G	G	T	rs75429795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	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	
ELTD1	64123	hgsc.bcm.edu	37	1	79392756	79392756	+	Missense_Mutation	SNP	C	C	A	rs12754818	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	98	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	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	
SIAE	54414	hgsc.bcm.edu	37	11	124524627	124524627	+	Silent	SNP	A	A	G	rs1942663	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	84	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	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	
ZNF423	23090	hgsc.bcm.edu	37	16	49671218	49671218	+	Silent	SNP	C	C	T	rs16947741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:49671218C>T	ENST00000561648.1	-	4	1898	c.1845G>A	c.(1843-1845)ccG>ccA	p.P615P	ZNF423_ENST00000567169.1_Silent_p.P498P|ZNF423_ENST00000262383.2_Silent_p.P615P|ZNF423_ENST00000563137.2_Silent_p.P555P|ZNF423_ENST00000562871.1_Silent_p.P555P|ZNF423_ENST00000562520.1_Silent_p.P555P|ZNF423_ENST00000535559.1_Silent_p.P498P	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	615					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|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)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GCTGCCGCTTCGGGGAAGACA	0.552													C|||	113	0.0225639	0.0144	0.0144	5008	,	,		22588	0.0149		0.0398	False		,,,				2504	0.0297				p.P615P		Atlas-SNP	.											ZNF423_ENST00000262383,NS,carcinoma,0,2	ZNF423	463	2	0			c.G1845A						scavenged	.	C		91,4305	75.7+/-113.9	0,91,2107	88.0	74.0	79.0		1845	-9.6	0.8	16	dbSNP_123	79	274,8326	104.6+/-165.6	4,266,4030	no	coding-synonymous	ZNF423	NM_015069.2		4,357,6137	TT,TC,CC		3.186,2.0701,2.8086		615/1285	49671218	365,12631	2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			CCGCTTCGGGGAA	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1845G>A	16.37:g.49671218C>T		Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	224	104	0.464286	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	37	CCDS32445.1																																																																																			C|0.973;T|0.027	0.027	strong		0.552	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
CDH23	64072	hgsc.bcm.edu	37	10	73501556	73501556	+	Missense_Mutation	SNP	G	G	A	rs1227051	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73501556G>A	ENST00000224721.6	+	37	4743	c.4738G>A	c.(4738-4740)Gcc>Acc	p.A1580T		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1575	Cadherin 15. {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						CAAGGACATGGCCTTCCGCAT	0.622													A|||	3650	0.728834	0.5582	0.6902	5008	,	,		20019	0.8254		0.7903	False		,,,				2504	0.8241				p.A1575T		Atlas-SNP	.											.	CDH23	365	.	0			c.G4723A						PASS	.	A	THR/ALA	2783,1607		897,989,309	71.0	71.0	71.0		4723	5.1	1.0	10	dbSNP_87	71	6814,1746		2724,1366,190	yes	missense	CDH23	NM_022124.5	58	3621,2355,499	AA,AG,GG		20.3972,36.6059,25.8919	probably-damaging	1575/3355	73501556	9597,3353	2195	4280	6475	SO:0001583	missense	64072	exon36			GACATGGCCTTCC	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.4738G>A	10.37:g.73501556G>A	ENSP00000224721:p.Ala1580Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		1628	0.7454212454212454	275	0.5589430894308943	261	0.7209944751381215	488	0.8531468531468531	604	0.7968337730870713	A	4.299	0.054691	0.08291	0.633941	0.796028	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398792	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	7	0.12766	T	0.61	.	10.8831	0.46951	0.9262:0.0:0.0738:0.0	rs1227051;rs60465380;rs1227051	395	E7ERT0	.	T	1580;1575;1578;395	.	ENSP00000224721:A1580T	A	+	1	0	CDH23	73171562	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	6.202000	0.72131	0.798000	0.33994	-0.254000	0.11334	GCC	G|0.250;T|0.003	.	strong		0.622	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
CATSPER4	378807	hgsc.bcm.edu	37	1	26517891	26517891	+	Silent	SNP	C	C	T	rs11247867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26517891C>T	ENST00000456354.2	+	2	394	c.327C>T	c.(325-327)atC>atT	p.I109I		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	109					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		CCATCACCATCGCTCTCCGTA	0.592													C|||	586	0.117013	0.2042	0.0893	5008	,	,		19617	0.0089		0.1879	False		,,,				2504	0.0573				p.I109I		Atlas-SNP	.											CATSPER4,caecum,carcinoma,0,1	CATSPER4	59	1	0			c.C327T						PASS	.	C		921,3485	354.6+/-312.7	111,699,1393	92.0	75.0	80.0		327	-0.8	1.0	1	dbSNP_120	80	1628,6972	301.0+/-305.2	152,1324,2824	no	coding-synonymous	CATSPER4	NM_198137.1		263,2023,4217	TT,TC,CC		18.9302,20.9033,19.5986		109/473	26517891	2549,10457	2203	4300	6503	SO:0001819	synonymous_variant	378807	exon2			CACCATCGCTCTC	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.327C>T	1.37:g.26517891C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_198137	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																			C|0.822;T|0.178	0.178	strong		0.592	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
MYH7B	57644	hgsc.bcm.edu	37	20	33587198	33587198	+	Missense_Mutation	SNP	G	G	C	rs3746435	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:33587198G>C	ENST00000262873.7	+	34	4748	c.4656G>C	c.(4654-4656)aaG>aaC	p.K1552N		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1510						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)			GGGAGAACAAGAACCTGCAGG	0.672													G|||	859	0.171526	0.1566	0.1311	5008	,	,		15468	0.1071		0.1938	False		,,,				2504	0.2638				p.K1552N		Atlas-SNP	.											.	MYH7B	145	.	0			c.G4656C						PASS	.	G	ASN/LYS	602,3460		38,526,1467	11.0	17.0	15.0		4656	4.2	1.0	20	dbSNP_107	15	1586,6814		156,1274,2770	yes	missense	MYH7B	NM_020884.3	94	194,1800,4237	CC,CG,GG		18.881,14.8203,17.5574	probably-damaging	1552/1984	33587198	2188,10274	2031	4200	6231	SO:0001583	missense	57644	exon36			GAACAAGAACCTG	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.4656G>C	20.37:g.33587198G>C	ENSP00000262873:p.Lys1552Asn	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	359	0.16437728937728938	82	0.16666666666666666	55	0.15193370165745856	69	0.12062937062937062	153	0.20184696569920843	G	18.15	3.559949	0.65538	0.148203	0.18881	ENSG00000078814	ENST00000262873	D	0.84589	-1.87	4.19	4.19	0.49359	Myosin tail (1);	.	.	.	.	T	0.01092	0.0036	H	0.95187	3.635	0.20873	P	0.99983557	D	0.62365	0.991	P	0.59825	0.864	T	0.30446	-0.9978	8	0.87932	D	0	.	10.7054	0.45952	0.088:0.0:0.912:0.0	rs3746435;rs59345834;rs3746435	1510	A7E2Y1	MYH7B_HUMAN	N	1552	ENSP00000262873:K1552N	ENSP00000262873:K1552N	K	+	3	2	MYH7B	33050859	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.715000	0.54897	2.326000	0.78906	0.561000	0.74099	AAG	G|0.830;C|0.170	0.170	strong		0.672	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
ARID1B	57492	hgsc.bcm.edu	37	6	157405930	157405930	+	Silent	SNP	G	G	A	rs3734441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:157405930G>A	ENST00000350026.5	+	5	2134	c.2133G>A	c.(2131-2133)gcG>gcA	p.A711A	ARID1B_ENST00000346085.5_Silent_p.A724A|ARID1B_ENST00000275248.4_Silent_p.A653A|ARID1B_ENST00000367148.1_Silent_p.A711A	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	711	Ser-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CCCCACATGCGTCCCCTCATC	0.607													G|||	2480	0.495208	0.2806	0.6254	5008	,	,		14523	0.5734		0.5239	False		,,,				2504	0.5828				p.A724A		Atlas-SNP	.											ARID1B_ENST00000346085,NS,carcinoma,0,2	ARID1B	320	2	0			c.G2172A						PASS	.	G	,	1512,2894	481.9+/-359.3	253,1006,944	91.0	88.0	89.0		2133,2172	-11.3	0.1	6	dbSNP_107	89	4635,3965	602.5+/-394.5	1260,2115,925	no	coding-synonymous,coding-synonymous	ARID1B	NM_017519.2,NM_020732.3	,	1513,3121,1869	AA,AG,GG		46.1047,34.3168,47.2628	,	711/2237,724/2250	157405930	6147,6859	2203	4300	6503	SO:0001819	synonymous_variant	57492	exon6			ACATGCGTCCCCT	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.2133G>A	6.37:g.157405930G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	37	CCDS5251.2																																																																																			G|0.515;A|0.485	0.485	strong		0.607	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
USP48	84196	hgsc.bcm.edu	37	1	22084201	22084201	+	Silent	SNP	A	A	G	rs150521027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:22084201A>G	ENST00000308271.9	-	2	858	c.210T>C	c.(208-210)aaT>aaC	p.N70N	USP48_ENST00000529637.1_Silent_p.N70N|USP48_ENST00000421625.2_Silent_p.N70N|USP48_ENST00000400301.1_Silent_p.N70N	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	70					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		TATGAAAACTATTTTCATCTA	0.333													A|||	6	0.00119808	0.0	0.0	5008	,	,		19681	0.0		0.006	False		,,,				2504	0.0				p.N70N		Atlas-SNP	.											.	USP48	91	.	0			c.T210C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	108.0	102.0	104.0		210,210	1.8	1.0	1	dbSNP_134	104	55,8545	35.9+/-90.5	0,55,4245	no	coding-synonymous,coding-synonymous	USP48	NM_001032730.1,NM_032236.5	,	0,60,6443	GG,GA,AA		0.6395,0.1135,0.4613	,	70/486,70/1036	22084201	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	84196	exon2			AAAACTATTTTCA	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.210T>C	1.37:g.22084201A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			A|0.996;G|0.004	0.004	strong		0.333	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
FMN2	56776	hgsc.bcm.edu	37	1	240370995	240370995	+	Silent	SNP	G	G	A	rs201866430	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240370995G>A	ENST00000319653.9	+	5	3113	c.2883G>A	c.(2881-2883)ggG>ggA	p.G961G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	961	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)			CTCTTCCCGGGGCAGGCATAC	0.692																																					p.G961G		Atlas-SNP	.											FMN2,NS,carcinoma,0,1	FMN2	451	1	0			c.G2883A						scavenged	.						20.0	23.0	22.0					1																	240370995		2199	4297	6496	SO:0001819	synonymous_variant	56776	exon5			TCCCGGGGCAGGC	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.2883G>A	1.37:g.240370995G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	117	13	0.111111	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			G|0.993;A|0.007	0.007	strong		0.692	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
CCL4	6351	hgsc.bcm.edu	37	17	34432663	34432663	+	Silent	SNP	A	A	G	rs1049807|rs386796798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:34432663A>G	ENST00000250151.4	+	3	553	c.237A>G	c.(235-237)gaA>gaG	p.E79E	CCL4_ENST00000394495.1_Missense_Mutation_p.N41S	NM_002984.2	NP_002975.1	P13236	CCL4_HUMAN	chemokine (C-C motif) ligand 4	79					cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|establishment or maintenance of cell polarity (GO:0007163)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of natural killer cell chemotaxis (GO:2000503)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemokine activity (GO:0008009)|cytokine activity (GO:0005125)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(1)|lung(2)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATCCCAGTGAATCCTGGGTCC	0.498													G|||	1096	0.21885	0.1732	0.1254	5008	,	,		21052	0.3036		0.2485	False		,,,				2504	0.229				p.E79E	Colon(139;824 1752 21188 21615 24765)	Atlas-SNP	.											.	CCL4	14	.	0			c.A237G						PASS	.	G		480,3926		54,372,1777	200.0	184.0	190.0		237	-10.1	0.0	17	dbSNP_86	190	278,8322		96,86,4118	no	coding-synonymous	CCL4	NM_002984.2		150,458,5895	GG,GA,AA		3.2326,10.8942,5.8281		79/93	34432663	758,12248	2203	4300	6503	SO:0001819	synonymous_variant	6351	exon3			CAGTGAATCCTGG	M23502	CCDS11308.1	17q21-q23	2014-05-06	2002-08-22	2002-08-23	ENSG00000129277	ENSG00000275302		"""Chemokine ligands"", ""Endogenous ligands"""	10630	protein-coding gene	gene with protein product		182284	"""small inducible cytokine A4 (homologous to mouse Mip-1b)"""	LAG1, SCYA4		1972563	Standard	NM_002984		Approved	MIP-1-beta, Act-2, AT744.1	uc002hkw.1	P13236	OTTHUMG00000188414	ENST00000250151.4:c.237A>G	17.37:g.34432663A>G		Somatic	437	1	0.00228833		WXS	Illumina HiSeq	Phase_I	459	252	0.54902	NM_002984	P22617|Q13704|Q3SXL8|Q6FGI8	Silent	SNP	ENST00000250151.4	37	CCDS11308.1	380	0.17399267399267399	58	0.11788617886178862	48	0.13259668508287292	137	0.2395104895104895	137	0.18073878627968337	.	0.859	-0.736020	0.03111	0.108942	0.032326	ENSG00000129277	ENST00000394495	T	0.71222	-0.55	5.03	-10.1	0.00402	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.29822	-0.9999	5	0.87932	D	0	.	2.3631	0.04312	0.1849:0.3061:0.1036:0.4054	rs1049807;rs1719151;rs52827317;rs56801182;rs1049807	.	.	.	S	41	ENSP00000378004:N41S	ENSP00000378004:N41S	N	+	2	0	CCL4	31456776	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.376000	0.01070	-3.251000	0.00204	-0.768000	0.03414	AAT	A|0.816;G|0.184	0.184	strong		0.498	CCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256592.2	NM_002984	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37442591	37442591	+	Splice_Site	SNP	G	G	T	rs200154690		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:37442591G>T	ENST00000602533.1	+	13	1729		c.e13+1		ANKRD30A_ENST00000361713.1_Splice_Site|ANKRD30A_ENST00000374660.1_Splice_Site			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A						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						AAATTAGAAGGTAAGAACCGT	0.333																																					.		Atlas-SNP	.											ANKRD30A,NS,carcinoma,+1,2	ANKRD30A	448	2	0			c.1630+1G>T						scavenged	.																																			SO:0001630	splice_region_variant	91074	exon13			TAGAAGGTAAGAA	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.1630+1G>T	10.37:g.37442591G>T		Somatic	545	0	0		WXS	Illumina HiSeq	Phase_I	429	59	0.137529	NM_052997	Q5W025	Splice_Site	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	g	5.237	0.229225	0.09916	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	.	.	.	1.71	0.759	0.18438	.	.	.	.	.	.	.	.	.	.	.	0.31905	N	0.615401	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.0426	0.09758	0.2275:0.0:0.7725:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANKRD30A	37482597	1.000000	0.71417	0.354000	0.25760	0.045000	0.14185	2.444000	0.44890	0.281000	0.22233	0.384000	0.25694	.	G|0.999;T|0.001	0.001	weak		0.333	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	Intron
LMO7	4008	hgsc.bcm.edu	37	13	76335109	76335109	+	Silent	SNP	A	A	G	rs17706535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:76335109A>G	ENST00000341547.4	+	5	1668	c.408A>G	c.(406-408)ggA>ggG	p.G136G	LMO7_ENST00000377534.3_Silent_p.G136G|LMO7_ENST00000357063.3_Silent_p.G136G|LMO7_ENST00000526202.1_Silent_p.G45G|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000465261.2_5'UTR|LMO7_ENST00000321797.8_5'UTR	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	136	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)		AACAGATTGGATTGAAAGAAG	0.358													A|||	341	0.0680911	0.0053	0.0922	5008	,	,		16064	0.003		0.1292	False		,,,				2504	0.1401				p.G136G		Atlas-SNP	.											.	LMO7	334	.	0			c.A408G						PASS	.	A	,	99,4307	76.8+/-115.0	4,91,2108	77.0	76.0	76.0		408,	4.4	1.0	13	dbSNP_123	76	982,7618	212.5+/-252.8	56,870,3374	no	coding-synonymous,utr-5	LMO7	NM_005358.5,NM_015842.2	,	60,961,5482	GG,GA,AA		11.4186,2.2469,8.3115	,	136/1350,	76335109	1081,11925	2203	4300	6503	SO:0001819	synonymous_variant	4008	exon5			GATTGGATTGAAA	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.408A>G	13.37:g.76335109A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	ENST00000341547.4	37	CCDS9454.1																																																																																			A|0.921;G|0.079	0.079	strong		0.358	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358	
ASPH	444	hgsc.bcm.edu	37	8	62489334	62489334	+	Silent	SNP	C	C	T	rs16927574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:62489334C>T	ENST00000379454.4	-	16	1333	c.1146G>A	c.(1144-1146)gcG>gcA	p.A382A	ASPH_ENST00000541428.1_Silent_p.A353A	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	382					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	AGAATACCTGCGCCTTCCCAT	0.383													C|||	654	0.130591	0.1551	0.0994	5008	,	,		16528	0.2371		0.0795	False		,,,				2504	0.0624				p.A382A		Atlas-SNP	.											.	ASPH	87	.	0			c.G1146A						PASS	.	C	,	587,3819	259.2+/-262.9	43,501,1659	171.0	153.0	159.0		1059,1146	-9.1	0.9	8	dbSNP_123	159	557,8043	153.0+/-207.5	13,531,3756	no	coding-synonymous,coding-synonymous	ASPH	NM_001164750.1,NM_004318.3	,	56,1032,5415	TT,TC,CC		6.4767,13.3227,8.7959	,	353/730,382/759	62489334	1144,11862	2203	4300	6503	SO:0001819	synonymous_variant	444	exon16			TACCTGCGCCTTC	AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"""junctin"", ""humbug"", ""junctate"""	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.1146G>A	8.37:g.62489334C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_004318	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Silent	SNP	ENST00000379454.4	37	CCDS34898.1																																																																																			C|0.883;N|0.000	.	strong		0.383	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318	
NAV3	89795	hgsc.bcm.edu	37	12	78400884	78400884	+	Silent	SNP	G	G	A	rs34276383	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:78400884G>A	ENST00000397909.2	+	8	1739	c.1566G>A	c.(1564-1566)ccG>ccA	p.P522P	NAV3_ENST00000228327.6_Silent_p.P522P|NAV3_ENST00000536525.2_Silent_p.P522P|NAV3_ENST00000266692.7_Silent_p.P522P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	522						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.P522P(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GCTTAATTCCGTCTTCCAGTG	0.448										HNSCC(70;0.22)			A|||	744	0.148562	0.0908	0.1095	5008	,	,		19238	0.2143		0.1322	False		,,,				2504	0.2035				p.P522P		Atlas-SNP	.											NAV3,NS,carcinoma,0,1	NAV3	506	1	1	Substitution - coding silent(1)	stomach(1)	c.G1566A						PASS	.	A		405,3417		31,343,1537	66.0	66.0	66.0		1566	-5.4	0.7	12	dbSNP_126	66	1037,7193		61,915,3139	no	coding-synonymous	NAV3	NM_014903.4		92,1258,4676	AA,AG,GG		12.6002,10.5965,11.9648		522/2364	78400884	1442,10610	1911	4115	6026	SO:0001819	synonymous_variant	89795	exon8			AATTCCGTCTTCC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1566G>A	12.37:g.78400884G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																				G|0.867;A|0.133	0.133	strong		0.448	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
KIRREL2	84063	hgsc.bcm.edu	37	19	36352906	36352906	+	Missense_Mutation	SNP	A	A	G	rs144457307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36352906A>G	ENST00000360202.5	+	11	1688	c.1490A>G	c.(1489-1491)cAg>cGg	p.Q497R	KIRREL2_ENST00000347900.6_Missense_Mutation_p.Q447R|KIRREL2_ENST00000262625.7_Missense_Mutation_p.Q497R|KIRREL2_ENST00000592409.1_Missense_Mutation_p.Q497R|NPHS1_ENST00000591817.1_Intron	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	497	Ig-like C2-type 5.				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)			GGAGGTGCCCAGGCCAGCCTG	0.622													A|||	4	0.000798722	0.0	0.0029	5008	,	,		14080	0.0		0.002	False		,,,				2504	0.0				p.Q497R		Atlas-SNP	.											.	KIRREL2	170	.	0			c.A1490G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN	1,4401		0,1,2200	21.0	24.0	23.0		1490,1340,1490	-6.2	0.0	19	dbSNP_134	23	22,8576		0,22,4277	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	43,43,43	0,23,6477	GG,GA,AA		0.2559,0.0227,0.1769	benign,benign,benign	497/634,447/584,497/709	36352906	23,12977	2201	4299	6500	SO:0001583	missense	84063	exon11			GTGCCCAGGCCAG	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.1490A>G	19.37:g.36352906A>G	ENSP00000353331:p.Gln497Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	A	0.272	-0.992131	0.02162	2.27E-4	0.002559	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658;ENST00000270294	T;T;T	0.13420	2.59;2.59;2.59	4.95	-6.2	0.02072	Immunoglobulin-like (1);	1.079580	0.07284	N	0.871301	T	0.03348	0.0097	N	0.08118	0	0.09310	N	0.999999	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.001	T	0.44483	-0.9325	10	0.13853	T	0.58	0.5967	7.0983	0.25321	0.6265:0.0:0.2415:0.1321	.	497;477;497;447;497	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	R	497;447;497;477;43	ENSP00000262625:Q497R;ENSP00000345067:Q447R;ENSP00000353331:Q497R	ENSP00000262625:Q497R	Q	+	2	0	KIRREL2	41044746	0.205000	0.23458	0.003000	0.11579	0.258000	0.26162	-0.122000	0.10627	-1.211000	0.02624	-0.253000	0.11424	CAG	A|0.999;G|0.001	0.001	strong		0.622	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
TMC5	79838	hgsc.bcm.edu	37	16	19492752	19492752	+	Silent	SNP	C	C	T	rs35421097	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:19492752C>T	ENST00000396229.2	+	15	3077	c.2328C>T	c.(2326-2328)aaC>aaT	p.N776N	TMC5_ENST00000542583.2_Silent_p.N776N|TMC5_ENST00000564959.1_Silent_p.N459N|TMC5_ENST00000219821.5_Silent_p.N530N|TMC5_ENST00000381414.4_Silent_p.N776N|TMC5_ENST00000541464.1_Silent_p.N724N|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000561503.1_Silent_p.N417N	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	776					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTGCCAGGAACGTTCTAGAAC	0.443													C|||	62	0.0123802	0.0	0.0115	5008	,	,		18652	0.0		0.0308	False		,,,				2504	0.0235				p.N776N		Atlas-SNP	.											.	TMC5	169	.	0			c.C2328T						PASS	.	C	,,	24,4370	31.7+/-61.6	0,24,2173	188.0	157.0	167.0		2328,2328,1590	-9.3	0.8	16	dbSNP_126	167	273,8327	103.3+/-164.5	5,263,4032	no	coding-synonymous,coding-synonymous,coding-synonymous	TMC5	NM_001105248.1,NM_001105249.1,NM_024780.4	,,	5,287,6205	TT,TC,CC		3.1744,0.5462,2.2857	,,	776/1007,776/949,530/761	19492752	297,12697	2197	4300	6497	SO:0001819	synonymous_variant	79838	exon15			CAGGAACGTTCTA	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.2328C>T	16.37:g.19492752C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Silent	SNP	ENST00000396229.2	37	CCDS45431.1																																																																																			C|0.981;T|0.019	0.019	strong		0.443	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
FRG1	2483	hgsc.bcm.edu	37	4	190876257	190876257	+	Missense_Mutation	SNP	G	G	A	rs75585360		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:190876257G>A	ENST00000226798.4	+	5	605	c.383G>A	c.(382-384)cGt>cAt	p.R128H	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	128					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.R128H(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GTTGTTGGGCGTTCAGATGCA	0.353																																					p.R128H		Atlas-SNP	.											FRG1,NS,carcinoma,0,1	FRG1	76	1	1	Substitution - Missense(1)	endometrium(1)	c.G383A						scavenged	.						93.0	92.0	93.0					4																	190876257		2203	4300	6503	SO:0001583	missense	2483	exon5			TTGGGCGTTCAGA	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.383G>A	4.37:g.190876257G>A	ENSP00000226798:p.Arg128His	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	291	5	0.0171821	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	17.27	3.347229	0.61183	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.48522	1.93;0.81	4.04	4.04	0.47022	Actin cross-linking (1);	0.047916	0.85682	D	0.000000	T	0.42653	0.1212	.	.	.	0.80722	D	1	B	0.22414	0.069	B	0.26770	0.073	T	0.45381	-0.9265	9	0.59425	D	0.04	2.3578	14.145	0.65344	0.0:0.0:1.0:0.0	.	128	Q14331	FRG1_HUMAN	H	128;65	ENSP00000226798:R128H;ENSP00000435943:R65H	ENSP00000226798:R128H	R	+	2	0	FRG1	191113251	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.226000	0.72277	1.964000	0.57103	0.567000	0.79289	CGT	.	.	weak		0.353	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
CDC27	996	hgsc.bcm.edu	37	17	45234300	45234300	+	Missense_Mutation	SNP	G	G	T	rs199588670		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45234300G>T	ENST00000066544.3	-	7	914	c.821C>A	c.(820-822)gCt>gAt	p.A274D	CDC27_ENST00000527547.1_Missense_Mutation_p.A274D|CDC27_ENST00000446365.2_Missense_Mutation_p.A213D|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Missense_Mutation_p.A274D	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.A274D(11)		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						TGGACTAAGAGCTGCTGGTCC	0.363																																					p.A274D		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,10	CDC27	337	10	11	Substitution - Missense(11)	prostate(9)|skin(2)	c.C821A						scavenged	.						61.0	65.0	63.0					17																	45234300		2201	4292	6493	SO:0001583	missense	996	exon7			CTAAGAGCTGCTG	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.821C>A	17.37:g.45234300G>T	ENSP00000066544:p.Ala274Asp	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	61	2	0.0327869	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.604295	0.66445	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.69175	-0.38;-0.38;-0.13;-0.38;0.68	5.64	5.64	0.86602	.	0.058237	0.64402	D	0.000002	T	0.64735	0.2625	N	0.24115	0.695	0.58432	D	0.999999	P;P;P;B	0.51351	0.704;0.886;0.944;0.363	B;P;P;B	0.51615	0.216;0.495;0.675;0.143	T	0.64685	-0.6349	10	0.40728	T	0.16	-20.3108	17.2083	0.86924	0.0:0.0:1.0:0.0	.	213;274;274;274	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	D	274;274;213;274;274	ENSP00000066544:A274D;ENSP00000434614:A274D;ENSP00000392802:A213D;ENSP00000437339:A274D;ENSP00000432105:A274D	ENSP00000066544:A274D	A	-	2	0	CDC27	42589299	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.260000	0.95568	2.665000	0.90641	0.460000	0.39030	GCT	.	.	weak		0.363	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
MYOM3	127294	hgsc.bcm.edu	37	1	24418768	24418768	+	Silent	SNP	T	T	C	rs7556176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24418768T>C	ENST00000374434.3	-	11	1290	c.1128A>G	c.(1126-1128)ccA>ccG	p.P376P	MYOM3_ENST00000329601.7_Silent_p.P376P|MYOM3_ENST00000330966.7_Silent_p.P377P|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	376	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GGACGTTCAGTGGGGAGCCTG	0.642													C|||	1884	0.376198	0.472	0.3199	5008	,	,		14860	0.3522		0.4662	False		,,,				2504	0.2188				p.P376P		Atlas-SNP	.											.	MYOM3	131	.	0			c.A1128G						PASS	.	C		1692,2080		382,928,576	44.0	50.0	48.0		1128	-10.7	0.0	1	dbSNP_116	48	3646,4546		827,1992,1277	no	coding-synonymous	MYOM3	NM_152372.3		1209,2920,1853	CC,CT,TT		44.5068,44.8568,44.6172		376/1438	24418768	5338,6626	1886	4096	5982	SO:0001819	synonymous_variant	127294	exon11			GTTCAGTGGGGAG	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.1128A>G	1.37:g.24418768T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			T|0.586;C|0.414	0.414	strong		0.642	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
COQ6	51004	hgsc.bcm.edu	37	14	74428445	74428445	+	Missense_Mutation	SNP	G	G	A	rs8500	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74428445G>A	ENST00000334571.2	+	11	1256	c.1216G>A	c.(1216-1218)Gtg>Atg	p.V406M	COQ6_ENST00000554920.1_Intron|COQ6_ENST00000394026.4_Missense_Mutation_p.V381M|COQ6_ENST00000238709.4_Missense_Mutation_p.V331M|ENTPD5_ENST00000557325.1_Intron	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	406			V -> M (in dbSNP:rs8500). {ECO:0000269|Ref.4}.		small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TTCAGGTTCCGTGAGCCACCT	0.438													A|||	1730	0.345447	0.1868	0.4251	5008	,	,		20118	0.1984		0.4821	False		,,,				2504	0.5143				p.V406M		Atlas-SNP	.											.	COQ6	27	.	0			c.G1216A						PASS	.	A	MET/VAL,MET/VAL	940,3466	736.9+/-410.8	109,722,1372	136.0	132.0	133.0		1216,991	4.1	1.0	14	dbSNP_52	133	4061,4539	594.4+/-393.3	951,2159,1190	yes	missense,missense	COQ6	NM_182476.2,NM_182480.2	21,21	1060,2881,2562	AA,AG,GG		47.2209,21.3345,38.4515	benign,benign	406/469,331/394	74428445	5001,8005	2203	4300	6503	SO:0001583	missense	51004	exon11			GGTTCCGTGAGCC	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"""coenzyme Q6 homolog (yeast)"", ""coenzyme Q6 homolog, monooxygenase (yeast)"", ""coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"""			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.1216G>A	14.37:g.74428445G>A	ENSP00000333946:p.Val406Met	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Missense_Mutation	SNP	ENST00000334571.2	37	CCDS9823.1	745	0.3411172161172161	89	0.18089430894308944	161	0.4447513812154696	129	0.22552447552447552	366	0.48284960422163586	A	8.409	0.843656	0.16963	0.213345	0.472209	ENSG00000119723	ENST00000394026;ENST00000555376;ENST00000238709;ENST00000334571;ENST00000556299	T;T;T	0.51574	0.7;0.7;0.7	5.34	4.14	0.48551	Monooxygenase, FAD-binding (1);	0.168630	0.64402	N	0.000003	T	0.00012	0.0000	N	0.12569	0.235	0.09310	P	0.9999999999998209	B;B;B;B	0.15719	0.014;0.003;0.012;0.008	B;B;B;B	0.20184	0.013;0.006;0.016;0.028	T	0.46233	-0.9206	9	0.31617	T	0.26	-10.2637	6.8788	0.24160	0.7218:0.0:0.0763:0.2019	rs8500;rs1139778;rs2074929;rs3179799;rs3203830;rs52834700;rs60262625;rs8500	381;406;331;331	B7Z3K8;Q9Y2Z9;G3XA86;Q86U30	.;COQ6_HUMAN;.;.	M	381;331;331;406;94	ENSP00000377594:V381M;ENSP00000238709:V331M;ENSP00000333946:V406M	ENSP00000238709:V331M	V	+	1	0	COQ6	73498198	0.993000	0.37304	0.997000	0.53966	0.777000	0.43975	2.062000	0.41413	1.049000	0.40321	-0.254000	0.11334	GTG	G|0.641;A|0.359	0.359	strong		0.438	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1		
SPPL2C	162540	hgsc.bcm.edu	37	17	43923683	43923683	+	Missense_Mutation	SNP	A	A	G	rs12185268	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43923683A>G	ENST00000329196.5	+	1	1428	c.1411A>G	c.(1411-1413)Atc>Gtc	p.I471V	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	471			I -> V (in dbSNP:rs12185268).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTCCCGTCAGATCTACTTCGT	0.582													G|||	432	0.086262	0.0151	0.1585	5008	,	,		22310	0.001		0.2396	False		,,,				2504	0.0613				p.I471V		Atlas-SNP	.											.	.	.	.	0			c.A1411G						PASS	.	G	VAL/ILE	203,4203	807.6+/-415.9	5,193,2005	134.0	101.0	112.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1411	0.8	0.3	17	dbSNP_120	112	1928,6672	726.4+/-406.6	221,1486,2593	yes	missense	IMP5	NM_175882.2	29	226,1679,4598	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	22.4186,4.6074,16.3847	benign	471/685	43923683	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			CGTCAGATCTACT		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1411A>G	17.37:g.43923683A>G	ENSP00000332488:p.Ile471Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	0	-2.736907	0.00088	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.17213	2.29	5.2	0.828	0.18841	.	0.406531	0.17861	N	0.159532	T	0.00012	0.0000	N	0.00869	-1.13	0.58432	P	8.000000000008E-6	B	0.11235	0.004	B	0.15484	0.013	T	0.41431	-0.9509	9	0.02654	T	1	-17.3089	4.7545	0.13077	0.3353:0.3144:0.3503:0.0	rs12185268;rs17763723;rs60640757;rs12185268	471	Q8IUH8	IMP5_HUMAN	V	471	ENSP00000332488:I471V	ENSP00000332488:I471V	I	+	1	0	AC217771.1	41279463	0.049000	0.20398	0.302000	0.25058	0.000000	0.00434	0.337000	0.19841	-0.152000	0.11156	-0.971000	0.02607	ATC	A|0.853;G|0.147	0.147	strong		0.582	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
GTF2A1L	11036	hgsc.bcm.edu	37	2	48873978	48873978	+	Missense_Mutation	SNP	A	A	G	rs10432667	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48873978A>G	ENST00000403751.3	+	6	812	c.775A>G	c.(775-777)Aat>Gat	p.N259D	STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.N963D|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.N963D|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.N963D|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.N916D|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.N225D|LHCGR_ENST00000420913.3_Intron|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.N963D	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	259				N -> D (in Ref. 1; AAD39634 and 4; AAH64585). {ECO:0000305}.	cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AACAAATTCTAATGTGGAGTC	0.468													A|||	1014	0.202476	0.0696	0.1945	5008	,	,		17718	0.2768		0.3052	False		,,,				2504	0.2055				p.N963D		Atlas-SNP	.											.	STON1-GTF2A1L	180	.	0			c.A2887G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	482,3924	226.2+/-241.8	32,418,1753	99.0	97.0	97.0		673,2887,2746,775,2887	0.8	0.0	2	dbSNP_119	97	2415,6185	400.1+/-346.7	339,1737,2224	yes	missense,missense,missense,missense,missense	GTF2A1L,STON1-GTF2A1L	NM_001193487.1,NM_001198593.1,NM_001198594.1,NM_006872.3,NM_172311.2	23,23,23,23,23	371,2155,3977	GG,GA,AA		28.0814,10.9396,22.2743	benign,benign,benign,benign,benign	225/445,963/1159,916/1136,259/479,963/1183	48873978	2897,10109	2203	4300	6503	SO:0001583	missense	286749	exon8			AATTCTAATGTGG	AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"""TFIIA alpha/beta like factor"""	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.775A>G	2.37:g.48873978A>G	ENSP00000384597:p.Asn259Asp	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	178	77	0.432584	NM_001198593	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	486	0.22252747252747251	35	0.07113821138211382	90	0.24861878453038674	145	0.2534965034965035	216	0.2849604221635884	A	7.228	0.598742	0.13939	0.109396	0.280814	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000437125;ENST00000430487;ENST00000403751	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	4.69	0.795	0.18643	.	1.024610	0.07778	N	0.952863	T	0.00012	0.0000	L	0.58101	1.795	0.80722	P	0.0	B;B;B;B;B	0.29301	0.241;0.023;0.08;0.183;0.08	B;B;B;B;B	0.28916	0.037;0.007;0.043;0.096;0.042	T	0.33189	-0.9878	9	0.09084	T	0.74	.	12.5595	0.56273	0.3489:0.6511:0.0:0.0	rs10432667;rs17846669;rs17859766;rs52792807;rs59591396;rs10432667	225;916;963;259;963	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	D	963;963;963;963;916;258;268;225;259	ENSP00000385499:N963D;ENSP00000385701:N963D;ENSP00000378236:N963D;ENSP00000311493:N963D;ENSP00000378234:N916D;ENSP00000396702:N268D;ENSP00000387896:N225D;ENSP00000384597:N259D	ENSP00000384597:N259D	N	+	1	0	STON1-GTF2A1L;GTF2A1L	48727482	0.000000	0.05858	0.000000	0.03702	0.453000	0.32348	0.323000	0.19593	-0.018000	0.14079	0.482000	0.46254	AAT	A|0.780;G|0.220	0.220	strong		0.468	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872	
CD8B	926	hgsc.bcm.edu	37	2	87042825	87042825	+	Missense_Mutation	SNP	T	T	C	rs35555413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:87042825T>C	ENST00000349455.3	-	5	596	c.547A>G	c.(547-549)Ata>Gta	p.I183V	CD8B_ENST00000331469.2_Missense_Mutation_p.I213V|CD8B_ENST00000393759.2_3'UTR|CD8B_ENST00000393761.2_Silent_p.V170V	NM_172102.3	NP_742100.1	P10966	CD8B_HUMAN	CD8b molecule	0					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)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	13						GTTCCTGATATACCTTCCCCT	0.413													T|||	553	0.110423	0.0061	0.2666	5008	,	,		20804	0.0357		0.2028	False		,,,				2504	0.1227				p.I213V		Atlas-SNP	.											.	CD8B	37	.	0			c.A637G						PASS	.	T	,,VAL/ILE,VAL/ILE	203,4203	125.3+/-162.5	5,193,2005	272.0	250.0	257.0		510,,547,637	0.8	0.0	2	dbSNP_126	257	1702,6898	311.0+/-310.2	173,1356,2771	yes	coding-synonymous,utr-3,missense,missense	CD8B	NM_001178100.1,NM_172101.3,NM_172102.3,NM_172213.3	,,29,29	178,1549,4776	CC,CT,TT		19.7907,4.6074,14.6471	,,,	170/199,,183/214,213/244	87042825	1905,11101	2203	4300	6503	SO:0001583	missense	926	exon6			CTGATATACCTTC		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	ENST00000349455.3:c.547A>G	2.37:g.87042825T>C	ENSP00000340592:p.Ile183Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	NM_172213	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Missense_Mutation	SNP	ENST00000349455.3	37	CCDS1994.1	277	0.12683150183150182	6	0.012195121951219513	84	0.23204419889502761	25	0.043706293706293704	162	0.21372031662269128	T	6.659	0.490110	0.12702	0.046074	0.197907	ENSG00000172116	ENST00000349455;ENST00000331469;ENST00000534926	.	.	.	2.0	0.758	0.18432	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P;P	0.34587	0.458;0.458	B;B	0.28232	0.087;0.087	T	0.33523	-0.9865	6	0.25751	T	0.34	.	5.1473	0.14991	0.0:0.0:0.4277:0.5723	rs35555413;rs35555413	183;213	P10966-3;P10966-6	.;.	V	183;213;21	.	ENSP00000331172:I213V	I	-	1	0	CD8B	86896336	0.000000	0.05858	0.005000	0.12908	0.055000	0.15305	-0.282000	0.08445	0.190000	0.20209	0.454000	0.30748	ATA	T|0.864;C|0.136	0.136	strong		0.413	CD8B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252594.1	NM_172099	
PANK4	55229	hgsc.bcm.edu	37	1	2445832	2445832	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:2445832T>C	ENST00000378466.3	-	11	1460	c.1448A>G	c.(1447-1449)aAg>aGg	p.K483R	PANK4_ENST00000435556.3_Missense_Mutation_p.K444R	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	483					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		GTTCCAGTACTTCTGCCGGAA	0.627																																					p.K483R		Atlas-SNP	.											.	PANK4	64	.	0			c.A1448G						PASS	.						72.0	75.0	74.0					1																	2445832		2203	4300	6503	SO:0001583	missense	55229	exon11			CAGTACTTCTGCC	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.1448A>G	1.37:g.2445832T>C	ENSP00000367727:p.Lys483Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	t	14.68	2.609185	0.46527	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.18810	2.19;2.19	5.1	5.1	0.69264	Domain of unknown function DUF89 (2);	0.000000	0.85682	D	0.000000	T	0.32912	0.0845	L	0.33485	1.01	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.99	T	0.03503	-1.1030	10	0.22109	T	0.4	-33.6939	14.0447	0.64698	0.0:0.0:0.0:1.0	.	444;483	E9PHT6;Q9NVE7	.;PANK4_HUMAN	R	483;444	ENSP00000367727:K483R;ENSP00000421433:K444R	ENSP00000367727:K483R	K	-	2	0	PANK4	2435692	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	5.751000	0.68720	1.933000	0.56026	0.454000	0.30748	AAG	.	.	none		0.627	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
SLC25A29	123096	hgsc.bcm.edu	37	14	100759277	100759277	+	Silent	SNP	C	C	T	rs3742379	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:100759277C>T	ENST00000359232.3	-	4	555	c.255G>A	c.(253-255)cgG>cgA	p.R85R	RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000554912.1_Silent_p.R19R|SLC25A29_ENST00000392908.3_Missense_Mutation_p.G71S|AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000555927.1_Silent_p.R19R|SLC25A29_ENST00000539621.1_Silent_p.R19R|SLC25A29_ENST00000556505.1_Silent_p.R19R	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	85						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	GGCCCAGGGCCCGGAGGGTGT	0.701													C|||	1400	0.279553	0.1876	0.2565	5008	,	,		14810	0.5317		0.3121	False		,,,				2504	0.1268				p.R85R		Atlas-SNP	.											SLC25A29,NS,carcinoma,0,1	SLC25A29	14	1	0			c.G255A						PASS	.	C		816,3446		90,636,1405	10.0	13.0	12.0		255	2.0	1.0	14	dbSNP_107	12	2498,5870		389,1720,2075	no	coding-synonymous	SLC25A29	NM_001039355.1		479,2356,3480	TT,TC,CC		29.8518,19.1459,26.2391		85/304	100759277	3314,9316	2131	4184	6315	SO:0001819	synonymous_variant	123096	exon4			CAGGGCCCGGAGG	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"""Solute carriers"""	20116	protein-coding gene	gene with protein product		615064	"""chromosome 14 open reading frame 69"", ""solute carrier family 25, member 29"""	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.255G>A	14.37:g.100759277C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_001039355	A3KMR5|Q541V0	Silent	SNP	ENST00000359232.3	37	CCDS32156.1	697	0.3191391941391941	77	0.1565040650406504	90	0.24861878453038674	307	0.5367132867132867	223	0.2941952506596306	C	6.911	0.537720	0.13188	0.191459	0.298518	ENSG00000197119	ENST00000392908;ENST00000554060	.	.	.	4.99	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45775	-0.9238	4	0.87932	D	0	-41.4631	3.2678	0.06871	0.3516:0.3279:0.2417:0.0788	rs3742379	.	.	.	S	71	.	ENSP00000376640:G71S	G	-	1	0	SLC25A29	99829030	0.824000	0.29247	0.983000	0.44433	0.355000	0.29361	0.082000	0.14847	0.111000	0.17947	-0.302000	0.09304	GGC	C|0.688;G|0.000;T|0.312	0.312	strong		0.701	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3		
GDPD4	220032	hgsc.bcm.edu	37	11	76954812	76954812	+	Missense_Mutation	SNP	T	T	C	rs11237145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76954812T>C	ENST00000376217.2	-	12	1418	c.1168A>G	c.(1168-1170)Att>Gtt	p.I390V	GDPD4_ENST00000315938.4_Missense_Mutation_p.I390V			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	390	GP-PDE.		I -> V (in dbSNP:rs11237145).		glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						AGGGTTTCAATGGATACTAAA	0.413													C|||	1274	0.254393	0.0514	0.1916	5008	,	,		16179	0.256		0.3738	False		,,,				2504	0.4489				p.I390V		Atlas-SNP	.											.	GDPD4	49	.	0			c.A1168G						PASS	.	C	VAL/ILE	458,3942	784.3+/-414.7	30,398,1772	117.0	108.0	111.0		1168	-8.5	0.0	11	dbSNP_120	111	3083,5501	658.5+/-401.6	536,2011,1745	yes	missense	GDPD4	NM_182833.1	29	566,2409,3517	CC,CT,TT		35.9157,10.4091,27.272	benign	390/521	76954812	3541,9443	2200	4292	6492	SO:0001583	missense	220032	exon12			TTTCAATGGATAC	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1168A>G	11.37:g.76954812T>C	ENSP00000365390:p.Ile390Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		501	0.22939560439560439	25	0.0508130081300813	76	0.20994475138121546	130	0.22727272727272727	270	0.3562005277044855	C	0.016	-1.522396	0.00967	0.104091	0.359157	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.10763	2.84;2.84	4.27	-8.54	0.00912	.	0.708347	0.13925	N	0.353264	T	0.00012	0.0000	N	0.05351	-0.065	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32955	-0.9887	9	0.06099	T	0.92	-2.8135	3.1474	0.06477	0.0959:0.3517:0.1943:0.3581	rs11237145;rs17824220;rs52820078;rs11237145	390	Q6W3E5-2	.	V	390	ENSP00000365390:I390V;ENSP00000320815:I390V	ENSP00000320815:I390V	I	-	1	0	GDPD4	76632460	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.063000	0.00622	-2.006000	0.00958	-1.874000	0.00550	ATT	C|0.254;N|0.000	0.254	strong		0.413	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
MED16	10025	hgsc.bcm.edu	37	19	890165	890165	+	Silent	SNP	G	G	A	rs6678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:890165G>A	ENST00000589119.1	-	2	248	c.249C>T	c.(247-249)gcC>gcT	p.A83A	MED16_ENST00000325464.1_Silent_p.A83A|MED16_ENST00000312090.6_Silent_p.A83A|MED16_ENST00000269814.4_Silent_p.A83A|MED16_ENST00000395808.3_Silent_p.A83A|MED16_ENST00000606828.1_Intron			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	83					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCAGGTGATGGCCTCGTGGT	0.682													G|||	891	0.177915	0.2693	0.1931	5008	,	,		17255	0.0208		0.2604	False		,,,				2504	0.1207				p.A83A		Atlas-SNP	.											.	MED16	61	.	0			c.C249T						PASS	.	G		1045,3267		149,747,1260	87.0	69.0	75.0		249	1.2	1.0	19	dbSNP_52	75	2043,6395		254,1535,2430	no	coding-synonymous	MED16	NM_005481.2		403,2282,3690	AA,AG,GG		24.2119,24.2347,24.2196		83/878	890165	3088,9662	2156	4219	6375	SO:0001819	synonymous_variant	10025	exon3			GGTGATGGCCTCG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.249C>T	19.37:g.890165G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			G|0.765;A|0.235	0.235	strong		0.682	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
KDM4B	23030	hgsc.bcm.edu	37	19	5110794	5110794	+	Silent	SNP	A	A	G	rs2613739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5110794A>G	ENST00000159111.4	+	10	1298	c.1080A>G	c.(1078-1080)gcA>gcG	p.A360A	KDM4B_ENST00000536461.1_Silent_p.A360A|KDM4B_ENST00000381759.4_Silent_p.A360A	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	360					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CCTGGAGTGCATCCCGGGCCT	0.701													G|||	3178	0.634585	0.6838	0.5706	5008	,	,		14508	0.6677		0.5656	False		,,,				2504	0.6503				p.A360A		Atlas-SNP	.											.	KDM4B	120	.	0			c.A1080G						PASS	.	G		2819,1581		904,1011,285	23.0	22.0	22.0		1080	-2.6	0.9	19	dbSNP_100	22	4747,3847		1318,2111,868	no	coding-synonymous	KDM4B	NM_015015.2		2222,3122,1153	GG,GA,AA		44.7638,35.9318,41.7731		360/1097	5110794	7566,5428	2200	4297	6497	SO:0001819	synonymous_variant	23030	exon10			GAGTGCATCCCGG	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1080A>G	19.37:g.5110794A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																			A|0.406;G|0.594	0.594	strong		0.701	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
KIAA1109	84162	hgsc.bcm.edu	37	4	123268859	123268859	+	Missense_Mutation	SNP	A	A	G	rs2306369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123268859A>G	ENST00000264501.4	+	76	13427	c.13054A>G	c.(13054-13056)Aca>Gca	p.T4352A	KIAA1109_ENST00000388738.3_Missense_Mutation_p.T4352A			Q2LD37	K1109_HUMAN	KIAA1109	4352			T -> A (in dbSNP:rs2306369).		regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GTCACCAGGGACAGTAGGACA	0.478													A|||	325	0.0648962	0.0424	0.0346	5008	,	,		19319	0.1518		0.0318	False		,,,				2504	0.0613				p.T4352A		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A13054G						PASS	.	A	ALA/THR	195,3931		3,189,1871	118.0	120.0	120.0		13054	5.0	1.0	4	dbSNP_100	120	297,8075		7,283,3896	yes	missense	KIAA1109	NM_015312.3	58	10,472,5767	GG,GA,AA		3.5475,4.7261,3.9366	benign	4352/5006	123268859	492,12006	2063	4186	6249	SO:0001583	missense	84162	exon74			CCAGGGACAGTAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.13054A>G	4.37:g.123268859A>G	ENSP00000264501:p.Thr4352Ala	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	206	107	0.519417	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	128	0.05860805860805861	22	0.044715447154471545	12	0.03314917127071823	72	0.1258741258741259	22	0.029023746701846966	A	5.759	0.324490	0.10900	0.047261	0.035475	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707	T;T;T	0.29142	2.57;2.57;1.58	6.16	5.03	0.67393	.	0.231131	0.45606	D	0.000348	T	0.00109	0.0003	N	0.03608	-0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34304	-0.9834	10	0.13853	T	0.58	.	8.277	0.31879	0.8328:0.0:0.1672:0.0	rs2306369;rs52836370;rs2306369	4351;4352	Q2LD37-4;Q2LD37	.;K1109_HUMAN	A	4352;4352;1021	ENSP00000264501:T4352A;ENSP00000373390:T4352A;ENSP00000410874:T1021A	ENSP00000264501:T4352A	T	+	1	0	KIAA1109	123488309	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.013000	0.40942	2.367000	0.80283	0.528000	0.53228	ACA	A|0.944;G|0.056	0.056	strong		0.478	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
AGMAT	79814	hgsc.bcm.edu	37	1	15909744	15909744	+	Missense_Mutation	SNP	C	C	T	rs11580170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15909744C>T	ENST00000375826.3	-	2	561	c.419G>A	c.(418-420)cGa>cAa	p.R140Q	DNAJC16_ENST00000483270.1_Intron|RP4-680D5.2_ENST00000428945.1_RNA	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	140			R -> Q (in dbSNP:rs11580170). {ECO:0000269|PubMed:11804860}.		agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		CTCTTGAATTCGCCGGCAGCT	0.527													C|||	1364	0.272364	0.5492	0.2133	5008	,	,		18278	0.0565		0.2326	False		,,,				2504	0.2035				p.R140Q	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.G419A						PASS	.	C	GLN/ARG	2311,2095	603.0+/-390.0	608,1095,500	64.0	65.0	65.0		419	1.2	0.4	1	dbSNP_120	65	2130,6470	365.7+/-334.0	252,1626,2422	yes	missense	AGMAT	NM_024758.4	43	860,2721,2922	TT,TC,CC		24.7674,47.5488,34.1458	benign	140/353	15909744	4441,8565	2203	4300	6503	SO:0001583	missense	79814	exon2			TGAATTCGCCGGC	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.419G>A	1.37:g.15909744C>T	ENSP00000364986:p.Arg140Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	57	0.564356	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	575	0.2632783882783883	260	0.5284552845528455	99	0.27348066298342544	37	0.06468531468531469	179	0.23614775725593667	C	8.173	0.792103	0.16258	0.524512	0.247674	ENSG00000116771	ENST00000375826	D	0.83992	-1.79	5.17	1.23	0.21249	Ureohydrolase domain (1);	0.437097	0.21674	N	0.070839	T	0.00012	0.0000	N	0.20445	0.575	0.53005	P	3.100000000000325E-5	B	0.16166	0.016	B	0.22880	0.042	T	0.41520	-0.9504	9	0.12430	T	0.62	-1.7129	8.4855	0.33069	0.3127:0.5585:0.0:0.1288	rs11580170;rs59956736;rs11580170	140	Q9BSE5	SPEB_HUMAN	Q	140	ENSP00000364986:R140Q	ENSP00000364986:R140Q	R	-	2	0	AGMAT	15782331	0.113000	0.22115	0.431000	0.26735	0.563000	0.35712	0.542000	0.23222	0.280000	0.22209	-0.457000	0.05445	CGA	C|0.690;T|0.310	0.310	strong		0.527	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
TPR	7175	hgsc.bcm.edu	37	1	186314809	186314809	+	Missense_Mutation	SNP	G	G	A	rs200209324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:186314809G>A	ENST00000367478.4	-	24	3412	c.3116C>T	c.(3115-3117)aCa>aTa	p.T1039I		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1039					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ACTAGAAAGTGTTTTCTTCAA	0.348			T	NTRK1	papillary thyroid																																p.T1039I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.C3116T						PASS	.	G	ILE/THR	2,3686		0,2,1842	107.0	94.0	99.0		3116	4.3	1.0	1		99	16,8154		0,16,4069	yes	missense	TPR	NM_003292.2	89	0,18,5911	AA,AG,GG		0.1958,0.0542,0.1518	benign	1039/2364	186314809	18,11840	1844	4085	5929	SO:0001583	missense	7175	exon24			GAAAGTGTTTTCT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3116C>T	1.37:g.186314809G>A	ENSP00000356448:p.Thr1039Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.713644	0.48517	5.42E-4	0.001958	ENSG00000047410	ENST00000367478	T	0.23348	1.91	5.31	4.34	0.51931	Prefoldin (1);Tetratricopeptide, MLP1/MLP2-like (1);	0.083000	0.85682	D	0.000000	T	0.16769	0.0403	N	0.08118	0	0.28533	N	0.912504	P	0.35821	0.523	B	0.42798	0.398	T	0.07252	-1.0782	10	0.56958	D	0.05	.	9.3043	0.37865	0.0:0.3079:0.566:0.1261	.	1039	P12270	TPR_HUMAN	I	1039	ENSP00000356448:T1039I	ENSP00000356448:T1039I	T	-	2	0	TPR	184581432	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.135000	0.50546	2.630000	0.89119	0.650000	0.86243	ACA	G|0.998;A|0.002	0.002	strong		0.348	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
OGFR	11054	hgsc.bcm.edu	37	20	61444693	61444693	+	Missense_Mutation	SNP	G	G	A	rs35813009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	9	1	0.111111		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	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		
CACNA1I	8911	hgsc.bcm.edu	37	22	40058393	40058393	+	Missense_Mutation	SNP	A	A	T	rs58021347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:40058393A>T	ENST00000402142.3	+	17	3325	c.3325A>T	c.(3325-3327)Atg>Ttg	p.M1109L	CACNA1I_ENST00000401624.1_Missense_Mutation_p.M1109L|CACNA1I_ENST00000404898.1_Missense_Mutation_p.M1074L|CACNA1I_ENST00000336649.4_Missense_Mutation_p.M1115L|CACNA1I_ENST00000400164.3_Missense_Mutation_p.M1074L|CACNA1I_ENST00000407673.1_Missense_Mutation_p.M1074L	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1109					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)	CTTCACCAAGATGGGCGACCG	0.692													A|||	5	0.000998403	0.0008	0.0	5008	,	,		12372	0.0		0.004	False		,,,				2504	0.0				p.M1109L		Atlas-SNP	.											.	CACNA1I	264	.	0			c.A3325T						PASS	.	A	LEU/MET,LEU/MET	2,2518		0,2,1258	3.0	4.0	4.0		3220,3325	5.1	1.0	22	dbSNP_129	4	28,5348		0,28,2660	yes	missense,missense	CACNA1I	NM_001003406.1,NM_021096.3	15,15	0,30,3918	TT,TA,AA		0.5208,0.0794,0.3799	benign,benign	1074/2189,1109/2224	40058393	30,7866	1260	2688	3948	SO:0001583	missense	8911	exon17			ACCAAGATGGGCG	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.3325A>T	22.37:g.40058393A>T	ENSP00000385019:p.Met1109Leu	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	37	CCDS46710.1	7	0.003205128205128205	2	0.0040650406504065045	0	0.0	0	0.0	5	0.006596306068601583	A	18.52	3.641292	0.67244	7.94E-4	0.005208	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.96459	-4.0;-3.97;-3.97;-3.94;-4.02;-3.94	5.1	5.1	0.69264	.	0.452723	0.26173	N	0.025902	D	0.94368	0.8189	L	0.31207	0.915	0.29689	N	0.841121	B;P;B;B	0.48407	0.001;0.91;0.002;0.025	B;D;B;B	0.62955	0.003;0.909;0.005;0.012	D	0.90560	0.4515	10	0.19147	T	0.46	.	14.8805	0.70528	1.0:0.0:0.0:0.0	rs58021347	1074;1109;1074;1109	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	L	1109;1074;1109;1074;1115;1074	ENSP00000385019:M1109L;ENSP00000384093:M1074L;ENSP00000383887:M1109L;ENSP00000385680:M1074L;ENSP00000337829:M1115L;ENSP00000383028:M1074L	ENSP00000337829:M1115L	M	+	1	0	CACNA1I	38388339	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.403000	0.59729	1.918000	0.55548	0.459000	0.35465	ATG	A|0.997;T|0.003	0.003	strong		0.692	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412138	105412138	+	Missense_Mutation	SNP	A	A	G	rs200384326		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	225	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	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	
HRNR	388697	hgsc.bcm.edu	37	1	152188999	152188999	+	Silent	SNP	G	G	A	rs149648668	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152188999G>A	ENST00000368801.2	-	3	5181	c.5106C>T	c.(5104-5106)caC>caT	p.H1702H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1702					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.H1702H(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTTGTCGGCCGTGGCCCGAAG	0.632																																					p.H1702H		Atlas-SNP	.											HRNR,NS,carcinoma,0,2	HRNR	403	2	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C5106T						scavenged	.	G		87,3097		0,87,1505	50.0	74.0	66.0		5106	-6.0	0.0	1	dbSNP_134	66	354,5964		0,354,2805	no	coding-synonymous	HRNR	NM_001009931.1		0,441,4310	AA,AG,GG		5.603,2.7324,4.6411		1702/2851	152188999	441,9061	1592	3159	4751	SO:0001819	synonymous_variant	388697	exon3			TCGGCCGTGGCCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5106C>T	1.37:g.152188999G>A		Somatic	452	2	0.00442478		WXS	Illumina HiSeq	Phase_I	426	48	0.112676	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.947;A|0.053	0.053	strong		0.632	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
TRIM65	201292	hgsc.bcm.edu	37	17	73888423	73888423	+	Silent	SNP	A	A	G	rs7222755	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73888423A>G	ENST00000269383.3	-	3	734	c.669T>C	c.(667-669)caT>caC	p.H223H		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	223						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAGCCTCCAAATGGACCCGCA	0.647													G|||	2044	0.408147	0.7859	0.2709	5008	,	,		16113	0.2212		0.2972	False		,,,				2504	0.3016				p.H223H		Atlas-SNP	.											.	TRIM65	23	.	0			c.T669C						PASS	.	G		3126,1276		1135,856,210	23.0	27.0	26.0		669	3.2	0.9	17	dbSNP_116	26	2536,6062		386,1764,2149	no	coding-synonymous	TRIM65	NM_173547.2		1521,2620,2359	GG,GA,AA		29.4952,28.9868,43.5538		223/518	73888423	5662,7338	2201	4299	6500	SO:0001819	synonymous_variant	201292	exon3			CTCCAAATGGACC	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.669T>C	17.37:g.73888423A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Silent	SNP	ENST00000269383.3	37	CCDS11732.1	843|843	0.385989010989011|0.385989010989011	374|374	0.7601626016260162|0.7601626016260162	109|109	0.3011049723756906|0.3011049723756906	147|147	0.256993006993007|0.256993006993007	213|213	0.28100263852242746|0.28100263852242746	G|G	0.396|0.396	-0.920654|-0.920654	0.02396|0.02396	0.710132|0.710132	0.294952|0.294952	ENSG00000141569|ENSG00000141569	ENST00000540128|ENST00000543309	.|.	.|.	.|.	4.23|4.23	3.23|3.23	0.37069|0.37069	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999999509411|0.99999999509411	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24728|0.24728	-1.0152|-1.0152	3|3	.|.	.|.	.|.	.|.	7.3708|7.3708	0.26800|0.26800	0.0908:0.3209:0.5883:0.0|0.0908:0.3209:0.5883:0.0	rs7222755;rs60028486|rs7222755;rs60028486	.|.	.|.	.|.	L|T	215|97	.|.	.|.	F|I	-|-	1|2	0|0	TRIM65|TRIM65	71400018|71400018	0.927000|0.927000	0.31430|0.31430	0.939000|0.939000	0.37840|0.37840	0.013000|0.013000	0.08279|0.08279	0.449000|0.449000	0.21744|0.21744	0.429000|0.429000	0.26202|0.26202	-0.355000|-0.355000	0.07637|0.07637	TTT|ATT	A|0.591;G|0.409	0.409	strong		0.647	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
WDR62	284403	hgsc.bcm.edu	37	19	36594369	36594369	+	Silent	SNP	C	C	T	rs45470992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36594369C>T	ENST00000270301.7	+	30	3624	c.3624C>T	c.(3622-3624)tcC>tcT	p.S1208S	WDR62_ENST00000401500.2_Silent_p.S1213S			O43379	WDR62_HUMAN	WD repeat domain 62	1208					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)			ATGCCCCCTCCACCTGTTCCT	0.647													C|||	247	0.0493211	0.0083	0.0331	5008	,	,		19456	0.1062		0.0358	False		,,,				2504	0.0716				p.S1213S		Atlas-SNP	.											.	WDR62	102	.	0			c.C3639T						PASS	.	C	,	71,4335	64.1+/-101.4	0,71,2132	96.0	87.0	90.0		3639,3624	-2.0	0.0	19	dbSNP_127	90	336,8264	115.0+/-174.9	3,330,3967	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	3,401,6099	TT,TC,CC		3.907,1.6114,3.1293	,	1213/1524,1208/1519	36594369	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon30			CCCCTCCACCTGT	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.3624C>T	19.37:g.36594369C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			C|0.963;T|0.037	0.037	strong		0.647	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
SNW1	22938	hgsc.bcm.edu	37	14	78205189	78205189	+	Silent	SNP	T	T	C	rs147154490		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:78205189T>C	ENST00000261531.7	-	5	527	c.465A>G	c.(463-465)gtA>gtG	p.V155V	SNW1_ENST00000554775.1_5'UTR|SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000555761.1_Silent_p.V155V	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	155					cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|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 by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CCTTCTGTGATACAGATTTTT	0.403													T|||	1	0.000199681	0.0	0.0	5008	,	,		18116	0.0		0.001	False		,,,				2504	0.0				p.V155V		Atlas-SNP	.											.	SNW1	44	.	0			c.A465G						PASS	.	T		0,4406		0,0,2203	90.0	93.0	92.0		465	-2.5	1.0	14	dbSNP_134	92	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	SNW1	NM_012245.2		0,20,6483	CC,CT,TT		0.2326,0.0,0.1538		155/537	78205189	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	22938	exon5			CTGTGATACAGAT	AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"""SKI interacting protein"""	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.465A>G	14.37:g.78205189T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	168	70	0.416667	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Silent	SNP	ENST00000261531.7	37	CCDS9867.1																																																																																			T|0.999;C|0.001	0.001	strong		0.403	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245	
PMFBP1	83449	hgsc.bcm.edu	37	16	72184566	72184566	+	Missense_Mutation	SNP	C	C	T	rs35370634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72184566C>T	ENST00000237353.10	-	5	838	c.577G>A	c.(577-579)Gag>Aag	p.E193K	PMFBP1_ENST00000537465.1_Missense_Mutation_p.E193K|PMFBP1_ENST00000355636.6_Missense_Mutation_p.E48K	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	193			E -> K (in dbSNP:rs35370634).			cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCTAGTAACTCGATGTTGCTC	0.532													C|||	439	0.0876597	0.0151	0.0634	5008	,	,		20294	0.0218		0.162	False		,,,				2504	0.1943				p.E193K		Atlas-SNP	.											.	PMFBP1	101	.	0			c.G577A						PASS	.	C	LYS/GLU,LYS/GLU	158,4238	107.3+/-145.7	6,146,2046	166.0	152.0	157.0		142,577	6.2	1.0	16	dbSNP_126	157	1404,7196	271.1+/-289.3	127,1150,3023	yes	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	56,56	133,1296,5069	TT,TC,CC		16.3256,3.5942,12.0191	probably-damaging,probably-damaging	48/883,193/1008	72184566	1562,11434	2198	4300	6498	SO:0001583	missense	83449	exon5			GTAACTCGATGTT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.577G>A	16.37:g.72184566C>T	ENSP00000237353:p.Glu193Lys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	121	73	0.603306	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	178	0.0815018315018315	8	0.016260162601626018	27	0.07458563535911603	11	0.019230769230769232	132	0.1741424802110818	C	33	5.203928	0.95033	0.035942	0.163256	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.79247	-1.25;-1.25;2.47	6.17	6.17	0.99709	.	0.000000	0.52532	D	0.000062	T	0.00666	0.0022	N	0.24115	0.695	0.29957	P	0.819727	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.989;0.989	T	0.33727	-0.9857	9	0.08837	T	0.75	-33.6909	16.3795	0.83443	0.0:1.0:0.0:0.0	rs35370634	193;193;193	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	K	193;193;48	ENSP00000443817:E193K;ENSP00000237353:E193K;ENSP00000347854:E48K	ENSP00000237353:E193K	E	-	1	0	PMFBP1	70742067	0.830000	0.29337	0.996000	0.52242	0.917000	0.54804	3.761000	0.55242	2.941000	0.99782	0.655000	0.94253	GAG	C|0.891;T|0.109	0.109	strong		0.532	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
OR5L2	26338	hgsc.bcm.edu	37	11	55595018	55595018	+	Silent	SNP	A	A	G	rs61745634|rs34954823|rs386753700	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	131	0	0		WXS	Illumina HiSeq	Phase_I	121	30	0.247934	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	
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280900T>G	ENST00000368799.1	-	3	6497	c.6462A>C	c.(6460-6462)caA>caC	p.Q2154H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2154	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGATTGCTCTTGGTGGGACC	0.592									Ichthyosis				-|||	1722	0.34385	0.3843	0.3487	5008	,	,		25148	0.4444		0.1541	False		,,,				2504	0.3773				p.Q2154H		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	0			c.A6462C						scavenged	.						380.0	322.0	342.0					1																	152280900		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGCTCTTGGTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6462A>C	1.37:g.152280900T>G	ENSP00000357789:p.Gln2154His	Somatic	325	1	0.00307692		WXS	Illumina HiSeq	Phase_I	496	136	0.274194	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411260	105411260	+	Missense_Mutation	SNP	A	A	G	rs2819425	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105411260A>G	ENST00000333244.5	-	7	10647	c.10528T>C	c.(10528-10530)Tcc>Ccc	p.S3510P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3510						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGCATGGAGGAGAGGCTCACG	0.637													.|||	103	0.0205671	0.0371	0.013	5008	,	,		18098	0.003		0.0278	False		,,,				2504	0.0143				p.S3510P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,+1,1	AHNAK2	719	1	0			c.T10528C						PASS	.	A	PRO/SER	96,3774		4,88,1843	124.0	134.0	131.0		10528	1.1	0.0	14	dbSNP_100	131	134,8102		1,132,3985	no	missense	AHNAK2	NM_138420.2	74	5,220,5828	GG,GA,AA		1.627,2.4806,1.8999	benign	3510/5796	105411260	230,11876	1935	4118	6053	SO:0001583	missense	113146	exon7			TGGAGGAGAGGCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.10528T>C	14.37:g.105411260A>G	ENSP00000353114:p.Ser3510Pro	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	190	100	0.526316	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	54	0.024725274725274724	26	0.052845528455284556	5	0.013812154696132596	6	0.01048951048951049	17	0.022427440633245383	a	0.017	-1.504266	0.00992	0.024806	0.01627	ENSG00000185567	ENST00000333244	T	0.00543	6.68	4.08	1.14	0.20703	.	.	.	.	.	T	0.00012	0.0000	N	0.00008	-3.105	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	3.7815	0.08682	0.091:0.2962:0.4609:0.1519	rs2819425	3510	Q8IVF2	AHNK2_HUMAN	P	3510	ENSP00000353114:S3510P	ENSP00000353114:S3510P	S	-	1	0	AHNAK2	104482305	0.105000	0.21958	0.000000	0.03702	0.004000	0.04260	0.097000	0.15168	-0.074000	0.12820	-1.216000	0.01612	TCC	A|0.978;G|0.022	0.022	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
RIC3	79608	hgsc.bcm.edu	37	11	8132301	8132301	+	Missense_Mutation	SNP	C	C	T	rs11826236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8132301C>T	ENST00000309737.6	-	6	1053	c.1054G>A	c.(1054-1056)Gat>Aat	p.D352N	RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000425599.2_Missense_Mutation_p.D271N|RIC3_ENST00000539720.1_Missense_Mutation_p.D303N|RIC3_ENST00000343202.4_Missense_Mutation_p.D351N|RIC3_ENST00000335425.7_Missense_Mutation_p.D170N|RIC3_ENST00000396677.2_Missense_Mutation_p.D190N			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	352					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)		TATGCTTTATCGGTGCTGATG	0.483													C|||	493	0.0984425	0.143	0.0821	5008	,	,		22078	0.0615		0.0656	False		,,,				2504	0.1217				p.D352N		Atlas-SNP	.											.	RIC3	42	.	0			c.G1054A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	554,3848	250.0+/-257.2	31,492,1678	162.0	143.0	149.0		508,1054,811,1051	5.2	0.0	11	dbSNP_120	149	541,8051	149.1+/-204.2	19,503,3774	yes	missense,missense,missense,missense	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	23,23,23,23	50,995,5452	TT,TC,CC		6.2966,12.5852,8.427	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	170/188,352/370,271/289,351/369	8132301	1095,11899	2201	4296	6497	SO:0001583	missense	79608	exon6			CTTTATCGGTGCT		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.1054G>A	11.37:g.8132301C>T	ENSP00000308820:p.Asp352Asn	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	181	92	0.508287	NM_001206671	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	175	0.08012820512820513	60	0.12195121951219512	28	0.07734806629834254	37	0.06468531468531469	50	0.06596306068601583	C	4.538	0.099878	0.08681	0.125852	0.062966	ENSG00000166405	ENST00000396677;ENST00000335425;ENST00000343202;ENST00000309737;ENST00000539720;ENST00000425599	T;T;T;T	0.33865	1.4;1.4;1.4;1.39	6.06	5.15	0.70609	.	0.742415	0.13006	N	0.421296	T	0.00328	0.0010	L	0.57536	1.79	0.80722	P	0.0	B;B;P;P;B	0.44946	0.017;0.03;0.709;0.846;0.054	B;B;B;B;B	0.32724	0.007;0.013;0.151;0.151;0.007	T	0.11817	-1.0572	9	0.27082	T	0.32	.	11.8453	0.52381	0.0:0.8506:0.0:0.1494	rs11826236;rs52800090;rs56624447;rs58123107;rs11826236	271;170;352;351;190	B0B1U0;Q7Z5B4-3;Q7Z5B4;Q7Z5B4-5;D3DQU6	.;.;RIC3_HUMAN;.;.	N	190;170;351;352;303;271	ENSP00000344904:D351N;ENSP00000308820:D352N;ENSP00000443871:D303N;ENSP00000395320:D271N	ENSP00000308820:D352N	D	-	1	0	RIC3	8088877	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	0.681000	0.25320	1.582000	0.49881	0.655000	0.94253	GAT	C|0.914;T|0.086	0.086	strong		0.483	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
GRID2IP	392862	hgsc.bcm.edu	37	7	6591009	6591009	+	Missense_Mutation	SNP	C	C	T	rs11761490	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:6591009C>T	ENST00000457091.2	-	1	58	c.59G>A	c.(58-60)cGg>cAg	p.R20Q		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						GCCACCTAGCCGGAAGCCAAA	0.652													C|||	315	0.0628994	0.003	0.0994	5008	,	,		11873	0.006		0.0984	False		,,,				2504	0.1401				p.R20Q		Atlas-SNP	.											GRID2IP_ENST00000457091,NS,carcinoma,+1,2	GRID2IP	82	2	0			c.G59A						PASS	.	C	GLN/ARG	26,1348		0,26,661	7.0	10.0	9.0		59	0.8	1.0	7	dbSNP_120	9	319,2849		17,285,1282	yes	missense	GRID2IP	NM_001145118.1	43	17,311,1943	TT,TC,CC		10.0694,1.8923,7.5958	benign	20/1212	6591009	345,4197	687	1584	2271	SO:0001583	missense	392862	exon1			CCTAGCCGGAAGC		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.59G>A	7.37:g.6591009C>T	ENSP00000397351:p.Arg20Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_001145118		Missense_Mutation	SNP	ENST00000457091.2	37	CCDS47537.1	111	0.050824175824175824	1	0.0020325203252032522	31	0.0856353591160221	1	0.0017482517482517483	78	0.10290237467018469	C	12.44	1.940133	0.34283	0.018923	0.100694	ENSG00000215045	ENST00000457091	T	0.27256	1.68	4.75	0.844	0.18943	PDZ/DHR/GLGF (4);	3.055710	0.03609	N	0.234527	T	0.00412	0.0013	N	0.11698	0.16	0.45172	P	0.001811000000000007	B	0.02656	0.0	B	0.04013	0.001	T	0.23440	-1.0188	9	0.24483	T	0.36	.	8.0869	0.30777	0.0:0.6395:0.0:0.3605	rs11761490;rs11761490	20	A4D2P6	GRD2I_HUMAN	Q	20	ENSP00000397351:R20Q	ENSP00000397351:R20Q	R	-	2	0	GRID2IP	6557534	0.046000	0.20272	0.977000	0.42913	0.974000	0.67602	0.341000	0.19909	-0.053000	0.13289	0.555000	0.69702	CGG	C|0.950;T|0.050	0.050	strong		0.652	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
TMEM140	55281	hgsc.bcm.edu	37	7	134849577	134849577	+	Silent	SNP	A	A	C	rs2288237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:134849577A>C	ENST00000275767.3	+	2	607	c.384A>C	c.(382-384)gcA>gcC	p.A128A	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	128						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						TGCTGCTGGCAGGCGGCCTGG	0.647													c|||	2283	0.455871	0.4009	0.4798	5008	,	,		16747	0.2589		0.4821	False		,,,				2504	0.6892				p.A128A		Atlas-SNP	.											TMEM140,NS,carcinoma,+1,1	TMEM140	18	1	0			c.A384C						PASS	.	T		1931,2475	618.7+/-393.2	434,1063,706	38.0	37.0	37.0		384	2.5	0.2	7	dbSNP_100	37	4363,4237	568.8+/-389.1	1120,2123,1057	no	coding-synonymous	TMEM140	NM_018295.3		1554,3186,1763	CC,CA,AA		49.2674,43.8266,48.393		128/186	134849577	6294,6712	2203	4300	6503	SO:0001819	synonymous_variant	55281	exon2			GCTGGCAGGCGGC	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.384A>C	7.37:g.134849577A>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_018295	A4D1P9|Q8WUC3	Silent	SNP	ENST00000275767.3	37	CCDS5837.1																																																																																			A|0.538;C|0.462	0.462	strong		0.647	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295	
FANCA	2175	hgsc.bcm.edu	37	16	89858417	89858417	+	Silent	SNP	C	C	A	rs1800331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89858417C>A	ENST00000389301.3	-	13	1173	c.1143G>T	c.(1141-1143)acG>acT	p.T381T	FANCA_ENST00000568369.1_Silent_p.T381T	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	381					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)		GAACCTCCTGCGTTTCCAGAA	0.507			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	360	0.071885	0.0091	0.0187	5008	,	,		22316	0.254		0.0626	False		,,,				2504	0.0164				p.T381T		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.G1143T						PASS	.	C		91,4305	74.1+/-112.3	0,91,2107	117.0	106.0	110.0		1143	-11.0	0.0	16	dbSNP_89	110	697,7903	172.6+/-223.3	26,645,3629	no	coding-synonymous	FANCA	NM_000135.2		26,736,5736	AA,AC,CC		8.1047,2.0701,6.0634		381/1456	89858417	788,12208	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon13	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTCCTGCGTTTCC	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.1143G>T	16.37:g.89858417C>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	184	88	0.478261	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.934;A|0.066	0.066	strong		0.507	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105408030	105408030	+	Silent	SNP	A	A	G	rs9671643	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	137	0	0		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	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	
PRDM16	63976	hgsc.bcm.edu	37	1	3102852	3102852	+	Silent	SNP	G	G	A	rs199614349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3102852G>A	ENST00000270722.5	+	2	250	c.201G>A	c.(199-201)ccG>ccA	p.P67P	PRDM16_ENST00000514189.1_Silent_p.P67P|PRDM16_ENST00000511072.1_Silent_p.P67P|PRDM16_ENST00000442529.2_Silent_p.P67P|PRDM16_ENST00000378398.3_Silent_p.P67P|PRDM16_ENST00000441472.2_Silent_p.P67P|PRDM16_ENST00000378391.2_Silent_p.P67P			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	67					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)		AGGGCTCGCCGTACGAGGCCC	0.672			T	EVI1	"""MDS, AML"""								G|||	6	0.00119808	0.0	0.0029	5008	,	,		14984	0.0		0.003	False		,,,				2504	0.001				p.P67P		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.G201A						PASS	.	G	,	0,4074		0,0,2037	49.0	60.0	56.0		201,201	-2.7	1.0	1		56	24,8284		0,24,4130	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	0,24,6167	AA,AG,GG		0.2889,0.0,0.1938	,	67/1277,67/1258	3102852	24,12358	2037	4154	6191	SO:0001819	synonymous_variant	63976	exon2			CTCGCCGTACGAG	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.201G>A	1.37:g.3102852G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	240	123	0.5125	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			G|0.989;A|0.011	0.011	strong		0.672	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
OR5P2	120065	hgsc.bcm.edu	37	11	7817856	7817856	+	Missense_Mutation	SNP	C	C	T	rs78460198	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7817856C>T	ENST00000329434.2	-	1	664	c.634G>A	c.(634-636)Gtc>Atc	p.V212I	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V212I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATGTAGCAGACGGCTATGACA	0.493													C|||	1185	0.236621	0.3472	0.2911	5008	,	,		18815	0.128		0.2763	False		,,,				2504	0.1196				p.V212I		Atlas-SNP	.											OR5P2,colon,carcinoma,0,2	OR5P2	68	2	1	Substitution - Missense(1)	large_intestine(1)	c.G634A						PASS	.	C	ILE/VAL	1371,2839		401,569,1135	99.0	104.0	102.0		634	-11.0	0.0	11	dbSNP_131	102	2425,6159		393,1639,2260	no	missense	OR5P2	NM_153444.1	29	794,2208,3395	TT,TC,CC		28.2502,32.5653,29.6702	benign	212/323	7817856	3796,8998	2105	4292	6397	SO:0001583	missense	120065	exon1			AGCAGACGGCTAT	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.634G>A	11.37:g.7817856C>T	ENSP00000331823:p.Val212Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	166	166	1	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	C	0.005	-2.119520	0.00346	0.325653	0.282502	ENSG00000183303	ENST00000329434	T	0.37235	1.21	5.5	-11.0	0.00169	GPCR, rhodopsin-like superfamily (1);	0.814212	0.11083	N	0.601638	T	0.00012	0.0000	N	0.11000	0.08	0.80722	P	0.0	B	0.13594	0.008	B	0.18263	0.021	T	0.36578	-0.9742	9	0.02654	T	1	-5.754	20.7759	0.99721	0.0:0.328:0.0:0.672	.	212	Q8WZ92	OR5P2_HUMAN	I	212	ENSP00000331823:V212I	ENSP00000331823:V212I	V	-	1	0	OR5P2	7774432	0.000000	0.05858	0.000000	0.03702	0.379000	0.30106	-6.285000	0.00072	-3.387000	0.00174	-1.300000	0.01332	GTC	C|0.739;T|0.261	0.261	strong		0.493	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
FLG	2312	hgsc.bcm.edu	37	1	152279920	152279920	+	Missense_Mutation	SNP	A	A	G	rs55650366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152279920A>G	ENST00000368799.1	-	3	7477	c.7442T>C	c.(7441-7443)tTg>tCg	p.L2481S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2481	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)			TCTATCTACCAATTGCTCGTA	0.572									Ichthyosis				a|||	1715	0.342452	0.1203	0.4207	5008	,	,		19633	0.6071		0.171	False		,,,				2504	0.4908				p.L2481S		Atlas-SNP	.											.	FLG	900	.	0			c.T7442C						PASS	.	A	SER/LEU	608,3798	267.7+/-268.0	43,522,1638	354.0	327.0	336.0		7442	-1.7	0.0	1	dbSNP_129	336	1442,7158	276.5+/-292.4	124,1194,2982	no	missense	FLG	NM_002016.1	145	167,1716,4620	GG,GA,AA		16.7674,13.7994,15.762	benign	2481/4062	152279920	2050,10956	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTACCAATTGCT	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.7442T>C	1.37:g.152279920A>G	ENSP00000357789:p.Leu2481Ser	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	343	181	0.527697	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	680	0.31135531135531136	68	0.13821138211382114	125	0.3453038674033149	356	0.6223776223776224	131	0.17282321899736147	a	6.576	0.474569	0.12521	0.137994	0.167674	ENSG00000143631	ENST00000368799	T	0.00882	5.58	3.18	-1.66	0.08265	.	.	.	.	.	T	0.00039	0.0001	N	0.00029	-2.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22836	-1.0205	8	0.02654	T	1	.	4.5928	0.12315	0.2877:0.1568:0.5555:0.0	rs55650366	2481	P20930	FILA_HUMAN	S	2481	ENSP00000357789:L2481S	ENSP00000357789:L2481S	L	-	2	0	FLG	150546544	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.345000	0.02637	-0.883000	0.03982	-3.056000	0.00068	TTG	A|0.792;G|0.208	0.208	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR52B6	340980	hgsc.bcm.edu	37	11	5602605	5602605	+	Missense_Mutation	SNP	G	G	A	rs2341433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5602605G>A	ENST00000345043.2	+	1	499	c.499G>A	c.(499-501)Gcc>Acc	p.A167T	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	167			A -> T (in dbSNP:rs2341433).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CGTCACTGCCGCCCTGAGCCA	0.507													G|||	2831	0.565296	0.6142	0.562	5008	,	,		24980	0.7659		0.331	False		,,,				2504	0.5358				p.A167T		Atlas-SNP	.											.	OR52B6	37	.	0			c.G499A						PASS	.	G	THR/ALA	2408,1994	582.3+/-385.5	657,1094,450	191.0	200.0	196.0		499	1.6	0.0	11	dbSNP_100	196	2694,5898	421.6+/-353.8	427,1840,2029	yes	missense	OR52B6	NM_001005162.2	58	1084,2934,2479	AA,AG,GG		31.3547,45.2976,39.2643	benign	167/336	5602605	5102,7892	2201	4296	6497	SO:0001583	missense	340980	exon1			ACTGCCGCCCTGA	AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"""GPCR / Class A : Olfactory receptors"""	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.499G>A	11.37:g.5602605G>A	ENSP00000341581:p.Ala167Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	37	CCDS41611.1	1182	0.5412087912087912	298	0.6056910569105691	191	0.5276243093922652	436	0.7622377622377622	257	0.3390501319261214	G	3.422	-0.117846	0.06838	0.547024	0.313547	ENSG00000187747	ENST00000345043	T	0.37584	1.19	5.15	1.57	0.23409	GPCR, rhodopsin-like superfamily (1);	0.372331	0.19199	N	0.120223	T	0.00012	0.0000	N	0.25789	0.76	0.80722	P	0.0	B	0.15473	0.013	B	0.18561	0.022	T	0.34179	-0.9839	9	0.09338	T	0.73	.	8.4941	0.33117	0.679:0.0:0.321:0.0	rs2341433;rs16933207;rs60635257;rs2341433	167	Q8NGF0	O52B6_HUMAN	T	167	ENSP00000341581:A167T	ENSP00000341581:A167T	A	+	1	0	OR52B6	5559181	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.549000	0.06041	0.101000	0.17610	-1.656000	0.00753	GCC	G|0.494;A|0.506	0.506	strong		0.507	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162	
CC2D1A	54862	hgsc.bcm.edu	37	19	14024269	14024269	+	Missense_Mutation	SNP	C	C	T	rs61740117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14024269C>T	ENST00000318003.7	+	6	807	c.566C>T	c.(565-567)gCg>gTg	p.A189V	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A189V	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	189					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)			ATTGACGAAGCGGACATCCCG	0.602													C|||	15	0.00299521	0.0	0.0029	5008	,	,		17181	0.0		0.0119	False		,,,				2504	0.001				p.A189V		Atlas-SNP	.											.	CC2D1A	67	.	0			c.C566T						PASS	.	C	VAL/ALA	7,4065		0,7,2029	35.0	44.0	41.0		566	-10.4	0.0	19	dbSNP_129	41	100,8246		0,100,4073	yes	missense	CC2D1A	NM_017721.4	64	0,107,6102	TT,TC,CC		1.1982,0.1719,0.8617	benign	189/952	14024269	107,12311	2036	4173	6209	SO:0001583	missense	54862	exon6			ACGAAGCGGACAT	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.566C>T	19.37:g.14024269C>T	ENSP00000313601:p.Ala189Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	10.62	1.400963	0.25291	0.001719	0.011982	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	T	0.22539	1.95	5.2	-10.4	0.00318	Domain of unknown function DM14 (1);	0.466636	0.22488	N	0.059413	T	0.07279	0.0184	L	0.46157	1.445	0.24389	N	0.994752	P;P	0.37731	0.489;0.607	B;B	0.32724	0.151;0.143	T	0.01791	-1.1273	10	0.59425	D	0.04	-4.4191	6.3202	0.21213	0.5862:0.255:0.0806:0.0783	rs61740117	189;189	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	V	189;27;164	ENSP00000313601:A189V	ENSP00000254346:A27V	A	+	2	0	CC2D1A	13885269	0.983000	0.35010	0.037000	0.18230	0.014000	0.08584	0.328000	0.19681	-2.793000	0.00355	-1.555000	0.00892	GCG	C|0.995;T|0.005	0.005	strong		0.602	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
LVRN	206338	hgsc.bcm.edu	37	5	115338958	115338958	+	Missense_Mutation	SNP	G	G	T	rs17138632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:115338958G>T	ENST00000357872.4	+	12	2042	c.1918G>T	c.(1918-1920)Gtt>Ttt	p.V640F	AQPEP_ENST00000395528.2_Missense_Mutation_p.V157F	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		640			V -> F (in dbSNP:rs17138632).			integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AGAAATGCAAGTTTCAGATTC	0.289													G|||	130	0.0259585	0.0015	0.0836	5008	,	,		14198	0.001		0.0298	False		,,,				2504	0.0399				p.V640F		Atlas-SNP	.											FLJ90650,NS,carcinoma,0,1	.	.	1	0			c.G1918T						PASS	.	G	PHE/VAL	25,4377	31.7+/-61.6	0,25,2176	51.0	56.0	55.0		1918	-0.9	1.0	5	dbSNP_123	55	272,8304	100.1+/-161.6	4,264,4020	yes	missense	AQPEP	NM_173800.4	50	4,289,6196	TT,TG,GG		3.1716,0.5679,2.2885	benign	640/991	115338958	297,12681	2201	4288	6489	SO:0001583	missense	0	exon12			ATGCAAGTTTCAG																												ENST00000357872.4:c.1918G>T	5.37:g.115338958G>T	ENSP00000350541:p.Val640Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	59	0.027014652014652016	3	0.006097560975609756	31	0.0856353591160221	1	0.0017482517482517483	24	0.0316622691292876	G	11.64	1.698549	0.30142	0.005679	0.031716	ENSG00000172901	ENST00000395528;ENST00000357872;ENST00000379578	T;T	0.23552	1.9;1.9	5.03	-0.942	0.10398	.	0.861260	0.10039	N	0.723709	T	0.00580	0.0019	L	0.57536	1.79	0.24475	N	0.994371	P	0.39282	0.666	B	0.33521	0.165	T	0.14144	-1.0483	10	0.09843	T	0.71	.	4.9292	0.13909	0.4644:0.3211:0.2146:0.0	rs17138632;rs52805082;rs17138632	640	Q6Q4G3	AMPQ_HUMAN	F	157;640;629	ENSP00000378899:V157F;ENSP00000350541:V640F	ENSP00000350541:V640F	V	+	1	0	AC010282.1	115366857	0.986000	0.35501	0.999000	0.59377	0.995000	0.86356	0.095000	0.15127	0.102000	0.17638	0.460000	0.39030	GTT	G|0.972;T|0.028	0.028	strong		0.289	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
TACC2	10579	hgsc.bcm.edu	37	10	123845211	123845211	+	Missense_Mutation	SNP	G	G	A	rs11200387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123845211G>A	ENST00000369005.1	+	4	3536	c.3196G>A	c.(3196-3198)Gcc>Acc	p.A1066T	TACC2_ENST00000334433.3_Missense_Mutation_p.A1066T|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.A1066T|TACC2_ENST00000453444.2_Missense_Mutation_p.A1066T|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.A1066T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1066					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCTGGCGCCCGCCAGCCCCGG	0.647													G|||	694	0.138578	0.1929	0.1499	5008	,	,		15541	0.0913		0.17	False		,,,				2504	0.0736				p.A1066T		Atlas-SNP	.											.	TACC2	271	.	0			c.G3196A						PASS	.	G	,THR/ALA	992,3414	350.3+/-310.7	115,762,1326	37.0	43.0	41.0		,3196	2.5	0.0	10	dbSNP_120	41	1441,7157	262.0+/-284.2	117,1207,2975	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	232,1969,4301	AA,AG,GG		16.7597,22.5148,18.7096	,benign	,1066/2949	123845211	2433,10571	2203	4299	6502	SO:0001583	missense	10579	exon4			GCGCCCGCCAGCC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3196G>A	10.37:g.123845211G>A	ENSP00000358001:p.Ala1066Thr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	349	0.15979853479853479	92	0.18699186991869918	63	0.17403314917127072	66	0.11538461538461539	128	0.16886543535620052	G	11.06	1.528723	0.27387	0.225148	0.167597	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03242	4.06;4.01;4.0;4.06;4.01	5.37	2.46	0.29980	.	0.496053	0.15164	N	0.276983	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	P;P;P	0.35872	0.525;0.525;0.525	B;B;B	0.28638	0.092;0.092;0.092	T	0.46359	-0.9197	9	0.12430	T	0.62	-0.0562	5.8983	0.18951	0.1754:0.1576:0.667:0.0	rs11200387;rs58225650	1066;1066;1066	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1066;1066;1066;1066;1066;1056	ENSP00000358001:A1066T;ENSP00000424467:A1066T;ENSP00000427618:A1066T;ENSP00000334280:A1066T;ENSP00000395048:A1066T	ENSP00000334280:A1066T	A	+	1	0	TACC2	123835201	0.001000	0.12720	0.005000	0.12908	0.048000	0.14542	0.705000	0.25675	0.240000	0.21263	0.478000	0.44815	GCC	G|0.826;A|0.174	0.174	strong		0.647	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
MEPE	56955	hgsc.bcm.edu	37	4	88767008	88767008	+	Missense_Mutation	SNP	G	G	A	rs17013285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88767008G>A	ENST00000424957.3	+	4	1061	c.988G>A	c.(988-990)Gtt>Att	p.V330I	MEPE_ENST00000540395.1_Missense_Mutation_p.V217I|MEPE_ENST00000395102.4_Missense_Mutation_p.V361I|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000560249.1_Missense_Mutation_p.V217I|MEPE_ENST00000361056.3_Missense_Mutation_p.V330I|MEPE_ENST00000497649.2_Missense_Mutation_p.V306I	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	330			V -> I (in dbSNP:rs17013285).		biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		GGCAGATGCTGTTGATGTCAG	0.458													G|||	863	0.172324	0.0484	0.1801	5008	,	,		20635	0.2827		0.164	False		,,,				2504	0.229				p.V330I		Atlas-SNP	.											.	MEPE	86	.	0			c.G988A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	286,4120	158.1+/-190.9	8,270,1925	65.0	64.0	64.0		988,649,649,649,988	0.4	0.0	4	dbSNP_123	64	1468,7132	274.2+/-291.1	134,1200,2966	yes	missense,missense,missense,missense,missense	MEPE	NM_001184694.1,NM_001184695.1,NM_001184696.1,NM_001184697.1,NM_020203.3	29,29,29,29,29	142,1470,4891	AA,AG,GG		17.0698,6.4911,13.4861	benign,benign,benign,benign,benign	330/526,217/413,217/413,217/413,330/526	88767008	1754,11252	2203	4300	6503	SO:0001583	missense	56955	exon4			GATGCTGTTGATG	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"""matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"""			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.988G>A	4.37:g.88767008G>A	ENSP00000416984:p.Val330Ile	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	385	0.1762820512820513	25	0.0508130081300813	54	0.14917127071823205	171	0.29895104895104896	135	0.17810026385224276	G	9.102	1.004490	0.19199	0.064911	0.170698	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.95;0.94	4.68	0.436	0.16549	.	0.506936	0.16629	N	0.206152	T	0.00012	0.0000	L	0.31207	0.915	0.80722	P	0.0	B	0.15719	0.014	B	0.10450	0.005	T	0.34650	-0.9820	9	0.31617	T	0.26	-0.3551	3.377	0.07241	0.3818:0.2037:0.4145:0.0	rs17013285;rs52799941;rs17013285	330	Q9NQ76	MEPE_HUMAN	I	330;361;306;217;330	ENSP00000416984:V330I;ENSP00000378534:V361I;ENSP00000422747:V306I;ENSP00000443491:V217I;ENSP00000354341:V330I	ENSP00000354341:V330I	V	+	1	0	MEPE	88986032	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.389000	0.20751	0.161000	0.19458	0.655000	0.94253	GTT	G|0.854;A|0.146	0.146	strong		0.458	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1		
PLG	5340	hgsc.bcm.edu	37	6	161152240	161152240	+	Missense_Mutation	SNP	G	G	A	rs4252125	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	95	0	0		WXS	Illumina HiSeq	Phase_I	95	38	0.4	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	
SMU1	55234	hgsc.bcm.edu	37	9	33071879	33071879	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33071879T>C	ENST00000397149.3	-	3	299	c.249A>G	c.(247-249)gaA>gaG	p.E83E	SMU1_ENST00000536631.1_Intron	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	83	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		GCTCTATCAATTCCAGAACAA	0.368																																					p.E83E		Atlas-SNP	.											.	SMU1	29	.	0			c.A249G						PASS	.						74.0	72.0	73.0					9																	33071879		2203	4300	6503	SO:0001819	synonymous_variant	55234	exon3			TATCAATTCCAGA	AK001667	CCDS6534.1	9p12	2013-01-10			ENSG00000122692	ENSG00000122692		"""WD repeat domain containing"""	18247	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 57"""					11438655, 11410362	Standard	NM_018225		Approved	SMU-1, FLJ10805, BWD, fSAP57	uc003zsf.1	Q2TAY7	OTTHUMG00000019757	ENST00000397149.3:c.249A>G	9.37:g.33071879T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_018225	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	Silent	SNP	ENST00000397149.3	37	CCDS6534.1																																																																																			.	.	none		0.368	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052022.1	NM_018225	
IP6K2	51447	hgsc.bcm.edu	37	3	48727112	48727112	+	Silent	SNP	G	G	A	rs4858798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:48727112G>A	ENST00000328631.5	-	5	862	c.639C>T	c.(637-639)taC>taT	p.Y213Y		NM_001005909.2|NM_016291.3	NP_001005909.1|NP_057375.2	Q9UHH9	IP6K2_HUMAN	inositol hexakisphosphate kinase 2	213					cytokine-mediated signaling pathway (GO:0019221)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell growth (GO:0030308)|phosphate ion transport (GO:0006817)|phosphatidylinositol phosphorylation (GO:0046854)|positive regulation of apoptotic process (GO:0043065)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|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-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	15						AAGGCACCTCGTAGCGGGAAG	0.483													G|||	3692	0.73722	0.4977	0.745	5008	,	,		21814	0.9484		0.6521	False		,,,				2504	0.9254				p.Y213Y		Atlas-SNP	.											.	IP6K2	63	.	0			c.C639T						PASS	.	G	,	2305,2101	602.0+/-389.8	604,1097,502	130.0	110.0	116.0		639,639	-1.4	1.0	3	dbSNP_111	116	5454,3146	656.5+/-401.4	1721,2012,567	no	coding-synonymous,coding-synonymous	IP6K2	NM_001005909.2,NM_016291.3	,	2325,3109,1069	AA,AG,GG		36.5814,47.685,40.3429	,	213/427,213/427	48727112	7759,5247	2203	4300	6503	SO:0001819	synonymous_variant	51447	exon5			CACCTCGTAGCGG	AF177145	CCDS2777.1, CCDS33752.1, CCDS54579.1, CCDS54580.1, CCDS54581.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000068745	ENSG00000068745			17313	protein-coding gene	gene with protein product		606992	"""inositol hexaphosphate kinase 2"""	IHPK2		10574768	Standard	NM_016291		Approved		uc003cup.3	Q9UHH9	OTTHUMG00000133543	ENST00000328631.5:c.639C>T	3.37:g.48727112G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_016291	A8K3B1|B4E3G6|G8JLL6|Q6P0N8|Q9BSZ6|Q9BUW3|Q9H4P7|Q9NT63|Q9UFU6	Silent	SNP	ENST00000328631.5	37	CCDS2777.1																																																																																			G|0.348;A|0.652	0.652	strong		0.483	IP6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257521.2	NM_016291	
COG6	57511	hgsc.bcm.edu	37	13	40229957	40229957	+	Missense_Mutation	SNP	T	T	A	rs3812883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	73	0	0		WXS	Illumina HiSeq	Phase_I	92	56	0.608696	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		
ZP1	22917	hgsc.bcm.edu	37	11	60638461	60638461	+	Silent	SNP	C	C	T	rs10897122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60638461C>T	ENST00000278853.5	+	5	858	c.858C>T	c.(856-858)ttC>ttT	p.F286F		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	286	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						ATGGCTACTTCGTCCTCGTAG	0.577													C|||	1551	0.309704	0.034	0.3098	5008	,	,		20608	0.626		0.2207	False		,,,				2504	0.4479				p.F286F		Atlas-SNP	.											.	ZP1	69	.	0			c.C858T						PASS	.	C		298,4108	162.5+/-194.5	11,276,1916	249.0	216.0	227.0		858	-1.5	0.0	11	dbSNP_120	227	1961,6637	345.4+/-325.7	228,1505,2566	no	coding-synonymous	ZP1	NM_207341.2		239,1781,4482	TT,TC,CC		22.8076,6.7635,17.3716		286/639	60638461	2259,10745	2203	4299	6502	SO:0001819	synonymous_variant	22917	exon5			CTACTTCGTCCTC	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"""Zona pellucida glycoproteins"""	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.858C>T	11.37:g.60638461C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_207341		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																			C|0.776;N|0.000	.	strong		0.577	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341	
AKR7A3	22977	hgsc.bcm.edu	37	1	19615023	19615023	+	Silent	SNP	G	G	A	rs115242113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19615023G>A	ENST00000361640.4	-	1	721	c.181C>T	c.(181-183)Ctg>Ttg	p.L61L		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	61					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)	p.L61L(1)		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)		CGGAGCCCCAGGCCGCCAAGG	0.692																																					p.L61L		Atlas-SNP	.											AKR7A3,NS,lymphoid_neoplasm,0,1	AKR7A3	30	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C181T						PASS	.						23.0	25.0	25.0					1																	19615023		2202	4298	6500	SO:0001819	synonymous_variant	22977	exon1			GCCCCAGGCCGCC	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.181C>T	1.37:g.19615023G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	247	51	0.206478	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Silent	SNP	ENST00000361640.4	37	CCDS193.1																																																																																			G|0.985;A|0.015	0.015	strong		0.692	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
KANSL3	55683	hgsc.bcm.edu	37	2	97297114	97297114	+	Silent	SNP	G	G	A	rs35809433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97297114G>A	ENST00000431828.1	-	3	397	c.321C>T	c.(319-321)gtC>gtT	p.V107V	KANSL3_ENST00000440133.1_5'UTR|KANSL3_ENST00000435669.1_Silent_p.V20V|KANSL3_ENST00000599854.1_Silent_p.V20V|KANSL3_ENST00000441706.2_Silent_p.V20V|KANSL3_ENST00000487070.1_5'UTR			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	107					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TGGCAAAGATGACATGCCGTT	0.542													G|||	25	0.00499201	0.0008	0.0043	5008	,	,		21590	0.0		0.0139	False		,,,				2504	0.0072				p.V107V		Atlas-SNP	.											.	.	.	.	0			c.C321T						PASS	.	G	,	7,4143		0,7,2068	97.0	97.0	97.0		321,60	4.7	1.0	2	dbSNP_126	97	61,8351		0,61,4145	no	coding-synonymous,coding-synonymous	KIAA1310	NM_001115016.1,NM_017991.4	,	0,68,6213	AA,AG,GG		0.7252,0.1687,0.5413	,	107/879,20/792	97297114	68,12494	2075	4206	6281	SO:0001819	synonymous_variant	55683	exon3			AAAGATGACATGC	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"""KIAA1310"""	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.321C>T	2.37:g.97297114G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	212	120	0.566038	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Silent	SNP	ENST00000431828.1	37	CCDS46361.1																																																																																			G|0.991;A|0.009	0.009	strong		0.542	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991	
AURKAIP1	54998	hgsc.bcm.edu	37	1	1309803	1309803	+	Silent	SNP	G	G	A	rs9554		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:1309803G>A	ENST00000338370.3	-	2	475	c.75C>T	c.(73-75)gtC>gtT	p.V25V	AURKAIP1_ENST00000338338.5_Silent_p.V25V|AURKAIP1_ENST00000321751.5_Silent_p.V25V|AURKAIP1_ENST00000489799.1_5'UTR|AURKAIP1_ENST00000378853.3_Silent_p.V25V			Q9NWT8	AKIP_HUMAN	aurora kinase A interacting protein 1	25					negative regulation of mitosis (GO:0045839)|positive regulation of proteolysis (GO:0045862)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				kidney(1)|lung(2)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.82e-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;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCACTCCAGAGACGGGCCAAG	0.716																																					p.V25V		Atlas-SNP	.											.	AURKAIP1	12	.	0			c.C75T						PASS	.						2.0	4.0	3.0					1																	1309803		1684	3642	5326	SO:0001819	synonymous_variant	54998	exon3			TCCAGAGACGGGC		CCDS25.1	1p36.33	2014-02-12			ENSG00000175756	ENSG00000175756			24114	protein-coding gene	gene with protein product		609183				12244051	Standard	NM_017900		Approved	AKIP, AIP, FLJ20608	uc009vkb.1	Q9NWT8	OTTHUMG00000001413	ENST00000338370.3:c.75C>T	1.37:g.1309803G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	10	9	0.9	NM_001127230	Q5TA36|Q8TBD3	Silent	SNP	ENST00000338370.3	37	CCDS25.1																																																																																			.	.	weak		0.716	AURKAIP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008273.1	NM_017900	
STRA6	64220	hgsc.bcm.edu	37	15	74488424	74488424	+	Silent	SNP	G	G	A	rs11857410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:74488424G>A	ENST00000323940.5	-	5	576	c.331C>T	c.(331-333)Ctg>Ttg	p.L111L	STRA6_ENST00000395105.4_Silent_p.L111L|STRA6_ENST00000535552.1_Silent_p.L148L|STRA6_ENST00000416286.3_Silent_p.L111L|STRA6_ENST00000449139.2_Silent_p.L111L|STRA6_ENST00000423167.2_Silent_p.L102L|STRA6_ENST00000563965.1_Silent_p.L150L|STRA6_ENST00000574278.1_Silent_p.L126L|STRA6_ENST00000574439.1_5'UTR|STRA6_ENST00000432245.2_Silent_p.L111L	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	111					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						AGGGAGCTCAGGAGGACCATG	0.637													A|||	309	0.0617013	0.0333	0.072	5008	,	,		17589	0.0		0.1809	False		,,,				2504	0.0337				p.L150L		Atlas-SNP	.											.	STRA6	66	.	0			c.C448T						PASS	.	A	,,,,,,,	290,4106	792.7+/-415.2	10,270,1918	94.0	77.0	83.0		331,331,304,331,442,376,448,331	4.1	1.0	15	dbSNP_120	83	1841,6753	728.8+/-406.7	191,1459,2647	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STRA6	NM_001142617.1,NM_001142618.1,NM_001142619.1,NM_001142620.1,NM_001199040.1,NM_001199041.1,NM_001199042.1,NM_022369.3	,,,,,,,	201,1729,4565	AA,AG,GG		21.4219,6.5969,16.4049	,,,,,,,	111/668,111/668,102/659,111/160,148/705,126/683,150/707,111/668	74488424	2131,10859	2198	4297	6495	SO:0001819	synonymous_variant	64220	exon5			AGCTCAGGAGGAC	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.331C>T	15.37:g.74488424G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Silent	SNP	ENST00000323940.5	37	CCDS10261.1																																																																																			G|0.878;A|0.122	0.122	strong		0.637	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605957	1605957	+	Missense_Mutation	SNP	C	C	T	rs151275365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1605957C>T	ENST00000382171.2	-	1	556	c.523G>A	c.(523-525)Ggg>Agg	p.G175R	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	175	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)		CCACAGCCCCCCTTGGAGCCC	0.677																																					p.G175R		Atlas-SNP	.											.	KRTAP5-1	74	.	0			c.G523A						PASS	.	C	ARG/GLY	12,4390		0,12,2189	46.0	62.0	57.0		523	2.9	1.0	11	dbSNP_134	57	111,8487		1,109,4189	no	missense	KRTAP5-1	NM_001005922.1	125	1,121,6378	TT,TC,CC		1.291,0.2726,0.9462	possibly-damaging	175/279	1605957	123,12877	2201	4299	6500	SO:0001583	missense	387264	exon1			AGCCCCCCTTGGA	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.523G>A	11.37:g.1605957C>T	ENSP00000371606:p.Gly175Arg	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	163	57	0.349693	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	c	0.039	-1.291524	0.01375	0.002726	0.01291	ENSG00000205869	ENST00000382171	T	0.05199	3.48	2.91	2.91	0.33838	.	.	.	.	.	T	0.03263	0.0095	M	0.62266	1.93	0.26033	N	0.981718	P	0.40332	0.713	B	0.40375	0.327	T	0.17592	-1.0364	9	0.12103	T	0.63	.	5.9746	0.19371	0.0:0.8455:0.0:0.1545	.	175	Q6L8H4	KRA51_HUMAN	R	175	ENSP00000371606:G175R	ENSP00000371606:G175R	G	-	1	0	KRTAP5-1	1562533	0.000000	0.05858	0.998000	0.56505	0.319000	0.28217	-1.117000	0.03283	1.185000	0.42971	0.271000	0.19318	GGG	C|0.989;T|0.011	0.011	strong		0.677	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
CSMD2	114784	hgsc.bcm.edu	37	1	34208948	34208948	+	Silent	SNP	G	G	A	rs117716479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:34208948G>A	ENST00000373381.4	-	14	2282	c.2106C>T	c.(2104-2106)caC>caT	p.H702H		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	662	Sushi 4. {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)				GACGGGCCACGTGGCCACTGC	0.602													G|||	225	0.0449281	0.0023	0.134	5008	,	,		18012	0.0377		0.0129	False		,,,				2504	0.0798				p.H662H		Atlas-SNP	.											CSMD2,rectum,carcinoma,-1,1	CSMD2	946	1	0			c.C1986T						PASS	.	G		13,4393	19.1+/-41.9	0,13,2190	58.0	51.0	53.0		1986	-3.5	1.0	1	dbSNP_132	53	74,8526	44.0+/-102.2	0,74,4226	no	coding-synonymous	CSMD2	NM_052896.3		0,87,6416	AA,AG,GG		0.8605,0.2951,0.6689		662/3488	34208948	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon14			GGCCACGTGGCCA	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	ENST00000373381.4:c.2106C>T	1.37:g.34208948G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	37																																																																																				G|0.986;A|0.014	0.014	strong		0.602	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
PPP6R1	22870	hgsc.bcm.edu	37	19	55748092	55748092	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55748092C>T	ENST00000412770.2	-	17	2473	c.1907G>A	c.(1906-1908)gGg>gAg	p.G636E	PPP6R1_ENST00000587283.1_Missense_Mutation_p.G636E|AC010327.1_ENST00000581390.1_RNA	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	636	Glu-rich.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)	p.G636E(1)		breast(1)	1						ATCAGACTCCCCTGAGCCCTG	0.622																																					p.G636E		Atlas-SNP	.											PPP6R1_ENST00000412770,NS,carcinoma,0,1	PPP6R1	63	1	1	Substitution - Missense(1)	kidney(1)	c.G1907A						scavenged	.						53.0	55.0	54.0					19																	55748092		1982	4151	6133	SO:0001583	missense	22870	exon17			GACTCCCCTGAGC	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1907G>A	19.37:g.55748092C>T	ENSP00000414202:p.Gly636Glu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	139	3	0.0215827	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392411	0.42410	.	.	ENSG00000105063	ENST00000412770	T	0.41400	1.0	4.95	1.52	0.23074	.	0.162599	0.29355	N	0.012390	T	0.18002	0.0432	N	0.19112	0.55	0.25168	N	0.990306	B	0.20052	0.041	B	0.19666	0.026	T	0.23762	-1.0179	10	0.02654	T	1	-23.7426	2.9102	0.05734	0.1807:0.528:0.1898:0.1015	.	636	Q9UPN7	PP6R1_HUMAN	E	636	ENSP00000414202:G636E	ENSP00000414202:G636E	G	-	2	0	PPP6R1	60439904	0.994000	0.37717	0.950000	0.38849	0.971000	0.66376	1.515000	0.35845	0.551000	0.29008	0.563000	0.77884	GGG	.	.	none		0.622	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
PCDHB10	56126	hgsc.bcm.edu	37	5	140574209	140574209	+	Missense_Mutation	SNP	C	C	G	rs138601077	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140574209C>G	ENST00000239446.4	+	1	2268	c.2084C>G	c.(2083-2085)gCg>gGg	p.A695G		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	695					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)			CTGGTGGTGGCGTTGGCCTCG	0.711													C|||	26	0.00519169	0.0	0.0029	5008	,	,		12365	0.0		0.0169	False		,,,				2504	0.0072				p.A695G		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C2084G						PASS	.	C	GLY/ALA	14,4232		0,14,2109	30.0	39.0	36.0		2084	3.0	0.0	5	dbSNP_134	36	127,8097		2,123,3987	no	missense	PCDHB10	NM_018930.3	60	2,137,6096	GG,GC,CC		1.5443,0.3297,1.1307	probably-damaging	695/801	140574209	141,12329	2123	4112	6235	SO:0001583	missense	56126	exon1			TGGTGGCGTTGGC	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.2084C>G	5.37:g.140574209C>G	ENSP00000239446:p.Ala695Gly	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	c	19.74	3.882989	0.72410	0.003297	0.015443	ENSG00000120324	ENST00000239446	T	0.24908	1.83	3.03	3.03	0.35002	.	.	.	.	.	T	0.48909	0.1526	H	0.97829	4.085	0.22571	N	0.998974	D	0.89917	1.0	D	0.91635	0.999	T	0.54912	-0.8222	9	0.87932	D	0	.	11.2418	0.48974	0.0:0.8128:0.1872:0.0	.	695	Q9UN67	PCDBA_HUMAN	G	695	ENSP00000239446:A695G	ENSP00000239446:A695G	A	+	2	0	PCDHB10	140554393	0.612000	0.27000	0.036000	0.18154	0.404000	0.30871	3.755000	0.55197	1.704000	0.51252	0.298000	0.19748	GCG	C|0.991;G|0.009	0.009	strong		0.711	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769228	43769228	+	Silent	SNP	A	A	C	rs10506226	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	162	0	0		WXS	Illumina HiSeq	Phase_I	153	152	0.993464	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	
ALDH18A1	5832	hgsc.bcm.edu	37	10	97388162	97388162	+	Missense_Mutation	SNP	G	G	A	rs2275272	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:97388162G>A	ENST00000371224.2	-	8	1033	c.896C>T	c.(895-897)aCc>aTc	p.T299I	ALDH18A1_ENST00000371221.3_Missense_Mutation_p.T297I	NM_002860.3	NP_002851.2	P54886	P5CS_HUMAN	aldehyde dehydrogenase 18 family, member A1	299	Glutamate 5-kinase.		T -> I (in dbSNP:rs2275272). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.	T -> P (in Ref. 1; CAA64224). {ECO:0000305}.	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)		TCTAGACTTGGTTCCAAATGT	0.413													G|||	359	0.0716853	0.0439	0.0922	5008	,	,		18912	0.0377		0.1421	False		,,,				2504	0.0573				p.T299I		Atlas-SNP	.											.	ALDH18A1	63	.	0			c.C896T						PASS	.	G	ILE/THR,ILE/THR	232,4174	138.4+/-174.2	6,220,1977	140.0	137.0	138.0		890,896	6.0	1.0	10	dbSNP_100	138	1084,7516	226.9+/-262.5	74,936,3290	yes	missense,missense	ALDH18A1	NM_001017423.1,NM_002860.3	89,89	80,1156,5267	AA,AG,GG		12.6047,5.2655,10.1184	benign,benign	297/794,299/796	97388162	1316,11690	2203	4300	6503	SO:0001583	missense	5832	exon8			GACTTGGTTCCAA	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.896C>T	10.37:g.97388162G>A	ENSP00000360268:p.Thr299Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_002860	B2R5Q4|B7Z350|B7Z5X8|B7ZLP1|D3DR44|O95952|Q3KQU2|Q5T566|Q5T567|Q9UM72	Missense_Mutation	SNP	ENST00000371224.2	37	CCDS7443.1	185	0.08470695970695971	24	0.04878048780487805	37	0.10220994475138122	20	0.03496503496503497	104	0.13720316622691292	G	17.42	3.385973	0.61956	0.052655	0.126047	ENSG00000059573	ENST00000371224;ENST00000371221	T;T	0.77620	-1.11;-1.11	5.97	5.97	0.96955	Aspartate/glutamate/uridylate kinase (3);	0.047339	0.85682	D	0.000000	T	0.01627	0.0052	L	0.39397	1.21	0.09310	P	0.9999997726	B;B	0.21071	0.051;0.041	B;B	0.32583	0.148;0.091	T	0.39292	-0.9621	9	0.56958	D	0.05	-24.3606	17.9326	0.89002	0.0:0.0:1.0:0.0	rs2275272;rs17539447;rs52791494;rs60885636;rs2275272	299;297	P54886;P54886-2	P5CS_HUMAN;.	I	299;297	ENSP00000360268:T299I;ENSP00000360265:T297I	ENSP00000360265:T297I	T	-	2	0	ALDH18A1	97378152	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.152000	0.71812	2.836000	0.97738	0.655000	0.94253	ACC	G|0.912;A|0.088	0.088	strong		0.413	ALDH18A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049552.1	NM_002860	
SHD	56961	hgsc.bcm.edu	37	19	4280186	4280186	+	Silent	SNP	C	C	T	rs10419363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4280186C>T	ENST00000543264.2	+	1	1589	c.126C>T	c.(124-126)ttC>ttT	p.F42F	SHD_ENST00000599689.1_Silent_p.F42F	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	42										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)		ACCTGGACTTCGAGGACCCCT	0.677													C|||	1627	0.32488	0.2821	0.2565	5008	,	,		12837	0.4038		0.3549	False		,,,				2504	0.319				p.F42F		Atlas-SNP	.											.	SHD	33	.	0			c.C126T						PASS	.	C		1316,3088	397.4+/-330.4	194,928,1080	25.0	30.0	28.0		126	-3.0	1.0	19	dbSNP_119	28	2929,5669	429.2+/-356.1	500,1929,1870	no	coding-synonymous	SHD	NM_020209.3		694,2857,2950	TT,TC,CC		34.0661,29.8819,32.6488		42/341	4280186	4245,8757	2202	4299	6501	SO:0001819	synonymous_variant	56961	exon1			GGACTTCGAGGAC	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.126C>T	19.37:g.4280186C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	108	0.964286	NM_020209	Q96NC2	Silent	SNP	ENST00000543264.2	37	CCDS12125.1																																																																																			C|0.681;N|0.000	.	strong		0.677	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
SLC2A9	56606	hgsc.bcm.edu	37	4	10027542	10027542	+	Missense_Mutation	SNP	C	C	T	rs6820230	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	140	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	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		
HIST1H3C	8352	hgsc.bcm.edu	37	6	26045737	26045737	+	Silent	SNP	C	C	G	rs3752418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26045737C>G	ENST00000540144.1	+	1	99	c.99C>G	c.(97-99)acC>acG	p.T33T	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	33					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						CTCCGGCCACCGGTGGCGTGA	0.617													c|||	1086	0.216853	0.0734	0.2695	5008	,	,		16517	0.5149		0.0676	False		,,,				2504	0.2198				p.T33T		Atlas-SNP	.											.	HIST1H3C	34	.	0			c.C99G						PASS	.	G		400,4006	186.7+/-213.5	19,362,1822	41.0	44.0	43.0		99	-9.3	0.1	6	dbSNP_107	43	578,8020	146.3+/-201.9	15,548,3736	no	coding-synonymous	HIST1H3C	NM_003531.2		34,910,5558	GG,GC,CC		6.7225,9.0785,7.5208		33/137	26045737	978,12026	2203	4299	6502	SO:0001819	synonymous_variant	8352	exon1			GGCCACCGGTGGC	X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"""Histones / Replication-dependent"""	4768	protein-coding gene	gene with protein product		602812	"""H3 histone family, member C"", ""histone 1, H3c"""	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.99C>G	6.37:g.26045737C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_003531	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000540144.1	37	CCDS4576.1																																																																																			C|0.881;G|0.119	0.119	strong		0.617	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531	
TPCN2	219931	hgsc.bcm.edu	37	11	68840399	68840399	+	Missense_Mutation	SNP	G	G	A	rs386754584|rs61746574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:68840399G>A	ENST00000294309.3	+	13	1261	c.1160G>A	c.(1159-1161)gGc>gAc	p.G387D	TPCN2_ENST00000442692.2_Intron|TPCN2_ENST00000542467.1_Missense_Mutation_p.G387D	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	387					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CGTTCCTATGGCAGTGTTCTG	0.607													G|||	442	0.0882588	0.0545	0.098	5008	,	,		17561	0.0744		0.1173	False		,,,				2504	0.1115				p.G387D		Atlas-SNP	.											.	TPCN2	63	.	0			c.G1160A						PASS	.	G	ASP/GLY	334,4066	175.5+/-204.9	15,304,1881	103.0	99.0	100.0		1160	-1.1	0.0	11	dbSNP_129	100	1062,7526	223.1+/-260.0	63,936,3295	yes	missense	TPCN2	NM_139075.3	94	78,1240,5176	AA,AG,GG		12.3661,7.5909,10.7484	benign	387/753	68840399	1396,11592	2200	4294	6494	SO:0001583	missense	219931	exon13			CCTATGGCAGTGT	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1160G>A	11.37:g.68840399G>A	ENSP00000294309:p.Gly387Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	189	0.08653846153846154	35	0.07113821138211382	30	0.08287292817679558	38	0.06643356643356643	86	0.11345646437994723	G	5.466	0.271017	0.10349	0.075909	0.123661	ENSG00000162341	ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.97529	-4.38;-4.42	5.24	-1.1	0.09872	.	1.713730	0.02856	N	0.129735	T	0.18087	0.0434	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.34399	0.323;0.131;0.452	B;B;B	0.29862	0.05;0.035;0.108	T	0.75915	-0.3149	9	0.13108	T	0.6	0.0938	6.1816	0.20474	0.5438:0.2373:0.2189:0.0	rs61746574	387;387;302	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	D	387;302;387	ENSP00000294309:G387D;ENSP00000445551:G387D	ENSP00000294309:G387D	G	+	2	0	TPCN2	68596975	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.436000	0.21526	-0.147000	0.11254	-0.258000	0.10820	GGC	G|0.896;A|0.104	0.104	strong		0.607	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
METTL13	51603	hgsc.bcm.edu	37	1	171753039	171753039	+	Missense_Mutation	SNP	A	A	G	rs2232816	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171753039A>G	ENST00000361735.3	+	2	579	c.313A>G	c.(313-315)Atg>Gtg	p.M105V	METTL13_ENST00000362019.3_Missense_Mutation_p.M19V|METTL13_ENST00000458517.1_Missense_Mutation_p.M104V|METTL13_ENST00000367737.5_Missense_Mutation_p.M105V	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	105			M -> V (in dbSNP:rs2232816). {ECO:0000269|PubMed:14702039}.				methyltransferase activity (GO:0008168)			breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GAAGATGGACATGACGCAGAT	0.502													A|||	1537	0.306909	0.2829	0.2867	5008	,	,		23620	0.5238		0.2445	False		,,,				2504	0.1943				p.M105V		Atlas-SNP	.											.	METTL13	67	.	0			c.A313G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	1364,3042	453.0+/-350.2	221,922,1060	135.0	121.0	126.0		313,55,313	5.3	1.0	1	dbSNP_98	126	2340,6260	392.4+/-344.0	334,1672,2294	yes	missense,missense,missense	METTL13	NM_001007239.1,NM_014955.2,NM_015935.4	21,21,21	555,2594,3354	GG,GA,AA		27.2093,30.9578,28.4792	benign,benign,benign	105/544,19/614,105/700	171753039	3704,9302	2203	4300	6503	SO:0001583	missense	51603	exon2			ATGGACATGACGC	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.313A>G	1.37:g.171753039A>G	ENSP00000354920:p.Met105Val	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	176	74	0.420455	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	37	CCDS1299.1	739	0.3383699633699634	148	0.3008130081300813	106	0.292817679558011	301	0.5262237762237763	184	0.24274406332453827	A	7.848	0.723345	0.15439	0.309578	0.272093	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000367737;ENST00000361735;ENST00000367736;ENST00000341850	T;T;T;T;T	0.61980	1.07;1.07;0.06;1.07;1.07	5.33	5.33	0.75918	Methyltransferase type 11 (1);	0.102000	0.64402	D	0.000001	T	0.15219	0.0367	N	0.05441	-0.05	0.34695	P	0.27388999999999997	B;B;B	0.17667	0.015;0.023;0.012	B;B;B	0.17979	0.02;0.006;0.014	T	0.09618	-1.0666	9	0.02654	T	1	-10.4348	7.7142	0.28694	0.841:0.0:0.159:0.0	rs2232816;rs52814698;rs60790489;rs2232816	104;105;105	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	V	104;19;105;105;22;19	ENSP00000401955:M104V;ENSP00000355393:M19V;ENSP00000356711:M105V;ENSP00000354920:M105V;ENSP00000356710:M22V	ENSP00000341732:M19V	M	+	1	0	METTL13	170019662	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	3.514000	0.53422	1.987000	0.57996	0.533000	0.62120	ATG	A|0.685;G|0.315	0.315	strong		0.502	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
C1QTNF6	114904	hgsc.bcm.edu	37	22	37581485	37581485	+	Missense_Mutation	SNP	C	C	A	rs229527	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37581485C>A	ENST00000337843.2	-	2	137	c.62G>T	c.(61-63)gGg>gTg	p.G21V	C1QTNF6_ENST00000397110.2_Missense_Mutation_p.G21V|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000255836.6_5'Flank|C1QTNF6_ENST00000470655.1_5'UTR	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	2					protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						GGCGGCTGTCCCCATGGTGAC	0.597													C|||	2254	0.45008	0.3457	0.3934	5008	,	,		19305	0.6548		0.4225	False		,,,				2504	0.4489				p.G21V		Atlas-SNP	.											.	C1QTNF6	32	.	0			c.G62T						PASS	.	C	VAL/GLY,VAL/GLY	1517,2889	446.3+/-348.0	282,953,968	31.0	33.0	32.0	http://www.ncbi.nlm.nih.gov/pubmed?term	62,62	1.0	1.0	22	dbSNP_79	32	3638,4962	490.1+/-372.8	726,2186,1388	yes	missense,missense	C1QTNF6	NM_031910.3,NM_182486.1	109,109	1008,3139,2356	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	42.3023,34.4303,39.6356	possibly-damaging,possibly-damaging	21/279,21/279	37581485	5155,7851	2203	4300	6503	SO:0001583	missense	114904	exon2			GCTGTCCCCATGG	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.62G>T	22.37:g.37581485C>A	ENSP00000338812:p.Gly21Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_182486	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	1008	0.46153846153846156	173	0.3516260162601626	144	0.39779005524861877	393	0.6870629370629371	298	0.39313984168865435	C	12.29	1.893803	0.33442	0.344303	0.423023	ENSG00000133466	ENST00000397110;ENST00000337843	T;T	0.37058	1.22;1.22	4.49	1.04	0.20106	.	0.701851	0.12983	N	0.423108	T	0.00012	0.0000	L	0.36672	1.1	0.19300	P	0.9999713074	B;B	0.16396	0.017;0.01	B;B	0.12156	0.007;0.003	T	0.37337	-0.9710	9	0.33141	T	0.24	.	0.4518	0.00502	0.1844:0.3243:0.2094:0.2819	rs229527;rs11538251;rs17851791;rs58952189;rs229527	21;2	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	V	21	ENSP00000380299:G21V;ENSP00000338812:G21V	ENSP00000338812:G21V	G	-	2	0	C1QTNF6	35911431	0.997000	0.39634	0.983000	0.44433	0.794000	0.44872	0.776000	0.26704	0.876000	0.35872	0.491000	0.48974	GGG	T|0.004;G|0.002	.	strong		0.597	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486	
PITX3	5309	hgsc.bcm.edu	37	10	103991518	103991518	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103991518C>T	ENST00000370002.3	-	3	301	c.148G>A	c.(148-150)Ggc>Agc	p.G50S	PITX3_ENST00000539804.1_Missense_Mutation_p.G50S	NM_005029.3	NP_005020.1	O75364	PITX3_HUMAN	paired-like homeodomain 3	50					dopaminergic neuron differentiation (GO:0071542)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|locomotory behavior (GO:0007626)|midbrain development (GO:0030901)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)	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)			endometrium(1)|large_intestine(2)|lung(2)	5		Colorectal(252;0.00957)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		GGGGAGCCGCCGGGCAGCGAA	0.662																																					p.G50S		Atlas-SNP	.											PITX3,colon,carcinoma,+2,1	PITX3	9	1	0			c.G148A						scavenged	.						16.0	17.0	17.0					10																	103991518		2200	4297	6497	SO:0001583	missense	5309	exon3			AGCCGCCGGGCAG		CCDS7532.1	10q24.32	2013-11-14	2007-07-12		ENSG00000107859	ENSG00000107859		"""Homeoboxes / PRD class"""	9006	protein-coding gene	gene with protein product		602669	"""paired-like homeodomain transcription factor 3"", ""anterior segment mesenchymal dysgenesis"""	ASMD		9620774	Standard	NM_005029		Approved		uc001kuu.1	O75364	OTTHUMG00000018952	ENST00000370002.3:c.148G>A	10.37:g.103991518C>T	ENSP00000359019:p.Gly50Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	2	0.0307692	NM_005029	Q5VZL2	Missense_Mutation	SNP	ENST00000370002.3	37	CCDS7532.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.170570	0.78452	.	.	ENSG00000107859	ENST00000370002;ENST00000539804	D;D	0.95377	-3.69;-3.69	5.32	4.42	0.53409	Homeodomain-related (1);	0.095493	0.64402	N	0.000002	D	0.88112	0.6349	N	0.08118	0	0.46749	D	0.999185	B	0.22541	0.071	B	0.16289	0.015	T	0.83353	-0.0002	10	0.20046	T	0.44	.	13.9339	0.64012	0.0:0.9265:0.0:0.0735	.	50	O75364	PITX3_HUMAN	S	50	ENSP00000359019:G50S;ENSP00000439383:G50S	ENSP00000359019:G50S	G	-	1	0	PITX3	103981508	0.993000	0.37304	0.763000	0.31416	0.934000	0.57294	5.036000	0.64164	1.260000	0.44134	0.455000	0.32223	GGC	.	.	none		0.662	PITX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050031.1		
ALS2CR11	151254	hgsc.bcm.edu	37	2	202430584	202430584	+	Missense_Mutation	SNP	G	G	A	rs73991652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202430584G>A	ENST00000286195.3	-	9	889	c.845C>T	c.(844-846)aCa>aTa	p.T282I	ALS2CR11_ENST00000439802.1_Missense_Mutation_p.T282I|ALS2CR11_ENST00000439140.1_Missense_Mutation_p.T282I|ALS2CR11_ENST00000450242.1_Missense_Mutation_p.T282I	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	282										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						TGTCTGTGGTGTAATAACTTT	0.393													G|||	219	0.04373	0.0991	0.0476	5008	,	,		14690	0.0		0.0477	False		,,,				2504	0.0072				p.T282I		Atlas-SNP	.											.	ALS2CR11	194	.	0			c.C845T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	342,4064	178.7+/-207.4	15,312,1876	72.0	72.0	72.0		845,845,845,845	-3.5	0.0	2	dbSNP_130	72	463,8137	137.1+/-194.1	14,435,3851	yes	missense,missense,missense,missense	ALS2CR11	NM_001168216.1,NM_001168217.1,NM_001168221.1,NM_152525.5	89,89,89,89	29,747,5727	AA,AG,GG		5.3837,7.7621,6.1895	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	282/396,282/551,282/1821,282/624	202430584	805,12201	2203	4300	6503	SO:0001583	missense	151254	exon9			TGTGGTGTAATAA	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.845C>T	2.37:g.202430584G>A	ENSP00000286195:p.Thr282Ile	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	22	0.366667	NM_001168217	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Missense_Mutation	SNP	ENST00000286195.3	37	CCDS2349.1	87	0.03983516483516483	32	0.06504065040650407	16	0.04419889502762431	0	0.0	39	0.051451187335092345	G	0.033	-1.320890	0.01320	0.077621	0.053837	ENSG00000155754	ENST00000286195;ENST00000439802;ENST00000439140;ENST00000450242	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.88	-3.54	0.04653	.	2.050610	0.01917	N	0.040204	T	0.01695	0.0054	N	0.25890	0.77	0.09310	N	1	B;B;B	0.28470	0.018;0.213;0.2	B;B;B	0.25506	0.011;0.029;0.061	T	0.12967	-1.0527	10	0.35671	T	0.21	.	11.585	0.50912	0.2363:0.0:0.6546:0.1091	.	282;282;282	Q53TS8-2;E9PGG4;Q53TS8	.;.;AL2SA_HUMAN	I	282	ENSP00000286195:T282I;ENSP00000400672:T282I;ENSP00000409937:T282I;ENSP00000399016:T282I	ENSP00000286195:T282I	T	-	2	0	ALS2CR11	202138829	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	-0.378000	0.07446	-0.455000	0.07054	-0.302000	0.09304	ACA	G|0.948;A|0.052	0.052	strong		0.393	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525	
OR52J3	119679	hgsc.bcm.edu	37	11	5068137	5068137	+	Missense_Mutation	SNP	G	G	A	rs2500017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	194	0	0		WXS	Illumina HiSeq	Phase_I	264	137	0.518939	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	
SLK	9748	hgsc.bcm.edu	37	10	105763026	105763026	+	Missense_Mutation	SNP	C	C	T	rs3740469	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105763026C>T	ENST00000369755.3	+	9	2635	c.2090C>T	c.(2089-2091)aCt>aTt	p.T697I	SLK_ENST00000335753.4_Missense_Mutation_p.T697I	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	697			T -> I (in dbSNP:rs3740469). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CCTGAAGTTACTGTAGTTTCA	0.358													C|||	821	0.163938	0.0688	0.2147	5008	,	,		19569	0.1379		0.2256	False		,,,				2504	0.2198				p.T697I	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.C2090T						PASS	.	C	ILE/THR	470,3936	218.7+/-236.7	30,410,1763	69.0	71.0	70.0		2090	3.5	0.0	10	dbSNP_107	70	2065,6535	356.6+/-330.4	232,1601,2467	yes	missense	SLK	NM_014720.2	89	262,2011,4230	TT,TC,CC		24.0116,10.6673,19.491	possibly-damaging	697/1236	105763026	2535,10471	2203	4300	6503	SO:0001583	missense	9748	exon9			AAGTTACTGTAGT		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.2090C>T	10.37:g.105763026C>T	ENSP00000358770:p.Thr697Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	340	0.15567765567765568	31	0.06300813008130081	67	0.1850828729281768	78	0.13636363636363635	164	0.21635883905013192	C	3.803	-0.041303	0.07452	0.106673	0.240116	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.69435	-0.4;-0.39	5.71	3.54	0.40534	Protein kinase-like domain (1);	0.452476	0.25264	N	0.031929	T	0.00039	0.0001	N	0.16478	0.41	0.48040	P	4.3000000000004146E-4	B;B	0.10296	0.003;0.002	B;B	0.09377	0.004;0.002	T	0.06144	-1.0843	9	0.48119	T	0.1	.	13.2602	0.60101	0.0:0.8499:0.0:0.1501	rs3740469;rs52790565;rs61191900;rs3740469	697;697	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	I	697	ENSP00000336824:T697I;ENSP00000358770:T697I	ENSP00000336824:T697I	T	+	2	0	SLK	105753016	0.001000	0.12720	0.022000	0.16811	0.181000	0.23173	0.268000	0.18571	1.430000	0.47334	0.555000	0.69702	ACT	C|0.822;T|0.178	0.178	strong		0.358	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
MAEL	84944	hgsc.bcm.edu	37	1	166958710	166958710	+	Missense_Mutation	SNP	T	T	G	rs11578336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:166958710T>G	ENST00000367872.4	+	1	365	c.121T>G	c.(121-123)Tca>Gca	p.S41A	MAEL_ENST00000367870.2_Missense_Mutation_p.S41A	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	41			S -> A (in dbSNP:rs11578336).		cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						TTACTGCTCCTCAGACTGGGC	0.632													G|||	1245	0.248602	0.3661	0.1513	5008	,	,		14443	0.248		0.2256	False		,,,				2504	0.183				p.S41A		Atlas-SNP	.											MAEL,NS,carcinoma,0,1	MAEL	95	1	0			c.T121G						PASS	.	G	ALA/SER	1568,2832		281,1006,913	35.0	31.0	33.0		121	2.5	0.0	1	dbSNP_120	33	2107,6485		254,1599,2443	yes	missense	MAEL	NM_032858.1	99	535,2605,3356	GG,GT,TT		24.5228,35.6364,28.2866	benign	41/435	166958710	3675,9317	2200	4296	6496	SO:0001583	missense	84944	exon1			TGCTCCTCAGACT	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"""cancer/testis antigen 128"", ""spermatogenesis associated 35"""	611368	"""maelstrom homolog (Drosophila)"""			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.121T>G	1.37:g.166958710T>G	ENSP00000356846:p.Ser41Ala	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	37	CCDS1257.1	556	0.25457875457875456	176	0.35772357723577236	58	0.16022099447513813	159	0.27797202797202797	163	0.21503957783641162	G	0.004	-2.240398	0.00274	0.356364	0.245228	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.40756	1.02;2.53;2.53	5.49	2.46	0.29980	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);Domain of unknown function DUF1898 (1);	0.462954	0.20595	N	0.089278	T	0.04815	0.0130	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	0.37911	-0.9685	9	0.07644	T	0.81	.	9.1724	0.37091	0.0672:0.0:0.5427:0.3901	rs11578336;rs17552415;rs57781349;rs11578336	41;41	E9JVC3;Q96JY0	.;MAEL_HUMAN	A	41	ENSP00000356846:S41A;ENSP00000356844:S41A;ENSP00000402143:S41A	ENSP00000356844:S41A	S	+	1	0	MAEL	165225334	0.000000	0.05858	0.011000	0.14972	0.016000	0.09150	-0.371000	0.07513	0.429000	0.26202	-2.444000	0.00210	TCA	T|0.743;G|0.257	0.257	strong		0.632	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858	
WNK1	65125	hgsc.bcm.edu	37	12	988894	988894	+	Silent	SNP	G	G	A	rs9804992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000530271.2_Silent_p.Q1341Q|WNK1_ENST00000537687.1_Intron|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	132	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	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	
FLG	2312	hgsc.bcm.edu	37	1	152276282	152276282	+	Missense_Mutation	SNP	C	C	G	rs55707024	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276282C>G	ENST00000368799.1	-	3	11115	c.11080G>C	c.(11080-11082)Gag>Cag	p.E3694Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3694	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.E3694Q(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGTGTGGACTCTTGGTGGCTC	0.587									Ichthyosis				C|||	911	0.181909	0.0772	0.232	5008	,	,		20697	0.3452		0.1004	False		,,,				2504	0.2035				p.E3694Q		Atlas-SNP	.											FLG,extremity,malignant_melanoma,0,1	FLG	900	1	1	Substitution - Missense(1)	skin(1)	c.G11080C						scavenged	.						50.0	56.0	54.0					1																	152276282		2202	4278	6480	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGACTCTTGGTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11080G>C	1.37:g.152276282C>G	ENSP00000357789:p.Glu3694Gln	Somatic	340	1	0.00294118		WXS	Illumina HiSeq	Phase_I	371	48	0.12938	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	8.701	0.909632	0.17833	.	.	ENSG00000143631	ENST00000368799	T	0.01787	4.64	2.52	-3.46	0.04767	.	.	.	.	.	T	0.01454	0.0047	M	0.75447	2.3	0.09310	N	1	D	0.65815	0.995	P	0.61070	0.883	T	0.34254	-0.9836	9	0.20519	T	0.43	.	0.3502	0.00348	0.1921:0.291:0.2301:0.2868	rs55707024;rs58436539	3694	P20930	FILA_HUMAN	Q	3694	ENSP00000357789:E3694Q	ENSP00000357789:E3694Q	E	-	1	0	FLG	150542906	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.189000	0.03061	-0.738000	0.04817	0.552000	0.68991	GAG	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184102	26184102	+	Missense_Mutation	SNP	G	G	A	rs7766641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26184102G>A	ENST00000356530.3	+	1	145	c.79G>A	c.(79-81)Ggc>Agc	p.G27S		NM_003523.2	NP_003514.2	P62807	H2B1C_HUMAN	histone cluster 1, H2be	27			G -> S (in dbSNP:rs7766641). {ECO:0000269|PubMed:9119399}.		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						GAAGAAGGACGGCAAGAAGCG	0.582													G|||	1767	0.352835	0.0204	0.3732	5008	,	,		18763	0.7579		0.2833	False		,,,				2504	0.4417				p.G27S		Atlas-SNP	.											.	HIST1H2BE	10	.	0			c.G79A						PASS	.	G	SER/GLY	287,4119		7,273,1923	141.0	129.0	133.0		79	4.2	1.0	6	dbSNP_116	133	2418,6182		325,1768,2207	no	missense	HIST1H2BE	NM_003523.2	56	332,2041,4130	AA,AG,GG		28.1163,6.5138,20.7981	benign	27/127	26184102	2705,10301	2203	4300	6503	SO:0001583	missense	8344	exon1			AAGGACGGCAAGA	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.79G>A	6.37:g.26184102G>A	ENSP00000348924:p.Gly27Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_003523	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000356530.3	37	CCDS4588.1	797	0.3649267399267399	17	0.034552845528455285	119	0.3287292817679558	441	0.7709790209790209	220	0.29023746701846964	.	15.08	2.728194	0.48833	0.065138	0.281163	ENSG00000197697	ENST00000356530	T	0.22539	1.95	5.05	4.18	0.49190	.	0.000000	0.34700	U	0.003742	T	0.20455	0.0492	.	.	.	0.28334	P	0.9216307	.	.	.	.	.	.	T	0.02477	-1.1153	6	0.46703	T	0.11	.	12.9072	0.58160	0.0791:0.0:0.9209:0.0	rs7766641;rs58684673	.	.	.	S	27	ENSP00000348924:G27S	ENSP00000348924:G27S	G	+	1	0	HIST1H2BE	26292081	1.000000	0.71417	0.986000	0.45419	0.042000	0.13812	7.554000	0.82212	1.280000	0.44463	-0.199000	0.12753	GGC	G|0.744;A|0.256	0.256	strong		0.582	HIST1H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040090.1	NM_003523	
TF	7018	hgsc.bcm.edu	37	3	133486958	133486958	+	Silent	SNP	G	G	C	rs8649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:133486958G>C	ENST00000402696.3	+	13	2057	c.1572G>C	c.(1570-1572)ctG>ctC	p.L524L	TF_ENST00000264998.3_Silent_p.L397L	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	524	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)	GCCTAAACCTGTGTGAACCCA	0.463													G|||	1064	0.21246	0.3457	0.1787	5008	,	,		19543	0.0714		0.2614	False		,,,				2504	0.1513				p.L524L		Atlas-SNP	.											.	TF	116	.	0			c.G1572C						PASS	.	G		1359,3047	452.0+/-349.9	224,911,1068	93.0	94.0	94.0		1572	2.3	0.2	3	dbSNP_52	94	2225,6375	376.6+/-338.2	287,1651,2362	no	coding-synonymous	TF	NM_001063.3		511,2562,3430	CC,CG,GG		25.8721,30.8443,27.5565		524/699	133486958	3584,9422	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon13			AAACCTGTGTGAA		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.1572G>C	3.37:g.133486958G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			G|0.752;C|0.248	0.248	strong		0.463	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
LMNB2	84823	hgsc.bcm.edu	37	19	2433890	2433890	+	Silent	SNP	A	A	G	rs11084940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2433890A>G	ENST00000582871.1	-	8	1442	c.1356T>C	c.(1354-1356)ggT>ggC	p.G452G	LMNB2_ENST00000475819.1_5'Flank|LMNB2_ENST00000325327.3_Silent_p.G472G	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	452	LTD.|Tail.			LEVEEPLGSGPSVLGTGTGGSGGFHLAQQASASGSVS -> WRWRSPWQRPKRPGHGHGWQRWLPPGPAGLGLGQRH (in Ref. 5; AAA80979). {ECO:0000305}.		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)		TGCTGACGCTACCCGAGGCCG	0.667													G|||	3193	0.63758	0.8502	0.6643	5008	,	,		14382	0.6349		0.4374	False		,,,				2504	0.5399				p.G472G		Atlas-SNP	.											LMNB2,NS,carcinoma,0,1	LMNB2	40	1	0			c.T1416C						PASS	.	G		3538,866	334.1+/-303.3	1419,700,83	66.0	63.0	64.0		1356	-0.8	0.0	19	dbSNP_120	64	3888,4712	604.9+/-394.9	902,2084,1314	no	coding-synonymous	LMNB2	NM_032737.2		2321,2784,1397	GG,GA,AA		45.2093,19.6639,42.8945		452/601	2433890	7426,5578	2202	4300	6502	SO:0001819	synonymous_variant	84823	exon8			GACGCTACCCGAG	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.1356T>C	19.37:g.2433890A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_032737	O75292|Q14734|Q96DF6	Silent	SNP	ENST00000582871.1	37																																																																																				A|0.401;G|0.599	0.599	strong		0.667	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737	
ADAMTS1	9510	hgsc.bcm.edu	37	21	28216674	28216674	+	Silent	SNP	G	G	C	rs409630	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:28216674G>C	ENST00000284984.3	-	1	1054	c.600C>G	c.(598-600)gtC>gtG	p.V200V		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	200					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)		CGTCGTCCACGACCCCGCACG	0.721											OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	885	0.176717	0.0151	0.1527	5008	,	,		11842	0.2847		0.1849	False		,,,				2504	0.2924				p.V200V		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.C600G						PASS	.	G		220,4070		10,200,1935	12.0	10.0	11.0		600	0.7	0.1	21	dbSNP_80	11	1779,6645		188,1403,2621	no	coding-synonymous	ADAMTS1	NM_006988.3		198,1603,4556	CC,CG,GG		21.1182,5.1282,15.7228		200/968	28216674	1999,10715	2145	4212	6357	SO:0001819	synonymous_variant	9510	exon1			GTCCACGACCCCG	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.600C>G	21.37:g.28216674G>C		Somatic	33	0	0	800	WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	37	CCDS33524.1																																																																																			G|0.825;C|0.175	0.175	strong		0.721	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
CACNA1B	774	hgsc.bcm.edu	37	9	140777299	140777299	+	Missense_Mutation	SNP	G	G	T	rs71238527	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140777299G>T	ENST00000371372.1	+	3	639	c.494G>T	c.(493-495)gGc>gTc	p.G165V	CACNA1B_ENST00000371357.1_Missense_Mutation_p.G165V|CACNA1B_ENST00000277551.2_Missense_Mutation_p.G165V|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371363.1_Missense_Mutation_p.G165V|CACNA1B_ENST00000371355.4_Missense_Mutation_p.G165V	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	165					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CTGCGGAACGGCTGGAACGTC	0.587																																					p.G165V		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G494T						PASS	.	G	VAL/GLY	95,4135		0,95,2020	195.0	208.0	204.0		494	4.6	1.0	9	dbSNP_130	204	992,7488		0,992,3248	yes	missense	CACNA1B	NM_000718.3	109	0,1087,5268	TT,TG,GG		11.6981,2.2459,8.5523	probably-damaging	165/2340	140777299	1087,11623	2115	4240	6355	SO:0001583	missense	774	exon3			GGAACGGCTGGAA	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.494G>T	9.37:g.140777299G>T	ENSP00000360423:p.Gly165Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	33	0.230769	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.738315	0.30774	0.022459	0.116981	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98381	-4.9;-4.9;-4.9;-4.9;-4.9	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.66005	0.2746	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60490	-0.7253	10	0.62326	D	0.03	.	17.3563	0.87336	0.0:0.0:1.0:0.0	.	165	B1AQK6	.	V	165	ENSP00000360423:G165V;ENSP00000277551:G165V;ENSP00000360414:G165V;ENSP00000360408:G165V;ENSP00000360406:G165V	ENSP00000277551:G165V	G	+	2	0	CACNA1B	139897120	1.000000	0.71417	0.999000	0.59377	0.154000	0.21943	9.633000	0.98432	2.070000	0.61991	0.467000	0.42956	GGC	G|0.947;T|0.053	0.053	strong		0.587	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
ABCC1	4363	hgsc.bcm.edu	37	16	16138322	16138322	+	Silent	SNP	T	T	C	rs246221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:16138322T>C	ENST00000399410.3	+	8	1000	c.825T>C	c.(823-825)gtT>gtC	p.V275V	ABCC1_ENST00000345148.5_Silent_p.V275V|ABCC1_ENST00000346370.5_Silent_p.V275V|ABCC1_ENST00000399408.2_Silent_p.V275V|ABCC1_ENST00000351154.5_Silent_p.V275V|ABCC1_ENST00000349029.5_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	143	0	0		WXS	Illumina HiSeq	Phase_I	122	69	0.565574	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	
RGCC	28984	hgsc.bcm.edu	37	13	42032572	42032572	+	Silent	SNP	T	T	C	rs7136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	36	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	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	
KIFC1	3833	hgsc.bcm.edu	37	6	33373341	33373341	+	Missense_Mutation	SNP	C	C	T	rs7770412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33373341C>T	ENST00000428849.2	+	7	1919	c.1469C>T	c.(1468-1470)gCa>gTa	p.A490V		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	490	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|minus-end-directed microtubule motor activity (GO:0008569)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						ATTCGCCGTGCAGGGCCAGGG	0.562													C|||	43	0.00858626	0.0098	0.0014	5008	,	,		19788	0.0099		0.0109	False		,,,				2504	0.0082				p.A490V		Atlas-SNP	.											.	KIFC1	47	.	0			c.C1469T						PASS	.	C	VAL/ALA	21,4385	25.3+/-52.1	0,21,2182	28.0	29.0	29.0		1469	5.2	1.0	6	dbSNP_116	29	72,8528	42.6+/-100.3	0,72,4228	yes	missense	KIFC1	NM_002263.3	64	0,93,6410	TT,TC,CC		0.8372,0.4766,0.7151	benign	490/674	33373341	93,12913	2203	4300	6503	SO:0001583	missense	3833	exon7			GCCGTGCAGGGCC	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"""Kinesins"""	6389	protein-coding gene	gene with protein product		603763	"""kinesin-like 2"""	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.1469C>T	6.37:g.33373341C>T	ENSP00000393963:p.Ala490Val	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	37	CCDS34430.1	23	0.010531135531135532	8	0.016260162601626018	1	0.0027624309392265192	8	0.013986013986013986	6	0.0079155672823219	C	10.18	1.279858	0.23392	0.004766	0.008372	ENSG00000237649	ENST00000428849	T	0.75367	-0.93	5.22	5.22	0.72569	Kinesin, motor domain (4);	0.346115	0.29900	N	0.010904	T	0.41650	0.1168	N	0.20610	0.595	0.45502	D	0.998463	B;B	0.28400	0.21;0.21	B;B	0.26094	0.066;0.066	T	0.39143	-0.9628	10	0.22109	T	0.4	-17.1298	9.6556	0.39923	0.0:0.9081:0.0:0.0919	rs7770412	482;490	B4E063;Q9BW19	.;KIFC1_HUMAN	V	490	ENSP00000393963:A490V	ENSP00000393963:A490V	A	+	2	0	KIFC1	33481319	0.997000	0.39634	1.000000	0.80357	0.952000	0.60782	2.994000	0.49433	2.720000	0.93068	0.655000	0.94253	GCA	C|0.993;T|0.007	0.007	strong		0.562	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	
LRRC8B	23507	hgsc.bcm.edu	37	1	90049577	90049577	+	Silent	SNP	C	C	T	rs140158391		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:90049577C>T	ENST00000330947.2	+	5	1728	c.1368C>T	c.(1366-1368)ccC>ccT	p.P456P	LRRC8B_ENST00000358200.4_Silent_p.P456P|LRRC8B_ENST00000439853.1_Silent_p.P456P|RP5-1007M22.2_ENST00000443562.1_RNA	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	456					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)		TGAAGCTGCCCTCTGCAGTCT	0.473																																					p.P456P		Atlas-SNP	.											.	LRRC8B	49	.	0			c.C1368T						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	52.0	52.0	52.0		1368,1368	0.8	1.0	1	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,	456/804,456/804	90049577	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			GCTGCCCTCTGCA	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.1368C>T	1.37:g.90049577C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	4	0.0625	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			C|1.000;T|0.000	0.000	weak		0.473	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
FLG2	388698	hgsc.bcm.edu	37	1	152331240	152331240	+	Missense_Mutation	SNP	G	G	A	rs3818831	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152331240G>A	ENST00000388718.5	-	2	193	c.121C>T	c.(121-123)Ctt>Ttt	p.L41F	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	41	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.|S-100-like. {ECO:0000250}.		L -> F (in dbSNP:rs3818831).		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)			ACTGGATGAAGCTCTTTCTCC	0.468													A|||	1862	0.371805	0.4493	0.4222	5008	,	,		17511	0.501		0.1461	False		,,,				2504	0.3303				p.L41F		Atlas-SNP	.											.	FLG2	431	.	0			c.C121T						PASS	.	A	PHE/LEU	1777,2629	643.9+/-397.9	337,1103,763	164.0	160.0	161.0		121	5.3	0.9	1	dbSNP_107	161	1386,7214	754.3+/-407.5	137,1112,3051	yes	missense	FLG2	NM_001014342.2	22	474,2215,3814	AA,AG,GG		16.1163,40.3314,24.3195	benign	41/2392	152331240	3163,9843	2203	4300	6503	SO:0001583	missense	388698	exon2			GATGAAGCTCTTT	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.121C>T	1.37:g.152331240G>A	ENSP00000373370:p.Leu41Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	732	0.33516483516483514	209	0.4247967479674797	129	0.356353591160221	283	0.49475524475524474	111	0.14643799472295516	A	2.168	-0.390521	0.04932	0.403314	0.161163	ENSG00000143520	ENST00000388718	T	0.16196	2.36	5.26	5.26	0.73747	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.01627	0.0052	N	0.03891	-0.335	0.53005	P	3.6000000000036E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44267	-0.9339	8	0.02654	T	1	-9.6106	8.2973	0.31993	0.9092:0.0:0.0908:0.0	rs3818831;rs52802943;rs58052569;rs3818831	41	Q5D862	FILA2_HUMAN	F	41	ENSP00000373370:L41F	ENSP00000373370:L41F	L	-	1	0	FLG2	150597864	0.992000	0.36948	0.945000	0.38365	0.555000	0.35460	1.519000	0.35888	0.946000	0.37632	-0.269000	0.10298	CTT	G|0.706;A|0.294	0.294	strong		0.468	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
OR51G1	79324	hgsc.bcm.edu	37	11	4945233	4945233	+	Missense_Mutation	SNP	C	C	T	rs35264256	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4945233C>T	ENST00000321961.2	-	1	404	c.337G>A	c.(337-339)Gag>Aag	p.E113K	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACTGATGACTCCATTGAAGAC	0.502													C|||	385	0.076877	0.062	0.1527	5008	,	,		22495	0.0079		0.1083	False		,,,				2504	0.0818				p.E113K		Atlas-SNP	.											.	OR51G1	74	.	0			c.G337A						PASS	.	C	LYS/GLU	277,4125	154.8+/-188.1	3,271,1927	101.0	94.0	97.0		337	4.2	0.5	11	dbSNP_126	97	930,7666	206.2+/-248.4	61,808,3429	no	missense	OR51G1	NM_001005237.1	56	64,1079,5356	TT,TC,CC		10.819,6.2926,9.286	probably-damaging	113/322	4945233	1207,11791	2201	4298	6499	SO:0001583	missense	79324	exon1			ATGACTCCATTGA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.337G>A	11.37:g.4945233C>T	ENSP00000322546:p.Glu113Lys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	171	0.0782967032967033	34	0.06910569105691057	30	0.08287292817679558	5	0.008741258741258742	102	0.1345646437994723	C	12.66	2.005934	0.35415	0.062926	0.10819	ENSG00000176879	ENST00000321961	T	0.40225	1.04	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39475	U	0.001355	T	0.02119	0.0066	H	0.95504	3.68	0.36263	P	0.145324	D	0.89917	1.0	D	0.91635	0.999	T	0.58092	-0.7697	9	0.87932	D	0	.	15.2651	0.73654	0.0:1.0:0.0:0.0	rs35264256;rs61737945	113	Q8NGK1	O51G1_HUMAN	K	113	ENSP00000322546:E113K	ENSP00000322546:E113K	E	-	1	0	OR51G1	4901809	0.634000	0.27190	0.508000	0.27688	0.043000	0.13939	1.261000	0.32980	2.169000	0.68431	0.557000	0.71058	GAG	C|0.912;T|0.088	0.088	strong		0.502	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
LAMC1	3915	hgsc.bcm.edu	37	1	183105705	183105705	+	Silent	SNP	G	G	A	rs20561	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:183105705G>A	ENST00000258341.4	+	25	4556	c.4299G>A	c.(4297-4299)gcG>gcA	p.A1433A	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1433	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						AGAGGATCGCGAGCGCTGTCC	0.567													G|||	1762	0.351837	0.1702	0.3833	5008	,	,		16519	0.5109		0.4433	False		,,,				2504	0.317				p.A1433A		Atlas-SNP	.											.	LAMC1	176	.	0			c.G4299A						PASS	.	G		954,3452	345.1+/-308.4	98,758,1347	52.0	54.0	54.0		4299	-1.7	0.8	1	dbSNP_67	54	3712,4888	509.6+/-377.3	798,2116,1386	no	coding-synonymous	LAMC1	NM_002293.3		896,2874,2733	AA,AG,GG		43.1628,21.6523,35.8757		1433/1610	183105705	4666,8340	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon25			GATCGCGAGCGCT	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4299G>A	1.37:g.183105705G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			G|0.636;A|0.364	0.364	strong		0.567	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
DSPP	1834	hgsc.bcm.edu	37	4	88537288	88537288	+	Silent	SNP	C	C	T	rs368208607		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537288C>T	ENST00000282478.7	+	4	3507	c.3474C>T	c.(3472-3474)gaC>gaT	p.D1158D	DSPP_ENST00000399271.1_Silent_p.D1158D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1158	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)		acagcagcgacagcagtgaca	0.557																																					p.D1158D		Atlas-SNP	.											.	DSPP	174	.	0			c.C3474T						PASS	.						46.0	59.0	54.0					4																	88537288		1591	2859	4450	SO:0001819	synonymous_variant	1834	exon5			CAGCGACAGCAGT	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.3474C>T	4.37:g.88537288C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	175	9	0.0514286	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	
KANSL3	55683	hgsc.bcm.edu	37	2	97271090	97271090	+	Missense_Mutation	SNP	G	G	A	rs35715176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97271090G>A	ENST00000431828.1	-	15	1976	c.1900C>T	c.(1900-1902)Cct>Tct	p.P634S	KANSL3_ENST00000440133.1_Missense_Mutation_p.P454S|KANSL3_ENST00000599854.1_Missense_Mutation_p.P547S|KANSL3_ENST00000441706.2_Intron|KANSL3_ENST00000487070.1_5'UTR			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	660					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GGAGCACAAGGCCCTCCAGCT	0.537													G|||	216	0.043131	0.0008	0.013	5008	,	,		21220	0.1438		0.0249	False		,,,				2504	0.0368				p.P634S		Atlas-SNP	.											.	.	.	.	0			c.C1900T						PASS	.	G	SER/PRO,SER/PRO	19,3929		0,19,1955	81.0	82.0	81.0		1900,1639	2.6	0.0	2	dbSNP_126	81	128,8174		1,126,4024	yes	missense,missense	KIAA1310	NM_001115016.1,NM_017991.4	74,74	1,145,5979	AA,AG,GG		1.5418,0.4813,1.2	benign,benign	634/879,547/792	97271090	147,12103	1974	4151	6125	SO:0001583	missense	55683	exon15			CACAAGGCCCTCC	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"""KIAA1310"""	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1900C>T	2.37:g.97271090G>A	ENSP00000396749:p.Pro634Ser	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	197	86	0.436548	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	37	CCDS46361.1	132	0.06043956043956044	1	0.0020325203252032522	6	0.016574585635359115	107	0.18706293706293706	18	0.023746701846965697	G	9.096	1.002849	0.19121	0.004813	0.015418	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000440133;ENST00000444759	T;T	0.40476	1.03;1.05	5.42	2.62	0.31277	.	0.617048	0.17418	N	0.174938	T	0.00039	0.0001	N	0.04508	-0.205	0.54753	P	1.399999999995849E-5	B;B;B;B	0.06786	0.0;0.001;0.001;0.001	B;B;B;B	0.06405	0.0;0.001;0.001;0.002	T	0.25433	-1.0132	9	0.08179	T	0.78	.	5.0282	0.14396	0.1843:0.1741:0.6416:0.0	rs35715176	428;634;547;522	B4E1W4;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;.;.;.	S	547;522;634;454;428	ENSP00000396749:P634S;ENSP00000406207:P454S	ENSP00000346144:P547S	P	-	1	0	KIAA1310	96634817	0.052000	0.20516	0.033000	0.17914	0.996000	0.88848	0.518000	0.22847	0.658000	0.30925	0.655000	0.94253	CCT	G|0.949;A|0.051	0.051	strong		0.537	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991	
SPATA22	84690	hgsc.bcm.edu	37	17	3352331	3352331	+	Missense_Mutation	SNP	C	C	T	rs1488690	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3352331C>T	ENST00000573128.1	-	6	925	c.442G>A	c.(442-444)Gtg>Atg	p.V148M	SPATA22_ENST00000541913.1_Missense_Mutation_p.V132M|SPATA22_ENST00000397168.3_Missense_Mutation_p.V148M|SPATA22_ENST00000572969.1_Missense_Mutation_p.V148M|SPATA22_ENST00000575375.1_Missense_Mutation_p.V148M|SPATA22_ENST00000355380.4_Missense_Mutation_p.V105M|SPATA22_ENST00000268981.5_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	232	0	0		WXS	Illumina HiSeq	Phase_I	226	121	0.535398	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	
ZBED6CL	113763	hgsc.bcm.edu	37	7	150027802	150027802	+	Silent	SNP	C	C	T	rs75555338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150027802C>T	ENST00000343855.4	+	1	865	c.309C>T	c.(307-309)ctC>ctT	p.L103L	LRRC61_ENST00000323078.7_Intron|LRRC61_ENST00000493307.1_Intron|LRRC61_ENST00000359623.4_Intron	NM_138434.2	NP_612443.1	Q96FA7	ZB6CL_HUMAN	ZBED6 C-terminal like	103																	AGCAAGTCCTCGTGTACAAGG	0.567													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		19715	0.0		0.0099	False		,,,				2504	0.0				p.L103L		Atlas-SNP	.											.	C7orf29	18	.	0			c.C309T						PASS	.	C	,,	7,4399	12.9+/-30.5	0,7,2196	74.0	75.0	75.0		,,309	-7.5	0.0	7	dbSNP_133	75	138,8462	68.4+/-130.8	2,134,4164	no	intron,intron,coding-synonymous	LRRC61,C7orf29	NM_001142928.1,NM_023942.2,NM_138434.2	,,	2,141,6360	TT,TC,CC		1.6047,0.1589,1.1149	,,	,,103/237	150027802	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	113763	exon1			AGTCCTCGTGTAC	BC011406	CCDS5900.1	7q35	2013-05-03	2013-05-03	2013-05-03	ENSG00000188707	ENSG00000188707			21720	protein-coding gene	gene with protein product		615252	"""chromosome 7 open reading frame 29"""	C7orf29		23533661	Standard	NM_138434		Approved			Q96FA7	OTTHUMG00000158328	ENST00000343855.4:c.309C>T	7.37:g.150027802C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_138434		Silent	SNP	ENST00000343855.4	37	CCDS5900.1																																																																																			C|0.990;T|0.010	0.010	strong		0.567	ZBED6CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350702.1	NM_138434	
C9orf43	257169	hgsc.bcm.edu	37	9	116181419	116181419	+	Missense_Mutation	SNP	A	A	G	rs113088354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:116181419A>G	ENST00000288462.4	+	4	765	c.319A>G	c.(319-321)Atc>Gtc	p.I107V	C9orf43_ENST00000490544.1_3'UTR|C9orf43_ENST00000374165.1_Missense_Mutation_p.I107V	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	107										breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						CAAAAGTTTGATCAACTGTAC	0.318													A|||	57	0.0113818	0.0008	0.0187	5008	,	,		21227	0.003		0.0169	False		,,,				2504	0.0235				p.I107V		Atlas-SNP	.											.	C9orf43	49	.	0			c.A319G						PASS	.	A	VAL/ILE	20,4386	27.2+/-55.0	0,20,2183	98.0	98.0	98.0		319	2.8	0.0	9	dbSNP_132	98	182,8418	81.5+/-144.1	1,180,4119	yes	missense	C9orf43	NM_152786.1	29	1,200,6302	GG,GA,AA		2.1163,0.4539,1.5531	benign	107/462	116181419	202,12804	2203	4300	6503	SO:0001583	missense	257169	exon4			AGTTTGATCAACT	BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.319A>G	9.37:g.116181419A>G	ENSP00000288462:p.Ile107Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_152786		Missense_Mutation	SNP	ENST00000288462.4	37	CCDS6796.1	26	0.011904761904761904	0	0.0	11	0.03038674033149171	1	0.0017482517482517483	14	0.018469656992084433	A	7.848	0.723287	0.15439	0.004539	0.021163	ENSG00000157653	ENST00000374165;ENST00000288462	T;T	0.46819	0.86;0.86	5.16	2.84	0.33178	.	2.056080	0.02302	N	0.071249	T	0.10809	0.0264	N	0.14661	0.345	0.09310	N	1	B	0.24721	0.11	B	0.20184	0.028	T	0.19844	-1.0293	10	0.05351	T	0.99	0.2011	6.613	0.22761	0.8143:0.0:0.1857:0.0	.	107	Q8TAL5	CI043_HUMAN	V	107	ENSP00000363280:I107V;ENSP00000288462:I107V	ENSP00000288462:I107V	I	+	1	0	C9orf43	115221240	0.000000	0.05858	0.000000	0.03702	0.268000	0.26511	0.300000	0.19156	0.527000	0.28560	0.533000	0.62120	ATC	A|0.986;G|0.014	0.014	strong		0.318	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786	
CHL1	10752	hgsc.bcm.edu	37	3	361493	361493	+	Missense_Mutation	SNP	G	G	A	rs142251617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:361493G>A	ENST00000256509.2	+	3	676	c.34G>A	c.(34-36)Gta>Ata	p.V12I	CHL1_ENST00000397491.2_Missense_Mutation_p.V12I	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)			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)		AGGACTAATCGTATATCTAAT	0.348													G|||	66	0.0131789	0.0015	0.0634	5008	,	,		16221	0.001		0.0089	False		,,,				2504	0.0102				p.V12I		Atlas-SNP	.											.	CHL1	242	.	0			c.G34A						PASS	.	G	ILE/VAL	13,4391	20.2+/-43.8	0,13,2189	65.0	68.0	67.0		34	-9.8	0.0	3	dbSNP_134	67	106,8494	57.9+/-119.4	0,106,4194	yes	missense	CHL1	NM_006614.2	29	0,119,6383	AA,AG,GG		1.2326,0.2952,0.9151	benign	12/1225	361493	119,12885	2202	4300	6502	SO:0001583	missense	10752	exon1			CTAATCGTATATC	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.34G>A	3.37:g.361493G>A	ENSP00000256509:p.Val12Ile	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	29	0.013278388278388278	3	0.006097560975609756	18	0.049723756906077346	1	0.0017482517482517483	7	0.009234828496042216	G	2.914	-0.224798	0.06022	0.002952	0.012326	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;T;T;T	0.61627	0.34;0.34;1.06;0.43;0.31;0.09	4.91	-9.82	0.00484	.	2.380520	0.01454	N	0.015608	T	0.04861	0.0131	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.0;0.001;0.002	B;B;B	0.04013	0.0;0.001;0.001	T	0.10941	-1.0608	10	0.11794	T	0.64	.	4.8623	0.13590	0.1328:0.4054:0.0618:0.4	.	12;12;12	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	I	12	ENSP00000256509:V12I;ENSP00000380628:V12I;ENSP00000403311:V12I;ENSP00000413628:V12I;ENSP00000397445:V12I;ENSP00000390440:V12I	ENSP00000256509:V12I	V	+	1	0	CHL1	336493	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.238000	0.01199	-3.536000	0.00145	-0.238000	0.12139	GTA	G|0.990;A|0.010	0.010	strong		0.348	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
C9orf84	158401	hgsc.bcm.edu	37	9	114468966	114468966	+	Missense_Mutation	SNP	A	A	C	rs7036568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114468966A>C	ENST00000318737.4	-	18	2555	c.2427T>G	c.(2425-2427)aaT>aaG	p.N809K	C9orf84_ENST00000394777.4_Missense_Mutation_p.N735K|C9orf84_ENST00000374287.3_Missense_Mutation_p.N809K|C9orf84_ENST00000394779.3_Missense_Mutation_p.N770K	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	809			N -> K (in dbSNP:rs7036568).							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						CAAATGAGAAATTACTCCAGG	0.358													C|||	1089	0.217452	0.3275	0.2205	5008	,	,		16153	0.0476		0.2475	False		,,,				2504	0.2106				p.N809K		Atlas-SNP	.											C9orf84_ENST00000374287,colon,carcinoma,0,2	C9orf84	207	2	0			c.T2427G						PASS	.	C	LYS/ASN,LYS/ASN	1478,2928	675.8+/-403.1	246,986,971	143.0	159.0	153.0		2310,2427	-3.9	0.1	9	dbSNP_116	153	2164,6434	712.1+/-405.9	264,1636,2399	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	94,94	510,2622,3370	CC,CA,AA		25.1686,33.5452,28.0068	benign,benign	770/1406,809/1445	114468966	3642,9362	2203	4299	6502	SO:0001583	missense	158401	exon18			TGAGAAATTACTC	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.2427T>G	9.37:g.114468966A>C	ENSP00000322108:p.Asn809Lys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	469	0.21474358974358973	168	0.34146341463414637	78	0.2154696132596685	33	0.057692307692307696	190	0.25065963060686014	C	0.082	-1.181676	0.01633	0.335452	0.251686	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.04156	3.69;3.7;3.7;3.7	4.84	-3.94	0.04130	.	1.009520	0.07955	N	0.981503	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.45877	-0.9231	9	0.02654	T	1	-0.0067	2.5329	0.04707	0.3654:0.196:0.3348:0.1039	rs7036568;rs57781556;rs7036568	735;809;770	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	K	770;735;423;809;809	ENSP00000378259:N770K;ENSP00000378257:N735K;ENSP00000363405:N809K;ENSP00000322108:N809K	ENSP00000322108:N809K	N	-	3	2	C9orf84	113508787	0.001000	0.12720	0.098000	0.21074	0.807000	0.45602	-0.190000	0.09615	-0.675000	0.05246	-1.740000	0.00687	AAT	A|0.750;C|0.250	0.250	strong		0.358	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
NCKAP5	344148	hgsc.bcm.edu	37	2	133489601	133489601	+	Silent	SNP	A	A	G	rs56284623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133489601A>G	ENST00000409261.1	-	17	5525	c.5152T>C	c.(5152-5154)Ttg>Ctg	p.L1718L	NCKAP5_ENST00000405974.3_Silent_p.L399L|NCKAP5_ENST00000317721.6_Silent_p.L1718L|NCKAP5_ENST00000409213.1_Silent_p.L399L|NCKAP5_ENST00000473859.1_5'UTR	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1718										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CCACTGTCCAATGTTCTCATC	0.502													A|||	784	0.15655	0.0492	0.1499	5008	,	,		19816	0.1002		0.2634	False		,,,				2504	0.2546				p.L1718L		Atlas-SNP	.											.	NCKAP5	322	.	0			c.T5152C						PASS	.	A	,	316,3612		15,286,1663	51.0	53.0	52.0		5152,1195	-2.9	0.0	2	dbSNP_129	52	2221,6087		298,1625,2231	no	coding-synonymous,coding-synonymous	NCKAP5	NM_207363.2,NM_207481.3	,	313,1911,3894	GG,GA,AA		26.7333,8.0448,20.7339	,	1718/1910,399/591	133489601	2537,9699	1964	4154	6118	SO:0001819	synonymous_variant	344148	exon17			TGTCCAATGTTCT	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.5152T>C	2.37:g.133489601A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			A|0.822;G|0.178	0.178	strong		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
ZNF429	353088	hgsc.bcm.edu	37	19	21719401	21719401	+	Silent	SNP	T	T	C	rs35782355	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	46	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	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	
CDON	50937	hgsc.bcm.edu	37	11	125891269	125891269	+	Missense_Mutation	SNP	C	C	T	rs3740912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	156	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	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	
DDX27	55661	hgsc.bcm.edu	37	20	47859217	47859217	+	Splice_Site	SNP	G	G	A	rs1130146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:47859217G>A	ENST00000371764.4	+	19	2305	c.2296G>A	c.(2296-2298)Ggc>Agc	p.G766S	ZNFX1_ENST00000469991.1_Intron|DDX27_ENST00000484427.1_3'UTR|ZNFX1_ENST00000371754.4_Intron	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	766			G -> S (in dbSNP:rs1130146). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			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)			GTATCGAGCTGGGTAGGATTT	0.443													G|||	1365	0.272564	0.0567	0.3271	5008	,	,		18301	0.3234		0.4085	False		,,,				2504	0.3333				p.G766S		Atlas-SNP	.											.	DDX27	74	.	0			c.G2296A						PASS	.	G	SER/GLY	468,3938	220.7+/-238.1	26,416,1761	114.0	118.0	116.0		2296	4.9	1.0	20	dbSNP_86	116	3283,5317	491.9+/-373.2	631,2021,1648	yes	missense-near-splice	DDX27	NM_017895.7	56	657,2437,3409	AA,AG,GG		38.1744,10.6219,28.8405	possibly-damaging	766/797	47859217	3751,9255	2203	4300	6503	SO:0001630	splice_region_variant	55661	exon19			CGAGCTGGGTAGG	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.2297+1G>A	20.37:g.47859217G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	634	0.2902930402930403	32	0.06504065040650407	124	0.3425414364640884	165	0.28846153846153844	313	0.4129287598944591	G	27.8	4.860053	0.91433	0.106219	0.381744	ENSG00000124228	ENST00000371764	T	0.01438	4.89	5.91	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	1.0	D	0.58620	0.983	P	0.54312	0.748	T	0.63954	-0.6520	9	0.23891	T	0.37	-21.6264	14.2585	0.66067	0.0:0.0:0.8498:0.1502	rs1130146;rs3188714;rs6063377;rs8116791;rs11553386;rs17416057;rs17722253;rs52796221;rs58594349;rs6063377	766	Q96GQ7	DDX27_HUMAN	S	766	ENSP00000360828:G766S	ENSP00000360828:G766S	G	+	1	0	DDX27	47292624	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.104000	0.77024	1.487000	0.48415	0.655000	0.94253	GGC	G|0.716;A|0.284	0.284	strong		0.443	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		Missense_Mutation
MUC2	4583	hgsc.bcm.edu	37	11	1080391	1080391	+	Missense_Mutation	SNP	G	G	A	rs41521547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1080391G>A	ENST00000441003.2	+	8	1138	c.1111G>A	c.(1111-1113)Gag>Aag	p.E371K	MUC2_ENST00000359061.5_Missense_Mutation_p.E371K	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	371					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CAATGACTGCGAGCAGTGGTG	0.662													G|||	242	0.0483227	0.0333	0.0461	5008	,	,		16331	0.0496		0.0915	False		,,,				2504	0.0245				p.E371K		Atlas-SNP	.											.	MUC2	614	.	0			c.G1111A						PASS	.	G	LYS/GLU	155,4047		4,147,1950	21.0	25.0	24.0		1111	0.8	0.0	11	dbSNP_127	24	746,7658		36,674,3492	yes	missense	MUC2	NM_002457.2	56	40,821,5442	AA,AG,GG		8.8767,3.6887,7.1474	benign	371/2813	1080391	901,11705	2101	4202	6303	SO:0001583	missense	4583	exon8			GACTGCGAGCAGT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1111G>A	11.37:g.1080391G>A	ENSP00000415183:p.Glu371Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		115	0.052655677655677656	14	0.028455284552845527	10	0.027624309392265192	25	0.043706293706293704	66	0.0870712401055409	G	13.29	2.193112	0.38707	0.036887	0.088767	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.64991	-0.13;-0.13	3.85	0.768	0.18487	.	0.340707	0.21166	U	0.079072	T	0.01627	0.0052	N	0.17800	0.525	0.80722	P	0.0	B	0.29646	0.253	B	0.27608	0.081	T	0.11084	-1.0602	9	0.13108	T	0.6	.	7.7094	0.28669	0.3541:0.0:0.6459:0.0	rs41521547;rs61732151	371	E7EUV1	.	K	371	ENSP00000415183:E371K;ENSP00000351956:E371K	ENSP00000351956:E371K	E	+	1	0	MUC2	1070391	0.207000	0.23482	0.040000	0.18447	0.145000	0.21501	2.397000	0.44477	0.296000	0.22592	0.491000	0.48974	GAG	G|0.947;A|0.053	0.053	strong		0.662	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390086	208390086	+	Silent	SNP	G	G	C	rs1664227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:208390086G>C	ENST00000367033.3	-	2	1939	c.1182C>G	c.(1180-1182)acC>acG	p.T394T		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	394	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTACCGCCTTGGTGCACTGGA	0.622													G|||	1839	0.367212	0.3623	0.3343	5008	,	,		20651	0.4048		0.3042	False		,,,				2504	0.4233				p.T394T		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C1182G						PASS	.	G		1551,2855	488.5+/-361.2	287,977,939	80.0	74.0	76.0		1182	4.9	1.0	1	dbSNP_89	76	2810,5790	443.7+/-360.5	479,1852,1969	no	coding-synonymous	PLXNA2	NM_025179.3		766,2829,2908	CC,CG,GG		32.6744,35.202,33.5307		394/1895	208390086	4361,8645	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			CGCCTTGGTGCAC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1182C>G	1.37:g.208390086G>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			G|0.664;C|0.336	0.336	strong		0.622	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2408486	2408486	+	Silent	SNP	T	T	C	rs62120712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2408486T>C	ENST00000332578.3	+	7	873	c.873T>C	c.(871-873)ttT>ttC	p.F291F		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	291	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)		CGGCCGACTTTGACGTGGCTG	0.667													C|||	710	0.141773	0.1838	0.0663	5008	,	,		7183	0.2351		0.0427	False		,,,				2504	0.1442				p.F291F		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.T873C						PASS	.	C		753,3653	753.4+/-412.4	72,609,1522	104.0	89.0	94.0		873	2.2	1.0	19	dbSNP_129	94	376,8224	801.2+/-407.4	3,370,3927	no	coding-synonymous	TMPRSS9	NM_182973.1		75,979,5449	CC,CT,TT		4.3721,17.0903,8.6806		291/1060	2408486	1129,11877	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon7			CGACTTTGACGTG	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.873T>C	19.37:g.2408486T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			T|0.901;C|0.099	0.099	strong		0.667	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
TYW1	55253	hgsc.bcm.edu	37	7	66648199	66648199	+	Silent	SNP	G	G	A	rs55756354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	80	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	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	
ETFB	2109	hgsc.bcm.edu	37	19	51857738	51857738	+	Intron	SNP	G	G	A	rs79338777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51857738G>A	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.P52L|CTD-2616J11.11_ENST00000600067.1_Intron	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		tgtaggcagGGGCAGGTCACC	0.582													g|||	387	0.0772764	0.0439	0.0403	5008	,	,		16395	0.1181		0.0696	False		,,,				2504	0.1145				p.P52L		Atlas-SNP	.											.	ETFB	46	.	0			c.C155T						PASS	.	G	LEU/PRO,	196,4210	122.5+/-159.9	3,190,2010	79.0	72.0	74.0		155,	-5.5	0.0	19	dbSNP_131	74	591,8009	156.7+/-210.5	22,547,3731	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	98,	25,737,5741	AA,AG,GG		6.8721,4.4485,6.0511	probably-damaging,	52/347,	51857738	787,12219	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			GGCAGGGGCAGGT	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-176C>T	19.37:g.51857738G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	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		
JAGN1	84522	hgsc.bcm.edu	37	3	9934753	9934753	+	Missense_Mutation	SNP	A	A	G	rs35365817	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:9934753A>G	ENST00000307768.4	+	2	413	c.244A>G	c.(244-246)Att>Gtt	p.I82V		NM_032492.3	NP_115881.3			jagunal homolog 1 (Drosophila)											breast(1)|central_nervous_system(1)|endometrium(4)|lung(3)|ovary(1)	10	Medulloblastoma(99;0.227)					TTTGCTGAGCATTTTGCCCTC	0.532													A|||	66	0.0131789	0.0	0.0288	5008	,	,		21516	0.0		0.0368	False		,,,				2504	0.0092				p.I82V		Atlas-SNP	.											.	JAGN1	18	.	0			c.A244G						PASS	.	A	VAL/ILE	27,4379	34.3+/-65.2	0,27,2176	201.0	151.0	168.0		244	-0.0	0.9	3	dbSNP_126	168	300,8300	108.0+/-168.7	6,288,4006	yes	missense	JAGN1	NM_032492.3	29	6,315,6182	GG,GA,AA		3.4884,0.6128,2.5142	benign	82/184	9934753	327,12679	2203	4300	6503	SO:0001583	missense	84522	exon2			CTGAGCATTTTGC	AK074760	CCDS2588.1	3p25.2	2010-03-23			ENSG00000171135	ENSG00000171135			26926	protein-coding gene	gene with protein product						12477932	Standard	NM_032492		Approved	GL009, FLJ14602	uc003btt.4	Q8N5M9	OTTHUMG00000128523	ENST00000307768.4:c.244A>G	3.37:g.9934753A>G	ENSP00000306106:p.Ile82Val	Somatic	505	0	0		WXS	Illumina HiSeq	Phase_I	556	267	0.480216	NM_032492		Missense_Mutation	SNP	ENST00000307768.4	37	CCDS2588.1	33	0.01510989010989011	0	0.0	11	0.03038674033149171	0	0.0	22	0.029023746701846966	A	12.93	2.084957	0.36758	0.006128	0.034884	ENSG00000171135	ENST00000307768;ENST00000543379	.	.	.	5.52	-0.00938	0.14001	.	0.369005	0.29451	N	0.012102	T	0.30198	0.0757	M	0.67953	2.075	0.45594	D	0.99853	B	0.22983	0.078	B	0.28553	0.091	T	0.26608	-1.0098	9	0.46703	T	0.11	-14.8775	5.783	0.18318	0.4909:0.141:0.3681:0.0	rs35365817	82	Q8N5M9	JAGN1_HUMAN	V	82	.	ENSP00000306106:I82V	I	+	1	0	JAGN1	9909753	1.000000	0.71417	0.912000	0.35992	0.933000	0.57130	2.581000	0.46077	-0.231000	0.09825	0.402000	0.26972	ATT	A|0.979;G|0.021	0.021	strong		0.532	JAGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250335.1	NM_032492	
MUC4	4585	hgsc.bcm.edu	37	3	195507129	195507129	+	Silent	SNP	G	G	T	rs74201433		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195507129G>T	ENST00000463781.3	-	2	11781	c.11322C>A	c.(11320-11322)gcC>gcA	p.A3774A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.A3774A	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)		GAAGAGGCGTGGCGTGACCTG	0.607																																					p.A3774A		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11322A						PASS	.						25.0	19.0	21.0					3																	195507129		686	1585	2271	SO:0001819	synonymous_variant	4585	exon2			AGGCGTGGCGTGA	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.11322C>A	3.37:g.195507129G>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	163	30	0.184049	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|0.910;T|0.090	0.090	strong		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR2T1	26696	hgsc.bcm.edu	37	1	248569369	248569369	+	Missense_Mutation	SNP	A	A	G	rs28599722	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248569369A>G	ENST00000366474.1	+	1	74	c.74A>G	c.(73-75)cAt>cGt	p.H25R		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	25			H -> R (in dbSNP:rs28599722).			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(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	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)			ATTAATTCACATGTTGTTATT	0.338													.|||	1634	0.326278	0.0424	0.4078	5008	,	,		20971	0.3135		0.503	False		,,,				2504	0.4836				p.H25R		Atlas-SNP	.											.	OR2T1	89	.	0			c.A74G						PASS	.	A	ARG/HIS	608,3798	265.3+/-266.6	37,534,1632	105.0	106.0	106.0		74	1.4	0.0	1	dbSNP_125	106	4832,3768	613.7+/-396.1	1358,2116,826	yes	missense	OR2T1	NM_030904.1	29	1395,2650,2458	GG,GA,AA		43.814,13.7994,41.8268	benign	25/370	248569369	5440,7566	2203	4300	6503	SO:0001583	missense	26696	exon1			ATTCACATGTTGT	U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"""GPCR / Class A : Olfactory receptors"""	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.74A>G	1.37:g.248569369A>G	ENSP00000355430:p.His25Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_030904	Q6IEZ9	Missense_Mutation	SNP	ENST00000366474.1	37	CCDS31115.1	730	0.3342490842490842	23	0.046747967479674794	149	0.4116022099447514	175	0.30594405594405594	383	0.5052770448548812	A	5.526	0.281939	0.10458	0.137994	0.56186	ENSG00000175143	ENST00000366474	T	0.02656	4.21	3.8	1.44	0.22558	.	.	.	.	.	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	0.18618	-1.0331	8	0.51188	T	0.08	.	6.1623	0.20370	0.7501:0.0:0.2499:0.0	rs28599722;rs28599722	25	O43869	OR2T1_HUMAN	R	25	ENSP00000355430:H25R	ENSP00000355430:H25R	H	+	2	0	OR2T1	246635992	0.000000	0.05858	0.002000	0.10522	0.037000	0.13140	-0.603000	0.05674	0.295000	0.22570	0.528000	0.53228	CAT	A|0.624;G|0.376	0.376	strong		0.338	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2		
QRFP	347148	hgsc.bcm.edu	37	9	133768827	133768827	+	Silent	SNP	G	G	A	rs139926605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133768827G>A	ENST00000343079.1	-	1	398	c.399C>T	c.(397-399)ttC>ttT	p.F133F		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)		ACCGCCGACCGAAGCGGAAGC	0.607													G|||	23	0.00459265	0.0068	0.0043	5008	,	,		18715	0.0		0.001	False		,,,				2504	0.0102				p.F133F		Atlas-SNP	.											.	QRFP	14	.	0			c.C399T						PASS	.	G		16,4388		0,16,2186	57.0	68.0	64.0		399	-7.2	0.6	9	dbSNP_134	64	10,8588		0,10,4289	no	coding-synonymous	QRFP	NM_198180.1		0,26,6475	AA,AG,GG		0.1163,0.3633,0.2		133/137	133768827	26,12976	2202	4299	6501	SO:0001819	synonymous_variant	347148	exon1			CCGACCGAAGCGG	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.399C>T	9.37:g.133768827G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_198180		Silent	SNP	ENST00000343079.1	37	CCDS6936.1																																																																																			G|0.998;A|0.002	0.002	strong		0.607	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180	
MPP6	51678	hgsc.bcm.edu	37	7	24703298	24703298	+	Silent	SNP	G	G	A	rs1053962	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:24703298G>A	ENST00000222644.5	+	6	991	c.741G>A	c.(739-741)gaG>gaA	p.E247E	MPP6_ENST00000409761.1_Silent_p.E135E|MPP6_ENST00000396475.2_Silent_p.E247E			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						CCAAAGGAGAGATTCTTCAGA	0.338													A|||	3233	0.645567	0.9153	0.4409	5008	,	,		18088	0.7996		0.3499	False		,,,				2504	0.5716				p.E247E		Atlas-SNP	.											.	MPP6	62	.	0			c.G741A						PASS	.	A		3577,829	327.5+/-300.1	1452,673,78	99.0	110.0	106.0		741	4.9	1.0	7	dbSNP_86	106	2851,5749	672.5+/-402.9	465,1921,1914	no	coding-synonymous	MPP6	NM_016447.2		1917,2594,1992	AA,AG,GG		33.1512,18.8153,49.4233		247/541	24703298	6428,6578	2203	4300	6503	SO:0001819	synonymous_variant	51678	exon7			AGGAGAGATTCTT	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.741G>A	7.37:g.24703298G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_016447	B2RAF0	Silent	SNP	ENST00000222644.5	37	CCDS5388.1																																																																																			A|0.556;C|0.001	0.556	strong		0.338	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4		
ANKLE1	126549	hgsc.bcm.edu	37	19	17392894	17392894	+	Missense_Mutation	SNP	G	G	A	rs8100241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17392894G>A	ENST00000394458.3	+	2	367	c.91G>A	c.(91-93)Gcg>Acg	p.A31T	ANKLE1_ENST00000433424.2_Missense_Mutation_p.A85T|ANKLE1_ENST00000594072.1_Missense_Mutation_p.A20T|ANKLE1_ENST00000598347.1_Missense_Mutation_p.A31T|ANKLE1_ENST00000404085.1_Missense_Mutation_p.A53T|CTD-2278I10.6_ENST00000596542.1_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	31			A -> T (in dbSNP:rs8100241). {ECO:0000269|Ref.1}.							large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						GCGCTGCGGCGCGGACCCTAA	0.736													G|||	2140	0.427316	0.3865	0.3761	5008	,	,		10836	0.3115		0.5716	False		,,,				2504	0.4898				p.A31T		Atlas-SNP	.											FLJ39369,NS,carcinoma,0,4	ANKLE1	27	4	0			c.G91A						PASS	.	G	THR/ALA	1171,2027		272,627,700	4.0	6.0	6.0		91	1.6	0.3	19	dbSNP_116	6	2712,3014		694,1324,845	yes	missense	ANKLE1	NM_152363.4	58	966,1951,1545	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	47.3629,36.6166,43.5119	probably-damaging	31/616	17392894	3883,5041	1599	2863	4462	SO:0001583	missense	126549	exon2			TGCGGCGCGGACC	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.91G>A	19.37:g.17392894G>A	ENSP00000377971:p.Ala31Thr	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_152363	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	37	CCDS12354.2	947	0.4336080586080586	186	0.3780487804878049	156	0.430939226519337	163	0.28496503496503495	442	0.58311345646438	G	15.15	2.747219	0.49257	0.366166	0.473629	ENSG00000160117	ENST00000404261;ENST00000433424;ENST00000404085;ENST00000394458;ENST00000438921	T;T;T	0.70869	-0.52;-0.52;-0.52	4.06	1.65	0.23941	Ankyrin repeat-containing domain (4);	0.076309	0.50627	D	0.000109	T	0.00012	0.0000	M	0.87456	2.885	0.48762	P	2.910000000000412E-4	P;D;D	0.89917	0.634;1.0;0.998	B;D;P	0.87578	0.302;0.998;0.884	T	0.47446	-0.9117	9	0.48119	T	0.1	-10.2519	6.5304	0.22324	0.0:0.1999:0.5941:0.2059	rs8100241;rs61305143;rs8100241	31;17;31	E7ETZ9;Q8NAG6-1;Q8NAG6	.;.;ANKL1_HUMAN	T	31;85;53;20;31	ENSP00000384753:A31T;ENSP00000394460:A85T;ENSP00000384008:A53T	ENSP00000377971:A20T	A	+	1	0	ANKLE1	17253894	0.981000	0.34729	0.273000	0.24645	0.084000	0.17831	5.063000	0.64332	0.873000	0.35799	0.484000	0.47621	GCG	G|0.574;A|0.426	0.426	strong		0.736	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363	
SLC9C1	285335	hgsc.bcm.edu	37	3	111985107	111985107	+	Missense_Mutation	SNP	T	T	C	rs9872691	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:111985107T>C	ENST00000305815.5	-	8	1108	c.856A>G	c.(856-858)Att>Gtt	p.I286V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I286V	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	286			I -> V (in dbSNP:rs9872691). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										GTTTCTTCAATTGCTGCTTTA	0.289													T|||	1648	0.329073	0.3449	0.4035	5008	,	,		15497	0.3393		0.2376	False		,,,				2504	0.3384				p.I286V		Atlas-SNP	.											.	.	.	.	0			c.A856G						PASS	.	T	VAL/ILE	1483,2923	464.7+/-354.0	256,971,976	67.0	75.0	72.0		856	3.2	1.0	3	dbSNP_119	72	2324,6268	385.5+/-341.5	322,1680,2294	yes	missense	SLC9A10	NM_183061.1	29	578,2651,3270	CC,CT,TT		27.0484,33.6586,29.2891	benign	286/1178	111985107	3807,9191	2203	4296	6499	SO:0001583	missense	285335	exon8			CTTCAATTGCTGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.856A>G	3.37:g.111985107T>C	ENSP00000306627:p.Ile286Val	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	217	107	0.493088	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	679	0.3108974358974359	171	0.3475609756097561	138	0.3812154696132597	185	0.32342657342657344	185	0.24406332453825857	T	0.009	-1.855283	0.00558	0.336586	0.270484	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.03386	3.95;3.95	5.04	3.23	0.37069	Cation/H+ exchanger (1);	0.574613	0.15538	N	0.257133	T	0.00012	0.0000	N	0.01297	-0.9	0.53005	P	3.500000000000725E-5	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.37526	-0.9702	9	0.09843	T	0.71	-2.2326	7.8574	0.29491	0.0:0.8079:0.0:0.1921	rs9872691;rs52814342;rs56679245;rs9872691	286;286	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	286	ENSP00000306627:I286V;ENSP00000420688:I286V	ENSP00000306627:I286V	I	-	1	0	SLC9A10	113467797	0.992000	0.36948	0.997000	0.53966	0.235000	0.25334	0.291000	0.18994	0.647000	0.30713	-0.186000	0.12905	ATT	T|0.705;C|0.295	0.295	strong		0.289	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
CPNE1	8904	hgsc.bcm.edu	37	20	34220755	34220755	+	Missense_Mutation	SNP	C	C	T	rs11543244	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34220755C>T	ENST00000317619.3	-	4	485	c.91G>A	c.(91-93)Gtc>Atc	p.V31I	RP1-309K20.6_ENST00000541176.2_3'UTR|CPNE1_ENST00000397442.1_Missense_Mutation_p.V31I|CPNE1_ENST00000397443.1_Missense_Mutation_p.V31I|CPNE1_ENST00000397446.1_Missense_Mutation_p.V31I|CPNE1_ENST00000317677.5_Missense_Mutation_p.V36I|CPNE1_ENST00000397445.1_Missense_Mutation_p.V31I|CPNE1_ENST00000352393.4_Missense_Mutation_p.V31I			Q99829	CPNE1_HUMAN	copine I	31	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TGTAAAAGGACGCAGAGTGGG	0.552													C|||	397	0.0792732	0.0658	0.0259	5008	,	,		20843	0.0516		0.0517	False		,,,				2504	0.1922				p.V36I		Atlas-SNP	.											.	CPNE1	44	.	0			c.G106A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	280,4126	157.4+/-190.3	11,258,1934	161.0	153.0	156.0		91,106,91,91,91,91	4.7	1.0	20	dbSNP_120	156	419,8181	130.2+/-188.1	14,391,3895	yes	missense,missense,missense,missense,missense,missense	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	29,29,29,29,29,29	25,649,5829	TT,TC,CC		4.8721,6.355,5.3744	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	31/537,36/543,31/538,31/538,31/538,31/538	34220755	699,12307	2203	4300	6503	SO:0001583	missense	8904	exon2			AAAGGACGCAGAG	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.91G>A	20.37:g.34220755C>T	ENSP00000326126:p.Val31Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	136	56	0.411765	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	121	0.0554029304029304	43	0.08739837398373984	13	0.03591160220994475	22	0.038461538461538464	43	0.05672823218997362	C	24.6	4.550870	0.86127	0.06355	0.048721	ENSG00000214078	ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570;ENST00000412056;ENST00000414664;ENST00000416778;ENST00000439806;ENST00000420363;ENST00000434795;ENST00000440240;ENST00000458038;ENST00000437100;ENST00000414711;ENST00000435747	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	5.66	4.66	0.58398	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000002	T	0.05823	0.0152	M	0.71920	2.185	0.22629	P	0.99891048	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;1.0	D;D;D;D;D	0.85130	0.936;0.936;0.936;0.924;0.997	T	0.41752	-0.9491	9	0.62326	D	0.03	-2.1566	15.7329	0.77819	0.0:0.8631:0.1369:0.0	rs11543244;rs52809749;rs11543244	36;31;31;31;35	B0QZ18;E7ENH5;A6PVH9;Q99829;Q59EI4	.;.;.;CPNE1_HUMAN;.	I	31;36;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31;31	ENSP00000336945:V31I;ENSP00000317257:V36I;ENSP00000326126:V31I;ENSP00000380588:V31I;ENSP00000380587:V31I;ENSP00000380585:V31I;ENSP00000380584:V31I;ENSP00000415597:V31I;ENSP00000390626:V31I;ENSP00000416962:V31I;ENSP00000404355:V31I;ENSP00000389662:V31I;ENSP00000387434:V31I;ENSP00000401915:V31I;ENSP00000409794:V31I;ENSP00000397638:V31I;ENSP00000390141:V31I;ENSP00000391483:V31I;ENSP00000409955:V31I;ENSP00000412806:V31I	ENSP00000326126:V31I	V	-	1	0	CPNE1	33684169	0.991000	0.36638	0.984000	0.44739	0.969000	0.65631	3.784000	0.55416	2.665000	0.90641	0.637000	0.83480	GTC	T|0.057;C|0.943	0.057	strong		0.552	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
MFSD6	54842	hgsc.bcm.edu	37	2	191301908	191301908	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:191301908G>A	ENST00000392328.1	+	3	1477	c.1153G>A	c.(1153-1155)Gtt>Att	p.V385I	MFSD6_ENST00000281416.7_Missense_Mutation_p.V385I	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	385					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						GGCCTTGATCGTTGCCACTCA	0.502																																					p.V385I		Atlas-SNP	.											MFSD6,colon,carcinoma,0,1	MFSD6	58	1	0			c.G1153A						scavenged	.						80.0	69.0	73.0					2																	191301908		2203	4300	6503	SO:0001583	missense	54842	exon3			TTGATCGTTGCCA		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.1153G>A	2.37:g.191301908G>A	ENSP00000376141:p.Val385Ile	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	245	3	0.0122449	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.836628	0.71373	.	.	ENSG00000151690	ENST00000392328;ENST00000281416	T;T	0.80738	-1.41;-1.41	6.16	6.16	0.99307	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.75946	0.3919	L	0.32530	0.975	0.80722	D	1	P	0.51791	0.948	B	0.43413	0.419	T	0.73582	-0.3937	10	0.30078	T	0.28	-27.0038	19.848	0.96722	0.0:0.0:1.0:0.0	.	385	Q6ZSS7	MFSD6_HUMAN	I	385	ENSP00000376141:V385I;ENSP00000281416:V385I	ENSP00000281416:V385I	V	+	1	0	MFSD6	191010153	1.000000	0.71417	0.226000	0.23910	0.607000	0.37147	7.954000	0.87848	2.937000	0.99478	0.650000	0.86243	GTT	.	.	none		0.502	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
IFT74	80173	hgsc.bcm.edu	37	9	26978170	26978170	+	Missense_Mutation	SNP	A	A	G	rs10812505	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:26978170A>G	ENST00000443698.1	+	3	336	c.165A>G	c.(163-165)atA>atG	p.I55M	IFT74_ENST00000380062.5_Missense_Mutation_p.I55M|IFT74_ENST00000433700.1_Missense_Mutation_p.I55M|IFT74_ENST00000429045.2_Missense_Mutation_p.I55M	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	55	Basic region.		I -> M (in dbSNP:rs10812505).		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)		GTTGTCCCATAGGGACTGGTG	0.428													A|||	857	0.171126	0.0038	0.1671	5008	,	,		14430	0.5655		0.0457	False		,,,				2504	0.1227				p.I55M		Atlas-SNP	.											.	IFT74	46	.	0			c.A165G						PASS	.	A	MET/ILE,MET/ILE,MET/ILE,MET/ILE	45,3717		1,43,1837	87.0	82.0	84.0		165,165,165,165	-2.9	0.1	9	dbSNP_120	84	311,7927		9,293,3817	yes	missense,missense,missense,missense	IFT74	NM_001099222.1,NM_001099223.1,NM_001099224.1,NM_025103.2	10,10,10,10	10,336,5654	GG,GA,AA		3.7752,1.1962,2.9667	benign,benign,benign,benign	55/601,55/601,55/373,55/601	26978170	356,11644	1881	4119	6000	SO:0001583	missense	80173	exon3			TCCCATAGGGACT	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.165A>G	9.37:g.26978170A>G	ENSP00000404122:p.Ile55Met	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_001099222	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Missense_Mutation	SNP	ENST00000443698.1	37	CCDS43793.1	420	0.19230769230769232	2	0.0040650406504065045	46	0.1270718232044199	338	0.5909090909090909	34	0.044854881266490766	A	6.595	0.478081	0.12521	0.011962	0.037752	ENSG00000096872	ENST00000519968;ENST00000433700;ENST00000517444;ENST00000443698;ENST00000380062;ENST00000544022;ENST00000518614;ENST00000429045;ENST00000517866	T;T;T;T;T;T;T;T	0.57436	0.4;2.76;1.92;2.76;2.76;1.5;0.4;0.4	5.57	-2.92	0.05615	.	0.597513	0.16966	N	0.192294	T	0.00012	0.0000	N	0.03115	-0.41	0.43588	P	0.004070000000000018	B;B	0.16396	0.003;0.017	B;B	0.12837	0.005;0.008	T	0.44832	-0.9302	9	0.31617	T	0.26	-0.5621	5.7077	0.17917	0.3679:0.0:0.4124:0.2198	rs10812505;rs52810846;rs61213081;rs10812505	55;55	Q96LB3;Q96LB3-2	IFT74_HUMAN;.	M	55;55;55;55;55;55;55;55;17	ENSP00000430004:I55M;ENSP00000389224:I55M;ENSP00000430096:I55M;ENSP00000404122:I55M;ENSP00000369402:I55M;ENSP00000430526:I55M;ENSP00000393907:I55M;ENSP00000430742:I17M	ENSP00000369402:I55M	I	+	3	3	IFT74	26968170	0.084000	0.21492	0.133000	0.22050	0.312000	0.27988	-0.511000	0.06321	-0.435000	0.07264	-0.468000	0.05107	ATA	A|0.836;G|0.164	0.164	strong		0.428	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103	
XAB2	56949	hgsc.bcm.edu	37	19	7685843	7685843	+	Silent	SNP	G	G	A	rs794078	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7685843G>A	ENST00000358368.4	-	14	1897	c.1860C>T	c.(1858-1860)acC>acT	p.T620T	XAB2_ENST00000534844.1_Silent_p.T617T	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	620					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						CCACGGCCCTGGTGGCACGCT	0.657								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	738	0.147364	0.1135	0.183	5008	,	,		10661	0.1062		0.2376	False		,,,				2504	0.1176				p.T620T		Atlas-SNP	.											XAB2,NS,carcinoma,0,1	XAB2	69	1	0			c.C1860T						PASS	.	G		618,3776		46,526,1625	17.0	17.0	17.0		1860	2.0	0.8	19	dbSNP_86	17	1708,6878		138,1432,2723	no	coding-synonymous	XAB2	NM_020196.2		184,1958,4348	AA,AG,GG		19.8928,14.0646,17.9199		620/856	7685843	2326,10654	2197	4293	6490	SO:0001819	synonymous_variant	56949	exon14			GGCCCTGGTGGCA	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.1860C>T	19.37:g.7685843G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			A|0.158;C|0.007	0.158	strong		0.657	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
GPATCH1	55094	hgsc.bcm.edu	37	19	33579128	33579128	+	Silent	SNP	T	T	C	rs7259333	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	124	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	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	
GPR4	2828	hgsc.bcm.edu	37	19	46094597	46094597	+	Silent	SNP	G	G	A	rs3745820	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46094597G>A	ENST00000323040.4	-	2	1472	c.528C>T	c.(526-528)ggC>ggT	p.G176G	GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	176					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)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		AGGCCACCCAGCCTTCCATGG	0.642													g|||	827	0.165136	0.0303	0.1787	5008	,	,		15664	0.1895		0.2763	False		,,,				2504	0.1984				p.G176G	Esophageal Squamous(117;181 1612 1673 14956 42937)	Atlas-SNP	.											.	GPR4	54	.	0			c.C528T						PASS	.			305,4097		11,283,1907	72.0	64.0	67.0		528	4.2	1.0	19	dbSNP_107	67	2283,6311		311,1661,2325	no	coding-synonymous	GPR4	NM_005282.2		322,1944,4232	AA,AG,GG		26.565,6.9287,19.9138		176/363	46094597	2588,10408	2201	4297	6498	SO:0001819	synonymous_variant	2828	exon2			CACCCAGCCTTCC	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"""GPCR / Class A : Orphans"""	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.528C>T	19.37:g.46094597G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_005282	A8K3T3|B0M0K1|Q6NWM4	Silent	SNP	ENST00000323040.4	37	CCDS12669.1																																																																																			G|0.820;A|0.180	0.180	strong		0.642	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435058	7435058	+	Missense_Mutation	SNP	C	C	T	rs60816800	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:7435058C>T	ENST00000319098.4	-	1	1642	c.1549G>A	c.(1549-1551)Gct>Act	p.A517T	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)	517					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						TGTTCCCCAGCGTGGAGGTGC	0.597													C|||	516	0.103035	0.0144	0.1282	5008	,	,		20237	0.0764		0.1909	False		,,,				2504	0.1421				p.A517T		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G1549A						PASS	.	C	THR/ALA,	149,3999		3,143,1928	22.0	25.0	24.0		1549,	-2.3	0.0	4	dbSNP_129	24	1497,6867		126,1245,2811	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	58,	129,1388,4739	TT,TC,CC		17.8981,3.5921,13.1554	benign,	517/522,	7435058	1646,10866	2074	4182	6256	SO:0001583	missense	768239	exon1			CCCCAGCGTGGAG	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.1549G>A	4.37:g.7435058C>T	ENSP00000317445:p.Ala517Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	235	0.10760073260073261	9	0.018292682926829267	52	0.143646408839779	33	0.057692307692307696	141	0.18601583113456466	C	4.446	0.082652	0.08533	0.035921	0.178981	ENSG00000178597	ENST00000319098	T	0.66638	-0.22	2.65	-2.31	0.06765	.	.	.	.	.	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	8	0.10636	T	0.68	.	4.4357	0.11549	0.1609:0.4725:0.0:0.3667	rs60816800;rs61730429	517	Q6NUJ1	SAPL1_HUMAN	T	517	ENSP00000317445:A517T	ENSP00000317445:A517T	A	-	1	0	PSAPL1	7485959	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.780000	0.00773	-1.078000	0.03117	-1.119000	0.02030	GCT	C|0.893;T|0.107	0.107	strong		0.597	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
COL12A1	1303	hgsc.bcm.edu	37	6	75848181	75848181	+	Missense_Mutation	SNP	A	A	G	rs240736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000483888.2_Missense_Mutation_p.I1738T|COL12A1_ENST00000345356.6_Missense_Mutation_p.I574T	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	90	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	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	
MICALL1	85377	hgsc.bcm.edu	37	22	38323507	38323507	+	Missense_Mutation	SNP	G	G	T	rs9610875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38323507G>T	ENST00000215957.6	+	9	1681	c.1555G>T	c.(1555-1557)Gcc>Tcc	p.A519S	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	519	Pro-rich.		A -> S (in dbSNP:rs9610875). {ECO:0000269|PubMed:17974005}.		endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					GTCTGAGAGCGCCAGCCAGAC	0.677													G|||	840	0.167732	0.0265	0.2637	5008	,	,		15751	0.1349		0.2336	False		,,,				2504	0.2566				p.A519S		Atlas-SNP	.											.	MICALL1	53	.	0			c.G1555T						PASS	.	G	SER/ALA	252,4154	146.1+/-180.8	10,232,1961	67.0	61.0	63.0		1555	1.6	0.2	22	dbSNP_119	63	2080,6520	359.8+/-331.7	267,1546,2487	yes	missense	MICALL1	NM_033386.3	99	277,1778,4448	TT,TG,GG		24.186,5.7195,17.9302	benign	519/864	38323507	2332,10674	2203	4300	6503	SO:0001583	missense	85377	exon9			GAGAGCGCCAGCC	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.1555G>T	22.37:g.38323507G>T	ENSP00000215957:p.Ala519Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	380|380	0.17399267399267399|0.17399267399267399	11|11	0.022357723577235773|0.022357723577235773	103|103	0.2845303867403315|0.2845303867403315	84|84	0.14685314685314685|0.14685314685314685	182|182	0.24010554089709762|0.24010554089709762	G|G	3.806|3.806	-0.040672|-0.040672	0.07497|0.07497	0.057195|0.057195	0.24186|0.24186	ENSG00000100139|ENSG00000100139	ENST00000215957|ENST00000454685	T|.	0.47177|.	0.85|.	4.99|4.99	1.63|1.63	0.23807|0.23807	.|.	0.441509|.	0.21510|.	N|.	0.073393|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00082|0.00082	-2.215|-2.215	0.23174|0.23174	P|P	0.99817006|0.99817006	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.41378|0.41378	-0.9512|-0.9512	9|4	0.02654|.	T|.	1|.	.|.	7.7553|7.7553	0.28921|0.28921	0.0:0.0694:0.2627:0.6679|0.0:0.0694:0.2627:0.6679	rs9610875;rs57936345;rs9610875|rs9610875;rs57936345;rs9610875	519|.	Q8N3F8|.	MILK1_HUMAN|.	S|L	519|96	ENSP00000215957:A519S|.	ENSP00000215957:A519S|.	A|R	+|+	1|2	0|0	MICALL1|MICALL1	36653453|36653453	0.620000|0.620000	0.27068|0.27068	0.236000|0.236000	0.24074|0.24074	0.259000|0.259000	0.26198|0.26198	2.468000|2.468000	0.45102|0.45102	-0.039000|-0.039000	0.13602|0.13602	-0.385000|-0.385000	0.06624|0.06624	GCC|CGC	G|0.829;T|0.171	0.171	strong		0.677	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
DNAH14	127602	hgsc.bcm.edu	37	1	225565073	225565073	+	Silent	SNP	C	C	T	rs3856155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225565073C>T	ENST00000445597.2	+	54	9321	c.9321C>T	c.(9319-9321)ggC>ggT	p.G3107G	DNAH14_ENST00000439375.2_Silent_p.G4115G|DNAH14_ENST00000430092.1_Silent_p.G4115G			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	3107					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						AGACCCAGGGCGAAAAGTTTA	0.453													c|||	2463	0.491813	0.171	0.7118	5008	,	,		17842	0.7411		0.6123	False		,,,				2504	0.3885				p.G4115G		Atlas-SNP	.											.	DNAH14	300	.	0			c.C12345T						PASS	.	T		315,1069		38,239,415	85.0	81.0	82.0		12345	4.3	0.0	1	dbSNP_108	82	1923,1259		574,775,242	no	coding-synonymous	DNAH14	NM_001373.1		612,1014,657	TT,TC,CC		39.5663,22.7601,49.0145		4115/4516	225565073	2238,2328	692	1591	2283	SO:0001819	synonymous_variant	127602	exon77			CCAGGGCGAAAAG	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.9321C>T	1.37:g.225565073C>T		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	319	310	0.971787	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Silent	SNP	ENST00000445597.2	37																																																																																				C|0.457;T|0.543	0.543	strong		0.453	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
KRT28	162605	hgsc.bcm.edu	37	17	38950272	38950272	+	Silent	SNP	T	T	C	rs2250671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38950272T>C	ENST00000306658.7	-	6	1070	c.1005A>G	c.(1003-1005)acA>acG	p.T335T		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)				TCTCGGTCTCTGTCAAGGAGC	0.552													C|||	3097	0.618411	0.8116	0.5259	5008	,	,		18684	0.4196		0.6213	False		,,,				2504	0.6247				p.T335T	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.A1005G						PASS	.	C		3393,1013	378.0+/-322.7	1305,783,115	109.0	113.0	111.0		1005	-11.4	0.0	17	dbSNP_100	111	5012,3588	520.0+/-379.6	1437,2138,725	no	coding-synonymous	KRT28	NM_181535.3		2742,2921,840	CC,CT,TT		41.7209,22.9914,35.376		335/465	38950272	8405,4601	2203	4300	6503	SO:0001819	synonymous_variant	162605	exon6			GGTCTCTGTCAAG	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.1005A>G	17.37:g.38950272T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_181535		Silent	SNP	ENST00000306658.7	37	CCDS11376.1																																																																																			T|0.373;C|0.627	0.627	strong		0.552	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
VSIG4	11326	hgsc.bcm.edu	37	X	65253454	65253454	+	Missense_Mutation	SNP	C	C	A	rs41306131	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65253454C>A	ENST00000374737.4	-	2	382	c.274G>T	c.(274-276)Gtt>Ttt	p.V92F	VSIG4_ENST00000412866.2_Missense_Mutation_p.V92F|VSIG4_ENST00000455586.2_Missense_Mutation_p.V92F	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	92	Ig-like 1.				complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCTCCTGGAACCTTGTGGCTC	0.547													C|||	14	0.00370861	0.0	0.0058	3775	,	,		14684	0.0		0.007	False		,,,				2504	0.0031				p.V92F		Atlas-SNP	.											.	VSIG4	54	.	0			c.G274T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL	5,3830		0,4,1,1628,570	136.0	115.0	122.0		274,274,274,274	-0.5	0.1	X	dbSNP_127	122	55,6673		0,35,20,2393,1852	yes	missense,missense,missense,missense	VSIG4	NM_001100431.1,NM_001184830.1,NM_001184831.1,NM_007268.2	50,50,50,50	0,39,21,4021,2422	AA,AC,A,CC,C		0.8175,0.1304,0.568	probably-damaging,probably-damaging,probably-damaging,probably-damaging	92/306,92/322,92/228,92/400	65253454	60,10503	2203	4300	6503	SO:0001583	missense	11326	exon2			CTGGAACCTTGTG	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.274G>T	X.37:g.65253454C>A	ENSP00000363869:p.Val92Phe	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_001100431	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	10|10	0.006027727546714889|0.006027727546714889	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	4|4	0.005305039787798408|0.005305039787798408	C|C	9.614|9.614	1.131982|1.131982	0.21041|0.21041	0.001304|0.001304	0.008175|0.008175	ENSG00000155659|ENSG00000155659	ENST00000427538|ENST00000374737;ENST00000455586;ENST00000412866	.|T;T;T	.|0.04156	.|3.69;3.69;3.69	4.93|4.93	-0.487|-0.487	0.12060|0.12060	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.656229	.|0.14136	.|N	.|0.339047	T|T	0.08358|0.08358	0.0208|0.0208	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	.|P;D;D;P;D	.|0.65815	.|0.825;0.994;0.995;0.889;0.995	.|P;P;D;P;D	.|0.69307	.|0.597;0.884;0.963;0.543;0.929	T|T	0.11275|0.11275	-1.0594|-1.0594	5|10	.|0.56958	.|D	.|0.05	-3.6037|-3.6037	4.5823|4.5823	0.12264|0.12264	0.0:0.4461:0.2494:0.3045|0.0:0.4461:0.2494:0.3045	rs41306131|rs41306131	.|92;92;82;92;92	.|C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279	.|.;.;.;.;VSIG4_HUMAN	V|F	18|92	.|ENSP00000363869:V92F;ENSP00000411581:V92F;ENSP00000394143:V92F	.|ENSP00000363869:V92F	G|V	-|-	2|1	0|0	VSIG4|VSIG4	65170179|65170179	0.000000|0.000000	0.05858|0.05858	0.076000|0.076000	0.20297|0.20297	0.004000|0.004000	0.04260|0.04260	-1.190000|-1.190000	0.03058|0.03058	0.038000|0.038000	0.15604|0.15604	-0.198000|-0.198000	0.12761|0.12761	GGT|GTT	C|0.994;A|0.006	0.006	strong		0.547	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268	
NAV2	89797	hgsc.bcm.edu	37	11	19970501	19970501	+	Silent	SNP	T	T	C	rs11025335	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:19970501T>C	ENST00000396087.3	+	11	2688	c.2589T>C	c.(2587-2589)caT>caC	p.H863H	NAV2_ENST00000349880.4_Silent_p.H840H|NAV2_ENST00000396085.1_Silent_p.H840H|NAV2_ENST00000360655.4_Silent_p.H776H|NAV2_ENST00000540292.1_Silent_p.H794H|NAV2_ENST00000527559.2_Silent_p.H792H	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	863					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						GTGTCTGCCATGTGGACGTCT	0.587													T|||	1308	0.261182	0.1036	0.2608	5008	,	,		18337	0.4395		0.2406	False		,,,				2504	0.3119				p.H863H		Atlas-SNP	.											.	NAV2	255	.	0			c.T2589C						PASS	.	T	,,	505,3893	231.7+/-245.5	26,453,1720	76.0	72.0	73.0		2328,2520,2520	-4.9	0.8	11	dbSNP_120	73	1906,6680	335.9+/-321.6	213,1480,2600	no	coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	239,1933,4320	CC,CT,TT		22.1989,11.4825,18.569	,,	776/2366,840/2430,840/2433	19970501	2411,10573	2199	4293	6492	SO:0001819	synonymous_variant	89797	exon11			CTGCCATGTGGAC	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.2589T>C	11.37:g.19970501T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	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																																																																																			T|0.792;C|0.208	0.208	strong		0.587	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
OR5L1	219437	hgsc.bcm.edu	37	11	55579182	55579182	+	Silent	SNP	A	A	G	rs139708815	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.						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	192	0	0		WXS	Illumina HiSeq	Phase_I	189	13	0.0687831	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	
FAM63A	55793	hgsc.bcm.edu	37	1	150974971	150974971	+	Missense_Mutation	SNP	T	T	A	rs41310885	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:150974971T>A	ENST00000361936.5	-	3	1077	c.123A>T	c.(121-123)agA>agT	p.R41S	FAM63A_ENST00000493834.2_Intron|FAM63A_ENST00000312210.5_Intron|FAM63A_ENST00000361738.6_Missense_Mutation_p.R89S|FAM63A_ENST00000470877.1_Intron	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	41						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	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)			CATCAGCATCTCTTGCATCTG	0.582													T|||	267	0.0533147	0.1309	0.0331	5008	,	,		19006	0.0		0.0646	False		,,,				2504	0.0061				p.R89S		Atlas-SNP	.											.	FAM63A	42	.	0			c.A267T						PASS	.	T	,SER/ARG,,,SER/ARG	584,3822	259.2+/-262.9	48,488,1667	139.0	128.0	132.0		,267,,,123	-0.1	0.0	1	dbSNP_127	132	614,7986	160.1+/-213.3	23,568,3709	yes	intron,missense,intron,intron,missense	FAM63A	NM_001040217.2,NM_001163258.1,NM_001163259.1,NM_001163260.1,NM_018379.4	,110,,,110	71,1056,5376	AA,AT,TT		7.1395,13.2547,9.2111	,benign,,,benign	,89/518,,,41/470	150974971	1198,11808	2203	4300	6503	SO:0001583	missense	55793	exon3			AGCATCTCTTGCA	BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.123A>T	1.37:g.150974971T>A	ENSP00000354814:p.Arg41Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_001163258	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	Missense_Mutation	SNP	ENST00000361936.5	37	CCDS976.1	133	0.060897435897435896	65	0.13211382113821138	12	0.03314917127071823	0	0.0	56	0.07387862796833773	T	13.14	2.148898	0.37923	0.132547	0.071395	ENSG00000143409	ENST00000361936;ENST00000361738	T;T	0.41758	1.01;0.99	5.18	-0.0985	0.13628	.	1.776210	0.02596	N	0.100509	T	0.06872	0.0175	N	0.19112	0.55	0.80722	P	0.0	B;B	0.17465	0.022;0.013	B;B	0.18871	0.023;0.006	T	0.06445	-1.0826	9	0.08381	T	0.77	7.5208	0.829	0.01126	0.1642:0.2922:0.1699:0.3737	rs41310885	89;41	Q8N5J2-3;Q8N5J2	.;FA63A_HUMAN	S	41;89	ENSP00000354814:R41S;ENSP00000354669:R89S	ENSP00000354669:R89S	R	-	3	2	FAM63A	149241595	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.099000	0.11007	-0.171000	0.10797	0.533000	0.62120	AGA	T|0.919;A|0.081	0.081	strong		0.582	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379	
CPT1C	126129	hgsc.bcm.edu	37	19	50212024	50212024	+	Silent	SNP	C	C	T	rs61747405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50212024C>T	ENST00000392518.4	+	14	1866	c.1494C>T	c.(1492-1494)gaC>gaT	p.D498D	CPT1C_ENST00000354199.5_Silent_p.D498D|CPT1C_ENST00000323446.5_Silent_p.D498D|CPT1C_ENST00000405931.2_Silent_p.D487D|CPT1C_ENST00000598293.1_Silent_p.D498D	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	498					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		ACTCAACAGACGGCCACTGCA	0.607													c|||	75	0.014976	0.0272	0.0101	5008	,	,		15016	0.001		0.0278	False		,,,				2504	0.0031				p.D498D		Atlas-SNP	.											.	CPT1C	93	.	0			c.C1494T						PASS	.	C	,,,	81,4325	72.5+/-110.5	1,79,2123	121.0	110.0	114.0		1461,1494,1494,1494	-4.4	0.7	19	dbSNP_129	114	206,8394	89.2+/-151.4	3,200,4097	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	,,,	4,279,6220	TT,TC,CC		2.3953,1.8384,2.2067	,,,	487/793,498/804,498/804,498/804	50212024	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	126129	exon14			AACAGACGGCCAC	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.1494C>T	19.37:g.50212024C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	63	0.583333	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Silent	SNP	ENST00000392518.4	37	CCDS12779.1																																																																																			C|0.978;T|0.022	0.022	strong		0.607	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414629	105414629	+	Missense_Mutation	SNP	G	G	A	rs72702027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	185	0	0		WXS	Illumina HiSeq	Phase_I	179	177	0.988827	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	
ZCCHC4	29063	hgsc.bcm.edu	37	4	25314478	25314478	+	Missense_Mutation	SNP	G	G	C	rs201763036	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:25314478G>C	ENST00000302874.4	+	1	71	c.47G>C	c.(46-48)aGc>aCc	p.S16T	ZCCHC4_ENST00000505451.1_3'UTR	NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	16							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				GCAGAGGGCAGCGCAGGGTGC	0.642											OREG0016141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0	0.0	5008	,	,		14396	0.0		0.002	False		,,,				2504	0.0				p.S16T		Atlas-SNP	.											.	ZCCHC4	34	.	0			c.G47C						PASS	.	G	THR/SER	2,4098		0,2,2048	70.0	89.0	83.0		47	-5.7	0.0	4		83	6,8382		0,6,4188	yes	missense	ZCCHC4	NM_024936.2	58	0,8,6236	CC,CG,GG		0.0715,0.0488,0.0641	benign	16/514	25314478	8,12480	2050	4194	6244	SO:0001583	missense	29063	exon1			AGGGCAGCGCAGG	AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"""Zinc fingers, CCHC domain containing"""	22917	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 4"""	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.47G>C	4.37:g.25314478G>C	ENSP00000303468:p.Ser16Thr	Somatic	95	0	0	778	WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Missense_Mutation	SNP	ENST00000302874.4	37	CCDS43218.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	11.08	1.534797	0.27475	4.88E-4	7.15E-4	ENSG00000168228	ENST00000302874	T	0.30981	1.51	5.18	-5.71	0.02413	.	1.862370	0.01786	N	0.032033	T	0.14270	0.0345	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.16897	-1.0387	10	0.11182	T	0.66	-5.9509	1.3284	0.02130	0.2451:0.1002:0.2206:0.4341	.	16	Q9H5U6	ZCHC4_HUMAN	T	16	ENSP00000303468:S16T	ENSP00000303468:S16T	S	+	2	0	ZCCHC4	24923576	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.725000	0.01863	-1.763000	0.01307	0.655000	0.94253	AGC	G|0.999;C|0.001	0.001	strong		0.642	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1		
MOV10	4343	hgsc.bcm.edu	37	1	113239382	113239382	+	Silent	SNP	G	G	A	rs17030651	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:113239382G>A	ENST00000413052.2	+	14	2502	c.2112G>A	c.(2110-2112)gaG>gaA	p.E704E	MOV10_ENST00000369645.1_Silent_p.E704E|MOV10_ENST00000357443.2_Silent_p.E704E|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.E648E|RP11-426L16.3_ENST00000421943.1_RNA	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	704					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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		CACTGCTGGAGCGGCTGCTCA	0.607													G|||	1175	0.234625	0.0787	0.281	5008	,	,		18993	0.4425		0.2346	False		,,,				2504	0.1984				p.E704E		Atlas-SNP	.											MOV10,NS,carcinoma,+2,1	MOV10	74	1	0			c.G2112A						PASS	.	G	,	425,3981	193.0+/-218.2	26,373,1804	63.0	49.0	53.0		2112,2112	1.2	1.0	1	dbSNP_123	53	1748,6852	294.4+/-301.9	179,1390,2731	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	205,1763,4535	AA,AG,GG		20.3256,9.6459,16.7077	,	704/1004,704/1004	113239382	2173,10833	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon14			GCTGGAGCGGCTG	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2112G>A	1.37:g.113239382G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			G|0.803;A|0.197	0.197	strong		0.607	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183191	11183191	+	Silent	SNP	T	T	C	rs116737741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:11183191T>C	ENST00000390675.2	-	1	815	c.744A>G	c.(742-744)tcA>tcG	p.S248S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	248					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						AACTCCAAACTGATATCATTA	0.408													.|||	414	0.0826677	0.0847	0.085	5008	,	,		20364	0.002		0.1203	False		,,,				2504	0.1227				p.S248S		Atlas-SNP	.											.	TAS2R31	24	.	0			c.A744G						PASS	.	T		457,3929		30,397,1766	198.0	206.0	203.0		744	-2.6	0.0	12	dbSNP_132	203	1314,7276		119,1076,3100	no	coding-synonymous	TAS2R31	NM_176885.2		149,1473,4866	CC,CT,TT		15.2969,10.4195,13.6483		248/310	11183191	1771,11205	2193	4295	6488	SO:0001819	synonymous_variant	259290	exon1			CCAAACTGATATC	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.744A>G	12.37:g.11183191T>C		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	340	161	0.473529	NM_176885	P59547|Q17R84|Q645X5	Silent	SNP	ENST00000390675.2	37	CCDS53747.1																																																																																			T|0.912;C|0.088	0.088	strong		0.408	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
VCAN	1462	hgsc.bcm.edu	37	5	82786194	82786194	+	Silent	SNP	T	T	C	rs12332199	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000502527.2_Silent_p.T116T|VCAN_ENST00000342785.4_Silent_p.T116T|VCAN_ENST00000343200.5_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	82	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	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	
MYOM3	127294	hgsc.bcm.edu	37	1	24421950	24421950	+	Missense_Mutation	SNP	C	C	G	rs4319261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24421950C>G	ENST00000374434.3	-	8	934	c.772G>C	c.(772-774)Gat>Cat	p.D258H	MYOM3_ENST00000329601.7_Missense_Mutation_p.D258H|MYOM3_ENST00000330966.7_Missense_Mutation_p.D259H|MYOM3_ENST00000475306.1_5'UTR	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	93	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	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	
USP51	158880	hgsc.bcm.edu	37	X	55514818	55514818	+	Silent	SNP	C	C	T	rs3126255	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:55514818C>T	ENST00000500968.3	-	2	637	c.555G>A	c.(553-555)gaG>gaA	p.E185E	USP51_ENST00000586165.1_Intron	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	185					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CAAACTCGACCTCCAGCAACC	0.587													.|||	1754	0.464636	0.0507	0.3501	3775	,	,		7246	0.4712		0.5149	False		,,,				2504	0.4611				p.E185E		Atlas-SNP	.											.	USP51	71	.	0			c.G555A						PASS	.	C		500,3335		30,369,71,1233,500	35.0	30.0	32.0		555	2.9	1.0	X	dbSNP_103	32	4634,2094		1149,1055,1281,224,591	no	coding-synonymous	USP51	NM_201286.3		1179,1424,1352,1457,1091	TT,TC,T,CC,C		31.1237,13.0378,48.6036		185/712	55514818	5134,5429	2203	4300	6503	SO:0001819	synonymous_variant	158880	exon2			CTCGACCTCCAGC	BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.555G>A	X.37:g.55514818C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_201286	Q8IWJ8	Silent	SNP	ENST00000500968.3	37	CCDS14370.1																																																																																			C|0.528;T|0.472	0.472	strong		0.587	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286	
MAPT	4137	hgsc.bcm.edu	37	17	44073973	44073973	+	Silent	SNP	T	T	C	rs17652121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44073973T>C	ENST00000571987.1	+	9	1716	c.1716T>C	c.(1714-1716)aaT>aaC	p.N572N	MAPT_ENST00000347967.5_Silent_p.N161N|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000576518.1_Silent_p.N186N|MAPT_ENST00000351559.5_Silent_p.N255N|MAPT_ENST00000334239.8_Silent_p.N197N|MAPT_ENST00000431008.3_Silent_p.N255N|MAPT_ENST00000344290.5_Silent_p.N590N|MAPT_ENST00000420682.2_Silent_p.N226N|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000340799.5_Silent_p.N226N|MAPT_ENST00000415613.2_Silent_p.N590N|MAPT_ENST00000574436.1_Silent_p.N255N|MAPT_ENST00000446361.3_Silent_p.N197N|MAPT_ENST00000262410.5_Silent_p.N572N|MAPT_ENST00000535772.1_Silent_p.N255N			P10636	TAU_HUMAN	microtubule-associated protein tau	572					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)	ACCTGAAGAATGTCAAGTCCA	0.652													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		13729	0.001		0.2406	False		,,,				2504	0.0613				p.N590N		Atlas-SNP	.											.	MAPT	135	.	0			c.T1770C						PASS	.	C	,,,,,,,	226,4180	793.7+/-415.2	6,214,1983	43.0	37.0	39.0		1770,678,678,765,765,591,1716,591	1.8	1.0	17	dbSNP_123	39	1925,6675	718.0+/-406.2	220,1485,2595	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,	226,1699,4578	CC,CT,TT		22.3837,5.1294,16.5385	,,,,,,,	590/777,226/413,226/382,255/411,255/442,197/384,572/759,197/353	44073973	2151,10855	2203	4300	6503	SO:0001819	synonymous_variant	4137	exon11			GAAGAATGTCAAG	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.1716T>C	17.37:g.44073973T>C		Somatic	205	2	0.0097561		WXS	Illumina HiSeq	Phase_I	195	195	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			T|0.860;C|0.140	0.140	strong		0.652	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
STOM	2040	hgsc.bcm.edu	37	9	124103523	124103523	+	Missense_Mutation	SNP	A	A	G	rs41273438	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:124103523A>G	ENST00000286713.2	-	7	841	c.824T>C	c.(823-825)aTg>aCg	p.M275T	STOM_ENST00000538954.1_Missense_Mutation_p.M224T|AL161784.1_ENST00000594963.1_5'Flank|STOM_ENST00000347359.2_Missense_Mutation_p.M110T	NM_001270526.1|NM_004099.5	NP_001257455.1|NP_004090.4	P27105	STOM_HUMAN	stomatin	275	Interaction with LANCL1.				protein homooligomerization (GO:0051260)|regulation of acid-sensing ion channel activity (GO:1901585)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|vesicle (GO:0031982)				endometrium(1)|large_intestine(1)|lung(3)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)		TCCTTGCAGCATATCTATGGG	0.488													A|||	97	0.019369	0.0045	0.0216	5008	,	,		19063	0.0		0.0368	False		,,,				2504	0.0399				p.M275T		Atlas-SNP	.											STOM,NS,carcinoma,-1,1	STOM	15	1	0			c.T824C						PASS	.	A	THR/MET,THR/MET	40,4366	43.8+/-77.6	1,38,2164	190.0	179.0	183.0		824,329	4.9	1.0	9	dbSNP_127	183	340,8260	116.6+/-176.3	10,320,3970	yes	missense,missense	STOM	NM_004099.4,NM_198194.1	81,81	11,358,6134	GG,GA,AA		3.9535,0.9079,2.9217	benign,benign	275/289,110/124	124103523	380,12626	2203	4300	6503	SO:0001583	missense	2040	exon7			TGCAGCATATCTA		CCDS6830.1, CCDS6831.1, CCDS75892.1	9q34.1	2008-07-21	2002-11-11	2002-11-15	ENSG00000148175	ENSG00000148175			3383	protein-coding gene	gene with protein product		133090	"""erythrocyte membrane protein band 7.2 (stomatin)"""	EPB7, EPB72		1883838	Standard	NM_198194		Approved	BND7	uc004blh.4	P27105	OTTHUMG00000020590	ENST00000286713.2:c.824T>C	9.37:g.124103523A>G	ENSP00000286713:p.Met275Thr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	162	82	0.506173	NM_004099	B1AM77|Q14087|Q15609|Q5VX96|Q96FK4	Missense_Mutation	SNP	ENST00000286713.2	37	CCDS6830.1	41	0.018772893772893772	4	0.008130081300813009	8	0.022099447513812154	0	0.0	29	0.03825857519788918	A	16.46	3.130373	0.56721	0.009079	0.039535	ENSG00000148175	ENST00000286713;ENST00000538954;ENST00000347359	D;D;D	0.99571	-6.19;-6.19;-4.51	4.86	4.86	0.63082	.	0.088931	0.85682	D	0.000000	D	0.95999	0.8697	L	0.48877	1.53	0.54753	D	0.999989	B;B	0.24963	0.115;0.041	B;B	0.40199	0.322;0.03	D	0.91311	0.5074	10	0.66056	D	0.02	.	13.7961	0.63171	1.0:0.0:0.0:0.0	rs41273438;rs62640058	110;275	B1AM77;P27105	.;STOM_HUMAN	T	275;224;110	ENSP00000286713:M275T;ENSP00000445764:M224T;ENSP00000339607:M110T	ENSP00000286713:M275T	M	-	2	0	STOM	123143344	1.000000	0.71417	0.963000	0.40424	0.924000	0.55760	8.856000	0.92245	2.032000	0.59987	0.454000	0.30748	ATG	A|0.971;G|0.029	0.029	strong		0.488	STOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053889.1	NM_004099	
SLC23A2	9962	hgsc.bcm.edu	37	20	4880308	4880308	+	Silent	SNP	G	G	A	rs1776964	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:4880308G>A	ENST00000379333.1	-	6	767	c.375C>T	c.(373-375)gcC>gcT	p.A125A	SLC23A2_ENST00000424750.2_Silent_p.A125A|SLC23A2_ENST00000338244.1_Silent_p.A125A|SLC23A2_ENST00000468355.1_5'UTR	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	125					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						ACATGGCATCGGCCAACAGGA	0.532													G|||	2256	0.450479	0.3638	0.4236	5008	,	,		19147	0.5446		0.4622	False		,,,				2504	0.4775				p.A125A		Atlas-SNP	.											.	SLC23A2	62	.	0			c.C375T						PASS	.	G	,	1723,2683	519.1+/-369.9	334,1055,814	163.0	140.0	148.0		375,375	-10.2	0.0	20	dbSNP_89	148	3934,4666	548.9+/-385.4	890,2154,1256	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1224,3209,2070	AA,AG,GG		45.7442,39.1058,43.4953	,	125/651,125/651	4880308	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon6			GGCATCGGCCAAC	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.375C>T	20.37:g.4880308G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1																																																																																			G|0.545;A|0.455	0.455	strong		0.532	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
TAS2R50	259296	hgsc.bcm.edu	37	12	11138935	11138935	+	Silent	SNP	T	T	C	rs66679979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:11138935T>C	ENST00000506868.1	-	1	576	c.525A>G	c.(523-525)tcA>tcG	p.S175S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	175					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						CAGTCAAATATGAAAGATGTA	0.388													T|||	493	0.0984425	0.1346	0.0908	5008	,	,		20092	0.002		0.1252	False		,,,				2504	0.1268				p.S175S		Atlas-SNP	.											.	TAS2R50	37	.	0			c.A525G						PASS	.	T		631,3775	272.5+/-270.8	52,527,1624	150.0	130.0	137.0		525	-3.1	0.0	12	dbSNP_130	137	1309,7291	257.9+/-281.7	111,1087,3102	no	coding-synonymous	TAS2R50	NM_176890.2		163,1614,4726	CC,CT,TT		15.2209,14.3214,14.9162		175/300	11138935	1940,11066	2203	4300	6503	SO:0001819	synonymous_variant	259296	exon1			CAAATATGAAAGA	AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.525A>G	12.37:g.11138935T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_176890	P59545|Q2M255|Q645Y0	Silent	SNP	ENST00000506868.1	37	CCDS8638.1																																																																																			T|0.870;C|0.130	0.130	strong		0.388	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890	
DRC7	84229	hgsc.bcm.edu	37	16	57762401	57762401	+	Missense_Mutation	SNP	T	T	C	rs2923147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57762401T>C	ENST00000360716.3	+	17	2517	c.2296T>C	c.(2296-2298)Tgc>Cgc	p.C766R	CCDC135_ENST00000394337.4_Missense_Mutation_p.C766R|CCDC135_ENST00000336825.8_Missense_Mutation_p.C701R			Q8IY82	CC135_HUMAN		766			C -> R (in dbSNP:rs2923147). {ECO:0000269|PubMed:11230166}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						GAAACTAACATGCTGGCAGGC	0.622													c|||	1976	0.394569	0.7133	0.2954	5008	,	,		16930	0.3839		0.2256	False		,,,				2504	0.2188				p.C766R		Atlas-SNP	.											CCDC135,NS,carcinoma,0,1	CCDC135	97	1	0			c.T2296C						PASS	.	C	ARG/CYS	2798,1594	487.6+/-361.0	900,998,298	46.0	51.0	49.0		2296	4.2	0.8	16	dbSNP_101	49	1710,6882	732.0+/-406.8	169,1372,2755	yes	missense	CCDC135	NM_032269.5	180	1069,2370,3053	CC,CT,TT		19.9022,36.2933,34.7197	benign	766/875	57762401	4508,8476	2196	4296	6492	SO:0001583	missense	84229	exon16			CTAACATGCTGGC																												ENST00000360716.3:c.2296T>C	16.37:g.57762401T>C	ENSP00000353942:p.Cys766Arg	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	233	117	0.502146	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		
PPFIBP1	8496	hgsc.bcm.edu	37	12	27788021	27788021	+	Silent	SNP	G	G	A	rs2075378	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:27788021G>A	ENST00000318304.8	+	4	526	c.243G>A	c.(241-243)acG>acA	p.T81T	PPFIBP1_ENST00000228425.6_Silent_p.T81T|PPFIBP1_ENST00000542629.1_Silent_p.T81T|PPFIBP1_ENST00000537927.1_Intron|PPFIBP1_ENST00000535047.1_Silent_p.T81T|PPFIBP1_ENST00000545334.1_Silent_p.T81T	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	81					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					CAGCAGAAACGCTTGTTGAAT	0.418													G|||	1745	0.348442	0.2572	0.2997	5008	,	,		18892	0.4008		0.3757	False		,,,				2504	0.4243				p.T81T		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.G243A						PASS	.	G	,,,	1215,3191	425.1+/-340.7	170,875,1158	82.0	87.0	86.0		,243,243,243	-8.6	0.0	12	dbSNP_96	86	3018,5582	466.2+/-366.7	552,1914,1834	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	722,2789,2992	AA,AG,GG		35.093,27.576,32.5465	,,,	,81/981,81/1006,81/1012	27788021	4233,8773	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon4			AGAAACGCTTGTT	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.243G>A	12.37:g.27788021G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_003622	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			G|0.671;A|0.329	0.329	strong		0.418	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
CCDC141	285025	hgsc.bcm.edu	37	2	179914649	179914649	+	Missense_Mutation	SNP	G	G	A	rs115554157	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179914649G>A	ENST00000409284.1	-	1	137	c.20C>T	c.(19-21)cCt>cTt	p.P7L	CCDC141_ENST00000420890.2_Missense_Mutation_p.P7L			Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	7										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			CGCAACACTAGGACTTCCTTG	0.478													G|||	11	0.00219649	0.0	0.0029	5008	,	,		19174	0.0		0.006	False		,,,				2504	0.0031				p.P7L		Atlas-SNP	.											.	CCDC141	362	.	0			c.C20T						PASS	.																																			SO:0001583	missense	285025	exon1			ACACTAGGACTTC	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26821	protein-coding gene	gene with protein product	"""coiled-coil protein associated with myosin II and DISC1"""					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000409284.1:c.20C>T	2.37:g.179914649G>A	ENSP00000386503:p.Pro7Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000409284.1	37		8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	G	10.95	1.495499	0.26774	.	.	ENSG00000163492	ENST00000420890;ENST00000443758;ENST00000446116;ENST00000409284	T;T	0.41065	1.01;1.62	5.73	3.95	0.45737	.	.	.	.	.	T	0.20333	0.0489	N	0.19112	0.55	0.25521	N	0.987361	B	0.12630	0.006	B	0.09377	0.004	T	0.14420	-1.0473	8	.	.	.	.	11.2749	0.49161	0.2026:0.0:0.7974:0.0	.	7	B8ZZB3	.	L	7	ENSP00000395995:P7L;ENSP00000390190:P7L	.	P	-	2	0	CCDC141	179622894	0.467000	0.25831	0.032000	0.17829	0.544000	0.35116	2.172000	0.42463	0.782000	0.33613	0.561000	0.74099	CCT	G|0.992;A|0.008	0.008	strong		0.478	CCDC141-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000335873.1	NM_173648	
NSUN4	387338	hgsc.bcm.edu	37	1	46827485	46827485	+	Silent	SNP	C	C	T	rs1053624	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46827485C>T	ENST00000474844.1	+	6	1772	c.1122C>T	c.(1120-1122)ccC>ccT	p.P374P	NSUN4_ENST00000536062.1_Silent_p.P325P|NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_Silent_p.P325P	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	374					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)					ATTTTGGCCCCATGTACTTCT	0.453																																					p.P374P		Atlas-SNP	.											.	NSUN4	26	.	0			c.C1122T						PASS	.	C		672,3734	284.6+/-277.7	58,556,1589	138.0	128.0	132.0		1122	-0.9	1.0	1	dbSNP_86	132	2493,6107	409.3+/-349.8	360,1773,2167	no	coding-synonymous	NSUN4	NM_199044.2		418,2329,3756	TT,TC,CC		28.9884,15.2519,24.3349		374/385	46827485	3165,9841	2203	4300	6503	SO:0001819	synonymous_variant	387338	exon6			TGGCCCCATGTAC	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.1122C>T	1.37:g.46827485C>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	255	125	0.490196	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Silent	SNP	ENST00000474844.1	37	CCDS534.1																																																																																			C|0.804;T|0.196	0.196	strong		0.453	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
SYNE1	23345	hgsc.bcm.edu	37	6	152615200	152615200	+	Silent	SNP	G	G	A	rs12664753	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:152615200G>A	ENST00000367255.5	-	94	18346	c.17745C>T	c.(17743-17745)caC>caT	p.H5915H	SYNE1_ENST00000448038.1_Silent_p.H5844H|SYNE1_ENST00000423061.1_Silent_p.H5844H|SYNE1_ENST00000356820.4_Silent_p.H439H|SYNE1_ENST00000265368.4_Silent_p.H5915H|SYNE1_ENST00000341594.5_Silent_p.H5527H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5915					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)		ATGTGCTGGGGTGAATTTTTG	0.468										HNSCC(10;0.0054)			G|||	740	0.147764	0.0129	0.1729	5008	,	,		16177	0.1677		0.1938	False		,,,				2504	0.2444				p.H5915H		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C17745T						PASS	.	G	,	205,4201	127.4+/-164.3	11,183,2009	101.0	91.0	94.0		17532,17745	-1.7	0.1	6	dbSNP_120	94	1649,6951	304.9+/-307.2	151,1347,2802	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	162,1530,4811	AA,AG,GG		19.1744,4.6527,14.255	,	5844/8750,5915/8798	152615200	1854,11152	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon94			GCTGGGGTGAATT	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.17745C>T	6.37:g.152615200G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	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|0.856;A|0.144	0.144	strong		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
NBPF4	148545	hgsc.bcm.edu	37	1	108769307	108769307	+	Silent	SNP	G	G	A	rs367656931	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:108769307G>A	ENST00000415641.3	-	14	2072	c.1869C>T	c.(1867-1869)agC>agT	p.S623S		NM_001143989.2	NP_001137461.1	Q96M43	NBPF4_HUMAN	neuroblastoma breakpoint family, member 4	623						cytoplasm (GO:0005737)		p.S623S(2)		endometrium(2)|lung(1)|skin(1)	4						TTACCTCTGCGCTCTCAGCAT	0.493													G|||	1100	0.219649	0.025	0.3429	5008	,	,		14496	0.3611		0.1859	False		,,,				2504	0.2843				p.S623S		Atlas-SNP	.											NBPF4,NS,carcinoma,0,2	NBPF4	4	2	2	Substitution - coding silent(2)	endometrium(2)	c.C1869T						scavenged	.						94.0	74.0	81.0					1																	108769307		647	1398	2045	SO:0001819	synonymous_variant	148545	exon14			CTCTGCGCTCTCA	AK057395	CCDS44182.1	1p13.3	2013-01-17			ENSG00000196427	ENSG00000196427		"""neuroblastoma breakpoint family"""	26550	protein-coding gene	gene with protein product		613994				16079250	Standard	NM_001143989		Approved	FLJ32833	uc009weo.2	Q96M43	OTTHUMG00000011318	ENST00000415641.3:c.1869C>T	1.37:g.108769307G>A		Somatic	727	0	0		WXS	Illumina HiSeq	Phase_I	32	22	0.6875	NM_001143989	Q5T483	Silent	SNP	ENST00000415641.3	37	CCDS44182.1																																																																																			G|0.500;A|0.500	0.500	weak		0.493	NBPF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031255.5	NM_152488	
COL6A5	256076	hgsc.bcm.edu	37	3	130098349	130098349	+	Silent	SNP	G	G	A	rs16845861	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:130098349G>A	ENST00000432398.2	+	4	1250	c.756G>A	c.(754-756)agG>agA	p.R252R	COL6A5_ENST00000265379.6_Silent_p.R252R	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	252	Nonhelical region.|VWFA 2. {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						GAAATTTAAGGCATCTTCAGA	0.468													G|||	1956	0.390575	0.4697	0.4553	5008	,	,		20494	0.5099		0.2008	False		,,,				2504	0.3098				p.R252R		Atlas-SNP	.											COL6A5,colon,carcinoma,+1,1	COL6A5	205	1	0			c.G756A						PASS	.	G		583,801		114,355,223	95.0	85.0	88.0		756	4.2	0.0	3	dbSNP_123	88	696,2486		84,528,979	no	coding-synonymous	COL6A5	NM_153264.5		198,883,1202	AA,AG,GG		21.873,42.1243,28.0114		252/2527	130098349	1279,3287	692	1591	2283	SO:0001819	synonymous_variant	256076	exon4			TTTAAGGCATCTT	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.756G>A	3.37:g.130098349G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				G|0.632;A|0.368	0.368	strong		0.468	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
KCNK10	54207	hgsc.bcm.edu	37	14	88651962	88651962	+	Missense_Mutation	SNP	C	C	T	rs17762463	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:88651962C>T	ENST00000340700.5	-	7	1985	c.1534G>A	c.(1534-1536)Gct>Act	p.A512T	KCNK10_ENST00000312350.5_Missense_Mutation_p.A517T|KCNK10_ENST00000319231.5_Missense_Mutation_p.A517T	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	512			A -> T (in dbSNP:rs17762463). {ECO:0000269|PubMed:14702039}.		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						TCCAACTCAGCGTGCTGCTGG	0.498													C|||	512	0.102236	0.0151	0.1412	5008	,	,		19750	0.0089		0.2942	False		,,,				2504	0.091				p.A517T		Atlas-SNP	.											.	KCNK10	273	.	0			c.G1549A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	285,4121	158.1+/-190.9	14,257,1932	164.0	155.0	158.0		1534,1549,1549	3.5	0.0	14	dbSNP_123	158	2382,6218	396.7+/-345.5	334,1714,2252	yes	missense,missense,missense	KCNK10	NM_021161.4,NM_138317.2,NM_138318.2	58,58,58	348,1971,4184	TT,TC,CC		27.6977,6.4685,20.5059	benign,benign,benign	512/539,517/544,517/544	88651962	2667,10339	2203	4300	6503	SO:0001583	missense	54207	exon7			ACTCAGCGTGCTG	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.1534G>A	14.37:g.88651962C>T	ENSP00000343104:p.Ala512Thr	Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	274	145	0.529197	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	37	CCDS9880.1	310	0.14194139194139194	10	0.02032520325203252	60	0.16574585635359115	9	0.015734265734265736	231	0.30474934036939316	C	6.980	0.550869	0.13374	0.064685	0.276977	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231	D;D;D	0.90955	-2.76;-2.76;-2.75	5.5	3.49	0.39957	.	1.607370	0.03015	N	0.149895	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.20261	0.043;0.043;0.012	B;B;B	0.14023	0.01;0.005;0.01	T	0.15954	-1.0419	9	0.62326	D	0.03	.	12.4173	0.55500	0.4059:0.5941:0.0:0.0	rs17762463;rs52818966;rs17762463	512;517;517	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	T	512;517;517	ENSP00000343104:A512T;ENSP00000310568:A517T;ENSP00000312811:A517T	ENSP00000310568:A517T	A	-	1	0	KCNK10	87721715	0.178000	0.23122	0.016000	0.15963	0.150000	0.21749	2.380000	0.44327	0.657000	0.30906	0.655000	0.94253	GCT	C|0.833;T|0.167	0.167	strong		0.498	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
KRT4	3851	hgsc.bcm.edu	37	12	53207628	53207628	+	Missense_Mutation	SNP	G	G	A	rs2638525	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53207628G>A	ENST00000551956.1	-	1	707	c.215C>T	c.(214-216)gCc>gTc	p.A72V	KRT4_ENST00000458244.2_Missense_Mutation_p.A52V|KRT4_ENST00000293774.4_Missense_Mutation_p.A146V			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	52	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	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	
PKP1	5317	hgsc.bcm.edu	37	1	201282573	201282573	+	Missense_Mutation	SNP	A	A	G	rs35507614	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201282573A>G	ENST00000352845.3	+	3	586	c.586A>G	c.(586-588)Ata>Gta	p.I196V	PKP1_ENST00000367324.3_Missense_Mutation_p.I196V|PKP1_ENST00000263946.3_Missense_Mutation_p.I196V			Q13835	PKP1_HUMAN	plakophilin 1	196			I -> V (in dbSNP:rs35507614).		apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						TCAGAAGGCCATAAAGAAGTG	0.617													A|||	520	0.103834	0.2814	0.0677	5008	,	,		17311	0.0		0.0616	False		,,,				2504	0.0399				p.I196V		Atlas-SNP	.											.	PKP1	127	.	0			c.A586G						PASS	.	A	VAL/ILE,VAL/ILE	1022,3384	352.8+/-311.9	120,782,1301	52.0	53.0	52.0		586,586	-4.2	0.0	1	dbSNP_126	52	501,8099	138.7+/-195.5	11,479,3810	yes	missense,missense	PKP1	NM_000299.3,NM_001005337.2	29,29	131,1261,5111	GG,GA,AA		5.8256,23.1956,11.71	benign,benign	196/748,196/727	201282573	1523,11483	2203	4300	6503	SO:0001583	missense	5317	exon3			AAGGCCATAAAGA	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.586A>G	1.37:g.201282573A>G	ENSP00000295597:p.Ile196Val	Somatic	281	1	0.00355872		WXS	Illumina HiSeq	Phase_I	289	140	0.484429	NM_001005337	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	218	0.09981684981684982	143	0.29065040650406504	29	0.08011049723756906	0	0.0	46	0.06068601583113457	A	0.006	-2.037916	0.00402	0.231956	0.058256	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.72615	-0.67;-0.55;-0.55	4.13	-4.2	0.03823	.	2.434390	0.01442	N	0.015125	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11036	-1.0604	9	0.11794	T	0.64	-10.7048	14.7395	0.69442	0.8255:0.0:0.1745:0.0	rs35507614	196;196	Q13835-2;Q13835	.;PKP1_HUMAN	V	196	ENSP00000356293:I196V;ENSP00000263946:I196V;ENSP00000295597:I196V	ENSP00000263946:I196V	I	+	1	0	PKP1	199549196	0.000000	0.05858	0.002000	0.10522	0.483000	0.33249	-0.092000	0.11129	-1.103000	0.03019	-0.344000	0.07964	ATA	A|0.887;G|0.113	0.113	strong		0.617	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
ZNF565	147929	hgsc.bcm.edu	37	19	36674305	36674305	+	Missense_Mutation	SNP	A	A	G	rs4805162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36674305A>G	ENST00000355114.5	-	5	1409	c.683T>C	c.(682-684)aTt>aCt	p.I228T	ZNF565_ENST00000392173.2_Missense_Mutation_p.I188T|ZNF565_ENST00000304116.5_Missense_Mutation_p.I188T			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	228			I -> T (in dbSNP:rs4805162). {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)			large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			ACCAGTGTGAATTTTCTGATG	0.468													G|||	3157	0.630391	0.8548	0.6398	5008	,	,		21793	0.6002		0.5219	False		,,,				2504	0.4632				p.I188T		Atlas-SNP	.											.	ZNF565	46	.	0			c.T563C						PASS	.	G	THR/ILE,THR/ILE	3456,950	360.9+/-315.4	1356,744,103	116.0	101.0	106.0		563,563	0.7	0.7	19	dbSNP_111	106	4524,4076	560.7+/-387.6	1196,2132,972	yes	missense,missense	ZNF565	NM_001042474.1,NM_152477.3	89,89	2552,2876,1075	GG,GA,AA		47.3953,21.5615,38.6437	benign,benign	188/500,188/500	36674305	7980,5026	2203	4300	6503	SO:0001583	missense	147929	exon5			GTGTGAATTTTCT	AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"""Zinc fingers, C2H2-type"", ""-"""	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.683T>C	19.37:g.36674305A>G	ENSP00000347234:p.Ile228Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001042474	B3KQ35|Q6NUS2	Missense_Mutation	SNP	ENST00000355114.5	37		1408	0.6446886446886447	421	0.8556910569105691	216	0.5966850828729282	371	0.6486013986013986	400	0.5277044854881267	g	9.197	1.027608	0.19512	0.784385	0.526047	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	T;T;T	0.04015	3.73;3.73;3.73	4.24	0.744	0.18353	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.361979	0.20251	N	0.096063	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B	0.10296	0.003	B	0.17433	0.018	T	0.03202	-1.1061	9	0.34782	T	0.22	.	7.8911	0.29677	0.3948:0.0:0.6052:0.0	rs4805162;rs58124195;rs4805162	188	Q8N9K5	ZN565_HUMAN	T	188;188;228	ENSP00000376013:I188T;ENSP00000306869:I188T;ENSP00000347234:I228T	ENSP00000306869:I188T	I	-	2	0	ZNF565	41366145	0.000000	0.05858	0.678000	0.29963	0.875000	0.50365	0.064000	0.14437	-0.075000	0.12798	-0.220000	0.12472	ATT	A|0.373;G|0.627	0.627	strong		0.468	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477	
TFAP4	7023	hgsc.bcm.edu	37	16	4310468	4310468	+	Missense_Mutation	SNP	C	C	G	rs251732	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4310468C>G	ENST00000204517.6	-	5	982	c.654G>C	c.(652-654)caG>caC	p.Q218H		NM_003223.2	NP_003214.1	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer binding protein 4)	218	Gln-rich.		Q -> H (in dbSNP:rs251732). {ECO:0000269|PubMed:15616553}.		cellular response to dexamethasone stimulus (GO:0071549)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|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 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)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						GGGTccgcagctgctgctgtt	0.647													G|||	3369	0.672724	0.8336	0.6369	5008	,	,		13091	0.7589		0.506	False		,,,				2504	0.5634				p.Q218H		Atlas-SNP	.											TFAP4,colon,carcinoma,0,1	TFAP4	31	1	0			c.G654C						PASS	.	G	HIS/GLN	3457,937		1372,713,112	21.0	21.0	21.0		654	2.1	1.0	16	dbSNP_79	21	4293,4307		1081,2131,1088	no	missense	TFAP4	NM_003223.2	24	2453,2844,1200	GG,GC,CC		49.9186,21.3245,40.3571	benign	218/339	4310468	7750,5244	2197	4300	6497	SO:0001583	missense	7023	exon5			CCGCAGCTGCTGC	X57435	CCDS10510.1	16p13	2013-05-21	2001-11-28		ENSG00000090447	ENSG00000090447		"""Basic helix-loop-helix proteins"""	11745	protein-coding gene	gene with protein product		600743	"""transcription factor AP-4 (activating enhancer-binding protein 4)"""			2123466	Standard	NM_003223		Approved	AP-4, bHLHc41	uc010uxg.2	Q01664	OTTHUMG00000129435	ENST00000204517.6:c.654G>C	16.37:g.4310468C>G	ENSP00000204517:p.Gln218His	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_003223	O60409	Missense_Mutation	SNP	ENST00000204517.6	37	CCDS10510.1	1457	0.6671245421245421	405	0.823170731707317	223	0.6160220994475138	440	0.7692307692307693	389	0.5131926121372031	G	11.24	1.579246	0.28180	0.786755	0.499186	ENSG00000090447	ENST00000204517	D	0.98717	-5.09	4.26	2.12	0.27331	.	0.467927	0.21148	N	0.079367	T	0.00012	0.0000	N	0.02011	-0.69	0.54753	P	1.0999999999983245E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.46925	-0.9156	9	0.14252	T	0.57	.	3.1819	0.06587	0.1617:0.1383:0.5578:0.1423	rs251732;rs1126923;rs61656003;rs251732	218	Q01664	TFAP4_HUMAN	H	218	ENSP00000204517:Q218H	ENSP00000204517:Q218H	Q	-	3	2	TFAP4	4250469	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	0.599000	0.24089	0.552000	0.29026	-0.986000	0.02555	CAG	C|0.381;G|0.619	0.619	strong		0.647	TFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251595.2	NM_003223	
ITGA4	3676	hgsc.bcm.edu	37	2	182322938	182322938	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:182322938G>A	ENST00000397033.2	+	2	643	c.213G>A	c.(211-213)gcG>gcA	p.A71A	ITGA4_ENST00000339307.4_Silent_p.A71A	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	71					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)	p.A71A(1)		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)	TAGTGGGTGCGCCCACTGCCA	0.612																																					p.A71A		Atlas-SNP	.											ITGA4,NS,carcinoma,0,1	ITGA4	142	1	1	Substitution - coding silent(1)	lung(1)	c.G213A						scavenged	.						28.0	31.0	30.0					2																	182322938		2099	4220	6319	SO:0001819	synonymous_variant	3676	exon2			GGGTGCGCCCACT		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.213G>A	2.37:g.182322938G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	238	3	0.012605	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	37	CCDS42788.1																																																																																			.	.	none		0.612	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
ARSH	347527	hgsc.bcm.edu	37	X	2945477	2945477	+	Missense_Mutation	SNP	C	C	T	rs61751925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:2945477C>T	ENST00000381130.2	+	7	1160	c.1160C>T	c.(1159-1161)aCg>aTg	p.T387M		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	387					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)				ATCTATCCGACGCTGTCTTAT	0.493													C|||	143	0.0378808	0.0008	0.036	3775	,	,		13676	0.0089		0.0706	False		,,,				2504	0.0378				p.T387M		Atlas-SNP	.											.	ARSH	72	.	0			c.C1160T						PASS	.	C	MET/THR	64,3771		0,51,13,1581,558	151.0	119.0	130.0		1160	3.4	0.0	X	dbSNP_129	130	650,6078		24,436,166,1968,1706	yes	missense	ARSH	NM_001011719.1	81	24,487,179,3549,2264	TT,TC,T,CC,C		9.6611,1.6688,6.7594	probably-damaging	387/563	2945477	714,9849	2203	4300	6503	SO:0001583	missense	347527	exon7			ATCCGACGCTGTC	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.1160C>T	X.37:g.2945477C>T	ENSP00000370522:p.Thr387Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	37	CCDS35198.1	82	0.04942736588306208	2	0.0040650406504065045	14	0.03977272727272727	3	0.005263157894736842	40	0.055248618784530384	C	11.44	1.639794	0.29157	0.016688	0.096611	ENSG00000205667	ENST00000381130	D	0.99150	-5.49	3.4	3.4	0.38934	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.90335	0.6976	H	0.99464	4.58	0.27978	P	0.9361375	D	0.89917	1.0	D	0.91635	0.999	T	0.68221	-0.5466	9	0.87932	D	0	.	14.2922	0.66286	0.0:1.0:0.0:0.0	rs61751925	387	Q5FYA8	ARSH_HUMAN	M	387	ENSP00000370522:T387M	ENSP00000370522:T387M	T	+	2	0	ARSH	2955477	0.999000	0.42202	0.004000	0.12327	0.010000	0.07245	4.677000	0.61634	1.328000	0.45358	0.596000	0.82720	ACG	C|0.940;T|0.060	0.060	strong		0.493	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
POLH	5429	hgsc.bcm.edu	37	6	43581586	43581586	+	Silent	SNP	G	G	A	rs3734690	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	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	
GLRX3	10539	hgsc.bcm.edu	37	10	131934747	131934747	+	Missense_Mutation	SNP	G	G	C	rs13991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:131934747G>C	ENST00000368644.1	+	1	85	c.63G>C	c.(61-63)caG>caC	p.Q21H	GLRX3_ENST00000331244.5_Missense_Mutation_p.Q21H	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	21	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.		Q -> H (in dbSNP:rs13991). {ECO:0000269|PubMed:10636891, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		CAGCCGGGCAGTTTGAGGAGC	0.726													G|||	814	0.16254	0.1233	0.0893	5008	,	,		9451	0.1091		0.2326	False		,,,				2504	0.2505				p.Q21H		Atlas-SNP	.											TXNL2,NS,carcinoma,0,2	GLRX3	39	2	0			c.G63C						PASS	.	G	HIS/GLN,HIS/GLN	308,2812		15,278,1267	7.0	10.0	9.0		63,63	2.9	1.0	10	dbSNP_52	9	885,4637		75,735,1951	no	missense,missense	GLRX3	NM_001199868.1,NM_006541.4	24,24	90,1013,3218	CC,CG,GG		16.0268,9.8718,13.8047	possibly-damaging,possibly-damaging	21/336,21/336	131934747	1193,7449	1560	2761	4321	SO:0001583	missense	10539	exon1			CGGGCAGTTTGAG	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"""glutaredoxin 4"""	612754	"""thioredoxin-like 2"""	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.63G>C	10.37:g.131934747G>C	ENSP00000357633:p.Gln21His	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	25	7	0.28	NM_006541	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	334	0.15293040293040294	64	0.13008130081300814	39	0.10773480662983426	52	0.09090909090909091	179	0.23614775725593667	G	16.20	3.054661	0.55325	0.098718	0.160268	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.14893	2.47;2.47	3.85	2.92	0.33932	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.077404	0.53938	D	0.000052	T	0.00012	0.0000	L	0.50993	1.605	0.20307	P	0.999915407	P	0.39862	0.692	P	0.50590	0.645	T	0.33954	-0.9848	9	0.24483	T	0.36	-2.8845	8.5365	0.33366	0.0:0.0:0.7694:0.2306	rs13991;rs1047395;rs3187400;rs13991	21	O76003	GLRX3_HUMAN	H	21	ENSP00000330836:Q21H;ENSP00000357633:Q21H	ENSP00000330836:Q21H	Q	+	3	2	GLRX3	131824737	0.996000	0.38824	0.997000	0.53966	0.810000	0.45777	0.140000	0.16056	0.802000	0.34089	0.313000	0.20887	CAG	G|0.849;C|0.151	0.151	strong		0.726	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541	
SLC47A2	146802	hgsc.bcm.edu	37	17	19607432	19607432	+	Silent	SNP	C	C	T	rs34169093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	59	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	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	
OR9Q2	219957	hgsc.bcm.edu	37	11	57958775	57958775	+	Silent	SNP	C	C	T	rs7120468	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57958775C>T	ENST00000311591.3	+	1	870	c.813C>T	c.(811-813)gaC>gaT	p.D271D		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D271D(1)		breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(24)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41		Breast(21;0.0589)				CCGAGGGAGACCGAGTGGTGT	0.557													C|||	2123	0.423922	0.2209	0.3847	5008	,	,		19568	0.752		0.3082	False		,,,				2504	0.5072				p.D271D		Atlas-SNP	.											OR9Q2,NS,carcinoma,0,1	OR9Q2	78	1	1	Substitution - coding silent(1)	stomach(1)	c.C813T						PASS	.	C		1068,3334	390.0+/-327.5	126,816,1259	102.0	94.0	97.0		813	3.1	0.4	11	dbSNP_116	97	2749,5843	437.8+/-358.7	458,1833,2005	no	coding-synonymous	OR9Q2	NM_001005283.2		584,2649,3264	TT,TC,CC		31.9949,24.2617,29.3751		271/315	57958775	3817,9177	2201	4296	6497	SO:0001819	synonymous_variant	219957	exon1			GGGAGACCGAGTG	AB065859	CCDS31544.1	11q12.1	2012-08-09		2004-03-10	ENSG00000186513	ENSG00000186513		"""GPCR / Class A : Olfactory receptors"""	15328	protein-coding gene	gene with protein product				OR9Q2P			Standard	NM_001005283		Approved		uc010rka.2	Q8NGE9	OTTHUMG00000167414	ENST00000311591.3:c.813C>T	11.37:g.57958775C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	142	73	0.514085	NM_001005283		Silent	SNP	ENST00000311591.3	37	CCDS31544.1																																																																																			C|0.651;T|0.349	0.349	strong		0.557	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283	
CNR2	1269	hgsc.bcm.edu	37	1	24201262	24201262	+	Silent	SNP	A	A	G	rs2502993	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201262A>G	ENST00000374472.4	-	2	1007	c.846T>C	c.(844-846)gcT>gcC	p.A282A	CNR2_ENST00000536471.1_Silent_p.A282A	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	282					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)	p.A282A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	TGGAGCAGAAAGCAAAGGCCT	0.572													G|||	3272	0.653355	0.7943	0.6383	5008	,	,		22050	0.502		0.5875	False		,,,				2504	0.6973				p.A282A		Atlas-SNP	.											CNR2_ENST00000374472,NS,carcinoma,-2,3	CNR2	78	3	1	Substitution - coding silent(1)	stomach(1)	c.T846C						PASS	.	G		3310,1096	395.8+/-329.8	1261,788,154	92.0	82.0	85.0		846	1.3	1.0	1	dbSNP_100	85	4934,3666	526.1+/-380.9	1402,2130,768	no	coding-synonymous	CNR2	NM_001841.2		2663,2918,922	GG,GA,AA		42.6279,24.8752,36.6139		282/361	24201262	8244,4762	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			GCAGAAAGCAAAG	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.846T>C	1.37:g.24201262A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			A|0.359;G|0.641	0.641	strong		0.572	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
DYNC1LI1	51143	hgsc.bcm.edu	37	3	32586521	32586521	+	Missense_Mutation	SNP	C	C	T	rs138677120	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:32586521C>T	ENST00000273130.4	-	4	518	c.415G>A	c.(415-417)Gta>Ata	p.V139I	DYNC1LI1_ENST00000432458.2_Intron	NM_016141.3	NP_057225.2	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain 1	139					microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(1)|lung(3)|ovary(1)	7						TTCAGAGATACGGCATCCAGT	0.383													C|||	48	0.00958466	0.0061	0.0072	5008	,	,		20209	0.001		0.0139	False		,,,				2504	0.0204				p.V139I		Atlas-SNP	.											.	DYNC1LI1	23	.	0			c.G415A						PASS	.	C	ILE/VAL	11,4395	17.9+/-39.9	0,11,2192	95.0	93.0	94.0		415	-9.2	0.2	3	dbSNP_134	94	127,8473	65.3+/-127.6	0,127,4173	yes	missense	DYNC1LI1	NM_016141.3	29	0,138,6365	TT,TC,CC		1.4767,0.2497,1.061	benign	139/524	32586521	138,12868	2203	4300	6503	SO:0001583	missense	51143	exon4			GAGATACGGCATC	AF078849	CCDS2654.1	3p23	2013-01-18	2005-11-25	2005-11-25	ENSG00000144635	ENSG00000144635		"""Cytoplasmic dyneins"""	18745	protein-coding gene	gene with protein product		615890	"""dynein, cytoplasmic, light intermediate polypeptide 1"""	DNCLI1		16260502	Standard	NM_016141		Approved		uc003cfb.4	Q9Y6G9	OTTHUMG00000130750	ENST00000273130.4:c.415G>A	3.37:g.32586521C>T	ENSP00000273130:p.Val139Ile	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_016141	A2RRG7|Q53HC8|Q53HK7	Missense_Mutation	SNP	ENST00000273130.4	37	CCDS2654.1	22	0.010073260073260074	8	0.016260162601626018	2	0.0055248618784530384	1	0.0017482517482517483	11	0.014511873350923483	C	12.53	1.965818	0.34659	0.002497	0.014767	ENSG00000144635	ENST00000273130;ENST00000413350;ENST00000424991	T;T;T	0.16897	2.31;2.31;2.31	5.52	-9.18	0.00688	.	0.495135	0.25851	N	0.027897	T	0.03477	0.0100	N	0.24115	0.695	0.09310	N	0.999996	B	0.09022	0.002	B	0.04013	0.001	T	0.07177	-1.0786	10	0.45353	T	0.12	-0.4528	10.3669	0.44030	0.0:0.4081:0.0947:0.4972	.	139	Q9Y6G9	DC1L1_HUMAN	I	139;88;180	ENSP00000273130:V139I;ENSP00000390507:V88I;ENSP00000409019:V180I	ENSP00000273130:V139I	V	-	1	0	DYNC1LI1	32561525	0.323000	0.24643	0.201000	0.23476	0.774000	0.43823	-0.181000	0.09740	-1.960000	0.01017	-1.119000	0.02030	GTA	C|0.989;T|0.011	0.011	strong		0.383	DYNC1LI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253250.1	NM_016141	
NISCH	11188	hgsc.bcm.edu	37	3	52524743	52524743	+	Silent	SNP	C	C	T	rs377533055		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:52524743C>T	ENST00000479054.1	+	20	3708	c.3636C>T	c.(3634-3636)acC>acT	p.T1212T	NISCH_ENST00000345716.4_Silent_p.T1212T			Q9Y2I1	NISCH_HUMAN	nischarin	1212					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	AGAAAAACACCGACTACAACA	0.532																																					p.T1212T		Atlas-SNP	.											NISCH,face,carcinoma,+1,3	NISCH	97	3	0			c.C3636T						scavenged	.	C		0,4406		0,0,2203	151.0	151.0	151.0		3636	-10.8	0.1	3		151	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NISCH	NM_007184.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1212/1505	52524743	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11188	exon19			AAACACCGACTAC	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"""imidazoline receptor candidate"", ""I-1 receptor candidate protein"", ""imidazoline receptor antisera selected"""	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.3636C>T	3.37:g.52524743C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	190	2	0.0105263	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	37	CCDS33767.1																																																																																			.	.	weak		0.532	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184	
EPHA8	2046	hgsc.bcm.edu	37	1	22927408	22927408	+	Silent	SNP	G	G	A	rs56055011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:22927408G>A	ENST00000166244.3	+	15	2628	c.2556G>A	c.(2554-2556)gaG>gaA	p.E852E		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	852	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCTCTGTGGAGGAGGGGTACC	0.706													g|||	265	0.0529153	0.003	0.0331	5008	,	,		14858	0.0456		0.0795	False		,,,				2504	0.1145				p.E852E		Atlas-SNP	.											EPHA8,NS,carcinoma,0,1	EPHA8	221	1	0			c.G2556A						PASS	.			70,4336	62.9+/-100.1	0,70,2133	44.0	48.0	46.0		2556	3.0	1.0	1	dbSNP_129	46	611,7987	157.5+/-211.1	30,551,3718	no	coding-synonymous	EPHA8	NM_020526.3		30,621,5851	AA,AG,GG		7.1063,1.5887,5.2369		852/1006	22927408	681,12323	2203	4299	6502	SO:0001819	synonymous_variant	2046	exon15			TGTGGAGGAGGGG	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2556G>A	1.37:g.22927408G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																			G|0.947;A|0.053	0.053	strong		0.706	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464558	39464558	+	Silent	SNP	G	G	A	rs72828117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	86	0	0		WXS	Illumina HiSeq	Phase_I	84	48	0.571429	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	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45258343	45258343	+	Silent	SNP	C	C	T	rs41278889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45258343C>T	ENST00000389774.2	+	13	1404	c.1263C>T	c.(1261-1263)caC>caT	p.H421H	PRR5-ARHGAP8_ENST00000352766.7_Silent_p.H600H|ARHGAP8_ENST00000356099.6_Silent_p.H390H|ARHGAP8_ENST00000389773.5_Silent_p.H512H|ARHGAP8_ENST00000336963.4_3'UTR|ARHGAP8_ENST00000517296.3_Silent_p.H600H|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.H521H	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	421					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)		CTGGGGAGCACGGCCTGGCAC	0.612													C|||	33	0.00658946	0.0212	0.0014	5008	,	,		17491	0.001		0.003	False		,,,				2504	0.0				p.H512H		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C1536T						PASS	.	C	,,,	52,4354	53.6+/-89.4	1,50,2152	50.0	49.0	49.0		1263,,1536,1170	-6.1	0.0	22	dbSNP_127	49	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,utr-3,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	1,71,6431	TT,TC,CC		0.2442,1.1802,0.5613	,,,	421/465,,512/556,390/434	45258343	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	553158	exon15			GGAGCACGGCCTG	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.1263C>T	22.37:g.45258343C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	10	0.004578754578754579	6	0.012195121951219513	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	C	2.018	-0.425336	0.04701	0.011802	0.002442	ENSG00000248405	ENST00000515632	.	.	.	3.04	-6.08	0.02151	.	.	.	.	.	T	0.10937	0.0267	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	.	0.5	0.00578	0.2906:0.2175:0.2876:0.2043	rs41278889	.	.	.	M	461	.	.	T	+	2	0	PRR5-ARHGAP8	43637007	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.542000	0.06091	-1.256000	0.02478	-0.964000	0.02622	ACG	C|0.995;T|0.005	0.005	strong		0.612	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
PLXNA2	5362	hgsc.bcm.edu	37	1	208391254	208391254	+	Missense_Mutation	SNP	C	C	T	rs2782948	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:208391254C>T	ENST00000367033.3	-	2	771	c.14G>A	c.(13-15)cGg>cAg	p.R5Q		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	5			R -> Q (in dbSNP:rs2782948). {ECO:0000269|PubMed:12975309}.		axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R5Q(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGGCCAGGGCCGCCTCTGTTC	0.667													C|||	1826	0.364617	0.3601	0.3314	5008	,	,		14354	0.4018		0.3022	False		,,,				2504	0.4202				p.R5Q		Atlas-SNP	.											PLXNA2,NS,carcinoma,0,1	PLXNA2	178	1	1	Substitution - Missense(1)	prostate(1)	c.G14A						scavenged	.	C	GLN/ARG	1475,2785		301,873,956	14.0	18.0	17.0		14	5.5	1.0	1	dbSNP_100	17	2702,5660		522,1658,2001	yes	missense	PLXNA2	NM_025179.3	43	823,2531,2957	TT,TC,CC		32.3128,34.6244,33.093	probably-damaging	5/1895	208391254	4177,8445	2130	4181	6311	SO:0001583	missense	5362	exon2			CAGGGCCGCCTCT	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.14G>A	1.37:g.208391254C>T	ENSP00000356000:p.Arg5Gln	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	787	0.36034798534798534	172	0.34959349593495936	127	0.35082872928176795	261	0.4562937062937063	227	0.2994722955145119	C	12.54	1.969753	0.34754	0.346244	0.323128	ENSG00000076356	ENST00000367033	T	0.00902	5.56	5.5	5.5	0.81552	.	1.704600	0.03240	N	0.180311	T	0.00012	0.0000	N	0.19112	0.55	0.36191	P	0.14992899999999998	P;B	0.46706	0.883;0.029	B;B	0.34038	0.174;0.011	T	0.48570	-0.9024	9	0.66056	D	0.02	.	13.6821	0.62491	0.0:0.9266:0.0:0.0734	rs2782948;rs3748736;rs2782948	59;5	O75051-2;O75051	.;PLXA2_HUMAN	Q	5	ENSP00000356000:R5Q	ENSP00000356000:R5Q	R	-	2	0	PLXNA2	206457877	0.994000	0.37717	0.985000	0.45067	0.023000	0.10783	0.519000	0.22862	2.588000	0.87417	0.650000	0.86243	CGG	C|0.660;T|0.340	0.340	strong		0.667	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
CYB5R2	51700	hgsc.bcm.edu	37	11	7686674	7686674	+	Silent	SNP	T	T	C	rs13854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7686674T>C	ENST00000533558.1	-	9	1318	c.762A>G	c.(760-762)ctA>ctG	p.L254L	CYB5R2_ENST00000299498.6_Silent_p.L254L|CYB5R2_ENST00000524790.1_3'UTR|CYB5R2_ENST00000528585.1_5'UTR			Q6BCY4	NB5R2_HUMAN	cytochrome b5 reductase 2	254					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)		CCGTCTGGATTAGTGGTGGCG	0.547											OREG0020724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3874	0.773562	0.854	0.67	5008	,	,		19373	0.7728		0.7604	False		,,,				2504	0.7526				p.L254L		Atlas-SNP	.											.	CYB5R2	23	.	0			c.A762G						PASS	.	C		3757,645	274.9+/-272.2	1590,577,34	74.0	65.0	68.0		762	6.0	1.0	11	dbSNP_52	68	6597,1995	345.6+/-325.8	2526,1545,225	no	coding-synonymous	CYB5R2	NM_016229.3		4116,2122,259	CC,CT,TT		23.2193,14.6524,20.3171		254/277	7686674	10354,2640	2201	4296	6497	SO:0001819	synonymous_variant	51700	exon9			CTGGATTAGTGGT	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.762A>G	11.37:g.7686674T>C		Somatic	131	0	0	643	WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_016229	Q9BVA3|Q9UF68|Q9UHJ0	Silent	SNP	ENST00000533558.1	37	CCDS7780.1																																																																																			T|0.208;C|0.792	0.792	strong		0.547	CYB5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385679.1	NM_016229	
ZNF133	7692	hgsc.bcm.edu	37	20	18296473	18296473	+	Silent	SNP	C	C	T	rs1050475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:18296473C>T	ENST00000316358.4	+	4	1075	c.978C>T	c.(976-978)taC>taT	p.Y326Y	ZNF133_ENST00000535822.1_Silent_p.Y231Y|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000402618.2_Silent_p.Y263Y|ZNF133_ENST00000377671.3_Silent_p.Y325Y|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000396026.3_Silent_p.Y329Y|ZNF133_ENST00000538547.1_Silent_p.Y231Y|ZNF133_ENST00000401790.1_Silent_p.Y326Y	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	326					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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						AAAAGCCTTACGTGTGCCGGG	0.542													C|||	351	0.0700879	0.0923	0.0735	5008	,	,		21795	0.0149		0.0726	False		,,,				2504	0.092				p.Y325Y		Atlas-SNP	.											.	ZNF133	63	.	0			c.C975T						PASS	.	C	,	386,4020	194.7+/-219.5	12,362,1829	75.0	69.0	71.0		975,975	-6.9	0.5	20	dbSNP_86	71	706,7894	173.0+/-223.6	36,634,3630	yes	coding-synonymous,coding-synonymous	ZNF133	NM_001083330.1,NM_003434.4	,	48,996,5459	TT,TC,CC		8.2093,8.7608,8.3961	,	325/654,325/654	18296473	1092,11914	2203	4300	6503	SO:0001819	synonymous_variant	7692	exon4			GCCTTACGTGTGC	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.978C>T	20.37:g.18296473C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Silent	SNP	ENST00000316358.4	37																																																																																				C|0.920;T|0.080	0.080	strong		0.542	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
GDPD4	220032	hgsc.bcm.edu	37	11	76954833	76954833	+	Missense_Mutation	SNP	G	G	A	rs11237146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76954833G>A	ENST00000376217.2	-	12	1397	c.1147C>T	c.(1147-1149)Cat>Tat	p.H383Y	GDPD4_ENST00000315938.4_Missense_Mutation_p.H383Y			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	383	GP-PDE.		H -> Y (in dbSNP:rs11237146).		glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						CGGCCCACATGCTGAAAACCA	0.408													G|||	1213	0.242212	0.0257	0.1873	5008	,	,		15839	0.256		0.3608	False		,,,				2504	0.4376				p.H383Y		Atlas-SNP	.											.	GDPD4	49	.	0			c.C1147T						PASS	.	G	TYR/HIS	361,4039	183.3+/-210.9	23,315,1862	97.0	92.0	93.0		1147	3.3	0.9	11	dbSNP_120	93	2937,5647	459.0+/-364.8	484,1969,1839	yes	missense	GDPD4	NM_182833.1	83	507,2284,3701	AA,AG,GG		34.2148,8.2045,25.4005	possibly-damaging	383/521	76954833	3298,9686	2200	4292	6492	SO:0001583	missense	220032	exon12			CCACATGCTGAAA	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1147C>T	11.37:g.76954833G>A	ENSP00000365390:p.His383Tyr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		475	0.2174908424908425	13	0.026422764227642278	74	0.20441988950276244	130	0.22727272727272727	258	0.3403693931398417	G	14.59	2.581875	0.46006	0.082045	0.342148	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.10960	2.82;2.82	4.27	3.34	0.38264	.	0.431410	0.27433	N	0.019382	T	0.00012	0.0000	M	0.62723	1.935	0.36466	P	0.13304899999999997	P	0.52316	0.952	P	0.47075	0.536	T	0.51196	-0.8736	9	0.36615	T	0.2	-1.6698	10.9709	0.47438	0.0:0.0:0.8135:0.1865	rs11237146;rs17824232;rs58856218;rs11237146	383	Q6W3E5-2	.	Y	383	ENSP00000365390:H383Y;ENSP00000320815:H383Y	ENSP00000320815:H383Y	H	-	1	0	GDPD4	76632481	1.000000	0.71417	0.883000	0.34634	0.439000	0.31926	3.107000	0.50329	1.112000	0.41740	0.655000	0.94253	CAT	G|0.770;A|0.229	0.229	strong		0.408	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
TEC	7006	hgsc.bcm.edu	37	4	48172266	48172266	+	Splice_Site	SNP	G	G	A	rs2271173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:48172266G>A	ENST00000381501.3	-	5	610	c.453C>T	c.(451-453)agC>agT	p.S151S		NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	151					B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						AATACTTACTGCTCTCAAAAA	0.313													A|||	2608	0.520767	0.3381	0.4942	5008	,	,		18392	0.8929		0.3579	False		,,,				2504	0.5706				p.S151S		Atlas-SNP	.											.	TEC	81	.	0			c.C453T						PASS	.	A		1474,2926	667.6+/-401.9	247,980,973	64.0	72.0	70.0		453	1.8	1.0	4	dbSNP_100	70	2955,5629	660.9+/-401.8	531,1893,1868	yes	coding-synonymous-near-splice	TEC	NM_003215.2		778,2873,2841	AA,AG,GG		34.4245,33.5,34.1112		151/632	48172266	4429,8555	2200	4292	6492	SO:0001630	splice_region_variant	7006	exon5			CTTACTGCTCTCA	D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.454+1C>T	4.37:g.48172266G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	185	185	1	NM_003215	B7ZKZ6|Q3MIS5	Silent	SNP	ENST00000381501.3	37	CCDS3481.1																																																																																			G|0.583;A|0.417	0.417	strong		0.313	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3		Silent
CEP128	145508	hgsc.bcm.edu	37	14	81251255	81251255	+	Missense_Mutation	SNP	T	T	C	rs327463	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:81251255T>C	ENST00000555265.1	-	15	2570	c.2195A>G	c.(2194-2196)cAt>cGt	p.H732R	CEP128_ENST00000281129.3_Missense_Mutation_p.H732R			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	732			H -> R (in dbSNP:rs327463).			centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)		p.H732R(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						AGTCCTGATATGATTCTCAGC	0.373													T|||	1664	0.332268	0.2383	0.3602	5008	,	,		20879	0.1806		0.3827	False		,,,				2504	0.544				p.H732R		Atlas-SNP	.											CEP128,NS,carcinoma,0,1	CEP128	146	1	1	Substitution - Missense(1)	stomach(1)	c.A2195G						PASS	.	T	ARG/HIS	1182,3224	413.5+/-336.5	154,874,1175	108.0	102.0	104.0		2195	4.9	1.0	14	dbSNP_79	104	3475,5125	505.0+/-376.3	698,2079,1523	yes	missense	CEP128	NM_152446.3	29	852,2953,2698	CC,CT,TT		40.407,26.8271,35.8066	probably-damaging	732/1095	81251255	4657,8349	2203	4300	6503	SO:0001583	missense	145508	exon14			CTGATATGATTCT	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2195A>G	14.37:g.81251255T>C	ENSP00000451162:p.His732Arg	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	268	268	1	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	634	0.2902930402930403	112	0.22764227642276422	128	0.35359116022099446	106	0.1853146853146853	288	0.37994722955145116	T	11.43	1.637792	0.29157	0.268271	0.40407	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619	T;T	0.29917	1.55;1.55	6.06	4.88	0.63580	.	0.163302	0.42548	D	0.000692	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	1.0	D	0.67145	0.996	P	0.61533	0.89	T	0.47315	-0.9127	9	0.17832	T	0.49	.	12.7799	0.57471	0.1224:0.0:0.0:0.8776	rs327463;rs328219;rs57357691;rs327463	732	Q6ZU80	CE128_HUMAN	R	732	ENSP00000281129:H732R;ENSP00000451162:H732R	ENSP00000281129:H732R	H	-	2	0	CEP128	80321008	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.088000	0.41663	2.326000	0.78906	0.472000	0.43445	CAT	T|0.657;C|0.343	0.343	strong		0.373	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
FER	2241	hgsc.bcm.edu	37	5	108281909	108281909	+	Missense_Mutation	SNP	C	C	G	rs2229086	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:108281909C>G	ENST00000281092.4	+	11	1699	c.1315C>G	c.(1315-1317)Ctg>Gtg	p.L439V	FER_ENST00000438717.2_Missense_Mutation_p.L264V|FER_ENST00000536402.1_3'UTR	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	439			L -> V (in dbSNP:rs34499946). {ECO:0000269|PubMed:1651563, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2725517}.		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)		AAAATCTGCACTGGGCTCTTC	0.378													C|||	291	0.058107	0.0045	0.0259	5008	,	,		16093	0.0863		0.0537	False		,,,				2504	0.1288				p.L439V	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.C1315G						PASS	.	C	VAL/LEU	42,4362	44.6+/-78.6	0,42,2160	111.0	118.0	116.0		1315	0.2	0.0	5	dbSNP_126	116	482,8118	139.8+/-196.4	10,462,3828	yes	missense	FER	NM_005246.2	32	10,504,5988	GG,GC,CC		5.6047,0.9537,4.0295	benign	439/823	108281909	524,12480	2202	4300	6502	SO:0001583	missense	2241	exon11			TCTGCACTGGGCT	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.1315C>G	5.37:g.108281909C>G	ENSP00000281092:p.Leu439Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	41	0.61194	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	104	0.047619047619047616	4	0.008130081300813009	10	0.027624309392265192	48	0.08391608391608392	42	0.055408970976253295	C	0.358	-0.941189	0.02322	0.009537	0.056047	ENSG00000151422	ENST00000281092;ENST00000438717	T;T	0.76578	-1.03;-0.99	5.45	0.156	0.14910	.	0.305350	0.32028	N	0.006695	T	0.07728	0.0194	L	0.58669	1.825	0.27111	P	0.9623734	B	0.31383	0.321	B	0.20577	0.03	T	0.34428	-0.9829	9	0.10111	T	0.7	0.8458	4.8822	0.13685	0.1422:0.3896:0.0:0.4682	rs41318630	439	P16591	FER_HUMAN	V	439;264	ENSP00000281092:L439V;ENSP00000394297:L264V	ENSP00000281092:L439V	L	+	1	2	FER	108309808	0.694000	0.27738	0.004000	0.12327	0.485000	0.33311	-0.134000	0.10436	0.022000	0.15160	0.491000	0.48974	CTG	C|0.956;G|0.044	0.044	strong		0.378	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
ADRB2	154	hgsc.bcm.edu	37	5	148207633	148207633	+	Silent	SNP	G	G	A	rs1042720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:148207633G>A	ENST00000305988.4	+	1	1478	c.1239G>A	c.(1237-1239)ctG>ctA	p.L413L		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	413					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	ACTCACTGCTGTAAAGCAGTT	0.403													G|||	2548	0.508786	0.5847	0.4438	5008	,	,		15122	0.6429		0.3131	False		,,,				2504	0.5153				p.L413L		Atlas-SNP	.											.	ADRB2	42	.	0			c.G1239A						PASS	.	G		2363,2043	560.0+/-380.4	646,1071,486	51.0	54.0	53.0		1239	1.6	1.0	5	dbSNP_86	53	2810,5788	431.4+/-356.8	453,1904,1942	no	coding-synonymous	ADRB2	NM_000024.5		1099,2975,2428	AA,AG,GG		32.682,46.3686,39.7801		413/414	148207633	5173,7831	2203	4299	6502	SO:0001819	synonymous_variant	154	exon1			ACTGCTGTAAAGC	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.1239G>A	5.37:g.148207633G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	133	74	0.556391	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																			A|0.411;G|0.589	0.411	strong		0.403	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408827	105408827	+	Missense_Mutation	SNP	A	A	C	rs11850949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	173	0	0		WXS	Illumina HiSeq	Phase_I	171	171	1	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	
SLC9C2	284525	hgsc.bcm.edu	37	1	173474429	173474429	+	Silent	SNP	T	T	C	rs12026637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:173474429T>C	ENST00000367714.3	-	26	3689	c.3267A>G	c.(3265-3267)caA>caG	p.Q1089Q	SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	1089					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										GCTCAGATGCTTGGATTATCA	0.398													T|||	1524	0.304313	0.0136	0.3213	5008	,	,		20902	0.6448		0.2087	False		,,,				2504	0.4325				p.Q1089Q		Atlas-SNP	.											.	.	.	.	0			c.A3267G						PASS	.	T		212,4194	127.8+/-164.7	7,198,1998	126.0	115.0	118.0		3267	2.8	0.0	1	dbSNP_120	118	1782,6818	320.8+/-314.8	185,1412,2703	no	coding-synonymous	SLC9A11	NM_178527.3		192,1610,4701	CC,CT,TT		20.7209,4.8116,15.3314		1089/1125	173474429	1994,11012	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon26			AGATGCTTGGATT	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.3267A>G	1.37:g.173474429T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			T|0.805;C|0.195	0.195	strong		0.398	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
N6AMT1	29104	hgsc.bcm.edu	37	21	30255347	30255347	+	Missense_Mutation	SNP	C	C	A	rs61735765	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:30255347C>A	ENST00000303775.5	-	2	206	c.181G>T	c.(181-183)Gca>Tca	p.A61S	N6AMT1_ENST00000351429.3_Missense_Mutation_p.A61S	NM_013240.4	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1 (putative)	61					positive regulation of cell growth (GO:0030307)|protein methylation (GO:0006479)	protein complex (GO:0043234)	nucleic acid binding (GO:0003676)|protein methyltransferase activity (GO:0008276)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)	12						GCTAGGAATGCAGATACTACA	0.358													C|||	682	0.136182	0.0953	0.1254	5008	,	,		15258	0.1101		0.1531	False		,,,				2504	0.2086				p.A61S		Atlas-SNP	.											.	N6AMT1	31	.	0			c.G181T						PASS	.	C	SER/ALA,SER/ALA	446,3960	214.5+/-233.7	16,414,1773	102.0	92.0	95.0		181,181	4.5	1.0	21	dbSNP_129	95	1193,7407	242.1+/-272.2	77,1039,3184	yes	missense,missense	N6AMT1	NM_013240.3,NM_182749.2	99,99	93,1453,4957	AA,AC,CC		13.8721,10.1226,12.6019	benign,benign	61/215,61/187	30255347	1639,11367	2203	4300	6503	SO:0001583	missense	29104	exon2			GGAATGCAGATAC	AF139682	CCDS33525.1, CCDS33526.1	21q21.3	2006-12-14	2006-12-14	2006-12-14	ENSG00000156239	ENSG00000156239	2.1.1.72		16021	protein-coding gene	gene with protein product		614553	"""chromosome 21 open reading frame 127"", ""HemK methyltransferase family member 2"""	C21orf127, HEMK2			Standard	NM_013240		Approved	PRED28, N6AMT, MTQ2	uc002ymo.2	Q9Y5N5	OTTHUMG00000078750	ENST00000303775.5:c.181G>T	21.37:g.30255347C>A	ENSP00000303584:p.Ala61Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_182749	Q96F73	Missense_Mutation	SNP	ENST00000303775.5	37	CCDS33526.1	264	0.12087912087912088	50	0.1016260162601626	41	0.1132596685082873	62	0.10839160839160839	111	0.14643799472295516	C	15.07	2.723926	0.48728	0.101226	0.138721	ENSG00000156239	ENST00000303775;ENST00000351429	T;T	0.17691	2.5;2.26	5.34	4.46	0.54185	Methyltransferase small (1);	0.104934	0.64402	D	0.000003	T	0.00073	0.0002	L	0.46567	1.45	0.23070	P	0.99834097	B;B	0.17667	0.023;0.014	B;B	0.22152	0.029;0.038	T	0.22487	-1.0215	9	0.15499	T	0.54	-16.1928	12.8662	0.57941	0.0:0.9213:0.0:0.0787	.	61;61	Q9Y5N5-2;Q9Y5N5	.;HEMK2_HUMAN	S	61	ENSP00000303584:A61S;ENSP00000286764:A61S	ENSP00000303584:A61S	A	-	1	0	N6AMT1	29177218	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	1.278000	0.33179	1.489000	0.48450	0.650000	0.86243	GCA	C|0.881;A|0.119	0.119	strong		0.358	N6AMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171738.1	NM_013240	
PREX1	57580	hgsc.bcm.edu	37	20	47361610	47361610	+	Silent	SNP	G	G	A	rs55952330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:47361610G>A	ENST00000371941.3	-	3	388	c.366C>T	c.(364-366)caC>caT	p.H122H	PREX1_ENST00000396220.1_Silent_p.H122H	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	122	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)			GCGGCTCCGGGTGTAAACAAT	0.483													G|||	119	0.023762	0.0023	0.0303	5008	,	,		18122	0.002		0.0716	False		,,,				2504	0.0215				p.H122H		Atlas-SNP	.											.	PREX1	441	.	0			c.C366T						PASS	.	G		33,4373	37.6+/-69.7	0,33,2170	144.0	149.0	147.0		366	-9.7	0.1	20	dbSNP_129	147	385,8215	125.3+/-183.9	11,363,3926	no	coding-synonymous	PREX1	NM_020820.3		11,396,6096	AA,AG,GG		4.4767,0.749,3.2139		122/1660	47361610	418,12588	2203	4300	6503	SO:0001819	synonymous_variant	57580	exon3			CTCCGGGTGTAAA	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.366C>T	20.37:g.47361610G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			G|0.966;A|0.034	0.034	strong		0.483	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
FBF1	85302	hgsc.bcm.edu	37	17	73922941	73922941	+	Missense_Mutation	SNP	T	T	C	rs2305913	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73922941T>C	ENST00000586717.1	-	9	724	c.451A>G	c.(451-453)Aga>Gga	p.R151G	FBF1_ENST00000319129.5_Missense_Mutation_p.R151G|FBF1_ENST00000389570.4_Missense_Mutation_p.R151G			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	151			R -> G (in dbSNP:rs2305913). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:18838552}.		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						AGAAGTCCTCTCAATGGGTCT	0.522													C|||	2265	0.452276	0.8396	0.3213	5008	,	,		20258	0.2202		0.3549	False		,,,				2504	0.3609				p.R151G		Atlas-SNP	.											.	FBF1	48	.	0			c.A451G						PASS	.	C	GLY/ARG	2928,1030		1084,760,135	53.0	51.0	52.0		451	4.3	0.9	17	dbSNP_100	52	2887,5423		518,1851,1786	yes	missense	FBF1	NM_001080542.1	125	1602,2611,1921	CC,CT,TT		34.7413,26.0232,47.3997	benign	151/1134	73922941	5815,6453	1979	4155	6134	SO:0001583	missense	85302	exon9			GTCCTCTCAATGG	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.451A>G	17.37:g.73922941T>C	ENSP00000465132:p.Arg151Gly	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	166	80	0.481928	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		935	0.4281135531135531	407	0.8272357723577236	130	0.35911602209944754	145	0.2534965034965035	253	0.3337730870712401	C	6.969	0.548733	0.13312	0.739768	0.347413	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.17054	2.3;2.3	5.28	4.31	0.51392	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.09729	-1.0661	8	0.45353	T	0.12	-2.1032	8.3301	0.32180	0.0:0.8185:0.0:0.1815	rs2305913;rs17856694;rs57572964;rs2305913	165;151;151	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	G	151;151;151;164	ENSP00000374221:R151G;ENSP00000324292:R151G	ENSP00000324292:R151G	R	-	1	2	FBF1	71434536	1.000000	0.71417	0.905000	0.35620	0.016000	0.09150	2.331000	0.43894	0.632000	0.30432	-0.119000	0.15052	AGA	T|0.549;C|0.451	0.451	strong		0.522	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
TOP3B	8940	hgsc.bcm.edu	37	22	22323003	22323003	+	Silent	SNP	C	C	A	rs114760416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:22323003C>A	ENST00000398793.2	-	7	1160	c.726G>T	c.(724-726)gtG>gtT	p.V242V	TOP3B_ENST00000413067.2_5'UTR|TOP3B_ENST00000357179.5_Silent_p.V242V	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	242					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		TGGCCTGCAGCACCCAGTAGG	0.532													C|||	4	0.000798722	0.0	0.0	5008	,	,		19610	0.0		0.004	False		,,,				2504	0.0				p.V242V		Atlas-SNP	.											.	TOP3B	107	.	0			c.G726T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	122.0	119.0	120.0		726	4.0	1.0	22	dbSNP_132	120	16,8584	12.6+/-44.7	0,16,4284	no	coding-synonymous	TOP3B	NM_003935.3		0,18,6485	AA,AC,CC		0.186,0.0454,0.1384		242/863	22323003	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	8940	exon7			CTGCAGCACCCAG	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.726G>T	22.37:g.22323003C>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_003935	A0M8Q3|Q9BUP5	Silent	SNP	ENST00000398793.2	37	CCDS13797.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	9.680	1.148957	0.21288	4.54E-4	0.00186	ENSG00000100038	ENST00000457270	.	.	.	5.04	4.01	0.46588	.	.	.	.	.	T	0.48095	0.1481	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49908	-0.8889	4	.	.	.	.	6.9623	0.24603	0.0:0.7019:0.1436:0.1544	.	.	.	.	F	37	.	.	C	-	2	0	TOP3B	20653003	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.312000	0.33574	1.318000	0.45170	0.555000	0.69702	TGC	C|0.998;A|0.002	0.002	strong		0.532	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
SEZ6L2	26470	hgsc.bcm.edu	37	16	29899021	29899021	+	Missense_Mutation	SNP	C	C	T	rs117448844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:29899021C>T	ENST00000308713.5	-	7	1684	c.1157G>A	c.(1156-1158)cGc>cAc	p.R386H	SEZ6L2_ENST00000562159.1_5'Flank|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.R316H|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.R272H|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.R342H	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	386	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTGCAGCCGGCGCCCCTCAGC	0.637													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15751	0.0		0.003	False		,,,				2504	0.0				p.R386H		Atlas-SNP	.											SEZ6L2_ENST00000350527,NS,carcinoma,0,2	SEZ6L2	137	2	0			c.G1157A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	4,4390	8.1+/-20.4	0,4,2193	78.0	72.0	74.0		947,815,947,1157	5.7	1.0	16	dbSNP_132	74	26,8574	19.8+/-62.0	0,26,4274	yes	missense,missense,missense,missense	SEZ6L2	NM_001114099.2,NM_001114100.2,NM_012410.3,NM_201575.3	29,29,29,29	0,30,6467	TT,TC,CC		0.3023,0.091,0.2309	benign,benign,benign,benign	316/841,272/810,316/854,386/911	29899021	30,12964	2197	4300	6497	SO:0001583	missense	26470	exon7			AGCCGGCGCCCCT	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1157G>A	16.37:g.29899021C>T	ENSP00000312550:p.Arg386His	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	114	62	0.54386	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	21.9	4.221861	0.79464	9.1E-4	0.003023	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.72	5.72	0.89469	CUB (4);	0.000000	0.56097	D	0.000031	T	0.13798	0.0334	N	0.02296	-0.605	0.35617	D	0.809155	B;B;B;B;B;B	0.24963	0.039;0.07;0.07;0.115;0.07;0.115	B;B;B;B;B;B	0.14023	0.01;0.003;0.002;0.006;0.003;0.006	T	0.30475	-0.9977	10	0.15066	T	0.55	.	8.9111	0.35555	0.0:0.8417:0.0:0.1583	.	342;386;272;316;386;316	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	H	316;386;272;342	ENSP00000310206:R316H;ENSP00000312550:R386H;ENSP00000319215:R272H;ENSP00000439412:R342H	ENSP00000312550:R386H	R	-	2	0	SEZ6L2	29806522	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.553000	0.67287	2.720000	0.93068	0.555000	0.69702	CGC	C|0.998;T|0.002	0.002	strong		0.637	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410	
GPR82	27197	hgsc.bcm.edu	37	X	41587218	41587218	+	Silent	SNP	T	T	C	rs587783365|rs1023065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:41587218T>C	ENST00000302548.4	+	3	1179	c.939T>C	c.(937-939)gaT>gaC	p.D313D	CASK_ENST00000378154.1_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000442742.2_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	313						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	10						TTTTATTAGATAAAACATTCA	0.318													T|||	3266	0.865166	0.6641	0.6787	3775	,	,		12785	0.7411		0.5388	False		,,,				2504	0.6421				p.D313D		Atlas-SNP	.											.	GPR82	52	.	0			c.T939C						PASS	.	T	,,,	3322,508		1230,374,488,26,82	23.0	23.0	23.0		,,,939	1.7	1.0	X	dbSNP_86	23	5170,1533		1448,838,1436,136,423	no	intron,intron,intron,coding-synonymous	CASK,GPR82	NM_001126054.2,NM_001126055.2,NM_003688.3,NM_080817.4	,,,	2678,1212,1924,162,505	CC,CT,C,TT,T		22.8704,13.2637,19.3772	,,,	,,,313/337	41587218	8492,2041	2200	4281	6481	SO:0001819	synonymous_variant	27197	exon3			ATTAGATAAAACA	AF411111	CCDS14259.1	Xp11.4	2012-08-21			ENSG00000171657	ENSG00000171657		"""GPCR / Class A : Orphans"""	4533	protein-coding gene	gene with protein product		300748				11574155	Standard	NM_080817		Approved		uc004dft.3	Q96P67	OTTHUMG00000021373	ENST00000302548.4:c.939T>C	X.37:g.41587218T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_080817	Q5VT13	Silent	SNP	ENST00000302548.4	37	CCDS14259.1																																																																																			T|0.167;C|0.833	0.833	strong		0.318	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817	
STYK1	55359	hgsc.bcm.edu	37	12	10783729	10783729	+	Silent	SNP	A	A	G	rs2290717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:10783729A>G	ENST00000075503.3	-	5	886	c.366T>C	c.(364-366)agT>agC	p.S122S		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						CACAGCTACCACTGCAAATCT	0.507										HNSCC(73;0.22)			A|||	1268	0.253195	0.1097	0.2378	5008	,	,		15618	0.2063		0.3787	False		,,,				2504	0.3773				p.S122S		Atlas-SNP	.											.	STYK1	55	.	0			c.T366C						PASS	.	A		701,3705	294.7+/-283.3	52,597,1554	77.0	74.0	75.0		366	-1.7	0.0	12	dbSNP_100	75	3696,4904	527.5+/-381.2	799,2098,1403	no	coding-synonymous	STYK1	NM_018423.2		851,2695,2957	GG,GA,AA		42.9767,15.9101,33.8075		122/423	10783729	4397,8609	2203	4300	6503	SO:0001819	synonymous_variant	55359	exon5			GCTACCACTGCAA	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.366T>C	12.37:g.10783729A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	125	49	0.392	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Silent	SNP	ENST00000075503.3	37	CCDS8629.1																																																																																			A|0.701;G|0.299	0.299	strong		0.507	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423	
CLEC18B	497190	hgsc.bcm.edu	37	16	74451960	74451960	+	Silent	SNP	C	C	T	rs201007386	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:74451960C>T	ENST00000339953.5	-	3	574	c.453G>A	c.(451-453)acG>acA	p.T151T		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	151	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CACTCACCTGCGTGTAGTGGG	0.592																																					p.T151T		Atlas-SNP	.											CLEC18B,NS,carcinoma,-1,4	CLEC18B	45	4	0			c.G453A						scavenged	.						8.0	9.0	8.0					16																	74451960		1773	3617	5390	SO:0001819	synonymous_variant	497190	exon3			CACCTGCGTGTAG	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"""C-type lectin domain containing"""	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.453G>A	16.37:g.74451960C>T		Somatic	514	0	0		WXS	Illumina HiSeq	Phase_I	651	30	0.046083	NM_001011880	B4DF90	Silent	SNP	ENST00000339953.5	37	CCDS32484.1																																																																																			.	.	weak		0.592	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880	
SNAPC4	6621	hgsc.bcm.edu	37	9	139275294	139275294	+	Missense_Mutation	SNP	G	G	C	rs3812571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139275294G>C	ENST00000298532.2	-	19	2765	c.2397C>G	c.(2395-2397)caC>caG	p.H799Q		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)		CAGTATCGATGTGGAACAGCT	0.637													C|||	2034	0.40615	0.3631	0.6066	5008	,	,		19093	0.3224		0.4155	False		,,,				2504	0.3988				p.H799Q		Atlas-SNP	.											SNAPC4,NS,carcinoma,0,2	SNAPC4	82	2	0			c.C2397G						PASS	.	C	GLN/HIS	1604,2798	656.1+/-400.0	287,1030,884	49.0	45.0	47.0		2397	4.2	1.0	9	dbSNP_107	47	3805,4791	609.2+/-395.5	844,2117,1337	yes	missense	SNAPC4	NM_003086.2	24	1131,3147,2221	CC,CG,GG		44.2648,36.438,41.6141	benign	799/1470	139275294	5409,7589	2201	4298	6499	SO:0001583	missense	6621	exon19			ATCGATGTGGAAC	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.2397C>G	9.37:g.139275294G>C	ENSP00000298532:p.His799Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	870	0.3983516483516483	184	0.37398373983739835	190	0.5248618784530387	177	0.3094405594405594	319	0.420844327176781	C	0.022	-1.406691	0.01155	0.36438	0.442648	ENSG00000165684	ENST00000298532	T	0.24538	1.85	4.15	4.15	0.48705	.	0.206990	0.35708	N	0.003030	T	0.00012	0.0000	N	0.00260	-1.75	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47142	-0.9140	9	0.02654	T	1	-18.3209	11.0145	0.47681	0.0:0.634:0.366:0.0	rs3812571;rs13298729;rs17602983;rs3812571	799	Q5SXM2	SNPC4_HUMAN	Q	799	ENSP00000298532:H799Q	ENSP00000298532:H799Q	H	-	3	2	SNAPC4	138395115	0.967000	0.33354	0.979000	0.43373	0.337000	0.28794	0.133000	0.15912	0.877000	0.35895	-0.120000	0.15030	CAC	G|0.591;C|0.409	0.409	strong		0.637	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
EMR1	2015	hgsc.bcm.edu	37	19	6906469	6906469	+	Silent	SNP	T	T	C	rs78491083	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6906469T>C	ENST00000312053.4	+	9	1012	c.975T>C	c.(973-975)gaT>gaC	p.D325D	EMR1_ENST00000381404.4_Silent_p.D273D|EMR1_ENST00000250572.8_Silent_p.D325D|EMR1_ENST00000381407.5_Silent_p.D184D|EMR1_ENST00000450315.3_Silent_p.D148D	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	325	Ser/Thr-rich.				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)					GTAAGGAAGATGTGATACCCG	0.383													T|||	20	0.00399361	0.0008	0.0058	5008	,	,		20677	0.0		0.0109	False		,,,				2504	0.0041				p.D325D		Atlas-SNP	.											EMR1,NS,carcinoma,+1,1	EMR1	153	1	0			c.T975C						PASS	.	T		11,4395	17.9+/-39.9	0,11,2192	143.0	136.0	138.0		975	-0.2	0.2	19	dbSNP_133	138	78,8522	46.3+/-105.2	1,76,4223	no	coding-synonymous	EMR1	NM_001974.3		1,87,6415	CC,CT,TT		0.907,0.2497,0.6843		325/887	6906469	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	2015	exon9			GGAAGATGTGATA	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.975T>C	19.37:g.6906469T>C		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	259	130	0.50193	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Silent	SNP	ENST00000312053.4	37	CCDS12175.1																																																																																			T|0.994;C|0.006	0.006	strong		0.383	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
TTC27	55622	hgsc.bcm.edu	37	2	32961858	32961858	+	Missense_Mutation	SNP	A	A	G	rs2273660	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:32961858A>G	ENST00000317907.4	+	12	1658	c.1427A>G	c.(1426-1428)tAt>tGt	p.Y476C		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	476			Y -> C (in dbSNP:rs2273660).							breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						GTCATTTGTTATGAAAGAGCC	0.433													A|||	643	0.128395	0.1997	0.111	5008	,	,		15672	0.0923		0.1133	False		,,,				2504	0.0971				p.Y476C		Atlas-SNP	.											.	TTC27	71	.	0			c.A1427G						PASS	.	A	CYS/TYR,CYS/TYR	760,3646	311.6+/-292.2	62,636,1505	105.0	102.0	103.0		1277,1427	5.7	1.0	2	dbSNP_100	103	975,7625	211.5+/-252.1	60,855,3385	yes	missense,missense	TTC27	NM_001193509.1,NM_017735.4	194,194	122,1491,4890	GG,GA,AA		11.3372,17.2492,13.34	probably-damaging,probably-damaging	426/794,476/844	32961858	1735,11271	2203	4300	6503	SO:0001583	missense	55622	exon12			TTTGTTATGAAAG	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"""Tetratricopeptide (TTC) repeat domain containing"""	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1427A>G	2.37:g.32961858A>G	ENSP00000313953:p.Tyr476Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	37	CCDS33176.1	276	0.12637362637362637	88	0.17886178861788618	40	0.11049723756906077	68	0.11888111888111888	80	0.10554089709762533	A	21.2	4.106295	0.77096	0.172492	0.113372	ENSG00000018699	ENST00000317907	T	0.28895	1.59	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);	0.266971	0.38164	N	0.001786	T	0.00109	0.0003	L	0.51422	1.61	0.18873	P	0.9999863401	D	0.71674	0.998	P	0.57371	0.819	T	0.01024	-1.1477	9	0.52906	T	0.07	-5.3293	14.9571	0.71124	1.0:0.0:0.0:0.0	rs2273660;rs58045822;rs2273660	476	Q6P3X3	TTC27_HUMAN	C	476	ENSP00000313953:Y476C	ENSP00000313953:Y476C	Y	+	2	0	TTC27	32815362	1.000000	0.71417	0.986000	0.45419	0.960000	0.62799	3.107000	0.50329	2.168000	0.68352	0.533000	0.62120	TAT	A|0.866;G|0.134	0.134	strong		0.433	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	
CCDC170	80129	hgsc.bcm.edu	37	6	151914265	151914265	+	Silent	SNP	T	T	C	rs17081470	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151914265T>C	ENST00000239374.7	+	8	1416	c.1317T>C	c.(1315-1317)ctT>ctC	p.L439L	CCDC170_ENST00000367290.5_Silent_p.L439L	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	439																	TGGATCAGCTTTCTCAGAAAA	0.428													T|||	482	0.096246	0.1581	0.0447	5008	,	,		19213	0.0794		0.0527	False		,,,				2504	0.1115				p.L439L		Atlas-SNP	.											.	.	.	.	0			c.T1317C						PASS	.	T		594,3146		56,482,1332	104.0	94.0	97.0		1317	-3.7	1.0	6	dbSNP_123	97	579,7651		19,541,3555	no	coding-synonymous	C6orf97	NM_025059.3		75,1023,4887	CC,CT,TT		7.0352,15.8824,9.7995		439/716	151914265	1173,10797	1870	4115	5985	SO:0001819	synonymous_variant	80129	exon8			TCAGCTTTCTCAG	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1317T>C	6.37:g.151914265T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Silent	SNP	ENST00000239374.7	37	CCDS43515.1																																																																																			T|0.914;C|0.086	0.086	strong		0.428	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
DOCK9	23348	hgsc.bcm.edu	37	13	99554621	99554621	+	Missense_Mutation	SNP	G	G	A	rs62620184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:99554621G>A	ENST00000376460.1	-	12	1381	c.1301C>T	c.(1300-1302)gCg>gTg	p.A434V	DOCK9_ENST00000448493.2_Missense_Mutation_p.A446V|DOCK9_ENST00000339416.2_Missense_Mutation_p.A435V|DOCK9_ENST00000442173.1_Missense_Mutation_p.A434V	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	435					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ATTCATCAGCGCCGGGGACGT	0.542													G|||	151	0.0301518	0.003	0.0259	5008	,	,		18436	0.002		0.0378	False		,,,				2504	0.091				p.A435V		Atlas-SNP	.											DOCK9_ENST00000448493,rectum,carcinoma,+1,3	DOCK9	311	3	0			c.C1304T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	37,4223		0,37,2093	70.0	76.0	74.0		1301,1304,1301,1304	0.3	0.0	13	dbSNP_129	74	386,8096		5,376,3860	yes	missense,missense,missense,missense	DOCK9	NM_001130048.1,NM_001130049.1,NM_001130050.1,NM_015296.2	64,64,64,64	5,413,5953	AA,AG,GG		4.5508,0.8685,3.3197	benign,benign,benign,benign	434/2069,435/1255,434/1254,435/2070	99554621	423,12319	2130	4241	6371	SO:0001583	missense	23348	exon12			ATCAGCGCCGGGG	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.1301C>T	13.37:g.99554621G>A	ENSP00000365643:p.Ala434Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	14.14	2.445235	0.43429	0.008685	0.045508	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	5.36	0.314	0.15847	.	1.035550	0.07591	N	0.921988	T	0.04588	0.0125	N	0.17082	0.46	0.09310	N	1	B;B;B;B;B	0.09022	0.002;0.002;0.001;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.001	T	0.12915	-1.0529	9	.	.	.	.	4.1252	0.10125	0.3458:0.0:0.3684:0.2857	.	435;434;434;434;435	A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;DOCK9_HUMAN	V	434;435;435;435;434;435;446;434	ENSP00000365643:A434V;ENSP00000341086:A435V;ENSP00000401958:A446V;ENSP00000406883:A434V	.	A	-	2	0	DOCK9	98352622	0.011000	0.17503	0.002000	0.10522	0.052000	0.14988	1.383000	0.34385	0.325000	0.23359	0.650000	0.86243	GCG	G|0.975;A|0.025	0.025	strong		0.542	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414790	105414790	+	Missense_Mutation	SNP	A	A	G	rs2582513|rs386781095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105414790A>G	ENST00000333244.5	-	7	7117	c.6998T>C	c.(6997-6999)cTt>cCt	p.L2333P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2333						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)			GGACTTGCCAAGGGCAGACAC	0.592													.|||	2820	0.563099	0.6528	0.536	5008	,	,		20158	0.4276		0.5338	False		,,,				2504	0.6309				p.L2333P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T6998C						PASS	.	G	PRO/LEU	2728,1374		971,786,294	186.0	207.0	200.0		6998	1.8	0.0	14	dbSNP_100	200	4582,3818		1274,2034,892	yes	missense	AHNAK2	NM_138420.2	98	2245,2820,1186	GG,GA,AA		45.4524,33.4959,41.5294	benign	2333/5796	105414790	7310,5192	2051	4200	6251	SO:0001583	missense	113146	exon7			TTGCCAAGGGCAG	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.6998T>C	14.37:g.105414790A>G	ENSP00000353114:p.Leu2333Pro	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1176	0.5384615384615384	331	0.6727642276422764	211	0.5828729281767956	235	0.41083916083916083	399	0.5263852242744064	-	0.274	-0.990626	0.02162	0.665041	0.545476	ENSG00000185567	ENST00000333244	T	0.00514	6.88	3.92	1.84	0.25277	.	.	.	.	.	T	0.00012	0.0000	N	0.00003	-3.425	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37314	-0.9711	8	0.19147	T	0.46	.	4.4358	0.11550	0.0968:0.2459:0.532:0.1253	rs61996038	2333	Q8IVF2	AHNK2_HUMAN	P	2333	ENSP00000353114:L2333P	ENSP00000353114:L2333P	L	-	2	0	AHNAK2	104485835	0.028000	0.19301	0.000000	0.03702	0.018000	0.09664	-0.260000	0.08708	0.140000	0.18849	-0.330000	0.08379	CTT	A|0.456;G|0.544	0.544	strong		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SMTNL2	342527	hgsc.bcm.edu	37	17	4495682	4495682	+	Silent	SNP	G	G	A	rs4790654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4495682G>A	ENST00000389313.4	+	2	493	c.426G>A	c.(424-426)gaG>gaA	p.E142E	SMTNL2_ENST00000338859.4_5'UTR	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	142										breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		AGGCCAGTGAGTCGGAGATGA	0.592													G|||	866	0.172923	0.2065	0.1369	5008	,	,		13659	0.126		0.1799	False		,,,				2504	0.1943				p.E142E		Atlas-SNP	.											.	SMTNL2	57	.	0			c.G426A						PASS	.	G	,	866,3540	338.1+/-305.1	87,692,1424	81.0	81.0	81.0		426,	1.8	0.0	17	dbSNP_111	81	1521,7079	286.6+/-297.8	126,1269,2905	no	coding-synonymous,utr-5	SMTNL2	NM_001114974.1,NM_198501.2	,	213,1961,4329	AA,AG,GG		17.686,19.655,18.3531	,	142/462,	4495682	2387,10619	2203	4300	6503	SO:0001819	synonymous_variant	342527	exon2			CAGTGAGTCGGAG	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.426G>A	17.37:g.4495682G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	44	0.6875	NM_001114974	Q6ZVK6	Silent	SNP	ENST00000389313.4	37	CCDS45583.1																																																																																			G|0.837;A|0.163	0.163	strong		0.592	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501	
OR5L2	26338	hgsc.bcm.edu	37	11	55595115	55595115	+	Missense_Mutation	SNP	C	C	T	rs35214936|rs71490506|rs386753701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	272	0	0		WXS	Illumina HiSeq	Phase_I	245	115	0.469388	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	
C12orf50	160419	hgsc.bcm.edu	37	12	88379788	88379788	+	Missense_Mutation	SNP	C	C	T	rs11104703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:88379788C>T	ENST00000298699.2	-	11	1145	c.965G>A	c.(964-966)cGc>cAc	p.R322H	C12orf50_ENST00000550553.1_Missense_Mutation_p.R283H	NM_152589.1	NP_689802.1	Q8NA57	CL050_HUMAN	chromosome 12 open reading frame 50	322			R -> H (in dbSNP:rs11104703).							NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|urinary_tract(2)	34						TTTATTATTGCGGTGATAACT	0.468													C|||	136	0.0271565	0.0053	0.036	5008	,	,		18367	0.0		0.0567	False		,,,				2504	0.0481				p.R322H		Atlas-SNP	.											.	C12orf50	70	.	0			c.G965A						PASS	.	C	HIS/ARG	44,4362	46.0+/-80.4	1,42,2160	174.0	168.0	170.0		965	3.0	0.7	12	dbSNP_120	170	599,8001	158.3+/-211.8	23,553,3724	yes	missense	C12orf50	NM_152589.1	29	24,595,5884	TT,TC,CC		6.9651,0.9986,4.9439	benign	322/415	88379788	643,12363	2203	4300	6503	SO:0001583	missense	160419	exon11			TTATTGCGGTGAT	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.965G>A	12.37:g.88379788C>T	ENSP00000298699:p.Arg322His	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	328	172	0.52439	NM_152589	Q6P674	Missense_Mutation	SNP	ENST00000298699.2	37	CCDS9031.1	51	0.023351648351648352	5	0.01016260162601626	11	0.03038674033149171	0	0.0	35	0.04617414248021108	C	6.954	0.545931	0.13312	0.009986	0.069651	ENSG00000165805	ENST00000298699;ENST00000550553;ENST00000551944	T;T	0.32515	1.46;1.45	5.91	2.99	0.34606	.	0.451068	0.23039	N	0.052640	T	0.01287	0.0042	N	0.25890	0.77	0.22796	N	0.998722	B;B	0.10296	0.003;0.003	B;B	0.08055	0.003;0.002	T	0.13872	-1.0493	10	0.32370	T	0.25	.	6.7773	0.23626	0.0:0.5651:0.0:0.4349	rs11104703;rs52797551;rs59006881;rs11104703	337;322	G3V208;Q8NA57	.;CL050_HUMAN	H	322;283;337	ENSP00000298699:R322H;ENSP00000448344:R283H	ENSP00000298699:R322H	R	-	2	0	C12orf50	86903919	0.856000	0.29760	0.691000	0.30163	0.098000	0.18820	0.314000	0.19432	0.330000	0.23485	0.650000	0.86243	CGC	C|0.959;T|0.041	0.041	strong		0.468	C12orf50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406328.1	NM_152589	
TNRC18	84629	hgsc.bcm.edu	37	7	5347749	5347749	+	Silent	SNP	G	G	A	rs9639976	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:5347749G>A	ENST00000430969.1	-	30	9243	c.8895C>T	c.(8893-8895)ccC>ccT	p.P2965P	TNRC18_ENST00000399537.4_Silent_p.P2965P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2965							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		AGCAGAGCACGGGCACGCCGT	0.682													G|||	646	0.128994	0.0552	0.17	5008	,	,		14507	0.1151		0.2565	False		,,,				2504	0.0828				p.P2965P		Atlas-SNP	.											.	TNRC18	311	.	0			c.C8895T						PASS	.	G		313,3739		24,265,1737	21.0	24.0	23.0		8895	-9.2	1.0	7	dbSNP_119	23	2092,6130		286,1520,2305	no	coding-synonymous	TNRC18	NM_001080495.2		310,1785,4042	AA,AG,GG		25.4439,7.7246,19.5943		2965/2969	5347749	2405,9869	2026	4111	6137	SO:0001819	synonymous_variant	84629	exon30			GAGCACGGGCACG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8895C>T	7.37:g.5347749G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.833;A|0.167	0.167	strong		0.682	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
DOCK4	9732	hgsc.bcm.edu	37	7	111512589	111512589	+	Silent	SNP	G	G	A	rs10257550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:111512589G>A	ENST00000437633.1	-	18	2032	c.1776C>T	c.(1774-1776)acC>acT	p.T592T	DOCK4_ENST00000428084.1_Silent_p.T592T|DOCK4_ENST00000476846.1_5'UTR	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	66	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	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	
OR6S1	341799	hgsc.bcm.edu	37	14	21109278	21109278	+	Silent	SNP	A	A	T	rs11627438	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21109278A>T	ENST00000320704.3	-	1	572	c.573T>A	c.(571-573)gcT>gcA	p.A191A		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TGTTGGTGCAAGCCAGGCGGA	0.562													T|||	2266	0.452476	0.4902	0.5461	5008	,	,		23005	0.251		0.5338	False		,,,				2504	0.4591				p.A191A		Atlas-SNP	.											OR6S1,NS,carcinoma,0,1	OR6S1	49	1	0			c.T573A						PASS	.	T		2257,2149	581.8+/-385.5	560,1137,506	68.0	69.0	68.0		573	-1.8	1.0	14	dbSNP_120	68	4783,3817	539.5+/-383.6	1334,2115,851	no	coding-synonymous	OR6S1	NM_001001968.1		1894,3252,1357	TT,TA,AA		44.3837,48.7744,45.8711		191/332	21109278	7040,5966	2203	4300	6503	SO:0001819	synonymous_variant	341799	exon1			GGTGCAAGCCAGG	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.573T>A	14.37:g.21109278A>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001001968	Q6IFJ9	Silent	SNP	ENST00000320704.3	37	CCDS32038.1																																																																																			A|0.484;T|0.516	0.516	strong		0.562	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
MUC16	94025	hgsc.bcm.edu	37	19	9001835	9001835	+	Silent	SNP	G	G	A	rs12985778|rs386806621	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9001835G>A	ENST00000397910.4	-	53	40616	c.40413C>T	c.(40411-40413)ccC>ccT	p.P13471P	MUC16_ENST00000380951.5_Silent_p.P112P	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13473					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						ACTCACTCATGGGTCCAGACA	0.448													-|||	2997	0.598442	0.3812	0.7219	5008	,	,		22058	0.6071		0.7177	False		,,,				2504	0.6728				p.P13471P		Atlas-SNP	.											.	MUC16	4315	.	0			c.C40413T						PASS	.			1868,2128		455,958,585	83.0	80.0	81.0		40413	-2.1	0.0	19	dbSNP_121	81	6099,2233		2297,1505,364	no	coding-synonymous	MUC16	NM_024690.2		2752,2463,949	AA,AG,GG		26.8003,46.7467,35.3748		13471/14508	9001835	7967,4361	1998	4166	6164	SO:0001819	synonymous_variant	94025	exon53			ACTCATGGGTCCA	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.40413C>T	19.37:g.9001835G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	1378	0.6309523809523809	210	0.4268292682926829	258	0.712707182320442	383	0.6695804195804196	527	0.6952506596306068	.	1.947	-0.442185	0.04604	0.467467	0.731997	ENSG00000181143	ENST00000542240	.	.	.	1.04	-2.08	0.07254	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.37033	-0.9723	4	0.12430	T	0.62	.	4.6521	0.12599	0.467:0.0:0.533:0.0	rs12985778	.	.	.	L	311	.	ENSP00000370334:P311L	P	-	2	0	MUC16	8862835	0.000000	0.05858	0.001000	0.08648	0.087000	0.18053	-0.128000	0.10531	-0.730000	0.04869	-0.798000	0.03219	CCA	G|0.353;A|0.647	0.647	strong		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PHYH	5264	hgsc.bcm.edu	37	10	13340236	13340236	+	Missense_Mutation	SNP	G	G	A	rs28938169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:13340236G>A	ENST00000263038.4	-	2	143	c.85C>T	c.(85-87)Ccc>Tcc	p.P29S	PHYH_ENST00000396913.2_Intron|PHYH_ENST00000396920.3_Missense_Mutation_p.P10S	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	29			P -> S (in RD; unknown pathological significance; dbSNP:rs28938169). {ECO:0000269|PubMed:10767344}.		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)	CCTGAAGTGGGATGAGCTACC	0.398													G|||	489	0.0976438	0.1165	0.0965	5008	,	,		16847	0.0238		0.173	False		,,,				2504	0.0716				p.P29S		Atlas-SNP	.											PHYH,NS,malignant_melanoma,+2,2	PHYH	50	2	0			c.C85T	GRCh37	CM001290	PHYH	M	rs28938169	PASS	.	G	,SER/PRO	539,3867	240.9+/-251.5	36,467,1700	51.0	51.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,85	3.3	0.0	10	dbSNP_125	51	1524,7076	285.7+/-297.3	136,1252,2912	yes	intron,missense	PHYH	NM_001037537.1,NM_006214.3	,74	172,1719,4612	AA,AG,GG		17.7209,12.2333,15.8619	,benign	,29/339	13340236	2063,10943	2203	4300	6503	SO:0001583	missense	5264	exon2			AAGTGGGATGAGC		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.85C>T	10.37:g.13340236G>A	ENSP00000263038:p.Pro29Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	131	53	0.40458	NM_006214	A8MTS8|B1ALH5	Missense_Mutation	SNP	ENST00000263038.4	37	CCDS7097.1	233	0.10668498168498168	50	0.1016260162601626	39	0.10773480662983426	13	0.022727272727272728	131	0.17282321899736147	G	8.826	0.938836	0.18281	0.122333	0.177209	ENSG00000107537	ENST00000263038;ENST00000396920;ENST00000479604	D;D;D	0.94376	-2.66;-2.68;-3.41	5.13	3.26	0.37387	.	0.388527	0.31673	N	0.007247	T	0.01254	0.0041	L	0.58669	1.825	0.27550	P	0.950518	B;B	0.26672	0.156;0.047	B;B	0.20384	0.029;0.017	T	0.50448	-0.8827	9	0.17832	T	0.49	-5.4561	9.8156	0.40851	0.1635:0.0:0.8365:0.0	rs28938169	10;29	B1ALH6;O14832	.;PAHX_HUMAN	S	29;10;29	ENSP00000263038:P29S;ENSP00000380126:P10S;ENSP00000420117:P29S	ENSP00000263038:P29S	P	-	1	0	PHYH	13380242	0.991000	0.36638	0.004000	0.12327	0.201000	0.24016	2.237000	0.43061	0.542000	0.28846	0.561000	0.74099	CCC	G|0.858;A|0.142	0.142	strong		0.398	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2		
ZNF57	126295	hgsc.bcm.edu	37	19	2917522	2917522	+	Silent	SNP	G	G	A	rs61754924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917522G>A	ENST00000306908.5	+	4	1051	c.903G>A	c.(901-903)acG>acA	p.T301T	ZNF57_ENST00000523428.1_Silent_p.T269T|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	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)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGAGAAGACGCACACGGGAG	0.488													G|||	130	0.0259585	0.0257	0.0288	5008	,	,		19252	0.0		0.0169	False		,,,				2504	0.0603				p.T301T	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G903A						PASS	.	G		95,4311	77.3+/-115.6	0,95,2108	75.0	79.0	78.0		903	-4.5	0.0	19	dbSNP_129	78	209,8391	88.6+/-150.9	4,201,4095	no	coding-synonymous	ZNF57	NM_173480.2		4,296,6203	AA,AG,GG		2.4302,2.1562,2.3374		301/556	2917522	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	126295	exon4			GAAGACGCACACG	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.903G>A	19.37:g.2917522G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_173480	Q8N6R9	Silent	SNP	ENST00000306908.5	37	CCDS12098.1																																																																																			G|0.973;A|0.027	0.027	strong		0.488	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
DCHS1	8642	hgsc.bcm.edu	37	11	6648424	6648424	+	Missense_Mutation	SNP	G	G	A	rs4758443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6648424G>A	ENST00000299441.3	-	14	6257	c.5846C>T	c.(5845-5847)aCg>aTg	p.T1949M		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1949	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> M (in dbSNP:rs4758443).		branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCGCGCACCGTGATGGTGAC	0.612													G|||	1490	0.297524	0.1233	0.3372	5008	,	,		18735	0.4236		0.3728	False		,,,				2504	0.2975				p.T1949M		Atlas-SNP	.											DCHS1,colon,carcinoma,0,1	DCHS1	277	1	0			c.C5846T						PASS	.	G	MET/THR	758,3644	302.4+/-287.4	78,602,1521	88.0	73.0	78.0		5846	2.3	0.4	11	dbSNP_111	78	3160,5432	468.9+/-367.4	568,2024,1704	yes	missense	DCHS1	NM_003737.2	81	646,2626,3225	AA,AG,GG		36.7784,17.2194,30.1524	benign	1949/3299	6648424	3918,9076	2201	4296	6497	SO:0001583	missense	8642	exon14			CGCACCGTGATGG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.5846C>T	11.37:g.6648424G>A	ENSP00000299441:p.Thr1949Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	728	0.3333333333333333	61	0.12398373983739837	124	0.3425414364640884	254	0.44405594405594406	289	0.3812664907651715	G	0.539	-0.854540	0.02630	0.172194	0.367784	ENSG00000166341	ENST00000299441	T	0.01838	4.61	5.18	2.32	0.28847	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.48286	D	0.000181	T	0.00012	0.0000	M	0.75447	2.3	0.53005	P	3.6999999999953737E-5	B	0.17667	0.023	B	0.14023	0.01	T	0.41875	-0.9484	9	0.41790	T	0.15	.	5.9633	0.19310	0.2566:0.0:0.6189:0.1246	rs4758443;rs52796770;rs61481044;rs4758443	1949	Q96JQ0	PCD16_HUMAN	M	1949	ENSP00000299441:T1949M	ENSP00000299441:T1949M	T	-	2	0	DCHS1	6605000	0.423000	0.25482	0.399000	0.26333	0.063000	0.16089	0.935000	0.28924	0.359000	0.24239	-1.450000	0.01041	ACG	G|0.687;A|0.313	0.313	strong		0.612	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
TJP3	27134	hgsc.bcm.edu	37	19	3738971	3738971	+	Silent	SNP	A	A	G	rs600986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3738971A>G	ENST00000541714.2	+	13	1932	c.1470A>G	c.(1468-1470)ccA>ccG	p.P490P	TJP3_ENST00000262968.9_Silent_p.P523P|TJP3_ENST00000589378.1_Silent_p.P499P|TJP3_ENST00000587686.1_Silent_p.P509P|TJP3_ENST00000382008.3_Silent_p.P504P|TJP3_ENST00000539908.2_Silent_p.P454P	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	490	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)		AGCCCAGTCCACCGTCTGGCC	0.657													G|||	3498	0.698482	0.7179	0.8112	5008	,	,		18069	0.6181		0.667	False		,,,				2504	0.7076				p.P499P		Atlas-SNP	.											.	TJP3	79	.	0			c.A1497G						PASS	.	G		3173,1233	424.0+/-340.3	1134,905,164	56.0	55.0	55.0		1569	-8.6	0.3	19	dbSNP_83	55	5683,2917	454.4+/-363.5	1871,1941,488	no	coding-synonymous	TJP3	NM_014428.1		3005,2846,652	GG,GA,AA		33.9186,27.9846,31.9083		523/953	3738971	8856,4150	2203	4300	6503	SO:0001819	synonymous_variant	27134	exon13			CAGTCCACCGTCT	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.1470A>G	19.37:g.3738971A>G		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	209	102	0.488038	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			A|0.311;G|0.689	0.689	strong		0.657	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
SEMA6D	80031	hgsc.bcm.edu	37	15	48058071	48058071	+	Missense_Mutation	SNP	G	G	A	rs532598	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000536845.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000389432.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000358066.4_Missense_Mutation_p.S478N|SEMA6D_ENST00000389433.2_Missense_Mutation_p.S478N|SEMA6D_ENST00000558014.1_Missense_Mutation_p.S478N|SEMA6D_ENST00000355997.3_Missense_Mutation_p.S478N|SEMA6D_ENST00000354744.4_Missense_Mutation_p.S478N|SEMA6D_ENST00000558816.1_Missense_Mutation_p.S478N|SEMA6D_ENST00000389428.3_Missense_Mutation_p.S478N	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	478	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		S -> N (in dbSNP:rs532598).		axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AATAGGTGCAGTGCTGAGAAT	0.408													g|||	2332	0.465655	0.5817	0.3617	5008	,	,		20797	0.6032		0.3509	False		,,,				2504	0.3589				p.S478N		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G1433A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	2581,1815	637.1+/-396.7	752,1077,369	155.0	133.0	140.0		1433,1433,1433,1433,1433,1433	-1.9	0.8	15	dbSNP_83	140	2874,5720	451.8+/-362.8	490,1894,1913	yes	missense,missense,missense,missense,missense,missense	SEMA6D	NM_001198999.1,NM_020858.1,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	46,46,46,46,46,46	1242,2971,2282	AA,AG,GG		33.4419,41.2875,41.9938	benign,benign,benign,benign,benign,benign	478/1012,478/1012,478/999,478/1018,478/1074,478/598	48058071	5455,7535	2198	4297	6495	SO:0001583	missense	80031	exon14			GGTGCAGTGCTGA	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1433G>A	15.37:g.48058071G>A	ENSP00000324857:p.Ser478Asn	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	112	69	0.616071	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	
KIAA0895	23366	hgsc.bcm.edu	37	7	36396735	36396735	+	Missense_Mutation	SNP	G	G	C	rs199774798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:36396735G>C	ENST00000297063.6	-	3	693	c.643C>G	c.(643-645)Cca>Gca	p.P215A	KIAA0895_ENST00000317020.6_Missense_Mutation_p.P164A|KIAA0895_ENST00000415803.2_Missense_Mutation_p.P202A|KIAA0895_ENST00000453212.1_Intron|KIAA0895_ENST00000338533.5_Missense_Mutation_p.P202A|KIAA0895_ENST00000436884.1_Missense_Mutation_p.P64A|KIAA0895_ENST00000440378.1_Missense_Mutation_p.P164A|KIAA0895_ENST00000480192.1_Intron	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	215										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TTTGGCTTTGGAAGAGTGGAG	0.413													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21233	0.0		0.001	False		,,,				2504	0.0				p.P215A		Atlas-SNP	.											.	KIAA0895	89	.	0			c.C643G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	3,3749		0,3,1873	93.0	88.0	90.0		643,490,604,190,490	3.7	0.4	7		90	0,8236		0,0,4118	yes	missense,missense,missense,missense,missense	KIAA0895	NM_001100425.1,NM_001199706.1,NM_001199707.1,NM_001199708.1,NM_015314.2	27,27,27,27,27	0,3,5991	CC,CG,GG		0.0,0.08,0.025	benign,benign,benign,benign,benign	215/521,164/518,202/508,64/418,164/470	36396735	3,11985	1876	4118	5994	SO:0001583	missense	23366	exon3			GCTTTGGAAGAGT	BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.643C>G	7.37:g.36396735G>C	ENSP00000297063:p.Pro215Ala	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	235	105	0.446809	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	.	.	.	.	.	.	.	.	.	.	G	2.506	-0.314008	0.05422	8.0E-4	0.0	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000415803;ENST00000429651	.	.	.	5.65	3.69	0.42338	.	0.385185	0.30028	N	0.010586	T	0.24236	0.0587	N	0.15975	0.35	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.001;0.001;0.001;0.0	T	0.13124	-1.0521	9	0.20046	T	0.44	-27.7009	11.557	0.50755	0.0:0.2899:0.5506:0.1596	.	164;164;64;202;215;202;164	B4DGN6;B7ZLT4;B4DF35;Q8NCT3-4;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;.;.;K0895_HUMAN;.;.	A	215;202;164;164;64;202;82	.	ENSP00000297063:P215A	P	-	1	0	KIAA0895	36363260	0.003000	0.15002	0.448000	0.26945	0.245000	0.25701	0.026000	0.13599	1.365000	0.46057	0.563000	0.77884	CCA	.	.	weak		0.413	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314	
MYH7B	57644	hgsc.bcm.edu	37	20	33574765	33574765	+	Silent	SNP	T	T	C	rs3746446	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:33574765T>C	ENST00000262873.7	+	13	1199	c.1107T>C	c.(1105-1107)aaT>aaC	p.N369N		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	327	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)			ACAACATGAATGATGGGGAGG	0.607													T|||	874	0.174521	0.1649	0.134	5008	,	,		19281	0.1071		0.1948	False		,,,				2504	0.2648				p.N369N		Atlas-SNP	.											.	MYH7B	145	.	0			c.T1107C						PASS	.	T		739,3525		55,629,1448	96.0	95.0	96.0		1107	-4.6	0.4	20	dbSNP_107	96	1653,6811		158,1337,2737	no	coding-synonymous	MYH7B	NM_020884.3		213,1966,4185	CC,CT,TT		19.5298,17.3311,18.7932		369/1984	33574765	2392,10336	2132	4232	6364	SO:0001819	synonymous_variant	57644	exon15			CATGAATGATGGG	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.1107T>C	20.37:g.33574765T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			T|0.819;C|0.181	0.181	strong		0.607	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
PLB1	151056	hgsc.bcm.edu	37	2	28865760	28865760	+	Silent	SNP	T	T	C	rs2272387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:28865760T>C	ENST00000327757.5	+	58	4254	c.4210T>C	c.(4210-4212)Ttg>Ctg	p.L1404L	AC074011.2_ENST00000431376.1_RNA|PLB1_ENST00000422425.2_Silent_p.L1393L|PLB1_ENST00000541605.1_Silent_p.L369L	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1404	Necessary for membrane localization. {ECO:0000250}.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					GAACAGCCGATTGCTCCCAGA	0.617													C|||	1940	0.38738	0.4962	0.2637	5008	,	,		16583	0.3591		0.4125	False		,,,				2504	0.3313				p.L1404L		Atlas-SNP	.											.	PLB1	255	.	0			c.T4210C						PASS	.	C	,	2160,2246		501,1158,544	37.0	35.0	35.0		4177,4210	2.8	0.0	2	dbSNP_100	35	3329,5271		657,2015,1628	no	coding-synonymous,coding-synonymous	PLB1	NM_001170585.1,NM_153021.4	,	1158,3173,2172	CC,CT,TT		38.7093,49.0241,42.2036	,	1393/1448,1404/1459	28865760	5489,7517	2203	4300	6503	SO:0001819	synonymous_variant	151056	exon58			AGCCGATTGCTCC		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.4210T>C	2.37:g.28865760T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	876	0.4010989010989011	253	0.5142276422764228	104	0.287292817679558	193	0.3374125874125874	326	0.43007915567282323	C	4.832	0.154611	0.09236	0.490241	0.387093	ENSG00000163803	ENST00000436775	.	.	.	5.7	2.85	0.33270	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.46762	-0.9168	3	.	.	.	-0.39	2.6537	0.05005	0.1504:0.5432:0.1454:0.1611	rs2272387;rs2272387	.	.	.	T	106	.	.	I	+	2	0	PLB1	28719264	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.364000	0.07583	0.053000	0.16036	-0.119000	0.15052	ATT	T|0.595;C|0.405	0.405	strong		0.617	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
IGFN1	91156	hgsc.bcm.edu	37	1	201190732	201190732	+	Silent	SNP	G	G	A	rs3738269	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201190732G>A	ENST00000335211.4	+	19	10189	c.10059G>A	c.(10057-10059)gtG>gtA	p.V3353V	RP11-567E21.3_ENST00000453155.1_RNA|IGFN1_ENST00000295591.8_Silent_p.V513V	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	896						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CGTGCCATGTGGGCACCGTGC	0.637													G|||	1105	0.220647	0.1135	0.2464	5008	,	,		18470	0.255		0.2694	False		,,,				2504	0.2618				p.V3353V		Atlas-SNP	.											IGFN1_ENST00000335211,NS,carcinoma,0,4	IGFN1	220	4	0			c.G10059A						PASS	.	G		663,3743	277.5+/-273.7	53,557,1593	51.0	42.0	45.0		10059	-2.2	0.1	1	dbSNP_107	45	2373,6227	388.2+/-342.5	339,1695,2266	no	coding-synonymous	IGFN1	NM_001164586.1		392,2252,3859	AA,AG,GG		27.593,15.0477,23.3431		3353/3709	201190732	3036,9970	2203	4300	6503	SO:0001819	synonymous_variant	91156	exon19			CCATGTGGGCACC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.10059G>A	1.37:g.201190732G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	199	99	0.497487	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	528	0.24175824175824176	64	0.13008130081300814	90	0.24861878453038674	151	0.263986013986014	223	0.2941952506596306	G	5.257	0.232928	0.09969	0.150477	0.27593	ENSG00000163395	ENST00000412892	.	.	.	4.64	-2.23	0.06930	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41142	-0.9525	3	.	.	.	.	1.0589	0.01596	0.4369:0.1254:0.2305:0.2072	rs3738269;rs3738269	.	.	.	R	771	.	.	G	+	1	0	IGFN1	199457355	0.000000	0.05858	0.070000	0.20053	0.049000	0.14656	-1.111000	0.03303	0.082000	0.17018	-0.727000	0.03589	GGG	G|0.775;A|0.225	0.225	strong		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
ILK	3611	hgsc.bcm.edu	37	11	6630833	6630833	+	Silent	SNP	G	G	A	rs1043390	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6630833G>A	ENST00000396751.2	+	8	1275	c.819G>A	c.(817-819)ccG>ccA	p.P273P	ILK_ENST00000537806.1_Silent_p.P139P|ILK_ENST00000299421.4_Silent_p.P273P|ILK_ENST00000528995.1_Silent_p.P212P|ILK_ENST00000526711.1_3'UTR|ILK_ENST00000420936.2_Silent_p.P273P|TAF10_ENST00000531760.1_5'Flank|RP11-732A19.2_ENST00000527398.1_RNA	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	223	0	0		WXS	Illumina HiSeq	Phase_I	237	122	0.514768	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	
TAF8	129685	hgsc.bcm.edu	37	6	42044945	42044945	+	Silent	SNP	G	G	A	rs3800286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42044945G>A	ENST00000372977.3	+	8	906	c.888G>A	c.(886-888)cgG>cgA	p.R296R	TAF8_ENST00000456846.2_Silent_p.R296R|TAF8_ENST00000465926.1_Silent_p.R220R|TAF8_ENST00000372982.4_Missense_Mutation_p.G337D|TAF8_ENST00000494547.1_Missense_Mutation_p.G337D	NM_138572.2	NP_612639.2	Q7Z7C8	TAF8_HUMAN	TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa	296					cell differentiation (GO:0030154)|inner cell mass cell proliferation (GO:0001833)|maintenance of protein location in nucleus (GO:0051457)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fat cell differentiation (GO:0045598)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcription factor TFIID complex (GO:0005669)				endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)			CTTATCTGCGGCCGGTGAAGA	0.577													G|||	3380	0.67492	0.441	0.7291	5008	,	,		17844	0.8988		0.6928	False		,,,				2504	0.7035				p.R296R		Atlas-SNP	.											.	TAF8	25	.	0			c.G888A						PASS	.	G		1941,1929		488,965,482	77.0	80.0	79.0		888	-6.4	0.1	6	dbSNP_107	79	5890,2380		2084,1722,329	no	coding-synonymous	TAF8	NM_138572.2		2572,2687,811	AA,AG,GG		28.7787,49.845,35.4942		296/311	42044945	7831,4309	1935	4135	6070	SO:0001819	synonymous_variant	129685	exon8			TCTGCGGCCGGTG	AK057383	CCDS43462.1	6p21.1	2008-10-23	2007-07-30	2007-07-30	ENSG00000137413	ENSG00000137413			17300	protein-coding gene	gene with protein product		609514	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 45/50kDa"", ""taube nuss homolog (mouse)"""	TBN			Standard	NM_138572		Approved	FLJ32821, TAF(II)43	uc003ors.3	Q7Z7C8	OTTHUMG00000014692	ENST00000372977.3:c.888G>A	6.37:g.42044945G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	140	0.985915	NM_138572	Q5T0K1|Q8N4R9|Q96M52	Silent	SNP	ENST00000372977.3	37	CCDS43462.1	1537	0.7037545787545788	230	0.46747967479674796	266	0.7348066298342542	508	0.8881118881118881	533	0.7031662269129287	G	18.31	3.595707	0.66219	0.50155	0.712213	ENSG00000137413	ENST00000494547;ENST00000372982	.	.	.	5.85	-6.41	0.01938	.	.	.	.	.	T	0.09202	0.0227	.	.	.	0.09310	P	0.9999999999997656	B	0.02656	0.0	B	0.08055	0.003	T	0.27297	-1.0078	6	0.87932	D	0	.	3.1284	0.06415	0.4255:0.2999:0.181:0.0936	rs3800286;rs59113735;rs3800286	337	Q7Z7C8-4	.	D	337	.	ENSP00000362073:G337D	G	+	2	0	TAF8	42152923	0.122000	0.22280	0.055000	0.19348	0.858000	0.48976	-0.539000	0.06113	-1.955000	0.01023	-0.345000	0.07892	GGC	G|0.303;A|0.697	0.697	strong		0.577	TAF8-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357901.1	NM_138572	
VENTX	27287	hgsc.bcm.edu	37	10	135053721	135053721	+	Missense_Mutation	SNP	C	C	A	rs9419033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:135053721C>A	ENST00000325980.9	+	3	1199	c.688C>A	c.(688-690)Cct>Act	p.P230T		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	230					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)		GTCCCACCCCCCTACCCCAGG	0.697													C|||	512	0.102236	0.1157	0.1354	5008	,	,		8556	0.0823		0.0586	False		,,,				2504	0.1258				p.P230T		Atlas-SNP	.											.	VENTX	24	.	0			c.C688A						PASS	.	C	THR/PRO	455,3869		21,413,1728	10.0	12.0	11.0		688	0.2	0.0	10	dbSNP_119	11	498,7952		18,462,3745	no	missense	VENTX	NM_014468.2	38	39,875,5473	AA,AC,CC		5.8935,10.5227,7.4605	probably-damaging	230/259	135053721	953,11821	2162	4225	6387	SO:0001583	missense	27287	exon3			CACCCCCCTACCC	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.688C>A	10.37:g.135053721C>A	ENSP00000357556:p.Pro230Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	197	0.0902014652014652	63	0.12804878048780488	46	0.1270718232044199	47	0.08216783216783216	41	0.05408970976253298	C	12.69	2.015024	0.35511	0.105227	0.058935	ENSG00000151650	ENST00000325980	D	0.91686	-2.89	2.3	0.163	0.14986	.	0.155217	0.42420	U	0.000701	T	0.04497	0.0123	N	0.24115	0.695	0.80722	P	0.0	D	0.57899	0.981	B	0.43783	0.431	T	0.59354	-0.7470	9	0.87932	D	0	.	4.5335	0.12017	0.2529:0.4995:0.2476:0.0	rs9419033	230	O95231	VENTX_HUMAN	T	230	ENSP00000357556:P230T	ENSP00000357556:P230T	P	+	1	0	VENTX	134903711	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.502000	0.22594	0.042000	0.15717	0.442000	0.29010	CCT	C|0.917;A|0.083	0.083	strong		0.697	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
GSG1L	146395	hgsc.bcm.edu	37	16	27840271	27840271	+	Silent	SNP	C	C	T	rs117918036	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:27840271C>T	ENST00000447459.2	-	5	753	c.669G>A	c.(667-669)gcG>gcA	p.A223A	GSG1L_ENST00000380898.2_Silent_p.A68A|GSG1L_ENST00000569166.1_Silent_p.A68A|GSG1L_ENST00000395724.3_Silent_p.A172A|GSG1L_ENST00000380897.3_Silent_p.A68A	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	223					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						AGGAGCCCCACGCCAGGCTGC	0.562													C|||	53	0.0105831	0.0	0.0173	5008	,	,		18026	0.001		0.0348	False		,,,				2504	0.0051				p.A223A		Atlas-SNP	.											.	GSG1L	82	.	0			c.G669A						PASS	.	C	,	29,4365	35.2+/-66.4	0,29,2168	47.0	38.0	41.0		669,204	0.4	1.0	16	dbSNP_132	41	325,8275	114.2+/-174.2	7,311,3982	no	coding-synonymous,coding-synonymous	GSG1L	NM_001109763.1,NM_144675.2	,	7,340,6150	TT,TC,CC		3.7791,0.66,2.7243	,	223/332,68/177	27840271	354,12640	2197	4300	6497	SO:0001819	synonymous_variant	146395	exon5			GCCCCACGCCAGG	AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.669G>A	16.37:g.27840271C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_001109763	Q7Z6F8|Q8TB81	Silent	SNP	ENST00000447459.2	37	CCDS45450.1																																																																																			C|0.977;T|0.023	0.023	strong		0.562	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675	
BBS12	166379	hgsc.bcm.edu	37	4	123664446	123664446	+	Missense_Mutation	SNP	G	G	A	rs13135778	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123664446G>A	ENST00000314218.3	+	2	1592	c.1399G>A	c.(1399-1401)Gac>Aac	p.D467N	BBS12_ENST00000542236.1_Missense_Mutation_p.D467N	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	467			D -> N (in dbSNP:rs13135778). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TTGTGTGGGCGACGGGGTCTG	0.468									Bardet-Biedl syndrome				A|||	464	0.0926518	0.0514	0.1052	5008	,	,		19474	0.0		0.2127	False		,,,				2504	0.1115				p.D467N		Atlas-SNP	.											.	BBS12	63	.	0			c.G1399A						PASS	.	A	ASN/ASP,ASN/ASP	304,4102	798.2+/-415.5	15,274,1914	80.0	79.0	79.0		1399,1399	1.9	0.0	4	dbSNP_121	79	1941,6659	725.5+/-406.6	230,1481,2589	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	23,23	245,1755,4503	AA,AG,GG		22.5698,6.8997,17.2613	benign,benign	467/711,467/711	123664446	2245,10761	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GTGGGCGACGGGG	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1399G>A	4.37:g.123664446G>A	ENSP00000319062:p.Asp467Asn	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	142	51	0.359155	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	238	0.10897435897435898	32	0.06504065040650407	42	0.11602209944751381	0	0.0	164	0.21635883905013192	A	0.015	-1.552873	0.00918	0.068997	0.225698	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.78246	-1.16;-1.16	5.69	1.9	0.25705	.	1.320260	0.04713	N	0.418035	T	0.00039	0.0001	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05099	-1.0906	9	0.07813	T	0.8	-38.0042	9.6017	0.39607	0.7363:0.0:0.2637:0.0	rs13135778;rs17857450;rs13135778	467	Q6ZW61	BBS12_HUMAN	N	467	ENSP00000319062:D467N;ENSP00000438273:D467N	ENSP00000319062:D467N	D	+	1	0	BBS12	123883896	0.000000	0.05858	0.033000	0.17914	0.138000	0.21146	0.602000	0.24134	-0.117000	0.11872	-0.269000	0.10298	GAC	G|0.857;A|0.143	0.143	strong		0.468	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
PLCL2	23228	hgsc.bcm.edu	37	3	17051328	17051328	+	Silent	SNP	T	T	C	rs7653834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:17051328T>C	ENST00000418129.2	+	2	577	c.112T>C	c.(112-114)Tta>Cta	p.L38L	PLCL2_ENST00000460467.1_3'UTR|PLCL2_ENST00000396755.2_Silent_p.L38L|PLCL2_ENST00000432376.1_Silent_p.L38L	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	166	0	0		WXS	Illumina HiSeq	Phase_I	163	90	0.552147	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		
KNG1	3827	hgsc.bcm.edu	37	3	186459475	186459475	+	Missense_Mutation	SNP	C	C	G	rs5030084	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:186459475C>G	ENST00000265023.4	+	10	1502	c.1290C>G	c.(1288-1290)gaC>gaG	p.D430E	KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_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	118	0	0		WXS	Illumina HiSeq	Phase_I	132	48	0.363636	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	
UPK1A	11045	hgsc.bcm.edu	37	19	36157740	36157740	+	Missense_Mutation	SNP	C	C	T	rs61741212	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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|UPK1A-AS1_ENST00000443196.1_RNA|RN7SL765P_ENST00000580260.1_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	169	0	0		WXS	Illumina HiSeq	Phase_I	216	97	0.449074	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		
SLC17A4	10050	hgsc.bcm.edu	37	6	25779392	25779392	+	Silent	SNP	A	A	G	rs9358890	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25779392A>G	ENST00000377905.4	+	12	1589	c.1470A>G	c.(1468-1470)aaA>aaG	p.K490K	SLC17A4_ENST00000397076.2_3'UTR|SLC17A4_ENST00000439485.2_Silent_p.K260K	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	490					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						ACTGGGCTAAAGAGCAGACAT	0.473													A|||	973	0.194289	0.0408	0.245	5008	,	,		20093	0.4921		0.0398	False		,,,				2504	0.2178				p.K490K		Atlas-SNP	.											.	SLC17A4	79	.	0			c.A1470G						PASS	.	A		208,4198	128.6+/-165.4	8,192,2003	184.0	173.0	177.0		1470	0.3	0.0	6	dbSNP_119	177	394,8206	126.0+/-184.5	5,384,3911	no	coding-synonymous	SLC17A4	NM_005495.2		13,576,5914	GG,GA,AA		4.5814,4.7208,4.6286		490/498	25779392	602,12404	2203	4300	6503	SO:0001819	synonymous_variant	10050	exon12			GGCTAAAGAGCAG	AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"""Solute carriers"""	10932	protein-coding gene	gene with protein product		604216	"""solute carrier family 17 (sodium phosphate), member 4"""			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.1470A>G	6.37:g.25779392A>G		Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	249	116	0.465863	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Silent	SNP	ENST00000377905.4	37	CCDS4564.1																																																																																			A|0.877;G|0.123	0.123	strong		0.473	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1		
NXPH4	11247	hgsc.bcm.edu	37	12	57619362	57619362	+	Silent	SNP	G	G	A	rs10783816	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	96	40	0.416667	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	
EPB41L5	57669	hgsc.bcm.edu	37	2	120848049	120848049	+	Missense_Mutation	SNP	C	C	T	rs28930677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:120848049C>T	ENST00000263713.5	+	12	1214	c.1000C>T	c.(1000-1002)Cat>Tat	p.H334Y	EPB41L5_ENST00000443902.2_Missense_Mutation_p.H334Y|EPB41L5_ENST00000331393.4_Missense_Mutation_p.H334Y|EPB41L5_ENST00000452780.1_Missense_Mutation_p.H334Y|EPB41L5_ENST00000443124.1_Missense_Mutation_p.H334Y	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	334			H -> Y (in dbSNP:rs28930677).		actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						AAAGAGTTCTCATCGATCAGG	0.388													C|||	109	0.0217652	0.003	0.0173	5008	,	,		19043	0.001		0.0467	False		,,,				2504	0.046				p.H334Y		Atlas-SNP	.											.	EPB41L5	98	.	0			c.C1000T						PASS	.	C	TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS	51,4355	50.9+/-86.3	0,51,2152	149.0	140.0	143.0		1000,1000,1000,1000	4.4	1.0	2	dbSNP_125	143	409,8191	128.8+/-187.0	14,381,3905	yes	missense,missense,missense,missense	EPB41L5	NM_001184937.1,NM_001184938.1,NM_001184939.1,NM_020909.3	83,83,83,83	14,432,6057	TT,TC,CC		4.7558,1.1575,3.5368	benign,benign,benign,benign	334/688,334/506,334/506,334/734	120848049	460,12546	2203	4300	6503	SO:0001583	missense	57669	exon12			AGTTCTCATCGAT	AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.1000C>T	2.37:g.120848049C>T	ENSP00000263713:p.His334Tyr	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	121	66	0.545455	NM_020909	Q7Z5S1|Q8IZ12|Q9H975	Missense_Mutation	SNP	ENST00000263713.5	37	CCDS2130.1	52	0.023809523809523808	0	0.0	8	0.022099447513812154	0	0.0	44	0.05804749340369393	C	4.886	0.164702	0.09287	0.011575	0.047558	ENSG00000115109	ENST00000263713;ENST00000443902;ENST00000331393;ENST00000443124;ENST00000452780	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.41	4.41	0.53225	.	0.529047	0.19160	N	0.121216	T	0.23370	0.0565	L	0.32530	0.975	0.33877	D	0.63565	B;B;B;B	0.34264	0.134;0.446;0.059;0.318	B;B;B;B	0.34346	0.045;0.18;0.028;0.087	T	0.63319	-0.6664	10	0.33141	T	0.24	.	11.2184	0.48840	0.3907:0.6093:0.0:0.0	rs28930677;rs28930677	334;334;334;334	Q9HCM4-3;Q9HCM4-4;Q9HCM4-2;Q9HCM4	.;.;.;E41L5_HUMAN	Y	334	ENSP00000263713:H334Y;ENSP00000393856:H334Y;ENSP00000329687:H334Y;ENSP00000393722:H334Y;ENSP00000390439:H334Y	ENSP00000263713:H334Y	H	+	1	0	EPB41L5	120564519	0.848000	0.29623	0.951000	0.38953	0.953000	0.61014	2.512000	0.45485	2.704000	0.92352	0.585000	0.79938	CAT	C|0.971;T|0.029	0.029	strong		0.388	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909	
MCMDC2	157777	hgsc.bcm.edu	37	8	67786633	67786633	+	Missense_Mutation	SNP	C	C	T	rs79944926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:67786633C>T	ENST00000422365.2	+	3	338	c.167C>T	c.(166-168)gCt>gTt	p.A56V	MCMDC2_ENST00000469823.1_3'UTR|MCMDC2_ENST00000492775.1_Missense_Mutation_p.A56V|MCMDC2_ENST00000541540.1_Intron|MCMDC2_ENST00000313616.5_Missense_Mutation_p.A56V|MCMDC2_ENST00000396592.3_Missense_Mutation_p.A56V	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	56					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						GAATTAGATGCTGAGCTTGGA	0.294													C|||	162	0.0323482	0.0038	0.0648	5008	,	,		16014	0.0		0.0785	False		,,,				2504	0.0337				p.A56V		Atlas-SNP	.											.	MCMDC2	84	.	0			c.C167T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	69,4337	61.1+/-98.1	2,65,2136	75.0	76.0	76.0		167,167,167	4.4	1.0	8	dbSNP_131	76	773,7825	182.8+/-231.1	43,687,3569	yes	missense,missense,missense	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	64,64,64	45,752,5705	TT,TC,CC		8.9905,1.566,6.4749	probably-damaging,probably-damaging,probably-damaging	56/633,56/591,56/682	67786633	842,12162	2203	4299	6502	SO:0001583	missense	157777	exon3			TAGATGCTGAGCT	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.167C>T	8.37:g.67786633C>T	ENSP00000413632:p.Ala56Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	75	0.034340659340659344	0	0.0	23	0.06353591160220995	0	0.0	52	0.06860158311345646	C	24.4	4.530143	0.85706	0.01566	0.089905	ENSG00000178460	ENST00000396592;ENST00000422365;ENST00000492775;ENST00000313616	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	4.4	4.4	0.53042	.	0.058197	0.64402	D	0.000001	T	0.02193	0.0068	L	0.60455	1.87	0.80722	D	1	B;B;B	0.28760	0.141;0.141;0.221	B;B;B	0.34652	0.091;0.091;0.187	T	0.03017	-1.1082	10	0.29301	T	0.29	-6.2505	17.3371	0.87285	0.0:1.0:0.0:0.0	.	56;56;56	Q4G0Z9;B4DXX4;G3XAN3	CH045_HUMAN;.;.	V	56	ENSP00000379837:A56V;ENSP00000413632:A56V;ENSP00000428037:A56V;ENSP00000317234:A56V	ENSP00000317234:A56V	A	+	2	0	C8orf45	67949187	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.188000	0.77739	2.158000	0.67659	0.557000	0.71058	GCT	C|0.946;T|0.054	0.054	strong		0.294	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518	
VENTX	27287	hgsc.bcm.edu	37	10	135053773	135053773	+	Missense_Mutation	SNP	G	G	A	rs9418953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:135053773G>A	ENST00000325980.9	+	3	1251	c.740G>A	c.(739-741)gGc>gAc	p.G247D		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	247			G -> D (in dbSNP:rs9418953).		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)		GGGCCCCGGGGCCTGTGTGCT	0.682													G|||	514	0.102636	0.1172	0.134	5008	,	,		9006	0.0833		0.0586	False		,,,				2504	0.1258				p.G247D		Atlas-SNP	.											.	VENTX	24	.	0			c.G740A						PASS	.	G	ASP/GLY	406,3688		18,370,1659	14.0	16.0	15.0		740	1.4	0.0	10	dbSNP_119	15	468,7704		17,434,3635	yes	missense	VENTX	NM_014468.2	94	35,804,5294	AA,AG,GG		5.7269,9.917,7.1254	benign	247/259	135053773	874,11392	2047	4086	6133	SO:0001583	missense	27287	exon3			CCCGGGGCCTGTG	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.740G>A	10.37:g.135053773G>A	ENSP00000357556:p.Gly247Asp	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	197	0.0902014652014652	63	0.12804878048780488	46	0.1270718232044199	47	0.08216783216783216	41	0.05408970976253298	G	6.517	0.463521	0.12402	0.09917	0.057269	ENSG00000151650	ENST00000325980	D	0.90732	-2.72	2.3	1.35	0.21983	.	0.745690	0.10930	U	0.618472	T	0.02571	0.0078	N	0.12182	0.205	0.80722	P	0.0	B	0.27951	0.195	B	0.25759	0.063	T	0.40887	-0.9539	9	0.16420	T	0.52	.	4.2397	0.10642	0.2123:0.0:0.7877:0.0	rs9418953	247	O95231	VENTX_HUMAN	D	247	ENSP00000357556:G247D	ENSP00000357556:G247D	G	+	2	0	VENTX	134903763	0.000000	0.05858	0.002000	0.10522	0.059000	0.15707	-0.781000	0.04648	0.508000	0.28173	0.442000	0.29010	GGC	G|0.919;A|0.081	0.081	strong		0.682	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
ABCC1	4363	hgsc.bcm.edu	37	16	16139714	16139714	+	Silent	SNP	T	T	C	rs35587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:16139714T>C	ENST00000399410.3	+	9	1237	c.1062T>C	c.(1060-1062)aaT>aaC	p.N354N	ABCC1_ENST00000345148.5_Silent_p.N354N|ABCC1_ENST00000346370.5_Silent_p.N354N|ABCC1_ENST00000399408.2_Silent_p.N354N|ABCC1_ENST00000351154.5_Silent_p.N354N|ABCC1_ENST00000349029.5_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	84	0	0	708	WXS	Illumina HiSeq	Phase_I	94	56	0.595745	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	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39497452	39497452	+	Missense_Mutation	SNP	A	A	G	rs139298	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39497452A>G	ENST00000401756.1	+	3	437	c.361A>G	c.(361-363)Aag>Gag	p.K121E	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.K121E|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.K121E|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.K121E	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	121			K -> E (in allele A3H-Var; haplotype 2; allele presenting a higher expression and more effective in retrotransposons and HIV-1 restriction; dbSNP:rs139298).|K -> N (in dbSNP:rs139299).	K -> D (in Ref. 2; CAG30367). {ECO:0000305}.	cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					GCCCCAGCAGAAGGGGCTGCG	0.592													G|||	2653	0.529752	0.8752	0.3876	5008	,	,		6308	0.3155		0.4771	False		,,,				2504	0.4387				p.K121E		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.A361G						PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	3557,849		1464,629,110	51.0	49.0	50.0		361,361,361,361	-6.7	0.0	22	dbSNP_78	50	3922,4678		899,2124,1277	yes	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	56,56,56,56	2363,2753,1387	GG,GA,AA		45.6047,19.2692,42.4958	benign,benign,benign,benign	121/183,121/201,121/155,121/184	39497452	7479,5527	2203	4300	6503	SO:0001583	missense	164668	exon3			CAGCAGAAGGGGC	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.361A>G	22.37:g.39497452A>G	ENSP00000385741:p.Lys121Glu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	1096	0.5018315018315018	427	0.8678861788617886	129	0.356353591160221	170	0.2972027972027972	370	0.48812664907651715	.	0.011	-1.720768	0.00700	0.807308	0.456047	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	3.33	-6.67	0.01783	.	.	.	.	.	T	0.00012	0.0000	N	0.02368	-0.58	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.18777	-1.0326	8	0.02654	T	1	-5.078	8.7069	0.34360	0.5333:0.1391:0.3276:0.0	rs139298;rs60094352;rs139298	121	B7TQM3	.	E	121	ENSP00000216123:K121E;ENSP00000411754:K121E;ENSP00000393520:K121E;ENSP00000385741:K121E	ENSP00000216123:K121E	K	+	1	0	APOBEC3H	37827398	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.684000	0.01932	-3.352000	0.00181	-1.473000	0.01005	AAG	A|0.449;G|0.551	0.551	strong		0.592	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
PTX4	390667	hgsc.bcm.edu	37	16	1537510	1537510	+	Silent	SNP	C	C	T	rs201970670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1537510C>T	ENST00000447419.2	-	2	628	c.603G>A	c.(601-603)ccG>ccA	p.P201P	PTX4_ENST00000293922.1_Silent_p.P196P|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long	201						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						TCAGGGAGGTCGGGCCCAGCT	0.726													C|||	13	0.00259585	0.0	0.0058	5008	,	,		14445	0.0		0.0089	False		,,,				2504	0.0				p.P196P		Atlas-SNP	.											.	PTX4	46	.	0			c.G588A						PASS	.	C		12,4368		0,12,2178	11.0	13.0	13.0		588	-10.4	0.0	16		13	113,8431		0,113,4159	no	coding-synonymous	PTX4	NM_001013658.1		0,125,6337	TT,TC,CC		1.3226,0.274,0.9672		196/474	1537510	125,12799	2190	4272	6462	SO:0001819	synonymous_variant	390667	exon2			GGAGGTCGGGCCC		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.603G>A	16.37:g.1537510C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				C|0.997;T|0.003	0.003	strong		0.726	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
FAM161A	84140	hgsc.bcm.edu	37	2	62067433	62067433	+	Missense_Mutation	SNP	T	T	C	rs17513722	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:62067433T>C	ENST00000405894.3	-	3	807	c.706A>G	c.(706-708)Att>Gtt	p.I236V	FAM161A_ENST00000404929.1_Missense_Mutation_p.I236V	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	236			I -> V (in dbSNP:rs17513722).		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						GGTACTGTAATTGTGGGCACC	0.383													T|||	583	0.116414	0.0408	0.1427	5008	,	,		20146	0.0863		0.2227	False		,,,				2504	0.1217				p.I236V		Atlas-SNP	.											FAM161A_ENST00000405894,colon,carcinoma,+2,3	FAM161A	200	3	0			c.A706G						PASS	.	T	VAL/ILE,VAL/ILE	273,3413		10,253,1580	155.0	138.0	143.0		706,706	4.4	0.4	2	dbSNP_123	143	1956,6208		238,1480,2364	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	29,29	248,1733,3944	CC,CT,TT		23.9588,7.4064,18.8101	benign,benign	236/717,236/661	62067433	2229,9621	1843	4082	5925	SO:0001583	missense	84140	exon3			CTGTAATTGTGGG		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.706A>G	2.37:g.62067433T>C	ENSP00000385893:p.Ile236Val	Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	231	117	0.506494	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	317	0.14514652014652016	23	0.046747967479674794	64	0.17679558011049723	56	0.0979020979020979	174	0.22955145118733508	T	12.18	1.860464	0.32884	0.074064	0.239588	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.30981	1.51;1.51	5.55	4.38	0.52667	.	0.219735	0.44285	D	0.000470	T	0.00012	0.0000	L	0.58428	1.81	0.34238	P	0.32269899999999996	P;B	0.49447	0.924;0.354	P;B	0.46543	0.52;0.138	T	0.26849	-1.0091	9	0.17369	T	0.5	-28.9171	7.9646	0.30091	0.0:0.0723:0.1388:0.7889	rs17513722;rs52827054;rs17513722	236;236	Q3B820;Q3B820-3	F161A_HUMAN;.	V	236	ENSP00000385158:I236V;ENSP00000385893:I236V	ENSP00000385158:I236V	I	-	1	0	FAM161A	61920937	0.782000	0.28689	0.442000	0.26870	0.375000	0.29983	1.029000	0.30140	0.919000	0.36945	0.533000	0.62120	ATT	T|0.844;C|0.156	0.156	strong		0.383	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
SCAF11	9169	hgsc.bcm.edu	37	12	46321514	46321514	+	Missense_Mutation	SNP	A	A	T	rs7315731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:46321514A>T	ENST00000369367.3	-	11	2203	c.1970T>A	c.(1969-1971)tTc>tAc	p.F657Y	SCAF11_ENST00000465950.1_Missense_Mutation_p.F342Y|SCAF11_ENST00000549162.1_Missense_Mutation_p.F465Y|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000419565.2_Missense_Mutation_p.F657Y	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	657			F -> Y (in dbSNP:rs7315731).		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						AATATTATTGAAATCTTCATT	0.323													A|||	1953	0.389976	0.1127	0.3674	5008	,	,		15472	0.5397		0.501	False		,,,				2504	0.5123				p.F657Y		Atlas-SNP	.											.	SCAF11	145	.	0			c.T1970A						PASS	.	A	TYR/PHE	729,3677	281.9+/-276.2	62,605,1536	56.0	58.0	57.0		1970	1.7	0.0	12	dbSNP_116	57	4337,4261	559.4+/-387.4	1118,2101,1080	yes	missense	SCAF11	NM_004719.2	22	1180,2706,2616	TT,TA,AA		49.558,16.5456,38.9572	benign	657/1464	46321514	5066,7938	2203	4299	6502	SO:0001583	missense	9169	exon11			TTATTGAAATCTT	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.1970T>A	12.37:g.46321514A>T	ENSP00000358374:p.Phe657Tyr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	877	0.4015567765567766	57	0.11585365853658537	131	0.36187845303867405	301	0.5262237762237763	388	0.5118733509234829	A	9.614	1.132054	0.21041	0.165456	0.50442	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.51325	1.36;2.09;1.35;2.09;0.71	5.4	1.74	0.24563	.	0.926509	0.09138	N	0.843359	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P;P	0.39391	0.531;0.671	B;B	0.40410	0.145;0.328	T	0.47032	-0.9148	9	0.49607	T	0.09	6.224	7.4396	0.27174	0.7465:0.0:0.2535:0.0	rs7315731;rs52792104;rs61371925;rs7315731	465;657	F8VXG7;Q99590	.;SCAFB_HUMAN	Y	342;657;465;657;597	ENSP00000449812:F342Y;ENSP00000358374:F657Y;ENSP00000448864:F465Y;ENSP00000413036:F657Y;ENSP00000446746:F597Y	ENSP00000358374:F657Y	F	-	2	0	SCAF11	44607781	0.000000	0.05858	0.000000	0.03702	0.276000	0.26787	-0.214000	0.09292	0.110000	0.17919	0.460000	0.39030	TTC	A|0.591;T|0.409	0.409	strong		0.323	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
C8A	731	hgsc.bcm.edu	37	1	57383357	57383357	+	Missense_Mutation	SNP	C	C	T	rs41285938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:57383357C>T	ENST00000361249.3	+	11	1819	c.1723C>T	c.(1723-1725)Cca>Tca	p.P575S		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	575	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		P -> L (in dbSNP:rs17300936).	P -> S (in Ref. 3; AAA82124). {ECO:0000305}.	complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GGCCTCGTGTCCAGGGCGGAA	0.567													C|||	17	0.00339457	0.0015	0.0043	5008	,	,		17631	0.0		0.0119	False		,,,				2504	0.0				p.P575S		Atlas-SNP	.											.	C8A	103	.	0			c.C1723T						PASS	.	C	SER/PRO	9,4397	15.5+/-35.6	0,9,2194	57.0	57.0	57.0		1723	4.8	0.5	1	dbSNP_127	57	94,8506	53.1+/-113.8	0,94,4206	yes	missense	C8A	NM_000562.2	74	0,103,6400	TT,TC,CC		1.093,0.2043,0.7919	benign	575/585	57383357	103,12903	2203	4300	6503	SO:0001583	missense	731	exon11			TCGTGTCCAGGGC	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.1723C>T	1.37:g.57383357C>T	ENSP00000354458:p.Pro575Ser	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	291	151	0.5189	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	11	0.005036630036630037	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	3.443	-0.113740	0.06881	0.002043	0.01093	ENSG00000157131	ENST00000361249	T	0.51574	0.7	4.82	4.82	0.62117	.	0.346426	0.30879	N	0.008683	T	0.14917	0.0360	N	0.04043	-0.29	0.09310	N	1	B	0.16603	0.018	B	0.12837	0.008	T	0.16837	-1.0389	10	0.08599	T	0.76	-1.0877	8.4137	0.32659	0.1563:0.5983:0.2454:0.0	rs41285938	575	P07357	CO8A_HUMAN	S	575	ENSP00000354458:P575S	ENSP00000354458:P575S	P	+	1	0	C8A	57155945	0.118000	0.22208	0.474000	0.27266	0.015000	0.08874	0.833000	0.27504	2.487000	0.83934	0.563000	0.77884	CCA	C|0.992;T|0.008	0.008	strong		0.567	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
TNC	3371	hgsc.bcm.edu	37	9	117804544	117804544	+	Silent	SNP	T	T	C	rs1061495	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000537320.1_Silent_p.T1097T|TNC_ENST00000542877.1_Silent_p.T1371T|TNC_ENST00000341037.4_Silent_p.T1552T|TNC_ENST00000340094.3_Silent_p.T1370T|TNC_ENST00000423613.2_Silent_p.T1461T|TNC_ENST00000345230.3_Silent_p.T1097T|TNC_ENST00000346706.3_Silent_p.T1188T	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	107	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	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	
SEC16A	9919	hgsc.bcm.edu	37	9	139371234	139371234	+	Silent	SNP	G	G	A	rs10781497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139371234G>A	ENST00000371706.3	-	1	333	c.300C>T	c.(298-300)gaC>gaT	p.D100D	SEC16A_ENST00000313050.7_Silent_p.D278D|SEC16A_ENST00000290037.6_Silent_p.D100D|SEC16A_ENST00000431893.2_Silent_p.D100D			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	100					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)		CGTCTCTTCCGTCACTGGGCA	0.552													G|||	696	0.138978	0.0386	0.2997	5008	,	,		18123	0.1577		0.1233	False		,,,				2504	0.1575				p.D278D		Atlas-SNP	.											.	SEC16A	249	.	0			c.C834T						PASS	.	G		216,3704		5,206,1749	30.0	35.0	33.0		834	-9.5	0.0	9	dbSNP_120	33	1165,7137		77,1011,3063	no	coding-synonymous	SEC16A	NM_014866.1		82,1217,4812	AA,AG,GG		14.0328,5.5102,11.2993		278/2358	139371234	1381,10841	1960	4151	6111	SO:0001819	synonymous_variant	9919	exon3			TCTTCCGTCACTG	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.300C>T	9.37:g.139371234G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.869;A|0.131	0.131	strong		0.552	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
SDCCAG8	10806	hgsc.bcm.edu	37	1	243579112	243579112	+	Silent	SNP	G	G	A	rs10927011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:243579112G>A	ENST00000366541.3	+	14	1843	c.1725G>A	c.(1723-1725)gaG>gaA	p.E575E	SDCCAG8_ENST00000355875.4_Silent_p.E532E|SDCCAG8_ENST00000343783.6_Silent_p.E430E	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	575	Gln-rich.|Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				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)		AGCAAATGGAGGCCCAGCATG	0.512													G|||	2201	0.439497	0.0938	0.5403	5008	,	,		19283	0.7847		0.498	False		,,,				2504	0.4192				p.E575E		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.G1725A						PASS	.	G		724,3682	297.3+/-284.7	64,596,1543	80.0	72.0	75.0		1725	1.5	1.0	1	dbSNP_120	75	4377,4223	582.0+/-391.3	1102,2173,1025	no	coding-synonymous	SDCCAG8	NM_006642.3		1166,2769,2568	AA,AG,GG		49.1047,16.4321,39.2204		575/714	243579112	5101,7905	2203	4300	6503	SO:0001819	synonymous_variant	10806	exon14			AATGGAGGCCCAG	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.1725G>A	1.37:g.243579112G>A		Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	302	133	0.440397	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Silent	SNP	ENST00000366541.3	37	CCDS31075.1																																																																																			G|0.576;A|0.424	0.424	strong		0.512	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	
STK33	65975	hgsc.bcm.edu	37	11	8486310	8486310	+	Silent	SNP	C	C	A	rs1446464	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8486310C>A	ENST00000447869.1	-	3	1317	c.399G>T	c.(397-399)gcG>gcT	p.A133A	STK33_ENST00000534493.1_Silent_p.A92A|STK33_ENST00000396672.1_Silent_p.A133A|STK33_ENST00000358872.3_5'UTR|STK33_ENST00000315204.1_Silent_p.A133A|STK33_ENST00000396673.1_Silent_p.A133A			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A133A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		CCTTGTCTGTCGCTTCAATGA	0.393													C|||	2229	0.445088	0.3411	0.3703	5008	,	,		16305	0.4871		0.4245	False		,,,				2504	0.6166				p.A133A		Atlas-SNP	.											STK33_ENST00000447869,NS,adenoma,0,2	STK33	147	2	1	Substitution - coding silent(1)	stomach(1)	c.G399T						PASS	.	C		1449,2953	467.0+/-354.7	248,953,1000	295.0	247.0	263.0		399	-5.1	0.1	11	dbSNP_88	263	3518,5074	512.9+/-378.0	721,2076,1499	no	coding-synonymous	STK33	NM_030906.2		969,3029,2499	AA,AC,CC		40.9451,32.9169,38.2253		133/515	8486310	4967,8027	2201	4296	6497	SO:0001819	synonymous_variant	65975	exon5			GTCTGTCGCTTCA	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.399G>T	11.37:g.8486310C>A		Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	377	150	0.397878	NM_030906	Q658S6|Q8NEF5	Silent	SNP	ENST00000447869.1	37	CCDS7789.1																																																																																			C|0.587;A|0.413	0.413	strong		0.393	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906	
NIPAL2	79815	hgsc.bcm.edu	37	8	99208190	99208190	+	Silent	SNP	A	A	C	rs3779721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:99208190A>C	ENST00000341166.3	-	9	1179	c.924T>G	c.(922-924)acT>acG	p.T308T	NIPAL2_ENST00000430223.2_Silent_p.T308T|NIPAL2_ENST00000520545.1_5'UTR	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	308						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						ATATAAATACAGTGAGAAAAG	0.328													A|||	2040	0.407348	0.3026	0.4841	5008	,	,		15920	0.4325		0.3479	False		,,,				2504	0.5297				p.T308T		Atlas-SNP	.											.	NIPAL2	23	.	0			c.T924G						PASS	.	A		1347,3059	436.8+/-344.8	198,951,1054	51.0	52.0	51.0		924	0.5	0.4	8	dbSNP_107	51	3080,5518	464.2+/-366.2	564,1952,1783	yes	coding-synonymous	NIPAL2	NM_024759.1		762,2903,2837	CC,CA,AA		35.8223,30.5719,34.0434		308/369	99208190	4427,8577	2203	4299	6502	SO:0001819	synonymous_variant	79815	exon9			AAATACAGTGAGA	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.924T>G	8.37:g.99208190A>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_024759	A2RTY8	Silent	SNP	ENST00000341166.3	37	CCDS6278.1																																																																																			A|0.642;C|0.358	0.358	strong		0.328	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291597	1291597	+	Missense_Mutation	SNP	C	C	G	rs144979264	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1291597C>G	ENST00000338844.3	+	4	429	c.396C>G	c.(394-396)aaC>aaG	p.N132K	TPSAB1_ENST00000461509.2_Missense_Mutation_p.N139K	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	132	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		N -> K (in dbSNP:rs1800991). {ECO:0000269|PubMed:10898108, ECO:0000269|PubMed:15489334}.		defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				AGCCGGTGAACGTCTCCAGCC	0.662													C|||	2475	0.494209	0.4092	0.3991	5008	,	,		15322	0.754		0.4563	False		,,,				2504	0.4479				p.N132K		Atlas-SNP	.											.	TPSAB1	24	.	0			c.C396G						PASS	.	C	LYS/ASN	1538,2778		228,1082,848	17.0	13.0	14.0		396	-0.1	0.0	16	dbSNP_134	14	3309,5111		655,1999,1556	no	missense	TPSAB1	NM_003294.3	94	883,3081,2404	GG,GC,CC		39.2993,35.6348,38.0575	benign	132/276	1291597	4847,7889	2158	4210	6368	SO:0001583	missense	7177	exon4			GGTGAACGTCTCC	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.396C>G	16.37:g.1291597C>G	ENSP00000343577:p.Asn132Lys	Somatic	521	0	0		WXS	Illumina HiSeq	Phase_I	350	319	0.911429	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Missense_Mutation	SNP	ENST00000338844.3	37	CCDS10431.1	976	0.4468864468864469	144	0.2926829268292683	123	0.3397790055248619	410	0.7167832167832168	299	0.3944591029023747	C	0.004	-2.348130	0.00219	0.356348	0.392993	ENSG00000172236	ENST00000338844;ENST00000461509	D;D	0.87966	-2.32;-2.32	3.51	-0.139	0.13460	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.707462	0.12783	N	0.439558	T	0.00012	0.0000	N	0.01649	-0.78	0.80722	P	0.0	B;B	0.20780	0.017;0.048	B;B	0.25506	0.024;0.061	T	0.42732	-0.9434	9	0.17832	T	0.49	.	1.0697	0.01619	0.177:0.4138:0.1741:0.235	.	123;132	Q15661-2;Q15661	.;TRYB1_HUMAN	K	132;139	ENSP00000343577:N132K;ENSP00000418247:N139K	ENSP00000343577:N132K	N	+	3	2	TPSAB1	1231598	0.000000	0.05858	0.010000	0.14722	0.028000	0.11728	-2.880000	0.00715	0.121000	0.18284	-0.492000	0.04666	AAC	C|0.500;G|0.500	0.500	strong		0.662	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
CLEC18C	283971	hgsc.bcm.edu	37	16	70211370	70211370	+	Missense_Mutation	SNP	C	C	G	rs3869428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70211370C>G	ENST00000569347.2	+	3	697	c.443C>G	c.(442-444)aCc>aGc	p.T148S	CLEC18C_ENST00000314151.8_Missense_Mutation_p.T148S|CLEC18C_ENST00000536907.2_Missense_Mutation_p.T148S|CLEC18C_ENST00000541793.2_Missense_Mutation_p.T148S|CLEC18C_ENST00000561612.1_Intron	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	148	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.T148S(1)		endometrium(3)|large_intestine(6)|lung(1)	10						GCCACCTGCACCCACTACACG	0.602																																					p.T148S		Atlas-SNP	.											CLEC18C,rectum,carcinoma,0,1	CLEC18C	15	1	1	Substitution - Missense(1)	large_intestine(1)	c.C443G						scavenged	.						12.0	11.0	11.0					16																	70211370		2072	4009	6081	SO:0001583	missense	283971	exon3			CCTGCACCCACTA	AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.443C>G	16.37:g.70211370C>G	ENSP00000455920:p.Thr148Ser	Somatic	466	0	0		WXS	Illumina HiSeq	Phase_I	357	82	0.229692	NM_173619	Q8IUW8	Missense_Mutation	SNP	ENST00000569347.2	37	CCDS32473.1	.	.	.	.	.	.	.	.	.	.	c	6.117	0.389845	0.11581	.	.	ENSG00000157335	ENST00000541793;ENST00000314151;ENST00000433156;ENST00000539438;ENST00000536907	T;T;T	0.07688	3.17;3.17;3.17	4.32	2.09	0.27110	CAP domain (3);	0.557277	0.19650	N	0.109248	T	0.06508	0.0167	L	0.28344	0.845	0.21802	N	0.999531	B	0.10296	0.003	B	0.12837	0.008	T	0.30851	-0.9964	10	0.51188	T	0.08	.	10.1296	0.42672	0.0:0.6029:0.3971:0.0	.	148	Q8NCF0	CL18C_HUMAN	S	148;148;148;144;148	ENSP00000444875:T148S;ENSP00000326538:T148S;ENSP00000444726:T148S	ENSP00000326538:T148S	T	+	2	0	CLEC18C	68768871	0.141000	0.22595	1.000000	0.80357	0.135000	0.20990	1.141000	0.31528	0.903000	0.36546	0.298000	0.19748	ACC	.	.	weak		0.602	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
SYNE1	23345	hgsc.bcm.edu	37	6	152529260	152529260	+	Silent	SNP	G	G	A	rs3798756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:152529260G>A	ENST00000367255.5	-	125	23272	c.22671C>T	c.(22669-22671)atC>atT	p.I7557I	SYNE1_ENST00000448038.1_Silent_p.I7486I|SYNE1_ENST00000423061.1_Silent_p.I7486I|SYNE1_ENST00000356820.4_Silent_p.I2081I|SYNE1_ENST00000265368.4_Silent_p.I7557I|SYNE1_ENST00000341594.5_Silent_p.I7169I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7557					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)		GGCTGTCAATGATCCCCCGCC	0.502										HNSCC(10;0.0054)			G|||	777	0.155152	0.1067	0.2378	5008	,	,		15324	0.2133		0.1272	False		,,,				2504	0.1309				p.I7557I		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C22671T						PASS	.	G	,	524,3882	241.5+/-251.9	22,480,1701	96.0	88.0	91.0		22458,22671	5.6	1.0	6	dbSNP_107	91	1153,7447	237.1+/-269.0	76,1001,3223	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	98,1481,4924	AA,AG,GG		13.407,11.8929,12.894	,	7486/8750,7557/8798	152529260	1677,11329	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon125			GTCAATGATCCCC	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.22671C>T	6.37:g.152529260G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	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|0.854;A|0.146	0.146	strong		0.502	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
OR13C8	138802	hgsc.bcm.edu	37	9	107332377	107332377	+	Missense_Mutation	SNP	T	T	A	rs76017116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:107332377T>A	ENST00000335040.1	+	1	929	c.929T>A	c.(928-930)aTa>aAa	p.I310K		NM_001004483.1	NP_001004483.1	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C, member 8	310						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|skin(1)	25						GTCAAAAACATACTGTGTAGG	0.368													T|||	18	0.00359425	0.0008	0.0029	5008	,	,		21213	0.0		0.0109	False		,,,				2504	0.0041				p.I310K		Atlas-SNP	.											.	OR13C8	77	.	0			c.T929A						PASS	.	T	LYS/ILE	10,4396	15.5+/-35.6	0,10,2193	49.0	50.0	50.0		929	4.9	0.8	9	dbSNP_131	50	128,8472	63.9+/-126.0	3,122,4175	yes	missense	OR13C8	NM_001004483.1	102	3,132,6368	AA,AT,TT		1.4884,0.227,1.061	benign	310/321	107332377	138,12868	2203	4300	6503	SO:0001583	missense	138802	exon1			AAAACATACTGTG		CCDS35090.1	9q31.1	2013-09-24			ENSG00000186943	ENSG00000186943		"""GPCR / Class A : Olfactory receptors"""	15103	protein-coding gene	gene with protein product							Standard	NM_001004483		Approved		uc011lvo.2	Q8NGS7	OTTHUMG00000020409	ENST00000335040.1:c.929T>A	9.37:g.107332377T>A	ENSP00000334068:p.Ile310Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	37	0.362745	NM_001004483	Q5VVG0|Q96R44	Missense_Mutation	SNP	ENST00000335040.1	37	CCDS35090.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	10.68	1.418173	0.25552	0.00227	0.014884	ENSG00000186943	ENST00000335040	T	0.39056	1.1	4.9	4.9	0.64082	.	0.163089	0.43747	D	0.000521	T	0.25195	0.0612	L	0.33624	1.015	0.09310	N	1	B	0.26975	0.165	B	0.22880	0.042	T	0.31024	-0.9958	10	0.87932	D	0	.	12.791	0.57534	0.0:0.0:0.0:1.0	.	310	Q8NGS7	O13C8_HUMAN	K	310	ENSP00000334068:I310K	ENSP00000334068:I310K	I	+	2	0	OR13C8	106372198	0.376000	0.25098	0.786000	0.31890	0.692000	0.40212	2.353000	0.44089	2.181000	0.69327	0.459000	0.35465	ATA	T|0.992;A|0.008	0.008	strong		0.368	OR13C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053480.1		
NAV3	89795	hgsc.bcm.edu	37	12	78562618	78562618	+	Silent	SNP	A	A	G	rs383190	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:78562618A>G	ENST00000397909.2	+	24	5126	c.4953A>G	c.(4951-4953)gcA>gcG	p.A1651A	NAV3_ENST00000228327.6_Silent_p.A1651A|NAV3_ENST00000536525.2_Silent_p.A1651A|NAV3_ENST00000266692.7_Silent_p.A1474A			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1651						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						TTCAGGGAGCACTGAATGGTC	0.378										HNSCC(70;0.22)			G|||	168	0.0335463	0.0106	0.036	5008	,	,		15664	0.0218		0.0706	False		,,,				2504	0.0368				p.A1651A		Atlas-SNP	.											NAV3,NS,carcinoma,+2,1	NAV3	506	1	0			c.A4953G						PASS	.	G		80,3580		1,78,1751	76.0	78.0	77.0		4953	-10.8	0.0	12	dbSNP_80	77	584,7560		22,540,3510	no	coding-synonymous	NAV3	NM_014903.4		23,618,5261	GG,GA,AA		7.1709,2.1858,5.6252		1651/2364	78562618	664,11140	1830	4072	5902	SO:0001819	synonymous_variant	89795	exon24			GGGAGCACTGAAT	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.4953A>G	12.37:g.78562618A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37		92	0.04212454212454213	8	0.016260162601626018	16	0.04419889502762431	15	0.026223776223776224	53	0.06992084432717678	G	7.985	0.751979	0.15778	0.021858	0.071709	ENSG00000067798	ENST00000552895	.	.	.	5.41	-10.8	0.00216	.	.	.	.	.	T	0.04003	0.0112	.	.	.	0.53005	D	0.999969	.	.	.	.	.	.	T	0.55692	-0.8101	4	.	.	.	-17.7105	4.2647	0.10757	0.1743:0.3133:0.3487:0.1636	rs383190	.	.	.	A	546	.	.	T	+	1	0	NAV3	77086749	0.000000	0.05858	0.018000	0.16275	0.945000	0.59286	-6.094000	0.00081	-4.671000	0.00037	-1.929000	0.00512	ACT	A|0.947;G|0.053	0.053	strong		0.378	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
TECPR1	25851	hgsc.bcm.edu	37	7	97852443	97852443	+	Silent	SNP	C	C	T	rs61745947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97852443C>T	ENST00000447648.2	-	21	3086	c.2787G>A	c.(2785-2787)gtG>gtA	p.V929V	TECPR1_ENST00000479975.1_5'UTR|TECPR1_ENST00000379795.3_Silent_p.V931V			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	929					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						CGATGGGGGGCACCTCCAGCC	0.682													C|||	81	0.0161741	0.0008	0.0101	5008	,	,		10604	0.001		0.0219	False		,,,				2504	0.0511				p.V929V		Atlas-SNP	.											.	TECPR1	77	.	0			c.G2787A						PASS	.	C		16,4018		0,16,2001	20.0	26.0	24.0		2787	4.0	1.0	7	dbSNP_129	24	238,8088		4,230,3929	no	coding-synonymous	TECPR1	NM_015395.1		4,246,5930	TT,TC,CC		2.8585,0.3966,2.055		929/1166	97852443	254,12106	2017	4163	6180	SO:0001819	synonymous_variant	25851	exon21			GGGGGGCACCTCC		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.2787G>A	7.37:g.97852443C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			C|0.985;T|0.015	0.015	strong		0.682	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
HHATL	57467	hgsc.bcm.edu	37	3	42735150	42735150	+	Missense_Mutation	SNP	T	T	C	rs11079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42735150T>C	ENST00000441594.1	-	10	1468	c.1207A>G	c.(1207-1209)Atg>Gtg	p.M403V	HHATL_ENST00000310417.5_Missense_Mutation_p.M403V	NM_020707.3	NP_065758.3	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like	403			M -> V (in dbSNP:rs11079).		negative regulation of N-terminal protein palmitoylation (GO:0060262)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(3)	19				KIRC - Kidney renal clear cell carcinoma(284;0.215)		AGTTTTTGCATCCAGAGCTCA	0.572													C|||	3251	0.649161	0.6785	0.6787	5008	,	,		17935	0.7113		0.5924	False		,,,				2504	0.5828				p.M403V		Atlas-SNP	.											.	HHATL	49	.	0			c.A1207G						PASS	.		VAL/MET	2878,1528	483.9+/-359.9	934,1010,259	50.0	46.0	47.0		1207	4.3	1.0	3	dbSNP_52	47	5072,3528	513.4+/-378.2	1462,2148,690	yes	missense	HHATL	NM_020707.3	21	2396,3158,949	CC,CT,TT		41.0233,34.68,38.8744	benign	403/505	42735150	7950,5056	2203	4300	6503	SO:0001583	missense	57467	exon10			TTTGCATCCAGAG	AB042554	CCDS2704.1	3p22	2009-10-06	2007-02-06	2007-02-06	ENSG00000010282	ENSG00000010282			13242	protein-coding gene	gene with protein product	"""membrane bound O-acyltransferase domain containing 3"""	608116	"""chromosome 3 open reading frame 3"", ""GUP1, glycerol uptake/transporter homolog (yeast)"""	C3orf3, GUP1		11374908	Standard	NM_020707		Approved	KIAA1173, OACT3, MSTP002, MBOAT3	uc003clx.3	Q9HCP6	OTTHUMG00000133043	ENST00000441594.1:c.1207A>G	3.37:g.42735150T>C	ENSP00000405423:p.Met403Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_020707	Q8TBG3|Q9ULP7	Missense_Mutation	SNP	ENST00000441594.1	37	CCDS2704.1	1409	0.6451465201465202	338	0.6869918699186992	236	0.6519337016574586	393	0.6870629370629371	442	0.58311345646438	c	4.841	0.156349	0.09236	0.6532	0.589767	ENSG00000010282	ENST00000310417;ENST00000441594	T;T	0.72394	-0.65;-0.65	4.35	4.35	0.52113	.	0.060080	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00044	-2.455	0.39949	P	0.025487000000000037	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	9	0.07030	T	0.85	-3.6735	12.4847	0.55866	0.0:0.9175:0.0:0.0825	rs11079;rs1046552;rs3172382;rs17237886;rs60079680;rs11079	403	Q9HCP6	HHATL_HUMAN	V	403	ENSP00000310621:M403V;ENSP00000405423:M403V	ENSP00000310621:M403V	M	-	1	0	HHATL	42710154	1.000000	0.71417	0.999000	0.59377	0.630000	0.37929	3.125000	0.50469	0.827000	0.34685	-0.404000	0.06349	ATG	T|0.381;C|0.619	0.619	strong		0.572	HHATL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343627.1	NM_020707	
METTL25	84190	hgsc.bcm.edu	37	12	82792666	82792666	+	Silent	SNP	C	C	T	rs10506872	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:82792666C>T	ENST00000248306.3	+	4	693	c.624C>T	c.(622-624)acC>acT	p.T208T	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	208							methyltransferase activity (GO:0008168)										CTTCAAATACCAATACTCATG	0.363													C|||	212	0.0423323	0.0189	0.0591	5008	,	,		13940	0.002		0.0805	False		,,,				2504	0.0644				p.T208T		Atlas-SNP	.											.	.	.	.	0			c.C624T						PASS	.	C		147,4259	99.4+/-138.0	3,141,2059	48.0	47.0	47.0		624	0.9	0.9	12	dbSNP_119	47	818,7780	186.0+/-233.6	43,732,3524	no	coding-synonymous	C12orf26	NM_032230.2		46,873,5583	TT,TC,CC		9.5138,3.3364,7.4208		208/604	82792666	965,12039	2203	4299	6502	SO:0001819	synonymous_variant	84190	exon4			AAATACCAATACT	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.624C>T	12.37:g.82792666C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_032230	Q9H5Y3	Silent	SNP	ENST00000248306.3	37	CCDS9024.1	89	0.04075091575091575	11	0.022357723577235773	22	0.06077348066298342	1	0.0017482517482517483	55	0.07255936675461741	C	7.250	0.603078	0.13939	0.033364	0.095138	ENSG00000127720	ENST00000550058	.	.	.	5.3	0.871	0.19107	.	.	.	.	.	T	0.02342	0.0072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00896	-1.1523	4	.	.	.	-0.1742	7.0117	0.24865	0.1109:0.5787:0.0:0.3105	rs10506872;rs17774639;rs10506872	.	.	.	L	167	.	.	P	+	2	0	C12orf26	81316797	1.000000	0.71417	0.941000	0.38009	0.953000	0.61014	0.943000	0.29030	-0.274000	0.09232	-1.128000	0.01989	CCA	C|0.955;T|0.045	0.045	strong		0.363	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
CALB2	794	hgsc.bcm.edu	37	16	71411636	71411636	+	Missense_Mutation	SNP	G	G	A	rs11545954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71411636G>A	ENST00000302628.4	+	4	405	c.328G>A	c.(328-330)Gcc>Acc	p.A110T	CALB2_ENST00000349553.5_Missense_Mutation_p.A110T	NM_001740.4	NP_001731.2	P22676	CALB2_HUMAN	calbindin 2	110	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.			A -> T (in Ref. 5; AAH15484). {ECO:0000305}.	cytosolic calcium ion homeostasis (GO:0051480)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18		Ovarian(137;0.125)				GGGCTCCAGCGCCGAGTTTAT	0.572													G|||	690	0.13778	0.1861	0.1052	5008	,	,		19624	0.0298		0.1292	False		,,,				2504	0.2157				p.A110T		Atlas-SNP	.											.	CALB2	46	.	0			c.G328A						PASS	.	G	THR/ALA,THR/ALA	751,3645	306.9+/-289.7	63,625,1510	94.0	84.0	88.0		328,328	1.2	0.9	16	dbSNP_120	88	1117,7483	232.6+/-266.2	72,973,3255	yes	missense,missense	CALB2	NM_001740.4,NM_007088.3	58,58	135,1598,4765	AA,AG,GG		12.9884,17.0837,14.3737	benign,benign	110/272,110/193	71411636	1868,11128	2198	4300	6498	SO:0001583	missense	794	exon4			TCCAGCGCCGAGT	X56667	CCDS10899.1	16q22.2	2013-01-10	2008-05-19		ENSG00000172137	ENSG00000172137		"""EF-hand domain containing"""	1435	protein-coding gene	gene with protein product	"""calretinin"""	114051	"""calbindin 2, 29kDa (calretinin)"""			1906795	Standard	NM_001740		Approved	CAL2	uc002faa.4	P22676	OTTHUMG00000137589	ENST00000302628.4:c.328G>A	16.37:g.71411636G>A	ENSP00000307508:p.Ala110Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_007088	A8K4Y1|Q53HD2|Q96BK4	Missense_Mutation	SNP	ENST00000302628.4	37	CCDS10899.1	264	0.12087912087912088	103	0.20934959349593496	51	0.1408839779005525	21	0.03671328671328671	89	0.11741424802110818	G	10.06	1.246691	0.22796	0.170837	0.129884	ENSG00000172137	ENST00000349553;ENST00000302628	T;T	0.68479	-0.33;-0.33	5.48	1.17	0.20885	EF-hand-like domain (1);	0.565985	0.20929	N	0.083122	T	0.00039	0.0001	L	0.41573	1.285	0.38374	P	0.05504600000000004	B;B	0.12013	0.005;0.003	B;B	0.11329	0.006;0.002	T	0.05517	-1.0880	9	0.27785	T	0.31	-1.4052	7.9909	0.30239	0.4237:0.0:0.5763:0.0	rs11545954;rs17851296;rs58508901	110;110	A6NER6;P22676	.;CALB2_HUMAN	T	110	ENSP00000340294:A110T;ENSP00000307508:A110T	ENSP00000307508:A110T	A	+	1	0	CALB2	69969137	0.811000	0.29063	0.926000	0.36857	0.935000	0.57460	0.203000	0.17315	0.057000	0.16193	0.603000	0.83216	GCC	G|0.867;A|0.133	0.133	strong		0.572	CALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268988.1	NM_001740	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43545893	43545893	+	Silent	SNP	T	T	C	rs1879581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43545893T>C	ENST00000430334.3	-	5	1123	c.990A>G	c.(988-990)acA>acG	p.T330T	PLEKHM1_ENST00000421073.2_Silent_p.T241T|RN7SL730P_ENST00000583727.1_RNA	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	330					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					TGGGGATCTCTGTTTCTTGGC	0.537													C|||	412	0.0822684	0.0378	0.1556	5008	,	,		19822	0.001		0.1958	False		,,,				2504	0.0573				p.T330T		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.A990G						PASS	.	C		281,4125	800.6+/-415.6	10,261,1932	140.0	137.0	138.0		990	-5.9	0.0	17	dbSNP_92	138	1646,6954	741.1+/-407.1	155,1336,2809	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1597,4741	CC,CT,TT		19.1395,6.3777,14.8162		330/1057	43545893	1927,11079	2203	4300	6503	SO:0001819	synonymous_variant	9842	exon5			GATCTCTGTTTCT	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.990A>G	17.37:g.43545893T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	143	140	0.979021	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			T|0.863;C|0.137	0.137	strong		0.537	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
RGS9BP	388531	hgsc.bcm.edu	37	19	33167837	33167837	+	Missense_Mutation	SNP	C	C	T	rs35413309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33167837C>T	ENST00000334176.3	+	1	1525	c.668C>T	c.(667-669)gCg>gTg	p.A223V	ANKRD27_ENST00000587352.1_5'Flank|ANKRD27_ENST00000306065.4_5'Flank	NM_207391.2	NP_997274.2	Q6ZS82	R9BP_HUMAN	regulator of G protein signaling 9 binding protein	223					detection of light stimulus involved in visual perception (GO:0050908)|negative regulation of signal transduction (GO:0009968)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	integral component of membrane (GO:0016021)				central_nervous_system(1)|lung(2)	3	Esophageal squamous(110;0.137)					GTGCTGCTGGCGGCTGTGGCC	0.716													C|||	188	0.0375399	0.0015	0.0202	5008	,	,		11942	0.121		0.0288	False		,,,				2504	0.0215				p.A223V		Atlas-SNP	.											.	RGS9BP	9	.	0			c.C668T						PASS	.	C	VAL/ALA	26,3558		0,26,1766	7.0	9.0	9.0		668	-0.5	1.0	19	dbSNP_126	9	209,7131		0,209,3461	yes	missense	RGS9BP	NM_207391.2	64	0,235,5227	TT,TC,CC		2.8474,0.7254,2.1512	possibly-damaging	223/236	33167837	235,10689	1792	3670	5462	SO:0001583	missense	388531	exon1			TGCTGGCGGCTGT	AW302149	CCDS12424.1	19q13.11	2008-02-05	2007-08-14			ENSG00000186326			30304	protein-coding gene	gene with protein product		607814	"""regulator of G protein signalling 9 binding protein"""			12119397, 8889548	Standard	NM_207391		Approved	FLJ45744, PERRS, R9AP, RGS9	uc002ntp.1	Q6ZS82		ENST00000334176.3:c.668C>T	19.37:g.33167837C>T	ENSP00000334134:p.Ala223Val	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	10	6	0.6	NM_207391	Q6ZVJ6	Missense_Mutation	SNP	ENST00000334176.3	37	CCDS12424.1	85	0.03891941391941392	1	0.0020325203252032522	6	0.016574585635359115	57	0.09965034965034965	21	0.027704485488126648	C	9.498	1.102552	0.20632	0.007254	0.028474	ENSG00000186326	ENST00000334176	T	0.35421	1.31	4.24	-0.461	0.12172	.	0.301451	0.28209	N	0.016198	T	0.00300	0.0009	N	0.04203	-0.255	0.23568	N	0.997398	B	0.13145	0.007	B	0.06405	0.002	T	0.21861	-1.0233	10	0.02654	T	1	-15.9998	7.3136	0.26488	0.0:0.2712:0.0:0.7288	rs35413309	223	Q6ZS82	R9BP_HUMAN	V	223	ENSP00000334134:A223V	ENSP00000334134:A223V	A	+	2	0	RGS9BP	37859677	0.972000	0.33761	0.996000	0.52242	0.882000	0.50991	1.953000	0.40352	0.104000	0.17725	0.462000	0.41574	GCG	C|0.962;T|0.038	0.038	strong		0.716	RGS9BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450337.1	NM_207391	
FLG2	388698	hgsc.bcm.edu	37	1	152323132	152323132	+	Nonsense_Mutation	SNP	G	G	T	rs12568784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152323132G>T	ENST00000388718.5	-	3	7202	c.7130C>A	c.(7129-7131)tCa>tAa	p.S2377*	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2377					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)			TGTTGACCATGAAAGGTGAGA	0.433													G|||	1587	0.316893	0.2905	0.4049	5008	,	,		24138	0.4554		0.1421	False		,,,				2504	0.3272				p.S2377X		Atlas-SNP	.											.	FLG2	431	.	0			c.C7130A						PASS	.	G	stop/SER	1148,3258	406.9+/-334.0	128,892,1183	169.0	161.0	164.0		7130	0.1	0.0	1	dbSNP_120	164	1368,7232	266.9+/-287.0	135,1098,3067	yes	stop-gained	FLG2	NM_001014342.2		263,1990,4250	TT,TG,GG		15.907,26.0554,19.3449		2377/2392	152323132	2516,10490	2203	4300	6503	SO:0001587	stop_gained	388698	exon3			GACCATGAAAGGT	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.7130C>A	1.37:g.152323132G>T	ENSP00000373370:p.Ser2377*	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	282	132	0.468085	NM_001014342	Q9H4U1	Nonsense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	653	0.298992673992674	144	0.2926829268292683	123	0.3397790055248619	278	0.486013986013986	108	0.1424802110817942	G	45	11.361751	0.99551	0.260554	0.15907	ENSG00000143520	ENST00000388718	.	.	.	4.14	0.129	0.14739	.	.	.	.	.	.	.	.	.	.	.	0.39661	P	0.02938799999999997	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	12.2763	2.5897	0.04839	0.5432:0.0:0.2581:0.1986	rs12568784;rs12568784	.	.	.	X	2377	.	ENSP00000373370:S2377X	S	-	2	0	FLG2	150589756	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.411000	0.21115	-0.057000	0.13199	0.460000	0.39030	TCA	G|0.756;T|0.244	0.244	strong		0.433	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
CCDC186	55088	hgsc.bcm.edu	37	10	115905428	115905428	+	Missense_Mutation	SNP	C	C	A	rs367843443		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:115905428C>A	ENST00000369287.3	-	5	1247	c.981G>T	c.(979-981)aaG>aaT	p.K327N	C10orf118_ENST00000543782.1_5'Flank	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		327										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)		TCTCTTTTTCCTTTCGAAGAT	0.368																																					p.K327N		Atlas-SNP	.											.	C10orf118	70	.	0			c.G981T						PASS	.	C	ASN/LYS	0,4406		0,0,2203	196.0	183.0	187.0		981	2.3	1.0	10		187	1,8599	1.2+/-3.3	0,1,4299	no	missense	C10orf118	NM_018017.2	94	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	327/899	115905428	1,13005	2203	4300	6503	SO:0001583	missense	55088	exon5			TTTTTCCTTTCGA																												ENST00000369287.3:c.981G>T	10.37:g.115905428C>A	ENSP00000358293:p.Lys327Asn	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	156	91	0.583333	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.075041	0.76415	0.0	1.16E-4	ENSG00000165813	ENST00000369287;ENST00000430353	T	0.53857	0.6	5.52	2.29	0.28610	.	0.099180	0.64402	D	0.000002	T	0.60248	0.2254	M	0.68593	2.085	0.80722	D	1	D	0.56746	0.977	P	0.55923	0.787	T	0.60900	-0.7171	10	0.72032	D	0.01	.	8.5338	0.33351	0.0:0.7277:0.0:0.2723	.	327	Q7Z3E2	CJ118_HUMAN	N	327;433	ENSP00000358293:K327N	ENSP00000358293:K327N	K	-	3	2	C10orf118	115895418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.972000	0.29409	0.518000	0.28383	0.650000	0.86243	AAG	.	.	none		0.368	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		
GP1BA	2811	hgsc.bcm.edu	37	17	4836973	4836973	+	Silent	SNP	A	A	G	rs6067	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4836973A>G	ENST00000329125.5	+	2	1149	c.1074A>G	c.(1072-1074)agA>agG	p.R358R		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	358	Pro/Thr-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						TCCCACCTAGATGGACCCCAA	0.493													A|||	446	0.0890575	0.0151	0.1412	5008	,	,		15845	0.2073		0.0268	False		,,,				2504	0.0941				p.R358R		Atlas-SNP	.											.	GP1BA	53	.	0			c.A1074G						PASS	.	A		108,3808		0,108,1850	180.0	176.0	177.0		1074	-0.4	0.0	17	dbSNP_52	177	315,8021		8,299,3861	no	coding-synonymous	GP1BA	NM_000173.5		8,407,5711	GG,GA,AA		3.7788,2.7579,3.4525		358/653	4836973	423,11829	1958	4168	6126	SO:0001819	synonymous_variant	2811	exon2			ACCTAGATGGACC		CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.1074A>G	17.37:g.4836973A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_000173	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Silent	SNP	ENST00000329125.5	37	CCDS54068.1																																																																																			A|0.940;G|0.060	0.060	strong		0.493	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
CLCN1	1180	hgsc.bcm.edu	37	7	143042837	143042837	+	Silent	SNP	C	C	T	rs2272251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:143042837C>T	ENST00000343257.2	+	17	2241	c.2154C>T	c.(2152-2154)gaC>gaT	p.D718D		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	718					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					AGGACGAAGACCTCTCTGGCA	0.677											OREG0018402	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2395	0.478235	0.3593	0.585	5008	,	,		13451	0.6141		0.4592	False		,,,				2504	0.4427				p.D718D		Atlas-SNP	.											CLCN1,NS,carcinoma,0,1	CLCN1	141	1	0			c.C2154T						PASS	.	C		1498,2778		328,842,968	7.0	8.0	8.0		2154	-1.8	0.1	7	dbSNP_100	8	3583,4875		839,1905,1485	no	coding-synonymous	CLCN1	NM_000083.2		1167,2747,2453	TT,TC,CC		42.3623,35.0327,39.9011		718/989	143042837	5081,7653	2138	4229	6367	SO:0001819	synonymous_variant	1180	exon17			CGAAGACCTCTCT	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2154C>T	7.37:g.143042837C>T		Somatic	53	0	0	1676	WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																			C|0.502;T|0.498	0.498	strong		0.677	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	
KISS1	3814	hgsc.bcm.edu	37	1	204161947	204161947	+	Missense_Mutation	SNP	C	C	T	rs12998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204161947C>T	ENST00000367194.4	-	2	206	c.58G>A	c.(58-60)Gag>Aag	p.E20K		NM_002256.3	NP_002247.3	Q15726	KISS1_HUMAN	KiSS-1 metastasis-suppressor	20			E -> K (in dbSNP:rs12998). {ECO:0000269|PubMed:15598687}.		cytoskeleton organization (GO:0007010)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of synaptic transmission (GO:0050806)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				large_intestine(1)|lung(1)|ovary(1)	3	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)		TCTAATGGCTCCCCAAAGTGG	0.522													C|||	116	0.0231629	0.0038	0.0317	5008	,	,		20686	0.0238		0.0408	False		,,,				2504	0.0245				p.E20K		Atlas-SNP	.											.	KISS1	6	.	0			c.G58A						PASS	.	C	LYS/GLU	19,3689		1,17,1836	32.0	32.0	32.0		58	2.9	0.1	1	dbSNP_52	32	282,7922		5,272,3825	yes	missense	KISS1	NM_002256.3	56	6,289,5661	TT,TC,CC		3.4373,0.5124,2.5269	possibly-damaging	20/139	204161947	301,11611	1854	4102	5956	SO:0001583	missense	3814	exon2			ATGGCTCCCCAAA	U43527	CCDS41454.1	1q32	2014-01-30			ENSG00000170498	ENSG00000170498		"""Endogenous ligands"""	6341	protein-coding gene	gene with protein product	"""prepro-kisspeptin"", ""kisspeptin"""	603286				9192814, 9806840	Standard	NM_002256		Approved		uc001har.3	Q15726	OTTHUMG00000036060	ENST00000367194.4:c.58G>A	1.37:g.204161947C>T	ENSP00000356162:p.Glu20Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_002256	A8K6N0|Q9HBP1	Missense_Mutation	SNP	ENST00000367194.4	37	CCDS41454.1	71	0.03250915750915751	4	0.008130081300813009	19	0.052486187845303865	17	0.02972027972027972	31	0.040897097625329816	C	14.53	2.562509	0.45694	0.005124	0.034373	ENSG00000170498	ENST00000367194	T	0.72942	-0.7	5.82	2.94	0.34122	.	0.142074	0.31601	N	0.007372	T	0.25827	0.0629	M	0.64404	1.975	0.21355	N	0.999719	P	0.40909	0.732	B	0.41988	0.372	T	0.48055	-0.9068	10	0.87932	D	0	-15.2579	5.9641	0.19315	0.0:0.6745:0.1572:0.1683	rs12998;rs17686;rs3209575;rs11548219;rs52790042;rs12998	20	Q15726	KISS1_HUMAN	K	20	ENSP00000356162:E20K	ENSP00000356162:E20K	E	-	1	0	KISS1	202428570	0.974000	0.33945	0.051000	0.19133	0.124000	0.20399	2.266000	0.43320	0.369000	0.24510	-0.182000	0.12963	GAG	C|0.968;T|0.032	0.032	strong		0.522	KISS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087892.1	NM_002256	
FDFT1	2222	hgsc.bcm.edu	37	8	11687923	11687923	+	Silent	SNP	T	T	A	rs73207296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11687923T>A	ENST00000220584.4	+	6	1095	c.873T>A	c.(871-873)atT>atA	p.I291I	FDFT1_ENST00000443614.2_Silent_p.I248I|FDFT1_ENST00000530664.1_Silent_p.I227I|FDFT1_ENST00000538689.1_Silent_p.I180I|FDFT1_ENST00000525777.1_Silent_p.I206I|FDFT1_ENST00000528643.1_Silent_p.I206I|FDFT1_ENST00000528812.1_Silent_p.I227I|FDFT1_ENST00000525900.1_Silent_p.I284I|FDFT1_ENST00000446331.2_3'UTR	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	291					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		TCTGTGCTATTCCACAGGTAG	0.483													T|||	25	0.00499201	0.0008	0.0058	5008	,	,		19213	0.0		0.0179	False		,,,				2504	0.002				p.I291I		Atlas-SNP	.											.	FDFT1	25	.	0			c.T873A						PASS	.	T		17,4389	24.3+/-50.5	0,17,2186	122.0	105.0	111.0		873	-6.2	0.5	8	dbSNP_130	111	208,8392	88.6+/-150.9	4,200,4096	no	coding-synonymous	FDFT1	NM_004462.3		4,217,6282	AA,AT,TT		2.4186,0.3858,1.73		291/418	11687923	225,12781	2203	4300	6503	SO:0001819	synonymous_variant	2222	exon6			TGCTATTCCACAG	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.873T>A	8.37:g.11687923T>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			T|0.985;A|0.015	0.015	strong		0.483	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
CNTD2	79935	hgsc.bcm.edu	37	19	40732484	40732484	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40732484G>T	ENST00000430325.2	-	1	113	c.65C>A	c.(64-66)gCc>gAc	p.A22D	CNTD2_ENST00000433940.1_Missense_Mutation_p.A22D|CNTD2_ENST00000513948.1_5'Flank	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	22					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						GGGCCTGGGGGCCCAGCGCCT	0.711																																					p.A22D		Atlas-SNP	.											.	CNTD2	22	.	0			c.C65A						PASS	.						7.0	10.0	9.0					19																	40732484		2153	4229	6382	SO:0001583	missense	79935	exon1			CTGGGGGCCCAGC	AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"""cyclin P"""					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.65C>A	19.37:g.40732484G>T	ENSP00000396755:p.Ala22Asp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_024877	B4DX65	Missense_Mutation	SNP	ENST00000430325.2	37	CCDS12551.2	.	.	.	.	.	.	.	.	.	.	G	2.608	-0.291537	0.05568	.	.	ENSG00000105219	ENST00000430325;ENST00000433940	T	0.34859	1.34	2.44	-0.257	0.12979	.	3.315080	0.01764	N	0.030742	T	0.22085	0.0532	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10268	-1.0637	9	0.22706	T	0.39	.	4.6612	0.12643	0.1483:0.0:0.6432:0.2085	.	22	B4DX65	.	D	22	ENSP00000396755:A22D	ENSP00000221818:A22D	A	-	2	0	CNTD2	45424324	0.011000	0.17503	0.000000	0.03702	0.002000	0.02628	0.152000	0.16302	-0.034000	0.13713	-1.134000	0.01955	GCC	.	.	none		0.711	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360785.1	NM_024877	
NLRP8	126205	hgsc.bcm.edu	37	19	56467167	56467167	+	Silent	SNP	C	C	T	rs375534172		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56467167C>T	ENST00000291971.3	+	3	1814	c.1743C>T	c.(1741-1743)ttC>ttT	p.F581F	NLRP8_ENST00000590542.1_Silent_p.F581F	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	581					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)		AGGTGTCTTTCGGTAATAAGA	0.488																																					p.F581F		Atlas-SNP	.											.	NLRP8	225	.	0			c.C1743T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	49.0	46.0	47.0		1743	-0.4	0.0	19		47	0,8600		0,0,4300	no	coding-synonymous	NLRP8	NM_176811.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		581/1049	56467167	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	126205	exon3			GTCTTTCGGTAAT	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.1743C>T	19.37:g.56467167C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	150	58	0.386667	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			.	.	weak		0.488	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ZNF311	282890	hgsc.bcm.edu	37	6	28963248	28963248	+	Missense_Mutation	SNP	T	T	G	rs6456880	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:28963248T>G	ENST00000377179.3	-	7	2043	c.1531A>C	c.(1531-1533)Aag>Cag	p.K511Q	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	511			K -> Q (in dbSNP:rs6456880). {ECO:0000269|PubMed:14574404}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						AGGCAGTGCTTATCTTGGAAG	0.463													G|||	3341	0.667133	0.9539	0.5692	5008	,	,		23712	0.6508		0.4354	False		,,,				2504	0.6043				p.K511Q		Atlas-SNP	.											ZNF311,colon,carcinoma,0,2	ZNF311	59	2	0			c.A1531C						PASS	.	G	GLN/LYS	2586,436		1113,360,38	87.0	83.0	84.0		1531	1.8	0.0	6	dbSNP_116	84	2247,3171		468,1311,930	yes	missense	ZNF311	NM_001010877.2	53	1581,1671,968	GG,GT,TT		41.4729,14.4275,42.737	benign	511/667	28963248	4833,3607	1511	2709	4220	SO:0001583	missense	282890	exon7			AGTGCTTATCTTG	AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935		"""Zinc fingers, C2H2-type"", ""-"""	13847	protein-coding gene	gene with protein product							Standard	XM_006715067		Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.1531A>C	6.37:g.28963248T>G	ENSP00000366384:p.Lys511Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_001010877	A2BFK5|B0S7Y4|Q92971	Missense_Mutation	SNP	ENST00000377179.3	37	CCDS34357.1	1350	0.6181318681318682	467	0.9491869918699187	203	0.5607734806629834	375	0.6555944055944056	305	0.4023746701846966	G	0.364	-0.938000	0.02340	0.855725	0.414729	ENSG00000197935	ENST00000377179;ENST00000535083	T	0.13538	2.58	3.69	1.82	0.25136	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03053	0.0090	L	0.38692	1.165	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41875	-0.9484	8	0.30854	T	0.27	-0.5211	5.6026	0.17361	0.0993:0.0:0.4055:0.4951	rs6456880;rs17340289;rs59778525;rs6456880	511	Q5JNZ3	ZN311_HUMAN	Q	511;419	ENSP00000366384:K511Q	ENSP00000366384:K511Q	K	-	1	0	ZNF311	29071227	0.021000	0.18746	0.000000	0.03702	0.035000	0.12851	0.492000	0.22435	0.009000	0.14813	-0.195000	0.12781	AAG	G|0.602;N|0.000	0.602	strong		0.463	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581	
GSTO2	119391	hgsc.bcm.edu	37	10	106039185	106039185	+	Missense_Mutation	SNP	A	A	G	rs156697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:106039185A>G	ENST00000338595.2	+	5	744	c.424A>G	c.(424-426)Aat>Gat	p.N142D	GSTO2_ENST00000477078.2_3'UTR|GSTO2_ENST00000450629.2_Intron|GSTO2_ENST00000429569.2_Intron|GSTO2_ENST00000401888.2_Missense_Mutation_p.N142D|GSTO2_ENST00000369707.2_Missense_Mutation_p.N114D	NM_183239.1	NP_899062.1	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	142	GST C-terminal.		N -> D (in dbSNP:rs156697). {ECO:0000269|PubMed:12618591}.		cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)	p.N142D(1)		NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)	AGAATGCACTAATCTGAAGGC	0.527													G|||	2207	0.440695	0.8048	0.2752	5008	,	,		21195	0.255		0.3668	False		,,,				2504	0.3333				p.N142D		Atlas-SNP	.											GSTO2,NS,carcinoma,0,1	GSTO2	23	1	1	Substitution - Missense(1)	stomach(1)	c.A424G						PASS	.	G	,ASP/ASN,,ASP/ASN	3273,1133	405.8+/-333.6	1225,823,155	150.0	132.0	138.0		,340,,424	4.0	0.1	10	dbSNP_79	138	2929,5671	669.5+/-402.7	498,1933,1869	yes	intron,missense,intron,missense	GSTO2	NM_001191013.1,NM_001191014.1,NM_001191015.1,NM_183239.1	,23,,23	1723,2756,2024	GG,GA,AA		34.0581,25.7149,47.6857	,benign,,benign	,114/216,,142/244	106039185	6202,6804	2203	4300	6503	SO:0001583	missense	119391	exon5			TGCACTAATCTGA	AY191318	CCDS7556.1, CCDS53574.1, CCDS53575.1	10q25.1	2012-06-21			ENSG00000065621	ENSG00000065621	2.5.1.18, 1.8.5.1, 1.20.4.2	"""Glutathione S-transferases / Soluble"""	23064	protein-coding gene	gene with protein product		612314				12618591	Standard	NM_001191013		Approved		uc001kyb.3	Q9H4Y5	OTTHUMG00000019006	ENST00000338595.2:c.424A>G	10.37:g.106039185A>G	ENSP00000345023:p.Asn142Asp	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_183239	A8K771|B4DJW6|E7ESD6|Q49TW5|Q5GM70|Q5JU15|Q86WP3	Missense_Mutation	SNP	ENST00000338595.2	37	CCDS7556.1	936	0.42857142857142855	399	0.8109756097560976	114	0.3149171270718232	152	0.26573426573426573	271	0.3575197889182058	G	0.500	-0.871174	0.02570	0.742851	0.340581	ENSG00000065621	ENST00000369708;ENST00000338595;ENST00000401888;ENST00000369707	T;T;T	0.12774	2.65;3.17;2.65	5.87	3.96	0.45880	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.333001	0.34986	N	0.003530	T	0.00012	0.0000	N	0.01048	-1.04	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.16660	-1.0395	9	0.12103	T	0.63	-7.1748	7.3566	0.26723	0.1496:0.1367:0.7137:0.0	rs156697;rs601755;rs11565111;rs17826262;rs60436392;rs156697	142	Q9H4Y5	GSTO2_HUMAN	D	142;142;142;114	ENSP00000345023:N142D;ENSP00000386011:N142D;ENSP00000358721:N114D	ENSP00000345023:N142D	N	+	1	0	GSTO2	106029175	0.009000	0.17119	0.081000	0.20488	0.253000	0.25986	0.748000	0.26305	0.851000	0.35264	-0.733000	0.03571	AAT	A|0.537;G|0.463	0.463	strong		0.527	GSTO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050210.2	NM_183239	
OPLAH	26873	hgsc.bcm.edu	37	8	145114844	145114844	+	Missense_Mutation	SNP	C	C	T	rs7004867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145114844C>T	ENST00000426825.1	-	2	173	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	31					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTTTAAGACCCGCACGTGCCC	0.667													C|||	309	0.0617013	0.1195	0.0504	5008	,	,		16649	0.001		0.0865	False		,,,				2504	0.0286				p.R31Q		Atlas-SNP	.											OPLAH,NS,carcinoma,0,2	OPLAH	78	2	0			c.G92A						PASS	.	C	GLN/ARG	424,3430		22,380,1525	34.0	40.0	38.0		92	4.4	1.0	8	dbSNP_116	38	584,7650		18,548,3551	yes	missense	OPLAH	NM_017570.3	43	40,928,5076	TT,TC,CC		7.0925,11.0016,8.3388	possibly-damaging	31/1289	145114844	1008,11080	1927	4117	6044	SO:0001583	missense	26873	exon2			AAGACCCGCACGT	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.92G>A	8.37:g.145114844C>T	ENSP00000475943:p.Arg31Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		155	0.07097069597069597	68	0.13821138211382114	23	0.06353591160220995	1	0.0017482517482517483	63	0.08311345646437995	C	10.24	1.294808	0.23564	0.110016	0.070925	ENSG00000178814	ENST00000426825	.	.	.	5.24	4.37	0.52481	Hydantoinaseoxoprolinase, N-terminal (1);	0.100597	0.64402	N	0.000007	T	0.00271	0.0008	.	.	.	0.43771	P	0.003707000000000016	P	0.43169	0.8	B	0.37198	0.243	T	0.08207	-1.0733	7	0.29301	T	0.29	.	11.8979	0.52665	0.0:0.914:0.0:0.086	rs7004867;rs7004867	31	O14841	OPLA_HUMAN	Q	31	.	ENSP00000412071:R31Q	R	-	2	0	OPLAH	145186832	0.998000	0.40836	0.992000	0.48379	0.136000	0.21042	4.204000	0.58460	1.221000	0.43506	-0.369000	0.07265	CGG	C|0.921;T|0.079	0.079	strong		0.667	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520330	72520330	+	Silent	SNP	A	A	G	rs10823615	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:72520330A>G	ENST00000373207.1	+	22	3393	c.3393A>G	c.(3391-3393)gcA>gcG	p.A1131A	ADAMTS14_ENST00000373208.1_Silent_p.A1134A	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1131	Pro-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CAGATGCTGCAGAGCCTCCTG	0.652													G|||	1933	0.385982	0.4637	0.3386	5008	,	,		15750	0.3075		0.3091	False		,,,				2504	0.4744				p.A1134A		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.A3402G						PASS	.	G	,	1760,2646	643.8+/-397.9	374,1012,817	54.0	56.0	55.0		3393,3402	2.6	0.4	10	dbSNP_120	55	2977,5623	666.1+/-402.3	546,1885,1869	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	920,2897,2686	GG,GA,AA		34.6163,39.9455,36.4217	,	1131/1224,1134/1227	72520330	4737,8269	2203	4300	6503	SO:0001819	synonymous_variant	140766	exon22			TGCTGCAGAGCCT	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.3393A>G	10.37:g.72520330A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			A|0.634;G|0.366	0.366	strong		0.652	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
KBTBD6	89890	hgsc.bcm.edu	37	13	41705110	41705110	+	Missense_Mutation	SNP	T	T	C	rs200203929		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:41705110T>C	ENST00000379485.1	-	1	1772	c.1538A>G	c.(1537-1539)aAt>aGt	p.N513S	KBTBD6_ENST00000499385.2_Missense_Mutation_p.N447S	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	513										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)		CTGAAAGTCATTGCGCTTCAG	0.448																																					p.N513S		Atlas-SNP	.											.	KBTBD6	83	.	0			c.A1538G						PASS	.						87.0	84.0	85.0					13																	41705110		2203	4300	6503	SO:0001583	missense	89890	exon1			AAGTCATTGCGCT	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.1538A>G	13.37:g.41705110T>C	ENSP00000368799:p.Asn513Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	t	0.006	-2.062628	0.00386	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.64618	-0.11;-0.11	3.8	1.68	0.24146	Kelch-type beta propeller (1);	0.396703	0.27349	N	0.019776	T	0.25457	0.0619	N	0.01168	-0.975	0.23023	N	0.998416	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.20505	-1.0273	10	0.15066	T	0.55	.	5.5596	0.17135	0.0:0.6244:0.0:0.3756	.	447;513	F5GZN7;Q86V97	.;KBTB6_HUMAN	S	513;447	ENSP00000368799:N513S;ENSP00000444326:N447S	ENSP00000368799:N513S	N	-	2	0	KBTBD6	40603110	0.993000	0.37304	0.379000	0.26080	0.527000	0.34593	0.732000	0.26072	0.208000	0.20626	-0.464000	0.05259	AAT	T|0.999;C|0.001	0.001	weak		0.448	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903	
PLK4	10733	hgsc.bcm.edu	37	4	128811038	128811038	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:128811038A>G	ENST00000270861.5	+	7	1751	c.1477A>G	c.(1477-1479)Act>Gct	p.T493A	PLK4_ENST00000507249.1_Missense_Mutation_p.T459A|PLK4_ENST00000514379.1_Missense_Mutation_p.T452A|PLK4_ENST00000515069.1_Intron|PLK4_ENST00000513090.1_Missense_Mutation_p.T461A|RNU6-583P_ENST00000516012.1_RNA	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	493					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						AAGAAAAACTACTGAATATGA	0.358																																					p.T493A	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.A1477G						PASS	.						36.0	38.0	37.0					4																	128811038		2201	4296	6497	SO:0001583	missense	10733	exon7			AAAACTACTGAAT	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.1477A>G	4.37:g.128811038A>G	ENSP00000270861:p.Thr493Ala	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	37	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	A	0.176	-1.066534	0.01934	.	.	ENSG00000142731	ENST00000270861;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	4.57	0.741	0.18336	.	0.520099	0.21520	N	0.073224	T	0.11110	0.0271	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.29336	-1.0015	10	0.06625	T	0.88	-2.5911	3.9503	0.09366	0.3168:0.399:0.2842:0.0	.	461;493	O00444-2;O00444	.;PLK4_HUMAN	A	493;461;459;452	ENSP00000270861:T493A;ENSP00000427554:T461A;ENSP00000423412:T459A;ENSP00000423582:T452A	ENSP00000270861:T493A	T	+	1	0	PLK4	129030488	0.335000	0.24748	0.921000	0.36526	0.022000	0.10575	0.100000	0.15231	0.787000	0.33731	0.482000	0.46254	ACT	.	.	none		0.358	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3		
TTBK1	84630	hgsc.bcm.edu	37	6	43250710	43250710	+	Missense_Mutation	SNP	G	G	C	rs3800295	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43250710G>C	ENST00000259750.4	+	14	2315	c.2232G>C	c.(2230-2232)gaG>gaC	p.E744D		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	744	Glu-rich.		E -> D (in dbSNP:rs3800295). {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)			atgaggaagaggaagaagagg	0.582													g|||	393	0.0784744	0.031	0.0735	5008	,	,		16818	0.1062		0.0656	False		,,,				2504	0.1309				p.E744D		Atlas-SNP	.											.	TTBK1	124	.	0			c.G2232C						PASS	.	A	ASP/GLU	152,4254	97.1+/-135.8	2,148,2053	21.0	21.0	21.0		2232	-5.7	0.0	6	dbSNP_107	21	551,8047	140.1+/-196.7	19,513,3767	no	missense	TTBK1	NM_032538.1	45	21,661,5820	CC,CG,GG		6.4085,3.4498,5.406	benign	744/1322	43250710	703,12301	2203	4299	6502	SO:0001583	missense	84630	exon14			GGAAGAGGAAGAA	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.2232G>C	6.37:g.43250710G>C	ENSP00000259750:p.Glu744Asp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	174	0.07967032967032966	23	0.046747967479674794	32	0.08839779005524862	66	0.11538461538461539	53	0.06992084432717678	g	0.016	-1.533948	0.00951	0.034498	0.064085	ENSG00000146216	ENST00000259750	T	0.11712	2.75	2.85	-5.7	0.02421	.	1.090820	0.07179	N	0.853654	T	0.01029	0.0034	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46261	-0.9204	9	0.13470	T	0.59	.	2.3024	0.04165	0.4622:0.1228:0.2918:0.1233	rs3800295;rs34933052;rs56496037;rs3800295	744	Q5TCY1	TTBK1_HUMAN	D	744	ENSP00000259750:E744D	ENSP00000259750:E744D	E	+	3	2	TTBK1	43358688	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-3.395000	0.00486	-2.547000	0.00482	-2.148000	0.00335	GAG	G|0.937;C|0.063	0.063	strong		0.582	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
C7	730	hgsc.bcm.edu	37	5	40955561	40955561	+	Missense_Mutation	SNP	G	G	C	rs1063499	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:40955561G>C	ENST00000313164.9	+	10	1525	c.1166G>C	c.(1165-1167)aGt>aCt	p.S389T		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	389	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		S -> T (polymorphism confirmed at protein level; dbSNP:rs1063499). {ECO:0000269|PubMed:22028381, ECO:0000269|PubMed:7730625}.		cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				TCTGGCCTTAGTTACCTAGAG	0.443													G|||	2410	0.48123	0.3048	0.5317	5008	,	,		18284	0.5218		0.5855	False		,,,				2504	0.5348				p.S389T		Atlas-SNP	.											.	C7	136	.	0			c.G1166C						PASS	.	G	THR/SER	1310,2488		218,874,807	127.0	125.0	126.0		1166	1.4	0.0	5	dbSNP_86	126	5060,3192		1557,1946,623	yes	missense	C7	NM_000587.2	58	1775,2820,1430	CC,CG,GG		38.6815,34.4918,47.1369	probably-damaging	389/844	40955561	6370,5680	1899	4126	6025	SO:0001583	missense	730	exon10			GCCTTAGTTACCT	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.1166G>C	5.37:g.40955561G>C	ENSP00000322061:p.Ser389Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	1118	0.5119047619047619	162	0.32926829268292684	198	0.5469613259668509	301	0.5262237762237763	457	0.6029023746701847	G	15.03	2.712446	0.48517	0.344918	0.613185	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.64438	-0.1	5.26	1.41	0.22369	Membrane attack complex component/perforin (MACPF) domain (3);	0.492287	0.23504	N	0.047475	T	0.00012	0.0000	M	0.81497	2.545	0.51767	P	6.799999999995698E-5	P	0.50819	0.939	P	0.51324	0.666	T	0.48525	-0.9028	9	0.45353	T	0.12	-1.6355	7.182	0.25778	0.2061:0.1232:0.6707:0.0	rs1063499;rs1801080;rs3828508;rs56494548;rs57733938;rs1063499	389	P10643	CO7_HUMAN	T	389;229	ENSP00000322061:S389T	ENSP00000322061:S389T	S	+	2	0	C7	40991318	0.790000	0.28787	0.049000	0.19019	0.789000	0.44602	1.379000	0.34340	0.031000	0.15407	0.655000	0.94253	AGT	G|0.499;C|0.499	0.499	strong		0.443	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
MUC7	4589	hgsc.bcm.edu	37	4	71347185	71347185	+	Missense_Mutation	SNP	T	T	C	rs79807294	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71347185T>C	ENST00000304887.5	+	3	914	c.724T>C	c.(724-726)Tct>Cct	p.S242P	MUC7_ENST00000413702.1_Missense_Mutation_p.S242P|MUC7_ENST00000456088.1_Missense_Mutation_p.S242P	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	242	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			ACCCACACCTTCTGCAACTAC	0.592																																					p.S242P		Atlas-SNP	.											MUC7,right_upper_lobe,carcinoma,0,4	MUC7	91	4	0			c.T724C						scavenged	.						422.0	341.0	368.0					4																	71347185		2203	4300	6503	SO:0001583	missense	4589	exon4			ACACCTTCTGCAA	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.724T>C	4.37:g.71347185T>C	ENSP00000302021:p.Ser242Pro	Somatic	409	6	0.0146699		WXS	Illumina HiSeq	Phase_I	293	44	0.150171	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	T	9.595	1.127046	0.20959	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.52754	0.65;0.65;0.65	1.88	-3.76	0.04359	.	.	.	.	.	T	0.26048	0.0635	N	0.24115	0.695	0.09310	N	1	B	0.24823	0.112	B	0.17722	0.019	T	0.17837	-1.0356	8	.	.	.	0.6471	6.6904	0.23167	0.7198:0.0:0.0:0.2802	.	242	Q8TAX7	MUC7_HUMAN	P	242	ENSP00000407422:S242P;ENSP00000400585:S242P;ENSP00000302021:S242P	.	S	+	1	0	MUC7	71381774	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.151000	0.01289	-0.798000	0.04444	-0.438000	0.05819	TCT	T|0.993;C|0.007	0.007	strong		0.592	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
B3GAT2	135152	hgsc.bcm.edu	37	6	71665986	71665986	+	Silent	SNP	G	G	A	rs1574490	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:71665986G>A	ENST00000230053.6	-	1	755	c.147C>T	c.(145-147)ggC>ggT	p.G49G		NM_080742.2	NP_542780.1	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2	49					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						GGAGTCGGGCGCCCCCGCGGC	0.711													A|||	2668	0.532748	0.6104	0.6066	5008	,	,		11241	0.6448		0.3926	False		,,,				2504	0.4039				p.G49G		Atlas-SNP	.											B3GAT2,bladder,carcinoma,-1,1	B3GAT2	33	1	0			c.C147T						PASS	.	A		2383,1877		699,985,446	11.0	14.0	13.0		147	-1.9	0.0	6	dbSNP_88	13	3542,4666		858,1826,1420	no	coding-synonymous	B3GAT2	NM_080742.2		1557,2811,1866	AA,AG,GG		43.153,44.061,47.5217		49/324	71665986	5925,6543	2130	4104	6234	SO:0001819	synonymous_variant	135152	exon1			TCGGGCGCCCCCG	AB075843	CCDS4974.1	6q12	2014-07-08	2014-07-08		ENSG00000112309	ENSG00000112309	2.4.1.135	"""Beta-1,3-glucuronyltransferases"""	922	protein-coding gene	gene with protein product	"""glucuronosyltransferase S"", ""galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2"""	607497				12383500	Standard	NM_080742		Approved	GlcAT-S	uc003pfv.3	Q9NPZ5	OTTHUMG00000014997	ENST00000230053.6:c.147C>T	6.37:g.71665986G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_080742	Q5JS09|Q8TF38|Q96NK4	Silent	SNP	ENST00000230053.6	37	CCDS4974.1																																																																																			G|0.463;A|0.537	0.537	strong		0.711	B3GAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041150.2	NM_080742	
ERCC5	2073	hgsc.bcm.edu	37	13	103528002	103528002	+	Missense_Mutation	SNP	G	G	C	rs17655	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103528002G>C	ENST00000355739.4	+	15	4733	c.3310G>C	c.(3310-3312)Gat>Cat	p.D1104H	ERCC5_ENST00000472247.1_3'UTR|ERCC5_ENST00000375954.1_Missense_Mutation_p.D337H	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	1104			D -> H (in dbSNP:rs17655). {ECO:0000269|PubMed:8483504}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTCAAGTGAAGATGCTGAAAG	0.428			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1810	0.361422	0.5008	0.2709	5008	,	,		19196	0.4623		0.2495	False		,,,				2504	0.2485				p.D1558H		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	.	.	0			c.G4672C	GRCh37	CM063964	ERCC5	M	rs17655	PASS	.	G	HIS/ASP,HIS/ASP	2009,2397	558.4+/-380.0	460,1089,654	53.0	55.0	54.0		3310,4672	4.1	0.0	13	dbSNP_63	54	1968,6632	344.4+/-325.3	237,1494,2569	yes	missense,missense	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	81,81	697,2583,3223	CC,CG,GG		22.8837,45.5969,30.5782	,	1104/1187,1558/1641	103528002	3977,9029	2203	4300	6503	SO:0001583	missense	0	exon23	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGTGAAGATGCTG	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.3310G>C	13.37:g.103528002G>C	ENSP00000347978:p.Asp1104His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	823	0.3768315018315018	245	0.49796747967479676	98	0.27071823204419887	283	0.49475524475524474	197	0.2598944591029024	G	18.44	3.624019	0.66901	0.455969	0.228837	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955;ENST00000375954	T;T	0.08807	3.27;3.05	4.96	4.11	0.48088	.	0.687220	0.14782	N	0.298701	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	1.0	D	0.65815	0.995	P	0.57371	0.819	T	0.48514	-0.9029	9	0.40728	T	0.16	-12.1551	13.3474	0.60582	0.0764:0.0:0.9236:0.0	rs17655;rs3188002;rs3825521;rs16960665;rs52825398;rs17655	1104	P28715	ERCC5_HUMAN	H	1529;1104;936;337	ENSP00000347978:D1104H;ENSP00000365121:D337H	ENSP00000347978:D1104H	D	+	1	0	ERCC5	102326003	1.000000	0.71417	0.047000	0.18901	0.012000	0.07955	3.757000	0.55212	1.221000	0.43506	0.650000	0.86243	GAT	G|0.655;C|0.345	0.345	strong		0.428	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
GPRC6A	222545	hgsc.bcm.edu	37	6	117114025	117114025	+	Silent	SNP	G	G	A	rs6901250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	85	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	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		
SORCS1	114815	hgsc.bcm.edu	37	10	108380213	108380213	+	Silent	SNP	G	G	A	rs4917481	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000478809.2_5'Flank|SORCS1_ENST00000369698.1_Silent_p.Y458Y	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	85	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	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	
EIF2AK3	9451	hgsc.bcm.edu	37	2	88879131	88879131	+	Silent	SNP	T	T	C	rs1805164	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:88879131T>C	ENST00000303236.3	-	11	2092	c.1791A>G	c.(1789-1791)caA>caG	p.Q597Q	EIF2AK3_ENST00000419748.1_Silent_p.Q446Q	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	597	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						GTCCCAGGCATTGAATTGGCT	0.338													T|||	1293	0.258187	0.1989	0.3617	5008	,	,		17972	0.3115		0.3062	False		,,,				2504	0.1605				p.Q597Q	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A1791G						PASS	.	T		955,3451	361.1+/-315.5	104,747,1352	84.0	82.0	83.0		1791	3.2	1.0	2	dbSNP_89	83	2597,6003	420.0+/-353.3	404,1789,2107	no	coding-synonymous	EIF2AK3	NM_004836.5		508,2536,3459	CC,CT,TT		30.1977,21.675,27.3105		597/1117	88879131	3552,9454	2203	4300	6503	SO:0001819	synonymous_variant	9451	exon11			CAGGCATTGAATT	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.1791A>G	2.37:g.88879131T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Silent	SNP	ENST00000303236.3	37	CCDS33241.1																																																																																			T|0.725;C|0.275	0.275	strong		0.338	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331549	21331549	+	Missense_Mutation	SNP	T	T	C	rs4149056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21331549T>C	ENST00000256958.2	+	6	617	c.521T>C	c.(520-522)gTg>gCg	p.V174A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	174			V -> A (decreased transport activity; dbSNP:rs4149056). {ECO:0000269|PubMed:11477075, ECO:0000269|PubMed:12130747}.		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)	TGGATATATGTGTTCATGGGT	0.343													T|||	439	0.0876597	0.0136	0.134	5008	,	,		15111	0.123		0.161	False		,,,				2504	0.0429				p.V174A		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.T521C	GRCh37	CM043777	SLCO1B1	M	rs4149056	PASS	.	T	ALA/VAL	159,4247	108.6+/-147.0	3,153,2047	144.0	135.0	138.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	521	3.6	0.1	12	dbSNP_110	138	1336,7264	261.4+/-283.8	119,1098,3083	yes	missense	SLCO1B1	NM_006446.4	64	122,1251,5130	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	15.5349,3.6087,11.4947	probably-damaging	174/692	21331549	1495,11511	2203	4300	6503	SO:0001583	missense	10599	exon6			TATATGTGTTCAT		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.521T>C	12.37:g.21331549T>C	ENSP00000256958:p.Val174Ala	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	201	89	0.442786	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	268	0.1227106227106227	13	0.026422764227642278	50	0.13812154696132597	73	0.12762237762237763	132	0.1741424802110818	T	12.39	1.923669	0.34002	0.036087	0.155349	ENSG00000134538	ENST00000256958	T	0.43294	0.95	3.62	3.62	0.41486	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.163062	0.39687	N	0.001300	T	0.00440	0.0014	M	0.92833	3.35	0.54753	P	1.4999999999987246E-5	D	0.89917	1.0	D	0.83275	0.996	T	0.43196	-0.9406	9	0.87932	D	0	.	12.6758	0.56893	0.0:0.0:0.0:1.0	rs4149056;rs52816141;rs60037639;rs4149056	174	Q9Y6L6	SO1B1_HUMAN	A	174	ENSP00000256958:V174A	ENSP00000256958:V174A	V	+	2	0	SLCO1B1	21222816	1.000000	0.71417	0.058000	0.19502	0.015000	0.08874	7.326000	0.79133	1.641000	0.50575	0.260000	0.18958	GTG	T|0.890;C|0.110	0.110	strong		0.343	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
SPAG16	79582	hgsc.bcm.edu	37	2	214794743	214794743	+	Missense_Mutation	SNP	A	A	C	rs12623569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:214794743A>C	ENST00000331683.5	+	12	1369	c.1274A>C	c.(1273-1275)aAa>aCa	p.K425T	SPAG16_ENST00000374309.3_Missense_Mutation_p.K331T	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	425			K -> T (in dbSNP:rs12623569). {ECO:0000269|PubMed:11867345, ECO:0000269|PubMed:12391165}.		cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		GATCTATGTAAAGGCGATTGC	0.428													A|||	1386	0.276757	0.2738	0.3112	5008	,	,		17159	0.4067		0.2843	False		,,,				2504	0.1145				p.K425T		Atlas-SNP	.											.	SPAG16	134	.	0			c.A1274C						PASS	.	A	THR/LYS	1197,3209	419.6+/-338.7	147,903,1153	119.0	117.0	118.0		1274	4.3	0.6	2	dbSNP_120	118	2253,6347	382.3+/-340.3	295,1663,2342	yes	missense	SPAG16	NM_024532.3	78	442,2566,3495	CC,CA,AA		26.1977,27.1675,26.5262	benign	425/632	214794743	3450,9556	2203	4300	6503	SO:0001583	missense	79582	exon12			TATGTAAAGGCGA	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1274A>C	2.37:g.214794743A>C	ENSP00000332592:p.Lys425Thr	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	209	110	0.526316	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	653	0.298992673992674	114	0.23170731707317074	110	0.30386740331491713	220	0.38461538461538464	209	0.2757255936675462	A	9.017	0.983924	0.18889	0.271675	0.261977	ENSG00000144451	ENST00000331683;ENST00000374309	T;T	0.78707	-1.2;-1.2	5.48	4.29	0.51040	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.277074	0.29466	N	0.012065	T	0.00012	0.0000	N	0.02181	-0.65	0.27912	P	0.9385632	B;B;B;B	0.17667	0.008;0.023;0.002;0.008	B;B;B;B	0.19391	0.011;0.025;0.002;0.011	T	0.12708	-1.0537	9	0.02654	T	1	.	11.4259	0.50009	0.8484:0.1516:0.0:0.0	rs12623569;rs52808897;rs59619307;rs12623569	331;276;365;425	B4DYB5;Q8N0X2-2;Q4G1A2;Q8N0X2	.;.;.;SPG16_HUMAN	T	425;331	ENSP00000332592:K425T;ENSP00000363428:K331T	ENSP00000332592:K425T	K	+	2	0	SPAG16	214502988	0.999000	0.42202	0.563000	0.28383	0.260000	0.26232	2.907000	0.48743	0.864000	0.35578	0.533000	0.62120	AAA	A|0.722;C|0.278	0.278	strong		0.428	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
HOMER3	9454	hgsc.bcm.edu	37	19	19049198	19049198	+	Silent	SNP	G	G	A	rs1064351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19049198G>A	ENST00000539827.1	-	3	919	c.267C>T	c.(265-267)taC>taT	p.Y89Y	AC005932.1_ENST00000601106.1_RNA|HOMER3_ENST00000594439.1_Silent_p.Y89Y|HOMER3_ENST00000594794.1_Intron|HOMER3_ENST00000392351.3_Silent_p.Y89Y|HOMER3_ENST00000542541.2_Silent_p.Y89Y|HOMER3_ENST00000221222.11_Silent_p.Y89Y|HOMER3_ENST00000355887.6_Silent_p.Y89Y|HOMER3_ENST00000433218.2_Silent_p.Y89Y			Q9NSC5	HOME3_HUMAN	homer homolog 3 (Drosophila)	89	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				G-protein coupled glutamate receptor signaling pathway (GO:0007216)|protein targeting (GO:0006605)	basal part of cell (GO:0045178)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(3)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10			Epithelial(12;0.0107)			AGCCCAGGCCGTAGACTGTGT	0.597													G|||	1405	0.280551	0.1051	0.5231	5008	,	,		15444	0.1736		0.4423	False		,,,				2504	0.2894				p.Y89Y		Atlas-SNP	.											.	HOMER3	19	.	0			c.C267T						PASS	.	G	,,,	657,3749	278.7+/-274.4	47,563,1593	110.0	103.0	106.0		267,267,267,267	-4.1	0.7	19	dbSNP_86	106	3755,4845	533.5+/-382.4	810,2135,1355	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HOMER3	NM_001145721.1,NM_001145722.1,NM_001145724.1,NM_004838.3	,,,	857,2698,2948	AA,AG,GG		43.6628,14.9115,33.9228	,,,	89/359,89/362,89/326,89/362	19049198	4412,8594	2203	4300	6503	SO:0001819	synonymous_variant	9454	exon4			CAGGCCGTAGACT	Y18894	CCDS12391.1, CCDS46022.1, CCDS46023.1	19p13.1	2008-02-05				ENSG00000051128			17514	protein-coding gene	gene with protein product		604800				10653696, 9808459	Standard	NM_004838		Approved	HOMER-3	uc002nkv.2	Q9NSC5		ENST00000539827.1:c.267C>T	19.37:g.19049198G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	132	52	0.393939	NM_001145722	E9PCW9|O14580|O95350|Q9NSB9|Q9NSC0|Q9NSC1	Silent	SNP	ENST00000539827.1	37	CCDS12391.1																																																																																			G|0.682;A|0.318	0.318	strong		0.597	HOMER3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464607.1		
BTBD10	84280	hgsc.bcm.edu	37	11	13441126	13441126	+	Silent	SNP	A	A	G	rs7114113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:13441126A>G	ENST00000278174.5	-	4	710	c.465T>C	c.(463-465)aaT>aaC	p.N155N	BTBD10_ENST00000532261.1_5'UTR|BTBD10_ENST00000530907.1_Silent_p.N163N|BTBD10_ENST00000528120.1_Silent_p.N107N	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	155	Interaction with AKT family members. {ECO:0000250|UniProtKB:Q80X66}.					nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		CTTCTTTTGCATTTTCATATA	0.428													A|||	742	0.148163	0.084	0.3012	5008	,	,		16577	0.1687		0.1481	False		,,,				2504	0.1053				p.N155N		Atlas-SNP	.											.	BTBD10	43	.	0			c.T465C						PASS	.	A		379,4021	191.6+/-217.2	19,341,1840	238.0	229.0	232.0		465	4.2	1.0	11	dbSNP_116	232	1493,7095	284.4+/-296.6	117,1259,2918	no	coding-synonymous	BTBD10	NM_032320.5		136,1600,4758	GG,GA,AA		17.3847,8.6136,14.4133		155/476	13441126	1872,11116	2200	4294	6494	SO:0001819	synonymous_variant	84280	exon4			TTTTGCATTTTCA	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.465T>C	11.37:g.13441126A>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	192	80	0.416667	NM_032320	B7Z228|Q86WG1	Silent	SNP	ENST00000278174.5	37	CCDS7811.1																																																																																			A|0.855;G|0.145	0.145	strong		0.428	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
PEPD	5184	hgsc.bcm.edu	37	19	33878837	33878837	+	Missense_Mutation	SNP	G	G	A	rs17570	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33878837G>A	ENST00000244137.7	-	14	1336	c.1303C>T	c.(1303-1305)Ctt>Ttt	p.L435F	PEPD_ENST00000436370.3_Missense_Mutation_p.L371F|PEPD_ENST00000591968.1_5'UTR|PEPD_ENST00000397032.4_Missense_Mutation_p.L394F	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	435			L -> F (in dbSNP:rs17570). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)					TCGCGGTTAAGGAAGGAGGCG	0.662													A|||	1394	0.278355	0.4932	0.2176	5008	,	,		16600	0.1915		0.2565	False		,,,				2504	0.1431				p.L435F		Atlas-SNP	.											.	PEPD	48	.	0			c.C1303T						PASS	.	A	PHE/LEU,PHE/LEU,PHE/LEU	1543,2345		326,891,727	9.0	14.0	12.0		1303,1180,1111	3.4	1.0	19	dbSNP_63	12	1977,6269		270,1437,2416	yes	missense,missense,missense	PEPD	NM_000285.3,NM_001166056.1,NM_001166057.1	22,22,22	596,2328,3143	AA,AG,GG		23.9753,39.6862,29.0094	benign,benign,benign	435/494,394/453,371/430	33878837	3520,8614	1944	4123	6067	SO:0001583	missense	5184	exon14			GGTTAAGGAAGGA	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.1303C>T	19.37:g.33878837G>A	ENSP00000244137:p.Leu435Phe	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	37	CCDS42544.1	646	0.2957875457875458	259	0.5264227642276422	87	0.24033149171270718	100	0.17482517482517482	200	0.2638522427440633	A	4.177	0.031489	0.08101	0.396862	0.239753	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	T;T;T	0.79749	-1.3;-0.93;-1.29	5.52	3.36	0.38483	Peptidase M24, structural domain (3);	0.090943	0.85682	N	0.000000	T	0.00012	0.0000	N	0.25380	0.74	0.09310	P	1.0	B;B;B;B	0.09022	0.001;0.002;0.001;0.001	B;B;B;B	0.17722	0.019;0.019;0.019;0.019	T	0.43376	-0.9395	9	0.07990	T	0.79	-9.2384	3.6997	0.08378	0.4988:0.0:0.1906:0.3105	rs17570;rs2303102;rs16968055;rs17398453;rs17856803;rs59385819	371;394;435;435	E9PCE8;A8MX47;P12955;A8K3Z1	.;.;PEPD_HUMAN;.	F	435;394;371	ENSP00000244137:L435F;ENSP00000380226:L394F;ENSP00000391890:L371F	ENSP00000244137:L435F	L	-	1	0	PEPD	38570677	1.000000	0.71417	0.996000	0.52242	0.881000	0.50899	2.274000	0.43390	0.388000	0.25054	-0.490000	0.04691	CTT	G|0.706;A|0.294	0.294	strong		0.662	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285	
MYO18B	84700	hgsc.bcm.edu	37	22	26222454	26222454	+	Missense_Mutation	SNP	C	C	T	rs9624909	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26222454C>T	ENST00000407587.2	+	14	2943	c.2774C>T	c.(2773-2775)tCa>tTa	p.S925L	MYO18B_ENST00000536101.1_Missense_Mutation_p.S925L|MYO18B_ENST00000335473.7_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	182	0	0		WXS	Illumina HiSeq	Phase_I	213	101	0.474178	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	
OGFOD3	79701	hgsc.bcm.edu	37	17	80373452	80373452	+	Silent	SNP	C	C	T	rs4789769	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80373452C>T	ENST00000313056.5	-	2	277	c.126G>A	c.(124-126)ccG>ccA	p.P42P	HEXDC_ENST00000337014.6_5'Flank|OGFOD3_ENST00000329197.5_Silent_p.P42P|Y_RNA_ENST00000364369.1_RNA	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	42						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										TCCTTAGCCACGGCCTCTGCC	0.672													C|||	1640	0.327476	0.2678	0.2464	5008	,	,		15837	0.6687		0.2515	False		,,,				2504	0.1922				p.P42P		Atlas-SNP	.											.	.	.	.	0			c.G126A						PASS	.	C	,	1174,3232	395.4+/-329.6	140,894,1169	29.0	32.0	31.0		126,126	-4.3	0.0	17	dbSNP_111	31	1897,6703	325.9+/-317.1	198,1501,2601	no	coding-synonymous,coding-synonymous	C17orf101	NM_024648.2,NM_175902.4	,	338,2395,3770	TT,TC,CC		22.0581,26.6455,23.6122	,	42/320,42/332	80373452	3071,9935	2203	4300	6503	SO:0001819	synonymous_variant	79701	exon2			TAGCCACGGCCTC	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 101"""	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.126G>A	17.37:g.80373452C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Silent	SNP	ENST00000313056.5	37	CCDS11811.1																																																																																			C|0.728;T|0.272	0.272	strong		0.672	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
PLG	5340	hgsc.bcm.edu	37	6	161139857	161139857	+	Silent	SNP	A	A	G	rs13231	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	87	0	0		WXS	Illumina HiSeq	Phase_I	85	48	0.564706	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	
MMP14	4323	hgsc.bcm.edu	37	14	23312554	23312554	+	Silent	SNP	C	C	G	rs2236302	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23312554C>G	ENST00000311852.6	+	5	1038	c.777C>G	c.(775-777)ccC>ccG	p.P259P	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	259					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)	TCATGGCACCCTTTTACCAGT	0.587													C|||	815	0.16274	0.3048	0.1383	5008	,	,		18326	0.13		0.1163	False		,,,				2504	0.0695				p.P259P		Atlas-SNP	.											.	MMP14	40	.	0			c.C777G						PASS	.	C		1263,3143	432.8+/-343.4	196,871,1136	107.0	104.0	105.0		777	-0.9	0.6	14	dbSNP_98	105	947,7653	208.7+/-250.1	50,847,3403	no	coding-synonymous	MMP14	NM_004995.2		246,1718,4539	GG,GC,CC		11.0116,28.6655,16.9922		259/583	23312554	2210,10796	2203	4300	6503	SO:0001819	synonymous_variant	4323	exon5			GGCACCCTTTTAC		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.777C>G	14.37:g.23312554C>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	37	CCDS9577.1																																																																																			C|0.833;G|0.167	0.167	strong		0.587	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
LAMA1	284217	hgsc.bcm.edu	37	18	6986259	6986259	+	Silent	SNP	G	G	A	rs62081531	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:6986259G>A	ENST00000389658.3	-	37	5349	c.5256C>T	c.(5254-5256)caC>caT	p.H1752H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1752	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.H1752H(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTGAAAGGACGTGGCTTGCTG	0.468													g|||	690	0.13778	0.0068	0.147	5008	,	,		17245	0.1915		0.2326	False		,,,				2504	0.1554				p.H1752H		Atlas-SNP	.											LAMA1,colon,carcinoma,0,2	LAMA1	458	2	1	Substitution - coding silent(1)	stomach(1)	c.C5256T						scavenged	.	G		233,4173	138.4+/-174.2	7,219,1977	154.0	133.0	140.0		5256	3.2	0.8	18	dbSNP_129	140	2248,6352	381.0+/-339.9	295,1658,2347	no	coding-synonymous	LAMA1	NM_005559.3		302,1877,4324	AA,AG,GG		26.1395,5.2882,19.0758		1752/3076	6986259	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon37			AAGGACGTGGCTT	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.5256C>T	18.37:g.6986259G>A		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	180	81	0.45	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.810;A|0.190	0.190	strong		0.468	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
TTN	7273	hgsc.bcm.edu	37	2	179464527	179464527	+	Missense_Mutation	SNP	T	T	C	rs1001238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179464527T>C	ENST00000591111.1	-	239	51402	c.51178A>G	c.(51178-51180)Aat>Gat	p.N17060D	TTN_ENST00000589042.1_Missense_Mutation_p.N18701D|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N9761D|TTN_ENST00000460472.2_Missense_Mutation_p.N9636D|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N9828D|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N16133D|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17060	Ig-like 102.		N -> D. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTTAACATTGGTTCCTTCT	0.383													C|||	2568	0.51278	0.5688	0.4078	5008	,	,		19770	0.7252		0.2535	False		,,,				2504	0.5593				p.N18701D		Atlas-SNP	.											.	TTN	18412	.	0			c.A56101G						PASS	.	C	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	1980,1734		541,898,418	95.0	87.0	90.0		29482,29281,48397,28906	5.6	1.0	2	dbSNP_86	90	1846,6320		195,1456,2432	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	23,23,23,23	736,2354,2850	CC,CT,TT		22.6059,46.6882,32.2054	benign,benign,benign,benign	9828/27119,9761/27052,16133/33424,9636/26927	179464527	3826,8054	1857	4083	5940	SO:0001583	missense	7273	exon289			TAACATTGGTTCC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.51178A>G	2.37:g.179464527T>C	ENSP00000465570:p.Asn17060Asp	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		998	0.45695970695970695	285	0.5792682926829268	131	0.36187845303867405	395	0.6905594405594405	187	0.24670184696569922	C	15.22	2.767580	0.49574	0.533118	0.226059	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.6	5.6	0.85130	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02751	-0.505	0.38372	P	0.05510300000000001	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.34030	-0.9845	8	0.87932	D	0	.	14.7926	0.69854	0.0:0.9306:0.0:0.0694	rs1001238;rs52825036;rs60652051;rs1001238	9636;9761;9828;17060	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	16133;9636;9828;9761;9634	ENSP00000343764:N16133D;ENSP00000434586:N9636D;ENSP00000340554:N9828D;ENSP00000352154:N9761D	ENSP00000340554:N9828D	N	-	1	0	TTN	179172772	1.000000	0.71417	0.998000	0.56505	0.770000	0.43624	6.042000	0.70996	1.386000	0.46466	-0.226000	0.12346	AAT	T|0.561;C|0.439	0.439	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
WNK1	65125	hgsc.bcm.edu	37	12	939302	939302	+	Silent	SNP	A	A	G	rs10774466	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:939302A>G	ENST00000315939.6	+	4	1930	c.1287A>G	c.(1285-1287)gcA>gcG	p.A429A	WNK1_ENST00000530271.2_Silent_p.A429A|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000537687.1_Silent_p.A429A|WNK1_ENST00000535572.1_Silent_p.A429A	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	429	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			AAAATGCTGCACAGATCTACC	0.443													G|||	3473	0.69349	0.5076	0.7594	5008	,	,		22184	0.871		0.7406	False		,,,				2504	0.6667				p.A429A	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											WNK1_ENST00000537687,NS,carcinoma,+1,2	WNK1	403	2	0			c.A1287G						PASS	.	G	,,,	2475,1931	551.5+/-378.3	686,1103,414	189.0	153.0	165.0		1287,1287,1287,1287	-10.1	0.1	12	dbSNP_120	165	6441,2159	369.9+/-335.7	2427,1587,286	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	3113,2690,700	GG,GA,AA		25.1047,43.8266,31.447	,,,	429/2643,429/2135,429/2383,429/2635	939302	8916,4090	2203	4300	6503	SO:0001819	synonymous_variant	65125	exon4			TGCTGCACAGATC	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.1287A>G	12.37:g.939302A>G		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			A|0.298;G|0.702	0.702	strong		0.443	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73142296	73142296	+	Missense_Mutation	SNP	C	C	T	rs2973571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73142296C>T	ENST00000426542.2	+	11	1651	c.1631C>T	c.(1630-1632)tCg>tTg	p.S544L	ARHGEF28_ENST00000437974.1_Missense_Mutation_p.S544L|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.S544L|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.S231L|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.S544L|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.S544L|ARHGEF28_ENST00000513841.1_3'UTR|ARHGEF28_ENST00000287898.5_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	113	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	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		
TRPV3	162514	hgsc.bcm.edu	37	17	3422032	3422032	+	Silent	SNP	G	G	A	rs7216486	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3422032G>A	ENST00000576742.1	-	15	2244	c.1923C>T	c.(1921-1923)gaC>gaT	p.D641D	TRPV3_ENST00000572519.1_Silent_p.D641D|TRPV3_ENST00000301365.4_Silent_p.D641D	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	641					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GGATGTTCAGGTCACCCAGGC	0.507													g|||	3350	0.66893	0.5219	0.5994	5008	,	,		21621	0.9524		0.5517	False		,,,				2504	0.7454				p.D641D		Atlas-SNP	.											.	TRPV3	85	.	0			c.C1923T						PASS	.	G		2403,2003	614.0+/-392.3	658,1087,458	165.0	130.0	142.0		1923	5.7	1.0	17	dbSNP_116	142	4483,4117	590.3+/-392.7	1160,2163,977	no	coding-synonymous	TRPV3	NM_145068.2		1818,3250,1435	AA,AG,GG		47.8721,45.4607,47.0552		641/791	3422032	6886,6120	2203	4300	6503	SO:0001819	synonymous_variant	162514	exon15			GTTCAGGTCACCC	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.1923C>T	17.37:g.3422032G>A		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	185	185	1	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	37	CCDS11029.1																																																																																			G|0.418;A|0.582	0.582	strong		0.507	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
ASCC2	84164	hgsc.bcm.edu	37	22	30200801	30200801	+	Silent	SNP	G	G	C	rs117333854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:30200801G>C	ENST00000397771.2	-	14	1356	c.1179C>G	c.(1177-1179)gcC>gcG	p.A393A	ASCC2_ENST00000307790.3_Silent_p.A393A|ASCC2_ENST00000542393.1_Silent_p.A317A|ASCC2_ENST00000478812.1_5'Flank			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			GGAGGATGTAGGCAGTCCGCG	0.552													G|||	46	0.0091853	0.0015	0.0014	5008	,	,		20721	0.0		0.008	False		,,,				2504	0.0358				p.A393A		Atlas-SNP	.											.	ASCC2	53	.	0			c.C1179G						PASS	.	G	,	7,4399	12.9+/-30.5	0,7,2196	275.0	235.0	248.0		951,1179	2.9	1.0	22	dbSNP_132	248	54,8546	34.3+/-88.2	0,54,4246	no	coding-synonymous,coding-synonymous	ASCC2	NM_001242906.1,NM_032204.4	,	0,61,6442	CC,CG,GG		0.6279,0.1589,0.469	,	317/682,393/758	30200801	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	84164	exon13			GATGTAGGCAGTC	AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"""ASC 1 complex subunit P100"""	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.1179C>G	22.37:g.30200801G>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	216	103	0.476852	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Silent	SNP	ENST00000397771.2	37	CCDS13869.1																																																																																			G|0.996;C|0.004	0.004	strong		0.552	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204	
SRP72	6731	hgsc.bcm.edu	37	4	57333822	57333822	+	Silent	SNP	G	G	T	rs12513091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:57333822G>T	ENST00000342756.5	+	1	742	c.21G>T	c.(19-21)ggG>ggT	p.G7G	SRP72_ENST00000510663.1_Silent_p.G7G|SRP72_ENST00000504757.1_Silent_p.G7G	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	7					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)					GCGGCAGCGGGGGGGTGTCAG	0.642													G|||	1156	0.230831	0.1036	0.4092	5008	,	,		14542	0.2282		0.2127	False		,,,				2504	0.2975				p.G7G		Atlas-SNP	.											SRP72,NS,carcinoma,0,1	SRP72	59	1	0			c.G21T						PASS	.	G		515,3883		23,469,1707	15.0	17.0	16.0		21	1.5	1.0	4	dbSNP_120	16	1547,7047		120,1307,2870	no	coding-synonymous	SRP72	NM_006947.3		143,1776,4577	TT,TG,GG		18.0009,11.7099,15.8713		7/672	57333822	2062,10930	2199	4297	6496	SO:0001819	synonymous_variant	6731	exon1			CAGCGGGGGGGTG	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.21G>T	4.37:g.57333822G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	115	73	0.634783	NM_006947	G5E9Z8|Q7Z3C0	Silent	SNP	ENST00000342756.5	37	CCDS3506.1																																																																																			A|0.000;C|0.000;G|0.800;T|0.199	0.199	strong		0.642	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
SERPINI2	5276	hgsc.bcm.edu	37	3	167164187	167164187	+	Silent	SNP	A	A	G	rs2272138	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000264677.4_Silent_p.N378N|SERPINI2_ENST00000461846.1_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	47	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	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	
UBXN6	80700	hgsc.bcm.edu	37	19	4454083	4454083	+	Missense_Mutation	SNP	C	C	T	rs1127888	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4454083C>T	ENST00000301281.6	-	2	215	c.91G>A	c.(91-93)Gcc>Acc	p.A31T	UBXN6_ENST00000394765.3_5'UTR|CTB-50L17.9_ENST00000592034.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	31			A -> T (in dbSNP:rs1127888).			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						TCTTTGTGGGCCTTTTCCCTG	0.662													C|||	836	0.166933	0.09	0.3213	5008	,	,		14937	0.0645		0.2624	False		,,,				2504	0.1687				p.A31T		Atlas-SNP	.											.	UBXN6	27	.	0			c.G91A						PASS	.	C	,THR/ALA	527,3879	242.1+/-252.3	30,467,1706	103.0	117.0	112.0		,91	2.0	1.0	19	dbSNP_86	112	2330,6270	388.9+/-342.7	319,1692,2289	yes	utr-5,missense	UBXN6	NM_001171091.1,NM_025241.2	,58	349,2159,3995	TT,TC,CC		27.093,11.961,21.9668	,benign	,31/442	4454083	2857,10149	2203	4300	6503	SO:0001583	missense	80700	exon2			TGTGGGCCTTTTC	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.91G>A	19.37:g.4454083C>T	ENSP00000301281:p.Ala31Thr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	28	26	0.928571	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	381	0.17445054945054944	48	0.0975609756097561	104	0.287292817679558	37	0.06468531468531469	192	0.2532981530343008	C	8.633	0.894076	0.17613	0.11961	0.27093	ENSG00000167671	ENST00000301281	T	0.43294	0.95	4.13	1.96	0.26148	.	1.015050	0.07885	N	0.970198	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	1.0	B	0.06786	0.001	B	0.08055	0.003	T	0.33929	-0.9849	9	0.10902	T	0.67	-9.49	6.9264	0.24418	0.0:0.7783:0.0:0.2217	rs1127888;rs11558243	31	Q9BZV1	UBXN6_HUMAN	T	31	ENSP00000301281:A31T	ENSP00000301281:A31T	A	-	1	0	UBXN6	4405083	0.996000	0.38824	0.990000	0.47175	0.138000	0.21146	0.552000	0.23376	0.211000	0.20683	0.484000	0.47621	GCC	T|0.211;G|0.000;C|0.788	0.211	strong		0.662	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
VWDE	221806	hgsc.bcm.edu	37	7	12401021	12401021	+	Missense_Mutation	SNP	C	C	T	rs80272295	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	112	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	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	
WDR93	56964	hgsc.bcm.edu	37	15	90246336	90246336	+	Silent	SNP	A	A	G	rs16974175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90246336A>G	ENST00000268130.7	+	3	560	c.459A>G	c.(457-459)ttA>ttG	p.L153L	RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Silent_p.L153L|WDR93_ENST00000558000.1_Silent_p.L153L	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	153					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)			CCACAGATTTAGGGAATGAAA	0.388													G|||	1964	0.392173	0.5061	0.3631	5008	,	,		20249	0.2063		0.4016	False		,,,				2504	0.4407				p.L153L		Atlas-SNP	.											.	WDR93	63	.	0			c.A459G						PASS	.	G		2142,2258	594.6+/-388.3	529,1084,587	187.0	183.0	185.0		459	0.2	1.0	15	dbSNP_123	185	3848,4750	609.9+/-395.6	846,2156,1297	no	coding-synonymous	WDR93	NM_020212.1		1375,3240,1884	GG,GA,AA		44.7546,48.6818,46.084		153/687	90246336	5990,7008	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon3			AGATTTAGGGAAT		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.459A>G	15.37:g.90246336A>G		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			A|0.575;G|0.425	0.425	strong		0.388	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
UGT2B4	7363	hgsc.bcm.edu	37	4	70346565	70346565	+	Missense_Mutation	SNP	A	A	T	rs13119049|rs67904882	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70346565A>T	ENST00000305107.6	-	6	1420	c.1374T>A	c.(1372-1374)gaT>gaA	p.D458E	UGT2B4_ENST00000506580.1_5'UTR|AC108078.1_ENST00000583573.1_RNA|UGT2B4_ENST00000381096.3_Missense_Mutation_p.D322E|UGT2B4_ENST00000512583.1_3'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	458			D -> E (in dbSNP:rs13119049). {ECO:0000269|PubMed:10376768, ECO:0000269|Ref.7}.		cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	AGACTGCTCGATCAAGGGGCT	0.428													a|||	654	0.130591	0.1362	0.2205	5008	,	,		17820	0.0		0.2266	False		,,,				2504	0.0951				p.D458E		Atlas-SNP	.											.	UGT2B4	105	.	0			c.T1374A						PASS	.	A	GLU/ASP	628,3778		44,540,1619	112.0	113.0	112.0		1374	-3.8	0.0	4	dbSNP_121	112	2045,6555		261,1523,2516	no	missense	UGT2B4	NM_021139.2	45	305,2063,4135	TT,TA,AA		23.7791,14.2533,20.5521	possibly-damaging	458/529	70346565	2673,10333	2203	4300	6503	SO:0001583	missense	7363	exon6			TGCTCGATCAAGG	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.1374T>A	4.37:g.70346565A>T	ENSP00000305221:p.Asp458Glu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Missense_Mutation	SNP	ENST00000305107.6	37	CCDS43234.1	257	0.11767399267399267	52	0.10569105691056911	71	0.19613259668508287	0	0.0	134	0.17678100263852242	A	13.26	2.184106	0.38609	0.142533	0.237791	ENSG00000156096	ENST00000305107;ENST00000381096	T;T	0.72282	-0.64;-0.64	2.11	-3.83	0.04269	.	0.000000	0.64402	U	0.000002	T	0.00039	0.0001	L	0.45352	1.415	0.58432	P	5.999999999950489E-6	B;B	0.33413	0.411;0.388	P;P	0.50162	0.633;0.513	T	0.50101	-0.8867	9	0.87932	D	0	.	11.9884	0.53161	0.1949:0.0:0.8051:0.0	rs13119049;rs52797972	322;458	A6NCP7;P06133	.;UD2B4_HUMAN	E	458;322	ENSP00000305221:D458E;ENSP00000370486:D322E	ENSP00000305221:D458E	D	-	3	2	UGT2B4	70381154	0.392000	0.25229	0.004000	0.12327	0.636000	0.38137	0.578000	0.23773	-1.145000	0.02858	0.254000	0.18369	GAT	A|0.853;T|0.147	0.147	strong		0.428	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12888397	12888397	+	Missense_Mutation	SNP	C	C	T	rs202156326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12888397C>T	ENST00000535591.1	-	2	322	c.127G>A	c.(127-129)Gat>Aat	p.D43N		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	43					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.D43N(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						TCAAGCCCATCGAGCACAGCT	0.627													.|||	63	0.0125799	0.0454	0.0043	5008	,	,		16628	0.0		0.0	False		,,,				2504	0.0				p.D43N		Atlas-SNP	.											PRAMEF11,NS,other,0,1	PRAMEF11	72	1	1	Substitution - Missense(1)	pancreas(1)	c.G127A						scavenged	.																																			SO:0001583	missense	440560	exon2			GCCCATCGAGCAC	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.127G>A	1.37:g.12888397C>T	ENSP00000439551:p.Asp43Asn	Somatic	341	45	0.131965		WXS	Illumina HiSeq	Phase_I	511	126	0.246575	NM_001146344		Missense_Mutation	SNP	ENST00000535591.1	37	CCDS53268.1	.	.	.	.	.	.	.	.	.	.	.	13.12	2.143414	0.37825	.	.	ENSG00000204513	ENST00000535591;ENST00000331684;ENST00000437584	T;T	0.05996	3.36;3.36	1.45	1.45	0.22620	.	0.744226	0.12606	N	0.454302	T	0.10766	0.0263	M	0.77712	2.385	0.09310	N	1	D	0.53745	0.962	P	0.44921	0.464	T	0.18366	-1.0339	10	0.87932	D	0	.	6.4008	0.21638	0.0:1.0:0.0:0.0	.	43	O60813	PRA11_HUMAN	N	43;84;43	ENSP00000439551:D43N;ENSP00000391839:D43N	ENSP00000328783:D84N	D	-	1	0	PRAMEF11	12810984	0.004000	0.15560	0.007000	0.13788	0.013000	0.08279	0.287000	0.18920	1.122000	0.41944	0.380000	0.24917	GAT	C|0.250;T|0.750	0.750	weak		0.627	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
FLG	2312	hgsc.bcm.edu	37	1	152281039	152281039	+	Missense_Mutation	SNP	G	G	A	rs7522925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281039G>A	ENST00000368799.1	-	3	6358	c.6323C>T	c.(6322-6324)gCg>gTg	p.A2108V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2108	Ser-rich.		A -> V (in dbSNP:rs7522925).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTGCTGGGCGCAGACTGTCC	0.567									Ichthyosis																												p.A2108V		Atlas-SNP	.											.	FLG	900	.	0			c.C6323T						PASS	.	G	VAL/ALA	1572,2834		0,1572,631	307.0	228.0	255.0		6323	-6.7	0.0	1	dbSNP_116	255	1153,7447		0,1153,3147	yes	missense	FLG	NM_002016.1	64	0,2725,3778	AA,AG,GG		13.407,35.6786,20.9519	benign	2108/4062	152281039	2725,10281	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGGGCGCAGACT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6323C>T	1.37:g.152281039G>A	ENSP00000357789:p.Ala2108Val	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	528	160	0.30303	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	
TMEM63A	9725	hgsc.bcm.edu	37	1	226046974	226046974	+	Silent	SNP	T	T	C	rs2292561	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226046974T>C	ENST00000366835.3	-	15	1569	c.1299A>G	c.(1297-1299)ctA>ctG	p.L433L	TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	433					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)					TCAGGAAAAATAGCCCCAGGA	0.542													C|||	548	0.109425	0.1452	0.0965	5008	,	,		17585	0.1577		0.0497	False		,,,				2504	0.0818				p.L433L		Atlas-SNP	.											.	TMEM63A	75	.	0			c.A1299G						PASS	.	C		628,3778	767.6+/-413.5	44,540,1619	131.0	118.0	122.0		1299	-4.3	0.9	1	dbSNP_100	122	354,8246	803.7+/-407.3	3,348,3949	no	coding-synonymous	TMEM63A	NM_014698.2		47,888,5568	CC,CT,TT		4.1163,14.2533,7.5504		433/808	226046974	982,12024	2203	4300	6503	SO:0001819	synonymous_variant	9725	exon15			GAAAAATAGCCCC		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.1299A>G	1.37:g.226046974T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	220	125	0.568182	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			T|0.916;C|0.084	0.084	strong		0.542	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
OR51B5	282763	hgsc.bcm.edu	37	11	5364431	5364431	+	Silent	SNP	G	G	A	rs58233587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364431G>A	ENST00000300773.2	-	1	378	c.324C>T	c.(322-324)ctC>ctT	p.L108L	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	108					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCAGACTCGAGAAAGGAAA	0.493													G|||	486	0.0970447	0.3041	0.0476	5008	,	,		20358	0.0		0.0457	False		,,,				2504	0.0051				p.L108L		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.C324T						PASS	.	G		1214,3188	413.5+/-336.5	164,886,1151	46.0	45.0	46.0		324	-8.8	0.1	11	dbSNP_129	46	454,8140	135.6+/-192.8	13,428,3856	no	coding-synonymous	OR51B5	NM_001005567.2		177,1314,5007	AA,AG,GG		5.2828,27.5784,12.8347		108/313	5364431	1668,11328	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			AGACTCGAGAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.324C>T	11.37:g.5364431G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			G|0.886;A|0.114	0.114	strong		0.493	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
OMP	4975	hgsc.bcm.edu	37	11	76813961	76813961	+	Missense_Mutation	SNP	C	C	T	rs2233546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76813961C>T	ENST00000529803.1	+	1	76	c.76C>T	c.(76-78)Cgg>Tgg	p.R26W	CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000456580.2_Intron|CAPN5_ENST00000278559.3_Intron|CAPN5_ENST00000529629.1_Intron	NM_006189.1	NP_006180.1	P47874	OMP_HUMAN	olfactory marker protein	26			R -> W (in dbSNP:rs2233546).		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						CAGGCAGATGCGGCTACGCGT	0.672													C|||	201	0.0401358	0.003	0.1873	5008	,	,		17170	0.0		0.0517	False		,,,				2504	0.0153				p.R26W		Atlas-SNP	.											.	OMP	14	.	0			c.C76T						PASS	.	C	,TRP/ARG	55,4161		1,53,2054	25.0	32.0	29.0		,76	2.0	1.0	11	dbSNP_98	29	443,7971		12,419,3776	yes	intron,missense	CAPN5,OMP	NM_004055.4,NM_006189.1	,101	13,472,5830	TT,TC,CC		5.265,1.3046,3.943	,probably-damaging	,26/164	76813961	498,12132	2108	4207	6315	SO:0001583	missense	4975	exon1			CAGATGCGGCTAC	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.76C>T	11.37:g.76813961C>T	ENSP00000436376:p.Arg26Trp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	138	67	0.485507	NM_006189	Q562G2	Missense_Mutation	SNP	ENST00000529803.1	37	CCDS53682.1	100	0.045787545787545784	5	0.01016260162601626	55	0.15193370165745856	0	0.0	40	0.052770448548812667	C	14.13	2.442956	0.43326	0.013046	0.05265	ENSG00000254550	ENST00000529803	T	0.47177	0.85	5.12	1.95	0.26073	.	.	.	.	.	T	0.00468	0.0015	L	0.32530	0.975	0.46954	D	0.999266	D	0.89917	1.0	D	0.91635	0.999	T	0.02471	-1.1154	9	0.87932	D	0	.	14.5845	0.68315	0.3817:0.6183:0.0:0.0	rs2233546	26	P47874	OMP_HUMAN	W	26	ENSP00000436376:R26W	ENSP00000436376:R26W	R	+	1	2	OMP	76491609	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	1.236000	0.32683	0.736000	0.32559	0.462000	0.41574	CGG	C|0.955;T|0.045	0.045	strong		0.672	OMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382570.1	NM_006189	
MST1L	11223	hgsc.bcm.edu	37	1	17085592	17085592	+	RNA	SNP	G	G	A	rs371449598		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17085592G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.Q376_R377delQR(1)|p.Q366_R367delQR(1)									GCGGACCAGCGCTGGCACTGG	0.706																																					p.R377C		Atlas-SNP	.											.	.	.	.	2	Deletion - In frame(2)	breast(2)	c.C1129T						PASS	.																																					11223	exon9			ACCAGCGCTGGCA	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.17085592G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	114	27	0.236842	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	12.29	1.894372	0.33442	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	1.304990	0.05479	N	0.554513	T	0.47619	0.1455	.	.	.	.	.	.	D	0.76494	0.999	P	0.55785	0.784	T	0.38001	-0.9681	6	0.56958	D	0.05	.	2.8176	0.05461	3.0E-4:3.0E-4:0.4997:0.4997	.	377	Q2TV78-2	.	C	367;377;377	.	ENSP00000439273:R377C	R	-	1	0	MST1P9	16958179	0.833000	0.29383	0.000000	0.03702	0.000000	0.00434	0.760000	0.26475	-0.000000	0.14550	0.000000	0.15137	CGC	.	.	none		0.706	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
IL22RA1	58985	hgsc.bcm.edu	37	1	24460797	24460797	+	Silent	SNP	T	T	G	rs17852649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24460797T>G	ENST00000270800.1	-	4	473	c.435A>C	c.(433-435)ccA>ccC	p.P145P		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	145	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		CTGCACGGATTGGCGTGGGGG	0.527													G|||	2622	0.523562	0.6989	0.4625	5008	,	,		18825	0.2956		0.6123	False		,,,				2504	0.4734				p.P145P		Atlas-SNP	.											.	IL22RA1	62	.	0			c.A435C						PASS	.	G		3055,1351	449.2+/-349.0	1059,937,207	111.0	98.0	102.0		435	-4.6	0.0	1	dbSNP_123	102	5181,3419	503.7+/-376.0	1571,2039,690	no	coding-synonymous	IL22RA1	NM_021258.3		2630,2976,897	GG,GT,TT		39.7558,30.6627,36.6754		145/575	24460797	8236,4770	2203	4300	6503	SO:0001819	synonymous_variant	58985	exon4			ACGGATTGGCGTG	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	13700	protein-coding gene	gene with protein product		605457	"""interleukin 22 receptor"""	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.435A>C	1.37:g.24460797T>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_021258	A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	37	CCDS247.1																																																																																			T|0.401;G|0.599	0.599	strong		0.527	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
EYA2	2139	hgsc.bcm.edu	37	20	45717954	45717954	+	Silent	SNP	C	C	T	rs866937	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:45717954C>T	ENST00000327619.5	+	8	1112	c.738C>T	c.(736-738)gaC>gaT	p.D246D	EYA2_ENST00000317304.6_Silent_p.D246D|EYA2_ENST00000357410.3_Silent_p.D246D	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	246					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)				GGGCCTCCGACGGGAAGCTCC	0.582													C|||	1262	0.251997	0.1445	0.3329	5008	,	,		18244	0.253		0.2575	False		,,,				2504	0.3333				p.D246D	Pancreas(120;56 1725 18501 25218 43520)	Atlas-SNP	.											.	EYA2	85	.	0			c.C738T						PASS	.	C	,	719,3687	299.8+/-286.0	60,599,1544	74.0	75.0	75.0		738,738	-4.2	0.9	20	dbSNP_86	75	2328,6272	390.8+/-343.4	320,1688,2292	no	coding-synonymous,coding-synonymous	EYA2	NM_005244.4,NM_172110.3	,	380,2287,3836	TT,TC,CC		27.0698,16.3187,23.4276	,	246/539,246/460	45717954	3047,9959	2203	4300	6503	SO:0001819	synonymous_variant	2139	exon8			CTCCGACGGGAAG		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.738C>T	20.37:g.45717954C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_172110	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Silent	SNP	ENST00000327619.5	37	CCDS13403.1																																																																																			C|0.768;T|0.232	0.232	strong		0.582	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244	
FGF6	2251	hgsc.bcm.edu	37	12	4554630	4554630	+	Missense_Mutation	SNP	A	A	G	rs11613495	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4554630A>G	ENST00000228837.2	-	1	150	c.107T>C	c.(106-108)gTg>gCg	p.V36A		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	36			V -> A (in dbSNP:rs11613495). {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)			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)			AGGCGAGGGCACCACCATGCC	0.642													A|||	467	0.0932508	0.09	0.0994	5008	,	,		16764	0.0139		0.1461	False		,,,				2504	0.1207				p.V36A		Atlas-SNP	.											.	FGF6	40	.	0			c.T107C						PASS	.	A	ALA/VAL	466,3940	219.7+/-237.4	38,390,1775	71.0	78.0	76.0		107	3.3	1.0	12	dbSNP_120	76	1399,7201	271.1+/-289.3	134,1131,3035	yes	missense	FGF6	NM_020996.1	64	172,1521,4810	GG,GA,AA		16.2674,10.5765,14.3395	benign	36/209	4554630	1865,11141	2203	4300	6503	SO:0001583	missense	2251	exon1			GAGGGCACCACCA	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.107T>C	12.37:g.4554630A>G	ENSP00000228837:p.Val36Ala	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	37	CCDS8527.1	210	0.09615384615384616	50	0.1016260162601626	30	0.08287292817679558	9	0.015734265734265736	121	0.15963060686015831	A	5.776	0.327498	0.10956	0.105765	0.162674	ENSG00000111241	ENST00000228837	T	0.24723	1.84	4.47	3.3	0.37823	.	0.307478	0.36002	N	0.002841	T	0.00039	0.0001	N	0.19112	0.55	0.40264	P	0.021788999999999947	B	0.02656	0.0	B	0.01281	0.0	T	0.29119	-1.0022	9	0.06365	T	0.9	.	5.7882	0.18345	0.7595:0.0:0.0889:0.1516	rs11613495;rs17183522;rs57277343;rs11613495	36	P10767	FGF6_HUMAN	A	36	ENSP00000228837:V36A	ENSP00000228837:V36A	V	-	2	0	FGF6	4424891	0.984000	0.35163	1.000000	0.80357	0.657000	0.38888	1.317000	0.33631	0.840000	0.34995	0.459000	0.35465	GTG	A|0.879;G|0.121	0.121	strong		0.642	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
FLNB	2317	hgsc.bcm.edu	37	3	58154327	58154327	+	Silent	SNP	C	C	T	rs8640	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58154327C>T	ENST00000295956.4	+	44	7524	c.7359C>T	c.(7357-7359)agC>agT	p.S2453S	FLNB_ENST00000493452.1_Silent_p.S2260S|FLNB_ENST00000357272.4_3'UTR|FLNB_ENST00000429972.2_Silent_p.S2442S|FLNB-AS1_ENST00000488720.1_RNA|FLNB_ENST00000348383.5_Silent_p.S2412S|FLNB_ENST00000484981.1_3'UTR|FLNB_ENST00000358537.3_Silent_p.S2429S|FLNB_ENST00000490882.1_Silent_p.S2484S|FLNB_ENST00000419752.2_Silent_p.S2273S	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2453	Interaction with INPPL1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		ACCTGATCAGCGTCAAATACG	0.537													C|||	2861	0.571286	0.5719	0.4597	5008	,	,		20342	0.9216		0.2664	False		,,,				2504	0.6022				p.S2484S		Atlas-SNP	.											.	FLNB	430	.	0			c.C7452T						PASS	.	C	,,,	2213,2193	592.1+/-387.7	532,1149,522	113.0	95.0	101.0		7452,7326,7287,7359	-4.1	0.2	3	dbSNP_52	101	2167,6433	371.5+/-336.3	275,1617,2408	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	807,2766,2930	TT,TC,CC		25.1977,49.773,33.6768	,,,	2484/2634,2442/2592,2429/2579,2453/2603	58154327	4380,8626	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon45			GATCAGCGTCAAA	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.7359C>T	3.37:g.58154327C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	145	59	0.406897	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			C|0.573;T|0.427	0.427	strong		0.537	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
CRHR1	1394	hgsc.bcm.edu	37	17	43907896	43907896	+	Silent	SNP	T	T	C	rs16940665	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43907896T>C	ENST00000398285.3	+	8	756	c.756T>C	c.(754-756)acT>acC	p.T252T	CRHR1_ENST00000314537.5_Silent_p.T223T|CRHR1_ENST00000352855.5_Silent_p.T183T|CRHR1_ENST00000577353.1_Silent_p.T223T|CRHR1_ENST00000293493.7_Silent_p.T48T|CRHR1_ENST00000339069.5_Silent_p.T122T	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	252					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCTACTCCACTGACCGGCTGC	0.622													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		20880	0.001		0.2396	False		,,,				2504	0.0613				p.T252T	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.T756C						PASS	.	C	,,,	200,4202	777.7+/-414.2	5,190,2006	91.0	94.0	93.0		756,549,669,669	-4.0	0.9	17	dbSNP_123	93	1925,6675	717.6+/-406.2	221,1483,2596	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRHR1	NM_001145146.1,NM_001145147.1,NM_001145148.1,NM_004382.4	,,,	226,1673,4602	CC,CT,TT		22.3837,4.5434,16.3436	,,,	252/445,183/376,223/402,223/416	43907896	2125,10877	2201	4300	6501	SO:0001819	synonymous_variant	1394	exon8			CTCCACTGACCGG	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2357	protein-coding gene	gene with protein product	"""corticotropin-releasing factor receptor"""	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.756T>C	17.37:g.43907896T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_001145146	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	37	CCDS45712.1																																																																																			T|0.862;C|0.138	0.138	strong		0.622	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
SACS	26278	hgsc.bcm.edu	37	13	23905711	23905711	+	Silent	SNP	A	A	G	rs2737699	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:23905711A>G	ENST00000382292.3	-	9	12577	c.12304T>C	c.(12304-12306)Ttg>Ctg	p.L4102L	SACS_ENST00000402364.1_Silent_p.L3352L|SACS_ENST00000382298.3_Silent_p.L4102L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4102					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)		GTCATTGCCAATGCTAACAGG	0.343													A|||	1294	0.258387	0.053	0.3617	5008	,	,		22100	0.3145		0.2783	False		,,,				2504	0.3845				p.L4102L		Atlas-SNP	.											.	SACS	871	.	0			c.T12304C						PASS	.	A		426,3980	206.8+/-228.3	21,384,1798	94.0	90.0	91.0		12304	0.2	0.1	13	dbSNP_100	91	2234,6364	375.8+/-337.9	291,1652,2356	no	coding-synonymous	SACS	NM_014363.4		312,2036,4154	GG,GA,AA		25.9828,9.6686,20.4552		4102/4580	23905711	2660,10344	2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			TTGCCAATGCTAA	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.12304T>C	13.37:g.23905711A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			G|0.232;N|0.000	0.232	strong		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
TG	7038	hgsc.bcm.edu	37	8	134108546	134108546	+	Missense_Mutation	SNP	T	T	C	rs2069569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:134108546T>C	ENST00000220616.4	+	43	7541	c.7501T>C	c.(7501-7503)Tgg>Cgg	p.W2501R	SLA_ENST00000518565.1_Intron|SLA_ENST00000517648.1_Intron|TG_ENST00000542445.1_Missense_Mutation_p.W871R|TG_ENST00000519543.1_Missense_Mutation_p.W634R|SLA_ENST00000524345.1_Intron|SLA_ENST00000395352.3_Intron|TG_ENST00000377869.1_Missense_Mutation_p.W2444R|SLA_ENST00000338087.5_Intron	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	113	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	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	
OVGP1	5016	hgsc.bcm.edu	37	1	111966291	111966291	+	Silent	SNP	C	C	T	rs954739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:111966291C>T	ENST00000369732.3	-	5	412	c.357G>A	c.(355-357)aaG>aaA	p.K119K	OVGP1_ENST00000540696.1_Silent_p.K59K|OVGP1_ENST00000481495.1_5'Flank	NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	119					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		AAGCAATAAACTTTTCACGGT	0.448													C|||	752	0.15016	0.0598	0.1282	5008	,	,		20675	0.1389		0.2366	False		,,,				2504	0.2106				p.K119K		Atlas-SNP	.											.	OVGP1	177	.	0			c.G357A						PASS	.	C		390,4016	196.4+/-220.7	13,364,1826	128.0	111.0	117.0		357	1.3	0.0	1	dbSNP_86	117	2274,6326	384.6+/-341.2	280,1714,2306	no	coding-synonymous	OVGP1	NM_002557.3		293,2078,4132	TT,TC,CC		26.4419,8.8516,20.4829		119/679	111966291	2664,10342	2203	4300	6503	SO:0001819	synonymous_variant	5016	exon5			AATAAACTTTTCA	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.357G>A	1.37:g.111966291C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	171	88	0.51462	NM_002557	A0AV19|B9EGE1|Q15841	Silent	SNP	ENST00000369732.3	37	CCDS834.1																																																																																			C|0.825;T|0.175	0.175	strong		0.448	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
IFNA4	3441	hgsc.bcm.edu	37	9	21187311	21187311	+	Missense_Mutation	SNP	C	C	T	rs1062571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21187311C>T	ENST00000421715.1	-	1	287	c.220G>A	c.(220-222)Gct>Act	p.A74T		NM_021068.2	NP_066546.1	P05014	IFNA4_HUMAN	interferon, alpha 4	74			A -> T (in alpha-4B; dbSNP:rs1062571). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:4057246, ECO:0000269|Ref.4}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17				GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		ATGGCTTGAGCCTTCTGGAAC	0.507													c|||	3405	0.679912	0.6142	0.6326	5008	,	,		19521	0.8611		0.5517	False		,,,				2504	0.7474				p.A74T	NSCLC(154;890 1986 23660 27800 51138)	Atlas-SNP	.											.	IFNA4	34	.	0			c.G220A						PASS	.						80.0	79.0	79.0					9																	21187311		2203	4300	6503	SO:0001583	missense	3441	exon1			CTTGAGCCTTCTG		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.220G>A	9.37:g.21187311C>T	ENSP00000412897:p.Ala74Thr	Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	345	147	0.426087	NM_021068	P13358|Q14CS4|Q5VV15	Missense_Mutation	SNP	ENST00000421715.1	37	CCDS6498.1	1416	0.6483516483516484	296	0.6016260162601627	234	0.6464088397790055	484	0.8461538461538461	402	0.5303430079155673	c	9.495	1.101676	0.20632	.	.	ENSG00000236637	ENST00000421715	T	0.03920	3.76	2.96	1.06	0.20224	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.403303	0.25313	N	0.031561	T	0.00012	0.0000	L	0.47016	1.485	0.80722	P	0.0	B	0.06786	0.001	B	0.22753	0.041	T	0.03296	-1.1051	9	0.44086	T	0.13	.	6.4897	0.22109	0.0:0.7509:0.0:0.2491	rs1062571;rs3750481;rs6475509;rs61596122	74	P05014	IFNA4_HUMAN	T	74	ENSP00000412897:A74T	ENSP00000412897:A74T	A	-	1	0	IFNA4	21177311	0.006000	0.16342	0.116000	0.21606	0.056000	0.15407	0.193000	0.17116	0.132000	0.18615	-0.329000	0.08387	GCT	C|0.402;T|0.598	0.598	strong		0.507	IFNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051889.1	NM_021068	
FABP3	2170	hgsc.bcm.edu	37	1	31842320	31842320	+	Missense_Mutation	SNP	T	T	C	rs2228194	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:31842320T>C	ENST00000373713.2	-	2	219	c.158A>G	c.(157-159)aAa>aGa	p.K53R	FABP3_ENST00000497275.1_5'UTR	NM_004102.3	NP_004093.1	P05413	FABPH_HUMAN	fatty acid binding protein 3, muscle and heart (mammary-derived growth inhibitor)	53			K -> R (in dbSNP:rs2228194).		cholesterol homeostasis (GO:0042632)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid import (GO:0044539)|negative regulation of cell proliferation (GO:0008285)|phospholipid homeostasis (GO:0055091)|positive regulation of phospholipid biosynthetic process (GO:0071073)|regulation of fatty acid oxidation (GO:0046320)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to insulin (GO:0032868)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasm (GO:0016528)	cytoskeletal protein binding (GO:0008092)|icosatetraenoic acid binding (GO:0050543)|long-chain fatty acid binding (GO:0036041)|long-chain fatty acid transporter activity (GO:0005324)|oleic acid binding (GO:0070538)			large_intestine(1)|lung(2)|ovary(2)	5		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0185)|READ - Rectum adenocarcinoma(331;0.149)		GCTGTGTGTTTTTAGGGTGAG	0.502													T|||	68	0.0135783	0.0008	0.0144	5008	,	,		21390	0.0		0.0457	False		,,,				2504	0.0112				p.K53R		Atlas-SNP	.											.	FABP3	12	.	0			c.A158G						PASS	.	T	ARG/LYS	24,4382	31.7+/-61.6	0,24,2179	438.0	374.0	396.0		158	3.9	1.0	1	dbSNP_98	396	324,8276	112.7+/-172.9	7,310,3983	yes	missense	FABP3	NM_004102.3	26	7,334,6162	CC,CT,TT		3.7674,0.5447,2.6757	benign	53/134	31842320	348,12658	2203	4300	6503	SO:0001583	missense	2170	exon2			TGTGTTTTTAGGG	U57623	CCDS342.1	1p33-p32	2013-03-01	2003-09-10		ENSG00000121769	ENSG00000121769		"""Fatty acid binding protein family"""	3557	protein-coding gene	gene with protein product		134651	"""fatty acid binding protein 11"""	MDGI, FABP11		8661024	Standard	NM_004102		Approved	H-FABP, O-FABP	uc001bss.1	P05413	OTTHUMG00000003797	ENST00000373713.2:c.158A>G	1.37:g.31842320T>C	ENSP00000362817:p.Lys53Arg	Somatic	502	0	0		WXS	Illumina HiSeq	Phase_I	469	218	0.464819	NM_004102	B2RAB6|Q5VV93|Q99957	Missense_Mutation	SNP	ENST00000373713.2	37	CCDS342.1	42	0.019230769230769232	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	36	0.047493403693931395	T	7.813	0.716132	0.15306	0.005447	0.037674	ENSG00000121769	ENST00000373713	T	0.48836	0.8	5.0	3.87	0.44632	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.083093	0.85682	N	0.000000	T	0.09862	0.0242	L	0.46157	1.445	0.47698	D	0.99949	B	0.18461	0.028	B	0.32465	0.146	T	0.04294	-1.0962	10	0.24483	T	0.36	.	10.6904	0.45867	0.0:0.076:0.0:0.924	rs2228194;rs11588069;rs52798601;rs11588069	53	P05413	FABPH_HUMAN	R	53	ENSP00000362817:K53R	ENSP00000362817:K53R	K	-	2	0	FABP3	31614907	1.000000	0.71417	0.996000	0.52242	0.337000	0.28794	2.696000	0.47052	1.045000	0.40225	-0.262000	0.10625	AAA	T|0.890;G|0.002;C|0.024;A|0.084	0.024	strong		0.502	FABP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010683.1	NM_004102	
SPPL2C	162540	hgsc.bcm.edu	37	17	43922942	43922942	+	Missense_Mutation	SNP	T	T	C	rs62621252	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43922942T>C	ENST00000329196.5	+	1	687	c.670T>C	c.(670-672)Tct>Cct	p.S224P	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	224						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)										AGGAGGGGGGTCTGGTGGTCA	0.647													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		18327	0.001		0.2396	False		,,,				2504	0.0613				p.S224P		Atlas-SNP	.											.	.	.	.	0			c.T670C						PASS	.	C	PRO/SER	202,4204		5,192,2006	37.0	39.0	38.0		670	0.8	0.0	17	dbSNP_129	38	1909,6689		217,1475,2607	yes	missense	IMP5	NM_175882.2	74	222,1667,4613	CC,CT,TT		22.2028,4.5847,16.2335	benign	224/685	43922942	2111,10893	2203	4299	6502	SO:0001583	missense	162540	exon1			GGGGGGTCTGGTG		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.670T>C	17.37:g.43922942T>C	ENSP00000332488:p.Ser224Pro	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	0.013	-1.632921	0.00806	0.045847	0.222028	ENSG00000185294	ENST00000329196	T	0.05258	3.47	5.24	0.827	0.18835	.	0.807093	0.10116	N	0.714047	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	0.48885	-0.8995	9	0.26408	T	0.33	-34.9333	1.2817	0.02042	0.1516:0.4416:0.1475:0.2594	rs62621252	224	Q8IUH8	IMP5_HUMAN	P	224	ENSP00000332488:S224P	ENSP00000332488:S224P	S	+	1	0	AC217771.1	41278722	0.062000	0.20869	0.006000	0.13384	0.004000	0.04260	0.475000	0.22164	0.358000	0.24211	-0.119000	0.15052	TCT	T|0.851;C|0.149	0.149	strong		0.647	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
BZRAP1	9256	hgsc.bcm.edu	37	17	56383744	56383744	+	Missense_Mutation	SNP	T	T	C	rs11079346	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56383744T>C	ENST00000343736.4	-	26	5346	c.5183A>G	c.(5182-5184)cAc>cGc	p.H1728R	BZRAP1_ENST00000268893.6_Missense_Mutation_p.H1668R|BZRAP1_ENST00000355701.3_Missense_Mutation_p.H1728R			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	76	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	
ALKBH3	221120	hgsc.bcm.edu	37	11	43913604	43913604	+	Silent	SNP	G	G	A	rs16937692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:43913604G>A	ENST00000302708.4	+	7	795	c.384G>A	c.(382-384)caG>caA	p.Q128Q	ALKBH3_ENST00000378840.4_Intron|ALKBH3_ENST00000532410.1_Intron	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	128					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	TAACTTATCAGCAACCAAGAC	0.368								Direct reversal of damage					G|||	303	0.0605032	0.0393	0.2046	5008	,	,		20438	0.0248		0.0268	False		,,,				2504	0.0583				p.Q128Q		Atlas-SNP	.											.	ALKBH3	33	.	0			c.G384A						PASS	.	G		145,4261	102.1+/-140.7	2,141,2060	119.0	109.0	112.0		384	3.0	1.0	11	dbSNP_123	112	264,8336	101.6+/-162.9	5,254,4041	no	coding-synonymous	ALKBH3	NM_139178.3		7,395,6101	AA,AG,GG		3.0698,3.291,3.1447		128/287	43913604	409,12597	2203	4300	6503	SO:0001819	synonymous_variant	221120	exon7			TTATCAGCAACCA	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"""Alkylation repair homologs"""	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.384G>A	11.37:g.43913604G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Silent	SNP	ENST00000302708.4	37	CCDS7906.1																																																																																			G|0.961;A|0.039	0.039	strong		0.368	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178	
RPTOR	57521	hgsc.bcm.edu	37	17	78865546	78865546	+	Silent	SNP	T	T	C	rs2289764	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78865546T>C	ENST00000306801.3	+	18	2372	c.2010T>C	c.(2008-2010)ctT>ctC	p.L670L	RPTOR_ENST00000544334.2_Silent_p.L512L|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	670					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						TGAGTCATCTTGTGGTTCAGT	0.517													C|||	1910	0.38139	0.7057	0.2435	5008	,	,		17130	0.2262		0.2247	False		,,,				2504	0.362				p.L670L		Atlas-SNP	.											.	RPTOR	122	.	0			c.T2010C						PASS	.	C	,	2806,1600	496.5+/-363.6	894,1018,291	182.0	158.0	166.0		1536,2010	-9.4	0.0	17	dbSNP_100	166	2029,6571	720.4+/-406.3	254,1521,2525	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	1148,2539,2816	CC,CT,TT		23.593,36.3141,37.1751	,	512/1178,670/1336	78865546	4835,8171	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon18			TCATCTTGTGGTT		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.2010T>C	17.37:g.78865546T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			T|0.634;C|0.366	0.366	strong		0.517	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
CACNA1H	8912	hgsc.bcm.edu	37	16	1271890	1271890	+	IGR	SNP	G	G	T	rs1004041	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1271890G>T	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.F288L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CGGGGAGGAAGAAGCCAGCCA	0.637													g|||	3072	0.613419	0.5946	0.6297	5008	,	,		13798	0.8472		0.5209	False		,,,				2504	0.4816				p.F288L		Atlas-SNP	.											.	TPSG1	19	.	0			c.C864A						PASS	.		LEU/PHE	2595,1789	610.2+/-391.5	752,1091,349	29.0	35.0	33.0		864	2.5	0.1	16	dbSNP_86	33	4112,4484	544.4+/-384.6	985,2142,1171	yes	missense	TPSG1	NM_012467.3	22	1737,3233,1520	TT,TG,GG		47.8362,40.8075,48.3282	benign	288/322	1271890	6707,6273	2192	4298	6490	SO:0001628	intergenic_variant	25823	exon6			GAGGAAGAAGCCA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180			16.37:g.1271890G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	1372	0.6282051282051282	264	0.5365853658536586	212	0.585635359116022	510	0.8916083916083916	386	0.5092348284960422	g	2.595	-0.294270	0.05568	0.591925	0.478362	ENSG00000116176	ENST00000234798	D	0.86627	-2.15	3.48	2.49	0.30216	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.39820	-0.9595	5	0.02654	T	1	.	8.0755	0.30714	0.0:0.0:0.7576:0.2424	rs1004041;rs17745458;rs59475748;rs1004041	.	.	.	L	288	ENSP00000234798:F288L	ENSP00000234798:F288L	F	-	3	2	TPSG1	1211891	0.488000	0.25996	0.104000	0.21259	0.071000	0.16799	1.439000	0.35013	0.744000	0.32741	-0.300000	0.09419	TTC	G|0.435;T|0.558	0.558	strong		0.637	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
PTPRH	5794	hgsc.bcm.edu	37	19	55715342	55715342	+	Missense_Mutation	SNP	C	C	T	rs55870162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55715342C>T	ENST00000376350.3	-	5	716	c.694G>A	c.(694-696)Gat>Aat	p.D232N	PTPRH_ENST00000263434.5_Intron|PTPRH_ENST00000588559.1_5'UTR	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	232	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		D -> N (in dbSNP:rs55870162).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TCTGTGCCATCGGGGACCTCC	0.542													C|||	90	0.0179712	0.0038	0.0115	5008	,	,		16192	0.001		0.0278	False		,,,				2504	0.0491				p.D232N		Atlas-SNP	.											.	PTPRH	139	.	0			c.G694A						PASS	.	C	,ASN/ASP	41,4365	43.8+/-77.6	0,41,2162	127.0	103.0	111.0		,694	-2.1	0.0	19	dbSNP_129	111	262,8338	101.6+/-162.9	3,256,4041	yes	intron,missense	PTPRH	NM_001161440.1,NM_002842.3	,23	3,297,6203	TT,TC,CC		3.0465,0.9305,2.3297	,benign	,232/1116	55715342	303,12703	2203	4300	6503	SO:0001583	missense	5794	exon5			TGCCATCGGGGAC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.694G>A	19.37:g.55715342C>T	ENSP00000365528:p.Asp232Asn	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	27	0.012362637362637362	4	0.008130081300813009	3	0.008287292817679558	0	0.0	20	0.026385224274406333	C	10.62	1.400532	0.25291	0.009305	0.030465	ENSG00000080031	ENST00000376350	T	0.57436	0.4	3.74	-2.09	0.07232	Fibronectin, type III (4);Immunoglobulin-like fold (1);	3.343480	0.01398	N	0.013509	T	0.11965	0.0291	N	0.22421	0.69	0.09310	N	0.999996	B;P	0.37594	0.01;0.601	B;B	0.23852	0.002;0.049	T	0.08472	-1.0720	10	0.23302	T	0.38	.	5.7879	0.18343	0.0:0.5648:0.2178:0.2174	rs55870162	54;232	Q9HD43-2;Q9HD43	.;PTPRH_HUMAN	N	232	ENSP00000365528:D232N	ENSP00000365528:D232N	D	-	1	0	PTPRH	60407154	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.476000	0.02333	-0.264000	0.09365	-0.301000	0.09380	GAT	C|0.980;T|0.020	0.020	strong		0.542	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
CEP350	9857	hgsc.bcm.edu	37	1	179972337	179972337	+	Silent	SNP	A	A	C	rs17371159	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:179972337A>C	ENST00000367607.3	+	7	1465	c.1047A>C	c.(1045-1047)cgA>cgC	p.R349R		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	349					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						CCAAGATTCGAACACCTGATG	0.368													A|||	258	0.0515176	0.0045	0.062	5008	,	,		19022	0.0139		0.1123	False		,,,				2504	0.0838				p.R349R		Atlas-SNP	.											.	CEP350	418	.	0			c.A1047C						PASS	.	A		114,4292	85.3+/-124.0	1,112,2090	85.0	79.0	81.0		1047	1.4	1.0	1	dbSNP_123	81	1035,7565	218.1+/-256.6	80,875,3345	no	coding-synonymous	CEP350	NM_014810.4		81,987,5435	CC,CA,AA		12.0349,2.5874,8.8344		349/3118	179972337	1149,11857	2203	4300	6503	SO:0001819	synonymous_variant	9857	exon7			GATTCGAACACCT	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.1047A>C	1.37:g.179972337A>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	97	42	0.43299	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1																																																																																			A|0.930;C|0.070	0.070	strong		0.368	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
TLR10	81793	hgsc.bcm.edu	37	4	38774889	38774889	+	Missense_Mutation	SNP	T	T	C	rs4129009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:38774889T>C	ENST00000308973.4	-	4	2928	c.2323A>G	c.(2323-2325)Att>Gtt	p.I775V	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Missense_Mutation_p.I775V|TLR10_ENST00000506111.1_Missense_Mutation_p.I775V|TLR10_ENST00000361424.2_Missense_Mutation_p.I775V	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	775	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.		I -> F (in dbSNP:rs4129009).|I -> L (in dbSNP:rs4129009).|I -> V (in dbSNP:rs4129009). {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						TTAACATTAATAGCAGCTCGA	0.408													T|||	734	0.146565	0.0106	0.1398	5008	,	,		18119	0.2688		0.2068	False		,,,				2504	0.1472				p.I775V		Atlas-SNP	.											.	TLR10	87	.	0			c.A2323G	GRCh37	CM057767	TLR10	M	rs4129009	PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	129,4277	93.0+/-131.7	4,121,2078	84.0	83.0	84.0		2323,2323,2323,2281,2323	-5.3	0.0	4	dbSNP_108	84	1492,7108	283.2+/-296.0	126,1240,2934	yes	missense,missense,missense,missense,missense	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	29,29,29,29,29	130,1361,5012	CC,CT,TT		17.3488,2.9278,12.4635	benign,benign,benign,benign,benign	775/812,775/812,775/812,761/798,775/812	38774889	1621,11385	2203	4300	6503	SO:0001583	missense	81793	exon2			CATTAATAGCAGC	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.2323A>G	4.37:g.38774889T>C	ENSP00000308925:p.Ile775Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	412	0.18864468864468864	8	0.016260162601626018	51	0.1408839779005525	215	0.3758741258741259	138	0.1820580474934037	T	3.040	-0.197715	0.06219	0.029278	0.173488	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.25085	1.82;1.82;1.82;1.82	5.38	-5.34	0.02705	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.420019	0.19121	N	0.122185	T	0.00012	0.0000	L	0.35854	1.095	0.43364	P	0.0045600000000000085	B	0.02656	0.0	B	0.01281	0.0	T	0.44467	-0.9326	9	0.34782	T	0.22	.	7.1692	0.25708	0.0:0.3023:0.2997:0.398	rs4129009;rs52824627;rs4129009	775	Q9BXR5	TLR10_HUMAN	V	775	ENSP00000308925:I775V;ENSP00000421483:I775V;ENSP00000354459:I775V;ENSP00000424923:I775V	ENSP00000308925:I775V	I	-	1	0	TLR10	38451284	0.006000	0.16342	0.010000	0.14722	0.011000	0.07611	0.012000	0.13287	-0.961000	0.03609	-1.221000	0.01599	ATT	T|0.840;C|0.160	0.160	strong		0.408	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155244475	155244475	+	Intron	SNP	G	G	T	rs12500437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155244475G>T	ENST00000357232.4	-	13	2653				DCHS2_ENST00000339452.1_Missense_Mutation_p.P1342H	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2						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)		CAGAGGCATAGGTCTAGCTGC	0.433													T|||	3951	0.788938	0.4501	0.9135	5008	,	,		13824	0.8849		0.9105	False		,,,				2504	0.9346				p.P1342H		Atlas-SNP	.											.	DCHS2	594	.	0			c.C4025A						PASS	.						39.0	29.0	32.0					4																	155244475		692	1591	2283	SO:0001627	intron_variant	54798	exon8			GGCATAGGTCTAG	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.2654-835C>A	4.37:g.155244475G>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	1728	0.7912087912087912	208	0.42276422764227645	334	0.9226519337016574	496	0.8671328671328671	690	0.9102902374670184	T	4.296	0.054247	0.08291	.	.	ENSG00000197410	ENST00000339452;ENST00000544161	T	0.58940	0.3	1.88	-0.914	0.10497	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32771	-0.9894	7	0.40728	T	0.16	.	4.6307	0.12500	0.1647:0.0:0.258:0.5774	rs12500437;rs58003514;rs12500437	1342	E9PC11	.	H	1342	ENSP00000345062:P1342H	ENSP00000345062:P1342H	P	-	2	0	DCHS2	155463925	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.301000	0.08232	-2.272000	0.00682	-4.807000	0.00003	CCT	G|0.235;T|0.765	0.765	strong		0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
PELP1	27043	hgsc.bcm.edu	37	17	4574751	4574751	+	Missense_Mutation	SNP	T	T	A	rs9436	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000436683.2_Missense_Mutation_p.T902S|PELP1_ENST00000269230.7_Missense_Mutation_p.T1036S|PELP1_ENST00000572293.1_Missense_Mutation_p.T1176S			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	75	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	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	
SPHK1	8877	hgsc.bcm.edu	37	17	74383648	74383648	+	Missense_Mutation	SNP	C	C	T	rs56341546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74383648C>T	ENST00000545180.1	+	8	1945	c.1136C>T	c.(1135-1137)cCg>cTg	p.P379L	SPHK1_ENST00000392496.3_Missense_Mutation_p.P379L|SPHK1_ENST00000592299.1_Missense_Mutation_p.P379L|SPHK1_ENST00000323374.4_Missense_Mutation_p.P465L|SPHK1_ENST00000590959.1_Missense_Mutation_p.P393L			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	379					'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)	CAGATGCCACCGCCAGAAGAG	0.647													C|||	24	0.00479233	0.0	0.0043	5008	,	,		17320	0.0		0.0119	False		,,,				2504	0.0092				p.P465L	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.C1394T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400		0,6,2197	27.0	30.0	29.0		1136,1136,1178,1394	0.9	0.0	17	dbSNP_129	29	52,8544		0,52,4246	yes	missense,missense,missense,missense	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	98,98,98,98	0,58,6443	TT,TC,CC		0.6049,0.1362,0.4461	benign,benign,benign,benign	379/385,379/385,393/399,465/471	74383648	58,12944	2203	4298	6501	SO:0001583	missense	8877	exon6			TGCCACCGCCAGA	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.1136C>T	17.37:g.74383648C>T	ENSP00000440970:p.Pro379Leu	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	27	15	0.555556	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	37	CCDS45785.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	12.92	2.081367	0.36758	0.001362	0.006049	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.24350	1.96;1.86;1.96	4.64	0.926	0.19430	.	1.925830	0.02640	N	0.105239	T	0.14917	0.0360	L	0.32530	0.975	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.23904	-1.0175	10	0.54805	T	0.06	0.009	4.5549	0.12131	0.1711:0.5944:0.0:0.2345	rs56341546;rs61751848	465;393;379	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	L	379;465;379;378	ENSP00000440970:P379L;ENSP00000313681:P465L;ENSP00000376285:P379L	ENSP00000313681:P465L	P	+	2	0	SPHK1	71895243	0.000000	0.05858	0.005000	0.12908	0.032000	0.12392	0.093000	0.15086	0.480000	0.27534	0.558000	0.71614	CCG	C|0.994;T|0.006	0.006	strong		0.647	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
DHX37	57647	hgsc.bcm.edu	37	12	125438713	125438713	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:125438713C>T	ENST00000308736.2	-	19	2596	c.2498G>A	c.(2497-2499)cGg>cAg	p.R833Q	DHX37_ENST00000544745.1_Missense_Mutation_p.R620Q	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	833							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)		CACCCGGGCCCGCTTGCTCTT	0.657																																					p.R833Q		Atlas-SNP	.											DHX37,NS,carcinoma,+1,1	DHX37	114	1	0			c.G2498A						scavenged	.						32.0	36.0	35.0					12																	125438713		2203	4300	6503	SO:0001583	missense	57647	exon19			CGGGCCCGCTTGC	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.2498G>A	12.37:g.125438713C>T	ENSP00000311135:p.Arg833Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	123	2	0.0162602	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.560197	0.45590	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.29917	1.55;1.55	5.33	4.24	0.50183	Helicase-associated domain (2);	0.193729	0.46758	D	0.000273	T	0.25082	0.0609	M	0.66939	2.045	0.30885	N	0.731001	P	0.37276	0.589	B	0.21546	0.035	T	0.28396	-1.0045	10	0.27785	T	0.31	-5.9232	11.1417	0.48406	0.0:0.7958:0.0:0.2042	.	833	Q8IY37	DHX37_HUMAN	Q	833;620	ENSP00000311135:R833Q;ENSP00000439009:R620Q	ENSP00000311135:R833Q	R	-	2	0	DHX37	124004666	0.999000	0.42202	0.997000	0.53966	0.753000	0.42808	1.186000	0.32078	2.489000	0.83994	0.455000	0.32223	CGG	.	.	none		0.657	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
DAAM1	23002	hgsc.bcm.edu	37	14	59797373	59797373	+	Silent	SNP	G	G	A	rs28927674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:59797373G>A	ENST00000395125.1	+	12	1550	c.1527G>A	c.(1525-1527)gcG>gcA	p.A509A	DAAM1_ENST00000351081.1_Silent_p.A509A|DAAM1_ENST00000360909.3_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	152	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	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	
ECI2	10455	hgsc.bcm.edu	37	6	4116262	4116262	+	Splice_Site	SNP	G	G	A	rs7166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:4116262G>A	ENST00000380118.3	-	10	1067	c.1031C>T	c.(1030-1032)gCc>gTc	p.A344V	C6orf201_ENST00000380175.4_Intron|ECI2_ENST00000465828.1_Splice_Site_p.A314V|C6orf201_ENST00000333388.5_Intron|ECI2_ENST00000361538.2_Splice_Site_p.A314V|ECI2_ENST00000380125.2_Splice_Site_p.A314V|C6orf201_ENST00000430835.2_Intron|ECI2_ENST00000413766.2_Splice_Site_p.A177V			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	344			A -> V (in dbSNP:rs7166). {ECO:0000269|PubMed:10354522, ECO:0000269|PubMed:12097419}.		fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						AATTCTCAAGGCCTGGAAAAA	0.463													G|||	1543	0.308107	0.292	0.3573	5008	,	,		20514	0.3581		0.332	False		,,,				2504	0.2188				p.A344V		Atlas-SNP	.											.	ECI2	59	.	0			c.C1031T						PASS	.	G	,VAL/ALA,VAL/ALA,VAL/ALA	1254,3152	429.5+/-342.2	186,882,1135	72.0	67.0	69.0		,941,941,1031	3.6	0.8	6	dbSNP_52	69	2616,5984	421.7+/-353.8	394,1828,2078	yes	intron,missense-near-splice,missense-near-splice,missense-near-splice	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,64,64,64	580,2710,3213	AA,AG,GG		30.4186,28.4612,29.7555	,benign,benign,benign	,314/365,314/365,344/395	4116262	3870,9136	2203	4300	6503	SO:0001630	splice_region_variant	10455	exon10			CTCAAGGCCTGGA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"""acyl-Coenzyme A binding domain containing 2"", "" Hepatocellular carcinoma-associated antigen 88"""	608024	"""peroxisomal D3,D2-enoyl-CoA isomerase"""	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.1030-1C>T	6.37:g.4116262G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	37	CCDS43420.2	736	0.336996336996337	138	0.2804878048780488	128	0.35359116022099446	210	0.36713286713286714	260	0.34300791556728233	G	15.37	2.814243	0.50527	0.284612	0.304186	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000413766;ENST00000361538;ENST00000465828	T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68	5.44	3.6	0.41247	.	0.517099	0.23282	N	0.049892	T	0.23054	0.0557	L	0.48362	1.52	0.38998	P	0.04071899999999995	B	0.14438	0.01	B	0.14578	0.011	T	0.11792	-1.0573	9	0.48119	T	0.1	.	10.1077	0.42544	0.0759:0.1368:0.7872:0.0	rs7166;rs605312;rs1128188;rs3184842;rs13209353;rs17294765;rs17349268;rs17734713;rs7166	344	O75521	ECI2_HUMAN	V	344;314;177;314;314	ENSP00000369461:A344V;ENSP00000369468:A314V;ENSP00000406969:A177V;ENSP00000354737:A314V;ENSP00000420309:A314V	ENSP00000354737:A314V	A	-	2	0	ECI2	4061261	0.994000	0.37717	0.820000	0.32676	0.830000	0.47004	4.146000	0.58072	1.293000	0.44690	0.655000	0.94253	GCC	G|0.699;A|0.301	0.301	strong		0.463	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117	Missense_Mutation
UGT3A1	133688	hgsc.bcm.edu	37	5	35965970	35965970	+	Missense_Mutation	SNP	A	A	C	rs3756669	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:35965970A>C	ENST00000274278.3	-	4	718	c.361T>G	c.(361-363)Tgt>Ggt	p.C121G	UGT3A1_ENST00000333811.4_Missense_Mutation_p.C67G|UGT3A1_ENST00000507113.1_Missense_Mutation_p.C87G|UGT3A1_ENST00000503189.1_Missense_Mutation_p.C121G|UGT3A1_ENST00000513233.1_Intron	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	121			C -> G (in dbSNP:rs3756669).			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)			AAATAACTACATTGAGTCCCA	0.294													A|||	1066	0.212859	0.0166	0.2233	5008	,	,		18203	0.3849		0.1392	False		,,,				2504	0.3691				p.C121G		Atlas-SNP	.											.	UGT3A1	95	.	0			c.T361G						PASS	.	A	GLY/CYS,GLY/CYS	157,4247		3,151,2048	37.0	38.0	38.0		199,361	3.0	0.0	5	dbSNP_107	38	1201,7391		93,1015,3188	yes	missense,missense	UGT3A1	NM_001171873.1,NM_152404.3	159,159	96,1166,5236	CC,CA,AA		13.9781,3.5649,10.4494	probably-damaging,probably-damaging	67/253,121/524	35965970	1358,11638	2202	4296	6498	SO:0001583	missense	133688	exon4			AACTACATTGAGT		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.361T>G	5.37:g.35965970A>C	ENSP00000274278:p.Cys121Gly	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Missense_Mutation	SNP	ENST00000274278.3	37	CCDS3913.1	384	0.17582417582417584	10	0.02032520325203252	65	0.17955801104972377	203	0.3548951048951049	106	0.13984168865435356	A	17.10	3.303970	0.60305	0.035649	0.139781	ENSG00000145626	ENST00000274278;ENST00000503189;ENST00000507113;ENST00000333811	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	3.0	3.0	0.34707	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.93854	3.465	0.25104	P	0.99076174	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;0.999	T	0.00028	-1.2296	9	0.87932	D	0	.	10.7944	0.46451	1.0:0.0:0.0:0.0	rs3756669;rs11566673;rs16902668;rs57097474;rs3756669	87;121;67;121	E9PD17;B7Z8Q8;G5E961;Q6NUS8	.;.;.;UD3A1_HUMAN	G	121;121;87;67	ENSP00000274278:C121G;ENSP00000427079:C121G;ENSP00000426100:C87G;ENSP00000328033:C67G	ENSP00000274278:C121G	C	-	1	0	UGT3A1	36001727	0.021000	0.18746	0.007000	0.13788	0.656000	0.38851	1.899000	0.39818	1.318000	0.45170	0.260000	0.18958	TGT	C|0.152;N|0.000	0.152	strong		0.294	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404	
MCM8	84515	hgsc.bcm.edu	37	20	5953815	5953815	+	Silent	SNP	A	A	G	rs34464794	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:5953815A>G	ENST00000378896.3	+	12	1745	c.1368A>G	c.(1366-1368)ccA>ccG	p.P456P	MCM8_ENST00000265187.4_Silent_p.P440P|MCM8_ENST00000378883.1_Intron|MCM8_ENST00000378886.2_Silent_p.P496P	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	456	MCM.				cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						TTGGAGATCCAGGCCTAGGAA	0.403													A|||	98	0.0195687	0.003	0.013	5008	,	,		19499	0.0		0.0646	False		,,,				2504	0.0204				p.P456P		Atlas-SNP	.											MCM8_ENST00000378896,NS,carcinoma,+2,2	MCM8	125	2	0			c.A1368G						PASS	.	A	,	58,4348	54.9+/-90.9	0,58,2145	131.0	123.0	126.0		1368,1320	3.9	1.0	20	dbSNP_126	126	552,8048	152.7+/-207.2	16,520,3764	no	coding-synonymous,coding-synonymous	MCM8	NM_032485.4,NM_182802.1	,	16,578,5909	GG,GA,AA		6.4186,1.3164,4.6901	,	456/841,440/825	5953815	610,12396	2203	4300	6503	SO:0001819	synonymous_variant	84515	exon12			AGATCCAGGCCTA	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.1368A>G	20.37:g.5953815A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Silent	SNP	ENST00000378896.3	37	CCDS13094.1																																																																																			A|0.960;G|0.040	0.040	strong		0.403	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
CUL7	9820	hgsc.bcm.edu	37	6	43008298	43008298	+	Silent	SNP	C	C	T	rs2273917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43008298C>T	ENST00000265348.3	-	21	4078	c.3993G>A	c.(3991-3993)ctG>ctA	p.L1331L	CUL7_ENST00000535468.1_Silent_p.L1415L			Q14999	CUL7_HUMAN	cullin 7	1331					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCTCCAGCTTCAGGAGTTCCT	0.567													T|||	1628	0.32508	0.6377	0.2406	5008	,	,		21471	0.2202		0.1203	False		,,,				2504	0.2812				p.L1415L		Atlas-SNP	.											.	CUL7	133	.	0			c.G4245A						PASS	.	T	,	2540,1866	539.1+/-375.2	732,1076,395	146.0	160.0	155.0		4245,3993	3.5	1.0	6	dbSNP_100	155	1136,7464	765.8+/-407.6	74,988,3238	no	coding-synonymous,coding-synonymous	CUL7	NM_001168370.1,NM_014780.4	,	806,2064,3633	TT,TC,CC		13.2093,42.3513,28.2639	,	1415/1783,1331/1699	43008298	3676,9330	2203	4300	6503	SO:0001819	synonymous_variant	9820	exon21			CAGCTTCAGGAGT	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.3993G>A	6.37:g.43008298C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	37	CCDS4881.1																																																																																			C|0.709;T|0.291	0.291	strong		0.567	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
PSMC5	5705	hgsc.bcm.edu	37	17	61903445	61903445	+	5'Flank	SNP	G	G	C	rs2584625	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:61903445G>C	ENST00000310144.6	+	0	0				PSMC5_ENST00000375812.4_5'Flank|FTSJ3_ENST00000427159.2_Missense_Mutation_p.Q91E|PSMC5_ENST00000580864.1_5'Flank|PSMC5_ENST00000581882.1_5'Flank|FTSJ3_ENST00000580295.1_5'Flank	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						GTGATGTCCTGCTGGAGAGTC	0.478													C|||	3670	0.732827	0.9796	0.6816	5008	,	,		20984	0.5556		0.5984	False		,,,				2504	0.7566				p.Q91E		Atlas-SNP	.											.	FTSJ3	63	.	0			c.C271G						PASS	.	C	GLU/GLN	4014,392	196.0+/-220.5	1829,356,18	143.0	145.0	145.0		271	4.7	1.0	17	dbSNP_100	145	5216,3384	501.5+/-375.5	1599,2018,683	yes	missense	FTSJ3	NM_017647.3	29	3428,2374,701	CC,CG,GG		39.3488,8.897,29.0328	benign	91/848	61903445	9230,3776	2203	4300	6503	SO:0001631	upstream_gene_variant	117246	exon5			TGTCCTGCTGGAG	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			17.37:g.61903445G>C	Exception_encountered	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	110	108	0.981818	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	1496	0.684981684981685	477	0.9695121951219512	230	0.6353591160220995	333	0.5821678321678322	456	0.6015831134564644	C	15.39	2.818139	0.50633	0.91103	0.606512	ENSG00000108592	ENST00000427159	T	0.28454	1.61	4.74	4.74	0.60224	Ribosomal RNA methyltransferase RrmJ/FtsJ (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00246	-1.78	0.49389	P	2.1099999999996122E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.40720	-0.9548	9	0.02654	T	1	-24.6385	13.1779	0.59637	0.0:0.8383:0.1617:0.0	rs2584625;rs3760246;rs17552334;rs52828289;rs57321735;rs2584625	91	Q8IY81	RRMJ3_HUMAN	E	91	ENSP00000396673:Q91E	ENSP00000396673:Q91E	Q	-	1	0	FTSJ3	59257177	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.111000	0.64628	1.367000	0.46095	-0.216000	0.12614	CAG	G|0.317;C|0.682	0.682	strong		0.478	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
KIAA1755	85449	hgsc.bcm.edu	37	20	36856616	36856616	+	Missense_Mutation	SNP	G	G	A	rs16987188	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36856616G>A	ENST00000279024.4	-	6	2169	c.1898C>T	c.(1897-1899)gCg>gTg	p.A633V		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	633			A -> V (in dbSNP:rs16987188).							breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AATCAGGACCGCCAGCCCCTT	0.612													G|||	269	0.0537141	0.0893	0.0259	5008	,	,		17350	0.0456		0.0249	False		,,,				2504	0.0634				p.A633V		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1898T						PASS	.	G	VAL/ALA	380,4026	189.5+/-215.6	19,342,1842	44.0	40.0	42.0		1898	-0.5	0.5	20	dbSNP_123	42	275,8325	102.5+/-163.7	7,261,4032	yes	missense	KIAA1755	NM_001029864.1	64	26,603,5874	AA,AG,GG		3.1977,8.6246,5.0361	benign	633/1201	36856616	655,12351	2203	4300	6503	SO:0001583	missense	85449	exon6			AGGACCGCCAGCC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1898C>T	20.37:g.36856616G>A	ENSP00000279024:p.Ala633Val	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	103	0.04716117216117216	48	0.0975609756097561	14	0.03867403314917127	24	0.04195804195804196	17	0.022427440633245383	G	0.487	-0.877142	0.02550	0.086246	0.031977	ENSG00000149633	ENST00000279024;ENST00000373398	T	0.14266	2.52	4.8	-0.471	0.12119	.	0.949823	0.08653	N	0.913657	T	0.00241	0.0007	L	0.28115	0.83	0.80722	P	0.0	B	0.13594	0.008	B	0.12837	0.008	T	0.44877	-0.9299	9	0.14252	T	0.57	.	8.381	0.32472	0.5547:0.0:0.4453:0.0	rs16987188;rs52805884;rs16987188	633	Q5JYT7	K1755_HUMAN	V	633;180	ENSP00000279024:A633V	ENSP00000279024:A633V	A	-	2	0	KIAA1755	36290030	0.003000	0.15002	0.546000	0.28166	0.186000	0.23388	0.141000	0.16076	-0.220000	0.09988	-0.812000	0.03155	GCG	G|0.949;A|0.051	0.051	strong		0.612	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
SLC45A4	57210	hgsc.bcm.edu	37	8	142222445	142222445	+	Missense_Mutation	SNP	T	T	C	rs3739238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:142222445T>C	ENST00000024061.3	-	7	2306	c.1999A>G	c.(1999-2001)Aac>Gac	p.N667D	SLC45A4_ENST00000519067.1_Missense_Mutation_p.N667D|SLC45A4_ENST00000433583.2_Missense_Mutation_p.N660D|SLC45A4_ENST00000517878.1_Missense_Mutation_p.N718D	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)			TCTGACACGTTGGGATAGATC	0.637													C|||	3559	0.710663	0.8374	0.5807	5008	,	,		12253	0.8145		0.5875	False		,,,				2504	0.6513				p.N667D		Atlas-SNP	.											.	SLC45A4	71	.	0			c.A1999G						PASS	.	C	ASP/ASN	3598,808	318.8+/-295.8	1474,650,79	50.0	52.0	51.0		1999	4.4	0.2	8	dbSNP_107	51	4895,3705	527.6+/-381.2	1391,2113,796	yes	missense	SLC45A4	NM_001080431.1	23	2865,2763,875	CC,CT,TT		43.0814,18.3386,34.6994	benign	667/799	142222445	8493,4513	2203	4300	6503	SO:0001583	missense	57210	exon7			ACACGTTGGGATA	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.1999A>G	8.37:g.142222445T>C	ENSP00000024061:p.Asn667Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	1530	0.7005494505494505	408	0.8292682926829268	231	0.638121546961326	463	0.8094405594405595	428	0.5646437994722955	C	1.445	-0.566589	0.03910	0.816614	0.569186	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061	T;T;T;T	0.13778	2.58;2.57;2.57;2.56	5.27	4.39	0.52855	.	0.790431	0.12085	N	0.500962	T	0.00012	0.0000	N	0.00170	-1.935	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	0.29150	-1.0021	9	0.06494	T	0.89	-11.7036	11.7476	0.51830	0.0:0.8568:0.0:0.1432	rs3739238;rs17830998;rs52802420;rs59594486;rs3739238	718;667;667	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	D	667;718;660;667	ENSP00000429059:N667D;ENSP00000428137:N718D;ENSP00000400799:N660D;ENSP00000024061:N667D	ENSP00000024061:N667D	N	-	1	0	SLC45A4	142291627	0.173000	0.23056	0.157000	0.22605	0.485000	0.33311	1.197000	0.32211	0.615000	0.30124	-0.119000	0.15052	AAC	T|0.321;C|0.679	0.679	strong		0.637	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
FGF6	2251	hgsc.bcm.edu	37	12	4553383	4553383	+	Silent	SNP	A	A	G	rs2241279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4553383A>G	ENST00000228837.2	-	2	409	c.366T>C	c.(364-366)acT>acC	p.T122T		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	122					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)			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)			CTCGCTCCACAGTGGAAATTT	0.532													G|||	2402	0.479633	0.6021	0.3473	5008	,	,		20091	0.4206		0.3857	False		,,,				2504	0.5654				p.T122T		Atlas-SNP	.											.	FGF6	40	.	0			c.T366C						PASS	.	G		2566,1840	535.4+/-374.2	753,1060,390	70.0	60.0	64.0		366	-11.3	0.2	12	dbSNP_98	64	3433,5167	637.0+/-399.2	666,2101,1533	no	coding-synonymous	FGF6	NM_020996.1		1419,3161,1923	GG,GA,AA		39.9186,41.7612,46.1249		122/209	4553383	5999,7007	2203	4300	6503	SO:0001819	synonymous_variant	2251	exon2			CTCCACAGTGGAA	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.366T>C	12.37:g.4553383A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_020996	Q0VAE1	Silent	SNP	ENST00000228837.2	37	CCDS8527.1																																																																																			A|0.548;G|0.452	0.452	strong		0.532	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
EP300	2033	hgsc.bcm.edu	37	22	41542753	41542753	+	Silent	SNP	A	A	G	rs61756763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:41542753A>G	ENST00000263253.7	+	11	3283	c.2064A>G	c.(2062-2064)ctA>ctG	p.L688L		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	688					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ATGGCCCTCTACCTGACCCAA	0.368			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	7	0.00139776	0.0	0.0	5008	,	,		16320	0.0		0.006	False		,,,				2504	0.001				p.L688L		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A2064G						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	95.0	93.0	93.0		2064	-11.5	0.3	22	dbSNP_129	93	41,8559	25.1+/-72.6	1,39,4260	no	coding-synonymous	EP300	NM_001429.3		1,43,6459	GG,GA,AA		0.4767,0.0908,0.346		688/2415	41542753	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	2033	exon11	Familial Cancer Database	Broad Thumb-Hallux syndrome	CCCTCTACCTGAC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2064A>G	22.37:g.41542753A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																			A|0.997;G|0.003	0.003	strong		0.368	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
ADAMTS4	9507	hgsc.bcm.edu	37	1	161167989	161167989	+	Silent	SNP	G	G	A	rs12740751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161167989G>A	ENST00000367996.5	-	1	857	c.429C>T	c.(427-429)caC>caT	p.H143H	ADAMTS4_ENST00000478394.1_5'Flank|NDUFS2_ENST00000367993.3_5'Flank|ADAMTS4_ENST00000367995.3_Silent_p.H143H	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	143					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	CCCCATCCCAGTGCAGAGATG	0.637													G|||	40	0.00798722	0.0015	0.0115	5008	,	,		17379	0.0		0.0229	False		,,,				2504	0.0072				p.H143H		Atlas-SNP	.											.	ADAMTS4	171	.	0			c.C429T						PASS	.	G		25,4381	29.9+/-59.1	0,25,2178	61.0	62.0	62.0		429	2.7	1.0	1	dbSNP_121	62	229,8371	93.5+/-155.5	2,225,4073	no	coding-synonymous	ADAMTS4	NM_005099.4		2,250,6251	AA,AG,GG		2.6628,0.5674,1.9529		143/838	161167989	254,12752	2203	4300	6503	SO:0001819	synonymous_variant	9507	exon1			ATCCCAGTGCAGA	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.429C>T	1.37:g.161167989G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Silent	SNP	ENST00000367996.5	37	CCDS1223.1																																																																																			G|0.986;A|0.014	0.014	strong		0.637	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
ROS1	6098	hgsc.bcm.edu	37	6	117686840	117686840	+	Silent	SNP	T	T	C	rs2229078	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:117686840T>C	ENST00000368508.3	-	19	3075	c.2877A>G	c.(2875-2877)gaA>gaG	p.E959E	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Silent_p.E954E	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	959	Fibronectin type-III 4. {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)		AAGCATTTCCTTCAATCCTAA	0.383			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								T|||	121	0.0241613	0.0	0.0303	5008	,	,		18336	0.001		0.0577	False		,,,				2504	0.0419				p.E959E		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.A2877G						PASS	.	T		48,4358	48.2+/-83.0	0,48,2155	52.0	50.0	51.0		2877	-0.7	1.0	6	dbSNP_98	51	464,8136	135.4+/-192.6	10,444,3846	no	coding-synonymous	ROS1	NM_002944.2		10,492,6001	CC,CT,TT		5.3953,1.0894,3.9366		959/2348	117686840	512,12494	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon19			ATTTCCTTCAATC	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.2877A>G	6.37:g.117686840T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			T|0.968;C|0.032	0.032	strong		0.383	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
OR6B1	135946	hgsc.bcm.edu	37	7	143701389	143701389	+	Missense_Mutation	SNP	A	A	T	rs182442940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:143701389A>T	ENST00000408922.2	+	1	368	c.300A>T	c.(298-300)caA>caT	p.Q100H		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	100						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)					GTATGATACAACTGTACTTCT	0.483													A|||	13	0.00259585	0.0015	0.0086	5008	,	,		23655	0.0		0.004	False		,,,				2504	0.001				p.Q100H		Atlas-SNP	.											.	OR6B1	60	.	0			c.A300T						PASS	.	A	HIS/GLN	7,4285		0,7,2139	161.0	162.0	162.0		300	-3.1	0.9	7		162	18,8526		0,18,4254	yes	missense	OR6B1	NM_001005281.1	24	0,25,6393	TT,TA,AA		0.2107,0.1631,0.1948	probably-damaging	100/312	143701389	25,12811	2146	4272	6418	SO:0001583	missense	135946	exon1			GATACAACTGTAC		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.300A>T	7.37:g.143701389A>T	ENSP00000386151:p.Gln100His	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	37	CCDS43667.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	A	18.27	3.587495	0.66105	0.001631	0.002107	ENSG00000221813	ENST00000408922	T	0.02121	4.44	5.13	-3.13	0.05266	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35349	U	0.003273	T	0.12220	0.0297	H	0.96691	3.865	0.33578	D	0.599454	D	0.89917	1.0	D	0.97110	1.0	T	0.36237	-0.9756	10	0.87932	D	0	.	13.9112	0.63869	0.3076:0.0:0.6924:0.0	.	100	O95007	OR6B1_HUMAN	H	100	ENSP00000386151:Q100H	ENSP00000386151:Q100H	Q	+	3	2	OR6B1	143332322	0.000000	0.05858	0.908000	0.35775	0.981000	0.71138	-1.271000	0.02828	-0.425000	0.07371	0.455000	0.32223	CAA	A|0.997;T|0.003	0.003	strong		0.483	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1		
ECE2	9718	hgsc.bcm.edu	37	3	183996068	183996068	+	Silent	SNP	C	C	T	rs3752904	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:183996068C>T	ENST00000402825.3	+	6	1071	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A	ECE2_ENST00000359140.4_Silent_p.A210A|ECE2_ENST00000404464.3_Silent_p.A239A|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000357474.5_Silent_p.A285A	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	357	Endothelin-converting enzyme 2 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)			ACATCAGTGCCGACTCTAAGA	0.542													C|||	2514	0.501997	0.593	0.6095	5008	,	,		16408	0.4157		0.5308	False		,,,				2504	0.362				p.A357A		Atlas-SNP	.											.	ECE2	303	.	0			c.C1071T						PASS	.	C	,,,	2666,1740	647.2+/-398.5	823,1020,360	75.0	73.0	73.0		630,855,717,1071	-7.3	0.7	3	dbSNP_107	73	4504,4096	591.6+/-392.9	1175,2154,971	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	,,,	1998,3174,1331	TT,TC,CC		47.6279,39.4916,44.8716	,,,	210/737,285/812,239/766,357/884	183996068	7170,5836	2203	4300	6503	SO:0001819	synonymous_variant	9718	exon6			CAGTGCCGACTCT	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.1071C>T	3.37:g.183996068C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			C|0.451;T|0.549	0.549	strong		0.542	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
QRFPR	84109	hgsc.bcm.edu	37	4	122254014	122254014	+	Silent	SNP	A	A	G	rs55975435	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	224	0	0		WXS	Illumina HiSeq	Phase_I	208	104	0.5	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	
ZFP69B	65243	hgsc.bcm.edu	37	1	40929087	40929087	+	Silent	SNP	C	C	T	rs142494383	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40929087C>T	ENST00000411995.2	+	6	1806	c.1431C>T	c.(1429-1431)tgC>tgT	p.C477C	RP1-228H13.5_ENST00000565390.1_RNA|ZFP69B_ENST00000361584.3_Silent_p.C375C|ZFP69B_ENST00000484445.1_3'UTR	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B	477					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)										CTTATGAATGCAGTCATTGTG	0.373													C|||	17	0.00339457	0.0023	0.0086	5008	,	,		21479	0.0		0.007	False		,,,				2504	0.001				p.C477C		Atlas-SNP	.											.	.	.	.	0			c.C1431T						PASS	.	C		9,4397		0,9,2194	92.0	89.0	90.0		1431	0.4	0.9	1	dbSNP_134	90	93,8507		0,93,4207	no	coding-synonymous	ZNF643	NM_023070.2		0,102,6401	TT,TC,CC		1.0814,0.2043,0.7843		477/535	40929087	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	65243	exon5			TGAATGCAGTCAT	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.1431C>T	1.37:g.40929087C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_023070	Q5QPL4	Silent	SNP	ENST00000411995.2	37	CCDS452.2																																																																																			C|0.991;T|0.009	0.009	strong		0.373	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2	NM_023070	
OR56B1	387748	hgsc.bcm.edu	37	11	5757785	5757785	+	Silent	SNP	C	C	T	rs12792180	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5757785C>T	ENST00000317121.3	+	1	105	c.39C>T	c.(37-39)agC>agT	p.S13S	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		TCTCCAATAGCTCCAAATTCC	0.443													C|||	566	0.113019	0.09	0.1268	5008	,	,		18374	0.1399		0.1133	False		,,,				2504	0.1063				p.S13S		Atlas-SNP	.											.	OR56B1	38	.	0			c.C39T						PASS	.	C		405,3997	200.1+/-223.5	18,369,1814	77.0	77.0	77.0		39	0.7	1.0	11	dbSNP_121	77	868,7726	196.8+/-241.6	45,778,3474	no	coding-synonymous	OR56B1	NM_001005180.2		63,1147,5288	TT,TC,CC		10.1001,9.2004,9.7953		13/325	5757785	1273,11723	2201	4297	6498	SO:0001819	synonymous_variant	387748	exon1			CAATAGCTCCAAA	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"""GPCR / Class A : Olfactory receptors"""	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.39C>T	11.37:g.5757785C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	134	58	0.432836	NM_001005180	B2RNY6|B3KV42|Q6IF76	Silent	SNP	ENST00000317121.3	37	CCDS31395.1																																																																																			C|0.895;T|0.105	0.105	strong		0.443	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180	
CSNK1G1	53944	hgsc.bcm.edu	37	15	64508763	64508763	+	Silent	SNP	G	G	A	rs6494466	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	74	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	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	
MOV10L1	54456	hgsc.bcm.edu	37	22	50599466	50599466	+	Missense_Mutation	SNP	C	C	A	rs2272843	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50599466C>A	ENST00000262794.5	+	26	3619	c.3536C>A	c.(3535-3537)gCa>gAa	p.A1179E	MOV10L1_ENST00000395858.3_Missense_Mutation_p.A1133E|MOV10L1_ENST00000540615.1_Intron|MOV10L1_ENST00000545383.1_Missense_Mutation_p.A1179E|MOV10L1_ENST00000395852.1_Missense_Mutation_p.A306E	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	1179			A -> E (in dbSNP:rs2272843). {ECO:0000269|PubMed:17974005}.		ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TTACCTCCTGCACTGCAGTCT	0.522													A|||	624	0.124601	0.031	0.2017	5008	,	,		20039	0.1488		0.1372	False		,,,				2504	0.1585				p.A1179E		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C3536A						PASS	.	A	GLU/ALA,,GLU/ALA,GLU/ALA	245,4161		9,227,1967	223.0	207.0	212.0		3398,,917,3536	5.1	0.2	22	dbSNP_100	212	1276,7324		93,1090,3117	yes	missense,intron,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_001164106.1,NM_018995.2	107,,107,107	102,1317,5084	AA,AC,CC		14.8372,5.5606,11.6946	benign,,benign,benign	1133/1166,,306/339,1179/1212	50599466	1521,11485	2203	4300	6503	SO:0001583	missense	54456	exon26			CTCCTGCACTGCA	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.3536C>A	22.37:g.50599466C>A	ENSP00000262794:p.Ala1179Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	118	69	0.584746	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	289	0.13232600732600733	15	0.03048780487804878	63	0.17403314917127072	108	0.1888111888111888	103	0.1358839050131926	.	0.005	-2.223352	0.00283	0.055606	0.148372	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000395852	D;D;T;D	0.92348	-1.72;-1.72;-1.22;-3.02	5.14	5.14	0.70334	.	0.228388	0.45361	N	0.000368	T	0.00241	0.0007	N	0.01048	-1.04	0.49130	P	2.4199999999996447E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.40136	-0.9579	9	0.02654	T	1	-29.185	5.4416	0.16511	0.7323:0.1784:0.0892:0.0	rs2272843;rs3188620;rs17412558;rs17836649;rs52811465;rs61473516;rs2272843	306;1133;1179	Q9BXT6-2;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	E	1179;1179;1133;306	ENSP00000438978:A1179E;ENSP00000262794:A1179E;ENSP00000379199:A1133E;ENSP00000379193:A306E	ENSP00000262794:A1179E	A	+	2	0	MOV10L1	48941593	0.833000	0.29383	0.241000	0.24154	0.060000	0.15804	2.379000	0.44318	0.804000	0.34136	-0.471000	0.05019	GCA	C|0.878;A|0.122	0.122	strong		0.522	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
SHMT2	6472	hgsc.bcm.edu	37	12	57624701	57624701	+	Missense_Mutation	SNP	C	C	T	rs73338162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57624701C>T	ENST00000328923.3	+	2	601	c.149C>T	c.(148-150)tCg>tTg	p.S50L	Y_RNA_ENST00000365197.1_RNA|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Missense_Mutation_p.S29L|SHMT2_ENST00000557487.1_Missense_Mutation_p.S50L|SHMT2_ENST00000393827.4_5'UTR|SHMT2_ENST00000414700.3_Missense_Mutation_p.S29L|SHMT2_ENST00000449049.3_Missense_Mutation_p.S29L	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	50					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)	GAGAGCCTGTCGGACAGTGAT	0.622													C|||	118	0.0235623	0.0756	0.0144	5008	,	,		18639	0.0		0.008	False		,,,				2504	0.0				p.S50L	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.C149T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	343,4063	179.4+/-207.9	9,325,1869	101.0	84.0	90.0		149,86,86,86,149	3.9	0.5	12	dbSNP_130	90	72,8528	43.1+/-100.9	0,72,4228	yes	missense,missense,missense,missense,missense	SHMT2	NM_001166356.1,NM_001166357.1,NM_001166358.1,NM_001166359.1,NM_005412.5	145,145,145,145,145	9,397,6097	TT,TC,CC		0.8372,7.7848,3.1908	benign,benign,benign,benign,benign	50/495,29/484,29/484,29/484,50/505	57624701	415,12591	2203	4300	6503	SO:0001583	missense	6472	exon2			GCCTGTCGGACAG	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.149C>T	12.37:g.57624701C>T	ENSP00000333667:p.Ser50Leu	Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	241	108	0.448133	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	37	CCDS8934.1	52	0.023809523809523808	41	0.08333333333333333	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	16.72	3.201341	0.58234	0.077848	0.008372	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000556689;ENST00000414700;ENST00000557703;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	4.81	3.92	0.45320	Pyridoxal phosphate-dependent transferase, major domain (1);	0.198794	0.43579	D	0.000549	T	0.01940	0.0061	L	0.37630	1.12	0.80722	D	1	B;B	0.24092	0.06;0.097	B;B	0.26202	0.067;0.052	T	0.01739	-1.1284	10	0.37606	T	0.19	-8.0204	12.6117	0.56554	0.0:0.9176:0.0:0.0824	.	50;50	Q8N1A5;P34897	.;GLYM_HUMAN	L	50;50;50;29;29;29;29;29;29;29;29;29;29	ENSP00000333667:S50L;ENSP00000452315:S50L;ENSP00000452035:S50L;ENSP00000406881:S29L;ENSP00000450452:S29L;ENSP00000452161:S29L;ENSP00000450893:S29L;ENSP00000452045:S29L;ENSP00000452419:S29L;ENSP00000451968:S29L;ENSP00000452404:S29L;ENSP00000413770:S29L;ENSP00000451495:S29L	ENSP00000333667:S50L	S	+	2	0	SHMT2	55910968	0.961000	0.32948	0.531000	0.27976	0.967000	0.64934	2.233000	0.43027	1.399000	0.46721	-0.137000	0.14449	TCG	C|0.970;T|0.030	0.030	strong		0.622	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	
SLC20A1	6574	hgsc.bcm.edu	37	2	113404708	113404708	+	Silent	SNP	G	G	A	rs4849091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:113404708G>A	ENST00000272542.3	+	2	842	c.303G>A	c.(301-303)ctG>ctA	p.L101L	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	101					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	high-affinity inorganic phosphate:sodium symporter activity (GO:0005316)|inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|sodium:phosphate symporter activity (GO:0005436)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3)	28						CTCAAGGGCTGCTGATGGCCG	0.483													G|||	1806	0.360623	0.1573	0.4481	5008	,	,		18952	0.2202		0.5497	False		,,,				2504	0.5235				p.L101L		Atlas-SNP	.											SLC20A1,NS,carcinoma,+2,1	SLC20A1	59	1	0			c.G303A						PASS	.	G		922,3484	355.1+/-312.9	104,714,1385	166.0	145.0	152.0		303	5.5	0.7	2	dbSNP_111	152	4807,3793	613.7+/-396.1	1328,2151,821	no	coding-synonymous	SLC20A1	NM_005415.4		1432,2865,2206	AA,AG,GG		44.1047,20.926,44.0489		101/680	113404708	5729,7277	2203	4300	6503	SO:0001819	synonymous_variant	6574	exon2			AGGGCTGCTGATG		CCDS2099.1	2q13	2013-05-22			ENSG00000144136	ENSG00000144136		"""Solute carriers"""	10946	protein-coding gene	gene with protein product	"""gibbon ape leukemia virus receptor 1"""	137570		GLVR1		8041748	Standard	NM_005415		Approved	PiT-1, Glvr-1	uc002tib.3	Q8WUM9	OTTHUMG00000131317	ENST00000272542.3:c.303G>A	2.37:g.113404708G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_005415	Q08344|Q6DHX8|Q9UQ82	Silent	SNP	ENST00000272542.3	37	CCDS2099.1																																																																																			G|0.602;A|0.398	0.398	strong		0.483	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415	
HPCAL4	51440	hgsc.bcm.edu	37	1	40150156	40150156	+	Silent	SNP	G	G	A	rs9662128	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40150156G>A	ENST00000372844.3	-	2	511	c.120C>T	c.(118-120)agC>agT	p.S40S		NM_001282396.1|NM_001282397.1|NM_016257.2	NP_001269325.1|NP_001269326.1|NP_057341.1	Q9UM19	HPCL4_HUMAN	hippocalcin like 4	40	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				central nervous system development (GO:0007417)|signal transduction (GO:0007165)	intracellular (GO:0005622)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)	p.S40S(1)		breast(1)|central_nervous_system(1)|lung(5)|stomach(1)	8	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGAGGATGCCGCTGGGGCAGT	0.622													G|||	1782	0.355831	0.4811	0.2406	5008	,	,		14737	0.2698		0.3519	False		,,,				2504	0.3609				p.S40S		Atlas-SNP	.											HPCAL4,NS,carcinoma,0,1	HPCAL4	20	1	1	Substitution - coding silent(1)	stomach(1)	c.C120T						PASS	.	G		2018,2388	561.9+/-380.8	482,1054,667	64.0	53.0	57.0		120	1.1	1.0	1	dbSNP_119	57	2855,5745	447.0+/-361.4	460,1935,1905	no	coding-synonymous	HPCAL4	NM_016257.2		942,2989,2572	AA,AG,GG		33.1977,45.8012,37.4673		40/192	40150156	4873,8133	2203	4300	6503	SO:0001819	synonymous_variant	51440	exon2			GATGCCGCTGGGG	AB001105	CCDS441.1, CCDS72761.1	1p34.2	2013-01-10			ENSG00000116983	ENSG00000116983		"""EF-hand domain containing"""	18212	protein-coding gene	gene with protein product						10520747	Standard	NM_016257		Approved	HLP4, DKFZp761G122	uc001cdr.3	Q9UM19	OTTHUMG00000009246	ENST00000372844.3:c.120C>T	1.37:g.40150156G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_016257	B2R5U2|D3DPU1|Q5TG97|Q8N611	Silent	SNP	ENST00000372844.3	37	CCDS441.1																																																																																			G|0.645;A|0.355	0.355	strong		0.622	HPCAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025640.1	NM_016257	
DIP2A	23181	hgsc.bcm.edu	37	21	47974582	47974582	+	Silent	SNP	A	A	G	rs1107065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47974582A>G	ENST00000417564.2	+	27	3270	c.3249A>G	c.(3247-3249)acA>acG	p.T1083T	DIP2A_ENST00000427143.2_Silent_p.T1019T|DIP2A_ENST00000318711.7_Silent_p.T1084T|DIP2A_ENST00000400274.1_Silent_p.T1079T			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1083					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)		TCGGCACCACACTGCCCACCG	0.657													A|||	1661	0.331669	0.1634	0.389	5008	,	,		10149	0.3433		0.3986	False		,,,				2504	0.4376				p.T1083T		Atlas-SNP	.											.	DIP2A	332	.	0			c.A3249G						PASS	.	A	,,	979,3315		143,693,1311	29.0	34.0	32.0		3057,3237,3249	-10.9	0.8	21	dbSNP_86	32	3557,4925		800,1957,1484	no	coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146116.1,NM_015151.3	,,	943,2650,2795	GG,GA,AA		41.9359,22.7993,35.5041	,,	1019/1111,1079/1568,1083/1572	47974582	4536,8240	2147	4241	6388	SO:0001819	synonymous_variant	23181	exon27			CACCACACTGCCC	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.3249A>G	21.37:g.47974582A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			A|0.650;G|0.348	0.348	strong		0.657	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
SLC5A9	200010	hgsc.bcm.edu	37	1	48708278	48708278	+	Silent	SNP	G	G	A	rs75538709	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:48708278G>A	ENST00000438567.2	+	13	1879	c.1827G>A	c.(1825-1827)gaG>gaA	p.E609E	SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000236495.5_Silent_p.E634E|SLC5A9_ENST00000533824.1_Silent_p.E630E	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	609					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						TGGGCCAGGAGCAGCCTGAAG	0.642													G|||	253	0.0505192	0.0129	0.0648	5008	,	,		15903	0.001		0.1113	False		,,,				2504	0.0798				p.E634E		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G1902A						PASS	.	G	,	113,4293		1,111,2091	21.0	25.0	24.0		1827,1902	0.4	0.0	1	dbSNP_132	24	1005,7589		60,885,3352	no	coding-synonymous,coding-synonymous	SLC5A9	NM_001011547.2,NM_001135181.1	,	61,996,5443	AA,AG,GG		11.6942,2.5647,8.6	,	609/682,634/707	48708278	1118,11882	2203	4297	6500	SO:0001819	synonymous_variant	200010	exon14			CCAGGAGCAGCCT	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.1827G>A	1.37:g.48708278G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	62	0.579439	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Silent	SNP	ENST00000438567.2	37	CCDS30709.2																																																																																			G|0.920;A|0.080	0.080	strong		0.642	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
DSPP	1834	hgsc.bcm.edu	37	4	88537357	88537357	+	Silent	SNP	T	T	C	rs146317878	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537357T>C	ENST00000282478.7	+	4	3576	c.3543T>C	c.(3541-3543)agT>agC	p.S1181S	DSPP_ENST00000399271.1_Silent_p.S1181S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1181	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)		gcaatagcagtgatagcagcg	0.567													t|||	285	0.0569089	0.0091	0.0879	5008	,	,		25184	0.003		0.168	False		,,,				2504	0.0409				p.S1181S		Atlas-SNP	.											DSPP,rectum,carcinoma,0,1	DSPP	174	1	0			c.T3543C						scavenged	.	C		80,3200		0,80,1560	55.0	74.0	67.0		3543	1.2	0.0	4	dbSNP_134	67	750,5074		47,656,2209	no	coding-synonymous	DSPP	NM_014208.3		47,736,3769	CC,CT,TT		12.8777,2.439,9.1169		1181/1302	88537357	830,8274	1640	2912	4552	SO:0001819	synonymous_variant	1834	exon5			TAGCAGTGATAGC	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.3543T>C	4.37:g.88537357T>C		Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	201	78	0.38806	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			T|0.922;C|0.078	0.078	strong		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
PKD1L1	168507	hgsc.bcm.edu	37	7	47969072	47969072	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:47969072C>T	ENST00000289672.2	-	7	839	c.789G>A	c.(787-789)tcG>tcA	p.S263S		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	263					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						AACCAGACTGCGATGCCGTGA	0.547																																					p.S263S		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G789A						PASS	.						64.0	68.0	66.0					7																	47969072		2203	4300	6503	SO:0001819	synonymous_variant	168507	exon7			AGACTGCGATGCC	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.789G>A	7.37:g.47969072C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			.	.	none		0.547	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
INHA	3623	hgsc.bcm.edu	37	2	220439634	220439634	+	Missense_Mutation	SNP	G	G	A	rs149916845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220439634G>A	ENST00000243786.2	+	2	667	c.487G>A	c.(487-489)Gtg>Atg	p.V163M	INHA_ENST00000489456.1_3'UTR	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	163					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)		GGGAGGACCCGTGGCTGTGCC	0.667													G|||	4	0.000798722	0.0	0.0	5008	,	,		19117	0.0		0.004	False		,,,				2504	0.0				p.V163M		Atlas-SNP	.											INHA,NS,carcinoma,-1,1	INHA	30	1	0			c.G487A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	65.0	59.0	61.0		487	-0.8	0.0	2	dbSNP_134	61	16,8584	11.2+/-40.8	0,16,4284	yes	missense	INHA	NM_002191.3	21	0,17,6486	AA,AG,GG		0.186,0.0227,0.1307	benign	163/367	220439634	17,12989	2203	4300	6503	SO:0001583	missense	3623	exon2			GGACCCGTGGCTG		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.487G>A	2.37:g.220439634G>A	ENSP00000243786:p.Val163Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	0.133	-1.111751	0.01813	2.27E-4	0.00186	ENSG00000123999	ENST00000243786	D	0.85556	-2.0	4.84	-0.764	0.11027	.	0.785011	0.12700	N	0.446402	T	0.65883	0.2734	N	0.05608	-0.01	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.53809	-0.8386	10	0.40728	T	0.16	0.0079	5.5726	0.17204	0.3651:0.1689:0.4659:0.0	.	163	P05111	INHA_HUMAN	M	163	ENSP00000243786:V163M	ENSP00000243786:V163M	V	+	1	0	INHA	220147878	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.549000	0.06041	0.025000	0.15241	-0.459000	0.05422	GTG	G|0.998;A|0.002	0.002	strong		0.667	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1		
OR1Q1	158131	hgsc.bcm.edu	37	9	125377087	125377087	+	Missense_Mutation	SNP	A	A	G	rs972925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125377087A>G	ENST00000297913.2	+	1	140	c.71A>G	c.(70-72)cAa>cGa	p.Q24R	RP11-64P14.7_ENST00000431442.1_RNA	NM_012364.1	NP_036496.1	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q, member 1	24			Q -> R (in dbSNP:rs972925).		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)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	17						CCAGAAGAGCAAATCCCACTC	0.453													G|||	4120	0.822684	0.6256	0.8573	5008	,	,		21199	0.9444		0.8141	False		,,,				2504	0.9479				p.Q24R		Atlas-SNP	.											.	OR1Q1	46	.	0			c.A71G						PASS	.	G	ARG/GLN	2951,1455	471.8+/-356.2	986,979,238	211.0	193.0	199.0		71	2.9	0.0	9	dbSNP_86	199	7047,1553	291.9+/-300.6	2895,1257,148	yes	missense	OR1Q1	NM_012364.1	43	3881,2236,386	GG,GA,AA		18.0581,33.0232,23.1278	benign	24/315	125377087	9998,3008	2203	4300	6503	SO:0001583	missense	158131	exon1			AAGAGCAAATCCC		CCDS35125.1	9q33.2	2013-09-20			ENSG00000165202	ENSG00000165202		"""GPCR / Class A : Olfactory receptors"""	8223	protein-coding gene	gene with protein product				OR1Q2, OR1Q3			Standard	NM_012364		Approved	OST226, OR9-A, HSTPCR106, OST226OR9-A, TPCR106	uc011lyy.2	Q15612	OTTHUMG00000020615	ENST00000297913.2:c.71A>G	9.37:g.125377087A>G	ENSP00000297913:p.Gln24Arg	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_012364	Q6IFN4|Q8NGR7|Q96R82	Missense_Mutation	SNP	ENST00000297913.2	37	CCDS35125.1	1765	0.8081501831501832	308	0.6260162601626016	295	0.8149171270718232	539	0.9423076923076923	623	0.8218997361477572	G	10.48	1.362570	0.24684	0.669768	0.819419	ENSG00000165202	ENST00000297913	T	0.00594	6.33	5.43	2.94	0.34122	.	0.146450	0.31797	N	0.007044	T	0.00012	0.0000	L	0.58969	1.84	0.80722	P	0.0	B	0.09022	0.002	B	0.12156	0.007	T	0.34850	-0.9812	9	0.62326	D	0.03	-6.5594	9.5462	0.39282	0.808:0.1221:0.0699:0.0	rs972925;rs52824498;rs61649599;rs972925	24	Q15612	OR1Q1_HUMAN	R	24	ENSP00000297913:Q24R	ENSP00000297913:Q24R	Q	+	2	0	OR1Q1	124416908	0.053000	0.20554	0.046000	0.18839	0.848000	0.48234	2.624000	0.46444	0.144000	0.18951	-1.088000	0.02184	CAA	A|0.217;G|0.783	0.783	strong		0.453	OR1Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053946.1		
INPP5E	56623	hgsc.bcm.edu	37	9	139327034	139327034	+	Silent	SNP	A	A	G	rs10870194	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139327034A>G	ENST00000371712.3	-	6	1686	c.1284T>C	c.(1282-1284)ggT>ggC	p.G428G		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		CCTTCCCGTCACCTGCTGTGG	0.632													G|||	1892	0.377796	0.3911	0.6182	5008	,	,		16010	0.1925		0.4115	False		,,,				2504	0.3456				p.G428G		Atlas-SNP	.											.	INPP5E	18	.	0			c.T1284C						PASS	.	G		1559,2627		308,943,842	52.0	36.0	42.0		1284	-8.3	0.2	9	dbSNP_120	42	3413,4611		789,1835,1388	no	coding-synonymous	INPP5E	NM_019892.4		1097,2778,2230	GG,GA,AA		42.5349,37.2432,40.7207		428/645	139327034	4972,7238	2093	4012	6105	SO:0001819	synonymous_variant	56623	exon6			CCCGTCACCTGCT	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1284T>C	9.37:g.139327034A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			A|0.612;G|0.388	0.388	strong		0.632	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
COL6A5	256076	hgsc.bcm.edu	37	3	130104062	130104062	+	Silent	SNP	T	T	C	rs10212241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:130104062T>C	ENST00000432398.2	+	5	2210	c.1716T>C	c.(1714-1716)acT>acC	p.T572T	COL6A5_ENST00000265379.6_Silent_p.T572T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	572	Nonhelical region.|VWFA 3. {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						AGCAAATCACTGTTCATGCAG	0.453													T|||	2102	0.419728	0.4834	0.4597	5008	,	,		18666	0.6022		0.2087	False		,,,				2504	0.3344				p.T572T		Atlas-SNP	.											.	COL6A5	205	.	0			c.T1716C						PASS	.	T		589,795		118,353,221	72.0	59.0	63.0		1716	1.9	0.0	3	dbSNP_119	63	696,2484		87,522,981	no	coding-synonymous	COL6A5	NM_153264.5		205,875,1202	CC,CT,TT		21.8868,42.5578,28.1551		572/2527	130104062	1285,3279	692	1590	2282	SO:0001819	synonymous_variant	256076	exon5			AATCACTGTTCAT	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.1716T>C	3.37:g.130104062T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				T|0.605;C|0.395	0.395	strong		0.453	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
VN1R4	317703	hgsc.bcm.edu	37	19	53770764	53770764	+	Missense_Mutation	SNP	G	G	A	rs74429916	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53770764G>A	ENST00000311170.4	-	1	208	c.155C>T	c.(154-156)gCc>gTc	p.A52V	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	52			A -> V (in allele VN1R4*3; dbSNP:rs112711591). {ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		TAAGAAGTTGGCTACAATCAG	0.453										HNSCC(26;0.072)																											p.A52V		Atlas-SNP	.											VN1R4,NS,carcinoma,-1,1	VN1R4	65	1	0			c.C155T						PASS	.	G	VAL/ALA	1197,3209		125,947,1131	43.0	44.0	44.0		155	0.1	0.1	19	dbSNP_132	44	1999,6597		219,1561,2518	no	missense	VN1R4	NM_173857.2	64	344,2508,3649	AA,AG,GG		23.255,27.1675,24.5808	probably-damaging	52/302	53770764	3196,9806	2203	4298	6501	SO:0001583	missense	317703	exon1			AAGTTGGCTACAA	AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.155C>T	19.37:g.53770764G>A	ENSP00000310856:p.Ala52Val	Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	261	122	0.467433	NM_173857	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	452	0.20695970695970695	155	0.3150406504065041	74	0.20441988950276244	48	0.08391608391608392	175	0.23087071240105542	G	14.88	2.666556	0.47677	0.271675	0.23255	ENSG00000228567	ENST00000311170	T	0.46451	0.87	2.49	0.0798	0.14418	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33346	U	0.005015	T	0.00012	0.0000	L	0.56199	1.76	0.49915	P	1.6899999999997473E-4	D	0.65815	0.995	D	0.63877	0.919	T	0.14420	-1.0473	9	0.72032	D	0.01	.	4.7929	0.13257	0.1357:0.4481:0.4162:0.0	.	52	Q7Z5H5	VN1R4_HUMAN	V	52	ENSP00000310856:A52V	ENSP00000310856:A52V	A	-	2	0	VN1R4	58462576	0.827000	0.29292	0.104000	0.21259	0.028000	0.11728	0.705000	0.25675	0.118000	0.18165	0.545000	0.68477	GCC	.	.	weak		0.453	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857	
DNAH1	25981	hgsc.bcm.edu	37	3	52394055	52394055	+	Missense_Mutation	SNP	G	G	A	rs61734638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:52394055G>A	ENST00000420323.2	+	27	4792	c.4531G>A	c.(4531-4533)Gtg>Atg	p.V1511M		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1511	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)		CCAGGAGAACGTGGTCAGCGT	0.617													G|||	42	0.00838658	0.0	0.0058	5008	,	,		21824	0.001		0.0239	False		,,,				2504	0.0133				p.V1511M		Atlas-SNP	.											.	DNAH1	534	.	0			c.G4531A						PASS	.	G	MET/VAL	27,4279		0,27,2126	135.0	138.0	137.0		4531	4.2	0.9	3	dbSNP_129	137	248,8278		2,244,4017	yes	missense	DNAH1	NM_015512.4	21	2,271,6143	AA,AG,GG		2.9087,0.627,2.1431	possibly-damaging	1511/4266	52394055	275,12557	2153	4263	6416	SO:0001583	missense	25981	exon27			GAGAACGTGGTCA	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.4531G>A	3.37:g.52394055G>A	ENSP00000401514:p.Val1511Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	129	52	0.403101	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	24	0.01098901098901099	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	19	0.025065963060686015	G	19.35	3.811702	0.70797	0.00627	0.029087	ENSG00000114841	ENST00000420323	T	0.32023	1.47	5.13	4.23	0.50019	.	0.163888	0.29145	N	0.013006	T	0.42314	0.1197	H	0.97874	4.095	0.40450	D	0.980138	D	0.67145	0.996	P	0.60068	0.868	T	0.74325	-0.3702	10	0.87932	D	0	.	12.9182	0.58216	0.0811:0.0:0.9189:0.0	rs61734638	1511	C9JXH6	.	M	1511	ENSP00000401514:V1511M	ENSP00000401514:V1511M	V	+	1	0	DNAH1	52369095	1.000000	0.71417	0.859000	0.33776	0.584000	0.36387	3.854000	0.55949	1.335000	0.45486	0.561000	0.74099	GTG	G|0.984;A|0.016	0.016	strong		0.617	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
KIAA0195	9772	hgsc.bcm.edu	37	17	73493217	73493217	+	Silent	SNP	G	G	A	rs372068615		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73493217G>A	ENST00000314256.7	+	26	3739	c.3345G>A	c.(3343-3345)ctG>ctA	p.L1115L	KIAA0195_ENST00000375248.5_Silent_p.L1125L|AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000579208.1_Silent_p.L766L	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1115						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)			TGGTCCAGCTGCCGCCACTCC	0.542																																					p.L1115L		Atlas-SNP	.											.	KIAA0195	102	.	0			c.G3345A						PASS	.	G		1,4405		0,1,2202	164.0	141.0	149.0		3345	2.8	1.0	17		149	0,8600		0,0,4300	no	coding-synonymous	KIAA0195	NM_014738.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1115/1357	73493217	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9772	exon26			CCAGCTGCCGCCA		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.3345G>A	17.37:g.73493217G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_014738	O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	CCDS32732.1																																																																																			.	.	weak		0.542	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
DFNA5	1687	hgsc.bcm.edu	37	7	24758795	24758795	+	Silent	SNP	T	T	C	rs78941420|rs876305	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:24758795T>C	ENST00000342947.3	-	4	872	c.447A>G	c.(445-447)gaA>gaG	p.E149E	DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR|DFNA5_ENST00000409775.3_Silent_p.E149E|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	149					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						CATTCCTTCCTTCCAGCACCT	0.493													C|||	3694	0.73762	0.8275	0.6643	5008	,	,		23268	0.9841		0.4135	False		,,,				2504	0.7474				p.E149E	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.A447G						PASS	.	C	,,	3370,1036	379.0+/-323.1	1295,780,128	161.0	143.0	149.0		447,,447	3.3	0.9	7	dbSNP_86	149	3619,4981	624.4+/-397.6	755,2109,1436	no	coding-synonymous,utr-5,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	2050,2889,1564	CC,CT,TT		42.0814,23.5134,46.2633	,,	149/497,,149/497	24758795	6989,6017	2203	4300	6503	SO:0001819	synonymous_variant	1687	exon4			CCTTCCTTCCAGC	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.447A>G	7.37:g.24758795T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1																																																																																			T|0.394;C|0.606	0.606	strong		0.493	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
PSPH	5723	hgsc.bcm.edu	37	7	56088786	56088786	+	Silent	SNP	A	A	T	rs202027697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	149	0	0		WXS	Illumina HiSeq	Phase_I	152	22	0.144737	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	
ARSB	411	hgsc.bcm.edu	37	5	78181477	78181477	+	Missense_Mutation	SNP	C	C	T	rs1065757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:78181477C>T	ENST00000264914.4	-	5	1608	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	ARSB_ENST00000521800.1_5'UTR|ARSB_ENST00000396151.3_Missense_Mutation_p.V358M|ARSB_ENST00000565165.1_Missense_Mutation_p.V358M	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	358			V -> L (in dbSNP:rs1065757).|V -> M (in dbSNP:rs1065757). {ECO:0000269|PubMed:10036316, ECO:0000269|PubMed:11802522, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14974081, ECO:0000269|PubMed:7687847, ECO:0000269|PubMed:9582121}.		autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		GCCAGCTTCACGAGTGTTGGC	0.587													C|||	1430	0.285543	0.0371	0.4294	5008	,	,		14652	0.372		0.4662	False		,,,				2504	0.2444				p.V358M	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											.	ARSB	47	.	0			c.G1072A						PASS	.	C	MET/VAL,MET/VAL	504,3902	232.6+/-246.1	30,444,1729	109.0	100.0	103.0		1072,1072	5.5	0.4	5	dbSNP_86	103	3719,4881	531.8+/-382.1	819,2081,1400	yes	missense,missense	ARSB	NM_000046.3,NM_198709.2	21,21	849,2525,3129	TT,TC,CC		43.2442,11.4389,32.4696	possibly-damaging,possibly-damaging	358/534,358/414	78181477	4223,8783	2203	4300	6503	SO:0001583	missense	411	exon6			GCTTCACGAGTGT	M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"""Arylsulfatase family"""	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.1072G>A	5.37:g.78181477C>T	ENSP00000264914:p.Val358Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_198709	B2RC20|Q8N322|Q9UDI9	Missense_Mutation	SNP	ENST00000264914.4	37	CCDS4043.1	743	0.3402014652014652	21	0.042682926829268296	155	0.4281767955801105	225	0.39335664335664333	342	0.45118733509234826	C	21.3	4.121790	0.77436	0.114389	0.432442	ENSG00000113273	ENST00000264914;ENST00000396151	D;D	0.98493	-4.96;-4.96	5.46	5.46	0.80206	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.058789	0.64402	D	0.000002	T	0.00012	0.0000	L	0.49571	1.57	0.09310	P	0.99999737313	D;D	0.89917	1.0;0.997	D;D	0.80764	0.994;0.91	T	0.00000	-1.5423	9	0.44086	T	0.13	.	18.2841	0.90108	0.0:1.0:0.0:0.0	rs1065757;rs1801060;rs17819819;rs52799154;rs1065757	358;358	Q8N322;P15848	.;ARSB_HUMAN	M	358	ENSP00000264914:V358M;ENSP00000379455:V358M	ENSP00000264914:V358M	V	-	1	0	ARSB	78217233	0.997000	0.39634	0.410000	0.26471	0.986000	0.74619	3.985000	0.56930	2.555000	0.86185	0.561000	0.74099	GTG	T|0.311;C|0.689	0.311	strong		0.587	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
MED16	10025	hgsc.bcm.edu	37	19	871135	871135	+	Silent	SNP	A	A	G	rs1683569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:871135A>G	ENST00000589119.1	-	12	2216	c.2217T>C	c.(2215-2217)gtT>gtC	p.V739V	MED16_ENST00000325464.1_Silent_p.V739V|MED16_ENST00000312090.6_Silent_p.V758V|MED16_ENST00000269814.4_Missense_Mutation_p.L675S|MED16_ENST00000395808.3_Silent_p.V739V|MED16_ENST00000606828.1_5'Flank			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	739					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGGCGGCTAACCAGGCCGT	0.701													g|||	1326	0.264776	0.5008	0.2205	5008	,	,		12505	0.0317		0.2873	False		,,,				2504	0.1943				p.V739V		Atlas-SNP	.											MED16,NS,carcinoma,0,1	MED16	61	1	0			c.T2217C						PASS	.			1482,2440		291,900,770	9.0	11.0	10.0		2217	3.1	1.0	19	dbSNP_89	10	1843,5871		223,1397,2237	no	coding-synonymous	MED16	NM_005481.2		514,2297,3007	GG,GA,AA		23.8916,37.7868,28.5751		739/878	871135	3325,8311	1961	3857	5818	SO:0001819	synonymous_variant	10025	exon13			GCGGCTAACCAGG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2217T>C	19.37:g.871135A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1	567	0.25961538461538464	240	0.4878048780487805	89	0.24585635359116023	20	0.03496503496503497	218	0.287598944591029	g	18.38	3.611665	0.66558	0.377868	0.238916	ENSG00000175221	ENST00000269814	.	.	.	4.13	3.06	0.35304	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47065	P	6.960000000000299E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44711	-0.9310	6	0.09590	T	0.72	-40.3568	9.783	0.40660	0.177:0.0:0.823:0.0	rs1683569;rs59662712;rs1683569	675	Q9Y2X0-4	.	S	675	.	ENSP00000269814:L675S	L	-	2	0	MED16	822135	1.000000	0.71417	0.984000	0.44739	0.793000	0.44817	2.176000	0.42500	0.718000	0.32166	-0.258000	0.10820	TTA	A|0.743;G|0.257	0.257	strong		0.701	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
OR4K17	390436	hgsc.bcm.edu	37	14	20586042	20586042	+	Missense_Mutation	SNP	G	G	C	rs8005245	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20586042G>C	ENST00000315543.4	+	1	477	c.477G>C	c.(475-477)aaG>aaC	p.K159N		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		CCATTTGTAAGCCCCTACACT	0.458													G|||	2141	0.427516	0.3268	0.4135	5008	,	,		20287	0.5437		0.4294	False		,,,				2504	0.4519				p.K159N		Atlas-SNP	.											.	OR4K17	58	.	0			c.G477C						PASS	.	G	ASN/LYS	1596,2810		285,1026,892	185.0	156.0	166.0		477	2.0	1.0	14	dbSNP_116	166	3585,5015		736,2113,1451	yes	missense	OR4K17	NM_001004715.1	94	1021,3139,2343	CC,CG,GG		41.686,36.2233,39.8355	probably-damaging	159/344	20586042	5181,7825	2203	4300	6503	SO:0001583	missense	390436	exon1			TTGTAAGCCCCTA		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"""GPCR / Class A : Olfactory receptors"""	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.477G>C	14.37:g.20586042G>C	ENSP00000319197:p.Lys159Asn	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_001004715	Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	37	CCDS32030.1	928	0.4249084249084249	147	0.29878048780487804	152	0.4198895027624309	307	0.5367132867132867	322	0.42480211081794195	.	13.61	2.287217	0.40494	0.362233	0.41686	ENSG00000176230	ENST00000315543	T	0.00392	7.58	2.86	1.95	0.26073	GPCR, rhodopsin-like superfamily (1);	0.561453	0.12470	U	0.466129	T	0.00012	0.0000	L	0.39566	1.225	0.39937	P	0.02563700000000002	D	0.69078	0.997	D	0.64687	0.928	T	0.09885	-1.0654	9	0.72032	D	0.01	.	5.0304	0.14407	0.1331:0.3717:0.4952:0.0	rs8005245;rs17308178;rs52832107;rs8005245	131	Q8NGC6	OR4KH_HUMAN	N	159	ENSP00000319197:K159N	ENSP00000319197:K159N	K	+	3	2	OR4K17	19655882	0.000000	0.05858	0.963000	0.40424	0.765000	0.43378	-6.214000	0.00075	0.511000	0.28236	0.404000	0.27445	AAG	G|0.599;C|0.401	0.401	strong		0.458	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1		
KIF26A	26153	hgsc.bcm.edu	37	14	104640098	104640098	+	Silent	SNP	G	G	A	rs61745565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104640098G>A	ENST00000423312.2	+	10	1923	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	KIF26A_ENST00000315264.7_Silent_p.A502A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	641	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GTGAGGCGGCGGCTGGCAGGG	0.687													G|||	83	0.0165735	0.0015	0.0288	5008	,	,		15832	0.0		0.0388	False		,,,				2504	0.0225				p.A641A		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1923A						PASS	.	G		24,3842		0,24,1909	17.0	24.0	22.0		1923	-2.2	0.0	14	dbSNP_129	22	289,7937		9,271,3833	no	coding-synonymous	KIF26A	NM_015656.1		9,295,5742	AA,AG,GG		3.5133,0.6208,2.5885		641/1883	104640098	313,11779	1933	4113	6046	SO:0001819	synonymous_variant	26153	exon10			GGCGGCGGCTGGC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.1923G>A	14.37:g.104640098G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
CENPE	1062	hgsc.bcm.edu	37	4	104066461	104066461	+	Missense_Mutation	SNP	A	A	G	rs2615542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	68	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	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			
MTR	4548	hgsc.bcm.edu	37	1	237048500	237048500	+	Missense_Mutation	SNP	A	A	G	rs1805087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237048500A>G	ENST00000366577.5	+	26	3150	c.2756A>G	c.(2755-2757)gAc>gGc	p.D919G	MTR_ENST00000535889.1_Missense_Mutation_p.D868G	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	919			D -> G (may be associated with susceptibility to FS-NTD; dbSNP:rs1805087). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9013615}.		cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	ATTAGACAGGACCATTATGAG	0.318													A|||	1093	0.218251	0.2844	0.1772	5008	,	,		20140	0.1052		0.173	False		,,,				2504	0.3211				p.D919G		Atlas-SNP	.											MTR,rectum,carcinoma,+1,1	MTR	127	1	0			c.A2756G	GRCh37	CM983303	MTR	M	rs1805087	PASS	.	A	GLY/ASP	1164,3242	407.1+/-334.1	154,856,1193	91.0	95.0	94.0		2756	6.0	1.0	1	dbSNP_89	94	1702,6898	309.6+/-309.4	177,1348,2775	yes	missense	MTR	NM_000254.2	94	331,2204,3968	GG,GA,AA		19.7907,26.4185,22.036	benign	919/1266	237048500	2866,10140	2203	4300	6503	SO:0001583	missense	4548	exon26			GACAGGACCATTA	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2756A>G	1.37:g.237048500A>G	ENSP00000355536:p.Asp919Gly	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	ENST00000366577.5	37	CCDS1614.1	421	0.19276556776556777	154	0.3130081300813008	67	0.1850828729281768	74	0.12937062937062938	126	0.1662269129287599	A	14.35	2.510220	0.44660	0.264185	0.197907	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576	T;T;T	0.72051	-0.62;-0.62;-0.62	5.99	5.99	0.97316	Cobalamin (vitamin B12)-binding (2);	0.149441	0.64402	D	0.000017	T	0.00012	0.0000	L	0.28694	0.88	0.20196	P	0.9999212773	B;P;B	0.37176	0.159;0.586;0.159	B;B;B	0.35770	0.161;0.21;0.161	T	0.07046	-1.0793	9	0.59425	D	0.04	-19.2895	16.4943	0.84223	1.0:0.0:0.0:0.0	rs1805087;rs17658739;rs56618494;rs61036243;rs1805087	919;868;919	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	G	773;919;868;473	ENSP00000355536:D919G;ENSP00000441845:D868G;ENSP00000355535:D473G	ENSP00000355535:D473G	D	+	2	0	MTR	235115123	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.545000	0.90657	2.291000	0.77112	0.533000	0.62120	GAC	A|0.786;G|0.214	0.214	strong		0.318	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
LILRA4	23547	hgsc.bcm.edu	37	19	54849481	54849481	+	Silent	SNP	T	T	G	rs7256494	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54849481T>G	ENST00000291759.4	-	4	437	c.381A>C	c.(379-381)gcA>gcC	p.A127A	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	127	Ig-like C2-type 2.				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)		GGCTTGGCAGTGCGGACAGGG	0.572													G|||	1951	0.389577	0.4554	0.4251	5008	,	,		18707	0.2589		0.3638	False		,,,				2504	0.4366				p.A127A		Atlas-SNP	.											LILRA4,colon,carcinoma,0,4	LILRA4	91	4	0			c.A381C						PASS	.	G		1958,2448		426,1106,671	49.0	52.0	51.0		381	0.3	0.1	19	dbSNP_116	51	3240,5360		604,2032,1664	no	coding-synonymous	LILRA4	NM_012276.3		1030,3138,2335	GG,GT,TT		37.6744,44.4394,39.9662		127/500	54849481	5198,7808	2203	4300	6503	SO:0001819	synonymous_variant	23547	exon4			TGGCAGTGCGGAC	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.381A>C	19.37:g.54849481T>G		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			T|0.611;G|0.389	0.389	strong		0.572	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
BPIFB6	128859	hgsc.bcm.edu	37	20	31622083	31622083	+	Missense_Mutation	SNP	G	G	A	rs2070317	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31622083G>A	ENST00000349552.1	+	3	289	c.289G>A	c.(289-291)Gtc>Atc	p.V97I		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	97			V -> I (in dbSNP:rs2070317).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										AGGCATGACCGTCACTGGCAA	0.547													A|||	2850	0.569089	0.4592	0.5303	5008	,	,		20988	0.7579		0.5179	False		,,,				2504	0.6033				p.V97I		Atlas-SNP	.											.	.	.	.	0			c.G289A						PASS	.	A	ILE/VAL	1962,2444	619.7+/-393.4	449,1064,690	125.0	98.0	107.0		289	4.7	1.0	20	dbSNP_96	107	4389,4211	571.1+/-389.5	1131,2127,1042	yes	missense	BPIFB6	NM_174897.2	29	1580,3191,1732	AA,AG,GG		48.9651,44.5302,48.8313	benign	97/454	31622083	6351,6655	2203	4300	6503	SO:0001583	missense	128859	exon3			ATGACCGTCACTG	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.289G>A	20.37:g.31622083G>A	ENSP00000344929:p.Val97Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	1246	0.5705128205128205	239	0.48577235772357724	181	0.5	429	0.75	397	0.5237467018469657	A	4.462	0.085670	0.08583	0.445302	0.510349	ENSG00000167104	ENST00000349552	T	0.04275	3.66	4.7	4.7	0.59300	.	0.109676	0.40385	N	0.001117	T	0.00012	0.0000	N	0.00188	-1.89	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.16867	-1.0388	9	0.07813	T	0.8	.	7.2204	0.25983	0.8961:0.0:0.1039:0.0	rs2070317;rs17373278;rs2070317	97	Q8NFQ5	BPIB6_HUMAN	I	97	ENSP00000344929:V97I	ENSP00000344929:V97I	V	+	1	0	BPIFB6	31085744	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.180000	0.42537	0.649000	0.30751	-0.361000	0.07541	GTC	G|0.480;A|0.520	0.520	strong		0.547	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
CDHR3	222256	hgsc.bcm.edu	37	7	105662690	105662690	+	Silent	SNP	T	T	C	rs10258293	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:105662690T>C	ENST00000317716.9	+	14	1952	c.1872T>C	c.(1870-1872)aaT>aaC	p.N624N	CDHR3_ENST00000478080.1_Silent_p.N536N|CDHR3_ENST00000542731.1_Silent_p.N624N|CDHR3_ENST00000343407.5_Intron|CDHR3_ENST00000470188.1_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	624	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						CTGGTTCCAATGTCACACGCC	0.428													t|||	879	0.175519	0.2186	0.1311	5008	,	,		23774	0.0813		0.2018	False		,,,				2504	0.2188				p.N624N		Atlas-SNP	.											.	CDHR3	153	.	0			c.T1872C						PASS	.	T		846,3206		81,684,1261	185.0	172.0	176.0		1872	-6.0	0.0	7	dbSNP_119	176	1404,6972		132,1140,2916	no	coding-synonymous	CDHR3	NM_152750.4		213,1824,4177	CC,CT,TT		16.7622,20.8786,18.1043		624/886	105662690	2250,10178	2026	4188	6214	SO:0001819	synonymous_variant	222256	exon14			TTCCAATGTCACA	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1872T>C	7.37:g.105662690T>C		Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	339	339	1	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1	347	0.15888278388278387	98	0.1991869918699187	58	0.16022099447513813	40	0.06993006993006994	151	0.19920844327176782	C	5.913	0.352602	0.11182	0.208786	0.167622	ENSG00000128536	ENST00000468477	.	.	.	5.23	-5.99	0.02213	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999885036	.	.	.	.	.	.	T	0.33394	-0.9870	3	.	.	.	-18.1293	18.9616	0.92679	0.0:0.252:0.0:0.748	rs10258293;rs56524808;rs10258293	.	.	.	T	93	.	.	M	+	2	0	CDHR3	105449926	0.000000	0.05858	0.002000	0.10522	0.787000	0.44495	-1.882000	0.01624	-1.794000	0.01256	-0.699000	0.03677	ATG	T|0.839;C|0.161	0.161	strong		0.428	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
ZNF571	51276	hgsc.bcm.edu	37	19	38056763	38056763	+	Missense_Mutation	SNP	C	C	G	rs8111790	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38056763C>G	ENST00000328550.2	-	4	666	c.567G>C	c.(565-567)caG>caC	p.Q189H	ZNF571-AS1_ENST00000589750.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571_ENST00000593133.1_Missense_Mutation_p.Q189H|ZNF571_ENST00000451802.2_Missense_Mutation_p.Q189H|ZNF571-AS1_ENST00000587121.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000589802.1_RNA|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571_ENST00000358744.3_Missense_Mutation_p.Q189H|ZNF571-AS1_ENST00000586013.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	189			Q -> H (in dbSNP:rs8111790). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCTCACCAGTCTGAATTCTCT	0.343													C|||	901	0.179912	0.0885	0.2651	5008	,	,		21454	0.0288		0.3618	False		,,,				2504	0.2117				p.Q189H		Atlas-SNP	.											ZNF571,colon,carcinoma,0,1	ZNF571	54	1	0			c.G567C						PASS	.	C	HIS/GLN	587,3819	258.6+/-262.5	37,513,1653	93.0	93.0	93.0		567	-7.0	0.0	19	dbSNP_116	93	3138,5462	476.9+/-369.5	580,1978,1742	yes	missense	ZNF571	NM_016536.3	24	617,2491,3395	GG,GC,CC		36.4884,13.3227,28.6406	benign	189/610	38056763	3725,9281	2203	4300	6503	SO:0001583	missense	51276	exon4			ACCAGTCTGAATT	AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"""Zinc fingers, C2H2-type"", ""-"""	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.567G>C	19.37:g.38056763C>G	ENSP00000333660:p.Gln189His	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_016536	Q2HIY0|Q3ZCU3|Q9NZX7	Missense_Mutation	SNP	ENST00000328550.2	37	CCDS12505.1	437	0.2000915750915751	42	0.08536585365853659	95	0.26243093922651933	21	0.03671328671328671	279	0.36807387862796836	C	0.983	-0.696452	0.03279	0.133227	0.364884	ENSG00000180479	ENST00000328550;ENST00000451802;ENST00000358744	T;T;T	0.01584	4.75;4.75;4.75	3.49	-6.98	0.01611	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00022	-2.725	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.44651	-0.9314	8	0.02654	T	1	.	3.9809	0.09495	0.5001:0.1224:0.2896:0.0879	rs8111790;rs52805879;rs8111790	189	Q7Z3V5	ZN571_HUMAN	H	189	ENSP00000333660:Q189H;ENSP00000392638:Q189H;ENSP00000351594:Q189H	ENSP00000333660:Q189H	Q	-	3	2	ZNF571	42748603	0.000000	0.05858	0.000000	0.03702	0.706000	0.40770	-2.048000	0.01406	-1.791000	0.01261	0.313000	0.20887	CAG	C|0.737;G|0.263	0.263	strong		0.343	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536	
TRABD	80305	hgsc.bcm.edu	37	22	50632869	50632869	+	Silent	SNP	C	C	T	rs4838813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50632869C>T	ENST00000303434.4	+	4	332	c.213C>T	c.(211-213)gaC>gaT	p.D71D	TRABD_ENST00000380909.4_Silent_p.D71D|RP3-402G11.25_ENST00000607943.1_RNA|TRABD_ENST00000395827.1_Silent_p.D71D|TRABD_ENST00000395829.1_Silent_p.D71D	NM_025204.2	NP_079480.2	Q9H4I3	TRABD_HUMAN	TraB domain containing	71										breast(1)|central_nervous_system(1)|large_intestine(1)|liver(2)|lung(1)|upper_aerodigestive_tract(1)	7		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)		TGGCTGAGGACGGGAGCAGGG	0.667													C|||	140	0.0279553	0.0045	0.0432	5008	,	,		16345	0.005		0.0716	False		,,,				2504	0.0276				p.D71D		Atlas-SNP	.											.	TRABD	21	.	0			c.C213T						PASS	.	C		55,4347	52.3+/-87.9	0,55,2146	46.0	46.0	46.0		213	-5.1	0.9	22	dbSNP_111	46	587,8007	152.1+/-206.7	17,553,3727	no	coding-synonymous	TRABD	NM_025204.2		17,608,5873	TT,TC,CC		6.8303,1.2494,4.94		71/377	50632869	642,12354	2201	4297	6498	SO:0001819	synonymous_variant	80305	exon4			TGAGGACGGGAGC	AL449244	CCDS14086.1	22q13.33	2006-07-06			ENSG00000170638	ENSG00000170638			28805	protein-coding gene	gene with protein product						12477932	Standard	NM_025204		Approved	PP2447	uc003bjs.1	Q9H4I3	OTTHUMG00000044644	ENST00000303434.4:c.213C>T	22.37:g.50632869C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_025204	Q19CC5|Q96ED8|Q9H7N1|Q9UGX6|Q9UGX7	Silent	SNP	ENST00000303434.4	37	CCDS14086.1																																																																																			C|0.956;T|0.044	0.044	strong		0.667	TRABD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316987.1	NM_025204	
GPR18	2841	hgsc.bcm.edu	37	13	99907568	99907568	+	Missense_Mutation	SNP	G	G	T	rs41279138	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:99907568G>T	ENST00000340807.3	-	3	1115	c.559C>A	c.(559-561)Ctg>Atg	p.L187M	GPR18_ENST00000397473.2_Missense_Mutation_p.L187M|UBAC2_ENST00000403766.3_Intron|GPR18_ENST00000397470.2_Missense_Mutation_p.L187M|UBAC2_ENST00000376440.2_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	187					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(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	GTGAGGTTCAGCACGTTCACA	0.448													G|||	9	0.00179712	0.0	0.0014	5008	,	,		22667	0.0		0.003	False		,,,				2504	0.0051				p.L187M		Atlas-SNP	.											.	GPR18	23	.	0			c.C559A						PASS	.	G	MET/LEU,,MET/LEU,	6,4400	11.4+/-27.6	0,6,2197	139.0	135.0	137.0		559,,559,	0.6	0.0	13	dbSNP_127	137	52,8548	32.3+/-84.9	0,52,4248	yes	missense,intron,missense,intron	GPR18,UBAC2	NM_001098200.1,NM_001144072.1,NM_005292.3,NM_177967.3	15,,15,	0,58,6445	TT,TG,GG		0.6047,0.1362,0.4459	possibly-damaging,,possibly-damaging,	187/332,,187/332,	99907568	58,12948	2203	4300	6503	SO:0001583	missense	2841	exon2			GGTTCAGCACGTT	L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"""GPCR / Class A : Orphans"""	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.559C>A	13.37:g.99907568G>T	ENSP00000343428:p.Leu187Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_001098200	Q6GTM3|Q96HI6|Q9H2L2	Missense_Mutation	SNP	ENST00000340807.3	37	CCDS9491.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	6.772	0.511433	0.12944	0.001362	0.006047	ENSG00000125245	ENST00000397473;ENST00000397470;ENST00000340807	T;T;T	0.38887	1.11;1.11;1.11	5.88	0.605	0.17553	GPCR, rhodopsin-like superfamily (1);	0.076851	0.51477	D	0.000081	T	0.35422	0.0931	L	0.33485	1.01	0.22127	N	0.999347	D	0.69078	0.997	D	0.64877	0.93	T	0.25916	-1.0118	9	.	.	.	-15.9702	7.814	0.29247	0.4787:0.1063:0.415:0.0	rs41279138	187	Q14330	GPR18_HUMAN	M	187	ENSP00000380613:L187M;ENSP00000380610:L187M;ENSP00000343428:L187M	.	L	-	1	2	GPR18	98705569	0.010000	0.17322	0.012000	0.15200	0.009000	0.06853	0.226000	0.17776	-0.209000	0.10156	-0.768000	0.03414	CTG	G|0.997;T|0.003	0.003	strong		0.448	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1		
NALCN	259232	hgsc.bcm.edu	37	13	101720300	101720300	+	Silent	SNP	T	T	G	rs1289556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	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	
PLXDC1	57125	hgsc.bcm.edu	37	17	37243927	37243927	+	Silent	SNP	A	A	G	rs12602945	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:37243927A>G	ENST00000315392.4	-	8	1051	c.840T>C	c.(838-840)taT>taC	p.Y280Y	PLXDC1_ENST00000493200.1_5'UTR|PLXDC1_ENST00000539608.1_Silent_p.Y207Y|PLXDC1_ENST00000444911.2_Silent_p.Y240Y|PLXDC1_ENST00000394316.2_Silent_p.Y280Y	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	280					angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)			kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTATGCGGTGATATTCAAAGA	0.567													G|||	1459	0.291334	0.1067	0.4496	5008	,	,		21447	0.3492		0.3032	False		,,,				2504	0.3569				p.Y280Y		Atlas-SNP	.											PLXDC1,NS,carcinoma,0,1	PLXDC1	45	1	0			c.T840C						scavenged	.	G		636,3770	767.7+/-413.5	53,530,1620	85.0	64.0	71.0		840	-0.4	1.0	17	dbSNP_120	71	2523,6077	693.3+/-404.6	374,1775,2151	no	coding-synonymous	PLXDC1	NM_020405.4		427,2305,3771	GG,GA,AA		29.3372,14.4349,24.2888		280/501	37243927	3159,9847	2203	4300	6503	SO:0001819	synonymous_variant	57125	exon8			GCGGTGATATTCA	AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381			20945	protein-coding gene	gene with protein product	"""tumor endothelial marker 7 precursor"""	606826				10947988, 11559528	Standard	NM_020405		Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.840T>C	17.37:g.37243927A>G		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_020405	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	Silent	SNP	ENST00000315392.4	37	CCDS11333.1																																																																																			A|0.747;G|0.253	0.253	strong		0.567	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256892.2	NM_020405	
ABHD8	79575	hgsc.bcm.edu	37	19	17412399	17412399	+	Silent	SNP	G	G	A	rs11086067	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17412399G>A	ENST00000247706.3	-	2	266	c.27C>T	c.(25-27)atC>atT	p.I9I	MRPL34_ENST00000594999.1_5'Flank|MRPL34_ENST00000595444.1_Intron|MRPL34_ENST00000600434.1_Intron	NM_024527.4	NP_078803.4	Q96I13	ABHD8_HUMAN	abhydrolase domain containing 8	9							hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	9						GGCAACAGAAGATACCGTCGG	0.637													G|||	1195	0.238618	0.1309	0.2277	5008	,	,		15449	0.1319		0.329	False		,,,				2504	0.409				p.I9I	Ovarian(156;1368 2543 15275 41187)	Atlas-SNP	.											.	ABHD8	26	.	0			c.C27T						PASS	.	G		712,3626		64,584,1521	25.0	27.0	26.0		27	4.0	1.0	19	dbSNP_120	26	2408,5992		361,1686,2153	no	coding-synonymous	ABHD8	NM_024527.4		425,2270,3674	AA,AG,GG		28.6667,16.4131,24.4936		9/440	17412399	3120,9618	2169	4200	6369	SO:0001819	synonymous_variant	79575	exon2			ACAGAAGATACCG	AK021805	CCDS12355.1	19p13.12	2010-12-09			ENSG00000127220	ENSG00000127220		"""Abhydrolase domain containing"""	23759	protein-coding gene	gene with protein product						12477932	Standard	NM_024527		Approved	FLJ11743, MGC14280, MGC2512	uc002ngb.4	Q96I13		ENST00000247706.3:c.27C>T	19.37:g.17412399G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_024527	Q9HAE9	Silent	SNP	ENST00000247706.3	37	CCDS12355.1																																																																																			G|0.778;A|0.222	0.222	strong		0.637	ABHD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462937.1	NM_024527	
FGF6	2251	hgsc.bcm.edu	37	12	4553332	4553332	+	Silent	SNP	A	A	G	rs2241280	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4553332A>G	ENST00000228837.2	-	2	460	c.417T>C	c.(415-417)gtT>gtC	p.V139V		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	139					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)			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)			TGTTCATGGCAACGAAGAGGG	0.507													A|||	2365	0.472244	0.5749	0.3487	5008	,	,		21392	0.4177		0.3857	False		,,,				2504	0.5665				p.V139V		Atlas-SNP	.											FGF6,NS,carcinoma,-2,1	FGF6	40	1	0			c.T417C						PASS	.	A		2464,1942	622.5+/-394.0	693,1078,432	106.0	81.0	90.0		417	-7.1	0.1	12	dbSNP_98	90	3432,5168	503.5+/-375.9	667,2098,1535	no	coding-synonymous	FGF6	NM_020996.1		1360,3176,1967	GG,GA,AA		39.907,44.0763,45.3329		139/209	4553332	5896,7110	2203	4300	6503	SO:0001819	synonymous_variant	2251	exon2			CATGGCAACGAAG	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.417T>C	12.37:g.4553332A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	178	88	0.494382	NM_020996	Q0VAE1	Silent	SNP	ENST00000228837.2	37	CCDS8527.1																																																																																			A|0.554;G|0.446	0.446	strong		0.507	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
SUGCT	79783	hgsc.bcm.edu	37	7	40314165	40314165	+	Silent	SNP	G	G	A	rs12669315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:40314165G>A	ENST00000335693.4	+	8	674	c.651G>A	c.(649-651)ctG>ctA	p.L217L	C7orf10_ENST00000309930.5_Silent_p.L217L|C7orf10_ENST00000401647.2_Intron	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		217					metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						CCACTGGCCTGTATGCATATG	0.398													G|||	1583	0.316094	0.1074	0.3285	5008	,	,		16841	0.4524		0.3648	False		,,,				2504	0.3988				p.L217L		Atlas-SNP	.											.	C7orf10	99	.	0			c.G651A						PASS	.	G	,,,	518,3256		31,456,1400	80.0	77.0	78.0		651,,651,540	-0.9	0.9	7	dbSNP_120	78	2898,5342		526,1846,1748	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	C7orf10	NM_001193311.1,NM_001193312.1,NM_001193313.1,NM_024728.2	,,,	557,2302,3148	AA,AG,GG		35.1699,13.7255,28.4335	,,,	217/472,,217/446,180/435	40314165	3416,8598	1887	4120	6007	SO:0001819	synonymous_variant	79783	exon8			TGGCCTGTATGCA																												ENST00000335693.4:c.651G>A	7.37:g.40314165G>A		Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_001193313	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Silent	SNP	ENST00000335693.4	37	CCDS55105.1	705	0.3228021978021978	55	0.11178861788617886	120	0.3314917127071823	255	0.4458041958041958	275	0.3627968337730871	G	6.398	0.441542	0.12164	0.137255	0.351699	ENSG00000175600	ENST00000416370	.	.	.	5.45	-0.951	0.10369	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47509	-0.9112	3	.	.	.	-3.9105	4.7505	0.13057	0.2558:0.0:0.3904:0.3538	rs12669315;rs12669315	.	.	.	Y	212	.	.	C	+	2	0	C7orf10	40280690	0.992000	0.36948	0.934000	0.37439	0.672000	0.39443	0.164000	0.16542	-0.410000	0.07542	-0.136000	0.14681	TGT	G|0.683;A|0.317	0.317	strong		0.398	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1		
PRIMA1	145270	hgsc.bcm.edu	37	14	94245652	94245652	+	Silent	SNP	C	C	T	rs4900195	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:94245652C>T	ENST00000393140.1	-	3	201	c.99G>A	c.(97-99)acG>acA	p.T33T	PRIMA1_ENST00000393143.1_Silent_p.T33T|PRIMA1_ENST00000316227.3_Silent_p.T33T	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	33					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)		GCTCACCATGCGTCACCTGTA	0.647													C|||	1818	0.363019	0.3949	0.3573	5008	,	,		9432	0.2302		0.4692	False		,,,				2504	0.3517				p.T33T		Atlas-SNP	.											PRIMA1,rectum,carcinoma,0,1	PRIMA1	21	1	0			c.G99A						PASS	.	C		1764,2638		367,1030,804	40.0	34.0	36.0		99	-8.8	0.2	14	dbSNP_111	36	4098,4500		978,2142,1179	no	coding-synonymous	PRIMA1	NM_178013.3		1345,3172,1983	TT,TC,CC		47.6622,40.0727,45.0923		33/154	94245652	5862,7138	2201	4299	6500	SO:0001819	synonymous_variant	145270	exon3			ACCATGCGTCACC		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.99G>A	14.37:g.94245652C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_178013	Q86XR6	Silent	SNP	ENST00000393140.1	37	CCDS9912.1																																																																																			C|0.579;T|0.421	0.421	strong		0.647	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013	
ERCC6	2074	hgsc.bcm.edu	37	10	50732280	50732280	+	Missense_Mutation	SNP	C	C	T	rs2228528	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50732280C>T	ENST00000355832.5	-	5	1274	c.1196G>A	c.(1195-1197)gGt>gAt	p.G399D	ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.G399D|PGBD3_ENST00000374127.3_5'Flank|ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.G399D|PGBD3_ENST00000603152.1_Missense_Mutation_p.G399D	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	399			G -> D (in dbSNP:rs2228528). {ECO:0000269|PubMed:9443879, ECO:0000269|Ref.3}.		activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						ATAGTCAGTACCATCTCCAGA	0.547								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	1191	0.237819	0.1793	0.2378	5008	,	,		17237	0.4911		0.1581	False		,,,				2504	0.138				p.L399H		Atlas-SNP	.											.	ERCC6	162	.	0			c.T1196A						PASS	.	C	ASP/GLY,	729,3677	302.1+/-287.2	62,605,1536	72.0	70.0	70.0		1196,	-3.8	0.0	10	dbSNP_98	70	1382,7218	268.2+/-287.7	112,1158,3030	yes	missense,utr-5	ERCC6,PGBD3	NM_000124.2,NM_170753.2	94,	174,1763,4566	TT,TC,CC		16.0698,16.5456,16.231	benign,	399/1494,	50732280	2111,10895	2203	4300	6503	SO:0001583	missense	2074	exon5			TCAGTACCATCTC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.1196G>A	10.37:g.50732280C>T	ENSP00000348089:p.Gly399Asp	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	553	0.2532051282051282	83	0.16869918699186992	75	0.20718232044198895	276	0.4825174825174825	119	0.15699208443271767	C	7.256	0.604123	0.14002	0.165456	0.160698	ENSG00000225830;ENSG00000258838;ENSG00000258838	ENST00000355832;ENST00000515869;ENST00000447839	D;T;T	0.81579	-1.51;3.62;3.62	5.93	-3.85	0.04243	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.54753	P	1.8999999999991246E-5	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.18967	-1.0320	8	0.06757	T	0.87	-1.3641	9.5029	0.39028	0.0:0.26:0.1064:0.6336	rs2228528;rs3829171;rs61043658;rs2228528	399;399	E7EV46;Q03468	.;ERCC6_HUMAN	D	399	ENSP00000348089:G399D;ENSP00000423550:G399D;ENSP00000387966:G399D	ENSP00000348089:G399D	G	-	2	0	ERCC6;RP11-123B3.6	50402286	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.130000	0.15850	-0.609000	0.05724	-0.140000	0.14226	GGT	C|0.794;T|0.206	0.206	strong		0.547	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
CROCC	9696	hgsc.bcm.edu	37	1	17275337	17275337	+	Missense_Mutation	SNP	C	C	T	rs143866013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17275337C>T	ENST00000375541.5	+	19	2821	c.2752C>T	c.(2752-2754)Cgg>Tgg	p.R918W	CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.R918W(2)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TGAGGTGCAACGGCAGCTGGC	0.677																																					p.R918W		Atlas-SNP	.											CROCC,NS,haematopoietic_neoplasm,0,6	CROCC	185	6	2	Substitution - Missense(2)	skin(2)	c.C2752T						scavenged	.						38.0	43.0	41.0					1																	17275337		2203	4298	6501	SO:0001583	missense	9696	exon19			GTGCAACGGCAGC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2752C>T	1.37:g.17275337C>T	ENSP00000364691:p.Arg918Trp	Somatic	347	2	0.00576369		WXS	Illumina HiSeq	Phase_I	291	59	0.202749	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.216169	0.58452	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.23552	1.9	4.38	2.36	0.29203	.	.	.	.	.	T	0.39886	0.1095	L	0.50333	1.59	0.34311	D	0.68543	D;D	0.76494	0.999;0.999	D;D	0.63488	0.915;0.915	T	0.53143	-0.8480	9	0.72032	D	0.01	.	10.9364	0.47247	0.41:0.59:0.0:0.0	.	221;918	Q5TZA2-2;Q5TZA2	.;CROCC_HUMAN	W	918;799	ENSP00000364691:R918W	ENSP00000364691:R918W	R	+	1	2	CROCC	17147924	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	1.205000	0.32308	0.452000	0.26830	0.557000	0.71058	CGG	C|0.900;T|0.100	0.100	strong		0.677	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
SDCCAG3	10807	hgsc.bcm.edu	37	9	139298580	139298580	+	Missense_Mutation	SNP	C	C	T	rs1131992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139298580C>T	ENST00000357365.3	-	9	1264	c.1135G>A	c.(1135-1137)Gtg>Atg	p.V379M	SDCCAG3_ENST00000298537.7_Missense_Mutation_p.V356M|SDCCAG3_ENST00000461693.1_5'UTR|SDCCAG3_ENST00000371725.3_Missense_Mutation_p.V306M	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	379			V -> M (in dbSNP:rs1131992). {ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		TGCTTCACCACGGTCAGGCTG	0.642													C|||	571	0.114018	0.0098	0.2464	5008	,	,		19227	0.1369		0.1223	False		,,,				2504	0.1288				p.V379M		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.G1135A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	108,3908		2,104,1902	93.0	101.0	98.0		1135,916,1066	2.6	0.2	9	dbSNP_86	98	1124,7208		81,962,3123	no	missense,missense,missense	SDCCAG3	NM_001039707.1,NM_001039708.1,NM_006643.3	21,21,21	83,1066,5025	TT,TC,CC		13.4902,2.6892,9.9773	benign,benign,benign	379/436,306/363,356/413	139298580	1232,11116	2008	4166	6174	SO:0001583	missense	10807	exon9			TCACCACGGTCAG	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.1135G>A	9.37:g.139298580C>T	ENSP00000349929:p.Val379Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	205	90	0.439024	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	37	CCDS43904.1	254	0.1163003663003663	6	0.012195121951219513	71	0.19613259668508287	74	0.12937062937062938	103	0.1358839050131926	C	8.788	0.929837	0.18131	0.026892	0.134902	ENSG00000165689	ENST00000357365;ENST00000298537;ENST00000371725	T;T;T	0.30182	1.54;2.48;1.54	4.52	2.63	0.31362	.	0.333726	0.26692	N	0.022995	T	0.00039	0.0001	L	0.31294	0.92	0.80722	P	0.0	D;D;D	0.59767	0.968;0.986;0.986	B;P;P	0.51945	0.332;0.685;0.685	T	0.11542	-1.0583	9	0.41790	T	0.15	-15.6461	9.6119	0.39668	0.0:0.8267:0.0:0.1733	rs1131992;rs3192341;rs16847756;rs59757485	306;356;379	Q96C92-4;Q96C92-2;Q96C92	.;.;SDCG3_HUMAN	M	379;356;306	ENSP00000349929:V379M;ENSP00000298537:V356M;ENSP00000360790:V306M	ENSP00000298537:V356M	V	-	1	0	SDCCAG3	138418401	0.122000	0.22280	0.190000	0.23270	0.006000	0.05464	0.883000	0.28200	0.993000	0.38866	0.655000	0.94253	GTG	C|0.878;T|0.122	0.122	strong		0.642	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	
TDRD9	122402	hgsc.bcm.edu	37	14	104481083	104481083	+	Silent	SNP	T	T	C	rs11160779	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104481083T>C	ENST00000409874.4	+	21	2176	c.2128T>C	c.(2128-2130)Ttg>Ctg	p.L710L	TDRD9_ENST00000339063.5_Silent_p.L710L|RN7SL634P_ENST00000485467.2_RNA	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	710					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L425L(1)|p.L710L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ATATGAAGAATTGAAGACTAG	0.378													T|||	1604	0.320288	0.2769	0.3444	5008	,	,		18980	0.3393		0.3479	False		,,,				2504	0.3139				p.L710L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,-1,4	TDRD9	175	4	2	Substitution - coding silent(2)	stomach(2)	c.T2128C						PASS	.	T		1323,3083	446.9+/-348.2	188,947,1068	128.0	127.0	128.0		2128	-3.2	0.0	14	dbSNP_120	128	2888,5712	451.8+/-362.8	481,1926,1893	no	coding-synonymous	TDRD9	NM_153046.2		669,2873,2961	CC,CT,TT		33.5814,30.0272,32.3774		710/1383	104481083	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	122402	exon21			GAAGAATTGAAGA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.2128T>C	14.37:g.104481083T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2	698	0.31959706959706957	131	0.266260162601626	114	0.3149171270718232	187	0.3269230769230769	266	0.35092348284960423	T	3.482	-0.105587	0.06967	0.300272	0.335814	ENSG00000156414	ENST00000557332	.	.	.	5.09	-3.15	0.05233	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999855393	.	.	.	.	.	.	T	0.23904	-1.0175	3	.	.	.	.	14.7852	0.69796	0.0:0.3035:0.0:0.6965	rs11160779;rs11160779	.	.	.	T	436	.	.	I	+	2	0	TDRD9	103550836	0.000000	0.05858	0.033000	0.17914	0.595000	0.36748	-0.448000	0.06820	-0.934000	0.03733	-0.376000	0.06991	ATT	T|0.678;C|0.322	0.322	strong		0.378	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
TULP3	7289	hgsc.bcm.edu	37	12	3049698	3049698	+	3'UTR	SNP	T	T	C	rs998814	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:3049698T>C	ENST00000448120.2	+	0	2468				TULP3_ENST00000397132.2_Missense_Mutation_p.C438R	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3						anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CTTCCCAGAATGTATCCAAAC	0.498													C|||	1389	0.277356	0.4085	0.2046	5008	,	,		20215	0.2183		0.2058	False		,,,				2504	0.2863				p.C438R		Atlas-SNP	.											.	TULP3	45	.	0			c.T1312C						PASS	.	C	,ARG/CYS	517,867		96,325,271	49.0	44.0	46.0		,1312	-0.3	0.0	12	dbSNP_86	46	691,2491		69,553,969	yes	utr-3,missense	TULP3	NM_003324.4,NM_001160408.1	,180	165,878,1240	CC,CT,TT		21.7159,37.3555,26.4564	,benign	,438/502	3049698	1208,3358	692	1591	2283	SO:0001624	3_prime_UTR_variant	7289	exon12			CCAGAATGTATCC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.*1088T>C	12.37:g.3049698T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_001160408	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	537	0.24587912087912087	186	0.3780487804878049	75	0.20718232044198895	110	0.19230769230769232	166	0.21899736147757257	C	0.107	-1.143619	0.01728	0.373555	0.217159	ENSG00000078246	ENST00000397132	D	0.91351	-2.83	3.48	-0.313	0.12754	.	.	.	.	.	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10314	-1.0635	8	0.46703	T	0.11	.	4.1363	0.10172	0.0:0.2335:0.1803:0.5862	rs998814;rs3210448;rs998814	438	F8WBZ9	.	R	438	ENSP00000380321:C438R	ENSP00000380321:C438R	C	+	1	0	TULP3	2919959	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.057000	0.03486	-0.212000	0.10109	-1.259000	0.01468	TGT	A|0.008;C|0.256	0.256	strong		0.498	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417225	105417225	+	Silent	SNP	C	C	G	rs2894635	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105417225C>G	ENST00000333244.5	-	7	4682	c.4563G>C	c.(4561-4563)ccG>ccC	p.P1521P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1521						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)			CCTCCACCTTCGGCGCAGACA	0.612													.|||	1216	0.242812	0.1278	0.2752	5008	,	,		14856	0.0585		0.4742	False		,,,				2504	0.3272				p.P1521P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4563C						PASS	.						141.0	101.0	114.0					14																	105417225		1901	3757	5658	SO:0001819	synonymous_variant	113146	exon7			CACCTTCGGCGCA	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.4563G>C	14.37:g.105417225C>G		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	106	102	0.962264	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.822;G|0.178	0.178	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
BZRAP1	9256	hgsc.bcm.edu	37	17	56405046	56405046	+	Missense_Mutation	SNP	C	C	T	rs61743284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56405046C>T	ENST00000343736.4	-	1	399	c.236G>A	c.(235-237)gGa>gAa	p.G79E	BZRAP1_ENST00000268893.6_Missense_Mutation_p.G79E|BZRAP1-AS1_ENST00000579527.1_RNA|BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000580515.1_RNA|BZRAP1_ENST00000355701.3_Missense_Mutation_p.G79E|BZRAP1-AS1_ENST00000580633.1_RNA			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	79						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)					AGCCTCTGCTCCTTCAGGGTC	0.622													C|||	79	0.0157748	0.0015	0.013	5008	,	,		17888	0.0		0.0338	False		,,,				2504	0.0348				p.G79E		Atlas-SNP	.											.	BZRAP1	287	.	0			c.G236A						PASS	.	C	GLU/GLY,GLU/GLY	33,4373	38.4+/-70.7	0,33,2170	59.0	53.0	55.0		236,236	0.9	0.0	17	dbSNP_129	55	224,8376	92.6+/-154.6	3,218,4079	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	98,98	3,251,6249	TT,TC,CC		2.6047,0.749,1.976	possibly-damaging,possibly-damaging	79/1858,79/1798	56405046	257,12749	2203	4300	6503	SO:0001583	missense	9256	exon1			TCTGCTCCTTCAG	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.236G>A	17.37:g.56405046C>T	ENSP00000345824:p.Gly79Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_024418	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	33	0.01510989010989011	0	0.0	4	0.011049723756906077	0	0.0	29	0.03825857519788918	C	9.261	1.043284	0.19748	0.00749	0.026047	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04917	3.64;3.65;3.53	5.19	0.886	0.19194	.	0.524608	0.17491	N	0.172355	T	0.01092	0.0036	L	0.44542	1.39	0.09310	N	1	B;P;B	0.39480	0.005;0.675;0.001	B;B;B	0.40940	0.006;0.344;0.003	T	0.29761	-1.0001	10	0.07482	T	0.82	.	6.3771	0.21513	0.0:0.6127:0.136:0.2513	.	79;79;79	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	E	79	ENSP00000347929:G79E;ENSP00000345824:G79E;ENSP00000268893:G79E	ENSP00000268893:G79E	G	-	2	0	BZRAP1	53760045	0.807000	0.29009	0.014000	0.15608	0.004000	0.04260	0.719000	0.25881	-0.036000	0.13669	-1.598000	0.00824	GGA	C|0.982;T|0.018	0.018	strong		0.622	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
ENTPD7	57089	hgsc.bcm.edu	37	10	101451259	101451259	+	Missense_Mutation	SNP	T	T	C	rs11190245	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:101451259T>C	ENST00000370489.4	+	8	1005	c.827T>C	c.(826-828)gTc>gCc	p.V276A		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	276			V -> A (in dbSNP:rs11190245). {ECO:0000269|PubMed:14702039}.			cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		TCAACCTCTGTCCTTCCTGCA	0.463													T|||	1155	0.230631	0.1785	0.2118	5008	,	,		17738	0.2956		0.3022	False		,,,				2504	0.1738				p.V276A		Atlas-SNP	.											.	ENTPD7	44	.	0			c.T827C						PASS	.	T	ALA/VAL	840,3566	332.8+/-302.6	77,686,1440	111.0	101.0	104.0		827	-1.6	0.9	10	dbSNP_120	104	2540,6060	416.0+/-352.0	380,1780,2140	yes	missense	ENTPD7	NM_020354.3	64	457,2466,3580	CC,CT,TT		29.5349,19.0649,25.988	benign	276/605	101451259	3380,9626	2203	4300	6503	SO:0001583	missense	57089	exon8			CCTCTGTCCTTCC	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.827T>C	10.37:g.101451259T>C	ENSP00000359520:p.Val276Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	571	0.26144688644688646	93	0.18902439024390244	78	0.2154696132596685	163	0.28496503496503495	237	0.31266490765171506	T	10.00	1.233309	0.22626	0.190649	0.295349	ENSG00000198018	ENST00000370489	T	0.11277	2.79	5.05	-1.58	0.08479	.	0.421504	0.25352	N	0.031284	T	0.00012	0.0000	N	0.04508	-0.205	0.48040	P	4.290000000000127E-4	B	0.09022	0.002	B	0.08055	0.003	T	0.37979	-0.9682	9	0.07325	T	0.83	-0.0184	0.8258	0.01120	0.3396:0.1366:0.128:0.3958	rs11190245;rs57104982;rs11190245	276	Q9NQZ7	ENTP7_HUMAN	A	276	ENSP00000359520:V276A	ENSP00000359520:V276A	V	+	2	0	ENTPD7	101441249	0.918000	0.31147	0.880000	0.34516	0.918000	0.54935	0.223000	0.17719	-0.462000	0.06984	-1.054000	0.02325	GTC	T|0.752;C|0.248	0.248	strong		0.463	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100692845	100692845	+	Missense_Mutation	SNP	A	A	G	rs28567966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:100692845A>G	ENST00000268070.4	-	10	1550	c.1445T>C	c.(1444-1446)aTg>aCg	p.M482T		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	482	Disintegrin.		M -> T (in dbSNP:rs28567966). {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)		GGTGGCATTCATGCCAAACAG	0.607													G|||	730	0.145767	0.2005	0.0865	5008	,	,		18574	0.0665		0.1441	False		,,,				2504	0.1973				p.M482T		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.T1445C						PASS	.	G	THR/MET	881,3525	742.8+/-411.4	102,677,1424	102.0	87.0	92.0		1445	2.6	1.0	15	dbSNP_125	92	1279,7321	759.5+/-407.6	105,1069,3126	yes	missense	ADAMTS17	NM_139057.2	81	207,1746,4550	GG,GA,AA		14.8721,19.9955,16.6077	benign	482/1096	100692845	2160,10846	2203	4300	6503	SO:0001583	missense	170691	exon10			GCATTCATGCCAA	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.1445T>C	15.37:g.100692845A>G	ENSP00000268070:p.Met482Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	289	0.13232600732600733	107	0.21747967479674796	36	0.09944751381215469	38	0.06643356643356643	108	0.1424802110817942	G	0.095	-1.160366	0.01686	0.199955	0.148721	ENSG00000140470	ENST00000268070;ENST00000378898	T	0.03468	3.92	5.52	2.64	0.31445	.	0.193656	0.42294	N	0.000724	T	0.00012	0.0000	N	0.01134	-0.995	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45366	-0.9266	9	0.09084	T	0.74	.	8.4343	0.32778	0.1399:0.2329:0.6272:0.0	rs28567966	239;482	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	T	482;239	ENSP00000268070:M482T	ENSP00000268070:M482T	M	-	2	0	ADAMTS17	98510368	1.000000	0.71417	0.987000	0.45799	0.422000	0.31414	2.515000	0.45512	0.043000	0.15746	-0.716000	0.03619	ATG	A|0.840;G|0.160	0.160	strong		0.607	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48917384	48917384	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48917384G>A	ENST00000311378.4	+	2	1263	c.735G>A	c.(733-735)aaG>aaA	p.K245K	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Silent_p.K152K	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	245	Ig-like C2-type.				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)			CCTGGGAGAAGCAGTTGGAGG	0.597																																					p.K245K		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G735A						PASS	.						107.0	103.0	104.0					17																	48917384		2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			GGAGAAGCAGTTG	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.735G>A	17.37:g.48917384G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	46	0.40708	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			.	.	none		0.597	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
MYBPC3	4607	hgsc.bcm.edu	37	11	47371442	47371442	+	Silent	SNP	G	G	A	rs11570051	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47371442G>A	ENST00000545968.1	-	5	591	c.537C>T	c.(535-537)gcC>gcT	p.A179A	MYBPC3_ENST00000399249.2_Silent_p.A179A|MYBPC3_ENST00000256993.4_Silent_p.A179A	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	179	Ig-like C2-type 1.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		GGCTGGCGCCGGCCACGCGGG	0.667													g|||	125	0.0249601	0.0015	0.0764	5008	,	,		14880	0.005		0.0408	False		,,,				2504	0.0245				p.A179A		Atlas-SNP	.											.	MYBPC3	102	.	0			c.C537T						PASS	.	A		38,4102		0,38,2032	25.0	31.0	29.0		537	-9.6	0.3	11	dbSNP_120	29	389,8009		8,373,3818	no	coding-synonymous	MYBPC3	NM_000256.3		8,411,5850	AA,AG,GG		4.6321,0.9179,3.4056		179/1275	47371442	427,12111	2070	4199	6269	SO:0001819	synonymous_variant	4607	exon5			GGCGCCGGCCACG	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.537C>T	11.37:g.47371442G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	32	0.333333	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Silent	SNP	ENST00000545968.1	37	CCDS53621.1																																																																																			G|0.976;A|0.024	0.024	strong		0.667	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
EFS	10278	hgsc.bcm.edu	37	14	23829164	23829164	+	Missense_Mutation	SNP	G	G	A	rs2231805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23829164G>A	ENST00000216733.3	-	4	1130	c.523C>T	c.(523-525)Cgg>Tgg	p.R175W	RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000429593.2_Missense_Mutation_p.R82W|EFS_ENST00000351354.3_Missense_Mutation_p.R82W	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	175	Pro-rich.				cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		GGGGCAACCCGGGTCAGAGGG	0.647													G|||	614	0.122604	0.3011	0.0749	5008	,	,		13281	0.0		0.0954	False		,,,				2504	0.0695				p.R175W		Atlas-SNP	.											EFS,NS,carcinoma,0,2	EFS	37	2	0			c.C523T						PASS	.	G	TRP/ARG,TRP/ARG	921,3263		82,757,1253	35.0	44.0	41.0		523,244	-2.8	0.0	14	dbSNP_98	41	928,7176		57,814,3181	yes	missense,missense	EFS	NM_005864.2,NM_032459.1	101,101	139,1571,4434	AA,AG,GG		11.4511,22.0124,15.0472	probably-damaging,probably-damaging	175/562,82/469	23829164	1849,10439	2092	4052	6144	SO:0001583	missense	10278	exon4			CAACCCGGGTCAG	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.523C>T	14.37:g.23829164G>A	ENSP00000216733:p.Arg175Trp	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	37	CCDS9595.1	267	0.12225274725274725	158	0.32113821138211385	35	0.09668508287292818	0	0.0	74	0.09762532981530343	G	4.309	0.056599	0.08291	0.220124	0.114511	ENSG00000100842	ENST00000216733;ENST00000351354;ENST00000429593	T;T;T	0.58210	0.35;0.85;0.72	4.92	-2.79	0.05841	.	4.233020	0.00357	N	0.000021	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.13594	0.001;0.008;0.002	B;B;B	0.08055	0.0;0.003;0.0	T	0.23762	-1.0179	9	0.51188	T	0.08	4.9719	6.4106	0.21688	0.4459:0.1204:0.4337:0.0	rs2231805;rs60687060	82;82;175	B4DJ56;O43281-2;O43281	.;.;EFS_HUMAN	W	175;82;82	ENSP00000216733:R175W;ENSP00000340607:R82W;ENSP00000416684:R82W	ENSP00000216733:R175W	R	-	1	2	EFS	22899004	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.237000	0.08990	-0.859000	0.04105	-1.218000	0.01608	CGG	G|0.872;A|0.128	0.128	strong		0.647	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		
HIVEP3	59269	hgsc.bcm.edu	37	1	42050366	42050366	+	Missense_Mutation	SNP	C	C	T	rs2146315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:42050366C>T	ENST00000372583.1	-	4	988	c.103G>A	c.(103-105)Gtc>Atc	p.V35I	HIVEP3_ENST00000247584.5_Missense_Mutation_p.V35I|HIVEP3_ENST00000429157.2_Missense_Mutation_p.V35I|HIVEP3_ENST00000372584.1_Missense_Mutation_p.V35I	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	35			V -> I (in dbSNP:rs2146315).		positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GGGTATGGGACGCTGGAAGAA	0.612													C|||	1549	0.309305	0.3215	0.1945	5008	,	,		16176	0.4345		0.2326	False		,,,				2504	0.3241				p.V35I		Atlas-SNP	.											HIVEP3,colon,carcinoma,0,1	HIVEP3	235	1	0			c.G103A						PASS	.	C	ILE/VAL,ILE/VAL	1310,3096	432.8+/-343.4	208,894,1101	111.0	126.0	121.0		103,103	-2.9	0.0	1	dbSNP_96	121	2006,6594	349.8+/-327.6	244,1518,2538	yes	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	29,29	452,2412,3639	TT,TC,CC		23.3256,29.7322,25.4959	benign,benign	35/2406,35/2407	42050366	3316,9690	2203	4300	6503	SO:0001583	missense	59269	exon4			ATGGGACGCTGGA	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.103G>A	1.37:g.42050366C>T	ENSP00000361664:p.Val35Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	637	0.2916666666666667	148	0.3008130081300813	79	0.21823204419889503	237	0.4143356643356643	173	0.22823218997361477	C	0.410	-0.913671	0.02415	0.297322	0.233256	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.05649	3.42;3.41;3.41;3.42	4.55	-2.92	0.05615	.	1.488660	0.04134	N	0.318452	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	0.47824	-0.9087	9	0.21014	T	0.42	-3.7482	10.9259	0.47191	0.0:0.4412:0.0:0.5588	rs2146315;rs58344483;rs2146315	35;35	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	I	35	ENSP00000361665:V35I;ENSP00000361664:V35I;ENSP00000247584:V35I;ENSP00000410828:V35I	ENSP00000247584:V35I	V	-	1	0	HIVEP3	41822953	0.000000	0.05858	0.000000	0.03702	0.303000	0.27691	-0.973000	0.03798	-0.735000	0.04837	-0.244000	0.11960	GTC	C|0.726;T|0.274	0.274	strong		0.612	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
EPYC	1833	hgsc.bcm.edu	37	12	91363909	91363909	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:91363909T>C	ENST00000261172.3	-	6	802	c.710A>G	c.(709-711)tAt>tGt	p.Y237C		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	237					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						ATGGAGATCATACATGTCCTG	0.408																																					p.Y237C		Atlas-SNP	.											.	EPYC	35	.	0			c.A710G						PASS	.						175.0	176.0	175.0					12																	91363909		2203	4300	6503	SO:0001583	missense	1833	exon6			AGATCATACATGT	AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	3053	protein-coding gene	gene with protein product	"""epiphycan proteoglycan"""	601657	"""dermatan sulphate proteoglycan 3"", ""dermatan sulfate proteoglycan 3"""	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.710A>G	12.37:g.91363909T>C	ENSP00000261172:p.Tyr237Cys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_004950	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.059179	0.36373	.	.	ENSG00000083782	ENST00000261172	T	0.02395	4.31	5.33	5.33	0.75918	.	0.379586	0.30556	N	0.009374	T	0.02012	0.0063	N	0.08118	0	0.29020	N	0.886362	P	0.44521	0.837	B	0.38562	0.276	T	0.42310	-0.9459	10	0.56958	D	0.05	.	11.9016	0.52687	0.0:0.0:0.1455:0.8545	.	237	Q99645	EPYC_HUMAN	C	237	ENSP00000261172:Y237C	ENSP00000261172:Y237C	Y	-	2	0	EPYC	89888040	0.977000	0.34250	1.000000	0.80357	0.979000	0.70002	1.131000	0.31406	2.016000	0.59253	0.383000	0.25322	TAT	.	.	none		0.408	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950	
TTC5	91875	hgsc.bcm.edu	37	14	20757804	20757804	+	Silent	SNP	C	C	A	rs3737220	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	74	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	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	
PPP1R36	145376	hgsc.bcm.edu	37	14	65054858	65054858	+	Silent	SNP	T	T	C	rs723594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:65054858T>C	ENST00000298705.1	+	11	1023	c.927T>C	c.(925-927)gcT>gcC	p.A309A	RP11-973N13.3_ENST00000556634.1_RNA|RP11-973N13.3_ENST00000554454.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	309					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TTAAAAAAGCTATCAACATGC	0.428													C|||	213	0.0425319	0.0469	0.0461	5008	,	,		21889	0.0129		0.0845	False		,,,				2504	0.0215				p.A309A		Atlas-SNP	.											.	.	.	.	0			c.T927C						PASS	.	C		198,4208	808.1+/-415.9	4,190,2009	100.0	99.0	99.0		927	3.2	1.0	14	dbSNP_86	99	670,7930	788.6+/-407.6	30,610,3660	no	coding-synonymous	C14orf50	NM_172365.1		34,800,5669	CC,CT,TT		7.7907,4.4939,6.6738		309/423	65054858	868,12138	2203	4300	6503	SO:0001819	synonymous_variant	145376	exon11			AAAAGCTATCAAC		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.927T>C	14.37:g.65054858T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_172365	Q6NTH6	Silent	SNP	ENST00000298705.1	37	CCDS9767.1																																																																																			T|0.940;C|0.060	0.060	strong		0.428	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
KALRN	8997	hgsc.bcm.edu	37	3	124201699	124201699	+	Silent	SNP	C	C	T	rs61740058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:124201699C>T	ENST00000240874.3	+	28	4387	c.4230C>T	c.(4228-4230)taC>taT	p.Y1410Y	KALRN_ENST00000460856.1_Silent_p.Y1401Y|KALRN_ENST00000360013.3_Silent_p.Y1410Y	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1410	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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						TCTCTTCCTACCTAATTAAGC	0.527													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		19189	0.0		0.0179	False		,,,				2504	0.0092				p.Y1410Y		Atlas-SNP	.											.	KALRN	556	.	0			c.C4230T						PASS	.	C	,	45,4361	46.7+/-81.2	0,45,2158	247.0	197.0	214.0		4230,4230	3.5	1.0	3	dbSNP_129	214	323,8277	113.7+/-173.7	7,309,3984	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	7,354,6142	TT,TC,CC		3.7558,1.0213,2.8295	,	1410/2987,1410/1664	124201699	368,12638	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon28			TTCCTACCTAATT	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.4230C>T	3.37:g.124201699C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	169	88	0.52071	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	23	0.010531135531135532	0	0.0	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	8.830	0.939650	0.18281	0.010213	0.037558	ENSG00000160145	ENST00000354186	.	.	.	5.31	3.53	0.40419	.	.	.	.	.	T	0.25754	0.0627	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27938	-1.0059	4	.	.	.	.	8.0382	0.30506	0.0:0.7055:0.0:0.2945	rs61740058	.	.	.	I	1379	.	.	T	+	2	0	KALRN	125684389	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.928000	0.40104	0.819000	0.34492	0.655000	0.94253	ACC	C|0.979;T|0.021	0.021	strong		0.527	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
CPNE8	144402	hgsc.bcm.edu	37	12	39299249	39299249	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:39299249C>T	ENST00000331366.5	-	1	184	c.88G>A	c.(88-90)Gtg>Atg	p.V30M	RP11-396F22.1_ENST00000551152.1_RNA|CPNE8_ENST00000360449.3_Intron	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	30	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				CTGCAGGACACGGACACCTCC	0.647																																					p.V30M		Atlas-SNP	.											.	CPNE8	66	.	0			c.G88A						PASS	.						62.0	50.0	54.0					12																	39299249		2195	4284	6479	SO:0001583	missense	144402	exon1			AGGACACGGACAC	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.88G>A	12.37:g.39299249C>T	ENSP00000329748:p.Val30Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_153634	Q2TB41|Q86VY2	Missense_Mutation	SNP	ENST00000331366.5	37	CCDS8733.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.377756	0.82682	.	.	ENSG00000139117	ENST00000331366	T	0.55234	0.53	4.53	4.53	0.55603	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.102804	0.38959	N	0.001514	T	0.67126	0.2860	M	0.76938	2.355	0.80722	D	1	P	0.50710	0.938	P	0.54856	0.762	T	0.72798	-0.4184	10	0.72032	D	0.01	-11.5212	15.0267	0.71674	0.0:1.0:0.0:0.0	.	30	Q86YQ8	CPNE8_HUMAN	M	30	ENSP00000329748:V30M	ENSP00000329748:V30M	V	-	1	0	CPNE8	37585516	0.990000	0.36364	0.966000	0.40874	0.994000	0.84299	3.827000	0.55745	2.448000	0.82819	0.563000	0.77884	GTG	.	.	none		0.647	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634	
CARD9	64170	hgsc.bcm.edu	37	9	139266405	139266405	+	Silent	SNP	G	G	A	rs10781499	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139266405G>A	ENST00000371732.5	-	2	291	c.126C>T	c.(124-126)ccC>ccT	p.P42P	CARD9_ENST00000315908.7_Silent_p.P42P|CARD9_ENST00000371734.3_Silent_p.P42P	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	42	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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)		CCTCATCATCGGGGTTCAGGA	0.642													G|||	1834	0.366214	0.2504	0.572	5008	,	,		17535	0.3185		0.3976	False		,,,				2504	0.3937				p.P42P		Atlas-SNP	.											CARD9,NS,carcinoma,0,1	CARD9	47	1	0			c.C126T						PASS	.	G	,	1227,3179	424.7+/-340.5	166,895,1142	171.0	150.0	157.0	http://www.ncbi.nlm.nih.gov/pubmed?term	126,126	-2.2	0.8	9	dbSNP_120	157	3641,4959	523.9+/-380.4	767,2107,1426	yes	coding-synonymous,coding-synonymous	CARD9	NM_052813.4,NM_052814.3	,	933,3002,2568	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	42.3372,27.8484,37.4289	,	42/537,42/493	139266405	4868,8138	2203	4300	6503	SO:0001819	synonymous_variant	64170	exon2			ATCATCGGGGTTC	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.126C>T	9.37:g.139266405G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			G|0.634;A|0.366	0.366	strong		0.642	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
ACSM4	341392	hgsc.bcm.edu	37	12	7463241	7463241	+	Silent	SNP	A	A	T	rs7968241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:7463241A>T	ENST00000399422.4	+	3	567	c.519A>T	c.(517-519)ccA>ccT	p.P173P		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	173					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						AGGTGGCCCCAGCGGTGGAGT	0.537													A|||	1618	0.323083	0.1997	0.3156	5008	,	,		-128	0.3502		0.5487	False		,,,				2504	0.2352				p.P173P		Atlas-SNP	.											.	ACSM4	98	.	0			c.A519T						PASS	.	A		994,2972		154,686,1143	48.0	48.0	48.0		519	-4.9	0.0	12	dbSNP_116	48	4313,4013		1119,2075,969	no	coding-synonymous	ACSM4	NM_001080454.1		1273,2761,2112	TT,TA,AA		48.1984,25.063,43.1744		173/581	7463241	5307,6985	1983	4163	6146	SO:0001819	synonymous_variant	341392	exon3			GGCCCCAGCGGTG		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.519A>T	12.37:g.7463241A>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	39	0.619048	NM_001080454	A8MTI6	Silent	SNP	ENST00000399422.4	37	CCDS44825.1																																																																																			A|0.570;T|0.430	0.430	strong		0.537	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454	
UBC	7316	hgsc.bcm.edu	37	12	125397364	125397364	+	Silent	SNP	A	A	G	rs8963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:125397364A>G	ENST00000536769.1	-	1	2530	c.954T>C	c.(952-954)acT>acC	p.T318T	UBC_ENST00000538617.1_Intron|UBC_ENST00000536661.1_5'Flank|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000546120.1_Silent_p.T242T|UBC_ENST00000339647.5_Silent_p.T318T			P0CG48	UBC_HUMAN	ubiquitin C	318	Ubiquitin-like 5. {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)			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)		CCACTTCGAGAGTGATGGTCT	0.522													G|||	2306	0.460463	0.1778	0.5476	5008	,	,		27904	0.2083		0.7714	False		,,,				2504	0.7209				p.T318T		Atlas-SNP	.											.	UBC	79	.	0			c.T954C						PASS	.						92.0	78.0	82.0					12																	125397364		2202	4286	6488	SO:0001819	synonymous_variant	7316	exon2			TTCGAGAGTGATG		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		ENST00000536769.1:c.954T>C	12.37:g.125397364A>G		Somatic	449	0	0		WXS	Illumina HiSeq	Phase_I	477	192	0.402516	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	37	CCDS9260.1																																																																																			A|0.537;G|0.463	0.463	strong		0.522	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009	
OGFOD1	55239	hgsc.bcm.edu	37	16	56485554	56485554	+	Silent	SNP	C	C	G	rs11076155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:56485554C>G	ENST00000566157.1	+	1	153	c.30C>G	c.(28-30)ggC>ggG	p.G10G	OGFOD1_ENST00000568397.1_Silent_p.G10G|NUDT21_ENST00000300291.5_5'Flank	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	10					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)	CGGAGCCCGGCCCAGCCCGGG	0.587													C|||	265	0.0529153	0.0015	0.049	5008	,	,		15751	0.0724		0.0835	False		,,,				2504	0.0736				p.G10G		Atlas-SNP	.											.	OGFOD1	31	.	0			c.C30G						PASS	.	C		75,4321	54.9+/-90.9	0,75,2123	72.0	87.0	82.0		30	1.1	0.0	16	dbSNP_120	82	597,8003	144.0+/-200.0	18,561,3721	no	coding-synonymous	OGFOD1	NM_018233.3		18,636,5844	GG,GC,CC		6.9419,1.7061,5.1708		10/543	56485554	672,12324	2198	4300	6498	SO:0001819	synonymous_variant	55239	exon1			GCCCGGCCCAGCC	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.30C>G	16.37:g.56485554C>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	25	0.694444	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Silent	SNP	ENST00000566157.1	37	CCDS10761.2																																																																																			C|0.948;G|0.052	0.052	strong		0.587	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
EDN1	1906	hgsc.bcm.edu	37	6	12296255	12296255	+	Missense_Mutation	SNP	G	G	T	rs5370	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:12296255G>T	ENST00000379375.5	+	5	861	c.594G>T	c.(592-594)aaG>aaT	p.K198N		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	198			K -> N (polymorphism associated with HDL cholesterol levels is some populations and in a sex-specific manner; dbSNP:rs5370). {ECO:0000269|PubMed:10334806, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17357073, ECO:0000269|PubMed:18288492, ECO:0000269|Ref.5}.		artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)	p.K198N(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				TGAAAGGCAAGCCCTCCAGAG	0.483													G|||	1239	0.247404	0.1619	0.147	5008	,	,		18203	0.2857		0.2127	False		,,,				2504	0.4305				p.K198N		Atlas-SNP	.											EDN1,NS,carcinoma,0,1	EDN1	23	1	1	Substitution - Missense(1)	stomach(1)	c.G594T	GRCh37	CM993569	EDN1	M	rs5370	PASS	.	G	ASN/LYS,ASN/LYS	865,3541	337.0+/-304.7	98,669,1436	158.0	150.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	591,594	2.2	0.1	6	dbSNP_52	152	1817,6783	326.9+/-317.6	185,1447,2668	yes	missense,missense	EDN1	NM_001168319.1,NM_001955.4	94,94	283,2116,4104	TT,TG,GG		21.1279,19.6323,20.6213	benign,benign	197/212,198/213	12296255	2682,10324	2203	4300	6503	SO:0001583	missense	1906	exon5			AGGCAAGCCCTCC	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"""Endogenous ligands"""	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.594G>T	6.37:g.12296255G>T	ENSP00000368683:p.Lys198Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	37	CCDS4522.1	449	0.20558608058608058	68	0.13821138211382114	63	0.17403314917127072	158	0.2762237762237762	160	0.21108179419525067	G	7.695	0.691892	0.15039	0.196323	0.211279	ENSG00000078401	ENST00000379375	D	0.84589	-1.87	5.93	2.18	0.27775	.	0.551151	0.21002	N	0.081852	T	0.60894	0.2304	L	0.38175	1.15	0.45452	P	0.001570999999999989	P;P	0.34462	0.454;0.454	B;B	0.26614	0.071;0.071	T	0.49532	-0.8930	9	0.51188	T	0.08	-14.7064	9.471	0.38842	0.276:0.0:0.724:0.0	rs5370;rs2229566;rs17845238;rs17858054;rs57072783;rs5370	198;198	Q6FH53;P05305	.;EDN1_HUMAN	N	198	ENSP00000368683:K198N	ENSP00000368683:K198N	K	+	3	2	EDN1	12404241	0.001000	0.12720	0.141000	0.22245	0.005000	0.04900	0.049000	0.14099	0.116000	0.18110	0.655000	0.94253	AAG	G|0.787;T|0.213	0.213	strong		0.483	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955	
GET4	51608	hgsc.bcm.edu	37	7	930689	930689	+	Silent	SNP	C	C	T	rs13171	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:930689C>T	ENST00000265857.3	+	5	685	c.591C>T	c.(589-591)gcC>gcT	p.A197A	GET4_ENST00000407192.1_Silent_p.A144A	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	197					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						TGTTCGTGGCCCAGGCCGTGC	0.617													C|||	1007	0.201078	0.0862	0.2435	5008	,	,		17773	0.2669		0.1879	False		,,,				2504	0.272				p.A197A		Atlas-SNP	.											GET4,NS,carcinoma,0,1	GET4	17	1	0			c.C591T						PASS	.	C		437,3969	207.5+/-228.8	23,391,1789	110.0	88.0	95.0		591	-2.1	1.0	7	dbSNP_52	95	1435,7165	275.4+/-291.8	116,1203,2981	no	coding-synonymous	GET4	NM_015949.2		139,1594,4770	TT,TC,CC		16.686,9.9183,14.3934		197/328	930689	1872,11134	2203	4300	6503	SO:0001819	synonymous_variant	51608	exon5			CGTGGCCCAGGCC	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.591C>T	7.37:g.930689C>T		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	310	152	0.490323	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																			C|0.831;T|0.169	0.169	strong		0.617	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949	
MUM1	84939	hgsc.bcm.edu	37	19	1360575	1360575	+	Missense_Mutation	SNP	G	G	A	rs3826942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1360575G>A	ENST00000415183.3	+	4	684	c.658G>A	c.(658-660)Gga>Aga	p.G220R	MUM1_ENST00000591806.1_Missense_Mutation_p.G220R|MUM1_ENST00000344663.3_Missense_Mutation_p.G220R|MUM1_ENST00000311401.5_Missense_Mutation_p.G151R			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	219					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TAAGAGGGGAGGAAACTCAGC	0.567													A|||	3370	0.672923	0.6831	0.7349	5008	,	,		19187	0.5149		0.7187	False		,,,				2504	0.7311				p.G220R		Atlas-SNP	.											.	MUM1	54	.	0			c.G658A						PASS	.	A	ARG/GLY	3019,1387	457.1+/-351.5	1057,905,241	64.0	61.0	62.0		658	-0.3	0.0	19	dbSNP_107	62	6510,2090	360.3+/-331.9	2454,1602,244	yes	missense	MUM1	NM_032853.3	125	3511,2507,485	AA,AG,GG		24.3023,31.4798,26.7338	benign	220/712	1360575	9529,3477	2203	4300	6503	SO:0001583	missense	84939	exon5			AGGGGAGGAAACT	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.658G>A	19.37:g.1360575G>A	ENSP00000394925:p.Gly220Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	37		1439	0.6588827838827839	320	0.6504065040650406	272	0.7513812154696132	299	0.5227272727272727	548	0.7229551451187335	A	0.020	-1.444469	0.01089	0.685202	0.756977	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183;ENST00000542512	T;T;T	0.25749	1.78;1.78;1.78	4.25	-0.31	0.12765	.	0.608195	0.15609	N	0.253470	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	0.28713	-1.0035	9	0.07482	T	0.82	.	0.8159	0.01102	0.3633:0.1728:0.2966:0.1673	rs3826942;rs12981386;rs17684638;rs56573020;rs60556983;rs3826942	151;219	Q2TAK8-2;Q2TAK8	.;MUM1_HUMAN	R	220;151;220;149	ENSP00000345789:G220R;ENSP00000309135:G151R;ENSP00000394925:G220R	ENSP00000309135:G151R	G	+	1	0	MUM1	1311575	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.389000	0.20751	-0.289000	0.09038	-1.007000	0.02485	GGA	G|0.297;A|0.703	0.703	strong		0.567	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853	
COL28A1	340267	hgsc.bcm.edu	37	7	7495735	7495735	+	Missense_Mutation	SNP	T	T	C	rs55745506	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	70	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	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	
SLC4A2	6522	hgsc.bcm.edu	37	7	150768280	150768280	+	Missense_Mutation	SNP	G	G	A	rs201086697		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150768280G>A	ENST00000485713.1	+	13	2911	c.1871G>A	c.(1870-1872)cGc>cAc	p.R624H	SLC4A2_ENST00000392826.2_Missense_Mutation_p.R615H|SLC4A2_ENST00000461735.1_Missense_Mutation_p.R610H|SLC4A2_ENST00000413384.2_Missense_Mutation_p.R624H|SLC4A2_ENST00000310317.5_Missense_Mutation_p.R542H	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	624					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)		GAGCTGCTGCGCTCTGTGGCC	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15698	0.0		0.0	False		,,,				2504	0.001				p.R624H		Atlas-SNP	.											SLC4A2,NS,carcinoma,0,1	SLC4A2	98	1	0			c.G1871A						PASS	.						24.0	24.0	24.0					7																	150768280		2203	4299	6502	SO:0001583	missense	6522	exon13			TGCTGCGCTCTGT		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.1871G>A	7.37:g.150768280G>A	ENSP00000419412:p.Arg624His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.382529	0.42207	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35	5.21	2.16	0.27623	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.063739	0.64402	N	0.000005	T	0.67002	0.2847	L	0.38175	1.15	0.54753	D	0.999986	B;B;B	0.22480	0.07;0.031;0.031	B;B;B	0.18561	0.022;0.013;0.006	T	0.59925	-0.7362	10	0.46703	T	0.11	.	5.0009	0.14264	0.0834:0.1465:0.6191:0.151	.	615;610;624	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	H	624;624;542;615;610	ENSP00000419412:R624H;ENSP00000405600:R624H;ENSP00000311402:R542H;ENSP00000376571:R615H;ENSP00000419164:R610H	ENSP00000311402:R542H	R	+	2	0	SLC4A2	150399213	0.537000	0.26386	0.656000	0.29637	0.780000	0.44128	1.414000	0.34736	0.668000	0.31126	-0.145000	0.13849	CGC	.	.	weak		0.652	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
NCLN	56926	hgsc.bcm.edu	37	19	3207422	3207422	+	Silent	SNP	T	T	C	rs3816054	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	86	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	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	
PNKD	25953	hgsc.bcm.edu	37	2	219205471	219205471	+	Silent	SNP	G	G	A	rs34014804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	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		
CRYBG3	131544	hgsc.bcm.edu	37	3	97634465	97634465	+	Missense_Mutation	SNP	A	A	G	rs17302349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:97634465A>G	ENST00000182096.4	+	14	2346	c.2282A>G	c.(2281-2283)tAt>tGt	p.Y761C		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2709							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TGGCTCCTCTATTACCAAGAA	0.438													A|||	18	0.00359425	0.0	0.0014	5008	,	,		18952	0.0		0.0169	False		,,,				2504	0.0				p.Y2709C		Atlas-SNP	.											.	CRYBG3	86	.	0			c.A8126G						PASS	.	A	CYS/TYR	13,3869		0,13,1928	131.0	124.0	127.0		8126	-0.7	0.7	3	dbSNP_123	127	101,8169		2,97,4036	no	missense	CRYBG3	XM_003118522.2	194	2,110,5964	GG,GA,AA		1.2213,0.3349,0.9381	benign	2709/2971	97634465	114,12038	1941	4135	6076	SO:0001583	missense	131544	exon17			TCCTCTATTACCA			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.2282A>G	3.37:g.97634465A>G	ENSP00000182096:p.Tyr761Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	4.996	0.184921	0.09495	0.003349	0.012213	ENSG00000080200	ENST00000182096	D	0.85702	-2.02	5.87	-0.682	0.11339	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.997902	0.08115	N	0.995570	T	0.66076	0.2753	L	0.60845	1.875	0.52501	D	0.999956	B	0.11235	0.004	B	0.09377	0.004	T	0.65919	-0.6051	10	0.51188	T	0.08	.	1.6488	0.02767	0.4574:0.1336:0.2803:0.1287	rs17302349;rs52818309;rs17302349	761	Q68DQ2	CRBG3_HUMAN	C	761	ENSP00000182096:Y761C	ENSP00000182096:Y761C	Y	+	2	0	CRYBG3	99117155	0.999000	0.42202	0.672000	0.29872	0.069000	0.16628	0.555000	0.23422	-0.105000	0.12132	-1.437000	0.01076	TAT	A|0.994;G|0.006	0.006	strong		0.438	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
CDKAL1	54901	hgsc.bcm.edu	37	6	21065450	21065450	+	Silent	SNP	A	A	G	rs56087852	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:21065450A>G	ENST00000378610.1	+	10	1237	c.1227A>G	c.(1225-1227)ccA>ccG	p.P409P	CDKAL1_ENST00000378624.4_Silent_p.P339P|CDKAL1_ENST00000274695.4_Silent_p.P409P			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	409					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)	p.P409P(1)		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)			AACAAGTTCCAGCACAAGTGG	0.388													A|||	941	0.187899	0.239	0.1369	5008	,	,		16097	0.1627		0.1998	False		,,,				2504	0.1687				p.P409P		Atlas-SNP	.											CDKAL1,NS,carcinoma,0,1	CDKAL1	55	1	1	Substitution - coding silent(1)	stomach(1)	c.A1227G						PASS	.	A		963,3443	359.1+/-314.7	114,735,1354	90.0	87.0	88.0		1227	-0.0	1.0	6	dbSNP_129	88	1633,6967	298.3+/-303.9	147,1339,2814	no	coding-synonymous	CDKAL1	NM_017774.3		261,2074,4168	GG,GA,AA		18.9884,21.8566,19.96		409/580	21065450	2596,10410	2203	4300	6503	SO:0001819	synonymous_variant	54901	exon12			AGTTCCAGCACAA	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.1227A>G	6.37:g.21065450A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Silent	SNP	ENST00000378610.1	37	CCDS4546.1																																																																																			A|0.809;G|0.191	0.191	strong		0.388	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774	
IGFN1	91156	hgsc.bcm.edu	37	1	201175274	201175274	+	Missense_Mutation	SNP	A	A	G	rs9651057	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201175274A>G	ENST00000335211.4	+	12	1383	c.1253A>G	c.(1252-1254)cAg>cGg	p.Q418R	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Intron	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	583						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CAAGGAGCCCAGGCATCAGGA	0.587													A|||	1882	0.375799	0.1467	0.4063	5008	,	,		18973	0.5903		0.4821	False		,,,				2504	0.3333				p.Q418R		Atlas-SNP	.											.	IGFN1	220	.	0			c.A1253G						PASS	.	A	ARG/GLN	279,1105		38,203,451	24.0	28.0	27.0		1253	-2.1	0.0	1	dbSNP_119	27	1476,1706		359,758,474	yes	missense	IGFN1	NM_001164586.1	43	397,961,925	GG,GA,AA		46.3859,20.159,38.4363		418/3709	201175274	1755,2811	692	1591	2283	SO:0001583	missense	91156	exon12			GAGCCCAGGCATC	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.1253A>G	1.37:g.201175274A>G	ENSP00000334714:p.Gln418Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	943	0.4317765567765568	84	0.17073170731707318	158	0.43646408839779005	327	0.5716783216783217	374	0.49340369393139843	A	12.00	1.807715	0.31961	0.20159	0.463859	ENSG00000163395	ENST00000335211	T	0.52526	0.66	4.0	-2.08	0.07254	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.46830	-0.9163	5	.	.	.	.	1.3995	0.02267	0.3901:0.3308:0.1054:0.1737	rs9651057;rs12740703;rs52837570;rs9651057	.	.	.	R	418	ENSP00000334714:Q418R	.	Q	+	2	0	IGFN1	199441897	0.044000	0.20184	0.000000	0.03702	0.041000	0.13682	0.064000	0.14437	-0.179000	0.10654	-0.313000	0.08912	CAG	A|0.571;G|0.429	0.429	strong		0.587	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
CR1	1378	hgsc.bcm.edu	37	1	207787796	207787796	+	Missense_Mutation	SNP	T	T	C	rs61822976		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:207787796T>C	ENST00000367049.4	+	40	6623	c.6623T>C	c.(6622-6624)aTg>aCg	p.M2208T	CR1_ENST00000367051.1_Missense_Mutation_p.M1758T|CR1_ENST00000400960.2_Missense_Mutation_p.M1758T|CR1_ENST00000367053.1_Missense_Mutation_p.M1758T|CR1_ENST00000367052.1_Missense_Mutation_p.M1758T	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1758					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.M1758T(1)|p.M2208T(1)|p.M1763T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTGGCTGGAATGAAAGCCCTT	0.408																																					p.M2208T		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,4	CR1	354	4	3	Substitution - Missense(3)	prostate(3)	c.T6623C						PASS	.						128.0	121.0	123.0					1																	207787796		1882	4112	5994	SO:0001583	missense	1378	exon40			CTGGAATGAAAGC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6623T>C	1.37:g.207787796T>C	ENSP00000356016:p.Met2208Thr	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	295	12	0.040678	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	T	3.803	-0.041226	0.07452	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	4.29	-5.87	0.02297	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.09335	0.0230	N	0.20986	0.625	0.09310	N	1	B;P	0.46457	0.043;0.878	B;B	0.42422	0.009;0.387	T	0.19614	-1.0300	9	0.18276	T	0.48	.	1.2481	0.01977	0.4109:0.0944:0.2677:0.2271	rs61822976	1758;2208	P17927;E9PDY4	CR1_HUMAN;.	T	1758;1758;1758;1758;2208	ENSP00000356019:M1758T;ENSP00000356018:M1758T;ENSP00000356020:M1758T;ENSP00000383744:M1758T;ENSP00000356016:M2208T	ENSP00000356016:M2208T	M	+	2	0	CR1	205854419	0.002000	0.14202	0.000000	0.03702	0.554000	0.35429	-0.327000	0.07955	-0.793000	0.04475	0.358000	0.22013	ATG	.	.	weak		0.408	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
NME8	51314	hgsc.bcm.edu	37	7	37936530	37936530	+	Silent	SNP	T	T	C	rs3213975	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:37936530T>C	ENST00000199447.4	+	17	1975	c.1603T>C	c.(1603-1605)Ttg>Ctg	p.L535L	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Silent_p.L535L	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	535	NDK 3.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										ATGGAGACGATTGATGGGCCC	0.463													T|||	1034	0.20647	0.1672	0.2017	5008	,	,		16821	0.2292		0.2396	False		,,,				2504	0.2055				p.L535L		Atlas-SNP	.											.	.	.	.	0			c.T1603C						PASS	.	T		907,3499	348.2+/-309.8	94,719,1390	116.0	111.0	113.0		1603	-4.0	0.8	7	dbSNP_106	113	2077,6523	359.8+/-331.7	256,1565,2479	no	coding-synonymous	TXNDC3	NM_016616.4		350,2284,3869	CC,CT,TT		24.1512,20.5856,22.9433		535/589	37936530	2984,10022	2203	4300	6503	SO:0001819	synonymous_variant	51314	exon17			AGACGATTGATGG	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1603T>C	7.37:g.37936530T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	153	82	0.535948	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			T|0.770;C|0.230	0.230	strong		0.463	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
OR8G5	219865	hgsc.bcm.edu	37	11	124135677	124135677	+	Missense_Mutation	SNP	A	A	G	rs10893192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124135677A>G	ENST00000524943.2	+	1	955	c.955A>G	c.(955-957)Atg>Gtg	p.M319V	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	319						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)		TGTTGTGCCCATGCTGAACCC	0.458													A|||	432	0.086262	0.1437	0.0346	5008	,	,		19241	0.0516		0.0169	False		,,,				2504	0.1524				p.M319V	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.A955G						PASS	.	A	VAL/MET	483,3583		28,427,1578	80.0	78.0	79.0		955	3.0	1.0	11	dbSNP_120	79	229,8231		4,221,4005	no	missense	OR8G5	NM_001005198.1	21	32,648,5583	GG,GA,AA		2.7069,11.879,5.6842		319/347	124135677	712,11814	2033	4230	6263	SO:0001583	missense	219865	exon1			GTGCCCATGCTGA	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.955A>G	11.37:g.124135677A>G	ENSP00000477014:p.Met319Val	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	289	124	0.429066	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				A|0.945;G|0.055	0.055	strong		0.458	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
SPNS3	201305	hgsc.bcm.edu	37	17	4352636	4352636	+	Missense_Mutation	SNP	G	G	A	rs34457931	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4352636G>A	ENST00000355530.2	+	7	1157	c.877G>A	c.(877-879)Ggg>Agg	p.G293R	SPNS3_ENST00000333476.2_Missense_Mutation_p.G166R|SPNS3_ENST00000576069.1_Intron	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	293			G -> R (in dbSNP:rs34457931). {ECO:0000269|PubMed:14702039}.		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						CGTGGTTCACGGGCTGCAGCC	0.682													g|||	481	0.0960463	0.0159	0.1138	5008	,	,		15672	0.0694		0.1372	False		,,,				2504	0.1769				p.G293R		Atlas-SNP	.											.	SPNS3	52	.	0			c.G877A						PASS	.		ARG/GLY	149,4257	103.4+/-141.9	3,143,2057	51.0	45.0	47.0		877	2.9	0.4	17	dbSNP_126	47	1055,7545	221.9+/-259.1	71,913,3316	yes	missense	SPNS3	NM_182538.4	125	74,1056,5373	AA,AG,GG		12.2674,3.3818,9.2573	benign	293/513	4352636	1204,11802	2203	4300	6503	SO:0001583	missense	201305	exon7			GTTCACGGGCTGC		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.877G>A	17.37:g.4352636G>A	ENSP00000347721:p.Gly293Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	195	0.08928571428571429	4	0.008130081300813009	49	0.13535911602209943	40	0.06993006993006994	102	0.1345646437994723	g	14.56	2.572599	0.45798	0.033818	0.122674	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.71579	-0.58;-0.58	5.05	2.94	0.34122	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.01156	0.0038	M	0.70903	2.155	0.30053	P	0.811621	D;P	0.60160	0.987;0.801	P;B	0.50049	0.629;0.362	T	0.38415	-0.9662	9	0.33940	T	0.23	-16.8041	5.8944	0.18931	0.1814:0.16:0.6585:0.0	rs34457931	166;293	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	R	293;166	ENSP00000347721:G293R;ENSP00000333207:G166R	ENSP00000333207:G166R	G	+	1	0	SPNS3	4299385	1.000000	0.71417	0.415000	0.26534	0.465000	0.32709	3.821000	0.55700	1.253000	0.44018	0.651000	0.88453	GGG	G|0.906;A|0.094	0.094	strong		0.682	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
VPS13C	54832	hgsc.bcm.edu	37	15	62254989	62254989	+	Missense_Mutation	SNP	T	T	C	rs3784635	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:62254989T>C	ENST00000261517.5	-	33	3467	c.3394A>G	c.(3394-3396)Att>Gtt	p.I1132V	VPS13C_ENST00000249837.3_Missense_Mutation_p.I1089V|VPS13C_ENST00000395898.3_Missense_Mutation_p.I1089V|VPS13C_ENST00000395896.4_Missense_Mutation_p.I1132V	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						GTGACAATAATATTTTCTAGT	0.338													T|||	485	0.096845	0.0038	0.196	5008	,	,		13637	0.2054		0.0298	False		,,,				2504	0.1094				p.I1132V		Atlas-SNP	.											.	VPS13C	506	.	0			c.A3394G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	36,4370	39.2+/-71.8	1,34,2168	74.0	76.0	75.0		3394,3265,3265,3394	3.5	1.0	15	dbSNP_107	75	213,8387	89.2+/-151.4	3,207,4090	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	29,29,29,29	4,241,6258	CC,CT,TT		2.4767,0.8171,1.9145	benign,benign,benign,benign	1132/3629,1089/3711,1089/3586,1132/3754	62254989	249,12757	2203	4300	6503	SO:0001583	missense	54832	exon33			CAATAATATTTTC	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.3394A>G	15.37:g.62254989T>C	ENSP00000261517:p.Ile1132Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	181	84	0.464088	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	190	0.08699633699633699	2	0.0040650406504065045	43	0.11878453038674033	116	0.20279720279720279	29	0.03825857519788918	T	9.239	1.037820	0.19669	0.008171	0.024767	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.42900	0.96;0.96;0.96	5.8	3.47	0.39725	.	0.221564	0.38897	N	0.001527	T	0.00039	0.0001	M	0.77486	2.375	0.31812	P	0.627054	B;B;B;B	0.32365	0.124;0.367;0.124;0.048	B;B;B;B	0.28232	0.038;0.087;0.065;0.025	T	0.11446	-1.0587	9	0.20519	T	0.43	.	6.7067	0.23254	0.1147:0.1287:0.0:0.7566	rs3784635;rs17304003;rs52829205;rs57619309;rs3784635	1089;1132;1089;1132	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	V	1089;1132;1132;1132	ENSP00000249837:I1089V;ENSP00000261517:I1132V;ENSP00000379233:I1132V	ENSP00000249837:I1089V	I	-	1	0	VPS13C	60042281	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	1.378000	0.34328	0.444000	0.26612	-0.374000	0.07098	ATT	T|0.948;C|0.052	0.052	strong		0.338	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
POLN	353497	hgsc.bcm.edu	37	4	2210065	2210065	+	Missense_Mutation	SNP	C	C	A	rs2353552	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2210065C>A	ENST00000511885.2	-	5	716	c.363G>T	c.(361-363)caG>caT	p.Q121H	POLN_ENST00000515357.1_5'UTR|POLN_ENST00000382865.1_Missense_Mutation_p.Q121H			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	121			Q -> H (in dbSNP:rs2353552). {ECO:0000269|PubMed:12794064, ECO:0000269|Ref.3}.		double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			CTTGATTATACTGTGGAATTA	0.373								DNA polymerases (catalytic subunits)					C|||	220	0.0439297	0.0068	0.0677	5008	,	,		17286	0.003		0.1262	False		,,,				2504	0.0348				p.Q121H		Atlas-SNP	.											.	POLN	82	.	0			c.G363T						PASS	.	C	HIS/GLN	106,4288	70.3+/-108.2	1,104,2092	79.0	84.0	83.0		363	-0.1	0.0	4	dbSNP_100	83	1103,7495	217.1+/-255.9	86,931,3282	yes	missense	POLN	NM_181808.2	24	87,1035,5374	AA,AC,CC		12.8286,2.4124,9.3057	probably-damaging	121/901	2210065	1209,11783	2197	4299	6496	SO:0001583	missense	353497	exon3			ATTATACTGTGGA	AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.363G>T	4.37:g.2210065C>A	ENSP00000435506:p.Gln121His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	136	0.06227106227106227	5	0.01016260162601626	31	0.0856353591160221	1	0.0017482517482517483	99	0.13060686015831136	C	18.60	3.658914	0.67586	0.024124	0.128286	ENSG00000130997	ENST00000511885;ENST00000382865	T;T	0.48522	0.81;0.81	5.27	-0.11	0.13580	.	3.066540	0.00644	N	0.000537	T	0.00496	0.0016	L	0.32530	0.975	0.80722	P	0.0	D;D	0.56521	0.976;0.976	P;P	0.49999	0.628;0.628	T	0.04976	-1.0914	9	0.66056	D	0.02	-0.2253	1.232	0.01945	0.2965:0.3839:0.1448:0.1748	rs2353552;rs17767504;rs60397785;rs2353552	121;121	E7ERY2;Q7Z5Q5	.;DPOLN_HUMAN	H	121	ENSP00000435506:Q121H;ENSP00000372316:Q121H	ENSP00000372316:Q121H	Q	-	3	2	POLN	2179863	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	-0.704000	0.05058	0.219000	0.20840	-0.258000	0.10820	CAG	C|0.924;A|0.076	0.076	strong		0.373	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
ZNF99	7652	hgsc.bcm.edu	37	19	22941617	22941617	+	Missense_Mutation	SNP	T	T	C	rs58653025	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	41	1	0.0243902		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	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	
BSPH1	100131137	hgsc.bcm.edu	37	19	48495304	48495304	+	Missense_Mutation	SNP	G	G	A	rs60213124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48495304G>A	ENST00000344839.3	-	1	123	c.35C>T	c.(34-36)aCg>aTg	p.T12M	ELSPBP1_ENST00000339841.2_5'Flank|ELSPBP1_ENST00000597519.1_5'Flank	NM_001128326.2	NP_001121798.1	Q075Z2	BSPH1_HUMAN	binder of sperm protein homolog 1	12					single fertilization (GO:0007338)|sperm capacitation (GO:0048240)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)	p.T12M(1)		stomach(2)	2						GGAATTTCGCGTCGTTTCCAC	0.458													g|||	930	0.185703	0.1543	0.1643	5008	,	,		15663	0.2004		0.1829	False		,,,				2504	0.2311				p.T12M		Atlas-SNP	.											BSPH1,NS,carcinoma,0,1	BSPH1	6	1	1	Substitution - Missense(1)	stomach(1)	c.C35T						PASS	.						83.0	69.0	73.0					19																	48495304		692	1591	2283	SO:0001583	missense	100131137	exon1			TTTCGCGTCGTTT	DQ227497	CCDS46135.1	19q13.32	2012-09-20				ENSG00000188334			33906	protein-coding gene	gene with protein product	"""epididymal sperm binding protein 2"", ""bovine seminal plasma protein homolog 1"""	612213				17085770, 18923155	Standard	NM_001128326		Approved	ELSPBP2, BSP1	uc002phs.1	Q075Z2		ENST00000344839.3:c.35C>T	19.37:g.48495304G>A	ENSP00000341762:p.Thr12Met	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	104	43	0.413462	NM_001128326	A6NIZ5	Missense_Mutation	SNP	ENST00000344839.3	37	CCDS46135.1	380	0.17399267399267399	76	0.15447154471544716	61	0.1685082872928177	115	0.20104895104895104	128	0.16886543535620052	G	6.353	0.433325	0.12045	.	.	ENSG00000188334	ENST00000344839	T	0.42513	0.97	1.71	-0.642	0.11486	.	1.614220	0.04353	U	0.356014	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.53745	0.962	B	0.28916	0.096	T	0.10428	-1.0630	9	0.46703	T	0.11	-2.6895	2.3933	0.04384	0.186:0.0:0.5229:0.2911	rs60213124	12	Q075Z2	BSPH1_HUMAN	M	12	ENSP00000341762:T12M	ENSP00000341762:T12M	T	-	2	0	BSPH1	53187116	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.368000	0.20399	-0.066000	0.12998	-0.310000	0.09108	ACG	G|0.818;A|0.182	0.182	strong		0.458	BSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465206.1	NM_001128326	
DISP1	84976	hgsc.bcm.edu	37	1	223116474	223116474	+	Missense_Mutation	SNP	G	G	T	rs71583926|rs2789975	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:223116474G>T	ENST00000284476.6	+	2	473	c.309G>T	c.(307-309)gaG>gaT	p.E103D	DISP1_ENST00000360254.2_Missense_Mutation_p.E103D|DISP1_ENST00000495684.1_Intron	NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	103			E -> K (in dbSNP:rs2609383).		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)		GCCATCCCGAGGCTGGCCCTG	0.522													G|||	1060	0.211661	0.1566	0.1715	5008	,	,		23499	0.2907		0.1352	False		,,,				2504	0.3119				p.E103D		Atlas-SNP	.											.	DISP1	145	.	0			c.G309T						PASS	.	G	ASP/GLU	738,3668	304.1+/-288.3	59,620,1524	140.0	120.0	127.0		309	4.5	1.0	1	dbSNP_100	127	1176,7424	239.7+/-270.7	86,1004,3210	yes	missense	DISP1	NM_032890.3	45	145,1624,4734	TT,TG,GG		13.6744,16.7499,14.7163	benign	103/1525	223116474	1914,11092	2203	4300	6503	SO:0001583	missense	84976	exon4			TCCCGAGGCTGGC	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.309G>T	1.37:g.223116474G>T	ENSP00000284476:p.Glu103Asp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	145	84	0.57931	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	399	0.18269230769230768	70	0.14227642276422764	64	0.17679558011049723	156	0.2727272727272727	109	0.1437994722955145	G	11.48	1.650644	0.29336	0.167499	0.136744	ENSG00000154309	ENST00000360254;ENST00000284476	T;D	0.91843	0.85;-2.92	5.62	4.51	0.55191	.	0.682047	0.14375	N	0.323515	T	0.00073	0.0002	L	0.51422	1.61	0.43982	P	0.003322999999999965	B	0.23937	0.094	B	0.16722	0.016	T	0.27297	-1.0078	9	0.14252	T	0.57	-28.9434	15.411	0.74917	0.0781:0.0:0.9219:0.0	rs2789975;rs3814305	103	Q96F81	DISP1_HUMAN	D	103	ENSP00000355848:E103D;ENSP00000284476:E103D	ENSP00000284476:E103D	E	+	3	2	DISP1	221183097	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.341000	0.52151	2.652000	0.90054	0.650000	0.86243	GAG	G|0.844;T|0.156	0.156	strong		0.522	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
LHCGR	3973	hgsc.bcm.edu	37	2	48921375	48921375	+	Missense_Mutation	SNP	T	T	C	rs2293275	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48921375T>C	ENST00000294954.7	-	10	956	c.935A>G	c.(934-936)aAt>aGt	p.N312S	LHCGR_ENST00000405626.1_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000403273.1_Missense_Mutation_p.N312S|LHCGR_ENST00000401907.1_Missense_Mutation_p.N312S|LHCGR_ENST00000344775.3_Missense_Mutation_p.N250S	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	312			N -> S (in dbSNP:rs2293275). {ECO:0000269|PubMed:2244890, ECO:0000269|PubMed:7556872}.	Missing (in Ref. 3; AAA70231). {ECO:0000305}.	activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TGTTTTGTTATTCACTTTCCT	0.323													T|||	2960	0.591054	0.2352	0.6657	5008	,	,		18928	0.9276		0.6402	False		,,,				2504	0.6217				p.N312S		Atlas-SNP	.											.	LHCGR	154	.	0			c.A935G						PASS	.	T	SER/ASN,	1307,3093	429.3+/-342.2	203,901,1096	137.0	102.0	114.0		935,	3.9	0.8	2	dbSNP_100	114	5074,3516	612.9+/-396.0	1492,2090,713	yes	missense,intron	LHCGR,STON1-GTF2A1L	NM_000233.3,NM_001198593.1	46,	1695,2991,1809	CC,CT,TT		40.9313,29.7045,49.1224	benign,	312/700,	48921375	6381,6609	2200	4295	6495	SO:0001583	missense	3973	exon10			TTGTTATTCACTT		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.935A>G	2.37:g.48921375T>C	ENSP00000294954:p.Asn312Ser	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	186	100	0.537634	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	37	CCDS1842.1	1387	0.63507326007326	125	0.2540650406504065	262	0.7237569060773481	529	0.9248251748251748	471	0.6213720316622692	T	4.051	0.007198	0.07866	0.297045	0.590687	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000403273;ENST00000401907	T;T;T;T	0.78003	-0.95;-0.77;-1.14;-0.97	5.09	3.9	0.45041	.	0.636684	0.17257	N	0.180938	T	0.00012	0.0000	N	0.17564	0.495	0.35412	P	0.20750199999999996	B	0.11235	0.004	B	0.08055	0.003	T	0.34030	-0.9845	8	.	.	.	.	9.9216	0.41468	0.0:0.0:0.3586:0.6414	rs2293275;rs17398177;rs52807977;rs60456102;rs2293275	312	P22888	LSHR_HUMAN	S	250;312;312;312	ENSP00000344301:N250S;ENSP00000294954:N312S;ENSP00000385847:N312S;ENSP00000385406:N312S	.	N	-	2	0	LHCGR	48774879	0.889000	0.30405	0.794000	0.32065	0.151000	0.21798	1.185000	0.32065	0.848000	0.35191	0.460000	0.39030	AAT	T|0.446;C|0.554	0.554	strong		0.323	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
TATDN1	83940	hgsc.bcm.edu	37	8	125499134	125499134	+	IGR	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:125499134C>T	ENST00000276692.6	-	0	1018				RP11-158K1.3_ENST00000518639.1_RNA|RNF139_ENST00000303545.3_Missense_Mutation_p.A415V	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)			CATCACTATGCACTAAATACA	0.373																																					p.A415V		Atlas-SNP	.											RNF139,colon,carcinoma,+1,1	RNF139	57	1	0			c.C1244T						scavenged	.						281.0	269.0	273.0					8																	125499134		2203	4300	6503	SO:0001628	intergenic_variant	11236	exon2			ACTATGCACTAAA	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.125499134C>T		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	244	4	0.0163934	NM_007218	B2R5J0|Q8TD02|Q9BY40	Missense_Mutation	SNP	ENST00000276692.6	37	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.718834	0.30503	.	.	ENSG00000170881	ENST00000303545	T	0.24538	1.85	5.25	5.25	0.73442	.	0.053948	0.64402	D	0.000001	T	0.31513	0.0799	L	0.60455	1.87	0.58432	D	0.999999	B	0.19445	0.036	B	0.23018	0.043	T	0.06409	-1.0828	10	0.46703	T	0.11	-9.2619	19.2104	0.93751	0.0:1.0:0.0:0.0	.	415	Q8WU17	RN139_HUMAN	V	415	ENSP00000304051:A415V	ENSP00000304051:A415V	A	+	2	0	RNF139	125568315	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	2.681000	0.46926	2.590000	0.87494	0.655000	0.94253	GCA	.	.	none		0.373	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026	
CCDC84	338657	hgsc.bcm.edu	37	11	118886117	118886117	+	Silent	SNP	C	C	T	rs10111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	141	0	0		WXS	Illumina HiSeq	Phase_I	189	76	0.402116	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	
ANKRD52	283373	hgsc.bcm.edu	37	12	56638455	56638455	+	Silent	SNP	G	G	A	rs201117129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56638455G>A	ENST00000267116.7	-	24	2824	c.2703C>T	c.(2701-2703)aaC>aaT	p.N901N	ANKRD52_ENST00000548241.1_5'UTR	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	901										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						CGGTCTGCCCGTTCTCAGCCG	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		17818	0.0		0.003	False		,,,				2504	0.0				p.N901N		Atlas-SNP	.											.	ANKRD52	81	.	0			c.C2703T						PASS	.	G		1,4327		0,1,2163	43.0	47.0	45.0		2703	-4.6	0.9	12		45	36,8510		1,34,4238	no	coding-synonymous	ANKRD52	NM_173595.3		1,35,6401	AA,AG,GG		0.4212,0.0231,0.2874		901/1077	56638455	37,12837	2164	4273	6437	SO:0001819	synonymous_variant	283373	exon24			CTGCCCGTTCTCA	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	26614	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit C"""						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.2703C>T	12.37:g.56638455G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	180	112	0.622222	NM_173595	A6NE79|B1Q2K2	Silent	SNP	ENST00000267116.7	37	CCDS44920.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595	
NAGK	55577	hgsc.bcm.edu	37	2	71304738	71304738	+	Silent	SNP	G	G	A	rs1043701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71304738G>A	ENST00000244204.6	+	9	878	c.816G>A	c.(814-816)gtG>gtA	p.V272V	NAGK_ENST00000443938.2_Silent_p.V268V|NAGK_ENST00000418807.3_Silent_p.V221V|NAGK_ENST00000443872.2_Silent_p.V124V|NAGK_ENST00000455662.2_Silent_p.V318V			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	272					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	TGGGCTCTGTGTGGAAGAGCT	0.612													G|||	250	0.0499201	0.0068	0.049	5008	,	,		16621	0.002		0.1153	False		,,,				2504	0.091				p.V318V		Atlas-SNP	.											.	NAGK	34	.	0			c.G954A						PASS	.	G		85,4321	68.7+/-106.4	2,81,2120	54.0	47.0	50.0		954	3.8	1.0	2	dbSNP_86	50	964,7636	201.1+/-244.7	56,852,3392	no	coding-synonymous	NAGK	NM_017567.4		58,933,5512	AA,AG,GG		11.2093,1.9292,8.0655		318/391	71304738	1049,11957	2203	4300	6503	SO:0001819	synonymous_variant	55577	exon9			CTCTGTGTGGAAG	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.816G>A	2.37:g.71304738G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Silent	SNP	ENST00000244204.6	37		108|108	0.04945054945054945|0.04945054945054945	3|3	0.006097560975609756|0.006097560975609756	19|19	0.052486187845303865|0.052486187845303865	0|0	0.0|0.0	86|86	0.11345646437994723|0.11345646437994723	G|G	10.65|10.65	1.410214|1.410214	0.25465|0.25465	0.019292|0.019292	0.112093|0.112093	ENSG00000124357|ENSG00000124357	ENST00000443938|ENST00000524537	.|.	.|.	.|.	5.63|5.63	3.81|3.81	0.43845|0.43845	.|.	.|0.060021	.|0.64402	.|D	.|0.000003	T|T	0.02727|0.02727	0.0082|0.0082	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.52283|0.52283	-0.8596|-0.8596	3|5	.|0.87932	.|D	.|0	-36.4269|-36.4269	10.4487|10.4487	0.44509|0.44509	0.1623:0.0:0.8377:0.0|0.1623:0.0:0.8377:0.0	rs1043701;rs3171860;rs1043701|rs1043701;rs3171860;rs1043701	.|.	.|.	.|.	Y|M	290|37	.|.	.|ENSP00000437192:V37M	C|V	+|+	2|1	0|0	NAGK|NAGK	71158246|71158246	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	2.907000|2.907000	0.48743|0.48743	1.376000|1.376000	0.46267|0.46267	0.655000|0.655000	0.94253|0.94253	TGT|GTG	G|0.935;A|0.065	0.065	strong		0.612	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1		
DDX53	168400	hgsc.bcm.edu	37	X	23019317	23019317	+	Missense_Mutation	SNP	G	G	T	rs5925720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	37	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	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	
MTRR	4552	hgsc.bcm.edu	37	5	7893005	7893005	+	Silent	SNP	C	C	T	rs34172797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7893005C>T	ENST00000264668.2	+	11	1647	c.1617C>T	c.(1615-1617)agC>agT	p.S539S	MTRR_ENST00000440940.2_Silent_p.S512S	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	539	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ATGAAGACAGCGGGAAAGCCC	0.458													C|||	45	0.00898562	0.0045	0.0259	5008	,	,		18337	0.0		0.0189	False		,,,				2504	0.002				p.S539S		Atlas-SNP	.											.	MTRR	74	.	0			c.C1617T						PASS	.	C	,	66,4340	61.7+/-98.7	0,66,2137	84.0	71.0	75.0		1536,1617	0.2	0.0	5	dbSNP_126	75	207,8393	89.4+/-151.6	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,269,6232	TT,TC,CC		2.407,1.498,2.099	,	512/699,539/726	7893005	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			AGACAGCGGGAAA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1617C>T	5.37:g.7893005C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.981;T|0.019	0.019	strong		0.458	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
FAM86B1	85002	hgsc.bcm.edu	37	8	12044264	12044264	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:12044264C>T	ENST00000448228.2	-	4	368	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	FAM86B1_ENST00000533513.1_Missense_Mutation_p.A141T|FAM86B1_ENST00000533852.2_Missense_Mutation_p.A141T|FAM86B1_ENST00000534520.1_Missense_Mutation_p.A107T|FAM86B1_ENST00000321602.8_Start_Codon_SNP_p.M1I	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	107										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TAGAGGGCGGCATCCCATGTG	0.612																																					p.A107T		Atlas-SNP	.											FAM86B1,NS,carcinoma,+2,1	FAM86B1	7	1	0			c.G319A						scavenged	.						1.0	1.0	1.0					8																	12044264		461	1070	1531	SO:0001583	missense	85002	exon4			GGGCGGCATCCCA	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.319G>A	8.37:g.12044264C>T	ENSP00000407067:p.Ala107Thr	Somatic	533	0	0		WXS	Illumina HiSeq	Phase_I	559	35	0.0626118	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	11.97|11.97	1.796969|1.796969	0.31777|0.31777	.|.	.|.	ENSG00000186523|ENSG00000186523	ENST00000431227;ENST00000340537;ENST00000448228;ENST00000534520;ENST00000526708;ENST00000524571;ENST00000533513|ENST00000321602;ENST00000526802	T;T;T;T;T|T	0.36340|0.24350	1.26;2.52;1.26;1.56;4.06|1.86	1.17|1.17	1.17|1.17	0.20885|0.20885	.|.	10.022600|.	0.01570|.	U|.	0.020538|.	T|T	0.33731|0.33731	0.0873|0.0873	M|M	0.90309|0.90309	3.105|3.105	0.80722|0.80722	D|D	1|1	P;P|B;B	0.46457|0.15719	0.878;0.749|0.014;0.003	D;P|B;B	0.64144|0.08055	0.922;0.624|0.003;0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	10|9	0.72032|0.87932	D|D	0.01|0	.|.	8.2654|8.2654	0.31810|0.31810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107;141|1;38	Q8N7N1;E9PN63|F6QN85;Q4KMP3	F86B1_HUMAN;.|.;.	T|I	141;107;107;107;141;79;141|1;102	ENSP00000342610:A107T;ENSP00000407067:A107T;ENSP00000431362:A107T;ENSP00000432790:A79T;ENSP00000435201:A141T|ENSP00000439686:M1I	ENSP00000342610:A107T|ENSP00000439686:M1I	A|M	-|-	1|3	0|0	FAM86B1|FAM86B1	12081673|12081673	1.000000|1.000000	0.71417|0.71417	0.088000|0.088000	0.20740|0.20740	0.049000|0.049000	0.14656|0.14656	6.283000|6.283000	0.72646|0.72646	0.950000|0.950000	0.37743|0.37743	0.173000|0.173000	0.16961|0.16961	GCC|ATG	.	.	none		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522388	144522388	+	Missense_Mutation	SNP	A	A	T	rs2272753	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144522388A>T	ENST00000262577.5	-	11	2669	c.2638T>A	c.(2638-2640)Tca>Aca	p.S880T		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	880	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			ggaggggatgaggaggaggag	0.652													A|||	560	0.111821	0.0363	0.1167	5008	,	,		16934	0.2431		0.1461	False		,,,				2504	0.0399				p.S880T		Atlas-SNP	.											.	ZC3H3	75	.	0			c.T2638A						PASS	.	A	THR/SER	208,4198		8,192,2003	29.0	28.0	29.0		2638	-8.5	0.0	8	dbSNP_100	29	945,7653		118,709,3472	no	missense	ZC3H3	NM_015117.2	58	126,901,5475	TT,TA,AA		10.9909,4.7208,8.8665	possibly-damaging	880/949	144522388	1153,11851	2203	4299	6502	SO:0001583	missense	23144	exon11			GGGATGAGGAGGA	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2638T>A	8.37:g.144522388A>T	ENSP00000262577:p.Ser880Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	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	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84611367	84611367	+	Missense_Mutation	SNP	G	G	C	rs34047645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:84611367G>C	ENST00000286744.5	+	18	2361	c.2137G>C	c.(2137-2139)Ggg>Cgg	p.G713R	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.G713R	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	713	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		G -> R (in dbSNP:rs34047645).			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)			GGGCTCTTGGGGGCCCTGCTC	0.542													G|||	271	0.0541134	0.0076	0.0879	5008	,	,		18592	0.001		0.168	False		,,,				2504	0.0307				p.G713R		Atlas-SNP	.											ADAMTSL3,NS,carcinoma,-2,2	ADAMTSL3	290	2	0			c.G2137C						PASS	.	G	ARG/GLY	161,4245	107.3+/-145.7	3,155,2045	83.0	85.0	84.0		2137	3.6	1.0	15	dbSNP_126	84	1369,7231	264.3+/-285.5	107,1155,3038	yes	missense	ADAMTSL3	NM_207517.2	125	110,1310,5083	CC,CG,GG		15.9186,3.6541,11.7638	benign	713/1692	84611367	1530,11476	2203	4300	6503	SO:0001583	missense	57188	exon18			TCTTGGGGGCCCT	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.2137G>C	15.37:g.84611367G>C	ENSP00000286744:p.Gly713Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	170	0.07783882783882784	4	0.008130081300813009	34	0.09392265193370165	0	0.0	132	0.1741424802110818	G	10.65	1.410885	0.25465	0.036541	0.159186	ENSG00000156218	ENST00000286744	T	0.53857	0.6	5.7	3.61	0.41365	.	2.009030	0.02079	N	0.052181	T	0.00109	0.0003	N	0.17564	0.495	0.23956	P	0.99635721	B;B	0.18863	0.002;0.031	B;B	0.23419	0.011;0.046	T	0.05886	-1.0858	9	0.33141	T	0.24	.	4.2229	0.10567	0.4509:0.0:0.5491:0.0	rs34047645	713;713	P82987-2;P82987	.;ATL3_HUMAN	R	713	ENSP00000286744:G713R	ENSP00000286744:G713R	G	+	1	0	ADAMTSL3	82402371	1.000000	0.71417	0.993000	0.49108	0.526000	0.34562	3.442000	0.52900	1.409000	0.46915	0.655000	0.94253	GGG	G|0.892;C|0.108	0.108	strong		0.542	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
TLR5	7100	hgsc.bcm.edu	37	1	223284599	223284599	+	Missense_Mutation	SNP	T	T	C	rs2072493	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:223284599T>C	ENST00000540964.1	-	4	2236	c.1775A>G	c.(1774-1776)aAt>aGt	p.N592S	TLR5_ENST00000342210.6_Missense_Mutation_p.N592S			O60602	TLR5_HUMAN	toll-like receptor 5	592	LRRCT.		Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.|N -> S (in dbSNP:rs2072493). {ECO:0000269|PubMed:14623910, ECO:0000269|PubMed:16027372}.		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)	p.N592S(1)		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)		ATTAAGCCAATTGATAAAAGT	0.413													T|||	702	0.140176	0.0045	0.2089	5008	,	,		21205	0.2728		0.162	False		,,,				2504	0.1155				p.N592S		Atlas-SNP	.											TLR5,NS,carcinoma,0,1	TLR5	86	1	1	Substitution - Missense(1)	stomach(1)	c.A1775G						PASS	.	T	SER/ASN	144,4262	102.1+/-140.7	1,142,2060	82.0	78.0	79.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1775	-10.0	0.0	1	dbSNP_96	79	1373,7227	265.4+/-286.1	112,1149,3039	yes	missense	TLR5	NM_003268.5	46	113,1291,5099	CC,CT,TT		15.9651,3.2683,11.6638	benign	592/859	223284599	1517,11489	2203	4300	6503	SO:0001583	missense	7100	exon6			AGCCAATTGATAA		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.1775A>G	1.37:g.223284599T>C	ENSP00000440643:p.Asn592Ser	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	180	77	0.427778	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	37	CCDS31033.1	362	0.16575091575091574	5	0.01016260162601626	67	0.1850828729281768	161	0.28146853146853146	129	0.17018469656992086	T	0.009	-1.858160	0.00558	0.032683	0.159651	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	T;T;T	0.23348	1.91;1.91;1.91	5.49	-10.0	0.00425	Cysteine-rich flanking region, C-terminal (1);	4.505430	0.00751	N	0.001067	T	0.00012	0.0000	N	0.11673	0.155	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28522	-1.0041	9	0.08599	T	0.76	.	0.5765	0.00704	0.2526:0.2392:0.143:0.3652	rs2072493;rs17748241	592	O60602	TLR5_HUMAN	S	592	ENSP00000440643:N592S;ENSP00000355846:N592S;ENSP00000340089:N592S	ENSP00000340089:N592S	N	-	2	0	TLR5	221351222	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-2.960000	0.00673	-1.542000	0.01725	-0.256000	0.11100	AAT	.	.	none		0.413	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
PPP2R1B	5519	hgsc.bcm.edu	37	11	111608216	111608216	+	IGR	SNP	T	T	A	rs61756429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:111608216T>A	ENST00000527614.1	-	0	5587				PPP2R1B_ENST00000311129.5_Missense_Mutation_p.N623Y|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.N559Y|PPP2R1B_ENST00000530787.1_5'Flank	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta						apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		GGGAAGTGGTTCTTGTCAGCC	0.597													T|||	10	0.00199681	0.0	0.0043	5008	,	,		20031	0.0		0.007	False		,,,				2504	0.0				p.N623Y		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1867T						PASS	.	T	TYR/ASN,TYR/ASN	13,4389	21.2+/-45.6	0,13,2188	155.0	128.0	137.0		1867,1675	4.1	1.0	11	dbSNP_129	137	86,8508	48.9+/-108.6	0,86,4211	yes	missense,missense	PPP2R1B	NM_181699.2,NM_181700.1	143,143	0,99,6399	AA,AT,TT		1.0007,0.2953,0.7618	possibly-damaging,possibly-damaging	623/668,559/604	111608216	99,12897	2201	4297	6498	SO:0001628	intergenic_variant	5519	exon15			AGTGGTTCTTGTC	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9303	protein-coding gene	gene with protein product	"""PP2A-A-beta"", ""protein phosphatase 2A, regulatory subunit A, beta isoform"""	603113	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"""			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741		11.37:g.111608216T>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_181699	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	10.82	1.458179	0.26161	0.002953	0.010007	ENSG00000137713	ENST00000311129;ENST00000426998	.	.	.	5.25	4.13	0.48395	.	0.617749	0.15812	N	0.243438	T	0.27933	0.0688	N	0.08118	0	0.80722	D	1	P;D	0.54207	0.94;0.965	P;P	0.51135	0.459;0.66	T	0.18493	-1.0335	9	0.87932	D	0	-10.7806	7.9175	0.29827	0.0:0.0914:0.0:0.9086	rs61756429	559;623	B4DWW5;P30154-2	.;.	Y	623;559	.	ENSP00000311344:N623Y	N	-	1	0	PPP2R1B	111113426	1.000000	0.71417	0.991000	0.47740	0.214000	0.24535	1.866000	0.39489	1.132000	0.42129	0.496000	0.49642	AAC	T|0.992;A|0.008	0.008	strong		0.597	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716	
FRMD7	90167	hgsc.bcm.edu	37	X	131212512	131212512	+	Silent	SNP	A	A	G	rs5977623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	105	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	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	
ZGPAT	84619	hgsc.bcm.edu	37	20	62339959	62339959	+	Silent	SNP	C	C	G	rs148155917		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62339959C>G	ENST00000328969.5	+	2	154	c.27C>G	c.(25-27)gcC>gcG	p.A9A	ARFRP1_ENST00000324228.2_5'Flank|ZGPAT_ENST00000357119.4_Silent_p.A9A|ARFRP1_ENST00000440854.1_5'Flank|ZGPAT_ENST00000355969.6_Silent_p.A9A|ARFRP1_ENST00000609142.1_5'Flank|ZGPAT_ENST00000448100.2_Silent_p.A9A|ZGPAT_ENST00000369967.3_Silent_p.A9A|ARFRP1_ENST00000607873.1_5'Flank|RP4-583P15.15_ENST00000490623.2_5'Flank|ARFRP1_ENST00000359715.5_5'Flank	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	9					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					TGGAGTCGGCCTTGCAGACCT	0.687																																					p.A9A		Atlas-SNP	.											.	ZGPAT	57	.	0			c.C27G						PASS	.						22.0	24.0	24.0					20																	62339959		2194	4282	6476	SO:0001819	synonymous_variant	84619	exon2			GTCGGCCTTGCAG	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"""Zinc fingers, CCCH-type domain containing"", ""G patch domain containing"""	15948	protein-coding gene	gene with protein product			"""KIAA1847"""	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.27C>G	20.37:g.62339959C>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	37	CCDS13534.1																																																																																			C|1.000;T|0.000	.	alt		0.687	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484	
SDHA	6389	hgsc.bcm.edu	37	5	236617	236617	+	Silent	SNP	G	G	T	rs200223188	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:236617G>T	ENST00000264932.6	+	10	1450	c.1335G>T	c.(1333-1335)tcG>tcT	p.S445S	SDHA_ENST00000504309.1_Silent_p.S445S|SDHA_ENST00000510361.1_Silent_p.S397S	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	445					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)	p.S445S(1)		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)	CCTGTGCCTCGGTACATGGTG	0.597									Familial Paragangliomas				G|||	2	0.000399361	0.0015	0.0	5008	,	,		17972	0.0		0.0	False		,,,				2504	0.0				p.S445S		Atlas-SNP	.											SDHA,NS,carcinoma,0,1	SDHA	80	1	1	Substitution - coding silent(1)	breast(1)	c.G1335T						scavenged	.						73.0	67.0	69.0					5																	236617		2203	4300	6503	SO:0001819	synonymous_variant	6389	exon10	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	TGCCTCGGTACAT	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.1335G>T	5.37:g.236617G>T		Somatic	324	1	0.00308642		WXS	Illumina HiSeq	Phase_I	310	7	0.0225806	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			A|0.002;G|0.988;T|0.011	0.011	strong		0.597	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
KMT2B	9757	hgsc.bcm.edu	37	19	36222857	36222857	+	Missense_Mutation	SNP	C	C	T	rs16970649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36222857C>T	ENST00000222270.7	+	27	5486	c.5486C>T	c.(5485-5487)cCt>cTt	p.P1829L	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.P1829L	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1829			P -> L (in dbSNP:rs16970649).		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)										GTTCTTGTCCCTGGAGCTCCT	0.627													C|||	502	0.10024	0.0794	0.0994	5008	,	,		15311	0.0883		0.1203	False		,,,				2504	0.1207				p.P1829L		Atlas-SNP	.											.	MLL4	229	.	0			c.C5486T						PASS	.	C	LEU/PRO	307,3673		10,287,1693	38.0	44.0	42.0		5486	4.3	0.9	19	dbSNP_123	42	797,7501		33,731,3385	yes	missense	MLL4	NM_014727.1	98	43,1018,5078	TT,TC,CC		9.6047,7.7136,8.9917	benign	1829/2716	36222857	1104,11174	1990	4149	6139	SO:0001583	missense	8085	exon27			TTGTCCCTGGAGC	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.5486C>T	19.37:g.36222857C>T	ENSP00000222270:p.Pro1829Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	223	0.1021062271062271	45	0.09146341463414634	36	0.09944751381215469	48	0.08391608391608392	94	0.12401055408970976	C	8.457	0.854334	0.17106	0.077136	0.096047	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.84146	-1.81;-1.81	5.33	4.3	0.51218	.	0.338090	0.21603	N	0.071911	T	0.05777	0.0151	L	0.49126	1.545	0.09310	P	1.0	B	0.12630	0.006	B	0.12156	0.007	T	0.61724	-0.7004	9	0.66056	D	0.02	.	13.0361	0.58873	0.0:0.9206:0.0:0.0794	rs16970649;rs56612720;rs60126381;rs16970649	1829	Q9UMN6	MLL4_HUMAN	L	1829	ENSP00000222270:P1829L;ENSP00000398837:P1829L	ENSP00000222270:P1829L	P	+	2	0	AD000671.1	40914697	0.132000	0.22450	0.860000	0.33809	0.622000	0.37654	1.659000	0.37387	1.390000	0.46547	0.655000	0.94253	CCT	C|0.902;T|0.098	0.098	strong		0.627	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
PNPO	55163	hgsc.bcm.edu	37	17	46023694	46023694	+	Silent	SNP	G	G	A	rs4378657	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:46023694G>A	ENST00000225573.4	+	6	657	c.552G>A	c.(550-552)ctG>ctA	p.L184L	PNPO_ENST00000434554.2_Silent_p.L141L|RP11-6N17.6_ENST00000582142.1_RNA|RP11-6N17.6_ENST00000580372.1_RNA|RP11-6N17.9_ENST00000582262.1_RNA|PNPO_ENST00000544840.1_Silent_p.L166L|PNPO_ENST00000534893.1_Silent_p.L89L	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	184					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						GACAGTATCTGAGAAAGAAAA	0.498													G|||	211	0.0421326	0.0219	0.0533	5008	,	,		19781	0.0		0.0775	False		,,,				2504	0.0685				p.L184L		Atlas-SNP	.											.	PNPO	18	.	0			c.G552A						PASS	.	G		162,4244	108.6+/-147.0	3,156,2044	77.0	80.0	79.0		552	4.2	1.0	17	dbSNP_111	79	677,7923	169.1+/-220.5	24,629,3647	no	coding-synonymous	PNPO	NM_018129.3		27,785,5691	AA,AG,GG		7.8721,3.6768,6.4509		184/262	46023694	839,12167	2203	4300	6503	SO:0001819	synonymous_variant	55163	exon6			GTATCTGAGAAAG	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.552G>A	17.37:g.46023694G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Silent	SNP	ENST00000225573.4	37	CCDS11522.1																																																																																			G|0.940;A|0.060	0.060	strong		0.498	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
MCAM	4162	hgsc.bcm.edu	37	11	119183067	119183067	+	Silent	SNP	C	C	T	rs35607515	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:119183067C>T	ENST00000264036.4	-	8	947	c.933G>A	c.(931-933)cgG>cgA	p.R311R	MCAM_ENST00000392814.1_Silent_p.R260R|MCAM_ENST00000530144.2_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	311	Ig-like C2-type 1.				anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		TGTGTTCCTTCCGGGCAGGCT	0.587													C|||	67	0.0133786	0.0	0.0259	5008	,	,		18127	0.0		0.0457	False		,,,				2504	0.0031				p.R311R		Atlas-SNP	.											MCAM,rectum,carcinoma,-2,4	MCAM	57	4	0			c.G933A						scavenged	.	C		42,4356	46.0+/-80.4	0,42,2157	88.0	82.0	84.0		933	1.6	0.5	11	dbSNP_126	84	338,8252	117.0+/-176.6	5,328,3962	no	coding-synonymous	MCAM	NM_006500.2		5,370,6119	TT,TC,CC		3.9348,0.955,2.9258		311/647	119183067	380,12608	2199	4295	6494	SO:0001819	synonymous_variant	4162	exon8			TTCCTTCCGGGCA	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6934	protein-coding gene	gene with protein product	"""Gicerin"""	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.933G>A	11.37:g.119183067C>T		Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	232	104	0.448276	NM_006500	O95812|Q59E86|Q6PHR3|Q6ZTR2	Silent	SNP	ENST00000264036.4	37	CCDS31690.1																																																																																			C|0.973;T|0.027	0.027	strong		0.587	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2		
EGFR	1956	hgsc.bcm.edu	37	7	55268916	55268916	+	Silent	SNP	C	C	T	rs2293347|rs587778251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:55268916C>T	ENST00000275493.2	+	25	3159	c.2982C>T	c.(2980-2982)gaC>gaT	p.D994D	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Silent_p.D941D|EGFR_ENST00000455089.1_Silent_p.D949D	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	994					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)	GTCCTACAGACTCCAACTTCT	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			t|||	710	0.141773	0.0129	0.1542	5008	,	,		18651	0.247		0.1113	False		,,,				2504	0.2301				p.D994D		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.C2982T						PASS	.	T		121,4285	90.6+/-129.3	1,119,2083	151.0	139.0	143.0		2982	3.8	1.0	7	dbSNP_100	143	795,7805	185.7+/-233.4	42,711,3547	no	coding-synonymous	EGFR	NM_005228.3		43,830,5630	TT,TC,CC		9.2442,2.7463,7.0429		994/1211	55268916	916,12090	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon25	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	TACAGACTCCAAC		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.2982C>T	7.37:g.55268916C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.894;T|0.106	0.106	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
C10orf71	118461	hgsc.bcm.edu	37	10	50534862	50534862	+	Silent	SNP	T	T	C	rs12411843	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50534862T>C	ENST00000374144.3	+	3	4560	c.4272T>C	c.(4270-4272)gaT>gaC	p.D1424D	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1424										endometrium(1)	1						TCTCCACTGATGACCTAGAGG	0.602													C|||	1521	0.303714	0.1316	0.3818	5008	,	,		14631	0.4127		0.333	False		,,,				2504	0.3384				p.D1424D		Atlas-SNP	.											.	C10orf71	179	.	0			c.T4272C						PASS	.	C	,	239,1145		19,201,472	29.0	33.0	32.0		4272,	-6.5	0.0	10	dbSNP_120	32	1018,2164		162,694,735	no	coding-synonymous,intron	C10orf71	NM_001135196.1,NM_199459.3	,	181,895,1207	CC,CT,TT		31.9925,17.2688,27.5296	,	1424/1436,	50534862	1257,3309	692	1591	2283	SO:0001819	synonymous_variant	118461	exon3			CACTGATGACCTA	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.4272T>C	10.37:g.50534862T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			T|0.690;C|0.310	0.310	strong		0.602	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
DSPP	1834	hgsc.bcm.edu	37	4	88537384	88537384	+	Silent	SNP	T	T	C	rs201295377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537384T>C	ENST00000282478.7	+	4	3603	c.3570T>C	c.(3568-3570)agT>agC	p.S1190S	DSPP_ENST00000399271.1_Silent_p.S1190S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1190	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)		gtgatagcagtgacagcagcg	0.572													-|||	804	0.160543	0.0817	0.245	5008	,	,		24963	0.1032		0.2744	False		,,,				2504	0.1493				p.S1190S		Atlas-SNP	.											DSPP,rectum,carcinoma,+1,1	DSPP	174	1	0			c.T3570C						PASS	.	T		300,2970		10,280,1345	48.0	68.0	61.0		3570		0.4	4	dbSNP_134	61	1176,4626		111,954,1836	no	coding-synonymous	DSPP	NM_014208.3		121,1234,3181	CC,CT,TT		20.2689,9.1743,16.2698		1190/1302	88537384	1476,7596	1635	2901	4536	SO:0001819	synonymous_variant	1834	exon5			TAGCAGTGACAGC	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.3570T>C	4.37:g.88537384T>C		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	211	91	0.43128	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.572	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
DHX36	170506	hgsc.bcm.edu	37	3	154018887	154018887	+	Missense_Mutation	SNP	G	G	C	rs9438	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:154018887G>C	ENST00000496811.1	-	10	1327	c.1247C>G	c.(1246-1248)tCc>tGc	p.S416C	DHX36_ENST00000544526.1_Missense_Mutation_p.S416C|DHX36_ENST00000308361.6_Missense_Mutation_p.S416C|DHX36_ENST00000329463.5_Missense_Mutation_p.S416C	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	416			S -> C (in dbSNP:rs9438). {ECO:0000269|PubMed:12198572, ECO:0000269|PubMed:14731398, ECO:0000269|PubMed:15489334}.		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)			CTTAAACTGGGATCTGTGTTC	0.318													G|||	2075	0.414337	0.3949	0.4049	5008	,	,		16991	0.4841		0.4115	False		,,,				2504	0.3783				p.S416C		Atlas-SNP	.											.	DHX36	98	.	0			c.C1247G	GRCh37	CM065110	DHX36	M	rs9438	PASS	.	G	CYS/SER,CYS/SER	1576,2830	480.8+/-358.9	297,982,924	82.0	85.0	84.0		1247,1247	5.9	1.0	3	dbSNP_52	84	3461,5139	504.9+/-376.3	716,2029,1555	yes	missense,missense	DHX36	NM_001114397.1,NM_020865.2	112,112	1013,3011,2479	CC,CG,GG		40.2442,35.7694,38.7283	benign,benign	416/995,416/1009	154018887	5037,7969	2203	4300	6503	SO:0001583	missense	170506	exon10			AACTGGGATCTGT	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.1247C>G	3.37:g.154018887G>C	ENSP00000417078:p.Ser416Cys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	74	0.435294	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	37	CCDS3171.1	890	0.4075091575091575	185	0.37601626016260165	143	0.39502762430939226	261	0.4562937062937063	301	0.3970976253298153	G	13.42	2.231610	0.39399	0.357694	0.402442	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.14640	2.49;2.49;2.49;2.49;2.49	5.89	5.89	0.94794	.	0.045801	0.85682	D	0.000000	T	0.00012	0.0000	L	0.39898	1.24	0.27372	P	0.9556698	B;D;B	0.55172	0.007;0.97;0.001	B;P;B	0.52424	0.015;0.698;0.003	T	0.55335	-0.8157	9	0.42905	T	0.14	.	16.4981	0.84250	0.0:0.0:0.8686:0.1314	rs9438;rs355766;rs1043835;rs3172333;rs17857087;rs52805216;rs59981318;rs9438	416;416;416	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	C	416;416;416;416;330	ENSP00000417078:S416C;ENSP00000309296:S416C;ENSP00000444247:S416C;ENSP00000330113:S416C;ENSP00000419862:S330C	ENSP00000309296:S416C	S	-	2	0	DHX36	155501581	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.847000	0.62867	2.788000	0.95919	0.557000	0.71058	TCC	G|0.613;C|0.387	0.387	strong		0.318	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865	
MADD	8567	hgsc.bcm.edu	37	11	47306585	47306585	+	Missense_Mutation	SNP	G	G	A	rs1051006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47306585G>A	ENST00000311027.5	+	13	2416	c.2251G>A	c.(2251-2253)Gtg>Atg	p.V751M	MADD_ENST00000402192.2_Missense_Mutation_p.V751M|MADD_ENST00000407859.3_Missense_Mutation_p.V751M|MADD_ENST00000349238.3_Missense_Mutation_p.V751M|MADD_ENST00000402799.1_Missense_Mutation_p.V751M|MADD_ENST00000406482.1_Missense_Mutation_p.V751M|MADD_ENST00000395336.3_Missense_Mutation_p.V751M|MADD_ENST00000395344.3_Missense_Mutation_p.V751M|MADD_ENST00000342922.4_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	59	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	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		
SPHKAP	80309	hgsc.bcm.edu	37	2	228855866	228855866	+	Missense_Mutation	SNP	G	G	C	rs16824283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228855866G>C	ENST00000392056.3	-	11	4855	c.4809C>G	c.(4807-4809)agC>agG	p.S1603R	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S1574R	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1603			S -> R (in dbSNP:rs16824283).			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCCTCTGGGGGCTGGCTGTTC	0.577													G|||	879	0.175519	0.0303	0.1931	5008	,	,		14524	0.2282		0.3022	False		,,,				2504	0.1748				p.S1603R		Atlas-SNP	.											SPHKAP_ENST00000392056,colon,carcinoma,0,2	SPHKAP	750	2	0			c.C4809G						PASS	.	G	ARG/SER,ARG/SER	296,4110	158.9+/-191.5	11,274,1918	43.0	45.0	44.0		4809,4722	-2.2	0.0	2	dbSNP_123	44	2318,6282	381.5+/-340.0	321,1676,2303	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	110,110	332,1950,4221	CC,CG,GG		26.9535,6.7181,20.0984	probably-damaging,probably-damaging	1603/1701,1574/1672	228855866	2614,10392	2203	4300	6503	SO:0001583	missense	80309	exon11			CTGGGGGCTGGCT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4809C>G	2.37:g.228855866G>C	ENSP00000375909:p.Ser1603Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	435	0.19917582417582416	17	0.034552845528455285	77	0.212707182320442	120	0.2097902097902098	221	0.29155672823219	G	11.64	1.699048	0.30142	0.067181	0.269535	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.06608	3.28;3.28	6.17	-2.19	0.07015	A-kinase anchor 110kDa, C-terminal (1);	0.300797	0.43919	D	0.000501	T	0.00012	0.0000	L	0.48362	1.52	0.80722	P	0.0	D;P	0.54397	0.966;0.935	P;P	0.55923	0.787;0.613	T	0.19614	-1.0300	9	0.59425	D	0.04	.	13.8991	0.63792	0.6506:0.0:0.3494:0.0	rs16824283;rs16824283	1603;1574	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	R	1603;1574	ENSP00000375909:S1603R;ENSP00000339886:S1574R	ENSP00000339886:S1574R	S	-	3	2	SPHKAP	228564110	0.088000	0.21588	0.000000	0.03702	0.090000	0.18270	0.210000	0.17455	-0.511000	0.06514	-0.137000	0.14449	AGC	G|0.803;C|0.197	0.197	strong		0.577	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
GALNS	2588	hgsc.bcm.edu	37	16	88902183	88902183	+	Silent	SNP	G	G	A	rs1064315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88902183G>A	ENST00000268695.5	-	7	796	c.708C>T	c.(706-708)caC>caT	p.H236H	GALNS_ENST00000542788.1_Silent_p.H161H	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	236	Catalytic domain.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		AGACGGGTGCGTGCGTGGCGT	0.617													G|||	1586	0.316693	0.211	0.2767	5008	,	,		17738	0.5486		0.2724	False		,,,				2504	0.2945				p.H236H	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.C708T						PASS	.	G		920,3476	351.6+/-311.3	84,752,1362	135.0	112.0	119.0		708	-4.9	0.2	16	dbSNP_86	119	2205,6395	375.8+/-337.9	257,1691,2352	no	coding-synonymous	GALNS	NM_000512.4		341,2443,3714	AA,AG,GG		25.6395,20.9281,24.0459		236/523	88902183	3125,9871	2198	4300	6498	SO:0001819	synonymous_variant	2588	exon7			GGGTGCGTGCGTG	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.708C>T	16.37:g.88902183G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	93	91	0.978495	NM_000512	Q86VK3	Silent	SNP	ENST00000268695.5	37	CCDS10970.1																																																																																			G|0.715;A|0.285	0.285	strong		0.617	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
OR13J1	392309	hgsc.bcm.edu	37	9	35870001	35870001	+	Missense_Mutation	SNP	T	T	C	rs7044405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35870001T>C	ENST00000377981.2	-	1	460	c.398A>G	c.(397-399)cAc>cGc	p.H133R		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	133			H -> R (in dbSNP:rs7044405).			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(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			CATGAGCACGTGGTACCTGAG	0.622													t|||	3234	0.645767	0.7239	0.5951	5008	,	,		21305	0.6369		0.6193	False		,,,				2504	0.6125				p.H133R		Atlas-SNP	.											OR13J1,colon,carcinoma,-1,1	OR13J1	37	1	0			c.A398G						PASS	.	C	ARG/HIS	3255,1151	403.5+/-332.8	1197,861,145	49.0	58.0	55.0		398	1.8	0.2	9	dbSNP_116	55	5225,3375	497.7+/-374.6	1565,2095,640	yes	missense	OR13J1	NM_001004487.1	29	2762,2956,785	CC,CT,TT		39.2442,26.1235,34.7993	benign	133/313	35870001	8480,4526	2203	4300	6503	SO:0001583	missense	392309	exon1			AGCACGTGGTACC		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"""GPCR / Class A : Olfactory receptors"""	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.398A>G	9.37:g.35870001T>C	ENSP00000367219:p.His133Arg	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_001004487	B2RN66|Q6IF20|Q96R40	Missense_Mutation	SNP	ENST00000377981.2	37	CCDS35011.1	1427	0.6533882783882784	370	0.7520325203252033	232	0.6408839779005525	368	0.6433566433566433	457	0.6029023746701847	C	6.564	0.472352	0.12461	0.738765	0.607558	ENSG00000168828	ENST00000377981	T	0.01323	5.01	4.62	1.76	0.24704	GPCR, rhodopsin-like superfamily (1);	0.112691	0.40302	N	0.001130	T	0.00012	0.0000	N	0.20845	0.615	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04178	-1.0971	9	0.54805	T	0.06	.	9.2108	0.37318	0.0:0.1349:0.4611:0.404	rs7044405;rs52813667;rs61017639;rs7044405	133	Q8NGT2	O13J1_HUMAN	R	133	ENSP00000367219:H133R	ENSP00000367219:H133R	H	-	2	0	OR13J1	35860001	0.000000	0.05858	0.215000	0.23724	0.365000	0.29674	-0.105000	0.10907	0.143000	0.18926	-1.964000	0.00472	CAC	T|0.347;C|0.653	0.653	strong		0.622	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1		
APOL5	80831	hgsc.bcm.edu	37	22	36122433	36122433	+	Silent	SNP	T	T	C	rs16996023	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36122433T>C	ENST00000249044.2	+	3	318	c.318T>C	c.(316-318)ttT>ttC	p.F106F		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	106					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						TCTCATATTTTCCTTTGCACA	0.438													T|||	208	0.0415335	0.0923	0.0245	5008	,	,		22372	0.0		0.0268	False		,,,				2504	0.0429				p.F106F		Atlas-SNP	.											.	APOL5	45	.	0			c.T318C						PASS	.	T		306,4100	165.4+/-196.9	10,286,1907	79.0	75.0	77.0		318	-4.0	0.0	22	dbSNP_123	77	217,8383	90.2+/-152.3	6,205,4089	no	coding-synonymous	APOL5	NM_030642.1		16,491,5996	CC,CT,TT		2.5233,6.9451,4.0212		106/434	36122433	523,12483	2203	4300	6503	SO:0001819	synonymous_variant	80831	exon3			ATATTTTCCTTTG	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.318T>C	22.37:g.36122433T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	28	0.35	NM_030642	Q5TFL9|Q9UGW5	Silent	SNP	ENST00000249044.2	37	CCDS13920.1																																																																																			T|0.960;C|0.040	0.040	strong		0.438	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
DNAJC16	23341	hgsc.bcm.edu	37	1	15892415	15892415	+	Splice_Site	SNP	A	A	C	rs2236215	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15892415A>C	ENST00000375847.3	+	12	1764	c.1600A>C	c.(1600-1602)Agg>Cgg	p.R534R	DNAJC16_ENST00000483270.1_3'UTR|DNAJC16_ENST00000375838.1_Splice_Site_p.R534R|DNAJC16_ENST00000375849.1_Splice_Site_p.R534R|RP4-680D5.8_ENST00000606186.1_RNA	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	534					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TGGTTTTAGGAGGGAAATGAT	0.408													C|||	1443	0.288139	0.6082	0.219	5008	,	,		17020	0.0565		0.2326	False		,,,				2504	0.2004				p.R534R		Atlas-SNP	.											.	DNAJC16	59	.	0			c.A1600C						PASS	.	C		2537,1869	540.2+/-375.5	739,1059,405	276.0	305.0	295.0		1600	5.0	1.0	1	dbSNP_98	295	2129,6471	715.6+/-406.1	253,1623,2424	yes	coding-synonymous-near-splice	DNAJC16	NM_015291.2		992,2682,2829	CC,CA,AA		24.7558,42.4194,35.8757		534/783	15892415	4666,8340	2203	4300	6503	SO:0001630	splice_region_variant	23341	exon12			TTTAGGAGGGAAA	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"""Heat shock proteins / DNAJ (HSP40)"""	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.1599-1A>C	1.37:g.15892415A>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	154	58	0.376623	NM_015291	Q68D57|Q86X32|Q8N5P4	Silent	SNP	ENST00000375847.3	37	CCDS30606.1																																																																																			A|0.668;C|0.332	0.332	strong		0.408	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291	Silent
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119938782	119938782	+	Silent	SNP	T	T	C	rs2228568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:119938782T>C	ENST00000297350.4	-	4	1146	c.768A>G	c.(766-768)ttA>ttG	p.L256L		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	256	Death 1.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			GATGTTTCCATAACTTCAGCA	0.373													T|||	394	0.0786741	0.0461	0.0663	5008	,	,		20402	0.0069		0.1223	False		,,,				2504	0.1605				p.L256L		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.A768G						PASS	.	T		252,4154	144.6+/-179.5	2,248,1953	230.0	222.0	225.0		768	3.4	1.0	8	dbSNP_98	225	1139,7459	234.7+/-267.5	88,963,3248	no	coding-synonymous	TNFRSF11B	NM_002546.3		90,1211,5201	CC,CT,TT		13.2473,5.7195,10.6967		256/402	119938782	1391,11613	2203	4299	6502	SO:0001819	synonymous_variant	4982	exon4			TTTCCATAACTTC	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.768A>G	8.37:g.119938782T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	169	63	0.372781	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Silent	SNP	ENST00000297350.4	37	CCDS6326.1																																																																																			T|0.902;C|0.098	0.098	strong		0.373	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
KRT20	54474	hgsc.bcm.edu	37	17	39037000	39037000	+	Missense_Mutation	SNP	G	G	A	rs143378689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39037000G>A	ENST00000167588.3	-	3	537	c.496C>T	c.(496-498)Cgt>Tgt	p.R166C		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	166	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				ACTGTTAGACGTATTCCTCTC	0.373													G|||	8	0.00159744	0.0	0.0014	5008	,	,		18332	0.0		0.007	False		,,,				2504	0.0				p.R166C		Atlas-SNP	.											.	KRT20	38	.	0			c.C496T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	147.0	136.0	140.0		496	0.3	0.0	17	dbSNP_134	140	34,8566	23.4+/-69.3	0,34,4266	yes	missense	KRT20	NM_019010.2	180	0,40,6463	AA,AG,GG		0.3953,0.1362,0.3076	possibly-damaging	166/425	39037000	40,12966	2203	4300	6503	SO:0001583	missense	54474	exon3			TTAGACGTATTCC	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.496C>T	17.37:g.39037000G>A	ENSP00000167588:p.Arg166Cys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	37	CCDS11379.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	11.51	1.659928	0.29515	0.001362	0.003953	ENSG00000171431	ENST00000167588	D	0.91792	-2.91	5.45	0.338	0.15974	Filament (1);	0.496636	0.16942	N	0.193234	D	0.83529	0.5274	L	0.56199	1.76	0.19300	N	0.999978	B	0.29886	0.26	B	0.24974	0.057	T	0.77332	-0.2627	10	0.62326	D	0.03	.	8.0078	0.30336	0.0704:0.0844:0.6039:0.2414	.	166	P35900	K1C20_HUMAN	C	166	ENSP00000167588:R166C	ENSP00000167588:R166C	R	-	1	0	KRT20	36290526	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.030000	0.13688	0.242000	0.21303	0.591000	0.81541	CGT	G|0.996;A|0.004	0.004	strong		0.373	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
CFAP46	54777	hgsc.bcm.edu	37	10	134659612	134659612	+	Silent	SNP	G	G	A	rs143293571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:134659612G>A	ENST00000368586.5	-	44	6487	c.6387C>T	c.(6385-6387)acC>acT	p.T2129T	TTC40_ENST00000263170.5_Silent_p.T290T	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GGCTGGTGGTGGTCCTGTCTT	0.672													G|||	3	0.000599042	0.0	0.0029	5008	,	,		13261	0.0		0.0	False		,,,				2504	0.001				p.T2129T		Atlas-SNP	.											.	TTC40	100	.	0			c.C6387T						PASS	.	G		0,4398		0,0,2199	34.0	35.0	34.0		1323	-6.1	0.0	10	dbSNP_134	34	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	C10orf92	NM_001200049.1		0,5,6494	AA,AG,GG		0.0581,0.0,0.0385		441/1028	134659612	5,12993	2199	4300	6499	SO:0001819	synonymous_variant	54777	exon44			GGTGGTGGTCCTG																												ENST00000368586.5:c.6387C>T	10.37:g.134659612G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.999;A|0.001	0.001	strong		0.672	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
KCNJ12	3768	hgsc.bcm.edu	37	17	21318770	21318770	+	Missense_Mutation	SNP	G	G	A	rs3752033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:21318770G>A	ENST00000583088.1	+	3	1011	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R39Q	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	39					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GTGCACACGCGGCGCAGGTGC	0.617										Prostate(3;0.18)			.|||	1734	0.346246	0.1505	0.366	5008	,	,		36674	0.4812		0.3559	False		,,,				2504	0.4479				p.R39Q		Atlas-SNP	.											.	.	.	.	0			c.G116A						PASS	.	G	GLN/ARG	526,3880		0,526,1677	114.0	87.0	96.0		116	5.3	1.0	17	dbSNP_107	96	2294,6306		0,2294,2006	yes	missense	KCNJ12	NM_021012.4	43	0,2820,3683	AA,AG,GG		26.6744,11.9383,21.6823	possibly-damaging	39/434	21318770	2820,10186	2203	4300	6503	SO:0001583	missense	100134444	exon3			ACACGCGGCGCAG	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.116G>A	17.37:g.21318770G>A	ENSP00000463778:p.Arg39Gln	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	160	31	0.19375	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	714	0.3269230769230769	78	0.15853658536585366	121	0.3342541436464088	267	0.46678321678321677	248	0.32717678100263853	G	22.8	4.332021	0.81801	0.119383	0.266744	ENSG00000184185	ENST00000331718	T	0.61980	0.06	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.193728	0.40385	U	0.001108	T	0.00012	0.0000	L	0.52759	1.655	0.58432	D	0.999999	P	0.37276	0.589	B	0.36766	0.232	T	0.43909	-0.9362	10	0.42905	T	0.14	.	19.026	0.92932	0.0:0.0:1.0:0.0	rs3752033;rs3752033	39	Q14500	IRK12_HUMAN	Q	39	ENSP00000328150:R39Q	ENSP00000328150:R39Q	R	+	2	0	KCNJ12	21259363	1.000000	0.71417	0.985000	0.45067	0.979000	0.70002	9.690000	0.98676	2.506000	0.84524	0.591000	0.81541	CGG	G|0.743;A|0.257	0.257	strong		0.617	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
AGBL4	84871	hgsc.bcm.edu	37	1	49511424	49511424	+	Silent	SNP	A	A	G	rs3934240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:49511424A>G	ENST00000371839.1	-	5	542	c.426T>C	c.(424-426)caT>caC	p.H142H	RP11-141A19.1_ENST00000456002.1_RNA|AGBL4_ENST00000371838.1_Silent_p.H142H|AGBL4_ENST00000371836.1_Silent_p.H142H	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	142					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.H142H(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		AGTTCTTCCTATGGTCCGGGC	0.403													A|||	1127	0.22504	0.0401	0.2608	5008	,	,		18029	0.4246		0.1889	False		,,,				2504	0.2812				p.H142H		Atlas-SNP	.											AGBL4,NS,carcinoma,0,1	AGBL4	54	1	1	Substitution - coding silent(1)	stomach(1)	c.T426C						PASS	.	A		103,1281		3,97,592	97.0	82.0	87.0		426	-0.5	1.0	1	dbSNP_108	87	703,2479		82,539,970	no	coding-synonymous	AGBL4	NM_032785.3		85,636,1562	GG,GA,AA		22.093,7.4422,17.6522		142/504	49511424	806,3760	692	1591	2283	SO:0001819	synonymous_variant	84871	exon5			CTTCCTATGGTCC	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 6"""					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.426T>C	1.37:g.49511424A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_032785	B3KT26|B4DG37	Silent	SNP	ENST00000371839.1	37	CCDS44137.1																																																																																			A|0.796;G|0.204	0.204	strong		0.403	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785	
ANKEF1	63926	hgsc.bcm.edu	37	20	10030452	10030452	+	Missense_Mutation	SNP	G	G	A	rs524625	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:10030452G>A	ENST00000378380.3	+	6	1564	c.1235G>A	c.(1234-1236)gGa>gAa	p.G412E	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.G412E|ANKEF1_ENST00000488991.1_3'UTR	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	412			G -> E (in dbSNP:rs524625).				calcium ion binding (GO:0005509)										GGATCGTATGGACCTAAGAAA	0.413													G|||	980	0.195687	0.2799	0.1556	5008	,	,		19334	0.0069		0.2604	False		,,,				2504	0.2382				p.G412E		Atlas-SNP	.											.	.	.	.	0			c.G1235A						PASS	.	G	GLU/GLY,GLU/GLY	1155,3247		155,845,1201	45.0	53.0	50.0		1235,1235	5.9	1.0	20	dbSNP_83	50	2224,6370		292,1640,2365	yes	missense,missense	ANKRD5	NM_022096.4,NM_198798.1	98,98	447,2485,3566	AA,AG,GG		25.8785,26.2381,26.0003	probably-damaging,probably-damaging	412/777,412/777	10030452	3379,9617	2201	4297	6498	SO:0001583	missense	63926	exon6			CGTATGGACCTAA	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1235G>A	20.37:g.10030452G>A	ENSP00000367631:p.Gly412Glu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_198798	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	387	0.1771978021978022	122	0.24796747967479674	65	0.17955801104972377	5	0.008741258741258742	195	0.25725593667546176	G	12.66	2.005879	0.35415	0.262381	0.258785	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.64991	-0.13;-0.13	5.86	5.86	0.93980	Ankyrin repeat-containing domain (1);	0.194693	0.53938	D	0.000057	T	0.00039	0.0001	L	0.52011	1.625	0.09310	P	0.999999164682	D	0.89917	1.0	D	0.71414	0.973	T	0.00294	-1.1840	9	0.26408	T	0.33	-20.6073	20.5632	0.99335	0.0:0.0:1.0:0.0	rs524625;rs52809150;rs58343015;rs524625	412	Q9NU02	ANKR5_HUMAN	E	412	ENSP00000367644:G412E;ENSP00000367631:G412E	ENSP00000367631:G412E	G	+	2	0	ANKRD5	9978452	0.997000	0.39634	0.995000	0.50966	0.044000	0.14063	1.841000	0.39240	2.937000	0.99478	0.650000	0.86243	GGA	G|0.769;A|0.231	0.231	strong		0.413	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
ARHGAP4	393	hgsc.bcm.edu	37	X	153174934	153174934	+	Missense_Mutation	SNP	T	T	G	rs145982906	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:153174934T>G	ENST00000350060.5	-	20	2511	c.2470A>C	c.(2470-2472)Agt>Cgt	p.S824R	ARHGAP4_ENST00000537206.1_Missense_Mutation_p.S801R|ARHGAP4_ENST00000370016.1_Missense_Mutation_p.S803R|ARHGAP4_ENST00000467421.1_5'Flank|ARHGAP4_ENST00000370028.3_Missense_Mutation_p.S864R|ARHGAP4_ENST00000393721.1_Missense_Mutation_p.S646R	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	824					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)					CCCTCGGGACTGCTCCCAGAC	0.672													T|||	15	0.00397351	0.0	0.0058	3775	,	,		11336	0.0		0.0109	False		,,,				2504	0.0				p.S864R		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.A2590C						PASS	.	T	ARG/SER,ARG/SER	8,3826		0,7,1,1625,569	34.0	32.0	32.0		2590,2470	-1.1	0.0	X	dbSNP_134	32	103,6623		1,80,21,2347,1849	yes	missense,missense	ARHGAP4	NM_001164741.1,NM_001666.4	110,110	1,87,22,3972,2418	GG,GT,G,TT,T		1.5314,0.2087,1.0511	benign,benign	864/987,824/947	153174934	111,10449	2202	4298	6500	SO:0001583	missense	393	exon21			CGGGACTGCTCCC	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.2470A>C	X.37:g.153174934T>G	ENSP00000203786:p.Ser824Arg	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001164741	Q14144|Q86UY3	Missense_Mutation	SNP	ENST00000350060.5	37	CCDS14736.1	8	0.004822182037371911	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010582010582010581	T	12.23	1.874696	0.33069	0.002087	0.015314	ENSG00000089820	ENST00000393721;ENST00000370028;ENST00000350060;ENST00000370016;ENST00000537206	T;T;T;T;T	0.10192	2.9;2.9;2.91;2.9;2.91	3.72	-1.07	0.09968	.	0.660669	0.12584	N	0.456216	T	0.02342	0.0072	N	0.24115	0.695	0.09310	N	1	B;B	0.23490	0.086;0.007	B;B	0.21917	0.037;0.002	T	0.43621	-0.9380	10	0.17369	T	0.5	.	3.6767	0.08294	0.0:0.2536:0.3356:0.4108	.	864;824	Q86UY3;P98171	.;RHG04_HUMAN	R	646;864;824;803;801	ENSP00000377322:S646R;ENSP00000359045:S864R;ENSP00000203786:S824R;ENSP00000359033:S803R;ENSP00000444169:S801R	ENSP00000203786:S824R	S	-	1	0	ARHGAP4	152828128	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.858000	0.04281	-0.444000	0.07170	0.427000	0.28365	AGT	T|0.993;G|0.007	0.007	strong		0.672	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666	
PRCP	5547	hgsc.bcm.edu	37	11	82564294	82564294	+	Missense_Mutation	SNP	T	T	G	rs2229437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:82564294T>G	ENST00000313010.3	-	3	530	c.336A>C	c.(334-336)gaA>gaC	p.E112D	PRCP_ENST00000535099.1_Missense_Mutation_p.E7D|PRCP_ENST00000393399.2_Missense_Mutation_p.E133D	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	112			E -> D (in dbSNP:rs2298668). {ECO:0000269|PubMed:14702039}.		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						TAGCTTTCAGTTCCTCAGCCA	0.383													T|||	698	0.139377	0.1051	0.1297	5008	,	,		17253	0.1131		0.1869	False		,,,				2504	0.1708				p.E133D		Atlas-SNP	.											.	PRCP	69	.	0			c.A399C						PASS	.	T	ASP/GLU,ASP/GLU	565,3841	250.0+/-257.2	43,479,1681	115.0	96.0	103.0		336,399	2.9	1.0	11	dbSNP_100	103	1545,7055	290.4+/-299.8	144,1257,2899	yes	missense,missense	PRCP	NM_005040.2,NM_199418.2	45,45	187,1736,4580	GG,GT,TT		17.9651,12.8234,16.2233	benign,benign	112/497,133/518	82564294	2110,10896	2203	4300	6503	SO:0001583	missense	5547	exon4			TTTCAGTTCCTCA	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.336A>C	11.37:g.82564294T>G	ENSP00000317362:p.Glu112Asp	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	252	113	0.448413	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Missense_Mutation	SNP	ENST00000313010.3	37	CCDS8262.1	302	0.1382783882783883	51	0.10365853658536585	52	0.143646408839779	57	0.09965034965034965	142	0.18733509234828497	T	14.55	2.569018	0.45798	0.128234	0.179651	ENSG00000137509	ENST00000313010;ENST00000393399;ENST00000535099;ENST00000531801;ENST00000534631;ENST00000527444;ENST00000531128;ENST00000534396;ENST00000529671;ENST00000528082;ENST00000532809;ENST00000533126;ENST00000534264	T;T;T;T;T;T;T;T;T;T;T;T;T	0.15718	2.4;2.4;2.4;2.4;2.4;2.4;2.4;2.4;2.4;2.4;2.4;2.4;2.4	5.27	2.94	0.34122	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.65677	2.01	0.23304	P	0.99794875	B;B	0.23540	0.001;0.087	B;B	0.27608	0.005;0.081	T	0.16041	-1.0416	8	.	.	.	-22.6635	7.2281	0.26026	0.0:0.3153:0.0:0.6847	rs2298668;rs17649579;rs52813874;rs2298668	112;133	P42785;A8MU24	PCP_HUMAN;.	D	112;133;7;7;7;7;7;7;71;7;58;7;7	ENSP00000317362:E112D;ENSP00000377055:E133D;ENSP00000442077:E7D;ENSP00000432004:E7D;ENSP00000431559:E7D;ENSP00000436141:E7D;ENSP00000431435:E7D;ENSP00000432506:E7D;ENSP00000434771:E71D;ENSP00000435071:E7D;ENSP00000437169:E58D;ENSP00000431496:E7D;ENSP00000436095:E7D	.	E	-	3	2	PRCP	82241942	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	0.547000	0.23299	0.864000	0.35578	0.528000	0.53228	GAA	T|0.854;G|0.146;A|0.000	0.146	strong		0.383	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040	
IQCB1	9657	hgsc.bcm.edu	37	3	121507231	121507231	+	Missense_Mutation	SNP	A	A	T	rs1141528	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:121507231A>T	ENST00000310864.6	-	12	1392	c.1178T>A	c.(1177-1179)aTt>aAt	p.I393N	IQCB1_ENST00000349820.6_Missense_Mutation_p.I260N	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	393	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.		I -> N (in dbSNP:rs1141528). {ECO:0000269|PubMed:15723066}.		cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TTTCTGGATAATCAGTGCTGA	0.403													A|||	214	0.0427316	0.0234	0.0533	5008	,	,		18049	0.004		0.1252	False		,,,				2504	0.0164				p.I393N		Atlas-SNP	.											.	IQCB1	50	.	0			c.T1178A						PASS	.	A	ASN/ILE,ASN/ILE	163,4243	109.1+/-147.4	2,159,2042	265.0	254.0	258.0		1178,779	2.2	1.0	3	dbSNP_86	258	1118,7482	231.1+/-265.2	74,970,3256	no	missense,missense	IQCB1	NM_001023570.2,NM_001023571.2	149,149	76,1129,5298	TT,TA,AA		13.0,3.6995,9.8493	benign,benign	393/599,260/466	121507231	1281,11725	2203	4300	6503	SO:0001583	missense	9657	exon12			TGGATAATCAGTG	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"""nephrocystin-5"""	609237	"""IQ calmodulin-binding motif containing 1"""			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1178T>A	3.37:g.121507231A>T	ENSP00000311505:p.Ile393Asn	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	212	114	0.537736	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	SNP	ENST00000310864.6	37	CCDS33837.1	130	0.05952380952380952	8	0.016260162601626018	19	0.052486187845303865	4	0.006993006993006993	99	0.13060686015831136	A	18.02	3.529303	0.64860	0.036995	0.13	ENSG00000173226	ENST00000310864;ENST00000349820	T;T	0.28069	1.63;1.63	5.76	2.19	0.27852	.	0.641392	0.17163	N	0.184591	T	0.00241	0.0007	L	0.34521	1.04	0.43110	P	0.005187000000000053	P;P	0.43542	0.81;0.744	B;B	0.44044	0.172;0.439	T	0.08953	-1.0697	9	0.30078	T	0.28	-1.7379	6.8388	0.23951	0.6371:0.0:0.3629:0.0	rs1141528;rs1141528	393;260	Q15051;Q15051-2	IQCB1_HUMAN;.	N	393;260	ENSP00000311505:I393N;ENSP00000323756:I260N	ENSP00000311505:I393N	I	-	2	0	IQCB1	122989921	1.000000	0.71417	0.992000	0.48379	0.971000	0.66376	1.142000	0.31540	0.555000	0.29079	0.528000	0.53228	ATT	.	.	weak		0.403	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642	
ADAM33	80332	hgsc.bcm.edu	37	20	3650234	3650234	+	Missense_Mutation	SNP	A	A	G	rs2280091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	127	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	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	
KRT35	3886	hgsc.bcm.edu	37	17	39633354	39633354	+	Missense_Mutation	SNP	C	C	T	rs12451652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39633354C>T	ENST00000393989.1	-	7	1364	c.1322G>A	c.(1321-1323)tGc>tAc	p.C441Y	KRT35_ENST00000246639.2_Missense_Mutation_p.C411Y	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	441	Tail.		C -> Y (in dbSNP:rs12451652).		anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				GCGGGGGCTGCAGTTTGTGCG	0.622													C|||	871	0.173922	0.0741	0.1225	5008	,	,		15175	0.2956		0.172	False		,,,				2504	0.2219				p.C441Y		Atlas-SNP	.											.	KRT35	58	.	0			c.G1322A						PASS	.	C	TYR/CYS	350,3512		14,322,1595	45.0	52.0	50.0		1322	4.4	1.0	17	dbSNP_120	50	1397,6857		107,1183,2837	no	missense	KRT35	NM_002280.4	194	121,1505,4432	TT,TC,CC		16.9251,9.0627,14.419	benign	441/456	39633354	1747,10369	1931	4127	6058	SO:0001583	missense	3886	exon7			GGGCTGCAGTTTG	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6453	protein-coding gene	gene with protein product	"""hard keratin type I 5"""	602764	"""keratin, hair, acidic, 5"""	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.1322G>A	17.37:g.39633354C>T	ENSP00000377558:p.Cys441Tyr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	CCDS11394.2	382	0.1749084249084249	36	0.07317073170731707	50	0.13812154696132597	164	0.2867132867132867	132	0.1741424802110818	C	12.96	2.095527	0.36952	0.090627	0.169251	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.83075	-1.68;-1.6	5.41	4.43	0.53597	.	0.094013	0.47852	D	0.000220	T	0.00039	0.0001	M	0.84219	2.685	0.29739	P	0.8372580000000001	B	0.14805	0.011	B	0.18561	0.022	T	0.11179	-1.0598	9	0.72032	D	0.01	.	11.9926	0.53184	0.0:0.8264:0.1736:0.0	rs12451652;rs59654549;rs12451652	441	Q92764	KRT35_HUMAN	Y	411;441	ENSP00000246639:C411Y;ENSP00000377558:C441Y	ENSP00000246639:C411Y	C	-	2	0	KRT35	36886880	0.991000	0.36638	0.996000	0.52242	0.696000	0.40369	1.906000	0.39887	1.496000	0.48567	0.563000	0.77884	TGC	C|0.825;T|0.175	0.175	strong		0.622	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
RTP2	344892	hgsc.bcm.edu	37	3	187416634	187416634	+	Silent	SNP	C	C	A	rs1973791	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:187416634C>A	ENST00000358241.1	-	2	758	c.330G>T	c.(328-330)ctG>ctT	p.L110L		NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	110					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			large_intestine(3)|lung(14)|skin(1)	18	all_cancers(143;4.06e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0515)		TGTTCTCCTCCAGCATGCTGG	0.672													C|||	2446	0.488419	0.0461	0.5893	5008	,	,		10353	0.7133		0.6362	False		,,,				2504	0.6309				p.L110L		Atlas-SNP	.											.	RTP2	38	.	0			c.G330T						PASS	.	C		670,3736		67,536,1600	25.0	22.0	23.0		330	4.0	1.0	3	dbSNP_92	23	5261,3331		1618,2025,653	no	coding-synonymous	RTP2	NM_001004312.2		1685,2561,2253	AA,AC,CC		38.7686,15.2065,45.6301		110/226	187416634	5931,7067	2203	4296	6499	SO:0001819	synonymous_variant	344892	exon2			CTCCTCCAGCATG	AY562236	CCDS33911.1	3q27.3	2014-02-20	2006-11-21		ENSG00000198471	ENSG00000198471		"""Receptor transporter proteins"""	32486	protein-coding gene	gene with protein product	"""receptor transporting protein 2"", ""zinc finger, 3CxxC-type 2"""	609138	"""receptor transporter protein 2"""			16271481, 15550249, 16720576	Standard	NM_001004312		Approved	MGC78665, Z3CXXC2	uc003fro.1	Q5QGT7	OTTHUMG00000156458	ENST00000358241.1:c.330G>T	3.37:g.187416634C>A		Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	252	225	0.892857	NM_001004312	Q6NVH4	Silent	SNP	ENST00000358241.1	37	CCDS33911.1																																																																																			C|0.468;A|0.532	0.532	strong		0.672	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312	
ACADS	35	hgsc.bcm.edu	37	12	121176083	121176083	+	Splice_Site	SNP	G	G	A	rs1799958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:121176083G>A	ENST00000242592.4	+	6	776	c.625G>A	c.(625-627)Ggc>Agc	p.G209S	ACADS_ENST00000411593.2_Splice_Site_p.G205S|RP11-173P15.7_ENST00000542620.1_RNA	NM_000017.2	NP_000008.1	P16219	ACADS_HUMAN	acyl-CoA dehydrogenase, C-2 to C-3 short chain	209			G -> S (86% of wild-type activity; confers susceptibility to ethylmalonicaciduria; dbSNP:rs1799958). {ECO:0000269|PubMed:11134486, ECO:0000269|PubMed:9499414}.		butyrate catabolic process (GO:0046359)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|protein homotetramerization (GO:0051289)|response to glucocorticoid (GO:0051384)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|butyryl-CoA dehydrogenase activity (GO:0004085)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)			central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			Flavin adenine dinucleotide(DB03147)	CTCCTTTCAGGGCATCAGTGC	0.627													G|||	913	0.182308	0.0333	0.3473	5008	,	,		7200	0.1052		0.2654	False		,,,				2504	0.2607				p.G209S		Atlas-SNP	.											.	ACADS	39	.	0			c.G625A	GRCh37	CM980010	ACADS	M	rs1799958	PASS	.	G	SER/GLY	284,4122	155.2+/-188.4	7,270,1926	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	625	4.6	1.0	12	dbSNP_89	61	2276,6324	384.0+/-341.0	313,1650,2337	yes	missense-near-splice	ACADS	NM_000017.2	56	320,1920,4263	AA,AG,GG		26.4651,6.4458,19.6832	probably-damaging	209/413	121176083	2560,10446	2203	4300	6503	SO:0001630	splice_region_variant	35	exon6			TTTCAGGGCATCA	M26393	CCDS9207.1	12q24.31	2012-07-13	2010-04-30		ENSG00000122971	ENSG00000122971	1.3.8.1		90	protein-coding gene	gene with protein product		606885	"""acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain"""			2565344	Standard	NM_000017		Approved	SCAD, ACAD3	uc001tza.4	P16219	OTTHUMG00000169203	ENST00000242592.4:c.625-1G>A	12.37:g.121176083G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_000017	P78331	Missense_Mutation	SNP	ENST00000242592.4	37	CCDS9207.1	386	0.17673992673992675	16	0.032520325203252036	114	0.3149171270718232	62	0.10839160839160839	194	0.2559366754617414	G	25.1	4.605761	0.87157	0.064458	0.264651	ENSG00000122971	ENST00000242592;ENST00000411593	D;D	0.99394	-5.82;-5.12	4.64	4.64	0.57946	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.00241	0.0007	M	0.67700	2.07	0.09310	P	0.9999999999969358	P;P;P	0.48350	0.909;0.664;0.664	P;B;B	0.54629	0.757;0.332;0.332	T	0.00000	-2.0058	8	.	.	.	.	17.4923	0.87708	0.0:0.0:1.0:0.0	rs1799958;rs2228408;rs11557837;rs17848088	205;209;209	E9PE82;E5KSD5;P16219	.;.;ACADS_HUMAN	S	209;205	ENSP00000242592:G209S;ENSP00000401045:G205S	.	G	+	1	0	ACADS	119660466	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	9.429000	0.97481	2.145000	0.66743	0.462000	0.41574	GGC	G|0.805;A|0.195	0.195	strong		0.627	ACADS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402861.1	NM_000017	Missense_Mutation
CARD10	29775	hgsc.bcm.edu	37	22	37906262	37906262	+	Missense_Mutation	SNP	C	C	T	rs9610775	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37906262C>T	ENST00000403299.1	-	5	1082	c.866G>A	c.(865-867)cGg>cAg	p.R289Q	CARD10_ENST00000406271.3_5'Flank|CARD10_ENST00000251973.5_Missense_Mutation_p.R289Q|CARD10_ENST00000494166.1_5'UTR			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	289			R -> Q (in dbSNP:rs9610775). {ECO:0000269|PubMed:11259443, ECO:0000269|PubMed:11356195}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CGCCGTCAGCCGCTGGTTCTC	0.662													C|||	1085	0.216653	0.2579	0.1282	5008	,	,		14625	0.1915		0.1948	False		,,,				2504	0.272				p.R289Q		Atlas-SNP	.											.	CARD10	55	.	0			c.G866A						PASS	.	C	GLN/ARG	1053,3353	366.6+/-317.9	134,785,1284	38.0	38.0	38.0		866	4.9	1.0	22	dbSNP_119	38	1557,7039	278.4+/-293.4	166,1225,2907	yes	missense	CARD10	NM_014550.3	43	300,2010,4191	TT,TC,CC		18.1131,23.8992,20.0738	probably-damaging	289/1033	37906262	2610,10392	2203	4298	6501	SO:0001583	missense	29775	exon4			GTCAGCCGCTGGT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.866G>A	22.37:g.37906262C>T	ENSP00000384570:p.Arg289Gln	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	392	0.1794871794871795	94	0.1910569105691057	46	0.1270718232044199	104	0.18181818181818182	148	0.19525065963060687	C	15.72	2.915945	0.52546	0.238992	0.181131	ENSG00000100065	ENST00000403299;ENST00000251973	T;T	0.34472	1.36;1.36	4.86	4.86	0.63082	.	0.252547	0.31909	N	0.006875	T	0.00012	0.0000	L	0.60455	1.87	0.35512	P	0.199303	D	0.67145	0.996	P	0.45829	0.494	T	0.20739	-1.0266	9	0.19590	T	0.45	-16.9506	18.0032	0.89203	0.0:1.0:0.0:0.0	rs9610775;rs9610775	289	Q9BWT7	CAR10_HUMAN	Q	289	ENSP00000384570:R289Q;ENSP00000251973:R289Q	ENSP00000251973:R289Q	R	-	2	0	CARD10	36236208	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	4.785000	0.62418	2.250000	0.74265	0.655000	0.94253	CGG	C|0.806;T|0.194	0.194	strong		0.662	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
SRCIN1	80725	hgsc.bcm.edu	37	17	36700163	36700163	+	Silent	SNP	C	C	T	rs35262222	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:36700163C>T	ENST00000264659.7	-	18	3536	c.3312G>A	c.(3310-3312)ccG>ccA	p.P1104P	SRCIN1_ENST00000398579.4_5'UTR|SRCIN1_ENST00000578925.1_Silent_p.P1138P	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	976					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						GAGAGGCCCCCGGAGTCACCA	0.632													C|||	412	0.0822684	0.1097	0.0634	5008	,	,		642	0.0615		0.0785	False		,,,				2504	0.0838				p.P1104P		Atlas-SNP	.											.	SRCIN1	66	.	0			c.G3312A						PASS	.	C		399,3865		21,357,1754	21.0	25.0	24.0		3312	-10.5	0.5	17	dbSNP_126	24	604,7888		22,560,3664	no	coding-synonymous	SRCIN1	NM_025248.2		43,917,5418	TT,TC,CC		7.1126,9.3574,7.863		1104/1184	36700163	1003,11753	2132	4246	6378	SO:0001819	synonymous_variant	80725	exon18			GGCCCCCGGAGTC		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.3312G>A	17.37:g.36700163C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_025248	Q75T46|Q8N4W8	Silent	SNP	ENST00000264659.7	37	CCDS45660.1																																																																																			C|0.926;T|0.074	0.074	strong		0.632	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	
TOPBP1	11073	hgsc.bcm.edu	37	3	133342218	133342218	+	Silent	SNP	C	C	T	rs4854738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:133342218C>T	ENST00000260810.5	-	18	3143	c.3012G>A	c.(3010-3012)gtG>gtA	p.V1004V		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1004					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						GGCCATCTTGCACTGCGCTGA	0.428								Other conserved DNA damage response genes					C|||	723	0.144369	0.1135	0.147	5008	,	,		17080	0.2222		0.0825	False		,,,				2504	0.1677				p.V1004V	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.G3012A						PASS	.	C		429,3491		22,385,1553	75.0	72.0	73.0		3012	2.8	1.0	3	dbSNP_111	73	614,7708		23,568,3570	no	coding-synonymous	TOPBP1	NM_007027.3		45,953,5123	TT,TC,CC		7.378,10.9439,8.5198		1004/1523	133342218	1043,11199	1960	4161	6121	SO:0001819	synonymous_variant	11073	exon18			ATCTTGCACTGCG	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.3012G>A	3.37:g.133342218C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	54	0.388489	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																			C|0.871;T|0.129	0.129	strong		0.428	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
TLK2	11011	hgsc.bcm.edu	37	17	60683503	60683503	+	Silent	SNP	A	A	G	rs8078132	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:60683503A>G	ENST00000326270.9	+	21	2206	c.1938A>G	c.(1936-1938)ccA>ccG	p.P646P	TLK2_ENST00000542523.1_Silent_p.P592P|TLK2_ENST00000582809.1_Silent_p.P475P|TLK2_ENST00000343388.7_Silent_p.P592P|TLK2_ENST00000346027.5_Silent_p.P624P	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	646	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						ATTTACCACCAGAGTGTTTTG	0.333													A|||	2636	0.526358	0.18	0.5086	5008	,	,		16721	0.8135		0.6153	False		,,,				2504	0.6196				p.P624P		Atlas-SNP	.											.	TLK2	223	.	0			c.A1872G						PASS	.	A	,	1162,3244	405.1+/-333.4	145,872,1186	72.0	66.0	68.0		1776,1872	4.9	1.0	17	dbSNP_116	68	5207,3393	637.4+/-399.2	1565,2077,658	no	coding-synonymous,coding-synonymous	TLK2	NM_001112707.1,NM_006852.3	,	1710,2949,1844	GG,GA,AA		39.4535,26.3731,48.9697	,	592/719,624/751	60683503	6369,6637	2203	4300	6503	SO:0001819	synonymous_variant	11011	exon20			ACCACCAGAGTGT	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1938A>G	17.37:g.60683503A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	29	0.337209	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Silent	SNP	ENST00000326270.9	37																																																																																				A|0.486;G|0.514	0.514	strong		0.333	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852	
SMARCAD1	56916	hgsc.bcm.edu	37	4	95170839	95170839	+	Missense_Mutation	SNP	G	G	A	rs11722476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:95170839G>A	ENST00000354268.4	+	7	813	c.740G>A	c.(739-741)aGt>aAt	p.S247N	SMARCAD1_ENST00000457823.2_Missense_Mutation_p.S247N			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	247			S -> N (in dbSNP:rs11722476). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17081983}.		ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.S247N(2)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		GAATCTAGCAGTAATTGGGAA	0.328													G|||	2311	0.461462	0.2012	0.5447	5008	,	,		17242	0.7024		0.3837	False		,,,				2504	0.5859				p.S247N		Atlas-SNP	.											SMARCAD1,NS,carcinoma,0,2	SMARCAD1	97	2	2	Substitution - Missense(2)	prostate(2)	c.G740A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	1071,3335	387.7+/-326.6	127,817,1259	95.0	100.0	99.0		740,740,740	0.2	1.0	4	dbSNP_120	99	3353,5239	494.8+/-373.9	661,2031,1604	yes	missense,missense,missense	SMARCAD1	NM_001128429.1,NM_001128430.1,NM_020159.3	46,46,46	788,2848,2863	AA,AG,GG		39.0247,24.3078,34.036	benign,benign,benign	247/1029,247/1029,247/1027	95170839	4424,8574	2203	4296	6499	SO:0001583	missense	56916	exon7			CTAGCAGTAATTG	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.740G>A	4.37:g.95170839G>A	ENSP00000346217:p.Ser247Asn	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	185	184	0.994595	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	37	CCDS3639.1	979	0.4482600732600733	99	0.20121951219512196	179	0.494475138121547	409	0.715034965034965	292	0.38522427440633245	G	9.170	1.020885	0.19433	0.243078	0.390247	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000536267;ENST00000354268	T;T;T	0.05319	3.46;3.46;3.46	6.16	0.199	0.15175	UBA-like (1);	0.738216	0.11822	N	0.526156	T	0.00012	0.0000	N	0.22421	0.69	0.27126	P	0.9620168	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13980	-1.0489	9	0.17369	T	0.5	-5.763	2.2078	0.03940	0.4369:0.122:0.3179:0.1232	rs11722476;rs17854343;rs52806084;rs60379623;rs11722476	247;247	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	N	247	ENSP00000351947:S247N;ENSP00000415576:S247N;ENSP00000346217:S247N	ENSP00000346217:S247N	S	+	2	0	SMARCAD1	95389862	0.990000	0.36364	0.987000	0.45799	0.998000	0.95712	0.160000	0.16462	0.069000	0.16605	0.650000	0.86243	AGT	G|0.609;A|0.391	0.391	strong		0.328	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159	
PARD3B	117583	hgsc.bcm.edu	37	2	206480393	206480393	+	Silent	SNP	C	C	T	rs17682782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:206480393C>T	ENST00000406610.2	+	23	3681	c.3474C>T	c.(3472-3474)gaC>gaT	p.D1158D	PARD3B_ENST00000349953.3_Silent_p.D1057D|PARD3B_ENST00000351153.1_Silent_p.D1089D|PARD3B_ENST00000358768.2_Silent_p.D1096D|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	1158					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)		TTCGACAAGACGTTCCGCCTT	0.632													C|||	173	0.0345447	0.0061	0.0447	5008	,	,		15892	0.0		0.1083	False		,,,				2504	0.0256				p.D1096D		Atlas-SNP	.											.	PARD3B	314	.	0			c.C3288T						PASS	.	C	,,	72,3878		2,68,1905	73.0	85.0	81.0		3267,3288,3171	-1.6	1.0	2	dbSNP_123	81	873,7407		52,769,3319	no	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	54,837,5224	TT,TC,CC		10.5435,1.8228,7.7269	,,	1089/1137,1096/1144,1057/1105	206480393	945,11285	1975	4140	6115	SO:0001819	synonymous_variant	117583	exon22			ACAAGACGTTCCG	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.3474C>T	2.37:g.206480393C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	205	98	0.478049	NM_152526	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				C|0.933;T|0.067	0.067	strong		0.632	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
ELAC2	60528	hgsc.bcm.edu	37	17	12898295	12898295	+	Silent	SNP	T	T	C	rs17552022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:12898295T>C	ENST00000338034.4	-	20	2132	c.1893A>G	c.(1891-1893)acA>acG	p.T631T	ELAC2_ENST00000426905.3_Silent_p.T591T|ELAC2_ENST00000395962.2_Silent_p.T612T	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	631					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CCAAATCACATGTTCGCAACA	0.532													T|||	252	0.0503195	0.0053	0.0793	5008	,	,		19149	0.001		0.1203	False		,,,				2504	0.0695				p.T631T		Atlas-SNP	.											.	ELAC2	48	.	0			c.A1893G						PASS	.	T	,,	99,4307	78.8+/-117.2	3,93,2107	178.0	185.0	183.0		1773,1893,1890	-10.6	0.0	17	dbSNP_123	183	1095,7505	228.6+/-263.6	76,943,3281	no	coding-synonymous,coding-synonymous,coding-synonymous	ELAC2	NM_001165962.1,NM_018127.6,NM_173717.1	,,	79,1036,5388	CC,CT,TT		12.7326,2.2469,9.1804	,,	591/787,631/827,630/826	12898295	1194,11812	2203	4300	6503	SO:0001819	synonymous_variant	60528	exon20			ATCACATGTTCGC	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1893A>G	17.37:g.12898295T>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	165	66	0.4	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	37	CCDS11164.1																																																																																			T|0.921;C|0.079	0.079	strong		0.532	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
TNS1	7145	hgsc.bcm.edu	37	2	218674614	218674614	+	Silent	SNP	C	C	T	rs13417442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:218674614C>T	ENST00000171887.4	-	30	5345	c.4893G>A	c.(4891-4893)acG>acA	p.T1631T	TNS1_ENST00000430930.1_Silent_p.T1610T|TNS1_ENST00000419504.1_Silent_p.T1617T	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	233	0	0		WXS	Illumina HiSeq	Phase_I	221	121	0.547511	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	
FLG	2312	hgsc.bcm.edu	37	1	152276889	152276889	+	Silent	SNP	A	A	G	rs3126067	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276889A>G	ENST00000368799.1	-	3	10508	c.10473T>C	c.(10471-10473)aaT>aaC	p.N3491N	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3491	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATTGTTCGTCATTACGAGTTT	0.577									Ichthyosis				a|||	2617	0.522564	0.7912	0.4553	5008	,	,		19155	0.6498		0.1511	False		,,,				2504	0.4581				p.N3491N		Atlas-SNP	.											.	FLG	900	.	0			c.T10473C						PASS	.	G		3036,1370	690.8+/-405.3	1065,906,232	295.0	287.0	289.0		10473	0.8	0.0	1	dbSNP_103	289	1298,7296	256.5+/-280.9	126,1046,3125	no	coding-synonymous	FLG	NM_002016.1		1191,1952,3357	GG,GA,AA		15.1036,31.094,33.3385		3491/4062	152276889	4334,8666	2203	4297	6500	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTCGTCATTACGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10473T>C	1.37:g.152276889A>G		Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	280	142	0.507143	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	
RASGEF1C	255426	hgsc.bcm.edu	37	5	179529124	179529124	+	Silent	SNP	G	G	A	rs7725201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:179529124G>A	ENST00000393371.2	-	12	1619	c.1323C>T	c.(1321-1323)taC>taT	p.Y441Y	RASGEF1C_ENST00000522500.1_Silent_p.Y290Y|RASGEF1C_ENST00000361132.4_Silent_p.Y441Y			Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	441	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	12	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCTCACTTTCGTAAGAAGCCA	0.443													A|||	4137	0.826078	0.8139	0.7882	5008	,	,		19228	0.7966		0.7684	False		,,,				2504	0.9591				p.Y441Y		Atlas-SNP	.											.	RASGEF1C	81	.	0			c.C1323T						PASS	.	A		3502,904	351.1+/-311.1	1384,734,85	91.0	83.0	85.0		1323	4.0	1.0	5	dbSNP_116	85	6706,1894	336.8+/-322.0	2617,1472,211	no	coding-synonymous	RASGEF1C	NM_175062.3		4001,2206,296	AA,AG,GG		22.0233,20.5175,21.5131		441/467	179529124	10208,2798	2203	4300	6503	SO:0001819	synonymous_variant	255426	exon13			ACTTTCGTAAGAA	AK093160	CCDS4452.1	5q35.3	2005-08-16			ENSG00000146090	ENSG00000146090			27400	protein-coding gene	gene with protein product						12477932	Standard	XM_006714839		Approved	FLJ35841	uc003mlr.3	Q8N431	OTTHUMG00000130914	ENST00000393371.2:c.1323C>T	5.37:g.179529124G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_175062	D3DWQ7|Q7Z4T0|Q8NA49	Silent	SNP	ENST00000393371.2	37	CCDS4452.1																																																																																			G|0.210;A|0.790	0.790	strong		0.443	RASGEF1C-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253506.2	NM_175062	
IQCE	23288	hgsc.bcm.edu	37	7	2644607	2644607	+	Silent	SNP	G	G	T	rs2293405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2644607G>T	ENST00000402050.2	+	19	1909	c.1725G>T	c.(1723-1725)gtG>gtT	p.V575V	IQCE_ENST00000404984.1_Silent_p.V524V|IQCE_ENST00000438376.2_Silent_p.V559V|IQCE_ENST00000325979.7_Silent_p.V510V	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	575						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)		CACCCAGCGTGCCAGGCCTCC	0.612													G|||	533	0.10643	0.1036	0.1527	5008	,	,		17926	0.0526		0.171	False		,,,				2504	0.0665				p.V575V		Atlas-SNP	.											IQCE,caecum,carcinoma,+2,2	IQCE	66	2	0			c.G1725T						PASS	.	G	,	399,3925		22,355,1785	38.0	45.0	43.0		1677,1725	1.1	0.0	7	dbSNP_100	43	1232,7270		96,1040,3115	no	coding-synonymous,coding-synonymous	IQCE	NM_001100390.1,NM_152558.3	,	118,1395,4900	TT,TG,GG		14.4907,9.2276,12.7164	,	559/680,575/696	2644607	1631,11195	2162	4251	6413	SO:0001819	synonymous_variant	23288	exon19			CAGCGTGCCAGGC	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.1725G>T	7.37:g.2644607G>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	61	23	0.377049	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	37	CCDS43542.1																																																																																			G|0.871;T|0.129	0.129	strong		0.612	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
PLEK	5341	hgsc.bcm.edu	37	2	68622914	68622914	+	Missense_Mutation	SNP	G	G	A	rs1063479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:68622914G>A	ENST00000234313.7	+	9	1198	c.1019G>A	c.(1018-1020)aGa>aAa	p.R340K		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	340	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.		R -> K (in dbSNP:rs1063479). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2768345, ECO:0000269|PubMed:2897630, ECO:0000269|Ref.3}.		actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		GAGTGGATCAGAGCCATCCAG	0.537													A|||	4294	0.857428	0.9554	0.817	5008	,	,		18760	0.9315		0.7087	False		,,,				2504	0.8303				p.R340K		Atlas-SNP	.											.	PLEK	64	.	0			c.G1019A						PASS	.	A	LYS/ARG	4073,333	174.8+/-204.3	1883,307,13	103.0	99.0	100.0		1019	4.5	1.0	2	dbSNP_86	100	6232,2368	394.4+/-344.7	2274,1684,342	yes	missense	PLEK	NM_002664.2	26	4157,1991,355	AA,AG,GG		27.5349,7.5579,20.7673	benign	340/351	68622914	10305,2701	2203	4300	6503	SO:0001583	missense	5341	exon9			GGATCAGAGCCAT	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.1019G>A	2.37:g.68622914G>A	ENSP00000234313:p.Arg340Lys	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	259	115	0.444015	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	1816	0.8315018315018315	462	0.9390243902439024	289	0.7983425414364641	525	0.9178321678321678	540	0.712401055408971	A	7.631	0.678873	0.14841	0.924421	0.724651	ENSG00000115956	ENST00000234313	T	0.74737	-0.87	5.65	4.49	0.54785	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.175903	0.64402	N	0.000010	T	0.00012	0.0000	N	0.04132	-0.27	0.53005	P	3.2000000000032E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45396	-0.9264	9	0.02654	T	1	.	10.0186	0.42029	0.8618:0.0:0.1382:0.0	rs1063479;rs2070172;rs3204524;rs17530441;rs17856568;rs52794830;rs57431189;rs1063479	340	P08567	PLEK_HUMAN	K	340	ENSP00000234313:R340K	ENSP00000234313:R340K	R	+	2	0	PLEK	68476418	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	4.577000	0.60922	0.430000	0.26230	-1.322000	0.01289	AGA	G|0.182;A|0.818	0.818	strong		0.537	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664	
FUT10	84750	hgsc.bcm.edu	37	8	33246685	33246685	+	Silent	SNP	G	G	A	rs16880852	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:33246685G>A	ENST00000327671.5	-	4	1639	c.1008C>T	c.(1006-1008)taC>taT	p.Y336Y	FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Silent_p.Y274Y|FUT10_ENST00000524021.1_Silent_p.Y308Y|FUT10_ENST00000518672.1_Silent_p.Y308Y	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	336					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.Y336Y(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		GTCGTCTGATGTAACTTGCCA	0.463													G|||	1496	0.298722	0.1808	0.17	5008	,	,		21121	0.4683		0.1938	False		,,,				2504	0.4826				p.Y336Y		Atlas-SNP	.											FUT10,NS,carcinoma,0,1	FUT10	62	1	1	Substitution - coding silent(1)	stomach(1)	c.C1008T						PASS	.	G		916,3490	349.5+/-310.4	76,764,1363	96.0	89.0	91.0		1008	3.2	0.4	8	dbSNP_123	91	1747,6853	316.6+/-312.8	177,1393,2730	no	coding-synonymous	FUT10	NM_032664.3		253,2157,4093	AA,AG,GG		20.314,20.7898,20.4752		336/480	33246685	2663,10343	2203	4300	6503	SO:0001819	synonymous_variant	84750	exon4			TCTGATGTAACTT	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1008C>T	8.37:g.33246685G>A		Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	264	132	0.5	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Silent	SNP	ENST00000327671.5	37	CCDS6088.1																																																																																			G|0.768;A|0.232	0.232	strong		0.463	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
CDC42EP4	23580	hgsc.bcm.edu	37	17	71282132	71282132	+	Missense_Mutation	SNP	C	C	T	rs375486831		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:71282132C>T	ENST00000335793.3	-	2	902	c.508G>A	c.(508-510)Gcg>Acg	p.A170T	CDC42EP4_ENST00000581014.1_Intron|CDC42EP4_ENST00000439510.2_Missense_Mutation_p.A100T			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	170					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(7)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			TGTGGACCCGCGGCCCCATTC	0.662																																					p.A170T		Atlas-SNP	.											CDC42EP4,colon,carcinoma,0,1	CDC42EP4	19	1	0			c.G508A						PASS	.	C	THR/ALA	0,4406		0,0,2203	46.0	41.0	43.0		508	-5.5	0.0	17		43	1,8599	1.2+/-3.3	0,1,4299	no	missense	CDC42EP4	NM_012121.4	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	170/357	71282132	1,13005	2203	4300	6503	SO:0001583	missense	23580	exon2			GACCCGCGGCCCC	AB042237	CCDS11695.1	17q24-q25	2008-07-18				ENSG00000179604			17147	protein-coding gene	gene with protein product	"""Cdc42 effector protein 4"", ""binder of Rho GTPases 4"""	605468				11035016, 10490598	Standard	NM_012121		Approved	CEP4, KAIA1777, BORG4, MGC3740, MGC17125	uc002jjo.3	Q9H3Q1		ENST00000335793.3:c.508G>A	17.37:g.71282132C>T	ENSP00000338258:p.Ala170Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	141	68	0.482269	NM_012121	B3KUS7|O95828|Q96FT3	Missense_Mutation	SNP	ENST00000335793.3	37	CCDS11695.1	.	.	.	.	.	.	.	.	.	.	C	4.875	0.162607	0.09287	0.0	1.16E-4	ENSG00000179604	ENST00000335793;ENST00000439510	T;T	0.34275	1.37;1.37	4.5	-5.48	0.02592	.	1.452830	0.05166	N	0.498676	T	0.20292	0.0488	L	0.28115	0.83	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.01281	0.0;0.0	T	0.23726	-1.0180	10	0.12766	T	0.61	-1.5257	6.8507	0.24012	0.118:0.3419:0.0:0.5401	.	100;170	B3KUS7;Q9H3Q1	.;BORG4_HUMAN	T	170;100	ENSP00000338258:A170T;ENSP00000404270:A100T	ENSP00000338258:A170T	A	-	1	0	CDC42EP4	68793727	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.321000	0.08018	-1.673000	0.01462	-0.678000	0.03780	GCG	.	.	weak		0.662	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121	
DYNAP	284254	hgsc.bcm.edu	37	18	52258548	52258548	+	Missense_Mutation	SNP	T	T	C	rs35428499	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:52258548T>C	ENST00000321600.1	+	1	159	c.113T>C	c.(112-114)gTt>gCt	p.V38A	DYNAP_ENST00000585973.1_Missense_Mutation_p.V41A	NM_173629.1	NP_775900.1	Q8N1N2	DYNAP_HUMAN	dynactin associated protein	38			V -> A (in dbSNP:rs35428499).		activation of protein kinase B activity (GO:0032148)|cellular response to ergosterol (GO:1901625)|positive regulation of cell proliferation (GO:0008284)|regulation of apoptotic process (GO:0042981)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											ATATTGAACGTTGAGCACTCT	0.368													T|||	584	0.116613	0.1483	0.0865	5008	,	,		15927	0.0288		0.1551	False		,,,				2504	0.1462				p.V38A		Atlas-SNP	.											.	.	.	.	0			c.T113C						PASS	.	T	ALA/VAL	679,3727		48,583,1572	146.0	144.0	145.0		113	-1.3	0.0	18	dbSNP_126	145	1300,7300		101,1098,3101	yes	missense	C18orf26	NM_173629.1	64	149,1681,4673	CC,CT,TT		15.1163,15.4108,15.2161	possibly-damaging	38/211	52258548	1979,11027	2203	4300	6503	SO:0001583	missense	284254	exon1			TGAACGTTGAGCA	AK096425	CCDS11957.1	18q21.2	2012-10-24	2012-10-24	2012-10-24	ENSG00000178690	ENSG00000178690			26808	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 26"""	C18orf26		20978158	Standard	NM_173629		Approved	FLJ39106	uc002lfq.1	Q8N1N2	OTTHUMG00000132709	ENST00000321600.1:c.113T>C	18.37:g.52258548T>C	ENSP00000315265:p.Val38Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_173629		Missense_Mutation	SNP	ENST00000321600.1	37	CCDS11957.1	245	0.11217948717948718	67	0.13617886178861788	42	0.11602209944751381	15	0.026223776223776224	121	0.15963060686015831	.	3.925	-0.017299	0.07681	0.154108	0.151163	ENSG00000178690	ENST00000321600	T	0.21191	2.02	5.21	-1.32	0.09201	.	1.146150	0.06450	N	0.727527	T	0.00039	0.0001	N	0.04959	-0.14	0.80722	P	0.0	B	0.23891	0.093	B	0.27170	0.077	T	0.38672	-0.9650	9	0.66056	D	0.02	-0.8943	9.2704	0.37668	0.0:0.4461:0.0:0.5539	rs35428499;rs35428499	38	Q8N1N2	CR026_HUMAN	A	38	ENSP00000315265:V38A	ENSP00000315265:V38A	V	+	2	0	C18orf26	50409546	0.000000	0.05858	0.003000	0.11579	0.012000	0.07955	-0.159000	0.10056	-0.133000	0.11537	0.496000	0.49642	GTT	T|0.861;C|0.139	0.139	strong		0.368	DYNAP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256007.1	NM_173629	
VENTX	27287	hgsc.bcm.edu	37	10	135053604	135053604	+	Missense_Mutation	SNP	G	G	A	rs9418952	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:135053604G>A	ENST00000325980.9	+	3	1082	c.571G>A	c.(571-573)Ggg>Agg	p.G191R		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	191			G -> R (in dbSNP:rs9418952).		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)		ACCCCTGTCCGGGCCCCAGGC	0.667													G|||	510	0.101837	0.1165	0.134	5008	,	,		11353	0.0823		0.0586	False		,,,				2504	0.1237				p.G191R		Atlas-SNP	.											.	VENTX	24	.	0			c.G571A						PASS	.	G	ARG/GLY	508,3894		31,446,1724	26.0	30.0	28.0		571	-2.1	0.0	10	dbSNP_119	28	569,8029		28,513,3758	no	missense	VENTX	NM_014468.2	125	59,959,5482	AA,AG,GG		6.6178,11.5402,8.2846	probably-damaging	191/259	135053604	1077,11923	2201	4299	6500	SO:0001583	missense	27287	exon3			CTGTCCGGGCCCC	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.571G>A	10.37:g.135053604G>A	ENSP00000357556:p.Gly191Arg	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	197	0.0902014652014652	63	0.12804878048780488	46	0.1270718232044199	47	0.08216783216783216	41	0.05408970976253298	G	6.686	0.495235	0.12762	0.115402	0.066178	ENSG00000151650	ENST00000325980	D	0.91237	-2.81	2.44	-2.11	0.07187	.	1.099270	0.07198	N	0.857031	T	0.03220	0.0094	N	0.24115	0.695	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.30060	-0.9991	9	0.25106	T	0.35	.	2.7017	0.05150	0.4498:0.0:0.3229:0.2274	rs9418952;rs9418952	191	O95231	VENTX_HUMAN	R	191	ENSP00000357556:G191R	ENSP00000357556:G191R	G	+	1	0	VENTX	134903594	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.997000	0.03705	-0.556000	0.06134	-0.497000	0.04613	GGG	G|0.916;A|0.084	0.084	strong		0.667	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
ZNF189	7743	hgsc.bcm.edu	37	9	104162272	104162272	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:104162272A>G	ENST00000339664.2	+	2	269	c.140A>G	c.(139-141)tAt>tGt	p.Y47C	ZNF189_ENST00000374861.3_Missense_Mutation_p.Y33C|MRPL50_ENST00000374865.4_5'Flank|ZNF189_ENST00000259395.4_Missense_Mutation_p.Y5C|MRPL50_ENST00000539624.1_5'Flank	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	47	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)				ATGGAGAATTATGGAAACCTG	0.413																																					p.Y47C		Atlas-SNP	.											ZNF189,NS,carcinoma,+1,1	ZNF189	79	1	0			c.A140G						PASS	.						125.0	126.0	126.0					9																	104162272		2203	4300	6503	SO:0001583	missense	7743	exon2			AGAATTATGGAAA	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.140A>G	9.37:g.104162272A>G	ENSP00000342019:p.Tyr47Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.348923	0.61183	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.08193	4.26;4.26;3.12	4.79	3.61	0.41365	Krueppel-associated box (4);	0.191487	0.25958	N	0.027201	T	0.22627	0.0546	M	0.74467	2.265	0.34073	D	0.65865	P;D;D	0.63046	0.946;0.966;0.992	P;B;P	0.62184	0.749;0.338;0.899	T	0.29119	-1.0022	10	0.59425	D	0.04	.	9.0762	0.36522	0.8355:0.0:0.0:0.1645	.	32;33;47	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	C	33;47;5	ENSP00000363995:Y33C;ENSP00000342019:Y47C;ENSP00000259395:Y5C	ENSP00000259395:Y5C	Y	+	2	0	ZNF189	103202093	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.826000	0.62715	0.924000	0.37069	0.528000	0.53228	TAT	.	.	none		0.413	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
ANKRD17	26057	hgsc.bcm.edu	37	4	73942678	73942678	+	Silent	SNP	C	C	T	rs2306058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:73942678C>T	ENST00000358602.4	-	33	7847	c.7731G>A	c.(7729-7731)acG>acA	p.T2577T	ANKRD17_ENST00000330838.6_Silent_p.T2326T|ANKRD17_ENST00000509867.2_Silent_p.T2464T	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2577					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)			CATTATTTTCCGTGGAGCTGG	0.433													C|||	884	0.176518	0.0136	0.2205	5008	,	,		17906	0.2877		0.165	False		,,,				2504	0.2628				p.T2577T		Atlas-SNP	.											.	ANKRD17	214	.	0			c.G7731A						PASS	.	C	,	171,4235	111.6+/-149.8	4,163,2036	131.0	129.0	130.0		7731,6978	0.0	1.0	4	dbSNP_100	130	1415,7185	273.1+/-290.5	95,1225,2980	no	coding-synonymous,coding-synonymous	ANKRD17	NM_032217.3,NM_198889.1	,	99,1388,5016	TT,TC,CC		16.4535,3.8811,12.1944	,	2577/2604,2326/2353	73942678	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	26057	exon33			ATTTTCCGTGGAG	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.7731G>A	4.37:g.73942678C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																			C|0.852;T|0.148	0.148	strong		0.433	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
C14orf159	80017	hgsc.bcm.edu	37	14	91636395	91636395	+	Silent	SNP	C	C	T	rs4900071	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:91636395C>T	ENST00000523771.1	+	5	909	c.306C>T	c.(304-306)ggC>ggT	p.G102G	C14orf159_ENST00000518868.1_Silent_p.G102G|C14orf159_ENST00000520328.1_Silent_p.G102G|C14orf159_ENST00000523816.1_Silent_p.G102G|C14orf159_ENST00000412671.2_Silent_p.G102G|C14orf159_ENST00000256324.10_Silent_p.G102G|C14orf159_ENST00000521077.2_Silent_p.G102G|C14orf159_ENST00000428926.2_Silent_p.G102G|C14orf159_ENST00000525393.2_Intron|C14orf159_ENST00000522322.1_Silent_p.G102G			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	102						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)		CCTGCACCGGCAGCCTGGCTT	0.627													C|||	837	0.167133	0.1036	0.2262	5008	,	,		17755	0.0585		0.3241	False		,,,				2504	0.1616				p.G102G		Atlas-SNP	.											C14orf159,NS,carcinoma,0,1	C14orf159	57	1	0			c.C306T						scavenged	.	C	,,,,	711,3695	295.3+/-283.6	62,587,1554	84.0	89.0	87.0		306,306,306,306,306	2.0	0.4	14	dbSNP_111	87	2897,5703	453.6+/-363.3	492,1913,1895	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	554,2500,3449	TT,TC,CC		33.686,16.1371,27.741	,,,,	102/617,102/617,102/622,102/565,102/617	91636395	3608,9398	2203	4300	6503	SO:0001819	synonymous_variant	80017	exon7			CACCGGCAGCCTG	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.306C>T	14.37:g.91636395C>T		Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_001102366	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1																																																																																			C|0.767;T|0.233	0.233	strong		0.627	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
SH2D3A	10045	hgsc.bcm.edu	37	19	6760974	6760974	+	Missense_Mutation	SNP	T	T	C	rs7258236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6760974T>C	ENST00000245908.6	-	3	363	c.94A>G	c.(94-96)Aat>Gat	p.N32D	SH2D3A_ENST00000437152.3_Intron|SH2D3A_ENST00000599563.1_5'UTR	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	81	0	0		WXS	Illumina HiSeq	Phase_I	88	33	0.375	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	
P2RX3	5024	hgsc.bcm.edu	37	11	57137424	57137424	+	Missense_Mutation	SNP	C	C	T	rs2276038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57137424C>T	ENST00000263314.2	+	12	1182	c.1148C>T	c.(1147-1149)gCg>gTg	p.A383V		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	383			A -> V (in dbSNP:rs2276038). {ECO:0000269|Ref.2}.		behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|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 homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CAGACCACAGCGGAGAAGCAG	0.587													C|||	2163	0.431909	0.0696	0.4914	5008	,	,		19306	0.7163		0.3926	False		,,,				2504	0.6268				p.A383V		Atlas-SNP	.											.	P2RX3	55	.	0			c.C1148T						PASS	.	C	VAL/ALA	546,3856	241.8+/-252.1	42,462,1697	102.0	87.0	92.0		1148	0.1	0.1	11	dbSNP_100	92	3319,5273	490.5+/-372.9	657,2005,1634	yes	missense	P2RX3	NM_002559.3	64	699,2467,3331	TT,TC,CC		38.629,12.4035,29.7445	benign	383/398	57137424	3865,9129	2201	4296	6497	SO:0001583	missense	5024	exon12			CCACAGCGGAGAA	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.1148C>T	11.37:g.57137424C>T	ENSP00000263314:p.Ala383Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	37	CCDS7953.1	905	0.4143772893772894	42	0.08536585365853659	160	0.4419889502762431	397	0.6940559440559441	306	0.40369393139841686	C	5.453	0.268630	0.10349	0.124035	0.38629	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.04275	3.66	5.4	0.0746	0.14396	.	0.735097	0.13141	N	0.410610	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	0.06232	-1.0838	9	0.28530	T	0.3	-15.7114	2.1232	0.03731	0.4489:0.3135:0.0883:0.1493	rs2276038;rs17574631;rs2276038	383	P56373	P2RX3_HUMAN	V	382;383	ENSP00000263314:A383V	ENSP00000263314:A383V	A	+	2	0	P2RX3	56894000	0.879000	0.30193	0.065000	0.19835	0.101000	0.19017	0.300000	0.19156	-0.241000	0.09681	-0.457000	0.05445	GCG	C|0.650;T|0.349	0.349	strong		0.587	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
SYT16	83851	hgsc.bcm.edu	37	14	62463214	62463214	+	Silent	SNP	C	C	T	rs1889806	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:62463214C>T	ENST00000430451.2	+	1	674	c.477C>T	c.(475-477)gaC>gaT	p.D159D	SYT16_ENST00000446982.2_Silent_p.D159D	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	159					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		ATGGCTTTGACAGCCAGCTCC	0.453													C|||	2806	0.560304	0.6195	0.5879	5008	,	,		20252	0.749		0.4036	False		,,,				2504	0.4274				p.D159D		Atlas-SNP	.											SYT16,NS,carcinoma,+2,1	SYT16	144	1	0			c.C477T						PASS	.	C		2098,1630		592,914,358	119.0	115.0	116.0		477	2.3	1.0	14	dbSNP_92	116	3356,4864		687,1982,1441	no	coding-synonymous	SYT16	NM_031914.2		1279,2896,1799	TT,TC,CC		40.8273,43.7232,45.6478		159/646	62463214	5454,6494	1864	4110	5974	SO:0001819	synonymous_variant	83851	exon1			CTTTGACAGCCAG	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.477C>T	14.37:g.62463214C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																			C|0.433;T|0.567	0.567	strong		0.453	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
FAM186A	121006	hgsc.bcm.edu	37	12	50746166	50746166	+	Silent	SNP	G	G	C	rs368983791		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	243	8	0.0329218	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	
EGFLAM	133584	hgsc.bcm.edu	37	5	38406251	38406251	+	Missense_Mutation	SNP	C	C	T	rs113400125	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:38406251C>T	ENST00000354891.3	+	7	1082	c.736C>T	c.(736-738)Cgc>Tgc	p.R246C	EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000322350.5_Missense_Mutation_p.R246C|EGFLAM-AS2_ENST00000512603.1_RNA|EGFLAM_ENST00000336740.6_Missense_Mutation_p.R12C|EGFLAM-AS2_ENST00000514377.1_RNA	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	246					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)					GGGAAGTGGCCGCTATGGACC	0.493													C|||	44	0.00878594	0.0023	0.0173	5008	,	,		17786	0.0		0.0249	False		,,,				2504	0.0041				p.R246C	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C736T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	27,4379	33.5+/-64.1	0,27,2176	100.0	99.0	99.0		736,736,34	3.2	0.6	5	dbSNP_132	99	285,8315	105.6+/-166.5	5,275,4020	yes	missense,missense,missense	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	180,180,180	5,302,6196	TT,TC,CC		3.314,0.6128,2.3989	benign,benign,benign	246/1018,246/1010,12/776	38406251	312,12694	2203	4300	6503	SO:0001583	missense	133584	exon7			AGTGGCCGCTATG	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.736C>T	5.37:g.38406251C>T	ENSP00000346964:p.Arg246Cys	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	272	129	0.474265	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	33	0.01510989010989011	3	0.006097560975609756	11	0.03038674033149171	0	0.0	19	0.025065963060686015	C	8.227	0.803877	0.16467	0.006128	0.03314	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	T;T;T	0.79749	0.77;0.6;-1.3	5.29	3.23	0.37069	.	0.603585	0.18447	N	0.140954	T	0.45915	0.1366	L	0.31294	0.92	0.09310	N	0.999992	B;B;B	0.15141	0.002;0.007;0.012	B;B;B	0.06405	0.001;0.001;0.002	T	0.52931	-0.8509	10	0.44086	T	0.13	-6.8818	10.6031	0.45379	0.5607:0.4393:0.0:0.0	.	12;246;246	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	C	246;246;12;12	ENSP00000346964:R246C;ENSP00000313084:R246C;ENSP00000337607:R12C	ENSP00000313084:R246C	R	+	1	0	EGFLAM	38442008	0.008000	0.16893	0.578000	0.28575	0.235000	0.25334	1.070000	0.30653	1.142000	0.42291	0.462000	0.41574	CGC	C|0.978;T|0.022	0.022	strong		0.493	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
KIF16B	55614	hgsc.bcm.edu	37	20	16352344	16352344	+	Missense_Mutation	SNP	C	C	T	rs75989969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:16352344C>T	ENST00000354981.2	-	21	3570	c.3413G>A	c.(3412-3414)aGt>aAt	p.S1138N	KIF16B_ENST00000378003.2_Missense_Mutation_p.S364N|KIF16B_ENST00000408042.1_Missense_Mutation_p.S1138N|KIF16B_ENST00000355755.3_Missense_Mutation_p.S1138N	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1138					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						GCAGCCTTCACTAATCACACG	0.408													c|||	65	0.0129792	0.0454	0.0072	5008	,	,		20897	0.0		0.0	False		,,,				2504	0.0				p.S1138N		Atlas-SNP	.											.	KIF16B	305	.	0			c.G3413A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER	148,4258	103.0+/-141.5	2,144,2057	143.0	118.0	126.0		3260,3413,3413	3.8	0.0	20	dbSNP_131	126	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	46,46,46	2,148,6353	TT,TC,CC		0.0465,3.3591,1.1687	benign,benign,benign	1087/1267,1138/1393,1138/1318	16352344	152,12854	2203	4300	6503	SO:0001583	missense	55614	exon21			CCTTCACTAATCA	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.3413G>A	20.37:g.16352344C>T	ENSP00000347076:p.Ser1138Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	155	80	0.516129	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	30	0.013736263736263736	25	0.0508130081300813	5	0.013812154696132596	0	0.0	0	0.0	c	10.36	1.329121	0.24167	0.033591	4.65E-4	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000378003;ENST00000408042	T;T;T;T	0.70986	-0.53;-0.52;2.51;-0.47	5.8	3.8	0.43715	.	0.550979	0.21055	N	0.080929	T	0.16085	0.0387	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.0	T	0.07028	-1.0794	10	0.18710	T	0.47	.	8.6668	0.34125	0.0:0.6904:0.0:0.3096	.	1138;1138;1138	Q96L93-2;Q96L93-6;Q96L93	.;.;KI16B_HUMAN	N	1138;1138;982;364;1138	ENSP00000347076:S1138N;ENSP00000347995:S1138N;ENSP00000367242:S364N;ENSP00000384164:S1138N	ENSP00000347076:S1138N	S	-	2	0	KIF16B	16300344	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.629000	0.24538	0.743000	0.32719	-1.124000	0.02001	AGT	C|0.989;T|0.011	0.011	strong		0.408	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
PLCD1	5333	hgsc.bcm.edu	37	3	38051941	38051941	+	Silent	SNP	T	T	C	rs9857730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:38051941T>C	ENST00000334661.4	-	6	1125	c.903A>G	c.(901-903)ccA>ccG	p.P301P	PLCD1_ENST00000479619.1_5'Flank|PLCD1_ENST00000463876.1_Silent_p.P322P	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	151	0	0		WXS	Illumina HiSeq	Phase_I	153	75	0.490196	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		
ASAH2	56624	hgsc.bcm.edu	37	10	52002980	52002980	+	Silent	SNP	T	T	G	rs3739979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:52002980T>G	ENST00000395526.4	-	3	491	c.492A>C	c.(490-492)tcA>tcC	p.S164S	ASAH2_ENST00000329428.6_Silent_p.S145S|ASAH2_ENST00000447815.1_Silent_p.S164S|ASAH2_ENST00000443575.1_5'Flank	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	164					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						TGAGCCTTTGTGATACCATGC	0.448													G|||	1524	0.304313	0.4766	0.1715	5008	,	,		20544	0.4276		0.0924	False		,,,				2504	0.2566				p.S164S		Atlas-SNP	.											.	ASAH2	69	.	0			c.A492C						PASS	.	G	,	1910,2496	626.8+/-394.8	424,1062,717	241.0	212.0	222.0		492,492	-2.5	0.3	10	dbSNP_107	222	808,7792	782.7+/-407.6	34,740,3526	no	coding-synonymous,coding-synonymous	ASAH2	NM_001143974.1,NM_019893.2	,	458,1802,4243	GG,GT,TT		9.3953,43.35,20.898	,	164/746,164/781	52002980	2718,10288	2203	4300	6503	SO:0001819	synonymous_variant	56624	exon3			CCTTTGTGATACC	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.492A>C	10.37:g.52002980T>G		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	199	85	0.427136	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Silent	SNP	ENST00000395526.4	37	CCDS7239.2																																																																																			T|0.747;G|0.253	0.253	strong		0.448	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893	
PLEKHS1	79949	hgsc.bcm.edu	37	10	115529576	115529576	+	Missense_Mutation	SNP	T	T	A	rs41292632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:115529576T>A	ENST00000369310.3	+	6	1013	c.451T>A	c.(451-453)Ttc>Atc	p.F151I	PLEKHS1_ENST00000369309.1_5'Flank|PLEKHS1_ENST00000361048.1_Missense_Mutation_p.F157I|PLEKHS1_ENST00000354462.3_5'Flank|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.F69I	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	151																	AAGAACCCTCTTCTACTCCAG	0.502													T|||	1003	0.20028	0.1195	0.1628	5008	,	,		18665	0.3175		0.162	False		,,,				2504	0.2546				p.F157I		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.T469A						PASS	.	T	ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE	532,3874	242.1+/-252.3	37,458,1708	125.0	119.0	121.0		205,205,469,451	4.8	0.0	10	dbSNP_127	121	1430,7170	275.6+/-291.8	138,1154,3008	yes	missense,missense,missense,missense	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4,NM_182601.1	21,21,21,21	175,1612,4716	AA,AT,TT		16.6279,12.0744,15.0853	benign,benign,benign,benign	69/367,69/367,157/364,151/466	115529576	1962,11044	2203	4300	6503	SO:0001583	missense	79949	exon7			ACCCTCTTCTACT	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.451T>A	10.37:g.115529576T>A	ENSP00000358316:p.Phe151Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	37	CCDS53580.1	410	0.18772893772893773	67	0.13617886178861788	55	0.15193370165745856	175	0.30594405594405594	113	0.14907651715039577	T	14.13	2.444684	0.43429	0.120744	0.166279	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310	T;T;T	0.28666	1.6;1.6;1.6	5.93	4.76	0.60689	.	0.459548	0.23019	N	0.052872	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;P;P	0.47302	0.893;0.63;0.744	B;B;B	0.42653	0.394;0.131;0.196	T	0.39702	-0.9601	9	0.52906	T	0.07	-34.7055	10.0062	0.41959	0.0:0.0:0.1698:0.8302	rs41292632;rs57607073	151;151;157	Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	.;.;.	I	157;69;151	ENSP00000354332:F157I;ENSP00000358318:F69I;ENSP00000358316:F151I	ENSP00000354332:F157I	F	+	1	0	C10orf81	115519566	0.359000	0.24955	0.009000	0.14445	0.001000	0.01503	2.190000	0.42630	1.015000	0.39444	0.533000	0.62120	TTC	T|0.838;A|0.162	0.162	strong		0.502	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
NTF3	4908	hgsc.bcm.edu	37	12	5603632	5603632	+	Silent	SNP	G	G	A	rs6332	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:5603632G>A	ENST00000331010.6	+	1	335	c.252G>A	c.(250-252)ccG>ccA	p.P84P	NTF3_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Silent_p.P97P	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	29	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	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		
KRT31	3881	hgsc.bcm.edu	37	17	39553547	39553547	+	Missense_Mutation	SNP	G	G	A	rs6503627	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	120	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	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	
CREB3L4	148327	hgsc.bcm.edu	37	1	153941514	153941514	+	Missense_Mutation	SNP	C	C	T	rs11264743	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153941514C>T	ENST00000368607.3	+	3	549	c.283C>T	c.(283-285)Ccc>Tcc	p.P95S	CREB3L4_ENST00000271889.4_Missense_Mutation_p.P95S|CREB3L4_ENST00000405694.3_Intron|CREB3L4_ENST00000368601.1_Missense_Mutation_p.P95S|CREB3L4_ENST00000368600.3_Missense_Mutation_p.P75S|RP11-422P24.10_ENST00000608147.1_RNA|CREB3L4_ENST00000368603.1_Missense_Mutation_p.P95S|SLC39A1_ENST00000310483.6_5'Flank	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	95			P -> S (in dbSNP:rs11264743).		response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|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(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CTCTGAGGACCCCTGCCATCC	0.552													C|||	1287	0.256989	0.0832	0.4107	5008	,	,		18583	0.2837		0.2853	False		,,,				2504	0.3262				p.P95S		Atlas-SNP	.											.	CREB3L4	36	.	0			c.C283T						PASS	.	C	SER/PRO	544,3862	249.6+/-257.0	18,508,1677	84.0	82.0	83.0		283	3.9	1.0	1	dbSNP_120	83	2436,6164	404.5+/-348.2	340,1756,2204	yes	missense	CREB3L4	NM_130898.2	74	358,2264,3881	TT,TC,CC		28.3256,12.3468,22.9125	probably-damaging	95/396	153941514	2980,10026	2203	4300	6503	SO:0001583	missense	148327	exon3			GAGGACCCCTGCC	AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"""basic leucine zipper proteins"""	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.283C>T	1.37:g.153941514C>T	ENSP00000357596:p.Pro95Ser	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	182	95	0.521978	NM_001255978	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	37	CCDS1056.1	588	0.2692307692307692	51	0.10365853658536585	138	0.3812154696132597	173	0.30244755244755245	226	0.29815303430079154	C	21.5	4.156309	0.78114	0.123468	0.283256	ENSG00000143578	ENST00000449724;ENST00000368607;ENST00000271889;ENST00000368601;ENST00000368603;ENST00000368600;ENST00000431292	T;T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39;1.39	4.84	3.86	0.44501	.	0.062472	0.64402	D	0.000006	T	0.46092	0.1375	M	0.71581	2.175	0.09310	P	1.0	D;P;D	0.76494	0.999;0.931;0.99	D;P;P	0.65140	0.932;0.476;0.449	T	0.42565	-0.9444	8	.	.	.	.	13.0533	0.58966	0.0:0.8366:0.1634:0.0	rs11264743;rs52800624;rs61331066;rs11264743	95;75;95	B4E2G3;Q5T4L0;Q8TEY5	.;.;CR3L4_HUMAN	S	75;95;95;95;95;75;95	ENSP00000391847:P75S;ENSP00000357596:P95S;ENSP00000271889:P95S;ENSP00000357590:P95S;ENSP00000357592:P95S;ENSP00000357589:P75S;ENSP00000402308:P95S	.	P	+	1	0	CREB3L4	152208138	0.995000	0.38212	0.996000	0.52242	0.829000	0.46940	4.348000	0.59379	2.666000	0.90696	0.561000	0.74099	CCC	C|0.760;T|0.240	0.240	strong		0.552	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898	
MYH2	4620	hgsc.bcm.edu	37	17	10448769	10448769	+	Silent	SNP	A	A	T	rs11078850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10448769A>T	ENST00000245503.5	-	5	783	c.399T>A	c.(397-399)ccT>ccA	p.P133P	CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000532183.2_Silent_p.P133P|MYH2_ENST00000397183.2_Silent_p.P133P	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	133	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GCTTATACACAGGCAGCCACT	0.502													T|||	2588	0.516773	0.3018	0.5144	5008	,	,		16718	0.8333		0.3847	False		,,,				2504	0.6186				p.P133P		Atlas-SNP	.											.	MYH2	390	.	0			c.T399A						PASS	.	T	,	1463,2943	680.4+/-403.8	244,975,984	90.0	94.0	92.0		399,399	-4.2	0.9	17	dbSNP_120	92	3511,5089	632.4+/-398.6	734,2043,1523	no	coding-synonymous,coding-synonymous	MYH2	NM_001100112.1,NM_017534.5	,	978,3018,2507	TT,TA,AA		40.8256,33.2047,38.2439	,	133/1942,133/1942	10448769	4974,8032	2203	4300	6503	SO:0001819	synonymous_variant	4620	exon5			ATACACAGGCAGC		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.399T>A	17.37:g.10448769A>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	171	74	0.432749	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			A|0.586;T|0.414	0.414	strong		0.502	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
OR51A4	401666	hgsc.bcm.edu	37	11	4967834	4967834	+	Missense_Mutation	SNP	C	C	G	rs201205025	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4967834C>G	ENST00000380373.2	-	1	522	c.497G>C	c.(496-498)aGa>aCa	p.R166T	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	166						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(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTCAAGTTTCTTAAAGTGAA	0.413													.|||	12	0.00239617	0.003	0.0029	5008	,	,		24981	0.0		0.003	False		,,,				2504	0.0031				p.R166T		Atlas-SNP	.											OR51A4,colon,carcinoma,-1,1	OR51A4	73	1	0			c.G497C						scavenged	.						212.0	198.0	203.0					11																	4967834		2177	4245	6422	SO:0001583	missense	401666	exon1			AAGTTTCTTAAAG	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"""GPCR / Class A : Olfactory receptors"""	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.497G>C	11.37:g.4967834C>G	ENSP00000369731:p.Arg166Thr	Somatic	614	12	0.019544		WXS	Illumina HiSeq	Phase_I	388	15	0.0386598	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	.	.	.	.	.	.	.	.	.	.	C	9.411	1.080491	0.20309	.	.	ENSG00000205497	ENST00000380373	T	0.71817	-0.6	3.44	-3.66	0.04489	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.59046	0.2165	L	0.41027	1.25	0.09310	N	1	B	0.23249	0.082	B	0.27608	0.081	T	0.52041	-0.8628	9	0.66056	D	0.02	.	9.2359	0.37466	0.0:0.303:0.0:0.697	.	166	Q8NGJ6	O51A4_HUMAN	T	166	ENSP00000369731:R166T	ENSP00000369731:R166T	R	-	2	0	OR51A4	4924410	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.905000	0.04075	-1.059000	0.03193	0.479000	0.44913	AGA	.	.	weak		0.413	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329	
POLH	5429	hgsc.bcm.edu	37	6	43582091	43582091	+	Missense_Mutation	SNP	A	A	T	rs6941583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43582091A>T	ENST00000372236.4	+	11	2234	c.1939A>T	c.(1939-1941)Atg>Ttg	p.M647L	POLH_ENST00000372226.1_3'UTR|POLH_ENST00000535400.1_Missense_Mutation_p.M585L	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	177	0	0		WXS	Illumina HiSeq	Phase_I	170	89	0.523529	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	
HOXC11	3227	hgsc.bcm.edu	37	12	54367690	54367690	+	Missense_Mutation	SNP	C	C	T	rs12427129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:54367690C>T	ENST00000546378.1	+	1	781	c.665C>T	c.(664-666)gCc>gTc	p.A222V	HOXC11_ENST00000243082.4_Missense_Mutation_p.A222V|HOTAIR_ENST00000455246.1_RNA|HOTAIR_ENST00000424518.1_RNA			O43248	HXC11_HUMAN	homeobox C11	222			A -> V (in dbSNP:rs12427129).		anterior/posterior pattern specification (GO:0009952)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal joint morphogenesis (GO:0060272)|endoderm development (GO:0007492)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			large_intestine(1)|ovary(1)	2						AAGGAGCCGGCCAAAGGAGCC	0.716			T	NUP98	AML								C|||	328	0.0654952	0.0061	0.1153	5008	,	,		9813	0.0833		0.0696	False		,,,				2504	0.0879				p.A222V		Atlas-SNP	.		Dom	yes		12	12q13.3	3227	homeo box C11		L	.	HOXC11	32	.	0			c.C665T						PASS	.	C	VAL/ALA	39,3043		0,39,1502	2.0	3.0	3.0		665	2.2	1.0	12	dbSNP_120	3	363,5283		3,357,2463	yes	missense	HOXC11	NM_014212.3	64	3,396,3965	TT,TC,CC		6.4293,1.2654,4.6059	benign	222/305	54367690	402,8326	1541	2823	4364	SO:0001583	missense	3227	exon1			AGCCGGCCAAAGG		CCDS8867.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123388	ENSG00000123388		"""Homeoboxes / ANTP class : HOXL subclass"""	5123	protein-coding gene	gene with protein product		605559	"""homeo box C11"""	HOX3H		1973146, 1358459	Standard	NM_014212		Approved		uc001sem.3	O43248	OTTHUMG00000160011	ENST00000546378.1:c.665C>T	12.37:g.54367690C>T	ENSP00000446680:p.Ala222Val	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_014212	A8K7D1|Q96DH2	Missense_Mutation	SNP	ENST00000546378.1	37	CCDS8867.1	152	0.0695970695970696	5	0.01016260162601626	46	0.1270718232044199	47	0.08216783216783216	54	0.0712401055408971	C	11.96	1.794544	0.31777	0.012654	0.064293	ENSG00000123388	ENST00000546378;ENST00000243082	D;T	0.95588	-3.75;1.83	4.22	2.24	0.28232	Homeodomain-related (1);Homeodomain-like (1);	0.306670	0.38111	N	0.001816	T	0.07143	0.0181	N	0.08118	0	0.37475	P	0.08421400000000001	B	0.17465	0.022	B	0.20184	0.028	T	0.64820	-0.6317	9	0.54805	T	0.06	.	7.8855	0.29648	0.0:0.6473:0.2562:0.0965	rs12427129	222	O43248	HXC11_HUMAN	V	222	ENSP00000446680:A222V;ENSP00000243082:A222V	ENSP00000243082:A222V	A	+	2	0	HOXC11	52653957	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.208000	0.42797	1.127000	0.42034	0.561000	0.74099	GCC	C|0.931;T|0.069	0.069	strong		0.716	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2		
MUC16	94025	hgsc.bcm.edu	37	19	9070402	9070402	+	Missense_Mutation	SNP	G	G	T	rs12150888	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9070402G>T	ENST00000397910.4	-	3	17247	c.17044C>A	c.(17044-17046)Ccc>Acc	p.P5682T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5684	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCGTTACGGGCTCTGGGCTT	0.512													g|||	819	0.163538	0.1142	0.2536	5008	,	,		20669	0.0089		0.2634	False		,,,				2504	0.2229				p.P5682T		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	0			c.C17044A						scavenged	.	A	THR/PRO	518,3486		33,452,1517	145.0	139.0	141.0		17044	-2.5	0.0	19	dbSNP_120	141	2434,5912		372,1690,2111	yes	missense	MUC16	NM_024690.2	38	405,2142,3628	TT,TG,GG		29.1637,12.9371,23.9028	probably-damaging	5682/14508	9070402	2952,9398	2002	4173	6175	SO:0001583	missense	94025	exon3			TTACGGGCTCTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17044C>A	19.37:g.9070402G>T	ENSP00000381008:p.Pro5682Thr	Somatic	277	2	0.00722022		WXS	Illumina HiSeq	Phase_I	276	147	0.532609	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	353	0.16163003663003664	53	0.10772357723577236	92	0.2541436464088398	5	0.008741258741258742	203	0.2678100263852243	g	1.261	-0.615735	0.03663	0.129371	0.291637	ENSG00000181143	ENST00000397910	T	0.35048	1.33	1.87	-2.48	0.06423	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	D	0.71674	0.998	P	0.58454	0.839	T	0.08126	-1.0737	7	0.87932	D	0	.	0.9034	0.01279	0.1587:0.2289:0.3795:0.2329	rs12150888;rs52815216;rs12150888	5682	B5ME49	.	T	5682	ENSP00000381008:P5682T	ENSP00000381008:P5682T	P	-	1	0	MUC16	8931402	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.309000	0.01130	-0.422000	0.07405	-1.549000	0.00901	CCC	G|0.815;T|0.185	0.185	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PCGF3	10336	hgsc.bcm.edu	37	4	755129	755129	+	Silent	SNP	C	C	T	rs2242234	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:755129C>T	ENST00000362003.5	+	9	920	c.525C>T	c.(523-525)cgC>cgT	p.R175R	PCGF3_ENST00000521023.2_Silent_p.R141R|PCGF3_ENST00000505655.2_Silent_p.R175R|RP11-440L14.1_ENST00000503571.1_RNA|PCGF3_ENST00000470161.2_Silent_p.R175R	NM_006315.4	NP_006306.2	Q3KNV8	PCGF3_HUMAN	polycomb group ring finger 3	175					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(1)	7						AGTGGATCCGCTGCTCAGCCC	0.542													C|||	283	0.0565096	0.0121	0.049	5008	,	,		17446	0.125		0.0577	False		,,,				2504	0.0501				p.R175R		Atlas-SNP	.											.	PCGF3	23	.	0			c.C525T						PASS	.	C		61,3893		1,59,1917	62.0	68.0	66.0		525	3.2	1.0	4	dbSNP_98	66	510,7788		13,484,3652	no	coding-synonymous	PCGF3	NM_006315.4		14,543,5569	TT,TC,CC		6.1461,1.5427,4.6605		175/243	755129	571,11681	1977	4149	6126	SO:0001819	synonymous_variant	10336	exon9			GATCCGCTGCTCA	AK093869	CCDS3339.2	4p16.3	2013-01-09	2005-01-17	2005-01-19	ENSG00000185619	ENSG00000185619		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	10066	protein-coding gene	gene with protein product			"""ring finger protein 3"""	RNF3			Standard	XM_005272250		Approved	FLJ36550, DONG1, RNF3A, MGC40413	uc003gbe.3	Q3KNV8	OTTHUMG00000119000	ENST00000362003.5:c.525C>T	4.37:g.755129C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	150	80	0.533333	NM_006315	D3DVN1|O15262	Silent	SNP	ENST00000362003.5	37	CCDS3339.2																																																																																			C|0.930;T|0.070	0.070	strong		0.542	PCGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239197.2	NM_006315	
BZRAP1	9256	hgsc.bcm.edu	37	17	56388238	56388238	+	Missense_Mutation	SNP	C	C	G	rs2680704	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	75	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	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	
KCNV2	169522	hgsc.bcm.edu	37	9	2718654	2718654	+	Silent	SNP	G	G	A	rs7859993	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:2718654G>A	ENST00000382082.3	+	1	1153	c.915G>A	c.(913-915)gtG>gtA	p.V305V		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	305					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)		TGGAGCACGTGGAGATGCTGT	0.692													G|||	133	0.0265575	0.0386	0.0317	5008	,	,		17166	0.0		0.0467	False		,,,				2504	0.0133				p.V305V		Atlas-SNP	.											.	KCNV2	72	.	0			c.G915A						PASS	.	G		180,4222	107.3+/-145.7	6,168,2027	38.0	43.0	41.0		915	4.2	1.0	9	dbSNP_116	41	429,8169	126.3+/-184.8	10,409,3880	no	coding-synonymous	KCNV2	NM_133497.3		16,577,5907	AA,AG,GG		4.9895,4.0891,4.6846		305/546	2718654	609,12391	2201	4299	6500	SO:0001819	synonymous_variant	169522	exon1			GCACGTGGAGATG	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.915G>A	9.37:g.2718654G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	109	41	0.376147	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	37	CCDS6447.1	72	0.03296703296703297	19	0.03861788617886179	15	0.04143646408839779	0	0.0	38	0.05013192612137203	G	8.471	0.857550	0.17106	0.040891	0.049895	ENSG00000168263	ENST00000423608	.	.	.	5.11	4.18	0.49190	.	.	.	.	.	T	0.26955	0.0660	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55036	-0.8203	5	0.62326	D	0.03	.	11.4245	0.50003	0.0:0.1258:0.7279:0.1463	rs7859993;rs17656699;rs7859993	.	.	.	R	256	.	ENSP00000409635:G256R	G	+	1	0	KCNV2	2708654	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	0.314000	0.19432	2.362000	0.80069	0.563000	0.77884	GGA	G|0.957;A|0.043	0.043	strong		0.692	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
CHD5	26038	hgsc.bcm.edu	37	1	6209363	6209363	+	Silent	SNP	T	T	C	rs12565328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	116	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	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	
RPTN	126638	hgsc.bcm.edu	37	1	152129100	152129100	+	Missense_Mutation	SNP	C	C	T	rs200003389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152129100C>T	ENST00000316073.3	-	3	539	c.475G>A	c.(475-477)Ggt>Agt	p.G159S		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	159	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TCAGACTGACCATGGTGGGAA	0.502																																					p.G159S		Atlas-SNP	.											RPTN,NS,carcinoma,0,1	RPTN	123	1	1	Deletion - In frame(1)	stomach(1)	c.G475A						scavenged	.	C	SER/GLY	0,3128		0,0,1564	469.0	409.0	427.0		475	-0.8	0.0	1	dbSNP_134	427	1,7133		0,1,3566	yes	missense	RPTN	NM_001122965.1	56	0,1,5130	TT,TC,CC		0.014,0.0,0.0097	benign	159/785	152129100	1,10261	1564	3567	5131	SO:0001583	missense	126638	exon3			ACTGACCATGGTG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.475G>A	1.37:g.152129100C>T	ENSP00000317895:p.Gly159Ser	Somatic	324	3	0.00925926		WXS	Illumina HiSeq	Phase_I	291	45	0.154639	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.350341	0.24512	0.0	1.4E-4	ENSG00000215853	ENST00000316073	T	0.12569	2.67	4.57	-0.815	0.10843	.	0.522245	0.14186	U	0.335665	T	0.02418	0.0074	L	0.33245	0.995	0.09310	N	1	P	0.47350	0.894	B	0.38500	0.275	T	0.39820	-0.9595	10	0.33940	T	0.23	0.6761	4.3811	0.11295	0.0:0.4509:0.1612:0.3879	.	159	Q6XPR3	RPTN_HUMAN	S	159	ENSP00000317895:G159S	ENSP00000317895:G159S	G	-	1	0	RPTN	150395724	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.352000	0.07701	-0.522000	0.06417	-0.272000	0.10252	GGT	C|0.966;T|0.034	0.034	strong		0.502	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
LPXN	9404	hgsc.bcm.edu	37	11	58318619	58318619	+	Silent	SNP	C	C	G	rs1047979	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58318619C>G	ENST00000395074.2	-	5	493	c.405G>C	c.(403-405)ctG>ctC	p.L135L	LPXN_ENST00000528489.1_Silent_p.L115L|LPXN_ENST00000528954.1_Silent_p.L140L	NM_004811.2	NP_004802.1	O60711	LPXN_HUMAN	leupaxin	135					cell adhesion (GO:0007155)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell adhesion (GO:0007162)|protein complex assembly (GO:0006461)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|podosome (GO:0002102)	transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				ATTCCTGCTCCAGACCCCCAA	0.552													C|||	2545	0.508187	0.2753	0.5576	5008	,	,		16402	0.6905		0.5616	False		,,,				2504	0.545				p.L140L		Atlas-SNP	.											.	LPXN	55	.	0			c.G420C						PASS	.	C	,	1534,2868	484.8+/-360.1	275,984,942	108.0	88.0	95.0		420,405	5.7	1.0	11	dbSNP_86	95	4999,3591	627.2+/-397.9	1474,2051,770	no	coding-synonymous,coding-synonymous	LPXN	NM_001143995.1,NM_004811.2	,	1749,3035,1712	GG,GC,CC		41.8044,34.8478,49.7152	,	140/392,135/387	58318619	6533,6459	2201	4295	6496	SO:0001819	synonymous_variant	9404	exon5			CTGCTCCAGACCC	AF062075	CCDS7969.1, CCDS53635.1	11q12.1	2013-09-20			ENSG00000110031	ENSG00000110031			14061	protein-coding gene	gene with protein product		605390				9565592	Standard	NM_004811		Approved	LDPL	uc001nmw.3	O60711	OTTHUMG00000167466	ENST00000395074.2:c.405G>C	11.37:g.58318619C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_001143995	B2R8B4|B4DV71|Q53FW6|Q6FI07	Silent	SNP	ENST00000395074.2	37	CCDS7969.1																																																																																			C|0.480;G|0.520	0.520	strong		0.552	LPXN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394709.1	NM_004811	
ACER1	125981	hgsc.bcm.edu	37	19	6312290	6312290	+	Missense_Mutation	SNP	T	T	C	rs72981971	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6312290T>C	ENST00000301452.4	-	3	297	c.220A>G	c.(220-222)Atg>Gtg	p.M74V		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	74					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						TGGAAATACATGGAGAACAGG	0.622													T|||	801	0.159944	0.0113	0.1354	5008	,	,		17950	0.3194		0.1332	False		,,,				2504	0.2413				p.M74V		Atlas-SNP	.											.	ACER1	38	.	0			c.A220G						PASS	.	T	VAL/MET	160,4246	106.9+/-145.3	2,156,2045	86.0	78.0	81.0		220	2.4	1.0	19	dbSNP_130	81	1078,7522	225.1+/-261.3	71,936,3293	yes	missense	ACER1	NM_133492.2	21	73,1092,5338	CC,CT,TT		12.5349,3.6314,9.5187	possibly-damaging	74/265	6312290	1238,11768	2203	4300	6503	SO:0001583	missense	125981	exon3			AATACATGGAGAA	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.220A>G	19.37:g.6312290T>C	ENSP00000301452:p.Met74Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_133492		Missense_Mutation	SNP	ENST00000301452.4	37	CCDS12161.1	381	0.17445054945054944	8	0.016260162601626018	50	0.13812154696132597	220	0.38461538461538464	103	0.1358839050131926	T	1.543	-0.541318	0.04053	0.036314	0.125349	ENSG00000167769	ENST00000301452	T	0.41065	1.01	5.01	2.4	0.29515	.	0.291305	0.41823	D	0.000803	T	0.00012	0.0000	N	0.16903	0.455	0.30627	P	0.757875	B	0.14438	0.01	B	0.17433	0.018	T	0.43845	-0.9366	9	0.07644	T	0.81	-37.8911	3.7919	0.08724	0.1841:0.139:0.0:0.6769	.	74	Q8TDN7	ACER1_HUMAN	V	74	ENSP00000301452:M74V	ENSP00000301452:M74V	M	-	1	0	ACER1	6263290	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	1.588000	0.36633	1.884000	0.54569	0.402000	0.26972	ATG	T|0.883;C|0.117	0.117	strong		0.622	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492	
C5orf34	375444	hgsc.bcm.edu	37	5	43505993	43505993	+	Silent	SNP	A	A	G	rs7710628	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:43505993A>G	ENST00000306862.2	-	4	1164	c.789T>C	c.(787-789)aaT>aaC	p.N263N	RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34	263										breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					TGCTGATTTTATTATGAAAAT	0.373													A|||	2013	0.401957	0.6271	0.3818	5008	,	,		20847	0.0893		0.503	False		,,,				2504	0.3303				p.N263N		Atlas-SNP	.											.	C5orf34	47	.	0			c.T789C						PASS	.	A		2603,1803	640.0+/-397.2	788,1027,388	97.0	100.0	99.0		789	1.1	0.1	5	dbSNP_116	99	4196,4404	570.1+/-389.3	1017,2162,1121	no	coding-synonymous	C5orf34	NM_198566.2		1805,3189,1509	GG,GA,AA		48.7907,40.9215,47.7241		263/639	43505993	6799,6207	2203	4300	6503	SO:0001819	synonymous_variant	375444	exon4			GATTTTATTATGA	AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.789T>C	5.37:g.43505993A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	130	55	0.423077	NM_198566		Silent	SNP	ENST00000306862.2	37	CCDS3946.1																																																																																			A|0.526;G|0.474	0.474	strong		0.373	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566	
C16orf96	342346	hgsc.bcm.edu	37	16	4626215	4626215	+	Silent	SNP	C	C	T	rs79448011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4626215C>T	ENST00000444310.4	+	5	1734	c.1734C>T	c.(1732-1734)taC>taT	p.Y578Y		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						ccgcagcctacgccgctgccA	0.647													C|||	79	0.0157748	0.0038	0.0259	5008	,	,		14408	0.0		0.0427	False		,,,				2504	0.0133				p.Y578Y		Atlas-SNP	.											.	C16orf96	28	.	0			c.C1734T						PASS	.						8.0	18.0	15.0					16																	4626215		671	1539	2210	SO:0001819	synonymous_variant	342346	exon5			AGCCTACGCCGCT		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.1734C>T	16.37:g.4626215C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_001145011		Silent	SNP	ENST00000444310.4	37	CCDS53986.1																																																																																			C|0.982;T|0.018	0.018	strong		0.647	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
LAD1	3898	hgsc.bcm.edu	37	1	201355669	201355669	+	Missense_Mutation	SNP	T	T	C	rs68021059	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201355669T>C	ENST00000391967.2	-	3	1121	c.820A>G	c.(820-822)Act>Gct	p.T274A	LAD1_ENST00000488842.1_5'Flank|LAD1_ENST00000367313.3_Missense_Mutation_p.T288A	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	136	0	0		WXS	Illumina HiSeq	Phase_I	199	78	0.39196	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	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189215	11189215	+	Silent	SNP	C	C	A	rs151245433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11189215C>A	ENST00000382435.4	+	1	819	c.600C>A	c.(598-600)ggC>ggA	p.G200G		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	200						integral component of membrane (GO:0016021)		p.G200G(1)									TCCTGGGAGGCCTGGCGCTGT	0.592																																					p.G200G		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C600A						scavenged	.						106.0	112.0	110.0					8																	11189215		2203	4300	6503	SO:0001819	synonymous_variant	83650	exon1			GGGAGGCCTGGCG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.600C>A	8.37:g.11189215C>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	233	25	0.107296	NM_054028	A2RRL6	Silent	SNP	ENST00000382435.4	37	CCDS5980.1																																																																																			C|0.988;A|0.011	0.011	strong		0.592	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
EXD3	54932	hgsc.bcm.edu	37	9	140247229	140247229	+	Missense_Mutation	SNP	C	C	T	rs199618022		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140247229C>T	ENST00000340951.4	-	11	1075	c.880G>A	c.(880-882)Ggg>Agg	p.G294R	EXD3_ENST00000342129.4_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						GGGCTCTGCCCCACCAGGCCC	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		15015	0.0		0.001	False		,,,				2504	0.0				p.G294R		Atlas-SNP	.											.	EXD3	86	.	0			c.G880A						PASS	.	C	ARG/GLY	0,4056		0,0,2028	8.0	11.0	10.0		880	1.1	0.5	9		10	4,8308		0,4,4152	yes	missense	EXD3	NM_017820.3	125	0,4,6180	TT,TC,CC		0.0481,0.0,0.0323	probably-damaging	294/877	140247229	4,12364	2028	4156	6184	SO:0001583	missense	54932	exon11			TCTGCCCCACCAG		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.880G>A	9.37:g.140247229C>T	ENSP00000340474:p.Gly294Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008915	0.35415	0.0	4.81E-4	ENSG00000187609	ENST00000340951	T	0.54071	0.59	3.3	1.08	0.20341	.	0.478752	0.20256	N	0.095973	T	0.36580	0.0972	L	0.50333	1.59	0.80722	D	1	P	0.37441	0.595	B	0.31016	0.123	T	0.26395	-1.0104	10	0.72032	D	0.01	.	3.4786	0.07594	0.0:0.564:0.2713:0.1647	.	294	Q8N9H8	MUT7_HUMAN	R	294	ENSP00000340474:G294R	ENSP00000340474:G294R	G	-	1	0	EXD3	139367050	0.000000	0.05858	0.493000	0.27502	0.261000	0.26267	0.259000	0.18405	0.646000	0.30693	0.491000	0.48974	GGG	.	.	weak		0.672	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
SPEF2	79925	hgsc.bcm.edu	37	5	35695844	35695844	+	Silent	SNP	T	T	C	rs78576797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:35695844T>C	ENST00000356031.3	+	14	2137	c.1983T>C	c.(1981-1983)aaT>aaC	p.N661N	SPEF2_ENST00000440995.2_Silent_p.N656N|CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000509059.1_Silent_p.N656N	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	661					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAGGTGCTAATGCTGATAAAA	0.323													T|||	104	0.0207668	0.0159	0.0159	5008	,	,		19276	0.002		0.0229	False		,,,				2504	0.0481				p.N661N		Atlas-SNP	.											.	SPEF2	324	.	0			c.T1983C						PASS	.	T		68,3614		1,66,1774	124.0	113.0	116.0		1983	-2.6	0.0	5	dbSNP_132	116	202,7978		3,196,3891	no	coding-synonymous	SPEF2	NM_024867.3		4,262,5665	CC,CT,TT		2.4694,1.8468,2.2762		661/1823	35695844	270,11592	1841	4090	5931	SO:0001819	synonymous_variant	79925	exon14			TGCTAATGCTGAT	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.1983T>C	5.37:g.35695844T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Silent	SNP	ENST00000356031.3	37	CCDS43309.1																																																																																			T|0.979;C|0.021	0.021	strong		0.323	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
RAD51AP2	729475	hgsc.bcm.edu	37	2	17696573	17696573	+	Missense_Mutation	SNP	C	C	T	rs834514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:17696573C>T	ENST00000399080.2	-	1	3133	c.3110G>A	c.(3109-3111)gGt>gAt	p.G1037D		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	1037			G -> D (in dbSNP:rs834514).							endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CATATTAGGACCTGCTATAGT	0.358													C|||	2908	0.580671	0.1339	0.6326	5008	,	,		19259	0.8849		0.6183	False		,,,				2504	0.7955				p.G1037D		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.G3110A						PASS	.	C	ASP/GLY	955,2719		136,683,1018	151.0	138.0	142.0		3110	2.3	0.0	2	dbSNP_86	142	5110,3072		1605,1900,586	yes	missense	RAD51AP2	NM_001099218.2	94	1741,2583,1604	TT,TC,CC		37.5458,25.9935,48.8445	probably-damaging	1037/1160	17696573	6065,5791	1837	4091	5928	SO:0001583	missense	729475	exon1			TTAGGACCTGCTA	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.3110G>A	2.37:g.17696573C>T	ENSP00000382030:p.Gly1037Asp	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	254	136	0.535433	NM_001099218		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	1264	0.5787545787545788	85	0.17276422764227642	220	0.6077348066298343	500	0.8741258741258742	459	0.6055408970976254	C	8.123	0.781475	0.16120	0.259935	0.624542	ENSG00000214842	ENST00000399080	T	0.32515	1.45	5.15	2.29	0.28610	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.23540	0.087	B	0.25759	0.063	T	0.08700	-1.0709	8	0.30078	T	0.28	-0.2348	5.6724	0.17729	0.0:0.5727:0.1336:0.2937	rs834514;rs1619596;rs2139384;rs17380198;rs52804587;rs834514	1037	Q09MP3	R51A2_HUMAN	D	1037	ENSP00000382030:G1037D	ENSP00000382030:G1037D	G	-	2	0	RAD51AP2	17560054	0.000000	0.05858	0.002000	0.10522	0.043000	0.13939	0.320000	0.19540	0.246000	0.21394	0.655000	0.94253	GGT	C|0.409;T|0.591	0.591	strong		0.358	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
WDR33	55339	hgsc.bcm.edu	37	2	128464116	128464116	+	Silent	SNP	G	G	A	rs34550770	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:128464116G>A	ENST00000322313.4	-	22	3950	c.3792C>T	c.(3790-3792)ggC>ggT	p.G1264G		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1264					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CAGGTCCTGGGCCCCCTCGGC	0.493													G|||	191	0.038139	0.0053	0.0519	5008	,	,		18704	0.0		0.1143	False		,,,				2504	0.0337				p.G1264G		Atlas-SNP	.											.	WDR33	136	.	0			c.C3792T						PASS	.	G		89,4317	75.2+/-113.4	0,89,2114	47.0	51.0	50.0		3792	4.2	1.0	2	dbSNP_126	50	802,7798	186.7+/-234.1	45,712,3543	no	coding-synonymous	WDR33	NM_018383.4		45,801,5657	AA,AG,GG		9.3256,2.02,6.8507		1264/1337	128464116	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	55339	exon22			TCCTGGGCCCCCT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3792C>T	2.37:g.128464116G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	37	CCDS2150.1																																																																																			G|0.935;A|0.065	0.065	strong		0.493	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
RPH3A	22895	hgsc.bcm.edu	37	12	113325629	113325629	+	Silent	SNP	T	T	C	rs4141253	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:113325629T>C	ENST00000389385.4	+	17	1961	c.1464T>C	c.(1462-1464)ttT>ttC	p.F488F	RPH3A_ENST00000447659.2_Silent_p.F439F|RPH3A_ENST00000548866.1_Silent_p.F439F|RPH3A_ENST00000543106.2_Silent_p.F488F|RPH3A_ENST00000551052.1_Silent_p.F484F|RPH3A_ENST00000415485.3_Silent_p.F488F|RPH3A_ENST00000420983.2_Silent_p.F488F|RPH3A_ENST00000549913.2_3'UTR	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	488	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		AGGACAAATTTGGCCACAATG	0.468													T|||	2612	0.521565	0.5446	0.5735	5008	,	,		19581	0.623		0.4165	False		,,,				2504	0.4571				p.F488F		Atlas-SNP	.											.	RPH3A	98	.	0			c.T1464C						PASS	.	T	,	2210,2196	591.0+/-387.5	558,1094,551	157.0	159.0	159.0		1464,1452	1.6	1.0	12	dbSNP_110	159	3390,5210	500.6+/-375.3	724,1942,1634	yes	coding-synonymous,coding-synonymous	RPH3A	NM_001143854.1,NM_014954.3	,	1282,3036,2185	CC,CT,TT		39.4186,49.8411,43.0571	,	488/695,484/691	113325629	5600,7406	2203	4300	6503	SO:0001819	synonymous_variant	22895	exon17			CAAATTTGGCCAC	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.1464T>C	12.37:g.113325629T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_001143854	B7Z3C3|Q96AE0	Silent	SNP	ENST00000389385.4	37	CCDS44979.1																																																																																			T|0.535;C|0.465	0.465	strong		0.468	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954	
USP45	85015	hgsc.bcm.edu	37	6	99894086	99894086	+	Missense_Mutation	SNP	C	C	G	rs41288947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:99894086C>G	ENST00000327681.6	-	14	2094	c.1562G>C	c.(1561-1563)aGa>aCa	p.R521T	USP45_ENST00000539675.1_Intron|USP45_ENST00000369233.2_Missense_Mutation_p.R473T|USP45_ENST00000392738.2_Missense_Mutation_p.R201T|USP45_ENST00000500704.2_Missense_Mutation_p.R521T	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	521	USP.		R -> T (in dbSNP:rs41288947). {ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			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)		ACTACTGGATCTGAACAGCCC	0.488													C|||	1102	0.220048	0.1566	0.3386	5008	,	,		18812	0.0923		0.3171	False		,,,				2504	0.2536				p.R521T		Atlas-SNP	.											.	USP45	56	.	0			c.G1562C						PASS	.	C	THR/ARG	807,3599	323.7+/-298.2	81,645,1477	83.0	69.0	74.0		1562	4.2	0.0	6	dbSNP_127	74	2833,5767	446.1+/-361.2	481,1871,1948	yes	missense	USP45	NM_001080481.1	71	562,2516,3425	GG,GC,CC		32.9419,18.3159,27.9871	benign	521/815	99894086	3640,9366	2203	4300	6503	SO:0001583	missense	85015	exon14			CTGGATCTGAACA	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.1562G>C	6.37:g.99894086C>G	ENSP00000333376:p.Arg521Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	132	51	0.386364	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	492	0.22527472527472528	79	0.16056910569105692	121	0.3342541436464088	54	0.0944055944055944	238	0.31398416886543534	C	12.74	2.029739	0.35797	0.183159	0.329419	ENSG00000123552	ENST00000392738;ENST00000500704;ENST00000327681;ENST00000369233	T;T;T;T	0.17054	2.3;3.81;3.81;3.78	5.09	4.2	0.49525	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.629809	0.15993	N	0.234732	T	0.06735	0.0172	L	0.40543	1.245	0.38176	P	0.06051399999999996	P;P	0.39404	0.669;0.672	B;B	0.38225	0.265;0.268	T	0.20605	-1.0270	9	0.14656	T	0.56	.	15.0365	0.71751	0.0:0.7131:0.2869:0.0	rs41288947;rs62432293	521;201	Q70EL2;Q70EL2-3	UBP45_HUMAN;.	T	201;521;521;473	ENSP00000376495:R201T;ENSP00000424372:R521T;ENSP00000333376:R521T;ENSP00000358236:R473T	ENSP00000333376:R521T	R	-	2	0	USP45	100000807	0.004000	0.15560	0.002000	0.10522	0.079000	0.17450	1.774000	0.38573	1.320000	0.45209	0.655000	0.94253	AGA	C|0.737;G|0.263	0.263	strong		0.488	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
DOCK3	1795	hgsc.bcm.edu	37	3	51386357	51386357	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:51386357C>T	ENST00000266037.9	+	39	4013	c.3990C>T	c.(3988-3990)ctC>ctT	p.L1330L		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1330	DHR-2.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACCAGAGCCTCAGCTGGATTC	0.562																																					p.L1330L		Atlas-SNP	.											.	DOCK3	397	.	0			c.C3990T						PASS	.						67.0	67.0	67.0					3																	51386357		1965	4145	6110	SO:0001819	synonymous_variant	1795	exon39			GAGCCTCAGCTGG	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.3990C>T	3.37:g.51386357C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_004947	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																			.	.	none		0.562	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	
OR51F1	256892	hgsc.bcm.edu	37	11	4790671	4790671	+	Silent	SNP	C	C	T	rs11033795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790671C>T	ENST00000380383.1	-	1	497	c.498G>A	c.(496-498)ttG>ttA	p.L166L	OR51F1_ENST00000343430.3_Silent_p.L159L|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	166						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)		AAAGTAGTGGCAATATTAGTA	0.403													T|||	1080	0.215655	0.4569	0.2017	5008	,	,		22619	0.0		0.2704	False		,,,				2504	0.0654				p.L159L		Atlas-SNP	.											.	OR51F1	60	.	0			c.G477A						PASS	.	T		1968,2434	618.7+/-393.2	445,1078,678	115.0	115.0	115.0		477	-8.8	0.0	11	dbSNP_120	115	2179,6417	712.2+/-405.9	291,1597,2410	no	coding-synonymous	OR51F1	NM_001004752.1		736,2675,3088	TT,TC,CC		25.349,44.707,31.9049		159/313	4790671	4147,8851	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			TAGTGGCAATATT	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.498G>A	11.37:g.4790671C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				C|0.706;T|0.294	0.294	strong		0.403	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
ITIH2	3698	hgsc.bcm.edu	37	10	7759595	7759595	+	Silent	SNP	C	C	T	rs7072478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	36	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	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	
KRT75	9119	hgsc.bcm.edu	37	12	52818377	52818377	+	Missense_Mutation	SNP	C	C	T	rs61730614	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52818377C>T	ENST00000252245.5	-	9	1800	c.1580G>A	c.(1579-1581)cGg>cAg	p.R527Q	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	527	Tail.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R527Q(1)		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)		CCCTAAGCCCCGGTTGCTGGT	0.622													C|||	816	0.162939	0.09	0.2493	5008	,	,		18615	0.1558		0.164	False		,,,				2504	0.2065				p.R527Q		Atlas-SNP	.											KRT75,rectum,NS,0,2	KRT75	75	2	1	Substitution - Missense(1)	large_intestine(1)	c.G1580A						PASS	.	C	GLN/ARG	495,3911	230.4+/-244.6	28,439,1736	159.0	158.0	158.0		1580	4.8	1.0	12	dbSNP_129	158	1401,7199	270.1+/-288.8	115,1171,3014	yes	missense	KRT75	NM_004693.2	43	143,1610,4750	TT,TC,CC		16.2907,11.2347,14.5779	probably-damaging	527/552	52818377	1896,11110	2203	4300	6503	SO:0001583	missense	9119	exon9			AAGCCCCGGTTGC	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.1580G>A	12.37:g.52818377C>T	ENSP00000252245:p.Arg527Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	171	90	0.526316	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	346	0.15842490842490842	41	0.08333333333333333	78	0.2154696132596685	95	0.1660839160839161	132	0.1741424802110818	C	15.92	2.976106	0.53720	0.112347	0.162907	ENSG00000170454	ENST00000252245	D	0.87809	-2.3	4.83	4.83	0.62350	.	0.000000	0.40064	N	0.001187	T	0.00328	0.0010	L	0.43152	1.355	0.30791	P	0.7408779999999999	D	0.89917	1.0	D	0.74023	0.982	T	0.18935	-1.0321	9	0.16420	T	0.52	.	13.2889	0.60260	0.0:1.0:0.0:0.0	.	527	O95678	K2C75_HUMAN	Q	527	ENSP00000252245:R527Q	ENSP00000252245:R527Q	R	-	2	0	KRT75	51104644	0.574000	0.26684	0.995000	0.50966	0.493000	0.33554	1.022000	0.30052	2.503000	0.84419	0.561000	0.74099	CGG	C|0.848;T|0.152	0.152	strong		0.622	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
NELL1	4745	hgsc.bcm.edu	37	11	21392487	21392487	+	Silent	SNP	C	C	T	rs4151056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:21392487C>T	ENST00000357134.5	+	15	1790	c.1638C>T	c.(1636-1638)tgC>tgT	p.C546C	NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000298925.5_Silent_p.C574C|NELL1_ENST00000325319.5_Silent_p.C489C|NELL1_ENST00000532434.1_Silent_p.C546C	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	546	EGF-like 3. {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						GAAGCCACTGCGAGAAAGGTA	0.433													C|||	801	0.159944	0.2216	0.0735	5008	,	,		18435	0.2698		0.0726	False		,,,				2504	0.1145				p.C546C		Atlas-SNP	.											.	NELL1	179	.	0			c.C1638T						PASS	.	C	,	831,3575	325.3+/-299.0	81,669,1453	93.0	88.0	90.0		1638,1638	-7.8	0.6	11	dbSNP_110	90	469,8131	137.6+/-194.5	12,445,3843	no	coding-synonymous,coding-synonymous	NELL1	NM_006157.3,NM_201551.1	,	93,1114,5296	TT,TC,CC		5.4535,18.8606,9.9954	,	546/811,546/764	21392487	1300,11706	2203	4300	6503	SO:0001819	synonymous_variant	4745	exon15			CCACTGCGAGAAA	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.1638C>T	11.37:g.21392487C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	100	61	0.61	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	37	CCDS7855.1																																																																																			C|0.868;T|0.132	0.132	strong		0.433	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
PER3	8863	hgsc.bcm.edu	37	1	7890153	7890153	+	Missense_Mutation	SNP	C	C	T	rs144178755	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:7890153C>T	ENST00000361923.2	+	18	3294	c.3119C>T	c.(3118-3120)aCt>aTt	p.T1040I	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.T1049I	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1040	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.				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)		TCCCATCCTACTGCCACTGTT	0.547													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18916	0.0		0.0	False		,,,				2504	0.0				p.T1040I		Atlas-SNP	.											.	PER3	95	.	0			c.C3119T						PASS	.	C	ILE/THR	0,4406		0,0,2203	142.0	115.0	124.0		3119	0.4	0.0	1	dbSNP_134	124	24,8576	17.3+/-56.4	0,24,4276	yes	missense	PER3	NM_016831.1	89	0,24,6479	TT,TC,CC		0.2791,0.0,0.1845	benign	1040/1202	7890153	24,12982	2203	4300	6503	SO:0001583	missense	8863	exon18			ATCCTACTGCCAC	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.3119C>T	1.37:g.7890153C>T	ENSP00000355031:p.Thr1040Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	7.381	0.628779	0.14257	0.0	0.002791	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.11495	2.77;2.83	1.61	0.359	0.16088	Period circadian-like, C-terminal (1);	7.092960	0.01606	U	0.022261	T	0.08891	0.0220	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.30889	0.075;0.054;0.299;0.248;0.054	B;B;B;B;B	0.27500	0.013;0.05;0.08;0.067;0.05	T	0.31166	-0.9953	10	0.52906	T	0.07	.	2.8786	0.05640	0.0:0.6047:0.0:0.3953	.	89;1040;1049;1049;1040	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	I	1049;1040;233	ENSP00000366755:T1049I;ENSP00000355031:T1040I	ENSP00000355031:T1040I	T	+	2	0	PER3	7812740	0.086000	0.21541	0.017000	0.16124	0.014000	0.08584	-0.079000	0.11357	0.692000	0.31613	0.305000	0.20034	ACT	C|0.998;T|0.002	0.002	strong		0.547	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
B4GALT3	8703	hgsc.bcm.edu	37	1	161145005	161145005	+	Silent	SNP	C	C	T	rs3813620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161145005C>T	ENST00000319769.5	-	4	489	c.267G>A	c.(265-267)tcG>tcA	p.S89S	PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000367998.1_Silent_p.S89S|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|B4GALT3_ENST00000470882.1_5'UTR	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	89					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	TAAAGGACACCGACACAGGAC	0.572													C|||	456	0.0910543	0.1044	0.0663	5008	,	,		19458	0.0675		0.0736	False		,,,				2504	0.1329				p.S89S		Atlas-SNP	.											.	B4GALT3	39	.	0			c.G267A						PASS	.	C	,,	510,3896	234.2+/-247.1	34,442,1727	46.0	45.0	45.0		267,267,267	-1.7	1.0	1	dbSNP_107	45	680,7920	169.3+/-220.7	31,618,3651	no	coding-synonymous,coding-synonymous,coding-synonymous	B4GALT3	NM_001199873.1,NM_001199874.1,NM_003779.3	,,	65,1060,5378	TT,TC,CC		7.907,11.5751,9.1496	,,	89/394,89/394,89/394	161145005	1190,11816	2203	4300	6503	SO:0001819	synonymous_variant	8703	exon4			GGACACCGACACA	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.267G>A	1.37:g.161145005C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Silent	SNP	ENST00000319769.5	37	CCDS1222.1																																																																																			C|0.918;T|0.082	0.082	strong		0.572	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
MUC2	4583	hgsc.bcm.edu	37	11	1092953	1092953	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1092953C>T	ENST00000441003.2	+	30	4799	c.4772C>T	c.(4771-4773)aCg>aTg	p.T1591M	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Splice_Site_p.T1592M|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1592M(1)|p.T1591M(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accaccactacggtgacccca	0.627																																					p.T1591M		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,-1,4	MUC2	614	4	2	Substitution - Missense(2)	endometrium(2)	c.C4772T						scavenged	.						54.0	86.0	74.0					11																	1092953		1812	3313	5125	SO:0001583	missense	4583	exon30			CCACTACGGTGAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4772C>T	11.37:g.1092953C>T	ENSP00000415183:p.Thr1591Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	77	3	0.038961	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.179	-0.168424	0.06461	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.16743	2.32;2.56	1.75	-0.619	0.11572	.	6.725620	0.00827	U	0.001636	T	0.08846	0.0219	.	.	.	0.09310	N	1	D	0.60575	0.988	B	0.34489	0.184	T	0.24548	-1.0157	9	0.32370	T	0.25	.	3.3423	0.07123	0.2481:0.5888:0.0:0.163	.	1591	E7EUV1	.	M	1591;1592	ENSP00000415183:T1591M;ENSP00000351956:T1592M	ENSP00000351956:T1592M	T	+	2	0	MUC2	1082953	0.064000	0.20934	0.000000	0.03702	0.189000	0.23516	1.615000	0.36922	-0.313000	0.08728	0.121000	0.15741	ACG	.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SMURF1	57154	hgsc.bcm.edu	37	7	98650051	98650051	+	Silent	SNP	G	G	C	rs219797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:98650051G>C	ENST00000361125.1	-	7	817	c.498C>G	c.(496-498)tcC>tcG	p.S166S	SMURF1_ENST00000361368.2_Silent_p.S166S|SMURF1_ENST00000480055.1_5'UTR	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	166					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCCCAGGCCCGGAGTCTTCAT	0.597													C|||	3413	0.68151	0.9561	0.5375	5008	,	,		18187	0.6498		0.504	False		,,,				2504	0.6278				p.S166S		Atlas-SNP	.											.	SMURF1	58	.	0			c.C498G						PASS	.	C	,,	3959,447	213.5+/-233.1	1782,395,26	35.0	35.0	35.0		498,498,498	-10.5	0.0	7	dbSNP_79	35	4367,4233	567.1+/-388.8	1133,2101,1066	no	coding-synonymous,coding-synonymous,coding-synonymous	SMURF1	NM_001199847.1,NM_020429.2,NM_181349.2	,,	2915,2496,1092	CC,CG,GG		49.2209,10.1453,35.9834	,,	166/729,166/758,166/732	98650051	8326,4680	2203	4300	6503	SO:0001819	synonymous_variant	57154	exon7			AGGCCCGGAGTCT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.498C>G	7.37:g.98650051G>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Silent	SNP	ENST00000361125.1	37	CCDS34690.1																																																																																			G|0.362;C|0.638	0.638	strong		0.597	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
RAD21	5885	hgsc.bcm.edu	37	8	117864217	117864217	+	Silent	SNP	A	A	G	rs1050838	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:117864217A>G	ENST00000297338.2	-	11	1727	c.1440T>C	c.(1438-1440)gcT>gcC	p.A480A	RAD21_ENST00000518055.1_Silent_p.A25A|RAD21_ENST00000523986.1_5'UTR|RAD21_ENST00000517749.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	480	Pro-rich.				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)		p.A480A(1)		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)					CAATTTGTCCAGCTTTTCGCT	0.473													A|||	667	0.133187	0.0076	0.2536	5008	,	,		18166	0.1696		0.1501	False		,,,				2504	0.1626				p.A480A		Atlas-SNP	.											RAD21,NS,carcinoma,0,1	RAD21	95	1	1	Substitution - coding silent(1)	stomach(1)	c.T1440C						PASS	.	A		150,4256	104.7+/-143.2	3,144,2056	140.0	125.0	130.0		1440	-11.4	0.0	8	dbSNP_86	130	1464,7136	279.8+/-294.2	128,1208,2964	yes	coding-synonymous	RAD21	NM_006265.2		131,1352,5020	GG,GA,AA		17.0233,3.4044,12.4097		480/632	117864217	1614,11392	2203	4300	6503	SO:0001819	synonymous_variant	5885	exon11			TTGTCCAGCTTTT	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.1440T>C	8.37:g.117864217A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	185	91	0.491892	NM_006265	A8K0E0|Q15001|Q99568	Silent	SNP	ENST00000297338.2	37	CCDS6321.1																																																																																			A|0.871;G|0.129	0.129	strong		0.473	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265	
WNK2	65268	hgsc.bcm.edu	37	9	96055063	96055063	+	Silent	SNP	C	C	T	rs41278286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96055063C>T	ENST00000297954.4	+	23	5427	c.5427C>T	c.(5425-5427)gaC>gaT	p.D1809D	WNK2_ENST00000427277.2_Silent_p.D1384D|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000356055.3_Silent_p.D136D|WNK2_ENST00000349097.3_Silent_p.D1421D|WNK2_ENST00000395477.2_Silent_p.D1772D	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1809					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CCCCACCCGACGTCTACCTGG	0.692													C|||	1965	0.392372	0.3487	0.2954	5008	,	,		13856	0.4206		0.3131	False		,,,				2504	0.5726				p.D1772D		Atlas-SNP	.											WNK2_ENST00000297954,colon,carcinoma,+2,4	WNK2	277	4	0			c.C5316T						PASS	.	C		1467,2891		252,963,964	15.0	15.0	15.0		5316	-1.8	0.9	9	dbSNP_127	15	2457,6027		393,1671,2178	no	coding-synonymous	WNK2	NM_006648.3		645,2634,3142	TT,TC,CC		28.9604,33.6622,30.556		1772/2218	96055063	3924,8918	2179	4242	6421	SO:0001819	synonymous_variant	65268	exon22			ACCCGACGTCTAC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.5427C>T	9.37:g.96055063C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	144	70	0.486111	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		777|777	0.3557692307692308|0.3557692307692308	176|176	0.35772357723577236|0.35772357723577236	105|105	0.2900552486187845|0.2900552486187845	256|256	0.44755244755244755|0.44755244755244755	240|240	0.316622691292876|0.316622691292876	C|C	0.625|0.625	-0.819743|-0.819743	0.02776|0.02776	0.336622|0.336622	0.289604|0.289604	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251;ENST00000453718	.|.	.|.	.|.	5.39|5.39	-1.75|-1.75	0.08031|0.08031	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999996005|0.9999999999996005	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46005|0.46005	-0.9222|-0.9222	3|3	.|.	.|.	.|.	.|.	11.3977|11.3977	0.49851|0.49851	0.0:0.3577:0.0:0.6423|0.0:0.3577:0.0:0.6423	rs41278286;rs57682323;rs61738874|rs41278286;rs57682323;rs61738874	.|.	.|.	.|.	C|M	1376|1768;569;294	.|.	.|.	R|T	+|+	1|2	0|0	WNK2|WNK2	95094884|95094884	0.000000|0.000000	0.05858|0.05858	0.908000|0.908000	0.35775|0.35775	0.064000|0.064000	0.16182|0.16182	-2.297000|-2.297000	0.01141|0.01141	-0.195000|-0.195000	0.10382|0.10382	-1.010000|-1.010000	0.02471|0.02471	CGT|ACG	C|0.672;T|0.328	0.328	strong		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
RAB3GAP2	25782	hgsc.bcm.edu	37	1	220331205	220331205	+	Missense_Mutation	SNP	C	C	G	rs2289189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:220331205C>G	ENST00000358951.2	-	30	3391	c.3275G>C	c.(3274-3276)aGt>aCt	p.S1092T		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	1092			S -> T (in dbSNP:rs2289189).		establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TGCTGTGTCACTCATTCCCAC	0.408													C|||	302	0.0603035	0.0076	0.0519	5008	,	,		18060	0.0486		0.0885	False		,,,				2504	0.1207				p.S1092T		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.G3275C						PASS	.	C	THR/SER	95,4311	76.2+/-114.5	2,91,2110	103.0	95.0	97.0		3275	5.6	1.0	1	dbSNP_100	97	805,7795	186.9+/-234.3	40,725,3535	yes	missense	RAB3GAP2	NM_012414.3	58	42,816,5645	GG,GC,CC		9.3605,2.1562,6.9199	probably-damaging	1092/1394	220331205	900,12106	2203	4300	6503	SO:0001583	missense	25782	exon30			GTGTCACTCATTC	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.3275G>C	1.37:g.220331205C>G	ENSP00000351832:p.Ser1092Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	37	CCDS31028.1	130	0.05952380952380952	7	0.014227642276422764	24	0.06629834254143646	34	0.05944055944055944	65	0.08575197889182058	C	29.6	5.018157	0.93404	0.021562	0.093605	ENSG00000118873	ENST00000358951	T	0.38560	1.13	5.59	5.59	0.84812	.	0.040952	0.85682	D	0.000000	T	0.04318	0.0119	L	0.55990	1.75	0.18873	P	0.9999822873	D;D	0.61080	0.989;0.989	P;P	0.59357	0.856;0.856	T	0.00802	-1.1560	9	0.39692	T	0.17	.	19.5886	0.95498	0.0:1.0:0.0:0.0	rs2289189;rs52789504;rs2289189	1092;1092	Q9H2M9;A6H8V0	RBGPR_HUMAN;.	T	1092	ENSP00000351832:S1092T	ENSP00000351832:S1092T	S	-	2	0	RAB3GAP2	218397828	1.000000	0.71417	0.967000	0.41034	0.995000	0.86356	7.430000	0.80321	2.642000	0.89623	0.591000	0.81541	AGT	C|0.932;G|0.068	0.068	strong		0.408	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414	
JAG1	182	hgsc.bcm.edu	37	20	10620386	10620386	+	Silent	SNP	A	A	G	rs1051419	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	272	144	0.529412	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	
SLC25A10	1468	hgsc.bcm.edu	37	17	79686879	79686879	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79686879G>A	ENST00000350690.5	+	10	810	c.724G>A	c.(724-726)Gtg>Atg	p.V242M	SLC25A10_ENST00000545862.1_Missense_Mutation_p.V199M|SLC25A10_ENST00000571730.1_Missense_Mutation_p.V397M|SLC25A10_ENST00000541223.1_Missense_Mutation_p.V397M|SLC25A10_ENST00000331531.5_Missense_Mutation_p.V251M	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	242					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)	p.V242L(1)		endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	CCACTGCGCCGTGGAGACAGC	0.602																																					p.V251M		Atlas-SNP	.											SLC25A10,NS,carcinoma,0,1	SLC25A10	24	1	1	Substitution - Missense(1)	lung(1)	c.G751A						PASS	.						156.0	180.0	172.0					17																	79686879		2203	4300	6503	SO:0001583	missense	1468	exon10			TGCGCCGTGGAGA		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"""Solute carriers"""	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.724G>A	17.37:g.79686879G>A	ENSP00000345580:p.Val242Met	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Missense_Mutation	SNP	ENST00000350690.5	37	CCDS11786.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.320337	0.23994	.	.	ENSG00000183048	ENST00000541223;ENST00000331531;ENST00000350690;ENST00000545862	T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26	4.36	-8.72	0.00845	Mitochondrial carrier domain (2);	0.647462	0.14300	N	0.328340	T	0.48696	0.1514	N	0.25286	0.73	0.09310	N	1	B;B;B	0.20988	0.018;0.05;0.025	B;B;B	0.20184	0.028;0.017;0.028	T	0.46373	-0.9196	10	0.14656	T	0.56	-2.2797	1.993	0.03450	0.3866:0.2096:0.2979:0.1059	.	397;251;242	B4DLN1;Q9UBX3-2;Q9UBX3	.;.;DIC_HUMAN	M	397;251;242;199	ENSP00000439565:V397M;ENSP00000328403:V251M;ENSP00000345580:V242M;ENSP00000446242:V199M	ENSP00000328403:V251M	V	+	1	0	SLC25A10	77297284	0.000000	0.05858	0.004000	0.12327	0.372000	0.29890	-1.990000	0.01479	-1.305000	0.02327	0.655000	0.94253	GTG	.	.	none		0.602	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155250786	155250786	+	Silent	SNP	G	G	A	rs34249493	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155250786G>A	ENST00000357232.4	-	11	2441	c.2442C>T	c.(2440-2442)cgC>cgT	p.R814R	DCHS2_ENST00000339452.1_Silent_p.R1269R	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	814	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(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)		GTGGGGAGCCGCGGTCTGTCA	0.547													G|||	51	0.0101837	0.0038	0.0187	5008	,	,		16009	0.0		0.0258	False		,,,				2504	0.0072				p.R1269R		Atlas-SNP	.											DCHS2_ENST00000339452,lower_third,carcinoma,-1,2	DCHS2	594	2	0			c.C3807T						PASS	.	G	,	19,4387	28.1+/-56.4	0,19,2184	102.0	79.0	87.0		3807,2442	-3.2	0.9	4	dbSNP_126	87	323,8277	113.9+/-173.9	6,311,3983	no	coding-synonymous,coding-synonymous	DCHS2	NM_001142552.1,NM_017639.3	,	6,330,6167	AA,AG,GG		3.7558,0.4312,2.6296	,	1269/1370,814/2917	155250786	342,12664	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon6			GGAGCCGCGGTCT	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.2442C>T	4.37:g.155250786G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			G|0.978;A|0.022	0.022	strong		0.547	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
ALG10B	144245	hgsc.bcm.edu	37	12	38715000	38715000	+	Silent	SNP	A	A	G	rs35518352	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:38715000A>G	ENST00000308742.4	+	3	1723	c.1407A>G	c.(1405-1407)caA>caG	p.Q469Q	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	469					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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				AGGACATTCAAAGGTTTATGT	0.318													A|||	1259	0.251398	0.1377	0.2867	5008	,	,		16352	0.1429		0.4513	False		,,,				2504	0.2863				p.Q469Q		Atlas-SNP	.											ALG10B,colon,carcinoma,0,1	ALG10B	58	1	0			c.A1407G						PASS	.	A		716,3688	278.7+/-274.4	65,586,1551	118.0	120.0	119.0		1407	-0.6	1.0	12	dbSNP_126	119	3877,4717	533.8+/-382.5	859,2159,1279	no	coding-synonymous	ALG10B	NM_001013620.3		924,2745,2830	GG,GA,AA		45.1129,16.2579,35.3362		469/474	38715000	4593,8405	2202	4297	6499	SO:0001819	synonymous_variant	144245	exon3			CATTCAAAGGTTT	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"""potassium channel regulator 1"", ""dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"""		"""asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"""				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.1407A>G	12.37:g.38715000A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	170	170	1	NM_001013620	B2RPF4	Silent	SNP	ENST00000308742.4	37	CCDS31772.1																																																																																			A|0.664;G|0.336	0.336	strong		0.318	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620	
MAP2	4133	hgsc.bcm.edu	37	2	210517915	210517915	+	Silent	SNP	T	T	C	rs2271252	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:210517915T>C	ENST00000360351.4	+	4	527	c.21T>C	c.(19-21)gaT>gaC	p.D7D	MAP2_ENST00000392194.1_Silent_p.D7D|MAP2_ENST00000199940.6_Silent_p.D7D|MAP2_ENST00000447185.1_Silent_p.D7D|MAP2_ENST00000361559.4_Silent_p.D7D	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	7					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)	AACGGAAAGATGAAGCAAAGG	0.463													C|||	1265	0.252596	0.562	0.1023	5008	,	,		19906	0.1974		0.1093	False		,,,				2504	0.1452				p.D7D	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.T21C						PASS	.	C	,,,	2261,2145	579.9+/-385.0	591,1079,533	75.0	56.0	63.0		21,21,21,21	0.1	1.0	2	dbSNP_100	63	895,7705	777.9+/-407.7	49,797,3454	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAP2	NM_001039538.1,NM_002374.3,NM_031845.2,NM_031847.2	,,,	640,1876,3987	CC,CT,TT		10.407,48.6836,24.2657	,,,	7/560,7/1828,7/472,7/503	210517915	3156,9850	2203	4300	6503	SO:0001819	synonymous_variant	4133	exon5			GAAAGATGAAGCA		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.21T>C	2.37:g.210517915T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	136	79	0.580882	NM_001039538	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	37	CCDS2384.1																																																																																			T|0.756;C|0.244	0.244	strong		0.463	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
LAMA2	3908	hgsc.bcm.edu	37	6	129833568	129833568	+	Missense_Mutation	SNP	C	C	A	rs145842163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:129833568C>A	ENST00000421865.2	+	63	8967	c.8918C>A	c.(8917-8919)aCg>aAg	p.T2973K		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2973	Laminin G-like 5. {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)		ACAACTACAACGACTGGAGTT	0.363																																					p.T2973K		Atlas-SNP	.											.	LAMA2	481	.	0			c.C8918A						PASS	.	C	LYS/THR,LYS/THR	0,4406		0,0,2203	151.0	148.0	149.0		8918,8906	3.9	0.5	6	dbSNP_134	149	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	78,78	0,3,6500	AA,AC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	2973/3123,2969/3119	129833568	3,13003	2203	4300	6503	SO:0001583	missense	3908	exon63			CTACAACGACTGG	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.8918C>A	6.37:g.129833568C>A	ENSP00000400365:p.Thr2973Lys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	172	78	0.453488	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	C	0.026	-1.373086	0.01214	0.0	3.49E-4	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.76839	-1.05	5.73	3.93	0.45458	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.207503	0.48767	D	0.000175	T	0.47655	0.1457	N	0.17674	0.51	0.09310	N	1	P;P	0.47484	0.896;0.896	P;P	0.44696	0.458;0.458	T	0.37820	-0.9689	9	.	.	.	.	7.8481	0.29437	0.1468:0.7266:0.0:0.1266	.	2974;2973	A6NF00;P24043	.;LAMA2_HUMAN	K	2973;2972;2973;991	ENSP00000400365:T2973K	.	T	+	2	0	LAMA2	129875261	0.986000	0.35501	0.534000	0.28014	0.194000	0.23727	1.787000	0.38704	1.406000	0.46857	0.655000	0.94253	ACG	C|1.000;A|0.000	0.000	strong		0.363	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
TIRAP	114609	hgsc.bcm.edu	37	11	126162862	126162862	+	Silent	SNP	C	C	T	rs7932766	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126162862C>T	ENST00000392680.2	+	5	963	c.558C>T	c.(556-558)gcC>gcT	p.A186A	TIRAP_ENST00000392678.3_Silent_p.A186A|TIRAP_ENST00000392679.1_Silent_p.A186A|RP11-712L6.5_ENST00000528876.1_5'Flank|RP11-712L6.7_ENST00000533378.1_RNA	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	186	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)			breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		GCAGAGCTGCCTACCCACCTG	0.607													C|||	671	0.133986	0.1225	0.1398	5008	,	,		18114	0.0397		0.2227	False		,,,				2504	0.1513				p.A186A		Atlas-SNP	.											.	TIRAP	37	.	0			c.C558T						PASS	.	C	,	577,3825	240.9+/-251.5	40,497,1664	44.0	47.0	46.0		558,558	3.5	1.0	11	dbSNP_116	46	2070,6524	350.1+/-327.7	264,1542,2491	no	coding-synonymous,coding-synonymous	TIRAP	NM_001039661.1,NM_148910.2	,	304,2039,4155	TT,TC,CC		24.0866,13.1077,20.3678	,	186/222,186/236	126162862	2647,10349	2201	4297	6498	SO:0001819	synonymous_variant	114609	exon5			AGCTGCCTACCCA	AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.558C>T	11.37:g.126162862C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	117	69	0.589744	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Silent	SNP	ENST00000392680.2	37	CCDS8472.1																																																																																			C|0.822;T|0.178	0.178	strong		0.607	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
ATXN1	6310	hgsc.bcm.edu	37	6	16327921	16327921	+	Missense_Mutation	SNP	C	C	A	rs201030692		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:16327921C>A	ENST00000244769.4	-	8	1557	c.621G>T	c.(619-621)caG>caT	p.Q207H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q207H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	207	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.Q207H(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgatgctgctgctgctgct	0.662																																					p.Q207H		Atlas-SNP	.											ATXN1,NS,carcinoma,0,1	ATXN1	117	1	2	Substitution - Missense(2)	lung(1)|prostate(1)	c.G621T						PASS	.						5.0	8.0	7.0					6																	16327921		1605	3502	5107	SO:0001583	missense	6310	exon7			ATGCTGCTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.621G>T	6.37:g.16327921C>A	ENSP00000244769:p.Gln207His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	10	0.16129	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	c	0.699	-0.791581	0.02884	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.56275	0.47;0.47	0.0465	-0.093	0.13652	.	.	.	.	.	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	D	0.54964	0.969	B	0.38106	0.265	T	0.21042	-1.0257	8	0.35671	T	0.21	.	.	.	.	.	207	P54253	ATX1_HUMAN	H	207	ENSP00000244769:Q207H;ENSP00000416360:Q207H	ENSP00000244769:Q207H	Q	-	3	2	ATXN1	16435900	0.128000	0.22383	0.017000	0.16124	0.068000	0.16541	-0.076000	0.11412	-1.412000	0.02030	-1.404000	0.01136	CAG	.	.	weak		0.662	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
OR10W1	81341	hgsc.bcm.edu	37	11	58034543	58034543	+	Missense_Mutation	SNP	C	C	T	rs10792156	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58034543C>T	ENST00000395079.2	-	1	1189	c.788G>A	c.(787-789)cGg>cAg	p.R263Q		NM_207374.3	NP_997257.2	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W, member 1	263			R -> Q (in dbSNP:rs10792156). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(1)	26		Breast(21;0.0589)				TGAGATGAACCGATCTTGCTT	0.547													t|||	2572	0.513578	0.4841	0.4942	5008	,	,		20037	0.6954		0.3787	False		,,,				2504	0.5184				p.R263Q		Atlas-SNP	.											OR10W1,NS,malignant_melanoma,-1,1	OR10W1	58	1	0			c.G788A						PASS	.	T	GLN/ARG	2180,2222	591.8+/-387.6	530,1120,551	97.0	89.0	92.0		788	-2.6	0.0	11	dbSNP_120	92	3483,5107	633.6+/-398.8	698,2087,1510	yes	missense	OR10W1	NM_207374.3	43	1228,3207,2061	TT,TC,CC		40.5471,49.5229,43.5884	benign	263/306	58034543	5663,7329	2201	4295	6496	SO:0001583	missense	81341	exon1			ATGAACCGATCTT	AB065850	CCDS7968.1	11q12.1	2012-08-09	2004-03-04	2004-03-05		ENSG00000172772		"""GPCR / Class A : Olfactory receptors"""	15139	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily W, member 1 pseudogene"""	OR10W1P			Standard	NM_207374		Approved		uc001nmq.1	Q8NGF6		ENST00000395079.2:c.788G>A	11.37:g.58034543C>T	ENSP00000378516:p.Arg263Gln	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	215	117	0.544186	NM_207374	A2RUD2|A8MTE1|Q6UXQ2	Missense_Mutation	SNP	ENST00000395079.2	37	CCDS7968.1	1099	0.5032051282051282	257	0.5223577235772358	181	0.5	373	0.6520979020979021	288	0.37994722955145116	T	5.977	0.364124	0.11296	0.495229	0.405471	ENSG00000172772	ENST00000395079	T	0.00084	8.75	5.7	-2.59	0.06209	GPCR, rhodopsin-like superfamily (1);	0.444434	0.19155	N	0.121349	T	0.00012	0.0000	L	0.28776	0.89	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48937	-0.8990	9	0.52906	T	0.07	.	4.216	0.10535	0.0956:0.3595:0.0984:0.4466	rs10792156;rs52791449;rs60718842;rs10792156	263	Q8NGF6	O10W1_HUMAN	Q	263	ENSP00000378516:R263Q	ENSP00000378516:R263Q	R	-	2	0	OR10W1	57791119	0.000000	0.05858	0.013000	0.15412	0.397000	0.30659	-0.521000	0.06245	-0.762000	0.04664	-1.062000	0.02293	CGG	C|0.523;T|0.477	0.477	strong		0.547	OR10W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394704.1	NM_207374	
SQLE	6713	hgsc.bcm.edu	37	8	126021414	126021414	+	Splice_Site	SNP	A	A	T	rs118130263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:126021414A>T	ENST00000265896.5	+	6	1835	c.937A>T	c.(937-939)Aat>Tat	p.N313Y	SQLE_ENST00000523430.1_Splice_Site_p.N218Y	NM_003129.3	NP_003120.2	Q14534	ERG1_HUMAN	squalene epoxidase	313					cellular aromatic compound metabolic process (GO:0006725)|cholesterol biosynthetic process (GO:0006695)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|squalene monooxygenase activity (GO:0004506)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	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)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	TTTGTTTTAGAATGCACCACA	0.308													A|||	23	0.00459265	0.0	0.0043	5008	,	,		16879	0.0		0.0109	False		,,,				2504	0.0092				p.N313Y		Atlas-SNP	.											.	SQLE	29	.	0			c.A937T						PASS	.	A	TYR/ASN	7,3605		0,7,1799	81.0	76.0	77.0		937	0.1	1.0	8	dbSNP_132	77	146,7992		3,140,3926	yes	missense-near-splice	SQLE	NM_003129.3	143	3,147,5725	TT,TA,AA		1.7941,0.1938,1.3021	possibly-damaging	313/575	126021414	153,11597	1806	4069	5875	SO:0001630	splice_region_variant	6713	exon6			TTTTAGAATGCAC	D78130	CCDS47918.1	8q24.1	2014-06-23			ENSG00000104549	ENSG00000104549	1.14.13.132		11279	protein-coding gene	gene with protein product	"""squalene monooxygenase"""	602019				9286711	Standard	NM_003129		Approved		uc011liq.2	Q14534	OTTHUMG00000164990	ENST00000265896.5:c.937-1A>T	8.37:g.126021414A>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_003129	Q9UEK6	Missense_Mutation	SNP	ENST00000265896.5	37	CCDS47918.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	A	17.34	3.365599	0.61513	0.001938	0.017941	ENSG00000104549	ENST00000523430;ENST00000265896;ENST00000541193	.	.	.	5.53	0.0813	0.14424	Squalene epoxidase (1);	0.261140	0.49916	D	0.000137	T	0.56659	0.2000	M	0.87381	2.88	0.37690	D	0.923809	D	0.64830	0.994	D	0.67231	0.95	T	0.67007	-0.5779	8	.	.	.	-11.547	5.7116	0.17938	0.5363:0.1409:0.3227:0.0	.	313	Q14534	ERG1_HUMAN	Y	218;313;118	.	.	N	+	1	0	SQLE	126090596	0.998000	0.40836	0.999000	0.59377	0.965000	0.64279	0.652000	0.24888	0.139000	0.18822	0.459000	0.35465	AAT	A|0.992;T|0.008	0.008	strong		0.308	SQLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381362.1	NM_003129	Missense_Mutation
MYLK	4638	hgsc.bcm.edu	37	3	123419573	123419573	+	Missense_Mutation	SNP	G	G	T	rs3732487	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:123419573G>T	ENST00000475616.1	-	15	2741	c.2742C>A	c.(2740-2742)gaC>gaA	p.D914E	MYLK_ENST00000346322.5_Missense_Mutation_p.D845E|MYLK_ENST00000360772.3_Missense_Mutation_p.D914E|MYLK_ENST00000359169.1_Missense_Mutation_p.D914E|MYLK_ENST00000360304.3_Missense_Mutation_p.D914E|MYLK_ENST00000510775.1_5'Flank			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	136	65	0.477941	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	
HERC5	51191	hgsc.bcm.edu	37	4	89397091	89397091	+	Missense_Mutation	SNP	A	A	G	rs7699006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:89397091A>G	ENST00000264350.3	+	12	1645	c.1492A>G	c.(1492-1494)Atg>Gtg	p.M498V	HERC5_ENST00000508159.1_Missense_Mutation_p.M136V	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	498				M -> V (in Ref. 1; BAA88519, 2; AAR00320 and 3; AAI40717). {ECO:0000305}.	cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		AGAATGTCCTATGATGCATAT	0.413													G|||	3070	0.613019	0.8101	0.4914	5008	,	,		18078	0.8026		0.335	False		,,,				2504	0.5235				p.M498V	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.A1492G						PASS	.	G	VAL/MET	3214,1192	417.6+/-338.0	1182,850,171	138.0	139.0	138.0		1492	-0.1	0.5	4	dbSNP_116	138	2701,5899	683.2+/-403.9	434,1833,2033	yes	missense	HERC5	NM_016323.2	21	1616,2683,2204	GG,GA,AA		31.407,27.054,45.479	benign	498/1025	89397091	5915,7091	2203	4300	6503	SO:0001583	missense	51191	exon12			TGTCCTATGATGC	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1492A>G	4.37:g.89397091A>G	ENSP00000264350:p.Met498Val	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	NM_016323	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	1246	0.5705128205128205	390	0.7926829268292683	160	0.4419889502762431	444	0.7762237762237763	252	0.3324538258575198	G	0.017	-1.495983	0.01009	0.72946	0.31407	ENSG00000138646	ENST00000264350;ENST00000508159	T;T	0.33654	1.4;1.45	4.79	-0.0846	0.13689	.	0.406837	0.20337	N	0.094320	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	0.37478	-0.9704	9	0.02654	T	1	.	8.6127	0.33813	0.6012:0.0:0.3988:0.0	rs7699006;rs52808145;rs56581085;rs57596219;rs7699006	498	Q9UII4	HERC5_HUMAN	V	498;136	ENSP00000264350:M498V;ENSP00000424129:M136V	ENSP00000264350:M498V	M	+	1	0	HERC5	89616114	0.031000	0.19500	0.519000	0.27824	0.812000	0.45895	-0.303000	0.08210	-0.162000	0.10964	-0.186000	0.12905	ATG	A|0.481;G|0.519	0.519	strong		0.413	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
GSTA2	2939	hgsc.bcm.edu	37	6	52615415	52615415	+	Missense_Mutation	SNP	T	T	G	rs6577	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	109	0	0		WXS	Illumina HiSeq	Phase_I	166	88	0.53012	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	
KPNB1	3837	hgsc.bcm.edu	37	17	45735975	45735975	+	Silent	SNP	G	G	A	rs1136613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45735975G>A	ENST00000290158.4	+	5	992	c.585G>A	c.(583-585)acG>acA	p.T195T	KPNB1_ENST00000535458.2_Silent_p.T50T|KPNB1_ENST00000577918.1_3'UTR|KPNB1_ENST00000537679.1_Silent_p.T50T|KPNB1_ENST00000540627.1_Silent_p.T50T	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	195					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						TAGCTGCTACGAATGCACTCC	0.403													T|||	301	0.0601038	0.053	0.0807	5008	,	,		20610	0.1101		0.0109	False		,,,				2504	0.0542				p.Y195X		Atlas-SNP	.											.	KPNB1	58	.	0			c.T585A						PASS	.	T		209,4197		6,197,2000	98.0	92.0	94.0		585	-7.2	0.7	17	dbSNP_86	94	170,8430		4,162,4134	no	coding-synonymous	KPNB1	NM_002265.4		10,359,6134	AA,AG,GG		1.9767,4.7435,2.914		195/877	45735975	379,12627	2203	4300	6503	SO:0001819	synonymous_variant	3837	exon5			TGCTACGAATGCA	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"""Importins"", ""Armadillo repeat containing"""	6400	protein-coding gene	gene with protein product	"""importin 1"""	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.585G>A	17.37:g.45735975G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	34	12	0.352941	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Nonsense_Mutation	SNP	ENST00000290158.4	37	CCDS11513.1																																																																																			G|0.956;A|0.044	0.044	strong		0.403	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265	
OSBPL1A	114876	hgsc.bcm.edu	37	18	21750298	21750298	+	Missense_Mutation	SNP	C	C	T	rs145164093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:21750298C>T	ENST00000319481.3	-	24	2617	c.2411G>A	c.(2410-2412)aGc>aAc	p.S804N	OSBPL1A_ENST00000357041.4_Missense_Mutation_p.S422N|RNA5SP452_ENST00000363004.1_RNA|OSBPL1A_ENST00000399443.3_Missense_Mutation_p.S291N	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	804					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)					CACCTGTTTGCTGTTCTTCTT	0.403													C|||	9	0.00179712	0.0	0.0058	5008	,	,		21057	0.0		0.005	False		,,,				2504	0.0				p.S804N		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.G2411A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	1,4405	2.1+/-5.4	0,1,2202	308.0	268.0	282.0		1265,872,2411	5.9	1.0	18	dbSNP_134	282	31,8569	22.2+/-67.0	0,31,4269	yes	missense,missense,missense	OSBPL1A	NM_001242508.1,NM_018030.4,NM_080597.3	46,46,46	0,32,6471	TT,TC,CC		0.3605,0.0227,0.246	benign,benign,benign	422/569,291/438,804/951	21750298	32,12974	2203	4300	6503	SO:0001583	missense	114876	exon24			TGTTTGCTGTTCT	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.2411G>A	18.37:g.21750298C>T	ENSP00000320291:p.Ser804Asn	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	108	41	0.37963	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Missense_Mutation	SNP	ENST00000319481.3	37	CCDS11884.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	12.90	2.075390	0.36662	2.27E-4	0.003605	ENSG00000141447	ENST00000319481;ENST00000399443;ENST00000357041	T;T;T	0.46063	0.88;0.92;0.9	5.89	5.89	0.94794	.	0.178386	0.64402	D	0.000007	T	0.19127	0.0459	N	0.16130	0.375	0.80722	D	1	B	0.12013	0.005	B	0.16722	0.016	T	0.05616	-1.0874	10	0.41790	T	0.15	-22.6708	9.3406	0.38079	0.1448:0.7834:0.0:0.0718	.	804	Q9BXW6	OSBL1_HUMAN	N	804;291;422	ENSP00000320291:S804N;ENSP00000382372:S291N;ENSP00000349545:S422N	ENSP00000320291:S804N	S	-	2	0	OSBPL1A	20004296	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.275000	0.43399	2.784000	0.95788	0.650000	0.86243	AGC	C|0.997;T|0.003	0.003	strong		0.403	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
PITPNA	5306	hgsc.bcm.edu	37	17	1456318	1456318	+	Silent	SNP	G	G	A	rs2230463	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1456318G>A	ENST00000313486.7	-	3	432	c.177C>T	c.(175-177)caC>caT	p.H59H	PITPNA_ENST00000539476.1_Silent_p.H59H	NM_006224.3	NP_006215.1	Q00169	PIPNA_HUMAN	phosphatidylinositol transfer protein, alpha	59					axon guidance (GO:0007411)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)|phosphatidylcholine transporter activity (GO:0008525)|phosphatidylinositol transporter activity (GO:0008526)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)		GGTAGATCTTGTGTGTGTACT	0.512													G|||	194	0.038738	0.0189	0.0418	5008	,	,		16861	0.0069		0.0954	False		,,,				2504	0.0378				p.H59H		Atlas-SNP	.											.	PITPNA	14	.	0			c.C177T						PASS	.	G		120,4058		2,116,1971	176.0	178.0	178.0		177	6.2	1.0	17	dbSNP_98	178	892,7546		47,798,3374	yes	coding-synonymous	PITPNA	NM_006224.3		49,914,5345	AA,AG,GG		10.5712,2.8722,8.0216		59/271	1456318	1012,11604	2089	4219	6308	SO:0001819	synonymous_variant	5306	exon3			GATCTTGTGTGTG	M73704	CCDS45563.1	17p13.3	2012-06-29	2003-05-09	2004-09-03	ENSG00000174238	ENSG00000174238			9001	protein-coding gene	gene with protein product		600174	"""phosphotidylinositol transfer protein"""	PITPN		8255295	Standard	NM_006224		Approved	VIB1A	uc021tnf.1	Q00169	OTTHUMG00000177779	ENST00000313486.7:c.177C>T	17.37:g.1456318G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	32	0.367816	NM_006224		Silent	SNP	ENST00000313486.7	37	CCDS45563.1																																																																																			G|0.940;C|0.000;A|0.060	0.060	strong		0.512	PITPNA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438927.3		
IL12RB2	3595	hgsc.bcm.edu	37	1	67852335	67852335	+	Silent	SNP	G	G	A	rs2228420	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:67852335G>A	ENST00000262345.1	+	14	2569	c.1929G>A	c.(1927-1929)acG>acA	p.T643T	IL12RB2_ENST00000465396.1_3'UTR|IL12RB2_ENST00000544434.1_Silent_p.T557T|IL12RB2_ENST00000371000.1_Silent_p.T643T|IL12RB2_ENST00000541374.1_Silent_p.T643T	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	643					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						TTTTCTCAACGCATTACTTCC	0.428													G|||	2071	0.413538	0.1989	0.4697	5008	,	,		16651	0.3442		0.5845	False		,,,				2504	0.5593				p.T643T		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G1929A						PASS	.	G		1023,3383	377.8+/-322.6	127,769,1307	210.0	178.0	189.0		1929	-3.9	0.0	1	dbSNP_111	189	4908,3692	621.0+/-397.1	1405,2098,797	no	coding-synonymous	IL12RB2	NM_001559.2		1532,2867,2104	AA,AG,GG		42.9302,23.2183,45.602		643/863	67852335	5931,7075	2203	4300	6503	SO:0001819	synonymous_variant	3595	exon14			CTCAACGCATTAC	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1929G>A	1.37:g.67852335G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	37	CCDS638.1																																																																																			G|0.567;A|0.433	0.433	strong		0.428	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
CD109	135228	hgsc.bcm.edu	37	6	74493432	74493432	+	Missense_Mutation	SNP	A	A	C	rs10455097	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:74493432A>C	ENST00000287097.5	+	19	2220	c.2108A>C	c.(2107-2109)tAc>tCc	p.Y703S	CD109_ENST00000437994.2_Missense_Mutation_p.Y703S|CD109_ENST00000422508.2_Missense_Mutation_p.Y626S			Q6YHK3	CD109_HUMAN	CD109 molecule	703			Y -> S (in allele Gov(b); dbSNP:rs10455097). {ECO:0000269|PubMed:11861285, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GACTTCAGTTACAGGATTTAC	0.333													C|||	2582	0.515575	0.6551	0.5072	5008	,	,		16327	0.5268		0.495	False		,,,				2504	0.3425				p.Y703S		Atlas-SNP	.											.	CD109	170	.	0			c.A2108C	GRCh37	CM020385	CD109	M	rs10455097	PASS	.	C	SER/TYR,SER/TYR,SER/TYR	2841,1565	490.3+/-361.7	914,1013,276	95.0	86.0	89.0		2108,1877,2108	5.2	0.7	6	dbSNP_119	89	4395,4205	568.4+/-389.0	1142,2111,1047	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	144,144,144	2056,3124,1323	CC,CA,AA		48.8953,35.5197,44.3641	benign,benign,benign	703/1429,626/1369,703/1446	74493432	7236,5770	2203	4300	6503	SO:0001583	missense	135228	exon19			TCAGTTACAGGAT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2108A>C	6.37:g.74493432A>C	ENSP00000287097:p.Tyr703Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	59	59	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	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377071	168377071	+	lincRNA	SNP	G	G	A	rs201618689		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168377071G>A	ENST00000538528.1	-	0	548																											AAGACAGTGGGGGTCATTCCC	0.642																																					p.P88S		Atlas-SNP	.											.	.	.	.	0			c.C262T						PASS	.						3.0	4.0	4.0					6																	168377071		539	1376	1915			0	exon1			CAGTGGGGGTCAT																													6.37:g.168377071G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	213	17	0.0798122	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				.	.	weak		0.642	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
POLRMT	5442	hgsc.bcm.edu	37	19	622336	622336	+	Missense_Mutation	SNP	T	T	G	rs2238549	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:622336T>G	ENST00000588649.2	-	9	1748	c.1664A>C	c.(1663-1665)gAg>gCg	p.E555A	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	555			E -> A (in dbSNP:rs2238549).		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)		CGCCCCCAGCTCCTCCCAGTA	0.736													G|||	3107	0.620407	0.7421	0.3905	5008	,	,		13238	0.5804		0.505	False		,,,				2504	0.7791				p.E555A		Atlas-SNP	.											POLRMT,rectum,carcinoma,0,1	POLRMT	91	1	0			c.A1664C						scavenged	.	G	ALA/GLU	2180,1784		674,832,476	3.0	4.0	4.0		1664	0.8	0.2	19	dbSNP_98	4	3162,4714		735,1692,1511	no	missense	POLRMT	NM_005035.3	107	1409,2524,1987	GG,GT,TT		40.1473,45.005,45.1182	benign	555/1231	622336	5342,6498	1982	3938	5920	SO:0001583	missense	5442	exon9			CCCAGCTCCTCCC		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.1664A>C	19.37:g.622336T>G	ENSP00000465759:p.Glu555Ala	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	1206	0.5521978021978022	355	0.7215447154471545	157	0.43370165745856354	311	0.5437062937062938	383	0.5052770448548812	.	0.101	-1.151710	0.01700	0.54995	0.401473	ENSG00000099821	ENST00000215591	T	0.38887	1.11	4.15	0.782	0.18567	.	1.028080	0.07721	N	0.943661	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	0.39563	-0.9608	9	0.07175	T	0.84	-7.4541	3.713	0.08427	0.2656:0.0:0.3311:0.4033	rs2238549;rs60424827	555	O00411	RPOM_HUMAN	A	555	ENSP00000215591:E555A	ENSP00000215591:E555A	E	-	2	0	POLRMT	573336	0.000000	0.05858	0.177000	0.23020	0.499000	0.33736	0.188000	0.17018	-0.062000	0.13088	-0.217000	0.12591	GAG	T|0.450;G|0.550	0.550	strong		0.736	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
FAT1	2195	hgsc.bcm.edu	37	4	187510280	187510280	+	Silent	SNP	G	G	A	rs3775307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187510280G>A	ENST00000441802.2	-	27	13442	c.13233C>T	c.(13231-13233)ccC>ccT	p.P4411P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4411					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CTGAGTACAGGGGTGTCTGCT	0.517										HNSCC(5;0.00058)			G|||	276	0.0551118	0.0023	0.1023	5008	,	,		18712	0.1587		0.0328	False		,,,				2504	0.0092				p.P4411P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C13233T						PASS	.	G		31,4047		0,31,2008	201.0	198.0	199.0		13233	0.3	1.0	4	dbSNP_107	199	250,8140		3,244,3948	no	coding-synonymous	FAT1	NM_005245.3		3,275,5956	AA,AG,GG		2.9797,0.7602,2.2538		4411/4589	187510280	281,12187	2039	4195	6234	SO:0001819	synonymous_variant	2195	exon27			GTACAGGGGTGTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.13233C>T	4.37:g.187510280G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1	162	0.07417582417582418	2	0.0040650406504065045	22	0.06077348066298342	109	0.19055944055944055	29	0.03825857519788918	G	6.987	0.552195	0.13374	0.007602	0.029797	ENSG00000083857	ENST00000512772;ENST00000507105	T;T	0.63913	-0.07;-0.07	5.37	0.336	0.15958	.	0.052622	0.85682	D	0.000000	T	0.00144	0.0004	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09684	-1.0663	6	0.66056	D	0.02	.	6.7536	0.23501	0.1987:0.3605:0.4408:0.0	rs3775307;rs17692347;rs60346763;rs3775307	.	.	.	S	191;179	ENSP00000424157:P191S;ENSP00000423801:P179S	ENSP00000423801:P179S	P	-	1	0	FAT1	187747274	0.988000	0.35896	0.997000	0.53966	0.864000	0.49448	0.229000	0.17833	0.101000	0.17610	0.455000	0.32223	CCT	G|0.920;A|0.080	0.080	strong		0.517	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
WDR46	9277	hgsc.bcm.edu	37	6	33256397	33256397	+	Silent	SNP	G	G	A	rs9277965	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33256397G>A	ENST00000374617.4	-	3	710	c.354C>T	c.(352-354)tcC>tcT	p.S118S	PFDN6_ENST00000374610.2_5'Flank|WDR46_ENST00000477718.1_5'UTR|PFDN6_ENST00000374606.5_5'Flank|PFDN6_ENST00000374607.1_5'Flank|PFDN6_ENST00000463584.1_5'Flank|PFDN6_ENST00000395131.1_5'Flank	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	118							poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						TCACCTTTCGGGATTTGTCAA	0.597													G|||	638	0.127396	0.0356	0.134	5008	,	,		18883	0.1071		0.165	False		,,,				2504	0.229				p.S118S		Atlas-SNP	.											.	WDR46	43	.	0			c.C354T						PASS	.	G	,	312,4094	162.5+/-194.5	8,296,1899	44.0	46.0	45.0		192,354	2.6	1.0	6	dbSNP_118	45	1432,7168	273.8+/-290.9	116,1200,2984	yes	coding-synonymous,coding-synonymous	WDR46	NM_001164267.1,NM_005452.5	,	124,1496,4883	AA,AG,GG		16.6512,7.0813,13.4092	,	64/557,118/611	33256397	1744,11262	2203	4300	6503	SO:0001819	synonymous_variant	9277	exon3			CTTTCGGGATTTG	Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"""WD repeat domain containing"""	13923	protein-coding gene	gene with protein product		611440	"""chromosome 6 open reading frame 11"""	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.354C>T	6.37:g.33256397G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	159	84	0.528302	NM_005452	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Silent	SNP	ENST00000374617.4	37	CCDS4772.1																																																																																			G|0.874;A|0.126	0.126	strong		0.597	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452	
NOX3	50508	hgsc.bcm.edu	37	6	155761246	155761246	+	Missense_Mutation	SNP	G	G	T	rs3749930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:155761246G>T	ENST00000159060.2	-	6	614	c.512C>A	c.(511-513)aCa>aAa	p.T171K		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	171	Ferric oxidoreductase.		T -> K (in dbSNP:rs3749930).		detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GCCTGCTATTGTCCTTAGCAA	0.393													G|||	989	0.197484	0.0734	0.1873	5008	,	,		17556	0.4821		0.0527	False		,,,				2504	0.228				p.T171K		Atlas-SNP	.											.	NOX3	93	.	0			c.C512A						PASS	.	G	LYS/THR	313,4093	165.1+/-196.6	8,297,1898	102.0	100.0	101.0		512	5.8	0.2	6	dbSNP_107	101	367,8233	121.3+/-180.4	3,361,3936	yes	missense	NOX3	NM_015718.2	78	11,658,5834	TT,TG,GG		4.2674,7.1039,5.2284	probably-damaging	171/569	155761246	680,12326	2203	4300	6503	SO:0001583	missense	50508	exon6			GCTATTGTCCTTA	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.512C>A	6.37:g.155761246G>T	ENSP00000159060:p.Thr171Lys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_015718	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	430	0.19688644688644688	28	0.056910569105691054	53	0.1464088397790055	301	0.5262237762237763	48	0.0633245382585752	G	22.4	4.284765	0.80803	0.071039	0.042674	ENSG00000074771	ENST00000159060	D	0.95756	-3.8	5.79	5.79	0.91817	Flavoprotein transmembrane component (1);	0.000000	0.64402	D	0.000004	D	0.95965	0.8686	M	0.74467	2.265	0.25165	P	0.99032905	D	0.58268	0.982	P	0.57620	0.824	D	0.95255	0.8363	9	0.41790	T	0.15	-21.7527	13.3132	0.60393	0.072:0.0:0.928:0.0	rs3749930;rs59445351;rs3749930	171	Q9HBY0	NOX3_HUMAN	K	171	ENSP00000159060:T171K	ENSP00000159060:T171K	T	-	2	0	NOX3	155802938	1.000000	0.71417	0.154000	0.22540	0.132000	0.20833	5.010000	0.64004	2.757000	0.94681	0.644000	0.83932	ACA	G|0.878;T|0.122	0.122	strong		0.393	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84639350	84639350	+	Missense_Mutation	SNP	C	C	T	rs2277849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	113	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	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	
FAT4	79633	hgsc.bcm.edu	37	4	126402890	126402890	+	Silent	SNP	G	G	A	rs6824160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:126402890G>A	ENST00000394329.3	+	15	12826	c.12813G>A	c.(12811-12813)gtG>gtA	p.V4271V	FAT4_ENST00000335110.5_Silent_p.V2512V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4271	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ACACTACTGTGAAGGTGAGAT	0.403													G|||	673	0.134385	0.0068	0.1124	5008	,	,		18179	0.2579		0.1302	False		,,,				2504	0.1994				p.V4271V		Atlas-SNP	.											.	FAT4	1752	.	0			c.G12813A						PASS	.	G		124,4282	92.0+/-130.7	5,114,2084	70.0	65.0	67.0		12813	4.9	1.0	4	dbSNP_116	67	1039,7561	219.2+/-257.4	59,921,3320	no	coding-synonymous	FAT4	NM_024582.4		64,1035,5404	AA,AG,GG		12.0814,2.8143,8.942		4271/4982	126402890	1163,11843	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon15			TACTGTGAAGGTG	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.12813G>A	4.37:g.126402890G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	22	0.338462	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			G|0.890;A|0.110	0.110	strong		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
TGFBI	7045	hgsc.bcm.edu	37	5	135388663	135388663	+	Silent	SNP	A	A	G	rs1054124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:135388663A>G	ENST00000442011.2	+	8	1142	c.981A>G	c.(979-981)gtA>gtG	p.V327V	TGFBI_ENST00000305126.8_Silent_p.V327V	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	327	FAS1 2. {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)			GGCTGTCTGTAGAGACCCTGG	0.557													G|||	1939	0.387181	0.5446	0.3631	5008	,	,		21375	0.3433		0.2594	False		,,,				2504	0.3681				p.V327V		Atlas-SNP	.											.	TGFBI	76	.	0			c.A981G						PASS	.	G		2109,2145		546,1017,564	74.0	84.0	81.0		981	5.7	1.0	5	dbSNP_86	81	2293,6195		329,1635,2280	no	coding-synonymous	TGFBI	NM_000358.2		875,2652,2844	GG,GA,AA		27.0146,49.5769,34.5472		327/684	135388663	4402,8340	2127	4244	6371	SO:0001819	synonymous_variant	7045	exon8			GTCTGTAGAGACC	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.981A>G	5.37:g.135388663A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1	779	0.3566849816849817	259	0.5264227642276422	124	0.3425414364640884	195	0.3409090909090909	201	0.26517150395778366	G	5.696	0.312930	0.10789	0.495769	0.270146	ENSG00000120708	ENST00000514554	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48603	-0.9021	3	.	.	.	-4.4285	15.1618	0.72791	0.0679:0.0:0.932:0.0	rs1054124;rs2228405;rs3173020;rs3749783;rs7723764;rs17849889;rs17857531;rs61124579;rs1054124	.	.	.	G	45	.	.	R	+	1	2	TGFBI	135416562	1.000000	0.71417	0.987000	0.45799	0.302000	0.27658	5.704000	0.68347	1.532000	0.49169	-0.119000	0.15052	AGA	A|0.650;G|0.350	0.350	strong		0.557	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
CCDC102B	79839	hgsc.bcm.edu	37	18	66542006	66542006	+	Missense_Mutation	SNP	G	G	T	rs745894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:66542006G>T	ENST00000360242.5	+	5	1154	c.1037G>T	c.(1036-1038)tGt>tTt	p.C346F	CCDC102B_ENST00000584156.1_Missense_Mutation_p.C346F|CCDC102B_ENST00000358653.5_Missense_Mutation_p.C346F|CCDC102B_ENST00000577772.1_3'UTR|CCDC102B_ENST00000319445.6_Missense_Mutation_p.C346F	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	60	0	0		WXS	Illumina HiSeq	Phase_I	39	12	0.307692	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	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1857548	1857548	+	Silent	SNP	T	T	C	rs2294038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:1857548T>C	ENST00000398564.1	+	18	2130	c.2130T>C	c.(2128-2130)taT>taC	p.Y710Y	ARHGEF10_ENST00000520359.1_Silent_p.Y647Y|ARHGEF10_ENST00000518288.1_Silent_p.Y709Y|ARHGEF10_ENST00000349830.3_Silent_p.Y685Y|ARHGEF10_ENST00000262112.6_Silent_p.Y710Y			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	710					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)		CCATCGAGTATGGCAGCAGCG	0.602													T|||	786	0.156949	0.115	0.2248	5008	,	,		18080	0.1746		0.171	False		,,,				2504	0.1329				p.Y685Y		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.T2055C						PASS	.	T		572,3834	254.0+/-259.7	35,502,1666	126.0	113.0	117.0		2055	-3.9	0.0	8	dbSNP_100	117	1328,7272	260.6+/-283.4	105,1118,3077	no	coding-synonymous	ARHGEF10	NM_014629.2		140,1620,4743	CC,CT,TT		15.4419,12.9823,14.6086		685/1345	1857548	1900,11106	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon18			CGAGTATGGCAGC	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.2130T>C	8.37:g.1857548T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				T|0.853;C|0.147	0.147	strong		0.602	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
FRMD1	79981	hgsc.bcm.edu	37	6	168457966	168457966	+	Silent	SNP	G	G	A	rs3734899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168457966G>A	ENST00000283309.6	-	11	1525	c.1461C>T	c.(1459-1461)gaC>gaT	p.D487D	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000440994.2_Silent_p.D419D|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	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	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	
ZNF490	57474	hgsc.bcm.edu	37	19	12691335	12691335	+	Silent	SNP	G	G	A	rs3745652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12691335G>A	ENST00000311437.6	-	5	1676	c.1554C>T	c.(1552-1554)caC>caT	p.H518H	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_Missense_Mutation_p.T152M	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						TTTCGTGCACGTGCAAAGACT	0.388													G|||	112	0.0223642	0.003	0.036	5008	,	,		21518	0.001		0.0765	False		,,,				2504	0.0051				p.H518H		Atlas-SNP	.											.	ZNF490	42	.	0			c.C1554T						PASS	.	G		86,4320	73.1+/-111.1	3,80,2120	182.0	163.0	169.0		1554	-1.7	0.0	19	dbSNP_107	169	585,8015	156.1+/-210.0	15,555,3730	no	coding-synonymous	ZNF490	NM_020714.2		18,635,5850	AA,AG,GG		6.8023,1.9519,5.1592		518/530	12691335	671,12335	2203	4300	6503	SO:0001819	synonymous_variant	57474	exon5			GTGCACGTGCAAA	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.1554C>T	19.37:g.12691335G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_020714		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																			G|0.954;A|0.046	0.046	strong		0.388	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854401	12854401	+	Nonsense_Mutation	SNP	G	G	T	rs201717831		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12854401G>T	ENST00000332296.7	+	3	728	c.625G>T	c.(625-627)Gag>Tag	p.E209*	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	209					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TAGTATTCAAGAGCTGGAAAT	0.398																																					p.E209X		Atlas-SNP	.											PRAMEF1,NS,carcinoma,0,2	PRAMEF1	78	2	0			c.G625T						scavenged	.						363.0	333.0	343.0					1																	12854401		2203	4300	6503	SO:0001587	stop_gained	65121	exon3			ATTCAAGAGCTGG	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.625G>T	1.37:g.12854401G>T	ENSP00000332134:p.Glu209*	Somatic	562	1	0.00177936		WXS	Illumina HiSeq	Phase_I	482	52	0.107884	NM_023013	Q9UQP2	Nonsense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	16.09	3.023241	0.54683	.	.	ENSG00000116721	ENST00000332296	.	.	.	1.74	0.76	0.18442	.	0.742629	0.12834	N	0.435382	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.5875	0.07977	0.2694:0.0:0.7306:0.0	.	.	.	.	X	209	.	ENSP00000332134:E209X	E	+	1	0	PRAMEF1	12776988	0.002000	0.14202	0.001000	0.08648	0.004000	0.04260	0.426000	0.21363	0.256000	0.21614	0.543000	0.68304	GAG	G|0.500;C|0.500	.	alt		0.398	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
TRPM5	29850	hgsc.bcm.edu	37	11	2435956	2435956	+	Missense_Mutation	SNP	C	C	T	rs4929982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000452833.1_Missense_Mutation_p.R580Q|TRPM5_ENST00000528453.1_Missense_Mutation_p.R578Q	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	8	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	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	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921277	12921277	+	Silent	SNP	A	A	G	rs3204826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12921277A>G	ENST00000240189.2	+	4	1155	c.1068A>G	c.(1066-1068)ttA>ttG	p.L356L		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	356					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.L356F(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)		CCCTCGTGTTAGAGGGCTGTC	0.542													.|||	93	0.0185703	0.0091	0.0115	5008	,	,		23369	0.0437		0.008	False		,,,				2504	0.0215				p.L356L		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	1	Substitution - Missense(1)	prostate(1)	c.A1068G						scavenged	.						161.0	158.0	159.0					1																	12921277		2201	4291	6492	SO:0001819	synonymous_variant	65122	exon4			CGTGTTAGAGGGC		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.1068A>G	1.37:g.12921277A>G		Somatic	320	3	0.009375		WXS	Illumina HiSeq	Phase_I	350	7	0.02	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			A|0.996;G|0.004	0.004	strong		0.542	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
MUC16	94025	hgsc.bcm.edu	37	19	9057896	9057896	+	Missense_Mutation	SNP	G	G	C	rs12984471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9057896G>C	ENST00000397910.4	-	3	29753	c.29550C>G	c.(29548-29550)gaC>gaG	p.D9850E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9852	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGTGGTATCGTCCACAGCGG	0.473													C|||	1046	0.208866	0.2352	0.219	5008	,	,		21466	0.0258		0.3121	False		,,,				2504	0.2485				p.D9850E		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29550G						PASS	.	C	GLU/ASP	931,3103		102,727,1188	156.0	149.0	151.0		29550	-1.6	0.0	19	dbSNP_121	151	2825,5553		499,1827,1863	yes	missense	MUC16	NM_024690.2	45	601,2554,3051	CC,CG,GG		33.7193,23.0788,30.261	benign	9850/14508	9057896	3756,8656	2017	4189	6206	SO:0001583	missense	94025	exon3			GGTATCGTCCACA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29550C>G	19.37:g.9057896G>C	ENSP00000381008:p.Asp9850Glu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	197	101	0.51269	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	455	0.20833333333333334	123	0.25	82	0.2265193370165746	11	0.019230769230769232	239	0.3153034300791557	c	5.757	0.324052	0.10900	0.230788	0.337193	ENSG00000181143	ENST00000397910	T	0.19806	2.12	2.43	-1.59	0.08453	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.45687	-0.9244	8	0.87932	D	0	.	4.2005	0.10464	0.0:0.4824:0.185:0.3325	rs12984471;rs52797430;rs57305113;rs12984471	9850	B5ME49	.	E	9850	ENSP00000381008:D9850E	ENSP00000381008:D9850E	D	-	3	2	MUC16	8918896	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.110000	0.00293	-0.660000	0.05352	-0.224000	0.12420	GAC	G|0.760;C|0.240	0.240	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
AKR7A3	22977	hgsc.bcm.edu	37	1	19615030	19615030	+	Silent	SNP	A	A	C	rs199899317	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19615030A>C	ENST00000361640.4	-	1	714	c.174T>G	c.(172-174)ctT>ctG	p.L58L		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	58					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)		CCAGGCCGCCAAGGATGGTCT	0.697																																					p.L58L		Atlas-SNP	.											AKR7A3,NS,carcinoma,0,1	AKR7A3	30	1	0			c.T174G						scavenged	.						24.0	26.0	25.0					1																	19615030		2202	4298	6500	SO:0001819	synonymous_variant	22977	exon1			GCCGCCAAGGATG	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.174T>G	1.37:g.19615030A>C		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	240	51	0.2125	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Silent	SNP	ENST00000361640.4	37	CCDS193.1																																																																																			A|0.988;C|0.013	0.013	strong		0.697	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
HDAC10	83933	hgsc.bcm.edu	37	22	50686371	50686371	+	Missense_Mutation	SNP	C	C	T	rs34402301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50686371C>T	ENST00000216271.5	-	13	1637	c.1285G>A	c.(1285-1287)Gtc>Atc	p.V429I	MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000349505.4_Missense_Mutation_p.V409I|HDAC10_ENST00000498366.1_5'UTR|HDAC10_ENST00000448072.1_Missense_Mutation_p.V379I|TUBGCP6_ENST00000439308.2_5'Flank	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	429			V -> I (in dbSNP:rs34402301).		chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGTTGGATGACGTCAGGGGGC	0.657													C|||	96	0.0191693	0.003	0.0432	5008	,	,		20936	0.0		0.0557	False		,,,				2504	0.0061				p.V429I		Atlas-SNP	.											.	HDAC10	29	.	0			c.G1285A						PASS	.	C	ILE/VAL,ILE/VAL	48,4358	47.5+/-82.1	0,48,2155	40.0	37.0	38.0		1225,1285	1.1	0.0	22	dbSNP_126	38	516,8084	143.6+/-199.6	21,474,3805	yes	missense,missense	HDAC10	NM_001159286.1,NM_032019.5	29,29	21,522,5960	TT,TC,CC		6.0,1.0894,4.3365	probably-damaging,probably-damaging	409/650,429/670	50686371	564,12442	2203	4300	6503	SO:0001583	missense	83933	exon13			GGATGACGTCAGG	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.1285G>A	22.37:g.50686371C>T	ENSP00000216271:p.Val429Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Missense_Mutation	SNP	ENST00000216271.5	37	CCDS14088.1	64	0.029304029304029304	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	44	0.05804749340369393	C	13.95	2.388992	0.42308	0.010894	0.06	ENSG00000100429	ENST00000216271;ENST00000448072;ENST00000349505	T;T;T	0.29397	1.57;1.57;1.57	4.33	1.1	0.20463	.	1.989150	0.03993	N	0.295219	T	0.05777	0.0151	M	0.76574	2.34	0.20403	N	0.99991	D;P;D;D;D	0.61697	0.99;0.928;0.969;0.957;0.982	P;B;P;B;B	0.47705	0.555;0.225;0.453;0.399;0.352	T	0.09684	-1.0663	10	0.23891	T	0.37	-16.585	6.0518	0.19789	0.0:0.6718:0.0:0.3282	rs34402301	409;419;379;429;429	Q969S8-2;E2QRD2;C9J8B8;Q969S8-4;Q969S8	.;.;.;.;HDA10_HUMAN	I	429;379;409	ENSP00000216271:V429I;ENSP00000397542:V379I;ENSP00000343540:V409I	ENSP00000216271:V429I	V	-	1	0	HDAC10	49028498	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.055000	0.14229	0.204000	0.20548	0.591000	0.81541	GTC	C|0.961;T|0.039	0.039	strong		0.657	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36654047	36654047	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:36654047C>T	ENST00000431231.2	+	21	3365	c.3297C>T	c.(3295-3297)gaC>gaT	p.D1099D	ARHGAP23_ENST00000443378.1_Silent_p.D1005D|ARHGAP23_ENST00000437668.3_Silent_p.D1099D	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	1099					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)	p.D1424D(3)		breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						TCTTCAGTGACGAAGAGGACA	0.587																																					p.D1099D		Atlas-SNP	.											ARHGAP23,NS,carcinoma,0,3	ARHGAP23	48	3	3	Substitution - coding silent(3)	kidney(3)	c.C3297T						scavenged	.						37.0	32.0	34.0					17																	36654047		692	1591	2283	SO:0001819	synonymous_variant	57636	exon21			CAGTGACGAAGAG	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.3297C>T	17.37:g.36654047C>T		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	413	5	0.0121065	NM_001199417		Silent	SNP	ENST00000431231.2	37	CCDS56027.1	.	.	.	.	.	.	.	.	.	.	C	7.121	0.577917	0.13686	.	.	ENSG00000225485	ENST00000548703	.	.	.	4.66	-6.46	0.01908	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.9385	0.35715	0.0:0.137:0.2125:0.6505	.	.	.	.	X	80	.	.	R	+	1	2	ARHGAP23	33907573	0.000000	0.05858	0.011000	0.14972	0.976000	0.68499	-3.675000	0.00396	-0.942000	0.03695	-0.252000	0.11476	CGA	.	.	none		0.587	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
TPSD1	23430	hgsc.bcm.edu	37	16	1306873	1306873	+	Silent	SNP	G	G	A	rs113333718	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306873G>A	ENST00000211076.3	+	3	478	c.330G>A	c.(328-330)ccG>ccA	p.P110P	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.P103P	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	110	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)				AGCTGCTGCCGGTCAGCAGGA	0.632																																					p.P110P		Atlas-SNP	.											.	TPSD1	47	.	0			c.G330A						PASS	.						59.0	62.0	61.0					16																	1306873		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			GCTGCCGGTCAGC	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.330G>A	16.37:g.1306873G>A		Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	649	113	0.174114	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			G|0.884;A|0.116	0.116	strong		0.632	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
FLG2	388698	hgsc.bcm.edu	37	1	152329435	152329435	+	Missense_Mutation	SNP	C	C	T	rs2282303	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152329435C>T	ENST00000388718.5	-	3	899	c.827G>A	c.(826-828)cGa>cAa	p.R276Q	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	276	Ser-rich.		R -> Q (in dbSNP:rs2282303).		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)			TGCATGACTTCGCCTCCCACT	0.448													C|||	1744	0.348243	0.3631	0.4164	5008	,	,		23197	0.502		0.1441	False		,,,				2504	0.3313				p.R276Q		Atlas-SNP	.											.	FLG2	431	.	0			c.G827A						PASS	.	C	GLN/ARG	1436,2970	466.4+/-354.5	210,1016,977	167.0	150.0	156.0		827	3.4	0.4	1	dbSNP_100	156	1378,7222	268.2+/-287.7	136,1106,3058	yes	missense	FLG2	NM_001014342.2	43	346,2122,4035	TT,TC,CC		16.0233,32.5919,21.6362	benign	276/2392	152329435	2814,10192	2203	4300	6503	SO:0001583	missense	388698	exon3			TGACTTCGCCTCC	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.827G>A	1.37:g.152329435C>T	ENSP00000373370:p.Arg276Gln	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	691	0.3163919413919414	168	0.34146341463414637	129	0.356353591160221	284	0.4965034965034965	110	0.14511873350923482	C	0.012	-1.684393	0.00745	0.325919	0.160233	ENSG00000143520	ENST00000388718	T	0.00705	5.81	5.9	3.44	0.39384	.	.	.	.	.	T	0.00144	0.0004	N	0.02802	-0.49	0.80722	P	0.0	B	0.12013	0.005	B	0.01281	0.0	T	0.05209	-1.0899	8	0.10636	T	0.68	-6.2395	7.9192	0.29835	0.0:0.1693:0.0:0.8307	rs2282303;rs52807030;rs2282303	276	Q5D862	FILA2_HUMAN	Q	276	ENSP00000373370:R276Q	ENSP00000373370:R276Q	R	-	2	0	FLG2	150596059	0.035000	0.19736	0.389000	0.26208	0.018000	0.09664	1.178000	0.31981	1.051000	0.40369	-0.300000	0.09419	CGA	C|0.750;T|0.250	0.250	strong		0.448	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
KCNH6	81033	hgsc.bcm.edu	37	17	61607708	61607708	+	Silent	SNP	T	T	C	rs7221517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:61607708T>C	ENST00000583023.1	+	4	491	c.480T>C	c.(478-480)caT>caC	p.H160H	KCNH6_ENST00000314672.5_Silent_p.H160H|KCNH6_ENST00000456941.2_Silent_p.H160H|KCNH6_ENST00000581784.1_Silent_p.H160H|KCNH6_ENST00000580652.1_Silent_p.H160H	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	160					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	AGGGCTCTCATGGCAGGCCAG	0.642													C|||	1439	0.28734	0.27	0.3141	5008	,	,		17600	0.2252		0.3797	False		,,,				2504	0.2607				p.H160H		Atlas-SNP	.											.	KCNH6	122	.	0			c.T480C						PASS	.	C	,	1337,3069	690.5+/-405.3	181,975,1047	84.0	73.0	77.0		480,480	-9.4	0.0	17	dbSNP_116	77	3044,5556	659.9+/-401.7	586,1872,1842	no	coding-synonymous,coding-synonymous	KCNH6	NM_030779.2,NM_173092.1	,	767,2847,2889	CC,CT,TT		35.3953,30.345,33.6845	,	160/995,160/906	61607708	4381,8625	2203	4300	6503	SO:0001819	synonymous_variant	81033	exon4			CTCTCATGGCAGG	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.480T>C	17.37:g.61607708T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	50	0.423729	NM_030779	Q9BRD7	Silent	SNP	ENST00000583023.1	37	CCDS11638.1																																																																																			T|0.671;C|0.329	0.329	strong		0.642	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
LRRK1	79705	hgsc.bcm.edu	37	15	101606890	101606890	+	Silent	SNP	C	C	A	rs375358524|rs386787404|rs2959197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:101606890C>A	ENST00000388948.3	+	33	6173	c.5814C>A	c.(5812-5814)ggC>ggA	p.G1938G	LRRK1_ENST00000284395.5_Silent_p.G1935G|LRRK1_ENST00000532145.1_3'UTR|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AGGATTCTGGCGCCCAGCGGG	0.587													C|||	1363	0.272165	0.0794	0.3559	5008	,	,		18904	0.3403		0.3201	False		,,,				2504	0.3538				p.G1938G		Atlas-SNP	.											.	LRRK1	310	.	0			c.C5814A						PASS	.	C		420,3726		13,394,1666	159.0	174.0	169.0		5814	-11.0	0.0	15	dbSNP_129	169	2549,5889		369,1811,2039	no	coding-synonymous	LRRK1	NM_024652.3		382,2205,3705	AA,AC,CC		30.2086,10.1302,23.5935		1938/2016	101606890	2969,9615	2073	4219	6292	SO:0001819	synonymous_variant	79705	exon33			TTCTGGCGCCCAG	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.5814C>A	15.37:g.101606890C>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1	494	0.2261904761904762	38	0.07723577235772358	93	0.2569060773480663	177	0.3094405594405594	186	0.24538258575197888	C	0.154	-1.088496	0.01873	0.101302	0.302086	ENSG00000154237	ENST00000542170	.	.	.	5.51	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49582	P	1.9499999999994522E-4	.	.	.	.	.	.	T	0.20042	-1.0287	3	.	.	.	.	1.1282	0.01740	0.2185:0.2416:0.1407:0.3992	rs56193104;rs61738396	.	.	.	E	492	.	.	A	+	2	0	LRRK1	99424413	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-2.718000	0.00813	-2.962000	0.00289	-2.086000	0.00376	GCG	C|0.740;A|0.260	0.260	strong		0.587	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
KLK12	43849	hgsc.bcm.edu	37	19	51535130	51535130	+	Splice_Site	SNP	A	A	G	rs3745540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51535130A>G	ENST00000525263.1	-	3	577		c.e3+1		CTC-518B2.9_ENST00000594910.1_RNA|KLK12_ENST00000319590.4_Splice_Site|KLK12_ENST00000250352.11_Intron|KLK12_ENST00000529888.1_Intron|KLK12_ENST00000250351.4_Splice_Site			Q9UKR0	KLK12_HUMAN	kallikrein-related peptidase 12						proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	12		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		TGGGCCCCTTACTCCGTGGGT	0.617													A|||	2675	0.534145	0.357	0.5591	5008	,	,		13289	0.6369		0.5656	False		,,,				2504	0.6176				.		Atlas-SNP	.											KLK12,NS,carcinoma,0,2	KLK12	30	2	0			c.457+2T>C	GRCh37	CS042543	KLK12	S	rs3745540	PASS	.	A	,,	1660,2740		316,1028,856	87.0	97.0	94.0		,,	4.3	1.0	19	dbSNP_107	94	5049,3543		1514,2021,761	yes	splice-5,splice-5,intron	KLK12	NM_019598.2,NM_145894.1,NM_145895.1	,,	1830,3049,1617	GG,GA,AA		41.236,37.7273,48.3605	,,	,,	51535130	6709,6283	2200	4296	6496	SO:0001630	splice_region_variant	43849	exon5			CCCCTTACTCCGT		CCDS12820.1, CCDS12821.1, CCDS54298.1	19q13.33	2008-02-05	2006-10-27		ENSG00000186474	ENSG00000186474		"""Kallikreins"""	6360	protein-coding gene	gene with protein product		605539	"""kallikrein 12"""			16800724, 16800723	Standard	NM_019598		Approved	KLK-L5	uc002pvh.1	Q9UKR0	OTTHUMG00000165806	ENST00000525263.1:c.457+1T>C	19.37:g.51535130A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_145894	Q9UKR1|Q9UKR2	Splice_Site	SNP	ENST00000525263.1	37	CCDS12821.1	1141	0.5224358974358975	168	0.34146341463414637	208	0.574585635359116	350	0.6118881118881119	415	0.5474934036939314	A	11.67	1.708772	0.30322	0.377273	0.58764	ENSG00000186474	ENST00000525263;ENST00000319590;ENST00000250351	.	.	.	4.27	4.27	0.50696	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9845	0.41832	1.0:0.0:0.0:0.0	rs3745540;rs3926726;rs17715045;rs61507153;rs3745540	.	.	.	.	-1	.	.	.	-	.	.	KLK12	56226942	0.780000	0.28664	1.000000	0.80357	0.355000	0.29361	0.937000	0.28951	1.949000	0.56562	0.528000	0.53228	.	A|0.476;G|0.524	0.524	strong		0.617	KLK12-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386288.1	NM_019598	Intron
CENPE	1062	hgsc.bcm.edu	37	4	104059542	104059542	+	Missense_Mutation	SNP	G	G	A	rs2243682	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	82	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	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			
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331573	28331573	+	Missense_Mutation	SNP	T	T	A	rs213227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	75	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	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	
OR52N1	79473	hgsc.bcm.edu	37	11	5809811	5809811	+	Missense_Mutation	SNP	G	G	T	rs12365487	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5809811G>T	ENST00000317078.1	-	1	235	c.236C>A	c.(235-237)aCc>aAc	p.T79N	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	79			T -> N (in dbSNP:rs12365487).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(15)|prostate(2)|skin(3)	31		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		GTTGGGAAGGGTGCTGGTGCA	0.468													G|||	653	0.130391	0.0287	0.1254	5008	,	,		25136	0.2321		0.1123	False		,,,				2504	0.1851				p.T79N		Atlas-SNP	.											.	OR52N1	70	.	0			c.C236A						PASS	.	G	ASN/THR	202,4200	127.0+/-164.0	7,188,2006	150.0	135.0	140.0		236	4.6	0.9	11	dbSNP_120	140	989,7603	214.6+/-254.2	55,879,3362	yes	missense	OR52N1	NM_001001913.1	65	62,1067,5368	TT,TG,GG		11.5107,4.5888,9.1658	possibly-damaging	79/321	5809811	1191,11803	2201	4296	6497	SO:0001583	missense	79473	exon1			GGAAGGGTGCTGG	AB065538	CCDS31398.1	11p15.4	2012-08-09			ENSG00000181001	ENSG00000181001		"""GPCR / Class A : Olfactory receptors"""	14853	protein-coding gene	gene with protein product							Standard	NM_001001913		Approved		uc010qzo.2	Q8NH53	OTTHUMG00000168800	ENST00000317078.1:c.236C>A	11.37:g.5809811G>T	ENSP00000322823:p.Thr79Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	143	71	0.496504	NM_001001913	Q6IFF6	Missense_Mutation	SNP	ENST00000317078.1	37	CCDS31398.1	302	0.1382783882783883	17	0.034552845528455285	56	0.15469613259668508	143	0.25	86	0.11345646437994723	G	17.82	3.483698	0.63962	0.045888	0.115107	ENSG00000181001	ENST00000317078	T	0.04083	3.71	4.59	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000095	T	0.00012	0.0000	M	0.88906	2.99	0.41515	P	0.011638999999999955	P	0.44380	0.834	P	0.50970	0.655	T	0.08249	-1.0731	9	0.87932	D	0	.	16.492	0.84203	0.0:0.0:1.0:0.0	rs12365487;rs52838163;rs57766475;rs12365487	79	Q8NH53	O52N1_HUMAN	N	79	ENSP00000322823:T79N	ENSP00000322823:T79N	T	-	2	0	OR52N1	5766387	0.000000	0.05858	0.948000	0.38648	0.982000	0.71751	0.744000	0.26245	2.528000	0.85240	0.609000	0.83330	ACC	G|0.886;T|0.114	0.114	strong		0.468	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
MON2	23041	hgsc.bcm.edu	37	12	62959137	62959137	+	Missense_Mutation	SNP	A	A	G	rs11174549	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:62959137A>G	ENST00000393632.2	+	27	4544	c.4153A>G	c.(4153-4155)Att>Gtt	p.I1385V	MON2_ENST00000552738.1_Missense_Mutation_p.I1362V|MON2_ENST00000393630.3_Missense_Mutation_p.I1386V|MON2_ENST00000546600.1_Missense_Mutation_p.I1385V|MON2_ENST00000393629.2_Missense_Mutation_p.I1385V|MON2_ENST00000280379.6_Missense_Mutation_p.I1386V	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1385					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		AACAAAGCACATTGCAAATGC	0.323													A|||	291	0.058107	0.0386	0.0476	5008	,	,		17704	0.0585		0.1183	False		,,,				2504	0.0297				p.I1385V		Atlas-SNP	.											.	MON2	160	.	0			c.A4153G						PASS	.	A	VAL/ILE	239,4167	138.8+/-174.5	5,229,1969	111.0	110.0	110.0		4153	5.8	1.0	12	dbSNP_120	110	953,7647	209.8+/-250.9	59,835,3406	yes	missense	MON2	NM_015026.2	29	64,1064,5375	GG,GA,AA		11.0814,5.4244,9.165	benign	1385/1718	62959137	1192,11814	2203	4300	6503	SO:0001583	missense	23041	exon27			AAGCACATTGCAA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4153A>G	12.37:g.62959137A>G	ENSP00000377252:p.Ile1385Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	170	0.07783882783882784	19	0.03861788617886179	19	0.052486187845303865	37	0.06468531468531469	95	0.12532981530343007	A	11.89	1.774762	0.31411	0.054244	0.110814	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.55052	0.55;0.54;0.55;0.55;0.58;0.57	5.76	5.76	0.90799	.	0.058459	0.64402	D	0.000001	T	0.00300	0.0009	N	0.03608	-0.345	0.18873	P	0.9999817629	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.0	B;B;B;B;B	0.09377	0.001;0.002;0.004;0.004;0.001	T	0.07009	-1.0795	8	.	.	.	-21.6838	16.3695	0.83350	1.0:0.0:0.0:0.0	rs11174549;rs56625845;rs57809371;rs11174549	1385;1362;1385;260;1385	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	V	1385;1386;1386;1385;1362;1385	ENSP00000377252:I1385V;ENSP00000377250:I1386V;ENSP00000280379:I1386V;ENSP00000447407:I1385V;ENSP00000449215:I1362V;ENSP00000377249:I1385V	.	I	+	1	0	MON2	61245404	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.131000	0.71670	2.315000	0.78130	0.533000	0.62120	ATT	A|0.924;G|0.076	0.076	strong		0.323	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
PIGN	23556	hgsc.bcm.edu	37	18	59768375	59768375	+	Silent	SNP	A	A	G	rs17714063	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:59768375A>G	ENST00000357637.5	-	22	2425	c.2010T>C	c.(2008-2010)acT>acC	p.T670T	PIGN_ENST00000400334.3_Silent_p.T670T	NM_176787.4	NP_789744.1	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class N	670					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22		Colorectal(73;0.187)				GACTACTCTGAGTGCTATACA	0.413													G|||	479	0.095647	0.0144	0.1239	5008	,	,		17793	0.0069		0.2694	False		,,,				2504	0.0982				p.T670T		Atlas-SNP	.											.	PIGN	62	.	0			c.T2010C						PASS	.	G	,	216,3574		5,206,1684	99.0	89.0	92.0		2010,2010	-0.1	0.5	18	dbSNP_123	92	2056,6194		246,1564,2315	no	coding-synonymous,coding-synonymous	PIGN	NM_012327.5,NM_176787.4	,	251,1770,3999	GG,GA,AA		24.9212,5.6992,18.8704	,	670/932,670/932	59768375	2272,9768	1895	4125	6020	SO:0001819	synonymous_variant	23556	exon22			ACTCTGAGTGCTA	AF109219	CCDS45879.1	18q21.33	2013-02-26	2006-06-28		ENSG00000197563	ENSG00000197563		"""Phosphatidylinositol glycan anchor biosynthesis"""	8967	protein-coding gene	gene with protein product		606097	"""phosphatidylinositol glycan, class N"""			10069808, 10574991	Standard	NM_012327		Approved	MDC4, PIG-N	uc021ulb.1	O95427	OTTHUMG00000180098	ENST00000357637.5:c.2010T>C	18.37:g.59768375A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	15	0.348837	NM_176787	Q7L8F8|Q8TC01|Q9NT05	Silent	SNP	ENST00000357637.5	37	CCDS45879.1																																																																																			A|0.851;G|0.149	0.149	strong		0.413	PIGN-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449757.2	NM_176787	
ZNF700	90592	hgsc.bcm.edu	37	19	12059645	12059645	+	Missense_Mutation	SNP	A	A	G	rs12327617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12059645A>G	ENST00000254321.5	+	4	949	c.806A>G	c.(805-807)gAa>gGa	p.E269G	ZNF700_ENST00000482090.1_Missense_Mutation_p.E251G|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000590798.1_Intron|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	269			E -> G (in dbSNP:rs12327617).		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						CAAATACATGAAAGAACTCAC	0.358													a|||	181	0.0361422	0.0045	0.0591	5008	,	,		20641	0.0		0.0964	False		,,,				2504	0.0378				p.E272G		Atlas-SNP	.											.	ZNF700	81	.	0			c.A815G						PASS	.	A	GLY/GLU	95,4311	74.1+/-112.3	1,93,2109	46.0	45.0	45.0		806	0.7	0.6	19	dbSNP_120	45	823,7777	184.6+/-232.5	42,739,3519	yes	missense	ZNF700	NM_144566.1	98	43,832,5628	GG,GA,AA		9.5698,2.1562,7.0583	probably-damaging	269/743	12059645	918,12088	2203	4300	6503	SO:0001583	missense	90592	exon4			TACATGAAAGAAC	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.806A>G	19.37:g.12059645A>G	ENSP00000254321:p.Glu269Gly	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_001271848	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	92	0.04212454212454213	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	70	0.09234828496042216	a	17.26	3.344785	0.61073	0.021562	0.095698	ENSG00000196757	ENST00000254321	T	0.07444	3.19	0.672	0.672	0.17935	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00356	0.0011	L	0.38531	1.155	0.24211	N	0.995479	D	0.53462	0.96	P	0.61722	0.893	T	0.24728	-1.0152	9	0.66056	D	0.02	.	6.9083	0.24321	1.0:0.0:0.0:0.0	rs12327617;rs52820867;rs12327617	269	Q9H0M5	ZN700_HUMAN	G	269	ENSP00000254321:E269G	ENSP00000254321:E269G	E	+	2	0	ZNF700	11920645	0.000000	0.05858	0.631000	0.29282	0.972000	0.66771	-0.911000	0.04050	0.524000	0.28502	0.254000	0.18369	GAA	A|0.938;G|0.062	0.062	strong		0.358	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552921	43552921	+	Silent	SNP	C	C	T	rs12452273	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	225	0	0		WXS	Illumina HiSeq	Phase_I	206	203	0.985437	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	
PCNT	5116	hgsc.bcm.edu	37	21	47851796	47851796	+	Silent	SNP	G	G	A	rs9983522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47851796G>A	ENST00000359568.5	+	38	8525	c.8418G>A	c.(8416-8418)gcG>gcA	p.A2806A	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2806					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)					ACTTGCAAGCGATGCTTGAAA	0.582													G|||	734	0.146565	0.0666	0.1801	5008	,	,		20552	0.1984		0.1252	False		,,,				2504	0.1994				p.A2806A		Atlas-SNP	.											.	PCNT	283	.	0			c.G8418A						PASS	.	G		279,4127	155.2+/-188.4	11,257,1935	59.0	58.0	58.0		8418	-10.6	0.0	21	dbSNP_119	58	1054,7546	221.6+/-259.0	63,928,3309	no	coding-synonymous	PCNT	NM_006031.5		74,1185,5244	AA,AG,GG		12.2558,6.3323,10.2491		2806/3337	47851796	1333,11673	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon38			GCAAGCGATGCTT	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.8418G>A	21.37:g.47851796G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			G|0.887;A|0.113	0.113	strong		0.582	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743235	22743235	+	Silent	SNP	A	A	G	rs371649333		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:22743235A>G	ENST00000560659.2	+	8	1470	c.1470A>G	c.(1468-1470)cgA>cgG	p.R490R	GOLGA6L1_ENST00000316397.3_Silent_p.R540R			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	534								p.R540R(1)		NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						agaagatacgagagcaggagg	0.532																																					p.R540R		Atlas-SNP	.											GOLGA6L1,NS,carcinoma,0,5	GOLGA6L1	20	5	1	Substitution - coding silent(1)	endometrium(1)	c.A1620G						PASS	.						2.0	1.0	1.0					15																	22743235		605	798	1403	SO:0001819	synonymous_variant	283767	exon8			GATACGAGAGCAG	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.1470A>G	15.37:g.22743235A>G		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	47	13	0.276596	NM_001001413		Silent	SNP	ENST00000560659.2	37																																																																																				.	.	weak		0.532	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
C8orf86	389649	hgsc.bcm.edu	37	8	38385914	38385914	+	Missense_Mutation	SNP	C	C	T	rs1378332	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:38385914C>T	ENST00000358138.1	-	1	266	c.242G>A	c.(241-243)cGc>cAc	p.R81H	C8orf86_ENST00000437935.2_Missense_Mutation_p.R81H	NM_207412.1	NP_997295.1	Q6ZUL3	CH086_HUMAN	chromosome 8 open reading frame 86	81			R -> H (in dbSNP:rs1378332).							breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						CTCTCGCCAGCGGCGTCTGCA	0.557													C|||	634	0.126597	0.2481	0.0576	5008	,	,		21363	0.127		0.0378	False		,,,				2504	0.1022				p.R81H		Atlas-SNP	.											.	C8orf86	17	.	0			c.G242A						PASS	.	C	HIS/ARG	1025,3381	378.7+/-323.0	118,789,1296	165.0	134.0	145.0		242	-1.4	0.0	8	dbSNP_88	145	323,8277	114.2+/-174.2	14,295,3991	yes	missense	C8orf86	NM_207412.1	29	132,1084,5287	TT,TC,CC		3.7558,23.2637,10.3644	probably-damaging	81/224	38385914	1348,11658	2203	4300	6503	SO:0001583	missense	389649	exon1			CGCCAGCGGCGTC	BC137511	CCDS6108.1	8p12-p11.23	2009-03-03			ENSG00000196166	ENSG00000196166			33774	protein-coding gene	gene with protein product							Standard	NM_207412		Approved	FLJ43582	uc003xlx.1	Q6ZUL3	OTTHUMG00000163992	ENST00000358138.1:c.242G>A	8.37:g.38385914C>T	ENSP00000350856:p.Arg81His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_207412	A4QPB7	Missense_Mutation	SNP	ENST00000358138.1	37	CCDS6108.1	262	0.11996336996336997	140	0.2845528455284553	16	0.04419889502762431	72	0.1258741258741259	34	0.044854881266490766	C	6.445	0.450244	0.12223	0.232637	0.037558	ENSG00000196166	ENST00000358138;ENST00000437935	T;T	0.57107	0.47;0.42	0.893	-1.44	0.08856	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22851	0.076	B	0.08055	0.003	T	0.24048	-1.0171	8	0.87932	D	0	.	1.6882	0.02846	0.3282:0.4135:0.0:0.2582	rs61726163	81	Q6ZUL3	CH086_HUMAN	H	81	ENSP00000350856:R81H;ENSP00000389615:R81H	ENSP00000350856:R81H	R	-	2	0	C8orf86	38505071	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-0.259000	0.08721	-0.610000	0.05716	-0.895000	0.02911	CGC	C|0.885;T|0.115	0.115	strong		0.557	C8orf86-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376668.1	NM_207412	
TUBB8	347688	hgsc.bcm.edu	37	10	94026	94026	+	Silent	SNP	G	G	A	rs10904032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:94026G>A	ENST00000309812.4	-	4	368	c.306C>T	c.(304-306)gcC>gcT	p.A102A	TUBB8_ENST00000332708.5_Missense_Mutation_p.P66L|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.A30A	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	102					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		AGTGTCCCTTGGCCCAGTTGT	0.572																																					p.A102A	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.C306T						PASS	.	G		693,3713		18,657,1528	68.0	56.0	60.0		306		0.4	10	dbSNP_120	60	3519,5081		504,2511,1285	no	coding-synonymous	TUBB8	NM_177987.2		522,3168,2813	AA,AG,GG		40.9186,15.7286,32.3851		102/445	94026	4212,8794	2203	4300	6503	SO:0001819	synonymous_variant	347688	exon4			TCCCTTGGCCCAG	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.306C>T	10.37:g.94026G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	242	106	0.438017	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	587	0.26877289377289376	72	0.14634146341463414	129	0.356353591160221	89	0.1555944055944056	297	0.391820580474934	G	10.07	1.248892	0.22880	0.157286	0.409186	ENSG00000173876	ENST00000309812;ENST00000332708	.	.	.	.	.	.	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40997	-0.9533	3	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	rs10904032;rs59810031	.	.	.	L	110;66	.	ENSP00000311042:P110L	P	-	2	0	RP11-631M21.2	84026	0.240000	0.23847	0.361000	0.25849	0.365000	0.29674	-3.811000	0.00360	0.119000	0.18210	0.121000	0.15741	CCA	G|0.731;A|0.269	0.269	strong		0.572	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
TLK2	11011	hgsc.bcm.edu	37	17	60601664	60601664	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:60601664C>T	ENST00000326270.9	+	6	603	c.335C>T	c.(334-336)cCg>cTg	p.P112L	TLK2_ENST00000542523.1_Intron|TLK2_ENST00000582809.1_5'UTR|TLK2_ENST00000343388.7_Intron|TLK2_ENST00000346027.5_Missense_Mutation_p.P112L	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	112					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						CGATCCTCACCGCAACATTCC	0.493																																					p.P112L		Atlas-SNP	.											TLK2_ENST00000346027,NS,carcinoma,-1,3	TLK2	223	3	0			c.C335T						scavenged	.						29.0	31.0	30.0					17																	60601664		2203	4296	6499	SO:0001583	missense	11011	exon6			CCTCACCGCAACA	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.335C>T	17.37:g.60601664C>T	ENSP00000316512:p.Pro112Leu	Somatic	553	1	0.00180832		WXS	Illumina HiSeq	Phase_I	533	5	0.00938086	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	37		.	.	.	.	.	.	.	.	.	.	C	15.41	2.824974	0.50739	.	.	ENSG00000146872	ENST00000346027;ENST00000326270	T;T	0.73789	-0.68;-0.78	5.5	4.5	0.54988	.	0.298250	0.42682	D	0.000663	D	0.83580	0.5285	M	0.72894	2.215	0.80722	D	1	D;B	0.64830	0.994;0.025	D;B	0.65010	0.931;0.021	D	0.84634	0.0691	10	0.54805	T	0.06	.	14.8371	0.70192	0.1439:0.8561:0.0:0.0	.	112;112	Q86UE8;Q86UE8-2	TLK2_HUMAN;.	L	112	ENSP00000275780:P112L;ENSP00000316512:P112L	ENSP00000316512:P112L	P	+	2	0	TLK2	57955396	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.192000	0.72069	2.579000	0.87056	0.563000	0.77884	CCG	.	.	none		0.493	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852	
ALPK2	115701	hgsc.bcm.edu	37	18	56204417	56204417	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:56204417G>A	ENST00000361673.3	-	5	3215	c.3002C>T	c.(3001-3003)gCg>gTg	p.A1001V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1001						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CTCCCTGGTCGCTTGAAAGCA	0.488																																					p.A1001V		Atlas-SNP	.											.	ALPK2	487	.	0			c.C3002T						PASS	.						111.0	96.0	101.0					18																	56204417		2203	4299	6502	SO:0001583	missense	115701	exon5			CTGGTCGCTTGAA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3002C>T	18.37:g.56204417G>A	ENSP00000354991:p.Ala1001Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	1.106	-0.659520	0.03454	.	.	ENSG00000198796	ENST00000361673	T	0.37752	1.18	5.08	-2.78	0.05859	.	4.754620	0.00550	N	0.000240	T	0.07098	0.0180	N	0.00289	-1.7	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39722	-0.9600	10	0.02654	T	1	-3.639	1.1061	0.01694	0.3981:0.281:0.1835:0.1373	.	1001;1001	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	V	1001	ENSP00000354991:A1001V	ENSP00000354991:A1001V	A	-	2	0	ALPK2	54355397	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.073000	0.14640	-0.244000	0.09639	-0.383000	0.06682	GCG	.	.	none		0.488	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ABCC3	8714	hgsc.bcm.edu	37	17	48745035	48745035	+	Silent	SNP	A	A	C	rs11568601	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48745035A>C	ENST00000285238.8	+	12	1632	c.1552A>C	c.(1552-1554)Agg>Cgg	p.R518R	ABCC3_ENST00000427699.1_Silent_p.R518R	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	518	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	GGAGGGCATCAGGCAGGGTGA	0.622													A|||	26	0.00519169	0.0015	0.0058	5008	,	,		22136	0.0		0.0189	False		,,,				2504	0.001				p.R518R		Atlas-SNP	.											.	ABCC3	138	.	0			c.A1552C						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	72.0	58.0	63.0		1552,1552	1.7	1.0	17	dbSNP_126	63	219,8381	91.1+/-153.3	3,213,4084	no	coding-synonymous,coding-synonymous	ABCC3	NM_001144070.1,NM_003786.3	,	3,234,6266	CC,CA,AA		2.5465,0.4766,1.8453	,	518/573,518/1528	48745035	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon12			GGCATCAGGCAGG	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.1552A>C	17.37:g.48745035A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			A|0.984;C|0.016	0.016	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
CRIP1	1396	hgsc.bcm.edu	37	14	105954705	105954705	+	Missense_Mutation	SNP	C	C	T	rs55633823	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105954705C>T	ENST00000330233.7	+	3	1116	c.173C>T	c.(172-174)gCa>gTa	p.A58V	C14orf80_ENST00000392527.1_5'Flank|CRIP1_ENST00000409393.2_Missense_Mutation_p.A58V|CRIP1_ENST00000392531.3_Missense_Mutation_p.A58V|C14orf80_ENST00000392523.4_5'Flank|C14orf80_ENST00000392522.3_5'Flank|CRIP1_ENST00000551180.1_Silent_p.R26R|C14orf80_ENST00000334656.7_5'Flank|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000329886.7_5'Flank			P50238	CRIP1_HUMAN	cysteine-rich protein 1 (intestinal)	58	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.			A -> V (in Ref. 1; AAA64537). {ECO:0000305}.	cell proliferation (GO:0008283)|cellular response to antibiotic (GO:0071236)|cellular response to UV-B (GO:0071493)|heart development (GO:0007507)|immune response (GO:0006955)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|prostate gland stromal morphogenesis (GO:0060741)|regulation of gene expression (GO:0010468)|response to organic substance (GO:0010033)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)	AT DNA binding (GO:0003680)|DNA binding, bending (GO:0008301)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)						Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.235)		CCCTGCTACGCAGCCATGTTT	0.632													C|||	390	0.0778754	0.0076	0.121	5008	,	,		9817	0.0		0.2177	False		,,,				2504	0.0787				p.A58V		Atlas-SNP	.											.	CRIP1	1	.	0			c.C173T						PASS	.	C	VAL/ALA	220,4184	129.8+/-166.5	7,206,1989	47.0	61.0	56.0		173	3.3	0.0	14	dbSNP_129	56	2111,6489	358.8+/-331.3	260,1591,2449	yes	missense	CRIP1	NM_001311.4	64	267,1797,4438	TT,TC,CC		24.5465,4.9955,17.9253	benign	58/78	105954705	2331,10673	2202	4300	6502	SO:0001583	missense	1396	exon4			GCTACGCAGCCAT		CCDS10004.1	14q32.33	2004-06-18			ENSG00000213145	ENSG00000213145			2360	protein-coding gene	gene with protein product		123875				9480758	Standard	NM_001311		Approved	CRIP	uc001yri.4	P50238	OTTHUMG00000029908	ENST00000330233.7:c.173C>T	14.37:g.105954705C>T	ENSP00000332449:p.Ala58Val	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	148	144	0.972973	NM_001311	H3BPI2|Q13628|Q53XY7|Q96J34	Missense_Mutation	SNP	ENST00000330233.7	37	CCDS10004.1	225	0.10302197802197802	8	0.016260162601626018	46	0.1270718232044199	0	0.0	171	0.22559366754617413	C	8.914	0.959358	0.18507	0.049955	0.245465	ENSG00000213145	ENST00000330233;ENST00000409393;ENST00000392531	D;D;D	0.87179	-2.22;-2.22;-2.22	4.24	3.35	0.38373	Zinc finger, LIM-type (3);	0.239612	0.24508	U	0.037904	T	0.00073	0.0002	.	.	.	0.58432	P	9.99999999995449E-6	B	0.17465	0.022	B	0.29440	0.102	T	0.19844	-1.0293	8	0.72032	D	0.01	-11.1404	6.9571	0.24578	0.0:0.727:0.1761:0.0969	rs7824;rs1128313;rs3185152;rs3185188;rs11544872;rs12882865;rs17029668;rs17029674;rs17294933	58	P50238	CRIP1_HUMAN	V	58	ENSP00000332449:A58V;ENSP00000386340:A58V;ENSP00000376315:A58V	ENSP00000447493:A58V	A	+	2	0	CRIP1	105025750	0.004000	0.15560	0.045000	0.18777	0.001000	0.01503	1.652000	0.37313	1.000000	0.39049	-0.142000	0.14014	GCA	C|0.838;T|0.162	0.162	strong		0.632	CRIP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335466.2	NM_001311	
SMPD2	6610	hgsc.bcm.edu	37	6	109764535	109764535	+	Missense_Mutation	SNP	G	G	T	rs1476387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:109764535G>T	ENST00000258052.3	+	9	1154	c.795G>T	c.(793-795)agG>agT	p.R265S	PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank|PPIL6_ENST00000440797.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	265			R -> S (in dbSNP:rs1476387). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9520418}.		apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		ACCCTCACAGGGGCACCCCCC	0.527													T|||	2769	0.552915	0.7549	0.4928	5008	,	,		15276	0.4534		0.4314	False		,,,				2504	0.5501				p.R265S		Atlas-SNP	.											SMPD2,NS,carcinoma,0,1	SMPD2	25	1	0			c.G795T						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	160	0	0		WXS	Illumina HiSeq	Phase_I	194	103	0.530928	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		
CDON	50937	hgsc.bcm.edu	37	11	125851181	125851181	+	Silent	SNP	G	G	A	rs684805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:125851181G>A	ENST00000392693.3	-	17	3166	c.3039C>T	c.(3037-3039)aaC>aaT	p.N1013N	CDON_ENST00000263577.7_Silent_p.N1013N|CDON_ENST00000531738.1_Silent_p.N390N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1013					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)				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)		CCATCTGCCCGTTCATATCTG	0.473													A|||	1340	0.267572	0.4955	0.2161	5008	,	,		18332	0.0655		0.2604	False		,,,				2504	0.2117				p.N1013N		Atlas-SNP	.											.	CDON	137	.	0			c.C3039T						PASS	.	A		2015,2387	613.7+/-392.2	465,1085,651	121.0	113.0	116.0		3039	-7.0	0.0	11	dbSNP_83	116	2327,6271	703.8+/-405.4	318,1691,2290	no	coding-synonymous	CDON	NM_016952.4		783,2776,2941	AA,AG,GG		27.0644,45.7746,33.4		1013/1265	125851181	4342,8658	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon17			CTGCCCGTTCATA	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.3039C>T	11.37:g.125851181G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			G|0.695;A|0.305	0.305	strong		0.473	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
NSUN4	387338	hgsc.bcm.edu	37	1	46810530	46810530	+	Missense_Mutation	SNP	A	A	G	rs3737744	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_Missense_Mutation_p.T2A	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	200	0	0		WXS	Illumina HiSeq	Phase_I	240	121	0.504167	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	
ZFAND4	93550	hgsc.bcm.edu	37	10	46143958	46143958	+	Missense_Mutation	SNP	T	T	G	rs17854567	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:46143958T>G	ENST00000344646.5	-	5	568	c.353A>C	c.(352-354)aAg>aCg	p.K118T	ZFAND4_ENST00000374371.2_Missense_Mutation_p.K118T|ZFAND4_ENST00000374366.3_Missense_Mutation_p.K44T|ZFAND4_ENST00000374370.1_5'UTR	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	118			K -> T (in dbSNP:rs17854567). {ECO:0000269|PubMed:14702039}.				zinc ion binding (GO:0008270)										CTCTGCCATCTTCCTAAGTGG	0.393													T|||	495	0.0988419	0.0068	0.2205	5008	,	,		18196	0.0317		0.1521	False		,,,				2504	0.1513				p.K118T		Atlas-SNP	.											.	.	.	.	0			c.A353C						PASS	.	T	THR/LYS,THR/LYS	133,4273	95.3+/-134.0	4,125,2074	101.0	97.0	98.0		353,353	5.8	1.0	10	dbSNP_123	98	1094,7506	228.0+/-263.2	69,956,3275	yes	missense,missense	ANUBL1	NM_001128324.1,NM_174890.2	78,78	73,1081,5349	GG,GT,TT		12.7209,3.0186,9.4341	benign,benign	118/728,118/728	46143958	1227,11779	2203	4300	6503	SO:0001583	missense	93550	exon5			GCCATCTTCCTAA	AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"""Zinc fingers, AN1-type domain containing"""	23504	protein-coding gene	gene with protein product			"""AN1, ubiquitin-like, homolog (Xenopus laevis)"""	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.353A>C	10.37:g.46143958T>G	ENSP00000339484:p.Lys118Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_001128324	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	201	0.09203296703296704	6	0.012195121951219513	67	0.1850828729281768	14	0.024475524475524476	114	0.1503957783641161	T	16.40	3.113419	0.56398	0.030186	0.127209	ENSG00000172671	ENST00000344646;ENST00000374371;ENST00000374366;ENST00000374376	T;T;T	0.46819	1.91;0.86;1.96	5.78	5.78	0.91487	.	2.856830	0.01859	N	0.036460	T	0.00073	0.0002	N	0.14661	0.345	0.29438	P	0.859326	B;B	0.23937	0.002;0.094	B;B	0.15870	0.001;0.014	T	0.04065	-1.0980	9	0.87932	D	0	-18.3348	14.0663	0.64831	0.0:0.0:0.0:1.0	rs17854567;rs17854567	118;118	Q5VVY4;Q86XD8	.;ANUB1_HUMAN	T	118;118;44;118	ENSP00000339484:K118T;ENSP00000363491:K118T;ENSP00000363486:K44T	ENSP00000339484:K118T	K	-	2	0	ANUBL1	45463964	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	4.665000	0.61547	2.198000	0.70561	0.477000	0.44152	AAG	T|0.909;G|0.091	0.091	strong		0.393	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890	
SENP7	57337	hgsc.bcm.edu	37	3	101085413	101085413	+	Silent	SNP	G	G	A	rs939443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:101085413G>A	ENST00000394095.2	-	9	1232	c.1179C>T	c.(1177-1179)acC>acT	p.T393T	SENP7_ENST00000394094.2_Silent_p.T328T|SENP7_ENST00000348610.3_Silent_p.T360T|SENP7_ENST00000314261.7_Silent_p.T327T|SENP7_ENST00000358203.3_Silent_p.T229T|SENP7_ENST00000394091.1_Silent_p.T229T	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	393						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						AGTTCTCAACGGTTTCAGTGG	0.403													A|||	2139	0.427117	0.3502	0.5533	5008	,	,		18015	0.4831		0.4125	False		,,,				2504	0.3988				p.T393T		Atlas-SNP	.											.	SENP7	170	.	0			c.C1179T						PASS	.	A	,	1414,2992	685.4+/-404.6	236,942,1025	101.0	101.0	101.0		984,1179	-4.7	0.0	3	dbSNP_86	101	3472,5128	634.7+/-398.9	705,2062,1533	no	coding-synonymous,coding-synonymous	SENP7	NM_001077203.1,NM_020654.3	,	941,3004,2558	AA,AG,GG		40.3721,32.0926,37.5673	,	328/986,393/1051	101085413	4886,8120	2203	4300	6503	SO:0001819	synonymous_variant	57337	exon9			CTCAACGGTTTCA		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.1179C>T	3.37:g.101085413G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	132	0.977778	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																			G|0.603;A|0.397	0.397	strong		0.403	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525466	48525466	+	Missense_Mutation	SNP	C	C	T	rs35700000	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:48525466C>T	ENST00000339841.2	+	6	732	c.554C>T	c.(553-555)cCg>cTg	p.P185L	ELSPBP1_ENST00000597519.1_Missense_Mutation_p.P37L	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	185	Fibronectin type-II 4. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		TGTCACTTTCCGTTCAACTAT	0.443													c|||	69	0.013778	0.0023	0.0072	5008	,	,		20502	0.0		0.0288	False		,,,				2504	0.0327				p.P185L		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.C554T						PASS	.	C	LEU/PRO	19,4387	27.2+/-55.0	0,19,2184	192.0	171.0	178.0		554	3.7	0.9	19	dbSNP_126	178	252,8348	99.5+/-161.0	5,242,4053	yes	missense	ELSPBP1	NM_022142.4	98	5,261,6237	TT,TC,CC		2.9302,0.4312,2.0837	probably-damaging	185/224	48525466	271,12735	2203	4300	6503	SO:0001583	missense	64100	exon6			ACTTTCCGTTCAA	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.554C>T	19.37:g.48525466C>T	ENSP00000340660:p.Pro185Leu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	223	102	0.457399	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	35	0.016025641025641024	4	0.008130081300813009	7	0.019337016574585635	0	0.0	24	0.0316622691292876	C	15.92	2.973836	0.53720	0.004312	0.029302	ENSG00000169393	ENST00000339841	D	0.93488	-3.23	3.66	3.66	0.41972	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.000000	0.48286	D	0.000187	D	0.92593	0.7647	H	0.94658	3.565	0.39211	D	0.963313	D	0.89917	1.0	D	0.87578	0.998	D	0.91856	0.5495	10	0.87932	D	0	.	7.6915	0.28571	0.0:0.8769:0.0:0.1231	rs35700000	185	Q96BH3	ESPB1_HUMAN	L	185	ENSP00000340660:P185L	ENSP00000340660:P185L	P	+	2	0	ELSPBP1	53217278	0.967000	0.33354	0.940000	0.37924	0.712000	0.41017	2.829000	0.48128	1.968000	0.57251	0.609000	0.83330	CCG	C|0.980;T|0.020	0.020	strong		0.443	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
KIF24	347240	hgsc.bcm.edu	37	9	34257095	34257095	+	Missense_Mutation	SNP	G	G	A	rs41274041	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:34257095G>A	ENST00000402558.2	-	10	2534	c.2510C>T	c.(2509-2511)tCt>tTt	p.S837F	KIF24_ENST00000379166.2_Missense_Mutation_p.S837F|KIF24_ENST00000379174.3_Missense_Mutation_p.S703F|KIF24_ENST00000345050.2_Missense_Mutation_p.S703F			Q5T7B8	KIF24_HUMAN	kinesin family member 24	837			S -> F (in dbSNP:rs41274041). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			CCTCTGACTAGAGATGTGTGA	0.493													G|||	676	0.134984	0.0416	0.17	5008	,	,		21202	0.0516		0.2107	False		,,,				2504	0.2444				p.S837F		Atlas-SNP	.											.	KIF24	64	.	0			c.C2510T						PASS	.	G	PHE/SER	316,4090	166.5+/-197.7	12,292,1899	88.0	74.0	79.0		2510	4.7	0.1	9	dbSNP_127	79	1740,6860	317.2+/-313.1	186,1368,2746	yes	missense	KIF24	NM_194313.2	155	198,1660,4645	AA,AG,GG		20.2326,7.172,15.8081	benign	837/1369	34257095	2056,10950	2203	4300	6503	SO:0001583	missense	347240	exon11			TGACTAGAGATGT	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.2510C>T	9.37:g.34257095G>A	ENSP00000384433:p.Ser837Phe	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	37	CCDS6551.2	274	0.12545787545787546	16	0.032520325203252036	63	0.17403314917127072	32	0.055944055944055944	163	0.21503957783641162	G	13.85	2.359768	0.41801	0.07172	0.202326	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.57	4.66	0.58398	.	0.000000	0.40302	N	0.001138	T	0.00039	0.0001	L	0.52364	1.645	0.80722	P	0.0	D	0.76494	0.999	D	0.68192	0.956	T	0.02728	-1.1118	9	0.52906	T	0.07	.	11.3343	0.49494	0.0723:0.1342:0.7935:0.0	rs41274041;rs62556599	837	Q5T7B8	KIF24_HUMAN	F	837;703;837;703;837	ENSP00000384433:S837F;ENSP00000368472:S703F;ENSP00000368464:S837F;ENSP00000340179:S703F	ENSP00000340179:S703F	S	-	2	0	KIF24	34247095	0.942000	0.31987	0.105000	0.21289	0.678000	0.39670	2.608000	0.46308	2.624000	0.88883	0.563000	0.77884	TCT	G|0.861;A|0.139	0.139	strong		0.493	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
TBC1D2	55357	hgsc.bcm.edu	37	9	100971348	100971348	+	Silent	SNP	T	T	C	rs3739666	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100971348T>C	ENST00000375064.1	-	9	1790	c.1752A>G	c.(1750-1752)gcA>gcG	p.A584A	TBC1D2_ENST00000493589.2_5'UTR|TBC1D2_ENST00000375066.5_Silent_p.A584A|TBC1D2_ENST00000375063.1_Silent_p.A124A|TBC1D2_ENST00000342112.5_Silent_p.A366A	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	584					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)		GTGACTCCAATGCCTGGATCT	0.612													C|||	3002	0.599441	0.7731	0.5418	5008	,	,		17823	0.498		0.5706	False		,,,				2504	0.5399				p.A584A		Atlas-SNP	.											TBC1D2,colon,carcinoma,0,1	TBC1D2	70	1	0			c.A1752G						PASS	.	C		3286,1120	394.9+/-329.4	1220,846,137	193.0	200.0	198.0		1752	-11.4	0.0	9	dbSNP_107	198	4819,3779	526.0+/-380.9	1339,2141,819	no	coding-synonymous	TBC1D2	NM_018421.3		2559,2987,956	CC,CT,TT		43.9521,25.4199,37.673		584/918	100971348	8105,4899	2203	4299	6502	SO:0001819	synonymous_variant	55357	exon9			CTCCAATGCCTGG	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.1752A>G	9.37:g.100971348T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	146	76	0.520548	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Silent	SNP	ENST00000375064.1	37																																																																																				T|0.384;C|0.616	0.616	strong		0.612	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
SPTBN2	6712	hgsc.bcm.edu	37	11	66468469	66468469	+	Missense_Mutation	SNP	A	A	G	rs506028	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66468469A>G	ENST00000533211.1	-	17	3432	c.3101T>C	c.(3100-3102)gTg>gCg	p.V1034A	SPTBN2_ENST00000529997.1_Missense_Mutation_p.V1034A|SPTBN2_ENST00000309996.2_Missense_Mutation_p.V1034A			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1034			V -> A (in dbSNP:rs506028).		actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GTTGATGGCCACTGCCTGAGC	0.721													G|||	1030	0.205671	0.3268	0.1268	5008	,	,		16267	0.2827		0.1133	False		,,,				2504	0.1135				p.V1034A		Atlas-SNP	.											.	SPTBN2	188	.	0			c.T3101C						PASS	.	G	ALA/VAL	1146,3250		141,864,1193	24.0	27.0	26.0		3101	4.5	0.2	11	dbSNP_83	26	793,7787		40,713,3537	yes	missense	SPTBN2	NM_006946.2	64	181,1577,4730	GG,GA,AA		9.2424,26.0692,14.943	benign	1034/2391	66468469	1939,11037	2198	4290	6488	SO:0001583	missense	6712	exon16			ATGGCCACTGCCT	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.3101T>C	11.37:g.66468469A>G	ENSP00000432568:p.Val1034Ala	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	436	0.19963369963369965	134	0.27235772357723576	47	0.1298342541436464	164	0.2867132867132867	91	0.12005277044854881	G	0.019	-1.452569	0.01080	0.260692	0.092424	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.46451	0.87;0.87;0.87	4.51	4.51	0.55191	.	0.893857	0.09833	N	0.749901	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35624	-0.9781	9	0.15066	T	0.55	.	11.7619	0.51908	0.0879:0.0:0.9121:0.0	rs506028;rs60296906;rs506028	1034	O15020	SPTN2_HUMAN	A	1034	ENSP00000432568:V1034A;ENSP00000311489:V1034A;ENSP00000433593:V1034A	ENSP00000311489:V1034A	V	-	2	0	SPTBN2	66225045	0.000000	0.05858	0.154000	0.22540	0.002000	0.02628	-0.102000	0.10956	1.137000	0.42214	-0.320000	0.08662	GTG	A|0.829;G|0.171	0.171	strong		0.721	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
ZNF500	26048	hgsc.bcm.edu	37	16	4815602	4815602	+	Silent	SNP	T	T	C	rs12919587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4815602T>C	ENST00000219478.6	-	2	677	c.378A>G	c.(376-378)gaA>gaG	p.E126E	ZNF500_ENST00000545009.1_Silent_p.E126E			O60304	ZN500_HUMAN	zinc finger protein 500	126	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)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						GCTGCAGCCCTTCCACAAGGA	0.657													T|||	2459	0.491014	0.3389	0.4755	5008	,	,		17027	0.4177		0.504	False		,,,				2504	0.7699				p.E126E		Atlas-SNP	.											.	ZNF500	45	.	0			c.A378G						PASS	.	T		1666,2728	479.9+/-358.7	344,978,875	46.0	45.0	45.0		378	-1.5	1.0	16	dbSNP_121	45	4681,3919	573.5+/-389.9	1264,2153,883	no	coding-synonymous	ZNF500	NM_021646.1		1608,3131,1758	CC,CT,TT		45.5698,37.9153,48.8456		126/481	4815602	6347,6647	2197	4300	6497	SO:0001819	synonymous_variant	26048	exon2			CAGCCCTTCCACA	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.378A>G	16.37:g.4815602T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	207	97	0.468599	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Silent	SNP	ENST00000219478.6	37	CCDS32383.1																																																																																			T|0.523;C|0.477	0.477	strong		0.657	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507	
C3orf20	84077	hgsc.bcm.edu	37	3	14745857	14745857	+	Missense_Mutation	SNP	G	G	A	rs17040196	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:14745857G>A	ENST00000253697.3	+	7	1344	c.892G>A	c.(892-894)Gcc>Acc	p.A298T	C3orf20_ENST00000412910.1_Missense_Mutation_p.A176T|C3orf20_ENST00000435614.1_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	81	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	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	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955861	18955861	+	Silent	SNP	C	C	T	rs72890000	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:18955861C>T	ENST00000302797.3	-	1	695	c.471G>A	c.(469-471)gaG>gaA	p.E157E	MRGPRX1_ENST00000526914.1_5'UTR|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	157					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						ATAACATCCACTCCAGGATGC	0.557													C|||	499	0.0996406	0.0076	0.0865	5008	,	,		26150	0.2073		0.1292	False		,,,				2504	0.092				p.E157E		Atlas-SNP	.											.	MRGPRX1	84	.	0			c.G471A						PASS	.	C		113,4275		5,103,2086	101.0	84.0	90.0		471	-4.2	0.0	11	dbSNP_130	90	1046,7526		73,900,3313	no	coding-synonymous	MRGPRX1	NM_147199.3		78,1003,5399	TT,TC,CC		12.2025,2.5752,8.9429		157/323	18955861	1159,11801	2194	4286	6480	SO:0001819	synonymous_variant	259249	exon1			CATCCACTCCAGG		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.471G>A	11.37:g.18955861C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	80	47	0.5875	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	37	CCDS7846.1																																																																																			C|0.905;T|0.095	0.095	strong		0.557	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43685357	43685357	+	Missense_Mutation	SNP	C	C	A	rs372133350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:43685357C>A	ENST00000377564.3	+	1	456	c.63C>A	c.(61-63)agC>agA	p.S21R	CNTNAP3B_ENST00000276974.6_Missense_Mutation_p.S21R	NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	21					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.S21R(1)		central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						AGACTTGGAGCCCCGTAGGAG	0.522													c|||	1096	0.21885	0.1339	0.3199	5008	,	,		16332	0.1329		0.2863	False		,,,				2504	0.2812				p.S21R		Atlas-SNP	.											CNTNAP3B,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CNTNAP3B	37	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C63A						scavenged	.																																			SO:0001583	missense	728577	exon1			TTGGAGCCCCGTA	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.63C>A	9.37:g.43685357C>A	ENSP00000366787:p.Ser21Arg	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	187	95	0.508021	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.685|9.685	1.150274|1.150274	0.21371|0.21371	.|.	.|.	ENSG00000154529|ENSG00000154529	ENST00000377561|ENST00000377564;ENST00000276974;ENST00000341990;ENST00000403166	.|D;D	.|0.95103	.|-2.56;-3.61	1.69|1.69	1.69|1.69	0.24217|0.24217	.|.	.|.	.|.	.|.	.|.	D|D	0.91744|0.91744	0.7389|0.7389	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	D|D	0.89794|0.89794	0.3970|0.3970	4|6	.|0.28530	.|T	.|0.3	.|.	8.2934|8.2934	0.31971|0.31971	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|R	70|21	.|ENSP00000366787:S21R;ENSP00000276974:S21R	.|ENSP00000276974:S21R	A|S	+|+	2|3	0|2	CNTNAP3B|CNTNAP3B	43625353|43625353	0.012000|0.012000	0.17670|0.17670	0.004000|0.004000	0.12327|0.12327	0.390000|0.390000	0.30446|0.30446	1.022000|1.022000	0.30052|0.30052	0.914000|0.914000	0.36822|0.36822	0.184000|0.184000	0.17185|0.17185	GCC|AGC	C|0.500;A|0.500	0.500	strong		0.522	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
CARD9	64170	hgsc.bcm.edu	37	9	139266496	139266496	+	Missense_Mutation	SNP	C	C	T	rs4077515	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139266496C>T	ENST00000371732.5	-	2	200	c.35G>A	c.(34-36)aGc>aAc	p.S12N	CARD9_ENST00000315908.7_Missense_Mutation_p.S12N|CARD9_ENST00000371734.3_Missense_Mutation_p.S12N	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	12	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		S -> N (in dbSNP:rs4077515). {ECO:0000269|PubMed:11053425, ECO:0000269|PubMed:14702039}.		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)		CTCCAGGACGCTCCAGCACTC	0.647													C|||	1836	0.366613	0.2519	0.5706	5008	,	,		18895	0.3214		0.3966	False		,,,				2504	0.3926				p.S12N		Atlas-SNP	.											CARD9,NS,carcinoma,0,1	CARD9	47	1	0			c.G35A						PASS	.	C	ASN/SER,ASN/SER	1227,3179	422.3+/-339.7	165,897,1141	116.0	80.0	92.0	http://www.ncbi.nlm.nih.gov/pubmed?term	35,35	-0.6	0.1	9	dbSNP_108	92	3625,4975	521.0+/-379.8	760,2105,1435	yes	missense,missense	CARD9	NM_052813.4,NM_052814.3	46,46	925,3002,2576	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	42.1512,27.8484,37.3059	benign,benign	12/537,12/493	139266496	4852,8154	2203	4300	6503	SO:0001583	missense	64170	exon2			AGGACGCTCCAGC	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.35G>A	9.37:g.139266496C>T	ENSP00000360797:p.Ser12Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Missense_Mutation	SNP	ENST00000371732.5	37	CCDS6997.1	803	0.3676739926739927	144	0.2926829268292683	170	0.4696132596685083	177	0.3094405594405594	312	0.41160949868073876	C	6.546	0.468978	0.12461	0.278484	0.421512	ENSG00000187796	ENST00000371734;ENST00000371732;ENST00000315908	T;T;T	0.20463	2.07;2.07;2.07	4.88	-0.553	0.11815	DEATH-like (2);Caspase Recruitment (2);	0.565475	0.18338	N	0.144278	T	0.00012	0.0000	N	0.03115	-0.41	0.54753	P	1.399999999995849E-5	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.08055	0.002;0.003;0.003	T	0.46400	-0.9194	9	0.27082	T	0.32	-14.5962	4.5111	0.11912	0.0:0.2509:0.3177:0.4314	rs4077515;rs60359505;rs4077515	12;12;12	Q9H257-2;Q5SXM5;Q9H257	.;.;CARD9_HUMAN	N	12	ENSP00000360799:S12N;ENSP00000360797:S12N;ENSP00000323719:S12N	ENSP00000323719:S12N	S	-	2	0	CARD9	138386317	0.005000	0.15991	0.100000	0.21137	0.252000	0.25951	-0.134000	0.10436	0.013000	0.14918	-0.326000	0.08463	AGC	C|0.634;T|0.366	0.366	strong		0.647	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
KDM5A	5927	hgsc.bcm.edu	37	12	427575	427575	+	Missense_Mutation	SNP	A	A	G	rs11062385	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:427575A>G	ENST00000399788.2	-	19	2956	c.2594T>C	c.(2593-2595)aTg>aCg	p.M865T	KDM5A_ENST00000382815.4_Missense_Mutation_p.M865T	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	865			M -> T (in dbSNP:rs11062385).		chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GGTTTCATCCATCATGGCCTC	0.393			T	NUP98	AML								A|||	1768	0.353035	0.3321	0.3199	5008	,	,		21745	0.5109		0.2326	False		,,,				2504	0.3661				p.M865T		Atlas-SNP	.		Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	.	KDM5A	307	.	0			c.T2594C						PASS	.	A	THR/MET	1180,2546		203,774,886	108.0	105.0	106.0		2594	4.0	1.0	12	dbSNP_120	106	2085,6131		276,1533,2299	yes	missense	KDM5A	NM_001042603.1	81	479,2307,3185	GG,GA,AA		25.3773,31.6694,27.3405	benign	865/1691	427575	3265,8677	1863	4108	5971	SO:0001583	missense	5927	exon19			TCATCCATCATGG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.2594T>C	12.37:g.427575A>G	ENSP00000382688:p.Met865Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	768	0.3516483516483517	181	0.3678861788617886	116	0.32044198895027626	289	0.5052447552447552	182	0.24010554089709762	A	6.591	0.477457	0.12521	0.316694	0.253773	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	T;T;T	0.39997	1.05;1.05;1.05	5.18	3.99	0.46301	Lysine-specific demethylase-like domain (1);	0.270105	0.38217	N	0.001762	T	0.00012	0.0000	N	0.01874	-0.695	0.32953	P	0.479989	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.001;0.001;0.004	T	0.46965	-0.9153	9	0.21014	T	0.42	-7.7721	6.1802	0.20468	0.7533:0.1572:0.0895:0.0	rs11062385;rs52835808;rs60765971;rs11062385	865;865;865	F5H1F7;P29375;P29375-2	.;KDM5A_HUMAN;.	T	484;824;865;865;484	ENSP00000382688:M865T;ENSP00000372265:M865T;ENSP00000440622:M484T	ENSP00000261253:M484T	M	-	2	0	KDM5A	297836	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.908000	0.56355	0.760000	0.33108	0.482000	0.46254	ATG	A|0.651;G|0.349	0.349	strong		0.393	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	
CCDC27	148870	hgsc.bcm.edu	37	1	3679775	3679775	+	Missense_Mutation	SNP	C	C	T	rs10910024	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3679775C>T	ENST00000294600.2	+	7	1142	c.1058C>T	c.(1057-1059)aCg>aTg	p.T353M		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	353	Glu-rich.		T -> M (in dbSNP:rs10910024). {ECO:0000269|PubMed:15489334}.							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)		GTGGAGGACACGGGTGCCTGG	0.667													C|||	744	0.148562	0.1074	0.2738	5008	,	,		16229	0.003		0.2435	False		,,,				2504	0.1677				p.T353M		Atlas-SNP	.											.	CCDC27	79	.	0			c.C1058T						PASS	.	C	MET/THR	547,3823		32,483,1670	57.0	57.0	57.0		1058	-5.1	0.0	1	dbSNP_120	57	2072,6486		256,1560,2463	yes	missense	CCDC27	NM_152492.2	81	288,2043,4133	TT,TC,CC		24.2113,12.5172,20.2584	probably-damaging	353/657	3679775	2619,10309	2185	4279	6464	SO:0001583	missense	148870	exon7			AGGACACGGGTGC		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.1058C>T	1.37:g.3679775C>T	ENSP00000294600:p.Thr353Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	323	0.1478937728937729	48	0.0975609756097561	87	0.24033149171270718	0	0.0	188	0.24802110817941952	C	5.949	0.359090	0.11239	0.125172	0.242113	ENSG00000162592	ENST00000294600	T	0.18960	2.18	2.93	-5.07	0.02938	.	3.906960	0.00575	N	0.000301	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.19583	0.037	B	0.12156	0.007	T	0.28267	-1.0049	9	0.41790	T	0.15	.	1.2646	0.02008	0.1856:0.2133:0.1286:0.4725	rs10910024;rs57282654;rs10910024	353	Q2M243	CCD27_HUMAN	M	353	ENSP00000294600:T353M	ENSP00000294600:T353M	T	+	2	0	CCDC27	3669635	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.171000	0.00281	-1.283000	0.02393	-1.406000	0.01132	ACG	C|0.836;T|0.164	0.164	strong		0.667	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
TMEM144	55314	hgsc.bcm.edu	37	4	159158677	159158677	+	Splice_Site	SNP	G	G	A	rs12504074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:159158677G>A	ENST00000296529.6	+	9	1084	c.564G>A	c.(562-564)gtG>gtA	p.V188V	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	188						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(7)|lung(9)|prostate(1)	19	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		GTTTTGTAAGGGGCTGCAGTC	0.363													G|||	391	0.0780751	0.0492	0.1484	5008	,	,		17204	0.0417		0.1352	False		,,,				2504	0.046				p.V188V		Atlas-SNP	.											.	TMEM144	34	.	0			c.G564A						PASS	.	G		259,4147	148.0+/-182.4	6,247,1950	163.0	159.0	160.0		564	2.8	1.0	4	dbSNP_120	160	969,7631	210.0+/-251.0	49,871,3380	yes	coding-synonymous-near-splice	TMEM144	NM_018342.4		55,1118,5330	AA,AG,GG		11.2674,5.8783,9.4418		188/346	159158677	1228,11778	2203	4300	6503	SO:0001630	splice_region_variant	55314	exon9			TGTAAGGGGCTGC	AK002017	CCDS3799.1	4q32.1	2008-02-05			ENSG00000164124	ENSG00000164124			25633	protein-coding gene	gene with protein product						12477932	Standard	NM_018342		Approved	FLJ11155	uc003ipx.3	Q7Z5S9	OTTHUMG00000162013	ENST00000296529.6:c.564-1G>A	4.37:g.159158677G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_018342	D3DP24|Q49A05|Q9NUT3	Silent	SNP	ENST00000296529.6	37	CCDS3799.1																																																																																			G|0.912;A|0.088	0.088	strong		0.363	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342	Silent
RPS6KA2	6196	hgsc.bcm.edu	37	6	166873010	166873010	+	Silent	SNP	C	C	T	rs2230729	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:166873010C>T	ENST00000265678.4	-	12	1225	c.1002G>A	c.(1000-1002)ccG>ccA	p.P334P	RPS6KA2_ENST00000503859.1_Silent_p.P342P|RPS6KA2-IT1_ENST00000416770.1_RNA|RPS6KA2_ENST00000510118.1_Silent_p.P359P|RPS6KA2_ENST00000405189.3_Silent_p.P245P|RPS6KA2_ENST00000481261.2_Silent_p.P245P	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	334	AGC-kinase C-terminal.				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)		CTGGTTTGAACGGTGGCTTGA	0.557													C|||	755	0.150759	0.112	0.196	5008	,	,		17552	0.1746		0.161	False		,,,				2504	0.136				p.P342P		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.G1026A						PASS	.	C	,	579,3827	253.4+/-259.3	30,519,1654	188.0	140.0	156.0		1026,1002	-7.2	0.4	6	dbSNP_107	156	1312,7288	257.5+/-281.5	110,1092,3098	no	coding-synonymous,coding-synonymous	RPS6KA2	NM_001006932.1,NM_021135.4	,	140,1611,4752	TT,TC,CC		15.2558,13.1412,14.5394	,	342/742,334/734	166873010	1891,11115	2203	4300	6503	SO:0001819	synonymous_variant	6196	exon13			TTTGAACGGTGGC	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.1002G>A	6.37:g.166873010C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																			C|0.849;T|0.151	0.151	strong		0.557	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
LINGO3	645191	hgsc.bcm.edu	37	19	2290870	2290870	+	Silent	SNP	G	G	C	rs8111892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2290870G>C	ENST00000585527.1	-	1	1153	c.906C>G	c.(904-906)gcC>gcG	p.A302A	LINGO3_ENST00000404279.1_Silent_p.A302A			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	302						integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						GCAGGGCCCCGGCCAGGTGCA	0.687													G|||	1212	0.242013	0.3828	0.2781	5008	,	,		14359	0.2421		0.1183	False		,,,				2504	0.1534				p.A302A		Atlas-SNP	.											.	LINGO3	19	.	0			c.C906G						PASS	.	G		1256,2676		198,860,908	12.0	15.0	14.0		906	-9.0	0.2	19	dbSNP_116	14	848,7400		46,756,3322	no	coding-synonymous	LINGO3	NM_001101391.1		244,1616,4230	CC,CG,GG		10.2813,31.943,17.2742		302/593	2290870	2104,10076	1966	4124	6090	SO:0001819	synonymous_variant	645191	exon2			GGCCCCGGCCAGG	AK091795	CCDS45905.1	19p13.3	2013-01-11	2007-02-01	2007-02-01		ENSG00000220008		"""Immunoglobulin superfamily / I-set domain containing"""	21206	protein-coding gene	gene with protein product		609792	"""leucine rich repeat neuronal 6B"""	LRRN6B		14686891	Standard	NM_001101391		Approved	LERN2	uc010dsx.1	P0C6S8		ENST00000585527.1:c.906C>G	19.37:g.2290870G>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_001101391		Silent	SNP	ENST00000585527.1	37	CCDS45905.1																																																																																			G|0.803;C|0.197	0.197	strong		0.687	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391	
DHDH	27294	hgsc.bcm.edu	37	19	49445817	49445817	+	Missense_Mutation	SNP	T	T	C	rs11666105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49445817T>C	ENST00000221403.2	+	5	780	c.740T>C	c.(739-741)gTa>gCa	p.V247A	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Missense_Mutation_p.V108A	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	247			V -> A (in dbSNP:rs11666105).		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)		AAGGGCATGGTACAGGTGAGG	0.612													C|||	2271	0.453474	0.6967	0.2954	5008	,	,		19234	0.5704		0.2058	False		,,,				2504	0.3712				p.V247A		Atlas-SNP	.											.	DHDH	35	.	0			c.T740C						PASS	.	C	ALA/VAL	2770,1636	497.6+/-363.9	892,986,325	53.0	48.0	50.0		740	2.5	0.7	19	dbSNP_120	50	1489,7111	745.4+/-407.3	130,1229,2941	yes	missense	DHDH	NM_014475.3	64	1022,2215,3266	CC,CT,TT		17.314,37.1312,32.7464	benign	247/335	49445817	4259,8747	2203	4300	6503	SO:0001583	missense	27294	exon5			GCATGGTACAGGT	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.740T>C	19.37:g.49445817T>C	ENSP00000221403:p.Val247Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	903	0.41346153846153844	325	0.6605691056910569	94	0.2596685082872928	313	0.5472027972027972	171	0.22559366754617413	C	3.572	-0.087501	0.07097	0.628688	0.17314	ENSG00000104808	ENST00000221403;ENST00000523250	T;T	0.23552	1.9;1.9	4.67	2.52	0.30459	.	0.241349	0.41712	N	0.000836	T	0.00012	0.0000	N	0.03238	-0.38	0.22500	P	0.999045546	B	0.02656	0.0	B	0.06405	0.002	T	0.30060	-0.9991	9	0.49607	T	0.09	-9.8612	4.3945	0.11356	0.0:0.5637:0.1657:0.2706	rs11666105;rs52799598;rs61101818;rs11666105	247	Q9UQ10	DHDH_HUMAN	A	247;108	ENSP00000221403:V247A;ENSP00000428935:V108A	ENSP00000221403:V247A	V	+	2	0	DHDH	54137629	0.981000	0.34729	0.748000	0.31131	0.041000	0.13682	2.693000	0.47027	0.301000	0.22738	-0.684000	0.03749	GTA	T|0.634;C|0.366	0.366	strong		0.612	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
USH2A	7399	hgsc.bcm.edu	37	1	216073505	216073505	+	Silent	SNP	C	C	T	rs12404427	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:216073505C>T	ENST00000307340.3	-	40	7892	c.7506G>A	c.(7504-7506)ccG>ccA	p.P2502P	USH2A_ENST00000366943.2_Silent_p.P2502P|RP5-1111A8.3_ENST00000414995.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2502	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACTCTGTGTACGGTTGGAGAT	0.418										HNSCC(13;0.011)			C|||	295	0.0589058	0.0923	0.0836	5008	,	,		19389	0.0		0.0746	False		,,,				2504	0.0409				p.P2502P		Atlas-SNP	.											.	USH2A	1168	.	0			c.G7506A						PASS	.	C		383,4023	192.3+/-217.7	18,347,1838	132.0	110.0	118.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7506	-7.8	0.0	1	dbSNP_120	118	724,7876	176.3+/-226.2	36,652,3612	no	coding-synonymous	USH2A	NM_206933.2		54,999,5450	TT,TC,CC		8.4186,8.6927,8.5115		2502/5203	216073505	1107,11899	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon40			TGTGTACGGTTGG	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.7506G>A	1.37:g.216073505C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			C|0.926;T|0.074	0.074	strong		0.418	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
NLGN2	57555	hgsc.bcm.edu	37	17	7320581	7320581	+	Silent	SNP	C	C	T	rs78081080	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7320581C>T	ENST00000302926.2	+	7	2044	c.1971C>T	c.(1969-1971)ccC>ccT	p.P657P	RP11-104H15.7_ENST00000575310.1_RNA|NLGN2_ENST00000575301.1_Silent_p.P657P	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	657					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)				AGCCCGAGCCCGGCCCAAGGG	0.756													C|||	331	0.0660942	0.0061	0.0735	5008	,	,		8417	0.0397		0.0895	False		,,,				2504	0.1452				p.P657P		Atlas-SNP	.											.	NLGN2	61	.	0			c.C1971T						PASS	.	C		72,4248		1,70,2089	9.0	9.0	9.0		1971	-6.0	0.9	17	dbSNP_131	9	612,7866		13,586,3640	no	coding-synonymous	NLGN2	NM_020795.2		14,656,5729	TT,TC,CC		7.2187,1.6667,5.3446		657/836	7320581	684,12114	2160	4239	6399	SO:0001819	synonymous_variant	57555	exon7			CGAGCCCGGCCCA	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.1971C>T	17.37:g.7320581C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	26	20	0.769231	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																			C|0.948;T|0.052	0.052	strong		0.756	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
DACT1	51339	hgsc.bcm.edu	37	14	59113537	59113537	+	Silent	SNP	C	C	G	rs61755641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:59113537C>G	ENST00000335867.4	+	4	2220	c.2196C>G	c.(2194-2196)tcC>tcG	p.S732S	DACT1_ENST00000395153.3_Silent_p.S695S|DACT1_ENST00000556859.1_Silent_p.S451S|DACT1_ENST00000541264.2_Silent_p.S451S			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	732					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						AGTGCGAGTCCCTGTTCCACT	0.642													C|||	168	0.0335463	0.0303	0.0375	5008	,	,		11194	0.003		0.0616	False		,,,				2504	0.0378				p.S732S		Atlas-SNP	.											.	DACT1	119	.	0			c.C2196G						PASS	.	C	,	143,4263	99.4+/-138.0	2,139,2062	82.0	78.0	80.0		2085,2196	-1.3	1.0	14	dbSNP_129	80	473,8127	137.8+/-194.7	10,453,3837	no	coding-synonymous,coding-synonymous	DACT1	NM_001079520.1,NM_016651.5	,	12,592,5899	GG,GC,CC		5.5,3.2456,4.7363	,	695/800,732/837	59113537	616,12390	2203	4300	6503	SO:0001819	synonymous_variant	51339	exon4			CGAGTCCCTGTTC	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.2196C>G	14.37:g.59113537C>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	37	CCDS9736.1																																																																																			C|0.956;G|0.044	0.044	strong		0.642	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237953	239237953	+	Missense_Mutation	SNP	G	G	T	rs12464423	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:239237953G>T	ENST00000373327.4	+	5	1107	c.885G>T	c.(883-885)aaG>aaT	p.K295N	TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.K295N|TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.K295N	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	295	Abolishes microtubules-binding when missing.|DISC1-interaction domain.		K -> N (in dbSNP:rs12464423).		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)		ACAGGGAGAAGAACAGAGAGC	0.512													G|||	1027	0.205072	0.0219	0.3516	5008	,	,		19671	0.2351		0.3012	False		,,,				2504	0.2188				p.K295N		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.G885T						PASS	.	G	ASN/LYS,ASN/LYS	295,4105	157.4+/-190.3	8,279,1913	66.0	76.0	73.0		885,885	2.5	0.1	2	dbSNP_120	73	2745,5829	408.0+/-349.4	449,1847,1991	yes	missense,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	94,94	457,2126,3904	TT,TG,GG		32.0154,6.7045,23.4315	possibly-damaging,possibly-damaging	295/626,295/692	239237953	3040,9934	2200	4287	6487	SO:0001583	missense	26146	exon5			GGAGAAGAACAGA	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.885G>T	2.37:g.239237953G>T	ENSP00000362424:p.Lys295Asn	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	521	0.23855311355311357	18	0.036585365853658534	123	0.3397790055248619	138	0.24125874125874125	242	0.31926121372031663	G	9.896	1.205530	0.22205	0.067045	0.320154	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.20200	2.09;2.09;2.09	4.37	2.52	0.30459	.	0.711349	0.14189	N	0.335508	T	0.00012	0.0000	L	0.55481	1.735	0.29484	P	0.856105	P;B	0.48016	0.904;0.136	P;B	0.49887	0.625;0.048	T	0.42327	-0.9458	9	0.46703	T	0.11	-12.9035	8.2169	0.31516	0.2696:0.0:0.7304:0.0	rs12464423;rs61180925;rs12464423	295;295	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	N	295	ENSP00000375851:K295N;ENSP00000362424:K295N;ENSP00000375852:K295N	ENSP00000362424:K295N	K	+	3	2	TRAF3IP1	238902692	0.955000	0.32602	0.123000	0.21794	0.439000	0.31926	0.808000	0.27154	0.395000	0.25257	0.655000	0.94253	AAG	A|0.000;G|0.758;T|0.242	0.242	strong		0.512	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
EBLN2	55096	hgsc.bcm.edu	37	3	73111973	73111973	+	Silent	SNP	A	A	G	rs2231928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:73111973A>G	ENST00000533473.1	+	1	1164	c.741A>G	c.(739-741)ccA>ccG	p.P247P	PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000394284.3_Intron	NM_018029.3	NP_060499.3	Q6P2I7	EBLN2_HUMAN	endogenous Bornavirus-like nucleoprotein 2	247										endometrium(1)|large_intestine(3)|lung(1)|prostate(1)	6						GCTCAAGACCATGGGTTGGAG	0.438													G|||	3079	0.614816	0.888	0.3991	5008	,	,		21782	0.4931		0.5099	False		,,,				2504	0.6319				p.P247P		Atlas-SNP	.											.	EBLN2	18	.	0			c.A741G						PASS	.	G	,	3237,615		1373,491,62	184.0	189.0	188.0		741,	-0.9	0.0	3	dbSNP_98	188	4245,4013		1087,2071,971	yes	coding-synonymous,intron	EBLN2,PPP4R2	NM_018029.3,NM_174907.2	,	2460,2562,1033	GG,GA,AA		48.5953,15.9657,38.2164	,	247/273,	73111973	7482,4628	1926	4129	6055	SO:0001819	synonymous_variant	55096	exon1			AAGACCATGGGTT		CCDS54608.1	3p13	2011-06-03			ENSG00000255423	ENSG00000255423			25493	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 2"""	613250				20054395, 20686665	Standard	NM_018029		Approved		uc003dpj.3	Q6P2I7	OTTHUMG00000165897	ENST00000533473.1:c.741A>G	3.37:g.73111973A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_018029	Q8WWH3|Q9NW89	Silent	SNP	ENST00000533473.1	37	CCDS54608.1																																																																																			A|0.395;G|0.605	0.605	strong		0.438	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029	
ANPEP	290	hgsc.bcm.edu	37	15	90334240	90334240	+	Silent	SNP	A	A	G	rs25654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90334240A>G	ENST00000300060.6	-	19	2926	c.2613T>C	c.(2611-2613)atT>atC	p.I871I		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	871	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	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)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GACCTTGCCCAATGACGTTGT	0.542													G|||	1570	0.313498	0.3812	0.2493	5008	,	,		20459	0.2341		0.2952	False		,,,				2504	0.3681				p.I871I	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.T2613C						PASS	.	G		1584,2816	665.6+/-401.6	290,1004,906	154.0	134.0	141.0		2613	-9.0	0.0	15	dbSNP_72	141	2734,5864	680.3+/-403.6	405,1924,1970	no	coding-synonymous	ANPEP	NM_001150.2		695,2928,2876	GG,GA,AA		31.7981,36.0,33.2205		871/968	90334240	4318,8680	2200	4299	6499	SO:0001819	synonymous_variant	290	exon19			TTGCCCAATGACG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2613T>C	15.37:g.90334240A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	207	91	0.439614	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																			A|0.675;G|0.325	0.325	strong		0.542	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
AGTR1	185	hgsc.bcm.edu	37	3	148459129	148459129	+	Missense_Mutation	SNP	A	A	T	rs201745152		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148459129A>T	ENST00000497524.1	+	2	698	c.307A>T	c.(307-309)Att>Ttt	p.I103F	AGTR1_ENST00000349243.3_Missense_Mutation_p.I103F|AGTR1_ENST00000461609.1_Missense_Mutation_p.I103F|AGTR1_ENST00000418473.2_Missense_Mutation_p.I103F|AGTR1_ENST00000475347.1_Missense_Mutation_p.I103F|AGTR1_ENST00000474935.1_Missense_Mutation_p.I103F|AGTR1_ENST00000542281.1_Missense_Mutation_p.I103F|AGTR1_ENST00000404754.2_Missense_Mutation_p.I103F|AGTR1_ENST00000402260.1_Missense_Mutation_p.I103F	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	103					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)			breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	CCTATGTAAGATTGCTTCAGC	0.458																																					p.I138F		Atlas-SNP	.											.	AGTR1	63	.	0			c.A412T						PASS	.						84.0	81.0	82.0					3																	148459129		2203	4300	6503	SO:0001583	missense	185	exon4			TGTAAGATTGCTT	M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"""GPCR / Class A : Angiotensin receptors"""	336	protein-coding gene	gene with protein product		106165	"""angiotensin receptor 1B"""	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.307A>T	3.37:g.148459129A>T	ENSP00000419422:p.Ile103Phe	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_031850	Q13725|Q8TBK4	Missense_Mutation	SNP	ENST00000497524.1	37	CCDS3137.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069842	0.36566	.	.	ENSG00000144891	ENST00000497524;ENST00000349243;ENST00000542281;ENST00000418473;ENST00000404754;ENST00000475347;ENST00000474935;ENST00000461609;ENST00000402260	T;T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.326257	0.29616	N	0.011648	T	0.26195	0.0639	N	0.17345	0.48	0.36625	D	0.875957	B	0.29270	0.24	B	0.38921	0.285	T	0.31943	-0.9925	10	0.48119	T	0.1	-17.5731	6.1718	0.20421	0.5754:0.1271:0.0:0.2975	.	103	P30556	AGTR1_HUMAN	F	103	ENSP00000419422:I103F;ENSP00000273430:I103F;ENSP00000443186:I103F;ENSP00000398832:I103F;ENSP00000385612:I103F;ENSP00000419783:I103F;ENSP00000418084:I103F;ENSP00000418851:I103F;ENSP00000385641:I103F	ENSP00000273430:I103F	I	+	1	0	AGTR1	149941819	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.369000	0.34227	2.071000	0.62044	0.533000	0.62120	ATT	A|0.999;T|0.001	0.001	weak		0.458	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1		
BDKRB2	624	hgsc.bcm.edu	37	14	96703484	96703484	+	Missense_Mutation	SNP	C	C	T	rs1046248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:96703484C>T	ENST00000306005.3	+	2	236	c.40C>T	c.(40-42)Cgt>Tgt	p.R14C	BDKRB2_ENST00000554311.1_Missense_Mutation_p.R14C|RP11-404P21.8_ENST00000553811.1_Missense_Mutation_p.R14C|BDKRB2_ENST00000542454.2_5'UTR|BDKRB2_ENST00000539359.1_5'UTR	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	14			R -> C (in dbSNP:rs1046248). {ECO:0000269|PubMed:7779090, ECO:0000269|Ref.8}.		arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	TCTGTCTGTTCGTGAGGACTC	0.527													C|||	213	0.0425319	0.056	0.0548	5008	,	,		21774	0.002		0.0865	False		,,,				2504	0.0123				p.R14C		Atlas-SNP	.											.	BDKRB2	56	.	0			c.C40T						PASS	.	C	CYS/ARG	224,4182	133.3+/-169.7	3,218,1982	200.0	159.0	173.0		40	1.8	0.0	14	dbSNP_86	173	839,7761	191.8+/-238.0	51,737,3512	yes	missense	BDKRB2	NM_000623.3	180	54,955,5494	TT,TC,CC		9.7558,5.084,8.1732	probably-damaging	14/392	96703484	1063,11943	2203	4300	6503	SO:0001583	missense	624	exon2			TCTGTTCGTGAGG	S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"""GPCR / Class A : Bradykinin receptors"""	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.40C>T	14.37:g.96703484C>T	ENSP00000307713:p.Arg14Cys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_000623		Missense_Mutation	SNP	ENST00000306005.3	37	CCDS9942.1	120	0.054945054945054944	30	0.06097560975609756	21	0.058011049723756904	0	0.0	69	0.09102902374670185	C	14.42	2.529529	0.44969	0.05084	0.097558	ENSG00000168398;ENSG00000168398;ENSG00000258691	ENST00000554311;ENST00000306005;ENST00000553811	T;T;T	0.72282	-0.64;-0.64;1.69	3.71	1.77	0.24775	.	2.399830	0.01945	N	0.042183	T	0.01592	0.0051	N	0.08118	0	0.80722	P	0.0	P	0.46277	0.875	B	0.32211	0.142	T	0.24404	-1.0161	9	0.40728	T	0.16	.	5.1894	0.15201	0.0:0.7153:0.0:0.2847	rs1046248;rs1800772;rs3186219;rs17191331;rs52804895;rs57649699;rs1046248	14	P30411	BKRB2_HUMAN	C	14	ENSP00000450482:R14C;ENSP00000307713:R14C;ENSP00000450984:R14C	ENSP00000307713:R14C	R	+	1	0	RP11-404P21.8;BDKRB2	95773237	0.014000	0.17966	0.000000	0.03702	0.006000	0.05464	0.961000	0.29267	0.489000	0.27749	0.655000	0.94253	CGT	C|0.933;T|0.067	0.067	strong		0.527	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1		
SIRT3	23410	hgsc.bcm.edu	37	11	233067	233067	+	Missense_Mutation	SNP	C	C	T	rs11246020	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:233067C>T	ENST00000382743.4	-	3	724	c.622G>A	c.(622-624)Gtc>Atc	p.V208I	SIRT3_ENST00000529382.1_Missense_Mutation_p.V66I|SIRT3_ENST00000532956.1_Missense_Mutation_p.V208I|SIRT3_ENST00000524564.1_Missense_Mutation_p.V144I|SIRT3_ENST00000525319.1_Missense_Mutation_p.V127I|SIRT3_ENST00000528702.1_5'UTR	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	208	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.		V -> I (in dbSNP:rs11246020).		aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		TAGTGAGTGACGTTGGGCTTG	0.532													c|||	575	0.114816	0.0151	0.1484	5008	,	,		17968	0.0942		0.2048	False		,,,				2504	0.1544				p.V208I		Atlas-SNP	.											.	SIRT3	28	.	0			c.G622A						PASS	.		ILE/VAL,ILE/VAL	191,4215	120.0+/-157.7	6,179,2018	109.0	104.0	106.0		196,622	-3.3	0.0	11	dbSNP_120	106	1831,6769	328.2+/-318.2	179,1473,2648	yes	missense,missense	SIRT3	NM_001017524.2,NM_012239.5	29,29	185,1652,4666	TT,TC,CC		21.2907,4.335,15.5467	benign,benign	66/258,208/400	233067	2022,10984	2203	4300	6503	SO:0001583	missense	23410	exon3			GAGTGACGTTGGG	AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3"", ""sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"""			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.622G>A	11.37:g.233067C>T	ENSP00000372191:p.Val208Ile	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	222	222	1	NM_012239	B7Z5U6|Q9Y6E8	Missense_Mutation	SNP	ENST00000382743.4	37	CCDS7691.1	279	0.12774725274725274	12	0.024390243902439025	54	0.14917127071823205	66	0.11538461538461539	147	0.19393139841688653	c	0.008	-1.872500	0.00542	0.04335	0.212907	ENSG00000142082	ENST00000382743;ENST00000525319;ENST00000524564;ENST00000532956;ENST00000529382;ENST00000528469	T;T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31;2.31	5.37	-3.33	0.04958	.	1.847400	0.03050	N	0.154442	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B;B;B;B;B	0.25609	0.13;0.002;0.001;0.004;0.002	B;B;B;B;B	0.15484	0.013;0.001;0.001;0.003;0.001	T	0.34551	-0.9824	9	0.21540	T	0.41	-5.4653	1.3502	0.02171	0.2453:0.2876:0.093:0.3741	rs11246020;rs52815403;rs61432625;rs11246020	208;208;127;144;208	E9PM75;B7Z7G4;E9PK80;E9PN58;Q9NTG7	.;.;.;.;SIRT3_HUMAN	I	208;127;144;208;66;66	ENSP00000372191:V208I;ENSP00000435464:V127I;ENSP00000432937:V144I;ENSP00000433077:V208I;ENSP00000437216:V66I;ENSP00000432857:V66I	ENSP00000372191:V208I	V	-	1	0	SIRT3	223067	0.000000	0.05858	0.000000	0.03702	0.194000	0.23727	-0.858000	0.04281	-0.565000	0.06061	-0.810000	0.03169	GTC	T|0.146;C|0.854	0.146	strong		0.532	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3		
CNN2	1265	hgsc.bcm.edu	37	19	1036456	1036456	+	Silent	SNP	C	C	G	rs1064410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1036456C>G	ENST00000263097.4	+	6	912	c.549C>G	c.(547-549)gcC>gcG	p.A183A	CNN2_ENST00000565096.2_Silent_p.A172A|CNN2_ENST00000606983.1_3'UTR|CNN2_ENST00000348419.3_Silent_p.A144A|CNN2_ENST00000562958.2_Silent_p.A204A|AC011558.5_ENST00000585757.1_RNA	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	183				TA -> HL (in Ref. 6; BAA20887). {ECO:0000305}.	actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCATGACTGCCTACGGCACGA	0.597													G|||	570	0.113818	0.0855	0.0951	5008	,	,		17735	0.0962		0.1968	False		,,,				2504	0.0982				p.A183A		Atlas-SNP	.											.	CNN2	26	.	0			c.C549G						PASS	.	G	,	449,3957	784.1+/-414.7	24,401,1778	71.0	66.0	68.0		549,432	-8.4	0.0	19	dbSNP_86	68	1807,6793	732.3+/-406.8	177,1453,2670	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	201,1854,4448	GG,GC,CC		21.0116,10.1906,17.3458	,	183/310,144/271	1036456	2256,10750	2203	4300	6503	SO:0001819	synonymous_variant	1265	exon6			GACTGCCTACGGC	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.549C>G	19.37:g.1036456C>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	188	79	0.420213	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			C|0.837;G|0.163	0.163	strong		0.597	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
KLHL17	339451	hgsc.bcm.edu	37	1	900505	900505	+	Silent	SNP	G	G	C	rs28705211	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:900505G>C	ENST00000338591.3	+	12	1970	c.1863G>C	c.(1861-1863)gtG>gtC	p.V621V	PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379410.3_5'Flank|PLEKHN1_ENST00000379409.2_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	621	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GTGTGGCGGTGCTGGAGCTGC	0.642													G|||	845	0.16873	0.0174	0.2017	5008	,	,		10946	0.0913		0.2903	False		,,,				2504	0.3047				p.V621V		Atlas-SNP	.											KLHL17,NS,carcinoma,0,1	KLHL17	31	1	0			c.G1863C						scavenged	.						107.0	82.0	90.0					1																	900505		2198	4298	6496	SO:0001819	synonymous_variant	339451	exon12			GGCGGTGCTGGAG	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"""Kelch-like"", ""BTB/POZ domain containing"""	24023	protein-coding gene	gene with protein product	"""actinfilin"""		"""kelch-like 17 (Drosophila)"""			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1863G>C	1.37:g.900505G>C		Somatic	126	3	0.0238095		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_198317	Q5SV94	Silent	SNP	ENST00000338591.3	37	CCDS30550.1																																																																																			G|0.802;C|0.198	0.198	strong		0.642	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317	
SNAPC4	6621	hgsc.bcm.edu	37	9	139273288	139273288	+	Silent	SNP	C	C	T	rs3829112	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139273288C>T	ENST00000298532.2	-	21	3359	c.2991G>A	c.(2989-2991)gaG>gaA	p.E997E		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)		GGGCTGTGCCCTCGGCCTCTG	0.667													C|||	945	0.188698	0.0893	0.2594	5008	,	,		10947	0.2738		0.161	False		,,,				2504	0.2137				p.E997E		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G2991A						PASS	.	C		382,4000		17,348,1826	15.0	18.0	17.0		2991	1.9	0.0	9	dbSNP_107	17	1323,7263		102,1119,3072	no	coding-synonymous	SNAPC4	NM_003086.2		119,1467,4898	TT,TC,CC		15.4088,8.7175,13.1477		997/1470	139273288	1705,11263	2191	4293	6484	SO:0001819	synonymous_variant	6621	exon21			TGTGCCCTCGGCC	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.2991G>A	9.37:g.139273288C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	189	93	0.492063	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			C|0.845;T|0.155	0.155	strong		0.667	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
HIPK2	28996	hgsc.bcm.edu	37	7	139415775	139415775	+	Silent	SNP	G	G	C	rs7456421	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:139415775G>C	ENST00000406875.3	-	2	1153	c.1059C>G	c.(1057-1059)gtC>gtG	p.V353V	HIPK2_ENST00000428878.2_Silent_p.V353V|HIPK2_ENST00000342645.6_Silent_p.V353V	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	353	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					CAGCCTTGGAGACGTGGCTGG	0.512													C|||	1986	0.396565	0.7995	0.4784	5008	,	,		21469	0.2669		0.2127	False		,,,				2504	0.1166				p.V353V		Atlas-SNP	.											.	HIPK2	192	.	0			c.C1059G						PASS	.	C	,	2196,940		777,642,149	93.0	79.0	83.0		1059,1059	3.2	1.0	7	dbSNP_116	83	1421,5743		125,1171,2286	yes	coding-synonymous,coding-synonymous	HIPK2	NM_001113239.2.dup,NM_022740.4.dup	,	902,1813,2435	CC,CG,GG		19.8353,29.9745,35.1165	,	353/368,353/368	139415775	3617,6683	1568	3582	5150	SO:0001819	synonymous_variant	28996	exon2			CTTGGAGACGTGG	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1059C>G	7.37:g.139415775G>C		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	194	111	0.572165	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	37																																																																																				G|0.630;C|0.370	0.370	strong		0.512	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54645411	54645411	+	Silent	SNP	G	G	A	rs2061242	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54645411G>A	ENST00000230640.5	+	12	1505	c.1251G>A	c.(1249-1251)aaG>aaA	p.K417K	SKIV2L2_ENST00000545714.1_Silent_p.K316K	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	417	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				ATGAAGAAAAGAAGATGGTTG	0.333													G|||	912	0.182109	0.289	0.0937	5008	,	,		19365	0.2867		0.0984	False		,,,				2504	0.0787				p.K417K	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.G1251A						PASS	.	G		990,3416	357.6+/-314.0	107,776,1320	72.0	78.0	76.0		1251	4.7	1.0	5	dbSNP_94	76	848,7752	193.4+/-239.1	44,760,3496	no	coding-synonymous	SKIV2L2	NM_015360.4		151,1536,4816	AA,AG,GG		9.8605,22.4694,14.1319		417/1043	54645411	1838,11168	2203	4300	6503	SO:0001819	synonymous_variant	23517	exon12			AGAAAAGAAGATG	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1251G>A	5.37:g.54645411G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	165	84	0.509091	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	37	CCDS3967.1																																																																																			G|0.840;A|0.160	0.160	strong		0.333	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
COX6A2	1339	hgsc.bcm.edu	37	16	31439170	31439170	+	Silent	SNP	G	G	A	rs12240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31439170G>A	ENST00000287490.4	-	3	321	c.219C>T	c.(217-219)ccC>ccT	p.P73P		NM_005205.3	NP_005196.1	Q02221	CX6A2_HUMAN	cytochrome c oxidase subunit VIa polypeptide 2	73					generation of precursor metabolites and energy (GO:0006091)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)|large_intestine(2)|lung(1)	5						CGTCCCCCCAGGGGTAGGGCT	0.731													G|||	421	0.0840655	0.1036	0.0461	5008	,	,		6488	0.0486		0.0746	False		,,,				2504	0.1309				p.P73P		Atlas-SNP	.											.	COX6A2	7	.	0			c.C219T						PASS	.	G		390,4004	174.4+/-204.0	13,364,1820	36.0	37.0	37.0		219	1.0	0.3	16	dbSNP_52	37	650,7950	148.2+/-203.4	17,616,3667	no	coding-synonymous	COX6A2	NM_005205.3		30,980,5487	AA,AG,GG		7.5581,8.8757,8.0037		73/98	31439170	1040,11954	2197	4300	6497	SO:0001819	synonymous_variant	1339	exon3			CCCCCAGGGGTAG	U66875, M83308	CCDS10712.1	16p11.12	2011-07-04			ENSG00000156885	ENSG00000156885	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2279	protein-coding gene	gene with protein product		602009				1327966, 9177785	Standard	NM_005205		Approved		uc002ebx.2	Q02221	OTTHUMG00000132463	ENST00000287490.4:c.219C>T	16.37:g.31439170G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_005205	O00761|Q6GTW6	Silent	SNP	ENST00000287490.4	37	CCDS10712.1																																																																																			G|0.928;A|0.072	0.072	strong		0.731	COX6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255626.2	NM_005205	
ADAM21	8747	hgsc.bcm.edu	37	14	70924696	70924696	+	Silent	SNP	G	G	A	rs77892318|rs386778613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:70924696G>A	ENST00000603540.1	+	2	738	c.480G>A	c.(478-480)aaG>aaA	p.K160K	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.K160K	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	146	0	0		WXS	Illumina HiSeq	Phase_I	86	25	0.290698	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		
AHNAK2	113146	hgsc.bcm.edu	37	14	105414238	105414238	+	Missense_Mutation	SNP	C	C	A	rs60754080	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	198	0	0		WXS	Illumina HiSeq	Phase_I	209	206	0.985646	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	
CAPRIN2	65981	hgsc.bcm.edu	37	12	30868002	30868002	+	Silent	SNP	C	C	T	rs13656	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:30868002C>T	ENST00000395805.2	-	14	2920	c.2373G>A	c.(2371-2373)gtG>gtA	p.V791V	CAPRIN2_ENST00000417045.1_Silent_p.V846V|CAPRIN2_ENST00000308433.5_Silent_p.V513V|CAPRIN2_ENST00000298892.5_Silent_p.V797V|CAPRIN2_ENST00000251071.5_Silent_p.V847V	NM_001206856.1	NP_001193785.1			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GTCTGGGAAACACATTCGTCT	0.448													T|||	2985	0.596046	0.8729	0.3818	5008	,	,		16760	0.4633		0.5905	False		,,,				2504	0.5164				p.V847V		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.G2541A						PASS	.	T	,,,	3637,769	310.8+/-291.8	1511,615,77	152.0	143.0	146.0		2541,2373,2391,2538	-3.6	1.0	12	dbSNP_52	146	5162,3438	505.6+/-376.4	1542,2078,680	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAPRIN2	NM_001002259.1,NM_001206856.1,NM_023925.3,NM_032156.3	,,,	3053,2693,757	TT,TC,CC		39.9767,17.4535,32.3466	,,,	847/1128,791/906,797/1078,846/961	30868002	8799,4207	2203	4300	6503	SO:0001819	synonymous_variant	65981	exon15			GGGAAACACATTC	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"""C1q domain containing 1"""	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.2373G>A	12.37:g.30868002C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	174	99	0.568965	NM_001002259		Silent	SNP	ENST00000395805.2	37	CCDS55816.1																																																																																			C|0.347;T|0.653	0.653	strong		0.448	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925	
XPO4	64328	hgsc.bcm.edu	37	13	21374333	21374333	+	Silent	SNP	A	A	G	rs9579954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	151	0	0		WXS	Illumina HiSeq	Phase_I	168	91	0.541667	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	
DMBT1	1755	hgsc.bcm.edu	37	10	124390721	124390721	+	Silent	SNP	T	T	C	rs72836136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:124390721T>C	ENST00000338354.3	+	46	5989	c.5883T>C	c.(5881-5883)acT>acC	p.T1961T	DMBT1_ENST00000330163.4_Silent_p.T1333T|DMBT1_ENST00000344338.3_Silent_p.T1951T|DMBT1_ENST00000368909.3_Silent_p.T1961T|DMBT1_ENST00000368956.2_Silent_p.T1333T|DMBT1_ENST00000368955.3_Silent_p.T1951T|DMBT1_ENST00000359586.6_Silent_p.T681T			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1961	SRCR 14. {ECO:0000255|PROSITE- ProRule:PRU00196}.		T -> P. {ECO:0000269|PubMed:12185598}.		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)				CGGAATCCACTCTCTGGCAGT	0.557													T|||	61	0.0121805	0.0015	0.0202	5008	,	,		20337	0.0		0.0408	False		,,,				2504	0.0041				p.T1961T	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,+2,3	DMBT1	677	3	0			c.T5883C						scavenged	.	T	,,	26,4064		0,26,2019	154.0	151.0	152.0		3999,5883,5853	-10.8	0.0	10	dbSNP_130	152	360,8016		4,352,3832	no	coding-synonymous,coding-synonymous,coding-synonymous	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	,,	4,378,5851	CC,CT,TT		4.298,0.6357,3.0964	,,	1333/1786,1961/2414,1951/2404	124390721	386,12080	2045	4188	6233	SO:0001819	synonymous_variant	1755	exon46			ATCCACTCTCTGG		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.5883T>C	10.37:g.124390721T>C		Somatic	116	2	0.0172414		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	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																																																																																				T|0.981;C|0.019	0.019	strong		0.557	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
KNSTRN	90417	hgsc.bcm.edu	37	15	40675493	40675493	+	Missense_Mutation	SNP	C	C	T	rs7169262	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:40675493C>T	ENST00000249776.8	+	2	389	c.274C>T	c.(274-276)Ccc>Tcc	p.P92S	KNSTRN_ENST00000448395.2_Missense_Mutation_p.P92S|KNSTRN_ENST00000416151.2_Missense_Mutation_p.P92S|KNSTRN_ENST00000608100.1_Missense_Mutation_p.P14S	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		CCTGCAGCCCCCCTCTGCGCT	0.652													C|||	223	0.0445288	0.0083	0.1066	5008	,	,		14251	0.0179		0.0974	False		,,,				2504	0.0225				p.P92S		Atlas-SNP	.											.	.	.	.	0			c.C274T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	89,3825		2,85,1870	47.0	51.0	49.0		274,274,274	-1.8	0.0	15	dbSNP_116	49	988,7296		56,876,3210	yes	missense,missense,missense	C15orf23	NM_001142761.1,NM_001142762.1,NM_033286.3	74,74,74	58,961,5080	TT,TC,CC		11.9266,2.2739,8.8293	benign,benign,benign	92/287,92/242,92/317	40675493	1077,11121	1957	4142	6099	SO:0001583	missense	90417	exon2			CAGCCCCCCTCTG	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"""small kinetochore-associated protein"", ""kinetochore-localized astrin-binding protein"", ""TRAF4 associated factor 1"""	614718	"""chromosome 15 open reading frame 23"""	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.274C>T	15.37:g.40675493C>T	ENSP00000249776:p.Pro92Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_033286		Missense_Mutation	SNP	ENST00000249776.8	37	CCDS42021.1	126	0.057692307692307696	2	0.0040650406504065045	36	0.09944751381215469	12	0.02097902097902098	76	0.10026385224274406	C	5.237	0.229217	0.09916	0.022739	0.119266	ENSG00000128944	ENST00000249776;ENST00000416151;ENST00000448395	T;T;T	0.21543	2.0;2.0;2.0	4.89	-1.78	0.07957	.	1.160740	0.06152	N	0.674383	T	0.00144	0.0004	N	0.12182	0.205	0.80722	P	0.0	B;B;B	0.12630	0.006;0.001;0.002	B;B;B	0.12156	0.007;0.003;0.004	T	0.29397	-1.0013	9	0.08179	T	0.78	-4.7508	2.6725	0.05071	0.1102:0.4263:0.2421:0.2215	rs7169262;rs56763191;rs7169262	92;92;92	Q9Y448-2;Q9Y448-3;Q9Y448	.;.;T4AF1_HUMAN	S	92	ENSP00000249776:P92S;ENSP00000391233:P92S;ENSP00000393001:P92S	ENSP00000249776:P92S	P	+	1	0	C15orf23	38462785	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.494000	0.06451	-0.709000	0.05008	-3.374000	0.00041	CCC	C|0.934;T|0.066	0.066	strong		0.652	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761	
TSPAN9	10867	hgsc.bcm.edu	37	12	3389601	3389601	+	Silent	SNP	C	C	T	rs66501720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:3389601C>T	ENST00000011898.5	+	6	545	c.384C>T	c.(382-384)acC>acT	p.T128T	TSPAN9_ENST00000492305.1_3'UTR|TSPAN9_ENST00000537971.1_Silent_p.T128T|TSPAN9_ENST00000407263.1_Silent_p.T128T	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	128						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)			TGTACCACACCGAGAACAACG	0.657													c|||	212	0.0423323	0.0045	0.0562	5008	,	,		18607	0.0		0.1093	False		,,,				2504	0.0583				p.T128T		Atlas-SNP	.											.	TSPAN9	20	.	0			c.C384T						PASS	.		,	104,4302	82.4+/-120.9	1,102,2100	142.0	99.0	113.0		384,384	-9.6	0.1	12	dbSNP_130	113	836,7764	191.8+/-238.0	41,754,3505	no	coding-synonymous,coding-synonymous	TSPAN9	NM_001168320.1,NM_006675.4	,	42,856,5605	TT,TC,CC		9.7209,2.3604,7.2274	,	128/240,128/240	3389601	940,12066	2203	4300	6503	SO:0001819	synonymous_variant	10867	exon6			CCACACCGAGAAC	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.384C>T	12.37:g.3389601C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_006675	D3DUQ7|Q53FV2|Q6FGJ8	Silent	SNP	ENST00000011898.5	37	CCDS8520.1																																																																																			C|0.932;T|0.068	0.068	strong		0.657	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675	
KANK1	23189	hgsc.bcm.edu	37	9	738503	738503	+	Splice_Site	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:738503C>T	ENST00000382303.1	+	12	4204	c.3552C>T	c.(3550-3552)gcC>gcT	p.A1184A	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Splice_Site_p.A1026A|KANK1_ENST00000382297.2_Splice_Site_p.A1184A	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1184	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)		TGTTAGATGCCGGTATGTTGG	0.517																																					p.A1184A		Atlas-SNP	.											.	KANK1	231	.	0			c.C3552T						PASS	.						103.0	78.0	87.0					9																	738503		2203	4300	6503	SO:0001630	splice_region_variant	23189	exon12			AGATGCCGGTATG	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.3553+1C>T	9.37:g.738503C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			.	.	none		0.517	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	Silent
FKBP10	60681	hgsc.bcm.edu	37	17	39976713	39976713	+	Splice_Site	SNP	C	C	T	rs146422412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39976713C>T	ENST00000321562.4	+	7	1360	c.1256C>T	c.(1255-1257)tCg>tTg	p.S419L	FKBP10_ENST00000544340.1_Splice_Site_p.S192L	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	419	PPIase FKBP-type 4. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		CTGTTCACCTCGTGGGTCCGG	0.632													C|||	3	0.000599042	0.0008	0.0	5008	,	,		12871	0.0		0.001	False		,,,				2504	0.001				p.S419L		Atlas-SNP	.											.	FKBP10	57	.	0			c.C1256T						PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	79.0	85.0	83.0		1256	4.9	1.0	17	dbSNP_134	83	9,8591	7.1+/-27.0	0,9,4291	yes	missense-near-splice	FKBP10	NM_021939.3	145	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	probably-damaging	419/583	39976713	11,12995	2203	4300	6503	SO:0001630	splice_region_variant	60681	exon7			TCACCTCGTGGGT	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"""EF-hand domain containing"""	18169	protein-coding gene	gene with protein product		607063	"""FK506 binding protein 10 (65 kDa)"""			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.1256+1C>T	17.37:g.39976713C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Missense_Mutation	SNP	ENST00000321562.4	37	CCDS11409.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	27.5|27.5	4.836108|4.836108	0.91117|0.91117	4.54E-4|4.54E-4	0.001047|0.001047	ENSG00000141756|ENSG00000141756	ENST00000455106|ENST00000269598;ENST00000321562;ENST00000414352;ENST00000544340	.|T;T	.|0.61980	.|0.06;0.06	4.89|4.89	4.89|4.89	0.63831|0.63831	.|Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.86016|0.86016	0.5832|0.5832	H|H	0.96333|0.96333	3.805|3.805	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.99;1.0	.|P;D	.|0.91635	.|0.874;0.999	D|D	0.90651|0.90651	0.4582|0.4582	5|10	.|0.72032	.|D	.|0.01	-20.3857|-20.3857	18.0311|18.0311	0.89285|0.89285	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|192;419	.|Q9H6J3;Q96AY3	.|.;FKB10_HUMAN	C|L	223|307;419;419;192	.|ENSP00000317232:S419L;ENSP00000442009:S192L	.|ENSP00000269598:S307L	R|S	+|+	1|2	0|0	FKBP10|FKBP10	37230239|37230239	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	5.928000|5.928000	0.70088|0.70088	2.439000|2.439000	0.82584|0.82584	0.655000|0.655000	0.94253|0.94253	CGC|TCG	C|0.999;T|0.001	0.001	strong		0.632	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939	Missense_Mutation
UBASH3B	84959	hgsc.bcm.edu	37	11	122665437	122665437	+	Silent	SNP	A	A	G	rs872414	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:122665437A>G	ENST00000284273.5	+	7	1383	c.1008A>G	c.(1006-1008)tcA>tcG	p.S336S		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	336					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)		ATACATCGTCATCCAACTCTC	0.512													G|||	2816	0.5623	0.7602	0.5317	5008	,	,		19279	0.5615		0.3917	False		,,,				2504	0.4928				p.S336S		Atlas-SNP	.											.	UBASH3B	73	.	0			c.A1008G						PASS	.	G		3077,1327	447.7+/-348.4	1079,919,204	153.0	157.0	156.0		1008	-7.8	0.0	11	dbSNP_86	156	3446,5152	637.3+/-399.2	704,2038,1557	no	coding-synonymous	UBASH3B	NM_032873.4		1783,2957,1761	GG,GA,AA		40.0791,30.1317,49.8308		336/650	122665437	6523,6479	2202	4299	6501	SO:0001819	synonymous_variant	84959	exon7			ATCGTCATCCAAC	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.1008A>G	11.37:g.122665437A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Silent	SNP	ENST00000284273.5	37	CCDS31694.1																																																																																			A|0.478;G|0.522	0.522	strong		0.512	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	
HERC5	51191	hgsc.bcm.edu	37	4	89421086	89421086	+	Silent	SNP	A	A	G	rs10516809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:89421086A>G	ENST00000264350.3	+	19	2607	c.2454A>G	c.(2452-2454)caA>caG	p.Q818Q	HERC5_ENST00000508159.1_Silent_p.Q456Q	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	818	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		GGAATTTGCAAACACTTCTGG	0.294													A|||	174	0.0347444	0.0053	0.0418	5008	,	,		19912	0.0		0.0815	False		,,,				2504	0.0573				p.Q818Q	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.A2454G						PASS	.	A		79,4323	65.8+/-103.3	1,77,2123	98.0	106.0	104.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2454	-9.0	0.0	4	dbSNP_119	104	807,7789	187.0+/-234.4	39,729,3530	no	coding-synonymous	HERC5	NM_016323.2		40,806,5653	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	9.3881,1.7946,6.8164		818/1025	89421086	886,12112	2201	4298	6499	SO:0001819	synonymous_variant	51191	exon19			TTTGCAAACACTT	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.2454A>G	4.37:g.89421086A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_016323	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	37	CCDS3630.1																																																																																			A|0.947;G|0.053	0.053	strong		0.294	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
DUOX1	53905	hgsc.bcm.edu	37	15	45444518	45444518	+	Silent	SNP	A	A	G	rs1706804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:45444518A>G	ENST00000321429.4	+	26	3635	c.3228A>G	c.(3226-3228)acA>acG	p.T1076T	DUOX1_ENST00000389037.3_Silent_p.T1076T|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000561166.1_Silent_p.T722T	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1076	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)	p.T1076T(1)		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)		CGGGCATCACAGACACCACCC	0.607													G|||	2888	0.576677	0.466	0.513	5008	,	,		18277	0.4921		0.665	False		,,,				2504	0.7679				p.T1076T		Atlas-SNP	.											DUOX1,NS,carcinoma,0,1	DUOX1	125	1	1	Substitution - coding silent(1)	stomach(1)	c.A3228G						PASS	.	G	,	2117,2279	598.5+/-389.1	518,1081,599	151.0	110.0	124.0		3228,3228	-8.1	0.3	15	dbSNP_89	124	5827,2769	440.1+/-359.4	1978,1871,449	no	coding-synonymous,coding-synonymous	DUOX1	NM_017434.3,NM_175940.1	,	2496,2952,1048	GG,GA,AA		32.2127,48.1574,38.8547	,	1076/1552,1076/1552	45444518	7944,5048	2198	4298	6496	SO:0001819	synonymous_variant	53905	exon26			CATCACAGACACC	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.3228A>G	15.37:g.45444518A>G		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			A|0.405;G|0.595	0.595	strong		0.607	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508450	37508450	+	Silent	SNP	A	A	C	rs1148259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:37508450A>C	ENST00000602533.1	+	34	3741	c.3642A>C	c.(3640-3642)gcA>gcC	p.A1214A	ANKRD30A_ENST00000361713.1_Silent_p.A1214A|ANKRD30A_ENST00000374660.1_Silent_p.A1333A			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1270					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						TCAATTATGCAGGAGATGCTC	0.368													A|||	2672	0.533546	0.382	0.5	5008	,	,		19799	0.6746		0.4125	False		,,,				2504	0.7413				p.A1214A		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A3642C						PASS	.	A		1406,2328		267,872,728	60.0	52.0	54.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3642	-1.5	0.0	10	dbSNP_87	54	3465,4723		725,2015,1354	yes	coding-synonymous	ANKRD30A	NM_052997.2		992,2887,2082	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	42.318,37.654,40.8572		1214/1342	37508450	4871,7051	1867	4094	5961	SO:0001819	synonymous_variant	91074	exon34			TTATGCAGGAGAT	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.3642A>C	10.37:g.37508450A>C		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																				A|0.458;C|0.542	0.542	strong		0.368	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
ASAH2	56624	hgsc.bcm.edu	37	10	51978270	51978270	+	Splice_Site	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:51978270C>T	ENST00000395526.4	-	7	1013	c.1014G>A	c.(1012-1014)caG>caA	p.Q338Q	ASAH2_ENST00000329428.6_Splice_Site_p.Q319Q|ASAH2_ENST00000447815.1_Splice_Site_p.Q338Q|ASAH2_ENST00000443575.1_Splice_Site_p.Q180Q	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	338					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						AAATTCTCACCTGTCCAGGTA	0.393																																					p.Q338Q		Atlas-SNP	.											ASAH2_ENST00000395526,NS,carcinoma,-1,2	ASAH2	69	2	0			c.G1014A						scavenged	.						27.0	20.0	25.0					10																	51978270		1947	1111	3058	SO:0001630	splice_region_variant	56624	exon7			TCTCACCTGTCCA	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.1014+1G>A	10.37:g.51978270C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	177	2	0.0112994	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Silent	SNP	ENST00000395526.4	37	CCDS7239.2																																																																																			.	.	none		0.393	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893	Silent
SNAP47	116841	hgsc.bcm.edu	37	1	227935762	227935762	+	Missense_Mutation	SNP	G	G	A	rs2236358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:227935762G>A	ENST00000366759.4	+	2	874	c.460G>A	c.(460-462)Gtg>Atg	p.V154M	SNAP47_ENST00000366760.1_Intron|SNAP47_ENST00000315781.5_Missense_Mutation_p.V154M|SNAP47-AS1_ENST00000413347.2_RNA	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	154	t-SNARE coiled-coil homology 1. {ECO:0000255|PROSITE-ProRule:PRU00202}.		V -> M (in dbSNP:rs2236358). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GCCTGGAGCCGTGGCAGACGC	0.622													G|||	738	0.147364	0.0998	0.1311	5008	,	,		20552	0.3462		0.0457	False		,,,				2504	0.1227				p.V154M		Atlas-SNP	.											.	SNAP47	42	.	0			c.G460A						PASS	.	G	MET/VAL	479,3927	222.0+/-238.9	29,421,1753	51.0	47.0	48.0		460	1.0	0.0	1	dbSNP_98	48	390,8210	124.6+/-183.3	10,370,3920	yes	missense	SNAP47	NM_053052.3	21	39,791,5673	AA,AG,GG		4.5349,10.8715,6.6815	possibly-damaging	154/465	227935762	869,12137	2203	4300	6503	SO:0001583	missense	116841	exon2			GGAGCCGTGGCAG	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 142"""	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.460G>A	1.37:g.227935762G>A	ENSP00000355721:p.Val154Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	326|326	0.14926739926739926|0.14926739926739926	43|43	0.08739837398373984|0.08739837398373984	49|49	0.13535911602209943|0.13535911602209943	196|196	0.34265734265734266|0.34265734265734266	38|38	0.05013192612137203|0.05013192612137203	G|G	7.600|7.600	0.672676|0.672676	0.14776|0.14776	0.108715|0.108715	0.045349|0.045349	ENSG00000143740|ENSG00000143740	ENST00000426344|ENST00000366759;ENST00000315781	.|T;T	.|0.21361	.|2.01;2.01	4.17|4.17	1.01|1.01	0.19927|0.19927	.|.	.|1.463730	.|0.03873	.|N	.|0.276012	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	P|P	0.0|0.0	.|D;D	.|0.61697	.|0.98;0.99	.|P;P	.|0.47744	.|0.454;0.556	T|T	0.38329|0.38329	-0.9666|-0.9666	4|9	.|0.31617	.|T	.|0.26	-9.6172|-9.6172	7.1714|7.1714	0.25721|0.25721	0.1066:0.4776:0.4158:0.0|0.1066:0.4776:0.4158:0.0	rs2236358;rs17844903;rs17857623;rs59029860;rs2236358|rs2236358;rs17844903;rs17857623;rs59029860;rs2236358	.|154;154	.|Q5SQN1;Q5SQN1-2	.|SNP47_HUMAN;.	H|M	145|154	.|ENSP00000355721:V154M;ENSP00000314157:V154M	.|ENSP00000314157:V154M	R|V	+|+	2|1	0|0	SNAP47|SNAP47	226002385|226002385	0.006000|0.006000	0.16342|0.16342	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	1.326000|1.326000	0.33735|0.33735	0.408000|0.408000	0.25621|0.25621	-0.256000|-0.256000	0.11100|0.11100	CGT|GTG	G|0.899;A|0.101	0.101	strong		0.622	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052	
KIDINS220	57498	hgsc.bcm.edu	37	2	8877042	8877042	+	Silent	SNP	G	G	A	rs61742863	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:8877042G>A	ENST00000256707.3	-	27	3854	c.3673C>T	c.(3673-3675)Ctg>Ttg	p.L1225L	KIDINS220_ENST00000473731.1_Silent_p.L1206L|KIDINS220_ENST00000418530.1_Silent_p.L1126L|KIDINS220_ENST00000427284.1_Silent_p.L1206L	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1225					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTCTGGTCCAGCCCTTCTATT	0.527													G|||	263	0.052516	0.0227	0.0548	5008	,	,		16320	0.004		0.1064	False		,,,				2504	0.0859				p.L1225L		Atlas-SNP	.											.	KIDINS220	136	.	0			c.C3673T						PASS	.	G		132,3832		2,128,1852	118.0	113.0	114.0		3673	3.9	1.0	2	dbSNP_129	114	651,7661		26,599,3531	no	coding-synonymous	KIDINS220	NM_020738.2		28,727,5383	AA,AG,GG		7.8321,3.33,6.3783		1225/1772	8877042	783,11493	1982	4156	6138	SO:0001819	synonymous_variant	57498	exon27			GGTCCAGCCCTTC	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"""Ankyrin repeat domain containing"""	29508	protein-coding gene	gene with protein product	"""ankyrin repeat-rich membrane-spanning protein"""	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.3673C>T	2.37:g.8877042G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	168	72	0.428571	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Silent	SNP	ENST00000256707.3	37	CCDS42650.1																																																																																			G|0.938;A|0.062	0.062	strong		0.527	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738	
CALU	813	hgsc.bcm.edu	37	7	128394606	128394606	+	Intron	SNP	C	C	T	rs2307040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128394606C>T	ENST00000249364.4	+	3	517				CALU_ENST00000542996.2_Missense_Mutation_p.A90V|CALU_ENST00000535623.1_3'UTR|CALU_ENST00000479257.1_Intron|CALU_ENST00000538546.1_Intron|CALU_ENST00000535011.2_Intron|CALU_ENST00000449187.2_Missense_Mutation_p.A82V	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin						blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)	p.A90V(1)		kidney(2)|large_intestine(3)|lung(5)	10						AAAATAGACGCGGATAAAGAT	0.443													C|||	888	0.177316	0.1127	0.2233	5008	,	,		19129	0.0585		0.3728	False		,,,				2504	0.1534				p.A90V		Atlas-SNP	.											CALU_ENST00000542996,NS,carcinoma,0,1	CALU	42	1	1	Substitution - Missense(1)	stomach(1)	c.C269T						PASS	.	C	VAL/ALA,,VAL/ALA,,,	181,1203		11,159,522	83.0	74.0	76.0		245,,269,,,	0.2	1.0	7	dbSNP_100	76	1182,2000		224,734,633	yes	missense,intron,missense,intron,intron,intron	CALU	NM_001130674.2,NM_001199671.1,NM_001199672.1,NM_001199673.1,NM_001199674.1,NM_001219.4	64,,64,,,	235,893,1155	TT,TC,CC		37.1464,13.078,29.8511	,,,,,	82/316,,90/324,,,	128394606	1363,3203	692	1591	2283	SO:0001627	intron_variant	813	exon4			TAGACGCGGATAA	AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"""EF-hand domain containing"""	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.415+97C>T	7.37:g.128394606C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_001199672	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Missense_Mutation	SNP	ENST00000249364.4	37	CCDS5805.1	459	0.21016483516483517	62	0.12601626016260162	95	0.26243093922651933	28	0.04895104895104895	274	0.36147757255936674	C	10.84	1.465452	0.26335	0.13078	0.371464	ENSG00000128595	ENST00000542996;ENST00000537667;ENST00000537014;ENST00000449187	T;T	0.70399	-0.48;-0.48	5.96	0.244	0.15507	.	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.13145	0.007	B	0.12837	0.008	T	0.32693	-0.9897	8	0.22109	T	0.4	.	5.664	0.17684	0.0:0.4412:0.1377:0.4211	rs2307040;rs11545530;rs52803804;rs2307040	90	D6QS48	.	V	90;82;82;82	ENSP00000438248:A90V;ENSP00000408838:A82V	ENSP00000408838:A82V	A	+	2	0	CALU	128181842	0.000000	0.05858	0.959000	0.39883	0.990000	0.78478	-0.365000	0.07573	0.092000	0.17331	-0.136000	0.14681	GCG	C|0.785;T|0.215	0.215	strong		0.443	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	rs201290098		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E|SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E			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	66	0	0		WXS	Illumina HiSeq	Phase_I	52	6	0.115385	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	
OR13D1	286365	hgsc.bcm.edu	37	9	107457275	107457275	+	Missense_Mutation	SNP	A	A	C	rs10820709	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	335	1	0.00298507		WXS	Illumina HiSeq	Phase_I	297	296	0.996633	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		
TUBG2	27175	hgsc.bcm.edu	37	17	40818451	40818451	+	Silent	SNP	G	G	A	rs1554227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40818451G>A	ENST00000251412.7	+	10	1306	c.1107G>A	c.(1105-1107)tcG>tcA	p.S369S	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	369					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		ACCTGCCCTCGGCCCACCGGG	0.612													G|||	2523	0.503794	0.4365	0.4726	5008	,	,		18996	0.4633		0.5189	False		,,,				2504	0.6431				p.S369S		Atlas-SNP	.											TUBG2,bladder,carcinoma,+1,1	TUBG2	43	1	0			c.G1107A						scavenged	.						71.0	74.0	73.0					17																	40818451		2203	4297	6500	SO:0001819	synonymous_variant	27175	exon10			GCCCTCGGCCCAC	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.1107G>A	17.37:g.40818451G>A		Somatic	284	2	0.00704225		WXS	Illumina HiSeq	Phase_I	385	152	0.394805	NM_016437	A6NDI4|Q32NB2	Silent	SNP	ENST00000251412.7	37	CCDS32658.1																																																																																			.	.	weak		0.612	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
OPLAH	26873	hgsc.bcm.edu	37	8	145114643	145114643	+	Silent	SNP	G	G	A	rs6558292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145114643G>A	ENST00000426825.1	-	3	303	c.222C>T	c.(220-222)atC>atT	p.I74I	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	74					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGATGCTGGCGATATGACTGG	0.692													G|||	335	0.066893	0.1399	0.0548	5008	,	,		15951	0.001		0.0815	False		,,,				2504	0.0297				p.I74I		Atlas-SNP	.											.	OPLAH	78	.	0			c.C222T						PASS	.	G		541,3803		33,475,1664	25.0	32.0	30.0		222	-10.5	0.1	8	dbSNP_116	30	568,7942		13,542,3700	no	coding-synonymous	OPLAH	NM_017570.3		46,1017,5364	AA,AG,GG		6.6745,12.454,8.6277		74/1289	145114643	1109,11745	2172	4255	6427	SO:0001819	synonymous_variant	26873	exon3			GCTGGCGATATGA	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.222C>T	8.37:g.145114643G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	37																																																																																				G|0.920;A|0.080	0.080	strong		0.692	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
PKD1L2	114780	hgsc.bcm.edu	37	16	81248745	81248745	+	RNA	SNP	A	A	G	rs8060294	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:81248745A>G	ENST00000525539.1	-	0	517				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						GACCTGCCCCAAGCCACAGTG	0.627											OREG0023964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1954	0.390176	0.5454	0.3473	5008	,	,		17841	0.4345		0.2962	False		,,,				2504	0.2618				p.L173S		Atlas-SNP	.											PKD1L2_ENST00000525539,rectum,carcinoma,0,2	PKD1L2	361	2	0			c.T518C						PASS	.	G	SER/LEU,SER/LEU	1980,1928		535,910,509	17.0	22.0	20.0		518,518	3.8	0.5	16	dbSNP_116	20	2300,5980		328,1644,2168	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	145,145	863,2554,2677	GG,GA,AA		27.7778,49.3347,35.1165	benign,benign	173/992,173/2460	81248745	4280,7908	1954	4140	6094			114780	exon3			TGCCCCAAGCCAC	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.81248745A>G		Somatic	114	0	0	1204	WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		863	0.39514652014652013	269	0.5467479674796748	124	0.3425414364640884	233	0.40734265734265734	237	0.31266490765171506	G	11.07	1.529240	0.27387	0.506653	0.277778	ENSG00000166473	ENST00000337114	T	0.15487	2.42	4.76	3.79	0.43588	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.357637	0.26183	N	0.025853	T	0.00012	0.0000	.	.	.	0.39104	P	0.038654999999999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45220	-0.9276	8	0.02654	T	1	-0.5244	10.2659	0.43455	0.0742:0.1356:0.7902:0.0	rs8060294;rs52836656;rs8060294	173;173	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	S	173	ENSP00000337397:L173S	ENSP00000337397:L173S	L	-	2	0	PKD1L2	79806246	1.000000	0.71417	0.457000	0.27056	0.360000	0.29518	5.197000	0.65141	0.438000	0.26450	-0.134000	0.14843	TTG	A|0.619;G|0.381	0.381	strong		0.627	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
AMZ1	155185	hgsc.bcm.edu	37	7	2752152	2752152	+	Silent	SNP	G	G	A	rs798565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2752152G>A	ENST00000312371.4	+	7	1505	c.1137G>A	c.(1135-1137)tcG>tcA	p.S379S	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_3'UTR	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	379							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)		CCTTCGCCTCGGGGCCAGAGG	0.687													G|||	900	0.179712	0.0794	0.2464	5008	,	,		16592	0.2004		0.2793	False		,,,				2504	0.1442				p.S379S		Atlas-SNP	.											AMZ1,colon,carcinoma,0,3	AMZ1	41	3	0			c.G1137A						PASS	.	G		440,3958		30,380,1789	20.0	23.0	22.0		1137	-6.0	0.0	7	dbSNP_86	22	2435,6163		364,1707,2228	no	coding-synonymous	AMZ1	NM_133463.1		394,2087,4017	AA,AG,GG		28.3205,10.0045,22.1222		379/499	2752152	2875,10121	2199	4299	6498	SO:0001819	synonymous_variant	155185	exon7			CGCCTCGGGGCCA	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.1137G>A	7.37:g.2752152G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1																																																																																			G|0.793;A|0.207	0.207	strong		0.687	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
DNM3	26052	hgsc.bcm.edu	37	1	171956803	171956803	+	Silent	SNP	C	C	T	rs3736790	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171956803C>T	ENST00000355305.5	+	3	400	c.243C>T	c.(241-243)gcC>gcT	p.A81A	DNM3_ENST00000367731.1_Silent_p.A81A|DNM3_ENST00000367733.2_Silent_p.A81A|DNM3_ENST00000358155.4_Silent_p.A81A|DNM3_ENST00000520906.1_Silent_p.A81A			Q9UQ16	DYN3_HUMAN	dynamin 3	81	Dynamin-type G.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TAGAATATGCCGAGTTTCTAC	0.308													T|||	1685	0.336462	0.736	0.2205	5008	,	,		16808	0.1974		0.164	False		,,,				2504	0.1994				p.A81A		Atlas-SNP	.											.	DNM3	85	.	0			c.C243T						PASS	.	T	,	2212,1404		674,864,270	106.0	122.0	117.0		243,243	1.5	1.0	1	dbSNP_107	117	1301,6859		99,1103,2878	no	coding-synonymous,coding-synonymous	DNM3	NM_001136127.1,NM_015569.3	,	773,1967,3148	TT,TC,CC		15.9436,38.8274,29.8319	,	81/860,81/864	171956803	3513,8263	1808	4080	5888	SO:0001819	synonymous_variant	26052	exon3			ATATGCCGAGTTT	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"""Pleckstrin homology (PH) domain containing"""	29125	protein-coding gene	gene with protein product	"""Dyna III"""	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.243C>T	1.37:g.171956803C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_001136127	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Silent	SNP	ENST00000355305.5	37																																																																																				C|0.681;T|0.319	0.319	strong		0.308	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569	
PTPN12	5782	hgsc.bcm.edu	37	7	77256713	77256713	+	Missense_Mutation	SNP	A	A	G	rs3750050	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:77256713A>G	ENST00000248594.6	+	13	1989	c.1717A>G	c.(1717-1719)Aca>Gca	p.T573A	PTPN12_ENST00000435495.2_Missense_Mutation_p.T443A|PTPN12_ENST00000415482.2_Missense_Mutation_p.T454A	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	573			T -> A (in dbSNP:rs3750050). {ECO:0000269|PubMed:14702039}.		protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						ACCAAGTCCTACAACACAAGT	0.403													A|||	1828	0.365016	0.2171	0.4366	5008	,	,		22259	0.6905		0.16	False		,,,				2504	0.3896				p.T573A		Atlas-SNP	.											.	PTPN12	83	.	0			c.A1717G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	949,3457	358.6+/-314.5	116,717,1370	167.0	152.0	157.0		1360,1327,1717	-0.4	0.0	7	dbSNP_107	157	1303,7297	256.8+/-281.1	106,1091,3103	yes	missense,missense,missense	PTPN12	NM_001131008.1,NM_001131009.1,NM_002835.3	58,58,58	222,1808,4473	GG,GA,AA		15.1512,21.5388,17.3151	benign,benign,benign	454/662,443/651,573/781	77256713	2252,10754	2203	4300	6503	SO:0001583	missense	5782	exon13			AGTCCTACAACAC		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1717A>G	7.37:g.77256713A>G	ENSP00000248594:p.Thr573Ala	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	153	77	0.503268	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	749	0.34294871794871795	93	0.18902439024390244	150	0.4143646408839779	387	0.6765734265734266	119	0.15699208443271767	A	4.040	0.005088	0.07866	0.215388	0.151512	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495;ENST00000407343	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	6.04	-0.387	0.12463	.	0.428092	0.25765	N	0.028452	T	0.00012	0.0000	L	0.28740	0.885	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.42241	-0.9463	9	0.13470	T	0.59	.	1.0381	0.01553	0.4387:0.1514:0.2294:0.1805	rs3750050;rs11540138;rs60753265;rs3750050	573	Q05209	PTN12_HUMAN	A	573;454;454;443;81	ENSP00000248594:T573A;ENSP00000392429:T454A;ENSP00000397991:T443A;ENSP00000385079:T81A	ENSP00000248594:T573A	T	+	1	0	PTPN12	77094649	0.000000	0.05858	0.001000	0.08648	0.756000	0.42949	-0.275000	0.08525	-0.319000	0.08652	-1.961000	0.00478	ACA	A|0.745;G|0.255	0.255	strong		0.403	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
TULP2	7288	hgsc.bcm.edu	37	19	49398405	49398405	+	Missense_Mutation	SNP	C	C	T	rs34378208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49398405C>T	ENST00000221399.3	-	6	508	c.364G>A	c.(364-366)Ggt>Agt	p.G122S		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	122			G -> S (in dbSNP:rs34378208).		visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		GACTGGAGACCGAGATTCCTG	0.542													C|||	260	0.0519169	0.0113	0.0648	5008	,	,		19540	0.002		0.0805	False		,,,				2504	0.1196				p.G122S		Atlas-SNP	.											.	TULP2	60	.	0			c.G364A						PASS	.	C	SER/GLY	87,4319	73.1+/-111.1	2,83,2118	64.0	62.0	63.0		364	-3.8	0.0	19	dbSNP_126	63	688,7912	170.1+/-221.3	25,638,3637	yes	missense	TULP2	NM_003323.2	56	27,721,5755	TT,TC,CC		8.0,1.9746,5.9588	benign	122/521	49398405	775,12231	2203	4300	6503	SO:0001583	missense	7288	exon6			GGAGACCGAGATT	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.364G>A	19.37:g.49398405C>T	ENSP00000221399:p.Gly122Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	99	0.04532967032967033	5	0.01016260162601626	27	0.07458563535911603	1	0.0017482517482517483	66	0.0870712401055409	C	10.91	1.485510	0.26686	0.019746	0.08	ENSG00000104804	ENST00000221399;ENST00000518572;ENST00000522945;ENST00000520977	D;T;T;T	0.83755	-1.76;2.11;1.26;0.68	4.92	-3.78	0.04333	.	4.406720	0.00567	N	0.000298	T	0.05364	0.0142	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.12156	0.007	T	0.30909	-0.9962	10	0.19147	T	0.46	11.6829	2.3847	0.04363	0.1423:0.2474:0.4186:0.1917	rs34378208	122	O00295	TULP2_HUMAN	S	122;76;119;103	ENSP00000221399:G122S;ENSP00000428420:G76S;ENSP00000430040:G119S;ENSP00000428535:G103S	ENSP00000221399:G122S	G	-	1	0	TULP2	54090217	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.132000	0.00590	-0.814000	0.04352	-0.311000	0.09066	GGT	C|0.945;T|0.055	0.055	strong		0.542	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
NEU4	129807	hgsc.bcm.edu	37	2	242757411	242757411	+	Silent	SNP	C	C	T	rs36111671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242757411C>T	ENST00000391969.2	+	5	1203	c.492C>T	c.(490-492)ggC>ggT	p.G164G	NEU4_ENST00000405370.1_Silent_p.G164G|NEU4_ENST00000407683.1_Silent_p.G164G|NEU4_ENST00000325935.6_Silent_p.G177G|NEU4_ENST00000404257.1_Silent_p.G176G	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	164					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)		CCGGCCACGGCGTGCAGCTGC	0.697													C|||	1083	0.216254	0.118	0.1571	5008	,	,		12056	0.2222		0.2237	False		,,,				2504	0.3773				p.G177G		Atlas-SNP	.											.	NEU4	39	.	0			c.C531T						PASS	.		,,,,	714,3680		71,572,1554	36.0	28.0	31.0		531,492,492,492,528	-2.6	0.5	2	dbSNP_126	31	1901,6693		211,1479,2607	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	282,2051,4161	TT,TC,CC		22.1201,16.2494,20.134	,,,,	177/498,164/485,164/485,164/485,176/497	242757411	2615,10373	2197	4297	6494	SO:0001819	synonymous_variant	129807	exon4			CCACGGCGTGCAG	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.492C>T	2.37:g.242757411C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1	405	0.18543956043956045	66	0.13414634146341464	61	0.1685082872928177	102	0.17832167832167833	176	0.23218997361477572	C	15.63	2.889694	0.52014	0.162494	0.221201	ENSG00000204099	ENST00000415936;ENST00000426032	T;T	0.38240	1.15;1.15	4.47	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.28618	-1.0038	5	0.45353	T	0.12	-24.8925	0.4689	0.00529	0.2954:0.2317:0.2665:0.2065	rs36111671	.	.	.	V	79;91	ENSP00000397167:A79V;ENSP00000406678:A91V	ENSP00000397167:A79V	A	+	2	0	NEU4	242406084	0.855000	0.29742	0.491000	0.27477	0.281000	0.26958	-0.030000	0.12308	-0.497000	0.06641	0.443000	0.29094	GCG	C|0.817;T|0.183	0.183	strong		0.697	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
DNAH3	55567	hgsc.bcm.edu	37	16	21145648	21145648	+	Silent	SNP	C	C	T	rs11074483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:21145648C>T	ENST00000261383.3	-	7	1013	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K	DNAH3_ENST00000415178.1_Silent_p.K338K	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	338	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.K338K(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCTCGTTCCACTTCTTGGCGC	0.522													C|||	1251	0.2498	0.1853	0.3646	5008	,	,		18455	0.2946		0.2336	False		,,,				2504	0.226				p.K338K		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,0,2	DNAH3	1142	2	2	Substitution - coding silent(2)	stomach(2)	c.G1014A						PASS	.	C		915,3487	351.3+/-311.2	97,721,1383	112.0	106.0	108.0		1014	3.9	1.0	16	dbSNP_120	108	2100,6500	363.6+/-333.2	263,1574,2463	no	coding-synonymous	DNAH3	NM_017539.1		360,2295,3846	TT,TC,CC		24.4186,20.786,23.1887		338/4117	21145648	3015,9987	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon7			GTTCCACTTCTTG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1014G>A	16.37:g.21145648C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			C|0.759;T|0.241	0.241	strong		0.522	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
STH	246744	hgsc.bcm.edu	37	17	44076665	44076665	+	Missense_Mutation	SNP	A	A	G	rs62063857	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44076665A>G	ENST00000537309.1	+	1	50	c.20A>G	c.(19-21)cAa>cGa	p.Q7R	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000535772.1_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	7			Q -> R (in dbSNP:rs62063857). {ECO:0000269|PubMed:12032355, ECO:0000269|PubMed:12402275, ECO:0000269|PubMed:12913211}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						ggtggaggccaagtctcatgc	0.532													G|||	439	0.0876597	0.0204	0.1571	5008	,	,		18794	0.001		0.2406	False		,,,				2504	0.0613				p.Q7R		Atlas-SNP	.											STH,rectum,carcinoma,+1,1	STH	14	1	0			c.A20G	GRCh37	CM032397	STH	M	rs62063857	PASS	.	G	ARG/GLN,,,,,,,,	187,3759		7,173,1793	50.0	49.0	49.0		20,,,,,,,,	-0.9	0.0	17	dbSNP_129	49	1836,6500		201,1434,2533	yes	missense,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	43,,,,,,,,	208,1607,4326	GG,GA,AA		22.025,4.739,16.4713	benign,,,,,,,,	7/129,,,,,,,,	44076665	2023,10259	1973	4168	6141	SO:0001583	missense	246744	exon1			GAGGCCAAGTCTC	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.20A>G	17.37:g.44076665A>G	ENSP00000443168:p.Gln7Arg	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	172	170	0.988372	NM_001007532	A1L3X7	Missense_Mutation	SNP	ENST00000537309.1	37	CCDS54136.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	0.974	-0.699349	0.03279	0.04739	0.22025	ENSG00000256762	ENST00000537309	T	0.51817	0.69	1.27	-0.939	0.10408	.	.	.	.	.	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	0.17471	-1.0368	8	0.87932	D	0	.	5.2426	0.15479	0.5798:0.0:0.4202:0.0	rs62063857	7	Q8IWL8	STH_HUMAN	R	7	ENSP00000443168:Q7R	ENSP00000443168:Q7R	Q	+	2	0	STH	41432502	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.093000	0.01353	-0.835000	0.04234	-1.668000	0.00747	CAA	A|0.159;C|0.093	.	strong		0.532	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1		
PALD1	27143	hgsc.bcm.edu	37	10	72289778	72289778	+	Missense_Mutation	SNP	C	C	T	rs2275060	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:72289778C>T	ENST00000263563.6	+	4	690	c.422C>T	c.(421-423)tCa>tTa	p.S141L		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	141			S -> L (in dbSNP:rs2275060). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:15489334}.			cytosol (GO:0005829)											CCCAGCCTCTCAGGGTTCAGG	0.627													C|||	641	0.127995	0.0113	0.1816	5008	,	,		17426	0.2173		0.2147	False		,,,				2504	0.0665				p.S141L		Atlas-SNP	.											.	.	.	.	0			c.C422T						PASS	.	C	LEU/SER	190,4216	120.0+/-157.7	5,180,2018	45.0	45.0	45.0		422	-4.2	0.0	10	dbSNP_100	45	1720,6880	312.5+/-310.9	177,1366,2757	yes	missense	KIAA1274	NM_014431.2	145	182,1546,4775	TT,TC,CC		20.0,4.3123,14.6855	benign	141/857	72289778	1910,11096	2203	4300	6503	SO:0001583	missense	27143	exon4			GCCTCTCAGGGTT	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.422C>T	10.37:g.72289778C>T	ENSP00000263563:p.Ser141Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	369	0.16895604395604397	7	0.014227642276422764	57	0.1574585635359116	131	0.229020979020979	174	0.22955145118733508	C	10.13	1.266029	0.23136	0.043123	0.2	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.37411	1.2	5.34	-4.24	0.03777	.	0.800301	0.11499	N	0.557882	T	0.00012	0.0000	L	0.28192	0.835	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.34825	-0.9813	9	0.22706	T	0.39	0.3488	2.882	0.05650	0.1589:0.5736:0.1337:0.1338	rs2275060;rs17598395;rs52838028;rs59062283;rs2275060	141	Q9ULE6	PALD_HUMAN	L	141	ENSP00000263563:S141L	ENSP00000263563:S141L	S	+	2	0	KIAA1274	71959784	0.000000	0.05858	0.001000	0.08648	0.814000	0.46013	-0.330000	0.07925	-0.596000	0.05821	-0.484000	0.04775	TCA	C|0.843;N|0.001	.	strong		0.627	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
CLEC10A	10462	hgsc.bcm.edu	37	17	6981353	6981353	+	Silent	SNP	G	G	C	rs732828	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	160	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	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	
KIAA0226L	80183	hgsc.bcm.edu	37	13	46946157	46946157	+	Missense_Mutation	SNP	C	C	T	rs1408184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46946157C>T	ENST00000429979.1	-	3	1058	c.454G>A	c.(454-456)Ggg>Agg	p.G152R	KIAA0226L_ENST00000534925.1_Missense_Mutation_p.G17R|KIAA0226L_ENST00000378787.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000480935.1_5'Flank|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.G85R|KIAA0226L_ENST00000378781.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000378797.2_Missense_Mutation_p.G152R|KIAA0226L_ENST00000409879.2_Intron|KIAA0226L_ENST00000322896.6_Intron|RNU2-6P_ENST00000411404.1_RNA	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	169	0	0		WXS	Illumina HiSeq	Phase_I	201	98	0.487562	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	
ZNF230	7773	hgsc.bcm.edu	37	19	44514422	44514422	+	Splice_Site	SNP	C	C	T	rs146185685		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44514422C>T	ENST00000429154.2	+	5	459	c.231C>T	c.(229-231)ggC>ggT	p.G77G		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	77					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)				TCCTTATAGGCGGCAAGACTA	0.428													c|||	1	0.000199681	0.0	0.0	5008	,	,		19264	0.0		0.0	False		,,,				2504	0.001				p.G77G	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.C231T						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	51.0	49.0	50.0		231	-2.3	0.0	19	dbSNP_134	50	0,8600		0,0,4300	yes	coding-synonymous-near-splice	ZNF230	NM_006300.3		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		77/475	44514422	7,12999	2203	4300	6503	SO:0001630	splice_region_variant	7773	exon5			TATAGGCGGCAAG	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.230-1C>T	19.37:g.44514422C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Silent	SNP	ENST00000429154.2	37	CCDS33044.1																																																																																			C|1.000;T|0.000	0.000	weak		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		Silent
ACOXL	55289	hgsc.bcm.edu	37	2	111850515	111850515	+	Missense_Mutation	SNP	C	C	T	rs17041850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:111850515C>T	ENST00000389811.4	+	18	1828	c.1604C>T	c.(1603-1605)cCc>cTc	p.P535L	ACOXL_ENST00000439055.1_Missense_Mutation_p.P505L			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	535			P -> L (in dbSNP:rs17041850).		fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						TACTTGACTCCCATGGCCAGC	0.463													C|||	373	0.0744808	0.0129	0.0879	5008	,	,		15389	0.2331		0.0378	False		,,,				2504	0.0225				p.P505L		Atlas-SNP	.											ACOXL_ENST00000439055,right_upper_lobe,carcinoma,-1,2	ACOXL	93	2	0			c.C1514T						PASS	.	C	LEU/PRO	95,4311	76.8+/-115.0	0,95,2108	95.0	92.0	93.0		1514	6.0	0.2	2	dbSNP_123	93	412,8188	130.3+/-188.3	11,390,3899	yes	missense	ACOXL	NM_001142807.1	98	11,485,6007	TT,TC,CC		4.7907,2.1562,3.8982	probably-damaging	505/581	111850515	507,12499	2203	4300	6503	SO:0001583	missense	55289	exon17			TGACTCCCATGGC		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"""acyl-Coenzyme A oxidase-like"""				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.1604C>T	2.37:g.111850515C>T	ENSP00000374461:p.Pro535Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		188	0.08608058608058608	6	0.012195121951219513	14	0.03867403314917127	144	0.2517482517482518	24	0.0316622691292876	C	16.59	3.166862	0.57476	0.021562	0.047907	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000422487;ENST00000417074	T;T;T	0.47528	0.84;0.84;0.84	5.97	5.97	0.96955	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.000000	0.64402	D	0.000007	T	0.00039	0.0001	M	0.79693	2.465	0.09310	P	1.0	D;D;P	0.56968	0.978;0.973;0.949	P;P;P	0.57620	0.823;0.73;0.824	T	0.00158	-1.1975	9	0.28530	T	0.3	-0.2987	17.9177	0.88957	0.0:1.0:0.0:0.0	rs17041850;rs59233521;rs17041850	505;505;535	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	L	535;505;356;343	ENSP00000374461:P535L;ENSP00000407761:P505L;ENSP00000387832:P343L	ENSP00000374461:P535L	P	+	2	0	ACOXL	111566986	0.070000	0.21116	0.216000	0.23742	0.193000	0.23685	2.041000	0.41213	2.828000	0.97474	0.655000	0.94253	CCC	C|0.930;T|0.070	0.070	strong		0.463	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
AHNAK2	113146	hgsc.bcm.edu	37	14	105407798	105407798	+	Missense_Mutation	SNP	T	T	C	rs4465542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	70	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	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	
MUC16	94025	hgsc.bcm.edu	37	19	9057750	9057750	+	Missense_Mutation	SNP	T	T	A	rs12982113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9057750T>A	ENST00000397910.4	-	3	29899	c.29696A>T	c.(29695-29697)tAt>tTt	p.Y9899F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9901	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGCACTCCATAAAGGACTGC	0.468													A|||	1095	0.21865	0.2352	0.2896	5008	,	,		21423	0.0258		0.3121	False		,,,				2504	0.2485				p.Y9899F		Atlas-SNP	.											.	MUC16	4315	.	0			c.A29696T						PASS	.	A	PHE/TYR	916,2978		99,718,1130	132.0	124.0	127.0		29696	-1.0	0.0	19	dbSNP_121	127	2816,5470		497,1822,1824	yes	missense	MUC16	NM_024690.2	22	596,2540,2954	AA,AT,TT		33.985,23.5234,30.6404	benign	9899/14508	9057750	3732,8448	1947	4143	6090	SO:0001583	missense	94025	exon3			ACTCCATAAAGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29696A>T	19.37:g.9057750T>A	ENSP00000381008:p.Tyr9899Phe	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	245	130	0.530612	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	474	0.21703296703296704	123	0.25	101	0.27900552486187846	11	0.019230769230769232	239	0.3153034300791557	a	5.303	0.241363	0.10077	0.235234	0.33985	ENSG00000181143	ENST00000397910	T	0.02631	4.22	2.62	-1.0	0.10196	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.47736	-0.9094	8	0.87932	D	0	.	2.3546	0.04293	0.2955:0.0:0.2972:0.4073	rs12982113;rs52835804;rs12982113	9899	B5ME49	.	F	9899	ENSP00000381008:Y9899F	ENSP00000381008:Y9899F	Y	-	2	0	MUC16	8918750	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.375000	0.07475	-0.471000	0.06891	-2.479000	0.00199	TAT	T|0.754;A|0.246	0.246	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NEFH	4744	hgsc.bcm.edu	37	22	29885473	29885473	+	Missense_Mutation	SNP	C	C	T	rs5763269	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:29885473C>T	ENST00000310624.6	+	4	1877	c.1844C>T	c.(1843-1845)cCg>cTg	p.P615L		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	615	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.		P -> L (in dbSNP:rs5763269).		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						gcaaagtcaccggctgagGCC	0.557													C|||	754	0.150559	0.1346	0.232	5008	,	,		22581	0.0744		0.2306	False		,,,				2504	0.1104				p.P615L		Atlas-SNP	.											.	NEFH	178	.	0			c.C1844T						PASS	.	C	LEU/PRO	752,3654	305.2+/-288.9	68,616,1519	65.0	64.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1844	4.6	0.1	22	dbSNP_114	64	1862,6738	326.0+/-317.2	200,1462,2638	no	missense	NEFH	NM_021076.3	98	268,2078,4157	TT,TC,CC		21.6512,17.0676,20.0984	possibly-damaging	615/1021	29885473	2614,10392	2203	4300	6503	SO:0001583	missense	4744	exon4			AGTCACCGGCTGA		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.1844C>T	22.37:g.29885473C>T	ENSP00000311997:p.Pro615Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	371	0.16987179487179488	77	0.1565040650406504	69	0.19060773480662985	53	0.09265734265734266	172	0.22691292875989447	C	8.422	0.846715	0.16963	0.170676	0.216512	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.99586	-6.23	4.6	4.6	0.57074	.	0.000000	0.49916	D	0.000133	T	0.02571	0.0078	M	0.72894	2.215	0.48975	P	2.6199999999998447E-4	P	0.39404	0.672	B	0.28011	0.085	T	0.00000	-1.2872	9	0.87932	D	0	.	17.564	0.87914	0.0:1.0:0.0:0.0	rs5763269;rs52807263;rs58303921;rs5763269	615	P12036	NFH_HUMAN	L	615	ENSP00000311997:P615L	ENSP00000311997:P615L	P	+	2	0	NEFH	28215473	0.853000	0.29707	0.055000	0.19348	0.005000	0.04900	2.462000	0.45049	2.568000	0.86640	0.650000	0.86243	CCG	C|0.815;T|0.185	0.185	strong		0.557	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
ASPA	443	hgsc.bcm.edu	37	17	3397702	3397702	+	Silent	SNP	C	C	T	rs12948217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3397702C>T	ENST00000263080.2	+	5	851	c.693C>T	c.(691-693)taC>taT	p.Y231Y	SPATA22_ENST00000541913.1_Intron|ASPA_ENST00000456349.2_Silent_p.Y231Y	NM_000049.2	NP_000040.1	P45381	ACY2_HUMAN	aspartoacylase	231			Y -> C (in CAND). {ECO:0000269|PubMed:10564886}.		aspartate catabolic process (GO:0006533)|central nervous system myelination (GO:0022010)|positive regulation of oligodendrocyte differentiation (GO:0048714)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminoacylase activity (GO:0004046)|aspartoacylase activity (GO:0019807)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(6)|lung(5)|stomach(1)|urinary_tract(1)	17					L-Aspartic Acid(DB00128)	AAGTTGATTACCCCCGGGATG	0.343													t|||	1020	0.203674	0.2345	0.1844	5008	,	,		20080	0.0496		0.3101	False		,,,				2504	0.2249				p.Y231Y		Atlas-SNP	.											.	ASPA	37	.	0			c.C693T	GRCh37	CM940123	ASPA	M	rs12948217	PASS	.	T	,	1075,3331	722.2+/-409.3	127,821,1255	179.0	200.0	192.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	693,693	3.5	1.0	17	dbSNP_121	192	2687,5913	683.3+/-403.9	446,1795,2059	no	coding-synonymous,coding-synonymous	ASPA	NM_000049.2,NM_001128085.1	,	573,2616,3314	TT,TC,CC		31.2442,24.3985,28.9251	,	231/314,231/314	3397702	3762,9244	2203	4300	6503	SO:0001819	synonymous_variant	443	exon5			TGATTACCCCCGG	S67156	CCDS11028.1	17p13.3	2010-06-24	2010-06-24		ENSG00000108381	ENSG00000108381	3.5.1.15		756	protein-coding gene	gene with protein product	"""aminoacylase 2"", ""Canavan disease"""	608034	"""aspartoacylase (aminoacylase 2, Canavan disease)"""			8252036	Standard	NM_001128085		Approved	ASP, ACY2	uc002fvq.3	P45381	OTTHUMG00000090655	ENST00000263080.2:c.693C>T	17.37:g.3397702C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_000049		Silent	SNP	ENST00000263080.2	37	CCDS11028.1																																																																																			C|0.732;T|0.268	0.268	strong		0.343	ASPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207315.1	NM_000049	
EFHB	151651	hgsc.bcm.edu	37	3	19930130	19930130	+	Missense_Mutation	SNP	A	A	T	rs76305623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:19930130A>T	ENST00000295824.9	-	10	1900	c.1739T>A	c.(1738-1740)aTg>aAg	p.M580K	EFHB_ENST00000344838.4_Missense_Mutation_p.M450K	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	580	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TTTATCTATCATCCCATCTCC	0.398													A|||	600	0.119808	0.1233	0.085	5008	,	,		13955	0.0833		0.0974	False		,,,				2504	0.2004				p.M580K		Atlas-SNP	.											EFHB_ENST00000295824,NS,haematopoietic_neoplasm,0,2	EFHB	186	2	0			c.T1739A						PASS	.	A	LYS/MET	483,3923	222.0+/-238.9	24,435,1744	61.0	56.0	58.0		1739	0.4	0.5	3	dbSNP_132	58	1033,7567	209.6+/-250.7	58,917,3325	yes	missense	EFHB	NM_144715.3	95	82,1352,5069	TT,TA,AA		12.0116,10.9623,11.6562	benign	580/834	19930130	1516,11490	2203	4300	6503	SO:0001583	missense	151651	exon10			TCTATCATCCCAT	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.1739T>A	3.37:g.19930130A>T	ENSP00000295824:p.Met580Lys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	217	0.09935897435897435	63	0.12804878048780488	31	0.0856353591160221	50	0.08741258741258741	73	0.09630606860158311	A	5.610	0.297219	0.10622	0.109623	0.120116	ENSG00000163576	ENST00000295824;ENST00000344838	T;T	0.69306	-0.39;-0.39	5.72	0.447	0.16608	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	1.174970	0.06034	N	0.653700	T	0.00300	0.0009	N	0.00389	-1.56	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.04165	-1.0972	8	.	.	.	-1.0624	4.6971	0.12809	0.5355:0.0:0.236:0.2285	.	450;580	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	K	580;450	ENSP00000295824:M580K;ENSP00000342263:M450K	.	M	-	2	0	EFHB	19905134	0.001000	0.12720	0.480000	0.27341	0.619000	0.37552	0.802000	0.27069	0.124000	0.18369	0.533000	0.62120	ATG	A|0.888;T|0.112	0.112	strong		0.398	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
CASZ1	54897	hgsc.bcm.edu	37	1	10720305	10720305	+	Missense_Mutation	SNP	A	A	G	rs138985539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10720305A>G	ENST00000377022.3	-	6	1111	c.794T>C	c.(793-795)gTg>gCg	p.V265A	CASZ1_ENST00000478728.2_5'Flank|CASZ1_ENST00000344008.5_Missense_Mutation_p.V265A	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	265					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)		CTCCTTGCCCACCCGCTCCTC	0.692													A|||	15	0.00299521	0.0	0.0072	5008	,	,		13239	0.0		0.005	False		,,,				2504	0.0051				p.V265A		Atlas-SNP	.											.	CASZ1	150	.	0			c.T794C						PASS	.	A	ALA/VAL,ALA/VAL	6,4396	11.4+/-27.6	0,6,2195	28.0	33.0	31.0		794,794	1.3	0.0	1	dbSNP_134	31	84,8516	48.1+/-107.5	0,84,4216	no	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	64,64	0,90,6411	GG,GA,AA		0.9767,0.1363,0.6922	benign,benign	265/1760,265/1167	10720305	90,12912	2201	4300	6501	SO:0001583	missense	54897	exon6			TTGCCCACCCGCT	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.794T>C	1.37:g.10720305A>G	ENSP00000366221:p.Val265Ala	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	0.003	-2.556568	0.00138	0.001363	0.009767	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.38	1.3	0.21679	.	0.492755	0.20891	N	0.083835	T	0.05502	0.0145	N	0.02539	-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;0.0;0.0;0.0	T	0.33803	-0.9854	9	0.02654	T	1	-4.3668	3.9612	0.09412	0.4216:0.0:0.4186:0.1597	.	289;265;265;265	B7Z1S3;B3KRV8;Q86V15-2;Q86V15	.;.;.;CASZ1_HUMAN	A	265	.	ENSP00000339445:V265A	V	-	2	0	CASZ1	10642892	0.454000	0.25728	0.020000	0.16555	0.084000	0.17831	0.831000	0.27476	0.082000	0.17018	-0.589000	0.04120	GTG	A|0.994;G|0.006	0.006	strong		0.692	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
WFIKKN1	117166	hgsc.bcm.edu	37	16	681284	681284	+	Silent	SNP	C	C	T	rs8062289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:681284C>T	ENST00000319070.2	+	1	353	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	11					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				CCTGCCGCTCCTGCTCCTCCT	0.741													c|||	1093	0.218251	0.3986	0.0965	5008	,	,		11117	0.0357		0.1859	False		,,,				2504	0.2822				p.L11L		Atlas-SNP	.											WFIKKN1,rectum,carcinoma,0,2	WFIKKN1	30	2	0			c.C31T						PASS	.			1488,2824		287,914,955	10.0	11.0	11.0		31	0.8	0.0	16	dbSNP_116	11	1579,6943		165,1249,2847	no	coding-synonymous	WFIKKN1	NM_053284.2		452,2163,3802	TT,TC,CC		18.5285,34.5083,23.8975		11/549	681284	3067,9767	2156	4261	6417	SO:0001819	synonymous_variant	117166	exon1			CCGCTCCTGCTCC	AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30912	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20A"""	608021	"""chromosome 16 open reading frame 12"""	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.31C>T	16.37:g.681284C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_053284	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																			C|0.799;T|0.201	0.201	strong		0.741	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284	
RP1L1	94137	hgsc.bcm.edu	37	8	10466089	10466089	+	Missense_Mutation	SNP	G	G	C	rs77968698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10466089G>C	ENST00000382483.3	-	4	5742	c.5519C>G	c.(5518-5520)gCt>gGt	p.A1840G		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1920					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)		CTCCCCTTCAGCCTCCGGGGC	0.632													G|||	151	0.0301518	0.0348	0.0159	5008	,	,		16114	0.002		0.0348	False		,,,				2504	0.0583				p.A1840G		Atlas-SNP	.											.	RP1L1	453	.	0			c.C5519G						PASS	.	G	GLY/ALA	118,3800		1,116,1842	150.0	167.0	162.0		5519	3.4	0.0	8	dbSNP_131	162	330,7932		5,320,3806	yes	missense	RP1L1	NM_178857.5	60	6,436,5648	CC,CG,GG		3.9942,3.0117,3.6782	probably-damaging	1840/2401	10466089	448,11732	1959	4131	6090	SO:0001583	missense	94137	exon4			CCTTCAGCCTCCG	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.5519C>G	8.37:g.10466089G>C	ENSP00000371923:p.Ala1840Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	46	0.021062271062271064	14	0.028455284552845527	5	0.013812154696132596	2	0.0034965034965034965	25	0.032981530343007916	G	10.75	1.439108	0.25900	0.030117	0.039942	ENSG00000183638	ENST00000382483	T	0.08807	3.05	3.44	3.44	0.39384	.	.	.	.	.	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	D	0.58268	0.982	P	0.49853	0.624	T	0.37709	-0.9694	9	0.39692	T	0.17	.	6.6991	0.23215	0.1379:0.0:0.8621:0.0	.	1840	A6NKC6	.	G	1840	ENSP00000371923:A1840G	ENSP00000371923:A1840G	A	-	2	0	RP1L1	10503499	0.000000	0.05858	0.006000	0.13384	0.004000	0.04260	0.060000	0.14342	1.450000	0.47717	0.455000	0.32223	GCT	G|0.972;C|0.028	0.028	strong		0.632	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
NKX1-2	390010	hgsc.bcm.edu	37	10	126136239	126136239	+	Missense_Mutation	SNP	A	A	G	rs146495217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:126136239A>G	ENST00000451024.3	-	2	932	c.692T>C	c.(691-693)gTg>gCg	p.V231A	NKX1-2_ENST00000440536.2_Missense_Mutation_p.V253A|RP13-238F13.3_ENST00000604581.1_RNA|RP13-238F13.5_ENST00000602332.1_lincRNA	NM_001146340.1	NP_001139812.1	Q9UD57	NKX12_HUMAN	NK1 homeobox 2	231	Gly-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)										gccaccccccacctgcgccgc	0.731													A|||	576	0.115016	0.0227	0.1268	5008	,	,		5896	0.1022		0.1918	False		,,,				2504	0.1656				p.V231A		Atlas-SNP	.											.	NKX1-2	6	.	0			c.T692C						PASS	.						13.0	10.0	11.0					10																	126136239		692	1582	2274	SO:0001583	missense	390010	exon2			CCCCCCACCTGCG	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.692T>C	10.37:g.126136239A>G	ENSP00000451945:p.Val231Ala	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_001146340		Missense_Mutation	SNP	ENST00000451024.3	37	CCDS59221.1	254	0.1163003663003663	18	0.036585365853658534	37	0.10220994475138122	68	0.11888111888111888	131	0.17282321899736147	A	0.003	-2.467059	0.00169	.	.	ENSG00000229544	ENST00000451024;ENST00000440536	D;D	0.88509	-2.35;-2.39	3.05	1.07	0.20283	Homeodomain-like (1);	.	.	.	.	T	0.00412	0.0013	N	0.04655	-0.195	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.10567	-1.0624	7	.	.	.	.	1.4615	0.02397	0.1346:0.2139:0.4331:0.2183	.	231	Q9UD57	NKX12_HUMAN	A	231;253	ENSP00000451945:V231A;ENSP00000450924:V253A	.	V	-	2	0	NKX1-2	126126229	.	.	0.047000	0.18901	0.034000	0.12701	.	.	0.282000	0.22254	-0.475000	0.04921	GTG	A|0.883;G|0.117	0.117	strong		0.731	NKX1-2-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050861.3	XM_372331	
ITSN2	50618	hgsc.bcm.edu	37	2	24432839	24432839	+	Silent	SNP	A	A	G	rs2303296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:24432839A>G	ENST00000355123.4	-	35	4764	c.4321T>C	c.(4321-4323)Tta>Cta	p.L1441L	ITSN2_ENST00000361999.3_Silent_p.L1414L	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1441	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)					GTCTTGTATAATTTCCCACTG	0.443													A|||	707	0.141174	0.0197	0.1354	5008	,	,		19423	0.124		0.2634	False		,,,				2504	0.2014				p.L1441L		Atlas-SNP	.											.	ITSN2	224	.	0			c.T4321C						PASS	.	A	,	267,4139	149.2+/-183.4	9,249,1945	169.0	160.0	163.0		4321,4240	-5.1	0.0	2	dbSNP_100	163	2131,6469	367.2+/-334.6	264,1603,2433	no	coding-synonymous,coding-synonymous	ITSN2	NM_006277.2,NM_019595.3	,	273,1852,4378	GG,GA,AA		24.7791,6.0599,18.4376	,	1441/1698,1414/1671	24432839	2398,10608	2203	4300	6503	SO:0001819	synonymous_variant	50618	exon35			TGTATAATTTCCC	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.4321T>C	2.37:g.24432839A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																			A|0.824;G|0.176	0.176	strong		0.443	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
ZBTB17	7709	hgsc.bcm.edu	37	1	16271260	16271260	+	Silent	SNP	G	G	A	rs9661939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16271260G>A	ENST00000375743.4	-	8	1234	c.1002C>T	c.(1000-1002)ttC>ttT	p.F334F	ZBTB17_ENST00000537142.1_Silent_p.F252F|ZBTB17_ENST00000448462.2_Silent_p.F271F|ZBTB17_ENST00000375733.2_Silent_p.F334F|ZBTB17_ENST00000479282.1_5'Flank	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	334				F -> S (in Ref. 2; BAG63326). {ECO:0000305}.	activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		CCCGGCACGAGAAGGGCTTCT	0.667													G|||	1043	0.208267	0.0779	0.3098	5008	,	,		16462	0.0169		0.3052	False		,,,				2504	0.41				p.F334F		Atlas-SNP	.											.	ZBTB17	45	.	0			c.C1002T						PASS	.	G	,	478,3928	216.4+/-235.1	27,424,1752	42.0	43.0	43.0		756,1002	5.5	1.0	1	dbSNP_119	43	2602,5998	412.5+/-350.8	413,1776,2111	no	coding-synonymous,coding-synonymous	ZBTB17	NM_001242884.1,NM_003443.2	,	440,2200,3863	AA,AG,GG		30.2558,10.8488,23.6814	,	252/722,334/804	16271260	3080,9926	2203	4300	6503	SO:0001819	synonymous_variant	7709	exon8			GCACGAGAAGGGC	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12936	protein-coding gene	gene with protein product		604084	"""zinc finger protein 151 (pHZ-67)"", ""zinc finger protein 60"""	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.1002C>T	1.37:g.16271260G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Silent	SNP	ENST00000375743.4	37	CCDS165.1																																																																																			G|0.802;A|0.198	0.198	strong		0.667	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443	
ZNF772	400720	hgsc.bcm.edu	37	19	57984918	57984918	+	Silent	SNP	A	A	G	rs2074058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57984918A>G	ENST00000343280.4	-	5	1454	c.1194T>C	c.(1192-1194)agT>agC	p.S398S	ZNF772_ENST00000600175.1_Intron|ZNF772_ENST00000356584.3_Silent_p.S357S|AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000425074.3_3'UTR|ZNF772_ENST00000427512.2_Silent_p.S286S|ZNF772_ENST00000601768.1_Intron|AC004076.9_ENST00000596831.1_Intron	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	398					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		CAGTATGAACACTCCAATGTT	0.413													A|||	2073	0.413938	0.3154	0.4524	5008	,	,		22319	0.5893		0.2783	False		,,,				2504	0.4785				p.S398S	Melanoma(5;289 436 14293 15924 30817)	Atlas-SNP	.											.	ZNF772	42	.	0			c.T1194C						PASS	.	A	,	1364,3042	454.2+/-350.6	198,968,1037	132.0	121.0	125.0		1194,1071	-1.1	1.0	19	dbSNP_96	125	2446,6154	402.6+/-347.5	329,1788,2183	no	coding-synonymous,coding-synonymous	ZNF772	NM_001024596.2,NM_001144068.1	,	527,2756,3220	GG,GA,AA		28.4419,30.9578,29.2942	,	398/490,357/449	57984918	3810,9196	2203	4300	6503	SO:0001819	synonymous_variant	400720	exon5			ATGAACACTCCAA	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"""Zinc fingers, C2H2-type"", ""-"""	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.1194T>C	19.37:g.57984918A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001024596	A6NJK9|B4DH56|B4DYS0	Silent	SNP	ENST00000343280.4	37	CCDS33133.1																																																																																			A|0.659;G|0.341	0.341	strong		0.413	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
CTBP2	1488	hgsc.bcm.edu	37	10	126715629	126715629	+	Intron	SNP	C	C	T	rs3781409	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:126715629C>T	ENST00000337195.5	-	3	458				CTBP2_ENST00000309035.6_Missense_Mutation_p.V234M|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000411419.2_Intron|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)		CTGGGGTCCACAACCAGGCAC	0.667													C|||	1010	0.201677	0.0998	0.2651	5008	,	,		17616	0.2431		0.2823	False		,,,				2504	0.1687				p.V234M		Atlas-SNP	.											.	CTBP2	100	.	0			c.G700A						PASS	.	C	,,MET/VAL	541,3865		30,481,1692	40.0	47.0	44.0		,,700	3.6	1.0	10	dbSNP_107	44	2280,6318		321,1638,2340	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,21	351,2119,4032	TT,TC,CC		26.5178,12.2787,21.6933	,,benign	,,234/986	126715629	2821,10183	2203	4299	6502	SO:0001627	intron_variant	1488	exon1			GGTCCACAACCAG	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+11936G>A	10.37:g.126715629C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	525	0.2403846153846154	42	0.08536585365853659	111	0.30662983425414364	152	0.26573426573426573	220	0.29023746701846964	C	20.6	4.024336	0.75390	0.122787	0.265178	ENSG00000175029	ENST00000309035	D	0.88664	-2.41	4.54	3.64	0.41730	.	0.201012	0.30649	N	0.009162	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.28350	0.208	B	0.30572	0.117	T	0.01909	-1.1249	8	0.59425	D	0.04	.	12.9826	0.58572	0.0:0.9215:0.0:0.0785	rs3781409;rs17710610;rs3781409	234	P56545-2	.	M	234	ENSP00000311825:V234M	ENSP00000311825:V234M	V	-	1	0	CTBP2	126705619	0.997000	0.39634	0.956000	0.39512	0.967000	0.64934	3.490000	0.53245	1.283000	0.44513	0.655000	0.94253	GTG	C|0.782;T|0.218	0.218	strong		0.667	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
CLEC10A	10462	hgsc.bcm.edu	37	17	6981397	6981397	+	Missense_Mutation	SNP	A	A	G	rs90951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:6981397A>G	ENST00000254868.4	-	3	431	c.103T>C	c.(103-105)Tgc>Cgc	p.C35R	CLEC10A_ENST00000571664.1_Missense_Mutation_p.C35R|CLEC10A_ENST00000416562.2_Missense_Mutation_p.C35R|CLEC10A_ENST00000576617.1_Missense_Mutation_p.C35R	NM_182906.2	NP_878910.1	Q8IUN9	CLC10_HUMAN	C-type lectin domain family 10, member A	35			C -> R (in dbSNP:rs90951). {ECO:0000269|PubMed:8598452}.		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						GGCCCAGAGCAGAGACGCTGC	0.627													G|||	2604	0.519968	0.9266	0.3473	5008	,	,		16452	0.4702		0.3608	False		,,,				2504	0.3078				p.C35R		Atlas-SNP	.											.	CLEC10A	40	.	0			c.T103C						PASS	.	G	ARG/CYS,ARG/CYS	3608,798	320.4+/-296.6	1492,624,87	102.0	106.0	104.0		103,103	-0.4	0.0	17	dbSNP_80	104	3053,5547	661.7+/-401.9	556,1941,1803	yes	missense,missense	CLEC10A	NM_006344.2,NM_182906.2	180,180	2048,2565,1890	GG,GA,AA		35.5,18.1117,48.7852	benign,benign	35/293,35/317	6981397	6661,6345	2203	4300	6503	SO:0001583	missense	10462	exon3			CAGAGCAGAGACG	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.103T>C	17.37:g.6981397A>G	ENSP00000254868:p.Cys35Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_182906	A8K8J8|Q14538|Q6PIW3	Missense_Mutation	SNP	ENST00000254868.4	37	CCDS11087.1	1115	0.5105311355311355	443	0.9004065040650406	119	0.3287292817679558	283	0.49475524475524474	270	0.3562005277044855	G	7.930	0.740365	0.15642	0.818883	0.355	ENSG00000132514	ENST00000254868;ENST00000416562	T;T	0.20738	2.05;2.05	4.43	-0.382	0.12481	Hepatic lectin, N-terminal (1);	0.629715	0.15066	N	0.282488	T	0.00012	0.0000	L	0.31371	0.925	0.80722	P	0.0	B;B;B	0.10296	0.003;0.0;0.003	B;B;B	0.21708	0.002;0.001;0.036	T	0.08432	-1.0722	9	0.37606	T	0.19	.	8.7412	0.34558	0.547:0.0:0.453:0.0	rs90951;rs747025;rs1048153;rs3765149;rs17806200;rs52801524;rs61010712;rs90951	35;35;35	Q8IUN9-3;Q8IUN9;Q8IUN9-2	.;CLC10_HUMAN;.	R	35	ENSP00000254868:C35R;ENSP00000414938:C35R	ENSP00000254868:C35R	C	-	1	0	CLEC10A	6922121	0.081000	0.21417	0.000000	0.03702	0.013000	0.08279	0.674000	0.25218	-0.472000	0.06881	-1.140000	0.01884	TGC	A|0.467;G|0.532	0.532	strong		0.627	CLEC10A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439837.2	NM_006344	
ATP13A5	344905	hgsc.bcm.edu	37	3	193080414	193080414	+	Missense_Mutation	SNP	C	C	G	rs6797429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:193080414C>G	ENST00000342358.4	-	4	514	c.397G>C	c.(397-399)Gaa>Caa	p.E133Q		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	133			E -> Q (in dbSNP:rs6797429).			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TTCTGCACTTCCATGCACCGC	0.483													G|||	2573	0.513778	0.646	0.5259	5008	,	,		21621	0.3859		0.5288	False		,,,				2504	0.4427				p.E133Q		Atlas-SNP	.											.	ATP13A5	171	.	0			c.G397C						PASS	.	G	GLN/GLU	2716,1690	513.1+/-368.2	845,1026,332	142.0	137.0	138.0		397	5.6	0.8	3	dbSNP_116	138	4451,4149	566.6+/-388.7	1179,2093,1028	yes	missense	ATP13A5	NM_198505.2	29	2024,3119,1360	GG,GC,CC		48.2442,38.3568,44.8947	benign	133/1219	193080414	7167,5839	2203	4300	6503	SO:0001583	missense	344905	exon4			GCACTTCCATGCA	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.397G>C	3.37:g.193080414C>G	ENSP00000341942:p.Glu133Gln	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	1159	0.5306776556776557	317	0.6443089430894309	202	0.5580110497237569	233	0.40734265734265734	407	0.5369393139841688	G	0.411	-0.913282	0.02415	0.616432	0.517558	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.26223	1.75;1.75	5.6	5.6	0.85130	.	0.268854	0.32548	N	0.005941	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31392	-0.9945	9	0.09590	T	0.72	-2.1229	13.3521	0.60607	0.0:0.3026:0.6974:0.0	rs6797429;rs59343082;rs6797429	133	Q4VNC0	AT135_HUMAN	Q	133;155	ENSP00000341942:E133Q;ENSP00000389416:E155Q	ENSP00000341942:E133Q	E	-	1	0	ATP13A5	194563108	1.000000	0.71417	0.815000	0.32552	0.069000	0.16628	2.617000	0.46385	1.534000	0.49203	-0.120000	0.15030	GAA	C|0.453;G|0.547	0.547	strong		0.483	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
CYP2J2	1573	hgsc.bcm.edu	37	1	60392271	60392271	+	Silent	SNP	G	G	A	rs11572191	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:60392271G>A	ENST00000371204.3	-	1	191	c.148C>T	c.(148-150)Ctg>Ttg	p.L50L		NM_000775.2	NP_000766.2	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J, polypeptide 2	50					arachidonic acid metabolic process (GO:0019369)|epoxygenase P450 pathway (GO:0019373)|icosanoid metabolic process (GO:0006690)|linoleic acid metabolic process (GO:0043651)|regulation of heart contraction (GO:0008016)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	arachidonic acid 11,12-epoxygenase activity (GO:0008405)|arachidonic acid 14,15-epoxygenase activity (GO:0008404)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|linoleic acid epoxygenase activity (GO:0071614)			NS(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|skin(1)	26	all_cancers(7;0.000396)				Apixaban(DB06605)|Astemizole(DB00637)|Cholecalciferol(DB00169)|Levomilnacipran(DB08918)|Masoprocol(DB00179)|Rivaroxaban(DB06228)	AGGAAGGGCAGGCGCCAGGGC	0.607													G|||	200	0.0399361	0.0098	0.0908	5008	,	,		15786	0.0		0.0984	False		,,,				2504	0.0256				p.L50L		Atlas-SNP	.											.	CYP2J2	34	.	0			c.C148T						PASS	.	G		98,4308	82.4+/-120.9	2,94,2107	60.0	67.0	65.0		148	4.4	0.1	1	dbSNP_120	65	985,7615	209.7+/-250.8	63,859,3378	no	coding-synonymous	CYP2J2	NM_000775.2		65,953,5485	AA,AG,GG		11.4535,2.2242,8.3269		50/503	60392271	1083,11923	2203	4300	6503	SO:0001819	synonymous_variant	1573	exon1			AGGGCAGGCGCCA	BC032594	CCDS613.1	1p31.3-p31.2	2008-02-05	2003-01-14		ENSG00000134716	ENSG00000134716		"""Cytochrome P450s"""	2634	protein-coding gene	gene with protein product		601258	"""cytochrome P450, subfamily IIJ (arachidonic acid epoxygenase) polypeptide 2"""			9570962	Standard	NM_000775		Approved		uc001czq.3	P51589	OTTHUMG00000008991	ENST00000371204.3:c.148C>T	1.37:g.60392271G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	224	112	0.5	NM_000775	B2RD33|Q8TF13	Silent	SNP	ENST00000371204.3	37	CCDS613.1																																																																																			G|0.932;A|0.068	0.068	strong		0.607	CYP2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024940.1	NM_000775	
HERC1	8925	hgsc.bcm.edu	37	15	63988400	63988400	+	Missense_Mutation	SNP	G	G	C	rs74814914	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:63988400G>C	ENST00000443617.2	-	27	5131	c.5044C>G	c.(5044-5046)Cta>Gta	p.L1682V	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1682					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CACCCTGCTAGGAACTGCAGC	0.512													G|||	51	0.0101837	0.0023	0.0202	5008	,	,		16282	0.0		0.0288	False		,,,				2504	0.0051				p.L1682V		Atlas-SNP	.											.	HERC1	624	.	0			c.C5044G						PASS	.	G	VAL/LEU	30,3990		0,30,1980	87.0	86.0	86.0		5044	5.5	1.0	15	dbSNP_132	86	304,8028		5,294,3867	yes	missense	HERC1	NM_003922.3	32	5,324,5847	CC,CG,GG		3.6486,0.7463,2.704	possibly-damaging	1682/4862	63988400	334,12018	2010	4166	6176	SO:0001583	missense	8925	exon27			CTGCTAGGAACTG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.5044C>G	15.37:g.63988400G>C	ENSP00000390158:p.Leu1682Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	27	0.012362637362637362	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	19	0.025065963060686015	G	22.5	4.299964	0.81136	0.007463	0.036486	ENSG00000103657	ENST00000443617;ENST00000425434	T	0.49139	0.79	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000019	T	0.24661	0.0598	L	0.34521	1.04	0.58432	D	0.999997	D;D	0.67145	0.996;0.993	D;D	0.72625	0.978;0.967	T	0.45425	-0.9262	10	0.87932	D	0	.	12.7906	0.57530	0.0749:0.0:0.9251:0.0	.	666;1682	B4DKS2;Q15751	.;HERC1_HUMAN	V	1682;666	ENSP00000390158:L1682V	ENSP00000389613:L666V	L	-	1	2	HERC1	61775453	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.658000	0.68003	2.607000	0.88179	0.650000	0.86243	CTA	G|0.985;C|0.015	0.015	strong		0.512	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46105889	46105889	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46105889G>A	ENST00000290795.3	-	7	1958	c.737C>T	c.(736-738)cCt>cTt	p.P246L	GPBP1L1_ENST00000355105.3_Missense_Mutation_p.P246L			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	246					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					TACCTTGGAAGGAGGTGGTAC	0.408																																					p.P246L		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.C737T						PASS	.						114.0	110.0	111.0					1																	46105889		2203	4300	6503	SO:0001583	missense	60313	exon8			TTGGAAGGAGGTG		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.737C>T	1.37:g.46105889G>A	ENSP00000290795:p.Pro246Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_021639	D3DQ10|Q9H751	Missense_Mutation	SNP	ENST00000290795.3	37	CCDS528.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903432	0.72754	.	.	ENSG00000159592	ENST00000290795;ENST00000355105	T;T	0.28069	1.63;1.63	5.85	4.94	0.65067	.	0.053159	0.85682	D	0.000000	T	0.33469	0.0864	M	0.66939	2.045	0.58432	D	0.999999	P	0.35155	0.487	B	0.30943	0.122	T	0.25882	-1.0119	10	0.87932	D	0	-24.6457	15.1693	0.72858	0.0678:0.0:0.9322:0.0	.	246	Q9HC44	GPBL1_HUMAN	L	246	ENSP00000290795:P246L;ENSP00000347224:P246L	ENSP00000290795:P246L	P	-	2	0	GPBP1L1	45878476	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.439000	0.97543	1.478000	0.48253	0.655000	0.94253	CCT	.	.	none		0.408	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
PCOLCE2	26577	hgsc.bcm.edu	37	3	142548681	142548681	+	Missense_Mutation	SNP	C	C	T	rs140721173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:142548681C>T	ENST00000295992.3	-	6	1024	c.718G>A	c.(718-720)Gtg>Atg	p.V240M	PCOLCE2_ENST00000485766.1_Intron	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	240	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						CTCTCAGACACAATTGGCCTA	0.313													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16702	0.0		0.001	False		,,,				2504	0.002				p.V240M		Atlas-SNP	.											.	PCOLCE2	63	.	0			c.G718A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	75.0	78.0	77.0		718	3.5	1.0	3	dbSNP_134	77	8,8592	6.4+/-24.3	0,8,4292	yes	missense	PCOLCE2	NM_013363.3	21	0,9,6494	TT,TC,CC		0.093,0.0227,0.0692	possibly-damaging	240/416	142548681	9,12997	2203	4300	6503	SO:0001583	missense	26577	exon6			CAGACACAATTGG	AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.718G>A	3.37:g.142548681C>T	ENSP00000295992:p.Val240Met	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_013363	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	13.63	2.294192	0.40594	2.27E-4	9.3E-4	ENSG00000163710	ENST00000295992	T	0.30714	1.52	5.3	3.5	0.40072	CUB (5);	0.127288	0.51477	D	0.000085	T	0.37652	0.1011	M	0.69823	2.125	0.80722	D	1	P	0.48407	0.91	P	0.49561	0.615	T	0.10800	-1.0614	10	0.44086	T	0.13	-4.6795	6.5558	0.22460	0.125:0.5656:0.2418:0.0675	.	240	Q9UKZ9	PCOC2_HUMAN	M	240	ENSP00000295992:V240M	ENSP00000295992:V240M	V	-	1	0	PCOLCE2	144031371	0.876000	0.30132	0.999000	0.59377	0.724000	0.41520	-0.015000	0.12634	0.618000	0.30179	-0.226000	0.12346	GTG	C|0.999;T|0.001	0.001	strong		0.313	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363	
LAMC1	3915	hgsc.bcm.edu	37	1	183086757	183086757	+	Silent	SNP	A	A	C	rs2296292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:183086757A>C	ENST00000258341.4	+	10	2033	c.1776A>C	c.(1774-1776)gcA>gcC	p.A592A		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	592	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GCCTCTCTGCAGAAGACCTTG	0.493													A|||	2663	0.531749	0.3321	0.6254	5008	,	,		21081	0.628		0.5636	False		,,,				2504	0.6033				p.A592A		Atlas-SNP	.											.	LAMC1	176	.	0			c.A1776C						PASS	.	A		1651,2755	504.1+/-365.7	334,983,886	125.0	115.0	119.0		1776	2.9	1.0	1	dbSNP_100	119	4898,3702	619.9+/-397.0	1352,2194,754	no	coding-synonymous	LAMC1	NM_002293.3		1686,3177,1640	CC,CA,AA		43.0465,37.4716,49.6463		592/1610	183086757	6549,6457	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon10			CTCTGCAGAAGAC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1776A>C	1.37:g.183086757A>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			A|0.489;C|0.511	0.511	strong		0.493	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
YIF1B	90522	hgsc.bcm.edu	37	19	38800165	38800165	+	Silent	SNP	C	C	T	rs3900981	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38800165C>T	ENST00000339413.6	-	2	222	c.177G>A	c.(175-177)ctG>ctA	p.L59L	YIF1B_ENST00000392124.3_Silent_p.L28L|YIF1B_ENST00000329420.8_Silent_p.L44L|YIF1B_ENST00000591755.1_Silent_p.L56L|YIF1B_ENST00000592246.1_Silent_p.L28L|YIF1B_ENST00000337679.8_Silent_p.L56L|YIF1B_ENST00000587361.1_5'UTR|YIF1B_ENST00000591784.1_Silent_p.L28L|YIF1B_ENST00000592694.1_Silent_p.L28L	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	59						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAGGATAACTCAGGCCACCAG	0.672													T|||	1112	0.222045	0.1407	0.3213	5008	,	,		14481	0.2331		0.2296	False		,,,				2504	0.2423				p.L59L		Atlas-SNP	.											.	YIF1B	47	.	0			c.G177A						PASS	.	T	,,,,,,	723,3679		50,623,1528	26.0	30.0	28.0		132,177,168,126,84,168,84	1.0	1.0	19	dbSNP_108	28	1697,6897		156,1385,2756	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YIF1B	NM_001039671.2,NM_001039672.2,NM_001039673.2,NM_001145461.1,NM_001145462.1,NM_001145463.1,NM_033557.3	,,,,,,	206,2008,4284	TT,TC,CC		19.7463,16.4244,18.6211	,,,,,,	44/300,59/315,56/312,42/298,28/284,56/292,28/284	38800165	2420,10576	2201	4297	6498	SO:0001819	synonymous_variant	90522	exon2			ATAACTCAGGCCA	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.177G>A	19.37:g.38800165C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	166	88	0.53012	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Silent	SNP	ENST00000339413.6	37	CCDS33010.1																																																																																			C|0.803;T|0.197	0.197	strong		0.672	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557	
C10orf12	26148	hgsc.bcm.edu	37	10	98742750	98742750	+	Missense_Mutation	SNP	A	A	C	rs3829856	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:98742750A>C	ENST00000286067.2	+	1	1710	c.1603A>C	c.(1603-1605)Atc>Ctc	p.I535L		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	535			I -> L (in dbSNP:rs3829856).							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)		TTGTCTTGAAATCAAAGTTCC	0.453													A|||	509	0.101637	0.0832	0.0476	5008	,	,		18675	0.1915		0.0646	False		,,,				2504	0.1104				p.I535L		Atlas-SNP	.											.	C10orf12	94	.	0			c.A1603C						PASS	.	A	LEU/ILE	333,4073	160.7+/-193.0	9,315,1879	71.0	80.0	77.0		1603	-2.5	0.4	10	dbSNP_107	77	503,8095	141.1+/-197.5	16,471,3812	yes	missense	C10orf12	NM_015652.2	5	25,786,5691	CC,CA,AA		5.8502,7.5579,6.4288	benign	535/1248	98742750	836,12168	2203	4299	6502	SO:0001583	missense	26148	exon1			CTTGAAATCAAAG	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.1603A>C	10.37:g.98742750A>C	ENSP00000286067:p.Ile535Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	212	0.09706959706959707	40	0.08130081300813008	20	0.055248618784530384	104	0.18181818181818182	48	0.0633245382585752	A	10.88	1.475286	0.26511	0.075579	0.058502	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.10382	2.88	5.82	-2.46	0.06461	.	0.278980	0.24499	U	0.037985	T	0.00012	0.0000	N	0.19112	0.55	0.41806	P	0.01005900000000004	B	0.14805	0.011	B	0.16289	0.015	T	0.41124	-0.9526	9	0.36615	T	0.2	-0.0766	6.6806	0.23117	0.5194:0.1323:0.3484:0.0	rs3829856;rs52834733;rs61155862;rs3829856	535	Q8N655	CJ012_HUMAN	L	535;369	ENSP00000286067:I535L	ENSP00000286067:I535L	I	+	1	0	C10orf12	98732740	0.995000	0.38212	0.426000	0.26672	0.191000	0.23601	0.418000	0.21230	-0.712000	0.04988	-0.396000	0.06452	ATC	A|0.918;C|0.082	0.082	strong		0.453	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
LAMB3	3914	hgsc.bcm.edu	37	1	209807972	209807972	+	Silent	SNP	G	G	A	rs1130667	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:209807972G>A	ENST00000356082.4	-	6	518	c.384C>T	c.(382-384)ccC>ccT	p.P128P	LAMB3_ENST00000391911.1_Silent_p.P128P|LAMB3_ENST00000367030.3_Silent_p.P128P	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	128	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCATGCCGGCGGGCATGGGCC	0.652													G|||	1229	0.245407	0.0908	0.2421	5008	,	,		16590	0.2381		0.3887	False		,,,				2504	0.317				p.P128P		Atlas-SNP	.											.	LAMB3	136	.	0			c.C384T						PASS	.	G	,,	678,3728	275.4+/-272.5	54,570,1579	32.0	28.0	30.0		384,384,384	-8.5	0.4	1	dbSNP_86	30	3402,5198	476.1+/-369.3	669,2064,1567	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	723,2634,3146	AA,AG,GG		39.5581,15.3881,31.3701	,,	128/1173,128/1173,128/1173	209807972	4080,8926	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon6			GCCGGCGGGCATG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.384C>T	1.37:g.209807972G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			G|0.713;A|0.287	0.287	strong		0.652	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924200	43924200	+	Missense_Mutation	SNP	C	C	G	rs12373142	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43924200C>G	ENST00000329196.5	+	1	1945	c.1928C>G	c.(1927-1929)cCg>cGg	p.P643R	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	643			P -> R (in dbSNP:rs12373142).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTGATGCCCCCGCCCTCAGAG	0.627													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		18729	0.001		0.2396	False		,,,				2504	0.0613				p.P643R		Atlas-SNP	.											.	.	.	.	0			c.C1928G						PASS	.	C	ARG/PRO	200,4206	121.3+/-158.8	5,190,2008	43.0	41.0	42.0		1928	-0.3	0.0	17	dbSNP_120	42	1916,6684	328.1+/-318.2	221,1474,2605	yes	missense	IMP5	NM_175882.2	103	226,1664,4613	GG,GC,CC		22.2791,4.5393,16.2694	possibly-damaging	643/685	43924200	2116,10890	2203	4300	6503	SO:0001583	missense	162540	exon1			TGCCCCCGCCCTC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1928C>G	17.37:g.43924200C>G	ENSP00000332488:p.Pro643Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	253	0.11584249084249085	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	174	0.22955145118733508	C	0.238	-1.015902	0.02078	0.045393	0.222791	ENSG00000185294	ENST00000329196	T	0.04406	3.63	4.23	-0.281	0.12882	.	0.237510	0.22293	N	0.061965	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.21309	0.054	B	0.14023	0.01	T	0.48490	-0.9031	9	0.48119	T	0.1	-18.8908	2.3936	0.04384	0.382:0.3664:0.1536:0.098	rs12373142;rs12373142	643	Q8IUH8	IMP5_HUMAN	R	643	ENSP00000332488:P643R	ENSP00000332488:P643R	P	+	2	0	AC217771.1	41279980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.094000	0.11094	-0.001000	0.14495	-1.047000	0.02352	CCG	C|0.473;G|0.527	0.527	strong		0.627	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415279	105415279	+	Missense_Mutation	SNP	T	T	C	rs386781098|rs201127689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105415279T>C	ENST00000333244.5	-	7	6628	c.6509A>G	c.(6508-6510)aAg>aGg	p.K2170R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2170						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)			CTCGATGGACTTGCCTGGGGC	0.582													.|||	632	0.126198	0.0439	0.1398	5008	,	,		16935	0.0446		0.2744	False		,,,				2504	0.1595				p.K2170R		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,lymphoid_neoplasm,0,3	AHNAK2	719	3	0			c.A6509G						scavenged	.						195.0	128.0	150.0					14																	105415279		1944	4029	5973	SO:0001583	missense	113146	exon7			ATGGACTTGCCTG	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.6509A>G	14.37:g.105415279T>C	ENSP00000353114:p.Lys2170Arg	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	15.79	2.937373	0.52972	.	.	ENSG00000185567	ENST00000333244	T	0.01821	4.62	3.99	3.99	0.46301	.	.	.	.	.	T	0.08802	0.0218	M	0.88450	2.955	0.45108	P	0.0018730000000000135	D	0.65815	0.995	D	0.81914	0.995	T	0.21075	-1.0256	8	0.12766	T	0.61	.	6.8711	0.24121	0.0:0.1178:0.0:0.8822	.	2170	Q8IVF2	AHNK2_HUMAN	R	2170	ENSP00000353114:K2170R	ENSP00000353114:K2170R	K	-	2	0	AHNAK2	104486324	0.000000	0.05858	0.928000	0.36995	0.203000	0.24098	0.264000	0.18497	1.692000	0.51112	0.397000	0.26171	AAG	.	.	weak		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TRPV2	51393	hgsc.bcm.edu	37	17	16325968	16325968	+	Silent	SNP	A	A	G	rs8121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	80	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	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	
FMN2	56776	hgsc.bcm.edu	37	1	240370985	240370985	+	Missense_Mutation	SNP	C	C	T	rs111896385	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240370985C>T	ENST00000319653.9	+	5	3103	c.2873C>T	c.(2872-2874)cCt>cTt	p.P958L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	958	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)			CCTCCGCCCCCTCTTCCCGGG	0.692																																					p.P958L		Atlas-SNP	.											.	FMN2	451	.	0			c.C2873T						PASS	.						20.0	23.0	22.0					1																	240370985		2203	4296	6499	SO:0001583	missense	56776	exon5			CGCCCCCTCTTCC	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.2873C>T	1.37:g.240370985C>T	ENSP00000318884:p.Pro958Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	126	38	0.301587	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	398	0.18223443223443223	65	0.13211382113821138	59	0.16298342541436464	125	0.21853146853146854	149	0.19656992084432717	C	10.82	1.457343	0.26161	.	.	ENSG00000155816	ENST00000319653	T	0.65549	-0.16	3.8	2.88	0.33553	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.00144	0.0004	M	0.89904	3.07	0.09310	P	1.0	D	0.60575	0.988	P	0.59056	0.851	T	0.09997	-1.0649	7	.	.	.	.	8.7103	0.34380	0.0:0.8893:0.0:0.1107	.	958	Q9NZ56	FMN2_HUMAN	L	958	ENSP00000318884:P958L	.	P	+	2	0	FMN2	238437608	0.002000	0.14202	0.036000	0.18154	0.002000	0.02628	1.177000	0.31969	0.978000	0.38470	-0.385000	0.06624	CCT	C|0.803;T|0.197	0.197	strong		0.692	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
PRSS58	136541	hgsc.bcm.edu	37	7	141955128	141955128	+	Silent	SNP	C	C	T	rs1894317	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:141955128C>T	ENST00000552471.1	-	3	502	c.183G>A	c.(181-183)aaG>aaA	p.K61K	PRSS58_ENST00000547058.2_Silent_p.K61K			Q8IYP2	PRS58_HUMAN	protease, serine, 58	61	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						TCACCCGAAGCTTTCTGGAAC	0.428													C|||	1000	0.199681	0.3359	0.2565	5008	,	,		19977	0.1409		0.1044	False		,,,				2504	0.1339				p.K61K		Atlas-SNP	.											.	PRSS58	41	.	0			c.G183A						PASS	.	C		1456,2950	465.9+/-354.3	260,936,1007	110.0	107.0	108.0		183	-5.0	0.0	7	dbSNP_92	108	867,7733	194.5+/-239.9	40,787,3473	no	coding-synonymous	PRSS58	NM_001001317.3		300,1723,4480	TT,TC,CC		10.0814,33.0458,17.861		61/242	141955128	2323,10683	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon4			CCGAAGCTTTCTG		CCDS5871.1	7q34	2012-10-03			ENSG00000258223	ENSG00000258223	3.4.21.4	"""Serine peptidases / Serine peptidases"""	39125	protein-coding gene	gene with protein product	"""trypsin X3"""						Standard	NM_001001317		Approved	TRYX3	uc003vxc.4	Q8IYP2	OTTHUMG00000158565	ENST00000552471.1:c.183G>A	7.37:g.141955128C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	150	84	0.56	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			C|0.819;T|0.181	0.181	strong		0.428	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317	
DHX29	54505	hgsc.bcm.edu	37	5	54572163	54572163	+	Silent	SNP	T	T	C	rs3761764	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54572163T>C	ENST00000251636.5	-	14	2506	c.2358A>G	c.(2356-2358)aaA>aaG	p.K786K	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	786						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				CTTCCAGAAATTTCTGACAAT	0.313													C|||	924	0.184505	0.2943	0.0965	5008	,	,		15312	0.2877		0.0994	False		,,,				2504	0.0798				p.K786K		Atlas-SNP	.											.	DHX29	116	.	0			c.A2358G						PASS	.	C		984,3420	714.7+/-408.4	115,754,1333	75.0	78.0	77.0		2358	-0.0	1.0	5	dbSNP_107	77	869,7721	772.4+/-407.7	45,779,3471	no	coding-synonymous	DHX29	NM_019030.2		160,1533,4804	CC,CT,TT		10.1164,22.3433,14.2604		786/1370	54572163	1853,11141	2202	4295	6497	SO:0001819	synonymous_variant	54505	exon14			CAGAAATTTCTGA	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"""DEAH-boxes"""	15815	protein-coding gene	gene with protein product		612720	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"""	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.2358A>G	5.37:g.54572163T>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	219	106	0.484018	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Silent	SNP	ENST00000251636.5	37	CCDS34158.1																																																																																			T|0.831;C|0.169	0.169	strong		0.313	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030	
RAET1E	135250	hgsc.bcm.edu	37	6	150211100	150211100	+	Silent	SNP	T	T	C	rs3798763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:150211100T>C	ENST00000357183.4	-	2	399	c.267A>G	c.(265-267)gaA>gaG	p.E89E	RAET1E_ENST00000532335.1_Silent_p.E89E|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000367363.3_Silent_p.E53E|RAET1E_ENST00000529948.1_Silent_p.E89E|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000605899.1_RNA	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	89	MHC class I alpha-1 like.				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)		TTTGGGTCAATTCTCCCCAAG	0.498													t|||	1122	0.224042	0.0386	0.3689	5008	,	,		20232	0.3333		0.2604	False		,,,				2504	0.2219				p.E89E		Atlas-SNP	.											.	RAET1E	20	.	0			c.A267G						PASS	.	T		302,4104	163.6+/-195.4	16,270,1917	116.0	107.0	110.0		267	-4.1	0.0	6	dbSNP_107	110	2245,6355	380.1+/-339.5	283,1679,2338	yes	coding-synonymous	RAET1E	NM_139165.2		299,1949,4255	CC,CT,TT		26.1047,6.8543,19.5833		89/264	150211100	2547,10459	2203	4300	6503	SO:0001819	synonymous_variant	135250	exon2			GGTCAATTCTCCC	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.267A>G	6.37:g.150211100T>C		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	180	179	0.994444	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Silent	SNP	ENST00000357183.4	37	CCDS5221.1																																																																																			T|0.790;C|0.210	0.210	strong		0.498	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
SLU7	10569	hgsc.bcm.edu	37	5	159835658	159835658	+	Splice_Site	SNP	A	A	G	rs17856337|rs2961944	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:159835658A>G	ENST00000297151.4	-	7	1073	c.686T>C	c.(685-687)aTg>aCg	p.M229T		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)	229			M -> T (in dbSNP:rs2961944). {ECO:0000269|PubMed:10197984, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17081983, ECO:0000269|PubMed:20068231, ECO:0000269|Ref.3}.		alternative mRNA splicing, via spliceosome (GO:0000380)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	pre-mRNA 3'-splice site binding (GO:0030628)|second spliceosomal transesterification activity (GO:0000386)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20	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)			ATGTATTACCATCTGAGAATT	0.299																																					p.M229T		Atlas-SNP	.											.	SLU7	35	.	0			c.T686C						PASS	.	G	THR/MET	2465,1941	541.1+/-375.7	689,1087,427	62.0	65.0	64.0		686	-2.5	0.6	5	dbSNP_101	64	6333,2257	375.8+/-337.9	2338,1657,300	yes	missense-near-splice	SLU7	NM_006425.4	81	3027,2744,727	GG,GA,AA		26.2747,44.0536,32.3022	benign	229/587	159835658	8798,4198	2203	4295	6498	SO:0001630	splice_region_variant	10569	exon7			ATTACCATCTGAG	AF101074	CCDS4352.1	5q33.3	2010-04-13			ENSG00000164609	ENSG00000164609			16939	protein-coding gene	gene with protein product	zinc knuckle motif containing	605974				10197984, 15728250	Standard	NM_006425		Approved	9G8	uc003lyg.3	O95391	OTTHUMG00000130324	ENST00000297151.4:c.687+1T>C	5.37:g.159835658A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_006425	D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Missense_Mutation	SNP	ENST00000297151.4	37	CCDS4352.1	1342	0.6144688644688645	239	0.48577235772357724	261	0.7209944751381215	298	0.5209790209790209	544	0.7176781002638523	G	8.258	0.810550	0.16537	0.559464	0.737253	ENSG00000164609	ENST00000297151	T	0.39997	1.05	6.16	-2.46	0.06461	Pre-mRNA splicing Prp18-interacting factor (1);	0.594399	0.19697	N	0.108130	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	9	0.12766	T	0.61	-19.8753	13.1096	0.59267	0.5674:0.0:0.4326:0.0	rs2961944;rs52792577;rs57779922;rs2961944	229	O95391	SLU7_HUMAN	T	229	ENSP00000297151:M229T	ENSP00000297151:M229T	M	-	2	0	SLU7	159768236	0.995000	0.38212	0.620000	0.29132	0.430000	0.31655	0.560000	0.23500	-0.918000	0.03808	-1.636000	0.00776	ATG	A|0.368;G|0.632	0.632	strong		0.299	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	NM_006425	Missense_Mutation
TRIM33	51592	hgsc.bcm.edu	37	1	114973429	114973429	+	Silent	SNP	T	T	C	rs12083584	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:114973429T>C	ENST00000358465.2	-	6	1229	c.1146A>G	c.(1144-1146)caA>caG	p.Q382Q	TRIM33_ENST00000369543.2_Silent_p.Q382Q|TRIM33_ENST00000450349.2_5'UTR	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	382	Necessary for oligomerization.				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)		CCTCTAGCTGTTGTAAGAGAG	0.313			T	RET	papillary thyroid								C|||	1481	0.295727	0.4697	0.2392	5008	,	,		16876	0.0446		0.325	False		,,,				2504	0.3292				p.Q382Q		Atlas-SNP	.		Dom	yes		1	1p13	51592	""" tripartite motif-containing 33 (PTC7,TIF1G)"""		E	.	TRIM33	115	.	0			c.A1146G						PASS	.	C	,	1945,2459	622.6+/-394.0	413,1119,670	123.0	127.0	126.0		1146,1146	3.8	1.0	1	dbSNP_120	126	2836,5762	673.9+/-403.1	475,1886,1938	no	coding-synonymous,coding-synonymous	TRIM33	NM_015906.3,NM_033020.2	,	888,3005,2608	CC,CT,TT		32.9844,44.1644,36.7713	,	382/1128,382/1111	114973429	4781,8221	2202	4299	6501	SO:0001819	synonymous_variant	51592	exon6			TAGCTGTTGTAAG	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.1146A>G	1.37:g.114973429T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Silent	SNP	ENST00000358465.2	37	CCDS872.1	573	0.2623626373626374	214	0.4349593495934959	95	0.26243093922651933	21	0.03671328671328671	243	0.32058047493403696	C	8.121	0.780930	0.16120	0.441644	0.329844	ENSG00000197323	ENST00000448034	.	.	.	5.68	3.77	0.43336	.	.	.	.	.	T	0.38719	0.1051	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26326	-1.0106	3	.	.	.	-7.4498	10.7422	0.46160	0.0:0.7296:0.0:0.2704	rs12083584;rs12083584	.	.	.	S	119	.	.	N	-	2	0	TRIM33	114774952	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.835000	0.39181	0.745000	0.32763	-0.186000	0.12905	AAC	T|0.669;C|0.331	0.331	strong		0.313	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906	
C19orf45	374877	hgsc.bcm.edu	37	19	7573287	7573287	+	Missense_Mutation	SNP	C	C	T	rs1133378	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7573287C>T	ENST00000361664.2	+	9	1630	c.1489C>T	c.(1489-1491)Cct>Tct	p.P497S	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	497			P -> S (in dbSNP:rs1133378). {ECO:0000269|PubMed:14702039}.							endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CCCCCAGCCCCCTATGTACCT	0.602													C|||	1198	0.239217	0.1725	0.3285	5008	,	,		17721	0.1746		0.337	False		,,,				2504	0.2321				p.P497S		Atlas-SNP	.											.	C19orf45	36	.	0			c.C1489T						PASS	.	C	SER/PRO	842,3562	313.0+/-292.9	92,658,1452	29.0	28.0	28.0		1489	3.6	0.0	19	dbSNP_86	28	2849,5751	417.1+/-352.3	471,1907,1922	yes	missense	C19orf45	NM_198534.2	74	563,2565,3374	TT,TC,CC		33.1279,19.119,28.3836	probably-damaging	497/506	7573287	3691,9313	2202	4300	6502	SO:0001583	missense	374877	exon9			CAGCCCCCTATGT	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.1489C>T	19.37:g.7573287C>T	ENSP00000355241:p.Pro497Ser	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	605	0.27701465201465203	98	0.1991869918699187	133	0.3674033149171271	112	0.1958041958041958	262	0.34564643799472294	C	16.86	3.239811	0.58995	0.19119	0.331279	ENSG00000198723	ENST00000361664	T	0.13901	2.55	3.62	3.62	0.41486	.	0.417387	0.20234	N	0.096427	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	D	0.63046	0.992	P	0.60541	0.876	T	0.48246	-0.9052	9	0.41790	T	0.15	-2.9932	11.0656	0.47974	0.0:1.0:0.0:0.0	rs1133378;rs3178370;rs3195126;rs3745354;rs1133378	497	Q8NA69	CS045_HUMAN	S	497	ENSP00000355241:P497S	ENSP00000355241:P497S	P	+	1	0	C19orf45	7479287	0.001000	0.12720	0.008000	0.14137	0.035000	0.12851	1.017000	0.29989	2.325000	0.78763	0.462000	0.41574	CCT	C|0.736;T|0.264	0.264	strong		0.602	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
VSIG10L	147645	hgsc.bcm.edu	37	19	51841364	51841364	+	Missense_Mutation	SNP	G	G	A	rs201452734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51841364G>A	ENST00000335624.4	-	6	1827	c.1828C>T	c.(1828-1830)Cgg>Tgg	p.R610W	CTD-2616J11.16_ENST00000601148.1_RNA|CTD-2616J11.16_ENST00000594311.1_RNA	NM_001163922.1	NP_001157394.1	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10 like	610						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)	4						CAGGATGCCCGTGAGGGTGGG	0.682													G|||	3	0.000599042	0.0	0.0043	5008	,	,		13375	0.0		0.0	False		,,,				2504	0.0				p.R610W		Atlas-SNP	.											.	VSIG10L	40	.	0			c.C1828T						PASS	.	G	TRP/ARG	0,1384		0,0,692	19.0	20.0	20.0		1828	-10.1	0.0	19		20	5,3177		0,5,1586	yes	missense	VSIG10L	NM_001163922.1	101	0,5,2278	AA,AG,GG		0.1571,0.0,0.1095	probably-damaging	610/868	51841364	5,4561	692	1591	2283	SO:0001583	missense	147645	exon6			ATGCCCGTGAGGG		CCDS54300.1	19q13.41	2013-01-11				ENSG00000186806		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27111	protein-coding gene	gene with protein product						12477932	Standard	NM_001163922		Approved		uc002pwf.3	Q86VR7		ENST00000335624.4:c.1828C>T	19.37:g.51841364G>A	ENSP00000335623:p.Arg610Trp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_001163922		Missense_Mutation	SNP	ENST00000335624.4	37	CCDS54300.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974353	0.74246	0.0	0.001571	ENSG00000186806	ENST00000335624	T	0.30981	1.51	5.03	-10.1	0.00402	Immunoglobulin-like fold (1);	0.123933	0.34853	N	0.003621	T	0.47820	0.1466	M	0.75447	2.3	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.64976	-0.6280	10	0.87932	D	0	-4.0204	19.2219	0.93801	0.0:0.0:0.1206:0.8794	.	610	Q86VR7	VS10L_HUMAN	W	610	ENSP00000335623:R610W	ENSP00000335623:R610W	R	-	1	2	VSIG10L	56533176	0.001000	0.12720	0.001000	0.08648	0.955000	0.61496	-0.437000	0.06914	-1.560000	0.01686	0.561000	0.74099	CGG	.	.	weak		0.682	VSIG10L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464535.1	NM_001163922	
SLC10A1	6554	hgsc.bcm.edu	37	14	70263648	70263648	+	Silent	SNP	C	C	T	rs4646285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:70263648C>T	ENST00000216540.4	-	1	358	c.225G>A	c.(223-225)acG>acA	p.T75T		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	75					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	GCACAAAGGCCGTGAGGGGCA	0.567													C|||	500	0.0998403	0.0083	0.134	5008	,	,		22636	0.1726		0.0855	False		,,,				2504	0.1391				p.T75T		Atlas-SNP	.											.	SLC10A1	32	.	0			c.G225A						PASS	.	C		122,4284	91.6+/-130.3	0,122,2081	94.0	77.0	83.0		225	-10.0	0.6	14	dbSNP_111	83	745,7855	179.0+/-228.3	37,671,3592	no	coding-synonymous	SLC10A1	NM_003049.3		37,793,5673	TT,TC,CC		8.6628,2.769,6.6662		75/350	70263648	867,12139	2203	4300	6503	SO:0001819	synonymous_variant	6554	exon1			AAAGGCCGTGAGG	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"""Solute carriers"""	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.225G>A	14.37:g.70263648C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_003049	B9EGB6|Q2TU29	Silent	SNP	ENST00000216540.4	37	CCDS9797.1																																																																																			C|0.920;T|0.080	0.080	strong		0.567	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1		
ARMC2	84071	hgsc.bcm.edu	37	6	109197379	109197379	+	Missense_Mutation	SNP	T	T	C	rs9386758	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:109197379T>C	ENST00000392644.4	+	5	665	c.497T>C	c.(496-498)aTg>aCg	p.M166T	ARMC2_ENST00000368972.3_Start_Codon_SNP_p.M1T	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	166			M -> T (in dbSNP:rs9386758).							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)		GAAACAGTTATGATGGGGGAC	0.333													T|||	407	0.08127	0.0053	0.0548	5008	,	,		17142	0.1964		0.0219	False		,,,				2504	0.1452				p.M166T		Atlas-SNP	.											.	ARMC2	56	.	0			c.T497C						PASS	.	T	THR/MET	35,4371	39.2+/-71.8	0,35,2168	43.0	45.0	44.0		497	-5.0	0.0	6	dbSNP_119	44	163,8437	76.3+/-139.0	2,159,4139	yes	missense	ARMC2	NM_032131.4	81	2,194,6307	CC,CT,TT		1.8953,0.7944,1.5224	benign	166/868	109197379	198,12808	2203	4300	6503	SO:0001583	missense	84071	exon5			CAGTTATGATGGG	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.497T>C	6.37:g.109197379T>C	ENSP00000376417:p.Met166Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	127	56	0.440945	NM_032131	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Missense_Mutation	SNP	ENST00000392644.4	37	CCDS5069.2	170|170	0.07783882783882784|0.07783882783882784	2|2	0.0040650406504065045|0.0040650406504065045	17|17	0.04696132596685083|0.04696132596685083	134|134	0.23426573426573427|0.23426573426573427	17|17	0.022427440633245383|0.022427440633245383	T|T	6.475|6.475	0.455864|0.455864	0.12283|0.12283	0.007944|0.007944	0.018953|0.018953	ENSG00000118690|ENSG00000118690	ENST00000368972;ENST00000392644;ENST00000237512|ENST00000414610	T;T;T|.	0.38887|.	1.11;1.11;1.11|.	5.01|5.01	-4.98|-4.98	0.03019|0.03019	.|.	1.156990|.	0.06067|.	N|.	0.659427|.	T|.	0.04137|.	0.0115|.	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.33111|.	-0.9881|.	9|.	0.30854|.	T|.	0.27|.	.|.	1.947|1.947	0.03358|0.03358	0.1229:0.3285:0.266:0.2826|0.1229:0.3285:0.266:0.2826	rs9386758;rs52803792;rs9386758|rs9386758;rs52803792;rs9386758	166|.	Q8NEN0|.	ARMC2_HUMAN|.	T|R	1;166;166|18	ENSP00000357968:M1T;ENSP00000376417:M166T;ENSP00000237512:M166T|.	ENSP00000237512:M166T|.	M|X	+|+	2|1	0|0	ARMC2|ARMC2	109304072|109304072	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.352000|0.352000	0.29268|0.29268	-1.573000|-1.573000	0.02134|0.02134	-1.055000|-1.055000	0.03209|0.03209	0.260000|0.260000	0.18958|0.18958	ATG|TGA	T|0.953;C|0.047	0.047	strong		0.333	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131	
PAG1	55824	hgsc.bcm.edu	37	8	81905397	81905397	+	Silent	SNP	A	A	G	rs2016465	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	42	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	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	
SNN	8303	hgsc.bcm.edu	37	16	11769963	11769963	+	Silent	SNP	C	C	T	rs1050069	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:11769963C>T	ENST00000329565.5	+	2	260	c.48C>T	c.(46-48)atC>atT	p.I16I	TXNDC11_ENST00000570917.1_5'Flank	NM_003498.5	NP_003489.1	O75324	SNN_HUMAN	stannin	16					response to abiotic stimulus (GO:0009628)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				endometrium(1)	1						TCACAGTCATCGTCATCCTCA	0.637													C|||	1281	0.255791	0.0688	0.2032	5008	,	,		18820	0.252		0.4672	False		,,,				2504	0.3323				p.I16I		Atlas-SNP	.											.	SNN	7	.	0			c.C48T						PASS	.	C		567,3827	252.1+/-258.6	42,483,1672	66.0	53.0	57.0		48	-3.7	1.0	16	dbSNP_86	57	4033,4567	556.7+/-386.9	903,2227,1170	no	coding-synonymous	SNN	NM_003498.5		945,2710,2842	TT,TC,CC		46.8953,12.904,35.401		16/89	11769963	4600,8394	2197	4300	6497	SO:0001819	synonymous_variant	8303	exon2			AGTCATCGTCATC	AF030196	CCDS10549.1	16p13	2008-02-05			ENSG00000184602	ENSG00000184602			11149	protein-coding gene	gene with protein product		603032				9657854	Standard	NM_003498		Approved		uc002dbf.3	O75324	OTTHUMG00000090535	ENST00000329565.5:c.48C>T	16.37:g.11769963C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_003498	D3DUG4|Q6FGI0	Silent	SNP	ENST00000329565.5	37	CCDS10549.1																																																																																			C|0.685;T|0.315	0.315	strong		0.637	SNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207059.1	NM_003498	
SLC41A1	254428	hgsc.bcm.edu	37	1	205764031	205764031	+	Silent	SNP	G	G	A	rs151305052	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205764031G>A	ENST00000367137.3	-	10	2337	c.1323C>T	c.(1321-1323)ttC>ttT	p.F441F	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	441					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)			AGAAGATGATGAAGATGAGTG	0.597													G|||	2	0.000399361	0.0	0.0	5008	,	,		21049	0.0		0.0	False		,,,				2504	0.002				p.F441F		Atlas-SNP	.											.	SLC41A1	46	.	0			c.C1323T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	92.0	81.0	85.0		1323	4.8	1.0	1	dbSNP_134	85	10,8590	8.4+/-32.0	0,10,4290	no	coding-synonymous	SLC41A1	NM_173854.4		0,12,6491	AA,AG,GG		0.1163,0.0454,0.0923		441/514	205764031	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	254428	exon10			GATGATGAAGATG	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.1323C>T	1.37:g.205764031G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Silent	SNP	ENST00000367137.3	37	CCDS30988.1																																																																																			G|0.998;A|0.002	0.002	strong		0.597	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1		
ZBTB42	100128927	hgsc.bcm.edu	37	14	105267934	105267934	+	Missense_Mutation	SNP	G	G	A	rs34284721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105267934G>A	ENST00000342537.7	+	1	685	c.400G>A	c.(400-402)Gca>Aca	p.A134T	ZBTB42_ENST00000555360.1_Missense_Mutation_p.A134T	NM_001137601.1	NP_001131073.1	B2RXF5	ZBT42_HUMAN	zinc finger and BTB domain containing 42	134	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TGCCCCTGGGGCAGAACCTGC	0.657													G|||	213	0.0425319	0.003	0.0706	5008	,	,		16804	0.0		0.1133	False		,,,				2504	0.047				p.A134T		Atlas-SNP	.											.	ZBTB42	10	.	0			c.G400A						PASS	.	G	THR/ALA	29,1353		2,25,664	21.0	25.0	24.0		400	-2.4	0.0	14	dbSNP_126	24	376,2802		19,338,1232	yes	missense	ZBTB42	NM_001137601.1	58	21,363,1896	AA,AG,GG		11.8313,2.0984,8.8816	benign	134/423	105267934	405,4155	691	1589	2280	SO:0001583	missense	100128927	exon2			CCTGGGGCAGAAC	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.400G>A	14.37:g.105267934G>A	ENSP00000409107:p.Ala134Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001137601	B7ZW21	Missense_Mutation	SNP	ENST00000342537.7	37	CCDS45174.1	121	0.0554029304029304	2	0.0040650406504065045	33	0.09116022099447514	0	0.0	86	0.11345646437994723	G	0.669	-0.802607	0.02841	0.020984	0.118313	ENSG00000179627	ENST00000555360;ENST00000342537	T;T	0.12361	2.69;2.69	3.09	-2.4	0.06583	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.44528	-0.9322	8	0.17369	T	0.5	.	1.9749	0.03414	0.2171:0.142:0.4775:0.1634	rs34284721	134	B2RXF5	ZBT42_HUMAN	T	134	ENSP00000450673:A134T;ENSP00000409107:A134T	ENSP00000409107:A134T	A	+	1	0	ZBTB42	104338979	0.021000	0.18746	0.003000	0.11579	0.002000	0.02628	1.115000	0.31209	-0.266000	0.09339	-0.379000	0.06801	GCA	G|0.930;A|0.070	0.070	strong		0.657	ZBTB42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410372.1		
EHBP1L1	254102	hgsc.bcm.edu	37	11	65348725	65348725	+	Silent	SNP	G	G	A	rs79021529	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:65348725G>A	ENST00000309295.4	+	8	1012	c.747G>A	c.(745-747)gtG>gtA	p.V249V		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	249						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CAGCCCCTGTGAGTGCTCCTG	0.657													G|||	178	0.0355431	0.0045	0.0432	5008	,	,		15454	0.0		0.0924	False		,,,				2504	0.0501				p.V249V		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G747A						PASS	.	G		67,3785		0,67,1859	29.0	33.0	32.0		747	3.3	1.0	11	dbSNP_132	32	669,7547		24,621,3463	no	coding-synonymous	EHBP1L1	NM_001099409.1		24,688,5322	AA,AG,GG		8.1426,1.7394,6.0988		249/1524	65348725	736,11332	1926	4108	6034	SO:0001819	synonymous_variant	254102	exon8			CCCTGTGAGTGCT	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.747G>A	11.37:g.65348725G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	44	0.611111	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.951;A|0.049	0.049	strong		0.657	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
OR7A5	26659	hgsc.bcm.edu	37	19	14938616	14938616	+	Silent	SNP	T	T	C	rs2190686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14938616T>C	ENST00000322301.3	-	2	525	c.438A>G	c.(436-438)ctA>ctG	p.L146L	OR7A5_ENST00000594432.1_Silent_p.L146L|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	146					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						TCCAGGATGCTAGAACCAGCA	0.507													.|||	2800	0.559105	0.6218	0.428	5008	,	,		20351	0.6815		0.3917	False		,,,				2504	0.6135				p.L146L		Atlas-SNP	.											.	OR7A5	43	.	0			c.A438G						PASS	.	C		2699,1707	514.1+/-368.5	825,1049,329	74.0	68.0	70.0		438	0.8	0.0	19	dbSNP_96	70	3404,5196	639.0+/-399.4	692,2020,1588	no	coding-synonymous	OR7A5	NM_017506.1		1517,3069,1917	CC,CT,TT		39.5814,38.7426,46.9245		146/320	14938616	6103,6903	2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			GGATGCTAGAACC	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"""GPCR / Class A : Olfactory receptors"""	8368	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily A, member 5 pseudogene"""				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.438A>G	19.37:g.14938616T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			T|0.505;C|0.495	0.495	strong		0.507	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
TMPRSS5	80975	hgsc.bcm.edu	37	11	113570385	113570385	+	Missense_Mutation	SNP	C	C	T	rs11601425	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:113570385C>T	ENST00000299882.5	-	3	285	c.137G>A	c.(136-138)cGa>cAa	p.R46Q	TMPRSS5_ENST00000540540.1_Intron|TMPRSS5_ENST00000544476.1_Missense_Mutation_p.R2Q|TMPRSS5_ENST00000538955.1_Missense_Mutation_p.R2Q|TMPRSS5_ENST00000545579.1_Missense_Mutation_p.R37Q|TMPRSS5_ENST00000544634.1_Missense_Mutation_p.R46Q|TMPRSS5_ENST00000536856.1_Intron	NM_030770.2	NP_110397.2	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	46			R -> Q (in dbSNP:rs11601425). {ECO:0000269|PubMed:17918732}.		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)		ACAGCCACGTCGCATGGAACG	0.632													c|||	210	0.0419329	0.0061	0.0764	5008	,	,		16592	0.001		0.0905	False		,,,				2504	0.0583				p.R46Q		Atlas-SNP	.											.	TMPRSS5	69	.	0			c.G137A						PASS	.		GLN/ARG	93,4151		2,89,2031	18.0	25.0	23.0		137	3.1	0.4	11	dbSNP_120	23	919,7551		52,815,3368	yes	missense	TMPRSS5	NM_030770.2	43	54,904,5399	TT,TC,CC		10.8501,2.1913,7.9597	benign	46/458	113570385	1012,11702	2122	4235	6357	SO:0001583	missense	80975	exon3			CCACGTCGCATGG	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.137G>A	11.37:g.113570385C>T	ENSP00000299882:p.Arg46Gln	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	207	102	0.492754	NM_030770		Missense_Mutation	SNP	ENST00000299882.5	37	CCDS44735.1	107	0.04899267399267399	6	0.012195121951219513	27	0.07458563535911603	0	0.0	74	0.09762532981530343	c	16.55	3.155673	0.57259	0.021913	0.108501	ENSG00000166682	ENST00000299882;ENST00000545579;ENST00000538955;ENST00000544634;ENST00000544476	D;D;D;D;D	0.88896	-2.44;-2.44;-2.37;-2.42;-2.43	4.02	3.09	0.35607	.	0.350692	0.23859	N	0.043867	T	0.05273	0.0140	N	0.17082	0.46	0.20489	N	0.999895	B;B;B	0.31318	0.201;0.319;0.005	B;B;B	0.17433	0.012;0.018;0.002	T	0.15292	-1.0442	10	0.38643	T	0.18	.	6.9714	0.24650	0.0:0.8679:0.0:0.1321	rs11601425;rs17533506;rs52821493;rs11601425	46;37;46	F5GYA3;F5GX83;Q9H3S3	.;.;TMPS5_HUMAN	Q	46;37;2;46;2	ENSP00000299882:R46Q;ENSP00000441104:R37Q;ENSP00000445528:R2Q;ENSP00000440783:R46Q;ENSP00000445930:R2Q	ENSP00000299882:R46Q	R	-	2	0	TMPRSS5	113075595	0.000000	0.05858	0.354000	0.25760	0.035000	0.12851	-0.348000	0.07740	1.001000	0.39076	0.450000	0.29827	CGA	C|0.946;T|0.054	0.054	strong		0.632	TMPRSS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398652.1	NM_030770	
SLC12A6	9990	hgsc.bcm.edu	37	15	34543185	34543185	+	Silent	SNP	T	T	C	rs558676261		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:34543185T>C	ENST00000354181.3	-	11	1899	c.1407A>G	c.(1405-1407)ttA>ttG	p.L469L	SLC12A6_ENST00000560164.1_Silent_p.L281L|SLC12A6_ENST00000397702.2_Silent_p.L410L|SLC12A6_ENST00000458406.2_Silent_p.L410L|SLC12A6_ENST00000290209.5_Silent_p.L418L|SLC12A6_ENST00000451844.2_Silent_p.L281L|SLC12A6_ENST00000397707.2_Silent_p.L454L|SLC12A6_ENST00000558589.1_Silent_p.L460L|SLC12A6_ENST00000558667.1_Silent_p.L469L|SLC12A6_ENST00000560611.1_Silent_p.L469L			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	469					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)	TTAAGCTGCCTAAGACATCAG	0.428													T|||	1	0.000199681	0.0	0.0	5008	,	,		17280	0.0		0.0	False		,,,				2504	0.001				p.L469L		Atlas-SNP	.											SLC12A6,NS,carcinoma,-1,1	SLC12A6	205	1	0			c.A1407G						scavenged	.						158.0	137.0	144.0					15																	34543185		2201	4298	6499	SO:0001819	synonymous_variant	9990	exon10			GCTGCCTAAGACA	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.1407A>G	15.37:g.34543185T>C		Somatic	202	2	0.00990099		WXS	Illumina HiSeq	Phase_I	199	3	0.0150754	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																			.	.	none		0.428	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
SLC6A1	6529	hgsc.bcm.edu	37	3	11064091	11064091	+	Silent	SNP	G	G	A	rs6344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:11064091G>A	ENST00000287766.4	+	7	1072	c.651G>A	c.(649-651)acG>acA	p.T217T	SLC6A1_ENST00000536032.1_Silent_p.T39T	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	217					gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	26		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Clobazam(DB00349)|Tiagabine(DB00906)	TGGCCATCACGCTGGCCATCG	0.552													G|||	9	0.00179712	0.0008	0.0058	5008	,	,		20511	0.0		0.004	False		,,,				2504	0.0				p.T217T		Atlas-SNP	.											.	SLC6A1	88	.	0			c.G651A						PASS	.						85.0	76.0	79.0					3																	11064091		2203	4300	6503	SO:0001819	synonymous_variant	6529	exon7			CATCACGCTGGCC		CCDS2603.1	3p25.3	2013-07-19	2013-07-19		ENSG00000157103	ENSG00000157103		"""Solute carriers"""	11042	protein-coding gene	gene with protein product	"""GABA transporter 1"""	137165	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 1"""			8530094	Standard	NM_003042		Approved	GAT1, GABATR, GABATHG	uc010hdq.3	P30531	OTTHUMG00000044208	ENST00000287766.4:c.651G>A	3.37:g.11064091G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	104	59	0.567308	NM_003042	Q8N4K8	Silent	SNP	ENST00000287766.4	37	CCDS2603.1																																																																																			A|0.000;G|0.954;T|0.046	0.000	strong		0.552	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042	
ATP2A3	489	hgsc.bcm.edu	37	17	3846802	3846802	+	Silent	SNP	A	A	G	rs758641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3846802A>G	ENST00000352011.3	-	11	1356	c.1302T>C	c.(1300-1302)taT>taC	p.Y434Y	ATP2A3_ENST00000309890.7_Silent_p.Y434Y|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000397043.3_Silent_p.Y434Y|ATP2A3_ENST00000359983.3_Silent_p.Y434Y|ATP2A3_ENST00000397041.3_Silent_p.Y434Y|ATP2A3_ENST00000397035.3_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	115	0	0		WXS	Illumina HiSeq	Phase_I	104	104	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	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73205463	73205463	+	Missense_Mutation	SNP	G	G	A	rs17634853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73205463G>A	ENST00000426542.2	+	33	4408	c.4388G>A	c.(4387-4389)cGg>cAg	p.R1463Q	ARHGEF28_ENST00000437974.1_Missense_Mutation_p.R1463Q|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.R1463Q|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.R383Q|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.R1150Q|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.R1463Q|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.R1463Q|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.R1419Q			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1463	Interaction with microtubules. {ECO:0000250}.				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)										CAGCAGCAGCGGGCGCAGGCG	0.706													G|||	176	0.0351438	0.0484	0.0288	5008	,	,		15344	0.0		0.0378	False		,,,				2504	0.0552				p.R1463Q		Atlas-SNP	.											.	.	.	.	0			c.G4388A						PASS	.	G	GLN/ARG,GLN/ARG	103,3775		1,101,1837	4.0	4.0	4.0		4388,4388	5.2	1.0	5	dbSNP_123	4	199,7719		0,199,3760	no	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	43,43	1,300,5597	AA,AG,GG		2.5133,2.656,2.5602	benign,benign	1463/1732,1463/1706	73205463	302,11494	1939	3959	5898	SO:0001583	missense	64283	exon34			AGCAGCGGGCGCA		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.4388G>A	5.37:g.73205463G>A	ENSP00000412175:p.Arg1463Gln	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	63	0.028846153846153848	29	0.05894308943089431	11	0.03038674033149171	0	0.0	23	0.030343007915567283	G	14.26	2.482813	0.44147	0.02656	0.025133	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06	5.21	5.21	0.72293	.	0.000000	0.28803	U	0.014098	T	0.01976	0.0062	L	0.53249	1.67	0.27348	N	0.956312	B;B;B;B;B	0.31655	0.222;0.226;0.226;0.33;0.334	B;B;B;B;B	0.24848	0.019;0.017;0.025;0.043;0.056	T	0.04360	-1.0957	10	0.30854	T	0.27	.	11.8212	0.52238	0.1277:0.0:0.8723:0.0	rs17634853	1150;1463;1463;383;1463	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	Q	1463;1463;1463;1419;1463;1463;1150;383	ENSP00000296794:R1463Q;ENSP00000441913:R1463Q;ENSP00000441436:R1463Q;ENSP00000287898:R1419Q;ENSP00000411459:R1463Q;ENSP00000412175:R1463Q;ENSP00000296799:R1150Q;ENSP00000421081:R383Q	ENSP00000287898:R1419Q	R	+	2	0	RP11-428C6.1	73241219	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	4.106000	0.57804	2.440000	0.82611	0.455000	0.32223	CGG	G|0.973;A|0.027	0.027	strong		0.706	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
ENTPD2	954	hgsc.bcm.edu	37	9	139943429	139943429	+	Silent	SNP	G	G	A	rs7873815	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139943429G>A	ENST00000355097.2	-	8	1295	c.1248C>T	c.(1246-1248)gaC>gaT	p.D416D	NPDC1_ENST00000488145.1_5'Flank|ENTPD2_ENST00000460614.1_5'UTR|NPDC1_ENST00000371601.4_5'Flank|ENTPD2_ENST00000312665.5_Silent_p.D393D	NM_001246.3|NM_203468.2	NP_001237.1|NP_982293.1	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2	416					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)		AGGCGCGCTCGTCGAAGCCGT	0.736													G|||	2187	0.436701	0.5756	0.389	5008	,	,		8947	0.5327		0.329	False		,,,				2504	0.2945				p.D416D		Atlas-SNP	.											.	ENTPD2	30	.	0			c.C1248T						PASS	.	G	,	1368,1734		336,696,519	2.0	2.0	2.0		1179,1248	-2.2	0.8	9	dbSNP_116	2	1856,4576		380,1096,1740	no	coding-synonymous,coding-synonymous	ENTPD2	NM_001246.2,NM_203468.1	,	716,1792,2259	AA,AG,GG		28.8557,44.1006,33.8158	,	393/473,416/496	139943429	3224,6310	1551	3216	4767	SO:0001819	synonymous_variant	954	exon8			GCGCTCGTCGAAG	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.1248C>T	9.37:g.139943429G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	16	14	0.875	NM_203468	O15464|Q5SPY6|Q5SPY7	Silent	SNP	ENST00000355097.2	37	CCDS7026.1																																																																																			G|0.564;A|0.436	0.436	strong		0.736	ENTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055169.1	NM_203468	
BUB1B	701	hgsc.bcm.edu	37	15	40462780	40462780	+	Silent	SNP	G	G	A	rs1801389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:40462780G>A	ENST00000287598.6	+	4	477	c.282G>A	c.(280-282)aaG>aaA	p.K94K	BUB1B_ENST00000412359.3_Silent_p.K108K|BUB1B_ENST00000560120.1_3'UTR	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	94	BUB1 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00822}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		AAGGTGGGAAGGAGAGTAATA	0.358			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				G|||	438	0.0874601	0.1422	0.0879	5008	,	,		18598	0.003		0.1342	False		,,,				2504	0.0521				p.K94K		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.G282A						PASS	.	G		603,3803	265.0+/-266.4	40,523,1640	113.0	107.0	109.0		282	1.3	1.0	15	dbSNP_89	109	1266,7334	252.2+/-278.4	83,1100,3117	no	coding-synonymous	BUB1B	NM_001211.5		123,1623,4757	AA,AG,GG		14.7209,13.6859,14.3703		94/1051	40462780	1869,11137	2203	4300	6503	SO:0001819	synonymous_variant	701	exon4	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	TGGGAAGGAGAGT	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.282G>A	15.37:g.40462780G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	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		
HTRA2	27429	hgsc.bcm.edu	37	2	74756548	74756548	+	5'UTR	SNP	G	G	C	rs1183739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:74756548G>C	ENST00000258080.3	+	0	45				HTRA2_ENST00000352222.3_5'Flank|AUP1_ENST00000377526.3_Silent_p.L43L	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2						adult walking behavior (GO:0007628)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|ceramide metabolic process (GO:0006672)|execution phase of apoptosis (GO:0097194)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitochondrion organization (GO:0007005)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|pentacyclic triterpenoid metabolic process (GO:0019742)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell death (GO:0010942)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of mitochondrion degradation (GO:1903146)|regulation of multicellular organism growth (GO:0040014)|response to herbicide (GO:0009635)	CD40 receptor complex (GO:0035631)|chromatin (GO:0000785)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)|unfolded protein binding (GO:0051082)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						TCCCGAGAAAGAGGCGCAGGA	0.662													G|||	234	0.0467252	0.0068	0.0432	5008	,	,		18412	0.0		0.169	False		,,,				2504	0.0256				p.L43L		Atlas-SNP	.											.	AUP1	29	.	0			c.C129G						PASS	.	G	,,	117,4199		4,109,2045	23.0	34.0	30.0		,,129	1.9	1.0	2	dbSNP_87	30	1206,7292		88,1030,3131	no	utr-5,utr-5,coding-synonymous	AUP1,HTRA2	NM_013247.4,NM_145074.2,NM_181575.3	,,	92,1139,5176	CC,CG,GG		14.1916,2.7108,10.3246	,,	,,43/411	74756548	1323,11491	2158	4249	6407	SO:0001623	5_prime_UTR_variant	550	exon2			GAGAAAGAGGCGC		CCDS1951.1, CCDS1952.1	2p13.1	2011-07-21	2005-08-19	2005-08-19	ENSG00000115317	ENSG00000115317		"""Serine peptidases / Serine peptidases"", ""Parkinson disease"""	14348	protein-coding gene	gene with protein product		606441	"""protease, serine, 25"""	PRSS25		10644717, 10971580	Standard	XM_005264266		Approved	OMI, PARK13	uc002smi.1	O43464	OTTHUMG00000129957	ENST00000258080.3:c.-586G>C	2.37:g.74756548G>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	187	87	0.465241	NM_181575	Q9HBZ4|Q9P0Y3|Q9P0Y4	Silent	SNP	ENST00000258080.3	37	CCDS1951.1																																																																																			G|0.924;C|0.076	0.076	strong		0.662	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247	
OR7C1	26664	hgsc.bcm.edu	37	19	14910573	14910573	+	Missense_Mutation	SNP	C	C	T	rs10415562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14910573C>T	ENST00000248073.2	-	1	450	c.376G>A	c.(376-378)Gtc>Atc	p.V126I	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	126			V -> I (in dbSNP:rs10415562).		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						GGGTGACAGACGGCCACGAAG	0.517													T|||	4202	0.839058	0.8797	0.7925	5008	,	,		18273	0.8869		0.7366	False		,,,				2504	0.8732				p.V126I		Atlas-SNP	.											.	OR7C1	58	.	0			c.G376A						PASS	.	T	ILE/VAL	3762,644	273.7+/-271.5	1604,554,45	90.0	85.0	86.0		376	2.6	1.0	19	dbSNP_119	86	6542,2058	357.4+/-330.7	2464,1614,222	no	missense	OR7C1	NM_198944.1	29	4068,2168,267	TT,TC,CC		23.9302,14.6164,20.775	benign	126/321	14910573	10304,2702	2203	4300	6503	SO:0001583	missense	26664	exon1			GACAGACGGCCAC	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.376G>A	19.37:g.14910573C>T	ENSP00000248073:p.Val126Ile	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	1769	0.809981684981685	422	0.8577235772357723	278	0.7679558011049724	498	0.8706293706293706	571	0.7532981530343008	t	0.013	-1.641372	0.00799	0.853836	0.760698	ENSG00000127530	ENST00000248073	T	0.26518	1.73	3.64	2.59	0.31030	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37304	N	0.002142	T	0.00012	0.0000	N	0.00025	-2.68	0.54753	P	1.0999999999983245E-5	B	0.13145	0.007	B	0.04013	0.001	T	0.31696	-0.9934	9	0.02654	T	1	.	4.3132	0.10981	0.1752:0.1037:0.0:0.7211	rs10415562;rs17295872;rs52801034;rs61619364	126	O76099	OR7C1_HUMAN	I	126	ENSP00000248073:V126I	ENSP00000248073:V126I	V	-	1	0	OR7C1	14771573	1.000000	0.71417	0.999000	0.59377	0.052000	0.14988	1.716000	0.37981	0.115000	0.18071	-0.408000	0.06270	GTC	C|0.206;T|0.794	0.794	strong		0.517	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1		
RAB36	9609	hgsc.bcm.edu	37	22	23503121	23503121	+	Silent	SNP	G	G	A	rs5759611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:23503121G>A	ENST00000263116.2	+	10	913	c.873G>A	c.(871-873)tcG>tcA	p.S291S	RAB36_ENST00000341989.4_Silent_p.S269S	NM_004914.2	NP_004905.2	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family	291					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		TCGAGCAGTCGGTGCTGCAGG	0.607													G|||	1138	0.227236	0.0976	0.3501	5008	,	,		20790	0.3413		0.2396	False		,,,				2504	0.1851				p.S291S		Atlas-SNP	.											.	RAB36	26	.	0			c.G873A						PASS	.	G		535,3871	242.5+/-252.5	36,463,1704	80.0	69.0	73.0		873	-11.3	0.3	22	dbSNP_114	73	2217,6383	377.2+/-338.5	288,1641,2371	no	coding-synonymous	RAB36	NM_004914.2		324,2104,4075	AA,AG,GG		25.7791,12.1425,21.1595		291/334	23503121	2752,10254	2203	4300	6503	SO:0001819	synonymous_variant	9609	exon10			GCAGTCGGTGCTG	AB023061	CCDS13805.1	22q11.22	2008-06-11			ENSG00000100228	ENSG00000100228		"""RAB, member RAS oncogene"""	9775	protein-coding gene	gene with protein product		605662				9920784, 10591208	Standard	NM_004914		Approved		uc002zwv.1	O95755	OTTHUMG00000150601	ENST00000263116.2:c.873G>A	22.37:g.23503121G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_004914	Q2M390|Q7Z4A9|Q9UHP5	Silent	SNP	ENST00000263116.2	37	CCDS13805.1																																																																																			G|0.776;A|0.224	0.224	strong		0.607	RAB36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319046.1	NM_004914	
C2orf70	339778	hgsc.bcm.edu	37	2	26800422	26800422	+	Silent	SNP	G	G	A	rs1053807	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:26800422G>A	ENST00000329615.3	+	3	418	c.387G>A	c.(385-387)acG>acA	p.T129T	C2orf70_ENST00000409392.1_Missense_Mutation_p.G117R	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	129						nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						AAGACAAGACGGGCACAGTGC	0.567											OREG0014506	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1709	0.341254	0.2035	0.5821	5008	,	,		20403	0.2183		0.4642	False		,,,				2504	0.3569				p.T129T		Atlas-SNP	.											C2orf70,NS,adenocarcinoma,+1,1	C2orf70	26	1	0			c.G387A						PASS	.	G		998,3174		125,748,1213	96.0	99.0	98.0		387	-10.5	0.0	2	dbSNP_86	98	4018,4402		979,2060,1171	no	coding-synonymous	C2orf70	NM_001105519.1		1104,2808,2384	AA,AG,GG		47.7197,23.9214,39.8348		129/202	26800422	5016,7576	2086	4210	6296	SO:0001819	synonymous_variant	339778	exon3			CAAGACGGGCACA		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"""hypothetical protein LOC339778"""						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.387G>A	2.37:g.26800422G>A		Somatic	78	0	0	789	WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001105519		Silent	SNP	ENST00000329615.3	37	CCDS42661.1	813|813	0.37225274725274726|0.37225274725274726	99|99	0.20121951219512196|0.20121951219512196	217|217	0.5994475138121547|0.5994475138121547	145|145	0.2534965034965035|0.2534965034965035	352|352	0.46437994722955145|0.46437994722955145	G|G	0.031|0.031	-1.334981|-1.334981	0.01287|0.01287	0.239214|0.239214	0.477197|0.477197	ENSG00000173557|ENSG00000173557	ENST00000409392|ENST00000453368	.|.	.|.	.|.	5.27|5.27	-10.5|-10.5	0.00291|0.00291	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.19128|0.19128	-1.0315|-1.0315	4|3	0.87932|.	D|.	0|.	-12.7985|-12.7985	1.084|1.084	0.01648|0.01648	0.2936:0.1433:0.3399:0.2233|0.2936:0.1433:0.3399:0.2233	rs1053807;rs1148955;rs3180971;rs17713753;rs52823718;rs61136298;rs1053807|rs1053807;rs1148955;rs3180971;rs17713753;rs52823718;rs61136298;rs1053807	.|.	.|.	.|.	R|Q	117|30	.|.	ENSP00000386615:G117R|.	G|R	+|+	1|2	0|0	C2orf70|C2orf70	26653926|26653926	0.000000|0.000000	0.05858|0.05858	0.023000|0.023000	0.16930|0.16930	0.003000|0.003000	0.03518|0.03518	-5.452000|-5.452000	0.00121|0.00121	-4.527000|-4.527000	0.00044|0.00044	-3.125000|-3.125000	0.00061|0.00061	GGG|CGG	G|0.621;A|0.379	0.379	strong		0.567	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519	
G6PC2	57818	hgsc.bcm.edu	37	2	169764546	169764546	+	Missense_Mutation	SNP	C	C	G	rs2232328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:169764546C>G	ENST00000375363.3	+	5	1117	c.1025C>G	c.(1024-1026)tCt>tGt	p.S342C	SPC25_ENST00000472216.2_Intron|G6PC2_ENST00000461586.1_3'UTR	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	65	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418194	105418194	+	Silent	SNP	A	A	G	rs78447535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105418194A>G	ENST00000333244.5	-	7	3713	c.3594T>C	c.(3592-3594)agT>agC	p.S1198S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1198						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)			TGGAGGGGAGACTCACGTCGG	0.632													.|||	1264	0.252396	0.0862	0.3012	5008	,	,		16594	0.0714		0.4841	False		,,,				2504	0.3906				p.S1198S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T3594C						PASS	.						130.0	116.0	120.0					14																	105418194		1960	4110	6070	SO:0001819	synonymous_variant	113146	exon7			GGGGAGACTCACG	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.3594T>C	14.37:g.105418194A>G		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.697;G|0.303	0.303	strong		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CCDC146	57639	hgsc.bcm.edu	37	7	76888362	76888362	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:76888362A>G	ENST00000285871.4	+	7	862	c.735A>G	c.(733-735)atA>atG	p.I245M	AC073635.5_ENST00000476561.2_RNA|CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	245										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GAAAAGAGATAGAAAAAATAA	0.363																																					p.I245M		Atlas-SNP	.											CCDC146,NS,carcinoma,0,1	CCDC146	87	1	0			c.A735G						scavenged	.						72.0	66.0	68.0					7																	76888362		2203	4300	6503	SO:0001583	missense	57639	exon7			AGAGATAGAAAAA	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.735A>G	7.37:g.76888362A>G	ENSP00000285871:p.Ile245Met	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	112	2	0.0178571	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	11.53	1.665669	0.29604	.	.	ENSG00000135205	ENST00000285871	T	0.23147	1.92	5.71	1.93	0.25924	.	0.458425	0.25704	N	0.028845	T	0.15219	0.0367	L	0.33485	1.01	0.80722	D	1	B	0.18610	0.029	B	0.17979	0.02	T	0.09596	-1.0667	10	0.41790	T	0.15	-23.9903	2.8406	0.05528	0.5062:0.0:0.1444:0.3493	.	245	Q8IYE0	CC146_HUMAN	M	245	ENSP00000285871:I245M	ENSP00000285871:I245M	I	+	3	3	AC007000.1	76726298	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.522000	0.22909	0.371000	0.24564	0.460000	0.39030	ATA	.	.	none		0.363	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
C10orf11	83938	hgsc.bcm.edu	37	10	78084184	78084184	+	Missense_Mutation	SNP	C	C	T	rs35349706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:78084184C>T	ENST00000372499.1	+	5	673	c.458C>T	c.(457-459)tCc>tTc	p.S153F	C10orf11_ENST00000593699.1_3'UTR|C10orf11_ENST00000496424.2_Missense_Mutation_p.S10F	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	153			S -> F (in dbSNP:rs35349706).		melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					GTTGCCAGCTCCCCGGAGCGC	0.512													C|||	296	0.0591054	0.1248	0.0115	5008	,	,		16701	0.0198		0.0169	False		,,,				2504	0.0879				p.S153F		Atlas-SNP	.											.	C10orf11	19	.	0			c.C458T						PASS	.	C	PHE/SER	399,4007	199.1+/-222.7	18,363,1822	228.0	208.0	215.0		458	4.6	0.1	10	dbSNP_126	215	123,8477	63.1+/-125.2	1,121,4178	yes	missense	C10orf11	NM_032024.3	155	19,484,6000	TT,TC,CC		1.4302,9.0558,4.0135	possibly-damaging	153/199	78084184	522,12484	2203	4300	6503	SO:0001583	missense	83938	exon5			CCAGCTCCCCGGA	AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655			23405	protein-coding gene	gene with protein product	"""oculocutaneous albinism 7, autosomal recessive"""	614537				23395477	Standard	NM_032024		Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.458C>T	10.37:g.78084184C>T	ENSP00000361577:p.Ser153Phe	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	169	88	0.52071	NM_032024	B1AVW6	Missense_Mutation	SNP	ENST00000372499.1	37	CCDS7351.1	77	0.035256410256410256	48	0.0975609756097561	4	0.011049723756906077	10	0.017482517482517484	15	0.01978891820580475	C	13.18	2.158899	0.38119	0.090558	0.014302	ENSG00000148655	ENST00000354343;ENST00000372499	T	0.35605	1.3	5.49	4.59	0.56863	.	0.559655	0.18495	N	0.139525	T	0.01454	0.0047	L	0.50333	1.59	0.24650	N	0.993526	P	0.47484	0.896	P	0.50860	0.652	T	0.00274	-1.1857	10	0.56958	D	0.05	-28.6113	12.6652	0.56837	0.0:0.9235:0.0:0.0765	rs35349706	153	Q9H2I8	CJ011_HUMAN	F	181;153	ENSP00000361577:S153F	ENSP00000346310:S181F	S	+	2	0	C10orf11	77754190	0.995000	0.38212	0.062000	0.19696	0.001000	0.01503	3.203000	0.51075	1.448000	0.47680	0.561000	0.74099	TCC	C|0.961;T|0.039	0.039	strong		0.512	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048839.1	NM_032024	
OR5T2	219464	hgsc.bcm.edu	37	11	56000079	56000079	+	Missense_Mutation	SNP	C	C	T	rs77295387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56000079C>T	ENST00000313264.4	-	1	658	c.583G>A	c.(583-585)Gct>Act	p.A195T		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, 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)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TGTATAGTAGCATGTAAAATG	0.433													c|||	34	0.00678914	0.0015	0.0029	5008	,	,		23389	0.0		0.0268	False		,,,				2504	0.0031				p.A195T		Atlas-SNP	.											.	OR5T2	107	.	0			c.G583A						PASS	.	C	THR/ALA	21,4381	26.2+/-53.5	0,21,2180	193.0	169.0	177.0		583	4.1	0.1	11	dbSNP_131	177	237,8355	96.6+/-158.3	1,235,4060	yes	missense	OR5T2	NM_001004746.1	58	1,256,6240	TT,TC,CC		2.7584,0.4771,1.9855	probably-damaging	195/360	56000079	258,12736	2201	4296	6497	SO:0001583	missense	219464	exon1			TAGTAGCATGTAA	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.583G>A	11.37:g.56000079C>T	ENSP00000323688:p.Ala195Thr	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	255	118	0.462745	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	C	12.15	1.852226	0.32699	0.004771	0.027584	ENSG00000181718	ENST00000313264	T	0.39056	1.1	5.07	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.184659	0.26013	U	0.026862	T	0.23054	0.0557	L	0.41356	1.27	0.09310	N	1	P	0.45986	0.87	P	0.53102	0.718	T	0.11155	-1.0599	10	0.49607	T	0.09	.	12.8779	0.57999	0.3516:0.6484:0.0:0.0	.	195	Q8NGG2	OR5T2_HUMAN	T	195	ENSP00000323688:A195T	ENSP00000323688:A195T	A	-	1	0	OR5T2	55756655	0.000000	0.05858	0.078000	0.20375	0.029000	0.11900	-0.966000	0.03825	1.207000	0.43291	0.478000	0.44815	GCT	C|0.981;T|0.019	0.019	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
FANCA	2175	hgsc.bcm.edu	37	16	89805914	89805914	+	Missense_Mutation	SNP	T	T	C	rs9282681	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89805914T>C	ENST00000389301.3	-	40	4012	c.3982A>G	c.(3982-3984)Acc>Gcc	p.T1328A	ZNF276_ENST00000289816.5_3'UTR|FANCA_ENST00000568369.1_Missense_Mutation_p.T1328A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1328			T -> A (in dbSNP:rs9282681). {ECO:0000269|PubMed:9371798}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AGCAGCCTGGTGTGCTGATCC	0.607			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	362	0.0722843	0.0038	0.0202	5008	,	,		18297	0.2599		0.0646	False		,,,				2504	0.0164				p.T1328A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.A3982G						PASS	.	T	ALA/THR,,	57,4137		0,57,2040	21.0	18.0	19.0		3982,,	-1.7	0.0	16	dbSNP_118	19	579,7621		12,555,3533	yes	missense,utr-3,utr-3	FANCA,ZNF276	NM_000135.2,NM_001113525.1,NM_152287.3	58,,	12,612,5573	CC,CT,TT		7.061,1.3591,5.1315	benign,,	1328/1456,,	89805914	636,11758	2097	4100	6197	SO:0001583	missense	2175	exon40	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GCCTGGTGTGCTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3982A>G	16.37:g.89805914T>C	ENSP00000373952:p.Thr1328Ala	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	182	0.08333333333333333	3	0.006097560975609756	10	0.027624309392265192	119	0.20804195804195805	50	0.06596306068601583	T	1.996	-0.430624	0.04669	0.013591	0.07061	ENSG00000187741	ENST00000389301	D	0.84442	-1.85	5.25	-1.66	0.08265	.	0.642380	0.14965	N	0.288135	T	0.00144	0.0004	L	0.44542	1.39	0.58432	P	6.999999999979245E-6	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.03619	-1.1019	9	0.28530	T	0.3	-7.1655	6.8317	0.23913	0.0:0.3146:0.1159:0.5695	rs9282681;rs11643682;rs17233776;rs9282681	1328;1328	B4DRI7;O15360	.;FANCA_HUMAN	A	1328	ENSP00000373952:T1328A	ENSP00000373952:T1328A	T	-	1	0	FANCA	88333415	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	-1.022000	0.03611	-0.515000	0.06479	-0.408000	0.06270	ACC	T|0.933;C|0.067	0.067	strong		0.607	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
EID2	163126	hgsc.bcm.edu	37	19	40030704	40030704	+	Missense_Mutation	SNP	C	C	T	rs7252027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40030704C>T	ENST00000390658.2	-	1	166	c.16G>A	c.(16-18)Gca>Aca	p.A6T		NM_153232.3	NP_694964.3			EP300 interacting inhibitor of differentiation 2											large_intestine(2)|lung(1)|urinary_tract(1)	4	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;3.2e-25)|all cancers(26;8.83e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			CTGCTGTCTGCGGGCAGCTTG	0.687													.|||	995	0.198682	0.0666	0.1686	5008	,	,		11622	0.244		0.2396	False		,,,				2504	0.3098				p.A6T		Atlas-SNP	.											.	EID2	14	.	0			c.G16A						PASS	.	C	THR/ALA	263,2765		12,239,1263	29.0	33.0	32.0		16	0.2	0.3	19	dbSNP_116	32	1280,5000		127,1026,1987	yes	missense	EID2	NM_153232.3	58	139,1265,3250	TT,TC,CC		20.3822,8.6856,16.5771	possibly-damaging	6/237	40030704	1543,7765	1514	3140	4654	SO:0001583	missense	163126	exon1			TGTCTGCGGGCAG	BC030137	CCDS12540.2	19q13.2	2008-10-24	2006-10-12	2006-10-12	ENSG00000176396	ENSG00000176396			28292	protein-coding gene	gene with protein product		609773	"""CREBBP/EP300 inhibitory protein 2"", ""CREBBP/EP300 inhibitor 2"""	CRI2		14585496	Standard	NM_153232		Approved	EID-2, MGC20452	uc002oma.3	Q8N6I1	OTTHUMG00000074073	ENST00000390658.2:c.16G>A	19.37:g.40030704C>T	ENSP00000375073:p.Ala6Thr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_153232		Missense_Mutation	SNP	ENST00000390658.2	37	CCDS12540.2	443	0.20283882783882784	20	0.04065040650406504	78	0.2154696132596685	149	0.26048951048951047	196	0.25857519788918204	.	17.90	3.503009	0.64298	0.086856	0.203822	ENSG00000176396	ENST00000390658;ENST00000539700	D	0.87412	-2.25	3.64	0.166	0.14999	.	1.449310	0.05067	U	0.480957	T	0.00039	0.0001	L	0.44542	1.39	0.44611	P	0.0024199999999999777	P	0.50710	0.938	B	0.41666	0.363	T	0.04178	-1.0971	9	0.37606	T	0.19	.	3.5746	0.07930	0.0:0.5451:0.2124:0.2426	rs7252027;rs58112765;rs7252027	6	Q8N6I1	EID2_HUMAN	T	6	ENSP00000375073:A6T	ENSP00000375073:A6T	A	-	1	0	EID2	44722544	0.634000	0.27190	0.337000	0.25536	0.424000	0.31475	0.100000	0.15231	0.140000	0.18849	0.485000	0.47835	GCA	C|0.788;T|0.212	0.212	strong		0.687	EID2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157251.1	NM_153232	
BNIP1	662	hgsc.bcm.edu	37	5	172581387	172581387	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:172581387A>G	ENST00000351486.5	+	3	271	c.240A>G	c.(238-240)gaA>gaG	p.E80E	BNIP1_ENST00000352523.6_Silent_p.E123E|BNIP1_ENST00000231668.9_Silent_p.E123E|BNIP1_ENST00000393770.4_Silent_p.E80E	NM_001205.2	NP_001196.2	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 1	80					apoptotic process (GO:0006915)|autophagy (GO:0006914)|endoplasmic reticulum membrane fusion (GO:0016320)|endoplasmic reticulum organization (GO:0007029)|execution phase of apoptosis (GO:0097194)|negative regulation of apoptotic process (GO:0043066)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	11	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TACTCCAGGAAGTGGAGAATC	0.478																																					p.E123E		Atlas-SNP	.											.	BNIP1	30	.	0			c.A369G						PASS	.						68.0	66.0	67.0					5																	172581387		2203	4300	6503	SO:0001819	synonymous_variant	662	exon4			CCAGGAAGTGGAG	AF083957	CCDS4384.1, CCDS4385.1, CCDS4386.1, CCDS43400.1	5q33-q34	2008-02-05	2002-08-29		ENSG00000113734	ENSG00000113734			1082	protein-coding gene	gene with protein product		603291	"""BCL2/adenovirus E1B 19kD-interacting protein 1"""			7954800, 15272311	Standard	NM_013979		Approved	Nip1, SEC20	uc003mcj.4	Q12981	OTTHUMG00000130521	ENST00000351486.5:c.240A>G	5.37:g.172581387A>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	240	119	0.495833	NM_013979	D3DQM3|D3DQM4|D3DQM5|D3DQM6|O75622|O75623|O75624|Q6K044|Q96FG4	Silent	SNP	ENST00000351486.5	37	CCDS4384.1																																																																																			.	.	none		0.478	BNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252939.1	NM_013979	
EPHA2	1969	hgsc.bcm.edu	37	1	16459787	16459787	+	Silent	SNP	C	C	A	rs56043737	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16459787C>A	ENST00000358432.5	-	11	2095	c.1941G>T	c.(1939-1941)acG>acT	p.T647T		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	647	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)	CGGCTTTCAGCGTCTTGATGG	0.612													C|||	35	0.00698882	0.0	0.0144	5008	,	,		18100	0.0		0.0249	False		,,,				2504	0.0				p.T647T		Atlas-SNP	.											EPHA2,colon,carcinoma,-1,1	EPHA2	102	1	0			c.G1941T						PASS	.	C		11,4395	17.9+/-39.9	0,11,2192	96.0	87.0	90.0		1941	-8.0	0.8	1	dbSNP_129	90	132,8468	67.0+/-129.4	0,132,4168	no	coding-synonymous	EPHA2	NM_004431.3		0,143,6360	AA,AC,CC		1.5349,0.2497,1.0995		647/977	16459787	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon11			TTTCAGCGTCTTG	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.1941G>T	1.37:g.16459787C>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			C|0.989;A|0.011	0.011	strong		0.612	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
C1orf106	55765	hgsc.bcm.edu	37	1	200867572	200867572	+	Missense_Mutation	SNP	T	T	A	rs41269923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:200867572T>A	ENST00000367342.4	+	2	499	c.299T>A	c.(298-300)aTc>aAc	p.I100N	C1orf106_ENST00000413687.2_Missense_Mutation_p.I15N	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	100										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						AGTGGCATCATCCTGCAGTCT	0.617													T|||	22	0.00439297	0.0	0.0101	5008	,	,		18319	0.0		0.0149	False		,,,				2504	0.0				p.I114N		Atlas-SNP	.											.	C1orf106	59	.	0			c.T341A						PASS	.	T	ASN/ILE,ASN/ILE	7,4399	12.9+/-30.5	0,7,2196	124.0	106.0	112.0		44,299	5.0	1.0	1	dbSNP_127	112	99,8501	55.2+/-116.2	1,97,4202	yes	missense,missense	C1orf106	NM_001142569.2,NM_018265.3	149,149	1,104,6398	AA,AT,TT		1.1512,0.1589,0.815	probably-damaging,probably-damaging	15/579,100/664	200867572	106,12900	2203	4300	6503	SO:0001583	missense	55765	exon2			GCATCATCCTGCA	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.299T>A	1.37:g.200867572T>A	ENSP00000356311:p.Ile100Asn	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	37		12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	T	20.4	3.991502	0.74703	0.001589	0.011512	ENSG00000163362	ENST00000532631;ENST00000451872;ENST00000367342;ENST00000413687	T;T	0.58358	0.34;0.47	4.97	4.97	0.65823	.	0.128098	0.50627	D	0.000103	T	0.59582	0.2204	L	0.60455	1.87	0.42617	D	0.993332	D	0.71674	0.998	D	0.79784	0.993	T	0.67245	-0.5719	10	0.59425	D	0.04	-13.828	12.1482	0.54036	0.0:0.0:0.0:1.0	rs41269923	100	Q3KP66	CA106_HUMAN	N	15;15;100;15	ENSP00000356311:I100N;ENSP00000392105:I15N	ENSP00000356311:I100N	I	+	2	0	C1orf106	199134195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.875000	0.69660	1.884000	0.54569	0.482000	0.46254	ATC	T|0.993;A|0.007	0.007	strong		0.617	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
PKD1L1	168507	hgsc.bcm.edu	37	7	47968927	47968927	+	Missense_Mutation	SNP	C	C	A	rs2686817	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:47968927C>A	ENST00000289672.2	-	7	984	c.934G>T	c.(934-936)Gtt>Ttt	p.V312F		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	312			V -> F (in dbSNP:rs2686817).		detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GCCATATGAACACGGAATCCC	0.498													C|||	2428	0.484824	0.5136	0.5072	5008	,	,		19692	0.5089		0.505	False		,,,				2504	0.3845				p.V312F		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G934T						PASS	.	C	PHE/VAL	2182,2224	586.2+/-386.4	556,1070,577	156.0	162.0	160.0		934	2.0	0.0	7	dbSNP_100	160	4220,4380	571.8+/-389.6	1029,2162,1109	yes	missense	PKD1L1	NM_138295.3	50	1585,3232,1686	AA,AC,CC		49.0698,49.5234,49.2234	probably-damaging	312/2850	47968927	6402,6604	2203	4300	6503	SO:0001583	missense	168507	exon7			TATGAACACGGAA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.934G>T	7.37:g.47968927C>A	ENSP00000289672:p.Val312Phe	Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	188	187	0.994681	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	1075	0.49221611721611724	230	0.46747967479674796	174	0.48066298342541436	279	0.48776223776223776	392	0.5171503957783641	C	13.77	2.335500	0.41398	0.495234	0.490698	ENSG00000158683	ENST00000289672	T	0.42131	0.98	3.97	2.03	0.26663	.	3.865810	0.00589	N	0.000357	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D	0.89917	1.0	D	0.80764	0.994	T	0.42882	-0.9425	9	0.87932	D	0	-11.5068	5.4202	0.16396	0.0:0.68:0.2049:0.1151	rs2686817;rs2686817	312	Q8TDX9	PK1L1_HUMAN	F	312	ENSP00000289672:V312F	ENSP00000289672:V312F	V	-	1	0	PKD1L1	47935452	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.448000	0.21726	0.395000	0.25257	0.579000	0.79373	GTT	C|0.513;A|0.487	0.487	strong		0.498	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
RNF32	140545	hgsc.bcm.edu	37	7	156469133	156469133	+	Missense_Mutation	SNP	C	C	G	rs2302147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:156469133C>G	ENST00000405335.1	+	10	1282	c.873C>G	c.(871-873)caC>caG	p.H291Q	RNF32_ENST00000311822.8_3'UTR|LMBR1_ENST00000430825.2_5'UTR|RNF32_ENST00000317955.5_Missense_Mutation_p.H291Q|RNF32_ENST00000432459.2_Missense_Mutation_p.H291Q|RNF32_ENST00000392743.2_Missense_Mutation_p.H291Q|RNF32_ENST00000343665.4_Missense_Mutation_p.H267Q			Q9H0A6	RNF32_HUMAN	ring finger protein 32	291			H -> Q (in dbSNP:rs2302147).			aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GGGAGACCCACGAGTGCTCCA	0.617													C|||	2009	0.401158	0.5303	0.4121	5008	,	,		13424	0.4097		0.3479	False		,,,				2504	0.2648				p.H291Q		Atlas-SNP	.											.	RNF32	77	.	0			c.C873G						PASS	.	C	GLN/HIS,GLN/HIS,GLN/HIS	2153,2253	569.4+/-382.6	550,1053,600	38.0	37.0	37.0		873,873,873	-3.8	0.0	7	dbSNP_100	37	2970,5630	451.5+/-362.7	519,1932,1849	no	missense,missense,missense	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	24,24,24	1069,2985,2449	GG,GC,CC		34.5349,48.8652,39.3895	benign,benign,benign	291/363,291/363,291/363	156469133	5123,7883	2203	4300	6503	SO:0001583	missense	140545	exon9			GACCCACGAGTGC		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.873C>G	7.37:g.156469133C>G	ENSP00000385285:p.His291Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001184996	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Missense_Mutation	SNP	ENST00000405335.1	37	CCDS5944.1	911	0.41712454212454214	262	0.532520325203252	134	0.3701657458563536	236	0.4125874125874126	279	0.36807387862796836	C	8.510	0.866371	0.17250	0.488652	0.345349	ENSG00000105982	ENST00000432459;ENST00000317955;ENST00000405335;ENST00000392743;ENST00000343665	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.71	-3.84	0.04256	Zinc finger, RING/FYVE/PHD-type (1);	1.357730	0.04194	N	0.328751	T	0.00012	0.0000	N	0.02315	-0.6	0.09310	P	0.99999542511	B	0.19073	0.033	B	0.11329	0.006	T	0.39522	-0.9610	9	0.27785	T	0.31	0.9631	12.4771	0.55821	0.0:0.2759:0.0:0.7241	rs2302147;rs10372879;rs2302147	291	Q9H0A6	RNF32_HUMAN	Q	291;291;291;291;267	ENSP00000405588:H291Q;ENSP00000315950:H291Q;ENSP00000385285:H291Q;ENSP00000376499:H291Q;ENSP00000341185:H267Q	ENSP00000315950:H291Q	H	+	3	2	RNF32	156161894	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-1.452000	0.02385	-0.967000	0.03582	-0.222000	0.12452	CAC	C|0.601;G|0.399	0.399	strong		0.617	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	
WRAP73	49856	hgsc.bcm.edu	37	1	3548136	3548136	+	Silent	SNP	T	T	C	rs2760321	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	63	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	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		
PKD1L2	114780	hgsc.bcm.edu	37	16	81253745	81253745	+	RNA	SNP	C	C	G	rs9934272	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:81253745C>G	ENST00000525539.1	-	0	230				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						GGGAGATGTGCTTCTGCAGAA	0.567													C|||	1540	0.307508	0.2587	0.3256	5008	,	,		22486	0.4306		0.2903	False		,,,				2504	0.2515				p.K77N		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G231C						PASS	.	C	ASN/LYS,ASN/LYS	1136,2946		165,806,1070	99.0	98.0	99.0		231,231	-0.6	0.9	16	dbSNP_119	99	2294,6096		315,1664,2216	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	94,94	480,2470,3286	GG,GC,CC		27.3421,27.8295,27.5016	possibly-damaging,possibly-damaging	77/992,77/2460	81253745	3430,9042	2041	4195	6236			114780	exon1			GATGTGCTTCTGC	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.81253745C>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		707	0.32371794871794873	127	0.258130081300813	117	0.32320441988950277	231	0.40384615384615385	232	0.30606860158311344	C	11.30	1.598639	0.28445	0.278295	0.273421	ENSG00000166473	ENST00000337114	T	0.17054	2.3	4.03	-0.596	0.11657	C-type lectin fold (1);C-type lectin (3);	0.356714	0.24265	N	0.040050	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.31256	0.091;0.316	B;B	0.32864	0.018;0.154	T	0.49551	-0.8928	8	0.33141	T	0.24	-4.7996	5.3754	0.16162	0.0:0.402:0.147:0.451	rs9934272;rs52827307;rs9934272	77;77	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	N	77	ENSP00000337397:K77N	ENSP00000337397:K77N	K	-	3	2	PKD1L2	79811246	0.365000	0.25006	0.911000	0.35937	0.862000	0.49288	-0.351000	0.07711	0.034000	0.15491	-0.251000	0.11542	AAG	C|0.685;G|0.315	0.315	strong		0.567	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
ATM	472	hgsc.bcm.edu	37	11	108141988	108141988	+	Missense_Mutation	SNP	T	T	C	rs139552233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:108141988T>C	ENST00000452508.2	+	21	3121	c.2932T>C	c.(2932-2934)Tct>Cct	p.S978P	ATM_ENST00000278616.4_Missense_Mutation_p.S978P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	978					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.S978P(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)	CAATGTGTGTTCTTTGTATCG	0.313			"""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)			T|||	3	0.000599042	0.0	0.0	5008	,	,		16164	0.0		0.001	False		,,,				2504	0.002				p.S978P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-2,5	ATM	1657	5	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T2932C						scavenged	.	T	PRO/SER	0,4402		0,0,2201	90.0	88.0	89.0		2932	5.5	1.0	11	dbSNP_134	89	4,8592	3.7+/-12.6	0,4,4294	yes	missense	ATM	NM_000051.3	74	0,4,6495	CC,CT,TT		0.0465,0.0,0.0308	probably-damaging	978/3057	108141988	4,12994	2201	4298	6499	SO:0001583	missense	472	exon20	Familial Cancer Database	AT, Louis-Bar syndrome	GTGTGTTCTTTGT	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.2932T>C	11.37:g.108141988T>C	ENSP00000388058:p.Ser978Pro	Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	24.8	4.565967	0.86439	0.0	4.65E-4	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.74106	-0.81;-0.81;-0.81	5.5	5.5	0.81552	Armadillo-type fold (1);	0.102849	0.64402	D	0.000001	D	0.85388	0.5685	M	0.70275	2.135	0.45567	D	0.998516	D	0.89917	1.0	D	0.87578	0.998	D	0.86822	0.2005	10	0.66056	D	0.02	.	15.8922	0.79309	0.0:0.0:0.0:1.0	.	978	Q13315	ATM_HUMAN	P	978	ENSP00000435747:S978P;ENSP00000278616:S978P;ENSP00000388058:S978P	ENSP00000278616:S978P	S	+	1	0	ATM	107647198	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.434000	0.73408	2.203000	0.70933	0.459000	0.35465	TCT	T|1.000;C|0.000	0.000	strong		0.313	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
AFP	174	hgsc.bcm.edu	37	4	74318177	74318177	+	Silent	SNP	T	T	C	rs35920062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:74318177T>C	ENST00000395792.2	+	12	1588	c.1488T>C	c.(1486-1488)ggT>ggC	p.G496G	AFP_ENST00000226359.2_Silent_p.G496G	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	496	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)			TAAACCCTGGTGTTGGCCAGT	0.453									Alpha-Fetoprotein, Hereditary Persistence of				T|||	128	0.0255591	0.0038	0.0259	5008	,	,		19934	0.0		0.0716	False		,,,				2504	0.0337				p.G496G		Atlas-SNP	.											.	AFP	60	.	0			c.T1488C						PASS	.	T		54,4352	52.9+/-88.7	0,54,2149	137.0	128.0	131.0		1488	-5.2	0.0	4	dbSNP_126	131	549,8051	150.6+/-205.5	24,501,3775	no	coding-synonymous	AFP	NM_001134.1		24,555,5924	CC,CT,TT		6.3837,1.2256,4.6363		496/610	74318177	603,12403	2203	4300	6503	SO:0001819	synonymous_variant	174	exon12	Familial Cancer Database	HPAFP	CCCTGGTGTTGGC	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.1488T>C	4.37:g.74318177T>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	234	118	0.504274	NM_001134	B2RBU3	Silent	SNP	ENST00000395792.2	37	CCDS3556.1																																																																																			T|0.955;C|0.045	0.045	strong		0.453	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3		
TBC1D28	254272	hgsc.bcm.edu	37	17	18542519	18542519	+	Missense_Mutation	SNP	T	T	G	rs74452761		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:18542519T>G	ENST00000345096.4	-	5	866	c.167A>C	c.(166-168)gAg>gCg	p.E56A	TBC1D28_ENST00000575570.1_5'Flank|TBC1D28_ENST00000405044.1_Missense_Mutation_p.E56A			Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28	56				E -> A (in Ref. 1; AAI12013). {ECO:0000305}.			Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(5)|lung(2)|ovary(1)	9						GCGGGGCAGCTCCATCTCACT	0.647																																					p.E56A		Atlas-SNP	.											.	TBC1D28	14	.	0			c.A167C						PASS	.						92.0	101.0	98.0					17																	18542519		2192	4297	6489	SO:0001583	missense	254272	exon6			GGCAGCTCCATCT		CCDS42273.1	17p11.2	2008-10-27			ENSG00000189375	ENSG00000189375			26858	protein-coding gene	gene with protein product							Standard	NM_001039397		Approved	FLJ40244	uc002gud.2	Q2M2D7	OTTHUMG00000059054	ENST00000345096.4:c.167A>C	17.37:g.18542519T>G	ENSP00000339973:p.Glu56Ala	Somatic	538	2	0.00371747		WXS	Illumina HiSeq	Phase_I	362	251	0.69337	NM_001039397	Q2M2E1	Missense_Mutation	SNP	ENST00000345096.4	37	CCDS42273.1	1125	0.5151098901098901	248	0.5040650406504065	183	0.505524861878453	377	0.6590909090909091	317	0.4182058047493404	N	7.143	0.582264	0.13749	.	.	ENSG00000189375	ENST00000345096;ENST00000405044	T;T	0.44881	0.91;0.91	0.418	0.418	0.16429	.	0.321547	0.28187	U	0.016280	T	0.00012	0.0000	M	0.78916	2.43	0.80722	P	0.0	B	0.19331	0.035	B	0.08055	0.003	T	0.36578	-0.9742	8	0.59425	D	0.04	.	.	.	.	.	56	Q2M2D7	TBC28_HUMAN	A	56	ENSP00000339973:E56A;ENSP00000385821:E56A	ENSP00000339973:E56A	E	-	2	0	TBC1D28	18483244	0.334000	0.24739	0.001000	0.08648	0.001000	0.01503	0.493000	0.22451	0.402000	0.25451	0.392000	0.25879	GAG	T|0.485;G|0.515	0.515	strong		0.647	TBC1D28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130672.2	NM_001039397	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54674296	54674296	+	Silent	SNP	A	A	G	rs10471413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54674296A>G	ENST00000230640.5	+	17	2219	c.1965A>G	c.(1963-1965)caA>caG	p.Q655Q	SKIV2L2_ENST00000545714.1_Silent_p.Q554Q	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	655					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				CTTTTCTACAACCAGGTCGTT	0.269													A|||	914	0.182508	0.292	0.0937	5008	,	,		15535	0.2857		0.0974	False		,,,				2504	0.0787				p.Q655Q	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A1965G						PASS	.	A		1014,3390	364.1+/-316.8	114,786,1302	51.0	54.0	53.0		1965	0.4	1.0	5	dbSNP_119	53	850,7742	193.8+/-239.4	43,764,3489	no	coding-synonymous	SKIV2L2	NM_015360.4		157,1550,4791	GG,GA,AA		9.8929,23.0245,14.3429		655/1043	54674296	1864,11132	2202	4296	6498	SO:0001819	synonymous_variant	23517	exon17			TCTACAACCAGGT	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1965A>G	5.37:g.54674296A>G		Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	324	161	0.496914	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	37	CCDS3967.1																																																																																			A|0.841;G|0.159	0.159	strong		0.269	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
EDEM2	55741	hgsc.bcm.edu	37	20	33703607	33703607	+	Missense_Mutation	SNP	C	C	T	rs3746429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:33703607C>T	ENST00000374492.3	-	11	1471	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	SNORD56_ENST00000364281.1_RNA|EDEM2_ENST00000542871.1_Missense_Mutation_p.A180T|EDEM2_ENST00000541621.1_Missense_Mutation_p.A235T|EDEM2_ENST00000374491.3_Missense_Mutation_p.A419T	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	456			A -> T (in dbSNP:rs3746429). {ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|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)			GTGATCACCGCGTCGAAGGTG	0.582													C|||	570	0.113818	0.0045	0.1052	5008	,	,		19848	0.0952		0.1799	False		,,,				2504	0.2188				p.A456T	Esophageal Squamous(51;906 1021 24535 36410 39145)	Atlas-SNP	.											.	EDEM2	46	.	0			c.G1366A						PASS	.	C	THR/ALA,THR/ALA	149,4257	100.7+/-139.4	4,141,2058	66.0	59.0	61.0		1255,1366	-0.3	0.0	20	dbSNP_107	61	1521,7079	287.8+/-298.4	128,1265,2907	yes	missense,missense	EDEM2	NM_001145025.1,NM_018217.2	58,58	132,1406,4965	TT,TC,CC		17.686,3.3818,12.8402	benign,benign	419/542,456/579	33703607	1670,11336	2203	4300	6503	SO:0001583	missense	55741	exon11			TCACCGCGTCGAA	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.1366G>A	20.37:g.33703607C>T	ENSP00000363616:p.Ala456Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	212	99	0.466981	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	37	CCDS13247.1	253	0.11584249084249085	3	0.006097560975609756	40	0.11049723756906077	64	0.11188811188811189	146	0.19261213720316622	C	0.803	-0.754627	0.03041	0.033818	0.17686	ENSG00000088298	ENST00000374491;ENST00000374492;ENST00000541621;ENST00000542871	T;T;T;T	0.56776	0.44;0.44;2.01;2.0	5.51	-0.269	0.12930	.	0.558647	0.20758	N	0.086220	T	0.00039	0.0001	N	0.03608	-0.345	0.58432	P	9.99999999995449E-6	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.08055	0.001;0.002;0.003	T	0.14980	-1.0453	9	0.14656	T	0.56	-0.5186	2.7101	0.05173	0.2015:0.4771:0.0948:0.2265	rs3746429;rs17320275;rs17849471;rs17851384;rs56594383;rs58920275;rs3746429	235;419;456	G3V1Q0;Q9BV94-2;Q9BV94	.;.;EDEM2_HUMAN	T	419;456;235;180	ENSP00000363615:A419T;ENSP00000363616:A456T;ENSP00000443528:A235T;ENSP00000441642:A180T	ENSP00000363615:A419T	A	-	1	0	EDEM2	33167268	0.118000	0.22208	0.008000	0.14137	0.067000	0.16453	0.203000	0.17315	-0.384000	0.07845	-1.267000	0.01435	GCG	C|0.874;T|0.126	0.126	strong		0.582	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217	
MRS2	57380	hgsc.bcm.edu	37	6	24418348	24418348	+	Silent	SNP	G	G	A	rs2793422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:24418348G>A	ENST00000378386.3	+	8	966	c.873G>A	c.(871-873)gaG>gaA	p.E291E	MRS2_ENST00000378353.1_Silent_p.E291E|MRS2_ENST00000543597.1_De_novo_Start_InFrame|MRS2_ENST00000535061.1_Silent_p.E241E|MRS2_ENST00000443868.2_Silent_p.E294E|MRS2_ENST00000274747.7_3'UTR|MRS2_ENST00000483634.1_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	291						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						ATGCAGAAGAGATGGAGTTGC	0.388													G|||	1143	0.228235	0.0923	0.2464	5008	,	,		14391	0.2272		0.3618	False		,,,				2504	0.2628				p.E291E		Atlas-SNP	.											.	MRS2	31	.	0			c.G873A						PASS	.	G		592,3814	261.6+/-264.4	44,504,1655	146.0	132.0	137.0		873	4.3	1.0	6	dbSNP_100	137	3334,5266	497.0+/-374.4	649,2036,1615	no	coding-synonymous	MRS2	NM_020662.2		693,2540,3270	AA,AG,GG		38.7674,13.4362,30.1861		291/444	24418348	3926,9080	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon8			AGAAGAGATGGAG	AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"""MRS2-like, magnesium homeostasis factor (S. cerevisiae)"", ""MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"""	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.873G>A	6.37:g.24418348G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1	505	0.23122710622710624	33	0.06707317073170732	96	0.26519337016574585	111	0.19405594405594406	265	0.3496042216358839	G	10.03	1.237670	0.22711	0.134362	0.387674	ENSG00000124532	ENST00000446191	.	.	.	6.06	4.3	0.51218	.	.	.	.	.	T	0.39436	0.1078	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.32322	-0.9911	3	.	.	.	-21.2535	10.6715	0.45762	0.2184:0.0:0.7816:0.0	rs2793422;rs3736797;rs17305417;rs61074641;rs2793422	.	.	.	K	110	.	.	R	+	2	0	MRS2	24526327	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.113000	0.57851	0.910000	0.36722	-0.245000	0.11935	AGA	G|0.730;A|0.270	0.270	strong		0.388	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
TRIAP1	51499	hgsc.bcm.edu	37	12	120884328	120884328	+	5'Flank	SNP	C	C	T	rs2235217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120884328C>T	ENST00000546954.1	-	0	0				TRIAP1_ENST00000302432.3_5'Flank|AL021546.6_ENST00000551806.1_Intron|GATC_ENST00000551765.1_Silent_p.G15G	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCCTCTGGGCGGGCGCCAGG	0.706													C|||	1299	0.259385	0.0794	0.2579	5008	,	,		14028	0.4901		0.2783	False		,,,				2504	0.2464				p.G15G		Atlas-SNP	.											.	GATC	12	.	0			c.C45T						PASS	.	C		466,3940	217.8+/-236.0	23,420,1760	46.0	52.0	50.0		45	-0.2	0.0	12	dbSNP_98	50	2719,5877	419.6+/-353.1	426,1867,2005	no	coding-synonymous	GATC	NM_176818.2		449,2287,3765	TT,TC,CC		31.631,10.5765,24.4962		15/137	120884328	3185,9817	2203	4298	6501	SO:0001631	upstream_gene_variant	283459	exon1			TCTGGGCGGGCGC		CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"""p53-inducible cell-survival factor"", ""mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"""	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		12.37:g.120884328C>T	Exception_encountered	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_176818	B2R4Z7|Q5RKS5|Q6LCA7	Silent	SNP	ENST00000546954.1	37	CCDS9198.1																																																																																			C|0.744;T|0.256	0.256	strong		0.706	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3	NM_016399	
CELSR2	1952	hgsc.bcm.edu	37	1	109806834	109806834	+	Silent	SNP	C	C	T	rs6698843	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109806834C>T	ENST00000271332.3	+	10	5197	c.5136C>T	c.(5134-5136)ccC>ccT	p.P1712P		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1712	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GCGGGGGGCCCGGCCATGCCA	0.657											OREG0013632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1770	0.353435	0.0764	0.4654	5008	,	,		12448	0.498		0.4751	False		,,,				2504	0.3742				p.P1712P	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C5136T						PASS	.	C		587,3819	247.8+/-255.9	39,509,1655	33.0	48.0	43.0		5136	-9.9	0.7	1	dbSNP_116	43	4016,4584	536.2+/-383.0	938,2140,1222	no	coding-synonymous	CELSR2	NM_001408.2		977,2649,2877	TT,TC,CC		46.6977,13.3227,35.3914		1712/2924	109806834	4603,8403	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon10			GGGGCCCGGCCAT	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.5136C>T	1.37:g.109806834C>T		Somatic	48	0	0	1422	WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			C|0.633;T|0.367	0.367	strong		0.657	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
SIAE	54414	hgsc.bcm.edu	37	11	124539273	124539273	+	Missense_Mutation	SNP	T	T	C	rs12282107	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	161	0	0	1535	WXS	Illumina HiSeq	Phase_I	146	69	0.472603	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	
USH2A	7399	hgsc.bcm.edu	37	1	216595306	216595306	+	Missense_Mutation	SNP	C	C	T	rs10779261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:216595306C>T	ENST00000307340.3	-	2	759	c.373G>A	c.(373-375)Gca>Aca	p.A125T	USH2A_ENST00000366942.3_Missense_Mutation_p.A125T|USH2A_ENST00000366943.2_Missense_Mutation_p.A125T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	125			A -> T (in dbSNP:rs10779261). {ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, 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)		ATAAAACTTGCAGAATTGCTA	0.453										HNSCC(13;0.011)			T|||	3812	0.761182	0.764	0.7089	5008	,	,		19002	0.8125		0.7326	False		,,,				2504	0.771				p.A125T		Atlas-SNP	.											.	USH2A	1168	.	0			c.G373A						PASS	.	T	THR/ALA,THR/ALA	3339,1067	387.9+/-326.7	1253,833,117	97.0	94.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	373,373	-1.4	0.0	1	dbSNP_120	95	6012,2588	420.6+/-353.4	2087,1838,375	yes	missense,missense	USH2A	NM_007123.5,NM_206933.2	58,58	3340,2671,492	TT,TC,CC		30.093,24.217,28.1024	benign,benign	125/1547,125/5203	216595306	9351,3655	2203	4300	6503	SO:0001583	missense	7399	exon2			AACTTGCAGAATT	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.373G>A	1.37:g.216595306C>T	ENSP00000305941:p.Ala125Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	1665	0.7623626373626373	397	0.806910569105691	258	0.712707182320442	458	0.8006993006993007	552	0.7282321899736148	T	6.393	0.440630	0.12104	0.75783	0.69907	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.64438	-0.1;-0.1;-0.1	5.14	-1.4	0.08968	Concanavalin A-like lectin/glucanase (1);	0.808293	0.10384	N	0.681154	T	0.00012	0.0000	N	0.00677	-1.265	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39563	-0.9608	9	0.02654	T	1	.	0.8739	0.01220	0.3718:0.2019:0.0989:0.3274	rs10779261;rs52819716;rs58109158;rs10779261	125;125	O75445-2;O75445	.;USH2A_HUMAN	T	125	ENSP00000305941:A125T;ENSP00000355910:A125T;ENSP00000355909:A125T	ENSP00000305941:A125T	A	-	1	0	USH2A	214661929	0.031000	0.19500	0.001000	0.08648	0.733000	0.41908	0.355000	0.20163	-0.953000	0.03645	-0.332000	0.08345	GCA	C|0.261;T|0.739	0.739	strong		0.453	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
MRC1	4360	hgsc.bcm.edu	37	10	18122716	18122716	+	Silent	SNP	A	A	G	rs111490411		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	287	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	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	
UBC	7316	hgsc.bcm.edu	37	12	125397061	125397061	+	Silent	SNP	G	G	A	rs17840844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:125397061G>A	ENST00000536769.1	-	1	2833	c.1257C>T	c.(1255-1257)gaC>gaT	p.D419D	UBC_ENST00000538617.1_Intron|UBC_ENST00000536661.1_5'Flank|UBC_ENST00000546120.1_Silent_p.D343D|UBC_ENST00000339647.5_Silent_p.D419D			P0CG48	UBC_HUMAN	ubiquitin C	419	Ubiquitin-like 6. {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)			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)		ACCTCTGCTGGTCAGGAGGGA	0.537													G|||	1838	0.367013	0.1657	0.4308	5008	,	,		31861	0.2103		0.5686	False		,,,				2504	0.5481				p.D419D		Atlas-SNP	.											UBC,NS,carcinoma,-2,1	UBC	79	1	0			c.C1257T						scavenged	.						54.0	52.0	53.0					12																	125397061		2150	4211	6361	SO:0001819	synonymous_variant	7316	exon2			CTGCTGGTCAGGA		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		ENST00000536769.1:c.1257C>T	12.37:g.125397061G>A		Somatic	400	1	0.0025		WXS	Illumina HiSeq	Phase_I	495	162	0.327273	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	37	CCDS9260.1																																																																																			G|0.625;A|0.375	0.375	strong		0.537	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009	
GPAM	57678	hgsc.bcm.edu	37	10	113940329	113940329	+	Missense_Mutation	SNP	T	T	C	rs2792751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:113940329T>C	ENST00000348367.4	-	4	324	c.127A>G	c.(127-129)Atc>Gtc	p.I43V	GPAM_ENST00000480130.1_5'UTR|GPAM_ENST00000369425.1_Missense_Mutation_p.I43V|GPAM_ENST00000423155.1_Missense_Mutation_p.I43V			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	43			I -> V (in dbSNP:rs2792751).		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)		GATCTGAAGATGGTGGGTCTA	0.388													C|||	4041	0.806909	0.9561	0.6671	5008	,	,		16776	0.7629		0.6918	False		,,,				2504	0.8681				p.I43V	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.A127G						PASS	.	C	VAL/ILE	4081,325	171.6+/-201.8	1895,291,17	89.0	77.0	81.0		127	2.8	0.2	10	dbSNP_100	81	6076,2524	412.4+/-350.8	2155,1766,379	yes	missense	GPAM	NM_020918.4	29	4050,2057,396	CC,CT,TT		29.3488,7.3763,21.9053	benign	43/829	113940329	10157,2849	2203	4300	6503	SO:0001583	missense	57678	exon4			TGAAGATGGTGGG	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.127A>G	10.37:g.113940329T>C	ENSP00000265276:p.Ile43Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_001244949	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	1653	0.7568681318681318	469	0.9532520325203252	247	0.6823204419889503	421	0.736013986013986	516	0.6807387862796834	C	0.015	-1.553994	0.00918	0.926237	0.706512	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.25749	1.78;1.78;1.78	5.91	2.8	0.32819	.	0.286536	0.33110	N	0.005278	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	0.32534	-0.9903	9	0.02654	T	1	-4.486	4.2806	0.10831	0.2976:0.4174:0.2147:0.0703	rs2792751;rs17256186;rs52805997;rs56676671;rs2792751	43;43	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	V	43	ENSP00000265276:I43V;ENSP00000409242:I43V;ENSP00000358433:I43V	ENSP00000265276:I43V	I	-	1	0	GPAM	113930319	0.888000	0.30383	0.223000	0.23860	0.083000	0.17756	1.587000	0.36622	0.013000	0.14918	-0.119000	0.15052	ATC	T|0.224;C|0.776	0.776	strong		0.388	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
MGME1	92667	hgsc.bcm.edu	37	20	17968923	17968923	+	Silent	SNP	T	T	C	rs28455091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:17968923T>C	ENST00000377710.5	+	4	1134	c.846T>C	c.(844-846)gaT>gaC	p.D282D	MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377709.1_Silent_p.D202D|MGME1_ENST00000377704.4_Intron	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1																		TGAACCATGATACCAACTACA	0.443													C|||	1562	0.311901	0.1823	0.2349	5008	,	,		19600	0.4345		0.2624	False		,,,				2504	0.4663				p.D282D		Atlas-SNP	.											.	.	.	.	0			c.T846C						PASS	.	C		953,3453	735.6+/-410.7	114,725,1364	104.0	93.0	97.0		846	0.7	0.9	20	dbSNP_125	97	2500,6100	695.0+/-404.8	350,1800,2150	no	coding-synonymous	C20orf72	NM_052865.2		464,2525,3514	CC,CT,TT		29.0698,21.6296,26.5493		282/345	17968923	3453,9553	2203	4300	6503	SO:0001819	synonymous_variant	92667	exon4			CCATGATACCAAC		CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871			16205	protein-coding gene	gene with protein product		615076	"""chromosome 20 open reading frame 72"""	C20orf72		23313956, 23358826, 23434322	Standard	NM_052865		Approved	bA504H3.4, DDK1	uc002wqh.3	Q9BQP7	OTTHUMG00000031955	ENST00000377710.5:c.846T>C	20.37:g.17968923T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	37	0.389474	NM_052865		Silent	SNP	ENST00000377710.5	37	CCDS13131.1																																																																																			T|0.732;C|0.268	0.268	strong		0.443	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1	NM_052865	
MC5R	4161	hgsc.bcm.edu	37	18	13826391	13826391	+	Missense_Mutation	SNP	C	C	G	rs2236700	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:13826391C>G	ENST00000324750.3	+	1	849	c.627C>G	c.(625-627)ttC>ttG	p.F209L	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	209			F -> L (in dbSNP:rs2236700). {ECO:0000269|PubMed:11286624, ECO:0000269|PubMed:15489334}.		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						TACACATGTTCCTCCTGGCGC	0.597													C|||	1329	0.265375	0.3154	0.3573	5008	,	,		21468	0.3433		0.172	False		,,,				2504	0.1483				p.F209L		Atlas-SNP	.											.	MC5R	83	.	0			c.C627G						PASS	.	C	LEU/PHE	1304,3102	440.0+/-345.9	207,890,1106	448.0	375.0	400.0		627	3.2	1.0	18	dbSNP_98	400	1537,7063	289.4+/-299.3	138,1261,2901	yes	missense	MC5R	NM_005913.2	22	345,2151,4007	GG,GC,CC		17.8721,29.596,21.8438	probably-damaging	209/326	13826391	2841,10165	2203	4300	6503	SO:0001583	missense	4161	exon1			CATGTTCCTCCTG	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.627C>G	18.37:g.13826391C>G	ENSP00000318077:p.Phe209Leu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	183	105	0.57377	NM_005913	B0YJ34|Q502V1	Missense_Mutation	SNP	ENST00000324750.3	37	CCDS11868.1	593	0.2715201465201465	142	0.2886178861788618	108	0.2983425414364641	214	0.3741258741258741	129	0.17018469656992086	C	18.97	3.736421	0.69189	0.29596	0.178721	ENSG00000176136	ENST00000324750	T	0.34667	1.35	5.01	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.80746	2.51	0.09310	P	0.99999841368	D	0.89917	1.0	D	0.83275	0.996	T	0.41770	-0.9490	9	0.12766	T	0.61	.	10.5883	0.45296	0.0:0.8386:0.0:0.1614	rs2236700;rs17848293;rs2236700	209	P33032	MC5R_HUMAN	L	209	ENSP00000318077:F209L	ENSP00000318077:F209L	F	+	3	2	MC5R	13816391	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	1.790000	0.38734	1.086000	0.41228	0.455000	0.32223	TTC	C|0.764;G|0.236	0.236	strong		0.597	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913	
OR4K17	390436	hgsc.bcm.edu	37	14	20586432	20586432	+	Silent	SNP	C	C	T	rs9323534	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20586432C>T	ENST00000315543.4	+	1	867	c.867C>T	c.(865-867)taC>taT	p.Y289Y		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		TCTTTATCTACATTTGGCCCT	0.423													T|||	2369	0.473043	0.3873	0.4424	5008	,	,		18583	0.5823		0.4433	False		,,,				2504	0.5286				p.Y289Y		Atlas-SNP	.											.	OR4K17	58	.	0			c.C867T						PASS	.	T		1829,2577		385,1059,759	107.0	97.0	100.0		867	-5.7	0.0	14	dbSNP_119	100	3778,4822		830,2118,1352	no	coding-synonymous	OR4K17	NM_001004715.1		1215,3177,2111	TT,TC,CC		43.9302,41.5116,43.1109		289/344	20586432	5607,7399	2203	4300	6503	SO:0001819	synonymous_variant	390436	exon1			TATCTACATTTGG		CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"""GPCR / Class A : Olfactory receptors"""	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.867C>T	14.37:g.20586432C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	169	83	0.491124	NM_001004715	Q6IF12	Silent	SNP	ENST00000315543.4	37	CCDS32030.1																																																																																			C|0.566;T|0.434	0.434	strong		0.423	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1		
EML2	24139	hgsc.bcm.edu	37	19	46141845	46141845	+	Missense_Mutation	SNP	T	T	C	rs12151009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46141845T>C	ENST00000245925.3	-	3	147	c.97A>G	c.(97-99)Atg>Gtg	p.M33V	EML2_ENST00000589876.1_Missense_Mutation_p.M33V|EML2_ENST00000536630.1_Missense_Mutation_p.M180V|EML2_ENST00000587152.1_Missense_Mutation_p.M234V|MIR330_ENST00000362196.1_RNA	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	33	Tandem atypical propeller in EMLs. {ECO:0000250}.		M -> V (in dbSNP:rs12151009).		negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		TCTGGGATCATCATGGGCACA	0.607													T|||	431	0.0860623	0.0061	0.1196	5008	,	,		15465	0.1032		0.1103	False		,,,				2504	0.1278				p.M234V		Atlas-SNP	.											.	EML2	64	.	0			c.A700G						PASS	.		VAL/MET,VAL/MET,VAL/MET	122,4284	89.7+/-128.4	3,116,2084	73.0	67.0	69.0		97,538,700	-4.5	0.9	19	dbSNP_120	69	1138,7462	234.3+/-267.3	81,976,3243	yes	missense,missense,missense	EML2	NM_012155.2,NM_001193269.1,NM_001193268.1	21,21,21	84,1092,5327	CC,CT,TT		13.2326,2.769,9.6878	benign,benign,benign	33/650,180/797,234/851	46141845	1260,11746	2203	4300	6503	SO:0001583	missense	24139	exon6			GGATCATCATGGG	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.97A>G	19.37:g.46141845T>C	ENSP00000245925:p.Met33Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	179	0.08195970695970696	3	0.006097560975609756	44	0.12154696132596685	53	0.09265734265734266	79	0.10422163588390501	T	15.12	2.739504	0.49045	0.02769	0.132326	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.26957	1.7;1.7;1.7	4.6	-4.54	0.03452	HELP (1);	0.462809	0.21249	N	0.077664	T	0.00144	0.0004	N	0.22421	0.69	0.54753	P	2.0000000000020002E-5	B;B;B;B;B	0.21821	0.061;0.001;0.001;0.03;0.001	B;B;B;B;B	0.29440	0.102;0.016;0.01;0.034;0.027	T	0.16217	-1.0410	9	0.66056	D	0.02	-5.0507	3.8011	0.08758	0.3982:0.0:0.2021:0.3996	rs12151009;rs57737116;rs12151009	33;199;180;191;33	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	V	180;33;234;191	ENSP00000442365:M180V;ENSP00000245925:M33V;ENSP00000382503:M191V	ENSP00000245925:M33V	M	-	1	0	EML2	50833685	1.000000	0.71417	0.929000	0.37066	0.932000	0.56968	1.910000	0.39927	-0.283000	0.09115	-0.889000	0.02933	ATG	T|0.908;C|0.092	0.092	strong		0.607	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
C19orf48	84798	hgsc.bcm.edu	37	19	51301395	51301395	+	Missense_Mutation	SNP	C	C	T	rs4801853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51301395C>T	ENST00000598463.1	-	5	1409	c.311G>A	c.(310-312)gGg>gAg	p.G104E	C19orf48_ENST00000391812.1_Missense_Mutation_p.G104E|SNORD88B_ENST00000408454.1_RNA|C19orf48_ENST00000596655.1_Missense_Mutation_p.G104E|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000595794.1_5'Flank|C19orf48_ENST00000345523.4_Missense_Mutation_p.G104E			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48	104			G -> E (in dbSNP:rs4801853).							endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		CTGCTTCACCCCTGGAGCACC	0.617													c|||	1652	0.329872	0.1309	0.2161	5008	,	,		21442	0.6538		0.3012	False		,,,				2504	0.3753				p.G104E		Atlas-SNP	.											.	C19orf48	11	.	0			c.G311A						PASS	.	T	GLU/GLY,GLU/GLY	680,3726	290.4+/-280.9	45,590,1568	87.0	89.0	88.0		311,311	-2.2	0.0	19	dbSNP_111	88	2413,6187	397.0+/-345.6	350,1713,2237	yes	missense,missense	C19orf48	NM_199249.1,NM_199250.1	98,98	395,2303,3805	TT,TC,CC		28.0581,15.4335,23.7813	probably-damaging,probably-damaging	104/118,104/118	51301395	3093,9913	2203	4300	6503	SO:0001583	missense	84798	exon5			TTCACCCCTGGAG	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"""multidrug resistance-related protein"""					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		ENST00000598463.1:c.311G>A	19.37:g.51301395C>T	ENSP00000471463:p.Gly104Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	95	58	0.610526	NM_199249		Missense_Mutation	SNP	ENST00000598463.1	37	CCDS12803.1	769	0.35210622710622713	71	0.1443089430894309	80	0.22099447513812154	383	0.6695804195804196	235	0.3100263852242744	c	3.466	-0.108946	0.06924	0.154335	0.280581	ENSG00000167747	ENST00000391812;ENST00000345523	T;T	0.35048	1.33;1.33	1.67	-2.21	0.06973	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.55172	0.97	B	0.41332	0.354	T	0.41645	-0.9497	8	0.87932	D	0	.	2.7674	0.05324	0.0:0.4002:0.2503:0.3495	rs4801853;rs17657787;rs58154692;rs4801853	104	Q6RUI8	CS048_HUMAN	E	104	ENSP00000375688:G104E;ENSP00000301419:G104E	ENSP00000301419:G104E	G	-	2	0	C19orf48	55993207	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.508000	0.06344	-0.483000	0.06772	-0.215000	0.12644	GGG	C|0.714;N|0.001	.	strong		0.617	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712	
RYR3	6263	hgsc.bcm.edu	37	15	33842400	33842400	+	Silent	SNP	A	A	T	rs41279202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33842400A>T	ENST00000389232.4	+	10	925	c.855A>T	c.(853-855)cgA>cgT	p.R285R	RYR3_ENST00000415757.3_Silent_p.R285R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	285	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGGCTTTCCGACTCCGGCATC	0.483													A|||	68	0.0135783	0.0	0.0187	5008	,	,		17879	0.001		0.0447	False		,,,				2504	0.0092				p.R285R		Atlas-SNP	.											.	RYR3	760	.	0			c.A855T						PASS	.	A		34,4350	34.3+/-65.2	0,34,2158	40.0	42.0	41.0		855	-1.1	1.0	15	dbSNP_127	41	369,8219	120.2+/-179.5	8,353,3933	no	coding-synonymous	RYR3	NM_001036.3		8,387,6091	TT,TA,AA		4.2967,0.7755,3.1067		285/4871	33842400	403,12569	2192	4294	6486	SO:0001819	synonymous_variant	6263	exon10			TTTCCGACTCCGG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.855A>T	15.37:g.33842400A>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.970;T|0.030	0.030	strong		0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
TMEM216	51259	hgsc.bcm.edu	37	11	61161359	61161359	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:61161359T>C	ENST00000515837.2	+	3	1085	c.140T>C	c.(139-141)gTc>gCc	p.V47A	TMEM216_ENST00000398979.3_5'UTR|TMEM216_ENST00000334888.5_Missense_Mutation_p.V47A			Q9P0N5	TM216_HUMAN	transmembrane protein 216	47					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				endometrium(1)|large_intestine(2)|lung(1)|prostate(2)	6						TTGGCAGGTGTCCTGCTACCA	0.433																																					p.V47A		Atlas-SNP	.											.	TMEM216	14	.	0			c.T140C						PASS	.						84.0	93.0	90.0					11																	61161359		1968	4156	6124	SO:0001583	missense	51259	exon3			CAGGTGTCCTGCT		CCDS53640.1	11q13.1	2014-09-17			ENSG00000187049	ENSG00000187049			25018	protein-coding gene	gene with protein product		613277	"""cerebello-oculo-renal syndrome 2"", ""Meckel syndrome, type 2"""	CORS2, MKS2		11042152, 20036350, 20512146	Standard	NM_016499		Approved	MGC13379, HSPC244, JBTS2	uc021qkf.1	Q9P0N5		ENST00000515837.2:c.140T>C	11.37:g.61161359T>C	ENSP00000440638:p.Val47Ala	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	231	91	0.393939	NM_001173990	A8MZ23|B7Z8N1	Missense_Mutation	SNP	ENST00000515837.2	37	CCDS53640.1	.	.	.	.	.	.	.	.	.	.	T	7.289	0.610705	0.14066	.	.	ENSG00000187049	ENST00000515837;ENST00000334888	D;D	0.88124	-2.34;-2.34	5.95	5.95	0.96441	.	.	.	.	.	T	0.77212	0.4097	N	0.14661	0.345	0.28495	N	0.914285	B	0.11235	0.004	B	0.12837	0.008	T	0.63229	-0.6684	9	0.15499	T	0.54	.	13.9469	0.64091	0.0:0.0:0.0:1.0	.	40	Q9P0N5	TM216_HUMAN	A	47	ENSP00000440638:V47A;ENSP00000334844:V47A	ENSP00000334844:V47A	V	+	2	0	TMEM216	60917935	0.988000	0.35896	0.929000	0.37066	0.003000	0.03518	3.612000	0.54142	2.279000	0.76181	0.533000	0.62120	GTC	.	.	none		0.433	TMEM216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398430.1	NM_016499	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14752957	14752957	+	Silent	SNP	G	G	A	rs12457503	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:14752957G>A	ENST00000358984.4	+	3	636	c.456G>A	c.(454-456)ttG>ttA	p.L152L	ANKRD30B_ENST00000447268.2_Silent_p.L152L|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	152										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						GTGAGAATTTGTTAATGGTGG	0.383													G|||	2604	0.519968	0.5068	0.6124	5008	,	,		15940	0.5883		0.4513	False		,,,				2504	0.4724				p.L152L		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,+2,2	ANKRD30B	237	2	0			c.G456A						PASS	.	G		681,703		164,353,175	178.0	158.0	164.0		456	-3.2	0.0	18	dbSNP_120	164	1533,1649		354,825,412	yes	coding-synonymous	ANKRD30B	NM_001145029.1		518,1178,587	AA,AG,GG		48.1772,49.2052,48.4888		152/1393	14752957	2214,2352	692	1591	2283	SO:0001819	synonymous_variant	374860	exon3			GAATTTGTTAATG	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.456G>A	18.37:g.14752957G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																			G|0.493;A|0.507	0.507	strong		0.383	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
ITGA1	3672	hgsc.bcm.edu	37	5	52214581	52214581	+	Missense_Mutation	SNP	G	G	A	rs2279587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:52214581G>A	ENST00000282588.6	+	16	2466	c.2008G>A	c.(2008-2010)Gtt>Att	p.V670I		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	670			V -> I (in dbSNP:rs2279587).		activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)	p.V670I(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TGTGGCCGTAGTTAAAGTGAC	0.373													G|||	489	0.0976438	0.0182	0.2709	5008	,	,		17535	0.1548		0.0616	False		,,,				2504	0.0603				p.V670I		Atlas-SNP	.											ITGA1,NS,carcinoma,0,1	ITGA1	112	1	1	Substitution - Missense(1)	stomach(1)	c.G2008A						PASS	.	G	ILE/VAL	141,4265	98.5+/-137.1	0,141,2062	119.0	105.0	110.0		2008	5.5	1.0	5	dbSNP_100	110	546,8052	150.6+/-205.5	18,510,3771	yes	missense	ITGA1	NM_181501.1	29	18,651,5833	AA,AG,GG		6.3503,3.2002,5.283	benign	670/1180	52214581	687,12317	2203	4299	6502	SO:0001583	missense	3672	exon16			GCCGTAGTTAAAG	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"""CD molecules"", ""Integrins"""	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.2008G>A	5.37:g.52214581G>A	ENSP00000282588:p.Val670Ile	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	150	76	0.506667	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	37	CCDS3955.1	220	0.10073260073260074	12	0.024390243902439025	70	0.19337016574585636	90	0.15734265734265734	48	0.0633245382585752	G	15.38	2.817003	0.50633	0.032002	0.063503	ENSG00000213949	ENST00000282588	T	0.38722	1.12	5.51	5.51	0.81932	Integrin alpha-2 (1);	0.128298	0.53938	D	0.000051	T	0.00073	0.0002	L	0.39397	1.21	0.26078	P	0.9811302	P	0.40578	0.722	P	0.48400	0.576	T	0.05784	-1.0864	9	0.19147	T	0.46	.	13.0533	0.58966	0.0737:0.0:0.9263:0.0	rs2279587;rs56692098;rs2279587	670	P56199	ITA1_HUMAN	I	670	ENSP00000282588:V670I	ENSP00000282588:V670I	V	+	1	0	ITGA1	52250338	0.993000	0.37304	1.000000	0.80357	0.998000	0.95712	1.855000	0.39378	2.738000	0.93877	0.655000	0.94253	GTT	G|0.928;A|0.072	0.072	strong		0.373	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501	
MYO19	80179	hgsc.bcm.edu	37	17	34854280	34854280	+	Missense_Mutation	SNP	G	G	A	rs2306590	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:34854280G>A	ENST00000431794.3	-	25	3109	c.2587C>T	c.(2587-2589)Ctc>Ttc	p.L863F	ZNHIT3_ENST00000588253.1_3'UTR|MYO19_ENST00000268852.9_Missense_Mutation_p.L663F	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	863	Mitochondrial targeting.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.L863F(1)		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)		AGGGGCCAGAGGCGGATTATT	0.582													G|||	1285	0.256589	0.0295	0.2925	5008	,	,		18386	0.3462		0.3946	False		,,,				2504	0.3037				p.L863F		Atlas-SNP	.											MYO19_ENST00000431794,NS,carcinoma,0,1	MYO19	130	1	1	Substitution - Missense(1)	stomach(1)	c.C2587T						PASS	.	G	PHE/LEU,PHE/LEU	294,3554		13,268,1643	84.0	83.0	84.0		2587,1987	1.8	0.4	17	dbSNP_100	84	3459,4797		718,2023,1387	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	22,22	731,2291,3030	AA,AG,GG		41.8968,7.6403,31.0063	benign,benign	863/971,663/771	34854280	3753,8351	1924	4128	6052	SO:0001583	missense	80179	exon26			GCCAGAGGCGGAT	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.2587C>T	17.37:g.34854280G>A	ENSP00000409936:p.Leu863Phe	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	53	0.540816	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	648	0.2967032967032967	22	0.044715447154471545	107	0.2955801104972376	221	0.38636363636363635	298	0.39313984168865435	G	10.96	1.499610	0.26861	0.076403	0.418968	ENSG00000141140	ENST00000415126;ENST00000431794;ENST00000268852	T;T	0.74209	-0.82;-0.82	5.91	1.75	0.24633	.	0.195325	0.25261	N	0.031945	T	0.00012	0.0000	L	0.39633	1.23	0.44234	P	0.002927000000000013	B;B	0.14805	0.007;0.011	B;B	0.14578	0.005;0.011	T	0.27020	-1.0086	9	0.07030	T	0.85	.	9.0125	0.36150	0.3407:0.0:0.6593:0.0	rs2306590;rs3169822;rs52822111;rs61306860;rs2306590	863;663	Q96H55;Q96H55-4	MYO19_HUMAN;.	F	321;863;663	ENSP00000409936:L863F;ENSP00000268852:L663F	ENSP00000268852:L663F	L	-	1	0	MYO19	31928393	0.993000	0.37304	0.364000	0.25888	0.767000	0.43475	1.305000	0.33493	0.139000	0.18822	0.485000	0.47835	CTC	G|0.695;A|0.305	0.305	strong		0.582	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
KRT37	8688	hgsc.bcm.edu	37	17	39580562	39580562	+	Missense_Mutation	SNP	T	T	C	rs9916484	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39580562T>C	ENST00000225550.3	-	1	213	c.214A>G	c.(214-216)Acc>Gcc	p.T72A	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	72	Head.		T -> A (in dbSNP:rs9916484).			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)				GTGTGACTGGTTGGGGGCAGA	0.612													T|||	1960	0.391374	0.1846	0.3415	5008	,	,		21245	0.4067		0.4592	False		,,,				2504	0.6207				p.T72A		Atlas-SNP	.											.	KRT37	61	.	0			c.A214G						PASS	.	T	ALA/THR	985,3421		111,763,1329	48.0	45.0	46.0		214	4.7	0.5	17	dbSNP_119	46	4175,4425		1020,2135,1145	no	missense	KRT37	NM_003770.4	58	1131,2898,2474	CC,CT,TT		48.5465,22.3559,39.674	benign	72/450	39580562	5160,7846	2203	4300	6503	SO:0001583	missense	8688	exon1			GACTGGTTGGGGG	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.214A>G	17.37:g.39580562T>C	ENSP00000225550:p.Thr72Ala	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	812	0.3717948717948718	101	0.20528455284552846	145	0.4005524861878453	227	0.3968531468531469	339	0.4472295514511873	.	9.918	1.211427	0.22289	0.223559	0.485465	ENSG00000108417	ENST00000225550	T	0.81247	-1.47	4.69	4.69	0.59074	.	0.207707	0.33938	N	0.004415	T	0.00012	0.0000	L	0.29908	0.895	0.45883	P	0.0012670000000000181	B	0.16802	0.019	B	0.09377	0.004	T	0.35599	-0.9782	9	0.51188	T	0.08	.	12.0874	0.53706	0.0:0.0:0.0:1.0	rs9916484;rs59543665;rs9916484	72	O76014	KRT37_HUMAN	A	72	ENSP00000225550:T72A	ENSP00000225550:T72A	T	-	1	0	KRT37	36834088	0.311000	0.24536	0.517000	0.27799	0.004000	0.04260	0.986000	0.29590	1.760000	0.52011	0.533000	0.62120	ACC	T|0.611;C|0.389	0.389	strong		0.612	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
ETV7	51513	hgsc.bcm.edu	37	6	36341294	36341294	+	Silent	SNP	C	C	T	rs3213530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:36341294C>T	ENST00000340181.4	-	4	610	c.369G>A	c.(367-369)ggG>ggA	p.G123G	ETV7_ENST00000373738.1_Silent_p.G68G|ETV7_ENST00000339796.5_Silent_p.G123G|ETV7_ENST00000538992.1_5'UTR|ETV7_ENST00000373737.4_Silent_p.G123G	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	123					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						CAAAAAAGGGCCCACACACCA	0.627													C|||	1094	0.21845	0.2179	0.3415	5008	,	,		11130	0.2391		0.1501	False		,,,				2504	0.181				p.G123G		Atlas-SNP	.											.	ETV7	31	.	0			c.G369A						PASS	.	C	,,,,,,,	871,3531		87,697,1417	28.0	25.0	26.0		369,204,192,369,204,126,,369	-2.0	0.1	6	dbSNP_106	26	1331,7267		105,1121,3073	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-5,coding-synonymous	ETV7	NM_001207035.1,NM_001207036.1,NM_001207037.1,NM_001207038.1,NM_001207039.1,NM_001207040.1,NM_001207041.1,NM_016135.3	,,,,,,,	192,1818,4490	TT,TC,CC		15.4803,19.7865,16.9385	,,,,,,,	123/318,68/287,64/283,123/265,68/263,42/261,,123/342	36341294	2202,10798	2201	4299	6500	SO:0001819	synonymous_variant	51513	exon4			AAAGGGCCCACAC	AF116508	CCDS4819.1, CCDS56422.1, CCDS56423.1, CCDS56424.1, CCDS56425.1, CCDS75440.1, CCDS75441.1	6p21	2008-09-12	2008-09-12		ENSG00000010030	ENSG00000010030			18160	protein-coding gene	gene with protein product	"""TEL2 oncogene"""	605255	"""ets variant gene 7 (TEL2 oncogene)"""			10828014, 11108721	Standard	NM_016135		Approved	TEL2, TEL-2	uc003omb.3	Q9Y603	OTTHUMG00000014594	ENST00000340181.4:c.369G>A	6.37:g.36341294C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Silent	SNP	ENST00000340181.4	37	CCDS4819.1																																																																																			C|0.813;T|0.187	0.187	strong		0.627	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
C2orf91	400950	hgsc.bcm.edu	37	2	42165754	42165754	+	Splice_Site	SNP	C	C	T	rs10192292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	160	0	0		WXS	Illumina HiSeq	Phase_I	169	97	0.573964	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
NBEAL2	23218	hgsc.bcm.edu	37	3	47043538	47043538	+	Silent	SNP	C	C	T	rs2305634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47043538C>T	ENST00000450053.3	+	31	5090	c.4911C>T	c.(4909-4911)tcC>tcT	p.S1637S	NBEAL2_ENST00000292309.5_Silent_p.S1453S|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1637					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		ACACCTCTTCCTTGGAGTCAG	0.652													C|||	2362	0.471645	0.2383	0.5216	5008	,	,		18720	0.5387		0.5865	False		,,,				2504	0.5644				p.S1637S		Atlas-SNP	.											NBEAL2_ENST00000450053,NS,carcinoma,0,4	NBEAL2	267	4	0			c.C4911T						scavenged	.	C		1134,3064		214,706,1179	6.0	7.0	7.0		4911	-5.6	0.0	3	dbSNP_100	7	4527,3787		1331,1865,961	no	coding-synonymous	NBEAL2	NM_015175.1		1545,2571,2140	TT,TC,CC		45.5497,27.0129,45.2446		1637/2755	47043538	5661,6851	2099	4157	6256	SO:0001819	synonymous_variant	23218	exon31			CTCTTCCTTGGAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4911C>T	3.37:g.47043538C>T		Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	1089|1089	0.49862637362637363|0.49862637362637363	143|143	0.29065040650406504|0.29065040650406504	197|197	0.5441988950276243|0.5441988950276243	305|305	0.5332167832167832|0.5332167832167832	444|444	0.5857519788918206|0.5857519788918206	C|C	0.102|0.102	-1.151030|-1.151030	0.01700|0.01700	0.270129|0.270129	0.544503|0.544503	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.62|4.62	-5.57|-5.57	0.02521|0.02521	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45190|0.45190	-0.9278|-0.9278	3|3	.|.	.|.	.|.	.|.	3.3322|3.3322	0.07088|0.07088	0.1082:0.3229:0.1069:0.4621|0.1082:0.3229:0.1069:0.4621	rs2305634;rs17223724;rs2305634|rs2305634;rs17223724;rs2305634	.|.	.|.	.|.	F|L	6|925	.|.	.|.	L|P	+|+	1|2	0|0	NBEAL2|NBEAL2	47018542|47018542	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.150000|0.150000	0.21749|0.21749	-1.477000|-1.477000	0.02331|0.02331	-1.080000|-1.080000	0.03109|0.03109	-0.145000|-0.145000	0.13849|0.13849	CTT|CCT	C|0.518;G|0.000;T|0.481	0.481	strong		0.652	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
KIRREL2	84063	hgsc.bcm.edu	37	19	36349736	36349736	+	Silent	SNP	G	G	C	rs34006827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36349736G>C	ENST00000360202.5	+	4	690	c.492G>C	c.(490-492)ggG>ggC	p.G164G	KIRREL2_ENST00000347900.6_Silent_p.G114G|KIRREL2_ENST00000262625.7_Silent_p.G164G|KIRREL2_ENST00000592409.1_Silent_p.G164G|NPHS1_ENST00000591817.1_Intron	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	227	0	0		WXS	Illumina HiSeq	Phase_I	237	97	0.409283	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	
FGF6	2251	hgsc.bcm.edu	37	12	4554413	4554413	+	Silent	SNP	C	C	T	rs11611403	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4554413C>T	ENST00000228837.2	-	1	367	c.324G>A	c.(322-324)ggG>ggA	p.G108G		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	108					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)			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)			CCTCGTGGGTCCCGCTGATCC	0.632													C|||	777	0.155152	0.3018	0.1196	5008	,	,		16677	0.0129		0.1451	False		,,,				2504	0.1391				p.G108G		Atlas-SNP	.											.	FGF6	40	.	0			c.G324A						PASS	.	C		1169,3237		163,843,1197	27.0	27.0	27.0		324	-2.6	0.8	12	dbSNP_120	27	1380,7220		129,1122,3049	no	coding-synonymous	FGF6	NM_020996.1		292,1965,4246	TT,TC,CC		16.0465,26.532,19.5986		108/209	4554413	2549,10457	2203	4300	6503	SO:0001819	synonymous_variant	2251	exon1			GTGGGTCCCGCTG	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.324G>A	12.37:g.4554413C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_020996	Q0VAE1	Silent	SNP	ENST00000228837.2	37	CCDS8527.1																																																																																			C|0.833;T|0.167	0.167	strong		0.632	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
TKT	7086	hgsc.bcm.edu	37	3	53269046	53269046	+	Silent	SNP	T	T	C	rs1051485|rs200778000	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:53269046T>C	ENST00000462138.1	-	5	670	c.582A>G	c.(580-582)ccA>ccG	p.P194P	TKT_ENST00000296289.6_Silent_p.P147P|TKT_ENST00000423525.2_Silent_p.P194P|TKT_ENST00000423516.1_Silent_p.P202P|TKT_ENST00000461139.1_5'Flank			P29401	TKT_HUMAN	transketolase	194					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		GGTGCTGCAGTGGGGCCGGGT	0.592													C|||	880	0.175719	0.1165	0.1427	5008	,	,		15418	0.1567		0.168	False		,,,				2504	0.3067				p.P202P	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.A606G						PASS	.	C	,	664,3742	764.2+/-413.3	55,554,1594	86.0	88.0	88.0		582,582	-11.1	0.0	3	dbSNP_86	88	1662,6938	740.5+/-407.1	161,1340,2799	no	coding-synonymous,coding-synonymous	TKT	NM_001064.3,NM_001135055.2	,	216,1894,4393	CC,CT,TT		19.3256,15.0704,17.8841	,	194/624,194/624	53269046	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	7086	exon6			CTGCAGTGGGGCC		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"""Wernicke-Korsakoff syndrome"""	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.582A>G	3.37:g.53269046T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	37	CCDS2871.1																																																																																			T|0.837;C|0.163	0.163	strong		0.592	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
CCL4	6351	hgsc.bcm.edu	37	17	34432664	34432664	+	Missense_Mutation	SNP	T	T	A	rs1719152|rs386796798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:34432664T>A	ENST00000250151.4	+	3	554	c.238T>A	c.(238-240)Tcc>Acc	p.S80T	CCL4_ENST00000394495.1_Missense_Mutation_p.N41K	NM_002984.2	NP_002975.1	P13236	CCL4_HUMAN	chemokine (C-C motif) ligand 4	80			S -> T (in dbSNP:rs1719152). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2809212}.		cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|establishment or maintenance of cell polarity (GO:0007163)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of natural killer cell chemotaxis (GO:2000503)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemokine activity (GO:0008009)|cytokine activity (GO:0005125)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(1)|lung(2)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCCCAGTGAATCCTGGGTCCA	0.498													A|||	898	0.179313	0.0492	0.1182	5008	,	,		21017	0.2758		0.2485	False		,,,				2504	0.228				p.S80T	Colon(139;824 1752 21188 21615 24765)	Atlas-SNP	.											.	CCL4	14	.	0			c.T238A						PASS	.	A	THR/SER	14,4392		3,8,2192	199.0	183.0	188.0		238	-10.1	0.7	17	dbSNP_89	188	113,8487		33,47,4220	no	missense	CCL4	NM_002984.2	58	36,55,6412	AA,AT,TT		1.314,0.3177,0.9765	benign	80/93	34432664	127,12879	2203	4300	6503	SO:0001583	missense	6351	exon3			AGTGAATCCTGGG	M23502	CCDS11308.1	17q21-q23	2014-05-06	2002-08-22	2002-08-23	ENSG00000129277	ENSG00000275302		"""Chemokine ligands"", ""Endogenous ligands"""	10630	protein-coding gene	gene with protein product		182284	"""small inducible cytokine A4 (homologous to mouse Mip-1b)"""	LAG1, SCYA4		1972563	Standard	NM_002984		Approved	MIP-1-beta, Act-2, AT744.1	uc002hkw.1	P13236	OTTHUMG00000188414	ENST00000250151.4:c.238T>A	17.37:g.34432664T>A	ENSP00000250151:p.Ser80Thr	Somatic	437	1	0.00228833		WXS	Illumina HiSeq	Phase_I	450	241	0.535556	NM_002984	P22617|Q13704|Q3SXL8|Q6FGI8	Missense_Mutation	SNP	ENST00000250151.4	37	CCDS11308.1	314|314	0.14377289377289376|0.14377289377289376	13|13	0.026422764227642278|0.026422764227642278	43|43	0.11878453038674033|0.11878453038674033	122|122	0.21328671328671328|0.21328671328671328	136|136	0.17941952506596306|0.17941952506596306	.|.	0.132|0.132	-1.112281|-1.112281	0.01799|0.01799	0.003177|0.003177	0.01314|0.01314	ENSG00000129277|ENSG00000129277	ENST00000394495|ENST00000250151	T|T	0.71698|0.04551	-0.59|3.6	5.03|5.03	-10.1|-10.1	0.00402|0.00402	.|Chemokine interleukin-8-like domain (3);	.|0.947069	.|0.08503	.|N	.|0.936124	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.50813|0.50813	P|P	1.020000000000465E-4|1.020000000000465E-4	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.40098|0.40098	-0.9581|-0.9581	5|8	0.87932|0.20519	D|T	0|0.43	.|.	2.6529|2.6529	0.05003|0.05003	0.1602:0.1173:0.3049:0.4176|0.1602:0.1173:0.3049:0.4176	rs1719152;rs52821607;rs1719152|rs1719152;rs52821607;rs1719152	.|80	.|P13236	.|CCL4_HUMAN	K|T	41|80	ENSP00000378004:N41K|ENSP00000250151:S80T	ENSP00000378004:N41K|ENSP00000250151:S80T	N|S	+|+	3|1	2|0	CCL4|CCL4	31456777|31456777	0.000000|0.000000	0.05858|0.05858	0.651000|0.651000	0.29564|0.29564	0.096000|0.096000	0.18686|0.18686	-6.619000|-6.619000	0.00059|0.00059	-3.661000|-3.661000	0.00124|0.00124	-2.948000|-2.948000	0.00085|0.00085	AAT|TCC	T|0.845;A|0.155	0.155	strong		0.498	CCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256592.2	NM_002984	
FBXL13	222235	hgsc.bcm.edu	37	7	102665620	102665620	+	Missense_Mutation	SNP	C	C	G	rs61749912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:102665620C>G	ENST00000313221.4	-	6	811	c.385G>C	c.(385-387)Gct>Cct	p.A129P	FBXL13_ENST00000379306.3_Missense_Mutation_p.A129P|FBXL13_ENST00000379305.3_Missense_Mutation_p.A129P|FBXL13_ENST00000455112.2_Missense_Mutation_p.A129P|FBXL13_ENST00000456695.1_Missense_Mutation_p.A129P|FBXL13_ENST00000471074.1_5'UTR|FBXL13_ENST00000393772.2_Missense_Mutation_p.A129P|FBXL13_ENST00000436908.1_Missense_Mutation_p.A129P|FBXL13_ENST00000379308.3_Missense_Mutation_p.A129P	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	129										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						TCTGCAGCAGCTCTTTTGAGT	0.318													C|||	531	0.10603	0.0166	0.0259	5008	,	,		14420	0.2847		0.0437	False		,,,				2504	0.1636				p.A129P		Atlas-SNP	.											.	FBXL13	65	.	0			c.G385C						PASS	.	C	PRO/ALA,PRO/ALA	143,4259	98.0+/-136.7	1,141,2059	53.0	51.0	51.0		385,385	-7.0	0.0	7	dbSNP_129	51	589,8007	154.3+/-208.6	18,553,3727	yes	missense,missense	FBXL13	NM_001111038.1,NM_145032.3	27,27	19,694,5786	GG,GC,CC		6.852,3.2485,5.6316	benign,benign	129/691,129/736	102665620	732,12266	2201	4298	6499	SO:0001583	missense	222235	exon6			CAGCAGCTCTTTT	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.385G>C	7.37:g.102665620C>G	ENSP00000321927:p.Ala129Pro	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_001111038	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Missense_Mutation	SNP	ENST00000313221.4	37	CCDS5726.1	222	0.10164835164835165	9	0.018292682926829267	11	0.03038674033149171	165	0.28846153846153844	37	0.048812664907651716	C	5.516	0.280075	0.10458	0.032485	0.06852	ENSG00000161040	ENST00000393772;ENST00000379308;ENST00000379306;ENST00000349747;ENST00000379305;ENST00000436908;ENST00000313221;ENST00000456695;ENST00000455112	T;T;T;T;T;T;T;T	0.08807	3.21;3.21;3.05;3.21;3.21;3.21;3.05;3.21	3.51	-7.01	0.01594	.	1.872960	0.03013	N	0.149748	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B;B	0.11235	0.004;0.004;0.003	B;B;B	0.14023	0.01;0.006;0.002	T	0.38757	-0.9646	9	0.27785	T	0.31	.	1.5385	0.02550	0.1952:0.1111:0.2866:0.4071	rs61749912	129;129;129	Q8NEE6-3;Q8NEE6-2;Q8NEE6	.;.;FXL13_HUMAN	P	129;129;129;56;129;129;129;129;129	ENSP00000377367:A129P;ENSP00000368610:A129P;ENSP00000368608:A129P;ENSP00000368607:A129P;ENSP00000388608:A129P;ENSP00000321927:A129P;ENSP00000409716:A129P;ENSP00000391550:A129P	ENSP00000321927:A129P	A	-	1	0	FBXL13	102452856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.492000	0.00225	-3.315000	0.00189	0.561000	0.74099	GCT	C|0.935;G|0.065	0.065	strong		0.318	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032	
EDNRA	1909	hgsc.bcm.edu	37	4	148461037	148461037	+	Silent	SNP	T	T	C	rs5333	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:148461037T>C	ENST00000324300.5	+	6	1484	c.969T>C	c.(967-969)caT>caC	p.H323H	EDNRA_ENST00000358556.4_Silent_p.H214H|EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000506066.1_Silent_p.H214H|EDNRA_ENST00000511804.1_Silent_p.H98H|EDNRA_ENST00000503721.1_3'UTR	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	323					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TCCCTCTTCATTTAAGCCGTA	0.378													T|||	1925	0.384385	0.6498	0.3386	5008	,	,		19262	0.2381		0.2237	False		,,,				2504	0.3742				p.H323H		Atlas-SNP	.											.	EDNRA	48	.	0			c.T969C						PASS	.	T	,	2444,1962	621.4+/-393.7	684,1076,443	193.0	193.0	193.0		642,969	-1.1	1.0	4	dbSNP_52	193	2140,6460	367.5+/-334.7	275,1590,2435	no	coding-synonymous,coding-synonymous	EDNRA	NM_001166055.1,NM_001957.3	,	959,2666,2878	CC,CT,TT		24.8837,44.5302,35.2453	,	214/319,323/428	148461037	4584,8422	2203	4300	6503	SO:0001819	synonymous_variant	1909	exon6			TCTTCATTTAAGC	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"""GPCR / Class A : Endothelin receptors"""	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.969T>C	4.37:g.148461037T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	203	101	0.497537	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Silent	SNP	ENST00000324300.5	37	CCDS3769.1																																																																																			T|0.642;C|0.358	0.358	strong		0.378	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1		
HS3ST6	64711	hgsc.bcm.edu	37	16	1961674	1961674	+	Missense_Mutation	SNP	G	G	C	rs337285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1961674G>C	ENST00000293937.3	-	2	945	c.946C>G	c.(946-948)Ctg>Gtg	p.L316V	HS3ST6_ENST00000454677.2_Missense_Mutation_p.L333V|HS3ST6_ENST00000443547.1_Missense_Mutation_p.L285V			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	316				L -> V (in Ref. 1). {ECO:0000305}.	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						CGCCGGACCAGGGCCTGGGGC	0.706													C|||	2983	0.595647	0.6293	0.4914	5008	,	,		14433	0.5188		0.5676	False		,,,				2504	0.7321				p.L285V		Atlas-SNP	.											.	HS3ST6	26	.	0			c.C853G						PASS	.	C	VAL/LEU	2516,1716		749,1018,349	17.0	20.0	19.0		853	1.8	0.1	16	dbSNP_79	19	4601,3835		1296,2009,913	yes	missense	HS3ST6	NM_001009606.2	32	2045,3027,1262	CC,CG,GG		45.4599,40.5482,43.8191	benign	285/312	1961674	7117,5551	2116	4218	6334	SO:0001583	missense	64711	exon2			GGACCAGGGCCTG			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.946C>G	16.37:g.1961674G>C	ENSP00000293937:p.Leu316Val	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_001009606	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	37		1230	0.5631868131868132	325	0.6605691056910569	183	0.505524861878453	309	0.5402097902097902	413	0.5448548812664907	C	0.006	-2.057386	0.00390	0.594518	0.545401	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	D;D	0.82526	-1.62;-1.62	4.99	1.84	0.25277	Sulfotransferase domain (1);	0.059383	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00254	-1.765	0.49687	P	1.8700000000004824E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.43327	-0.9398	9	0.02654	T	1	.	5.4486	0.16550	0.2565:0.5498:0.1239:0.0698	rs337285;rs3751826;rs58968312;rs337285	316	Q96QI5	HS3S6_HUMAN	V	316;285;355	ENSP00000293937:L316V;ENSP00000390354:L285V	ENSP00000293937:L316V	L	-	1	2	HS3ST6	1901675	0.998000	0.40836	0.111000	0.21465	0.022000	0.10575	3.181000	0.50903	-0.082000	0.12640	-1.565000	0.00878	CTG	G|0.448;C|0.552	0.552	strong		0.706	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
UNC45A	55898	hgsc.bcm.edu	37	15	91496233	91496233	+	Missense_Mutation	SNP	G	G	A	rs149872991		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:91496233G>A	ENST00000418476.2	+	18	2418	c.2378G>A	c.(2377-2379)cGg>cAg	p.R793Q	AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000556618.1_5'Flank|RCCD1_ENST00000555155.1_5'Flank|UNC45A_ENST00000394275.2_Missense_Mutation_p.R778Q|RCCD1_ENST00000394258.2_5'Flank	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	793					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)			ATGATCCGCCGGGCAGCCACG	0.582													g|||	1	0.000199681	0.0	0.0	5008	,	,		22008	0.0		0.001	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											.	UNC45A	57	.	0			c.G2378A						PASS	.		GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	83.0	62.0	69.0		2333,2378	4.9	1.0	15	dbSNP_134	69	7,8589	5.7+/-21.5	0,7,4291	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	43,43	0,8,6488	AA,AG,GG		0.0814,0.0227,0.0616	benign,benign	778/930,793/945	91496233	8,12984	2198	4298	6496	SO:0001583	missense	55898	exon18			TCCGCCGGGCAGC		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.2378G>A	15.37:g.91496233G>A	ENSP00000407487:p.Arg793Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	g	15.13	2.742516	0.49151	2.27E-4	8.14E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.49720	0.77;0.77	4.88	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.457993	0.23413	N	0.048457	T	0.28830	0.0715	N	0.25992	0.78	0.37116	D	0.900608	P;P	0.48640	0.913;0.913	B;B	0.33799	0.17;0.17	T	0.30909	-0.9962	10	0.40728	T	0.16	-27.8398	10.8602	0.46823	0.0:0.0:0.7065:0.2935	.	793;778	Q9H3U1;A8K6F7	UN45A_HUMAN;.	Q	778;793	ENSP00000377816:R778Q;ENSP00000407487:R793Q	ENSP00000377816:R778Q	R	+	2	0	UNC45A	89297237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.880000	0.39628	2.549000	0.85964	0.645000	0.84053	CGG	G|1.000;A|0.000	0.000	strong		0.582	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
EEA1	8411	hgsc.bcm.edu	37	12	93202801	93202801	+	Silent	SNP	C	C	T	rs7970286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	89	0	0		WXS	Illumina HiSeq	Phase_I	115	61	0.530435	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	
OR14C36	127066	hgsc.bcm.edu	37	1	248512094	248512094	+	Silent	SNP	C	C	T	rs28728105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248512094C>T	ENST00000317861.1	+	1	18	c.18C>T	c.(16-18)acC>acT	p.T6T		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						ATTCAACCACCGTGATGGAAT	0.403													c|||	2325	0.464257	0.3744	0.4885	5008	,	,		19251	0.4315		0.5239	False		,,,				2504	0.5409				p.T6T		Atlas-SNP	.											.	OR14C36	113	.	0			c.C18T						PASS	.	C		1837,2569	537.1+/-374.7	382,1073,748	128.0	119.0	122.0		18	-7.9	0.0	1	dbSNP_125	122	4898,3702	619.7+/-397.0	1392,2114,794	no	coding-synonymous	OR14C36	NM_001001918.1		1774,3187,1542	TT,TC,CC		43.0465,41.6931,48.2162		6/313	248512094	6735,6271	2203	4300	6503	SO:0001819	synonymous_variant	127066	exon1			AACCACCGTGATG	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.18C>T	1.37:g.248512094C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	180	74	0.411111	NM_001001918	Q6IEZ6	Silent	SNP	ENST00000317861.1	37	CCDS31112.1																																																																																			C|0.513;T|0.487	0.487	strong		0.403	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918	
ABCF2	10061	hgsc.bcm.edu	37	7	150915948	150915948	+	Silent	SNP	C	C	T	rs7782699	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150915948C>T	ENST00000287844.2	-	9	1138	c.1029G>A	c.(1027-1029)gcG>gcA	p.A343A	ABCF2_ENST00000473874.1_5'UTR|ABCF2_ENST00000222388.2_Silent_p.A343A	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	343					transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GACCAAACCTCGCAATGTAGT	0.483													C|||	269	0.0537141	0.0363	0.072	5008	,	,		17485	0.0		0.0984	False		,,,				2504	0.0736				p.A343A		Atlas-SNP	.											.	ABCF2	54	.	0			c.G1029A						PASS	.	C	,	257,4149	147.3+/-181.8	6,245,1952	94.0	90.0	92.0		1029,1029	-1.0	1.0	7	dbSNP_116	92	983,7617	213.6+/-253.5	54,875,3371	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	60,1120,5323	TT,TC,CC		11.4302,5.833,9.5341	,	343/635,343/624	150915948	1240,11766	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon9			AAACCTCGCAATG	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.1029G>A	7.37:g.150915948C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			C|0.909;T|0.091	0.091	strong		0.483	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
IL1R1	3554	hgsc.bcm.edu	37	2	102781629	102781629	+	Silent	SNP	G	G	A	rs3917286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102781629G>A	ENST00000410023.1	+	5	669	c.351G>A	c.(349-351)gaG>gaA	p.E117E	IL1R1_ENST00000233946.3_Silent_p.E117E|IL1R1_ENST00000409288.1_Silent_p.E117E|IL1R1_ENST00000424272.1_Silent_p.E117E|IL1R1_ENST00000409589.1_Silent_p.E117E|IL1R1_ENST00000409329.1_Silent_p.E117E|IL1R1_ENST00000409929.1_Silent_p.E117E			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	117					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)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	TGGAGAATGAGCCTAACTTAT	0.313													G|||	225	0.0449281	0.0083	0.0072	5008	,	,		12413	0.0714		0.006	False		,,,				2504	0.1339				p.E117E		Atlas-SNP	.											.	IL1R1	52	.	0			c.G351A						PASS	.	G		47,4359	48.9+/-83.8	0,47,2156	50.0	51.0	50.0		351	-10.0	0.1	2	dbSNP_108	50	43,8555	27.4+/-76.7	0,43,4256	no	coding-synonymous	IL1R1	NM_000877.2		0,90,6412	AA,AG,GG		0.5001,1.0667,0.6921		117/570	102781629	90,12914	2203	4299	6502	SO:0001819	synonymous_variant	3554	exon4			GAATGAGCCTAAC	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.351G>A	2.37:g.102781629G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	186	89	0.478495	NM_000877	Q587I7	Silent	SNP	ENST00000410023.1	37	CCDS2055.1																																																																																			G|0.984;A|0.016	0.016	strong		0.313	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
ZSCAN22	342945	hgsc.bcm.edu	37	19	58849789	58849789	+	Silent	SNP	G	G	A	rs368211476		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58849789G>A	ENST00000329665.4	+	3	720	c.573G>A	c.(571-573)ggG>ggA	p.G191G		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	191					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)		GACTATCAGGGGAGATCTGGA	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		20257	0.0		0.0	False		,,,				2504	0.001				p.G191G		Atlas-SNP	.											ZSCAN22,NS,carcinoma,+1,1	ZSCAN22	47	1	0			c.G573A						PASS	.						114.0	112.0	112.0					19																	58849789		2203	4300	6503	SO:0001819	synonymous_variant	342945	exon3			ATCAGGGGAGATC	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.573G>A	19.37:g.58849789G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_181846	Q15922|Q7Z3L8	Silent	SNP	ENST00000329665.4	37	CCDS12975.1																																																																																			.	.	weak		0.537	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846	
KRTAP9-3	83900	hgsc.bcm.edu	37	17	39388811	39388811	+	Missense_Mutation	SNP	C	C	A	rs112082369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39388811C>A	ENST00000411528.2	+	1	97	c.58C>A	c.(58-60)Cag>Aag	p.Q20K		NM_031962.2	NP_114168.1	Q9BYQ3	KRA93_HUMAN	keratin associated protein 9-3	20	16 X 5 AA repeats of C-C-[RQVSHE]-[SPTN]- [TASPI].					keratin filament (GO:0045095)				breast(1)|endometrium(3)|lung(2)|ovary(1)|prostate(1)	8		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CACCTGCTGGCAGCCCACCAC	0.602													.|||	979	0.195487	0.1505	0.1354	5008	,	,		17008	0.3194		0.1918	False		,,,				2504	0.1748				p.Q20K		Atlas-SNP	.											.	KRTAP9-3	11	.	0			c.C58A						PASS	.	C	LYS/GLN	756,3454		177,402,1526	71.0	79.0	76.0		58	-2.4	0.0	17	dbSNP_132	76	1565,7035		136,1293,2871	no	missense	KRTAP9-3	NM_031962.2	53	313,1695,4397	AA,AC,CC		18.1977,17.9572,18.1187		20/160	39388811	2321,10489	2105	4300	6405	SO:0001583	missense	83900	exon1			TGCTGGCAGCCCA	AJ406947	CCDS11385.1	17q21.2	2013-06-25			ENSG00000204873	ENSG00000204873		"""Keratin associated proteins"""	16927	protein-coding gene	gene with protein product						11279113	Standard	NM_031962		Approved	KAP9.3	uc021txg.1	Q9BYQ3	OTTHUMG00000133427	ENST00000411528.2:c.58C>A	17.37:g.39388811C>A	ENSP00000392189:p.Gln20Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_031962		Missense_Mutation	SNP	ENST00000411528.2	37	CCDS11385.1	375	0.1717032967032967	65	0.13211382113821138	46	0.1270718232044199	154	0.2692307692307692	110	0.14511873350923482	.	0.003	-2.481142	0.00165	0.179572	0.181977	ENSG00000204873	ENST00000411528	T	0.01455	4.87	1.22	-2.44	0.06502	.	.	.	.	.	T	0.00012	0.0000	L	0.43598	1.365	0.80722	P	0.0	.	.	.	.	.	.	T	0.42120	-0.9470	6	0.19147	T	0.46	.	5.0219	0.14365	0.2322:0.5773:0.0:0.1905	.	.	.	.	K	20	ENSP00000392189:Q20K	ENSP00000392189:Q20K	Q	+	1	0	KRTAP9-3	36642337	0.784000	0.28713	0.047000	0.18901	0.087000	0.18053	-0.050000	0.11904	-2.202000	0.00745	-1.432000	0.01085	CAG	C|0.828;A|0.172	0.172	strong		0.602	KRTAP9-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257290.1		
MUC2	4583	hgsc.bcm.edu	37	11	1084362	1084362	+	Missense_Mutation	SNP	G	G	A	rs11245936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1084362G>A	ENST00000441003.2	+	19	2521	c.2494G>A	c.(2494-2496)Ggc>Agc	p.G832S	MUC2_ENST00000359061.5_Missense_Mutation_p.G832S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	832			G -> S (in dbSNP:rs11245936).		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.G832R(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)	GTATTCTTCCGGCGCCAAGAT	0.642													G|||	273	0.0545128	0.0363	0.0461	5008	,	,		19772	0.0496		0.0905	False		,,,				2504	0.0532				p.G832S		Atlas-SNP	.											MUC2_ENST00000441003,mouth,carcinoma,0,2	MUC2	614	2	2	Substitution - Missense(2)	upper_aerodigestive_tract(2)	c.G2494A						scavenged	.	G	SER/GLY	168,4110		4,160,1975	82.0	92.0	89.0		2494	4.2	0.0	11	dbSNP_120	89	758,7724		34,690,3517	yes	missense	MUC2	NM_002457.2	56	38,850,5492	AA,AG,GG		8.9366,3.9271,7.2571	probably-damaging	832/2813	1084362	926,11834	2139	4241	6380	SO:0001583	missense	4583	exon19			TCTTCCGGCGCCA	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.2494G>A	11.37:g.1084362G>A	ENSP00000415183:p.Gly832Ser	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		118	0.05402930402930403	15	0.03048780487804878	10	0.027624309392265192	26	0.045454545454545456	67	0.08839050131926121	G	12.65	2.003040	0.35320	0.039271	0.089366	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.28895	1.59;1.59	4.22	4.22	0.49857	.	0.000000	0.64402	D	0.000006	T	0.06962	0.0177	H	0.95004	3.61	0.22842	P	0.99866543	D	0.89917	1.0	D	0.87578	0.998	T	0.61686	-0.7012	9	0.87932	D	0	.	16.7715	0.85538	0.0:0.0:1.0:0.0	rs11245936;rs57489587;rs11245936	832	E7EUV1	.	S	832	ENSP00000415183:G832S;ENSP00000351956:G832S	ENSP00000351956:G832S	G	+	1	0	MUC2	1074362	1.000000	0.71417	0.038000	0.18304	0.006000	0.05464	6.454000	0.73493	2.175000	0.68902	0.555000	0.69702	GGC	G|0.945;A|0.055	0.055	strong		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
IL12B	3593	hgsc.bcm.edu	37	5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	rs3213096	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:158750329C>T	ENST00000231228.2	-	3	552	c.97G>A	c.(97-99)Gta>Ata	p.V33I		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	33	Ig-like C2-type.		V -> I (in dbSNP:rs3213096). {ECO:0000269|Ref.5}.		cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|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-17 production (GO:0032740)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|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 Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCAATTCTACGACATAAACT	0.502													C|||	19	0.00379393	0.0	0.0043	5008	,	,		20539	0.0		0.0099	False		,,,				2504	0.0061				p.V33I		Atlas-SNP	.											.	IL12B	30	.	0			c.G97A						PASS	.	C	ILE/VAL	7,4399	12.9+/-30.5	0,7,2196	61.0	56.0	58.0		97	5.2	0.9	5	dbSNP_106	58	49,8551	31.2+/-83.2	0,49,4251	yes	missense	IL12B	NM_002187.2	29	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	benign	33/329	158750329	56,12950	2203	4300	6503	SO:0001583	missense	3593	exon3			ATTCTACGACATA	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5970	protein-coding gene	gene with protein product	"""natural killer cell stimulatory factor-2"", ""cytotoxic lymphocyte maturation factor 2, p40"", ""interleukin 12, p40"", ""natural killer cell stimulatory factor, 40 kD subunit"", ""interleukin-12 beta chain"", ""IL12, subunit p40"""	161561	"""interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"""	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.97G>A	5.37:g.158750329C>T	ENSP00000231228:p.Val33Ile	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	37	CCDS4346.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.248	1.040122	0.19669	0.001589	0.005698	ENSG00000113302	ENST00000231228	T	0.22743	1.94	6.02	5.16	0.70880	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054974	0.64402	D	0.000001	T	0.20210	0.0486	M	0.79475	2.455	0.45791	D	0.998676	B	0.09022	0.002	B	0.12156	0.007	T	0.03473	-1.1033	10	0.46703	T	0.11	-3.6912	11.4605	0.50208	0.0:0.9177:0.0:0.0823	rs3213096;rs17056679;rs17875310;rs52806839;rs56592501;rs3213096	33	P29460	IL12B_HUMAN	I	33	ENSP00000231228:V33I	ENSP00000231228:V33I	V	-	1	0	IL12B	158682907	0.822000	0.29219	0.877000	0.34402	0.087000	0.18053	1.240000	0.32731	1.568000	0.49683	-0.137000	0.14449	GTA	C|0.994;T|0.006	0.006	strong		0.502	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187	
AASDH	132949	hgsc.bcm.edu	37	4	57211352	57211352	+	Missense_Mutation	SNP	T	T	C	rs12498340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:57211352T>C	ENST00000205214.6	-	12	2773	c.2593A>G	c.(2593-2595)Acc>Gcc	p.T865A	AASDH_ENST00000434343.2_Missense_Mutation_p.T380A|AASDH_ENST00000513376.1_Missense_Mutation_p.T765A|AASDH_ENST00000451613.1_Intron|AASDH_ENST00000602986.1_Intron	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	865			T -> A (in dbSNP:rs12498340).		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				AGTCCTGTGGTTGGATCCATG	0.393													T|||	1101	0.219848	0.1974	0.3775	5008	,	,		18367	0.2173		0.1302	False		,,,				2504	0.2331				p.T865A		Atlas-SNP	.											.	AASDH	101	.	0			c.A2593G						PASS	.	T	ALA/THR	842,3564	332.5+/-302.5	80,682,1441	201.0	186.0	191.0		2593	3.4	1.0	4	dbSNP_120	191	1096,7504	228.3+/-263.4	70,956,3274	yes	missense	AASDH	NM_181806.2	58	150,1638,4715	CC,CT,TT		12.7442,19.1103,14.9008	benign	865/1099	57211352	1938,11068	2203	4300	6503	SO:0001583	missense	132949	exon12			CTGTGGTTGGATC	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.2593A>G	4.37:g.57211352T>C	ENSP00000205214:p.Thr865Ala	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	424	0.19413919413919414	89	0.18089430894308944	117	0.32320441988950277	119	0.20804195804195805	99	0.13060686015831136	T	13.89	2.371977	0.42003	0.191103	0.127442	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343	T;T;T	0.60299	1.01;0.2;1.01	6.03	3.43	0.39272	Quinonprotein alcohol dehydrogenase-like (2);	0.846265	0.11368	N	0.571223	T	0.00012	0.0000	N	0.17631	0.505	0.20975	P	0.999810126	B	0.28178	0.202	B	0.33846	0.171	T	0.30001	-0.9993	9	0.40728	T	0.16	-1.2383	5.8582	0.18732	0.4903:0.0:0.1117:0.398	rs12498340;rs52797375;rs57654214;rs12498340	865	Q4L235	ACSF4_HUMAN	A	865;765;380	ENSP00000205214:T865A;ENSP00000423760:T765A;ENSP00000392158:T380A	ENSP00000205214:T865A	T	-	1	0	AASDH	56906109	0.029000	0.19370	0.987000	0.45799	0.967000	0.64934	0.122000	0.15687	1.052000	0.40392	0.533000	0.62120	ACC	T|0.830;C|0.170	0.170	strong		0.393	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
ATP8A2	51761	hgsc.bcm.edu	37	13	26043182	26043182	+	Silent	SNP	A	A	C	rs7317185	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:26043182A>C	ENST00000381655.2	+	2	286	c.144A>C	c.(142-144)ggA>ggC	p.G48G	ATP8A2_ENST00000255283.8_Silent_p.G8G	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	8					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		CGTCTGTTGGAGACCAGCTGG	0.582													A|||	1022	0.204073	0.354	0.1484	5008	,	,		9431	0.119		0.1998	False		,,,				2504	0.1329				p.G48G		Atlas-SNP	.											ATP8A2,colon,carcinoma,0,1	ATP8A2	181	1	0			c.A144C						PASS	.	A		1226,2880		185,856,1012	77.0	86.0	83.0		144	0.1	1.0	13	dbSNP_116	83	1789,6605		191,1407,2599	no	coding-synonymous	ATP8A2	NM_016529.4		376,2263,3611	CC,CA,AA		21.3128,29.8587,24.12		48/1189	26043182	3015,9485	2053	4197	6250	SO:0001819	synonymous_variant	51761	exon2			TGTTGGAGACCAG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.144A>C	13.37:g.26043182A>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent	SNP	ENST00000381655.2	37	CCDS41873.1	455	0.20833333333333334	166	0.33739837398373984	68	0.1878453038674033	75	0.13111888111888112	146	0.19261213720316622	A	12.71	2.020365	0.35606	0.298587	0.213128	ENSG00000132932	ENST00000544544	.	.	.	4.16	0.119	0.14685	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42310	-0.9459	4	0.11485	T	0.65	.	0.3655	0.00371	0.3332:0.1995:0.2735:0.1938	rs7317185;rs7317185	.	.	.	A	10	.	ENSP00000444329:E10A	E	+	2	0	ATP8A2	24941182	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	1.074000	0.30703	0.144000	0.18951	0.329000	0.21502	GAG	A|0.790;C|0.210	0.210	strong		0.582	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
NIN	51199	hgsc.bcm.edu	37	14	51204996	51204996	+	Silent	SNP	C	C	T	rs11376	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:51204996C>T	ENST00000382041.3	-	27	5827	c.5637G>A	c.(5635-5637)caG>caA	p.Q1879Q	NIN_ENST00000453196.1_Silent_p.Q1879Q|NIN_ENST00000245441.5_Silent_p.Q1879Q|NIN_ENST00000530997.2_Silent_p.Q1879Q|NIN_ENST00000382043.4_Silent_p.Q1166Q|NIN_ENST00000389868.3_Silent_p.Q1166Q|NIN_ENST00000324330.9_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	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	205	204	0.995122	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	
DMWD	1762	hgsc.bcm.edu	37	19	46289503	46289503	+	Silent	SNP	C	C	T	rs8109951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46289503C>T	ENST00000270223.6	-	3	1296	c.1251G>A	c.(1249-1251)ccG>ccA	p.P417P	AC011530.4_ENST00000593999.1_5'Flank|DMWD_ENST00000377735.3_Silent_p.P417P|DMWD_ENST00000601370.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	417										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		GTGGAGAGAGCGGGGCGCCCC	0.692													C|||	1455	0.290535	0.3079	0.2291	5008	,	,		12564	0.2887		0.329	False		,,,				2504	0.273				p.P417P		Atlas-SNP	.											DMWD,rectum,carcinoma,0,1	DMWD	46	1	0			c.G1251A						PASS	.	C		1250,3120		209,832,1144	15.0	18.0	17.0		1251	-8.4	0.0	19	dbSNP_116	17	3086,5450		602,1882,1784	no	coding-synonymous	DMWD	NM_004943.1		811,2714,2928	TT,TC,CC		36.1528,28.6041,33.5968		417/675	46289503	4336,8570	2185	4268	6453	SO:0001819	synonymous_variant	1762	exon3			AGAGAGCGGGGCG	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"""WD repeat domain containing"""	2936	protein-coding gene	gene with protein product		609857	"""dystrophia myotonica-containing WD repeat motif"""			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1251G>A	19.37:g.46289503C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_004943		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																			C|0.701;T|0.299	0.299	strong		0.692	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943	
REP15	387849	hgsc.bcm.edu	37	12	27850113	27850113	+	Missense_Mutation	SNP	A	A	T	rs12819160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:27850113A>T	ENST00000310791.2	+	1	686	c.618A>T	c.(616-618)gaA>gaT	p.E206D	RP11-1060J15.4_ENST00000536922.1_RNA|RP11-1060J15.4_ENST00000542660.1_RNA|RP11-1060J15.4_ENST00000536317.1_RNA	NM_001029874.1	NP_001025045.1	Q6BDI9	REP15_HUMAN	RAB15 effector protein	206			E -> D (in dbSNP:rs12819160).		receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	endosome membrane (GO:0010008)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)				breast(1)|cervix(1)|large_intestine(2)|lung(4)|ovary(1)	9	Lung SC(9;0.0873)					TGGAAACTGAAGATTGTGTGT	0.483													A|||	451	0.0900559	0.0068	0.0994	5008	,	,		19167	0.0506		0.175	False		,,,				2504	0.1493				p.E206D		Atlas-SNP	.											.	REP15	13	.	0			c.A618T						PASS	.	A	ASP/GLU	169,4237	112.9+/-151.0	3,163,2037	99.0	100.0	100.0		618	1.3	0.0	12	dbSNP_121	100	1526,7074	287.8+/-298.4	125,1276,2899	yes	missense	REP15	NM_001029874.1	45	128,1439,4936	TT,TA,AA		17.7442,3.8357,13.0324	benign	206/237	27850113	1695,11311	2203	4300	6503	SO:0001583	missense	387849	exon1			AACTGAAGATTGT	BC140921	CCDS31762.1	12p11.22	2010-09-02			ENSG00000174236	ENSG00000174236			33748	protein-coding gene	gene with protein product		610848				16195351	Standard	NM_001029874		Approved	RAB15EP	uc001rig.1	Q6BDI9		ENST00000310791.2:c.618A>T	12.37:g.27850113A>T	ENSP00000310335:p.Glu206Asp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	23	0.383333	NM_001029874	B2RU16	Missense_Mutation	SNP	ENST00000310791.2	37	CCDS31762.1	212	0.09706959706959707	7	0.014227642276422764	38	0.10497237569060773	34	0.05944055944055944	133	0.17546174142480211	A	4.863	0.160403	0.09287	0.038357	0.177442	ENSG00000174236	ENST00000310791	T	0.32753	1.44	4.91	1.3	0.21679	.	0.598204	0.16508	N	0.211344	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.27571	-1.0070	9	0.12766	T	0.61	-20.553	1.1719	0.01827	0.2933:0.2663:0.2981:0.1423	rs12819160;rs52834046;rs12819160	206	Q6BDI9	REP15_HUMAN	D	206	ENSP00000310335:E206D	ENSP00000310335:E206D	E	+	3	2	REP15	27741380	0.000000	0.05858	0.005000	0.12908	0.464000	0.32679	-0.146000	0.10250	0.387000	0.25024	0.533000	0.62120	GAA	A|0.877;T|0.123	0.123	strong		0.483	REP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402894.1	NM_001029874	
ADAM9	8754	hgsc.bcm.edu	37	8	38854660	38854660	+	Silent	SNP	C	C	A	rs148707472	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:38854660C>A	ENST00000487273.2	+	1	156	c.78C>A	c.(76-78)gtC>gtA	p.V26V	TM2D2_ENST00000412303.1_5'Flank|TM2D2_ENST00000456845.2_5'Flank|ADAM9_ENST00000466936.1_Silent_p.V26V|TM2D2_ENST00000522434.1_5'Flank|TM2D2_ENST00000397070.2_5'Flank|TM2D2_ENST00000456397.2_5'Flank|ADAM9_ENST00000481513.1_Silent_p.V26V	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	26				Missing (in Ref. 2; no nucleotide entry). {ECO:0000305}.	activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|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)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			TGGGCCCAGTCCTCGGTGCGG	0.706													C|||	110	0.0219649	0.0038	0.049	5008	,	,		11618	0.0		0.0666	False		,,,				2504	0.0041				p.V26V		Atlas-SNP	.											.	ADAM9	66	.	0			c.C78A						PASS	.	C		54,4348	52.9+/-88.7	1,52,2148	50.0	44.0	46.0		78	0.9	1.0	8	dbSNP_134	46	452,8146	131.2+/-189.0	9,434,3856	no	coding-synonymous	ADAM9	NM_003816.2		10,486,6004	AA,AC,CC		5.257,1.2267,3.8923		26/820	38854660	506,12494	2201	4299	6500	SO:0001819	synonymous_variant	8754	exon1			CCCAGTCCTCGGT	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"""ADAM metallopeptidase domain containing"""	216	protein-coding gene	gene with protein product	"""meltrin gamma"""	602713	"""a disintegrin and metalloproteinase domain 9 (meltrin gamma)"", ""cone rod dystrophy 9"""	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.78C>A	8.37:g.38854660C>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_003816	B7ZLN7|Q10718|Q8NFM6	Silent	SNP	ENST00000487273.2	37	CCDS6112.1																																																																																			C|0.964;A|0.036	0.036	strong		0.706	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2		
CCZ1B	221960	hgsc.bcm.edu	37	7	6844574	6844574	+	Missense_Mutation	SNP	C	C	G	rs62441800	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:6844574C>G	ENST00000316731.8	-	12	1673	c.1101G>C	c.(1099-1101)atG>atC	p.M367I	CCZ1B_ENST00000538180.1_Missense_Mutation_p.M224I	NM_198097.3	NP_932765.1	P86790	CCZ1B_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog B (S. cerevisiae)	367						lysosome (GO:0005764)|membrane (GO:0016020)											CAAACCCAGACATCCTCTTGT	0.453																																					p.M367I		Atlas-SNP	.											.	.	.	.	0			c.G1101C						PASS	.	C	ILE/MET	1349,2815		277,795,1010	194.0	176.0	182.0		1101	-6.1	0.1	7	dbSNP_131	182	2675,5379		439,1797,1791	no	missense	C7orf28B	NM_198097.3	10	716,2592,2801	GG,GC,CC		33.2133,32.3967,32.935	benign	367/483	6844574	4024,8194	2082	4027	6109	SO:0001583	missense	221960	exon12			CCCAGACATCCTC	BC010130	CCDS5354.1	7p22.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000146574	ENSG00000146574			21717	protein-coding gene	gene with protein product	"""similar to CGI-43 protein"""		"""chromosome 7 open reading frame 28B"""	C7orf28B		12477932	Standard	NM_198097		Approved	DKFZP586I1023, H_NH0577018.2, MGC19819	uc003sqx.2	P86790	OTTHUMG00000152441	ENST00000316731.8:c.1101G>C	7.37:g.6844574C>G	ENSP00000314544:p.Met367Ile	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	472	207	0.438559	NM_198097	A2RU45|O95766|Q9UG65|Q9Y359	Missense_Mutation	SNP	ENST00000316731.8	37	CCDS5354.1	461	0.21108058608058608	120	0.24390243902439024	75	0.20718232044198895	38	0.06643356643356643	228	0.3007915567282322	C	0.117	-1.131089	0.01756	0.323967	0.332133	ENSG00000146574	ENST00000316731;ENST00000538180	.	.	.	3.03	-6.06	0.02165	.	0.198789	0.51477	N	0.000083	T	0.00012	0.0000	.	.	.	0.44611	P	0.0024159999999999737	.	.	.	.	.	.	T	0.31971	-0.9924	5	0.21540	T	0.41	-1.3097	2.0781	0.03628	0.1264:0.1554:0.1341:0.5842	.	.	.	.	I	367;224	.	ENSP00000314544:M367I	M	-	3	0	C7orf28B	6811099	0.850000	0.29656	0.088000	0.20740	0.887000	0.51463	-0.147000	0.10234	-1.682000	0.01446	0.506000	0.49869	ATG	C|0.694;G|0.306	0.306	strong		0.453	CCZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246858.1	NM_198097	
GRK7	131890	hgsc.bcm.edu	37	3	141535608	141535608	+	Missense_Mutation	SNP	C	C	A	rs33928105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:141535608C>A	ENST00000264952.2	+	4	1515	c.1378C>A	c.(1378-1380)Cct>Act	p.P460T		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	460	AGC-kinase C-terminal.		P -> T (in dbSNP:rs33928105). {ECO:0000269|PubMed:17344846}.		protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						GATCAACTTTCCTCGCCTGGA	0.428													C|||	321	0.0640974	0.0817	0.0677	5008	,	,		17376	0.0139		0.1054	False		,,,				2504	0.047				p.P460T		Atlas-SNP	.											.	GRK7	65	.	0			c.C1378A						PASS	.	C	THR/PRO	369,4037	188.8+/-215.1	17,335,1851	112.0	113.0	113.0		1378	2.5	1.0	3	dbSNP_126	113	1105,7495	230.1+/-264.6	66,973,3261	yes	missense	GRK7	NM_139209.2	38	83,1308,5112	AA,AC,CC		12.8488,8.3749,11.3332	benign	460/554	141535608	1474,11532	2203	4300	6503	SO:0001583	missense	131890	exon4			AACTTTCCTCGCC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.1378C>A	3.37:g.141535608C>A	ENSP00000264952:p.Pro460Thr	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	165	0.07554945054945054	42	0.08536585365853659	33	0.09116022099447514	5	0.008741258741258742	85	0.11213720316622691	C	14.10	2.434647	0.43224	0.083749	0.128488	ENSG00000114124	ENST00000264952	T	0.24723	1.84	5.4	2.52	0.30459	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.279721	0.36444	N	0.002584	T	0.00210	0.0006	L	0.45581	1.43	0.37836	P	0.07110899999999998	B	0.28128	0.201	B	0.25140	0.058	T	0.08207	-1.0733	9	0.46703	T	0.11	-3.9809	7.2857	0.26337	0.124:0.6777:0.1298:0.0685	rs33928105	460	Q8WTQ7	GRK7_HUMAN	T	460	ENSP00000264952:P460T	ENSP00000264952:P460T	P	+	1	0	GRK7	143018298	1.000000	0.71417	0.991000	0.47740	0.898000	0.52572	3.309000	0.51903	0.210000	0.20664	0.467000	0.42956	CCT	C|0.899;A|0.101	0.101	strong		0.428	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
CSMD3	114788	hgsc.bcm.edu	37	8	113241088	113241088	+	Missense_Mutation	SNP	T	T	G	rs1592624	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:113241088T>G	ENST00000297405.5	-	70	11105	c.10861A>C	c.(10861-10863)Aat>Cat	p.N3621H	CSMD3_ENST00000343508.3_Missense_Mutation_p.N3581H|CSMD3_ENST00000455883.2_Missense_Mutation_p.N3452H|CSMD3_ENST00000352409.3_Missense_Mutation_p.N3551H	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3621			N -> H (in dbSNP:rs1592624). {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						TGAGGTTGATTTGAAGAATTT	0.279										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	3567	0.71226	0.944	0.585	5008	,	,		15262	0.7619		0.5676	False		,,,				2504	0.5869				p.N3621H		Atlas-SNP	.											CSMD3_ENST00000343508,caecum,carcinoma,0,4	CSMD3	2325	4	0			c.A10861C						PASS	.	T	HIS/ASN,HIS/ASN,HIS/ASN	3881,525	777.3+/-414.2	1723,435,45	75.0	77.0	76.0		10354,10861,10741	5.6	1.0	8	dbSNP_88	76	4800,3794	610.9+/-395.7	1347,2106,844	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	68,68,68	3070,2541,889	GG,GT,TT		44.1471,11.9156,33.2231	benign,benign,benign	3452/3539,3621/3708,3581/3668	113241088	8681,4319	2203	4297	6500	SO:0001583	missense	114788	exon70			GTTGATTTGAAGA	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.10861A>C	8.37:g.113241088T>G	ENSP00000297405:p.Asn3621His	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	1517	0.6945970695970696	458	0.9308943089430894	227	0.6270718232044199	419	0.7325174825174825	413	0.5448548812664907	T	17.83	3.485126	0.63962	0.880844	0.558529	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.26373	2.04;2.04;2.06;1.74;2.06	5.63	5.63	0.86233	.	0.212969	0.38381	N	0.001710	T	0.00012	0.0000	L	0.50333	1.59	0.27220	P	0.9596862	P;P;D	0.64830	0.928;0.883;0.994	P;P;P	0.60789	0.73;0.541;0.879	T	0.02933	-1.1092	9	0.39692	T	0.17	.	16.1263	0.81397	0.0:0.0:0.0:1.0	rs1592624;rs17553856;rs52833020;rs59602589;rs1592624	3452;3621;3581	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	H	3581;3621;2891;3452;3551	ENSP00000345799:N3581H;ENSP00000297405:N3621H;ENSP00000341558:N2891H;ENSP00000412263:N3452H;ENSP00000343124:N3551H	ENSP00000297405:N3621H	N	-	1	0	CSMD3	113310264	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.181000	0.58303	2.257000	0.74773	0.533000	0.62120	AAT	G|0.698;N|0.000	0.698	strong		0.279	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
IL2RB	3560	hgsc.bcm.edu	37	22	37524619	37524619	+	Missense_Mutation	SNP	G	G	T	rs228942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37524619G>T	ENST00000216223.5	-	10	1371	c.1173C>A	c.(1171-1173)gaC>gaA	p.D391E		NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	391			D -> E (in dbSNP:rs228942). {ECO:0000269|Ref.3}.		cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	CCTCATCAGGGTCTTCCTCTG	0.612													G|||	903	0.180312	0.0764	0.3098	5008	,	,		17234	0.2341		0.1839	False		,,,				2504	0.1697				p.D391E		Atlas-SNP	.											.	IL2RB	44	.	0			c.C1173A						PASS	.	G	GLU/ASP	406,4000	200.8+/-224.0	16,374,1813	59.0	60.0	59.0		1173	2.2	0.2	22	dbSNP_79	59	1585,7015	295.4+/-302.4	158,1269,2873	yes	missense	IL2RB	NM_000878.2	45	174,1643,4686	TT,TG,GG		18.4302,9.2147,15.3083	benign	391/552	37524619	1991,11015	2203	4300	6503	SO:0001583	missense	3560	exon10			ATCAGGGTCTTCC	M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"""Interleukins and interleukin receptors"", ""CD molecules"""	6009	protein-coding gene	gene with protein product		146710	"""interleukin 15 receptor, beta"""	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.1173C>A	22.37:g.37524619G>T	ENSP00000216223:p.Asp391Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	79	77	0.974684	NM_000878	B2R765	Missense_Mutation	SNP	ENST00000216223.5	37	CCDS13942.1	438	0.20054945054945056	40	0.08130081300813008	110	0.30386740331491713	144	0.2517482517482518	144	0.18997361477572558	G	0.759	-0.769881	0.02974	0.092147	0.184302	ENSG00000100385	ENST00000216223	T	0.06849	3.25	4.28	2.16	0.27623	.	1.830200	0.02534	N	0.093949	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40156	-0.9578	9	0.02654	T	1	-6.2193	7.4522	0.27244	0.0:0.738:0.1698:0.0922	rs228942;rs57366109;rs228942	391	P14784	IL2RB_HUMAN	E	391	ENSP00000216223:D391E	ENSP00000216223:D391E	D	-	3	2	IL2RB	35854565	0.000000	0.05858	0.226000	0.23910	0.001000	0.01503	-2.511000	0.00958	0.543000	0.28864	-0.766000	0.03442	GAC	G|0.839;T|0.161	0.161	strong		0.612	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1		
PLEKHG7	440107	hgsc.bcm.edu	37	12	93150102	93150102	+	Missense_Mutation	SNP	T	T	C	rs924326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	355	0	0		WXS	Illumina HiSeq	Phase_I	400	191	0.4775	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	
DAPK1	1612	hgsc.bcm.edu	37	9	90265015	90265015	+	Silent	SNP	C	C	T	rs3818584	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90265015C>T	ENST00000408954.3	+	16	1943	c.1608C>T	c.(1606-1608)gaC>gaT	p.D536D	DAPK1_ENST00000472284.1_Silent_p.D536D|DAPK1_ENST00000469640.2_Silent_p.D536D|DAPK1_ENST00000358077.5_Silent_p.D536D|DAPK1_ENST00000491893.1_Silent_p.D536D	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	536					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						ATGGAGCCGACCTTAATGCTT	0.552									Chronic Lymphocytic Leukemia, Familial Clustering of				C|||	1773	0.354034	0.1241	0.5432	5008	,	,		16292	0.5784		0.3748	False		,,,				2504	0.2781				p.D536D		Atlas-SNP	.											DAPK1_ENST00000408954,NS,carcinoma,0,4	DAPK1	329	4	0			c.C1608T						PASS	.	C		603,3323		46,511,1406	50.0	50.0	50.0		1608	1.6	0.9	9	dbSNP_107	50	3141,5141		587,1967,1587	no	coding-synonymous	DAPK1	NM_004938.2		633,2478,2993	TT,TC,CC		37.9256,15.3591,30.6684		536/1431	90265015	3744,8464	1963	4141	6104	SO:0001819	synonymous_variant	1612	exon16	Familial Cancer Database	Familial CLL	AGCCGACCTTAAT	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.1608C>T	9.37:g.90265015C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			C|0.634;T|0.365	0.365	strong		0.552	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011720	46011720	+	Missense_Mutation	SNP	G	G	A	rs9977124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46011720G>A	ENST00000400368.1	-	1	666	c.646C>T	c.(646-648)Cca>Tca	p.P216S	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	216	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.P216S(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						CAGCAAGTTGGCTGGCAGCTA	0.672													.|||	290	0.0579073	0.1543	0.0476	5008	,	,		21953	0.0446		0.003	False		,,,				2504	0.0051				p.P216S		Atlas-SNP	.											KRTAP10-6,caecum,carcinoma,0,1	KRTAP10-6	57	1	1	Substitution - Missense(1)	large_intestine(1)	c.C646T						scavenged	.	G	,SER/PRO	227,4163		25,177,1993	92.0	120.0	111.0		,646	0.2	0.0	21	dbSNP_119	111	0,8600		0,0,4300	no	intron,missense	TSPEAR,KRTAP10-6	NM_144991.2,NM_198688.2	,74	25,177,6293	AA,AG,GG		0.0,5.1708,1.7475	,benign	,216/366	46011720	227,12763	2195	4300	6495	SO:0001583	missense	386674	exon1			AAGTTGGCTGGCA	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.646C>T	21.37:g.46011720G>A	ENSP00000383219:p.Pro216Ser	Somatic	273	2	0.00732601		WXS	Illumina HiSeq	Phase_I	311	12	0.0385852	NM_198688		Missense_Mutation	SNP	ENST00000400368.1	37	CCDS42959.1	69	0.03159340659340659	43	0.08739837398373984	12	0.03314917127071823	14	0.024475524475524476	0	0.0	-	10.25	1.298149	0.23650	0.051708	0.0	ENSG00000188155	ENST00000400368	T	0.01887	4.58	3.12	0.189	0.15119	.	.	.	.	.	T	0.00144	0.0004	L	0.49640	1.575	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.43458	-0.9390	9	0.49607	T	0.09	.	6.7771	0.23626	0.3716:0.0:0.6284:0.0	rs9977124	216	P60371	KR106_HUMAN	S	216	ENSP00000383219:P216S	ENSP00000383219:P216S	P	-	1	0	KRTAP10-6	44836148	0.000000	0.05858	0.006000	0.13384	0.237000	0.25408	-0.250000	0.08830	0.184000	0.20083	0.508000	0.49915	CCA	G|0.968;A|0.032	0.032	strong		0.672	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
SLC39A11	201266	hgsc.bcm.edu	37	17	70645032	70645032	+	Missense_Mutation	SNP	G	G	A	rs61736066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:70645032G>A	ENST00000542342.2	-	9	948	c.860C>T	c.(859-861)gCt>gTt	p.A287V	SLC39A11_ENST00000255559.3_Missense_Mutation_p.A280V|SLC39A11_ENST00000579988.1_5'UTR	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	287					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GATGGGCTCAGCCAGCACCAC	0.607													G|||	526	0.105032	0.062	0.1412	5008	,	,		18518	0.1647		0.0895	False		,,,				2504	0.092				p.A287V	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.C860T						PASS	.	G	VAL/ALA,VAL/ALA	283,4123	156.3+/-189.4	11,261,1931	62.0	57.0	59.0		860,839	4.5	0.8	17	dbSNP_129	59	702,7898	173.5+/-223.9	29,644,3627	yes	missense,missense	SLC39A11	NM_001159770.1,NM_139177.3	64,64	40,905,5558	AA,AG,GG		8.1628,6.4231,7.5734	probably-damaging,probably-damaging	287/343,280/336	70645032	985,12021	2203	4300	6503	SO:0001583	missense	201266	exon9			GGCTCAGCCAGCA	AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"""Solute carriers"""	14463	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 26"""	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.860C>T	17.37:g.70645032G>A	ENSP00000445829:p.Ala287Val	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	31	0.659574	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	37	CCDS54160.1	246	0.11263736263736264	29	0.05894308943089431	54	0.14917127071823205	95	0.1660839160839161	68	0.08970976253298153	G	13.90	2.375913	0.42105	0.064231	0.081628	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.52754	0.65;0.65	5.5	4.5	0.54988	.	0.125962	0.52532	D	0.000072	T	0.00178	0.0005	L	0.31664	0.95	0.09310	P	1.0	D;P	0.54601	0.967;0.92	P;P	0.58391	0.838;0.615	T	0.02064	-1.1220	9	0.06494	T	0.89	.	15.3722	0.74573	0.0:0.0:0.8594:0.1406	.	287;280	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	V	287;280	ENSP00000445829:A287V;ENSP00000255559:A280V	ENSP00000255559:A280V	A	-	2	0	SLC39A11	68156627	1.000000	0.71417	0.831000	0.32960	0.996000	0.88848	8.972000	0.93424	1.258000	0.44101	0.655000	0.94253	GCT	G|0.911;A|0.089	0.089	strong		0.607	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1		
LAMA1	284217	hgsc.bcm.edu	37	18	6993673	6993673	+	Missense_Mutation	SNP	T	T	C	rs62081533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:6993673T>C	ENST00000389658.3	-	35	5068	c.4975A>G	c.(4975-4977)Ata>Gta	p.I1659V		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1659	Domain II and I.			I -> V (in Ref. 1 and 3; CAA41418). {ECO:0000305}.	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)				TCAATGGCTATGGCCAGGTCT	0.443													T|||	568	0.113419	0.0371	0.1239	5008	,	,		17190	0.0903		0.1958	False		,,,				2504	0.1483				p.I1659V		Atlas-SNP	.											.	LAMA1	458	.	0			c.A4975G						PASS	.	T	VAL/ILE	318,4088	170.5+/-200.9	10,298,1895	196.0	176.0	183.0		4975	-3.5	0.0	18	dbSNP_129	183	1903,6697	338.1+/-322.6	214,1475,2611	yes	missense	LAMA1	NM_005559.3	29	224,1773,4506	CC,CT,TT		22.1279,7.2174,17.0767	benign	1659/3076	6993673	2221,10785	2203	4300	6503	SO:0001583	missense	284217	exon35			TGGCTATGGCCAG	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.4975A>G	18.37:g.6993673T>C	ENSP00000374309:p.Ile1659Val	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	239	115	0.481172	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	298	0.13644688644688643	26	0.052845528455284556	53	0.1464088397790055	59	0.10314685314685315	160	0.21108179419525067	T	9.069	0.996472	0.19043	0.072174	0.221279	ENSG00000101680	ENST00000389658	T	0.09163	3.01	5.95	-3.46	0.04767	Laminin I (1);	1.037100	0.07550	N	0.915181	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.47535	-0.9110	9	0.32370	T	0.25	.	9.4009	0.38431	0.1089:0.5229:0.0:0.3682	rs62081533	1659	P25391	LAMA1_HUMAN	V	1659	ENSP00000374309:I1659V	ENSP00000374309:I1659V	I	-	1	0	LAMA1	6983673	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.037000	0.12164	-0.707000	0.05022	-0.242000	0.12053	ATA	T|0.834;C|0.166	0.166	strong		0.443	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
ORAI1	84876	hgsc.bcm.edu	37	12	122079441	122079441	+	Silent	SNP	T	T	C	rs3825175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:122079441T>C	ENST00000330079.7	+	2	997	c.804T>C	c.(802-804)acT>acC	p.T268T		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	266					blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		GCCATAAGACTGACCGACAGT	0.612													C|||	2783	0.555711	0.7269	0.4755	5008	,	,		19656	0.5823		0.3976	False		,,,				2504	0.5164				p.T268T		Atlas-SNP	.											.	ORAI1	66	.	0			c.T804C						PASS	.	C		2972,1284		1057,858,213	73.0	84.0	81.0		804	-2.2	1.0	12	dbSNP_107	81	3562,4922		746,2070,1426	no	coding-synonymous	ORAI1	NM_032790.3		1803,2928,1639	CC,CT,TT		41.9849,30.1692,48.7127		268/304	122079441	6534,6206	2128	4242	6370	SO:0001819	synonymous_variant	84876	exon2			TAAGACTGACCGA	AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.804T>C	12.37:g.122079441T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	145	56	0.386207	NM_032790	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	Silent	SNP	ENST00000330079.7	37	CCDS41851.1																																																																																			T|0.470;C|0.530	0.530	strong		0.612	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
ATAD5	79915	hgsc.bcm.edu	37	17	29221584	29221584	+	Missense_Mutation	SNP	A	A	G	rs114345202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:29221584A>G	ENST00000321990.4	+	22	5678	c.5300A>G	c.(5299-5301)aAt>aGt	p.N1767S	TEFM_ENST00000579183.1_5'Flank	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1767					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)				TTTTACAGCAATGCTTGGAAG	0.368													A|||	27	0.00539137	0.0189	0.0029	5008	,	,		18155	0.0		0.0	False		,,,				2504	0.0				p.N1767S		Atlas-SNP	.											.	ATAD5	150	.	0			c.A5300G						PASS	.	A	SER/ASN	64,4342	59.3+/-96.0	0,64,2139	79.0	77.0	78.0		5300	-0.4	0.4	17	dbSNP_132	78	11,8589	8.4+/-32.0	0,11,4289	yes	missense	ATAD5	NM_024857.3	46	0,75,6428	GG,GA,AA		0.1279,1.4526,0.5767	benign	1767/1845	29221584	75,12931	2203	4300	6503	SO:0001583	missense	79915	exon22			ACAGCAATGCTTG		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.5300A>G	17.37:g.29221584A>G	ENSP00000313171:p.Asn1767Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	11	0.005036630036630037	9	0.018292682926829267	2	0.0055248618784530384	0	0.0	0	0.0	A	3.076	-0.190144	0.06299	0.014526	0.001279	ENSG00000176208	ENST00000321990	T	0.07800	3.16	5.59	-0.38	0.12490	.	0.706131	0.15070	N	0.282249	T	0.01061	0.0035	N	0.01267	-0.92	0.21256	N	0.999741	B	0.10296	0.003	B	0.08055	0.003	T	0.46062	-0.9218	10	0.21540	T	0.41	.	5.7512	0.18148	0.4172:0.0:0.441:0.1418	.	1767	Q96QE3	ATAD5_HUMAN	S	1767	ENSP00000313171:N1767S	ENSP00000313171:N1767S	N	+	2	0	ATAD5	26245710	0.924000	0.31332	0.415000	0.26534	0.785000	0.44390	0.700000	0.25601	-0.099000	0.12263	-0.334000	0.08254	AAT	A|0.994;G|0.006	0.006	strong		0.368	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
HNRNPDL	9987	hgsc.bcm.edu	37	4	83347266	83347266	+	Silent	SNP	A	A	G	rs79373393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:83347266A>G	ENST00000295470.5	-	7	1384	c.1209T>C	c.(1207-1209)taT>taC	p.Y403Y	HNRNPDL_ENST00000514511.1_5'UTR|HNRNPDL_ENST00000502762.1_Silent_p.Y403Y|HNRNPDL_ENST00000602300.1_Silent_p.Y284Y|HNRNPDL_ENST00000349655.4_Silent_p.Y227Y	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	403	Gly-rich.|Necessary for interaction with TNPO1.|Necessary for its nuclear import and export.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										ATGCCTTGCCATAAGTGCTCT	0.363													a|||	62	0.0123802	0.0038	0.0202	5008	,	,		16669	0.0		0.0398	False		,,,				2504	0.0031				p.Y403Y		Atlas-SNP	.											.	HNRPDL	35	.	0			c.T1209C						PASS	.	A	,	44,4362	43.8+/-77.6	0,44,2159	135.0	123.0	127.0		1038,1209	-11.7	0.1	4	dbSNP_132	127	286,8314	107.8+/-168.5	3,280,4017	no	coding-synonymous,coding-synonymous	HNRPDL	NM_001207000.1,NM_031372.3	,	3,324,6176	GG,GA,AA		3.3256,0.9986,2.5373	,	346/364,403/421	83347266	330,12676	2203	4300	6503	SO:0001819	synonymous_variant	9987	exon7			CTTGCCATAAGTG	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"""RNA binding motif (RRM) containing"""	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.1209T>C	4.37:g.83347266A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Silent	SNP	ENST00000295470.5	37	CCDS3593.1																																																																																			A|0.975;G|0.025	0.025	strong		0.363	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455978	5455978	+	Missense_Mutation	SNP	T	T	C	rs386806230|rs8107825	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5455978T>C	ENST00000222033.4	+	1	553	c.476T>C	c.(475-477)gTg>gCg	p.V159A		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	159	PA.		V -> A (in dbSNP:rs8107825).	AIV -> SIA (in Ref. 4; AAH17592). {ECO:0000305}.		cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		GGCGCCATCGTGCTGATCCGC	0.677													C|||	2726	0.544329	0.3744	0.4957	5008	,	,		15728	0.752		0.5219	False		,,,				2504	0.6176				p.V159A		Atlas-SNP	.											.	ZNRF4	59	.	0			c.T476C						PASS	.	C	ALA/VAL	1603,2649		348,907,871	28.0	31.0	30.0		476	-3.1	0.0	19	dbSNP_116	30	4077,4391		1076,1925,1233	yes	missense	ZNRF4	NM_181710.3	64	1424,2832,2104	CC,CT,TT		48.146,37.6999,44.6541	benign	159/430	5455978	5680,7040	2126	4234	6360	SO:0001583	missense	148066	exon1			CCATCGTGCTGAT	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.476T>C	19.37:g.5455978T>C	ENSP00000222033:p.Val159Ala	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	1232	0.5641025641025641	191	0.3882113821138211	201	0.5552486187845304	447	0.7814685314685315	393	0.5184696569920845	C	0.375	-0.931828	0.02359	0.376999	0.48146	ENSG00000105428	ENST00000222033	T	0.10668	2.85	4.65	-3.08	0.05347	Protease-associated domain, PA (1);	0.244527	0.32503	N	0.006003	T	0.00012	0.0000	N	0.17248	0.465	0.80722	P	0.0	B	0.10296	0.003	B	0.14578	0.011	T	0.39035	-0.9633	9	0.02654	T	1	-7.3391	12.8579	0.57897	0.0:0.5818:0.0:0.4182	rs8107825;rs17856547;rs60068947;rs8107825	159	Q8WWF5	ZNRF4_HUMAN	A	159	ENSP00000222033:V159A	ENSP00000222033:V159A	V	+	2	0	ZNRF4	5406978	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	-0.987000	0.03743	-0.981000	0.03520	-1.140000	0.01884	GTG	T|0.460;C|0.540	0.540	strong		0.677	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
LILRB1	10859	hgsc.bcm.edu	37	19	55143395	55143395	+	Missense_Mutation	SNP	T	T	G	rs370374304		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55143395T>G	ENST00000396331.1	+	6	725	c.368T>G	c.(367-369)aTc>aGc	p.I123S	LILRB1_ENST00000396315.1_Missense_Mutation_p.I123S|LILRB1_ENST00000427581.2_Missense_Mutation_p.I159S|LILRB1_ENST00000324602.7_Missense_Mutation_p.I123S|LILRB1_ENST00000396327.3_Missense_Mutation_p.I123S|LILRB1_ENST00000434867.2_Missense_Mutation_p.I123S|LILRB1_ENST00000396321.2_Missense_Mutation_p.I123S|LILRB1_ENST00000396332.4_Missense_Mutation_p.I123S|LILRB1_ENST00000418536.2_Missense_Mutation_p.I123S|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396317.1_Missense_Mutation_p.I123S|LILRB1_ENST00000448689.1_Missense_Mutation_p.I123S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	123	Ig-like C2-type 2.				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)		GGAGCCTACATCAAACCCACC	0.587										HNSCC(37;0.09)			N|||	1	0.000199681	0.0008	0.0	5008	,	,		17815	0.0		0.0	False		,,,				2504	0.0				p.I123S		Atlas-SNP	.											.	LILRB1	140	.	0			c.T368G						PASS	.	G	SER/ILE,SER/ILE,SER/ILE,SER/ILE	0,4406		0,0,2203	72.0	75.0	74.0		368,368,368,368	-3.0	0.0	19		74	2,8598	818.7+/-406.8	0,2,4298	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	142,142,142,142	0,2,6501	GG,GT,TT		0.0233,0.0,0.0154	benign,benign,benign,benign	123/653,123/652,123/652,123/651	55143395	2,13004	2203	4300	6503	SO:0001583	missense	10859	exon5			CCTACATCAAACC	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.368T>G	19.37:g.55143395T>G	ENSP00000379622:p.Ile123Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.736760	0.00088	0.0	2.33E-4	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02	1.57	-2.95	0.05564	Immunoglobulin-like fold (1);	1.339760	0.04742	N	0.422960	T	0.02929	0.0087	N	0.00121	-2.07	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	0.04013	0.0;0.001;0.0;0.0;0.0	T	0.35525	-0.9785	10	0.02654	T	1	.	2.0172	0.03500	0.3909:0.0:0.3453:0.2638	.	123;123;123;123;123	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	S	123;123;123;123;123;123;123;123;159;123;123	ENSP00000379614:I123S;ENSP00000391514:I123S;ENSP00000409968:I123S;ENSP00000379622:I123S;ENSP00000379618:I123S;ENSP00000315997:I123S;ENSP00000405243:I123S;ENSP00000379623:I123S;ENSP00000395004:I159S;ENSP00000379610:I123S;ENSP00000379608:I123S	ENSP00000315997:I123S	I	+	2	0	LILRB1	59835207	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.408000	0.00124	-0.614000	0.05687	-3.867000	0.00017	ATC	.	.	weak		0.587	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
KNG1	3827	hgsc.bcm.edu	37	3	186459646	186459646	+	Silent	SNP	G	G	A	rs5030085	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:186459646G>A	ENST00000265023.4	+	10	1673	c.1461G>A	c.(1459-1461)ggG>ggA	p.G487G	KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_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	88	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	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	
ABCA3	21	hgsc.bcm.edu	37	16	2327929	2327929	+	Silent	SNP	T	T	C	rs540282149	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2327929T>C	ENST00000301732.5	-	31	5560	c.4860A>G	c.(4858-4860)caA>caG	p.Q1620Q	ABCA3_ENST00000382381.3_Silent_p.Q1562Q	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1620					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)	GCGCCTCCTGTTGCCCTTCAC	0.672													T|||	2	0.000399361	0.0	0.0	5008	,	,		16834	0.0		0.0	False		,,,				2504	0.002				p.Q1620Q		Atlas-SNP	.											.	ABCA3	176	.	0			c.A4860G						PASS	.						28.0	29.0	28.0					16																	2327929		2198	4300	6498	SO:0001819	synonymous_variant	21	exon31			CTCCTGTTGCCCT	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.4860A>G	16.37:g.2327929T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			.	.	none		0.672	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
GAS8	2622	hgsc.bcm.edu	37	16	90106746	90106746	+	Silent	SNP	C	C	T	rs61734731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90106746C>T	ENST00000268699.4	+	9	1172	c.1050C>T	c.(1048-1050)acC>acT	p.T350T	GAS8_ENST00000540721.1_3'UTR|URAHP_ENST00000517889.1_RNA|GAS8_ENST00000536122.1_Silent_p.T325T	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	350					cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		GGAAGTTCACCGCAGCCATCC	0.627													c|||	136	0.0271565	0.0091	0.0115	5008	,	,		19539	0.0446		0.0487	False		,,,				2504	0.0225				p.T350T		Atlas-SNP	.											GAS8,NS,carcinoma,0,1	GAS8	29	1	0			c.C1050T						PASS	.	C		65,4323		0,65,2129	61.0	45.0	51.0		1050	-11.6	0.0	16	dbSNP_129	51	507,8091		15,477,3807	no	coding-synonymous	GAS8	NM_001481.2		15,542,5936	TT,TC,CC		5.8967,1.4813,4.4047		350/479	90106746	572,12414	2194	4299	6493	SO:0001819	synonymous_variant	2622	exon9			GTTCACCGCAGCC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.1050C>T	16.37:g.90106746C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			C|0.963;T|0.037	0.037	strong		0.627	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
WDR93	56964	hgsc.bcm.edu	37	15	90281278	90281278	+	Missense_Mutation	SNP	A	A	C	rs35365973	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90281278A>C	ENST00000268130.7	+	16	1873	c.1772A>C	c.(1771-1773)tAt>tCt	p.Y591S	WDR93_ENST00000444934.2_Missense_Mutation_p.Y308S|WDR93_ENST00000560294.1_Missense_Mutation_p.Y563S	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	591					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)			ACAGGAGACTATTCACATGAA	0.463													A|||	79	0.0157748	0.0023	0.0202	5008	,	,		18309	0.0		0.0507	False		,,,				2504	0.0112				p.Y591S		Atlas-SNP	.											.	WDR93	63	.	0			c.A1772C						PASS	.	A	SER/TYR	36,4364	41.6+/-74.8	1,34,2165	271.0	268.0	269.0		1772	-2.9	0.0	15	dbSNP_126	269	439,8159	134.7+/-192.1	13,413,3873	yes	missense	WDR93	NM_020212.1	144	14,447,6038	CC,CA,AA		5.1058,0.8182,3.6544	benign	591/687	90281278	475,12523	2200	4299	6499	SO:0001583	missense	56964	exon16			GAGACTATTCACA		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.1772A>C	15.37:g.90281278A>C	ENSP00000268130:p.Tyr591Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	53	0.024267399267399268	3	0.006097560975609756	8	0.022099447513812154	0	0.0	42	0.055408970976253295	A	8.700	0.909492	0.17833	0.008182	0.051058	ENSG00000140527	ENST00000268130;ENST00000444934	T;T	0.40476	2.03;1.03	4.68	-2.93	0.05598	.	1.368680	0.04786	N	0.430633	T	0.03136	0.0092	N	0.22421	0.69	0.09310	N	1	B;B	0.22211	0.027;0.066	B;B	0.18871	0.015;0.023	T	0.12604	-1.0541	10	0.23891	T	0.37	1.3311	9.9447	0.41602	0.4348:0.0:0.5652:0.0	rs35365973;rs62023384	563;591	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	S	591;308	ENSP00000268130:Y591S;ENSP00000403871:Y308S	ENSP00000268130:Y591S	Y	+	2	0	WDR93	88082282	0.000000	0.05858	0.005000	0.12908	0.002000	0.02628	-0.457000	0.06745	-0.443000	0.07180	-0.296000	0.09543	TAT	A|0.966;C|0.034	0.034	strong		0.463	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
CDH9	1007	hgsc.bcm.edu	37	5	26885964	26885964	+	Silent	SNP	T	T	G	rs35328154	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:26885964T>G	ENST00000231021.4	-	11	1813	c.1641A>C	c.(1639-1641)gcA>gcC	p.A547A		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	547	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TCATGATTCCTGCTGTATTAT	0.318													T|||	49	0.00978435	0.0	0.0187	5008	,	,		17688	0.0		0.0109	False		,,,				2504	0.0256				p.A547A	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1641C						PASS	.	T		7,4399	11.4+/-27.6	0,7,2196	55.0	58.0	57.0		1641	-4.3	1.0	5	dbSNP_126	57	82,8518	44.0+/-102.2	0,82,4218	no	coding-synonymous	CDH9	NM_016279.3		0,89,6414	GG,GT,TT		0.9535,0.1589,0.6843		547/790	26885964	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	1007	exon11			GATTCCTGCTGTA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1641A>C	5.37:g.26885964T>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	37	CCDS3893.1																																																																																			T|0.992;G|0.008	0.008	strong		0.318	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
TPH2	121278	hgsc.bcm.edu	37	12	72416235	72416235	+	Silent	SNP	A	A	T	rs4290270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:72416235A>T	ENST00000333850.3	+	9	1266	c.1125A>T	c.(1123-1125)gcA>gcT	p.A375A		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	375					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)	AACTGCGGGCATATGGAGCAG	0.428													A|||	2440	0.48722	0.385	0.4899	5008	,	,		18272	0.4663		0.6233	False		,,,				2504	0.5051				p.A375A		Atlas-SNP	.											.	TPH2	81	.	0			c.A1125T						PASS	.	A		1829,2577	534.0+/-373.9	378,1073,752	116.0	108.0	111.0		1125	-12.0	0.7	12	dbSNP_111	111	5535,3065	660.9+/-401.8	1768,1999,533	no	coding-synonymous	TPH2	NM_173353.3		2146,3072,1285	TT,TA,AA		35.6395,41.5116,43.38		375/491	72416235	7364,5642	2203	4300	6503	SO:0001819	synonymous_variant	121278	exon9			GCGGGCATATGGA	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.1125A>T	12.37:g.72416235A>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_173353	A6NGA4|Q14CB0	Silent	SNP	ENST00000333850.3	37	CCDS31859.1																																																																																			A|0.450;T|0.550	0.550	strong		0.428	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145015877	145015877	+	Missense_Mutation	SNP	G	G	T	rs77741369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:145015877G>T	ENST00000530740.1	-	3	462	c.424C>A	c.(424-426)Ctt>Att	p.L142I	PDE4DIP_ENST00000369348.3_Missense_Mutation_p.L142I|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.L71I|PDE4DIP_ENST00000493130.2_Missense_Mutation_p.L71I|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.L142I|RP11-326G21.1_ENST00000610119.1_RNA|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.L71I			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	5					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAGTCTCGAAGAGCCTGGGTC	0.438			T	PDGFRB	MPD																																p.L142I		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369348,NS,carcinoma,0,2	PDE4DIP	817	2	0			c.C424A						PASS	.	G	ILE/LEU,ILE/LEU	351,4055		0,351,1852	501.0	587.0	558.0		211,424	5.3	1.0	1	dbSNP_131	558	2135,6465		0,2135,2165	yes	missense,missense	PDE4DIP	NM_001198832.1,NM_022359.5	5,5	0,2486,4017	TT,TG,GG		24.8256,7.9664,19.1143	,	71/2241,142/311	145015877	2486,10520	2203	4300	6503	SO:0001583	missense	9659	exon3			CTCGAAGAGCCTG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.424C>A	1.37:g.145015877G>T	ENSP00000435654:p.Leu142Ile	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	269	31	0.115242	NM_022359	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000530740.1	37		419	0.19184981684981686	18	0.036585365853658534	88	0.2430939226519337	49	0.08566433566433566	264	0.3482849604221636	G	19.22	3.784896	0.70222	0.079664	0.248256	ENSG00000178104	ENST00000313382;ENST00000530740;ENST00000369359;ENST00000530078;ENST00000369348;ENST00000531369;ENST00000493130;ENST00000478649	T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19	5.26	5.26	0.73747	.	.	.	.	.	T	0.42017	0.1184	M	0.74467	2.265	0.80722	D	1	D;B;P	0.53619	0.961;0.445;0.931	P;B;P	0.53224	0.721;0.282;0.699	T	0.26573	-1.0099	9	0.42905	T	0.14	.	14.2417	0.65961	0.0:0.0:1.0:0.0	.	71;142;71	Q5VU43-3;E9PJ64;E9PQH9	.;.;.	I	71;142;142;71;142;72;71;71	ENSP00000327209:L71I;ENSP00000435654:L142I;ENSP00000358366:L142I;ENSP00000358354:L142I;ENSP00000435616:L72I	ENSP00000327209:L71I	L	-	1	0	PDE4DIP	143727234	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.501000	0.60393	2.727000	0.93392	0.655000	0.94253	CTT	G|0.821;T|0.179	0.179	strong		0.438	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
LRIT1	26103	hgsc.bcm.edu	37	10	85992511	85992511	+	Silent	SNP	T	T	C	rs3814209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85992511T>C	ENST00000372105.3	-	4	1065	c.1044A>G	c.(1042-1044)ccA>ccG	p.P348P		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	348						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						TGGAAGTCGGTGGCTCAGTGA	0.567													C|||	2468	0.492812	0.8661	0.4798	5008	,	,		21416	0.2579		0.3976	False		,,,				2504	0.3374				p.P348P		Atlas-SNP	.											LRIT1,right_upper_lobe,carcinoma,-1,1	LRIT1	73	1	0			c.A1044G						scavenged	.	C		3428,978	367.8+/-318.4	1342,744,117	57.0	48.0	51.0		1044	-8.9	0.0	10	dbSNP_107	51	3357,5243	640.7+/-399.6	681,1995,1624	no	coding-synonymous	LRIT1	NM_015613.2		2023,2739,1741	CC,CT,TT		39.0349,22.197,47.8318		348/624	85992511	6785,6221	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon4			AGTCGGTGGCTCA	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.1044A>G	10.37:g.85992511T>C		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	129	68	0.527132	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			T|0.496;C|0.503	0.503	strong		0.567	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
OR5V1	81696	hgsc.bcm.edu	37	6	29323276	29323276	+	Missense_Mutation	SNP	C	C	T	rs61742983	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	45	0	0		WXS	Illumina HiSeq	Phase_I	42	30	0.714286	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		
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31838085	31838085	+	Silent	SNP	G	G	A	rs5997988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31838085G>A	ENST00000397525.1	-	17	2449	c.2226C>T	c.(2224-2226)agC>agT	p.S742S	EIF4ENIF1_ENST00000344710.5_Silent_p.S568S|EIF4ENIF1_ENST00000330125.5_Silent_p.S742S|EIF4ENIF1_ENST00000382180.2_Silent_p.S397S|EIF4ENIF1_ENST00000441289.1_5'Flank|EIF4ENIF1_ENST00000397523.1_Silent_p.S718S	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	195	0	0		WXS	Illumina HiSeq	Phase_I	168	79	0.470238	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	
ZNF419	79744	hgsc.bcm.edu	37	19	58002924	58002924	+	Missense_Mutation	SNP	G	G	A	rs145680611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58002924G>A	ENST00000221735.7	+	3	344	c.158G>A	c.(157-159)cGc>cAc	p.R53H	ZNF419_ENST00000347466.6_Missense_Mutation_p.R54H|ZNF419_ENST00000442920.2_Missense_Mutation_p.R40H|AC003005.4_ENST00000601674.1_Missense_Mutation_p.R40H|ZNF419_ENST00000518999.1_Missense_Mutation_p.R54H|ZNF419_ENST00000520540.1_Missense_Mutation_p.R41H|ZNF419_ENST00000426954.2_Missense_Mutation_p.R41H|ZNF419_ENST00000354197.4_Missense_Mutation_p.R41H|ZNF419_ENST00000415379.2_Missense_Mutation_p.R40H|ZNF419_ENST00000424930.2_Missense_Mutation_p.R54H			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	53	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CTCCTCTACCGCAATGTGATG	0.532													G|||	34	0.00678914	0.0	0.0101	5008	,	,		19458	0.0		0.0229	False		,,,				2504	0.0041				p.R54H		Atlas-SNP	.											ZNF419_ENST00000424930,colon,carcinoma,0,8	ZNF419	134	8	0			c.G161A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	19,4387	26.2+/-53.5	0,19,2184	109.0	106.0	107.0		161,122,119,161,122,119,158	-2.6	0.0	19	dbSNP_134	107	179,8415	81.5+/-144.1	0,179,4118	no	missense,missense,missense,missense,missense,missense,missense	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	29,29,29,29,29,29,29	0,198,6302	AA,AG,GG		2.0828,0.4312,1.5231	benign,benign,benign,benign,benign,benign,benign	54/512,41/499,40/498,54/479,41/466,40/465,53/511	58002924	198,12802	2203	4297	6500	SO:0001583	missense	79744	exon3			TCTACCGCAATGT	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.158G>A	19.37:g.58002924G>A	ENSP00000221735:p.Arg53His	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	227	95	0.418502	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	G	1.463	-0.561777	0.03939	0.004312	0.020828	ENSG00000105136	ENST00000284020;ENST00000524372;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000427558;ENST00000523882;ENST00000520540;ENST00000442920;ENST00000523312;ENST00000517598;ENST00000347466;ENST00000523138;ENST00000415379;ENST00000521754;ENST00000221735;ENST00000518999;ENST00000521137	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.02737	4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18;4.18	2.79	-2.61	0.06171	Krueppel-associated box (4);	.	.	.	.	T	0.01222	0.0040	L	0.43646	1.37	0.09310	N	1	B;B;B;B;B;B;P	0.41041	0.005;0.005;0.002;0.001;0.026;0.003;0.736	B;B;B;B;B;B;B	0.38655	0.002;0.002;0.002;0.002;0.009;0.002;0.278	T	0.34477	-0.9827	9	0.59425	D	0.04	.	3.4635	0.07541	0.3514:0.0:0.4706:0.1779	.	40;40;40;41;54;54;53	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	H	33;41;54;41;41;53;54;41;40;40;54;54;53;40;41;53;54;53	ENSP00000388864:R54H;ENSP00000390916:R41H;ENSP00000346136:R41H;ENSP00000428181:R54H;ENSP00000429471:R41H;ENSP00000414709:R40H;ENSP00000428515:R40H;ENSP00000299860:R54H;ENSP00000429504:R53H;ENSP00000392129:R40H;ENSP00000428523:R41H;ENSP00000221735:R53H;ENSP00000427723:R54H;ENSP00000429628:R53H	ENSP00000221735:R53H	R	+	2	0	ZNF419	62694736	0.000000	0.05858	0.000000	0.03702	0.196000	0.23810	-1.838000	0.01687	-0.662000	0.05338	0.511000	0.50034	CGC	G|0.983;A|0.017	0.017	strong		0.532	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
PHYHD1	254295	hgsc.bcm.edu	37	9	131689361	131689361	+	Silent	SNP	G	G	A	rs751340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	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	
LYST	1130	hgsc.bcm.edu	37	1	235952009	235952009	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:235952009A>G	ENST00000389794.3	-	13	4854	c.4680T>C	c.(4678-4680)ctT>ctC	p.L1560L	LYST_ENST00000389793.2_Silent_p.L1560L|LYST_ENST00000536965.1_3'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1560					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)			ACCGAAAGATAAGAGTGGCAT	0.358																																					p.L1560L		Atlas-SNP	.											LYST,bladder,carcinoma,-2,1	LYST	370	1	0			c.T4680C						scavenged	.						89.0	76.0	81.0					1																	235952009		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon13			AAAGATAAGAGTG	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.4680T>C	1.37:g.235952009A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.	.	none		0.358	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
ANTXR2	118429	hgsc.bcm.edu	37	4	80905991	80905991	+	Silent	SNP	G	G	T	rs386676514|rs72653288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:80905991G>T	ENST00000307333.7	-	13	1070	c.1068C>A	c.(1066-1068)ccC>ccA	p.P356P	ANTXR2_ENST00000404191.1_Silent_p.P279P|ANTXR2_ENST00000346652.6_Silent_p.P253P|ANTXR2_ENST00000403729.2_Silent_p.P356P	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	356	Poly-Pro.				reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						GTGCAGGGGCGGGTGGTGGTG	0.353									Juvenile Hyaline Fibromatosis				g|||	231	0.0461262	0.0242	0.0519	5008	,	,		13030	0.0109		0.0915	False		,,,				2504	0.0613				p.P356P		Atlas-SNP	.											.	ANTXR2	97	.	0			c.C1068A						PASS	.						67.0	70.0	69.0					4																	80905991		1796	4063	5859	SO:0001819	synonymous_variant	118429	exon13	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	AGGGGCGGGTGGT	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"""capillary morphogenesis protein 2"""	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.1068C>A	4.37:g.80905991G>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	231	101	0.437229	NM_001145794	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Silent	SNP	ENST00000307333.7	37	CCDS47086.1																																																																																			C|0.000;G|0.947;T|0.053	0.053	strong		0.353	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172	
CCDC27	148870	hgsc.bcm.edu	37	1	3677933	3677933	+	Missense_Mutation	SNP	T	T	C	rs1181883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3677933T>C	ENST00000294600.2	+	5	884	c.800T>C	c.(799-801)aTg>aCg	p.M267T		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	267			M -> T (in dbSNP:rs1181883). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							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)		GCCCTGAAGATGCAGCTGAAA	0.577													C|||	2384	0.476038	0.6944	0.4683	5008	,	,		18850	0.2788		0.4354	False		,,,				2504	0.4315				p.M267T		Atlas-SNP	.											.	CCDC27	79	.	0			c.T800C						PASS	.	C	THR/MET	2721,1685	508.9+/-367.1	851,1019,333	80.0	77.0	78.0		800	-1.3	0.3	1	dbSNP_87	78	3371,5229	641.1+/-399.7	666,2039,1595	yes	missense	CCDC27	NM_152492.2	81	1517,3058,1928	CC,CT,TT		39.1977,38.2433,46.8399	benign	267/657	3677933	6092,6914	2203	4300	6503	SO:0001583	missense	148870	exon5			TGAAGATGCAGCT		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.800T>C	1.37:g.3677933T>C	ENSP00000294600:p.Met267Thr	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	194	85	0.438144	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	994	0.4551282051282051	356	0.7235772357723578	164	0.4530386740331492	148	0.25874125874125875	326	0.43007915567282323	C	0.025	-1.378822	0.01204	0.617567	0.391977	ENSG00000162592	ENST00000294600	T	0.16897	2.31	3.75	-1.31	0.09230	.	0.477568	0.17824	N	0.160777	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	0.24870	-1.0148	9	0.17832	T	0.49	-30.5079	0.0397	0.00008	0.2978:0.1762:0.2037:0.3224	rs1181883;rs17371673;rs52791836;rs58427864;rs1181883	267	Q2M243	CCD27_HUMAN	T	267	ENSP00000294600:M267T	ENSP00000294600:M267T	M	+	2	0	CCDC27	3667793	0.039000	0.19947	0.345000	0.25642	0.018000	0.09664	-0.489000	0.06490	-0.433000	0.07286	-3.293000	0.00046	ATG	T|0.530;C|0.470	0.470	strong		0.577	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
PKD1	5310	hgsc.bcm.edu	37	16	2165395	2165395	+	Missense_Mutation	SNP	G	G	A	rs138575342		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2165395G>A	ENST00000262304.4	-	10	2289	c.2081C>T	c.(2080-2082)cCc>cTc	p.P694L	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.P694L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	694					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTGCGCGGGGGGCCCCGCGGG	0.682																																					p.P694L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	1	0			c.C2081T						scavenged	.						3.0	5.0	4.0					16																	2165395		1659	3504	5163	SO:0001583	missense	5310	exon10			GCGGGGGGCCCCG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.2081C>T	16.37:g.2165395G>A	ENSP00000262304:p.Pro694Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	120	34	0.283333	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.606219	0.46527	.	.	ENSG00000008710	ENST00000262304;ENST00000423118	T;T	0.37915	1.17;1.17	5.17	5.17	0.71159	Polycystin cation channel (1);	0.333966	0.29587	N	0.011721	T	0.57725	0.2073	M	0.76002	2.32	0.52099	D	0.999947	D;D	0.89917	1.0;1.0	D;D	0.79108	0.984;0.992	T	0.61202	-0.7110	10	0.72032	D	0.01	.	10.8459	0.46743	0.0877:0.0:0.9123:0.0	.	694;694	P98161-3;P98161	.;PKD1_HUMAN	L	694	ENSP00000262304:P694L;ENSP00000399501:P694L	ENSP00000262304:P694L	P	-	2	0	PKD1	2105396	0.999000	0.42202	0.746000	0.31095	0.102000	0.19082	4.544000	0.60691	2.384000	0.81235	0.557000	0.71058	CCC	.	.	weak		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
HPS3	84343	hgsc.bcm.edu	37	3	148872987	148872987	+	Silent	SNP	G	G	A	rs6440589	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148872987G>A	ENST00000296051.2	+	8	1634	c.1494G>A	c.(1492-1494)caG>caA	p.Q498Q	HPS3_ENST00000460120.1_Silent_p.Q333Q	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	498					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)			CACCAGTGCAGCTGTACAAAG	0.333									Hermansky-Pudlak syndrome				A|||	2455	0.490216	0.7042	0.3501	5008	,	,		16917	0.3631		0.4254	False		,,,				2504	0.498				p.Q498Q		Atlas-SNP	.											.	HPS3	104	.	0			c.G1494A						PASS	.	A		2913,1493	475.2+/-357.2	943,1027,233	141.0	147.0	145.0		1494	-6.1	0.0	3	dbSNP_116	145	3771,4829	614.4+/-396.2	860,2051,1389	no	coding-synonymous	HPS3	NM_032383.3		1803,3078,1622	AA,AG,GG		43.8488,33.8856,48.6083		498/1005	148872987	6684,6322	2203	4300	6503	SO:0001819	synonymous_variant	84343	exon8	Familial Cancer Database	HPS, HPS1-8	AGTGCAGCTGTAC	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.1494G>A	3.37:g.148872987G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1																																																																																			G|0.497;A|0.503	0.503	strong		0.333	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
CD109	135228	hgsc.bcm.edu	37	6	74497009	74497009	+	Missense_Mutation	SNP	A	A	G	rs2351528	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:74497009A>G	ENST00000287097.5	+	21	2502	c.2390A>G	c.(2389-2391)aAt>aGt	p.N797S	CD109_ENST00000437994.2_Missense_Mutation_p.N797S|CD109_ENST00000422508.2_Missense_Mutation_p.N720S			Q6YHK3	CD109_HUMAN	CD109 molecule	797			N -> S (in dbSNP:rs2351528). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ATGACTTCAAATGAAATAAAT	0.378													G|||	1865	0.372404	0.4675	0.4049	5008	,	,		19371	0.4087		0.339	False		,,,				2504	0.2178				p.N797S		Atlas-SNP	.											CD109,caecum,carcinoma,0,1	CD109	170	1	0			c.A2390G						PASS	.	G	SER/ASN,SER/ASN,SER/ASN	2051,2355	608.2+/-391.1	495,1061,647	65.0	68.0	67.0		2390,2159,2390	1.6	0.1	6	dbSNP_100	67	3057,5543	660.2+/-401.7	552,1953,1795	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	46,46,46	1047,3014,2442	GG,GA,AA		35.5465,46.5502,39.2742	benign,benign,benign	797/1429,720/1369,797/1446	74497009	5108,7898	2203	4300	6503	SO:0001583	missense	135228	exon21			CTTCAAATGAAAT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.2390A>G	6.37:g.74497009A>G	ENSP00000287097:p.Asn797Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	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	
HSD3B2	3284	hgsc.bcm.edu	37	1	119964933	119964933	+	Missense_Mutation	SNP	T	T	C	rs75429891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:119964933T>C	ENST00000543831.1	+	4	1058	c.809T>C	c.(808-810)aTc>aCc	p.I270T	HSD3B2_ENST00000369416.3_Missense_Mutation_p.I270T	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	270					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)	CTTAATTACATCCTGAGCAAA	0.498													T|||	2	0.000399361	0.0	0.0	5008	,	,		20150	0.0		0.002	False		,,,				2504	0.0				p.I270T		Atlas-SNP	.											.	HSD3B2	48	.	0			c.T809C						PASS	.	T	THR/ILE,THR/ILE	1,4405		0,1,2202	75.0	79.0	77.0		809,809	-8.0	0.0	1	dbSNP_131	77	6,8594		0,6,4294	no	missense,missense	HSD3B2	NM_000198.3,NM_001166120.1	89,89	0,7,6496	CC,CT,TT		0.0698,0.0227,0.0538	benign,benign	270/373,270/373	119964933	7,12999	2203	4300	6503	SO:0001583	missense	3284	exon4			ATTACATCCTGAG	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.809T>C	1.37:g.119964933T>C	ENSP00000445122:p.Ile270Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	170	72	0.423529	NM_001166120	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Missense_Mutation	SNP	ENST00000543831.1	37	CCDS902.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	-	0.003	-2.490832	0.00161	2.27E-4	6.98E-4	ENSG00000203859	ENST00000543831;ENST00000369416	D;D	0.88124	-2.34;-2.34	3.98	-7.97	0.01139	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.703655	0.13486	N	0.384300	T	0.28101	0.0693	N	0.00496	-1.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.55976	-0.8055	9	.	.	.	-2.0251	7.6517	0.28352	0.592:0.2386:0.0:0.1694	.	270	P26439	3BHS2_HUMAN	T	270	ENSP00000445122:I270T;ENSP00000358424:I270T	.	I	+	2	0	HSD3B2	119766456	0.000000	0.05858	0.034000	0.17996	0.257000	0.26127	-0.688000	0.05150	-1.777000	0.01283	-0.782000	0.03352	ATC	T|1.000;C|0.000	0.000	strong		0.498	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198	
EXTL3	2137	hgsc.bcm.edu	37	8	28574803	28574803	+	Silent	SNP	G	G	A	rs240951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:28574803G>A	ENST00000220562.4	+	3	2129	c.1227G>A	c.(1225-1227)ccG>ccA	p.P409P	EXTL3_ENST00000523149.1_Silent_p.P25P|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	409					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)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		CCAGCCTGCCGACTGAGTGGG	0.592													G|||	1314	0.26238	0.1876	0.2738	5008	,	,		19422	0.3472		0.2813	False		,,,				2504	0.2485				p.P409P		Atlas-SNP	.											.	EXTL3	83	.	0			c.G1227A						PASS	.	G		920,3486	345.4+/-308.5	89,742,1372	61.0	50.0	54.0		1227	-3.8	1.0	8	dbSNP_79	54	2248,6352	372.4+/-336.6	290,1668,2342	no	coding-synonymous	EXTL3	NM_001440.2		379,2410,3714	AA,AG,GG		26.1395,20.8806,24.358		409/920	28574803	3168,9838	2203	4300	6503	SO:0001819	synonymous_variant	2137	exon3			CCTGCCGACTGAG	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"""Exostosin glycosyltransferase family"""	3518	protein-coding gene	gene with protein product	"""REG receptor"", ""glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"""	605744	"""exostoses (multiple)-like 3"""			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.1227G>A	8.37:g.28574803G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_001440	D3DST8|O00225|Q53XT3	Silent	SNP	ENST00000220562.4	37	CCDS6070.1																																																																																			A|0.256;C|0.004	0.256	strong		0.592	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440	
WDR93	56964	hgsc.bcm.edu	37	15	90260145	90260145	+	Missense_Mutation	SNP	T	T	A	rs7163367	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90260145T>A	ENST00000268130.7	+	7	861	c.760T>A	c.(760-762)Tcc>Acc	p.S254T	RNU6-132P_ENST00000383863.1_RNA|WDR93_ENST00000560294.1_Missense_Mutation_p.S254T	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	254			S -> T (in dbSNP:rs7163367).		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)			TTCTCAGAACTCCCTTGGTCC	0.338													A|||	1879	0.3752	0.4766	0.3112	5008	,	,		15609	0.2044		0.3956	False		,,,				2504	0.4387				p.S254T		Atlas-SNP	.											WDR93,NS,carcinoma,-1,2	WDR93	63	2	0			c.T760A						PASS	.	A	THR/SER	2074,2326	603.5+/-390.1	483,1108,609	100.0	100.0	100.0		760	-2.3	0.0	15	dbSNP_116	100	3788,4810	613.1+/-396.1	816,2156,1327	yes	missense	WDR93	NM_020212.1	58	1299,3264,1936	AA,AT,TT		44.0568,47.1364,45.0992	benign	254/687	90260145	5862,7136	2200	4299	6499	SO:0001583	missense	56964	exon7			CAGAACTCCCTTG		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.760T>A	15.37:g.90260145T>A	ENSP00000268130:p.Ser254Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	53	50	0.943396	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	757	0.3466117216117216	201	0.40853658536585363	125	0.3453038674033149	132	0.23076923076923078	299	0.3944591029023747	A	0.011	-1.739211	0.00681	0.471364	0.440568	ENSG00000140527	ENST00000268130	T	0.21361	2.01	3.21	-2.28	0.06826	WD40 repeat-like-containing domain (1);	0.687039	0.13286	N	0.399397	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	0.32798	-0.9893	9	0.02654	T	1	-0.901	0.9508	0.01376	0.2657:0.319:0.1032:0.3121	rs7163367;rs52812393;rs7163367	254;254	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	T	254	ENSP00000268130:S254T	ENSP00000268130:S254T	S	+	1	0	WDR93	88061149	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.435000	0.06931	-0.913000	0.03832	-0.336000	0.08194	TCC	A|0.415;N|0.000	0.415	strong		0.338	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
BPIFB4	149954	hgsc.bcm.edu	37	20	31673846	31673846	+	Missense_Mutation	SNP	A	A	G	rs2070325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31673846A>G	ENST00000375483.3	+	5	802	c.802A>G	c.(802-804)Atc>Gtc	p.I268V		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	268			I -> V (in dbSNP:rs2070325).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CTTCCTGGACATCGCAGTAGA	0.612													A|||	2331	0.465455	0.2693	0.4611	5008	,	,		20190	0.7569		0.3797	False		,,,				2504	0.5215				p.I268V		Atlas-SNP	.											.	.	.	.	0			c.A802G						PASS	.	A	VAL/ILE	1173,3233	414.1+/-336.7	172,829,1202	138.0	121.0	127.0		802	3.9	1.0	20	dbSNP_96	127	3112,5488	475.3+/-369.1	575,1962,1763	yes	missense	BPIFB4	NM_182519.2	29	747,2791,2965	GG,GA,AA		36.186,26.6228,32.9463	possibly-damaging	268/615	31673846	4285,8721	2203	4300	6503	SO:0001583	missense	149954	exon5			CTGGACATCGCAG	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.802A>G	20.37:g.31673846A>G	ENSP00000364632:p.Ile268Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	1025	0.4693223443223443	141	0.2865853658536585	155	0.4281767955801105	435	0.7604895104895105	294	0.38786279683377306	A	15.21	2.766176	0.49574	0.266228	0.36186	ENSG00000186191	ENST00000375483	T	0.06528	3.29	3.94	3.94	0.45596	.	0.165701	0.40818	N	0.001009	T	0.00012	0.0000	L	0.46157	1.445	0.32473	P	0.542564	P	0.39535	0.677	B	0.43445	0.42	T	0.00414	-1.1754	9	0.41790	T	0.15	-16.0856	9.1151	0.36753	1.0:0.0:0.0:0.0	rs2070325;rs61233760;rs2070325	268	P59827	BPIB4_HUMAN	V	268	ENSP00000364632:I268V	ENSP00000364632:I268V	I	+	1	0	BPIFB4	31137507	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.418000	0.52721	1.649000	0.50652	0.402000	0.26972	ATC	A|0.615;G|0.385	0.385	strong		0.612	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
MICAL3	57553	hgsc.bcm.edu	37	22	18379640	18379640	+	Silent	SNP	C	C	T	rs61739477	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:18379640C>T	ENST00000441493.2	-	8	1408	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	MICAL3_ENST00000585038.1_Silent_p.P352P|MICAL3_ENST00000207726.7_Silent_p.P352P|MICAL3_ENST00000414725.2_Silent_p.P352P|MICAL3_ENST00000429452.1_Silent_p.P352P|MICAL3_ENST00000444520.1_Silent_p.P352P|MICAL3_ENST00000400561.2_Silent_p.P352P|MICAL3_ENST00000383094.3_Silent_p.P352P	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	352	Monooxygenase domain. {ECO:0000250}.				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)		AATCCAGAGACGGCAGCTGCT	0.582											OREG0026285	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	56	0.0111821	0.0	0.0029	5008	,	,		19187	0.0248		0.0149	False		,,,				2504	0.0143				p.P352P		Atlas-SNP	.											.	MICAL3	53	.	0			c.G1056A						PASS	.	C	,,	7,3129		0,7,1561	58.0	56.0	57.0		1056,1056,1056	-11.7	0.0	22	dbSNP_129	57	108,7056		1,106,3475	no	coding-synonymous,coding-synonymous,coding-synonymous	MICAL3	NM_001122731.1,NM_001136004.1,NM_015241.2	,,	1,113,5036	TT,TC,CC		1.5075,0.2232,1.1165	,,	352/967,352/1074,352/2003	18379640	115,10185	1568	3582	5150	SO:0001819	synonymous_variant	57553	exon8			CAGAGACGGCAGC	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.1056G>A	22.37:g.18379640C>T		Somatic	64	0	0	725	WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1																																																																																			C|0.987;T|0.013	0.013	strong		0.582	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
AKR7A3	22977	hgsc.bcm.edu	37	1	19615051	19615051	+	Missense_Mutation	SNP	C	C	G	rs201237444		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19615051C>G	ENST00000361640.4	-	1	693	c.153G>C	c.(151-153)gaG>gaC	p.E51D		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	51				E -> D (in Ref. 1; AAD02195). {ECO:0000305}.	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)		CGGACTGGCCCTCGCTGTACA	0.701																																					p.E51D		Atlas-SNP	.											AKR7A3,NS,carcinoma,0,1	AKR7A3	30	1	0			c.G153C						PASS	.						25.0	27.0	26.0					1																	19615051		2201	4299	6500	SO:0001583	missense	22977	exon1			CTGGCCCTCGCTG	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.153G>C	1.37:g.19615051C>G	ENSP00000355377:p.Glu51Asp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	206	46	0.223301	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Missense_Mutation	SNP	ENST00000361640.4	37	CCDS193.1	.	.	.	.	.	.	.	.	.	.	g	0.014	-1.578956	0.00879	.	.	ENSG00000162482	ENST00000361640	T	0.24350	1.86	3.11	-0.31	0.12765	NADP-dependent oxidoreductase domain (3);	0.107680	0.64402	N	0.000008	T	0.06826	0.0174	.	.	.	0.21220	N	0.99975	B	0.02656	0.0	B	0.01281	0.0	T	0.27773	-1.0064	9	0.02654	T	1	.	1.1645	0.01812	0.2187:0.3146:0.3071:0.1595	.	51	O95154	ARK73_HUMAN	D	51	ENSP00000355377:E51D	ENSP00000355377:E51D	E	-	3	2	AKR7A3	19487638	0.240000	0.23847	0.773000	0.31616	0.086000	0.17979	-0.588000	0.05774	-0.215000	0.10063	-0.699000	0.03677	GAG	C|0.996;G|0.004	0.004	weak		0.701	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
HLX	3142	hgsc.bcm.edu	37	1	221057831	221057831	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:221057831G>A	ENST00000366903.6	+	4	2753	c.1252G>A	c.(1252-1254)Gcc>Acc	p.A418T	HLX_ENST00000549319.1_Missense_Mutation_p.A204T	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	418	Ser-rich.				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)	p.A418T(1)		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)		CCTCATTACCGCcagcagtgc	0.627																																					p.A418T		Atlas-SNP	.											HLX,NS,carcinoma,0,1	HLX	67	1	1	Substitution - Missense(1)	endometrium(1)	c.G1252A						scavenged	.						36.0	33.0	34.0					1																	221057831		2203	4300	6503	SO:0001583	missense	3142	exon4			ATTACCGCCAGCA	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.1252G>A	1.37:g.221057831G>A	ENSP00000355870:p.Ala418Thr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	144	3	0.0208333	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.034418	0.35893	.	.	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;D;T	0.93426	-2.64;-3.22;0.52	4.72	-2.37	0.06643	.	0.404477	0.18290	N	0.145748	T	0.80204	0.4580	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.65936	-0.6047	10	0.09338	T	0.73	-5.6412	1.6364	0.02743	0.3472:0.1334:0.3835:0.1359	.	418	Q14774	HLX_HUMAN	T	418;151;204	ENSP00000355870:A418T;ENSP00000408248:A151T;ENSP00000449882:A204T	ENSP00000355870:A418T	A	+	1	0	HLX	219124454	0.008000	0.16893	0.000000	0.03702	0.017000	0.09413	0.132000	0.15891	-0.081000	0.12662	0.561000	0.74099	GCC	.	.	none		0.627	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
OR1S2	219958	hgsc.bcm.edu	37	11	57971195	57971195	+	Silent	SNP	G	G	A	rs11229279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57971195G>A	ENST00000302592.6	-	1	458	c.459C>T	c.(457-459)ttC>ttT	p.F153F		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F153F(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				GCAAAGTGCCGAACCTGGCCC	0.483													G|||	2137	0.426717	0.2239	0.3876	5008	,	,		21853	0.752		0.3161	False		,,,				2504	0.5072				p.F153F		Atlas-SNP	.											OR1S2,caecum,carcinoma,-2,2	OR1S2	119	2	1	Substitution - coding silent(1)	stomach(1)	c.C459T						PASS	.	G		1096,3306	396.5+/-330.1	131,834,1236	175.0	164.0	168.0		459	1.5	0.0	11	dbSNP_120	168	2804,5788	443.7+/-360.5	477,1850,1969	no	coding-synonymous	OR1S2	NM_001004459.1		608,2684,3205	AA,AG,GG		32.635,24.8978,30.0139		153/326	57971195	3900,9094	2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			AGTGCCGAACCTG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.459C>T	11.37:g.57971195G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	252	99	0.392857	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.677;A|0.323	0.323	strong		0.483	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
CCDC57	284001	hgsc.bcm.edu	37	17	80151881	80151881	+	Silent	SNP	G	G	A	rs4789722	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80151881G>A	ENST00000389641.4	-	5	789	c.753C>T	c.(751-753)gaC>gaT	p.D251D	CCDC57_ENST00000392347.1_Silent_p.D251D|CCDC57_ENST00000392343.3_Silent_p.D251D			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	251										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TGGCCTCCAGGTCCTGGAGCT	0.677													g|||	2998	0.598642	0.525	0.6282	5008	,	,		14366	0.8631		0.4821	False		,,,				2504	0.5245				p.D251D		Atlas-SNP	.											.	CCDC57	102	.	0			c.C753T						PASS	.			1759,2149		388,983,583	20.0	23.0	22.0		753	-0.5	0.1	17	dbSNP_111	22	3514,4776		777,1960,1408	no	coding-synonymous	CCDC57	NM_198082.2		1165,2943,1991	AA,AG,GG		42.3884,45.0102,43.2284		251/916	80151881	5273,6925	1954	4145	6099	SO:0001819	synonymous_variant	284001	exon5			CTCCAGGTCCTGG	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.753C>T	17.37:g.80151881G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				G|0.414;A|0.586	0.586	strong		0.677	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
DPP6	1804	hgsc.bcm.edu	37	7	154561188	154561188	+	Silent	SNP	C	C	T	rs56091483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:154561188C>T	ENST00000377770.3	+	9	1086	c.945C>T	c.(943-945)taC>taT	p.Y315Y	DPP6_ENST00000332007.3_Silent_p.Y253Y|DPP6_ENST00000427557.1_Silent_p.Y208Y|DPP6_ENST00000404039.1_Silent_p.Y251Y			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	315					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GACTCGCCTACGCCGCCATCA	0.522													C|||	485	0.096845	0.1104	0.0533	5008	,	,		18877	0.12		0.0964	False		,,,				2504	0.0859				p.Y315Y	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.C945T						PASS	.	C	,,	422,3630		26,370,1630	75.0	79.0	78.0		399,318,318	-4.7	0.9	7	dbSNP_129	78	671,7673		27,617,3528	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	53,987,5158	TT,TC,CC		8.0417,10.4146,8.8174	,,	133/684,106/657,106/657	154561188	1093,11303	2026	4172	6198	SO:0001819	synonymous_variant	1804	exon9			CGCCTACGCCGCC	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.945C>T	7.37:g.154561188C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				C|0.910;T|0.090	0.090	strong		0.522	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
FUT2	2524	hgsc.bcm.edu	37	19	49206985	49206985	+	Missense_Mutation	SNP	G	G	A	rs602662	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49206985G>A	ENST00000425340.2	+	2	889	c.772G>A	c.(772-774)Ggt>Agt	p.G258S	FUT2_ENST00000391876.4_Missense_Mutation_p.G258S	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	258			G -> S (in dbSNP:rs602662). {ECO:0000269|Ref.4}.		carbohydrate metabolic process (GO:0005975)|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)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		CACCTCCCACGGTGATGTGGT	0.552													G|||	1647	0.328874	0.4924	0.3516	5008	,	,		19101	0.004		0.4682	False		,,,				2504	0.2832				p.G258S		Atlas-SNP	.											.	FUT2	30	.	0			c.G772A	GRCh37	CM042988	FUT2	M	rs602662	PASS	.	G	SER/GLY,SER/GLY	2210,2196	588.3+/-386.9	560,1090,553	227.0	190.0	203.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	772,772	5.2	0.2	19	dbSNP_83	203	4457,4143	589.3+/-392.5	1165,2127,1008	yes	missense,missense	FUT2	NM_000511.5,NM_001097638.2	56,56	1725,3217,1561	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	48.1744,49.8411,48.739	probably-damaging,probably-damaging	258/344,258/344	49206985	6667,6339	2203	4300	6503	SO:0001583	missense	2524	exon2			TCCCACGGTGATG		CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"""Fucosyltransferases"""	4013	protein-coding gene	gene with protein product	"""alpha (1,2) fucosyltransferase"", ""galactoside 2-alpha-L-fucosyltransferase 2"", ""GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2"", ""alpha(1,2)FT2"", ""secretor factor"", ""secretor blood group alpha-2-fucosyltransferase"""	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.772G>A	19.37:g.49206985G>A	ENSP00000387498:p.Gly258Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_001097638	Q0VAG5|Q14338|Q5D0G2	Missense_Mutation	SNP	ENST00000425340.2	37	CCDS33069.1	737	0.3374542124542125	242	0.491869918699187	144	0.39779005524861877	3	0.005244755244755245	348	0.45910290237467016	G	15.68	2.905937	0.52333	0.501589	0.518256	ENSG00000176920	ENST00000425340;ENST00000391876	D;D	0.96459	-4.02;-4.02	5.25	5.25	0.73442	.	.	.	.	.	T	0.00012	0.0000	M	0.83852	2.665	0.24734	P	0.99307017	D	0.89917	1.0	D	0.74023	0.982	T	0.00000	-1.3673	7	.	.	.	.	16.7225	0.85413	0.0:0.0:1.0:0.0	rs602662;rs17297331;rs58593496;rs602662	258	Q10981	FUT2_HUMAN	S	258	ENSP00000387498:G258S;ENSP00000375748:G258S	.	G	+	1	0	FUT2	53898797	0.998000	0.40836	0.166000	0.22797	0.012000	0.07955	3.274000	0.51631	2.615000	0.88500	0.549000	0.68633	GGT	G|0.559;A|0.441	0.441	strong		0.552	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511	
PLCE1	51196	hgsc.bcm.edu	37	10	95931087	95931087	+	Missense_Mutation	SNP	G	G	T	rs17417407	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:95931087G>T	ENST00000371380.3	+	3	1878	c.1643G>T	c.(1642-1644)cGc>cTc	p.R548L	PLCE1_ENST00000371385.3_Missense_Mutation_p.R240L|PLCE1_ENST00000371375.1_Missense_Mutation_p.R240L|PLCE1_ENST00000260766.3_Missense_Mutation_p.R548L			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	548	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.		R -> L (in dbSNP:rs17417407).		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)				ACTATTTACCGCAGGGTCTTG	0.552													G|||	1007	0.201078	0.1967	0.111	5008	,	,		20216	0.1319		0.1859	False		,,,				2504	0.3579				p.R548L		Atlas-SNP	.											.	PLCE1	543	.	0			c.G1643T						PASS	.	G	LEU/ARG,LEU/ARG	711,3365		58,595,1385	157.0	157.0	157.0		719,1643	4.9	0.9	10	dbSNP_123	157	1427,6947		133,1161,2893	yes	missense,missense	PLCE1	NM_001165979.1,NM_016341.3	102,102	191,1756,4278	TT,TG,GG		17.0408,17.4436,17.1727	probably-damaging,probably-damaging	240/1995,548/2303	95931087	2138,10312	2038	4187	6225	SO:0001583	missense	51196	exon4			TTTACCGCAGGGT		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.1643G>T	10.37:g.95931087G>T	ENSP00000360431:p.Arg548Leu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	237	106	0.447257	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	360	0.16483516483516483	92	0.18699186991869918	45	0.12430939226519337	89	0.1555944055944056	134	0.17678100263852242	G	19.85	3.903982	0.72754	0.174436	0.170408	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.84	4.91	0.64330	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.249629	0.34268	N	0.004113	T	0.00073	0.0002	L	0.44542	1.39	0.25843	P	0.9840336	D;D;D	0.69078	0.997;0.985;0.997	D;P;D	0.68765	0.96;0.795;0.933	T	0.01706	-1.1291	9	0.45353	T	0.12	.	14.1024	0.65065	0.0746:0.0:0.9254:0.0	rs17417407;rs17417407	548;240;548	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	L	548;548;240;240	ENSP00000260766:R548L;ENSP00000360431:R548L;ENSP00000360438:R240L;ENSP00000360426:R240L	ENSP00000260766:R548L	R	+	2	0	PLCE1	95921077	1.000000	0.71417	0.937000	0.37676	0.699000	0.40488	4.671000	0.61590	1.404000	0.46819	0.655000	0.94253	CGC	G|0.828;N|0.001	.	strong		0.552	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
LIPH	200879	hgsc.bcm.edu	37	3	185229464	185229464	+	Silent	SNP	T	T	C	rs61730237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	55	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	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		
TJP3	27134	hgsc.bcm.edu	37	19	3738649	3738649	+	Silent	SNP	A	A	C	rs599587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3738649A>C	ENST00000541714.2	+	12	1843	c.1381A>C	c.(1381-1383)Agg>Cgg	p.R461R	TJP3_ENST00000262968.9_Silent_p.R494R|TJP3_ENST00000589378.1_Silent_p.R470R|TJP3_ENST00000587686.1_Silent_p.R480R|TJP3_ENST00000382008.3_Silent_p.R475R|TJP3_ENST00000539908.2_Silent_p.R425R	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	461					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)		GGTGACGCAGAGGAAGCAGGA	0.627													C|||	3532	0.705272	0.7451	0.8098	5008	,	,		20974	0.6181		0.665	False		,,,				2504	0.7086				p.R470R		Atlas-SNP	.											.	TJP3	79	.	0			c.A1408C						PASS	.	C		3257,1149	407.3+/-334.2	1201,855,147	162.0	106.0	125.0		1480	-0.2	1.0	19	dbSNP_83	125	5682,2918	456.3+/-364.0	1871,1940,489	no	coding-synonymous	TJP3	NM_014428.1		3072,2795,636	CC,CA,AA		33.9302,26.0781,31.2702		494/953	3738649	8939,4067	2203	4300	6503	SO:0001819	synonymous_variant	27134	exon12			ACGCAGAGGAAGC	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.1381A>C	19.37:g.3738649A>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			A|0.306;C|0.694	0.694	strong		0.627	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
KRT84	3890	hgsc.bcm.edu	37	12	52774305	52774305	+	Silent	SNP	A	A	G	rs1732293	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	82	0	0	987	WXS	Illumina HiSeq	Phase_I	111	44	0.396396	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	
MBD1	4152	hgsc.bcm.edu	37	18	47800179	47800179	+	Missense_Mutation	SNP	G	G	C	rs125555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:47800179G>C	ENST00000591416.1	-	12	1632	c.1201C>G	c.(1201-1203)Cca>Gca	p.P401A	MBD1_ENST00000398493.1_Missense_Mutation_p.P345A|MBD1_ENST00000398488.1_Missense_Mutation_p.P345A|MBD1_ENST00000585672.1_Missense_Mutation_p.P351A|MBD1_ENST00000588937.1_Missense_Mutation_p.P378A|MBD1_ENST00000590208.1_Missense_Mutation_p.P401A|MBD1_ENST00000436910.1_Missense_Mutation_p.P378A|MBD1_ENST00000398495.2_Missense_Mutation_p.P370A|MBD1_ENST00000591535.1_Missense_Mutation_p.P378A|MBD1_ENST00000585595.1_Missense_Mutation_p.P426A|MBD1_ENST00000347968.3_Missense_Mutation_p.P345A|MBD1_ENST00000349085.2_Missense_Mutation_p.P345A|MBD1_ENST00000339998.6_Missense_Mutation_p.P401A|MBD1_ENST00000424334.2_Missense_Mutation_p.P452A|MBD1_ENST00000353909.3_Missense_Mutation_p.P352A|MBD1_ENST00000587605.1_Missense_Mutation_p.P345A|MBD1_ENST00000269471.5_Missense_Mutation_p.P378A|MBD1_ENST00000269468.5_Missense_Mutation_p.P401A|MBD1_ENST00000457839.2_Missense_Mutation_p.P426A|MBD1_ENST00000382948.5_Missense_Mutation_p.P401A			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	401			P -> A (in dbSNP:rs125555). {ECO:0000269|PubMed:10441743}.		negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						CGGTAAGGTGGGGGCGATCCT	0.607													G|||	890	0.177716	0.1407	0.17	5008	,	,		16641	0.1806		0.1829	False		,,,				2504	0.2249				p.P426A		Atlas-SNP	.											.	MBD1	228	.	0			c.C1276G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	604,3802	261.3+/-264.2	49,506,1648	89.0	86.0	87.0		1201,1276,1273,1201,1108,1051,1201,1033,1132,1033,1033,1132,1201,1054	1.9	0.1	18	dbSNP_78	87	1692,6908	309.3+/-309.3	171,1350,2779	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	MBD1	NM_001204136.1,NM_001204137.1,NM_001204138.1,NM_001204139.1,NM_001204140.1,NM_001204141.1,NM_001204142.1,NM_001204143.1,NM_001204151.1,NM_002384.2,NM_015844.2,NM_015845.3,NM_015846.3,NM_015847.3	27,27,27,27,27,27,27,27,27,27,27,27,27,27	220,1856,4427	CC,CG,GG		19.6744,13.7086,17.6534	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	401/656,426/631,425/630,401/606,370/575,351/568,401/551,345/536,378/537,345/504,345/550,378/587,401/606,352/557	47800179	2296,10710	2203	4300	6503	SO:0001583	missense	4152	exon13			AAGGTGGGGGCGA	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.1201C>G	18.37:g.47800179G>C	ENSP00000467017:p.Pro401Ala	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	37	CCDS11943.1	385	0.1762820512820513	74	0.15040650406504066	66	0.18232044198895028	102	0.17832167832167833	143	0.18865435356200527	G	10.33	1.319949	0.23994	0.137086	0.196744	ENSG00000141644	ENST00000382948;ENST00000353909;ENST00000349085;ENST00000269468;ENST00000347968;ENST00000436910;ENST00000269471;ENST00000424334;ENST00000339998;ENST00000398495;ENST00000457839;ENST00000398493;ENST00000398488	D;D;D;D;D;D;D;D;D;D;D;D;D	0.98633	-3.89;-3.93;-4.78;-3.89;-5.04;-3.82;-3.82;-3.9;-3.84;-3.88;-3.88;-5.04;-4.78	4.98	1.89	0.25635	.	0.218980	0.32081	N	0.006607	T	0.02156	0.0067	L	0.32530	0.975	0.53688	P	2.599999999997049E-5	P;B;B;B;P;P;B;B;B;P;B;P	0.43314	0.803;0.409;0.081;0.245;0.51;0.644;0.359;0.433;0.154;0.681;0.245;0.681	B;B;B;B;B;B;B;B;B;B;B;B	0.44133	0.338;0.188;0.073;0.118;0.167;0.335;0.234;0.164;0.118;0.442;0.08;0.442	T	0.48514	-0.9029	9	0.44086	T	0.13	-0.1939	5.6276	0.17490	0.1987:0.1579:0.6434:0.0	rs125555;rs760283;rs52805720;rs60253010;rs125555	345;452;378;401;401;378;352;345;401;345;426;345	B4DUR3;B4DI41;Q9UIS9-8;A8K654;Q9UIS9-6;Q9UIS9-2;Q9UIS9-5;Q9UIS9-4;Q9UIS9;Q9UIS9-7;B4DXJ5;Q9UIS9-3	.;.;.;.;.;.;.;.;MBD1_HUMAN;.;.;.	A	401;352;345;401;345;378;378;452;401;401;426;345;345	ENSP00000372407:P401A;ENSP00000269469:P352A;ENSP00000342531:P345A;ENSP00000269468:P401A;ENSP00000285102:P345A;ENSP00000409561:P378A;ENSP00000269471:P378A;ENSP00000408846:P452A;ENSP00000339546:P401A;ENSP00000381508:P401A;ENSP00000405268:P426A;ENSP00000381506:P345A;ENSP00000381502:P345A	ENSP00000269468:P401A	P	-	1	0	MBD1	46054177	0.343000	0.24818	0.126000	0.21872	0.987000	0.75469	0.249000	0.18216	0.254000	0.21573	0.555000	0.69702	CCA	G|0.819;C|0.181	0.181	strong		0.607	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
SEMA4C	54910	hgsc.bcm.edu	37	2	97532152	97532152	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97532152T>C	ENST00000305476.5	-	3	258	c.126A>G	c.(124-126)gtA>gtG	p.V42V		NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	42	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell migration in hindbrain (GO:0021535)|cerebellum development (GO:0021549)|muscle cell differentiation (GO:0042692)|neural tube closure (GO:0001843)|positive regulation of stress-activated MAPK cascade (GO:0032874)|semaphorin-plexin signaling pathway (GO:0071526)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle membrane (GO:0030672)	receptor activity (GO:0004872)			NS(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	17						AGAACCGCCGTACTACCGTGG	0.657																																					p.V42V		Atlas-SNP	.											SEMA4C,caecum,carcinoma,-2,1	SEMA4C	56	1	0			c.A126G						scavenged	.						73.0	73.0	73.0					2																	97532152		2203	4300	6503	SO:0001819	synonymous_variant	54910	exon3			CCGCCGTACTACC	AB051526	CCDS2029.1	2q11.2	2013-01-11			ENSG00000168758	ENSG00000168758		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10731	protein-coding gene	gene with protein product	"""M-Sema F"""	604462		SEMAI		7656991	Standard	NM_017789		Approved	Semacl1, Semaf	uc002sxh.4	Q9C0C4	OTTHUMG00000130535	ENST00000305476.5:c.126A>G	2.37:g.97532152T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	149	2	0.0134228	NM_017789	Q32MJ3|Q7Z5X0	Silent	SNP	ENST00000305476.5	37	CCDS2029.1																																																																																			.	.	none		0.657	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252957.1	NM_017789	
TXNDC8	255220	hgsc.bcm.edu	37	9	113091523	113091523	+	Missense_Mutation	SNP	T	T	G	rs7041938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	28	0	0		WXS	Illumina HiSeq	Phase_I	35	12	0.342857	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	
SLC37A1	54020	hgsc.bcm.edu	37	21	43982247	43982247	+	Silent	SNP	C	C	A	rs77485357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43982247C>A	ENST00000352133.2	+	12	2023	c.1041C>A	c.(1039-1041)ctC>ctA	p.L347L	AP001625.6_ENST00000442605.1_RNA|SLC37A1_ENST00000398341.3_Silent_p.L347L			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	347					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						ATACTTTCCTCTTCTGGCTGC	0.512													C|||	195	0.0389377	0.0076	0.0259	5008	,	,		20068	0.0327		0.0447	False		,,,				2504	0.091				p.L347L		Atlas-SNP	.											.	SLC37A1	48	.	0			c.C1041A						PASS	.	C		38,4368	41.6+/-74.8	0,38,2165	255.0	209.0	225.0		1041	-6.1	1.0	21	dbSNP_132	225	349,8251	119.2+/-178.6	1,347,3952	no	coding-synonymous	SLC37A1	NM_018964.3		1,385,6117	AA,AC,CC		4.0581,0.8625,2.9755		347/534	43982247	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	54020	exon13			TTTCCTCTTCTGG	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.1041C>A	21.37:g.43982247C>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	164	87	0.530488	NM_018964	D3DSJ7|Q9HAQ1	Silent	SNP	ENST00000352133.2	37	CCDS13689.1																																																																																			C|0.968;A|0.032	0.032	strong		0.512	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
GAB4	128954	hgsc.bcm.edu	37	22	17446157	17446157	+	Splice_Site	SNP	G	G	T	rs1541529	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:17446157G>T	ENST00000400588.1	-	7	1397	c.1290C>A	c.(1288-1290)gcC>gcA	p.A430A	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	430										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GTGTTGGGTTGGCTGGAGCAG	0.557													T|||	163	0.0325479	0.0008	0.0317	5008	,	,		18394	0.0069		0.0686	False		,,,				2504	0.0654				p.A430A		Atlas-SNP	.											.	GAB4	95	.	0			c.C1290A						PASS	.	T		75,4029		0,75,1977	151.0	160.0	157.0		1290	0.8	0.9	22	dbSNP_88	157	592,7856		17,558,3649	yes	coding-synonymous-near-splice	GAB4	NM_001037814.1		17,633,5626	TT,TG,GG		7.0076,1.8275,5.3139		430/575	17446157	667,11885	2052	4224	6276	SO:0001630	splice_region_variant	128954	exon7			TGGGTTGGCTGGA	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1289-1C>A	22.37:g.17446157G>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	180	81	0.45	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			G|0.960;T|0.040	0.040	strong		0.557	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	Silent
MYOM3	127294	hgsc.bcm.edu	37	1	24419496	24419496	+	Missense_Mutation	SNP	A	A	G	rs4233050	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24419496A>G	ENST00000374434.3	-	10	1193	c.1031T>C	c.(1030-1032)aTg>aCg	p.M344T	MYOM3_ENST00000329601.7_Missense_Mutation_p.M344T|MYOM3_ENST00000330966.7_Missense_Mutation_p.M345T|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	344	Ig-like C2-type 2.		M -> T (in dbSNP:rs4233050). {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)		CACCCGGACCATGTAGAGCCC	0.637													A|||	1898	0.378994	0.4486	0.3242	5008	,	,		18829	0.3512		0.496	False		,,,				2504	0.2321				p.M344T		Atlas-SNP	.											.	MYOM3	131	.	0			c.T1031C						PASS	.	A	THR/MET	1736,2212		389,958,627	35.0	40.0	38.0		1031	-3.2	0.0	1	dbSNP_111	38	3934,4346		946,2042,1152	yes	missense	MYOM3	NM_152372.3	81	1335,3000,1779	GG,GA,AA		47.5121,43.9716,46.369	benign	344/1438	24419496	5670,6558	1974	4140	6114	SO:0001583	missense	127294	exon10			CGGACCATGTAGA	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.1031T>C	1.37:g.24419496A>G	ENSP00000363557:p.Met344Thr	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	940	0.43040293040293043	232	0.4715447154471545	130	0.35911602209944754	185	0.32342657342657344	393	0.5184696569920845	A	0.003	-2.444953	0.00178	0.439716	0.475121	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.35789	1.29;1.29;1.29	5.36	-3.19	0.05171	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.256906	0.43919	N	0.000514	T	0.00012	0.0000	N	0.00030	-2.605	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	0.31503	-0.9941	9	0.02654	T	1	.	6.2063	0.20604	0.358:0.3113:0.3307:0.0	rs4233050;rs17184609;rs61100288;rs4233050	1;344;344	Q6ZU56;Q5VTT5-2;Q5VTT5	.;.;MYOM3_HUMAN	T	344;345;344	ENSP00000363557:M344T;ENSP00000332670:M345T;ENSP00000328415:M344T	ENSP00000328415:M344T	M	-	2	0	MYOM3	24292083	0.134000	0.22483	0.007000	0.13788	0.189000	0.23516	0.243000	0.18106	-0.586000	0.05898	-0.777000	0.03380	ATG	A|0.582;G|0.418	0.418	strong		0.637	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
OR5P2	120065	hgsc.bcm.edu	37	11	7817665	7817665	+	Silent	SNP	T	T	C	rs72484720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7817665T>C	ENST00000329434.2	-	1	855	c.825A>G	c.(823-825)acA>acG	p.T275T	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAATCACCACTGTGTACAACA	0.448													C|||	1185	0.236621	0.3472	0.2911	5008	,	,		18498	0.128		0.2763	False		,,,				2504	0.1196				p.T275T		Atlas-SNP	.											.	OR5P2	68	.	0			c.A825G						PASS	.	C		1371,2845		401,569,1138	114.0	122.0	120.0		825	2.4	1.0	11	dbSNP_130	120	2425,6159		393,1639,2260	no	coding-synonymous	OR5P2	NM_153444.1		794,2208,3398	CC,CT,TT		28.2502,32.519,29.6562		275/323	7817665	3796,9004	2108	4292	6400	SO:0001819	synonymous_variant	120065	exon1			CACCACTGTGTAC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.825A>G	11.37:g.7817665T>C		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	236	233	0.987288	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			T|0.738;C|0.262	0.262	strong		0.448	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
EVC	2121	hgsc.bcm.edu	37	4	5721049	5721049	+	Silent	SNP	A	A	G	rs35870680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:5721049A>G	ENST00000264956.6	+	2	433	c.249A>G	c.(247-249)tcA>tcG	p.S83S	EVC_ENST00000382674.2_Silent_p.S83S|EVC_ENST00000509451.1_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	127	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	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		
GAS6	2621	hgsc.bcm.edu	37	13	114524944	114524944	+	Silent	SNP	A	A	G	rs7400002	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:114524944A>G	ENST00000327773.6	-	14	2015	c.1869T>C	c.(1867-1869)gcT>gcC	p.A623A	GAS6_ENST00000357389.3_Silent_p.A666A|GAS6_ENST00000355761.4_Silent_p.A569A|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000450766.1_Silent_p.A350A|GAS6_ENST00000418959.3_Silent_p.A324A	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	666	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		S -> L. {ECO:0000269|Ref.4}.		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)				GCAGGCCGCCAGCAAAGGTGA	0.692													G|||	2219	0.443091	0.5166	0.4568	5008	,	,		16218	0.4008		0.2416	False		,,,				2504	0.5849				p.A623A		Atlas-SNP	.											GAS6_ENST00000327773,NS,carcinoma,0,1	GAS6	75	1	0			c.T1869C						PASS	.	G	,,	1755,2389		386,983,703	7.0	9.0	8.0		1869,1050,972	-8.0	0.0	13	dbSNP_116	8	1720,6538		240,1240,2649	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS6	NM_000820.2,NM_001143945.1,NM_001143946.1	,,	626,2223,3352	GG,GA,AA		20.8283,42.3504,28.0197	,,	623/679,350/406,324/380	114524944	3475,8927	2072	4129	6201	SO:0001819	synonymous_variant	2621	exon14			GCCGCCAGCAAAG		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.1869T>C	13.37:g.114524944A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Silent	SNP	ENST00000327773.6	37	CCDS45072.1																																																																																			A|0.641;G|0.359	0.359	strong		0.692	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820	
PTCHD4	442213	hgsc.bcm.edu	37	6	47846603	47846603	+	Silent	SNP	C	C	T	rs41273690	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:47846603C>T	ENST00000339488.4	-	3	2010	c.1977G>A	c.(1975-1977)gtG>gtA	p.V659V		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	659						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										TCAGAACAGGCACTGTGACAG	0.478													C|||	88	0.0175719	0.0091	0.0159	5008	,	,		19850	0.0		0.0606	False		,,,				2504	0.0041				p.V659V		Atlas-SNP	.											.	.	.	.	0			c.G1977A						PASS	.	C		94,4312	76.8+/-115.0	0,94,2109	132.0	123.0	126.0		1977	5.9	1.0	6	dbSNP_127	126	386,8214	125.0+/-183.6	12,362,3926	no	coding-synonymous	C6orf138	NM_001013732.3		12,456,6035	TT,TC,CC		4.4884,2.1335,3.6906		659/847	47846603	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	442213	exon3			AACAGGCACTGTG		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 138"""	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1977G>A	6.37:g.47846603C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_001013732	B0QZ29|B4DRK3|Q5T884	Silent	SNP	ENST00000339488.4	37	CCDS34473.2																																																																																			C|0.965;T|0.035	0.035	strong		0.478	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732	
APOL1	8542	hgsc.bcm.edu	37	22	36661842	36661842	+	Silent	SNP	G	G	A	rs136177	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36661842G>A	ENST00000397278.3	+	6	1189	c.960G>A	c.(958-960)agG>agA	p.R320R	APOL1_ENST00000397279.4_Silent_p.R320R|APOL1_ENST00000426053.1_Silent_p.R302R|APOL1_ENST00000319136.4_Silent_p.R336R|APOL1_ENST00000422706.1_Silent_p.R320R|APOL1_ENST00000347595.7_Silent_p.R199R	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	320					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						AGGTGGAGAGGGTTAATGAAC	0.552													a|||	4273	0.853235	0.9486	0.8847	5008	,	,		19407	0.7966		0.7813	False		,,,				2504	0.8344				p.R336R		Atlas-SNP	.											.	APOL1	35	.	0			c.G1008A						PASS	.	G	,,,	4065,341	177.6+/-206.5	1877,311,15	87.0	75.0	80.0		960,906,960,1008	-2.3	0.0	22	dbSNP_78	80	6857,1743	315.4+/-312.2	2725,1407,168	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APOL1	NM_001136540.1,NM_001136541.1,NM_003661.3,NM_145343.2	,,,	4602,1718,183	AA,AG,GG		20.2674,7.7394,16.0234	,,,	320/399,302/381,320/399,336/415	36661842	10922,2084	2203	4300	6503	SO:0001819	synonymous_variant	8542	exon7			GGAGAGGGTTAAT	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.960G>A	22.37:g.36661842G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_145343	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Silent	SNP	ENST00000397278.3	37	CCDS13926.1																																																																																			G|0.164;A|0.836	0.836	strong		0.552	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343	
CARD11	84433	hgsc.bcm.edu	37	7	2983971	2983971	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2983971G>A	ENST00000396946.4	-	5	962	c.559C>T	c.(559-561)Cgg>Tgg	p.R187W	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	187					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)		TAGCTGTCCCGCTCTTCCTTC	0.557			Mis		DLBCL																																p.R187W		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,NS,carcinoma,0,1	CARD11	339	1	0			c.C559T						scavenged	.						248.0	154.0	186.0					7																	2983971		2203	4300	6503	SO:0001583	missense	84433	exon5			TGTCCCGCTCTTC	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.559C>T	7.37:g.2983971G>A	ENSP00000380150:p.Arg187Trp	Somatic	276	2	0.00724638		WXS	Illumina HiSeq	Phase_I	273	3	0.010989	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	15.02	2.710363	0.48517	.	.	ENSG00000198286	ENST00000396946	T	0.36157	1.27	4.46	2.25	0.28309	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	N	0.20881	0.62	0.52099	D	0.999945	B	0.27971	0.196	B	0.17722	0.019	T	0.05632	-1.0873	10	0.37606	T	0.19	-27.5118	7.2254	0.26012	0.0992:0.0:0.6097:0.2911	.	187	Q9BXL7	CAR11_HUMAN	W	187	ENSP00000380150:R187W	ENSP00000380150:R187W	R	-	1	2	CARD11	2950497	1.000000	0.71417	0.994000	0.49952	0.976000	0.68499	2.135000	0.42112	1.000000	0.39049	0.561000	0.74099	CGG	.	.	none		0.557	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
EIF2AK1	27102	hgsc.bcm.edu	37	7	6066450	6066450	+	Missense_Mutation	SNP	T	T	C	rs2640	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:6066450T>C	ENST00000199389.6	-	14	1819	c.1673A>G	c.(1672-1674)aAg>aGg	p.K558R	EIF2AK1_ENST00000536084.1_Missense_Mutation_p.K434R	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	558	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (in dbSNP:rs2640). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.13}.		negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)	p.K558R(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CTGGATATACTTGGCTTGCAC	0.468													T|||	605	0.120807	0.0106	0.0562	5008	,	,		19849	0.3323		0.0606	False		,,,				2504	0.1595				p.K558R		Atlas-SNP	.											EIF2AK1,NS,carcinoma,0,1	EIF2AK1	76	1	1	Substitution - Missense(1)	stomach(1)	c.A1673G						PASS	.	T	ARG/LYS,ARG/LYS	106,4300	82.9+/-121.4	0,106,2097	142.0	130.0	134.0		1670,1673	4.6	1.0	7	dbSNP_36	134	398,8202	127.5+/-185.8	13,372,3915	yes	missense,missense	EIF2AK1	NM_001134335.1,NM_014413.3	26,26	13,478,6012	CC,CT,TT		4.6279,2.4058,3.8751	probably-damaging,probably-damaging	557/630,558/631	6066450	504,12502	2203	4300	6503	SO:0001583	missense	27102	exon14			ATATACTTGGCTT	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1673A>G	7.37:g.6066450T>C	ENSP00000199389:p.Lys558Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	37	CCDS5345.1	268	0.1227106227106227	6	0.012195121951219513	21	0.058011049723756904	197	0.34440559440559443	44	0.05804749340369393	T	18.69	3.677390	0.68042	0.024058	0.046279	ENSG00000086232	ENST00000199389;ENST00000536084	T;T	0.24538	1.97;1.85	5.72	4.57	0.56435	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.096359	0.64402	N	0.000001	T	0.00012	0.0000	L	0.46670	1.46	0.20563	P	0.999886333	B;P;B	0.37864	0.095;0.61;0.025	B;B;B	0.37780	0.126;0.258;0.076	T	0.46938	-0.9155	9	0.36615	T	0.2	-24.9445	11.6281	0.51158	0.0:0.0694:0.0:0.9306	rs2640;rs11567128;rs17136312;rs17136313;rs52808510;rs60637318;rs2640	434;557;558	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	R	558;434	ENSP00000199389:K558R;ENSP00000445784:K434R	ENSP00000199389:K558R	K	-	2	0	EIF2AK1	6032976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.974000	0.70465	1.005000	0.39183	0.533000	0.62120	AAG	T|0.918;C|0.082	0.082	strong		0.468	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
DPP6	1804	hgsc.bcm.edu	37	7	154681050	154681050	+	Silent	SNP	C	C	T	rs1129300	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:154681050C>T	ENST00000377770.3	+	24	2514	c.2373C>T	c.(2371-2373)gcC>gcT	p.A791A	DPP6_ENST00000332007.3_Silent_p.A729A|DPP6_ENST00000427557.1_Silent_p.A684A|DPP6_ENST00000404039.1_Silent_p.A727A			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	791					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)	p.A727A(1)		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)			ATCCCACTGCCGATGGTAAGG	0.483													C|||	808	0.161342	0.0053	0.0922	5008	,	,		19575	0.4673		0.1074	False		,,,				2504	0.1616				p.A791A	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											DPP6,NS,carcinoma,0,1	DPP6	383	1	1	Substitution - coding silent(1)	stomach(1)	c.C2373T						PASS	.	C	,,	106,3898		0,106,1896	53.0	54.0	54.0		1827,1746,1746	-9.0	0.0	7	dbSNP_86	54	965,7381		50,865,3258	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	50,971,5154	TT,TC,CC		11.5624,2.6474,8.6721	,,	609/684,582/657,582/657	154681050	1071,11279	2002	4173	6175	SO:0001819	synonymous_variant	1804	exon24			CACTGCCGATGGT	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.2373C>T	7.37:g.154681050C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				C|0.837;G|0.000;T|0.163	0.163	strong		0.483	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
DNAI1	27019	hgsc.bcm.edu	37	9	34500821	34500821	+	Missense_Mutation	SNP	G	G	A	rs11793196	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:34500821G>A	ENST00000242317.4	+	11	1174	c.1003G>A	c.(1003-1005)Gtc>Atc	p.V335I		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	335			V -> I (in dbSNP:rs11793196).		cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		GCGCCTGTCCGTCACTGCCCT	0.537									Kartagener syndrome		OREG0019152	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	884	0.176518	0.3601	0.1455	5008	,	,		18776	0.0119		0.1561	False		,,,				2504	0.1411				p.V335I		Atlas-SNP	.											.	DNAI1	72	.	0			c.G1003A						PASS	.	G	ILE/VAL	1420,2986	463.2+/-353.5	229,962,1012	61.0	61.0	61.0		1003	5.0	1.0	9	dbSNP_120	61	1308,7292	258.4+/-282.1	114,1080,3106	yes	missense	DNAI1	NM_012144.2	29	343,2042,4118	AA,AG,GG		15.2093,32.2288,20.9749	probably-damaging	335/700	34500821	2728,10278	2203	4300	6503	SO:0001583	missense	27019	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CTGTCCGTCACTG	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"""Axonemal dyneins"", ""WD repeat domain containing"""	2954	protein-coding gene	gene with protein product		604366	"""dynein, axonemal, intermediate polypeptide 1"""			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1003G>A	9.37:g.34500821G>A	ENSP00000242317:p.Val335Ile	Somatic	83	0	0	848	WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	350	0.16025641025641027	168	0.34146341463414637	53	0.1464088397790055	8	0.013986013986013986	121	0.15963060686015831	G	17.37	3.372643	0.61624	0.322288	0.152093	ENSG00000122735	ENST00000242317	T	0.71579	-0.58	4.99	4.99	0.66335	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.065937	0.64402	D	0.000011	T	0.00012	0.0000	M	0.85710	2.77	0.09310	P	1.0	B	0.27700	0.186	B	0.25405	0.06	T	0.07635	-1.0762	9	0.54805	T	0.06	.	16.1322	0.81449	0.0:0.0:1.0:0.0	rs11793196;rs59607272;rs11793196	335	Q9UI46	DNAI1_HUMAN	I	335	ENSP00000242317:V335I	ENSP00000242317:V335I	V	+	1	0	DNAI1	34490821	1.000000	0.71417	0.979000	0.43373	0.880000	0.50808	7.069000	0.76755	2.470000	0.83445	0.462000	0.41574	GTC	G|0.812;A|0.188	0.188	strong		0.537	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1		
KBTBD6	89890	hgsc.bcm.edu	37	13	41705897	41705897	+	Missense_Mutation	SNP	G	G	C	rs150633583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:41705897G>C	ENST00000379485.1	-	1	985	c.751C>G	c.(751-753)Ccc>Gcc	p.P251A	KBTBD6_ENST00000499385.2_Missense_Mutation_p.P185A	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	251								p.P251A(1)		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)		CGCTCTTTGGGAGCAGCCTCC	0.587													G|||	4	0.000798722	0.003	0.0	5008	,	,		19033	0.0		0.0	False		,,,				2504	0.0				p.P251A		Atlas-SNP	.											KBTBD6,trunk,malignant_melanoma,0,2	KBTBD6	83	2	1	Substitution - Missense(1)	skin(1)	c.C751G						scavenged	.	G	ALA/PRO	14,4392	19.1+/-41.9	0,14,2189	64.0	65.0	65.0		751	3.7	1.0	13	dbSNP_134	65	0,8600		0,0,4300	yes	missense	KBTBD6	NM_152903.4	27	0,14,6489	CC,CG,GG		0.0,0.3177,0.1076	benign	251/675	41705897	14,12992	2203	4300	6503	SO:0001583	missense	89890	exon1			CTTTGGGAGCAGC	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.751C>G	13.37:g.41705897G>C	ENSP00000368799:p.Pro251Ala	Somatic	273	3	0.010989		WXS	Illumina HiSeq	Phase_I	270	4	0.0148148	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	g	3.422	-0.117976	0.06838	0.003177	0.0	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.67523	-0.27;-0.27	3.68	3.68	0.42216	BTB/Kelch-associated (2);	0.074945	0.53938	D	0.000048	T	0.51193	0.1660	L	0.31926	0.97	0.38217	D	0.940638	B;B	0.10296	0.003;0.001	B;B	0.15052	0.012;0.006	T	0.48328	-0.9045	10	0.08837	T	0.75	.	13.263	0.60117	0.0:0.0:1.0:0.0	.	185;251	F5GZN7;Q86V97	.;KBTB6_HUMAN	A	251;185	ENSP00000368799:P251A;ENSP00000444326:P185A	ENSP00000368799:P251A	P	-	1	0	KBTBD6	40603897	0.817000	0.29147	0.996000	0.52242	0.966000	0.64601	1.519000	0.35888	2.060000	0.61445	0.455000	0.32223	CCC	G|0.998;C|0.002	0.002	strong		0.587	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903	
TARBP1	6894	hgsc.bcm.edu	37	1	234529570	234529570	+	Silent	SNP	G	G	A	rs2175593	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:234529570G>A	ENST00000040877.1	-	27	4256	c.4257C>T	c.(4255-4257)gtC>gtT	p.V1419V	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1419					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TATCTGCTTCGACCAAATTAG	0.383													G|||	2524	0.503994	0.6089	0.5677	5008	,	,		17325	0.494		0.4334	False		,,,				2504	0.3998				p.V1419V		Atlas-SNP	.											.	TARBP1	111	.	0			c.C4257T						PASS	.	G		2501,1905	621.0+/-393.7	735,1031,437	61.0	66.0	64.0		4257	-9.0	0.0	1	dbSNP_96	64	3675,4925	524.7+/-380.6	779,2117,1404	no	coding-synonymous	TARBP1	NM_005646.3		1514,3148,1841	AA,AG,GG		42.7326,43.2365,47.4858		1419/1622	234529570	6176,6830	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon27			TGCTTCGACCAAA		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.4257C>T	1.37:g.234529570G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	111	39	0.351351	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			G|0.519;A|0.481	0.481	strong		0.383	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
FMN2	56776	hgsc.bcm.edu	37	1	240371106	240371106	+	Silent	SNP	C	C	T	rs11586155		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371106C>T	ENST00000319653.9	+	5	3224	c.2994C>T	c.(2992-2994)ccC>ccT	p.P998P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	998	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)			CGGGCATACCCCCTCCGCCCC	0.711																																					p.P998P		Atlas-SNP	.											.	FMN2	451	.	0			c.C2994T						PASS	.						5.0	7.0	7.0					1																	240371106		2012	4075	6087	SO:0001819	synonymous_variant	56776	exon5			CATACCCCCTCCG	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.2994C>T	1.37:g.240371106C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.783;T|0.217	0.217	strong		0.711	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
EML3	256364	hgsc.bcm.edu	37	11	62378801	62378801	+	Silent	SNP	T	T	C	rs11553576	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:62378801T>C	ENST00000394773.2	-	3	517	c.210A>G	c.(208-210)ccA>ccG	p.P70P	EML3_ENST00000531557.1_5'Flank|EML3_ENST00000494176.2_Silent_p.P42P|ROM1_ENST00000534093.1_5'Flank|ROM1_ENST00000278833.3_5'Flank|EML3_ENST00000278845.4_Silent_p.P71P|EML3_ENST00000529309.1_Silent_p.P70P	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	70						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GTGGCAGTCCTGGGGGGGCTG	0.602													T|||	1051	0.209864	0.1989	0.2075	5008	,	,		17102	0.0913		0.3221	False		,,,				2504	0.2331				p.P70P		Atlas-SNP	.											.	EML3	61	.	0			c.A210G						PASS	.	T		1034,3364		117,800,1282	27.0	30.0	29.0		210	-3.4	1.0	11	dbSNP_120	29	3114,5476		585,1944,1766	no	coding-synonymous	EML3	NM_153265.2		702,2744,3048	CC,CT,TT		36.2515,23.5107,31.9372		70/897	62378801	4148,8840	2199	4295	6494	SO:0001819	synonymous_variant	256364	exon3			CAGTCCTGGGGGG	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.210A>G	11.37:g.62378801T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_153265	Q6ZQW7|Q8NA55	Silent	SNP	ENST00000394773.2	37	CCDS8023.2	511	0.23397435897435898	116	0.23577235772357724	91	0.2513812154696133	61	0.10664335664335664	243	0.32058047493403696	T	4.044	0.005745	0.07866	0.235107	0.362515	ENSG00000149499	ENST00000394776	.	.	.	5.05	-3.38	0.04883	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999990846	.	.	.	.	.	.	T	0.45498	-0.9257	3	.	.	.	-3.1771	1.755	0.02980	0.1498:0.363:0.1544:0.3328	rs11553576;rs11553576	.	.	.	G	65	.	.	R	-	1	2	EML3	62135377	0.781000	0.28676	0.996000	0.52242	0.277000	0.26821	-0.823000	0.04443	-0.206000	0.10203	0.379000	0.24179	AGG	T|0.718;C|0.282	0.282	strong		0.602	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
KRT28	162605	hgsc.bcm.edu	37	17	38955173	38955173	+	Silent	SNP	G	G	A	rs7222207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38955173G>A	ENST00000306658.7	-	2	594	c.529C>T	c.(529-531)Cta>Tta	p.L177L		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)				ACTTACTTTAGCCTGAAATCA	0.318													G|||	661	0.131989	0.0711	0.1801	5008	,	,		15102	0.0377		0.2306	False		,,,				2504	0.1759				p.L177L	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.C529T						PASS	.	G		448,3958	210.5+/-231.0	30,388,1785	106.0	107.0	107.0		529	3.3	1.0	17	dbSNP_116	107	1964,6634	343.5+/-324.9	219,1526,2554	no	coding-synonymous	KRT28	NM_181535.3		249,1914,4339	AA,AG,GG		22.8425,10.168,18.5481		177/465	38955173	2412,10592	2203	4299	6502	SO:0001819	synonymous_variant	162605	exon2			ACTTTAGCCTGAA	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.529C>T	17.37:g.38955173G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	203	95	0.46798	NM_181535		Silent	SNP	ENST00000306658.7	37	CCDS11376.1																																																																																			G|0.838;A|0.162	0.162	strong		0.318	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
PPL	5493	hgsc.bcm.edu	37	16	4935985	4935985	+	Missense_Mutation	SNP	C	C	G	rs35869286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4935985C>G	ENST00000345988.2	-	22	2760	c.2671G>C	c.(2671-2673)Gag>Cag	p.E891Q	PPL_ENST00000590782.2_Missense_Mutation_p.E889Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	891			E -> Q (in dbSNP:rs35869286).		keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.E891K(1)		breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TTCCACGCCTCCTCCACTCCA	0.557													C|||	164	0.0327476	0.0303	0.0245	5008	,	,		19112	0.006		0.0706	False		,,,				2504	0.0307				p.E891Q		Atlas-SNP	.											PPL,NS,carcinoma,0,1	PPL	168	1	1	Substitution - Missense(1)	lung(1)	c.G2671C						PASS	.	C	GLN/GLU	191,4203	116.7+/-154.6	5,181,2011	71.0	74.0	73.0		2671	3.8	0.1	16	dbSNP_126	73	638,7960	153.4+/-207.8	27,584,3688	yes	missense	PPL	NM_002705.4	29	32,765,5699	GG,GC,CC		7.4203,4.3468,6.3808	benign	891/1757	4935985	829,12163	2197	4299	6496	SO:0001583	missense	5493	exon22			ACGCCTCCTCCAC	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.2671G>C	16.37:g.4935985C>G	ENSP00000340510:p.Glu891Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	78	0.03571428571428571	10	0.02032520325203252	7	0.019337016574585635	3	0.005244755244755245	58	0.07651715039577836	C	7.631	0.678938	0.14841	0.043468	0.074203	ENSG00000118898	ENST00000345988	T	0.58652	0.32	4.71	3.75	0.43078	.	0.060179	0.64402	N	0.000004	T	0.07593	0.0191	M	0.74881	2.28	0.40865	D	0.983862	B	0.16396	0.017	B	0.17433	0.018	T	0.37979	-0.9682	10	0.62326	D	0.03	.	17.7271	0.88368	0.0:0.8745:0.1255:0.0	rs35869286	891	O60437	PEPL_HUMAN	Q	891	ENSP00000340510:E891Q	ENSP00000340510:E891Q	E	-	1	0	PPL	4875986	1.000000	0.71417	0.050000	0.19076	0.032000	0.12392	6.068000	0.71201	0.430000	0.26230	-2.039000	0.00418	GAG	C|0.942;G|0.058	0.058	strong		0.557	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
SLC9A8	23315	hgsc.bcm.edu	37	20	48491258	48491258	+	Silent	SNP	T	T	G	rs542234	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:48491258T>G	ENST00000361573.2	+	11	1017	c.975T>G	c.(973-975)ctT>ctG	p.L325L	SLC9A8_ENST00000417961.1_Silent_p.L341L|SLC9A8_ENST00000541138.1_Silent_p.L25L|SLC9A8_ENST00000539601.1_Silent_p.L106L			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	325					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TGGCCATCCTTTTCTCAGGCA	0.562													G|||	4121	0.822883	0.8033	0.8256	5008	,	,		18879	0.8373		0.7952	False		,,,				2504	0.8609				p.L341L		Atlas-SNP	.											.	SLC9A8	63	.	0			c.T1023G						PASS	.	G		3476,930	355.6+/-313.1	1363,750,90	250.0	173.0	199.0		975	3.8	1.0	20	dbSNP_83	199	6819,1781	321.2+/-315.0	2705,1409,186	no	coding-synonymous	SLC9A8	NM_015266.1		4068,2159,276	GG,GT,TT		20.7093,21.1076,20.8442		325/582	48491258	10295,2711	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon11			CATCCTTTTCTCA	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"""Solute carriers"""	20728	protein-coding gene	gene with protein product		612730	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 8"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 8"""			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.975T>G	20.37:g.48491258T>G		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	288	287	0.996528	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			T|0.200;G|0.800	0.800	strong		0.562	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360625	71360625	+	Missense_Mutation	SNP	G	G	T	rs1813160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71360625G>T	ENST00000244230.2	+	2	1039	c.687G>T	c.(685-687)gaG>gaT	p.E229D	MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.E229D	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	229	Poly-Glu.		E -> D (in dbSNP:rs1813160).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						ATAATGATGAGGAGGAGGAAG	0.323													g|||	1782	0.355831	0.4251	0.4035	5008	,	,		19873	0.2738		0.2982	False		,,,				2504	0.3722				p.E229D		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.G687T						PASS	.	G	ASP/GLU	1653,2753	483.2+/-359.6	298,1057,848	72.0	79.0	76.0		687	-5.8	0.0	2	dbSNP_92	76	2557,6043	408.0+/-349.4	400,1757,2143	yes	missense	MPHOSPH10	NM_005791.2	45	698,2814,2991	TT,TG,GG		29.7326,37.517,32.3697	possibly-damaging	229/682	71360625	4210,8796	2203	4300	6503	SO:0001583	missense	10199	exon2			TGATGAGGAGGAG	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.687G>T	2.37:g.71360625G>T	ENSP00000244230:p.Glu229Asp	Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	338	164	0.485207	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	751	0.34386446886446886	214	0.4349593495934959	139	0.3839779005524862	180	0.3146853146853147	218	0.287598944591029	G	0.023	-1.395481	0.01175	0.37517	0.297326	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.09723	2.95;2.95	4.88	-5.84	0.02318	.	1.151000	0.06097	N	0.664775	T	0.00012	0.0000	N	0.11789	0.175	0.80722	P	0.0	B	0.10296	0.003	B	0.16289	0.015	T	0.49244	-0.8960	9	0.10377	T	0.69	.	5.1731	0.15120	0.0813:0.0935:0.2794:0.5458	rs1813160;rs35147470;rs52810143;rs58460570;rs1813160	229	O00566	MPP10_HUMAN	D	229;89	ENSP00000244230:E229D;ENSP00000393034:E89D	ENSP00000244230:E229D	E	+	3	2	MPHOSPH10	71214133	0.017000	0.18338	0.001000	0.08648	0.189000	0.23516	-2.557000	0.00924	-0.696000	0.05098	-1.893000	0.00533	GAG	G|0.673;T|0.327	0.327	strong		0.323	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
LTF	4057	hgsc.bcm.edu	37	3	46501268	46501268	+	Missense_Mutation	SNP	C	C	T	rs1126477	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:46501268C>T	ENST00000231751.4	-	2	380	c.85G>A	c.(85-87)Gcc>Acc	p.A29T	LTF_ENST00000417439.1_Missense_Mutation_p.A29T|LTF_ENST00000426532.2_5'UTR	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	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	189	87	0.460317	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	
SCARB1	949	hgsc.bcm.edu	37	12	125284748	125284748	+	Silent	SNP	A	A	G	rs5888	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:125284748A>G	ENST00000415380.2	-	8	1175	c.1050T>C	c.(1048-1050)gcT>gcC	p.A350A	SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000261693.6_Silent_p.A350A|SCARB1_ENST00000376788.1_Silent_p.A250A|SCARB1_ENST00000546215.1_Silent_p.A350A|SCARB1_ENST00000544327.1_Silent_p.A296A|SCARB1_ENST00000540495.1_Silent_p.A313A|SCARB1_ENST00000541205.1_Silent_p.A309A|SCARB1_ENST00000339570.5_Silent_p.A350A			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	350					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)	GAACCGGGTCAGCGTTGAGGA	0.597													G|||	3391	0.677117	0.8306	0.6715	5008	,	,		18630	0.7599		0.5417	False		,,,				2504	0.5276				p.A350A		Atlas-SNP	.											.	SCARB1	40	.	0			c.T1050C	GRCh37	CM994636	SCARB1	M	rs5888	PASS	.	G	,	3595,811	322.3+/-297.6	1467,661,75	92.0	88.0	89.0		1050,1050	-10.6	0.0	12	dbSNP_52	89	4448,4152	565.7+/-388.5	1139,2170,991	no	coding-synonymous,coding-synonymous	SCARB1	NM_001082959.1,NM_005505.4	,	2606,2831,1066	GG,GA,AA		48.2791,18.4067,38.1593	,	350/507,350/510	125284748	8043,4963	2203	4300	6503	SO:0001819	synonymous_variant	949	exon8			CGGGTCAGCGTTG	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.1050T>C	12.37:g.125284748A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_005505	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Silent	SNP	ENST00000415380.2	37																																																																																				T|0.004;G|0.645	0.645	strong		0.597	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505	
MEGF9	1955	hgsc.bcm.edu	37	9	123367681	123367681	+	Silent	SNP	C	C	G	rs56019987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123367681C>G	ENST00000373930.3	-	6	1707	c.1596G>C	c.(1594-1596)gtG>gtC	p.V532V	MEGF9_ENST00000426959.1_Silent_p.V569V	NM_001080497.2	NP_001073966.2	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	532						integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	16						ATACAGCCCCCACAAATCCCA	0.433													C|||	112	0.0223642	0.0038	0.0303	5008	,	,		21435	0.0		0.0706	False		,,,				2504	0.0153				p.V532V		Atlas-SNP	.											.	MEGF9	33	.	0			c.G1596C						PASS	.	C		53,3811		0,53,1879	129.0	124.0	125.0		1596	1.7	1.0	9	dbSNP_129	125	558,7748		21,516,3616	no	coding-synonymous	MEGF9	NM_001080497.2		21,569,5495	GG,GC,CC		6.718,1.3716,5.0205		532/603	123367681	611,11559	1932	4153	6085	SO:0001819	synonymous_variant	1955	exon6			AGCCCCCACAAAT	AB011542	CCDS48010.1, CCDS48010.2	9q32-q33.3	2008-07-21	2006-03-31	2006-03-31	ENSG00000106780	ENSG00000106780			3234	protein-coding gene	gene with protein product		604268	"""EGF-like-domain, multiple 5"""	EGFL5		9693030	Standard	NM_001080497		Approved		uc022bms.1	Q9H1U4	OTTHUMG00000021039	ENST00000373930.3:c.1596G>C	9.37:g.123367681C>G		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	237	114	0.481013	NM_001080497	B7Z315|O75098	Silent	SNP	ENST00000373930.3	37	CCDS48010.2																																																																																			C|0.936;G|0.064	0.064	strong		0.433	MEGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055513.1	NM_001080497	
DNAH5	1767	hgsc.bcm.edu	37	5	13913885	13913885	+	Silent	SNP	A	A	G	rs3213936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	98	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	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	
HELQ	113510	hgsc.bcm.edu	37	4	84370091	84370091	+	Silent	SNP	A	A	G	rs13141136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:84370091A>G	ENST00000295488.3	-	3	1198	c.1036T>C	c.(1036-1038)Ttg>Ctg	p.L346L	HELQ_ENST00000510985.1_Silent_p.L346L	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	346	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ACAGAATTCAATGTTAAACAA	0.318								Other identified genes with known or suspected DNA repair function					A|||	2076	0.414537	0.1059	0.5245	5008	,	,		16998	0.6766		0.3787	False		,,,				2504	0.5204				p.L346L		Atlas-SNP	.											.	HELQ	95	.	0			c.T1036C						PASS	.	A		687,3715	266.2+/-267.1	54,579,1568	37.0	37.0	37.0		1036	-6.4	0.3	4	dbSNP_121	37	3504,5090	492.3+/-373.3	712,2080,1505	no	coding-synonymous	HELQ	NM_133636.2		766,2659,3073	GG,GA,AA		40.7726,15.6065,32.2484		346/1102	84370091	4191,8805	2201	4297	6498	SO:0001819	synonymous_variant	113510	exon3			AATTCAATGTTAA	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1036T>C	4.37:g.84370091A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.654;G|0.346	0.346	strong		0.318	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
NR1H3	10062	hgsc.bcm.edu	37	11	47282024	47282024	+	Silent	SNP	C	C	T	rs2279238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47282024C>T	ENST00000467728.1	+	3	1535	c.297C>T	c.(295-297)agC>agT	p.S99S	NR1H3_ENST00000405576.1_Silent_p.S54S|NR1H3_ENST00000441012.2_Silent_p.S99S|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000481889.2_Silent_p.S54S|NR1H3_ENST00000405853.3_Silent_p.S99S|NR1H3_ENST00000527949.1_Silent_p.S8S|NR1H3_ENST00000395397.3_Silent_p.S54S|NR1H3_ENST00000407404.1_Silent_p.S99S			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	92	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	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		
WNT2B	7482	hgsc.bcm.edu	37	1	113063125	113063125	+	Silent	SNP	A	A	G	rs910697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:113063125A>G	ENST00000369684.4	+	5	1655	c.1170A>G	c.(1168-1170)caA>caG	p.Q390Q	WNT2B_ENST00000369686.5_Silent_p.Q371Q|WNT2B_ENST00000256640.5_Silent_p.Q298Q|RP4-671G15.2_ENST00000608357.1_RNA	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	93	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	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	
TMEM63A	9725	hgsc.bcm.edu	37	1	226034774	226034774	+	Silent	SNP	C	C	T	rs2292559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226034774C>T	ENST00000366835.3	-	24	2661	c.2391G>A	c.(2389-2391)acG>acA	p.T797T	RP11-285F7.2_ENST00000424332.1_RNA	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	797					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)					CCACACTGCCCGTGGCGCTCT	0.662													C|||	353	0.0704872	0.0008	0.0735	5008	,	,		18801	0.1587		0.0487	False		,,,				2504	0.0941				p.T797T		Atlas-SNP	.											.	TMEM63A	75	.	0			c.G2391A						PASS	.	C		32,4372	36.8+/-68.6	0,32,2170	51.0	52.0	52.0		2391	0.3	0.0	1	dbSNP_100	52	349,8251	114.8+/-174.7	4,341,3955	no	coding-synonymous	TMEM63A	NM_014698.2		4,373,6125	TT,TC,CC		4.0581,0.7266,2.9299		797/808	226034774	381,12623	2202	4300	6502	SO:0001819	synonymous_variant	9725	exon24			ACTGCCCGTGGCG		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.2391G>A	1.37:g.226034774C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			C|0.957;T|0.043	0.043	strong		0.662	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
SPATC1L	84221	hgsc.bcm.edu	37	21	47581423	47581423	+	Missense_Mutation	SNP	C	C	T	rs14378	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47581423C>T	ENST00000291672.5	-	5	1954	c.893G>A	c.(892-894)aGc>aAc	p.S298N	SPATC1L_ENST00000330205.6_Missense_Mutation_p.S144N	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	298			S -> N (in dbSNP:rs14378).														GGCCGGGCTGCTGTGCAGGGG	0.672													C|||	510	0.101837	0.1551	0.0735	5008	,	,		11263	0.0179		0.1034	False		,,,				2504	0.135				p.S298N		Atlas-SNP	.											.	.	.	.	0			c.G893A						PASS	.	C	ASN/SER,ASN/SER	597,3787		44,509,1639	21.0	24.0	23.0		893,431	3.3	1.0	21	dbSNP_52	23	809,7773		34,741,3516	yes	missense,missense	C21orf56	NM_001142854.1,NM_032261.4	46,46	78,1250,5155	TT,TC,CC		9.4267,13.6177,10.8437	benign,benign	298/341,144/187	47581423	1406,11560	2192	4291	6483	SO:0001583	missense	84221	exon5			GGGCTGCTGTGCA	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.893G>A	21.37:g.47581423C>T	ENSP00000291672:p.Ser298Asn	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	178	0.0815018315018315	59	0.11991869918699187	33	0.09116022099447514	10	0.017482517482517484	76	0.10026385224274406	C	9.667	1.145700	0.21288	0.136177	0.094267	ENSG00000160284	ENST00000330205;ENST00000291672	T;T	0.55234	0.53;0.53	4.37	3.32	0.38043	.	0.221171	0.36555	N	0.002526	T	0.00144	0.0004	N	0.03608	-0.345	0.36796	P	0.11489799999999994	B	0.02656	0.0	B	0.04013	0.001	T	0.08186	-1.0734	9	0.15066	T	0.55	-26.4506	3.818	0.08824	0.0:0.7011:0.0:0.2989	rs14378;rs17343698;rs60647255;rs14378	298	Q9H0A9	CU056_HUMAN	N	144;298	ENSP00000333869:S144N;ENSP00000291672:S298N	ENSP00000291672:S298N	S	-	2	0	C21orf56	46405851	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.804000	0.27098	1.990000	0.58119	0.591000	0.81541	AGC	C|0.896;T|0.104	0.104	strong		0.672	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
SH3BP2	6452	hgsc.bcm.edu	37	4	2831383	2831383	+	Silent	SNP	T	T	G	rs231399	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2831383T>G	ENST00000356331.5	+	8	1011	c.750T>G	c.(748-750)gcT>gcG	p.A250A	SH3BP2_ENST00000511747.1_Silent_p.A250A|SH3BP2_ENST00000435136.2_Silent_p.A250A|SH3BP2_ENST00000503393.2_Silent_p.A307A|SH3BP2_ENST00000442312.2_Silent_p.A278A|SH3BP2_ENST00000452765.2_Silent_p.A250A|SH3BP2_ENST00000515183.1_3'UTR	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	250					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)	p.A250A(1)		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)		TTGGCCTGGCTGCTGAGGACT	0.677									Cherubism				T|||	2335	0.466254	0.3533	0.5245	5008	,	,		10753	0.4712		0.4851	False		,,,				2504	0.5532				p.A307A		Atlas-SNP	.											SH3BP2,NS,carcinoma,0,1	SH3BP2	43	1	1	Substitution - coding silent(1)	prostate(1)	c.T921G						scavenged	.	T	,,,	1649,2757	491.7+/-362.2	285,1079,839	39.0	44.0	42.0		750,834,921,750	-9.2	0.0	4	dbSNP_79	42	4260,4340	561.2+/-387.7	1083,2094,1123	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	1368,3173,1962	GG,GT,TT		49.5349,37.4262,45.4329	,,,	250/562,278/590,307/619,250/562	2831383	5909,7097	2203	4300	6503	SO:0001819	synonymous_variant	6452	exon8	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CCTGGCTGCTGAG	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.750T>G	4.37:g.2831383T>G		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			T|0.554;G|0.446	0.446	strong		0.677	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
FAM69C	125704	hgsc.bcm.edu	37	18	72103782	72103782	+	Missense_Mutation	SNP	T	T	C	rs2278154	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	63	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	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	
GBP6	163351	hgsc.bcm.edu	37	1	89844035	89844035	+	Missense_Mutation	SNP	T	T	C	rs35837853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89844035T>C	ENST00000370456.4	+	5	581	c.488T>C	c.(487-489)gTa>gCa	p.V163A	GBP6_ENST00000535065.1_Missense_Mutation_p.V33A	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	163	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		CCTGATGGAGTAGAAGATTCC	0.458													T|||	511	0.102037	0.0045	0.134	5008	,	,		18582	0.2758		0.0666	False		,,,				2504	0.0685				p.V163A		Atlas-SNP	.											.	GBP6	87	.	0			c.T488C						PASS	.	T	ALA/VAL	52,4354	51.6+/-87.1	0,52,2151	121.0	129.0	127.0		488	-3.5	0.0	1	dbSNP_126	127	349,8251	119.4+/-178.7	1,347,3952	yes	missense	GBP6	NM_198460.2	64	1,399,6103	CC,CT,TT		4.0581,1.1802,3.0832	benign	163/634	89844035	401,12605	2203	4300	6503	SO:0001583	missense	163351	exon5			ATGGAGTAGAAGA	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.488T>C	1.37:g.89844035T>C	ENSP00000359485:p.Val163Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	261	0.11950549450549451	3	0.006097560975609756	42	0.11602209944751381	162	0.28321678321678323	54	0.0712401055408971	T	8.949	0.967628	0.18659	0.011802	0.040581	ENSG00000183347	ENST00000544311;ENST00000370456;ENST00000535065	T;T	0.76709	-1.04;-1.04	4.24	-3.55	0.04639	Guanylate-binding protein, N-terminal (1);	1.126930	0.06713	N	0.773473	T	0.40979	0.1139	L	0.33792	1.035	0.80722	P	0.0	B	0.09022	0.002	B	0.12156	0.007	T	0.16276	-1.0408	9	0.36615	T	0.2	-0.5825	4.2396	0.10642	0.522:0.1695:0.0:0.3085	rs35837853	163	Q6ZN66	GBP6_HUMAN	A	134;163;33	ENSP00000359485:V163A;ENSP00000442530:V33A	ENSP00000359485:V163A	V	+	2	0	GBP6	89616623	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.277000	0.02812	-0.793000	0.04475	-0.334000	0.08254	GTA	T|0.945;C|0.055	0.055	strong		0.458	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
TNR	7143	hgsc.bcm.edu	37	1	175324711	175324711	+	Silent	SNP	G	G	A	rs61731115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:175324711G>A	ENST00000367674.2	-	17	3885	c.3177C>T	c.(3175-3177)atC>atT	p.I1059I	TNR_ENST00000263525.2_Silent_p.I1059I			Q92752	TENR_HUMAN	tenascin R	1059	Fibronectin type-III 9. {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)					GCTGCCAGGAGATCAGGGCAC	0.537													G|||	627	0.1252	0.1702	0.0692	5008	,	,		22049	0.0933		0.0964	False		,,,				2504	0.1667				p.I1059I		Atlas-SNP	.											.	TNR	399	.	0			c.C3177T						PASS	.	G		583,3823	259.5+/-263.1	52,479,1672	89.0	92.0	91.0		3177	3.0	1.0	1	dbSNP_129	91	799,7801	187.6+/-234.8	44,711,3545	no	coding-synonymous	TNR	NM_003285.2		96,1190,5217	AA,AG,GG		9.2907,13.232,10.6259		1059/1359	175324711	1382,11624	2203	4300	6503	SO:0001819	synonymous_variant	7143	exon17			CCAGGAGATCAGG	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.3177C>T	1.37:g.175324711G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																			G|0.894;A|0.106	0.106	strong		0.537	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
RBM19	9904	hgsc.bcm.edu	37	12	114377835	114377835	+	Missense_Mutation	SNP	A	A	G	rs2290788	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:114377835A>G	ENST00000545145.2	-	15	1946	c.1868T>C	c.(1867-1869)aTc>aCc	p.I623T	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.I623T|RBM19_ENST00000392561.3_Missense_Mutation_p.I623T	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	623	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		I -> T (in dbSNP:rs2290788). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GATGGCAGTGATTCCGCCCTC	0.642													A|||	965	0.192692	0.3245	0.0735	5008	,	,		16454	0.1885		0.1133	False		,,,				2504	0.1851				p.I623T		Atlas-SNP	.											.	RBM19	117	.	0			c.T1868C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	1342,3064	436.1+/-344.5	224,894,1085	54.0	60.0	58.0		1868,1868,1868	3.1	0.7	12	dbSNP_100	58	888,7712	196.3+/-241.3	39,810,3451	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	89,89,89	263,1704,4536	GG,GA,AA		10.3256,30.4585,17.1459	benign,benign,benign	623/961,623/961,623/961	114377835	2230,10776	2203	4300	6503	SO:0001583	missense	9904	exon15			GCAGTGATTCCGC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1868T>C	12.37:g.114377835A>G	ENSP00000442053:p.Ile623Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	23	0.315068	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	
FAM107A	11170	hgsc.bcm.edu	37	3	58552997	58552997	+	Missense_Mutation	SNP	C	C	A	rs1043942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58552997C>A	ENST00000394481.1	-	4	823	c.265G>T	c.(265-267)Gcc>Tcc	p.A89S	FAM107A_ENST00000474531.1_Missense_Mutation_p.A120S|FAM107A_ENST00000360997.2_Missense_Mutation_p.A89S|FAM107A_ENST00000464064.1_Missense_Mutation_p.A89S|FAM107A_ENST00000447756.2_Missense_Mutation_p.A117S	NM_001282713.1|NM_007177.2	NP_001269642.1|NP_009108.1	O95990	F107A_HUMAN	family with sequence similarity 107, member A	89			A -> S (in dbSNP:rs1043942).		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)		AGCCGCTTGGCTTCCAGCTCC	0.642													C|||	302	0.0603035	0.1089	0.0403	5008	,	,		19707	0.002		0.0477	False		,,,				2504	0.0818				p.A89S		Atlas-SNP	.											.	FAM107A	33	.	0			c.G265T						PASS	.	C	SER/ALA,SER/ALA	504,3902	229.1+/-243.8	34,436,1733	42.0	36.0	38.0		265,265	4.2	1.0	3	dbSNP_86	38	560,8040	151.5+/-206.2	19,522,3759	yes	missense,missense	FAM107A	NM_001076778.1,NM_007177.2	99,99	53,958,5492	AA,AC,CC		6.5116,11.4389,8.1808	possibly-damaging,possibly-damaging	89/145,89/145	58552997	1064,11942	2203	4300	6503	SO:0001583	missense	11170	exon3			GCTTGGCTTCCAG	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.265G>T	3.37:g.58552997C>A	ENSP00000377991:p.Ala89Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	176	92	0.522727	NM_001076778	B3KNQ4|B7ZAY5|J3KR61|Q96NH4	Missense_Mutation	SNP	ENST00000394481.1	37	CCDS2892.1	118	0.05402930402930403	68	0.13821138211382114	11	0.03038674033149171	1	0.0017482517482517483	38	0.05013192612137203	C	21.8	4.201418	0.79015	0.114389	0.065116	ENSG00000168309	ENST00000360997;ENST00000394481;ENST00000464064;ENST00000474531;ENST00000447756;ENST00000465970	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.05	4.16	0.48862	.	0.158084	0.56097	D	0.000032	T	0.00468	0.0015	M	0.78916	2.43	0.22835	P	0.99867395	P;D;P;P	0.54207	0.626;0.965;0.749;0.749	B;P;P;B	0.48454	0.298;0.578;0.492;0.396	T	0.18304	-1.0341	9	0.44086	T	0.13	-11.19	10.1437	0.42751	0.0:0.8417:0.0:0.1583	rs1043942;rs3183624;rs52819386;rs1043942	117;89;120;89	B7ZAY5;O95990-2;B3KNQ4;O95990	.;.;.;F107A_HUMAN	S	89;89;89;120;117;89	ENSP00000354270:A89S;ENSP00000377991:A89S;ENSP00000419529:A89S;ENSP00000419124:A120S;ENSP00000400858:A117S;ENSP00000418038:A89S	ENSP00000354270:A89S	A	-	1	0	FAM107A	58528037	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.013000	0.64023	1.233000	0.43693	0.591000	0.81541	GCC	G|0.000;C|0.931;A|0.069	0.069	strong		0.642	FAM107A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353585.1	NM_007177	
TMEM260	54916	hgsc.bcm.edu	37	14	57075920	57075920	+	Missense_Mutation	SNP	G	G	T	rs17776256	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:57075920G>T	ENST00000261556.6	+	6	855	c.733G>T	c.(733-735)Gcc>Tcc	p.A245S	TMEM260_ENST00000536419.1_5'UTR|TMEM260_ENST00000538838.1_Missense_Mutation_p.A245S	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	245			A -> S (in dbSNP:rs17776256). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)											CCTTAATCACGCCCGGTGGAC	0.478													G|||	545	0.108826	0.1324	0.098	5008	,	,		17824	0.004		0.1521	False		,,,				2504	0.1483				p.A245S		Atlas-SNP	.											.	.	.	.	0			c.G733T						PASS	.	G	SER/ALA	549,3857	249.6+/-257.0	36,477,1690	221.0	211.0	215.0		733	6.1	1.0	14	dbSNP_123	215	1121,7479	232.1+/-265.8	87,947,3266	yes	missense	C14orf101	NM_017799.3	99	123,1424,4956	TT,TG,GG		13.0349,12.4603,12.8402	probably-damaging	245/708	57075920	1670,11336	2203	4300	6503	SO:0001583	missense	0	exon6			AATCACGCCCGGT	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 101"""	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.733G>T	14.37:g.57075920G>T	ENSP00000261556:p.Ala245Ser	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	199	107	0.537688	NM_017799	A8KAN4|B3KPF5|Q86XE1	Missense_Mutation	SNP	ENST00000261556.6	37	CCDS9727.2	221	0.10119047619047619	61	0.12398373983739837	42	0.11602209944751381	1	0.0017482517482517483	117	0.15435356200527706	G	25.9	4.690097	0.88735	0.124603	0.130349	ENSG00000070269	ENST00000261556;ENST00000538838	T;T	0.44881	1.47;0.91	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.00666	0.0022	M	0.72894	2.215	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00086	-1.2095	9	0.34782	T	0.22	-12.3979	20.6397	0.99537	0.0:0.0:1.0:0.0	rs17776256;rs52803469;rs17776256	245	Q9NX78	CN101_HUMAN	S	245	ENSP00000261556:A245S;ENSP00000441934:A245S	ENSP00000261556:A245S	A	+	1	0	C14orf101	56145673	1.000000	0.71417	0.972000	0.41901	0.517000	0.34286	9.730000	0.98797	2.880000	0.98712	0.650000	0.86243	GCC	G|0.880;T|0.120	0.120	strong		0.478	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799	
CNR2	1269	hgsc.bcm.edu	37	1	24201109	24201109	+	Silent	SNP	C	C	T	rs2229580	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201109C>T	ENST00000374472.4	-	2	1160	c.999G>A	c.(997-999)ccG>ccA	p.P333P	CNR2_ENST00000536471.1_Silent_p.P333P	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	333					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)	p.P333P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	CTGAGGATCTCGGGGCTTCTT	0.557													C|||	3272	0.653355	0.7943	0.6383	5008	,	,		21148	0.502		0.5875	False		,,,				2504	0.6973				p.P333P		Atlas-SNP	.											CNR2,NS,carcinoma,0,1	CNR2	78	1	1	Substitution - coding silent(1)	stomach(1)	c.G999A						PASS	.	C		3311,1095	720.0+/-409.0	1261,789,153	97.0	106.0	103.0		999	-9.5	0.0	1	dbSNP_98	103	4935,3665	622.6+/-397.3	1402,2131,767	no	coding-synonymous	CNR2	NM_001841.2		2663,2920,920	TT,TC,CC		42.6163,24.8525,36.5985		333/361	24201109	8246,4760	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			GGATCTCGGGGCT	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.999G>A	1.37:g.24201109C>T		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	230	106	0.46087	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			C|0.368;T|0.632	0.632	strong		0.557	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
SLC7A13	157724	hgsc.bcm.edu	37	8	87226700	87226700	+	Missense_Mutation	SNP	A	A	G	rs9656982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87226700A>G	ENST00000297524.3	-	4	1458	c.1355T>C	c.(1354-1356)aTg>aCg	p.M452T	SLC7A13_ENST00000419776.2_3'UTR|CTD-3118D11.3_ENST00000523112.1_RNA	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	452			M -> T (in dbSNP:rs9656982).			integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						ATAGCAAGTCATCTTCTCAAA	0.328													A|||	848	0.169329	0.1967	0.2363	5008	,	,		17057	0.1419		0.0835	False		,,,				2504	0.2014				p.M452T		Atlas-SNP	.											.	SLC7A13	97	.	0			c.T1355C						PASS	.	A	THR/MET	768,3638	301.0+/-286.6	66,636,1501	63.0	69.0	67.0		1355	4.2	0.4	8	dbSNP_119	67	779,7821	183.9+/-232.0	31,717,3552	yes	missense	SLC7A13	NM_138817.2	81	97,1353,5053	GG,GA,AA		9.0581,17.4308,11.8945	benign	452/471	87226700	1547,11459	2203	4300	6503	SO:0001583	missense	157724	exon4			CAAGTCATCTTCT	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1355T>C	8.37:g.87226700A>G	ENSP00000297524:p.Met452Thr	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	302	0.1382783882783883	81	0.16463414634146342	80	0.22099447513812154	67	0.11713286713286714	74	0.09762532981530343	A	12.56	1.973178	0.34848	0.174308	0.090581	ENSG00000164893	ENST00000297524	D	0.87966	-2.32	4.15	4.15	0.48705	.	0.647706	0.14488	N	0.316524	T	0.00109	0.0003	N	0.08118	0	0.09310	P	1.0	B	0.19817	0.039	B	0.18263	0.021	T	0.08066	-1.0740	9	0.27785	T	0.31	.	11.775	0.51981	1.0:0.0:0.0:0.0	rs9656982;rs52795070;rs61261684;rs9656982	452	Q8TCU3	S7A13_HUMAN	T	452	ENSP00000297524:M452T	ENSP00000297524:M452T	M	-	2	0	SLC7A13	87295816	0.152000	0.22762	0.373000	0.26003	0.957000	0.61999	3.243000	0.51392	1.808000	0.52836	0.533000	0.62120	ATG	A|0.866;G|0.134	0.134	strong		0.328	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
DPH1	1801	hgsc.bcm.edu	37	17	1940232	1940232	+	Missense_Mutation	SNP	A	A	G	rs1131600	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1940232A>G	ENST00000263083.6	+	6	722	c.677A>G	c.(676-678)aAa>aGa	p.K226R	DPH1_ENST00000576891.2_3'UTR|DPH1_ENST00000570477.1_Missense_Mutation_p.K146R	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	226			K -> R (in dbSNP:rs1131600). {ECO:0000269|PubMed:8616839}.		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						CGACTGTCCAAAGAGGTGGAG	0.577													A|||	508	0.101438	0.0098	0.2968	5008	,	,		18911	0.0565		0.1541	False		,,,				2504	0.0787				p.K226R		Atlas-SNP	.											DPH1,NS,carcinoma,0,1	DPH1	32	1	0			c.A677G						PASS	.	A	ARG/LYS	131,3721		4,123,1799	45.0	50.0	48.0		677	4.6	1.0	17	dbSNP_86	48	1340,6922		122,1096,2913	yes	missense	DPH1	NM_001383.3	26	126,1219,4712	GG,GA,AA		16.2188,3.4008,12.143	benign	226/444	1940232	1471,10643	1926	4131	6057	SO:0001583	missense	1801	exon6			TGTCCAAAGAGGT	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.677A>G	17.37:g.1940232A>G	ENSP00000263083:p.Lys226Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	37	CCDS42228.1	254	0.1163003663003663	8	0.016260162601626018	88	0.2430939226519337	43	0.07517482517482517	115	0.1517150395778364	A	8.856	0.945819	0.18356	0.034008	0.162188	ENSG00000108963	ENST00000263083	T	0.43294	0.95	5.71	4.63	0.57726	.	0.512553	0.22244	N	0.062645	T	0.00012	0.0000	N	0.20766	0.605	0.37302	P	0.09124399999999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.003;0.005;0.005	T	0.25847	-1.0120	9	0.22706	T	0.39	-2.2955	8.3377	0.32224	0.7959:0.1339:0.0702:0.0	rs1131600;rs1804588;rs3191649;rs11551145;rs16951861;rs17413902;rs1131600	236;236;226	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	R	226	ENSP00000263083:K226R	ENSP00000263083:K226R	K	+	2	0	DPH1	1886982	0.913000	0.31002	0.987000	0.45799	0.423000	0.31445	1.942000	0.40243	0.989000	0.38761	-0.346000	0.07831	AAA	A|0.885;G|0.115	0.115	strong		0.577	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
LY6G5B	58496	hgsc.bcm.edu	37	6	31639979	31639979	+	Missense_Mutation	SNP	C	C	T	rs9267532	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31639979C>T	ENST00000375864.4	+	3	1310	c.526C>T	c.(526-528)Cgc>Tgc	p.R176C	LY6G5B_ENST00000409525.1_Missense_Mutation_p.R121C|CSNK2B-LY6G5B-1181_ENST00000375880.2_3'UTR	NM_021221.2	NP_067044.2	Q8NDX9	LY65B_HUMAN	lymphocyte antigen 6 complex, locus G5B	176			R -> C (in dbSNP:rs9267532). {ECO:0000269|PubMed:14574404}.			extracellular region (GO:0005576)				lung(4)	4						TGCTGAGCTGCGCCGCATGTA	0.547													c|||	397	0.0792732	0.1036	0.0447	5008	,	,		20366	0.0565		0.0666	False		,,,				2504	0.1074				p.R176C		Atlas-SNP	.											.	LY6G5B	8	.	0			c.C526T						PASS	.	T	CYS/ARG	289,2733		17,255,1239	121.0	111.0	114.0		526	2.9	0.4	6	dbSNP_118	114	378,5040		13,352,2344	yes	missense	LY6G5B	NM_021221.2	180	30,607,3583	TT,TC,CC		6.9767,9.5632,7.9028	probably-damaging	176/202	31639979	667,7773	1511	2709	4220	SO:0001583	missense	58496	exon3			GAGCTGCGCCGCA	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.526C>T	6.37:g.31639979C>T	ENSP00000365024:p.Arg176Cys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_021221	B0UXB2|B0UZ65|B0UZP8|B7ZCA3|Q5SQ62|Q5SST3|Q9UKT0|Q9UMQ0	Missense_Mutation	SNP	ENST00000375864.4	37	CCDS34400.1	153	0.07005494505494506	51	0.10365853658536585	17	0.04696132596685083	33	0.057692307692307696	52	0.06860158311345646	c	6.314	0.426030	0.11987	0.095632	0.069767	ENSG00000240053	ENST00000409691;ENST00000375864;ENST00000409525	T;T	0.27557	1.67;1.66	3.79	2.92	0.33932	.	.	.	.	.	T	0.22551	0.0544	L	0.32530	0.975	.	.	.	D	0.89917	1.0	P	0.60886	0.88	T	0.05582	-1.0876	8	0.56958	D	0.05	-11.6129	7.5746	0.27928	0.0:0.8811:0.0:0.1189	rs9267532;rs57853456;rs9267532	176	Q8NDX9	LY65B_HUMAN	C	173;176;121	ENSP00000365024:R176C;ENSP00000386365:R121C	ENSP00000365024:R176C	R	+	1	0	LY6G5B	31747958	0.498000	0.26075	0.416000	0.26546	0.292000	0.27327	0.568000	0.23623	0.959000	0.37980	-0.355000	0.07637	CGC	C|0.924;T|0.076	0.076	strong		0.547	LY6G5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000124389.4		
CNRIP1	25927	hgsc.bcm.edu	37	2	68546449	68546449	+	Silent	SNP	G	G	A	rs13025842	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:68546449G>A	ENST00000263655.3	-	1	689	c.84C>T	c.(82-84)gaC>gaT	p.D28D	CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409862.1_Silent_p.D28D|CNRIP1_ENST00000409559.3_Silent_p.D28D	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	28										kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						AGCGCTGCCCGTCCACCTTGT	0.632													G|||	1044	0.208466	0.1589	0.3026	5008	,	,		15369	0.0794		0.331	False		,,,				2504	0.2157				p.D28D		Atlas-SNP	.											.	CNRIP1	45	.	0			c.C84T						PASS	.	G	,	718,3632		64,590,1521	47.0	36.0	40.0		84,84	2.9	1.0	2	dbSNP_121	40	2642,5878		429,1784,2047	no	coding-synonymous,coding-synonymous	CNRIP1	NM_001111101.1,NM_015463.2	,	493,2374,3568	AA,AG,GG		31.0094,16.5057,26.1072	,	28/129,28/165	68546449	3360,9510	2175	4260	6435	SO:0001819	synonymous_variant	25927	exon1			CTGCCCGTCCACC	AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 32"""	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.84C>T	2.37:g.68546449G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	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	
ALDH4A1	8659	hgsc.bcm.edu	37	1	19202896	19202896	+	Silent	SNP	G	G	A	rs2230707	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19202896G>A	ENST00000375341.3	-	12	1508	c.1251C>T	c.(1249-1251)gcC>gcT	p.A417A	ALDH4A1_ENST00000538839.1_Intron|ALDH4A1_ENST00000538309.1_Silent_p.A357A|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000290597.5_Silent_p.A417A	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	417					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		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;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ACTTGCCCCCGGCCAGGATGG	0.627													G|||	2584	0.515974	0.4569	0.6513	5008	,	,		19095	0.6002		0.4453	False		,,,				2504	0.4857				p.A417A		Atlas-SNP	.											.	ALDH4A1	72	.	0			c.C1251T						PASS	.	G	,,	1917,2489	542.7+/-376.1	427,1063,713	53.0	42.0	46.0		1071,1251,1251	-8.6	0.7	1	dbSNP_98	46	3997,4603	548.6+/-385.4	907,2183,1210	yes	coding-synonymous,coding-synonymous,coding-synonymous	ALDH4A1	NM_001161504.1,NM_003748.3,NM_170726.2	,,	1334,3246,1923	AA,AG,GG		46.4767,43.5089,45.4713	,,	357/504,417/564,417/564	19202896	5914,7092	2203	4300	6503	SO:0001819	synonymous_variant	8659	exon12			GCCCCCGGCCAGG	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.1251C>T	1.37:g.19202896G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Silent	SNP	ENST00000375341.3	37	CCDS188.1																																																																																			G|0.522;A|0.478	0.478	strong		0.627	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1		
PBX1	5087	hgsc.bcm.edu	37	1	164529120	164529120	+	Missense_Mutation	SNP	G	G	A	rs2275558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:164529120G>A	ENST00000420696.2	+	1	249	c.61G>A	c.(61-63)Ggc>Agc	p.G21S	PBX1_ENST00000540236.1_Missense_Mutation_p.G21S|PBX1_ENST00000559240.1_Missense_Mutation_p.G21S|PBX1_ENST00000485769.1_Missense_Mutation_p.G21S|PBX1_ENST00000401534.1_Missense_Mutation_p.G21S|PBX1_ENST00000367897.1_Missense_Mutation_p.G21S	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	21					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						CGGACACCCCGGCCTGTCCCA	0.627			T	"""TCF3, EWSR1"""	"""pre B-ALL, myoepithelioma"""								G|||	1539	0.307308	0.0159	0.4308	5008	,	,		6892	0.6101		0.1968	False		,,,				2504	0.4151				p.G21S		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"""L, M"""	PBX1_ENST00000420696,colon,carcinoma,0,1	PBX1	60	1	0			c.G61A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	168,3946		3,162,1892	10.0	11.0	11.0		61,61,61	5.2	1.0	1	dbSNP_100	11	1503,6483		141,1221,2631	yes	missense,missense,missense	PBX1	NM_001204961.1,NM_001204963.1,NM_002585.3	56,56,56	144,1383,4523	AA,AG,GG		18.8204,4.0836,13.8099	benign,benign,benign	21/348,21/421,21/431	164529120	1671,10429	2057	3993	6050	SO:0001583	missense	5087	exon1			CACCCCGGCCTGT	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"""Homeoboxes / TALE class"""	8632	protein-coding gene	gene with protein product		176310	"""pre-B-cell leukemia transcription factor 1"""				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.61G>A	1.37:g.164529120G>A	ENSP00000405890:p.Gly21Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	181	76	0.41989	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	37	CCDS1246.1	666	0.30494505494505497	21	0.042682926829268296	130	0.35911602209944754	372	0.6503496503496503	143	0.18865435356200527	G	12.17	1.858419	0.32791	0.040836	0.188204	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534	T;D;D;D;D	0.89681	0.79;-2.51;-2.43;-2.55;-2.43	5.18	5.18	0.71444	.	0.063231	0.64402	D	0.000005	T	0.71005	0.3289	L	0.45137	1.4	0.09310	N	1.0	B;P;B	0.35226	0.054;0.491;0.066	B;B;B	0.19391	0.006;0.025;0.004	T	0.69884	-0.5024	9	0.20519	T	0.43	-8.1196	11.0309	0.47772	0.0866:0.0:0.9134:0.0	rs2275558;rs59646304	21;21;21	F5H4U9;P40424;Q53YC7	.;PBX1_HUMAN;.	S	21	ENSP00000341455:G21S;ENSP00000405890:G21S;ENSP00000356872:G21S;ENSP00000439943:G21S;ENSP00000384856:G21S	ENSP00000341455:G21S	G	+	1	0	PBX1	162795744	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	7.826000	0.86716	2.409000	0.81822	0.561000	0.74099	GGC	G|0.695;A|0.305	0.305	strong		0.627	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585	
DCHS1	8642	hgsc.bcm.edu	37	11	6655433	6655433	+	Silent	SNP	G	G	A	rs997263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6655433G>A	ENST00000299441.3	-	3	2313	c.1902C>T	c.(1900-1902)caC>caT	p.H634H	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	634	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATCACCGCTGTGGGCATCAA	0.592													G|||	1735	0.346446	0.2572	0.3631	5008	,	,		21138	0.4296		0.3777	False		,,,				2504	0.3374				p.H634H		Atlas-SNP	.											.	DCHS1	277	.	0			c.C1902T						PASS	.	G		1277,3125	434.1+/-343.8	202,873,1126	99.0	97.0	97.0		1902	1.7	1.0	11	dbSNP_86	97	3238,5354	487.5+/-372.1	598,2042,1656	no	coding-synonymous	DCHS1	NM_003737.2		800,2915,2782	AA,AG,GG		37.6862,29.0095,34.7468		634/3299	6655433	4515,8479	2201	4296	6497	SO:0001819	synonymous_variant	8642	exon3			ACCGCTGTGGGCA	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.1902C>T	11.37:g.6655433G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			G|0.642;A|0.358	0.358	strong		0.592	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
PYROXD2	84795	hgsc.bcm.edu	37	10	100148176	100148176	+	Missense_Mutation	SNP	A	A	G	rs2147896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	95	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	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	
RABEP1	9135	hgsc.bcm.edu	37	17	5284719	5284719	+	Silent	SNP	T	T	C	rs1065482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5284719T>C	ENST00000546142.2	+	17	2593	c.2406T>C	c.(2404-2406)aaT>aaC	p.N802N	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000408982.2_Silent_p.N769N|RABEP1_ENST00000262477.6_Silent_p.N802N|RABEP1_ENST00000537505.1_Silent_p.N759N|RABEP1_ENST00000341923.6_Silent_p.N769N			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	74	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	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	
METTL13	51603	hgsc.bcm.edu	37	1	171755170	171755170	+	Silent	SNP	G	G	A	rs2232818	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171755170G>A	ENST00000361735.3	+	3	1331	c.1065G>A	c.(1063-1065)tcG>tcA	p.S355S	METTL13_ENST00000362019.3_Silent_p.S269S|METTL13_ENST00000458517.1_Silent_p.S354S|METTL13_ENST00000367737.5_Silent_p.S199S	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	355							methyltransferase activity (GO:0008168)			breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						CTGAGCTGTCGGCTAGAGTCA	0.562													G|||	1593	0.318091	0.323	0.2911	5008	,	,		20059	0.5238		0.2445	False		,,,				2504	0.1943				p.S355S		Atlas-SNP	.											.	METTL13	67	.	0			c.G1065A						PASS	.	G	,,	1528,2878	479.9+/-358.7	277,974,952	54.0	45.0	48.0		597,807,1065	-10.7	0.5	1	dbSNP_98	48	2341,6259	389.4+/-342.9	334,1673,2293	no	coding-synonymous,coding-synonymous,coding-synonymous	METTL13	NM_001007239.1,NM_014955.2,NM_015935.4	,,	611,2647,3245	AA,AG,GG		27.2209,34.68,29.7478	,,	199/544,269/614,355/700	171755170	3869,9137	2203	4300	6503	SO:0001819	synonymous_variant	51603	exon3			GCTGTCGGCTAGA	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1065G>A	1.37:g.171755170G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	172	94	0.546512	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Silent	SNP	ENST00000361735.3	37	CCDS1299.1																																																																																			G|0.680;A|0.320	0.320	strong		0.562	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
CSMD1	64478	hgsc.bcm.edu	37	8	2820745	2820745	+	Splice_Site	SNP	G	G	C	rs667859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:2820745G>C	ENST00000520002.1	-	61	10011	c.9456C>G	c.(9454-9456)ctC>ctG	p.L3152L	CSMD1_ENST00000537824.1_Splice_Site_p.L3151L|CSMD1_ENST00000602723.1_Splice_Site_p.L2975L|CSMD1_ENST00000400186.3_Splice_Site_p.L2975L|CSMD1_ENST00000542608.1_Splice_Site_p.L2974L|CSMD1_ENST00000602557.1_Splice_Site_p.L3152L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3152	Sushi 25. {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)		AGAACTTACGGAGACACTGGG	0.547													C|||	2177	0.434704	0.5401	0.2954	5008	,	,		16782	0.5456		0.339	False		,,,				2504	0.3753				p.L3151L		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C9453G						PASS	.	C		1807,2111		436,935,588	86.0	91.0	90.0		9453	2.9	1.0	8	dbSNP_83	90	2682,5608		446,1790,1909	yes	coding-synonymous-near-splice	CSMD1	NM_033225.5		882,2725,2497	CC,CG,GG		32.3522,46.1205,36.771		3151/3565	2820745	4489,7719	1959	4145	6104	SO:0001630	splice_region_variant	64478	exon60			CTTACGGAGACAC			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.9457+1C>G	8.37:g.2820745G>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	26	0.634146	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		957	0.4381868131868132	265	0.5386178861788617	102	0.281767955801105	337	0.5891608391608392	253	0.3337730870712401	C	2.887	-0.230506	0.05983	0.461205	0.323522	ENSG00000183117	ENST00000335551	.	.	.	5.69	2.93	0.34026	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46582	-0.9181	3	.	.	.	.	6.1603	0.20360	0.0:0.6111:0.1234:0.2655	rs667859;rs59362929	.	.	.	A	2569	.	.	P	-	1	0	CSMD1	2808152	0.072000	0.21174	0.998000	0.56505	0.133000	0.20885	-0.504000	0.06375	0.082000	0.17018	-0.120000	0.15030	CCC	G|0.566;C|0.434	0.434	strong		0.547	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	Silent
KIF27	55582	hgsc.bcm.edu	37	9	86504027	86504027	+	Missense_Mutation	SNP	A	A	C	rs146702826		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:86504027A>C	ENST00000297814.2	-	7	2094	c.1951T>G	c.(1951-1953)Tca>Gca	p.S651A	KIF27_ENST00000334204.2_Missense_Mutation_p.S651A|KIF27_ENST00000413982.1_Missense_Mutation_p.S651A|KIF27_ENST00000376347.1_Missense_Mutation_p.S42A	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	651					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TGGCCTTCTGATTCTTCATCA	0.348													A|||	1	0.000199681	0.0	0.0	5008	,	,		17259	0.0		0.001	False		,,,				2504	0.0				p.S651A		Atlas-SNP	.											.	KIF27	103	.	0			c.T1951G						PASS	.	A	ALA/SER	2,4404	4.2+/-10.8	0,2,2201	78.0	77.0	77.0		1951	0.7	1.0	9	dbSNP_134	77	39,8557	25.7+/-73.6	0,39,4259	no	missense	KIF27	NM_017576.1	99	0,41,6460	CC,CA,AA		0.4537,0.0454,0.3153	benign	651/1402	86504027	41,12961	2203	4298	6501	SO:0001583	missense	55582	exon7			CTTCTGATTCTTC	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.1951T>G	9.37:g.86504027A>C	ENSP00000297814:p.Ser651Ala	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	173	85	0.491329	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	A	4.222	0.039963	0.08148	4.54E-4	0.004537	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204;ENST00000376347	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.95	0.686	0.18015	.	0.846284	0.09495	N	0.794425	T	0.24547	0.0595	N	0.12182	0.205	0.20563	N	0.999886	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.23368	-1.0190	10	0.18276	T	0.48	.	5.1501	0.15005	0.3051:0.3749:0.0:0.32	.	651;651;651	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	A	651;651;651;42	ENSP00000297814:S651A;ENSP00000401688:S651A;ENSP00000333928:S651A;ENSP00000365525:S42A	ENSP00000297814:S651A	S	-	1	0	KIF27	85693847	0.933000	0.31639	0.997000	0.53966	0.861000	0.49209	0.489000	0.22387	0.300000	0.22699	-0.472000	0.04984	TCA	A|0.998;C|0.002	0.002	strong		0.348	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
VPS52	6293	hgsc.bcm.edu	37	6	33234454	33234454	+	Silent	SNP	G	G	A	rs34933266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33234454G>A	ENST00000445902.2	-	12	1379	c.1161C>T	c.(1159-1161)taC>taT	p.Y387Y	VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000436044.2_Silent_p.Y262Y|VPS52_ENST00000482399.1_3'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	387					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						CTAGGAGGGCGTAGTGCTGGC	0.517													G|||	33	0.00658946	0.003	0.0014	5008	,	,		18785	0.0129		0.008	False		,,,				2504	0.0072				p.Y387Y		Atlas-SNP	.											.	VPS52	56	.	0			c.C1161T						PASS	.	G		13,3007		0,13,1497	61.0	64.0	63.0		1161	-5.7	1.0	6	dbSNP_126	63	31,5387		0,31,2678	no	coding-synonymous	VPS52	NM_022553.4		0,44,4175	AA,AG,GG		0.5722,0.4305,0.5215		387/724	33234454	44,8394	1510	2709	4219	SO:0001819	synonymous_variant	6293	exon12			GAGGGCGTAGTGC	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.1161C>T	6.37:g.33234454G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			G|0.994;A|0.006	0.006	strong		0.517	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
TBC1D15	64786	hgsc.bcm.edu	37	12	72307637	72307637	+	Silent	SNP	C	C	G	rs11178983	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000319106.8_Silent_p.S452S|TBC1D15_ENST00000548679.1_3'UTR|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	72	0	0		WXS	Illumina HiSeq	Phase_I	81	26	0.320988	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	
CHI3L2	1117	hgsc.bcm.edu	37	1	111783982	111783982	+	Silent	SNP	C	C	A	rs13721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:111783982C>A	ENST00000445067.2	+	11	1723	c.952C>A	c.(952-954)Cgg>Agg	p.R318R	CHI3L2_ENST00000369748.4_Silent_p.R318R|CHI3L2_ENST00000369744.2_Silent_p.R308R|CHI3L2_ENST00000529459.1_3'UTR|CHI3L2_ENST00000466741.1_Silent_p.R239R|CHI3L2_ENST00000524472.1_Silent_p.R239R			Q15782	CH3L2_HUMAN	chitinase 3-like 2	318			R -> W (in dbSNP:rs13721).		carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		CAAGATCACGCGGCTCCAGGA	0.537													A|||	953	0.190296	0.0507	0.1729	5008	,	,		20313	0.1974		0.333	False		,,,				2504	0.2372				p.R318R		Atlas-SNP	.											.	CHI3L2	38	.	0			c.C952A						PASS	.	A	,,	458,3948		30,398,1775	97.0	87.0	90.0		922,715,952	3.6	0.0	1	dbSNP_52	90	2572,6028		536,1500,2264	no	coding-synonymous,coding-synonymous,coding-synonymous	CHI3L2	NM_001025197.1,NM_001025199.1,NM_004000.2	,,	566,1898,4039	AA,AC,CC		29.907,10.3949,23.2969	,,	308/381,239/312,318/391	111783982	3030,9976	2203	4300	6503	SO:0001819	synonymous_variant	1117	exon9			ATCACGCGGCTCC	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.952C>A	1.37:g.111783982C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_004000	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Silent	SNP	ENST00000445067.2	37	CCDS30802.1																																																																																			A|0.280;C|0.697;T|0.022	0.280	strong		0.537	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000	
UMODL1	89766	hgsc.bcm.edu	37	21	43531632	43531632	+	Missense_Mutation	SNP	T	T	C	rs220129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43531632T>C	ENST00000408910.2	+	12	1916	c.1916T>C	c.(1915-1917)aTc>aCc	p.I639T	UMODL1_ENST00000400427.1_Missense_Mutation_p.I695T|UMODL1_ENST00000400424.2_Missense_Mutation_p.I567T|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000408989.2_Missense_Mutation_p.I767T	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	639			I -> T (in dbSNP:rs220129). {ECO:0000269|PubMed:15194491, ECO:0000269|PubMed:16026467}.		adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GGAAACTCCATCATGGAGCCA	0.637													C|||	3908	0.780351	0.6104	0.8617	5008	,	,		16363	0.8621		0.8211	False		,,,				2504	0.8262				p.I767T	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T2300C						PASS	.	C	THR/ILE,THR/ILE,THR/ILE,THR/ILE	2624,1322		883,858,232	50.0	56.0	54.0		1916,2084,1700,2300	1.7	0.0	21	dbSNP_79	54	6756,1538		2762,1232,153	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	89,89,89,89	3645,2090,385	CC,CT,TT		18.5435,33.5023,23.366	benign,benign,benign,benign	639/1319,695/1375,567/1247,767/1447	43531632	9380,2860	1973	4147	6120	SO:0001583	missense	89766	exon11			ACTCCATCATGGA		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.1916T>C	21.37:g.43531632T>C	ENSP00000386147:p.Ile639Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	1712	0.7838827838827839	290	0.5894308943089431	308	0.850828729281768	480	0.8391608391608392	634	0.8364116094986808	C	0.017	-1.492611	0.01009	0.664977	0.814565	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.71461	-0.57;-0.49;-0.57;-0.49	4.6	1.72	0.24424	.	0.550783	0.16034	N	0.232739	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40251	-0.9573	9	0.02654	T	1	-15.9453	6.8287	0.23897	0.0:0.522:0.3115:0.1665	rs220129;rs480934;rs1153357;rs61249621;rs220129	767;639	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	T	695;567;767;639	ENSP00000383279:I695T;ENSP00000383276:I567T;ENSP00000386126:I767T;ENSP00000386147:I639T	ENSP00000383276:I567T	I	+	2	0	UMODL1	42404701	0.027000	0.19231	0.000000	0.03702	0.034000	0.12701	0.060000	0.14342	-0.010000	0.14271	-1.318000	0.01297	ATC	T|0.225;C|0.775	0.775	strong		0.637	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
SRPRB	58477	hgsc.bcm.edu	37	3	133524717	133524717	+	Missense_Mutation	SNP	G	G	C	rs1107413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:133524717G>C	ENST00000466490.2	+	2	310	c.25G>C	c.(25-27)Gtg>Ctg	p.V9L		NM_021203.3	NP_067026.3	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, B subunit	9			V -> L (in dbSNP:rs1107413). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|small GTPase mediated signal transduction (GO:0007264)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(2)	12						CTCGCGCCGGGTGGCAGATGG	0.677													G|||	867	0.173123	0.0825	0.2363	5008	,	,		15824	0.2262		0.2038	False		,,,				2504	0.1646				p.V9L		Atlas-SNP	.											.	SRPRB	28	.	0			c.G25C						PASS	.	G	LEU/VAL	506,3900	219.4+/-237.2	31,444,1728	43.0	45.0	45.0		25	0.8	0.0	3	dbSNP_86	45	2154,6444	342.7+/-324.6	297,1560,2442	yes	missense	SRPRB	NM_021203.3	32	328,2004,4170	CC,CG,GG		25.0523,11.4843,20.4552	benign	9/272	133524717	2660,10344	2203	4299	6502	SO:0001583	missense	58477	exon2			CGCCGGGTGGCAG	AK075531	CCDS3081.1	3q22.1	2004-01-29			ENSG00000144867	ENSG00000144867			24085	protein-coding gene	gene with protein product						7844142, 10859309	Standard	NM_021203		Approved	APMCF1	uc003epx.2	Q9Y5M8	OTTHUMG00000159753	ENST00000466490.2:c.25G>C	3.37:g.133524717G>C	ENSP00000418401:p.Val9Leu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_021203	Q6P595|Q8N2D8	Missense_Mutation	SNP	ENST00000466490.2	37	CCDS3081.1	402	0.18406593406593408	38	0.07723577235772358	86	0.23756906077348067	126	0.2202797202797203	152	0.20052770448548812	G	4.670	0.124636	0.08931	0.114843	0.250523	ENSG00000144867	ENST00000466490;ENST00000484684	T;T	0.47528	2.54;0.84	4.91	0.767	0.18482	.	3.007370	0.02176	U	0.060084	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10894	-1.0610	9	0.35671	T	0.21	-0.5703	6.6806	0.23117	0.2138:0.164:0.6222:0.0	rs1107413;rs17855773;rs1107413	9	Q9Y5M8	SRPRB_HUMAN	L	9	ENSP00000418401:V9L;ENSP00000417096:V9L	ENSP00000418401:V9L	V	+	1	0	SRPRB	135007407	0.000000	0.05858	0.011000	0.14972	0.111000	0.19643	-1.023000	0.03607	0.256000	0.21614	0.650000	0.86243	GTG	G|0.795;C|0.205	0.205	strong		0.677	SRPRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357170.2		
PEX6	5190	hgsc.bcm.edu	37	6	42933526	42933526	+	Splice_Site	SNP	C	C	T	rs2274515	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42933526C>T	ENST00000304611.8	-	13	2433	c.2364G>A	c.(2362-2364)gtG>gtA	p.V788V	PEX6_ENST00000244546.4_Splice_Site_p.C706Y	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	788					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			CCCTGGCAAACACTGAAGAGA	0.577													C|||	549	0.109625	0.0582	0.1671	5008	,	,		15330	0.1379		0.0437	False		,,,				2504	0.1769				p.V788V		Atlas-SNP	.											.	PEX6	44	.	0			c.G2364A						PASS	.	C		250,4156	138.4+/-174.2	9,232,1962	57.0	66.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2364	3.1	1.0	6	dbSNP_100	63	384,8216	121.7+/-180.7	5,374,3921	yes	coding-synonymous-near-splice	PEX6	NM_000287.3		14,606,5883	TT,TC,CC		4.4651,5.6741,4.8747		788/981	42933526	634,12372	2203	4300	6503	SO:0001630	splice_region_variant	5190	exon13			GGCAAACACTGAA	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"""ATPases / AAA-type"""	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2363-1G>A	6.37:g.42933526C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Silent	SNP	ENST00000304611.8	37	CCDS4877.1	192	0.08791208791208792	24	0.04878048780487805	52	0.143646408839779	80	0.13986013986013987	36	0.047493403693931395	C	14.26	2.482455	0.44147	0.056741	0.044651	ENSG00000124587	ENST00000244546	D	0.94966	-3.57	5.86	3.11	0.35812	.	.	.	.	.	D	0.92417	0.7593	.	.	.	0.38098	P	0.062832	.	.	.	.	.	.	D	0.90084	0.4172	5	0.87932	D	0	.	8.7772	0.34769	0.0:0.7383:0.1252:0.1364	rs2274515;rs17854562;rs52825508;rs2274515	.	.	.	Y	706	ENSP00000244546:C706Y	ENSP00000244546:C706Y	C	-	2	0	PEX6	43041504	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.952000	0.29149	0.378000	0.24764	0.563000	0.77884	TGT	C|0.937;T|0.063	0.063	strong		0.577	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	Silent
PRKD1	5587	hgsc.bcm.edu	37	14	30066929	30066929	+	Silent	SNP	A	A	G	rs2230505	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:30066929A>G	ENST00000331968.5	-	16	2431	c.2202T>C	c.(2200-2202)atT>atC	p.I734I	PRKD1_ENST00000415220.2_Silent_p.I742I	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	734	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|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)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		ACTTCTCTCCAATGATCCGGG	0.478													A|||	2563	0.511781	0.851	0.4568	5008	,	,		14241	0.2113		0.3837	False		,,,				2504	0.5337				p.I734I		Atlas-SNP	.											.	PRKD1	316	.	0			c.T2202C						PASS	.	A		3369,1037	726.8+/-409.8	1298,773,132	58.0	62.0	61.0		2202	2.1	1.0	14	dbSNP_98	61	3258,5342	488.6+/-372.4	595,2068,1637	no	coding-synonymous	PRKD1	NM_002742.2		1893,2841,1769	GG,GA,AA		37.8837,23.5361,49.0466		734/913	30066929	6627,6379	2203	4300	6503	SO:0001819	synonymous_variant	5587	exon16			CTCTCCAATGATC		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2202T>C	14.37:g.30066929A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																			T|0.088;G|0.396;C|0.100;A|0.416	0.396	strong		0.478	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
SHANK2	22941	hgsc.bcm.edu	37	11	70331716	70331716	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:70331716G>C	ENST00000423696.2	-	15	3581	c.3545C>G	c.(3544-3546)gCa>gGa	p.A1182G	SHANK2_ENST00000409161.1_Missense_Mutation_p.A965G|SHANK2_ENST00000338508.4_Missense_Mutation_p.A1562G|SHANK2_ENST00000449833.2_Missense_Mutation_p.A966G			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1182					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			TTGATAAAGTGCATTGCTTTT	0.552																																					p.A973G		Atlas-SNP	.											.	SHANK2	340	.	0			c.C2918G						PASS	.						147.0	145.0	145.0					11																	70331716		2200	4294	6494	SO:0001583	missense	22941	exon10			TAAAGTGCATTGC	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.3545C>G	11.37:g.70331716G>C	ENSP00000394536:p.Ala1182Gly	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	153	76	0.496732	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	37		.	.	.	.	.	.	.	.	.	.	G	11.04	1.520786	0.27211	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13	5.42	4.51	0.55191	.	0.353602	0.31872	N	0.006936	T	0.20333	0.0489	L	0.32530	0.975	0.80722	D	1	B;P;P	0.43287	0.437;0.802;0.573	B;B;B	0.43536	0.137;0.423;0.267	T	0.01561	-1.1324	10	0.37606	T	0.19	.	14.1457	0.65349	0.0721:0.0:0.9279:0.0	.	1182;1561;966	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	G	966;965;840;1562;1182;1200;1185	ENSP00000399423:A966G;ENSP00000386491:A965G;ENSP00000402944:A840G;ENSP00000345193:A1562G;ENSP00000394536:A1182G;ENSP00000294018:A1185G	ENSP00000294018:A1185G	A	-	2	0	SHANK2	70009364	1.000000	0.71417	0.013000	0.15412	0.999000	0.98932	6.103000	0.71492	1.294000	0.44707	0.655000	0.94253	GCA	.	.	none		0.552	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
FIGNL1	63979	hgsc.bcm.edu	37	7	50514577	50514577	+	Missense_Mutation	SNP	C	C	T	rs10235371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:50514577C>T	ENST00000419119.1	-	2	1962	c.409G>A	c.(409-411)Gtg>Atg	p.V137M	FIGNL1_ENST00000435566.1_3'UTR|FIGNL1_ENST00000395556.2_Missense_Mutation_p.V137M|FIGNL1_ENST00000356889.4_Missense_Mutation_p.V137M|FIGNL1_ENST00000433017.1_Missense_Mutation_p.V137M			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	137			V -> M (in dbSNP:rs10235371). {ECO:0000269|PubMed:15489334}.		ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				TGGATTACCACTGATGCAAGA	0.383													C|||	316	0.063099	0.0446	0.0836	5008	,	,		21357	0.0377		0.1153	False		,,,				2504	0.046				p.V137M		Atlas-SNP	.											.	FIGNL1	73	.	0			c.G409A						PASS	.	C	MET/VAL,MET/VAL	206,4200	126.6+/-163.6	5,196,2002	104.0	104.0	104.0		409,409	-4.6	0.0	7	dbSNP_119	104	895,7705	200.3+/-244.1	50,795,3455	yes	missense,missense	FIGNL1	NM_001042762.1,NM_022116.3	21,21	55,991,5457	TT,TC,CC		10.407,4.6754,8.4653	possibly-damaging,possibly-damaging	137/675,137/675	50514577	1101,11905	2203	4300	6503	SO:0001583	missense	63979	exon4			TTACCACTGATGC	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"""ATPases / AAA-type"""	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.409G>A	7.37:g.50514577C>T	ENSP00000410811:p.Val137Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001042762	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	159	0.07280219780219781	32	0.06504065040650407	29	0.08011049723756906	23	0.04020979020979021	75	0.09894459102902374	C	11.45	1.642477	0.29246	0.046754	0.10407	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.49	-4.56	0.03431	.	0.659654	0.14095	N	0.341751	T	0.00384	0.0012	L	0.50333	1.59	0.58432	P	5.000000000032756E-6	B	0.34103	0.437	B	0.30401	0.115	T	0.05053	-1.0909	9	0.46703	T	0.11	-4.6804	10.0545	0.42237	0.0:0.3473:0.4724:0.1803	rs10235371;rs52821479;rs10235371	137	Q6PIW4	FIGL1_HUMAN	M	137	ENSP00000349356:V137M;ENSP00000378924:V137M;ENSP00000399997:V137M;ENSP00000410811:V137M	ENSP00000349356:V137M	V	-	1	0	FIGNL1	50482071	0.001000	0.12720	0.000000	0.03702	0.877000	0.50540	0.561000	0.23515	-0.842000	0.04195	-0.344000	0.07964	GTG	C|0.920;T|0.080	0.080	strong		0.383	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762	
DSC3	1825	hgsc.bcm.edu	37	18	28586964	28586964	+	Silent	SNP	A	A	G	rs1313586	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	123	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	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	
SCP2D1	140856	hgsc.bcm.edu	37	20	18794714	18794714	+	Silent	SNP	C	C	T	rs1053834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:18794714C>T	ENST00000377428.2	+	1	345	c.255C>T	c.(253-255)acC>acT	p.T85T	C20orf78_ENST00000463425.1_5'Flank|C20orf78_ENST00000278779.4_Intron	NM_178483.2	NP_848578.1	Q9UJQ7	SCP2D_HUMAN	SCP2 sterol-binding domain containing 1	85	SCP2.																TGCGGTGGACCATTGATCTGA	0.507													C|||	1060	0.211661	0.4062	0.1643	5008	,	,		18810	0.0308		0.175	False		,,,				2504	0.2065				p.T85T		Atlas-SNP	.											.	.	.	.	0			c.C255T						PASS	.	C	,	1598,2808	497.1+/-363.7	303,992,908	100.0	97.0	98.0		,255	1.8	1.0	20	dbSNP_86	98	1462,7138	279.3+/-293.9	129,1204,2967	no	intron,coding-synonymous	C20orf79,LOC100128496	NM_001242671.1,NM_178483.2	,	432,2196,3875	TT,TC,CC		17.0,36.2687,23.5276	,	,85/157	18794714	3060,9946	2203	4300	6503	SO:0001819	synonymous_variant	140856	exon1			GTGGACCATTGAT	AL035563	CCDS13139.1	20p11.23	2012-10-29	2012-10-29	2012-10-29	ENSG00000132631	ENSG00000132631			16211	protein-coding gene	gene with protein product	"""sterol carrier protein 2-like protein"""		"""chromosome 20 open reading frame 79"""	C20orf79		16501878	Standard	NM_178483		Approved	dJ1068E13.2, HSD22	uc002wrk.3	Q9UJQ7	OTTHUMG00000031983	ENST00000377428.2:c.255C>T	20.37:g.18794714C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_178483	Q548A4	Silent	SNP	ENST00000377428.2	37	CCDS13139.1																																																																																			C|0.788;T|0.212	0.212	strong		0.507	SCP2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078193.1	NM_178483	
CCDC155	147872	hgsc.bcm.edu	37	19	49910869	49910869	+	Splice_Site	SNP	C	C	T	rs199889676		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49910869C>T	ENST00000447857.3	+	12	1139	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	312						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						GCTTTCCTAGCGCACTCGCGA	0.647																																					p.R312C		Atlas-SNP	.											CCDC155,colon,carcinoma,0,1	CCDC155	46	1	0			c.C934T						scavenged	.		CYS/ARG	0,3872		0,0,1936	38.0	41.0	40.0		934	3.7	1.0	19		40	5,8261		0,5,4128	yes	missense-near-splice	CCDC155	NM_144688.4	180	0,5,6064	TT,TC,CC		0.0605,0.0,0.0412	probably-damaging	312/563	49910869	5,12133	1936	4133	6069	SO:0001630	splice_region_variant	147872	exon12			TCCTAGCGCACTC		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.934-1C>T	19.37:g.49910869C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	124	3	0.0241935	NM_144688	Q96MC3	Missense_Mutation	SNP	ENST00000447857.3	37	CCDS46140.1	.	.	.	.	.	.	.	.	.	.	c	16.01	3.001820	0.54254	0.0	6.05E-4	ENSG00000161609	ENST00000447857	T	0.36340	1.26	4.83	3.7	0.42460	.	0.274240	0.30101	N	0.010402	T	0.55577	0.1929	M	0.75447	2.3	0.45087	D	0.998105	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.54860	-0.8230	9	.	.	.	-18.8095	9.6852	0.40094	0.207:0.793:0.0:0.0	.	312;312	C9JGW3;Q8N6L0	.;CC155_HUMAN	C	312	ENSP00000404220:R312C	.	R	+	1	0	CCDC155	54602681	1.000000	0.71417	1.000000	0.80357	0.349000	0.29174	1.976000	0.40579	2.636000	0.89361	0.645000	0.84053	CGC	.	.	weak		0.647	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	Missense_Mutation
THADA	63892	hgsc.bcm.edu	37	2	43571347	43571347	+	Silent	SNP	G	G	A	rs35422033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:43571347G>A	ENST00000405006.4	-	30	4608	c.4257C>T	c.(4255-4257)gaC>gaT	p.D1419D	THADA_ENST00000330266.7_Intron|THADA_ENST00000485353.1_5'UTR|THADA_ENST00000405975.2_Silent_p.D1419D|THADA_ENST00000415080.2_Silent_p.D1100D	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1419										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)				CGTGTTTGGAGTCTGAGTAGG	0.398													G|||	91	0.0181709	0.0484	0.0187	5008	,	,		19017	0.0		0.006	False		,,,				2504	0.0082				p.D1419D		Atlas-SNP	.											.	THADA	131	.	0			c.C4257T						PASS	.	G	,	136,3678		3,130,1774	75.0	68.0	70.0		4257,4257	4.8	1.0	2	dbSNP_126	70	54,8200		0,54,4073	no	coding-synonymous,coding-synonymous	THADA	NM_001083953.1,NM_022065.4	,	3,184,5847	AA,AG,GG		0.6542,3.5658,1.5744	,	1419/1954,1419/1954	43571347	190,11878	1907	4127	6034	SO:0001819	synonymous_variant	63892	exon30			TTTGGAGTCTGAG	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.4257C>T	2.37:g.43571347G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	166	87	0.524096	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Silent	SNP	ENST00000405006.4	37	CCDS46268.1	43	0.019688644688644688	31	0.06300813008130081	7	0.019337016574585635	0	0.0	5	0.006596306068601583	G	8.144	0.785827	0.16189	0.035658	0.006542	ENSG00000115970	ENST00000407351	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	T	0.13543	0.0328	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18650	-1.0330	4	.	.	.	-20.2203	8.2927	0.31967	0.0846:0.1598:0.7556:0.0	rs35422033	.	.	.	I	659	.	.	T	-	2	0	THADA	43424851	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.449000	0.35123	2.494000	0.84150	0.585000	0.79938	ACT	G|0.983;A|0.017	0.017	strong		0.398	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
ARAP3	64411	hgsc.bcm.edu	37	5	141052416	141052416	+	Silent	SNP	G	G	T	rs1057371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:141052416G>T	ENST00000239440.4	-	8	1235	c.1170C>A	c.(1168-1170)ccC>ccA	p.P390P	ARAP3_ENST00000513878.1_Silent_p.P52P|ARAP3_ENST00000508305.1_Silent_p.P312P	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	390					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GGGGTGGTTGGGGGGGCCGGG	0.662													G|||	436	0.0870607	0.0877	0.072	5008	,	,		9998	0.0556		0.0835	False		,,,				2504	0.1329				p.P390P		Atlas-SNP	.											.	ARAP3	139	.	0			c.C1170A						PASS	.	G		377,3959		15,347,1806	11.0	12.0	12.0		1170	-8.7	0.0	5	dbSNP_86	12	763,7747		47,669,3539	no	coding-synonymous	ARAP3	NM_022481.5		62,1016,5345	TT,TG,GG		8.9659,8.6946,8.8744		390/1545	141052416	1140,11706	2168	4255	6423	SO:0001819	synonymous_variant	64411	exon8			TGGTTGGGGGGGC	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.1170C>A	5.37:g.141052416G>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			G|0.915;T|0.085	0.085	strong		0.662	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
SVEP1	79987	hgsc.bcm.edu	37	9	113252011	113252011	+	Missense_Mutation	SNP	T	T	C	rs74597491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:113252011T>C	ENST00000401783.2	-	9	2185	c.1849A>G	c.(1849-1851)Att>Gtt	p.I617V	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.I594V|SVEP1_ENST00000374461.1_Missense_Mutation_p.I594V|SVEP1_ENST00000302728.8_Missense_Mutation_p.I617V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	617	HYR 1. {ECO:0000255|PROSITE- ProRule:PRU00113}.				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						ACATCTCCAATTGGGAAAAGG	0.413													T|||	64	0.0127796	0.0023	0.0173	5008	,	,		19765	0.0		0.0358	False		,,,				2504	0.0133				p.I617V		Atlas-SNP	.											.	SVEP1	326	.	0			c.A1849G						PASS	.	T	VAL/ILE	14,3864		0,14,1925	147.0	143.0	145.0		1849	4.8	1.0	9	dbSNP_132	145	199,8091		3,193,3949	yes	missense	SVEP1	NM_153366.3	29	3,207,5874	CC,CT,TT		2.4005,0.361,1.7505	benign	617/3572	113252011	213,11955	1939	4145	6084	SO:0001583	missense	79987	exon9			CTCCAATTGGGAA	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.1849A>G	9.37:g.113252011T>C	ENSP00000384917:p.Ile617Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	167	89	0.532934	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	33	0.01510989010989011	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	23	0.030343007915567283	T	24.0	4.482021	0.84747	0.00361	0.024005	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	4.85	4.85	0.62838	Hyalin (2);	0.000000	0.85682	D	0.000000	T	0.13628	0.0330	L	0.45422	1.42	0.35687	D	0.814545	D;D;D	0.69078	0.958;0.997;0.991	D;D;D	0.80764	0.97;0.994;0.978	T	0.25293	-1.0136	10	0.62326	D	0.03	.	14.413	0.67128	0.0:0.0:0.0:1.0	.	617;617;617	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	V	617;594;617;594	ENSP00000384917:I617V;ENSP00000363593:I594V;ENSP00000304118:I617V;ENSP00000363585:I594V	ENSP00000304118:I617V	I	-	1	0	SVEP1	112291832	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.499000	0.81566	1.822000	0.53115	0.460000	0.39030	ATT	T|0.983;C|0.017	0.017	strong		0.413	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MTRR	4552	hgsc.bcm.edu	37	5	7897319	7897319	+	Silent	SNP	G	G	A	rs1802059	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7897319G>A	ENST00000264668.2	+	14	2022	c.1992G>A	c.(1990-1992)gcG>gcA	p.A664A	MTRR_ENST00000440940.2_Silent_p.A637A	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	664					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	AGCAGGTGGCGAGAATCCTCC	0.512													G|||	1334	0.266374	0.2557	0.2133	5008	,	,		16470	0.13		0.336	False		,,,				2504	0.3875				p.A664A		Atlas-SNP	.											MTRR,NS,carcinoma,+1,1	MTRR	74	1	0			c.G1992A						PASS	.	G	,	1122,3284	402.4+/-332.3	145,832,1226	109.0	105.0	106.0		1911,1992	-10.8	0.0	5	dbSNP_89	106	3087,5513	472.7+/-368.4	578,1931,1791	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	723,2763,3017	AA,AG,GG		35.8953,25.4653,32.362	,	637/699,664/726	7897319	4209,8797	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon14			GGTGGCGAGAATC	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1992G>A	5.37:g.7897319G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			G|0.703;A|0.297	0.297	strong		0.512	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
PXN	5829	hgsc.bcm.edu	37	12	120650264	120650264	+	Silent	SNP	G	G	A	rs25664	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120650264G>A	ENST00000228307.7	-	12	1770	c.1629C>T	c.(1627-1629)acC>acT	p.T543T	PXN_ENST00000458477.2_Silent_p.T376T|PXN-AS1_ENST00000538804.1_RNA|PXN-AS1_ENST00000542314.1_RNA|PXN-AS1_ENST00000542265.1_RNA|PXN_ENST00000538144.1_5'UTR|PXN_ENST00000424649.2_Silent_p.T509T|PXN-AS1_ENST00000539446.1_RNA|PXN_ENST00000267257.7_Silent_p.T557T|PXN_ENST00000536957.1_Silent_p.T541T|PXN_ENST00000397506.3_Silent_p.T355T|PXN-AS1_ENST00000535200.1_RNA	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	543	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGCAGCGGCCGGTGATGGGCT	0.622													G|||	59	0.0117812	0.0023	0.0115	5008	,	,		12974	0.0		0.0417	False		,,,				2504	0.0061				p.T557T		Atlas-SNP	.											.	PXN	69	.	0			c.C1671T						PASS	.	G	,,	33,4163		1,31,2066	54.0	65.0	61.0		1629,1527,1128	-5.4	0.9	12	dbSNP_72	61	347,8085		5,337,3874	no	coding-synonymous,coding-synonymous,coding-synonymous	PXN	NM_001080855.2,NM_002859.3,NM_025157.4	,,	6,368,5940	AA,AG,GG		4.1153,0.7865,3.0092	,,	543/592,509/558,376/425	120650264	380,12248	2098	4216	6314	SO:0001819	synonymous_variant	5829	exon11			GCGGCCGGTGATG	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.1629C>T	12.37:g.120650264G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	178	83	0.466292	NM_001243756	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Silent	SNP	ENST00000228307.7	37	CCDS44997.1																																																																																			G|0.980;A|0.020	0.020	strong		0.622	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859	
MMP27	64066	hgsc.bcm.edu	37	11	102573569	102573569	+	Silent	SNP	C	C	A	rs3809018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102573569C>A	ENST00000260229.4	-	4	625	c.534G>T	c.(532-534)gtG>gtT	p.V178V		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	178					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	CATGGCCAAGCACTCCCAAGG	0.478													C|||	542	0.108227	0.0076	0.1859	5008	,	,		18072	0.1081		0.1789	False		,,,				2504	0.1166				p.V178V		Atlas-SNP	.											.	MMP27	84	.	0			c.G534T						PASS	.	C		173,4233	112.5+/-150.6	4,165,2034	86.0	87.0	87.0		534	0.5	1.0	11	dbSNP_107	87	1704,6894	312.5+/-310.9	166,1372,2761	no	coding-synonymous	MMP27	NM_022122.2		170,1537,4795	AA,AC,CC		19.8186,3.9265,14.434		178/514	102573569	1877,11127	2203	4299	6502	SO:0001819	synonymous_variant	64066	exon4			GCCAAGCACTCCC	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.534G>T	11.37:g.102573569C>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																			C|0.870;A|0.130	0.130	strong		0.478	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
MYRIP	25924	hgsc.bcm.edu	37	3	40286017	40286017	+	Silent	SNP	T	T	C	rs4618168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:40286017T>C	ENST00000302541.6	+	13	2523	c.2181T>C	c.(2179-2181)agT>agC	p.S727S	MYRIP_ENST00000425621.1_Silent_p.S662S|MYRIP_ENST00000396217.3_Silent_p.S638S|MYRIP_ENST00000539167.1_Silent_p.S540S|MYRIP_ENST00000444716.1_Silent_p.S727S|MYRIP_ENST00000459828.1_3'UTR	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	727	Actin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		GCATCCACAGTGGCACTGATG	0.582													C|||	3248	0.648562	0.7965	0.4712	5008	,	,		17394	0.7629		0.4254	False		,,,				2504	0.6861				p.S727S		Atlas-SNP	.											.	MYRIP	98	.	0			c.T2181C						PASS	.	C		3259,1147	406.6+/-333.9	1212,835,156	64.0	61.0	62.0		2181	-5.1	0.8	3	dbSNP_111	62	3823,4777	611.0+/-395.8	882,2059,1359	no	coding-synonymous	MYRIP	NM_015460.2		2094,2894,1515	CC,CT,TT		44.4535,26.0327,45.5482		727/860	40286017	7082,5924	2203	4300	6503	SO:0001819	synonymous_variant	25924	exon13			CCACAGTGGCACT	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"""A-kinase anchor proteins"""	19156	protein-coding gene	gene with protein product	"""synaptotagmin-like protein homologue lacking C2 domains-c"", ""rab effector MYRIP"", ""Slp homologue lacking C2 domains"""	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.2181T>C	3.37:g.40286017T>C		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	252	121	0.480159	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Silent	SNP	ENST00000302541.6	37	CCDS2689.1																																																																																			T|0.418;C|0.582	0.582	strong		0.582	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
GRM6	2916	hgsc.bcm.edu	37	5	178408828	178408828	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:178408828C>T	ENST00000517717.1	-	11	2502	c.2464G>A	c.(2464-2466)Gtg>Atg	p.V822M	GRM6_ENST00000231188.5_Missense_Mutation_p.V822M|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	822					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.V822M(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CTCAAGGACACGGTTAGCGTG	0.572																																					p.V822M		Atlas-SNP	.											GRM6,NS,carcinoma,0,1	GRM6	149	1	1	Substitution - Missense(1)	lung(1)	c.G2464A						scavenged	.						184.0	156.0	166.0					5																	178408828		2203	4300	6503	SO:0001583	missense	2916	exon10			AGGACACGGTTAG	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.2464G>A	5.37:g.178408828C>T	ENSP00000430767:p.Val822Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	133	5	0.037594	NM_000843		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.531950	0.85706	.	.	ENSG00000113262	ENST00000231188;ENST00000517717	D;D	0.89123	-2.47;-2.47	5.28	5.28	0.74379	GPCR, family 3, C-terminal (2);	.	.	.	.	D	0.91546	0.7330	L	0.41824	1.3	0.58432	D	0.999995	P;D	0.63046	0.924;0.992	B;D	0.67900	0.438;0.954	D	0.91838	0.5481	9	0.56958	D	0.05	.	16.7914	0.85590	0.0:1.0:0.0:0.0	.	822;116	O15303;Q5HYM4	GRM6_HUMAN;.	M	822	ENSP00000231188:V822M;ENSP00000430767:V822M	ENSP00000231188:V822M	V	-	1	0	GRM6	178341434	0.998000	0.40836	0.986000	0.45419	0.679000	0.39708	3.912000	0.56386	2.643000	0.89663	0.462000	0.41574	GTG	.	.	none		0.572	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
SMARCA5	8467	hgsc.bcm.edu	37	4	144442611	144442611	+	Silent	SNP	T	T	C	rs11100790	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:144442611T>C	ENST00000283131.3	+	3	744	c.282T>C	c.(280-282)taT>taC	p.Y94Y		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	94					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					GATTCGAGTATTTATTAAAGC	0.353													T|||	1463	0.292133	0.2247	0.2594	5008	,	,		16713	0.6052		0.2078	False		,,,				2504	0.1708				p.Y94Y		Atlas-SNP	.											.	SMARCA5	73	.	0			c.T282C						PASS	.	T		963,3443	357.9+/-314.1	100,763,1340	54.0	59.0	58.0		282	5.6	1.0	4	dbSNP_120	58	1655,6945	304.8+/-307.1	163,1329,2808	no	coding-synonymous	SMARCA5	NM_003601.3		263,2092,4148	CC,CT,TT		19.2442,21.8566,20.1292		94/1053	144442611	2618,10388	2203	4300	6503	SO:0001819	synonymous_variant	8467	exon3			CGAGTATTTATTA	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.282T>C	4.37:g.144442611T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_003601		Silent	SNP	ENST00000283131.3	37	CCDS3761.1																																																																																			A|0.000;C|0.252;T|0.748	0.252	strong		0.353	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3		
CHD4	1108	hgsc.bcm.edu	37	12	6707526	6707526	+	Silent	SNP	G	G	A	rs11539543	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6707526G>A	ENST00000357008.2	-	11	1711	c.1548C>T	c.(1546-1548)ccC>ccT	p.P516P	CHD4_ENST00000544484.1_Silent_p.P513P|CHD4_ENST00000309577.6_Silent_p.P516P|CHD4_ENST00000544040.1_Silent_p.P509P	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	516	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						GCACTGGTGTGGGAGATGGTG	0.542													G|||	488	0.0974441	0.1263	0.0634	5008	,	,		19415	0.004		0.1322	False		,,,				2504	0.1431				p.P516P	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C1548T						PASS	.	G		571,3835	254.9+/-260.3	39,493,1671	147.0	149.0	148.0		1548	0.9	1.0	12	dbSNP_120	148	1396,7204	271.9+/-289.8	121,1154,3025	no	coding-synonymous	CHD4	NM_001273.2		160,1647,4696	AA,AG,GG		16.2326,12.9596,15.1238		516/1913	6707526	1967,11039	2203	4300	6503	SO:0001819	synonymous_variant	1108	exon11			TGGTGTGGGAGAT	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.1548C>T	12.37:g.6707526G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_001273	Q8IXZ5	Silent	SNP	ENST00000357008.2	37	CCDS8552.1																																																																																			G|0.870;C|0.000;A|0.130	0.130	strong		0.542	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
S100P	6286	hgsc.bcm.edu	37	4	6698664	6698664	+	Silent	SNP	G	G	A	rs11737783	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:6698664G>A	ENST00000296370.3	+	2	1047	c.183G>A	c.(181-183)ctG>ctA	p.L61L	S100P_ENST00000513778.1_3'UTR	NM_005980.2	NP_005971.1	P25815	S100P_HUMAN	S100 calcium binding protein P	61	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				endothelial cell migration (GO:0043542)|response to organic substance (GO:0010033)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|magnesium ion binding (GO:0000287)			prostate(1)	1		Myeloproliferative disorder(84;0.0255)		Colorectal(103;0.011)	Cromoglicic acid(DB01003)	TCAAGGACCTGGATGCCAATG	0.532													G|||	144	0.028754	0.0023	0.0331	5008	,	,		21956	0.001		0.0427	False		,,,				2504	0.0757				p.L61L		Atlas-SNP	.											.	S100P	7	.	0			c.G183A						PASS	.	G		34,4372	40.8+/-73.8	0,34,2169	242.0	226.0	231.0		183	-0.2	0.5	4	dbSNP_120	231	340,8260	116.3+/-176.0	1,338,3961	no	coding-synonymous	S100P	NM_005980.2		1,372,6130	AA,AG,GG		3.9535,0.7717,2.8756		61/96	6698664	374,12632	2203	4300	6503	SO:0001819	synonymous_variant	6286	exon2			GGACCTGGATGCC	X65614	CCDS3391.1	4p16	2013-01-10	2001-11-28		ENSG00000163993	ENSG00000163993		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10504	protein-coding gene	gene with protein product		600614	"""S100 calcium-binding protein P"""			8341667, 7759097	Standard	NM_005980		Approved		uc003gjl.3	P25815	OTTHUMG00000090491	ENST00000296370.3:c.183G>A	4.37:g.6698664G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	172	80	0.465116	NM_005980	Q5J7W2	Silent	SNP	ENST00000296370.3	37	CCDS3391.1																																																																																			G|0.972;A|0.028	0.028	strong		0.532	S100P-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206979.1	NM_005980	
IQSEC3	440073	hgsc.bcm.edu	37	12	248155	248155	+	Silent	SNP	C	C	T	rs55923022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:248155C>T	ENST00000538872.1	+	4	1744	c.1626C>T	c.(1624-1626)gcC>gcT	p.A542A	RP11-598F7.4_ENST00000505893.2_RNA|IQSEC3_ENST00000326261.4_Silent_p.A542A|IQSEC3_ENST00000382841.2_Silent_p.A239A|RP11-598F7.4_ENST00000508953.2_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	542					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)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.A542A(1)|p.A239A(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		AAGCCCCCGCCGTGGGCCGGG	0.746													T|||	657	0.13119	0.2882	0.0908	5008	,	,		10438	0.0258		0.0974	False		,,,				2504	0.091				p.A542A		Atlas-SNP	.											IQSEC3_ENST00000538872,NS,carcinoma,0,2	IQSEC3	154	2	2	Substitution - coding silent(2)	prostate(2)	c.C1626T						PASS	.						4.0	5.0	4.0					12																	248155		1929	3805	5734	SO:0001819	synonymous_variant	440073	exon4			CCCCGCCGTGGGC	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.1626C>T	12.37:g.248155C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	37	CCDS53728.1																																																																																			C|0.880;T|0.120	0.120	strong		0.746	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
RIOK1	83732	hgsc.bcm.edu	37	6	7393452	7393452	+	Silent	SNP	C	C	T	rs2274212|rs368069269	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:7393452C>T	ENST00000379834.2	+	2	699	c.192C>T	c.(190-192)gaC>gaT	p.D64D		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	64							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					agggttatgacgatgatgatg	0.433													T|||	2307	0.460663	0.261	0.4798	5008	,	,		15160	0.4554		0.5586	False		,,,				2504	0.6217				p.D64D		Atlas-SNP	.											RIOK1,colon,carcinoma,+1,1	RIOK1	36	1	0			c.C192T						PASS	.	T		1305,3101	697.6+/-406.2	198,909,1096	188.0	158.0	168.0		192	-2.6	0.0	6	dbSNP_100	168	4848,3752	534.7+/-382.7	1358,2132,810	no	coding-synonymous	RIOK1	NM_031480.2		1556,3041,1906	TT,TC,CC		43.6279,29.6187,47.3089		64/569	7393452	6153,6853	2203	4300	6503	SO:0001819	synonymous_variant	83732	exon2			TTATGACGATGAT	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"""RIO kinase 1 (yeast)"""				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.192C>T	6.37:g.7393452C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_031480	B2RB28|Q8NDC8|Q96NV9	Silent	SNP	ENST00000379834.2	37	CCDS4500.1																																																																																			C|0.560;T|0.440	0.440	strong		0.433	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037424	33037424	+	Missense_Mutation	SNP	T	T	C	rs1126542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33037424T>C	ENST00000419277.1	-	3	469	c.340A>G	c.(340-342)Acc>Gcc	p.T114A	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.T114A|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	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	155	0	0		WXS	Illumina HiSeq	Phase_I	167	62	0.371257	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	
UPK3A	7380	hgsc.bcm.edu	37	22	45691594	45691594	+	Silent	SNP	A	A	G	rs1057356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	44	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	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	
CCDC7	79741	hgsc.bcm.edu	37	10	32807434	32807434	+	Splice_Site	SNP	G	G	T	rs41276068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:32807434G>T	ENST00000362006.5	+	12	1536		c.e12+1		CCDC7_ENST00000277657.6_Splice_Site	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7											NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				GGACAAAGAGGTTGGAAAAAT	0.299													G|||	435	0.086861	0.0151	0.0937	5008	,	,		13256	0.1597		0.1004	False		,,,				2504	0.09				.		Atlas-SNP	.											.	CCDC7	47	.	0			c.993+1G>T						PASS	.	G	,	132,4274	91.1+/-129.8	2,128,2073	74.0	82.0	79.0		,	3.8	1.0	10	dbSNP_127	79	820,7778	184.6+/-232.5	31,758,3510	yes	splice-5,splice-5	CCDC7	NM_001026383.1,NM_145023.4	,	33,886,5583	TT,TG,GG		9.5371,2.9959,7.3208	,	,	32807434	952,12052	2203	4299	6502	SO:0001630	splice_region_variant	221016	exon12			AAAGAGGTTGGAA	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.993+1G>T	10.37:g.32807434G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Splice_Site	SNP	ENST00000362006.5	37	CCDS7173.1	208	0.09523809523809523	11	0.022357723577235773	31	0.0856353591160221	91	0.1590909090909091	75	0.09894459102902374	G	8.934	0.964089	0.18583	0.029959	0.095371	ENSG00000216937	ENST00000277657;ENST00000362006	.	.	.	4.77	3.85	0.44370	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999717	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2805	0.49192	0.0:0.1852:0.8148:0.0	rs41276068	.	.	.	.	-1	.	.	.	+	.	.	CCDC7	32847440	1.000000	0.71417	0.974000	0.42286	0.175000	0.22909	2.483000	0.45233	1.094000	0.41399	0.650000	0.86243	.	G|0.921;T|0.079	0.079	strong		0.299	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	Intron
C9orf84	158401	hgsc.bcm.edu	37	9	114462322	114462322	+	Missense_Mutation	SNP	A	A	G	rs6477845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114462322A>G	ENST00000318737.4	-	22	3031	c.2903T>C	c.(2902-2904)cTg>cCg	p.L968P	C9orf84_ENST00000394777.4_Missense_Mutation_p.L894P|C9orf84_ENST00000374287.3_Missense_Mutation_p.L968P|C9orf84_ENST00000394779.3_Missense_Mutation_p.L929P	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	968			L -> P (in dbSNP:rs6477845).							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						TTCTGTAAGCAGATACCTACA	0.279													G|||	4169	0.832468	0.7995	0.8674	5008	,	,		14313	0.9266		0.7962	False		,,,				2504	0.7924				p.L968P		Atlas-SNP	.											.	C9orf84	207	.	0			c.T2903C						PASS	.	G	PRO/LEU,PRO/LEU	3574,832	327.5+/-300.1	1465,644,94	83.0	85.0	84.0		2786,2903	-0.7	0.0	9	dbSNP_116	84	6754,1842	329.0+/-318.6	2653,1448,197	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	98,98	4118,2092,291	GG,GA,AA		21.4286,18.8833,20.5661	benign,benign	929/1406,968/1445	114462322	10328,2674	2203	4298	6501	SO:0001583	missense	158401	exon22			GTAAGCAGATACC	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.2903T>C	9.37:g.114462322A>G	ENSP00000322108:p.Leu968Pro	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	1855	0.8493589743589743	409	0.8313008130081301	314	0.8674033149171271	526	0.9195804195804196	606	0.7994722955145118	G	5.730	0.319163	0.10845	0.811167	0.785714	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.04970	3.52;3.52;3.52;3.52	6.08	-0.713	0.11223	.	0.725023	0.12896	N	0.430146	T	0.00012	0.0000	N	0.14661	0.345	0.42561	P	0.006854000000000027	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04781	-1.0927	9	0.26408	T	0.33	0.4561	2.0073	0.03480	0.145:0.3498:0.3062:0.199	rs6477845;rs17270491;rs57084802;rs6477845	894;968;929	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	P	929;894;582;968;968	ENSP00000378259:L929P;ENSP00000378257:L894P;ENSP00000363405:L968P;ENSP00000322108:L968P	ENSP00000322108:L968P	L	-	2	0	C9orf84	113502143	0.029000	0.19370	0.040000	0.18447	0.288000	0.27193	0.328000	0.19681	-0.304000	0.08843	-1.059000	0.02297	CTG	A|0.164;G|0.836	0.836	strong		0.279	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
SATB1	6304	hgsc.bcm.edu	37	3	18427924	18427924	+	Silent	SNP	G	G	T	rs2229261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:18427924G>T	ENST00000338745.6	-	8	3120	c.1386C>A	c.(1384-1386)ccC>ccA	p.P462P	SATB1_ENST00000454909.2_Silent_p.P462P|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000417717.2_Silent_p.P462P	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	462					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						TGCTGATGAGGGGGGCAGGAC	0.517													G|||	3451	0.689097	0.5809	0.7291	5008	,	,		16692	0.9226		0.5716	False		,,,				2504	0.6871				p.P462P		Atlas-SNP	.											.	SATB1	96	.	0			c.C1386A						PASS	.	G	,,	2573,1833	636.9+/-396.7	739,1095,369	160.0	171.0	167.0		1386,1386,1386	-5.8	0.9	3	dbSNP_119	167	4985,3615	625.1+/-397.7	1459,2067,774	no	coding-synonymous,coding-synonymous,coding-synonymous	SATB1	NM_001131010.2,NM_001195470.1,NM_002971.4	,,	2198,3162,1143	TT,TG,GG		42.0349,41.6024,41.8884	,,	462/764,462/796,462/764	18427924	7558,5448	2203	4300	6503	SO:0001819	synonymous_variant	6304	exon8			GATGAGGGGGGCA		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"""Homeoboxes / CUT class"""	10541	protein-coding gene	gene with protein product		602075	"""special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"""			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.1386C>A	3.37:g.18427924G>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Silent	SNP	ENST00000338745.6	37	CCDS2631.1																																																																																			T|0.613;G|0.387;A|0.000	0.613	strong		0.517	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010	
CUBN	8029	hgsc.bcm.edu	37	10	16967586	16967586	+	Missense_Mutation	SNP	C	C	G	rs62619939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:16967586C>G	ENST00000377833.4	-	42	6524	c.6459G>C	c.(6457-6459)ttG>ttC	p.L2153F		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2153	CUB 15. {ECO:0000255|PROSITE- ProRule:PRU00059}.		L -> F (in dbSNP:rs62619939). {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)	GACCTACCACCAAGTAATCCC	0.423													C|||	674	0.134585	0.1543	0.147	5008	,	,		18857	0.0595		0.1233	False		,,,				2504	0.1881				p.L2153F		Atlas-SNP	.											.	CUBN	515	.	0			c.G6459C						PASS	.	C	PHE/LEU	586,3820	251.5+/-258.2	33,520,1650	48.0	50.0	49.0		6459	0.6	0.9	10	dbSNP_129	49	1036,7564	216.0+/-255.2	66,904,3330	yes	missense	CUBN	NM_001081.3	22	99,1424,4980	GG,GC,CC		12.0465,13.3,12.4712	probably-damaging	2153/3624	16967586	1622,11384	2203	4300	6503	SO:0001583	missense	8029	exon42			TACCACCAAGTAA	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.6459G>C	10.37:g.16967586C>G	ENSP00000367064:p.Leu2153Phe	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	267	0.12225274725274725	78	0.15853658536585366	55	0.15193370165745856	40	0.06993006993006994	94	0.12401055408970976	C	16.47	3.132179	0.56828	0.133	0.120465	ENSG00000107611	ENST00000377833	T	0.46063	0.88	5.65	0.617	0.17619	CUB (5);	0.000000	0.36101	N	0.002789	T	0.00440	0.0014	M	0.91717	3.235	0.09310	P	0.9999999999999996	D	0.89917	1.0	D	0.76575	0.988	T	0.18967	-1.0320	9	0.72032	D	0.01	.	6.132	0.20211	0.1235:0.3866:0.0:0.4899	rs62619939	2153	O60494	CUBN_HUMAN	F	2153	ENSP00000367064:L2153F	ENSP00000367064:L2153F	L	-	3	2	CUBN	17007592	0.904000	0.30761	0.939000	0.37840	0.971000	0.66376	0.050000	0.14120	0.083000	0.17047	-0.123000	0.14984	TTG	C|0.878;G|0.122	0.122	strong		0.423	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
TGOLN2	10618	hgsc.bcm.edu	37	2	85553784	85553784	+	Silent	SNP	C	C	T	rs1044973	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:85553784C>T	ENST00000409232.3	-	2	1132	c.1071G>A	c.(1069-1071)ggG>ggA	p.G357G	TGOLN2_ENST00000377386.3_Silent_p.G357G|TGOLN2_ENST00000444342.2_Silent_p.G357G|TGOLN2_ENST00000282120.2_Silent_p.G201G|TGOLN2_ENST00000398263.2_Silent_p.G299G|TGOLN2_ENST00000409015.1_Silent_p.G357G			O43493	TGON2_HUMAN	trans-golgi network protein 2	357						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CCGAAAGTGTCCCTTCACGGT	0.527													C|||	3299	0.658746	0.5522	0.7205	5008	,	,		20073	0.875		0.5348	False		,,,				2504	0.6636				p.G357G		Atlas-SNP	.											.	TGOLN2	32	.	0			c.G1071A						PASS	.	C	,,,	2188,1616		630,928,344	92.0	90.0	91.0		1071,1071,897,1071	-2.1	0.0	2	dbSNP_86	91	4474,3780		1214,2046,867	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TGOLN2	NM_001206840.1,NM_001206841.1,NM_001206844.1,NM_006464.3	,,,	1844,2974,1211	TT,TC,CC		45.796,42.4816,44.7504	,,,	357/481,357/454,299/380,357/438	85553784	6662,5396	1902	4127	6029	SO:0001819	synonymous_variant	10618	exon2			AAGTGTCCCTTCA	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"""trans-Golgi network protein (46, 48, 51kD isoforms)"""	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.1071G>A	2.37:g.85553784C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	204	96	0.470588	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Silent	SNP	ENST00000409232.3	37	CCDS56126.1																																																																																			C|0.360;T|0.640	0.640	strong		0.527	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464	
RSL1D1	26156	hgsc.bcm.edu	37	16	11940390	11940390	+	Silent	SNP	T	T	C	rs8052900	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	74	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	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	
SWT1	54823	hgsc.bcm.edu	37	1	185240474	185240474	+	Missense_Mutation	SNP	A	A	G	rs12041704	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:185240474A>G	ENST00000367500.4	+	17	2626	c.2461A>G	c.(2461-2463)Aat>Gat	p.N821D	SWT1_ENST00000367501.3_Missense_Mutation_p.N821D	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	821			N -> D (in dbSNP:rs12041704). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						CCCAAACAGTAATTATCAAGA	0.284													A|||	1743	0.348043	0.2428	0.3963	5008	,	,		13198	0.245		0.4433	False		,,,				2504	0.4642				p.N821D		Atlas-SNP	.											SWT1,NS,carcinoma,0,1	SWT1	88	1	0			c.A2461G						PASS	.	A	ASP/ASN,ASP/ASN	1203,3175	380.2+/-323.6	164,875,1150	38.0	39.0	39.0		2461,2461	4.8	1.0	1	dbSNP_120	39	3641,4921	504.5+/-376.2	786,2069,1426	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	23,23	950,2944,2576	GG,GA,AA		42.5251,27.4783,37.4343	benign,benign	821/901,821/901	185240474	4844,8096	2189	4281	6470	SO:0001583	missense	54823	exon17			AACAGTAATTATC	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.2461A>G	1.37:g.185240474A>G	ENSP00000356470:p.Asn821Asp	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	204	103	0.504902	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	763	0.34935897435897434	132	0.2682926829268293	134	0.3701657458563536	170	0.2972027972027972	327	0.4313984168865435	A	16.44	3.123324	0.56613	0.274783	0.425251	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.20200	2.09;2.09	6.02	4.8	0.61643	.	0.263012	0.43747	D	0.000535	T	0.00012	0.0000	N	0.24115	0.695	0.41524	P	0.011584000000000039	P	0.49090	0.919	B	0.42692	0.395	T	0.42068	-0.9473	9	0.11794	T	0.64	.	9.9289	0.41510	0.838:0.0:0.0:0.162	rs12041704;rs12756341;rs17578728;rs17852826;rs52806916;rs60303559;rs12041704	821	Q5T5J6	SWT1_HUMAN	D	821	ENSP00000356471:N821D;ENSP00000356470:N821D	ENSP00000356470:N821D	N	+	1	0	SWT1	183507097	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.076000	0.50081	2.299000	0.77371	0.528000	0.53228	AAT	A|0.637;G|0.363	0.363	strong		0.284	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
NPHS1	4868	hgsc.bcm.edu	37	19	36334419	36334419	+	Silent	SNP	G	G	A	rs437168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	126	0	0		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	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		
CDH11	1009	hgsc.bcm.edu	37	16	65038674	65038674	+	Silent	SNP	G	G	A	rs35182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:65038674G>A	ENST00000268603.4	-	3	714	c.99C>T	c.(97-99)ccC>ccT	p.P33P	CDH11_ENST00000569624.1_5'UTR|CDH11_ENST00000394156.3_Silent_p.P33P|CDH11_ENST00000566827.1_Intron	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	33					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CATGGAAGGAGGGCCGCAGGT	0.607			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	313	0.0625	0.0061	0.0865	5008	,	,		14916	0.0675		0.1054	False		,,,				2504	0.0726				p.P33P		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	CDH11	260	.	0			c.C99T						PASS	.	G		87,4317	69.2+/-107.0	2,83,2117	29.0	26.0	27.0		99	2.2	1.0	16	dbSNP_76	27	969,7631	198.5+/-242.8	56,857,3387	no	coding-synonymous	CDH11	NM_001797.2		58,940,5504	AA,AG,GG		11.2674,1.9755,8.1206		33/797	65038674	1056,11948	2202	4300	6502	SO:0001819	synonymous_variant	1009	exon3			GAAGGAGGGCCGC	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.99C>T	16.37:g.65038674G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																			G|0.923;A|0.077	0.077	strong		0.607	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
DNAH9	1770	hgsc.bcm.edu	37	17	11757355	11757355	+	Silent	SNP	G	G	A	rs117483481	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:11757355G>A	ENST00000262442.4	+	50	9611	c.9543G>A	c.(9541-9543)ccG>ccA	p.P3181P	DNAH9_ENST00000454412.2_Silent_p.P3181P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3181	Stalk. {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)		TTGGCTCTCCGCCTCTGGCCG	0.567													G|||	56	0.0111821	0.0	0.0058	5008	,	,		17967	0.0427		0.003	False		,,,				2504	0.0061				p.P3181P		Atlas-SNP	.											DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	0			c.G9543A						scavenged	.	G		6,4400	12.9+/-30.5	0,6,2197	80.0	79.0	79.0		9543	-11.0	0.0	17	dbSNP_132	79	33,8567	22.8+/-68.1	0,33,4267	no	coding-synonymous	DNAH9	NM_001372.3		0,39,6464	AA,AG,GG		0.3837,0.1362,0.2999		3181/4487	11757355	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon50			CTCTCCGCCTCTG	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.9543G>A	17.37:g.11757355G>A		Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.995;A|0.005	0.005	strong		0.567	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
RNF112	7732	hgsc.bcm.edu	37	17	19319353	19319353	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19319353C>T	ENST00000461366.1	+	14	1976	c.1761C>T	c.(1759-1761)gcC>gcT	p.A587A	CTB-187M2.2_ENST00000579897.1_RNA|AC004448.2_ENST00000437646.1_lincRNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	587						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						CTGGAGCTGCCGTGGGGGCCA	0.701																																					p.A587A		Atlas-SNP	.											.	RNF112	37	.	0			c.C1761T						PASS	.						3.0	4.0	4.0					17																	19319353		1690	3667	5357	SO:0001819	synonymous_variant	7732	exon14			AGCTGCCGTGGGG	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.1761C>T	17.37:g.19319353C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_007148	O60633|Q7Z5V9	Silent	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			.	.	none		0.701	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
SLFN13	146857	hgsc.bcm.edu	37	17	33772550	33772550	+	Silent	SNP	C	C	T	rs76192030	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:33772550C>T	ENST00000285013.6	-	3	425	c.150G>A	c.(148-150)gcG>gcA	p.A50A	SLFN13_ENST00000360502.2_Intron|SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000533791.1_Silent_p.A50A|SLFN13_ENST00000542635.1_Silent_p.A50A|SLFN13_ENST00000526861.1_Silent_p.A50A	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	50			A -> T (in dbSNP:rs7216628).			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)		ATAAAGCACACGCGGCCCGTA	0.478													C|||	545	0.108826	0.0197	0.0749	5008	,	,		16941	0.0208		0.0994	False		,,,				2504	0.3538				p.A50A		Atlas-SNP	.											SLFN13,rectum,carcinoma,-2,1	SLFN13	79	1	0			c.G150A						PASS	.	C		147,4259	102.1+/-140.7	4,139,2060	118.0	122.0	121.0		150	-6.6	0.1	17	dbSNP_132	121	765,7835	182.6+/-231.0	28,709,3563	no	coding-synonymous	SLFN13	NM_144682.5		32,848,5623	TT,TC,CC		8.8953,3.3364,7.0121		50/898	33772550	912,12094	2203	4300	6503	SO:0001819	synonymous_variant	146857	exon3			AGCACACGCGGCC	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.150G>A	17.37:g.33772550C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	37	CCDS32620.1																																																																																			C|0.930;T|0.070	0.070	strong		0.478	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
RAET1G	353091	hgsc.bcm.edu	37	6	150239484	150239484	+	Missense_Mutation	SNP	C	C	T	rs4870111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:150239484C>T	ENST00000367360.2	-	4	735	c.668G>A	c.(667-669)aGg>aAg	p.R223K	RAET1E-AS1_ENST00000446954.2_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000605899.1_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)		GGCCGTGGCCCTGGGTTGGGC	0.587													c|||	133	0.0265575	0.003	0.0937	5008	,	,		22030	0.0		0.0408	False		,,,				2504	0.0235				p.R223K		Atlas-SNP	.											.	RAET1G	31	.	0			c.G668A						PASS	.	C	LYS/ARG	23,4383	29.9+/-59.1	0,23,2180	234.0	219.0	224.0		668	-4.5	0.0	6	dbSNP_111	224	307,8293	109.8+/-170.3	6,295,3999	yes	missense	RAET1G	NM_001001788.2	26	6,318,6179	TT,TC,CC		3.5698,0.522,2.5373	benign	223/335	150239484	330,12676	2203	4300	6503	SO:0001583	missense	353091	exon4			GTGGCCCTGGGTT	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.668G>A	6.37:g.150239484C>T	ENSP00000356329:p.Arg223Lys	Somatic	533	1	0.00187617		WXS	Illumina HiSeq	Phase_I	559	276	0.493739	NM_001001788		Missense_Mutation	SNP	ENST00000367360.2	37	CCDS43514.1	66	0.03021978021978022	3	0.006097560975609756	32	0.08839779005524862	0	0.0	31	0.040897097625329816	C	1.063	-0.672272	0.03403	0.00522	0.035698	ENSG00000203722	ENST00000367360	T	0.00730	5.77	2.24	-4.47	0.03525	.	.	.	.	.	T	0.00144	0.0004	N	0.04880	-0.145	0.80722	P	0.0	B	0.15719	0.014	B	0.15870	0.014	T	0.38243	-0.9670	8	0.66056	D	0.02	.	4.4879	0.11799	0.0:0.2331:0.3214:0.4455	rs4870111	223	Q6H3X3	RET1G_HUMAN	K	223	ENSP00000356329:R223K	ENSP00000356329:R223K	R	-	2	0	RAET1G	150281177	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.889000	0.00341	-1.749000	0.01330	-1.294000	0.01345	AGG	C|0.968;T|0.032	0.032	strong		0.587	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2		
TIGD2	166815	hgsc.bcm.edu	37	4	90034686	90034686	+	Silent	SNP	A	A	G	rs17015027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:90034686A>G	ENST00000317005.2	+	1	719	c.561A>G	c.(559-561)ccA>ccG	p.P187P	RP11-84C13.1_ENST00000603357.1_lincRNA|FAM13A_ENST00000502459.1_5'Flank	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	187	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		aatgtctaccaTCAAGGACAT	0.383													a|||	1104	0.220447	0.1097	0.2579	5008	,	,		20280	0.3889		0.2038	False		,,,				2504	0.1871				p.P187P		Atlas-SNP	.											.	TIGD2	36	.	0			c.A561G						PASS	.			622,3784	261.9+/-264.6	44,534,1625	59.0	63.0	62.0		561	-5.5	1.0	4	dbSNP_123	62	1858,6742	326.4+/-317.4	205,1448,2647	no	coding-synonymous	TIGD2	NM_145715.2		249,1982,4272	GG,GA,AA		21.6047,14.1171,19.0681		187/526	90034686	2480,10526	2203	4300	6503	SO:0001819	synonymous_variant	166815	exon1			TCTACCATCAAGG	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.561A>G	4.37:g.90034686A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_145715		Silent	SNP	ENST00000317005.2	37	CCDS3633.1																																																																																			A|0.795;G|0.205	0.205	strong		0.383	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715	
SLURP1	57152	hgsc.bcm.edu	37	8	143823241	143823241	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:143823241G>A	ENST00000246515.1	-	2	183	c.158C>T	c.(157-159)aCg>aTg	p.T53M		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	53	UPAR/Ly6.				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)					CGTCACCAGCGTGGTCATGCA	0.652																																					p.T53M		Atlas-SNP	.											SLURP1,NS,carcinoma,0,1	SLURP1	16	1	0			c.C158T						PASS	.						100.0	87.0	91.0					8																	143823241		2203	4299	6502	SO:0001583	missense	57152	exon2			ACCAGCGTGGTCA	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.158C>T	8.37:g.143823241G>A	ENSP00000246515:p.Thr53Met	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_020427	Q53YJ6|Q6PUA6|Q92483	Missense_Mutation	SNP	ENST00000246515.1	37	CCDS6387.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212927	0.39102	.	.	ENSG00000126233	ENST00000246515	T	0.70749	-0.51	4.17	-1.92	0.07618	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.602070	0.04459	N	0.374005	T	0.66137	0.2759	M	0.78456	2.415	0.09310	N	1	B	0.34313	0.448	B	0.29440	0.102	T	0.55623	-0.8112	10	0.72032	D	0.01	-20.1734	3.9364	0.09307	0.2058:0.0:0.356:0.4382	.	53	P55000	SLUR1_HUMAN	M	53	ENSP00000246515:T53M	ENSP00000246515:T53M	T	-	2	0	SLURP1	143820243	0.000000	0.05858	0.001000	0.08648	0.057000	0.15508	-0.051000	0.11885	-0.259000	0.09432	-0.704000	0.03662	ACG	.	.	none		0.652	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427	
ABCA4	24	hgsc.bcm.edu	37	1	94476388	94476388	+	Silent	SNP	C	C	G	rs1801574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:94476388C>G	ENST00000370225.3	-	40	5768	c.5682G>C	c.(5680-5682)ctG>ctC	p.L1894L	ABCA4_ENST00000465352.1_5'UTR|ABCA4_ENST00000536513.1_Silent_p.L164L|ABCA4_ENST00000535881.1_Silent_p.L13L	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1894					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)	p.L1894L(1)		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)		GCTGGACCAGCAGGGTCAGGA	0.582													G|||	1005	0.200679	0.2738	0.2075	5008	,	,		17831	0.12		0.2495	False		,,,				2504	0.1299				p.L1894L		Atlas-SNP	.											ABCA4,NS,carcinoma,0,1	ABCA4	275	1	1	Substitution - coding silent(1)	stomach(1)	c.G5682C						PASS	.	G		1077,3329	722.2+/-409.3	146,785,1272	193.0	146.0	162.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5682	-1.1	1.0	1	dbSNP_89	162	2165,6435	712.8+/-405.9	257,1651,2392	no	coding-synonymous	ABCA4	NM_000350.2		403,2436,3664	GG,GC,CC		25.1744,24.4439,24.927		1894/2274	94476388	3242,9764	2203	4300	6503	SO:0001819	synonymous_variant	24	exon40			GACCAGCAGGGTC	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.5682G>C	1.37:g.94476388C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			C|0.758;G|0.242	0.242	strong		0.582	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
TTC16	158248	hgsc.bcm.edu	37	9	130489558	130489558	+	Silent	SNP	A	A	G	rs472144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130489558A>G	ENST00000373289.3	+	12	1658	c.1578A>G	c.(1576-1578)aaA>aaG	p.K526K	PTRH1_ENST00000429848.1_5'Flank|PTRH1_ENST00000419060.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	526										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GGATGCTTAAACGGCACGAGT	0.607													G|||	3098	0.61861	0.7844	0.6037	5008	,	,		21776	0.3661		0.6173	False		,,,				2504	0.6667				p.K526K		Atlas-SNP	.											TTC16,NS,carcinoma,0,1	TTC16	55	1	0			c.A1578G						PASS	.	G		3259,1147	393.3+/-328.8	1211,837,155	33.0	31.0	32.0		1578	1.3	0.0	9	dbSNP_83	32	5006,3592	506.6+/-376.6	1456,2094,749	no	coding-synonymous	TTC16	NM_144965.1		2667,2931,904	GG,GA,AA		41.7772,26.0327,36.4426		526/874	130489558	8265,4739	2203	4299	6502	SO:0001819	synonymous_variant	158248	exon12			GCTTAAACGGCAC	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.1578A>G	9.37:g.130489558A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	150	65	0.433333	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Silent	SNP	ENST00000373289.3	37	CCDS6875.1																																																																																			A|0.377;G|0.623	0.623	strong		0.607	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
CTAGE1	64693	hgsc.bcm.edu	37	18	19995731	19995731	+	5'Flank	SNP	T	T	C	rs9946136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:19995731T>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.I682V			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					CCTCTTCTTATGAACGGGCCC	0.522													T|||	937	0.187101	0.2481	0.1787	5008	,	,		15959	0.0387		0.2346	False		,,,				2504	0.2147				p.I682V		Atlas-SNP	.											.	CTAGE1	146	.	0			c.A2044G						PASS	.	T	VAL/ILE	1107,3269		155,797,1236	79.0	88.0	85.0		2044	0.6	0.0	18	dbSNP_119	85	1994,6562		248,1498,2532	yes	missense	CTAGE1	NM_172241.2	29	403,2295,3768	CC,CT,TT		23.3053,25.2971,23.9793	benign	682/746	19995731	3101,9831	2188	4278	6466	SO:0001631	upstream_gene_variant	64693	exon1			TTCTTATGAACGG	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19995731T>C	Exception_encountered	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	155	92	0.593548	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	37		392	0.1794871794871795	115	0.23373983739837398	73	0.20165745856353592	25	0.043706293706293704	179	0.23614775725593667	T	3.003	-0.205701	0.06180	0.252971	0.233053	ENSG00000212710	ENST00000391403	T	0.07444	3.19	0.614	0.614	0.17603	.	.	.	.	.	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47886	-0.9082	6	.	.	.	.	.	.	.	rs9946136;rs16966941;rs59362725;rs9946136	682	Q96RT6	CTGE2_HUMAN	V	682	ENSP00000375220:I682V	.	I	-	1	0	CTAGE1	18249729	0.266000	0.24112	0.013000	0.15412	0.009000	0.06853	0.319000	0.19522	0.486000	0.27676	0.248000	0.18094	ATA	T|0.813;C|0.187	0.187	strong		0.522	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
VPS52	6293	hgsc.bcm.edu	37	6	33239423	33239423	+	Silent	SNP	C	C	G	rs17221618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33239423C>G	ENST00000445902.2	-	1	248	c.30G>C	c.(28-30)gcG>gcC	p.A10A	VPS52_ENST00000478934.1_Intron|RPS18_ENST00000439602.2_5'Flank|VPS52_ENST00000436044.2_Intron|RPS18_ENST00000474973.1_5'Flank|VPS52_ENST00000482399.1_Silent_p.A10A	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	10					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						GTTCCCGGGCCGCAGCCGCCA	0.672													G|||	213	0.0425319	0.1044	0.0144	5008	,	,		14678	0.0387		0.0149	False		,,,				2504	0.0112				p.A10A		Atlas-SNP	.											.	VPS52	56	.	0			c.G30C						PASS	.	G		340,4058		9,322,1868	15.0	17.0	16.0		30	-7.9	0.4	6	dbSNP_123	16	166,8426		1,164,4131	no	coding-synonymous	VPS52	NM_022553.4		10,486,5999	GG,GC,CC		1.932,7.7308,3.8953		10/724	33239423	506,12484	2199	4296	6495	SO:0001819	synonymous_variant	6293	exon1			CCGGGCCGCAGCC	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.30G>C	6.37:g.33239423C>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			C|0.956;G|0.044	0.044	strong		0.672	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
GPRC6A	222545	hgsc.bcm.edu	37	6	117113653	117113653	+	Silent	SNP	T	T	C	rs615199	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	128	0	0		WXS	Illumina HiSeq	Phase_I	127	72	0.566929	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		
GCNT4	51301	hgsc.bcm.edu	37	5	74325101	74325101	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:74325101C>T	ENST00000322348.4	-	1	1623	c.762G>A	c.(760-762)acG>acA	p.T254T		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	254					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		GGGGTTTCACCGTCTCCAACA	0.378																																					p.T254T		Atlas-SNP	.											GCNT4,NS,carcinoma,-2,1	GCNT4	46	1	0			c.G762A						PASS	.						85.0	88.0	87.0					5																	74325101		2203	4300	6503	SO:0001819	synonymous_variant	51301	exon1			TTTCACCGTCTCC	AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	17973	protein-coding gene	gene with protein product	"""core 2 beta-1,6-N-acetylglucosaminyltransferase 3"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"""		"""glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.762G>A	5.37:g.74325101C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_016591		Silent	SNP	ENST00000322348.4	37	CCDS4026.1																																																																																			.	.	none		0.378	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591	
GABRP	2568	hgsc.bcm.edu	37	5	170215638	170215638	+	Silent	SNP	T	T	C	rs10036156	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:170215638T>C	ENST00000518525.1	+	3	483	c.19T>C	c.(19-21)Ttg>Ctg	p.L7L	MIR4454_ENST00000518172.1_RNA|GABRP_ENST00000519598.1_Silent_p.L7L|GABRP_ENST00000265294.4_Silent_p.L7L|GABRP_ENST00000519385.1_Silent_p.L7L			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	7					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)	CAGCCTCCACTTGGCCTTCGT	0.552													T|||	1230	0.245607	0.5159	0.1816	5008	,	,		17098	0.1647		0.0696	False		,,,				2504	0.1902				p.L7L		Atlas-SNP	.											.	GABRP	65	.	0			c.T19C						PASS	.	T		1983,2423	559.0+/-380.1	444,1095,664	180.0	157.0	165.0		19	-1.5	0.0	5	dbSNP_119	165	618,7982	160.4+/-213.5	22,574,3704	no	coding-synonymous	GABRP	NM_014211.2		466,1669,4368	CC,CT,TT		7.186,45.0068,19.9985		7/441	170215638	2601,10405	2203	4300	6503	SO:0001819	synonymous_variant	2568	exon2			CTCCACTTGGCCT	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.19T>C	5.37:g.170215638T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	165	78	0.472727	NM_014211	A8KA36|D3DQL2|Q32MJ1	Silent	SNP	ENST00000518525.1	37	CCDS4375.1																																																																																			T|0.788;C|0.212	0.212	strong		0.552	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
HP	3240	hgsc.bcm.edu	37	16	72094348	72094348	+	Silent	SNP	G	G	A	rs5475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72094348G>A	ENST00000355906.5	+	7	838	c.780G>A	c.(778-780)gaG>gaA	p.E260E	HPR_ENST00000356967.5_Intron|HP_ENST00000565574.1_Silent_p.E201E|HP_ENST00000562526.1_Intron|HPR_ENST00000561690.1_5'Flank|HP_ENST00000398131.2_Silent_p.E201E|HP_ENST00000357763.4_Silent_p.E296E|HPR_ENST00000540303.2_5'Flank|HP_ENST00000570083.1_Silent_p.E201E	NM_005143.3	NP_005134.1	P00738	HPT_HUMAN	haptoglobin	260	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute-phase response (GO:0006953)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|immune system process (GO:0002376)|negative regulation of hydrogen peroxide catabolic process (GO:2000296)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of cell death (GO:0010942)|response to hydrogen peroxide (GO:0042542)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)	antioxidant activity (GO:0016209)|hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)		CTGTTAATGAGAGAGTGATGC	0.438													G|||	72	0.014377	0.0015	0.0331	5008	,	,		21745	0.0		0.0427	False		,,,				2504	0.0041				p.E260E		Atlas-SNP	.											.	HP	27	.	0			c.G780A						PASS	.	G	,	36,3832		0,36,1898	102.0	99.0	100.0		603,780	3.1	1.0	16	dbSNP_52	100	403,7885		15,373,3756	no	coding-synonymous,coding-synonymous	HP	NM_001126102.1,NM_005143.3	,	15,409,5654	AA,AG,GG		4.8625,0.9307,3.6114	,	201/348,260/407	72094348	439,11717	1934	4144	6078	SO:0001819	synonymous_variant	3240	exon7			TAATGAGAGAGTG		CCDS45524.1, CCDS45525.1	16q22.2	2012-10-02			ENSG00000257017	ENSG00000257017			5141	protein-coding gene	gene with protein product		140100				11109501, 9352226	Standard	NM_005143		Approved		uc002fbr.4	P00738		ENST00000355906.5:c.780G>A	16.37:g.72094348G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	255	120	0.470588	NM_005143	B0AZL5|P00737|Q0VAC4|Q0VAC5|Q2PP15|Q3B7J0|Q6LBY9|Q9UC67	Silent	SNP	ENST00000355906.5	37	CCDS45524.1																																																																																			G|0.978;A|0.022	0.022	strong		0.438	HP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421680.1	NM_005143	
AMZ1	155185	hgsc.bcm.edu	37	7	2748803	2748803	+	Silent	SNP	C	C	T	rs58726146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:2748803C>T	ENST00000312371.4	+	5	1064	c.696C>T	c.(694-696)gaC>gaT	p.D232D	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	232							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CAGCAGCAGACGGCCCCGAGG	0.687													C|||	1451	0.289736	0.3011	0.1297	5008	,	,		14749	0.5714		0.1252	False		,,,				2504	0.2669				p.D232D		Atlas-SNP	.											AMZ1,NS,carcinoma,0,1	AMZ1	41	1	0			c.C696T						PASS	.	C		1183,3211		177,829,1191	14.0	18.0	16.0		696	-8.6	0.0	7	dbSNP_129	16	1168,7426		83,1002,3212	no	coding-synonymous	AMZ1	NM_133463.1		260,1831,4403	TT,TC,CC		13.5909,26.9231,18.1013		232/499	2748803	2351,10637	2197	4297	6494	SO:0001819	synonymous_variant	155185	exon5			AGCAGACGGCCCC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.696C>T	7.37:g.2748803C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1																																																																																			C|0.791;T|0.209	0.209	strong		0.687	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
TRIM34	53840	hgsc.bcm.edu	37	11	5663706	5663706	+	Missense_Mutation	SNP	G	G	C	rs3740997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5663706G>C	ENST00000514226.1	+	6	1181	c.844G>C	c.(844-846)Gat>Cat	p.D282H	HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Missense_Mutation_p.D636H|TRIM34_ENST00000495668.1_3'UTR|TRIM34_ENST00000429814.2_Missense_Mutation_p.D282H|TRIM6-TRIM34_ENST00000457787.2_Missense_Mutation_p.D282H	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	282			D -> H (in dbSNP:rs3740997).		positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.D282H(1)|p.D636H(1)		NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCATGCTCCAGATCTGAGTAG	0.433													G|||	333	0.0664936	0.0098	0.1167	5008	,	,		21356	0.1597		0.0278	False		,,,				2504	0.0511				p.D636H		Atlas-SNP	.											TRIM6-TRIM34,NS,carcinoma,0,2	TRIM6-TRIM34	68	2	2	Substitution - Missense(2)	stomach(2)	c.G1906C						scavenged	.	G	HIS/ASP,HIS/ASP,HIS/ASP	71,4331	62.9+/-100.1	2,67,2132	79.0	74.0	76.0		1906,844,844	3.0	0.0	11	dbSNP_107	76	226,8368	94.0+/-155.9	1,224,4072	yes	missense,missense,missense	TRIM34,TRIM6-TRIM34	NM_001003819.3,NM_001003827.1,NM_021616.5	81,81,81	3,291,6204	CC,CG,GG		2.6297,1.6129,2.2853	probably-damaging,probably-damaging,probably-damaging	636/843,282/489,282/489	5663706	297,12699	2201	4297	6498	SO:0001583	missense	445372	exon12			GCTCCAGATCTGA	AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10063	protein-coding gene	gene with protein product		605684	"""tripartite motif-containing 34"""	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.844G>C	11.37:g.5663706G>C	ENSP00000422947:p.Asp282His	Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	37	CCDS31391.1	136	0.06227106227106227	7	0.014227642276422764	34	0.09392265193370165	74	0.12937062937062938	21	0.027704485488126648	G	19.05	3.752877	0.69648	0.016129	0.026297	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	3.02	3.02	0.34903	.	.	.	.	.	T	0.00178	0.0005	M	0.75777	2.31	0.80722	P	0.0	D;D	0.89917	0.996;1.0	D;D	0.79784	0.923;0.993	T	0.03068	-1.1076	8	0.54805	T	0.06	.	9.7454	0.40444	0.0:0.0:1.0:0.0	rs3740997;rs52801003;rs3740997	282;636	Q9BYJ4;B2RNG4	TRI34_HUMAN;.	H	636;282;282;282;636	ENSP00000422947:D282H;ENSP00000402595:D282H;ENSP00000395982:D282H;ENSP00000346916:D636H	ENSP00000402595:D282H	D	+	1	0	TRIM34;TRIM6-TRIM34	5620282	0.013000	0.17824	0.025000	0.17156	0.914000	0.54420	1.188000	0.32102	1.988000	0.58038	0.460000	0.39030	GAT	G|0.965;C|0.035	0.035	strong		0.433	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827	
KLHL28	54813	hgsc.bcm.edu	37	14	45403616	45403616	+	Missense_Mutation	SNP	T	T	C	rs35728857	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:45403616T>C	ENST00000396128.4	-	3	1164	c.1045A>G	c.(1045-1047)Atc>Gtc	p.I349V	KLHL28_ENST00000355081.2_Missense_Mutation_p.I363V	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	349			I -> V (in dbSNP:rs35728857).							breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGTTTTCTGATAGTGACGCCA	0.388													T|||	6	0.00119808	0.0	0.0029	5008	,	,		19647	0.0		0.003	False		,,,				2504	0.001				p.I349V		Atlas-SNP	.											.	KLHL28	53	.	0			c.A1045G						PASS	.	T	VAL/ILE	6,4400	11.4+/-27.6	0,6,2197	116.0	108.0	111.0		1045	-1.1	1.0	14	dbSNP_126	111	36,8564	25.1+/-72.6	0,36,4264	yes	missense	KLHL28	NM_017658.3	29	0,42,6461	CC,CT,TT		0.4186,0.1362,0.3229	benign	349/572	45403616	42,12964	2203	4300	6503	SO:0001583	missense	54813	exon3			TTCTGATAGTGAC	AK000088	CCDS9680.1	14q21.1	2013-02-22	2013-02-22	2007-01-09	ENSG00000179454	ENSG00000179454		"""Kelch-like"", ""BTB/POZ domain containing"""	19741	protein-coding gene	gene with protein product			"""BTB (POZ) domain containing 5"", ""kelch-like 28 (Drosophila)"""	BTBD5			Standard	NM_017658		Approved	FLJ20081	uc001wvr.3	Q9NXS3	OTTHUMG00000140263	ENST00000396128.4:c.1045A>G	14.37:g.45403616T>C	ENSP00000379434:p.Ile349Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_017658	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	37	CCDS9680.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	10.34	1.322698	0.23994	0.001362	0.004186	ENSG00000179454	ENST00000396128;ENST00000355081	T;T	0.77229	-1.08;-1.08	5.38	-1.07	0.09968	Kelch-type beta propeller (1);	0.305531	0.37136	N	0.002234	T	0.48040	0.1478	N	0.12746	0.255	0.23515	N	0.997516	B	0.06786	0.001	B	0.14023	0.01	T	0.15407	-1.0438	10	0.14252	T	0.57	.	0.81	0.01091	0.3527:0.0965:0.2311:0.3196	rs35728857	349	Q9NXS3	KLH28_HUMAN	V	349;363	ENSP00000379434:I349V;ENSP00000347193:I363V	ENSP00000347193:I363V	I	-	1	0	KLHL28	44473366	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	1.815000	0.38981	0.060000	0.16281	0.455000	0.32223	ATC	T|0.997;C|0.003	0.003	strong		0.388	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3		
HIST1H4B	8366	hgsc.bcm.edu	37	6	26027433	26027433	+	Silent	SNP	G	G	A	rs3752419	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26027433G>A	ENST00000377364.3	-	1	47	c.48C>T	c.(46-48)gcC>gcT	p.A16A		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	16					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			large_intestine(4)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	13						GGTGACGCTTGGCACCTCCCT	0.542													G|||	1975	0.394369	0.1309	0.4524	5008	,	,		16190	0.7123		0.3956	False		,,,				2504	0.3804				p.A16A		Atlas-SNP	.											.	HIST1H4B	27	.	0			c.C48T						PASS	.	G		847,3559	333.6+/-303.0	82,683,1438	67.0	61.0	63.0		48	-9.1	0.1	6	dbSNP_107	63	3484,5116	509.7+/-377.3	735,2014,1551	no	coding-synonymous	HIST1H4B	NM_003544.2		817,2697,2989	AA,AG,GG		40.5116,19.2238,33.3		16/104	26027433	4331,8675	2203	4300	6503	SO:0001819	synonymous_variant	8366	exon1			ACGCTTGGCACCT	X67081	CCDS4572.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124529	ENSG00000278705		"""Histones / Replication-dependent"""	4789	protein-coding gene	gene with protein product		602829	"""H4 histone family, member I"", ""histone 1, H4b"""	H4FI		9119399, 12408966	Standard	NM_003544		Approved	H4/I	uc003nfr.3	P62805	OTTHUMG00000014417	ENST00000377364.3:c.48C>T	6.37:g.26027433G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_003544	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377364.3	37	CCDS4572.1																																																																																			G|0.628;A|0.372	0.372	strong		0.542	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544	
TACC2	10579	hgsc.bcm.edu	37	10	123846288	123846288	+	Missense_Mutation	SNP	G	G	A	rs4752642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123846288G>A	ENST00000369005.1	+	4	4613	c.4273G>A	c.(4273-4275)Gcc>Acc	p.A1425T	TACC2_ENST00000334433.3_Missense_Mutation_p.A1425T|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.A1425T|TACC2_ENST00000453444.2_Missense_Mutation_p.A1425T|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.A1425T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1425			A -> T (in dbSNP:rs4752642).		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)				CGGAGCCCTGGCCACACCTGG	0.587													A|||	1025	0.204673	0.3071	0.1844	5008	,	,		19126	0.1002		0.2117	False		,,,				2504	0.181				p.A1425T		Atlas-SNP	.											.	TACC2	271	.	0			c.G4273A						PASS	.	A	,THR/ALA	1515,2891	673.4+/-402.8	257,1001,945	45.0	46.0	45.0		,4273	-1.9	0.0	10	dbSNP_111	45	1931,6669	725.9+/-406.6	215,1501,2584	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	472,2502,3529	AA,AG,GG		22.4535,34.3849,26.4955	,benign	,1425/2949	123846288	3446,9560	2203	4300	6503	SO:0001583	missense	10579	exon4			GCCCTGGCCACAC	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.4273G>A	10.37:g.123846288G>A	ENSP00000358001:p.Ala1425Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	128	51	0.398438	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	462	0.21153846153846154	157	0.31910569105691056	79	0.21823204419889503	70	0.12237762237762238	156	0.20580474934036938	A	2.047	-0.418747	0.04766	0.343849	0.224535	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02606	4.23;4.25;4.24;4.23;4.25	4.42	-1.87	0.07737	.	0.725799	0.11366	N	0.571365	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	0.41662	-0.9496	9	0.07644	T	0.81	-0.7154	11.5586	0.50764	0.3549:0.0:0.6451:0.0	rs4752642;rs52796433;rs57437888;rs4752642	1425;1425;1425	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1425;1425;1425;1425;1425;1415	ENSP00000358001:A1425T;ENSP00000424467:A1425T;ENSP00000427618:A1425T;ENSP00000334280:A1425T;ENSP00000395048:A1425T	ENSP00000334280:A1425T	A	+	1	0	TACC2	123836278	0.009000	0.17119	0.000000	0.03702	0.001000	0.01503	0.072000	0.14617	-0.939000	0.03709	-0.380000	0.06706	GCC	G|0.754;A|0.246	0.246	strong		0.587	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
WDR27	253769	hgsc.bcm.edu	37	6	170058374	170058374	+	Missense_Mutation	SNP	C	C	T	rs3800544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170058374C>T	ENST00000448612.1	-	13	1509	c.1400G>A	c.(1399-1401)cGt>cAt	p.R467H	WDR27_ENST00000423258.1_Missense_Mutation_p.R340H|WDR27_ENST00000333572.6_Missense_Mutation_p.R467H|WDR27_ENST00000546525.1_5'UTR	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	437						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)		GTACTGACCACGTCGCTGTTC	0.483													C|||	400	0.0798722	0.1014	0.049	5008	,	,		20160	0.0903		0.0716	False		,,,				2504	0.0706				p.R467H		Atlas-SNP	.											.	WDR27	129	.	0			c.G1400A						PASS	.	C	HIS/ARG,HIS/ARG	364,3848		17,330,1759	78.0	78.0	78.0		1400,1019	1.5	0.0	6	dbSNP_107	78	604,7838		23,558,3640	yes	missense,missense	WDR27	NM_182552.4,NM_001202550.1	29,29	40,888,5399	TT,TC,CC		7.1547,8.642,7.6498	benign,benign	467/896,340/731	170058374	968,11686	2106	4221	6327	SO:0001583	missense	253769	exon13			TGACCACGTCGCT	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.1400G>A	6.37:g.170058374C>T	ENSP00000416289:p.Arg467His	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	184|184	0.08424908424908426|0.08424908424908426	48|48	0.0975609756097561|0.0975609756097561	21|21	0.058011049723756904|0.058011049723756904	61|61	0.10664335664335664|0.10664335664335664	54|54	0.0712401055408971|0.0712401055408971	C|C	4.979|4.979	0.181740|0.181740	0.09495|0.09495	0.08642|0.08642	0.071547|0.071547	ENSG00000184465|ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258|ENST00000441385	T;T;T|.	0.24538|.	1.92;2.17;1.85|.	4.56|4.56	1.5|1.5	0.22942|0.22942	.|.	1.649040|.	0.03431|.	N|.	0.207806|.	T|T	0.10121|0.10121	0.0248|0.0248	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B;B;B|.	0.06786|.	0.001;0.0;0.001;0.001|.	B;B;B;B|.	0.08055|.	0.0;0.0;0.003;0.001|.	T|T	0.26815|0.26815	-1.0092|-1.0092	9|4	0.14252|.	T|.	0.57|.	-13.7184|-13.7184	7.3373|7.3373	0.26617|0.26617	0.0:0.3557:0.4646:0.1796|0.0:0.3557:0.4646:0.1796	rs3800544;rs52796940;rs58816624;rs3800544|rs3800544;rs52796940;rs58816624;rs3800544	467;437;340;467|.	F2Z2U5;A2RRH5;A2RRH5-2;C9JGV0|.	.;WDR27_HUMAN;.;.|.	H|M	467;467;340|101	ENSP00000416289:R467H;ENSP00000330265:R467H;ENSP00000397869:R340H|.	ENSP00000330265:R467H|.	R|V	-|-	2|1	0|0	WDR27|WDR27	169800299|169800299	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	0.443000|0.443000	0.21644|0.21644	0.049000|0.049000	0.15920|0.15920	-0.344000|-0.344000	0.07964|0.07964	CGT|GTG	C|0.910;T|0.090	0.090	strong		0.483	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
SPP1	6696	hgsc.bcm.edu	37	4	88903889	88903889	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88903889T>C	ENST00000395080.3	+	7	913	c.786T>C	c.(784-786)gaT>gaC	p.D262D	SPP1_ENST00000360804.4_Silent_p.D235D|SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000237623.7_Silent_p.D248D	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	262					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)		ATGTGATTGATAGTCAGGAAC	0.448																																					p.D275D		Atlas-SNP	.											SPP1,NS,carcinoma,+2,1	SPP1	35	1	0			c.T825C						scavenged	.						146.0	145.0	145.0					4																	88903889		2203	4300	6503	SO:0001819	synonymous_variant	6696	exon8			GATTGATAGTCAG		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.786T>C	4.37:g.88903889T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	182	4	0.021978	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	37	CCDS43250.1																																																																																			.	.	none		0.448	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011298	46011298	+	Silent	SNP	G	G	A	rs113437209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46011298G>A	ENST00000400368.1	-	1	1088	c.1068C>T	c.(1066-1068)agC>agT	p.S356S	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	356						keratin filament (GO:0045095)		p.S356S(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						CAGAGCAGAGGCTGTAGCAGG	0.677																																					p.S356S		Atlas-SNP	.											KRTAP10-6,NS,carcinoma,0,1	KRTAP10-6	57	1	1	Substitution - coding silent(1)	stomach(1)	c.C1068T						scavenged	.						29.0	38.0	35.0					21																	46011298		2194	4298	6492	SO:0001819	synonymous_variant	386674	exon1			GCAGAGGCTGTAG	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.1068C>T	21.37:g.46011298G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	251	5	0.0199203	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			A|1.000;|0.000	1.000	weak		0.677	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
DHX38	9785	hgsc.bcm.edu	37	16	72135014	72135014	+	Silent	SNP	T	T	C	rs1050363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72135014T>C	ENST00000268482.3	+	10	1817	c.1308T>C	c.(1306-1308)gcT>gcC	p.A436A	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	436					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.A436A(1)		endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				TGAAGGATGCTACTTCTGACC	0.542													C|||	2794	0.557907	0.823	0.3963	5008	,	,		19009	0.3591		0.5	False		,,,				2504	0.5787				p.A436A	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,NS,carcinoma,0,1	DHX38	91	1	1	Substitution - coding silent(1)	stomach(1)	c.T1308C						PASS	.	C		3313,1083	392.6+/-328.5	1262,789,147	128.0	133.0	131.0		1308	2.3	1.0	16	dbSNP_86	131	4556,4044	558.4+/-387.2	1204,2148,948	no	coding-synonymous	DHX38	NM_014003.3		2466,2937,1095	CC,CT,TT		47.0233,24.636,39.4506		436/1228	72135014	7869,5127	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon10			GGATGCTACTTCT	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"""DEAH-boxes"""	17211	protein-coding gene	gene with protein product		605584	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"""	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.1308T>C	16.37:g.72135014T>C		Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	328	140	0.426829	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			T|0.421;C|0.579	0.579	strong		0.542	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
E2F3	1871	hgsc.bcm.edu	37	6	20490428	20490428	+	Missense_Mutation	SNP	G	G	A	rs4134982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:20490428G>A	ENST00000346618.3	+	7	1231	c.1165G>A	c.(1165-1167)Gat>Aat	p.D389N	E2F3_ENST00000535432.1_Missense_Mutation_p.D258N	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	389			D -> N (in dbSNP:rs4134982). {ECO:0000269|Ref.2}.		mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			AGGACATAGCGATTGCTCAGT	0.408													G|||	15	0.00299521	0.0	0.0043	5008	,	,		19775	0.0		0.0119	False		,,,				2504	0.0				p.D389N		Atlas-SNP	.											E2F3,NS,carcinoma,-2,1	E2F3	30	1	0			c.G1165A						PASS	.	G	ASN/ASP	12,4394	17.9+/-39.9	0,12,2191	75.0	75.0	75.0		1165	5.5	0.8	6	dbSNP_108	75	99,8501	54.0+/-114.7	0,99,4201	yes	missense	E2F3	NM_001949.4	23	0,111,6392	AA,AG,GG		1.1512,0.2724,0.8535	benign	389/466	20490428	111,12895	2203	4300	6503	SO:0001583	missense	1871	exon7			CATAGCGATTGCT	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.1165G>A	6.37:g.20490428G>A	ENSP00000262904:p.Asp389Asn	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	137	57	0.416058	NM_001949	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	37	CCDS4545.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	9.602	1.129011	0.21041	0.002724	0.011512	ENSG00000112242	ENST00000346618;ENST00000535432	T;T	0.06933	3.24;3.26	5.49	5.49	0.81192	.	0.338236	0.35378	N	0.003255	T	0.02304	0.0071	N	0.21097	0.63	0.42665	D	0.993494	B	0.16396	0.017	B	0.08055	0.003	T	0.45760	-0.9239	10	0.27082	T	0.32	.	9.5533	0.39324	0.0743:0.1436:0.782:0.0	rs4134982;rs52820498;rs4134982	389	O00716	E2F3_HUMAN	N	389;258	ENSP00000262904:D389N;ENSP00000443418:D258N	ENSP00000262904:D389N	D	+	1	0	E2F3	20598407	1.000000	0.71417	0.808000	0.32385	0.973000	0.67179	3.942000	0.56614	2.746000	0.94184	0.561000	0.74099	GAT	G|0.993;A|0.007	0.007	strong		0.408	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1		
ACAT1	38	hgsc.bcm.edu	37	11	108009660	108009660	+	Silent	SNP	C	C	A	rs35188041	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:108009660C>A	ENST00000265838.4	+	6	562	c.471C>A	c.(469-471)tcC>tcA	p.S157S		NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	157					adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	AGAGCATGTCCAATGTTCCAT	0.408													C|||	636	0.126997	0.1929	0.0965	5008	,	,		19189	0.0198		0.1581	False		,,,				2504	0.138				p.S157S		Atlas-SNP	.											ACAT1,colon,carcinoma,0,1	ACAT1	35	1	0			c.C471A						scavenged	.	C		862,3540	338.4+/-305.3	91,680,1430	218.0	191.0	200.0		471	1.8	1.0	11	dbSNP_126	200	1501,7095	284.4+/-296.6	127,1247,2924	no	coding-synonymous	ACAT1	NM_000019.3		218,1927,4354	AA,AC,CC		17.4616,19.582,18.1797		157/428	108009660	2363,10635	2201	4298	6499	SO:0001819	synonymous_variant	38	exon6			CATGTCCAATGTT	D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	2.3.1.9		93	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	607809	"""acetyl-Coenzyme A acetyltransferase 1"""	ACAT		1979337	Standard	NM_000019		Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.471C>A	11.37:g.108009660C>A		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	138	76	0.550725	NM_000019	B2R6H1|G3XAB4|Q96FG8	Silent	SNP	ENST00000265838.4	37	CCDS8339.1	273	0.125	94	0.1910569105691057	41	0.1132596685082873	13	0.022727272727272728	125	0.16490765171503957	C	15.57	2.873841	0.51695	0.19582	0.174616	ENSG00000075239	ENST00000528370	.	.	.	5.74	1.76	0.24704	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11616	-1.0580	3	.	.	.	-18.5574	7.7441	0.28858	0.1131:0.6655:0.0:0.2213	rs35188041	.	.	.	K	93	.	.	Q	+	1	0	ACAT1	107514870	0.977000	0.34250	0.993000	0.49108	0.960000	0.62799	0.158000	0.16422	0.775000	0.33450	0.603000	0.83216	CAA	A|0.168;C|0.832;G|0.000	0.168	strong		0.408	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389474.1	NM_000019	
KDM5C	8242	hgsc.bcm.edu	37	X	53223819	53223819	+	Silent	SNP	C	C	T	rs76525703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53223819C>T	ENST00000375401.3	-	23	4072	c.3540G>A	c.(3538-3540)acG>acA	p.T1180T	KDM5C_ENST00000452825.3_Silent_p.T1113T|KDM5C_ENST00000375383.3_Silent_p.T1139T|KDM5C_ENST00000404049.3_Silent_p.T1179T|KDM5C_ENST00000375379.3_Silent_p.T1180T	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1180					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|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)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						TAGAGGAGGCCGTGCTCGATG	0.612			"""N, F, S"""		clear cell renal carcinoma								c|||	18	0.00476821	0.0136	0.0	3775	,	,		14232	0.0		0.0	False		,,,				2504	0.0				p.T1180T		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G3540A						PASS	.	C	,	37,3798		0,28,9,1604,562	221.0	158.0	179.0		3339,3540	-4.5	0.0	X	dbSNP_131	179	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	KDM5C	NM_001146702.1,NM_004187.3	,	0,28,10,4032,2433	TT,TC,T,CC,C		0.0149,0.9648,0.3597	,	1113/1380,1180/1561	53223819	38,10525	2203	4300	6503	SO:0001819	synonymous_variant	8242	exon23			GGAGGCCGTGCTC	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.3540G>A	X.37:g.53223819C>T		Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	279	278	0.996416	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	37	CCDS14351.1																																																																																			C|0.996;T|0.004	0.004	strong		0.612	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
MTRNR2L7	100288485	hgsc.bcm.edu	37	10	37890955	37890955	+	Silent	SNP	G	G	A	rs2180706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:37890955G>A	ENST00000544824.1	-	1	904	c.18C>T	c.(16-18)ttC>ttT	p.F6F		NM_001190489.1	NP_001177418.1			MT-RNR2-like 7																		AGAGGCAGCCGAACCCTCCTG	0.408													a|||	3355	0.669928	0.6278	0.6715	5008	,	,		18486	0.6032		0.6372	False		,,,				2504	0.8282				p.F6F		Atlas-SNP	.											.	.	.	.	0			c.C18T						PASS	.																																			SO:0001819	synonymous_variant	100288485	exon1			GCAGCCGAACCCT		CCDS53524.1	10p11.21	2014-02-18			ENSG00000256892	ENSG00000256892			37164	protein-coding gene	gene with protein product	"""humanin-like 7"""					19477263	Standard	NM_001190489		Approved		uc021ppd.1	P0CJ74	OTTHUMG00000184979	ENST00000544824.1:c.18C>T	10.37:g.37890955G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001190489		Silent	SNP	ENST00000544824.1	37	CCDS53524.1																																																																																			G|0.434;A|0.566	0.566	strong		0.408	MTRNR2L7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469397.1	NM_001190489	
MICAL1	64780	hgsc.bcm.edu	37	6	109767930	109767930	+	Missense_Mutation	SNP	G	G	T	rs552227069|rs9320288|rs35260632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:109767930G>T	ENST00000358807.3	-	18	2584	c.2273C>A	c.(2272-2274)gCg>gAg	p.A758E	MICAL1_ENST00000368952.4_Missense_Mutation_p.A777E|MICAL1_ENST00000358577.3_Missense_Mutation_p.A672E	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	227	0	0		WXS	Illumina HiSeq	Phase_I	221	96	0.434389	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412335	105412335	+	Silent	SNP	C	C	T	rs202104959	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105412335C>T	ENST00000333244.5	-	7	9572	c.9453G>A	c.(9451-9453)ccG>ccA	p.P3151P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3151						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.P3151P(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)			CCCCGAACGACGGCATCTTGA	0.602																																					p.P3151P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	1	Substitution - coding silent(1)	endometrium(1)	c.G9453A						scavenged	.						198.0	138.0	157.0					14																	105412335		1921	4005	5926	SO:0001819	synonymous_variant	113146	exon7			GAACGACGGCATC	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.9453G>A	14.37:g.105412335C>T		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	21	4	0.190476	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.963;T|0.037	0.037	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CNNM4	26504	hgsc.bcm.edu	37	2	97465379	97465379	+	Missense_Mutation	SNP	C	C	T	rs144495984		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97465379C>T	ENST00000377075.2	+	5	2040	c.1942C>T	c.(1942-1944)Ccc>Tcc	p.P648S	CNNM4_ENST00000540067.1_Missense_Mutation_p.P135S|CNNM4_ENST00000496186.1_3'UTR|MIR3127_ENST00000583925.1_RNA	NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	648					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						GACCTCGGTCCCCTCCGGTGA	0.602																																					p.P648S		Atlas-SNP	.											.	CNNM4	48	.	0			c.C1942T						PASS	.	C	SER/PRO	0,4340		0,0,2170	85.0	72.0	77.0		1942	-1.7	0.0	2	dbSNP_134	77	2,8374		0,2,4186	yes	missense	CNNM4	NM_020184.3	74	0,2,6356	TT,TC,CC		0.0239,0.0,0.0157	benign	648/776	97465379	2,12714	2170	4188	6358	SO:0001583	missense	26504	exon5			TCGGTCCCCTCCG	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1942C>T	2.37:g.97465379C>T	ENSP00000366275:p.Pro648Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800104	0.31869	0.0	2.39E-4	ENSG00000158158	ENST00000377075;ENST00000540067	T	0.73047	-0.71	4.78	-1.71	0.08133	RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.773363	0.12569	N	0.457447	T	0.36082	0.0954	N	0.03281	-0.365	0.18873	N	0.999989	B;B	0.14438	0.01;0.0	B;B	0.17433	0.018;0.0	T	0.18053	-1.0349	10	0.17369	T	0.5	-9.342	0.8361	0.01140	0.2255:0.3422:0.2194:0.2129	.	135;648	B7Z1U0;Q6P4Q7	.;CNNM4_HUMAN	S	648;135	ENSP00000366275:P648S	ENSP00000366275:P648S	P	+	1	0	CNNM4	96829106	0.000000	0.05858	0.000000	0.03702	0.230000	0.25150	-1.945000	0.01537	-0.484000	0.06763	-0.291000	0.09656	CCC	C|1.000;T|0.000	0.000	weak		0.602	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184	
PSMD5	5711	hgsc.bcm.edu	37	9	123605139	123605139	+	Missense_Mutation	SNP	C	C	A	rs113345820	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123605139C>A	ENST00000210313.3	-	1	123	c.49G>T	c.(49-51)Gcg>Tcg	p.A17S	PSMD5-AS1_ENST00000588973.1_RNA|PSMD5-AS1_ENST00000608862.1_RNA|PSMD5-AS1_ENST00000432640.1_RNA|PSMD5-AS1_ENST00000609388.1_RNA|PSMD5-AS1_ENST00000586907.1_RNA|PSMD5-AS1_ENST00000447891.1_RNA|PSMD5-AS1_ENST00000589026.1_RNA|PSMD5_ENST00000373904.5_Missense_Mutation_p.A17S|PSMD5-AS1_ENST00000442982.1_RNA	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	17					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)|proteasome regulatory particle assembly (GO:0070682)|protein folding (GO:0006457)|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)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)				endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)	10						TCCAGCGGCGCTTCCAGCCTC	0.706													C|||	9	0.00179712	0.0	0.0	5008	,	,		15272	0.0		0.0089	False		,,,				2504	0.0				p.A17S		Atlas-SNP	.											.	PSMD5	34	.	0			c.G49T						PASS	.	C	SER/ALA	5,4381		0,5,2188	11.0	12.0	11.0		49	5.2	1.0	9	dbSNP_132	11	39,8525		0,39,4243	yes	missense	PSMD5	NM_005047.2	99	0,44,6431	AA,AC,CC		0.4554,0.114,0.3398	benign	17/505	123605139	44,12906	2193	4282	6475	SO:0001583	missense	5711	exon1			GCGGCGCTTCCAG	AK001065	CCDS6824.1, CCDS59143.1	9q34.11	2008-02-05			ENSG00000095261	ENSG00000095261		"""Proteasome (prosome, macropain) subunits"""	9563	protein-coding gene	gene with protein product		604452				7559544	Standard	NM_005047		Approved	S5B, KIAA0072	uc004bko.4	Q16401	OTTHUMG00000020573	ENST00000210313.3:c.49G>T	9.37:g.123605139C>A	ENSP00000210313:p.Ala17Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_005047	B4DZM8|Q15045|Q4VXG8	Missense_Mutation	SNP	ENST00000210313.3	37	CCDS6824.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	20.9	4.062032	0.76187	0.00114	0.004554	ENSG00000095261	ENST00000210313;ENST00000373904	T;T	0.31510	1.55;1.49	5.22	5.22	0.72569	.	0.221292	0.45606	D	0.000360	T	0.26231	0.0640	L	0.41236	1.265	0.37143	D	0.901819	B;B	0.30542	0.284;0.284	B;B	0.38458	0.274;0.184	T	0.24012	-1.0172	10	0.45353	T	0.12	.	17.5286	0.87808	0.0:1.0:0.0:0.0	.	17;17	B4DZM8;Q16401	.;PSMD5_HUMAN	S	17	ENSP00000210313:A17S;ENSP00000363011:A17S	ENSP00000210313:A17S	A	-	1	0	PSMD5	122644960	0.998000	0.40836	1.000000	0.80357	0.922000	0.55478	2.583000	0.46094	2.725000	0.93324	0.655000	0.94253	GCG	C|0.997;A|0.003	0.003	strong		0.706	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047	
TTN	7273	hgsc.bcm.edu	37	2	179447848	179447848	+	Silent	SNP	T	T	C	rs4894029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179447848T>C	ENST00000591111.1	-	263	60983	c.60759A>G	c.(60757-60759)acA>acG	p.T20253T	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.T21894T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Silent_p.T12954T|TTN_ENST00000460472.2_Silent_p.T12829T|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.T13021T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.T19326T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20253	Ig-like 111.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCAAGAAACTGTTGGCATCG	0.458													C|||	2573	0.513778	0.5749	0.4078	5008	,	,		18418	0.7202		0.2555	False		,,,				2504	0.5593				p.T21894T		Atlas-SNP	.											.	TTN	18412	.	0			c.A65682G						PASS	.	C	,,,	2050,1812		558,934,439	63.0	60.0	61.0		38487,57978,38862,39063	-6.8	0.4	2	dbSNP_111	61	1860,6430		195,1470,2480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	753,2404,2919	CC,CT,TT		22.4367,46.9187,32.1758	,,,	12829/26927,19326/33424,12954/27052,13021/27119	179447848	3910,8242	1931	4145	6076	SO:0001819	synonymous_variant	7273	exon313			AGAAACTGTTGGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.60759A>G	2.37:g.179447848T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	166	70	0.421687	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.555;C|0.445	0.445	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
BAIAP2	10458	hgsc.bcm.edu	37	17	79089590	79089590	+	Missense_Mutation	SNP	A	A	G	rs4969391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79089590A>G	ENST00000321300.6	+	14	1649	c.1556A>G	c.(1555-1557)cAg>cGg	p.Q519R	BAIAP2_ENST00000575245.1_3'UTR|BAIAP2_ENST00000392411.3_Missense_Mutation_p.Q441R|BAIAP2_ENST00000428708.2_Missense_Mutation_p.Q519R|BAIAP2_ENST00000435091.3_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	78	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	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		
APBA2	321	hgsc.bcm.edu	37	15	29346468	29346468	+	Silent	SNP	C	C	T	rs137995892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29346468C>T	ENST00000558402.1	+	5	980	c.381C>T	c.(379-381)caC>caT	p.H127H	APBA2_ENST00000411764.1_Silent_p.H127H|APBA2_ENST00000558259.1_Silent_p.H127H|APBA2_ENST00000558330.1_Silent_p.H127H|APBA2_ENST00000561069.1_Silent_p.H127H			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	127					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)		ACAGTGCACACCCTGTGGACA	0.652													C|||	25	0.00499201	0.0008	0.0115	5008	,	,		19471	0.0		0.0129	False		,,,				2504	0.0031				p.H127H		Atlas-SNP	.											.	APBA2	132	.	0			c.C381T						PASS	.	C	,	10,4396	16.8+/-37.8	0,10,2193	98.0	82.0	87.0		381,381	-1.4	0.0	15	dbSNP_134	87	75,8525	44.9+/-103.4	0,75,4225	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	0,85,6418	TT,TC,CC		0.8721,0.227,0.6535	,	127/738,127/750	29346468	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	321	exon3			TGCACACCCTGTG	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.381C>T	15.37:g.29346468C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	28	0.329412	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			C|0.994;T|0.006	0.006	strong		0.652	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
ASXL3	80816	hgsc.bcm.edu	37	18	31320229	31320229	+	Missense_Mutation	SNP	A	A	G	rs2282632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:31320229A>G	ENST00000269197.5	+	11	2861	c.2861A>G	c.(2860-2862)aAt>aGt	p.N954S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	954			N -> S (in dbSNP:rs2282632). {ECO:0000269|PubMed:11214970, 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)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GGGATAAGAAATGAAAGTAGA	0.403													A|||	3522	0.703275	0.8094	0.6916	5008	,	,		18519	0.8988		0.5249	False		,,,				2504	0.5501				p.N954S		Atlas-SNP	.											.	ASXL3	405	.	0			c.A2861G						PASS	.	A	SER/ASN	2900,796		1133,634,81	58.0	55.0	56.0		2861	0.4	0.9	18	dbSNP_100	56	4246,3954		1084,2078,938	yes	missense	ASXL3	NM_030632.1	46	2217,2712,1019	GG,GA,AA		48.2195,21.5368,39.9294	benign	954/2249	31320229	7146,4750	1848	4100	5948	SO:0001583	missense	80816	exon11			TAAGAAATGAAAG	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.2861A>G	18.37:g.31320229A>G	ENSP00000269197:p.Asn954Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	1533	0.7019230769230769	385	0.782520325203252	239	0.6602209944751382	516	0.9020979020979021	393	0.5184696569920845	A	9.879	1.200986	0.22121	0.784632	0.517805	ENSG00000141431	ENST00000269197	T	0.48522	0.81	5.72	0.361	0.16107	.	1.491830	0.03855	N	0.272982	T	0.00012	0.0000	L	0.29908	0.895	0.44352	P	0.0027599999999999847	B	0.10296	0.003	B	0.06405	0.002	T	0.35475	-0.9787	9	0.07813	T	0.8	.	5.8836	0.18868	0.4169:0.3758:0.2073:0.0	rs2282632;rs17746901;rs60259995;rs2282632	954	Q9C0F0	ASXL3_HUMAN	S	954	ENSP00000269197:N954S	ENSP00000269197:N954S	N	+	2	0	ASXL3	29574227	0.996000	0.38824	0.907000	0.35723	0.870000	0.49936	0.405000	0.21015	0.109000	0.17891	0.533000	0.62120	AAT	G|0.767;N|0.000	0.767	strong		0.403	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
IL21	59067	hgsc.bcm.edu	37	4	123536963	123536963	+	Silent	SNP	G	G	A	rs4833837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123536963G>A	ENST00000264497.3	-	3	291	c.234C>T	c.(232-234)tgC>tgT	p.C78C		NM_001207006.2|NM_021803.3	NP_001193935.1|NP_068575.1	Q9HBE4	IL21_HUMAN	interleukin 21	71					cell maturation (GO:0048469)|immune response (GO:0006955)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	cytokine receptor binding (GO:0005126)|interleukin-2 receptor binding (GO:0005134)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(3)	8						CCTTCTGAAAGCAGGAAAAAG	0.343													A|||	4209	0.840455	0.9531	0.817	5008	,	,		20616	0.8869		0.6581	False		,,,				2504	0.8446				p.C78C		Atlas-SNP	.											.	IL21	16	.	0			c.C234T						PASS	.	A	,	4045,361	183.6+/-211.2	1861,323,19	122.0	120.0	121.0		234,234	5.1	1.0	4	dbSNP_111	121	5909,2691	430.5+/-356.5	2021,1867,412	no	coding-synonymous,coding-synonymous	IL21	NM_001207006.1,NM_021803.2	,	3882,2190,431	AA,AG,GG		31.2907,8.1934,23.4661	,	78/154,78/163	123536963	9954,3052	2203	4300	6503	SO:0001819	synonymous_variant	59067	exon3			CTGAAAGCAGGAA	AF254069	CCDS3727.1, CCDS75189.1	4q26-q27	2011-07-15			ENSG00000138684	ENSG00000138684		"""Interleukins and interleukin receptors"""	6005	protein-coding gene	gene with protein product		605384				11081504, 17947662	Standard	NM_001207006		Approved	Za11, IL-21	uc003ies.3	Q9HBE4	OTTHUMG00000133073	ENST00000264497.3:c.234C>T	4.37:g.123536963G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_001207006	A5J0L4	Silent	SNP	ENST00000264497.3	37	CCDS3727.1																																																																																			G|0.208;A|0.792	0.792	strong		0.343	IL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256713.1	NM_021803	
EFCAB13	124989	hgsc.bcm.edu	37	17	45447832	45447832	+	Missense_Mutation	SNP	A	A	G	rs55853213	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45447832A>G	ENST00000331493.2	+	11	1246	c.835A>G	c.(835-837)Ata>Gta	p.I279V	EFCAB13_ENST00000517484.1_Missense_Mutation_p.I183V	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	279			I -> V (in dbSNP:rs55853213).			cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TGGGGATATTATATTTACTTT	0.299													A|||	312	0.0623003	0.0257	0.0821	5008	,	,		15853	0.1091		0.0517	False		,,,				2504	0.0603				p.I279V		Atlas-SNP	.											C17orf57,NS,carcinoma,-2,1	.	.	1	0			c.A835G						scavenged	.	A	VAL/ILE,VAL/ILE	129,4277	96.2+/-134.9	5,119,2079	134.0	143.0	140.0		547,835	-4.0	0.1	17	dbSNP_129	140	508,8088	144.2+/-200.1	18,472,3808	yes	missense,missense	C17orf57	NM_001195192.1,NM_152347.4	29,29	23,591,5887	GG,GA,AA		5.9097,2.9278,4.8992	benign,benign	183/785,279/974	45447832	637,12365	2203	4298	6501	SO:0001583	missense	124989	exon11			GATATTATATTTA	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.835A>G	17.37:g.45447832A>G	ENSP00000332111:p.Ile279Val	Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_152347	G3V128|Q49AG9	Missense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	138	0.06318681318681318	14	0.028455284552845527	21	0.058011049723756904	62	0.10839160839160839	41	0.05408970976253298	A	10.46	1.356387	0.24598	0.029278	0.059097	ENSG00000178852	ENST00000331493;ENST00000517484;ENST00000344176	T;T	0.66638	0.81;-0.22	3.86	-4.0	0.04057	EF-hand-like domain (1);	0.289542	0.24573	N	0.037371	T	0.00967	0.0032	N	0.21097	0.63	0.51767	P	6.20000000000065E-5	B;B;B	0.22541	0.041;0.071;0.026	B;B;B	0.20955	0.022;0.032;0.019	T	0.01545	-1.1328	9	0.87932	D	0	-4.0559	5.0206	0.14360	0.3941:0.0:0.4512:0.1547	rs55853213	231;279;183	Q8N7U2;Q8IY85;G3V128	.;CQ057_HUMAN;.	V	279;183;231	ENSP00000332111:I279V;ENSP00000430048:I183V	ENSP00000332111:I279V	I	+	1	0	C17orf57	42802831	0.018000	0.18449	0.132000	0.22025	0.326000	0.28443	-1.738000	0.01842	-1.067000	0.03160	-1.573000	0.00871	ATA	A|0.942;G|0.058	0.058	strong		0.299	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10574796	10574796	+	Missense_Mutation	SNP	C	C	T	rs9932051	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10574796C>T	ENST00000396560.2	+	11	1837	c.1610C>T	c.(1609-1611)aCc>aTc	p.T537I	ATF7IP2_ENST00000543967.1_Missense_Mutation_p.T81I|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.P515S|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.P515S|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.T537I	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	537			T -> I (in dbSNP:rs9932051).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AAGGAAACAACCCCATTGGCA	0.408													C|||	506	0.101038	0.1921	0.0216	5008	,	,		16818	0.126		0.0219	False		,,,				2504	0.09				p.T537I		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.C1610T						PASS	.	C	ILE/THR	778,3616	314.9+/-293.9	73,632,1492	110.0	110.0	110.0		1610	-6.5	0.0	16	dbSNP_119	110	205,8395	87.9+/-150.2	4,197,4099	yes	missense	ATF7IP2	NM_024997.2	89	77,829,5591	TT,TC,CC		2.3837,17.706,7.565	benign	537/683	10574796	983,12011	2197	4300	6497	SO:0001583	missense	80063	exon11			AAACAACCCCATT	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.1610C>T	16.37:g.10574796C>T	ENSP00000379808:p.Thr537Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	186|186	0.08516483516483517|0.08516483516483517	100|100	0.2032520325203252|0.2032520325203252	12|12	0.03314917127071823|0.03314917127071823	66|66	0.11538461538461539|0.11538461538461539	8|8	0.010554089709762533|0.010554089709762533	C|C	3.500|3.500	-0.102086|-0.102086	0.06967|0.06967	0.17706|0.17706	0.023837|0.023837	ENSG00000166669|ENSG00000166669	ENST00000396559;ENST00000324570|ENST00000543967;ENST00000396560;ENST00000356427	.|T;T;T	.|0.23950	.|1.9;1.88;1.88	4.56|4.56	-6.53|-6.53	0.01866|0.01866	.|.	.|0.923454	.|0.09035	.|N	.|0.858155	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.17082|0.17082	0.46|0.46	0.80722|0.80722	P|P	0.0|0.0	B|B	0.06786|0.10296	0.001|0.003	B|B	0.04013|0.11329	0.001|0.006	T|T	0.40232|0.40232	-0.9574|-0.9574	7|9	0.87932|0.33940	D|T	0|0.23	0.0216|0.0216	0.0575|0.0575	0.00014|0.00014	0.3008:0.1907:0.2347:0.2737|0.3008:0.1907:0.2347:0.2737	rs9932051;rs52804635;rs9932051|rs9932051;rs52804635;rs9932051	515|537	Q5U623-2|Q5U623	.|MCAF2_HUMAN	S|I	515|81;537;537	.|ENSP00000446119:T81I;ENSP00000379808:T537I;ENSP00000348799:T537I	ENSP00000322811:P515S|ENSP00000348799:T537I	P|T	+|+	1|2	0|0	ATF7IP2|ATF7IP2	10482297|10482297	0.001000|0.001000	0.12720|0.12720	0.009000|0.009000	0.14445|0.14445	0.133000|0.133000	0.20885|0.20885	-0.945000|-0.945000	0.03909|0.03909	-0.831000|-0.831000	0.04256|0.04256	-0.244000|-0.244000	0.11960|0.11960	CCC|ACC	C|0.913;N|0.001	.	strong		0.408	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
ZNF880	400713	hgsc.bcm.edu	37	19	52888049	52888049	+	Missense_Mutation	SNP	C	C	A	rs75346003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:52888049C>A	ENST00000422689.2	+	4	1231	c.1216C>A	c.(1216-1218)Caa>Aaa	p.Q406K		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	406					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						CACGGGAGAGCAACCTTACAA	0.398																																					p.Q406K		Atlas-SNP	.											ZNF880,colon,carcinoma,-1,2	ZNF880	45	2	0			c.C1216A						scavenged	.						69.0	63.0	65.0					19																	52888049		1568	3582	5150	SO:0001583	missense	400713	exon4			GGAGAGCAACCTT	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.1216C>A	19.37:g.52888049C>A	ENSP00000406318:p.Gln406Lys	Somatic	20	4	0.2		WXS	Illumina HiSeq	Phase_I	38	9	0.236842	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.634723	0.00114	.	.	ENSG00000221923	ENST00000422689	T	0.10860	2.83	1.84	0.731	0.18277	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01835	0.0058	N	0.00128	-2.045	0.20638	N	0.999879	B	0.17667	0.023	B	0.14023	0.01	T	0.46105	-0.9215	8	.	.	.	.	6.7224	0.23338	0.7399:0.2601:0.0:0.0	.	406	Q6PDB4	ZN880_HUMAN	K	406	ENSP00000406318:Q406K	.	Q	+	1	0	ZNF880	57579861	0.006000	0.16342	0.407000	0.26434	0.151000	0.21798	0.708000	0.25719	0.007000	0.14760	-0.493000	0.04662	CAA	C|0.872;A|0.128	0.128	strong		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43891639	43891639	+	Silent	SNP	G	G	A	rs200586830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:43891639G>A	ENST00000377564.3	+	17	3075	c.2682G>A	c.(2680-2682)caG>caA	p.Q894Q		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	894	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						AAGTTGATCAGCTTCCTCAGA	0.507													G|||	1197	0.239018	0.0885	0.3703	5008	,	,		15500	0.1508		0.338	False		,,,				2504	0.3384				p.Q894Q		Atlas-SNP	.											CNTNAP3B,NS,carcinoma,0,1	CNTNAP3B	37	1	0			c.G2682A						scavenged	.																																			SO:0001819	synonymous_variant	728577	exon17			TGATCAGCTTCCT	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.2682G>A	9.37:g.43891639G>A		Somatic	567	0	0		WXS	Illumina HiSeq	Phase_I	830	283	0.340964	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Silent	SNP	ENST00000377564.3	37	CCDS55312.1	.	.	.	.	.	.	.	.	.	.	G	3.543	-0.093219	0.07053	.	.	ENSG00000154529	ENST00000377561	.	.	.	2.67	0.632	0.17705	.	.	.	.	.	T	0.39572	0.1083	.	.	.	0.09310	P	0.999999999870063	.	.	.	.	.	.	T	0.45977	-0.9224	3	.	.	.	.	6.8519	0.24020	0.3621:0.0:0.6379:0.0	.	.	.	.	N	943	.	.	S	+	2	0	CNTNAP3B	43831635	0.966000	0.33281	0.086000	0.20670	0.722000	0.41435	1.539000	0.36104	0.030000	0.15379	0.121000	0.15741	AGC	.	.	weak		0.507	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
DMBX1	127343	hgsc.bcm.edu	37	1	46976717	46976717	+	Silent	SNP	C	C	T	rs12045245	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46976717C>T	ENST00000360032.3	+	3	458	c.444C>T	c.(442-444)gcC>gcT	p.A148A	DMBX1_ENST00000371956.4_Silent_p.A153A	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					AAGGCAAGGCCGAGGCCCCCA	0.637													C|||	1516	0.302716	0.4924	0.1916	5008	,	,		17349	0.2718		0.175	False		,,,				2504	0.2883				p.A153A		Atlas-SNP	.											.	DMBX1	50	.	0			c.C459T						PASS	.	C	,	1891,2515	537.0+/-374.6	392,1107,704	51.0	61.0	58.0		459,444	-9.7	0.0	1	dbSNP_120	58	1401,7199	269.1+/-288.2	146,1109,3045	no	coding-synonymous,coding-synonymous	DMBX1	NM_147192.2,NM_172225.1	,	538,2216,3749	TT,TC,CC		16.2907,42.9187,25.3114	,	153/383,148/378	46976717	3292,9714	2203	4300	6503	SO:0001819	synonymous_variant	127343	exon3			CAAGGCCGAGGCC	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"""Homeoboxes / PRD class"""	19026	protein-coding gene	gene with protein product		607410	"""orthodenticle homolog 3 (Drosophila)"""	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.444C>T	1.37:g.46976717C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	148	62	0.418919	NM_147192		Silent	SNP	ENST00000360032.3	37	CCDS536.1																																																																																			C|0.749;T|0.251	0.251	strong		0.637	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1		
ADAMTS18	170692	hgsc.bcm.edu	37	16	77323235	77323235	+	Missense_Mutation	SNP	C	C	G	rs3743749	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:77323235C>G	ENST00000282849.5	-	22	3894	c.3476G>C	c.(3475-3477)aGt>aCt	p.S1159T	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1159	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		S -> T (in dbSNP:rs3743749).		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GAGCAGACAACTTGAGGAAGG	0.547													C|||	911	0.181909	0.2103	0.1254	5008	,	,		16523	0.2212		0.1451	False		,,,				2504	0.181				p.S1159T		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G3476C						PASS	.	C	THR/SER	923,3473	352.3+/-311.7	94,735,1369	113.0	119.0	117.0		3476	4.8	0.0	16	dbSNP_107	117	1217,7383	247.4+/-275.4	84,1049,3167	yes	missense	ADAMTS18	NM_199355.2	58	178,1784,4536	GG,GC,CC		14.1512,20.9964,16.4666	possibly-damaging	1159/1222	77323235	2140,10856	2198	4300	6498	SO:0001583	missense	170692	exon22			AGACAACTTGAGG	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3476G>C	16.37:g.77323235C>G	ENSP00000282849:p.Ser1159Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	366	0.16758241758241757	108	0.21951219512195122	53	0.1464088397790055	105	0.18356643356643357	100	0.13192612137203166	C	19.99	3.928362	0.73327	0.209964	0.141512	ENSG00000140873	ENST00000282849	T	0.61274	0.12	5.77	4.82	0.62117	.	0.154637	0.56097	D	0.000026	T	0.00039	0.0001	L	0.41415	1.275	0.47037	P	7.059999999999844E-4	B	0.25007	0.116	B	0.30401	0.115	T	0.07347	-1.0777	9	0.28530	T	0.3	.	13.7821	0.63089	0.0:0.9264:0.0:0.0736	rs3743749;rs17687094;rs3743749	1159	Q8TE60	ATS18_HUMAN	T	1159	ENSP00000282849:S1159T	ENSP00000282849:S1159T	S	-	2	0	ADAMTS18	75880736	0.197000	0.23362	0.006000	0.13384	0.821000	0.46438	3.104000	0.50306	1.443000	0.47586	0.557000	0.71058	AGT	C|0.827;G|0.173	0.173	strong		0.547	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
ZDBF2	57683	hgsc.bcm.edu	37	2	207175070	207175070	+	Missense_Mutation	SNP	G	G	A	rs138061259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:207175070G>A	ENST00000374423.3	+	5	6204	c.5818G>A	c.(5818-5820)Gcg>Acg	p.A1940T		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1940							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						ATGCCAGACAGCGAAAATCAG	0.448													G|||	52	0.0103834	0.0015	0.0115	5008	,	,		19095	0.0		0.0268	False		,,,				2504	0.0153				p.A1940T		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G5818A						PASS	.	G	THR/ALA	32,3824		1,30,1897	76.0	76.0	76.0		5818	3.7	0.0	2	dbSNP_134	76	303,7979		11,281,3849	yes	missense	ZDBF2	NM_020923.1	58	12,311,5746	AA,AG,GG		3.6585,0.8299,2.7599	benign	1940/2355	207175070	335,11803	1928	4141	6069	SO:0001583	missense	57683	exon5			CAGACAGCGAAAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5818G>A	2.37:g.207175070G>A	ENSP00000363545:p.Ala1940Thr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	161	67	0.416149	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	27	0.012362637362637362	0	0.0	3	0.008287292817679558	0	0.0	24	0.0316622691292876	G	6.504	0.461202	0.12342	0.008299	0.036585	ENSG00000204186	ENST00000374423	T	0.44482	0.92	5.56	3.68	0.42216	.	.	.	.	.	T	0.07548	0.0190	N	0.22421	0.69	0.09310	N	1	B	0.30326	0.276	B	0.25614	0.062	T	0.05289	-1.0894	9	0.54805	T	0.06	.	10.475	0.44659	0.0746:0.1338:0.7915:0.0	.	1940	Q9HCK1	ZDBF2_HUMAN	T	1940	ENSP00000363545:A1940T	ENSP00000363545:A1940T	A	+	1	0	ZDBF2	206883315	0.873000	0.30073	0.000000	0.03702	0.002000	0.02628	2.510000	0.45468	0.654000	0.30846	0.558000	0.71614	GCG	G|0.981;A|0.019	0.019	strong		0.448	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
COL5A3	50509	hgsc.bcm.edu	37	19	10106936	10106936	+	Silent	SNP	G	G	C	rs1559186	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10106936G>C	ENST00000264828.3	-	14	1510	c.1425C>G	c.(1423-1425)ctC>ctG	p.L475L	CTD-2553C6.1_ENST00000592332.1_RNA	NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	475	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CTTTCATAGAGAGCTGGAAAG	0.597													G|||	1978	0.394968	0.6256	0.3689	5008	,	,		16292	0.3403		0.3221	False		,,,				2504	0.2331				p.L475L		Atlas-SNP	.											.	COL5A3	243	.	0			c.C1425G						PASS	.	G		2545,1855		749,1047,404	20.0	24.0	23.0		1425	-11.3	0.1	19	dbSNP_88	23	2898,5686		493,1912,1887	no	coding-synonymous	COL5A3	NM_015719.3		1242,2959,2291	CC,CG,GG		33.7605,42.1591,41.9208		475/1746	10106936	5443,7541	2200	4292	6492	SO:0001819	synonymous_variant	50509	exon14			CATAGAGAGCTGG	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.1425C>G	19.37:g.10106936G>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			G|0.601;C|0.399	0.399	strong		0.597	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
ROS1	6098	hgsc.bcm.edu	37	6	117708971	117708971	+	Silent	SNP	C	C	T	rs9489143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:117708971C>T	ENST00000368508.3	-	13	2184	c.1986G>A	c.(1984-1986)gaG>gaA	p.E662E	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Silent_p.E657E	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	662	Fibronectin type-III 3. {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)		CCACTGAGGGCTCTGACCAGG	0.488			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								C|||	323	0.0644968	0.0295	0.0778	5008	,	,		17947	0.0308		0.0924	False		,,,				2504	0.1084				p.E662E		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.G1986A						PASS	.	C		156,4250	106.0+/-144.5	5,146,2052	86.0	89.0	88.0		1986	-0.6	1.0	6	dbSNP_119	88	652,7948	165.5+/-217.6	23,606,3671	no	coding-synonymous	ROS1	NM_002944.2		28,752,5723	TT,TC,CC		7.5814,3.5406,6.2125		662/2348	117708971	808,12198	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon13			TGAGGGCTCTGAC	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.1986G>A	6.37:g.117708971C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	157	77	0.490446	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			C|0.933;T|0.067	0.067	strong		0.488	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
CDHR2	54825	hgsc.bcm.edu	37	5	176002542	176002542	+	Silent	SNP	C	C	T	rs41275281	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:176002542C>T	ENST00000510636.1	+	10	1078	c.804C>T	c.(802-804)ggC>ggT	p.G268G	CDHR2_ENST00000261944.5_Silent_p.G268G|CDHR2_ENST00000506348.1_Silent_p.G268G	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	268	Cadherin 3. {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						CTGTGGATGGCGACAAAGGCA	0.652													C|||	606	0.121006	0.118	0.085	5008	,	,		17369	0.1597		0.0706	False		,,,				2504	0.1626				p.G268G		Atlas-SNP	.											CDHR2,NS,carcinoma,0,1	CDHR2	152	1	0			c.C804T						PASS	.	C	,	470,3936	222.0+/-238.9	22,426,1755	102.0	109.0	107.0		804,804	-8.6	0.0	5	dbSNP_127	107	483,8117	140.8+/-197.2	10,463,3827	no	coding-synonymous,coding-synonymous	CDHR2	NM_001171976.1,NM_017675.4	,	32,889,5582	TT,TC,CC		5.6163,10.6673,7.3274	,	268/1311,268/1311	176002542	953,12053	2203	4300	6503	SO:0001819	synonymous_variant	54825	exon10			GGATGGCGACAAA	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.804C>T	5.37:g.176002542C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_017675	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	37	CCDS34297.1																																																																																			C|0.917;T|0.083	0.083	strong		0.652	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
VWC2	375567	hgsc.bcm.edu	37	7	49842377	49842377	+	Missense_Mutation	SNP	A	A	C	rs79731913	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:49842377A>C	ENST00000340652.4	+	3	1323	c.767A>C	c.(766-768)cAg>cCg	p.Q256P		NM_198570.3	NP_940972.2	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	256	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|basement membrane (GO:0005604)|cell junction (GO:0030054)|extracellular space (GO:0005615)|interstitial matrix (GO:0005614)|synapse (GO:0045202)				cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8						GCGTGTCCCCAGACGGAGTGT	0.562													A|||	96	0.0191693	0.0015	0.036	5008	,	,		21290	0.0		0.0636	False		,,,				2504	0.0051				p.Q256P		Atlas-SNP	.											.	VWC2	30	.	0			c.A767C						PASS	.	A	PRO/GLN	51,4355	52.9+/-88.7	0,51,2152	289.0	198.0	229.0		767	5.3	1.0	7	dbSNP_131	229	512,8088	145.6+/-201.3	20,472,3808	yes	missense	VWC2	NM_198570.3	76	20,523,5960	CC,CA,AA		5.9535,1.1575,4.3288	benign	256/326	49842377	563,12443	2203	4300	6503	SO:0001583	missense	375567	exon3			GTCCCCAGACGGA	AY358393	CCDS5508.1	7p12.3-p12.2	2007-07-19			ENSG00000188730	ENSG00000188730			30200	protein-coding gene	gene with protein product	"""brorin"", ""brain-specific chordin-like"""	611108				17400546	Standard	NM_198570		Approved	PSST739, UNQ739	uc003tot.1	Q2TAL6	OTTHUMG00000129265	ENST00000340652.4:c.767A>C	7.37:g.49842377A>C	ENSP00000341819:p.Gln256Pro	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_198570	Q6UXE2	Missense_Mutation	SNP	ENST00000340652.4	37	CCDS5508.1	58	0.026556776556776556	0	0.0	14	0.03867403314917127	0	0.0	44	0.05804749340369393	A	13.13	2.146361	0.37923	0.011575	0.059535	ENSG00000188730	ENST00000340652	T	0.14266	2.52	5.32	5.32	0.75619	von Willebrand factor, type C (4);	0.000000	0.64402	D	0.000001	T	0.00524	0.0017	N	0.00869	-1.13	0.49051	D	0.99974	B	0.23185	0.081	B	0.26094	0.066	T	0.49532	-0.8930	10	0.15066	T	0.55	.	15.299	0.73931	1.0:0.0:0.0:0.0	.	256	Q2TAL6	VWC2_HUMAN	P	256	ENSP00000341819:Q256P	ENSP00000341819:Q256P	Q	+	2	0	VWC2	49812923	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.175000	0.65021	2.011000	0.59026	0.528000	0.53228	CAG	A|0.958;C|0.042	0.042	strong		0.562	VWC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251375.2	NM_198570	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362104	105362104	+	Silent	SNP	G	G	A	rs111908946|rs11191741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105362104G>A	ENST00000369774.4	-	15	3147	c.2871C>T	c.(2869-2871)ttC>ttT	p.F957F	SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000540321.1_Silent_p.F824F|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000538130.1_Silent_p.F792F|SH3PXD2A_ENST00000355946.2_Silent_p.F929F			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	957					superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		AGGTCTTGCCGAAGCCCCCGG	0.642													G|||	1618	0.323083	0.1067	0.3559	5008	,	,		18050	0.3502		0.3519	False		,,,				2504	0.5348				p.F929F		Atlas-SNP	.											SH3PXD2A,NS,neuroblastoma,0,1	SH3PXD2A	90	1	0			c.C2787T						PASS	.	G		686,3720	284.9+/-277.9	56,574,1573	58.0	54.0	55.0		2787	1.1	0.5	10	dbSNP_120	55	3046,5554	457.7+/-364.4	553,1940,1807	no	coding-synonymous	SH3PXD2A	NM_014631.2		609,2514,3380	AA,AG,GG		35.4186,15.5697,28.6944		929/1106	105362104	3732,9274	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			CTTGCCGAAGCCC	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.2871C>T	10.37:g.105362104G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		605	0.27701465201465203	61	0.12398373983739837	122	0.3370165745856354	163	0.28496503496503495	259	0.341688654353562	G	0.009	-1.848781	0.00563	0.155697	0.354186	ENSG00000107957	ENST00000420222	.	.	.	5.02	1.13	0.20643	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999883335	.	.	.	.	.	.	T	0.39099	-0.9630	3	.	.	.	-29.7996	8.6238	0.33877	0.544:0.0:0.456:0.0	rs11191741;rs17339506;rs11191741	.	.	.	W	884	.	.	R	-	1	2	SH3PXD2A	105352094	0.074000	0.21230	0.499000	0.27577	0.147000	0.21601	0.484000	0.22308	-0.041000	0.13558	-0.969000	0.02612	CGG	G|0.718;A|0.282	0.282	strong		0.642	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
HLA-A	3105	hgsc.bcm.edu	37	6	29911119	29911119	+	Missense_Mutation	SNP	G	G	C	rs3173419	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29911119G>C	ENST00000396634.1	+	5	759	c.418G>C	c.(418-420)Gac>Cac	p.D140H	HLA-A_ENST00000376809.5_Missense_Mutation_p.D140H|HLA-A_ENST00000376806.5_Missense_Mutation_p.D140H|HLA-A_ENST00000376802.2_Missense_Mutation_p.D140H			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	140	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GTACCGGCAGGACGCCTACGA	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	273	0.0545128	0.1399	0.0461	5008	,	,		11816	0.0159		0.0308	False		,,,				2504	0.0092				p.D140H		Atlas-SNP	.											.	HLA-A	89	.	0			c.G418C						PASS	.						36.0	27.0	30.0					6																	29911119		1496	2698	4194	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGGCAGGACGCCT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.418G>C	6.37:g.29911119G>C	ENSP00000379873:p.Asp140His	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	185	62	0.335135	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	0.014	-1.580111	0.00879	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00009	9.49;9.49;9.49;9.49	3.78	-7.56	0.01322	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	79.907900	0.01339	U	0.011517	T	0.00039	0.0001	L	0.47190	1.495	0.09310	N	1	B;B;B;B;B;B	0.16603	0.018;0.001;0.001;0.003;0.003;0.001	B;B;B;B;B;B	0.26969	0.064;0.051;0.061;0.075;0.075;0.051	T	0.10706	-1.0618	10	0.23302	T	0.38	.	5.3314	0.15934	0.102:0.2286:0.5197:0.1496	rs3173419;rs3175999;rs16896879;rs28749152;rs41549418	19;140;140;140;140;140	B4DVB9;P13746;Q5SRN7;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;.;1A36_HUMAN;1A03_HUMAN	H	140	ENSP00000379873:D140H;ENSP00000366002:D140H;ENSP00000366005:D140H;ENSP00000365998:D140H	ENSP00000365998:D140H	D	+	1	0	HLA-A	30019098	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-9.138000	0.00013	-2.332000	0.00632	-4.658000	0.00004	GAC	C|0.006;G|0.577;T|0.416	0.006	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
MAP7D3	79649	hgsc.bcm.edu	37	X	135313034	135313034	+	Missense_Mutation	SNP	T	T	G	rs1055497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:135313034T>G	ENST00000316077.9	-	9	1725	c.1505A>C	c.(1504-1506)gAa>gCa	p.E502A	MAP7D3_ENST00000495432.1_5'Flank|MAP7D3_ENST00000370661.1_Missense_Mutation_p.E467A|MAP7D3_ENST00000370663.5_Missense_Mutation_p.E484A	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	502			E -> A (in dbSNP:rs1055497). {ECO:0000269|PubMed:15489334}.		microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					ACAAGCATTTTCAGGAGATGA	0.413													g|||	2070	0.548344	0.3676	0.3732	3775	,	,		12866	0.5427		0.4105	False		,,,				2504	0.3732				p.E502A		Atlas-SNP	.											.	MAP7D3	102	.	0			c.A1505C						PASS	.		ALA/GLU,ALA/GLU,ALA/GLU	1761,1645		385,701,290,332,280	162.0	143.0	149.0		1451,1400,1505	1.0	0.0	X	dbSNP_86	149	3552,2957		744,1111,953,501,844	yes	missense,missense,missense	MAP7D3	NM_001173516.1,NM_001173517.1,NM_024597.3	107,107,107	1129,1812,1243,833,1124	GG,GT,G,TT,T		45.4294,48.2971,46.4145	benign,benign,benign	484/859,467/842,502/877	135313034	5313,4602	1988	4153	6141	SO:0001583	missense	79649	exon9			GCATTTTCAGGAG	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1505A>C	X.37:g.135313034T>G	ENSP00000318086:p.Glu502Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	943	0.568414707655214	112	0.2916666666666667	95	0.35984848484848486	202	0.543010752688172	227	0.4127272727272727	g	0.095	-1.160453	0.01686	0.517029	0.545706	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.04317	4.28;3.65;3.65;3.82	5.8	1.03	0.20045	.	0.900171	0.09038	N	0.857688	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.41998	-0.9477	9	0.02654	T	1	-0.5443	3.6492	0.08196	0.3154:0.0:0.4123:0.2723	rs1055497;rs3174434;rs17846288;rs17859312;rs52828368;rs60930052;rs1055497	484;461;502;467	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	A	467;502;484;461	ENSP00000359695:E467A;ENSP00000318086:E502A;ENSP00000359697:E484A;ENSP00000359694:E461A	ENSP00000318086:E502A	E	-	2	0	MAP7D3	135140700	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.932000	0.28884	-0.527000	0.06374	-1.902000	0.00527	GAA	0|0.026;G|0.527	0.527	strong		0.413	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
DCHS2	54798	hgsc.bcm.edu	37	4	155243573	155243573	+	Silent	SNP	C	C	T	rs13109747	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155243573C>T	ENST00000357232.4	-	13	2720	c.2721G>A	c.(2719-2721)tcG>tcA	p.S907S		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	907	Cadherin 7. {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)		TATAATCATACGAAAGTATTG	0.378													T|||	3951	0.788938	0.4501	0.9135	5008	,	,		19859	0.8849		0.9105	False		,,,				2504	0.9346				p.S907S		Atlas-SNP	.											DCHS2,NS,carcinoma,-1,2	DCHS2	594	2	0			c.G2721A						PASS	.	T		2321,2085	573.5+/-383.5	624,1073,506	177.0	149.0	159.0		2721	-11.5	0.0	4	dbSNP_121	159	7874,726	176.5+/-226.3	3601,672,27	no	coding-synonymous	DCHS2	NM_017639.3		4225,1745,533	TT,TC,CC		8.4419,47.3218,21.6131		907/2917	155243573	10195,2811	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon13			ATCATACGAAAGT	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.2721G>A	4.37:g.155243573C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			C|0.217;T|0.783	0.783	strong		0.378	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101815888	101815888	+	Silent	SNP	T	T	C	rs150189521	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:101815888T>C	ENST00000506729.1	-	2	780	c.609A>G	c.(607-609)ggA>ggG	p.G203G	SLCO6A1_ENST00000514551.1_Intron|SLCO6A1_ENST00000379807.3_Silent_p.G203G|SLCO6A1_ENST00000513675.1_Silent_p.G203G|SLCO6A1_ENST00000389019.3_Silent_p.G203G|SLCO6A1_ENST00000379810.1_Silent_p.G203G			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	203						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)		TACCTTCAATTCCTACCTTAC	0.299													T|||	12	0.00239617	0.0008	0.0029	5008	,	,		18321	0.0		0.0089	False		,,,				2504	0.0				p.G203G		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.A609G						PASS	.	T		8,4394	11.4+/-27.6	0,8,2193	66.0	68.0	68.0		609	0.4	0.0	5	dbSNP_134	68	81,8513	37.8+/-93.5	0,81,4216	no	coding-synonymous	SLCO6A1	NM_173488.3		0,89,6409	CC,CT,TT		0.9425,0.1817,0.6848		203/720	101815888	89,12907	2201	4297	6498	SO:0001819	synonymous_variant	133482	exon2			TTCAATTCCTACC	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.609A>G	5.37:g.101815888T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																			T|0.994;C|0.006	0.006	strong		0.299	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
PLIN4	729359	hgsc.bcm.edu	37	19	4510560	4510560	+	Missense_Mutation	SNP	C	C	T	rs7251858	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4510560C>T	ENST00000301286.3	-	3	3369	c.3370G>A	c.(3370-3372)Gcc>Acc	p.A1124T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1124			A -> T (in dbSNP:rs7251858). {ECO:0000269|PubMed:11572484}.			cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TGTGTGGTGGCCAAAAGCCCC	0.657													C|||	1776	0.354633	0.27	0.304	5008	,	,		15490	0.5645		0.3091	False		,,,				2504	0.3354				p.A1124T		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.G3370A						PASS	.	C	THR/ALA	1202,3044		173,856,1094	38.0	44.0	42.0		3370	1.5	0.0	19	dbSNP_116	42	2576,5880		397,1782,2049	yes	missense	PLIN4	NM_001080400.1	58	570,2638,3143	TT,TC,CC		30.4636,28.309,29.7433	possibly-damaging	1124/1358	4510560	3778,8924	2123	4228	6351	SO:0001583	missense	729359	exon3			TGGTGGCCAAAAG	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.3370G>A	19.37:g.4510560C>T	ENSP00000301286:p.Ala1124Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	131	128	0.977099	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	792	0.3626373626373626	121	0.2459349593495935	119	0.3287292817679558	322	0.5629370629370629	230	0.3034300791556728	C	15.40	2.823443	0.50739	0.28309	0.304636	ENSG00000167676	ENST00000301286	T	0.10763	2.84	2.67	1.51	0.23008	.	0.243249	0.21268	N	0.077365	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.47762	0.9	P	0.44518	0.452	T	0.31052	-0.9957	9	0.27082	T	0.32	.	3.8559	0.08974	0.0:0.7687:0.0:0.2313	rs7251858;rs61171079;rs7251858	1124	Q96Q06	PLIN4_HUMAN	T	1124	ENSP00000301286:A1124T	ENSP00000301286:A1124T	A	-	1	0	PLIN4	4461560	0.000000	0.05858	0.015000	0.15790	0.007000	0.05969	0.396000	0.20867	1.353000	0.45828	0.511000	0.50034	GCC	C|0.660;T|0.340	0.340	strong		0.657	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ZNF354B	117608	hgsc.bcm.edu	37	5	178294060	178294060	+	Missense_Mutation	SNP	G	G	A	rs11955074|rs386695542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:178294060G>A	ENST00000322434.3	+	4	470	c.244G>A	c.(244-246)Gtc>Atc	p.V82I		NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGTTCTGGTGTCTCCTCTCT	0.507													G|||	592	0.118211	0.2655	0.1066	5008	,	,		17688	0.0		0.1213	False		,,,				2504	0.046				p.V82I		Atlas-SNP	.											.	ZNF354B	67	.	0			c.G244A						PASS	.	G	ILE/VAL	925,3481		122,681,1400	147.0	138.0	141.0		244	0.8	0.0	5	dbSNP_120	141	911,7689		64,783,3453	yes	missense	ZNF354B	NM_058230.2	29	186,1464,4853	AA,AG,GG		10.593,20.9941,14.1166	benign	82/613	178294060	1836,11170	2203	4300	6503	SO:0001583	missense	117608	exon4			TCTGGTGTCTCCT	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.244G>A	5.37:g.178294060G>A	ENSP00000327143:p.Val82Ile	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	240	125	0.520833	NM_058230	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	37	CCDS4439.1	218	0.09981684981684982	113	0.22967479674796748	35	0.09668508287292818	0	0.0	70	0.09234828496042216	G	3.804	-0.041079	0.07452	0.209941	0.10593	ENSG00000178338	ENST00000322434;ENST00000520377	T;T	0.05580	3.42;6.24	3.74	0.785	0.18584	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.14012	0.009	B	0.11329	0.006	T	0.46091	-0.9216	8	0.48119	T	0.1	.	4.3661	0.11225	0.211:0.0:0.6034:0.1855	rs11955074;rs57002972	82	Q96LW1	Z354B_HUMAN	I	82	ENSP00000327143:V82I;ENSP00000429827:V82I	ENSP00000327143:V82I	V	+	1	0	ZNF354B	178226666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.168000	0.16622	0.027000	0.15297	-0.671000	0.03813	GTC	G|0.854;A|0.146	0.146	strong		0.507	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
CLEC4C	170482	hgsc.bcm.edu	37	12	7894056	7894056	+	Missense_Mutation	SNP	G	G	A	rs73056605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:7894056G>A	ENST00000542353.1	-	4	686	c.196C>T	c.(196-198)Cca>Tca	p.P66S	CLEC4C_ENST00000354629.5_Missense_Mutation_p.P35S|CLEC4C_ENST00000360345.3_Missense_Mutation_p.P66S|CLEC4C_ENST00000540085.1_Missense_Mutation_p.P35S	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	121	0	0		WXS	Illumina HiSeq	Phase_I	148	61	0.412162	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	
MKI67	4288	hgsc.bcm.edu	37	10	129921195	129921195	+	Silent	SNP	A	A	T	rs1063536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	178	0	0		WXS	Illumina HiSeq	Phase_I	205	97	0.473171	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	
EML1	2009	hgsc.bcm.edu	37	14	100317272	100317272	+	Silent	SNP	C	C	T	rs34803725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:100317272C>T	ENST00000262233.6	+	2	289	c.150C>T	c.(148-150)gaC>gaT	p.D50D	EML1_ENST00000334192.4_Silent_p.D50D|EML1_ENST00000556758.1_3'UTR|EML1_ENST00000327921.9_Silent_p.D19D	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	50					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)				TGCAAGAAGACGACATCCAGC	0.507													C|||	23	0.00459265	0.0008	0.0058	5008	,	,		21445	0.0		0.0139	False		,,,				2504	0.0041				p.D50D		Atlas-SNP	.											.	EML1	97	.	0			c.C150T						PASS	.	C	,	19,4387	25.3+/-52.1	0,19,2184	137.0	119.0	125.0		150,150	-8.2	0.4	14	dbSNP_126	125	225,8375	94.7+/-156.6	3,219,4078	no	coding-synonymous,coding-synonymous	EML1	NM_001008707.1,NM_004434.2	,	3,238,6262	TT,TC,CC		2.6163,0.4312,1.8761	,	50/835,50/816	100317272	244,12762	2203	4300	6503	SO:0001819	synonymous_variant	2009	exon2			AGAAGACGACATC	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.150C>T	14.37:g.100317272C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	150	63	0.42	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Silent	SNP	ENST00000262233.6	37	CCDS32155.1																																																																																			C|0.985;T|0.015	0.015	strong		0.507	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707	
SON	6651	hgsc.bcm.edu	37	21	34925689	34925689	+	Silent	SNP	G	G	A	rs61739710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:34925689G>A	ENST00000356577.4	+	3	4627	c.4152G>A	c.(4150-4152)ctG>ctA	p.L1384L	SON_ENST00000381679.4_Silent_p.L1384L|SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Silent_p.L1384L|SON_ENST00000290239.6_Silent_p.L1384L	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1384	4 X 8 AA tandem repeats of V-L-E-SS- [AVT]-VT.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						TAACTGTCCTGGAGCCTTCGG	0.567													G|||	881	0.175919	0.0189	0.2421	5008	,	,		20839	0.1637		0.3082	False		,,,				2504	0.2178				p.L1384L		Atlas-SNP	.											.	SON	343	.	0			c.G4152A						PASS	.	G	,	281,4125	156.6+/-189.7	10,261,1932	80.0	72.0	75.0		4152,4152	-5.8	0.0	21	dbSNP_129	75	2385,6215	396.7+/-345.5	322,1741,2237	no	coding-synonymous,coding-synonymous	SON	NM_032195.1,NM_138927.1	,	332,2002,4169	AA,AG,GG		27.7326,6.3777,20.4982	,	1384/2304,1384/2427	34925689	2666,10340	2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			TGTCCTGGAGCCT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.4152G>A	21.37:g.34925689G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	185	76	0.410811	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	37	CCDS13629.1	421	0.19276556776556777	14	0.028455284552845527	97	0.26795580110497236	86	0.15034965034965034	224	0.2955145118733509	G	3.643	-0.073046	0.07228	0.063777	0.277326	ENSG00000159140	ENST00000436227	.	.	.	4.95	-5.81	0.02340	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999058328	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.1717	0.15114	0.1924:0.0:0.3331:0.4745	rs61739710	.	.	.	X	379	.	.	W	+	2	0	SON	33847559	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.279000	0.02807	-1.193000	0.02688	-1.077000	0.02231	TGG	G|0.792;A|0.208	0.208	strong		0.567	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
FASN	2194	hgsc.bcm.edu	37	17	80045086	80045086	+	Silent	SNP	G	G	C	rs4485435	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80045086G>C	ENST00000306749.2	-	21	3485	c.3267C>G	c.(3265-3267)gcC>gcG	p.A1089A		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1089					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)	GGACGCCTCCGGCCACTGTGA	0.672													.|||	1117	0.223043	0.3222	0.4092	5008	,	,		11177	0.1121		0.2217	False		,,,				2504	0.0726				p.A1089A	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C3267G						PASS	.						18.0	19.0	19.0					17																	80045086		2185	4286	6471	SO:0001819	synonymous_variant	2194	exon21			GCCTCCGGCCACT	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.3267C>G	17.37:g.80045086G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			G|0.762;C|0.238	0.238	strong		0.672	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
DMP1	1758	hgsc.bcm.edu	37	4	88584148	88584148	+	Silent	SNP	C	C	T	rs2615498	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88584148C>T	ENST00000339673.6	+	6	1317	c.1218C>T	c.(1216-1218)agC>agT	p.S406S	DMP1_ENST00000282479.7_Silent_p.S390S|RP11-742B18.1_ENST00000507894.1_RNA|RP11-742B18.1_ENST00000506480.1_RNA|RP11-742B18.1_ENST00000506814.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	406					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)		AAGCAGACAGCGAATCCAGTG	0.557													C|||	880	0.175719	0.0431	0.1527	5008	,	,		20684	0.2401		0.1968	False		,,,				2504	0.2832				p.S406S		Atlas-SNP	.											.	DMP1	72	.	0			c.C1218T						PASS	.	C	,	322,4084	170.1+/-200.6	11,300,1892	91.0	95.0	94.0		1170,1218	-2.9	0.0	4	dbSNP_100	94	1646,6954	304.6+/-307.0	141,1364,2795	no	coding-synonymous,coding-synonymous	DMP1	NM_001079911.2,NM_004407.3	,	152,1664,4687	TT,TC,CC		19.1395,7.3082,15.1315	,	390/498,406/514	88584148	1968,11038	2203	4300	6503	SO:0001819	synonymous_variant	1758	exon6			AGACAGCGAATCC	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.1218C>T	4.37:g.88584148C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	66	0.594595	NM_004407	A1L4L3|O43265	Silent	SNP	ENST00000339673.6	37	CCDS3623.1																																																																																			C|0.850;T|0.150	0.150	strong		0.557	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1		
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296152	39296152	+	Silent	SNP	A	A	G	rs551614044	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39296152A>G	ENST00000345847.4	-	1	587	c.588T>C	c.(586-588)cgT>cgC	p.R196R		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	196						keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						AGCACAAGGGACGGGGGCAGG	0.597													a|||	234	0.0467252	0.0726	0.0504	5008	,	,		18042	0.0179		0.0298	False		,,,				2504	0.0562				p.R196R		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,0,1	KRTAP4-6	46	1	0			c.T588C						scavenged	.																																			SO:0001819	synonymous_variant	81871	exon1			CAAGGGACGGGGG	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.588T>C	17.37:g.39296152A>G		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	222	7	0.0315315	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			.	.	none		0.597	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
F11	2160	hgsc.bcm.edu	37	4	187205301	187205301	+	Silent	SNP	T	T	C	rs5970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187205301T>C	ENST00000403665.2	+	11	1543	c.1191T>C	c.(1189-1191)ggT>ggC	p.G397G	F11-AS1_ENST00000505103.1_RNA|F11_ENST00000264692.4_Silent_p.G345G	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	397	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	CTGTTCGTGGTGAGTGGCCGT	0.527													T|||	848	0.169329	0.2587	0.1369	5008	,	,		17990	0.0387		0.166	False		,,,				2504	0.2096				p.G397G		Atlas-SNP	.											.	F11	65	.	0			c.T1191C						PASS	.	T		947,3459	358.9+/-314.6	108,731,1364	145.0	130.0	135.0		1191	-9.9	0.0	4	dbSNP_52	135	1224,7376	245.8+/-274.5	91,1042,3167	no	coding-synonymous	F11	NM_000128.3		199,1773,4531	CC,CT,TT		14.2326,21.4934,16.6923		397/626	187205301	2171,10835	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon11			TCGTGGTGAGTGG	M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"""plasma thromboplastin antecedent"""	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.1191T>C	4.37:g.187205301T>C		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1																																																																																			T|0.839;C|0.161	0.161	strong		0.527	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4		
TBC1D32	221322	hgsc.bcm.edu	37	6	121629167	121629167	+	Silent	SNP	G	G	A	rs9398629	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:121629167G>A	ENST00000398212.2	-	5	694	c.645C>T	c.(643-645)tgC>tgT	p.C215C	TBC1D32_ENST00000275159.6_Silent_p.C215C	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	215					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCAGTTTTTCGCAGAGAGTAG	0.358													G|||	1581	0.315695	0.0885	0.2118	5008	,	,		15123	0.5863		0.2644	False		,,,				2504	0.4703				p.C215C		Atlas-SNP	.											.	C6orf170	146	.	0			c.C645T						PASS	.	G		468,3224		31,406,1409	107.0	100.0	102.0		645	0.8	1.0	6	dbSNP_119	102	2136,6054		270,1596,2229	no	coding-synonymous	C6orf170	NM_152730.4		301,2002,3638	AA,AG,GG		26.0806,12.6761,21.9155		215/1258	121629167	2604,9278	1846	4095	5941	SO:0001819	synonymous_variant	221322	exon5			TTTTTCGCAGAGA	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.645C>T	6.37:g.121629167G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	196	84	0.428571	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			G|0.704;A|0.296	0.296	strong		0.358	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
CREB3L1	90993	hgsc.bcm.edu	37	11	46339011	46339011	+	Missense_Mutation	SNP	G	G	A	rs35652107	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:46339011G>A	ENST00000529193.1	+	10	1682	c.1231G>A	c.(1231-1233)Gca>Aca	p.A411T	CREB3L1_ENST00000534616.1_3'UTR|CREB3L1_ENST00000288400.3_Missense_Mutation_p.A411T			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	47	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	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	
DIO1	1733	hgsc.bcm.edu	37	1	54359922	54359922	+	Silent	SNP	C	C	T	rs2294510	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:54359922C>T	ENST00000361921.3	+	1	63	c.39C>T	c.(37-39)ctC>ctT	p.L13L	DIO1_ENST00000388876.3_Silent_p.L13L|DIO1_ENST00000322679.6_Silent_p.L13L|DIO1_ENST00000524406.1_5'UTR|DIO1_ENST00000532493.1_Silent_p.L13L|DIO1_ENST00000534069.1_Intron|DIO1_ENST00000525202.1_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	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	175	95	0.542857	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		
DDHD2	23259	hgsc.bcm.edu	37	8	38095662	38095662	+	Missense_Mutation	SNP	C	C	T	rs2306899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:38095662C>T	ENST00000397166.2	+	5	1082	c.557C>T	c.(556-558)aCg>aTg	p.T186M	DDHD2_ENST00000520272.2_Missense_Mutation_p.T186M	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	186			T -> M (in dbSNP:rs2306899). {ECO:0000269|PubMed:9872452}.		cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TCAACACCCACGGAGCAGGGT	0.408													C|||	860	0.171725	0.0227	0.2392	5008	,	,		20303	0.3194		0.2545	False		,,,				2504	0.0879				p.T186M		Atlas-SNP	.											DDHD2,NS,carcinoma,-1,1	DDHD2	60	1	0			c.C557T						PASS	.	C	MET/THR,MET/THR,MET/THR	297,4109	161.8+/-193.9	14,269,1920	209.0	190.0	196.0		557,557,557	5.0	0.2	8	dbSNP_100	196	1977,6623	347.8+/-326.7	225,1527,2548	yes	missense,missense,missense	DDHD2	NM_001164232.1,NM_001164234.1,NM_015214.2	81,81,81	239,1796,4468	TT,TC,CC		22.9884,6.7408,17.4842	probably-damaging,probably-damaging,probably-damaging	186/712,186/228,186/712	38095662	2274,10732	2203	4300	6503	SO:0001583	missense	23259	exon5			CACCCACGGAGCA	AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"""Sterile alpha motif (SAM) domain containing"""	29106	protein-coding gene	gene with protein product		615003	"""SAM, WWE and DDHD domain containing 1"""	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.557C>T	8.37:g.38095662C>T	ENSP00000380352:p.Thr186Met	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	235	119	0.506383	NM_001164232	B3KWV2|B3KXB5|Q9H8X7	Missense_Mutation	SNP	ENST00000397166.2	37	CCDS34883.1	481	0.22023809523809523	13	0.026422764227642278	91	0.2513812154696133	189	0.3304195804195804	188	0.24802110817941952	C	11.77	1.738693	0.30774	0.067408	0.229884	ENSG00000085788	ENST00000397166;ENST00000532222;ENST00000520272	T;T;T	0.49139	0.79;1.43;0.79	5.91	5.03	0.67393	.	0.398117	0.28114	N	0.016542	T	0.00012	0.0000	L	0.50333	1.59	0.52501	P	4.4000000000044004E-5	P;B	0.45634	0.863;0.017	B;B	0.39531	0.302;0.009	T	0.35748	-0.9776	9	0.51188	T	0.08	-7.3516	9.7953	0.40731	0.0:0.7869:0.1398:0.0732	rs2306899;rs52819565;rs58300296;rs2306899	186;186	O94830;E9PKE6	DDHD2_HUMAN;.	M	186	ENSP00000380352:T186M;ENSP00000433578:T186M;ENSP00000429932:T186M	ENSP00000380352:T186M	T	+	2	0	DDHD2	38214819	0.001000	0.12720	0.236000	0.24074	0.069000	0.16628	1.292000	0.33342	1.510000	0.48803	0.558000	0.71614	ACG	C|0.805;T|0.195	0.195	strong		0.408	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291	
SLC22A16	85413	hgsc.bcm.edu	37	6	110778128	110778128	+	Missense_Mutation	SNP	T	T	C	rs714368	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:110778128T>C	ENST00000368919.3	-	2	212	c.146A>G	c.(145-147)cAt>cGt	p.H49R	SLC22A16_ENST00000439654.1_Missense_Mutation_p.H49R|SLC22A16_ENST00000330550.4_Missense_Mutation_p.H47R|SLC22A16_ENST00000461487.1_5'UTR|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	84	44	0.52381	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	
DAPK1	1612	hgsc.bcm.edu	37	9	90322023	90322023	+	Missense_Mutation	SNP	G	G	A	rs1056719	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90322023G>A	ENST00000408954.3	+	26	4372	c.4037G>A	c.(4036-4038)aGt>aAt	p.S1346N	DAPK1_ENST00000472284.1_Missense_Mutation_p.S1346N|DAPK1_ENST00000469640.2_Missense_Mutation_p.S1371N|DAPK1_ENST00000358077.5_Missense_Mutation_p.S1346N|DAPK1_ENST00000491893.1_Missense_Mutation_p.S1280N	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1346	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.		S -> N (in dbSNP:rs1056719). {ECO:0000269|PubMed:15164053, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:7828849, ECO:0000269|Ref.5}.		apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TACAACACCAGTAACGGGGCT	0.632									Chronic Lymphocytic Leukemia, Familial Clustering of				A|||	3285	0.65595	0.3986	0.6974	5008	,	,		17270	0.8323		0.6372	False		,,,				2504	0.8119				p.S1346N		Atlas-SNP	.											.	DAPK1	329	.	0			c.G4037A	GRCh37	CM071685	DAPK1	M	rs1056719	PASS	.	A	ASN/SER	1834,2142		451,932,605	64.0	70.0	68.0		4037	-2.0	0.0	9	dbSNP_86	68	5356,2942		1728,1900,521	yes	missense	DAPK1	NM_004938.2	46	2179,2832,1126	AA,AG,GG		35.4543,46.1268,41.4209	benign	1346/1431	90322023	7190,5084	1988	4149	6137	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	ACACCAGTAACGG	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.4037G>A	9.37:g.90322023G>A	ENSP00000386135:p.Ser1346Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	1397	0.6396520146520146	192	0.3902439024390244	245	0.6767955801104972	474	0.8286713286713286	486	0.6411609498680739	A	0.005	-2.140561	0.00332	0.461268	0.645457	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	D;D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98;-1.98	5.45	-2.04	0.07343	Death (3);DEATH-like (2);	0.236488	0.26143	N	0.026082	T	0.00012	0.0000	N	0.03268	-0.37	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	0.42882	-0.9425	9	0.13108	T	0.6	.	12.6085	0.56538	0.5557:0.0:0.4443:0.0	rs1056719;rs3197321;rs36220449;rs56966233;rs1056719	1280;1346;1346	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	N	1346;1346;1371;1346;1280	ENSP00000350785:S1346N;ENSP00000417076:S1346N;ENSP00000418885:S1371N;ENSP00000386135:S1346N;ENSP00000419026:S1280N	ENSP00000350785:S1346N	S	+	2	0	DAPK1	89511843	0.240000	0.23847	0.003000	0.11579	0.001000	0.01503	0.776000	0.26704	-0.509000	0.06532	-0.972000	0.02603	AGT	G|0.362;A|0.638	0.638	strong		0.632	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
PTPRS	5802	hgsc.bcm.edu	37	19	5273571	5273571	+	Silent	SNP	T	T	G	rs1141371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5273571T>G	ENST00000587303.1	-	3	360	c.261A>C	c.(259-261)gcA>gcC	p.A87A	PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000590509.1_Silent_p.A87A|PTPRS_ENST00000588012.1_Silent_p.A87A|PTPRS_ENST00000353284.2_Silent_p.A87A|PTPRS_ENST00000348075.2_Silent_p.A87A|PTPRS_ENST00000592099.1_Silent_p.A87A|PTPRS_ENST00000357368.4_Silent_p.A87A|PTPRS_ENST00000262963.6_Silent_p.A87A|PTPRS_ENST00000372412.4_Silent_p.A87A			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	87	Ig-like C2-type 1.				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)	GCACTGCCCCTGCACTCTCAT	0.582													T|||	819	0.163538	0.2943	0.1527	5008	,	,		20134	0.002		0.2266	False		,,,				2504	0.0961				p.A87A		Atlas-SNP	.											.	PTPRS	169	.	0			c.A261C						PASS	.	T	,,,	1168,3238	412.4+/-336.1	151,866,1186	94.0	82.0	86.0		261,261,261,261	-8.0	0.6	19	dbSNP_86	86	1924,6676	339.9+/-323.4	208,1508,2584	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	359,2374,3770	GG,GT,TT		22.3721,26.5093,23.7736	,,,	87/1949,87/1502,87/1911,87/1506	5273571	3092,9914	2203	4300	6503	SO:0001819	synonymous_variant	5802	exon4			TGCCCCTGCACTC	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.261A>C	19.37:g.5273571T>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_130854	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			T|0.785;G|0.215;A|0.000	0.215	strong		0.582	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
KRT82	3888	hgsc.bcm.edu	37	12	52788814	52788814	+	Missense_Mutation	SNP	C	C	T	rs61730587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52788814C>T	ENST00000257974.2	-	9	1564	c.1487G>A	c.(1486-1488)cGg>cAg	p.R496Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	496	Tail.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GCTGGATTTCCGCCCGCTCCC	0.642													c|||	21	0.00419329	0.0023	0.0072	5008	,	,		16513	0.0		0.0089	False		,,,				2504	0.0041				p.R496Q		Atlas-SNP	.											KRT82,NS,carcinoma,-1,1	KRT82	45	1	0			c.G1487A						scavenged	.	T	GLN/ARG	14,4392	21.2+/-45.6	0,14,2189	48.0	48.0	48.0		1487	-0.4	0.0	12	dbSNP_129	48	113,8487	58.7+/-120.3	1,111,4188	yes	missense	KRT82	NM_033033.3	43	1,125,6377	TT,TC,CC		1.314,0.3177,0.9765	benign	496/514	52788814	127,12879	2203	4300	6503	SO:0001583	missense	3888	exon9			GATTTCCGCCCGC	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1487G>A	12.37:g.52788814C>T	ENSP00000257974:p.Arg496Gln	Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	c	11.54	1.670563	0.29693	0.003177	0.01314	ENSG00000161850	ENST00000257974	D	0.82255	-1.59	4.59	-0.424	0.12321	.	0.753921	0.10873	N	0.624709	T	0.52933	0.1765	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.39800	-0.9596	10	0.25106	T	0.35	.	4.4613	0.11668	0.1481:0.4148:0.0:0.4371	rs61730587	496	Q9NSB4	KRT82_HUMAN	Q	496	ENSP00000257974:R496Q	ENSP00000257974:R496Q	R	-	2	0	KRT82	51075081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.155000	0.16362	-0.326000	0.08564	-0.215000	0.12644	CGG	C|0.991;T|0.009	0.009	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
ZNF839	55778	hgsc.bcm.edu	37	14	102807671	102807671	+	Missense_Mutation	SNP	C	C	T	rs9464	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:102807671C>T	ENST00000558850.1	+	8	1941	c.1591C>T	c.(1591-1593)Cca>Tca	p.P531S	ZNF839_ENST00000442396.2_Missense_Mutation_p.P647S|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000262236.5_Missense_Mutation_p.P533S|ZNF839_ENST00000559185.1_Missense_Mutation_p.P531S	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	204	0	0		WXS	Illumina HiSeq	Phase_I	208	98	0.471154	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	
RNF32	140545	hgsc.bcm.edu	37	7	156469190	156469190	+	Silent	SNP	A	A	G	rs2302145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:156469190A>G	ENST00000405335.1	+	10	1339	c.930A>G	c.(928-930)gcA>gcG	p.A310A	RNF32_ENST00000311822.8_3'UTR|LMBR1_ENST00000430825.2_5'UTR|RNF32_ENST00000317955.5_Silent_p.A310A|RNF32_ENST00000432459.2_Silent_p.A310A|RNF32_ENST00000392743.2_Silent_p.A310A|RNF32_ENST00000343665.4_Silent_p.A286A			Q9H0A6	RNF32_HUMAN	ring finger protein 32	310						aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GCGTGGGTGCAGGCAGGCGTT	0.657													G|||	2666	0.532348	0.8646	0.4597	5008	,	,		12418	0.5248		0.4006	False		,,,				2504	0.2781				p.A310A		Atlas-SNP	.											.	RNF32	77	.	0			c.A930G						PASS	.	G	,,	3413,993	369.5+/-319.1	1336,741,126	56.0	47.0	50.0		930,930,930	-2.9	0.0	7	dbSNP_100	50	3246,5354	647.9+/-400.4	615,2016,1669	no	coding-synonymous,coding-synonymous,coding-synonymous	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	,,	1951,2757,1795	GG,GA,AA		37.7442,22.5374,48.8006	,,	310/363,310/363,310/363	156469190	6659,6347	2203	4300	6503	SO:0001819	synonymous_variant	140545	exon9			GGGTGCAGGCAGG		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.930A>G	7.37:g.156469190A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	63	0.543103	NM_001184996	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Silent	SNP	ENST00000405335.1	37	CCDS5944.1																																																																																			A|0.477;G|0.523	0.523	strong		0.657	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	
SPECC1	92521	hgsc.bcm.edu	37	17	20217375	20217375	+	Silent	SNP	G	G	A	rs75296798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:20217375G>A	ENST00000261503.5	+	15	3255	c.3204G>A	c.(3202-3204)acG>acA	p.T1068T	AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395527.4_Silent_p.T1068T|SPECC1_ENST00000536879.1_Silent_p.T408T|SPECC1_ENST00000395530.2_Silent_p.T987T	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	1068					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		ACTTTGAGACGTAACCCTGGA	0.587													g|||	186	0.0371406	0.0045	0.0836	5008	,	,		19090	0.0		0.1024	False		,,,				2504	0.0194				p.T1068T		Atlas-SNP	.											.	SPECC1	100	.	0			c.G3204A						PASS	.	A	,	101,4305	79.3+/-117.8	2,97,2104	76.0	62.0	67.0		3204,2961	-6.7	0.1	17	dbSNP_132	67	1037,7563	219.4+/-257.5	71,895,3334	no	coding-synonymous,coding-synonymous	SPECC1	NM_001033553.2,NM_001033555.2	,	73,992,5438	AA,AG,GG		12.0581,2.2923,8.7498	,	1068/1069,987/988	20217375	1138,11868	2203	4300	6503	SO:0001819	synonymous_variant	92521	exon15			TGAGACGTAACCC	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.3204G>A	17.37:g.20217375G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																			G|0.923;A|0.077	0.077	strong		0.587	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
VSIG4	11326	hgsc.bcm.edu	37	X	65242157	65242157	+	Missense_Mutation	SNP	G	G	A	rs41307375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65242157G>A	ENST00000374737.4	-	8	1256	c.1148C>T	c.(1147-1149)aCa>aTa	p.T383I	VSIG4_ENST00000412866.2_Missense_Mutation_p.T289I|VSIG4_ENST00000455586.2_3'UTR	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	383					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGAGGAACTGTGTCCAGCAG	0.507													G|||	14	0.00370861	0.0	0.0058	3775	,	,		15026	0.0		0.007	False		,,,				2504	0.0031				p.T383I		Atlas-SNP	.											.	VSIG4	54	.	0			c.C1148T						PASS	.	G	ILE/THR,,,ILE/THR	5,3830		0,4,1,1628,570	81.0	68.0	73.0		866,,,1148	2.7	0.0	X	dbSNP_127	73	55,6673		0,35,20,2393,1852	yes	missense,utr-3,utr-3,missense	VSIG4	NM_001100431.1,NM_001184830.1,NM_001184831.1,NM_007268.2	89,,,89	0,39,21,4021,2422	AA,AG,A,GG,G		0.8175,0.1304,0.568	probably-damaging,,,probably-damaging	289/306,,,383/400	65242157	60,10503	2203	4300	6503	SO:0001583	missense	11326	exon8			GGAACTGTGTCCA	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.1148C>T	X.37:g.65242157G>A	ENSP00000363869:p.Thr383Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_007268	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	10	0.006027727546714889	0	0.0	4	0.011049723756906077	0	0.0	4	0.005305039787798408	G	6.391	0.440248	0.12104	0.001304	0.008175	ENSG00000155659	ENST00000374737;ENST00000412866	T;T	0.29142	1.58;2.06	4.55	2.69	0.31865	.	0.562854	0.14925	N	0.290449	T	0.23532	0.0569	L	0.57536	1.79	0.09310	N	0.999995	P;B	0.35908	0.527;0.232	B;B	0.37989	0.262;0.082	T	0.13045	-1.0524	10	0.72032	D	0.01	-2.997	8.7467	0.34591	0.0:0.0:0.5888:0.4112	rs41307375	289;383	Q9Y279-3;Q9Y279	.;VSIG4_HUMAN	I	383;289	ENSP00000363869:T383I;ENSP00000394143:T289I	ENSP00000363869:T383I	T	-	2	0	VSIG4	65158882	0.010000	0.17322	0.007000	0.13788	0.011000	0.07611	0.952000	0.29149	0.423000	0.26033	0.513000	0.50165	ACA	G|0.994;A|0.006	0.006	strong		0.507	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268	
DGAT1	8694	hgsc.bcm.edu	37	8	145541766	145541766	+	Missense_Mutation	SNP	G	G	T	rs55962377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145541766G>T	ENST00000332324.4	-	8	1016	c.743C>A	c.(742-744)aCc>aAc	p.T248N	GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000527438.1_5'Flank|DGAT1_ENST00000531896.1_Missense_Mutation_p.D278E	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	248					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	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;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			ACCGCGGTAGGTCAGATTGTC	0.637													G|||	180	0.0359425	0.0023	0.0418	5008	,	,		17354	0.0		0.1014	False		,,,				2504	0.047				p.T248N		Atlas-SNP	.											.	DGAT1	26	.	0			c.C743A						PASS	.	G	ASN/THR	81,4325	62.9+/-100.1	1,79,2123	60.0	63.0	62.0		743	3.8	1.0	8	dbSNP_129	62	859,7733	190.1+/-236.7	60,739,3497	yes	missense	DGAT1	NM_012079.4	65	61,818,5620	TT,TG,GG		9.9977,1.8384,7.2319	benign	248/489	145541766	940,12058	2203	4296	6499	SO:0001583	missense	8694	exon8			CGGTAGGTCAGAT	AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"""diacylglycerol O-acyltransferase homolog 1 (mouse)"""			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.743C>A	8.37:g.145541766G>T	ENSP00000332258:p.Thr248Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	37	CCDS6420.1	86|86	0.039377289377289376|0.039377289377289376	1|1	0.0020325203252032522|0.0020325203252032522	15|15	0.04143646408839779|0.04143646408839779	0|0	0.0|0.0	70|70	0.09234828496042216|0.09234828496042216	G|G	14.39|14.39	2.521800|2.521800	0.44866|0.44866	0.018384|0.018384	0.099977|0.099977	ENSG00000185000|ENSG00000185000	ENST00000531896|ENST00000332324	.|T	.|0.73047	.|-0.71	4.68|4.68	3.77|3.77	0.43336|0.43336	.|.	.|0.165053	.|0.52532	.|D	.|0.000071	T|T	0.04952|0.04952	0.0133|0.0133	L|L	0.50919|0.50919	1.6|1.6	0.22081|0.22081	N|N	0.999376|0.999376	.|B	.|0.23650	.|0.089	.|B	.|0.35770	.|0.21	T|T	0.21008|0.21008	-1.0258|-1.0258	6|10	0.56958|0.42905	D|T	0.05|0.14	-13.2441|-13.2441	11.641|11.641	0.51233|0.51233	0.0:0.0:0.8211:0.1789|0.0:0.0:0.8211:0.1789	rs55962377|rs55962377	.|248	.|O75907	.|DGAT1_HUMAN	E|N	278|248	.|ENSP00000332258:T248N	ENSP00000432795:D278E|ENSP00000332258:T248N	D|T	-|-	3|2	2|0	DGAT1|DGAT1	145512574|145512574	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.641000|0.641000	0.38312|0.38312	2.525000|2.525000	0.45598|0.45598	1.130000|1.130000	0.42092|0.42092	0.484000|0.484000	0.47621|0.47621	GAC|ACC	G|0.941;T|0.059	0.059	strong		0.637	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079	
PPL	5493	hgsc.bcm.edu	37	16	4934564	4934564	+	Silent	SNP	C	C	G	rs1049207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4934564C>G	ENST00000345988.2	-	22	4181	c.4092G>C	c.(4090-4092)ctG>ctC	p.L1364L	PPL_ENST00000590782.2_Silent_p.L1362L	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1364					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						CCTCGGCCCGCAGGCCTGGCT	0.677													C|||	2107	0.420727	0.1014	0.4697	5008	,	,		15767	0.6478		0.5308	False		,,,				2504	0.4703				p.L1364L		Atlas-SNP	.											.	PPL	168	.	0			c.G4092C						PASS	.	C		688,3706	285.5+/-278.2	56,576,1565	114.0	125.0	121.0		4092	2.4	0.4	16	dbSNP_86	121	4759,3841	607.2+/-395.2	1317,2125,858	no	coding-synonymous	PPL	NM_002705.4		1373,2701,2423	GG,GC,CC		44.6628,15.6577,41.9193		1364/1757	4934564	5447,7547	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			GGCCCGCAGGCCT	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.4092G>C	16.37:g.4934564C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			C|0.573;G|0.427	0.427	strong		0.677	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
SLC38A8	146167	hgsc.bcm.edu	37	16	84050776	84050776	+	Missense_Mutation	SNP	T	T	C	rs142821762		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:84050776T>C	ENST00000299709.3	-	7	921	c.922A>G	c.(922-924)Act>Gct	p.T308A		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	308					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						GGGTAGACAGTTACGATGGAG	0.537													T|||	1	0.000199681	0.0	0.0	5008	,	,		19595	0.0		0.001	False		,,,				2504	0.0				p.T308A		Atlas-SNP	.											.	SLC38A8	60	.	0			c.A922G						PASS	.	T	ALA/THR	0,4400		0,0,2200	113.0	88.0	97.0		922	4.8	0.2	16	dbSNP_134	97	8,8592	6.4+/-24.3	0,8,4292	yes	missense	SLC38A8	NM_001080442.1	58	0,8,6492	CC,CT,TT		0.093,0.0,0.0615	probably-damaging	308/436	84050776	8,12992	2200	4300	6500	SO:0001583	missense	146167	exon7			AGACAGTTACGAT		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.922A>G	16.37:g.84050776T>C	ENSP00000299709:p.Thr308Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	77	51	0.662338	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.893044	0.72524	0.0	9.3E-4	ENSG00000166558	ENST00000299709	T	0.02236	4.38	4.75	4.75	0.60458	.	0.110120	0.64402	D	0.000009	T	0.09642	0.0237	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36696	-0.9737	10	0.06099	T	0.92	-17.5765	13.2419	0.60002	0.0:0.0:0.0:1.0	.	308	A6NNN8	S38A8_HUMAN	A	308	ENSP00000299709:T308A	ENSP00000299709:T308A	T	-	1	0	SLC38A8	82608277	1.000000	0.71417	0.184000	0.23157	0.920000	0.55202	7.230000	0.78097	1.773000	0.52216	0.391000	0.25812	ACT	T|1.000;C|0.000	0.000	strong		0.537	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
CPAMD8	27151	hgsc.bcm.edu	37	19	17113147	17113147	+	Silent	SNP	A	A	G	rs3745345	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17113147A>G	ENST00000443236.1	-	9	859	c.828T>C	c.(826-828)ttT>ttC	p.F276F	CPAMD8_ENST00000388925.4_Silent_p.F229F	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	229						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						TCAGAAGCTCAAACTTGGGCA	0.597													N|||	929	0.185503	0.379	0.0994	5008	,	,		16169	0.121		0.1471	False		,,,				2504	0.091				p.F276F		Atlas-SNP	.											.	CPAMD8	192	.	0			c.T828C						PASS	.	G		1229,2655		185,859,898	29.0	30.0	30.0		828	1.4	0.6	19	dbSNP_107	30	1168,7088		82,1004,3042	yes	coding-synonymous	CPAMD8	NM_015692.2		267,1863,3940	GG,GA,AA		14.1473,31.6426,19.7446		276/1933	17113147	2397,9743	1942	4128	6070	SO:0001819	synonymous_variant	27151	exon9			AAGCTCAAACTTG	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.828T>C	19.37:g.17113147A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	392	0.1794871794871795	190	0.3861788617886179	32	0.08839779005524862	61	0.10664335664335664	109	0.1437994722955145	N	1.453	-0.564591	0.03939	0.316426	0.141473	ENSG00000160111	ENST00000443236	.	.	.	2.46	1.39	0.22231	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43718	-0.9374	3	.	.	.	.	8.3204	0.32126	0.876:0.0:0.124:0.0	rs3745345;rs58677535;rs3745345	.	.	.	S	287	.	.	L	-	2	0	CPAMD8	16974147	1.000000	0.71417	0.582000	0.28627	0.227000	0.25037	2.475000	0.45162	-0.386000	0.07821	-1.305000	0.01319	TTG	A|0.822;G|0.178	0.178	strong		0.597	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
ZNF229	7772	hgsc.bcm.edu	37	19	44933947	44933947	+	Missense_Mutation	SNP	G	G	A	rs12151338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44933947G>A	ENST00000588931.1	-	6	1442	c.1009C>T	c.(1009-1011)Cgt>Tgt	p.R337C	ZNF229_ENST00000291187.4_Missense_Mutation_p.R331C|ZNF229_ENST00000591289.1_Intron|CTC-512J12.4_ENST00000588655.1_RNA	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	337			R -> C (in dbSNP:rs12151338).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				GGGTGGTTACGTATGTGCGTG	0.498													G|||	1441	0.28774	0.028	0.2651	5008	,	,		19954	0.3343		0.3678	False		,,,				2504	0.5245				p.R337C		Atlas-SNP	.											ZNF229,NS,carcinoma,+1,1	ZNF229	123	1	0			c.C1009T						PASS	.	G	CYS/ARG	295,3621		15,265,1678	66.0	64.0	65.0		1009	0.6	0.0	19	dbSNP_120	65	2916,5400		520,1876,1762	yes	missense	ZNF229	NM_014518.2	180	535,2141,3440	AA,AG,GG		35.0649,7.5332,26.2508	possibly-damaging	337/826	44933947	3211,9021	1958	4158	6116	SO:0001583	missense	7772	exon6			GGTTACGTATGTG	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1009C>T	19.37:g.44933947G>A	ENSP00000466519:p.Arg337Cys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	576	0.26373626373626374	12	0.024390243902439025	97	0.26795580110497236	185	0.32342657342657344	282	0.3720316622691293	G	8.511	0.866580	0.17250	0.075332	0.350649	ENSG00000167383	ENST00000291187	.	.	.	3.16	0.592	0.17471	.	.	.	.	.	T	0.00012	0.0000	M	0.69523	2.12	0.80722	P	0.0	P	0.40970	0.734	B	0.38921	0.285	T	0.36625	-0.9740	7	0.38643	T	0.18	.	9.6208	0.39721	0.0:0.5592:0.4408:0.0	rs12151338;rs17281928;rs60383343;rs12151338	337	Q9UJW7	ZN229_HUMAN	C	337	.	ENSP00000291187:R337C	R	-	1	0	ZNF229	49625787	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-3.507000	0.00448	0.609000	0.30018	0.609000	0.83330	CGT	G|0.732;A|0.268	0.268	strong		0.498	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
ZNF814	730051	hgsc.bcm.edu	37	19	58385762	58385762	+	Silent	SNP	C	C	G	rs199732634		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58385762C>G	ENST00000435989.2	-	3	1230	c.996G>C	c.(994-996)tcG>tcC	p.S332S	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	332					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)	p.S332S(2)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						ATTTGCTAAACGATTTCCCAC	0.358																																					p.S332S		Atlas-SNP	.											ZNF814,NS,carcinoma,0,15	ZNF814	93	15	2	Substitution - coding silent(2)	kidney(2)	c.G996C						PASS	.						25.0	25.0	25.0					19																	58385762		692	1589	2281	SO:0001819	synonymous_variant	730051	exon3			GCTAAACGATTTC		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.996G>C	19.37:g.58385762C>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	179	51	0.284916	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			.	.	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
FUK	197258	hgsc.bcm.edu	37	16	70515355	70515355	+	IGR	SNP	C	C	T	rs11054	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:70515355C>T	ENST00000288078.6	+	0	4081				COG4_ENST00000323786.5_Silent_p.S714S	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase							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)				AGGCAATGAGCGACCTCAGCT	0.592													T|||	1872	0.373802	0.5083	0.3847	5008	,	,		18714	0.2222		0.4692	False		,,,				2504	0.2423				p.S714S		Atlas-SNP	.											.	COG4	64	.	0			c.G2142A						PASS	.	T	,	2275,2121	575.9+/-384.1	574,1127,497	91.0	83.0	86.0		2079,2142	-2.1	1.0	16	dbSNP_52	86	4016,4584	597.2+/-393.7	944,2128,1228	no	coding-synonymous,coding-synonymous	COG4	NM_001195139.1,NM_015386.2	,	1518,3255,1725	TT,TC,CC		46.6977,48.2484,48.4072	,	693/769,714/790	70515355	6291,6705	2198	4300	6498	SO:0001628	intergenic_variant	25839	exon18			AATGAGCGACCTC		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		16.37:g.70515355C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_015386	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Silent	SNP	ENST00000288078.6	37	CCDS10891.2																																																																																			C|0.538;A|0.002	.	strong		0.592	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
CABP2	51475	hgsc.bcm.edu	37	11	67288594	67288594	+	Missense_Mutation	SNP	C	C	T	rs2276118	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:67288594C>T	ENST00000294288.4	-	4	350	c.281G>A	c.(280-282)cGg>cAg	p.R94Q	CABP2_ENST00000353903.5_Missense_Mutation_p.R37Q	NM_016366.2	NP_057450.2	Q9NPB3	CABP2_HUMAN	calcium binding protein 2	94	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> Q (in dbSNP:rs2276118). {ECO:0000269|PubMed:10625670}.		signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	9						GTAGCCGTCCCGGTCTCGGTC	0.632													C|||	2152	0.429712	0.0303	0.3775	5008	,	,		18420	0.6558		0.5606	False		,,,				2504	0.6391				p.R94Q		Atlas-SNP	.											.	CABP2	25	.	0			c.G281A						PASS	.	C	GLN/ARG	558,3842	249.3+/-256.8	37,484,1679	79.0	73.0	75.0		281	3.6	1.0	11	dbSNP_100	75	4879,3711	618.5+/-396.8	1393,2093,809	yes	missense	CABP2	NM_016366.2	43	1430,2577,2488	TT,TC,CC		43.2014,12.6818,41.8553	benign	94/221	67288594	5437,7553	2200	4295	6495	SO:0001583	missense	51475	exon4			CCGTCCCGGTCTC	AF169154	CCDS8170.1	11q13.1	2013-01-10			ENSG00000167791	ENSG00000167791		"""EF-hand domain containing"""	1385	protein-coding gene	gene with protein product		607314				10625670	Standard	NM_016366		Approved		uc001omc.1	Q9NPB3	OTTHUMG00000168014	ENST00000294288.4:c.281G>A	11.37:g.67288594C>T	ENSP00000294288:p.Arg94Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_016366		Missense_Mutation	SNP	ENST00000294288.4	37	CCDS8170.1	960	0.43956043956043955	21	0.042682926829268296	147	0.40607734806629836	382	0.6678321678321678	410	0.5408970976253298	C	9.221	1.033505	0.19590	0.126818	0.567986	ENSG00000167791	ENST00000353903;ENST00000294288	T;T	0.63417	-0.04;-0.04	4.53	3.61	0.41365	EF-hand-like domain (1);	0.072995	0.53938	D	0.000041	T	0.00012	0.0000	N	0.17564	0.495	0.29008	P	0.88707	B;B;P	0.42123	0.422;0.265;0.771	B;B;B	0.35510	0.091;0.02;0.204	T	0.40098	-0.9581	9	0.66056	D	0.02	-22.6172	6.2025	0.20583	0.0:0.7112:0.0:0.2888	rs2276118;rs17472820;rs58486160;rs2276118	100;37;94	F1T0K2;Q9NPB3-2;Q9NPB3	.;.;CABP2_HUMAN	Q	37;94	ENSP00000312037:R37Q;ENSP00000294288:R94Q	ENSP00000294288:R94Q	R	-	2	0	CABP2	67045170	0.135000	0.22499	0.992000	0.48379	0.109000	0.19521	0.618000	0.24373	1.256000	0.44068	0.555000	0.69702	CGG	C|0.573;T|0.427	0.427	strong		0.632	CABP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397516.1		
PCNT	5116	hgsc.bcm.edu	37	21	47811272	47811272	+	Silent	SNP	C	C	T	rs3737438	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47811272C>T	ENST00000359568.5	+	21	4304	c.4197C>T	c.(4195-4197)gaC>gaT	p.D1399D	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1399					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CAGCCACGGACGCCGAGGCCA	0.701													C|||	1510	0.301518	0.2073	0.2262	5008	,	,		16283	0.4008		0.3907	False		,,,				2504	0.2883				p.D1399D		Atlas-SNP	.											PCNT,NS,carcinoma,0,1	PCNT	283	1	0			c.C4197T						PASS	.	C		798,3288		84,630,1329	6.0	7.0	6.0		4197	-9.4	0.0	21	dbSNP_107	6	2727,5429		466,1795,1817	no	coding-synonymous	PCNT	NM_006031.5		550,2425,3146	TT,TC,CC		33.4355,19.5301,28.7943		1399/3337	47811272	3525,8717	2043	4078	6121	SO:0001819	synonymous_variant	5116	exon21			CACGGACGCCGAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.4197C>T	21.37:g.47811272C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.650;T|0.350	0.350	strong		0.701	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
PPL	5493	hgsc.bcm.edu	37	16	4934549	4934549	+	Silent	SNP	G	G	A	rs1049208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4934549G>A	ENST00000345988.2	-	22	4196	c.4107C>T	c.(4105-4107)agC>agT	p.S1369S	PPL_ENST00000590782.2_Silent_p.S1367S	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1369					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						CGGCAAAGGCGCTCGCCTCGG	0.682													G|||	2035	0.40635	0.0598	0.4726	5008	,	,		15868	0.6339		0.5298	False		,,,				2504	0.4663				p.S1369S		Atlas-SNP	.											.	PPL	168	.	0			c.C4107T						PASS	.	G		574,3820	251.2+/-258.0	41,492,1664	100.0	109.0	106.0		4107	-0.4	0.3	16	dbSNP_86	106	4754,3846	604.9+/-394.9	1316,2122,862	no	coding-synonymous	PPL	NM_002705.4		1357,2614,2526	AA,AG,GG		44.7209,13.0633,41.0035		1369/1757	4934549	5328,7666	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			AAAGGCGCTCGCC	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.4107C>T	16.37:g.4934549G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			G|0.589;A|0.411	0.411	strong		0.682	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
SVIL	6840	hgsc.bcm.edu	37	10	29754535	29754535	+	Missense_Mutation	SNP	G	G	A	rs17694739	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:29754535G>A	ENST00000355867.4	-	34	6874	c.6122C>T	c.(6121-6123)gCg>gTg	p.A2041V	PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.A955V|SVIL_ENST00000375400.3_Missense_Mutation_p.A1615V|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000375398.2_Missense_Mutation_p.A2041V	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2041			A -> V (in dbSNP:rs17694739).		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)				TGGCTGGGGCGCGCTGTACAG	0.542													G|||	246	0.0491214	0.0189	0.0504	5008	,	,		17538	0.0198		0.1352	False		,,,				2504	0.0307				p.A2041V		Atlas-SNP	.											SVIL,colon,carcinoma,+1,1	SVIL	226	1	0			c.C6122T						PASS	.	G	VAL/ALA,VAL/ALA	151,4255	99.4+/-138.0	0,151,2052	38.0	41.0	40.0		4844,6122	4.7	0.2	10	dbSNP_123	40	1126,7472	211.1+/-251.8	82,962,3255	no	missense,missense	SVIL	NM_003174.3,NM_021738.2	64,64	82,1113,5307	AA,AG,GG		13.0961,3.4271,9.8201	benign,benign	1615/1789,2041/2215	29754535	1277,11727	2203	4299	6502	SO:0001583	missense	6840	exon34			TGGGGCGCGCTGT	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.6122C>T	10.37:g.29754535G>A	ENSP00000348128:p.Ala2041Val	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	207	100	0.483092	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	139	0.06364468864468864	8	0.016260162601626018	23	0.06353591160220995	7	0.012237762237762238	101	0.13324538258575197	G	16.70	3.195070	0.58017	0.034271	0.130961	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393	T;T;T;T	0.14640	2.49;2.49;2.49;2.49	4.72	4.72	0.59763	.	0.046563	0.85682	D	0.000000	T	0.00210	0.0006	M	0.74258	2.255	0.09310	P	1.0	P;P;P	0.46656	0.882;0.582;0.791	B;B;B	0.39152	0.292;0.245;0.177	T	0.14671	-1.0464	9	0.42905	T	0.14	-23.0313	17.8597	0.88777	0.0:0.0:1.0:0.0	rs17694739	955;1615;2041	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	V	1615;2041;2041;955	ENSP00000364549:A1615V;ENSP00000364547:A2041V;ENSP00000348128:A2041V;ENSP00000445472:A955V	ENSP00000348128:A2041V	A	-	2	0	SVIL	29794541	1.000000	0.71417	0.245000	0.24217	0.158000	0.22134	7.706000	0.84615	2.428000	0.82296	0.650000	0.86243	GCG	G|0.917;A|0.083	0.083	strong		0.542	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
CNGA2	1260	hgsc.bcm.edu	37	X	150912502	150912502	+	Silent	SNP	G	G	A	rs113295831	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	111	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	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	
PPP3R1	5534	hgsc.bcm.edu	37	2	68415767	68415767	+	Silent	SNP	G	G	A	rs687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:68415767G>A	ENST00000234310.3	-	3	502	c.99C>T	c.(97-99)gaC>gaT	p.D33D	PPP3R1_ENST00000409377.1_Silent_p.D23D|RP11-474G23.1_ENST00000406334.3_Silent_p.D23D|PPP3R1_ENST00000409752.1_Silent_p.D52D	NM_000945.3	NP_000936.1	P63098	CANB1_HUMAN	protein phosphatase 3, regulatory subunit B, alpha	33	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				apoptotic process (GO:0006915)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lung epithelial cell differentiation (GO:0060487)|NFAT protein import into nucleus (GO:0051531)|patterning of blood vessels (GO:0001569)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein dephosphorylation (GO:0006470)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|protein domain specific binding (GO:0019904)			large_intestine(1)	1						AACCAGAATTGTCCAAATCAA	0.353													G|||	2582	0.515575	0.5227	0.4798	5008	,	,		15459	0.494		0.4195	False		,,,				2504	0.6524				p.D33D		Atlas-SNP	.											.	PPP3R1	14	.	0			c.C99T						PASS	.	G		1763,1895		425,913,491	78.0	74.0	75.0		99	5.9	1.0	2	dbSNP_120	75	3226,4950		658,1910,1520	no	coding-synonymous	PPP3R1	NM_000945.3		1083,2823,2011	AA,AG,GG		39.4569,48.1957,42.1582		33/171	68415767	4989,6845	1829	4088	5917	SO:0001819	synonymous_variant	5534	exon3			AGAATTGTCCAAA	M30773	CCDS46310.1	2p14	2013-01-10	2010-04-14		ENSG00000221823	ENSG00000221823	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 3, regulatory subunits"", ""EF-hand domain containing"""	9317	protein-coding gene	gene with protein product	"""calcineurin B, type I (19kDa)"", ""protein phosphatase 2B regulatory subunit B alpha"""	601302	"""protein phosphatase 3 (formerly 2B), regulatory subunit B (19kD), alpha isoform (calcineurin B, type I)"", ""protein phosphatase 3 (formerly 2B), regulatory subunit B, 19kDa, alpha isoform (calcineurin B, type I)"", ""protein phosphatase 3 (formerly 2B), regulatory subunit B, alpha isoform"""			8978785, 2558868	Standard	NM_000945		Approved	CALNB1, CNB, CNB1	uc002sei.1	P63098	OTTHUMG00000129561	ENST00000234310.3:c.99C>T	2.37:g.68415767G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	207	100	0.483092	NM_000945	B2RC10|B5MDU4|P06705|P15117|Q08044|Q53SL0	Silent	SNP	ENST00000234310.3	37	CCDS46310.1																																																																																			G|0.502;A|0.498	0.498	strong		0.353	PPP3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326765.4	NM_000945	
TBC1D5	9779	hgsc.bcm.edu	37	3	17208267	17208267	+	Missense_Mutation	SNP	T	T	C	rs1138454	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:17208267T>C	ENST00000253692.7	-	21	3750	c.2086A>G	c.(2086-2088)Att>Gtt	p.I696V	TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000446818.2_Missense_Mutation_p.I718V|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	129	0	0		WXS	Illumina HiSeq	Phase_I	154	80	0.519481	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	
TONSL	4796	hgsc.bcm.edu	37	8	145657840	145657840	+	Missense_Mutation	SNP	G	G	A	rs146566654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145657840G>A	ENST00000409379.3	-	23	3592	c.3563C>T	c.(3562-3564)gCt>gTt	p.A1188V	AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1188					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CAGGTGCTCAGCATCTGCACC	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		15419	0.0		0.0	False		,,,				2504	0.002				p.A1188V		Atlas-SNP	.											.	TONSL	128	.	0			c.C3563T						PASS	.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	49.0	56.0	54.0		3563	5.0	0.9	8	dbSNP_134	54	8,8592	6.4+/-24.3	0,8,4292	yes	missense	TONSL	NM_013432.4	64	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	possibly-damaging	1188/1379	145657840	9,12997	2203	4300	6503	SO:0001583	missense	4796	exon23			TGCTCAGCATCTG		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"""Ankyrin repeat domain containing"""	7801	protein-coding gene	gene with protein product		604546	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"""	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.3563C>T	8.37:g.145657840G>A	ENSP00000386239:p.Ala1188Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	37	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	g	0.591	-0.833165	0.02713	2.27E-4	9.3E-4	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.52526	0.66	4.99	4.99	0.66335	.	0.277567	0.33650	N	0.004684	T	0.44953	0.1318	L	0.51853	1.615	0.40916	D	0.984272	B	0.25390	0.125	B	0.22753	0.041	T	0.48175	-0.9058	10	0.66056	D	0.02	-9.63	15.8111	0.78565	0.0:0.0:1.0:0.0	.	1188	Q96HA7	TONSL_HUMAN	V	1188;1187	ENSP00000386239:A1188V	ENSP00000386239:A1188V	A	-	2	0	TONSL	145628648	0.970000	0.33590	0.868000	0.34077	0.114000	0.19823	2.838000	0.48199	2.324000	0.78689	0.456000	0.33151	GCT	G|1.000;A|0.000	0.000	strong		0.667	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
GBE1	2632	hgsc.bcm.edu	37	3	81698130	81698130	+	Missense_Mutation	SNP	T	T	C	rs2229519	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:81698130T>C	ENST00000429644.2	-	5	1211	c.568A>G	c.(568-570)Aga>Gga	p.R190G	GBE1_ENST00000489715.1_Missense_Mutation_p.R149G	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	190			R -> G (in dbSNP:rs2229519).		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)		TTCTTTGGTCTGGAATGCTTA	0.328									Glycogen Storage Disease, type IV				T|||	1610	0.321486	0.2579	0.3026	5008	,	,		15982	0.4425		0.3052	False		,,,				2504	0.3129				p.R190G		Atlas-SNP	.											.	GBE1	111	.	0			c.A568G						PASS	.	T	GLY/ARG	992,2594		147,698,948	33.0	31.0	32.0		568	4.8	1.0	3	dbSNP_98	32	2441,5681		368,1705,1988	yes	missense	GBE1	NM_000158.3	125	515,2403,2936	CC,CT,TT		30.0542,27.6631,29.3218	benign	190/703	81698130	3433,8275	1793	4061	5854	SO:0001583	missense	2632	exon5	Familial Cancer Database	Andersen Disease, Brancher deficiency	TTGGTCTGGAATG		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.568A>G	3.37:g.81698130T>C	ENSP00000410833:p.Arg190Gly	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_000158	B3KWV3|Q96EN0	Missense_Mutation	SNP	ENST00000429644.2	37	CCDS54612.1	713	0.32646520146520147	133	0.2703252032520325	100	0.27624309392265195	252	0.4405594405594406	228	0.3007915567282322	T	13.56	2.272762	0.40194	0.276631	0.300542	ENSG00000114480	ENST00000429644;ENST00000264326;ENST00000489715	D;D	0.86627	-2.15;-2.15	5.92	4.81	0.61882	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.336569	0.34932	N	0.003563	T	0.00012	0.0000	M	0.87827	2.91	0.32208	P	0.576845	B;B	0.18461	0.028;0.013	B;B	0.13407	0.009;0.006	T	0.45527	-0.9255	9	0.66056	D	0.02	-20.1415	3.4755	0.07583	0.1231:0.0796:0.1596:0.6378	rs2229519;rs2305246;rs60933752;rs2229519	149;190	E9PGM4;Q04446	.;GLGB_HUMAN	G	190;241;149	ENSP00000410833:R190G;ENSP00000419638:R149G	ENSP00000264326:R241G	R	-	1	2	GBE1	81780820	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.477000	0.53151	2.255000	0.74692	0.533000	0.62120	AGA	T|0.679;C|0.320;N|0.000	0.320	strong		0.328	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73148481	73148481	+	Missense_Mutation	SNP	G	G	A	rs2973566	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73148481G>A	ENST00000426542.2	+	13	1774	c.1754G>A	c.(1753-1755)aGa>aAa	p.R585K	ARHGEF28_ENST00000437974.1_Missense_Mutation_p.R585K|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.R585K|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.R272K|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.R585K|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.R585K|ARHGEF28_ENST00000287898.5_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	163	0	0		WXS	Illumina HiSeq	Phase_I	165	77	0.466667	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		
MYOC	4653	hgsc.bcm.edu	37	1	171605387	171605387	+	Missense_Mutation	SNP	T	T	C	rs56314834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171605387T>C	ENST00000037502.6	-	3	1264	c.1193A>G	c.(1192-1194)aAa>aGa	p.K398R		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	398	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.		K -> R (in dbSNP:rs56314834). {ECO:0000269|PubMed:10916185, ECO:0000269|PubMed:11004290, ECO:0000269|PubMed:11774072, ECO:0000269|PubMed:12189160, ECO:0000269|PubMed:12872267}.		bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					AATGGCACCTTTGGCCTCATC	0.522													T|||	10	0.00199681	0.0008	0.0029	5008	,	,		19133	0.0		0.007	False		,,,				2504	0.0				p.K398R		Atlas-SNP	.											.	MYOC	69	.	0			c.A1193G	GRCh37	CM004363	MYOC	M	rs56314834	PASS	.	T	ARG/LYS	5,4401	9.9+/-24.2	0,5,2198	156.0	145.0	149.0		1193	-1.2	0.8	1	dbSNP_129	149	48,8552	31.7+/-84.0	0,48,4252	yes	missense	MYOC	NM_000261.1	26	0,53,6450	CC,CT,TT		0.5581,0.1135,0.4075	benign	398/505	171605387	53,12953	2203	4300	6503	SO:0001583	missense	4653	exon3			GCACCTTTGGCCT	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.1193A>G	1.37:g.171605387T>C	ENSP00000037502:p.Lys398Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_000261	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	37	CCDS1297.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	T	9.364	1.068750	0.20147	0.001135	0.005581	ENSG00000034971	ENST00000037502;ENST00000357746;ENST00000536591	D	0.89939	-2.59	5.31	-1.17	0.09648	Olfactomedin-like (3);	0.227351	0.50627	N	0.000107	T	0.64681	0.2620	L	0.28014	0.82	0.37961	D	0.932985	B;B	0.24258	0.049;0.1	B;B	0.28465	0.038;0.09	T	0.49744	-0.8907	10	0.12430	T	0.62	.	9.8677	0.41154	0.0:0.3679:0.0:0.6321	rs56314834	340;398	B4DV44;Q99972	.;MYOC_HUMAN	R	398;351;331	ENSP00000037502:K398R	ENSP00000037502:K398R	K	-	2	0	MYOC	169872010	0.319000	0.24607	0.824000	0.32777	0.507000	0.33981	0.524000	0.22940	-0.149000	0.11215	0.454000	0.30748	AAA	T|0.995;C|0.005	0.005	strong		0.522	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261	
KANSL1	284058	hgsc.bcm.edu	37	17	44248783	44248783	+	Missense_Mutation	SNP	G	G	T	rs142096969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44248783G>T	ENST00000262419.6	-	2	1197	c.727C>A	c.(727-729)Caa>Aaa	p.Q243K	KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000572904.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000575318.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000432791.1_Missense_Mutation_p.Q243K	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	243					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.Q243E(2)									CTGCTTCCTTGAAGTGCCGGC	0.438													G|||	4	0.000798722	0.0	0.0043	5008	,	,		25143	0.0		0.001	False		,,,				2504	0.0				p.Q243K		Atlas-SNP	.											KIAA1267,NS,carcinoma,0,1	.	.	1	2	Substitution - Missense(2)	prostate(2)	c.C727A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN	1,4405	2.1+/-5.4	0,1,2202	97.0	122.0	114.0		727,727,727	6.0	1.0	17	dbSNP_134	114	21,8579	14.0+/-48.4	0,21,4279	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	53,53,53	0,22,6481	TT,TG,GG		0.2442,0.0227,0.1692	benign,benign,benign	243/1105,243/1106,243/1106	44248783	22,12984	2203	4300	6503	SO:0001583	missense	284058	exon2			TTCCTTGAAGTGC	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.727C>A	17.37:g.44248783G>T	ENSP00000262419:p.Gln243Lys	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	354	110	0.310734	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.556207	0.27827	2.27E-4	0.002442	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.12039	2.72;2.72	6.04	6.04	0.98038	.	0.144262	0.47852	D	0.000202	T	0.08980	0.0222	N	0.14661	0.345	0.80722	D	1	B;B	0.24426	0.103;0.07	B;B	0.25140	0.058;0.033	T	0.36016	-0.9765	10	0.17369	T	0.5	-9.4613	13.6782	0.62467	0.0:0.1543:0.8457:0.0	.	243;243	C9JHY2;Q7Z3B3	.;K1267_HUMAN	K	243	ENSP00000262419:Q243K;ENSP00000387393:Q243K	ENSP00000262419:Q243K	Q	-	1	0	KIAA1267	41604560	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.286000	0.43496	2.873000	0.98535	0.561000	0.74099	CAA	G|0.998;T|0.002	0.002	strong		0.438	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
C2orf49	79074	hgsc.bcm.edu	37	2	105954140	105954140	+	Silent	SNP	G	G	A	rs55772482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:105954140G>A	ENST00000258457.2	+	1	325	c.96G>A	c.(94-96)gaG>gaA	p.E32E	C2orf49_ENST00000410049.1_Silent_p.E32E|RP11-332H14.2_ENST00000610036.1_lincRNA|C2orf49_ENST00000437250.2_Silent_p.E70E			Q9BVC5	ASHWN_HUMAN	chromosome 2 open reading frame 49	32					embryonic morphogenesis (GO:0048598)	tRNA-splicing ligase complex (GO:0072669)				endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6						TCACTCTGGAGCAGGTTGGGC	0.677													G|||	277	0.0553115	0.0076	0.1138	5008	,	,		5061	0.0238		0.1193	False		,,,				2504	0.045				p.E32E		Atlas-SNP	.											C2orf49,NS,carcinoma,+2,1	C2orf49	19	1	0			c.G96A						scavenged	.	G		117,4279		1,115,2082	12.0	13.0	13.0		96	5.5	1.0	2	dbSNP_129	13	1114,7448		68,978,3235	no	coding-synonymous	C2orf49	NM_024093.1		69,1093,5317	AA,AG,GG		13.011,2.6615,9.4999		32/233	105954140	1231,11727	2198	4281	6479	SO:0001819	synonymous_variant	79074	exon1			TCTGGAGCAGGTT	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.96G>A	2.37:g.105954140G>A		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_024093	B3KXN3|B4E2G9	Silent	SNP	ENST00000258457.2	37	CCDS2068.1																																																																																			G|0.927;A|0.073	0.073	strong		0.677	C2orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253353.2	NM_024093	
FAM200B	285550	hgsc.bcm.edu	37	4	15689632	15689632	+	Silent	SNP	G	G	A	rs11729955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:15689632G>A	ENST00000422728.2	+	2	1870	c.1032G>A	c.(1030-1032)gaG>gaA	p.E344E	FAM200B_ENST00000504137.1_Intron	NM_001145191.1	NP_001138663.1	P0CF97	F200B_HUMAN	family with sequence similarity 200, member B	344							nucleic acid binding (GO:0003676)	p.E344E(2)		endometrium(1)|kidney(1)	2						atctcatggaggtattgaaaa	0.328													A|||	1502	0.29992	0.3858	0.3098	5008	,	,		17540	0.1379		0.4056	False		,,,				2504	0.2352				p.E344E		Atlas-SNP	.											FAM200B_ENST00000422728,NS,carcinoma,0,2	FAM200B	56	2	2	Substitution - coding silent(2)	kidney(2)	c.G1032A						PASS	.	A		529,855		110,309,273	52.0	48.0	49.0		1032	2.6	1.0	4	dbSNP_120	49	1257,1925		249,759,583	no	coding-synonymous	FAM200B	NM_001145191.1		359,1068,856	AA,AG,GG		39.5035,38.2225,39.1152		344/658	15689632	1786,2780	692	1591	2283	SO:0001819	synonymous_variant	285550	exon2			CATGGAGGTATTG	BC048993	CCDS47028.1	4p15.32	2014-04-02			ENSG00000237765	ENSG00000237765			27740	protein-coding gene	gene with protein product	"""chromosome 4 open reading frame 53"""						Standard	NM_001145191		Approved	C4orf53	uc003gof.4	P0CF97	OTTHUMG00000160279	ENST00000422728.2:c.1032G>A	4.37:g.15689632G>A		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	174	172	0.988506	NM_001145191		Silent	SNP	ENST00000422728.2	37	CCDS47028.1																																																																																			G|0.683;A|0.317	0.317	strong		0.328	FAM200B-005	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360100.1	NM_001145191	
PAG1	55824	hgsc.bcm.edu	37	8	81897200	81897200	+	Silent	SNP	C	C	T	rs7006101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	352	1	0.00284091		WXS	Illumina HiSeq	Phase_I	328	163	0.496951	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	
TRMT12	55039	hgsc.bcm.edu	37	8	125463544	125463544	+	Silent	SNP	T	T	C	rs11556913	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	103	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	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	
FNDC1	84624	hgsc.bcm.edu	37	6	159672419	159672419	+	Silent	SNP	G	G	C	rs551392	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	84	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	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	
RRP9	9136	hgsc.bcm.edu	37	3	51969389	51969389	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:51969389C>T	ENST00000232888.6	-	10	1013	c.940G>A	c.(940-942)Gag>Aag	p.E314K		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	314					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		TGGGACTCCTCGGGGATCTTC	0.652																																					p.E314K		Atlas-SNP	.											.	RRP9	40	.	0			c.G940A						PASS	.						40.0	40.0	40.0					3																	51969389		2203	4300	6503	SO:0001583	missense	9136	exon10			ACTCCTCGGGGAT	AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"""WD repeat domain containing"""	16829	protein-coding gene	gene with protein product			"""RNA, U3 small nucleolar interacting protein 2"""	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.940G>A	3.37:g.51969389C>T	ENSP00000232888:p.Glu314Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146212	0.94603	.	.	ENSG00000114767	ENST00000232888	T	0.80909	-1.43	4.36	4.36	0.52297	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051372	0.85682	D	0.000000	D	0.90748	0.7096	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	D	0.91266	0.5040	10	0.38643	T	0.18	-33.3696	16.7078	0.85377	0.0:1.0:0.0:0.0	.	314	O43818	U3IP2_HUMAN	K	314	ENSP00000232888:E314K	ENSP00000232888:E314K	E	-	1	0	RRP9	51944429	1.000000	0.71417	0.936000	0.37596	0.950000	0.60333	7.083000	0.76859	2.278000	0.76064	0.561000	0.74099	GAG	.	.	none		0.652	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	
MC5R	4161	hgsc.bcm.edu	37	18	13826508	13826508	+	Silent	SNP	C	C	T	rs2236701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:13826508C>T	ENST00000324750.3	+	1	966	c.744C>T	c.(742-744)acC>acT	p.T248T	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	248					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						GCGTGTTTACCGTGTGCTGGG	0.587													C|||	1324	0.264377	0.3109	0.3573	5008	,	,		20387	0.3433		0.173	False		,,,				2504	0.1483				p.T248T		Atlas-SNP	.											.	MC5R	83	.	0			c.C744T						PASS	.	C		1258,3148	430.6+/-342.6	192,874,1137	219.0	172.0	188.0		744	-0.9	0.7	18	dbSNP_98	188	1536,7064	288.9+/-299.0	139,1258,2903	no	coding-synonymous	MC5R	NM_005913.2		331,2132,4040	TT,TC,CC		17.8605,28.552,21.4824		248/326	13826508	2794,10212	2203	4300	6503	SO:0001819	synonymous_variant	4161	exon1			GTTTACCGTGTGC	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.744C>T	18.37:g.13826508C>T		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	167	96	0.57485	NM_005913	B0YJ34|Q502V1	Silent	SNP	ENST00000324750.3	37	CCDS11868.1																																																																																			C|0.775;T|0.225	0.225	strong		0.587	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913	
SCIN	85477	hgsc.bcm.edu	37	7	12620804	12620804	+	Silent	SNP	C	C	T	rs17283717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:12620804C>T	ENST00000297029.5	+	3	575	c.474C>T	c.(472-474)gaC>gaT	p.D158D		NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	158	Actin-severing. {ECO:0000255}.				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)		TTAGCTGGGACAGTTTCAACA	0.443													C|||	1275	0.254593	0.1778	0.3386	5008	,	,		19419	0.2123		0.3598	False		,,,				2504	0.2342				p.D158D		Atlas-SNP	.											.	SCIN	105	.	0			c.C474T						PASS	.	C		269,1115		30,209,453	146.0	114.0	124.0		474	2.2	1.0	7	dbSNP_123	124	1186,1996		227,732,632	no	coding-synonymous	SCIN	NM_001112706.2		257,941,1085	TT,TC,CC		37.2722,19.4364,31.866		158/716	12620804	1455,3111	692	1591	2283	SO:0001819	synonymous_variant	85477	exon3			CTGGGACAGTTTC	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.474C>T	7.37:g.12620804C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	37	CCDS47545.1																																																																																			C|0.733;T|0.267	0.267	strong		0.443	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
KLKB1	3818	hgsc.bcm.edu	37	4	187173012	187173012	+	Missense_Mutation	SNP	T	T	G	rs4253301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187173012T>G	ENST00000264690.6	+	10	1328	c.1141T>G	c.(1141-1143)Tct>Gct	p.S381A	KLKB1_ENST00000513864.1_Missense_Mutation_p.S381A	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	381			S -> A (in dbSNP:rs4253301). {ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		TGGGGACAACTCTGGTGAGTA	0.423													.|||	565	0.112819	0.0484	0.1095	5008	,	,		21668	0.0675		0.1342	False		,,,				2504	0.227				p.S381A		Atlas-SNP	.											KLKB1_ENST00000264690,bladder,carcinoma,-1,2	KLKB1	155	2	0			c.T1141G						PASS	.	T	ALA/SER	275,4131	153.7+/-187.2	5,265,1933	122.0	127.0	125.0		1141	-2.6	0.6	4	dbSNP_111	125	1004,7596	215.3+/-254.7	70,864,3366	yes	missense	KLKB1	NM_000892.3	99	75,1129,5299	GG,GT,TT		11.6744,6.2415,9.8339	benign	381/639	187173012	1279,11727	2203	4300	6503	SO:0001583	missense	3818	exon10			GACAACTCTGGTG	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.1141T>G	4.37:g.187173012T>G	ENSP00000264690:p.Ser381Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	205	0.09386446886446886	18	0.036585365853658534	48	0.13259668508287292	35	0.06118881118881119	104	0.13720316622691292	t	11.95	1.792986	0.31685	0.062415	0.116744	ENSG00000164344	ENST00000264690;ENST00000513864;ENST00000418715	D;D	0.92752	-2.47;-3.1	5.15	-2.63	0.06133	.	0.575398	0.16596	N	0.207553	T	0.01976	0.0062	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.34015	0.028;0.304;0.435	B;B;B	0.27887	0.01;0.077;0.084	T	0.49103	-0.8974	9	0.20046	T	0.44	.	0.948	0.01369	0.2601:0.3092:0.1211:0.3096	rs4253301;rs52817049;rs58196317;rs4253301	343;381;381	E7EQA8;A8K9A9;P03952	.;.;KLKB1_HUMAN	A	381;381;343	ENSP00000264690:S381A;ENSP00000424469:S381A	ENSP00000264690:S381A	S	+	1	0	KLKB1	187410006	0.218000	0.23608	0.578000	0.28575	0.687000	0.40016	0.685000	0.25378	-0.204000	0.10235	-0.348000	0.07805	TCT	T|0.904;G|0.096	0.096	strong		0.423	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	
TGM1	7051	hgsc.bcm.edu	37	14	24729687	24729687	+	Silent	SNP	C	C	T	rs35755034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24729687C>T	ENST00000206765.6	-	4	849	c.726G>A	c.(724-726)gaG>gaA	p.E242E	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	242					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	GGATGTAGATCTCATTGCGGG	0.587													C|||	291	0.058107	0.0923	0.0231	5008	,	,		20751	0.0754		0.0199	False		,,,				2504	0.0583				p.E242E		Atlas-SNP	.											.	TGM1	73	.	0			c.G726A						PASS	.	C		445,3961	215.8+/-234.7	19,407,1777	103.0	90.0	95.0		726	3.6	1.0	14	dbSNP_126	95	196,8404	85.6+/-148.0	3,190,4107	no	coding-synonymous	TGM1	NM_000359.2		22,597,5884	TT,TC,CC		2.2791,10.0999,4.9285		242/818	24729687	641,12365	2203	4300	6503	SO:0001819	synonymous_variant	7051	exon4			GTAGATCTCATTG	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"""Transglutaminases"""	11777	protein-coding gene	gene with protein product	"""K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"""	190195	"""transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"""	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.726G>A	14.37:g.24729687C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_000359	B4DWR7|Q197M4	Silent	SNP	ENST00000206765.6	37	CCDS9622.1																																																																																			C|0.952;T|0.048	0.048	strong		0.587	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359	
PTPN12	5782	hgsc.bcm.edu	37	7	77247821	77247821	+	Missense_Mutation	SNP	G	G	A	rs9640663	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:77247821G>A	ENST00000248594.6	+	12	1236	c.964G>A	c.(964-966)Gtc>Atc	p.V322I	PTPN12_ENST00000435495.2_Missense_Mutation_p.V192I|PTPN12_ENST00000415482.2_Missense_Mutation_p.V203I	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	31	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	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		
PCSK5	5125	hgsc.bcm.edu	37	9	78936358	78936358	+	Missense_Mutation	SNP	G	G	A	rs1110222	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	70	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	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			
KLK2	3817	hgsc.bcm.edu	37	19	51379893	51379893	+	Silent	SNP	C	C	T	rs198972	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51379893C>T	ENST00000325321.3	+	3	597	c.372C>T	c.(370-372)ctC>ctT	p.L124L	KLK2_ENST00000391810.2_Silent_p.L22L|KLK2_ENST00000358049.4_Silent_p.L124L|AC037199.1_ENST00000594218.1_5'Flank			P20151	KLK2_HUMAN	kallikrein-related peptidase 2	124	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)		KLK2/ETV1(3)|KLK2/ETV4(2)	large_intestine(3)|lung(6)|ovary(1)|skin(1)	11		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.00871)		TCATGCTGCTCCGCCTGTCAG	0.587			T	ETV4	prostate								C|||	2214	0.442093	0.6558	0.3545	5008	,	,		19482	0.2877		0.332	False		,,,				2504	0.4877				p.L124L		Atlas-SNP	.		Dom	yes		19	19q13.41	3817	kallikrein-related peptidase 2		E	.	KLK2	66	.	0			c.C372T						PASS	.	C	,	2707,1699	651.8+/-399.3	845,1017,341	62.0	57.0	59.0		372,372	-5.2	0.0	19	dbSNP_79	59	2686,5914	430.0+/-356.4	414,1858,2028	no	coding-synonymous,coding-synonymous	KLK2	NM_001002231.1,NM_005551.3	,	1259,2875,2369	TT,TC,CC		31.2326,38.5611,41.4655	,	124/224,124/262	51379893	5393,7613	2203	4300	6503	SO:0001819	synonymous_variant	3817	exon3			GCTGCTCCGCCTG	M18157	CCDS12808.1, CCDS42597.1, CCDS58675.1	19q13.33	2008-02-05	2006-10-27				3.4.21.35	"""Kallikreins"""	6363	protein-coding gene	gene with protein product		147960	"""kallikrein 2, prostatic"""			2468530, 16800724, 16800723	Standard	NM_005551		Approved		uc002ptv.3	P20151		ENST00000325321.3:c.372C>T	19.37:g.51379893C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	98	58	0.591837	NM_001002231	B4DU93|B4DUB0|F5H8L3|Q15946|Q9UJZ9	Silent	SNP	ENST00000325321.3	37	CCDS12808.1																																																																																			C|0.585;T|0.415	0.415	strong		0.587	KLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464438.3	NM_005551.3	
PRUNE2	158471	hgsc.bcm.edu	37	9	79320095	79320095	+	Missense_Mutation	SNP	T	T	G	rs3739524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79320095T>G	ENST00000376718.3	-	8	7218	c.7095A>C	c.(7093-7095)ttA>ttC	p.L2365F	PRUNE2_ENST00000428286.1_Missense_Mutation_p.L2006F	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2365					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						GCTCTCTCAGTAAATCTTCAT	0.478													T|||	1415	0.282548	0.3495	0.1787	5008	,	,		21606	0.4673		0.173	False		,,,				2504	0.1881				p.L2365F		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A7095C						PASS	.	T	PHE/LEU	952,2184		142,668,758	176.0	167.0	170.0		7095	-6.0	0.0	9	dbSNP_107	170	1051,6113		68,915,2599	yes	missense	PRUNE2	NM_015225.2	22	210,1583,3357	GG,GT,TT		14.6706,30.3571,19.4466	benign	2365/3089	79320095	2003,8297	1568	3582	5150	SO:0001583	missense	158471	exon8			TCTCAGTAAATCT	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.7095A>C	9.37:g.79320095T>G	ENSP00000365908:p.Leu2365Phe	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	664|664	0.304029304029304|0.304029304029304	185|185	0.37601626016260165|0.37601626016260165	60|60	0.16574585635359115|0.16574585635359115	286|286	0.5|0.5	133|133	0.17546174142480211|0.17546174142480211	T|T	6.441|6.441	0.449511|0.449511	0.12223|0.12223	0.303571|0.303571	0.146706|0.146706	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.49139|.	0.79;0.79|.	5.93|5.93	-6.03|-6.03	0.02185|0.02185	.|.	1.139740|.	0.06556|.	N|.	0.745923|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.56769|0.56769	1.78|1.78	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	B|.	0.12630|.	0.006|.	B|.	0.08055|.	0.003|.	T|T	0.36625|0.36625	-0.9740|-0.9740	9|4	0.42905|.	T|.	0.14|.	-0.0066|-0.0066	4.0518|4.0518	0.09798|0.09798	0.1932:0.1249:0.4936:0.1882|0.1932:0.1249:0.4936:0.1882	rs3739524;rs17180760;rs52795993;rs61003206;rs3739524|rs3739524;rs17180760;rs52795993;rs61003206;rs3739524	2365|.	Q8WUY3|.	PRUN2_HUMAN|.	F|P	2365;2006;2364|1687	ENSP00000365908:L2365F;ENSP00000397425:L2006F|.	ENSP00000365908:L2365F|.	L|T	-|-	3|1	2|0	PRUNE2|PRUNE2	78509915|78509915	0.000000|0.000000	0.05858|0.05858	0.032000|0.032000	0.17829|0.17829	0.256000|0.256000	0.26092|0.26092	-0.885000|-0.885000	0.04161|0.04161	-1.146000|-1.146000	0.02854|0.02854	-1.243000|-1.243000	0.01532|0.01532	TTA|ACT	G|0.303;N|0.000	0.303	strong		0.478	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
CCDC110	256309	hgsc.bcm.edu	37	4	186379735	186379735	+	Missense_Mutation	SNP	T	T	C	rs6827370	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	51	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	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	
FNDC1	84624	hgsc.bcm.edu	37	6	159672542	159672542	+	Silent	SNP	C	C	T	rs550443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	81	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	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	
PRR21	643905	hgsc.bcm.edu	37	2	240982247	240982247	+	Silent	SNP	A	A	G	rs75044548	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:240982247A>G	ENST00000408934.1	-	1	152	c.153T>C	c.(151-153)caT>caC	p.H51H		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	51	Pro-rich.							p.H51H(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						AGAGCCGTGGATGAAGGGCCA	0.577																																					p.H51H		Atlas-SNP	.											PRR21,NS,carcinoma,0,2	PRR21	53	2	2	Substitution - coding silent(2)	ovary(2)	c.T153C						PASS	.						118.0	104.0	109.0					2																	240982247		2203	4299	6502	SO:0001819	synonymous_variant	643905	exon1			CCGTGGATGAAGG	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.153T>C	2.37:g.240982247A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	28	22	0.785714	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			A|0.813;G|0.187	0.187	strong		0.577	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
FAM89A	375061	hgsc.bcm.edu	37	1	231155682	231155682	+	Missense_Mutation	SNP	C	C	T	rs141463019	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:231155682C>T	ENST00000366654.4	-	2	516	c.482G>A	c.(481-483)cGa>cAa	p.R161Q	MIR1182_ENST00000408363.1_RNA|FAM89A_ENST00000494111.1_5'UTR	NM_198552.2	NP_940954.1	Q96GI7	FA89A_HUMAN	family with sequence similarity 89, member A	161										endometrium(1)|upper_aerodigestive_tract(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AGGAGGGCCTCGGTCCCTCCT	0.582													C|||	4	0.000798722	0.0015	0.0	5008	,	,		20019	0.0		0.002	False		,,,				2504	0.0				p.R161Q		Atlas-SNP	.											.	FAM89A	8	.	0			c.G482A						PASS	.	C	GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	81.0	79.0	80.0		482	-0.1	0.0	1	dbSNP_134	80	16,8584	11.9+/-42.8	0,16,4284	yes	missense	FAM89A	NM_198552.2	43	0,22,6481	TT,TC,CC		0.186,0.1362,0.1692	benign	161/185	231155682	22,12984	2203	4300	6503	SO:0001583	missense	375061	exon2			GGGCCTCGGTCCC	BC009447	CCDS1590.1	1q42.2	2008-02-05	2005-09-13	2005-09-13	ENSG00000182118	ENSG00000182118			25057	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 153"""	C1orf153		12477932	Standard	NM_198552		Approved	MGC15887	uc001hui.2	Q96GI7	OTTHUMG00000037960	ENST00000366654.4:c.482G>A	1.37:g.231155682C>T	ENSP00000355614:p.Arg161Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_198552		Missense_Mutation	SNP	ENST00000366654.4	37	CCDS1590.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.03	3.285071	0.59867	0.001362	0.00186	ENSG00000182118	ENST00000366654	.	.	.	5.6	-0.0557	0.13808	.	1.086610	0.07184	N	0.854580	T	0.26159	0.0638	N	0.19112	0.55	0.09310	N	1	B	0.22346	0.068	B	0.12837	0.008	T	0.22871	-1.0204	9	0.19147	T	0.46	5.0E-4	9.7002	0.40182	0.0:0.4293:0.0:0.5707	.	161	Q96GI7	FA89A_HUMAN	Q	161	.	ENSP00000355614:R161Q	R	-	2	0	FAM89A	229222305	0.000000	0.05858	0.001000	0.08648	0.968000	0.65278	-0.990000	0.03732	0.163000	0.19507	0.453000	0.30009	CGA	C|0.999;T|0.001	0.001	strong		0.582	FAM89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092652.1	NM_198552	
CCDC38	120935	hgsc.bcm.edu	37	12	96284650	96284650	+	Silent	SNP	A	A	G	rs6538681	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:96284650A>G	ENST00000344280.3	-	9	1388	c.831T>C	c.(829-831)gcT>gcC	p.A277A	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	277										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTGAAAGGACAGCTGTCCTCC	0.443													G|||	3778	0.754393	0.9145	0.536	5008	,	,		21217	0.745		0.7058	False		,,,				2504	0.7526				p.A277A		Atlas-SNP	.											.	CCDC38	45	.	0			c.T831C						PASS	.	G		3874,532	244.3+/-253.7	1705,464,34	87.0	80.0	82.0		831	-5.0	0.0	12	dbSNP_116	82	6036,2564	418.2+/-352.7	2111,1814,375	no	coding-synonymous	CCDC38	NM_182496.2		3816,2278,409	GG,GA,AA		29.814,12.0744,23.8044		277/564	96284650	9910,3096	2203	4300	6503	SO:0001819	synonymous_variant	120935	exon9			AAGGACAGCTGTC	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.831T>C	12.37:g.96284650A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_182496	Q8N835	Silent	SNP	ENST00000344280.3	37	CCDS9056.1																																																																																			A|0.248;G|0.752	0.752	strong		0.443	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
ATG4B	23192	hgsc.bcm.edu	37	2	242606080	242606080	+	Missense_Mutation	SNP	G	G	A	rs35613684	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242606080G>A	ENST00000404914.3	+	8	662	c.559G>A	c.(559-561)Gtt>Att	p.V187I	ATG4B_ENST00000402096.1_Missense_Mutation_p.V113I|ATG4B_ENST00000396411.3_Missense_Mutation_p.V113I|ATG4B_ENST00000405546.3_Missense_Mutation_p.V187I|ATG4B_ENST00000474739.2_Missense_Mutation_p.V173I	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	187					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)		CAGGACCAGCGTTCCCTGTGC	0.567													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18650	0.0		0.006	False		,,,				2504	0.0				p.V187I	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.G559A						PASS	.	G	ILE/VAL,ILE/VAL	7,4269		0,7,2131	33.0	36.0	35.0		559,559	-3.0	0.0	2	dbSNP_126	35	60,8384		2,56,4164	yes	missense,missense	ATG4B	NM_013325.4,NM_178326.2	29,29	2,63,6295	AA,AG,GG		0.7106,0.1637,0.5267	benign,benign	187/394,187/381	242606080	67,12653	2138	4222	6360	SO:0001583	missense	23192	exon8			ACCAGCGTTCCCT	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.559G>A	2.37:g.242606080G>A	ENSP00000384259:p.Val187Ile	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_178326	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Missense_Mutation	SNP	ENST00000404914.3	37	CCDS46564.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	12.75	2.032450	0.35893	0.001637	0.007106	ENSG00000168397	ENST00000405546;ENST00000337606;ENST00000402096;ENST00000404914;ENST00000474739;ENST00000396411;ENST00000400771;ENST00000429899;ENST00000311517;ENST00000428861	T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.79	-2.96	0.05547	.	1.522260	0.03648	N	0.240580	T	0.15609	0.0376	N	0.12920	0.275	0.09310	N	1	B;B;B;B;B	0.25235	0.121;0.067;0.055;0.009;0.007	B;B;B;B;B	0.20184	0.016;0.028;0.024;0.008;0.01	T	0.07328	-1.0778	10	0.21540	T	0.41	0.9712	3.7127	0.08425	0.1122:0.134:0.4743:0.2795	rs35613684	173;304;275;187;113	F5H7P2;B4DZK0;Q9Y4P1-2;Q9Y4P1;Q9Y4P1-4	.;.;.;ATG4B_HUMAN;.	I	187;304;113;187;173;113;136;113;113;24	ENSP00000383964:V187I;ENSP00000384661:V113I;ENSP00000384259:V187I;ENSP00000442378:V173I;ENSP00000379692:V113I;ENSP00000383582:V136I;ENSP00000410526:V113I;ENSP00000404783:V24I	ENSP00000309348:V113I	V	+	1	0	ATG4B	242254753	0.000000	0.05858	0.000000	0.03702	0.431000	0.31685	-0.503000	0.06383	-0.406000	0.07588	-1.053000	0.02334	GTT	G|0.998;A|0.002	0.002	strong		0.567	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325	
GPRC5C	55890	hgsc.bcm.edu	37	17	72436949	72436949	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72436949T>C	ENST00000392627.1	+	2	2295	c.1169T>C	c.(1168-1170)aTg>aCg	p.M390T	GPRC5C_ENST00000481232.1_Intron|GPRC5C_ENST00000392629.2_Missense_Mutation_p.M357T|GPRC5C_ENST00000342648.5_Missense_Mutation_p.M30T	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	345					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						GCCTTTTCCATGGATGAGCCG	0.577																																					p.M390T		Atlas-SNP	.											.	GPRC5C	92	.	0			c.T1169C						PASS	.						84.0	82.0	83.0					17																	72436949		2203	4300	6503	SO:0001583	missense	55890	exon2			TTTCCATGGATGA	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"""GPCR / Class C : Orphans"""	13309	protein-coding gene	gene with protein product		605949	"""G protein-coupled receptor, family C, group 5, member C"""			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000392627.1:c.1169T>C	17.37:g.72436949T>C	ENSP00000376403:p.Met390Thr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000392627.1	37	CCDS11699.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.089028	0.36855	.	.	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000262616;ENST00000392629;ENST00000392628	T	0.20463	2.07	5.42	5.42	0.78866	.	0.125962	0.85682	D	0.000000	T	0.26340	0.0643	L	0.59436	1.845	0.80722	D	1	B;B;B	0.25772	0.134;0.072;0.118	B;B;B	0.29267	0.075;0.046;0.1	T	0.04621	-1.0938	10	0.87932	D	0	-11.5631	14.6481	0.68774	0.0:0.0:0.0:1.0	.	345;345;357	A8MXZ4;Q9NQ84;Q9NQ84-2	.;GPC5C_HUMAN;.	T	345;390;56;357;345	ENSP00000376405:M357T	ENSP00000262616:M56T	M	+	2	0	GPRC5C	69948544	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	6.106000	0.71511	2.061000	0.61500	0.459000	0.35465	ATG	.	.	none		0.577	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2		
ZCCHC2	54877	hgsc.bcm.edu	37	18	60231851	60231851	+	Silent	SNP	A	A	G	rs12956093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:60231851A>G	ENST00000269499.5	+	10	2152	c.1734A>G	c.(1732-1734)ggA>ggG	p.G578G	ZCCHC2_ENST00000586834.1_Silent_p.G257G	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	578						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						AGAAGAAAGGAAAGCCACAAA	0.308													A|||	414	0.0826677	0.0068	0.1816	5008	,	,		16285	0.001		0.2386	False		,,,				2504	0.0389				p.G578G		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.A1734G						PASS	.	A		138,3382		3,132,1625	50.0	42.0	44.0		1734	3.6	1.0	18	dbSNP_121	44	1460,6500		123,1214,2643	no	coding-synonymous	ZCCHC2	NM_017742.4		126,1346,4268	GG,GA,AA		18.3417,3.9205,13.9199		578/1179	60231851	1598,9882	1760	3980	5740	SO:0001819	synonymous_variant	54877	exon10			GAAAGGAAAGCCA	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.1734A>G	18.37:g.60231851A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Silent	SNP	ENST00000269499.5	37	CCDS45880.1																																																																																			A|0.878;G|0.122	0.122	strong		0.308	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742	
SMCR8	140775	hgsc.bcm.edu	37	17	18220268	18220268	+	Missense_Mutation	SNP	A	A	G	rs79875842	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:18220268A>G	ENST00000406438.3	+	1	1645	c.1165A>G	c.(1165-1167)Ata>Gta	p.I389V	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	389						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						ACAAGAAAGCATACCCTCTAA	0.418													A|||	17	0.00339457	0.0015	0.0058	5008	,	,		22155	0.0		0.0099	False		,,,				2504	0.001				p.I389V		Atlas-SNP	.											.	SMCR8	62	.	0			c.A1165G						PASS	.	A	VAL/ILE	14,4392	21.2+/-45.6	0,14,2189	118.0	113.0	115.0		1165	-11.8	0.0	17	dbSNP_131	115	121,8479	62.4+/-124.4	2,117,4181	yes	missense	SMCR8	NM_144775.2	29	2,131,6370	GG,GA,AA		1.407,0.3177,1.038	benign	389/938	18220268	135,12871	2203	4300	6503	SO:0001583	missense	140775	exon1			GAAAGCATACCCT	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1165A>G	17.37:g.18220268A>G	ENSP00000385025:p.Ile389Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	A	0.010	-1.786354	0.00628	0.003177	0.01407	ENSG00000176994	ENST00000406438	T	0.20881	2.04	5.9	-11.8	0.00035	.	1.175130	0.06061	N	0.658377	T	0.02571	0.0078	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10567	-1.0624	10	0.02654	T	1	-20.6322	7.2119	0.25939	0.2449:0.1412:0.5438:0.0701	.	389	Q8TEV9	SMCR8_HUMAN	V	389	ENSP00000385025:I389V	ENSP00000385025:I389V	I	+	1	0	SMCR8	18160993	0.000000	0.05858	0.000000	0.03702	0.233000	0.25261	-0.704000	0.05058	-3.114000	0.00240	-0.291000	0.09656	ATA	A|0.991;G|0.009	0.009	strong		0.418	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
DNAH7	56171	hgsc.bcm.edu	37	2	196822004	196822004	+	Missense_Mutation	SNP	A	A	G	rs62623378	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:196822004A>G	ENST00000312428.6	-	19	3159	c.3059T>C	c.(3058-3060)aTa>aCa	p.I1020T		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1020	Stem. {ECO:0000250}.			I -> T (in Ref. 2; BAA76788). {ECO:0000305}.	cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						ACTTCTCATTATATCTCTCCA	0.388													A|||	239	0.0477236	0.0068	0.0778	5008	,	,		20305	0.001		0.1074	False		,,,				2504	0.0685				p.I1020T		Atlas-SNP	.											.	DNAH7	512	.	0			c.T3059C						PASS	.	A	THR/ILE	77,3669		1,75,1797	120.0	108.0	111.0		3059	4.4	0.9	2	dbSNP_129	111	972,7268		59,854,3207	yes	missense	DNAH7	NM_018897.2	89	60,929,5004	GG,GA,AA		11.7961,2.0555,8.7519	benign	1020/4025	196822004	1049,10937	1873	4120	5993	SO:0001583	missense	56171	exon19			CTCATTATATCTC	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.3059T>C	2.37:g.196822004A>G	ENSP00000311273:p.Ile1020Thr	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	431	235	0.545244	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	110	0.05036630036630037	2	0.0040650406504065045	33	0.09116022099447514	1	0.0017482517482517483	74	0.09762532981530343	A	8.570	0.879782	0.17467	0.020555	0.117961	ENSG00000118997	ENST00000312428	T	0.64085	-0.08	5.57	4.41	0.53225	Dynein heavy chain, domain-2 (1);	0.529435	0.20211	N	0.096913	T	0.00998	0.0033	L	0.38692	1.165	0.20563	P	0.999884684	B	0.12013	0.005	B	0.16722	0.016	T	0.15665	-1.0429	9	0.40728	T	0.16	.	11.7773	0.51993	0.9308:0.0:0.0692:0.0	rs62623378	1020	Q8WXX0	DYH7_HUMAN	T	1020	ENSP00000311273:I1020T	ENSP00000311273:I1020T	I	-	2	0	DNAH7	196530249	0.507000	0.26146	0.939000	0.37840	0.485000	0.33311	2.482000	0.45224	1.044000	0.40200	0.533000	0.62120	ATA	A|0.921;G|0.079	0.079	strong		0.388	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
PI4KA	5297	hgsc.bcm.edu	37	22	21066789	21066789	+	Silent	SNP	A	A	G	rs5996654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21066789A>G	ENST00000572273.1	-	50	5843	c.5613T>C	c.(5611-5613)acT>acC	p.T1871T	PI4KA_ENST00000255882.6_Silent_p.T1929T|PI4KA_ENST00000414196.3_Silent_p.T681T			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1871	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.T1871T(1)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			GGAAGGCCAGAGTGGACTCAT	0.662																																					p.T1929T	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	1	Substitution - coding silent(1)	stomach(1)	c.T5787C						PASS	.						23.0	25.0	24.0					22																	21066789		2198	4284	6482	SO:0001819	synonymous_variant	5297	exon50			GGCCAGAGTGGAC	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5613T>C	22.37:g.21066789A>G		Somatic	336	1	0.00297619		WXS	Illumina HiSeq	Phase_I	247	222	0.898785	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|0.618;G|0.382	0.382	strong		0.662	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
SBSPON	157869	hgsc.bcm.edu	37	8	74005131	74005131	+	Missense_Mutation	SNP	A	A	G	rs59331088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:74005131A>G	ENST00000297354.6	-	1	376	c.172T>C	c.(172-174)Ttc>Ctc	p.F58L	SBSPON_ENST00000519697.1_Intron	NM_153225.3	NP_694957.3	Q8IVN8	SBSPO_HUMAN	somatomedin B and thrombospondin, type 1 domain containing	58	SMB. {ECO:0000255|PROSITE- ProRule:PRU00350}.		F -> L (in dbSNP:rs59331088). {ECO:0000269|PubMed:12107410}.		immune response (GO:0006955)	proteinaceous extracellular matrix (GO:0005578)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)										TCCCCGGTGAAGCGACAGGCT	0.711													G|||	1839	0.367212	0.649	0.2738	5008	,	,		9492	0.2966		0.2873	False		,,,				2504	0.2076				p.F58L		Atlas-SNP	.											.	.	.	.	0			c.T172C						PASS	.	G	LEU/PHE	2242,1716		657,928,394	26.0	38.0	34.0		172	3.2	1.0	8	dbSNP_129	34	2237,6025		307,1623,2201	yes	missense	C8orf84	NM_153225.3	22	964,2551,2595	GG,GA,AA		27.0758,43.3552,36.653	benign	58/265	74005131	4479,7741	1979	4131	6110	SO:0001583	missense	157869	exon1			CGGTGAAGCGACA		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.172T>C	8.37:g.74005131A>G	ENSP00000297354:p.Phe58Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_153225	A8KAA5|Q96J64	Missense_Mutation	SNP	ENST00000297354.6	37	CCDS43747.2	800	0.3663003663003663	324	0.6585365853658537	111	0.30662983425414364	163	0.28496503496503495	202	0.26649076517150394	G	10.70	1.423153	0.25639	0.566448	0.270758	ENSG00000164764	ENST00000297354	T	0.20738	2.05	5.15	3.25	0.37280	Somatomedin B domain (2);	0.526255	0.19119	N	0.122227	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	0.35351	-0.9792	9	0.07990	T	0.79	-14.5554	7.5784	0.27950	0.1573:0.1376:0.7051:0.0	rs59331088;rs62510382	58	Q8IVN8	RPESP_HUMAN	L	58	ENSP00000297354:F58L	ENSP00000297354:F58L	F	-	1	0	C8orf84	74167685	0.163000	0.22920	0.998000	0.56505	0.992000	0.81027	0.807000	0.27140	1.175000	0.42826	-0.220000	0.12472	TTC	A|0.660;G|0.340	0.340	strong		0.711	SBSPON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347584.2	NM_153225	
UNC5CL	222643	hgsc.bcm.edu	37	6	40998141	40998141	+	Silent	SNP	G	G	A	rs736795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:40998141G>A	ENST00000373164.1	-	7	1380	c.1320C>T	c.(1318-1320)tgC>tgT	p.C440C	UNC5CL_ENST00000244565.3_Silent_p.C440C|UNC5CL_ENST00000470102.1_5'UTR			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	440	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCTTCATGCCGCAAAGCCCCA	0.597													G|||	1385	0.276558	0.2368	0.268	5008	,	,		19416	0.2778		0.2038	False		,,,				2504	0.41				p.C440C		Atlas-SNP	.											.	UNC5CL	52	.	0			c.C1320T						PASS	.	G		1033,3373	380.9+/-323.9	131,771,1301	82.0	74.0	76.0		1320	-5.8	0.9	6	dbSNP_86	76	2098,6502	363.7+/-333.3	254,1590,2456	no	coding-synonymous	UNC5CL	NM_173561.2		385,2361,3757	AA,AG,GG		24.3953,23.4453,24.0735		440/519	40998141	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	222643	exon8			CATGCCGCAAAGC	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"""ZU5 and death domain containing"""					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1320C>T	6.37:g.40998141G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_173561	Q5TGU1	Silent	SNP	ENST00000373164.1	37	CCDS4847.1																																																																																			G|0.767;A|0.233	0.233	strong		0.597	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561	
PADI1	29943	hgsc.bcm.edu	37	1	17550121	17550121	+	Silent	SNP	G	G	A	rs2293912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17550121G>A	ENST00000375471.4	+	3	371	c.279G>A	c.(277-279)agG>agA	p.R93R		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	93					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	TGCAGGTGAGGGTCTCCTACT	0.587													G|||	735	0.146765	0.0477	0.3084	5008	,	,		19558	0.1567		0.1402	False		,,,				2504	0.1626				p.R93R	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.G279A						PASS	.	G		241,4165	141.1+/-176.5	9,223,1971	116.0	94.0	101.0		279	2.8	1.0	1	dbSNP_100	101	1374,7226	267.8+/-287.5	113,1148,3039	no	coding-synonymous	PADI1	NM_013358.2		122,1371,5010	AA,AG,GG		15.9767,5.4698,12.4173		93/664	17550121	1615,11391	2203	4300	6503	SO:0001819	synonymous_variant	29943	exon3			GGTGAGGGTCTCC	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.279G>A	1.37:g.17550121G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_013358	A1L4K6|Q70SX6	Silent	SNP	ENST00000375471.4	37	CCDS178.1																																																																																			G|0.877;A|0.121	0.121	strong		0.587	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
C1orf27	54953	hgsc.bcm.edu	37	1	186363119	186363119	+	Missense_Mutation	SNP	C	C	G	rs12084264	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:186363119C>G	ENST00000287859.6	+	9	877	c.752C>G	c.(751-753)tCt>tGt	p.S251C	C1orf27_ENST00000419367.3_Missense_Mutation_p.S219C|C1orf27_ENST00000432021.3_Intron|C1orf27_ENST00000367470.3_Intron	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	251			S -> C (in dbSNP:rs12084264). {ECO:0000269|PubMed:14702039}.			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						ACTAGTCATTCTTTTGATGTC	0.279													C|||	1164	0.232428	0.149	0.4078	5008	,	,		14393	0.127		0.335	False		,,,				2504	0.2239				p.S251C		Atlas-SNP	.											C1orf27_ENST00000287859,NS,carcinoma,0,2	C1orf27	41	2	0			c.C752G						PASS	.	C	,CYS/SER,CYS/SER	581,2775		48,485,1145	27.0	24.0	25.0		,656,752	3.4	0.9	1	dbSNP_120	25	2399,5149		385,1629,1760	yes	intron,missense,missense	C1orf27	NM_001164245.1,NM_001164246.1,NM_017847.5	,112,112	433,2114,2905	GG,GC,CC		31.7833,17.3123,27.3294	,benign,benign	,219/423,251/455	186363119	2980,7924	1678	3774	5452	SO:0001583	missense	54953	exon9			GTCATTCTTTTGA	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.752C>G	1.37:g.186363119C>G	ENSP00000287859:p.Ser251Cys	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	266	130	0.488722	NM_017847	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	557	0.25503663003663	65	0.13211382113821138	148	0.4088397790055249	77	0.1346153846153846	267	0.35224274406332456	C	15.80	2.939210	0.52972	0.173123	0.317833	ENSG00000157181	ENST00000419367;ENST00000432021;ENST00000287859	T;T	0.46451	0.87;0.87	5.34	3.43	0.39272	.	0.556512	0.18307	N	0.145224	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.99999999387866	D;B	0.57899	0.981;0.0	P;B	0.53062	0.717;0.003	T	0.43702	-0.9375	9	0.37606	T	0.19	-3.9611	6.5884	0.22634	0.0:0.5515:0.3334:0.1151	rs12084264;rs17521893;rs12084264	219;251	E9PFR7;Q5SWX8	.;ODR4_HUMAN	C	219;251;251	ENSP00000395084:S219C;ENSP00000287859:S251C	ENSP00000287859:S251C	S	+	2	0	C1orf27	184629742	0.008000	0.16893	0.940000	0.37924	0.976000	0.68499	0.050000	0.14120	0.605000	0.29947	-0.300000	0.09419	TCT	C|0.756;G|0.244	0.244	strong		0.279	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847	
COL4A3	1285	hgsc.bcm.edu	37	2	228160027	228160027	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228160027C>T	ENST00000396578.3	+	41	3722	c.3560C>T	c.(3559-3561)gCt>gTt	p.A1187V	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1187	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)		AACCCTGGTGCTCAAGGTAAG	0.393																																					p.A1187V		Atlas-SNP	.											COL4A3_ENST00000328380,NS,carcinoma,+1,2	COL4A3	293	2	0			c.C3560T						scavenged	.						101.0	100.0	100.0					2																	228160027		1841	4089	5930	SO:0001583	missense	1285	exon41			CTGGTGCTCAAGG		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.3560C>T	2.37:g.228160027C>T	ENSP00000379823:p.Ala1187Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	101	3	0.029703	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.952818	0.34471	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.93712	-3.27	5.32	-2.61	0.06171	.	2.012170	0.01995	N	0.045785	D	0.87253	0.6131	L	0.38649	1.16	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.10450	0.003;0.003;0.003;0.005	T	0.73959	-0.3818	10	0.13108	T	0.6	.	4.5628	0.12168	0.2429:0.3032:0.0:0.4539	.	1187;1187;1187;1187	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	V	1187	ENSP00000379823:A1187V	ENSP00000323334:A1187V	A	+	2	0	COL4A3	227868271	0.000000	0.05858	0.003000	0.11579	0.229000	0.25112	-2.051000	0.01402	-0.488000	0.06726	0.563000	0.77884	GCT	.	.	none		0.393	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
NDUFS7	374291	hgsc.bcm.edu	37	19	1388538	1388538	+	Missense_Mutation	SNP	C	C	T	rs1142530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1388538C>T	ENST00000233627.9	+	3	364	c.68C>T	c.(67-69)cCg>cTg	p.P23L	NDUFS7_ENST00000313408.7_Missense_Mutation_p.P23L|NDUFS7_ENST00000539480.1_Missense_Mutation_p.P23L|NDUFS7_ENST00000546283.1_Missense_Mutation_p.P23L|NDUFS7_ENST00000414651.2_Missense_Mutation_p.P23L|NDUFS7_ENST00000540530.1_3'UTR	NM_024407.4	NP_077718.3	O75251	NDUS7_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzyme Q reductase)	23			P -> L (in dbSNP:rs1142530). {ECO:0000269|PubMed:15489334}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|synaptic membrane (GO:0097060)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|quinone binding (GO:0048038)			ovary(1)	1		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)|Breast(49;0.00186)|Lung NSC(49;0.00292)|all_lung(49;0.00419)		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)	Doxorubicin(DB00997)	AGCGTGGGCCCGGCTGTGCAG	0.701													C|||	2282	0.455671	0.3585	0.4813	5008	,	,		15897	0.3264		0.5974	False		,,,				2504	0.5562				p.P23L		Atlas-SNP	.											.	NDUFS7	4	.	0			c.C68T						PASS	.	C	LEU/PRO	1674,2730		306,1062,834	26.0	28.0	27.0		68	0.8	0.0	19	dbSNP_86	27	5353,3241		1675,2003,619	yes	missense	NDUFS7	NM_024407.4	98	1981,3065,1453	TT,TC,CC		37.7124,38.0109,45.9378	benign	23/214	1388538	7027,5971	2202	4297	6499	SO:0001583	missense	374291	exon3			TGGGCCCGGCTGT	AF115969	CCDS12063.1	19p13	2011-07-04	2002-08-29		ENSG00000115286	ENSG00000115286		"""Mitochondrial respiratory chain complex / Complex I"""	7714	protein-coding gene	gene with protein product	"""complex I 20kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial"""	601825	"""NADH dehydrogenase (ubiquinone) Fe-S protein 7 (20kD) (NADH-coenzyme Q reductase)"""			8938450	Standard	NM_024407		Approved	PSST, FLJ46880, FLJ45860, CI-20	uc002lse.4	O75251	OTTHUMG00000168077	ENST00000233627.9:c.68C>T	19.37:g.1388538C>T	ENSP00000233627:p.Pro23Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_024407	B3KRI2|Q2T9H7|Q9BV17	Missense_Mutation	SNP	ENST00000233627.9	37	CCDS12063.1	969	0.44368131868131866	143	0.29065040650406504	172	0.47513812154696133	189	0.3304195804195804	465	0.6134564643799473	C	6.986	0.551973	0.13374	0.380109	0.622876	ENSG00000115286	ENST00000546283;ENST00000233627;ENST00000539480;ENST00000313408;ENST00000435801;ENST00000450862;ENST00000414651	T;T;T;T;T	0.63913	0.07;0.11;0.09;0.07;-0.07	4.25	0.837	0.18896	.	0.797288	0.10735	U	0.640146	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.14438	0.001;0.01;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.46498	-0.9187	9	0.17832	T	0.49	.	4.5671	0.12191	0.0:0.5386:0.164:0.2973	rs1142530;rs1801315;rs3180032;rs3206107;rs11551665;rs17401746;rs17845065;rs17857847;rs56861343;rs1142530	23;23;23	F5H5N1;B3KRI2;O75251	.;.;NDUS7_HUMAN	L	23	ENSP00000440348:P23L;ENSP00000233627:P23L;ENSP00000443273:P23L;ENSP00000364262:P23L;ENSP00000406630:P23L	ENSP00000233627:P23L	P	+	2	0	NDUFS7	1339538	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.885000	0.28227	0.164000	0.19529	0.561000	0.74099	CCG	C|0.511;T|0.489	0.489	strong		0.701	NDUFS7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397984.1	NM_024407	
CUL7	9820	hgsc.bcm.edu	37	6	43020188	43020188	+	Silent	SNP	G	G	A	rs4711738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43020188G>A	ENST00000265348.3	-	2	424	c.339C>T	c.(337-339)gaC>gaT	p.D113D	CUL7_ENST00000535468.1_Silent_p.D165D			Q14999	CUL7_HUMAN	cullin 7	113					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			GGGACTTCACGTCGGTTTCCA	0.612													A|||	1413	0.282149	0.5613	0.2205	5008	,	,		19600	0.2054		0.0905	False		,,,				2504	0.2249				p.D165D		Atlas-SNP	.											.	CUL7	133	.	0			c.C495T						PASS	.	A	,	2133,2273	597.5+/-388.9	504,1125,574	91.0	78.0	83.0		495,339	-9.3	0.0	6	dbSNP_111	83	790,7810	783.7+/-407.6	37,716,3547	no	coding-synonymous,coding-synonymous	CUL7	NM_001168370.1,NM_014780.4	,	541,1841,4121	AA,AG,GG		9.186,48.4113,22.4742	,	165/1783,113/1699	43020188	2923,10083	2203	4300	6503	SO:0001819	synonymous_variant	9820	exon2			CTTCACGTCGGTT	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.339C>T	6.37:g.43020188G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	92	33	0.358696	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Silent	SNP	ENST00000265348.3	37	CCDS4881.1																																																																																			G|0.755;A|0.245	0.245	strong		0.612	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
CHST1	8534	hgsc.bcm.edu	37	11	45672261	45672261	+	Silent	SNP	A	A	G	rs3802762	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:45672261A>G	ENST00000308064.2	-	4	883	c.213T>C	c.(211-213)agT>agC	p.S71S	CHST1_ENST00000533673.1_5'Flank|RP11-495O11.1_ENST00000525563.1_RNA	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	71					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		AGGAGGAGCCACTGCGCGTGG	0.637													G|||	3441	0.687101	0.3986	0.7795	5008	,	,		15939	0.6716		0.828	False		,,,				2504	0.8824				p.S71S		Atlas-SNP	.											.	CHST1	81	.	0			c.T213C						PASS	.	G		1995,2411	616.7+/-392.8	450,1095,658	78.0	73.0	75.0		213	2.7	1.0	11	dbSNP_107	75	7328,1270	251.2+/-277.8	3122,1084,93	no	coding-synonymous	CHST1	NM_003654.5		3572,2179,751	GG,GA,AA		14.7709,45.2792,28.3067		71/412	45672261	9323,3681	2203	4299	6502	SO:0001819	synonymous_variant	8534	exon4			GGAGCCACTGCGC	U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"""Sulfotransferases, membrane-bound"""	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.213T>C	11.37:g.45672261A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	223	221	0.991031	NM_003654	D3DQP2	Silent	SNP	ENST00000308064.2	37	CCDS7913.1																																																																																			G|0.689;N|0.000	0.689	strong		0.637	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802325	24802325	+	Missense_Mutation	SNP	C	C	T	rs3803716	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:24802325C>T	ENST00000395799.3	+	6	2491	c.2362C>T	c.(2362-2364)Cct>Tct	p.P788S	TNRC6A_ENST00000315183.7_Missense_Mutation_p.P788S	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	788	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.		P -> S (in dbSNP:rs3803716).		cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CGATCCCAAACCTGCTCTGAG	0.502													C|||	788	0.157348	0.1884	0.1455	5008	,	,		17985	0.126		0.162	False		,,,				2504	0.1513				p.P788S		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2362T						PASS	.	C	SER/PRO	767,3621		67,633,1494	36.0	39.0	38.0		2362	5.8	1.0	16	dbSNP_107	38	1632,6966		155,1322,2822	yes	missense	TNRC6A	NM_014494.2	74	222,1955,4316	TT,TC,CC		18.9812,17.4795,18.4737	benign	788/1963	24802325	2399,10587	2194	4299	6493	SO:0001583	missense	27327	exon6			CCCAAACCTGCTC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2362C>T	16.37:g.24802325C>T	ENSP00000379144:p.Pro788Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	301	0.13782051282051283	77	0.1565040650406504	55	0.15193370165745856	59	0.10314685314685315	110	0.14511873350923482	C	6.894	0.534394	0.13188	0.174795	0.189812	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.12569	2.67;2.68	5.85	5.85	0.93711	.	0.242162	0.39146	N	0.001457	T	0.00012	0.0000	N	0.10809	0.05	0.09310	P	1.0	B;B;B	0.19706	0.002;0.011;0.038	B;B;B	0.17979	0.02;0.013;0.018	T	0.42849	-0.9427	9	0.13853	T	0.58	-9.2271	7.6837	0.28528	0.0:0.8077:0.0:0.1923	rs3803716;rs17771305;rs61587441;rs3803716	535;788;788	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	S	788	ENSP00000326900:P788S;ENSP00000379144:P788S	ENSP00000326900:P788S	P	+	1	0	TNRC6A	24709826	1.000000	0.71417	0.969000	0.41365	0.862000	0.49288	2.213000	0.42844	2.768000	0.95171	0.655000	0.94253	CCT	C|0.850;T|0.150	0.150	strong		0.502	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
ENPP6	133121	hgsc.bcm.edu	37	4	185012387	185012387	+	Silent	SNP	C	C	T	rs28495394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:185012387C>T	ENST00000296741.2	-	8	1407	c.1266G>A	c.(1264-1266)ccG>ccA	p.P422P		NM_153343.3	NP_699174.1	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 6	422					choline metabolic process (GO:0019695)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glycerophosphocholine cholinephosphodiesterase activity (GO:0047390)|glycerophosphodiester phosphodiesterase activity (GO:0008889)|phosphoric diester hydrolase activity (GO:0008081)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	15		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		GCCAGACAGGCGGGGCAGTGC	0.552													c|||	585	0.116813	0.3616	0.0591	5008	,	,		15709	0.004		0.0398	False		,,,				2504	0.0225				p.P422P		Atlas-SNP	.											.	ENPP6	61	.	0			c.G1266A						PASS	.	C		1263,3143	417.8+/-338.1	175,913,1115	66.0	68.0	67.0		1266	-10.5	0.0	4	dbSNP_125	67	303,8297	109.0+/-169.6	3,297,4000	no	coding-synonymous	ENPP6	NM_153343.3		178,1210,5115	TT,TC,CC		3.5233,28.6655,12.0406		422/441	185012387	1566,11440	2203	4300	6503	SO:0001819	synonymous_variant	133121	exon8			GACAGGCGGGGCA	AK057370	CCDS3834.1	4q35.1	2008-02-05			ENSG00000164303	ENSG00000164303			23409	protein-coding gene	gene with protein product							Standard	NM_153343		Approved	MGC33971	uc003iwc.3	Q6UWR7	OTTHUMG00000160617	ENST00000296741.2:c.1266G>A	4.37:g.185012387C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_153343	Q4W5Q1|Q96M57	Silent	SNP	ENST00000296741.2	37	CCDS3834.1																																																																																			C|0.898;T|0.102	0.102	strong		0.552	ENPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361428.1	NM_153343	
CYP3A43	64816	hgsc.bcm.edu	37	7	99457605	99457605	+	Missense_Mutation	SNP	C	C	G	rs680055	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99457605C>G	ENST00000354829.2	+	10	1121	c.1018C>G	c.(1018-1020)Ccc>Gcc	p.P340A	CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000444905.1_Missense_Mutation_p.P87A|CYP3A43_ENST00000342499.4_Missense_Mutation_p.P200A|CYP3A43_ENST00000312017.5_Missense_Mutation_p.P340A|CYP3A43_ENST00000417625.1_Missense_Mutation_p.P230A|CYP3A43_ENST00000222382.5_Missense_Mutation_p.P340A|CYP3A43_ENST00000415413.1_Missense_Mutation_p.P129A	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	114	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	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		
ARHGAP9	64333	hgsc.bcm.edu	37	12	57867907	57867907	+	Silent	SNP	G	G	A	rs61754174	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57867907G>A	ENST00000356411.2	-	16	2031	c.1893C>T	c.(1891-1893)acC>acT	p.T631T	ARHGAP9_ENST00000424809.2_Silent_p.T612T|ARHGAP9_ENST00000430041.2_Silent_p.T428T|ARHGAP9_ENST00000393791.3_Silent_p.T612T|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000393797.2_Silent_p.T702T|ARHGAP9_ENST00000550288.1_Silent_p.T691T			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	631	Lipid binding.|Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			TCAGGGCTCCGGTGACCACAT	0.557													G|||	23	0.00459265	0.0	0.0115	5008	,	,		15812	0.0		0.0139	False		,,,				2504	0.001				p.T612T		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1836T						PASS	.	G	,,	9,4397	15.5+/-35.6	0,9,2194	45.0	48.0	47.0		1284,1836,1836	-4.7	1.0	12	dbSNP_129	47	72,8528	42.6+/-100.3	0,72,4228	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP9	NM_001080156.1,NM_001080157.1,NM_032496.2	,,	0,81,6422	AA,AG,GG		0.8372,0.2043,0.6228	,,	428/548,612/641,612/732	57867907	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	64333	exon15			GGCTCCGGTGACC	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1893C>T	12.37:g.57867907G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Silent	SNP	ENST00000356411.2	37																																																																																				G|0.994;A|0.006	0.006	strong		0.557	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
KIAA0753	9851	hgsc.bcm.edu	37	17	6513329	6513329	+	Missense_Mutation	SNP	G	G	A	rs2304977	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:6513329G>A	ENST00000361413.3	-	9	2055	c.1697C>T	c.(1696-1698)cCa>cTa	p.P566L	KIAA0753_ENST00000572370.1_Missense_Mutation_p.P267L|KIAA0753_ENST00000542606.1_Missense_Mutation_p.P267L|KIAA0753_ENST00000589033.1_Missense_Mutation_p.P22L	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	566			P -> L (in dbSNP:rs2304977).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		AGGAGACGCTGGTGGGGATGT	0.473													G|||	1361	0.271765	0.0303	0.3876	5008	,	,		16778	0.3562		0.3459	False		,,,				2504	0.3528				p.P566L		Atlas-SNP	.											.	KIAA0753	63	.	0			c.C1697T						PASS	.	G	LEU/PRO	325,3485		15,295,1595	155.0	154.0	154.0		1697	4.2	1.0	17	dbSNP_100	154	3087,5129		548,1991,1569	yes	missense	KIAA0753	NM_014804.2	98	563,2286,3164	AA,AG,GG		37.573,8.5302,28.3719	probably-damaging	566/968	6513329	3412,8614	1905	4108	6013	SO:0001583	missense	9851	exon9			GACGCTGGTGGGG		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1697C>T	17.37:g.6513329G>A	ENSP00000355250:p.Pro566Leu	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	291	290	0.996564	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	601	0.2751831501831502	20	0.04065040650406504	148	0.4088397790055249	178	0.3111888111888112	255	0.33641160949868076	G	18.74	3.688818	0.68271	0.085302	0.37573	ENSG00000198920	ENST00000361413;ENST00000542606;ENST00000542826	D;D	0.85702	-2.02;-2.02	5.14	4.15	0.48705	.	0.112488	0.64402	D	0.000007	T	0.00012	0.0000	M	0.78916	2.43	0.20563	P	0.99988895	D	0.57257	0.979	P	0.54270	0.747	T	0.01409	-1.1362	9	0.27785	T	0.31	-9.5145	11.2919	0.49256	0.0:0.0:0.8174:0.1826	rs2304977;rs17731495;rs52796942;rs60289833;rs2304977	566	Q2KHM9	K0753_HUMAN	L	566;267;22	ENSP00000355250:P566L;ENSP00000444634:P267L	ENSP00000355250:P566L	P	-	2	0	KIAA0753	6454053	0.999000	0.42202	0.998000	0.56505	0.886000	0.51366	2.037000	0.41174	1.275000	0.44379	0.650000	0.86243	CCA	G|0.714;A|0.286	0.286	strong		0.473	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
MYH10	4628	hgsc.bcm.edu	37	17	8416982	8416982	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:8416982C>T	ENST00000269243.4	-	21	2664	c.2526G>A	c.(2524-2526)aaG>aaA	p.K842K	MYH10_ENST00000396239.1_Silent_p.K863K|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000379980.4_Silent_p.K858K|MYH10_ENST00000360416.3_Silent_p.K873K	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	842					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GTAGAAGCGGCTTCACCTATG	0.443																																					p.K873K		Atlas-SNP	.											.	MYH10	148	.	0			c.G2619A						PASS	.						166.0	159.0	161.0					17																	8416982		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon23			AAGCGGCTTCACC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2526G>A	17.37:g.8416982C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.	.	none		0.443	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
YAF2	10138	hgsc.bcm.edu	37	12	42554505	42554505	+	Silent	SNP	A	A	G	rs1059360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:42554505A>G	ENST00000534854.2	-	4	496	c.429T>C	c.(427-429)gcT>gcC	p.A143A	YAF2_ENST00000380788.3_Silent_p.A134A|YAF2_ENST00000442791.3_Silent_p.A167A|YAF2_ENST00000327791.4_Silent_p.A119A|YAF2_ENST00000380790.4_Silent_p.A101A	NM_005748.4	NP_005739.2	Q8IY57	YAF2_HUMAN	YY1 associated factor 2	143					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)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)	8	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)		GATCTGCAGAAGCAGCACTAG	0.458													A|||	1832	0.365815	0.2451	0.2896	5008	,	,		17235	0.4573		0.3946	False		,,,				2504	0.4591				p.A167A		Atlas-SNP	.											.	YAF2	16	.	0			c.T501C						PASS	.	A	,,	1187,3219	415.2+/-337.1	147,893,1163	91.0	79.0	83.0		303,501,429	0.6	1.0	12	dbSNP_86	83	3258,5342	487.8+/-372.2	593,2072,1635	no	coding-synonymous,coding-synonymous,coding-synonymous	YAF2	NM_001190977.1,NM_001190979.1,NM_005748.4	,,	740,2965,2798	GG,GA,AA		37.8837,26.9405,34.1765	,,	101/139,167/205,143/181	42554505	4445,8561	2203	4300	6503	SO:0001819	synonymous_variant	10138	exon5			TGCAGAAGCAGCA	U72209	CCDS31775.1, CCDS53778.1, CCDS53779.1, CCDS53780.1	12q12	2014-09-04			ENSG00000015153	ENSG00000015153			17363	protein-coding gene	gene with protein product		607534				9016636	Standard	NM_001190977		Approved		uc001rmw.3	Q8IY57	OTTHUMG00000169380	ENST00000534854.2:c.429T>C	12.37:g.42554505A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	138	48	0.347826	NM_001190979	A8K5P0|B4DFU3|G3V465|Q99710	Silent	SNP	ENST00000534854.2	37	CCDS31775.1																																																																																			A|0.654;G|0.346	0.346	strong		0.458	YAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403781.1		
VPS13D	55187	hgsc.bcm.edu	37	1	12401868	12401868	+	Silent	SNP	A	A	C	rs28551666	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12401868A>C	ENST00000358136.3	+	41	8788	c.8658A>C	c.(8656-8658)ccA>ccC	p.P2886P	VPS13D_ENST00000356315.4_Silent_p.P2861P	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)		GCCGGCAGCCATTTGTCCCCT	0.567													A|||	3990	0.796725	0.7398	0.7579	5008	,	,		16866	0.8978		0.7913	False		,,,				2504	0.8027				p.P2886P		Atlas-SNP	.											.	VPS13D	316	.	0			c.A8658C						PASS	.	A	,	3345,1061	724.7+/-409.5	1279,787,137	95.0	97.0	96.0		8658,8583	-11.6	0.4	1	dbSNP_125	96	6911,1689	738.5+/-407.1	2773,1365,162	no	coding-synonymous,coding-synonymous	VPS13D	NM_015378.2,NM_018156.2	,	4052,2152,299	CC,CA,AA		19.6395,24.0808,21.1441	,	2886/4389,2861/4364	12401868	10256,2750	2203	4300	6503	SO:0001819	synonymous_variant	55187	exon41			GCAGCCATTTGTC	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.8658A>C	1.37:g.12401868A>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_015378		Silent	SNP	ENST00000358136.3	37	CCDS30588.1	1741	0.7971611721611722	357	0.725609756097561	276	0.7624309392265194	515	0.9003496503496503	593	0.7823218997361477	A	9.971	1.225393	0.22457	0.759192	0.803605	ENSG00000048707	ENST00000011700	.	.	.	5.82	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999438343	.	.	.	.	.	.	T	0.19976	-1.0289	3	.	.	.	.	8.5071	0.33195	0.176:0.4005:0.3599:0.0637	rs28551666;rs60764499;rs28551666	.	.	.	P	1708	.	.	H	+	2	0	VPS13D	12324455	0.000000	0.05858	0.440000	0.26846	0.986000	0.74619	-3.659000	0.00401	-2.202000	0.00745	-0.256000	0.11100	CAT	A|0.203;C|0.797	0.797	strong		0.567	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
FLNB	2317	hgsc.bcm.edu	37	3	58109162	58109162	+	Missense_Mutation	SNP	G	G	A	rs1131356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58109162G>A	ENST00000295956.4	+	21	3634	c.3469G>A	c.(3469-3471)Gac>Aac	p.D1157N	FLNB_ENST00000493452.1_Missense_Mutation_p.D988N|FLNB_ENST00000357272.4_Missense_Mutation_p.D1157N|FLNB_ENST00000429972.2_Missense_Mutation_p.D1157N|FLNB_ENST00000348383.5_Missense_Mutation_p.D1157N|FLNB_ENST00000358537.3_Missense_Mutation_p.D1157N|FLNB_ENST00000490882.1_Missense_Mutation_p.D1157N|FLNB_ENST00000419752.2_Missense_Mutation_p.D988N	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1157	Interaction with FBLP1.		D -> N (in dbSNP:rs1131356). {ECO:0000269|PubMed:11153914, ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:9651345}.		actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCTTAGCGTCGACTGCTCGGA	0.582													G|||	2735	0.546126	0.4758	0.4726	5008	,	,		16378	0.9187		0.2803	False		,,,				2504	0.5828				p.D1157N		Atlas-SNP	.											.	FLNB	430	.	0			c.G3469A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1813,2593	529.0+/-372.6	370,1073,760	64.0	72.0	69.0		3469,3469,3469,3469	5.1	0.9	3	dbSNP_86	69	2097,6503	360.6+/-332.0	263,1571,2466	yes	missense,missense,missense,missense	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	23,23,23,23	633,2644,3226	AA,AG,GG		24.3837,41.1484,30.063	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1157/2634,1157/2592,1157/2579,1157/2603	58109162	3910,9096	2203	4300	6503	SO:0001583	missense	2317	exon21			AGCGTCGACTGCT	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.3469G>A	3.37:g.58109162G>A	ENSP00000295956:p.Asp1157Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	1105	0.5059523809523809	232	0.4715447154471545	145	0.4005524861878453	521	0.9108391608391608	207	0.27308707124010556	G	18.92	3.725331	0.68959	0.411484	0.243837	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.95	5.08	0.68730	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.69248	2.105	0.09310	P	0.9999999382633	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.987;1.0;1.0	D;D;D;P;D;D	0.91635	0.985;0.918;0.998;0.863;0.999;0.999	T	0.39251	-0.9623	9	0.54805	T	0.06	.	15.2231	0.73330	0.0672:0.0:0.9328:0.0	rs1131356;rs17058842;rs56425027;rs58310728;rs1131356	1157;1157;988;988;1157;1157	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	N	1157;1157;1157;1157;1157;1157;988;988	ENSP00000295956:D1157N;ENSP00000420213:D1157N;ENSP00000351339:D1157N;ENSP00000415599:D1157N;ENSP00000232447:D1157N;ENSP00000349819:D1157N;ENSP00000418510:D988N;ENSP00000414532:D988N	ENSP00000295956:D1157N	D	+	1	0	FLNB	58084202	1.000000	0.71417	0.888000	0.34837	0.016000	0.09150	9.869000	0.99810	1.537000	0.49254	0.563000	0.77884	GAC	G|0.596;A|0.404	0.404	strong		0.582	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
ACSF3	197322	hgsc.bcm.edu	37	16	89167138	89167138	+	Missense_Mutation	SNP	G	G	C	rs11547019	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89167138G>C	ENST00000317447.4	+	3	426	c.49G>C	c.(49-51)Gcg>Ccg	p.A17P	ACSF3_ENST00000406948.3_Missense_Mutation_p.A17P|ACSF3_ENST00000378345.4_Intron	NM_001127214.2|NM_001243279.1|NM_001284316.1|NM_174917.3	NP_001120686.1|NP_001230208.1|NP_001271245.1|NP_777577.2	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	17			A -> P (in dbSNP:rs11547019). {ECO:0000269|PubMed:15489334}.		fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		CTGCGCCTTGGCGTCCTGCCG	0.682													G|||	282	0.0563099	0.0015	0.0317	5008	,	,		14874	0.1597		0.0577	False		,,,				2504	0.0399				p.A17P		Atlas-SNP	.											ACSF3,colon,carcinoma,-2,1	ACSF3	40	1	0			c.G49C						PASS	.	G	PRO/ALA,PRO/ALA	30,4298		0,30,2134	16.0	18.0	17.0		49,49	0.4	0.0	16	dbSNP_120	17	334,8134		7,320,3907	yes	missense,missense	ACSF3	NM_001127214.2,NM_174917.3	27,27	7,350,6041	CC,CG,GG		3.9443,0.6932,2.8446	benign,benign	17/577,17/577	89167138	364,12432	2164	4234	6398	SO:0001583	missense	197322	exon3			GCCTTGGCGTCCT	AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715		"""Acyl-CoA synthetase family"""	27288	protein-coding gene	gene with protein product	"""malonyl-CoA synthetase"""	614245				17762044, 21846720	Standard	XM_005256293		Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000317447.4:c.49G>C	16.37:g.89167138G>C	ENSP00000320646:p.Ala17Pro	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	26	7	0.269231	NM_174917	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Missense_Mutation	SNP	ENST00000317447.4	37	CCDS10974.1	150	0.06868131868131869	0	0.0	5	0.013812154696132596	96	0.16783216783216784	49	0.06464379947229551	G	12.21	1.870413	0.33069	0.006932	0.039443	ENSG00000176715	ENST00000317447;ENST00000537290;ENST00000406948	T;T;T	0.57595	0.81;0.39;0.81	5.02	0.452	0.16634	.	1.418140	0.04327	N	0.351700	T	0.00144	0.0004	L	0.48362	1.52	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.04427	-1.0952	10	0.35671	T	0.21	-22.3275	2.9079	0.05727	0.0869:0.3051:0.3296:0.2784	rs11547019	17	Q4G176	ACSF3_HUMAN	P	17	ENSP00000320646:A17P;ENSP00000440734:A17P;ENSP00000384627:A17P	ENSP00000320646:A17P	A	+	1	0	ACSF3	87694639	0.000000	0.05858	0.009000	0.14445	0.070000	0.16714	-0.170000	0.09897	0.149000	0.19098	0.650000	0.86243	GCG	G|0.956;C|0.044	0.044	strong		0.682	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917	
CD81	975	hgsc.bcm.edu	37	11	2417893	2417893	+	Silent	SNP	C	C	T	rs14077	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:2417893C>T	ENST00000263645.5	+	7	853	c.597C>T	c.(595-597)tcC>tcT	p.S199S	CD81_ENST00000492627.1_Silent_p.S128S|CD81_ENST00000381036.3_Silent_p.S237S|CD81_ENST00000526072.1_Silent_p.S128S|CD81_ENST00000481687.1_Silent_p.S205S	NM_004356.3	NP_004347.1	P60033	CD81_HUMAN	CD81 molecule	199					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of 1-phosphatidylinositol 4-kinase activity (GO:0043128)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization (GO:0008104)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of immune response (GO:0050776)|viral entry into host cell (GO:0046718)	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)|vesicle (GO:0031982)	MHC class II protein complex binding (GO:0023026)			endometrium(1)|lung(3)|skin(1)	5		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;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)		ACCTCTTCTCCGGGAAGCTGT	0.677													C|||	446	0.0890575	0.2617	0.0288	5008	,	,		15769	0.0317		0.0129	False		,,,				2504	0.0358				p.S199S		Atlas-SNP	.											.	CD81	11	.	0			c.C597T						PASS	.	C		1006,3398	367.1+/-318.1	115,776,1311	94.0	89.0	91.0		597	-6.8	0.9	11	dbSNP_52	91	90,8506	50.2+/-110.2	0,90,4208	no	coding-synonymous	CD81	NM_004356.3		115,866,5519	TT,TC,CC		1.047,22.8429,8.4308		199/237	2417893	1096,11904	2202	4298	6500	SO:0001819	synonymous_variant	975	exon7			CTTCTCCGGGAAG		CCDS7734.1, CCDS73240.1	11p15.5	2014-09-17	2006-03-28		ENSG00000110651	ENSG00000110651		"""CD molecules"", ""Tetraspanins"""	1701	protein-coding gene	gene with protein product		186845	"""CD81 antigen (target of antiproliferative antibody 1)"""	TAPA1		1650385	Standard	XM_005253260		Approved	TAPA-1, TSPAN28	uc001lwf.1	P60033	OTTHUMG00000009892	ENST00000263645.5:c.597C>T	11.37:g.2417893C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_004356	P18582|Q5U0J6	Silent	SNP	ENST00000263645.5	37	CCDS7734.1	161	0.07371794871794872	132	0.2682926829268293	10	0.027624309392265192	13	0.022727272727272728	6	0.0079155672823219	C	9.285	1.049210	0.19827	0.228429	0.01047	ENSG00000110651	ENST00000464784	.	.	.	3.39	-6.79	0.01715	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999843166	.	.	.	.	.	.	T	0.32534	-0.9903	3	.	.	.	.	3.2627	0.06854	0.0893:0.3026:0.1493:0.4588	rs14077;rs1047947;rs2229750;rs16928233;rs17355940	.	.	.	L	184	.	.	P	+	2	0	CD81	2374469	0.000000	0.05858	0.908000	0.35775	0.950000	0.60333	-3.607000	0.00416	-1.601000	0.01601	-0.467000	0.05162	CCG	C|0.922;T|0.078	0.078	strong		0.677	CD81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027357.4	NM_004356	
OR5L1	219437	hgsc.bcm.edu	37	11	55578991	55578991	+	Silent	SNP	C	C	T	rs61732387|rs386753698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	93	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	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	
ZNF521	25925	hgsc.bcm.edu	37	18	22775185	22775185	+	Silent	SNP	C	C	T	rs1140026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:22775185C>T	ENST00000361524.3	-	5	3745	c.3597G>A	c.(3595-3597)aaG>aaA	p.K1199K	ZNF521_ENST00000538137.2_Silent_p.K1199K|ZNF521_ENST00000584787.1_Silent_p.K979K	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1199					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CCATCTGACACTTGATGCATT	0.323			T	PAX5	ALL								C|||	1135	0.226637	0.1316	0.2089	5008	,	,		19650	0.2768		0.2535	False		,,,				2504	0.2883				p.K1199K		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G3597A						PASS	.	C		631,3773	271.6+/-270.3	33,565,1604	145.0	126.0	133.0		3597	5.6	1.0	18	dbSNP_86	133	2084,6516	357.9+/-330.9	254,1576,2470	no	coding-synonymous	ZNF521	NM_015461.2		287,2141,4074	TT,TC,CC		24.2326,14.3279,20.8782		1199/1312	22775185	2715,10289	2202	4300	6502	SO:0001819	synonymous_variant	25925	exon5			CTGACACTTGATG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3597G>A	18.37:g.22775185C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	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	
PDCD11	22984	hgsc.bcm.edu	37	10	105194086	105194086	+	Missense_Mutation	SNP	C	C	T	rs2986014	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105194086C>T	ENST00000369797.3	+	24	3740	c.3646C>T	c.(3646-3648)Ctc>Ttc	p.L1216F		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1216	S1 motif 10. {ECO:0000255|PROSITE- ProRule:PRU00180}.		L -> F (in dbSNP:rs2986014). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8724849}.		mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CTCCAAGACCCTCTTATGTCT	0.552													T|||	2396	0.478435	0.4803	0.402	5008	,	,		16763	0.4236		0.4235	False		,,,				2504	0.6431				p.L1216F		Atlas-SNP	.											.	PDCD11	160	.	0			c.C3646T						PASS	.	T	PHE/LEU	1975,2431	618.4+/-393.2	414,1147,642	94.0	96.0	96.0		3646	5.2	1.0	10	dbSNP_101	96	3395,5205	639.6+/-399.5	654,2087,1559	yes	missense	PDCD11	NM_014976.1	22	1068,3234,2201	TT,TC,CC		39.4767,44.8252,41.2886	benign	1216/1872	105194086	5370,7636	2203	4300	6503	SO:0001583	missense	22984	exon24			AAGACCCTCTTAT	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.3646C>T	10.37:g.105194086C>T	ENSP00000358812:p.Leu1216Phe	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	19	0.365385	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	926	0.423992673992674	230	0.46747967479674796	138	0.3812154696132597	243	0.42482517482517484	315	0.4155672823218997	T	0.710	-0.787661	0.02884	0.448252	0.394767	ENSG00000148843	ENST00000369797	T	0.17691	2.26	5.23	5.23	0.72850	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (1);	0.333692	0.35555	N	0.003121	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	0.45454	-0.9260	9	0.09843	T	0.71	-12.7858	5.2262	0.15396	0.1666:0.0853:0.0:0.7481	rs2986014;rs3765527;rs11558730;rs52819868;rs57673953;rs2986014	1216	Q14690	RRP5_HUMAN	F	1216	ENSP00000358812:L1216F	ENSP00000358812:L1216F	L	+	1	0	PDCD11	105184076	0.302000	0.24454	1.000000	0.80357	0.439000	0.31926	0.859000	0.27858	0.947000	0.37659	-0.361000	0.07541	CTC	C|0.578;T|0.422	0.422	strong		0.552	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
PPP1R12C	54776	hgsc.bcm.edu	37	19	55614923	55614923	+	Silent	SNP	T	T	C	rs2532060	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55614923T>C	ENST00000263433.3	-	4	600	c.585A>G	c.(583-585)gaA>gaG	p.E195E	PPP1R12C_ENST00000435544.2_Silent_p.E121E|PPP1R12C_ENST00000376393.2_Silent_p.E195E	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		GCTTGGCTGCTTCCACATCCA	0.617													C|||	3413	0.68151	0.9145	0.5072	5008	,	,		16289	0.754		0.4056	False		,,,				2504	0.6994				p.E195E		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.A585G						PASS	.	C		3774,632		1637,500,66	45.0	37.0	39.0		585	3.1	1.0	19	dbSNP_100	39	3643,4951		816,2011,1470	no	coding-synonymous	PPP1R12C	NM_017607.2		2453,2511,1536	CC,CT,TT		42.39,14.3441,42.9462		195/783	55614923	7417,5583	2203	4297	6500	SO:0001819	synonymous_variant	54776	exon4			GGCTGCTTCCACA	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.585A>G	19.37:g.55614923T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	171	77	0.450292	NM_017607		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																			T|0.385;C|0.615	0.615	strong		0.617	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
KRBOX4	55634	hgsc.bcm.edu	37	X	46332301	46332301	+	Silent	SNP	A	A	C	rs144294150	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:46332301A>C	ENST00000344302.4	+	6	1001	c.370A>C	c.(370-372)Aga>Cga	p.R124R	KRBOX4_ENST00000487081.1_3'UTR|KRBOX4_ENST00000298190.6_Silent_p.R119R|KRBOX4_ENST00000360017.5_3'UTR|KRBOX4_ENST00000478600.1_Intron	NM_001129898.1|NM_017776.2	NP_001123370.1|NP_060246.2	Q5JUW0	KRBX4_HUMAN	KRAB box domain containing 4	124					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)										TCAAGAATCCAGAACATGTAG	0.393													A|||	26	0.00688742	0.0061	0.0058	3775	,	,		14788	0.0099		0.001	False		,,,				2504	0.0031				p.R124R		Atlas-SNP	.											.	.	.	.	0			c.A370C						PASS	.	A	,,,	19,3816		0,19,0,1613,571	100.0	86.0	91.0		370,,,355	1.4	0.1	X	dbSNP_134	91	41,6687		0,28,13,2400,1859	no	coding-synonymous,utr-3,utr-3,coding-synonymous	ZNF673	NM_001129898.1,NM_001129899.1,NM_001129900.1,NM_017776.2	,,,	0,47,13,4013,2430	CC,CA,C,AA,A		0.6094,0.4954,0.568	,,,	124/172,,,119/167	46332301	60,10503	2203	4300	6503	SO:0001819	synonymous_variant	55634	exon6			GAATCCAGAACAT		CCDS14267.1, CCDS48097.1, CCDS48098.1	Xp11.3	2013-01-08	2013-01-08	2013-01-08	ENSG00000147121	ENSG00000147121		"""-"""	26007	protein-coding gene	gene with protein product	"""hypothetical protein FLJ20344"""	300585	"""zinc finger protein 673"", ""zinc finger family member 673"""	ZNF673		11944989	Standard	NM_001129898		Approved	FLJ20344	uc004dgn.4	Q5JUW0	OTTHUMG00000021421	ENST00000344302.4:c.370A>C	X.37:g.46332301A>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_001129898	A8K0Y8|B3KU22|Q96EA3|Q9NXB1	Silent	SNP	ENST00000344302.4	37	CCDS48097.1																																																																																			A|0.995;C|0.005	0.005	strong		0.393	KRBOX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056359.2	NM_017776	
CAND2	23066	hgsc.bcm.edu	37	3	12861608	12861608	+	Missense_Mutation	SNP	G	G	A	rs3817121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12861608G>A	ENST00000456430.2	+	11	3009	c.2968G>A	c.(2968-2970)Gtc>Atc	p.V990I	CAND2_ENST00000295989.5_Missense_Mutation_p.V897I	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	990			V -> I (in dbSNP:rs3817121).		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						CCGGAGCACCGTCATCACAGC	0.597													G|||	689	0.13758	0.0257	0.2911	5008	,	,		18400	0.1151		0.174	False		,,,				2504	0.1656				p.V990I	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,NS,carcinoma,-2,2	CAND2	138	2	0			c.G2968A						PASS	.	G	ILE/VAL,ILE/VAL	146,4178		2,142,2018	134.0	146.0	142.0		2968,2689	5.1	0.9	3	dbSNP_107	142	1485,7001		141,1203,2899	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	29,29	143,1345,4917	AA,AG,GG		17.4994,3.3765,12.7322	benign,benign	990/1237,897/1120	12861608	1631,11179	2162	4243	6405	SO:0001583	missense	23066	exon11			AGCACCGTCATCA		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.2968G>A	3.37:g.12861608G>A	ENSP00000387641:p.Val990Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	55	0.591398	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	311	0.1423992673992674	19	0.03861788617886179	106	0.292817679558011	67	0.11713286713286714	119	0.15699208443271767	G	19.76	3.886690	0.72410	0.033765	0.174994	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.25414	1.8;1.8	5.09	5.09	0.68999	Armadillo-like helical (1);Armadillo-type fold (1);	0.234553	0.34460	N	0.003952	T	0.00012	0.0000	L	0.56124	1.755	0.09310	P	1.0	P;P	0.43909	0.468;0.821	B;B	0.39027	0.065;0.288	T	0.40059	-0.9583	9	0.41790	T	0.15	-19.3095	15.9818	0.80116	0.0:0.0:1.0:0.0	rs3817121;rs52799778;rs59821400;rs3817121	990;897	O75155;O75155-2	CAND2_HUMAN;.	I	897;990	ENSP00000295989:V897I;ENSP00000387641:V990I	ENSP00000295989:V897I	V	+	1	0	CAND2	12836608	1.000000	0.71417	0.855000	0.33649	0.985000	0.73830	5.587000	0.67510	2.391000	0.81399	0.561000	0.74099	GTC	A|0.144;G|0.856	0.144	strong		0.597	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
CELF5	60680	hgsc.bcm.edu	37	19	3281298	3281298	+	Silent	SNP	G	G	A	rs36030381	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3281298G>A	ENST00000292672.2	+	6	742	c.705G>A	c.(703-705)ccG>ccA	p.P235P	CELF5_ENST00000541430.2_Silent_p.P235P	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	235					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						TCCTGACGCCGTCCCTCACAT	0.652													G|||	403	0.0804712	0.0295	0.072	5008	,	,		18514	0.0218		0.1044	False		,,,				2504	0.1912				p.P235P		Atlas-SNP	.											.	CELF5	32	.	0			c.G705A						PASS	.	G	,	140,4266	98.9+/-137.6	2,136,2065	101.0	89.0	93.0		705,705	-7.2	0.9	19	dbSNP_126	93	1018,7582	217.0+/-255.8	55,908,3337	no	coding-synonymous,coding-synonymous	CELF5	NM_001172673.1,NM_021938.3	,	57,1044,5402	AA,AG,GG		11.8372,3.1775,8.9036	,	235/410,235/486	3281298	1158,11848	2203	4300	6503	SO:0001819	synonymous_variant	60680	exon6			GACGCCGTCCCTC	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.705G>A	19.37:g.3281298G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Silent	SNP	ENST00000292672.2	37	CCDS12106.1																																																																																			G|0.917;A|0.083	0.083	strong		0.652	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938	
UGT2B28	54490	hgsc.bcm.edu	37	4	70160338	70160338	+	Silent	SNP	G	G	C	rs72552703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70160338G>C	ENST00000335568.5	+	6	1403	c.1401G>C	c.(1399-1401)gtG>gtC	p.V467V	UGT2B28_ENST00000511240.1_3'UTR	NM_053039.1	NP_444267.1	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B28	467					metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31						TTGAATTTGTGATGTGCCACA	0.443													N|||	1214	0.242412	0.2632	0.2161	5008	,	,		12627	0.2034		0.2813	False		,,,				2504	0.2331				p.V467V		Atlas-SNP	.											.	UGT2B28	101	.	0			c.G1401C						PASS	.	C	,	830,3228		274,282,1473	72.0	81.0	78.0		,1401	0.7	1.0	4	dbSNP_130	78	1619,6833		436,747,3043	no	utr-3,coding-synonymous	UGT2B28	NM_001207004.1,NM_053039.1	,	710,1029,4516	CC,CG,GG		19.1552,20.4534,19.5763	,	,467/530	70160338	2449,10061	2029	4226	6255	SO:0001819	synonymous_variant	54490	exon6			ATTTGTGATGTGC	AF177272	CCDS3528.1, CCDS56330.1	4q13.3	2011-02-09	2005-07-20		ENSG00000135226	ENSG00000135226		"""UDP glucuronosyltransferases"""	13479	protein-coding gene	gene with protein product		606497	"""UDP glycosyltransferase 2 family, polypeptide B28"""			11300766	Standard	NM_053039		Approved		uc003hej.3	Q9BY64	OTTHUMG00000129401	ENST00000335568.5:c.1401G>C	4.37:g.70160338G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	119	42	0.352941	NM_053039	B5BUM0|Q9BY62|Q9BY63	Silent	SNP	ENST00000335568.5	37	CCDS3528.1																																																																																			G|0.792;C|0.208	0.208	strong		0.443	UGT2B28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251557.2	NM_053039	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887149	9887149	+	Missense_Mutation	SNP	G	G	C	rs11662946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	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		
OR52J3	119679	hgsc.bcm.edu	37	11	5067984	5067984	+	Missense_Mutation	SNP	A	A	G	rs2500016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	192	0	0		WXS	Illumina HiSeq	Phase_I	249	120	0.481928	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	
LY6G6C	80740	hgsc.bcm.edu	37	6	31687008	31687008	+	Silent	SNP	G	G	A	rs1065356	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	119	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	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		
TYR	7299	hgsc.bcm.edu	37	11	88911696	88911696	+	Missense_Mutation	SNP	C	C	A	rs1042602	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:88911696C>A	ENST00000263321.5	+	1	1077	c.575C>A	c.(574-576)tCt>tAt	p.S192Y	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	192			S -> Y (associated with SHEP3; light/dark skin; dbSNP:rs1042602). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:11153699, ECO:0000269|PubMed:11214319, ECO:0000269|PubMed:15146472, ECO:0000269|PubMed:17952075, ECO:0000269|PubMed:17999355, ECO:0000269|PubMed:2342539}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CTTGGGGGATCTGAAATCTGG	0.423													C|||	618	0.123403	0.0121	0.2378	5008	,	,		21077	0.001		0.3718	False		,,,				2504	0.0634				p.S192Y		Atlas-SNP	.											TYR,NS,carcinoma,0,1	TYR	130	1	0			c.C575A	GRCh37	CM076581	TYR	M	rs1042602	PASS	.	C	TYR/SER	333,4069	174.4+/-204.0	13,307,1881	193.0	181.0	185.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	575	6.1	0.0	11	dbSNP_86	185	3239,5359	486.7+/-371.9	592,2055,1652	yes	missense	TYR	NM_000372.4	144	605,2362,3533	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	37.6716,7.5647,27.4769	probably-damaging	192/530	88911696	3572,9428	2201	4299	6500	SO:0001583	missense	7299	exon1			GGGGATCTGAAAT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.575C>A	11.37:g.88911696C>A	ENSP00000263321:p.Ser192Tyr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	399	0.18269230769230768	7	0.014227642276422764	112	0.30939226519337015	1	0.0017482517482517483	279	0.36807387862796836	C	17.00	3.275960	0.59649	0.075647	0.376716	ENSG00000077498	ENST00000263321	D	0.98732	-5.1	6.07	6.07	0.98685	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.065875	0.64402	D	0.000008	T	0.00039	0.0001	M	0.70275	2.135	0.47737	P	4.92000000000048E-4	D	0.69078	0.997	D	0.71656	0.974	T	0.00000	-1.7843	8	.	.	.	.	15.3849	0.74691	0.1393:0.8607:0.0:0.0	rs61569485	192	P14679	TYRO_HUMAN	Y	192	ENSP00000263321:S192Y	.	S	+	2	0	TYR	88551344	0.660000	0.27420	0.028000	0.17463	0.775000	0.43874	4.436000	0.59948	2.885000	0.99019	0.655000	0.94253	TCT	C|0.751;A|0.249	0.249	strong		0.423	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
C9orf84	158401	hgsc.bcm.edu	37	9	114464487	114464487	+	Missense_Mutation	SNP	T	T	C	rs1407390	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114464487T>C	ENST00000318737.4	-	21	2923	c.2795A>G	c.(2794-2796)tAt>tGt	p.Y932C	C9orf84_ENST00000394777.4_Missense_Mutation_p.Y858C|C9orf84_ENST00000374287.3_Missense_Mutation_p.Y932C|C9orf84_ENST00000394779.3_Missense_Mutation_p.Y893C	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	932			Y -> C (in dbSNP:rs1407390).							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						TGCCTTCTCATAATTCAATTC	0.259													C|||	4258	0.85024	0.8646	0.8732	5008	,	,		19267	0.9266		0.7952	False		,,,				2504	0.7924				p.Y932C		Atlas-SNP	.											.	C9orf84	207	.	0			c.A2795G						PASS	.	C	CYS/TYR,CYS/TYR	3769,629	262.2+/-264.8	1625,519,55	50.0	52.0	51.0		2678,2795	-2.5	0.9	9	dbSNP_88	51	6770,1822	322.0+/-315.3	2666,1438,192	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	194,194	4291,1957,247	CC,CT,TT		21.2058,14.302,18.8684	benign,benign	893/1406,932/1445	114464487	10539,2451	2199	4296	6495	SO:0001583	missense	158401	exon21			TTCTCATAATTCA	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.2795A>G	9.37:g.114464487T>C	ENSP00000322108:p.Tyr932Cys	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	99	97	0.979798	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	1880	0.8608058608058609	432	0.8780487804878049	316	0.8729281767955801	526	0.9195804195804196	606	0.7994722955145118	C	0.223	-1.027272	0.02045	0.85698	0.787942	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.04360	3.64;3.64;3.65;3.65	5.27	-2.51	0.06365	.	0.704505	0.13229	N	0.403794	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	1.2000000000012001E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.13072	-1.0523	9	0.09590	T	0.72	2.0848	9.9315	0.41525	0.0:0.237:0.1047:0.6583	rs1407390;rs17342605;rs57393014;rs1407390	858;932;893	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	C	893;858;546;932;932	ENSP00000378259:Y893C;ENSP00000378257:Y858C;ENSP00000363405:Y932C;ENSP00000322108:Y932C	ENSP00000322108:Y932C	Y	-	2	0	C9orf84	113504308	0.012000	0.17670	0.930000	0.37139	0.823000	0.46562	-1.044000	0.03532	-0.868000	0.04058	-0.186000	0.12905	TAT	T|0.152;C|0.848	0.848	strong		0.259	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
MUC16	94025	hgsc.bcm.edu	37	19	9074265	9074265	+	Missense_Mutation	SNP	G	G	A	rs10406209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9074265G>A	ENST00000397910.4	-	3	13384	c.13181C>T	c.(13180-13182)aCt>aTt	p.T4394I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4396	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCAGCTCCAGTAGGACCTGT	0.468													G|||	768	0.153355	0.1142	0.183	5008	,	,		23652	0.0089		0.2634	False		,,,				2504	0.2209				p.T4394I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C13181T						PASS	.	G	ILE/THR	502,3590		32,438,1576	145.0	141.0	142.0		13181	0.5	0.0	19	dbSNP_119	142	2429,5961		370,1689,2136	yes	missense	MUC16	NM_024690.2	89	402,2127,3712	AA,AG,GG		28.9511,12.2678,23.4818	possibly-damaging	4394/14508	9074265	2931,9551	2046	4195	6241	SO:0001583	missense	94025	exon3			GCTCCAGTAGGAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13181C>T	19.37:g.9074265G>A	ENSP00000381008:p.Thr4394Ile	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	319	152	0.476489	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	334	0.15293040293040294	53	0.10772357723577236	73	0.20165745856353592	5	0.008741258741258742	203	0.2678100263852243	g	3.708	-0.060188	0.07317	0.122678	0.289511	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.67	0.509	0.16977	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	P	0.46020	0.871	B	0.34346	0.18	T	0.52170	-0.8611	8	0.87932	D	0	.	5.6254	0.17480	0.0:0.3493:0.6507:0.0	rs10406209;rs17515888;rs52837265;rs59614183;rs10406209	4394	B5ME49	.	I	4394	ENSP00000381008:T4394I	ENSP00000381008:T4394I	T	-	2	0	MUC16	8935265	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	0.366000	0.20365	0.231000	0.21079	0.305000	0.20034	ACT	G|0.826;A|0.174	0.174	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DISP1	84976	hgsc.bcm.edu	37	1	223116472	223116472	+	Missense_Mutation	SNP	G	G	A	rs2609383|rs71583926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:223116472G>A	ENST00000284476.6	+	2	471	c.307G>A	c.(307-309)Gag>Aag	p.E103K	DISP1_ENST00000360254.2_Missense_Mutation_p.E103K|DISP1_ENST00000495684.1_Intron	NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	103			E -> K (in dbSNP:rs2609383).		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)		GTGCCATCCCGAGGCTGGCCC	0.522													G|||	1060	0.211661	0.1566	0.1715	5008	,	,		23581	0.2907		0.1352	False		,,,				2504	0.3119				p.E103K		Atlas-SNP	.											.	DISP1	145	.	0			c.G307A						PASS	.	G	LYS/GLU	738,3668	304.1+/-288.3	59,620,1524	139.0	120.0	126.0		307	4.7	1.0	1	dbSNP_100	126	1176,7424	239.7+/-270.7	86,1004,3210	yes	missense	DISP1	NM_032890.3	56	145,1624,4734	AA,AG,GG		13.6744,16.7499,14.7163	benign	103/1525	223116472	1914,11092	2203	4300	6503	SO:0001583	missense	84976	exon4			CATCCCGAGGCTG	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.307G>A	1.37:g.223116472G>A	ENSP00000284476:p.Glu103Lys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	148	85	0.574324	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	399	0.18269230769230768	70	0.14227642276422764	64	0.17679558011049723	156	0.2727272727272727	109	0.1437994722955145	G	9.041	0.989600	0.18966	0.167499	0.136744	ENSG00000154309	ENST00000360254;ENST00000284476	T;D	0.91577	0.92;-2.87	5.62	4.68	0.58851	.	0.682047	0.14375	N	0.323515	T	0.00039	0.0001	L	0.51422	1.61	0.42105	P	0.00864699999999996	B	0.28880	0.226	B	0.17098	0.017	T	0.43114	-0.9411	9	0.07030	T	0.85	-28.9434	15.3736	0.74587	0.0:0.2638:0.7362:0.0	rs2609383;rs3814304;rs2609383	103	Q96F81	DISP1_HUMAN	K	103	ENSP00000355848:E103K;ENSP00000284476:E103K	ENSP00000284476:E103K	E	+	1	0	DISP1	221183095	0.968000	0.33430	0.997000	0.53966	0.973000	0.67179	1.811000	0.38942	2.652000	0.90054	0.650000	0.86243	GAG	AAT|0.500;GAG|0.500	.	alt		0.522	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
DND1	373863	hgsc.bcm.edu	37	5	140050926	140050926	+	Silent	SNP	G	G	A	rs62384220	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140050926G>A	ENST00000542735.1	-	4	1057	c.1014C>T	c.(1012-1014)aaC>aaT	p.N338N	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	338					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)	p.N338N(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCACAGGAGGTTGGCCCCAG	0.587													G|||	20	0.00399361	0.0008	0.0072	5008	,	,		20122	0.0		0.0109	False		,,,				2504	0.0031				p.N338N		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	1	Substitution - coding silent(1)	prostate(1)	c.C1014T						scavenged	.						73.0	65.0	67.0					5																	140050926		1984	4006	5990	SO:0001819	synonymous_variant	373863	exon4			CAGGAGGTTGGCC	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1014C>T	5.37:g.140050926G>A		Somatic	503	0	0		WXS	Illumina HiSeq	Phase_I	869	174	0.20023	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.970;A|0.030	0.030	strong		0.587	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
HRNR	388697	hgsc.bcm.edu	37	1	152185750	152185750	+	Silent	SNP	G	G	A	rs12729662	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152185750G>A	ENST00000368801.2	-	3	8430	c.8355C>T	c.(8353-8355)taC>taT	p.Y2785Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2785					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGTTGGCCGTAGCTGGAAG	0.562													G|||	1716	0.342652	0.1172	0.415	5008	,	,		15303	0.6181		0.17	False		,,,				2504	0.4898				p.Y2785Y		Atlas-SNP	.											HRNR,colon,carcinoma,0,1	HRNR	403	1	0			c.C8355T						PASS	.						92.0	83.0	86.0					1																	152185750		2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			TTGGCCGTAGCTG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.8355C>T	1.37:g.152185750G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	214	136	0.635514	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.723;A|0.277	0.277	strong		0.562	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
ACVR1C	130399	hgsc.bcm.edu	37	2	158443889	158443889	+	Silent	SNP	G	G	A	rs4556933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:158443889G>A	ENST00000243349.8	-	2	474	c.114C>T	c.(112-114)ttC>ttT	p.F38F	ACVR1C_ENST00000335450.7_Silent_p.F38F|ACVR1C_ENST00000409680.3_5'UTR|ACVR1C_ENST00000348328.5_Silent_p.F38F	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						TTTGGCAGGTGAAGTTTGAAG	0.398													A|||	2205	0.440296	0.6974	0.4323	5008	,	,		18794	0.3185		0.3936	False		,,,				2504	0.272				p.F38F		Atlas-SNP	.											.	ACVR1C	85	.	0			c.C114T						PASS	.	A	,,,	2902,1504	478.8+/-358.3	966,970,267	213.0	205.0	207.0		,114,114,114	-2.7	1.0	2	dbSNP_111	207	3401,5199	639.6+/-399.5	691,2019,1590	no	utr-5,coding-synonymous,coding-synonymous,coding-synonymous	ACVR1C	NM_001111031.1,NM_001111032.1,NM_001111033.1,NM_145259.2	,,,	1657,2989,1857	AA,AG,GG		39.5465,34.1353,48.4622	,,,	,38/414,38/337,38/494	158443889	6303,6703	2203	4300	6503	SO:0001819	synonymous_variant	130399	exon2			GCAGGTGAAGTTT	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.114C>T	2.37:g.158443889G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	177	84	0.474576	NM_145259		Silent	SNP	ENST00000243349.8	37	CCDS2205.1																																																																																			G|0.540;A|0.460	0.460	strong		0.398	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259	
GRM4	2914	hgsc.bcm.edu	37	6	34008006	34008006	+	Silent	SNP	A	A	G	rs2229900	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:34008006A>G	ENST00000538487.2	-	8	1898	c.1455T>C	c.(1453-1455)gaT>gaC	p.D485D	GRM4_ENST00000544773.2_Silent_p.D316D|GRM4_ENST00000374177.3_Silent_p.D369D|GRM4_ENST00000535756.1_Silent_p.D352D|GRM4_ENST00000455714.2_Silent_p.D345D|GRM4_ENST00000609222.1_Silent_p.D352D|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000374181.4_Silent_p.D485D	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	485					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						ACTCGGCAGAATCGTTGCGCA	0.572													G|||	2417	0.482628	0.7632	0.4899	5008	,	,		18082	0.5139		0.2296	False		,,,				2504	0.3262				p.D485D		Atlas-SNP	.											GRM4_ENST00000374181,NS,carcinoma,-2,3	GRM4	317	3	0			c.T1455C						PASS	.	G		3040,1366	452.4+/-350.0	1063,914,226	153.0	147.0	149.0		1455	3.6	1.0	6	dbSNP_98	149	1982,6618	724.0+/-406.5	237,1508,2555	no	coding-synonymous	GRM4	NM_000841.1		1300,2422,2781	GG,GA,AA		23.0465,31.0032,38.6129		485/913	34008006	5022,7984	2203	4300	6503	SO:0001819	synonymous_variant	2914	exon8			GGCAGAATCGTTG	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.1455T>C	6.37:g.34008006A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Silent	SNP	ENST00000538487.2	37	CCDS4787.1																																																																																			T|0.098;G|0.315	0.315	strong		0.572	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
TCF4	6925	hgsc.bcm.edu	37	18	52895531	52895531	+	Silent	SNP	T	T	C	rs8766	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:52895531T>C	ENST00000356073.4	-	19	2540	c.1929A>G	c.(1927-1929)tcA>tcG	p.S643S	TCF4_ENST00000540999.1_Silent_p.S619S|TCF4_ENST00000564999.1_Silent_p.S643S|TCF4_ENST00000566286.1_Silent_p.S640S|TCF4_ENST00000537856.3_Silent_p.S513S|TCF4_ENST00000544241.2_Silent_p.S576S|TCF4_ENST00000457482.3_Silent_p.S487S|TCF4_ENST00000570287.2_Silent_p.S483S|TCF4_ENST00000565018.2_Silent_p.S647S|TCF4_ENST00000537578.1_Silent_p.S623S|TCF4_ENST00000564403.2_Silent_p.S653S|TCF4_ENST00000568673.1_Silent_p.S623S|TCF4_ENST00000567880.1_Silent_p.S583S|TCF4_ENST00000566279.1_Silent_p.S587S|TCF4_ENST00000568740.1_Silent_p.S618S|TCF4_ENST00000543082.1_Silent_p.S601S|TCF4_ENST00000570177.2_Silent_p.S513S|TCF4_ENST00000561831.3_Silent_p.S483S|TCF4_ENST00000561992.1_Silent_p.S513S|TCF4_ENST00000564228.1_Silent_p.S572S|TCF4_ENST00000398339.1_Silent_p.S749S|TCF4_ENST00000354452.3_Silent_p.S647S	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	643					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GGGGAGGCTCTGAGGACACCT	0.498													C|||	1715	0.342452	0.2965	0.366	5008	,	,		17666	0.4008		0.4155	False		,,,				2504	0.2526				p.S749S		Atlas-SNP	.											.	TCF4	178	.	0			c.A2247G						PASS	.	C	,	1401,3005	687.2+/-404.8	221,959,1023	125.0	114.0	118.0		1941,1929	-5.4	0.5	18	dbSNP_52	118	3342,5258	643.2+/-399.9	658,2026,1616	no	coding-synonymous,coding-synonymous	TCF4	NM_001083962.1,NM_003199.2	,	879,2985,2639	CC,CT,TT		38.8605,31.7975,36.4678	,	647/672,643/668	52895531	4743,8263	2203	4300	6503	SO:0001819	synonymous_variant	6925	exon20			AGGCTCTGAGGAC	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1929A>G	18.37:g.52895531T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	37	CCDS11960.1																																																																																			T|0.626;C|0.374	0.374	strong		0.498	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
OR1S2	219958	hgsc.bcm.edu	37	11	57971190	57971190	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57971190G>A	ENST00000302592.6	-	1	463	c.464C>T	c.(463-465)aCt>aTt	p.T155I		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T155I(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGTGAGCAAAGTGCCGAACCT	0.488																																					p.T155I		Atlas-SNP	.											OR1S2,trunk,malignant_melanoma,0,1	OR1S2	119	1	1	Substitution - Missense(1)	skin(1)	c.C464T						scavenged	.						183.0	172.0	176.0					11																	57971190		2201	4296	6497	SO:0001583	missense	219958	exon1			AGCAAAGTGCCGA	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.464C>T	11.37:g.57971190G>A	ENSP00000305469:p.Thr155Ile	Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	253	12	0.0474308	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	.	.	.	.	.	.	.	.	.	.	g	0.008	-1.862128	0.00552	.	.	ENSG00000197887	ENST00000302592	T	0.35421	1.31	4.47	0.804	0.18697	GPCR, rhodopsin-like superfamily (1);	1.024400	0.07804	N	0.956995	T	0.11367	0.0277	N	0.00525	-1.395	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.24440	-1.0160	10	0.34782	T	0.22	.	7.5141	0.27590	0.6178:0.0:0.3822:0.0	.	155	Q8NGQ3	OR1S2_HUMAN	I	155	ENSP00000305469:T155I	ENSP00000305469:T155I	T	-	2	0	OR1S2	57727766	0.000000	0.05858	0.013000	0.15412	0.026000	0.11368	-0.153000	0.10144	0.277000	0.22141	-0.285000	0.09966	ACT	.	.	none		0.488	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
DSCAM	1826	hgsc.bcm.edu	37	21	41725630	41725630	+	Missense_Mutation	SNP	G	G	C	rs2297270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:41725630G>C	ENST00000400454.1	-	5	1173	c.696C>G	c.(694-696)gaC>gaG	p.D232E		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	232	Ig-like C2-type 3.		D -> E (in dbSNP:rs2297270).		cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CTTTGCGATGGTCAAACCCAT	0.537													G|||	714	0.142572	0.2065	0.1499	5008	,	,		17892	0.2093		0.0755	False		,,,				2504	0.0511				p.D232E	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C696G						PASS	.	G	GLU/ASP	630,3164		55,520,1322	24.0	24.0	24.0		696	-10.1	0.7	21	dbSNP_100	24	638,7626		29,580,3523	yes	missense	DSCAM	NM_001389.3	45	84,1100,4845	CC,CG,GG		7.7202,16.6052,10.5158	benign	232/2013	41725630	1268,10790	1897	4132	6029	SO:0001583	missense	1826	exon5			GCGATGGTCAAAC	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.696C>G	21.37:g.41725630G>C	ENSP00000383303:p.Asp232Glu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	347	0.15888278388278387	95	0.19308943089430894	56	0.15469613259668508	139	0.243006993006993	57	0.07519788918205805	G	1.753	-0.488713	0.04352	0.166052	0.077202	ENSG00000171587	ENST00000400454	T	0.65916	-0.18	5.31	-10.1	0.00402	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.164825	0.53938	D	0.000058	T	0.00012	0.0000	N	0.01267	-0.92	0.44635	P	0.0023809999999999665	B	0.02656	0.0	B	0.04013	0.001	T	0.07177	-1.0786	9	0.02654	T	1	.	12.5074	0.55989	0.0941:0.1349:0.6959:0.0751	rs2297270;rs2297270	232	O60469	DSCAM_HUMAN	E	232	ENSP00000383303:D232E	ENSP00000383303:D232E	D	-	3	2	DSCAM	40647500	0.193000	0.23313	0.690000	0.30148	0.975000	0.68041	-0.492000	0.06467	-1.752000	0.01325	-0.806000	0.03193	GAC	G|0.854;C|0.146	0.146	strong		0.537	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
STK17A	9263	hgsc.bcm.edu	37	7	43664198	43664198	+	Silent	SNP	A	A	G	rs10233697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:43664198A>G	ENST00000319357.5	+	7	1181	c.1002A>G	c.(1000-1002)gaA>gaG	p.E334E		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	334					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						TCAGGATGGAAAAGGCACTAG	0.433													A|||	467	0.0932508	0.0174	0.1354	5008	,	,		19180	0.0119		0.2157	False		,,,				2504	0.1237				p.E334E		Atlas-SNP	.											.	STK17A	31	.	0			c.A1002G						PASS	.	A		191,4215	120.8+/-158.4	6,179,2018	86.0	76.0	79.0		1002	2.3	0.5	7	dbSNP_119	79	1820,6780	325.8+/-317.1	195,1430,2675	no	coding-synonymous	STK17A	NM_004760.2		201,1609,4693	GG,GA,AA		21.1628,4.335,15.4621		334/415	43664198	2011,10995	2203	4300	6503	SO:0001819	synonymous_variant	9263	exon7			GATGGAAAAGGCA	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 1"""	604726	"""serine/threonine kinase 17a (apoptosis-inducing)"""			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.1002A>G	7.37:g.43664198A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_004760	A4D1V6|Q8IVC8	Silent	SNP	ENST00000319357.5	37	CCDS5470.1																																																																																			A|0.868;G|0.132	0.132	strong		0.433	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
FRMD7	90167	hgsc.bcm.edu	37	X	131212944	131212944	+	Silent	SNP	A	A	G	rs7051368	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:131212944A>G	ENST00000298542.4	-	12	1276	c.1101T>C	c.(1099-1101)aaT>aaC	p.N367N	FRMD7_ENST00000370879.1_Silent_p.N247N|FRMD7_ENST00000464296.1_Silent_p.N352N	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	367					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)					cGTGCACTCCATTCACATTTT	0.483													A|||	179	0.0474172	0.0628	0.0231	3775	,	,		13883	0.0		0.0726	False		,,,				2504	0.0072				p.N367N		Atlas-SNP	.											.	FRMD7	69	.	0			c.T1101C						PASS	.	A		379,3456		11,295,62,1326,509	174.0	160.0	165.0		1101	-0.6	0.9	X	dbSNP_116	165	659,6069		23,440,173,1965,1699	no	coding-synonymous	FRMD7	NM_194277.2		34,735,235,3291,2208	GG,GA,G,AA,A		9.7949,9.8827,9.8268		367/715	131212944	1038,9525	2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			CACTCCATTCACA	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.1101T>C	X.37:g.131212944A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																			A|0.911;G|0.089	0.089	strong		0.483	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
KRT72	140807	hgsc.bcm.edu	37	12	52992743	52992743	+	Missense_Mutation	SNP	C	C	T	rs142970524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52992743C>T	ENST00000537672.2	-	2	590	c.580G>A	c.(580-582)Ggg>Agg	p.G194R	KRT72_ENST00000293745.2_Missense_Mutation_p.G194R|KRT72_ENST00000398066.3_Missense_Mutation_p.G6R|KRT72_ENST00000354310.4_Missense_Mutation_p.G194R|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	194	Coil 1B.|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)		AGCCTCACCCCGTCCCCAGAC	0.547																																					p.G194R		Atlas-SNP	.											.	KRT72	70	.	0			c.G580A						PASS	.	T	ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	194.0	177.0	183.0		580,580,580	-4.3	1.0	12	dbSNP_134	183	10,8590	818.8+/-406.8	0,10,4290	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	125,125,125	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign,benign,benign	194/512,194/470,194/512	52992743	10,12996	2203	4300	6503	SO:0001583	missense	140807	exon2			TCACCCCGTCCCC	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.580G>A	12.37:g.52992743C>T	ENSP00000441160:p.Gly194Arg	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	215	110	0.511628	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.962|3.962	-0.010160|-0.010160	0.07727|0.07727	0.0|0.0	0.001163|0.001163	ENSG00000170486|ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066|ENST00000549979	D;D;D;D|.	0.86432|.	-2.12;-2.12;-2.12;-2.12|.	5.25|5.25	-4.29|-4.29	0.03721|0.03721	Filament (1);|.	0.000000|.	0.47852|.	N|.	0.000214|.	T|T	0.08846|0.08846	0.0219|0.0219	N|N	0.00191|0.00191	-1.88|-1.88	0.19575|0.19575	N|N	0.999963|0.999963	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|T	0.42396|0.42396	-0.9454|-0.9454	10|5	0.02654|.	T|.	1|.	.|.	16.5611|16.5611	0.84566|0.84566	0.0:0.0582:0.6555:0.2862|0.0:0.0582:0.6555:0.2862	.|.	194;194|.	B4DEI8;Q14CN4|.	.;K2C72_HUMAN|.	R|Q	194;194;194;6|190	ENSP00000441160:G194R;ENSP00000293745:G194R;ENSP00000346269:G194R;ENSP00000446151:G6R|.	ENSP00000293745:G194R|.	G|R	-|-	1|2	0|0	KRT72|KRT72	51279010|51279010	0.000000|0.000000	0.05858|0.05858	0.951000|0.951000	0.38953|0.38953	0.767000|0.767000	0.43475|0.43475	-0.184000|-0.184000	0.09698|0.09698	-0.750000|-0.750000	0.04740|0.04740	-0.361000|-0.361000	0.07541|0.07541	GGG|CGG	C|0.999;T|0.001	0.001	strong		0.547	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
OR5P2	120065	hgsc.bcm.edu	37	11	7818151	7818151	+	Silent	SNP	G	G	A	rs73406606	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7818151G>A	ENST00000329434.2	-	1	369	c.339C>T	c.(337-339)gcC>gcT	p.A113A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CATAGGCCATGGCAGCCAGAA	0.478													G|||	1185	0.236621	0.348	0.2911	5008	,	,		18204	0.128		0.2763	False		,,,				2504	0.1186				p.A113A		Atlas-SNP	.											OR5P2,brain,glioma,0,1	OR5P2	68	1	0			c.C339T						PASS	.	G		1371,2837		401,569,1134	89.0	103.0	99.0		339	2.4	1.0	11	dbSNP_130	99	2425,6159		393,1639,2260	no	coding-synonymous	OR5P2	NM_153444.1		794,2208,3394	AA,AG,GG		28.2502,32.5808,29.6748		113/323	7818151	3796,8996	2104	4292	6396	SO:0001819	synonymous_variant	120065	exon1			GGCCATGGCAGCC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.339C>T	11.37:g.7818151G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			G|0.739;A|0.261	0.261	strong		0.478	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
MYZAP	100820829	hgsc.bcm.edu	37	15	57925836	57925836	+	Missense_Mutation	SNP	C	C	T	rs16977629	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:57925836C>T	ENST00000267853.5	+	8	924	c.830C>T	c.(829-831)gCg>gTg	p.A277V	GCOM1_ENST00000572390.1_Missense_Mutation_p.A277V|GCOM1_ENST00000396180.1_Missense_Mutation_p.A246V|GCOM1_ENST00000380560.2_Missense_Mutation_p.A208V|GCOM1_ENST00000587652.1_Missense_Mutation_p.A277V|GCOM1_ENST00000380569.2_Missense_Mutation_p.A277V|POLR2M_ENST00000380563.2_5'UTR|MYZAP_ENST00000380565.4_Missense_Mutation_p.A277V|GCOM1_ENST00000380568.3_Missense_Mutation_p.A277V|GCOM1_ENST00000574161.1_Missense_Mutation_p.A277V|GCOM1_ENST00000380561.2_Missense_Mutation_p.A246V			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	277			A -> V (in dbSNP:rs16977629). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:20093627}.		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)		p.A277V(1)									TTTCTGAAAGCGATTGAAGAA	0.483													C|||	929	0.185503	0.2126	0.0605	5008	,	,		17328	0.3244		0.0736	False		,,,				2504	0.2096				p.A277V		Atlas-SNP	.											GCOM1,NS,carcinoma,0,1	GCOM1	66	1	1	Substitution - Missense(1)	stomach(1)	c.C830T						scavenged	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	767,3617	309.7+/-291.2	71,625,1496	99.0	106.0	103.0		830,830,830,830	5.7	0.9	15	dbSNP_123	103	515,8069	145.6+/-201.3	17,481,3794	yes	missense,missense,missense,missense	GCOM1	NM_001018090.3,NM_001018091.3,NM_001018100.3,NM_152451.6	64,64,64,64	88,1106,5290	TT,TC,CC		5.9995,17.4954,9.8859	probably-damaging,probably-damaging,probably-damaging,probably-damaging	277/551,277/446,277/467,277/439	57925836	1282,11686	2192	4292	6484	SO:0001583	missense	145781	exon8			TGAAAGCGATTGA	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.830C>T	15.37:g.57925836C>T	ENSP00000267853:p.Ala277Val	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	125	51	0.408	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	374	0.17124542124542125	104	0.21138211382113822	17	0.04696132596685083	199	0.3479020979020979	54	0.0712401055408971	C	23.2	4.386058	0.82902	0.174954	0.059995	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.68	5.68	0.88126	.	0.168555	0.53938	D	0.000059	T	0.00012	0.0000	L	0.41236	1.265	0.09310	P	1.0	D;P;D;P	0.60575	0.988;0.866;0.988;0.942	P;B;P;P	0.51615	0.675;0.388;0.675;0.642	T	0.42783	-0.9431	9	0.32370	T	0.25	-13.0405	18.5497	0.91058	0.0:1.0:0.0:0.0	rs16977629;rs52810917;rs57381984;rs16977629	277;277;277;277	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	V	277;246;246;208;277;277;277	ENSP00000369943:A277V;ENSP00000369935:A246V;ENSP00000379483:A246V;ENSP00000369933:A208V;ENSP00000267853:A277V;ENSP00000369939:A277V;ENSP00000369942:A277V	ENSP00000267853:A277V	A	+	2	0	GCOM1	55713128	0.987000	0.35691	0.944000	0.38274	0.981000	0.71138	4.540000	0.60664	2.676000	0.91093	0.563000	0.77884	GCG	C|0.862;N|0.000	.	strong		0.483	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
PIGQ	9091	hgsc.bcm.edu	37	16	630902	630902	+	Silent	SNP	C	C	G	rs1045274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:630902C>G	ENST00000026218.5	+	9	1549	c.1461C>G	c.(1459-1461)ctC>ctG	p.L487L	PIGQ_ENST00000321878.5_Silent_p.L487L|PIGQ_ENST00000409527.2_Silent_p.L487L	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	487	Leu-rich.				C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				TCCATCTGCTCGTGGACCTCA	0.667													C|||	691	0.137979	0.1369	0.0807	5008	,	,		17865	0.0248		0.1759	False		,,,				2504	0.2577				p.L487L		Atlas-SNP	.											PIGQ,NS,carcinoma,0,1	PIGQ	43	1	0			c.C1461G						PASS	.	C	,	690,3712	289.5+/-280.5	49,592,1560	143.0	136.0	139.0		1461,1461	-4.0	1.0	16	dbSNP_86	139	1588,7012	296.3+/-302.9	149,1290,2861	no	coding-synonymous,coding-synonymous	PIGQ	NM_004204.3,NM_148920.1	,	198,1882,4421	GG,GC,CC		18.4651,15.6747,17.5204	,	487/582,487/761	630902	2278,10724	2201	4300	6501	SO:0001819	synonymous_variant	9091	exon9			TCTGCTCGTGGAC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.1461C>G	16.37:g.630902C>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Silent	SNP	ENST00000026218.5	37	CCDS10411.1																																																																																			C|0.846;G|0.154	0.154	strong		0.667	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048640	33048640	+	Missense_Mutation	SNP	A	A	G	rs1042140	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.K98E	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	57	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	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	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965173	49965173	+	Silent	SNP	A	A	T	rs7259560	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49965173A>T	ENST00000293350.4	+	7	955	c.792A>T	c.(790-792)ggA>ggT	p.G264G	ALDH16A1_ENST00000433981.2_Silent_p.G99G|CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000540132.1_Silent_p.G101G|ALDH16A1_ENST00000455361.2_Intron	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	264						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)		GCCTGGCGGGAGAGTGTGCGG	0.731													c|||	1507	0.300919	0.1422	0.2061	5008	,	,		10303	0.2817		0.4165	False		,,,				2504	0.4836				p.G264G		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.A792T						PASS	.	T	,	796,3562		89,618,1472	19.0	19.0	19.0		,792	-5.6	0.0	19	dbSNP_116	19	3356,5190		682,1992,1599	no	intron,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	771,2610,3071	TT,TA,AA		39.2698,18.2653,32.1761	,	,264/803	49965173	4152,8752	2179	4273	6452	SO:0001819	synonymous_variant	126133	exon7			GGCGGGAGAGTGT	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.792A>T	19.37:g.49965173A>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			A|0.718;T|0.282	0.282	strong		0.731	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
SLC25A17	10478	hgsc.bcm.edu	37	22	41195082	41195082	+	Silent	SNP	G	G	A	rs117487309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:41195082G>A	ENST00000435456.2	-	2	193	c.60C>T	c.(58-60)agC>agT	p.S20S	SLC25A17_ENST00000544408.1_5'UTR|SLC25A17_ENST00000491545.1_5'UTR|SLC25A17_ENST00000542412.1_Silent_p.S20S	NM_006358.2	NP_006349.1	O43808	PM34_HUMAN	solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17	20	Necessary for targeting to peroxisomes and interaction with PEX19.				ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|cellular lipid metabolic process (GO:0044255)|coenzyme A transmembrane transport (GO:0035349)|FAD transmembrane transport (GO:0035350)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|fatty acid transport (GO:0015908)|NAD transport (GO:0043132)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)	integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|chaperone binding (GO:0051087)|coenzyme A transmembrane transporter activity (GO:0015228)|FAD transmembrane transporter activity (GO:0015230)|FMN transmembrane transporter activity (GO:0044610)|NAD transporter activity (GO:0051724)			central_nervous_system(1)|large_intestine(4)|lung(2)|skin(1)	8						TTGCTGTCACGCTTCCCTGAA	0.398													G|||	280	0.0559105	0.0038	0.3602	5008	,	,		19575	0.004		0.0199	False		,,,				2504	0.001				p.S20S		Atlas-SNP	.											.	SLC25A17	25	.	0			c.C60T						PASS	.	G		43,4363	45.3+/-79.5	1,41,2161	83.0	70.0	74.0		60	-7.3	0.5	22	dbSNP_132	74	173,8427	79.8+/-142.4	3,167,4130	no	coding-synonymous	SLC25A17	NM_006358.2		4,208,6291	AA,AG,GG		2.0116,0.9759,1.6608		20/308	41195082	216,12790	2203	4300	6503	SO:0001819	synonymous_variant	10478	exon2			TGTCACGCTTCCC	Y12860	CCDS14005.1, CCDS74868.1	22q13.2	2013-05-22	2002-08-29		ENSG00000100372	ENSG00000100372		"""Solute carriers"""	10987	protein-coding gene	gene with protein product	"""peroxisomal membrane protein (34kD)"""	606795	"""solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kD), member 17"""			9874197	Standard	NM_006358		Approved	PMP34	uc003azc.3	O43808	OTTHUMG00000151139	ENST00000435456.2:c.60C>T	22.37:g.41195082G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	217	110	0.506912	NM_006358	A8KA59|Q5TFL0|Q9UGW8|Q9UGY7	Silent	SNP	ENST00000435456.2	37	CCDS14005.1																																																																																			G|0.971;A|0.029	0.029	strong		0.398	SLC25A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321487.1	NM_006358	
NLRP5	126206	hgsc.bcm.edu	37	19	56565127	56565127	+	Silent	SNP	G	G	A	rs392801	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56565127G>A	ENST00000390649.3	+	13	3252	c.3252G>A	c.(3250-3252)gcG>gcA	p.A1084A		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	1084					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GGGTTGCTGCGCTGTGCGAGG	0.627													G|||	464	0.0926518	0.0272	0.1052	5008	,	,		17855	0.0149		0.2286	False		,,,				2504	0.1125				p.A1084A		Atlas-SNP	.											.	NLRP5	217	.	0			c.G3252A						PASS	.	G		197,4017		5,187,1915	93.0	97.0	96.0		3252	-7.4	0.0	19	dbSNP_80	96	1740,6706		189,1362,2672	no	coding-synonymous	NLRP5	NM_153447.4		194,1549,4587	AA,AG,GG		20.6015,4.6749,15.3002		1084/1201	56565127	1937,10723	2107	4223	6330	SO:0001819	synonymous_variant	126206	exon13			TGCTGCGCTGTGC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.3252G>A	19.37:g.56565127G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	183	94	0.513661	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			G|0.876;A|0.124	0.124	strong		0.627	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
PSMG4	389362	hgsc.bcm.edu	37	6	3264526	3264526	+	Intron	SNP	C	C	T	rs200271803|rs4959788	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3264526C>T	ENST00000438998.2	+	2	379				PSMG4_ENST00000380306.4_Intron|PSMG4_ENST00000419065.2_Missense_Mutation_p.L112F|PSMG4_ENST00000380305.4_Intron|PSMG4_ENST00000451246.2_Intron|PSMG4_ENST00000473000.2_3'UTR	NM_001128591.1	NP_001122063.1	Q5JS54	PSMG4_HUMAN	proteasome (prosome, macropain) assembly chaperone 4											endometrium(1)	1						ATGCTCCACTCTTCCCACACC	0.597													C|||	2665	0.532149	0.1074	0.7464	5008	,	,		23472	0.5635		0.832	False		,,,				2504	0.6135				p.L112F		Atlas-SNP	.											PSMG4_ENST00000419065,colon,carcinoma,-1,4	PSMG4	23	4	0			c.C334T						PASS	.	C	,PHE/LEU	55,1329		21,13,658	204.0	157.0	171.0		,334	-3.3	0.0	6	dbSNP_111	171	1752,1430		757,238,596	yes	intron,missense	PSMG4	NM_001128591.1,NM_001128592.1	,22	778,251,1254	TT,TC,CC		44.9403,3.974,39.5751	,benign	,112/163	3264526	1807,2759	692	1591	2283	SO:0001627	intron_variant	389362	exon3			TCCACTCTTCCCA		CCDS47360.1, CCDS47361.1, CCDS47362.1	6p25.2	2010-06-23	2008-02-25	2008-02-25	ENSG00000180822	ENSG00000180822			21108	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 86"""	C6orf86		17707236	Standard	NM_001128591		Approved	PAC4	uc010jnl.1	Q5JS54	OTTHUMG00000014142	ENST00000438998.2:c.250+533C>T	6.37:g.3264526C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_001128592	C9J2F8|F8WBZ2|Q5JS53|Q5JS56	Missense_Mutation	SNP	ENST00000438998.2	37	CCDS47361.1	1043	0.4775641025641026	53	0.10772357723577236	226	0.6243093922651933	265	0.4632867132867133	499	0.658311345646438	C	0.647	-0.811136	0.02798	0.03974	0.550597	ENSG00000180822	ENST00000419065	.	.	.	3.38	-3.28	0.05033	.	.	.	.	.	T	0.07143	0.0181	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30707	-0.9969	7	0.87932	D	0	.	5.5524	0.17097	0.0:0.6086:0.1614:0.23	rs4959788	112	C9J2F8	.	F	112	.	ENSP00000392353:L112F	L	+	1	0	PSMG4	3209525	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.019000	0.13444	-0.816000	0.04340	0.462000	0.41574	CTT	C|0.522;T|0.478	0.478	strong		0.597	PSMG4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039678.2		
FLG	2312	hgsc.bcm.edu	37	1	152281007	152281007	+	Missense_Mutation	SNP	A	A	G	rs7512553	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281007A>G	ENST00000368799.1	-	3	6390	c.6355T>C	c.(6355-6357)Tat>Cat	p.Y2119H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2119	Ser-rich.		Y -> H (in dbSNP:rs7512553).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCTGATCATAATGGGATCCT	0.572									Ichthyosis				-|||	1641	0.327676	0.3843	0.3357	5008	,	,		29956	0.4355		0.1282	False		,,,				2504	0.3395				p.Y2119H		Atlas-SNP	.											FLG,brain,glioma,+2,1	FLG	900	1	0			c.T6355C						PASS	.	G	HIS/TYR	1451,2955		0,1451,752	349.0	263.0	292.0		6355	1.3	0.0	1	dbSNP_116	292	1089,7511		0,1089,3211	yes	missense	FLG	NM_002016.1	83	0,2540,3963	GG,GA,AA		12.6628,32.9324,19.5294	benign	2119/4062	152281007	2540,10466	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATCATAATGGGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6355T>C	1.37:g.152281007A>G	ENSP00000357789:p.Tyr2119His	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	544	178	0.327206	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1268579	1268579	+	Missense_Mutation	SNP	T	T	G	rs190148881	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1268579T>G	ENST00000529681.1	+	31	10527	c.10469T>G	c.(10468-10470)gTg>gGg	p.V3490G	MUC5B_ENST00000447027.1_Missense_Mutation_p.V3493G|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3490	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.|V -> G (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)		p.V3469G(1)		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)		CCTTCCACGGTGACTTCCCAC	0.667																																					p.V3490G		Atlas-SNP	.											MUC5B,NS,carcinoma,0,5	MUC5B	473	5	1	Substitution - Missense(1)	skin(1)	c.T10469G						scavenged	.						101.0	122.0	115.0					11																	1268579		2134	4215	6349	SO:0001583	missense	727897	exon31			CCACGGTGACTTC	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.10469T>G	11.37:g.1268579T>G	ENSP00000436812:p.Val3490Gly	Somatic	422	1	0.00236967		WXS	Illumina HiSeq	Phase_I	402	25	0.0621891	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	29	0.013278388278388278	10	0.02032520325203252	7	0.019337016574585635	2	0.0034965034965034965	10	0.013192612137203167	t	2.632	-0.286071	0.05605	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21932	1.98;2.17	1.44	-1.72	0.08107	.	.	.	.	.	T	0.10165	0.0249	L	0.43152	1.355	0.09310	N	1	P;P	0.44090	0.826;0.563	P;B	0.48571	0.582;0.032	T	0.14504	-1.0470	9	0.87932	D	0	.	2.5883	0.04836	0.0:0.381:0.2946:0.3243	.	4018;3493	A7Y9J9;E9PBJ0	.;.	G	3490;3493;3462;3395	ENSP00000436812:V3490G;ENSP00000415793:V3493G	ENSP00000343037:V3462G	V	+	2	0	MUC5B	1225155	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	-2.439000	0.01016	-0.179000	0.10654	0.246000	0.17985	GTG	T|0.984;G|0.016	0.016	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
NF2	4771	hgsc.bcm.edu	37	22	30051596	30051596	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:30051596A>G	ENST00000338641.4	+	6	971	c.530A>G	c.(529-531)tAt>tGt	p.Y177C	NF2_ENST00000361452.4_Missense_Mutation_p.Y136C|NF2_ENST00000403999.3_Missense_Mutation_p.Y177C|NF2_ENST00000334961.7_Missense_Mutation_p.Y94C|NF2_ENST00000361676.4_Missense_Mutation_p.Y135C|NF2_ENST00000403435.1_Missense_Mutation_p.Y177C|NF2_ENST00000347330.5_Intron|NF2_ENST00000413209.2_Intron|NF2_ENST00000397789.3_Missense_Mutation_p.Y177C|NF2_ENST00000353887.4_Missense_Mutation_p.Y94C|NF2_ENST00000361166.4_Missense_Mutation_p.Y177C	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	177	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						ATAAATCTGTATCAGATGACT	0.388			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																												p.Y177C		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	NF2_ENST00000403999,colon,carcinoma,-1,8	NF2	1312	8	3	Unknown(3)	large_intestine(1)|stomach(1)|central_nervous_system(1)	c.A530G						scavenged	.						94.0	97.0	96.0					22																	30051596		2203	4299	6502	SO:0001583	missense	4771	exon6	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	ATCTGTATCAGAT	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.530A>G	22.37:g.30051596A>G	ENSP00000344666:p.Tyr177Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	187	5	0.026738	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.379930	0.82682	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	T;T;T;T;T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11;-1.11	5.41	5.41	0.78517	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.89298	0.6675	M	0.86651	2.83	0.80722	D	1	D;D;D;D;P;D	0.89917	1.0;1.0;1.0;1.0;0.947;1.0	D;D;D;D;P;D	0.87578	0.998;0.992;0.987;0.991;0.552;0.987	D	0.90723	0.4636	9	.	.	.	.	15.4334	0.75121	1.0:0.0:0.0:0.0	.	136;177;177;135;94;177	P35240-5;P35240;P35240-2;P35240-6;P35240-4;P35240-3	.;MERL_HUMAN;.;.;.;.	C	177;177;136;177;177;94;94;177;135;177	ENSP00000344666:Y177C;ENSP00000384029:Y177C;ENSP00000354897:Y136C;ENSP00000384797:Y177C;ENSP00000335652:Y94C;ENSP00000340626:Y94C;ENSP00000380891:Y177C;ENSP00000355183:Y135C;ENSP00000354529:Y177C	.	Y	+	2	0	NF2	28381596	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.137000	0.94496	2.039000	0.60335	0.454000	0.30748	TAT	.	.	none		0.388	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	
DDX20	11218	hgsc.bcm.edu	37	1	112308953	112308953	+	Missense_Mutation	SNP	T	T	C	rs197412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	105	0	0		WXS	Illumina HiSeq	Phase_I	95	38	0.4	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	
CPNE1	8904	hgsc.bcm.edu	37	20	34214173	34214173	+	Missense_Mutation	SNP	G	G	A	rs11543239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34214173G>A	ENST00000317619.3	-	18	1998	c.1604C>T	c.(1603-1605)cCc>cTc	p.P535L	CPNE1_ENST00000397442.1_Missense_Mutation_p.P479L|CPNE1_ENST00000397443.1_Missense_Mutation_p.P535L|CPNE1_ENST00000397446.1_Missense_Mutation_p.P535L|CPNE1_ENST00000317677.5_Missense_Mutation_p.P540L|CPNE1_ENST00000397445.1_Missense_Mutation_p.P535L|CPNE1_ENST00000352393.4_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	55	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	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	
CDC14A	8556	hgsc.bcm.edu	37	1	100949860	100949860	+	Silent	SNP	G	G	A	rs2270694	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:100949860G>A	ENST00000336454.3	+	11	1345	c.990G>A	c.(988-990)tcG>tcA	p.S330S	CDC14A_ENST00000542213.1_Silent_p.S272S|RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000361544.6_Silent_p.S330S|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000370124.3_Silent_p.S330S|CDC14A_ENST00000544534.1_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	38	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	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	
GRID1	2894	hgsc.bcm.edu	37	10	87489318	87489318	+	Silent	SNP	G	G	C	rs3812644|rs386746181	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:87489318G>C	ENST00000327946.7	-	9	1372	c.1287C>G	c.(1285-1287)ccC>ccG	p.P429P	GRID1_ENST00000536331.1_5'UTR	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	429					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)	p.P429P(1)		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						GGCTGCCCATGGGCCTCTCTT	0.527										Multiple Myeloma(13;0.14)			G|||	334	0.0666933	0.1566	0.0173	5008	,	,		15969	0.0516		0.0239	False		,,,				2504	0.0399				p.P429P		Atlas-SNP	.											GRID1,NS,carcinoma,0,1	GRID1	204	1	1	Substitution - coding silent(1)	stomach(1)	c.C1287G						PASS	.	G		676,3730	283.7+/-277.2	45,586,1572	81.0	78.0	79.0		1287	-0.2	1.0	10	dbSNP_107	79	174,8426	77.2+/-139.8	0,174,4126	no	coding-synonymous	GRID1	NM_017551.2		45,760,5698	CC,CG,GG		2.0233,15.3427,6.5354		429/1010	87489318	850,12156	2203	4300	6503	SO:0001819	synonymous_variant	2894	exon9			GCCCATGGGCCTC	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.1287C>G	10.37:g.87489318G>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	96	35	0.364583	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																			G|0.944;C|0.056	0.056	strong		0.527	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
RELN	5649	hgsc.bcm.edu	37	7	103205779	103205779	+	Missense_Mutation	SNP	G	G	A	rs115913736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:103205779G>A	ENST00000428762.1	-	34	5315	c.5156C>T	c.(5155-5157)tCg>tTg	p.S1719L	RELN_ENST00000424685.2_Missense_Mutation_p.S1719L|RELN_ENST00000343529.5_Missense_Mutation_p.S1719L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1719					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)		GAATCTTTCCGAGGTGTAAAT	0.463													G|||	17	0.00339457	0.0008	0.0	5008	,	,		19094	0.0		0.0089	False		,,,				2504	0.0072				p.S1719L	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											RELN,NS,lymphoid_neoplasm,+1,1	RELN	593	1	0			c.C5156T						PASS	.	G	LEU/SER,LEU/SER	3,4403	6.2+/-15.9	0,3,2200	129.0	114.0	119.0		5156,5156	5.2	0.9	7	dbSNP_132	119	70,8530	42.2+/-99.7	2,66,4232	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	145,145	2,69,6432	AA,AG,GG		0.814,0.0681,0.5613	probably-damaging,probably-damaging	1719/3461,1719/3459	103205779	73,12933	2203	4300	6503	SO:0001583	missense	5649	exon34			CTTTCCGAGGTGT		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.5156C>T	7.37:g.103205779G>A	ENSP00000392423:p.Ser1719Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	23.4	4.410786	0.83340	6.81E-4	0.00814	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.43688	1.75;0.94;1.75	6.02	5.15	0.70609	Neuraminidase (1);	0.066420	0.64402	N	0.000006	T	0.51261	0.1664	L	0.60455	1.87	0.54753	D	0.999988	D;D	0.76494	0.999;0.998	P;D	0.69307	0.889;0.963	T	0.56486	-0.7971	10	0.42905	T	0.14	.	15.254	0.73571	0.0668:0.0:0.9332:0.0	.	1719;1719	P78509-2;P78509	.;RELN_HUMAN	L	1719	ENSP00000392423:S1719L;ENSP00000345694:S1719L;ENSP00000388446:S1719L	ENSP00000345694:S1719L	S	-	2	0	RELN	102993015	1.000000	0.71417	0.913000	0.36048	0.978000	0.69477	9.139000	0.94554	1.569000	0.49696	0.655000	0.94253	TCG	G|0.994;A|0.006	0.006	strong		0.463	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
MLXIP	22877	hgsc.bcm.edu	37	12	122617989	122617989	+	Missense_Mutation	SNP	A	A	G	rs7978353	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:122617989A>G	ENST00000319080.7	+	9	1319	c.1187A>G	c.(1186-1188)gAg>gGg	p.E396G	MLXIP_ENST00000377037.2_Missense_Mutation_p.E3G|MLXIP_ENST00000538698.1_Missense_Mutation_p.E3G					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		CACATGGATGAGCAGGGCTGT	0.642													G|||	2283	0.455871	0.5113	0.3934	5008	,	,		13429	0.3581		0.4742	False		,,,				2504	0.5072				p.E396G	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											MLXIP,colon,carcinoma,0,2	MLXIP	46	2	0			c.A1187G						PASS	.	G	GLY/GLU	1981,2079		503,975,552	31.0	35.0	33.0		777	-0.2	0.0	12	dbSNP_116	33	3278,5086		632,2014,1536	yes	missense	MLXIP	NM_014938.3	98	1135,2989,2088	GG,GA,AA		39.1918,48.7931,42.3294	benign	396/920	122617989	5259,7165	2030	4182	6212	SO:0001583	missense	22877	exon9			TGGATGAGCAGGG	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1187A>G	12.37:g.122617989A>G	ENSP00000312834:p.Glu396Gly	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	37		936	0.42857142857142855	236	0.4796747967479675	142	0.39226519337016574	209	0.36538461538461536	349	0.4604221635883905	G	4.856	0.159087	0.09236	0.487931	0.391918	ENSG00000175727	ENST00000319080;ENST00000538698;ENST00000539039;ENST00000377037	T;T;T	0.30981	2.51;1.96;1.51	5.04	-0.212	0.13169	.	2.273020	0.01378	N	0.012813	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45454	-0.9260	8	0.13470	T	0.59	0.7027	6.0635	0.19850	0.4415:0.1246:0.4339:0.0	rs7978353;rs60448207;rs7978353	396;396	Q9HAP2-3;Q9HAP2	.;MLXIP_HUMAN	G	396;3;3;3	ENSP00000312834:E396G;ENSP00000440769:E3G;ENSP00000366236:E3G	ENSP00000312834:E396G	E	+	2	0	MLXIP	121183942	0.265000	0.24102	0.000000	0.03702	0.006000	0.05464	0.805000	0.27112	-0.658000	0.05366	-0.898000	0.02899	GAG	A|0.566;G|0.434	0.434	strong		0.642	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
SLC7A9	11136	hgsc.bcm.edu	37	19	33355081	33355081	+	Silent	SNP	G	G	A	rs35170371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33355081G>A	ENST00000023064.4	-	4	590	c.399C>T	c.(397-399)tcC>tcT	p.S133S	SLC7A9_ENST00000587772.1_Silent_p.S133S|SLC7A9_ENST00000590341.1_Silent_p.S133S|RN7SKP22_ENST00000365097.1_RNA	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	133					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)	ACACATACTCGGAGAAGCTGA	0.607													G|||	1059	0.211462	0.3079	0.1124	5008	,	,		20091	0.1994		0.2207	False		,,,				2504	0.1544				p.S133S	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.C399T						PASS	.	G	,	1275,3131	432.2+/-343.2	187,901,1115	119.0	92.0	101.0		399,399	-9.9	0.0	19	dbSNP_126	101	1726,6874	314.2+/-311.7	162,1402,2736	no	coding-synonymous,coding-synonymous	SLC7A9	NM_001126335.1,NM_014270.4	,	349,2303,3851	AA,AG,GG		20.0698,28.9378,23.074	,	133/488,133/488	33355081	3001,10005	2203	4300	6503	SO:0001819	synonymous_variant	11136	exon4			ATACTCGGAGAAG	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.399C>T	19.37:g.33355081G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																			G|0.782;A|0.218	0.218	strong		0.607	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
UCHL1	7345	hgsc.bcm.edu	37	4	41259633	41259633	+	Missense_Mutation	SNP	C	C	A	rs5030732	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:41259633C>A	ENST00000284440.4	+	3	197	c.53C>A	c.(52-54)tCc>tAc	p.S18Y	UCHL1_ENST00000503431.1_Missense_Mutation_p.S18Y|UCHL1_ENST00000504818.1_3'UTR|UCHL1_ENST00000512788.1_Missense_Mutation_p.S18Y|UCHL1-AS1_ENST00000510073.1_RNA|UCHL1_ENST00000508768.1_Missense_Mutation_p.S18Y|UCHL1-AS1_ENST00000507190.1_RNA	NM_004181.4	NP_004172.2	P09936	UCHL1_HUMAN	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	18			S -> Y (found in patients with cataract; unknown pathological significance; loss of dimerization ability; impaired ligase activity; confers an antioxidant protective function when expressed at physiological levels in neuroblastoma cells and primary cortical neurons; dbSNP:rs5030732). {ECO:0000269|PubMed:10203348, ECO:0000269|PubMed:11027850, ECO:0000269|PubMed:15048890, ECO:0000269|PubMed:16450370, ECO:0000269|PubMed:21268678}.		adult walking behavior (GO:0007628)|axon target recognition (GO:0007412)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|cell proliferation (GO:0008283)|eating behavior (GO:0042755)|muscle fiber development (GO:0048747)|negative regulation of MAP kinase activity (GO:0043407)|neuromuscular process (GO:0050905)|protein deubiquitination (GO:0016579)|response to ischemia (GO:0002931)|sensory perception of pain (GO:0019233)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	alpha-2A adrenergic receptor binding (GO:0031694)|cysteine-type endopeptidase activity (GO:0004197)|ligase activity (GO:0016874)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(2)	8						CAGGTGCTGTCCCGGCTGGGG	0.766													C|||	1272	0.253994	0.0121	0.2939	5008	,	,		10899	0.5437		0.1809	False		,,,				2504	0.3292				p.S18Y		Atlas-SNP	.											.	UCHL1	19	.	0			c.C53A	GRCh37	CM994452	UCHL1	M	rs5030732	PASS	.	C	TYR/SER	114,4064		2,110,1977	6.0	8.0	7.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	53	2.8	0.9	4	dbSNP_113	7	1114,7164		61,992,3086	no	missense	UCHL1	NM_004181.4	144	63,1102,5063	AA,AC,CC		13.4574,2.7286,9.8587	benign	18/224	41259633	1228,11228	2089	4139	6228	SO:0001583	missense	7345	exon3			TGCTGTCCCGGCT	BC000332	CCDS3462.1	4p13	2011-07-21			ENSG00000154277	ENSG00000154277	3.4.19.12	"""Parkinson disease"""	12513	protein-coding gene	gene with protein product		191342		PARK5		1840236	Standard	NM_004181		Approved	PGP9.5, Uch-L1	uc003gvo.3	P09936	OTTHUMG00000099377	ENST00000284440.4:c.53C>A	4.37:g.41259633C>A	ENSP00000284440:p.Ser18Tyr	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_004181	Q4W5K6|Q71UM0	Missense_Mutation	SNP	ENST00000284440.4	37	CCDS3462.1	528	0.24175824175824176	16	0.032520325203252036	97	0.26795580110497236	282	0.493006993006993	133	0.17546174142480211	C	8.406	0.842968	0.16963	0.027286	0.134574	ENSG00000154277	ENST00000514924;ENST00000503431;ENST00000284440;ENST00000508768;ENST00000512788	T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47	3.7	2.84	0.33178	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	1.003210	0.08035	N	0.994193	T	0.00012	0.0000	L	0.37697	1.125	0.28202	P	0.9273172	P	0.38300	0.626	B	0.36567	0.228	T	0.44406	-0.9330	9	0.23891	T	0.37	-1.0546	13.1671	0.59577	0.0:0.8388:0.1611:0.0	rs5030732	18	P09936	UCHL1_HUMAN	Y	18	ENSP00000426634:S18Y;ENSP00000422542:S18Y;ENSP00000284440:S18Y;ENSP00000426895:S18Y;ENSP00000423623:S18Y	ENSP00000284440:S18Y	S	+	2	0	UCHL1	40954390	0.422000	0.25473	0.940000	0.37924	0.849000	0.48306	1.040000	0.30278	0.724000	0.32296	0.462000	0.41574	TCC	C|0.758;A|0.242	0.242	strong		0.766	UCHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216827.1	NM_004181	
BCO1	53630	hgsc.bcm.edu	37	16	81301694	81301694	+	Missense_Mutation	SNP	A	A	T	rs12934922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:81301694A>T	ENST00000258168.2	+	6	1262	c.801A>T	c.(799-801)agA>agT	p.R267S	BCMO1_ENST00000425577.2_Missense_Mutation_p.R198S	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						ACATCCGGAGAATGAGCTGGG	0.562													a|||	1138	0.227236	0.0893	0.3199	5008	,	,		20516	0.128		0.4404	False		,,,				2504	0.2311				p.R267S		Atlas-SNP	.											.	BCMO1	53	.	0			c.A801T						PASS	.		SER/ARG	718,3686	299.0+/-285.6	67,584,1551	88.0	78.0	82.0		801	-7.5	1.0	16	dbSNP_121	82	3866,4734	542.9+/-384.3	893,2080,1327	yes	missense	BCMO1	NM_017429.2	110	960,2664,2878	TT,TA,AA		44.9535,16.3034,35.2507	benign	267/548	81301694	4584,8420	2202	4300	6502	SO:0001583	missense	53630	exon6			CCGGAGAATGAGC																												ENST00000258168.2:c.801A>T	16.37:g.81301694A>T	ENSP00000258168:p.Arg267Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_017429		Missense_Mutation	SNP	ENST00000258168.2	37	CCDS10934.1	589	0.2696886446886447	48	0.0975609756097561	127	0.35082872928176795	79	0.1381118881118881	335	0.4419525065963061	a	14.54	2.565170	0.45694	0.163034	0.449535	ENSG00000135697	ENST00000258168;ENST00000425577	D;D	0.94650	-3.48;-3.1	5.22	-7.5	0.01351	.	0.110635	0.64402	D	0.000009	T	0.00012	0.0000	N	0.12746	0.255	0.58432	P	1.0000000000287557E-6	B;B	0.15719	0.014;0.002	B;B	0.13407	0.009;0.002	T	0.46638	-0.9177	9	0.49607	T	0.09	-11.2666	0.3682	0.00375	0.2329:0.2626:0.1757:0.3288	rs12934922;rs52815018;rs59284946;rs12934922	198;267	E7EM88;Q9HAY6	.;BCDO1_HUMAN	S	267;198	ENSP00000258168:R267S;ENSP00000400586:R198S	ENSP00000258168:R267S	R	+	3	2	BCMO1	79859195	0.000000	0.05858	0.976000	0.42696	0.887000	0.51463	-2.352000	0.01091	-0.659000	0.05359	0.319000	0.21371	AGA	A|0.670;T|0.330	0.330	strong		0.562	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1		
EXOSC3	51010	hgsc.bcm.edu	37	9	37780831	37780831	+	Missense_Mutation	SNP	A	A	G	rs3208406	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:37780831A>G	ENST00000327304.5	-	4	685	c.673T>C	c.(673-675)Tat>Cat	p.Y225H	EXOSC3_ENST00000490516.1_5'UTR|EXOSC3_ENST00000396521.3_3'UTR|RP11-613M10.9_ENST00000540557.1_Intron	NM_016042.3	NP_057126.2	Q9NQT5	EXOS3_HUMAN	exosome component 3	225			Y -> H (in dbSNP:rs3208406).		CUT catabolic process (GO:0071034)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of isotype switching (GO:0045830)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(1)	4				GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221)		TCCAGTGGATAGAGTTTTCCC	0.383													A|||	179	0.0357428	0.0015	0.049	5008	,	,		20262	0.003		0.1113	False		,,,				2504	0.0286				p.Y225H		Atlas-SNP	.											.	EXOSC3	8	.	0			c.T673C						PASS	.	A	,HIS/TYR	89,4317	73.6+/-111.7	1,87,2115	85.0	78.0	80.0		,673	5.7	1.0	9	dbSNP_105	80	848,7752	193.5+/-239.2	44,760,3496	yes	utr-3,missense	EXOSC3	NM_001002269.1,NM_016042.2	,83	45,847,5611	GG,GA,AA		9.8605,2.02,7.2044	,possibly-damaging	,225/276	37780831	937,12069	2203	4300	6503	SO:0001583	missense	51010	exon4			GTGGATAGAGTTT	BC002437	CCDS35016.1, CCDS43805.1	9p11	2009-01-20			ENSG00000107371	ENSG00000107371			17944	protein-coding gene	gene with protein product	"""exosome component Rrp40"", ""CGI-102 protein"""	606489				10810093, 11110791	Standard	NM_016042		Approved	hRrp40p, Rrp40p, RRP40, CGI-102, p10, hRrp-40	uc004aal.3	Q9NQT5	OTTHUMG00000019932	ENST00000327304.5:c.673T>C	9.37:g.37780831A>G	ENSP00000323046:p.Tyr225His	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	131	58	0.442748	NM_016042	A8K0K6|Q5QP85|Q9Y3A8	Missense_Mutation	SNP	ENST00000327304.5	37	CCDS35016.1	100	0.045787545787545784	2	0.0040650406504065045	20	0.055248618784530384	1	0.0017482517482517483	77	0.10158311345646438	A	21.0	4.074761	0.76415	0.0202	0.098605	ENSG00000107371	ENST00000327304	T	0.16897	2.31	5.66	5.66	0.87406	.	0.167853	0.52532	D	0.000074	T	0.00936	0.0031	M	0.66939	2.045	0.09310	P	1.0	D	0.65815	0.995	P	0.61201	0.885	T	0.06862	-1.0803	9	0.15499	T	0.54	-10.691	14.1342	0.65276	1.0:0.0:0.0:0.0	rs3208406;rs17586551;rs52820434;rs59118498;rs3208406	225	Q9NQT5	EXOS3_HUMAN	H	225	ENSP00000323046:Y225H	ENSP00000323046:Y225H	Y	-	1	0	EXOSC3	37770831	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.782000	0.75073	2.270000	0.75569	0.533000	0.62120	TAT	A|0.941;G|0.059	0.059	strong		0.383	EXOSC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052478.3	NM_016042	
NUP37	79023	hgsc.bcm.edu	37	12	102494849	102494849	+	Silent	SNP	T	T	C	rs17438178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102494849T>C	ENST00000552283.1	-	4	454	c.315A>G	c.(313-315)agA>agG	p.R105R	NUP37_ENST00000251074.1_Silent_p.R105R|NUP37_ENST00000543021.1_5'UTR			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	105					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						AAGTAAATAATCTAATTTTCA	0.308													T|||	110	0.0219649	0.0401	0.0058	5008	,	,		16106	0.0		0.0308	False		,,,				2504	0.0225				p.R105R		Atlas-SNP	.											.	NUP37	26	.	0			c.A315G						PASS	.	T		130,4262		4,122,2070	29.0	31.0	31.0		315	0.3	1.0	12	dbSNP_123	31	211,8361		2,207,4077	no	coding-synonymous	NUP37	NM_024057.2		6,329,6147	CC,CT,TT		2.4615,2.9599,2.6304		105/327	102494849	341,12623	2196	4286	6482	SO:0001819	synonymous_variant	79023	exon3			AAATAATCTAATT	AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188		"""WD repeat domain containing"""	29929	protein-coding gene	gene with protein product		609264				12196509	Standard	NM_024057		Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.315A>G	12.37:g.102494849T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_024057	Q9H644	Silent	SNP	ENST00000552283.1	37	CCDS9089.1																																																																																			T|0.976;C|0.024	0.024	strong		0.308	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057	
ZNF57	126295	hgsc.bcm.edu	37	19	2917509	2917509	+	Missense_Mutation	SNP	G	G	A	rs61754927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917509G>A	ENST00000306908.5	+	4	1038	c.890G>A	c.(889-891)aGa>aAa	p.R297K	ZNF57_ENST00000523428.1_Missense_Mutation_p.R265K|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	297					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTTTTCAAAGACATGAGAAG	0.488													G|||	130	0.0259585	0.0257	0.0288	5008	,	,		19431	0.0		0.0169	False		,,,				2504	0.0603				p.R297K	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G890A						PASS	.	G	LYS/ARG	95,4311	76.8+/-115.0	0,95,2108	74.0	80.0	78.0		890	-4.1	0.0	19	dbSNP_129	78	208,8392	88.1+/-150.5	4,200,4096	yes	missense	ZNF57	NM_173480.2	26	4,295,6204	AA,AG,GG		2.4186,2.1562,2.3297	benign	297/556	2917509	303,12703	2203	4300	6503	SO:0001583	missense	126295	exon4			TTCAAAGACATGA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.890G>A	19.37:g.2917509G>A	ENSP00000303696:p.Arg297Lys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	40	0.018315018315018316	17	0.034552845528455285	13	0.03591160220994475	0	0.0	10	0.013192612137203167	G	2.867	-0.234775	0.05983	0.021562	0.024186	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.02197	4.4;4.4	2.25	-4.14	0.03892	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00384	0.0012	L	0.31207	0.915	0.09310	N	1	B	0.33171	0.4	B	0.37943	0.261	T	0.41787	-0.9489	9	0.05721	T	0.95	.	0.9159	0.01304	0.2475:0.1759:0.3978:0.1788	rs61754927	297	Q68EA5	ZNF57_HUMAN	K	297;299;265	ENSP00000303696:R297K;ENSP00000430223:R265K	ENSP00000303696:R297K	R	+	2	0	ZNF57	2868509	0.000000	0.05858	0.001000	0.08648	0.558000	0.35554	-7.471000	0.00035	-1.087000	0.03081	0.511000	0.50034	AGA	G|0.974;A|0.026	0.026	strong		0.488	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
C5	727	hgsc.bcm.edu	37	9	123769200	123769200	+	Missense_Mutation	SNP	C	C	T	rs17611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123769200C>T	ENST00000223642.1	-	19	2433	c.2404G>A	c.(2404-2406)Gtt>Att	p.V802I	C5_ENST00000466280.1_5'UTR	NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	802			V -> I (in dbSNP:rs17611). {ECO:0000269|PubMed:15488949, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1984448, ECO:0000269|PubMed:2579066, ECO:0000269|PubMed:3365401, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		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)	GAAATGCCAACGCCTTGAATT	0.328													C|||	2027	0.404752	0.0287	0.5	5008	,	,		17327	0.5685		0.4583	False		,,,				2504	0.6217				p.V802I		Atlas-SNP	.											.	C5	124	.	0			c.G2404A						PASS	.	C	ILE/VAL	396,4010	196.7+/-221.0	25,346,1832	105.0	98.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2404	1.1	1.0	9	dbSNP_63	101	3829,4771	539.6+/-383.6	888,2053,1359	yes	missense	C5	NM_001735.2	29	913,2399,3191	TT,TC,CC		44.5233,8.9877,32.485	benign	802/1677	123769200	4225,8781	2203	4300	6503	SO:0001583	missense	727	exon19			TGCCAACGCCTTG	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.2404G>A	9.37:g.123769200C>T	ENSP00000223642:p.Val802Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	890	0.4075091575091575	20	0.04065040650406504	181	0.5	333	0.5821678321678322	356	0.46965699208443273	C	10.61	1.399024	0.25291	0.089877	0.445233	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.26223	1.75	5.8	1.06	0.20224	Alpha-2-macroglobulin (1);	0.493963	0.22107	N	0.064536	T	0.00012	0.0000	N	0.12663	0.25	0.38389	P	0.054643	B	0.25486	0.127	B	0.20577	0.03	T	0.40327	-0.9569	9	0.32370	T	0.25	.	5.6286	0.17497	0.1408:0.5487:0.0:0.3105	rs17611;rs2900182;rs3789309;rs17398509;rs52790382;rs59537886;rs17611	802	P01031	CO5_HUMAN	I	802;873	ENSP00000223642:V802I	ENSP00000223642:V802I	V	-	1	0	C5	122809021	0.430000	0.25538	0.986000	0.45419	0.471000	0.32888	0.100000	0.15231	0.277000	0.22141	0.563000	0.77884	GTT	C|0.644;T|0.356	0.356	strong		0.328	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
PLA2G3	50487	hgsc.bcm.edu	37	22	31536133	31536133	+	Missense_Mutation	SNP	A	A	C	rs2232176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31536133A>C	ENST00000215885.3	-	1	460	c.208T>G	c.(208-210)Tca>Gca	p.S70A		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	70			S -> A (in dbSNP:rs2232176). {ECO:0000269|PubMed:10713052, ECO:0000269|PubMed:15489334}.		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						CAGCTACATGACTGCAGCCTC	0.642													C|||	4167	0.832069	0.7231	0.8646	5008	,	,		18627	0.9325		0.7873	False		,,,				2504	0.8988				p.S70A		Atlas-SNP	.											PLA2G3_ENST00000215885,NS,carcinoma,0,4	PLA2G3	85	4	0			c.T208G						PASS	.	C	ALA/SER	3100,1306	431.6+/-343.0	1086,928,189	66.0	69.0	68.0		208	3.6	0.1	22	dbSNP_98	68	6684,1916	333.3+/-320.5	2596,1492,212	yes	missense	PLA2G3	NM_015715.3	99	3682,2420,401	CC,CA,AA		22.2791,29.6414,24.7732	benign	70/510	31536133	9784,3222	2203	4300	6503	SO:0001583	missense	50487	exon1			TACATGACTGCAG	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.208T>G	22.37:g.31536133A>C	ENSP00000215885:p.Ser70Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	37	CCDS13889.1	1786	0.8177655677655677	358	0.7276422764227642	306	0.8453038674033149	529	0.9248251748251748	593	0.7823218997361477	C	1.301	-0.605006	0.03717	0.703586	0.777209	ENSG00000100078	ENST00000215885	T	0.11712	2.75	5.69	3.58	0.41010	.	1.051720	0.07391	N	0.889048	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	0.21348	-1.0248	9	0.06625	T	0.88	-3.9647	7.1186	0.25431	0.3019:0.6191:0.0:0.079	rs2232176;rs17856726;rs61572667;rs2232176	70	Q9NZ20	PA2G3_HUMAN	A	70	ENSP00000215885:S70A	ENSP00000215885:S70A	S	-	1	0	PLA2G3	29866133	0.335000	0.24748	0.103000	0.21229	0.560000	0.35617	0.989000	0.29629	0.342000	0.23796	-0.121000	0.15023	TCA	A|0.211;C|0.789	0.789	strong		0.642	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
TRPC4	7223	hgsc.bcm.edu	37	13	38237564	38237564	+	Silent	SNP	A	A	G	rs75514550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:38237564A>G	ENST00000379705.3	-	6	2534	c.1677T>C	c.(1675-1677)aaT>aaC	p.N559N	TRPC4_ENST00000447043.1_Silent_p.N559N|TRPC4_ENST00000358477.2_Silent_p.N559N|TRPC4_ENST00000379681.3_Silent_p.N559N|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000355779.2_Silent_p.N559N|TRPC4_ENST00000379673.2_Silent_p.N559N|TRPC4_ENST00000338947.5_Silent_p.N386N|TRPC4_ENST00000494529.1_Intron|TRPC4_ENST00000379679.1_Silent_p.N386N			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	559					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)		TTGAAAATGCATTATTCTGCT	0.348													A|||	34	0.00678914	0.0008	0.0187	5008	,	,		19000	0.0		0.0179	False		,,,				2504	0.002				p.N559N		Atlas-SNP	.											.	TRPC4	389	.	0			c.T1677C						PASS	.	A	,,,,,	11,4395	20.2+/-43.8	0,11,2192	79.0	74.0	75.0		1677,1677,1677,1158,1677,1677	2.2	1.0	13	dbSNP_132	75	165,8435	77.8+/-140.4	2,161,4137	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	,,,,,	2,172,6329	GG,GA,AA		1.9186,0.2497,1.3532	,,,,,	559/894,559/829,559/837,386/805,559/983,559/978	38237564	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon6			AAATGCATTATTC	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.1677T>C	13.37:g.38237564A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	148	91	0.614865	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			A|0.988;G|0.012	0.012	strong		0.348	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
MYPN	84665	hgsc.bcm.edu	37	10	69908157	69908157	+	Missense_Mutation	SNP	T	T	C	rs11596653	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:69908157T>C	ENST00000358913.5	+	5	1666	c.1178T>C	c.(1177-1179)gTc>gCc	p.V393A	MYPN_ENST00000540630.1_Missense_Mutation_p.V393A|MYPN_ENST00000373675.3_Missense_Mutation_p.V393A|MYPN_ENST00000354393.2_Missense_Mutation_p.V118A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	393	Interaction with CARP.		V -> A (in dbSNP:rs11596653). {ECO:0000269|PubMed:22286171, ECO:0000269|PubMed:22892539}.		sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						ACCTCTGCAGTCATTCCTCCA	0.453													C|||	604	0.120607	0.4077	0.049	5008	,	,		19266	0.0		0.0159	False		,,,				2504	0.0153				p.V393A		Atlas-SNP	.											.	MYPN	189	.	0			c.T1178C						PASS	.	C	ALA/VAL	1464,2942	680.1+/-403.8	242,980,981	104.0	96.0	99.0		1178	2.5	1.0	10	dbSNP_120	99	126,8474	813.8+/-407.0	0,126,4174	yes	missense	MYPN	NM_032578.2	64	242,1106,5155	CC,CT,TT		1.4651,33.2274,12.2251	benign	393/1321	69908157	1590,11416	2203	4300	6503	SO:0001583	missense	84665	exon5			CTGCAGTCATTCC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1178T>C	10.37:g.69908157T>C	ENSP00000351790:p.Val393Ala	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	184	98	0.532609	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	237	0.10851648351648352	203	0.41260162601626016	21	0.058011049723756904	0	0.0	13	0.017150395778364115	C	10.18	1.278846	0.23307	0.332274	0.014651	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630;ENST00000373675	T;T;T;T	0.60171	0.44;0.58;0.55;0.21	5.86	2.55	0.30701	.	0.577822	0.18475	N	0.140105	T	0.00012	0.0000	N	0.02011	-0.69	0.51233	P	8.300000000005525E-5	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	0.44605	-0.9317	8	.	.	.	.	5.8113	0.18467	0.0:0.5922:0.146:0.2618	rs11596653;rs52808892;rs58050908;rs11596653	393;393;118;393	F5GWA6;Q86TC9-3;Q86TC9-2;Q86TC9	.;.;.;MYPN_HUMAN	A	118;118;393;393;393	ENSP00000346369:V118A;ENSP00000351790:V393A;ENSP00000441668:V393A;ENSP00000362779:V393A	.	V	+	2	0	MYPN	69578163	0.993000	0.37304	1.000000	0.80357	0.831000	0.47069	0.253000	0.18296	0.393000	0.25203	-0.119000	0.15052	GTC	T|0.874;C|0.126	0.126	strong		0.453	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
ANPEP	290	hgsc.bcm.edu	37	15	90335788	90335788	+	Missense_Mutation	SNP	C	C	T	rs25651	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90335788C>T	ENST00000300060.6	-	17	2568	c.2255G>A	c.(2254-2256)aGc>aAc	p.S752N		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	752	Metalloprotease.		S -> N (in dbSNP:rs25651).		angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	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)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	ATTAACCTCGCTGTACCTGCC	0.577													T|||	1756	0.350639	0.5144	0.2622	5008	,	,		17122	0.2331		0.2962	False		,,,				2504	0.3691				p.S752N	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.G2255A						PASS	.	T	ASN/SER	2142,2258	595.9+/-388.5	542,1058,600	104.0	85.0	91.0		2255	-4.4	0.0	15	dbSNP_72	91	2737,5861	679.9+/-403.6	405,1927,1967	yes	missense	ANPEP	NM_001150.2	46	947,2985,2567	TT,TC,CC		31.833,48.6818,37.5365	benign	752/968	90335788	4879,8119	2200	4299	6499	SO:0001583	missense	290	exon17			ACCTCGCTGTACC	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2255G>A	15.37:g.90335788C>T	ENSP00000300060:p.Ser752Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	689	0.31547619047619047	231	0.4695121951219512	94	0.2596685082872928	144	0.2517482517482518	220	0.29023746701846964	T	0.008	-1.901246	0.00517	0.486818	0.31833	ENSG00000166825	ENST00000300060	T	0.05513	3.43	4.58	-4.38	0.03622	.	0.497865	0.21743	N	0.069790	T	0.00012	0.0000	N	0.01405	-0.89	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45411	-0.9263	9	0.22706	T	0.39	.	14.2567	0.66058	0.0:0.6451:0.0:0.3549	rs25651;rs1126609;rs3181738;rs8179194;rs16943596;rs17402988;rs52810845;rs25651	752	P15144	AMPN_HUMAN	N	752	ENSP00000300060:S752N	ENSP00000300060:S752N	S	-	2	0	ANPEP	88136792	0.002000	0.14202	0.006000	0.13384	0.005000	0.04900	-0.012000	0.12699	-1.792000	0.01259	-1.271000	0.01417	AGC	C|0.642;T|0.358	0.358	strong		0.577	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
GRK4	2868	hgsc.bcm.edu	37	4	2990499	2990499	+	Missense_Mutation	SNP	G	G	T	rs2960306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2990499G>T	ENST00000398052.4	+	3	537	c.194G>T	c.(193-195)cGt>cTt	p.R65L	GRK4_ENST00000398051.4_Missense_Mutation_p.R33L|GRK4_ENST00000504933.1_Missense_Mutation_p.R65L|GRK4_ENST00000345167.6_Missense_Mutation_p.R33L	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	65	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		R -> L (in dbSNP:rs2960306). {ECO:0000269|PubMed:17344846}.		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)		ATAGGAAGACGTCTCTTCAGG	0.433													.|||	1565	0.3125	0.5371	0.3285	5008	,	,		20266	0.0942		0.3777	False		,,,				2504	0.1554				p.R65L		Atlas-SNP	.											.	GRK4	72	.	0			c.G194T	GRCh37	CM025429	GRK4	M	rs2960306	PASS	.	T	LEU/ARG,LEU/ARG,LEU/ARG	2167,2239	594.5+/-388.2	508,1151,544	144.0	143.0	143.0		98,194,194	5.6	1.0	4	dbSNP_101	143	3086,5514	659.9+/-401.7	581,1924,1795	yes	missense,missense,missense	GRK4	NM_001004056.1,NM_001004057.1,NM_182982.2	102,102,102	1089,3075,2339	TT,TG,GG		35.8837,49.1829,40.3891	benign,benign,benign	33/547,65/533,65/579	2990499	5253,7753	2203	4300	6503	SO:0001583	missense	2868	exon3			GAAGACGTCTCTT		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.194G>T	4.37:g.2990499G>T	ENSP00000381129:p.Arg65Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_182982	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Missense_Mutation	SNP	ENST00000398052.4	37	CCDS33946.1	736	0.336996336996337	264	0.5365853658536586	124	0.3425414364640884	57	0.09965034965034965	291	0.3839050131926121	T	10.94	1.492816	0.26774	0.491829	0.358837	ENSG00000125388	ENST00000398051;ENST00000398052;ENST00000345167;ENST00000504933	T;T;T;T	0.01902	4.57;4.57;4.57;4.57	5.56	5.56	0.83823	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.089250	0.47093	N	0.000243	T	0.00012	0.0000	N	0.00114	-2.085	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	0.0;0.001;0.0;0.001	T	0.14671	-1.0464	9	0.15952	T	0.53	-12.4212	11.1954	0.48709	0.0:0.0:0.1541:0.8459	rs2960306;rs57066640;rs2960306	33;33;65;65	P32298-3;P32298-2;P32298-4;P32298	.;.;.;GRK4_HUMAN	L	33;65;33;65	ENSP00000381128:R33L;ENSP00000381129:R65L;ENSP00000264764:R33L;ENSP00000427445:R65L	ENSP00000264764:R33L	R	+	2	0	GRK4	2960297	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.228000	0.51270	0.934000	0.37316	-0.376000	0.06991	CGT	G|0.638;T|0.362	0.362	strong		0.433	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307	
MUC2	4583	hgsc.bcm.edu	37	11	1080954	1080954	+	Silent	SNP	G	G	A	rs11245929	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1080954G>A	ENST00000441003.2	+	10	1365	c.1338G>A	c.(1336-1338)acG>acA	p.T446T	MUC2_ENST00000359061.5_Silent_p.T446T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	446	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GCCTGAAGACGGTGGTGCTGC	0.632													G|||	396	0.0790735	0.1233	0.0519	5008	,	,		15776	0.0506		0.0934	False		,,,				2504	0.0532				p.T446T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G1338A						PASS	.	G		495,3653		33,429,1612	69.0	80.0	76.0		1338	-7.2	0.7	11	dbSNP_120	76	764,7612		35,694,3459	no	coding-synonymous	MUC2	NM_002457.2		68,1123,5071	AA,AG,GG		9.1213,11.9335,10.0527		446/2813	1080954	1259,11265	2074	4188	6262	SO:0001819	synonymous_variant	4583	exon10			GAAGACGGTGGTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1338G>A	11.37:g.1080954G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	134	74	0.552239	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				G|0.919;A|0.081	0.081	strong		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
GTPBP4	23560	hgsc.bcm.edu	37	10	1061767	1061767	+	Silent	SNP	G	G	A	rs2306405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:1061767G>A	ENST00000360803.4	+	16	1765	c.1683G>A	c.(1681-1683)ccG>ccA	p.P561P	GTPBP4_ENST00000538293.1_Silent_p.P445P|GTPBP4_ENST00000545048.1_Silent_p.P514P	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	561					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		CTGCTCCCCCGTCCTCTGTGG	0.527													G|||	402	0.0802716	0.0492	0.0576	5008	,	,		19065	0.0972		0.0805	False		,,,				2504	0.1207				p.P561P		Atlas-SNP	.											.	GTPBP4	57	.	0			c.G1683A						PASS	.	G		297,4109	164.4+/-196.0	13,271,1919	146.0	132.0	137.0		1683	0.3	0.0	10	dbSNP_100	137	829,7771	191.3+/-237.5	42,745,3513	no	coding-synonymous	GTPBP4	NM_012341.2		55,1016,5432	AA,AG,GG		9.6395,6.7408,8.6575		561/635	1061767	1126,11880	2203	4300	6503	SO:0001819	synonymous_variant	23560	exon16			TCCCCCGTCCTCT	AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"""G protein-binding protein CRFG"", "" GTP-binding protein"""					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.1683G>A	10.37:g.1061767G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_012341	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Silent	SNP	ENST00000360803.4	37	CCDS31132.1																																																																																			G|0.914;A|0.086	0.086	strong		0.527	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68925094	68925094	+	Missense_Mutation	SNP	G	G	A	rs142412240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:68925094G>A	ENST00000356291.2	-	9	1167	c.1108C>T	c.(1108-1110)Cca>Tca	p.P370S	RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000500538.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	370	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					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						AACATTCCTGGAGTTATCAGG	0.393													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18312	0.0		0.001	False		,,,				2504	0.0				p.P370S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.C1108T						PASS	.	G	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	216.0	188.0	197.0		1108	0.3	1.0	4	dbSNP_134	197	14,8586	10.5+/-38.8	0,14,4286	yes	missense	TMPRSS11F	NM_207407.2	74	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	benign	370/439	68925094	15,12991	2203	4300	6503	SO:0001583	missense	389208	exon9			TTCCTGGAGTTAT	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.1108C>T	4.37:g.68925094G>A	ENSP00000348639:p.Pro370Ser	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	201	87	0.432836	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	3.434	-0.115545	0.06881	2.27E-4	0.001628	ENSG00000198092	ENST00000356291	D	0.92545	-3.06	5.2	0.258	0.15578	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.014630	0.07912	N	0.974403	T	0.81754	0.4889	N	0.16903	0.455	0.29686	N	0.841319	B	0.02656	0.0	B	0.06405	0.002	T	0.68303	-0.5444	10	0.18276	T	0.48	.	4.0738	0.09894	0.2767:0.0:0.4486:0.2746	.	370	Q6ZWK6	TM11F_HUMAN	S	370	ENSP00000348639:P370S	ENSP00000348639:P370S	P	-	1	0	TMPRSS11F	68607689	0.878000	0.30173	0.997000	0.53966	0.986000	0.74619	0.300000	0.19156	0.093000	0.17368	0.591000	0.81541	CCA	G|0.999;A|0.001	0.001	strong		0.393	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
UVRAG	7405	hgsc.bcm.edu	37	11	75852448	75852448	+	Silent	SNP	C	C	T	rs636420	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:75852448C>T	ENST00000356136.3	+	15	2332	c.2091C>T	c.(2089-2091)tcC>tcT	p.S697S	UVRAG_ENST00000528420.1_Silent_p.S596S|UVRAG_ENST00000531818.1_Silent_p.S325S|UVRAG_ENST00000532130.1_Silent_p.S325S|UVRAG_ENST00000538870.1_Silent_p.S253S|UVRAG_ENST00000533454.1_Silent_p.S325S|UVRAG_ENST00000539288.1_Silent_p.S325S	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	697					DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						GCAGGAGTTCCGATAAGTGAA	0.478													C|||	480	0.0958466	0.0038	0.0274	5008	,	,		20840	0.2698		0.0606	False		,,,				2504	0.1258				p.S697S		Atlas-SNP	.											.	UVRAG	69	.	0			c.C2091T						PASS	.	C		78,4322	62.3+/-99.4	0,78,2122	39.0	41.0	40.0		2091	-9.5	0.1	11	dbSNP_83	40	537,8047	139.8+/-196.4	16,505,3771	no	coding-synonymous	UVRAG	NM_003369.3		16,583,5893	TT,TC,CC		6.2558,1.7727,4.7366		697/700	75852448	615,12369	2200	4292	6492	SO:0001819	synonymous_variant	7405	exon15			GAGTTCCGATAAG	X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"""beclin 1 binding protein"""	602493	"""UV radiation resistance associated gene"""			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.2091C>T	11.37:g.75852448C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_003369	B3KTC1|O00392	Silent	SNP	ENST00000356136.3	37	CCDS8241.1																																																																																			C|0.920;T|0.080	0.080	strong		0.478	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369	
INADL	10207	hgsc.bcm.edu	37	1	62579891	62579891	+	Missense_Mutation	SNP	G	G	T	rs12140153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:62579891G>T	ENST00000371158.2	+	35	4742	c.4628G>T	c.(4627-4629)gGc>gTc	p.G1543V	INADL_ENST00000316485.6_Missense_Mutation_p.G1573V|INADL_ENST00000543708.1_Missense_Mutation_p.G357V|INADL_ENST00000545929.1_Missense_Mutation_p.G188V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1543	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GCTGGCCGGGGCCTGGGCCTG	0.542													G|||	133	0.0265575	0.0038	0.0216	5008	,	,		18042	0.0		0.0666	False		,,,				2504	0.047				p.G1543V		Atlas-SNP	.											.	INADL	179	.	0			c.G4628T						PASS	.	G	VAL/GLY	64,4342	60.5+/-97.4	0,64,2139	58.0	62.0	61.0		4628	5.5	1.0	1	dbSNP_120	61	757,7843	182.2+/-230.7	36,685,3579	yes	missense	INADL	NM_176877.2	109	36,749,5718	TT,TG,GG		8.8023,1.4526,6.3125	probably-damaging	1543/1802	62579891	821,12185	2203	4300	6503	SO:0001583	missense	10207	exon35			GCCGGGGCCTGGG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4628G>T	1.37:g.62579891G>T	ENSP00000360200:p.Gly1543Val	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	211	107	0.507109	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	66	0.03021978021978022	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	55	0.07255936675461741	G	25.5	4.645815	0.87958	0.014526	0.088023	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000543708;ENST00000545929	T;T;T;T	0.34859	1.69;2.61;1.69;1.34	5.5	5.5	0.81552	PDZ/DHR/GLGF (4);	0.080609	0.47093	D	0.000244	T	0.07999	0.0200	M	0.90369	3.11	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999;0.999	D;D;D;D;D;D	0.97110	1.0;0.99;0.998;0.998;0.995;0.996	T	0.54576	-0.8273	10	0.87932	D	0	.	19.425	0.94737	0.0:0.0:1.0:0.0	rs12140153	188;357;1002;1573;1543;1515	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	V	1543;1573;1573;1515;357;188	ENSP00000360200:G1543V;ENSP00000326199:G1573V;ENSP00000445790:G357V;ENSP00000440094:G188V	ENSP00000326199:G1573V	G	+	2	0	INADL	62352479	1.000000	0.71417	0.999000	0.59377	0.662000	0.39071	9.772000	0.98984	2.584000	0.87258	0.563000	0.77884	GGC	G|0.943;T|0.057	0.057	strong		0.542	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
F10	2159	hgsc.bcm.edu	37	13	113801737	113801737	+	Silent	SNP	C	C	T	rs5960	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:113801737C>T	ENST00000375559.3	+	7	830	c.792C>T	c.(790-792)acC>acT	p.T264T	F10_ENST00000409306.1_Silent_p.T264T|F10_ENST00000375551.3_Silent_p.T264T	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	264	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)|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)	p.T264T(1)		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)	GTGGTGGAACCATTCTGAGCG	0.562													C|||	3121	0.623203	0.4463	0.6715	5008	,	,		19363	0.5238		0.8648	False		,,,				2504	0.682				p.T264T		Atlas-SNP	.											F10,NS,carcinoma,0,1	F10	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C792T						PASS	.	C		2188,2218	586.1+/-386.4	556,1076,571	129.0	99.0	109.0		792	-0.2	1.0	13	dbSNP_52	109	7425,1175	764.4+/-407.6	3212,1001,87	no	coding-synonymous	F10	NM_000504.3		3768,2077,658	TT,TC,CC		13.6628,49.6596,26.088		264/489	113801737	9613,3393	2203	4300	6503	SO:0001819	synonymous_variant	2159	exon7			TGGAACCATTCTG		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.792C>T	13.37:g.113801737C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_000504	Q14340	Silent	SNP	ENST00000375559.3	37	CCDS9530.1																																																																																			C|0.292;T|0.708	0.708	strong		0.562	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3		
ZNF101	94039	hgsc.bcm.edu	37	19	19790690	19790690	+	Missense_Mutation	SNP	C	C	T	rs35358946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19790690C>T	ENST00000592502.1	+	4	1002	c.892C>T	c.(892-894)Cac>Tac	p.H298Y	ZNF101_ENST00000415784.2_Missense_Mutation_p.H178Y|ZNF101_ENST00000444249.2_3'UTR			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						CAGTTCCCTTCACAGACATGA	0.453													C|||	29	0.00579073	0.0008	0.0115	5008	,	,		19424	0.0		0.007	False		,,,				2504	0.0133				p.H298Y		Atlas-SNP	.											.	ZNF101	43	.	0			c.C892T						PASS	.	C	TYR/HIS	8,4398	12.9+/-30.5	0,8,2195	48.0	46.0	47.0		892	0.2	0.0	19	dbSNP_126	47	63,8537	38.8+/-94.9	1,61,4238	yes	missense	ZNF101	NM_033204.2	83	1,69,6433	TT,TC,CC		0.7326,0.1816,0.5459	benign	298/437	19790690	71,12935	2203	4300	6503	SO:0001583	missense	94039	exon4			TCCCTTCACAGAC	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"""Zinc fingers, C2H2-type"", ""-"""	12881	protein-coding gene	gene with protein product		603983	"""zinc finger protein 101 (Y2)"""			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.892C>T	19.37:g.19790690C>T	ENSP00000468049:p.His298Tyr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_033204	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	C	4.392	0.072382	0.08436	0.001816	0.007326	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.27557	1.66;1.66	0.235	0.235	0.15431	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07098	0.0180	N	0.04245	-0.25	0.09310	N	0.999997	B	0.33940	0.433	B	0.29663	0.105	T	0.21042	-1.0257	8	.	.	.	.	3.123	0.06397	0.4753:0.5244:1.0E-4:1.0E-4	rs35358946;rs35358946	298	Q8IZC7	ZN101_HUMAN	Y	298;298;178	ENSP00000319716:H298Y;ENSP00000400952:H178Y	.	H	+	1	0	ZNF101	19651690	0.000000	0.05858	0.047000	0.18901	0.047000	0.14425	-0.669000	0.05262	0.308000	0.22923	0.313000	0.20887	CAC	C|0.994;T|0.006	0.006	strong		0.453	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204	
GIMAP4	55303	hgsc.bcm.edu	37	7	150269542	150269542	+	Missense_Mutation	SNP	G	G	T	rs2293172	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150269542G>T	ENST00000255945.2	+	3	559	c.384G>T	c.(382-384)gaG>gaT	p.E128D	GIMAP4_ENST00000461940.1_Missense_Mutation_p.E142D|GIMAP4_ENST00000494750.1_3'UTR	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	128	AIG1-type G.		E -> D (in dbSNP:rs2293172).			cytosol (GO:0005829)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTTACACTGAGGAAGAGCACA	0.488													G|||	685	0.136781	0.0734	0.1412	5008	,	,		20430	0.2173		0.1561	False		,,,				2504	0.1166				p.E128D		Atlas-SNP	.											.	GIMAP4	61	.	0			c.G384T						PASS	.	G	ASP/GLU	348,4058	179.4+/-207.9	14,320,1869	81.0	78.0	79.0		384	2.9	0.8	7	dbSNP_100	79	1353,7247	265.7+/-286.3	109,1135,3056	yes	missense	GIMAP4	NM_018326.2	45	123,1455,4925	TT,TG,GG		15.7326,7.8983,13.0786	benign	128/330	150269542	1701,11305	2203	4300	6503	SO:0001583	missense	55303	exon3			CACTGAGGAAGAG	AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"""GTPases, IMAP"""	21872	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 1"""	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.384G>T	7.37:g.150269542G>T	ENSP00000255945:p.Glu128Asp	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_018326		Missense_Mutation	SNP	ENST00000255945.2	37	CCDS5904.1	338	0.15476190476190477	30	0.06097560975609756	60	0.16574585635359115	120	0.2097902097902098	128	0.16886543535620052	G	4.023	0.001695	0.07819	0.078983	0.157326	ENSG00000133574	ENST00000255945;ENST00000461940;ENST00000479232	T;T;T	0.62498	0.02;0.02;0.02	4.72	2.86	0.33363	AIG1 (1);	2.302990	0.01535	N	0.018966	T	0.00039	0.0001	N	0.21097	0.63	0.58432	P	1.0000000000287557E-6	B;B	0.19817	0.039;0.008	B;B	0.17979	0.014;0.02	T	0.03025	-1.1081	9	0.29301	T	0.29	.	7.4594	0.27285	0.203:0.0:0.797:0.0	rs2293172;rs11539192;rs52811237;rs57984509;rs2293172	142;128	G5E9W9;Q9NUV9	.;GIMA4_HUMAN	D	128;142;142	ENSP00000255945:E128D;ENSP00000419545:E142D;ENSP00000418615:E142D	ENSP00000255945:E128D	E	+	3	2	GIMAP4	149900475	0.000000	0.05858	0.821000	0.32701	0.011000	0.07611	-0.964000	0.03833	1.226000	0.43582	0.655000	0.94253	GAG	G|0.866;T|0.134	0.134	strong		0.488	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326	
ACOX3	8310	hgsc.bcm.edu	37	4	8375342	8375342	+	Silent	SNP	G	G	A	rs2280571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:8375342G>A	ENST00000356406.5	-	16	1919	c.1842C>T	c.(1840-1842)tcC>tcT	p.S614S	ACOX3_ENST00000413009.2_Intron|ACOX3_ENST00000503233.1_Silent_p.S614S|ACOX3_ENST00000515797.1_5'UTR	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	614					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						CCTGCTCACCGGAGAAGTATC	0.572													g|||	709	0.141573	0.1664	0.0951	5008	,	,		15745	0.1319		0.1272	False		,,,				2504	0.1656				p.S614S		Atlas-SNP	.											.	ACOX3	70	.	0			c.C1842T						PASS	.	A	,	731,3675	297.6+/-284.8	66,599,1538	90.0	72.0	78.0		,1842	-8.6	0.0	4	dbSNP_100	78	1166,7434	233.3+/-266.6	88,990,3222	no	intron,coding-synonymous	ACOX3	NM_001101667.1,NM_003501.2	,	154,1589,4760	AA,AG,GG		13.5581,16.591,14.5856	,	,614/701	8375342	1897,11109	2203	4300	6503	SO:0001819	synonymous_variant	8310	exon16			CTCACCGGAGAAG	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.1842C>T	4.37:g.8375342G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_003501	Q96AJ8	Silent	SNP	ENST00000356406.5	37	CCDS3401.1																																																																																			G|0.864;A|0.136	0.136	strong		0.572	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4		
OR5L2	26338	hgsc.bcm.edu	37	11	55595114	55595114	+	Silent	SNP	G	G	T	rs34929168|rs386753701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	274	0	0		WXS	Illumina HiSeq	Phase_I	239	110	0.460251	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	
OR14C36	127066	hgsc.bcm.edu	37	1	248512637	248512637	+	Silent	SNP	C	C	T	rs2039824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248512637C>T	ENST00000317861.1	+	1	561	c.561C>T	c.(559-561)tgC>tgT	p.C187C		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						AGCTCTCTTGCTCTGACACCT	0.488													c|||	2306	0.460463	0.3601	0.4885	5008	,	,		22340	0.4315		0.5239	False		,,,				2504	0.5409				p.C187C		Atlas-SNP	.											.	OR14C36	113	.	0			c.C561T						PASS	.	C		1764,2642	525.5+/-371.6	352,1060,791	159.0	143.0	148.0		561	1.1	0.9	1	dbSNP_94	148	4894,3706	619.6+/-396.9	1390,2114,796	no	coding-synonymous	OR14C36	NM_001001918.1		1742,3174,1587	TT,TC,CC		43.093,40.0363,48.8082		187/313	248512637	6658,6348	2203	4300	6503	SO:0001819	synonymous_variant	127066	exon1			CTCTTGCTCTGAC	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.561C>T	1.37:g.248512637C>T		Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	237	109	0.459916	NM_001001918	Q6IEZ6	Silent	SNP	ENST00000317861.1	37	CCDS31112.1																																																																																			C|0.518;T|0.482	0.482	strong		0.488	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918	
C5orf60	285679	hgsc.bcm.edu	37	5	179071947	179071947	+	Silent	SNP	A	A	G	rs4645306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:179071947A>G	ENST00000448248.2	-	1	100	c.75T>C	c.(73-75)atT>atC	p.I25I	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	25						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GCTCTGTACCAATAACACTGT	0.517																																					p.I25I		Atlas-SNP	.											.	C5orf60	24	.	0			c.T75C						PASS	.						72.0	71.0	71.0					5																	179071947		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			TGTACCAATAACA	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.75T>C	5.37:g.179071947A>G		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	286	169	0.590909	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			A|0.743;G|0.257	0.257	strong		0.517	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
INPP4A	3631	hgsc.bcm.edu	37	2	99179971	99179971	+	Silent	SNP	C	C	G	rs61748143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:99179971C>G	ENST00000523221.1	+	17	1914	c.1914C>G	c.(1912-1914)acC>acG	p.T638T	INPP4A_ENST00000409540.3_Silent_p.T599T|INPP4A_ENST00000409016.4_Silent_p.T599T|INPP4A_ENST00000409851.3_Silent_p.T633T|INPP4A_ENST00000074304.5_Silent_p.T638T|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000545415.1_Silent_p.T599T			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	638					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						CCACTCTCACCGACTGCGTGG	0.552													C|||	21	0.00419329	0.0	0.0058	5008	,	,		18327	0.0		0.0119	False		,,,				2504	0.0051				p.T638T		Atlas-SNP	.											INPP4A_ENST00000409540,caecum,carcinoma,+2,3	INPP4A	205	3	0			c.C1914G						scavenged	.	C	,,,	5,4177		0,5,2086	36.0	41.0	39.0		1914,1899,1797,1797	-10.9	0.0	2	dbSNP_129	39	104,8340		1,102,4119	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	1,107,6205	GG,GC,CC		1.2316,0.1196,0.8633	,,,	638/978,633/973,599/955,599/939	99179971	109,12517	2091	4222	6313	SO:0001819	synonymous_variant	3631	exon19			TCTCACCGACTGC	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.1914C>G	2.37:g.99179971C>G		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	171	83	0.48538	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			C|0.994;G|0.006	0.006	strong		0.552	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
UFL1	23376	hgsc.bcm.edu	37	6	96999725	96999725	+	Silent	SNP	C	C	T	rs1127175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:96999725C>T	ENST00000369278.4	+	17	1977	c.1911C>T	c.(1909-1911)gaC>gaT	p.D637D		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	637					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										GCATAGAAGACTTTATTTCTT	0.299													C|||	1636	0.326677	0.326	0.2911	5008	,	,		16341	0.3075		0.3698	False		,,,				2504	0.3282				p.D637D		Atlas-SNP	.											KIAA0776,NS,carcinoma,0,2	.	.	2	0			c.C1911T						PASS	.	C		1470,2934	455.5+/-351.0	239,992,971	86.0	95.0	92.0		1911	-0.4	1.0	6	dbSNP_86	92	2996,5600	455.3+/-363.7	536,1924,1838	no	coding-synonymous	UFL1	NM_015323.4		775,2916,2809	TT,TC,CC		34.8534,33.3787,34.3538		637/795	96999725	4466,8534	2202	4298	6500	SO:0001819	synonymous_variant	23376	exon17			AGAAGACTTTATT	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1911C>T	6.37:g.96999725C>T		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	204	95	0.465686	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																			C|0.662;T|0.338	0.338	strong		0.299	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
ANKEF1	63926	hgsc.bcm.edu	37	20	10030188	10030188	+	Missense_Mutation	SNP	T	T	A	rs652633	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:10030188T>A	ENST00000378380.3	+	6	1300	c.971T>A	c.(970-972)cTg>cAg	p.L324Q	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.L324Q|ANKEF1_ENST00000488991.1_3'UTR	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	324			L -> Q (in dbSNP:rs652633).				calcium ion binding (GO:0005509)										CCAAATCCACTGTGGGCCCTT	0.517													T|||	990	0.197684	0.2685	0.1571	5008	,	,		16990	0.0069		0.2744	False		,,,				2504	0.2485				p.L324Q		Atlas-SNP	.											.	.	.	.	0			c.T971A						PASS	.	T	GLN/LEU,GLN/LEU	1128,3278	405.1+/-333.4	145,838,1220	77.0	80.0	79.0		971,971	3.2	0.0	20	dbSNP_83	79	2417,6183	401.6+/-347.2	345,1727,2228	yes	missense,missense	ANKRD5	NM_022096.4,NM_198798.1	113,113	490,2565,3448	AA,AT,TT		28.1047,25.6015,27.2567	benign,benign	324/777,324/777	10030188	3545,9461	2203	4300	6503	SO:0001583	missense	63926	exon6			ATCCACTGTGGGC	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.971T>A	20.37:g.10030188T>A	ENSP00000367631:p.Leu324Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_198798	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	391	0.17902930402930403	116	0.23577235772357724	65	0.17955801104972377	5	0.008741258741258742	205	0.2704485488126649	T	3.673	-0.067203	0.07273	0.256015	0.281047	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.68331	-0.32;-0.32	5.6	3.19	0.36642	Ankyrin repeat-containing domain (1);	0.632290	0.16702	N	0.203072	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.08953	-1.0697	9	0.29301	T	0.29	0.0049	3.4295	0.07422	0.1276:0.108:0.1193:0.645	rs652633;rs52838052;rs652633	324	Q9NU02	ANKR5_HUMAN	Q	324	ENSP00000367644:L324Q;ENSP00000367631:L324Q	ENSP00000367631:L324Q	L	+	2	0	ANKRD5	9978188	0.000000	0.05858	0.017000	0.16124	0.073000	0.16967	-0.618000	0.05578	1.044000	0.40200	0.528000	0.53228	CTG	T|0.761;A|0.239	0.239	strong		0.517	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201822	32201822	+	RNA	SNP	G	G	T	rs9982910	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	177	0	0		WXS	Illumina HiSeq	Phase_I	172	171	0.994186	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	
ZNF35	7584	hgsc.bcm.edu	37	3	44700347	44700347	+	Silent	SNP	G	G	A	rs139090092	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:44700347G>A	ENST00000396056.2	+	4	727	c.492G>A	c.(490-492)agG>agA	p.R164R	ZNF35_ENST00000453164.1_3'UTR|RP11-944L7.4_ENST00000457331.1_RNA|ZNF35_ENST00000542250.1_Silent_p.R4R|ZNF35_ENST00000399560.2_3'UTR|ZNF35_ENST00000296092.3_3'UTR	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	164	Globular domain.				cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		TGTTAAAGAGGCAGAGAATAA	0.383													.|||	28	0.00559105	0.0008	0.0043	5008	,	,		20715	0.0		0.0139	False		,,,				2504	0.0102				p.R164R		Atlas-SNP	.											.	ZNF35	34	.	0			c.G492A						PASS	.	G		9,4397	16.8+/-37.8	0,9,2194	80.0	83.0	82.0		492	-0.7	0.4	3	dbSNP_134	82	86,8514	49.4+/-109.1	0,86,4214	no	coding-synonymous	ZNF35	NM_003420.3		0,95,6408	AA,AG,GG		1.0,0.2043,0.7304		164/528	44700347	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	7584	exon4			AAAGAGGCAGAGA	X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"""Zinc fingers, C2H2-type"""	13099	protein-coding gene	gene with protein product		194533	"""zinc finger protein 35 (clone HF.10)"""			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.492G>A	3.37:g.44700347G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	202	94	0.465347	NM_003420	B2RBU6|Q53Y54|Q96D01	Silent	SNP	ENST00000396056.2	37	CCDS2718.2																																																																																			G|0.993;A|0.007	0.007	strong		0.383	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420	
MAP3K5	4217	hgsc.bcm.edu	37	6	136977568	136977568	+	Silent	SNP	T	T	C	rs2076260	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	56	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	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		
PAPLN	89932	hgsc.bcm.edu	37	14	73727509	73727509	+	Missense_Mutation	SNP	T	T	G	rs177389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:73727509T>G	ENST00000554301.1	+	16	2241	c.2078T>G	c.(2077-2079)aTg>aGg	p.M693R	PAPLN_ENST00000381166.3_Missense_Mutation_p.M693R|PAPLN_ENST00000427855.1_Missense_Mutation_p.M693R|PAPLN_ENST00000555445.1_Missense_Mutation_p.M693R|PAPLN_ENST00000340738.5_Missense_Mutation_p.M666R			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	693				M -> R (in Ref. 2; BAG57757, 5; CAD97826 and 6; BAC85123). {ECO:0000305}.		basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		ACCGGGGGCATGCCCAGGTCA	0.647													G|||	3286	0.65615	0.7481	0.6801	5008	,	,		15634	0.7103		0.4841	False		,,,				2504	0.636				p.M666R		Atlas-SNP	.											.	PAPLN	180	.	0			c.T1997G						PASS	.	G	ARG/MET	3585,821		1484,617,102	44.0	42.0	43.0		1997	3.7	0.0	14	dbSNP_79	43	4465,4135		1180,2105,1015	yes	missense	PAPLN	NM_173462.3	91	2664,2722,1117	GG,GT,TT		48.0814,18.6337,38.1055	benign	666/1252	73727509	8050,4956	2203	4300	6503	SO:0001583	missense	89932	exon16			GGGGCATGCCCAG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2078T>G	14.37:g.73727509T>G	ENSP00000451803:p.Met693Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	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	
VPS37C	55048	hgsc.bcm.edu	37	11	60906279	60906279	+	Missense_Mutation	SNP	G	G	T	rs80029472	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60906279G>T	ENST00000301765.5	-	2	255	c.23C>A	c.(22-24)aCc>aAc	p.T8N		NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)	8					endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						CTCCTGCAGGGTCTTATCCTT	0.577													G|||	75	0.014976	0.0015	0.0317	5008	,	,		17343	0.0		0.0437	False		,,,				2504	0.0072				p.T8N		Atlas-SNP	.											.	VPS37C	30	.	0			c.C23A						PASS	.	G	ASN/THR	38,4368	42.3+/-75.8	0,38,2165	118.0	104.0	109.0		23	4.9	1.0	11	dbSNP_132	109	494,8104	143.0+/-199.1	12,470,3817	yes	missense	VPS37C	NM_017966.4	65	12,508,5982	TT,TG,GG		5.7455,0.8625,4.091	probably-damaging	8/356	60906279	532,12472	2203	4299	6502	SO:0001583	missense	55048	exon2			TGCAGGGTCTTAT	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"""vacuolar protein sorting 37C (yeast)"""			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.23C>A	11.37:g.60906279G>T	ENSP00000301765:p.Thr8Asn	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_017966	Q8N3K4	Missense_Mutation	SNP	ENST00000301765.5	37	CCDS31573.1	52	0.023809523809523808	1	0.0020325203252032522	17	0.04696132596685083	0	0.0	34	0.044854881266490766	G	18.15	3.560117	0.65538	0.008625	0.057455	ENSG00000167987	ENST00000301765;ENST00000540084;ENST00000538036	T;T	0.80304	-1.36;-1.36	5.8	4.88	0.63580	Modifier of rudimentary, Modr (1);	0.048025	0.85682	D	0.000000	T	0.41190	0.1148	N	0.20766	0.605	0.40128	D	0.976689	D;D	0.89917	0.997;1.0	D;D	0.91635	0.954;0.999	T	0.73534	-0.3952	10	0.54805	T	0.06	-27.5021	14.88	0.70525	0.0:0.1432:0.8568:0.0	.	8;8	B4DYD9;A5D8V6	.;VP37C_HUMAN	N	8	ENSP00000301765:T8N;ENSP00000446013:T8N	ENSP00000301765:T8N	T	-	2	0	VPS37C	60662855	0.973000	0.33851	0.996000	0.52242	0.582000	0.36321	1.778000	0.38614	1.433000	0.47394	-0.175000	0.13238	ACC	C|0.000;G|0.965;T|0.035	0.035	strong		0.577	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966	
TNRC18	84629	hgsc.bcm.edu	37	7	5391702	5391702	+	Missense_Mutation	SNP	C	C	G	rs3801048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	93	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	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			
C1QTNF9	338872	hgsc.bcm.edu	37	13	24890157	24890157	+	Missense_Mutation	SNP	C	C	T	rs1974332	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:24890157C>T	ENST00000382071.2	+	2	101	c.16C>T	c.(16-18)Ctt>Ttt	p.L6F	RP11-307N16.6_ENST00000382141.4_3'UTR|C1QTNF9_ENST00000332018.4_Missense_Mutation_p.L6F|C1QTNF9-AS1_ENST00000449656.1_RNA			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	184	0	0		WXS	Illumina HiSeq	Phase_I	207	78	0.376812	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	
ABCC2	1244	hgsc.bcm.edu	37	10	101604207	101604207	+	Silent	SNP	C	C	T	rs3740066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:101604207C>T	ENST00000370449.4	+	28	4085	c.3972C>T	c.(3970-3972)atC>atT	p.I1324I		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1324	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.I1324I(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CTTGTGACATCGGTAGCATGG	0.542													C|||	1443	0.288139	0.2163	0.3415	5008	,	,		20904	0.247		0.3708	False		,,,				2504	0.3047				p.I1324I		Atlas-SNP	.											ABCC2,NS,carcinoma,0,1	ABCC2	160	1	1	Substitution - coding silent(1)	stomach(1)	c.C3972T	GRCh37	CM080009	ABCC2	M	rs3740066	PASS	.			1145,3261	407.3+/-334.2	151,843,1209	144.0	126.0	132.0		3972	0.7	0.8	10	dbSNP_107	132	3193,5407	483.7+/-371.2	605,1983,1712	no	coding-synonymous	ABCC2	NM_000392.3		756,2826,2921	TT,TC,CC		37.1279,25.9873,33.3538		1324/1546	101604207	4338,8668	2203	4300	6503	SO:0001819	synonymous_variant	1244	exon28			TGACATCGGTAGC	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3972C>T	10.37:g.101604207C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																			C|0.678;T|0.322	0.322	strong		0.542	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
ELMO1	9844	hgsc.bcm.edu	37	7	36895342	36895342	+	Silent	SNP	C	C	T	rs13246439	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:36895342C>T	ENST00000310758.4	-	22	2645	c.1998G>A	c.(1996-1998)acG>acA	p.T666T	ELMO1_ENST00000396045.3_Silent_p.T186T|ELMO1_ENST00000396040.2_Silent_p.T186T|ELMO1_ENST00000341056.3_Silent_p.T368T|ELMO1_ENST00000448602.1_Silent_p.T666T|ELMO1_ENST00000442504.1_Silent_p.T666T	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	666	PH.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						TCAGTCCATCCGTCCAGATAC	0.493													C|||	400	0.0798722	0.115	0.1268	5008	,	,		21598	0.0139		0.0974	False		,,,				2504	0.0491				p.T666T		Atlas-SNP	.											.	ELMO1	141	.	0			c.G1998A						PASS	.	C	,,,	448,3958	216.1+/-234.9	25,398,1780	142.0	117.0	125.0		558,1998,1998,1998	-9.8	0.5	7	dbSNP_121	125	939,7661	206.6+/-248.6	61,817,3422	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ELMO1	NM_001039459.2,NM_001206480.1,NM_001206482.1,NM_014800.10	,,,	86,1215,5202	TT,TC,CC		10.9186,10.168,10.6643	,,,	186/248,666/728,666/728,666/728	36895342	1387,11619	2203	4300	6503	SO:0001819	synonymous_variant	9844	exon22			TCCATCCGTCCAG	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"""Engulfment and cell motility proteins"""	16286	protein-coding gene	gene with protein product		606420	"""engulfment and cell motility 1 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1998G>A	7.37:g.36895342C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	178	103	0.578652	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Silent	SNP	ENST00000310758.4	37	CCDS5449.1																																																																																			C|0.903;T|0.097	0.097	strong		0.493	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442	
KNG1	3827	hgsc.bcm.edu	37	3	186459775	186459775	+	Silent	SNP	C	C	T	rs5030086	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:186459775C>T	ENST00000265023.4	+	10	1802	c.1590C>T	c.(1588-1590)gaC>gaT	p.D530D	KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|RP11-573D15.8_ENST00000609726.1_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	144	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	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	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149008484	149008484	+	Silent	SNP	G	G	A	rs3733661	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149008484G>A	ENST00000333677.6	+	12	1936	c.1773G>A	c.(1771-1773)ccG>ccA	p.P591P		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	591						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GTCTAACACCGGAGCCCAGCC	0.612													G|||	285	0.0569089	0.0023	0.0	5008	,	,		18098	0.247		0.004	False		,,,				2504	0.0297				p.P591P		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.G1773A						PASS	.	G		12,3904		0,12,1946	46.0	50.0	48.0		1773	-0.2	0.8	5	dbSNP_107	48	39,8257		0,39,4109	no	coding-synonymous	ARHGEF37	NM_001001669.2		0,51,6055	AA,AG,GG		0.4701,0.3064,0.4176		591/676	149008484	51,12161	1958	4148	6106	SO:0001819	synonymous_variant	389337	exon12			AACACCGGAGCCC	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.1773G>A	5.37:g.149008484G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	90	53	0.588889	NM_001001669	Q6ZW51	Silent	SNP	ENST00000333677.6	37	CCDS43385.1																																																																																			G|0.941;A|0.059	0.059	strong		0.612	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
DIDO1	11083	hgsc.bcm.edu	37	20	61542863	61542863	+	Silent	SNP	G	G	A	rs11907248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61542863G>A	ENST00000266070.4	-	3	427	c.102C>T	c.(100-102)atC>atT	p.I34I	DIDO1_ENST00000370371.4_Silent_p.I34I|DIDO1_ENST00000370366.1_Silent_p.I34I|DIDO1_ENST00000354665.4_Silent_p.I34I|DIDO1_ENST00000370368.1_Silent_p.I34I|DIDO1_ENST00000395335.2_Silent_p.I34I|DIDO1_ENST00000395343.1_Silent_p.I34I|DIDO1_ENST00000395340.1_Silent_p.I34I|DIDO1_ENST00000266071.5_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	97	0.530055	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	
MUC16	94025	hgsc.bcm.edu	37	19	8982212	8982212	+	Silent	SNP	A	A	G	rs78717907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8982212A>G	ENST00000397910.4	-	70	42266	c.42063T>C	c.(42061-42063)caT>caC	p.H14021H	MUC16_ENST00000380951.5_Silent_p.H662H	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	14046	SEA 13. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGTGATGCCATGGGTCTGCT	0.637													G|||	89	0.0177716	0.0265	0.0072	5008	,	,		15617	0.0218		0.0159	False		,,,				2504	0.0112				p.H14021H		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-2,2	MUC16	4315	2	0			c.T42063C						PASS	.	G		122,3914		0,122,1896	50.0	54.0	53.0		42063	-7.8	0.0	19	dbSNP_132	53	201,8147		0,201,3973	no	coding-synonymous	MUC16	NM_024690.2		0,323,5869	GG,GA,AA		2.4078,3.0228,2.6082		14021/14508	8982212	323,12061	2018	4174	6192	SO:0001819	synonymous_variant	94025	exon70			GATGCCATGGGTC	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.42063T>C	19.37:g.8982212A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	38	0.0173992673992674	15	0.03048780487804878	5	0.013812154696132596	8	0.013986013986013986	10	0.013192612137203167	G	0.014	-1.599328	0.00849	0.030228	0.024078	ENSG00000181143	ENST00000542240	.	.	.	3.89	-7.78	0.01223	.	.	.	.	.	T	0.08223	0.0205	.	.	.	.	.	.	.	.	.	.	.	.	T	0.10636	-1.0621	3	.	.	.	.	5.2862	0.15702	0.2947:0.1044:0.4976:0.1033	.	.	.	.	T	861	.	.	M	-	2	0	MUC16	8843212	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-4.638000	0.00205	-2.981000	0.00283	-1.952000	0.00485	ATG	A|0.981;G|0.019	0.019	strong		0.637	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SLC4A9	83697	hgsc.bcm.edu	37	5	139740454	139740454	+	Silent	SNP	C	C	T	rs34507975	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:139740454C>T	ENST00000230993.6	+	2	395	c.360C>T	c.(358-360)caC>caT	p.H120H	SLC4A9_ENST00000506545.1_Silent_p.H96H|SLC4A9_ENST00000507527.1_Silent_p.H120H|SLC4A9_ENST00000506757.2_Silent_p.H96H|SLC4A9_ENST00000432095.2_Silent_p.H96H	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	120					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGCCCCCCACGTGCCCACCC	0.627													C|||	1008	0.201278	0.0772	0.2104	5008	,	,		16034	0.2728		0.2326	False		,,,				2504	0.2566				p.H120H		Atlas-SNP	.											.	SLC4A9	125	.	0			c.C360T						PASS	.	C		354,3576		15,324,1626	18.0	21.0	20.0		288	-4.0	1.0	5	dbSNP_126	20	1941,6367		238,1465,2451	no	coding-synonymous	SLC4A9	NM_031467.2		253,1789,4077	TT,TC,CC		23.363,9.0076,18.7531		96/960	139740454	2295,9943	1965	4154	6119	SO:0001819	synonymous_variant	83697	exon2			CCCCCACGTGCCC	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"""Solute carriers"""	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.360C>T	5.37:g.139740454C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Silent	SNP	ENST00000230993.6	37	CCDS58973.1																																																																																			C|0.790;T|0.210	0.210	strong		0.627	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467	
OR52R1	119695	hgsc.bcm.edu	37	11	4825010	4825010	+	Missense_Mutation	SNP	T	T	A	rs6578533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4825010T>A	ENST00000356069.2	-	1	600	c.601A>T	c.(601-603)Aat>Tat	p.N201Y	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.N280Y	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	201			N -> Y (in dbSNP:rs6578533). {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)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGAGCCCATTCCCACGACTT	0.493													A|||	1551	0.309704	0.559	0.2795	5008	,	,		23742	0.0129		0.3907	False		,,,				2504	0.2168				p.N201Y		Atlas-SNP	.											.	OR52R1	81	.	0			c.A601T						PASS	.	A	TYR/ASN	2267,2135	577.8+/-384.5	595,1077,529	152.0	115.0	128.0		601	4.4	0.8	11	dbSNP_116	128	3013,5583	663.9+/-402.1	551,1911,1836	yes	missense	OR52R1	NM_001005177.3	143	1146,2988,2365	AA,AT,TT		35.0512,48.5007,40.6216	benign	201/316	4825010	5280,7718	2201	4298	6499	SO:0001583	missense	119695	exon1			GCCCATTCCCACG	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.601A>T	11.37:g.4825010T>A	ENSP00000348368:p.Asn201Tyr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	682	0.31227106227106227	270	0.5487804878048781	117	0.32320441988950277	10	0.017482517482517484	285	0.3759894459102902	A	0.009	-1.845698	0.00568	0.514993	0.350512	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.28255	1.62;1.62	5.57	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	N	0.000407	T	0.00012	0.0000	N	0.00002	-3.515	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47586	-0.9106	9	0.02654	T	1	.	10.3189	0.43753	0.739:0.0:0.0:0.261	rs6578533;rs57223245;rs6578533	201	Q8NGF1	O52R1_HUMAN	Y	201;280	ENSP00000348368:N201Y;ENSP00000369742:N280Y	ENSP00000348368:N201Y	N	-	1	0	OR52R1	4781586	0.002000	0.14202	0.753000	0.31225	0.302000	0.27658	1.733000	0.38156	1.130000	0.42092	-0.265000	0.10407	AAT	A|0.369;N|0.000	0.369	strong		0.493	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
GSPT1	2935	hgsc.bcm.edu	37	16	12009304	12009304	+	Intron	SNP	C	C	A	rs11544193	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12009304C>A	ENST00000420576.2	-	1	41				AC007216.1_ENST00000583357.1_RNA|GSPT1_ENST00000434724.2_Missense_Mutation_p.G92C|GSPT1_ENST00000439887.2_Missense_Mutation_p.G92C	NM_001130007.1	NP_001123479.1	P15170	ERF3A_HUMAN	G1 to S phase transition 1						G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						GCTGCCGGGCCCCGCAGGAAG	0.731													c|||	1516	0.302716	0.0847	0.4438	5008	,	,		5136	0.2063		0.5507	False		,,,				2504	0.3415				p.G92C		Atlas-SNP	.											.	GSPT1	71	.	0			c.G274T						PASS	.	C	CYS/GLY,CYS/GLY,	508,2572		49,410,1081	8.0	11.0	10.0		274,274,	4.6	1.0	16	dbSNP_120	10	4104,2970		1245,1614,678	no	missense,missense,intron	GSPT1	NM_001130006.1,NM_002094.3,NM_001130007.1	159,159,	1294,2024,1759	AA,AC,CC		41.9847,16.4935,45.4205	probably-damaging,probably-damaging,	92/637,92/638,	12009304	4612,5542	1540	3537	5077	SO:0001627	intron_variant	2935	exon1			CCGGGCCCCGCAG	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000420576.2:c.61+594G>T	16.37:g.12009304C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_001130006	J3KQG6|Q96GF2	Missense_Mutation	SNP	ENST00000420576.2	37	CCDS45414.1	734	0.3360805860805861	54	0.10975609756097561	171	0.4723756906077348	85	0.1486013986013986	424	0.5593667546174143	c	16.39	3.109685	0.56398	0.164935	0.580153	ENSG00000103342	ENST00000434724;ENST00000439887	T;T	0.32023	1.47;1.47	4.57	4.57	0.56435	.	0.720518	0.12766	U	0.440919	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999979	D	0.89917	1.0	D	0.83275	0.996	T	0.48681	-0.9014	8	0.72032	D	0.01	-5.0676	12.7153	0.57111	0.0:0.833:0.167:0.0	rs11544193	92	E7EQZ3	.	C	92	ENSP00000398131:G92C;ENSP00000408399:G92C	ENSP00000398131:G92C	G	-	1	0	GSPT1	11916805	0.983000	0.35010	0.988000	0.46212	0.011000	0.07611	1.202000	0.32271	2.062000	0.61559	0.556000	0.70494	GGC	C|0.663;A|0.337	0.337	strong		0.731	GSPT1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421514.1	NM_002094	
CNGA4	1262	hgsc.bcm.edu	37	11	6262909	6262909	+	Missense_Mutation	SNP	G	G	A	rs61745230	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	121	0	0		WXS	Illumina HiSeq	Phase_I	124	70	0.564516	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	
FAM160B1	57700	hgsc.bcm.edu	37	10	116602805	116602805	+	Silent	SNP	A	A	G	rs17092491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:116602805A>G	ENST00000369248.4	+	6	971	c.636A>G	c.(634-636)gaA>gaG	p.E212E	FAM160B1_ENST00000369250.3_Silent_p.E212E	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	212										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						AACCAGAGGAACTATCTGGTG	0.448													A|||	494	0.0986422	0.0227	0.1455	5008	,	,		13286	0.1974		0.0875	False		,,,				2504	0.0777				p.E212E		Atlas-SNP	.											.	FAM160B1	107	.	0			c.A636G						PASS	.	A	,	211,4195	129.0+/-165.8	5,201,1997	136.0	110.0	119.0		636,636	-6.6	0.0	10	dbSNP_123	119	860,7740	195.6+/-240.8	48,764,3488	no	coding-synonymous,coding-synonymous	FAM160B1	NM_001135051.1,NM_020940.3	,	53,965,5485	GG,GA,AA		10.0,4.7889,8.2347	,	212/739,212/766	116602805	1071,11935	2203	4300	6503	SO:0001819	synonymous_variant	57700	exon6			AGAGGAACTATCT	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"""KIAA1600"""	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.636A>G	10.37:g.116602805A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Silent	SNP	ENST00000369248.4	37	CCDS31290.1																																																																																			A|0.908;G|0.092	0.092	strong		0.448	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351	
LY75	4065	hgsc.bcm.edu	37	2	160737621	160737621	+	Silent	SNP	C	C	T	rs11675155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160737621C>T	ENST00000263636.4	-	8	1404	c.1377G>A	c.(1375-1377)acG>acA	p.T459T	LY75_ENST00000553424.1_Silent_p.T459T|LY75-CD302_ENST00000504764.1_Silent_p.T459T|LY75-CD302_ENST00000505052.1_Silent_p.T459T|LY75_ENST00000554112.1_Silent_p.T459T	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	459	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)	p.T459T(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		CACAGTTGGGCGTCTTATTGT	0.368													C|||	1097	0.21905	0.1218	0.3746	5008	,	,		19539	0.3224		0.165	False		,,,				2504	0.1892				p.T459T		Atlas-SNP	.											LY75,NS,carcinoma,0,1	LY75	151	1	1	Substitution - coding silent(1)	prostate(1)	c.G1377A						PASS	.	C	,,	598,3808	264.1+/-265.8	45,508,1650	171.0	154.0	160.0		1377,1377,1377	-0.8	1.0	2	dbSNP_120	160	1508,7092	285.8+/-297.4	120,1268,2912	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	165,1776,4562	TT,TC,CC		17.5349,13.5724,16.1925	,,	459/1874,459/1818,459/1723	160737621	2106,10900	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon8			GTTGGGCGTCTTA	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.1377G>A	2.37:g.160737621C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			C|0.818;T|0.182	0.182	strong		0.368	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
DOCK10	55619	hgsc.bcm.edu	37	2	225669996	225669996	+	Silent	SNP	A	A	G	rs4674940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:225669996A>G	ENST00000258390.7	-	36	4045	c.3978T>C	c.(3976-3978)ttT>ttC	p.F1326F	DOCK10_ENST00000409592.3_Silent_p.F1320F	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1326					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		CTAACTTGTCAAATCGAAGAG	0.393													G|||	424	0.0846645	0.2383	0.0447	5008	,	,		20916	0.0		0.0398	False		,,,				2504	0.0389				p.F1326F		Atlas-SNP	.											.	DOCK10	308	.	0			c.T3978C						PASS	.	G		667,3057		67,533,1262	138.0	132.0	133.0		3978	4.6	1.0	2	dbSNP_111	133	252,7932		8,236,3848	no	coding-synonymous	DOCK10	NM_014689.2		75,769,5110	GG,GA,AA		3.0792,17.9108,7.7175		1326/2187	225669996	919,10989	1862	4092	5954	SO:0001819	synonymous_variant	55619	exon36			CTTGTCAAATCGA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3978T>C	2.37:g.225669996A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	185	82	0.443243	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1	145	0.06639194139194139	96	0.1951219512195122	19	0.052486187845303865	0	0.0	30	0.0395778364116095	G	7.315	0.615829	0.14129	0.179108	0.030792	ENSG00000135905	ENST00000422684	.	.	.	5.74	4.58	0.56647	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	0.9999999999999993	.	.	.	.	.	.	T	0.00763	-1.1576	3	.	.	.	.	14.174	0.65529	0.9361:0.0:0.0639:0.0	rs4674940;rs57043404;rs4674940	.	.	.	S	208	.	.	L	-	2	0	DOCK10	225378240	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	1.314000	0.33597	0.540000	0.28808	-1.195000	0.01675	TTG	A|0.924;G|0.076	0.076	strong		0.393	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
TMPRSS9	360200	hgsc.bcm.edu	37	19	2396556	2396556	+	Silent	SNP	C	C	T	rs7252886	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2396556C>T	ENST00000332578.3	+	2	162	c.162C>T	c.(160-162)ggC>ggT	p.G54G	TMPRSS9_ENST00000592650.1_3'UTR	NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	54					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)		CTACACAGGGCTTCCACGTGG	0.697													C|||	2157	0.430711	0.5696	0.464	5008	,	,		15889	0.504		0.2306	False		,,,				2504	0.3497				p.G54G		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C162T						PASS	.	C		2330,2076		614,1102,487	30.0	26.0	27.0		162	-3.4	0.4	19	dbSNP_116	27	2123,6477		274,1575,2451	no	coding-synonymous	TMPRSS9	NM_182973.1		888,2677,2938	TT,TC,CC		24.686,47.1176,34.238		54/1060	2396556	4453,8553	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon2			ACAGGGCTTCCAC	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.162C>T	19.37:g.2396556C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.631;T|0.369	0.369	strong		0.697	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
COL5A3	50509	hgsc.bcm.edu	37	19	10088271	10088271	+	Splice_Site	SNP	C	C	G	rs2161468	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	80	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	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
PHF2	5253	hgsc.bcm.edu	37	9	96436037	96436037	+	Missense_Mutation	SNP	G	G	A	rs41276200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96436037G>A	ENST00000359246.4	+	18	2886	c.2519G>A	c.(2518-2520)aGt>aAt	p.S840N	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	840				SGKSA -> NKGT (in Ref. 1; AAD21791). {ECO:0000305}.	liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		AGTGGCAAGAGTGCAGGCAAA	0.627													G|||	36	0.0071885	0.0	0.0029	5008	,	,		19197	0.0129		0.0169	False		,,,				2504	0.0041				p.S840N		Atlas-SNP	.											.	PHF2	113	.	0			c.G2519A						PASS	.	G	ASN/SER	11,4395	20.2+/-43.8	0,11,2192	88.0	74.0	78.0		2519	3.3	0.0	9	dbSNP_127	78	120,8480	62.4+/-124.4	2,116,4182	yes	missense	PHF2	NM_005392.3	46	2,127,6374	AA,AG,GG		1.3953,0.2497,1.0072	benign	840/1097	96436037	131,12875	2203	4300	6503	SO:0001583	missense	5253	exon18			GCAAGAGTGCAGG	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2519G>A	9.37:g.96436037G>A	ENSP00000352185:p.Ser840Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	150	75	0.5	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	37	CCDS35069.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	6	0.01048951048951049	13	0.017150395778364115	G	10.03	1.237840	0.22711	0.002497	0.013953	ENSG00000197724	ENST00000359246	T	0.18502	2.21	5.18	3.32	0.38043	.	0.515497	0.21501	N	0.073536	T	0.02807	0.0084	N	0.11560	0.145	0.80722	D	1	B;B	0.13594	0.008;0.001	B;B	0.14578	0.011;0.003	T	0.22871	-1.0204	10	0.07990	T	0.79	-3.0171	3.472	0.07570	0.1562:0.0:0.4214:0.4224	rs41276200;rs61739260	259;840	Q8N359;O75151	.;PHF2_HUMAN	N	840	ENSP00000352185:S840N	ENSP00000352185:S840N	S	+	2	0	PHF2	95475858	0.998000	0.40836	0.019000	0.16419	0.398000	0.30690	2.824000	0.48088	1.149000	0.42402	0.561000	0.74099	AGT	G|0.990;A|0.010	0.010	strong		0.627	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
FLG	2312	hgsc.bcm.edu	37	1	152282311	152282311	+	Missense_Mutation	SNP	C	C	T	rs12407807	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152282311C>T	ENST00000368799.1	-	3	5086	c.5051G>A	c.(5050-5052)cGc>cAc	p.R1684H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1684	Ser-rich.		R -> H (in dbSNP:rs12407807).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTGGTGGCGGGATCCATG	0.562									Ichthyosis				C|||	1486	0.296725	0.0461	0.3905	5008	,	,		20240	0.5843		0.1421	False		,,,				2504	0.4315				p.R1684H		Atlas-SNP	.											.	FLG	900	.	0			c.G5051A						PASS	.	C	HIS/ARG	303,4103	164.4+/-196.0	5,293,1905	303.0	304.0	304.0		5051	-5.0	0.0	1	dbSNP_120	304	1241,7359	249.0+/-276.5	97,1047,3156	no	missense	FLG	NM_002016.1	29	102,1340,5061	TT,TC,CC		14.4302,6.877,11.8714	probably-damaging	1684/4062	152282311	1544,11462	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGGCGGGATC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5051G>A	1.37:g.152282311C>T	ENSP00000357789:p.Arg1684His	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	232	118	0.508621	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	596	0.27289377289377287	32	0.06504065040650407	118	0.3259668508287293	335	0.5856643356643356	111	0.14643799472295516	C	11.22	1.575161	0.28092	0.06877	0.144302	ENSG00000143631	ENST00000368799	T	0.04015	3.73	2.9	-5.01	0.02991	.	.	.	.	.	T	0.01976	0.0062	N	0.12746	0.255	0.80722	P	0.0	D	0.76494	0.999	D	0.71656	0.974	T	0.23476	-1.0187	8	0.28530	T	0.3	.	5.6496	0.17608	0.0:0.5734:0.1604:0.2663	rs12407807;rs59897311	1684	P20930	FILA_HUMAN	H	1684	ENSP00000357789:R1684H	ENSP00000357789:R1684H	R	-	2	0	FLG	150548935	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.483000	0.00980	-0.996000	0.03455	0.306000	0.20318	CGC	C|0.829;T|0.171	0.171	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CES1	1066	hgsc.bcm.edu	37	16	55855361	55855361	+	Missense_Mutation	SNP	G	G	T	rs2307227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:55855361G>T	ENST00000361503.4	-	5	739	c.609C>A	c.(607-609)gaC>gaA	p.D203E	CES1_ENST00000422046.2_Missense_Mutation_p.D203E|CES1_ENST00000566555.1_5'UTR|CES1_ENST00000360526.3_Missense_Mutation_p.D204E			P23141	EST1_HUMAN	carboxylesterase 1	203			D -> E (in dbSNP:rs2307227).		epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	TGGCAATGTTGTCCTGGACCC	0.577													.|||	229	0.0457268	0.0877	0.0202	5008	,	,		25071	0.0149		0.0388	False		,,,				2504	0.046				p.D204E	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.C612A						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP	366,4030		17,332,1849	59.0	60.0	60.0		609,612,609	2.1	1.0	16	dbSNP_100	60	283,8317		4,275,4021	no	missense,missense,missense	CES1	NM_001025194.1,NM_001025195.1,NM_001266.4	45,45,45	21,607,5870	TT,TG,GG		3.2907,8.3258,4.9938	benign,benign,benign	203/568,204/569,203/567	55855361	649,12347	2198	4300	6498	SO:0001583	missense	1066	exon5			AATGTTGTCCTGG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.609C>A	16.37:g.55855361G>T	ENSP00000355193:p.Asp203Glu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	83	0.038003663003663	35	0.07113821138211382	9	0.024861878453038673	7	0.012237762237762238	32	0.04221635883905013	.	10.14	1.268247	0.23136	0.083258	0.032907	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046;ENST00000426667	T;T;T	0.09073	3.2;3.2;3.02	4.18	2.08	0.27032	Carboxylesterase, type B (1);	0.196139	0.36200	N	0.002728	T	0.00271	0.0008	N	0.13352	0.335	0.35876	D	0.828558	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.12837	0.008;0.008;0.004	T	0.41161	-0.9524	10	0.08837	T	0.75	.	12.7562	0.57336	0.0:0.3336:0.6663:0.0	rs2307227;rs52803818;rs2307227	203;203;204	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	E	204;203;203;68	ENSP00000353720:D204E;ENSP00000355193:D203E;ENSP00000390492:D203E	ENSP00000353720:D204E	D	-	3	2	CES1	54412862	0.998000	0.40836	1.000000	0.80357	0.851000	0.48451	0.493000	0.22451	0.761000	0.33130	0.456000	0.33151	GAC	G|0.956;T|0.044	0.044	strong		0.577	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
AKR7A3	22977	hgsc.bcm.edu	37	1	19612477	19612477	+	Missense_Mutation	SNP	C	C	T	rs2231198	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	186	0	0		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	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	
KIAA0922	23240	hgsc.bcm.edu	37	4	154533506	154533506	+	Missense_Mutation	SNP	C	C	G	rs36113034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:154533506C>G	ENST00000409663.3	+	26	3570	c.3518C>G	c.(3517-3519)tCt>tGt	p.S1173C	KIAA0922_ENST00000440693.1_Missense_Mutation_p.S1090C|KIAA0922_ENST00000409959.3_Missense_Mutation_p.S1174C	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1173						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)				CACAAAACATCTAGAGAAGAC	0.343													C|||	27	0.00539137	0.0008	0.0058	5008	,	,		18587	0.0		0.0169	False		,,,				2504	0.0051				p.S1174C		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C3521G						PASS	.	C	CYS/SER,CYS/SER	21,4385	27.2+/-55.0	0,21,2182	72.0	74.0	73.0		3521,3518	5.6	0.6	4	dbSNP_126	73	163,8435	76.9+/-139.5	2,159,4138	yes	missense,missense	KIAA0922	NM_001131007.1,NM_015196.3	112,112	2,180,6320	GG,GC,CC		1.8958,0.4766,1.4149	possibly-damaging,possibly-damaging	1174/1611,1173/1610	154533506	184,12820	2203	4299	6502	SO:0001583	missense	23240	exon26			AAACATCTAGAGA	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.3518C>G	4.37:g.154533506C>G	ENSP00000386574:p.Ser1173Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	18	0.008241758241758242	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	14.57	2.576303	0.45902	0.004766	0.018958	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.20463	2.35;2.07;2.35;2.07	5.62	5.62	0.85841	.	0.724620	0.13870	N	0.357041	T	0.23330	0.0564	L	0.43152	1.355	0.21553	N	0.999645	D;D;P	0.76494	0.999;0.963;0.939	D;P;P	0.66716	0.946;0.73;0.541	T	0.08411	-1.0723	10	0.62326	D	0.03	-4.8155	14.9005	0.70675	0.0:0.7872:0.2128:0.0	rs36113034	1090;1174;1173	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	C	1173;1090;1174;951	ENSP00000386574:S1173C;ENSP00000409663:S1090C;ENSP00000386787:S1174C;ENSP00000240487:S951C	ENSP00000240487:S951C	S	+	2	0	KIAA0922	154752956	0.279000	0.24239	0.615000	0.29064	0.921000	0.55340	1.785000	0.38684	2.648000	0.89879	0.557000	0.71058	TCT	C|0.988;G|0.012	0.012	strong		0.343	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
MAP1B	4131	hgsc.bcm.edu	37	5	71494906	71494906	+	Silent	SNP	G	G	A	rs61734262	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:71494906G>A	ENST00000296755.7	+	5	6022	c.5724G>A	c.(5722-5724)aaG>aaA	p.K1908K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1908					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)		ACTATGAGAAGATAGAGAGAA	0.448													G|||	412	0.0822684	0.1021	0.0461	5008	,	,		19259	0.0317		0.1173	False		,,,				2504	0.0971				p.K1908K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.G5724A						PASS	.	G		482,3924	203.5+/-225.9	20,442,1741	61.0	65.0	64.0		5724	3.5	0.7	5	dbSNP_129	64	1019,7581	206.8+/-248.7	62,895,3343	no	coding-synonymous	MAP1B	NM_005909.3		82,1337,5084	AA,AG,GG		11.8488,10.9396,11.5408		1908/2469	71494906	1501,11505	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			TGAGAAGATAGAG	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.5724G>A	5.37:g.71494906G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			G|0.900;A|0.100	0.100	strong		0.448	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
MANEA	79694	hgsc.bcm.edu	37	6	96034560	96034560	+	Missense_Mutation	SNP	C	C	T	rs62417812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:96034560C>T	ENST00000358812.4	+	2	379	c.245C>T	c.(244-246)aCt>aTt	p.T82I	MANEA_ENST00000369293.1_Missense_Mutation_p.T82I	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	82	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		GTTGAAATCACTATGAAACCT	0.328													C|||	251	0.0501198	0.0605	0.0346	5008	,	,		17245	0.003		0.1103	False		,,,				2504	0.0337				p.T82I		Atlas-SNP	.											.	MANEA	58	.	0			c.C245T						PASS	.	C	ILE/THR	314,4092	164.0+/-195.7	13,288,1902	97.0	100.0	99.0		245	2.9	0.2	6	dbSNP_129	99	984,7616	210.3+/-251.2	68,848,3384	yes	missense	MANEA	NM_024641.3	89	81,1136,5286	TT,TC,CC		11.4419,7.1266,9.98	benign	82/463	96034560	1298,11708	2203	4300	6503	SO:0001583	missense	79694	exon2			AAATCACTATGAA	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.245C>T	6.37:g.96034560C>T	ENSP00000351669:p.Thr82Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	37	CCDS5032.1	136	0.06227106227106227	27	0.054878048780487805	12	0.03314917127071823	2	0.0034965034965034965	95	0.12532981530343007	C	10.52	1.372093	0.24857	0.071266	0.114419	ENSG00000172469	ENST00000358812;ENST00000369293;ENST00000542500	.	.	.	5.82	2.87	0.33458	.	0.440545	0.27563	N	0.018819	T	0.29524	0.0736	M	0.67953	2.075	0.80722	P	0.0	B;B	0.24823	0.091;0.112	B;B	0.23716	0.022;0.048	T	0.13926	-1.0491	8	0.34782	T	0.22	-10.0816	7.6663	0.28432	0.1285:0.6836:0.1141:0.0738	rs62417812	82;82	Q5SRI9;Q8WWX4	MANEA_HUMAN;.	I	82	.	ENSP00000351669:T82I	T	+	2	0	MANEA	96141281	0.018000	0.18449	0.174000	0.22961	0.996000	0.88848	-0.000000	0.12993	1.459000	0.47892	0.650000	0.86243	ACT	C|0.917;T|0.083	0.083	strong		0.328	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
CSMD1	64478	hgsc.bcm.edu	37	8	3351147	3351147	+	Silent	SNP	G	G	A	rs17066296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:3351147G>A	ENST00000520002.1	-	12	2004	c.1449C>T	c.(1447-1449)taC>taT	p.Y483Y	CSMD1_ENST00000537824.1_Silent_p.Y482Y|CSMD1_ENST00000602723.1_Silent_p.Y483Y|CSMD1_ENST00000400186.3_Silent_p.Y483Y|CSMD1_ENST00000542608.1_Silent_p.Y482Y|CSMD1_ENST00000602557.1_Silent_p.Y483Y|CSMD1_ENST00000539096.1_Silent_p.Y482Y			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	483	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ATACTCACACGTACAAGACCG	0.527													G|||	558	0.111422	0.0446	0.0476	5008	,	,		16184	0.2312		0.0716	False		,,,				2504	0.1646				p.Y482Y		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C1446T						PASS	.	G		210,4148		7,196,1976	86.0	91.0	89.0		1446	-7.4	0.6	8	dbSNP_123	89	651,7941		27,597,3672	no	coding-synonymous	CSMD1	NM_033225.5		34,793,5648	AA,AG,GG		7.5768,4.8187,6.6486		482/3565	3351147	861,12089	2179	4296	6475	SO:0001819	synonymous_variant	64478	exon11			TCACACGTACAAG			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.1449C>T	8.37:g.3351147G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37																																																																																				G|0.914;A|0.086	0.086	strong		0.527	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
TRIOBP	11078	hgsc.bcm.edu	37	22	38130459	38130459	+	Missense_Mutation	SNP	G	G	T	rs8140207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	178	0	0		WXS	Illumina HiSeq	Phase_I	164	68	0.414634	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		
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855752	12855752	+	Silent	SNP	G	G	A	rs80197258	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12855752G>A	ENST00000332296.7	+	4	1135	c.1032G>A	c.(1030-1032)ctG>ctA	p.L344L	PRAMEF1_ENST00000400814.3_Silent_p.L99L	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	344					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.L344L(2)		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)		GAGCTCTGCTGGAGAAAATTG	0.557																																					p.L344L		Atlas-SNP	.											PRAMEF1,NS,carcinoma,0,2	PRAMEF1	78	2	2	Substitution - coding silent(2)	prostate(2)	c.G1032A						scavenged	.						188.0	192.0	191.0					1																	12855752		2203	4300	6503	SO:0001819	synonymous_variant	65121	exon4			TCTGCTGGAGAAA	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.1032G>A	1.37:g.12855752G>A		Somatic	400	5	0.0125		WXS	Illumina HiSeq	Phase_I	489	10	0.0204499	NM_023013	Q9UQP2	Silent	SNP	ENST00000332296.7	37	CCDS148.1																																																																																			G|0.997;A|0.003	0.003	strong		0.557	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
GEMIN4	50628	hgsc.bcm.edu	37	17	649067	649067	+	Missense_Mutation	SNP	A	A	G	rs1062923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:649067A>G	ENST00000319004.5	-	2	2334	c.2216T>C	c.(2215-2217)aTt>aCt	p.I739T	GEMIN4_ENST00000576778.1_Missense_Mutation_p.I728T	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	739			I -> T (in dbSNP:rs1062923).		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)		GGCTGATACAATCTCACACAG	0.542													A|||	372	0.0742812	0.0113	0.0865	5008	,	,		19699	0.002		0.1918	False		,,,				2504	0.1043				p.I739T		Atlas-SNP	.											.	GEMIN4	116	.	0			c.T2216C						PASS	.	A	THR/ILE	134,3788		2,130,1829	25.0	25.0	25.0		2216	-2.2	0.0	17	dbSNP_86	25	1404,6894		137,1130,2882	yes	missense	GEMIN4	NM_015721.2	89	139,1260,4711	GG,GA,AA		16.9197,3.4166,12.5859	benign	739/1059	649067	1538,10682	1961	4149	6110	SO:0001583	missense	50628	exon2			GATACAATCTCAC	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.2216T>C	17.37:g.649067A>G	ENSP00000321706:p.Ile739Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	176	0.08058608058608059	3	0.006097560975609756	30	0.08287292817679558	0	0.0	143	0.18865435356200527	A	1.201	-0.632507	0.03584	0.034166	0.169197	ENSG00000179409	ENST00000319004	T	0.07021	3.23	5.46	-2.19	0.07015	.	0.822055	0.10990	N	0.611688	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.33574	-0.9863	9	0.40728	T	0.16	-0.1052	12.0072	0.53265	0.5095:0.0:0.4905:0.0	rs1062923;rs3169635;rs56633576;rs1062923	739	P57678	GEMI4_HUMAN	T	739	ENSP00000321706:I739T	ENSP00000321706:I739T	I	-	2	0	GEMIN4	595817	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	1.057000	0.30492	-0.811000	0.04369	0.533000	0.62120	ATT	A|0.912;G|0.088	0.088	strong		0.542	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
PRAMEF13	400736	hgsc.bcm.edu	37	1	13448351	13448351	+	Missense_Mutation	SNP	T	T	C	rs71183793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:13448351T>C	ENST00000376132.3	-	4	1226	c.1124A>G	c.(1123-1125)cAc>cGc	p.H375R		NM_001024661.1	NP_001019832.1	Q5VWM6	PRA13_HUMAN	PRAME family member 13	375					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)|large_intestine(1)|lung(3)|skin(2)	7	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;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGAGCAGTGGCTCAGGCC	0.547																																					p.H375R		Atlas-SNP	.											PRAMEF13,brain,glioma,0,1	PRAMEF13	10	1	0			c.A1124G						scavenged	.						10.0	10.0	10.0					1																	13448351		1832	3466	5298	SO:0001583	missense	400736	exon4			GAGCAGTGGCTCA			1p36.21	2013-01-17			ENSG00000204495			"""-"""	13262	protein-coding gene	gene with protein product							Standard	NG_005159		Approved	OTTHUMG00000008034	uc010obi.1	Q5VWM6	OTTHUMG00000008034	ENST00000376132.3:c.1124A>G	1.37:g.13448351T>C	ENSP00000365302:p.His375Arg	Somatic	354	26	0.0734463		WXS	Illumina HiSeq	Phase_I	576	428	0.743056	NM_001024661		Missense_Mutation	SNP	ENST00000376132.3	37	CCDS41257.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.668736	0.00105	.	.	ENSG00000204495	ENST00000376132	T	0.08984	3.03	1.2	-2.41	0.06562	.	1.164400	0.06173	N	0.678136	T	0.02455	0.0075	N	0.01729	-0.75	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40979	-0.9534	9	0.02654	T	1	.	6.0386	0.19722	0.0:0.3485:0.0:0.6515	.	375;375	Q5VWM6;A6NFR9	PRA13_HUMAN;.	R	375	ENSP00000365302:H375R	ENSP00000365302:H375R	H	-	2	0	PRAMEF13	13320938	0.064000	0.20934	0.069000	0.20011	0.009000	0.06853	-0.393000	0.07305	-1.586000	0.01632	-1.964000	0.00472	CAC	T|0.131;C|0.869	0.869	strong		0.547	PRAMEF13-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022040.1	XM_375688	
FLG	2312	hgsc.bcm.edu	37	1	152280782	152280782	+	Missense_Mutation	SNP	A	A	G	rs2184953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280782A>G	ENST00000368799.1	-	3	6615	c.6580T>C	c.(6580-6582)Tat>Cat	p.Y2194H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2194	Ser-rich.		Y -> H (in dbSNP:rs2184953).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCTTGTCATATGTTTTTCTG	0.547									Ichthyosis				-|||	2703	0.539736	0.7897	0.4683	5008	,	,		29126	0.6607		0.1759	False		,,,				2504	0.502				p.Y2194H		Atlas-SNP	.											.	FLG	900	.	0			c.T6580C						PASS	.						483.0	407.0	432.0					1																	152280782		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGTCATATGTTTT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6580T>C	1.37:g.152280782A>G	ENSP00000357789:p.Tyr2194His	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	489	317	0.648262	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	
TPSB2	64499	hgsc.bcm.edu	37	16	1279704	1279704	+	RNA	SNP	A	A	G	rs202107419	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1279704A>G	ENST00000339687.6	-	0	118				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				CCTGACCCCCAACGATGCCCA	0.697																																					p.V32V		Atlas-SNP	.											.	TPSB2	8	.	0			c.T96C						PASS	.						30.0	38.0	35.0					16																	1279704		2182	4298	6480			64499	exon3			ACCCCCAACGATG	AF099143		16p13.3	2009-11-20	2009-11-18		ENSG00000197253	ENSG00000197253			14120	protein-coding gene	gene with protein product	"""tryptase beta II"", ""tryptase beta III"""	191081	"""tryptase beta 2"""			19748655	Standard	NM_024164		Approved		uc002cky.3	P20231	OTTHUMG00000155926		16.37:g.1279704A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	94	66	0.702128	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Silent	SNP	ENST00000339687.6	37																																																																																				.	.	weak		0.697	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376110	113376110	+	Silent	SNP	T	T	C	rs59601191|rs112313093|rs10606566|rs59990801|rs397990842		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:113376110T>C	ENST00000478658.1	-	5	4436	c.4419A>G	c.(4417-4419)caA>caG	p.Q1473Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1473Q			Q68DE3	K2018_HUMAN	KIAA2018	1473	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgttgctgttgctgctgct	0.507																																					p.Q1473Q		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A4419G						PASS	.						84.0	92.0	89.0					3																	113376110		2193	4281	6474	SO:0001819	synonymous_variant	205717	exon7			TTGCTGTTGCTGC	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.4419A>G	3.37:g.113376110T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	137	12	0.0875912	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	none		0.507	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
PHF2	5253	hgsc.bcm.edu	37	9	96411414	96411414	+	Silent	SNP	G	G	A	rs16912641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96411414G>A	ENST00000359246.4	+	5	889	c.522G>A	c.(520-522)ctG>ctA	p.L174L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	174					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		AGATGAAGCTGAAGGAGTTTG	0.572													G|||	177	0.0353435	0.0862	0.0101	5008	,	,		14042	0.0139		0.0298	False		,,,				2504	0.0123				p.L174L		Atlas-SNP	.											.	PHF2	113	.	0			c.G522A						PASS	.	G		330,3782		6,318,1732	110.0	71.0	84.0		522	3.7	1.0	9	dbSNP_123	84	140,7862		1,138,3862	no	coding-synonymous	PHF2	NM_005392.3		7,456,5594	AA,AG,GG		1.7496,8.0253,3.8798		174/1097	96411414	470,11644	2056	4001	6057	SO:0001819	synonymous_variant	5253	exon5			GAAGCTGAAGGAG	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.522G>A	9.37:g.96411414G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	194	81	0.417526	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			G|0.954;A|0.046	0.046	strong		0.572	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
GDF5	8200	hgsc.bcm.edu	37	20	34022387	34022387	+	Missense_Mutation	SNP	A	A	C	rs224331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34022387A>C	ENST00000374372.1	-	4	1329	c.826T>G	c.(826-828)Tcc>Gcc	p.S276A	GDF5_ENST00000374369.3_Missense_Mutation_p.S276A|GDF5OS_ENST00000374375.1_Missense_Mutation_p.E144A			P43026	GDF5_HUMAN	growth differentiation factor 5	276			S -> A (in dbSNP:rs224331). {ECO:0000269|PubMed:7961761, ECO:0000269|Ref.4}.		cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			TCCAGCAAGGAGGCCGGCTGC	0.682													C|||	1923	0.383986	0.466	0.2608	5008	,	,		13219	0.2857		0.3539	False		,,,				2504	0.4928				p.S276A		Atlas-SNP	.											GDF5OS_ENST00000374375,NS,carcinoma,0,3	GDF5	66	3	0			c.T826G						PASS	.	C	ALA/SER	1790,2526		429,932,797	11.0	14.0	13.0		826	3.5	1.0	20	dbSNP_79	13	2951,5579		595,1761,1909	yes	missense	GDF5	NM_000557.2	99	1024,2693,2706	CC,CA,AA		34.5955,41.4736,36.9064	benign	276/502	34022387	4741,8105	2158	4265	6423	SO:0001583	missense	8200	exon2			GCAAGGAGGCCGG	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"""cartilage-derived morphogenetic protein-1"""	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.826T>G	20.37:g.34022387A>C	ENSP00000363492:p.Ser276Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_000557	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	733|733	0.3356227106227106|0.3356227106227106	221|221	0.4491869918699187|0.4491869918699187	105|105	0.2900552486187845|0.2900552486187845	137|137	0.2395104895104895|0.2395104895104895	270|270	0.3562005277044855|0.3562005277044855	C|C	8.146|8.146	0.786387|0.786387	0.16189|0.16189	0.414736|0.414736	0.345955|0.345955	ENSG00000204183|ENSG00000125965	ENST00000374375|ENST00000374369;ENST00000374372	.|T;T	.|0.64438	.|-0.1;-0.1	4.56|4.56	3.54|3.54	0.40534|0.40534	.|Transforming growth factor-beta, N-terminal (1);	.|0.399875	.|0.24606	.|N	.|0.037095	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.43442|0.43442	-0.9391|-0.9391	5|9	0.87932|0.09338	D|T	0|0.73	.|.	1.8889|1.8889	0.03243|0.03243	0.3052:0.4336:0.0:0.2612|0.3052:0.4336:0.0:0.2612	rs224331;rs3748436;rs224331|rs224331;rs3748436;rs224331	.|276	.|P43026	.|GDF5_HUMAN	A|A	144|276	.|ENSP00000363489:S276A;ENSP00000363492:S276A	ENSP00000363495:E144A|ENSP00000363489:S276A	E|S	+|-	2|1	0|0	GDF5OS|GDF5	33485801|33485801	0.974000|0.974000	0.33945|0.33945	1.000000|1.000000	0.80357|0.80357	0.917000|0.917000	0.54804|0.54804	1.594000|1.594000	0.36697|0.36697	1.145000|1.145000	0.42336|0.42336	-0.323000|-0.323000	0.08544|0.08544	GAG|TCC	A|0.641;C|0.359	0.359	strong		0.682	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2		
TARBP1	6894	hgsc.bcm.edu	37	1	234546245	234546245	+	Silent	SNP	C	C	T	rs1141264	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	246	0	0		WXS	Illumina HiSeq	Phase_I	236	103	0.436441	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	
DSEL	92126	hgsc.bcm.edu	37	18	65179657	65179657	+	Missense_Mutation	SNP	T	T	C	rs12953840	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:65179657T>C	ENST00000310045.7	-	2	3692	c.2219A>G	c.(2218-2220)tAt>tGt	p.Y740C	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	730					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)				GAATCCCAGATAATTGAATCT	0.403													T|||	4	0.000798722	0.0008	0.0029	5008	,	,		18544	0.0		0.001	False		,,,				2504	0.0				p.Y740C		Atlas-SNP	.											.	DSEL	196	.	0			c.A2219G						PASS	.	T	CYS/TYR	3,4403	6.2+/-15.9	0,3,2200	52.0	54.0	53.0		2219	5.1	1.0	18	dbSNP_121	53	30,8570	21.6+/-65.8	1,28,4271	yes	missense	DSEL	NM_032160.2	194	1,31,6471	CC,CT,TT		0.3488,0.0681,0.2537	probably-damaging	740/1223	65179657	33,12973	2203	4300	6503	SO:0001583	missense	92126	exon2			CCCAGATAATTGA	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.2219A>G	18.37:g.65179657T>C	ENSP00000310565:p.Tyr740Cys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	15.14	2.743790	0.49151	6.81E-4	0.003488	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.26373	1.74	5.09	5.09	0.68999	.	0.000000	0.64402	U	0.000002	T	0.44201	0.1282	M	0.70595	2.14	0.45806	D	0.99868	D	0.71674	0.998	P	0.60789	0.879	T	0.44406	-0.9330	10	0.87932	D	0	.	10.1284	0.42663	0.1494:0.0:0.0:0.8506	rs12953840;rs12953840	730	Q8IZU8	DSEL_HUMAN	C	740;730	ENSP00000310565:Y740C	ENSP00000310565:Y740C	Y	-	2	0	DSEL	63330637	1.000000	0.71417	0.986000	0.45419	0.966000	0.64601	5.986000	0.70563	2.060000	0.61445	0.374000	0.22700	TAT	T|0.998;C|0.002	0.002	strong		0.403	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
GRIN3B	116444	hgsc.bcm.edu	37	19	1008683	1008683	+	Missense_Mutation	SNP	G	G	A	rs2285906	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1008683G>A	ENST00000234389.3	+	7	2552	c.2533G>A	c.(2533-2535)Gct>Act	p.A845T		NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	845			A -> T (in dbSNP:rs2285906).		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)	CCTGGGCAGCGCTCTGCTCAG	0.677													g|||	545	0.108826	0.0378	0.1383	5008	,	,		11007	0.1329		0.161	False		,,,				2504	0.1053				p.A845T		Atlas-SNP	.											GRIN3B,NS,carcinoma,0,1	GRIN3B	46	1	0			c.G2533A						PASS	.	G	THR/ALA	261,4145	146.1+/-180.8	8,245,1950	41.0	35.0	37.0		2533	1.2	1.0	19	dbSNP_100	37	1416,7184	268.7+/-288.0	121,1174,3005	yes	missense	GRIN3B	NM_138690.1	58	129,1419,4955	AA,AG,GG		16.4651,5.9237,12.894	possibly-damaging	845/1044	1008683	1677,11329	2203	4300	6503	SO:0001583	missense	116444	exon7			GGCAGCGCTCTGC		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.2533G>A	19.37:g.1008683G>A	ENSP00000234389:p.Ala845Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	259	0.11858974358974358	21	0.042682926829268296	47	0.1298342541436464	70	0.12237762237762238	121	0.15963060686015831	G	21.1	4.091740	0.76756	0.059237	0.164651	ENSG00000116032	ENST00000234389	T	0.16073	2.37	3.78	1.22	0.21188	.	0.136063	0.49305	U	0.000143	T	0.00073	0.0002	L	0.55481	1.735	0.09310	P	0.9999999999999997	D	0.62365	0.991	P	0.50314	0.637	T	0.11665	-1.0578	9	0.72032	D	0.01	.	9.4558	0.38753	0.0:0.0:0.548:0.452	rs2285906	845	O60391	NMD3B_HUMAN	T	845	ENSP00000234389:A845T	ENSP00000234389:A845T	A	+	1	0	GRIN3B	959683	0.994000	0.37717	0.954000	0.39281	0.981000	0.71138	2.365000	0.44196	1.661000	0.50771	0.462000	0.41574	GCT	G|0.875;A|0.125	0.125	strong		0.677	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
CILP	8483	hgsc.bcm.edu	37	15	65494212	65494212	+	Missense_Mutation	SNP	A	A	G	rs2073711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:65494212A>G	ENST00000261883.4	-	8	1350	c.1184T>C	c.(1183-1185)aTa>aCa	p.I395T		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	395	Ig-like C2-type.		I -> T (common polymorphism; associated with susceptibility to lumbar disk disease in Japanese; increases binding and inhibition of TGFB1; dbSNP:rs2073711). {ECO:0000269|PubMed:10319588, ECO:0000269|PubMed:10601732, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9722584}.		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						AGGCTTACCTATGACAATCAG	0.562													A|||	2487	0.496605	0.6732	0.6254	5008	,	,		17127	0.1429		0.6471	False		,,,				2504	0.3763				p.I395T		Atlas-SNP	.											.	CILP	124	.	0			c.T1184C	GRCh37	CM051412	CILP	M	rs2073711	PASS	.	A	THR/ILE	2801,1603	663.3+/-401.2	883,1035,284	59.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1184	3.4	1.0	15	dbSNP_96	57	5471,3127	656.4+/-401.4	1756,1959,584	yes	missense	CILP	NM_003613.3	89	2639,2994,868	GG,GA,AA		36.3689,36.3987,36.379	probably-damaging	395/1185	65494212	8272,4730	2202	4299	6501	SO:0001583	missense	8483	exon8			TTACCTATGACAA	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.1184T>C	15.37:g.65494212A>G	ENSP00000261883:p.Ile395Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	CCDS10203.1	1122	0.5137362637362637	319	0.6483739837398373	220	0.6077348066298343	92	0.16083916083916083	491	0.6477572559366754	A	11.26	1.587634	0.28268	0.636013	0.636311	ENSG00000138615	ENST00000261883	T	0.37584	1.19	5.71	3.4	0.38934	.	0.188488	0.52532	N	0.000073	T	0.00012	0.0000	M	0.68593	2.085	0.24642	P	0.99356269	B	0.02656	0.0	B	0.04013	0.001	T	0.34329	-0.9833	9	0.41790	T	0.15	-9.539	9.4938	0.38976	0.8569:0.0:0.1431:0.0	rs2073711;rs16948551;rs59476856;rs2073711	395	O75339	CILP1_HUMAN	T	395	ENSP00000261883:I395T	ENSP00000261883:I395T	I	-	2	0	CILP	63281265	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	4.093000	0.57714	0.523000	0.28482	-0.263000	0.10527	ATA	A|0.431;G|0.569	0.569	strong		0.562	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37469591	37469591	+	Silent	SNP	G	G	A	rs4820268	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37469591G>A	ENST00000346753.3	-	13	1679	c.1563C>T	c.(1561-1563)gaC>gaT	p.D521D	TMPRSS6_ENST00000381792.2_Silent_p.D512D|TMPRSS6_ENST00000406856.1_Silent_p.D512D|TMPRSS6_ENST00000406725.1_Silent_p.D512D	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	521	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.		D -> N (in IRIDA; reduced expression at the cell surface; partially retained in the Golgi apparatus; does not undergo proteolytic processing; able to interact with HFE2; results in reduced inhibition of HAMP promoter; dbSNP:rs137853120). {ECO:0000269|PubMed:18408718, ECO:0000269|PubMed:19357398}.		angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.D521D(1)		breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						ACTGCTCTTCGTCGCTGCCGT	0.552													A|||	2722	0.54353	0.7239	0.4669	5008	,	,		19397	0.4365		0.5775	False		,,,				2504	0.4294				p.D521D		Atlas-SNP	.											TMPRSS6,NS,carcinoma,0,2	TMPRSS6	99	2	1	Substitution - coding silent(1)	stomach(1)	c.C1563T						PASS	.	A		3233,1173	413.0+/-336.3	1180,873,150	172.0	128.0	143.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1563	-4.7	0.1	22	dbSNP_111	143	4634,3966	551.0+/-385.8	1278,2078,944	yes	coding-synonymous	TMPRSS6	NM_153609.2		2458,2951,1094	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	46.1163,26.6228,39.5125		521/812	37469591	7867,5139	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon13			CTCTTCGTCGCTG	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.1563C>T	22.37:g.37469591G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			G|0.418;A|0.582	0.582	strong		0.552	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
WDR62	284403	hgsc.bcm.edu	37	19	36549684	36549684	+	Silent	SNP	G	G	A	rs61742664	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36549684G>A	ENST00000270301.7	+	2	180	c.180G>A	c.(178-180)gtG>gtA	p.V60V	WDR62_ENST00000401500.2_Silent_p.V60V|WDR62_ENST00000388999.3_Silent_p.V60V|WDR62_ENST00000378860.4_3'UTR			O43379	WDR62_HUMAN	WD repeat domain 62	60					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)			CTTTGCAGGTGTCACTCGAGA	0.582													G|||	568	0.113419	0.0189	0.0865	5008	,	,		19086	0.2173		0.0358	False		,,,				2504	0.2331				p.V60V		Atlas-SNP	.											.	WDR62	102	.	0			c.G180A						PASS	.	G	,	124,4282	91.6+/-130.3	0,124,2079	81.0	70.0	74.0		180,180	-0.4	1.0	19	dbSNP_129	74	346,8254	116.5+/-176.2	3,340,3957	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	3,464,6036	AA,AG,GG		4.0233,2.8143,3.6137	,	60/1524,60/1519	36549684	470,12536	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon2			GCAGGTGTCACTC	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.180G>A	19.37:g.36549684G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			G|0.947;A|0.053	0.053	strong		0.582	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
SIX5	147912	hgsc.bcm.edu	37	19	46268902	46268902	+	Missense_Mutation	SNP	C	C	T	rs2341097	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46268902C>T	ENST00000317578.6	-	3	2458	c.2077G>A	c.(2077-2079)Gtg>Atg	p.V693M	AC074212.5_ENST00000559756.1_RNA|AC074212.6_ENST00000590076.1_RNA|AC074212.5_ENST00000592217.2_RNA|SIX5_ENST00000560168.1_3'UTR	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	693			V -> M (in dbSNP:rs2341097).		lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		AGCCTCAGCACGGTGTGGGGG	0.682													C|||	1493	0.298123	0.3298	0.2305	5008	,	,		15903	0.2937		0.3231	False		,,,				2504	0.2822				p.V693M		Atlas-SNP	.											SIX5,NS,carcinoma,0,1	SIX5	35	1	0			c.G2077A						PASS	.	C	MET/VAL	1342,3064	415.4+/-337.2	214,914,1075	34.0	40.0	38.0		2077	3.1	0.8	19	dbSNP_100	38	3127,5471	449.9+/-362.2	577,1973,1749	yes	missense	SIX5	NM_175875.4	21	791,2887,2824	TT,TC,CC		36.3689,30.4585,34.3663	possibly-damaging	693/740	46268902	4469,8535	2203	4299	6502	SO:0001583	missense	147912	exon3			TCAGCACGGTGTG	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"""Homeoboxes / SINE class"""	10891	protein-coding gene	gene with protein product		600963	"""sine oculis homeobox (Drosophila) homolog 5"", ""sine oculis homeobox homolog 5 (Drosophila)"""	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.2077G>A	19.37:g.46268902C>T	ENSP00000316842:p.Val693Met	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	143	58	0.405594	NM_175875		Missense_Mutation	SNP	ENST00000317578.6	37	CCDS12673.1	635	0.2907509157509158	148	0.3008130081300813	100	0.27624309392265195	138	0.24125874125874125	249	0.32849604221635886	c	10.08	1.253473	0.22965	0.304585	0.363689	ENSG00000177045	ENST00000317578	D	0.91295	-2.82	4.24	3.14	0.36123	.	1.198060	0.06087	N	0.663052	T	0.00012	0.0000	N	0.08118	0	0.44635	P	0.0023849999999999705	P	0.38420	0.63	B	0.33750	0.169	T	0.04140	-1.0974	9	0.59425	D	0.04	-4.6308	9.0942	0.36629	0.0:0.7536:0.2464:0.0	rs2341097;rs17846041;rs17859030;rs57436149;rs2341097	693	Q8N196	SIX5_HUMAN	M	693	ENSP00000316842:V693M	ENSP00000316842:V693M	V	-	1	0	SIX5	50960742	0.430000	0.25538	0.843000	0.33291	0.480000	0.33159	0.682000	0.25335	2.199000	0.70637	0.561000	0.74099	GTG	C|0.678;T|0.322	0.322	strong		0.682	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875	
SETD5	55209	hgsc.bcm.edu	37	3	9517369	9517369	+	Missense_Mutation	SNP	C	C	T	rs11542009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:9517369C>T	ENST00000406341.1	+	22	4113	c.3923C>T	c.(3922-3924)aCa>aTa	p.T1308I	SETD5_ENST00000402198.1_Missense_Mutation_p.T1308I|SETD5_ENST00000302463.6_Missense_Mutation_p.T1210I|SETD5_ENST00000402466.1_Missense_Mutation_p.T1210I|SETD5_ENST00000407969.1_Missense_Mutation_p.T1327I			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1308	Ser-rich.		T -> I (in dbSNP:rs11542009).							NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CCTGTGTCCACAGACTCGTTG	0.567													C|||	197	0.0393371	0.0098	0.0533	5008	,	,		18375	0.001		0.0875	False		,,,				2504	0.0593				p.T1308I		Atlas-SNP	.											.	SETD5	210	.	0			c.C3923T						PASS	.	C	ILE/THR	104,3712		1,102,1805	44.0	44.0	44.0		3923	5.2	1.0	3	dbSNP_120	44	904,7346		48,808,3269	yes	missense	SETD5	NM_001080517.1	89	49,910,5074	TT,TC,CC		10.9576,2.7254,8.3541	possibly-damaging	1308/1443	9517369	1008,11058	1908	4125	6033	SO:0001583	missense	55209	exon23			TGTCCACAGACTC	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.3923C>T	3.37:g.9517369C>T	ENSP00000383939:p.Thr1308Ile	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	146	60	0.410959	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	99	0.04532967032967033	6	0.012195121951219513	23	0.06353591160220995	1	0.0017482517482517483	69	0.09102902374670185	C	16.85	3.236147	0.58886	0.027254	0.109576	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.93307	-2.86;-3.2;-2.86;-2.85;-3.2	5.23	5.23	0.72850	.	0.163740	0.42964	D	0.000636	T	0.17874	0.0429	N	0.19112	0.55	0.36809	D	0.885795	P;P	0.48294	0.908;0.689	P;B	0.46543	0.52;0.242	T	0.66697	-0.5858	10	0.41790	T	0.15	-11.7016	12.5086	0.55995	0.0:0.9233:0.0:0.0767	rs11542009	1210;1308	Q9C0A6-3;Q9C0A6	.;SETD5_HUMAN	I	1308;1210;1308;1327;1210	ENSP00000385852:T1308I;ENSP00000384429:T1210I;ENSP00000383939:T1308I;ENSP00000384114:T1327I;ENSP00000302028:T1210I	ENSP00000302028:T1210I	T	+	2	0	SETD5	9492369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.376000	0.52417	2.586000	0.87340	0.591000	0.81541	ACA	T|0.068;G|0.000;C|0.932	0.068	strong		0.567	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614	
PCDHGA12	26025	hgsc.bcm.edu	37	5	140858245	140858245	+	Intron	SNP	C	C	T	rs3805695	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140858245C>T	ENST00000252085.3	+	2	2566				PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGB7_ENST00000398594.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB1_ENST00000523390.1_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)			TTCAACTGGCCCTTCCTAGAT	0.438											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1089	0.217452	0.4032	0.2075	5008	,	,		21412	0.1131		0.1382	False		,,,				2504	0.1626				p.A854A		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.C2562T						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,,	860,1408		179,502,453	150.0	141.0	144.0		,,,,,,,,,,,,,,,,,,,,,2562,	-5.3	0.0	5	dbSNP_107	144	710,3692		52,606,1543	no	intron,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	,,,,,,,,,,,,,,,,,,,,,,	231,1108,1996	TT,TC,CC		16.129,37.9189,23.5382	,,,,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,,,,854/864,	140858245	1570,5100	1134	2201	3335	SO:0001627	intron_variant	5098	exon1			ACTGGCCCTTCCT	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.2425-16129C>T	5.37:g.140858245C>T		Somatic	189	0	0	1659	WXS	Illumina HiSeq	Phase_I	186	88	0.473118	NM_032402	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																			C|0.789;T|0.211	0.211	strong		0.438	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
ANKK1	255239	hgsc.bcm.edu	37	11	113270828	113270828	+	Missense_Mutation	SNP	G	G	A	rs1800497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:113270828G>A	ENST00000303941.3	+	8	2231	c.2137G>A	c.(2137-2139)Gag>Aag	p.E713K		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	713			E -> K (in dbSNP:rs1800497). {ECO:0000269|PubMed:14741327, ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		AGTGCTGGTCGAGGCAGGCGC	0.637													A|||	1631	0.325679	0.385	0.3112	5008	,	,		20348	0.4058		0.1879	False		,,,				2504	0.3149				p.E713K		Atlas-SNP	.											.	ANKK1	83	.	0			c.G2137A	GRCh37	CM041241	ANKK1	M	rs1800497	PASS	.	A	LYS/GLU	1351,2783		230,891,946	21.0	26.0	24.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2137	2.0	0.1	11	dbSNP_89	24	1598,6796		160,1278,2759	yes	missense	ANKK1	NM_178510.1	56	390,2169,3705	AA,AG,GG		19.0374,32.6802,23.5393	benign	713/766	113270828	2949,9579	2067	4197	6264	SO:0001583	missense	255239	exon8			CTGGTCGAGGCAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.2137G>A	11.37:g.113270828G>A	ENSP00000306678:p.Glu713Lys	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	192	80	0.416667	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	647	0.29624542124542125	188	0.3821138211382114	100	0.27624309392265195	222	0.3881118881118881	137	0.18073878627968337	A	0.006	-2.089378	0.00367	0.326802	0.190374	ENSG00000170209	ENST00000303941	T	0.65732	-0.17	4.42	1.98	0.26296	Ankyrin repeat-containing domain (3);	0.914415	0.09102	N	0.848445	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33137	-0.9880	9	0.05833	T	0.94	-2.6564	1.1851	0.01854	0.5313:0.1533:0.1676:0.1478	rs1800497;rs4134623;rs4245144;rs59538675;rs1800497	713	Q8NFD2	ANKK1_HUMAN	K	713	ENSP00000306678:E713K	ENSP00000306678:E713K	E	+	1	0	ANKK1	112776038	0.001000	0.12720	0.054000	0.19295	0.051000	0.14879	0.411000	0.21115	-0.053000	0.13289	-0.439000	0.05793	GAG	G|0.703;A|0.297	0.297	strong		0.637	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
OR10G3	26533	hgsc.bcm.edu	37	14	22038276	22038276	+	Silent	SNP	C	C	T	rs28436899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:22038276C>T	ENST00000303532.1	-	1	599	c.600G>A	c.(598-600)acG>acA	p.T200T		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	200						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)		TGTCTACAAACGTCACCAGCT	0.522													c|||	115	0.0229633	0.0794	0.013	5008	,	,		19542	0.0		0.0	False		,,,				2504	0.001				p.T200T		Atlas-SNP	.											.	OR10G3	40	.	0			c.G600A						PASS	.	T		261,4145	148.8+/-183.1	5,251,1947	196.0	188.0	191.0		600	-0.4	1.0	14	dbSNP_125	191	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	OR10G3	NM_001005465.1		5,261,6237	TT,TC,CC		0.1163,5.9237,2.0837		200/314	22038276	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			TACAAACGTCACC		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.600G>A	14.37:g.22038276C>T		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	239	132	0.552301	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			C|0.978;T|0.022	0.022	strong		0.522	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
WDR93	56964	hgsc.bcm.edu	37	15	90245253	90245253	+	Silent	SNP	C	C	T	rs4316730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90245253C>T	ENST00000268130.7	+	2	377	c.276C>T	c.(274-276)acC>acT	p.T92T	RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Silent_p.T92T|WDR93_ENST00000558000.1_Silent_p.T92T	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	92					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)			TCCAGCCCACCGTCTACCCTC	0.483													C|||	1986	0.396565	0.5234	0.3631	5008	,	,		19440	0.2063		0.4026	False		,,,				2504	0.4387				p.T92T		Atlas-SNP	.											.	WDR93	63	.	0			c.C276T						PASS	.	C		2200,2200	588.5+/-386.9	559,1082,559	51.0	55.0	53.0		276	-3.0	0.0	15	dbSNP_111	53	3847,4751	540.1+/-383.7	846,2155,1298	yes	coding-synonymous	WDR93	NM_020212.1		1405,3237,1857	TT,TC,CC		44.743,50.0,46.5225		92/687	90245253	6047,6951	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon2			GCCCACCGTCTAC		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.276C>T	15.37:g.90245253C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			C|0.564;T|0.436	0.436	strong		0.483	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
MFI2	4241	hgsc.bcm.edu	37	3	196743130	196743130	+	Silent	SNP	T	T	C	rs6779362	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:196743130T>C	ENST00000296350.5	-	8	1124	c.1011A>G	c.(1009-1011)acA>acG	p.T337T		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	337	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)	p.T337T(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		CATAGGTCTGTGTGGCGATGG	0.592													C|||	1598	0.319089	0.4743	0.2046	5008	,	,		20505	0.2976		0.2455	False		,,,				2504	0.2883				p.T337T		Atlas-SNP	.											MFI2,NS,carcinoma,0,1	MFI2	88	1	1	Substitution - coding silent(1)	prostate(1)	c.A1011G						PASS	.	C		1920,2486	626.5+/-394.7	422,1076,705	99.0	90.0	93.0		1011	-9.7	0.4	3	dbSNP_116	93	2006,6594	721.7+/-406.4	243,1520,2537	no	coding-synonymous	MFI2	NM_005929.5		665,2596,3242	CC,CT,TT		23.3256,43.5769,30.1861		337/739	196743130	3926,9080	2203	4300	6503	SO:0001819	synonymous_variant	4241	exon8			GGTCTGTGTGGCG		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.1011A>G	3.37:g.196743130T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_005929	Q9BQE2	Silent	SNP	ENST00000296350.5	37	CCDS3325.1																																																																																			T|0.686;C|0.314	0.314	strong		0.592	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
EMILIN3	90187	hgsc.bcm.edu	37	20	39991171	39991171	+	Silent	SNP	G	G	A	rs61739307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:39991171G>A	ENST00000332312.3	-	4	1230	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	346						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TCCGGCTGGCGGCCTGACCCT	0.672													G|||	405	0.0808706	0.059	0.1225	5008	,	,		14633	0.003		0.1799	False		,,,				2504	0.0593				p.A346A		Atlas-SNP	.											EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	0			c.C1038T						PASS	.	G		390,4012		16,358,1827	15.0	17.0	16.0		1038	-10.3	0.2	20	dbSNP_129	16	1433,7165		130,1173,2996	no	coding-synonymous	EMILIN3	NM_052846.1		146,1531,4823	AA,AG,GG		16.6667,8.8596,14.0231		346/767	39991171	1823,11177	2201	4299	6500	SO:0001819	synonymous_variant	90187	exon4			GCTGGCGGCCTGA	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1038C>T	20.37:g.39991171G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			G|0.883;A|0.117	0.117	strong		0.672	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
PPIL3	53938	hgsc.bcm.edu	37	2	201736166	201736166	+	Missense_Mutation	SNP	A	A	C	rs7562391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:201736166A>C	ENST00000392283.4	-	7	706	c.438T>G	c.(436-438)gaT>gaG	p.D146E	PPIL3_ENST00000465823.1_5'UTR|PPIL3_ENST00000409449.1_Missense_Mutation_p.D150E|PPIL3_ENST00000286175.8_Missense_Mutation_p.D150E|PPIL3_ENST00000409361.1_Missense_Mutation_p.D142E	NM_130906.2	NP_570981.1	Q9H2H8	PPIL3_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 3	146	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.		D -> E (in dbSNP:rs7562391). {ECO:0000269|PubMed:15489334}.		mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|lung(2)	3						TAATGTGTACATCATTAAGAG	0.383													A|||	882	0.176118	0.4523	0.1268	5008	,	,		18242	0.0139		0.1441	False		,,,				2504	0.0378				p.D150E		Atlas-SNP	.											.	PPIL3	20	.	0			c.T450G						PASS	.	A	GLU/ASP,GLU/ASP	1639,2767	502.9+/-365.4	312,1015,876	214.0	186.0	196.0		450,438	1.1	1.0	2	dbSNP_116	196	1100,7500	229.0+/-263.8	66,968,3266	yes	missense,missense	PPIL3	NM_032472.3,NM_130906.2	45,45	378,1983,4142	CC,CA,AA		12.7907,37.1993,21.0595	benign,benign	150/166,146/162	201736166	2739,10267	2203	4300	6503	SO:0001583	missense	53938	exon7			GTGTACATCATTA	AF251049	CCDS2332.1, CCDS2333.1	2q33.1	2008-02-05			ENSG00000240344	ENSG00000240344			9262	protein-coding gene	gene with protein product	"""Cyclophilin J"""	615811				11435694	Standard	NM_032472		Approved	CyPJ	uc002uwi.3	Q9H2H8	OTTHUMG00000132782	ENST00000392283.4:c.438T>G	2.37:g.201736166A>C	ENSP00000376107:p.Asp146Glu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_032472	Q86WF9|Q96IA9|Q9BXZ1	Missense_Mutation	SNP	ENST00000392283.4	37	CCDS2333.1	366	0.16758241758241757	203	0.41260162601626016	45	0.12430939226519337	2	0.0034965034965034965	116	0.15303430079155672	A	8.989	0.977153	0.18812	0.371993	0.127907	ENSG00000240344	ENST00000286175;ENST00000392283;ENST00000409264;ENST00000409361;ENST00000409449	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.94	1.14	0.20703	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.135826	0.64402	D	0.000003	T	0.00012	0.0000	N	0.16307	0.4	0.19945	P	0.9999463824	B;B	0.06786	0.001;0.0	B;B	0.09377	0.001;0.004	T	0.46456	-0.9190	9	0.10377	T	0.69	.	6.0387	0.19722	0.5787:0.0:0.306:0.1153	rs7562391;rs17856221;rs52806646;rs61324596;rs7562391	150;146	Q9H2H8-2;Q9H2H8	.;PPIL3_HUMAN	E	150;146;165;142;150	ENSP00000286175:D150E;ENSP00000376107:D146E;ENSP00000386893:D165E;ENSP00000386235:D142E;ENSP00000387012:D150E	ENSP00000286175:D150E	D	-	3	2	PPIL3	201444411	0.987000	0.35691	1.000000	0.80357	0.997000	0.91878	0.345000	0.19979	0.509000	0.28195	0.528000	0.53228	GAT	A|0.804;C|0.196	0.196	strong		0.383	PPIL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256190.3		
GPR55	9290	hgsc.bcm.edu	37	2	231775094	231775094	+	Missense_Mutation	SNP	C	C	A	rs3749073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:231775094C>A	ENST00000392040.1	-	2	776	c.584G>T	c.(583-585)gGc>gTc	p.G195V	GPR55_ENST00000392039.2_Missense_Mutation_p.G195V|AC012507.4_ENST00000454890.1_RNA	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	195			G -> V (in dbSNP:rs3749073).		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)		GCCCATGATGCCCATGGGAAG	0.557													C|||	1019	0.203474	0.3933	0.0706	5008	,	,		20006	0.1508		0.0795	False		,,,				2504	0.2229				p.G195V		Atlas-SNP	.											.	GPR55	46	.	0			c.G584T						PASS	.	C	VAL/GLY	1451,2955	467.2+/-354.7	249,953,1001	104.0	107.0	106.0		584	-0.7	0.1	2	dbSNP_107	106	798,7802	185.9+/-233.5	49,700,3551	yes	missense	GPR55	NM_005683.3	109	298,1653,4552	AA,AC,CC		9.2791,32.9324,17.292	benign	195/320	231775094	2249,10757	2203	4300	6503	SO:0001583	missense	9290	exon2			ATGATGCCCATGG	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.584G>T	2.37:g.231775094C>A	ENSP00000375894:p.Gly195Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_005683	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	37	CCDS2480.1	363	0.1662087912087912	185	0.37601626016260165	30	0.08287292817679558	88	0.15384615384615385	60	0.079155672823219	C	6.753	0.507776	0.12883	0.329324	0.092791	ENSG00000135898	ENST00000392040;ENST00000392039;ENST00000438398	T;T;T	0.34072	1.38;1.38;1.38	5.38	-0.722	0.11184	GPCR, rhodopsin-like superfamily (1);	0.956087	0.08756	N	0.898327	T	0.00012	0.0000	N	0.04260	-0.245	0.26930	P	0.9664926	B	0.18166	0.026	B	0.21546	0.035	T	0.48007	-0.9072	9	0.22109	T	0.4	-14.9729	11.6395	0.51224	0.2027:0.1763:0.6211:0.0	rs3749073;rs56725961;rs3749073	195	Q9Y2T6	GPR55_HUMAN	V	195	ENSP00000375894:G195V;ENSP00000375893:G195V;ENSP00000412768:G195V	ENSP00000375893:G195V	G	-	2	0	GPR55	231483338	0.000000	0.05858	0.056000	0.19401	0.989000	0.77384	0.008000	0.13197	-0.142000	0.11354	0.561000	0.74099	GGC	C|0.826;A|0.174	0.174	strong		0.557	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
DBX1	120237	hgsc.bcm.edu	37	11	20178717	20178717	+	Silent	SNP	G	G	T	rs831464	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	38	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	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	
RAB3GAP1	22930	hgsc.bcm.edu	37	2	135911422	135911422	+	Silent	SNP	T	T	C	rs17261772	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:135911422T>C	ENST00000264158.8	+	19	2308	c.2265T>C	c.(2263-2265)ttT>ttC	p.F755F	RAB3GAP1_ENST00000539493.1_Silent_p.F711F|ZRANB3_ENST00000412849.1_Intron|RAB3GAP1_ENST00000442034.1_Silent_p.F755F|RAB3GAP1_ENST00000487003.1_3'UTR	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	755					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		GGAGACTCTTTGATGATACAC	0.423													C|||	3940	0.786741	0.9705	0.6542	5008	,	,		19434	1.0		0.4145	False		,,,				2504	0.7955				p.F755F		Atlas-SNP	.											.	RAB3GAP1	87	.	0			c.T2265C						PASS	.	C	,	3724,682		1586,552,65	97.0	93.0	94.0		2265,2265	1.9	1.0	2	dbSNP_123	94	2658,5942		505,1648,2147	yes	coding-synonymous,coding-synonymous	RAB3GAP1	NM_001172435.1,NM_012233.2	,	2091,2200,2212	CC,CT,TT		30.907,15.4789,49.0697	,	755/989,755/982	135911422	6382,6624	2203	4300	6503	SO:0001819	synonymous_variant	22930	exon19			ACTCTTTGATGAT	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.2265T>C	2.37:g.135911422T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001172435	A6H8Z3|C9J837|Q659F5|Q8TBB4	Silent	SNP	ENST00000264158.8	37	CCDS33294.1																																																																																			C|0.626;G|0.000;T|0.374	0.626	strong		0.423	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233	
ARAP3	64411	hgsc.bcm.edu	37	5	141059868	141059868	+	Silent	SNP	T	T	C	rs11167756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:141059868T>C	ENST00000239440.4	-	2	251	c.186A>G	c.(184-186)ctA>ctG	p.L62L	ARAP3_ENST00000508305.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	62	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TGCCTGTCTGTAGCAGGCGTA	0.652													C|||	2332	0.465655	0.4493	0.4942	5008	,	,		15776	0.4683		0.4274	False		,,,				2504	0.5041				p.L62L		Atlas-SNP	.											.	ARAP3	139	.	0			c.A186G						PASS	.	C		1957,2449	619.1+/-393.3	439,1079,685	83.0	88.0	87.0		186	0.2	0.9	5	dbSNP_120	87	3613,4987	625.1+/-397.7	778,2057,1465	yes	coding-synonymous	ARAP3	NM_022481.5		1217,3136,2150	CC,CT,TT		42.0116,44.4167,42.8264		62/1545	141059868	5570,7436	2203	4300	6503	SO:0001819	synonymous_variant	64411	exon2			TGTCTGTAGCAGG	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.186A>G	5.37:g.141059868T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	225	107	0.475556	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			T|0.567;C|0.433	0.433	strong		0.652	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
LRRN2	10446	hgsc.bcm.edu	37	1	204587569	204587569	+	Missense_Mutation	SNP	G	G	C	rs3747631	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204587569G>C	ENST00000367175.1	-	1	3764	c.1552C>G	c.(1552-1554)Ctc>Gtc	p.L518V	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367176.3_Missense_Mutation_p.L518V|LRRN2_ENST00000367177.3_Missense_Mutation_p.L518V			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	518			L -> V (in dbSNP:rs3747631).		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GGCTGGAGGAGAGCACGGCCC	0.627													G|||	925	0.184704	0.0575	0.0922	5008	,	,		16939	0.3095		0.2237	False		,,,				2504	0.2536				p.L518V		Atlas-SNP	.											.	LRRN2	81	.	0			c.C1552G						PASS	.	G	VAL/LEU,VAL/LEU	358,4048	184.3+/-211.7	16,326,1861	77.0	73.0	74.0		1552,1552	3.5	0.9	1	dbSNP_107	74	1835,6765	329.0+/-318.6	182,1471,2647	yes	missense,missense	LRRN2	NM_006338.2,NM_201630.1	32,32	198,1797,4508	CC,CG,GG		21.3372,8.1253,16.8614	benign,benign	518/714,518/714	204587569	2193,10813	2203	4300	6503	SO:0001583	missense	10446	exon3			GGAGGAGAGCACG	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1552C>G	1.37:g.204587569G>C	ENSP00000356143:p.Leu518Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	418	0.19139194139194138	38	0.07723577235772358	39	0.10773480662983426	172	0.3006993006993007	169	0.22295514511873352	G	2.932	-0.220842	0.06061	0.081253	0.213372	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.59906	0.23;0.23;0.23	5.35	3.45	0.39498	.	0.433987	0.17130	N	0.185858	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.26326	-1.0106	9	0.16420	T	0.52	.	10.4948	0.44770	0.0738:0.1345:0.7917:0.0	rs3747631;rs57267382	518	O75325	LRRN2_HUMAN	V	518	ENSP00000356144:L518V;ENSP00000356145:L518V;ENSP00000356143:L518V	ENSP00000356143:L518V	L	-	1	0	LRRN2	202854192	0.998000	0.40836	0.865000	0.33974	0.693000	0.40251	2.784000	0.47774	0.624000	0.30286	-0.386000	0.06593	CTC	G|0.818;C|0.182	0.182	strong		0.627	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
GLYATL3	389396	hgsc.bcm.edu	37	6	49485266	49485266	+	Missense_Mutation	SNP	C	C	A	rs9367358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:49485266C>A	ENST00000371197.4	+	4	423	c.310C>A	c.(310-312)Caa>Aaa	p.Q104K		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	104				Q -> K (in Ref. 1; AK126371). {ECO:0000305}.		mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						TTTTCAAATACAAGGTGAGGT	0.328													C|||	1292	0.257987	0.0121	0.451	5008	,	,		18212	0.499		0.2018	False		,,,				2504	0.2628				p.Q104K		Atlas-SNP	.											.	GLYATL3	19	.	0			c.C310A						PASS	.	C	LYS/GLN	46,1338		0,46,646	163.0	136.0	144.0		310	6.0	1.0	6	dbSNP_119	144	624,2558		61,502,1028	yes	missense	GLYATL3	NM_001010904.1	53	61,548,1674	AA,AC,CC		19.6103,3.3237,14.6737	possibly-damaging	104/289	49485266	670,3896	692	1591	2283	SO:0001583	missense	389396	exon4			CAAATACAAGGTG		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.310C>A	6.37:g.49485266C>A	ENSP00000360240:p.Gln104Lys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	622	0.2847985347985348	12	0.024390243902439025	151	0.4171270718232044	319	0.5576923076923077	140	0.18469656992084432	C	17.64	3.440813	0.63067	0.033237	0.196103	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.22336	1.96;1.96	6.01	6.01	0.97437	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	.	.	.	.	T	0.13372	0.0324	M	0.76574	2.34	0.30797	P	0.740263	B	0.28419	0.211	B	0.31547	0.132	T	0.05818	-1.0862	8	0.07030	T	0.85	-4.5353	16.0184	0.80460	0.0:1.0:0.0:0.0	rs9367358;rs52838191;rs60437869;rs9367358	104	Q5SZD4	GLYL3_HUMAN	K	104	ENSP00000360240:Q104K;ENSP00000440029:Q104K	ENSP00000360240:Q104K	Q	+	1	0	GLYATL3	49593225	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.197000	0.58413	2.860000	0.98153	0.655000	0.94253	CAA	C|0.732;A|0.268	0.268	strong		0.328	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
NWD1	284434	hgsc.bcm.edu	37	19	16890243	16890243	+	Missense_Mutation	SNP	C	C	G	rs773930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:16890243C>G	ENST00000552788.1	+	10	2698	c.2698C>G	c.(2698-2700)Cag>Gag	p.Q900E	NWD1_ENST00000549814.1_Missense_Mutation_p.Q900E|NWD1_ENST00000524140.2_Missense_Mutation_p.Q900E|NWD1_ENST00000339803.6_Missense_Mutation_p.Q765E|NWD1_ENST00000523826.1_Missense_Mutation_p.Q694E|NWD1_ENST00000379808.3_Missense_Mutation_p.Q900E			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	57	0	0	713	WXS	Illumina HiSeq	Phase_I	68	23	0.338235	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	
SPZ1	84654	hgsc.bcm.edu	37	5	79616544	79616544	+	Missense_Mutation	SNP	G	G	A	rs2047589	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79616544G>A	ENST00000296739.4	+	1	755	c.510G>A	c.(508-510)atG>atA	p.M170I		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	170	Helix-loop-helix motif. {ECO:0000255}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		TCAATGAAATGTTATCAACAA	0.378													G|||	158	0.0315495	0.0045	0.0331	5008	,	,		18379	0.0		0.0905	False		,,,				2504	0.0389				p.M170I		Atlas-SNP	.											.	SPZ1	60	.	0			c.G510A						PASS	.	G	ILE/MET	84,3542		0,84,1729	55.0	48.0	50.0		510	-1.4	0.0	5	dbSNP_94	50	796,7342		38,720,3311	no	missense	SPZ1	NM_032567.3	10	38,804,5040	AA,AG,GG		9.7813,2.3166,7.4804	benign	170/431	79616544	880,10884	1813	4069	5882	SO:0001583	missense	84654	exon1			TGAAATGTTATCA		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.510G>A	5.37:g.79616544G>A	ENSP00000369611:p.Met170Ile	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	243	111	0.45679	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	90	0.04120879120879121	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	71	0.09366754617414248	G	1.860	-0.462981	0.04476	0.023166	0.097813	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.41400	1.0;1.65	2.67	-1.38	0.09027	.	0.851711	0.09948	N	0.735019	T	0.00524	0.0017	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.15435	-1.0437	9	0.36615	T	0.2	-14.9516	7.2498	0.26142	0.6148:0.0:0.3852:0.0	rs2047589	170	Q9BXG8	SPZ1_HUMAN	I	170	ENSP00000426530:M170I;ENSP00000369611:M170I	ENSP00000369611:M170I	M	+	3	0	SPZ1	79652300	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.535000	0.06142	-0.271000	0.09272	0.494000	0.49563	ATG	G|0.941;A|0.059	0.059	strong		0.378	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
MOV10L1	54456	hgsc.bcm.edu	37	22	50588131	50588131	+	Silent	SNP	C	C	T	rs138271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50588131C>T	ENST00000262794.5	+	20	2798	c.2715C>T	c.(2713-2715)gaC>gaT	p.D905D	MOV10L1_ENST00000395843.1_Silent_p.D3D|MOV10L1_ENST00000545383.1_Silent_p.D905D|MOV10L1_ENST00000395858.3_Silent_p.D905D|MOV10L1_ENST00000354853.2_Silent_p.D3D|MOV10L1_ENST00000540615.1_Silent_p.D885D|MOV10L1_ENST00000395852.1_Silent_p.D32D	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	905					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGATGTCGGACATCAGTGGCC	0.582											OREG0026674	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	641	0.127995	0.0431	0.1974	5008	,	,		18773	0.0109		0.2823	False		,,,				2504	0.1554				p.D905D		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C2715T						PASS	.	C	,,,	408,3996	201.1+/-224.2	15,378,1809	134.0	99.0	111.0		2715,2655,96,2715	-4.9	0.0	22	dbSNP_78	111	2783,5817	437.4+/-358.6	429,1925,1946	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_001164106.1,NM_018995.2	,,,	444,2303,3755	TT,TC,CC		32.3605,9.2643,24.5386	,,,	905/1166,885/1166,32/339,905/1212	50588131	3191,9813	2202	4300	6502	SO:0001819	synonymous_variant	54456	exon20			GTCGGACATCAGT	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2715C>T	22.37:g.50588131C>T		Somatic	110	0	0	970	WXS	Illumina HiSeq	Phase_I	123	71	0.577236	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.799;T|0.201	0.201	strong		0.582	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
MMP27	64066	hgsc.bcm.edu	37	11	102563739	102563739	+	Silent	SNP	C	C	T	rs1276289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102563739C>T	ENST00000260229.4	-	9	1318	c.1227G>A	c.(1225-1227)ggG>ggA	p.G409G		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	409					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TCTGCGGGAACCCTTTGTCCA	0.438													C|||	2254	0.45008	0.2186	0.5072	5008	,	,		19176	0.629		0.4453	False		,,,				2504	0.5429				p.G409G		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	0			c.G1227A						PASS	.	C		1205,3201	419.8+/-338.8	150,905,1148	193.0	181.0	185.0		1227	-5.4	0.3	11	dbSNP_87	185	3891,4707	544.7+/-384.6	858,2175,1266	no	coding-synonymous	MMP27	NM_022122.2		1008,3080,2414	TT,TC,CC		45.2547,27.3491,39.1879		409/514	102563739	5096,7908	2203	4299	6502	SO:0001819	synonymous_variant	64066	exon9			CGGGAACCCTTTG	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.1227G>A	11.37:g.102563739C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																			C|0.594;T|0.406	0.406	strong		0.438	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
SLC51A	200931	hgsc.bcm.edu	37	3	195956827	195956827	+	Silent	SNP	T	T	C	rs17852687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195956827T>C	ENST00000296327.5	+	7	884	c.675T>C	c.(673-675)ctT>ctC	p.L225L	PCYT1A_ENST00000419333.1_3'UTR	NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	225					bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	ACACTTTCCTTGGCGTGTCCA	0.537													C|||	2492	0.497604	0.3222	0.4914	5008	,	,		17557	0.7897		0.4394	False		,,,				2504	0.498				p.L225L		Atlas-SNP	.											.	.	.	.	0			c.T675C						PASS	.	C		1527,2879	674.0+/-402.9	244,1039,920	120.0	106.0	111.0		675	-11.7	0.0	3	dbSNP_123	111	3818,4782	612.9+/-396.0	870,2078,1352	no	coding-synonymous	OSTalpha	NM_152672.5		1114,3117,2272	CC,CT,TT		44.3953,34.6573,41.0964		225/341	195956827	5345,7661	2203	4300	6503	SO:0001819	synonymous_variant	200931	exon7			TTTCCTTGGCGTG		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"""Solute carriers"""	29955	protein-coding gene	gene with protein product	"""organic solute transporter, alpha subunit"""	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.675T>C	3.37:g.195956827T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_152672	Q6ZMC7	Silent	SNP	ENST00000296327.5	37	CCDS3314.1																																																																																			T|0.544;C|0.456	0.456	strong		0.537	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672	
DDX53	168400	hgsc.bcm.edu	37	X	23019346	23019346	+	Missense_Mutation	SNP	G	G	T	rs5926203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	35	0	0		WXS	Illumina HiSeq	Phase_I	45	45	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	
CARD10	29775	hgsc.bcm.edu	37	22	37900243	37900243	+	Silent	SNP	G	G	A	rs3817802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37900243G>A	ENST00000403299.1	-	10	1800	c.1584C>T	c.(1582-1584)gcC>gcT	p.A528A	CARD10_ENST00000406271.3_Silent_p.A242A|CARD10_ENST00000251973.5_Silent_p.A528A			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	528					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GGATGGAGCCGGCACTGGGGG	0.642													G|||	254	0.0507188	0.0885	0.0288	5008	,	,		17760	0.0347		0.0596	False		,,,				2504	0.0225				p.A528A		Atlas-SNP	.											.	CARD10	55	.	0			c.C1584T						PASS	.	G		306,4080		9,288,1896	46.0	45.0	45.0		1584	-10.9	0.0	22	dbSNP_107	45	465,8111		12,441,3835	no	coding-synonymous	CARD10	NM_014550.3		21,729,5731	AA,AG,GG		5.4221,6.9767,5.9482		528/1033	37900243	771,12191	2193	4288	6481	SO:0001819	synonymous_variant	29775	exon9			GGAGCCGGCACTG	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1584C>T	22.37:g.37900243G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			A|0.060;C|0.000;G|0.939	0.060	strong		0.642	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
ATP9B	374868	hgsc.bcm.edu	37	18	77067000	77067000	+	Silent	SNP	T	T	G	rs3760541	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:77067000T>G	ENST00000426216.2	+	15	1556	c.1539T>G	c.(1537-1539)gcT>gcG	p.A513A	ATP9B_ENST00000307671.7_Silent_p.A513A	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	513					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)		AGTCTCAAGCTGGTGGAAACA	0.358													T|||	2020	0.403355	0.3623	0.4481	5008	,	,		20069	0.38		0.4483	False		,,,				2504	0.4049				p.A513A		Atlas-SNP	.											.	ATP9B	96	.	0			c.T1539G						PASS	.	T		1699,2707	509.4+/-367.2	338,1023,842	69.0	65.0	66.0		1539	-1.6	0.0	18	dbSNP_107	66	3792,4808	536.0+/-382.9	855,2082,1363	no	coding-synonymous	ATP9B	NM_198531.3		1193,3105,2205	GG,GT,TT		44.093,38.5611,42.219		513/1148	77067000	5491,7515	2203	4300	6503	SO:0001819	synonymous_variant	374868	exon15			TCAAGCTGGTGGA	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.1539T>G	18.37:g.77067000T>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_198531	O60872|Q08AD8|Q08AD9	Silent	SNP	ENST00000426216.2	37	CCDS12014.1																																																																																			T|0.570;G|0.430	0.430	strong		0.358	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
DND1	373863	hgsc.bcm.edu	37	5	140050907	140050907	+	Missense_Mutation	SNP	C	C	T	rs148639416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140050907C>T	ENST00000542735.1	-	4	1076	c.1033G>A	c.(1033-1035)Gct>Act	p.A345T	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	345					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)			CCTGCCTCAGCCCCAGCAGAC	0.602																																					p.A345T		Atlas-SNP	.											.	DND1	15	.	0			c.G1033A						PASS	.						77.0	65.0	69.0					5																	140050907		1940	3940	5880	SO:0001583	missense	373863	exon4			CCTCAGCCCCAGC	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.1033G>A	5.37:g.140050907C>T	ENSP00000445366:p.Ala345Thr	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	764	132	0.172775	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.525451	0.27299	.	.	ENSG00000256453	ENST00000542735	T	0.34859	1.34	4.97	4.97	0.65823	.	0.357138	0.23704	N	0.045400	T	0.26268	0.0641	N	0.19112	0.55	0.27565	N	0.950072	B	0.26635	0.155	B	0.25759	0.063	T	0.24764	-1.0151	10	0.72032	D	0.01	-6.3441	13.9714	0.64242	0.0:1.0:0.0:0.0	.	345	Q8IYX4	DND1_HUMAN	T	345	ENSP00000445366:A345T	ENSP00000445366:A345T	A	-	1	0	DND1	140031091	0.814000	0.29104	1.000000	0.80357	0.382000	0.30200	0.973000	0.29422	2.750000	0.94351	0.551000	0.68910	GCT	.	.	weak		0.602	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
AKAP11	11215	hgsc.bcm.edu	37	13	42875258	42875258	+	Silent	SNP	T	T	C	rs61741710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42875258T>C	ENST00000025301.2	+	8	2551	c.2376T>C	c.(2374-2376)taT>taC	p.Y792Y		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	792					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)		TTCTCCCATATCATATTTCAT	0.418													T|||	55	0.0109824	0.003	0.0029	5008	,	,		19247	0.001		0.0099	False		,,,				2504	0.0389				p.Y792Y		Atlas-SNP	.											.	AKAP11	146	.	0			c.T2376C						PASS	.	T		19,4387	26.2+/-53.5	0,19,2184	145.0	129.0	135.0		2376	0.9	0.3	13	dbSNP_129	135	84,8516	48.5+/-108.0	0,84,4216	no	coding-synonymous	AKAP11	NM_016248.3		0,103,6400	CC,CT,TT		0.9767,0.4312,0.7919		792/1902	42875258	103,12903	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			CCCATATCATATT	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.2376T>C	13.37:g.42875258T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			T|0.992;C|0.008	0.008	strong		0.418	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
TAP2	6891	hgsc.bcm.edu	37	6	32800224	32800224	+	Silent	SNP	C	C	A	rs2228397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32800224C>A	ENST00000452392.2	-	7	1331	c.1158G>T	c.(1156-1158)ggG>ggT	p.G386G	TAP2_ENST00000374899.4_Silent_p.G386G|TAP2_ENST00000485701.1_5'UTR|TAP2_ENST00000374897.2_Silent_p.G386G			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	GCATCTGCACCCCCAAGTGCA	0.567													C|||	1223	0.244209	0.1967	0.3112	5008	,	,		17033	0.248		0.2227	False		,,,				2504	0.2791				p.G386G		Atlas-SNP	.											.	TAP2	98	.	0			c.G1158T						PASS	.	C	,	706,2312		90,526,893	41.0	37.0	38.0		1158,1158	-10.9	0.0	6	dbSNP_98	38	1342,4076		160,1022,1527	no	coding-synonymous,coding-synonymous	TAP2	NM_000544.3,NM_018833.2	,	250,1548,2420	AA,AC,CC		24.7693,23.393,24.2769	,	386/704,386/654	32800224	2048,6388	1509	2709	4218	SO:0001819	synonymous_variant	6891	exon7			CTGCACCCCCAAG	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1158G>T	6.37:g.32800224C>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000452392.2	37																																																																																				C|0.750;A|0.250	0.250	strong		0.567	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97922851	97922851	+	Silent	SNP	C	C	T	rs12728	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97922851C>T	ENST00000005260.8	-	14	1733	c.1518G>A	c.(1516-1518)tcG>tcA	p.S506S		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	506	Binds F-actin.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			TGATGGGTGCCGAGCGATCAT	0.562													C|||	1333	0.266174	0.1392	0.3458	5008	,	,		16342	0.2688		0.4801	False		,,,				2504	0.1585				p.S506S		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.G1518A						PASS	.	C		881,3525	341.2+/-306.6	84,713,1406	128.0	125.0	126.0		1518	-9.9	0.2	7	dbSNP_52	126	4338,4262	580.7+/-391.1	1103,2132,1065	no	coding-synonymous	BAIAP2L1	NM_018842.4		1187,2845,2471	TT,TC,CC		49.5581,19.9955,40.1276		506/512	97922851	5219,7787	2203	4300	6503	SO:0001819	synonymous_variant	55971	exon14			GGGTGCCGAGCGA	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1518G>A	7.37:g.97922851C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			C|0.634;T|0.366	0.366	strong		0.562	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
ABCC3	8714	hgsc.bcm.edu	37	17	48753423	48753423	+	Silent	SNP	C	C	T	rs4148416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48753423C>T	ENST00000285238.8	+	22	3119	c.3039C>T	c.(3037-3039)ggC>ggT	p.G1013G	ABCC3_ENST00000510891.1_3'UTR	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1013	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TGAGGCTGGGCGTCTATGCTG	0.562													C|||	686	0.136981	0.2254	0.0951	5008	,	,		21999	0.1567		0.0497	False		,,,				2504	0.1166				p.G1013G		Atlas-SNP	.											.	ABCC3	138	.	0			c.C3039T						PASS	.	C		850,3556	336.0+/-304.2	79,692,1432	84.0	74.0	77.0		3039	-11.8	0.0	17	dbSNP_110	77	463,8137	137.0+/-194.0	9,445,3846	no	coding-synonymous	ABCC3	NM_003786.3		88,1137,5278	TT,TC,CC		5.3837,19.2919,10.0953		1013/1528	48753423	1313,11693	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon22			GCTGGGCGTCTAT	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.3039C>T	17.37:g.48753423C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1	223	0.1021062271062271	80	0.16260162601626016	35	0.09668508287292818	75	0.13111888111888112	33	0.04353562005277045	C	0.502	-0.870347	0.02570	0.192919	0.053837	ENSG00000108846	ENST00000513745	.	.	.	5.88	-11.8	0.00035	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.99999999076842	.	.	.	.	.	.	T	0.02617	-1.1133	3	.	.	.	-18.5963	4.1202	0.10101	0.431:0.1244:0.0553:0.3894	rs4148416;rs4148416	.	.	.	C	162	.	.	R	+	1	0	ABCC3	46108422	0.000000	0.05858	0.028000	0.17463	0.177000	0.22998	-3.861000	0.00348	-3.862000	0.00098	-0.812000	0.03155	CGT	C|0.893;T|0.107	0.107	strong		0.562	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
MOV10	4343	hgsc.bcm.edu	37	1	113237171	113237171	+	Silent	SNP	A	A	G	rs883593	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:113237171A>G	ENST00000413052.2	+	9	1782	c.1392A>G	c.(1390-1392)acA>acG	p.T464T	MOV10_ENST00000369645.1_Silent_p.T464T|MOV10_ENST00000357443.2_Silent_p.T464T|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.T408T|RP11-426L16.3_ENST00000421943.1_RNA	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	464					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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		TGGAGCTGACAGGGCGCTGGC	0.617													G|||	1426	0.284744	0.1672	0.2911	5008	,	,		17708	0.5427		0.2346	False		,,,				2504	0.2249				p.T464T		Atlas-SNP	.											MOV10,NS,carcinoma,0,1	MOV10	74	1	0			c.A1392G						PASS	.	G	,	803,3603	743.3+/-411.4	83,637,1483	39.0	38.0	38.0		1392,1392	-10.2	0.3	1	dbSNP_86	38	1763,6837	726.8+/-406.6	180,1403,2717	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	263,2040,4200	GG,GA,AA		20.5,18.2251,19.7294	,	464/1004,464/1004	113237171	2566,10440	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon9			GCTGACAGGGCGC	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1392A>G	1.37:g.113237171A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			A|0.765;G|0.235	0.235	strong		0.617	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
IGSF5	150084	hgsc.bcm.edu	37	21	41137499	41137499	+	Silent	SNP	A	A	G	rs12626544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	76	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	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		
DNAJC15	29103	hgsc.bcm.edu	37	13	43639845	43639845	+	Silent	SNP	A	A	C	rs3783044	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:43639845A>C	ENST00000379221.2	+	2	556	c.132A>C	c.(130-132)ggA>ggC	p.G44G	DNAJC15_ENST00000474320.1_3'UTR	NM_013238.2	NP_037370.2	Q9Y5T4	DJC15_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 15	44					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)		TAGCTGTAGGACTGGGTGTTG	0.323													A|||	1285	0.256589	0.2005	0.2795	5008	,	,		16885	0.2212		0.2087	False		,,,				2504	0.4018				p.G44G		Atlas-SNP	.											.	DNAJC15	16	.	0			c.A132C						PASS	.	A		837,3569	330.7+/-301.6	66,705,1432	128.0	136.0	133.0		132	3.2	1.0	13	dbSNP_107	133	1721,6877	313.7+/-311.4	182,1357,2760	no	coding-synonymous	DNAJC15	NM_013238.2		248,2062,4192	CC,CA,AA		20.0163,18.9968,19.6709		44/151	43639845	2558,10446	2203	4299	6502	SO:0001819	synonymous_variant	29103	exon2			TGTAGGACTGGGT	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.132A>C	13.37:g.43639845A>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_013238	B2R4L0|Q5T219|Q6X963	Silent	SNP	ENST00000379221.2	37	CCDS9388.1																																																																																			A|0.790;C|0.210	0.210	strong		0.323	DNAJC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044709.2	NM_013238	
SMC5	23137	hgsc.bcm.edu	37	9	72933774	72933774	+	Missense_Mutation	SNP	A	A	G	rs11142365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:72933774A>G	ENST00000361138.5	+	15	2103	c.2045A>G	c.(2044-2046)cAt>cGt	p.H682R		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	682			H -> R (in dbSNP:rs11142365).		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						ACAAGCAAACATCTGGAGCAC	0.318													A|||	436	0.0870607	0.1664	0.0821	5008	,	,		16017	0.0139		0.1044	False		,,,				2504	0.0409				p.H682R		Atlas-SNP	.											.	SMC5	96	.	0			c.A2045G						PASS	.	A	ARG/HIS	670,3726		53,564,1581	48.0	50.0	49.0		2045	0.2	0.0	9	dbSNP_120	49	1012,7584		62,888,3348	no	missense	SMC5	NM_015110.3	29	115,1452,4929	GG,GA,AA		11.7729,15.2411,12.9464	benign	682/1102	72933774	1682,11310	2198	4298	6496	SO:0001583	missense	23137	exon15			GCAAACATCTGGA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.2045A>G	9.37:g.72933774A>G	ENSP00000354957:p.His682Arg	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	152	58	0.381579	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	210	0.09615384615384616	93	0.18902439024390244	32	0.08839779005524862	5	0.008741258741258742	80	0.10554089709762533	A	3.138	-0.176891	0.06380	0.152411	0.117729	ENSG00000198887	ENST00000361138	T	0.16196	2.36	5.3	0.161	0.14977	RecF/RecN/SMC (1);	1.282520	0.04800	N	0.433287	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.39375	-0.9617	9	0.17832	T	0.49	-0.7879	4.1705	0.10327	0.4124:0.0:0.2134:0.3742	rs11142365	682	Q8IY18	SMC5_HUMAN	R	682	ENSP00000354957:H682R	ENSP00000354957:H682R	H	+	2	0	SMC5	72123594	0.000000	0.05858	0.005000	0.12908	0.889000	0.51656	0.330000	0.19715	0.008000	0.14787	0.472000	0.43445	CAT	A|0.888;G|0.112	0.112	strong		0.318	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
OR14C36	127066	hgsc.bcm.edu	37	1	248512767	248512767	+	Missense_Mutation	SNP	G	G	T	rs28545014	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248512767G>T	ENST00000317861.1	+	1	691	c.691G>T	c.(691-693)Gac>Tac	p.D231Y		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	231			D -> Y (in dbSNP:rs28545014).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						AAGAGGAGCAGACAGAACAAA	0.517													g|||	2308	0.460863	0.3608	0.4885	5008	,	,		19287	0.4315		0.5249	False		,,,				2504	0.5409				p.D231Y		Atlas-SNP	.											OR14C36,NS,carcinoma,-2,2	OR14C36	113	2	0			c.G691T						PASS	.	G	TYR/ASP	1768,2638	526.2+/-371.8	354,1060,789	207.0	148.0	168.0		691	1.5	0.0	1	dbSNP_125	168	4894,3706	619.6+/-396.9	1390,2114,796	yes	missense	OR14C36	NM_001001918.1	160	1744,3174,1585	TT,TG,GG		43.093,40.1271,48.7775	probably-damaging	231/313	248512767	6662,6344	2203	4300	6503	SO:0001583	missense	127066	exon1			GGAGCAGACAGAA	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.691G>T	1.37:g.248512767G>T	ENSP00000324534:p.Asp231Tyr	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	350	166	0.474286	NM_001001918	Q6IEZ6	Missense_Mutation	SNP	ENST00000317861.1	37	CCDS31112.1	1007	0.4610805860805861	170	0.34552845528455284	179	0.494475138121547	253	0.4423076923076923	405	0.5343007915567283	G	16.83	3.232118	0.58777	0.401271	0.56907	ENSG00000177174	ENST00000317861	T	0.00130	8.69	3.61	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.473448	0.17741	N	0.163548	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	D	0.89917	1.0	D	0.76071	0.987	T	0.04140	-1.0974	9	0.87932	D	0	.	12.5964	0.56472	0.0:0.301:0.699:0.0	rs28545014	231	Q8NHC7	O14CZ_HUMAN	Y	231	ENSP00000324534:D231Y	ENSP00000324534:D231Y	D	+	1	0	OR14C36	246579390	0.000000	0.05858	0.000000	0.03702	0.747000	0.42532	0.042000	0.13949	0.183000	0.20059	0.395000	0.25975	GAC	G|0.502;T|0.498	0.498	strong		0.517	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918	
TEKT4	150483	hgsc.bcm.edu	37	2	95542433	95542433	+	Missense_Mutation	SNP	C	C	G	rs17120062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:95542433C>G	ENST00000295201.4	+	6	1364	c.1227C>G	c.(1225-1227)aaC>aaG	p.N409K	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	409			N -> K (in dbSNP:rs17120062).		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						CCATGACCAACAGTCTCTTCA	0.597													C|||	79	0.0157748	0.0008	0.0101	5008	,	,		19729	0.0228		0.0338	False		,,,				2504	0.0143				p.N409K		Atlas-SNP	.											TEKT4,brain,glioma,0,1	TEKT4	72	1	0			c.C1227G						PASS	.	C	LYS/ASN	30,4376		0,30,2173	82.0	59.0	67.0		1227	1.5	1.0	2	dbSNP_123	67	296,8304		3,290,4007	no	missense	TEKT4	NM_144705.2	94	3,320,6180	GG,GC,CC		3.4419,0.6809,2.5065	probably-damaging	409/436	95542433	326,12680	2203	4300	6503	SO:0001583	missense	150483	exon6			GACCAACAGTCTC	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.1227C>G	2.37:g.95542433C>G	ENSP00000295201:p.Asn409Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	40	0.018315018315018316	1	0.0020325203252032522	5	0.013812154696132596	10	0.017482517482517484	24	0.0316622691292876	.	15.60	2.882521	0.51908	0.006809	0.034419	ENSG00000163060	ENST00000295201	T	0.03004	4.08	2.43	1.46	0.22682	.	0.224645	0.43579	D	0.000552	T	0.06917	0.0176	M	0.93328	3.405	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00473	-1.1718	10	0.49607	T	0.09	-18.0548	7.7096	0.28669	0.0:0.8368:0.0:0.1632	rs17120062	409	Q8WW24	TEKT4_HUMAN	K	409	ENSP00000295201:N409K	ENSP00000295201:N409K	N	+	3	2	TEKT4	94906160	1.000000	0.71417	0.996000	0.52242	0.648000	0.38561	1.489000	0.35562	1.049000	0.40321	0.281000	0.19383	AAC	C|0.977;G|0.023	0.023	strong		0.597	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
MAP7D3	79649	hgsc.bcm.edu	37	X	135310785	135310785	+	Missense_Mutation	SNP	T	T	C	rs2273221	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:135310785T>C	ENST00000316077.9	-	11	2103	c.1883A>G	c.(1882-1884)cAa>cGa	p.Q628R	MAP7D3_ENST00000495432.1_5'UTR|MAP7D3_ENST00000370661.1_Missense_Mutation_p.Q593R|MAP7D3_ENST00000370663.5_Missense_Mutation_p.Q610R	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	628			Q -> R (in dbSNP:rs2273221). {ECO:0000269|PubMed:15489334}.		microtubule cytoskeleton organization (GO:0000226)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.Q925R(1)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(1)	44	Acute lymphoblastic leukemia(192;0.000127)					TGCTGACCTTTGCTGCATTTC	0.398													C|||	1846	0.489007	0.2126	0.3501	3775	,	,		12628	0.5427		0.4076	False		,,,				2504	0.3732				p.Q628R		Atlas-SNP	.											.	MAP7D3	102	.	1	Substitution - Missense(1)	prostate(1)	c.A1883G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN	937,2175		112,522,191,637,379	148.0	126.0	133.0		1829,1778,1883	-5.9	0.0	X	dbSNP_100	133	3433,2942		704,1087,938,509,837	yes	missense,missense,missense	MAP7D3	NM_001173516.1,NM_001173517.1,NM_024597.3	43,43,43	816,1609,1129,1146,1216	CC,CT,C,TT,T		46.149,30.1093,46.063	benign,benign,benign	610/859,593/842,628/877	135310785	4370,5117	1841	4075	5916	SO:0001583	missense	79649	exon11			GACCTTTGCTGCA	AL832120	CCDS44004.1, CCDS55508.1, CCDS55509.1	Xq26.3	2014-08-13			ENSG00000129680	ENSG00000129680			25742	protein-coding gene	gene with protein product		300930				24927501	Standard	NM_001173516		Approved	FLJ12649	uc004ezt.3	Q8IWC1	OTTHUMG00000022507	ENST00000316077.9:c.1883A>G	X.37:g.135310785T>C	ENSP00000318086:p.Gln628Arg	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	874	0.5268233875828813	75	0.1736111111111111	90	0.3409090909090909	202	0.543010752688172	224	0.4072727272727273	C	7.976	0.750132	0.15778	0.301093	0.53851	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.44	-5.9	0.02275	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.0;0.0;0.001	B;B;B;B	0.08055	0.002;0.001;0.002;0.003	T	0.44682	-0.9312	8	0.25751	T	0.34	.	6.02	0.19625	0.1559:0.0717:0.0997:0.6727	rs2273221;rs17330808;rs17846287;rs17859311;rs52825916;rs61380364;rs2273221	610;587;628;593	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	R	593;628;610;587	ENSP00000359695:Q593R;ENSP00000318086:Q628R;ENSP00000359697:Q610R;ENSP00000359694:Q587R	ENSP00000318086:Q628R	Q	-	2	0	MAP7D3	135138451	0.001000	0.12720	0.000000	0.03702	0.021000	0.10359	-0.479000	0.06567	-2.118000	0.00828	-0.879000	0.02964	CAA	0|0.030;C|0.478	0.478	strong		0.398	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2		
ZNF671	79891	hgsc.bcm.edu	37	19	58233008	58233008	+	Missense_Mutation	SNP	G	G	A	rs3746207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58233008G>A	ENST00000317398.6	-	4	541	c.446C>T	c.(445-447)gCa>gTa	p.A149V	ZNF671_ENST00000594803.1_5'Flank|AC003006.7_ENST00000599221.1_Intron|ZNF671_ENST00000335820.3_Missense_Mutation_p.A51V|AC003006.7_ENST00000594684.1_Intron	NM_024833.2	NP_079109.2	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	149			A -> V (in dbSNP:rs3746207). {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)			kidney(1)|large_intestine(6)|liver(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22		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;0.0257)		TGACACTCCTGCTACAAAAAT	0.453													G|||	767	0.153155	0.2814	0.111	5008	,	,		22236	0.0873		0.175	False		,,,				2504	0.0552				p.A149V		Atlas-SNP	.											.	ZNF671	55	.	0			c.C446T						PASS	.	G	VAL/ALA	1167,3239	410.9+/-335.5	145,877,1181	111.0	107.0	109.0		446	-0.6	0.0	19	dbSNP_107	109	1280,7320	254.4+/-279.7	90,1100,3110	yes	missense	ZNF671	NM_024833.2	64	235,1977,4291	AA,AG,GG		14.8837,26.4866,18.8144	possibly-damaging	149/535	58233008	2447,10559	2203	4300	6503	SO:0001583	missense	79891	exon4			ACTCCTGCTACAA		CCDS12961.1	19q13.43	2013-01-08				ENSG00000083814		"""Zinc fingers, C2H2-type"", ""-"""	26279	protein-coding gene	gene with protein product	"""hypothetical protein FLJ23506"""					12477932	Standard	NM_024833		Approved	FLJ23506	uc002qpz.4	Q8TAW3		ENST00000317398.6:c.446C>T	19.37:g.58233008G>A	ENSP00000321848:p.Ala149Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_024833	A6NF07|Q9H5E9	Missense_Mutation	SNP	ENST00000317398.6	37	CCDS12961.1	367	0.16804029304029305	126	0.25609756097560976	48	0.13259668508287292	57	0.09965034965034965	136	0.17941952506596306	G	9.713	1.157550	0.21454	0.264866	0.148837	ENSG00000083814	ENST00000317398;ENST00000335820	T;T	0.06142	3.46;3.34	1.66	-0.654	0.11443	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.399999999997849E-5	B	0.27192	0.171	B	0.15870	0.014	T	0.48875	-0.8996	8	0.32370	T	0.25	.	4.2045	0.10481	0.5669:0.0:0.4331:0.0	rs3746207;rs52832436;rs61034509;rs3746207	149	Q8TAW3	ZN671_HUMAN	V	149;51	ENSP00000321848:A149V;ENSP00000338670:A51V	ENSP00000321848:A149V	A	-	2	0	ZNF671	62924820	0.000000	0.05858	0.015000	0.15790	0.180000	0.23129	-2.628000	0.00873	-0.229000	0.09854	0.313000	0.20887	GCA	G|0.819;A|0.181	0.181	strong		0.453	ZNF671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466817.1	NM_024833	
ZNF37A	7587	hgsc.bcm.edu	37	10	38406359	38406359	+	Missense_Mutation	SNP	A	A	C	rs150470434	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:38406359A>C	ENST00000361085.5	+	7	625	c.280A>C	c.(280-282)Aat>Cat	p.N94H	ZNF37A_ENST00000351773.3_Missense_Mutation_p.N94H	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	94					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(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						AATGAAGTTCAATGAGTTTAA	0.294													A|||	4	0.000798722	0.0	0.0	5008	,	,		18981	0.0		0.004	False		,,,				2504	0.0				p.N94H		Atlas-SNP	.											.	ZNF37A	118	.	0			c.A280C						PASS	.	A	HIS/ASN,HIS/ASN,HIS/ASN	0,4396		0,0,2198	65.0	77.0	73.0		280,280,280	-4.3	0.1	10	dbSNP_134	73	17,8563	9.8+/-36.6	0,17,4273	yes	missense,missense,missense	ZNF37A	NM_001007094.2,NM_001178101.1,NM_003421.2	68,68,68	0,17,6471	CC,CA,AA		0.1981,0.0,0.131	benign,benign,benign	94/562,94/562,94/562	38406359	17,12959	2198	4290	6488	SO:0001583	missense	7587	exon7			AAGTTCAATGAGT	X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"""Zinc fingers, C2H2-type"", ""-"""	13102	protein-coding gene	gene with protein product			"""zinc finger protein 37a (KOX 21)"""			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.280A>C	10.37:g.38406359A>C	ENSP00000354377:p.Asn94His	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	187	81	0.433155	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Missense_Mutation	SNP	ENST00000361085.5	37	CCDS31183.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0.012	-1.647092	0.00792	0.0	0.001981	ENSG00000075407	ENST00000351773;ENST00000361085	T;T	0.07021	3.23;3.23	2.16	-4.33	0.03677	.	.	.	.	.	T	0.02571	0.0078	N	0.02213	-0.635	0.09310	N	1	B	0.23442	0.085	B	0.28011	0.085	T	0.46816	-0.9164	9	0.19147	T	0.46	.	4.1301	0.10146	0.3936:0.0:0.4349:0.1715	.	94	P17032	ZN37A_HUMAN	H	94	ENSP00000329141:N94H;ENSP00000354377:N94H	ENSP00000329141:N94H	N	+	1	0	ZNF37A	38446365	0.000000	0.05858	0.149000	0.22428	0.397000	0.30659	-1.717000	0.01876	-0.782000	0.04541	-0.376000	0.06991	AAT	A|0.998;C|0.002	0.002	strong		0.294	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421	
SUGP1	57794	hgsc.bcm.edu	37	19	19413092	19413092	+	Missense_Mutation	SNP	C	C	T	rs17751061	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19413092C>T	ENST00000247001.5	-	7	1216	c.869G>A	c.(868-870)cGt>cAt	p.R290H	SUGP1_ENST00000585763.1_Intron	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	290			R -> H (in dbSNP:rs17751061).		gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						CTGGTTCTCACGGTTGTTCTG	0.612													C|||	345	0.0688898	0.0061	0.1037	5008	,	,		16253	0.0		0.164	False		,,,				2504	0.1022				p.R290H		Atlas-SNP	.											.	SUGP1	63	.	0			c.G869A						PASS	.	C	HIS/ARG	134,4272	96.7+/-135.4	0,134,2069	183.0	151.0	162.0		869	5.0	1.0	19	dbSNP_123	162	1359,7241	266.0+/-286.5	104,1151,3045	yes	missense	SUGP1	NM_172231.3	29	104,1285,5114	TT,TC,CC		15.8023,3.0413,11.4793	probably-damaging	290/646	19413092	1493,11513	2203	4300	6503	SO:0001583	missense	57794	exon7			TTCTCACGGTTGT	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.869G>A	19.37:g.19413092C>T	ENSP00000247001:p.Arg290His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	130	50	0.384615	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	162	0.07417582417582418	7	0.014227642276422764	44	0.12154696132596685	0	0.0	111	0.14643799472295516	C	29.1	4.973750	0.92919	0.030413	0.158023	ENSG00000105705	ENST00000247001	T	0.44083	0.93	5.03	5.03	0.67393	SWAP/Surp (3);	0.000000	0.85682	D	0.000000	T	0.00468	0.0015	M	0.74881	2.28	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00857	-1.1538	9	0.54805	T	0.06	.	16.9243	0.86172	0.0:1.0:0.0:0.0	rs17751061;rs17751061	290	Q8IWZ8	SUGP1_HUMAN	H	290	ENSP00000247001:R290H	ENSP00000247001:R290H	R	-	2	0	SUGP1	19274092	1.000000	0.71417	0.964000	0.40570	0.985000	0.73830	5.788000	0.69020	2.350000	0.79820	0.563000	0.77884	CGT	C|0.891;T|0.109	0.109	strong		0.612	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	
ERAP2	64167	hgsc.bcm.edu	37	5	96228072	96228072	+	Missense_Mutation	SNP	C	C	T	rs75263594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:96228072C>T	ENST00000437043.3	+	6	1751	c.1040C>T	c.(1039-1041)aCg>aTg	p.T347M	CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000379904.4_Missense_Mutation_p.T302M	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	347					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TATAGGGAGACGTCACTGCTT	0.453													C|||	56	0.0111821	0.0023	0.0259	5008	,	,		19814	0.0		0.0308	False		,,,				2504	0.0041				p.T347M		Atlas-SNP	.											.	ERAP2	77	.	0			c.C1040T						PASS	.	C	MET/THR,MET/THR	38,4368	41.6+/-74.8	1,36,2166	175.0	159.0	164.0		1040,1040	3.6	0.3	5	dbSNP_132	164	268,8332	103.8+/-164.8	4,260,4036	yes	missense,missense	ERAP2	NM_001130140.1,NM_022350.3	81,81	5,296,6202	TT,TC,CC		3.1163,0.8625,2.3528	probably-damaging,probably-damaging	347/961,347/961	96228072	306,12700	2203	4300	6503	SO:0001583	missense	64167	exon6			GGGAGACGTCACT	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1040C>T	5.37:g.96228072C>T	ENSP00000400376:p.Thr347Met	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	224	109	0.486607	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	34	0.015567765567765568	0	0.0	10	0.027624309392265192	0	0.0	24	0.0316622691292876	C	15.89	2.966998	0.53507	0.008625	0.031163	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904	T;T;T;T	0.05382	3.45;3.45;3.45;3.45	4.49	3.61	0.41365	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.144593	0.45126	D	0.000400	T	0.11836	0.0288	M	0.92077	3.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.988;0.993	T	0.04115	-1.0976	10	0.87932	D	0	.	11.2326	0.48920	0.0:0.908:0.0:0.092	.	302;347	Q6P179-3;Q6P179	.;ERAP2_HUMAN	M	347;347;347;302	ENSP00000400376:T347M;ENSP00000421175:T347M;ENSP00000421849:T347M;ENSP00000369235:T302M	ENSP00000369235:T302M	T	+	2	0	ERAP2	96253828	0.999000	0.42202	0.260000	0.24451	0.334000	0.28698	4.351000	0.59398	1.015000	0.39444	0.563000	0.77884	ACG	C|0.975;T|0.025	0.025	strong		0.453	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
HUS1	3364	hgsc.bcm.edu	37	7	48004962	48004962	+	Silent	SNP	C	C	T	rs1056663	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:48004962C>T	ENST00000258774.5	-	8	857	c.834G>A	c.(832-834)gcG>gcA	p.A278A	HUS1_ENST00000432325.1_Silent_p.A257A	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	278					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				GCTAGGACAGCGCAGGGATGA	0.488								Direct reversal of damage;Other conserved DNA damage response genes					c|||	2120	0.423323	0.2799	0.4928	5008	,	,		20745	0.5119		0.5189	False		,,,				2504	0.3783				p.A278A	Ovarian(103;466 1517 21788 34610 43890)	Atlas-SNP	.											.	HUS1	36	.	0			c.G834A						PASS	.	G		1389,3017	457.8+/-351.8	236,917,1050	164.0	129.0	141.0		834	-10.3	0.0	7	dbSNP_86	141	4384,4216	584.4+/-391.7	1096,2192,1012	no	coding-synonymous	HUS1	NM_004507.3		1332,3109,2062	TT,TC,CC		49.0233,31.5252,44.3872		278/281	48004962	5773,7233	2203	4300	6503	SO:0001819	synonymous_variant	3364	exon8			GGACAGCGCAGGG	Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"""hus1+-like protein"""	603760	"""HUS1 (S. pombe) checkpoint homolog"""			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.834G>A	7.37:g.48004962C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_004507	B4DFI9	Silent	SNP	ENST00000258774.5	37	CCDS34635.1																																																																																			C|0.560;T|0.440	0.440	strong		0.488	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507	
TCHP	84260	hgsc.bcm.edu	37	12	110341933	110341933	+	Missense_Mutation	SNP	A	A	G	rs10774978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:110341933A>G	ENST00000312777.5	+	3	594	c.380A>G	c.(379-381)aAa>aGa	p.K127R	TCHP_ENST00000405876.4_Missense_Mutation_p.K127R	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						AAATCAGCCAAAGAAGAGCAG	0.562													G|||	1562	0.311901	0.674	0.1844	5008	,	,		19945	0.1438		0.1769	False		,,,				2504	0.2249				p.K127R		Atlas-SNP	.											.	TCHP	45	.	0			c.A380G						PASS	.	G	ARG/LYS,ARG/LYS	2603,1787		779,1045,371	50.0	45.0	47.0		380,380	3.3	1.0	12	dbSNP_120	47	1357,7219		108,1141,3039	yes	missense,missense	TCHP	NM_001143852.1,NM_032300.4	26,26	887,2186,3410	GG,GA,AA		15.8232,40.7062,30.5414	benign,benign	127/499,127/499	110341933	3960,9006	2195	4288	6483	SO:0001583	missense	84260	exon3			CAGCCAAAGAAGA	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.380A>G	12.37:g.110341933A>G	ENSP00000324404:p.Lys127Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	554	0.25366300366300365	301	0.6117886178861789	70	0.19337016574585636	54	0.0944055944055944	129	0.17018469656992086	G	0.176	-1.067266	0.01934	0.592938	0.158232	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.33865	2.2;2.2;1.39	5.21	3.3	0.37823	.	0.117657	0.56097	N	0.000036	T	0.00012	0.0000	N	0.00230	-1.795	0.09310	P	0.9999999999948324	B	0.02656	0.0	B	0.01281	0.0	T	0.47736	-0.9094	9	0.02654	T	1	-0.1723	8.7459	0.34587	0.2659:0.0:0.7341:0.0	rs10774978;rs61441019;rs10774978	127	Q9BT92	TCHP_HUMAN	R	127	ENSP00000384520:K127R;ENSP00000324404:K127R;ENSP00000441835:K127R	ENSP00000324404:K127R	K	+	2	0	TCHP	108826316	0.826000	0.29277	0.968000	0.41197	0.210000	0.24377	1.397000	0.34543	0.268000	0.21939	-1.101000	0.02118	AAA	A|0.700;G|0.300	0.300	strong		0.562	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
ITLN1	55600	hgsc.bcm.edu	37	1	160853312	160853312	+	Silent	SNP	C	C	T	rs79969862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	155	0	0		WXS	Illumina HiSeq	Phase_I	139	49	0.352518	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	
RPUSD4	84881	hgsc.bcm.edu	37	11	126074192	126074192	+	Silent	SNP	A	A	G	rs2276312	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126074192A>G	ENST00000298317.4	-	6	881	c.828T>C	c.(826-828)tcT>tcC	p.S276S	RPUSD4_ENST00000534393.1_5'Flank|RPUSD4_ENST00000533628.1_Silent_p.S245S	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	31	14	0.451613	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	
SLC35B3	51000	hgsc.bcm.edu	37	6	8413890	8413890	+	Silent	SNP	A	A	G	rs3757099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	57	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	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	
MATN2	4147	hgsc.bcm.edu	37	8	98991223	98991223	+	Silent	SNP	A	A	G	rs1869608	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:98991223A>G	ENST00000520016.1	+	5	1192	c.1068A>G	c.(1066-1068)aaA>aaG	p.K356K	MATN2_ENST00000521689.1_Silent_p.K356K|MATN2_ENST00000254898.5_Silent_p.K356K|MATN2_ENST00000524308.1_Silent_p.K356K|MATN2_ENST00000522025.2_Silent_p.K72K			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	76	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	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		
TRPV3	162514	hgsc.bcm.edu	37	17	3422077	3422077	+	Silent	SNP	G	G	A	rs12946883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3422077G>A	ENST00000576742.1	-	15	2199	c.1878C>T	c.(1876-1878)agC>agT	p.S626S	TRPV3_ENST00000572519.1_Silent_p.S626S|TRPV3_ENST00000301365.4_Silent_p.S626S	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	626					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)	p.S626S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GCACTGCGTCGCTGAAGCTGC	0.532													g|||	1641	0.327676	0.3427	0.2478	5008	,	,		20399	0.3333		0.2873	False		,,,				2504	0.3998				p.S626S		Atlas-SNP	.											TRPV3,NS,carcinoma,0,1	TRPV3	85	1	1	Substitution - coding silent(1)	stomach(1)	c.C1878T						scavenged	.	G		1496,2910	477.5+/-357.9	269,958,976	102.0	90.0	94.0		1878	-7.3	0.0	17	dbSNP_121	94	2365,6235	394.1+/-344.6	319,1727,2254	no	coding-synonymous	TRPV3	NM_145068.2		588,2685,3230	AA,AG,GG		27.5,33.9537,29.6863		626/791	3422077	3861,9145	2203	4300	6503	SO:0001819	synonymous_variant	162514	exon15			TGCGTCGCTGAAG	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.1878C>T	17.37:g.3422077G>A		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	37	CCDS11029.1																																																																																			G|0.699;A|0.301	0.301	strong		0.532	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
PPAN	56342	hgsc.bcm.edu	37	19	10218524	10218524	+	Silent	SNP	C	C	G	rs2305791	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10218524C>G	ENST00000253107.7	+	4	442	c.336C>G	c.(334-336)gtC>gtG	p.V112V	PPAN-P2RY11_ENST00000428358.1_Silent_p.V112V|PPAN_ENST00000556468.1_Silent_p.V112V|SNORD105_ENST00000386910.1_RNA|SNORD105B_ENST00000458770.1_RNA|PPAN-P2RY11_ENST00000393796.4_Silent_p.V112V|PPAN_ENST00000393793.1_Silent_p.V59V	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	112	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				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)			CCTTCCAGGTCAAGAAGGTGA	0.607													C|||	1351	0.269768	0.025	0.4135	5008	,	,		17177	0.3611		0.3628	False		,,,				2504	0.3088				p.V112V		Atlas-SNP	.											.	PPAN	43	.	0			c.C336G						PASS	.	C	,,	374,4028	168.0+/-198.9	23,328,1850	68.0	82.0	77.0		336,336,336	1.9	0.6	19	dbSNP_100	77	2894,5700	437.5+/-358.6	487,1920,1890	no	coding-synonymous,coding-synonymous,coding-synonymous	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	,,	510,2248,3740	GG,GC,CC		33.6747,8.4961,25.1462	,,	112/795,112/521,112/474	10218524	3268,9728	2201	4297	6498	SO:0001819	synonymous_variant	56342	exon4			CCAGGTCAAGAAG	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.336C>G	19.37:g.10218524C>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_020230	C9J3F9|Q9BW97|Q9H170	Silent	SNP	ENST00000253107.7	37	CCDS12225.1																																																																																			C|0.716;G|0.284	0.284	strong		0.607	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	
DNASE2	1777	hgsc.bcm.edu	37	19	12989560	12989560	+	Silent	SNP	G	G	A	rs2293682	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12989560G>A	ENST00000222219.3	-	4	527	c.435C>T	c.(433-435)agC>agT	p.S145S	DNASE2_ENST00000538460.1_Intron|CTD-2265O21.7_ENST00000592400.1_RNA	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal	145					apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						TATGAGGCCAGCTGTATGCAG	0.577													G|||	1857	0.370807	0.2451	0.2853	5008	,	,		18962	0.6181		0.2435	False		,,,				2504	0.4775				p.S145S		Atlas-SNP	.											DNASE2,NS,adenoma,0,1	DNASE2	23	1	0			c.C435T						PASS	.	G		1134,3272	403.5+/-332.8	141,852,1210	70.0	60.0	63.0		435	0.3	0.8	19	dbSNP_100	63	1989,6611	349.8+/-327.6	205,1579,2516	no	coding-synonymous	DNASE2	NM_001375.2		346,2431,3726	AA,AG,GG		23.1279,25.7376,24.012		145/361	12989560	3123,9883	2203	4300	6503	SO:0001819	synonymous_variant	1777	exon4			AGGCCAGCTGTAT	AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115		ENST00000222219.3:c.435C>T	19.37:g.12989560G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_001375	B2RD06|B7Z4K6|O43910	Silent	SNP	ENST00000222219.3	37	CCDS12284.1																																																																																			G|0.706;A|0.294	0.294	strong		0.577	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1		
ARHGAP39	80728	hgsc.bcm.edu	37	8	145806262	145806262	+	Silent	SNP	C	C	T	rs117042905	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145806262C>T	ENST00000276826.5	-	2	681	c.480G>A	c.(478-480)gcG>gcA	p.A160A	ARHGAP39_ENST00000377307.2_Silent_p.A160A|ARHGAP39_ENST00000540274.1_Silent_p.A160A			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	160					axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						TCCCAAACGCCGCGGGCCGCC	0.716													C|||	114	0.0227636	0.0023	0.0375	5008	,	,		8622	0.001		0.0736	False		,,,				2504	0.0102				p.A160A		Atlas-SNP	.											ARHGAP39,NS,carcinoma,0,1	ARHGAP39	80	1	0			c.G480A						PASS	.	C		36,4156		0,36,2060	11.0	13.0	12.0		480	-6.6	0.0	8	dbSNP_132	12	475,7733		10,455,3639	no	coding-synonymous	ARHGAP39	NM_025251.1		10,491,5699	TT,TC,CC		5.787,0.8588,4.121		160/1115	145806262	511,11889	2096	4104	6200	SO:0001819	synonymous_variant	80728	exon4			AAACGCCGCGGGC		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"""Rho GTPase activating proteins"""	29351	protein-coding gene	gene with protein product	"""RhoGAP93B homolog (Drosophila)"", ""crossGAP homolog (Drosophila)"""	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.480G>A	8.37:g.145806262C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_025251	B4E1I1	Silent	SNP	ENST00000276826.5	37																																																																																				C|0.960;T|0.040	0.040	strong		0.716	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1		
OR2J3	442186	hgsc.bcm.edu	37	6	29080004	29080004	+	Missense_Mutation	SNP	A	A	G	rs28757581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29080004A>G	ENST00000377169.1	+	1	337	c.337A>G	c.(337-339)Aca>Gca	p.T113A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	113			T -> A (in allele 6M1-3*02; decreased response to C3HEX; dbSNP:rs28757581). {ECO:0000269|PubMed:22714804, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						ACTGGGAACCACAGAGTGTGT	0.498													A|||	961	0.191893	0.3812	0.1499	5008	,	,		22982	0.1101		0.1193	False		,,,				2504	0.1247				p.T113A		Atlas-SNP	.											OR2J3,NS,carcinoma,0,1	OR2J3	53	1	0			c.A337G						PASS	.	A	ALA/THR	809,1911		118,573,669	297.0	340.0	325.0		337	2.8	1.0	6	dbSNP_125	325	569,4693		36,497,2098	no	missense	OR2J3	NM_001005216.2	58	154,1070,2767	GG,GA,AA		10.8134,29.7426,17.2638	benign	113/312	29080004	1378,6604	1360	2631	3991	SO:0001583	missense	442186	exon1			GGAACCACAGAGT		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.337A>G	6.37:g.29080004A>G	ENSP00000366374:p.Thr113Ala	Somatic	361	1	0.00277008		WXS	Illumina HiSeq	Phase_I	361	176	0.487535	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	407	0.18635531135531136	203	0.41260162601626016	48	0.13259668508287292	67	0.11713286713286714	89	0.11741424802110818	A	5.246	0.230828	0.09969	0.297426	0.108134	ENSG00000204701	ENST00000377169	T	0.01685	4.69	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00784	0.0026	L	0.45422	1.42	0.80722	P	0.0	B	0.11235	0.004	B	0.15052	0.012	T	0.39742	-0.9599	8	0.52906	T	0.07	.	7.2096	0.25927	0.8801:0.0:0.1199:0.0	rs28757581	113	O76001	OR2J3_HUMAN	A	113	ENSP00000366374:T113A	ENSP00000366374:T113A	T	+	1	0	OR2J3	29187983	0.000000	0.05858	0.988000	0.46212	0.407000	0.30961	0.679000	0.25291	1.268000	0.44264	0.358000	0.22013	ACA	A|0.839;G|0.161	0.161	strong		0.498	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
LATS2	26524	hgsc.bcm.edu	37	13	21562371	21562371	+	Silent	SNP	C	C	T	rs59928188	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:21562371C>T	ENST00000382592.4	-	4	1953	c.1548G>A	c.(1546-1548)ccG>ccA	p.P516P	LATS2_ENST00000542899.1_Silent_p.P516P|LATS2_ENST00000472754.1_5'Flank	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		TCGGGTAGGGCGGAGGCGGGC	0.711													C|||	219	0.04373	0.0605	0.0331	5008	,	,		8998	0.0665		0.0358	False		,,,				2504	0.0133				p.P516P		Atlas-SNP	.											LATS2_ENST00000382592,NS,carcinoma,-1,2	LATS2	176	2	0			c.G1548A						PASS	.	C		218,4186		11,196,1995	20.0	22.0	21.0		1548	-9.1	0.3	13	dbSNP_129	21	309,8285		7,295,3995	no	coding-synonymous	LATS2	NM_014572.2		18,491,5990	TT,TC,CC		3.5955,4.95,4.0545		516/1089	21562371	527,12471	2202	4297	6499	SO:0001819	synonymous_variant	26524	exon4			GTAGGGCGGAGGC	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.1548G>A	13.37:g.21562371C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_014572		Silent	SNP	ENST00000382592.4	37	CCDS9294.1																																																																																			C|0.959;T|0.041	0.041	strong		0.711	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
MYH4	4622	hgsc.bcm.edu	37	17	10346781	10346781	+	Missense_Mutation	SNP	T	T	C	rs3744554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10346781T>C	ENST00000255381.2	-	40	5841	c.5731A>G	c.(5731-5733)Aag>Gag	p.K1911E	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1911			K -> E (in dbSNP:rs3744554). {ECO:0000269|PubMed:10388558}.		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)			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						GCCCGTTCCTTGGCCTCCTCC	0.458													C|||	2670	0.533147	0.3336	0.5245	5008	,	,		18924	0.8631		0.3698	False		,,,				2504	0.637				p.K1911E		Atlas-SNP	.											.	MYH4	349	.	0			c.A5731G						PASS	.	C	GLU/LYS	1556,2850	669.2+/-402.1	271,1014,918	135.0	124.0	128.0		5731	4.2	0.9	17	dbSNP_107	128	3586,5014	627.6+/-398.0	761,2064,1475	yes	missense	MYH4	NM_017533.2	56	1032,3078,2393	CC,CT,TT		41.6977,35.3155,39.5356	benign	1911/1940	10346781	5142,7864	2203	4300	6503	SO:0001583	missense	4622	exon40			GTTCCTTGGCCTC		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.5731A>G	17.37:g.10346781T>C	ENSP00000255381:p.Lys1911Glu	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	231	112	0.484848	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1125	0.5151098901098901	157	0.31910569105691056	186	0.5138121546961326	498	0.8706293706293706	284	0.37467018469656993	C	2.548	-0.304632	0.05495	0.353155	0.416977	ENSG00000141048	ENST00000255381	D	0.82984	-1.67	5.19	4.23	0.50019	Myosin tail (1);	0.000000	0.36101	N	0.002785	T	0.00012	0.0000	N	0.00028	-2.63	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44697	-0.9311	9	0.02654	T	1	.	12.1163	0.53868	0.0:0.8614:0.0:0.1386	rs3744554;rs3744554	1911	Q9Y623	MYH4_HUMAN	E	1911	ENSP00000255381:K1911E	ENSP00000255381:K1911E	K	-	1	0	MYH4	10287506	0.929000	0.31497	0.884000	0.34674	0.594000	0.36715	1.988000	0.40697	0.912000	0.36772	-0.119000	0.15052	AAG	T|0.573;C|0.427	0.427	strong		0.458	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
FLG	2312	hgsc.bcm.edu	37	1	152280759	152280759	+	Silent	SNP	A	A	G	rs2338554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280759A>G	ENST00000368799.1	-	3	6638	c.6603T>C	c.(6601-6603)gaT>gaC	p.D2201D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2201	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCTAGAGCCATCTCCTGATT	0.552									Ichthyosis				-|||	1839	0.367212	0.472	0.3501	5008	,	,		27298	0.4454		0.1531	False		,,,				2504	0.3773				p.D2201D		Atlas-SNP	.											FLG,NS,carcinoma,-2,2	FLG	900	2	0			c.T6603C						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	317	0	0		WXS	Illumina HiSeq	Phase_I	525	114	0.217143	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	
IMMT	10989	hgsc.bcm.edu	37	2	86371883	86371883	+	Silent	SNP	T	T	C	rs8244	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:86371883T>C	ENST00000410111.3	-	15	2172	c.1785A>G	c.(1783-1785)gcA>gcG	p.A595A	IMMT_ENST00000449247.2_Silent_p.A584A|IMMT_ENST00000254636.5_Silent_p.A496A|IMMT_ENST00000409051.2_Silent_p.A548A|IMMT_ENST00000442664.2_Silent_p.A594A	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	595					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						TGGCCTCAACTGCACTACCCA	0.502													T|||	1306	0.260783	0.0582	0.3703	5008	,	,		18972	0.1488		0.4761	False		,,,				2504	0.3507				p.A595A		Atlas-SNP	.											IMMT,colon,carcinoma,-1,1	IMMT	65	1	0			c.A1785G						scavenged	.	T	,,	434,3420		27,380,1520	90.0	87.0	88.0		1782,1752,1785	-10.5	0.0	2	dbSNP_52	88	4158,4106		1034,2090,1008	no	coding-synonymous,coding-synonymous,coding-synonymous	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	,,	1061,2470,2528	CC,CT,TT		49.6854,11.261,37.894	,,	594/758,584/748,595/759	86371883	4592,7526	1927	4132	6059	SO:0001819	synonymous_variant	10989	exon15			CTCAACTGCACTA	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.1785A>G	2.37:g.86371883T>C		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	620	0.2838827838827839	32	0.06504065040650407	143	0.39502762430939226	94	0.16433566433566432	351	0.4630606860158311	T	0.334	-0.954617	0.02285	0.11261	0.503146	ENSG00000132305	ENST00000419070	.	.	.	5.27	-10.5	0.00291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999958	.	.	.	.	.	.	T	0.18085	-1.0348	3	.	.	.	-13.0405	5.2624	0.15582	0.1877:0.432:0.2424:0.1379	rs8244;rs17431880;rs17849575;rs8244	.	.	.	G	450	.	.	S	-	1	0	IMMT	86225394	0.000000	0.05858	0.002000	0.10522	0.292000	0.27327	-5.190000	0.00143	-3.336000	0.00184	-0.320000	0.08662	AGT	T|0.689;G|0.000;C|0.310;A|0.000	0.310	strong		0.502	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
CENPF	1063	hgsc.bcm.edu	37	1	214819980	214819980	+	Missense_Mutation	SNP	C	C	T	rs3748696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214819980C>T	ENST00000366955.3	+	13	7235	c.7067C>T	c.(7066-7068)gCt>gTt	p.A2356V		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2452	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)		GAGCATGCAGCTCTTGAGGCA	0.438													C|||	532	0.10623	0.1089	0.1066	5008	,	,		18387	0.1151		0.0507	False		,,,				2504	0.1503				p.A2356V	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.C7067T						PASS	.	C	VAL/ALA	435,3971	207.5+/-228.8	22,391,1790	43.0	45.0	44.0		7067	-2.8	0.0	1	dbSNP_107	44	462,8138	135.4+/-192.6	12,438,3850	yes	missense	CENPF	NM_016343.3	64	34,829,5640	TT,TC,CC		5.3721,9.8729,6.8968	benign	2356/3115	214819980	897,12109	2203	4300	6503	SO:0001583	missense	1063	exon13			ATGCAGCTCTTGA	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.7067C>T	1.37:g.214819980C>T	ENSP00000355922:p.Ala2356Val	Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	205	117	0.570732	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	223	0.1021062271062271	64	0.13008130081300814	40	0.11049723756906077	77	0.1346153846153846	42	0.055408970976253295	C	1.174	-0.640237	0.03557	0.098729	0.053721	ENSG00000117724	ENST00000366955	T	0.38401	1.14	5.03	-2.79	0.05841	Centromere protein Cenp-F, leucine-rich repeat-containing domain (1);	2.488010	0.01841	N	0.035318	T	0.00144	0.0004	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.10359	-1.0633	9	0.30078	T	0.28	.	2.785	0.05371	0.123:0.3725:0.1267:0.3778	rs3748696;rs52822419;rs3748696	2452	P49454	CENPF_HUMAN	V	2356	ENSP00000355922:A2356V	ENSP00000355922:A2356V	A	+	2	0	CENPF	212886603	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.510000	0.06328	-0.396000	0.07703	-0.320000	0.08662	GCT	C|0.919;G|0.000;T|0.080	0.080	strong		0.438	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
SLC37A2	219855	hgsc.bcm.edu	37	11	124951719	124951719	+	Missense_Mutation	SNP	G	G	A	rs34485243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124951719G>A	ENST00000403796.2	+	9	1103	c.802G>A	c.(802-804)Ggc>Agc	p.G268S	SLC37A2_ENST00000298280.5_Missense_Mutation_p.G268S|SLC37A2_ENST00000308074.4_Missense_Mutation_p.G268S|SLC37A2_ENST00000407458.1_Missense_Mutation_p.G268S	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	268			G -> S (in dbSNP:rs34485243).		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)		CAGGGAGAGCGGCCTTGAGAC	0.592													G|||	170	0.0339457	0.1248	0.0058	5008	,	,		18150	0.0		0.001	False		,,,				2504	0.0				p.G268S	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G802A						PASS	.	G	SER/GLY,SER/GLY	396,4006	198.7+/-222.5	15,366,1820	68.0	65.0	66.0		802,802	-8.0	0.0	11	dbSNP_126	66	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	56,56	15,368,6117	AA,AG,GG		0.0233,8.9959,3.0615	benign,benign	268/502,268/506	124951719	398,12602	2201	4299	6500	SO:0001583	missense	219855	exon9			GAGAGCGGCCTTG	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.802G>A	11.37:g.124951719G>A	ENSP00000384407:p.Gly268Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	27	0.355263	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	1.561	-0.536711	0.04082	0.089959	2.33E-4	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.31769	1.48;1.48;1.93;1.48	4.86	-7.96	0.01144	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.505550	0.03203	N	0.175066	T	0.00328	0.0010	N	0.01473	-0.845	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.003	T	0.15065	-1.0450	10	0.08599	T	0.76	-3.6249	6.3702	0.21477	0.2968:0.1007:0.5033:0.0992	rs34485243	268;268	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	S	268	ENSP00000384407:G268S;ENSP00000385126:G268S;ENSP00000298280:G268S;ENSP00000311833:G268S	ENSP00000298280:G268S	G	+	1	0	SLC37A2	124456929	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.394000	0.20834	-1.389000	0.02090	-0.880000	0.02959	GGC	G|0.965;A|0.035	0.035	strong		0.592	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
FLT4	2324	hgsc.bcm.edu	37	5	180051003	180051003	+	Missense_Mutation	SNP	T	T	C	rs307826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180051003T>C	ENST00000261937.6	-	11	1558	c.1480A>G	c.(1480-1482)Acg>Gcg	p.T494A	FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Missense_Mutation_p.T494A|FLT4_ENST00000393347.3_Missense_Mutation_p.T494A	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	494	Ig-like C2-type 5.		T -> A (in dbSNP:rs307826). {ECO:0000269|PubMed:11807987, 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)	GCATCCTGCGTGGTCACCGCC	0.642													T|||	265	0.0529153	0.0151	0.0605	5008	,	,		17541	0.0		0.1074	False		,,,				2504	0.0971				p.T494A	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.A1480G						PASS	.	T	ALA/THR,ALA/THR	132,4274	96.7+/-135.4	1,130,2072	87.0	72.0	77.0		1480,1480	2.2	0.7	5	dbSNP_79	77	1055,7545	222.3+/-259.4	46,963,3291	yes	missense,missense	FLT4	NM_002020.4,NM_182925.4	58,58	47,1093,5363	CC,CT,TT		12.2674,2.9959,9.1266	benign,benign	494/1299,494/1364	180051003	1187,11819	2203	4300	6503	SO:0001583	missense	2324	exon11			CCTGCGTGGTCAC	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.1480A>G	5.37:g.180051003T>C	ENSP00000261937:p.Thr494Ala	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	131	0.984962	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	114	0.0521978021978022	5	0.01016260162601626	27	0.07458563535911603	0	0.0	82	0.10817941952506596	T	5.503	0.277851	0.10403	0.029959	0.122674	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000376868	D;D;D	0.94417	-3.42;-3.42;-3.42	4.72	2.25	0.28309	Immunoglobulin subtype (1);Immunoglobulin-like (1);	.	.	.	.	T	0.11367	0.0277	L	0.38531	1.155	0.51482	P	7.80000000000225E-5	B;B;B;B	0.18610	0.029;0.0;0.0;0.0	B;B;B;B	0.16289	0.015;0.004;0.004;0.008	T	0.60772	-0.7197	8	0.16420	T	0.52	.	5.8076	0.18448	0.0:0.1796:0.2625:0.5579	rs307826;rs1309989;rs307826	494;304;494;494	P35916-3;E9PFB0;E9PD35;P35916	.;.;.;VGFR3_HUMAN	A	494;494;494;304	ENSP00000261937:T494A;ENSP00000377016:T494A;ENSP00000426057:T494A	ENSP00000261937:T494A	T	-	1	0	FLT4	179983609	0.003000	0.15002	0.724000	0.30704	0.064000	0.16182	0.557000	0.23454	0.768000	0.33290	0.459000	0.35465	ACG	T|0.920;G|0.006	.	strong		0.642	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
ATF6	22926	hgsc.bcm.edu	37	1	161751741	161751741	+	Missense_Mutation	SNP	A	A	G	rs1058405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161751741A>G	ENST00000367942.3	+	3	266	c.199A>G	c.(199-201)Atg>Gtg	p.M67V		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	67	Transcription activation.		M -> L (in dbSNP:rs1058405). {ECO:0000269|PubMed:9271374}.|M -> V (in dbSNP:rs1058405). {ECO:0000269|PubMed:15489334}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	TTTGGATTTGATGCCTTGGGA	0.284													A|||	836	0.166933	0.0113	0.17	5008	,	,		18662	0.2629		0.2724	False		,,,				2504	0.1677				p.M67V		Atlas-SNP	.											.	ATF6	84	.	0			c.A199G	GRCh37	CM077506	ATF6	M	rs1058405	PASS	.	A	VAL/MET	250,4156	145.0+/-179.8	6,238,1959	94.0	91.0	92.0		199	3.8	1.0	1	dbSNP_86	92	2505,6095	409.7+/-349.9	336,1833,2131	yes	missense	ATF6	NM_007348.3	21	342,2071,4090	GG,GA,AA		29.1279,5.6741,21.1825	possibly-damaging	67/671	161751741	2755,10251	2203	4300	6503	SO:0001583	missense	22926	exon3			GATTTGATGCCTT	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"""basic leucine zipper proteins"""	791	protein-coding gene	gene with protein product	"""activating transcription factor 6 alpha"""	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.199A>G	1.37:g.161751741A>G	ENSP00000356919:p.Met67Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	80	53	0.6625	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Missense_Mutation	SNP	ENST00000367942.3	37	CCDS1235.1	462	0.21153846153846154	11	0.022357723577235773	74	0.20441988950276244	169	0.29545454545454547	208	0.27440633245382584	A	9.163	1.019228	0.19355	0.056741	0.291279	ENSG00000118217	ENST00000367942	T	0.13901	2.55	5.04	3.83	0.44106	.	0.093620	0.85682	D	0.000000	T	0.05456	0.0144	L	0.53249	1.67	0.38764	P	0.04560299999999995	B	0.20887	0.049	B	0.22386	0.039	T	0.15752	-1.0426	9	0.27785	T	0.31	-7.2503	8.4476	0.32852	0.8028:0.1972:0.0:0.0	rs1058405;rs17407301;rs17845445;rs17858317;rs52823149;rs61419510;rs1058405	67	P18850	ATF6A_HUMAN	V	67	ENSP00000356919:M67V	ENSP00000356919:M67V	M	+	1	0	ATF6	160018365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.129000	0.42055	2.023000	0.59567	0.454000	0.30748	ATG	A|0.793;G|0.207	0.207	strong		0.284	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348	
OR4A5	81318	hgsc.bcm.edu	37	11	51411460	51411460	+	Silent	SNP	G	G	A	rs34285763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:51411460G>A	ENST00000319760.6	-	1	988	c.936C>T	c.(934-936)tcC>tcT	p.S312S		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				ACATGAGGACGGACACTCCTC	0.373													.|||	466	0.0930511	0.0938	0.0706	5008	,	,		17363	0.0863		0.1262	False		,,,				2504	0.0808				p.S312S		Atlas-SNP	.											OR4A5,NS,carcinoma,-1,1	OR4A5	116	1	0			c.C936T						PASS	.	G		385,3967		15,355,1806	18.0	19.0	18.0		936	-1.4	0.0	11	dbSNP_126	18	1029,7543		54,921,3311	no	coding-synonymous	OR4A5	NM_001005272.3		69,1276,5117	AA,AG,GG		12.0042,8.8465,10.9409		312/316	51411460	1414,11510	2176	4286	6462	SO:0001819	synonymous_variant	81318	exon1			GAGGACGGACACT	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.936C>T	11.37:g.51411460G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			G|0.897;A|0.103	0.103	strong		0.373	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
TRAK2	66008	hgsc.bcm.edu	37	2	202245423	202245423	+	Missense_Mutation	SNP	A	A	T	rs34594680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202245423A>T	ENST00000332624.3	-	16	3016	c.2588T>A	c.(2587-2589)aTt>aAt	p.I863N		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	863			I -> N (in dbSNP:rs34594680). {ECO:0000269|PubMed:15489334}.		protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						TTGAGGACCAATTTCTGCCTC	0.453													A|||	263	0.052516	0.1233	0.0562	5008	,	,		20783	0.001		0.0527	False		,,,				2504	0.0072				p.I863N		Atlas-SNP	.											.	TRAK2	62	.	0			c.T2588A						PASS	.	A	ASN/ILE	450,3956	214.5+/-233.7	19,412,1772	81.0	86.0	84.0		2588	-2.3	0.0	2	dbSNP_126	84	494,8106	141.7+/-198.0	16,462,3822	yes	missense	TRAK2	NM_015049.2	149	35,874,5594	TT,TA,AA		5.7442,10.2133,7.2582	benign	863/915	202245423	944,12062	2203	4300	6503	SO:0001583	missense	66008	exon16			GGACCAATTTCTG	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.2588T>A	2.37:g.202245423A>T	ENSP00000328875:p.Ile863Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	37	CCDS2347.1	115|115	0.052655677655677656|0.052655677655677656	52|52	0.10569105691056911|0.10569105691056911	18|18	0.049723756906077346|0.049723756906077346	1|1	0.0017482517482517483|0.0017482517482517483	44|44	0.05804749340369393|0.05804749340369393	A|A	1.705|1.705	-0.500469|-0.500469	0.04291|0.04291	0.102133|0.102133	0.057442|0.057442	ENSG00000115993|ENSG00000115993	ENST00000332624|ENST00000542292	T|.	0.06933|.	3.24|.	6.17|6.17	-2.31|-2.31	0.06765|0.06765	.|.	1.354340|.	0.04289|.	N|.	0.345106|.	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|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.17501|0.17501	-1.0367|-1.0367	10|6	0.15499|0.36615	T|T	0.54|0.2	.|.	4.7814|4.7814	0.13204|0.13204	0.4558:0.0:0.3155:0.2286|0.4558:0.0:0.3155:0.2286	rs34594680;rs59285166|rs34594680;rs59285166	863|.	O60296|.	TRAK2_HUMAN|.	N|M	863|769	ENSP00000328875:I863N|.	ENSP00000328875:I863N|ENSP00000445053:L769M	I|L	-|-	2|1	0|2	TRAK2|TRAK2	201953668|201953668	0.001000|0.001000	0.12720|0.12720	0.014000|0.014000	0.15608|0.15608	0.249000|0.249000	0.25844|0.25844	0.062000|0.062000	0.14389|0.14389	-0.627000|-0.627000	0.05589|0.05589	-0.290000|-0.290000	0.09829|0.09829	ATT|TTG	A|0.935;T|0.065	0.065	strong		0.453	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
FBXO4	26272	hgsc.bcm.edu	37	5	41925431	41925431	+	Missense_Mutation	SNP	G	G	A	rs2231916		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:41925431G>A	ENST00000281623.3	+	1	76	c.20G>A	c.(19-21)cGc>cAc	p.R7H	FBXO4_ENST00000509134.1_Missense_Mutation_p.R7H|FBXO4_ENST00000296812.2_Missense_Mutation_p.R7H	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	7					positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				AGCGAGCCGCGCAGCGGAACA	0.706																																					p.R7H		Atlas-SNP	.											.	FBXO4	42	.	0			c.G20A						PASS	.						3.0	5.0	4.0					5																	41925431		1448	2780	4228	SO:0001583	missense	26272	exon1			AGCCGCGCAGCGG	AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"""F-boxes /  ""other"""""	13583	protein-coding gene	gene with protein product		609090	"""F-box only protein 4"""			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.20G>A	5.37:g.41925431G>A	ENSP00000281623:p.Arg7His	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_033484	Q68CU8|Q86VT8|Q9UK98	Missense_Mutation	SNP	ENST00000281623.3	37	CCDS3938.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.601780	0.66445	.	.	ENSG00000151876	ENST00000296812;ENST00000281623;ENST00000509134	T;T;T	0.65364	-0.15;-0.15;-0.15	4.14	4.14	0.48551	.	0.532611	0.20854	N	0.084478	T	0.41789	0.1174	N	0.14661	0.345	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.04013	0.0;0.001;0.001	T	0.24440	-1.0160	10	0.49607	T	0.09	-12.9866	8.033	0.30476	0.1107:0.0:0.8893:0.0	.	7;7;7	D6RAJ6;Q9UKT5;Q9UKT5-2	.;FBX4_HUMAN;.	H	7	ENSP00000296812:R7H;ENSP00000281623:R7H;ENSP00000421749:R7H	ENSP00000281623:R7H	R	+	2	0	FBXO4	41961188	0.010000	0.17322	0.037000	0.18230	0.752000	0.42762	1.241000	0.32743	2.311000	0.77944	0.563000	0.77884	CGC	.	.	alt		0.706	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1		
MKI67	4288	hgsc.bcm.edu	37	10	129914162	129914162	+	Missense_Mutation	SNP	G	G	C	rs143381225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:129914162G>C	ENST00000368654.3	-	7	885	c.510C>G	c.(508-510)gaC>gaG	p.D170E	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	170					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)				TGTCTTTTGAGTCATCTGCGG	0.413													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18963	0.0		0.003	False		,,,				2504	0.0				p.D170E		Atlas-SNP	.											.	MKI67	363	.	0			c.C510G						PASS	.	G	,GLU/ASP	3,4403	6.2+/-15.9	0,3,2200	202.0	190.0	194.0		,510	2.6	0.0	10	dbSNP_134	194	21,8579	16.0+/-53.3	0,21,4279	yes	intron,missense	MKI67	NM_001145966.1,NM_002417.4	,45	0,24,6479	CC,CG,GG		0.2442,0.0681,0.1845	,possibly-damaging	,170/3257	129914162	24,12982	2203	4300	6503	SO:0001583	missense	4288	exon7			TTTTGAGTCATCT	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.510C>G	10.37:g.129914162G>C	ENSP00000357643:p.Asp170Glu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.09	2.133471	0.37630	6.81E-4	0.002442	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.21543	2.0	3.54	2.64	0.31445	.	1.326700	0.05140	N	0.494199	T	0.12263	0.0298	N	0.19112	0.55	0.09310	N	0.999994	P	0.37864	0.61	B	0.29353	0.101	T	0.20505	-1.0273	9	.	.	.	.	6.9772	0.24683	0.1232:0.0:0.8768:0.0	.	170	P46013	KI67_HUMAN	E	170	ENSP00000357643:D170E	.	D	-	3	2	MKI67	129804152	0.001000	0.12720	0.005000	0.12908	0.042000	0.13812	0.408000	0.21065	1.097000	0.41459	0.655000	0.94253	GAC	G|0.998;C|0.002	0.002	strong		0.413	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
PRR21	643905	hgsc.bcm.edu	37	2	240982271	240982271	+	Silent	SNP	G	G	A	rs76841013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:240982271G>A	ENST00000408934.1	-	1	128	c.129C>T	c.(127-129)caC>caT	p.H43H		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	43	Pro-rich.							p.H43H(4)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GTGAAGAGCCGTGGATGAAGG	0.577													N|||	1226	0.244808	0.1838	0.2061	5008	,	,		19244	0.4167		0.2555	False		,,,				2504	0.1667				p.H43H		Atlas-SNP	.											PRR21,NS,lymphoid_neoplasm,0,4	PRR21	53	4	4	Substitution - coding silent(4)	haematopoietic_and_lymphoid_tissue(4)	c.C129T						PASS	.						110.0	98.0	102.0					2																	240982271		2203	4300	6503	SO:0001819	synonymous_variant	643905	exon1			AGAGCCGTGGATG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.129C>T	2.37:g.240982271G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	35	30	0.857143	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			G|0.755;A|0.245	0.245	strong		0.577	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249984	3249984	+	Missense_Mutation	SNP	C	C	T	rs12295710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:3249984C>T	ENST00000389832.5	-	2	352	c.46G>A	c.(46-48)Ggc>Agc	p.G16S	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Missense_Mutation_p.G15S			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	16			G -> S (in dbSNP:rs12295710).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCTGGGCGCCGTTGGCGGCC	0.672													C|||	1660	0.33147	0.0567	0.3026	5008	,	,		17649	0.4692		0.495	False		,,,				2504	0.4131				p.G16S		Atlas-SNP	.											MRGPRE,colon,carcinoma,+2,1	MRGPRE	35	1	0			c.G46A						PASS	.	C	SER/GLY	484,3440		35,414,1513	31.0	34.0	33.0		43	-2.3	0.0	11	dbSNP_120	33	3932,4356		924,2084,1136	yes	missense	MRGPRE	NM_001039165.2	56	959,2498,2649	TT,TC,CC		47.4421,12.3344,36.1612	benign	15/312	3249984	4416,7796	1962	4144	6106	SO:0001583	missense	116534	exon2			GGGCGCCGTTGGC	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"""GPCR / Class A : Orphans"""	30694	protein-coding gene	gene with protein product		607232	"""G protein-coupled receptor 167"""	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.46G>A	11.37:g.3249984C>T	ENSP00000374482:p.Gly16Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	37		824	0.3772893772893773	34	0.06910569105691057	118	0.3259668508287293	292	0.5104895104895105	380	0.5013192612137203	c	8.567	0.879164	0.17395	0.123344	0.474421	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	2.63	-2.32	0.06745	.	0.918531	0.08824	N	0.888287	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45011	-0.9290	8	0.07030	T	0.85	-1.8484	6.7124	0.23284	0.0:0.2466:0.0:0.7534	rs12295710;rs59380296	15	Q86SM8	MRGRE_HUMAN	S	16;15	.	ENSP00000374482:G15S	G	-	1	0	MRGPRE	3206560	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.223000	0.09177	-0.503000	0.06586	-0.350000	0.07774	GGC	C|0.601;T|0.399	0.399	strong		0.672	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71376999	71376999	+	Missense_Mutation	SNP	G	G	A	rs6574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71376999G>A	ENST00000244230.2	+	11	2252	c.1900G>A	c.(1900-1902)Gaa>Aaa	p.E634K		NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	634			E -> K (in dbSNP:rs6574).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						ATTGCAGGATGAAGGTAAAGA	0.318													G|||	1429	0.285343	0.1838	0.3905	5008	,	,		17497	0.2649		0.2942	False		,,,				2504	0.3599				p.E634K		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.G1900A						PASS	.	G	LYS/GLU	834,3572	321.8+/-297.3	82,670,1451	138.0	144.0	142.0		1900	5.8	1.0	2	dbSNP_52	142	2537,6059	412.1+/-350.7	394,1749,2155	yes	missense	MPHOSPH10	NM_005791.2	56	476,2419,3606	AA,AG,GG		29.5137,18.9287,25.9268	possibly-damaging	634/682	71376999	3371,9631	2203	4298	6501	SO:0001583	missense	10199	exon11			CAGGATGAAGGTA	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1900G>A	2.37:g.71376999G>A	ENSP00000244230:p.Glu634Lys	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	302	132	0.437086	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	626	0.2866300366300366	101	0.20528455284552846	134	0.3701657458563536	175	0.30594405594405594	216	0.2849604221635884	G	21.4	4.150114	0.78001	0.189287	0.295137	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.13307	2.6;2.6	5.85	5.85	0.93711	.	0.111229	0.64402	D	0.000010	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.99999884409	D	0.54964	0.969	P	0.58077	0.832	T	0.52873	-0.8517	9	0.12103	T	0.63	.	18.0364	0.89305	0.0:0.0:1.0:0.0	rs6574;rs357743;rs1129261;rs3177500;rs3186969;rs11549403;rs17429514;rs52821931;rs58145471;rs6574	634	O00566	MPP10_HUMAN	K	634;494	ENSP00000244230:E634K;ENSP00000393034:E494K	ENSP00000244230:E634K	E	+	1	0	MPHOSPH10	71230507	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.869000	0.92326	2.941000	0.99782	0.655000	0.94253	GAA	G|0.736;T|0.001	.	strong		0.318	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
NEK2	4751	hgsc.bcm.edu	37	1	211840498	211840498	+	Missense_Mutation	SNP	T	T	C	rs2230489	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:211840498T>C	ENST00000366999.4	-	7	1199	c.1061A>G	c.(1060-1062)aAc>aGc	p.N354S	NEK2_ENST00000462283.1_5'UTR|NEK2_ENST00000540251.1_Missense_Mutation_p.N311S|NEK2_ENST00000366998.3_Missense_Mutation_p.N354S	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	354	Interaction with PCNT.|Necessary for interaction with MAD1L1.|Required for microtubule binding and for localization to the centrosomes.		N -> S (in dbSNP:rs2230489). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.5}.		blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		CAAGCTGTAGTTCTTCAACAG	0.413													T|||	863	0.172324	0.1778	0.2061	5008	,	,		17236	0.2242		0.1282	False		,,,				2504	0.1329				p.N354S		Atlas-SNP	.											.	NEK2	49	.	0			c.A1061G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	718,3688	297.0+/-284.5	69,580,1554	128.0	128.0	128.0		1061,1061,1061	4.9	1.0	1	dbSNP_98	128	1131,7469	233.5+/-266.7	81,969,3250	yes	missense,missense,missense	NEK2	NM_001204182.1,NM_001204183.1,NM_002497.3	46,46,46	150,1549,4804	CC,CT,TT		13.1512,16.296,14.2165	benign,benign,benign	354/389,354/385,354/446	211840498	1849,11157	2203	4300	6503	SO:0001583	missense	4751	exon7			CTGTAGTTCTTCA	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"""HsPK 21"", ""protein phosphatase 1, regulatory subunit 111"""	604043	"""NIMA (never in mitosis gene a)-related kinase 2"""			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.1061A>G	1.37:g.211840498T>C	ENSP00000355966:p.Asn354Ser	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	217	111	0.511521	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Missense_Mutation	SNP	ENST00000366999.4	37	CCDS1500.1	380	0.17399267399267399	84	0.17073170731707318	61	0.1685082872928177	135	0.23601398601398602	100	0.13192612137203166	T	12.22	1.874092	0.33069	0.16296	0.131512	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	T;T;T	0.36520	1.25;1.25;1.25	4.89	4.89	0.63831	.	0.199697	0.52532	D	0.000068	T	0.00012	0.0000	L	0.45581	1.43	0.24716	P	0.99317538	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.002	T	0.19647	-1.0299	9	0.20519	T	0.43	.	9.1214	0.36788	0.0:0.0829:0.0:0.9171	rs2230489;rs2289726;rs10429965;rs52795825;rs58622133;rs10429965	354;354;354	P51955-2;P51955;P51955-4	.;NEK2_HUMAN;.	S	354;311;354	ENSP00000355966:N354S;ENSP00000440237:N311S;ENSP00000355965:N354S	ENSP00000355965:N354S	N	-	2	0	NEK2	209907121	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	1.120000	0.31271	1.964000	0.57103	0.528000	0.53228	AAC	T|0.684;G|0.030	.	strong		0.413	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
KTN1	3895	hgsc.bcm.edu	37	14	56096686	56096686	+	Silent	SNP	A	A	C	rs74053638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:56096686A>C	ENST00000395314.3	+	7	1160	c.1092A>C	c.(1090-1092)acA>acC	p.T364T	KTN1_ENST00000416613.1_Silent_p.T364T|KTN1_ENST00000395308.1_Silent_p.T364T|KTN1_ENST00000395311.1_Silent_p.T364T|KTN1_ENST00000413890.2_Silent_p.T364T|KTN1_ENST00000395309.3_Silent_p.T364T|KTN1_ENST00000438792.2_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	154	0	0		WXS	Illumina HiSeq	Phase_I	160	72	0.45	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		
TKT	7086	hgsc.bcm.edu	37	3	53269163	53269163	+	Silent	SNP	G	G	A	rs1051483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:53269163G>A	ENST00000462138.1	-	5	553	c.465C>T	c.(463-465)gaC>gaT	p.D155D	TKT_ENST00000296289.6_Silent_p.D108D|TKT_ENST00000423525.2_Silent_p.D155D|TKT_ENST00000423516.1_Silent_p.D163D|TKT_ENST00000461139.1_5'Flank			P29401	TKT_HUMAN	transketolase	155					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		ACAGCTCCCCGTCTCCCAGCA	0.597													G|||	697	0.139177	0.1165	0.1427	5008	,	,		12635	0.1091		0.168	False		,,,				2504	0.1687				p.D163D	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.C489T						PASS	.	G	,	660,3746	281.1+/-275.7	55,550,1598	79.0	76.0	77.0		465,465	-9.1	0.3	3	dbSNP_86	77	1658,6942	304.9+/-307.2	160,1338,2802	no	coding-synonymous,coding-synonymous	TKT	NM_001064.3,NM_001135055.2	,	215,1888,4400	AA,AG,GG		19.2791,14.9796,17.8225	,	155/624,155/624	53269163	2318,10688	2203	4300	6503	SO:0001819	synonymous_variant	7086	exon6			CTCCCCGTCTCCC		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"""Wernicke-Korsakoff syndrome"""	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.465C>T	3.37:g.53269163G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	37	CCDS2871.1																																																																																			G|0.833;C|0.000;A|0.167	0.167	strong		0.597	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
WDR72	256764	hgsc.bcm.edu	37	15	53907948	53907948	+	Missense_Mutation	SNP	G	G	A	rs17730281	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:53907948G>A	ENST00000396328.1	-	15	2694	c.2455C>T	c.(2455-2457)Ctc>Ttc	p.L819F	WDR72_ENST00000557913.1_Missense_Mutation_p.L816F|WDR72_ENST00000559418.1_Missense_Mutation_p.L829F|WDR72_ENST00000360509.5_Missense_Mutation_p.L819F	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	819			L -> F (in dbSNP:rs17730281).							NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		AAAATATTGAGGTGCTTAATG	0.373													G|||	1337	0.266973	0.1248	0.3804	5008	,	,		18191	0.4851		0.2018	False		,,,				2504	0.2209				p.L819F		Atlas-SNP	.											.	WDR72	177	.	0			c.C2455T						PASS	.	G	PHE/LEU	692,3694	282.8+/-276.7	56,580,1557	103.0	105.0	104.0		2455	5.7	1.0	15	dbSNP_123	104	1896,6690	324.5+/-316.5	195,1506,2592	yes	missense	WDR72	NM_182758.2	22	251,2086,4149	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.0825,15.7775,19.9507	probably-damaging	819/1103	53907948	2588,10384	2193	4293	6486	SO:0001583	missense	256764	exon15			TATTGAGGTGCTT	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.2455C>T	15.37:g.53907948G>A	ENSP00000379619:p.Leu819Phe	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	611	0.27976190476190477	65	0.13211382113821138	121	0.3342541436464088	276	0.4825174825174825	149	0.19656992084432717	G	18.65	3.669478	0.67814	0.157775	0.220825	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.69561	-0.41;-0.41	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000004	T	0.00012	0.0000	M	0.80616	2.505	0.23168	P	0.99818646	D	0.76494	0.999	D	0.68765	0.96	T	0.51108	-0.8747	9	0.87932	D	0	.	10.4234	0.44363	0.1487:0.0:0.8513:0.0	rs17730281;rs52809867;rs17730281	819	Q3MJ13	WDR72_HUMAN	F	819	ENSP00000379619:L819F;ENSP00000353699:L819F	ENSP00000353699:L819F	L	-	1	0	WDR72	51695240	0.991000	0.36638	1.000000	0.80357	0.973000	0.67179	2.006000	0.40874	2.703000	0.92315	0.655000	0.94253	CTC	G|0.773;A|0.227	0.227	strong		0.373	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
ACSL1	2180	hgsc.bcm.edu	37	4	185687863	185687863	+	Silent	SNP	A	A	G	rs11727009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:185687863A>G	ENST00000515030.1	-	13	1501	c.1176T>C	c.(1174-1176)ttT>ttC	p.F392F	ACSL1_ENST00000507295.1_Silent_p.F358F|ACSL1_ENST00000454703.2_Silent_p.F221F|ACSL1_ENST00000281455.2_Silent_p.F392F|ACSL1_ENST00000513317.1_Silent_p.F392F|ACSL1_ENST00000437665.3_Silent_p.F221F|ACSL1_ENST00000504342.1_Silent_p.F392F			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	392					adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TCTTGGAGGCAAAGTCCAAGA	0.498													A|||	1076	0.214856	0.2073	0.2277	5008	,	,		20599	0.2153		0.2366	False		,,,				2504	0.1933				p.F392F		Atlas-SNP	.											.	ACSL1	77	.	0			c.T1176C						PASS	.	A		985,3421	368.6+/-318.7	112,761,1330	116.0	109.0	112.0		1176	-1.6	1.0	4	dbSNP_120	112	2018,6582	352.5+/-328.7	226,1566,2508	no	coding-synonymous	ACSL1	NM_001995.2		338,2327,3838	GG,GA,AA		23.4651,22.3559,23.0893		392/699	185687863	3003,10003	2203	4300	6503	SO:0001819	synonymous_variant	2180	exon13			GGAGGCAAAGTCC	BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"""Acyl-CoA synthetase family"""	3569	protein-coding gene	gene with protein product	"""lignoceroyl-CoA synthase"", ""long-chain fatty-acid-coenzyme A ligase 1"""	152425	"""fatty-acid-Coenzyme A ligase, long-chain 2"""	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.1176T>C	4.37:g.185687863A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Silent	SNP	ENST00000515030.1	37	CCDS3839.1																																																																																			A|0.768;G|0.232	0.232	strong		0.498	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
USP25	29761	hgsc.bcm.edu	37	21	17250244	17250244	+	Missense_Mutation	SNP	A	A	C	rs149241751		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:17250244A>C	ENST00000285679.6	+	23	3298	c.2929A>C	c.(2929-2931)Aag>Cag	p.K977Q	USP25_ENST00000285681.2_Missense_Mutation_p.K1009Q|USP25_ENST00000400183.2_Missense_Mutation_p.K1047Q|USP25_ENST00000351097.5_Missense_Mutation_p.K372Q	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	977					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		AATGGAAGAAAAGGATATACT	0.373													A|||	1	0.000199681	0.0	0.0	5008	,	,		15290	0.0		0.001	False		,,,				2504	0.0				p.K977Q		Atlas-SNP	.											.	USP25	156	.	0			c.A2929C						PASS	.	A	GLN/LYS	1,4405	2.1+/-5.4	0,1,2202	111.0	113.0	113.0		2929	4.5	1.0	21	dbSNP_134	113	14,8586	10.5+/-38.8	0,14,4286	yes	missense	USP25	NM_013396.3	53	0,15,6488	CC,CA,AA		0.1628,0.0227,0.1153	benign	977/1056	17250244	15,12991	2203	4300	6503	SO:0001583	missense	29761	exon23			GAAGAAAAGGATA	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2929A>C	21.37:g.17250244A>C	ENSP00000285679:p.Lys977Gln	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	177	98	0.553672	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	12.67	2.007030	0.35415	2.27E-4	0.001628	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.29917	1.94;1.95;1.55;1.95	5.67	4.51	0.55191	.	0.131563	0.64402	D	0.000001	T	0.29458	0.0734	L	0.51422	1.61	0.41488	D	0.9882	B;P;B;P	0.50272	0.082;0.862;0.214;0.933	B;B;B;B	0.41917	0.059;0.37;0.127;0.323	T	0.05037	-1.0910	10	0.49607	T	0.09	-20.4276	11.8858	0.52602	0.8691:0.0:0.0:0.1309	.	1047;372;1009;977	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	Q	1009;977;372;1047	ENSP00000285681:K1009Q;ENSP00000285679:K977Q;ENSP00000299574:K372Q;ENSP00000383044:K1047Q	ENSP00000285679:K977Q	K	+	1	0	USP25	16172115	1.000000	0.71417	0.999000	0.59377	0.173000	0.22820	8.932000	0.92897	0.970000	0.38263	-0.336000	0.08194	AAG	A|0.999;C|0.001	0.001	strong		0.373	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
CDKAL1	54901	hgsc.bcm.edu	37	6	21201493	21201493	+	Silent	SNP	G	G	A	rs9465994	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	44	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	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	
EMILIN3	90187	hgsc.bcm.edu	37	20	39991144	39991144	+	Silent	SNP	A	A	G	rs41307177	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:39991144A>G	ENST00000332312.3	-	4	1257	c.1065T>C	c.(1063-1065)ctT>ctC	p.L355L		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	355						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CCCGGCCATCAAGGCTCTGGT	0.682													A|||	406	0.0810703	0.0598	0.1225	5008	,	,		15115	0.003		0.1799	False		,,,				2504	0.0593				p.L355L		Atlas-SNP	.											EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	0			c.T1065C						PASS	.	A		377,4021		11,355,1833	13.0	16.0	15.0		1065	-1.5	1.0	20	dbSNP_127	15	1411,7175		132,1147,3014	no	coding-synonymous	EMILIN3	NM_052846.1		143,1502,4847	GG,GA,AA		16.4337,8.5721,13.7708		355/767	39991144	1788,11196	2199	4293	6492	SO:0001819	synonymous_variant	90187	exon4			GCCATCAAGGCTC	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1065T>C	20.37:g.39991144A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			A|0.888;G|0.112	0.112	strong		0.682	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
OR52N4	390072	hgsc.bcm.edu	37	11	5776595	5776595	+	Missense_Mutation	SNP	T	T	G	rs12363178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5776595T>G	ENST00000317254.3	+	1	673	c.625T>G	c.(625-627)Tgg>Ggg	p.W209G	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	209			W -> G (in dbSNP:rs12363178). {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)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		CCTCCTGATTTGGGGCTTTGA	0.493													G|||	914	0.182508	0.1475	0.1542	5008	,	,		22325	0.2341		0.1581	False		,,,				2504	0.2219				p.W209G		Atlas-SNP	.											.	OR52N4	55	.	0			c.T625G						PASS	.	G	GLY/TRP	667,3663	694.3+/-405.8	55,557,1553	198.0	183.0	188.0		625	6.1	1.0	11	dbSNP_120	188	1524,7044	726.2+/-406.6	132,1260,2892	yes	missense	OR52N4	NM_001005175.2	184	187,1817,4445	GG,GT,TT		17.7871,15.4042,16.9871	benign	209/322	5776595	2191,10707	2165	4284	6449	SO:0001583	missense	390072	exon1			CTGATTTGGGGCT	AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"""GPCR / Class A : Olfactory receptors"""	15230	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily N, member 4"""				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	ENST00000317254.3:c.625T>G	11.37:g.5776595T>G	ENSP00000323224:p.Trp209Gly	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	254	113	0.444882	NM_001005175	B2RNP8|Q6IF77	Missense_Mutation	SNP	ENST00000317254.3	37	CCDS44528.1	411	0.18818681318681318	80	0.16260162601626016	68	0.1878453038674033	144	0.2517482517482518	119	0.15699208443271767	G	1.009	-0.688422	0.03328	0.154042	0.177871	ENSG00000181074	ENST00000317254	T	0.36157	1.27	6.1	6.1	0.99115	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47455	N	0.000231	T	0.00012	0.0000	N	0.00110	-2.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22591	-1.0212	9	0.51188	T	0.08	.	15.7994	0.78439	0.0:0.0:0.8627:0.1373	rs12363178;rs59977720;rs12363178	209	Q8NGI2	O52N4_HUMAN	G	209	ENSP00000323224:W209G	ENSP00000323224:W209G	W	+	1	0	OR52N4	5733171	0.000000	0.05858	0.984000	0.44739	0.093000	0.18481	0.358000	0.20216	1.609000	0.50190	-0.127000	0.14921	TGG	T|0.816;G|0.184	0.184	strong		0.493	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175	
SEMA5B	54437	hgsc.bcm.edu	37	3	122646828	122646828	+	Missense_Mutation	SNP	A	A	G	rs2276774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:122646828A>G	ENST00000357599.3	-	8	1045	c.659T>C	c.(658-660)aTt>aCt	p.I220T	SEMA5B_ENST00000195173.4_Missense_Mutation_p.I220T|AC078794.1_ENST00000408284.1_RNA|SEMA5B_ENST00000451055.2_Missense_Mutation_p.I274T	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	220	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		I -> T (in dbSNP:rs2276774). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GATCTTCTCAATAGTCCGGCT	0.582													a|||	682	0.136182	0.1846	0.1744	5008	,	,		18987	0.0595		0.1392	False		,,,				2504	0.1196				p.I274T		Atlas-SNP	.											.	SEMA5B	303	.	0			c.T821C						PASS	.		THR/ILE	684,3722	289.2+/-280.3	57,570,1576	76.0	75.0	75.0		659	5.6	0.1	3	dbSNP_100	75	1301,7299	257.2+/-281.3	89,1123,3088	yes	missense	SEMA5B	NM_001031702.2	89	146,1693,4664	GG,GA,AA		15.1279,15.5243,15.2622	possibly-damaging	220/1152	122646828	1985,11021	2203	4300	6503	SO:0001583	missense	54437	exon8			TTCTCAATAGTCC	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.659T>C	3.37:g.122646828A>G	ENSP00000350215:p.Ile220Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	116	41	0.353448	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	282	0.12912087912087913	90	0.18292682926829268	60	0.16574585635359115	32	0.055944055944055944	100	0.13192612137203166	a	11.03	1.520285	0.27211	0.155243	0.151279	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.10382	2.88;2.88;2.88;2.88	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.347111	0.32687	N	0.005776	T	0.00012	0.0000	N	0.12502	0.225	0.36606	P	0.12503699999999995	B;B;B	0.22851	0.062;0.076;0.076	B;B;B	0.32022	0.085;0.139;0.139	T	0.51687	-0.8674	9	0.21014	T	0.42	.	13.7366	0.62821	1.0:0.0:0.0:0.0	rs2276774;rs52822678;rs59346924;rs2276774	162;220;220	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	T	220;220;162;274;220	ENSP00000350215:I220T;ENSP00000195173:I220T;ENSP00000389588:I274T;ENSP00000377208:I220T	ENSP00000195173:I220T	I	-	2	0	SEMA5B	124129518	0.992000	0.36948	0.056000	0.19401	0.862000	0.49288	6.819000	0.75262	2.368000	0.80403	0.529000	0.55759	ATT	A|0.858;G|0.142	0.142	strong		0.582	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
LAX1	54900	hgsc.bcm.edu	37	1	203743122	203743122	+	Silent	SNP	G	G	A	rs3820194	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:203743122G>A	ENST00000442561.2	+	5	900	c.510G>A	c.(508-510)tcG>tcA	p.S170S	LAX1_ENST00000367215.1_3'UTR|LAX1_ENST00000367217.5_Silent_p.S154S	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	170					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TCACTCCCTCGGCACACTGCA	0.532													G|||	1474	0.294329	0.3222	0.1657	5008	,	,		16855	0.2321		0.331	False		,,,				2504	0.3742				p.S170S		Atlas-SNP	.											LAX1,NS,carcinoma,+1,1	LAX1	48	1	0			c.G510A						scavenged	.	G	,	1395,3011	458.0+/-351.8	198,999,1006	100.0	90.0	94.0		462,510	-11.0	0.0	1	dbSNP_107	94	2800,5800	442.1+/-360.0	465,1870,1965	no	coding-synonymous,coding-synonymous	LAX1	NM_001136190.1,NM_017773.3	,	663,2869,2971	AA,AG,GG		32.5581,31.6614,32.2543	,	154/383,170/399	203743122	4195,8811	2203	4300	6503	SO:0001819	synonymous_variant	54900	exon5			TCCCTCGGCACAC	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"""LAT-like membrane associated protein"", ""linker for activation of x cells"""					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.510G>A	1.37:g.203743122G>A		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	157	68	0.433121	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Silent	SNP	ENST00000442561.2	37	CCDS1441.2																																																																																			G|0.691;A|0.309	0.309	strong		0.532	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773	
HLA-DMA	3108	hgsc.bcm.edu	37	6	32917544	32917544	+	Missense_Mutation	SNP	C	C	T	rs1063478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32917544C>T	ENST00000374843.4	-	3	581	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395305.3_Missense_Mutation_p.V71I|HLA-DMA_ENST00000464392.1_5'UTR|HLA-DMA_ENST00000395303.3_Missense_Mutation_p.V132I	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	166	Alpha-2.|Ig-like C1-type.		V -> I (in allele DMA*01:02 and allele DMA*01:04; dbSNP:rs1063478).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						TCCACAGGGACGGAATGATGC	0.498													c|||	870	0.173722	0.0915	0.1974	5008	,	,		20678	0.2391		0.1292	False		,,,				2504	0.2464				p.V166I		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G496A						PASS	.	T	ILE/VAL	283,2739		13,257,1241	78.0	71.0	73.0		496	1.5	0.0	6	dbSNP_86	73	696,4722		34,628,2047	yes	missense	HLA-DMA	NM_006120.3	29	47,885,3288	TT,TC,CC		12.8461,9.3647,11.5995	benign	166/262	32917544	979,7461	1511	2709	4220	SO:0001583	missense	3108	exon3			CAGGGACGGAATG		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.496G>A	6.37:g.32917544C>T	ENSP00000363976:p.Val166Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	37	CCDS4761.1	328	0.15018315018315018	50	0.1016260162601626	55	0.15193370165745856	129	0.22552447552447552	94	0.12401055408970976	c	2.325	-0.354828	0.05138	0.093647	0.128461	ENSG00000204257	ENST00000395305;ENST00000395303;ENST00000374843;ENST00000456800;ENST00000422832	T;T;T;T;T	0.03004	4.08;4.08;4.08;4.08;4.08	5.28	1.54	0.23209	.	1.512590	0.03389	N	0.201603	T	0.00784	0.0026	N	0.16130	0.375	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46830	-0.9163	9	0.33141	T	0.24	.	4.0461	0.09773	0.1635:0.5772:0.0:0.2594	rs1063478;rs13209997;rs17214050;rs17617501;rs17882348;rs45482294;rs52831176;rs1063478	166	Q31604	.	I	71;132;166;196;133	ENSP00000378716:V71I;ENSP00000378714:V132I;ENSP00000363976:V166I;ENSP00000409668:V196I;ENSP00000403122:V133I	ENSP00000363976:V166I	V	-	1	0	HLA-DMA	33025522	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.119000	0.10676	0.095000	0.17434	-0.131000	0.14894	GTC	.	.	weak		0.498	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120	
SRRM1	10250	hgsc.bcm.edu	37	1	24979487	24979487	+	Missense_Mutation	SNP	C	C	T	rs144082896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24979487C>T	ENST00000323848.9	+	8	1319	c.1004C>T	c.(1003-1005)cCa>cTa	p.P335L	SRRM1_ENST00000447431.2_Missense_Mutation_p.P335L|SRRM1_ENST00000374389.4_Missense_Mutation_p.P330L|SRRM1_ENST00000537199.1_Missense_Mutation_p.P204L|SRRM1_ENST00000479034.1_3'UTR	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	335	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		ATGCCTCCTCCACCAAGGCAT	0.448													C|||	7	0.00139776	0.0	0.0	5008	,	,		17867	0.0		0.004	False		,,,				2504	0.0031				p.P335L	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.C1004T						PASS	.	C	LEU/PRO	3,4403	6.2+/-15.9	0,3,2200	58.0	55.0	56.0		1004	5.4	1.0	1	dbSNP_134	56	33,8567	23.4+/-69.3	0,33,4267	yes	missense	SRRM1	NM_005839.3	98	0,36,6467	TT,TC,CC		0.3837,0.0681,0.2768	possibly-damaging	335/905	24979487	36,12970	2203	4300	6503	SO:0001583	missense	10250	exon8			CTCCTCCACCAAG	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1004C>T	1.37:g.24979487C>T	ENSP00000326261:p.Pro335Leu	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	237	100	0.421941	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	17.19	3.326020	0.60743	6.81E-4	0.003837	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389;ENST00000537199	T;T;T;T	0.53206	0.84;0.86;0.86;0.63	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000009	T	0.50120	0.1597	L	0.54323	1.7	0.53688	D	0.999977	P;P	0.50528	0.936;0.895	P;B	0.44477	0.451;0.264	T	0.50338	-0.8840	10	0.39692	T	0.17	.	19.065	0.93106	0.0:1.0:0.0:0.0	.	335;335	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	L	335;335;330;204	ENSP00000326261:P335L;ENSP00000391430:P335L;ENSP00000363510:P330L;ENSP00000441776:P204L	ENSP00000326261:P335L	P	+	2	0	SRRM1	24852074	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	3.240000	0.51368	2.500000	0.84329	0.585000	0.79938	CCA	C|0.997;T|0.003	0.003	strong		0.448	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
NCAPD2	9918	hgsc.bcm.edu	37	12	6635274	6635274	+	Missense_Mutation	SNP	G	G	A	rs10849482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6635274G>A	ENST00000315579.5	+	19	3188	c.2389G>A	c.(2389-2391)Gtg>Atg	p.V797M	NCAPD2_ENST00000542492.1_3'UTR|NCAPD2_ENST00000545962.1_Missense_Mutation_p.V752M	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	797			V -> M (in dbSNP:rs10849482).		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						AGACACACTGGTGAGCATAGG	0.517													G|||	540	0.107827	0.0242	0.1354	5008	,	,		20967	0.0089		0.2107	False		,,,				2504	0.1973				p.V797M		Atlas-SNP	.											.	NCAPD2	99	.	0			c.G2389A						PASS	.	G	MET/VAL	249,4157	143.8+/-178.8	9,231,1963	87.0	83.0	85.0		2389	5.6	1.0	12	dbSNP_120	85	2030,6570	354.8+/-329.6	236,1558,2506	yes	missense	NCAPD2	NM_014865.3	21	245,1789,4469	AA,AG,GG		23.6047,5.6514,17.5227	possibly-damaging	797/1402	6635274	2279,10727	2203	4300	6503	SO:0001583	missense	9918	exon19			ACACTGGTGAGCA	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.2389G>A	12.37:g.6635274G>A	ENSP00000325017:p.Val797Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	37	CCDS8548.1	250	0.11446886446886446	20	0.04065040650406504	64	0.17679558011049723	5	0.008741258741258742	161	0.21240105540897097	G	20.6	4.010233	0.75046	0.056514	0.236047	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.56444	0.46;0.46;0.46	5.62	5.62	0.85841	Armadillo-type fold (1);	0.106954	0.64402	D	0.000007	T	0.00039	0.0001	L	0.55743	1.74	0.30658	P	0.754738	P;P;P	0.51653	0.927;0.801;0.947	P;B;P	0.51135	0.66;0.387;0.536	T	0.01988	-1.1234	9	0.46703	T	0.11	-26.7934	13.8923	0.63747	0.0728:0.0:0.9272:0.0	rs10849482;rs17725920;rs60278952;rs10849482	752;758;797	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	M	797;669;752;669	ENSP00000325017:V797M;ENSP00000371895:V669M;ENSP00000444417:V752M	ENSP00000325017:V797M	V	+	1	0	NCAPD2	6505535	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.367000	0.44213	2.653000	0.90120	0.655000	0.94253	GTG	G|0.854;A|0.146	0.146	strong		0.517	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
CLEC10A	10462	hgsc.bcm.edu	37	17	6979179	6979179	+	Silent	SNP	A	A	G	rs364569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	105	0	0		WXS	Illumina HiSeq	Phase_I	103	41	0.398058	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	
ZNF839	55778	hgsc.bcm.edu	37	14	102808273	102808273	+	Missense_Mutation	SNP	C	C	A	rs1053019	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:102808273C>A	ENST00000558850.1	+	8	2543	c.2193C>A	c.(2191-2193)ttC>ttA	p.F731L	ZNF839_ENST00000442396.2_Missense_Mutation_p.F847L|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000262236.5_Missense_Mutation_p.F733L|ZNF839_ENST00000559185.1_Missense_Mutation_p.F731L	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	139	0	0		WXS	Illumina HiSeq	Phase_I	165	69	0.418182	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	
CPPED1	55313	hgsc.bcm.edu	37	16	12798778	12798778	+	Missense_Mutation	SNP	C	C	T	rs149102231	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12798778C>T	ENST00000381774.4	-	3	658	c.418G>A	c.(418-420)Gag>Aag	p.E140K	CPPED1_ENST00000261660.4_Intron|CPPED1_ENST00000433677.2_Intron	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	140	Catalytic.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						CAGAACTCCTCGACGGTCTCG	0.607													C|||	27	0.00539137	0.0045	0.013	5008	,	,		16941	0.0		0.0119	False		,,,				2504	0.0				p.E140K		Atlas-SNP	.											.	CPPED1	41	.	0			c.G418A						PASS	.	C	,LYS/GLU	10,4056		0,10,2023	58.0	62.0	61.0		,418	2.3	0.0	16	dbSNP_134	61	83,8267		0,83,4092	yes	intron,missense	CPPED1	NM_001099455.1,NM_018340.2	,56	0,93,6115	TT,TC,CC		0.994,0.2459,0.749	,benign	,140/315	12798778	93,12323	2033	4175	6208	SO:0001583	missense	55313	exon3			ACTCCTCGACGGT	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.418G>A	16.37:g.12798778C>T	ENSP00000371193:p.Glu140Lys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_018340	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Missense_Mutation	SNP	ENST00000381774.4	37	CCDS42120.1	26	0.011904761904761904	5	0.01016260162601626	8	0.022099447513812154	2	0.0034965034965034965	11	0.014511873350923483	C	0.678	-0.799366	0.02841	0.002459	0.00994	ENSG00000103381	ENST00000381774	D	0.84589	-1.87	5.32	2.26	0.28386	Metallophosphoesterase domain (1);	0.643319	0.17227	N	0.182096	T	0.58090	0.2098	L	0.46819	1.47	0.20489	N	0.999892	B	0.10296	0.003	B	0.13407	0.009	T	0.49263	-0.8958	10	0.06099	T	0.92	-1.2321	2.2291	0.03992	0.1582:0.5187:0.1534:0.1696	.	140	Q9BRF8	CPPED_HUMAN	K	140	ENSP00000371193:E140K	ENSP00000371193:E140K	E	-	1	0	CPPED1	12706279	0.071000	0.21146	0.001000	0.08648	0.085000	0.17905	1.041000	0.30291	0.229000	0.21039	-0.142000	0.14014	GAG	C|0.987;T|0.013	0.013	strong		0.607	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79069121	79069121	+	Silent	SNP	A	A	G	rs11854507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79069121A>G	ENST00000388820.4	-	10	1740	c.1530T>C	c.(1528-1530)gcT>gcC	p.A510A	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	510	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						TGCCGTCCACAGCTGCATCCA	0.627													G|||	1269	0.253395	0.2057	0.268	5008	,	,		16760	0.1399		0.4006	False		,,,				2504	0.273				p.A510A		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.T1530C						PASS	.	G		993,3275		131,731,1272	75.0	55.0	62.0		1530	-5.1	0.9	15	dbSNP_120	62	3203,5133		691,1821,1656	no	coding-synonymous	ADAMTS7	NM_014272.3		822,2552,2928	GG,GA,AA		38.4237,23.2662,33.291		510/1687	79069121	4196,8408	2134	4168	6302	SO:0001819	synonymous_variant	11173	exon10			GTCCACAGCTGCA	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.1530T>C	15.37:g.79069121A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			A|0.706;G|0.294	0.294	strong		0.627	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
NOMO1	23420	hgsc.bcm.edu	37	16	14969016	14969016	+	Missense_Mutation	SNP	T	T	A	rs62038475		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:14969016T>A	ENST00000287667.7	+	19	2349	c.2178T>A	c.(2176-2178)aaT>aaA	p.N726K		NM_014287.3	NP_055102.3	Q15155	NOMO1_HUMAN	NODAL modulator 1	726						integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(6)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|skin(2)	30						AAAACGGCAATGAGGAAGGCG	0.567																																					p.N726K		Atlas-SNP	.											.	NOMO1	60	.	0			c.T2178A						PASS	.						229.0	236.0	234.0					16																	14969016		2197	4299	6496	SO:0001583	missense	23420	exon19			CGGCAATGAGGAA	X57398	CCDS10556.1	16p13.11	2008-02-05			ENSG00000103512	ENSG00000103512			30060	protein-coding gene	gene with protein product		609157				1310294, 15257293	Standard	NM_014287		Approved	PM5	uc002dcv.3	Q15155	OTTHUMG00000090541	ENST00000287667.7:c.2178T>A	16.37:g.14969016T>A	ENSP00000287667:p.Asn726Lys	Somatic	603	1	0.00165837		WXS	Illumina HiSeq	Phase_I	870	263	0.302299	NM_014287	P78421|Q8IW21|Q96DG0	Missense_Mutation	SNP	ENST00000287667.7	37	CCDS10556.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.401964	0.00195	.	.	ENSG00000103512	ENST00000287667;ENST00000456867;ENST00000536948	T	0.03607	3.87	2.86	-1.44	0.08856	.	0.796012	0.12016	N	0.507432	T	0.00967	0.0032	N	0.01352	-0.895	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.41378	-0.9512	10	0.05620	T	0.96	1.8419	1.5646	0.02602	0.4027:0.3305:0.1058:0.161	.	726	Q15155	NOMO1_HUMAN	K	726;726;559	ENSP00000287667:N726K	ENSP00000287667:N726K	N	+	3	2	NOMO1	14876517	0.000000	0.05858	0.005000	0.12908	0.071000	0.16799	-0.760000	0.04756	-0.988000	0.03489	-1.489000	0.00976	AAT	.	.	weak		0.567	NOMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207065.1		
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10908893	10908893	+	Missense_Mutation	SNP	A	A	G	rs1198849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:10908893A>G	ENST00000272238.4	+	6	536	c.427A>G	c.(427-429)Aac>Gac	p.N143D	RP11-791G15.2_ENST00000606907.1_lincRNA|ATP6V1C2_ENST00000381661.3_Missense_Mutation_p.N143D	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	143			N -> D (in dbSNP:rs1198849). {ECO:0000269|PubMed:15489334}.		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)		GGCCGCCTACAACACTCTGAA	0.557													A|||	2266	0.452476	0.3434	0.438	5008	,	,		17633	0.6597		0.3648	False		,,,				2504	0.4867				p.N143D	NSCLC(188;1042 2136 10807 16813 47705)	Atlas-SNP	.											.	ATP6V1C2	73	.	0			c.A427G						PASS	.	A	ASP/ASN,ASP/ASN	1463,2943	470.0+/-355.6	248,967,988	68.0	75.0	73.0		427,427	4.5	0.6	2	dbSNP_87	73	3186,5414	481.3+/-370.6	596,1994,1710	yes	missense,missense	ATP6V1C2	NM_001039362.1,NM_144583.3	23,23	844,2961,2698	GG,GA,AA		37.0465,33.2047,35.745	benign,benign	143/428,143/382	10908893	4649,8357	2203	4300	6503	SO:0001583	missense	245973	exon6			GCCTACAACACTC	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.427A>G	2.37:g.10908893A>G	ENSP00000272238:p.Asn143Asp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001039362	Q96EL8	Missense_Mutation	SNP	ENST00000272238.4	37	CCDS42653.1	967	0.44276556776556775	166	0.33739837398373984	158	0.43646408839779005	356	0.6223776223776224	287	0.3786279683377309	A	14.76	2.630472	0.46944	0.332047	0.370465	ENSG00000143882	ENST00000272238;ENST00000381661	T;T	0.53857	0.6;0.6	5.65	4.48	0.54585	.	0.096395	0.64402	D	0.000001	T	0.00012	0.0000	M	0.92026	3.265	0.22754	P	0.99877951	B;B	0.24823	0.112;0.036	B;B	0.38156	0.266;0.163	T	0.44174	-0.9345	9	0.72032	D	0.01	-2.7858	10.7183	0.46026	0.8398:0.1602:0.0:0.0	rs1198849;rs1734463;rs17364715;rs17850878;rs61181462;rs1198849	143;143	Q8NEY4-2;Q8NEY4	.;VATC2_HUMAN	D	143	ENSP00000272238:N143D;ENSP00000371077:N143D	ENSP00000272238:N143D	N	+	1	0	ATP6V1C2	10826344	1.000000	0.71417	0.636000	0.29352	0.338000	0.28826	5.384000	0.66225	0.951000	0.37770	-0.313000	0.08912	AAC	A|0.600;G|0.400	0.400	strong		0.557	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583	
MUC16	94025	hgsc.bcm.edu	37	19	9005719	9005719	+	Silent	SNP	A	A	G	rs4804375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	127	125	0.984252	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	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205308368	205308368	+	Silent	SNP	C	C	T	rs1105387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205308368C>T	ENST00000367156.3	-	7	1527	c.711G>A	c.(709-711)cgG>cgA	p.R237R	KLHDC8A_ENST00000460687.1_Silent_p.R103R|KLHDC8A_ENST00000539253.1_Silent_p.R237R|KLHDC8A_ENST00000367155.3_Silent_p.R237R|KLHDC8A_ENST00000537168.1_Silent_p.R124R	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	237										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ACTTGGGCTGCCGGTAGAGGC	0.597													C|||	902	0.180112	0.2247	0.134	5008	,	,		19267	0.0308		0.2813	False		,,,				2504	0.2025				p.R237R		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.G711A						PASS	.	C		984,3422	370.3+/-319.5	108,768,1327	54.0	47.0	49.0		711	3.2	1.0	1	dbSNP_86	49	2558,6042	416.8+/-352.2	346,1866,2088	no	coding-synonymous	KLHDC8A	NM_018203.1		454,2634,3415	TT,TC,CC		29.7442,22.3332,27.2336		237/351	205308368	3542,9464	2203	4300	6503	SO:0001819	synonymous_variant	55220	exon4			GGGCTGCCGGTAG		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.711G>A	1.37:g.205308368C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_018203	B3KU70|Q9NVG5	Silent	SNP	ENST00000367156.3	37	CCDS30985.1																																																																																			C|0.754;T|0.246	0.246	strong		0.597	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
DOPEY2	9980	hgsc.bcm.edu	37	21	37664501	37664501	+	Silent	SNP	G	G	A	rs9978057	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:37664501G>A	ENST00000399151.3	+	36	6700	c.6615G>A	c.(6613-6615)agG>agA	p.R2205R		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	2205					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)		p.R2205R(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						ACACTGTCAGGATTCTAGAAC	0.428													G|||	974	0.194489	0.2799	0.2464	5008	,	,		16964	0.0407		0.2465	False		,,,				2504	0.1472				p.R2205R		Atlas-SNP	.											DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	1	Substitution - coding silent(1)	stomach(1)	c.G6615A						scavenged	.	G		1137,3269	402.8+/-332.5	143,851,1209	86.0	86.0	86.0		6615	3.8	1.0	21	dbSNP_119	86	2399,6201	398.5+/-346.1	360,1679,2261	no	coding-synonymous	DOPEY2	NM_005128.2		503,2530,3470	AA,AG,GG		27.8953,25.8057,27.1875		2205/2299	37664501	3536,9470	2203	4300	6503	SO:0001819	synonymous_variant	9980	exon36			TGTCAGGATTCTA	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.6615G>A	21.37:g.37664501G>A		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	37	CCDS13643.1																																																																																			G|0.751;A|0.249	0.249	strong		0.428	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
C2orf57	165100	hgsc.bcm.edu	37	2	232457880	232457880	+	Missense_Mutation	SNP	T	T	C	rs74460533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:232457880T>C	ENST00000313965.2	+	1	306	c.218T>C	c.(217-219)gTt>gCt	p.V73A		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	73										endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	19		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		AAGAGTGCAGTTGTTCCAGAA	0.517													T|||	163	0.0325479	0.0091	0.036	5008	,	,		20873	0.001		0.0775	False		,,,				2504	0.0481				p.V73A		Atlas-SNP	.											C2orf57,NS,carcinoma,+1,1	C2orf57	35	1	0			c.T218C						PASS	.	T	ALA/VAL	60,4346	58.1+/-94.6	0,60,2143	127.0	131.0	130.0		218	-7.2	0.0	2	dbSNP_131	130	666,7934	168.1+/-219.7	20,626,3654	yes	missense	C2orf57	NM_152614.2	64	20,686,5797	CC,CT,TT		7.7442,1.3618,5.582	benign	73/396	232457880	726,12280	2203	4300	6503	SO:0001583	missense	165100	exon1			GTGCAGTTGTTCC	BC034405	CCDS2487.1	2q37.1	2008-02-05			ENSG00000177673	ENSG00000177673			28563	protein-coding gene	gene with protein product						12477932	Standard	NM_152614		Approved	MGC35154	uc002vrz.3	Q53QW1	OTTHUMG00000133226	ENST00000313965.2:c.218T>C	2.37:g.232457880T>C	ENSP00000315557:p.Val73Ala	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	95	38	0.4	NM_152614	Q8N4F2	Missense_Mutation	SNP	ENST00000313965.2	37	CCDS2487.1	79	0.036172161172161175	5	0.01016260162601626	15	0.04143646408839779	0	0.0	59	0.07783641160949868	t	2.793	-0.250867	0.05867	0.013618	0.077442	ENSG00000177673	ENST00000313965	T	0.16196	2.36	3.62	-7.23	0.01480	.	1.814210	0.03502	N	0.218268	T	0.00271	0.0008	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.22452	-1.0216	10	0.02654	T	1	.	0.8686	0.01209	0.2365:0.3624:0.1623:0.2388	.	73	Q53QW1	CB057_HUMAN	A	73	ENSP00000315557:V73A	ENSP00000315557:V73A	V	+	2	0	C2orf57	232166124	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.775000	0.04679	-2.143000	0.00803	-0.376000	0.06991	GTT	T|0.948;C|0.052	0.052	strong		0.517	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614	
FAM111A	63901	hgsc.bcm.edu	37	11	58920492	58920492	+	Missense_Mutation	SNP	C	C	G	rs116918730	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58920492C>G	ENST00000528737.1	+	5	4169	c.1351C>G	c.(1351-1353)Caa>Gaa	p.Q451E	FAM111A_ENST00000420244.1_Missense_Mutation_p.Q451E|FAM111A_ENST00000361723.3_Missense_Mutation_p.Q451E|FAM111A_ENST00000531147.1_Missense_Mutation_p.Q451E|FAM111A_ENST00000533703.1_Missense_Mutation_p.Q451E			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	451	Interaction with SV40 large T antigen.				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)				AAATGGACAACAAGTACCTAT	0.363													C|||	77	0.0153754	0.0023	0.0288	5008	,	,		22708	0.001		0.0437	False		,,,				2504	0.0092				p.Q451E		Atlas-SNP	.											.	FAM111A	57	.	0			c.C1351G						PASS	.	C	GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN	38,4364	43.1+/-76.7	0,38,2163	90.0	93.0	92.0		1351,1351,1351,1351,1351	-1.8	0.0	11	dbSNP_132	92	413,8177	129.8+/-187.9	15,383,3897	yes	missense,missense,missense,missense,missense	FAM111A	NM_001142519.1,NM_001142520.1,NM_001142521.1,NM_022074.3,NM_198847.2	29,29,29,29,29	15,421,6060	GG,GC,CC		4.8079,0.8632,3.4714	benign,benign,benign,benign,benign	451/612,451/612,451/612,451/612,451/612	58920492	451,12541	2201	4295	6496	SO:0001583	missense	63901	exon5			GGACAACAAGTAC	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.1351C>G	11.37:g.58920492C>G	ENSP00000434435:p.Gln451Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_001142520	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Missense_Mutation	SNP	ENST00000528737.1	37	CCDS7973.1	52	0.023809523809523808	3	0.006097560975609756	15	0.04143646408839779	1	0.0017482517482517483	33	0.04353562005277045	C	0.427	-0.905422	0.02453	0.008632	0.048079	ENSG00000166801	ENST00000528737;ENST00000420244;ENST00000361723;ENST00000533703;ENST00000531147	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.04	-1.75	0.08031	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	1.264940	0.05268	N	0.516963	T	0.04092	0.0114	N	0.17474	0.49	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.15206	-1.0445	10	0.09843	T	0.71	-16.2634	9.6028	0.39615	0.4381:0.2104:0.3516:0.0	.	451	Q96PZ2	F111A_HUMAN	E	451	ENSP00000434435:Q451E;ENSP00000406683:Q451E;ENSP00000355264:Q451E;ENSP00000433154:Q451E;ENSP00000431631:Q451E	ENSP00000355264:Q451E	Q	+	1	0	FAM111A	58677068	0.000000	0.05858	0.000000	0.03702	0.180000	0.23129	-2.314000	0.01125	-0.376000	0.07943	-0.211000	0.12701	CAA	C|0.966;G|0.034	0.034	strong		0.363	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074	
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12087921G>C	ENST00000358987.3	+	2	199	c.72G>C	c.(70-72)tcG>tcC	p.S24S	ZNF763_ENST00000592625.1_Silent_p.S24S|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000538752.1_Silent_p.S44S|ZNF763_ENST00000343949.5_Silent_p.S27S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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						TGGATATTTCGCAGAGGAAAC	0.493													N|||	4	0.000798722	0.0023	0.0	5008	,	,		18630	0.0		0.001	False		,,,				2504	0.0				p.S27S		Atlas-SNP	.											ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	0			c.G81C						scavenged	.						150.0	152.0	151.0					19																	12087921		2203	4300	6503	SO:0001819	synonymous_variant	284390	exon2			TATTTCGCAGAGG	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.72G>C	19.37:g.12087921G>C		Somatic	174	3	0.0172414		WXS	Illumina HiSeq	Phase_I	193	15	0.0777202	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.	.	alt		0.493	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
CYB5RL	606495	hgsc.bcm.edu	37	1	54661150	54661150	+	Missense_Mutation	SNP	C	C	T	rs946448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:54661150C>T	ENST00000534324.1	-	1	139	c.140G>A	c.(139-141)aGg>aAg	p.R47K	CYB5RL_ENST00000497820.1_Missense_Mutation_p.R47K|CYB5RL_ENST00000537208.1_Missense_Mutation_p.R47K|CYB5RL_ENST00000401046.3_5'UTR|CYB5RL_ENST00000542737.1_Missense_Mutation_p.R47K|RP11-446E24.4_ENST00000311841.7_Missense_Mutation_p.R47K|CYB5RL_ENST00000419823.2_Missense_Mutation_p.R47K|CYB5RL_ENST00000287899.8_Missense_Mutation_p.R47K|MRPL37_ENST00000487096.1_Intron			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	47	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	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	
PM20D1	148811	hgsc.bcm.edu	37	1	205817018	205817018	+	Missense_Mutation	SNP	T	T	C	rs11540015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205817018T>C	ENST00000367136.4	-	2	295	c.251A>G	c.(250-252)cAt>cGt	p.H84R	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	84				H -> R (in Ref. 3; AAH39170). {ECO:0000305}.	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)			CTGACCTTTATGAATGTATTT	0.433													T|||	779	0.155551	0.0545	0.062	5008	,	,		19451	0.3978		0.0964	False		,,,				2504	0.1697				p.H84R		Atlas-SNP	.											.	PM20D1	56	.	0			c.A251G						PASS	.	T	ARG/HIS	252,4150	129.4+/-166.1	4,244,1953	45.0	40.0	42.0		251	-9.7	0.0	1	dbSNP_134	42	617,7939	152.8+/-207.3	8,601,3669	no	missense	PM20D1	NM_152491.4	29	12,845,5622	CC,CT,TT		7.2113,5.7247,6.7063	benign	84/503	205817018	869,12089	2201	4278	6479	SO:0001583	missense	148811	exon2			CCTTTATGAATGT		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.251A>G	1.37:g.205817018T>C	ENSP00000356104:p.His84Arg	Somatic	414	0	0		WXS	Illumina HiSeq	Phase_I	552	210	0.380435	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	352	0.16117216117216118	24	0.04878048780487805	23	0.06353591160220995	232	0.40559440559440557	73	0.09630606860158311	T	0.087	-1.173601	0.01646	0.057247	0.072113	ENSG00000162877	ENST00000367136	T	0.06933	3.24	4.86	-9.72	0.00515	.	0.648666	0.16780	N	0.199831	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	0.44802	-0.9304	9	0.12766	T	0.61	.	10.3431	0.43891	0.0:0.3064:0.0951:0.5986	rs11540015	84	Q6GTS8	P20D1_HUMAN	R	84	ENSP00000356104:H84R	ENSP00000356104:H84R	H	-	2	0	PM20D1	204083641	0.000000	0.05858	0.006000	0.13384	0.284000	0.27059	-2.964000	0.00671	-1.525000	0.01762	-0.337000	0.08149	CAT	.	.	weak		0.433	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
KRT77	374454	hgsc.bcm.edu	37	12	53090190	53090190	+	Silent	SNP	C	C	T	rs7138818	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53090190C>T	ENST00000341809.3	-	3	811	c.783G>A	c.(781-783)agG>agA	p.R261R	RP11-641A6.3_ENST00000547533.1_RNA|KRT77_ENST00000537195.1_Silent_p.R28R	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	261	Coil 1B.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R261R(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CGCTGCCAGTCCTCTTGTTGA	0.567													C|||	2038	0.406949	0.4826	0.4092	5008	,	,		21399	0.25		0.4026	False		,,,				2504	0.4693				p.R261R		Atlas-SNP	.											KRT77,NS,carcinoma,0,1	KRT77	58	1	1	Substitution - coding silent(1)	stomach(1)	c.G783A						PASS	.	C		1987,2419	557.0+/-379.6	439,1109,655	164.0	118.0	134.0		783	3.6	0.8	12	dbSNP_116	134	3625,4975	522.2+/-380.1	763,2099,1438	no	coding-synonymous	KRT77	NM_175078.2		1202,3208,2093	TT,TC,CC		42.1512,45.0976,43.1493		261/579	53090190	5612,7394	2203	4300	6503	SO:0001819	synonymous_variant	374454	exon3			GCCAGTCCTCTTG	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.783G>A	12.37:g.53090190C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																			C|0.590;T|0.410	0.410	strong		0.567	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
MDC1	9656	hgsc.bcm.edu	37	6	30672463	30672463	+	Silent	SNP	G	G	A	rs10947087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30672463G>A	ENST00000376406.3	-	10	5144	c.4497C>T	c.(4495-4497)tcC>tcT	p.S1499S	MDC1_ENST00000376405.2_Silent_p.S1235S|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1499	Interaction with the PRKDC complex.				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						CTGTGGAGGCGGAAGCCTGTA	0.562								Other conserved DNA damage response genes					G|||	144	0.028754	0.0711	0.0144	5008	,	,		20170	0.0159		0.0159	False		,,,				2504	0.0082				p.S1499S		Atlas-SNP	.											.	MDC1	218	.	0			c.C4497T						PASS	.	G		295,4111	155.5+/-188.7	10,275,1918	90.0	104.0	100.0		4497	-2.5	0.0	6	dbSNP_120	100	132,8466	65.6+/-127.9	1,130,4168	no	coding-synonymous	MDC1	NM_014641.2		11,405,6086	AA,AG,GG		1.5352,6.6954,3.2836		1499/2090	30672463	427,12577	2203	4299	6502	SO:0001819	synonymous_variant	9656	exon10			GGAGGCGGAAGCC	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.4497C>T	6.37:g.30672463G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	233	118	0.506438	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	37	CCDS34384.1																																																																																			G|0.962;A|0.038	0.038	strong		0.562	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
NUP88	4927	hgsc.bcm.edu	37	17	5290033	5290033	+	Silent	SNP	T	T	C	rs1071705	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	156	0	0		WXS	Illumina HiSeq	Phase_I	154	83	0.538961	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	
MLPH	79083	hgsc.bcm.edu	37	2	238443226	238443226	+	Missense_Mutation	SNP	A	A	G	rs2292884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238443226A>G	ENST00000264605.3	+	9	1334	c.1040A>G	c.(1039-1041)cAt>cGt	p.H347R	MLPH_ENST00000338530.4_Intron|MLPH_ENST00000409373.1_Intron|MLPH_ENST00000468178.1_Intron|MLPH_ENST00000445024.2_Missense_Mutation_p.H347R|MLPH_ENST00000410032.1_Intron	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	347			H -> R (in dbSNP:rs2292884).		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)		CTGAATAAGCATATTTCAGCT	0.552													G|||	1860	0.371406	0.621	0.3098	5008	,	,		20283	0.2748		0.2097	False		,,,				2504	0.3436				p.H347R		Atlas-SNP	.											.	MLPH	41	.	0			c.A1040G						PASS	.	G	,ARG/HIS	2503,1903	545.1+/-376.7	712,1079,412	132.0	126.0	128.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,1040	0.0	0.0	2	dbSNP_100	128	2189,6411	711.9+/-405.9	269,1651,2380	yes	intron,missense	MLPH	NM_001042467.1,NM_024101.5	,29	981,2730,2792	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	25.4535,43.1911,36.0757	,benign	,347/601	238443226	4692,8314	2203	4300	6503	SO:0001583	missense	79083	exon9			ATAAGCATATTTC	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.1040A>G	2.37:g.238443226A>G	ENSP00000264605:p.His347Arg	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	186	81	0.435484	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	723	0.33104395604395603	305	0.6199186991869918	98	0.27071823204419887	159	0.27797202797202797	161	0.21240105540897097	G	0.005	-2.149150	0.00328	0.568089	0.254535	ENSG00000115648	ENST00000264605;ENST00000445024;ENST00000437893	T;T;T	0.14144	3.1;3.01;2.53	3.99	0.0132	0.14094	.	0.873451	0.09484	N	0.795883	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	0.43015	-0.9417	9	0.02654	T	1	-1.4822	8.7039	0.34343	0.4573:0.0:0.5427:0.0	rs2292884;rs11539362;rs60898014;rs2292884	8;347	Q53QV8;Q9BV36	.;MELPH_HUMAN	R	347;347;107	ENSP00000264605:H347R;ENSP00000414849:H347R;ENSP00000412438:H107R	ENSP00000264605:H347R	H	+	2	0	MLPH	238107965	0.000000	0.05858	0.000000	0.03702	0.557000	0.35523	0.241000	0.18065	-0.177000	0.10690	-0.119000	0.15052	CAT	A|0.644;G|0.356	0.356	strong		0.552	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
PASK	23178	hgsc.bcm.edu	37	2	242054718	242054718	+	Silent	SNP	G	G	A	rs61748659	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242054718G>A	ENST00000405260.1	-	13	3881	c.3183C>T	c.(3181-3183)caC>caT	p.H1061H	PASK_ENST00000234040.4_Silent_p.H1061H|PASK_ENST00000475666.1_5'Flank|PASK_ENST00000358649.4_Silent_p.H1061H|PASK_ENST00000403638.3_Silent_p.H1061H|PASK_ENST00000544142.1_Silent_p.H875H|PASK_ENST00000539818.1_Silent_p.H845H	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1061	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)		TGATATTGGCGTGCTCCACCC	0.408													G|||	56	0.0111821	0.0023	0.0187	5008	,	,		21449	0.0		0.0298	False		,,,				2504	0.0102				p.H1061H		Atlas-SNP	.											.	PASK	230	.	0			c.C3183T						PASS	.	G		23,4383	29.0+/-57.7	0,23,2180	178.0	161.0	167.0		3183	-3.4	0.9	2	dbSNP_129	167	261,8339	101.2+/-162.5	3,255,4042	no	coding-synonymous	PASK	NM_015148.2		3,278,6222	AA,AG,GG		3.0349,0.522,2.1836		1061/1324	242054718	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon13			ATTGGCGTGCTCC	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.3183C>T	2.37:g.242054718G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			G|0.982;A|0.018	0.018	strong		0.408	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
BBS12	166379	hgsc.bcm.edu	37	4	123664427	123664427	+	Silent	SNP	G	G	C	rs13135766	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123664427G>C	ENST00000314218.3	+	2	1573	c.1380G>C	c.(1378-1380)gtG>gtC	p.V460V	BBS12_ENST00000542236.1_Silent_p.V460V	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	460					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TTACACAAGTGAATGAAGATT	0.478									Bardet-Biedl syndrome				G|||	474	0.0946486	0.0484	0.1081	5008	,	,		19718	0.0		0.2177	False		,,,				2504	0.1186				p.V460V		Atlas-SNP	.											.	BBS12	63	.	0			c.G1380C						PASS	.	G	,	294,4112	161.4+/-193.6	15,264,1924	79.0	79.0	79.0		1380,1380	3.0	0.2	4	dbSNP_121	79	1981,6619	347.3+/-326.5	241,1499,2560	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	256,1763,4484	CC,CG,GG		23.0349,6.6727,17.4919	,	460/711,460/711	123664427	2275,10731	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ACAAGTGAATGAA	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1380G>C	4.37:g.123664427G>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	145	53	0.365517	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			G|0.853;C|0.147	0.147	strong		0.478	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
GLDC	2731	hgsc.bcm.edu	37	9	6589230	6589230	+	Silent	SNP	C	C	T	rs121964976	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:6589230C>T	ENST00000321612.6	-	12	1695	c.1545G>A	c.(1543-1545)agG>agA	p.R515R		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	515			R -> S (in NKH; dbSNP:rs121964976). {ECO:0000269|PubMed:11286506}.		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)	ACGGGCTGGTCCTCTTGAACA	0.498													C|||	87	0.0173722	0.0197	0.0317	5008	,	,		15961	0.0		0.0358	False		,,,				2504	0.0031				p.R515R		Atlas-SNP	.											.	GLDC	118	.	0			c.G1545A	GRCh37	CM002029	GLDC	M	rs121964976	PASS	.	C		26,4380	31.7+/-61.6	0,26,2177	172.0	137.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1545	-2.2	0.9	9	dbSNP_133	149	264,8336	101.9+/-163.1	4,256,4040	no	coding-synonymous	GLDC	NM_000170.2		4,282,6217	TT,TC,CC		3.0698,0.5901,2.2297		515/1021	6589230	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon12			GCTGGTCCTCTTG	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.1545G>A	9.37:g.6589230C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			T|0.021;G|0.000;C|0.978	0.021	strong		0.498	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
KIF26A	26153	hgsc.bcm.edu	37	14	104633227	104633227	+	Silent	SNP	A	A	C	rs76304797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104633227A>C	ENST00000423312.2	+	5	955	c.955A>C	c.(955-957)Agg>Cgg	p.R319R	KIF26A_ENST00000315264.7_Silent_p.R180R	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	319					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GGCCTCCAAGAGGAAGAAGCC	0.697													c|||	114	0.0227636	0.0023	0.036	5008	,	,		13321	0.0		0.0586	False		,,,				2504	0.0276				p.R319R		Atlas-SNP	.											.	KIF26A	84	.	0			c.A955C						PASS	.			43,3959		0,43,1958	7.0	11.0	10.0		955	3.1	1.0	14	dbSNP_132	10	503,7777		18,467,3655	no	coding-synonymous	KIF26A	NM_015656.1		18,510,5613	CC,CA,AA		6.0749,1.0745,4.4455		319/1883	104633227	546,11736	2001	4140	6141	SO:0001819	synonymous_variant	26153	exon5			TCCAAGAGGAAGA	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.955A>C	14.37:g.104633227A>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			A|0.973;C|0.027	0.027	strong		0.697	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
SLC39A5	283375	hgsc.bcm.edu	37	12	56630764	56630764	+	Silent	SNP	G	G	A	rs17118409	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56630764G>A	ENST00000266980.4	+	9	1550	c.1257G>A	c.(1255-1257)gcG>gcA	p.A419A	ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_Silent_p.A419A|SLC39A5_ENST00000419232.1_3'UTR	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	419					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CCACCTTAGCGGTCTTCTGCC	0.587													G|||	161	0.0321486	0.0015	0.0519	5008	,	,		18625	0.0357		0.0676	False		,,,				2504	0.0194				p.A419A		Atlas-SNP	.											.	SLC39A5	52	.	0			c.G1257A						PASS	.	G	,	46,4360	47.5+/-82.1	1,44,2158	144.0	158.0	154.0		1257,1257	-8.0	0.8	12	dbSNP_123	154	532,8068	147.9+/-203.2	22,488,3790	no	coding-synonymous,coding-synonymous	SLC39A5	NM_001135195.1,NM_173596.2	,	23,532,5948	AA,AG,GG		6.186,1.044,4.4441	,	419/541,419/541	56630764	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	283375	exon11			CTTAGCGGTCTTC		CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"""Solute carriers"""	20502	protein-coding gene	gene with protein product		608730	"""solute carrier family 39 (metal ion transporter), member 5"""				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.1257G>A	12.37:g.56630764G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_173596	B2R808|Q8N6Y3	Silent	SNP	ENST00000266980.4	37	CCDS8912.2																																																																																			G|0.959;A|0.041	0.041	strong		0.587	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596	
RPLP0	6175	hgsc.bcm.edu	37	12	120637199	120637199	+	Silent	SNP	G	G	A	rs1045110	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120637199G>A	ENST00000551150.1	-	2	459	c.144C>T	c.(142-144)cgC>cgT	p.R48R	RPLP0_ENST00000550296.1_5'UTR|PXN-AS1_ENST00000538804.1_RNA|RPLP0_ENST00000546989.1_Silent_p.R48R|RPLP0_ENST00000392514.4_Silent_p.R48R|PXN-AS1_ENST00000542314.1_RNA|PXN-AS1_ENST00000542265.1_RNA|RPLP0_ENST00000228306.4_Silent_p.R48R|PXN-AS1_ENST00000539446.1_RNA|RPLP0_ENST00000552292.1_5'Flank|PXN-AS1_ENST00000535200.1_RNA|RPLP0_ENST00000313104.5_Silent_p.R48R			P05388	RLA0_HUMAN	ribosomal protein, large, P0	48					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAGCCTTCCCGCGAAGGGACA	0.527													G|||	288	0.057508	0.0045	0.1931	5008	,	,		20083	0.0		0.1064	False		,,,				2504	0.0419				p.R48R		Atlas-SNP	.											RPLP0,NS,carcinoma,-2,1	RPLP0	27	1	0			c.C144T						PASS	.	G	,	105,4301	81.9+/-120.4	1,103,2099	98.0	86.0	90.0		144,144	-10.9	0.2	12	dbSNP_86	90	896,7704	200.9+/-244.5	58,780,3462	no	coding-synonymous,coding-synonymous	RPLP0	NM_001002.3,NM_053275.3	,	59,883,5561	AA,AG,GG		10.4186,2.3831,7.6964	,	48/318,48/318	120637199	1001,12005	2203	4300	6503	SO:0001819	synonymous_variant	6175	exon3			CTTCCCGCGAAGG	AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"""L ribosomal proteins"""	10371	protein-coding gene	gene with protein product	"""acidic ribosomal phosphoprotein P0"""	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.144C>T	12.37:g.120637199G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	99	64	0.646465	NM_053275	Q3B7A4|Q9BVK4	Silent	SNP	ENST00000551150.1	37	CCDS9193.1																																																																																			G|0.926;A|0.074	0.074	strong		0.527	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275	
MAPT	4137	hgsc.bcm.edu	37	17	44060775	44060775	+	Missense_Mutation	SNP	C	C	T	rs63750417	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44060775C>T	ENST00000571987.1	+	5	605	c.605C>T	c.(604-606)cCg>cTg	p.P202L	MAPT_ENST00000347967.5_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.P202L|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.P202L|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.P202L|MAPT_ENST00000535772.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	202					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)	GAGGGGCCGCCGCTGAAGGGG	0.677													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		15400	0.001		0.2406	False		,,,				2504	0.0613				p.P202L		Atlas-SNP	.											.	MAPT	135	.	0			c.C605T						PASS	.	C	LEU/PRO,,,,,,LEU/PRO,	220,4094		7,206,1944	19.0	16.0	17.0		605,,,,,,605,	-0.9	0.0	17	dbSNP_130	17	1886,6602		231,1424,2589	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	98,,,,,,98,	238,1630,4533	TT,TC,CC		22.2196,5.0997,16.4506	probably-damaging,,,,,,probably-damaging,	202/777,,,,,,202/759,	44060775	2106,10696	2157	4244	6401	SO:0001583	missense	4137	exon6			GGCCGCCGCTGAA	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.605C>T	17.37:g.44060775C>T	ENSP00000458742:p.Pro202Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	15.24	2.774625	0.49786	0.050997	0.222196	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.12255	2.71;2.7;2.71	5.05	-0.928	0.10448	.	0.827349	0.10194	N	0.704208	T	0.00012	0.0000	L	0.59436	1.845	0.58432	P	1.0000000000287557E-6	D;D	0.71674	0.996;0.998	P;P	0.55871	0.786;0.688	T	0.24048	-1.0171	9	0.87932	D	0	0.2179	3.6703	0.08272	0.1676:0.4266:0.0:0.4058	rs63750417	202;202	P10636-9;P10636	.;TAU_HUMAN	L	202	ENSP00000340820:P202L;ENSP00000262410:P202L;ENSP00000410838:P202L	ENSP00000262410:P202L	P	+	2	0	MAPT	41416612	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.208000	0.17415	-0.048000	0.13401	-0.367000	0.07326	CCG	C|0.552;A|0.040	.	strong		0.677	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496336	39496336	+	Missense_Mutation	SNP	G	G	T	rs139293	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39496336G>T	ENST00000401756.1	+	2	129	c.53G>T	c.(52-54)cGc>cTc	p.R18L	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.R18L|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.R18L|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.R18L	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	18			R -> L (in dbSNP:rs139293). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					AACAAGCGCCGCCTCAGAAGG	0.522													G|||	1010	0.201677	0.0666	0.2421	5008	,	,		17467	0.1587		0.2932	False		,,,				2504	0.3057				p.R18L		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G53T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	365,4041		14,337,1852	82.0	73.0	76.0		53,53,53,53	-0.2	0.0	22	dbSNP_78	76	2353,6247		307,1739,2254	yes	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	102,102,102,102	321,2076,4106	TT,TG,GG		27.3605,8.2842,20.898	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	18/183,18/201,18/155,18/184	39496336	2718,10288	2203	4300	6503	SO:0001583	missense	164668	exon2			AGCGCCGCCTCAG	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.53G>T	22.37:g.39496336G>T	ENSP00000385741:p.Arg18Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	439	0.20100732600732601	30	0.06097560975609756	83	0.2292817679558011	89	0.1555944055944056	237	0.31266490765171506	.	12.72	2.022317	0.35701	0.082842	0.273605	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.63580	0.04;0.04;-0.05;0.01	3.01	-0.212	0.13169	.	.	.	.	.	T	0.00012	0.0000	M	0.64404	1.975	0.80722	P	0.0	D	0.61080	0.989	D	0.64410	0.925	T	0.24154	-1.0168	8	0.13470	T	0.59	2.1365	5.1589	0.15050	0.4171:0.0:0.5829:0.0	rs139293;rs52833502;rs139293	18	B7TQM3	.	L	18	ENSP00000216123:R18L;ENSP00000411754:R18L;ENSP00000393520:R18L;ENSP00000385741:R18L	ENSP00000216123:R18L	R	+	2	0	APOBEC3H	37826282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.120000	0.10660	0.030000	0.15379	-0.481000	0.04817	CGC	A|0.000;G|0.804;T|0.196	0.196	strong		0.522	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
TPCN2	219931	hgsc.bcm.edu	37	11	68855363	68855363	+	Missense_Mutation	SNP	G	G	A	rs3829241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:68855363G>A	ENST00000294309.3	+	25	2302	c.2201G>A	c.(2200-2202)gGg>gAg	p.G734E	TPCN2_ENST00000442692.2_3'UTR|TPCN2_ENST00000542467.1_Missense_Mutation_p.G552E	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	734			G -> E (associated with SHEP10; dbSNP:rs3829241). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:18488028, ECO:0000269|PubMed:19387438}.		calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GAGGAGCCCGGGGAGGATGAG	0.632													G|||	883	0.176318	0.0386	0.2205	5008	,	,		16887	0.2063		0.3817	False		,,,				2504	0.089				p.G734E		Atlas-SNP	.											.	TPCN2	63	.	0			c.G2201A	GRCh37	CM083200	TPCN2	M	rs3829241	PASS	.	G	GLU/GLY	466,3934	209.5+/-230.2	28,410,1762	27.0	32.0	30.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2201	-3.6	0.0	11	dbSNP_107	30	3292,5296	470.8+/-367.9	620,2052,1622	yes	missense	TPCN2	NM_139075.3	98	648,2462,3384	AA,AG,GG		38.3326,10.5909,28.9344	benign	734/753	68855363	3758,9230	2200	4294	6494	SO:0001583	missense	219931	exon25			AGCCCGGGGAGGA	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.2201G>A	11.37:g.68855363G>A	ENSP00000294309:p.Gly734Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	515	0.2358058608058608	23	0.046747967479674794	98	0.27071823204419887	119	0.20804195804195805	275	0.3627968337730871	G	0.005	-2.162036	0.00318	0.105909	0.383326	ENSG00000162341	ENST00000294309;ENST00000542467	D;D	0.96830	-4.07;-4.14	4.12	-3.6	0.04570	.	0.542623	0.16118	N	0.228770	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	0.38520	-0.9657	9	0.02654	T	1	-0.834	3.6019	0.08028	0.2148:0.4832:0.211:0.091	rs3829241;rs17399449;rs17855775;rs57492255;rs3829241	552;734	E7ETX0;Q8NHX9	.;TPC2_HUMAN	E	734;552	ENSP00000294309:G734E;ENSP00000445551:G552E	ENSP00000294309:G734E	G	+	2	0	TPCN2	68611939	0.575000	0.26692	0.027000	0.17364	0.018000	0.09664	1.094000	0.30951	-0.426000	0.07360	-0.672000	0.03802	GGG	G|0.756;A|0.244	0.244	strong		0.632	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
KRT79	338785	hgsc.bcm.edu	37	12	53227803	53227803	+	Missense_Mutation	SNP	A	A	G	rs2638497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	84	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	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	
PSD3	23362	hgsc.bcm.edu	37	8	18725428	18725428	+	Silent	SNP	A	A	G	rs17127370	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:18725428A>G	ENST00000327040.8	-	4	1492	c.1390T>C	c.(1390-1392)Tta>Cta	p.L464L	PSD3_ENST00000523619.1_Silent_p.L399L|PSD3_ENST00000440756.2_Silent_p.L464L	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	464					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		TCTGAGTATAATGTCTCCAGG	0.458													A|||	503	0.100439	0.2269	0.098	5008	,	,		18498	0.006		0.0507	False		,,,				2504	0.0798				p.L464L		Atlas-SNP	.											.	PSD3	142	.	0			c.T1390C						PASS	.	A		755,3095		77,601,1247	149.0	145.0	146.0		1390	1.6	0.0	8	dbSNP_123	146	453,7845		18,417,3714	no	coding-synonymous	PSD3	NM_015310.3		95,1018,4961	GG,GA,AA		5.4591,19.6104,9.944		464/1048	18725428	1208,10940	1925	4149	6074	SO:0001819	synonymous_variant	23362	exon4			AGTATAATGTCTC	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"""Pleckstrin homology (PH) domain containing"""	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.1390T>C	8.37:g.18725428A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	183	87	0.47541	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	ENST00000327040.8	37	CCDS43720.1																																																																																			A|0.898;G|0.102	0.102	strong		0.458	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	
ACTL7B	10880	hgsc.bcm.edu	37	9	111617650	111617650	+	Silent	SNP	G	G	A	rs11543179	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111617650G>A	ENST00000374667.3	-	1	1589	c.561C>T	c.(559-561)taC>taT	p.Y187Y		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	187						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TGCCGTAGGAGTAGATGGACA	0.652													G|||	1140	0.227636	0.2224	0.2378	5008	,	,		18645	0.2113		0.2097	False		,,,				2504	0.2628				p.Y187Y		Atlas-SNP	.											.	ACTL7B	57	.	0			c.C561T						PASS	.	G		962,3444	346.4+/-309.0	109,744,1350	44.0	43.0	43.0		561	2.8	1.0	9	dbSNP_120	43	1832,6762	306.5+/-307.9	195,1442,2660	no	coding-synonymous	ACTL7B	NM_006686.3		304,2186,4010	AA,AG,GG		21.3172,21.8339,21.4923		187/416	111617650	2794,10206	2203	4297	6500	SO:0001819	synonymous_variant	10880	exon1			GTAGGAGTAGATG	BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.561C>T	9.37:g.111617650G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	37	CCDS6771.1																																																																																			G|0.782;A|0.218	0.218	strong		0.652	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	
FRAS1	80144	hgsc.bcm.edu	37	4	79400868	79400868	+	Silent	SNP	C	C	T	rs11098194	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79400868C>T	ENST00000264895.6	+	56	8879	c.8439C>T	c.(8437-8439)gaC>gaT	p.D2813D		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2809	Calx-beta 3.				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						TCAGTGAGGACGCAGGTAATG	0.522													c|||	1459	0.291334	0.1422	0.4424	5008	,	,		21157	0.3284		0.3608	False		,,,				2504	0.2761				p.D2813D		Atlas-SNP	.											.	FRAS1	779	.	0			c.C8439T						PASS	.	T		728,3410		63,602,1404	49.0	52.0	51.0		8439	0.4	1.0	4	dbSNP_120	51	3175,5245		576,2023,1611	no	coding-synonymous	FRAS1	NM_025074.6		639,2625,3015	TT,TC,CC		37.7078,17.593,31.0798		2813/4013	79400868	3903,8655	2069	4210	6279	SO:0001819	synonymous_variant	80144	exon56			TGAGGACGCAGGT	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.8439C>T	4.37:g.79400868C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	704	0.32234432234432236	84	0.17073170731707318	157	0.43370165745856354	183	0.31993006993006995	280	0.36939313984168864	c	0.014	-1.599207	0.00849	0.17593	0.377078	ENSG00000138759	ENST00000512123	.	.	.	5.72	0.416	0.16416	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999977356	.	.	.	.	.	.	T	0.45101	-0.9284	3	.	.	.	.	11.7091	0.51614	0.0:0.1726:0.0:0.8274	rs11098194	.	.	.	C	1042	.	.	R	+	1	0	FRAS1	79619892	1.000000	0.71417	0.996000	0.52242	0.001000	0.01503	1.381000	0.34362	-0.110000	0.12022	-1.610000	0.00802	CGC	C|0.673;T|0.327	0.327	strong		0.522	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DEFB114	245928	hgsc.bcm.edu	37	6	49928116	49928116	+	Silent	SNP	G	G	A	rs17736782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:49928116G>A	ENST00000322066.3	-	2	98	c.99C>T	c.(97-99)taC>taT	p.Y33Y		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	33					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					TACAACGACCGTAACGTTTGG	0.353													G|||	297	0.0593051	0.0272	0.0648	5008	,	,		15618	0.0079		0.1282	False		,,,				2504	0.0808				p.Y33Y		Atlas-SNP	.											.	DEFB114	12	.	0			c.C99T						PASS	.	G		209,4197	128.6+/-165.4	5,199,1999	108.0	97.0	101.0		99	-7.1	0.0	6	dbSNP_123	101	1107,7491	230.3+/-264.7	68,971,3260	no	coding-synonymous	DEFB114	NM_001037499.1		73,1170,5259	AA,AG,GG		12.8751,4.7435,10.12		33/70	49928116	1316,11688	2203	4299	6502	SO:0001819	synonymous_variant	245928	exon2			ACGACCGTAACGT	DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"""Defensins, beta"""	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.99C>T	6.37:g.49928116G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_001037499	Q8NES9	Silent	SNP	ENST00000322066.3	37	CCDS34474.1																																																																																			G|0.916;A|0.084	0.084	strong		0.353	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499	
H6PD	9563	hgsc.bcm.edu	37	1	9323910	9323910	+	Missense_Mutation	SNP	G	G	A	rs6688832	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:9323910G>A	ENST00000377403.2	+	5	1660	c.1358G>A	c.(1357-1359)cGg>cAg	p.R453Q	H6PD_ENST00000602477.1_Missense_Mutation_p.R464Q	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	453	Glucose 1-dehydrogenase.		R -> Q (in CRD; less than 50% of activity than wild-type; dbSNP:rs6688832). {ECO:0000269|PubMed:12858176, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)		AGCCCTGTGCGGGAGCGGGAC	0.597													A|||	1951	0.389577	0.4932	0.3732	5008	,	,		18364	0.4812		0.2485	False		,,,				2504	0.3119				p.R453Q		Atlas-SNP	.											.	H6PD	71	.	0			c.G1358A	GRCh37	CM031993	H6PD	M	rs6688832	PASS	.	A	GLN/ARG	2017,2389	611.7+/-391.8	456,1105,642	64.0	74.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1358	-2.1	0.1	1	dbSNP_116	71	1971,6629	723.0+/-406.4	223,1525,2552	yes	missense	H6PD	NM_004285.3	43	679,2630,3194	AA,AG,GG		22.9186,45.7785,30.6628	benign	453/792	9323910	3988,9018	2203	4300	6503	SO:0001583	missense	9563	exon5			CTGTGCGGGAGCG	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.1358G>A	1.37:g.9323910G>A	ENSP00000366620:p.Arg453Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	795	0.364010989010989	225	0.4573170731707317	123	0.3397790055248619	260	0.45454545454545453	187	0.24670184696569922	A	0.078	-1.188930	0.01607	0.457785	0.229186	ENSG00000049239	ENST00000377403	D	0.98264	-4.83	5.53	-2.12	0.07165	.	0.705587	0.14737	N	0.301437	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32824	-0.9892	9	0.17832	T	0.49	-13.5512	4.5195	0.11952	0.3753:0.0952:0.4337:0.0958	rs6688832;rs17286908;rs52797480;rs58250722;rs6688832	453	O95479	G6PE_HUMAN	Q	453	ENSP00000366620:R453Q	ENSP00000366620:R453Q	R	+	2	0	H6PD	9246497	0.001000	0.12720	0.054000	0.19295	0.017000	0.09413	-0.091000	0.11146	-0.530000	0.06349	-1.197000	0.01672	CGG	G|0.662;A|0.338	0.338	strong		0.597	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
CAPN12	147968	hgsc.bcm.edu	37	19	39233146	39233146	+	Silent	SNP	A	A	G	rs936524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39233146A>G	ENST00000328867.4	-	3	638	c.330T>C	c.(328-330)gcT>gcC	p.A110A	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_5'UTR	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	110	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			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)			GGGAGGCGGCAGCTGCAAGGA	0.617													G|||	3361	0.671126	0.5386	0.6196	5008	,	,		15466	0.623		0.7694	False		,,,				2504	0.8354				p.A110A		Atlas-SNP	.											.	CAPN12	43	.	0			c.T330C						PASS	.	G		2395,2011	552.9+/-378.6	648,1099,456	68.0	57.0	61.0		330	-9.1	0.1	19	dbSNP_86	61	6413,2187	369.4+/-335.5	2412,1589,299	no	coding-synonymous	CAPN12	NM_144691.3		3060,2688,755	GG,GA,AA		25.4302,45.6423,32.2774		110/720	39233146	8808,4198	2203	4300	6503	SO:0001819	synonymous_variant	147968	exon3			GGCGGCAGCTGCA	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.330T>C	19.37:g.39233146A>G		Somatic	283	2	0.00706714		WXS	Illumina HiSeq	Phase_I	297	296	0.996633	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			A|0.326;G|0.674	0.674	strong		0.617	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
POSTN	10631	hgsc.bcm.edu	37	13	38138689	38138689	+	Missense_Mutation	SNP	C	C	T	rs9547952	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:38138689C>T	ENST00000379747.4	-	22	2557	c.2440G>A	c.(2440-2442)Gtg>Atg	p.V814M	POSTN_ENST00000379749.4_Missense_Mutation_p.V786M|POSTN_ENST00000541179.1_Missense_Mutation_p.V759M|POSTN_ENST00000379742.4_Missense_Mutation_p.V757M|POSTN_ENST00000379743.4_Missense_Mutation_p.V787M|POSTN_ENST00000541481.1_Missense_Mutation_p.V727M	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	814			V -> M (in dbSNP:rs9547952).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		AACTTCCTCACGGGTGTGTCT	0.348													C|||	496	0.0990415	0.1384	0.1758	5008	,	,		12858	0.0685		0.0706	False		,,,				2504	0.0521				p.V814M		Atlas-SNP	.											.	POSTN	161	.	0			c.G2440A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	535,3871	242.8+/-252.7	38,459,1706	154.0	140.0	145.0		2269,2275,2185,2440	5.2	1.0	13	dbSNP_119	145	508,8092	144.0+/-200.0	13,482,3805	yes	missense,missense,missense,missense	POSTN	NM_001135934.1,NM_001135935.1,NM_001135936.1,NM_006475.2	21,21,21,21	51,941,5511	TT,TC,CC		5.907,12.1425,8.0194	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	757/780,759/782,729/752,814/837	38138689	1043,11963	2203	4300	6503	SO:0001583	missense	10631	exon22			TCCTCACGGGTGT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.2440G>A	13.37:g.38138689C>T	ENSP00000369071:p.Val814Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	65	24	0.369231	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	212	0.09706959706959707	61	0.12398373983739837	48	0.13259668508287292	42	0.07342657342657342	61	0.08047493403693931	C	14.37	2.513934	0.44763	0.121425	0.05907	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.93763	-3.28;-3.08;-3.09;-3.09;-3.08;-3.12	5.18	5.18	0.71444	.	0.099518	0.44097	D	0.000491	T	0.14442	0.0349	L	0.47716	1.5	0.52099	P	5.8000000000002494E-5	P;P;B;B;P;P;B	0.49696	0.88;0.686;0.114;0.157;0.927;0.686;0.066	B;B;B;B;P;B;B	0.47528	0.26;0.178;0.041;0.046;0.549;0.178;0.054	T	0.62478	-0.6846	9	0.54805	T	0.06	.	15.7637	0.78106	0.0:1.0:0.0:0.0	rs9547952;rs52820352;rs57362419;rs9547952	699;727;787;759;729;757;814	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	M	759;786;814;787;757;727	ENSP00000437959:V759M;ENSP00000369073:V786M;ENSP00000369071:V814M;ENSP00000369067:V787M;ENSP00000369066:V757M;ENSP00000437953:V727M	ENSP00000369066:V757M	V	-	1	0	POSTN	37036689	0.998000	0.40836	0.998000	0.56505	0.868000	0.49771	1.879000	0.39618	2.562000	0.86427	0.555000	0.69702	GTG	C|0.916;T|0.084	0.084	strong		0.348	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
TJAP1	93643	hgsc.bcm.edu	37	6	43472708	43472708	+	Silent	SNP	T	T	C	rs3734689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43472708T>C	ENST00000372445.5	+	11	1165	c.789T>C	c.(787-789)caT>caC	p.H263H	TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000372444.2_Silent_p.H253H|TJAP1_ENST00000372452.1_Silent_p.H253H|TJAP1_ENST00000259751.1_Silent_p.H253H|TJAP1_ENST00000436109.2_Silent_p.H253H|TJAP1_ENST00000372449.1_Silent_p.H263H|TJAP1_ENST00000438588.2_Silent_p.H263H	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	263					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			TCTTTGTGCATGTGGACATGA	0.622													T|||	278	0.0555112	0.0961	0.0259	5008	,	,		15070	0.0347		0.0249	False		,,,				2504	0.0746				p.H263H		Atlas-SNP	.											.	TJAP1	35	.	0			c.T789C						PASS	.	T	,,,,,	350,4056	181.2+/-209.3	25,300,1878	64.0	63.0	63.0		789,789,759,759,759,759	-7.1	1.0	6	dbSNP_107	63	211,8389	89.4+/-151.6	3,205,4092	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJAP1	NM_001146016.1,NM_001146017.1,NM_001146018.1,NM_001146019.1,NM_001146020.1,NM_080604.2	,,,,,	28,505,5970	CC,CT,TT		2.4535,7.9437,4.3134	,,,,,	263/558,263/558,253/548,253/548,253/548,253/548	43472708	561,12445	2203	4300	6503	SO:0001819	synonymous_variant	93643	exon11			TGTGCATGTGGAC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"""tight junction protein 4 (peripheral)"""	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.789T>C	6.37:g.43472708T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_001146016	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Silent	SNP	ENST00000372445.5	37	CCDS55004.1																																																																																			T|0.953;C|0.047	0.047	strong		0.622	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604	
PMPCA	23203	hgsc.bcm.edu	37	9	139306467	139306467	+	Silent	SNP	C	C	T	rs10870144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139306467C>T	ENST00000371717.3	+	2	99	c.90C>T	c.(88-90)taC>taT	p.Y30Y	SDCCAG3_ENST00000298537.7_5'Flank|PMPCA_ENST00000399219.3_5'UTR|SDCCAG3_ENST00000371725.3_5'Flank|SDCCAG3_ENST00000357365.3_5'Flank|PMPCA_ENST00000371720.1_Silent_p.Y30Y	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	30					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		CTCCTGCGTACAGACGGTTTA	0.488													C|||	696	0.138978	0.0333	0.2651	5008	,	,		19777	0.1419		0.1581	False		,,,				2504	0.1697				p.Y30Y		Atlas-SNP	.											.	PMPCA	29	.	0			c.C90T						PASS	.	C		232,4174	138.0+/-173.8	6,220,1977	139.0	117.0	125.0		90	4.5	0.4	9	dbSNP_120	125	1496,7104	281.7+/-295.2	132,1232,2936	no	coding-synonymous	PMPCA	NM_015160.1		138,1452,4913	TT,TC,CC		17.3953,5.2655,13.2862		30/526	139306467	1728,11278	2203	4300	6503	SO:0001819	synonymous_variant	23203	exon2			TGCGTACAGACGG	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"""inositol polyphosphate-5-phosphatase, 72 kD"""	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.90C>T	9.37:g.139306467C>T		Somatic	333	1	0.003003		WXS	Illumina HiSeq	Phase_I	371	180	0.485175	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371717.3	37	CCDS35180.1																																																																																			C|0.870;T|0.130	0.130	strong		0.488	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
FUCA2	2519	hgsc.bcm.edu	37	6	143825104	143825104	+	Missense_Mutation	SNP	G	G	T	rs11155297	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:143825104G>T	ENST00000002165.6	-	3	753	c.698C>A	c.(697-699)gCa>gAa	p.A233E	RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|FUCA2_ENST00000438118.2_Intron|RP1-20N2.6_ENST00000593175.1_RNA|FUCA2_ENST00000367585.1_Intron|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	233			A -> E (in dbSNP:rs11155297).		fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TTGATCCGGTGCTCCTCCGTC	0.458													G|||	446	0.0890575	0.0144	0.1268	5008	,	,		18466	0.002		0.2724	False		,,,				2504	0.0644				p.A233E		Atlas-SNP	.											FUCA2,colon,carcinoma,0,1	FUCA2	28	1	0			c.C698A						scavenged	.	G	GLU/ALA	209,4197	126.6+/-163.6	8,193,2002	82.0	75.0	77.0		698	3.8	0.0	6	dbSNP_120	77	2282,6318	384.5+/-341.1	278,1726,2296	yes	missense	FUCA2	NM_032020.4	107	286,1919,4298	TT,TG,GG		26.5349,4.7435,19.1527	benign	233/468	143825104	2491,10515	2203	4300	6503	SO:0001583	missense	2519	exon3			TCCGGTGCTCCTC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.698C>A	6.37:g.143825104G>T	ENSP00000002165:p.Ala233Glu	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	164	92	0.560976	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	280	0.1282051282051282	10	0.02032520325203252	58	0.16022099447513813	2	0.0034965034965034965	210	0.2770448548812665	G	14.98	2.698181	0.48307	0.047435	0.265349	ENSG00000001036	ENST00000002165	T	0.56275	0.47	5.62	3.81	0.43845	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.58935	0.2157	M	0.81112	2.525	0.09310	P	1.0	D	0.76494	0.999	D	0.81914	0.995	T	0.61739	-0.7001	9	0.17369	T	0.5	-20.7489	11.8248	0.52261	0.0674:0.1219:0.8107:0.0	rs11155297;rs17286188;rs61663154;rs11155297	233	Q9BTY2	FUCO2_HUMAN	E	233	ENSP00000002165:A233E	ENSP00000002165:A233E	A	-	2	0	FUCA2	143866797	1.000000	0.71417	0.012000	0.15200	0.002000	0.02628	7.638000	0.83328	1.346000	0.45694	0.650000	0.86243	GCA	G|0.844;T|0.156	0.156	strong		0.458	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
FCHSD1	89848	hgsc.bcm.edu	37	5	141029072	141029072	+	Silent	SNP	G	G	A	rs11739451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:141029072G>A	ENST00000435817.2	-	5	315	c.265C>T	c.(265-267)Ctg>Ttg	p.L89L	FCHSD1_ENST00000522783.1_Silent_p.L87L|FCHSD1_ENST00000522126.1_Silent_p.L13L|FCHSD1_ENST00000519800.1_Silent_p.L87L|FCHSD1_ENST00000523856.1_5'Flank	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	89									FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCATCCAGCAGGCAGCGCCAG	0.657													g|||	556	0.111022	0.0522	0.1599	5008	,	,		15943	0.0992		0.1183	False		,,,				2504	0.1605				p.L89L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C265T						PASS	.	G		274,4018		8,258,1880	49.0	58.0	55.0		265	3.4	1.0	5	dbSNP_120	55	1080,7440		63,954,3243	no	coding-synonymous	FCHSD1	NM_033449.2		71,1212,5123	AA,AG,GG		12.6761,6.384,10.5682		89/691	141029072	1354,11458	2146	4260	6406	SO:0001819	synonymous_variant	89848	exon5			CCAGCAGGCAGCG	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.265C>T	5.37:g.141029072G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Silent	SNP	ENST00000435817.2	37	CCDS47295.1																																																																																			G|0.879;A|0.121	0.121	strong		0.657	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
GBP6	163351	hgsc.bcm.edu	37	1	89849268	89849268	+	Silent	SNP	T	T	C	rs41288387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89849268T>C	ENST00000370456.4	+	9	1516	c.1423T>C	c.(1423-1425)Ttg>Ctg	p.L475L	GBP6_ENST00000535065.1_Silent_p.L345L	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	475					cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		GGAATCCATCTTGCAGTCAGA	0.458													T|||	513	0.102436	0.0045	0.1326	5008	,	,		19583	0.2798		0.0666	False		,,,				2504	0.0675				p.L475L		Atlas-SNP	.											.	GBP6	87	.	0			c.T1423C						PASS	.	T		52,4354	51.6+/-87.1	0,52,2151	101.0	102.0	102.0		1423	-1.6	0.1	1	dbSNP_127	102	349,8251	119.2+/-178.6	1,347,3952	no	coding-synonymous	GBP6	NM_198460.2		1,399,6103	CC,CT,TT		4.0581,1.1802,3.0832		475/634	89849268	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	163351	exon9			TCCATCTTGCAGT	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.1423T>C	1.37:g.89849268T>C		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	343	183	0.533528	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Silent	SNP	ENST00000370456.4	37	CCDS723.1																																																																																			T|0.945;C|0.055	0.055	strong		0.458	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
MS4A14	84689	hgsc.bcm.edu	37	11	60184191	60184191	+	Missense_Mutation	SNP	G	G	A	rs3825020	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60184191G>A	ENST00000300187.6	+	5	2027	c.1750G>A	c.(1750-1752)Gga>Aga	p.G584R	MS4A14_ENST00000531787.1_Missense_Mutation_p.G472R|MS4A14_ENST00000395005.2_Missense_Mutation_p.G567R|MS4A14_ENST00000531783.1_Missense_Mutation_p.G617R	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	584	Gln-rich.		G -> R (in dbSNP:rs3825020). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			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						ATCTAAAGATGGACAAGTTAA	0.458													G|||	2495	0.498203	0.5182	0.6513	5008	,	,		21541	0.3433		0.6262	False		,,,				2504	0.3906				p.G617R		Atlas-SNP	.											.	MS4A14	120	.	0			c.G1849A						PASS	.	G	ARG/GLY,ARG/GLY	2155,2251	581.2+/-385.3	521,1113,569	72.0	62.0	65.0		1699,1750	-1.4	0.0	11	dbSNP_107	65	5324,3276	645.7+/-400.2	1639,2046,615	yes	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	125,125	2160,3159,1184	AA,AG,GG		38.093,48.9106,42.4958	benign,benign	567/663,584/680	60184191	7479,5527	2203	4300	6503	SO:0001583	missense	84689	exon6			AAAGATGGACAAG	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.1750G>A	11.37:g.60184191G>A	ENSP00000300187:p.Gly584Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	1179	0.5398351648351648	254	0.516260162601626	226	0.6243093922651933	228	0.3986013986013986	471	0.6213720316622692	G	5.096	0.203398	0.09704	0.489106	0.61907	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.30981	1.51;2.73;1.52;3.1	4.31	-1.43	0.08884	.	4.009310	0.00541	N	0.000226	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.13145	0.007;0.004	B;B	0.08055	0.003;0.001	T	0.45948	-0.9226	9	0.15499	T	0.54	4.9183	3.2257	0.06731	0.3862:0.0:0.3485:0.2652	rs3825020;rs52806143;rs60869380;rs3825020	567;584	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	R	472;584;567;617	ENSP00000437222:G472R;ENSP00000300187:G584R;ENSP00000378453:G567R;ENSP00000433761:G617R	ENSP00000300187:G584R	G	+	1	0	MS4A14	59940767	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.859000	0.04277	-0.031000	0.13781	0.655000	0.94253	GGA	G|0.445;A|0.555	0.555	strong		0.458	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
ZNF543	125919	hgsc.bcm.edu	37	19	57839567	57839567	+	Missense_Mutation	SNP	T	T	A	rs1968090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57839567T>A	ENST00000321545.4	+	4	1082	c.737T>A	c.(736-738)cTc>cAc	p.L246H		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	246			L -> H (in dbSNP:rs1968090). {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)			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)		CTTCAGCACCTCATCATCCAC	0.507													a|||	3414	0.681709	0.7716	0.7133	5008	,	,		21232	0.5843		0.7197	False		,,,				2504	0.5992				p.L246H		Atlas-SNP	.											.	ZNF543	61	.	0			c.T737A						PASS	.	A	HIS/LEU	3295,1111	397.0+/-330.2	1223,849,131	70.0	70.0	70.0		737	2.3	0.6	19	dbSNP_92	70	6414,2186	373.1+/-336.9	2402,1610,288	yes	missense	ZNF543	NM_213598.3	99	3625,2459,419	AA,AT,TT		25.4186,25.2156,25.3498	benign	246/601	57839567	9709,3297	2203	4300	6503	SO:0001583	missense	125919	exon4			AGCACCTCATCAT	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.737T>A	19.37:g.57839567T>A	ENSP00000322545:p.Leu246His	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	1508	0.6904761904761905	356	0.7235772357723578	261	0.7209944751381215	338	0.5909090909090909	553	0.7295514511873351	A	0.092	-1.165669	0.01673	0.747844	0.745814	ENSG00000178229	ENST00000321545	T	0.22336	1.96	2.33	2.33	0.28932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.73319	2.225	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15780	-1.0425	8	0.31617	T	0.26	.	7.18	0.25768	0.7995:0.0:0.0:0.2005	rs1968090;rs16987824;rs52796659;rs1968090	246	Q08ER8	ZN543_HUMAN	H	246	ENSP00000322545:L246H	ENSP00000322545:L246H	L	+	2	0	ZNF543	62531379	0.000000	0.05858	0.576000	0.28549	0.816000	0.46133	-0.576000	0.05854	0.328000	0.23435	-0.364000	0.07487	CTC	T|0.268;A|0.732	0.732	strong		0.507	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
CENPF	1063	hgsc.bcm.edu	37	1	214814778	214814778	+	Missense_Mutation	SNP	G	G	A	rs3795518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214814778G>A	ENST00000366955.3	+	12	3265	c.3097G>A	c.(3097-3099)Gga>Aga	p.G1033R		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0			G -> R (in dbSNP:rs3795518).		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)		TGAAGAAACCGGAAATGCATA	0.318													G|||	733	0.146366	0.2526	0.1124	5008	,	,		19617	0.126		0.0517	False		,,,				2504	0.1452				p.G1033R	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.G3097A						PASS	.	G	ARG/GLY	924,3454		98,728,1363	49.0	55.0	53.0		3097	2.2	0.0	1	dbSNP_107	53	476,8104		12,452,3826	yes	missense	CENPF	NM_016343.3	125	110,1180,5189	AA,AG,GG		5.5478,21.1055,10.8041	possibly-damaging	1033/3115	214814778	1400,11558	2189	4290	6479	SO:0001583	missense	1063	exon12			GAAACCGGAAATG	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.3097G>A	1.37:g.214814778G>A	ENSP00000355922:p.Gly1033Arg	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	175	70	0.4	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	287	0.13141025641025642	116	0.23577235772357724	45	0.12430939226519337	84	0.14685314685314685	42	0.055408970976253295	G	1.594	-0.528351	0.04112	0.211055	0.055478	ENSG00000117724	ENST00000366955	T	0.02974	4.09	4.86	2.22	0.28083	.	0.906463	0.09101	N	0.848461	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.44946	0.846	B	0.23716	0.048	T	0.50206	-0.8855	8	0.30078	T	0.28	.	4.5192	0.11950	0.357:0.0:0.4967:0.1463	rs3795518;rs52823889;rs57425713;rs3795518	1033	P49454	CENPF_HUMAN	R	1033	ENSP00000355922:G1033R	ENSP00000355922:G1033R	G	+	1	0	CENPF	212881401	0.000000	0.05858	0.002000	0.10522	0.778000	0.44026	0.140000	0.16056	0.261000	0.21753	-0.320000	0.08662	GGA	G|0.883;A|0.117	0.117	strong		0.318	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
CDH23	64072	hgsc.bcm.edu	37	10	73455273	73455273	+	Silent	SNP	T	T	C	rs3752751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73455273T>C	ENST00000224721.6	+	21	2408	c.2403T>C	c.(2401-2403)gaT>gaC	p.D801D	CDH23_ENST00000299366.7_Silent_p.D841D	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	796	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CAGACTCTGATGTGACCACGG	0.602													C|||	2774	0.553914	0.5038	0.5187	5008	,	,		18162	0.4345		0.7068	False		,,,				2504	0.6125				p.D796D		Atlas-SNP	.											.	CDH23	365	.	0			c.T2388C						PASS	.	C	,,	2281,1855		653,975,440	90.0	96.0	94.0		2388,2388,2388	-4.0	0.9	10	dbSNP_107	94	6124,2296		2222,1680,308	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	,,	2875,2655,748	CC,CT,TT		27.2684,44.8501,33.0599	,,	796/1382,796/1062,796/3355	73455273	8405,4151	2068	4210	6278	SO:0001819	synonymous_variant	64072	exon21			CTCTGATGTGACC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.2403T>C	10.37:g.73455273T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				T|0.408;C|0.591	0.591	strong		0.602	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
ANO2	57101	hgsc.bcm.edu	37	12	6030301	6030301	+	Missense_Mutation	SNP	G	G	A	rs3741901	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6030301G>A	ENST00000356134.5	-	3	498	c.427C>T	c.(427-429)Ccg>Tcg	p.P143S	ANO2_ENST00000546188.1_Missense_Mutation_p.P143S|ANO2_ENST00000327087.8_Missense_Mutation_p.P143S	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	147					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						GCATCGAGCGGTCCCAGCTCA	0.612													G|||	268	0.0535144	0.0045	0.0389	5008	,	,		16871	0.0139		0.1064	False		,,,				2504	0.1166				p.P143S		Atlas-SNP	.											ANO2_ENST00000327087,lower_third,carcinoma,+1,2	ANO2	309	2	0			c.C427T						scavenged	.	G	SER/PRO	83,3977		0,83,1947	78.0	75.0	76.0		427	4.8	0.6	12	dbSNP_107	76	1000,7336		67,866,3235	yes	missense	ANO2	NM_020373.2	74	67,949,5182	AA,AG,GG		11.9962,2.0443,8.7367	possibly-damaging	143/999	6030301	1083,11313	2030	4168	6198	SO:0001583	missense	57101	exon3			CGAGCGGTCCCAG	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.427C>T	12.37:g.6030301G>A	ENSP00000348453:p.Pro143Ser	Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	103	36	0.349515	NM_020373	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		108	0.04945054945054945	4	0.008130081300813009	18	0.049723756906077346	8	0.013986013986013986	78	0.10290237467018469	G	13.70	2.316264	0.40996	0.020443	0.119962	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277	T;T;T	0.65732	-0.17;-0.17;-0.17	4.84	4.84	0.62591	.	0.136253	0.49916	D	0.000133	T	0.01254	0.0041	L	0.57536	1.79	0.25697	P	0.9856276	B	0.28208	0.203	B	0.25291	0.059	T	0.28870	-1.0030	9	0.20046	T	0.44	.	15.0999	0.72266	0.0:0.0:1.0:0.0	rs3741901;rs3741901	143	Q9NQ90-3	.	S	143;143;143;147	ENSP00000314048:P143S;ENSP00000348453:P143S;ENSP00000440981:P143S	ENSP00000314048:P143S	P	-	1	0	ANO2	5900562	1.000000	0.71417	0.602000	0.28890	0.493000	0.33554	7.127000	0.77210	2.223000	0.72356	0.563000	0.77884	CCG	G|0.943;A|0.057	0.057	strong		0.612	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
DNAH14	127602	hgsc.bcm.edu	37	1	225528183	225528183	+	Missense_Mutation	SNP	C	C	A	rs377250670|rs3856145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225528183C>A	ENST00000445597.2	+	47	7770	c.7770C>A	c.(7768-7770)gaC>gaA	p.D2590E	DNAH14_ENST00000439375.2_Missense_Mutation_p.D3393E|DNAH14_ENST00000430092.1_Missense_Mutation_p.D3393E			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2590					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						CAGAAATAGACAACCCCCATT	0.318													C|||	2653	0.529752	0.643	0.4697	5008	,	,		17622	0.5089		0.4046	False		,,,				2504	0.5695				p.D3393E		Atlas-SNP	.											.	DNAH14	300	.	0			c.C10179A						PASS	.	C	GLU/ASP	846,538		270,306,116	113.0	99.0	103.0		10179	0.7	1.0	1	dbSNP_108	103	1403,1779		323,757,511	yes	missense	DNAH14	NM_001373.1	45	593,1063,627	AA,AC,CC		44.0918,38.8728,49.2554	possibly-damaging	3393/4516	225528183	2249,2317	692	1591	2283	SO:0001583	missense	127602	exon67			AATAGACAACCCC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.7770C>A	1.37:g.225528183C>A	ENSP00000409472:p.Asp2590Glu	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	314	137	0.436306	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1057	0.483974358974359	305	0.6199186991869918	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	13.41	2.229518	0.39399	0.611272	0.440918	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.21191	2.02;2.02;2.02	5.22	0.724	0.18236	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999854566	B	0.31817	0.341	B	0.32762	0.152	T	0.33214	-0.9877	7	0.32370	T	0.25	.	1.4675	0.02408	0.2894:0.3987:0.141:0.1709	rs3856145;rs52794541;rs58846503;rs3856145	3393	Q0VDD8-4	.	E	2590;3393;3393	ENSP00000409472:D2590E;ENSP00000414402:D3393E;ENSP00000392061:D3393E	ENSP00000414402:D3393E	D	+	3	2	DNAH14	223594806	1.000000	0.71417	0.981000	0.43875	0.977000	0.68977	0.462000	0.21956	-0.062000	0.13088	0.508000	0.49915	GAC	C|0.498;A|0.500	0.500	strong		0.318	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
CIB1	10519	hgsc.bcm.edu	37	15	90771704	90771704	+	IGR	SNP	G	G	A	rs3751656	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90771704G>A	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000411539.2_Silent_p.P781P|SEMA4B_ENST00000379122.3_Intron|SEMA4B_ENST00000332496.6_Silent_p.P781P	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)			CTAGCACCCCGCTCGATCACC	0.652													A|||	1128	0.22524	0.379	0.1729	5008	,	,		15349	0.1062		0.2406	False		,,,				2504	0.1616				p.P781P		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G2343A						PASS	.	A	,	1333,2557		238,857,850	21.0	24.0	23.0		2343,2343	-9.5	0.0	15	dbSNP_107	23	1777,6455		182,1413,2521	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	420,2270,3371	AA,AG,GG		21.5865,34.2674,25.6558	,	781/838,781/838	90771704	3110,9012	1945	4116	6061	SO:0001628	intergenic_variant	10509	exon15			CACCCCGCTCGAT	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.90771704G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_020210	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Silent	SNP	ENST00000328649.6	37	CCDS10360.1																																																																																			G|0.746;A|0.254	0.254	strong		0.652	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1		
CD101	9398	hgsc.bcm.edu	37	1	117560058	117560058	+	Missense_Mutation	SNP	C	C	G	rs17235773	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	148	0	0		WXS	Illumina HiSeq	Phase_I	139	77	0.553957	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	
TATDN2	9797	hgsc.bcm.edu	37	3	10302056	10302056	+	Missense_Mutation	SNP	A	A	G	rs2241314	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:10302056A>G	ENST00000287652.4	+	3	1701	c.650A>G	c.(649-651)cAt>cGt	p.H217R	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Missense_Mutation_p.H217R	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	217			H -> R (in dbSNP:rs2241314).		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						GCAGCAGAGCATCCCAGCCAT	0.557													G|||	1811	0.361621	0.2814	0.2334	5008	,	,		16636	0.6528		0.1024	False		,,,				2504	0.5276				p.H217R		Atlas-SNP	.											.	TATDN2	59	.	0			c.A650G						PASS	.	G	ARG/HIS	1113,3293	715.0+/-408.4	151,811,1241	47.0	49.0	48.0		650	-6.6	0.0	3	dbSNP_98	48	883,7717	778.1+/-407.7	44,795,3461	yes	missense	TATDN2	NM_014760.3	29	195,1606,4702	GG,GA,AA		10.2674,25.261,15.3468	benign	217/762	10302056	1996,11010	2203	4300	6503	SO:0001583	missense	9797	exon3			CAGAGCATCCCAG	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.650A>G	3.37:g.10302056A>G	ENSP00000287652:p.His217Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_014760	Q3MIL9|Q5BKU0	Missense_Mutation	SNP	ENST00000287652.4	37	CCDS33698.1	678	0.31043956043956045	136	0.2764227642276423	78	0.2154696132596685	387	0.6765734265734266	77	0.10158311345646438	G	3.651	-0.071494	0.07228	0.25261	0.102674	ENSG00000157014	ENST00000287652;ENST00000448281	T;T	0.20881	2.04;2.04	4.14	-6.61	0.01818	.	1.060550	0.07562	N	0.917220	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38802	-0.9644	9	0.07030	T	0.85	5.5314	16.2242	0.82283	0.7871:0.0:0.2129:0.0	rs2241314;rs60155787;rs2241314	217	Q93075	TATD2_HUMAN	R	217	ENSP00000287652:H217R;ENSP00000408736:H217R	ENSP00000287652:H217R	H	+	2	0	TATDN2	10277056	0.000000	0.05858	0.000000	0.03702	0.230000	0.25150	-0.768000	0.04715	-2.321000	0.00641	-1.767000	0.00664	CAT	A|0.772;G|0.228	0.228	strong		0.557	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
TECPR1	25851	hgsc.bcm.edu	37	7	97854393	97854393	+	Silent	SNP	G	G	A	rs2291745	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97854393G>A	ENST00000447648.2	-	18	2834	c.2535C>T	c.(2533-2535)taC>taT	p.Y845Y	TECPR1_ENST00000479975.1_5'UTR|TECPR1_ENST00000379795.3_Silent_p.Y847Y			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	845					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						CGCTCCACATGTACCGGTCCG	0.677													G|||	1445	0.288538	0.1573	0.196	5008	,	,		16332	0.4236		0.2266	False		,,,				2504	0.456				p.Y845Y		Atlas-SNP	.											.	TECPR1	77	.	0			c.C2535T						PASS	.	G		586,3620		43,500,1560	12.0	14.0	13.0		2535	3.2	1.0	7	dbSNP_100	13	1851,6553		235,1381,2586	no	coding-synonymous	TECPR1	NM_015395.1		278,1881,4146	AA,AG,GG		22.0252,13.9325,19.3259		845/1166	97854393	2437,10173	2103	4202	6305	SO:0001819	synonymous_variant	25851	exon18			CCACATGTACCGG		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.2535C>T	7.37:g.97854393G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	168	76	0.452381	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			G|0.727;A|0.273	0.273	strong		0.677	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
CILP2	148113	hgsc.bcm.edu	37	19	19656615	19656615	+	Silent	SNP	C	C	T	rs61744761	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	188	0	0		WXS	Illumina HiSeq	Phase_I	178	76	0.426966	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	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808056	18808056	+	Missense_Mutation	SNP	G	G	C	rs7515150	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:18808056G>C	ENST00000400664.1	+	1	633	c.581G>C	c.(580-582)cGt>cCt	p.R194P		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	194			R -> P (in dbSNP:rs7515150).			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)		AGTAAACCCCGTGAGCATCCA	0.607													C|||	473	0.0944489	0.1233	0.1239	5008	,	,		16821	0.0377		0.1233	False		,,,				2504	0.0634				p.R194P		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G581C						PASS	.	C	PRO/ARG	446,3960	777.6+/-414.2	21,404,1778	42.0	44.0	43.0		581	0.4	0.0	1	dbSNP_116	43	1052,7548	764.1+/-407.6	62,928,3310	yes	missense	KLHDC7A	NM_152375.2	103	83,1332,5088	CC,CG,GG		12.2326,10.1226,11.5178	benign	194/778	18808056	1498,11508	2203	4300	6503	SO:0001583	missense	127707	exon1			AACCCCGTGAGCA	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.581G>C	1.37:g.18808056G>C	ENSP00000383505:p.Arg194Pro	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	211	0.09661172161172162	45	0.09146341463414634	48	0.13259668508287292	29	0.050699300699300696	89	0.11741424802110818	C	1.227	-0.625166	0.03610	0.101226	0.122326	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.71934	-0.61	5.7	0.453	0.16639	.	0.560227	0.13516	N	0.382044	T	0.00384	0.0012	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04165	-1.0972	9	0.22109	T	0.4	.	2.3462	0.04272	0.1203:0.492:0.1171:0.2707	rs7515150;rs7515150	194	Q5VTJ3	KLD7A_HUMAN	P	194;131	ENSP00000383505:R194P	ENSP00000383505:R194P	R	+	2	0	KLHDC7A	18680643	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.137000	0.15995	-0.136000	0.11475	-0.187000	0.12897	CGT	G|0.888;C|0.112	0.112	strong		0.607	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
CHAF1A	10036	hgsc.bcm.edu	37	19	4409756	4409756	+	Splice_Site	SNP	A	A	G	rs2230636	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4409756A>G	ENST00000301280.5	+	3	1061	c.960A>G	c.(958-960)agA>agG	p.R320R		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	320					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCTCCGCAGAGTGAGTATCT	0.627								Chromatin Structure					A|||	692	0.138179	0.0492	0.3055	5008	,	,		18632	0.0198		0.2406	False		,,,				2504	0.1564				p.R320R		Atlas-SNP	.											.	CHAF1A	69	.	0			c.A960G						PASS	.	A		393,4013	194.3+/-219.2	17,359,1827	50.0	48.0	49.0		960	-2.2	0.8	19	dbSNP_126	49	2129,6471	350.0+/-327.7	262,1605,2433	yes	coding-synonymous-near-splice	CHAF1A	NM_005483.2		279,1964,4260	GG,GA,AA		24.7558,8.9197,19.3911		320/957	4409756	2522,10484	2203	4300	6503	SO:0001630	splice_region_variant	10036	exon3			CCGCAGAGTGAGT	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.960+1A>G	19.37:g.4409756A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Silent	SNP	ENST00000301280.5	37	CCDS32875.1																																																																																			A|0.809;G|0.191	0.191	strong		0.627	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	Silent
USP48	84196	hgsc.bcm.edu	37	1	22109370	22109370	+	Silent	SNP	G	G	A	rs10917042	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:22109370G>A	ENST00000308271.9	-	1	729	c.81C>T	c.(79-81)caC>caT	p.H27H	USP48_ENST00000529637.1_Silent_p.H27H|USP48_ENST00000421625.2_Silent_p.H27H|USP48_ENST00000400301.1_Silent_p.H27H	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	27					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CGGTCTCGATGTGCTCCTGCG	0.736													G|||	1411	0.281749	0.028	0.5274	5008	,	,		12624	0.5893		0.2197	False		,,,				2504	0.1973				p.H27H		Atlas-SNP	.											.	USP48	91	.	0			c.C81T						PASS	.	G	,	275,4053		11,253,1900	18.0	16.0	17.0		81,81	0.8	1.0	1	dbSNP_120	17	1858,6642		203,1452,2595	no	coding-synonymous,coding-synonymous	USP48	NM_001032730.1,NM_032236.5	,	214,1705,4495	AA,AG,GG		21.8588,6.354,16.6277	,	27/486,27/1036	22109370	2133,10695	2164	4250	6414	SO:0001819	synonymous_variant	84196	exon1			CTCGATGTGCTCC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.81C>T	1.37:g.22109370G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			G|0.772;A|0.228	0.228	strong		0.736	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
BRD7	29117	hgsc.bcm.edu	37	16	50368663	50368663	+	Silent	SNP	G	G	A	rs1062348	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:50368663G>A	ENST00000394688.3	-	7	1005	c.846C>T	c.(844-846)gcC>gcT	p.A282A	BRD7_ENST00000394689.2_Silent_p.A282A			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	282					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)				CGTGTGCTTCGGCATCTCCAG	0.473													G|||	1254	0.250399	0.2943	0.0893	5008	,	,		17016	0.497		0.1083	False		,,,				2504	0.1973				p.A282A		Atlas-SNP	.											.	BRD7	61	.	0			c.C846T						PASS	.	G	,	1156,3240	400.1+/-331.5	119,918,1161	135.0	141.0	139.0		846,846	-10.9	0.0	16	dbSNP_86	139	876,7724	195.8+/-240.9	41,794,3465	no	coding-synonymous,coding-synonymous	BRD7	NM_001173984.2,NM_013263.4	,	160,1712,4626	AA,AG,GG		10.186,26.2966,15.6356	,	282/653,282/652	50368663	2032,10964	2198	4300	6498	SO:0001819	synonymous_variant	29117	exon7			TGCTTCGGCATCT	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.846C>T	16.37:g.50368663G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Silent	SNP	ENST00000394688.3	37	CCDS10742.1																																																																																			G|0.826;A|0.174	0.174	strong		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
POM121L12	285877	hgsc.bcm.edu	37	7	53104078	53104078	+	Silent	SNP	G	G	A	rs72598686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	57	0	0		WXS	Illumina HiSeq	Phase_I	59	38	0.644068	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	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086718	46086718	+	Missense_Mutation	SNP	G	G	C	rs7275281|rs368303093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46086718G>C	ENST00000360770.3	-	1	126	c.86C>G	c.(85-87)tCc>tGc	p.S29C	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	29	23 X 5 AA approximate repeats.		S -> C (in dbSNP:rs7275281).|S -> P (in dbSNP:rs7276859).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						TGCCTGGCAGGAGCTGGGCAC	0.677													G|||	3070	0.613019	0.7262	0.5807	5008	,	,		16465	0.5675		0.5547	False		,,,				2504	0.59				p.S29C		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.C86G						PASS	.	G	CYS/SER,	1259,3073		510,239,1417	35.0	42.0	39.0		86,	-2.7	0.0	21	dbSNP_116	39	1526,6972		615,296,3338	no	missense,intron	TSPEAR,KRTAP12-2	NM_181684.2,NM_144991.2	112,	1125,535,4755	CC,CG,GG		17.9572,29.0628,21.7069	probably-damaging,	29/147,	46086718	2785,10045	2166	4249	6415	SO:0001583	missense	353323	exon1			TGGCAGGAGCTGG	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.86C>G	21.37:g.46086718G>C	ENSP00000354001:p.Ser29Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1165	0.5334249084249084	318	0.6463414634146342	199	0.5497237569060773	279	0.48776223776223776	369	0.4868073878627968	g	6.477	0.456248	0.12283	0.290628	0.179572	ENSG00000221864	ENST00000360770	T	0.03035	4.07	3.4	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	N	0.01761	-0.735	0.80722	P	0.0	D	0.58620	0.983	P	0.51297	0.665	T	0.36237	-0.9756	8	0.19147	T	0.46	.	3.0179	0.06066	0.0978:0.415:0.2069:0.2803	rs7275281	29	P59991	KR122_HUMAN	C	29	ENSP00000354001:S29C	ENSP00000354001:S29C	S	-	2	0	KRTAP12-2	44911146	0.004000	0.15560	0.000000	0.03702	0.019000	0.09904	-0.386000	0.07370	-1.078000	0.03117	0.462000	0.41574	TCC	.	.	alt		0.677	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104448	26104448	+	Silent	SNP	A	A	G	rs198852	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26104448A>G	ENST00000377803.2	+	1	345	c.273A>G	c.(271-273)ctA>ctG	p.L91L		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	91					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						TATATGCCCTAAAACGTCAGG	0.473													A|||	1232	0.246006	0.1059	0.3055	5008	,	,		18534	0.1379		0.3708	False		,,,				2504	0.3763				p.L91L		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.A273G						PASS	.	A		723,3683		59,605,1539	61.0	55.0	57.0		273	-1.0	1.0	6	dbSNP_79	57	3194,5406		598,1998,1704	no	coding-synonymous	HIST1H4C	NM_003542.3		657,2603,3243	GG,GA,AA		37.1395,16.4094,30.1169		91/104	26104448	3917,9089	2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			TGCCCTAAAACGT	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.273A>G	6.37:g.26104448A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	37	CCDS4583.1																																																																																			A|0.734;G|0.266	0.266	strong		0.473	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542	
MTIF2	4528	hgsc.bcm.edu	37	2	55476591	55476591	+	Silent	SNP	G	G	A	rs2576709	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:55476591G>A	ENST00000263629.4	-	9	1236	c.921C>T	c.(919-921)taC>taT	p.Y307Y	MTIF2_ENST00000394600.3_Silent_p.Y307Y|MTIF2_ENST00000403721.1_Silent_p.Y307Y	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	307	tr-type G.				formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						ATACCACATCGTAAGCCAGCA	0.428													A|||	78	0.0155751	0.0015	0.0403	5008	,	,		20499	0.001		0.0447	False		,,,				2504	0.002				p.Y307Y		Atlas-SNP	.											.	MTIF2	64	.	0			c.C921T						PASS	.	A	,	39,4367	822.7+/-416.5	0,39,2164	255.0	222.0	233.0		921,921	-7.0	0.3	2	dbSNP_100	233	435,8165	799.9+/-407.4	11,413,3876	no	coding-synonymous,coding-synonymous	MTIF2	NM_001005369.1,NM_002453.2	,	11,452,6040	AA,AG,GG		5.0581,0.8852,3.6445	,	307/728,307/728	55476591	474,12532	2203	4300	6503	SO:0001819	synonymous_variant	4528	exon9			CACATCGTAAGCC	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.921C>T	2.37:g.55476591G>A		Somatic	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	292	147	0.503425	NM_002453	D6W5D0	Silent	SNP	ENST00000263629.4	37	CCDS1853.1																																																																																			A|0.032;C|0.000;G|0.968	0.032	strong		0.428	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
INO80D	54891	hgsc.bcm.edu	37	2	206874339	206874339	+	Silent	SNP	G	G	A	rs817991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:206874339G>A	ENST00000403263.1	-	9	2126	c.1722C>T	c.(1720-1722)ccC>ccT	p.P574P	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	574					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						AGACGCTGGCGGGCATGCTGA	0.522													G|||	1941	0.38758	0.2035	0.3228	5008	,	,		15169	0.502		0.3499	False		,,,				2504	0.6033				p.P574P		Atlas-SNP	.											.	INO80D	134	.	0			c.C1722T						PASS	.	G		791,3167		78,635,1266	73.0	84.0	81.0		1722	4.9	1.0	2	dbSNP_86	81	2973,5367		543,1887,1740	no	coding-synonymous	INO80D	NM_017759.4		621,2522,3006	AA,AG,GG		35.6475,19.9848,30.6066		574/1028	206874339	3764,8534	1979	4170	6149	SO:0001819	synonymous_variant	54891	exon9			GCTGGCGGGCATG		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.1722C>T	2.37:g.206874339G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	138	76	0.550725	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			G|0.629;A|0.371	0.371	strong		0.522	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
KCNH2	3757	hgsc.bcm.edu	37	7	150649531	150649531	+	Silent	SNP	G	G	A	rs1805120	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150649531G>A	ENST00000262186.5	-	6	1940	c.1539C>T	c.(1537-1539)ttC>ttT	p.F513F	KCNH2_ENST00000330883.4_Silent_p.F173F|KCNH2_ENST00000392968.2_Silent_p.F417F|KCNH2_ENST00000430723.3_Silent_p.F513F	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	513					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGCCAGAGCCGAAGATGAGCA	0.647													G|||	1711	0.341653	0.2511	0.3357	5008	,	,		18979	0.622		0.2127	False		,,,				2504	0.3119				p.F513F	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.C1539T						PASS	.	G	,,,	1110,3296	395.6+/-329.7	146,818,1239	67.0	58.0	61.0		1539,519,1539,519	-9.4	0.8	7	dbSNP_89	61	1834,6766	328.4+/-318.3	202,1430,2668	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNH2	NM_000238.3,NM_001204798.1,NM_172056.2,NM_172057.2	,,,	348,2248,3907	AA,AG,GG		21.3256,25.1929,22.6357	,,,	513/1160,173/549,513/889,173/820	150649531	2944,10062	2203	4300	6503	SO:0001819	synonymous_variant	3757	exon6			AGAGCCGAAGATG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1539C>T	7.37:g.150649531G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	37	CCDS5910.1																																																																																			G|0.708;A|0.292	0.292	strong		0.647	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
OCA2	4948	hgsc.bcm.edu	37	15	28090173	28090173	+	Silent	SNP	C	C	T	rs12592307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:28090173C>T	ENST00000354638.3	-	23	2519	c.2364G>A	c.(2362-2364)tcG>tcA	p.S788S	OCA2_ENST00000353809.5_Silent_p.S764S	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	788					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)	p.S788S(1)		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)		CGACGTTTGCCGACGCGCCAA	0.388									Oculocutaneous Albinism				C|||	1416	0.282748	0.0802	0.3559	5008	,	,		16618	0.5635		0.2008	False		,,,				2504	0.2996				p.S788S		Atlas-SNP	.											OCA2,NS,carcinoma,0,1	OCA2	173	1	1	Substitution - coding silent(1)	stomach(1)	c.G2364A						PASS	.	C		505,3901	232.3+/-245.9	25,455,1723	61.0	61.0	61.0		2364	-5.0	0.7	15	dbSNP_120	61	1767,6833	320.4+/-314.6	181,1405,2714	no	coding-synonymous	OCA2	NM_000275.2		206,1860,4437	TT,TC,CC		20.5465,11.4616,17.4689		788/839	28090173	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	4948	exon23	Familial Cancer Database		GTTTGCCGACGCG		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.2364G>A	15.37:g.28090173C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	198	94	0.474747	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			C|0.769;T|0.231	0.231	strong		0.388	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
SYT15	83849	hgsc.bcm.edu	37	10	46968665	46968665	+	Silent	SNP	G	G	A	rs200814731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:46968665G>A	ENST00000374321.4	-	3	337	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000503753.1_Silent_p.L91L|SYT15_ENST00000374323.4_Silent_p.L144L|SYT15_ENST00000374325.3_Silent_p.L91L	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CCACTGTGCAGGGGCACCCAA	0.632													G|||	469	0.0936502	0.1051	0.0764	5008	,	,		35813	0.0496		0.1282	False		,,,				2504	0.1002				p.L91L	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000416127,colon,carcinoma,0,15	SYT15	165	15	0			c.C271T						PASS	.	G	,	277,3977		0,277,1850	55.0	65.0	62.0		271,271	2.7	0.2	10	dbSNP_132	62	613,7885		0,613,3636	no	coding-synonymous,coding-synonymous	SYT15	NM_031912.4,NM_181519.2	,	0,890,5486	AA,AG,GG		7.2135,6.5115,6.9793	,	91/422,91/391	46968665	890,11862	2127	4249	6376	SO:0001819	synonymous_variant	83849	exon3			TGTGCAGGGGCAC	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.271C>T	10.37:g.46968665G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	118	23	0.194915	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Silent	SNP	ENST00000374321.4	37	CCDS44376.1																																																																																			G|0.911;A|0.089	0.089	strong		0.632	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
INADL	10207	hgsc.bcm.edu	37	1	62380298	62380298	+	Missense_Mutation	SNP	G	G	A	rs1056513	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:62380298G>A	ENST00000371158.2	+	26	3646	c.3532G>A	c.(3532-3534)Ggt>Agt	p.G1178S	INADL_ENST00000316485.6_Missense_Mutation_p.G1178S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1178			G -> S (in dbSNP:rs1056513). {ECO:0000269|PubMed:11927608}.		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						CAAAATCACCGGTAACCAGAA	0.363													A|||	2229	0.445088	0.0862	0.5231	5008	,	,		16917	0.5655		0.6282	False		,,,				2504	0.5624				p.G1178S		Atlas-SNP	.											.	INADL	179	.	0			c.G3532A						PASS	.	A	SER/GLY	714,3692	752.8+/-412.3	71,572,1560	89.0	95.0	93.0		3532	2.3	0.0	1	dbSNP_86	93	5597,3003	463.5+/-366.0	1816,1965,519	yes	missense	INADL	NM_176877.2	56	1887,2537,2079	AA,AG,GG		34.9186,16.2052,48.5238	benign	1178/1802	62380298	6311,6695	2203	4300	6503	SO:0001583	missense	10207	exon26			ATCACCGGTAACC	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.3532G>A	1.37:g.62380298G>A	ENSP00000360200:p.Gly1178Ser	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	272	270	0.992647	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	1061	0.4858058608058608	47	0.09552845528455285	184	0.5082872928176796	347	0.6066433566433567	483	0.637203166226913	A	1.178	-0.638842	0.03557	0.162052	0.650814	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513	T;T	0.11930	2.84;2.73	4.69	2.27	0.28462	.	1.838150	0.02326	N	0.073429	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.40001	-0.9586	9	0.07990	T	0.79	.	6.0221	0.19634	0.5837:0.33:0.0863:0.0	rs1056513;rs3197111;rs52806717;rs1056513	1178;1178;1178	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	1178	ENSP00000360200:G1178S;ENSP00000326199:G1178S	ENSP00000326199:G1178S	G	+	1	0	INADL	62152886	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.416000	0.21198	0.059000	0.16252	-0.360000	0.07572	GGT	G|0.530;A|0.470	0.470	strong		0.363	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
C9orf84	158401	hgsc.bcm.edu	37	9	114490229	114490229	+	Silent	SNP	T	T	G	rs10512411	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114490229T>G	ENST00000318737.4	-	11	1454	c.1326A>C	c.(1324-1326)gcA>gcC	p.A442A	C9orf84_ENST00000394777.4_Silent_p.A403A|C9orf84_ENST00000374287.3_Silent_p.A442A|C9orf84_ENST00000394779.3_Silent_p.A403A	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	442										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						GTACTTCTTTTGCCAGAGATG	0.343													T|||	719	0.14357	0.1422	0.196	5008	,	,		18422	0.0278		0.2286	False		,,,				2504	0.1401				p.A442A		Atlas-SNP	.											C9orf84_ENST00000374287,NS,carcinoma,-2,2	C9orf84	207	2	0			c.A1326C						PASS	.	T	,	767,3637	308.0+/-290.3	67,633,1502	79.0	79.0	79.0		1209,1326	3.9	0.3	9	dbSNP_119	79	1992,6604	344.4+/-325.3	228,1536,2534	no	coding-synonymous,coding-synonymous	C9orf84	NM_001080551.1,NM_173521.3	,	295,2169,4036	GG,GT,TT		23.1736,17.416,21.2231	,	403/1406,442/1445	114490229	2759,10241	2202	4298	6500	SO:0001819	synonymous_variant	158401	exon11			TTCTTTTGCCAGA	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.1326A>C	9.37:g.114490229T>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			T|0.852;G|0.148	0.148	strong		0.343	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
CSGALNACT1	55790	hgsc.bcm.edu	37	8	19316086	19316086	+	Silent	SNP	G	G	A	rs12155539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:19316086G>A	ENST00000454498.2	-	5	1715	c.702C>T	c.(700-702)caC>caT	p.H234H	CSGALNACT1_ENST00000518542.1_5'UTR|CSGALNACT1_ENST00000544602.1_Silent_p.H234H|CSGALNACT1_ENST00000311540.4_Silent_p.H234H|CSGALNACT1_ENST00000332246.6_Silent_p.H234H|CSGALNACT1_ENST00000522854.1_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	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	324	156	0.481481	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	
TG	7038	hgsc.bcm.edu	37	8	133981746	133981746	+	Silent	SNP	G	G	A	rs17693031	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133981746G>A	ENST00000220616.4	+	32	5947	c.5907G>A	c.(5905-5907)ccG>ccA	p.P1969P	TG_ENST00000542445.1_Silent_p.P339P|TG_ENST00000519543.1_Silent_p.P123P|TG_ENST00000377869.1_Silent_p.P1912P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1969					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)		CTCGCCTGCCGTTCCAAAAAC	0.353													g|||	98	0.0195687	0.0121	0.0115	5008	,	,		17103	0.0		0.0467	False		,,,				2504	0.0276				p.P1969P		Atlas-SNP	.											TG,NS,carcinoma,+2,1	TG	416	1	0			c.G5907A						PASS	.	A		60,4346	58.1+/-94.6	0,60,2143	105.0	115.0	112.0		5907	-8.2	0.7	8	dbSNP_123	112	360,8240	120.2+/-179.5	6,348,3946	no	coding-synonymous	TG	NM_003235.4		6,408,6089	AA,AG,GG		4.186,1.3618,3.2293		1969/2769	133981746	420,12586	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon32			CCTGCCGTTCCAA	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.5907G>A	8.37:g.133981746G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	47	0.02152014652014652	5	0.01016260162601626	7	0.019337016574585635	0	0.0	35	0.04617414248021108	g	1.343	-0.593578	0.03771	0.013618	0.04186	ENSG00000042832	ENST00000519178	.	.	.	5.53	-8.19	0.01049	.	.	.	.	.	T	0.09818	0.0241	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38478	-0.9659	4	.	.	.	.	4.4853	0.11787	0.4043:0.1016:0.3944:0.0997	rs17693031;rs17693031	.	.	.	I	425	.	.	V	+	1	0	TG	134050928	0.000000	0.05858	0.708000	0.30435	0.193000	0.23685	-3.793000	0.00365	-1.867000	0.01144	-2.451000	0.00208	GTT	G|0.971;A|0.029	0.029	strong		0.353	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
DPP6	1804	hgsc.bcm.edu	37	7	154681216	154681216	+	Silent	SNP	G	G	A	rs1129301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:154681216G>A	ENST00000377770.3	+	25	2568	c.2427G>A	c.(2425-2427)agG>agA	p.R809R	DPP6_ENST00000332007.3_Silent_p.R747R|DPP6_ENST00000427557.1_Silent_p.R702R|DPP6_ENST00000404039.1_Silent_p.R745R			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	809					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)			AACTAATTAGGGGAAAGGCTA	0.378													G|||	1322	0.263978	0.351	0.1398	5008	,	,		16831	0.4663		0.1243	False		,,,				2504	0.1697				p.R809R	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G2427A						PASS	.	G	,,	1312,2482		240,832,825	92.0	84.0	86.0		1881,1800,1800	2.8	0.9	7	dbSNP_86	86	1155,7093		87,981,3056	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	327,1813,3881	AA,AG,GG		14.0034,34.5809,20.4866	,,	627/684,600/657,600/657	154681216	2467,9575	1897	4124	6021	SO:0001819	synonymous_variant	1804	exon25			AATTAGGGGAAAG	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.2427G>A	7.37:g.154681216G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				A|0.260;C|0.000;G|0.739;N|0.000	0.260	strong		0.378	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
NCKAP5	344148	hgsc.bcm.edu	37	2	133541454	133541454	+	Missense_Mutation	SNP	A	A	G	rs12691830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133541454A>G	ENST00000409261.1	-	14	3303	c.2930T>C	c.(2929-2931)aTt>aCt	p.I977T	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.I977T|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	977			I -> T (in dbSNP:rs12691830).							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						TGGAGCAGAAATTCCTTTCAG	0.498													G|||	3530	0.704872	0.8328	0.6657	5008	,	,		17934	0.871		0.493	False		,,,				2504	0.6063				p.I977T		Atlas-SNP	.											NCKAP5,colon,carcinoma,0,1	NCKAP5	322	1	0			c.T2930C						scavenged	.	G	THR/ILE,	3023,743		1237,549,97	28.0	30.0	29.0		2930,	4.2	0.0	2	dbSNP_121	29	4236,3964		1116,2004,980	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	89,	2353,2553,1077	GG,GA,AA		48.3415,19.7292,39.3365	benign,	977/1910,	133541454	7259,4707	1883	4100	5983	SO:0001583	missense	344148	exon14			GCAGAAATTCCTT	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.2930T>C	2.37:g.133541454A>G	ENSP00000387128:p.Ile977Thr	Somatic	166	2	0.0120482		WXS	Illumina HiSeq	Phase_I	204	204	1	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	1520	0.6959706959706959	407	0.8272357723577236	229	0.6325966850828729	511	0.8933566433566433	373	0.4920844327176781	G	0.075	-1.193811	0.01594	0.802708	0.516585	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.09163	3.01;3.01	5.03	4.16	0.48862	.	0.446841	0.16410	N	0.215659	T	0.00012	0.0000	N	0.03608	-0.345	0.29167	P	0.877392	B	0.02656	0.0	B	0.01281	0.0	T	0.19811	-1.0294	9	0.07990	T	0.79	.	10.8108	0.46547	0.1473:0.0:0.8527:0.0	rs12691830;rs17397631;rs58720662;rs12691830	977	O14513	NCKP5_HUMAN	T	977	ENSP00000387128:I977T;ENSP00000380603:I977T	ENSP00000380603:I977T	I	-	2	0	NCKAP5	133257924	0.079000	0.21365	0.012000	0.15200	0.006000	0.05464	1.847000	0.39299	0.727000	0.32360	-0.900000	0.02857	ATT	A|0.299;G|0.701	0.701	strong		0.498	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145248876	145248876	+	Missense_Mutation	SNP	A	A	G	rs200866084		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:145248876A>G	ENST00000369340.3	+	3	464	c.20A>G	c.(19-21)aAt>aGt	p.N7S	RP11-458D21.5_ENST00000468030.1_Missense_Mutation_p.N7S|NOTCH2NL_ENST00000344859.3_Missense_Mutation_p.N7S|NOTCH2NL_ENST00000362074.6_Missense_Mutation_p.N7S			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	7	EGF-like 1. {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)	p.N7S(2)		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						ACCTACCACAATGGCACAGGA	0.348																																					p.N7S		Atlas-SNP	.											NOTCH2NL_ENST00000362074,colon,carcinoma,0,2	NOTCH2NL	100	2	2	Substitution - Missense(2)	large_intestine(2)	c.A20G						scavenged	.						11.0	10.0	10.0					1																	145248876		2011	4104	6115	SO:0001583	missense	388677	exon2			ACCACAATGGCAC		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.20A>G	1.37:g.145248876A>G	ENSP00000358346:p.Asn7Ser	Somatic	2635	239	0.0907021		WXS	Illumina HiSeq	Phase_I	3113	520	0.167041	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.596096	0.46318	.	.	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	T;T;T	0.63255	-0.03;-0.03;-0.03	3.15	3.15	0.36227	Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.47432	0.1445	L	0.35793	1.09	0.22552	N	0.998997	D;D	0.63880	0.993;0.988	P;P	0.55391	0.775;0.6	T	0.26087	-1.0113	9	0.49607	T	0.09	.	7.9433	0.29971	1.0:0.0:0.0:0.0	.	7;7	Q7Z3S9-2;Q7Z3S9	.;NT2NL_HUMAN	S	7	ENSP00000354929:N7S;ENSP00000344557:N7S;ENSP00000358346:N7S	ENSP00000344557:N7S	N	+	2	0	NOTCH2NL	143960233	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.487000	0.60293	1.439000	0.47511	0.329000	0.21502	AAT	.	.	weak		0.348	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
RRN3	54700	hgsc.bcm.edu	37	16	15178499	15178499	+	Splice_Site	SNP	G	G	A	rs76732059	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:15178499G>A	ENST00000198767.6	-	7	679	c.596C>T	c.(595-597)tCg>tTg	p.S199L	RRN3_ENST00000429751.2_Splice_Site_p.S169L|RRN3_ENST00000564131.1_Splice_Site_p.S199L|RRN3_ENST00000327307.7_Splice_Site_p.S166L|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000540462.1_Splice_Site_p.S50L|RRN3_ENST00000563559.1_Splice_Site_p.S199L	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	199					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						GTATACTCACGATGGTACATA	0.294																																					p.S199L		Atlas-SNP	.											.	RRN3	36	.	0			c.C596T						PASS	.						65.0	55.0	59.0					16																	15178499		2197	4300	6497	SO:0001630	splice_region_variant	54700	exon7			ACTCACGATGGTA	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.596+1C>T	16.37:g.15178499G>A		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	374	87	0.23262	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	37	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	10.85	1.465668	0.26335	.	.	ENSG00000085721	ENST00000198767;ENST00000429751;ENST00000327307;ENST00000540462	T;T;T;T	0.42900	1.14;1.14;1.14;0.96	3.86	3.86	0.44501	.	0.193609	0.33980	U	0.004372	T	0.30324	0.0761	L	0.39514	1.22	0.58432	D	0.999998	B;B;B;P	0.35348	0.08;0.192;0.107;0.496	B;B;B;B	0.29176	0.017;0.041;0.05;0.099	T	0.09684	-1.0663	9	.	.	.	.	12.516	0.56032	0.0:0.0:1.0:0.0	.	169;100;199;199	F5H148;B4DZL9;Q3MHU9;Q9NYV6	.;.;.;RRN3_HUMAN	L	199;169;166;50	ENSP00000198767:S199L;ENSP00000402027:S169L;ENSP00000318484:S166L;ENSP00000437963:S50L	.	S	-	2	0	RRN3	15086000	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	4.366000	0.59492	1.700000	0.51204	0.313000	0.20887	TCG	G|0.960;A|0.040	0.040	strong		0.294	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	Missense_Mutation
DBNDD1	79007	hgsc.bcm.edu	37	16	90075226	90075226	+	Silent	SNP	C	C	T	rs4362387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90075226C>T	ENST00000002501.6	-	3	416	c.285G>A	c.(283-285)tcG>tcA	p.S95S	DBNDD1_ENST00000304733.3_Silent_p.S115S|DBNDD1_ENST00000568838.1_Silent_p.S215S|DBNDD1_ENST00000392973.3_Silent_p.S101S	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	95						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		TCTCGTCGTCCGAGTCAGCAA	0.642													C|||	285	0.0569089	0.0053	0.0706	5008	,	,		20383	0.1587		0.0457	False		,,,				2504	0.0235				p.S115S		Atlas-SNP	.											.	DBNDD1	9	.	0			c.G345A						PASS	.	C	,	47,4035		0,47,1994	40.0	44.0	43.0		285,345	-10.5	0.0	16	dbSNP_111	43	495,7867		14,467,3700	no	coding-synonymous,coding-synonymous	DBNDD1	NM_001042610.1,NM_024043.2	,	14,514,5694	TT,TC,CC		5.9196,1.1514,4.3555	,	95/159,115/179	90075226	542,11902	2041	4181	6222	SO:0001819	synonymous_variant	79007	exon3			GTCGTCCGAGTCA	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.285G>A	16.37:g.90075226C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_024043	B4DQS3|Q69YT2|Q9BW25	Silent	SNP	ENST00000002501.6	37	CCDS42223.1																																																																																			C|0.947;T|0.053	0.053	strong		0.642	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043	
MMACHC	25974	hgsc.bcm.edu	37	1	45973928	45973928	+	Silent	SNP	G	G	A	rs2275276	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:45973928G>A	ENST00000401061.4	+	3	601	c.321G>A	c.(319-321)gtG>gtA	p.V107V		NM_015506.2	NP_056321.2	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria	107					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)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACTACGAGGTGCACCCCAACC	0.552													G|||	2380	0.47524	0.3654	0.4957	5008	,	,		20592	0.5952		0.4771	False		,,,				2504	0.4836				p.V107V		Atlas-SNP	.											.	MMACHC	22	.	0			c.G321A						PASS	.	G		1467,2473		283,901,786	81.0	82.0	82.0		321	-0.2	1.0	1	dbSNP_100	82	3633,4681		775,2083,1299	no	coding-synonymous	MMACHC	NM_015506.2		1058,2984,2085	AA,AG,GG		43.6974,37.2335,41.6191		107/283	45973928	5100,7154	1970	4157	6127	SO:0001819	synonymous_variant	25974	exon3			CGAGGTGCACCCC		CCDS41324.1	1p34.1	2011-05-12			ENSG00000132763	ENSG00000132763			24525	protein-coding gene	gene with protein product		609831				16311595	Standard	NM_015506		Approved	DKFZP564I122, cblC	uc009vxv.3	Q9Y4U1	OTTHUMG00000007742	ENST00000401061.4:c.321G>A	1.37:g.45973928G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	186	86	0.462366	NM_015506	Q5T157|Q9BRQ7	Silent	SNP	ENST00000401061.4	37	CCDS41324.1																																																																																			G|0.526;A|0.474	0.474	strong		0.552	MMACHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020864.2	NM_015506	
FUT2	2524	hgsc.bcm.edu	37	19	49206674	49206674	+	Nonsense_Mutation	SNP	G	G	A	rs601338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49206674G>A	ENST00000425340.2	+	2	578	c.461G>A	c.(460-462)tGg>tAg	p.W154*	FUT2_ENST00000391876.4_Nonsense_Mutation_p.W154*	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	154					carbohydrate metabolic process (GO:0005975)|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)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		CCCTGCTCCTGGACCTTCTAC	0.642													G|||	1611	0.321685	0.4909	0.3415	5008	,	,		16779	0.004		0.4414	False		,,,				2504	0.2832				p.W154X		Atlas-SNP	.											FUT2,NS,carcinoma,0,2	FUT2	30	2	0			c.G461A	GRCh37	CM950483	FUT2	M	rs601338	PASS	.	G	stop/TRP,stop/TRP	2186,2220	560.2+/-380.4	554,1078,571	42.0	41.0	42.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	461,461	4.8	1.0	19	dbSNP_83	42	4231,4367	545.7+/-384.8	1051,2129,1119	no	stop-gained,stop-gained	FUT2	NM_000511.5,NM_001097638.2	,	1605,3207,1690	AA,AG,GG		49.2091,49.6142,49.3464	,	154/344,154/344	49206674	6417,6587	2203	4299	6502	SO:0001587	stop_gained	2524	exon2			GCTCCTGGACCTT		CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"""Fucosyltransferases"""	4013	protein-coding gene	gene with protein product	"""alpha (1,2) fucosyltransferase"", ""galactoside 2-alpha-L-fucosyltransferase 2"", ""GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2"", ""alpha(1,2)FT2"", ""secretor factor"", ""secretor blood group alpha-2-fucosyltransferase"""	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.461G>A	19.37:g.49206674G>A	ENSP00000387498:p.Trp154*	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_001097638	Q0VAG5|Q14338|Q5D0G2	Nonsense_Mutation	SNP	ENST00000425340.2	37	CCDS33069.1	708	0.3241758241758242	241	0.4898373983739837	139	0.3839779005524862	3	0.005244755244755245	325	0.4287598944591029	G	32	5.143978	0.94603	0.496142	0.492091	ENSG00000176920	ENST00000522966;ENST00000425340;ENST00000391876	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7492	0.77969	0.0:0.0:1.0:0.0	rs601338;rs17849550;rs58899004;rs601338	.	.	.	X	154	.	ENSP00000375748:W154X	W	+	2	0	FUT2	53898486	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.260000	0.58835	2.384000	0.81235	0.549000	0.68633	TGG	G|0.575;A|0.425	0.425	strong		0.642	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511	
MYBPH	4608	hgsc.bcm.edu	37	1	203144794	203144794	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:203144794G>A	ENST00000255416.4	-	1	147	c.90C>T	c.(88-90)ccC>ccT	p.P30P		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	30					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)		CCACTTCTCCGGGAGGCTCTG	0.617																																					p.P30P	NSCLC(32;174 1025 14462 23899 42933)	Atlas-SNP	.											MYBPH,NS,carcinoma,-2,1	MYBPH	41	1	0			c.C90T						scavenged	.						99.0	116.0	110.0					1																	203144794		2203	4300	6503	SO:0001819	synonymous_variant	4608	exon1			TTCTCCGGGAGGC	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.90C>T	1.37:g.203144794G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	242	5	0.0206612	NM_004997	Q16886|Q86YC5	Silent	SNP	ENST00000255416.4	37	CCDS30975.1																																																																																			.	.	none		0.617	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997	
PLXNA2	5362	hgsc.bcm.edu	37	1	208202279	208202279	+	Silent	SNP	G	G	A	rs113155197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:208202279G>A	ENST00000367033.3	-	30	6091	c.5334C>T	c.(5332-5334)ttC>ttT	p.F1778F	PLXNA2_ENST00000483048.1_5'UTR	NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1778					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)		AAGAGTCCATGAAGGTCTGGG	0.577													G|||	5	0.000998403	0.0	0.0	5008	,	,		20004	0.0		0.004	False		,,,				2504	0.001				p.F1778F		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C5334T						PASS	.	G		0,4406		0,0,2203	108.0	107.0	107.0		5334	3.5	1.0	1	dbSNP_132	107	40,8560	26.8+/-75.7	0,40,4260	no	coding-synonymous	PLXNA2	NM_025179.3		0,40,6463	AA,AG,GG		0.4651,0.0,0.3076		1778/1895	208202279	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon30			GTCCATGAAGGTC	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.5334C>T	1.37:g.208202279G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			G|0.997;A|0.003	0.003	strong		0.577	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2413961	2413961	+	Silent	SNP	G	G	C	rs10153475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2413961G>C	ENST00000332578.3	+	9	1416	c.1416G>C	c.(1414-1416)tcG>tcC	p.S472S		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	472					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)		CCACCAAATCGATGCAGGCCC	0.607													C|||	1969	0.393171	0.5923	0.2925	5008	,	,		16151	0.374		0.2594	False		,,,				2504	0.3528				p.S472S		Atlas-SNP	.											TMPRSS9,NS,carcinoma,0,1	TMPRSS9	79	1	0			c.G1416C						PASS	.	C		2490,1916	528.6+/-372.4	723,1044,436	30.0	30.0	30.0		1416	2.6	0.0	19	dbSNP_119	30	2278,6322	685.8+/-404.1	308,1662,2330	no	coding-synonymous	TMPRSS9	NM_182973.1		1031,2706,2766	CC,CG,GG		26.4884,43.4862,36.66		472/1060	2413961	4768,8238	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon9			CAAATCGATGCAG	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.1416G>C	19.37:g.2413961G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			G|0.632;C|0.368	0.368	strong		0.607	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
MCM10	55388	hgsc.bcm.edu	37	10	13230950	13230950	+	Silent	SNP	C	C	T	rs2296222	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:13230950C>T	ENST00000484800.2	+	10	1391	c.1288C>T	c.(1288-1290)Ctg>Ttg	p.L430L	MCM10_ENST00000378714.3_Silent_p.L429L|MCM10_ENST00000378694.1_Silent_p.L429L			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	430					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						GCGTGCGGATCTGCAGTCCAC	0.542													T|||	983	0.196286	0.1293	0.2896	5008	,	,		17923	0.1954		0.174	False		,,,				2504	0.2444				p.L430L		Atlas-SNP	.											.	MCM10	76	.	0			c.C1288T						PASS	.	T	,	624,3782	768.8+/-413.6	35,554,1614	140.0	130.0	133.0		1285,1288	-6.7	0.0	10	dbSNP_100	133	1255,7345	761.3+/-407.6	88,1079,3133	no	coding-synonymous,coding-synonymous	MCM10	NM_018518.4,NM_182751.2	,	123,1633,4747	TT,TC,CC		14.593,14.1625,14.4472	,	429/875,430/876	13230950	1879,11127	2203	4300	6503	SO:0001819	synonymous_variant	55388	exon10			GCGGATCTGCAGT	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.1288C>T	10.37:g.13230950C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Silent	SNP	ENST00000484800.2	37	CCDS7096.1																																																																																			C|0.837;T|0.163	0.163	strong		0.542	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
KCNH2	3757	hgsc.bcm.edu	37	7	150649603	150649603	+	Silent	SNP	G	G	A	rs740952	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150649603G>A	ENST00000262186.5	-	6	1868	c.1467C>T	c.(1465-1467)atC>atT	p.I489I	KCNH2_ENST00000330883.4_Silent_p.I149I|KCNH2_ENST00000392968.2_Silent_p.I393I|KCNH2_ENST00000430723.3_Silent_p.I489I	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	489					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGTGGACGGCGATGCGGCCGG	0.592													G|||	1716	0.342652	0.2632	0.3372	5008	,	,		19711	0.6131		0.2127	False		,,,				2504	0.3088				p.I489I	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.C1467T						PASS	.	G	,,,	1158,3248	409.1+/-334.9	154,850,1199	129.0	112.0	118.0		1467,447,1467,447	-1.3	1.0	7	dbSNP_86	118	1836,6764	329.6+/-318.8	201,1434,2665	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNH2	NM_000238.3,NM_001204798.1,NM_172056.2,NM_172057.2	,,,	355,2284,3864	AA,AG,GG		21.3488,26.2823,23.0201	,,,	489/1160,149/549,489/889,149/820	150649603	2994,10012	2203	4300	6503	SO:0001819	synonymous_variant	3757	exon6			GACGGCGATGCGG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1467C>T	7.37:g.150649603G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	163	70	0.429448	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	37	CCDS5910.1																																																																																			A|0.278;G|0.722;T|0.000	0.278	strong		0.592	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
LAMA1	284217	hgsc.bcm.edu	37	18	6985270	6985270	+	Missense_Mutation	SNP	C	C	T	rs11664063	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:6985270C>T	ENST00000389658.3	-	39	5719	c.5626G>A	c.(5626-5628)Gct>Act	p.A1876T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1876	Domain II and I.		A -> T (in dbSNP:rs11664063). {ECO:0000269|PubMed:1714537, ECO:0000269|PubMed:2049067}.		axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.A1876T(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGGAACTCAGCGGCATGGTCC	0.493													C|||	679	0.135583	0.0068	0.1383	5008	,	,		17821	0.1915		0.2276	False		,,,				2504	0.1554				p.A1876T		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	1	Substitution - Missense(1)	stomach(1)	c.G5626A						PASS	.	C	THR/ALA	225,4181	135.3+/-171.4	7,211,1985	200.0	163.0	176.0		5626	-0.6	0.0	18	dbSNP_120	176	2201,6399	375.3+/-337.7	281,1639,2380	yes	missense	LAMA1	NM_005559.3	58	288,1850,4365	TT,TC,CC		25.593,5.1067,18.6529	benign	1876/3076	6985270	2426,10580	2203	4300	6503	SO:0001583	missense	284217	exon39			ACTCAGCGGCATG	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.5626G>A	18.37:g.6985270C>T	ENSP00000374309:p.Ala1876Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	167	80	0.479042	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	347	0.15888278388278387	6	0.012195121951219513	63	0.17403314917127072	96	0.16783216783216784	182	0.24010554089709762	C	8.183	0.794177	0.16327	0.051067	0.25593	ENSG00000101680	ENST00000389658	T	0.17854	2.25	5.58	-0.587	0.11690	.	0.452259	0.22669	N	0.057082	T	0.00012	0.0000	M	0.68593	2.085	0.53688	P	2.199999999996649E-5	B	0.26547	0.152	B	0.15484	0.013	T	0.44112	-0.9349	9	0.15952	T	0.53	.	6.1433	0.20271	0.1159:0.4954:0.0:0.3887	rs11664063;rs52811359;rs58155506;rs11664063	1876	P25391	LAMA1_HUMAN	T	1876	ENSP00000374309:A1876T	ENSP00000374309:A1876T	A	-	1	0	LAMA1	6975270	0.009000	0.17119	0.016000	0.15963	0.006000	0.05464	0.065000	0.14466	-0.449000	0.07117	-0.123000	0.14984	GCT	C|0.823;T|0.177	0.177	strong		0.493	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
INADL	10207	hgsc.bcm.edu	37	1	62550230	62550230	+	Silent	SNP	C	C	T	rs17123051	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:62550230C>T	ENST00000371158.2	+	33	4401	c.4287C>T	c.(4285-4287)ccC>ccT	p.P1429P	INADL_ENST00000316485.6_Silent_p.P1429P|INADL_ENST00000543708.1_Silent_p.P213P|INADL_ENST00000545929.1_Silent_p.P102P	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1429					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						CAACGTGTCCCATTGTCCCTG	0.502													C|||	149	0.0297524	0.0393	0.0072	5008	,	,		16921	0.003		0.007	False		,,,				2504	0.0838				p.P1429P		Atlas-SNP	.											INADL_ENST00000543708,NS,carcinoma,+1,2	INADL	179	2	0			c.C4287T						scavenged	.	C		204,4202	125.7+/-162.9	4,196,2003	95.0	89.0	91.0		4287	3.1	1.0	1	dbSNP_123	91	16,8584	11.2+/-40.8	0,16,4284	no	coding-synonymous	INADL	NM_176877.2		4,212,6287	TT,TC,CC		0.186,4.63,1.6915		1429/1802	62550230	220,12786	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon33			GTGTCCCATTGTC	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.4287C>T	1.37:g.62550230C>T		Somatic	85	2	0.0235294		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			C|0.985;T|0.015	0.015	strong		0.502	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
CHRM4	1132	hgsc.bcm.edu	37	11	46406767	46406767	+	Silent	SNP	G	G	A	rs2067482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	213	0	0		WXS	Illumina HiSeq	Phase_I	192	87	0.453125	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	
NEIL2	252969	hgsc.bcm.edu	37	8	11640784	11640784	+	Silent	SNP	A	A	G	rs8191642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:11640784A>G	ENST00000284503.6	+	4	1163	c.564A>G	c.(562-564)ccA>ccG	p.P188P	NEIL2_ENST00000528323.1_Silent_p.P72P|NEIL2_ENST00000436750.3_Silent_p.P188P|NEIL2_ENST00000455213.2_Silent_p.P188P|NEIL2_ENST00000403422.3_Silent_p.P127P	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	188					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)		GCTCTTCCCCAGTGGTCACAC	0.512								Base excision repair (BER), DNA glycosylases					A|||	1075	0.214657	0.4175	0.1816	5008	,	,		23263	0.0109		0.2376	False		,,,				2504	0.1503				p.P188P		Atlas-SNP	.											.	NEIL2	14	.	0			c.A564G						PASS	.	A	,,,	1609,2797	498.9+/-364.3	284,1041,878	219.0	196.0	204.0		564,381,216,564	-7.4	0.0	8	dbSNP_117	204	1943,6657	343.0+/-324.7	224,1495,2581	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	508,2536,3459	GG,GA,AA		22.593,36.5184,27.3105	,,,	188/333,127/272,72/217,188/333	11640784	3552,9454	2203	4300	6503	SO:0001819	synonymous_variant	252969	exon4			TTCCCCAGTGGTC	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.564A>G	8.37:g.11640784A>G		Somatic	341	1	0.00293255		WXS	Illumina HiSeq	Phase_I	334	332	0.994012	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			A|0.751;G|0.249	0.249	strong		0.512	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043	
LRRC25	126364	hgsc.bcm.edu	37	19	18502835	18502835	+	Missense_Mutation	SNP	G	G	A	rs6512265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18502835G>A	ENST00000339007.3	-	2	1533	c.880C>T	c.(880-882)Cca>Tca	p.P294S	LRRC25_ENST00000595840.1_Missense_Mutation_p.P294S	NM_145256.2	NP_660299.2	Q8N386	LRC25_HUMAN	leucine rich repeat containing 25	294			P -> S (in dbSNP:rs6512265). {ECO:0000269|PubMed:12384430, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|skin(1)	8						TCATCCATTGGGGCCTGGCCC	0.562													G|||	3616	0.722045	0.8638	0.7046	5008	,	,		20103	0.6746		0.675	False		,,,				2504	0.6401				p.P294S		Atlas-SNP	.											.	LRRC25	16	.	0			c.C880T						PASS	.	G	SER/PRO	3679,727	758.4+/-412.8	1551,577,75	131.0	93.0	106.0		880	-1.6	0.0	19	dbSNP_116	106	5668,2932	668.8+/-402.6	1865,1938,497	yes	missense	LRRC25	NM_145256.2	74	3416,2515,572	AA,AG,GG		34.093,16.5002,28.1332	probably-damaging	294/306	18502835	9347,3659	2203	4300	6503	SO:0001583	missense	126364	exon2			CCATTGGGGCCTG	AK095435	CCDS12377.1	19p13.11	2013-09-20			ENSG00000175489	ENSG00000175489			29806	protein-coding gene	gene with protein product		607518				12384430	Standard	NM_145256		Approved	MAPA, FLJ38116	uc002niw.3	Q8N386	OTTHUMG00000183361	ENST00000339007.3:c.880C>T	19.37:g.18502835G>A	ENSP00000340983:p.Pro294Ser	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	221	108	0.488688	NM_145256	Q6IQ00|Q8N9A5	Missense_Mutation	SNP	ENST00000339007.3	37	CCDS12377.1	1599	0.7321428571428571	425	0.8638211382113821	263	0.7265193370165746	391	0.6835664335664335	520	0.6860158311345647	G	13.39	2.223873	0.39300	0.834998	0.65907	ENSG00000175489	ENST00000339007	T	0.33216	1.42	3.56	-1.63	0.08345	.	0.758877	0.11108	N	0.598887	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.18310	0.027	B	0.11329	0.006	T	0.14783	-1.0460	9	0.51188	T	0.08	-8.6308	1.1268	0.01736	0.2196:0.1739:0.4285:0.178	rs6512265;rs60176912;rs6512265	294	Q8N386	LRC25_HUMAN	S	294	ENSP00000340983:P294S	ENSP00000340983:P294S	P	-	1	0	LRRC25	18363835	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.491000	0.06474	-0.305000	0.08831	-1.080000	0.02220	CCA	G|0.273;A|0.727	0.727	strong		0.562	LRRC25-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466342.1	NM_145256	
CAPN9	10753	hgsc.bcm.edu	37	1	230903350	230903350	+	Silent	SNP	T	T	C	rs3828126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:230903350T>C	ENST00000271971.2	+	5	713	c.600T>C	c.(598-600)acT>acC	p.T200T	RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000366666.2_Silent_p.T137T|CAPN9_ENST00000354537.1_Silent_p.T200T	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	200	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)				AAGACTTCACTGGGGGTGTGG	0.552													C|||	1125	0.224641	0.1959	0.2939	5008	,	,		16928	0.1984		0.337	False		,,,				2504	0.1258				p.T200T		Atlas-SNP	.											.	CAPN9	116	.	0			c.T600C						PASS	.	C	,	855,3551	745.1+/-411.6	81,693,1429	89.0	92.0	91.0		600,600	-10.6	0.0	1	dbSNP_107	91	2820,5780	676.6+/-403.3	479,1862,1959	yes	coding-synonymous,coding-synonymous	CAPN9	NM_006615.2,NM_016452.1	,	560,2555,3388	CC,CT,TT		32.7907,19.4054,28.2562	,	200/691,200/665	230903350	3675,9331	2203	4300	6503	SO:0001819	synonymous_variant	10753	exon5			CTTCACTGGGGGT	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.600T>C	1.37:g.230903350T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	37	CCDS1586.1																																																																																			T|0.736;C|0.264	0.264	strong		0.552	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
MANSC4	100287284	hgsc.bcm.edu	37	12	27916206	27916206	+	Missense_Mutation	SNP	G	G	A	rs11049125	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:27916206G>A	ENST00000381273.3	-	3	487	c.488C>T	c.(487-489)aCg>aTg	p.T163M		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	163						integral component of membrane (GO:0016021)				kidney(1)	1						ACCATTTATCGTGGTGGTTTG	0.383													A|||	625	0.1248	0.0234	0.1023	5008	,	,		19906	0.2044		0.173	False		,,,				2504	0.1462				p.T163M		Atlas-SNP	.											.	MANSC4	9	.	0			c.C488T						PASS	.	A	MET/THR	63,1321		1,61,630	292.0	244.0	259.0		488	-9.5	0.0	12	dbSNP_120	259	485,2697		36,413,1142	yes	missense	MANSC4	NM_001146221.1	81	37,474,1772	AA,AG,GG		15.242,4.552,12.0018	benign	163/341	27916206	548,4018	692	1591	2283	SO:0001583	missense	100287284	exon3			TTTATCGTGGTGG		CCDS53770.1	12p11.22	2011-05-05			ENSG00000205693	ENSG00000205693			40023	protein-coding gene	gene with protein product							Standard	NM_001146221		Approved		uc010sjs.1	A6NHS7	OTTHUMG00000169216	ENST00000381273.3:c.488C>T	12.37:g.27916206G>A	ENSP00000370673:p.Thr163Met	Somatic	311	1	0.00321543		WXS	Illumina HiSeq	Phase_I	295	131	0.444068	NM_001146221		Missense_Mutation	SNP	ENST00000381273.3	37	CCDS53770.1	295	0.13507326007326007	17	0.034552845528455285	34	0.09392265193370165	112	0.1958041958041958	132	0.1741424802110818	A	4.507	0.094008	0.08632	0.04552	0.15242	ENSG00000205693	ENST00000381273	T	0.44881	0.91	5.58	-9.5	0.00584	.	1.354920	0.04623	N	0.402308	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.15809	-1.0424	9	0.36615	T	0.2	2.5148	4.6531	0.12605	0.2368:0.0978:0.4738:0.1916	rs11049125;rs61212329;rs11049125	163	A6NHS7	MANS4_HUMAN	M	163	ENSP00000370673:T163M	ENSP00000370673:T163M	T	-	2	0	MANSC4	27807473	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-0.138000	0.10374	-2.593000	0.00455	-0.360000	0.07572	ACG	G|0.869;A|0.131	0.131	strong		0.383	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
PJA2	9867	hgsc.bcm.edu	37	5	108714298	108714298	+	Missense_Mutation	SNP	T	T	C	rs1045706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:108714298T>C	ENST00000361189.2	-	4	1129	c.890A>G	c.(889-891)cAa>cGa	p.Q297R	PJA2_ENST00000361557.3_Missense_Mutation_p.Q297R|PJA2_ENST00000511624.1_5'Flank	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	297			Q -> R (in dbSNP:rs1045706). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455477}.		long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		ATTGGTATTTTGTTCACTACA	0.413													T|||	1607	0.320887	0.0643	0.4712	5008	,	,		22030	0.0565		0.5895	False		,,,				2504	0.5573				p.Q297R		Atlas-SNP	.											.	PJA2	53	.	0			c.A890G						PASS	.	T	ARG/GLN	690,3714	287.8+/-279.5	54,582,1566	139.0	147.0	144.0		890	2.9	1.0	5	dbSNP_86	144	5090,3510	632.9+/-398.7	1512,2066,722	yes	missense	PJA2	NM_014819.4	43	1566,2648,2288	CC,CT,TT		40.814,15.6676,44.4479	possibly-damaging	297/709	108714298	5780,7224	2202	4300	6502	SO:0001583	missense	9867	exon4			GTATTTTGTTCAC	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.890A>G	5.37:g.108714298T>C	ENSP00000354775:p.Gln297Arg	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	205	205	1	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	685	0.31364468864468864	41	0.08333333333333333	169	0.46685082872928174	25	0.043706293706293704	450	0.5936675461741425	T	0.040	-1.287968	0.01387	0.156676	0.59186	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.05513	3.43;3.43	5.61	2.88	0.33553	.	0.384034	0.24922	N	0.034535	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	8.000000000008E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.46105	-0.9215	9	0.07030	T	0.85	-15.05	1.7421	0.02955	0.2484:0.0888:0.1186:0.5443	rs1045706;rs3805437;rs17410526;rs17856899;rs52814571;rs56932049;rs1045706	297	O43164	PJA2_HUMAN	R	297	ENSP00000354775:Q297R;ENSP00000355284:Q297R	ENSP00000354775:Q297R	Q	-	2	0	PJA2	108742197	0.147000	0.22687	0.961000	0.40146	0.108000	0.19459	0.437000	0.21543	1.054000	0.40438	-0.274000	0.10170	CAA	T|0.639;C|0.361	0.361	strong		0.413	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
RPL27A	6157	hgsc.bcm.edu	37	11	8707233	8707233	+	Silent	SNP	C	C	T	rs6735	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8707233C>T	ENST00000314138.6	+	5	730	c.327C>T	c.(325-327)taC>taT	p.Y109Y	RPL27A_ENST00000524496.1_Silent_p.Y52Y|RPL27A_ENST00000532359.1_Silent_p.Y74Y|SNORA3_ENST00000364113.1_RNA|RPL27A_ENST00000530022.1_Silent_p.Y52Y|SNORA45_ENST00000391305.1_RNA|RPL27A_ENST00000526562.1_Silent_p.Y52Y|RPL27A_ENST00000530913.1_Silent_p.Y52Y	NM_000990.4	NP_000981.1	P46776	RL27A_HUMAN	ribosomal protein L27a	109					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGGGCTACTACAAAGTTCTGG	0.468													C|||	928	0.185304	0.0946	0.17	5008	,	,		19537	0.2798		0.1779	False		,,,				2504	0.229				p.Y109Y		Atlas-SNP	.											.	RPL27A	5	.	0			c.C327T						PASS	.	C		455,3947	207.5+/-228.8	22,411,1768	81.0	83.0	83.0		327	3.9	1.0	11	dbSNP_52	83	1464,7128	277.2+/-292.7	120,1224,2952	no	coding-synonymous	RPL27A	NM_000990.4		142,1635,4720	TT,TC,CC		17.0391,10.3362,14.7684		109/149	8707233	1919,11075	2201	4296	6497	SO:0001819	synonymous_variant	6157	exon5			CTACTACAAAGTT	U14968	CCDS7790.1	11p15	2011-04-06				ENSG00000166441		"""L ribosomal proteins"""	10329	protein-coding gene	gene with protein product		603637				7772601, 9582194	Standard	NM_000990		Approved	L27A	uc001mgs.4	P46776		ENST00000314138.6:c.327C>T	11.37:g.8707233C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	119	38	0.319328	NM_000990	B2R4B3	Silent	SNP	ENST00000314138.6	37	CCDS7790.1																																																																																			C|0.830;G|0.005	.	strong		0.468	RPL27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386506.1	NM_000990	
MRTO4	51154	hgsc.bcm.edu	37	1	19585207	19585207	+	Silent	SNP	G	G	A	rs2294939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19585207G>A	ENST00000330263.4	+	8	900	c.603G>A	c.(601-603)aaG>aaA	p.K201K		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	201					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K201K(2)		breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTGAATTCAAGGTGACCATCA	0.478													.|||	547	0.109225	0.087	0.0908	5008	,	,		19401	0.1012		0.1262	False		,,,				2504	0.1431				p.K201K	GBM(192;2418 3032 7540 48714)	Atlas-SNP	.											MRTO4,colon,carcinoma,0,2	MRTO4	17	2	2	Substitution - coding silent(2)	large_intestine(1)|stomach(1)	c.G603A						PASS	.	G		455,3951	215.8+/-234.7	22,411,1770	110.0	107.0	108.0		603	-2.8	1.0	1	dbSNP_100	108	1239,7361	248.3+/-276.0	102,1035,3163	no	coding-synonymous	MRTO4	NM_016183.3		124,1446,4933	AA,AG,GG		14.407,10.3268,13.0248		201/240	19585207	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	51154	exon8			ATTCAAGGTGACC	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.603G>A	1.37:g.19585207G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			G|1.000;|0.000	.	weak		0.478	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
ENPP5	59084	hgsc.bcm.edu	37	6	46135884	46135884	+	Missense_Mutation	SNP	C	C	G	rs34109856	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:46135884C>G	ENST00000371383.2	-	3	376	c.116G>C	c.(115-117)cGt>cCt	p.R39P	ENPP5_ENST00000492313.1_5'Flank|ENPP5_ENST00000230565.3_Missense_Mutation_p.R39P					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GTAATCCCAACGGAATCCATC	0.373													C|||	137	0.0273562	0.0015	0.0562	5008	,	,		17712	0.0		0.0696	False		,,,				2504	0.0266				p.R39P		Atlas-SNP	.											.	ENPP5	44	.	0			c.G116C						PASS	.	C	PRO/ARG	40,4366	40.0+/-72.8	0,40,2163	47.0	49.0	48.0		116	5.3	1.0	6	dbSNP_126	48	463,8135	132.0+/-189.7	15,433,3851	yes	missense	ENPP5	NM_021572.4	103	15,473,6014	GG,GC,CC		5.385,0.9079,3.868	probably-damaging	39/478	46135884	503,12501	2203	4299	6502	SO:0001583	missense	59084	exon2			TCCCAACGGAATC	AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.116G>C	6.37:g.46135884C>G	ENSP00000360436:p.Arg39Pro	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	86	52	0.604651	NM_021572		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	69	0.03159340659340659	0	0.0	20	0.055248618784530384	0	0.0	49	0.06464379947229551	C	20.6	4.018882	0.75275	0.009079	0.05385	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.78816	-1.21;-1.21	5.26	5.26	0.73747	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.90290	0.6963	H	0.95645	3.7	0.47905	D	0.999541	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92527	0.6030	10	0.87932	D	0	-17.0106	14.5296	0.67915	0.0:0.927:0.0:0.073	rs34109856	39;39	A8K9X7;Q9UJA9	.;ENPP5_HUMAN	P	39	ENSP00000360436:R39P;ENSP00000230565:R39P	ENSP00000230565:R39P	R	-	2	0	ENPP5	46243843	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.725000	0.68507	2.613000	0.88420	0.591000	0.81541	CGT	C|0.961;G|0.039	0.039	strong		0.373	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
ANXA6	309	hgsc.bcm.edu	37	5	150489390	150489390	+	Silent	SNP	A	A	G	rs1133202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150489390A>G	ENST00000354546.5	-	22	1835	c.1608T>C	c.(1606-1608)ccT>ccC	p.P536P	ANXA6_ENST00000521512.1_Silent_p.P323P|ANXA6_ENST00000356496.5_Silent_p.P530P|ANXA6_ENST00000523714.1_Silent_p.P504P|ANXA6_ENST00000377751.5_Silent_p.P193P	NM_001155.4	NP_001146.2	P08133	ANXA6_HUMAN	annexin A6	536					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|protein homooligomerization (GO:0051260)|regulation of muscle contraction (GO:0006937)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|cholesterol binding (GO:0015485)|GTP binding (GO:0005525)|ligand-gated ion channel activity (GO:0015276)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|lung(9)	12		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTCTCCACTAGGTGTGTCTG	0.522													G|||	3797	0.758187	0.8404	0.7637	5008	,	,		20406	0.6696		0.7555	False		,,,				2504	0.7372				p.P536P		Atlas-SNP	.											.	ANXA6	102	.	0			c.T1608C						PASS	.	G	,	3257,603		1387,483,60	83.0	88.0	86.0		1608,1512	3.6	0.5	5	dbSNP_86	86	6251,2029		2379,1493,268	no	coding-synonymous,coding-synonymous	ANXA6	NM_001155.4,NM_001193544.1	,	3766,1976,328	GG,GA,AA		24.5048,15.6218,21.6804	,	536/674,504/642	150489390	9508,2632	1930	4140	6070	SO:0001819	synonymous_variant	309	exon22			TCCACTAGGTGTG	J03578	CCDS47315.1, CCDS54941.1	5q33.1	2008-02-05			ENSG00000197043	ENSG00000197043		"""Annexins"""	544	protein-coding gene	gene with protein product		114070		ANX6		3258820	Standard	NM_001155		Approved		uc003ltl.2	P08133	OTTHUMG00000164179	ENST00000354546.5:c.1608T>C	5.37:g.150489390A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001155	B7Z8A7|D3DQH4|E9PGK1|Q6ZT79	Silent	SNP	ENST00000354546.5	37	CCDS47315.1																																																																																			A|0.234;G|0.766	0.766	strong		0.522	ANXA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377668.2	NM_001155	
OR1S1	219959	hgsc.bcm.edu	37	11	57982726	57982726	+	Silent	SNP	G	G	T	rs1993089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57982726G>T	ENST00000309433.6	+	1	510	c.510G>T	c.(508-510)ctG>ctT	p.L170L		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L170L(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTATTGCTCTGACACACACCC	0.478													G|||	2620	0.523163	0.2844	0.5418	5008	,	,		18215	0.8036		0.4225	False		,,,				2504	0.6472				p.L170L		Atlas-SNP	.											OR1S1,NS,carcinoma,0,1	OR1S1	139	1	1	Substitution - coding silent(1)	stomach(1)	c.G510T						PASS	.	G		1158,3244		197,764,1240	214.0	189.0	197.0		510	1.2	1.0	11	dbSNP_92	197	3386,5206		781,1824,1691	no	coding-synonymous	OR1S1	NM_001004458.1		978,2588,2931	TT,TG,GG		39.4088,26.3062,34.97		170/326	57982726	4544,8450	2201	4296	6497	SO:0001819	synonymous_variant	219959	exon1			TGCTCTGACACAC	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.510G>T	11.37:g.57982726G>T		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	244	98	0.401639	NM_001004458	Q6IFG3	Silent	SNP	ENST00000309433.6	37	CCDS31546.1																																																																																			G|0.609;T|0.391	0.391	strong		0.478	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
NPAS3	64067	hgsc.bcm.edu	37	14	34269167	34269167	+	Missense_Mutation	SNP	G	G	C	rs12434716	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:34269167G>C	ENST00000356141.4	+	12	1654	c.1654G>C	c.(1654-1656)Gcg>Ccg	p.A552P	NPAS3_ENST00000357798.5_Missense_Mutation_p.A539P|NPAS3_ENST00000346562.2_Missense_Mutation_p.A520P|NPAS3_ENST00000551492.1_Missense_Mutation_p.A557P|NPAS3_ENST00000548645.1_Missense_Mutation_p.A522P			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	552				A -> P (in Ref. 3; AAO17043). {ECO:0000305}.	locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		TGCTCTGGGCGCGATGCAGAT	0.647													C|||	609	0.121605	0.1876	0.2075	5008	,	,		12693	0.0099		0.1491	False		,,,				2504	0.0583				p.A552P		Atlas-SNP	.											.	NPAS3	266	.	0			c.G1654C						PASS	.	C	PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	863,3543	739.3+/-411.1	69,725,1409	48.0	50.0	49.0		1654,1564,1558,1615	2.0	0.3	14	dbSNP_120	49	1368,7232	753.1+/-407.4	114,1140,3046	yes	missense,missense,missense,missense	NPAS3	NM_001164749.1,NM_001165893.1,NM_022123.2,NM_173159.2	27,27,27,27	183,1865,4455	CC,CG,GG		15.907,19.5869,17.1536	benign,benign,benign,benign	552/934,522/904,520/902,539/921	34269167	2231,10775	2203	4300	6503	SO:0001583	missense	64067	exon12			CTGGGCGCGATGC	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"""Basic helix-loop-helix proteins"""	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1654G>C	14.37:g.34269167G>C	ENSP00000348460:p.Ala552Pro	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	37	CCDS53891.1	290	0.13278388278388278	95	0.19308943089430894	79	0.21823204419889503	7	0.012237762237762238	109	0.1437994722955145	C	4.439	0.081186	0.08533	0.195869	0.15907	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.72942	-0.7;3.39;3.38;3.38;3.38;3.25	5.3	2.01	0.26516	.	0.528965	0.20112	N	0.098988	T	0.00039	0.0001	N	0.03608	-0.345	0.09310	P	0.999999999966164	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	0.08146	-1.0736	9	0.02654	T	1	.	5.1868	0.15187	0.0:0.4487:0.3189:0.2324	rs12434716;rs12434716	522;552;520;539	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	P	526;557;520;522;552;539	ENSP00000448373:A526P;ENSP00000450392:A557P;ENSP00000319610:A520P;ENSP00000448916:A522P;ENSP00000348460:A552P;ENSP00000350446:A539P	ENSP00000319610:A520P	A	+	1	0	NPAS3	33338918	0.045000	0.20229	0.299000	0.25016	0.975000	0.68041	1.052000	0.30429	0.590000	0.29694	-0.225000	0.12378	GCG	G|0.846;C|0.154	0.154	strong		0.647	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1		
MOV10	4343	hgsc.bcm.edu	37	1	113241052	113241052	+	Silent	SNP	T	T	C	rs2306940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:113241052T>C	ENST00000413052.2	+	16	2850	c.2460T>C	c.(2458-2460)gcT>gcC	p.A820A	MOV10_ENST00000369645.1_Silent_p.A820A|MOV10_ENST00000357443.2_Silent_p.A820A|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.A764A|RP11-426L16.3_ENST00000421943.1_RNA	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	820					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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		AGGGCAAAGCTCGCCTGAGCC	0.607													C|||	1438	0.287141	0.1762	0.2911	5008	,	,		18562	0.5417		0.2346	False		,,,				2504	0.226				p.A820A		Atlas-SNP	.											.	MOV10	74	.	0			c.T2460C						PASS	.	C	,	827,3579	746.2+/-411.7	90,647,1466	59.0	47.0	51.0		2460,2460	0.9	1.0	1	dbSNP_100	51	1766,6834	731.5+/-406.8	181,1404,2715	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	271,2051,4181	CC,CT,TT		20.5349,18.7699,19.937	,	820/1004,820/1004	113241052	2593,10413	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon16			CAAAGCTCGCCTG	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2460T>C	1.37:g.113241052T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			T|0.747;G|0.002	.	strong		0.607	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
TNIP1	10318	hgsc.bcm.edu	37	5	150436503	150436503	+	Missense_Mutation	SNP	G	G	C	rs2233290	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000523200.1_Missense_Mutation_p.P151A|TNIP1_ENST00000523338.1_Missense_Mutation_p.P151A|TNIP1_ENST00000315050.7_Missense_Mutation_p.P151A|TNIP1_ENST00000520931.1_Missense_Mutation_p.P98A|TNIP1_ENST00000518977.1_Missense_Mutation_p.P151A|TNIP1_ENST00000522226.1_Missense_Mutation_p.P151A|TNIP1_ENST00000524280.1_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	60	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	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	
IFNE	338376	hgsc.bcm.edu	37	9	21481556	21481556	+	Missense_Mutation	SNP	T	T	G	rs1125488	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21481556T>G	ENST00000448696.3	-	1	756	c.138A>C	c.(136-138)caA>caC	p.Q46H	MIR31HG_ENST00000304425.3_RNA	NM_176891.4	NP_795372.1	Q86WN2	IFNE_HUMAN	interferon, epsilon	46			Q -> H (in dbSNP:rs1125488).		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(2)|lung(1)|skin(1)	4						TTGACAAGGTTTGCAACTTAT	0.408													T|||	249	0.0497204	0.0303	0.1009	5008	,	,		22045	0.0248		0.0547	False		,,,				2504	0.0603				p.Q46H		Atlas-SNP	.											.	IFNE	16	.	0			c.A138C						PASS	.	T	HIS/GLN	168,4238	110.8+/-149.0	2,164,2037	88.0	84.0	85.0		138	-8.9	0.0	9	dbSNP_86	85	605,7995	159.7+/-212.9	24,557,3719	yes	missense	IFNE	NM_176891.4	24	26,721,5756	GG,GT,TT		7.0349,3.813,5.9434	benign	46/209	21481556	773,12233	2203	4300	6503	SO:0001583	missense	338376	exon1			CAAGGTTTGCAAC	AY190045	CCDS34997.1	9p21.1	2008-12-12			ENSG00000184995	ENSG00000184995			18163	protein-coding gene	gene with protein product		615223				15546383, 17287131	Standard	NM_176891		Approved	IFNE1	uc003zpg.3	Q86WN2	OTTHUMG00000019672	ENST00000448696.3:c.138A>C	9.37:g.21481556T>G	ENSP00000418018:p.Gln46His	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	184	86	0.467391	NM_176891		Missense_Mutation	SNP	ENST00000448696.3	37	CCDS34997.1	101	0.04624542124542125	9	0.018292682926829267	35	0.09668508287292818	13	0.022727272727272728	44	0.05804749340369393	T	7.335	0.619629	0.14193	0.03813	0.070349	ENSG00000184995	ENST00000448696	T	0.03413	3.94	4.73	-8.88	0.00789	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.238330	0.06241	U	0.690404	T	0.00109	0.0003	L	0.45581	1.43	0.09310	N	1	B	0.22541	0.071	B	0.24006	0.05	T	0.45673	-0.9245	10	0.87932	D	0	.	5.6347	0.17530	0.1085:0.503:0.2199:0.1686	rs1125488;rs17729034;rs52826037;rs61637566;rs1125488	46	Q86WN2	IFNE_HUMAN	H	46	ENSP00000418018:Q46H	ENSP00000418018:Q46H	Q	-	3	2	IFNE	21471556	0.000000	0.05858	0.000000	0.03702	0.254000	0.26022	-2.452000	0.01005	-1.427000	0.01992	0.533000	0.62120	CAA	T|0.945;G|0.055	0.055	strong		0.408	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051901.2	NM_176891	
IFT74	80173	hgsc.bcm.edu	37	9	26978259	26978259	+	Missense_Mutation	SNP	A	A	G	rs11555693	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:26978259A>G	ENST00000443698.1	+	3	425	c.254A>G	c.(253-255)aAa>aGa	p.K85R	IFT74_ENST00000380062.5_Missense_Mutation_p.K85R|IFT74_ENST00000433700.1_Missense_Mutation_p.K85R|IFT74_ENST00000429045.2_Missense_Mutation_p.K85R	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	85	Basic region.		K -> R (in dbSNP:rs11555693).		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)		ACTGGGACGAAAGGTACCTAT	0.373													A|||	1172	0.234026	0.121	0.1888	5008	,	,		15995	0.6558		0.0457	False		,,,				2504	0.1779				p.K85R		Atlas-SNP	.											.	IFT74	46	.	0			c.A254G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	417,3287		19,379,1454	80.0	75.0	76.0		254,254,254,254	5.6	1.0	9	dbSNP_120	76	318,7882		9,300,3791	yes	missense,missense,missense,missense	IFT74	NM_001099222.1,NM_001099223.1,NM_001099224.1,NM_025103.2	26,26,26,26	28,679,5245	GG,GA,AA		3.878,11.2581,6.1744	benign,benign,benign,benign	85/601,85/601,85/373,85/601	26978259	735,11169	1852	4100	5952	SO:0001583	missense	80173	exon3			GGACGAAAGGTAC	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.254A>G	9.37:g.26978259A>G	ENSP00000404122:p.Lys85Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001099222	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Missense_Mutation	SNP	ENST00000443698.1	37	CCDS43793.1	556	0.25457875457875456	72	0.14634146341463414	52	0.143646408839779	397	0.6940559440559441	35	0.04617414248021108	A	13.58	2.278507	0.40294	0.112581	0.03878	ENSG00000096872	ENST00000519968;ENST00000433700;ENST00000517444;ENST00000443698;ENST00000380062;ENST00000544022;ENST00000518614;ENST00000429045;ENST00000517866	T;T;T;T;T;T;T;T	0.56103	0.48;2.79;1.94;2.79;2.79;1.47;0.48;0.77	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.25890	0.77	0.09310	P	0.999999417496	B;P	0.34615	0.226;0.459	B;B	0.30943	0.103;0.122	T	0.29792	-1.0000	9	0.22109	T	0.4	-29.1709	15.8195	0.78628	1.0:0.0:0.0:0.0	rs11555693;rs41306085;rs58559286	85;85	Q96LB3;Q96LB3-2	IFT74_HUMAN;.	R	85;85;85;85;85;85;85;85;47	ENSP00000430004:K85R;ENSP00000389224:K85R;ENSP00000430096:K85R;ENSP00000404122:K85R;ENSP00000369402:K85R;ENSP00000430526:K85R;ENSP00000393907:K85R;ENSP00000430742:K47R	ENSP00000369402:K85R	K	+	2	0	IFT74	26968259	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	8.810000	0.91950	2.146000	0.66826	0.383000	0.25322	AAA	A|0.823;G|0.177	0.177	strong		0.373	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103	
ARHGEF40	55701	hgsc.bcm.edu	37	14	21542753	21542753	+	Silent	SNP	G	G	A	rs1243472	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21542753G>A	ENST00000298694.4	+	3	991	c.864G>A	c.(862-864)gcG>gcA	p.A288A	ARHGEF40_ENST00000298693.3_Silent_p.A288A			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	288	Gly-rich.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GACACCGGGCGTGGATGCACC	0.721													G|||	1212	0.242013	0.1452	0.1369	5008	,	,		16369	0.4762		0.2117	False		,,,				2504	0.2372				p.A288A		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.G864A						PASS	.	G		628,3730		45,538,1596	9.0	12.0	11.0		864	-10.2	0.1	14	dbSNP_87	11	1636,6912		158,1320,2796	no	coding-synonymous	ARHGEF40	NM_018071.3		203,1858,4392	AA,AG,GG		19.139,14.4103,17.5422		288/1520	21542753	2264,10642	2179	4274	6453	SO:0001819	synonymous_variant	55701	exon3			CCGGGCGTGGATG		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.864G>A	14.37:g.21542753G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	16	8	0.5	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																			G|0.741;A|0.259	0.259	strong		0.721	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
OR2AG2	338755	hgsc.bcm.edu	37	11	6790028	6790028	+	Missense_Mutation	SNP	C	C	G	rs10839616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6790028C>G	ENST00000338569.2	-	1	258	c.161G>C	c.(160-162)cGg>cCg	p.R54P		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	54			R -> P (in dbSNP:rs10839616).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATGTGGAGCCGGGCTTCTAT	0.542													c|||	1445	0.288538	0.3654	0.1671	5008	,	,		21247	0.2143		0.2157	False		,,,				2504	0.4223				p.R54P		Atlas-SNP	.											OR2AG2,right_upper_lobe,carcinoma,-1,1	OR2AG2	55	1	0			c.G161C						PASS	.	T	PRO/ARG	1501,2901	479.0+/-358.4	246,1009,946	140.0	127.0	132.0		161	0.4	0.0	11	dbSNP_120	132	1890,6702	334.9+/-321.2	231,1428,2637	yes	missense	OR2AG2	NM_001004490.1	103	477,2437,3583	GG,GC,CC		21.9972,34.0981,26.0967	probably-damaging	54/317	6790028	3391,9603	2201	4296	6497	SO:0001583	missense	338755	exon1			TGGAGCCGGGCTT	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.161G>C	11.37:g.6790028C>G	ENSP00000342697:p.Arg54Pro	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	512	0.23443223443223443	162	0.32926829268292684	74	0.20441988950276244	109	0.19055944055944055	167	0.22031662269129287	c	7.698	0.692473	0.15039	0.340981	0.219972	ENSG00000188124	ENST00000338569	T	0.00449	7.37	4.28	0.401	0.16338	GPCR, rhodopsin-like superfamily (1);	0.497698	0.17054	N	0.188819	T	0.00012	0.0000	M	0.78049	2.395	0.80722	P	0.0	P	0.51147	0.942	P	0.53954	0.738	T	0.49041	-0.8980	9	0.72032	D	0.01	.	8.3017	0.32019	0.0:0.6516:0.0:0.3484	rs10839616;rs52830974;rs10839616	54	A6NM03	O2AG2_HUMAN	P	54	ENSP00000342697:R54P	ENSP00000342697:R54P	R	-	2	0	OR2AG2	6746604	0.000000	0.05858	0.006000	0.13384	0.004000	0.04260	-0.918000	0.04021	0.087000	0.17167	-1.594000	0.00841	CGG	C|0.737;G|0.263	0.263	strong		0.542	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
OR6M1	390261	hgsc.bcm.edu	37	11	123676413	123676413	+	Silent	SNP	G	G	A	rs7952150	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123676413G>A	ENST00000309154.2	-	1	682	c.645C>T	c.(643-645)taC>taT	p.Y215Y		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		TTATGTACACGTAGGACCCAG	0.488													G|||	1120	0.223642	0.3177	0.2666	5008	,	,		20315	0.1905		0.1869	False		,,,				2504	0.138				p.Y215Y		Atlas-SNP	.											.	OR6M1	60	.	0			c.C645T						PASS	.	G		1197,3207	417.8+/-338.1	173,851,1178	72.0	64.0	66.0		645	-0.8	0.1	11	dbSNP_116	66	1397,7201	270.9+/-289.3	107,1183,3009	no	coding-synonymous	OR6M1	NM_001005325.1		280,2034,4187	AA,AG,GG		16.248,27.1798,19.9508		215/314	123676413	2594,10408	2202	4299	6501	SO:0001819	synonymous_variant	390261	exon1			GTACACGTAGGAC	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"""GPCR / Class A : Olfactory receptors"""	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.645C>T	11.37:g.123676413G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Silent	SNP	ENST00000309154.2	37	CCDS31696.1																																																																																			G|0.788;A|0.212	0.212	strong		0.488	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
GNB5	10681	hgsc.bcm.edu	37	15	52446200	52446200	+	Silent	SNP	G	G	A	rs6493537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52446200G>A	ENST00000261837.7	-	4	377	c.312C>T	c.(310-312)caC>caT	p.H104H	GNB5_ENST00000560116.1_Silent_p.H62H|GNB5_ENST00000396335.4_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	54	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	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		
PGS1	9489	hgsc.bcm.edu	37	17	76421464	76421464	+	IGR	SNP	C	C	T	rs35422926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:76421464C>T	ENST00000262764.6	+	0	2201				DNAH17_ENST00000389840.5_Silent_p.P4391P|DNAH17_ENST00000585328.1_Silent_p.P4363P|DNAH17_ENST00000586052.1_5'UTR|AC061992.1_ENST00000600087.1_5'Flank	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)			AGCCCTCTCGCGGAGGAGCGG	0.552													C|||	744	0.148562	0.2315	0.134	5008	,	,		20016	0.0248		0.1809	False		,,,				2504	0.1411				p.P4368P	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.G13104A						PASS	.	C		1033,3373	381.6+/-324.1	110,813,1280	116.0	115.0	115.0		13104	-9.7	0.0	17	dbSNP_126	115	1495,7105	282.9+/-295.8	127,1241,2932	no	coding-synonymous	DNAH17	NM_173628.3		237,2054,4212	TT,TC,CC		17.3837,23.4453,19.4372		4368/4463	76421464	2528,10478	2203	4300	6503	SO:0001628	intergenic_variant	8632	exon80			CTCTCGCGGAGGA		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.76421464C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	37	CCDS42391.1																																																																																			C|0.818;T|0.182	0.182	strong		0.552	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
ATAD2B	54454	hgsc.bcm.edu	37	2	24149439	24149439	+	Silent	SNP	G	G	A	rs61739076	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:24149439G>A	ENST00000238789.5	-	1	545	c.202C>T	c.(202-204)Ctg>Ttg	p.L68L	UBXN2A_ENST00000404924.1_5'Flank	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	68						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCTCATCCAGAGTGACGCCG	0.711													G|||	479	0.095647	0.0507	0.0821	5008	,	,		13460	0.0536		0.1481	False		,,,				2504	0.1554				p.L68L		Atlas-SNP	.											.	ATAD2B	110	.	0			c.C202T						PASS	.	G	,	118,3002		2,114,1444	2.0	3.0	3.0		202,202	-0.6	0.3	2	dbSNP_129	3	672,6482		19,634,2924	no	coding-synonymous,coding-synonymous	ATAD2B	NM_001242338.1,NM_017552.2	,	21,748,4368	AA,AG,GG		9.3933,3.7821,7.6893	,	68/1454,68/1459	24149439	790,9484	1560	3577	5137	SO:0001819	synonymous_variant	54454	exon1			CATCCAGAGTGAC	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.202C>T	2.37:g.24149439G>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Silent	SNP	ENST00000238789.5	37	CCDS46227.1																																																																																			G|0.906;A|0.094	0.094	strong		0.711	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
ART3	419	hgsc.bcm.edu	37	4	77033590	77033590	+	Missense_Mutation	SNP	C	C	T	rs1128864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77033590C>T	ENST00000355810.4	+	12	1207	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	ART3_ENST00000349321.3_Missense_Mutation_p.S352L|ART3_ENST00000341029.5_Missense_Mutation_p.S341L	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	363			S -> L (in dbSNP:rs1128864). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TCTGCATCCTCGGGCAAACTG	0.418													C|||	2423	0.483826	0.7035	0.4035	5008	,	,		18814	0.5982		0.2346	False		,,,				2504	0.3824				p.S363L		Atlas-SNP	.											.	ART3	34	.	0			c.C1088T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	2772,1634	661.0+/-400.8	881,1010,312	224.0	200.0	208.0		1088,1022,1055	2.5	0.8	4	dbSNP_86	208	2074,6526	359.3+/-331.5	247,1580,2473	yes	missense,missense,missense	ART3	NM_001130016.1,NM_001130017.1,NM_001179.4	145,145,145	1128,2590,2785	TT,TC,CC		24.1163,37.0858,37.2597	benign,benign,benign	363/390,341/368,352/379	77033590	4846,8160	2203	4300	6503	SO:0001583	missense	419	exon12			CATCCTCGGGCAA	X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.1088C>T	4.37:g.77033590C>T	ENSP00000348064:p.Ser363Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	NM_001130016	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	37	CCDS47079.1	1031	0.47206959706959706	360	0.7317073170731707	139	0.3839779005524862	347	0.6066433566433567	185	0.24406332453825857	C	6.004	0.369077	0.11352	0.629142	0.241163	ENSG00000156219	ENST00000341029;ENST00000355810;ENST00000349321	T;T;T	0.11604	2.98;2.8;2.76	5.6	2.52	0.30459	.	1.300790	0.05293	N	0.521410	T	0.00012	0.0000	N	0.15975	0.35	0.58432	P	4.000000000004E-6	B;B;B;B	0.18013	0.015;0.004;0.007;0.025	B;B;B;B	0.11329	0.003;0.003;0.006;0.006	T	0.38672	-0.9650	9	0.37606	T	0.19	-13.2551	11.0566	0.47922	0.0:0.8105:0.0:0.1895	rs1128864;rs3186179;rs17001419;rs17845165;rs17857971;rs52804370;rs60186754;rs1128864	312;363;352;341	D6RBN3;Q13508;Q13508-3;Q13508-2	.;NAR3_HUMAN;.;.	L	341;363;352	ENSP00000343843:S341L;ENSP00000348064:S363L;ENSP00000304313:S352L	ENSP00000343843:S341L	S	+	2	0	ART3	77252614	0.275000	0.24201	0.818000	0.32626	0.003000	0.03518	0.816000	0.27267	0.741000	0.32674	-1.175000	0.01729	TCG	C|0.574;T|0.426	0.426	strong		0.418	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179	
PRR21	643905	hgsc.bcm.edu	37	2	240981375	240981375	+	Missense_Mutation	SNP	T	T	A	rs6732185	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:240981375T>A	ENST00000408934.1	-	1	1024	c.1025A>T	c.(1024-1026)aAg>aTg	p.K342M		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	342			K -> M (in dbSNP:rs6732185).							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						ATGAAGAGACTTGGATGAAGA	0.587													N|||	3630	0.72484	0.9251	0.5879	5008	,	,		21941	0.7817		0.6312	False		,,,				2504	0.589				p.K342M		Atlas-SNP	.											.	PRR21	53	.	0			c.A1025T						PASS	.	A	MET/LYS	3878,528		1700,478,25	161.0	143.0	149.0		1025	-1.2	0.0	2	dbSNP_116	149	5530,3070		1781,1968,551	yes	missense	PRR21	NM_001080835.1	95	3481,2446,576	AA,AT,TT		35.6977,11.9837,27.6642	possibly-damaging	342/390	240981375	9408,3598	2203	4300	6503	SO:0001583	missense	643905	exon1			AGAGACTTGGATG	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.1025A>T	2.37:g.240981375T>A	ENSP00000386166:p.Lys342Met	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	1598	0.7316849816849816	458	0.9308943089430894	218	0.6022099447513812	431	0.7534965034965035	491	0.6477572559366754	N	0.792	-0.758439	0.03019	0.880163	0.643023	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.28454	1.61;1.61	0.612	-1.22	0.09494	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.30236	0.274	B	0.08055	0.003	T	0.44787	-0.9305	8	0.54805	T	0.06	.	0.9984	0.01472	0.1999:0.3912:0.2111:0.1977	rs6732185;rs52797090;rs59866356;rs6732185	342	Q8WXC7	PRR21_HUMAN	M	342	ENSP00000386166:K342M;ENSP00000418240:K342M	ENSP00000386166:K342M	K	-	2	0	PRR21	240630048	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.269000	0.00262	-3.326000	0.00186	-2.852000	0.00102	AAG	T|0.277;A|0.723	0.723	strong		0.587	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
A4GALT	53947	hgsc.bcm.edu	37	22	43089400	43089400	+	Silent	SNP	G	G	A	rs139550090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:43089400G>A	ENST00000401850.1	-	2	1047	c.558C>T	c.(556-558)ttC>ttT	p.F186F	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000381278.3_Silent_p.F186F|A4GALT_ENST00000249005.2_Silent_p.F186F			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	186					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						AGATGCCGCCGAACTTCCACA	0.652													G|||	31	0.0061901	0.0008	0.0173	5008	,	,		14513	0.0		0.0139	False		,,,				2504	0.0041				p.F186F		Atlas-SNP	.											A4GALT,colon,carcinoma,0,2	A4GALT	35	2	0			c.C558T						PASS	.	G		6,4400	9.9+/-24.2	0,6,2197	65.0	56.0	59.0		558	-2.0	1.0	22	dbSNP_134	59	75,8525	42.6+/-100.3	0,75,4225	no	coding-synonymous	A4GALT	NM_017436.4		0,81,6422	AA,AG,GG		0.8721,0.1362,0.6228		186/354	43089400	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	53947	exon3			GCCGCCGAACTTC		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.558C>T	22.37:g.43089400G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_017436	B2R7C4|Q9P1X5	Silent	SNP	ENST00000401850.1	37	CCDS14041.1																																																																																			G|0.994;A|0.006	0.006	strong		0.652	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
SLC29A3	55315	hgsc.bcm.edu	37	10	73122284	73122284	+	Silent	SNP	G	G	A	rs373404056		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73122284G>A	ENST00000373189.5	+	6	1399	c.1347G>A	c.(1345-1347)acG>acA	p.T449T		NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	449			T -> R (in HLAS; results in reduced nucleoside transport). {ECO:0000269|PubMed:19336477}.		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						CTGAGGCCACGGGAGTGGTGA	0.602																																					p.T449T	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											SLC29A3,NS,carcinoma,+1,1	SLC29A3	51	1	0			c.G1347A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	86.0	60.0	69.0		,1347	-11.1	0.0	10		69	0,8600		0,0,4300	no	utr-3,coding-synonymous	SLC29A3	NM_001174098.1,NM_018344.5	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	,449/476	73122284	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55315	exon6			GGCCACGGGAGTG	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.1347G>A	10.37:g.73122284G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	144	79	0.548611	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Silent	SNP	ENST00000373189.5	37	CCDS7310.1																																																																																			.	.	none		0.602	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344	
COL23A1	91522	hgsc.bcm.edu	37	5	177674821	177674821	+	Missense_Mutation	SNP	T	T	C	rs200475672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:177674821T>C	ENST00000390654.3	-	21	1581	c.1224A>G	c.(1222-1224)atA>atG	p.I408M		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	408	Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CTGGCTCCACTATGAGCTGAG	0.632													T|||	2	0.000399361	0.0	0.0	5008	,	,		17262	0.0		0.002	False		,,,				2504	0.0				p.I408M		Atlas-SNP	.											.	COL23A1	47	.	0			c.A1224G						PASS	.	T	MET/ILE	0,3916		0,0,1958	19.0	22.0	21.0		1224	3.6	1.0	5		21	4,8254		0,4,4125	yes	missense	COL23A1	NM_173465.3	10	0,4,6083	CC,CT,TT		0.0484,0.0,0.0329	probably-damaging	408/541	177674821	4,12170	1958	4129	6087	SO:0001583	missense	91522	exon21			CTCCACTATGAGC	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"""Collagens"""	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.1224A>G	5.37:g.177674821T>C	ENSP00000375069:p.Ile408Met	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	146	68	0.465753	NM_173465	Q8IVR4|Q9NT93	Missense_Mutation	SNP	ENST00000390654.3	37	CCDS4436.1	.	.	.	.	.	.	.	.	.	.	T	7.999	0.754912	0.15846	0.0	4.84E-4	ENSG00000050767	ENST00000390654	D	0.93307	-3.2	4.76	3.57	0.40892	.	0.273854	0.26496	N	0.024047	D	0.89812	0.6823	L	0.47716	1.5	0.80722	D	1	P	0.44877	0.845	B	0.42522	0.39	D	0.86541	0.1828	10	0.48119	T	0.1	-4.3929	8.4416	0.32818	0.0:0.0:0.1982:0.8018	.	408	Q86Y22	CONA1_HUMAN	M	408	ENSP00000375069:I408M	ENSP00000375069:I408M	I	-	3	3	COL23A1	177607427	0.998000	0.40836	0.999000	0.59377	0.010000	0.07245	1.567000	0.36407	0.642000	0.30620	-0.460000	0.05396	ATA	.	.	weak		0.632	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465	
TTN	7273	hgsc.bcm.edu	37	2	179444939	179444939	+	Missense_Mutation	SNP	C	C	T	rs2303838	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179444939C>T	ENST00000591111.1	-	268	62376	c.62152G>A	c.(62152-62154)Gtc>Atc	p.V20718I	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V22359I|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V13419I|TTN_ENST00000460472.2_Missense_Mutation_p.V13294I|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V13486I|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V19791I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20718	Fibronectin type-III 50. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCACATTGACAGGTGGCCCA	0.348													C|||	1759	0.351238	0.3434	0.2147	5008	,	,		20260	0.631		0.1849	False		,,,				2504	0.3415				p.V22359I		Atlas-SNP	.											.	TTN	18412	.	0			c.G67075A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1207,2467		202,803,832	62.0	60.0	61.0		40456,40255,59371,39880	2.6	0.9	2	dbSNP_100	61	1445,6723		128,1189,2767	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	330,1992,3599	TT,TC,CC		17.691,32.8525,22.3949	benign,benign,benign,benign	13486/27119,13419/27052,19791/33424,13294/26927	179444939	2652,9190	1837	4084	5921	SO:0001583	missense	7273	exon318			CATTGACAGGTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.62152G>A	2.37:g.179444939C>T	ENSP00000465570:p.Val20718Ile	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		710	0.3250915750915751	157	0.31910569105691056	73	0.20165745856353592	344	0.6013986013986014	136	0.17941952506596306	C	9.291	1.050609	0.19827	0.328525	0.17691	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.41	2.61	0.31194	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.54965	1.715	0.27033	P	0.9641858	B;B;B;B	0.10296	0.003;0.003;0.003;0.003	B;B;B;B	0.14578	0.011;0.011;0.011;0.011	T	0.39396	-0.9616	8	0.87932	D	0	.	6.7606	0.23538	0.0:0.6119:0.1229:0.2652	rs2303838;rs52803332;rs59721271;rs2303838	13294;13419;13486;20718	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	19791;13294;13486;13419;13292	ENSP00000343764:V19791I;ENSP00000434586:V13294I;ENSP00000340554:V13486I;ENSP00000352154:V13419I	ENSP00000340554:V13486I	V	-	1	0	TTN	179153185	0.001000	0.12720	0.932000	0.37286	0.972000	0.66771	-0.020000	0.12525	0.261000	0.21753	-0.253000	0.11424	GTC	C|0.677;T|0.323	0.323	strong		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LRRC16A	55604	hgsc.bcm.edu	37	6	25600968	25600968	+	Silent	SNP	G	G	A	rs10456324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25600968G>A	ENST00000329474.6	+	33	3914	c.3546G>A	c.(3544-3546)gcG>gcA	p.A1182A		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1182					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)	p.A1182A(1)		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						CTGCGTGTGCGCAGAAGGTAA	0.453													A|||	2030	0.405351	0.3404	0.4179	5008	,	,		18673	0.372		0.4632	False		,,,				2504	0.4591				p.A1182A		Atlas-SNP	.											LRRC16A_ENST00000329474,NS,carcinoma,0,1	LRRC16A	168	1	1	Substitution - coding silent(1)	prostate(1)	c.G3546A						PASS	.	A	,	1375,2629		246,883,873	34.0	40.0	38.0		3546,3546	-10.1	0.0	6	dbSNP_119	38	3864,4496		908,2048,1224	no	coding-synonymous,coding-synonymous	LRRC16A	NM_001173977.1,NM_017640.5	,	1154,2931,2097	AA,AG,GG		46.2201,34.3407,42.373	,	1182/1366,1182/1372	25600968	5239,7125	2002	4180	6182	SO:0001819	synonymous_variant	55604	exon33			GTGTGCGCAGAAG	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.3546G>A	6.37:g.25600968G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Silent	SNP	ENST00000329474.6	37	CCDS54973.1																																																																																			G|0.607;A|0.393	0.393	strong		0.453	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296167	39296167	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39296167A>G	ENST00000345847.4	-	1	572	c.573T>C	c.(571-573)atT>atC	p.I191I		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	191						keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GGCAGGTGGAAATGACACAGG	0.627																																					p.I191I		Atlas-SNP	.											KRTAP4-6,bladder,carcinoma,0,9	KRTAP4-6	46	9	0			c.T573C						scavenged	.																																			SO:0001819	synonymous_variant	81871	exon1			GGTGGAAATGACA	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.573T>C	17.37:g.39296167A>G		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	203	7	0.0344828	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			.	.	none		0.627	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
ADH4	127	hgsc.bcm.edu	37	4	100047812	100047812	+	Silent	SNP	G	G	A	rs1126672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100047812G>A	ENST00000265512.7	-	8	1125	c.1051C>T	c.(1051-1053)Ctg>Ttg	p.L351L	ADH4_ENST00000423445.1_Silent_p.L370L|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Silent_p.L370L|ADH4_ENST00000505590.1_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	136	0	0		WXS	Illumina HiSeq	Phase_I	138	56	0.405797	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	
AIFM1	9131	hgsc.bcm.edu	37	X	129283520	129283520	+	Silent	SNP	A	A	G	rs1139851	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:129283520A>G	ENST00000287295.3	-	3	503	c.273T>C	c.(271-273)gaT>gaC	p.D91D	AIFM1_ENST00000346424.2_Intron|AIFM1_ENST00000535724.1_Silent_p.D4D|AIFM1_ENST00000319908.3_Silent_p.D87D	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	63	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	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		
LY75	4065	hgsc.bcm.edu	37	2	160743040	160743040	+	Splice_Site	SNP	T	T	A	rs2271381	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160743040T>A	ENST00000263636.4	-	5	831	c.804A>T	c.(802-804)gaA>gaT	p.E268D	LY75_ENST00000553424.1_Splice_Site_p.E268D|LY75-CD302_ENST00000504764.1_Splice_Site_p.E268D|LY75-CD302_ENST00000505052.1_Splice_Site_p.E268D|LY75_ENST00000554112.1_Splice_Site_p.E268D	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	268	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.		E -> D (in dbSNP:rs2271381). {ECO:0000269|PubMed:9862343}.		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)		TGCCTTCTTTTTCTGTAAGAA	0.318													T|||	1179	0.235423	0.0688	0.1916	5008	,	,		17719	0.1964		0.2555	False		,,,				2504	0.5112				p.E268D		Atlas-SNP	.											.	LY75	151	.	0			c.A804T						PASS	.	T	ASP/GLU,ASP/GLU,ASP/GLU	462,3944	214.8+/-234.0	26,410,1767	63.0	66.0	65.0		804,804,804	1.8	1.0	2	dbSNP_100	65	2094,6506	357.0+/-330.6	273,1548,2479	yes	missense-near-splice,missense-near-splice,missense-near-splice	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	45,45,45	299,1958,4246	AA,AT,TT		24.3488,10.4857,19.6525	benign,benign,benign	268/1874,268/1818,268/1723	160743040	2556,10450	2203	4300	6503	SO:0001630	splice_region_variant	4065	exon5			TTCTTTTTCTGTA	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.803-1A>T	2.37:g.160743040T>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	18	13	0.722222	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	429	0.19642857142857142	36	0.07317073170731707	82	0.2265193370165746	117	0.20454545454545456	194	0.2559366754617414	T	10.77	1.443503	0.25987	0.104857	0.243488	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	5.67	1.79	0.24919	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.484707	0.15317	N	0.268748	T	0.00012	0.0000	N	0.13235	0.315	0.44055	P	0.0032079999999999886	B;B;B	0.13594	0.003;0.008;0.007	B;B;B	0.16289	0.009;0.015;0.009	T	0.23868	-1.0176	9	0.16420	T	0.52	.	1.4472	0.02367	0.1854:0.1613:0.1156:0.5376	rs2271381;rs52809162;rs2271381	268;268;268	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	D	268	ENSP00000451511:E268D;ENSP00000451446:E268D;ENSP00000263636:E268D;ENSP00000423463:E268D;ENSP00000421035:E268D	ENSP00000423463:E268D	E	-	3	2	LY75;LY75-CD302	160451286	0.984000	0.35163	1.000000	0.80357	0.989000	0.77384	0.544000	0.23253	0.986000	0.38683	0.455000	0.32223	GAA	T|0.798;A|0.202	0.202	strong		0.318	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		Missense_Mutation
STARD6	147323	hgsc.bcm.edu	37	18	51858197	51858197	+	Silent	SNP	A	A	G	rs17470798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:51858197A>G	ENST00000581310.1	-	7	673	c.300T>C	c.(298-300)agT>agC	p.S100S	STARD6_ENST00000580990.2_Missense_Mutation_p.F8L|STARD6_ENST00000307844.3_Silent_p.S100S			P59095	STAR6_HUMAN	StAR-related lipid transfer (START) domain containing 6	100	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)	8				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)		CCACGGCAAAACTTTGTGTAA	0.373													A|||	636	0.126997	0.1172	0.1412	5008	,	,		17996	0.0248		0.1859	False		,,,				2504	0.1748				p.S100S		Atlas-SNP	.											.	STARD6	19	.	0			c.T300C						PASS	.	A		613,3793	267.7+/-268.0	40,533,1630	107.0	100.0	102.0		300	3.5	1.0	18	dbSNP_123	102	1745,6855	316.7+/-312.9	161,1423,2716	no	coding-synonymous	STARD6	NM_139171.1		201,1956,4346	GG,GA,AA		20.2907,13.9128,18.1301		100/221	51858197	2358,10648	2203	4300	6503	SO:0001819	synonymous_variant	147323	exon4			GGCAAAACTTTGT	AF480305	CCDS11955.1	18q21.2	2011-09-12	2007-08-16		ENSG00000174448	ENSG00000174448		"""StAR-related lipid transfer (START) domain containing"""	18066	protein-coding gene	gene with protein product		607051	"""START domain containing 6"""			12011452	Standard	NM_139171		Approved		uc010xdt.2	P59095	OTTHUMG00000132702	ENST00000581310.1:c.300T>C	18.37:g.51858197A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_139171		Silent	SNP	ENST00000581310.1	37	CCDS11955.1																																																																																			A|0.839;G|0.161	0.161	strong		0.373	STARD6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256000.3	NM_139171	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21742598	21742598	+	Missense_Mutation	SNP	G	G	A	rs468931		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21742598G>A	ENST00000434111.1	+	1	4936	c.4451G>A	c.(4450-4452)aGg>aAg	p.R1484K	SCARNA18_ENST00000516505.1_RNA|RN7SKP63_ENST00000363187.1_RNA|SCARNA17_ENST00000516211.1_RNA	NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	1484	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.																TTCCAGAAAAGGCAGTTGCTA	0.567																																					p.R1484K		Atlas-SNP	.											RIMBP3B,NS,carcinoma,0,3	RIMBP3C	6	3	0			c.G4451A						scavenged	.						1.0	1.0	1.0					22																	21742598		15	32	47	SO:0001583	missense	150221	exon1			AGAAAAGGCAGTT		CCDS46668.1	22q11.21	2008-10-23			ENSG00000196934	ENSG00000274600			33891	protein-coding gene	gene with protein product		612700				17855024	Standard	NM_001128635		Approved			A6NNM3	OTTHUMG00000150819	ENST00000434111.1:c.4451G>A	22.37:g.21742598G>A	ENSP00000407925:p.Arg1484Lys	Somatic	1045	1	0.000956938		WXS	Illumina HiSeq	Phase_I	1053	191	0.181387	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	
IGDCC4	57722	hgsc.bcm.edu	37	15	65676726	65676726	+	Missense_Mutation	SNP	C	C	T	rs33918653	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	16	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	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	
C1orf87	127795	hgsc.bcm.edu	37	1	60506744	60506744	+	Silent	SNP	G	G	A	rs10493277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:60506744G>A	ENST00000371201.3	-	4	509	c.402C>T	c.(400-402)tcC>tcT	p.S134S	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	134							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						CATGCACATAGGATAAGGACT	0.493													G|||	599	0.119609	0.031	0.1974	5008	,	,		20343	0.2222		0.1262	False		,,,				2504	0.0716				p.S134S	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.C402T						PASS	.	G		189,4217	123.7+/-161.0	4,181,2018	134.0	113.0	120.0		402	3.3	1.0	1	dbSNP_119	120	1242,7358	248.7+/-276.3	105,1032,3163	no	coding-synonymous	C1orf87	NM_152377.2		109,1213,5181	AA,AG,GG		14.4419,4.2896,11.0026		134/547	60506744	1431,11575	2203	4300	6503	SO:0001819	synonymous_variant	127795	exon4			CACATAGGATAAG	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"""carcinoma-related EF-hand protein"""					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.402C>T	1.37:g.60506744G>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	200	200	1	NM_152377	Q6ZU07|Q8IVS0	Silent	SNP	ENST00000371201.3	37	CCDS614.1																																																																																			G|0.861;A|0.139	0.139	strong		0.493	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	
KRT84	3890	hgsc.bcm.edu	37	12	52778947	52778947	+	Silent	SNP	A	A	G	rs1791631	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	94	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	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	
GPR142	350383	hgsc.bcm.edu	37	17	72368383	72368383	+	Silent	SNP	C	C	A	rs144235997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72368383C>A	ENST00000335666.4	+	4	1081	c.1033C>A	c.(1033-1035)Cgg>Agg	p.R345R		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	345						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						GAGGAGGGGCCGGAGTGGGCT	0.632													C|||	15	0.00299521	0.0	0.0086	5008	,	,		19090	0.0		0.008	False		,,,				2504	0.001				p.R345R		Atlas-SNP	.											GPR142,bladder,carcinoma,-2,1	GPR142	74	1	0			c.C1033A						PASS	.	C		2,4404	2.1+/-5.4	0,2,2201	93.0	75.0	81.0		1033	2.6	0.0	17	dbSNP_134	81	77,8523	44.9+/-103.4	0,77,4223	no	coding-synonymous	GPR142	NM_181790.1		0,79,6424	AA,AC,CC		0.8953,0.0454,0.6074		345/463	72368383	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	350383	exon4			AGGGGCCGGAGTG	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"""GPCR / Class A : Orphans"""	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.1033C>A	17.37:g.72368383C>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_181790	A4CYJ8|Q86SL3	Silent	SNP	ENST00000335666.4	37	CCDS11698.1																																																																																			C|0.994;A|0.006	0.006	strong		0.632	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790	
FNBP4	23360	hgsc.bcm.edu	37	11	47745589	47745589	+	Missense_Mutation	SNP	T	T	C	rs34242224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:47745589T>C	ENST00000263773.5	-	14	2467	c.2455A>G	c.(2455-2457)Ata>Gta	p.I819V	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	819						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						CCTGTAGCTATAGCTGACTGG	0.388													T|||	153	0.0305511	0.0053	0.0504	5008	,	,		18832	0.0		0.0875	False		,,,				2504	0.0235				p.I819V		Atlas-SNP	.											.	FNBP4	99	.	0			c.A2455G						PASS	.	T	VAL/ILE	58,3696		1,56,1820	107.0	106.0	106.0		2455	-6.8	0.7	11	dbSNP_126	106	721,7531		28,665,3433	yes	missense	FNBP4	NM_015308.2	29	29,721,5253	CC,CT,TT		8.7373,1.545,6.4884	benign	819/1018	47745589	779,11227	1877	4126	6003	SO:0001583	missense	23360	exon14			TAGCTATAGCTGA	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.2455A>G	11.37:g.47745589T>C	ENSP00000263773:p.Ile819Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	37	CCDS41644.1	97	0.044413919413919416	6	0.012195121951219513	24	0.06629834254143646	0	0.0	67	0.08839050131926121	T	6.862	0.528323	0.13127	0.01545	0.087373	ENSG00000109920	ENST00000263773	T	0.41758	0.99	5.07	-6.82	0.01698	.	1.374210	0.03891	N	0.278631	T	0.00580	0.0019	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05971	-1.0853	9	0.27785	T	0.31	-0.4376	0.5329	0.00631	0.2012:0.2622:0.2042:0.3325	rs34242224	819	Q8N3X1	FNBP4_HUMAN	V	819	ENSP00000263773:I819V	ENSP00000263773:I819V	I	-	1	0	FNBP4	47702165	0.000000	0.05858	0.694000	0.30210	0.903000	0.53119	-2.117000	0.01326	-0.837000	0.04223	0.459000	0.35465	ATA	T|0.943;C|0.057	0.057	strong		0.388	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
NR3C1	2908	hgsc.bcm.edu	37	5	142661490	142661490	+	Silent	SNP	A	A	G	rs6196	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:142661490A>G	ENST00000343796.2	-	9	3291	c.2298T>C	c.(2296-2298)aaT>aaC	p.N766N	NR3C1_ENST00000231509.3_Silent_p.N767N|NR3C1_ENST00000424646.2_Silent_p.N740N|NR3C1_ENST00000394464.2_Silent_p.N766N|NR3C1_ENST00000503201.1_Silent_p.N766N|NR3C1_ENST00000394466.2_Silent_p.N767N|NR3C1_ENST00000416954.2_Silent_p.N369N|NR3C1_ENST00000504572.1_Silent_p.N767N|NR3C1_ENST00000415690.2_Intron	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	766	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TGATATTTCCATTTGAATATT	0.303													A|||	595	0.11881	0.1929	0.1066	5008	,	,		18489	0.0873		0.1491	False		,,,				2504	0.0286				p.N767N		Atlas-SNP	.											.	NR3C1	124	.	0			c.T2301C	GRCh37	CS044090	NR3C1	S	rs6196	PASS	.	A	,,,,,,,,,,,,,	826,3580	324.2+/-298.5	80,666,1457	98.0	99.0	99.0		2298,2298,2298,2298,2298,,2301,2220,2043,2031,2007,1353,1308,1293	3.6	1.0	5	dbSNP_52	99	1320,7280	258.6+/-282.2	116,1088,3096	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NR3C1	NM_000176.2,NM_001018074.1,NM_001018075.1,NM_001018076.1,NM_001018077.1,NM_001020825.1,NM_001024094.1,NM_001204258.1,NM_001204259.1,NM_001204260.1,NM_001204261.1,NM_001204262.1,NM_001204263.1,NM_001204264.1	,,,,,,,,,,,,,	196,1754,4553	GG,GA,AA		15.3488,18.7472,16.5001	,,,,,,,,,,,,,	766/778,766/778,766/778,766/778,766/778,,767/779,740/752,681/693,677/689,669/681,451/463,436/448,431/443	142661490	2146,10860	2203	4300	6503	SO:0001819	synonymous_variant	2908	exon9			ATTTCCATTTGAA	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"""Nuclear hormone receptors"""	7978	protein-coding gene	gene with protein product		138040	"""nuclear receptor subfamily 3, group C, member 1"""	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.2298T>C	5.37:g.142661490A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_001024094	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Silent	SNP	ENST00000343796.2	37	CCDS4278.1																																																																																			A|0.852;G|0.148	0.148	strong		0.303	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1		
CPZ	8532	hgsc.bcm.edu	37	4	8605818	8605818	+	Silent	SNP	C	C	T	rs6852001	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:8605818C>T	ENST00000360986.4	+	4	786	c.612C>T	c.(610-612)tgC>tgT	p.C204C	CPZ_ENST00000382480.2_Silent_p.C67C|CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000315782.6_Silent_p.C193C	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	204					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCTCCCGCTGCGCCCACGTGG	0.692													C|||	807	0.161142	0.0204	0.1988	5008	,	,		16720	0.2976		0.2465	False		,,,				2504	0.0961				p.C204C		Atlas-SNP	.											CPZ,NS,carcinoma,0,1	CPZ	95	1	0			c.C612T						PASS	.	C	,,	237,4125		10,217,1954	19.0	16.0	17.0		612,201,579	1.0	1.0	4	dbSNP_116	17	2178,6368		284,1610,2379	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	294,1827,4333	TT,TC,CC		25.4856,5.4333,18.7093	,,	204/653,67/516,193/642	8605818	2415,10493	2181	4273	6454	SO:0001819	synonymous_variant	8532	exon4			CCGCTGCGCCCAC	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.612C>T	4.37:g.8605818C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	73	46	0.630137	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			C|0.812;T|0.188	0.188	strong		0.692	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
BMS1	9790	hgsc.bcm.edu	37	10	43292647	43292647	+	Missense_Mutation	SNP	A	A	G	rs787795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:43292647A>G	ENST00000374518.5	+	10	2018	c.1955A>G	c.(1954-1956)aAg>aGg	p.K652R		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	652			K -> R (in dbSNP:rs787795).		ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GAAGATTACAAGGAAGAAAAT	0.393													A|||	904	0.180511	0.1725	0.2392	5008	,	,		20648	0.1835		0.1571	False		,,,				2504	0.1708				p.K652R		Atlas-SNP	.											.	BMS1	132	.	0			c.A1955G						PASS	.	A	ARG/LYS	724,3566		68,588,1489	39.0	40.0	40.0		1955	2.6	1.0	10	dbSNP_86	40	1381,7161		131,1119,3021	yes	missense	BMS1	NM_014753.3	26	199,1707,4510	GG,GA,AA		16.1672,16.8765,16.4043	benign	652/1283	43292647	2105,10727	2145	4271	6416	SO:0001583	missense	9790	exon10			ATTACAAGGAAGA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.1955A>G	10.37:g.43292647A>G	ENSP00000363642:p.Lys652Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	385	0.1762820512820513	79	0.16056910569105692	72	0.19889502762430938	115	0.20104895104895104	119	0.15699208443271767	A	8.696	0.908575	0.17833	0.168765	0.161672	ENSG00000165733	ENST00000374518	T	0.26518	1.73	5.02	2.61	0.31194	.	0.519373	0.19428	N	0.114529	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.30387	-0.9980	9	0.18276	T	0.48	.	7.5141	0.27590	0.7816:0.1438:0.0747:0.0	rs787795;rs3740330;rs52813958;rs60228399;rs787795	652	Q14692	BMS1_HUMAN	R	652	ENSP00000363642:K652R	ENSP00000363642:K652R	K	+	2	0	BMS1	42612653	0.985000	0.35326	0.988000	0.46212	0.817000	0.46193	1.212000	0.32394	0.851000	0.35264	0.519000	0.50382	AAG	A|0.810;C|0.002	.	strong		0.393	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
PSMC4	5704	hgsc.bcm.edu	37	19	40486606	40486606	+	Silent	SNP	T	T	C	rs1127090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40486606T>C	ENST00000157812.2	+	10	1323	c.1125T>C	c.(1123-1125)atT>atC	p.I375I	PSMC4_ENST00000455878.2_Silent_p.I344I	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	375					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GAGCTGATATTAACTCCATCT	0.522													C|||	247	0.0493211	0.1127	0.0173	5008	,	,		19725	0.006		0.0328	False		,,,				2504	0.0481				p.I375I	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.T1125C						PASS	.	C	,	357,4049	794.3+/-415.3	14,329,1860	150.0	146.0	147.0		1125,1032	3.4	1.0	19	dbSNP_86	147	221,8379	809.6+/-407.2	5,211,4084	no	coding-synonymous,coding-synonymous	PSMC4	NM_006503.2,NM_153001.1	,	19,540,5944	CC,CT,TT		2.5698,8.1026,4.4441	,	375/419,344/388	40486606	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	5704	exon10			TGATATTAACTCC	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9551	protein-coding gene	gene with protein product	"""protease 26S subunit 6"", ""Tat-binding protein 7"", ""MB67 interacting protein"""	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.1125T>C	19.37:g.40486606T>C		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	229	101	0.441048	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																			T|0.960;C|0.040	0.040	strong		0.522	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503	
OR51F1	256892	hgsc.bcm.edu	37	11	4790948	4790948	+	Missense_Mutation	SNP	C	C	A	rs11033800	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790948C>A	ENST00000380383.1	-	1	220	c.221G>T	c.(220-222)aGg>aTg	p.R74M	OR51F1_ENST00000343430.3_Missense_Mutation_p.R67M|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	74			R -> M (in dbSNP:rs11033800).			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)		GGCTGATAGCCTGAAGAGGAA	0.438													A|||	1080	0.215655	0.4569	0.2017	5008	,	,		21734	0.0		0.2704	False		,,,				2504	0.0654				p.R67M		Atlas-SNP	.											.	OR51F1	60	.	0			c.G200T						PASS	.	A	MET/ARG	1967,2435	618.8+/-393.2	444,1079,678	69.0	65.0	66.0		200	3.7	0.7	11	dbSNP_120	66	2179,6417	711.6+/-405.8	291,1597,2410	yes	missense	OR51F1	NM_001004752.1	91	735,2676,3088	AA,AC,CC		25.349,44.6842,31.8972	benign	67/313	4790948	4146,8852	2201	4298	6499	SO:0001583	missense	256892	exon1			GATAGCCTGAAGA	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.221G>T	11.37:g.4790948C>A	ENSP00000369744:p.Arg74Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		494	0.2261904761904762	225	0.4573170731707317	82	0.2265193370165746	0	0.0	187	0.24670184696569922	A	0.008	-1.904301	0.00512	0.446842	0.25349	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.03035	4.07;4.07	4.81	3.66	0.41972	GPCR, rhodopsin-like superfamily (1);	0.189083	0.36628	N	0.002497	T	0.00012	0.0000	N	0.00000	-3.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41305	-0.9516	9	0.02654	T	1	.	6.5145	0.22240	0.5426:0.3089:0.0:0.1485	rs11033800;rs52809349;rs60993028;rs11033800	74	A6NGY5	O51F1_HUMAN	M	67;74	ENSP00000345163:R67M;ENSP00000369744:R74M	ENSP00000345163:R67M	R	-	2	0	OR51F1	4747524	0.947000	0.32204	0.679000	0.29978	0.608000	0.37181	2.960000	0.49161	0.324000	0.23333	-0.346000	0.07831	AGG	C|0.707;A|0.293	0.293	strong		0.438	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
TTLL4	9654	hgsc.bcm.edu	37	2	219602754	219602754	+	Missense_Mutation	SNP	C	C	T	rs114586336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:219602754C>T	ENST00000392102.1	+	3	695	c.355C>T	c.(355-357)Cgc>Tgc	p.R119C	TTLL4_ENST00000442769.1_Missense_Mutation_p.R119C|TTLL4_ENST00000258398.4_Missense_Mutation_p.R119C|TTLL4_ENST00000457313.1_5'UTR	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	119					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		CCTGCTATACCGCCGCTCCAG	0.522													C|||	15	0.00299521	0.0008	0.0072	5008	,	,		19799	0.0		0.0089	False		,,,				2504	0.0				p.R119C	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.C355T						PASS	.	C	CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	80.0	79.0	79.0		355	2.9	0.4	2	dbSNP_132	79	66,8534	40.3+/-97.0	0,66,4234	yes	missense	TTLL4	NM_014640.4	180	0,70,6433	TT,TC,CC		0.7674,0.0908,0.5382	probably-damaging	119/1200	219602754	70,12936	2203	4300	6503	SO:0001583	missense	9654	exon3			CTATACCGCCGCT		CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"""Tubulin tyrosine ligase-like family"""	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.355C>T	2.37:g.219602754C>T	ENSP00000375951:p.Arg119Cys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	10.28	1.306067	0.23736	9.08E-4	0.007674	ENSG00000135912	ENST00000392102;ENST00000437755;ENST00000442769;ENST00000258398	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	4.72	2.94	0.34122	.	0.531595	0.17480	N	0.172760	T	0.16128	0.0388	L	0.34521	1.04	0.32014	N	0.601669	B;B	0.18610	0.029;0.029	B;B	0.12156	0.007;0.005	T	0.12426	-1.0548	10	0.56958	D	0.05	.	8.4578	0.32910	0.0:0.818:0.0:0.182	.	119;119	E7EX20;Q14679	.;TTLL4_HUMAN	C	119	ENSP00000375951:R119C;ENSP00000391342:R119C;ENSP00000396555:R119C;ENSP00000258398:R119C	ENSP00000258398:R119C	R	+	1	0	TTLL4	219310998	0.772000	0.28567	0.365000	0.25901	0.007000	0.05969	2.692000	0.47018	0.614000	0.30107	-0.986000	0.02555	CGC	C|0.996;T|0.004	0.004	strong		0.522	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
TM7SF2	7108	hgsc.bcm.edu	37	11	64880743	64880743	+	Missense_Mutation	SNP	C	C	T	rs11539360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:64880743C>T	ENST00000279263.7	+	4	518	c.356C>T	c.(355-357)gCg>gTg	p.A119V	TM7SF2_ENST00000531029.1_3'UTR|TM7SF2_ENST00000345348.5_Missense_Mutation_p.A119V|TM7SF2_ENST00000540748.1_Missense_Mutation_p.A3V|AP003068.9_ENST00000528887.1_RNA	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	119			A -> V (in dbSNP:rs11539360).		cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GGGATGTCAGCGGGGCTGCCT	0.652											OREG0021072	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	140	0.0279553	0.003	0.0389	5008	,	,		15608	0.0655		0.0348	False		,,,				2504	0.0082				p.A119V		Atlas-SNP	.											.	TM7SF2	30	.	0			c.C356T						PASS	.	C	VAL/ALA	24,3984		0,24,1980	20.0	25.0	23.0		356	-5.6	0.0	11	dbSNP_120	23	274,8018		3,268,3875	yes	missense	TM7SF2	NM_003273.2	64	3,292,5855	TT,TC,CC		3.3044,0.5988,2.4228	benign	119/419	64880743	298,12002	2004	4146	6150	SO:0001583	missense	7108	exon4			TGTCAGCGGGGCT	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"""delta(14)-sterol reductase"""	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.356C>T	11.37:g.64880743C>T	ENSP00000279263:p.Ala119Val	Somatic	31	0	0	134	WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	37	CCDS41669.1	74	0.03388278388278388	8	0.016260162601626018	15	0.04143646408839779	21	0.03671328671328671	30	0.0395778364116095	C	8.231	0.804716	0.16467	0.005988	0.033044	ENSG00000149809	ENST00000279263;ENST00000524986;ENST00000540748;ENST00000525385;ENST00000345348;ENST00000529414	D;D;D;D;D;D	0.98075	-4.7;-4.7;-4.66;-4.7;-4.7;-4.7	4.81	-5.63	0.02474	.	1.058010	0.07252	N	0.866091	T	0.77391	0.4123	N	0.16266	0.395	0.09310	N	1	B;B;B	0.13145	0.007;0.003;0.007	B;B;B	0.13407	0.003;0.005;0.009	T	0.80650	-0.1288	10	0.17369	T	0.5	-8.2347	7.4336	0.27141	0.0:0.1618:0.3499:0.4882	rs11539360	3;119;119	F5GYV3;O76062-2;O76062	.;.;ERG24_HUMAN	V	119;90;3;90;119;119	ENSP00000279263:A119V;ENSP00000435972:A90V;ENSP00000441215:A3V;ENSP00000433325:A90V;ENSP00000329520:A119V;ENSP00000433275:A119V	ENSP00000279263:A119V	A	+	2	0	TM7SF2	64637319	0.000000	0.05858	0.000000	0.03702	0.394000	0.30568	-0.725000	0.04942	-0.920000	0.03799	-1.080000	0.02220	GCG	C|0.967;T|0.033	0.033	strong		0.652	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273	
PSMD3	5709	hgsc.bcm.edu	37	17	38137364	38137364	+	Silent	SNP	G	G	A	rs3087852	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38137364G>A	ENST00000264639.4	+	1	315	c.141G>A	c.(139-141)tcG>tcA	p.S47S	PSMD3_ENST00000541736.1_Intron	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	47					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					GTGGCGGGTCGACGGGGGAGG	0.711											OREG0024385	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2630	0.52516	0.677	0.5259	5008	,	,		12464	0.4325		0.4563	False		,,,				2504	0.4857				p.S47S	Ovarian(186;531 2051 6385 19668 48409)	Atlas-SNP	.											.	PSMD3	56	.	0			c.G141A						PASS	.	A		2556,1346		884,788,279	10.0	17.0	15.0		141	-4.1	0.0	17	dbSNP_102	15	3869,3747		1069,1731,1008	no	coding-synonymous	PSMD3	NM_002809.2		1953,2519,1287	AA,AG,GG		49.1991,34.4951,44.2177		47/535	38137364	6425,5093	1951	3808	5759	SO:0001819	synonymous_variant	5709	exon1			CGGGTCGACGGGG	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"""Proteasome (prosome, macropain) subunits"""	9560	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 2"""	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.141G>A	17.37:g.38137364G>A		Somatic	106	0	0	875	WXS	Illumina HiSeq	Phase_I	100	100	1	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Silent	SNP	ENST00000264639.4	37	CCDS11356.1																																																																																			G|0.491;A|0.509	0.509	strong		0.711	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809	
LRP1	4035	hgsc.bcm.edu	37	12	57601929	57601929	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57601929G>A	ENST00000243077.3	+	77	12434	c.11968G>A	c.(11968-11970)Gag>Aag	p.E3990K		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3990					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.E3990K(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)	GATGAAGGGCGAGAACCGCAA	0.642																																					p.E3990K		Atlas-SNP	.											LRP1,caecum,carcinoma,0,1	LRP1	428	1	1	Substitution - Missense(1)	large_intestine(1)	c.G11968A						scavenged	.						83.0	71.0	75.0					12																	57601929		2203	4300	6503	SO:0001583	missense	4035	exon77			AAGGGCGAGAACC	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.11968G>A	12.37:g.57601929G>A	ENSP00000243077:p.Glu3990Lys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	159	3	0.0188679	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.014100	0.35511	.	.	ENSG00000123384	ENST00000243077	D	0.93859	-3.3	4.6	4.6	0.57074	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.300615	0.28796	N	0.014114	T	0.74642	0.3743	N	0.00771	-1.2	0.80722	D	1	P	0.44006	0.824	B	0.31442	0.13	T	0.82542	-0.0405	10	0.06236	T	0.91	.	16.7144	0.85394	0.0:0.0:1.0:0.0	.	3990	Q07954	LRP1_HUMAN	K	3990	ENSP00000243077:E3990K	ENSP00000243077:E3990K	E	+	1	0	LRP1	55888196	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.059000	0.57470	2.543000	0.85770	0.655000	0.94253	GAG	.	.	none		0.642	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
ZNF57	126295	hgsc.bcm.edu	37	19	2917798	2917798	+	Silent	SNP	A	A	G	rs61755868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917798A>G	ENST00000306908.5	+	4	1327	c.1179A>G	c.(1177-1179)aaA>aaG	p.K393K	ZNF57_ENST00000523428.1_Silent_p.K361K|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCTCTATAAATGTGAACAAT	0.433													A|||	125	0.0249601	0.0219	0.0288	5008	,	,		22248	0.0		0.0169	False		,,,				2504	0.0603				p.K393K	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.A1179G						PASS	.	A		85,4321	71.4+/-109.4	0,85,2118	92.0	84.0	86.0		1179	-0.5	0.0	19	dbSNP_129	86	208,8392	88.6+/-150.9	4,200,4096	no	coding-synonymous	ZNF57	NM_173480.2		4,285,6214	GG,GA,AA		2.4186,1.9292,2.2528		393/556	2917798	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	126295	exon4			CTATAAATGTGAA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.1179A>G	19.37:g.2917798A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	NM_173480	Q8N6R9	Silent	SNP	ENST00000306908.5	37	CCDS12098.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
HIST1H2BA	255626	hgsc.bcm.edu	37	6	25727265	25727265	+	Silent	SNP	C	C	T	rs4712960	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25727265C>T	ENST00000274764.2	+	1	129	c.129C>T	c.(127-129)atC>atT	p.I43I	HIST1H2AA_ENST00000297012.3_5'Flank	NM_170610.2	NP_733759.1	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	43					cellular response to acid chemical (GO:0071229)|chromatin organization (GO:0006325)|inflammatory response (GO:0006954)|mononuclear cell migration (GO:0071674)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|plasminogen activation (GO:0031639)|positive regulation of binding (GO:0051099)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	extrinsic component of plasma membrane (GO:0019897)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)	2						CTATTTACATCTACAAAGTGC	0.433													C|||	1738	0.347045	0.0976	0.4366	5008	,	,		22101	0.6825		0.2922	False		,,,				2504	0.3313				p.I43I		Atlas-SNP	.											.	HIST1H2BA	25	.	0			c.C129T						PASS	.	C		605,3801	265.3+/-266.6	47,511,1645	351.0	287.0	308.0		129	-2.3	0.1	6	dbSNP_111	308	2391,6209	398.2+/-346.0	339,1713,2248	no	coding-synonymous	HIST1H2BA	NM_170610.2		386,2224,3893	TT,TC,CC		27.8023,13.7313,23.0355		43/128	25727265	2996,10010	2203	4300	6503	SO:0001819	synonymous_variant	255626	exon1			TTACATCTACAAA	AF397301	CCDS4563.1	6p22.2	2011-01-27	2006-10-11		ENSG00000146047	ENSG00000146047		"""Histones / Replication-dependent"""	18730	protein-coding gene	gene with protein product		609904	"""H2B histone family, member U, (testis-specific)"", ""histone 1, H2ba"""			12408966, 12213818	Standard	NM_170610		Approved	bA317E16.3, STBP, TSH2B, H2BFU	uc003nfd.3	Q96A08	OTTHUMG00000014408	ENST00000274764.2:c.129C>T	6.37:g.25727265C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	42	0.456522	NM_170610	B2R544|Q6NZ98|Q6NZA0|Q6NZA1	Silent	SNP	ENST00000274764.2	37	CCDS4563.1																																																																																			C|0.714;T|0.286	0.286	strong		0.433	HIST1H2BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040066.1	NM_170610	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18776819	18776819	+	Silent	SNP	G	G	A	rs2060363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:18776819G>A	ENST00000380548.4	+	19	2931	c.2592G>A	c.(2590-2592)gcG>gcA	p.A864A		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	864	Ig-like C2-type 1.					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)		CGCACATCGCGGCCGCCAGGA	0.647													G|||	257	0.0513179	0.0961	0.0403	5008	,	,		15557	0.0		0.0517	False		,,,				2504	0.0511				p.A864A		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.G2592A						PASS	.	G		285,3659		9,267,1696	8.0	10.0	9.0		2592	-10.5	0.0	9	dbSNP_94	9	422,7826		7,408,3709	no	coding-synonymous	ADAMTSL1	NM_001040272.5		16,675,5405	AA,AG,GG		5.1164,7.2262,5.7989		864/1763	18776819	707,11485	1972	4124	6096	SO:0001819	synonymous_variant	92949	exon19			CATCGCGGCCGCC	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.2592G>A	9.37:g.18776819G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	52	22	0.423077	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			G|0.953;A|0.047	0.047	strong		0.647	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
TMEM132D	121256	hgsc.bcm.edu	37	12	129559421	129559421	+	Missense_Mutation	SNP	C	C	T	rs73159540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:129559421C>T	ENST00000422113.2	-	9	2625	c.2299G>A	c.(2299-2301)Gtc>Atc	p.V767I	TMEM132D_ENST00000389441.4_Missense_Mutation_p.V305I	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	767					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)		TCCACCTTGACCAGGGTGCCT	0.463													C|||	414	0.0826677	0.0045	0.0778	5008	,	,		21102	0.1161		0.1173	False		,,,				2504	0.1217				p.V767I		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G2299A						PASS	.	C	ILE/VAL	88,4318	75.7+/-113.9	1,86,2116	146.0	128.0	134.0		2299	4.2	1.0	12	dbSNP_130	134	927,7673	204.9+/-247.5	54,819,3427	yes	missense	TMEM132D	NM_133448.2	29	55,905,5543	TT,TC,CC		10.7791,1.9973,7.8041	possibly-damaging	767/1100	129559421	1015,11991	2203	4300	6503	SO:0001583	missense	121256	exon9			CCTTGACCAGGGT	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.2299G>A	12.37:g.129559421C>T	ENSP00000408581:p.Val767Ile	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	198	103	0.520202	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	195	0.08928571428571429	4	0.008130081300813009	33	0.09116022099447514	64	0.11188811188811189	94	0.12401055408970976	C	9.353	1.066018	0.20067	0.019973	0.107791	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.14022	2.54;2.54	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000004	T	0.00241	0.0007	N	0.17345	0.48	0.18873	P	0.999981947	B;P	0.50528	0.211;0.936	B;P	0.56398	0.066;0.797	T	0.37126	-0.9719	8	.	.	.	-31.7501	16.8845	0.86072	0.0:1.0:0.0:0.0	.	767;305	Q14C87;Q14C87-2	T132D_HUMAN;.	I	305;767	ENSP00000374092:V305I;ENSP00000408581:V767I	.	V	-	1	0	TMEM132D	128125374	1.000000	0.71417	0.953000	0.39169	0.326000	0.28443	2.480000	0.45206	2.033000	0.60031	0.462000	0.41574	GTC	C|0.919;T|0.081	0.081	strong		0.463	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
LNX1	84708	hgsc.bcm.edu	37	4	54373579	54373579	+	Missense_Mutation	SNP	G	G	A	rs147992678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:54373579G>A	ENST00000263925.7	-	4	994	c.680C>T	c.(679-681)gCt>gTt	p.A227V	LNX1-AS1_ENST00000510785.1_RNA|LNX1_ENST00000306888.2_Missense_Mutation_p.A131V|FIP1L1_ENST00000507166.1_Intron|LNX1-AS1_ENST00000511989.1_RNA|LNX1-AS1_ENST00000514364.1_RNA	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	227	Interaction with MAGEB18.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AACACTCAAAGCTCGATTTAT	0.448													G|||	5	0.000998403	0.0	0.0014	5008	,	,		18395	0.0		0.004	False		,,,				2504	0.0				p.A227V		Atlas-SNP	.											.	LNX1	139	.	0			c.C680T						PASS	.	G	VAL/ALA,VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	89.0	88.0	88.0		680,392	4.9	0.2	4	dbSNP_134	88	18,8582	11.9+/-42.8	0,18,4282	yes	missense,missense	LNX1	NM_001126328.1,NM_032622.2	64,64	0,20,6483	AA,AG,GG		0.2093,0.0454,0.1538	probably-damaging,probably-damaging	227/729,131/633	54373579	20,12986	2203	4300	6503	SO:0001583	missense	84708	exon4			CTCAAAGCTCGAT	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"""RING-type (C3HC4) zinc fingers"""	6657	protein-coding gene	gene with protein product		609732	"""ligand of numb-protein X"", ""ligand of numb-protein X 1"""	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.680C>T	4.37:g.54373579G>A	ENSP00000263925:p.Ala227Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	26.6	4.752364	0.89753	4.54E-4	0.002093	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.09630	2.96;4.47	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.25344	0.0616	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;0.998	D;P	0.87578	0.998;0.904	T	0.00780	-1.1569	10	0.45353	T	0.12	.	18.345	0.90318	0.0:0.0:1.0:0.0	.	227;131	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	V	131;65;227	ENSP00000302879:A131V;ENSP00000263925:A227V	ENSP00000263925:A227V	A	-	2	0	LNX1	54068336	1.000000	0.71417	0.243000	0.24186	0.863000	0.49368	7.540000	0.82074	2.565000	0.86533	0.555000	0.69702	GCT	G|0.998;A|0.002	0.002	strong		0.448	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2		
FER	2241	hgsc.bcm.edu	37	5	108380419	108380419	+	Silent	SNP	T	T	C	rs919771	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:108380419T>C	ENST00000281092.4	+	15	2136	c.1752T>C	c.(1750-1752)gaT>gaC	p.D584D	FER_ENST00000438717.2_Silent_p.D409D	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	584	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		CATTAAAGGATAAAACTTCTG	0.299													T|||	358	0.0714856	0.062	0.0908	5008	,	,		16133	0.0		0.1561	False		,,,				2504	0.0573				p.D584D	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T1752C						PASS	.	T		325,4077	166.9+/-198.0	13,299,1889	89.0	96.0	94.0		1752	5.5	1.0	5	dbSNP_86	94	1246,7352	247.2+/-275.4	95,1056,3148	no	coding-synonymous	FER	NM_005246.2		108,1355,5037	CC,CT,TT		14.4917,7.383,12.0846		584/823	108380419	1571,11429	2201	4299	6500	SO:0001819	synonymous_variant	2241	exon15			AAAGGATAAAACT	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.1752T>C	5.37:g.108380419T>C		Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	330	139	0.421212	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			T|0.895;C|0.105	0.105	strong		0.299	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
IGSF3	3321	hgsc.bcm.edu	37	1	117156603	117156603	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:117156603A>T	ENST00000369486.3	-	4	1381	c.616T>A	c.(616-618)Tcc>Acc	p.S206T	IGSF3_ENST00000318837.6_Missense_Mutation_p.S206T|IGSF3_ENST00000369483.1_Missense_Mutation_p.S206T	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	206	Ig-like C2-type 2.				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)		TCGCTGCTGGAGTGAAGCATG	0.617																																					p.S206T		Atlas-SNP	.											.	IGSF3	294	.	0			c.T616A						PASS	.						56.0	57.0	57.0					1																	117156603		2203	4300	6503	SO:0001583	missense	3321	exon4			TGCTGGAGTGAAG	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.616T>A	1.37:g.117156603A>T	ENSP00000358498:p.Ser206Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.243549	0.39697	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.23552	1.9;1.9;1.9	5.02	5.02	0.67125	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.061231	0.64402	D	0.000002	T	0.13543	0.0328	L	0.27053	0.805	0.42061	D	0.991163	B;P	0.36183	0.387;0.542	P;B	0.45660	0.489;0.388	T	0.05451	-1.0884	10	0.66056	D	0.02	-47.2567	7.3497	0.26684	0.9046:0.0:0.0954:0.0	.	206;206	O75054;A6NJZ6	IGSF3_HUMAN;.	T	206	ENSP00000358498:S206T;ENSP00000358495:S206T;ENSP00000321184:S206T	ENSP00000321184:S206T	S	-	1	0	IGSF3	116958126	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	3.342000	0.52159	2.101000	0.63845	0.528000	0.53228	TCC	.	.	none		0.617	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
TRPM6	140803	hgsc.bcm.edu	37	9	77416972	77416972	+	Silent	SNP	C	C	T	rs11144089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:77416972C>T	ENST00000360774.1	-	16	2088	c.1851G>A	c.(1849-1851)ctG>ctA	p.L617L	TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Silent_p.L617L|TRPM6_ENST00000451710.3_Silent_p.L617L|TRPM6_ENST00000376872.3_Intron|RN7SKP47_ENST00000365347.1_RNA|TRPM6_ENST00000361255.3_Silent_p.L612L|TRPM6_ENST00000449912.2_Silent_p.L612L	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	617					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						GCCTTTTCATCAGCACAGCCC	0.473													C|||	447	0.0892572	0.025	0.1066	5008	,	,		18275	0.1558		0.1074	False		,,,				2504	0.0767				p.L617L		Atlas-SNP	.											.	TRPM6	377	.	0			c.G1851A						PASS	.	C	,,	170,4236	111.2+/-149.4	4,162,2037	124.0	98.0	107.0		1836,1836,1851	-4.8	1.0	9	dbSNP_120	107	798,7802	187.0+/-234.4	36,726,3538	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	40,888,5575	TT,TC,CC		9.2791,3.8584,7.4427	,,	612/2018,612/2018,617/2023	77416972	968,12038	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon16			TTTCATCAGCACA	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1851G>A	9.37:g.77416972C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			C|0.911;T|0.089	0.089	strong		0.473	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
PCSK9	255738	hgsc.bcm.edu	37	1	55505651	55505651	+	Silent	SNP	C	C	T	rs28385701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:55505651C>T	ENST00000302118.5	+	1	431	c.141C>T	c.(139-141)tcC>tcT	p.S47S	PCSK9_ENST00000452118.2_Silent_p.S47S|PCSK9_ENST00000543384.1_5'Flank	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	47					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						CCTTGCGTTCCGAGGAGGACG	0.706													C|||	20	0.00399361	0.0	0.0043	5008	,	,		14828	0.0		0.0099	False		,,,				2504	0.0072				p.S47S	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.C141T						PASS	.	C		8,4366		0,8,2179	35.0	28.0	30.0		141	-6.4	0.0	1	dbSNP_125	30	80,8460		0,80,4190	no	coding-synonymous	PCSK9	NM_174936.3		0,88,6369	TT,TC,CC		0.9368,0.1829,0.6814		47/693	55505651	88,12826	2187	4270	6457	SO:0001819	synonymous_variant	255738	exon1			GCGTTCCGAGGAG	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.141C>T	1.37:g.55505651C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	112	68	0.607143	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	37	CCDS603.1																																																																																			C|0.993;T|0.007	0.007	strong		0.706	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232574921	232574921	+	Missense_Mutation	SNP	T	T	C	rs2275307	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:232574921T>C	ENST00000366630.1	-	14	4322	c.3964A>G	c.(3964-3966)Acc>Gcc	p.T1322A	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.T396A|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.T1322A			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1322	Ser-rich.		T -> A (in dbSNP:rs2275307). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.4}.		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)				GCGGAGATGGTGGACGCGTAG	0.607													C|||	1764	0.352236	0.41	0.3473	5008	,	,		19452	0.4643		0.2008	False		,,,				2504	0.318				p.T1322A		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.A3964G						PASS	.	C	ALA/THR	1603,2551		312,979,786	32.0	35.0	34.0		3964	-1.9	0.0	1	dbSNP_100	34	1823,6619		204,1415,2602	yes	missense	SIPA1L2	NM_020808.3	58	516,2394,3388	CC,CT,TT		21.5944,38.5893,27.1991	benign	1322/1723	232574921	3426,9170	2077	4221	6298	SO:0001583	missense	57568	exon13			AGATGGTGGACGC	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.3964A>G	1.37:g.232574921T>C	ENSP00000355589:p.Thr1322Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	745	0.3411172161172161	206	0.4186991869918699	118	0.3259668508287293	274	0.479020979020979	147	0.19393139841688653	C	0.008	-1.930233	0.00488	0.385893	0.215944	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.76968	-1.06;-1.06;2.89	5.16	-1.91	0.07641	.	0.762839	0.12744	N	0.442752	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	0.17048	-1.0382	9	0.02654	T	1	-1.9707	7.3522	0.26697	0.0:0.3717:0.1155:0.5127	rs2275307;rs2275307	1322;396	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	A	1322;1322;396	ENSP00000355589:T1322A;ENSP00000262861:T1322A;ENSP00000309102:T396A	ENSP00000262861:T1322A	T	-	1	0	SIPA1L2	230641544	0.487000	0.25988	0.000000	0.03702	0.037000	0.13140	1.127000	0.31357	-0.905000	0.03871	-0.213000	0.12676	ACC	T|0.688;C|0.311	0.311	strong		0.607	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
NGEF	25791	hgsc.bcm.edu	37	2	233750074	233750074	+	Silent	SNP	C	C	T	rs2292725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:233750074C>T	ENST00000264051.3	-	10	1631	c.1353G>A	c.(1351-1353)gtG>gtA	p.V451V	NGEF_ENST00000373552.4_Silent_p.V359V|NGEF_ENST00000539537.1_Silent_p.V174V	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	451	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)		TGCATGCCTTCACCACCTGGG	0.577													C|||	773	0.154353	0.1861	0.1427	5008	,	,		19749	0.0992		0.2465	False		,,,				2504	0.0818				p.V451V		Atlas-SNP	.											.	NGEF	198	.	0			c.G1353A						PASS	.	C	,	803,3603	322.9+/-297.8	59,685,1459	199.0	167.0	178.0		1077,1353	-2.5	1.0	2	dbSNP_100	178	1937,6663	342.6+/-324.5	214,1509,2577	no	coding-synonymous,coding-synonymous	NGEF	NM_001114090.1,NM_019850.2	,	273,2194,4036	TT,TC,CC		22.5233,18.2251,21.0672	,	359/619,451/711	233750074	2740,10266	2203	4300	6503	SO:0001819	synonymous_variant	25791	exon10			TGCCTTCACCACC	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.1353G>A	2.37:g.233750074C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Silent	SNP	ENST00000264051.3	37	CCDS2500.1																																																																																			C|0.798;T|0.202	0.202	strong		0.577	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799	
GRID1	2894	hgsc.bcm.edu	37	10	87489317	87489317	+	Missense_Mutation	SNP	T	T	C	rs3812645|rs386746181	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:87489317T>C	ENST00000327946.7	-	9	1373	c.1288A>G	c.(1288-1290)Atg>Gtg	p.M430V	GRID1_ENST00000536331.1_Start_Codon_SNP_p.M1V	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	430					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)	p.M430V(1)		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						CGGCTGCCCATGGGCCTCTCT	0.522										Multiple Myeloma(13;0.14)			T|||	335	0.066893	0.1573	0.0173	5008	,	,		15994	0.0516		0.0239	False		,,,				2504	0.0399				p.M430V		Atlas-SNP	.											GRID1,NS,carcinoma,0,1	GRID1	204	1	1	Substitution - Missense(1)	stomach(1)	c.A1288G						PASS	.	T	VAL/MET	683,3723	286.0+/-278.5	46,591,1566	81.0	78.0	79.0		1288	5.4	1.0	10	dbSNP_107	79	173,8427	78.1+/-140.7	0,173,4127	yes	missense	GRID1	NM_017551.2	21	46,764,5693	CC,CT,TT		2.0116,15.5016,6.5816	benign	430/1010	87489317	856,12150	2203	4300	6503	SO:0001583	missense	2894	exon9			TGCCCATGGGCCT	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.1288A>G	10.37:g.87489317T>C	ENSP00000330148:p.Met430Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	95	36	0.378947	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	103	0.04716117216117216	56	0.11382113821138211	5	0.013812154696132596	29	0.050699300699300696	13	0.017150395778364115	T	13.82	2.352380	0.41700	0.155016	0.020116	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.12569	2.86;2.67	5.45	5.45	0.79879	.	0.320867	0.40640	N	0.001046	T	0.00039	0.0001	N	0.08118	0	0.09310	P	0.99999000953	B	0.02656	0.0	B	0.01281	0.0	T	0.35400	-0.9790	9	0.25751	T	0.34	.	6.6909	0.23171	0.1423:0.0:0.1682:0.6896	rs3812645	430	Q9ULK0	GRID1_HUMAN	V	430;1	ENSP00000330148:M430V;ENSP00000444455:M1V	ENSP00000330148:M430V	M	-	1	0	GRID1	87479297	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.777000	0.47717	2.057000	0.61298	0.482000	0.46254	ATG	T|0.964;C|0.036	0.036	strong		0.522	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
CD8B	926	hgsc.bcm.edu	37	2	87073852	87073852	+	Missense_Mutation	SNP	C	C	T	rs2228022	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:87073852C>T	ENST00000390655.6	-	4	596	c.538G>A	c.(538-540)Gtc>Atc	p.V180I	CD8B_ENST00000331469.2_Missense_Mutation_p.V180I|CD8B_ENST00000393759.2_Missense_Mutation_p.V180I|CD8B_ENST00000431506.2_Intron|CD8B_ENST00000393761.2_Intron|CD8B_ENST00000349455.3_Intron	NM_004931.4	NP_004922.1	P10966	CD8B_HUMAN	CD8b molecule	180				V -> I (in Ref. 6; AAI00915). {ECO:0000305}.	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)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	13						AGAACCAGGACGCCAGCCACC	0.537													C|||	876	0.17492	0.0764	0.2911	5008	,	,		16088	0.1577		0.2087	False		,,,				2504	0.2086				p.V180I		Atlas-SNP	.											.	CD8B	37	.	0			c.G538A						PASS	.	C	,ILE/VAL,ILE/VAL,,ILE/VAL	437,3931		15,407,1762	54.0	43.0	47.0		,538,538,,538	-0.7	0.0	2	dbSNP_131	47	1742,6818		176,1390,2714	no	intron,missense,missense,intron,missense	CD8B	NM_001178100.1,NM_004931.4,NM_172101.3,NM_172102.3,NM_172213.3	,29,29,,29	191,1797,4476	TT,TC,CC		20.3505,10.0046,16.8549	,benign,benign,,benign	,180/211,180/222,,180/244	87073852	2179,10749	2184	4280	6464	SO:0001583	missense	926	exon4			CCAGGACGCCAGC		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.538G>A	2.37:g.87073852C>T	ENSP00000375070:p.Val180Ile	Somatic	389	0	0		WXS	Illumina HiSeq	Phase_I	414	218	0.52657	NM_004931	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Missense_Mutation	SNP	ENST00000390655.6	37	CCDS1997.1	393	0.17994505494505494	42	0.08536585365853659	90	0.24861878453038674	94	0.16433566433566432	167	0.22031662269129287	C	0.008	-1.908834	0.00508	0.100046	0.203505	ENSG00000172116	ENST00000393759;ENST00000331469;ENST00000390655;ENST00000445248	.	.	.	4.91	-0.731	0.11151	.	0.850395	0.10380	N	0.681737	T	0.00012	0.0000	N	0.13098	0.295	0.80722	P	0.0	B;B;B;B	0.15719	0.014;0.003;0.005;0.005	B;B;B;B	0.10450	0.003;0.002;0.005;0.005	T	0.31998	-0.9923	8	0.05620	T	0.96	-5.3481	8.0987	0.30844	0.0:0.4499:0.0:0.5501	.	180;180;180;180	Q53QL8;P10966;P10966-2;P10966-6	.;CD8B_HUMAN;.;.	I	180	.	ENSP00000331172:V180I	V	-	1	0	CD8B	86927363	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.468000	0.02350	-0.242000	0.09667	-0.137000	0.14449	GTC	C|0.829;T|0.171	0.171	strong		0.537	CD8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330402.1	NM_172099	
CCDC93	54520	hgsc.bcm.edu	37	2	118771566	118771566	+	Silent	SNP	C	C	A	rs11545372	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:118771566C>A	ENST00000376300.2	-	1	143	c.6G>T	c.(4-6)ggG>ggT	p.G2G	AC009303.1_ENST00000588042.1_RNA|RN7SL111P_ENST00000468841.2_RNA|AC009303.1_ENST00000590516.1_RNA|CCDC93_ENST00000319432.5_Silent_p.G2G	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	2								p.G2G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						CCCTGGGCAACCCCATGATCC	0.692													C|||	1604	0.320288	0.4894	0.2421	5008	,	,		10351	0.1409		0.3459	False		,,,				2504	0.3057				p.G2G		Atlas-SNP	.											CCDC93,NS,carcinoma,0,1	CCDC93	70	1	1	Substitution - coding silent(1)	prostate(1)	c.G6T						PASS	.	C		1828,2574		393,1042,766	20.0	23.0	22.0		6	2.0	1.0	2	dbSNP_120	22	2829,5755		508,1813,1971	no	coding-synonymous	CCDC93	NM_019044.4		901,2855,2737	AA,AC,CC		32.9567,41.5266,35.8617		2/632	118771566	4657,8329	2201	4292	6493	SO:0001819	synonymous_variant	54520	exon1			GGGCAACCCCATG	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.6G>T	2.37:g.118771566C>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	119	49	0.411765	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Silent	SNP	ENST00000376300.2	37	CCDS2121.2																																																																																			C|0.673;A|0.327	0.327	strong		0.692	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044	
PDE6A	5145	hgsc.bcm.edu	37	5	149323906	149323906	+	Silent	SNP	T	T	G	rs2277925	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	125	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	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		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036959	33036959	+	Silent	SNP	G	G	A	rs201076982|rs2308929	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	91	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	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	
ZPLD1	131368	hgsc.bcm.edu	37	3	102181131	102181131	+	Missense_Mutation	SNP	A	A	G	rs12054046	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:102181131A>G	ENST00000491959.1	+	13	1471	c.589A>G	c.(589-591)Acc>Gcc	p.T197A	ZPLD1_ENST00000306176.1_Missense_Mutation_p.T213A|ZPLD1_ENST00000466937.1_Missense_Mutation_p.T197A			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	197	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		T -> A (in dbSNP:rs12054046).			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						TTAGGATTCAACCTACAACCA	0.343													A|||	481	0.0960463	0.0893	0.1585	5008	,	,		16495	0.0357		0.1372	False		,,,				2504	0.0808				p.T213A		Atlas-SNP	.											.	ZPLD1	82	.	0			c.A637G						PASS	.	A	ALA/THR	404,4002	200.4+/-223.7	18,368,1817	76.0	77.0	77.0		637	4.1	1.0	3	dbSNP_120	77	1328,7270	259.5+/-282.7	95,1138,3066	yes	missense	ZPLD1	NM_175056.1	58	113,1506,4883	GG,GA,AA		15.4455,9.1693,13.319	benign	213/432	102181131	1732,11272	2203	4299	6502	SO:0001583	missense	131368	exon6			GATTCAACCTACA	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.589A>G	3.37:g.102181131A>G	ENSP00000420265:p.Thr197Ala	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		219	0.10027472527472528	40	0.08130081300813008	58	0.16022099447513813	16	0.027972027972027972	105	0.13852242744063326	A	11.67	1.707151	0.30232	0.091693	0.154455	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	D;D;D	0.81996	-1.56;-1.56;-1.56	5.28	4.09	0.47781	Zona pellucida sperm-binding protein (3);	0.157465	0.56097	D	0.000021	T	0.00552	0.0018	N	0.16130	0.375	0.23260	P	0.99802135	B;B	0.19583	0.037;0.007	B;B	0.19666	0.022;0.026	T	0.17561	-1.0365	9	0.35671	T	0.21	4.2278	11.3184	0.49405	0.8635:0.0:0.0:0.1365	rs12054046;rs52822606;rs60979721;rs12054046	213;197	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	A	197;213;197	ENSP00000420265:T197A;ENSP00000307801:T213A;ENSP00000418253:T197A	ENSP00000307801:T213A	T	+	1	0	ZPLD1	103663821	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.357000	0.44125	0.797000	0.33971	0.482000	0.46254	ACC	A|0.884;G|0.116	0.116	strong		0.343	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056	
CENPF	1063	hgsc.bcm.edu	37	1	214820494	214820494	+	Silent	SNP	G	G	A	rs3790648	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214820494G>A	ENST00000366955.3	+	13	7749	c.7581G>A	c.(7579-7581)ctG>ctA	p.L2527L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2623	2 X 177 AA tandem repeats.|Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TCAGTAGACTGAAAAATCAAA	0.393													A|||	532	0.10623	0.1089	0.1066	5008	,	,		19726	0.1151		0.0507	False		,,,				2504	0.1503				p.L2527L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,bladder,carcinoma,+1,1	CENPF	321	1	0			c.G7581A						PASS	.	A		434,3972	784.6+/-414.7	22,390,1791	89.0	94.0	92.0		7581	-8.5	0.0	1	dbSNP_107	92	467,8133	797.3+/-407.5	12,443,3845	no	coding-synonymous	CENPF	NM_016343.3		34,833,5636	AA,AG,GG		5.4302,9.8502,6.9276		2527/3115	214820494	901,12105	2203	4300	6503	SO:0001819	synonymous_variant	1063	exon13			TAGACTGAAAAAT	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.7581G>A	1.37:g.214820494G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			G|0.910;A|0.090	0.090	strong		0.393	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
TTLL5	23093	hgsc.bcm.edu	37	14	76259376	76259376	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:76259376G>A	ENST00000298832.9	+	27	3309	c.3104G>A	c.(3103-3105)cGg>cAg	p.R1035Q	TTLL5_ENST00000554510.1_Missense_Mutation_p.R544Q|TTLL5_ENST00000557636.1_Missense_Mutation_p.R1050Q|TTLL5_ENST00000556893.1_Missense_Mutation_p.R586Q	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1035					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		GAACTTCAGCGGCTAGCTGAG	0.473																																					p.R1035Q		Atlas-SNP	.											.	TTLL5	102	.	0			c.G3104A						PASS	.						101.0	91.0	94.0					14																	76259376		2203	4300	6503	SO:0001583	missense	23093	exon27			TTCAGCGGCTAGC	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.3104G>A	14.37:g.76259376G>A	ENSP00000298832:p.Arg1035Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848322	0.51164	.	.	ENSG00000119685	ENST00000418433;ENST00000286653;ENST00000557636;ENST00000298832;ENST00000393826;ENST00000556893;ENST00000554510	T;T;T;T	0.27104	3.83;3.91;1.69;1.7	5.41	5.41	0.78517	.	0.711361	0.13654	N	0.372060	T	0.34658	0.0905	N	0.19112	0.55	0.29768	N	0.835037	P;D;P;P	0.76494	0.698;0.999;0.917;0.572	B;D;B;B	0.79784	0.098;0.993;0.202;0.045	T	0.13656	-1.0501	10	0.38643	T	0.18	.	11.7839	0.52030	0.0831:0.0:0.9169:0.0	.	1050;109;586;1035	G3V2J9;F8W7N3;Q6EMB2-2;Q6EMB2	.;.;.;TTLL5_HUMAN	Q	722;109;1050;1035;586;586;544	ENSP00000450713:R1050Q;ENSP00000298832:R1035Q;ENSP00000452524:R586Q;ENSP00000451946:R544Q	ENSP00000286653:R109Q	R	+	2	0	TTLL5	75329129	1.000000	0.71417	0.999000	0.59377	0.894000	0.52154	3.531000	0.53546	2.538000	0.85594	0.563000	0.77884	CGG	.	.	none		0.473	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
KCNU1	157855	hgsc.bcm.edu	37	8	36788479	36788479	+	Missense_Mutation	SNP	A	A	G	rs16885577	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	58	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	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	
ABHD10	55347	hgsc.bcm.edu	37	3	111710398	111710398	+	Missense_Mutation	SNP	A	A	G	rs17429033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:111710398A>G	ENST00000273359.3	+	5	778	c.751A>G	c.(751-753)Att>Gtt	p.I251V	ABHD10_ENST00000534857.1_Missense_Mutation_p.I94V	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	251			I -> V (in dbSNP:rs17429033).		glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						GAAGGATGACATTGTACCTTG	0.448													A|||	135	0.0269569	0.0023	0.0591	5008	,	,		19518	0.001		0.0835	False		,,,				2504	0.0061				p.I251V		Atlas-SNP	.											.	ABHD10	20	.	0			c.A751G						PASS	.	A	VAL/ILE	51,4355	51.6+/-87.1	0,51,2152	217.0	186.0	196.0		751	-11.1	0.0	3	dbSNP_123	196	582,8018	156.3+/-210.2	21,540,3739	yes	missense	ABHD10	NM_018394.2	29	21,591,5891	GG,GA,AA		6.7674,1.1575,4.867	benign	251/307	111710398	633,12373	2203	4300	6503	SO:0001583	missense	55347	exon5			GATGACATTGTAC	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"""Abhydrolase domain containing"""	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.751A>G	3.37:g.111710398A>G	ENSP00000273359:p.Ile251Val	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	356	173	0.485955	NM_018394	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Missense_Mutation	SNP	ENST00000273359.3	37	CCDS2963.1	84	0.038461538461538464	2	0.0040650406504065045	28	0.07734806629834254	0	0.0	54	0.0712401055408971	A	8.533	0.871406	0.17322	0.011575	0.067674	ENSG00000144827	ENST00000534857;ENST00000273359	T;T	0.66280	1.06;-0.2	5.53	-11.1	0.00147	.	0.495363	0.21716	N	0.070193	T	0.01870	0.0059	N	0.04746	-0.17	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.05937	-1.0855	10	0.15499	T	0.54	-10.6724	21.0401	0.99944	0.1269:0.0937:0.7794:0.0	rs17429033;rs56588673;rs17429033	251	Q9NUJ1	ABHDA_HUMAN	V	94;251	ENSP00000442932:I94V;ENSP00000273359:I251V	ENSP00000273359:I251V	I	+	1	0	ABHD10	113193088	0.628000	0.27138	0.000000	0.03702	0.457000	0.32468	0.763000	0.26517	-2.637000	0.00431	-1.039000	0.02377	ATT	A|0.961;G|0.039	0.039	strong		0.448	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394	
HSP90AB1	3326	hgsc.bcm.edu	37	6	44221316	44221316	+	Missense_Mutation	SNP	G	G	A	rs76772157	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:44221316G>A	ENST00000371554.1	+	12	2370	c.2156G>A	c.(2155-2157)cGc>cAc	p.R719H	HSP90AB1_ENST00000371646.5_Missense_Mutation_p.R719H|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000353801.3_Missense_Mutation_p.R719H|SLC35B2_ENST00000495706.1_5'Flank			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	719					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)	p.R719H(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GATGCGTCTCGCATGGAAGAA	0.522											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R719H		Atlas-SNP	.											HSP90AB1,extremity,malignant_melanoma,0,1	HSP90AB1	83	1	1	Substitution - Missense(1)	skin(1)	c.G2156A						PASS	.						72.0	75.0	74.0					6																	44221316		2203	4300	6503	SO:0001583	missense	3326	exon12			CGTCTCGCATGGA	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2156G>A	6.37:g.44221316G>A	ENSP00000360609:p.Arg719His	Somatic	198	0	0	922	WXS	Illumina HiSeq	Phase_I	225	34	0.151111	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	ENST00000371554.1	37	CCDS4909.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099702	0.56183	.	.	ENSG00000096384	ENST00000371646;ENST00000353801;ENST00000371554	T;T;T	0.09723	2.95;2.95;2.95	3.91	3.91	0.45181	.	0.000000	0.64402	U	0.000001	T	0.06554	0.0168	M	0.61703	1.905	0.80722	D	1	B;B;B	0.30584	0.004;0.286;0.002	B;B;B	0.30029	0.11;0.092;0.013	T	0.06499	-1.0823	10	0.44086	T	0.13	-1.7567	12.0789	0.53659	0.0881:0.0:0.9119:0.0	.	681;709;719	B4DMA2;B4DGL0;P08238	.;.;HS90B_HUMAN	H	719	ENSP00000360709:R719H;ENSP00000325875:R719H;ENSP00000360609:R719H	ENSP00000325875:R719H	R	+	2	0	HSP90AB1	44329294	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	5.571000	0.67404	2.188000	0.69820	0.609000	0.83330	CGC	G|0.986;A|0.014	0.014	strong		0.522	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
PHIP	55023	hgsc.bcm.edu	37	6	79688366	79688366	+	Silent	SNP	T	T	C	rs12209235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:79688366T>C	ENST00000275034.4	-	24	2999	c.2832A>G	c.(2830-2832)acA>acG	p.T944T	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	944	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CTGTAATCCATGTTGATGGCA	0.343													T|||	121	0.0241613	0.0045	0.0418	5008	,	,		15169	0.001		0.0746	False		,,,				2504	0.0102				p.T944T		Atlas-SNP	.											.	PHIP	177	.	0			c.A2832G						PASS	.	T		61,4345	58.1+/-94.6	0,61,2142	104.0	99.0	101.0		2832	-1.8	1.0	6	dbSNP_120	101	627,7973	163.3+/-215.9	31,565,3704	no	coding-synonymous	PHIP	NM_017934.5		31,626,5846	CC,CT,TT		7.2907,1.3845,5.2899		944/1822	79688366	688,12318	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon24			AATCCATGTTGAT	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.2832A>G	6.37:g.79688366T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			T|0.952;C|0.048	0.048	strong		0.343	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587103	15587103	+	Silent	SNP	C	C	T	rs35973013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	146	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	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	
NRCAM	4897	hgsc.bcm.edu	37	7	107849908	107849908	+	Silent	SNP	G	G	A	rs1269621	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:107849908G>A	ENST00000425651.2	-	9	1031	c.1032C>T	c.(1030-1032)aaC>aaT	p.N344N	NRCAM_ENST00000379024.4_Silent_p.N325N|NRCAM_ENST00000351718.4_Silent_p.N338N|NRCAM_ENST00000413765.2_Silent_p.N325N|NRCAM_ENST00000379028.3_Silent_p.N344N|NRCAM_ENST00000379022.4_Silent_p.N344N	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	344	Ig-like 3.				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						CTCCTAATGCGTTTTTTGCTA	0.353													G|||	2929	0.584864	0.5408	0.6066	5008	,	,		17628	0.8155		0.508	False		,,,				2504	0.4703				p.N344N		Atlas-SNP	.											.	NRCAM	267	.	0			c.C1032T						PASS	.	G	,,,,	2411,1995	615.6+/-392.6	638,1135,430	164.0	157.0	159.0		1032,1032,975,975,1014	2.2	0.3	7	dbSNP_87	159	4368,4232	583.1+/-391.5	1127,2114,1059	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	1765,3249,1489	AA,AG,GG		49.2093,45.2792,47.8779	,,,,	344/1305,344/1212,325/1193,325/1181,338/1184	107849908	6779,6227	2203	4300	6503	SO:0001819	synonymous_variant	4897	exon9			TAATGCGTTTTTT		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.1032C>T	7.37:g.107849908G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1																																																																																			G|0.434;A|0.566	0.566	strong		0.353	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
ODF3B	440836	hgsc.bcm.edu	37	22	50969647	50969647	+	Missense_Mutation	SNP	C	C	G	rs139023197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50969647C>G	ENST00000428989.2	-	3	390	c.391G>C	c.(391-393)Ggt>Cgt	p.G131R	TYMP_ENST00000395680.1_5'Flank|TYMP_ENST00000395681.1_5'Flank|ODF3B_ENST00000401779.1_Missense_Mutation_p.G107A|ODF3B_ENST00000329363.4_Missense_Mutation_p.G131R|ODF3B_ENST00000403326.1_Missense_Mutation_p.G63R|TYMP_ENST00000252029.3_5'Flank|TYMP_ENST00000395678.3_5'Flank|ODF3B_ENST00000405135.1_Missense_Mutation_p.G146A			A8MYP8	ODF3B_HUMAN	outer dense fiber of sperm tails 3B	131										lung(2)	2						GCCTGGACACCCCAGTTTCGG	0.682													C|||	101	0.0201677	0.0015	0.0202	5008	,	,		13778	0.0079		0.0437	False		,,,				2504	0.0337				p.G131R		Atlas-SNP	.											.	ODF3B	6	.	0			c.G391C						PASS	.	C	ARG/GLY	21,3985		0,21,1982	31.0	35.0	34.0		391	4.2	1.0	22	dbSNP_134	34	324,8002		11,302,3850	yes	missense	ODF3B	NM_001014440.3	125	11,323,5832	GG,GC,CC		3.8914,0.5242,2.7976	probably-damaging	131/254	50969647	345,11987	2003	4163	6166	SO:0001583	missense	440836	exon4			GGACACCCCAGTT		CCDS43039.1	22q13.33	2008-10-24			ENSG00000177989	ENSG00000177989			34388	protein-coding gene	gene with protein product							Standard	NM_001014440		Approved		uc003bmh.2	A8MYP8	OTTHUMG00000150334	ENST00000428989.2:c.391G>C	22.37:g.50969647C>G	ENSP00000390712:p.Gly131Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_001014440	A0PK18	Missense_Mutation	SNP	ENST00000428989.2	37	CCDS43039.1	41|41	0.018772893772893772|0.018772893772893772	0|0	0.0|0.0	5|5	0.013812154696132596|0.013812154696132596	4|4	0.006993006993006993|0.006993006993006993	32|32	0.04221635883905013|0.04221635883905013	C|C	12.83|12.83	2.055725|2.055725	0.36277|0.36277	0.005242|0.005242	0.038914|0.038914	ENSG00000177989|ENSG00000177989	ENST00000401779;ENST00000405135|ENST00000329363;ENST00000403326;ENST00000428989	T|T;T;T	0.52295|0.29917	0.67|1.55;1.6;1.55	4.21|4.21	4.21|4.21	0.49690|0.49690	.|.	.|.	.|.	.|.	.|.	T|T	0.11281|0.11281	0.0275|0.0275	L|L	0.47716|0.47716	1.5|1.5	0.32204|0.32204	N|N	0.57746|0.57746	D|D	0.60160|0.58268	0.987|0.982	P|P	0.61328|0.55011	0.887|0.766	T|T	0.04723|0.04723	-1.0931|-1.0931	9|9	0.59425|0.16420	D|T	0.04|0.52	-2.6159|-2.6159	12.2401|12.2401	0.54538|0.54538	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107|131	B5MD02|A8MYP8	.|ODF3B_HUMAN	A|R	107;146|131;63;131	ENSP00000384012:G146A|ENSP00000382804:G131R;ENSP00000385123:G63R;ENSP00000390712:G131R	ENSP00000384310:G107A|ENSP00000382804:G131R	G|G	-|-	2|1	0|0	ODF3B|ODF3B	49316513|49316513	0.579000|0.579000	0.26725|0.26725	0.996000|0.996000	0.52242|0.52242	0.471000|0.471000	0.32888|0.32888	1.708000|1.708000	0.37899|0.37899	2.329000|2.329000	0.79093|0.79093	0.561000|0.561000	0.74099|0.74099	GGG|GGT	C|0.969;G|0.031	0.031	strong		0.682	ODF3B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317626.2		
IRGC	56269	hgsc.bcm.edu	37	19	44223412	44223412	+	Silent	SNP	C	C	T	rs34471331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44223412C>T	ENST00000244314.5	+	2	901	c.702C>T	c.(700-702)caC>caT	p.H234H		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	234	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)				CCTGGGAGCACGACCTGCCCT	0.672													C|||	261	0.0521166	0.0242	0.0548	5008	,	,		16982	0.001		0.1292	False		,,,				2504	0.0613				p.H234H	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.C702T						PASS	.	C		184,4218		3,178,2020	22.0	21.0	21.0		702	-9.2	0.0	19	dbSNP_126	21	987,7607		53,881,3363	no	coding-synonymous	IRGC	NM_019612.3		56,1059,5383	TT,TC,CC		11.4848,4.1799,9.0105		234/464	44223412	1171,11825	2201	4297	6498	SO:0001819	synonymous_variant	56269	exon2			GGAGCACGACCTG	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.702C>T	19.37:g.44223412C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_019612	Q05BR8	Silent	SNP	ENST00000244314.5	37	CCDS12629.1																																																																																			C|0.924;T|0.076	0.076	strong		0.672	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612	
PPL	5493	hgsc.bcm.edu	37	16	4933907	4933907	+	Silent	SNP	T	T	C	rs17137389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4933907T>C	ENST00000345988.2	-	22	4838	c.4749A>G	c.(4747-4749)caA>caG	p.Q1583Q	PPL_ENST00000590782.2_Silent_p.Q1581Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1583					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						TGATTTCCGATTGGAGCCTTC	0.532													T|||	351	0.0700879	0.1604	0.036	5008	,	,		19681	0.006		0.0775	False		,,,				2504	0.0307				p.Q1583Q		Atlas-SNP	.											.	PPL	168	.	0			c.A4749G						PASS	.	T		668,3726	281.9+/-276.2	42,584,1571	120.0	119.0	119.0		4749	-3.7	0.7	16	dbSNP_123	119	665,7935	167.1+/-218.9	29,607,3664	no	coding-synonymous	PPL	NM_002705.4		71,1191,5235	CC,CT,TT		7.7326,15.2025,10.2586		1583/1757	4933907	1333,11661	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			TTCCGATTGGAGC	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.4749A>G	16.37:g.4933907T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			T|0.902;C|0.098	0.098	strong		0.532	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
ZNF17	7565	hgsc.bcm.edu	37	19	57932027	57932027	+	Silent	SNP	C	C	T	rs2158009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57932027C>T	ENST00000601808.1	+	3	1380	c.1167C>T	c.(1165-1167)aaC>aaT	p.N389N	ZNF17_ENST00000307658.7_Silent_p.N391N|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	389					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		ATGAATGCAACGAATGTGGGA	0.398													C|||	792	0.158147	0.0144	0.2061	5008	,	,		22756	0.253		0.174	False		,,,				2504	0.2045				p.N389N	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.C1167T						PASS	.	C		184,4200	103.8+/-142.4	6,172,2014	85.0	88.0	87.0		1167	-3.6	0.0	19	dbSNP_96	87	1703,6891	300.2+/-304.8	177,1349,2771	no	coding-synonymous	ZNF17	NM_006959.2		183,1521,4785	TT,TC,CC		19.8162,4.1971,14.54		389/663	57932027	1887,11091	2192	4297	6489	SO:0001819	synonymous_variant	7565	exon3			ATGCAACGAATGT	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.1167C>T	19.37:g.57932027C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Silent	SNP	ENST00000601808.1	37	CCDS42636.1																																																																																			C|0.820;T|0.180	0.180	strong		0.398	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	
CCDC13	152206	hgsc.bcm.edu	37	3	42772038	42772038	+	Missense_Mutation	SNP	A	A	T	rs12495805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42772038A>T	ENST00000310232.6	-	13	1722	c.1639T>A	c.(1639-1641)Tca>Aca	p.S547T	CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	547			S -> T (in dbSNP:rs12495805).							endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TTGATCTCTGACACTTGTGCC	0.592													T|||	1022	0.204073	0.2451	0.1844	5008	,	,		18415	0.1081		0.1849	False		,,,				2504	0.2812				p.S547T		Atlas-SNP	.											.	CCDC13	71	.	0			c.T1639A						PASS	.	T	THR/SER	1077,3329	722.4+/-409.3	108,861,1234	87.0	85.0	85.0		1639	-3.3	0.0	3	dbSNP_120	85	1567,7033	744.7+/-407.2	123,1321,2856	yes	missense	CCDC13	NM_144719.3	58	231,2182,4090	TT,TA,AA		18.2209,24.4439,20.3291	benign	547/716	42772038	2644,10362	2203	4300	6503	SO:0001583	missense	152206	exon13			TCTCTGACACTTG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1639T>A	3.37:g.42772038A>T	ENSP00000309836:p.Ser547Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	427	0.1955128205128205	139	0.28252032520325204	75	0.20718232044198895	71	0.12412587412587413	142	0.18733509234828497	T	0.599	-0.829686	0.02734	0.244439	0.182209	ENSG00000244607	ENST00000310232	T	0.10573	2.86	5.76	-3.26	0.05064	.	0.453819	0.24400	N	0.038850	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	9	0.12766	T	0.61	.	10.1473	0.42771	0.1103:0.5632:0.0:0.3265	rs12495805;rs52834773;rs12495805	547	Q8IYE1	CCD13_HUMAN	T	547	ENSP00000309836:S547T	ENSP00000309836:S547T	S	-	1	0	CCDC13	42747042	0.002000	0.14202	0.006000	0.13384	0.575000	0.36095	-0.454000	0.06770	-0.933000	0.03737	-1.051000	0.02340	TCA	A|0.792;T|0.208	0.208	strong		0.592	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
MUC2	4583	hgsc.bcm.edu	37	11	1092951	1092951	+	Silent	SNP	T	T	C	rs62649761		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1092951T>C	ENST00000441003.2	+	30	4797	c.4770T>C	c.(4768-4770)acT>acC	p.T1590T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1591T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccactacggtgaccc	0.632																																					p.T1590T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,+1,2	MUC2	614	2	0			c.T4770C						scavenged	.						55.0	88.0	76.0					11																	1092951		1822	3339	5161	SO:0001819	synonymous_variant	4583	exon30			CACCACTACGGTG	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.4770T>C	11.37:g.1092951T>C		Somatic	52	5	0.0961538		WXS	Illumina HiSeq	Phase_I	77	19	0.246753	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PHF21A	51317	hgsc.bcm.edu	37	11	45987091	45987091	+	Silent	SNP	A	A	T	rs151169176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:45987091A>T	ENST00000418153.2	-	9	967	c.768T>A	c.(766-768)gcT>gcA	p.A256A	PHF21A_ENST00000527753.1_5'Flank|PHF21A_ENST00000323180.6_Silent_p.A257A|PHF21A_ENST00000257821.4_Silent_p.A257A			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	256					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						TAAGCTGAGGAGCTGCGAGCA	0.537											OREG0020936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	15	0.00299521	0.0	0.0072	5008	,	,		19319	0.0		0.004	False		,,,				2504	0.0061				p.A257A		Atlas-SNP	.											.	PHF21A	107	.	0			c.T771A						PASS	.	A	,	6,4398	11.4+/-27.6	0,6,2196	72.0	57.0	62.0		768,771	3.7	1.0	11	dbSNP_134	62	61,8537	38.8+/-94.9	1,59,4239	no	coding-synonymous,coding-synonymous	PHF21A	NM_001101802.1,NM_016621.3	,	1,65,6435	TT,TA,AA		0.7095,0.1362,0.5153	,	256/681,257/635	45987091	67,12935	2202	4299	6501	SO:0001819	synonymous_variant	51317	exon9			CTGAGGAGCTGCG	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.768T>A	11.37:g.45987091A>T		Somatic	186	0	0	935	WXS	Illumina HiSeq	Phase_I	230	128	0.556522	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	37	CCDS44578.1																																																																																			A|0.994;T|0.006	0.006	strong		0.537	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
NFRKB	4798	hgsc.bcm.edu	37	11	129746707	129746707	+	Silent	SNP	G	G	T	rs2229650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:129746707G>T	ENST00000446488.3	-	16	1759	c.1656C>A	c.(1654-1656)ggC>ggA	p.G552G	NFRKB_ENST00000304521.5_Silent_p.G552G|NFRKB_ENST00000524746.1_Silent_p.G552G|NFRKB_ENST00000524794.1_Silent_p.G577G	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	552					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)		TGTCAAACACGCCCTTCACTG	0.587													G|||	1371	0.273762	0.2156	0.2349	5008	,	,		17938	0.3869		0.2018	False		,,,				2504	0.3374				p.G577G		Atlas-SNP	.											NFRKB,right_upper_lobe,carcinoma,-1,1	NFRKB	101	1	0			c.C1731A						scavenged	.	G	,	859,3543	335.7+/-304.0	81,697,1423	107.0	85.0	92.0		1656,1731	-11.9	0.3	11	dbSNP_98	92	1417,7177	272.2+/-289.9	107,1203,2987	no	coding-synonymous,coding-synonymous	NFRKB	NM_001143835.1,NM_006165.3	,	188,1900,4410	TT,TG,GG		16.4882,19.5139,17.5131	,	552/1300,577/1325	129746707	2276,10720	2201	4297	6498	SO:0001819	synonymous_variant	4798	exon15			AAACACGCCCTTC		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.1656C>A	11.37:g.129746707G>T		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																			T|0.203;G|0.797;A|0.000	0.203	strong		0.587	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
ITSN2	50618	hgsc.bcm.edu	37	2	24431184	24431184	+	Missense_Mutation	SNP	C	C	T	rs2303291	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:24431184C>T	ENST00000355123.4	-	37	5043	c.4600G>A	c.(4600-4602)Gcc>Acc	p.A1534T	ITSN2_ENST00000361999.3_Missense_Mutation_p.A1507T	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1534	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		A -> T (in dbSNP:rs2303291).		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)					TGCACCCAGGCGGTCCTACGG	0.592													C|||	696	0.138978	0.0204	0.134	5008	,	,		18660	0.123		0.2594	False		,,,				2504	0.1953				p.A1534T		Atlas-SNP	.											.	ITSN2	224	.	0			c.G4600A						PASS	.	C	THR/ALA,THR/ALA	261,4145	146.9+/-181.5	8,245,1950	96.0	90.0	92.0		4600,4519	4.9	1.0	2	dbSNP_100	92	2084,6516	361.3+/-332.3	254,1576,2470	yes	missense,missense	ITSN2	NM_006277.2,NM_019595.3	58,58	262,1821,4420	TT,TC,CC		24.2326,5.9237,18.0301	probably-damaging,probably-damaging	1534/1698,1507/1671	24431184	2345,10661	2203	4300	6503	SO:0001583	missense	50618	exon37			CCCAGGCGGTCCT	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.4600G>A	2.37:g.24431184C>T	ENSP00000347244:p.Ala1534Thr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	347	0.15888278388278387	20	0.04065040650406504	54	0.14917127071823205	71	0.12412587412587413	202	0.26649076517150394	C	14.81	2.646229	0.47258	0.059237	0.242326	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.44083	0.93;0.93;0.93	4.86	4.86	0.63082	Pleckstrin homology-type (1);Pleckstrin homology domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.36628	U	0.002485	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.999999852117	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.09487	-1.0672	9	0.35671	T	0.21	.	18.3604	0.90372	0.0:1.0:0.0:0.0	rs2303291;rs52805758;rs56718449;rs2303291	1507;1534	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	T	1507;1534;1507	ENSP00000354561:A1507T;ENSP00000347244:A1534T;ENSP00000370250:A1507T	ENSP00000347244:A1534T	A	-	1	0	ITSN2	24284688	1.000000	0.71417	0.978000	0.43139	0.526000	0.34562	7.308000	0.78929	2.397000	0.81536	0.542000	0.68232	GCC	C|0.829;T|0.171	0.171	strong		0.592	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
XCL2	6846	hgsc.bcm.edu	37	1	168511284	168511284	+	Silent	SNP	T	T	C	rs4282797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:168511284T>C	ENST00000367819.2	-	2	155	c.123A>G	c.(121-123)ccA>ccG	p.P41P		NM_003175.3	NP_003166.1	Q9UBD3	XCL2_HUMAN	chemokine (C motif) ligand 2	41					blood circulation (GO:0008015)|cell chemotaxis (GO:0060326)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			large_intestine(1)|lung(6)|ovary(1)	8	all_hematologic(923;0.215)					TTCTGCTAACTGGCAGTCGCT	0.478													T|||	1763	0.352037	0.2481	0.3818	5008	,	,		12214	0.6429		0.2117	False		,,,				2504	0.316				p.P41P		Atlas-SNP	.											XCL2,colon,carcinoma,-2,1	XCL2	18	1	0			c.A123G						PASS	.	T		779,3627		110,559,1534	139.0	116.0	124.0		123	-0.3	0.3	1	dbSNP_111	124	1024,7572		170,684,3444	yes	coding-synonymous	XCL2	NM_003175.3		280,1243,4978	CC,CT,TT		11.9125,17.6804,13.8671		41/115	168511284	1803,11199	2203	4298	6501	SO:0001819	synonymous_variant	6846	exon2			GCTAACTGGCAGT	BC070309	CCDS1273.1	1q24.2	2013-02-28	2002-08-22	2002-08-23	ENSG00000143185	ENSG00000143185		"""Endogenous ligands"""	10646	protein-coding gene	gene with protein product		604828	"""small inducible cytokine subfamily C, member 2"""	SCYC2		7875320	Standard	NM_003175		Approved	SCM-1b	uc001gfn.4	Q9UBD3	OTTHUMG00000034549	ENST00000367819.2:c.123A>G	1.37:g.168511284T>C		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	109	105	0.963303	NM_003175		Silent	SNP	ENST00000367819.2	37	CCDS1273.1																																																																																			T|0.709;C|0.291	0.291	strong		0.478	XCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083613.1	NM_003175	
UNC45B	146862	hgsc.bcm.edu	37	17	33513337	33513337	+	Missense_Mutation	SNP	T	T	A	rs11654824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:33513337T>A	ENST00000268876.5	+	20	2652	c.2555T>A	c.(2554-2556)aTc>aAc	p.I852N	UNC45B_ENST00000378449.1_Missense_Mutation_p.I771N|UNC45B_ENST00000433649.1_Missense_Mutation_p.I850N|RP11-799D4.2_ENST00000590144.1_RNA|UNC45B_ENST00000591048.1_Missense_Mutation_p.I771N|UNC45B_ENST00000394570.2_Missense_Mutation_p.I850N	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	852			I -> N (in dbSNP:rs11654824).		cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TGGTTGGAGATCCTCCAGCGG	0.567													T|||	169	0.033746	0.0053	0.0317	5008	,	,		19749	0.0		0.0905	False		,,,				2504	0.0501				p.I852N		Atlas-SNP	.											.	UNC45B	133	.	0			c.T2555A						PASS	.	T	ASN/ILE,ASN/ILE	65,4341	61.1+/-98.1	2,61,2140	82.0	82.0	82.0		2549,2555	6.0	1.0	17	dbSNP_120	82	627,7973	163.0+/-215.7	13,601,3686	yes	missense,missense	UNC45B	NM_001033576.1,NM_173167.2	149,149	15,662,5826	AA,AT,TT		7.2907,1.4753,5.3206	possibly-damaging,possibly-damaging	850/930,852/932	33513337	692,12314	2203	4300	6503	SO:0001583	missense	146862	exon20			TGGAGATCCTCCA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2555T>A	17.37:g.33513337T>A	ENSP00000268876:p.Ile852Asn	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	102	0.046703296703296704	5	0.01016260162601626	16	0.04419889502762431	0	0.0	81	0.10686015831134564	T	17.96	3.516186	0.64634	0.014753	0.072907	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.51574	0.7;1.45;0.7	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.03564	0.0102	M	0.75615	2.305	0.09310	P	0.999999791172	D;D;P	0.89917	0.999;1.0;0.93	D;D;P	0.91635	0.997;0.999;0.496	T	0.39961	-0.9588	9	0.87932	D	0	-26.2242	15.7258	0.77756	0.0:0.0:0.0:1.0	rs11654824;rs52819819;rs11654824	771;850;852	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	N	852;852;850;771	ENSP00000268876:I852N;ENSP00000412840:I850N;ENSP00000367710:I771N	ENSP00000268876:I852N	I	+	2	0	UNC45B	30537450	1.000000	0.71417	0.958000	0.39756	0.992000	0.81027	7.886000	0.87288	2.311000	0.77944	0.533000	0.62120	ATC	T|0.948;A|0.052	0.052	strong		0.567	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
UMOD	7369	hgsc.bcm.edu	37	16	20352532	20352532	+	Silent	SNP	G	G	A	rs141800038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:20352532G>A	ENST00000570689.1	-	7	1604	c.1458C>T	c.(1456-1458)taC>taT	p.Y486Y	UMOD_ENST00000396134.2_Silent_p.Y519Y|UMOD_ENST00000424589.1_Silent_p.Y519Y|UMOD_ENST00000396138.4_Silent_p.Y535Y|UMOD_ENST00000302509.4_Silent_p.Y486Y|UMOD_ENST00000570331.1_5'UTR|UMOD_ENST00000396142.2_Silent_p.Y486Y			P07911	UROM_HUMAN	uromodulin	486	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TGGTGCCCACGTAGAGAAAAG	0.597													G|||	13	0.00259585	0.0	0.0	5008	,	,		16645	0.0		0.0099	False		,,,				2504	0.0031				p.Y486Y		Atlas-SNP	.											.	UMOD	128	.	0			c.C1458T						PASS	.	G	,	7,4399	12.9+/-30.5	0,7,2196	96.0	75.0	82.0		1458,1458	-4.3	0.9	16	dbSNP_134	82	90,8510	52.3+/-112.8	0,90,4210	no	coding-synonymous,coding-synonymous	UMOD	NM_001008389.1,NM_003361.2	,	0,97,6406	AA,AG,GG		1.0465,0.1589,0.7458	,	486/641,486/641	20352532	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	7369	exon7			GCCCACGTAGAGA	M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"""Tamm-Horsfall glycoprotein"", ""uromucoid"""	191845	"""uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"""			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.1458C>T	16.37:g.20352532G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Silent	SNP	ENST00000570689.1	37	CCDS10583.1																																																																																			G|0.994;A|0.006	0.006	strong		0.597	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
SPATC1L	84221	hgsc.bcm.edu	37	21	47581835	47581835	+	Missense_Mutation	SNP	C	C	T	rs113710653	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47581835C>T	ENST00000291672.5	-	4	1752	c.691G>A	c.(691-693)Gag>Aag	p.E231K	SPATC1L_ENST00000330205.6_Missense_Mutation_p.E77K	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	231																	CGCACCTGCTCGATCTTCTCG	0.716													T|||	203	0.0405351	0.0106	0.0504	5008	,	,		12069	0.0139		0.0964	False		,,,				2504	0.044				p.E231K		Atlas-SNP	.											.	.	.	.	0			c.G691A						PASS	.	T	LYS/GLU,LYS/GLU	70,4316		0,70,2123	26.0	24.0	25.0		691,229	3.3	1.0	21	dbSNP_132	25	746,7838		27,692,3573	yes	missense,missense	C21orf56	NM_001142854.1,NM_032261.4	56,56	27,762,5696	TT,TC,CC		8.6906,1.596,6.2914	benign,benign	231/341,77/187	47581835	816,12154	2193	4292	6485	SO:0001583	missense	84221	exon4			CCTGCTCGATCTT	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.691G>A	21.37:g.47581835C>T	ENSP00000291672:p.Glu231Lys	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	22	14	0.636364	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	109	0.04990842490842491	6	0.012195121951219513	23	0.06353591160220995	8	0.013986013986013986	72	0.09498680738786279	T	7.612	0.674926	0.14841	0.01596	0.086906	ENSG00000160284	ENST00000330205;ENST00000291672	T;T	0.38401	1.14;1.14	4.45	3.27	0.37495	.	0.153324	0.42548	N	0.000698	T	0.00328	0.0010	N	0.00538	-1.39	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.28744	-1.0034	10	0.10902	T	0.67	-17.7276	4.5983	0.12341	0.1682:0.0949:0.0:0.7369	.	231	Q9H0A9	CU056_HUMAN	K	77;231	ENSP00000333869:E77K;ENSP00000291672:E231K	ENSP00000291672:E231K	E	-	1	0	C21orf56	46406263	0.914000	0.31030	0.999000	0.59377	0.986000	0.74619	1.022000	0.30052	0.117000	0.18138	-0.254000	0.11334	GAG	C|0.942;T|0.058	0.058	strong		0.716	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
PABPC1L	80336	hgsc.bcm.edu	37	20	43547677	43547677	+	Missense_Mutation	SNP	T	T	G	rs2075960	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:43547677T>G	ENST00000217073.2	+	4	634	c.634T>G	c.(634-636)Tcc>Gcc	p.S212A	PABPC1L_ENST00000217074.4_Missense_Mutation_p.S212A|PABPC1L_ENST00000537323.1_Missense_Mutation_p.S212A|PABPC1L_ENST00000255136.3_Missense_Mutation_p.S212A			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	212	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.		S -> A (in dbSNP:rs2075960).		mRNA polyadenylation (GO:0006378)|oocyte maturation (GO:0001556)	extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20						GGACCTCTTCTCCCAGTTTGG	0.627													T|||	1159	0.23143	0.1838	0.3458	5008	,	,		17408	0.2123		0.2515	False		,,,				2504	0.2137				p.S212A		Atlas-SNP	.											.	PABPC1L	59	.	0			c.T634G						PASS	.	T	ALA/SER	541,2595		43,455,1070	97.0	95.0	96.0		634	3.9	1.0	20	dbSNP_96	96	1744,5420		214,1316,2052	yes	missense	PABPC1L	NM_001124756.1	99	257,1771,3122	GG,GT,TT		24.3439,17.2513,22.1845	benign	212/615	43547677	2285,8015	1568	3582	5150	SO:0001583	missense	80336	exon4			CTCTTCTCCCAGT	AK026760	CCDS42878.1	20q12-q13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000101104	ENSG00000101104		"""RNA binding motif (RRM) containing"""	15797	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 119"""	C20orf119		11549316	Standard	NM_001124756		Approved	dJ1069P2.3, PABPC1L1, ePAB	uc010ggv.1	Q4VXU2	OTTHUMG00000032553	ENST00000217073.2:c.634T>G	20.37:g.43547677T>G	ENSP00000217073:p.Ser212Ala	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	37	CCDS42878.1	513	0.2348901098901099	83	0.16869918699186992	121	0.3342541436464088	125	0.21853146853146854	184	0.24274406332453827	T	10.66	1.411498	0.25465	0.172513	0.243439	ENSG00000101104	ENST00000217074;ENST00000255136;ENST00000537323;ENST00000217073	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.06	3.94	0.45596	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.281067	0.41097	D	0.000956	T	0.00012	0.0000	N	0.21583	0.68	0.31114	P	0.709589	B	0.15473	0.013	B	0.26094	0.066	T	0.04693	-1.0933	9	0.29301	T	0.29	.	12.1282	0.53928	0.0:0.0:0.1436:0.8564	rs2075960;rs60813358;rs2075960	212	Q4VXU2	PAP1L_HUMAN	A	212	ENSP00000217074:S212A;ENSP00000255136:S212A;ENSP00000445661:S212A;ENSP00000217073:S212A	ENSP00000217073:S212A	S	+	1	0	PABPC1L	42981091	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.107000	0.50329	0.929000	0.37192	0.460000	0.39030	TCC	T|0.781;G|0.219	0.219	strong		0.627	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2		
TSEN2	80746	hgsc.bcm.edu	37	3	12538040	12538040	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12538040A>G	ENST00000284995.6	+	4	682	c.295A>G	c.(295-297)Atc>Gtc	p.I99V	TSEN2_ENST00000402228.3_Missense_Mutation_p.I99V|TSEN2_ENST00000444864.1_Missense_Mutation_p.I99V|TSEN2_ENST00000454502.2_Missense_Mutation_p.I99V|TSEN2_ENST00000415684.1_Missense_Mutation_p.I99V|TSEN2_ENST00000314571.7_Missense_Mutation_p.I99V|TSEN2_ENST00000383797.5_Missense_Mutation_p.I99V	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	99					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						CATGCCTATCATCACATCAAA	0.368																																					p.I99V		Atlas-SNP	.											.	TSEN2	46	.	0			c.A295G						PASS	.						201.0	190.0	194.0					3																	12538040		2203	4300	6503	SO:0001583	missense	80746	exon4			CCTATCATCACAT	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.295A>G	3.37:g.12538040A>G	ENSP00000284995:p.Ile99Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_001145394	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Missense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	.	.	.	.	.	.	.	.	.	.	A	13.07	2.128557	0.37533	.	.	ENSG00000154743	ENST00000446004;ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000444864;ENST00000537959;ENST00000415684	T;T;T;T;T;T;T;T	0.59364	0.29;0.3;0.39;0.29;0.35;0.35;0.27;0.3	5.12	1.92	0.25849	.	0.308783	0.32935	N	0.005479	T	0.48466	0.1501	M	0.71581	2.175	0.27073	N	0.963277	B;B;B;B	0.32283	0.362;0.03;0.066;0.003	B;B;B;B	0.33121	0.158;0.047;0.094;0.003	T	0.32693	-0.9897	10	0.30854	T	0.27	-16.8333	3.9504	0.09366	0.4827:0.3484:0.1689:0.0	.	99;99;99;99	G5E9Q3;Q8NCE0;Q8NCE0-3;C9IZI7	.;SEN2_HUMAN;.;.	V	99;99;99;99;99;99;99;72;99	ENSP00000406238:I99V;ENSP00000323188:I99V;ENSP00000392029:I99V;ENSP00000373307:I99V;ENSP00000385976:I99V;ENSP00000284995:I99V;ENSP00000407974:I99V;ENSP00000416510:I99V	ENSP00000284995:I99V	I	+	1	0	TSEN2	12513040	0.985000	0.35326	0.991000	0.47740	0.982000	0.71751	0.964000	0.29306	1.943000	0.56356	0.529000	0.55759	ATC	.	.	none		0.368	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265	
BMP2K	55589	hgsc.bcm.edu	37	4	79832488	79832488	+	Silent	SNP	A	A	G	rs574665641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79832488A>G	ENST00000335016.5	+	16	2953	c.2787A>G	c.(2785-2787)gtA>gtG	p.V929V	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	929					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						CCAAAAGTGTAGATGTATTTG	0.438													A|||	2	0.000399361	0.0	0.0	5008	,	,		21116	0.0		0.0	False		,,,				2504	0.002				p.V929V		Atlas-SNP	.											.	BMP2K	169	.	0			c.A2787G						PASS	.						60.0	54.0	56.0					4																	79832488		1946	4127	6073	SO:0001819	synonymous_variant	55589	exon16			AAGTGTAGATGTA	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.2787A>G	4.37:g.79832488A>G		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	306	155	0.506536	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	A	5.217	0.225527	0.09916	.	.	ENSG00000138756	ENST00000502613	.	.	.	5.3	-4.97	0.03029	.	.	.	.	.	T	0.46964	0.1420	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44892	-0.9298	4	.	.	.	-9.7415	5.8121	0.18471	0.1496:0.2279:0.5104:0.1121	.	.	.	.	G	622	.	.	R	+	1	2	BMP2K	80051512	0.006000	0.16342	0.843000	0.33291	0.837000	0.47467	-1.136000	0.03222	-0.932000	0.03742	0.397000	0.26171	AGA	.	.	none		0.438	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
PODXL	5420	hgsc.bcm.edu	37	7	131191461	131191461	+	Silent	SNP	A	A	G	rs3212300	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:131191461A>G	ENST00000378555.3	-	6	1373	c.1126T>C	c.(1126-1128)Ttg>Ctg	p.L376L	PODXL_ENST00000541194.1_Silent_p.L378L|PODXL_ENST00000537928.1_Silent_p.L344L|PODXL_ENST00000322985.9_Silent_p.L344L			O00592	PODXL_HUMAN	podocalyxin-like	376					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)					AGTGAGATCAATTTCTCATCC	0.612											OREG0018320	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	205	0.0409345	0.0552	0.0389	5008	,	,		17593	0.0		0.0795	False		,,,				2504	0.0256				p.L376L		Atlas-SNP	.											.	PODXL	53	.	0			c.T1126C						PASS	.	A	,	204,4202	127.0+/-164.0	5,194,2004	124.0	116.0	118.0		1126,1030	-1.7	0.0	7	dbSNP_105	118	657,7943	167.1+/-218.9	27,603,3670	no	coding-synonymous,coding-synonymous	PODXL	NM_001018111.2,NM_005397.3	,	32,797,5674	GG,GA,AA		7.6395,4.63,6.62	,	376/559,344/527	131191461	861,12145	2203	4300	6503	SO:0001819	synonymous_variant	5420	exon6			AGATCAATTTCTC		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.1126T>C	7.37:g.131191461A>G		Somatic	128	0	0	1585	WXS	Illumina HiSeq	Phase_I	170	83	0.488235	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			A|0.940;G|0.060	0.060	strong		0.612	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
SMARCAD1	56916	hgsc.bcm.edu	37	4	95186055	95186055	+	Silent	SNP	A	A	G	rs2306802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:95186055A>G	ENST00000354268.4	+	10	1552	c.1479A>G	c.(1477-1479)caA>caG	p.Q493Q	SMARCAD1_ENST00000509418.1_Silent_p.Q63Q|SMARCAD1_ENST00000457823.2_Silent_p.Q493Q			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	493					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.Q493Q(2)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		TTCTAAACCAAAGGTAATCTT	0.308													A|||	1679	0.335264	0.0673	0.3501	5008	,	,		18015	0.499		0.3698	False		,,,				2504	0.4826				p.Q493Q		Atlas-SNP	.											SMARCAD1,NS,carcinoma,0,1	SMARCAD1	97	1	2	Substitution - coding silent(2)	prostate(2)	c.A1479G						PASS	.	A	,,	546,3858	239.6+/-250.7	36,474,1692	53.0	51.0	52.0		1479,1479,1479	3.2	1.0	4	dbSNP_100	52	3266,5330	480.4+/-370.4	628,2010,1660	no	coding-synonymous,coding-synonymous,coding-synonymous	SMARCAD1	NM_001128429.1,NM_001128430.1,NM_020159.3	,,	664,2484,3352	GG,GA,AA		37.9944,12.3978,29.3231	,,	493/1029,493/1029,493/1027	95186055	3812,9188	2202	4298	6500	SO:0001819	synonymous_variant	56916	exon10			AAACCAAAGGTAA	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.1479A>G	4.37:g.95186055A>G		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Silent	SNP	ENST00000354268.4	37	CCDS3639.1																																																																																			A|0.691;G|0.309	0.309	strong		0.308	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159	
EFCAB5	374786	hgsc.bcm.edu	37	17	28417576	28417576	+	Missense_Mutation	SNP	G	G	C	rs35724168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28417576G>C	ENST00000394835.3	+	20	4013	c.3821G>C	c.(3820-3822)aGg>aCg	p.R1274T	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Missense_Mutation_p.R1150T|RP11-1148O4.2_ENST00000582938.1_RNA	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1274			R -> T (in dbSNP:rs35724168).				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						GGCCAAAATAGGATGTTGTTG	0.438													G|||	94	0.01877	0.0681	0.0029	5008	,	,		20188	0.0		0.002	False		,,,				2504	0.0				p.R1274T		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3821C						PASS	.	G	THR/ARG	165,3525		8,149,1688	140.0	137.0	138.0		3821	-0.0	0.1	17	dbSNP_126	138	12,8184		0,12,4086	yes	missense	EFCAB5	NM_198529.3	71	8,161,5774	CC,CG,GG		0.1464,4.4715,1.4891	benign	1274/1504	28417576	177,11709	1845	4098	5943	SO:0001583	missense	374786	exon20			AAAATAGGATGTT	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.3821G>C	17.37:g.28417576G>C	ENSP00000378312:p.Arg1274Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	34	0.015567765567765568	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.356	0.832049	0.16820	0.044715	0.001464	ENSG00000176927	ENST00000394835;ENST00000320856;ENST00000419434	T;T;T	0.10960	2.82;2.84;2.85	5.35	-0.00624	0.14014	.	0.653292	0.15652	N	0.251330	T	0.00580	0.0019	L	0.40543	1.245	0.09310	N	1	P;P	0.41848	0.763;0.763	B;B	0.36608	0.229;0.21	T	0.26121	-1.0112	10	0.66056	D	0.02	-6.6532	8.972	0.35912	0.523:0.0:0.477:0.0	rs35724168	1150;1274	E7EVS9;A4FU69	.;EFCB5_HUMAN	T	1274;1150;956	ENSP00000378312:R1274T;ENSP00000322003:R1150T;ENSP00000417009:R956T	ENSP00000322003:R1150T	R	+	2	0	EFCAB5	25441702	0.038000	0.19896	0.079000	0.20413	0.150000	0.21749	0.447000	0.21710	0.094000	0.17404	0.655000	0.94253	AGG	G|0.984;C|0.016	0.016	strong		0.438	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
MOGAT1	116255	hgsc.bcm.edu	37	2	223536541	223536541	+	Missense_Mutation	SNP	G	G	A	rs35959734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:223536541G>A	ENST00000446656.3	+	1	37	c.37G>A	c.(37-39)Gcg>Acg	p.A13T		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	13			A -> T (in dbSNP:rs35959734).		diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|cervix(1)|endometrium(1)|lung(5)|urinary_tract(1)	9		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		CATCCAGCTGGCGCGGCGGCT	0.697													G|||	302	0.0603035	0.1657	0.0346	5008	,	,		14166	0.0208		0.0139	False		,,,				2504	0.0245				p.A13T	Ovarian(93;205 1446 2385 11581 25911)	Atlas-SNP	.											.	MOGAT1	47	.	0			c.G37A						PASS	.	G	THR/ALA	469,3329		21,427,1451	7.0	11.0	10.0		37	2.5	1.0	2	dbSNP_126	10	131,7799		1,129,3835	yes	missense	MOGAT1	NM_058165.2	58	22,556,5286	AA,AG,GG		1.652,12.3486,5.116	benign	13/336	223536541	600,11128	1899	3965	5864	SO:0001583	missense	116255	exon1			CAGCTGGCGCGGC	AF384163	CCDS46524.1	2q36.2	2006-10-06	2004-05-28	2004-05-28	ENSG00000124003	ENSG00000124003			18210	protein-coding gene	gene with protein product		610268	"""diacylglycerol O-acyltransferase 2 like 1"""	DGAT2L1		14970677	Standard	NM_058165		Approved	DGAT2L, MGAT1	uc010fws.1	Q96PD6	OTTHUMG00000153394	ENST00000446656.3:c.37G>A	2.37:g.223536541G>A	ENSP00000406674:p.Ala13Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_058165	Q6IEE5	Missense_Mutation	SNP	ENST00000446656.3	37	CCDS46524.1	113	0.051739926739926737	84	0.17073170731707318	13	0.03591160220994475	8	0.013986013986013986	8	0.010554089709762533	G	9.288	1.049899	0.19827	0.123486	0.01652	ENSG00000124003	ENST00000446656	T	0.34667	1.35	4.33	2.48	0.30137	.	0.407102	0.22179	N	0.063532	T	0.00073	0.0002	L	0.28740	0.885	0.28167	P	0.9287327	B	0.02656	0.0	B	0.04013	0.001	T	0.08411	-1.0723	9	0.48119	T	0.1	-1.029	6.3841	0.21552	0.0964:0.0:0.7235:0.18	rs35959734;rs35959734	13	Q96PD6	MOGT1_HUMAN	T	13	ENSP00000406674:A13T	ENSP00000406674:A13T	A	+	1	0	MOGAT1	223244785	0.953000	0.32496	0.978000	0.43139	0.004000	0.04260	1.177000	0.31969	0.435000	0.26365	-0.282000	0.10007	GCG	G|0.939;A|0.061	0.061	strong		0.697	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165	
RPH3A	22895	hgsc.bcm.edu	37	12	113307744	113307744	+	Silent	SNP	C	C	T	rs149945171	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:113307744C>T	ENST00000389385.4	+	10	1193	c.696C>T	c.(694-696)ccC>ccT	p.P232P	RPH3A_ENST00000447659.2_Silent_p.P183P|RPH3A_ENST00000548866.1_Silent_p.P183P|RPH3A_ENST00000543106.2_Silent_p.P232P|RPH3A_ENST00000551052.1_Silent_p.P228P|RPH3A_ENST00000415485.3_Silent_p.P232P|RPH3A_ENST00000420983.2_Silent_p.P232P|RPH3A_ENST00000549913.2_3'UTR	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	232	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)		ATGGGCCTCCCGTGCGCAGGG	0.607																																					p.P232P		Atlas-SNP	.											RPH3A,NS,carcinoma,0,1	RPH3A	98	1	0			c.C696T						scavenged	.	C	,	0,4406		0,0,2203	78.0	77.0	78.0		696,684	-11.4	0.0	12	dbSNP_134	78	6,8594	4.3+/-15.6	1,4,4295	no	coding-synonymous,coding-synonymous	RPH3A	NM_001143854.1,NM_014954.3	,	1,4,6498	TT,TC,CC		0.0698,0.0,0.0461	,	232/695,228/691	113307744	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	22895	exon10			GCCTCCCGTGCGC	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.696C>T	12.37:g.113307744C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	135	2	0.0148148	NM_001143854	B7Z3C3|Q96AE0	Silent	SNP	ENST00000389385.4	37	CCDS44979.1																																																																																			C|0.999;T|0.001	0.001	strong		0.607	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954	
RIPK3	11035	hgsc.bcm.edu	37	14	24806902	24806902	+	Splice_Site	SNP	G	G	A	rs34106261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24806902G>A	ENST00000216274.5	-	7	1117	c.899C>T	c.(898-900)aCg>aTg	p.T300M	RP11-934B9.3_ENST00000555591.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank|ADCY4_ENST00000418030.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	300			T -> M (in dbSNP:rs34106261). {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)		GGCACTCACCGTGGAGACAGC	0.532													G|||	274	0.0547125	0.0953	0.0403	5008	,	,		20870	0.001		0.0577	False		,,,				2504	0.0624				p.T300M	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C899T						PASS	.	G	MET/THR	437,3969	212.2+/-232.1	12,413,1778	142.0	120.0	127.0		899	-9.3	0.0	14	dbSNP_126	127	409,8191	128.5+/-186.7	19,371,3910	yes	missense-near-splice	RIPK3	NM_006871.3	81	31,784,5688	AA,AG,GG		4.7558,9.9183,6.5047	benign	300/519	24806902	846,12160	2203	4300	6503	SO:0001630	splice_region_variant	11035	exon7			CTCACCGTGGAGA	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.900+1C>T	14.37:g.24806902G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	133	74	0.556391	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	37	CCDS9628.1	99	0.04532967032967033	46	0.09349593495934959	17	0.04696132596685083	0	0.0	36	0.047493403693931395	G	1.086	-0.665569	0.03428	0.099183	0.047558	ENSG00000129465	ENST00000216274	T	0.78595	-1.19	4.67	-9.34	0.00636	Protein kinase-like domain (1);	2.639140	0.01142	N	0.006225	T	0.02807	0.0084	N	0.14661	0.345	0.80722	P	0.0	B	0.20780	0.048	B	0.06405	0.002	T	0.48559	-0.9025	9	0.52906	T	0.07	5.6667	5.3725	0.16146	0.4725:0.0611:0.0781:0.3882	rs34106261	300	Q9Y572	RIPK3_HUMAN	M	300	ENSP00000216274:T300M	ENSP00000216274:T300M	T	-	2	0	RIPK3	23876742	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.838000	0.00354	-6.642000	0.00003	-1.074000	0.02243	ACG	G|0.936;A|0.064	0.064	strong		0.532	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	Missense_Mutation
AIM1	202	hgsc.bcm.edu	37	6	106999822	106999822	+	Missense_Mutation	SNP	G	G	A	rs2297970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:106999822G>A	ENST00000369066.3	+	12	4671	c.4184G>A	c.(4183-4185)tGt>tAt	p.C1395Y	AIM1_ENST00000535438.1_Missense_Mutation_p.C214Y|AIM1_ENST00000487681.1_3'UTR	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)		p.C1395Y(1)		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)		GGCAAAAATTGTAAGATCTCT	0.353													G|||	997	0.199081	0.121	0.1988	5008	,	,		15007	0.0565		0.2873	False		,,,				2504	0.3609				p.C1395Y		Atlas-SNP	.											AIM1,NS,carcinoma,0,1	AIM1	161	1	1	Substitution - Missense(1)	stomach(1)	c.G4184A						PASS	.	G	TYR/CYS	658,3748	276.0+/-272.9	44,570,1589	93.0	102.0	99.0		4184	5.0	1.0	6	dbSNP_100	99	2629,5969	421.7+/-353.8	418,1793,2088	yes	missense	AIM1	NM_001624.2	194	462,2363,3677	AA,AG,GG		30.5769,14.9342,25.2768	benign	1395/1724	106999822	3287,9717	2203	4299	6502	SO:0001583	missense	202	exon12			AAAATTGTAAGAT	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.4184G>A	6.37:g.106999822G>A	ENSP00000358062:p.Cys1395Tyr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	143	60	0.41958	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	395	0.18086080586080586	65	0.13211382113821138	76	0.20994475138121546	29	0.050699300699300696	225	0.29683377308707126	G	10.73	1.432797	0.25813	0.149342	0.305769	ENSG00000112297	ENST00000369066;ENST00000457437;ENST00000535438	T;T;T	0.75589	-0.95;-0.95;-0.95	5.9	5.03	0.67393	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.376576	0.37483	N	0.002062	T	0.49167	0.1541	N	0.17723	0.515	0.30327	P	0.7869889999999999	B;B	0.30793	0.137;0.295	B;B	0.41374	0.115;0.355	T	0.52320	-0.8591	9	0.34782	T	0.22	.	8.4927	0.33110	0.0702:0.0:0.6658:0.264	rs2297970;rs17562712;rs2297970	214;1395	B4DU04;Q9Y4K1	.;AIM1_HUMAN	Y	1395;214;214	ENSP00000358062:C1395Y;ENSP00000391419:C214Y;ENSP00000439183:C214Y	ENSP00000358062:C1395Y	C	+	2	0	AIM1	107106515	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.941000	0.29005	1.489000	0.48450	0.563000	0.77884	TGT	G|0.768;A|0.232	0.232	strong		0.353	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
RABEP1	9135	hgsc.bcm.edu	37	17	5280440	5280440	+	Silent	SNP	T	T	C	rs3026101	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5280440T>C	ENST00000546142.2	+	14	2242	c.2055T>C	c.(2053-2055)cgT>cgC	p.R685R	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000408982.2_Silent_p.R685R|RABEP1_ENST00000262477.6_Silent_p.R685R|RABEP1_ENST00000537505.1_Silent_p.R642R|RABEP1_ENST00000341923.6_Silent_p.R685R			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	685					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						TAAAATACCGTGAGGACATCA	0.408													T|||	1963	0.391973	0.2315	0.3573	5008	,	,		18412	0.6012		0.3479	False		,,,				2504	0.4632				p.R685R		Atlas-SNP	.											RABEP1,NS,haematopoietic_neoplasm,+1,1	RABEP1	59	1	0			c.T2055C						PASS	.	T	,	907,2861		102,703,1079	141.0	135.0	137.0		2055,2055	-10.0	0.2	17	dbSNP_102	137	2497,5717		364,1769,1974	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	466,2472,3053	CC,CT,TT		30.3993,24.0711,28.4093	,	685/830,685/863	5280440	3404,8578	1884	4107	5991	SO:0001819	synonymous_variant	9135	exon14			ATACCGTGAGGAC	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.2055T>C	17.37:g.5280440T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			T|0.635;C|0.365	0.365	strong		0.408	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
MUC16	94025	hgsc.bcm.edu	37	19	9066259	9066259	+	Missense_Mutation	SNP	T	T	C	rs17000770	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9066259T>C	ENST00000397910.4	-	3	21390	c.21187A>G	c.(21187-21189)Act>Gct	p.T7063A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7065	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.T7063A(2)|p.T2696A(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATCTCTGAGTCAAAGTTGAA	0.498													T|||	1758	0.351038	0.388	0.3746	5008	,	,		22181	0.2768		0.3489	False		,,,				2504	0.363				p.T7063A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,3	MUC16	4315	3	3	Substitution - Missense(3)	prostate(3)	c.A21187G						PASS	.	T	ALA/THR	1449,2487		279,891,798	137.0	132.0	133.0		21187	-0.1	0.0	19	dbSNP_123	133	3095,5251		606,1883,1684	yes	missense	MUC16	NM_024690.2	58	885,2774,2482	CC,CT,TT		37.0836,36.814,36.9972	possibly-damaging	7063/14508	9066259	4544,7738	1968	4173	6141	SO:0001583	missense	94025	exon3			TCTGAGTCAAAGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21187A>G	19.37:g.9066259T>C	ENSP00000381008:p.Thr7063Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	156	82	0.525641	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	746	0.3415750915750916	167	0.3394308943089431	133	0.3674033149171271	174	0.3041958041958042	272	0.35883905013192613	t	4.731	0.136008	0.09032	0.36814	0.370836	ENSG00000181143	ENST00000397910	T	0.26223	1.75	2.54	-0.117	0.13551	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	.	.	.	P	0.39424	0.673	P	0.46975	0.533	T	0.45279	-0.9272	8	0.87932	D	0	.	5.3856	0.16216	0.5728:0.0:0.0:0.4272	rs17000770;rs52798269;rs58411266;rs17000770	7063	B5ME49	.	A	7063	ENSP00000381008:T7063A	ENSP00000381008:T7063A	T	-	1	0	MUC16	8927259	0.160000	0.22878	0.001000	0.08648	0.003000	0.03518	1.613000	0.36900	-0.128000	0.11641	0.334000	0.21626	ACT	T|0.643;C|0.357	0.357	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR2S2	56656	hgsc.bcm.edu	37	9	35957355	35957355	+	Silent	SNP	G	G	A	rs2233568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35957355G>A	ENST00000341959.2	-	1	796	c.741C>T	c.(739-741)acC>acT	p.T247T		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	247					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T237T(1)		central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			CGATCACCACGGTGAGGTGGG	0.498													A|||	1722	0.34385	0.4902	0.2968	5008	,	,		24532	0.2986		0.2793	False		,,,				2504	0.2924				p.T247T	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											OR2S2,NS,carcinoma,0,1	OR2S2	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C741T						PASS	.	A		2030,2376	611.7+/-391.8	445,1140,618	100.0	102.0	101.0		741	-3.0	0.6	9	dbSNP_98	101	2836,5764	675.0+/-403.2	508,1820,1972	no	coding-synonymous	OR2S2	NM_019897.2		953,2960,2590	AA,AG,GG		32.9767,46.0735,37.4135		247/320	35957355	4866,8140	2203	4300	6503	SO:0001819	synonymous_variant	56656	exon1			CACCACGGTGAGG	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"""GPCR / Class A : Olfactory receptors"""	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.741C>T	9.37:g.35957355G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_019897	Q2M3L0|Q6IF19|Q96R42	Silent	SNP	ENST00000341959.2	37	CCDS6596.2																																																																																			G|0.634;A|0.366	0.366	strong		0.498	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
FAT2	2196	hgsc.bcm.edu	37	5	150901209	150901209	+	Silent	SNP	G	G	T	rs142359154		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150901209G>T	ENST00000261800.5	-	18	10957	c.10945C>A	c.(10945-10947)Cgg>Agg	p.R3649R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3649					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)			TGCAGGTTCCGCCAGTGGTCA	0.607																																					p.R3649R		Atlas-SNP	.											.	FAT2	465	.	0			c.C10945A						PASS	.						34.0	30.0	32.0					5																	150901209		2203	4299	6502	SO:0001819	synonymous_variant	2196	exon18			GGTTCCGCCAGTG	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.10945C>A	5.37:g.150901209G>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	8.154	0.788009	0.16258	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.71	2.8	0.32819	.	.	.	.	.	T	0.68979	0.3060	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65821	-0.6075	4	.	.	.	.	14.5588	0.68120	0.0:0.0:0.5656:0.4344	.	.	.	.	E	507	.	.	A	-	2	0	FAT2	150881402	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.794000	0.47853	0.264000	0.21851	-0.475000	0.04921	GCG	G|0.999;A|0.001	.	alt		0.607	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
CYP2W1	54905	hgsc.bcm.edu	37	7	1023013	1023013	+	Silent	SNP	C	C	T	rs2272375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1023013C>T	ENST00000308919.7	+	1	179	c.166C>T	c.(166-168)Ctg>Ttg	p.L56L	CYP2W1_ENST00000340150.6_5'UTR	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	56					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GGACCGGTCCCTGATGGAGGT	0.711													C|||	1804	0.360224	0.5098	0.3343	5008	,	,		12799	0.3115		0.2744	False		,,,				2504	0.3149				p.L56L		Atlas-SNP	.											.	CYP2W1	28	.	0			c.C166T						PASS	.	C		1532,2094		347,838,628	11.0	10.0	10.0		166	4.5	0.8	7	dbSNP_100	10	1881,5021		306,1269,1876	no	coding-synonymous	CYP2W1	NM_017781.2		653,2107,2504	TT,TC,CC		27.253,42.2504,32.4183		56/491	1023013	3413,7115	1813	3451	5264	SO:0001819	synonymous_variant	54905	exon1			CGGTCCCTGATGG	AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"""Cytochrome P450s"""	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.166C>T	7.37:g.1023013C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	11	8	0.727273	NM_017781		Silent	SNP	ENST00000308919.7	37	CCDS5319.2																																																																																			C|0.645;T|0.355	0.355	strong		0.711	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781	
MUC2	4583	hgsc.bcm.edu	37	11	1093778	1093778	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093778C>G	ENST00000441003.2	+	30	5624	c.5597C>G	c.(5596-5598)tCt>tGt	p.S1866C	MUC2_ENST00000333592.6_Missense_Mutation_p.S154C|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4228					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)	CGGTCCACCTCTTCCCCTCTC	0.627																																					p.S1862C		Atlas-SNP	.											.	MUC2	614	.	0			c.C5585G						PASS	.						240.0	285.0	270.0					11																	1093778		2162	4255	6417	SO:0001583	missense	4583	exon31			CCACCTCTTCCCC	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.5597C>G	11.37:g.1093778C>G	ENSP00000415183:p.Ser1866Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	4	0.045977	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	8.146	0.786373	0.16189	.	.	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.12984	2.63;3.09	1.81	-0.426	0.12314	.	.	.	.	.	T	0.07503	0.0189	N	0.14661	0.345	0.09310	N	1	P	0.52463	0.953	B	0.43783	0.431	T	0.22487	-1.0215	9	0.59425	D	0.04	.	3.1045	0.06337	0.2592:0.5749:0.0:0.1658	.	1866	E7EUV1	.	C	1866;154	ENSP00000415183:S1866C;ENSP00000331373:S154C	ENSP00000331373:S154C	S	+	2	0	MUC2	1083778	0.000000	0.05858	0.002000	0.10522	0.152000	0.21847	-0.239000	0.08965	-0.281000	0.09141	0.305000	0.20034	TCT	.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR51F1	256892	hgsc.bcm.edu	37	11	4790758	4790758	+	Silent	SNP	G	G	A	rs11033796	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790758G>A	ENST00000380383.1	-	1	410	c.411C>T	c.(409-411)gaC>gaT	p.D137D	OR51F1_ENST00000343430.3_Silent_p.D130D|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, 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)			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)		ACCTCAGAGGGTCACAGATGG	0.418													A|||	1167	0.233027	0.5174	0.2104	5008	,	,		21796	0.0		0.2714	False		,,,				2504	0.0654				p.D130D		Atlas-SNP	.											.	OR51F1	60	.	0			c.C390T						PASS	.	A		2151,2251	595.0+/-388.3	532,1087,582	79.0	80.0	79.0		390	-0.9	0.5	11	dbSNP_120	79	2183,6413	712.0+/-405.9	292,1599,2407	no	coding-synonymous	OR51F1	NM_001004752.1		824,2686,2989	AA,AG,GG		25.3955,48.8642,33.3436		130/313	4790758	4334,8664	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			CAGAGGGTCACAG	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.411C>T	11.37:g.4790758G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	111	62	0.558559	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				G|0.690;A|0.310	0.310	strong		0.418	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
LSG1	55341	hgsc.bcm.edu	37	3	194373833	194373833	+	Silent	SNP	G	G	A	rs66771418|rs386669929|rs1705991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:194373833G>A	ENST00000265245.5	-	8	1112	c.798C>T	c.(796-798)acC>acT	p.T266T		NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	266	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)		GTCCAAACTTGGTTGTGTTGC	0.408													G|||	3176	0.634185	0.3253	0.6297	5008	,	,		22478	0.8651		0.7038	False		,,,				2504	0.7454				p.T266T		Atlas-SNP	.											.	LSG1	38	.	0			c.C798T						PASS	.	G		1763,2643	512.6+/-368.1	376,1011,816	118.0	94.0	102.0		798	-4.3	0.0	3	dbSNP_89	102	5883,2717	675.2+/-403.2	2035,1813,452	no	coding-synonymous	LSG1	NM_018385.2		2411,2824,1268	AA,AG,GG		31.593,40.0136,41.2117		266/659	194373833	7646,5360	2203	4300	6503	SO:0001819	synonymous_variant	55341	exon8			AAACTTGGTTGTG		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.798C>T	3.37:g.194373833G>A		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	247	125	0.506073	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1																																																																																			CA|1.000;|0.000	.	alt		0.408	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	
SLC39A5	283375	hgsc.bcm.edu	37	12	56630444	56630444	+	Missense_Mutation	SNP	G	G	C	rs74812296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56630444G>C	ENST00000266980.4	+	8	1414	c.1121G>C	c.(1120-1122)aGt>aCt	p.S374T	ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_Missense_Mutation_p.S374T|SLC39A5_ENST00000419232.1_3'UTR	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	374					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CAAGGCCACAGTCATGGGCAC	0.627													G|||	34	0.00678914	0.0015	0.0187	5008	,	,		20254	0.0		0.0179	False		,,,				2504	0.001				p.S374T		Atlas-SNP	.											.	SLC39A5	52	.	0			c.G1121C						PASS	.	G	THR/SER,THR/SER	12,4394	16.8+/-37.8	0,12,2191	109.0	96.0	101.0		1121,1121	5.0	1.0	12	dbSNP_131	101	168,8432	78.6+/-141.3	1,166,4133	yes	missense,missense	SLC39A5	NM_001135195.1,NM_173596.2	58,58	1,178,6324	CC,CG,GG		1.9535,0.2724,1.384	probably-damaging,probably-damaging	374/541,374/541	56630444	180,12826	2203	4300	6503	SO:0001583	missense	283375	exon10			GCCACAGTCATGG		CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"""Solute carriers"""	20502	protein-coding gene	gene with protein product		608730	"""solute carrier family 39 (metal ion transporter), member 5"""				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.1121G>C	12.37:g.56630444G>C	ENSP00000266980:p.Ser374Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_173596	B2R808|Q8N6Y3	Missense_Mutation	SNP	ENST00000266980.4	37	CCDS8912.2	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	G	18.19	3.569542	0.65765	0.002724	0.019535	ENSG00000139540	ENST00000454355;ENST00000266980	T;T	0.51071	0.72;0.72	4.96	4.96	0.65561	.	0.188002	0.37393	N	0.002110	T	0.43122	0.1233	M	0.62088	1.915	0.38031	D	0.935152	D	0.69078	0.997	P	0.62885	0.908	T	0.50575	-0.8812	10	0.21540	T	0.41	-0.8511	12.2396	0.54534	0.0:0.2787:0.7213:0.0	.	374	Q6ZMH5	S39A5_HUMAN	T	374	ENSP00000405360:S374T;ENSP00000266980:S374T	ENSP00000266980:S374T	S	+	2	0	SLC39A5	54916711	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	3.606000	0.54095	2.746000	0.94184	0.655000	0.94253	AGT	G|0.987;C|0.013	0.013	strong		0.627	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596	
MAVS	57506	hgsc.bcm.edu	37	20	3843027	3843027	+	Missense_Mutation	SNP	C	C	A	rs7262903	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3843027C>A	ENST00000428216.2	+	5	720	c.592C>A	c.(592-594)Cag>Aag	p.Q198K	MAVS_ENST00000416600.2_Missense_Mutation_p.Q57K|MAVS_ENST00000358134.6_3'UTR	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	198			Q -> K (in dbSNP:rs7262903). {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						GCATCAGGAGCAGGACACAGA	0.567													C|||	779	0.155551	0.2065	0.1052	5008	,	,		17920	0.0952		0.1561	False		,,,				2504	0.184				p.Q198K		Atlas-SNP	.											.	MAVS	34	.	0			c.C592A						PASS	.	C	LYS/GLN,LYS/GLN	825,3581	323.7+/-298.2	69,687,1447	67.0	65.0	66.0		169,592	1.1	0.1	20	dbSNP_116	66	1396,7204	269.7+/-288.6	103,1190,3007	yes	missense,missense	MAVS	NM_001206491.1,NM_020746.4	53,53	172,1877,4454	AA,AC,CC		16.2326,18.7245,17.0767	possibly-damaging,possibly-damaging	57/400,198/541	3843027	2221,10785	2203	4300	6503	SO:0001583	missense	57506	exon5			CAGGAGCAGGACA	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.592C>A	20.37:g.3843027C>A	ENSP00000401980:p.Gln198Lys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	324	0.14835164835164835	108	0.21951219512195122	48	0.13259668508287292	63	0.11013986013986014	105	0.13852242744063326	C	18.21	3.572603	0.65765	0.187245	0.162326	ENSG00000088888	ENST00000416600;ENST00000428216	T;T	0.34667	1.35;2.41	4.16	1.06	0.20224	.	0.850776	0.09996	N	0.729013	T	0.00039	0.0001	L	0.52573	1.65	0.58432	P	1.0000000000287557E-6	D	0.58268	0.982	P	0.55615	0.78	T	0.10847	-1.0612	9	0.08381	T	0.77	-9.8954	4.8663	0.13609	0.3777:0.5204:0.0:0.1019	rs7262903;rs17846372;rs17859409;rs52833926;rs59508677;rs7262903	198	Q7Z434	MAVS_HUMAN	K	57;198	ENSP00000413749:Q57K;ENSP00000401980:Q198K	ENSP00000413749:Q57K	Q	+	1	0	MAVS	3791027	0.953000	0.32496	0.137000	0.22149	0.360000	0.29518	0.217000	0.17603	0.263000	0.21812	0.655000	0.94253	CAG	C|0.840;A|0.160	0.160	strong		0.567	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
BPIFB3	359710	hgsc.bcm.edu	37	20	31656632	31656632	+	Missense_Mutation	SNP	C	C	G	rs6057717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31656632C>G	ENST00000375494.3	+	10	1002	c.1002C>G	c.(1000-1002)caC>caG	p.H334Q		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	334			H -> Q (in dbSNP:rs6057717).		innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGCCCCTGCACCAGCAACTCC	0.562													C|||	2414	0.482029	0.3086	0.4741	5008	,	,		17133	0.7698		0.3837	False		,,,				2504	0.5266				p.H334Q		Atlas-SNP	.											C20orf185,NS,carcinoma,0,1	.	.	1	0			c.C1002G						PASS	.	C	GLN/HIS	1307,3099	442.3+/-346.6	202,903,1098	89.0	66.0	74.0		1002	2.3	0.6	20	dbSNP_114	74	3124,5476	475.9+/-369.2	578,1968,1754	yes	missense	BPIFB3	NM_182658.1	24	780,2871,2852	GG,GC,CC		36.3256,29.6641,34.0689	benign	334/477	31656632	4431,8575	2203	4300	6503	SO:0001583	missense	359710	exon10			CCTGCACCAGCAA	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1002C>G	20.37:g.31656632C>G	ENSP00000364643:p.His334Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	1051	0.48122710622710624	163	0.3313008130081301	160	0.4419889502762431	438	0.7657342657342657	290	0.38258575197889183	C	2.285	-0.363791	0.05103	0.296641	0.363256	ENSG00000186190	ENST00000375494	T	0.08193	3.12	4.25	2.26	0.28386	.	2.005100	0.02461	N	0.086613	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	9.99999999995449E-6	B	0.26635	0.155	B	0.29785	0.107	T	0.28332	-1.0047	9	0.13853	T	0.58	0.2314	6.1232	0.20164	0.0:0.7579:0.0:0.2421	rs6057717;rs6057717	334	P59826	BPIB3_HUMAN	Q	334	ENSP00000364643:H334Q	ENSP00000364643:H334Q	H	+	3	2	BPIFB3	31120293	0.019000	0.18553	0.644000	0.29465	0.068000	0.16541	0.094000	0.15107	0.519000	0.28406	0.591000	0.81541	CAC	C|0.625;G|0.375	0.375	strong		0.562	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
SYNE2	23224	hgsc.bcm.edu	37	14	64686125	64686125	+	Silent	SNP	G	G	T	rs35648226	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64686125G>T	ENST00000344113.4	+	109	20000	c.19788G>T	c.(19786-19788)ctG>ctT	p.L6596L	SYNE2_ENST00000441438.2_Silent_p.L127L|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.L3253L|SYNE2_ENST00000358025.3_Silent_p.L6619L|SYNE2_ENST00000394768.2_Silent_p.L2981L|SYNE2_ENST00000555022.1_Silent_p.L474L|SYNE2_ENST00000554805.1_Silent_p.L379L|SYNE2_ENST00000554584.1_Silent_p.L6512L|SYNE2_ENST00000458046.2_Silent_p.L253L|SYNE2_ENST00000357395.3_Silent_p.L2981L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6596					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)		TGAAGAGACTGCAGGTGAGTT	0.473													G|||	1050	0.209665	0.2057	0.1974	5008	,	,		19636	0.1131		0.2744	False		,,,				2504	0.2566				p.L6619L		Atlas-SNP	.											.	SYNE2	577	.	0			c.G19857T						PASS	.	G	,,,	954,3452	360.6+/-315.3	86,782,1335	64.0	60.0	61.0		19788,381,759,19857	-0.1	1.0	14	dbSNP_126	61	2436,6164	402.7+/-347.6	340,1756,2204	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182910.2,NM_182913.2,NM_182914.2	,,,	426,2538,3539	TT,TG,GG		28.3256,21.6523,26.0649	,,,	6596/6886,127/430,253/557,6619/6908	64686125	3390,9616	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon110			GAGACTGCAGGTG	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.19788G>T	14.37:g.64686125G>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			G|0.752;T|0.248	0.248	strong		0.473	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
PRRC2B	84726	hgsc.bcm.edu	37	9	134351655	134351655	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134351655G>A	ENST00000357304.4	+	15	4194	c.4139G>A	c.(4138-4140)aGc>aAc	p.S1380N	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1380							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCCTCCGAAAGCAGCGACTTC	0.662											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1380N		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G4139A						PASS	.						16.0	19.0	18.0					9																	134351655		1954	4134	6088	SO:0001583	missense	84726	exon15			CCGAAAGCAGCGA	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4139G>A	9.37:g.134351655G>A	ENSP00000349856:p.Ser1380Asn	Somatic	78	0	0	1610	WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647371	0.67358	.	.	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.05447	3.44	5.93	5.93	0.95920	.	.	.	.	.	T	0.11537	0.0281	M	0.73962	2.25	0.80722	D	1	P;B;B	0.40970	0.734;0.347;0.236	B;B;B	0.35470	0.203;0.12;0.056	T	0.04565	-1.0942	9	0.33940	T	0.23	.	19.3291	0.94278	0.0:0.0:1.0:0.0	.	676;113;1380	Q5H9R5;Q5JSZ8;Q5JSZ5	.;.;PRC2B_HUMAN	N	1380;676	ENSP00000349856:S1380N	ENSP00000349856:S1380N	S	+	2	0	PRRC2B	133341476	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.145000	0.58065	2.814000	0.96858	0.655000	0.94253	AGC	.	.	none		0.662	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280691A>T	ENST00000368799.1	-	3	6706	c.6671T>A	c.(6670-6672)cTg>cAg	p.L2224Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2224	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGCCCACCAGTGAGTGTCT	0.542									Ichthyosis				-|||	959	0.191494	0.1936	0.1873	5008	,	,		22319	0.3026		0.0706	False		,,,				2504	0.2014				p.L2224Q		Atlas-SNP	.											FLG,NS,malignant_melanoma,+1,1	FLG	900	1	0			c.T6671A						scavenged	.						260.0	255.0	257.0					1																	152280691		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCACCAGTGAGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6671T>A	1.37:g.152280691A>T	ENSP00000357789:p.Leu2224Gln	Somatic	304	1	0.00328947		WXS	Illumina HiSeq	Phase_I	475	35	0.0736842	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	
OR8D1	283159	hgsc.bcm.edu	37	11	124180477	124180477	+	Silent	SNP	G	G	A	rs6590057	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124180477G>A	ENST00000357821.2	-	1	256	c.186C>T	c.(184-186)ttC>ttT	p.F62F		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, 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)			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)		AGCTGCTGAGGAAATAGTACA	0.468													G|||	127	0.0253594	0.0091	0.0375	5008	,	,		21105	0.0		0.0815	False		,,,				2504	0.0072				p.F62F		Atlas-SNP	.											.	OR8D1	53	.	0			c.C186T						PASS	.	G		88,4314	75.2+/-113.4	0,88,2113	87.0	81.0	84.0		186	1.4	0.2	11	dbSNP_116	84	910,7688	202.4+/-245.7	50,810,3439	no	coding-synonymous	OR8D1	NM_001002917.1		50,898,5552	AA,AG,GG		10.5839,1.9991,7.6769		62/309	124180477	998,12002	2201	4299	6500	SO:0001819	synonymous_variant	283159	exon1			GCTGAGGAAATAG	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.186C>T	11.37:g.124180477G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Silent	SNP	ENST00000357821.2	37	CCDS31706.1																																																																																			G|0.939;A|0.061	0.061	strong		0.468	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
MVK	4598	hgsc.bcm.edu	37	12	110019233	110019233	+	Silent	SNP	G	G	A	rs34368092|rs104895310	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:110019233G>A	ENST00000228510.3	+	5	481	c.405G>A	c.(403-405)tcG>tcA	p.S135S	MVK_ENST00000539575.1_Intron|MVK_ENST00000535044.1_Intron|MVK_ENST00000541384.1_Intron|MVK_ENST00000392727.3_Intron|MVK_ENST00000539696.1_Intron	NM_000431.2|NM_001114185.1	NP_000422.1|NP_001107657.1	Q03426	KIME_HUMAN	mevalonate kinase	135			S -> L (in HIDS). {ECO:0000269|PubMed:11313768}.		cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|negative regulation of inflammatory response (GO:0050728)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|mevalonate kinase activity (GO:0004496)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8						TAGTGTGGTCGGAGCTGCCCC	0.662													G|||	161	0.0321486	0.0499	0.0389	5008	,	,		17071	0.0		0.0616	False		,,,				2504	0.0061				p.S135S		Atlas-SNP	.											MVK,colon,carcinoma,+1,1	MVK	42	1	0			c.G405A						PASS	.	G	,	164,4242	109.1+/-147.4	1,162,2040	68.0	69.0	68.0		405,405	-10.3	0.1	12	dbSNP_126	68	506,8094	144.2+/-200.1	18,470,3812	no	coding-synonymous,coding-synonymous	MVK	NM_000431.2,NM_001114185.1	,	19,632,5852	AA,AG,GG		5.8837,3.7222,5.1515	,	135/397,135/397	110019233	670,12336	2203	4300	6503	SO:0001819	synonymous_variant	4598	exon5			GTGGTCGGAGCTG	M88468	CCDS9132.1, CCDS73522.1	12q24	2014-09-17	2008-01-30		ENSG00000110921	ENSG00000110921	2.7.1.36		7530	protein-coding gene	gene with protein product	"""LH receptor mRNA-binding protein"", ""mevalonic aciduria"""	251170	"""mevalonate kinase (mevalonic aciduria)"""			1377680	Standard	XM_005253883		Approved	LRBP, MK	uc001toy.4	Q03426	OTTHUMG00000169256	ENST00000228510.3:c.405G>A	12.37:g.110019233G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_000431		Silent	SNP	ENST00000228510.3	37	CCDS9132.1																																																																																			G|0.950;A|0.050	0.050	strong		0.662	MVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403143.1	NM_000431	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923703	43923703	+	Silent	SNP	C	C	T	rs12185235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43923703C>T	ENST00000329196.5	+	1	1448	c.1431C>T	c.(1429-1431)acC>acT	p.T477T	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	477						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TGGCCTGCACCGTGGCCTATG	0.577													C|||	430	0.0858626	0.0151	0.1571	5008	,	,		22489	0.001		0.2396	False		,,,				2504	0.0603				p.T477T		Atlas-SNP	.											.	.	.	.	0			c.C1431T						PASS	.	C		203,4203	127.0+/-164.0	6,191,2006	120.0	92.0	102.0		1431	-9.2	0.0	17	dbSNP_120	102	1927,6673	340.7+/-323.7	221,1485,2594	no	coding-synonymous	IMP5	NM_175882.2		227,1676,4600	TT,TC,CC		22.407,4.6074,16.3771		477/685	43923703	2130,10876	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			CTGCACCGTGGCC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1431C>T	17.37:g.43923703C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			C|0.853;T|0.147	0.147	strong		0.577	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
ITPR1	3708	hgsc.bcm.edu	37	3	4716811	4716811	+	Silent	SNP	A	A	C	rs2306877	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:4716811A>C	ENST00000443694.2	+	20	2613	c.2613A>C	c.(2611-2613)ctA>ctC	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|ITPR1_ENST00000456211.2_Silent_p.L871L			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	152	71	0.467105	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	
FLG	2312	hgsc.bcm.edu	37	1	152285099	152285099	+	Missense_Mutation	SNP	C	C	T	rs74129461	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152285099C>T	ENST00000368799.1	-	3	2298	c.2263G>A	c.(2263-2265)Gaa>Aaa	p.E755K	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	755	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTGAGTCTTCTGAATGTCCC	0.582									Ichthyosis				-|||	1641	0.327676	0.0681	0.415	5008	,	,		21625	0.6062		0.171	False		,,,				2504	0.4908				p.E755K		Atlas-SNP	.											.	FLG	900	.	0			c.G2263A						PASS	.	C	LYS/GLU	368,4038		15,338,1850	377.0	363.0	368.0		2263	1.0	0.0	1	dbSNP_130	368	1443,7157		124,1195,2981	yes	missense	FLG	NM_002016.1	56	139,1533,4831	TT,TC,CC		16.7791,8.3522,13.9243	probably-damaging	755/4062	152285099	1811,11195	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTCTTCTGAATG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2263G>A	1.37:g.152285099C>T	ENSP00000357789:p.Glu755Lys	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	226	110	0.486726	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	620	0.2838827838827839	41	0.08333333333333333	119	0.3287292817679558	330	0.5769230769230769	130	0.17150395778364116	-	9.927	1.213701	0.22289	0.083522	0.167791	ENSG00000143631	ENST00000368799	T	0.00695	5.83	4.25	1.02	0.19986	.	.	.	.	.	T	0.00412	0.0013	M	0.79123	2.44	0.80722	P	0.0	P	0.43477	0.808	B	0.36418	0.224	T	0.47724	-0.9095	8	0.41790	T	0.15	-3.6243	3.5386	0.07803	0.0:0.5395:0.2134:0.2471	.	755	P20930	FILA_HUMAN	K	755	ENSP00000357789:E755K	ENSP00000357789:E755K	E	-	1	0	FLG	150551723	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.308000	0.08156	0.439000	0.26476	0.479000	0.44913	GAA	C|0.815;T|0.185	0.185	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
AZU1	566	hgsc.bcm.edu	37	19	829568	829568	+	Silent	SNP	C	C	T	rs12460890	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:829568C>T	ENST00000233997.2	+	3	243	c.222C>T	c.(220-222)ccC>ccT	p.P74P		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	74	Hydrophobic.|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)		TCAGGAACCCCGGGGTTAGCA	0.637													C|||	1654	0.330272	0.1838	0.4251	5008	,	,		16386	0.4702		0.2972	False		,,,				2504	0.3507				p.P74P		Atlas-SNP	.											AZU1,NS,carcinoma,0,1	AZU1	31	1	0			c.C222T						PASS	.	C		895,3511	341.2+/-306.6	105,685,1413	79.0	76.0	77.0		222	-2.5	0.0	19	dbSNP_120	77	2494,6106	404.1+/-348.0	365,1764,2171	no	coding-synonymous	AZU1	NM_001700.3		470,2449,3584	TT,TC,CC		29.0,20.3132,26.0572		74/252	829568	3389,9617	2203	4300	6503	SO:0001819	synonymous_variant	566	exon3			GAACCCCGGGGTT	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.222C>T	19.37:g.829568C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	38	25	0.657895	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			C|0.714;T|0.286	0.286	strong		0.637	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
OR4K13	390433	hgsc.bcm.edu	37	14	20502120	20502120	+	Silent	SNP	C	C	T	rs17277032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20502120C>T	ENST00000315693.2	-	1	799	c.798G>A	c.(796-798)tcG>tcA	p.S266S	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TTTTATCTACCGAGTATCTGC	0.383													C|||	1332	0.265974	0.0877	0.3444	5008	,	,		18724	0.255		0.507	False		,,,				2504	0.2147				p.S266S		Atlas-SNP	.											.	OR4K13	68	.	0			c.G798A						PASS	.	C		782,3624		75,632,1496	61.0	61.0	61.0		798	1.0	0.2	14	dbSNP_123	61	4289,4311		1076,2137,1087	no	coding-synonymous	OR4K13	NM_001004714.1		1151,2769,2583	TT,TC,CC		49.8721,17.7485,38.9897		266/305	20502120	5071,7935	2203	4300	6503	SO:0001819	synonymous_variant	390433	exon1			ATCTACCGAGTAT		CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"""GPCR / Class A : Olfactory receptors"""	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.798G>A	14.37:g.20502120C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	43	0.641791	NM_001004714	Q6IF13	Silent	SNP	ENST00000315693.2	37	CCDS32028.1																																																																																			C|0.636;T|0.364	0.364	strong		0.383	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1		
IRF3	3661	hgsc.bcm.edu	37	19	50162909	50162909	+	Missense_Mutation	SNP	C	C	G	rs7251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50162909C>G	ENST00000597198.1	-	8	1661	c.1280G>C	c.(1279-1281)aGc>aCc	p.S427T	IRF3_ENST00000598808.1_Missense_Mutation_p.S281T|IRF3_ENST00000596765.1_Missense_Mutation_p.S154T|IRF3_ENST00000599680.1_5'UTR|IRF3_ENST00000593922.1_Missense_Mutation_p.S281T|IRF3_ENST00000601291.1_Missense_Mutation_p.E432D|IRF3_ENST00000599223.1_Missense_Mutation_p.S300T|IRF3_ENST00000600911.1_Missense_Mutation_p.E388D|IRF3_ENST00000599144.1_Missense_Mutation_p.S281T|IRF3_ENST00000377135.4_Missense_Mutation_p.S300T|IRF3_ENST00000377139.3_Missense_Mutation_p.S427T|IRF3_ENST00000600022.1_Missense_Mutation_p.S154T|IRF3_ENST00000309877.7_Missense_Mutation_p.S427T|IRF3_ENST00000596822.1_Missense_Mutation_p.E115D			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	72	0	0		WXS	Illumina HiSeq	Phase_I	86	86	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	
PIGH	5283	hgsc.bcm.edu	37	14	68060574	68060574	+	Silent	SNP	G	G	A	rs45474396	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:68060574G>A	ENST00000216452.4	-	2	359	c.276C>T	c.(274-276)atC>atT	p.I92I	PIGH_ENST00000560722.1_Silent_p.I92I|PIGH_ENST00000559581.1_Intron	NM_004569.3	NP_004560.1	Q14442	PIGH_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class H	92					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4				all cancers(60;0.000592)|OV - Ovarian serous cystadenocarcinoma(108;0.00395)|BRCA - Breast invasive adenocarcinoma(234;0.00933)		GGGAATCAATGATTAACAGAG	0.418													G|||	313	0.0625	0.0794	0.0648	5008	,	,		20187	0.0288		0.1034	False		,,,				2504	0.0307				p.I92I		Atlas-SNP	.											.	PIGH	13	.	0			c.C276T						PASS	.	G		383,4023	190.5+/-216.4	19,345,1839	84.0	71.0	75.0		276	3.2	1.0	14	dbSNP_127	75	913,7687	202.7+/-245.9	49,815,3436	no	coding-synonymous	PIGH	NM_004569.3		68,1160,5275	AA,AG,GG		10.6163,8.6927,9.9646		92/189	68060574	1296,11710	2203	4300	6503	SO:0001819	synonymous_variant	5283	exon2			ATCAATGATTAAC		CCDS9784.1	14q24.1	2013-02-26	2006-06-28		ENSG00000100564	ENSG00000100564	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	8964	protein-coding gene	gene with protein product	"""phosphatidylinositol N-acetylglucosaminyltransferase subunit"""	600154	"""phosphatidylinositol glycan, class H"""			8204896	Standard	NM_004569		Approved	GPI-H	uc001xjr.1	Q14442	OTTHUMG00000171806	ENST00000216452.4:c.276C>T	14.37:g.68060574G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	110	69	0.627273	NM_004569	B2RAA4	Silent	SNP	ENST00000216452.4	37	CCDS9784.1																																																																																			G|0.905;A|0.095	0.095	strong		0.418	PIGH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000415189.2	NM_004569	
DNAH12	201625	hgsc.bcm.edu	37	3	57494915	57494915	+	Missense_Mutation	SNP	G	G	T	rs115576589	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:57494915G>T	ENST00000351747.2	-	6	674	c.494C>A	c.(493-495)cCa>cAa	p.P165Q	DNAH12_ENST00000389536.4_Missense_Mutation_p.P165Q|DNAH12_ENST00000311202.6_Missense_Mutation_p.P165Q	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	165	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						CGATTTAACTGGTGGTTTCAC	0.313													G|||	23	0.00459265	0.0008	0.0115	5008	,	,		17393	0.0		0.0139	False		,,,				2504	0.0				p.P165Q		Atlas-SNP	.											.	DNAH12	182	.	0			c.C494A						PASS	.	G	GLN/PRO,GLN/PRO	12,4394	19.1+/-41.9	0,12,2191	83.0	85.0	84.0		494,494	2.7	0.8	3	dbSNP_132	84	109,8489	59.5+/-121.1	0,109,4190	yes	missense,missense	DNAH12	NM_178504.4,NM_198564.3	76,76	0,121,6381	TT,TG,GG		1.2677,0.2724,0.9305	probably-damaging,probably-damaging	165/3093,165/458	57494915	121,12883	2203	4299	6502	SO:0001583	missense	201625	exon6			TTAACTGGTGGTT	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.494C>A	3.37:g.57494915G>T	ENSP00000295937:p.Pro165Gln	Somatic	443	0	0		WXS	Illumina HiSeq	Phase_I	376	186	0.494681	NM_198564	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		19	0.0086996336996337	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	12	0.0158311345646438	G	7.794	0.712208	0.15306	0.002724	0.012677	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	T;T;T;T	0.20598	2.21;2.06;3.67;3.12	5.68	2.65	0.31530	.	0.476524	0.18836	N	0.129836	T	0.08935	0.0221	L	0.51422	1.61	0.09310	N	1	B;B	0.27559	0.181;0.047	B;B	0.24701	0.055;0.01	T	0.14035	-1.0487	10	0.24483	T	0.36	.	9.9707	0.41752	0.0:0.1115:0.3122:0.5764	.	165;165	Q6ZR08-4;Q6ZR08	.;DYH12_HUMAN	Q	165	ENSP00000295937:P165Q;ENSP00000418137:P165Q;ENSP00000374187:P165Q;ENSP00000312554:P165Q	ENSP00000312554:P165Q	P	-	2	0	DNAH12	57469955	0.055000	0.20627	0.754000	0.31244	0.998000	0.95712	0.763000	0.26517	0.706000	0.31912	0.585000	0.79938	CCA	G|0.990;T|0.010	0.010	strong		0.313	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
ARL17B	100506084	hgsc.bcm.edu	37	17	44430254	44430254	+	Missense_Mutation	SNP	G	G	C	rs35595570	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44430254G>C	ENST00000450673.3	-	3	296	c.191C>G	c.(190-192)gCt>gGt	p.A64G	ARL17B_ENST00000434041.2_Missense_Mutation_p.A64G|ARL17B_ENST00000575698.1_Missense_Mutation_p.A64G|ARL17B_ENST00000575960.1_Missense_Mutation_p.A64G|ARL17B_ENST00000571246.1_Missense_Mutation_p.A64G|ARL17B_ENST00000570618.1_Missense_Mutation_p.A64G	NM_001039083.3	NP_001034172.3	Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	64					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)	p.A64G(1)		pancreas(1)	1						ATCCCAGACAGCGAAGGTGTT	0.378																																					p.A64G		Atlas-SNP	.											ARL17B,NS,other,0,1	ARL17B	3	1	1	Substitution - Missense(1)	pancreas(1)	c.C191G						scavenged	.						3.0	3.0	3.0					17																	44430254		1275	3002	4277	SO:0001583	missense	100506084	exon3			CAGACAGCGAAGG	AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	32387	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 17"""	ARL17			Standard	NM_001039083		Approved			Q8IVW1	OTTHUMG00000178031	ENST00000450673.3:c.191C>G	17.37:g.44430254G>C	ENSP00000404247:p.Ala64Gly	Somatic	470	1	0.00212766		WXS	Illumina HiSeq	Phase_I	936	188	0.200855	NM_001039083	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	Missense_Mutation	SNP	ENST00000450673.3	37	CCDS58557.1	.	.	.	.	.	.	.	.	.	.	g	4.858	0.159467	0.09236	.	.	ENSG00000228696	ENST00000434041;ENST00000450673	T;T	0.63744	-0.06;-0.06	2.89	2.89	0.33648	.	.	.	.	.	T	0.51736	0.1692	.	.	.	0.29739	N	0.837233	B;B;B	0.31817	0.164;0.054;0.341	B;B;B	0.31686	0.134;0.038;0.08	T	0.55768	-0.8089	8	0.52906	T	0.07	.	11.9465	0.52930	0.0:0.0:1.0:0.0	.	64;64;64	Q8IVW1;Q8IVW1-2;F8VZA5	ARL17_HUMAN;.;.	G	64	ENSP00000391751:A64G;ENSP00000404247:A64G	ENSP00000391751:A64G	A	-	2	0	ARL17B	41786010	1.000000	0.71417	0.999000	0.59377	0.006000	0.05464	8.736000	0.91554	1.898000	0.54952	0.393000	0.25936	GCT	G|0.905;C|0.095	0.095	strong		0.378	ARL17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440297.1	NM_001039083	
KLHL12	59349	hgsc.bcm.edu	37	1	202888947	202888947	+	Silent	SNP	T	T	C	rs3182429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:202888947T>C	ENST00000367261.3	-	3	503	c.285A>G	c.(283-285)acA>acG	p.T95T	KLHL12_ENST00000435533.3_Silent_p.T133T	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	95	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			TCACATGTACTGTTTCTGTGT	0.398													T|||	1461	0.291733	0.0681	0.3271	5008	,	,		18036	0.5208		0.2326	False		,,,				2504	0.3937				p.T95T		Atlas-SNP	.											.	KLHL12	50	.	0			c.A285G						PASS	.	T		508,3898	233.0+/-246.3	35,438,1730	96.0	85.0	88.0		285	-6.0	0.5	1	dbSNP_105	88	1950,6650	344.7+/-325.5	234,1482,2584	no	coding-synonymous	KLHL12	NM_021633.2		269,1920,4314	CC,CT,TT		22.6744,11.5297,18.899		95/569	202888947	2458,10548	2203	4300	6503	SO:0001819	synonymous_variant	59349	exon3			ATGTACTGTTTCT	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"""Kelch-like"", ""BTB/POZ domain containing"""	19360	protein-coding gene	gene with protein product		614522	"""kelch-like 12 (Drosophila)"""			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.285A>G	1.37:g.202888947T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	188	77	0.409574	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	37	CCDS1429.1																																																																																			T|0.778;C|0.222	0.222	strong		0.398	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633	
MYBPC1	4604	hgsc.bcm.edu	37	12	102069077	102069077	+	Silent	SNP	A	A	G	rs764291	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102069077A>G	ENST00000550270.1	+	25	2796	c.2796A>G	c.(2794-2796)ccA>ccG	p.P932P	MYBPC1_ENST00000553190.1_Silent_p.P914P|MYBPC1_ENST00000441232.1_Silent_p.P932P|MYBPC1_ENST00000549145.1_Silent_p.P945P|MYBPC1_ENST00000547405.1_Silent_p.P888P|MYBPC1_ENST00000545503.2_Silent_p.P914P|MYBPC1_ENST00000547509.1_Silent_p.P900P|MYBPC1_ENST00000361466.2_Silent_p.P939P|MYBPC1_ENST00000452455.2_Silent_p.P932P|MYBPC1_ENST00000541119.1_Silent_p.P902P|MYBPC1_ENST00000536007.1_Silent_p.P895P|MYBPC1_ENST00000551300.1_Silent_p.P815P|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000392934.3_Silent_p.P901P|MYBPC1_ENST00000360610.2_Silent_p.P932P|MYBPC1_ENST00000361685.2_Silent_p.P939P			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	932					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						TAGACCGTCCAGGTCCACCCC	0.448													A|||	719	0.14357	0.0416	0.1297	5008	,	,		23895	0.1091		0.2525	False		,,,				2504	0.2147				p.P939P		Atlas-SNP	.											.	MYBPC1	235	.	0			c.A2817G						PASS	.	A	,,,	363,4043	185.3+/-212.5	15,333,1855	95.0	79.0	84.0		2817,2817,2796,2742	-11.5	0.9	12	dbSNP_86	84	2428,6172	401.6+/-347.2	330,1768,2202	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYBPC1	NM_002465.2,NM_206819.1,NM_206820.1,NM_206821.1	,,,	345,2101,4057	GG,GA,AA		28.2326,8.2388,21.4593	,,,	939/1172,939/1149,932/1142,914/1124	102069077	2791,10215	2203	4300	6503	SO:0001819	synonymous_variant	4604	exon26			CCGTCCAGGTCCA		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.2796A>G	12.37:g.102069077A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Silent	SNP	ENST00000550270.1	37	CCDS9085.1																																																																																			A|0.807;G|0.193	0.193	strong		0.448	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
TLDC1	57707	hgsc.bcm.edu	37	16	84516204	84516204	+	Silent	SNP	G	G	A	rs62640938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:84516204G>A	ENST00000343629.6	-	6	1253	c.1071C>T	c.(1069-1071)aaC>aaT	p.N357N	TLDC1_ENST00000535580.1_Silent_p.N330N	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	357	TLD.					lysosomal membrane (GO:0005765)											TCACCAGTCCGTTCGGGATCG	0.597													g|||	40	0.00798722	0.0	0.0202	5008	,	,		19775	0.0		0.0258	False		,,,				2504	0.0				p.N357N		Atlas-SNP	.											.	KIAA1609	39	.	0			c.C1071T						PASS	.	G		20,4380	27.2+/-55.0	0,20,2180	173.0	143.0	153.0		1071	-10.7	0.0	16	dbSNP_129	153	248,8352	99.3+/-160.8	6,236,4058	no	coding-synonymous	KIAA1609	NM_020947.3		6,256,6238	AA,AG,GG		2.8837,0.4545,2.0615		357/457	84516204	268,12732	2200	4300	6500	SO:0001819	synonymous_variant	57707	exon6			CAGTCCGTTCGGG	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.1071C>T	16.37:g.84516204G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	160	84	0.525	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Silent	SNP	ENST00000343629.6	37	CCDS32498.1																																																																																			G|0.981;A|0.019	0.019	strong		0.597	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
FAM228A	653140	hgsc.bcm.edu	37	2	24413298	24413298	+	Missense_Mutation	SNP	A	A	G	rs2288073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:24413298A>G	ENST00000295150.3	+	6	505	c.419A>G	c.(418-420)tAt>tGt	p.Y140C	RP11-507M3.1_ENST00000584973.1_3'UTR	NM_001040710.1	NP_001035800.1	Q86W67	F228A_HUMAN	family with sequence similarity 228, member A	140			Y -> C (in dbSNP:rs2288073).														AAGCTCATCTATGCAGACAAG	0.408													G|||	1073	0.214257	0.1437	0.147	5008	,	,		21745	0.1478		0.3131	False		,,,				2504	0.3241				p.Y140C		Atlas-SNP	.											C2orf84,NS,carcinoma,+1,1	.	.	1	0			c.A419G						PASS	.	G	CYS/TYR	607,3115		49,509,1303	32.0	32.0	32.0		419	-1.3	0.0	2	dbSNP_100	32	2376,5798		354,1668,2065	yes	missense	C2orf84	NM_001040710.1	194	403,2177,3368	GG,GA,AA		29.0678,16.3084,25.0757	benign	140/207	24413298	2983,8913	1861	4087	5948	SO:0001583	missense	653140	exon6			TCATCTATGCAGA		CCDS42659.1	2p23.3	2012-07-04	2012-07-04	2012-07-04	ENSG00000186453	ENSG00000186453			34418	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 84"""	C2orf84			Standard	NM_001040710		Approved	FLJ30851	uc002rfc.3	Q86W67	OTTHUMG00000151903	ENST00000295150.3:c.419A>G	2.37:g.24413298A>G	ENSP00000295150:p.Tyr140Cys	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	216	215	0.99537	NM_001040710		Missense_Mutation	SNP	ENST00000295150.3	37	CCDS42659.1	473|473	0.21657509157509158|0.21657509157509158	83|83	0.16869918699186992|0.16869918699186992	61|61	0.1685082872928177|0.1685082872928177	82|82	0.14335664335664336|0.14335664335664336	247|247	0.3258575197889182|0.3258575197889182	G|G	0.008|0.008	-1.917424|-1.917424	0.00503|0.00503	0.163084|0.163084	0.290678|0.290678	ENSG00000186453|ENSG00000186453	ENST00000432434|ENST00000295150;ENST00000415196	.|T;T	.|0.48201	.|0.82;0.87	3.64|3.64	-1.3|-1.3	0.09259|0.09259	.|.	.|0.177091	.|0.27851	.|N	.|0.017599	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11927|0.11927	0.2|0.2	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.35351|0.35351	-0.9792|-0.9792	4|9	.|0.56958	.|D	.|0.05	-1.3245|-1.3245	4.2867|4.2867	0.10858|0.10858	0.5053:0.0:0.3279:0.1668|0.5053:0.0:0.3279:0.1668	rs2288073;rs11545100;rs57437922;rs2288073|rs2288073;rs11545100;rs57437922;rs2288073	.|140	.|Q86W67	.|CB084_HUMAN	V|C	178|140;41	.|ENSP00000295150:Y140C;ENSP00000416595:Y41C	.|ENSP00000295150:Y140C	M|Y	+|+	1|2	0|0	C2orf84|C2orf84	24266802|24266802	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.018000|0.018000	0.09664|0.09664	-0.668000|-0.668000	0.05268|0.05268	-0.616000|-0.616000	0.05671|0.05671	-0.755000|-0.755000	0.03482|0.03482	ATG|TAT	A|0.776;G|0.224	0.224	strong		0.408	FAM228A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324342.1	NM_001040710	
DCSTAMP	81501	hgsc.bcm.edu	37	8	105368408	105368408	+	Silent	SNP	A	A	G	rs4734780	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:105368408A>G	ENST00000297581.2	+	4	1444	c.1395A>G	c.(1393-1395)gcA>gcG	p.A465A	DCSTAMP_ENST00000520080.1_3'UTR|DCSTAMP_ENST00000517991.1_3'UTR|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	465					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											TGGACATGGCAAGTGCAGACA	0.458													A|||	397	0.0792732	0.1331	0.0317	5008	,	,		20678	0.0744		0.0467	False		,,,				2504	0.0787				p.A465A		Atlas-SNP	.											.	.	.	.	0			c.A1395G						PASS	.	A		492,3914	228.8+/-243.5	27,438,1738	100.0	95.0	97.0		1395	-4.5	0.0	8	dbSNP_111	97	413,8187	129.5+/-187.6	13,387,3900	no	coding-synonymous	TM7SF4	NM_030788.2		40,825,5638	GG,GA,AA		4.8023,11.1666,6.9583		465/471	105368408	905,12101	2203	4300	6503	SO:0001819	synonymous_variant	81501	exon4			CATGGCAAGTGCA	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"""Dendritic cells (DC)-specific transmembrane protein"", ""IL-Four INDuced"""	605933	"""transmembrane 7 superfamily member 4"""	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.1395A>G	8.37:g.105368408A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_030788	B7ZVW2|E7ESG0|Q2M2D5	Silent	SNP	ENST00000297581.2	37	CCDS6301.1																																																																																			A|0.929;G|0.071	0.071	strong		0.458	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
ALPP	250	hgsc.bcm.edu	37	2	233245139	233245139	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:233245139T>C	ENST00000392027.2	+	7	1071	c.802T>C	c.(802-804)Tat>Cat	p.Y268H	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	268					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GGGTGCCCGGTATGTGTGGAA	0.667																																					p.Y268H		Atlas-SNP	.											ALPP,colon,carcinoma,-2,1	ALPP	53	1	0			c.T802C						scavenged	.						82.0	94.0	90.0					2																	233245139		2203	4300	6503	SO:0001583	missense	250	exon7			GCCCGGTATGTGT	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.802T>C	2.37:g.233245139T>C	ENSP00000375881:p.Tyr268His	Somatic	491	1	0.00203666		WXS	Illumina HiSeq	Phase_I	402	5	0.0124378	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	.	17.28	3.348946	0.61183	.	.	ENSG00000163283	ENST00000392027	D	0.97731	-4.51	3.2	3.2	0.36748	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	M	0.91972	3.26	0.53688	D	0.999978	D	0.76494	0.999	D	0.79784	0.993	D	0.99066	1.0832	10	0.87932	D	0	.	10.2922	0.43603	0.0:0.0:0.0:1.0	.	268	P05187	PPB1_HUMAN	H	268	ENSP00000375881:Y268H	ENSP00000375881:Y268H	Y	+	1	0	ALPP	232953383	1.000000	0.71417	0.091000	0.20842	0.091000	0.18340	6.285000	0.72658	1.212000	0.43366	0.254000	0.18369	TAT	.	.	none		0.667	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
CHD5	26038	hgsc.bcm.edu	37	1	6190315	6190315	+	Silent	SNP	C	C	T	rs17029184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:6190315C>T	ENST00000262450.3	-	22	3435	c.3336G>A	c.(3334-3336)gcG>gcA	p.A1112A	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)		TGACAGTGTCCGCCGTGGCCA	0.642													C|||	525	0.104832	0.0038	0.0375	5008	,	,		16076	0.3433		0.0785	False		,,,				2504	0.0706				p.A1112A		Atlas-SNP	.											.	CHD5	267	.	0			c.G3336A						PASS	.	C		90,4316	74.7+/-112.8	0,90,2113	102.0	91.0	95.0		3336	-9.6	0.0	1	dbSNP_123	95	698,7902	173.0+/-223.6	29,640,3631	no	coding-synonymous	CHD5	NM_015557.2		29,730,5744	TT,TC,CC		8.1163,2.0427,6.0587		1112/1955	6190315	788,12218	2203	4300	6503	SO:0001819	synonymous_variant	26038	exon22			AGTGTCCGCCGTG	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.3336G>A	1.37:g.6190315C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			C|0.905;T|0.095	0.095	strong		0.642	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
DOK2	9046	hgsc.bcm.edu	37	8	21766900	21766900	+	Silent	SNP	G	G	A	rs17853066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:21766900G>A	ENST00000276420.4	-	5	1419	c.1161C>T	c.(1159-1161)gcC>gcT	p.A387A	DOK2_ENST00000544659.1_Silent_p.A233A	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	387					blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		AATCCTGCCCGGCTGGCTGGA	0.602													G|||	719	0.14357	0.0991	0.0735	5008	,	,		17901	0.3274		0.1282	False		,,,				2504	0.0798				p.A387A		Atlas-SNP	.											.	DOK2	51	.	0			c.C1161T						PASS	.	G		421,3983	197.1+/-221.3	14,393,1795	49.0	52.0	51.0		1161	-8.2	0.0	8	dbSNP_123	51	976,7616	199.6+/-243.6	66,844,3386	no	coding-synonymous	DOK2	NM_003974.2		80,1237,5181	AA,AG,GG		11.3594,9.5595,10.7495		387/413	21766900	1397,11599	2202	4296	6498	SO:0001819	synonymous_variant	9046	exon5			CTGCCCGGCTGGC	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"""docking protein 2, 56kD"""			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.1161C>T	8.37:g.21766900G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_003974	Q8N5A4	Silent	SNP	ENST00000276420.4	37	CCDS6016.1																																																																																			G|0.869;A|0.131	0.131	strong		0.602	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974	
LRP1	4035	hgsc.bcm.edu	37	12	57569478	57569478	+	Silent	SNP	C	C	T	rs12814239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57569478C>T	ENST00000243077.3	+	23	4249	c.3783C>T	c.(3781-3783)tgC>tgT	p.C1261C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1261	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GCGAGAGCTGCCGCAGCCTGG	0.617											OREG0021937	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	130	0.0259585	0.0023	0.0317	5008	,	,		19081	0.0		0.0606	False		,,,				2504	0.045				p.C1261C		Atlas-SNP	.											.	LRP1	428	.	0			c.C3783T						PASS	.	C		54,4352	54.9+/-90.9	0,54,2149	89.0	91.0	90.0		3783	4.0	1.0	12	dbSNP_121	90	570,8030	153.7+/-208.1	20,530,3750	no	coding-synonymous	LRP1	NM_002332.2		20,584,5899	TT,TC,CC		6.6279,1.2256,4.7978		1261/4545	57569478	624,12382	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon23			GAGCTGCCGCAGC	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.3783C>T	12.37:g.57569478C>T		Somatic	95	0	0	1024	WXS	Illumina HiSeq	Phase_I	78	30	0.384615	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.956;T|0.044	0.044	strong		0.617	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
INPP1	3628	hgsc.bcm.edu	37	2	191231503	191231503	+	Silent	SNP	G	G	A	rs4940|rs10931450	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:191231503G>A	ENST00000322522.4	+	4	804	c.348G>A	c.(346-348)gtG>gtA	p.V116V	INPP1_ENST00000541441.1_Silent_p.V116V|INPP1_ENST00000392329.2_Silent_p.V116V	NM_002194.3	NP_002185.1	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase	116					dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-1,3,4-trisphosphate 1-phosphatase activity (GO:0052829)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|metal ion binding (GO:0046872)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)			GTAACAAGGTGGCATCTGAAG	0.463													G|||	1385	0.276558	0.2201	0.2233	5008	,	,		19977	0.4623		0.2316	False		,,,				2504	0.2454				p.V116V	Melanoma(130;184 1743 2185 19805 38428)	Atlas-SNP	.											.	INPP1	29	.	0			c.G348A						PASS	.	G	,	968,3438	367.1+/-318.1	110,748,1345	175.0	167.0	169.0		348,348	0.9	0.1	2	dbSNP_120	169	2050,6550	354.6+/-329.6	236,1578,2486	no	coding-synonymous,coding-synonymous	INPP1	NM_001128928.1,NM_002194.3	,	346,2326,3831	AA,AG,GG		23.8372,21.97,23.2047	,	116/400,116/400	191231503	3018,9988	2203	4300	6503	SO:0001819	synonymous_variant	3628	exon4			CAAGGTGGCATCT		CCDS2305.1	2q32	2008-02-07			ENSG00000151689	ENSG00000151689	3.1.3.57		6071	protein-coding gene	gene with protein product		147263				8390685	Standard	NM_002194		Approved		uc010fsb.3	P49441	OTTHUMG00000132672	ENST00000322522.4:c.348G>A	2.37:g.191231503G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	84	33	0.392857	NM_002194		Silent	SNP	ENST00000322522.4	37	CCDS2305.1																																																																																			G|0.733;A|0.267	0.267	strong		0.463	INPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255932.2		
HHLA2	11148	hgsc.bcm.edu	37	3	108095365	108095365	+	Silent	SNP	G	G	A	rs2124736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:108095365G>A	ENST00000357759.5	+	9	1599	c.1185G>A	c.(1183-1185)gaG>gaA	p.E395E	HHLA2_ENST00000467761.1_Silent_p.E395E|HHLA2_ENST00000491820.1_Silent_p.E378E|HHLA2_ENST00000467562.1_Silent_p.E331E|HHLA2_ENST00000489514.2_Silent_p.E395E	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	395					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						CTCCTGGTGAGCGCTGTCCCA	0.363													G|||	449	0.0896565	0.0136	0.1527	5008	,	,		19715	0.001		0.2326	False		,,,				2504	0.092				p.E395E		Atlas-SNP	.											.	HHLA2	95	.	0			c.G1185A						PASS	.	G		212,3540		5,202,1669	82.0	84.0	83.0		1185	-2.5	0.0	3	dbSNP_96	83	1901,6307		236,1429,2439	no	coding-synonymous	HHLA2	NM_007072.2		241,1631,4108	AA,AG,GG		23.1603,5.6503,17.6672		395/415	108095365	2113,9847	1876	4104	5980	SO:0001819	synonymous_variant	11148	exon9			TGGTGAGCGCTGT	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1185G>A	3.37:g.108095365G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Silent	SNP	ENST00000357759.5	37	CCDS46883.1	256	0.11721611721611722	7	0.014227642276422764	64	0.17679558011049723	0	0.0	185	0.24406332453825857	G	1.601	-0.526518	0.04141	0.056503	0.231603	ENSG00000114455	ENST00000482099	.	.	.	3.44	-2.48	0.06423	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34601	-0.9822	3	.	.	.	-15.1402	1.081	0.01643	0.2254:0.3121:0.3019:0.1606	rs2124736;rs17373363;rs2124736	.	.	.	T	298	.	.	A	+	1	0	HHLA2	109578055	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.141000	0.10327	-0.545000	0.06224	0.561000	0.74099	GCG	G|0.881;A|0.119	0.119	strong		0.363	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
CAMTA1	23261	hgsc.bcm.edu	37	1	7723957	7723957	+	Silent	SNP	G	G	A	rs12128526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:7723957G>A	ENST00000303635.7	+	9	1557	c.1350G>A	c.(1348-1350)tcG>tcA	p.S450S	CAMTA1_ENST00000439411.2_Silent_p.S450S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	450					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CGGGCAGCTCGGAGAGCCTGT	0.627			T	WWTR1	epitheliod hemangioendothelioma								G|||	2004	0.40016	0.3873	0.4539	5008	,	,		18084	0.3313		0.4304	False		,,,				2504	0.4192				p.S450S		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G1350A						PASS	.	G		1648,2758	504.4+/-365.8	297,1054,852	73.0	77.0	76.0		1350	-2.1	1.0	1	dbSNP_120	76	3944,4656	549.5+/-385.6	906,2132,1262	no	coding-synonymous	CAMTA1	NM_015215.2		1203,3186,2114	AA,AG,GG		45.8605,37.4035,42.9955		450/1674	7723957	5592,7414	2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			CAGCTCGGAGAGC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.1350G>A	1.37:g.7723957G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1																																																																																			G|0.581;A|0.419	0.419	strong		0.627	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
KRT37	8688	hgsc.bcm.edu	37	17	39578424	39578424	+	Missense_Mutation	SNP	G	G	T	rs2071607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39578424G>T	ENST00000225550.3	-	5	916	c.917C>A	c.(916-918)gCc>gAc	p.A306D	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	306	Coil 2.|Rod.		A -> D (in dbSNP:rs2071607).			extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				GCAGGACATGGCCTGCAGGCT	0.617													G|||	864	0.172524	0.0348	0.1268	5008	,	,		21797	0.3224		0.1759	False		,,,				2504	0.2331				p.A306D		Atlas-SNP	.											.	KRT37	61	.	0			c.C917A						PASS	.	G	ASP/ALA	245,4161		8,229,1966	140.0	106.0	118.0		917	-1.3	0.8	17	dbSNP_96	118	1520,7080		120,1280,2900	no	missense	KRT37	NM_003770.4	126	128,1509,4866	TT,TG,GG		17.6744,5.5606,13.5707	benign	306/450	39578424	1765,11241	2203	4300	6503	SO:0001583	missense	8688	exon5			GACATGGCCTGCA	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.917C>A	17.37:g.39578424G>T	ENSP00000225550:p.Ala306Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	381	0.17445054945054944	21	0.042682926829268296	48	0.13259668508287292	178	0.3111888111888112	134	0.17678100263852242	.	13.24	2.177273	0.38413	0.055606	0.176744	ENSG00000108417	ENST00000225550	D	0.90385	-2.66	4.83	-1.33	0.09172	Filament (1);	0.509712	0.16338	N	0.218833	T	0.00012	0.0000	M	0.62723	1.935	0.58432	P	4.000000000004E-6	B	0.13145	0.007	B	0.16289	0.015	T	0.15263	-1.0443	9	0.54805	T	0.06	.	3.5228	0.07748	0.3042:0.0:0.2986:0.3972	rs2071607	306	O76014	KRT37_HUMAN	D	306	ENSP00000225550:A306D	ENSP00000225550:A306D	A	-	2	0	KRT37	36831950	0.000000	0.05858	0.752000	0.31206	0.999000	0.98932	0.732000	0.26072	0.077000	0.16863	0.655000	0.94253	GCC	G|0.854;T|0.146	0.146	strong		0.617	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
MST1L	11223	hgsc.bcm.edu	37	1	17084066	17084066	+	RNA	SNP	G	G	A	rs201206414		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	1131	2	0.00176835		WXS	Illumina HiSeq	Phase_I	1252	81	0.0646965	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	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318912	21318912	+	Silent	SNP	C	C	A	rs35011501	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:21318912C>A	ENST00000583088.1	+	3	1153	c.258C>A	c.(256-258)atC>atA	p.I86I	KCNJ12_ENST00000331718.5_Silent_p.I86I	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	86					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TGCTGCTCATCTTCTCGCTGG	0.612										Prostate(3;0.18)																											p.I86I		Atlas-SNP	.											.	.	.	.	0			c.C258A						PASS	.						190.0	116.0	141.0					17																	21318912		2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			GCTCATCTTCTCG	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.258C>A	17.37:g.21318912C>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	258	41	0.158915	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			C|0.733;A|0.267	0.267	strong		0.612	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
TMEM44	93109	hgsc.bcm.edu	37	3	194349178	194349178	+	Silent	SNP	C	C	T	rs1563970	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:194349178C>T	ENST00000392432.2	-	2	403	c.198G>A	c.(196-198)gcG>gcA	p.A66A	TMEM44_ENST00000347147.4_Silent_p.A66A|TMEM44_ENST00000273580.7_Silent_p.A66A|TMEM44_ENST00000330115.3_De_novo_Start_OutOfFrame|TMEM44_ENST00000473092.1_Silent_p.A66A|TMEM44_ENST00000381975.3_Silent_p.A66A	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	66						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)		GGAGGCAGCACGCAGCACACA	0.582													C|||	1732	0.345847	0.2489	0.304	5008	,	,		19416	0.4385		0.325	False		,,,				2504	0.4325				p.A66A		Atlas-SNP	.											TMEM44_ENST00000392432,colon,carcinoma,0,2	TMEM44	42	2	0			c.G198A						PASS	.	C	,,,	1111,3295	397.2+/-330.3	148,815,1240	77.0	68.0	71.0		198,198,198,198	-10.5	0.2	3	dbSNP_88	71	2918,5682	450.2+/-362.3	504,1910,1886	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	,,,	652,2725,3126	TT,TC,CC		33.9302,25.2156,30.978	,,,	66/429,66/476,66/397,66/439	194349178	4029,8977	2203	4300	6503	SO:0001819	synonymous_variant	93109	exon2			GCAGCACGCAGCA	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.198G>A	3.37:g.194349178C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Silent	SNP	ENST00000392432.2	37	CCDS54699.1																																																																																			C|0.674;T|0.326	0.326	strong		0.582	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
SDC3	9672	hgsc.bcm.edu	37	1	31347399	31347399	+	Missense_Mutation	SNP	C	C	T	rs4949184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:31347399C>T	ENST00000339394.6	-	4	1081	c.907G>A	c.(907-909)Gat>Aat	p.D303N	SDC3_ENST00000336798.7_Missense_Mutation_p.D245N|SDC3_ENST00000471567.1_5'Flank	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	303			D -> N (in dbSNP:rs4949184). {ECO:0000269|PubMed:11527150}.		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)		TCTGGCTCATCCCGGATTGTG	0.587													C|||	1174	0.234425	0.3782	0.1628	5008	,	,		18096	0.0665		0.1799	False		,,,				2504	0.32				p.D303N		Atlas-SNP	.											.	SDC3	45	.	0			c.G907A						PASS	.	C	ASN/ASP	1367,3039	454.0+/-350.5	217,933,1053	108.0	106.0	107.0		907	4.7	1.0	1	dbSNP_111	107	1565,7035	292.4+/-300.8	137,1291,2872	yes	missense	SDC3	NM_014654.3	23	354,2224,3925	TT,TC,CC		18.1977,31.0259,22.5434	probably-damaging	303/443	31347399	2932,10074	2203	4300	6503	SO:0001583	missense	9672	exon4			GCTCATCCCGGAT	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.907G>A	1.37:g.31347399C>T	ENSP00000344468:p.Asp303Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Missense_Mutation	SNP	ENST00000339394.6	37	CCDS30661.1	385	0.1762820512820513	180	0.36585365853658536	56	0.15469613259668508	24	0.04195804195804196	125	0.16490765171503957	C	19.78	3.890788	0.72524	0.310259	0.181977	ENSG00000162512	ENST00000336798;ENST00000339394	T;T	0.25414	1.81;1.8	4.7	4.7	0.59300	.	0.266144	0.30809	N	0.008833	T	0.00012	0.0000	N	0.12182	0.205	0.48135	P	4.0200000000001346E-4	B;B	0.13594	0.008;0.008	B;B	0.16289	0.015;0.009	T	0.41680	-0.9495	9	0.36615	T	0.2	-1.9576	6.7554	0.23510	0.0:0.8463:0.0:0.1537	rs4949184;rs57147714;rs4949184	303;245	O75056;D3DPN2	SDC3_HUMAN;.	N	245;303	ENSP00000338346:D245N;ENSP00000344468:D303N	ENSP00000338346:D245N	D	-	1	0	SDC3	31119986	0.715000	0.27946	0.967000	0.41034	0.697000	0.40408	3.045000	0.49838	2.454000	0.82982	0.563000	0.77884	GAT	C|0.795;T|0.205	0.205	strong		0.587	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
KRT71	112802	hgsc.bcm.edu	37	12	52946498	52946498	+	Missense_Mutation	SNP	C	C	T	rs665470	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52946498C>T	ENST00000267119.5	-	1	433	c.364G>A	c.(364-366)Gag>Aag	p.E122K		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	122	Head.		E -> K (in dbSNP:rs665470).		hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		TTCTGGATCTCGGGGTCCAGC	0.607													C|||	1017	0.203075	0.3351	0.1556	5008	,	,		18005	0.0208		0.2286	False		,,,				2504	0.2198				p.E122K		Atlas-SNP	.											.	KRT71	70	.	0			c.G364A						PASS	.	C	LYS/GLU	1322,3084	445.5+/-347.7	196,930,1077	107.0	102.0	104.0		364	4.8	1.0	12	dbSNP_83	104	2038,6562	355.1+/-329.8	250,1538,2512	yes	missense	KRT71	NM_033448.2	56	446,2468,3589	TT,TC,CC		23.6977,30.0045,25.8342	benign	122/524	52946498	3360,9646	2203	4300	6503	SO:0001583	missense	112802	exon1			GGATCTCGGGGTC	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.364G>A	12.37:g.52946498C>T	ENSP00000267119:p.Glu122Lys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	186	78	0.419355	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	
VWDE	221806	hgsc.bcm.edu	37	7	12409327	12409327	+	Missense_Mutation	SNP	C	C	T	rs17165910	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	258	0	0		WXS	Illumina HiSeq	Phase_I	260	132	0.507692	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	
MYCBP2	23077	hgsc.bcm.edu	37	13	77738664	77738664	+	Silent	SNP	A	A	G	rs2274547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:77738664A>G	ENST00000544440.2	-	43	6375	c.6358T>C	c.(6358-6360)Ttg>Ctg	p.L2120L	MYCBP2_ENST00000407578.2_Silent_p.L2158L|MYCBP2_ENST00000357337.6_Silent_p.L2120L|MYCBP2_ENST00000360084.5_5'UTR					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	125	0	0		WXS	Illumina HiSeq	Phase_I	95	35	0.368421	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	
RBM33	155435	hgsc.bcm.edu	37	7	155530954	155530954	+	Silent	SNP	T	T	C	rs2178428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	140	0	0		WXS	Illumina HiSeq	Phase_I	158	88	0.556962	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	
CMYA5	202333	hgsc.bcm.edu	37	5	79028726	79028726	+	Missense_Mutation	SNP	A	A	G	rs13158477	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79028726A>G	ENST00000446378.2	+	2	4169	c.4138A>G	c.(4138-4140)Atc>Gtc	p.I1380V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1380			I -> V (in dbSNP:rs13158477).		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)		TTCATCTCTTATCACTCCTGT	0.398													G|||	557	0.111222	0.1172	0.1254	5008	,	,		21072	0.0188		0.164	False		,,,				2504	0.1339				p.I1380V		Atlas-SNP	.											.	CMYA5	643	.	0			c.A4138G						PASS	.	G	VAL/ILE	469,3255		33,403,1426	37.0	36.0	36.0		4138	-0.9	0.0	5	dbSNP_121	36	1285,6907		105,1075,2916	yes	missense	CMYA5	NM_153610.3	29	138,1478,4342	GG,GA,AA		15.686,12.594,14.7197	benign	1380/4070	79028726	1754,10162	1862	4096	5958	SO:0001583	missense	202333	exon2			TCTCTTATCACTC	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.4138A>G	5.37:g.79028726A>G	ENSP00000394770:p.Ile1380Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	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	244	0.11172161172161173	56	0.11382113821138211	50	0.13812154696132597	11	0.019230769230769232	127	0.16754617414248021	G	0.003	-2.531967	0.00145	0.12594	0.15686	ENSG00000164309	ENST00000446378	T	0.03413	3.94	6.17	-0.879	0.10613	.	0.706453	0.12896	N	0.430196	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.42832	-0.9428	9	0.02654	T	1	.	0.3063	0.00280	0.2386:0.2567:0.2478:0.2568	rs13158477;rs17254056;rs60369806;rs13158477	1380	Q8N3K9	CMYA5_HUMAN	V	1380	ENSP00000394770:I1380V	ENSP00000394770:I1380V	I	+	1	0	CMYA5	79064482	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.304000	0.02741	0.054000	0.16065	-0.119000	0.15052	ATC	A|0.895;G|0.105	0.105	strong		0.398	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
FLNB	2317	hgsc.bcm.edu	37	3	58112488	58112488	+	Splice_Site	SNP	C	C	T	rs2362904	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58112488C>T	ENST00000295956.4	+	24	4386	c.4221C>T	c.(4219-4221)ccC>ccT	p.P1407P	FLNB_ENST00000493452.1_Splice_Site_p.P1238P|FLNB_ENST00000357272.4_Splice_Site_p.P1407P|FLNB_ENST00000429972.2_Splice_Site_p.P1407P|FLNB_ENST00000348383.5_Splice_Site_p.P1407P|FLNB_ENST00000358537.3_Splice_Site_p.P1407P|FLNB_ENST00000490882.1_Splice_Site_p.P1407P|FLNB_ENST00000419752.2_Splice_Site_p.P1238P	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1407	Interaction with FBLP1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCCACATCCCCGGTGAGCTAT	0.458													T|||	3248	0.648562	0.7852	0.4942	5008	,	,		19177	0.9712		0.2833	False		,,,				2504	0.6166				p.P1407P		Atlas-SNP	.											.	FLNB	430	.	0			c.C4221T						PASS	.	T	,,,	3123,1283	436.4+/-344.6	1098,927,178	50.0	51.0	50.0		4221,4221,4221,4221	3.5	1.0	3	dbSNP_100	50	2111,6489	715.9+/-406.1	268,1575,2457	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	1366,2502,2635	TT,TC,CC		24.5465,29.1194,40.243	,,,	1407/2634,1407/2592,1407/2579,1407/2603	58112488	5234,7772	2203	4300	6503	SO:0001630	splice_region_variant	2317	exon24			CATCCCCGGTGAG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4222+1C>T	3.37:g.58112488C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			C|0.489;T|0.511	0.511	strong		0.458	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	Silent
TPSD1	23430	hgsc.bcm.edu	37	16	1306971	1306971	+	Missense_Mutation	SNP	A	A	G	rs72775466		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306971A>G	ENST00000211076.3	+	3	576	c.428A>G	c.(427-429)cAc>cGc	p.H143R	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.H136R	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	143	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				ATCTCCAGCCACATCCACACG	0.647																																					p.H143R		Atlas-SNP	.											TPSD1,NS,NS,0,1	TPSD1	47	1	0			c.A428G						PASS	.						49.0	47.0	47.0					16																	1306971		2198	4299	6497	SO:0001583	missense	23430	exon3			CCAGCCACATCCA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.428A>G	16.37:g.1306971A>G	ENSP00000211076:p.His143Arg	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	538	183	0.340149	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	a	0.006	-2.041578	0.00402	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	T;T	0.81330	-1.48;-1.48	2.55	1.26	0.21427	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.828860	0.02995	N	0.147379	T	0.68035	0.2957	N	0.20304	0.555	0.80722	P	0.0	B;B	0.10296	0.003;0.003	B;B	0.14578	0.011;0.011	T	0.55823	-0.8080	9	0.30078	T	0.28	.	5.9116	0.19031	0.767:0.0:0.0:0.233	.	127;143	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	R	136;143	ENSP00000380668:H136R;ENSP00000211076:H143R	ENSP00000211076:H143R	H	+	2	0	TPSD1	1246972	0.000000	0.05858	0.001000	0.08648	0.073000	0.16967	-0.594000	0.05733	1.156000	0.42514	0.155000	0.16302	CAC	.	.	strong		0.647	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
OR10G9	219870	hgsc.bcm.edu	37	11	123893757	123893757	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123893757C>T	ENST00000375024.1	+	1	38	c.38C>T	c.(37-39)aCg>aTg	p.T13M		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	13						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)		TTCATCCTCACGGGCCTTCCC	0.562																																					p.T13M		Atlas-SNP	.											OR10G9,NS,carcinoma,0,2	OR10G9	80	2	0			c.C38T						scavenged	.						175.0	170.0	172.0					11																	123893757		2201	4299	6500	SO:0001583	missense	219870	exon1			TCCTCACGGGCCT	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.38C>T	11.37:g.123893757C>T	ENSP00000364164:p.Thr13Met	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	387	29	0.0749354	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	7.277	0.608309	0.14002	.	.	ENSG00000236981	ENST00000375024	T	0.00421	7.46	3.33	-4.34	0.03666	.	1.118960	0.06817	N	0.791372	T	0.00178	0.0005	N	0.04260	-0.245	0.09310	N	0.999992	B	0.06786	0.001	B	0.04013	0.001	T	0.29640	-1.0005	10	0.40728	T	0.16	.	9.7201	0.40297	0.0:0.2623:0.0:0.7377	.	13	Q8NGN4	O10G9_HUMAN	M	13	ENSP00000364164:T13M	ENSP00000364164:T13M	T	+	2	0	OR10G9	123398967	0.000000	0.05858	0.149000	0.22428	0.069000	0.16628	-0.761000	0.04751	-1.009000	0.03400	-0.766000	0.03442	ACG	.	.	none		0.562	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
PDLIM5	10611	hgsc.bcm.edu	37	4	95561459	95561459	+	Missense_Mutation	SNP	A	A	G	rs7690296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:95561459A>G	ENST00000317968.4	+	9	1277	c.1141A>G	c.(1141-1143)Act>Gct	p.T381A	PDLIM5_ENST00000380176.3_3'UTR|PDLIM5_ENST00000542407.1_Missense_Mutation_p.T259A|PDLIM5_ENST00000437932.1_Missense_Mutation_p.T272A|PDLIM5_ENST00000514743.1_Missense_Mutation_p.T410A	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	381			T -> A (in dbSNP:rs7690296). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.9}.		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)		AAACAGCGCTACTTACTCAGG	0.443													A|||	1941	0.38758	0.1528	0.4265	5008	,	,		15460	0.3998		0.4354	False		,,,				2504	0.6155				p.T410A		Atlas-SNP	.											PDLIM5,colon,carcinoma,-2,1	PDLIM5	76	1	0			c.A1228G						PASS	.	A	ALA/THR,ALA/THR	821,3585	327.5+/-300.1	70,681,1452	79.0	71.0	74.0		814,1141	-11.3	0.0	4	dbSNP_116	74	3630,4970	523.2+/-380.3	762,2106,1432	yes	missense,missense	PDLIM5	NM_001011513.2,NM_006457.3	58,58	832,2787,2884	GG,GA,AA		42.2093,18.6337,34.2227	benign,benign	272/488,381/597	95561459	4451,8555	2203	4300	6503	SO:0001583	missense	10611	exon13			AGCGCTACTTACT	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.1141A>G	4.37:g.95561459A>G	ENSP00000321746:p.Thr381Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001256426	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	773	0.35393772893772896	74	0.15040650406504066	159	0.43922651933701656	223	0.38986013986013984	317	0.4182058047493404	A	0.006	-2.038621	0.00402	0.186337	0.422093	ENSG00000163110	ENST00000437932;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000514743	T;T;T;T;T	0.58652	0.53;0.71;0.53;0.32;0.53	5.67	-11.3	0.00108	.	1.765530	0.02790	N	0.121883	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B	0.09022	0.0;0.002;0.0;0.0	B;B;B;B	0.08055	0.0;0.003;0.0;0.001	T	0.05289	-1.0894	9	0.02654	T	1	.	6.2316	0.20738	0.1609:0.1746:0.4932:0.1713	rs7690296;rs17856261;rs52798084;rs61343931;rs7690296	278;410;381;272	E9PBF5;D6RB78;Q96HC4;Q96HC4-4	.;.;PDLI5_HUMAN;.	A	272;381;278;259;410	ENSP00000398469:T272A;ENSP00000321746:T381A;ENSP00000424297:T278A;ENSP00000442187:T259A;ENSP00000424360:T410A	ENSP00000321746:T381A	T	+	1	0	PDLIM5	95780482	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.359000	0.02602	-3.551000	0.00142	-1.004000	0.02495	ACT	A|0.655;G|0.345	0.345	strong		0.443	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
NEDD4L	23327	hgsc.bcm.edu	37	18	55816791	55816791	+	Intron	SNP	G	G	A	rs4149601	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:55816791G>A	ENST00000400345.3	+	2	331				NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000435432.2_5'UTR|NEDD4L_ENST00000256832.7_Intron|NEDD4L_ENST00000382850.4_Intron|NEDD4L_ENST00000256830.9_Intron|NEDD4L_ENST00000456986.1_Intron|NEDD4L_ENST00000588516.1_Intron|NEDD4L_ENST00000356462.6_Intron|NEDD4L_ENST00000586263.1_Splice_Site_p.Q8Q|NEDD4L_ENST00000357895.5_Splice_Site_p.Q8Q	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase						cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						CATTTGAGCAGGTAACACTCG	0.433													A|||	1383	0.276158	0.3608	0.2089	5008	,	,		21751	0.2113		0.3539	False		,,,				2504	0.1963				p.Q8Q		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G24A	GRCh37	CS024266	NEDD4L	S	rs4149601	PASS	.	A	,,,,,,	453,931		66,321,305	189.0	166.0	173.0		,,,24,24,,	2.8	0.0	18	dbSNP_110	173	1101,2081		196,709,686	yes	intron,utr-5,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,utr-5,intron	NEDD4L	NM_001144964.1,NM_001144965.1,NM_001144967.2,NM_001144968.1,NM_001144969.1,NM_001144971.1,NM_015277.5	,,,,,,	262,1030,991	AA,AG,GG		34.6009,32.7312,34.0342	,,,,,,	,,,8/968,8/948,,	55816791	1554,3012	692	1591	2283	SO:0001627	intron_variant	23327	exon1			TGAGCAGGTAACA	AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"""neural precursor cell expressed, developmentally down-regulated 4-like"""			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.49-16229G>A	18.37:g.55816791G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001144968	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	37	CCDS45872.1																																																																																			G|0.696;A|0.304	0.304	strong		0.433	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1		
APRT	353	hgsc.bcm.edu	37	16	88874632	88874632	+	IGR	SNP	C	C	G	rs572275	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	118	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	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	
OCA2	4948	hgsc.bcm.edu	37	15	28202804	28202804	+	Missense_Mutation	SNP	G	G	A	rs374415755		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:28202804G>A	ENST00000354638.3	-	16	1869	c.1714C>T	c.(1714-1716)Cgc>Tgc	p.R572C	OCA2_ENST00000353809.5_Missense_Mutation_p.R548C|OCA2_ENST00000382996.2_Missense_Mutation_p.R572C	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	572					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)		AGCAGGCGGCGCACAGCTGTC	0.662									Oculocutaneous Albinism																												p.R572C		Atlas-SNP	.											OCA2,caecum,carcinoma,0,1	OCA2	173	1	0			c.C1714T						PASS	.	G	CYS/ARG	0,4402		0,0,2201	27.0	30.0	29.0		1714	3.8	0.2	15		29	2,8588		0,2,4293	no	missense	OCA2	NM_000275.2	180	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	572/839	28202804	2,12990	2201	4295	6496	SO:0001583	missense	4948	exon16	Familial Cancer Database		GGCGGCGCACAGC		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.1714C>T	15.37:g.28202804G>A	ENSP00000346659:p.Arg572Cys	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784872	0.49997	0.0	2.33E-4	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.91894	-2.92;-2.74;-2.93	5.8	3.79	0.43588	Divalent ion symporter (1);	0.118953	0.53938	D	0.000046	D	0.93700	0.7987	M	0.64997	1.995	0.51012	D	0.999906	D;D	0.89917	0.998;1.0	P;D	0.74023	0.827;0.982	D	0.92961	0.6389	10	0.87932	D	0	-7.3542	6.2138	0.20644	0.0936:0.0:0.6114:0.295	.	548;572	Q04671-2;Q04671	.;P_HUMAN	C	572;548;572	ENSP00000346659:R572C;ENSP00000261276:R548C;ENSP00000372457:R572C	ENSP00000261276:R548C	R	-	1	0	OCA2	25876399	1.000000	0.71417	0.234000	0.24042	0.118000	0.20060	5.943000	0.70211	1.468000	0.48064	-0.229000	0.12294	CGC	.	.	weak		0.662	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
CDK11A	728642	hgsc.bcm.edu	37	1	1636044	1636044	+	Silent	SNP	G	G	A	rs1059822	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:1636044G>A	ENST00000378633.1	-	14	1597	c.1518C>T	c.(1516-1518)taC>taT	p.Y506Y	CDK11A_ENST00000358779.5_Silent_p.Y493Y|CDK11A_ENST00000378638.2_Silent_p.Y469Y|CDK11A_ENST00000404249.3_Silent_p.Y503Y|CDK11A_ENST00000356200.3_Silent_p.Y469Y|CDK11A_ENST00000357760.2_Silent_p.Y502Y|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000495016.1_5'Flank			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	506	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.Y502Y(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						CGTGCTCCACGTAGTTCATCA	0.622													-|||	3245	0.647963	0.9433	0.562	5008	,	,		12267	0.4643		0.5924	False		,,,				2504	0.5562				p.Y503Y	Pancreas(186;965 2119 30274 40311 50569)	Atlas-SNP	.											CDC2L2,NS,carcinoma,0,1	CDK11A	38	1	1	Substitution - coding silent(1)	stomach(1)	c.C1509T						PASS	.	A	,	3327,455		1515,297,79	47.0	79.0	69.0		1509,1479	-1.0	1.0	1	dbSNP_86	69	4669,3603		1482,1705,949	no	coding-synonymous,coding-synonymous	CDK11A	NM_024011.2,NM_033529.2	,	2997,2002,1028	AA,AG,GG		43.5566,12.0307,33.6652	,	503/781,493/771	1636044	7996,4058	1891	4136	6027	SO:0001819	synonymous_variant	728642	exon14			CTCCACGTAGTTC	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.1518C>T	1.37:g.1636044G>A		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	577	218	0.377816	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																																																																																				G|0.014;A|0.986	0.986	weak		0.622	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011	
KIAA1551	55196	hgsc.bcm.edu	37	12	32135186	32135186	+	Missense_Mutation	SNP	T	T	A	rs3759302	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32135186T>A	ENST00000312561.4	+	4	1711	c.1297T>A	c.(1297-1299)Tct>Act	p.S433T	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	433			S -> T (in dbSNP:rs3759302).														GACTAATACTTCTTATAGTGA	0.343													T|||	733	0.146366	0.0756	0.1254	5008	,	,		19387	0.121		0.1869	False		,,,				2504	0.2413				p.S433T		Atlas-SNP	.											.	.	.	.	0			c.T1297A						PASS	.	T	THR/SER	387,4019	180.5+/-208.7	15,357,1831	69.0	82.0	78.0		1297	-1.1	0.0	12	dbSNP_107	78	1720,6880	298.2+/-303.8	168,1384,2748	yes	missense	C12orf35	NM_018169.3	58	183,1741,4579	AA,AT,TT		20.0,8.7835,16.2002	possibly-damaging	433/1748	32135186	2107,10899	2203	4300	6503	SO:0001583	missense	55196	exon4			AATACTTCTTATA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1297T>A	12.37:g.32135186T>A	ENSP00000310338:p.Ser433Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	313	0.1433150183150183	43	0.08739837398373984	47	0.1298342541436464	85	0.1486013986013986	138	0.1820580474934037	T	9.919	1.211573	0.22289	0.087835	0.2	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.08807	3.7;3.05	5.72	-1.13	0.09775	.	0.495198	0.19035	N	0.124441	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.76494	0.999	D	0.65443	0.935	T	0.33599	-0.9862	8	.	.	.	.	5.5119	0.16886	0.0:0.2805:0.2503:0.4692	rs3759302;rs3759302	433	Q9HCM1	CL035_HUMAN	T	433	ENSP00000310338:S433T;ENSP00000370442:S433T	.	S	+	1	0	C12orf35	32026453	0.000000	0.05858	0.001000	0.08648	0.111000	0.19643	-0.055000	0.11807	-0.438000	0.07232	0.533000	0.62120	TCT	T|0.847;A|0.153	0.153	strong		0.343	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
VWA5B1	127731	hgsc.bcm.edu	37	1	20645086	20645086	+	Missense_Mutation	SNP	T	T	A	rs35480773	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:20645086T>A	ENST00000375079.2	+	6	909	c.713T>A	c.(712-714)gTg>gAg	p.V238E	RP4-745E8.2_ENST00000444923.1_RNA|VWA5B1_ENST00000289815.8_Missense_Mutation_p.V238E|VWA5B1_ENST00000375083.4_Missense_Mutation_p.V238E|VWA5B1_ENST00000289825.4_5'UTR	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	238						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						CACTCAGGGGTGGAGAGTCCC	0.592													T|||	96	0.0191693	0.0038	0.036	5008	,	,		18412	0.001		0.0487	False		,,,				2504	0.0164				p.V238E		Atlas-SNP	.											.	VWA5B1	44	.	0			c.T713A						PASS	.	T	GLU/VAL	15,1369		0,15,677	67.0	66.0	67.0		713	5.5	1.0	1	dbSNP_126	67	176,3006		6,164,1421	yes	missense	VWA5B1	NM_001039500.2	121	6,179,2098	AA,AT,TT		5.5311,1.0838,4.1831	probably-damaging	238/1216	20645086	191,4375	692	1591	2283	SO:0001583	missense	127731	exon6			CAGGGGTGGAGAG	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.713T>A	1.37:g.20645086T>A	ENSP00000364220:p.Val238Glu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	37		57	0.0260989010989011	1	0.0020325203252032522	17	0.04696132596685083	0	0.0	39	0.051451187335092345	T	23.0	4.366209	0.82463	0.010838	0.055311	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000375079	T;T;T	0.08984	3.32;3.03;3.3	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.03434	0.0099	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.00029	-1.2293	10	0.62326	D	0.03	-16.4276	14.5046	0.67743	0.0:0.0:0.0:1.0	rs35480773;rs61742671	238;238	Q5TIE3;Q5TIE3-2	VW5B1_HUMAN;.	E	238	ENSP00000289815:V238E;ENSP00000364224:V238E;ENSP00000364220:V238E	ENSP00000289815:V238E	V	+	2	0	VWA5B1	20517673	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	7.459000	0.80802	2.107000	0.64212	0.377000	0.23210	GTG	T|0.963;A|0.037	0.037	strong		0.592	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
OR2T33	391195	hgsc.bcm.edu	37	1	248437002	248437002	+	Missense_Mutation	SNP	C	C	T	rs146010336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248437002C>T	ENST00000318021.2	-	1	136	c.115G>A	c.(115-117)Ggc>Agc	p.G39S		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	39						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(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			AGGGAATTGCCAAACAGGGAG	0.498																																					p.G39S		Atlas-SNP	.											OR2T33,NS,carcinoma,+2,1	OR2T33	133	1	0			c.G115A						scavenged	.						33.0	35.0	35.0					1																	248437002		2200	4276	6476	SO:0001583	missense	391195	exon1			AATTGCCAAACAG		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"""GPCR / Class A : Olfactory receptors"""	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.115G>A	1.37:g.248437002C>T	ENSP00000324687:p.Gly39Ser	Somatic	669	11	0.0164425		WXS	Illumina HiSeq	Phase_I	709	89	0.125529	NM_001004695	B2RNN0	Missense_Mutation	SNP	ENST00000318021.2	37	CCDS31109.1	.	.	.	.	.	.	.	.	.	.	-	13.48	2.248585	0.39797	.	.	ENSG00000177212	ENST00000318021	T	0.00530	6.77	2.7	1.59	0.23543	GPCR, rhodopsin-like superfamily (1);	0.435769	0.16800	N	0.199012	T	0.00724	0.0024	M	0.81341	2.54	0.20489	N	0.999891	P	0.35307	0.494	B	0.36504	0.226	T	0.34825	-0.9813	10	0.49607	T	0.09	.	10.27	0.43477	0.1988:0.8012:0.0:0.0	.	39	Q8NG76	O2T33_HUMAN	S	39	ENSP00000324687:G39S	ENSP00000324687:G39S	G	-	1	0	OR2T33	246503625	0.003000	0.15002	0.087000	0.20705	0.236000	0.25371	1.373000	0.34272	1.437000	0.47472	0.494000	0.49563	GGC	C|0.992;T|0.008	0.008	strong		0.498	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695	
WNT6	7475	hgsc.bcm.edu	37	2	219736472	219736472	+	Silent	SNP	G	G	A	rs13417214	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:219736472G>A	ENST00000233948.3	+	3	784	c.567G>A	c.(565-567)gcG>gcA	p.A189A		NM_006522.3	NP_006513.1	Q9Y6F9	WNT6_HUMAN	wingless-type MMTV integration site family, member 6	189					axis specification (GO:0009798)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|epithelial-mesenchymal cell signaling (GO:0060684)|nephron tubule formation (GO:0072079)|neuron differentiation (GO:0030182)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of gene expression (GO:0010628)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription, DNA-templated (GO:0045893)|Wnt signaling pathway (GO:0016055)	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)	p.A189A(1)		large_intestine(1)|ovary(2)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.53e-07)|all cancers(144;9.3e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTATGGACGCGCGGCACAAGC	0.692													g|||	52	0.0103834	0.003	0.0231	5008	,	,		11643	0.0		0.0308	False		,,,				2504	0.001				p.A189A		Atlas-SNP	.											WNT6_ENST00000233948,NS,carcinoma,0,1	WNT6	21	1	1	Substitution - coding silent(1)	prostate(1)	c.G567A						PASS	.			26,4376	31.7+/-61.6	0,26,2175	25.0	28.0	27.0		567	-3.8	0.0	2	dbSNP_121	27	274,8326	99.7+/-161.2	2,270,4028	no	coding-synonymous	WNT6	NM_006522.3		2,296,6203	AA,AG,GG		3.186,0.5906,2.3073		189/366	219736472	300,12702	2201	4300	6501	SO:0001819	synonymous_variant	7475	exon3			GGACGCGCGGCAC	AF079522	CCDS2425.1	2q35	2008-05-23			ENSG00000115596	ENSG00000115596		"""Wingless-type MMTV integration sites"""	12785	protein-coding gene	gene with protein product		604663				10343101, 11350055	Standard	NM_006522		Approved		uc002vjc.1	Q9Y6F9	OTTHUMG00000133082	ENST00000233948.3:c.567G>A	2.37:g.219736472G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	181	93	0.513812	NM_006522	Q9H1J6|Q9H238	Silent	SNP	ENST00000233948.3	37	CCDS2425.1																																																																																			G|0.979;A|0.021	0.021	strong		0.692	WNT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256727.2	NM_006522	
DUSP4	1846	hgsc.bcm.edu	37	8	29207692	29207692	+	Missense_Mutation	SNP	C	C	T	rs527419472		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:29207692C>T	ENST00000240100.2	-	1	493	c.104G>A	c.(103-105)gGc>gAc	p.G35D	DUSP4_ENST00000240101.2_5'Flank|RP4-676L2.1_ENST00000567818.1_RNA	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	35					endoderm formation (GO:0001706)|innate immune response (GO:0045087)|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)|protein dephosphorylation (GO:0006470)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		CCCCAGGGTGCCGTGGCTGCC	0.682																																					p.G35D		Atlas-SNP	.											.	DUSP4	58	.	0			c.G104A						PASS	.						11.0	15.0	14.0					8																	29207692		1933	3796	5729	SO:0001583	missense	1846	exon1			AGGGTGCCGTGGC	U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3070	protein-coding gene	gene with protein product	"""VH1 homologous phosphatase 2"", ""MAP kinase phosphatase 2"""	602747				7535768, 9205128	Standard	NM_001394		Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240100.2:c.104G>A	8.37:g.29207692C>T	ENSP00000240100:p.Gly35Asp	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	37	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.284687	0.23392	.	.	ENSG00000120875	ENST00000240100	T	0.02552	4.25	3.26	3.26	0.37387	Rhodanese-like (3);	0.000000	0.51477	D	0.000081	T	0.01523	0.0049	N	0.08118	0	0.80722	D	1	P	0.37233	0.588	B	0.19946	0.027	T	0.65841	-0.6070	10	0.51188	T	0.08	.	12.7539	0.57323	0.0:1.0:0.0:0.0	.	35	Q13115	DUS4_HUMAN	D	35	ENSP00000240100:G35D	ENSP00000240100:G35D	G	-	2	0	DUSP4	29263611	0.826000	0.29277	1.000000	0.80357	0.425000	0.31504	-0.265000	0.08644	2.101000	0.63845	0.491000	0.48974	GGC	.	.	none		0.682	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394	
TTC24	164118	hgsc.bcm.edu	37	1	156551248	156551248	+	Missense_Mutation	SNP	G	G	A	rs192869620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156551248G>A	ENST00000368237.3	+	1	92	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	TTC24_ENST00000368236.3_Missense_Mutation_p.R31Q			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	31										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)					AAGTGGCTGCGGCAAGAAGCC	0.572													G|||	26	0.00519169	0.0	0.0173	5008	,	,		17596	0.0		0.0129	False		,,,				2504	0.001				p.R31Q		Atlas-SNP	.											TTC24,NS,carcinoma,0,2	TTC24	46	2	0			c.G92A						PASS	.						26.0	27.0	27.0					1																	156551248		692	1591	2283	SO:0001583	missense	164118	exon2			GGCTGCGGCAAGA		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.92G>A	1.37:g.156551248G>A	ENSP00000357220:p.Arg31Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	13	0.005952380952380952	0	0.0	7	0.019337016574585635	0	0.0	6	0.0079155672823219	G	2.638	-0.284842	0.05605	.	.	ENSG00000187862	ENST00000368236;ENST00000368237	T;T	0.76968	-1.06;-1.06	4.23	-1.72	0.08107	.	0.820698	0.10269	N	0.694981	T	0.19805	0.0476	N	0.02916	-0.46	0.09310	N	1	.	.	.	.	.	.	T	0.15321	-1.0441	8	0.11794	T	0.64	-1.6385	1.4317	0.02335	0.3363:0.1592:0.3497:0.1549	.	.	.	.	Q	31	ENSP00000357219:R31Q;ENSP00000357220:R31Q	ENSP00000357219:R31Q	R	+	2	0	TTC24	154817872	0.000000	0.05858	0.000000	0.03702	0.312000	0.27988	-0.224000	0.09164	-0.319000	0.08652	-0.672000	0.03802	CGG	G|0.994;A|0.006	0.006	strong		0.572	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
ELF1	1997	hgsc.bcm.edu	37	13	41517985	41517985	+	Silent	SNP	A	A	G	rs3764056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:41517985A>G	ENST00000239882.3	-	6	920	c.606T>C	c.(604-606)gaT>gaC	p.D202D	ELF1_ENST00000442101.1_Silent_p.D178D|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	202					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TACCCTTTCCATCTTTGTTTT	0.368													A|||	2071	0.413538	0.152	0.6657	5008	,	,		17100	0.1538		0.7097	False		,,,				2504	0.5511				p.D202D		Atlas-SNP	.											.	ELF1	65	.	0			c.T606C						PASS	.	A	,	976,3430	362.4+/-316.1	103,770,1330	222.0	184.0	197.0		534,606	3.6	1.0	13	dbSNP_107	197	5838,2762	678.9+/-403.5	1962,1914,424	yes	coding-synonymous,coding-synonymous	ELF1	NM_001145353.1,NM_172373.3	,	2065,2684,1754	GG,GA,AA		32.1163,22.1516,47.6088	,	178/596,202/620	41517985	6814,6192	2203	4300	6503	SO:0001819	synonymous_variant	1997	exon6			CTTTCCATCTTTG	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.606T>C	13.37:g.41517985A>G		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	256	127	0.496094	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Silent	SNP	ENST00000239882.3	37	CCDS9374.1																																																																																			A|0.521;G|0.479	0.479	strong		0.368	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
PSAPL1	768239	hgsc.bcm.edu	37	4	7436073	7436073	+	Silent	SNP	C	C	T	rs61740031	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:7436073C>T	ENST00000319098.4	-	1	627	c.534G>A	c.(532-534)gcG>gcA	p.A178A	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)	178					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CTCCTTCAGGCGCCTGGCGGG	0.627													C|||	637	0.127196	0.0976	0.1369	5008	,	,		17302	0.0764		0.1948	False		,,,				2504	0.1431				p.A178A		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G534A						PASS	.	C	,	464,3454		22,420,1517	12.0	14.0	13.0		534,	-3.3	0.0	4	dbSNP_129	13	1608,6656		161,1286,2685	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	183,1706,4202	TT,TC,CC		19.4579,11.8428,17.0087	,	178/522,	7436073	2072,10110	1959	4132	6091	SO:0001819	synonymous_variant	768239	exon1			TTCAGGCGCCTGG	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.534G>A	4.37:g.7436073C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	97	91	0.938144	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			C|0.870;T|0.130	0.130	strong		0.627	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
CDHR3	222256	hgsc.bcm.edu	37	7	105658460	105658460	+	Missense_Mutation	SNP	C	C	G	rs73195662	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000343407.5_Intron|CDHR3_ENST00000470188.1_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	56	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412542	105412542	+	Silent	SNP	A	A	G	rs386781092|rs12433815	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	200	1	0.005		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	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	
PTP4A3	11156	hgsc.bcm.edu	37	8	142441117	142441117	+	Silent	SNP	G	G	A	rs145258592	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:142441117G>A	ENST00000521578.1	+	6	1440	c.495G>A	c.(493-495)acG>acA	p.T165T	PTP4A3_ENST00000349124.1_Silent_p.T140T|PTP4A3_ENST00000520105.1_Silent_p.T140T|PTP4A3_ENST00000329397.1_Silent_p.T165T|PTP4A3_ENST00000524028.1_Silent_p.T79T|MROH5_ENST00000430863.1_RNA			O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	165					peptidyl-tyrosine dephosphorylation (GO:0035335)	endosome (GO:0005768)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)			endometrium(2)|large_intestine(1)|lung(3)	6	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)			ACCCACACACGCACAAGACCC	0.617													G|||	3	0.000599042	0.0	0.0	5008	,	,		19282	0.0		0.001	False		,,,				2504	0.002				p.T165T		Atlas-SNP	.											.	PTP4A3	19	.	0			c.G495A						PASS	.	G	,	0,4406		0,0,2203	139.0	114.0	123.0		420,495	-8.9	0.0	8	dbSNP_134	123	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous,coding-synonymous	PTP4A3	NM_007079.2,NM_032611.1	,	0,3,6499	AA,AG,GG		0.0349,0.0,0.0231	,	140/149,165/174	142441117	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	11156	exon5			ACACACGCACAAG	AF041434	CCDS6382.1, CCDS6383.1	8q24.3	2011-06-09				ENSG00000184489		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"""	9636	protein-coding gene	gene with protein product		606449					Standard	NM_032611		Approved	PRL-3, PRL-R, PRL3	uc003ywg.1	O75365		ENST00000521578.1:c.495G>A	8.37:g.142441117G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_032611	Q8IVN5|Q99849|Q9BTW5	Silent	SNP	ENST00000521578.1	37	CCDS6383.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	PTP4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378977.1	NM_032611	
RPL3L	6123	hgsc.bcm.edu	37	16	1996720	1996720	+	Missense_Mutation	SNP	C	C	T	rs147512517		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1996720C>T	ENST00000268661.7	-	7	951	c.857G>A	c.(856-858)cGc>cAc	p.R286H		NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	286					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						CCTGCCGATGCGGAAGATCTG	0.632																																					p.R286H		Atlas-SNP	.											RPL3L,caecum,carcinoma,-1,1	RPL3L	42	1	0			c.G857A						PASS	.	C	HIS/ARG	2,4394	4.2+/-10.8	0,2,2196	37.0	36.0	37.0		857	3.6	1.0	16	dbSNP_134	37	0,8598		0,0,4299	no	missense	RPL3L	NM_005061.2	29	0,2,6495	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging	286/408	1996720	2,12992	2198	4299	6497	SO:0001583	missense	6123	exon7			CCGATGCGGAAGA	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.857G>A	16.37:g.1996720C>T	ENSP00000268661:p.Arg286His	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	37	CCDS10450.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.594823	0.46318	4.55E-4	0.0	ENSG00000140986	ENST00000268661	T	0.26067	1.76	4.55	3.59	0.41128	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.117044	0.64402	D	0.000012	T	0.63861	0.2547	H	0.97240	3.965	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.75428	-0.3321	10	0.87932	D	0	-32.639	11.9539	0.52970	0.0:0.9145:0.0:0.0855	.	286	Q92901	RL3L_HUMAN	H	286	ENSP00000268661:R286H	ENSP00000268661:R286H	R	-	2	0	RPL3L	1936721	0.990000	0.36364	0.987000	0.45799	0.039000	0.13416	2.583000	0.46094	1.037000	0.40024	-0.258000	0.10820	CGC	C|1.000;T|0.000	0.000	weak		0.632	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061	
EXO5	64789	hgsc.bcm.edu	37	1	40981230	40981230	+	Silent	SNP	G	G	A	rs3795344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40981230G>A	ENST00000372703.1	+	2	2088	c.1014G>A	c.(1012-1014)gaG>gaA	p.E338E	EXO5_ENST00000296380.4_Silent_p.E338E|RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000358527.2_Silent_p.E338E|RP11-656D10.5_ENST00000453437.1_RNA			Q9H790	EXO5_HUMAN	exonuclease 5	338					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)										TTGACGTGGAGGAGGCTTGGA	0.547													G|||	216	0.043131	0.0598	0.0331	5008	,	,		19359	0.0208		0.0328	False		,,,				2504	0.0613				p.E338E		Atlas-SNP	.											.	.	.	.	0			c.G1014A						PASS	.	G		245,4161	140.8+/-176.2	9,227,1967	61.0	50.0	54.0		1014	-2.1	1.0	1	dbSNP_107	54	300,8300	107.4+/-168.2	5,290,4005	no	coding-synonymous	DEM1	NM_022774.1		14,517,5972	AA,AG,GG		3.4884,5.5606,4.1904		338/374	40981230	545,12461	2203	4300	6503	SO:0001819	synonymous_variant	64789	exon3			CGTGGAGGAGGCT	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.1014G>A	1.37:g.40981230G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Silent	SNP	ENST00000372703.1	37	CCDS453.1																																																																																			G|0.958;A|0.042	0.042	strong		0.547	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
CAAP1	79886	hgsc.bcm.edu	37	9	26892654	26892654	+	Silent	SNP	G	G	A	rs3739548	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:26892654G>A	ENST00000333916.5	-	1	148	c.60C>T	c.(58-60)gcC>gcT	p.A20A	CAAP1_ENST00000520187.1_Silent_p.A20A|CAAP1_ENST00000535437.1_5'Flank|CAAP1_ENST00000495958.1_5'Flank	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	20	Poly-Ala.				apoptotic process (GO:0006915)												CGAGCGCTGCGGCCGCCTCCT	0.677													G|||	1159	0.23143	0.1165	0.1844	5008	,	,		15465	0.6607		0.0388	False		,,,				2504	0.1759				p.A20A		Atlas-SNP	.											.	.	.	.	0			c.C60T						PASS	.	G	,	434,3910		17,400,1755	16.0	20.0	19.0		,60	1.3	0.0	9	dbSNP_107	19	240,8274		4,232,4021	no	utr-5,coding-synonymous	C9orf82	NM_001167575.1,NM_024828.3	,	21,632,5776	AA,AG,GG		2.8189,9.9908,5.2419	,	,20/362	26892654	674,12184	2172	4257	6429	SO:0001819	synonymous_variant	79886	exon1			CGCTGCGGCCGCC	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.60C>T	9.37:g.26892654G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Silent	SNP	ENST00000333916.5	37	CCDS6516.1																																																																																			G|0.879;C|0.000;A|0.121	0.121	strong		0.677	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828	
SCARF1	8578	hgsc.bcm.edu	37	17	1538669	1538669	+	Missense_Mutation	SNP	C	C	T	rs36108564	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:1538669C>T	ENST00000263071.4	-	11	1925	c.1876G>A	c.(1876-1878)Ggt>Agt	p.G626S	SCARF1_ENST00000348987.3_Missense_Mutation_p.G540S|SCARF1_ENST00000571272.1_3'UTR	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	626	Gly-rich.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCCTCAGGACCCGACTGCGCC	0.677													C|||	275	0.0549121	0.0076	0.1167	5008	,	,		14353	0.0079		0.1392	False		,,,				2504	0.0368				p.G626S		Atlas-SNP	.											.	SCARF1	46	.	0			c.G1876A						PASS	.	C	SER/GLY,,SER/GLY	131,4275	90.2+/-128.9	0,131,2072	26.0	30.0	29.0		1876,,1618	1.5	0.3	17	dbSNP_126	29	1204,7396	232.8+/-266.3	80,1044,3176	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	56,,56	80,1175,5248	TT,TC,CC		14.0,2.9732,10.2645	benign,,benign	626/831,,540/745	1538669	1335,11671	2203	4300	6503	SO:0001583	missense	8578	exon11			CAGGACCCGACTG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1876G>A	17.37:g.1538669C>T	ENSP00000263071:p.Gly626Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	165	0.07554945054945054	3	0.006097560975609756	51	0.1408839779005525	4	0.006993006993006993	107	0.14116094986807387	C	8.573	0.880576	0.17467	0.029732	0.14	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.36520	1.25;1.25	5.21	1.48	0.22813	.	0.771440	0.11051	N	0.605086	T	0.00241	0.0007	L	0.47716	1.5	0.80722	P	0.0	B;B	0.19583	0.037;0.027	B;B	0.15484	0.013;0.012	T	0.14035	-1.0487	9	0.22706	T	0.39	-4.2449	10.3537	0.43952	0.0:0.4454:0.403:0.1516	rs36108564	540;626	Q14162-2;Q14162	.;SREC_HUMAN	S	626;540	ENSP00000263071:G626S;ENSP00000323964:G540S	ENSP00000263071:G626S	G	-	1	0	SCARF1	1485419	0.000000	0.05858	0.327000	0.25402	0.015000	0.08874	0.444000	0.21661	0.477000	0.27464	0.555000	0.69702	GGT	C|0.913;T|0.087	0.087	strong		0.677	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
RIMS1	22999	hgsc.bcm.edu	37	6	73102442	73102442	+	Silent	SNP	C	C	T	rs2815738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:73102442C>T	ENST00000521978.1	+	31	4548	c.4548C>T	c.(4546-4548)ttC>ttT	p.F1516F	RIMS1_ENST00000523963.1_Silent_p.F641F|RIMS1_ENST00000522291.1_Silent_p.F1115F|RIMS1_ENST00000518273.1_Silent_p.F1195F|RIMS1_ENST00000517960.1_Silent_p.F1299F|RIMS1_ENST00000425662.2_Silent_p.F584F|RIMS1_ENST00000491071.2_Silent_p.F1339F|RIMS1_ENST00000414192.2_Silent_p.F43F|RIMS1_ENST00000538414.1_Silent_p.F322F|RIMS1_ENST00000517827.1_Silent_p.F650F|RIMS1_ENST00000348717.5_Silent_p.F1299F|RIMS1_ENST00000264839.7_Silent_p.F1365F|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000401910.3_Silent_p.F836F|RIMS1_ENST00000520567.1_Silent_p.F1166F	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1516					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				ACAGTCAATTCAGTGATTTTC	0.408													C|||	795	0.158746	0.1293	0.1052	5008	,	,		15470	0.0149		0.2435	False		,,,				2504	0.2975				p.F1516F		Atlas-SNP	.											.	RIMS1	278	.	0			c.C4548T						PASS	.	C	,,,,,	578,3128		46,486,1321	97.0	92.0	94.0		2508,1923,1752,1950,129,4548	4.6	1.0	6	dbSNP_100	94	1966,6244		263,1440,2402	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RIMS1	NM_001168407.1,NM_001168408.1,NM_001168409.1,NM_001168410.1,NM_001168411.1,NM_014989.4	,,,,,	309,1926,3723	TT,TC,CC		23.9464,15.5963,21.3494	,,,,,	836/1013,641/818,584/761,650/827,43/220,1516/1693	73102442	2544,9372	1853	4105	5958	SO:0001819	synonymous_variant	22999	exon31			TCAATTCAGTGAT	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4548C>T	6.37:g.73102442C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Silent	SNP	ENST00000521978.1	37	CCDS47449.1	315|315	0.14423076923076922|0.14423076923076922	70|70	0.14227642276422764|0.14227642276422764	45|45	0.12430939226519337|0.12430939226519337	6|6	0.01048951048951049|0.01048951048951049	194|194	0.2559366754617414|0.2559366754617414	C|C	10.49|10.49	1.365787|1.365787	0.24684|0.24684	0.155963|0.155963	0.239464|0.239464	ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000522211	.|.	.|.	.|.	5.5|5.5	4.63|4.63	0.57726|0.57726	.|.	.|.	.|.	.|.	.|.	.|T	.|0.53158	.|0.1779	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.56481	.|-0.7972	.|3	.|.	.|.	.|.	-14.4078|-14.4078	14.2864|14.2864	0.66249|0.66249	0.0:0.9282:0.0:0.0718|0.0:0.9282:0.0:0.0718	rs2815738;rs17747938;rs60438041;rs2815738|rs2815738;rs17747938;rs60438041;rs2815738	.|.	.|.	.|.	X|L	862|434	.|.	.|.	Q|S	+|+	1|2	0|0	RIMS1|RIMS1	73159163|73159163	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.642000|1.642000	0.37207|0.37207	1.320000|1.320000	0.45209|0.45209	0.591000|0.591000	0.81541|0.81541	CAG|TCA	T|0.158;C|0.842	0.158	strong		0.408	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
KDM5B	10765	hgsc.bcm.edu	37	1	202733238	202733238	+	Silent	SNP	C	C	T	rs3196669	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:202733238C>T	ENST00000367265.3	-	6	1911	c.747G>A	c.(745-747)acG>acA	p.T249T	KDM5B_ENST00000367264.2_Silent_p.T285T	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	249					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						TTCTGGCTTCCGTTGTCTCCT	0.313													T|||	3182	0.635383	0.323	0.8343	5008	,	,		16383	0.7679		0.7714	False		,,,				2504	0.6401				p.T249T		Atlas-SNP	.											.	KDM5B	166	.	0			c.G747A						PASS	.	T		1660,2746	657.7+/-400.3	320,1020,863	107.0	96.0	100.0		747	2.7	1.0	1	dbSNP_105	100	6691,1909	338.1+/-322.6	2616,1459,225	no	coding-synonymous	KDM5B	NM_006618.3		2936,2479,1088	TT,TC,CC		22.1977,37.6759,35.7912		249/1545	202733238	8351,4655	2203	4300	6503	SO:0001819	synonymous_variant	10765	exon6			GGCTTCCGTTGTC	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.747G>A	1.37:g.202733238C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_006618	O95811|Q15752|Q9Y3Q5	Silent	SNP	ENST00000367265.3	37	CCDS30974.1																																																																																			C|0.346;T|0.654	0.654	strong		0.313	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
HOXB6	3216	hgsc.bcm.edu	37	17	46675240	46675240	+	Silent	SNP	G	G	T	rs34438598	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:46675240G>T	ENST00000484302.2	-	2	895	c.273C>A	c.(271-273)tcC>tcA	p.S91S	HOXB-AS3_ENST00000477144.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000474040.1_RNA|HOXB6_ENST00000225648.3_Silent_p.S91S|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000476204.1_RNA			P17509	HXB6_HUMAN	homeobox B6	91					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						CGTCGGCGCCGGAGAGTGCGC	0.711													G|||	154	0.0307508	0.003	0.049	5008	,	,		11019	0.002		0.0815	False		,,,				2504	0.0327				p.S91S		Atlas-SNP	.											.	HOXB6	13	.	0			c.C273A						PASS	.	G		78,4274		1,76,2099	10.0	9.0	9.0		273	-6.3	0.9	17	dbSNP_126	9	693,7829		17,659,3585	no	coding-synonymous	HOXB6	NM_018952.4		18,735,5684	TT,TG,GG		8.1319,1.7923,5.9888		91/225	46675240	771,12103	2176	4261	6437	SO:0001819	synonymous_variant	3216	exon3			GGCGCCGGAGAGT		CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"""Homeoboxes / ANTP class : HOXL subclass"""	5117	protein-coding gene	gene with protein product		142961	"""homeo box B6"""	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.273C>A	17.37:g.46675240G>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_018952	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	Silent	SNP	ENST00000484302.2	37	CCDS11531.1																																																																																			G|0.956;T|0.044	0.044	strong		0.711	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2		
FAT1	2195	hgsc.bcm.edu	37	4	187542736	187542736	+	Silent	SNP	T	T	C	rs35753072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187542736T>C	ENST00000441802.2	-	10	5213	c.5004A>G	c.(5002-5004)acA>acG	p.T1668T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1668	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATTCTTTTGATGTAAACTTCG	0.398										HNSCC(5;0.00058)			T|||	342	0.0682907	0.003	0.1499	5008	,	,		19850	0.1796		0.0338	False		,,,				2504	0.0194				p.T1668T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A5004G						PASS	.	T		39,3709		0,39,1835	99.0	95.0	96.0		5004	-4.3	0.9	4	dbSNP_126	96	253,7975		4,245,3865	no	coding-synonymous	FAT1	NM_005245.3		4,284,5700	CC,CT,TT		3.0749,1.0406,2.4382		1668/4589	187542736	292,11684	1874	4114	5988	SO:0001819	synonymous_variant	2195	exon10			TTTTGATGTAAAC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.5004A>G	4.37:g.187542736T>C		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	202	92	0.455446	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			T|0.926;C|0.074	0.074	strong		0.398	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
USP10	9100	hgsc.bcm.edu	37	16	84778685	84778685	+	Missense_Mutation	SNP	A	A	G	rs1862792	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:84778685A>G	ENST00000219473.7	+	4	711	c.598A>G	c.(598-600)Atg>Gtg	p.M200V	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Missense_Mutation_p.M204V	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	200			M -> V (in dbSNP:rs1862792). {ECO:0000269|PubMed:17974005}.		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						TATGGGTGACATGCCCCCGTC	0.547													A|||	1017	0.203075	0.208	0.2334	5008	,	,		17509	0.1458		0.2197	False		,,,				2504	0.2168				p.M204V		Atlas-SNP	.											.	USP10	51	.	0			c.A610G						PASS	.	A	VAL/MET	879,3117		80,719,1199	32.0	31.0	32.0		598	-6.6	0.0	16	dbSNP_92	32	1906,6426		216,1474,2476	no	missense	USP10	NM_005153.2	21	296,2193,3675	GG,GA,AA		22.8757,21.997,22.5909	benign	200/799	84778685	2785,9543	1998	4166	6164	SO:0001583	missense	9100	exon5			GGTGACATGCCCC	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.598A>G	16.37:g.84778685A>G	ENSP00000219473:p.Met200Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	163	68	0.417178	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	437	0.2000915750915751	101	0.20528455284552846	89	0.24585635359116023	83	0.1451048951048951	164	0.21635883905013192	A	0.775	-0.764453	0.02996	0.21997	0.228757	ENSG00000103194	ENST00000219473	T	0.05717	3.4	5.17	-6.56	0.01848	.	1.153270	0.06206	N	0.684240	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50268	-0.8848	9	0.26408	T	0.33	-0.2777	6.1323	0.20211	0.6595:0.1056:0.1287:0.1062	rs1862792	204;200	Q14694-3;Q14694	.;UBP10_HUMAN	V	200	ENSP00000219473:M200V	ENSP00000219473:M200V	M	+	1	0	USP10	83336186	0.000000	0.05858	0.000000	0.03702	0.254000	0.26022	-0.116000	0.10724	-1.127000	0.02925	-0.415000	0.06103	ATG	A|0.797;G|0.203	0.203	strong		0.547	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
XKR4	114786	hgsc.bcm.edu	37	8	56270383	56270383	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:56270383C>T	ENST00000327381.6	+	2	1052	c.952C>T	c.(952-954)Ctg>Ttg	p.L318L		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	318						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			TGCTCCACAGCTGGTCCTGCA	0.463																																					p.L318L		Atlas-SNP	.											XKR4,NS,carcinoma,-2,1	XKR4	104	1	0			c.C952T						scavenged	.						136.0	118.0	124.0					8																	56270383		2203	4300	6503	SO:0001819	synonymous_variant	114786	exon2			CCACAGCTGGTCC	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 4"""				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.952C>T	8.37:g.56270383C>T		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	224	3	0.0133929	NM_052898	Q96PZ8	Silent	SNP	ENST00000327381.6	37	CCDS34893.1																																																																																			.	.	none		0.463	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898	
ERMARD	55780	hgsc.bcm.edu	37	6	170176146	170176146	+	Missense_Mutation	SNP	G	G	A	rs41265401	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170176146G>A	ENST00000366773.3	+	15	1538	c.1505G>A	c.(1504-1506)cGt>cAt	p.R502H	ERMARD_ENST00000418781.3_Missense_Mutation_p.R502H|ERMARD_ENST00000366772.2_Missense_Mutation_p.R502H|ERMARD_ENST00000392095.4_Missense_Mutation_p.R376H|ERMARD_ENST00000588451.1_Missense_Mutation_p.R366H	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	502					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											GACTTGGATCGTCTTCCTACT	0.388													G|||	393	0.0784744	0.0764	0.0562	5008	,	,		21820	0.1022		0.0785	False		,,,				2504	0.0726				p.R502H		Atlas-SNP	.											.	C6orf70	63	.	0			c.G1505A						PASS	.	G	HIS/ARG	277,4129		7,263,1933	151.0	123.0	133.0		1505	-10.5	0.0	6	dbSNP_127	133	686,7914		30,626,3644	yes	missense	C6orf70	NM_018341.1	29	37,889,5577	AA,AG,GG		7.9767,6.2869,7.4043	benign	502/679	170176146	963,12043	2203	4300	6503	SO:0001583	missense	55780	exon15			TGGATCGTCTTCC	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.1505G>A	6.37:g.170176146G>A	ENSP00000355735:p.Arg502His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	176	0.08058608058608059	27	0.054878048780487805	24	0.06629834254143646	65	0.11363636363636363	60	0.079155672823219	.	3.431	-0.116188	0.06881	0.062869	0.079767	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.42900	0.96;0.96	5.27	-10.5	0.00291	.	4.533170	0.00496	N	0.000154	T	0.04634	0.0126	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	0.31888	-0.9927	9	0.40728	T	0.16	.	12.4976	0.55937	0.1824:0.2637:0.5539:0.0	rs41265401;rs61747676	502;502;502	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	H	502;502;502;376;150	ENSP00000355735:R502H;ENSP00000375945:R376H	ENSP00000355733:R150H	R	+	2	0	C6orf70	169918071	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.948000	0.03897	-3.144000	0.00232	-1.533000	0.00918	CGT	G|0.925;A|0.075	0.075	strong		0.388	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
LAMC3	10319	hgsc.bcm.edu	37	9	133924451	133924451	+	Missense_Mutation	SNP	C	C	T	rs869457	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133924451C>T	ENST00000361069.4	+	9	1697	c.1564C>T	c.(1564-1566)Ccc>Tcc	p.P522S	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	522	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.		P -> S (in dbSNP:rs869457). {ECO:0000269|PubMed:10225960}.		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)		CTCTGAGCACCCCCCACAATG	0.657													C|||	1295	0.258586	0.2405	0.2133	5008	,	,		15143	0.246		0.3241	False		,,,				2504	0.2607				p.P522S		Atlas-SNP	.											.	LAMC3	167	.	0			c.C1564T						PASS	.	C	SER/PRO	945,3285		107,731,1277	20.0	23.0	22.0		1564	3.9	0.0	9	dbSNP_86	22	2470,5804		393,1684,2060	yes	missense	LAMC3	NM_006059.3	74	500,2415,3337	TT,TC,CC		29.8526,22.3404,27.3113	possibly-damaging	522/1576	133924451	3415,9089	2115	4137	6252	SO:0001583	missense	10319	exon9			GAGCACCCCCCAC	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.1564C>T	9.37:g.133924451C>T	ENSP00000354360:p.Pro522Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	546	0.25	116	0.23577235772357724	70	0.19337016574585636	131	0.229020979020979	229	0.3021108179419525	C	2.617	-0.289380	0.05605	0.223404	0.298526	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.27890	1.64	4.78	3.88	0.44766	Laminin B type IV (1);	0.313497	0.36854	N	0.002376	T	0.00012	0.0000	L	0.43554	1.36	0.80722	P	0.0	B	0.29378	0.243	B	0.26864	0.074	T	0.25257	-1.0137	9	0.06099	T	0.92	.	8.9877	0.36003	0.0:0.8999:0.0:0.1001	rs869457;rs61050238	522	Q9Y6N6	LAMC3_HUMAN	S	522	ENSP00000354360:P522S	ENSP00000347156:P522S	P	+	1	0	LAMC3	132914272	0.146000	0.22672	0.042000	0.18584	0.015000	0.08874	2.134000	0.42102	1.389000	0.46526	0.555000	0.69702	CCC	C|0.729;T|0.271	0.271	strong		0.657	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
HNRNPDL	9987	hgsc.bcm.edu	37	4	83348652	83348652	+	Silent	SNP	T	T	C	rs61729822	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:83348652T>C	ENST00000295470.5	-	4	1015	c.840A>G	c.(838-840)acA>acG	p.T280T	HNRNPDL_ENST00000514511.1_5'UTR|HNRNPDL_ENST00000502762.1_Silent_p.T280T|HNRNPDL_ENST00000602300.1_Silent_p.T161T|HNRNPDL_ENST00000349655.4_Silent_p.T161T	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	280	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										CATCAGTATATGTGATAAAAC	0.323													T|||	61	0.0121805	0.0038	0.0202	5008	,	,		17929	0.0		0.0388	False		,,,				2504	0.0031				p.T280T		Atlas-SNP	.											.	HNRPDL	35	.	0			c.A840G						PASS	.	T	,	45,4359	44.6+/-78.6	0,45,2157	77.0	76.0	76.0		840,840	3.1	1.0	4	dbSNP_129	76	287,8311	107.2+/-168.0	3,281,4015	no	coding-synonymous,coding-synonymous	HNRPDL	NM_001207000.1,NM_031372.3	,	3,326,6172	CC,CT,TT		3.338,1.0218,2.5535	,	280/364,280/421	83348652	332,12670	2202	4299	6501	SO:0001819	synonymous_variant	9987	exon4			AGTATATGTGATA	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"""RNA binding motif (RRM) containing"""	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.840A>G	4.37:g.83348652T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	179	68	0.379888	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Silent	SNP	ENST00000295470.5	37	CCDS3593.1																																																																																			T|0.975;C|0.025	0.025	strong		0.323	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463	
VWDE	221806	hgsc.bcm.edu	37	7	12414725	12414725	+	Nonsense_Mutation	SNP	G	G	A	rs17165936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:12414725G>A	ENST00000275358.3	-	8	1341	c.1153C>T	c.(1153-1155)Cga>Tga	p.R385*		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	385						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TCTCCATCTCGAGAAAAATCT	0.428													G|||	835	0.166733	0.1997	0.0893	5008	,	,		13901	0.2004		0.1034	False		,,,				2504	0.2076				p.R385X		Atlas-SNP	.											.	VWDE	123	.	0			c.C1153T						PASS	.	G	stop/ARG	289,1095		34,221,437	128.0	110.0	116.0		1153	3.8	0.6	7	dbSNP_123	116	362,2818		20,322,1248	yes	stop-gained	VWDE	NM_001135924.1		54,543,1685	AA,AG,GG		11.3836,20.8815,14.2638		385/1591	12414725	651,3913	692	1590	2282	SO:0001587	stop_gained	221806	exon8			CATCTCGAGAAAA		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.1153C>T	7.37:g.12414725G>A	ENSP00000275358:p.Arg385*	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	145	67	0.462069	NM_001135924	B7ZM77|Q96SQ3	Nonsense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	356	0.163003663003663	99	0.20121951219512196	33	0.09116022099447514	138	0.24125874125874125	86	0.11345646437994723	G	38	6.658276	0.97739	0.208815	0.113836	ENSG00000146530	ENST00000275358	.	.	.	4.68	3.78	0.43462	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2026	0.59776	0.0:0.3035:0.6965:0.0	rs17165936;rs57342406;rs17165936	.	.	.	X	385	.	ENSP00000275358:R385X	R	-	1	2	VWDE	12381250	0.012000	0.17670	0.601000	0.28877	0.592000	0.36648	1.788000	0.38714	1.164000	0.42652	0.585000	0.79938	CGA	G|0.840;A|0.160	0.160	strong		0.428	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421059	29421059	+	Missense_Mutation	SNP	A	A	C	rs200682124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29421059A>C	ENST00000261275.4	-	8	935	c.936T>G	c.(934-936)agT>agG	p.S312R		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	312	Pro-rich.					integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						GCTGACCTATACTTGTAACCT	0.557													A|||	9	0.00179712	0.0008	0.0029	5008	,	,		17039	0.0		0.004	False		,,,				2504	0.002				p.S312R		Atlas-SNP	.											.	FAM189A1	20	.	0			c.T936G						PASS	.	A	ARG/SER	0,1384		0,0,692	52.0	52.0	52.0		936	-6.1	0.0	15		52	8,3174		0,8,1583	yes	missense	FAM189A1	NM_015307.1	110	0,8,2275	CC,CA,AA		0.2514,0.0,0.1752	probably-damaging	312/540	29421059	8,4558	692	1591	2283	SO:0001583	missense	23359	exon8			ACCTATACTTGTA		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.936T>G	15.37:g.29421059A>C	ENSP00000261275:p.Ser312Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	52	16	0.307692	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.551072	0.27739	0.0	0.002514	ENSG00000104059	ENST00000261275	T	0.04049	3.72	5.07	-6.1	0.02138	.	0.258929	0.41194	N	0.000939	T	0.05686	0.0149	M	0.68952	2.095	0.09310	N	1	B	0.29612	0.251	B	0.26202	0.067	T	0.07751	-1.0756	10	0.42905	T	0.14	-31.8889	14.1806	0.65572	0.4236:0.0:0.5764:0.0	.	312	O60320	F1891_HUMAN	R	312	ENSP00000261275:S312R	ENSP00000261275:S312R	S	-	3	2	FAM189A1	27208351	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	0.073000	0.14640	-1.192000	0.02691	0.533000	0.62120	AGT	.	.	weak		0.557	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
C6orf211	79624	hgsc.bcm.edu	37	6	151789912	151789912	+	Silent	SNP	C	C	T	rs9397054	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151789912C>T	ENST00000367294.3	+	5	1252	c.993C>T	c.(991-993)caC>caT	p.H331H	C6orf211_ENST00000545879.1_Silent_p.H212H	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	331										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)		GGGTTTACCACAATCATATAT	0.383													C|||	1038	0.207268	0.1581	0.1354	5008	,	,		19474	0.4077		0.1153	False		,,,				2504	0.2127				p.H331H		Atlas-SNP	.											.	C6orf211	30	.	0			c.C993T						PASS	.	C		663,3743	278.1+/-274.1	54,555,1594	85.0	86.0	86.0		993	-12.3	0.0	6	dbSNP_119	86	899,7701	201.4+/-244.9	43,813,3444	no	coding-synonymous	C6orf211	NM_024573.1		97,1368,5038	TT,TC,CC		10.4535,15.0477,12.0098		331/442	151789912	1562,11444	2203	4300	6503	SO:0001819	synonymous_variant	79624	exon5			TTACCACAATCAT	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.993C>T	6.37:g.151789912C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_024573	Q96FC6|Q9UFY5	Silent	SNP	ENST00000367294.3	37	CCDS5233.1																																																																																			C|0.855;T|0.145	0.145	strong		0.383	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417147	105417147	+	Silent	SNP	A	A	G	rs2013445	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105417147A>G	ENST00000333244.5	-	7	4760	c.4641T>C	c.(4639-4641)tcT>tcC	p.S1547S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1547						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)			CCAGGTCAGCAGAAGGGGGCT	0.647													.|||	2149	0.429113	0.2496	0.4395	5008	,	,		14567	0.3512		0.5557	False		,,,				2504	0.6145				p.S1547S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T4641C						PASS	.	G		1099,2733		211,677,1028	108.0	105.0	106.0		4641	-8.3	0.0	14	dbSNP_92	106	4529,3635		1477,1575,1030	no	coding-synonymous	AHNAK2	NM_138420.2		1688,2252,2058	GG,GA,AA		44.5247,28.6795,46.9156		1547/5796	105417147	5628,6368	1916	4082	5998	SO:0001819	synonymous_variant	113146	exon7			GTCAGCAGAAGGG	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.4641T>C	14.37:g.105417147A>G		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	214	214	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.593;G|0.407	0.407	strong		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CBS	875	hgsc.bcm.edu	37	21	44480616	44480616	+	Silent	SNP	G	G	A	rs1801181	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44480616G>A	ENST00000398165.3	-	12	1339	c.1080C>T	c.(1078-1080)gcC>gcT	p.A360A	CBS_ENST00000398168.1_Silent_p.A360A|CBS_ENST00000398158.1_Silent_p.A360A|CBS_ENST00000352178.5_Silent_p.A360A|CBS_ENST00000359624.3_Silent_p.A360A|CBS_ENST00000544202.1_Silent_p.A272A	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	360					cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	GCTCCTGCGCGGCCTTCACGG	0.667													G|||	1480	0.295527	0.0204	0.1888	5008	,	,		18257	0.5744		0.3857	False		,,,				2504	0.363				p.A360A		Atlas-SNP	.											.	CBS	85	.	0			c.C1080T						PASS	.	G	,,	328,4078		12,304,1887	54.0	40.0	45.0		1080,1080,1080	-10.1	0.2	21	dbSNP_89	45	3087,5507		566,1955,1776	no	coding-synonymous,coding-synonymous,coding-synonymous	CBS	NM_000071.2,NM_001178008.1,NM_001178009.1	,,	578,2259,3663	AA,AG,GG		35.9204,7.4444,26.2692	,,	360/552,360/552,360/552	44480616	3415,9585	2203	4297	6500	SO:0001819	synonymous_variant	875	exon12			CTGCGCGGCCTTC	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.1080C>T	21.37:g.44480616G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Silent	SNP	ENST00000398165.3	37	CCDS13693.1	714	0.3269230769230769	16	0.032520325203252036	77	0.212707182320442	329	0.5751748251748252	292	0.38522427440633245	G	1.626	-0.520158	0.04171	0.074444	0.359204	ENSG00000160200	ENST00000430013	.	.	.	5.05	-10.1	0.00402	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999772428	.	.	.	.	.	.	T	0.31308	-0.9948	3	.	.	.	-17.1941	3.9564	0.09391	0.4527:0.3144:0.0758:0.157	rs1801181;rs17850632;rs17850743;rs57290520	.	.	.	L	14	.	.	P	-	2	0	CBS	43353685	0.000000	0.05858	0.239000	0.24122	0.024000	0.10985	-2.619000	0.00879	-2.547000	0.00482	-0.469000	0.05056	CCG	G|0.720;A|0.280	0.280	strong		0.667	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
SLC27A2	11001	hgsc.bcm.edu	37	15	50475035	50475035	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:50475035C>T	ENST00000267842.5	+	1	643	c.411C>T	c.(409-411)aaC>aaT	p.N137N	SLC27A2_ENST00000380902.4_Silent_p.N137N	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	137					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)		TCAATTACAACATCCGCGCGA	0.657																																					p.N137N		Atlas-SNP	.											.	SLC27A2	50	.	0			c.C411T						PASS	.						99.0	107.0	104.0					15																	50475035		2196	4295	6491	SO:0001819	synonymous_variant	11001	exon1			TTACAACATCCGC	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.411C>T	15.37:g.50475035C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_003645	A8K2J7|Q53FY6|Q6PF09	Silent	SNP	ENST00000267842.5	37	CCDS10133.1																																																																																			.	.	none		0.657	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645	
GALNT8	26290	hgsc.bcm.edu	37	12	4853806	4853806	+	Missense_Mutation	SNP	A	A	G	rs34776842	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:4853806A>G	ENST00000252318.2	+	4	1137	c.800A>G	c.(799-801)gAa>gGa	p.E267G		NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	267	Catalytic subdomain A.		E -> G (in dbSNP:rs34776842). {ECO:0000269|PubMed:10767557}.		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)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						ACTGGCTGGGAAGCTGCCACA	0.488													A|||	98	0.0195687	0.0008	0.0375	5008	,	,		21968	0.0		0.0626	False		,,,				2504	0.0082				p.E267G	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.A800G						PASS	.	A	GLY/GLU	60,4346		0,60,2143	62.0	49.0	53.0		800	2.0	0.9	12	dbSNP_126	53	637,7963		26,585,3689	yes	missense	GALNT8	NM_017417.1	98	26,645,5832	GG,GA,AA		7.407,1.3618,5.3591	benign	267/638	4853806	697,12309	2203	4300	6503	SO:0001583	missense	26290	exon4			GCTGGGAAGCTGC	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.800A>G	12.37:g.4853806A>G	ENSP00000252318:p.Glu267Gly	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	261	0.11950549450549451	26	0.052845528455284556	46	0.1270718232044199	85	0.1486013986013986	104	0.13720316622691292	A	13.01	2.109331	0.37242	0.013618	0.07407	ENSG00000130035	ENST00000252318	T	0.63096	-0.02	4.5	2.0	0.26442	Glycosyl transferase, family 2 (1);	0.531713	0.19101	N	0.122697	T	0.00384	0.0012	L	0.48174	1.505	0.25632	N	0.986292	B	0.19200	0.034	B	0.21917	0.037	T	0.01056	-1.1466	9	.	.	.	.	9.513	0.39089	0.6569:0.3431:0.0:0.0	rs34776842;rs61753192	267	Q9NY28	GALT8_HUMAN	G	267	ENSP00000252318:E267G	.	E	+	2	0	GALNT8	4724067	0.012000	0.17670	0.886000	0.34754	0.996000	0.88848	0.521000	0.22893	0.224000	0.20940	0.397000	0.26171	GAA	A|0.927;G|0.073	0.073	strong		0.488	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
OR5F1	338674	hgsc.bcm.edu	37	11	55761528	55761528	+	Missense_Mutation	SNP	T	T	C	rs35607186	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	120	0	0		WXS	Illumina HiSeq	Phase_I	120	51	0.425	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	
PPEF2	5470	hgsc.bcm.edu	37	4	76797739	76797739	+	Nonsense_Mutation	SNP	G	G	A	rs149631239		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:76797739G>A	ENST00000286719.7	-	11	1377	c.1021C>T	c.(1021-1023)Cag>Tag	p.Q341*		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	341	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)			ATGGGTCCCTGTGCAGAGCTC	0.547													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18236	0.0		0.0	False		,,,				2504	0.0				p.Q341X	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.C1021T						PASS	.	G	stop/GLN	1,4405	2.1+/-5.4	0,1,2202	95.0	98.0	97.0		1021	0.9	0.0	4	dbSNP_134	97	9,8591	7.1+/-27.0	0,9,4291	yes	stop-gained	PPEF2	NM_006239.2		0,10,6493	AA,AG,GG		0.1047,0.0227,0.0769		341/754	76797739	10,12996	2203	4300	6503	SO:0001587	stop_gained	5470	exon11			GTCCCTGTGCAGA	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.1021C>T	4.37:g.76797739G>A	ENSP00000286719:p.Gln341*	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	289	144	0.49827	NM_006239	O14831	Nonsense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	G	34	5.301613	0.95601	2.27E-4	0.001047	ENSG00000156194	ENST00000286719;ENST00000337500	.	.	.	3.63	0.893	0.19236	.	2.033460	0.02299	N	0.070992	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-0.1914	5.7028	0.17891	0.2626:0.4639:0.2735:0.0	.	.	.	.	X	341	.	ENSP00000286719:Q341X	Q	-	1	0	PPEF2	77016763	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.043000	0.13971	0.162000	0.19483	-0.339000	0.08088	CAG	G|0.999;A|0.001	0.001	strong		0.547	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
HLA-B	3106	hgsc.bcm.edu	37	6	31324057	31324057	+	Missense_Mutation	SNP	C	C	A	rs281864629|rs12697943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31324057C>A	ENST00000412585.2	-	3	534	c.506G>T	c.(505-507)cGc>cTc	p.R169L		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	169	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CTCCCACTTGCGCTGGGTGAT	0.667									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.R169L		Atlas-SNP	.											.	HLA-B	54	.	0			c.G506T						PASS	.						29.0	20.0	23.0					6																	31324057		2147	4208	6355	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	CACTTGCGCTGGG	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.506G>T	6.37:g.31324057C>A	ENSP00000399168:p.Arg169Leu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	289	118	0.408305	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	7.685	0.689875	0.15039	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00864	5.6;5.6	3.18	0.265	0.15612	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.208390	0.20930	U	0.083113	T	0.02342	0.0072	M	0.92691	3.335	0.09310	N	1	D;B	0.76494	0.999;0.007	D;B	0.79784	0.993;0.018	T	0.21211	-1.0252	10	0.87932	D	0	.	6.3785	0.21521	0.0:0.5259:0.0:0.4741	rs12697943	169;169	P30480;P01889	1B42_HUMAN;1B07_HUMAN	L	169;48;48;180	ENSP00000399168:R169L;ENSP00000405931:R180L	ENSP00000399168:R169L	R	-	2	0	HLA-B	31432036	0.001000	0.12720	0.009000	0.14445	0.002000	0.02628	-0.161000	0.10026	-0.079000	0.12707	0.297000	0.19635	CGC	C|0.990;A|0.010	0.010	strong		0.667	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
MS4A6A	64231	hgsc.bcm.edu	37	11	59940599	59940599	+	Missense_Mutation	SNP	T	T	A	rs7232	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:59940599T>A	ENST00000530839.1	-	7	1045	c.553A>T	c.(553-555)Act>Tct	p.T185S	MS4A6A_ENST00000528851.1_Missense_Mutation_p.T185S|MS4A6A_ENST00000426738.2_Missense_Mutation_p.T140S|MS4A6A_ENST00000420732.2_Missense_Mutation_p.N150I|MS4A6A_ENST00000412309.2_Missense_Mutation_p.T213S|MS4A6A_ENST00000323961.3_Missense_Mutation_p.T185S|MS4A6A_ENST00000529054.1_Missense_Mutation_p.T213S|MS4A6A_ENST00000533023.1_Missense_Mutation_p.N86I	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	185			T -> S (in dbSNP:rs7232). {ECO:0000269|PubMed:11401424}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGAGAGAGAGTTCCCTGAAAG	0.488													T|||	1072	0.214058	0.0401	0.2277	5008	,	,		21441	0.0575		0.3608	False		,,,				2504	0.4499				p.T213S		Atlas-SNP	.											.	MS4A6A	85	.	0			c.A637T	GRCh37	CM067701	MS4A6A	M	rs7232	PASS	.	T	SER/THR,ILE/ASN,SER/THR	428,3974	208.5+/-229.5	15,398,1788	115.0	103.0	107.0		553,449,553	-5.1	0.0	11	dbSNP_52	107	3180,5410	483.3+/-371.1	605,1970,1720	yes	missense,missense,missense	MS4A6A	NM_022349.2,NM_152851.1,NM_152852.1	58,149,58	620,2368,3508	AA,AT,TT		37.0198,9.7229,27.7709	benign,benign,benign	185/226,150/179,185/249	59940599	3608,9384	2201	4295	6496	SO:0001583	missense	64231	exon7			AGAGAGTTCCCTG	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.553A>T	11.37:g.59940599T>A	ENSP00000436979:p.Thr185Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Missense_Mutation	SNP	ENST00000530839.1	37	CCDS7981.1	428|428	0.19597069597069597|0.19597069597069597	19|19	0.03861788617886179|0.03861788617886179	93|93	0.2569060773480663|0.2569060773480663	38|38	0.06643356643356643|0.06643356643356643	278|278	0.36675461741424803|0.36675461741424803	T|T	12.82|12.82	2.051084|2.051084	0.36181|0.36181	0.097229|0.097229	0.370198|0.370198	ENSG00000110077|ENSG00000110077	ENST00000420732;ENST00000533023|ENST00000323961;ENST00000528851;ENST00000530839;ENST00000533989;ENST00000529054;ENST00000426738;ENST00000412309	T;T|T;T;T;T;T;T	0.23552|0.02216	3.09;1.9|4.39;4.39;4.39;4.39;4.39;4.39	4.66|4.66	-5.11|-5.11	0.02901|0.02901	.|.	.|1.816880	.|0.03459	.|N	.|0.211991	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|P;P;P;P	0.24368|0.44139	0.102|0.626;0.573;0.626;0.827	B|B;B;B;B	0.21151|0.43413	0.033|0.419;0.294;0.419;0.419	T|T	0.35325|0.35325	-0.9793|-0.9793	7|8	0.38643|0.51188	T|T	0.18|0.08	.|.	2.2928|2.2928	0.04143|0.04143	0.1302:0.3935:0.1901:0.2862|0.1302:0.3935:0.1901:0.2862	rs7232;rs1019670;rs1128323;rs3177289;rs3185181;rs17341520;rs17349303;rs17602417;rs17845711;rs17858658;rs52799801;rs56458515;rs1019670|rs7232;rs1019670;rs1128323;rs3177289;rs3185181;rs17341520;rs17349303;rs17602417;rs17845711;rs17858658;rs52799801;rs56458515;rs1019670	150|140;213;213;185	Q9H2W1-3|E7EMT7;F8W9K1;E9PSA9;Q9H2W1	.|.;.;.;M4A6A_HUMAN	I|S	150;86|185;185;185;85;213;140;213	ENSP00000392921:N150I;ENSP00000436172:N86I|ENSP00000315878:T185S;ENSP00000431901:T185S;ENSP00000436979:T185S;ENSP00000435844:T213S;ENSP00000392770:T140S;ENSP00000403212:T213S	ENSP00000392921:N150I|ENSP00000315878:T185S	N|T	-|-	2|1	0|0	MS4A6A|MS4A6A	59697175|59697175	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.131000|0.131000	0.20780|0.20780	-1.954000|-1.954000	0.01525|0.01525	-0.877000|-0.877000	0.04012|0.04012	-0.250000|-0.250000	0.11733|0.11733	AAC|ACT	T|0.641;A|0.359	0.359	strong		0.488	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
CDON	50937	hgsc.bcm.edu	37	11	125851055	125851055	+	Silent	SNP	A	A	G	rs564214	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:125851055A>G	ENST00000392693.3	-	17	3292	c.3165T>C	c.(3163-3165)aaT>aaC	p.N1055N	CDON_ENST00000263577.7_Silent_p.N1055N|CDON_ENST00000531738.1_Silent_p.N432N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1055					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)				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)		CATTGACTGCATTGGGGACCT	0.493													G|||	1343	0.268171	0.497	0.2161	5008	,	,		18390	0.0665		0.2604	False		,,,				2504	0.2117				p.N1055N		Atlas-SNP	.											CDON,brain,glioma,0,1	CDON	137	1	0			c.T3165C						PASS	.	G		2016,2386	613.5+/-392.2	466,1084,651	103.0	94.0	97.0		3165	-4.4	0.0	11	dbSNP_83	97	2326,6272	703.7+/-405.4	318,1690,2291	no	coding-synonymous	CDON	NM_016952.4		784,2774,2942	GG,GA,AA		27.0528,45.7974,33.4		1055/1265	125851055	4342,8658	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon17			GACTGCATTGGGG	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.3165T>C	11.37:g.125851055A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			A|0.698;G|0.302	0.302	strong		0.493	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
NFASC	23114	hgsc.bcm.edu	37	1	204924020	204924020	+	Missense_Mutation	SNP	C	C	T	rs3795564	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204924020C>T	ENST00000401399.1	+	6	675	c.476C>T	c.(475-477)aCg>aTg	p.T159M	NFASC_ENST00000367172.4_Missense_Mutation_p.T159M|NFASC_ENST00000367170.4_Missense_Mutation_p.T159M|NFASC_ENST00000404076.1_Missense_Mutation_p.T153M|NFASC_ENST00000360049.4_Missense_Mutation_p.T153M|NFASC_ENST00000404907.1_Missense_Mutation_p.T153M|NFASC_ENST00000403080.1_Missense_Mutation_p.T159M|NFASC_ENST00000539706.1_Missense_Mutation_p.T153M|NFASC_ENST00000513543.1_Missense_Mutation_p.T153M|NFASC_ENST00000367169.4_Missense_Mutation_p.T159M|NFASC_ENST00000367171.4_Missense_Mutation_p.T159M|NFASC_ENST00000339876.6_Missense_Mutation_p.T159M|NFASC_ENST00000338586.6_Missense_Mutation_p.T159M|NFASC_ENST00000338515.6_Missense_Mutation_p.T159M			O94856	NFASC_HUMAN	neurofascin	159	Ig-like C2-type 2.		T -> M (in dbSNP:rs3795564).		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)			GCTCCTTTGACGCTCCAGTGC	0.547													C|||	31	0.0061901	0.0	0.0043	5008	,	,		14488	0.0089		0.0089	False		,,,				2504	0.0102				p.T159M		Atlas-SNP	.											.	NFASC	396	.	0			c.C476T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	7,4399	12.9+/-30.5	0,7,2196	145.0	146.0	146.0		476,476,458,458,458,458	5.5	1.0	1	dbSNP_107	146	60,8540	38.3+/-94.2	0,60,4240	yes	missense,missense,missense,missense,missense,missense	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	81,81,81,81,81,81	0,67,6436	TT,TC,CC		0.6977,0.1589,0.5151	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	159/1241,159/620,153/1190,153/1175,153/614,153/1170	204924020	67,12939	2203	4300	6503	SO:0001583	missense	23114	exon7			CTTTGACGCTCCA	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.476C>T	1.37:g.204924020C>T	ENSP00000385637:p.Thr159Met	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	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	14|14	0.00641025641025641|0.00641025641025641	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	6|6	0.01048951048951049|0.01048951048951049	7|7	0.009234828496042216|0.009234828496042216	C|C	16.53|16.53	3.147785|3.147785	0.57151|0.57151	0.001589|0.001589	0.006977|0.006977	ENSG00000163531|ENSG00000163531	ENST00000367173|ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.17370	.|2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	.|0.118237	.|0.37715	.|N	.|0.001966	T|T	0.12008|0.12008	0.0292|0.0292	L|L	0.33710|0.33710	1.025|1.025	0.35996|0.35996	D|D	0.837036|0.837036	.|D;D;D;D;D;D	.|0.67145	.|0.991;0.972;0.996;0.995;0.989;0.969	.|B;B;P;P;P;P	.|0.49665	.|0.388;0.157;0.618;0.56;0.558;0.506	T|T	0.07214|0.07214	-1.0784|-1.0784	5|10	.|0.59425	.|D	.|0.04	.|.	6.1238|6.1238	0.20167|0.20167	0.0:0.6829:0.1622:0.1549|0.0:0.6829:0.1622:0.1549	rs3795564;rs52819361;rs3795564|rs3795564;rs52819361;rs3795564	.|153;153;255;159;153;159	.|O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.|.;.;.;.;.;.	C|M	129|159;159;159;159;159;159;153;153;153;159;159;159;153;159;153;153;129	.|ENSP00000356140:T159M;ENSP00000356139:T159M;ENSP00000356138:T159M;ENSP00000342128:T159M;ENSP00000344786:T159M;ENSP00000343509:T159M;ENSP00000438614:T153M;ENSP00000353154:T153M;ENSP00000356137:T159M;ENSP00000412161:T159M;ENSP00000384875:T159M;ENSP00000385676:T153M;ENSP00000385637:T159M;ENSP00000384061:T153M;ENSP00000425908:T153M;ENSP00000415031:T129M	.|ENSP00000295776:T153M	R|T	+|+	1|2	0|0	NFASC|NFASC	203190643|203190643	0.998000|0.998000	0.40836|0.40836	0.966000|0.966000	0.40874|0.40874	0.926000|0.926000	0.56050|0.56050	3.259000|3.259000	0.51515|0.51515	2.573000|2.573000	0.86826|0.86826	0.655000|0.655000	0.94253|0.94253	CGC|ACG	C|0.993;T|0.007	0.007	strong		0.547	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
LY75	4065	hgsc.bcm.edu	37	2	160711045	160711045	+	Splice_Site	SNP	G	G	C	rs3951216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160711045G>C	ENST00000263636.4	-	18	2448	c.2421C>G	c.(2419-2421)gaC>gaG	p.D807E	LY75_ENST00000553424.1_Splice_Site_p.D807E|LY75-CD302_ENST00000504764.1_Splice_Site_p.D807E|LY75-CD302_ENST00000505052.1_Splice_Site_p.D807E|LY75_ENST00000554112.1_Splice_Site_p.D807E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	807			D -> E (in dbSNP:rs3951216). {ECO:0000269|PubMed:9862343}.		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)		TTCCAGCACGGTCTAAAGAAG	0.358													C|||	2834	0.565895	0.3896	0.5778	5008	,	,		15355	0.7093		0.4304	False		,,,				2504	0.7873				p.D807E		Atlas-SNP	.											.	LY75	151	.	0			c.C2421G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	1718,2688	648.1+/-398.7	316,1086,801	61.0	61.0	61.0		2421,2421,2421	3.7	1.0	2	dbSNP_108	61	3765,4835	614.7+/-396.3	810,2145,1345	yes	missense-near-splice,missense-near-splice,missense-near-splice	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	45,45,45	1126,3231,2146	CC,CG,GG		43.7791,38.9923,42.1575	benign,benign,benign	807/1874,807/1818,807/1723	160711045	5483,7523	2203	4300	6503	SO:0001630	splice_region_variant	4065	exon18			AGCACGGTCTAAA	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.2420-1C>G	2.37:g.160711045G>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	1136	0.5201465201465202	193	0.39227642276422764	201	0.5552486187845304	413	0.722027972027972	329	0.4340369393139842	C	1.959	-0.439447	0.04636	0.389923	0.437791	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.09073	3.05;3.05;3.02;3.05;3.05	5.69	3.67	0.42095	.	0.242674	0.21217	N	0.078215	T	0.00012	0.0000	N	0.01482	-0.84	0.47009	P	7.190000000000252E-4	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.32322	-0.9911	9	0.02654	T	1	.	7.5174	0.27608	0.4063:0.4503:0.1434:0.0	rs3951216;rs52796448	807;807;807	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	E	807	ENSP00000451511:D807E;ENSP00000451446:D807E;ENSP00000263636:D807E;ENSP00000423463:D807E;ENSP00000421035:D807E	ENSP00000423463:D807E	D	-	3	2	LY75;LY75-CD302	160419291	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	1.124000	0.31320	0.715000	0.32103	-0.120000	0.15030	GAC	G|0.536;C|0.464	0.464	strong		0.358	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		Missense_Mutation
LDLRAD1	388633	hgsc.bcm.edu	37	1	54483792	54483792	+	5'UTR	SNP	G	G	T	rs116802374	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:54483792G>T	ENST00000371360.1	-	0	11				LDLRAD1_ENST00000420619.1_Silent_p.R20R|LDLRAD1_ENST00000545928.1_5'UTR|LDLRAD1_ENST00000371362.3_5'UTR	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1							integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						TCATGTCTTCGGTTTCCTGCT	0.592													G|||	80	0.0159744	0.0	0.036	5008	,	,		18046	0.0		0.0288	False		,,,				2504	0.0266				p.R20R		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.C58A						PASS	.	G		29,4377	34.3+/-65.2	0,29,2174	101.0	83.0	89.0			-2.3	0.0	1	dbSNP_132	89	215,8385	91.6+/-153.7	3,209,4088	no	utr-5	LDLRAD1	NM_001010978.2		3,238,6262	TT,TG,GG		2.5,0.6582,1.8761			54483792	244,12762	2203	4300	6503	SO:0001623	5_prime_UTR_variant	388633	exon1			GTCTTCGGTTTCC		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 1"""				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.-7C>A	1.37:g.54483792G>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_001276392	A0PJY0|B7ZME3|Q5T6Z9	Silent	SNP	ENST00000371360.1	37	CCDS30725.1																																																																																			G|0.979;T|0.021	0.021	strong		0.592	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455796	5455796	+	Silent	SNP	A	A	G	rs420325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5455796A>G	ENST00000222033.4	+	1	371	c.294A>G	c.(292-294)gcA>gcG	p.A98A		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	98						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		CCGCGCAGGCAGTGGTACGGG	0.697													G|||	3666	0.732029	0.8472	0.5908	5008	,	,		15479	0.8621		0.5795	False		,,,				2504	0.6994				p.A98A		Atlas-SNP	.											ZNRF4,colon,carcinoma,0,2	ZNRF4	59	2	0			c.A294G						PASS	.	G		3419,825		1402,615,105	46.0	55.0	52.0		294	-6.4	0.0	19	dbSNP_80	52	4732,3716		1347,2038,839	no	coding-synonymous	ZNRF4	NM_181710.3		2749,2653,944	GG,GA,AA		43.9867,19.4392,35.7784		98/430	5455796	8151,4541	2122	4224	6346	SO:0001819	synonymous_variant	148066	exon1			GCAGGCAGTGGTA	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.294A>G	19.37:g.5455796A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_181710	A8K886|O75866	Silent	SNP	ENST00000222033.4	37	CCDS42475.1																																																																																			A|0.316;G|0.684	0.684	strong		0.697	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
USH2A	7399	hgsc.bcm.edu	37	1	216592003	216592003	+	Silent	SNP	T	T	C	rs4253963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:216592003T>C	ENST00000307340.3	-	3	890	c.504A>G	c.(502-504)acA>acG	p.T168T	USH2A_ENST00000366942.3_Silent_p.T168T|USH2A_ENST00000366943.2_Silent_p.T168T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	168					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)		GCCCATCTACTGTCTTTTCTA	0.383										HNSCC(13;0.011)			t|||	3169	0.632788	0.4531	0.6614	5008	,	,		17096	0.8175		0.664	False		,,,				2504	0.6329				p.T168T		Atlas-SNP	.											USH2A,NS,carcinoma,-1,1	USH2A	1168	1	0			c.A504G						scavenged	.	C	,	2225,2181	592.2+/-387.7	562,1101,540	119.0	111.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	504,504	-9.8	0.0	1	dbSNP_111	114	5531,3069	659.9+/-401.7	1766,1999,535	no	coding-synonymous,coding-synonymous	USH2A	NM_007123.5,NM_206933.2	,	2328,3100,1075	CC,CT,TT		35.686,49.5007,40.366	,	168/1547,168/5203	216592003	7756,5250	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon3			ATCTACTGTCTTT	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.504A>G	1.37:g.216592003T>C		Somatic	129	2	0.0155039		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			T|0.380;C|0.620	0.620	strong		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
LRRK2	120892	hgsc.bcm.edu	37	12	40688695	40688695	+	Silent	SNP	T	T	C	rs7966550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:40688695T>C	ENST00000298910.7	+	22	2915	c.2857T>C	c.(2857-2859)Tta>Cta	p.L953L	LRRK2_ENST00000343742.2_Silent_p.L953L	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	953					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)	p.L953L(2)		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)				AAGAAAAATATTATCTTCAGA	0.289													T|||	451	0.0900559	0.0159	0.1282	5008	,	,		13787	0.1458		0.1292	False		,,,				2504	0.0654				p.L953L		Atlas-SNP	.											LRRK2_ENST00000298910,NS,carcinoma,0,2	LRRK2	763	2	2	Substitution - coding silent(2)	stomach(2)	c.T2857C						PASS	.	T		104,4302	78.3+/-116.7	1,102,2100	42.0	47.0	45.0		2857	-5.6	0.0	12	dbSNP_116	45	1127,7441	226.2+/-262.0	66,995,3223	no	coding-synonymous	LRRK2	NM_198578.3		67,1097,5323	CC,CT,TT		13.1536,2.3604,9.4882		953/2528	40688695	1231,11743	2203	4284	6487	SO:0001819	synonymous_variant	120892	exon22			AAAATATTATCTT	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.2857T>C	12.37:g.40688695T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	62	0.639175	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																			T|0.907;C|0.093	0.093	strong		0.289	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
RASAL3	64926	hgsc.bcm.edu	37	19	15574858	15574858	+	Silent	SNP	C	C	T	rs78677793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15574858C>T	ENST00000343625.7	-	2	397	c.312G>A	c.(310-312)ccG>ccA	p.P104P		NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	104	Pro-rich.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						CCTCCTGCTCCGGCTCCGGGT	0.647													C|||	474	0.0946486	0.0817	0.085	5008	,	,		13744	0.0694		0.167	False		,,,				2504	0.0706				p.P104P		Atlas-SNP	.											.	RASAL3	49	.	0			c.G312A						PASS	.	C		343,3561		22,299,1631	13.0	15.0	15.0		312	-7.9	0.0	19	dbSNP_132	15	1352,6896		126,1100,2898	no	coding-synonymous	RASAL3	NM_022904.1		148,1399,4529	TT,TC,CC		16.3919,8.7859,13.9483		104/1012	15574858	1695,10457	1952	4124	6076	SO:0001819	synonymous_variant	64926	exon2			CTGCTCCGGCTCC		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.312G>A	19.37:g.15574858C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	23	0.353846	NM_022904	Q8N2T9|Q9H735	Silent	SNP	ENST00000343625.7	37	CCDS46006.1																																																																																			C|0.894;T|0.106	0.106	strong		0.647	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
ZNF419	79744	hgsc.bcm.edu	37	19	58003488	58003488	+	Silent	SNP	A	A	G	rs2074070	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58003488A>G	ENST00000221735.7	+	4	393	c.207A>G	c.(205-207)gcA>gcG	p.A69A	ZNF419_ENST00000347466.6_Intron|ZNF419_ENST00000442920.2_Silent_p.A56A|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000518999.1_Silent_p.A70A|ZNF419_ENST00000520540.1_Silent_p.A57A|ZNF419_ENST00000426954.2_Silent_p.A57A|ZNF419_ENST00000354197.4_Silent_p.A57A|ZNF419_ENST00000415379.2_Intron|ZNF419_ENST00000424930.2_Silent_p.A70A			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TAGGACTTGCATCTTCCAAGA	0.468													A|||	2157	0.430711	0.2995	0.4611	5008	,	,		18486	0.5764		0.3161	False		,,,				2504	0.5542				p.A70A		Atlas-SNP	.											.	ZNF419	134	.	0			c.A210G						PASS	.						63.0	60.0	61.0					19																	58003488		2202	4280	6482	SO:0001819	synonymous_variant	79744	exon4			ACTTGCATCTTCC	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.207A>G	19.37:g.58003488A>G		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	163	138	0.846626	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			A|0.647;G|0.353	0.353	strong		0.468	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
MUC2	4583	hgsc.bcm.edu	37	11	1093368	1093368	+	Silent	SNP	G	G	A	rs111440994		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093368G>A	ENST00000441003.2	+	30	5214	c.5187G>A	c.(5185-5187)acG>acA	p.T1729T	MUC2_ENST00000333592.6_Silent_p.T17T|MUC2_ENST00000359061.5_Silent_p.T1696T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1696T(3)|p.T1729T(3)		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)	ccaccactacggtgaccccaa	0.647																																					p.T1729T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	6	Substitution - coding silent(6)	prostate(6)	c.G5187A						scavenged	.						175.0	224.0	207.0					11																	1093368		1971	3826	5797	SO:0001819	synonymous_variant	4583	exon30			CACTACGGTGACC	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.5187G>A	11.37:g.1093368G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	92	3	0.0326087	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	weak		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TRIM14	9830	hgsc.bcm.edu	37	9	100862339	100862339	+	Silent	SNP	C	C	A	rs35830621	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100862339C>A	ENST00000341469.2	-	3	420	c.411G>T	c.(409-411)acG>acT	p.T137T	TRIM14_ENST00000342043.3_Silent_p.T137T|TRIM14_ENST00000375098.3_Silent_p.T137T	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	137					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				GGGTAAGCTGCGTGTTTTTAT	0.468													C|||	176	0.0351438	0.0711	0.0288	5008	,	,		19176	0.001		0.0527	False		,,,				2504	0.0082				p.T137T	Colon(14;460 597 13826 51781)	Atlas-SNP	.											.	TRIM14	24	.	0			c.G411T						PASS	.	C	,,	251,4155	145.7+/-180.5	6,239,1958	135.0	128.0	131.0		411,411,411	-9.1	0.0	9	dbSNP_126	131	465,8135	137.9+/-194.8	8,449,3843	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM14	NM_014788.2,NM_033219.1,NM_033220.1	,,	14,688,5801	AA,AC,CC		5.407,5.6968,5.5052	,,	137/443,137/443,137/443	100862339	716,12290	2203	4300	6503	SO:0001819	synonymous_variant	9830	exon3			AAGCTGCGTGTTT	AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"""Tripartite motif containing / Tripartite motif containing"""	16283	protein-coding gene	gene with protein product		606556	"""tripartite motif-containing 14"""			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.411G>T	9.37:g.100862339C>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	165	75	0.454545	NM_033219	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Silent	SNP	ENST00000341469.2	37	CCDS6734.1																																																																																			C|0.951;A|0.049	0.049	strong		0.468	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788	
STRA6	64220	hgsc.bcm.edu	37	15	74473739	74473739	+	Missense_Mutation	SNP	C	C	T	rs736118	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:74473739C>T	ENST00000323940.5	-	17	1826	c.1581G>A	c.(1579-1581)atG>atA	p.M527I	RP11-665J16.1_ENST00000561647.1_RNA|STRA6_ENST00000395105.4_Missense_Mutation_p.M527I|STRA6_ENST00000535552.1_Missense_Mutation_p.M564I|STRA6_ENST00000416286.3_Missense_Mutation_p.M519I|STRA6_ENST00000449139.2_Missense_Mutation_p.M527I|STRA6_ENST00000423167.2_Missense_Mutation_p.M518I|STRA6_ENST00000563965.1_Missense_Mutation_p.M566I|STRA6_ENST00000574278.1_Missense_Mutation_p.M542I|STRA6_ENST00000574439.1_5'UTR	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	527			M -> I (in dbSNP:rs736118). {ECO:0000269|PubMed:11358845, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039}.		adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)	p.M527I(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						AGGTGGCCACCATGGCACCCA	0.622													C|||	999	0.199481	0.0825	0.1729	5008	,	,		20530	0.3631		0.0944	False		,,,				2504	0.316				p.M566I		Atlas-SNP	.											STRA6,NS,carcinoma,0,1	STRA6	66	1	1	Substitution - Missense(1)	stomach(1)	c.G1698A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	391,4005	194.7+/-219.5	20,351,1827	68.0	61.0	63.0		1581,1581,1554,1692,1626,1698,1581	3.8	0.1	15	dbSNP_86	63	739,7855	179.3+/-228.5	35,669,3593	yes	missense,missense,missense,missense,missense,missense,missense	STRA6	NM_001142617.1,NM_001142618.1,NM_001142619.1,NM_001199040.1,NM_001199041.1,NM_001199042.1,NM_022369.3	10,10,10,10,10,10,10	55,1020,5420	TT,TC,CC		8.599,8.8944,8.699	benign,benign,benign,benign,benign,benign,benign	527/668,527/668,518/659,564/705,542/683,566/707,527/668	74473739	1130,11860	2198	4297	6495	SO:0001583	missense	64220	exon17			GGCCACCATGGCA	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.1581G>A	15.37:g.74473739C>T	ENSP00000326085:p.Met527Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	37	CCDS10261.1	383	0.17536630036630035	38	0.07723577235772358	60	0.16574585635359115	209	0.36538461538461536	76	0.10026385224274406	C	11.40	1.627547	0.28978	0.088944	0.08599	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000416286;ENST00000545137;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000536129	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	4.72	3.79	0.43588	.	0.612179	0.17274	N	0.180272	T	0.00012	0.0000	L	0.33485	1.01	0.09310	P	1.0	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B	0.08055	0.003;0.003;0.001;0.001;0.003;0.001	T	0.13098	-1.0522	9	0.15066	T	0.55	-2.2341	11.9607	0.53007	0.0:0.9142:0.0:0.0858	rs736118;rs3743214;rs52818335;rs736118	564;565;518;527;566;336	F5GYI8;B7Z5G7;Q9BX79-3;Q9BX79;Q9BX79-4;B3KRT6	.;.;.;STRA6_HUMAN;.;.	I	527;527;459;336;566;518;564;417	ENSP00000378537:M527I;ENSP00000326085:M527I;ENSP00000413012:M518I;ENSP00000440238:M564I	ENSP00000326085:M527I	M	-	3	0	STRA6	72260792	0.856000	0.29760	0.128000	0.21923	0.860000	0.49131	0.320000	0.19540	0.956000	0.37904	0.561000	0.74099	ATG	C|0.873;T|0.127	0.127	strong		0.622	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
MYLK	4638	hgsc.bcm.edu	37	3	123419782	123419782	+	Missense_Mutation	SNP	G	G	A	rs3732485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:123419782G>A	ENST00000475616.1	-	15	2532	c.2533C>T	c.(2533-2535)Cgc>Tgc	p.R845C	MYLK_ENST00000346322.5_Missense_Mutation_p.R776C|MYLK_ENST00000360772.3_Missense_Mutation_p.R845C|MYLK_ENST00000359169.1_Missense_Mutation_p.R845C|MYLK_ENST00000360304.3_Missense_Mutation_p.R845C|MYLK_ENST00000510775.1_5'Flank			Q15746	MYLK_HUMAN	myosin light chain kinase	845			R -> C (in dbSNP:rs3732485).		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)		GACCCATAGCGGTCACTACCA	0.627													G|||	226	0.0451278	0.0318	0.0101	5008	,	,		13765	0.0526		0.0189	False		,,,				2504	0.1074				p.R845C		Atlas-SNP	.											.	MYLK	224	.	0			c.C2533T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	61,4341		0,61,2140	37.0	42.0	40.0		2533,2326,2533,2326	1.3	0.0	3	dbSNP_107	40	21,8569		0,21,4274	no	missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	180,180,180,180	0,82,6414	AA,AG,GG		0.2445,1.3857,0.6312	benign,benign,benign,benign	845/1915,776/1846,845/1864,776/1795	123419782	82,12910	2201	4295	6496	SO:0001583	missense	4638	exon18			CATAGCGGTCACT	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.2533C>T	3.37:g.123419782G>A	ENSP00000418335:p.Arg845Cys	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	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	61	0.027930402930402932	16	0.032520325203252036	4	0.011049723756906077	24	0.04195804195804196	17	0.022427440633245383	G	6.688	0.495469	0.12762	0.013857	0.002445	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67698	-0.28;-0.23;-0.28;-0.22;-0.23	5.45	1.3	0.21679	.	.	.	.	.	T	0.14056	0.0340	N	0.17082	0.46	0.09310	N	0.999992	B;B;B;B;B	0.17268	0.001;0.002;0.021;0.005;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.002;0.002;0.0	T	0.13926	-1.0491	9	0.45353	T	0.12	.	0.6904	0.00890	0.2428:0.1873:0.3784:0.1914	rs3732485;rs52814293;rs3732485	845;776;845;776;845	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	C	845;845;845;776;845	ENSP00000354004:R845C;ENSP00000353452:R845C;ENSP00000352088:R845C;ENSP00000320622:R776C;ENSP00000418335:R845C	ENSP00000320622:R776C	R	-	1	0	MYLK	124902472	0.005000	0.15991	0.002000	0.10522	0.625000	0.37756	-0.063000	0.11655	-0.056000	0.13221	-0.314000	0.08810	CGC	G|0.987;A|0.013	0.013	strong		0.627	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
CCDC65	85478	hgsc.bcm.edu	37	12	49312540	49312540	+	Missense_Mutation	SNP	C	C	T	rs78877829	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:49312540C>T	ENST00000320516.4	+	6	1068	c.880C>T	c.(880-882)Cgt>Tgt	p.R294C	CCDC65_ENST00000266984.5_Missense_Mutation_p.R294C|RP11-302B13.5_ENST00000398092.4_Intron	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	294										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						CCGGTATATCCGTAATGACAA	0.458													C|||	89	0.0177716	0.0023	0.0274	5008	,	,		19284	0.0		0.0567	False		,,,				2504	0.0102				p.R294C		Atlas-SNP	.											.	CCDC65	41	.	0			c.C880T						PASS	.	C	CYS/ARG	48,4358	48.2+/-83.0	0,48,2155	111.0	102.0	105.0		880	4.7	1.0	12	dbSNP_131	105	477,8123	140.3+/-196.8	14,449,3837	yes	missense	CCDC65	NM_033124.4	180	14,497,5992	TT,TC,CC		5.5465,1.0894,4.0366	probably-damaging	294/485	49312540	525,12481	2203	4300	6503	SO:0001583	missense	85478	exon6			TATATCCGTAATG		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.880C>T	12.37:g.49312540C>T	ENSP00000312706:p.Arg294Cys	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	66	0.03021978021978022	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	51	0.06728232189973615	C	18.72	3.684596	0.68157	0.010894	0.055465	ENSG00000139537	ENST00000266984;ENST00000552942;ENST00000320516	T;T;T	0.51071	1.34;0.72;1.35	4.72	4.72	0.59763	.	0.337418	0.30920	N	0.008603	T	0.14657	0.0354	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.69824	0.966	T	0.49399	-0.8944	10	0.59425	D	0.04	-7.8024	16.9918	0.86356	0.0:1.0:0.0:0.0	.	294	Q8IXS2	CCD65_HUMAN	C	294;191;294	ENSP00000266984:R294C;ENSP00000446569:R191C;ENSP00000312706:R294C	ENSP00000266984:R294C	R	+	1	0	CCDC65	47598807	0.989000	0.36119	0.985000	0.45067	0.508000	0.34012	2.687000	0.46976	2.630000	0.89119	0.655000	0.94253	CGT	C|0.965;T|0.035	0.035	strong		0.458	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
POPDC2	64091	hgsc.bcm.edu	37	3	119379186	119379186	+	Missense_Mutation	SNP	C	C	T	rs4688023	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:119379186C>T	ENST00000264231.3	-	1	251	c.85G>A	c.(85-87)Gtc>Atc	p.V29I	POPDC2_ENST00000468801.1_Missense_Mutation_p.V29I|POPDC2_ENST00000474523.1_Intron|POPDC2_ENST00000538678.1_Missense_Mutation_p.V29I|POPDC2_ENST00000493094.1_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	92	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	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	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386358	56386358	+	Silent	SNP	T	T	A	rs2526360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56386358T>A	ENST00000343736.4	-	22	4438	c.4275A>T	c.(4273-4275)cgA>cgT	p.R1425R	BZRAP1_ENST00000268893.6_Silent_p.R1365R|BZRAP1_ENST00000355701.3_Silent_p.R1425R			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1425						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCAGTGTTCTCGGGGATCTG	0.662													A|||	1407	0.28095	0.2973	0.2709	5008	,	,		15887	0.25		0.332	False		,,,				2504	0.2454				p.R1425R		Atlas-SNP	.											BZRAP1_ENST00000355701,NS,carcinoma,0,2	BZRAP1	287	2	0			c.A4275T						scavenged	.	A	,	1205,3139		177,851,1144	47.0	57.0	54.0		4275,4095	-9.9	0.9	17	dbSNP_100	54	2502,5968		398,1706,2131	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	575,2557,3275	AA,AT,TT		29.5396,27.7394,28.9293	,	1425/1858,1365/1798	56386358	3707,9107	2172	4235	6407	SO:0001819	synonymous_variant	9256	exon22			GTGTTCTCGGGGA	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4275A>T	17.37:g.56386358T>A		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	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	
CCDC170	80129	hgsc.bcm.edu	37	6	151907027	151907027	+	Missense_Mutation	SNP	G	G	A	rs41290243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:151907027G>A	ENST00000239374.7	+	7	1195	c.1096G>A	c.(1096-1098)Gtc>Atc	p.V366I	CCDC170_ENST00000367290.5_Missense_Mutation_p.V366I	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	366																	TTTCCAGATGGTCTCCCAGCT	0.448													G|||	54	0.0107827	0.0015	0.0144	5008	,	,		15905	0.0		0.0249	False		,,,				2504	0.0174				p.V366I		Atlas-SNP	.											.	.	.	.	0			c.G1096A						PASS	.	G	ILE/VAL	20,3792		0,20,1886	68.0	62.0	64.0		1096	4.9	1.0	6	dbSNP_127	64	285,7965		3,279,3843	yes	missense	C6orf97	NM_025059.3	29	3,299,5729	AA,AG,GG		3.4545,0.5247,2.5286	benign	366/716	151907027	305,11757	1906	4125	6031	SO:0001583	missense	80129	exon7			CAGATGGTCTCCC	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1096G>A	6.37:g.151907027G>A	ENSP00000239374:p.Val366Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	24	0.01098901098901099	0	0.0	7	0.019337016574585635	0	0.0	17	0.022427440633245383	G	9.672	1.146936	0.21288	0.005247	0.034545	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.09817	2.94;2.94	5.76	4.89	0.63831	.	0.475806	0.22581	N	0.058207	T	0.03434	0.0099	L	0.50333	1.59	0.26929	N	0.966503	B	0.29862	0.259	B	0.22753	0.041	T	0.34329	-0.9833	10	0.21540	T	0.41	-2.7206	10.5732	0.45212	0.1491:0.0:0.8509:0.0	rs41290243;rs61730722	366	Q8IYT3	CF097_HUMAN	I	366	ENSP00000239374:V366I;ENSP00000356259:V366I	ENSP00000239374:V366I	V	+	1	0	C6orf97	151948720	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.269000	0.51592	1.421000	0.47157	0.591000	0.81541	GTC	G|0.986;A|0.014	0.014	strong		0.448	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
ACACB	32	hgsc.bcm.edu	37	12	109684125	109684125	+	Missense_Mutation	SNP	G	G	A	rs61752535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109684125G>A	ENST00000338432.7	+	39	5562	c.5443G>A	c.(5443-5445)Gag>Aag	p.E1815K	ACACB_ENST00000377854.5_Missense_Mutation_p.E1745K|ACACB_ENST00000377848.3_Missense_Mutation_p.E1815K|ACACB_ENST00000543201.1_Missense_Mutation_p.E481K			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1815	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)	GCGGGCATCCGAGATGGCCCG	0.572													G|||	234	0.0467252	0.0991	0.0432	5008	,	,		15834	0.0		0.0596	False		,,,				2504	0.0133				p.E1815K		Atlas-SNP	.											.	ACACB	330	.	0			c.G5443A						PASS	.	G	LYS/GLU	392,4014	196.7+/-221.0	8,376,1819	71.0	75.0	74.0		5443	4.3	0.9	12	dbSNP_129	74	591,8009	157.2+/-210.9	17,557,3726	yes	missense	ACACB	NM_001093.3	56	25,933,5545	AA,AG,GG		6.8721,8.897,7.5581	benign	1815/2459	109684125	983,12023	2203	4300	6503	SO:0001583	missense	32	exon38			GCATCCGAGATGG	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.5443G>A	12.37:g.109684125G>A	ENSP00000341044:p.Glu1815Lys	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	212	96	0.45283	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	105	0.04807692307692308	45	0.09146341463414634	17	0.04696132596685083	0	0.0	43	0.05672823218997362	G	21.7	4.189029	0.78789	0.08897	0.068721	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201;ENST00000537347	D;D;D;D	0.97529	-4.42;-4.42;-4.42;-4.42	5.24	4.3	0.51218	Carboxyl transferase (1);Acetyl-coenzyme A carboxyltransferase, N-terminal (1);	0.047486	0.85682	D	0.000000	T	0.68604	0.3019	M	0.69248	2.105	0.51767	D	0.999936	D	0.67145	0.996	P	0.52627	0.704	T	0.75121	-0.3429	10	0.51188	T	0.08	.	16.5291	0.84353	0.0:0.1303:0.8697:0.0	rs61752535	1815	O00763	ACACB_HUMAN	K	1815;1815;1745;1046;481;140	ENSP00000341044:E1815K;ENSP00000367079:E1815K;ENSP00000367085:E1745K;ENSP00000444075:E481K	ENSP00000341044:E1815K	E	+	1	0	ACACB	108168508	1.000000	0.71417	0.949000	0.38748	0.688000	0.40055	4.600000	0.61083	2.618000	0.88619	0.561000	0.74099	GAG	G|0.937;A|0.063	0.063	strong		0.572	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
USPL1	10208	hgsc.bcm.edu	37	13	31231778	31231778	+	Missense_Mutation	SNP	G	G	C	rs17609459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:31231778G>C	ENST00000255304.4	+	9	1906	c.1564G>C	c.(1564-1566)Gct>Cct	p.A522P		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	522			A -> P (in dbSNP:rs17609459).		Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		TGACCAACACGCTCTCAGTAA	0.403													G|||	62	0.0123802	0.0204	0.013	5008	,	,		20603	0.0		0.0199	False		,,,				2504	0.0061				p.A522P	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.G1564C						PASS	.	G	PRO/ALA	101,4305	80.4+/-118.8	1,99,2103	135.0	131.0	133.0		1564	3.1	0.0	13	dbSNP_123	133	172,8428	79.5+/-142.1	4,164,4132	yes	missense	USPL1	NM_005800.4	27	5,263,6235	CC,CG,GG		2.0,2.2923,2.099	benign	522/1093	31231778	273,12733	2203	4300	6503	SO:0001583	missense	10208	exon9			CAACACGCTCTCA	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.1564G>C	13.37:g.31231778G>C	ENSP00000255304:p.Ala522Pro	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	36	0.016483516483516484	13	0.026422764227642278	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	13.09	2.132849	0.37630	0.022923	0.02	ENSG00000132952	ENST00000255304	T	0.08102	3.13	5.79	3.06	0.35304	.	0.937697	0.09093	N	0.849598	T	0.03053	0.0090	L	0.54323	1.7	0.09310	N	1	B	0.24186	0.099	B	0.23852	0.049	T	0.40924	-0.9537	10	0.22109	T	0.4	-4.288	9.692	0.40134	0.0:0.1844:0.3512:0.4644	rs17609459;rs52830887;rs56453321;rs17609459	522	Q5W0Q7	USPL1_HUMAN	P	522	ENSP00000255304:A522P	ENSP00000255304:A522P	A	+	1	0	USPL1	30129778	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.189000	0.09629	0.341000	0.23771	-0.169000	0.13324	GCT	C|0.020;G|0.980	0.020	strong		0.403	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
DNASE2	1777	hgsc.bcm.edu	37	19	12985576	12985576	+	IGR	SNP	A	A	G	rs11085822	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:12985576A>G	ENST00000222219.3	-	0	1955				AC020934.1_ENST00000578125.1_RNA|MAST1_ENST00000251472.4_Silent_p.S1535S	NM_001375.2	NP_001366.1	O00115	DNS2A_HUMAN	deoxyribonuclease II, lysosomal						apoptotic DNA fragmentation (GO:0006309)|DNA metabolic process (GO:0006259)|erythrocyte differentiation (GO:0030218)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)|DNA binding (GO:0003677)			breast(1)|large_intestine(1)|lung(4)|ovary(1)	7						TCTTGGGCTCAGGCACCAAGC	0.672													A|||	2190	0.4373	0.4304	0.3357	5008	,	,		14484	0.6181		0.2913	False		,,,				2504	0.4826				p.S1535S		Atlas-SNP	.											MAST1_ENST00000251472,NS,carcinoma,0,2	MAST1	214	2	0			c.A4605G						scavenged	.	A		1791,2609		382,1027,791	23.0	19.0	21.0		4605	-10.9	0.0	19	dbSNP_120	21	2313,6279		289,1735,2272	no	coding-synonymous	MAST1	NM_014975.2		671,2762,3063	GG,GA,AA		26.9204,40.7045,31.5887		1535/1571	12985576	4104,8888	2200	4296	6496	SO:0001628	intergenic_variant	22983	exon26			GGGCTCAGGCACC	AF045937	CCDS12284.1	19p13.2	2012-10-02			ENSG00000105612	ENSG00000105612	3.1.22.1		2960	protein-coding gene	gene with protein product		126350		DNL, DNL2		1586130	Standard	NM_001375		Approved		uc002mvn.1	O00115			19.37:g.12985576A>G		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	99	66	0.666667	NM_014975	B2RD06|B7Z4K6|O43910	Silent	SNP	ENST00000222219.3	37	CCDS12284.1																																																																																			A|0.639;G|0.361	0.361	strong		0.672	DNASE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451790.1		
ZNF98	148198	hgsc.bcm.edu	37	19	22574357	22574357	+	Missense_Mutation	SNP	C	C	G	rs200702907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	718	0	0		WXS	Illumina HiSeq	Phase_I	711	106	0.149086	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	
TEX101	83639	hgsc.bcm.edu	37	19	43922061	43922061	+	Silent	SNP	A	A	G	rs3816438	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43922061A>G	ENST00000598265.1	+	5	589	c.423A>G	c.(421-423)ccA>ccG	p.P141P	TEX101_ENST00000602198.1_Silent_p.P159P|TEX101_ENST00000253435.7_Silent_p.P159P|TEX101_ENST00000601707.1_3'UTR	NM_001130011.1	NP_001123483.1	Q9BY14	TX101_HUMAN	testis expressed 101	141	UPAR/Ly6.					acrosomal membrane (GO:0002080)|anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				large_intestine(1)|lung(12)|ovary(1)|skin(1)	15		Prostate(69;0.0199)				TCCATTGTCCAACCTGTGTGG	0.512													A|||	1440	0.28754	0.0287	0.2839	5008	,	,		21738	0.6091		0.2366	False		,,,				2504	0.3609				p.P159P		Atlas-SNP	.											.	TEX101	28	.	0			c.A477G						PASS	.	A	,	257,4149	146.1+/-180.8	5,247,1951	325.0	268.0	287.0		423,477	1.5	1.0	19	dbSNP_107	287	1964,6636	345.5+/-325.8	253,1458,2589	no	coding-synonymous,coding-synonymous	TEX101	NM_001130011.1,NM_031451.4	,	258,1705,4540	GG,GA,AA		22.8372,5.833,17.0767	,	141/250,159/268	43922061	2221,10785	2203	4300	6503	SO:0001819	synonymous_variant	83639	exon8			TTGTCCAACCTGT	AF241268	CCDS12619.1, CCDS59393.1	19q13.31	2013-06-06	2007-03-13			ENSG00000131126			30722	protein-coding gene	gene with protein product	"""cancer/testis antigen 131"", ""spermatogenesis associated 44"""	612665	"""testis expressed sequence 101"""			16388701, 16516155	Standard	NM_031451		Approved	MGC4766, SGRG, CT131, SPATA44	uc010xwo.2	Q9BY14		ENST00000598265.1:c.423A>G	19.37:g.43922061A>G		Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	403	206	0.511166	NM_031451	Q7L5R2|Q9BPY7	Silent	SNP	ENST00000598265.1	37	CCDS59393.1																																																																																			A|0.783;G|0.217	0.217	strong		0.512	TEX101-004	KNOWN	non_canonical_other|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000463176.1	NM_031451	
MC5R	4161	hgsc.bcm.edu	37	18	13826088	13826088	+	Silent	SNP	C	C	T	rs17848292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:13826088C>T	ENST00000324750.3	+	1	546	c.324C>T	c.(322-324)gaC>gaT	p.D108D	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	108					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						TGATAGCAGACGCCTTTGTGC	0.532													C|||	783	0.15635	0.1611	0.2464	5008	,	,		23692	0.1865		0.1372	False		,,,				2504	0.0746				p.D108D		Atlas-SNP	.											.	MC5R	83	.	0			c.C324T						PASS	.	C		721,3685	299.0+/-285.6	64,593,1546	156.0	127.0	137.0		324	-5.5	0.0	18	dbSNP_123	137	1228,7372	247.2+/-275.4	89,1050,3161	no	coding-synonymous	MC5R	NM_005913.2		153,1643,4707	TT,TC,CC		14.2791,16.364,14.9854		108/326	13826088	1949,11057	2203	4300	6503	SO:0001819	synonymous_variant	4161	exon1			AGCAGACGCCTTT	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.324C>T	18.37:g.13826088C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	152	91	0.598684	NM_005913	B0YJ34|Q502V1	Silent	SNP	ENST00000324750.3	37	CCDS11868.1																																																																																			C|0.850;T|0.150	0.150	strong		0.532	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913	
PADI4	23569	hgsc.bcm.edu	37	1	17668563	17668563	+	Missense_Mutation	SNP	G	G	A	rs35903413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17668563G>A	ENST00000375448.4	+	7	804	c.778G>A	c.(778-780)Gac>Aac	p.D260N	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	260			D -> N (in dbSNP:rs35903413).		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)	CCCGGACACCGACTTCCCGGG	0.627													G|||	263	0.052516	0.0129	0.0865	5008	,	,		16205	0.001		0.1531	False		,,,				2504	0.0317				p.D260N		Atlas-SNP	.											.	PADI4	70	.	0			c.G778A						PASS	.	G	ASN/ASP	131,4275	96.2+/-134.9	0,131,2072	85.0	80.0	82.0		778	1.3	0.1	1	dbSNP_126	82	1107,7493	231.1+/-265.2	77,953,3270	yes	missense	PADI4	NM_012387.2	23	77,1084,5342	AA,AG,GG		12.8721,2.9732,9.5187	benign	260/664	17668563	1238,11768	2203	4300	6503	SO:0001583	missense	23569	exon7			GACACCGACTTCC	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.778G>A	1.37:g.17668563G>A	ENSP00000364597:p.Asp260Asn	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	37	CCDS180.1	156	0.07142857142857142	4	0.008130081300813009	30	0.08287292817679558	1	0.0017482517482517483	121	0.15963060686015831	g	1.634	-0.518326	0.04171	0.029732	0.128721	ENSG00000159339	ENST00000375448	T	0.15372	2.43	4.63	1.27	0.21489	Protein-arginine deiminase (PAD), central domain (2);	0.532611	0.20775	N	0.085903	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.14805	0.011;0.011	B;B	0.12837	0.008;0.008	T	0.37009	-0.9724	9	0.20519	T	0.43	-13.0871	6.2085	0.20615	0.5552:0.0:0.4448:0.0	rs35903413	260;260	A8K392;Q9UM07	.;PADI4_HUMAN	N	260	ENSP00000364597:D260N	ENSP00000364597:D260N	D	+	1	0	PADI4	17541150	0.000000	0.05858	0.069000	0.20011	0.041000	0.13682	0.539000	0.23175	0.345000	0.23873	-0.355000	0.07637	GAC	G|0.908;A|0.092	0.092	strong		0.627	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
WRNIP1	56897	hgsc.bcm.edu	37	6	2770468	2770468	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:2770468C>T	ENST00000380773.4	+	3	1338	c.1129C>T	c.(1129-1131)Ctt>Ttt	p.L377F	WRNIP1_ENST00000380771.4_Missense_Mutation_p.L352F|WRNIP1_ENST00000380764.1_5'UTR|WRNIP1_ENST00000380769.4_Missense_Mutation_p.L157F	NM_020135.2	NP_064520.2			Werner helicase interacting protein 1											breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				AGTGATTGTTCTTGAGAAGCT	0.522																																					p.L377F		Atlas-SNP	.											WRNIP1,NS,carcinoma,-1,1	WRNIP1	39	1	0			c.C1129T						scavenged	.						141.0	125.0	130.0					6																	2770468		2203	4300	6503	SO:0001583	missense	56897	exon3			ATTGTTCTTGAGA	AB056152	CCDS4475.1, CCDS4476.1	6p25.2	2010-04-21			ENSG00000124535	ENSG00000124535		"""ATPases / AAA-type"""	20876	protein-coding gene	gene with protein product		608196				11301316	Standard	NM_020135		Approved	WHIP, FLJ22526, bA420G6.2	uc003mtz.3	Q96S55	OTTHUMG00000014126	ENST00000380773.4:c.1129C>T	6.37:g.2770468C>T	ENSP00000370150:p.Leu377Phe	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	134	3	0.0223881	NM_020135		Missense_Mutation	SNP	ENST00000380773.4	37	CCDS4475.1	.	.	.	.	.	.	.	.	.	.	C	31	5.059524	0.93846	.	.	ENSG00000124535	ENST00000380773;ENST00000380771;ENST00000380769	T;T;T	0.41758	0.99;0.99;0.99	6.06	5.19	0.71726	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.44244	0.1284	L	0.41415	1.275	0.80722	D	1	P;P	0.49961	0.89;0.93	P;D	0.63877	0.472;0.919	T	0.50074	-0.8870	10	0.87932	D	0	-36.0835	14.2448	0.65981	0.0:0.9294:0.0:0.0706	.	352;377	Q96S55-2;Q96S55	.;WRIP1_HUMAN	F	377;352;157	ENSP00000370150:L377F;ENSP00000370148:L352F;ENSP00000370146:L157F	ENSP00000370146:L157F	L	+	1	0	WRNIP1	2715467	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.927000	0.70080	1.578000	0.49821	0.650000	0.86243	CTT	.	.	none		0.522	WRNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039641.1	NM_130395	
TNFRSF10B	8795	hgsc.bcm.edu	37	8	22926313	22926313	+	Missense_Mutation	SNP	G	G	A	rs1129424	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:22926313G>A	ENST00000276431.4	-	1	379	c.95C>T	c.(94-96)cCc>cTc	p.P32L	RP11-875O11.2_ENST00000501897.1_RNA|TNFRSF10B_ENST00000542226.1_5'UTR|TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.P32L|RP11-875O11.3_ENST00000520840.1_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	15	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	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	
CNR2	1269	hgsc.bcm.edu	37	1	24201919	24201919	+	Silent	SNP	T	T	C	rs35761398|rs2502992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201919T>C	ENST00000374472.4	-	2	350	c.189A>G	c.(187-189)caA>caG	p.Q63Q	CNR2_ENST00000536471.1_Silent_p.Q63Q	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	63			Q -> R (high incidence in Japanese depressed subjects; dbSNP:rs2501432). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18286196}.		G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)	p.Q63Q(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	TCCGGCGGAGTTGGTGGGAGG	0.552													C|||	3275	0.653954	0.7958	0.6383	5008	,	,		19878	0.503		0.5875	False		,,,				2504	0.6973				p.Q63Q		Atlas-SNP	.											CNR2,NS,carcinoma,-1,2	CNR2	78	2	1	Substitution - coding silent(1)	stomach(1)	c.A189G						scavenged	.	C		3214,1192		1261,692,250	60.0	70.0	67.0		189	3.0	1.0	1	dbSNP_100	67	4758,3842		1403,1952,945	no	coding-synonymous	CNR2	NM_001841.2		2664,2644,1195	CC,CT,TT		44.6744,27.054,38.7052		63/361	24201919	7972,5034	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			GCGGAGTTGGTGG	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.189A>G	1.37:g.24201919T>C		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			CC|1.000;|0.000	.	alt		0.552	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
SEC14L5	9717	hgsc.bcm.edu	37	16	5050897	5050897	+	Silent	SNP	G	G	C	rs2286966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:5050897G>C	ENST00000251170.7	+	10	1281	c.1101G>C	c.(1099-1101)ggG>ggC	p.G367G		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	367	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						GGTGTGAGGGGAGCACAAGGC	0.612													G|||	1990	0.397364	0.413	0.4885	5008	,	,		17758	0.2609		0.4742	False		,,,				2504	0.3732				p.G367G		Atlas-SNP	.											.	SEC14L5	79	.	0			c.G1101C						PASS	.	G		1707,2497		362,983,757	25.0	29.0	27.0		1101	-0.4	1.0	16	dbSNP_100	27	4018,4450		963,2092,1179	no	coding-synonymous	SEC14L5	NM_014692.1		1325,3075,1936	CC,CG,GG		47.4492,40.6042,45.1783		367/697	5050897	5725,6947	2102	4234	6336	SO:0001819	synonymous_variant	9717	exon10			TGAGGGGAGCACA	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.1101G>C	16.37:g.5050897G>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			G|0.589;C|0.411	0.411	strong		0.612	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
ABCA4	24	hgsc.bcm.edu	37	1	94473845	94473845	+	Silent	SNP	T	T	C	rs2275029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:94473845T>C	ENST00000370225.3	-	42	5930	c.5844A>G	c.(5842-5844)ccA>ccG	p.P1948P	ABCA4_ENST00000465352.1_5'UTR|ABCA4_ENST00000536513.1_Silent_p.P218P|ABCA4_ENST00000535881.1_Silent_p.P67P	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1948	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		P -> L (in dbSNP:rs56142141). {ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11385708, ECO:0000269|PubMed:11527935, ECO:0000269|PubMed:11594993}.		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)	p.P1948P(1)		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)		TGGAGGTGCCTGGATAAATCT	0.542													T|||	837	0.167133	0.264	0.1585	5008	,	,		17654	0.12		0.1441	False		,,,				2504	0.1145				p.P1948P		Atlas-SNP	.											ABCA4,NS,carcinoma,0,1	ABCA4	275	1	1	Substitution - coding silent(1)	stomach(1)	c.A5844G						PASS	.	T		1033,3373	378.3+/-322.8	133,767,1303	71.0	72.0	72.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5844	-2.8	1.0	1	dbSNP_100	72	1564,7036	285.4+/-297.1	145,1274,2881	no	coding-synonymous	ABCA4	NM_000350.2		278,2041,4184	CC,CT,TT		18.186,23.4453,19.9677		1948/2274	94473845	2597,10409	2203	4300	6503	SO:0001819	synonymous_variant	24	exon42			GGTGCCTGGATAA	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.5844A>G	1.37:g.94473845T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			T|0.804;C|0.196	0.196	strong		0.542	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
ALDH3A1	218	hgsc.bcm.edu	37	17	19644472	19644472	+	Silent	SNP	A	A	T	rs2072330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19644472A>T	ENST00000457500.2	-	5	1070	c.741T>A	c.(739-741)ccT>ccA	p.P247P	ALDH3A1_ENST00000444455.1_Silent_p.P247P|ALDH3A1_ENST00000225740.6_Silent_p.P247P|RP11-311F12.2_ENST00000580884.1_RNA|ALDH3A1_ENST00000395555.3_Silent_p.P247P|ALDH3A1_ENST00000494157.2_Silent_p.P174P|ALDH3A1_ENST00000485231.1_5'Flank	NM_001135168.1	NP_001128640.1	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3 family, member A1	247					aging (GO:0007568)|cellular aldehyde metabolic process (GO:0006081)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|alcohol dehydrogenase (NADP+) activity (GO:0008106)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)		GGATGTAGTCAGGGGCCACGC	0.532													A|||	1456	0.290735	0.0923	0.3934	5008	,	,		11377	0.2956		0.3907	False		,,,				2504	0.3783				p.P247P		Atlas-SNP	.											.	ALDH3A1	40	.	0			c.T741A						PASS	.	A	,,	550,3856	246.8+/-255.3	33,484,1686	87.0	76.0	80.0		741,741,741	-10.4	0.1	17	dbSNP_96	80	3376,5224	502.0+/-375.6	640,2096,1564	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH3A1	NM_000691.4,NM_001135167.1,NM_001135168.1	,,	673,2580,3250	TT,TA,AA		39.2558,12.483,30.1861	,,	247/454,247/454,247/454	19644472	3926,9080	2203	4300	6503	SO:0001819	synonymous_variant	218	exon5			GTAGTCAGGGGCC	M74542	CCDS11212.1	17p11.2	2010-05-07	2010-05-07		ENSG00000108602	ENSG00000108602	1.2.1.5	"""Aldehyde dehydrogenases"""	405	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase, dimeric NADP-preferring"""	100660		ALDH3		7774944, 1737758	Standard	NM_000691		Approved		uc010cqu.3	P30838	OTTHUMG00000059469	ENST00000457500.2:c.741T>A	17.37:g.19644472A>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_001135168	A8K828|Q9BT37	Silent	SNP	ENST00000457500.2	37	CCDS11212.1																																																																																			A|0.701;T|0.299	0.299	strong		0.532	ALDH3A1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132265.4	NM_000691	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418155	105418155	+	Silent	SNP	G	G	C	rs141600524		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105418155G>C	ENST00000333244.5	-	7	3752	c.3633C>G	c.(3631-3633)ctC>ctG	p.L1211L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1211						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)			GCTGAATGCTGAGGTCAGTGG	0.647																																					p.L1211L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3633G						PASS	.	G		80,3750		19,42,1854	104.0	78.0	86.0		3633	-6.0	0.0	14	dbSNP_134	86	913,6543		290,333,3105	no	coding-synonymous	AHNAK2	NM_138420.2		309,375,4959	CC,CG,GG		12.2452,2.0888,8.7985		1211/5796	105418155	993,10293	1915	3728	5643	SO:0001819	synonymous_variant	113146	exon7			AATGCTGAGGTCA	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.3633C>G	14.37:g.105418155G>C		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.897;C|0.103	0.103	strong		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MCM8	84515	hgsc.bcm.edu	37	20	5966626	5966626	+	Missense_Mutation	SNP	G	G	T	rs150257637		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:5966626G>T	ENST00000378896.3	+	16	2389	c.2012G>T	c.(2011-2013)gGc>gTc	p.G671V	MCM8_ENST00000265187.4_Missense_Mutation_p.G655V|MCM8_ENST00000378883.1_Missense_Mutation_p.G624V|MCM8_ENST00000378886.2_Missense_Mutation_p.G711V	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	671					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						AAGTACATTGGCTATGCTCGG	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		18852	0.0		0.001	False		,,,				2504	0.0				p.G671V		Atlas-SNP	.											.	MCM8	125	.	0			c.G2012T						PASS	.	G	VAL/GLY,VAL/GLY	1,4405	2.1+/-5.4	0,1,2202	135.0	121.0	126.0		2012,1964	5.3	1.0	20	dbSNP_134	126	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	109,109	0,6,6497	TT,TG,GG		0.0581,0.0227,0.0461	possibly-damaging,possibly-damaging	671/841,655/825	5966626	6,13000	2203	4300	6503	SO:0001583	missense	84515	exon16			ACATTGGCTATGC	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.2012G>T	20.37:g.5966626G>T	ENSP00000368174:p.Gly671Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	156	70	0.448718	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.9	4.060936	0.76074	2.27E-4	5.81E-4	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.06068	3.35;3.35;3.35;3.35	5.33	5.33	0.75918	.	0.096141	0.64402	D	0.000001	T	0.10937	0.0267	L	0.39898	1.24	0.80722	D	1	P;P;B;P	0.47191	0.73;0.891;0.431;0.772	B;P;B;B	0.47346	0.219;0.544;0.219;0.326	T	0.12142	-1.0559	10	0.30078	T	0.28	-14.9313	19.4129	0.94683	0.0:0.0:1.0:0.0	.	624;711;655;671	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	V	671;624;711;655	ENSP00000368174:G671V;ENSP00000368161:G624V;ENSP00000368164:G711V;ENSP00000265187:G655V	ENSP00000265187:G655V	G	+	2	0	MCM8	5914626	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.648000	0.98483	2.652000	0.90054	0.655000	0.94253	GGC	G|0.999;T|0.001	0.001	strong		0.448	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
C16orf96	342346	hgsc.bcm.edu	37	16	4649300	4649300	+	Missense_Mutation	SNP	C	C	G	rs7195763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4649300C>G	ENST00000444310.4	+	15	3143	c.3143C>G	c.(3142-3144)tCt>tGt	p.S1048C		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						AAGGCTCCATCTCCCCCGTCA	0.612													G|||	631	0.125998	0.416	0.0432	5008	,	,		17238	0.003		0.0457	False		,,,				2504	0.002				p.S1048C		Atlas-SNP	.											.	C16orf96	28	.	0			c.C3143G						PASS	.	G	CYS/SER	481,903		90,301,301	210.0	181.0	190.0		3143	-1.5	0.0	16	dbSNP_116	190	114,3068		0,114,1477	yes	missense	C16orf96	NM_001145011.1	112	90,415,1778	GG,GC,CC		3.5827,34.7543,13.0311	benign	1048/1142	4649300	595,3971	692	1591	2283	SO:0001583	missense	342346	exon15			CTCCATCTCCCCC		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.3143C>G	16.37:g.4649300C>G	ENSP00000415027:p.Ser1048Cys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_001145011		Missense_Mutation	SNP	ENST00000444310.4	37	CCDS53986.1	239	0.10943223443223443	189	0.38414634146341464	20	0.055248618784530384	2	0.0034965034965034965	28	0.036939313984168866	G	4.007	-0.001415	0.07819	0.347543	0.035827	ENSG00000205832	ENST00000444310	T	0.63913	-0.07	3.24	-1.51	0.08664	.	.	.	.	.	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	0.36286	-0.9754	8	0.36615	T	0.2	.	4.8603	0.13581	0.2575:0.324:0.4185:0.0	rs7195763;rs59679953;rs7195763	1048	A6NNT2	CP096_HUMAN	C	1048	ENSP00000415027:S1048C	ENSP00000415027:S1048C	S	+	2	0	C16orf96	4589301	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.000000	0.12993	-0.596000	0.05821	-1.436000	0.01078	TCT	C|0.901;G|0.099	0.099	strong		0.612	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21174496	21174496	+	Missense_Mutation	SNP	C	C	T	rs12824121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21174496C>T	ENST00000421593.2	+	3	320	c.320C>T	c.(319-321)cCg>cTg	p.P107L	LST3_ENST00000540229.1_Intron|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.P154L|LST3_ENST00000381541.3_Missense_Mutation_p.P154L|SLCO1B3_ENST00000553473.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						AATAGAACACCGTCTGAGATA	0.254													C|||	21	0.00419329	0.0008	0.0029	5008	,	,		15614	0.0		0.0179	False		,,,				2504	0.0				p.P107L		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.C320T						PASS	.	C	LEU/PRO	14,3786		0,14,1886	38.0	34.0	35.0		320	2.8	0.0	12	dbSNP_121	35	139,8183		1,137,4023	yes	missense	SLCO1B7	NM_001009562.4	98	1,151,5909	TT,TC,CC		1.6703,0.3684,1.2622		107/641	21174496	153,11969	1900	4161	6061	SO:0001583	missense	338821	exon3			GAACACCGTCTGA	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.320C>T	12.37:g.21174496C>T	ENSP00000394168:p.Pro107Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	19	0.0086996336996337	0	0.0	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	.	7.606	0.673791	0.14841	0.003684	0.016703	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.37915	1.17;1.17;1.17	2.79	2.79	0.32731	.	1.095650	0.07077	U	0.836307	T	0.17152	0.0412	L	0.39147	1.195	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.13407	0.007;0.009	T	0.12941	-1.0528	10	0.37606	T	0.19	.	9.1237	0.36801	0.0:1.0:0.0:0.0	rs12824121;rs52800356;rs12824121	107;154	G3V0H7;F5H094	.;.	L	154;154;107	ENSP00000370952:P154L;ENSP00000452013:P154L;ENSP00000394168:P107L	ENSP00000370952:P154L	P	+	2	0	SLCO1B7;RP11-545J16.1	21065763	0.003000	0.15002	0.005000	0.12908	0.124000	0.20399	1.055000	0.30467	1.531000	0.49152	0.205000	0.17691	CCG	C|0.990;T|0.010	0.010	strong		0.254	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
CCT2	10576	hgsc.bcm.edu	37	12	69986788	69986788	+	Silent	SNP	A	A	G	rs1043434	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:69986788A>G	ENST00000299300.6	+	9	971	c.783A>G	c.(781-783)acA>acG	p.T261T	CCT2_ENST00000544368.2_Silent_p.T261T|CCT2_ENST00000543146.2_Silent_p.T214T	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	65	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1266537	1266537	+	Silent	SNP	G	G	T	rs199659189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1266537G>T	ENST00000529681.1	+	31	8485	c.8427G>T	c.(8425-8427)ctG>ctT	p.L2809L	MUC5B_ENST00000447027.1_Silent_p.L2812L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2809	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)		CTCCAGCCCTGTCCAGCCCTC	0.682													-|||	290	0.0579073	0.0401	0.1167	5008	,	,		17295	0.0387		0.0706	False		,,,				2504	0.047				p.L2809L		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.G8427T						scavenged	.																																			SO:0001819	synonymous_variant	727897	exon31			AGCCCTGTCCAGC	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.8427G>T	11.37:g.1266537G>T		Somatic	440	2	0.00454545		WXS	Illumina HiSeq	Phase_I	316	94	0.297468	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.790;T|0.211	0.211	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
EXPH5	23086	hgsc.bcm.edu	37	11	108383676	108383676	+	Missense_Mutation	SNP	A	A	G	rs10749920	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:108383676A>G	ENST00000265843.4	-	6	2668	c.2558T>C	c.(2557-2559)cTg>cCg	p.L853P	EXPH5_ENST00000443411.1_Missense_Mutation_p.L665P|EXPH5_ENST00000525344.1_Missense_Mutation_p.L846P|EXPH5_ENST00000428840.1_Missense_Mutation_p.L777P|EXPH5_ENST00000524840.1_5'Flank	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	149	0	0		WXS	Illumina HiSeq	Phase_I	161	77	0.478261	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	
RHPN2	85415	hgsc.bcm.edu	37	19	33499071	33499071	+	Silent	SNP	G	G	A	rs10410414	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33499071G>A	ENST00000254260.3	-	7	644	c.609C>T	c.(607-609)acC>acT	p.T203T	RHPN2_ENST00000400226.4_Silent_p.T52T	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	203	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					CCGGAACCCCGGTGAGAGAGT	0.473													G|||	1090	0.217652	0.2345	0.1744	5008	,	,		16699	0.1796		0.1988	False		,,,				2504	0.2843				p.T203T		Atlas-SNP	.											.	RHPN2	107	.	0			c.C609T						PASS	.	G		913,3493		96,721,1386	26.0	28.0	27.0		609	-6.8	0.8	19	dbSNP_119	27	1480,7120		129,1222,2949	no	coding-synonymous	RHPN2	NM_033103.4		225,1943,4335	AA,AG,GG		17.2093,20.7217,18.3992		203/687	33499071	2393,10613	2203	4300	6503	SO:0001819	synonymous_variant	85415	exon7			AACCCCGGTGAGA	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.609C>T	19.37:g.33499071G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Silent	SNP	ENST00000254260.3	37	CCDS12427.1																																																																																			G|0.809;A|0.191	0.191	strong		0.473	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
ADAM15	8751	hgsc.bcm.edu	37	1	155030557	155030557	+	Silent	SNP	A	A	C	rs11264303	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:155030557A>C	ENST00000356955.2	+	14	1748	c.1647A>C	c.(1645-1647)acA>acC	p.T549T	ADAM15_ENST00000531455.1_Silent_p.T559T|ADAM15_ENST00000359280.4_Silent_p.T549T|ADAM15_ENST00000447332.3_Silent_p.T533T|ADAM15_ENST00000271836.6_Silent_p.T549T|ADAM15_ENST00000368413.1_Silent_p.T255T|ADAM15_ENST00000368412.3_Silent_p.T549T|ADAM15_ENST00000355956.2_Silent_p.T549T|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000368410.2_Silent_p.T255T|ADAM15_ENST00000449910.2_Silent_p.T549T|ADAM15_ENST00000360674.4_Silent_p.T549T	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	549	Cys-rich.				angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GCCTCCAGACAGCTAATACTC	0.597													A|||	1625	0.324481	0.4508	0.3127	5008	,	,		19561	0.0069		0.5179	False		,,,				2504	0.2904				p.T559T		Atlas-SNP	.											.	ADAM15	92	.	0			c.A1677C						PASS	.	A	,,,,,	2119,2287	574.5+/-383.8	517,1085,601	56.0	60.0	59.0		1647,1647,1647,1647,1647,1647	0.5	0.4	1	dbSNP_120	59	4523,4077	591.2+/-392.8	1180,2163,957	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADAM15	NM_003815.3,NM_207191.1,NM_207194.1,NM_207195.1,NM_207196.1,NM_207197.1	,,,,,	1697,3248,1558	CC,CA,AA		47.407,48.0935,48.9313	,,,,,	549/815,549/773,549/840,549/839,549/863,549/864	155030557	6642,6364	2203	4300	6503	SO:0001819	synonymous_variant	8751	exon14			CCAGACAGCTAAT	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.1647A>C	1.37:g.155030557A>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001261464	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Silent	SNP	ENST00000356955.2	37	CCDS1087.1																																																																																			A|0.558;C|0.442	0.442	strong		0.597	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	
ZNF611	81856	hgsc.bcm.edu	37	19	53209554	53209554	+	Missense_Mutation	SNP	G	G	T	rs4085565|rs34846371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53209554G>T	ENST00000319783.1	-	7	1070	c.754C>A	c.(754-756)Ccc>Acc	p.P252T	ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000543227.1_Missense_Mutation_p.P252T|ZNF611_ENST00000595798.1_Missense_Mutation_p.P183T|ZNF611_ENST00000540744.1_Missense_Mutation_p.P252T|ZNF611_ENST00000453741.2_Missense_Mutation_p.P183T|ZNF611_ENST00000602162.1_Missense_Mutation_p.P183T	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	152	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	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	
UNC93A	54346	hgsc.bcm.edu	37	6	167709702	167709702	+	Nonsense_Mutation	SNP	G	G	A	rs2235197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:167709702G>A	ENST00000230256.3	+	3	627	c.452G>A	c.(451-453)tGg>tAg	p.W151*	UNC93A_ENST00000366829.2_Nonsense_Mutation_p.W151*	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	151						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)		TCCGGTGTGTGGGGCAACTTG	0.507													G|||	553	0.110423	0.0371	0.1037	5008	,	,		23147	0.1399		0.1223	False		,,,				2504	0.1718				p.W151X		Atlas-SNP	.											.	UNC93A	66	.	0			c.G452A	GRCh37	CM068095	UNC93A	M	rs2235197	PASS	.	G	stop/TRP,stop/TRP	170,4236	111.2+/-149.4	1,168,2034	211.0	196.0	201.0		452,452	2.3	0.7	6	dbSNP_98	201	757,7843	180.5+/-229.4	34,689,3577	yes	stop-gained,stop-gained	UNC93A	NM_001143947.1,NM_018974.3	,	35,857,5611	AA,AG,GG		8.8023,3.8584,7.1275	,	151/416,151/458	167709702	927,12079	2203	4300	6503	SO:0001587	stop_gained	54346	exon3			GTGTGTGGGGCAA	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.452G>A	6.37:g.167709702G>A	ENSP00000230256:p.Trp151*	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Nonsense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	224	0.10256410256410256	18	0.036585365853658534	27	0.07458563535911603	84	0.14685314685314685	95	0.12532981530343007	G	18.06	3.538517	0.65085	0.038584	0.088023	ENSG00000112494	ENST00000230256;ENST00000366829	.	.	.	5.2	2.35	0.29111	.	0.061393	0.64402	D	0.000001	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.2136	10.4457	0.44493	0.0:0.13:0.6002:0.2698	rs2235197;rs17618795;rs52834734;rs58978951;rs2235197	.	.	.	X	151	.	.	W	+	2	0	UNC93A	167629692	1.000000	0.71417	0.654000	0.29608	0.600000	0.36913	4.525000	0.60559	0.164000	0.19529	0.655000	0.94253	TGG	G|0.915;A|0.085	0.085	strong		0.507	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
KCNMB3	27094	hgsc.bcm.edu	37	3	178962463	178962463	+	Silent	SNP	C	C	T	rs372618559		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:178962463C>T	ENST00000314235.5	-	3	790	c.279G>A	c.(277-279)tcG>tcA	p.S93S	KCNMB3_ENST00000349697.2_Silent_p.S91S|KCNMB3_ENST00000485523.1_Silent_p.S71S|KCNMB3_ENST00000497599.1_Silent_p.S91S|KCNMB3_ENST00000392685.2_Silent_p.S89S|KCNMB3_ENST00000486944.1_5'Flank	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	93					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	CAGTGCAGGTCGATTCTTCTC	0.433																																					p.S93S		Atlas-SNP	.											KCNMB3_ENST00000497599,NS,carcinoma,0,4	KCNMB3	46	4	0			c.G279A						scavenged	.	C	,,,,	0,4406		0,0,2203	68.0	65.0	66.0		273,279,273,213,267	-10.3	0.2	3		66	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNMB3	NM_001163677.1,NM_014407.3,NM_171828.1,NM_171829.2,NM_171830.1	,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,	91/174,93/280,91/278,71/258,89/276	178962463	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	27094	exon3			GCAGGTCGATTCT	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"""Potassium channels"""	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.279G>A	3.37:g.178962463C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	234	8	0.034188	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000314235.5	37	CCDS3226.1																																																																																			.	.	weak		0.433	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1		
CNTNAP1	8506	hgsc.bcm.edu	37	17	40835922	40835922	+	Silent	SNP	A	A	C	rs2271029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40835922A>C	ENST00000264638.4	+	2	368	c.151A>C	c.(151-153)Aga>Cga	p.R51R	CTD-3193K9.4_ENST00000593139.1_RNA|CTD-3193K9.3_ENST00000592440.1_RNA|CCR10_ENST00000332438.4_5'Flank|CCR10_ENST00000591765.1_5'Flank	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	51	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				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)		TACTGCGCCGAGATTCGCCAG	0.667													C|||	2896	0.578275	0.6014	0.5245	5008	,	,		13914	0.4663		0.5775	False		,,,				2504	0.7014				p.R51R		Atlas-SNP	.											CNTNAP1,rectum,carcinoma,0,2	CNTNAP1	116	2	0			c.A151C						PASS	.	C		2624,1782	521.1+/-370.4	771,1082,350	37.0	35.0	36.0		151	4.8	0.6	17	dbSNP_100	36	5160,3440	502.5+/-375.7	1556,2048,696	no	coding-synonymous	CNTNAP1	NM_003632.2		2327,3130,1046	CC,CA,AA		40.0,40.4448,40.1507		51/1385	40835922	7784,5222	2203	4300	6503	SO:0001819	synonymous_variant	8506	exon2			GCGCCGAGATTCG	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.151A>C	17.37:g.40835922A>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_003632		Silent	SNP	ENST00000264638.4	37	CCDS11436.1																																																																																			A|0.417;C|0.583	0.583	strong		0.667	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79064143	79064143	+	Silent	SNP	C	C	G	rs11635870	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79064143C>G	ENST00000388820.4	-	15	2370	c.2160G>C	c.(2158-2160)gcG>gcC	p.A720A	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	720	Spacer.				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						CGCGTGCGCCCGCTGGGATCA	0.617													G|||	932	0.186102	0.0454	0.2579	5008	,	,		18925	0.0188		0.4185	False		,,,				2504	0.2587				p.A720A		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.G2160C						PASS	.	G		469,3923	777.1+/-414.2	37,395,1764	49.0	36.0	41.0		2160	-8.1	0.0	15	dbSNP_120	41	3668,4918	608.6+/-395.4	815,2038,1440	no	coding-synonymous	ADAMTS7	NM_014272.3		852,2433,3204	GG,GC,CC		42.7207,10.6785,31.877		720/1687	79064143	4137,8841	2196	4293	6489	SO:0001819	synonymous_variant	11173	exon15			TGCGCCCGCTGGG	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.2160G>C	15.37:g.79064143C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			C|0.715;G|0.285	0.285	strong		0.617	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
SLC17A2	10246	hgsc.bcm.edu	37	6	25916979	25916979	+	Silent	SNP	C	C	T	rs1865760	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25916979C>T	ENST00000265425.3	-	7	884	c.864G>A	c.(862-864)ttG>ttA	p.L288L	SLC17A2_ENST00000377850.3_Silent_p.L288L|SLC17A2_ENST00000360488.3_Silent_p.L288L			O00624	NPT3_HUMAN	solute carrier family 17, member 2	288					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						TGATGGTGCACAACCAGAAAT	0.448													C|||	2004	0.40016	0.143	0.4568	5008	,	,		22991	0.6964		0.4026	False		,,,				2504	0.3998				p.L288L		Atlas-SNP	.											.	SLC17A2	70	.	0			c.G864A						PASS	.	C		817,3589	325.6+/-299.2	73,671,1459	129.0	114.0	119.0		864	-5.0	0.9	6	dbSNP_96	119	3350,5250	498.8+/-374.8	670,2010,1620	no	coding-synonymous	SLC17A2	NM_005835.2		743,2681,3079	TT,TC,CC		38.9535,18.5429,32.0391		288/437	25916979	4167,8839	2203	4300	6503	SO:0001819	synonymous_variant	10246	exon8			GGTGCACAACCAG	U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"""Solute carriers"""	10930	protein-coding gene	gene with protein product		611049	"""solute carrier family 17 (sodium phosphate), member 2"""			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.864G>A	6.37:g.25916979C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_005835	A6NK81|A6NLD6|Q5TB84|Q76P85	Silent	SNP	ENST00000265425.3	37																																																																																				C|0.634;T|0.366	0.366	strong		0.448	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1		
ITGA1	3672	hgsc.bcm.edu	37	5	52201722	52201722	+	Missense_Mutation	SNP	C	C	T	rs4145748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:52201722C>T	ENST00000282588.6	+	12	1897	c.1439C>T	c.(1438-1440)aCg>aTg	p.T480M		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	480			T -> M (in dbSNP:rs4145748).		activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)	p.T480M(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				ATTCTCCAGACGCTCAGTGGA	0.348													C|||	481	0.0960463	0.0189	0.2695	5008	,	,		15323	0.1488		0.0596	False		,,,				2504	0.0603				p.T480M		Atlas-SNP	.											ITGA1,NS,carcinoma,0,1	ITGA1	112	1	1	Substitution - Missense(1)	stomach(1)	c.C1439T						PASS	.	C	MET/THR	137,4269	97.1+/-135.8	1,135,2067	100.0	98.0	99.0		1439	5.8	1.0	5	dbSNP_110	99	541,8059	150.0+/-205.0	18,505,3777	yes	missense	ITGA1	NM_181501.1	81	19,640,5844	TT,TC,CC		6.2907,3.1094,5.213	probably-damaging	480/1180	52201722	678,12328	2203	4300	6503	SO:0001583	missense	3672	exon12			TCCAGACGCTCAG	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"""CD molecules"", ""Integrins"""	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1439C>T	5.37:g.52201722C>T	ENSP00000282588:p.Thr480Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	165	89	0.539394	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	37	CCDS3955.1	218	0.09981684981684982	11	0.022357723577235773	71	0.19613259668508287	89	0.1555944055944056	47	0.06200527704485488	C	17.03	3.284520	0.59867	0.031094	0.062907	ENSG00000213949	ENST00000282588	T	0.12255	2.7	5.77	5.77	0.91146	.	0.154340	0.56097	D	0.000021	T	0.00039	0.0001	L	0.57536	1.79	0.23113	P	0.9982739	P	0.51057	0.941	P	0.48704	0.587	T	0.06023	-1.0850	9	0.48119	T	0.1	.	15.8297	0.78741	0.0:0.8261:0.1739:0.0	rs4145748;rs52796722;rs61318225;rs4145748	480	P56199	ITA1_HUMAN	M	480	ENSP00000282588:T480M	ENSP00000282588:T480M	T	+	2	0	ITGA1	52237479	0.974000	0.33945	0.992000	0.48379	0.921000	0.55340	1.784000	0.38674	2.890000	0.99128	0.650000	0.86243	ACG	C|0.929;T|0.071	0.071	strong		0.348	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501	
PDIA6	10130	hgsc.bcm.edu	37	2	10930903	10930903	+	Missense_Mutation	SNP	T	T	C	rs4807	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:10930903T>C	ENST00000272227.3	-	7	788	c.641A>G	c.(640-642)aAa>aGa	p.K214R	PDIA6_ENST00000381611.4_Missense_Mutation_p.K219R|PDIA6_ENST00000540494.1_Missense_Mutation_p.K211R|PDIA6_ENST00000404824.2_Missense_Mutation_p.K262R|PDIA6_ENST00000404371.2_Missense_Mutation_p.K266R	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	149	0	0		WXS	Illumina HiSeq	Phase_I	157	88	0.56051	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	
GAK	2580	hgsc.bcm.edu	37	4	882643	882643	+	Silent	SNP	G	G	A	rs2279181	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:882643G>A	ENST00000314167.4	-	11	1307	c.1197C>T	c.(1195-1197)tcC>tcT	p.S399S	GAK_ENST00000511163.1_Silent_p.S320S	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	399	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		ACTTAGCGACGGACTGGATGA	0.637													G|||	601	0.120008	0.0946	0.0634	5008	,	,		16076	0.0992		0.1183	False		,,,				2504	0.2178				p.S399S		Atlas-SNP	.											.	GAK	104	.	0			c.C1197T						PASS	.	G		374,4018		10,354,1832	89.0	70.0	77.0		1197	-4.0	0.6	4	dbSNP_100	77	909,7673		54,801,3436	no	coding-synonymous	GAK	NM_005255.2		64,1155,5268	AA,AG,GG		10.5919,8.5155,9.889		399/1312	882643	1283,11691	2196	4291	6487	SO:0001819	synonymous_variant	2580	exon11			AGCGACGGACTGG	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.1197C>T	4.37:g.882643G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1																																																																																			G|0.901;A|0.099	0.099	strong		0.637	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
HCN2	610	hgsc.bcm.edu	37	19	603625	603625	+	Silent	SNP	T	T	C	rs56342526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:603625T>C	ENST00000251287.2	+	2	767	c.714T>C	c.(712-714)gaT>gaC	p.D238D		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	238					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)		TCTTCAAGGATGAGACCACTG	0.562													c|||	1182	0.236022	0.236	0.0908	5008	,	,		16379	0.2837		0.0984	False		,,,				2504	0.4315				p.D238D	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.T714C						PASS	.	C		1041,3357		134,773,1292	88.0	80.0	82.0		714	-4.7	0.9	19	dbSNP_129	82	862,7732		48,766,3483	no	coding-synonymous	HCN2	NM_001194.3		182,1539,4775	CC,CT,TT		10.0303,23.6698,14.6475		238/890	603625	1903,11089	2199	4297	6496	SO:0001819	synonymous_variant	610	exon2			CAAGGATGAGACC	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.714T>C	19.37:g.603625T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			T|0.866;C|0.134	0.134	strong		0.562	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
SLC25A6	293	hgsc.bcm.edu	37	X	1510877	1510877	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:1510877G>C	ENST00000381401.5	-	1	740	c.26C>G	c.(25-27)gCc>gGc	p.A9G	SLC25A6_ENST00000475167.1_5'UTR	NM_001636.3	NP_001627.2	P12236	ADT3_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6	9					active induction of host immune response by virus (GO:0046732)|ADP transport (GO:0015866)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|modulation by virus of host morphology or physiology (GO:0019048)|protein targeting to mitochondrion (GO:0006626)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP:ADP antiporter activity (GO:0005471)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|upper_aerodigestive_tract(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Clodronate(DB00720)	GAAGTCTTTGGCGAAGGAGAT	0.692																																					p.A9G		Atlas-SNP	.											.	SLC25A6	27	.	0			c.C26G						PASS	.						36.0	37.0	36.0					X																	1510877		2202	4295	6497	SO:0001583	missense	293	exon1			TCTTTGGCGAAGG	AY007135	CCDS14114.1	Xp22.32 and Yp11.3	2013-05-22			ENSG00000169100	ENSG00000169100		"""Pseudoautosomal regions / PAR1"", ""Solute carriers"""	10992	protein-coding gene	gene with protein product		300151, 403000		ANT3			Standard	NM_001636		Approved	ANT3Y, MGC17525	uc004cpt.3	P12236	OTTHUMG00000021058	ENST00000381401.5:c.26C>G	X.37:g.1510877G>C	ENSP00000370808:p.Ala9Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_001636	Q96C49	Missense_Mutation	SNP	ENST00000381401.5	37	CCDS14114.1	.	.	.	.	.	.	.	.	.	.	g	8.851	0.944558	0.18356	.	.	ENSG00000169100	ENST00000381401;ENST00000447786	T	0.79454	-1.27	1.54	1.54	0.23209	Mitochondrial carrier domain (2);	0.000000	0.41500	U	0.000862	T	0.69575	0.3126	L	0.52364	1.645	0.09310	N	1	B	0.09022	0.002	B	0.21708	0.036	T	0.61068	-0.7137	10	0.40728	T	0.16	.	10.0455	0.42184	0.0:0.0:1.0:0.0	.	9	P12236	ADT3_HUMAN	G	9	ENSP00000370808:A9G	ENSP00000370808:A9G	A	-	2	0	SLC25A6	1470877	0.997000	0.39634	0.724000	0.30704	0.047000	0.14425	1.204000	0.32296	0.807000	0.34208	0.281000	0.19383	GCC	.	.	none		0.692	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636	
SCAPER	49855	hgsc.bcm.edu	37	15	76726465	76726465	+	Missense_Mutation	SNP	G	G	T	rs1607017|rs34441478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:76726465G>T	ENST00000563290.1	-	26	3360	c.3265C>A	c.(3265-3267)Ccc>Acc	p.P1089T	SCAPER_ENST00000324767.7_Missense_Mutation_p.P1089T|SCAPER_ENST00000538941.2_Missense_Mutation_p.P843T			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1089			P -> T (in dbSNP:rs1607017). {ECO:0000269|PubMed:10819331, ECO:0000269|Ref.7}.			endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						CCTTGTGAGGGTTTGTTTTTC	0.398													G|||	1783	0.35603	0.0938	0.3372	5008	,	,		16225	0.6131		0.327	False		,,,				2504	0.4888				p.P1089T		Atlas-SNP	.											.	SCAPER	160	.	0			c.C3265A						PASS	.	G	THR/PRO,THR/PRO	464,3200		23,418,1391	115.0	104.0	108.0		3265,2527	3.0	1.0	15	dbSNP_88	108	2519,5643		387,1745,1949	yes	missense,missense	SCAPER	NM_020843.2,NM_001145923.1	38,38	410,2163,3340	TT,TG,GG		30.8625,12.6638,25.2241	benign,benign	1089/1401,843/1155	76726465	2983,8843	1832	4081	5913	SO:0001583	missense	49855	exon25			GTGAGGGTTTGTT	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"""Zinc fingers, C2H2-type"""	13081	protein-coding gene	gene with protein product		611611	"""zinc finger protein 291"""	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.3265C>A	15.37:g.76726465G>T	ENSP00000454973:p.Pro1089Thr	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	166	165	0.993976	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	753	0.3447802197802198	43	0.08739837398373984	130	0.35911602209944754	334	0.583916083916084	246	0.3245382585751979	G	7.381	0.628737	0.14257	0.126638	0.308625	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.22743	1.96;1.94	5.93	2.97	0.34412	.	0.429133	0.27306	N	0.019963	T	0.00012	0.0000	L	0.57536	1.79	0.31641	P	0.648053	B;B	0.21071	0.007;0.051	B;B	0.18871	0.007;0.023	T	0.39981	-0.9587	9	0.30078	T	0.28	.	5.7223	0.17995	0.2163:0.2696:0.5142:0.0	rs1607017;rs52823383;rs1607017	1088;843	Q9BY12;F5H7X8	SCAPE_HUMAN;.	T	1089;843;1111	ENSP00000326924:P1089T;ENSP00000442190:P843T	ENSP00000303560:P1111T	P	-	1	0	SCAPER	74513520	0.999000	0.42202	0.998000	0.56505	0.997000	0.91878	0.687000	0.25407	0.815000	0.34398	0.655000	0.94253	CCC	G|0.674;T|0.326	0.326	strong		0.398	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843	
ZNF492	57615	hgsc.bcm.edu	37	19	22846867	22846867	+	Silent	SNP	G	G	A	rs74406853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:22846867G>A	ENST00000456783.2	+	4	640	c.396G>A	c.(394-396)acG>acA	p.T132T	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	132					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ACAGACATACGATAAGACATA	0.313													N|||	190	0.0379393	0.0295	0.0187	5008	,	,		15276	0.0813		0.0398	False		,,,				2504	0.0164				p.T132T		Atlas-SNP	.											.	ZNF492	129	.	0			c.G396A						PASS	.	G		80,4134		0,80,2027	35.0	37.0	36.0		396	0.3	0.0	19	dbSNP_131	36	249,8261		3,243,4009	no	coding-synonymous	ZNF492	NM_020855.2		3,323,6036	AA,AG,GG		2.926,1.8984,2.5857		132/532	22846867	329,12395	2107	4255	6362	SO:0001819	synonymous_variant	57615	exon4			ACATACGATAAGA	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.396G>A	19.37:g.22846867G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	185	110	0.594595	NM_020855	Q08EI7|Q08EI8	Silent	SNP	ENST00000456783.2	37	CCDS46032.1																																																																																			G|0.955;A|0.045	0.045	strong		0.313	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
ACPT	93650	hgsc.bcm.edu	37	19	51297826	51297826	+	Missense_Mutation	SNP	C	C	A	rs55735528|rs386810263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51297826C>A	ENST00000270593.1	+	9	974	c.974C>A	c.(973-975)gCc>gAc	p.A325D	CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Missense_Mutation_p.A232D	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	325						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GGGAATCCCGCCAAAGATGGA	0.617													A|||	1652	0.329872	0.1309	0.2161	5008	,	,		17428	0.6538		0.3012	False		,,,				2504	0.3753				p.A325D		Atlas-SNP	.											.	ACPT	43	.	0			c.C974A						PASS	.	C	ASP/ALA	673,3733		44,585,1574	39.0	39.0	39.0		974	2.9	0.0	19	dbSNP_129	39	2383,6217		348,1687,2265	yes	missense	ACPT	NM_033068.2	126	392,2272,3839	AA,AC,CC		27.7093,15.2746,23.4968	benign	325/427	51297826	3056,9950	2203	4300	6503	SO:0001583	missense	93650	exon9			ATCCCGCCAAAGA	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.974C>A	19.37:g.51297826C>A	ENSP00000270593:p.Ala325Asp	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	37	CCDS12802.1	640	0.29304029304029305	50	0.1016260162601626	71	0.19613259668508287	329	0.5751748251748252	190	0.25065963060686014	N	3.945	-0.013485	0.07727	0.152746	0.277093	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.76709	2.97;-1.04	3.9	2.88	0.33553	.	0.642945	0.14811	N	0.297051	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46638	-0.9177	9	0.14656	T	0.56	-10.0341	8.9577	0.35827	0.8111:0.1889:0.0:0.0	rs55735528;rs61505895	325	Q9BZG2	PPAT_HUMAN	D	325;232	ENSP00000270593:A325D;ENSP00000270594:A232D	ENSP00000270593:A325D	A	+	2	0	ACPT	55989638	0.004000	0.15560	0.017000	0.16124	0.002000	0.02628	1.783000	0.38664	0.688000	0.31529	-0.367000	0.07326	GCC	C|0.752;A|0.248	0.248	strong		0.617	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	
IL27	246778	hgsc.bcm.edu	37	16	28513403	28513403	+	Missense_Mutation	SNP	A	A	G	rs181206	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:28513403A>G	ENST00000356897.1	-	4	378	c.356T>C	c.(355-357)cTg>cCg	p.L119P		NM_145659.3	NP_663634.2	Q8TAD2	IL17D_HUMAN	interleukin 27	0					inflammatory response (GO:0006954)	extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	10						CCCTCCCAGCAGGGCATGGAA	0.657													A|||	801	0.159944	0.0151	0.3501	5008	,	,		20164	0.0833		0.2873	False		,,,				2504	0.1687				p.L119P		Atlas-SNP	.											.	IL27	27	.	0			c.T356C						PASS	.	A	PRO/LEU	320,4074	163.3+/-195.1	14,292,1891	53.0	54.0	54.0		356	3.0	0.9	16	dbSNP_79	54	2753,5847	419.4+/-353.1	453,1847,2000	yes	missense	IL27	NM_145659.3	98	467,2139,3891	GG,GA,AA		32.0116,7.2827,23.6494	possibly-damaging	119/244	28513403	3073,9921	2197	4300	6497	SO:0001583	missense	246778	exon4			CCCAGCAGGGCAT	AY099296	CCDS10633.1	16p11	2011-07-21	2003-12-17	2003-12-19	ENSG00000197272	ENSG00000197272		"""Interleukins and interleukin receptors"""	19157	protein-coding gene	gene with protein product		608273	"""interleukin 30"""	IL30		12121660	Standard	NM_145659		Approved	IL-27, p28, IL27p28, IL-27A, IL27A, MGC71873	uc002dqc.3	Q8NEV9	OTTHUMG00000097023	ENST00000356897.1:c.356T>C	16.37:g.28513403A>G	ENSP00000349365:p.Leu119Pro	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_145659	B1AM69	Missense_Mutation	SNP	ENST00000356897.1	37	CCDS10633.1	397	0.18177655677655677	10	0.02032520325203252	99	0.27348066298342544	59	0.10314685314685315	229	0.3021108179419525	A	14.22	2.471119	0.43942	0.072827	0.320116	ENSG00000197272	ENST00000356897	T	0.38560	1.13	4.33	2.97	0.34412	.	0.556457	0.13501	N	0.383273	T	0.00012	0.0000	L	0.40543	1.245	0.54753	P	1.2000000000012001E-5	D	0.61697	0.99	P	0.58266	0.836	T	0.25082	-1.0142	9	0.72032	D	0.01	-0.6238	6.3931	0.21597	0.8633:0.0:0.1366:0.0	rs181206;rs181206	119	Q8NEV9	IL27A_HUMAN	P	119	ENSP00000349365:L119P	ENSP00000349365:L119P	L	-	2	0	IL27	28420904	0.769000	0.28531	0.877000	0.34402	0.768000	0.43524	1.753000	0.38359	1.600000	0.50102	0.358000	0.22013	CTG	A|0.798;G|0.202	0.202	strong		0.657	IL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214114.1	NM_145659	
CES1	1066	hgsc.bcm.edu	37	16	55853545	55853545	+	Missense_Mutation	SNP	C	C	A	rs115629050	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:55853545C>A	ENST00000361503.4	-	7	935	c.805G>T	c.(805-807)Gct>Tct	p.A269S	CES1_ENST00000422046.2_Missense_Mutation_p.A269S|CES1_ENST00000566555.1_5'Flank|CES1_ENST00000360526.3_Missense_Mutation_p.A270S			P23141	EST1_HUMAN	carboxylesterase 1	269					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GCAGTGATAGCAATTTGCTGC	0.493													.|||	229	0.0457268	0.0877	0.0202	5008	,	,		23902	0.0149		0.0388	False		,,,				2504	0.046				p.A270S	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.G808T						PASS	.	C	SER/ALA,SER/ALA,SER/ALA	365,4031		17,331,1850	120.0	116.0	117.0		805,808,805	2.8	0.1	16	dbSNP_132	117	279,8321		4,271,4025	no	missense,missense,missense	CES1	NM_001025194.1,NM_001025195.1,NM_001266.4	99,99,99	21,602,5875	AA,AC,CC		3.2442,8.303,4.9554	possibly-damaging,possibly-damaging,possibly-damaging	269/568,270/569,269/567	55853545	644,12352	2198	4300	6498	SO:0001583	missense	1066	exon7			TGATAGCAATTTG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.805G>T	16.37:g.55853545C>A	ENSP00000355193:p.Ala269Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	83	0.038003663003663	35	0.07113821138211382	9	0.024861878453038673	7	0.012237762237762238	32	0.04221635883905013	.	16.26	3.073306	0.55646	0.08303	0.032442	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046;ENST00000426667	T;T;T	0.74526	-0.85;-0.85;-0.85	3.81	2.83	0.33086	Carboxylesterase, type B (1);	0.115830	0.39210	N	0.001430	T	0.20618	0.0496	M	0.73430	2.235	0.44587	D	0.99755	P;P;P	0.41748	0.528;0.761;0.718	P;P;P	0.53549	0.729;0.729;0.609	T	0.60311	-0.7288	10	0.66056	D	0.02	.	7.6658	0.28430	0.0:0.8726:0.0:0.1274	.	269;269;270	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	S	270;269;269;134	ENSP00000353720:A270S;ENSP00000355193:A269S;ENSP00000390492:A269S	ENSP00000353720:A270S	A	-	1	0	CES1	54411046	1.000000	0.71417	0.107000	0.21349	0.041000	0.13682	2.405000	0.44548	1.701000	0.51217	0.456000	0.33151	GCT	C|0.955;A|0.045	0.045	strong		0.493	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
FBXO11	80204	hgsc.bcm.edu	37	2	48059539	48059539	+	Silent	SNP	A	A	G	rs141756242		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48059539A>G	ENST00000403359.3	-	11	1419	c.1347T>C	c.(1345-1347)aaT>aaC	p.N449N	FBXO11_ENST00000316377.4_Silent_p.N365N|FBXO11_ENST00000402508.1_Silent_p.N365N|FBXO11_ENST00000434523.2_5'UTR	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	449					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GATGAATATGATTCCGTCTAA	0.333			"""Mis, F, D"""		DLBCL								A|||	1	0.000199681	0.0	0.0014	5008	,	,		16143	0.0		0.0	False		,,,				2504	0.0				p.N449N		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1347C						PASS	.	A	,	2,4402	4.2+/-10.8	0,2,2200	87.0	89.0	88.0		1347,1095	4.8	1.0	2	dbSNP_134	88	21,8577	16.0+/-53.3	0,21,4278	no	coding-synonymous,coding-synonymous	FBXO11	NM_001190274.1,NM_025133.4	,	0,23,6478	GG,GA,AA		0.2442,0.0454,0.1769	,	449/928,365/844	48059539	23,12979	2202	4299	6501	SO:0001819	synonymous_variant	80204	exon11			AATATGATTCCGT	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.1347T>C	2.37:g.48059539A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	102	35	0.343137	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Silent	SNP	ENST00000403359.3	37	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	A	7.851	0.724018	0.15439	4.54E-4	0.002442	ENSG00000138081	ENST00000493962	.	.	.	5.95	4.8	0.61643	.	.	.	.	.	T	0.63640	0.2528	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61187	-0.7113	4	.	.	.	-19.7747	11.946	0.52928	0.9324:0.0:0.0676:0.0	.	.	.	.	P	241	.	.	S	-	1	0	FBXO11	47913043	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.794000	0.55492	1.076000	0.40961	0.460000	0.39030	TCA	A|0.998;G|0.002	0.002	strong		0.333	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133	
PPFIA1	8500	hgsc.bcm.edu	37	11	70118489	70118489	+	Missense_Mutation	SNP	G	G	A	rs546502	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:70118489G>A	ENST00000253925.7	+	2	426	c.211G>A	c.(211-213)Gtt>Att	p.V71I	PPFIA1_ENST00000389547.3_Missense_Mutation_p.V71I	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	71			V -> I (in dbSNP:rs546502).		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)			GTTACACGAGGTTGGTCATGA	0.458													G|||	970	0.19369	0.1543	0.2493	5008	,	,		18725	0.1052		0.2187	False		,,,				2504	0.273				p.V71I		Atlas-SNP	.											.	PPFIA1	114	.	0			c.G211A						PASS	.	G	ILE/VAL,ILE/VAL	631,3769	273.4+/-271.3	44,543,1613	116.0	108.0	111.0		211,211	5.0	1.0	11	dbSNP_83	111	1874,6714	334.3+/-320.9	195,1484,2615	yes	missense,missense	PPFIA1	NM_003626.2,NM_177423.1	29,29	239,2027,4228	AA,AG,GG		21.8211,14.3409,19.287	benign,benign	71/1203,71/1186	70118489	2505,10483	2200	4294	6494	SO:0001583	missense	8500	exon2			CACGAGGTTGGTC	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.211G>A	11.37:g.70118489G>A	ENSP00000253925:p.Val71Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	387	0.1771978021978022	77	0.1565040650406504	90	0.24861878453038674	60	0.1048951048951049	160	0.21108179419525067	G	18.13	3.554908	0.65425	0.143409	0.218211	ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000530746;ENST00000532024	T;T;T;T	0.42513	0.97;0.97;0.97;0.98	4.99	4.99	0.66335	.	0.093477	0.42682	U	0.000678	T	0.00012	0.0000	L	0.28458	0.855	0.19575	P	0.9999670122	B;B	0.09022	0.001;0.002	B;B	0.15052	0.002;0.012	T	0.10019	-1.0648	9	0.42905	T	0.14	.	18.3704	0.90405	0.0:0.0:1.0:0.0	rs546502;rs3740718;rs57405546;rs546502	71;71	Q13136;Q13136-2	LIPA1_HUMAN;.	I	71	ENSP00000253925:V71I;ENSP00000374198:V71I;ENSP00000432722:V71I;ENSP00000432065:V71I	ENSP00000253925:V71I	V	+	1	0	PPFIA1	69796137	1.000000	0.71417	0.976000	0.42696	0.984000	0.73092	7.575000	0.82447	2.328000	0.79073	0.638000	0.83543	GTT	G|0.821;A|0.179	0.179	strong		0.458	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
OR2M7	391196	hgsc.bcm.edu	37	1	248487300	248487300	+	Missense_Mutation	SNP	C	C	T	rs4916129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248487300C>T	ENST00000317965.2	-	1	599	c.571G>A	c.(571-573)Gac>Aac	p.D191N		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	191			D -> N (in dbSNP:rs4916129).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATTGATGTGTCATTGCATGAG	0.428													c|||	2036	0.40655	0.1377	0.4539	5008	,	,		23334	0.494		0.5159	False		,,,				2504	0.5337				p.D191N		Atlas-SNP	.											.	OR2M7	84	.	0			c.G571A						PASS	.	C	ASN/ASP	975,3431	367.8+/-318.4	102,771,1330	222.0	218.0	220.0		571	1.5	0.2	1	dbSNP_111	220	4730,3866	607.2+/-395.2	1302,2126,870	no	missense	OR2M7	NM_001004691.1	23	1404,2897,2200	TT,TC,CC		44.9744,22.1289,43.8779	benign	191/313	248487300	5705,7297	2203	4298	6501	SO:0001583	missense	391196	exon1			ATGTGTCATTGCA	BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"""GPCR / Class A : Olfactory receptors"""	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.571G>A	1.37:g.248487300C>T	ENSP00000324557:p.Asp191Asn	Somatic	379	1	0.00263852		WXS	Illumina HiSeq	Phase_I	381	180	0.472441	NM_001004691	B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	37	CCDS31111.1	882	0.40384615384615385	70	0.14227642276422764	156	0.430939226519337	281	0.49125874125874125	375	0.4947229551451187	C	11.49	1.654451	0.29425	0.221289	0.550256	ENSG00000177186	ENST00000317965	T	0.00231	8.49	1.55	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33938	U	0.004419	T	0.00012	0.0000	M	0.76938	2.355	0.80722	P	0.0	B	0.20052	0.041	B	0.25405	0.06	T	0.38156	-0.9674	9	0.52906	T	0.07	.	5.9237	0.19096	0.0:0.8325:0.0:0.1675	rs4916129	191	Q8NG81	OR2M7_HUMAN	N	191	ENSP00000324557:D191N	ENSP00000324557:D191N	D	-	1	0	OR2M7	246553923	0.000000	0.05858	0.180000	0.23079	0.400000	0.30750	-0.532000	0.06164	0.850000	0.35239	0.194000	0.17425	GAC	C|0.571;T|0.429	0.429	strong		0.428	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691	
PTK2B	2185	hgsc.bcm.edu	37	8	27293865	27293865	+	Splice_Site	SNP	C	C	T	rs7005936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:27293865C>T	ENST00000397501.1	+	20	2149	c.1341C>T	c.(1339-1341)caC>caT	p.H447H	PTK2B_ENST00000346049.5_Splice_Site_p.H447H|PTK2B_ENST00000517339.1_Splice_Site_p.H447H|PTK2B_ENST00000397497.4_Splice_Site_p.H193H|PTK2B_ENST00000544172.1_Splice_Site_p.H447H|PTK2B_ENST00000338238.4_Splice_Site_p.H447H|PTK2B_ENST00000420218.2_Splice_Site_p.H447H	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	447	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|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 cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	ACACAAATCACGTGAGTTCTA	0.498													C|||	1854	0.370208	0.4607	0.3804	5008	,	,		21147	0.1954		0.3867	False		,,,				2504	0.4039				p.H447H		Atlas-SNP	.											PTK2B_ENST00000544172,brain,glioma,0,6	PTK2B	304	6	0			c.C1341T						PASS	.	C	,,,	1959,2447	554.2+/-379.0	444,1071,688	250.0	227.0	235.0		1341,1341,1341,1341	-0.6	1.0	8	dbSNP_116	235	3396,5204	502.2+/-375.6	689,2018,1593	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	1133,3089,2281	TT,TC,CC		39.4884,44.4621,41.1733	,,,	447/1010,447/1010,447/968,447/1010	27293865	5355,7651	2203	4300	6503	SO:0001630	splice_region_variant	2185	exon20			AAATCACGTGAGT	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.1341+1C>T	8.37:g.27293865C>T		Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	309	130	0.420712	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			C|0.638;T|0.362	0.362	strong		0.498	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	Silent
ZNF160	90338	hgsc.bcm.edu	37	19	53572494	53572494	+	Silent	SNP	G	G	T	rs11665677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53572494G>T	ENST00000429604.1	-	7	1708	c.1293C>A	c.(1291-1293)ggC>ggA	p.G431G	ZNF160_ENST00000599056.1_Silent_p.G431G|ZNF160_ENST00000418871.1_Silent_p.G431G|ZNF160_ENST00000601421.1_Silent_p.G395G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	431					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TAAAGACTTTGCCACATTCAT	0.428													g|||	1378	0.27516	0.4629	0.2795	5008	,	,		21830	0.0714		0.3022	False		,,,				2504	0.2004				p.G431G		Atlas-SNP	.											ZNF160,NS,carcinoma,-1,1	ZNF160	75	1	0			c.C1293A						PASS	.	A	,,	1816,2590	530.8+/-373.0	369,1078,756	130.0	131.0	131.0		1293,1293,1293	-4.3	0.0	19	dbSNP_120	131	2678,5922	429.5+/-356.2	418,1842,2040	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF160	NM_001102603.1,NM_033288.3,NM_198893.2	,,	787,2920,2796	TT,TG,GG		31.1395,41.2165,34.5533	,,	431/819,431/819,431/819	53572494	4494,8512	2203	4300	6503	SO:0001819	synonymous_variant	90338	exon7			GACTTTGCCACAT	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1293C>A	19.37:g.53572494G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	98	57	0.581633	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Silent	SNP	ENST00000429604.1	37	CCDS12859.1																																																																																			G|0.683;T|0.317	0.317	strong		0.428	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288	
PIEZO1	9780	hgsc.bcm.edu	37	16	88783100	88783100	+	Missense_Mutation	SNP	T	T	C	rs1803382	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88783100T>C	ENST00000301015.9	-	47	7039	c.6793A>G	c.(6793-6795)Atc>Gtc	p.I2265V	MIR4722_ENST00000578292.1_RNA|RP5-1142A6.9_ENST00000564984.1_RNA|PIEZO1_ENST00000327397.7_Missense_Mutation_p.I133V	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2265					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						GCCGTGACGATGTCCTCAGGG	0.647													T|||	993	0.198283	0.1029	0.1902	5008	,	,		19929	0.0913		0.326	False		,,,				2504	0.3119				p.I2265V		Atlas-SNP	.											.	PIEZO1	79	.	0			c.A6793G						PASS	.	T	VAL/ILE	186,1198		13,160,519	45.0	49.0	48.0		6793	2.3	1.0	16	dbSNP_89	48	1027,2145		150,727,709	yes	missense	PIEZO1	NM_001142864.2	29	163,887,1228	CC,CT,TT		32.377,13.4393,26.6242	probably-damaging	2265/2522	88783100	1213,3343	692	1586	2278	SO:0001583	missense	9780	exon47			TGACGATGTCCTC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.6793A>G	16.37:g.88783100T>C	ENSP00000301015:p.Ile2265Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	416|416	0.19047619047619047|0.19047619047619047	55|55	0.11178861788617886|0.11178861788617886	82|82	0.2265193370165746|0.2265193370165746	48|48	0.08391608391608392|0.08391608391608392	231|231	0.30474934036939316|0.30474934036939316	T|T	12.61|12.61	1.988341|1.988341	0.35036|0.35036	0.134393|0.134393	0.32377|0.32377	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015;ENST00000327397	.|T;T	.|0.72394	.|-0.65;-0.65	4.67|4.67	2.32|2.32	0.28847|0.28847	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25485|0.25485	0.75|0.75	0.24021|0.24021	P|P	0.99614979|0.99614979	.|B;D;D	.|0.65815	.|0.288;0.995;0.995	.|P;D;D	.|0.79108	.|0.578;0.992;0.992	T|T	0.09885|0.09885	-1.0654|-1.0654	4|9	.|0.24483	.|T	.|0.36	-37.9372|-37.9372	10.6074|10.6074	0.45402|0.45402	0.0:0.0:0.3085:0.6915|0.0:0.0:0.3085:0.6915	rs1803382;rs58765949;rs1803382|rs1803382;rs58765949;rs1803382	.|2265;133;133	.|Q92508;E7EUT2;Q96HU3	.|PIEZ1_HUMAN;.;.	R|V	2210|2265;133	.|ENSP00000301015:I2265V;ENSP00000333704:I133V	.|ENSP00000301015:I2265V	H|I	-|-	2|1	0|0	FAM38A|FAM38A	87310601|87310601	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.910000|0.910000	0.53928|0.53928	5.680000|5.680000	0.68168|0.68168	0.144000|0.144000	0.18951|0.18951	0.460000|0.460000	0.39030|0.39030	CAT|ATC	T|0.811;C|0.189	0.189	strong		0.647	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
SSBP2	23635	hgsc.bcm.edu	37	5	80736444	80736444	+	Silent	SNP	A	A	G	rs9596	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:80736444A>G	ENST00000320672.4	-	14	1071	c.861T>C	c.(859-861)ggT>ggC	p.G287G	SSBP2_ENST00000514493.1_Silent_p.G257G|SSBP2_ENST00000509053.1_Silent_p.G257G|SSBP2_ENST00000515395.1_Silent_p.G265G|SSBP2_ENST00000510060.1_5'UTR|SSBP2_ENST00000505980.1_Silent_p.G267G	NM_001256732.1|NM_001256733.1|NM_012446.3	NP_001243661.1|NP_001243662.1|NP_036578.2	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2	287	Gly-rich.|Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)		SSBP2/JAK2(4)	central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		CTGACCCAGGACCCATTGGAA	0.338													G|||	2270	0.453275	0.885	0.3948	5008	,	,		18494	0.1756		0.33	False		,,,				2504	0.3241				p.G295G		Atlas-SNP	.											.	SSBP2	25	.	0			c.T885C						PASS	.	G		3486,920	351.8+/-311.4	1391,704,108	65.0	70.0	69.0		861	3.3	1.0	5	dbSNP_52	69	2915,5685	669.3+/-402.6	503,1909,1888	no	coding-synonymous	SSBP2	NM_012446.2		1894,2613,1996	GG,GA,AA		33.8953,20.8806,49.2157		287/362	80736444	6401,6605	2203	4300	6503	SO:0001819	synonymous_variant	23635	exon14			CCCAGGACCCATT	AF077048	CCDS4056.1, CCDS58960.1, CCDS58961.1, CCDS58962.1, CCDS58963.1, CCDS75268.1	5q14.1	2012-05-25	2001-11-28		ENSG00000145687	ENSG00000145687			15831	protein-coding gene	gene with protein product		607389	"""single-stranded DNA-binding protein 2"""			11230166, 11042152	Standard	NM_001256732		Approved	HSPC116	uc003khp.4	P81877	OTTHUMG00000119039	ENST00000320672.4:c.861T>C	5.37:g.80736444A>G		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	305	121	0.396721	NM_001256732	B2R5W1|B7Z1J2|B7Z2L9|B7Z665|D6RH18|E9PB74|E9PDA8|Q8N2Q2|Q9BWW6|Q9Y4T7	Silent	SNP	ENST00000320672.4	37	CCDS4056.1																																																																																			A|0.544;G|0.456	0.456	strong		0.338	SSBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239249.1	NM_012446	
WDR4	10785	hgsc.bcm.edu	37	21	44283574	44283574	+	Silent	SNP	C	C	T	rs11911090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44283574C>T	ENST00000398208.2	-	4	488	c.429G>A	c.(427-429)ggG>ggA	p.G143G	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Silent_p.G143G	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	139	0	0		WXS	Illumina HiSeq	Phase_I	155	65	0.419355	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		
NCKAP5	344148	hgsc.bcm.edu	37	2	133539566	133539566	+	Silent	SNP	G	G	A	rs6730282	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133539566G>A	ENST00000409261.1	-	14	5191	c.4818C>T	c.(4816-4818)caC>caT	p.H1606H	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Silent_p.H1606H|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'UTR	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1606										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						CAACAGGGCTGTGTCTATTCC	0.448													G|||	2684	0.535942	0.4985	0.4813	5008	,	,		19229	0.745		0.4702	False		,,,				2504	0.4775				p.H1606H		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C4818T						PASS	.	G	,	2018,1822		541,936,443	264.0	231.0	241.0		4818,	4.4	1.0	2	dbSNP_116	241	4163,4107		1053,2057,1025	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	1594,2993,1468	AA,AG,GG		49.6614,47.4479,48.9595	,	1606/1910,	133539566	6181,5929	1920	4135	6055	SO:0001819	synonymous_variant	344148	exon14			AGGGCTGTGTCTA	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.4818C>T	2.37:g.133539566G>A		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	285	285	1	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			G|0.434;A|0.566	0.566	strong		0.448	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
C20orf196	149840	hgsc.bcm.edu	37	20	5843812	5843812	+	Silent	SNP	T	T	C	rs1699233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	154	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	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	
SCAPER	49855	hgsc.bcm.edu	37	15	77176158	77176158	+	Start_Codon_SNP	SNP	T	T	C	rs3812908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:77176158T>C	ENST00000563290.1	-	2	96	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	SCAPER_ENST00000324767.7_Start_Codon_SNP_p.M1V			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1				M -> V (in Ref. 1; AAK29205). {ECO:0000305}.		endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						CTTACCATCATTCTTTAAATT	0.284													T|||	2092	0.417732	0.3434	0.3256	5008	,	,		17908	0.5774		0.3101	False		,,,				2504	0.5297				p.M1V		Atlas-SNP	.											.	SCAPER	160	.	0			c.A1G						PASS	.	T	VAL/MET	1148,2456		188,772,842	102.0	106.0	105.0		1	3.9	1.0	15	dbSNP_107	105	2329,5803		333,1663,2070	yes	missense	SCAPER	NM_020843.2	21	521,2435,2912	CC,CT,TT		28.6399,31.8535,29.6268	benign	1/1401	77176158	3477,8259	1802	4066	5868	SO:0001582	initiator_codon_variant	49855	exon1			CCATCATTCTTTA	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"""Zinc fingers, C2H2-type"""	13081	protein-coding gene	gene with protein product		611611	"""zinc finger protein 291"""	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1A>G	15.37:g.77176158T>C	ENSP00000454973:p.Met1Val	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	37	CCDS53962.1	808|808	0.36996336996337|0.36996336996337	145|145	0.29471544715447157|0.29471544715447157	125|125	0.3453038674033149|0.3453038674033149	311|311	0.5437062937062938|0.5437062937062938	227|227	0.2994722955145119|0.2994722955145119	T|T	9.550|9.550	1.115590|1.115590	0.20795|0.20795	0.318535|0.318535	0.286399|0.286399	ENSG00000140386|ENSG00000140386	ENST00000324767|ENST00000303521	T|.	0.21031|.	2.03|.	3.87|3.87	3.87|3.87	0.44632|0.44632	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.36073|0.36073	P|P	0.157763|0.157763	P|.	0.43578|.	0.811|.	P|.	0.57846|.	0.828|.	T|T	0.52109|0.52109	-0.8619|-0.8619	7|4	0.40728|0.46703	T|T	0.16|0.11	.|.	9.3739|9.3739	0.38270|0.38270	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs3812908;rs60428850;rs3812908|rs3812908;rs60428850;rs3812908	1|.	Q6NSF1|.	.|.	V|S	1|55	ENSP00000326924:M1V|.	ENSP00000326924:M1V|ENSP00000303560:N55S	M|N	-|-	1|2	0|0	SCAPER|SCAPER	74963213|74963213	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.971000|0.971000	0.66376|0.66376	2.645000|2.645000	0.46621|0.46621	1.990000|1.990000	0.58119|0.58119	0.528000|0.528000	0.53228|0.53228	ATG|AAT	T|0.628;C|0.372	0.372	strong		0.284	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843	Missense_Mutation
FAM166B	730112	hgsc.bcm.edu	37	9	35562549	35562549	+	Silent	SNP	G	G	A	rs755774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35562549G>A	ENST00000399742.2	-	5	637	c.567C>T	c.(565-567)tgC>tgT	p.C189C	FAM166B_ENST00000492890.1_Intron	NM_001099951.2|NM_001164310.1	NP_001093421.1|NP_001157782.1	A8MTA8	F166B_HUMAN	family with sequence similarity 166, member B	189										kidney(3)|large_intestine(1)|lung(4)|ovary(1)	9						GGAAGCGGGCGCAGGGCACAT	0.627													G|||	1671	0.333666	0.2148	0.5778	5008	,	,		16151	0.2817		0.4433	False		,,,				2504	0.2618				p.C189C		Atlas-SNP	.											.	FAM166B	19	.	0			c.C567T						PASS	.	G	,	1052,3294		153,746,1274	42.0	51.0	48.0		,567	-5.5	0.9	9	dbSNP_86	48	4007,4555		926,2155,1200	no	intron,coding-synonymous	FAM166B	NM_001099951.2,NM_001164310.1	,	1079,2901,2474	AA,AG,GG		46.7998,24.2062,39.1927	,	,189/276	35562549	5059,7849	2173	4281	6454	SO:0001819	synonymous_variant	730112	exon5			GCGGGCGCAGGGC	BC129999	CCDS47963.1, CCDS56572.1	9p13.3	2008-06-10			ENSG00000215187	ENSG00000215187			34242	protein-coding gene	gene with protein product							Standard	NM_001099951		Approved		uc010mkr.3	A8MTA8	OTTHUMG00000019858	ENST00000399742.2:c.567C>T	9.37:g.35562549G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001164310	A1L3B2|B7ZBJ0	Silent	SNP	ENST00000399742.2	37	CCDS56572.1																																																																																			G|0.653;A|0.347	0.347	strong		0.627	FAM166B-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336563.1	NM_001099951	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458893	39458893	+	Missense_Mutation	SNP	G	G	A	rs758741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	87	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	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		
DDX55	57696	hgsc.bcm.edu	37	12	124102305	124102305	+	Splice_Site	SNP	T	T	A	rs147152712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124102305T>A	ENST00000238146.4	+	11	1100	c.1050T>A	c.(1048-1050)agT>agA	p.S350R	DDX55_ENST00000421670.3_5'Flank|SNORA9_ENST00000384170.1_RNA|DDX55_ENST00000541259.1_Intron|DDX55_ENST00000538744.1_Splice_Site_p.S319R	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	350	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					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)		GTTCTCACAGTGCCTTCGTGC	0.582																																					p.S350R		Atlas-SNP	.											.	DDX55	51	.	0			c.T1050A						PASS	.	T	ARG/SER	1,4405	2.1+/-5.4	0,1,2202	90.0	79.0	83.0		1050	-6.2	0.9	12	dbSNP_134	83	9,8591	7.1+/-27.0	0,9,4291	yes	missense-near-splice	DDX55	NM_020936.1	110	0,10,6493	AA,AT,TT		0.1047,0.0227,0.0769	probably-damaging	350/601	124102305	10,12996	2203	4300	6503	SO:0001630	splice_region_variant	57696	exon11			TCACAGTGCCTTC	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.1050-1T>A	12.37:g.124102305T>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.469762	0.84533	2.27E-4	0.001047	ENSG00000111364	ENST00000238146;ENST00000538744	T;D	0.92699	-0.93;-3.09	5.98	-6.16	0.02098	Helicase, C-terminal (3);	0.084790	0.85682	D	0.000000	D	0.90899	0.7140	L	0.33293	1	0.80722	D	1	P;D	0.58970	0.603;0.984	P;D	0.66847	0.516;0.947	D	0.88317	0.2960	9	.	.	.	.	15.8924	0.79309	0.0:0.5049:0.0:0.4951	.	350;350	B4DVE4;Q8NHQ9	.;DDX55_HUMAN	R	350;319	ENSP00000238146:S350R;ENSP00000443114:S319R	.	S	+	3	2	DDX55	122668258	0.229000	0.23729	0.920000	0.36463	0.971000	0.66376	-0.470000	0.06639	-0.950000	0.03659	-0.274000	0.10170	AGT	T|0.999;A|0.001	0.001	strong		0.582	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		Missense_Mutation
ENPP5	59084	hgsc.bcm.edu	37	6	46135283	46135283	+	Silent	SNP	A	A	G	rs34450398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:46135283A>G	ENST00000371383.2	-	3	977	c.717T>C	c.(715-717)caT>caC	p.H239H	ENPP5_ENST00000492313.1_5'UTR|ENPP5_ENST00000230565.3_Silent_p.H239H					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GCGTCATTCCATGATCACTTG	0.403													A|||	177	0.0353435	0.0303	0.0591	5008	,	,		22151	0.0		0.0696	False		,,,				2504	0.0266				p.H239H		Atlas-SNP	.											.	ENPP5	44	.	0			c.T717C						PASS	.	A		171,4235	112.1+/-150.2	3,165,2035	154.0	134.0	141.0		717	-10.4	0.6	6	dbSNP_126	141	474,8126	139.4+/-196.0	15,444,3841	no	coding-synonymous	ENPP5	NM_021572.4		18,609,5876	GG,GA,AA		5.5116,3.8811,4.9592		239/478	46135283	645,12361	2203	4300	6503	SO:0001819	synonymous_variant	59084	exon2			CATTCCATGATCA	AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.717T>C	6.37:g.46135283A>G		Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	275	144	0.523636	NM_021572		Silent	SNP	ENST00000371383.2	37	CCDS4915.1																																																																																			A|0.951;G|0.049	0.049	strong		0.403	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
PAM	5066	hgsc.bcm.edu	37	5	102345546	102345546	+	Silent	SNP	A	A	C	rs2230457	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:102345546A>C	ENST00000438793.3	+	20	2777	c.2307A>C	c.(2305-2307)atA>atC	p.I769I	PAM_ENST00000346918.2_Silent_p.I769I|PAM_ENST00000304400.7_Silent_p.I769I|PAM_ENST00000379787.4_Silent_p.I149I|PAM_ENST00000348126.2_Silent_p.I662I|PAM_ENST00000274392.9_Silent_p.I672I|PAM_ENST00000455264.2_Silent_p.I769I	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	769	Peptidyl-alpha-hydroxyglycine alpha- amidating lyase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	GGGAAATTATAGACATCTTCA	0.393													A|||	1176	0.234824	0.112	0.2277	5008	,	,		13755	0.4335		0.2763	False		,,,				2504	0.1585				p.I769I		Atlas-SNP	.											.	PAM	180	.	0			c.A2307C						PASS	.	A	,,,,	643,3763	275.4+/-272.5	44,555,1604	86.0	82.0	83.0		2307,2307,2307,1986,2307	0.7	1.0	5	dbSNP_120	83	2500,6100	409.3+/-349.8	354,1792,2154	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PAM	NM_000919.3,NM_001177306.1,NM_138766.2,NM_138821.2,NM_138822.2	,,,,	398,2347,3758	CC,CA,AA		29.0698,14.5937,24.1658	,,,,	769/975,769/974,769/906,662/867,769/888	102345546	3143,9863	2203	4300	6503	SO:0001819	synonymous_variant	5066	exon20			AATTATAGACATC	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"""peptidyl-alpha-hydroxyglycine alpha-amidating lyase"", ""peptidylglycine alpha-hydroxylating monooxygenase"""	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.2307A>C	5.37:g.102345546A>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Silent	SNP	ENST00000438793.3	37	CCDS54885.1	596	0.27289377289377287	50	0.1016260162601626	91	0.2513812154696133	239	0.4178321678321678	216	0.2849604221635884	A	6.874	0.530566	0.13127	0.145937	0.290698	ENSG00000145730	ENST00000504691	.	.	.	5.8	0.673	0.17941	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.7	0.02870	0.5417:0.1061:0.2066:0.1456	rs11544128;rs17154927;rs17851622	.	.	.	S	64	.	.	X	+	2	0	PAM	102373445	1.000000	0.71417	0.966000	0.40874	0.672000	0.39443	0.738000	0.26158	-0.097000	0.12307	-0.361000	0.07541	TAG	A|0.744;C|0.256;T|0.000	0.256	strong		0.393	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919	
STAB2	55576	hgsc.bcm.edu	37	12	104067812	104067812	+	Silent	SNP	C	C	T	rs11614418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:104067812C>T	ENST00000388887.2	+	23	2703	c.2499C>T	c.(2497-2499)taC>taT	p.Y833Y		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						GTGGGCCCTACGTGCAGTTCT	0.557													C|||	2112	0.421725	0.3177	0.389	5008	,	,		21847	0.5278		0.3817	False		,,,				2504	0.5174				p.Y833Y		Atlas-SNP	.											.	STAB2	370	.	0			c.C2499T						PASS	.	C		1330,3076	447.5+/-348.4	209,912,1082	131.0	103.0	113.0		2499	-2.6	0.0	12	dbSNP_120	113	3215,5385	485.4+/-371.6	598,2019,1683	no	coding-synonymous	STAB2	NM_017564.9		807,2931,2765	TT,TC,CC		37.3837,30.1861,34.9454		833/2552	104067812	4545,8461	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon23			GCCCTACGTGCAG	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.2499C>T	12.37:g.104067812C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.625;T|0.375	0.375	strong		0.557	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
MTR	4548	hgsc.bcm.edu	37	1	237058828	237058828	+	Silent	SNP	C	C	T	rs1131449	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237058828C>T	ENST00000366577.5	+	31	3970	c.3576C>T	c.(3574-3576)ctC>ctT	p.L1192L	MTR_ENST00000535889.1_Silent_p.L1141L|MTR_ENST00000470570.1_3'UTR	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	1192	AdoMet activation. {ECO:0000255|PROSITE- ProRule:PRU00346}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TGTGGAGACTCGCAGACATCG	0.592													C|||	2650	0.529153	0.4342	0.5922	5008	,	,		17413	0.5198		0.5358	False		,,,				2504	0.6155				p.L1192L		Atlas-SNP	.											MTR,NS,carcinoma,0,2	MTR	127	2	0			c.C3576T						PASS	.	C		2051,2349		475,1101,624	19.0	18.0	19.0		3576	-11.3	0.0	1	dbSNP_86	19	5038,3544		1496,2046,749	no	coding-synonymous	MTR	NM_000254.2		1971,3147,1373	TT,TC,CC		41.2957,46.6136,45.3936		1192/1266	237058828	7089,5893	2200	4291	6491	SO:0001819	synonymous_variant	4548	exon31			GAGACTCGCAGAC	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.3576C>T	1.37:g.237058828C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	193	108	0.559586	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Silent	SNP	ENST00000366577.5	37	CCDS1614.1																																																																																			C|0.456;G|0.000;T|0.544	0.544	strong		0.592	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36667022	36667022	+	Silent	SNP	C	C	T	rs15537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:36667022C>T	ENST00000431231.2	+	24	4358	c.4290C>T	c.(4288-4290)ccC>ccT	p.P1430P	ARHGAP23_ENST00000443378.1_Silent_p.P1336P	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	1430					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						GAGGGGGCCCCCCGGAGCCTG	0.731													C|||	356	0.0710863	0.1112	0.0504	5008	,	,		6979	0.0327		0.0736	False		,,,				2504	0.0685				p.P1430P		Atlas-SNP	.											.	ARHGAP23	48	.	0			c.C4290T						PASS	.						2.0	3.0	3.0					17																	36667022		407	1191	1598	SO:0001819	synonymous_variant	57636	exon24			GGGCCCCCCGGAG	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.4290C>T	17.37:g.36667022C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_001199417		Silent	SNP	ENST00000431231.2	37	CCDS56027.1																																																																																			C|0.926;T|0.074	0.074	strong		0.731	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
FLG	2312	hgsc.bcm.edu	37	1	152278689	152278689	+	Silent	SNP	C	C	A	rs57672167	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152278689C>A	ENST00000368799.1	-	3	8708	c.8673G>T	c.(8671-8673)gtG>gtT	p.V2891V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2891	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCCTGGCTCACACTGGATC	0.552									Ichthyosis				A|||	1985	0.396366	0.3147	0.4337	5008	,	,		31121	0.6101		0.171	False		,,,				2504	0.4918				p.V2891V		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.G8673T						PASS	.	A		847,3219		243,361,1429	85.0	137.0	120.0		8673	-5.2	0.0	1	dbSNP_129	120	1434,7156		126,1182,2987	no	coding-synonymous	FLG	NM_002016.1		369,1543,4416	AA,AC,CC		16.6938,20.8313,18.0231		2891/4062	152278689	2281,10375	2033	4295	6328	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGGCTCACACTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8673G>T	1.37:g.152278689C>A		Somatic	515	2	0.0038835		WXS	Illumina HiSeq	Phase_I	806	456	0.565757	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	
NBEAL1	65065	hgsc.bcm.edu	37	2	204073414	204073414	+	Missense_Mutation	SNP	A	A	G	rs140112414	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:204073414A>G	ENST00000449802.1	+	51	7807	c.7474A>G	c.(7474-7476)Acc>Gcc	p.T2492A		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2492										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TTATGGACACACCAACGAGGT	0.408													A|||	91	0.0181709	0.0023	0.0231	5008	,	,		18397	0.0		0.0487	False		,,,				2504	0.0235				p.T2492A		Atlas-SNP	.											NBEAL1_ENST00000449802,NS,carcinoma,0,2	NBEAL1	266	2	0			c.A7474G						PASS	.	A	ALA/THR	34,3756		0,34,1861	133.0	121.0	125.0		7474	5.9	1.0	2	dbSNP_134	125	456,7800		19,418,3691	yes	missense	NBEAL1	NM_001114132.1	58	19,452,5552	GG,GA,AA		5.5233,0.8971,4.0677	benign	2492/2695	204073414	490,11556	1895	4128	6023	SO:0001583	missense	65065	exon51			GGACACACCAACG	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.7474A>G	2.37:g.204073414A>G	ENSP00000399903:p.Thr2492Ala	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	46	0.021062271062271064	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	35	0.04617414248021108	A	21.0	4.074809	0.76415	0.008971	0.055233	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.64618	-0.11;-0.11	5.95	5.95	0.96441	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.042481	0.85682	D	0.000000	T	0.18383	0.0441	L	0.35288	1.05	0.53005	D	0.999965	P;D	0.64830	0.93;0.994	P;P	0.59115	0.659;0.852	T	0.40403	-0.9565	10	0.14656	T	0.56	.	16.0684	0.80907	1.0:0.0:0.0:0.0	.	2492;2481	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	A	2492;2423;507	ENSP00000399903:T2492A;ENSP00000388466:T507A	ENSP00000344985:T2423A	T	+	1	0	NBEAL1	203781659	1.000000	0.71417	0.998000	0.56505	0.712000	0.41017	6.930000	0.75858	2.272000	0.75746	0.460000	0.39030	ACC	A|0.964;G|0.036	0.036	strong		0.408	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
GLP2R	9340	hgsc.bcm.edu	37	17	9792872	9792872	+	Silent	SNP	T	T	C	rs17681708	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:9792872T>C	ENST00000262441.5	+	13	2025	c.1512T>C	c.(1510-1512)caT>caC	p.H504H	GLP2R_ENST00000574745.1_Silent_p.H324H	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	504					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	GGCTCCTACATCTAGCCATGC	0.627													C|||	504	0.100639	0.0212	0.1585	5008	,	,		18658	0.002		0.2763	False		,,,				2504	0.0879				p.H504H		Atlas-SNP	.											GLP2R,NS,carcinoma,0,1	GLP2R	90	1	0			c.T1512C						PASS	.	C		322,4084	771.1+/-413.8	11,300,1892	44.0	46.0	45.0		1512	-1.2	0.0	17	dbSNP_123	45	2702,5898	662.0+/-401.9	428,1846,2026	no	coding-synonymous	GLP2R	NM_004246.1		439,2146,3918	CC,CT,TT		31.4186,7.3082,23.2508		504/554	9792872	3024,9982	2203	4300	6503	SO:0001819	synonymous_variant	9340	exon13			CCTACATCTAGCC	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"""GPCR / Class B : Glucagon receptors"""	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1512T>C	17.37:g.9792872T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_004246	Q4VAT3	Silent	SNP	ENST00000262441.5	37	CCDS11150.1																																																																																			T|0.817;C|0.183	0.183	strong		0.627	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4		
OR52R1	119695	hgsc.bcm.edu	37	11	4824878	4824878	+	Missense_Mutation	SNP	A	A	C	rs2053116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4824878A>C	ENST00000356069.2	-	1	732	c.733T>G	c.(733-735)Tcc>Gcc	p.S245A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.S324A	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	245			S -> A (in dbSNP:rs2053116). {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)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATATGGGAGGAACGTGTGCTA	0.468													C|||	1553	0.310104	0.5598	0.2795	5008	,	,		22575	0.0129		0.3907	False		,,,				2504	0.2178				p.S245A		Atlas-SNP	.											.	OR52R1	81	.	0			c.T733G						PASS	.	C	ALA/SER	2268,2134	577.7+/-384.5	596,1076,529	86.0	86.0	86.0		733	4.7	1.0	11	dbSNP_94	86	3017,5579	663.6+/-402.1	550,1917,1831	yes	missense	OR52R1	NM_001005177.3	99	1146,2993,2360	CC,CA,AA		35.0977,48.478,40.6601	benign	245/316	4824878	5285,7713	2201	4298	6499	SO:0001583	missense	119695	exon1			GGGAGGAACGTGT	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.733T>G	11.37:g.4824878A>C	ENSP00000348368:p.Ser245Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	114	70	0.614035	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	683	0.31272893772893773	271	0.5508130081300813	117	0.32320441988950277	10	0.017482517482517484	285	0.3759894459102902	C	11.82	1.753870	0.31046	0.51522	0.350977	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.34667	1.35;1.35	5.57	4.65	0.58169	GPCR, rhodopsin-like superfamily (1);	0.134911	0.33419	N	0.004921	T	0.00012	0.0000	N	0.16708	0.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	9	0.44086	T	0.13	.	10.1867	0.43002	0.136:0.7919:0.0:0.072	rs2053116;rs52835851;rs60739270;rs2053116	245	Q8NGF1	O52R1_HUMAN	A	245;324	ENSP00000348368:S245A;ENSP00000369742:S324A	ENSP00000348368:S245A	S	-	1	0	OR52R1	4781454	0.000000	0.05858	0.984000	0.44739	0.902000	0.53008	0.023000	0.13533	1.609000	0.50190	-0.127000	0.14921	TCC	A|0.631;C|0.369	0.369	strong		0.468	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
OR5R1	219479	hgsc.bcm.edu	37	11	56185224	56185224	+	Missense_Mutation	SNP	A	A	G	rs12785840	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56185224A>G	ENST00000312253.1	-	1	484	c.485T>C	c.(484-486)aTc>aCc	p.I162T		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	162			I -> T (in dbSNP:rs12785840).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I162T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					ACGGAAAGTGATAACGGTGTG	0.453													A|||	621	0.124002	0.1944	0.0663	5008	,	,		21271	0.0933		0.1402	False		,,,				2504	0.0849				p.I162T		Atlas-SNP	.											OR5R1,NS,carcinoma,0,1	OR5R1	83	1	1	Substitution - Missense(1)	stomach(1)	c.T485C						PASS	.	A	THR/ILE	762,3640	313.0+/-292.9	67,628,1506	113.0	112.0	112.0		485	3.5	0.7	11	dbSNP_121	112	1191,7401	243.3+/-273.0	75,1041,3180	yes	missense	OR5R1	NM_001004744.1	89	142,1669,4686	GG,GA,AA		13.8617,17.3103,15.03	possibly-damaging	162/325	56185224	1953,11041	2201	4296	6497	SO:0001583	missense	219479	exon1			AAAGTGATAACGG	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"""GPCR / Class A : Olfactory receptors"""	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.485T>C	11.37:g.56185224A>G	ENSP00000308595:p.Ile162Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	294	0.1346153846153846	112	0.22764227642276422	38	0.10497237569060773	42	0.07342657342657342	102	0.1345646437994723	A	1.240	-0.621485	0.03636	0.173103	0.138617	ENSG00000174942	ENST00000312253	T	0.00123	8.7	5.91	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.249670	0.20616	U	0.088874	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.29955	0.263	B	0.33121	0.158	T	0.00030	-1.2284	9	0.22109	T	0.4	-14.6421	4.351	0.11155	0.613:0.0:0.1359:0.2511	rs12785840;rs17627213;rs61597384;rs12785840	162	Q8NH85	OR5R1_HUMAN	T	162	ENSP00000308595:I162T	ENSP00000308595:I162T	I	-	2	0	OR5R1	55941800	0.000000	0.05858	0.663000	0.29738	0.021000	0.10359	1.455000	0.35190	1.028000	0.39785	0.472000	0.43445	ATC	A|0.853;G|0.147	0.147	strong		0.453	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291188	1291188	+	Silent	SNP	C	C	T	rs17434400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1291188C>T	ENST00000338844.3	+	3	129	c.96C>T	c.(94-96)gtC>gtT	p.V32V	TPSAB1_ENST00000461509.2_Silent_p.V39V	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	32	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				TGGGCATCGTCGGGGGTCAGG	0.701																																					p.V32V		Atlas-SNP	.											TPSAB1,NS,carcinoma,0,1	TPSAB1	24	1	0			c.C96T						PASS	.						38.0	38.0	38.0					16																	1291188		2199	4299	6498	SO:0001819	synonymous_variant	7177	exon3			CATCGTCGGGGGT	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.96C>T	16.37:g.1291188C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	190	138	0.726316	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Silent	SNP	ENST00000338844.3	37	CCDS10431.1																																																																																			.	.	weak		0.701	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
VWA3B	200403	hgsc.bcm.edu	37	2	98736225	98736225	+	Splice_Site	SNP	C	C	T	rs2305355	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:98736225C>T	ENST00000477737.1	+	4	745	c.541C>T	c.(541-543)Cgg>Tgg	p.R181W	VWA3B_ENST00000451075.2_Intron|VWA3B_ENST00000435344.1_Splice_Site_p.R181W	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	181			R -> W (in dbSNP:rs2305355).							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						CAATATCATACGGTGAGTTCC	0.453													C|||	645	0.128794	0.2496	0.0548	5008	,	,		19824	0.1329		0.0656	False		,,,				2504	0.0787				p.R181W		Atlas-SNP	.											.	VWA3B	138	.	0			c.C541T						PASS	.	C	TRP/ARG	742,3066		69,604,1231	135.0	127.0	130.0		541	-2.8	1.0	2	dbSNP_100	130	602,7658		21,560,3549	yes	missense-near-splice	VWA3B	NM_144992.4	101	90,1164,4780	TT,TC,CC		7.2881,19.4853,11.1369	benign	181/1295	98736225	1344,10724	1904	4130	6034	SO:0001630	splice_region_variant	200403	exon4			ATCATACGGTGAG	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.542+1C>T	2.37:g.98736225C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	266	0.12179487179487179	114	0.23170731707317074	22	0.06077348066298342	81	0.14160839160839161	49	0.06464379947229551	C	15.15	2.749237	0.49257	0.194853	0.072881	ENSG00000168658	ENST00000435344;ENST00000477737	T;T	0.07908	3.15;3.15	6.02	-2.82	0.05787	.	0.999489	0.08098	N	0.998373	T	0.00012	0.0000	N	0.02916	-0.46	0.09310	P	0.9999999736373	B;B	0.24043	0.096;0.078	B;B	0.19148	0.016;0.024	T	0.48790	-0.9004	9	0.30078	T	0.28	.	3.9747	0.09468	0.1147:0.4827:0.1301:0.2726	rs2305355;rs60567239;rs2305355	181;181	Q502W6;Q502W6-8	VWA3B_HUMAN;.	W	181	ENSP00000401959:R181W;ENSP00000417955:R181W	ENSP00000411168:R181W	R	+	1	2	VWA3B	98102657	0.721000	0.28007	0.997000	0.53966	0.974000	0.67602	-0.354000	0.07681	-0.105000	0.12132	0.655000	0.94253	CGG	C|0.875;T|0.125	0.125	strong		0.453	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	Missense_Mutation
ANO2	57101	hgsc.bcm.edu	37	12	5841733	5841733	+	Missense_Mutation	SNP	A	A	C	rs1860961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:5841733A>C	ENST00000356134.5	-	16	1572	c.1501T>G	c.(1501-1503)Tct>Gct	p.S501A	ANO2_ENST00000546188.1_Missense_Mutation_p.S501A|ANO2_ENST00000538154.1_5'UTR|ANO2_ENST00000327087.8_Missense_Mutation_p.S500A	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	154	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	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	
SOAT2	8435	hgsc.bcm.edu	37	12	53509933	53509933	+	Missense_Mutation	SNP	C	C	T	rs2272296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53509933C>T	ENST00000301466.3	+	7	821	c.761C>T	c.(760-762)aCc>aTc	p.T254I		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	254			T -> I (in dbSNP:rs2272296). {ECO:0000269|PubMed:10846185, ECO:0000269|PubMed:15489334}.		cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)			endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	GTGCCTGGGACCCTTCGTGCC	0.527													C|||	1315	0.26258	0.416	0.2061	5008	,	,		20456	0.3165		0.172	False		,,,				2504	0.1329				p.T254I		Atlas-SNP	.											.	SOAT2	44	.	0			c.C761T						PASS	.	C	ILE/THR	1546,2860	488.0+/-361.1	274,998,931	154.0	133.0	140.0		761	-2.7	0.8	12	dbSNP_100	140	1327,7273	260.1+/-283.0	109,1109,3082	yes	missense	SOAT2	NM_003578.3	89	383,2107,4013	TT,TC,CC		15.4302,35.0885,22.0898	benign	254/523	53509933	2873,10133	2203	4300	6503	SO:0001583	missense	8435	exon7			CTGGGACCCTTCG	AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.761C>T	12.37:g.53509933C>T	ENSP00000301466:p.Thr254Ile	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_003578	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Missense_Mutation	SNP	ENST00000301466.3	37	CCDS8847.1	605	0.27701465201465203	197	0.40040650406504064	71	0.19613259668508287	198	0.34615384615384615	139	0.18337730870712401	C	6.504	0.461214	0.12342	0.350885	0.154302	ENSG00000167780	ENST00000301466	T	0.73897	-0.79	4.96	-2.65	0.06095	.	0.359684	0.24978	N	0.034088	T	0.00012	0.0000	N	0.04820	-0.15	0.40954	P	0.015436000000000005	B	0.09022	0.002	B	0.12156	0.007	T	0.35574	-0.9783	9	0.19147	T	0.46	-6.404	11.847	0.52389	0.0:0.3154:0.0:0.6846	rs2272296;rs58899375;rs2272296	254	O75908	SOAT2_HUMAN	I	254	ENSP00000301466:T254I	ENSP00000301466:T254I	T	+	2	0	SOAT2	51796200	0.002000	0.14202	0.790000	0.31976	0.963000	0.63663	0.383000	0.20651	-0.384000	0.07845	-0.140000	0.14226	ACC	C|0.751;T|0.249	0.249	strong		0.527	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1		
FLG	2312	hgsc.bcm.edu	37	1	152283283	152283283	+	Missense_Mutation	SNP	C	C	T	rs11586631	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152283283C>T	ENST00000368799.1	-	3	4114	c.4079G>A	c.(4078-4080)cGc>cAc	p.R1360H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1360	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTGGTGGCGGGATCCATG	0.537									Ichthyosis				C|||	1441	0.28774	0.0144	0.389	5008	,	,		20885	0.5823		0.1421	False		,,,				2504	0.4315				p.R1360H		Atlas-SNP	.											.	FLG	900	.	0			c.G4079A						PASS	.	C	HIS/ARG	163,4243	109.1+/-147.4	2,159,2042	375.0	355.0	362.0		4079	-7.6	0.0	1	dbSNP_120	362	1237,7359	248.6+/-276.2	97,1043,3158	no	missense	FLG	NM_002016.1	29	99,1202,5200	TT,TC,CC		14.3904,3.6995,10.7676	benign	1360/4062	152283283	1400,11602	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGGCGGGATC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4079G>A	1.37:g.152283283C>T	ENSP00000357789:p.Arg1360His	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	204	86	0.421569	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	505	0.23122710622710624	7	0.014227642276422764	104	0.287292817679558	300	0.5244755244755245	94	0.12401055408970976	C	11.44	1.640902	0.29157	0.036995	0.143904	ENSG00000143631	ENST00000368799	T	0.01474	4.85	3.78	-7.56	0.01322	.	.	.	.	.	T	0.00300	0.0009	L	0.29908	0.895	0.80722	P	0.0	B	0.33288	0.406	B	0.24155	0.051	T	0.49194	-0.8965	8	0.15066	T	0.55	.	1.3944	0.02257	0.1228:0.3039:0.2443:0.329	rs11586631	1360	P20930	FILA_HUMAN	H	1360	ENSP00000357789:R1360H	ENSP00000357789:R1360H	R	-	2	0	FLG	150549907	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-6.306000	0.00071	-1.837000	0.01189	-0.300000	0.09419	CGC	C|0.851;T|0.149	0.149	strong		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
UGCG	7357	hgsc.bcm.edu	37	9	114694486	114694486	+	Silent	SNP	A	A	G	rs7850023	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:114694486A>G	ENST00000374279.3	+	8	1311	c.861A>G	c.(859-861)acA>acG	p.T287T	MIR4668_ENST00000582284.1_RNA	NM_003358.1	NP_003349.1	Q16739	CEGT_HUMAN	UDP-glucose ceramide glucosyltransferase	287					epidermis development (GO:0008544)|glucosylceramide biosynthetic process (GO:0006679)|glycosphingolipid biosynthetic process (GO:0006688)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ceramide glucosyltransferase activity (GO:0008120)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	12				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)	TTCCTGCTACAATAATTTGTG	0.353													A|||	1660	0.33147	0.3759	0.4251	5008	,	,		19974	0.2986		0.2813	False		,,,				2504	0.2904				p.T287T		Atlas-SNP	.											.	UGCG	32	.	0			c.A861G						PASS	.	A		1539,2867	485.7+/-360.4	261,1017,925	144.0	140.0	141.0		861	2.3	1.0	9	dbSNP_116	141	2224,6376	378.0+/-338.7	293,1638,2369	no	coding-synonymous	UGCG	NM_003358.1		554,2655,3294	GG,GA,AA		25.8605,34.9296,28.9328		287/395	114694486	3763,9243	2203	4300	6503	SO:0001819	synonymous_variant	7357	exon8			TGCTACAATAATT	D50840	CCDS6782.1	9q31	2014-03-13			ENSG00000148154	ENSG00000148154	2.4.1.80	"""Glycosyltransferase family 2 domain containing"""	12524	protein-coding gene	gene with protein product	"""glucosylceramide synthase"", ""ceramide glucosyltransferase"""	602874				8643456, 9605861	Standard	NM_003358		Approved	GCS	uc004bft.3	Q16739	OTTHUMG00000020498	ENST00000374279.3:c.861A>G	9.37:g.114694486A>G		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	212	110	0.518868	NM_003358	Q5T258	Silent	SNP	ENST00000374279.3	37	CCDS6782.1																																																																																			A|0.701;G|0.299	0.299	strong		0.353	UGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053661.1	NM_003358	
GREB1	9687	hgsc.bcm.edu	37	2	11727507	11727507	+	Intron	SNP	G	G	A	rs13394619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:11727507G>A	ENST00000381486.2	+	10	1459				GREB1_ENST00000234142.5_Intron|RN7SL674P_ENST00000463397.2_RNA|GREB1_ENST00000263834.5_Splice_Site|GREB1_ENST00000381483.2_Intron	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral component of membrane (GO:0016021)		p.?(1)		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)		GCCCACTGCAGTATTTGTAAA	0.498													A|||	3101	0.619209	0.916	0.5893	5008	,	,		19435	0.4881		0.5278	False		,,,				2504	0.4683				.	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											GREB1_ENST00000263834,NS,carcinoma,0,1	GREB1	308	1	1	Unknown(1)	stomach(1)	c.1160-1G>A						PASS	.	A	,,	3700,704	294.4+/-283.1	1552,596,54	137.0	136.0	136.0		,,	-0.7	0.0	2	dbSNP_121	136	4294,4306	578.4+/-390.7	1057,2180,1063	yes	intron,intron,splice-3	GREB1	NM_014668.3,NM_033090.2,NM_148903.2	,,	2609,2776,1117	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	49.9302,15.9855,38.5266	,,	,,	11727507	7994,5010	2202	4300	6502	SO:0001627	intron_variant	9687	exon10			ACTGCAGTATTTG		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.1160-1365G>A	2.37:g.11727507G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Splice_Site	SNP	ENST00000381486.2	37	CCDS42655.1	1362	0.6236263736263736	454	0.9227642276422764	216	0.5966850828729282	303	0.5297202797202797	389	0.5131926121372031	A	1.031	-0.681773	0.03353	0.840145	0.499302	ENSG00000196208	ENST00000263834	.	.	.	2.02	-0.7	0.11273	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.295	0.21081	0.4356:0.0:0.5644:0.0	rs13394619;rs17529763;rs58035934;rs13394619	.	.	.	.	-1	.	.	.	+	.	.	GREB1	11644958	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.639000	0.05446	-0.592000	0.05851	-1.246000	0.01523	.	G|0.377;A|0.623	0.623	strong		0.498	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
PNPLA6	10908	hgsc.bcm.edu	37	19	7615903	7615903	+	Silent	SNP	G	G	A	rs8107538	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7615903G>A	ENST00000221249.6	+	20	2408	c.1977G>A	c.(1975-1977)ccG>ccA	p.P659P	PNPLA6_ENST00000600737.1_Silent_p.P698P|PNPLA6_ENST00000594864.1_3'UTR|PNPLA6_ENST00000545201.2_Silent_p.P633P|PNPLA6_ENST00000450331.3_Silent_p.P659P|PNPLA6_ENST00000414982.3_Silent_p.P707P	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	698					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						CCCGGCAGCCGCGAGCCACGA	0.687													G|||	1012	0.202077	0.3419	0.1758	5008	,	,		9640	0.0129		0.2386	False		,,,				2504	0.1892				p.P707P		Atlas-SNP	.											.	PNPLA6	163	.	0			c.G2121A						PASS	.	G	,,,,	1025,2749		156,713,1018	4.0	4.0	4.0		2121,1899,1977,2094,1977	-9.8	0.6	19	dbSNP_116	4	1552,5774		175,1202,2286	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PNPLA6	NM_001166111.1,NM_001166112.1,NM_001166113.1,NM_001166114.1,NM_006702.4	,,,,	331,1915,3304	AA,AG,GG		21.1848,27.1595,23.2162	,,,,	707/1376,633/1301,659/1328,698/1366,659/1328	7615903	2577,8523	1887	3663	5550	SO:0001819	synonymous_variant	10908	exon19			GCAGCCGCGAGCC	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1977G>A	19.37:g.7615903G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	15	12	0.8	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	37	CCDS32891.1																																																																																			G|0.793;A|0.207	0.207	strong		0.687	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
STRN4	29888	hgsc.bcm.edu	37	19	47223949	47223949	+	Silent	SNP	G	G	A	rs313841	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47223949G>A	ENST00000263280.6	-	17	2221	c.2172C>T	c.(2170-2172)caC>caT	p.H724H	STRN4_ENST00000594357.2_5'Flank|STRN4_ENST00000391910.3_Silent_p.H731H|STRN4_ENST00000539396.1_Silent_p.H605H	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	724						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)		TGGCCTCCTCGTGCTTCTTGC	0.627													G|||	389	0.0776757	0.0454	0.0663	5008	,	,		19982	0.0427		0.1421	False		,,,				2504	0.0992				p.H731H		Atlas-SNP	.											.	STRN4	33	.	0			c.C2193T						PASS	.	G	,	243,4163	140.8+/-176.2	5,233,1965	159.0	110.0	127.0		2193,2172	-6.1	0.9	19	dbSNP_79	127	1124,7476	232.1+/-265.8	76,972,3252	no	coding-synonymous,coding-synonymous	STRN4	NM_001039877.1,NM_013403.2	,	81,1205,5217	AA,AG,GG		13.0698,5.5152,10.5105	,	731/761,724/754	47223949	1367,11639	2203	4300	6503	SO:0001819	synonymous_variant	29888	exon17			CTCCTCGTGCTTC	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.2172C>T	19.37:g.47223949G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	198	97	0.489899	NM_001039877	A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Silent	SNP	ENST00000263280.6	37	CCDS12690.1																																																																																			G|0.913;N|0.000	.	strong		0.627	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2		
LILRB4	11006	hgsc.bcm.edu	37	19	55175009	55175009	+	Missense_Mutation	SNP	G	G	T	rs11540761	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55175009G>T	ENST00000391736.1	+	4	369	c.54G>T	c.(52-54)agG>agT	p.R18S	LILRB4_ENST00000391733.3_Missense_Mutation_p.R18S|LILRB4_ENST00000391734.3_Missense_Mutation_p.R18S|LILRB4_ENST00000270452.2_Missense_Mutation_p.R18S|LILRB4_ENST00000430952.2_Missense_Mutation_p.R18S	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	18			R -> S (in dbSNP:rs11574570).		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)		TGGGCCCCAGGACCCACATGC	0.592													G|||	979	0.195487	0.2118	0.2032	5008	,	,		12985	0.124		0.1799	False		,,,				2504	0.2577				p.R18S		Atlas-SNP	.											.	LILRB4	86	.	0			c.G54T						PASS	.	G	SER/ARG,SER/ARG	957,3449	359.4+/-314.8	94,769,1340	53.0	59.0	57.0		54,54	1.3	0.0	19	dbSNP_120	57	1598,7002	297.9+/-303.7	156,1286,2858	no	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	110,110	250,2055,4198	TT,TG,GG		18.5814,21.7204,19.6448	possibly-damaging,possibly-damaging	18/448,18/449	55175009	2555,10451	2203	4300	6503	SO:0001583	missense	11006	exon2			CCCCAGGACCCAC	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.54G>T	19.37:g.55175009G>T	ENSP00000375616:p.Arg18Ser	Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	336	182	0.541667	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	382	0.1749084249084249	104	0.21138211382113822	58	0.16022099447513813	77	0.1346153846153846	143	0.18865435356200527	G	9.489	1.100156	0.20552	0.217204	0.185814	ENSG00000186818	ENST00000420271;ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00477	7.2;7.2;7.2;7.17;7.22;7.14	2.4	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	M	0.87180	2.865	0.80722	P	0.0	B;D;B;B;D	0.89917	0.404;0.963;0.364;0.431;1.0	B;P;B;B;D	0.87578	0.254;0.885;0.341;0.358;0.998	T	0.49234	-0.8961	8	0.21014	T	0.42	.	6.8653	0.24091	0.0:0.2927:0.7073:0.0	rs11574570;rs11574570	18;18;18;18;59	C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6;C9JHA6	.;.;.;LIRB4_HUMAN;.	S	59;18;18;18;18;18;18	ENSP00000375616:R18S;ENSP00000270452:R18S;ENSP00000408995:R18S;ENSP00000375614:R18S;ENSP00000375613:R18S;ENSP00000401962:R18S	ENSP00000270452:R18S	R	+	3	2	LILRB4	59866821	0.001000	0.12720	0.002000	0.10522	0.145000	0.21501	0.498000	0.22530	0.312000	0.23038	0.407000	0.27541	AGG	G|0.810;T|0.190	0.190	strong		0.592	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
GPC1	2817	hgsc.bcm.edu	37	2	241404317	241404317	+	Silent	SNP	C	C	T	rs2229458	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241404317C>T	ENST00000264039.2	+	6	1307	c.1059C>T	c.(1057-1059)ccC>ccT	p.P353P		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	353					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)	p.P353P(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		CCCAGGGCCCCGGGCCTGAGG	0.701													C|||	2588	0.516773	0.6233	0.5274	5008	,	,		16409	0.3026		0.5696	False		,,,				2504	0.5317				p.P353P		Atlas-SNP	.											GPC1,NS,carcinoma,0,1	GPC1	32	1	1	Substitution - coding silent(1)	prostate(1)	c.C1059T						PASS	.	C		2707,1509		895,917,296	13.0	15.0	14.0		1059	-7.8	0.0	2	dbSNP_98	14	4791,3473		1486,1819,827	no	coding-synonymous	GPC1	NM_002081.2		2381,2736,1123	TT,TC,CC		42.0257,35.7922,39.9199		353/559	241404317	7498,4982	2108	4132	6240	SO:0001819	synonymous_variant	2817	exon6			GGGCCCCGGGCCT	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1059C>T	2.37:g.241404317C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	1102|1102	0.5045787545787546|0.5045787545787546	310|310	0.6300813008130082|0.6300813008130082	201|201	0.5552486187845304|0.5552486187845304	178|178	0.3111888111888112|0.3111888111888112	413|413	0.5448548812664907|0.5448548812664907	C|C	0.034|0.034	-1.315240|-1.315240	0.01331|0.01331	0.642078|0.642078	0.579743|0.579743	ENSG00000063660|ENSG00000063660	ENST00000425056|ENST00000420138;ENST00000455111	T|.	0.47528|.	0.84|.	3.88|3.88	-7.76|-7.76	0.01232|0.01232	.|.	191.155000|.	0.00357|.	U|.	0.000039|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.21930|0.21930	-1.0231|-1.0231	6|3	0.54805|.	T|.	0.06|.	-2.1006|-2.1006	5.4102|5.4102	0.16344|0.16344	0.325:0.4377:0.0:0.2373|0.325:0.4377:0.0:0.2373	rs2229458;rs13001312;rs17854675|rs2229458;rs13001312;rs17854675	.|.	.|.	.|.	L|W	349|393;105	ENSP00000392629:P349L|.	ENSP00000392629:P349L|.	P|R	+|+	2|1	0|2	GPC1|GPC1	241052990|241052990	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-7.128000|-7.128000	0.00043|0.00043	-2.805000|-2.805000	0.00350|0.00350	-1.239000|-1.239000	0.01543|0.01543	CCG|CGG	C|0.493;T|0.507	0.507	strong		0.701	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
KCNQ3	3786	hgsc.bcm.edu	37	8	133192521	133192521	+	Silent	SNP	A	A	G	rs41272389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133192521A>G	ENST00000388996.4	-	4	1080	c.660T>C	c.(658-660)aaT>aaC	p.N220N	KCNQ3_ENST00000519445.1_Silent_p.N220N|KCNQ3_ENST00000521134.1_Silent_p.N100N	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	220					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TGGCCAGAACATTGCCTTGGT	0.592													A|||	121	0.0241613	0.003	0.0303	5008	,	,		20790	0.0		0.0835	False		,,,				2504	0.0123				p.N220N		Atlas-SNP	.											.	KCNQ3	164	.	0			c.T660C						PASS	.	A	,	65,4341	62.3+/-99.4	0,65,2138	107.0	93.0	98.0		300,660	3.2	1.0	8	dbSNP_127	98	607,7993	158.8+/-212.2	27,553,3720	no	coding-synonymous,coding-synonymous	KCNQ3	NM_001204824.1,NM_004519.3	,	27,618,5858	GG,GA,AA		7.0581,1.4753,5.1668	,	100/753,220/873	133192521	672,12334	2203	4300	6503	SO:0001819	synonymous_variant	3786	exon4			CAGAACATTGCCT	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.660T>C	8.37:g.133192521A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																			A|0.951;G|0.049	0.049	strong		0.592	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
NPHP4	261734	hgsc.bcm.edu	37	1	5926507	5926507	+	Silent	SNP	T	T	C	rs555164	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	128	0	0		WXS	Illumina HiSeq	Phase_I	144	60	0.416667	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		
FLG	2312	hgsc.bcm.edu	37	1	152278856	152278856	+	Missense_Mutation	SNP	T	T	G	rs11582087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152278856T>G	ENST00000368799.1	-	3	8541	c.8506A>C	c.(8506-8508)Agt>Cgt	p.S2836R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2836	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTTGCACTTCTGGATCCT	0.562									Ichthyosis																												p.S2836R		Atlas-SNP	.											.	FLG	900	.	0			c.A8506C						PASS	.	T	ARG/SER	136,4198		0,136,2031	264.0	395.0	351.0		8506	-0.9	0.0	1	dbSNP_120	351	951,7643		0,951,3346	no	missense	FLG	NM_002016.1	110	0,1087,5377	GG,GT,TT		11.0659,3.138,8.4081	possibly-damaging	2836/4062	152278856	1087,11841	2167	4297	6464	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGCACTTCTGGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8506A>C	1.37:g.152278856T>G	ENSP00000357789:p.Ser2836Arg	Somatic	553	1	0.00180832		WXS	Illumina HiSeq	Phase_I	726	165	0.227273	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	419	0.19184981684981686	8	0.016260162601626018	92	0.2541436464088398	232	0.40559440559440557	87	0.11477572559366754	T	8.326	0.825345	0.16749	0.03138	0.110659	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.03745	3.82	1.87	-0.845	0.10737	.	.	.	.	.	T	0.01092	0.0036	M	0.76838	2.35	0.09310	N	1	P	0.42993	0.797	B	0.28305	0.088	T	0.45614	-0.9249	9	0.28530	T	0.3	-0.3021	2.3761	0.04342	0.0:0.1966:0.3031:0.5003	.	2836	P20930	FILA_HUMAN	R	2836;98	ENSP00000357789:S2836R	ENSP00000357786:S98R	S	-	1	0	FLG	150545480	.	.	0.000000	0.03702	0.028000	0.11728	.	.	-0.204000	0.10235	0.254000	0.18369	AGT	T|0.892;G|0.108	0.108	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
NFKBID	84807	hgsc.bcm.edu	37	19	36387378	36387378	+	Silent	SNP	C	C	G	rs73590883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36387378C>G	ENST00000396901.1	-	7	894	c.321G>C	c.(319-321)ctG>ctC	p.L107L	NFKBID_ENST00000606253.1_Silent_p.L107L|NFKBID_ENST00000352614.2_Silent_p.L259L|NFKBID_ENST00000585544.1_5'Flank	NM_139239.1	NP_640332.1	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta	107					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						GCTCTGCTCCCAGGTTCAACA	0.622													C|||	175	0.0349441	0.0681	0.0202	5008	,	,		14896	0.0119		0.0229	False		,,,				2504	0.0368				p.L107L		Atlas-SNP	.											.	NFKBID	30	.	0			c.G321C						PASS	.	C		257,3819		5,247,1786	49.0	58.0	55.0		321	2.5	1.0	19	dbSNP_130	55	261,8115		1,259,3928	no	coding-synonymous	NFKBID	NM_139239.1		6,506,5714	GG,GC,CC		3.116,6.3052,4.16		107/314	36387378	518,11934	2038	4188	6226	SO:0001819	synonymous_variant	84807	exon7			TGCTCCCAGGTTC	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.321G>C	19.37:g.36387378C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_139239	Q8NI39|Q9BRG9	Silent	SNP	ENST00000396901.1	37	CCDS42552.1																																																																																			C|0.972;G|0.028	0.028	strong		0.622	NFKBID-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452927.3	NM_032721	
EVPLL	645027	hgsc.bcm.edu	37	17	18291559	18291559	+	Silent	SNP	T	T	C	rs9890369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:18291559T>C	ENST00000399134.4	+	10	1261	c.903T>C	c.(901-903)caT>caC	p.H301H	RP1-37N7.1_ENST00000579352.1_RNA|EVPLL_ENST00000583003.1_3'UTR	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	301										NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CCTCTCCTCATTGACTCTGCA	0.463													.|||	1328	0.265176	0.4342	0.2032	5008	,	,		12834	0.1637		0.1849	False		,,,				2504	0.2679				p.H301H		Atlas-SNP	.											EVPLL,NS,NS,+2,1	EVPLL	10	1	0			c.T903C						PASS	.	T		503,881		91,321,280	73.0	63.0	66.0		903	0.1	0.0	17	dbSNP_119	66	659,2523		64,531,996	no	coding-synonymous	EVPLL	NM_001145127.1		155,852,1276	CC,CT,TT		20.7102,36.3439,25.449		301/302	18291559	1162,3404	692	1591	2283	SO:0001819	synonymous_variant	645027	exon10			TCCTCATTGACTC		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.903T>C	17.37:g.18291559T>C		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	439	175	0.398633	NM_001145127	B4DPD4	Silent	SNP	ENST00000399134.4	37	CCDS45626.1																																																																																			T|0.770;C|0.230	0.230	strong		0.463	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127	
COLEC12	81035	hgsc.bcm.edu	37	18	347254	347254	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:347254C>T	ENST00000400256.3	-	5	575	c.368G>A	c.(367-369)cGt>cAt	p.R123H		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	123					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)				TGTAATCTCACGAAGTTGCTG	0.463																																					p.R123H		Atlas-SNP	.											COLEC12,NS,carcinoma,-1,1	COLEC12	121	1	0			c.G368A						scavenged	.						139.0	123.0	129.0					18																	347254		2203	4300	6503	SO:0001583	missense	81035	exon5			ATCTCACGAAGTT	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.368G>A	18.37:g.347254C>T	ENSP00000383115:p.Arg123His	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	250	3	0.012	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.672119	0.29693	.	.	ENSG00000158270	ENST00000400256	T	0.38560	1.13	6.17	0.228	0.15364	.	0.489229	0.25668	N	0.029083	T	0.22975	0.0555	N	0.12182	0.205	0.22001	N	0.999428	B	0.06786	0.001	B	0.01281	0.0	T	0.17715	-1.0360	10	0.44086	T	0.13	-0.3801	11.3374	0.49511	0.0:0.4746:0.0:0.5254	.	123	Q5KU26	COL12_HUMAN	H	123	ENSP00000383115:R123H	ENSP00000383115:R123H	R	-	2	0	COLEC12	337254	0.013000	0.17824	0.654000	0.29608	0.995000	0.86356	0.078000	0.14761	-0.023000	0.13963	0.655000	0.94253	CGT	.	.	none		0.463	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		
PCSK5	5125	hgsc.bcm.edu	37	9	78938186	78938186	+	Missense_Mutation	SNP	G	G	C	rs2803429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	126	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	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			
AKNA	80709	hgsc.bcm.edu	37	9	117110046	117110046	+	Missense_Mutation	SNP	C	C	T	rs3748178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:117110046C>T	ENST00000307564.4	-	16	3517	c.3356G>A	c.(3355-3357)cGg>cAg	p.R1119Q	AKNA_ENST00000223791.3_Missense_Mutation_p.R579Q|AKNA_ENST00000492875.1_5'Flank|AKNA_ENST00000374088.3_Missense_Mutation_p.R1119Q|AKNA_ENST00000374075.5_Missense_Mutation_p.R1038Q|AKNA_ENST00000374079.4_Missense_Mutation_p.R64Q	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1119			R -> Q (in dbSNP:rs3748178). {ECO:0000269|PubMed:14702039}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GTCTGCTGGCCGGCCGCGGGT	0.662													C|||	533	0.10643	0.0106	0.1427	5008	,	,		13674	0.0685		0.2624	False		,,,				2504	0.089				p.R1119Q		Atlas-SNP	.											.	AKNA	119	.	0			c.G3356A						PASS	.	C	GLN/ARG	179,3903		8,163,1870	7.0	8.0	8.0		3356	1.0	0.0	9	dbSNP_107	8	1759,6341		177,1405,2468	yes	missense	AKNA	NM_030767.4	43	185,1568,4338	TT,TC,CC		21.716,4.3851,15.9087	probably-damaging	1119/1440	117110046	1938,10244	2041	4050	6091	SO:0001583	missense	80709	exon16			GCTGGCCGGCCGC	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.3356G>A	9.37:g.117110046C>T	ENSP00000303769:p.Arg1119Gln	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	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	300	0.13736263736263737	8	0.016260162601626018	62	0.1712707182320442	31	0.05419580419580419	199	0.262532981530343	C	18.55	3.649336	0.67358	0.043851	0.21716	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000320310;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.24350	2.37;1.86;2.37;2.13;2.36	5.01	0.963	0.19649	.	0.323271	0.22341	N	0.061322	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;P	0.36874	0.436;0.572	B;B	0.29267	0.027;0.1	T	0.24621	-1.0155	9	0.62326	D	0.03	-11.2927	4.2153	0.10531	0.0:0.5399:0.1702:0.2899	rs3748178;rs17230383;rs3748178	1119;1038	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	Q	1119;64;131;1119;579;1038	ENSP00000303769:R1119Q;ENSP00000363192:R64Q;ENSP00000363201:R1119Q;ENSP00000223791:R579Q;ENSP00000363188:R1038Q	ENSP00000223791:R579Q	R	-	2	0	AKNA	116149867	0.004000	0.15560	0.001000	0.08648	0.013000	0.08279	0.196000	0.17176	0.084000	0.17077	0.655000	0.94253	CGG	C|0.891;T|0.109	0.109	strong		0.662	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
GRIN1	2902	hgsc.bcm.edu	37	9	140051376	140051376	+	Silent	SNP	G	G	A	rs1126442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140051376G>A	ENST00000371561.3	+	6	1952	c.855G>A	c.(853-855)gtG>gtA	p.V285V	GRIN1_ENST00000350902.5_Silent_p.V285V|GRIN1_ENST00000315048.3_Silent_p.V285V|GRIN1_ENST00000371553.3_Silent_p.V306V|GRIN1_ENST00000371560.3_Silent_p.V306V|GRIN1_ENST00000371559.4_Silent_p.V285V|GRIN1_ENST00000371555.4_Silent_p.V306V|GRIN1_ENST00000371546.4_Silent_p.V306V|GRIN1_ENST00000371550.4_Silent_p.V285V|GRIN1_ENST00000471122.1_3'UTR	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	285					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|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 density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCGACGCCGTGGGCGTGGTGG	0.677													G|||	699	0.139577	0.0265	0.2017	5008	,	,		11686	0.002		0.336	False		,,,				2504	0.1881				p.V306V	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.G918A						PASS	.	G	,,,,	288,4106		12,264,1921	29.0	31.0	30.0		855,918,918,855,855	2.7	1.0	9	dbSNP_86	30	2741,5845		447,1847,1999	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRIN1	NM_000832.6,NM_001185090.1,NM_001185091.1,NM_007327.3,NM_021569.3	,,,,	459,2111,3920	AA,AG,GG		31.9241,6.5544,23.3359	,,,,	285/886,306/944,306/907,285/939,285/902	140051376	3029,9951	2197	4293	6490	SO:0001819	synonymous_variant	2902	exon7			CGCCGTGGGCGTG		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4584	protein-coding gene	gene with protein product		138249	"""N-methyl-D-aspartate receptor subunit NR1"""	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.855G>A	9.37:g.140051376G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Silent	SNP	ENST00000371561.3	37	CCDS7031.1																																																																																			G|0.800;A|0.200	0.200	strong		0.677	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144875979	144875979	+	Silent	SNP	G	G	C	rs71664005	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:144875979G>C	ENST00000369354.3	-	29	4890	c.4701C>G	c.(4699-4701)ctC>ctG	p.L1567L	RP4-791M13.5_ENST00000531288.1_RNA|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000369356.4_Silent_p.L1567L|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Silent_p.L1523L|PDE4DIP_ENST00000369359.4_Silent_p.L1703L|PDE4DIP_ENST00000530740.1_Silent_p.L1703L			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1567	NBPF. {ECO:0000255|PROSITE- ProRule:PRU00647}.				cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGAATTACCTGAGGGCCAGTG	0.468			T	PDGFRB	MPD																																p.L1567L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C4701G						PASS	.	G	,,	210,4196		0,210,1993	224.0	225.0	225.0		4569,4701,4701	4.2	1.0	1	dbSNP_130	225	1462,7130		0,1462,2834	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,1672,4827	CC,CG,GG		17.0158,4.7662,12.8635	,,	1523/2241,1567/2363,1567/2347	144875979	1672,11326	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon29			TTACCTGAGGGCC	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.4701C>G	1.37:g.144875979G>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	138	32	0.231884	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			G|0.216;C|0.784	0.784	strong		0.468	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
STRBP	55342	hgsc.bcm.edu	37	9	125895238	125895238	+	Missense_Mutation	SNP	C	C	T	rs79286922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125895238C>T	ENST00000348403.5	-	17	2212	c.1783G>A	c.(1783-1785)Gtt>Att	p.V595I	STRBP_ENST00000360998.3_Missense_Mutation_p.V581I|STRBP_ENST00000447404.2_Missense_Mutation_p.V595I	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	595					cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						GTATTCACAACGCCCTTTGCC	0.438													C|||	28	0.00559105	0.0061	0.0072	5008	,	,		20536	0.0		0.0129	False		,,,				2504	0.002				p.V595I		Atlas-SNP	.											.	STRBP	73	.	0			c.G1783A						PASS	.	C	ILE/VAL,ILE/VAL	30,4376	36.0+/-67.5	0,30,2173	90.0	84.0	86.0		1741,1783	4.0	1.0	9	dbSNP_131	86	160,8440	76.3+/-139.0	1,158,4141	yes	missense,missense	STRBP	NM_001171137.1,NM_018387.4	29,29	1,188,6314	TT,TC,CC		1.8605,0.6809,1.4609	benign,benign	581/659,595/673	125895238	190,12816	2203	4300	6503	SO:0001583	missense	55342	exon17			TCACAACGCCCTT	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.1783G>A	9.37:g.125895238C>T	ENSP00000321347:p.Val595Ile	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_018387	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Missense_Mutation	SNP	ENST00000348403.5	37	CCDS6851.1	18	0.008241758241758242	5	0.01016260162601626	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	15.15	2.746549	0.49257	0.006809	0.018605	ENSG00000165209	ENST00000447404;ENST00000348403;ENST00000360998	T;T;T	0.17054	2.56;2.56;2.3	5.96	4.03	0.46877	.	0.336970	0.34750	N	0.003716	T	0.05273	0.0140	N	0.24115	0.695	0.35920	D	0.831777	B;B	0.13145	0.004;0.007	B;B	0.08055	0.001;0.003	T	0.15752	-1.0426	10	0.30854	T	0.27	-1.5899	10.2451	0.43336	0.0:0.7752:0.0:0.2248	.	595;581	Q96SI9;Q96SI9-2	STRBP_HUMAN;.	I	595;595;581	ENSP00000415968:V595I;ENSP00000321347:V595I;ENSP00000354271:V581I	ENSP00000321347:V595I	V	-	1	0	STRBP	124935059	0.950000	0.32346	0.993000	0.49108	0.977000	0.68977	1.691000	0.37721	0.757000	0.33036	0.579000	0.79373	GTT	C|0.988;T|0.012	0.012	strong		0.438	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1		
LCT	3938	hgsc.bcm.edu	37	2	136590746	136590746	+	Missense_Mutation	SNP	C	C	T	rs386833838|rs3754689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	70	0	0		WXS	Illumina HiSeq	Phase_I	87	87	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	
TRIM17	51127	hgsc.bcm.edu	37	1	228602660	228602660	+	Silent	SNP	G	G	C	rs503203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228602660G>C	ENST00000366697.2	-	1	1070	c.114C>G	c.(112-114)gcC>gcG	p.A38A	TRIM17_ENST00000456946.2_Silent_p.A38A|TRIM17_ENST00000366698.2_Silent_p.A38A|TRIM17_ENST00000295033.3_Silent_p.A38A			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	38					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)				GCTGGATGCAGGCTCGGCAGA	0.597													C|||	1482	0.295927	0.6513	0.098	5008	,	,		18452	0.3095		0.1014	False		,,,				2504	0.1421				p.A38A		Atlas-SNP	.											.	TRIM17	66	.	0			c.C114G						PASS	.	C	,,	2358,2048	556.5+/-379.5	615,1128,460	35.0	31.0	33.0		114,114,114	1.4	0.5	1	dbSNP_83	33	824,7776	767.5+/-407.6	41,742,3517	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	,,	656,1870,3977	CC,CG,GG		9.5814,46.4821,24.4656	,,	38/478,38/344,38/478	228602660	3182,9824	2203	4300	6503	SO:0001819	synonymous_variant	51127	exon2			GATGCAGGCTCGG	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.114C>G	1.37:g.228602660G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_001024940	B4DVJ2|Q5VST8	Silent	SNP	ENST00000366697.2	37	CCDS1571.1																																																																																			G|0.745;C|0.255	0.255	strong		0.597	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102	
MTIF2	4528	hgsc.bcm.edu	37	2	55490788	55490788	+	Silent	SNP	T	T	C	rs1134722	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:55490788T>C	ENST00000263629.4	-	4	522	c.207A>G	c.(205-207)ctA>ctG	p.L69L	MTIF2_ENST00000394600.3_Silent_p.L69L|MTIF2_ENST00000403721.1_Silent_p.L69L|MTIF2_ENST00000446660.1_5'UTR	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	69					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.L69L(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TTTTTGTTACTAGAAGCCTAT	0.493													T|||	300	0.0599042	0.0711	0.0331	5008	,	,		16067	0.0645		0.0517	False		,,,				2504	0.0675				p.L69L		Atlas-SNP	.											MTIF2,NS,carcinoma,0,1	MTIF2	64	1	1	Substitution - coding silent(1)	stomach(1)	c.A207G						scavenged	.	T	,	302,4104	165.4+/-196.9	13,276,1914	66.0	64.0	65.0		207,207	-3.4	0.2	2	dbSNP_86	65	493,8107	141.9+/-198.1	20,453,3827	no	coding-synonymous,coding-synonymous	MTIF2	NM_001005369.1,NM_002453.2	,	33,729,5741	CC,CT,TT		5.7326,6.8543,6.1126	,	69/728,69/728	55490788	795,12211	2203	4300	6503	SO:0001819	synonymous_variant	4528	exon4			TGTTACTAGAAGC	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.207A>G	2.37:g.55490788T>C		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_002453	D6W5D0	Silent	SNP	ENST00000263629.4	37	CCDS1853.1																																																																																			T|0.941;C|0.059	0.059	strong		0.493	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
KDM5C	8242	hgsc.bcm.edu	37	X	53230909	53230909	+	Silent	SNP	C	C	T	rs74850270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53230909C>T	ENST00000375401.3	-	14	2416	c.1884G>A	c.(1882-1884)caG>caA	p.Q628Q	KDM5C_ENST00000452825.3_Silent_p.Q561Q|KDM5C_ENST00000375383.3_Silent_p.Q587Q|KDM5C_ENST00000404049.3_Silent_p.Q627Q|KDM5C_ENST00000375379.3_Silent_p.Q628Q|KDM5C_ENST00000465402.1_5'UTR	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	628	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|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)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						GCTCAATGCACTGGCGCCCAG	0.592			"""N, F, S"""		clear cell renal carcinoma								C|||	35	0.00927152	0.025	0.0029	3775	,	,		13930	0.0		0.0	False		,,,				2504	0.0				p.Q628Q		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G1884A						PASS	.	C	,	119,3716		1,96,21,1535,550	47.0	42.0	44.0		1683,1884	-0.3	1.0	X	dbSNP_131	44	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	KDM5C	NM_001146702.1,NM_004187.3	,	1,96,22,3963,2421	TT,TC,T,CC,C		0.0149,3.103,1.136	,	561/1380,628/1561	53230909	120,10443	2203	4300	6503	SO:0001819	synonymous_variant	8242	exon14			AATGCACTGGCGC	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.1884G>A	X.37:g.53230909C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	37	CCDS14351.1																																																																																			C|0.988;T|0.012	0.012	strong		0.592	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
TAS1R1	80835	hgsc.bcm.edu	37	1	6639073	6639073	+	Missense_Mutation	SNP	G	G	A	rs149418903	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:6639073G>A	ENST00000333172.6	+	6	2148	c.1955G>A	c.(1954-1956)cGc>cAc	p.R652H	ZBTB48_ENST00000377674.4_5'Flank|TAS1R1_ENST00000328191.4_3'UTR|TAS1R1_ENST00000351136.3_Missense_Mutation_p.R398H	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	652					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|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)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|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;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		CTGACAGTTCGCTCATTCCAA	0.522													G|||	4	0.000798722	0.0	0.0014	5008	,	,		22421	0.0		0.001	False		,,,				2504	0.002				p.R652H		Atlas-SNP	.											TAS1R1,colon,carcinoma,0,1	TAS1R1	76	1	0			c.G1955A						scavenged	.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	129.0	128.0	128.0		1955,1193	4.8	1.0	1	dbSNP_134	128	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	TAS1R1	NM_138697.3,NM_177540.2	29,29	0,14,6489	AA,AG,GG		0.1628,0.0,0.1076	probably-damaging,probably-damaging	652/842,398/588	6639073	14,12992	2203	4300	6503	SO:0001583	missense	80835	exon6			CAGTTCGCTCATT		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14448	protein-coding gene	gene with protein product		606225	"""G protein-coupled receptor 70"""	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.1955G>A	1.37:g.6639073G>A	ENSP00000331867:p.Arg652His	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	220	115	0.522727	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	37	CCDS81.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031876	0.93575	0.0	0.001628	ENSG00000173662	ENST00000333172;ENST00000351136	D;D	0.88664	-2.41;-2.41	4.85	4.85	0.62838	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.94532	0.8239	M	0.81614	2.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.989;0.999	D	0.95172	0.8291	10	0.87932	D	0	.	17.1499	0.86775	0.0:0.0:1.0:0.0	.	398;652	Q7RTX1-2;Q7RTX1	.;TS1R1_HUMAN	H	652;398	ENSP00000331867:R652H;ENSP00000312558:R398H	ENSP00000331867:R652H	R	+	2	0	TAS1R1	6561660	0.885000	0.30320	0.994000	0.49952	0.998000	0.95712	2.584000	0.46102	2.505000	0.84491	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.522	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1		
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57077464	57077464	+	Silent	SNP	T	T	C	rs10896602	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57077464T>C	ENST00000532437.1	-	5	3032	c.2721A>G	c.(2719-2721)caA>caG	p.Q907Q	TNKS1BP1_ENST00000530920.1_5'UTR|TNKS1BP1_ENST00000358252.3_Silent_p.Q907Q			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	907	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TCCCCAAATCTTGGCCCTGCT	0.537													T|||	1661	0.331669	0.4531	0.2522	5008	,	,		19426	0.2827		0.33	False		,,,				2504	0.2761				p.Q907Q		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A2721G						PASS	.	T		1893,2509	544.2+/-376.5	393,1107,701	190.0	185.0	186.0		2721	-1.2	0.0	11	dbSNP_120	186	2785,5807	442.5+/-360.1	456,1873,1967	no	coding-synonymous	TNKS1BP1	NM_033396.2		849,2980,2668	CC,CT,TT		32.4139,43.0032,36.0012		907/1730	57077464	4678,8316	2201	4296	6497	SO:0001819	synonymous_variant	85456	exon6			CAAATCTTGGCCC	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.2721A>G	11.37:g.57077464T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	180	86	0.477778	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	
LCN10	414332	hgsc.bcm.edu	37	9	139634451	139634451	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139634451A>G	ENST00000474369.1	-	4	485	c.486T>C	c.(484-486)gcT>gcC	p.A162A	LCN10_ENST00000527229.1_Silent_p.A139A|LCN6_ENST00000435202.1_3'UTR|LCN6_ENST00000480584.1_5'Flank|LCN10_ENST00000497771.1_Silent_p.A175A			Q6JVE6	LCN10_HUMAN	lipocalin 10	162					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)		GAATGTCACAAGCGTCCATGA	0.557																																					p.A175A		Atlas-SNP	.											.	LCN10	21	.	0			c.T525C						PASS	.						93.0	73.0	80.0					9																	139634451		2202	4300	6502	SO:0001819	synonymous_variant	414332	exon5			GTCACAAGCGTCC	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.486T>C	9.37:g.139634451A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001001712	A2RUU3|B0QZ79	Silent	SNP	ENST00000474369.1	37	CCDS35182.2																																																																																			.	.	none		0.557	LCN10-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318062.2	NM_001001712	
FNDC7	163479	hgsc.bcm.edu	37	1	109256135	109256135	+	Silent	SNP	T	T	C	rs11102279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109256135T>C	ENST00000370017.3	+	2	343	c.66T>C	c.(64-66)gtT>gtC	p.V22V	FNDC7_ENST00000271311.2_Silent_p.V23V	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	22						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)		CTTTTCAGGTTGCTTCAGCAA	0.328													T|||	385	0.076877	0.0015	0.085	5008	,	,		18496	0.3105		0.005	False		,,,				2504	0.0061				p.V22V		Atlas-SNP	.											.	FNDC7	113	.	0			c.T66C						PASS	.	T		4,1380		0,4,688	285.0	218.0	238.0		66	2.2	1.0	1	dbSNP_120	238	10,3172		0,10,1581	no	coding-synonymous	FNDC7	NM_001144937.1		0,14,2269	CC,CT,TT		0.3143,0.289,0.3066		22/734	109256135	14,4552	692	1591	2283	SO:0001819	synonymous_variant	163479	exon2			TCAGGTTGCTTCA		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.66T>C	1.37:g.109256135T>C		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	206	117	0.567961	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1																																																																																			T|0.865;C|0.135	0.135	strong		0.328	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
NRK	203447	hgsc.bcm.edu	37	X	105152282	105152282	+	Missense_Mutation	SNP	G	G	A	rs209373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	210	207	0.985714	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	
OR5L2	26338	hgsc.bcm.edu	37	11	55594869	55594869	+	Missense_Mutation	SNP	G	G	A	rs56711116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	200	0	0		WXS	Illumina HiSeq	Phase_I	217	104	0.479263	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	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036999	33036999	+	Missense_Mutation	SNP	T	T	C	rs1042190	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33036999T>C	ENST00000419277.1	-	4	554	c.425A>G	c.(424-426)aAg>aGg	p.K142R	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.K142R|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	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	84	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	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	
CARD10	29775	hgsc.bcm.edu	37	22	37915100	37915100	+	Silent	SNP	A	A	G	rs7287804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37915100A>G	ENST00000403299.1	-	2	324	c.108T>C	c.(106-108)caT>caC	p.H36H	CARD10_ENST00000251973.5_Silent_p.H36H			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	36	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GAGCCAGCCGATGCCGGACGC	0.736													G|||	564	0.11262	0.2973	0.072	5008	,	,		10615	0.0476		0.0487	False		,,,				2504	0.0245				p.H36H		Atlas-SNP	.											.	CARD10	55	.	0			c.T108C						PASS	.	G		1112,3172		141,830,1171	13.0	14.0	13.0		108	2.9	1.0	22	dbSNP_116	13	399,8047		6,387,3830	no	coding-synonymous	CARD10	NM_014550.3		147,1217,5001	GG,GA,AA		4.7241,25.957,11.8696		36/1033	37915100	1511,11219	2142	4223	6365	SO:0001819	synonymous_variant	29775	exon1			CAGCCGATGCCGG	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.108T>C	22.37:g.37915100A>G		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	20	4	0.2	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			A|0.879;G|0.121	0.121	strong		0.736	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
MEGF6	1953	hgsc.bcm.edu	37	1	3428608	3428608	+	Missense_Mutation	SNP	G	G	A	rs11585362	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3428608G>A	ENST00000356575.4	-	8	1164	c.938C>T	c.(937-939)gCg>gTg	p.A313V	MEGF6_ENST00000294599.4_Missense_Mutation_p.A208V	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	313	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		A -> V (in dbSNP:rs11585362).			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)		CTCATAGCCCGCGTGACACAC	0.672													G|||	1278	0.255192	0.3411	0.1945	5008	,	,		18825	0.4048		0.1501	False		,,,				2504	0.136				p.A313V	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C938T						PASS	.	G	VAL/ALA	1293,2947		193,907,1020	49.0	59.0	56.0		938	3.7	0.0	1	dbSNP_120	56	1229,7197		94,1041,3078	yes	missense	MEGF6	NM_001409.3	64	287,1948,4098	AA,AG,GG		14.5858,30.4953,19.9116	possibly-damaging	313/1542	3428608	2522,10144	2120	4213	6333	SO:0001583	missense	1953	exon8			TAGCCCGCGTGAC	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.938C>T	1.37:g.3428608G>A	ENSP00000348982:p.Ala313Val	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	306	160	0.522876	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	601	0.2751831501831502	179	0.3638211382113821	85	0.23480662983425415	233	0.40734265734265734	104	0.13720316622691292	G	10.15	1.271169	0.23221	0.304953	0.145858	ENSG00000162591	ENST00000294599;ENST00000356575	D;D	0.92299	-3.01;-3.01	4.63	3.71	0.42584	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.130150	0.51477	D	0.000097	T	0.00012	0.0000	L	0.41710	1.295	0.80722	P	0.0	P;P	0.52061	0.95;0.893	B;B	0.41571	0.36;0.3	T	0.02901	-1.1096	9	0.28530	T	0.3	-5.9456	8.4155	0.32668	0.0833:0.0:0.7611:0.1556	rs11585362;rs60818858;rs11585362	313;208	O75095;O75095-2	MEGF6_HUMAN;.	V	208;313	ENSP00000294599:A208V;ENSP00000348982:A313V	ENSP00000294599:A208V	A	-	2	0	MEGF6	3418468	0.969000	0.33509	0.015000	0.15790	0.038000	0.13279	5.545000	0.67237	0.909000	0.36697	-0.448000	0.05591	GCG	G|0.738;A|0.262	0.262	strong		0.672	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
OR10A6	390093	hgsc.bcm.edu	37	11	7950024	7950024	+	Silent	SNP	A	A	G	rs12272735	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7950024A>G	ENST00000309838.2	-	1	185	c.186T>C	c.(184-186)ttT>ttC	p.F62F		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGTTCAGGAGAAACAGGTACA	0.443													A|||	1669	0.333267	0.2617	0.4568	5008	,	,		17833	0.2698		0.3718	False		,,,				2504	0.3681				p.F62F		Atlas-SNP	.											.	OR10A6	49	.	0			c.T186C						PASS	.	A		1257,3145	430.8+/-342.7	187,883,1131	119.0	114.0	116.0		186	-3.1	0.9	11	dbSNP_120	116	3233,5359	486.1+/-371.8	643,1947,1706	no	coding-synonymous	OR10A6	NM_001004461.1		830,2830,2837	GG,GA,AA		37.628,28.5552,34.5544		62/315	7950024	4490,8504	2201	4296	6497	SO:0001819	synonymous_variant	390093	exon1			CAGGAGAAACAGG	AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"""GPCR / Class A : Olfactory receptors"""	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.186T>C	11.37:g.7950024A>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	253	114	0.450593	NM_001004461	Q6IF59	Silent	SNP	ENST00000309838.2	37	CCDS31420.1																																																																																			A|0.658;G|0.342	0.342	strong		0.443	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461	
KIAA1671	85379	hgsc.bcm.edu	37	22	25573431	25573431	+	Silent	SNP	G	G	A	rs12168578	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:25573431G>A	ENST00000406486.4	+	10	5403	c.5016G>A	c.(5014-5016)gaG>gaA	p.E1672E	KIAA1671_ENST00000358431.3_Silent_p.E1672E|KIAA1671_ENST00000401395.1_Silent_p.E179E			Q9BY89	K1671_HUMAN	KIAA1671	1672										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						GTGAGTCCGAGAGCAGATCAC	0.567													G|||	618	0.123403	0.149	0.0591	5008	,	,		15938	0.0913		0.0805	False		,,,				2504	0.2117				p.E1672E		Atlas-SNP	.											.	KIAA1671	28	.	0			c.G5016A						PASS	.	G		227,1157		15,197,480	82.0	78.0	79.0		5016	0.9	1.0	22	dbSNP_120	79	334,2848		16,302,1273	no	coding-synonymous	KIAA1671	NM_001145206.1		31,499,1753	AA,AG,GG		10.4965,16.4017,12.2865		1672/1807	25573431	561,4005	692	1591	2283	SO:0001819	synonymous_variant	85379	exon7			GTCCGAGAGCAGA		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.5016G>A	22.37:g.25573431G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	193	87	0.450777	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			G|0.899;A|0.101	0.101	strong		0.567	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
ZFAND2A	90637	hgsc.bcm.edu	37	7	1195215	1195215	+	Silent	SNP	A	A	C	rs1133116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1195215A>C	ENST00000316495.3	-	4	415	c.156T>G	c.(154-156)gtT>gtG	p.V52V	ZFAND2A_ENST00000401903.1_Silent_p.V52V	NM_182491.2	NP_872297.2	Q8N6M9	ZFN2A_HUMAN	zinc finger, AN1-type domain 2A	52					cellular response to arsenic-containing substance (GO:0071243)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	zinc ion binding (GO:0008270)			lung(2)|ovary(1)	3		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.82e-15)		CTGGGACGTGAACATCCTAAA	0.448													A|||	557	0.111222	0.0749	0.1816	5008	,	,		19995	0.0268		0.1481	False		,,,				2504	0.1595				p.V52V		Atlas-SNP	.											.	ZFAND2A	9	.	0			c.T156G						PASS	.			375,4031	190.9+/-216.7	18,339,1846	146.0	138.0	141.0		156	-8.2	0.1	7	dbSNP_86	141	1527,7073	287.0+/-298.0	131,1265,2904	no	coding-synonymous	ZFAND2A	NM_182491.2		149,1604,4750	CC,CA,AA		17.7558,8.5111,14.624		52/146	1195215	1902,11104	2203	4300	6503	SO:0001819	synonymous_variant	90637	exon4			GACGTGAACATCC	BC029558	CCDS5323.1	7p22.3	2010-04-23			ENSG00000178381	ENSG00000178381		"""Zinc fingers, AN1-type domain containing"""	28073	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein"""	610699				20185824	Standard	NM_182491		Approved	AIRAP	uc003skc.3	Q8N6M9	OTTHUMG00000119019	ENST00000316495.3:c.156T>G	7.37:g.1195215A>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_182491	A4D220	Silent	SNP	ENST00000316495.3	37	CCDS5323.1																																																																																			A|0.857;C|0.143	0.143	strong		0.448	ZFAND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239220.2	NM_182491	
FMN2	56776	hgsc.bcm.edu	37	1	240371223	240371223	+	Silent	SNP	C	C	T	rs71297737|rs575452021	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.						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	74	0	0		WXS	Illumina HiSeq	Phase_I	101	20	0.19802	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	
TFB2M	64216	hgsc.bcm.edu	37	1	246714587	246714587	+	Silent	SNP	G	G	A	rs10754526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:246714587G>A	ENST00000366514.4	-	5	908	c.723C>T	c.(721-723)ccC>ccT	p.P241P	TFB2M_ENST00000544618.1_3'UTR	NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	241					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(1)|kidney(12)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			CTGGATTTCCGGGATCTGCCA	0.318													G|||	2066	0.41254	0.4312	0.4063	5008	,	,		20072	0.3423		0.4702	False		,,,				2504	0.4049				p.P241P		Atlas-SNP	.											.	TFB2M	46	.	0			c.C723T						PASS	.	G		2049,2357	562.1+/-380.9	493,1063,647	69.0	72.0	71.0		723	-4.5	0.0	1	dbSNP_120	71	4096,4504	558.6+/-387.3	1012,2072,1216	no	coding-synonymous	TFB2M	NM_022366.2		1505,3135,1863	AA,AG,GG		47.6279,46.5048,47.2474		241/397	246714587	6145,6861	2203	4300	6503	SO:0001819	synonymous_variant	64216	exon5			ATTTCCGGGATCT	AK026835	CCDS1627.1	1q44	2008-02-05			ENSG00000162851	ENSG00000162851			18559	protein-coding gene	gene with protein product		607055					Standard	NM_022366		Approved	FLJ23182, FLJ22661, Hkp1	uc001ibn.3	Q9H5Q4	OTTHUMG00000040091	ENST00000366514.4:c.723C>T	1.37:g.246714587G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_022366	Q9H626	Silent	SNP	ENST00000366514.4	37	CCDS1627.1																																																																																			G|0.554;A|0.446	0.446	strong		0.318	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	NM_022366	
OR4E2	26686	hgsc.bcm.edu	37	14	22134018	22134018	+	Missense_Mutation	SNP	C	C	T	rs61732411	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:22134018C>T	ENST00000408935.1	+	1	722	c.722C>T	c.(721-723)tCg>tTg	p.S241L		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		TCTACCTGCTCGGCCCACTTC	0.527													C|||	699	0.139577	0.2526	0.1628	5008	,	,		21318	0.005		0.2038	False		,,,				2504	0.0429				p.S241L		Atlas-SNP	.											OR4E2,NS,carcinoma,-1,1	OR4E2	44	1	0			c.C722T						PASS	.	C	LEU/SER	921,2999		109,703,1148	96.0	93.0	94.0		722	4.8	1.0	14	dbSNP_129	94	1719,6581		190,1339,2621	yes	missense	OR4E2	NM_001001912.1	145	299,2042,3769	TT,TC,CC		20.7108,23.4949,21.6039	benign	241/314	22134018	2640,9580	1960	4150	6110	SO:0001583	missense	26686	exon1			CCTGCTCGGCCCA		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.722C>T	14.37:g.22134018C>T	ENSP00000386195:p.Ser241Leu	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	210	115	0.547619	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		
SNN	8303	hgsc.bcm.edu	37	16	11769948	11769948	+	Silent	SNP	C	C	T	rs1050068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:11769948C>T	ENST00000329565.5	+	2	245	c.33C>T	c.(31-33)ggC>ggT	p.G11G	TXNDC11_ENST00000570917.1_5'Flank	NM_003498.5	NP_003489.1	O75324	SNN_HUMAN	stannin	11					response to abiotic stimulus (GO:0009628)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				endometrium(1)	1						CCACCACGGGCGTGGTCACAG	0.632													C|||	1235	0.246605	0.0363	0.2017	5008	,	,		17973	0.254		0.4672	False		,,,				2504	0.3282				p.G11G		Atlas-SNP	.											.	SNN	7	.	0			c.C33T						PASS	.	C		473,3921	221.7+/-238.7	30,413,1754	54.0	46.0	49.0		33	-11.0	0.1	16	dbSNP_86	49	4027,4573	553.9+/-386.4	903,2221,1176	yes	coding-synonymous	SNN	NM_003498.5		933,2634,2930	TT,TC,CC		46.8256,10.7647,34.6314		11/89	11769948	4500,8494	2197	4300	6497	SO:0001819	synonymous_variant	8303	exon2			CACGGGCGTGGTC	AF030196	CCDS10549.1	16p13	2008-02-05			ENSG00000184602	ENSG00000184602			11149	protein-coding gene	gene with protein product		603032				9657854	Standard	NM_003498		Approved		uc002dbf.3	O75324	OTTHUMG00000090535	ENST00000329565.5:c.33C>T	16.37:g.11769948C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_003498	D3DUG4|Q6FGI0	Silent	SNP	ENST00000329565.5	37	CCDS10549.1																																																																																			C|0.695;T|0.305	0.305	strong		0.632	SNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207059.1	NM_003498	
ARHGEF37	389337	hgsc.bcm.edu	37	5	148996328	148996328	+	Splice_Site	SNP	G	G	A	rs57292511	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:148996328G>A	ENST00000333677.6	+	5	820	c.657G>A	c.(655-657)gtG>gtA	p.V219V		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	219						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GCAAGGAAGTGGGTAAGGACT	0.463													G|||	288	0.057508	0.0023	0.0	5008	,	,		23080	0.25		0.004	False		,,,				2504	0.0297				p.V219V		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.G657A						PASS	.	G		11,3877		0,11,1933	106.0	97.0	100.0		657	-0.4	1.0	5	dbSNP_129	100	39,8279		0,39,4120	yes	coding-synonymous-near-splice	ARHGEF37	NM_001001669.2		0,50,6053	AA,AG,GG		0.4689,0.2829,0.4096		219/676	148996328	50,12156	1944	4159	6103	SO:0001630	splice_region_variant	389337	exon5			GGAAGTGGGTAAG	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.658+1G>A	5.37:g.148996328G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	122	72	0.590164	NM_001001669	Q6ZW51	Silent	SNP	ENST00000333677.6	37	CCDS43385.1																																																																																			G|0.954;A|0.046	0.046	strong		0.463	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	Silent
LGI2	55203	hgsc.bcm.edu	37	4	25032135	25032135	+	Missense_Mutation	SNP	C	C	T	rs74901868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:25032135C>T	ENST00000382114.4	-	1	366	c.181G>A	c.(181-183)Ggc>Agc	p.G61S		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	61	LRRNT.					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)				CTGATGTCGCCCGGCACGATC	0.721													C|||	901	0.179912	0.1611	0.2133	5008	,	,		8134	0.2262		0.1879	False		,,,				2504	0.1258				p.G61S		Atlas-SNP	.											.	LGI2	62	.	0			c.G181A						PASS	.	C	SER/GLY	692,3688		54,584,1552	16.0	20.0	19.0		181	3.4	1.0	4	dbSNP_131	19	1686,6888		183,1320,2784	yes	missense	LGI2	NM_018176.3	56	237,1904,4336	TT,TC,CC		19.6641,15.7991,18.3573	benign	61/546	25032135	2378,10576	2190	4287	6477	SO:0001583	missense	55203	exon1			TGTCGCCCGGCAC	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.181G>A	4.37:g.25032135C>T	ENSP00000371548:p.Gly61Ser	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	37	CCDS3431.1	470	0.21520146520146521	83	0.16869918699186992	91	0.2513812154696133	151	0.263986013986014	145	0.19129287598944592	C	10.22	1.290577	0.23564	0.157991	0.196641	ENSG00000153012	ENST00000382114	T	0.61158	0.13	4.23	3.38	0.38709	.	0.300464	0.35677	N	0.003060	T	0.00012	0.0000	N	0.04880	-0.145	0.26571	P	0.9735612	B	0.06786	0.001	B	0.08055	0.003	T	0.13791	-1.0496	9	0.13108	T	0.6	-21.4882	11.5814	0.50894	0.0:0.9076:0.0:0.0924	.	61	Q8N0V4	LGI2_HUMAN	S	61	ENSP00000371548:G61S	ENSP00000371548:G61S	G	-	1	0	LGI2	24641233	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.122000	0.31295	0.880000	0.35969	0.561000	0.74099	GGC	C|0.806;T|0.194	0.194	strong		0.721	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		
FOXN1	8456	hgsc.bcm.edu	37	17	26864302	26864302	+	Missense_Mutation	SNP	G	G	C	rs532648	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	166	0	0		WXS	Illumina HiSeq	Phase_I	173	91	0.526012	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		
SPNS1	83985	hgsc.bcm.edu	37	16	28995145	28995145	+	Silent	SNP	C	C	T	rs4788114	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:28995145C>T	ENST00000311008.11	+	11	1736	c.1359C>T	c.(1357-1359)ttC>ttT	p.F453F	SPNS1_ENST00000334536.8_Silent_p.F401F|LAT_ENST00000354453.4_5'Flank|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000454369.2_5'Flank|SPNS1_ENST00000352260.7_Silent_p.F379F|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000323081.8_Silent_p.F380F|LAT_ENST00000566177.1_5'Flank|SPNS1_ENST00000565975.1_Silent_p.F498F|LAT_ENST00000360872.5_5'Flank|LAT_ENST00000395461.3_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	453					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CCCCCTCCTTCTTGTCCGAGT	0.637													C|||	272	0.0543131	0.0053	0.2363	5008	,	,		18278	0.0		0.0765	False		,,,				2504	0.0245				p.F453F		Atlas-SNP	.											.	SPNS1	47	.	0			c.C1359T						PASS	.	C	,,,,	89,4305	73.1+/-111.1	0,89,2108	61.0	66.0	64.0		1359,1137,1140,1203,1359	4.6	1.0	16	dbSNP_111	64	643,7957	157.5+/-211.1	31,581,3688	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPNS1	NM_001142448.1,NM_001142449.1,NM_001142450.1,NM_001142451.1,NM_032038.2	,,,,	31,670,5796	TT,TC,CC		7.4767,2.0255,5.6334	,,,,	453/529,379/455,380/456,401/477,453/529	28995145	732,12262	2197	4300	6497	SO:0001819	synonymous_variant	83985	exon12			CTCCTTCTTGTCC	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1359C>T	16.37:g.28995145C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																			C|0.943;T|0.057	0.057	strong		0.637	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
MUC16	94025	hgsc.bcm.edu	37	19	9057704	9057704	+	Silent	SNP	G	G	T	rs12984130	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9057704G>T	ENST00000397910.4	-	3	29945	c.29742C>A	c.(29740-29742)atC>atA	p.I9914I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9916	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TAGAGGACATGATTTCTGTCA	0.463													G|||	1046	0.208866	0.2352	0.219	5008	,	,		21195	0.0258		0.3121	False		,,,				2504	0.2485				p.I9914I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29742A						PASS	.	G		912,3046		97,718,1164	186.0	176.0	179.0		29742	1.4	0.0	19	dbSNP_121	179	2817,5499		498,1821,1839	no	coding-synonymous	MUC16	NM_024690.2		595,2539,3003	TT,TG,GG		33.8745,23.0419,30.3813		9914/14508	9057704	3729,8545	1979	4158	6137	SO:0001819	synonymous_variant	94025	exon3			GGACATGATTTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29742C>A	19.37:g.9057704G>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	218	113	0.518349	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.768;T|0.232	0.232	strong		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79089111	79089111	+	Missense_Mutation	SNP	A	A	G	rs3825807	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79089111A>G	ENST00000388820.4	-	4	850	c.640T>C	c.(640-642)Tct>Cct	p.S214P	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	214			S -> P (in dbSNP:rs3825807).		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						tcccgtcgAGACTCCAGCTCT	0.657													G|||	1253	0.2502	0.1112	0.2968	5008	,	,		14046	0.1518		0.4274	False		,,,				2504	0.3241				p.S214P		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.T640C						PASS	.	G	PRO/SER	678,3714		57,564,1575	22.0	21.0	22.0	http://www.ncbi.nlm.nih.gov/pubmed?term	640	-9.0	0.0	15	dbSNP_107	22	3816,4762		878,2060,1351	yes	missense	ADAMTS7	NM_014272.3	74	935,2624,2926	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	44.4859,15.4372,34.6492	benign	214/1687	79089111	4494,8476	2196	4289	6485	SO:0001583	missense	11173	exon4			GTCGAGACTCCAG	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.640T>C	15.37:g.79089111A>G	ENSP00000373472:p.Ser214Pro	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	584	0.2673992673992674	63	0.12804878048780488	123	0.3397790055248619	77	0.1346153846153846	321	0.4234828496042216	G	12.54	1.968180	0.34754	0.154372	0.444859	ENSG00000136378	ENST00000388820;ENST00000456326	T	0.60920	0.15	5.11	-8.98	0.00754	.	0.967066	0.08499	N	0.936716	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	0.04013	0.001;0.0;0.001	T	0.40384	-0.9566	9	0.30078	T	0.28	.	2.7518	0.05283	0.5523:0.0989:0.1616:0.1872	rs3825807;rs57075956;rs3825807	214;214;214	E7EP58;A8MQ00;Q9UKP4	.;.;ATS7_HUMAN	P	214	ENSP00000373472:S214P	ENSP00000373472:S214P	S	-	1	0	ADAMTS7	76876166	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-1.471000	0.02344	-1.596000	0.01611	-1.382000	0.01172	TCT	A|0.704;G|0.296	0.296	strong		0.657	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
TEK	7010	hgsc.bcm.edu	37	9	27190655	27190655	+	Missense_Mutation	SNP	G	G	A	rs1334811	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:27190655G>A	ENST00000380036.4	+	10	1898	c.1456G>A	c.(1456-1458)Gtt>Att	p.V486I	TEK_ENST00000519097.1_Missense_Mutation_p.V339I|TEK_ENST00000406359.4_Missense_Mutation_p.V443I	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	486	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs1334811). {ECO:0000269|PubMed:17344846}.		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)	ATACAAACCCGTTAATCACTA	0.438													G|||	394	0.0786741	0.121	0.0447	5008	,	,		18526	0.0109		0.0497	False		,,,				2504	0.1452				p.V486I		Atlas-SNP	.											.	TEK	250	.	0			c.G1456A						PASS	.	G	ILE/VAL	553,3853	249.6+/-257.0	35,483,1685	110.0	110.0	110.0		1456	4.7	1.0	9	dbSNP_88	110	422,8178	130.5+/-188.4	11,400,3889	yes	missense	TEK	NM_000459.3	29	46,883,5574	AA,AG,GG		4.907,12.5511,7.4965	benign	486/1125	27190655	975,12031	2203	4300	6503	SO:0001583	missense	7010	exon10			AAACCCGTTAATC	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.1456G>A	9.37:g.27190655G>A	ENSP00000369375:p.Val486Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	119	0.05448717948717949	66	0.13414634146341464	12	0.03314917127071823	5	0.008741258741258742	36	0.047493403693931395	G	10.66	1.413443	0.25465	0.125511	0.04907	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.73	4.65	0.58169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.585658	0.14019	N	0.346917	T	0.00468	0.0015	L	0.29908	0.895	0.21499	N	0.999661	B;P;B;B	0.35612	0.329;0.512;0.329;0.424	B;B;B;B	0.33568	0.062;0.166;0.098;0.119	T	0.00363	-1.1788	10	0.38643	T	0.18	.	13.8836	0.63696	0.0828:0.0:0.9172:0.0	rs1334811;rs61594018;rs1334811	339;519;443;486	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	I	339;486;443;443;296	ENSP00000430686:V339I;ENSP00000369375:V486I;ENSP00000383977:V443I;ENSP00000428337:V296I	ENSP00000343716:V443I	V	+	1	0	TEK	27180655	1.000000	0.71417	1.000000	0.80357	0.469000	0.32828	3.253000	0.51469	2.713000	0.92767	0.591000	0.81541	GTT	G|0.928;A|0.072	0.072	strong		0.438	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
CTDP1	9150	hgsc.bcm.edu	37	18	77474921	77474921	+	Silent	SNP	G	G	A	rs2126082	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:77474921G>A	ENST00000299543.7	+	8	1608	c.1461G>A	c.(1459-1461)ccG>ccA	p.P487P	CTDP1_ENST00000075430.7_Silent_p.P487P	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	487				KP -> NA (in Ref. 5; AAC64549). {ECO:0000305}.	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)		GGCAGAAGCCGAAGGCTGCCC	0.697													G|||	927	0.185104	0.2307	0.2075	5008	,	,		14787	0.1389		0.1759	False		,,,				2504	0.1646				p.P487P		Atlas-SNP	.											.	CTDP1	67	.	0			c.G1461A						PASS	.	G	,,	784,3440		78,628,1406	7.0	8.0	7.0		1104,1461,1461	-9.2	0.0	18	dbSNP_96	7	1297,7041		111,1075,2983	no	coding-synonymous,coding-synonymous,coding-synonymous	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,,	189,1703,4389	AA,AG,GG		15.5553,18.5606,16.5658	,,	368/843,487/962,487/868	77474921	2081,10481	2112	4169	6281	SO:0001819	synonymous_variant	9150	exon8			GAAGCCGAAGGCT	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.1461G>A	18.37:g.77474921G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																			G|0.813;A|0.187	0.187	strong		0.697	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
MICAL2	9645	hgsc.bcm.edu	37	11	12247813	12247813	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:12247813C>T	ENST00000256194.4	+	14	2072	c.1784C>T	c.(1783-1785)aCg>aTg	p.T595M	MICAL2_ENST00000537344.1_Missense_Mutation_p.T595M|MICAL2_ENST00000342902.5_Missense_Mutation_p.T595M|MICAL2_ENST00000379612.3_Missense_Mutation_p.T595M|MICAL2_ENST00000527546.1_Missense_Mutation_p.T595M	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	595	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		CCAGTGACCACGGGCAAAGAG	0.547																																					p.T595M		Atlas-SNP	.											MICAL2,NS,haematopoietic_neoplasm,0,1	MICAL2	114	1	0			c.C1784T						PASS	.						135.0	123.0	127.0					11																	12247813		2201	4294	6495	SO:0001583	missense	9645	exon14			TGACCACGGGCAA	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.1784C>T	11.37:g.12247813C>T	ENSP00000256194:p.Thr595Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	124	5	0.0403226	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.684033	0.88639	.	.	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	D;D;D;D;D	0.95588	-3.75;-3.75;-3.75;-3.75;-3.75	5.28	5.28	0.74379	Calponin homology domain (5);	0.062767	0.64402	D	0.000008	D	0.98074	0.9365	M	0.88450	2.955	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.76575	0.98;0.979;0.984;0.983;0.988	D	0.99019	1.0817	10	0.87932	D	0	.	18.526	0.90973	0.0:1.0:0.0:0.0	.	595;595;595;595;595	G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;MICA2_HUMAN	M	595;128;595;595;595;595	ENSP00000441689:T595M;ENSP00000256194:T595M;ENSP00000433965:T595M;ENSP00000344894:T595M;ENSP00000368932:T595M	ENSP00000256194:T595M	T	+	2	0	MICAL2	12204389	1.000000	0.71417	0.968000	0.41197	0.895000	0.52256	7.818000	0.86416	2.466000	0.83321	0.563000	0.77884	ACG	.	.	none		0.547	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
RIPK3	11035	hgsc.bcm.edu	37	14	24808388	24808388	+	Silent	SNP	A	A	G	rs3181247	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24808388A>G	ENST00000216274.5	-	3	522	c.304T>C	c.(304-306)Ttg>Ctg	p.L102L	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	102	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	p.L102L(1)		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)		AGCCCCGACAAGGAGCCGTTC	0.572													G|||	320	0.0638978	0.1286	0.0418	5008	,	,		17983	0.001		0.0596	False		,,,				2504	0.0613				p.L102L	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											RIPK3,NS,carcinoma,0,1	RIPK3	43	1	1	Substitution - coding silent(1)	prostate(1)	c.T304C						PASS	.	G		524,3882	773.8+/-414.0	21,482,1700	72.0	66.0	68.0		304	3.8	1.0	14	dbSNP_105	68	416,8184	799.0+/-407.4	19,378,3903	no	coding-synonymous	RIPK3	NM_006871.3		40,860,5603	GG,GA,AA		4.8372,11.8929,7.2274		102/519	24808388	940,12066	2203	4300	6503	SO:0001819	synonymous_variant	11035	exon3			CCGACAAGGAGCC	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.304T>C	14.37:g.24808388A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	37	CCDS9628.1																																																																																			A|0.926;G|0.074	0.074	strong		0.572	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
GSG2	83903	hgsc.bcm.edu	37	17	3628362	3628362	+	Missense_Mutation	SNP	T	T	C	rs3809806	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3628362T>C	ENST00000325418.4	+	1	1152	c.1133T>C	c.(1132-1134)gTc>gCc	p.V378A	ITGAE_ENST00000571185.1_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	378			V -> A (in dbSNP:rs3809806). {ECO:0000269|PubMed:11311556, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		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)	p.V378A(2)									TTACAGAATGTCTGCTTTTGG	0.483													C|||	2661	0.53135	0.6838	0.3473	5008	,	,		20813	0.3353		0.5477	False		,,,				2504	0.6411				p.V378A		Atlas-SNP	.											GSG2_ENST00000325418,NS,carcinoma,0,1	GSG2	48	1	2	Substitution - Missense(2)	prostate(2)	c.T1133C						PASS	.	C	,ALA/VAL	2807,1599	495.0+/-363.1	893,1021,289	74.0	74.0	74.0		,1133	1.0	0.0	17	dbSNP_107	74	4674,3926	547.8+/-385.2	1274,2126,900	yes	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,64	2167,3147,1189	CC,CT,TT		45.6512,36.2914,42.4804	,benign	,378/799	3628362	7481,5525	2203	4300	6503	SO:0001583	missense	83903	exon1			AGAATGTCTGCTT	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.1133T>C	17.37:g.3628362T>C	ENSP00000325290:p.Val378Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	1087	0.4977106227106227	333	0.676829268292683	140	0.3867403314917127	197	0.34440559440559443	417	0.5501319261213721	C	1.283	-0.609872	0.03690	0.637086	0.543488	ENSG00000177602	ENST00000325418	T	0.05258	3.47	4.23	0.989	0.19802	.	1.426380	0.05004	N	0.469640	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	0.35822	-0.9773	9	0.87932	D	0	-32.5476	4.2491	0.10686	0.1734:0.5639:0.0:0.2627	rs3809806;rs56614897;rs59995636;rs3809806	378	Q8TF76	HASP_HUMAN	A	378	ENSP00000325290:V378A	ENSP00000325290:V378A	V	+	2	0	GSG2	3575111	0.000000	0.05858	0.000000	0.03702	0.316000	0.28119	-0.223000	0.09177	-0.105000	0.12132	-0.726000	0.03593	GTC	T|0.447;C|0.553	0.553	strong		0.483	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
SYTL3	94120	hgsc.bcm.edu	37	6	159178345	159178345	+	Missense_Mutation	SNP	C	C	T	rs901363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:159178345C>T	ENST00000297239.9	+	13	1434	c.1240C>T	c.(1240-1242)Cct>Tct	p.P414S	SYTL3_ENST00000360448.3_Missense_Mutation_p.P346S|SYTL3_ENST00000367081.3_Missense_Mutation_p.P140S			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	414			P -> S (in dbSNP:rs901363).		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)		AGTGATCATTCCTCTGGCCAC	0.612													C|||	2249	0.449081	0.2753	0.598	5008	,	,		14777	0.7361		0.328	False		,,,				2504	0.407				p.P414S		Atlas-SNP	.											.	SYTL3	49	.	0			c.C1240T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	1241,3165	429.1+/-342.1	182,877,1144	92.0	78.0	83.0		1036,1240,1240,1036	5.1	1.0	6	dbSNP_86	83	2893,5707	452.8+/-363.1	496,1901,1903	yes	missense,missense,missense,missense	SYTL3	NM_001009991.3,NM_001242384.1,NM_001242394.1,NM_001242395.1	74,74,74,74	678,2778,3047	TT,TC,CC		33.6395,28.1661,31.7853	probably-damaging,probably-damaging,probably-damaging,probably-damaging	346/543,414/611,414/611,346/543	159178345	4134,8872	2203	4300	6503	SO:0001583	missense	94120	exon15			ATCATTCCTCTGG	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.1240C>T	6.37:g.159178345C>T	ENSP00000297239:p.Pro414Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001242384	Q496J4|Q496J6|Q5U3B9	Missense_Mutation	SNP	ENST00000297239.9	37	CCDS56458.1	1012	0.4633699633699634	146	0.2967479674796748	188	0.5193370165745856	437	0.763986013986014	241	0.3179419525065963	C	18.21	3.572424	0.65765	0.281661	0.336395	ENSG00000164674	ENST00000360448;ENST00000543689;ENST00000297239;ENST00000367081	T;T;T	0.08370	3.1;3.1;3.1	5.07	5.07	0.68467	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.06554	0.0168	M	0.74881	2.28	0.20563	P	0.999887067	P;P;P	0.45212	0.791;0.853;0.851	B;B;B	0.42692	0.332;0.288;0.395	T	0.29458	-1.0011	9	0.20519	T	0.43	-17.7371	12.8384	0.57786	0.0:0.9208:0.0:0.0792	rs901363;rs59429263;rs901363	140;414;346	F8W7H4;Q4VX76;Q4VX76-2	.;SYTL3_HUMAN;.	S	346;414;414;140	ENSP00000353631:P346S;ENSP00000297239:P414S;ENSP00000356048:P140S	ENSP00000297239:P414S	P	+	1	0	SYTL3	159098333	0.999000	0.42202	0.980000	0.43619	0.951000	0.60555	2.629000	0.46485	2.356000	0.79943	0.491000	0.48974	CCT	C|0.605;T|0.394	0.394	strong		0.612	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1		
CACNA1D	776	hgsc.bcm.edu	37	3	53845295	53845295	+	Silent	SNP	C	C	T	rs10154841	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:53845295C>T	ENST00000350061.5	+	48	6859	c.6348C>T	c.(6346-6348)aaC>aaT	p.N2116N	CACNA1D_ENST00000422281.2_Silent_p.N2092N|CACNA1D_ENST00000544977.1_3'UTR|CACNA1D_ENST00000288139.4_Silent_p.N2136N	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2116					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCCGAGCCAACGGGGATGTGG	0.597													C|||	1308	0.261182	0.646	0.1398	5008	,	,		19721	0.1498		0.1054	False		,,,				2504	0.1022				p.N2136N		Atlas-SNP	.											.	CACNA1D	324	.	0			c.C6408T						PASS	.	C	,,	2542,1864	629.6+/-395.3	734,1074,395	77.0	76.0	76.0		6408,6276,6348	-6.9	0.1	3	dbSNP_119	76	742,7858	178.6+/-228.0	29,684,3587	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1D	NM_000720.2,NM_001128839.1,NM_001128840.1	,,	763,1758,3982	TT,TC,CC		8.6279,42.3059,25.2499	,,	2136/2182,2092/2138,2116/2162	53845295	3284,9722	2203	4300	6503	SO:0001819	synonymous_variant	776	exon49			AGCCAACGGGGAT	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6348C>T	3.37:g.53845295C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	37	CCDS46848.1																																																																																			C|0.753;T|0.247	0.247	strong		0.597	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	
NDUFS2	4720	hgsc.bcm.edu	37	1	161172233	161172233	+	Missense_Mutation	SNP	C	C	A	rs11538340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161172233C>A	ENST00000367993.3	+	2	506	c.58C>A	c.(58-60)Cct>Act	p.P20T	NDUFS2_ENST00000392179.4_Missense_Mutation_p.P20T|NDUFS2_ENST00000476409.2_De_novo_Start_InFrame	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	20			P -> T (in dbSNP:rs11538340).		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	GGTGCTGCGGCCTGGGGCTGG	0.657													C|||	433	0.0864617	0.0643	0.0576	5008	,	,		15718	0.0764		0.0676	False		,,,				2504	0.1667				p.P20T		Atlas-SNP	.											.	NDUFS2	33	.	0			c.C58A						PASS	.	C	THR/PRO,THR/PRO	282,4122		9,264,1929	19.0	21.0	20.0		58,58	3.8	0.9	1	dbSNP_120	20	681,7917		29,623,3647	yes	missense,missense	NDUFS2	NM_001166159.1,NM_004550.4	38,38	38,887,5576	AA,AC,CC		7.9204,6.4033,7.4066	benign,benign	20/458,20/464	161172233	963,12039	2202	4299	6501	SO:0001583	missense	4720	exon1			CTGCGGCCTGGGG	BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7708	protein-coding gene	gene with protein product	"""complex I 49kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"""	602985	"""NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"""			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.58C>A	1.37:g.161172233C>A	ENSP00000356972:p.Pro20Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_001166159	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Missense_Mutation	SNP	ENST00000367993.3	37	CCDS1224.1	157	0.07188644688644688	42	0.08536585365853659	17	0.04696132596685083	45	0.07867132867132867	53	0.06992084432717678	C	11.61	1.689543	0.29962	0.064033	0.079204	ENSG00000158864	ENST00000367993;ENST00000392179	D;D	0.85013	-1.93;-1.93	5.7	3.83	0.44106	.	0.454461	0.23738	N	0.045056	T	0.51787	0.1695	N	0.08118	0	0.09310	P	0.9999999999701543	B;B	0.06786	0.001;0.001	B;B	0.09377	0.002;0.004	T	0.33675	-0.9859	9	0.38643	T	0.18	.	8.3945	0.32548	0.0:0.6261:0.2941:0.0798	rs11538340;rs17357375	20;20	Q53HG2;O75306	.;NDUS2_HUMAN	T	20	ENSP00000356972:P20T;ENSP00000376018:P20T	ENSP00000356972:P20T	P	+	1	0	NDUFS2	159438857	0.871000	0.30034	0.853000	0.33588	0.186000	0.23388	0.356000	0.20181	0.743000	0.32719	0.655000	0.94253	CCT	A|0.068;C|0.932;G|0.000	0.068	strong		0.657	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550	
ANKH	56172	hgsc.bcm.edu	37	5	14769103	14769103	+	Silent	SNP	G	G	A	rs17251667	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:14769103G>A	ENST00000284268.6	-	2	624	c.294C>T	c.(292-294)gcC>gcT	p.A98A		NM_054027.4	NP_473368.1	Q9HCJ1	ANKH_HUMAN	ANKH inorganic pyrophosphate transport regulator	98					locomotory behavior (GO:0007626)|regulation of bone mineralization (GO:0030500)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	inorganic diphosphate transmembrane transporter activity (GO:0030504)|inorganic phosphate transmembrane transporter activity (GO:0005315)|phosphate ion transmembrane transporter activity (GO:0015114)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						TGTGAAAGACGGCAGCGATGG	0.483													G|||	604	0.120607	0.0424	0.1225	5008	,	,		16145	0.0238		0.1829	False		,,,				2504	0.2607				p.A98A		Atlas-SNP	.											.	ANKH	64	.	0			c.C294T						PASS	.	G		264,4142	148.8+/-183.1	7,250,1946	73.0	72.0	72.0		294	-4.0	0.3	5	dbSNP_123	72	1672,6928	307.4+/-308.4	173,1326,2801	no	coding-synonymous	ANKH	NM_054027.4		180,1576,4747	AA,AG,GG		19.4419,5.9918,14.8854		98/493	14769103	1936,11070	2203	4300	6503	SO:0001819	synonymous_variant	56172	exon2			AAAGACGGCAGCG	AF274753	CCDS3885.1	5p15.2	2013-06-19	2013-06-19		ENSG00000154122	ENSG00000154122			15492	protein-coding gene	gene with protein product		605145	"""ankylosis, progressive (mouse) homolog"", ""craniometaphyseal dysplasia, Jackson type (dominant)"", ""ankylosis, progressive homolog (mouse)"""	CCAL2, CMDJ		10894769, 12297989, 11326338	Standard	NM_054027		Approved	HANK, ANK, CPPDD	uc003jfm.4	Q9HCJ1	OTTHUMG00000090539	ENST00000284268.6:c.294C>T	5.37:g.14769103G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	298	151	0.506711	NM_054027	B2RCA7|B3KMG4|D3DTD4|Q9NQW2	Silent	SNP	ENST00000284268.6	37	CCDS3885.1																																																																																			G|0.877;A|0.123	0.123	strong		0.483	ANKH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207063.1	NM_054027	
MRPS35	60488	hgsc.bcm.edu	37	12	27867727	27867727	+	Missense_Mutation	SNP	G	G	A	rs1127787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:27867727G>A	ENST00000081029.3	+	2	198	c.127G>A	c.(127-129)Gga>Aga	p.G43R	MRPS35_ENST00000538315.1_Missense_Mutation_p.G43R	NM_021821.3	NP_068593.2	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S35	0						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	6	Lung SC(9;0.0873)					AAGAACACCCGGAAATGAAAG	0.348													G|||	598	0.119409	0.0068	0.1009	5008	,	,		18221	0.1944		0.173	False		,,,				2504	0.1524				p.G43R		Atlas-SNP	.											.	MRPS35	26	.	0			c.G127A						PASS	.	G	ARG/GLY,ARG/GLY	148,4258	103.4+/-141.9	1,146,2056	101.0	104.0	103.0		127,127	2.0	0.0	12	dbSNP_86	103	1372,7228	266.9+/-287.0	108,1156,3036	yes	missense,missense	MRPS35	NM_001190864.1,NM_021821.3	125,125	109,1302,5092	AA,AG,GG		15.9535,3.3591,11.6869	benign,benign	43/195,43/324	27867727	1520,11486	2203	4300	6503	SO:0001583	missense	60488	exon2			ACACCCGGAAATG	AF182422	CCDS8714.1, CCDS53769.1	12p11	2012-09-13			ENSG00000061794	ENSG00000061794		"""Mitochondrial ribosomal proteins / small subunits"""	16635	protein-coding gene	gene with protein product		611995				11279123	Standard	NM_021821		Approved	MRPS28, MDS023	uc001rih.3	P82673	OTTHUMG00000169215	ENST00000081029.3:c.127G>A	12.37:g.27867727G>A	ENSP00000081029:p.Gly43Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_001190864	B2RDZ7|Q96Q21	Missense_Mutation	SNP	ENST00000081029.3	37	CCDS8714.1	282	0.12912087912087913	7	0.014227642276422764	37	0.10220994475138122	106	0.1853146853146853	132	0.1741424802110818	G	0.077	-1.191671	0.01607	0.033591	0.159535	ENSG00000061794	ENST00000081029;ENST00000321446;ENST00000538315	T;T	0.41758	1.0;0.99	4.42	1.99	0.26369	.	0.456688	0.23123	N	0.051666	T	0.00012	0.0000	N	0.00152	-1.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26608	-1.0098	9	0.08599	T	0.76	-4.1139	4.4065	0.11411	0.6957:0.2013:0.103:0.0	rs1127787;rs1801373;rs3177168;rs3184093;rs11545242;rs17404577;rs52803578;rs3177168	43;43	P82673-2;P82673	.;RT35_HUMAN	R	43	ENSP00000081029:G43R;ENSP00000445390:G43R	ENSP00000081029:G43R	G	+	1	0	MRPS35	27758994	0.008000	0.16893	0.007000	0.13788	0.008000	0.06430	1.190000	0.32126	0.438000	0.26450	-0.238000	0.12139	GGA	G|0.873;A|0.127	0.127	strong		0.348	MRPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402897.1	NM_021821	
GCNT1	2650	hgsc.bcm.edu	37	9	79118400	79118400	+	Missense_Mutation	SNP	C	C	T	rs147866228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79118400C>T	ENST00000376730.4	+	4	1586	c.1103C>T	c.(1102-1104)cCc>cTc	p.P368L	GCNT1_ENST00000444201.2_Missense_Mutation_p.P368L|GCNT1_ENST00000536223.1_Missense_Mutation_p.P368L|GCNT1_ENST00000442371.1_Missense_Mutation_p.P368L	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	368	Catalytic. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						AAGGGTGCTCCCTACCCGCCC	0.522													C|||	10	0.00199681	0.0015	0.0029	5008	,	,		13880	0.0		0.006	False		,,,				2504	0.0				p.P368L		Atlas-SNP	.											.	GCNT1	52	.	0			c.C1103T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400	12.9+/-30.5	0,6,2197	110.0	92.0	98.0		1103,1103,1103,1103,1103	5.3	1.0	9	dbSNP_134	98	89,8511	50.6+/-110.7	0,89,4211	yes	missense,missense,missense,missense,missense	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	98,98,98,98,98	0,95,6408	TT,TC,CC		1.0349,0.1362,0.7304	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	368/429,368/429,368/429,368/429,368/429	79118400	95,12911	2203	4300	6503	SO:0001583	missense	2650	exon4			GTGCTCCCTACCC	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.1103C>T	9.37:g.79118400C>T	ENSP00000365920:p.Pro368Leu	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	258	129	0.5	NM_001490	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	8	0.003663003663003663	2	0.0040650406504065045	0	0.0	0	0.0	6	0.0079155672823219	c	14.65	2.600144	0.46423	0.001362	0.010349	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11169	2.8;2.8;2.8;2.8	6.17	5.28	0.74379	.	0.179527	0.50627	D	0.000111	T	0.28995	0.0720	M	0.82823	2.61	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.16070	-1.0415	9	.	.	.	1.2848	15.5517	0.76158	0.0:0.9345:0.0:0.0655	.	368	Q02742	GCNT1_HUMAN	L	368	ENSP00000440883:P368L;ENSP00000415454:P368L;ENSP00000390703:P368L;ENSP00000365920:P368L	.	P	+	2	0	GCNT1	78308220	0.432000	0.25554	0.987000	0.45799	0.047000	0.14425	2.020000	0.41010	1.635000	0.50512	0.655000	0.94253	CCC	C|0.994;T|0.006	0.006	strong		0.522	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
ELP6	54859	hgsc.bcm.edu	37	3	47545911	47545911	+	Missense_Mutation	SNP	G	G	A	rs377204125		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47545911G>A	ENST00000296149.4	-	4	402	c.232C>T	c.(232-234)Cgt>Tgt	p.R78C	ELP6_ENST00000439305.1_Missense_Mutation_p.R5C|ELP6_ENST00000446787.1_Missense_Mutation_p.R5C	NM_001031703.2	NP_001026873.2	Q0PNE2	ELP6_HUMAN	elongator acetyltransferase complex subunit 6	78					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Elongator holoenzyme complex (GO:0033588)											AGCTGCCCACGCTCCCGCGCC	0.542																																					p.R78C		Atlas-SNP	.											.	.	.	.	0			c.C232T						PASS	.	G	CYS/ARG	0,4072		0,0,2036	57.0	61.0	60.0		232	2.1	0.0	3		60	1,8375		0,1,4187	no	missense	C3orf75	NM_001031703.2	180	0,1,6223	AA,AG,GG		0.0119,0.0,0.0080	benign	78/267	47545911	1,12447	2036	4188	6224	SO:0001583	missense	54859	exon4			GCCCACGCTCCCG	AK000218	CCDS43082.1	3p21.31	2012-08-14	2012-08-08	2012-08-08	ENSG00000163832	ENSG00000163832		"""Elongator acetyltransferase complex subunits"""	25976	protein-coding gene	gene with protein product		615020	"""transmembrane protein 103"", ""chromosome 3 open reading frame 75"""	TMEM103, C3orf75		22854966	Standard	XM_005265241		Approved	FLJ20211	uc003crk.3	Q0PNE2	OTTHUMG00000133521	ENST00000296149.4:c.232C>T	3.37:g.47545911G>A	ENSP00000296149:p.Arg78Cys	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001031703	Q9BW57|Q9NXJ3	Missense_Mutation	SNP	ENST00000296149.4	37	CCDS43082.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012549	0.35511	0.0	1.19E-4	ENSG00000163832	ENST00000296149;ENST00000450051;ENST00000446787;ENST00000439305;ENST00000412761;ENST00000444760;ENST00000425291;ENST00000449409;ENST00000414236	.	.	.	6.06	2.13	0.27403	.	0.296215	0.40064	N	0.001181	T	0.27489	0.0675	L	0.41027	1.25	0.09310	N	0.999998	B;B;B	0.25351	0.061;0.124;0.052	B;B;B	0.23018	0.019;0.043;0.027	T	0.21381	-1.0247	9	0.56958	D	0.05	-0.5247	2.3576	0.04300	0.2284:0.1263:0.5154:0.1298	.	54;78;78	B4DP60;C9JAS1;Q0PNE2	.;.;CC075_HUMAN	C	78;54;5;5;5;5;5;5;5	.	ENSP00000296149:R78C	R	-	1	0	C3orf75	47520915	0.001000	0.12720	0.012000	0.15200	0.638000	0.38207	0.871000	0.28023	0.398000	0.25338	0.655000	0.94253	CGT	.	.	weak		0.542	ELP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257493.1	NM_017713	
FLG	2312	hgsc.bcm.edu	37	1	152281523	152281523	+	Missense_Mutation	SNP	A	A	C	rs80059102	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281523A>C	ENST00000368799.1	-	3	5874	c.5839T>G	c.(5839-5841)Tgg>Ggg	p.W1947G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1947	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACTGCTCCCAAGCAGATCCA	0.572									Ichthyosis																												p.W1947G		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.T5839G						scavenged	.						253.0	240.0	245.0					1																	152281523		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCCCAAGCAGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5839T>G	1.37:g.152281523A>C	ENSP00000357789:p.Trp1947Gly	Somatic	338	2	0.00591716		WXS	Illumina HiSeq	Phase_I	510	151	0.296078	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	
SP100	6672	hgsc.bcm.edu	37	2	231331896	231331896	+	Silent	SNP	G	G	A	rs1050224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:231331896G>A	ENST00000264052.5	+	13	1612	c.1257G>A	c.(1255-1257)tcG>tcA	p.S419S	SP100_ENST00000409897.1_Silent_p.S384S|SP100_ENST00000409112.1_Silent_p.S419S|SP100_ENST00000427101.2_Silent_p.S394S|SP100_ENST00000341950.4_Silent_p.S419S|SP100_ENST00000409341.1_Silent_p.S419S|SP100_ENST00000340126.4_Silent_p.S419S|SP100_ENST00000409824.1_Silent_p.S394S	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	419	Sufficient to mediate interaction with ETS1.				cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CAGAAGCCTCGAGCGGGGCAC	0.537													A|||	3330	0.664936	0.6142	0.6484	5008	,	,		19443	0.4772		0.7555	False		,,,				2504	0.8456				p.S419S		Atlas-SNP	.											.	SP100	167	.	0			c.G1257A						PASS	.	A	,,,,,	2775,1631	501.3+/-365.0	887,1001,315	114.0	127.0	123.0		1257,1257,1257,1182,1152,1257	-0.1	0.0	2	dbSNP_86	123	6487,2113	363.5+/-333.2	2448,1591,261	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SP100	NM_001080391.1,NM_001206701.1,NM_001206702.1,NM_001206703.1,NM_001206704.1,NM_003113.3	,,,,,	3335,2592,576	AA,AG,GG		24.5698,37.0177,28.7867	,,,,,	419/886,419/689,419/481,394/453,384/446,419/880	231331896	9262,3744	2203	4300	6503	SO:0001819	synonymous_variant	6672	exon13			AGCCTCGAGCGGG	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.1257G>A	2.37:g.231331896G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	49	0.604938	NM_001206702	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Silent	SNP	ENST00000264052.5	37	CCDS2477.1	1405	0.6433150183150184	334	0.6788617886178862	232	0.6408839779005525	268	0.46853146853146854	571	0.7532981530343008	A	3.671	-0.067548	0.07273	0.629823	0.754302	ENSG00000067066	ENST00000413284	.	.	.	3.92	-0.0788	0.13713	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.27640	-1.0068	3	.	.	.	.	4.5515	0.12114	0.195:0.0:0.5066:0.2984	rs1050224;rs1050324;rs1649870;rs3172147;rs17850761;rs1050224	.	.	.	Q	67	.	.	R	+	2	0	SP100	231040140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.419000	0.07071	-0.254000	0.09500	-1.418000	0.01112	CGA	G|0.320;A|0.680	0.680	strong		0.537	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
HCN2	610	hgsc.bcm.edu	37	19	603874	603874	+	Silent	SNP	C	C	T	rs55780677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:603874C>T	ENST00000251287.2	+	2	1016	c.963C>T	c.(961-963)cgC>cgT	p.R321R		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	321					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)		AGACGGCACGCGCCCTGCGCA	0.607													c|||	1167	0.233027	0.2383	0.0908	5008	,	,		12078	0.2897		0.0974	False		,,,				2504	0.408				p.R321R	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.C963T						PASS	.	C		1116,3284		140,836,1224	96.0	75.0	82.0		963	0.5	1.0	19	dbSNP_129	82	886,7704		48,790,3457	no	coding-synonymous	HCN2	NM_001194.3		188,1626,4681	TT,TC,CC		10.3143,25.3636,15.4119		321/890	603874	2002,10988	2200	4295	6495	SO:0001819	synonymous_variant	610	exon2			GGCACGCGCCCTG	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.963C>T	19.37:g.603874C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			C|0.837;T|0.163	0.163	strong		0.607	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
DUSP10	11221	hgsc.bcm.edu	37	1	221912334	221912334	+	Silent	SNP	T	T	G	rs35552569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:221912334T>G	ENST00000366899.3	-	2	991	c.753A>C	c.(751-753)ccA>ccC	p.P251P	DUSP10_ENST00000544095.1_5'Flank|DUSP10_ENST00000468085.1_5'Flank|DUSP10_ENST00000323825.3_Intron	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10	251	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|oligodendrocyte differentiation (GO:0048709)|protein dephosphorylation (GO:0006470)|regulation of adaptive immune response (GO:0002819)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(131;0.0103)		CTATGTGAAGTGGCTGGGAGG	0.483													T|||	4	0.000798722	0.0	0.0	5008	,	,		21697	0.0		0.004	False		,,,				2504	0.0				p.P251P		Atlas-SNP	.											.	DUSP10	64	.	0			c.A753C						PASS	.	T	,	5,4401	9.9+/-24.2	0,5,2198	162.0	167.0	165.0		753,	-1.2	0.9	1	dbSNP_126	165	52,8548	32.8+/-85.7	1,50,4249	no	coding-synonymous,intron	DUSP10	NM_007207.4,NM_144729.2	,	1,55,6447	GG,GT,TT		0.6047,0.1135,0.4383	,	251/483,	221912334	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	11221	exon2			GTGAAGTGGCTGG	AB026436	CCDS1528.1	1q41	2011-06-09			ENSG00000143507	ENSG00000143507		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3065	protein-coding gene	gene with protein product		608867				10391943, 10597297	Standard	NM_007207		Approved	MKP-5, MKP5	uc001hmy.2	Q9Y6W6	OTTHUMG00000037269	ENST00000366899.3:c.753A>C	1.37:g.221912334T>G		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	235	102	0.434043	NM_007207	D3DTB4|Q6GSI4|Q9H9Z5	Silent	SNP	ENST00000366899.3	37	CCDS1528.1																																																																																			T|0.997;G|0.003	0.003	strong		0.483	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090716.1	NM_007207	
SUSD5	26032	hgsc.bcm.edu	37	3	33195284	33195284	+	Silent	SNP	G	G	A	rs61743511	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:33195284G>A	ENST00000309558.3	-	5	1257	c.840C>T	c.(838-840)ccC>ccT	p.P280P		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	280					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)	p.P280P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GTGAATCTGCGGGGACACTGC	0.547													G|||	810	0.161741	0.0862	0.1758	5008	,	,		18901	0.1905		0.1541	False		,,,				2504	0.2321				p.P280P		Atlas-SNP	.											SUSD5,NS,carcinoma,0,1	SUSD5	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C840T						PASS	.	G		346,3490		21,304,1593	47.0	48.0	48.0		840	3.0	0.0	3	dbSNP_129	48	1323,6933		106,1111,2911	no	coding-synonymous	SUSD5	NM_015551.1		127,1415,4504	AA,AG,GG		16.0247,9.0198,13.8025		280/630	33195284	1669,10423	1918	4128	6046	SO:0001819	synonymous_variant	26032	exon5			ATCTGCGGGGACA	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.840C>T	3.37:g.33195284G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_015551		Silent	SNP	ENST00000309558.3	37	CCDS46787.1	338	0.15476190476190477	43	0.08739837398373984	64	0.17679558011049723	117	0.20454545454545456	114	0.1503957783641161	G	0.009	-1.842924	0.00568	0.090198	0.160247	ENSG00000173705	ENST00000412539	T	0.11063	2.81	5.9	2.99	0.34606	.	0.323106	0.32852	N	0.005575	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.45542	-0.9254	6	0.16420	T	0.52	-6.8588	4.4684	0.11700	0.1477:0.1153:0.6059:0.131	.	.	.	.	L	216	ENSP00000406475:P216L	ENSP00000406475:P216L	P	-	2	0	SUSD5	33170288	1.000000	0.71417	0.002000	0.10522	0.000000	0.00434	1.206000	0.32321	0.418000	0.25898	-0.797000	0.03246	CCG	G|0.848;A|0.152	0.152	strong		0.547	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054	
MIEF2	125170	hgsc.bcm.edu	37	17	18167684	18167684	+	Missense_Mutation	SNP	G	G	A	rs12603700	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:18167684G>A	ENST00000323019.4	+	4	1182	c.971G>A	c.(970-972)gGg>gAg	p.G324E	MIEF2_ENST00000395706.2_Missense_Mutation_p.G335E|MIEF2_ENST00000395704.4_3'UTR	NM_001144900.1|NM_139162.3	NP_001138372.1|NP_631901.2	Q96C03	MID49_HUMAN	mitochondrial elongation factor 2	324			G -> E (in dbSNP:rs12603700).		mitochondrion organization (GO:0007005)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein targeting to membrane (GO:0090314)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)											CCCCTGGAGGGGCTGGCGGGG	0.682													G|||	700	0.139776	0.115	0.1484	5008	,	,		15991	0.1518		0.0924	False		,,,				2504	0.2035				p.G335E		Atlas-SNP	.											.	SMCR7	20	.	0			c.G1004A						PASS	.	G	GLU/GLY,GLU/GLY,	398,4008	185.0+/-212.2	18,362,1823	49.0	57.0	54.0		971,1004,	5.4	1.0	17	dbSNP_120	54	881,7713	189.1+/-236.0	50,781,3466	yes	missense,missense,utr-3	SMCR7	NM_139162.3,NM_148886.1,NM_001144900.1	98,98,	68,1143,5289	AA,AG,GG		10.2513,9.0331,9.8385	possibly-damaging,possibly-damaging,	324/455,335/466,	18167684	1279,11721	2203	4297	6500	SO:0001583	missense	125170	exon4			TGGAGGGGCTGGC	BC014973	CCDS11193.1, CCDS45624.1, CCDS45625.1	17p11.2	2013-09-23	2013-09-23	2013-09-23	ENSG00000177427	ENSG00000177427			17920	protein-coding gene	gene with protein product		615498	"""Smith-Magenis syndrome chromosome region, candidate 7"""	SMCR7		11997338, 21508961	Standard	NM_001144900		Approved	MGC23130, MiD49	uc010vxq.2	Q96C03	OTTHUMG00000059392	ENST00000323019.4:c.971G>A	17.37:g.18167684G>A	ENSP00000323591:p.Gly324Glu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	39	23	0.589744	NM_148886	J3KPT3|Q6ZRD4|Q96N07	Missense_Mutation	SNP	ENST00000323019.4	37	CCDS11193.1	279	0.12774725274725274	53	0.10772357723577236	47	0.1298342541436464	109	0.19055944055944055	70	0.09234828496042216	G	19.15	3.771076	0.69992	0.090331	0.102513	ENSG00000177427	ENST00000323019;ENST00000395706	T;T	0.11712	2.75;2.75	5.45	5.45	0.79879	.	0.282242	0.39909	N	0.001227	T	0.00039	0.0001	M	0.61703	1.905	0.22835	P	0.9986774	P	0.46020	0.871	P	0.53593	0.73	T	0.31503	-0.9941	9	0.23302	T	0.38	-45.0743	9.2938	0.37802	0.0762:0.1463:0.7776:0.0	rs12603700;rs59096125	324	Q96C03	MID49_HUMAN	E	324;335	ENSP00000323591:G324E;ENSP00000379057:G335E	ENSP00000323591:G324E	G	+	2	0	SMCR7	18108409	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.149000	0.58091	2.565000	0.86533	0.462000	0.41574	GGG	G|0.896;A|0.104	0.104	strong		0.682	MIEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132060.2	NM_139162	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253815	39253815	+	Silent	SNP	G	G	A	rs77163010	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39253815G>A	ENST00000333822.4	-	1	578	c.522C>T	c.(520-522)tgC>tgT	p.C174C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	174					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						CGGGGCGGGGGCAGGTGGAGA	0.632													G|||	2819	0.562899	0.6536	0.6081	5008	,	,		16773	0.4127		0.6183	False		,,,				2504	0.5061				p.C174C		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C522T						PASS	.						52.0	63.0	60.0					17																	39253815		691	1591	2282	SO:0001819	synonymous_variant	728224	exon1			GCGGGGGCAGGTG	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.522C>T	17.37:g.39253815G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	194	85	0.438144	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			G|0.983;A|0.017	0.017	strong		0.632	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
SFTPA1	653509	hgsc.bcm.edu	37	10	81373810	81373810	+	Missense_Mutation	SNP	G	G	A	rs548998131		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:81373810G>A	ENST00000398636.3	+	6	826	c.688G>A	c.(688-690)Gat>Aat	p.D230N	SFTPA1_ENST00000428376.2_Missense_Mutation_p.D230N|SFTPA1_ENST00000372308.3_Missense_Mutation_p.D230N|SFTPA1_ENST00000419470.2_Missense_Mutation_p.D245N|SFTPA1_ENST00000372313.5_Missense_Mutation_p.D171N	NM_001164644.1|NM_001164646.1|NM_005411.4	NP_001158116.1|NP_001158118.1|NP_005402.3	Q8IWL2	SFTA1_HUMAN	surfactant protein A1	230	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				lipid transport (GO:0006869)|respiratory gaseous exchange (GO:0007585)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|lipid transporter activity (GO:0005319)			endometrium(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			GATGTACACAGATGGGCAGTG	0.572													g|||	1	0.000199681	0.0	0.0	5008	,	,		19728	0.0		0.001	False		,,,				2504	0.0				p.D245N		Atlas-SNP	.											.	SFTPA1	23	.	0			c.G733A						PASS	.						141.0	128.0	132.0					10																	81373810		2203	4296	6499	SO:0001583	missense	653509	exon6			TACACAGATGGGC	BC026229	CCDS44444.1, CCDS44445.1, CCDS44444.2	10q22.3	2012-11-02	2008-08-26			ENSG00000122852		"""Collectins"""	10798	protein-coding gene	gene with protein product	"""surfactant, pulmonary-associated protein A1A"""	178630	"""surfactant, pulmonary-associated protein A1"""	SFTP1			Standard	NM_001093770		Approved	SP-A, SP-A1, COLEC4	uc009xry.3	Q8IWL2		ENST00000398636.3:c.688G>A	10.37:g.81373810G>A	ENSP00000381633:p.Asp230Asn	Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	432	218	0.50463	NM_001093770	A8K3T8|B7ZW50|E3VLD8|E3VLD9|E3VLE0|E3VLE1|G5E9J3|P07714|Q14DV4|Q5RIR5|Q5RIR7|Q6PIT0|Q8TC19	Missense_Mutation	SNP	ENST00000398636.3	37	CCDS44445.1	.	.	.	.	.	.	.	.	.	.	.	11.71	1.719016	0.30503	.	.	ENSG00000122852	ENST00000372308;ENST00000398636;ENST00000428376;ENST00000372313;ENST00000419470;ENST00000394569	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	2.89	1.98	0.26296	C-type lectin fold (2);C-type lectin, conserved site (2);C-type lectin-like (2);C-type lectin (6);	0.072464	0.56097	N	0.000034	T	0.61714	0.2369	L	0.52823	1.66	0.40129	D	0.976696	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.59337	-0.7473	10	0.40728	T	0.16	-9.4297	7.9528	0.30025	0.1308:0.0:0.8692:0.0	.	230;245;230	Q8IWL1;G5E9J3;Q8IWL2	SFPA2_HUMAN;.;SFTA1_HUMAN	N	230;230;230;171;245;230	ENSP00000361382:D230N;ENSP00000381633:D230N;ENSP00000411102:D230N;ENSP00000361387:D171N;ENSP00000397082:D245N	ENSP00000361382:D230N	D	+	1	0	SFTPA1	81043816	0.998000	0.40836	0.905000	0.35620	0.045000	0.14185	2.629000	0.46485	0.783000	0.33636	0.297000	0.19635	GAT	.	.	none		0.572	SFTPA1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_005411	
OR5AU1	390445	hgsc.bcm.edu	37	14	21623290	21623290	+	Missense_Mutation	SNP	T	T	C	rs7145814	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21623290T>C	ENST00000304418.3	-	1	932	c.895A>G	c.(895-897)Atc>Gtc	p.I299V		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	299			I -> V (in dbSNP:rs7145814). {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)			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)		AAGAGGCAGATGGCAGTGAGG	0.512													C|||	3622	0.723243	0.851	0.696	5008	,	,		21362	0.496		0.7942	False		,,,				2504	0.7311				p.I299V		Atlas-SNP	.											.	OR5AU1	46	.	0			c.A895G						PASS	.	C	VAL/ILE	3604,802	751.0+/-412.2	1482,640,81	160.0	134.0	143.0		895	2.6	0.3	14	dbSNP_116	143	6781,1819	732.6+/-406.8	2687,1407,206	yes	missense	OR5AU1	NM_001004731.1	29	4169,2047,287	CC,CT,TT		21.1512,18.2025,20.1522	benign	299/363	21623290	10385,2621	2203	4300	6503	SO:0001583	missense	390445	exon1			GGCAGATGGCAGT	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.895A>G	14.37:g.21623290T>C	ENSP00000302057:p.Ile299Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001004731	B2RP78|Q6IEU2|Q96R10	Missense_Mutation	SNP	ENST00000304418.3	37	CCDS32042.1	1562	0.7152014652014652	419	0.8516260162601627	263	0.7265193370165746	280	0.48951048951048953	600	0.7915567282321899	t	0.006	-2.064153	0.00386	0.817975	0.788488	ENSG00000169327	ENST00000304418	T	0.00009	9.46	4.48	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00380	-1.58	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41142	-0.9525	8	0.02654	T	1	.	9.1103	0.36723	0.0:0.7716:0.1371:0.0913	rs7145814;rs52792926;rs59287100;rs7145814	299	Q8NGC0	O5AU1_HUMAN	V	299	ENSP00000302057:I299V	ENSP00000302057:I299V	I	-	1	0	OR5AU1	20693130	0.385000	0.25172	0.251000	0.24312	0.588000	0.36517	1.190000	0.32126	0.160000	0.19432	-1.297000	0.01338	ATC	T|0.240;C|0.760	0.760	strong		0.512	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1		
DHDH	27294	hgsc.bcm.edu	37	19	49438363	49438363	+	Missense_Mutation	SNP	G	G	A	rs2270941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49438363G>A	ENST00000221403.2	+	2	237	c.197G>A	c.(196-198)aGc>aAc	p.S66N	DHDH_ENST00000522614.1_Missense_Mutation_p.S66N|DHDH_ENST00000523250.1_Missense_Mutation_p.S66N	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	66			S -> N (in dbSNP:rs2270941).		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)		AAGGACCCGAGCGTGGGTGAG	0.692													A|||	2561	0.511382	0.7958	0.4308	5008	,	,		14256	0.5456		0.2535	False		,,,				2504	0.4141				p.S66N		Atlas-SNP	.											DHDH,NS,carcinoma,0,1	DHDH	35	1	0			c.G197A						PASS	.	A	ASN/SER	3081,1311		1099,883,214	22.0	17.0	19.0		197	4.7	0.3	19	dbSNP_100	19	1842,6740		209,1424,2658	yes	missense	DHDH	NM_014475.3	46	1308,2307,2872	AA,AG,GG		21.4635,29.8497,37.9451	benign	66/335	49438363	4923,8051	2196	4291	6487	SO:0001583	missense	27294	exon2			ACCCGAGCGTGGG	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.197G>A	19.37:g.49438363G>A	ENSP00000221403:p.Ser66Asn	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	1018	0.4661172161172161	367	0.7459349593495935	141	0.38950276243093923	305	0.5332167832167832	205	0.2704485488126649	A	8.755	0.922187	0.17982	0.701503	0.214635	ENSG00000104808	ENST00000221403;ENST00000523250;ENST00000522614	T;T;T	0.21361	2.01;2.01;2.01	4.74	4.74	0.60224	Oxidoreductase, N-terminal (1);NAD(P)-binding domain (1);	0.254938	0.43919	N	0.000502	T	0.00012	0.0000	N	0.00966	-1.09	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38045	-0.9679	9	0.02654	T	1	-20.6016	8.936	0.35700	0.9105:0.0:0.0895:0.0	rs2270941;rs17239182;rs52799839;rs58054167;rs2270941	66	Q9UQ10	DHDH_HUMAN	N	66	ENSP00000221403:S66N;ENSP00000428935:S66N;ENSP00000428672:S66N	ENSP00000221403:S66N	S	+	2	0	DHDH	54130175	0.322000	0.24634	0.282000	0.24776	0.680000	0.39746	4.951000	0.63610	0.951000	0.37770	-0.556000	0.04195	AGC	G|0.533;A|0.467	0.467	strong		0.692	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
GPLD1	2822	hgsc.bcm.edu	37	6	24437408	24437408	+	Silent	SNP	G	G	A	rs61733145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:24437408G>A	ENST00000230036.1	-	21	2240	c.2130C>T	c.(2128-2130)agC>agT	p.S710S		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	710					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						GGCGGTCTCCGCTGAAGGTGC	0.557													G|||	120	0.0239617	0.028	0.0375	5008	,	,		19974	0.002		0.0398	False		,,,				2504	0.0153				p.S710S		Atlas-SNP	.											GPLD1,NS,adenoma,0,1	GPLD1	91	1	0			c.C2130T						PASS	.	G		134,4272	95.7+/-134.4	3,128,2072	112.0	96.0	102.0		2130	-6.3	0.9	6	dbSNP_129	102	409,8191	129.5+/-187.6	5,399,3896	no	coding-synonymous	GPLD1	NM_001503.2		8,527,5968	AA,AG,GG		4.7558,3.0413,4.175		710/841	24437408	543,12463	2203	4300	6503	SO:0001819	synonymous_variant	2822	exon21			GTCTCCGCTGAAG	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.2130C>T	6.37:g.24437408G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Silent	SNP	ENST00000230036.1	37	CCDS4553.1																																																																																			G|0.961;A|0.039	0.039	strong		0.557	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
ANKEF1	63926	hgsc.bcm.edu	37	20	10032413	10032413	+	Silent	SNP	T	T	G	rs683145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:10032413T>G	ENST00000378380.3	+	7	2075	c.1746T>G	c.(1744-1746)gcT>gcG	p.A582A	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Silent_p.A582A|ANKEF1_ENST00000488991.1_3'UTR	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	582							calcium ion binding (GO:0005509)										AATCTGGAGCTTTAATAGATG	0.393													T|||	1005	0.200679	0.2791	0.1585	5008	,	,		17241	0.0069		0.2744	False		,,,				2504	0.2485				p.A582A		Atlas-SNP	.											.	.	.	.	0			c.T1746G						PASS	.	T	,	1192,3214	418.7+/-338.4	160,872,1171	89.0	83.0	85.0		1746,1746	-4.1	0.0	20	dbSNP_83	85	2415,6185	400.5+/-346.8	344,1727,2229	no	coding-synonymous,coding-synonymous	ANKRD5	NM_022096.4,NM_198798.1	,	504,2599,3400	GG,GT,TT		28.0814,27.054,27.7334	,	582/777,582/777	10032413	3607,9399	2203	4300	6503	SO:0001819	synonymous_variant	63926	exon7			TGGAGCTTTAATA	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1746T>G	20.37:g.10032413T>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	29	0.371795	NM_198798	B3KUQ0|Q9H6Y9	Silent	SNP	ENST00000378380.3	37	CCDS13108.1																																																																																			T|0.752;G|0.248	0.248	strong		0.393	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
GJA4	2701	hgsc.bcm.edu	37	1	35260769	35260769	+	Missense_Mutation	SNP	C	C	T	rs1764391	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	44	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	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	
CLHC1	130162	hgsc.bcm.edu	37	2	55404883	55404883	+	Silent	SNP	T	T	C	rs13032294	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:55404883T>C	ENST00000401408.1	-	12	1764	c.1419A>G	c.(1417-1419)caA>caG	p.Q473Q	CLHC1_ENST00000406437.2_Silent_p.Q24Q|CLHC1_ENST00000406076.1_Silent_p.Q351Q|CLHC1_ENST00000494539.1_5'UTR|CLHC1_ENST00000407122.1_Silent_p.Q473Q	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	473								p.Q473Q(2)									TTAATTCAACTTGGGGACATG	0.343													T|||	374	0.0746805	0.09	0.0288	5008	,	,		18576	0.1181		0.0497	False		,,,				2504	0.0675				p.Q473Q		Atlas-SNP	.											C2orf63_ENST00000407122,NS,carcinoma,0,2	.	.	2	2	Substitution - coding silent(2)	stomach(2)	c.A1419G						PASS	.	T	,	372,4034	188.1+/-214.6	18,336,1849	86.0	83.0	84.0		1053,1419	-0.8	0.0	2	dbSNP_121	84	468,8130	137.1+/-194.1	17,434,3848	no	coding-synonymous,coding-synonymous	C2orf63	NM_001135598.1,NM_152385.2	,	35,770,5697	CC,CT,TT		5.4431,8.443,6.4596	,	351/465,473/587	55404883	840,12164	2203	4299	6502	SO:0001819	synonymous_variant	130162	exon12			TTCAACTTGGGGA		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.1419A>G	2.37:g.55404883T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_152385	B2RDV1|Q53R93|Q8N403	Silent	SNP	ENST00000401408.1	37	CCDS33201.1																																																																																			T|0.932;C|0.068	0.068	strong		0.343	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056072	26056072	+	Silent	SNP	G	G	C	rs8384	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26056072G>C	ENST00000343677.2	-	1	627	c.585C>G	c.(583-585)ccC>ccG	p.P195P		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	195					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						TAGCGGCCTTGGGCTTCACAG	0.537													G|||	582	0.116214	0.0484	0.121	5008	,	,		16450	0.1627		0.1958	False		,,,				2504	0.0746				p.P195P		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.C585G						PASS	.	G		316,4090	166.9+/-198.0	9,298,1896	73.0	78.0	77.0		585	1.2	1.0	6	dbSNP_52	77	1881,6719	331.9+/-319.9	207,1467,2626	no	coding-synonymous	HIST1H1C	NM_005319.3		216,1765,4522	CC,CG,GG		21.8721,7.172,16.8922		195/214	26056072	2197,10809	2203	4300	6503	SO:0001819	synonymous_variant	3006	exon1			GGCCTTGGGCTTC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.585C>G	6.37:g.26056072G>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_005319	A8K4I2	Silent	SNP	ENST00000343677.2	37	CCDS4577.1																																																																																			G|0.834;C|0.166	0.166	strong		0.537	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163831	73163831	+	Silent	SNP	C	C	T	rs2931423	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73163831C>T	ENST00000426542.2	+	18	2303	c.2283C>T	c.(2281-2283)ggC>ggT	p.G761G	ARHGEF28_ENST00000437974.1_Silent_p.G761G|ARHGEF28_ENST00000296794.6_Silent_p.G761G|ARHGEF28_ENST00000296799.4_Silent_p.G448G|ARHGEF28_ENST00000513042.2_Silent_p.G761G|ARHGEF28_ENST00000545377.1_Silent_p.G761G|ARHGEF28_ENST00000287898.5_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	110	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	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		
MON2	23041	hgsc.bcm.edu	37	12	62965212	62965212	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:62965212C>T	ENST00000393632.2	+	30	4755	c.4364C>T	c.(4363-4365)tCt>tTt	p.S1455F	MON2_ENST00000552738.1_Missense_Mutation_p.S1426F|MON2_ENST00000393630.3_Missense_Mutation_p.S1456F|MON2_ENST00000546600.1_Missense_Mutation_p.S1455F|MON2_ENST00000393629.2_Missense_Mutation_p.S1449F|MON2_ENST00000280379.6_Missense_Mutation_p.S1456F	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1455					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TCCTGCCCTTCTGAAAGCACA	0.383																																					p.S1455F		Atlas-SNP	.											.	MON2	160	.	0			c.C4364T						PASS	.						129.0	135.0	133.0					12																	62965212		2203	4300	6503	SO:0001583	missense	23041	exon30			GCCCTTCTGAAAG		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4364C>T	12.37:g.62965212C>T	ENSP00000377252:p.Ser1455Phe	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	4	0.04	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607945	0.87258	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.49	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.73289	0.3568	L	0.58810	1.83	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.994;0.996;0.984;0.998	P;D;D;P;D	0.65773	0.868;0.938;0.938;0.809;0.938	T	0.73294	-0.4028	9	.	.	.	-15.3521	14.0268	0.64590	0.0:0.9272:0.0:0.0728	.	1449;1426;1455;324;1455	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	F	1455;1456;1456;1455;1426;1449	ENSP00000377252:S1455F;ENSP00000377250:S1456F;ENSP00000280379:S1456F;ENSP00000447407:S1455F;ENSP00000449215:S1426F;ENSP00000377249:S1449F	.	S	+	2	0	MON2	61251479	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.814000	0.86154	1.316000	0.45131	0.650000	0.86243	TCT	.	.	none		0.383	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
SPTA1	6708	hgsc.bcm.edu	37	1	158604391	158604391	+	Missense_Mutation	SNP	T	T	C	rs16830483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158604391T>C	ENST00000368147.4	-	39	5687	c.5507A>G	c.(5506-5508)aAt>aGt	p.N1836S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1836			N -> S (in dbSNP:rs16830483).		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)					ATTCTTTTCATTGATCCAAGC	0.423													T|||	270	0.0539137	0.1407	0.0303	5008	,	,		22090	0.0		0.0229	False		,,,				2504	0.0409				p.N1836S		Atlas-SNP	.											.	SPTA1	720	.	0			c.A5507G						PASS	.	T	SER/ASN	544,3370		27,490,1440	197.0	180.0	185.0		5507	1.4	0.1	1	dbSNP_123	185	125,8155		2,121,4017	yes	missense	SPTA1	NM_003126.2	46	29,611,5457	CC,CT,TT		1.5097,13.8988,5.4863	benign	1836/2420	158604391	669,11525	1957	4140	6097	SO:0001583	missense	6708	exon39			TTTTCATTGATCC	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.5507A>G	1.37:g.158604391T>C	ENSP00000357129:p.Asn1836Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	101	0.04624542124542125	75	0.1524390243902439	10	0.027624309392265192	0	0.0	16	0.021108179419525065	T	10.38	1.332942	0.24167	0.138988	0.015097	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48836	0.8;0.8	5.64	1.39	0.22231	.	1.056520	0.07576	N	0.919371	T	0.05273	0.0140	N	0.03016	-0.435	0.19575	N	0.999963	B	0.09022	0.002	B	0.12156	0.007	T	0.36648	-0.9739	10	0.06365	T	0.9	.	3.7159	0.08438	0.0:0.4471:0.1822:0.3708	rs16830483;rs52794569;rs61613472;rs16830483	1836	P02549	SPTA1_HUMAN	S	1836	ENSP00000357130:N1836S;ENSP00000357129:N1836S	ENSP00000357129:N1836S	N	-	2	0	SPTA1	156871015	0.982000	0.34865	0.086000	0.20670	0.956000	0.61745	0.751000	0.26348	0.447000	0.26695	-0.248000	0.11899	AAT	T|0.947;C|0.053	0.053	strong		0.423	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
COG3	83548	hgsc.bcm.edu	37	13	46067593	46067593	+	Silent	SNP	G	G	A	rs2985959	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46067593G>A	ENST00000349995.5	+	12	1411	c.1299G>A	c.(1297-1299)gaG>gaA	p.E433E	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	433					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.E433E(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TTAAAAATGAGGTGCTTGAAG	0.343													G|||	1805	0.360423	0.1551	0.3818	5008	,	,		15875	0.495		0.4175	False		,,,				2504	0.4254				p.E433E	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											COG3,NS,carcinoma,0,1	COG3	52	1	1	Substitution - coding silent(1)	stomach(1)	c.G1299A						PASS	.	G		996,3410	373.7+/-320.9	117,762,1324	152.0	142.0	145.0		1299	3.7	1.0	13	dbSNP_101	145	3797,4803	538.1+/-383.3	856,2085,1359	no	coding-synonymous	COG3	NM_031431.3		973,2847,2683	AA,AG,GG		44.1512,22.6055,36.8522		433/829	46067593	4793,8213	2203	4300	6503	SO:0001819	synonymous_variant	83548	exon12			AAATGAGGTGCTT	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1299G>A	13.37:g.46067593G>A		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Silent	SNP	ENST00000349995.5	37	CCDS9398.1																																																																																			G|0.624;A|0.376	0.376	strong		0.343	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
ZNF202	7753	hgsc.bcm.edu	37	11	123600380	123600380	+	Missense_Mutation	SNP	C	C	T	rs145114988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123600380C>T	ENST00000529691.1	-	3	775	c.556G>A	c.(556-558)Gca>Aca	p.A186T	ZNF202_ENST00000336139.4_Missense_Mutation_p.A186T|ZNF202_ENST00000530393.1_Missense_Mutation_p.A186T			O95125	ZN202_HUMAN	zinc finger protein 202	186					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)		TCTGCCGGTGCCCCCAGATCT	0.612													C|||	5	0.000998403	0.0	0.0	5008	,	,		16399	0.0		0.004	False		,,,				2504	0.001				p.A186T		Atlas-SNP	.											.	ZNF202	72	.	0			c.G556A						PASS	.	C	THR/ALA	3,4401	6.2+/-15.9	0,3,2199	56.0	50.0	52.0		556	-0.4	0.0	11	dbSNP_134	52	31,8567	20.4+/-63.3	0,31,4268	yes	missense	ZNF202	NM_003455.2	58	0,34,6467	TT,TC,CC		0.3605,0.0681,0.2615	benign	186/649	123600380	34,12968	2202	4299	6501	SO:0001583	missense	7753	exon5			CCGGTGCCCCCAG	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.556G>A	11.37:g.123600380C>T	ENSP00000433881:p.Ala186Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Missense_Mutation	SNP	ENST00000529691.1	37	CCDS8443.1	.	.	.	.	.	.	.	.	.	.	C	2.375	-0.343496	0.05243	6.81E-4	0.003605	ENSG00000166261	ENST00000336139;ENST00000530393;ENST00000529691	T;T;T	0.06218	3.33;3.33;3.33	4.47	-0.403	0.12400	.	1.393600	0.04780	N	0.429575	T	0.02649	0.0080	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42949	-0.9421	10	0.10111	T	0.7	-0.2021	4.6895	0.12774	0.0:0.3235:0.415:0.2615	.	186	O95125	ZN202_HUMAN	T	186	ENSP00000337724:A186T;ENSP00000432504:A186T;ENSP00000433881:A186T	ENSP00000337724:A186T	A	-	1	0	ZNF202	123105590	0.000000	0.05858	0.049000	0.19019	0.384000	0.30261	-0.596000	0.05720	0.008000	0.14787	-0.310000	0.09108	GCA	C|0.998;T|0.002	0.002	strong		0.612	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
AMPH	273	hgsc.bcm.edu	37	7	38431481	38431481	+	Silent	SNP	C	C	A	rs1058655	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:38431481C>A	ENST00000356264.2	-	19	1961	c.1746G>T	c.(1744-1746)ccG>ccT	p.P582P	AMPH_ENST00000428293.2_Silent_p.P540P|AMPH_ENST00000325590.5_Silent_p.P540P|AMPH_ENST00000471913.1_5'Flank	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	582					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						TAGCCAGCTCCGGTGTCTCGC	0.617													C|||	663	0.132388	0.0401	0.1945	5008	,	,		13936	0.1736		0.1759	False		,,,				2504	0.1258				p.P582P		Atlas-SNP	.											.	AMPH	157	.	0			c.G1746T						PASS	.	C	,	259,4147	149.9+/-184.0	5,249,1949	56.0	51.0	53.0		1746,1620	-10.1	0.0	7	dbSNP_86	53	1851,6749	330.5+/-319.2	193,1465,2642	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	198,1714,4591	AA,AC,CC		21.5233,5.8783,16.2233	,	582/696,540/654	38431481	2110,10896	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			CAGCTCCGGTGTC		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1746G>T	7.37:g.38431481C>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1	337	0.1543040293040293	19	0.03861788617886179	67	0.1850828729281768	108	0.1888111888111888	143	0.18865435356200527	C	5.567	0.289367	0.10513	0.058783	0.215233	ENSG00000078053	ENST00000441628	.	.	.	5.24	-10.1	0.00402	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.5251	9.6967	0.40161	0.0:0.369:0.352:0.279	rs1058655;rs3199301;rs57321987;rs1058655	.	.	.	X	465	.	.	G	-	1	0	AMPH	38398006	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.106000	0.00602	-1.886000	0.01116	-1.937000	0.00501	GGA	C|0.852;A|0.148	0.148	strong		0.617	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
MAP2	4133	hgsc.bcm.edu	37	2	210558162	210558162	+	Missense_Mutation	SNP	G	G	A	rs741006	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	195	0	0		WXS	Illumina HiSeq	Phase_I	162	80	0.493827	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	
CUBN	8029	hgsc.bcm.edu	37	10	17130199	17130199	+	Silent	SNP	G	G	A	rs41289311	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:17130199G>A	ENST00000377833.4	-	15	1976	c.1911C>T	c.(1909-1911)ctC>ctT	p.L637L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	637	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CATGGTGCTCGAGGCTCAAGG	0.418													G|||	322	0.0642971	0.0113	0.0274	5008	,	,		17790	0.0179		0.0527	False		,,,				2504	0.2219				p.L637L		Atlas-SNP	.											.	CUBN	515	.	0			c.C1911T						PASS	.	G		53,4353	52.9+/-88.7	0,53,2150	106.0	97.0	100.0		1911	0.0	1.0	10	dbSNP_127	100	340,8260	115.9+/-175.7	10,320,3970	no	coding-synonymous	CUBN	NM_001081.3		10,373,6120	AA,AG,GG		3.9535,1.2029,3.0217		637/3624	17130199	393,12613	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon15			GTGCTCGAGGCTC	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.1911C>T	10.37:g.17130199G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	72	0.637168	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			G|0.968;A|0.032	0.032	strong		0.418	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
KDM5B	10765	hgsc.bcm.edu	37	1	202705455	202705455	+	Silent	SNP	G	G	C	rs1141109	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:202705455G>C	ENST00000367265.3	-	21	4314	c.3150C>G	c.(3148-3150)ccC>ccG	p.P1050P	KDM5B_ENST00000367264.2_Silent_p.P1086P	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1050					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						TCAGATGTACGGGGATAGATC	0.428													C|||	3203	0.639577	0.323	0.8343	5008	,	,		20197	0.7837		0.7714	False		,,,				2504	0.6452				p.P1050P		Atlas-SNP	.											.	KDM5B	166	.	0			c.C3150G						PASS	.	C		1659,2747	658.0+/-400.3	320,1019,864	107.0	100.0	102.0		3150	-11.3	0.1	1	dbSNP_86	102	6686,1914	338.7+/-322.9	2615,1456,229	no	coding-synonymous	KDM5B	NM_006618.3		2935,2475,1093	CC,CG,GG		22.2558,37.6532,35.8373		1050/1545	202705455	8345,4661	2203	4300	6503	SO:0001819	synonymous_variant	10765	exon21			ATGTACGGGGATA	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3150C>G	1.37:g.202705455G>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_006618	O95811|Q15752|Q9Y3Q5	Silent	SNP	ENST00000367265.3	37	CCDS30974.1																																																																																			T|0.000;G|0.349;C|0.651	0.651	strong		0.428	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
RSPH14	27156	hgsc.bcm.edu	37	22	23482460	23482460	+	Silent	SNP	A	A	G	rs4822360	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:23482460A>G	ENST00000216036.4	-	2	344	c.148T>C	c.(148-150)Ttg>Ctg	p.L50L	RTDR1_ENST00000406876.1_Silent_p.L50L	NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		50								p.L50L(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		AGGTCACACAAGGCCATGAGG	0.577													G|||	2628	0.52476	0.6354	0.5706	5008	,	,		18083	0.4038		0.5547	False		,,,				2504	0.4366				p.L50L		Atlas-SNP	.											RTDR1,NS,carcinoma,0,1	RTDR1	39	1	1	Substitution - coding silent(1)	stomach(1)	c.T148C						PASS	.	G		2827,1579	493.4+/-362.7	899,1029,275	151.0	114.0	126.0		148	3.9	1.0	22	dbSNP_111	126	4819,3781	536.0+/-382.9	1365,2089,846	no	coding-synonymous	RTDR1	NM_014433.2		2264,3118,1121	GG,GA,AA		43.9651,35.8375,41.2117		50/349	23482460	7646,5360	2203	4300	6503	SO:0001819	synonymous_variant	27156	exon2			CACACAAGGCCAT																												ENST00000216036.4:c.148T>C	22.37:g.23482460A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_014433		Silent	SNP	ENST00000216036.4	37	CCDS13803.1																																																																																			A|0.436;G|0.564	0.564	strong		0.577	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1		
ZFHX3	463	hgsc.bcm.edu	37	16	72830539	72830539	+	Missense_Mutation	SNP	C	C	G	rs62051555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72830539C>G	ENST00000268489.5	-	9	6714	c.6042G>C	c.(6040-6042)caG>caC	p.Q2014H	ZFHX3_ENST00000397992.5_Missense_Mutation_p.Q1100H	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2014					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)				ACCTCTCGAGCTGTTTGAAAG	0.498													C|||	72	0.014377	0.0015	0.036	5008	,	,		12747	0.0		0.0427	False		,,,				2504	0.002				p.Q2014H		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G6042C						PASS	.	C	HIS/GLN,HIS/GLN	36,4360	40.0+/-72.8	0,36,2162	96.0	99.0	98.0		3300,6042	4.8	1.0	16	dbSNP_129	98	338,8262	113.7+/-173.7	11,316,3973	yes	missense,missense	ZFHX3	NM_001164766.1,NM_006885.3	24,24	11,352,6135	GG,GC,CC		3.9302,0.8189,2.8778	probably-damaging,probably-damaging	1100/2790,2014/3704	72830539	374,12622	2198	4300	6498	SO:0001583	missense	463	exon9			CTCGAGCTGTTTG	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.6042G>C	16.37:g.72830539C>G	ENSP00000268489:p.Gln2014His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	49	0.022435897435897436	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	32	0.04221635883905013	C	8.314	0.822681	0.16678	0.008189	0.039302	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.73575	-0.76;-0.74	5.75	4.79	0.61399	.	0.000000	0.47852	D	0.000219	T	0.29389	0.0732	N	0.19112	0.55	0.38167	D	0.939201	P	0.51653	0.947	P	0.44561	0.453	T	0.57487	-0.7803	10	0.48119	T	0.1	.	11.3527	0.49598	0.0:0.8606:0.0:0.1394	rs62051555	2014	Q15911	ZFHX3_HUMAN	H	2014;1100	ENSP00000268489:Q2014H;ENSP00000438926:Q1100H	ENSP00000268489:Q2014H	Q	-	3	2	ZFHX3	71388040	1.000000	0.71417	1.000000	0.80357	0.555000	0.35460	2.250000	0.43178	2.696000	0.92011	0.655000	0.94253	CAG	C|0.973;G|0.027	0.027	strong		0.498	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
TTN	7273	hgsc.bcm.edu	37	2	179579822	179579822	+	Silent	SNP	T	T	A	rs2562836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179579822T>A	ENST00000591111.1	-	88	25364	c.25140A>T	c.(25138-25140)ctA>ctT	p.L8380L	TTN_ENST00000589042.1_Silent_p.L8697L|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.L7453L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12554	Ig-like 66.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGATACTGGTTAGGAAGTTCT	0.463													A|||	2226	0.444489	0.4644	0.379	5008	,	,		20441	0.6577		0.2237	False		,,,				2504	0.4714				p.L8697L		Atlas-SNP	.											.	TTN	18412	.	0			c.A26091T						PASS	.	A	,,,	1560,2344		323,914,715	314.0	300.0	305.0		,22359,,	-4.7	0.0	2	dbSNP_100	305	1660,6618		160,1340,2639	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	483,2254,3354	AA,AT,TT		20.0532,39.959,26.4324	,,,	,7453/33424,,	179579822	3220,8962	1952	4139	6091	SO:0001819	synonymous_variant	7273	exon90			ACTGGTTAGGAAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25140A>T	2.37:g.179579822T>A		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	233	114	0.48927	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.630;N|0.001	.	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF280C	55609	hgsc.bcm.edu	37	X	129349295	129349295	+	Silent	SNP	T	T	G	rs209238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	89	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	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	
NPTXR	23467	hgsc.bcm.edu	37	22	39222627	39222627	+	Missense_Mutation	SNP	G	G	A	rs34637063	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39222627G>A	ENST00000333039.2	-	3	1099	c.976C>T	c.(976-978)Cgg>Tgg	p.R326W		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	326	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.R326W(1)		central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					GACCTGGACCGCAGCCACATG	0.632													G|||	8	0.00159744	0.0	0.0	5008	,	,		18002	0.0		0.006	False		,,,				2504	0.002				p.R326W	Pancreas(139;2521 3281 36965)	Atlas-SNP	.											NPTXR,colon,carcinoma,0,2	NPTXR	34	2	1	Substitution - Missense(1)	prostate(1)	c.C976T						scavenged	.	G	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	78.0	71.0	73.0		976	4.6	1.0	22	dbSNP_126	73	42,8558	27.9+/-77.7	2,38,4260	yes	missense	NPTXR	NM_014293.3	101	2,42,6459	AA,AG,GG		0.4884,0.0908,0.3537	probably-damaging	326/501	39222627	46,12960	2203	4300	6503	SO:0001583	missense	23467	exon3			TGGACCGCAGCCA	AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.976C>T	22.37:g.39222627G>A	ENSP00000327545:p.Arg326Trp	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_014293		Missense_Mutation	SNP	ENST00000333039.2	37	CCDS33647.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	21.8	4.196556	0.79015	9.08E-4	0.004884	ENSG00000221890	ENST00000333039	T	0.61627	0.09	4.64	4.64	0.57946	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.277072	0.35067	N	0.003476	T	0.67230	0.2871	M	0.79123	2.44	0.37765	D	0.926466	D	0.89917	1.0	D	0.75484	0.986	T	0.78892	-0.2025	9	0.87932	D	0	-56.6397	11.0963	0.48145	0.0:0.0:0.6934:0.3066	rs34637063	326	O95502	NPTXR_HUMAN	W	326	ENSP00000327545:R326W	ENSP00000327545:R326W	R	-	1	2	NPTXR	37552573	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	5.441000	0.66569	2.861000	0.98227	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.632	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318194.2	NM_014293	
SLC14A1	6563	hgsc.bcm.edu	37	18	43319274	43319274	+	Splice_Site	SNP	G	G	A	rs17675299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:43319274G>A	ENST00000321925.4	+	7	1042	c.810G>A	c.(808-810)gcG>gcA	p.A270A	SLC14A1_ENST00000402943.2_Splice_Site_p.A165A|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000535474.1_Splice_Site_p.A138A|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000591541.1_5'Flank|SLC14A1_ENST00000436407.3_Splice_Site_p.A326A|SLC14A1_ENST00000589700.1_Intron|SLC14A1_ENST00000415427.3_Splice_Site_p.A326A|SLC14A1_ENST00000586142.1_Splice_Site_p.A270A|SLC14A1_ENST00000502059.2_Splice_Site_p.A162A	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)	270					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						GCATAGCAGCGGGTGAGCACA	0.532													g|||	132	0.0263578	0.0023	0.0274	5008	,	,		18819	0.0		0.0646	False		,,,				2504	0.046				p.A326A		Atlas-SNP	.											.	SLC14A1	84	.	0			c.G978A						PASS	.	G	,,,	52,4354	52.3+/-87.9	0,52,2151	68.0	60.0	63.0		978,810,978,810	-0.1	1.0	18	dbSNP_123	63	585,8015	156.4+/-210.3	15,555,3730	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SLC14A1	NM_001128588.3,NM_001146036.2,NM_001146037.1,NM_015865.6	,,,	15,607,5881	AA,AG,GG		6.8023,1.1802,4.8977	,,,	326/446,270/390,326/446,270/390	43319274	637,12369	2203	4300	6503	SO:0001630	splice_region_variant	6563	exon6			AGCAGCGGGTGAG	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.811+1G>A	18.37:g.43319274G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	145	63	0.434483	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Silent	SNP	ENST00000321925.4	37	CCDS11925.1																																																																																			G|0.960;A|0.040	0.040	strong		0.532	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	Silent
TNPO3	23534	hgsc.bcm.edu	37	7	128641226	128641226	+	Silent	SNP	G	G	C	rs2305324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128641226G>C	ENST00000265388.5	-	6	902	c.759C>G	c.(757-759)ctC>ctG	p.L253L	TNPO3_ENST00000393245.1_Silent_p.L253L|TNPO3_ENST00000471234.1_Silent_p.L253L|TNPO3_ENST00000471166.1_Silent_p.L253L|TNPO3_ENST00000482320.1_Silent_p.L187L			Q9Y5L0	TNPO3_HUMAN	transportin 3	253					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						CAATGGCATAGAGAGCTGAGC	0.488													G|||	1712	0.341853	0.1218	0.3199	5008	,	,		18821	0.3988		0.4801	False		,,,				2504	0.454				p.L253L	Pancreas(147;583 2585 39696 52331)	Atlas-SNP	.											.	TNPO3	148	.	0			c.C759G						PASS	.	G	,	773,3633	314.7+/-293.7	63,647,1493	269.0	231.0	244.0		759,759	-1.9	1.0	7	dbSNP_100	244	4060,4540	559.5+/-387.4	940,2180,1180	no	coding-synonymous,coding-synonymous	TNPO3	NM_001191028.2,NM_012470.3	,	1003,2827,2673	CC,CG,GG		47.2093,17.5443,37.1598	,	253/860,253/924	128641226	4833,8173	2203	4300	6503	SO:0001819	synonymous_variant	23534	exon6			GGCATAGAGAGCT	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"""Importins"""	17103	protein-coding gene	gene with protein product	"""importin 12"""	610032	"""limb girdle muscular dystrophy 1F (autosomal dominant)"""	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.759C>G	7.37:g.128641226G>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Silent	SNP	ENST00000265388.5	37	CCDS5809.1																																																																																			G|0.635;C|0.365	0.365	strong		0.488	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470	
PCSK5	5125	hgsc.bcm.edu	37	9	78506145	78506145	+	Silent	SNP	G	G	A	rs7020560	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:78506145G>A	ENST00000545128.1	+	1	586	c.48G>A	c.(46-48)ctG>ctA	p.L16L	PCSK5_ENST00000376767.3_Silent_p.L16L|PCSK5_ENST00000376752.4_Silent_p.L16L	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	16					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						TGGACCTGCTGTGCGTGCTGG	0.711													G|||	583	0.116414	0.3396	0.0476	5008	,	,		11968	0.0		0.0825	False		,,,				2504	0.0184				p.L16L		Atlas-SNP	.											.	PCSK5	329	.	0			c.G48A						PASS	.	G	,	1279,3125		176,927,1099	26.0	33.0	30.0		48,48	3.1	1.0	9	dbSNP_116	30	589,8005		17,555,3725	no	coding-synonymous,coding-synonymous	PCSK5	NM_001190482.1,NM_006200.3	,	193,1482,4824	AA,AG,GG		6.8536,29.0418,14.3714	,	16/1861,16/914	78506145	1868,11130	2202	4297	6499	SO:0001819	synonymous_variant	5125	exon1			CCTGCTGTGCGTG		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.48G>A	9.37:g.78506145G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			G|0.877;A|0.123	0.123	strong		0.711	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500627	90500627	+	Missense_Mutation	SNP	G	G	A	rs34946554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90500627G>A	ENST00000325643.5	+	4	1291	c.1225G>A	c.(1225-1227)Gtg>Atg	p.V409M		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	409			V -> M (in dbSNP:rs34946554).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTTCTGGAACGTGTCAACCCA	0.562													.|||	391	0.0780751	0.2337	0.0375	5008	,	,		13818	0.0		0.0497	False		,,,				2504	0.0061				p.V409M		Atlas-SNP	.											.	.	.	.	0			c.G1225A						PASS	.	G	MET/VAL	804,3602	295.6+/-283.7	65,674,1464	88.0	65.0	73.0		1225	-4.3	0.0	9	dbSNP_126	73	380,8218	117.0+/-176.6	6,368,3925	yes	missense	C9orf79	NM_178828.4	21	71,1042,5389	AA,AG,GG		4.4196,18.2478,9.1049	benign	409/1446	90500627	1184,11820	2203	4299	6502	SO:0001583	missense	286234	exon4			TGGAACGTGTCAA	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.1225G>A	9.37:g.90500627G>A	ENSP00000322640:p.Val409Met	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	168	0.07692307692307693	112	0.22764227642276422	16	0.04419889502762431	0	0.0	40	0.052770448548812667	g	0.448	-0.895324	0.02491	0.182478	0.044196	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.03358	3.96	2.16	-4.31	0.03698	.	3.449120	0.01027	N	0.004060	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.22604	0.072;0.049	B;B	0.13407	0.009;0.004	T	0.43310	-0.9399	9	0.44086	T	0.13	.	2.3846	0.04363	0.1753:0.4386:0.2409:0.1453	rs34946554	409;61	Q6ZUB1;Q8NA33	CI079_HUMAN;.	M	409;61	ENSP00000322640:V409M	ENSP00000322640:V409M	V	+	1	0	C9orf79	89690447	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.326000	0.07965	-2.871000	0.00323	-1.752000	0.00675	GTG	G|0.915;A|0.085	0.085	strong		0.562	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
VPS41	27072	hgsc.bcm.edu	37	7	38796570	38796570	+	Silent	SNP	G	G	A	rs2240350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:38796570G>A	ENST00000310301.4	-	19	1617	c.1563C>T	c.(1561-1563)gaC>gaT	p.D521D	VPS41_ENST00000395969.2_Silent_p.D496D	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	521					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CATAGTTCTTGTCATAGGTGT	0.299													G|||	1794	0.358227	0.2549	0.5965	5008	,	,		16905	0.4206		0.3469	False		,,,				2504	0.2761				p.D521D		Atlas-SNP	.											.	VPS41	102	.	0			c.C1563T						PASS	.	G	,	1278,3126	433.5+/-343.6	186,906,1110	103.0	106.0	105.0		1563,1488	4.1	1.0	7	dbSNP_98	105	3076,5516	469.7+/-367.6	510,2056,1730	no	coding-synonymous,coding-synonymous	VPS41	NM_014396.3,NM_080631.3	,	696,2962,2840	AA,AG,GG		35.8007,29.0191,33.5026	,	521/855,496/830	38796570	4354,8642	2202	4296	6498	SO:0001819	synonymous_variant	27072	exon19			GTTCTTGTCATAG	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1563C>T	7.37:g.38796570G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																			G|0.643;A|0.357	0.357	strong		0.299	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
NEK2	4751	hgsc.bcm.edu	37	1	211836789	211836789	+	Silent	SNP	T	T	C	rs12031285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:211836789T>C	ENST00000366999.4	-	8	1455	c.1317A>G	c.(1315-1317)agA>agG	p.R439R	NEK2_ENST00000462283.1_5'UTR|NEK2_ENST00000540251.1_Silent_p.R396R	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	439	Interaction with PCNT.|Interaction with SAV1 and STK3/MST2.|Necessary for interaction with MAD1L1.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		CCAGGATCTGTCTGCTTTTCA	0.463													T|||	1550	0.309505	0.3782	0.3501	5008	,	,		18557	0.2629		0.2286	False		,,,				2504	0.319				p.R439R		Atlas-SNP	.											.	NEK2	49	.	0			c.A1317G						PASS	.	T	,	1590,2816	486.4+/-360.6	301,988,914	43.0	39.0	41.0		,1317	-7.9	0.5	1	dbSNP_120	41	1976,6624	341.9+/-324.3	234,1508,2558	no	intron,coding-synonymous	NEK2	NM_001204182.1,NM_002497.3	,	535,2496,3472	CC,CT,TT		22.9767,36.0872,27.4181	,	,439/446	211836789	3566,9440	2203	4300	6503	SO:0001819	synonymous_variant	4751	exon8			GATCTGTCTGCTT	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"""HsPK 21"", ""protein phosphatase 1, regulatory subunit 111"""	604043	"""NIMA (never in mitosis gene a)-related kinase 2"""			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.1317A>G	1.37:g.211836789T>C		Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	308	143	0.464286	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Silent	SNP	ENST00000366999.4	37	CCDS1500.1																																																																																			T|0.733;C|0.267	0.267	strong		0.463	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
PTGS1	5742	hgsc.bcm.edu	37	9	125143973	125143973	+	Missense_Mutation	SNP	C	C	A	rs5789	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125143973C>A	ENST00000362012.2	+	7	714	c.709C>A	c.(709-711)Ctg>Atg	p.L237M	PTGS1_ENST00000223423.4_Missense_Mutation_p.L237M|PTGS1_ENST00000373698.5_Missense_Mutation_p.L128M|PTGS1_ENST00000540753.1_Missense_Mutation_p.L212M	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)	237			L -> M (in dbSNP:rs5789). {ECO:0000269|PubMed:15308583, ECO:0000269|Ref.8}.		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)			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)	TGGAGACAATCTGGAGCGTCA	0.582													C|||	65	0.0129792	0.0008	0.0274	5008	,	,		17236	0.0		0.0348	False		,,,				2504	0.0102				p.L237M		Atlas-SNP	.											.	PTGS1	84	.	0			c.C709A	GRCh37	CM071954	PTGS1	M	rs5789	PASS	.	C	MET/LEU,MET/LEU	21,4385	29.0+/-57.7	0,21,2182	52.0	51.0	52.0		709,709	4.8	1.0	9	dbSNP_52	52	242,8358	97.5+/-159.1	4,234,4062	yes	missense,missense	PTGS1	NM_000962.2,NM_080591.1	15,15	4,255,6244	AA,AC,CC		2.814,0.4766,2.0221	benign,benign	237/600,237/563	125143973	263,12743	2203	4300	6503	SO:0001583	missense	5742	exon7			GACAATCTGGAGC	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.709C>A	9.37:g.125143973C>A	ENSP00000354612:p.Leu237Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	37	CCDS6842.1	39	0.017857142857142856	0	0.0	14	0.03867403314917127	0	0.0	25	0.032981530343007916	C	15.52	2.858868	0.51376	0.004766	0.02814	ENSG00000095303	ENST00000540753;ENST00000362012;ENST00000223423;ENST00000426608;ENST00000373698	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	4.82	4.82	0.62117	.	0.067485	0.64402	D	0.000009	T	0.56187	0.1968	M	0.86420	2.815	0.58432	D	0.999999	D;B;B	0.76494	0.999;0.37;0.338	D;B;B	0.79108	0.992;0.177;0.26	T	0.75233	-0.3390	10	0.56958	D	0.05	-15.6693	10.6416	0.45596	0.0:0.9131:0.0:0.0869	rs5789;rs3842796;rs4987007;rs57008519;rs5789	212;237;237	B4DHQ2;P23219;P23219-2	.;PGH1_HUMAN;.	M	212;237;237;131;128	ENSP00000437709:L212M;ENSP00000354612:L237M;ENSP00000223423:L237M;ENSP00000411606:L131M;ENSP00000362802:L128M	ENSP00000223423:L237M	L	+	1	2	PTGS1	124183794	0.981000	0.34729	0.968000	0.41197	0.909000	0.53808	2.567000	0.45956	2.505000	0.84491	0.555000	0.69702	CTG	C|0.979;A|0.021	0.021	strong		0.582	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1		
RYR3	6263	hgsc.bcm.edu	37	15	34113010	34113010	+	Silent	SNP	C	C	T	rs2288613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:34113010C>T	ENST00000389232.4	+	78	10882	c.10812C>T	c.(10810-10812)ttC>ttT	p.F3604F	RYR3_ENST00000415757.3_Silent_p.F3599F	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3604					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)		AAAAAACATTCGAAGTAAGTT	0.433													c|||	1877	0.3748	0.3048	0.3689	5008	,	,		21183	0.3026		0.5159	False		,,,				2504	0.4029				p.F3604F		Atlas-SNP	.											RYR3,NS,carcinoma,0,1	RYR3	760	1	0			c.C10812T						PASS	.	T		1172,2602		208,756,923	64.0	56.0	59.0		10812	-1.0	1.0	15	dbSNP_100	59	4250,3992		1095,2060,966	no	coding-synonymous	RYR3	NM_001036.3		1303,2816,1889	TT,TC,CC		48.4348,31.0546,45.1232		3604/4871	34113010	5422,6594	1887	4121	6008	SO:0001819	synonymous_variant	6263	exon78			AACATTCGAAGTA		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.10812C>T	15.37:g.34113010C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			C|0.577;N|0.001	.	strong		0.433	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
MYOM3	127294	hgsc.bcm.edu	37	1	24416070	24416070	+	Silent	SNP	G	G	C	rs7533060	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24416070G>C	ENST00000374434.3	-	14	1734	c.1572C>G	c.(1570-1572)ccC>ccG	p.P524P	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000329601.7_Silent_p.P524P|MYOM3_ENST00000330966.7_Silent_p.P525P|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	524	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CCCGGGGGCTGGGCTCCTCCC	0.612													C|||	2507	0.500599	0.4561	0.4078	5008	,	,		17607	0.7321		0.5	False		,,,				2504	0.3885				p.P524P		Atlas-SNP	.											.	MYOM3	131	.	0			c.C1572G						PASS	.	C		1668,2232		381,906,663	29.0	33.0	31.0		1572	-7.1	0.0	1	dbSNP_116	31	4075,4177		1011,2053,1062	no	coding-synonymous	MYOM3	NM_152372.3		1392,2959,1725	CC,CG,GG		49.382,42.7692,47.2597		524/1438	24416070	5743,6409	1950	4126	6076	SO:0001819	synonymous_variant	127294	exon14			GGGGCTGGGCTCC	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.1572C>G	1.37:g.24416070G>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			G|0.447;C|0.553	0.553	strong		0.612	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
CYP3A43	64816	hgsc.bcm.edu	37	7	99447241	99447241	+	Silent	SNP	T	T	C	rs800667	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:99447241T>C	ENST00000354829.2	+	7	697	c.594T>C	c.(592-594)aaT>aaC	p.N198N	CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000342499.4_Missense_Mutation_p.S61P|CYP3A43_ENST00000312017.5_Silent_p.N198N|CYP3A43_ENST00000417625.1_Intron|CYP3A43_ENST00000222382.5_Silent_p.N198N|CYP3A43_ENST00000415413.1_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	149	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	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		
MACF1	23499	hgsc.bcm.edu	37	1	39908506	39908506	+	Missense_Mutation	SNP	G	G	A	rs587404	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:39908506G>A	ENST00000372915.3	+	77	19009	c.18922G>A	c.(18922-18924)Gcc>Acc	p.A6308T	MACF1_ENST00000545844.1_Missense_Mutation_p.A4350T|MACF1_ENST00000539005.1_Missense_Mutation_p.A4220T|MACF1_ENST00000289893.4_Missense_Mutation_p.A4852T|MACF1_ENST00000567887.1_Missense_Mutation_p.A6446T|MACF1_ENST00000361689.2_Missense_Mutation_p.A4350T|MACF1_ENST00000564288.1_Missense_Mutation_p.A6409T|MACF1_ENST00000317713.7_Missense_Mutation_p.A4350T			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	99	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	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	
MRPL9	65005	hgsc.bcm.edu	37	1	151733327	151733327	+	Missense_Mutation	SNP	T	T	C	rs74228558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:151733327T>C	ENST00000368830.3	-	6	721	c.637A>G	c.(637-639)Atc>Gtc	p.I213V	OAZ3_ENST00000321531.5_5'Flank|RP11-98D18.15_ENST00000601684.1_RNA|MRPL9_ENST00000368829.3_Missense_Mutation_p.I179V|OAZ3_ENST00000315067.8_5'Flank|MRPL9_ENST00000467306.1_5'UTR|OAZ3_ENST00000479764.1_5'Flank|OAZ3_ENST00000453029.2_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	213					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CACCGTGTGATAGGCTCTTCT	0.378													T|||	349	0.0696885	0.0794	0.0605	5008	,	,		15549	0.0228		0.1123	False		,,,				2504	0.0675				p.I213V		Atlas-SNP	.											.	MRPL9	21	.	0			c.A637G						PASS	.	T	VAL/ILE	350,4056	180.8+/-209.0	11,328,1864	93.0	89.0	91.0		637	5.3	1.0	1	dbSNP_130	91	937,7663	207.7+/-249.4	55,827,3418	yes	missense	MRPL9	NM_031420.2	29	66,1155,5282	CC,CT,TT		10.8953,7.9437,9.8954	benign	213/268	151733327	1287,11719	2203	4300	6503	SO:0001583	missense	65005	exon6			GTGTGATAGGCTC	AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"""Mitochondrial ribosomal proteins / large subunits"""	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.637A>G	1.37:g.151733327T>C	ENSP00000357823:p.Ile213Val	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	21	7	0.333333	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	154	0.07051282051282051	38	0.07723577235772358	23	0.06353591160220995	12	0.02097902097902098	81	0.10686015831134564	T	14.47	2.545365	0.45280	0.079437	0.108953	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.48201	0.82;1.31	5.27	5.27	0.74061	.	0.071468	0.56097	D	0.000025	T	0.29783	0.0744	M	0.65975	2.015	0.27917	P	0.9383854	P	0.40360	0.714	B	0.35039	0.194	T	0.42032	-0.9475	9	0.49607	T	0.09	-11.3137	11.5085	0.50481	0.0:0.0:0.0:1.0	.	213	Q9BYD2	RM09_HUMAN	V	213;179	ENSP00000357823:I213V;ENSP00000357822:I179V	ENSP00000357822:I179V	I	-	1	0	MRPL9	149999951	1.000000	0.71417	0.998000	0.56505	0.933000	0.57130	3.736000	0.55052	2.198000	0.70561	0.533000	0.62120	ATC	T|0.909;C|0.091	0.091	strong		0.378	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420	
DNAH14	127602	hgsc.bcm.edu	37	1	225237950	225237950	+	Missense_Mutation	SNP	A	A	G	rs78320839	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225237950A>G	ENST00000445597.2	+	12	1864	c.1864A>G	c.(1864-1866)Atc>Gtc	p.I622V	DNAH14_ENST00000439375.2_Missense_Mutation_p.I651V|DNAH14_ENST00000430092.1_Missense_Mutation_p.I651V			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	622					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						CCAGCTGTCTATCTTCATTGA	0.343													A|||	43	0.00858626	0.0008	0.0101	5008	,	,		16907	0.0129		0.007	False		,,,				2504	0.0153				p.I651V		Atlas-SNP	.											.	DNAH14	300	.	0			c.A1951G						PASS	.	A	VAL/ILE	2,1382		0,2,690	169.0	139.0	148.0		1951	-4.1	0.0	1	dbSNP_131	148	58,3124		1,56,1534	yes	missense	DNAH14	NM_001373.1	29	1,58,2224	GG,GA,AA		1.8228,0.1445,1.3141	benign	651/4516	225237950	60,4506	692	1591	2283	SO:0001583	missense	127602	exon16			CTGTCTATCTTCA	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.1864A>G	1.37:g.225237950A>G	ENSP00000409472:p.Ile622Val	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	193	84	0.435233	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		20	0.009157509157509158	1	0.0020325203252032522	6	0.016574585635359115	9	0.015734265734265736	4	0.005277044854881266	A	14.53	2.563703	0.45694	0.001445	0.018228	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.27890	2.61;1.64;1.64	5.49	-4.13	0.03904	.	.	.	.	.	T	0.06050	0.0157	N	0.08118	0	0.09310	N	0.999998	B	0.10296	0.003	B	0.12156	0.007	T	0.32134	-0.9918	9	0.21014	T	0.42	.	7.8316	0.29347	0.4385:0.1253:0.4362:0.0	.	651	Q0VDD8-4	.	V	622;651;651	ENSP00000409472:I622V;ENSP00000414402:I651V;ENSP00000392061:I651V	ENSP00000414402:I651V	I	+	1	0	DNAH14	223304573	0.000000	0.05858	0.005000	0.12908	0.439000	0.31926	-1.628000	0.02031	-0.704000	0.05042	0.338000	0.21704	ATC	A|0.991;G|0.009	0.009	strong		0.343	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
C16orf59	80178	hgsc.bcm.edu	37	16	2512523	2512523	+	Silent	SNP	G	G	A	rs3810794	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2512523G>A	ENST00000361837.4	+	7	923	c.858G>A	c.(856-858)tcG>tcA	p.S286S	RP11-715J22.2_ENST00000563775.1_RNA|C16orf59_ENST00000483320.1_Silent_p.S119S|C16orf59_ENST00000563531.1_Silent_p.S286S|C16orf59_ENST00000569496.1_Silent_p.S286S|RP11-715J22.4_ENST00000566085.1_lincRNA	NM_025108.2	NP_079384.2	Q7L2K0	CP059_HUMAN	chromosome 16 open reading frame 59	286										lung(1)|skin(1)|urinary_tract(1)	3		Ovarian(90;0.17)				AGGAGCTCTCGGCAGGTCAGT	0.687													G|||	1418	0.283147	0.0182	0.3357	5008	,	,		16577	0.6111		0.3052	False		,,,				2504	0.2434				p.S286S		Atlas-SNP	.											.	C16orf59	13	.	0			c.G858A						PASS	.	G		240,3982		7,226,1878	14.0	19.0	18.0		858	-9.0	0.0	16	dbSNP_107	18	2306,6136		327,1652,2242	no	coding-synonymous	C16orf59	NM_025108.2		334,1878,4120	AA,AG,GG		27.3158,5.6845,20.1042		286/434	2512523	2546,10118	2111	4221	6332	SO:0001819	synonymous_variant	80178	exon7			GCTCTCGGCAGGT	AK023971	CCDS10468.2	16p13.3	2008-10-30			ENSG00000162062	ENSG00000162062			25849	protein-coding gene	gene with protein product						12477932	Standard	XM_006720955		Approved	FLJ13909	uc002cqh.3	Q7L2K0	OTTHUMG00000128859	ENST00000361837.4:c.858G>A	16.37:g.2512523G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_025108	B4DXD7|Q96H61|Q9H872	Silent	SNP	ENST00000361837.4	37	CCDS10468.2																																																																																			G|0.724;A|0.276	0.276	strong		0.687	C16orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250802.3	NM_025108	
SIRT3	23410	hgsc.bcm.edu	37	11	233212	233212	+	Silent	SNP	C	C	A	rs11555236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:233212C>A	ENST00000382743.4	-	3	579	c.477G>T	c.(475-477)tcG>tcT	p.S159S	SIRT3_ENST00000529382.1_Silent_p.S17S|SIRT3_ENST00000532956.1_Silent_p.S159S|SIRT3_ENST00000524564.1_Silent_p.S95S|SIRT3_ENST00000525319.1_Silent_p.S78S|SIRT3_ENST00000528702.1_5'UTR	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	159	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		CACTCCCCGGCGATCTGCAGG	0.572													A|||	576	0.115016	0.0159	0.1484	5008	,	,		17030	0.0942		0.2048	False		,,,				2504	0.1544				p.S159S		Atlas-SNP	.											.	SIRT3	28	.	0			c.G477T						PASS	.		,	192,4214	808.3+/-415.9	6,180,2017	45.0	48.0	47.0		51,477	0.3	0.2	11	dbSNP_120	47	1830,6770	731.2+/-406.8	178,1474,2648	no	coding-synonymous,coding-synonymous	SIRT3	NM_001017524.2,NM_012239.5	,	184,1654,4665	AA,AC,CC		21.2791,4.3577,15.5467	,	17/258,159/400	233212	2022,10984	2203	4300	6503	SO:0001819	synonymous_variant	23410	exon3			CCCCGGCGATCTG	AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3"", ""sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"""			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.477G>T	11.37:g.233212C>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_012239	B7Z5U6|Q9Y6E8	Silent	SNP	ENST00000382743.4	37	CCDS7691.1																																																																																			C|0.849;A|0.151	0.151	strong		0.572	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3		
CRTAC1	55118	hgsc.bcm.edu	37	10	99625319	99625319	+	Missense_Mutation	SNP	C	C	T	rs56007204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99625319C>T	ENST00000370597.3	-	15	2327	c.1972G>A	c.(1972-1974)Gag>Aag	p.E658K	GOLGA7B_ENST00000596005.1_5'Flank|CRTAC1_ENST00000298819.4_3'UTR|GOLGA7B_ENST00000370602.1_Intron	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	658			E -> K (in dbSNP:rs56007204).			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)		CAGCTGGGCTCGCAGCTCTCC	0.622													C|||	396	0.0790735	0.0129	0.1484	5008	,	,		16528	0.0		0.2316	False		,,,				2504	0.044				p.E658K		Atlas-SNP	.											CRTAC1,NS,adenoma,0,2	CRTAC1	86	2	0			c.G1972A						PASS	.	C	,LYS/GLU	213,4193	130.6+/-167.2	7,199,1997	38.0	39.0	39.0		,1972	-1.5	0.0	10	dbSNP_129	39	1892,6708	334.9+/-321.2	199,1494,2607	yes	intron,missense	CRTAC1,GOLGA7B	NM_001010917.2,NM_018058.6	,56	206,1693,4604	TT,TC,CC		22.0,4.8343,16.1848	,benign	,658/662	99625319	2105,10901	2203	4300	6503	SO:0001583	missense	55118	exon15			TGGGCTCGCAGCT	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.1972G>A	10.37:g.99625319C>T	ENSP00000359629:p.Glu658Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	126	68	0.539683	NM_018058	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	241	0.11034798534798534	10	0.02032520325203252	69	0.19060773480662985	0	0.0	162	0.21372031662269128	C	17.52	3.410848	0.62399	0.048343	0.22	ENSG00000095713	ENST00000370597	T	0.74209	-0.82	3.19	-1.52	0.08637	.	1.841770	0.03457	N	0.211645	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.08638	-1.0712	9	0.87932	D	0	.	7.4764	0.27378	0.0:0.5166:0.0:0.4834	rs56007204;rs61874778	658	Q9NQ79	CRAC1_HUMAN	K	658	ENSP00000359629:E658K	ENSP00000359629:E658K	E	-	1	0	CRTAC1	99615309	0.004000	0.15560	0.000000	0.03702	0.840000	0.47671	-0.670000	0.05256	-0.329000	0.08527	0.462000	0.41574	GAG	C|0.846;T|0.154	0.154	strong		0.622	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
KDM7A	80853	hgsc.bcm.edu	37	7	139801777	139801777	+	Silent	SNP	T	T	G	rs1062277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:139801777T>G	ENST00000397560.2	-	12	1709	c.1612A>C	c.(1612-1614)Aga>Cga	p.R538R	JHDM1D_ENST00000006967.5_Silent_p.R538R	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		538					histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|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)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					ATCTCTAATCTTTTGAGGACC	0.398													T|||	1670	0.333466	0.416	0.281	5008	,	,		20517	0.245		0.335	False		,,,				2504	0.3487				p.R538R		Atlas-SNP	.											.	JHDM1D	54	.	0			c.A1612C						PASS	.	T		1448,2302		272,904,699	191.0	171.0	178.0		1612	5.9	0.8	7	dbSNP_86	178	2794,5418		479,1836,1791	no	coding-synonymous	JHDM1D	NM_030647.1		751,2740,2490	GG,GT,TT		34.0234,38.6133,35.4623		538/942	139801777	4242,7720	1875	4106	5981	SO:0001819	synonymous_variant	80853	exon12			CTAATCTTTTGAG																												ENST00000397560.2:c.1612A>C	7.37:g.139801777T>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	162	96	0.592593	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Silent	SNP	ENST00000397560.2	37	CCDS43658.1																																																																																			T|0.659;G|0.341	0.341	strong		0.398	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1		
ZNF543	125919	hgsc.bcm.edu	37	19	57839150	57839150	+	Missense_Mutation	SNP	A	A	G	rs8100491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57839150A>G	ENST00000321545.4	+	4	665	c.320A>G	c.(319-321)cAa>cGa	p.Q107R		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	107			Q -> R (in dbSNP:rs8100491). {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)			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)		CTCCAGGAACAACTGACACAA	0.478													g|||	3418	0.682508	0.7731	0.7133	5008	,	,		19133	0.5863		0.7197	False		,,,				2504	0.5992				p.Q107R		Atlas-SNP	.											ZNF543,NS,lymphoid_neoplasm,+1,2	ZNF543	61	2	0			c.A320G						PASS	.	G	ARG/GLN	3295,1111	397.6+/-330.5	1223,849,131	70.0	70.0	70.0		320	-5.7	0.0	19	dbSNP_116	70	6414,2186	373.7+/-337.1	2402,1610,288	yes	missense	ZNF543	NM_213598.3	43	3625,2459,419	GG,GA,AA		25.4186,25.2156,25.3498	benign	107/601	57839150	9709,3297	2203	4300	6503	SO:0001583	missense	125919	exon4			AGGAACAACTGAC	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.320A>G	19.37:g.57839150A>G	ENSP00000322545:p.Gln107Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	1508	0.6904761904761905	356	0.7235772357723578	261	0.7209944751381215	338	0.5909090909090909	553	0.7295514511873351	G	0.536	-0.855603	0.02630	0.747844	0.745814	ENSG00000178229	ENST00000321545	T	0.23754	1.89	2.87	-5.73	0.02398	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.42565	-0.9444	8	0.02654	T	1	.	6.0897	0.19987	0.4665:0.0:0.4063:0.1272	rs8100491;rs57192148;rs8100491	107	Q08ER8	ZN543_HUMAN	R	107	ENSP00000322545:Q107R	ENSP00000322545:Q107R	Q	+	2	0	ZNF543	62530962	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.431000	0.01023	-1.610000	0.01583	-2.030000	0.00424	CAA	A|0.278;G|0.722	0.722	strong		0.478	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
COX10	1352	hgsc.bcm.edu	37	17	13980058	13980058	+	Missense_Mutation	SNP	A	A	T	rs2230351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:13980058A>T	ENST00000261643.3	+	3	261	c.184A>T	c.(184-186)Aca>Tca	p.T62S	COX10_ENST00000537334.1_Intron|COX10_ENST00000429152.2_Missense_Mutation_p.T62S|COX10_ENST00000536205.1_5'UTR	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	62			T -> S (in dbSNP:rs2230351).		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)		TTAGTATGTCACACAGCTGAA	0.408													A|||	308	0.0615016	0.0061	0.1153	5008	,	,		16223	0.1032		0.0686	False		,,,				2504	0.0481				p.T62S		Atlas-SNP	.											.	COX10	36	.	0			c.A184T						PASS	.	A	SER/THR	63,4343	56.8+/-93.2	1,61,2141	60.0	57.0	58.0		184	5.3	1.0	17	dbSNP_98	58	586,8014	155.4+/-209.4	25,536,3739	yes	missense	COX10	NM_001303.3	58	26,597,5880	TT,TA,AA		6.814,1.4299,4.99	benign	62/444	13980058	649,12357	2203	4300	6503	SO:0001583	missense	1352	exon3			TATGTCACACAGC	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.184A>T	17.37:g.13980058A>T	ENSP00000261643:p.Thr62Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	37	CCDS11166.1	156|156	0.07142857142857142|0.07142857142857142	3|3	0.006097560975609756|0.006097560975609756	33|33	0.09116022099447514|0.09116022099447514	70|70	0.12237762237762238|0.12237762237762238	50|50	0.06596306068601583|0.06596306068601583	A|A	17.14|17.14	3.312828|3.312828	0.60414|0.60414	0.014299|0.014299	0.06814|0.06814	ENSG00000006695|ENSG00000006695	ENST00000429152|ENST00000261643	.|T	.|0.37411	.|1.2	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.122077	.|0.53938	.|D	.|0.000048	T|T	0.00608|0.00608	0.0020|0.0020	M|M	0.71581|0.71581	2.175|2.175	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.16396	.|0.017	.|B	.|0.15052	.|0.012	T|T	0.06881|0.06881	-1.0802|-1.0802	4|9	.|0.41790	.|T	.|0.15	-18.9765|-18.9765	14.2362|14.2362	0.65929|0.65929	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs2230351;rs34342426|rs2230351;rs34342426	.|62	.|Q12887	.|COX10_HUMAN	L|S	22|62	.|ENSP00000261643:T62S	.|ENSP00000261643:T62S	H|T	+|+	2|1	0|0	COX10|COX10	13920783|13920783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.042000|6.042000	0.70996|0.70996	2.163000|2.163000	0.67991|0.67991	0.529000|0.529000	0.55759|0.55759	CAC|ACA	A|0.940;T|0.060	0.060	strong		0.408	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
TACC2	10579	hgsc.bcm.edu	37	10	123847355	123847355	+	Silent	SNP	G	G	A	rs10788237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123847355G>A	ENST00000369005.1	+	4	5680	c.5340G>A	c.(5338-5340)ggG>ggA	p.G1780G	TACC2_ENST00000334433.3_Silent_p.G1780G|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.G1780G|TACC2_ENST00000453444.2_Silent_p.G1780G|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.G1780G	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1780					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)				AGCAGCCAGGGCCTGAGCGCC	0.642													G|||	1005	0.200679	0.2867	0.1844	5008	,	,		17167	0.1002		0.2187	False		,,,				2504	0.181				p.G1780G		Atlas-SNP	.											TACC2,colon,carcinoma,0,1	TACC2	271	1	0			c.G5340A						PASS	.	G	,	1413,2993	444.9+/-347.5	226,961,1016	35.0	35.0	35.0		,5340	0.6	0.0	10	dbSNP_120	35	1963,6637	330.1+/-319.0	223,1517,2560	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	449,2478,3576	AA,AG,GG		22.8256,32.0699,25.9573	,	,1780/2949	123847355	3376,9630	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			GCCAGGGCCTGAG	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.5340G>A	10.37:g.123847355G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			G|0.767;A|0.233	0.233	strong		0.642	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
ERICH6	131831	hgsc.bcm.edu	37	3	150391810	150391810	+	Missense_Mutation	SNP	A	A	C	rs73003074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:150391810A>C	ENST00000295910.6	-	11	1328	c.1276T>G	c.(1276-1278)Tta>Gta	p.L426V	FAM194A_ENST00000491361.1_Missense_Mutation_p.L280V	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						TGCTTCTCTAAGAGCTCATTC	0.368													A|||	879	0.175519	0.267	0.1744	5008	,	,		19262	0.1171		0.1481	False		,,,				2504	0.1411				p.L426V		Atlas-SNP	.											.	FAM194A	91	.	0			c.T1276G						PASS	.	A	VAL/LEU	1039,3367	381.4+/-324.0	111,817,1275	138.0	133.0	135.0		1276	-2.1	0.0	3	dbSNP_130	135	1240,7360	248.7+/-276.3	92,1056,3152	yes	missense	FAM194A	NM_152394.3	32	203,1873,4427	CC,CA,AA		14.4186,23.5815,17.5227	benign	426/664	150391810	2279,10727	2203	4300	6503	SO:0001583	missense	131831	exon11			TCTCTAAGAGCTC																												ENST00000295910.6:c.1276T>G	3.37:g.150391810A>C	ENSP00000295910:p.Leu426Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	385	0.1762820512820513	138	0.2804878048780488	59	0.16298342541436464	78	0.13636363636363635	110	0.14511873350923482	A	12.56	1.975122	0.34848	0.235815	0.144186	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.12147	2.71;2.71	4.81	-2.1	0.07210	.	0.960065	0.08422	N	0.948220	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	P	0.49961	0.93	P	0.50162	0.633	T	0.41645	-0.9497	9	0.27785	T	0.31	-0.718	11.0114	0.47665	0.5098:0.0:0.4902:0.0	.	426	Q7L0X2	F194A_HUMAN	V	426;280;384	ENSP00000295910:L426V;ENSP00000419366:L280V	ENSP00000295910:L426V	L	-	1	2	FAM194A	151874500	0.002000	0.14202	0.001000	0.08648	0.511000	0.34104	-1.259000	0.02861	-0.275000	0.09219	0.460000	0.39030	TTA	A|0.820;C|0.180	0.180	strong		0.368	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
NCAPD2	9918	hgsc.bcm.edu	37	12	6637941	6637941	+	Silent	SNP	C	C	T	rs10849484	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6637941C>T	ENST00000315579.5	+	26	4195	c.3396C>T	c.(3394-3396)agC>agT	p.S1132S	NCAPD2_ENST00000545962.1_Silent_p.S1087S	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1132					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						GGCAGGTCAGCGAGATGGCGG	0.597													C|||	524	0.104633	0.0182	0.1354	5008	,	,		17652	0.0089		0.2097	False		,,,				2504	0.1902				p.S1132S		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3396T						PASS	.	C		234,4172	138.0+/-173.8	9,216,1978	73.0	67.0	69.0		3396	1.5	1.0	12	dbSNP_120	69	2030,6570	354.9+/-329.7	236,1558,2506	no	coding-synonymous	NCAPD2	NM_014865.3		245,1774,4484	TT,TC,CC		23.6047,5.3109,17.4074		1132/1402	6637941	2264,10742	2203	4300	6503	SO:0001819	synonymous_variant	9918	exon26			GGTCAGCGAGATG	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.3396C>T	12.37:g.6637941C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			C|0.847;T|0.153	0.153	strong		0.597	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
LRP1B	53353	hgsc.bcm.edu	37	2	141751592	141751592	+	Silent	SNP	G	G	A	rs13007735	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:141751592G>A	ENST00000389484.3	-	16	3587	c.2616C>T	c.(2614-2616)gaC>gaT	p.D872D	Y_RNA_ENST00000365022.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	872	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CATCGCTTCCGTCTAGGCAGT	0.433										TSP Lung(27;0.18)			G|||	2552	0.509585	0.6059	0.3847	5008	,	,		17244	0.6141		0.3748	False		,,,				2504	0.499				p.D872D	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,lymphoid_neoplasm,-2,1	LRP1B	1315	1	0			c.C2616T						PASS	.	G		2406,2000	615.0+/-392.5	650,1106,447	129.0	122.0	125.0		2616	-5.2	0.7	2	dbSNP_121	125	2780,5820	440.7+/-359.6	451,1878,1971	no	coding-synonymous	LRP1B	NM_018557.2		1101,2984,2418	AA,AG,GG		32.3256,45.3926,39.8739		872/4600	141751592	5186,7820	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon16			GCTTCCGTCTAGG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2616C>T	2.37:g.141751592G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.558;A|0.442	0.442	strong		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
SCUBE1	80274	hgsc.bcm.edu	37	22	43614316	43614316	+	Silent	SNP	C	C	G	rs9620123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	71	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	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	
MUC2	4583	hgsc.bcm.edu	37	11	1083293	1083293	+	Silent	SNP	T	T	C	rs7394853	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1083293T>C	ENST00000441003.2	+	16	2220	c.2193T>C	c.(2191-2193)gaT>gaC	p.D731D	MUC2_ENST00000359061.5_Silent_p.D731D	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	731					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)	AGGCGGGGGATGTGGTCGTCA	0.672													C|||	1860	0.371406	0.444	0.366	5008	,	,		14043	0.3919		0.2167	False		,,,				2504	0.4151				p.D731D		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.T2193C						scavenged	.			1636,2364		342,952,706	25.0	30.0	28.0		2193	-8.5	0.0	11	dbSNP_116	28	1685,6627		181,1323,2652	no	coding-synonymous	MUC2	NM_002457.2		523,2275,3358	CC,CT,TT		20.2719,40.9,26.9737		731/2813	1083293	3321,8991	2000	4156	6156	SO:0001819	synonymous_variant	4583	exon16			GGGGGATGTGGTC	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.2193T>C	11.37:g.1083293T>C		Somatic	56	2	0.0357143		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.705;C|0.295	0.295	strong		0.672	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
MUC2	4583	hgsc.bcm.edu	37	11	1101078	1101078	+	Missense_Mutation	SNP	A	A	G	rs11245954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1101078A>G	ENST00000441003.2	+	41	7504	c.7477A>G	c.(7477-7479)Agc>Ggc	p.S2493G		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4855					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)	CAAGAGGTGCAGCCAGAAGCC	0.587													A|||	426	0.0850639	0.1573	0.0403	5008	,	,		20234	0.0456		0.0775	False		,,,				2504	0.0675				p.S2489G		Atlas-SNP	.											.	MUC2	614	.	0			c.A7465G						PASS	.	A	GLY/SER	506,3726		27,452,1637	81.0	90.0	87.0		7462	-2.3	0.0	11	dbSNP_120	87	594,7860		18,558,3651	yes	missense	MUC2	NM_002457.2	56	45,1010,5288	GG,GA,AA		7.0263,11.9565,8.671	benign	2488/2813	1101078	1100,11586	2116	4227	6343	SO:0001583	missense	4583	exon42			AGGTGCAGCCAGA	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.7477A>G	11.37:g.1101078A>G	ENSP00000415183:p.Ser2493Gly	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		164	0.07509157509157509	73	0.1483739837398374	15	0.04143646408839779	19	0.033216783216783216	57	0.07519788918205805	A	7.456	0.643762	0.14451	0.119565	0.070263	ENSG00000198788	ENST00000441003	T	0.42900	0.96	2.95	-2.26	0.06867	.	.	.	.	.	T	0.00144	0.0004	L	0.40543	1.245	0.80722	P	0.0	B	0.28470	0.213	B	0.21151	0.033	T	0.18840	-1.0324	8	0.20519	T	0.43	.	8.0542	0.30596	0.3112:0.5846:0.1042:0.0	rs11245954;rs11245954	2493	E7EUV1	.	G	2493	ENSP00000415183:S2493G	ENSP00000415183:S2493G	S	+	1	0	MUC2	1091078	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	-1.367000	0.02583	-0.205000	0.10219	0.392000	0.25879	AGC	A|0.924;G|0.076	0.076	strong		0.587	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CCDC13	152206	hgsc.bcm.edu	37	3	42799765	42799765	+	Missense_Mutation	SNP	G	G	A	rs17238798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42799765G>A	ENST00000310232.6	-	2	156	c.73C>T	c.(73-75)Cgg>Tgg	p.R25W	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	25			R -> W (in dbSNP:rs17238798).							endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TTCTGTAACCGTTTGTGCTGC	0.507													G|||	840	0.167732	0.0144	0.1571	5008	,	,		18102	0.1667		0.2694	False		,,,				2504	0.2791				p.R25W		Atlas-SNP	.											.	CCDC13	71	.	0			c.C73T						PASS	.	G	TRP/ARG	248,4158	145.4+/-180.2	9,230,1964	205.0	164.0	178.0		73	0.8	0.0	3	dbSNP_123	178	2344,6256	393.5+/-344.4	304,1736,2260	yes	missense	CCDC13	NM_144719.3	101	313,1966,4224	AA,AG,GG		27.2558,5.6287,19.9293	probably-damaging	25/716	42799765	2592,10414	2203	4300	6503	SO:0001583	missense	152206	exon2			GTAACCGTTTGTG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.73C>T	3.37:g.42799765G>A	ENSP00000309836:p.Arg25Trp	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	195	101	0.517949	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	385	0.1762820512820513	15	0.03048780487804878	71	0.19613259668508287	90	0.15734265734265734	209	0.2757255936675462	G	12.73	2.024097	0.35701	0.056287	0.272558	ENSG00000244607	ENST00000310232	T	0.37752	1.18	4.61	0.786	0.18590	.	0.050977	0.64402	D	0.000001	T	0.00012	0.0000	M	0.75447	2.3	0.58432	P	5.000000000032756E-6	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.995;0.977	T	0.12218	-1.0556	9	0.87932	D	0	.	12.9469	0.58376	0.0:0.0:0.6736:0.3264	rs17238798;rs17238798	25;25;25	B4DZD2;Q96LI1;Q8IYE1	.;.;CCD13_HUMAN	W	25	ENSP00000309836:R25W	ENSP00000309836:R25W	R	-	1	2	CCDC13	42774769	0.021000	0.18746	0.002000	0.10522	0.354000	0.29330	-0.396000	0.07278	-0.023000	0.13963	-0.457000	0.05445	CGG	G|0.817;A|0.183	0.183	strong		0.507	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
CUEDC1	404093	hgsc.bcm.edu	37	17	55950064	55950064	+	Silent	SNP	C	C	T	rs35704289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:55950064C>T	ENST00000577830.1	-	5	1157	c.744G>A	c.(742-744)gaG>gaA	p.E248E	CUEDC1_ENST00000577840.1_Silent_p.E111E|CUEDC1_ENST00000360238.2_Silent_p.E248E|CUEDC1_ENST00000578357.1_5'Flank|CUEDC1_ENST00000407144.2_Silent_p.E248E	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	106	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	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	
ZNF470	388566	hgsc.bcm.edu	37	19	57088850	57088850	+	Silent	SNP	T	T	C	rs3752180	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57088850T>C	ENST00000330619.8	+	6	1739	c.1053T>C	c.(1051-1053)gaT>gaC	p.D351D	ZNF470_ENST00000391709.3_Silent_p.D351D|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		CTTTTAGTGATTGCTCATCCC	0.438													T|||	1455	0.290535	0.1362	0.3401	5008	,	,		21092	0.379		0.3867	False		,,,				2504	0.274				p.D351D		Atlas-SNP	.											.	ZNF470	103	.	0			c.T1053C						PASS	.	T		801,3605	320.4+/-296.6	64,673,1466	86.0	82.0	84.0		1053	-2.2	0.7	19	dbSNP_107	84	3198,5402	482.3+/-370.9	598,2002,1700	no	coding-synonymous	ZNF470	NM_001001668.3		662,2675,3166	CC,CT,TT		37.186,18.1798,30.7473		351/718	57088850	3999,9007	2203	4300	6503	SO:0001819	synonymous_variant	388566	exon6			TAGTGATTGCTCA	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1053T>C	19.37:g.57088850T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Silent	SNP	ENST00000330619.8	37	CCDS33122.1																																																																																			T|0.693;C|0.307	0.307	strong		0.438	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086719	46086719	+	Missense_Mutation	SNP	A	A	G	rs7276859|rs368303093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46086719A>G	ENST00000360770.3	-	1	125	c.85T>C	c.(85-87)Tcc>Ccc	p.S29P	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	29	23 X 5 AA approximate repeats.		S -> C (in dbSNP:rs7275281).|S -> P (in dbSNP:rs7276859).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GCCTGGCAGGAGCTGGGCACA	0.682													G|||	3070	0.613019	0.7262	0.5807	5008	,	,		16573	0.5675		0.5547	False		,,,				2504	0.59				p.S29P		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.T85C						PASS	.	G	,PRO/SER	1221,3097		486,249,1424	33.0	40.0	38.0		,85	-6.8	0.0	21	dbSNP_129	38	1508,6988		620,268,3360	no	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,74	1106,517,4784	GG,GA,AA		17.7495,28.277,21.297	,benign	,29/147	46086719	2729,10085	2159	4248	6407	SO:0001583	missense	353323	exon1			GGCAGGAGCTGGG	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.85T>C	21.37:g.46086719A>G	ENSP00000354001:p.Ser29Pro	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1167	0.5343406593406593	320	0.6504065040650406	199	0.5497237569060773	279	0.48776223776223776	369	0.4868073878627968	g	1.782	-0.481680	0.04383	0.28277	0.177495	ENSG00000221864	ENST00000360770	T	0.03152	4.03	3.4	-6.8	0.01709	.	.	.	.	.	T	0.00012	0.0000	N	0.13003	0.285	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42799	-0.9430	8	0.05833	T	0.94	.	1.6096	0.02691	0.3939:0.0934:0.138:0.3746	rs7276859;rs34421715	29	P59991	KR122_HUMAN	P	29	ENSP00000354001:S29P	ENSP00000354001:S29P	S	-	1	0	KRTAP12-2	44911147	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.335000	0.00251	-4.007000	0.00082	-2.692000	0.00139	TCC	A|0.470;G|0.530	0.530	strong		0.682	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
DHRS11	79154	hgsc.bcm.edu	37	17	34958598	34958598	+	IGR	SNP	G	G	C	rs78943308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:34958598G>C	ENST00000251312.5	+	0	1598				MRM1_ENST00000250156.7_Missense_Mutation_p.C120S|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						CAGGGTGTCTGCATGGAGGTG	0.682													G|||	355	0.0708866	0.0038	0.0533	5008	,	,		15695	0.1627		0.0785	False		,,,				2504	0.0716				p.C120S		Atlas-SNP	.											MRM1,NS,carcinoma,0,1	MRM1	19	1	0			c.G359C						PASS	.	G	SER/CYS	37,4343		0,37,2153	20.0	23.0	22.0		359	4.9	1.0	17	dbSNP_131	22	388,8156		8,372,3892	yes	missense	MRM1	NM_024864.3	112	8,409,6045	CC,CG,GG		4.5412,0.8447,3.2885	probably-damaging	120/354	34958598	425,12499	2190	4272	6462	SO:0001628	intergenic_variant	79922	exon1			GTGTCTGCATGGA		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.34958598G>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Missense_Mutation	SNP	ENST00000251312.5	37	CCDS11315.2	166	0.076007326007326	3	0.006097560975609756	16	0.04419889502762431	87	0.1520979020979021	60	0.079155672823219	G	28.4	4.914261	0.92178	0.008447	0.045412	ENSG00000129282	ENST00000250156	T	0.30714	1.52	4.9	4.9	0.64082	RNA 2-O ribose methyltransferase, substrate binding (2);	0.000000	0.85682	D	0.000000	T	0.00384	0.0012	M	0.71581	2.175	0.80722	D	1	D	0.55385	0.971	P	0.62089	0.898	T	0.00045	-1.2216	10	0.87932	D	0	-16.6239	15.6051	0.76664	0.0:0.0:1.0:0.0	.	120	Q6IN84	MRM1_HUMAN	S	120	ENSP00000250156:C120S	ENSP00000250156:C120S	C	+	2	0	MRM1	32032711	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.332000	0.90024	2.423000	0.82170	0.555000	0.69702	TGC	G|0.947;C|0.053	0.053	strong		0.682	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308	
CENPI	2491	hgsc.bcm.edu	37	X	100395663	100395663	+	Silent	SNP	G	G	T	rs2273380	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:100395663G>T	ENST00000372927.1	+	15	1756	c.1479G>T	c.(1477-1479)gtG>gtT	p.V493V	CENPI_ENST00000423383.1_Silent_p.V493V|CENPI_ENST00000372926.1_Silent_p.V493V|CENPI_ENST00000218507.5_Silent_p.V493V	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	493					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						AGTGTAGTGTGCTTCAGAGTC	0.393													T|||	1238	0.327947	0.3472	0.2061	3775	,	,		14673	0.1994		0.1769	False		,,,				2504	0.2628				p.V493V		Atlas-SNP	.											.	CENPI	70	.	0			c.G1479T						PASS	.	T		1584,2251		266,800,252,566,319	224.0	211.0	215.0		1479	4.3	1.0	X	dbSNP_100	215	1659,5069		146,913,454,1369,1418	no	coding-synonymous	CENPI	NM_006733.2		412,1713,706,1935,1737	TT,TG,T,GG,G		24.6581,41.3038,30.7015		493/757	100395663	3243,7320	2203	4300	6503	SO:0001819	synonymous_variant	2491	exon15			TAGTGTGCTTCAG	X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384			3968	protein-coding gene	gene with protein product		300065	"""FSH primary response (LRPR1, rat) homolog 1"", ""FSH primary response (LRPR1 homolog, rat) 1"""	FSHPRH1		16622420	Standard	NM_006733		Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	ENST00000372927.1:c.1479G>T	X.37:g.100395663G>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	99	97	0.979798	NM_006733	Q5JWZ9|Q96ED0	Silent	SNP	ENST00000372927.1	37	CCDS14479.1																																																																																			G|0.697;0|0.002	.	strong		0.393	CENPI-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057519.1	NM_006733	
NLRP4	147945	hgsc.bcm.edu	37	19	56369215	56369215	+	Silent	SNP	C	C	T	rs395503|rs199476224	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56369215C>T	ENST00000301295.6	+	3	878	c.456C>T	c.(454-456)atC>atT	p.I152I	NLRP4_ENST00000346986.5_Silent_p.I152I|NLRP4_ENST00000587891.1_Silent_p.I77I	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	152	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GTACAGTGATCATTCAAGGAC	0.473													C|||	2584	0.515974	0.447	0.464	5008	,	,		20382	0.6657		0.3827	False		,,,				2504	0.6288				p.I152I		Atlas-SNP	.											.	NLRP4	331	.	0			c.C456T						PASS	.	C		1905,2501	546.1+/-377.0	413,1079,711	135.0	121.0	126.0		456	3.0	0.1	19	dbSNP_80	126	3180,5420	481.5+/-370.7	598,1984,1718	no	coding-synonymous	NLRP4	NM_134444.4		1011,3063,2429	TT,TC,CC		36.9767,43.2365,39.0973		152/995	56369215	5085,7921	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			AGTGATCATTCAA	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.456C>T	19.37:g.56369215C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	145	63	0.434483	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.574;T|0.426	0.426	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
TPSD1	23430	hgsc.bcm.edu	37	16	1306346	1306346	+	Missense_Mutation	SNP	C	C	G	rs3865205	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306346C>G	ENST00000211076.3	+	1	213	c.65C>G	c.(64-66)cCg>cGg	p.P22R	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.P15R	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	22			P -> R (in dbSNP:rs3865205). {ECO:0000269|PubMed:9920877}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CTGGCGAGCCCGGCCTACGTG	0.721													-|||	1100	0.219649	0.112	0.1571	5008	,	,		14799	0.3641		0.1938	False		,,,				2504	0.2873				p.P22R		Atlas-SNP	.											TPSD1,rectum,carcinoma,0,4	TPSD1	47	4	0			c.C65G						scavenged	.						32.0	40.0	37.0					16																	1306346		2197	4298	6495	SO:0001583	missense	23430	exon1			CGAGCCCGGCCTA	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.65C>G	16.37:g.1306346C>G	ENSP00000211076:p.Pro22Arg	Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	77	15	0.194805	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	-	3.814	-0.039033	0.07497	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.81579	-1.51;-1.51	2.55	0.112	0.14623	.	2.133630	0.02279	N	0.069280	T	0.64571	0.2610	N	0.08118	0	0.09310	N	1	B	0.22003	0.063	B	0.26693	0.072	T	0.51317	-0.8721	10	0.20046	T	0.44	.	6.9607	0.24595	0.0:0.3788:0.0:0.6212	rs3865205;rs3891050	22	Q9BZJ3	TRYD_HUMAN	R	15;22	ENSP00000380668:P15R;ENSP00000211076:P22R	ENSP00000211076:P22R	P	+	2	0	TPSD1	1246347	0.000000	0.05858	0.007000	0.13788	0.001000	0.01503	-2.678000	0.00839	-0.544000	0.06232	-2.646000	0.00150	CCG	C|0.851;T|0.149	.	strong		0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037557	33037557	+	Silent	SNP	C	C	T	rs1042177	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33037557C>T	ENST00000419277.1	-	3	336	c.207G>A	c.(205-207)aaG>aaA	p.K69K	HLA-DPA1_ENST00000428995.1_Silent_p.K69K|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	69	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CGGTCTCCTTCTTGTCCAGAT	0.453													.|||	1181	0.235823	0.3775	0.2363	5008	,	,		19499	0.1022		0.1551	False		,,,				2504	0.2648				p.K69K		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G207A						PASS	.	C	,,	807,2215		129,549,833	69.0	91.0	83.0		207,207,207	3.0	0.8	6	dbSNP_86	83	718,4700		45,628,2036	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	174,1177,2869	TT,TC,CC		13.2521,26.7042,18.0687	,,	69/261,69/261,69/261	33037557	1525,6915	1511	2709	4220	SO:0001819	synonymous_variant	3113	exon2			CTCCTTCTTGTCC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.207G>A	6.37:g.33037557C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	133	52	0.390977	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	
LRRK1	79705	hgsc.bcm.edu	37	15	101591923	101591923	+	Silent	SNP	A	A	G	rs4965778	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:101591923A>G	ENST00000388948.3	+	24	3806	c.3447A>G	c.(3445-3447)acA>acG	p.T1149T	LRRK1_ENST00000284395.5_Silent_p.T1146T|RP11-505E24.3_ENST00000558979.1_RNA|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			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	71	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	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	
COL18A1	80781	hgsc.bcm.edu	37	21	46911188	46911188	+	Missense_Mutation	SNP	C	C	G	rs79980197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46911188C>G	ENST00000359759.4	+	21	3383	c.3362C>G	c.(3361-3363)cCc>cGc	p.P1121R	COL18A1_ENST00000400337.2_Missense_Mutation_p.P706R|COL18A1_ENST00000355480.5_Missense_Mutation_p.P886R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1121	Triple-helical region 4 (COL4).		P -> R (in dbSNP:rs79980197). {ECO:0000269|PubMed:14695535, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:8188291}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CCTGGCCCCCCCGGACCCCCG	0.682													C|||	345	0.0688898	0.0227	0.0303	5008	,	,		10479	0.0873		0.0895	False		,,,				2504	0.1186				p.P886R		Atlas-SNP	.											.	COL18A1	129	.	0			c.C2657G						PASS	.	C	ARG/PRO,ARG/PRO	125,3713		2,121,1796	19.0	25.0	23.0		2657,2117	3.8	0.9	21	dbSNP_131	23	594,7590		18,558,3516	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	103,103	20,679,5312	GG,GC,CC		7.2581,3.2569,5.9807	probably-damaging,probably-damaging	886/1520,706/1340	46911188	719,11303	1919	4092	6011	SO:0001583	missense	80781	exon21			GCCCCCCCGGACC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3362C>G	21.37:g.46911188C>G	ENSP00000352798:p.Pro1121Arg	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	215	120	0.55814	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		129	0.059065934065934064	16	0.032520325203252036	13	0.03591160220994475	28	0.04895104895104895	72	0.09498680738786279	C	14.33	2.503088	0.44558	0.032569	0.072581	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	D;D;D;D	0.95447	-3.09;-3.09;-3.09;-3.71	3.85	3.85	0.44370	.	0.073580	0.56097	D	0.000037	T	0.62380	0.2423	L	0.52266	1.64	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.75243	-0.3386	10	0.27785	T	0.31	.	13.6811	0.62487	0.0:1.0:0.0:0.0	.	1121;886;706	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	R	706;706;886;1121;1121;53	ENSP00000383191:P706R;ENSP00000347665:P886R;ENSP00000352798:P1121R;ENSP00000339118:P53R	ENSP00000339118:P53R	P	+	2	0	COL18A1	45735616	0.222000	0.23652	0.916000	0.36221	0.128000	0.20619	3.287000	0.51732	2.159000	0.67721	0.561000	0.74099	CCC	C|0.938;G|0.062	0.062	strong		0.682	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
ZNF514	84874	hgsc.bcm.edu	37	2	95815306	95815306	+	Silent	SNP	C	C	T	rs36045840	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:95815306C>T	ENST00000295208.2	-	5	1386	c.924G>A	c.(922-924)agG>agA	p.R308R	MRPS5_ENST00000475040.1_5'Flank|ZNF514_ENST00000411425.1_Silent_p.R308R	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	308					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)			large_intestine(4)|lung(6)|urinary_tract(1)	11						CAGTATGAGTCCTCTGATGCT	0.438													C|||	113	0.0225639	0.0008	0.0101	5008	,	,		19729	0.0565		0.0298	False		,,,				2504	0.0184				p.R308R		Atlas-SNP	.											.	ZNF514	34	.	0			c.G924A						PASS	.	C		30,4376	36.0+/-67.5	0,30,2173	68.0	71.0	70.0		924	0.2	1.0	2	dbSNP_126	70	263,8337	101.9+/-163.1	3,257,4040	no	coding-synonymous	ZNF514	NM_032788.1		3,287,6213	TT,TC,CC		3.0581,0.6809,2.2528		308/401	95815306	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	84874	exon5			ATGAGTCCTCTGA	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"""Zinc fingers, C2H2-type"", ""-"""	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.924G>A	2.37:g.95815306C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_032788	Q5JPJ3	Silent	SNP	ENST00000295208.2	37	CCDS2011.1																																																																																			C|0.972;T|0.028	0.028	strong		0.438	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788	
ZNF714	148206	hgsc.bcm.edu	37	19	21300462	21300462	+	Missense_Mutation	SNP	A	A	G	rs2884554	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:21300462A>G	ENST00000596143.1	+	5	1317	c.992A>G	c.(991-993)aAa>aGa	p.K331R	ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	331			K -> R (in dbSNP:rs2884554). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						ACAAAACATAAAAGAATTCAT	0.348													.|||	3353	0.669529	0.2035	0.8084	5008	,	,		20909	0.8611		0.8191	False		,,,				2504	0.8497				p.K331R		Atlas-SNP	.											.	ZNF714	121	.	0			c.A992G						PASS	.	A	ARG/LYS	1513,2791		267,979,906	33.0	36.0	35.0		992	1.0	0.8	19	dbSNP_101	35	7198,1358		3030,1138,110	yes	missense	ZNF714	NM_182515.3	26	3297,2117,1016	GG,GA,AA		15.8719,35.1533,32.2628	benign	331/555	21300462	8711,4149	2152	4278	6430	SO:0001583	missense	148206	exon5			AACATAAAAGAAT	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.992A>G	19.37:g.21300462A>G	ENSP00000472368:p.Lys331Arg	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	1519	0.6955128205128205	120	0.24390243902439024	287	0.7928176795580111	503	0.8793706293706294	609	0.8034300791556728	.	11.58	1.680248	0.29872	0.351533	0.841281	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	0.955	0.19602	.	.	.	.	.	T	0.00012	0.0000	N	0.10972	0.075	0.53005	P	3.6000000000036E-5	D	0.76494	0.999	D	0.70487	0.969	T	0.38351	-0.9665	7	0.39692	T	0.17	.	4.6997	0.12822	0.6729:0.3271:0.0:0.0	rs2884554;rs52821377;rs2884554	331	A6NEM4	.	R	331	.	ENSP00000291770:K331R	K	+	2	0	ZNF714	21092302	0.000000	0.05858	0.766000	0.31476	0.755000	0.42902	0.131000	0.15870	0.378000	0.24764	0.369000	0.22263	AAA	A|0.264;G|0.736	0.736	strong		0.348	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
CPO	130749	hgsc.bcm.edu	37	2	207833983	207833983	+	Silent	SNP	A	A	G	rs7582305	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	0	0		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	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	
GFOD2	81577	hgsc.bcm.edu	37	16	67709262	67709262	+	Silent	SNP	G	G	A	rs34895002|rs139441064	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:67709262G>A	ENST00000268797.7	-	3	1299	c.954C>T	c.(952-954)ttC>ttT	p.F318F	GFOD2_ENST00000602377.1_5'UTR	NM_030819.3	NP_110446.3	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain containing 2	318					extracellular matrix organization (GO:0030198)	proteinaceous extracellular matrix (GO:0005578)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		CCTGCCCCTGGAAGGACTGGC	0.667													G|||	40	0.00798722	0.0015	0.013	5008	,	,		17536	0.0		0.0239	False		,,,				2504	0.0051				p.F318F		Atlas-SNP	.											.	GFOD2	36	.	0			c.C954T						PASS	.						65.0	60.0	61.0					16																	67709262		2198	4299	6497	SO:0001819	synonymous_variant	81577	exon3			CCCCTGGAAGGAC	AK074382	CCDS10845.1, CCDS59268.1	16q22.1	2008-02-05			ENSG00000141098	ENSG00000141098			28159	protein-coding gene	gene with protein product						12975309	Standard	NM_030819		Approved	FLJ23802, MGC11335	uc002eub.3	Q3B7J2	OTTHUMG00000137537	ENST00000268797.7:c.954C>T	16.37:g.67709262G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	40	0.555556	NM_030819	Q69YL9|Q6UXX6|Q7L648|Q8TE86|Q9BQ07|R4GNG5	Silent	SNP	ENST00000268797.7	37	CCDS10845.1																																																																																			G|0.980;A|0.020	0.020	strong		0.667	GFOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268868.2	NM_030819	
ZNF268	10795	hgsc.bcm.edu	37	12	133780033	133780033	+	Silent	SNP	C	C	T	rs189953075	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:133780033C>T	ENST00000536435.2	+	6	2091	c.1761C>T	c.(1759-1761)acC>acT	p.T587T	ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000536899.2_3'UTR|ZNF268_ENST00000537565.1_Silent_p.T426T|ZNF268_ENST00000228289.5_Silent_p.T587T|ZNF268_ENST00000542986.2_3'UTR	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	587					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		ATGAATGCACCGACTGTGGAA	0.438													C|||	20	0.00399361	0.0151	0.0	5008	,	,		20480	0.0		0.0	False		,,,				2504	0.0				p.T587T		Atlas-SNP	.											.	ZNF268	71	.	0			c.C1761T						PASS	.	C	,,,,,,,,	8,1376		0,8,684	44.0	42.0	42.0		1761,1512,,,,,,1761,	-1.4	0.0	12		42	0,3182		0,0,1591	no	coding-synonymous,coding-synonymous,utr-3,utr-3,utr-3,utr-3,utr-3,coding-synonymous,utr-3	ZNF268	NM_001165881.2,NM_001165882.2,NM_001165883.1,NM_001165884.2,NM_001165885.1,NM_001165886.1,NM_001165887.1,NM_003415.2,NM_152943.2	,,,,,,,,	0,8,2275	TT,TC,CC		0.0,0.578,0.1752	,,,,,,,,	587/948,504/865,,,,,,587/948,	133780033	8,4558	692	1591	2283	SO:0001819	synonymous_variant	10795	exon6			ATGCACCGACTGT	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.1761C>T	12.37:g.133780033C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	6	5	0.833333	NM_001165881	Q8TDG8|Q96RH4|Q9BZJ9	Silent	SNP	ENST00000536435.2	37	CCDS45012.1																																																																																			C|0.997;T|0.003	0.003	strong		0.438	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
PSMD13	5719	hgsc.bcm.edu	37	11	244141	244141	+	Intron	SNP	G	G	A	rs7128029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:244141G>A	ENST00000532097.1	+	4	713				PSMD13_ENST00000431206.2_Missense_Mutation_p.A66T|PSMD13_ENST00000352303.5_Intron	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13						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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		GTGCTCAAAGGCTGGTGGCTT	0.398													A|||	4083	0.815296	0.8918	0.83	5008	,	,		15776	0.8036		0.7306	False		,,,				2504	0.8006				p.A66T		Atlas-SNP	.											.	PSMD13	53	.	0			c.G196A						PASS	.	A	,THR/ALA	3853,553	229.4+/-244.0	1713,427,63	56.0	61.0	59.0		,196	-8.5	0.0	11	dbSNP_116	59	6267,2331	370.8+/-336.0	2369,1529,401	yes	intron,missense	PSMD13	NM_002817.3,NM_175932.2	,58	4082,1956,464	AA,AG,GG		27.111,12.5511,22.1778	,	,66/379	244141	10120,2884	2203	4299	6502	SO:0001627	intron_variant	5719	exon2			TCAAAGGCTGGTG	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.210-20G>A	11.37:g.244141G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	1756	0.8040293040293041	440	0.8943089430894309	295	0.8149171270718232	469	0.8199300699300699	552	0.7282321899736148	A	11.70	1.718273	0.30503	0.874489	0.72889	ENSG00000185627	ENST00000431206	T	0.16897	2.31	4.25	-8.5	0.00927	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09596	-1.0667	6	.	.	.	.	8.2539	0.31743	0.12:0.1884:0.5752:0.1164	rs7128029;rs60794392;rs7128029	66	Q9UNM6-2	.	T	66	ENSP00000396937:A66T	.	A	+	1	0	PSMD13	234141	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.204000	0.01233	-2.509000	0.00505	-1.326000	0.01283	GCT	G|0.202;N|0.000	.	strong		0.398	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
TIPIN	54962	hgsc.bcm.edu	37	15	66641417	66641417	+	Silent	SNP	T	T	C	rs11856320	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:66641417T>C	ENST00000261881.4	-	6	541	c.456A>G	c.(454-456)gaA>gaG	p.E152E	TIPIN_ENST00000367709.4_Silent_p.E51E|SCARNA14_ENST00000516903.1_RNA|Y_RNA_ENST00000411339.1_RNA	NM_017858.2	NP_060328	Q9BVW5	TIPIN_HUMAN	TIMELESS interacting protein	152					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						TAACAAAATCTTCATGTAAAA	0.333													T|||	182	0.0363419	0.0106	0.036	5008	,	,		20636	0.001		0.1064	False		,,,				2504	0.0358				p.E152E		Atlas-SNP	.											.	TIPIN	23	.	0			c.A456G						PASS	.	T		102,4300	75.7+/-113.9	4,94,2103	58.0	62.0	61.0		456	1.2	1.0	15	dbSNP_120	61	673,7923	165.2+/-217.4	28,617,3653	no	coding-synonymous	TIPIN	NM_017858.2		32,711,5756	CC,CT,TT		7.8292,2.3171,5.9625		152/302	66641417	775,12223	2201	4298	6499	SO:0001819	synonymous_variant	54962	exon6			AAAATCTTCATGT	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.456A>G	15.37:g.66641417T>C		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	328	174	0.530488	NM_017858	B2CW64|Q9NWZ6	Silent	SNP	ENST00000261881.4	37	CCDS10215.1																																																																																			T|0.945;C|0.055	0.055	strong		0.333	TIPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256897.2	NM_017858	
AKR1C2	1646	hgsc.bcm.edu	37	10	5043747	5043747	+	Missense_Mutation	SNP	C	C	G	rs142672563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:5043747C>G	ENST00000380753.4	-	2	398	c.211G>C	c.(211-213)Gat>Cat	p.D71H	AKR1C2_ENST00000421196.3_Missense_Mutation_p.D71H|AKR1C2_ENST00000407674.1_Missense_Mutation_p.D71H|AKR1C2_ENST00000455190.1_Missense_Mutation_p.D71H	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	71					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)	ACACTGCCATCTGCAATCTTG	0.443													C|||	13	0.00259585	0.0008	0.0043	5008	,	,		21249	0.0		0.001	False		,,,				2504	0.0082				p.D71H		Atlas-SNP	.											.	AKR1C2	68	.	0			c.G211C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP	0,4406		0,0,2203	133.0	114.0	120.0		211,211,211	2.3	1.0	10	dbSNP_134	120	11,8583	8.4+/-32.0	0,11,4286	no	missense,missense,missense	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	81,81,81	0,11,6489	GG,GC,CC		0.128,0.0,0.0846	probably-damaging,probably-damaging,probably-damaging	71/140,71/324,71/324	5043747	11,12989	2203	4297	6500	SO:0001583	missense	1646	exon4			TGCCATCTGCAAT	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.211G>C	10.37:g.5043747C>G	ENSP00000370129:p.Asp71His	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	327	158	0.48318	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Missense_Mutation	SNP	ENST00000380753.4	37	CCDS7062.1	4	0.0018315018315018315	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	0	0.0	C	12.09	1.834056	0.32421	0.0	0.00128	ENSG00000151632	ENST00000380753;ENST00000421196;ENST00000407674;ENST00000455190	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	2.35	2.35	0.29111	NADP-dependent oxidoreductase domain (3);	0.000000	0.56097	D	0.000030	T	0.53769	0.1817	M	0.72894	2.215	0.35214	D	0.775386	D;D;D	0.64830	0.989;0.994;0.988	D;P;P	0.65010	0.931;0.846;0.908	T	0.71735	-0.4503	10	0.87932	D	0	.	10.778	0.46361	0.0:1.0:0.0:0.0	.	71;71;71	B4DKR9;B4DK69;P52895	.;.;AK1C2_HUMAN	H	71	ENSP00000370129:D71H;ENSP00000392694:D71H;ENSP00000385221:D71H;ENSP00000408440:D71H	ENSP00000370129:D71H	D	-	1	0	AKR1C2	5033747	0.999000	0.42202	0.971000	0.41717	0.309000	0.27889	4.461000	0.60115	1.601000	0.50113	0.205000	0.17691	GAT	C|0.998;G|0.002	0.002	strong		0.443	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354	
CRYBG3	131544	hgsc.bcm.edu	37	3	97660106	97660106	+	Missense_Mutation	SNP	A	A	C	rs4857302	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:97660106A>C	ENST00000182096.4	+	17	2840	c.2776A>C	c.(2776-2778)Aat>Cat	p.N926H	CRYBG3_ENST00000485253.1_3'UTR|CRYBG3_ENST00000389622.2_Missense_Mutation_p.N133H	NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2874							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TAGTGGAAAGAATACTCAGAT	0.433													A|||	2411	0.48143	0.2648	0.5101	5008	,	,		15499	0.6875		0.5139	False		,,,				2504	0.5082				p.N2874H		Atlas-SNP	.											.	CRYBG3	86	.	0			c.A8620C						PASS	.	A	HIS/ASN	1101,2653		168,765,944	126.0	119.0	122.0		8620	3.3	0.2	3	dbSNP_111	122	4213,3989		1099,2015,987	no	missense	CRYBG3	XM_003118522.2	68	1267,2780,1931	CC,CA,AA		48.6345,29.3287,44.4463	benign	2874/2971	97660106	5314,6642	1877	4101	5978	SO:0001583	missense	131544	exon20			GGAAAGAATACTC			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.2776A>C	3.37:g.97660106A>C	ENSP00000182096:p.Asn926His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		1122	0.5137362637362637	142	0.2886178861788618	165	0.4558011049723757	418	0.7307692307692307	397	0.5237467018469657	A	10.97	1.501933	0.26949	0.293287	0.513655	ENSG00000080200	ENST00000182096;ENST00000389622	T;T	0.28666	1.6;1.6	6.07	3.35	0.38373	Ricin B-related lectin (1);Ricin B lectin (3);	0.424754	0.24247	N	0.040215	T	0.00012	0.0000	L	0.49778	1.585	0.80722	P	0.0	D	0.53885	0.963	P	0.51487	0.671	T	0.29212	-1.0019	9	0.62326	D	0.03	.	5.9919	0.19472	0.629:0.0:0.2565:0.1144	rs4857302;rs17302718;rs61639278;rs4857302	926	Q68DQ2	CRBG3_HUMAN	H	926;133	ENSP00000182096:N926H;ENSP00000374273:N133H	ENSP00000182096:N926H	N	+	1	0	CRYBG3	99142796	0.282000	0.24268	0.181000	0.23098	0.542000	0.35054	0.703000	0.25646	0.077000	0.16863	-1.463000	0.01021	AAT	A|0.498;C|0.502	0.502	strong		0.433	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
MMP10	4319	hgsc.bcm.edu	37	11	102643718	102643718	+	Silent	SNP	G	G	T	rs17359286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102643718G>T	ENST00000279441.4	-	8	1122	c.1086C>A	c.(1084-1086)atC>atA	p.I362I		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	362					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	CATTTCCTCTGATGGCCCAGA	0.368													G|||	56	0.0111821	0.0015	0.0159	5008	,	,		16199	0.0		0.0408	False		,,,				2504	0.002				p.I362I		Atlas-SNP	.											.	MMP10	44	.	0			c.C1086A						PASS	.	G		28,4378	33.5+/-64.1	0,28,2175	104.0	105.0	105.0		1086	2.4	0.8	11	dbSNP_123	105	332,8264	116.5+/-176.2	7,318,3973	no	coding-synonymous	MMP10	NM_002425.2		7,346,6148	TT,TG,GG		3.8623,0.6355,2.7688		362/477	102643718	360,12642	2203	4298	6501	SO:0001819	synonymous_variant	4319	exon8			TCCTCTGATGGCC	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.1086C>A	11.37:g.102643718G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_002425	B2R9X9|Q53HH9	Silent	SNP	ENST00000279441.4	37	CCDS8321.1																																																																																			G|0.976;T|0.024	0.024	strong		0.368	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
ACTL9	284382	hgsc.bcm.edu	37	19	8808900	8808900	+	Missense_Mutation	SNP	A	A	G	rs10410943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8808900A>G	ENST00000324436.3	-	1	272	c.152T>C	c.(151-153)gTg>gCg	p.V51A		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	51			V -> A (in dbSNP:rs10410943). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						AATAACCACCACGCCGGTCTT	0.657													G|||	3965	0.791733	0.7995	0.7219	5008	,	,		13806	0.874		0.7127	False		,,,				2504	0.8272				p.V51A		Atlas-SNP	.											.	ACTL9	74	.	0			c.T152C						PASS	.	G	ALA/VAL	3491,915	338.9+/-305.5	1392,707,104	44.0	51.0	49.0		152	3.1	0.0	19	dbSNP_119	49	5883,2717	415.8+/-351.9	1997,1889,414	yes	missense	ACTL9	NM_178525.3	64	3389,2596,518	GG,GA,AA		31.593,20.7671,27.9256	benign	51/417	8808900	9374,3632	2203	4300	6503	SO:0001583	missense	284382	exon1			ACCACCACGCCGG		CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.152T>C	19.37:g.8808900A>G	ENSP00000316674:p.Val51Ala	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	1696	0.7765567765567766	397	0.806910569105691	266	0.7348066298342542	493	0.8618881118881119	540	0.712401055408971	G	0.828	-0.746413	0.03065	0.792329	0.68407	ENSG00000181786	ENST00000324436	D	0.92805	-3.11	3.12	3.12	0.35913	.	0.586122	0.13895	N	0.355344	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	0.40327	-0.9569	9	0.02654	T	1	.	9.9865	0.41846	0.1073:0.0:0.8927:0.0	rs10410943;rs17845740;rs17858691;rs17859417;rs59846574;rs10410943	51	Q8TC94	ACTL9_HUMAN	A	51	ENSP00000316674:V51A	ENSP00000316674:V51A	V	-	2	0	ACTL9	8669900	1.000000	0.71417	0.005000	0.12908	0.026000	0.11368	4.998000	0.63927	0.907000	0.36646	-0.355000	0.07637	GTG	A|0.251;G|0.749	0.749	strong		0.657	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525	
GEMIN4	50628	hgsc.bcm.edu	37	17	650518	650518	+	Silent	SNP	G	G	A	rs35696687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:650518G>A	ENST00000319004.5	-	2	883	c.765C>T	c.(763-765)gaC>gaT	p.D255D	GEMIN4_ENST00000576778.1_Silent_p.D244D|GEMIN4_ENST00000437269.1_Missense_Mutation_p.T168M	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	255					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)		CCTGGGGGTCGTCCTCTGTCA	0.612													G|||	370	0.0738818	0.0098	0.0865	5008	,	,		19416	0.002		0.1918	False		,,,				2504	0.1043				p.D255D		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C765T						PASS	.	G		145,4211		2,141,2035	93.0	102.0	99.0		765	-10.7	0.6	17	dbSNP_126	99	1441,7091		136,1169,2961	no	coding-synonymous	GEMIN4	NM_015721.2		138,1310,4996	AA,AG,GG		16.8894,3.3287,12.306		255/1059	650518	1586,11302	2178	4266	6444	SO:0001819	synonymous_variant	50628	exon2			GGGGTCGTCCTCT	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.765C>T	17.37:g.650518G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	153	151	0.986928	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1	175	0.08012820512820513	2	0.0040650406504065045	30	0.08287292817679558	0	0.0	143	0.18865435356200527	G	0.561	-0.845209	0.02671	0.033287	0.168894	ENSG00000179409	ENST00000437269	T	0.10005	2.92	5.37	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.35151	-0.9800	7	0.02654	T	1	-5.5261	7.923	0.29857	0.0985:0.3416:0.4825:0.0775	rs35696687;rs61746325	168	E7EN12	.	M	168	ENSP00000392460:T168M	ENSP00000392460:T168M	T	-	2	0	GEMIN4	597268	0.000000	0.05858	0.616000	0.29078	0.664000	0.39144	-4.479000	0.00227	-2.233000	0.00716	0.557000	0.71058	ACG	G|0.897;A|0.103	0.103	strong		0.612	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
NF1	4763	hgsc.bcm.edu	37	17	29679401	29679401	+	Silent	SNP	A	A	G	rs55865524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:29679401A>G	ENST00000358273.4	+	51	7967	c.7584A>G	c.(7582-7584)caA>caG	p.Q2528Q	NF1_ENST00000417592.2_Intron|NF1_ENST00000356175.3_Silent_p.Q2507Q|NF1_ENST00000444181.2_Silent_p.Q321Q	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2528					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)		ACATGGGGCAACCTTCTCAGG	0.413			"""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|||	5	0.000998403	0.0023	0.0029	5008	,	,		14500	0.0		0.0	False		,,,				2504	0.0				p.Q2528Q		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.A7584G						PASS	.	G	,	4,4402	825.7+/-416.5	0,4,2199	56.0	53.0	54.0		7521,7584	4.9	1.0	17	dbSNP_129	54	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	0,12,6491	GG,GA,AA		0.093,0.0908,0.0923	,	2507/2819,2528/2840	29679401	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon51	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	GGGGCAACCTTCT		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.7584A>G	17.37:g.29679401A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	66	0.545455	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			A|0.999;G|0.001	0.001	strong		0.413	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
CHID1	66005	hgsc.bcm.edu	37	11	870446	870446	+	Missense_Mutation	SNP	G	G	A	rs6682	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:870446G>A	ENST00000449825.1	-	11	1369	c.1013C>T	c.(1012-1014)gCc>gTc	p.A338V	CHID1_ENST00000323578.8_Missense_Mutation_p.A338V|CHID1_ENST00000436108.2_Missense_Mutation_p.A338V|CHID1_ENST00000336845.5_Missense_Mutation_p.A363V|CHID1_ENST00000429789.2_Missense_Mutation_p.A307V|CHID1_ENST00000323541.7_Missense_Mutation_p.A368V|CHID1_ENST00000526714.1_5'UTR|CHID1_ENST00000528581.1_Missense_Mutation_p.A363V|CHID1_ENST00000454838.2_Missense_Mutation_p.A363V	NM_001142675.1	NP_001136147.1	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1	338			A -> V (in dbSNP:rs6682). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|innate immune response (GO:0045087)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	chitinase activity (GO:0004568)|oligosaccharide binding (GO:0070492)			endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	13		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;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735)		GTGCTCTGAGGCCTGGCTGTC	0.607													G|||	2849	0.56889	0.4077	0.4092	5008	,	,		17548	0.7639		0.4851	False		,,,				2504	0.7853				p.A363V	Pancreas(117;992 2327 5172 41921)	Atlas-SNP	.											.	CHID1	29	.	0			c.C1088T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1912,2492	537.0+/-374.6	424,1064,714	90.0	72.0	78.0		1013,1013,1088,920,1013	4.0	0.9	11	dbSNP_52	78	4285,4305	566.4+/-388.7	1068,2149,1078	yes	missense,missense,missense,missense,missense	CHID1	NM_001142674.1,NM_001142675.1,NM_001142676.1,NM_001142677.1,NM_023947.3	64,64,64,64,64	1492,3213,1792	AA,AG,GG		49.8836,43.4151,47.6912	benign,benign,benign,benign,benign	338/394,338/394,363/419,307/363,338/394	870446	6197,6797	2202	4295	6497	SO:0001583	missense	66005	exon12			TCTGAGGCCTGGC	AK124697	CCDS7722.1, CCDS44510.1, CCDS44511.1	11p15.5	2005-10-27			ENSG00000177830	ENSG00000177830			28474	protein-coding gene	gene with protein product		615692					Standard	NM_023947		Approved	MGC3234, FLJ42707	uc001lsm.3	Q9BWS9	OTTHUMG00000133314	ENST00000449825.1:c.1013C>T	11.37:g.870446G>A	ENSP00000391255:p.Ala338Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001142676	B3KWB0|Q8NBM9|Q96CZ3|Q96S93|Q96SK0|Q9BY52	Missense_Mutation	SNP	ENST00000449825.1	37	CCDS7722.1	1145	0.5242673992673993	203	0.41260162601626016	157	0.43370165745856354	416	0.7272727272727273	369	0.4868073878627968	G	15.69	2.908570	0.52439	0.434151	0.498836	ENSG00000177830	ENST00000323541;ENST00000449825;ENST00000454838;ENST00000323578;ENST00000429789;ENST00000528581;ENST00000336845;ENST00000436108	T;T;T;T;T;T;T;T	0.33865	1.39;1.41;1.83;1.41;1.43;1.83;1.83;1.41	3.99	3.99	0.46301	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.381500	0.25978	N	0.027088	T	0.00012	0.0000	M	0.72894	2.215	0.25636	P	0.9862583	P;B;B;B	0.39131	0.661;0.134;0.003;0.229	B;B;B;B	0.41666	0.363;0.027;0.009;0.166	T	0.27739	-1.0065	9	0.33141	T	0.24	-22.9675	11.9203	0.52787	0.0:0.0:1.0:0.0	rs6682;rs3210962;rs35207476;rs57796313;rs6682	368;307;363;338	B7Z705;Q9BWS9-3;Q9BWS9-2;Q9BWS9	.;.;.;CHID1_HUMAN	V	368;338;363;338;307;363;363;338	ENSP00000324821:A368V;ENSP00000391255:A338V;ENSP00000398722:A363V;ENSP00000325055:A338V;ENSP00000416034:A307V;ENSP00000435503:A363V;ENSP00000338838:A363V;ENSP00000388156:A338V	ENSP00000324821:A368V	A	-	2	0	CHID1	860446	0.465000	0.25815	0.946000	0.38457	0.772000	0.43724	2.460000	0.45031	1.935000	0.56089	0.462000	0.41574	GCC	G|0.487;A|0.513	0.513	strong		0.607	CHID1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257112.1	NM_023947	
SYT2	127833	hgsc.bcm.edu	37	1	202574784	202574784	+	Silent	SNP	G	G	A	rs1968583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:202574784G>A	ENST00000367267.1	-	2	309	c.117C>T	c.(115-117)agC>agT	p.S39S	RP11-569A11.1_ENST00000428573.1_RNA|SYT2_ENST00000367268.4_Silent_p.S39S	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	39					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)	TGTCCTCCTGGCTCTCCCCAG	0.557													G|||	1797	0.358826	0.0794	0.4597	5008	,	,		17852	0.3621		0.5746	False		,,,				2504	0.4397				p.S39S		Atlas-SNP	.											.	SYT2	51	.	0			c.C117T						PASS	.	G	,	693,3713	291.3+/-281.4	65,563,1575	70.0	67.0	68.0		117,117	2.1	1.0	1	dbSNP_92	68	4549,4051	595.3+/-393.4	1191,2167,942	no	coding-synonymous,coding-synonymous	SYT2	NM_001136504.1,NM_177402.4	,	1256,2730,2517	AA,AG,GG		47.1047,15.7286,40.3045	,	39/420,39/420	202574784	5242,7764	2203	4300	6503	SO:0001819	synonymous_variant	127833	exon2			CTCCTGGCTCTCC	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.117C>T	1.37:g.202574784G>A		Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	239	108	0.451883	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	37	CCDS1427.1																																																																																			G|0.596;A|0.404	0.404	strong		0.557	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
KIAA1755	85449	hgsc.bcm.edu	37	20	36869769	36869769	+	Missense_Mutation	SNP	C	C	T	rs41282824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36869769C>T	ENST00000279024.4	-	3	1035	c.764G>A	c.(763-765)cGg>cAg	p.R255Q		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	255										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CTCCCCACACCGGGCTTGCTC	0.577													C|||	161	0.0321486	0.0741	0.0231	5008	,	,		19097	0.002		0.0209	False		,,,				2504	0.0245				p.R255Q		Atlas-SNP	.											KIAA1755,colon,carcinoma,0,1	KIAA1755	145	1	0			c.G764A						PASS	.	C	GLN/ARG	329,4077	173.0+/-202.9	13,303,1887	137.0	121.0	126.0		764	5.3	0.3	20	dbSNP_127	126	216,8384	90.4+/-152.6	4,208,4088	yes	missense	KIAA1755	NM_001029864.1	43	17,511,5975	TT,TC,CC		2.5116,7.4671,4.1904	possibly-damaging	255/1201	36869769	545,12461	2203	4300	6503	SO:0001583	missense	85449	exon3			CCACACCGGGCTT	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.764G>A	20.37:g.36869769C>T	ENSP00000279024:p.Arg255Gln	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	217	103	0.474654	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	62	0.028388278388278388	34	0.06910569105691057	13	0.03591160220994475	0	0.0	15	0.01978891820580475	C	7.853	0.724435	0.15439	0.074671	0.025116	ENSG00000149633	ENST00000279024	T	0.05786	3.39	5.31	5.31	0.75309	.	0.347836	0.24952	N	0.034290	T	0.00845	0.0028	L	0.50333	1.59	0.09310	N	0.999999	D	0.71674	0.998	P	0.50860	0.652	T	0.15150	-1.0447	10	0.25106	T	0.35	.	16.293	0.82759	0.0:1.0:0.0:0.0	rs41282824;rs61735726	255	Q5JYT7	K1755_HUMAN	Q	255	ENSP00000279024:R255Q	ENSP00000279024:R255Q	R	-	2	0	KIAA1755	36303183	0.000000	0.05858	0.251000	0.24312	0.112000	0.19704	0.255000	0.18333	2.764000	0.94973	0.655000	0.94253	CGG	C|0.961;T|0.039	0.039	strong		0.577	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
FAM131C	348487	hgsc.bcm.edu	37	1	16385131	16385131	+	Missense_Mutation	SNP	C	C	A	rs1832151	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	442	0	0		WXS	Illumina HiSeq	Phase_I	485	168	0.346392	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	
PITPNM3	83394	hgsc.bcm.edu	37	17	6441376	6441376	+	Missense_Mutation	SNP	G	G	A	rs28493751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:6441376G>A	ENST00000262483.8	-	2	136	c.49C>T	c.(49-51)Ccc>Tcc	p.P17S	PITPNM3_ENST00000421306.3_Missense_Mutation_p.P17S	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	17			P -> S (in dbSNP:rs28493751).		phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)	p.P17S(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AGGTGCCAGGGGGCACCGCCG	0.552													G|||	267	0.0533147	0.0265	0.0648	5008	,	,		18689	0.002		0.1103	False		,,,				2504	0.0757				p.P17S		Atlas-SNP	.											PITPNM3,brain,glioma,0,1	PITPNM3	91	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C49T						scavenged	.	G	SER/PRO,SER/PRO	196,4210	119.6+/-157.3	4,188,2011	39.0	37.0	38.0		49,49	4.9	1.0	17	dbSNP_125	38	939,7661	200.3+/-244.1	62,815,3423	yes	missense,missense	PITPNM3	NM_001165966.1,NM_031220.3	74,74	66,1003,5434	AA,AG,GG		10.9186,4.4485,8.7267	possibly-damaging,possibly-damaging	17/939,17/975	6441376	1135,11871	2203	4300	6503	SO:0001583	missense	83394	exon2			GCCAGGGGGCACC	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.49C>T	17.37:g.6441376G>A	ENSP00000262483:p.Pro17Ser	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	200	106	0.53	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	127	0.05815018315018315	15	0.03048780487804878	28	0.07734806629834254	1	0.0017482517482517483	83	0.10949868073878628	G	18.04	3.534439	0.64972	0.044485	0.109186	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.41065	1.03;1.01	4.89	4.89	0.63831	.	0.182670	0.37219	N	0.002190	T	0.00496	0.0016	N	0.08118	0	0.36580	P	0.12648700000000002	P;P	0.42518	0.782;0.675	B;B	0.41174	0.349;0.19	T	0.08659	-1.0711	9	0.48119	T	0.1	0.2887	13.9315	0.63998	0.0:0.0:1.0:0.0	rs28493751	17;17	F8WEW5;Q9BZ71	.;PITM3_HUMAN	S	17	ENSP00000262483:P17S;ENSP00000407882:P17S	ENSP00000262483:P17S	P	-	1	0	PITPNM3	6382100	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.677000	0.54619	2.439000	0.82584	0.655000	0.94253	CCC	G|0.926;A|0.074	0.074	strong		0.552	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305800	39305800	+	Missense_Mutation	SNP	T	T	A	rs141998775		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39305800T>A	ENST00000343246.4	-	1	254	c.220A>T	c.(220-222)Agc>Tgc	p.S74C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	74	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			cggcagcagctggattcacag	0.657																																					p.S74C		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,4	KRTAP4-5	34	4	0			c.A220T						scavenged	.						12.0	18.0	16.0					17																	39305800		2056	4148	6204	SO:0001583	missense	85289	exon1			AGCAGCTGGATTC	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.220A>T	17.37:g.39305800T>A	ENSP00000340546:p.Ser74Cys	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	79	7	0.0886076	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		
DBH	1621	hgsc.bcm.edu	37	9	136522274	136522274	+	Missense_Mutation	SNP	C	C	T	rs6271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136522274C>T	ENST00000393056.2	+	11	1657	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	DBH-AS1_ENST00000425189.1_RNA	NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	549			R -> C (in dbSNP:rs6271). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:3443096}.		behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	CTCCTTCAACCGCGACGTACT	0.612													C|||	104	0.0207668	0.0053	0.0447	5008	,	,		16323	0.0		0.0606	False		,,,				2504	0.0051				p.R549C		Atlas-SNP	.											.	DBH	86	.	0			c.C1645T	GRCh37	CM054656	DBH	M	rs6271	PASS	.	C	CYS/ARG	57,4349	56.2+/-92.4	0,57,2146	166.0	120.0	136.0		1645	4.2	0.0	9	dbSNP_52	136	656,7944	166.4+/-218.3	25,606,3669	yes	missense	DBH	NM_000787.3	180	25,663,5815	TT,TC,CC		7.6279,1.2937,5.4821	possibly-damaging	549/618	136522274	713,12293	2203	4300	6503	SO:0001583	missense	1621	exon11			TTCAACCGCGACG	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.1645C>T	9.37:g.136522274C>T	ENSP00000376776:p.Arg549Cys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	156	66	0.423077	NM_000787	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	71	0.03250915750915751	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	44	0.05804749340369393	C	10.61	1.397932	0.25205	0.012937	0.076279	ENSG00000123454	ENST00000393056	T	0.49432	0.78	5.07	4.16	0.48862	.	0.346260	0.30492	N	0.009514	T	0.04815	0.0130	M	0.78223	2.4	0.19300	N	0.99997	D	0.57899	0.981	P	0.47162	0.54	T	0.07888	-1.0749	10	0.54805	T	0.06	-26.8568	8.555	0.33476	0.3682:0.5038:0.128:0.0	rs6271;rs6271	549	P09172	DOPO_HUMAN	C	549	ENSP00000376776:R549C	ENSP00000376776:R549C	R	+	1	0	DBH	135512095	0.996000	0.38824	0.028000	0.17463	0.046000	0.14306	3.394000	0.52551	1.109000	0.41680	-0.500000	0.04577	CGC	C|0.956;T|0.044	0.044	strong		0.612	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
FAM71F2	346653	hgsc.bcm.edu	37	7	128315791	128315791	+	Silent	SNP	C	C	G	rs61738927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128315791C>G	ENST00000480462.1	+	2	349	c.243C>G	c.(241-243)gtC>gtG	p.V81V	FAM71F2_ENST00000378704.3_Silent_p.V72V|FAM71F2_ENST00000477515.1_Silent_p.V81V|FAM71F2_ENST00000460349.1_3'UTR			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	81										NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						TCCTCGGGGTCACCTCCTCGG	0.597													.|||	1680	0.335463	0.1959	0.3098	5008	,	,		13009	0.5615		0.2903	False		,,,				2504	0.3558				p.V81V		Atlas-SNP	.											.	FAM71F2	19	.	0			c.C243G						PASS	.	G	,	814,3120		87,640,1240	49.0	51.0	50.0		243,216	1.7	1.0	7	dbSNP_129	50	2477,5833		382,1713,2060	no	coding-synonymous,coding-synonymous	FAM71F2	NM_001012454.3,NM_001128926.1	,	469,2353,3300	GG,GC,CC		29.8075,20.6914,26.8785	,	81/310,72/301	128315791	3291,8953	1967	4155	6122	SO:0001819	synonymous_variant	346653	exon2			CGGGGTCACCTCC	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.243C>G	7.37:g.128315791C>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Silent	SNP	ENST00000480462.1	37	CCDS47701.1																																																																																			C|0.679;G|0.321	0.321	strong		0.597	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
WWP2	11060	hgsc.bcm.edu	37	16	69967897	69967897	+	Silent	SNP	T	T	C	rs2270841	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:69967897T>C	ENST00000359154.2	+	17	1808	c.1707T>C	c.(1705-1707)caT>caC	p.H569H	WWP2_ENST00000448661.1_Silent_p.H569H|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000356003.2_Silent_p.H569H|WWP2_ENST00000568684.1_Silent_p.H130H|MIR140_ENST00000385282.1_RNA|WWP2_ENST00000542271.1_Silent_p.H453H	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	147	0	0		WXS	Illumina HiSeq	Phase_I	144	66	0.458333	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	
FAM189A1	23359	hgsc.bcm.edu	37	15	29416901	29416901	+	Missense_Mutation	SNP	A	A	G	rs2279482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29416901A>G	ENST00000261275.4	-	10	1291	c.1292T>C	c.(1291-1293)gTg>gCg	p.V431A		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	431			V -> A (in dbSNP:rs2279482).			integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						GCTCCCAGGCACAGCCTCAGA	0.562													a|||	858	0.171326	0.2315	0.1153	5008	,	,		16403	0.2202		0.0775	False		,,,				2504	0.1759				p.V431A		Atlas-SNP	.											.	FAM189A1	20	.	0			c.T1292C						PASS	.	G	ALA/VAL	311,1073		40,231,421	63.0	69.0	67.0		1292	-3.4	0.0	15	dbSNP_100	67	231,2951		9,213,1369	yes	missense	FAM189A1	NM_015307.1	64	49,444,1790	GG,GA,AA		7.2596,22.4711,11.8703	benign	431/540	29416901	542,4024	692	1591	2283	SO:0001583	missense	23359	exon10			CCAGGCACAGCCT		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.1292T>C	15.37:g.29416901A>G	ENSP00000261275:p.Val431Ala	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	330	0.1510989010989011	113	0.22967479674796748	40	0.11049723756906077	122	0.21328671328671328	55	0.07255936675461741	a	0.012	-1.672619	0.00758	0.224711	0.072596	ENSG00000104059	ENST00000261275	T	0.09630	2.96	4.28	-3.41	0.04839	.	2.367780	0.01632	N	0.023592	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43294	-0.9400	9	0.15066	T	0.55	-18.2153	3.3831	0.07261	0.2555:0.1122:0.508:0.1243	rs2279482;rs59311904;rs2279482	431	O60320	F1891_HUMAN	A	431	ENSP00000261275:V431A	ENSP00000261275:V431A	V	-	2	0	FAM189A1	27204193	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.069000	0.14552	-0.411000	0.07530	-3.557000	0.00030	GTG	A|0.843;G|0.157	0.157	strong		0.562	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
ACOT12	134526	hgsc.bcm.edu	37	5	80631642	80631642	+	Missense_Mutation	SNP	C	C	T	rs10371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:80631642C>T	ENST00000307624.3	-	12	1235	c.1207G>A	c.(1207-1209)Gct>Act	p.A403T	ACOT12_ENST00000508234.1_5'UTR	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	403	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.		A -> T (in dbSNP:rs10371).		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)		AGACGATAAGCCAAATGTGCT	0.343													C|||	602	0.120208	0.1815	0.134	5008	,	,		17733	0.002		0.159	False		,,,				2504	0.1094				p.A403T		Atlas-SNP	.											.	ACOT12	57	.	0			c.G1207A						PASS	.	C	THR/ALA	849,3557	333.9+/-303.2	73,703,1427	83.0	92.0	89.0		1207	4.3	0.2	5	dbSNP_52	89	1345,7255	262.5+/-284.5	100,1145,3055	yes	missense	ACOT12	NM_130767.2	58	173,1848,4482	TT,TC,CC		15.6395,19.2692,16.8691	benign	403/556	80631642	2194,10812	2203	4300	6503	SO:0001583	missense	134526	exon12			GATAAGCCAAATG	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.1207G>A	5.37:g.80631642C>T	ENSP00000303246:p.Ala403Thr	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	214	81	0.378505	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	253	0.11584249084249085	83	0.16869918699186992	51	0.1408839779005525	2	0.0034965034965034965	117	0.15435356200527706	C	7.282	0.609265	0.14066	0.192692	0.156395	ENSG00000172497	ENST00000307624	T	0.31247	1.5	5.24	4.34	0.51931	Lipid-binding START (2);START-like domain (1);	0.256266	0.37437	N	0.002099	T	0.00039	0.0001	N	0.25890	0.77	0.27235	P	0.9592961	B	0.21071	0.051	B	0.27170	0.077	T	0.17561	-1.0365	9	0.34782	T	0.22	5.4069	11.1453	0.48426	0.0:0.9049:0.0:0.0951	rs10371;rs1132753;rs3193840;rs52811470;rs56771708;rs10371	403	Q8WYK0	ACO12_HUMAN	T	403	ENSP00000303246:A403T	ENSP00000303246:A403T	A	-	1	0	ACOT12	80667398	0.913000	0.31002	0.208000	0.23602	0.034000	0.12701	1.926000	0.40084	1.275000	0.44379	0.561000	0.74099	GCT	C|0.852;T|0.148	0.148	strong		0.343	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767	
PRKCD	5580	hgsc.bcm.edu	37	3	53213657	53213657	+	Silent	SNP	T	T	C	rs2230493	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:53213657T>C	ENST00000394729.2	+	3	508	c.180T>C	c.(178-180)gaT>gaC	p.D60D	PRKCD_ENST00000330452.3_Silent_p.D60D	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	60	C2.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	CGACGTTCGATGCCCACATCT	0.592													T|||	410	0.081869	0.0416	0.0807	5008	,	,		21183	0.0159		0.1441	False		,,,				2504	0.1411				p.D60D		Atlas-SNP	.											.	PRKCD	124	.	0			c.T180C						PASS	.	T	,	258,4148	149.5+/-183.7	13,232,1958	92.0	77.0	82.0		180,180	-7.2	0.3	3	dbSNP_98	82	1428,7172	273.1+/-290.5	112,1204,2984	no	coding-synonymous,coding-synonymous	PRKCD	NM_006254.3,NM_212539.1	,	125,1436,4942	CC,CT,TT		16.6047,5.8557,12.9632	,	60/677,60/677	53213657	1686,11320	2203	4300	6503	SO:0001819	synonymous_variant	5580	exon3			GTTCGATGCCCAC		CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.180T>C	3.37:g.53213657T>C		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	174	68	0.390805	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Silent	SNP	ENST00000394729.2	37	CCDS2870.1																																																																																			T|0.897;C|0.103	0.103	strong		0.592	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1		
CPNE3	8895	hgsc.bcm.edu	37	8	87540872	87540872	+	Silent	SNP	G	G	A	rs10956871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87540872G>A	ENST00000521271.1	+	3	261	c.99G>A	c.(97-99)ttG>ttA	p.L33L	CPNE3_ENST00000198765.4_Silent_p.L33L	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	33	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						TATGTGTGTTGTTTTTGAATA	0.373													A|||	825	0.164736	0.2103	0.1383	5008	,	,		19358	0.0496		0.2555	False		,,,				2504	0.1472				p.L33L		Atlas-SNP	.											.	CPNE3	65	.	0			c.G99A						PASS	.	A		1068,3338	722.7+/-409.3	116,836,1251	116.0	115.0	116.0		99	-5.3	0.4	8	dbSNP_120	116	2330,6270	703.9+/-405.4	315,1700,2285	no	coding-synonymous	CPNE3	NM_003909.3		431,2536,3536	AA,AG,GG		27.093,24.2397,26.1264		33/538	87540872	3398,9608	2203	4300	6503	SO:0001819	synonymous_variant	8895	exon3			TGTGTTGTTTTTG	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.99G>A	8.37:g.87540872G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_003909	A8KA47|Q8IYA1	Silent	SNP	ENST00000521271.1	37	CCDS6243.1																																																																																			G|0.775;A|0.225	0.225	strong		0.373	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1		
NPHP4	261734	hgsc.bcm.edu	37	1	5937327	5937327	+	Silent	SNP	C	C	T	rs3747990	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:5937327C>T	ENST00000378156.4	-	20	2908	c.2643G>A	c.(2641-2643)gcG>gcA	p.A881A	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	881					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)		TGTCCACGTCCGCCAGCTTCT	0.647													C|||	448	0.0894569	0.0083	0.1153	5008	,	,		16487	0.0833		0.1571	False		,,,				2504	0.1176				p.A881A		Atlas-SNP	.											.	NPHP4	119	.	0			c.G2643A						PASS	.	C		124,4156		4,116,2020	27.0	27.0	27.0		2643	-10.2	0.0	1	dbSNP_107	27	1477,7005		141,1195,2905	no	coding-synonymous	NPHP4	NM_015102.3		145,1311,4925	TT,TC,CC		17.4133,2.8972,12.5451		881/1427	5937327	1601,11161	2140	4241	6381	SO:0001819	synonymous_variant	261734	exon20			CACGTCCGCCAGC	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.2643G>A	1.37:g.5937327C>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	200	105	0.525	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			C|0.906;T|0.094	0.094	strong		0.647	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
TXNDC2	84203	hgsc.bcm.edu	37	18	9887877	9887877	+	Silent	SNP	G	G	A	rs34362649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:9887877G>A	ENST00000306084.6	+	2	1600	c.1401G>A	c.(1399-1401)ggG>ggA	p.G467G	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Silent_p.G400G	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	467	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						AGGAGGCCGGGGAGAGGCTGG	0.567													G|||	78	0.0155751	0.0015	0.0173	5008	,	,		20053	0.0		0.0596	False		,,,				2504	0.0041				p.G467G		Atlas-SNP	.											.	TXNDC2	168	.	0			c.G1401A						PASS	.	G	,	31,4375	38.4+/-70.7	0,31,2172	61.0	50.0	54.0		1401,1200	-1.4	0.5	18	dbSNP_126	54	431,8169	130.7+/-188.6	12,407,3881	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	12,438,6053	AA,AG,GG		5.0116,0.7036,3.5522	,	467/554,400/487	9887877	462,12544	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			GGCCGGGGAGAGG	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.1401G>A	18.37:g.9887877G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	162	88	0.54321	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			G|0.960;A|0.040	0.040	strong		0.567	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
PKHD1	5314	hgsc.bcm.edu	37	6	51917968	51917968	+	Silent	SNP	T	T	G	rs4715271	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:51917968T>G	ENST00000371117.3	-	21	2321	c.2046A>C	c.(2044-2046)ccA>ccC	p.P682P	PKHD1_ENST00000340994.4_Silent_p.P682P	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	682					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAACCAGCACTGGGGAGTTTG	0.527													T|||	294	0.0587061	0.0242	0.0749	5008	,	,		19890	0.0407		0.1113	False		,,,				2504	0.0583				p.P682P		Atlas-SNP	.											PKHD1_ENST00000340994,NS,malignant_melanoma,-1,4	PKHD1	927	4	0			c.A2046C						PASS	.	T	,	168,4238	110.8+/-149.0	5,158,2040	71.0	73.0	72.0		2046,2046	-11.3	0.0	6	dbSNP_111	72	952,7648	207.9+/-249.5	60,832,3408	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	65,990,5448	GG,GT,TT		11.0698,3.813,8.6114	,	682/4075,682/3397	51917968	1120,11886	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon21			CAGCACTGGGGAG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2046A>C	6.37:g.51917968T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.921;G|0.079	0.079	strong		0.527	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
GPR158	57512	hgsc.bcm.edu	37	10	25701316	25701316	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:25701316C>T	ENST00000376351.3	+	4	1608	c.1249C>T	c.(1249-1251)Cga>Tga	p.R417*		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	417					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						TAAGTATTTACGACTTGCCAT	0.512																																					p.R417X		Atlas-SNP	.											GPR158,NS,carcinoma,0,2	GPR158	255	2	0			c.C1249T						scavenged	.						260.0	226.0	238.0					10																	25701316		2203	4300	6503	SO:0001587	stop_gained	57512	exon4			TATTTACGACTTG	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1249C>T	10.37:g.25701316C>T	ENSP00000365529:p.Arg417*	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	169	2	0.0118343	NM_020752	Q6QR81|Q9ULT3	Nonsense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	C	42	9.510353	0.99190	.	.	ENSG00000151025	ENST00000376351	.	.	.	6.16	3.25	0.37280	.	0.000000	0.53938	D	0.000042	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5634	0.76269	0.3616:0.6384:0.0:0.0	.	.	.	.	X	417	.	ENSP00000365529:R417X	R	+	1	2	GPR158	25741322	1.000000	0.71417	0.975000	0.42487	0.970000	0.65996	2.899000	0.48679	0.441000	0.26529	-0.158000	0.13435	CGA	.	.	none		0.512	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
RADIL	55698	hgsc.bcm.edu	37	7	4841318	4841318	+	Silent	SNP	G	G	A	rs6945581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:4841318G>A	ENST00000399583.3	-	12	2995	c.2808C>T	c.(2806-2808)aaC>aaT	p.N936N	RADIL_ENST00000538469.1_Silent_p.N696N|RADIL_ENST00000536091.1_3'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	936					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CGCTGAGTCCGTTCCTCTGCC	0.701													G|||	860	0.171725	0.4433	0.1196	5008	,	,		14271	0.001		0.1064	False		,,,				2504	0.0849				p.N936N		Atlas-SNP	.											RADIL,brain,glioma,0,2	RADIL	110	2	0			c.C2808T						PASS	.	G		1147,2629		163,821,904	7.0	9.0	8.0		2808	-4.4	0.0	7	dbSNP_116	8	815,7397		45,725,3336	no	coding-synonymous	RADIL	NM_018059.4		208,1546,4240	AA,AG,GG		9.9245,30.3761,16.3664		936/1076	4841318	1962,10026	1888	4106	5994	SO:0001819	synonymous_variant	55698	exon12			GAGTCCGTTCCTC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2808C>T	7.37:g.4841318G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.861;A|0.139	0.139	strong		0.701	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
TSHR	7253	hgsc.bcm.edu	37	14	81575005	81575005	+	Missense_Mutation	SNP	C	C	A	rs3783941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:81575005C>A	ENST00000342443.6	+	9	992	c.742C>A	c.(742-744)Cgc>Agc	p.R248S	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000554263.1_3'UTR|TSHR_ENST00000298171.2_Intron|TSHR_ENST00000541158.2_Intron|TSHR_ENST00000554435.1_Missense_Mutation_p.R269S	NM_001018036.2|NM_001142626.2	NP_001018046.1|NP_001136098.1	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	0					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)			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)	GAAGGCCCCACGCTCCAGTAT	0.502			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism						A|||	3056	0.610224	0.6354	0.6239	5008	,	,		15351	0.3889		0.671	False		,,,				2504	0.7321				p.R269S		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	.	TSHR	462	.	0			c.C805A						PASS	.	A	,SER/ARG,SER/ARG	2709,1697	512.4+/-368.1	844,1021,338	126.0	115.0	119.0		,742,805	-8.6	0.0	14	dbSNP_107	119	5647,2953	459.3+/-364.9	1871,1905,524	yes	intron,missense,missense	TSHR	NM_000369.2,NM_001018036.2,NM_001142626.2	,110,110	2715,2926,862	AA,AC,CC		34.3372,38.5157,35.7527	,,	,248/254,269/275	81575005	8356,4650	2203	4300	6503	SO:0001583	missense	7253	exon9			GCCCCACGCTCCA	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		ENST00000342443.6:c.742C>A	14.37:g.81575005C>A	ENSP00000340113:p.Arg248Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001142626	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000342443.6	37	CCDS32131.1	1262	0.5778388278388278	296	0.6016260162601627	229	0.6325966850828729	224	0.3916083916083916	513	0.6767810026385225	A	8.541	0.873263	0.17322	0.614843	0.656628	ENSG00000165409	ENST00000342443;ENST00000554435	T;T	0.78707	-1.17;-1.2	4.29	-8.59	0.00893	.	.	.	.	.	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	0.22765	-1.0207	8	0.08837	T	0.75	.	1.3539	0.02178	0.1267:0.208:0.245:0.4202	rs3783941;rs17845211;rs17858023;rs61159633;rs3783941	269;248	G3V2A9;P16473-2	.;.	S	248;269	ENSP00000340113:R248S;ENSP00000450549:R269S	ENSP00000340113:R248S	R	+	1	0	TSHR	80644758	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.988000	0.03739	-2.513000	0.00502	-0.346000	0.07831	CGC	C|0.384;A|0.616	0.616	strong		0.502	TSHR-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413366.1	NM_000369	
KAL1	3730	hgsc.bcm.edu	37	X	8504833	8504833	+	Missense_Mutation	SNP	C	C	T	rs808119	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:8504833C>T	ENST00000262648.3	-	11	1749	c.1600G>A	c.(1600-1602)Gtt>Att	p.V534I	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	534			V -> I (in dbSNP:rs808119). {ECO:0000269|PubMed:11297579, ECO:0000269|PubMed:15001591, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17223984, ECO:0000269|PubMed:1913827, ECO:0000269|PubMed:1922361, ECO:0000269|PubMed:8504298, ECO:0000269|PubMed:8989261, ECO:0000269|PubMed:9589672, ECO:0000269|Ref.5}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						AGGCAGCCAACAGGCTTGTGG	0.507													C|||	1843	0.488212	0.2458	0.3487	3775	,	,		14377	0.506		0.5089	False		,,,				2504	0.2597				p.V534I		Atlas-SNP	.											.	KAL1	78	.	0			c.G1600A						PASS	.	C	ILE/VAL	1441,2394		233,766,209,633,362	78.0	59.0	65.0		1600	-4.1	0.0	X	dbSNP_86	65	4512,2216		1099,1062,1252,267,620	no	missense	KAL1	NM_000216.2	29	1332,1828,1461,900,982	TT,TC,T,CC,C		32.937,37.575,43.6429	benign	534/681	8504833	5953,4610	2203	4300	6503	SO:0001583	missense	3730	exon11			AGCCAACAGGCTT		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1600G>A	X.37:g.8504833C>T	ENSP00000262648:p.Val534Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	913	0.5503315250150693	72	0.17391304347826086	79	0.3015267175572519	194	0.5418994413407822	247	0.4862204724409449	C	0.004	-2.328820	0.00229	0.37575	0.67063	ENSG00000011201	ENST00000262648	T	0.73363	-0.74	3.89	-4.09	0.03951	.	0.740248	0.12185	N	0.491758	T	0.00012	0.0000	N	0.03238	-0.38	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.27938	-1.0059	9	0.02654	T	1	-1.3626	7.395	0.26931	0.1398:0.1336:0.0:0.7266	rs808119;rs56908549	534	P23352	KALM_HUMAN	I	534	ENSP00000262648:V534I	ENSP00000262648:V534I	V	-	1	0	KAL1	8464833	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-0.458000	0.06737	-1.055000	0.03209	-0.198000	0.12761	GTT	C|0.447;T|0.553	0.553	strong		0.507	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
GRHL1	29841	hgsc.bcm.edu	37	2	10095185	10095185	+	Silent	SNP	T	T	C	rs16867251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:10095185T>C	ENST00000324907.9	+	2	298	c.162T>C	c.(160-162)gaT>gaC	p.D54D	GRHL1_ENST00000405379.2_Silent_p.D54D|GRHL1_ENST00000324883.5_5'UTR	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	54	Transcription activation.				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)		TCAATGGAGATGAAGACAGCG	0.527													C|||	873	0.174321	0.4365	0.1023	5008	,	,		19672	0.0109		0.1461	False		,,,				2504	0.0685				p.D54D		Atlas-SNP	.											.	GRHL1	95	.	0			c.T162C						PASS	.	C		1415,2699		234,947,876	58.0	64.0	62.0		162	-11.1	0.0	2	dbSNP_123	62	1127,7351		73,981,3185	no	coding-synonymous	GRHL1	NM_198182.2		307,1928,4061	CC,CT,TT		13.2932,34.3947,20.1874		54/619	10095185	2542,10050	2057	4239	6296	SO:0001819	synonymous_variant	29841	exon2			TGGAGATGAAGAC	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.162T>C	2.37:g.10095185T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	158	92	0.582278	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	37	CCDS33144.2																																																																																			T|0.810;C|0.190	0.190	strong		0.527	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552	
ATL2	64225	hgsc.bcm.edu	37	2	38604351	38604351	+	Missense_Mutation	SNP	A	A	G	rs3731847	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:38604351A>G	ENST00000378954.4	-	1	53	c.52T>C	c.(52-54)Tgg>Cgg	p.W18R	ATL2_ENST00000452935.2_5'Flank|ATL2_ENST00000419554.2_Missense_Mutation_p.W18R|ATL2_ENST00000332337.4_5'Flank|ATL2_ENST00000406122.1_5'UTR|ATL2_ENST00000402054.1_5'Flank|ATL2_ENST00000539122.1_5'UTR|ATL2_ENST00000546051.1_5'Flank	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	18			W -> R (in dbSNP:rs3731847). {ECO:0000269|Ref.1}.		endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						CGCCGGCGCCACAGCCCCTGG	0.682													G|||	2472	0.49361	0.82	0.3934	5008	,	,		7916	0.1974		0.4056	False		,,,				2504	0.5194				p.W18R		Atlas-SNP	.											.	ATL2	49	.	0			c.T52C						PASS	.	G	ARG/TRP,ARG/TRP	3238,1160		1209,820,170	18.0	23.0	22.0		52,52	0.4	1.0	2	dbSNP_107	22	3347,5239		606,2135,1552	no	missense,missense	ATL2	NM_001135673.1,NM_022374.2	101,101	1815,2955,1722	GG,GA,AA		38.9821,26.3756,49.2837	benign,benign	18/584,18/580	38604351	6585,6399	2199	4293	6492	SO:0001583	missense	64225	exon1			GGCGCCACAGCCC		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"""ADP-ribosylation factor-like 6 interacting protein 2"""	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.52T>C	2.37:g.38604351A>G	ENSP00000368237:p.Trp18Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	31	9	0.290323	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	963	0.4409340659340659	398	0.8089430894308943	148	0.4088397790055249	113	0.19755244755244755	304	0.40105540897097625	G	2.842	-0.240149	0.05944	0.736244	0.389821	ENSG00000119787	ENST00000378954;ENST00000419554;ENST00000449130;ENST00000451483	T;T;D;T	0.84070	-1.19;-1.23;-1.8;2.58	3.78	0.417	0.16421	.	0.332033	0.20851	N	0.084527	T	0.00012	0.0000	N	0.02916	-0.46	0.09310	P	0.9999999999927123	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38650	-0.9651	9	0.20046	T	0.44	-1.5765	0.6089	0.00757	0.2367:0.1829:0.3778:0.2026	rs3731847;rs59791873	18;18	Q8NHH9-2;Q8NHH9	.;ATLA2_HUMAN	R	18	ENSP00000368237:W18R;ENSP00000415336:W18R;ENSP00000409811:W18R;ENSP00000404921:W18R	ENSP00000368237:W18R	W	-	1	0	ATL2	38457855	1.000000	0.71417	0.998000	0.56505	0.029000	0.11900	1.309000	0.33539	0.006000	0.14734	-0.755000	0.03482	TGG	A|0.523;G|0.477	0.477	strong		0.682	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374	
TPSD1	23430	hgsc.bcm.edu	37	16	1306817	1306817	+	Missense_Mutation	SNP	G	G	A	rs3993983		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306817G>A	ENST00000211076.3	+	3	422	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.A85T	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	92	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A92T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				GGATCTGGCCGCCCTCAGGGT	0.652																																					p.A92T		Atlas-SNP	.											TPSD1,trunk,malignant_melanoma,0,1	TPSD1	47	1	1	Substitution - Missense(1)	skin(1)	c.G274A						PASS	.						42.0	48.0	46.0					16																	1306817		2199	4300	6499	SO:0001583	missense	23430	exon3			CTGGCCGCCCTCA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.274G>A	16.37:g.1306817G>A	ENSP00000211076:p.Ala92Thr	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	391	106	0.2711	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	-	0.599	-0.829982	0.02734	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.88975	-2.45;-2.45	2.55	-5.1	0.02911	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.840310	0.02910	N	0.136553	T	0.73442	0.3587	N	0.12920	0.275	0.09310	N	1	B	0.20459	0.045	B	0.11329	0.006	T	0.65977	-0.6037	10	0.10111	T	0.7	.	2.4616	0.04542	0.3598:0.0:0.2688:0.3714	rs3993983	92	Q9BZJ3	TRYD_HUMAN	T	85;92	ENSP00000380668:A85T;ENSP00000211076:A92T	ENSP00000211076:A92T	A	+	1	0	TPSD1	1246818	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.726000	0.01861	-1.446000	0.01945	0.185000	0.17295	GCC	G|0.999;A|0.001	0.001	weak		0.652	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
CPNE7	27132	hgsc.bcm.edu	37	16	89657630	89657630	+	Missense_Mutation	SNP	C	C	G	rs377056293		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89657630C>G	ENST00000268720.5	+	15	1619	c.1489C>G	c.(1489-1491)Cgc>Ggc	p.R497G	CPNE7_ENST00000319518.8_Missense_Mutation_p.R422G	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	497	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		CAAGGTGGCACGCGTGGCGGC	0.687																																					p.R497G		Atlas-SNP	.											.	CPNE7	56	.	0			c.C1489G						PASS	.						18.0	20.0	19.0					16																	89657630		2183	4285	6468	SO:0001583	missense	27132	exon15			GTGGCACGCGTGG	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.1489C>G	16.37:g.89657630C>G	ENSP00000268720:p.Arg497Gly	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940346	0.34283	.	.	ENSG00000178773	ENST00000319518;ENST00000268720;ENST00000529800	T;T;T	0.22945	1.93;1.93;1.93	3.9	1.73	0.24493	von Willebrand factor, type A (2);Copine (1);	0.305959	0.32161	N	0.006489	T	0.27697	0.0681	M	0.77313	2.365	0.38493	D	0.948011	P;B	0.36660	0.564;0.049	B;B	0.37304	0.246;0.087	T	0.14392	-1.0474	10	0.59425	D	0.04	0.9483	6.5897	0.22639	0.295:0.6139:0.0:0.0911	.	422;497	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	G	422;497;142	ENSP00000317374:R422G;ENSP00000268720:R497G;ENSP00000435876:R142G	ENSP00000268720:R497G	R	+	1	0	CPNE7	88185131	0.518000	0.26234	0.988000	0.46212	0.873000	0.50193	2.044000	0.41241	0.759000	0.33084	0.556000	0.70494	CGC	.	.	alt		0.687	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
SF3A3	10946	hgsc.bcm.edu	37	1	38449910	38449910	+	Silent	SNP	T	T	C	rs11210870	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:38449910T>C	ENST00000373019.4	-	6	1354	c.399A>G	c.(397-399)gaA>gaG	p.E133E	SF3A3_ENST00000489537.1_5'UTR|SF3A3_ENST00000448721.2_Silent_p.E80E	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	133					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)				CATATCCCTCTTCATCTGTGA	0.453													T|||	1467	0.292931	0.2511	0.3703	5008	,	,		20157	0.2421		0.2753	False		,,,				2504	0.365				p.E133E		Atlas-SNP	.											.	SF3A3	37	.	0			c.A399G						PASS	.	T		1139,3267	402.6+/-332.4	140,859,1204	115.0	88.0	97.0		399	4.3	1.0	1	dbSNP_120	97	2495,6105	405.2+/-348.4	341,1813,2146	no	coding-synonymous	SF3A3	NM_006802.2		481,2672,3350	CC,CT,TT		29.0116,25.8511,27.941		133/502	38449910	3634,9372	2203	4300	6503	SO:0001819	synonymous_variant	10946	exon6			TCCCTCTTCATCT	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.399A>G	1.37:g.38449910T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_006802	D3DPT5|Q15460|Q5VT87	Silent	SNP	ENST00000373019.4	37	CCDS428.1																																																																																			T|0.718;C|0.282	0.282	strong		0.453	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802	
TCFL5	10732	hgsc.bcm.edu	37	20	61488785	61488785	+	Silent	SNP	T	T	C	rs2294996	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61488785T>C	ENST00000335351.3	-	4	1292	c.1200A>G	c.(1198-1200)caA>caG	p.Q400Q	TCFL5_ENST00000217162.5_Silent_p.Q352Q	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	400	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					TCTCCCTACGTTGAGACCTTC	0.537													C|||	1139	0.227436	0.27	0.196	5008	,	,		19544	0.1597		0.2763	False		,,,				2504	0.2117				p.Q400Q		Atlas-SNP	.											.	TCFL5	43	.	0			c.A1200G						PASS	.	C		1244,3162	704.4+/-407.1	164,916,1123	198.0	169.0	179.0		1200	4.7	1.0	20	dbSNP_100	179	2379,6221	701.2+/-405.2	314,1751,2235	no	coding-synonymous	TCFL5	NM_006602.2		478,2667,3358	CC,CT,TT		27.6628,28.2342,27.8564		400/501	61488785	3623,9383	2203	4300	6503	SO:0001819	synonymous_variant	10732	exon4			CCTACGTTGAGAC	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"""Basic helix-loop-helix proteins"""	11646	protein-coding gene	gene with protein product	"""HPV-16 E2 binding protein 1"""	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.1200A>G	20.37:g.61488785T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_006602	O94771|Q9BYW0	Silent	SNP	ENST00000335351.3	37	CCDS13506.1																																																																																			A|0.005;C|0.255	0.255	strong		0.537	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602	
POP1	10940	hgsc.bcm.edu	37	8	99146261	99146261	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:99146261A>G	ENST00000401707.2	+	6	901	c.820A>G	c.(820-822)Aca>Gca	p.T274A	POP1_ENST00000349693.3_Missense_Mutation_p.T274A	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	274					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			TAACATAGACACAGGTAAACT	0.338																																					p.T274A		Atlas-SNP	.											POP1,NS,carcinoma,0,1	POP1	85	1	0			c.A820G						PASS	.						136.0	133.0	134.0					8																	99146261		2203	4300	6503	SO:0001583	missense	10940	exon6			ATAGACACAGGTA	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"""processing of precursors 1"""	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.820A>G	8.37:g.99146261A>G	ENSP00000385787:p.Thr274Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	A	7.548	0.662067	0.14645	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.35236	1.32;1.32	5.51	0.307	0.15811	.	0.441525	0.24174	N	0.040879	T	0.15912	0.0383	N	0.13235	0.315	0.36378	D	0.861726	B	0.02656	0.0	B	0.04013	0.001	T	0.37407	-0.9707	10	0.05525	T	0.97	0.0715	9.807	0.40799	0.6459:0.0:0.3541:0.0	.	274	Q99575	POP1_HUMAN	A	274	ENSP00000385787:T274A;ENSP00000339529:T274A	ENSP00000339529:T274A	T	+	1	0	POP1	99215437	0.205000	0.23458	0.931000	0.37212	0.838000	0.47535	0.840000	0.27600	-0.165000	0.10908	0.260000	0.18958	ACA	.	.	none		0.338	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029	
MGAT5B	146664	hgsc.bcm.edu	37	17	74921072	74921072	+	Silent	SNP	G	G	C	rs3889145	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	89	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	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	
TTLL7	79739	hgsc.bcm.edu	37	1	84372060	84372060	+	Silent	SNP	G	G	A	rs41301084	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:84372060G>A	ENST00000260505.8	-	17	2456	c.2079C>T	c.(2077-2079)atC>atT	p.I693I	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	693					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		CTGGAAACCGGATCTTCATGT	0.368													G|||	48	0.00958466	0.0038	0.0187	5008	,	,		15472	0.0		0.0288	False		,,,				2504	0.001				p.I693I		Atlas-SNP	.											.	TTLL7	93	.	0			c.C2079T						PASS	.	G		17,4389	25.3+/-52.1	0,17,2186	161.0	163.0	162.0		2079	3.9	1.0	1	dbSNP_127	162	204,8396	88.6+/-150.9	1,202,4097	no	coding-synonymous	TTLL7	NM_024686.4		1,219,6283	AA,AG,GG		2.3721,0.3858,1.6992		693/888	84372060	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	79739	exon17			AAACCGGATCTTC	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"""Tubulin tyrosine ligase-like family"""	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.2079C>T	1.37:g.84372060G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	171	87	0.508772	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Silent	SNP	ENST00000260505.8	37	CCDS690.2																																																																																			G|0.985;A|0.015	0.015	strong		0.368	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686	
RSF1	51773	hgsc.bcm.edu	37	11	77409568	77409568	+	Silent	SNP	T	T	C	rs4945203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:77409568T>C	ENST00000308488.6	-	7	2981	c.2679A>G	c.(2677-2679)ccA>ccG	p.P893P	RSF1_ENST00000480887.1_Silent_p.P641P|RSF1_ENST00000360355.2_Silent_p.P862P			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	893					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)			ATTTTTTGCATGGTTCATCAT	0.433													C|||	986	0.196885	0.3298	0.2161	5008	,	,		17411	0.1736		0.0984	False		,,,				2504	0.1288				p.P893P		Atlas-SNP	.											.	RSF1	105	.	0			c.A2679G						PASS	.	C		1343,3057	693.4+/-405.7	208,927,1065	223.0	203.0	210.0		2679	-8.3	0.4	11	dbSNP_111	210	832,7752	780.7+/-407.7	36,760,3496	no	coding-synonymous	RSF1	NM_016578.3		244,1687,4561	CC,CT,TT		9.6925,30.5227,16.7514		893/1442	77409568	2175,10809	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon7			TTTGCATGGTTCA	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.2679A>G	11.37:g.77409568T>C		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	338	170	0.502959	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1	421	0.19276556776556777	172	0.34959349593495936	67	0.1850828729281768	109	0.19055944055944055	73	0.09630606860158311	C	8.729	0.916226	0.17907	0.305227	0.096925	ENSG00000048649	ENST00000532556	.	.	.	4.68	-8.3	0.01005	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996607	.	.	.	.	.	.	T	0.33445	-0.9868	3	.	.	.	-7.7615	2.551	0.04749	0.1499:0.3493:0.2269:0.2739	rs4945203;rs4945203	.	.	.	R	147	.	.	H	-	2	0	RSF1	77087216	0.001000	0.12720	0.444000	0.26895	0.979000	0.70002	-1.814000	0.01723	-2.263000	0.00689	-0.930000	0.02707	CAT	T|0.813;C|0.187	0.187	strong		0.433	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
PGLYRP4	57115	hgsc.bcm.edu	37	1	153313044	153313044	+	Missense_Mutation	SNP	C	C	T	rs12063091	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153313044C>T	ENST00000359650.5	-	7	701	c.637G>A	c.(637-639)Gtt>Att	p.V213I	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.V209I	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	213			V -> I (in dbSNP:rs12063091). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.V213I(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CGTGGGACAACGCCGGGGCAA	0.592													c|||	295	0.0589058	0.1536	0.0389	5008	,	,		13931	0.0		0.0398	False		,,,				2504	0.0256				p.V213I		Atlas-SNP	.											PGLYRP4,NS,carcinoma,0,1	PGLYRP4	45	1	1	Substitution - Missense(1)	prostate(1)	c.G637A						PASS	.	C	ILE/VAL	580,3826	255.2+/-260.5	29,522,1652	46.0	45.0	45.0		637	-0.3	0.0	1	dbSNP_120	45	515,8085	145.7+/-201.4	9,497,3794	yes	missense	PGLYRP4	NM_020393.2	29	38,1019,5446	TT,TC,CC		5.9884,13.1639,8.4192	benign	213/374	153313044	1095,11911	2203	4300	6503	SO:0001583	missense	57115	exon7			GGACAACGCCGGG	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.637G>A	1.37:g.153313044C>T	ENSP00000352672:p.Val213Ile	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	126	0.057692307692307696	87	0.17682926829268292	13	0.03591160220994475	0	0.0	26	0.03430079155672823	c	0	-2.799602	0.00076	0.131639	0.059884	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.14640	2.49;2.49	3.64	-0.273	0.12915	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (2);	0.338684	0.23220	N	0.050576	T	0.00440	0.0014	N	0.00053	-2.39	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.39057	-0.9632	9	0.02654	T	1	-25.9949	6.3688	0.21469	0.0:0.3413:0.0:0.6587	rs12063091;rs12063091	209;213	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	I	209;213	ENSP00000357728:V209I;ENSP00000352672:V213I	ENSP00000352672:V213I	V	-	1	0	PGLYRP4	151579668	0.012000	0.17670	0.013000	0.15412	0.016000	0.09150	0.482000	0.22276	-0.183000	0.10585	-1.149000	0.01842	GTT	C|0.923;T|0.077	0.077	strong		0.592	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393	
MMP14	4323	hgsc.bcm.edu	37	14	23312594	23312594	+	Missense_Mutation	SNP	G	G	A	rs1042704	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23312594G>A	ENST00000311852.6	+	5	1078	c.817G>A	c.(817-819)Gat>Aat	p.D273N	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	273			D -> N (in dbSNP:rs1042704). {ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	TGTGCTGCCCGATGATGACCG	0.597													G|||	550	0.109824	0.0091	0.1311	5008	,	,		17770	0.0258		0.1988	False		,,,				2504	0.226				p.D273N		Atlas-SNP	.											.	MMP14	40	.	0			c.G817A						PASS	.	G	ASN/ASP	197,4209	122.5+/-159.9	2,193,2008	106.0	108.0	107.0		817	5.6	1.0	14	dbSNP_86	107	1747,6853	317.6+/-313.3	167,1413,2720	yes	missense	MMP14	NM_004995.2	23	169,1606,4728	AA,AG,GG		20.314,4.4712,14.9469	benign	273/583	23312594	1944,11062	2203	4300	6503	SO:0001583	missense	4323	exon5			CTGCCCGATGATG		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"""membrane type 1 metalloprotease"""	600754	"""matrix metalloproteinase 14 (membrane-inserted)"""			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.817G>A	14.37:g.23312594G>A	ENSP00000308208:p.Asp273Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	37	CCDS9577.1	231	0.10576923076923077	8	0.016260162601626018	53	0.1464088397790055	13	0.022727272727272728	157	0.20712401055408972	G	9.413	1.081018	0.20309	0.044712	0.20314	ENSG00000157227	ENST00000311852	T	0.20598	2.06	5.6	5.6	0.85130	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.143577	0.64402	D	0.000009	T	0.00012	0.0000	L	0.35414	1.06	0.18873	P	0.9999895192	B	0.12013	0.005	B	0.09377	0.004	T	0.29579	-1.0007	9	0.32370	T	0.25	.	18.3853	0.90464	0.0:0.0:1.0:0.0	rs1042704;rs3182168;rs17881628;rs52820031;rs60437546;rs1042704	273	P50281	MMP14_HUMAN	N	273	ENSP00000308208:D273N	ENSP00000308208:D273N	D	+	1	0	MMP14	22382434	1.000000	0.71417	0.979000	0.43373	0.140000	0.21249	4.763000	0.62257	2.644000	0.89710	0.563000	0.77884	GAT	G|0.873;A|0.127	0.127	strong		0.597	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
TECPR2	9895	hgsc.bcm.edu	37	14	102909991	102909991	+	Silent	SNP	C	C	T	rs17100923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	44	0	0		WXS	Illumina HiSeq	Phase_I	48	27	0.5625	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411700	105411700	+	Missense_Mutation	SNP	A	A	G	rs4264326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	209	209	1	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	
OR1K1	392392	hgsc.bcm.edu	37	9	125562527	125562527	+	Silent	SNP	T	T	C	rs10985782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125562527T>C	ENST00000277309.2	+	1	158	c.126T>C	c.(124-126)ggT>ggC	p.G42G		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, 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)	p.G42G(1)		endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						GCCTCCTGGGTAATGGACTCA	0.547													t|||	608	0.121406	0.1687	0.1282	5008	,	,		20797	0.0486		0.1282	False		,,,				2504	0.1207				p.G42G		Atlas-SNP	.											OR1K1,NS,carcinoma,0,1	OR1K1	34	1	1	Substitution - coding silent(1)	stomach(1)	c.T126C						PASS	.	C		585,3821	257.4+/-261.8	39,507,1657	118.0	93.0	102.0		126	-8.8	0.0	9	dbSNP_120	102	1094,7506	229.1+/-263.9	64,966,3270	no	coding-synonymous	OR1K1	NM_080859.1		103,1473,4927	CC,CT,TT		12.7209,13.2773,12.9094		42/317	125562527	1679,11327	2203	4300	6503	SO:0001819	synonymous_variant	392392	exon1			CCTGGGTAATGGA	AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"""GPCR / Class A : Olfactory receptors"""	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.126T>C	9.37:g.125562527T>C		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	202	99	0.490099	NM_080859	B9EH41|Q4VXB7|Q96R23	Silent	SNP	ENST00000277309.2	37	CCDS35132.1																																																																																			T|0.876;C|0.124	0.124	strong		0.547	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1		
TMEM101	84336	hgsc.bcm.edu	37	17	42092267	42092267	+	Silent	SNP	C	C	T	rs35301047	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42092267C>T	ENST00000589334.1	-	2	369	c.54G>A	c.(52-54)ttG>ttA	p.L18L	TMEM101_ENST00000542039.1_Intron|TMEM101_ENST00000587529.1_Silent_p.L18L|TMEM101_ENST00000206380.3_Silent_p.L18L			Q96IK0	TM101_HUMAN	transmembrane protein 101	18					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCACCGAACCCAACTGCATGA	0.612													C|||	43	0.00858626	0.025	0.0058	5008	,	,		18733	0.0		0.005	False		,,,				2504	0.001				p.L18L		Atlas-SNP	.											.	TMEM101	18	.	0			c.G54A						PASS	.	C		126,4280	93.9+/-132.6	1,124,2078	102.0	90.0	94.0		54	4.7	1.0	17	dbSNP_126	94	65,8535	40.3+/-97.0	1,63,4236	no	coding-synonymous	TMEM101	NM_032376.2		2,187,6314	TT,TC,CC		0.7558,2.8597,1.4686		18/258	42092267	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	84336	exon1			CGAACCCAACTGC	AK172826	CCDS11474.1	17q21.31	2005-12-16							28653	protein-coding gene	gene with protein product						12761501	Standard	NM_032376		Approved	MGC4251, FLJ23987	uc002ieu.3	Q96IK0		ENST00000589334.1:c.54G>A	17.37:g.42092267C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	243	102	0.419753	NM_032376	B2R9N6	Silent	SNP	ENST00000589334.1	37	CCDS11474.1																																																																																			C|0.988;T|0.012	0.012	strong		0.612	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376	
KAL1	3730	hgsc.bcm.edu	37	X	8538659	8538659	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:8538659A>C	ENST00000262648.3	-	7	1092	c.943T>G	c.(943-945)Tgg>Ggg	p.W315G		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	315	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						GGGAGATCCCAAACTATAGTG	0.542																																					p.W315G		Atlas-SNP	.											.	KAL1	78	.	0			c.T943G						PASS	.						81.0	60.0	67.0					X																	8538659		2203	4300	6503	SO:0001583	missense	3730	exon7			GATCCCAAACTAT		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.943T>G	X.37:g.8538659A>C	ENSP00000262648:p.Trp315Gly	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	218	9	0.0412844	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.950679	0.34377	.	.	ENSG00000011201	ENST00000262648	D	0.86297	-2.1	4.11	4.11	0.48088	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.125962	0.64402	D	0.000019	D	0.92034	0.7476	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	D	0.92526	0.6029	10	0.87932	D	0	-9.6393	11.7793	0.52003	1.0:0.0:0.0:0.0	.	315	P23352	KALM_HUMAN	G	315	ENSP00000262648:W315G	ENSP00000262648:W315G	W	-	1	0	KAL1	8498659	1.000000	0.71417	0.464000	0.27143	0.040000	0.13550	7.362000	0.79507	1.356000	0.45884	0.352000	0.21897	TGG	.	.	none		0.542	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
MFI2	4241	hgsc.bcm.edu	37	3	196742290	196742290	+	Silent	SNP	T	T	C	rs9855410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:196742290T>C	ENST00000296350.5	-	9	1292	c.1179A>G	c.(1177-1179)ccA>ccG	p.P393P		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	393	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		ACTGGATCTCTGGCTTGAGCC	0.672													t|||	1389	0.277356	0.3956	0.1931	5008	,	,		17562	0.2827		0.2217	False		,,,				2504	0.229				p.P393P		Atlas-SNP	.											.	MFI2	88	.	0			c.A1179G						PASS	.	C		1625,2775		299,1027,874	33.0	27.0	29.0		1179	-11.4	0.0	3	dbSNP_119	29	1892,6706		218,1456,2625	no	coding-synonymous	MFI2	NM_005929.5		517,2483,3499	CC,CT,TT		22.0051,36.9318,27.058		393/739	196742290	3517,9481	2200	4299	6499	SO:0001819	synonymous_variant	4241	exon9			GATCTCTGGCTTG		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.1179A>G	3.37:g.196742290T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	143	71	0.496504	NM_005929	Q9BQE2	Silent	SNP	ENST00000296350.5	37	CCDS3325.1																																																																																			T|0.712;C|0.288	0.288	strong		0.672	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
ATP2A3	489	hgsc.bcm.edu	37	17	3844787	3844787	+	Silent	SNP	C	C	G	rs1800912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3844787C>G	ENST00000352011.3	-	13	1761	c.1707G>C	c.(1705-1707)gcG>gcC	p.A569A	ATP2A3_ENST00000309890.7_Silent_p.A569A|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000397043.3_Silent_p.A569A|ATP2A3_ENST00000359983.3_Silent_p.A569A|ATP2A3_ENST00000397041.3_Silent_p.A569A|ATP2A3_ENST00000397035.3_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	97	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	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	
ZNF518B	85460	hgsc.bcm.edu	37	4	10445207	10445207	+	Missense_Mutation	SNP	T	T	C	rs75487798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:10445207T>C	ENST00000326756.3	-	3	3184	c.2746A>G	c.(2746-2748)Att>Gtt	p.I916V		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	916					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						ACCTGAAAAATTGAAGGATCC	0.413													T|||	48	0.00958466	0.0008	0.0072	5008	,	,		19593	0.0		0.0338	False		,,,				2504	0.0082				p.I916V		Atlas-SNP	.											.	ZNF518B	116	.	0			c.A2746G						PASS	.	T	VAL/ILE	33,4373	37.6+/-69.7	0,33,2170	102.0	103.0	103.0		2746	0.7	0.8	4	dbSNP_131	103	274,8326	103.8+/-164.8	6,262,4032	yes	missense	ZNF518B	NM_053042.2	29	6,295,6202	CC,CT,TT		3.186,0.749,2.3604	benign	916/1075	10445207	307,12699	2203	4300	6503	SO:0001583	missense	85460	exon3			GAAAAATTGAAGG	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.2746A>G	4.37:g.10445207T>C	ENSP00000317614:p.Ile916Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	160	62	0.3875	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	28	0.01282051282051282	0	0.0	2	0.0055248618784530384	0	0.0	26	0.03430079155672823	T	9.781	1.175242	0.21704	0.00749	0.03186	ENSG00000178163	ENST00000326756	T	0.01527	4.8	6.01	0.735	0.18300	.	0.680664	0.13438	N	0.387894	T	0.00412	0.0013	N	0.19112	0.55	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.48681	-0.9014	10	0.09338	T	0.73	-8.3754	3.6195	0.08090	0.2983:0.2973:0.0:0.4044	.	916	Q9C0D4	Z518B_HUMAN	V	916	ENSP00000317614:I916V	ENSP00000317614:I916V	I	-	1	0	ZNF518B	10054305	0.091000	0.21658	0.838000	0.33150	0.995000	0.86356	0.301000	0.19174	0.130000	0.18549	0.528000	0.53228	ATT	T|0.978;C|0.022	0.022	strong		0.413	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
MED16	10025	hgsc.bcm.edu	37	19	871987	871987	+	Silent	SNP	G	G	A	rs78047294	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:871987G>A	ENST00000589119.1	-	11	2036	c.2037C>T	c.(2035-2037)acC>acT	p.T679T	MED16_ENST00000325464.1_Silent_p.T679T|MED16_ENST00000312090.6_Silent_p.T679T|MED16_ENST00000269814.4_Intron|MED16_ENST00000395808.3_Silent_p.T679T|MED16_ENST00000606828.1_5'Flank			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	679					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGTATCCGAGGTGGCCGTAT	0.662													-|||	867	0.173123	0.2821	0.1744	5008	,	,		7668	0.0228		0.2346	False		,,,				2504	0.1166				p.T679T		Atlas-SNP	.											.	MED16	61	.	0			c.C2037T						PASS	.			1094,3248	383.0+/-324.7	152,790,1229	53.0	44.0	47.0		2037	0.1	1.0	19	dbSNP_131	47	2068,6486	353.4+/-329.1	242,1584,2451	no	coding-synonymous	MED16	NM_005481.2		394,2374,3680	AA,AG,GG		24.1758,25.1958,24.5192		679/878	871987	3162,9734	2171	4277	6448	SO:0001819	synonymous_variant	10025	exon12			ATCCGAGGTGGCC	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2037C>T	19.37:g.871987G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			G|0.771;A|0.229	0.229	strong		0.662	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
GRIN3B	116444	hgsc.bcm.edu	37	19	1008879	1008879	+	Silent	SNP	G	G	C	rs2285907	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1008879G>C	ENST00000234389.3	+	8	2674	c.2655G>C	c.(2653-2655)acG>acC	p.T885T		NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	885					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)	CCCTCAACACGGAGCCACCAG	0.711													a|||	548	0.109425	0.0371	0.1383	5008	,	,		11487	0.1369		0.161	False		,,,				2504	0.1053				p.T885T		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G2655C						PASS	.			257,4117		8,241,1938	36.0	29.0	32.0		2655	-7.4	0.5	19	dbSNP_100	32	1368,7222		115,1138,3042	no	coding-synonymous	GRIN3B	NM_138690.1		123,1379,4980	CC,CG,GG		15.9255,5.8756,12.5347		885/1044	1008879	1625,11339	2187	4295	6482	SO:0001819	synonymous_variant	116444	exon8			CAACACGGAGCCA		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.2655G>C	19.37:g.1008879G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			G|0.891;C|0.109	0.109	strong		0.711	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
RGS3	5998	hgsc.bcm.edu	37	9	116346287	116346287	+	Silent	SNP	C	C	T	rs3810927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:116346287C>T	ENST00000374140.2	+	21	2804	c.2595C>T	c.(2593-2595)taC>taT	p.Y865Y	RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000350696.5_Silent_p.Y865Y|RGS3_ENST00000343817.5_Silent_p.Y584Y|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000374134.3_Silent_p.Y186Y|RGS3_ENST00000462143.1_Silent_p.Y186Y	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	865					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)	p.Y865Y(1)|p.Y761Y(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						ATAGCACCTACAGCCAGAAGG	0.662													C|||	850	0.169728	0.1082	0.2421	5008	,	,		17767	0.2103		0.1869	False		,,,				2504	0.1421				p.Y865Y		Atlas-SNP	.											RGS3_ENST00000374140,NS,carcinoma,0,2	RGS3	251	2	2	Substitution - coding silent(2)	stomach(2)	c.C2595T						PASS	.	C	,,,	591,3815	259.5+/-263.1	55,481,1667	54.0	53.0	54.0		558,1752,,2595	2.6	1.0	9	dbSNP_107	54	1577,7023	290.5+/-299.9	144,1289,2867	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4	,,,	199,1770,4534	TT,TC,CC		18.3372,13.4135,16.6692	,,,	186/520,584/918,,865/1199	116346287	2168,10838	2203	4300	6503	SO:0001819	synonymous_variant	5998	exon21			CACCTACAGCCAG	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.2595C>T	9.37:g.116346287C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	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																																																																																			C|0.832;T|0.168	0.168	strong		0.662	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
TMEM132D	121256	hgsc.bcm.edu	37	12	130387850	130387850	+	Missense_Mutation	SNP	T	T	A	rs142888394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:130387850T>A	ENST00000422113.2	-	1	361	c.35A>T	c.(34-36)cAc>cTc	p.H12L		NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	12					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)		CGGCGACCAGTGGTGCCACAG	0.672													T|||	27	0.00539137	0.0008	0.0043	5008	,	,		12817	0.001		0.0099	False		,,,				2504	0.0123				p.H12L		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A35T						PASS	.	T	LEU/HIS	8,4268		0,8,2130	30.0	29.0	29.0		35	-4.3	0.3	12	dbSNP_134	29	70,8242		1,68,4087	yes	missense	TMEM132D	NM_133448.2	99	1,76,6217	AA,AT,TT		0.8422,0.1871,0.6196	benign	12/1100	130387850	78,12510	2138	4156	6294	SO:0001583	missense	121256	exon1			GACCAGTGGTGCC	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.35A>T	12.37:g.130387850T>A	ENSP00000408581:p.His12Leu	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	180	95	0.527778	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	4.656	0.122035	0.08931	0.001871	0.008422	ENSG00000151952	ENST00000422113	T	0.03553	3.89	5.2	-4.27	0.03744	.	0.452778	0.19129	N	0.121962	T	0.00637	0.0021	N	0.01352	-0.895	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.41016	-0.9532	9	.	.	.	-15.177	0.934	0.01340	0.4633:0.173:0.1254:0.2384	.	12	Q14C87	T132D_HUMAN	L	12	ENSP00000408581:H12L	.	H	-	2	0	TMEM132D	128953803	0.070000	0.21116	0.312000	0.25196	0.737000	0.42083	0.050000	0.14120	-0.792000	0.04480	0.482000	0.46254	CAC	T|0.996;A|0.004	0.004	strong		0.672	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
CDHR2	54825	hgsc.bcm.edu	37	5	176017639	176017639	+	Missense_Mutation	SNP	C	C	A	rs17078347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:176017639C>A	ENST00000510636.1	+	28	3764	c.3490C>A	c.(3490-3492)Ctg>Atg	p.L1164M	CDHR2_ENST00000261944.5_Missense_Mutation_p.L1164M|CDHR2_ENST00000506348.1_Missense_Mutation_p.L1164M	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1164			L -> M (in dbSNP:rs17078347). {ECO:0000269|PubMed:14702039}.		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						AGTGGCTTTGCTGCTGGTCCT	0.572													c|||	1193	0.238219	0.0182	0.2161	5008	,	,		19841	0.4395		0.2356	False		,,,				2504	0.3466				p.L1164M		Atlas-SNP	.											.	CDHR2	152	.	0			c.C3490A						PASS	.		MET/LEU,MET/LEU	220,4186	132.5+/-169.0	3,214,1986	240.0	196.0	211.0		3490,3490	-1.4	1.0	5	dbSNP_123	211	1884,6716	335.8+/-321.6	199,1486,2615	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	15,15	202,1700,4601	AA,AC,CC		21.907,4.9932,16.1771	benign,benign	1164/1311,1164/1311	176017639	2104,10902	2203	4300	6503	SO:0001583	missense	54825	exon28			GCTTTGCTGCTGG	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.3490C>A	5.37:g.176017639C>A	ENSP00000424565:p.Leu1164Met	Somatic	335	1	0.00298507		WXS	Illumina HiSeq	Phase_I	404	199	0.492574	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	524	0.23992673992673993	15	0.03048780487804878	73	0.20165745856353592	258	0.45104895104895104	178	0.23482849604221637	c	11.10	1.538851	0.27475	0.049932	0.21907	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.59083	0.29;0.29;0.29	4.61	-1.36	0.09085	.	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	D	0.54397	0.966	P	0.48030	0.564	T	0.46871	-0.9160	8	0.48119	T	0.1	-1.776	12.261	0.54651	0.1124:0.3188:0.5688:0.0	rs17078347;rs52836129;rs17078347	1164	Q9BYE9	CDHR2_HUMAN	M	1164	ENSP00000424565:L1164M;ENSP00000261944:L1164M;ENSP00000421078:L1164M	ENSP00000261944:L1164M	L	+	1	2	CDHR2	175950245	0.055000	0.20627	0.964000	0.40570	0.123000	0.20343	-1.193000	0.03049	0.033000	0.15463	-0.347000	0.07816	CTG	C|0.804;A|0.196	0.196	strong		0.572	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
SLC1A5	6510	hgsc.bcm.edu	37	19	47278938	47278938	+	Silent	SNP	G	G	A	rs1060043	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47278938G>A	ENST00000542575.2	-	8	2083	c.1455C>T	c.(1453-1455)taC>taT	p.Y485Y	SLC1A5_ENST00000434726.2_Silent_p.Y283Y|FKRP_ENST00000600646.1_Intron|SLC1A5_ENST00000412532.2_Silent_p.Y257Y|SLC1A5_ENST00000594991.1_Silent_p.Y309Y	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	485					amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	TACGGTCCACGTAATTTTGGA	0.557													-|||	295	0.0589058	0.0212	0.0677	5008	,	,		15671	0.0218		0.1093	False		,,,				2504	0.09				p.Y485Y		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C1455T						PASS	.		,,	135,4271		1,133,2069	102.0	90.0	94.0		771,849,1455	-6.2	0.1	19	dbSNP_86	94	898,7702		44,810,3446	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC1A5	NM_001145144.1,NM_001145145.1,NM_005628.2	,,	45,943,5515	AA,AG,GG		10.4419,3.064,7.9425	,,	257/314,283/340,485/542	47278938	1033,11973	2203	4300	6503	SO:0001819	synonymous_variant	6510	exon8			GTCCACGTAATTT	U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"""Solute carriers"""	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.1455C>T	19.37:g.47278938G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	167	76	0.45509	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	37	CCDS12692.1																																																																																			G|0.933;A|0.067	0.067	strong		0.557	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
ITGA11	22801	hgsc.bcm.edu	37	15	68695349	68695349	+	Silent	SNP	G	G	A	rs11629460	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:68695349G>A	ENST00000315757.7	-	2	158	c.72C>T	c.(70-72)aaC>aaT	p.N24N	ITGA11_ENST00000423218.2_Silent_p.N24N	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	24					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						TGGTGTCCATGTTGAAGGTGT	0.597													G|||	222	0.0443291	0.003	0.0749	5008	,	,		17967	0.0		0.1471	False		,,,				2504	0.0184				p.N24N		Atlas-SNP	.											.	ITGA11	110	.	0			c.C72T						PASS	.	G		112,4016		2,108,1954	48.0	53.0	52.0		72	3.2	1.0	15	dbSNP_120	52	1189,7221		90,1009,3106	no	coding-synonymous	ITGA11	NM_001004439.1		92,1117,5060	AA,AG,GG		14.1379,2.7132,10.3765		24/1189	68695349	1301,11237	2064	4205	6269	SO:0001819	synonymous_variant	22801	exon2			GTCCATGTTGAAG	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.72C>T	15.37:g.68695349G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.934;A|0.066	0.066	strong		0.597	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
EIF4G1	1981	hgsc.bcm.edu	37	3	184049143	184049143	+	Silent	SNP	C	C	T	rs76779558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184049143C>T	ENST00000346169.2	+	29	4522	c.4251C>T	c.(4249-4251)gtC>gtT	p.V1417V	EIF4G1_ENST00000427845.1_Silent_p.V1331V|EIF4G1_ENST00000424196.1_Silent_p.V1424V|EIF4G1_ENST00000414031.1_Silent_p.V1377V|EIF4G1_ENST00000435046.2_Silent_p.V1221V|EIF4G1_ENST00000350481.5_Silent_p.V1253V|EIF4G1_ENST00000382330.3_Silent_p.V1424V|EIF4G1_ENST00000411531.1_Silent_p.V1378V|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Silent_p.V1254V|EIF4G1_ENST00000434061.2_Silent_p.V1222V|EIF4G1_ENST00000352767.3_Silent_p.V1424V|EIF4G1_ENST00000342981.4_Silent_p.V1418V|EIF4G1_ENST00000392537.2_Silent_p.V1330V|EIF4G1_ENST00000319274.6_Silent_p.V1417V	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1417					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)			GTGCATTCGTCGCTGAACAGG	0.517													C|||	71	0.0141773	0.0008	0.0086	5008	,	,		19913	0.0179		0.0159	False		,,,				2504	0.0307				p.V1424V		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C4272T						PASS	.	C	,,,,,,	22,4384	29.9+/-59.1	0,22,2181	150.0	160.0	157.0		4272,4272,3666,4254,4251,3759,3990	-1.0	0.0	3	dbSNP_131	157	216,8384	92.1+/-154.2	1,214,4085	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	,,,,,,	1,236,6266	TT,TC,CC		2.5116,0.4993,1.8299	,,,,,,	1424/1607,1424/1607,1222/1405,1418/1601,1417/1600,1253/1436,1330/1513	184049143	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	1981	exon30			ATTCGTCGCTGAA	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.4251C>T	3.37:g.184049143C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			C|0.983;T|0.017	0.017	strong		0.517	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
CATSPERG	57828	hgsc.bcm.edu	37	19	38847431	38847431	+	Silent	SNP	T	T	C	rs2286475	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38847431T>C	ENST00000409235.3	+	11	1360	c.1245T>C	c.(1243-1245)acT>acC	p.T415T	CATSPERG_ENST00000410018.1_Intron|CATSPERG_ENST00000215069.4_Silent_p.T408T	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	415					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						GTGAGTATACTCTACTGCTGC	0.532													C|||	1648	0.329073	0.1573	0.3948	5008	,	,		19875	0.4544		0.2873	False		,,,				2504	0.4284				p.T415T		Atlas-SNP	.											.	CATSPERG	121	.	0			c.T1245C						PASS	.	C		779,3627	753.3+/-412.4	75,629,1499	204.0	184.0	191.0		1245	-8.2	0.0	19	dbSNP_100	191	2029,6571	720.5+/-406.3	239,1551,2510	no	coding-synonymous	CATSPERG	NM_021185.4		314,2180,4009	CC,CT,TT		23.593,17.6804,21.59		415/1160	38847431	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	57828	exon11			GTATACTCTACTG	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.1245T>C	19.37:g.38847431T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_021185	A6NEG6|Q659E1	Silent	SNP	ENST00000409235.3	37	CCDS12514.2																																																																																			T|0.735;C|0.265	0.265	strong		0.532	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
CUBN	8029	hgsc.bcm.edu	37	10	17157572	17157572	+	Silent	SNP	G	G	A	rs41289313	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:17157572G>A	ENST00000377833.4	-	7	683	c.618C>T	c.(616-618)taC>taT	p.Y206Y		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	206	EGF-like 2; 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)	p.Y206*(1)|p.Y206_G207>*(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)	ACTGGGGTCCGTACGTCTCAG	0.522													G|||	424	0.0846645	0.0227	0.0476	5008	,	,		20173	0.0198		0.0974	False		,,,				2504	0.2485				p.Y206Y		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	1	2	Substitution - Nonsense(1)|Complex - deletion inframe(1)	lung(2)	c.C618T						PASS	.	G		107,4299	83.9+/-122.4	2,103,2098	141.0	118.0	126.0		618	-11.5	0.0	10	dbSNP_127	126	708,7892	173.5+/-223.9	28,652,3620	no	coding-synonymous	CUBN	NM_001081.3		30,755,5718	AA,AG,GG		8.2326,2.4285,6.2663		206/3624	17157572	815,12191	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon7			GGGTCCGTACGTC	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.618C>T	10.37:g.17157572G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	164	76	0.463415	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			G|0.935;A|0.065	0.065	strong		0.522	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
OPRM1	4988	hgsc.bcm.edu	37	6	154360655	154360655	+	5'UTR	SNP	C	C	T	rs41292890	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:154360655C>T	ENST00000330432.7	+	0	213				OPRM1_ENST00000360422.4_5'UTR|OPRM1_ENST00000428397.2_5'UTR|OPRM1_ENST00000523520.1_3'UTR|OPRM1_ENST00000419506.2_5'UTR|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000524163.1_5'UTR|OPRM1_ENST00000452687.2_5'UTR|OPRM1_ENST00000337049.4_5'UTR|OPRM1_ENST00000435918.2_5'UTR|OPRM1_ENST00000414028.2_5'UTR|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000434900.2_Silent_p.S85S|OPRM1_ENST00000229768.5_5'UTR	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)	CCTCGCACAGCGGTGCCCGCC	0.622													C|||	12	0.00239617	0.0	0.0029	5008	,	,		17347	0.0		0.007	False		,,,				2504	0.0031				p.S85S		Atlas-SNP	.											.	OPRM1	241	.	0			c.C255T						PASS	.	C	,,,,,,,,,,,	2,4070		0,2,2034	20.0	28.0	26.0		,,,,255,,,,,,,	-10.2	0.0	6	dbSNP_127	26	29,8311		0,29,4141	no	utr-5,utr-5,utr-5,utr-5,coding-synonymous,intron,intron,utr-5,utr-5,utr-5,utr-5,utr-5	OPRM1	NM_000914.3,NM_001008503.1,NM_001008504.2,NM_001008505.1,NM_001145279.2,NM_001145280.2,NM_001145281.1,NM_001145282.1,NM_001145283.1,NM_001145284.2,NM_001145285.1,NM_001145286.1	,,,,,,,,,,,	0,31,6175	TT,TC,CC		0.3477,0.0491,0.2498	,,,,,,,,,,,	,,,,85/494,,,,,,,	154360655	31,12381	2036	4170	6206	SO:0001623	5_prime_UTR_variant	4988	exon3			GCACAGCGGTGCC	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.-25C>T	6.37:g.154360655C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Silent	SNP	ENST00000330432.7	37	CCDS55070.1																																																																																			C|0.998;T|0.002	0.002	strong		0.622	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914	
MCPH1	79648	hgsc.bcm.edu	37	8	6303025	6303025	+	Silent	SNP	G	G	A	rs2584	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:6303025G>A	ENST00000344683.5	+	8	1858	c.1782G>A	c.(1780-1782)acG>acA	p.T594T	MCPH1_ENST00000522905.1_Silent_p.T546T|MCPH1_ENST00000519480.1_Silent_p.T594T	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	594					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		ACATGGAGACGTCTACAGAAG	0.423													G|||	662	0.132188	0.0174	0.245	5008	,	,		20565	0.0268		0.338	False		,,,				2504	0.1043				p.T594T	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											MCPH1,caecum,carcinoma,+1,1	MCPH1	65	1	0			c.G1782A						scavenged	.	G	,,	248,3494		9,230,1632	61.0	55.0	57.0		1782,1638,1782	-9.1	0.0	8	dbSNP_36	57	2706,5502		452,1802,1850	no	coding-synonymous,coding-synonymous,coding-synonymous	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	,,	461,2032,3482	AA,AG,GG		32.9678,6.6275,24.7197	,,	594/611,546/563,594/836	6303025	2954,8996	1871	4104	5975	SO:0001819	synonymous_variant	79648	exon8			GGAGACGTCTACA	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1782G>A	8.37:g.6303025G>A		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			G|0.814;A|0.186	0.186	strong		0.423	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
C2orf43	60526	hgsc.bcm.edu	37	2	20974586	20974586	+	Missense_Mutation	SNP	C	C	T	rs114010802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:20974586C>T	ENST00000237822.3	-	4	531	c.452G>A	c.(451-453)cGa>cAa	p.R151Q	C2orf43_ENST00000440866.2_Missense_Mutation_p.R151Q|C2orf43_ENST00000541941.1_Missense_Mutation_p.R21Q|C2orf43_ENST00000435420.2_Missense_Mutation_p.R103Q|C2orf43_ENST00000381090.3_Missense_Mutation_p.R151Q|C2orf43_ENST00000403006.2_Missense_Mutation_p.R21Q	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	151										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCAGGGACTCGCTTCAGCAT	0.483													C|||	20	0.00399361	0.0008	0.0043	5008	,	,		19497	0.0		0.0159	False		,,,				2504	0.0				p.R151Q		Atlas-SNP	.											.	C2orf43	28	.	0			c.G452A						PASS	.	C	GLN/ARG	10,4396	16.8+/-37.8	0,10,2193	169.0	155.0	160.0		452	-5.1	0.0	2	dbSNP_132	160	71,8529	42.6+/-100.3	0,71,4229	yes	missense	C2orf43	NM_021925.2	43	0,81,6422	TT,TC,CC		0.8256,0.227,0.6228	probably-damaging	151/326	20974586	81,12925	2203	4300	6503	SO:0001583	missense	60526	exon4			GGGACTCGCTTCA	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.452G>A	2.37:g.20974586C>T	ENSP00000237822:p.Arg151Gln	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	202	102	0.504951	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	17	0.007783882783882784	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	12	0.0158311345646438	C	11.34	1.610511	0.28712	0.00227	0.008256	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000440866;ENST00000541941;ENST00000432947;ENST00000412261	T;T;T;T	0.71817	0.86;1.47;0.86;-0.6	5.73	-5.05	0.02955	.	0.589533	0.17377	N	0.176450	T	0.34832	0.0911	L	0.52759	1.655	0.24725	N	0.99312	P;P;B;B;P;P	0.45396	0.857;0.798;0.141;0.141;0.485;0.636	B;B;B;B;B;B	0.35859	0.176;0.179;0.013;0.013;0.212;0.206	T	0.45234	-0.9275	10	0.48119	T	0.1	-0.0561	5.7365	0.18069	0.3052:0.4799:0.0:0.2149	.	109;151;103;109;151;151	B4DS38;B4DRG3;B7ZAJ5;B4DWE2;Q9H6V9;B5MDU6	.;.;.;.;CB043_HUMAN;.	Q	21;151;151;103;151;21;21;103	ENSP00000384267:R21Q;ENSP00000388635:R103Q;ENSP00000440570:R21Q;ENSP00000396911:R21Q	ENSP00000237822:R151Q	R	-	2	0	C2orf43	20838067	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-0.373000	0.07494	-1.306000	0.02324	-0.157000	0.13467	CGA	C|0.993;T|0.007	0.007	strong		0.483	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376847	168376847	+	lincRNA	SNP	C	C	G	rs77867907		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168376847C>G	ENST00000538528.1	-	0	772																											GTGTGGGGAGCAGGAGGCAGT	0.617																																					p.L162L		Atlas-SNP	.											.	.	.	.	0			c.G486C						PASS	.						32.0	30.0	30.0					6																	168376847		692	1591	2283			0	exon1			GGGGAGCAGGAGG																													6.37:g.168376847C>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	189	32	0.169312	NM_001129895		Silent	SNP	ENST00000538528.1	37																																																																																				C|0.500;G|0.500	0.500	weak		0.617	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
FAM83E	54854	hgsc.bcm.edu	37	19	49107039	49107039	+	Silent	SNP	G	G	T	rs201027346	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49107039G>T	ENST00000263266.3	-	4	1077	c.888C>A	c.(886-888)ccC>ccA	p.P296P	SPACA4_ENST00000321762.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	296										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)		AGGGTTTCTGGGGGGGCGCAG	0.721																																					p.P296P		Atlas-SNP	.											.	FAM83E	34	.	0			c.C888A						PASS	.	G		0,3978		0,0,1989	12.0	13.0	13.0		888	1.2	0.0	19		13	2,8210		0,2,4104	no	coding-synonymous	FAM83E	NM_017708.3		0,2,6093	TT,TG,GG		0.0244,0.0,0.0164		296/479	49107039	2,12188	1989	4106	6095	SO:0001819	synonymous_variant	54854	exon4			TTTCTGGGGGGGC	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.888C>A	19.37:g.49107039G>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_017708	Q9NXK1	Silent	SNP	ENST00000263266.3	37	CCDS42587.1																																																																																			G|0.999;T|0.001	0.001	weak		0.721	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
USP34	9736	hgsc.bcm.edu	37	2	61647901	61647901	+	Silent	SNP	A	A	G	rs778155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:61647901A>G	ENST00000398571.2	-	2	187	c.111T>C	c.(109-111)taT>taC	p.Y37Y		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	37					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)			AGGAATTGATATAAGTAAATA	0.303													A|||	1680	0.335463	0.2375	0.4467	5008	,	,		17643	0.3284		0.3499	False		,,,				2504	0.3814				p.Y37Y		Atlas-SNP	.											USP34,colon,carcinoma,0,1	USP34	334	1	0			c.T111C						PASS	.	A		915,2803		116,683,1060	111.0	109.0	109.0		111	4.6	1.0	2	dbSNP_86	109	3058,5150		571,1916,1617	no	coding-synonymous	USP34	NM_014709.3		687,2599,2677	GG,GA,AA		37.2563,24.61,33.3138		37/3547	61647901	3973,7953	1859	4104	5963	SO:0001819	synonymous_variant	9736	exon2			ATTGATATAAGTA	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.111T>C	2.37:g.61647901A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1																																																																																			A|0.679;G|0.320	0.320	strong		0.303	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
IBA57	200205	hgsc.bcm.edu	37	1	228362923	228362923	+	Silent	SNP	C	C	T	rs202126055		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228362923C>T	ENST00000366711.3	+	3	782	c.780C>T	c.(778-780)taC>taT	p.Y260Y	IBA57_ENST00000546123.1_Silent_p.Y67Y|IBA57_ENST00000484749.1_3'UTR	NM_001010867.2	NP_001010867.1	Q5T440	CAF17_HUMAN	IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)	260					glycine catabolic process (GO:0006546)|heme biosynthetic process (GO:0006783)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|prostate(1)	11						AAGGCTGCTACATTGGCCAGG	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		17017	0.0		0.0	False		,,,				2504	0.001				p.Y260Y		Atlas-SNP	.											.	IBA57	22	.	0			c.C780T						PASS	.	C		0,4406		0,0,2203	69.0	66.0	67.0		780	2.0	0.5	1		67	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	IBA57	NM_001010867.2		0,3,6499	TT,TC,CC		0.0349,0.0,0.0231		260/357	228362923	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	200205	exon3			CTGCTACATTGGC	AK022796	CCDS31046.1	1q42.13	2011-03-11	2011-03-11	2011-03-11	ENSG00000181873	ENSG00000181873			27302	protein-coding gene	gene with protein product	"""iron-sulfur cluster assembly factor for biotin synthase- and aconitase-like mitochondrial proteins, with a mass of 57kDa"""	615316	"""chromosome 1 open reading frame 69"""	C1orf69			Standard	NM_001010867		Approved	FLJ12734	uc001hsl.4	Q5T440	OTTHUMG00000039769	ENST00000366711.3:c.780C>T	1.37:g.228362923C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_001010867		Silent	SNP	ENST00000366711.3	37	CCDS31046.1																																																																																			C|0.999;T|0.001	0.001	weak		0.647	IBA57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095980.1	NM_001010867	
MMP27	64066	hgsc.bcm.edu	37	11	102575442	102575442	+	Missense_Mutation	SNP	C	C	T	rs553456217		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102575442C>T	ENST00000260229.4	-	2	258	c.167G>A	c.(166-168)aGg>aAg	p.R56K		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	56					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TATGAGACTCCTATTCTTGCT	0.383																																					p.R56K		Atlas-SNP	.											.	MMP27	84	.	0			c.G167A						PASS	.						74.0	72.0	73.0					11																	102575442		2203	4299	6502	SO:0001583	missense	64066	exon2			AGACTCCTATTCT	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.167G>A	11.37:g.102575442C>T	ENSP00000260229:p.Arg56Lys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	C	1.324	-0.598646	0.03744	.	.	ENSG00000137675	ENST00000260229	T	0.36340	1.26	5.55	1.43	0.22495	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.764123	0.12270	N	0.483911	T	0.13628	0.0330	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.29518	-1.0009	10	0.10111	T	0.7	.	2.5257	0.04690	0.1265:0.4691:0.1116:0.2928	.	56	Q9H306	MMP27_HUMAN	K	56	ENSP00000260229:R56K	ENSP00000260229:R56K	R	-	2	0	MMP27	102080652	0.000000	0.05858	0.610000	0.28997	0.014000	0.08584	-0.364000	0.07583	0.473000	0.27368	0.591000	0.81541	AGG	.	.	none		0.383	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
DNAH17	8632	hgsc.bcm.edu	37	17	76521121	76521121	+	Silent	SNP	T	T	C	rs17729253	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	77	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	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	
MUC2	4583	hgsc.bcm.edu	37	11	1081438	1081438	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1081438C>T	ENST00000441003.2	+	12	1483	c.1456C>T	c.(1456-1458)Cgc>Tgc	p.R486C	MUC2_ENST00000359061.5_Missense_Mutation_p.R486C	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	486	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CTCTGTCTTCCGCCCGTCTTC	0.652																																					p.R486C		Atlas-SNP	.											MUC2_ENST00000441003,colon,carcinoma,-1,2	MUC2	614	2	0			c.C1456T						scavenged	.						74.0	79.0	77.0					11																	1081438		2089	4202	6291	SO:0001583	missense	4583	exon12			GTCTTCCGCCCGT	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.1456C>T	11.37:g.1081438C>T	ENSP00000415183:p.Arg486Cys	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	197	2	0.0101523	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	8.189	0.795524	0.16327	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.60424	0.19;0.19	3.17	2.23	0.28157	.	0.356853	0.21664	U	0.070961	T	0.70710	0.3255	M	0.67625	2.065	0.36476	D	0.86752	D	0.89917	1.0	D	0.79784	0.993	T	0.75733	-0.3214	10	0.87932	D	0	.	10.7623	0.46272	0.3598:0.6402:0.0:0.0	.	486	E7EUV1	.	C	486	ENSP00000415183:R486C;ENSP00000351956:R486C	ENSP00000351956:R486C	R	+	1	0	MUC2	1071438	0.000000	0.05858	0.563000	0.28383	0.352000	0.29268	-0.323000	0.07997	0.507000	0.28148	0.491000	0.48974	CGC	.	.	none		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
GDAP1	54332	hgsc.bcm.edu	37	8	75274141	75274141	+	Silent	SNP	T	T	G	rs11554166	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:75274141T>G	ENST00000220822.7	+	4	587	c.507T>G	c.(505-507)tcT>tcG	p.S169S	GDAP1_ENST00000434412.2_Silent_p.S101S|GDAP1_ENST00000521096.1_3'UTR	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	169	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			ACACAGAGTCTGAGCTGAAGA	0.378													T|||	1098	0.219249	0.093	0.1787	5008	,	,		19465	0.3026		0.3569	False		,,,				2504	0.1912				p.S169S		Atlas-SNP	.											.	GDAP1	36	.	0			c.T507G						PASS	.	T	,	564,3842	252.4+/-258.8	27,510,1666	108.0	102.0	104.0		303,507	0.1	1.0	8	dbSNP_120	104	2736,5864	436.4+/-358.3	437,1862,2001	no	coding-synonymous,coding-synonymous	GDAP1	NM_001040875.1,NM_018972.2	,	464,2372,3667	GG,GT,TT		31.814,12.8007,25.3729	,	101/291,169/359	75274141	3300,9706	2203	4300	6503	SO:0001819	synonymous_variant	54332	exon4			AGAGTCTGAGCTG		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"""Charcot-Marie-Tooth neuropathy 4A"""	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.507T>G	8.37:g.75274141T>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_018972	A8K957|E7FJF3|E7FJF4	Silent	SNP	ENST00000220822.7	37	CCDS34911.1																																																																																			T|0.753;G|0.247	0.247	strong		0.378	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972	
KRT72	140807	hgsc.bcm.edu	37	12	52984620	52984620	+	Splice_Site	SNP	C	C	T	rs12818575	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52984620C>T	ENST00000537672.2	-	6	1099	c.1089G>A	c.(1087-1089)caG>caA	p.Q363Q	KRT72_ENST00000293745.2_Splice_Site_p.Q363Q|KRT72_ENST00000398066.3_Splice_Site_p.Q175Q|KRT72_ENST00000354310.4_Intron	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	363	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)		TAGAACCCACCTGCTTCTTCA	0.478													C|||	891	0.177915	0.0968	0.1527	5008	,	,		22804	0.0655		0.2416	False		,,,				2504	0.3558				p.Q363Q		Atlas-SNP	.											.	KRT72	70	.	0			c.G1089A						PASS	.	C	,,	611,3795	267.7+/-268.0	47,517,1639	93.0	89.0	90.0		1089,,1089	5.1	1.0	12	dbSNP_121	90	2199,6401	374.8+/-337.5	277,1645,2378	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	,,	324,2162,4017	TT,TC,CC		25.5698,13.8675,21.6054	,,	363/512,,363/512	52984620	2810,10196	2203	4300	6503	SO:0001630	splice_region_variant	140807	exon6			ACCCACCTGCTTC	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.1089+1G>A	12.37:g.52984620C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	ENST00000537672.2	37	CCDS8833.1																																																																																			C|0.812;T|0.188	0.188	strong		0.478	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	Silent
C15orf52	388115	hgsc.bcm.edu	37	15	40630073	40630073	+	Missense_Mutation	SNP	G	G	A	rs78494549	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:40630073G>A	ENST00000559313.1	-	6	682	c.667C>T	c.(667-669)Cgg>Tgg	p.R223W	C15orf52_ENST00000397536.2_Missense_Mutation_p.R13W|C15orf52_ENST00000557973.1_5'Flank	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	223							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		CCCACCGGCCGGCTCCAGGGC	0.677													G|||	204	0.0407348	0.0053	0.0778	5008	,	,		12646	0.003		0.1153	False		,,,				2504	0.0245				p.R223W		Atlas-SNP	.											.	C15orf52	47	.	0			c.C667T						PASS	.	G	TRP/ARG	102,4190		4,94,2048	8.0	10.0	9.0		667	2.0	0.5	15	dbSNP_131	9	1052,7414		61,930,3242	yes	missense	C15orf52	NM_207380.2	101	65,1024,5290	AA,AG,GG		12.4262,2.3765,9.0453	probably-damaging	223/535	40630073	1154,11604	2146	4233	6379	SO:0001583	missense	388115	exon6			CCGGCCGGCTCCA	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.667C>T	15.37:g.40630073G>A	ENSP00000453969:p.Arg223Trp	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Missense_Mutation	SNP	ENST00000559313.1	37	CCDS10055.2	129	0.059065934065934064	4	0.008130081300813009	32	0.08839779005524862	3	0.005244755244755245	90	0.11873350923482849	G	17.32	3.358835	0.61403	0.023765	0.124262	ENSG00000188549	ENST00000382688;ENST00000397536;ENST00000397535	T	0.45276	0.9	3.01	1.96	0.26148	.	1.790160	0.03756	N	0.257310	T	0.00724	0.0024	L	0.47716	1.5	0.80722	P	0.0	D;B;B	0.71674	0.998;0.027;0.007	P;B;B	0.47744	0.556;0.005;0.005	T	0.14980	-1.0453	9	0.72032	D	0.01	-0.0185	6.6395	0.22901	0.0:0.0:0.7168:0.2832	.	13;155;223	Q6ZUT6-2;Q6ZUT6-3;Q6ZUT6	.;.;CO052_HUMAN	W	223;13;155	ENSP00000380670:R13W	ENSP00000372135:R223W	R	-	1	2	C15orf52	38417365	0.997000	0.39634	0.531000	0.27976	0.165000	0.22458	2.094000	0.41719	1.704000	0.51252	0.563000	0.77884	CGG	G|0.937;A|0.063	0.063	strong		0.677	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
OR51L1	119682	hgsc.bcm.edu	37	11	5020509	5020509	+	Silent	SNP	C	C	T	rs11035066	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5020509C>T	ENST00000321543.1	+	1	297	c.297C>T	c.(295-297)tgC>tgT	p.C99C		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	99						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)		CAAGTGCTTGCTATGCTCAGC	0.512													C|||	1155	0.230631	0.3011	0.1599	5008	,	,		24680	0.0694		0.3131	False		,,,				2504	0.2669				p.C99C		Atlas-SNP	.											.	OR51L1	60	.	0			c.C297T						PASS	.	C		1371,3031	455.5+/-351.0	199,973,1029	267.0	199.0	222.0		297	4.5	1.0	11	dbSNP_120	222	2566,6030	418.5+/-352.8	383,1800,2115	no	coding-synonymous	OR51L1	NM_001004755.1		582,2773,3144	TT,TC,CC		29.8511,31.1449,30.2893		99/316	5020509	3937,9061	2201	4298	6499	SO:0001819	synonymous_variant	119682	exon1			TGCTTGCTATGCT	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.297C>T	11.37:g.5020509C>T		Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	366	193	0.527322	NM_001004755	Q6IFE5	Silent	SNP	ENST00000321543.1	37	CCDS31369.1																																																																																			C|0.718;T|0.282	0.282	strong		0.512	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
ZFYVE9	9372	hgsc.bcm.edu	37	1	52703491	52703491	+	Missense_Mutation	SNP	G	G	C	rs35385323	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:52703491G>C	ENST00000371591.1	+	3	533	c.402G>C	c.(400-402)aaG>aaC	p.K134N	ZFYVE9_ENST00000357206.2_Missense_Mutation_p.K134N|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.K134N	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	134					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						TGGGAGAGAAGAAATGTGGAA	0.403													G|||	320	0.0638978	0.1135	0.0403	5008	,	,		22542	0.003		0.0517	False		,,,				2504	0.089				p.K134N		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.G402C						PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS	421,3985	205.2+/-227.1	15,391,1797	80.0	79.0	80.0		402,402,402	3.9	1.0	1	dbSNP_126	80	470,8130	138.7+/-195.5	13,444,3843	yes	missense,missense,missense	ZFYVE9	NM_004799.2,NM_007323.1,NM_007324.2	94,94,94	28,835,5640	CC,CG,GG		5.4651,9.5552,6.8507	benign,benign,benign	134/1426,134/763,134/1367	52703491	891,12115	2203	4300	6503	SO:0001583	missense	9372	exon4			AGAGAAGAAATGT	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.402G>C	1.37:g.52703491G>C	ENSP00000360647:p.Lys134Asn	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	37	CCDS563.1	115	0.052655677655677656	57	0.11585365853658537	15	0.04143646408839779	1	0.0017482517482517483	42	0.055408970976253295	G	11.18	1.563362	0.27915	0.095552	0.054651	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.55413	1.01;0.52;1.01;1.01	5.77	3.86	0.44501	.	0.407035	0.22551	N	0.058597	T	0.00412	0.0013	N	0.19112	0.55	0.41685	P	0.01068800000000003	P;B;P	0.41848	0.493;0.361;0.763	B;B;B	0.33620	0.109;0.051;0.167	T	0.06661	-1.0814	9	0.46703	T	0.11	.	5.8879	0.18892	0.2158:0.1414:0.6427:0.0	rs35385323;rs61753388	134;134;134	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	N	134	ENSP00000349737:K134N;ENSP00000355358:K134N;ENSP00000287727:K134N;ENSP00000360647:K134N	ENSP00000287727:K134N	K	+	3	2	ZFYVE9	52476079	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.776000	0.26704	0.756000	0.33013	0.655000	0.94253	AAG	G|0.935;C|0.065	0.065	strong		0.403	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
ALS2CR12	130540	hgsc.bcm.edu	37	2	202215492	202215492	+	Missense_Mutation	SNP	C	C	G	rs13014235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202215492C>G	ENST00000286190.5	-	2	173	c.127G>C	c.(127-129)Gta>Cta	p.V43L	ALS2CR12_ENST00000448967.1_5'UTR|ALS2CR12_ENST00000405148.2_Missense_Mutation_p.V43L|ALS2CR12_ENST00000392257.3_Missense_Mutation_p.V43L|ALS2CR12_ENST00000439709.1_Missense_Mutation_p.V43L			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	43			V -> L (in dbSNP:rs13014235). {ECO:0000269|PubMed:11586298, ECO:0000269|PubMed:15489334}.		regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						GGAGCTGGTACAAGAGGAGTT	0.348													G|||	3551	0.709065	0.7874	0.4971	5008	,	,		20725	0.7292		0.6054	False		,,,				2504	0.8395				p.V43L		Atlas-SNP	.											.	ALS2CR12	54	.	0			c.G127C						PASS	.	G	LEU/VAL,LEU/VAL	3287,1119	401.7+/-332.1	1227,833,143	138.0	139.0	139.0		127,127	-0.8	0.0	2	dbSNP_121	139	5116,3484	509.4+/-377.3	1515,2086,699	yes	missense,missense	ALS2CR12	NM_001127391.1,NM_139163.2	32,32	2742,2919,842	GG,GC,CC		40.5116,25.3972,35.3914	benign,benign	43/423,43/446	202215492	8403,4603	2203	4300	6503	SO:0001583	missense	130540	exon3			CTGGTACAAGAGG	AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.127G>C	2.37:g.202215492C>G	ENSP00000286190:p.Val43Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001127391	G5E9S3|Q53TT6|Q8N1B6	Missense_Mutation	SNP	ENST00000286190.5	37	CCDS2346.1	1421	0.6506410256410257	378	0.7682926829268293	179	0.494475138121547	406	0.7097902097902098	458	0.604221635883905	G	1.433	-0.569691	0.03910	0.746028	0.594884	ENSG00000155749	ENST00000286190;ENST00000405148;ENST00000392257;ENST00000439709;ENST00000418364	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.1	4.54	-0.808	0.10868	.	1.578820	0.03586	N	0.231085	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	0.34129	-0.9841	9	0.13108	T	0.6	8.2935	6.5755	0.22564	0.0828:0.5433:0.2538:0.1201	rs13014235;rs17383797;rs17856927;rs58498371;rs13014235	43;43	Q96Q35;G5E9S3	AL2SB_HUMAN;.	L	43	ENSP00000286190:V43L;ENSP00000385098:V43L;ENSP00000376086:V43L;ENSP00000412073:V43L;ENSP00000407585:V43L	ENSP00000286190:V43L	V	-	1	0	ALS2CR12	201923737	0.001000	0.12720	0.000000	0.03702	0.338000	0.28826	-1.077000	0.03416	-0.394000	0.07727	-0.120000	0.15030	GTA	C|0.340;G|0.660	0.660	strong		0.348	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163	
UNKL	64718	hgsc.bcm.edu	37	16	1416355	1416355	+	Silent	SNP	C	C	T	rs75956141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1416355C>T	ENST00000389221.4	-	15	1928	c.1929G>A	c.(1927-1929)cgG>cgA	p.R643R	UNKL_ENST00000508903.2_Silent_p.R696R|UNKL_ENST00000402641.2_Silent_p.R195R|UNKL_ENST00000248104.7_Silent_p.R192R|UNKL_ENST00000391893.2_Silent_p.R192R|UNKL_ENST00000403703.1_Silent_p.R195R|UNKL_ENST00000397464.1_Silent_p.R145R	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	643					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				GGGCCCGCTCCCGGCAGGCCA	0.697													C|||	179	0.0357428	0.0008	0.0014	5008	,	,		16863	0.1667		0.004	False		,,,				2504	0.0051				p.R646R		Atlas-SNP	.											.	UNKL	46	.	0			c.G1938A						PASS	.	C	,,	7,4371		0,7,2182	15.0	15.0	15.0		1929,435,585	-2.0	0.1	16	dbSNP_132	15	18,8552		0,18,4267	no	coding-synonymous,coding-synonymous,coding-synonymous	UNKL	NM_001193388.1,NM_001193389.1,NM_023076.4	,,	0,25,6449	TT,TC,CC		0.21,0.1599,0.1931	,,	643/681,145/183,195/233	1416355	25,12923	2189	4285	6474	SO:0001819	synonymous_variant	64718	exon15			CCGCTCCCGGCAG	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"""Zinc fingers, CCCH-type domain containing"""	14184	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 28"", ""unkempt homolog (Drosophila)-like"""	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.1929G>A	16.37:g.1416355C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Silent	SNP	ENST00000389221.4	37	CCDS53981.1																																																																																			C|0.982;T|0.018	0.018	strong		0.697	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125	
ZKSCAN7	55888	hgsc.bcm.edu	37	3	44607013	44607013	+	Missense_Mutation	SNP	T	T	C	rs13081859	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:44607013T>C	ENST00000273320.3	+	3	887	c.458T>C	c.(457-459)tTt>tCt	p.F153S	RP11-944L7.5_ENST00000419137.1_5'Flank|RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000431636.1_Missense_Mutation_p.F153S|ZKSCAN7_ENST00000426540.1_Missense_Mutation_p.F153S|ZKSCAN7_ENST00000341840.3_Missense_Mutation_p.F153S	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	153			F -> S (in dbSNP:rs13081859).		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)										GAAATGCATTTTGAGGAGACA	0.512													.|||	892	0.178115	0.3048	0.1556	5008	,	,		20728	0.001		0.3191	False		,,,				2504	0.0603				p.F153S		Atlas-SNP	.											.	.	.	.	0			c.T458C						PASS	.	T	SER/PHE,SER/PHE	1393,3013		215,963,1025	147.0	142.0	144.0		458,458	0.5	0.0	3	dbSNP_121	144	2684,5916		405,1874,2021	yes	missense,missense	ZNF167	NM_018651.2,NM_025169.1	155,155	620,2837,3046	CC,CT,TT		31.2093,31.616,31.3471	benign,benign	153/755,153/277	44607013	4077,8929	2203	4300	6503	SO:0001583	missense	55888	exon3			TGCATTTTGAGGA	L32164, AY280798	CCDS2714.1, CCDS2715.1, CCDS74924.1	3p21.32	2013-01-09	2013-01-09	2013-01-09	ENSG00000196345	ENSG00000196345		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12955	protein-coding gene	gene with protein product			"""zinc finger protein 64"", ""zinc finger protein 448"", ""zinc finger protein 167"""	ZNF64, ZNF448, ZNF167		7814019, 1505991	Standard	XM_005265323		Approved	FLJ12738, ZSCAN39	uc003cnj.3	Q9P0L1	OTTHUMG00000133094	ENST00000273320.3:c.458T>C	3.37:g.44607013T>C	ENSP00000273320:p.Phe153Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_018651	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Missense_Mutation	SNP	ENST00000273320.3	37	CCDS2715.1	441	0.20192307692307693	156	0.3170731707317073	59	0.16298342541436464	1	0.0017482517482517483	225	0.29683377308707126	.	0.768	-0.766811	0.02974	0.31616	0.312093	ENSG00000196345	ENST00000431636;ENST00000426540;ENST00000341840;ENST00000273320;ENST00000447279	T;T;T;T;T	0.05382	4.69;3.57;4.69;3.57;3.45	4.45	0.533	0.17121	Transcription regulator SCAN (1);	0.747100	0.10417	N	0.677186	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	0.47355	-0.9124	9	0.09084	T	0.74	0.8589	3.3799	0.07251	0.0:0.2179:0.2059:0.5761	rs13081859;rs57766763;rs13081859	24;153;153	A7MAY2;Q9P0L1;Q9P0L1-2	.;ZN167_HUMAN;.	S	153;153;153;153;3	ENSP00000416681:F153S;ENSP00000395524:F153S;ENSP00000345404:F153S;ENSP00000273320:F153S;ENSP00000405034:F3S	ENSP00000273320:F153S	F	+	2	0	ZNF167	44582017	0.113000	0.22115	0.018000	0.16275	0.053000	0.15095	-0.052000	0.11865	0.346000	0.23899	0.528000	0.53228	TTT	T|0.732;C|0.268	0.268	strong		0.512	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651	
CUL2	8453	hgsc.bcm.edu	37	10	35302705	35302705	+	Silent	SNP	C	C	T	rs12830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:35302705C>T	ENST00000374748.1	-	20	2224	c.1911G>A	c.(1909-1911)tcG>tcA	p.S637S	CUL2_ENST00000374749.3_Silent_p.S637S|CUL2_ENST00000374746.1_Silent_p.S637S|CUL2_ENST00000374751.3_Silent_p.S637S|CUL2_ENST00000537177.1_Silent_p.S656S|CUL2_ENST00000602371.1_Silent_p.S580S|CUL2_ENST00000374742.1_Silent_p.S637S			Q13617	CUL2_HUMAN	cullin 2	637					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						TTAATGAAAACGAAGATTCTG	0.264													C|||	1421	0.283746	0.1483	0.3314	5008	,	,		15043	0.3125		0.3598	False		,,,				2504	0.3252				p.S656S		Atlas-SNP	.											CUL2,colon,carcinoma,-1,1	CUL2	63	1	0			c.G1968A						PASS	.	C	,,,	739,3659	282.5+/-276.6	72,595,1532	104.0	88.0	94.0		1911,1968,1950,1911	0.6	1.0	10	dbSNP_52	94	2928,5654	423.6+/-354.4	495,1938,1858	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CUL2	NM_001198777.1,NM_001198778.1,NM_001198779.1,NM_003591.3	,,,	567,2533,3390	TT,TC,CC		34.1179,16.8031,28.2512	,,,	637/746,656/765,650/759,637/746	35302705	3667,9313	2199	4291	6490	SO:0001819	synonymous_variant	8453	exon19			TGAAAACGAAGAT	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.1911G>A	10.37:g.35302705C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Silent	SNP	ENST00000374748.1	37	CCDS7179.1																																																																																			T|0.272;G|0.012	0.272	strong		0.264	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591	
SPTB	6710	hgsc.bcm.edu	37	14	65242044	65242044	+	Silent	SNP	C	C	T	rs184528	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:65242044C>T	ENST00000389721.5	-	22	4673	c.4641G>A	c.(4639-4641)gcG>gcA	p.A1547A	SPTB_ENST00000556626.1_Silent_p.A1547A|SPTB_ENST00000389722.3_Silent_p.A1547A|SPTB_ENST00000542895.1_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	114	0	0		WXS	Illumina HiSeq	Phase_I	150	148	0.986667	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		
RAP1GAP	5909	hgsc.bcm.edu	37	1	21976289	21976289	+	5'UTR	SNP	C	C	T	rs141127873	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:21976289C>T	ENST00000374765.4	-	0	53				RAP1GAP_ENST00000542643.2_5'UTR|RAP1GAP_ENST00000374757.3_5'UTR|RAP1GAP_ENST00000290101.4_Splice_Site_p.G15G	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)		ACTTGTCCACCCTGAAACACA	0.592													C|||	17	0.00339457	0.0008	0.0072	5008	,	,		16650	0.0		0.008	False		,,,				2504	0.0031				p.G15G		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.G45A						PASS	.	C	,,	7,2927		0,7,1460	67.0	65.0	65.0		,45,	2.4	1.0	1	dbSNP_134	65	75,6603		0,75,3264	yes	utr-5,coding-synonymous-near-splice,utr-5	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	0,82,4724	TT,TC,CC		1.1231,0.2386,0.8531	,,	,15/728,	21976289	82,9530	1467	3339	4806	SO:0001623	5_prime_UTR_variant	5909	exon2			GTCCACCCTGAAA	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.-148G>A	1.37:g.21976289C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	140	58	0.414286	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			C|0.996;T|0.004	0.004	strong		0.592	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
FBXW5	54461	hgsc.bcm.edu	37	9	139835725	139835725	+	Missense_Mutation	SNP	C	C	T	rs374757784		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139835725C>T	ENST00000325285.3	-	8	1514	c.1435G>A	c.(1435-1437)Gtc>Atc	p.V479I	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	479					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		TCCCTGCTGACGTCCAGGAAG	0.697																																					p.V479I		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1435A						PASS	.	C	ILE/VAL	0,4404		0,0,2202	32.0	27.0	29.0		1435	4.2	1.0	9		29	1,8595	1.2+/-3.3	0,1,4297	no	missense	FBXW5	NM_018998.2	29	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	479/567	139835725	1,12999	2202	4298	6500	SO:0001583	missense	54461	exon8			TGCTGACGTCCAG	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.1435G>A	9.37:g.139835725C>T	ENSP00000313034:p.Val479Ile	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.002574	0.74932	0.0	1.16E-4	ENSG00000159069	ENST00000325285	T	0.65732	-0.17	4.24	4.24	0.50183	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.73118	0.3546	L	0.54323	1.7	0.80722	D	1	D;P	0.76494	0.999;0.751	D;B	0.72982	0.979;0.106	T	0.69401	-0.5155	10	0.21540	T	0.41	-10.464	16.8298	0.85941	0.0:1.0:0.0:0.0	.	344;479	Q59ET5;Q969U6	.;FBXW5_HUMAN	I	479	ENSP00000313034:V479I	ENSP00000313034:V479I	V	-	1	0	FBXW5	138955546	1.000000	0.71417	0.985000	0.45067	0.964000	0.63967	7.002000	0.76304	2.204000	0.70986	0.561000	0.74099	GTC	.	.	weak		0.697	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
PML	5371	hgsc.bcm.edu	37	15	74328116	74328116	+	Intron	SNP	A	A	G	rs743580	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:74328116A>G	ENST00000268058.3	+	7	1806				PML_ENST00000435786.2_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000354026.6_Missense_Mutation_p.S724G|PML_ENST00000395132.2_Intron|PML_ENST00000564428.1_Intron|PML_ENST00000436891.3_3'UTR|PML_ENST00000395135.3_Intron|PML_ENST00000268059.6_Missense_Mutation_p.S772G|PML_ENST00000359928.4_Intron|PML_ENST00000565898.1_Intron|PML_ENST00000563500.1_3'UTR	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						GGCAGGGGAAAGCAGAGCCCA	0.577			T	"""RARA, PAX5"""	"""APL, ALL"""								G|||	2764	0.551917	0.5272	0.5346	5008	,	,		15561	0.6379		0.5189	False		,,,				2504	0.5429				p.S772G		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.A2314G						PASS	.	G	,,GLY/SER,,,,,,GLY/SER	2250,2146	556.1+/-379.4	568,1114,516	47.0	55.0	53.0		,,2314,,,,,,2170	0.6	0.0	15	dbSNP_86	53	4233,4361	565.9+/-388.6	1023,2187,1087	yes	intron,intron,missense,utr-3,utr-3,intron,intron,intron,missense	PML	NM_002675.3,NM_033238.2,NM_033239.2,NM_033240.2,NM_033244.3,NM_033246.2,NM_033247.2,NM_033249.2,NM_033250.2	,,56,,,,,,56	1591,3301,1603	GG,GA,AA		49.2553,48.8171,49.9076	,,,,,,,,	,,772/830,,,,,,724/782	74328116	6483,6507	2198	4297	6495	SO:0001627	intron_variant	5371	exon8			GGGGAAAGCAGAG	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+1245A>G	15.37:g.74328116A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_033239	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	37	CCDS10255.1	1199	0.548992673992674	248	0.5040650406504065	179	0.494475138121547	373	0.6520979020979021	399	0.5263852242744064	G	0.009	-1.857524	0.00558	0.511829	0.492553	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	2.67	0.623	0.17654	.	.	.	.	.	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	0.44922	-0.9296	6	0.02654	T	1	.	2.4421	0.04497	0.2885:0.0:0.4641:0.2475	rs743580;rs3825940;rs17855993;rs17856627	724;772	P29590-13;P29590-8	.;.	G	772;724	.	ENSP00000268059:S772G	S	+	1	0	PML	72115169	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	0.137000	0.15995	-0.085000	0.12573	-0.355000	0.07637	AGC	A|0.492;C|0.000;G|0.508	0.508	strong		0.577	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
ABTB1	80325	hgsc.bcm.edu	37	3	127395817	127395817	+	Silent	SNP	G	G	A	rs35834653	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:127395817G>A	ENST00000232744.8	+	7	620	c.534G>A	c.(532-534)ctG>ctA	p.L178L	ABTB1_ENST00000393363.3_Silent_p.L36L|ABTB1_ENST00000453791.2_Silent_p.L36L|ABTB1_ENST00000468137.1_Silent_p.L36L					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						CAGGCCGCCTGGACATTGGCG	0.642													G|||	97	0.019369	0.0008	0.0418	5008	,	,		19736	0.001		0.0596	False		,,,				2504	0.0061				p.L178L		Atlas-SNP	.											.	ABTB1	36	.	0			c.G534A						PASS	.	G	,	56,4350	50.9+/-86.3	0,56,2147	40.0	39.0	40.0		108,534	2.5	1.0	3	dbSNP_126	40	547,8053	149.5+/-204.6	15,517,3768	no	coding-synonymous,coding-synonymous	ABTB1	NM_032548.3,NM_172027.2	,	15,573,5915	AA,AG,GG		6.3605,1.271,4.6363	,	36/337,178/479	127395817	603,12403	2203	4300	6503	SO:0001819	synonymous_variant	80325	exon7			CCGCCTGGACATT	AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.534G>A	3.37:g.127395817G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_172027		Silent	SNP	ENST00000232744.8	37	CCDS3045.1																																																																																			G|0.962;A|0.038	0.038	strong		0.642	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027	
CMTR2	55783	hgsc.bcm.edu	37	16	71319539	71319539	+	Silent	SNP	C	C	T	rs3826247	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71319539C>T	ENST00000338099.5	-	3	621	c.285G>A	c.(283-285)gcG>gcA	p.A95A	CMTR2_ENST00000434935.2_Silent_p.A95A			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	95					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)										TGATTTTCCCCGCTTTATTAG	0.373													T|||	2314	0.462061	0.3714	0.6628	5008	,	,		20347	0.245		0.675	False		,,,				2504	0.4468				p.A95A		Atlas-SNP	.											.	FTSJD1	70	.	0			c.G285A						PASS	.	T	,	1766,2630	640.0+/-397.2	352,1062,784	102.0	97.0	99.0		285,285	0.6	1.0	16	dbSNP_107	99	5609,2991	461.7+/-365.5	1836,1937,527	no	coding-synonymous,coding-synonymous	FTSJD1	NM_001099642.1,NM_018348.5	,	2188,2999,1311	TT,TC,CC		34.7791,40.1729,43.2518	,	95/771,95/771	71319539	7375,5621	2198	4300	6498	SO:0001819	synonymous_variant	55783	exon3			TTTCCCCGCTTTA	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.285G>A	16.37:g.71319539C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Silent	SNP	ENST00000338099.5	37	CCDS10898.1																																																																																			C|0.460;T|0.540	0.540	strong		0.373	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
AK9	221264	hgsc.bcm.edu	37	6	109827716	109827716	+	Missense_Mutation	SNP	C	C	T	rs2277114	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:109827716C>T	ENST00000424296.2	-	35	4739	c.4663G>A	c.(4663-4665)Gta>Ata	p.V1555I	AL109947.2_ENST00000517228.1_RNA|RP5-919F19.5_ENST00000423747.2_RNA	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1555	Adenylate kinase 3.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTGACAGCTACAATTTGTGCA	0.348													T|||	1905	0.380391	0.2814	0.4092	5008	,	,		20615	0.378		0.4105	False		,,,				2504	0.4652				p.V1555I		Atlas-SNP	.											.	AKD1	223	.	0			c.G4663A						PASS	.	T	ILE/VAL	399,985		60,279,353	186.0	133.0	149.0		4663	0.9	1.0	6	dbSNP_100	149	1222,1960		247,728,616	yes	missense	AKD1	NM_001145128.2	29	307,1007,969	TT,TC,CC		38.4035,28.8295,35.5015	benign	1555/1912	109827716	1621,2945	692	1591	2283	SO:0001583	missense	221264	exon35			CAGCTACAATTTG	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.4663G>A	6.37:g.109827716C>T	ENSP00000410186:p.Val1555Ile	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	865	0.39606227106227104	148	0.3008130081300813	146	0.40331491712707185	260	0.45454545454545453	311	0.4102902374670185	T	3.803	-0.041245	0.07452	0.288295	0.384035	ENSG00000155085	ENST00000424296	T	0.78003	-1.14	4.76	0.879	0.19155	ATPase, AAA+ type, core (1);	.	.	.	.	T	0.18341	0.0440	N	0.01048	-1.04	0.09310	P	0.999999999184006	B	0.02656	0.0	B	0.01281	0.0	T	0.07177	-1.0786	7	.	.	.	.	1.7741	0.03018	0.1123:0.184:0.3305:0.3733	rs2277114;rs61486674;rs2277114	1555	Q5TCS8	AKD1_HUMAN	I	1555	ENSP00000410186:V1555I	.	V	-	1	0	AKD1	109934409	1.000000	0.71417	0.978000	0.43139	0.024000	0.10985	1.754000	0.38369	0.269000	0.21961	-1.087000	0.02190	GTA	C|0.610;T|0.390	0.390	strong		0.348	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
EFNA3	1944	hgsc.bcm.edu	37	1	155058663	155058663	+	Missense_Mutation	SNP	G	G	A	rs17723260	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:155058663G>A	ENST00000368408.3	+	4	638	c.568G>A	c.(568-570)Gtg>Atg	p.V190M	EFNA3_ENST00000498667.1_3'UTR|EFNA3_ENST00000556931.1_Missense_Mutation_p.V185M|EFNA3_ENST00000505139.1_Missense_Mutation_p.V185M|EFNA3_ENST00000418360.2_Intron	NM_004952.4	NP_004943.1	P52797	EFNA3_HUMAN	ephrin-A3	190			V -> M (in dbSNP:rs17723260).		axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGGCCCCAATGTGAAGATCAA	0.687											OREG0013850	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	381	0.0760783	0.0234	0.0994	5008	,	,		13282	0.0109		0.1342	False		,,,				2504	0.138				p.V190M		Atlas-SNP	.											EFNA3,colon,carcinoma,0,1	EFNA3	15	1	0			c.G568A						PASS	.	G	MET/VAL	172,4234	109.9+/-148.2	1,170,2032	44.0	43.0	43.0		568	4.5	1.0	1	dbSNP_123	43	1202,7396	238.8+/-270.1	82,1038,3179	yes	missense	EFNA3	NM_004952.4	21	83,1208,5211	AA,AG,GG		13.98,3.9038,10.566	possibly-damaging	190/239	155058663	1374,11630	2203	4299	6502	SO:0001583	missense	1944	exon4			CCCAATGTGAAGA	BC017722	CCDS1090.1	1q21-q22	2011-03-09			ENSG00000143590	ENSG00000143590		"""Ephrins"""	3223	protein-coding gene	gene with protein product		601381		EPLG3		8660976	Standard	NM_004952		Approved	LERK3, Ehk1-L	uc001fhf.3	P52797	OTTHUMG00000035313	ENST00000368408.3:c.568G>A	1.37:g.155058663G>A	ENSP00000357393:p.Val190Met	Somatic	235	0	0	220	WXS	Illumina HiSeq	Phase_I	216	115	0.532407	NM_004952	B7ZAD3|D3DV85|Q0VGC9|Q5SR70	Missense_Mutation	SNP	ENST00000368408.3	37	CCDS1090.1	165	0.07554945054945054	12	0.024390243902439025	45	0.12430939226519337	3	0.005244755244755245	105	0.13852242744063326	G	16.17	3.046837	0.55110	0.039038	0.1398	ENSG00000143590;ENSG00000143590;ENSG00000251246	ENST00000556931;ENST00000368408;ENST00000505139	D;D;D	0.94897	-3.55;-3.53;-3.55	4.51	4.51	0.55191	.	0.000000	0.33534	N	0.004810	D	0.89326	0.6683	N	0.14661	0.345	0.09310	P	1.0	P;P	0.51351	0.944;0.936	P;P	0.51355	0.667;0.578	D	0.90589	0.4535	9	0.45353	T	0.12	-13.0846	15.1743	0.72899	0.0:0.0:1.0:0.0	rs17723260;rs17723260	185;190	B4DXG7;P52797	.;EFNA3_HUMAN	M	185;190;185	ENSP00000450814:V185M;ENSP00000357393:V190M;ENSP00000426741:V185M	ENSP00000357393:V190M	V	+	1	0	RP11-540D14.8;EFNA3	153325287	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.093000	0.50217	2.525000	0.85131	0.456000	0.33151	GTG	G|0.911;A|0.089	0.089	strong		0.687	EFNA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085429.1	NM_004952	
SPATA22	84690	hgsc.bcm.edu	37	17	3343519	3343519	+	Silent	SNP	T	T	C	rs17822627	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:3343519T>C	ENST00000573128.1	-	9	1497	c.1014A>G	c.(1012-1014)gaA>gaG	p.E338E	SPATA22_ENST00000541913.1_Silent_p.E322E|SPATA22_ENST00000397168.3_Silent_p.E338E|SPATA22_ENST00000572969.1_Silent_p.E338E|SPATA22_ENST00000575375.1_Silent_p.E338E|SPATA22_ENST00000355380.4_Silent_p.E295E			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	358	0	0		WXS	Illumina HiSeq	Phase_I	385	180	0.467532	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	
MIA2	117153	hgsc.bcm.edu	37	14	39722023	39722023	+	Missense_Mutation	SNP	G	G	C	rs10134365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	49	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	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	
SLC18A1	6570	hgsc.bcm.edu	37	8	20038466	20038466	+	Missense_Mutation	SNP	T	T	G	rs2270641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:20038466T>G	ENST00000276373.5	-	2	276	c.10A>C	c.(10-12)Acc>Ccc	p.T4P	SLC18A1_ENST00000440926.1_Missense_Mutation_p.T4P|SLC18A1_ENST00000381608.4_Missense_Mutation_p.T4P|SLC18A1_ENST00000265808.7_Missense_Mutation_p.T4P|SLC18A1_ENST00000437980.1_Missense_Mutation_p.T4P|SLC18A1_ENST00000519026.1_Missense_Mutation_p.T4P	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	4			T -> P (in dbSNP:rs2270641). {ECO:0000269|PubMed:15489334}.		monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)	p.T4P(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	TCCAGAATGGTCCGGAGCATG	0.607													T|||	1233	0.246206	0.1029	0.3012	5008	,	,		13281	0.248		0.3638	False		,,,				2504	0.2781				p.T4P		Atlas-SNP	.											SLC18A1,NS,lymphoid_neoplasm,0,1	SLC18A1	68	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A10C	GRCh37	CM057213	SLC18A1	M	rs2270641	PASS	.	T	PRO/THR,PRO/THR,PRO/THR,PRO/THR	686,3714		57,572,1571	49.0	40.0	43.0		10,10,10,10	0.6	0.0	8	dbSNP_100	43	3086,5506		573,1940,1783	yes	missense,missense,missense,missense	SLC18A1	NM_001135691.2,NM_001142324.1,NM_001142325.1,NM_003053.3	38,38,38,38	630,2512,3354	GG,GT,TT		35.9171,15.5909,29.0333	benign,benign,benign,benign	4/526,4/494,4/473,4/526	20038466	3772,9220	2200	4296	6496	SO:0001583	missense	6570	exon3			GAATGGTCCGGAG		CCDS6013.1, CCDS47814.1, CCDS47815.1	8p21.3	2013-07-18	2013-07-18		ENSG00000036565	ENSG00000036565		"""Solute carriers"""	10934	protein-coding gene	gene with protein product		193002		VMAT1, VAT1			Standard	NM_003053		Approved	CGAT	uc003wzm.3	P54219	OTTHUMG00000097017	ENST00000276373.5:c.10A>C	8.37:g.20038466T>G	ENSP00000276373:p.Thr4Pro	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_001142324	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000276373.5	37	CCDS6013.1	596	0.27289377289377287	63	0.12804878048780488	112	0.30939226519337015	152	0.26573426573426573	269	0.3548812664907652	T	7.431	0.638805	0.14386	0.155909	0.359171	ENSG00000036565	ENST00000265808;ENST00000276373;ENST00000440926;ENST00000437980;ENST00000519026;ENST00000381608;ENST00000522513	T;T;T;T;T;T;T	0.04454	3.93;3.93;3.93;3.89;3.93;3.89;3.62	5.71	0.564	0.17302	.	1.085600	0.06916	N	0.808479	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.27068	0.001;0.167;0.0	B;B;B	0.20384	0.001;0.029;0.0	T	0.47886	-0.9082	9	0.30078	T	0.28	0.6653	8.8235	0.35041	0.0:0.3955:0.0:0.6045	rs2270641;rs17222099;rs17490072;rs17856183;rs56575139;rs2270641	4;4;4	E9PB33;E9PDJ5;P54219	.;.;VMAT1_HUMAN	P	4	ENSP00000265808:T4P;ENSP00000276373:T4P;ENSP00000387549:T4P;ENSP00000413361:T4P;ENSP00000429664:T4P;ENSP00000371021:T4P;ENSP00000428999:T4P	ENSP00000265808:T4P	T	-	1	0	SLC18A1	20082746	0.000000	0.05858	0.002000	0.10522	0.100000	0.18952	-0.897000	0.04110	-0.183000	0.10585	0.533000	0.62120	ACC	A|0.013;C|0.004	.	strong		0.607	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1		
HIST1H1T	3010	hgsc.bcm.edu	37	6	26107790	26107790	+	Missense_Mutation	SNP	G	G	T	rs198845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26107790G>T	ENST00000338379.4	-	1	574	c.532C>A	c.(532-534)Cag>Aag	p.Q178K		NM_005323.3	NP_005314.2	P22492	H1T_HUMAN	histone cluster 1, H1t	178			Q -> K (in dbSNP:rs198845). {ECO:0000269|PubMed:8175896}.		binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|nucleosome assembly (GO:0006334)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(1)|lung(3)|ovary(2)|prostate(1)	9						CTCTTCTGCTGTTGCTTACCC	0.448													G|||	1224	0.244409	0.1059	0.304	5008	,	,		19764	0.1319		0.3708	False		,,,				2504	0.3753				p.Q178K		Atlas-SNP	.											.	HIST1H1T	40	.	0			c.C532A						PASS	.	G	LYS/GLN	724,3682		59,606,1538	145.0	134.0	138.0		532	4.2	0.0	6	dbSNP_79	138	3195,5405		598,1999,1703	yes	missense	HIST1H1T	NM_005323.3	53	657,2605,3241	TT,TG,GG		37.1512,16.4321,30.1322	benign	178/208	26107790	3919,9087	2203	4300	6503	SO:0001583	missense	3010	exon1			TCTGCTGTTGCTT	M60094	CCDS34349.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000187475	ENSG00000187475		"""Histones / Replication-dependent"""	4720	protein-coding gene	gene with protein product		142712	"""H1 histone family, member T (testis-specific)"", ""histone 1, H1t"""	H1FT		8175896, 12408966	Standard	NM_005323		Approved	H1t	uc003ngj.3	P22492	OTTHUMG00000014430	ENST00000338379.4:c.532C>A	6.37:g.26107790G>T	ENSP00000341214:p.Gln178Lys	Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	263	129	0.490494	NM_005323	Q6ISI1|Q8IUE8	Missense_Mutation	SNP	ENST00000338379.4	37	CCDS34349.1	518	0.23717948717948717	57	0.11585365853658537	111	0.30662983425414364	57	0.09965034965034965	293	0.3865435356200528	.	7.748	0.702736	0.15172	0.164321	0.371512	ENSG00000187475	ENST00000338379	T	0.03772	3.81	5.08	4.17	0.49024	.	0.472456	0.13025	U	0.419810	T	0.00967	0.0032	N	0.08118	0	0.80722	P	0.0	P	0.35077	0.483	B	0.33339	0.162	T	0.32161	-0.9917	9	0.06099	T	0.92	-14.8036	14.8221	0.70082	0.0:0.1437:0.8563:0.0	rs198845;rs1758681;rs3734529;rs17531286;rs52791787;rs56528463;rs57850971;rs198845	178	P22492	H1T_HUMAN	K	178	ENSP00000341214:Q178K	ENSP00000341214:Q178K	Q	-	1	0	HIST1H1T	26215769	0.000000	0.05858	0.006000	0.13384	0.046000	0.14306	0.731000	0.26058	2.656000	0.90262	0.655000	0.94253	CAG	G|0.742;T|0.258	0.258	strong		0.448	HIST1H1T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040093.2	NM_005323	
DMWD	1762	hgsc.bcm.edu	37	19	46289509	46289509	+	Silent	SNP	G	G	A	rs11545326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46289509G>A	ENST00000270223.6	-	3	1290	c.1245C>T	c.(1243-1245)ggC>ggT	p.G415G	AC011530.4_ENST00000593999.1_5'Flank|DMWD_ENST00000377735.3_Silent_p.G415G|DMWD_ENST00000601370.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	415										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		AGAGCGGGGCGCCCCCGGCCG	0.701													G|||	412	0.0822684	0.0045	0.111	5008	,	,		12595	0.0407		0.162	False		,,,				2504	0.1278				p.G415G		Atlas-SNP	.											.	DMWD	46	.	0			c.C1245T						PASS	.	G		95,4227		1,93,2067	15.0	18.0	17.0		1245	-7.3	0.0	19	dbSNP_120	17	1083,7415		69,945,3235	no	coding-synonymous	DMWD	NM_004943.1		70,1038,5302	AA,AG,GG		12.7442,2.1981,9.1888		415/675	46289509	1178,11642	2161	4249	6410	SO:0001819	synonymous_variant	1762	exon3			CGGGGCGCCCCCG	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"""WD repeat domain containing"""	2936	protein-coding gene	gene with protein product		609857	"""dystrophia myotonica-containing WD repeat motif"""			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1245C>T	19.37:g.46289509G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	78	30	0.384615	NM_004943		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																			G|0.917;A|0.083	0.083	strong		0.701	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943	
ZNF335	63925	hgsc.bcm.edu	37	20	44578674	44578674	+	Silent	SNP	T	T	A	rs16990951	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:44578674T>A	ENST00000322927.2	-	23	3622	c.3522A>T	c.(3520-3522)ccA>ccT	p.P1174P	ZNF335_ENST00000426788.1_Silent_p.P1019P	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1174					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GTAGCCGCTCTGGGCCCAGGA	0.612													T|||	1133	0.226238	0.3313	0.1009	5008	,	,		19525	0.3294		0.1004	False		,,,				2504	0.1963				p.P1174P		Atlas-SNP	.											.	ZNF335	115	.	0			c.A3522T						PASS	.	T		1162,3244	403.1+/-332.6	139,884,1180	36.0	35.0	35.0		3522	-2.2	1.0	20	dbSNP_123	35	987,7613	211.0+/-251.7	50,887,3363	no	coding-synonymous	ZNF335	NM_022095.3		189,1771,4543	AA,AT,TT		11.4767,26.3731,16.5231		1174/1343	44578674	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	63925	exon23			CCGCTCTGGGCCC	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3522A>T	20.37:g.44578674T>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																			T|0.821;A|0.179	0.179	strong		0.612	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
KRT79	338785	hgsc.bcm.edu	37	12	53217701	53217701	+	Silent	SNP	C	C	A	rs10876354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:53217701C>A	ENST00000330553.5	-	6	1150	c.1116G>T	c.(1114-1116)ctG>ctT	p.L372L		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	372	Coil 2.|Rod.					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						CCTCCCCCTGCAGCCTCTGGA	0.617													C|||	2407	0.480631	0.2557	0.5562	5008	,	,		18214	0.5099		0.5099	False		,,,				2504	0.6708				p.L372L		Atlas-SNP	.											.	KRT79	78	.	0			c.G1116T						PASS	.	C		1362,3044	450.0+/-349.2	235,892,1076	66.0	55.0	59.0		1116	3.8	1.0	12	dbSNP_120	59	4403,4197	584.0+/-391.6	1132,2139,1029	no	coding-synonymous	KRT79	NM_175834.2		1367,3031,2105	AA,AC,CC		48.8023,30.9124,44.3257		372/536	53217701	5765,7241	2203	4300	6503	SO:0001819	synonymous_variant	338785	exon6			CCCCTGCAGCCTC	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.1116G>T	12.37:g.53217701C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_175834	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	37	CCDS8839.1																																																																																			C|0.550;A|0.450	0.450	strong		0.617	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
IL25	64806	hgsc.bcm.edu	37	14	23844979	23844979	+	Silent	SNP	C	C	A	rs79877597	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23844979C>A	ENST00000329715.2	+	2	682	c.424C>A	c.(424-426)Cgg>Agg	p.R142R	CMTM5_ENST00000555731.1_5'Flank|CMTM5_ENST00000397227.3_5'Flank|CMTM5_ENST00000342473.4_5'Flank|CMTM5_ENST00000359320.3_5'Flank|IL25_ENST00000397242.2_Silent_p.R126R|CMTM5_ENST00000382809.2_5'Flank|CMTM5_ENST00000339180.4_5'Flank	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	142					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)		TGTCTTCTACCGGCGGCCATG	0.637													C|||	1337	0.266973	0.3873	0.1974	5008	,	,		16724	0.2639		0.2157	False		,,,				2504	0.2096				p.R142R		Atlas-SNP	.											IL25,NS,carcinoma,0,1	IL25	21	1	0			c.C424A						PASS	.	C	,	1620,2786	500.0+/-364.6	290,1040,873	87.0	80.0	83.0		424,376	3.6	1.0	14	dbSNP_131	83	1820,6780	324.2+/-316.4	192,1436,2672	no	coding-synonymous,coding-synonymous	IL25	NM_022789.3,NM_172314.1	,	482,2476,3545	AA,AC,CC		21.1628,36.768,26.4493	,	142/178,126/162	23844979	3440,9566	2203	4300	6503	SO:0001819	synonymous_variant	64806	exon2			TTCTACCGGCGGC	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.424C>A	14.37:g.23844979C>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_022789	Q2M3F0|Q8IZV3|Q8WXB0	Silent	SNP	ENST00000329715.2	37	CCDS9597.1																																																																																			A|0.271;C|0.727;T|0.002	0.271	strong		0.637	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417103	105417103	+	Missense_Mutation	SNP	G	G	A	rs61996045	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105417103G>A	ENST00000333244.5	-	7	4804	c.4685C>T	c.(4684-4686)cCa>cTa	p.P1562L	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)			AGGGCCCTCTGGGAGTTTCAC	0.632													.|||	1410	0.28155	0.0719	0.3746	5008	,	,		15026	0.0883		0.5427	False		,,,				2504	0.4294				p.P1562L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4685T						PASS	.	G	LEU/PRO	561,3197		82,397,1400	96.0	98.0	97.0		4685	2.9	0.0	14	dbSNP_129	97	4381,3737		1408,1565,1086	no	missense	AHNAK2	NM_138420.2	98	1490,1962,2486	AA,AG,GG		46.0335,14.9282,41.6133	benign	1562/5796	105417103	4942,6934	1879	4059	5938	SO:0001583	missense	113146	exon7			CCCTCTGGGAGTT	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.4685C>T	14.37:g.105417103G>A	ENSP00000353114:p.Pro1562Leu	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	241	241	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	486	0.22252747252747251	41	0.08333333333333333	121	0.3342541436464088	17	0.02972027972027972	307	0.4050131926121372	g	14.05	2.421062	0.42918	0.149282	0.539665	ENSG00000185567	ENST00000333244	T	0.02890	4.12	3.78	2.86	0.33363	.	.	.	.	.	T	0.00012	0.0000	M	0.84219	2.685	0.80722	P	0.0	P	0.50943	0.94	P	0.51135	0.66	T	0.17806	-1.0357	8	0.12766	T	0.61	.	3.4672	0.07554	0.0976:0.1691:0.5592:0.1741	rs61996045	1562	Q8IVF2	AHNK2_HUMAN	L	1562	ENSP00000353114:P1562L	ENSP00000353114:P1562L	P	-	2	0	AHNAK2	104488148	0.059000	0.20769	0.007000	0.13788	0.002000	0.02628	2.086000	0.41643	0.547000	0.28938	-0.515000	0.04445	CCA	G|0.702;A|0.298	0.298	strong		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TEKT5	146279	hgsc.bcm.edu	37	16	10788219	10788219	+	Missense_Mutation	SNP	G	G	A	rs141349037	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10788219G>A	ENST00000283025.2	-	1	583	c.512C>T	c.(511-513)aCg>aTg	p.T171M	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	171						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						CCTCTTGACCGTCTCCAAGTT	0.597													G|||	3	0.000599042	0.0	0.0	5008	,	,		18281	0.0		0.002	False		,,,				2504	0.001				p.T171M		Atlas-SNP	.											.	TEKT5	66	.	0			c.C512T						PASS	.	G	MET/THR	1,4393	2.1+/-5.4	0,1,2196	140.0	152.0	148.0		512	-1.3	0.0	16	dbSNP_134	148	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TEKT5	NM_144674.1	81	0,10,6487	AA,AG,GG		0.1047,0.0228,0.077	possibly-damaging	171/486	10788219	10,12984	2197	4300	6497	SO:0001583	missense	146279	exon1			TTGACCGTCTCCA		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.512C>T	16.37:g.10788219G>A	ENSP00000283025:p.Thr171Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	80	26	0.325	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.721	0.501787	0.12822	2.28E-4	0.001047	ENSG00000153060	ENST00000283025	T	0.02631	4.22	5.63	-1.29	0.09288	.	0.388807	0.24722	N	0.036122	T	0.03305	0.0096	L	0.59436	1.845	0.09310	N	1	B	0.31968	0.349	B	0.38020	0.263	T	0.35992	-0.9766	10	0.52906	T	0.07	-7.5255	1.0994	0.01680	0.2102:0.1177:0.3104:0.3617	.	171	Q96M29	TEKT5_HUMAN	M	171	ENSP00000283025:T171M	ENSP00000283025:T171M	T	-	2	0	TEKT5	10695720	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.881000	0.28173	-0.203000	0.10251	-0.143000	0.13931	ACG	G|0.999;A|0.001	0.001	strong		0.597	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
SULF2	55959	hgsc.bcm.edu	37	20	46385955	46385955	+	Silent	SNP	C	C	T	rs61730618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:46385955C>T	ENST00000359930.4	-	2	1004	c.153G>A	c.(151-153)acG>acA	p.T51T	SULF2_ENST00000361612.4_Silent_p.T51T|SULF2_ENST00000484875.1_Silent_p.T51T|SULF2_ENST00000467815.1_Silent_p.T51T	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	51					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						CCTGGTCGTCCGTCAGCACCA	0.657													C|||	83	0.0165735	0.0008	0.013	5008	,	,		17515	0.0		0.0388	False		,,,				2504	0.0348				p.T51T		Atlas-SNP	.											.	SULF2	131	.	0			c.G153A						PASS	.	C	,,	31,4351		0,31,2160	51.0	37.0	41.0		153,153,153	-9.5	0.1	20	dbSNP_129	41	218,8342		1,216,4063	no	coding-synonymous,coding-synonymous,coding-synonymous	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	,,	1,247,6223	TT,TC,CC		2.5467,0.7074,1.924	,,	51/871,51/871,51/868	46385955	249,12693	2191	4280	6471	SO:0001819	synonymous_variant	55959	exon2			GTCGTCCGTCAGC	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.153G>A	20.37:g.46385955C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Silent	SNP	ENST00000359930.4	37	CCDS13408.1																																																																																			C|0.982;T|0.018	0.018	strong		0.657	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
HTRA4	203100	hgsc.bcm.edu	37	8	38845602	38845602	+	Silent	SNP	T	T	G	rs62504414	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:38845602T>G	ENST00000302495.4	+	9	1516	c.1416T>G	c.(1414-1416)ccT>ccG	p.P472P		NM_153692.3	NP_710159.1	P83105	HTRA4_HUMAN	HtrA serine peptidase 4	472	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)	11		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			CAGTCATACCTGAAACAATCA	0.353													T|||	190	0.0379393	0.003	0.0418	5008	,	,		16888	0.001		0.0726	False		,,,				2504	0.0849				p.P472P		Atlas-SNP	.											.	HTRA4	25	.	0			c.T1416G						PASS	.	T		59,4347	56.2+/-92.4	1,57,2145	73.0	64.0	67.0		1416	4.9	1.0	8	dbSNP_129	67	681,7919	166.8+/-218.7	30,621,3649	no	coding-synonymous	HTRA4	NM_153692.3		31,678,5794	GG,GT,TT		7.9186,1.3391,5.6897		472/477	38845602	740,12266	2203	4300	6503	SO:0001819	synonymous_variant	203100	exon9			CATACCTGAAACA	AK075205	CCDS6110.1	8p11.23	2008-02-05			ENSG00000169495	ENSG00000169495			26909	protein-coding gene	gene with protein product		610700					Standard	NM_153692		Approved	FLJ90724	uc003xmj.3	P83105	OTTHUMG00000164070	ENST00000302495.4:c.1416T>G	8.37:g.38845602T>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_153692	Q542Z4|Q6PF13	Silent	SNP	ENST00000302495.4	37	CCDS6110.1																																																																																			T|0.950;G|0.050	0.050	strong		0.353	HTRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377077.1	NM_153692	
HDHD3	81932	hgsc.bcm.edu	37	9	116136155	116136155	+	Silent	SNP	G	G	A	rs17765613	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:116136155G>A	ENST00000238379.5	-	2	1377	c.480C>T	c.(478-480)tcC>tcT	p.S160S	HDHD3_ENST00000374180.3_Silent_p.S160S|HDHD3_ENST00000485934.1_5'Flank	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	160						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						CAGCAGCCTCGGAGGTCAGCA	0.602													G|||	209	0.0417332	0.0461	0.0144	5008	,	,		19469	0.0496		0.0219	False		,,,				2504	0.0675				p.S160S		Atlas-SNP	.											.	HDHD3	10	.	0			c.C480T						PASS	.	G		194,4212	122.5+/-159.9	5,184,2014	98.0	103.0	101.0		480	-6.2	0.9	9	dbSNP_123	101	302,8298	109.0+/-169.6	7,288,4005	no	coding-synonymous	HDHD3	NM_031219.2		12,472,6019	AA,AG,GG		3.5116,4.4031,3.8136		160/252	116136155	496,12510	2203	4300	6503	SO:0001819	synonymous_variant	81932	exon2			AGCCTCGGAGGTC	AK097067	CCDS6793.1	9q33.1	2006-04-12	2004-08-09	2004-08-12	ENSG00000119431	ENSG00000119431			28171	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 158"""	C9orf158		12477932	Standard	NM_031219		Approved	MGC12904	uc004bhi.1	Q9BSH5	OTTHUMG00000020524	ENST00000238379.5:c.480C>T	9.37:g.116136155G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_031219	B2RD47	Silent	SNP	ENST00000238379.5	37	CCDS6793.1																																																																																			G|0.965;A|0.035	0.035	strong		0.602	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219	
DNASE1L3	1776	hgsc.bcm.edu	37	3	58191266	58191266	+	Silent	SNP	C	C	T	rs2070117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58191266C>T	ENST00000394549.2	-	3	568	c.252G>A	c.(250-252)acG>acA	p.T84T	DNASE1L3_ENST00000483681.1_Silent_p.T84T|DNASE1L3_ENST00000318316.3_Silent_p.T84T|DNASE1L3_ENST00000486455.1_Intron	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	84					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		CATAGTTGTACGTTATGCCTC	0.388													C|||	1812	0.361821	0.1664	0.2997	5008	,	,		22701	0.6429		0.2237	False		,,,				2504	0.5225				p.T84T	Esophageal Squamous(96;1069 1424 4841 43466 52325)	Atlas-SNP	.											.	DNASE1L3	36	.	0			c.G252A						PASS	.	C		728,3676	300.4+/-286.3	54,620,1528	186.0	182.0	183.0		252	3.4	0.2	3	dbSNP_96	183	1709,6891	313.0+/-311.1	166,1377,2757	no	coding-synonymous	DNASE1L3	NM_004944.2		220,1997,4285	TT,TC,CC		19.8721,16.5304,18.7404		84/306	58191266	2437,10567	2202	4300	6502	SO:0001819	synonymous_variant	1776	exon3			GTTGTACGTTATG	AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"""DNase gamma"""	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.252G>A	3.37:g.58191266C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_004944	B2R8B1|B7Z707|O75803	Silent	SNP	ENST00000394549.2	37	CCDS2886.1																																																																																			C|0.747;T|0.253	0.253	strong		0.388	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944	
OTOP3	347741	hgsc.bcm.edu	37	17	72943126	72943126	+	Silent	SNP	G	G	A	rs8066909	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72943126G>A	ENST00000328801.4	+	6	1176	c.1176G>A	c.(1174-1176)gcG>gcA	p.A392A		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	392						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					CGTGCCTGGCGGGCACAGCCA	0.607													G|||	1456	0.290735	0.1672	0.4885	5008	,	,		18262	0.0655		0.5109	False		,,,				2504	0.3231				p.A392A		Atlas-SNP	.											OTOP3,NS,carcinoma,0,1	OTOP3	64	1	0			c.G1176A						PASS	.						74.0	66.0	69.0					17																	72943126		2203	4300	6503	SO:0001819	synonymous_variant	347741	exon6			CCTGGCGGGCACA	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.1176G>A	17.37:g.72943126G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_178233		Silent	SNP	ENST00000328801.4	37	CCDS11709.1																																																																																			G|0.683;A|0.317	0.317	strong		0.607	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
CCDC57	284001	hgsc.bcm.edu	37	17	80159566	80159566	+	Silent	SNP	T	T	C	rs8072670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80159566T>C	ENST00000389641.4	-	2	291	c.255A>G	c.(253-255)gaA>gaG	p.E85E	CCDC57_ENST00000392347.1_Silent_p.E85E|CCDC57_ENST00000392343.3_Silent_p.E85E			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	85										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GCCTGGCCTCTTCCCACTCCC	0.647													C|||	4124	0.823482	0.8828	0.817	5008	,	,		18894	0.9276		0.7087	False		,,,				2504	0.7587				p.E85E		Atlas-SNP	.											CCDC57_ENST00000389641,NS,carcinoma,-1,2	CCDC57	102	2	0			c.A255G						PASS	.	C		3743,553		1634,475,39	44.0	52.0	49.0		255	3.4	0.9	17	dbSNP_116	49	5847,2651		2015,1817,417	no	coding-synonymous	CCDC57	NM_198082.2		3649,2292,456	CC,CT,TT		31.1956,12.8724,25.043		85/916	80159566	9590,3204	2148	4249	6397	SO:0001819	synonymous_variant	284001	exon2			GGCCTCTTCCCAC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.255A>G	17.37:g.80159566T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	253	122	0.482213	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				T|0.203;C|0.797	0.797	strong		0.647	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
TPCN2	219931	hgsc.bcm.edu	37	11	68840412	68840412	+	Silent	SNP	C	C	G	rs1466220	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:68840412C>G	ENST00000294309.3	+	13	1274	c.1173C>G	c.(1171-1173)ctC>ctG	p.L391L	TPCN2_ENST00000442692.2_Intron|TPCN2_ENST00000542467.1_Silent_p.L391L	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	391					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GTGTTCTGCTCTCAGCTGAGG	0.597													C|||	1675	0.334465	0.3601	0.3271	5008	,	,		17797	0.2867		0.4841	False		,,,				2504	0.2004				p.L391L		Atlas-SNP	.											TPCN2,NS,carcinoma,+2,1	TPCN2	63	1	0			c.C1173G						PASS	.	C		1711,2689	515.0+/-368.8	335,1041,824	105.0	101.0	103.0		1173	1.1	0.0	11	dbSNP_88	103	4289,4299	576.1+/-390.3	1038,2213,1043	no	coding-synonymous	TPCN2	NM_139075.3		1373,3254,1867	GG,GC,CC		49.9418,38.8864,46.1965		391/753	68840412	6000,6988	2200	4294	6494	SO:0001819	synonymous_variant	219931	exon13			TCTGCTCTCAGCT	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1173C>G	11.37:g.68840412C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_139075	Q9NT82	Silent	SNP	ENST00000294309.3	37	CCDS8189.1																																																																																			C|0.563;G|0.437	0.437	strong		0.597	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
WDSUB1	151525	hgsc.bcm.edu	37	2	160112881	160112881	+	Missense_Mutation	SNP	G	G	T	rs7591849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160112881G>T	ENST00000409990.3	-	9	1214	c.958C>A	c.(958-960)Cgc>Agc	p.R320S	WDSUB1_ENST00000359774.4_Missense_Mutation_p.R320S|WDSUB1_ENST00000392796.3_Missense_Mutation_p.R320S|WDSUB1_ENST00000358147.4_Missense_Mutation_p.R228S|WDSUB1_ENST00000409124.1_Missense_Mutation_p.R320S	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	320			R -> S (in dbSNP:rs7591849). {ECO:0000269|PubMed:14702039}.				ubiquitin-protein transferase activity (GO:0004842)	p.R320S(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						TGTTCTGTGCGCCTTGCTTAA	0.318													T|||	2372	0.473642	0.7421	0.3689	5008	,	,		19381	0.2738		0.5398	False		,,,				2504	0.3231				p.R320S		Atlas-SNP	.											WDSUB1,colon,carcinoma,+1,2	WDSUB1	39	2	1	Substitution - Missense(1)	stomach(1)	c.C958A						PASS	.	T	SER/ARG,SER/ARG,SER/ARG	3163,1243	428.3+/-341.8	1127,909,167	79.0	76.0	77.0		958,958,958	4.4	0.6	2	dbSNP_116	77	4931,3669	525.5+/-380.8	1403,2125,772	yes	missense,missense,missense	WDSUB1	NM_001128212.1,NM_001128213.1,NM_152528.2	110,110,110	2530,3034,939	TT,TG,GG		42.6628,28.2115,37.7672	benign,benign,benign	320/477,320/477,320/477	160112881	8094,4912	2203	4300	6503	SO:0001583	missense	151525	exon9			CTGTGCGCCTTGC	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.958C>A	2.37:g.160112881G>T	ENSP00000387078:p.Arg320Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_152528	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	1087	0.4977106227106227	360	0.7317073170731707	153	0.42265193370165743	167	0.291958041958042	407	0.5369393139841688	T	11.20	1.568119	0.28003	0.717885	0.573372	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990;ENST00000409124	T;T;T;T;T	0.57273	0.66;0.41;0.66;0.66;0.65	5.54	4.37	0.52481	WD40/YVTN repeat-like-containing domain (1);	0.519406	0.23402	N	0.048580	T	0.00012	0.0000	N	0.04746	-0.17	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	0.42172	-0.9467	9	0.08599	T	0.76	.	6.6524	0.22969	0.0:0.1367:0.1305:0.7328	rs7591849;rs52801853;rs59900970;rs7591849	228;320;320	Q8N9V3-2;B8ZZF2;Q8N9V3	.;.;WSDU1_HUMAN	S	320;228;320;320;320	ENSP00000352820:R320S;ENSP00000350866:R228S;ENSP00000376545:R320S;ENSP00000387078:R320S;ENSP00000386891:R320S	ENSP00000350866:R228S	R	-	1	0	WDSUB1	159821127	0.000000	0.05858	0.639000	0.29394	0.984000	0.73092	0.383000	0.20651	0.378000	0.24764	-0.256000	0.11100	CGC	G|0.422;T|0.578	0.578	strong		0.318	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528	
ZNF729	100287226	hgsc.bcm.edu	37	19	22498943	22498943	+	Silent	SNP	T	T	C	rs8104705	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:22498943T>C	ENST00000601693.1	+	4	2842	c.2724T>C	c.(2722-2724)tgT>tgC	p.C908C	ZNF729_ENST00000357491.6_Intron			A6NN14	ZN729_HUMAN	zinc finger protein 729	908					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						AGAAACCCTGTAAATGTGAAG	0.353													C|||	3279	0.654752	0.6846	0.5403	5008	,	,		20307	0.6815		0.5477	False		,,,				2504	0.7781				p.C908C		Atlas-SNP	.											.	ZNF729	78	.	0			c.T2724C						PASS	.																																			SO:0001819	synonymous_variant	100287226	exon4			ACCCTGTAAATGT		CCDS59368.1	19p12	2014-02-14			ENSG00000196350	ENSG00000196350		"""Zinc fingers, C2H2-type"", ""-"""	32464	protein-coding gene	gene with protein product							Standard	NM_001242680		Approved		uc021urs.1	A6NN14	OTTHUMG00000182938	ENST00000601693.1:c.2724T>C	19.37:g.22498943T>C		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_001242680	M0QY45	Silent	SNP	ENST00000601693.1	37	CCDS59368.1																																																																																			T|0.467;C|0.533	0.533	strong		0.353	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464396.1	XM_496301	
ZNF407	55628	hgsc.bcm.edu	37	18	72344238	72344238	+	Silent	SNP	C	C	T	rs17817969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:72344238C>T	ENST00000299687.5	+	1	1263	c.1263C>T	c.(1261-1263)ctC>ctT	p.L421L	ZNF407_ENST00000582337.1_Silent_p.L421L|ZNF407_ENST00000577538.1_Silent_p.L421L|ZNF407_ENST00000309902.6_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	101	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	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	
DUSP12	11266	hgsc.bcm.edu	37	1	161721707	161721707	+	Silent	SNP	C	C	T	rs1063178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161721707C>T	ENST00000367943.4	+	3	542	c.510C>T	c.(508-510)taC>taT	p.Y170Y		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	170					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CAATGGGATACGAAGTGGATA	0.333													C|||	1803	0.360024	0.407	0.2464	5008	,	,		18522	0.4831		0.2922	False		,,,				2504	0.32				p.Y170Y		Atlas-SNP	.											.	DUSP12	20	.	0			c.C510T						PASS	.	C		1715,2691	513.7+/-368.4	344,1027,832	95.0	103.0	100.0		510	0.1	0.7	1	dbSNP_86	100	2889,5711	452.1+/-362.9	453,1983,1864	no	coding-synonymous	DUSP12	NM_007240.1		797,3010,2696	TT,TC,CC		33.593,38.9242,35.399		170/341	161721707	4604,8402	2203	4300	6503	SO:0001819	synonymous_variant	11266	exon3			GGGATACGAAGTG	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3067	protein-coding gene	gene with protein product	"""serine/threonine specific protein phosphatase"", ""YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"""	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.510C>T	1.37:g.161721707C>T		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	291	129	0.443299	NM_007240	Q5VXA8	Silent	SNP	ENST00000367943.4	37	CCDS1234.1																																																																																			C|0.639;N|0.000	.	strong		0.333	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240	
RGS7	6000	hgsc.bcm.edu	37	1	240975229	240975229	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240975229C>T	ENST00000407727.1	-	13	1070	c.1071G>A	c.(1069-1071)tcG>tcA	p.S357S	RGS7_ENST00000348120.2_Silent_p.S304S|RGS7_ENST00000446183.2_Silent_p.S273S|RGS7_ENST00000401882.1_Silent_p.S304S|RGS7_ENST00000366564.1_Silent_p.S357S|RGS7_ENST00000366562.4_Silent_p.S357S|RGS7_ENST00000366563.1_Silent_p.S357S|RGS7_ENST00000331110.7_Silent_p.S331S|RGS7_ENST00000366565.1_Silent_p.S357S			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	357	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			TTAAATTTTCCGAGCTGAATT	0.393																																					p.S357S		Atlas-SNP	.											RGS7_ENST00000366565,right_upper_lobe,carcinoma,-1,2	RGS7	308	2	0			c.G1071A						PASS	.						68.0	72.0	71.0					1																	240975229		2203	4299	6502	SO:0001819	synonymous_variant	6000	exon14			ATTTTCCGAGCTG	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"""Regulators of G-protein signaling"""	10003	protein-coding gene	gene with protein product		602517	"""regulator of G-protein signalling 7"""			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.1071G>A	1.37:g.240975229C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Silent	SNP	ENST00000407727.1	37																																																																																				.	.	none		0.393	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924	
SDHA	6389	hgsc.bcm.edu	37	5	231111	231111	+	Silent	SNP	T	T	C	rs1126417	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:231111T>C	ENST00000264932.6	+	7	1006	c.891T>C	c.(889-891)ccT>ccC	p.P297P	SDHA_ENST00000504309.1_Silent_p.P297P|SDHA_ENST00000510361.1_Silent_p.P249P	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	297					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)	AGTTCCACCCTACAGGTAGGG	0.547									Familial Paragangliomas				C|||	3272	0.653355	0.7874	0.6902	5008	,	,		19860	0.3363		0.7475	False		,,,				2504	0.6759				p.P297P		Atlas-SNP	.											.	SDHA	80	.	0			c.T891C						PASS	.	C		3477,929		1370,737,96	49.0	41.0	43.0		891	1.1	1.0	5	dbSNP_86	43	6519,2079		2498,1523,278	no	coding-synonymous	SDHA	NM_004168.2		3868,2260,374	CC,CT,TT		24.18,21.0849,23.1313		297/665	231111	9996,3008	2203	4299	6502	SO:0001819	synonymous_variant	6389	exon7	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	CCACCCTACAGGT	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.891T>C	5.37:g.231111T>C		Somatic	512	2	0.00390625		WXS	Illumina HiSeq	Phase_I	548	294	0.536496	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			T|0.273;C|0.727	0.727	strong		0.547	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
C3orf33	285315	hgsc.bcm.edu	37	3	155481609	155481609	+	Silent	SNP	G	G	A	rs7653384	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:155481609G>A	ENST00000340171.2	-	5	680	c.582C>T	c.(580-582)taC>taT	p.Y194Y	C3orf33_ENST00000534941.1_Silent_p.Y151Y			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	194					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)			GAACTGTCCAGTAGATTTTAG	0.343													A|||	2348	0.46885	0.5144	0.4755	5008	,	,		15789	0.3155		0.6352	False		,,,				2504	0.3896				p.Y151Y		Atlas-SNP	.											.	C3orf33	18	.	0			c.C453T						PASS	.	A		1906,1686		515,876,405	33.0	29.0	30.0		453	-4.8	0.9	3	dbSNP_116	30	5086,3022		1616,1854,584	no	coding-synonymous	C3orf33	NM_173657.1		2131,2730,989	AA,AG,GG		37.2718,46.9376,40.2393		151/252	155481609	6992,4708	1796	4054	5850	SO:0001819	synonymous_variant	285315	exon6			TGTCCAGTAGATT	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.582C>T	3.37:g.155481609G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_173657	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Silent	SNP	ENST00000340171.2	37																																																																																				G|0.508;A|0.492	0.492	strong		0.343	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657	
DNAAF3	352909	hgsc.bcm.edu	37	19	55673164	55673164	+	Silent	SNP	T	T	C	rs56726774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55673164T>C	ENST00000524407.2	-	6	543	c.510A>G	c.(508-510)gtA>gtG	p.V170V	DNAAF3_ENST00000455045.1_Silent_p.V116V|DNAAF3_ENST00000527223.2_Silent_p.V238V|DNAAF3_ENST00000587789.2_5'Flank|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000391720.4_Silent_p.V217V|CTD-2587H24.5_ENST00000591665.1_RNA			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	170					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											AGAAGCGGAATACGGCCTCCA	0.682													c|||	659	0.131589	0.0794	0.2666	5008	,	,		11907	0.2034		0.0169	False		,,,				2504	0.1503				p.V238V		Atlas-SNP	.											.	.	.	.	0			c.A714G						PASS	.	C		178,3498		2,174,1662	4.0	6.0	5.0		651	-0.1	0.4	19	dbSNP_129	5	194,7662		1,192,3735	no	coding-synonymous	C19orf51	NM_178837.3		3,366,5397	CC,CT,TT		2.4695,4.8422,3.2258		217/589	55673164	372,11160	1838	3928	5766	SO:0001819	synonymous_variant	352909	exon6			GCGGAATACGGCC	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.510A>G	19.37:g.55673164T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Silent	SNP	ENST00000524407.2	37	CCDS59422.1																																																																																			T|0.882;C|0.118	0.118	strong		0.682	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
NSUN4	387338	hgsc.bcm.edu	37	1	46806550	46806550	+	Missense_Mutation	SNP	C	C	T	rs41293277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46806550C>T	ENST00000474844.1	+	1	702	c.52C>T	c.(52-54)Ctc>Ttc	p.L18F	NSUN4_ENST00000536062.1_5'UTR|NSUN4_ENST00000537428.1_5'Flank	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	18					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)					GCGTGTGGACCTCGCGACGGT	0.602											OREG0013456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	637	0.127196	0.115	0.147	5008	,	,		15523	0.0179		0.2773	False		,,,				2504	0.0879				p.L18F		Atlas-SNP	.											.	NSUN4	26	.	0			c.C52T						PASS	.	T	PHE/LEU	604,3800	755.8+/-412.6	55,494,1653	29.0	30.0	30.0		52	2.9	0.1	1	dbSNP_127	30	2510,6088	680.6+/-403.7	367,1776,2156	yes	missense	NSUN4	NM_199044.2	22	422,2270,3809	TT,TC,CC		29.1928,13.7148,23.9502	benign	18/385	46806550	3114,9888	2202	4299	6501	SO:0001583	missense	387338	exon1			GTGGACCTCGCGA	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.52C>T	1.37:g.46806550C>T	ENSP00000419740:p.Leu18Phe	Somatic	99	0	0	942	WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	37	CCDS534.1	338	0.15476190476190477	59	0.11991869918699187	60	0.16574585635359115	11	0.019230769230769232	208	0.27440633245382584	T	5.578	0.291507	0.10567	0.137148	0.291928	ENSG00000117481	ENST00000474844	T	0.15017	2.46	4.09	2.93	0.34026	.	0.748109	0.13086	N	0.414936	T	0.00012	0.0000	N	0.08118	0	0.51767	P	6.700000000003925E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.46289	-0.9202	9	0.08179	T	0.78	-0.8149	4.8239	0.13407	0.0:0.4319:0.0:0.5681	rs41293277	18	Q96CB9	NSUN4_HUMAN	F	18	ENSP00000419740:L18F	ENSP00000419740:L18F	L	+	1	0	NSUN4	46579137	0.005000	0.15991	0.105000	0.21289	0.096000	0.18686	0.284000	0.18864	0.630000	0.30394	-0.490000	0.04691	CTC	C|0.790;T|0.210	0.210	strong		0.602	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
NAALADL2	254827	hgsc.bcm.edu	37	3	174814920	174814920	+	Missense_Mutation	SNP	A	A	G	rs9836841	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:174814920A>G	ENST00000454872.1	+	2	512	c.384A>G	c.(382-384)atA>atG	p.I128M	NAALADL2-AS3_ENST00000453180.1_RNA|NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	128			I -> M (in dbSNP:rs9836841). {ECO:0000269|PubMed:15168106, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TCTTAAAAATACTTTGCACAG	0.383													A|||	1985	0.396366	0.2912	0.4524	5008	,	,		19667	0.4375		0.4433	False		,,,				2504	0.408				p.I128M		Atlas-SNP	.											.	NAALADL2	86	.	0			c.A384G						PASS	.	A	MET/ILE	1037,2635		157,723,956	102.0	104.0	104.0		384	-1.5	0.1	3	dbSNP_119	104	3684,4500		838,2008,1246	yes	missense	NAALADL2	NM_207015.2	10	995,2731,2202	GG,GA,AA		45.0147,28.2407,39.8195	benign	128/796	174814920	4721,7135	1836	4092	5928	SO:0001583	missense	254827	exon2			AAAAATACTTTGC		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.384A>G	3.37:g.174814920A>G	ENSP00000404705:p.Ile128Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	883	0.4043040293040293	148	0.3008130081300813	172	0.47513812154696133	236	0.4125874125874126	327	0.4313984168865435	A	1.481	-0.557312	0.03967	0.282407	0.450147	ENSG00000177694	ENST00000434257;ENST00000454872	T;T	0.34472	1.42;1.36	5.63	-1.48	0.08745	.	0.315558	0.27008	N	0.021400	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.23316	0.083;0.017	B;B	0.17098	0.017;0.009	T	0.48151	-0.9060	9	0.44086	T	0.13	-1.755	6.1917	0.20528	0.5894:0.2263:0.1843:0.0	rs9836841;rs52822748;rs61284953;rs9836841	111;128	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	M	111;128	ENSP00000409858:I111M;ENSP00000404705:I128M	ENSP00000409858:I111M	I	+	3	3	NAALADL2	176297614	0.012000	0.17670	0.085000	0.20634	0.151000	0.21798	-0.003000	0.12901	-0.076000	0.12775	0.477000	0.44152	ATA	A|0.617;G|0.383	0.383	strong		0.383	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
ENPEP	2028	hgsc.bcm.edu	37	4	111409705	111409705	+	Missense_Mutation	SNP	T	T	C	rs1126483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:111409705T>C	ENST00000265162.5	+	2	995	c.653T>C	c.(652-654)gTg>gCg	p.V218A		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	218			V -> A (in dbSNP:rs1126483). {ECO:0000269|PubMed:8346219}.		angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V218A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		AGGAGCATAGTGGCCACCGAT	0.403													C|||	2554	0.509984	0.3722	0.5245	5008	,	,		16014	0.6488		0.5427	False		,,,				2504	0.5092				p.V218A		Atlas-SNP	.											ENPEP,NS,carcinoma,0,1	ENPEP	149	1	1	Substitution - Missense(1)	prostate(1)	c.T653C						scavenged	.	C	ALA/VAL	1883,2523	622.1+/-393.9	407,1069,727	52.0	48.0	49.0		653	4.2	1.0	4	dbSNP_86	49	4750,3850	533.8+/-382.5	1309,2132,859	no	missense	ENPEP	NM_001977.3	64	1716,3201,1586	CC,CT,TT		44.7674,42.7372,49.0005	benign	218/958	111409705	6633,6373	2203	4300	6503	SO:0001583	missense	2028	exon2			GCATAGTGGCCAC	L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"""CD molecules"""	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.653T>C	4.37:g.111409705T>C	ENSP00000265162:p.Val218Ala	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	37	CCDS3691.1	1194	0.5467032967032966	185	0.37601626016260165	200	0.5524861878453039	395	0.6905594405594405	414	0.5461741424802111	C	4.381	0.070357	0.08436	0.427372	0.552326	ENSG00000138792	ENST00000265162	T	0.02552	4.25	5.03	4.18	0.49190	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00049	-2.415	0.48511	P	3.4000000000000696E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.28839	-1.0031	9	0.02654	T	1	.	9.9421	0.41587	0.1383:0.7891:0.0:0.0726	rs1126483;rs2271876;rs17008395;rs57352639;rs1126483	218	Q07075	AMPE_HUMAN	A	218	ENSP00000265162:V218A	ENSP00000265162:V218A	V	+	2	0	ENPEP	111629154	1.000000	0.71417	0.992000	0.48379	0.687000	0.40016	5.788000	0.69020	0.515000	0.28320	-0.119000	0.15052	GTG	T|0.471;C|0.529	0.529	strong		0.403	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2		
ELAVL3	1995	hgsc.bcm.edu	37	19	11569316	11569316	+	Silent	SNP	G	G	A	rs2242112	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11569316G>A	ENST00000359227.3	-	4	868	c.444C>T	c.(442-444)taC>taT	p.Y148Y	ELAVL3_ENST00000438662.2_Silent_p.Y148Y	NM_001420.3|NM_032281.2	NP_001411.2|NP_115657.2	Q14576	ELAV3_HUMAN	ELAV like neuron-specific RNA binding protein 3	148	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)		AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15						TGATGCGGCCGTACTGGGAGA	0.627													g|||	285	0.0569089	0.0166	0.036	5008	,	,		20081	0.1339		0.0537	False		,,,				2504	0.0501				p.Y148Y		Atlas-SNP	.											ELAVL3,colon,carcinoma,0,1	ELAVL3	58	1	0			c.C444T						PASS	.	G	,	71,4335	64.7+/-102.0	1,69,2133	131.0	112.0	118.0		444,444	-3.8	0.9	19	dbSNP_98	118	376,8224	123.8+/-182.6	8,360,3932	no	coding-synonymous,coding-synonymous	ELAVL3	NM_001420.3,NM_032281.2	,	9,429,6065	AA,AG,GG		4.3721,1.6114,3.4369	,	148/368,148/361	11569316	447,12559	2203	4300	6503	SO:0001819	synonymous_variant	1995	exon4			GCGGCCGTACTGG		CCDS32912.1, CCDS45978.1	19p13.2	2013-10-03	2013-10-03			ENSG00000196361		"""RNA binding motif (RRM) containing"""	3314	protein-coding gene	gene with protein product	"""Hu antigen C"", ""paraneoplastic limbic encephalitis antigen 21"", ""paraneoplastic cerebellar degeneration-associated antigen"", ""ELAV-like protein 3"""	603458	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)"""			9799595	Standard	NM_001420		Approved	HUC, PLE21, DKFZp547J036, HUCL, MGC20653	uc002mry.1	Q14576		ENST00000359227.3:c.444C>T	19.37:g.11569316G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_032281	Q16135|Q96CL8|Q96QS9	Silent	SNP	ENST00000359227.3	37	CCDS32912.1																																																																																			G|0.956;A|0.044	0.044	strong		0.627	ELAVL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458827.2	NM_001420	
ST3GAL5	8869	hgsc.bcm.edu	37	2	86088311	86088311	+	Missense_Mutation	SNP	T	T	C	rs1138484	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:86088311T>C	ENST00000377332.3	-	3	419	c.311A>G	c.(310-312)cAt>cGt	p.H104R	ST3GAL5_ENST00000525834.2_Missense_Mutation_p.H104R|ST3GAL5_ENST00000393805.1_Missense_Mutation_p.H76R|ST3GAL5_ENST00000484728.1_5'UTR|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	86	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	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	
SPTBN5	51332	hgsc.bcm.edu	37	15	42171462	42171462	+	Missense_Mutation	SNP	C	C	T	rs12708402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:42171462C>T	ENST00000320955.6	-	16	3405	c.3178G>A	c.(3178-3180)Gta>Ata	p.V1060I		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1060					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)		CCGTACTTTACGACCACACTT	0.617													C|||	902	0.180112	0.1657	0.1888	5008	,	,		19056	0.0516		0.2684	False		,,,				2504	0.2352				p.V1025I		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G3073A						PASS	.	C	ILE/VAL	690,3428		66,558,1435	43.0	47.0	46.0		3073	-1.1	0.0	15	dbSNP_121	46	2192,6226		298,1596,2315	yes	missense	SPTBN5	NM_016642.2	29	364,2154,3750	TT,TC,CC		26.0394,16.7557,22.9898	benign	1025/3640	42171462	2882,9654	2059	4209	6268	SO:0001583	missense	51332	exon16			ACTTTACGACCAC	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.3178G>A	15.37:g.42171462C>T	ENSP00000317790:p.Val1060Ile	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		375	0.1717032967032967	79	0.16056910569105692	72	0.19889502762430938	19	0.033216783216783216	205	0.2704485488126649	.	11.20	1.568878	0.28003	0.167557	0.260394	ENSG00000137877	ENST00000320955	T	0.34667	1.35	4.26	-1.14	0.09741	.	2.753290	0.01702	N	0.027227	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	0.26155	-1.0111	9	0.35671	T	0.21	.	4.4363	0.11552	0.0:0.3366:0.3577:0.3057	rs12708402;rs56456804;rs12708402	1060	Q9NRC6	SPTN5_HUMAN	I	1060	ENSP00000317790:V1060I	ENSP00000317790:V1060I	V	-	1	0	SPTBN5	39958754	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-1.257000	0.02866	-0.245000	0.09625	-0.752000	0.03492	GTA	C|0.800;T|0.200	0.200	strong		0.617	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
PM20D1	148811	hgsc.bcm.edu	37	1	205810947	205810947	+	Missense_Mutation	SNP	C	C	T	rs11240573	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205810947C>T	ENST00000367136.4	-	9	1080	c.1036G>A	c.(1036-1038)Ggg>Agg	p.G346R	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	346			G -> R (in dbSNP:rs11240573). {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)			ACCTTGACCCCTGCTTTGAAT	0.468													C|||	592	0.118211	0.1339	0.0663	5008	,	,		21048	0.2113		0.0845	False		,,,				2504	0.0726				p.G346R		Atlas-SNP	.											.	PM20D1	56	.	0			c.G1036A						PASS	.	C	ARG/GLY	533,3873		34,465,1704	176.0	162.0	167.0		1036	5.4	0.9	1	dbSNP_120	167	490,8106		13,464,3821	yes	missense	PM20D1	NM_152491.4	125	47,929,5525	TT,TC,CC		5.7003,12.0971,7.868	probably-damaging	346/503	205810947	1023,11979	2203	4298	6501	SO:0001583	missense	148811	exon9			TGACCCCTGCTTT		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.1036G>A	1.37:g.205810947C>T	ENSP00000356104:p.Gly346Arg	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	321	155	0.482866	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	245	0.11217948717948718	62	0.12601626016260162	26	0.0718232044198895	96	0.16783216783216784	61	0.08047493403693931	C	18.62	3.662890	0.67700	0.120971	0.057003	ENSG00000162877	ENST00000367136	T	0.73789	-0.78	5.4	5.4	0.78164	Peptidase M20, dimerisation (2);	0.000000	0.85682	D	0.000000	T	0.01730	0.0055	H	0.94698	3.57	0.09310	P	0.99999999824732	P	0.50443	0.935	P	0.57244	0.816	T	0.44329	-0.9335	9	0.59425	D	0.04	.	18.7848	0.91949	0.0:1.0:0.0:0.0	rs11240573;rs52836737;rs11240573	346	Q6GTS8	P20D1_HUMAN	R	346	ENSP00000356104:G346R	ENSP00000356104:G346R	G	-	1	0	PM20D1	204077570	1.000000	0.71417	0.926000	0.36857	0.191000	0.23601	6.856000	0.75450	2.548000	0.85928	0.655000	0.94253	GGG	C|0.906;T|0.094	0.094	strong		0.468	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
FUT3	2525	hgsc.bcm.edu	37	19	5844792	5844792	+	Missense_Mutation	SNP	A	A	C	rs28362459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:5844792A>C	ENST00000303225.6	-	3	693	c.59T>G	c.(58-60)cTg>cGg	p.L20R	FUT3_ENST00000589620.1_Missense_Mutation_p.L20R|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000458379.2_Missense_Mutation_p.L20R|AC024592.9_ENST00000589276.1_RNA|FUT3_ENST00000589918.1_Missense_Mutation_p.L20R	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	188	0	0		WXS	Illumina HiSeq	Phase_I	202	114	0.564356	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	
ZC3H12D	340152	hgsc.bcm.edu	37	6	149795522	149795522	+	Missense_Mutation	SNP	G	G	A	rs7747948	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:149795522G>A	ENST00000409806.3	-	2	476	c.158C>T	c.(157-159)cCg>cTg	p.P53L	ZC3H12D_ENST00000416573.2_Missense_Mutation_p.P53L|ZC3H12D_ENST00000409948.1_Missense_Mutation_p.P53L|ZC3H12D_ENST00000389942.5_Missense_Mutation_p.P53L|ZC3H12D_ENST00000542614.1_Missense_Mutation_p.P53L			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	53			P -> L (in dbSNP:rs7747948). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:19531561}.		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)		GGGTGCAGCCGGGTGCTCCAG	0.716													G|||	903	0.180312	0.2965	0.1902	5008	,	,		14767	0.0169		0.2465	False		,,,				2504	0.1166				p.P53L		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.C158T						PASS	.	G	LEU/PRO	1027,2693		158,711,991	17.0	19.0	18.0		158	-0.3	0.0	6	dbSNP_116	18	2191,5983		305,1581,2201	no	missense	ZC3H12D	NM_207360.2	98	463,2292,3192	AA,AG,GG		26.8045,27.6075,27.0557	benign	53/528	149795522	3218,8676	1860	4087	5947	SO:0001583	missense	340152	exon2			GCAGCCGGGTGCT			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.158C>T	6.37:g.149795522G>A	ENSP00000386616:p.Pro53Leu	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	37		450	0.20604395604395603	175	0.3556910569105691	72	0.19889502762430938	11	0.019230769230769232	192	0.2532981530343008	G	8.967	0.971885	0.18736	0.276075	0.268045	ENSG00000178199	ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614;ENST00000409948	T;T;T;T;T	0.43688	1.49;1.53;1.49;1.54;0.94	4.46	-0.297	0.12820	.	.	.	.	.	T	0.09642	0.0237	L	0.39898	1.24	0.80722	P	0.0	B;P	0.36535	0.176;0.557	B;B	0.22880	0.012;0.042	T	0.11591	-1.0581	8	0.32370	T	0.25	-0.1115	5.0201	0.14356	0.0:0.2903:0.3337:0.376	rs7747948;rs17417830	53;53	A2A288;B7WNU7	ZC12D_HUMAN;.	L	53	ENSP00000374592:P53L;ENSP00000408686:P53L;ENSP00000386616:P53L;ENSP00000440813:P53L;ENSP00000387062:P53L	ENSP00000374592:P53L	P	-	2	0	ZC3H12D	149837215	0.000000	0.05858	0.001000	0.08648	0.046000	0.14306	-0.044000	0.12023	0.027000	0.15297	-0.457000	0.05445	CCG	G|0.788;A|0.212	0.212	strong		0.716	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360	
TPSB2	64499	hgsc.bcm.edu	37	16	1279574	1279574	+	RNA	SNP	C	C	G	rs199887053	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1279574C>G	ENST00000339687.6	-	0	248				TPSB2_ENST00000445910.1_RNA|TPSB2_ENST00000430512.2_RNA			P20231	TRYB2_HUMAN	tryptase beta 2 (gene/pseudogene)							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|upper_aerodigestive_tract(1)	2		Hepatocellular(780;0.00369)				CACGGTCCCACGCAGTGCGCT	0.706													C|||	2384	0.476038	0.3986	0.3847	5008	,	,		5384	0.6617		0.4622	False		,,,				2504	0.4683				p.V76L		Atlas-SNP	.											.	TPSB2	8	.	0			c.G226C						PASS	.						14.0	20.0	18.0					16																	1279574		2120	4269	6389			64499	exon3			GTCCCACGCAGTG	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.1279574C>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	52	49	0.942308	NM_024164	D2E6S0|D2E6S2|O95827|Q15664|Q9UQI6|Q9UQI7	Missense_Mutation	SNP	ENST00000339687.6	37		.	.	.	.	.	.	.	.	.	.	C	1.709	-0.499629	0.04291	.	.	ENSG00000197253	ENST00000430512	D	0.82255	-1.59	3.53	-4.6	0.03390	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.521995	0.16023	N	0.233229	T	0.63581	0.2523	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.47235	-0.9133	8	0.27082	T	0.32	.	3.8979	0.09147	0.129:0.174:0.5084:0.1887	.	76	P20231	TRYB2_HUMAN	L	76	ENSP00000412409:V76L	ENSP00000412409:V76L	V	-	1	0	TPSB2	1219575	0.000000	0.05858	0.220000	0.23810	0.348000	0.29142	-3.993000	0.00318	-0.479000	0.06813	-1.622000	0.00790	GTG	G|1.000;|0.000	1.000	weak		0.706	TPSB2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000342364.1	NM_024164	
SPATA16	83893	hgsc.bcm.edu	37	3	172835125	172835125	+	Missense_Mutation	SNP	T	T	C	rs1515442	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	242	2	0.00826446		WXS	Illumina HiSeq	Phase_I	225	106	0.471111	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	
FAM175A	84142	hgsc.bcm.edu	37	4	84383810	84383810	+	Missense_Mutation	SNP	C	C	T	rs12642536	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:84383810C>T	ENST00000321945.7	-	9	1150	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	MRPS18C_ENST00000509571.1_Intron|FAM175A_ENST00000506553.1_Missense_Mutation_p.A299T	NM_139076.2	NP_620775.2	Q6UWZ7	F175A_HUMAN	family with sequence similarity 175, member A	348			A -> T (common polymorphism not associated with susceptibility to breast cancer; dbSNP:rs12642536). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18695986}.		chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	13						AAGTCTAAGGCTTTATGCTTA	0.398													C|||	2098	0.41893	0.1225	0.5259	5008	,	,		19558	0.6756		0.3787	False		,,,				2504	0.5204				p.A348T		Atlas-SNP	.											.	FAM175A	36	.	0			c.G1042A						PASS	.	C	THR/ALA	747,3659	307.7+/-290.2	56,635,1512	240.0	205.0	217.0		1042	2.8	0.1	4	dbSNP_120	217	3509,5091	512.4+/-377.9	712,2085,1503	yes	missense	FAM175A	NM_139076.2	58	768,2720,3015	TT,TC,CC		40.8023,16.9542,32.7234	possibly-damaging	348/410	84383810	4256,8750	2203	4300	6503	SO:0001583	missense	84142	exon9			CTAAGGCTTTATG	AK023676	CCDS3605.2	4q21.23	2008-10-31	2008-07-02	2008-07-02	ENSG00000163322	ENSG00000163322			25829	protein-coding gene	gene with protein product	"""Abraxas protein"""	611143	"""coiled-coil domain containing 98"""	CCDC98		12975309, 17525340	Standard	NM_139076		Approved	FLJ13614, ABRA1	uc003hou.2	Q6UWZ7	OTTHUMG00000130429	ENST00000321945.7:c.1042G>A	4.37:g.84383810C>T	ENSP00000369857:p.Ala348Thr	Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	318	177	0.556604	NM_139076	A5JJ07|Q9H8I1|Q9H9N4	Missense_Mutation	SNP	ENST00000321945.7	37	CCDS3605.2	923	0.4226190476190476	72	0.14634146341463414	180	0.4972375690607735	370	0.6468531468531469	301	0.3970976253298153	C	16.97	3.268943	0.59540	0.169542	0.408023	ENSG00000163322	ENST00000321945;ENST00000506553	T;T	0.48522	0.81;0.82	5.61	2.75	0.32379	.	0.357727	0.26079	N	0.026478	T	0.00012	0.0000	L	0.57536	1.79	0.49687	P	1.8600000000001948E-4	P	0.43938	0.822	B	0.43916	0.436	T	0.44251	-0.9340	9	0.66056	D	0.02	-24.7011	10.914	0.47124	0.2669:0.6152:0.1179:0.0	rs12642536;rs52814022;rs12642536	348	Q6UWZ7	F175A_HUMAN	T	348;299	ENSP00000369857:A348T;ENSP00000426763:A299T	ENSP00000369857:A348T	A	-	1	0	FAM175A	84602834	0.270000	0.24152	0.139000	0.22197	0.030000	0.12068	0.499000	0.22546	1.330000	0.45394	-0.293000	0.09583	GCC	C|0.642;T|0.358	0.358	strong		0.398	FAM175A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252818.1	NM_139076	
TMCO4	255104	hgsc.bcm.edu	37	1	20009737	20009737	+	Silent	SNP	G	G	A	rs10917514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:20009737G>A	ENST00000294543.6	-	16	1942	c.1701C>T	c.(1699-1701)tcC>tcT	p.S567S	TMCO4_ENST00000375122.2_Silent_p.S527S|TMCO4_ENST00000489814.1_5'UTR|TMCO4_ENST00000375127.1_Intron	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	567						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		AGGTGTCTCCGGATATGGGAC	0.667													G|||	627	0.1252	0.0537	0.111	5008	,	,		16666	0.2113		0.1133	False		,,,				2504	0.1554				p.S567S		Atlas-SNP	.											.	TMCO4	46	.	0			c.C1701T						PASS	.	G		249,4157	145.4+/-180.2	7,235,1961	65.0	69.0	67.0		1701	-6.1	0.0	1	dbSNP_120	67	1129,7471	233.5+/-266.7	79,971,3250	no	coding-synonymous	TMCO4	NM_181719.4		86,1206,5211	AA,AG,GG		13.1279,5.6514,10.5951		567/635	20009737	1378,11628	2203	4300	6503	SO:0001819	synonymous_variant	255104	exon16			GTCTCCGGATATG		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.1701C>T	1.37:g.20009737G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	260	127	0.488462	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Silent	SNP	ENST00000294543.6	37	CCDS198.1																																																																																			G|0.888;A|0.112	0.112	strong		0.667	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
DCC	1630	hgsc.bcm.edu	37	18	50936994	50936994	+	Silent	SNP	T	T	C	rs2229082	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:50936994T>C	ENST00000442544.2	+	20	3724	c.3108T>C	c.(3106-3108)ccT>ccC	p.P1036P	DCC_ENST00000581580.1_Silent_p.P671P|DCC_ENST00000412726.1_Silent_p.P864P	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1036	Fibronectin type-III 6. {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)		TCTCTGATCCTATCCTCTTCA	0.368													C|||	1554	0.310304	0.174	0.3127	5008	,	,		18669	0.2262		0.5368	False		,,,				2504	0.3466				p.P1036P		Atlas-SNP	.											.	DCC	360	.	0			c.T3108C						PASS	.	C		1061,3345	720.2+/-409.0	124,813,1266	80.0	80.0	80.0		3108	2.1	1.0	18	dbSNP_126	80	4607,3991	547.8+/-385.2	1219,2169,911	no	coding-synonymous	DCC	NM_005215.3		1343,2982,2177	CC,CT,TT		46.4178,24.0808,43.5866		1036/1448	50936994	5668,7336	2203	4299	6502	SO:0001819	synonymous_variant	1630	exon20			TGATCCTATCCTC	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.3108T>C	18.37:g.50936994T>C		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			T|0.584;C|0.416	0.416	strong		0.368	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924073	43924073	+	Missense_Mutation	SNP	T	T	C	rs12373123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43924073T>C	ENST00000329196.5	+	1	1818	c.1801T>C	c.(1801-1803)Tcc>Ccc	p.S601P	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	601			S -> P (in dbSNP:rs12373123).			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)										CAGTGATAGCTCCGAGGGCTG	0.572													T|||	431	0.0860623	0.0151	0.1571	5008	,	,		21623	0.001		0.2396	False		,,,				2504	0.0613				p.S601P		Atlas-SNP	.											.	.	.	.	0			c.T1801C						PASS	.	T	PRO/SER	203,4203	127.0+/-164.0	5,193,2005	116.0	100.0	105.0		1801	4.9	0.3	17	dbSNP_120	105	1929,6671	340.8+/-323.8	221,1487,2592	yes	missense	IMP5	NM_175882.2	74	226,1680,4597	CC,CT,TT		22.4302,4.6074,16.3924	benign	601/685	43924073	2132,10874	2203	4300	6503	SO:0001583	missense	162540	exon1			GATAGCTCCGAGG		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.1801T>C	17.37:g.43924073T>C	ENSP00000332488:p.Ser601Pro	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	T	17.99	3.523276	0.64747	0.046074	0.224302	ENSG00000185294	ENST00000329196	T	0.07216	3.21	4.86	4.86	0.63082	.	0.338646	0.21560	N	0.072581	T	0.00012	0.0000	L	0.29908	0.895	0.51482	P	7.299999999998974E-5	D	0.58970	0.984	P	0.55161	0.77	T	0.53136	-0.8481	9	0.26408	T	0.33	-22.5877	11.0259	0.47744	0.0:0.0:0.0:1.0	rs12373123;rs17690528;rs12373123	601	Q8IUH8	IMP5_HUMAN	P	601	ENSP00000332488:S601P	ENSP00000332488:S601P	S	+	1	0	AC217771.1	41279853	0.920000	0.31207	0.275000	0.24674	0.091000	0.18340	2.208000	0.42797	2.153000	0.67306	0.533000	0.62120	TCC	T|0.853;C|0.147	0.147	strong		0.572	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
SPERT	220082	hgsc.bcm.edu	37	13	46288145	46288145	+	Missense_Mutation	SNP	A	A	G	rs7317245	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46288145A>G	ENST00000310521.1	+	3	1065	c.985A>G	c.(985-987)Aag>Gag	p.K329E	SPERT_ENST00000378966.3_Missense_Mutation_p.K293E	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	329			K -> E (in dbSNP:rs7317245).			cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		CGCCCTGCGGAAGATGGTCAG	0.716													g|||	2477	0.494609	0.3003	0.4914	5008	,	,		15278	0.5		0.6869	False		,,,				2504	0.5562				p.K329E		Atlas-SNP	.											.	SPERT	54	.	0			c.A985G						PASS	.		GLU/LYS	1638,2406		401,836,785	4.0	4.0	4.0		985	3.2	0.9	13	dbSNP_116	4	5608,2244		2132,1344,450	yes	missense	SPERT	NM_152719.1	56	2533,2180,1235	GG,GA,AA		28.5787,40.5045,39.0888	benign	329/449	46288145	7246,4650	2022	3926	5948	SO:0001583	missense	220082	exon3			CTGCGGAAGATGG	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"""spermatid flower-like structure protein"", ""testis specific leucine zipper protein nurit"", ""chibby homolog 2 (Drosophila)"""					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.985A>G	13.37:g.46288145A>G	ENSP00000309189:p.Lys329Glu	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	23	8	0.347826	NM_152719	A8K8I5|Q8NHV2	Missense_Mutation	SNP	ENST00000310521.1	37	CCDS9399.1	1169	0.5352564102564102	163	0.3313008130081301	196	0.5414364640883977	285	0.4982517482517482	525	0.6926121372031663	G	0.009	-1.812861	0.00600	0.405045	0.714213	ENSG00000174015	ENST00000310521;ENST00000378966	T;T	0.39056	1.1;1.19	4.9	3.16	0.36331	.	0.382628	0.22713	N	0.056559	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	0.44050	-0.9353	9	0.02654	T	1	.	5.0269	0.14389	0.19:0.1856:0.6243:0.0	rs7317245;rs61188622;rs7317245	293;329	Q8NA61-2;Q8NA61	.;SPERT_HUMAN	E	329;293	ENSP00000309189:K329E;ENSP00000368249:K293E	ENSP00000309189:K329E	K	+	1	0	SPERT	45186146	0.996000	0.38824	0.890000	0.34922	0.030000	0.12068	1.217000	0.32455	0.277000	0.22141	-0.119000	0.15052	AAG	A|0.488;G|0.512	0.512	strong		0.716	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719	
VMO1	284013	hgsc.bcm.edu	37	17	4689313	4689313	+	Missense_Mutation	SNP	G	G	C	rs2279961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4689313G>C	ENST00000328739.5	-	2	309	c.230C>G	c.(229-231)aCt>aGt	p.T77S	VMO1_ENST00000416307.2_Missense_Mutation_p.T77S|VMO1_ENST00000354194.4_Intron|VMO1_ENST00000441199.2_Missense_Mutation_p.T77S|GLTPD2_ENST00000331264.7_5'Flank	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)	77			T -> S (in dbSNP:rs2279961).			extracellular vesicular exosome (GO:0070062)				kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						ATTCAGTGCAGTGTCGTCGCC	0.622													G|||	474	0.0946486	0.115	0.1052	5008	,	,		18607	0.0992		0.0994	False		,,,				2504	0.0501				p.T77S		Atlas-SNP	.											.	VMO1	19	.	0			c.C230G						PASS	.	G	SER/THR,SER/THR,,SER/THR	551,3855	249.3+/-256.8	32,487,1684	755.0	684.0	708.0		230,230,,230	4.4	0.9	17	dbSNP_100	708	914,7686	203.0+/-246.1	59,796,3445	yes	missense,missense,intron,missense	VMO1	NM_001144939.1,NM_001144940.1,NM_001144941.1,NM_182566.2	58,58,,58	91,1283,5129	CC,CG,GG		10.6279,12.5057,11.264	probably-damaging,probably-damaging,,probably-damaging	77/115,77/103,,77/203	4689313	1465,11541	2203	4300	6503	SO:0001583	missense	284013	exon2			AGTGCAGTGTCGT	AF521892	CCDS11055.1, CCDS45585.1, CCDS45586.1, CCDS45587.1	17p13.2	2013-03-07	2005-11-14						30387	protein-coding gene	gene with protein product						22025569	Standard	NM_182566		Approved		uc002fyx.3	Q7Z5L0		ENST00000328739.5:c.230C>G	17.37:g.4689313G>C	ENSP00000328397:p.Thr77Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	85	32	0.376471	NM_182566	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Missense_Mutation	SNP	ENST00000328739.5	37	CCDS11055.1	241	0.11034798534798534	63	0.12804878048780488	36	0.09944751381215469	64	0.11188811188811189	78	0.10290237467018469	G	16.26	3.073061	0.55646	0.125057	0.106279	ENSG00000182853	ENST00000328739;ENST00000416307;ENST00000441199	T;T;T	0.52295	0.67;0.67;0.67	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.01523	0.0049	M	0.82132	2.575	0.09310	P	1.0	D;D;D	0.89917	1.0;1.0;0.98	D;D;P	0.97110	1.0;0.999;0.767	T	0.44952	-0.9294	9	0.66056	D	0.02	-14.9036	12.404	0.55428	0.0:0.0:1.0:0.0	rs2279961;rs4080467;rs17765171;rs2279961	77;77;77	C9JQ15;E9PAU9;Q7Z5L0	.;.;VMO1_HUMAN	S	77	ENSP00000328397:T77S;ENSP00000390450:T77S;ENSP00000408166:T77S	ENSP00000328397:T77S	T	-	2	0	VMO1	4636053	1.000000	0.71417	0.920000	0.36463	0.019000	0.09904	7.187000	0.77730	2.286000	0.76751	0.563000	0.77884	ACT	G|0.901;C|0.099	0.099	strong		0.622	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439587.1	NM_182566	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79064080	79064080	+	Silent	SNP	G	G	A	rs11635931	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:79064080G>A	ENST00000388820.4	-	15	2433	c.2223C>T	c.(2221-2223)agC>agT	p.S741S	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	741	Spacer.				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						CCGGGTCCTCGCTCCGCAGTG	0.632													G|||	932	0.186102	0.0454	0.2579	5008	,	,		18538	0.0188		0.4185	False		,,,				2504	0.2587				p.S741S		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C2223T						PASS	.	G		470,3922	219.4+/-237.2	37,396,1763	73.0	55.0	61.0		2223	-1.7	1.0	15	dbSNP_120	61	3669,4917	515.0+/-378.5	798,2073,1422	no	coding-synonymous	ADAMTS7	NM_014272.3		835,2469,3185	AA,AG,GG		42.7324,10.7013,31.8924		741/1687	79064080	4139,8839	2196	4293	6489	SO:0001819	synonymous_variant	11173	exon15			GTCCTCGCTCCGC	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.2223C>T	15.37:g.79064080G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			G|0.721;A|0.279	0.279	strong		0.632	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
DNAAF3	352909	hgsc.bcm.edu	37	19	55673654	55673654	+	Silent	SNP	T	T	C	rs3848618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55673654T>C	ENST00000524407.2	-	5	360	c.327A>G	c.(325-327)cgA>cgG	p.R109R	DNAAF3_ENST00000455045.1_Silent_p.R55R|DNAAF3_ENST00000527223.2_Silent_p.R177R|DNAAF3_ENST00000587789.2_5'Flank|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000391720.4_Silent_p.R156R|CTD-2587H24.5_ENST00000591665.1_RNA			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	109					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											AGGTCTCGCTTCGCTCTACGG	0.577													c|||	643	0.128395	0.0688	0.2651	5008	,	,		12792	0.2024		0.0169	False		,,,				2504	0.1503				p.R177R		Atlas-SNP	.											C19orf51,rectum,carcinoma,0,1	.	.	1	0			c.A531G						PASS	.	C		111,3373		2,107,1633	11.0	13.0	13.0		468	-4.6	0.1	19	dbSNP_108	13	158,7134		0,158,3488	yes	coding-synonymous	C19orf51	NM_178837.3		2,265,5121	CC,CT,TT		2.1668,3.186,2.4963		156/589	55673654	269,10507	1742	3646	5388	SO:0001819	synonymous_variant	352909	exon5			CTCGCTTCGCTCT	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.327A>G	19.37:g.55673654T>C		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Silent	SNP	ENST00000524407.2	37	CCDS59422.1																																																																																			T|0.892;C|0.108	0.108	strong		0.577	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
CENPF	1063	hgsc.bcm.edu	37	1	214818215	214818215	+	Missense_Mutation	SNP	G	G	A	rs3748692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214818215G>A	ENST00000366955.3	+	13	5470	c.5302G>A	c.(5302-5304)Gat>Aat	p.D1768N		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	1864					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)		GAATCAGGAAGATATCCATAA	0.398													A|||	543	0.108427	0.1089	0.1066	5008	,	,		19201	0.126		0.0507	False		,,,				2504	0.1503				p.D1768N	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.G5302A						PASS	.	A	ASN/ASP	433,3973	778.4+/-414.3	23,387,1793	44.0	46.0	46.0		5302	-3.8	0.0	1	dbSNP_107	46	465,8135	793.7+/-407.5	12,441,3847	yes	missense	CENPF	NM_016343.3	23	35,828,5640	AA,AG,GG		5.407,9.8275,6.9045	benign	1768/3115	214818215	898,12108	2203	4300	6503	SO:0001583	missense	1063	exon13			CAGGAAGATATCC	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.5302G>A	1.37:g.214818215G>A	ENSP00000355922:p.Asp1768Asn	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	123	47	0.382114	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	230	0.10531135531135531	64	0.13008130081300814	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	A	2.658	-0.280308	0.05642	0.098275	0.05407	ENSG00000117724	ENST00000366955	T	0.03035	4.07	5.56	-3.85	0.04243	.	0.630501	0.13206	N	0.405550	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	0.45026	-0.9289	9	0.21014	T	0.42	.	1.5864	0.02645	0.4337:0.0932:0.2673:0.2058	rs3748692;rs3748692	1864	P49454	CENPF_HUMAN	N	1768	ENSP00000355922:D1768N	ENSP00000355922:D1768N	D	+	1	0	CENPF	212884838	0.000000	0.05858	0.009000	0.14445	0.026000	0.11368	0.075000	0.14686	-0.822000	0.04306	-0.308000	0.09152	GAT	G|0.924;A|0.076	0.076	strong		0.398	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
WDFY4	57705	hgsc.bcm.edu	37	10	50098739	50098739	+	Missense_Mutation	SNP	G	G	C	rs41283283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50098739G>C	ENST00000325239.5	+	43	7310	c.7283G>C	c.(7282-7284)gGt>gCt	p.G2428A	RP11-523O18.7_ENST00000430438.1_RNA|WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2428						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						TCTCCCACGGGTGATGTCTAC	0.547													G|||	156	0.0311502	0.0098	0.0476	5008	,	,		22902	0.001		0.0865	False		,,,				2504	0.0225				p.G2428A		Atlas-SNP	.											.	WDFY4	205	.	0			c.G7283C						PASS	.	G	ALA/GLY	32,1352		0,32,660	118.0	91.0	99.0		7283	4.8	0.9	10	dbSNP_127	99	223,2959		4,215,1372	yes	missense	WDFY4	NM_020945.1	60	4,247,2032	CC,CG,GG		7.0082,2.3121,5.5848	probably-damaging	2428/3185	50098739	255,4311	692	1591	2283	SO:0001583	missense	57705	exon44			CCACGGGTGATGT	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.7283G>C	10.37:g.50098739G>C	ENSP00000320563:p.Gly2428Ala	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	197	110	0.558376	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	88|88	0.040293040293040296|0.040293040293040296	3|3	0.006097560975609756|0.006097560975609756	17|17	0.04696132596685083|0.04696132596685083	0|0	0.0|0.0	68|68	0.08970976253298153|0.08970976253298153	G|G	16.14|16.14	3.039273|3.039273	0.55003|0.55003	0.023121|0.023121	0.070082|0.070082	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000265453	T|.	0.60171|.	0.21|.	4.83|4.83	4.83|4.83	0.62350|0.62350	PH-BEACH domain (1);|.	0.069031|.	0.56097|.	D|.	0.000022|.	T|T	0.07773|0.07773	0.0195|0.0195	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D|.	0.67145|.	0.996|.	P|.	0.57720|.	0.826|.	T|T	0.17715|0.17715	-1.0360|-1.0360	9|5	.|.	.|.	.|.	.|.	13.7746|13.7746	0.63046|0.63046	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs41283283;rs61733232|rs41283283;rs61733232	2428|.	Q6ZS81|.	WDFY4_HUMAN|.	A|L	2428|515	ENSP00000320563:G2428A|.	.|.	G|V	+|+	2|1	0|0	WDFY4|WDFY4	49768745|49768745	0.993000|0.993000	0.37304|0.37304	0.945000|0.945000	0.38365|0.38365	0.933000|0.933000	0.57130|0.57130	3.689000|3.689000	0.54706|0.54706	2.373000|2.373000	0.80994|0.80994	0.561000|0.561000	0.74099|0.74099	GGT|GTG	G|0.957;C|0.043	0.043	strong		0.547	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
SYK	6850	hgsc.bcm.edu	37	9	93639973	93639973	+	Silent	SNP	G	G	C	rs2290888	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:93639973G>C	ENST00000375754.4	+	10	1450	c.1302G>C	c.(1300-1302)cgG>cgC	p.R434R	SYK_ENST00000375747.1_Silent_p.R411R|SYK_ENST00000375751.4_Silent_p.R411R|SYK_ENST00000375746.1_Silent_p.R434R	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	434	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						ACATCGTGCGGATGATCGGGA	0.483			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	984	0.196486	0.211	0.366	5008	,	,		21474	0.2321		0.1362	False		,,,				2504	0.0818				p.R434R		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.G1302C						PASS	.	C	,,,	935,3471	737.2+/-410.9	93,749,1361	132.0	115.0	121.0		1233,1302,1233,1302	-1.8	1.0	9	dbSNP_100	121	1214,7386	763.0+/-407.6	87,1040,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	180,1789,4534	CC,CG,GG		14.1163,21.2211,16.5231	,,,	411/613,434/636,411/613,434/636	93639973	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon10			CGTGCGGATGATC	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1302G>C	9.37:g.93639973G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	178	78	0.438202	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			G|0.789;C|0.211	0.211	strong		0.483	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278075	126278075	+	Silent	SNP	C	C	T	rs2230279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126278075C>T	ENST00000526727.1	+	6	797	c.423C>T	c.(421-423)taC>taT	p.Y141Y	ST3GAL4_ENST00000532243.1_Silent_p.Y140Y|ST3GAL4_ENST00000227495.6_Silent_p.Y137Y|ST3GAL4_ENST00000356132.4_Silent_p.Y147Y|ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000530591.1_Silent_p.Y137Y|ST3GAL4_ENST00000449406.2_Silent_p.Y130Y|ST3GAL4_ENST00000534457.1_Silent_p.Y136Y|ST3GAL4_ENST00000534083.1_Silent_p.Y141Y|ST3GAL4_ENST00000392669.2_Silent_p.Y141Y|ST3GAL4_ENST00000444328.2_Silent_p.Y141Y			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	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	152	150	0.986842	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	
ITGA4	3676	hgsc.bcm.edu	37	2	182374534	182374534	+	Splice_Site	SNP	A	A	G	rs1143674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:182374534A>G	ENST00000397033.2	+	16	2275	c.1845A>G	c.(1843-1845)acA>acG	p.T615T		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	615					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)	TGAAAAAAACAGTAGGAATAT	0.313													A|||	3313	0.661542	0.6634	0.6282	5008	,	,		15424	0.631		0.5328	False		,,,				2504	0.8466				p.T615T		Atlas-SNP	.											.	ITGA4	142	.	0			c.A1845G						PASS	.	A		2342,1250		750,842,204	49.0	46.0	47.0		1845	1.7	0.9	2	dbSNP_86	47	4693,3431		1383,1927,752	yes	coding-synonymous-near-splice	ITGA4	NM_000885.4		2133,2769,956	GG,GA,AA		42.2329,34.7996,39.9539		615/1033	182374534	7035,4681	1796	4062	5858	SO:0001630	splice_region_variant	3676	exon16			AAAAACAGTAGGA		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.1845+1A>G	2.37:g.182374534A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	37	CCDS42788.1																																																																																			A|0.407;G|0.593	0.593	strong		0.313	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		Silent
SNAPC4	6621	hgsc.bcm.edu	37	9	139289825	139289825	+	Silent	SNP	A	A	G	rs4266763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139289825A>G	ENST00000298532.2	-	4	764	c.396T>C	c.(394-396)gaT>gaC	p.D132D		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)		GGCTTTTGCCATCTTTCACCT	0.567													a|||	1983	0.395966	0.3593	0.5793	5008	,	,		18187	0.3214		0.3907	False		,,,				2504	0.3978				p.D132D		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T396C						PASS	.	G		1553,2853	666.9+/-401.8	266,1021,916	114.0	102.0	106.0		396	-9.4	0.0	9	dbSNP_111	106	3587,5013	626.9+/-397.9	742,2103,1455	no	coding-synonymous	SNAPC4	NM_003086.2		1008,3124,2371	GG,GA,AA		41.7093,35.2474,39.5202		132/1470	139289825	5140,7866	2203	4300	6503	SO:0001819	synonymous_variant	6621	exon4			TTTGCCATCTTTC	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.396T>C	9.37:g.139289825A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	194	93	0.479381	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.611;G|0.388	0.388	strong		0.567	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
COL6A5	256076	hgsc.bcm.edu	37	3	130103709	130103709	+	Missense_Mutation	SNP	G	G	A	rs1453241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:130103709G>A	ENST00000432398.2	+	5	1857	c.1363G>A	c.(1363-1365)Gag>Aag	p.E455K	COL6A5_ENST00000265379.6_Missense_Mutation_p.E455K	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	455	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		E -> K (in dbSNP:rs1453241). {ECO:0000269|PubMed:18276594}.		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						CAGCATCCAGGAGAAACAGTT	0.418													G|||	1987	0.396765	0.4728	0.4582	5008	,	,		19916	0.5149		0.2028	False		,,,				2504	0.3282				p.E455K		Atlas-SNP	.											.	COL6A5	205	.	0			c.G1363A	GRCh37	CM076121	COL6A5	M	rs1453241	PASS	.	G	LYS/GLU	586,798		116,354,222	86.0	78.0	81.0		1363	-6.1	0.0	3	dbSNP_88	81	697,2485		85,527,979	yes	missense	COL6A5	NM_153264.5	56	201,881,1201	AA,AG,GG		21.9045,42.341,28.099	benign	455/2527	130103709	1283,3283	692	1591	2283	SO:0001583	missense	256076	exon5			ATCCAGGAGAAAC	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.1363G>A	3.37:g.130103709G>A	ENSP00000390895:p.Glu455Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		795	0.364010989010989	206	0.4186991869918699	146	0.40331491712707185	294	0.513986013986014	149	0.19656992084432717	G	9.568	1.120335	0.20877	0.42341	0.219045	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.83837	-1.77;-1.77	5.5	-6.05	0.02172	.	.	.	.	.	T	0.00012	0.0000	N	0.05554	-0.025	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.16424	-1.0403	8	0.06365	T	0.9	.	3.7844	0.08694	0.289:0.1875:0.4308:0.0927	rs1453241;rs52804564;rs58043586;rs1453241	455	A8TX70-2	.	K	455	ENSP00000390895:E455K;ENSP00000265379:E455K	ENSP00000265379:E455K	E	+	1	0	COL6A5	131586399	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.626000	0.00874	-1.344000	0.02216	-0.262000	0.10625	GAG	G|0.619;A|0.381	0.381	strong		0.418	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
TOR2A	27433	hgsc.bcm.edu	37	9	130495633	130495633	+	Intron	SNP	C	C	G	rs564754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130495633C>G	ENST00000373284.5	-	3	640				TOR2A_ENST00000373281.5_Missense_Mutation_p.W208C|TOR2A_ENST00000458505.3_3'UTR|TOR2A_ENST00000472723.1_5'UTR|TOR2A_ENST00000336067.6_Intron	NM_001085347.2	NP_001078816	Q5JU69	TOR2A_HUMAN	torsin family 2, member A						chaperone mediated protein folding requiring cofactor (GO:0051085)|protein homooligomerization (GO:0051260)	endoplasmic reticulum lumen (GO:0005788)	ATP binding (GO:0005524)			NS(1)|endometrium(2)	3						AGTGGCCCCCCCACTGTGCCC	0.602													C|||	3124	0.623802	0.7844	0.6081	5008	,	,		17651	0.371		0.6332	False		,,,				2504	0.6687				p.W208C		Atlas-SNP	.											.	TOR2A	26	.	0			c.G624C						PASS	.	C	,,,CYS/TRP	3267,1139	711.3+/-408.0	1215,837,151	50.0	49.0	49.0		,,,624	-1.4	0.0	9	dbSNP_83	49	5087,3513	627.7+/-398.0	1505,2077,718	yes	intron,intron,utr-3,missense	TOR2A	NM_001085347.1,NM_001134430.1,NM_001134431.1,NM_130459.2	,,,215	2720,2914,869	GG,GC,CC		40.8488,25.8511,35.7681	,,,	,,,208/254	130495633	8354,4652	2203	4300	6503	SO:0001627	intron_variant	27433	exon3			GCCCCCCCACTGT	AA873275	CCDS6876.1, CCDS43879.1, CCDS48024.1	9q34.11	2010-08-20			ENSG00000160404	ENSG00000160404			11996	protein-coding gene	gene with protein product		608052				10644435	Standard	NM_001085347		Approved	FLJ14771, TORP1	uc004brs.4	Q5JU69	OTTHUMG00000020706	ENST00000373284.5:c.593+30G>C	9.37:g.130495633C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_130459	A4FU12|A4FU13|Q3ZCN9|Q3ZCP0|Q5JU68|Q66K87|Q6UXW6|Q8NAN5|Q96SL7	Missense_Mutation	SNP	ENST00000373284.5	37	CCDS43879.1	1311	0.6002747252747253	382	0.7764227642276422	219	0.6049723756906077	220	0.38461538461538464	490	0.6464379947229552	C	10.73	1.432873	0.25813	0.741489	0.591512	ENSG00000160404	ENST00000373281	T	0.69040	-0.37	5.39	-1.4	0.08968	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.35475	-0.9787	7	0.38643	T	0.18	.	5.8881	0.18892	0.137:0.2686:0.5145:0.0798	rs564754;rs1755665;rs3739813;rs57276118;rs564754	208	Q5JU69-2	.	C	208	ENSP00000362378:W208C	ENSP00000362378:W208C	W	-	3	0	TOR2A	129535454	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.060000	0.03475	-0.643000	0.05473	-0.311000	0.09066	TGG	C|0.370;G|0.630	0.630	strong		0.602	TOR2A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054205.1	NM_130459	
GPC1	2817	hgsc.bcm.edu	37	2	241405528	241405528	+	Missense_Mutation	SNP	A	A	G	rs2228331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241405528A>G	ENST00000264039.2	+	9	1746	c.1498A>G	c.(1498-1500)Agc>Ggc	p.S500G	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	500			S -> G (in dbSNP:rs2228331). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2148568}.		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)		TGACCTCTGCAGCCGGAAGGT	0.672													g|||	3327	0.664337	0.9244	0.6484	5008	,	,		13079	0.3383		0.7048	False		,,,				2504	0.6186				p.S500G		Atlas-SNP	.											.	GPC1	32	.	0			c.A1498G						PASS	.		GLY/SER	3936,470	217.8+/-236.0	1750,436,17	39.0	48.0	45.0		1498	2.0	0.0	2	dbSNP_98	45	6121,2477	404.0+/-348.0	2179,1763,357	yes	missense	GPC1	NM_002081.2	56	3929,2199,374	GG,GA,AA		28.809,10.6673,22.6623	benign	500/559	241405528	10057,2947	2203	4299	6502	SO:0001583	missense	2817	exon9			CTCTGCAGCCGGA	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.1498A>G	2.37:g.241405528A>G	ENSP00000264039:p.Ser500Gly	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	240	237	0.9875	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	37	CCDS2534.1	1406|1406	0.6437728937728938|0.6437728937728938	447|447	0.9085365853658537|0.9085365853658537	246|246	0.6795580110497238|0.6795580110497238	190|190	0.3321678321678322|0.3321678321678322	523|523	0.6899736147757256|0.6899736147757256	g|g	0.004|0.004	-2.325179|-2.325179	0.00229|0.00229	0.893327|0.893327	0.71191|0.71191	ENSG00000063660|ENSG00000063660	ENST00000420138;ENST00000455111|ENST00000264039	.|T	.|0.47869	.|0.83	3.82|3.82	1.97|1.97	0.26223|0.26223	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00855|0.00855	-1.145|-1.145	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.37079|0.37079	-0.9721|-0.9721	4|8	.|0.02654	.|T	.|1	-17.0512|-17.0512	7.9693|7.9693	0.30117|0.30117	0.296:0.0:0.704:0.0|0.296:0.0:0.704:0.0	rs2228331;rs6437345;rs17588505;rs17857396;rs60372239;rs2228331|rs2228331;rs6437345;rs17588505;rs17857396;rs60372239;rs2228331	.|500	.|P35052	.|GPC1_HUMAN	R|G	539;251|500	.|ENSP00000264039:S500G	.|ENSP00000264039:S500G	Q|S	+|+	2|1	0|0	GPC1|GPC1	241054201|241054201	0.846000|0.846000	0.29590|0.29590	0.019000|0.019000	0.16419|0.16419	0.003000|0.003000	0.03518|0.03518	1.350000|1.350000	0.34010|0.34010	-0.045000|-0.045000	0.13468|0.13468	-1.177000|-1.177000	0.01723|0.01723	CAG|AGC	A|0.294;G|0.706	0.706	strong		0.672	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
TXNDC2	84203	hgsc.bcm.edu	37	18	9886988	9886988	+	Missense_Mutation	SNP	C	C	T	rs34812912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	112	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	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		
LAPTM4B	55353	hgsc.bcm.edu	37	8	98788261	98788261	+	Silent	SNP	G	G	T	rs2449508	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:98788261G>T	ENST00000521545.2	+	1	258	c.24G>T	c.(22-24)acG>acT	p.T8T	RNU7-177P_ENST00000517101.1_RNA|LAPTM4B_ENST00000445593.2_Silent_p.T99T			Q86VI4	LAP4B_HUMAN	lysosomal protein transmembrane 4 beta	152					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	10	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)			CGCCCTGGACGCGGTTCTACT	0.716													G|||	419	0.0836661	0.0598	0.0908	5008	,	,		10836	0.0		0.1471	False		,,,				2504	0.1319				p.T99T		Atlas-SNP	.											LAPTM4B,rectum,carcinoma,0,1	LAPTM4B	26	1	0			c.G297T						PASS	.	G		258,4118		11,236,1941	18.0	20.0	19.0		297	0.8	1.0	8	dbSNP_100	19	1359,7205		99,1161,3022	no	coding-synonymous	LAPTM4B	NM_018407.4		110,1397,4963	TT,TG,GG		15.8688,5.8958,12.4961		99/318	98788261	1617,11323	2188	4282	6470	SO:0001819	synonymous_variant	55353	exon1			CTGGACGCGGTTC	AF317417	CCDS6275.1	8q22.1	2008-08-11	2008-08-11		ENSG00000104341	ENSG00000104341			13646	protein-coding gene	gene with protein product		613296					Standard	NM_018407		Approved	LC27	uc003yia.3	Q86VI4	OTTHUMG00000164740	ENST00000521545.2:c.24G>T	8.37:g.98788261G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_018407	Q3ZCV5|Q7L909|Q86VH8|Q9H060	Silent	SNP	ENST00000521545.2	37		168	0.07692307692307693	26	0.052845528455284556	37	0.10220994475138122	0	0.0	105	0.13852242744063326	G	4.659	0.122439	0.08931	0.058958	0.158688	ENSG00000104341	ENST00000517924	.	.	.	4.29	0.755	0.18415	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.999999999869745	.	.	.	.	.	.	T	0.15694	-1.0428	3	.	.	.	-7.5416	2.1512	0.03800	0.098:0.2843:0.2599:0.3577	rs2449508;rs4397375;rs61112322;rs2449508	.	.	.	L	62	.	.	R	+	2	0	LAPTM4B	98857437	1.000000	0.71417	0.996000	0.52242	0.001000	0.01503	0.802000	0.27069	0.269000	0.21961	-0.179000	0.13096	CGC	G|0.891;T|0.109	0.109	strong		0.716	LAPTM4B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000380016.2		
ITPR2	3709	hgsc.bcm.edu	37	12	26809412	26809412	+	Silent	SNP	T	T	G	rs2230378	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:26809412T>G	ENST00000381340.3	-	19	2678	c.2262A>C	c.(2260-2262)acA>acC	p.T754T		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	754					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)	CAGACAGCTGTGTAGAAATCT	0.488													T|||	157	0.0313498	0.0068	0.0346	5008	,	,		21167	0.001		0.0944	False		,,,				2504	0.0286				p.T754T		Atlas-SNP	.											.	ITPR2	270	.	0			c.A2262C						PASS	.	T		74,4016		2,70,1973	67.0	73.0	71.0		2262	-8.9	0.4	12	dbSNP_98	71	795,7583		43,709,3437	no	coding-synonymous	ITPR2	NM_002223.2		45,779,5410	GG,GT,TT		9.4891,1.8093,6.9698		754/2702	26809412	869,11599	2045	4189	6234	SO:0001819	synonymous_variant	3709	exon19			CAGCTGTGTAGAA	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.2262A>C	12.37:g.26809412T>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.946;G|0.054	0.054	strong		0.488	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
ATG14	22863	hgsc.bcm.edu	37	14	55864130	55864130	+	Silent	SNP	A	A	G	rs8003279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:55864130A>G	ENST00000247178.5	-	2	279	c.244T>C	c.(244-246)Tta>Cta	p.L82L		NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14	82					autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						AGTCGGCTTAACCTTTCCTTC	0.333													A|||	1045	0.208666	0.1142	0.1902	5008	,	,		21063	0.1617		0.329	False		,,,				2504	0.274				p.L82L		Atlas-SNP	.											.	ATG14	36	.	0			c.T244C						PASS	.	A		657,3747	277.8+/-273.9	45,567,1590	137.0	114.0	122.0		244	2.1	1.0	14	dbSNP_116	122	2762,5836	435.0+/-357.9	469,1824,2006	no	coding-synonymous	ATG14	NM_014924.4		514,2391,3596	GG,GA,AA		32.1237,14.9183,26.296		82/493	55864130	3419,9583	2202	4299	6501	SO:0001819	synonymous_variant	22863	exon2			GGCTTAACCTTTC	AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"""Barkor"", ""beclin 1-associated autophagy-related key regulator"""	613515	"""KIAA0831"", ""ATG14 autophagy related 14 homolog (S. cerevisiae)"""	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129	ENST00000247178.5:c.244T>C	14.37:g.55864130A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_014924	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Silent	SNP	ENST00000247178.5	37	CCDS32087.1																																																																																			A|0.760;G|0.240	0.240	strong		0.333	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416992.1	NM_014924	
COQ10B	80219	hgsc.bcm.edu	37	2	198327314	198327314	+	Silent	SNP	G	G	A	rs3754822	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:198327314G>A	ENST00000263960.2	+	3	444	c.306G>A	c.(304-306)aaG>aaA	p.K102K	COQ10B_ENST00000409010.1_Silent_p.K74K|COQ10B_ENST00000545340.1_Silent_p.K59K|COQ10B_ENST00000409398.1_Silent_p.K52K	NM_025147.3	NP_079423.1	Q9H8M1	CQ10B_HUMAN	coenzyme Q10 homolog B (S. cerevisiae)	102						mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(2)|lung(3)	6			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)			AGGATTACAAGCATTTTGTTC	0.318													G|||	730	0.145767	0.053	0.1729	5008	,	,		16503	0.2282		0.2157	False		,,,				2504	0.0951				p.K102K		Atlas-SNP	.											.	COQ10B	18	.	0			c.G306A						PASS	.	G		381,4025	193.6+/-218.7	20,341,1842	126.0	129.0	128.0		306	0.9	1.0	2	dbSNP_107	128	1697,6903	308.8+/-309.1	155,1387,2758	no	coding-synonymous	COQ10B	NM_025147.3		175,1728,4600	AA,AG,GG		19.7326,8.6473,15.9772		102/239	198327314	2078,10928	2203	4300	6503	SO:0001819	synonymous_variant	80219	exon3			TTACAAGCATTTT	AK023510	CCDS2319.1	2q33.1	2008-02-05	2006-04-04		ENSG00000115520	ENSG00000115520			25819	protein-coding gene	gene with protein product			"""coenzyme Q10 homolog B (yeast)"""				Standard	NM_025147		Approved	FLJ13448	uc002uuh.1	Q9H8M1	OTTHUMG00000132745	ENST00000263960.2:c.306G>A	2.37:g.198327314G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_025147	B7Z1Y4	Silent	SNP	ENST00000263960.2	37	CCDS2319.1																																																																																			G|0.833;A|0.167	0.167	strong		0.318	COQ10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256105.2	NM_025147	
ZNF814	730051	hgsc.bcm.edu	37	19	58385748	58385748	+	Missense_Mutation	SNP	G	G	A	rs145250945		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58385748G>A	ENST00000435989.2	-	3	1244	c.1010C>T	c.(1009-1011)gCt>gTt	p.A337V	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	337					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)	p.A337V(2)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						ACTGAAGCTAGCATATTTGCT	0.353																																					p.A337V		Atlas-SNP	.											ZNF814,NS,carcinoma,0,3	ZNF814	93	3	2	Substitution - Missense(2)	prostate(2)	c.C1010T						PASS	.						58.0	51.0	53.0					19																	58385748		692	1591	2283	SO:0001583	missense	730051	exon3			AAGCTAGCATATT		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.1010C>T	19.37:g.58385748G>A	ENSP00000410545:p.Ala337Val	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	197	74	0.375635	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	3.777	-0.046344	0.07407	.	.	ENSG00000204514	ENST00000435989	T	0.15372	2.43	2.11	-4.21	0.03812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07728	0.0194	N	0.21142	0.635	0.09310	N	1	B	0.32781	0.384	B	0.18561	0.022	T	0.05649	-1.0872	9	0.66056	D	0.02	.	3.5015	0.07674	0.0936:0.1206:0.3016:0.4843	.	337	B7Z6K7	ZN814_HUMAN	V	337	ENSP00000410545:A337V	ENSP00000410545:A337V	A	-	2	0	ZNF814	63077560	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.230000	0.01207	-3.525000	0.00147	-3.867000	0.00017	GCT	.	.	weak		0.353	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
HHATL	57467	hgsc.bcm.edu	37	3	42735274	42735274	+	Silent	SNP	A	A	G	rs339697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42735274A>G	ENST00000441594.1	-	10	1344	c.1083T>C	c.(1081-1083)gcT>gcC	p.A361A	HHATL_ENST00000310417.5_Silent_p.A361A	NM_020707.3	NP_065758.3	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like	361					negative regulation of N-terminal protein palmitoylation (GO:0060262)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(3)	19				KIRC - Kidney renal clear cell carcinoma(284;0.215)		CTGGGATCACAGCGGAATGCT	0.542													G|||	3508	0.700479	0.8525	0.6888	5008	,	,		19113	0.7133		0.5954	False		,,,				2504	0.5982				p.A361A		Atlas-SNP	.											.	HHATL	49	.	0			c.T1083C						PASS	.			3510,896	347.5+/-309.5	1400,710,93	71.0	59.0	63.0		1083	-8.2	0.0	3	dbSNP_79	63	5095,3505	512.1+/-377.9	1474,2147,679	no	coding-synonymous	HHATL	NM_020707.3		2874,2857,772	GG,GA,AA		40.7558,20.3359,33.8382		361/505	42735274	8605,4401	2203	4300	6503	SO:0001819	synonymous_variant	57467	exon10			GATCACAGCGGAA	AB042554	CCDS2704.1	3p22	2009-10-06	2007-02-06	2007-02-06	ENSG00000010282	ENSG00000010282			13242	protein-coding gene	gene with protein product	"""membrane bound O-acyltransferase domain containing 3"""	608116	"""chromosome 3 open reading frame 3"", ""GUP1, glycerol uptake/transporter homolog (yeast)"""	C3orf3, GUP1		11374908	Standard	NM_020707		Approved	KIAA1173, OACT3, MSTP002, MBOAT3	uc003clx.3	Q9HCP6	OTTHUMG00000133043	ENST00000441594.1:c.1083T>C	3.37:g.42735274A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_020707	Q8TBG3|Q9ULP7	Silent	SNP	ENST00000441594.1	37	CCDS2704.1																																																																																			A|0.333;G|0.667	0.667	strong		0.542	HHATL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343627.1	NM_020707	
RAD51D	5892	hgsc.bcm.edu	37	17	33445549	33445549	+	Silent	SNP	G	G	A	rs9901455	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:33445549G>A	ENST00000345365.6	-	3	489	c.234C>T	c.(232-234)tcC>tcT	p.S78S	RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000460118.2_5'UTR|RAD51D_ENST00000357906.3_Silent_p.S78S|RAD51D_ENST00000360276.3_Silent_p.S78S|RAD51D_ENST00000590016.1_Intron|RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000590380.1_Intron|RAD51D_ENST00000394589.4_Silent_p.S78S	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	54	0	0		WXS	Illumina HiSeq	Phase_I	73	44	0.60274	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	
ATCAY	85300	hgsc.bcm.edu	37	19	3908272	3908272	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3908272A>G	ENST00000450849.2	+	6	1018	c.551A>G	c.(550-552)tAc>tGc	p.Y184C	ATCAY_ENST00000398448.3_Missense_Mutation_p.Y190C|ATCAY_ENST00000600960.1_Missense_Mutation_p.Y184C|ATCAY_ENST00000301260.6_Missense_Mutation_p.Y184C	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	184	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)			breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		TCAGGGTACTACGGCGAAGGC	0.632																																					p.Y184C		Atlas-SNP	.											ATCAY_ENST00000450849,NS,carcinoma,-1,2	ATCAY	84	2	0			c.A551G						scavenged	.						28.0	36.0	33.0					19																	3908272		2147	4251	6398	SO:0001583	missense	85300	exon6			GGTACTACGGCGA		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"""Cayman ataxia"", ""caytaxin"""	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.551A>G	19.37:g.3908272A>G	ENSP00000390941:p.Tyr184Cys	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	146	2	0.0136986	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Missense_Mutation	SNP	ENST00000450849.2	37	CCDS45923.1	.	.	.	.	.	.	.	.	.	.	A	17.00	3.275820	0.59649	.	.	ENSG00000167654	ENST00000450849;ENST00000301260;ENST00000357694;ENST00000398448;ENST00000539301	T;T;T	0.25414	1.8;1.8;1.8	5.14	5.14	0.70334	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.183781	0.49305	D	0.000146	T	0.53449	0.1797	M	0.83483	2.645	0.51012	D	0.999906	P;D	0.89917	0.949;1.0	P;D	0.85130	0.884;0.997	T	0.56968	-0.7891	10	0.42905	T	0.14	-29.8697	14.2782	0.66194	1.0:0.0:0.0:0.0	.	190;184	B4DS11;Q86WG3	.;ATCAY_HUMAN	C	184;184;184;190;162	ENSP00000390941:Y184C;ENSP00000301260:Y184C;ENSP00000381466:Y190C	ENSP00000301260:Y184C	Y	+	2	0	ATCAY	3859272	1.000000	0.71417	1.000000	0.80357	0.308000	0.27856	8.669000	0.91163	1.973000	0.57446	0.524000	0.50904	TAC	.	.	none		0.632	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2		
TSPAN18	90139	hgsc.bcm.edu	37	11	44940828	44940828	+	Missense_Mutation	SNP	G	G	A	rs2291334	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:44940828G>A	ENST00000520358.2	+	7	812	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	TSPAN18_ENST00000340160.3_Missense_Mutation_p.V133I			Q96SJ8	TSN18_HUMAN	tetraspanin 18	133			V -> I (in dbSNP:rs2291334). {ECO:0000269|PubMed:12975309}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						CGACACAGACGTCTTCTCTGC	0.557													G|||	1738	0.347045	0.034	0.415	5008	,	,		21259	0.5575		0.329	False		,,,				2504	0.5235				p.V133I		Atlas-SNP	.											TSPAN18,colon,carcinoma,-2,1	TSPAN18	38	1	0			c.G397A						PASS	.	G	ILE/VAL	440,3966	212.5+/-232.4	25,390,1788	199.0	154.0	170.0		397	2.4	0.5	11	dbSNP_100	170	2937,5661	458.0+/-364.5	502,1933,1864	yes	missense	TSPAN18	NM_130783.4	29	527,2323,3652	AA,AG,GG		34.1591,9.9864,25.9689	benign	133/249	44940828	3377,9627	2203	4299	6502	SO:0001583	missense	90139	exon6			ACAGACGTCTTCT	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.397G>A	11.37:g.44940828G>A	ENSP00000429993:p.Val133Ile	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	141	68	0.482269	NM_130783	Q6UY44|Q8NBI9	Missense_Mutation	SNP	ENST00000520358.2	37	CCDS7910.1	743|743	0.3402014652014652|0.3402014652014652	20|20	0.04065040650406504|0.04065040650406504	154|154	0.425414364640884|0.425414364640884	316|316	0.5524475524475524|0.5524475524475524	253|253	0.3337730870712401|0.3337730870712401	G|G	11.55|11.55	1.671289|1.671289	0.29693|0.29693	0.099864|0.099864	0.341591|0.341591	ENSG00000157570|ENSG00000157570	ENST00000518429|ENST00000533786;ENST00000533080;ENST00000520358;ENST00000520999;ENST00000340160	.|T;D;D;T;D	.|0.86956	.|-1.27;-2.19;-2.19;-1.27;-2.19	5.29|5.29	2.4|2.4	0.29515|0.29515	.|Tetraspanin, EC2 domain (1);	.|0.405863	.|0.28989	.|N	.|0.013489	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38838|0.38838	1.175|1.175	0.09310|0.09310	P|P	0.9999999999999999|0.9999999999999999	.|B;B	.|0.32302	.|0.205;0.363	.|B;B	.|0.34385	.|0.04;0.181	T|T	0.44651|0.44651	-0.9314|-0.9314	4|9	.|0.36615	.|T	.|0.2	.|.	9.2617|9.2617	0.37616|0.37616	0.2416:0.0:0.7584:0.0|0.2416:0.0:0.7584:0.0	rs2291334;rs17787220;rs58600094;rs2291334|rs2291334;rs17787220;rs58600094;rs2291334	.|133;133	.|Q8WUV1;Q96SJ8	.|.;TSN18_HUMAN	H|I	136|133;68;133;143;133	.|ENSP00000433592:V133I;ENSP00000433362:V68I;ENSP00000429993:V133I;ENSP00000427942:V143I;ENSP00000339820:V133I	.|ENSP00000339820:V133I	R|V	+|+	2|1	0|0	TSPAN18|TSPAN18	44897404|44897404	1.000000|1.000000	0.71417|0.71417	0.546000|0.546000	0.28166|0.28166	0.227000|0.227000	0.25037|0.25037	5.142000|5.142000	0.64820|0.64820	0.622000|0.622000	0.30249|0.30249	0.462000|0.462000	0.41574|0.41574	CGT|GTC	G|0.711;A|0.289	0.289	strong		0.557	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
HCN2	610	hgsc.bcm.edu	37	19	603826	603826	+	Silent	SNP	C	C	T	rs56170955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:603826C>T	ENST00000251287.2	+	2	968	c.915C>T	c.(913-915)ttC>ttT	p.F305F		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	305					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)		ACTACATCTTCCTTATCGTGG	0.582													c|||	1186	0.236821	0.2368	0.0908	5008	,	,		14018	0.2897		0.0984	False		,,,				2504	0.4284				p.F305F	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.C915T						PASS	.	C		1119,3277		141,837,1220	141.0	108.0	119.0		915	2.8	1.0	19	dbSNP_129	119	900,7698		50,800,3449	no	coding-synonymous	HCN2	NM_001194.3		191,1637,4669	TT,TC,CC		10.4676,25.455,15.5379		305/890	603826	2019,10975	2198	4299	6497	SO:0001819	synonymous_variant	610	exon2			CATCTTCCTTATC	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.915C>T	19.37:g.603826C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			C|0.835;T|0.165	0.165	strong		0.582	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
INSR	3643	hgsc.bcm.edu	37	19	7166376	7166376	+	Silent	SNP	C	C	T	rs2059806	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7166376C>T	ENST00000302850.5	-	8	1792	c.1650G>A	c.(1648-1650)gcG>gcA	p.A550A	INSR_ENST00000341500.5_Silent_p.A550A	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	550					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.A550A(1)		breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	TGGAACCACACGCATCCTGCC	0.552													c|||	1226	0.244808	0.1793	0.2363	5008	,	,		19405	0.2798		0.2853	False		,,,				2504	0.2618				p.A550A		Atlas-SNP	.											INSR,NS,carcinoma,0,1	INSR	265	1	1	Substitution - coding silent(1)	stomach(1)	c.G1650A	GRCh37	CM004252	INSR	M	rs2059806	PASS	.	T	,	855,3551	335.5+/-303.9	87,681,1435	99.0	74.0	83.0		1650,1650	-10.2	0.0	19	dbSNP_94	83	2078,6522	359.6+/-331.6	252,1574,2474	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	339,2255,3909	TT,TC,CC		24.1628,19.4054,22.5511	,	550/1383,550/1371	7166376	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon8			ACCACACGCATCC	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.1650G>A	19.37:g.7166376C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			C|0.767;T|0.233	0.233	strong		0.552	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
LILRB5	10990	hgsc.bcm.edu	37	19	54755923	54755923	+	Silent	SNP	A	A	G	rs34889610|rs12976868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54755923A>G	ENST00000316219.5	-	12	1727	c.1620T>C	c.(1618-1620)gaT>gaC	p.D540D	LILRB5_ENST00000345866.6_Silent_p.D441D|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000449561.2_Silent_p.D541D|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	191	0	0		WXS	Illumina HiSeq	Phase_I	192	97	0.505208	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		
FLG	2312	hgsc.bcm.edu	37	1	152280032	152280032	+	Missense_Mutation	SNP	T	T	C	rs71625200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280032T>C	ENST00000368799.1	-	3	7365	c.7330A>G	c.(7330-7332)Aag>Gag	p.K2444E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2444	Ser-rich.			K -> Q (in Ref. 3; AAA52454). {ECO:0000305}.	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)			CGTGCCTGCTTGTGGTGGGAT	0.592									Ichthyosis				C|||	1718	0.343051	0.1218	0.4222	5008	,	,		21032	0.6071		0.171	False		,,,				2504	0.4908				p.K2444E		Atlas-SNP	.											FLG,larynx,carcinoma,+2,1	FLG	900	1	0			c.A7330G						PASS	.	C	GLU/LYS	599,3807	766.7+/-413.5	43,513,1647	304.0	277.0	286.0		7330	2.1	0.0	1	dbSNP_130	286	1407,7191	749.4+/-407.4	123,1161,3015	no	missense	FLG	NM_002016.1	56	166,1674,4662	CC,CT,TT		16.3643,13.5951,15.426	benign	2444/4062	152280032	2006,10998	2203	4299	6502	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTGCTTGTGGTG	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.7330A>G	1.37:g.152280032T>C	ENSP00000357789:p.Lys2444Glu	Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	324	166	0.512346	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	586	0.2683150183150183	51	0.10365853658536585	107	0.2955801104972376	319	0.5576923076923077	109	0.1437994722955145	C	7.499	0.652241	0.14580	0.135951	0.163643	ENSG00000143631	ENST00000368799	T	0.01647	4.71	4.1	2.1	0.27182	.	.	.	.	.	T	0.00109	0.0003	N	0.00036	-2.535	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26710	-1.0095	8	0.02654	T	1	.	3.9847	0.09511	0.0:0.5744:0.1996:0.226	.	2444	P20930	FILA_HUMAN	E	2444	ENSP00000357789:K2444E	ENSP00000357789:K2444E	K	-	1	0	FLG	150546656	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.889000	0.04144	0.313000	0.23062	-0.330000	0.08379	AAG	T|0.803;C|0.197	0.197	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CCDC109B	55013	hgsc.bcm.edu	37	4	110581363	110581363	+	Missense_Mutation	SNP	T	T	A	rs4698744	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	119	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	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	
MROH2B	133558	hgsc.bcm.edu	37	5	40998235	40998235	+	Silent	SNP	C	C	T	rs722575	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:40998235C>T	ENST00000399564.4	-	42	5127	c.4677G>A	c.(4675-4677)ccG>ccA	p.P1559P	MROH2B_ENST00000506092.2_Silent_p.P1114P	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1559								p.P1559P(1)									CACTAATACACGGATCTTGAC	0.483													C|||	1635	0.326478	0.295	0.3646	5008	,	,		21196	0.2956		0.3936	False		,,,				2504	0.3047				p.P1559P		Atlas-SNP	.											HEATR7B2,NS,carcinoma,-2,2	.	.	2	1	Substitution - coding silent(1)	stomach(1)	c.G4677A						PASS	.	C		1182,2674		181,820,927	181.0	169.0	172.0		4677	-0.2	1.0	5	dbSNP_86	172	3323,4985		669,1985,1500	no	coding-synonymous	HEATR7B2	NM_173489.4		850,2805,2427	TT,TC,CC		39.9976,30.6535,37.0355		1559/1586	40998235	4505,7659	1928	4154	6082	SO:0001819	synonymous_variant	133558	exon42			AATACACGGATCT		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.4677G>A	5.37:g.40998235C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	CCDS47202.1																																																																																			C|0.702;T|0.298	0.298	strong		0.483	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
PPL	5493	hgsc.bcm.edu	37	16	4942099	4942099	+	Missense_Mutation	SNP	C	C	T	rs1049205	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:4942099C>T	ENST00000345988.2	-	15	1855	c.1766G>A	c.(1765-1767)cGg>cAg	p.R589Q	PPL_ENST00000590782.2_Missense_Mutation_p.R587Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	589			R -> Q (in dbSNP:rs1049205). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9412476, ECO:0000269|PubMed:9628581, ECO:0000269|Ref.5}.		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						GTCCTCCACCCGGGTCCTCAG	0.642													C|||	2002	0.39976	0.034	0.4654	5008	,	,		17542	0.6399		0.5388	False		,,,				2504	0.4571				p.R589Q		Atlas-SNP	.											PPL,NS,carcinoma,0,1	PPL	168	1	0			c.G1766A						PASS	.	C	GLN/ARG	513,3881	233.3+/-246.5	36,441,1720	59.0	58.0	59.0		1766	5.3	1.0	16	dbSNP_86	59	4754,3846	609.6+/-395.6	1318,2118,864	yes	missense	PPL	NM_002705.4	43	1354,2559,2584	TT,TC,CC		44.7209,11.675,40.5341	possibly-damaging	589/1757	4942099	5267,7727	2197	4300	6497	SO:0001583	missense	5493	exon15			TCCACCCGGGTCC	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.1766G>A	16.37:g.4942099C>T	ENSP00000340510:p.Arg589Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	970	0.4441391941391941	24	0.04878048780487805	164	0.4530386740331492	370	0.6468531468531469	412	0.5435356200527705	C	14.43	2.534249	0.45073	0.11675	0.552791	ENSG00000118898	ENST00000345988	T	0.36520	1.25	5.35	5.35	0.76521	.	0.079955	0.51477	D	0.000092	T	0.00012	0.0000	L	0.44542	1.39	0.27437	P	0.9538222	P	0.41710	0.76	B	0.30401	0.115	T	0.40869	-0.9540	9	0.14656	T	0.56	.	6.9724	0.24656	0.0:0.7881:0.0:0.2119	rs1049205;rs3189307;rs56845948;rs1049205	589	O60437	PEPL_HUMAN	Q	589	ENSP00000340510:R589Q	ENSP00000340510:R589Q	R	-	2	0	PPL	4882100	1.000000	0.71417	1.000000	0.80357	0.352000	0.29268	5.278000	0.65592	2.519000	0.84933	0.549000	0.68633	CGG	C|0.588;T|0.412	0.412	strong		0.642	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
COL3A1	1281	hgsc.bcm.edu	37	2	189862995	189862995	+	Silent	SNP	T	T	C	rs41263757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:189862995T>C	ENST00000304636.3	+	28	2097	c.1927T>C	c.(1927-1929)Ttg>Ctg	p.L643L	COL3A1_ENST00000317840.5_Silent_p.L643L	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	643	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TTTCTAGGGCTTGCCTGGTAC	0.353													T|||	9	0.00179712	0.0	0.0014	5008	,	,		15368	0.0		0.008	False		,,,				2504	0.0				p.L643L		Atlas-SNP	.											.	COL3A1	292	.	0			c.T1927C						PASS	.	T		0,4406		0,0,2203	65.0	68.0	67.0		1927	-3.8	0.6	2	dbSNP_127	67	20,8580	14.0+/-48.4	0,20,4280	no	coding-synonymous	COL3A1	NM_000090.3		0,20,6483	CC,CT,TT		0.2326,0.0,0.1538		643/1467	189862995	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	1281	exon28			TAGGGCTTGCCTG	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.1927T>C	2.37:g.189862995T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1																																																																																			T|0.998;C|0.002	0.002	strong		0.353	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
MUC16	94025	hgsc.bcm.edu	37	19	9091771	9091771	+	Missense_Mutation	SNP	C	C	T	rs375862521		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9091771C>T	ENST00000397910.4	-	1	247	c.44G>A	c.(43-45)cGc>cAc	p.R15H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	15	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						CATCAAGGAGCGGGTGGGAGA	0.532																																					p.R15H		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	0			c.G44A						scavenged	.	C	HIS/ARG	1,4003		0,1,2001	76.0	73.0	74.0		44	-2.7	0.0	19		74	0,8326		0,0,4163	no	missense	MUC16	NM_024690.2	29	0,1,6164	TT,TC,CC		0.0,0.025,0.0081	benign	15/14508	9091771	1,12329	2002	4163	6165	SO:0001583	missense	94025	exon1			AAGGAGCGGGTGG	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.44G>A	19.37:g.9091771C>T	ENSP00000381008:p.Arg15His	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	0.061	-1.224947	0.01530	2.5E-4	0.0	ENSG00000181143	ENST00000397910	T	0.02916	4.11	1.35	-2.7	0.06004	.	.	.	.	.	T	0.01421	0.0046	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.47018	-0.9149	8	0.87932	D	0	.	0.3222	0.00305	0.1936:0.1814:0.2537:0.3713	.	15	B5ME49	.	H	15	ENSP00000381008:R15H	ENSP00000381008:R15H	R	-	2	0	MUC16	8952771	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.995000	0.00317	-2.527000	0.00494	-2.577000	0.00169	CGC	.	.	weak		0.532	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GPD2	2820	hgsc.bcm.edu	37	2	157406249	157406249	+	Missense_Mutation	SNP	G	G	A	rs2116665	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:157406249G>A	ENST00000310454.6	+	7	1163	c.791G>A	c.(790-792)cGt>cAt	p.R264H	GPD2_ENST00000540309.1_Missense_Mutation_p.R264H|GPD2_ENST00000438166.2_Missense_Mutation_p.R264H|GPD2_ENST00000409674.1_Missense_Mutation_p.R264H|GPD2_ENST00000409125.4_Missense_Mutation_p.R37H	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	264			R -> H (in dbSNP:rs2116665). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7821823, ECO:0000269|PubMed:8549872, ECO:0000269|PubMed:8682323, ECO:0000269|PubMed:9110174, ECO:0000269|Ref.4, ECO:0000269|Ref.6, ECO:0000269|Ref.8}.		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)	p.R264H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						GGGAAAGTGCGTGTGAGCGGC	0.522													G|||	3295	0.657947	0.4849	0.7032	5008	,	,		19139	0.7847		0.6889	False		,,,				2504	0.6973				p.R264H		Atlas-SNP	.											GPD2,caecum,carcinoma,0,2	GPD2	59	2	1	Substitution - Missense(1)	stomach(1)	c.G791A	GRCh37	CM012769	GPD2	M	rs2116665	PASS	.	G	HIS/ARG,HIS/ARG	2093,2313	572.1+/-383.2	503,1087,613	66.0	63.0	64.0		791,791	3.2	0.0	2	dbSNP_96	64	6102,2498	694.7+/-404.8	2144,1814,342	yes	missense,missense	GPD2	NM_000408.4,NM_001083112.2	29,29	2647,2901,955	AA,AG,GG		29.0465,47.5034,36.9906	possibly-damaging,possibly-damaging	264/728,264/728	157406249	8195,4811	2203	4300	6503	SO:0001583	missense	2820	exon7			AAGTGCGTGTGAG		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.791G>A	2.37:g.157406249G>A	ENSP00000308610:p.Arg264His	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	37	CCDS2202.1	1431	0.6552197802197802	228	0.4634146341463415	241	0.6657458563535912	441	0.7709790209790209	521	0.6873350923482849	G	7.674	0.687659	0.14973	0.475034	0.709535	ENSG00000115159	ENST00000310454;ENST00000409125;ENST00000438166;ENST00000540309;ENST00000409674	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	5.91	3.17	0.36434	FAD dependent oxidoreductase (1);	0.321794	0.38436	N	0.001700	T	0.00012	0.0000	L	0.51422	1.61	0.29245	P	0.872348	B	0.17038	0.02	B	0.15484	0.013	T	0.34800	-0.9814	9	0.51188	T	0.08	.	10.1454	0.42760	0.2664:0.0:0.7336:0.0	rs2116665;rs2228475;rs17847134;rs17858516;rs2116665	264	P43304	GPDM_HUMAN	H	264;37;264;264;264	ENSP00000308610:R264H;ENSP00000386484:R37H;ENSP00000409708:R264H;ENSP00000440892:R264H;ENSP00000386425:R264H	ENSP00000308610:R264H	R	+	2	0	GPD2	157114495	0.930000	0.31532	0.004000	0.12327	0.333000	0.28666	1.958000	0.40402	0.412000	0.25729	0.650000	0.86243	CGT	G|0.353;N|0.000	.	strong		0.522	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3		
KCNMA1	3778	hgsc.bcm.edu	37	10	78944590	78944590	+	Silent	SNP	G	G	A	rs1131824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:78944590G>A	ENST00000286628.8	-	4	686	c.687C>T	c.(685-687)ttC>ttT	p.F229F	KCNMA1_ENST00000372443.1_Silent_p.F229F|KCNMA1_ENST00000406533.3_Silent_p.F229F|KCNMA1_ENST00000286627.5_Silent_p.F229F|KCNMA1_ENST00000404771.3_Silent_p.F229F|KCNMA1_ENST00000404857.1_Silent_p.F229F|KCNMA1_ENST00000354353.5_Silent_p.F229F|KCNMA1_ENST00000372440.1_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	50	0	0		WXS	Illumina HiSeq	Phase_I	66	63	0.954545	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	
DNAAF3	352909	hgsc.bcm.edu	37	19	55673145	55673145	+	Missense_Mutation	SNP	C	C	T	rs58824375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55673145C>T	ENST00000524407.2	-	6	562	c.529G>A	c.(529-531)Ggc>Agc	p.G177S	DNAAF3_ENST00000455045.1_Missense_Mutation_p.G123S|DNAAF3_ENST00000527223.2_Missense_Mutation_p.G245S|DNAAF3_ENST00000587789.2_5'Flank|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000391720.4_Missense_Mutation_p.G224S|CTD-2587H24.5_ENST00000591665.1_RNA			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	177					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											CCTTTCTCGCCGCCAGCCCAG	0.716													a|||	645	0.128794	0.0688	0.2651	5008	,	,		11152	0.2034		0.0169	False		,,,				2504	0.1513				p.G245S		Atlas-SNP	.											.	.	.	.	0			c.G733A						PASS	.	C	SER/GLY	136,3542		2,132,1705	5.0	6.0	6.0		670	2.5	0.5	19	dbSNP_129	6	184,7672		1,182,3745	yes	missense	C19orf51	NM_178837.3	56	3,314,5450	TT,TC,CC		2.3422,3.6977,2.7744	possibly-damaging	224/589	55673145	320,11214	1839	3928	5767	SO:0001583	missense	352909	exon6			TCTCGCCGCCAGC	AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.529G>A	19.37:g.55673145C>T	ENSP00000432046:p.Gly177Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	37	CCDS59422.1	244	0.11172161172161173	36	0.07317073170731707	65	0.17955801104972377	129	0.22552447552447552	14	0.018469656992084433	C	8.896	0.955249	0.18507	0.036977	0.023422	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.16073	2.37;2.37	4.8	2.52	0.30459	.	0.361858	0.28067	N	0.016739	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;B;P;P	0.46220	0.874;0.414;0.708;0.621	B;B;B;B	0.35278	0.199;0.021;0.193;0.051	T	0.43572	-0.9383	9	0.11182	T	0.66	-18.1931	12.362	0.55209	0.3003:0.6997:0.0:0.0	rs58824375;rs62621003	245;123;198;177	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	S	245;123;224	ENSP00000394343:G123S;ENSP00000375600:G224S	ENSP00000301249:G245S	G	-	1	0	C19orf51	60364957	0.002000	0.14202	0.520000	0.27837	0.006000	0.05464	0.044000	0.13992	1.169000	0.42739	-0.233000	0.12211	GGC	C|0.886;T|0.114	0.114	strong		0.716	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
FANCA	2175	hgsc.bcm.edu	37	16	89825065	89825065	+	Silent	SNP	G	G	A	rs17226980	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89825065G>A	ENST00000389301.3	-	30	2931	c.2901C>T	c.(2899-2901)tcC>tcT	p.S967S	FANCA_ENST00000568369.1_Silent_p.S967S	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	967					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CTGAAGCCGAGGACTCAGGGA	0.537			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	361	0.0720847	0.0038	0.0187	5008	,	,		22388	0.2599		0.0646	False		,,,				2504	0.0164				p.S967S		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C2901T						PASS	.	G		76,4320	65.3+/-102.7	0,76,2122	121.0	110.0	114.0		2901	-4.4	0.0	16	dbSNP_123	114	696,7904	172.9+/-223.5	26,644,3630	no	coding-synonymous	FANCA	NM_000135.2		26,720,5752	AA,AG,GG		8.093,1.7288,5.9403		967/1456	89825065	772,12224	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon30	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGCCGAGGACTCA	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.2901C>T	16.37:g.89825065G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			G|0.933;A|0.067	0.067	strong		0.537	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
WIPF3	644150	hgsc.bcm.edu	37	7	29923970	29923970	+	Missense_Mutation	SNP	A	A	T	rs174965	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:29923970A>T	ENST00000409290.1	+	4	860	c.860A>T	c.(859-861)cAg>cTg	p.Q287L	WIPF3_ENST00000409123.1_Missense_Mutation_p.Q287L|WIPF3_ENST00000242140.5_Missense_Mutation_p.Q287L	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	287					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						CAAGATGCGCAGGAGCCTCCC	0.697													A|||	173	0.0345447	0.0015	0.0605	5008	,	,		4374	0.001		0.1213	False		,,,				2504	0.0061				p.Q287L		Atlas-SNP	.											.	WIPF3	46	.	0			c.A860T						PASS	.	A	LEU/GLN	27,2973		0,27,1473	3.0	3.0	3.0		860	-5.0	0.0	7	dbSNP_79	3	469,6569		17,435,3067	no	missense	WIPF3	NM_001080529.2	113	17,462,4540	TT,TA,AA		6.6638,0.9,4.9412	benign	287/484	29923970	496,9542	1500	3519	5019	SO:0001583	missense	644150	exon5			ATGCGCAGGAGCC	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.860A>T	7.37:g.29923970A>T	ENSP00000386878:p.Gln287Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_001080529	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	37	CCDS56472.1	131	0.059981684981684984	21	0.042682926829268296	27	0.07458563535911603	2	0.0034965034965034965	81	0.10686015831134564	A	7.463	0.645165	0.14451	0.009	0.066638	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.43294	0.95;0.95;0.95	3.74	-4.96	0.03038	.	0.805114	0.10114	N	0.714260	T	0.00328	0.0010	N	0.08118	0	0.09310	N	1	B	0.19817	0.039	B	0.15052	0.012	T	0.12477	-1.0546	10	0.31617	T	0.26	.	5.4435	0.16521	0.3404:0.4274:0.2321:0.0	rs174965	287	A6NGB9	WIPF3_HUMAN	L	287	ENSP00000386790:Q287L;ENSP00000386878:Q287L;ENSP00000242140:Q287L	ENSP00000242140:Q287L	Q	+	2	0	WIPF3	29890495	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.012000	0.12699	-1.305000	0.02327	-0.517000	0.04412	CAG	A|0.940;T|0.060	0.060	strong		0.697	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
CEP55	55165	hgsc.bcm.edu	37	10	95259979	95259979	+	Missense_Mutation	SNP	C	C	G	rs3740370	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	50	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	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	
FLG	2312	hgsc.bcm.edu	37	1	152277055	152277055	+	Missense_Mutation	SNP	C	C	G	rs2065955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152277055C>G	ENST00000368799.1	-	3	10342	c.10307G>C	c.(10306-10308)gGa>gCa	p.G3436A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3436	Ser-rich.		G -> A (in dbSNP:rs2065955).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCCGGGTGTCCACGAATGGT	0.597									Ichthyosis				C|||	2575	0.514177	0.7882	0.4481	5008	,	,		18425	0.6349		0.1481	False		,,,				2504	0.4427				p.G3436A		Atlas-SNP	.											.	FLG	900	.	0			c.G10307C						PASS	.	C	ALA/GLY	3017,1389	686.4+/-404.7	1050,917,236	295.0	296.0	295.0		10307	-1.1	0.0	1	dbSNP_94	295	1294,7306	254.0+/-279.5	122,1050,3128	no	missense	FLG	NM_002016.1	60	1172,1967,3364	GG,GC,CC		15.0465,31.5252,33.1462	possibly-damaging	3436/4062	152277055	4311,8695	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGGTGTCCACGAA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10307G>C	1.37:g.152277055C>G	ENSP00000357789:p.Gly3436Ala	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	260	111	0.426923	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	
NAAA	27163	hgsc.bcm.edu	37	4	76857309	76857309	+	Missense_Mutation	SNP	C	C	T	rs4859571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:76857309C>T	ENST00000286733.4	-	3	552	c.451G>A	c.(451-453)Gtc>Atc	p.V151I	NAAA_ENST00000399497.3_Missense_Mutation_p.V151I|NAAA_ENST00000507956.1_Missense_Mutation_p.V151I|NAAA_ENST00000507187.2_Missense_Mutation_p.V151I|NAAA_ENST00000505594.1_Missense_Mutation_p.V50I	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	151			V -> I (in dbSNP:rs4859571).		lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						TTGCGTAAGACATTCCCAAAA	0.408													T|||	1092	0.218051	0.084	0.2983	5008	,	,		17681	0.3581		0.2306	False		,,,				2504	0.1851				p.V151I		Atlas-SNP	.											.	NAAA	26	.	0			c.G451A						PASS	.	T	ILE/VAL,ILE/VAL	408,3322		19,370,1476	160.0	151.0	154.0		451,451	-10.3	0.0	4	dbSNP_111	154	1902,6306		221,1460,2423	yes	missense,missense	NAAA	NM_001042402.1,NM_014435.3	29,29	240,1830,3899	TT,TC,CC		23.1725,10.9383,19.35	benign,benign	151/324,151/360	76857309	2310,9628	1865	4104	5969	SO:0001583	missense	27163	exon3			GTAAGACATTCCC	M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"""N-acylsphingosine amidohydrolase (acid ceramidase)-like"""	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.451G>A	4.37:g.76857309C>T	ENSP00000286733:p.Val151Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_014435	Q5KTF2|Q96EY2|Q9BRA8	Missense_Mutation	SNP	ENST00000286733.4	37	CCDS43239.1	527	0.2413003663003663	34	0.06910569105691057	113	0.31215469613259667	219	0.38286713286713286	161	0.21240105540897097	T	0.031	-1.336236	0.01287	0.109383	0.231725	ENSG00000138744	ENST00000399497;ENST00000286733;ENST00000507956;ENST00000505594;ENST00000399490;ENST00000507187	T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;0.98	5.9	-10.3	0.00346	.	0.773311	0.12646	N	0.450872	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.08055	0.003;0.002;0.003	T	0.15235	-1.0444	9	0.18276	T	0.48	-0.2643	1.4382	0.02348	0.168:0.2887:0.258:0.2853	rs4859571;rs52819073;rs60609159;rs4859571	50;151;151	B4DVL2;D6R9S9;Q02083	.;.;NAAA_HUMAN	I	151;151;151;50;151;151	ENSP00000382420:V151I;ENSP00000286733:V151I;ENSP00000427641:V151I;ENSP00000426977:V50I;ENSP00000423142:V151I	ENSP00000286733:V151I	V	-	1	0	NAAA	77076333	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.818000	0.04467	-2.251000	0.00700	-3.866000	0.00017	GTC	C|0.772;N|0.000	.	strong		0.408	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4		
OR51F1	256892	hgsc.bcm.edu	37	11	4790471	4790471	+	Missense_Mutation	SNP	G	G	A	rs1030723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790471G>A	ENST00000380383.1	-	1	697	c.698C>T	c.(697-699)tCt>tTt	p.S233F	OR51F1_ENST00000343430.3_Missense_Mutation_p.S226F|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			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	134	0	0		WXS	Illumina HiSeq	Phase_I	136	74	0.544118	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	4790474	4790474	+	Missense_Mutation	SNP	T	T	C	rs11033793	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790474T>C	ENST00000380383.1	-	1	694	c.695A>G	c.(694-696)cAc>cGc	p.H232R	OR51F1_ENST00000343430.3_Missense_Mutation_p.H225R|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	232			H -> R (in dbSNP:rs11033793).			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)		GAGGACAGAGTGAATAATTAA	0.448													T|||	837	0.167133	0.4418	0.1052	5008	,	,		22196	0.0		0.1292	False		,,,				2504	0.0511				p.H225R		Atlas-SNP	.											.	OR51F1	60	.	0			c.A674G						PASS	.	T	ARG/HIS	1716,2686	506.9+/-366.5	356,1004,841	127.0	124.0	125.0		674	-0.4	0.1	11	dbSNP_120	125	1018,7578	217.7+/-256.3	74,870,3354	no	missense	OR51F1	NM_001004752.1	29	430,1874,4195	CC,CT,TT		11.8427,38.9823,21.034	benign	225/313	4790474	2734,10264	2201	4298	6499	SO:0001583	missense	256892	exon1			ACAGAGTGAATAA	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.695A>G	11.37:g.4790474T>C	ENSP00000369744:p.His232Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		325	0.1488095238095238	211	0.42886178861788615	34	0.09392265193370165	0	0.0	80	0.10554089709762533	T	0.004	-2.366994	0.00212	0.389823	0.118427	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.33865	1.39;1.39	5.24	-0.433	0.12287	GPCR, rhodopsin-like superfamily (1);	0.597682	0.15860	N	0.241076	T	0.00012	0.0000	N	0.02213	-0.635	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.45026	-0.9289	9	0.02654	T	1	.	9.7685	0.40576	0.0:0.5207:0.0:0.4792	rs11033793;rs52795109;rs57688765;rs11033793	232	A6NGY5	O51F1_HUMAN	R	225;232	ENSP00000345163:H225R;ENSP00000369744:H232R	ENSP00000345163:H225R	H	-	2	0	OR51F1	4747050	0.000000	0.05858	0.057000	0.19452	0.394000	0.30568	-3.406000	0.00482	-0.244000	0.09639	0.533000	0.62120	CAC	T|0.810;C|0.190	0.190	strong		0.448	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
MINA	84864	hgsc.bcm.edu	37	3	97664725	97664725	+	Missense_Mutation	SNP	C	C	T	rs2172257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:97664725C>T	ENST00000333396.7	-	9	1738	c.1156G>A	c.(1156-1158)Gct>Act	p.A386T	MINA_ENST00000360258.4_Missense_Mutation_p.A385T|MINA_ENST00000394198.2_Missense_Mutation_p.A386T	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						TTTTCTTGAGCTTCATCCTTT	0.378													C|||	2394	0.478035	0.2648	0.5101	5008	,	,		20013	0.6746		0.5119	False		,,,				2504	0.5061				p.A386T		Atlas-SNP	.											MINA,NS,carcinoma,0,1	MINA	39	1	0			c.G1156A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	1283,3123	433.1+/-343.5	193,897,1113	133.0	115.0	121.0		1156,1153,1156	1.6	1.0	3	dbSNP_96	121	4426,4172	583.6+/-391.6	1159,2108,1032	yes	missense,missense,missense	MINA	NM_001042533.1,NM_032778.4,NM_153182.2	58,58,58	1352,3005,2145	TT,TC,CC		48.5229,29.1194,43.9019	benign,benign,benign	386/466,385/465,386/466	97664725	5709,7295	2203	4299	6502	SO:0001583	missense	84864	exon9			CTTGAGCTTCATC	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.1156G>A	3.37:g.97664725C>T	ENSP00000328251:p.Ala386Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_001042533		Missense_Mutation	SNP	ENST00000333396.7	37	CCDS43114.1	1109	0.5077838827838828	142	0.2886178861788618	165	0.4558011049723757	405	0.708041958041958	397	0.5237467018469657	C	8.856	0.945657	0.18356	0.291194	0.514771	ENSG00000170854	ENST00000442492;ENST00000333396;ENST00000394198;ENST00000360258	T;T;T	0.12255	2.71;2.71;2.7	6.06	1.6	0.23607	.	0.621890	0.17779	N	0.162312	T	0.00012	0.0000	N	0.12569	0.235	0.53005	P	3.6999999999953737E-5	B;B	0.11235	0.004;0.002	B;B	0.14023	0.01;0.004	T	0.20706	-1.0267	9	0.11485	T	0.65	-4.6032	5.47	0.16664	0.141:0.4433:0.0:0.4158	rs2172257;rs3736365;rs11542931;rs17851250;rs52824313;rs57113083;rs2172257	385;386	Q8IUF8-4;Q8IUF8	.;MINA_HUMAN	T	132;386;386;385	ENSP00000328251:A386T;ENSP00000377748:A386T;ENSP00000353395:A385T	ENSP00000328251:A386T	A	-	1	0	MINA	99147415	0.066000	0.20996	0.999000	0.59377	0.733000	0.41908	-0.512000	0.06313	0.311000	0.23014	0.650000	0.86243	GCT	C|0.535;T|0.465	0.465	strong		0.378	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778	
WDR78	79819	hgsc.bcm.edu	37	1	67327894	67327894	+	Silent	SNP	A	A	G	rs34182923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:67327894A>G	ENST00000371026.3	-	7	1087	c.1032T>C	c.(1030-1032)agT>agC	p.S344S	WDR78_ENST00000371023.3_Silent_p.S344S|WDR78_ENST00000493572.1_5'UTR|WDR78_ENST00000431318.1_Silent_p.S90S	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	344					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						TTGCTTTACTACTTGACTCAA	0.338													A|||	87	0.0173722	0.0023	0.0159	5008	,	,		18825	0.0228		0.0189	False		,,,				2504	0.0317				p.S344S		Atlas-SNP	.											.	WDR78	102	.	0			c.T1032C						PASS	.	A	,	26,4380	33.5+/-64.1	0,26,2177	108.0	108.0	108.0		1032,1032	-2.6	0.0	1	dbSNP_126	108	218,8382	91.9+/-153.9	1,216,4083	yes	coding-synonymous,coding-synonymous	WDR78	NM_024763.4,NM_207014.2	,	1,242,6260	GG,GA,AA		2.5349,0.5901,1.8761	,	344/849,344/546	67327894	244,12762	2203	4300	6503	SO:0001819	synonymous_variant	79819	exon7			TTTACTACTTGAC	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.1032T>C	1.37:g.67327894A>G		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	341	167	0.489736	NM_207014	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Silent	SNP	ENST00000371026.3	37	CCDS635.1	33	0.01510989010989011	2	0.0040650406504065045	8	0.022099447513812154	12	0.02097902097902098	11	0.014511873350923483	A	3.430	-0.116389	0.06881	0.005901	0.025349	ENSG00000152763	ENST00000469450	.	.	.	4.38	-2.56	0.06268	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3879	5.1919	0.15214	0.5182:0.0:0.3481:0.1337	rs34182923	.	.	.	Q	78	.	.	X	-	1	0	WDR78	67100482	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.878000	0.04192	-0.390000	0.07774	-1.120000	0.02017	TAG	A|0.982;G|0.018	0.018	strong		0.338	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
FLG	2312	hgsc.bcm.edu	37	1	152276659	152276659	+	Missense_Mutation	SNP	T	T	C	rs7532285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276659T>C	ENST00000368799.1	-	3	10738	c.10703A>G	c.(10702-10704)cAg>cGg	p.Q3568R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3568	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGACTGCTCCTGAGCAGATCC	0.567									Ichthyosis				t|||	1035	0.206669	0.2133	0.1916	5008	,	,		18266	0.3403		0.0696	False		,,,				2504	0.2117				p.Q3568R		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A10703G						scavenged	.						148.0	201.0	183.0					1																	152276659		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCTCCTGAGCAG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10703A>G	1.37:g.152276659T>C	ENSP00000357789:p.Gln3568Arg	Somatic	380	0	0		WXS	Illumina HiSeq	Phase_I	296	36	0.121622	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	
FGF21	26291	hgsc.bcm.edu	37	19	49259529	49259529	+	Silent	SNP	A	A	G	rs838133	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49259529A>G	ENST00000593756.1	+	2	608	c.36A>G	c.(34-36)ggA>ggG	p.G12G	FUT1_ENST00000601931.1_5'Flank|FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Silent_p.G12G			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	12					cell-cell signaling (GO:0007267)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		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;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		AGCACTCAGGACTGTGGGTTT	0.607													A|||	3865	0.771765	0.739	0.7478	5008	,	,		15268	0.994		0.5746	False		,,,				2504	0.8067				p.G12G		Atlas-SNP	.											FGF21,NS,carcinoma,+1,1	FGF21	21	1	0			c.A36G						PASS	.	A		3090,1316	695.2+/-405.9	1090,910,203	76.0	57.0	64.0		36	0.8	1.0	19	dbSNP_86	64	4817,3783	612.2+/-395.9	1340,2137,823	no	coding-synonymous	FGF21	NM_019113.2		2430,3047,1026	GG,GA,AA		43.9884,29.8684,39.205		12/210	49259529	7907,5099	2203	4300	6503	SO:0001819	synonymous_variant	26291	exon1			CTCAGGACTGTGG	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.36A>G	19.37:g.49259529A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	172	91	0.52907	NM_019113	Q8N683	Silent	SNP	ENST00000593756.1	37	CCDS12734.1																																																																																			A|0.337;G|0.663	0.663	strong		0.607	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1		
LRGUK	136332	hgsc.bcm.edu	37	7	133884016	133884016	+	Silent	SNP	C	C	T	rs61749958		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:133884016C>T	ENST00000285928.2	+	14	1659	c.1590C>T	c.(1588-1590)atC>atT	p.I530I		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	530	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						CTCGTTATATCCTGGTGGTGC	0.368																																					p.I530I		Atlas-SNP	.											.	LRGUK	113	.	0			c.C1590T						PASS	.	C		0,4406		0,0,2203	93.0	98.0	96.0		1590	5.2	1.0	7	dbSNP_129	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	LRGUK	NM_144648.1		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		530/826	133884016	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon14			TTATATCCTGGTG	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.1590C>T	7.37:g.133884016C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	180	80	0.444444	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			C|1.000;T|0.000	0.000	weak		0.368	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
FAIM	55179	hgsc.bcm.edu	37	3	138347957	138347957	+	Missense_Mutation	SNP	G	G	A	rs641320	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:138347957G>A	ENST00000393035.2	+	4	458	c.349G>A	c.(349-351)Gct>Act	p.A117T	FAIM_ENST00000338446.4_Missense_Mutation_p.A151T|FAIM_ENST00000464668.1_Missense_Mutation_p.A117T|FAIM_ENST00000360570.3_Missense_Mutation_p.A139T|FAIM_ENST00000393034.2_Missense_Mutation_p.A117T	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule	117			A -> T (in dbSNP:rs641320). {ECO:0000269|PubMed:12107411, ECO:0000269|Ref.2}.		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						AGAAAAAGATGCTATGGACGT	0.313													A|||	1180	0.235623	0.7466	0.0994	5008	,	,		17034	0.0179		0.0606	False		,,,				2504	0.046				p.A151T		Atlas-SNP	.											.	FAIM	27	.	0			c.G451A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA,THR/ALA	2932,1474	474.6+/-357.0	970,992,241	113.0	132.0	126.0		451,415,349,349	4.9	1.0	3	dbSNP_83	126	592,8008	792.6+/-407.5	16,560,3724	yes	missense,missense,missense,missense	FAIM	NM_001033030.1,NM_001033031.1,NM_001033032.1,NM_018147.3	58,58,58,58	986,1552,3965	AA,AG,GG		6.8837,33.4544,27.0952	benign,benign,benign,benign	151/214,139/202,117/180,117/180	138347957	3524,9482	2203	4300	6503	SO:0001583	missense	55179	exon5			AAAGATGCTATGG	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.349G>A	3.37:g.138347957G>A	ENSP00000376755:p.Ala117Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	111	47	0.423423	NM_001033030	Q6IAN2	Missense_Mutation	SNP	ENST00000393035.2	37	CCDS3103.1	433	0.19826007326007325	347	0.7052845528455285	38	0.10497237569060773	7	0.012237762237762238	41	0.05408970976253298	A	8.813	0.935676	0.18206	0.665456	0.068837	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94	4.94	4.94	0.65067	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00086	-2.195	0.44762	P	0.002230999999999983	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	0.40646	-0.9552	9	0.02654	T	1	-9.6295	9.1785	0.37127	0.9132:0.0:0.0868:0.0	rs641320;rs1136173;rs1672961;rs52819534;rs56548670;rs61598503;rs641320	117;139;151;117	Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2;C9JDZ2	FAIM1_HUMAN;.;.;.	T	151;139;117;117;117;117	ENSP00000342805:A151T;ENSP00000353775:A139T;ENSP00000376755:A117T;ENSP00000376754:A117T;ENSP00000417642:A117T;ENSP00000420543:A117T	ENSP00000342805:A151T	A	+	1	0	FAIM	139830647	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.898000	0.75676	1.013000	0.39391	-0.254000	0.11334	GCT	G|0.743;T|0.004	.	strong		0.313	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032	
FLG	2312	hgsc.bcm.edu	37	1	152285930	152285930	+	Missense_Mutation	SNP	G	G	A	rs11584340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152285930G>A	ENST00000368799.1	-	3	1467	c.1432C>T	c.(1432-1434)Cct>Tct	p.P478S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	478	Ser-rich.		P -> S (in dbSNP:rs11584340).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCAGAGTCAGGCTGTTCATGA	0.612									Ichthyosis				-|||	1726	0.344649	0.1286	0.4222	5008	,	,		18652	0.6062		0.171	False		,,,				2504	0.4908				p.P478S		Atlas-SNP	.											.	FLG	900	.	0			c.C1432T	GRCh37	CM084968	FLG	M	rs11584340	PASS	.	A	SER/PRO	615,3791		44,527,1632	220.0	210.0	214.0		1432	-3.1	0.0	1	dbSNP_120	214	1444,7156		124,1196,2980	yes	missense	FLG	NM_002016.1	74	168,1723,4612	AA,AG,GG		16.7907,13.9582,15.8312	benign	478/4062	152285930	2059,10947	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTCAGGCTGTTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1432C>T	1.37:g.152285930G>A	ENSP00000357789:p.Pro478Ser	Somatic	300	1	0.00333333		WXS	Illumina HiSeq	Phase_I	337	171	0.507418	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	684	0.3131868131868132	72	0.14634146341463414	125	0.3453038674033149	355	0.6206293706293706	132	0.1741424802110818	-	4.251	0.045625	0.08196	0.139582	0.167907	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00873	5.59	3.05	-3.12	0.05282	.	.	.	.	.	T	0.00073	0.0002	N	0.00260	-1.75	0.80722	P	0.0	B	0.17038	0.02	B	0.21360	0.034	T	0.30149	-0.9988	8	0.02654	T	1	.	3.0665	0.06217	0.3181:0.0:0.3425:0.3394	rs11584340;rs52819317;rs11584340	478	P20930	FILA_HUMAN	S	478;10	ENSP00000357789:P478S	ENSP00000357789:P478S	P	-	1	0	FLG	150552554	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.893000	0.01609	-1.350000	0.02199	-1.441000	0.01070	CCT	G|0.785;A|0.215	0.215	strong		0.612	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
EPPK1	83481	hgsc.bcm.edu	37	8	144944379	144944379	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144944379A>G	ENST00000525985.1	-	2	3114	c.3043T>C	c.(3043-3045)Ttc>Ctc	p.F1015L				P58107	EPIPL_HUMAN	epiplakin 1	1015						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)			TTCCCAGAGAAGGGGTCTCTG	0.637																																					p.F1015L		Atlas-SNP	.											.	EPPK1	199	.	0			c.T3043C						PASS	.						14.0	17.0	16.0					8																	144944379		2067	4201	6268	SO:0001583	missense	83481	exon1			CAGAGAAGGGGTC	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.3043T>C	8.37:g.144944379A>G	ENSP00000436337:p.Phe1015Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	A	22.5	4.295045	0.81025	.	.	ENSG00000227184	ENST00000525985	T	0.67523	-0.27	4.67	3.52	0.40303	.	.	.	.	.	T	0.51890	0.1701	L	0.39898	1.24	0.24399	N	0.994711	B	0.16166	0.016	B	0.10450	0.005	T	0.35649	-0.9780	9	0.09843	T	0.71	.	8.3157	0.32100	0.9051:0.0:0.0949:0.0	.	1015	E9PPU0	.	L	1015	ENSP00000436337:F1015L	ENSP00000436337:F1015L	F	-	1	0	EPPK1	145016367	1.000000	0.71417	0.481000	0.27354	0.918000	0.54935	6.916000	0.75776	0.809000	0.34255	0.533000	0.62120	TTC	.	.	none		0.637	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ATG2B	55102	hgsc.bcm.edu	37	14	96829302	96829302	+	Silent	SNP	C	C	T	rs72706804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:96829302C>T	ENST00000359933.4	-	1	905	c.12G>A	c.(10-12)ccG>ccA	p.P4P	GSKIP_ENST00000555181.1_5'Flank|GSKIP_ENST00000554182.1_5'Flank|GSKIP_ENST00000556095.1_5'Flank	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	4					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)		ACTCCGAAAACGGCCAAGGCA	0.672													C|||	38	0.00758786	0.0008	0.013	5008	,	,		15753	0.001		0.0239	False		,,,				2504	0.0031				p.P4P		Atlas-SNP	.											.	ATG2B	169	.	0			c.G12A						PASS	.	C		17,4211		0,17,2097	52.0	56.0	54.0		12	0.9	0.7	14	dbSNP_130	54	195,8315		0,195,4060	no	coding-synonymous	ATG2B	NM_018036.5		0,212,6157	TT,TC,CC		2.2914,0.4021,1.6643		4/2079	96829302	212,12526	2114	4255	6369	SO:0001819	synonymous_variant	55102	exon1			CGAAAACGGCCAA	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.12G>A	14.37:g.96829302C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	142	63	0.443662	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	CCDS9944.2																																																																																			C|0.986;T|0.014	0.014	strong		0.672	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
ASB11	140456	hgsc.bcm.edu	37	X	15332558	15332558	+	Intron	SNP	A	A	G	rs5935944	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:15332558A>G	ENST00000480796.1	-	1	232				ASB11_ENST00000344384.4_Silent_p.R17R|ASB11_ENST00000537676.1_Silent_p.R17R|ASB11_ENST00000380470.3_Intron			Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box containing 11, E3 ubiquitin protein ligase						intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(1)	16	Hepatocellular(33;0.183)					ACCTTCTGATACGTTCTGAAA	0.363													A|||	1356	0.359205	0.1059	0.2161	3775	,	,		13644	0.3185		0.2952	False		,,,				2504	0.4581				p.R17R		Atlas-SNP	.											.	ASB11	79	.	0			c.T51C						PASS	.	A	,,	751,3084		61,504,125,1067,446	141.0	125.0	131.0		51,,	5.8	0.1	X	dbSNP_114	131	2634,4094		381,1177,695,870,1177	no	coding-synonymous,intron,intron	ASB11	NM_001012428.2,NM_001201583.1,NM_080873.2	,,	442,1681,820,1937,1623	GG,GA,G,AA,A		39.1498,19.5828,32.0458	,,	17/303,,	15332558	3385,7178	2203	4300	6503	SO:0001627	intron_variant	140456	exon1			TCTGATACGTTCT	AF425642	CCDS14164.1, CCDS35209.1, CCDS56596.1	Xp22.31	2014-02-10	2014-02-10		ENSG00000165192	ENSG00000165192		"""Ankyrin repeat domain containing"""	17186	protein-coding gene	gene with protein product		300626	"""ankyrin repeat and SOCS box-containing 11"", ""ankyrin repeat and SOCS box containing 11"""			24337577	Standard	NM_080873		Approved	DKFZp779E2460	uc004cwp.2	Q8WXH4	OTTHUMG00000021173	ENST00000480796.1:c.181+988T>C	X.37:g.15332558A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_001012428	E9PEN1|Q3SYC4|Q7Z667	Silent	SNP	ENST00000480796.1	37	CCDS14164.1																																																																																			A|0.680;0|0.003	.	strong		0.363	ASB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055852.2		
ATXN1	6310	hgsc.bcm.edu	37	6	16327903	16327903	+	Missense_Mutation	SNP	C	C	A	rs3817753		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:16327903C>A	ENST00000244769.4	-	8	1575	c.639G>T	c.(637-639)caG>caT	p.Q213H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q213H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	213	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)				gctgctgctgctgctgatgct	0.667																																					p.Q213H		Atlas-SNP	.											ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	0			c.G639T						scavenged	.						5.0	8.0	7.0					6																	16327903		1624	3504	5128	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGA	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.639G>T	6.37:g.16327903C>A	ENSP00000244769:p.Gln213His	Somatic	59	2	0.0338983		WXS	Illumina HiSeq	Phase_I	61	13	0.213115	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	221	0.10119047619047619	38	0.07723577235772358	47	0.1298342541436464	89	0.1555944055944056	47	0.06200527704485488	C	4.787	0.146322	0.09134	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.62941	-0.01;-0.01	.	.	.	.	.	.	.	.	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.19582	-1.0301	5	0.45353	T	0.12	.	.	.	.	rs3817753	213	P54253	ATX1_HUMAN	H	213	ENSP00000244769:Q213H;ENSP00000416360:Q213H	ENSP00000244769:Q213H	Q	-	3	2	ATXN1	16435882	0.034000	0.19679	0.018000	0.16275	0.072000	0.16883	0.306000	0.19279	0.000000	0.14550	0.000000	0.15137	CAG	C|0.899;A|0.101	0.101	strong		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
COLGALT1	79709	hgsc.bcm.edu	37	19	17670201	17670201	+	Silent	SNP	C	C	T	rs62119894	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17670201C>T	ENST00000252599.4	+	2	462	c.342C>T	c.(340-342)tcC>tcT	p.S114S		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	114					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										TGTACCATTCCGTGGAGTGGC	0.597													c|||	472	0.0942492	0.0053	0.2277	5008	,	,		15298	0.0714		0.0616	False		,,,				2504	0.1769				p.S114S		Atlas-SNP	.											.	.	.	.	0			c.C342T						PASS	.	C		63,4225		0,63,2081	123.0	93.0	103.0		342	-6.4	0.9	19	dbSNP_129	103	453,7929		8,437,3746	no	coding-synonymous	GLT25D1	NM_024656.2		8,500,5827	TT,TC,CC		5.4044,1.4692,4.0726		114/623	17670201	516,12154	2144	4191	6335	SO:0001819	synonymous_variant	79709	exon2			CCATTCCGTGGAG	AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"""glycosyltransferase 25 domain containing 1"""	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.342C>T	19.37:g.17670201C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_024656	Q8NC64	Silent	SNP	ENST00000252599.4	37	CCDS12363.1																																																																																			C|0.942;T|0.058	0.058	strong		0.597	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240511	39240511	+	Missense_Mutation	SNP	A	A	T	rs383835	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39240511A>T	ENST00000391417.4	+	1	53	c.53A>T	c.(52-54)gAc>gTc	p.D18V		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	18	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		D -> V. {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						TGCAGCCAAGACCTCTGTCAG	0.612													a|||	2763	0.551717	0.6445	0.6081	5008	,	,		14149	0.3879		0.6024	False		,,,				2504	0.5031				p.D18V		Atlas-SNP	.											.	KRTAP4-7	49	.	0			c.A53T						PASS	.						9.0	17.0	15.0					17																	39240511		677	1582	2259	SO:0001583	missense	100132476	exon1			GCCAAGACCTCTG	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.53A>T	17.37:g.39240511A>T	ENSP00000375236:p.Asp18Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	1033	0.47298534798534797	274	0.556910569105691	200	0.5524861878453039	184	0.32167832167832167	375	0.4947229551451187	.	0.459	-0.889937	0.02511	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00608	6.25	1.02	-1.55	0.08558	.	0.471385	0.15244	U	0.272684	T	0.00012	0.0000	.	.	.	0.53688	P	2.2999999999995246E-5	B	0.20261	0.043	B	0.12156	0.007	T	0.14924	-1.0455	8	0.45353	T	0.12	.	2.8192	0.05467	0.404:0.251:0.345:0.0	rs62068121	18	Q9BYR0	KRA47_HUMAN	V	18	ENSP00000375236:D18V	ENSP00000375236:D18V	D	+	2	0	KRTAP4-9;KRTAP4-7	36494037	0.086000	0.21541	0.114000	0.21550	0.074000	0.17049	0.065000	0.14466	-0.591000	0.05859	0.260000	0.18958	GAC	A|0.527;T|0.473	0.473	strong		0.612	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
ALG1	56052	hgsc.bcm.edu	37	16	5132636	5132636	+	Silent	SNP	C	C	T	rs1047732	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:5132636C>T	ENST00000262374.5	+	11	1180	c.1149C>T	c.(1147-1149)ttC>ttT	p.F383F	ALG1_ENST00000588623.1_Silent_p.F272F|ALG1_ENST00000544428.1_Silent_p.F272F	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	383					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				TGGACATGTTCGGGTGCTGTT	0.592													C|||	2603	0.519768	0.3903	0.415	5008	,	,		20459	0.629		0.495	False		,,,				2504	0.682				p.F383F		Atlas-SNP	.											.	ALG1	35	.	0			c.C1149T						PASS	.	C		1679,2475		348,983,746	87.0	66.0	73.0		1149	-3.4	1.0	16	dbSNP_86	73	3990,3934		1038,1914,1010	no	coding-synonymous	ALG1	NM_019109.4		1386,2897,1756	TT,TC,CC		49.6466,40.4189,46.9366		383/465	5132636	5669,6409	2077	3962	6039	SO:0001819	synonymous_variant	56052	exon11			CATGTTCGGGTGC	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.1149C>T	16.37:g.5132636C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Silent	SNP	ENST00000262374.5	37	CCDS10528.1																																																																																			C|0.536;T|0.464	0.464	strong		0.592	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
PTCHD4	442213	hgsc.bcm.edu	37	6	47847179	47847179	+	Silent	SNP	A	A	G	rs3799276	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:47847179A>G	ENST00000339488.4	-	3	1434	c.1401T>C	c.(1399-1401)gtT>gtC	p.V467V		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	467						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										AGAGGATGACAACAAATGGCT	0.443													G|||	3734	0.745607	0.6445	0.8516	5008	,	,		21602	0.8016		0.7475	False		,,,				2504	0.7474				p.V467V		Atlas-SNP	.											.	.	.	.	0			c.T1401C						PASS	.	G		2937,1469	473.1+/-356.6	988,961,254	110.0	100.0	104.0		1401	-11.3	0.1	6	dbSNP_107	104	6405,2195	373.7+/-337.1	2398,1609,293	no	coding-synonymous	C6orf138	NM_001013732.3		3386,2570,547	GG,GA,AA		25.5233,33.3409,28.1716		467/847	47847179	9342,3664	2203	4300	6503	SO:0001819	synonymous_variant	442213	exon3			GATGACAACAAAT		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 138"""	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1401T>C	6.37:g.47847179A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_001013732	B0QZ29|B4DRK3|Q5T884	Silent	SNP	ENST00000339488.4	37	CCDS34473.2																																																																																			A|0.279;G|0.721	0.721	strong		0.443	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732	
ZNF229	7772	hgsc.bcm.edu	37	19	44932972	44932972	+	Missense_Mutation	SNP	C	C	T	rs1434579	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44932972C>T	ENST00000588931.1	-	6	2417	c.1984G>A	c.(1984-1986)Gga>Aga	p.G662R	ZNF229_ENST00000291187.4_Missense_Mutation_p.G656R|ZNF229_ENST00000591289.1_Intron|CTC-512J12.4_ENST00000588655.1_RNA	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	662			G -> R (in dbSNP:rs1434579). {ECO:0000269|Ref.4}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AAGCCCTTTCCGCACTCTTGG	0.493													C|||	1442	0.287939	0.0484	0.2608	5008	,	,		22657	0.3294		0.3598	False		,,,				2504	0.5143				p.G662R		Atlas-SNP	.											ZNF229,NS,carcinoma,+1,1	ZNF229	123	1	0			c.G1984A						PASS	.	C	ARG/GLY	393,3919		20,353,1783	126.0	127.0	127.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1984	3.5	0.0	19	dbSNP_88	127	2912,5640		507,1898,1871	yes	missense	ZNF229	NM_014518.2	125	527,2251,3654	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	34.0505,9.1141,25.6919	probably-damaging	662/826	44932972	3305,9559	2156	4276	6432	SO:0001583	missense	7772	exon6			CCTTTCCGCACTC	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1984G>A	19.37:g.44932972C>T	ENSP00000466519:p.Gly662Arg	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	570	0.260989010989011	20	0.04065040650406504	94	0.2596685082872928	182	0.3181818181818182	274	0.36147757255936674	C	22.8	4.337383	0.81911	0.091141	0.340505	ENSG00000167383	ENST00000291187	.	.	.	3.5	3.5	0.40072	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.81497	2.545	0.26784	P	0.969539	D	0.89917	1.0	D	0.67231	0.95	T	0.04005	-1.0985	7	0.59425	D	0.04	.	14.1802	0.65568	0.0:1.0:0.0:0.0	rs1434579;rs17347602;rs52817635;rs59210988;rs1434579	662	Q9UJW7	ZN229_HUMAN	R	662	.	ENSP00000291187:G662R	G	-	1	0	ZNF229	49624812	0.197000	0.23362	0.030000	0.17652	0.143000	0.21401	1.720000	0.38022	1.677000	0.50941	0.609000	0.83330	GGA	C|0.728;T|0.272	0.272	strong		0.493	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
GPR126	57211	hgsc.bcm.edu	37	6	142691549	142691549	+	Missense_Mutation	SNP	A	A	C	rs11155242	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:142691549A>C	ENST00000230173.6	+	4	1164	c.688A>C	c.(688-690)Aaa>Caa	p.K230Q	GPR126_ENST00000367608.2_Missense_Mutation_p.K230Q|GPR126_ENST00000367609.3_Missense_Mutation_p.K230Q|GPR126_ENST00000296932.8_Missense_Mutation_p.K230Q|GPR126_ENST00000545477.1_Intron	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	230	Pentaxin.		K -> Q (in dbSNP:rs11155242). {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)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TTCTGATTCAAAATGTTTGTT	0.383													A|||	984	0.196486	0.23	0.196	5008	,	,		19300	0.0863		0.2276	False		,,,				2504	0.2331				p.K230Q		Atlas-SNP	.											.	GPR126	192	.	0			c.A688C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	761,2903		75,611,1146	57.0	55.0	56.0		688,688,688,688	4.3	0.8	6	dbSNP_120	56	1586,6596		178,1230,2683	yes	missense,missense,missense,missense	GPR126	NM_001032394.2,NM_001032395.2,NM_020455.5,NM_198569.2	53,53,53,53	253,1841,3829	CC,CA,AA		19.384,20.7697,19.8126	benign,benign,benign,benign	230/1194,230/1223,230/1222,230/1251	142691549	2347,9499	1832	4091	5923	SO:0001583	missense	57211	exon4			GATTCAAAATGTT	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"""-"", ""GPCR / Class B : Orphans"""	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.688A>C	6.37:g.142691549A>C	ENSP00000230173:p.Lys230Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	374	0.17124542124542125	102	0.2073170731707317	60	0.16574585635359115	56	0.0979020979020979	156	0.20580474934036938	A	2.081	-0.410801	0.04799	0.207697	0.19384	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609;ENST00000541199	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;3.12	5.4	4.27	0.50696	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.286838	0.30639	N	0.009188	T	0.20210	0.0486	L	0.28274	0.84	0.58432	P	2.9999999999752447E-6	B;B;B;B;B	0.19583	0.007;0.007;0.007;0.008;0.037	B;B;B;B;B	0.20955	0.019;0.019;0.019;0.032;0.008	T	0.06303	-1.0834	9	0.25751	T	0.34	.	4.2399	0.10643	0.3837:0.4537:0.1625:0.0	rs11155242;rs17280363;rs52807181;rs58038778;rs11155242	230;230;230;230;229	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4;F5H2L1	.;.;.;GP126_HUMAN;.	Q	230;230;230;230;229	ENSP00000230173:K230Q;ENSP00000356580:K230Q;ENSP00000296932:K230Q;ENSP00000356581:K230Q;ENSP00000446287:K229Q	ENSP00000230173:K230Q	K	+	1	0	GPR126	142733242	0.577000	0.26708	0.811000	0.32455	0.239000	0.25481	1.027000	0.30115	2.054000	0.61138	0.528000	0.53228	AAA	A|0.830;C|0.170	0.170	strong		0.383	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
FLT3	2322	hgsc.bcm.edu	37	13	28624294	28624294	+	Missense_Mutation	SNP	G	G	A	rs1933437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28624294G>A	ENST00000241453.7	-	6	761	c.680C>T	c.(679-681)aCg>aTg	p.T227M	FLT3_ENST00000380982.4_Missense_Mutation_p.T227M|FLT3_ENST00000537084.1_Missense_Mutation_p.T227M	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	227			T -> M (in dbSNP:rs1933437). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8394751, ECO:0000269|Ref.4}.		B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|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)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCTTATGTCCGTCCCAAATAA	0.398			"""Mis, O"""		"""AML, ALL"""								G|||	2798	0.558706	0.2844	0.6066	5008	,	,		21258	0.7688		0.5805	False		,,,				2504	0.6564				p.T227M		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C680T						PASS	.	G	MET/THR	1513,2893	481.0+/-359.0	264,985,954	162.0	136.0	145.0		680	3.8	0.6	13	dbSNP_92	145	5288,3312	646.4+/-400.3	1636,2016,648	yes	missense	FLT3	NM_004119.2	81	1900,3001,1602	AA,AG,GG		38.5116,34.3395,47.7087	probably-damaging	227/994	28624294	6801,6205	2203	4300	6503	SO:0001583	missense	2322	exon6			ATGTCCGTCCCAA	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.680C>T	13.37:g.28624294G>A	ENSP00000241453:p.Thr227Met	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	160	160	1	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	1241	0.5682234432234432	150	0.3048780487804878	220	0.6077348066298343	431	0.7534965034965035	440	0.5804749340369393	G	12.45	1.941805	0.34283	0.343395	0.614884	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.79749	-1.23;-1.3;-1.03	5.63	3.85	0.44370	.	0.166014	0.42821	D	0.000648	T	0.00012	0.0000	L	0.29908	0.895	0.32868	P	0.491131	D;D	0.76494	0.999;0.999	P;P	0.60789	0.879;0.743	T	0.48547	-0.9026	9	0.41790	T	0.15	.	11.1573	0.48495	0.0:0.1387:0.7168:0.1445	rs1933437;rs52828701;rs57444997;rs1933437	227;227	P36888-2;P36888	.;FLT3_HUMAN	M	227	ENSP00000241453:T227M;ENSP00000370369:T227M;ENSP00000438139:T227M	ENSP00000241453:T227M	T	-	2	0	FLT3	27522294	1.000000	0.71417	0.599000	0.28851	0.006000	0.05464	3.696000	0.54757	0.687000	0.31509	-0.311000	0.09066	ACG	G|0.465;A|0.535	0.535	strong		0.398	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
QPCT	25797	hgsc.bcm.edu	37	2	37599963	37599963	+	Missense_Mutation	SNP	A	A	C	rs4670696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:37599963A>C	ENST00000338415.3	+	7	1237	c.1079A>C	c.(1078-1080)cAt>cCt	p.H360P	QPCT_ENST00000537448.1_Missense_Mutation_p.H311P	NM_012413.3	NP_036545.1	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase	360			H -> P (in dbSNP:rs4670696). {ECO:0000269|PubMed:15489334}.		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.H360R(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)				GAATATCTTCATTTGTAATAC	0.318													A|||	672	0.134185	0.0023	0.2219	5008	,	,		19761	0.3839		0.0368	False		,,,				2504	0.093				p.H360P		Atlas-SNP	.											QPCT,colon,carcinoma,0,1	QPCT	34	1	1	Substitution - Missense(1)	large_intestine(1)	c.A1079C						PASS	.	A	PRO/HIS	59,4347	57.4+/-93.9	1,57,2145	70.0	66.0	67.0		1079	6.0	1.0	2	dbSNP_111	67	260,8340	100.3+/-161.8	2,256,4042	yes	missense	QPCT	NM_012413.3	77	3,313,6187	CC,CA,AA		3.0233,1.3391,2.4527	benign	360/362	37599963	319,12687	2203	4300	6503	SO:0001583	missense	25797	exon7			ATCTTCATTTGTA	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.1079A>C	2.37:g.37599963A>C	ENSP00000344829:p.His360Pro	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	32	0.340426	NM_012413	Q16770|Q3KRG6|Q53TR4	Missense_Mutation	SNP	ENST00000338415.3	37	CCDS1790.1	307	0.14056776556776557	3	0.006097560975609756	71	0.19613259668508287	208	0.36363636363636365	25	0.032981530343007916	A	19.26	3.794008	0.70452	0.013391	0.030233	ENSG00000115828	ENST00000338415;ENST00000537448	T;T	0.30182	2.26;1.54	5.96	5.96	0.96718	.	0.093684	0.64402	D	0.000001	T	0.00012	0.0000	L	0.49350	1.555	0.23780	P	0.99686459	D;P	0.56287	0.975;0.925	P;B	0.52424	0.698;0.406	T	0.39961	-0.9588	9	0.45353	T	0.12	0.5586	16.1181	0.81324	1.0:0.0:0.0:0.0	rs4670696;rs52824678;rs57682818;rs4670696	311;360	Q16769-2;Q16769	.;QPCT_HUMAN	P	360;311	ENSP00000344829:H360P;ENSP00000441606:H311P	ENSP00000344829:H360P	H	+	2	0	QPCT	37453467	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	3.941000	0.56607	2.284000	0.76573	0.528000	0.53228	CAT	A|0.925;C|0.075	0.075	strong		0.318	QPCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218572.2		
PLEK	5341	hgsc.bcm.edu	37	2	68613710	68613710	+	Silent	SNP	G	G	A	rs2070171	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:68613710G>A	ENST00000234313.7	+	5	728	c.549G>A	c.(547-549)tcG>tcA	p.S183S		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	183	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		TTGCTTCATCGCTGCTCAATG	0.522													G|||	1063	0.21226	0.18	0.2061	5008	,	,		19398	0.1726		0.3052	False		,,,				2504	0.2055				p.S183S		Atlas-SNP	.											.	PLEK	64	.	0			c.G549A						PASS	.	G		830,3576	330.2+/-301.4	76,678,1449	147.0	137.0	141.0		549	-10.8	0.0	2	dbSNP_96	141	2736,5864	437.7+/-358.7	456,1824,2020	no	coding-synonymous	PLEK	NM_002664.2		532,2502,3469	AA,AG,GG		31.814,18.8379,27.4181		183/351	68613710	3566,9440	2203	4300	6503	SO:0001819	synonymous_variant	5341	exon5			TTCATCGCTGCTC	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.549G>A	2.37:g.68613710G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Silent	SNP	ENST00000234313.7	37	CCDS1887.1																																																																																			G|0.746;A|0.254	0.254	strong		0.522	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664	
FASTKD3	79072	hgsc.bcm.edu	37	5	7867027	7867027	+	Silent	SNP	A	A	G	rs77130393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7867027A>G	ENST00000264669.5	-	2	1306	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000502509.1_Intron|FASTKD3_ENST00000513658.1_Intron	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	390					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CTGCCACTGCATTGAGGATGG	0.438													A|||	32	0.00638978	0.0	0.0173	5008	,	,		18240	0.0		0.0189	False		,,,				2504	0.001				p.N390N		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T1170C						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	63.0	64.0	63.0		1170	-5.6	0.0	5	dbSNP_134	63	199,8401	87.1+/-149.5	1,197,4102	no	coding-synonymous	FASTKD3	NM_024091.3		1,221,6281	GG,GA,AA		2.314,0.5447,1.7146		390/663	7867027	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			CACTGCATTGAGG	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1170T>C	5.37:g.7867027A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	68	0.450331	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			A|0.984;G|0.016	0.016	strong		0.438	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
AAMDC	28971	hgsc.bcm.edu	37	11	77553638	77553638	+	Silent	SNP	T	T	C	rs585721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:77553638T>C	ENST00000526415.1	+	3	269	c.96T>C	c.(94-96)ggT>ggC	p.G32G	AAMDC_ENST00000527134.1_Silent_p.G32G|AAMDC_ENST00000393427.2_Silent_p.G32G|AAMDC_ENST00000304716.8_Silent_p.G32G|AAMDC_ENST00000525409.1_Silent_p.G32G|AAMDC_ENST00000525034.1_Silent_p.G51G|RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000533193.1_Silent_p.G32G|AAMDC_ENST00000532481.1_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	65	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	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	
SECISBP2L	9728	hgsc.bcm.edu	37	15	49285001	49285001	+	Missense_Mutation	SNP	G	G	C	rs34895054	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:49285001G>C	ENST00000559471.1	-	18	3009	c.2746C>G	c.(2746-2748)Cca>Gca	p.P916A	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.P871A	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	916							poly(A) RNA binding (GO:0044822)	p.P871A(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTACCAATTGGGGGTGTGTCA	0.453													G|||	952	0.190096	0.0356	0.1844	5008	,	,		17781	0.2063		0.2823	False		,,,				2504	0.2914				p.P916A		Atlas-SNP	.											SECISBP2L,NS,carcinoma,0,1	SECISBP2L	118	1	1	Substitution - Missense(1)	stomach(1)	c.C2746G						PASS	.	G	ALA/PRO,ALA/PRO	341,4053	176.6+/-205.7	17,307,1873	174.0	164.0	167.0		2746,2611	-0.6	0.0	15	dbSNP_126	167	2134,6456	367.9+/-334.9	273,1588,2434	yes	missense,missense	SECISBP2L	NM_001193489.1,NM_014701.3	27,27	290,1895,4307	CC,CG,GG		24.8428,7.7606,19.0619	benign,benign	916/1102,871/1057	49285001	2475,10509	2197	4295	6492	SO:0001583	missense	9728	exon18			CAATTGGGGGTGT	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2746C>G	15.37:g.49285001G>C	ENSP00000453854:p.Pro916Ala	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	195	92	0.471795	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	428	0.19597069597069597	17	0.034552845528455285	72	0.19889502762430938	117	0.20454545454545456	222	0.2928759894459103	G	5.350	0.249933	0.10130	0.077606	0.248428	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.71579	-0.58	4.79	-0.566	0.11767	.	1.036750	0.07555	N	0.916156	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.23249	0.049;0.082	B;B	0.15484	0.01;0.013	T	0.04723	-1.0931	9	0.07990	T	0.79	.	1.6184	0.02708	0.2142:0.1032:0.4026:0.2799	rs34895054	916;871	Q93073;Q93073-2	SBP2L_HUMAN;.	A	871;916	ENSP00000261847:P871A	ENSP00000261847:P871A	P	-	1	0	SECISBP2L	47072293	0.015000	0.18098	0.000000	0.03702	0.811000	0.45836	0.874000	0.28065	-0.169000	0.10834	-0.152000	0.13540	CCA	G|0.812;C|0.188	0.188	strong		0.453	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
KCNQ3	3786	hgsc.bcm.edu	37	8	133184914	133184914	+	Silent	SNP	G	G	C	rs17575754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:133184914G>C	ENST00000388996.4	-	7	1491	c.1071C>G	c.(1069-1071)ctC>ctG	p.L357L	KCNQ3_ENST00000519445.1_Silent_p.L357L|KCNQ3_ENST00000521134.1_Silent_p.L237L	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	357					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CCTGCACCTTGAGGGCCAGCC	0.602													G|||	121	0.0241613	0.003	0.0303	5008	,	,		19240	0.0		0.0835	False		,,,				2504	0.0123				p.L357L		Atlas-SNP	.											.	KCNQ3	164	.	0			c.C1071G						PASS	.	G	,	65,4341	62.3+/-99.4	0,65,2138	145.0	114.0	125.0		711,1071	0.6	1.0	8	dbSNP_123	125	607,7993	158.9+/-212.3	28,551,3721	no	coding-synonymous,coding-synonymous	KCNQ3	NM_001204824.1,NM_004519.3	,	28,616,5859	CC,CG,GG		7.0581,1.4753,5.1668	,	237/753,357/873	133184914	672,12334	2203	4300	6503	SO:0001819	synonymous_variant	3786	exon7			CACCTTGAGGGCC	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1071C>G	8.37:g.133184914G>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																			G|0.954;C|0.046	0.046	strong		0.602	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
STPG1	90529	hgsc.bcm.edu	37	1	24718079	24718079	+	Missense_Mutation	SNP	C	C	A	rs560219	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24718079C>A	ENST00000374409.1	-	3	415	c.161G>T	c.(160-162)aGt>aTt	p.S54I	STPG1_ENST00000337248.4_Missense_Mutation_p.S54I|STPG1_ENST00000468303.1_5'UTR|STPG1_ENST00000440416.1_Intron|STPG1_ENST00000003583.8_Intron	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	54					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTTGGCTTGACTATTGAATCC	0.403											OREG0013240	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1173	0.234225	0.1906	0.2248	5008	,	,		18080	0.3145		0.2416	False		,,,				2504	0.2096				p.S54I		Atlas-SNP	.											.	.	.	.	0			c.G161T						PASS	.																																			SO:0001583	missense	90529	exon3			GCTTGACTATTGA	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 2"""	615826	"""chromosome 1 open reading frame 201"""	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.161G>T	1.37:g.24718079C>A	ENSP00000363530:p.Ser54Ile	Somatic	92	0	0	773	WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Missense_Mutation	SNP	ENST00000374409.1	37	CCDS55581.1	544|544	0.2490842490842491|0.2490842490842491	103|103	0.20934959349593496|0.20934959349593496	88|88	0.2430939226519337|0.2430939226519337	176|176	0.3076923076923077|0.3076923076923077	177|177	0.23350923482849603|0.23350923482849603	C|C	14.40|14.40	2.522665|2.522665	0.44866|0.44866	.|.	.|.	ENSG00000001460|ENSG00000001460	ENST00000374409;ENST00000337248;ENST00000437986|ENST00000435187	.|.	.|.	.|.	5.39|5.39	4.47|4.47	0.54385|0.54385	.|.	0.342231|.	0.29286|.	N|.	0.012599|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.74881|0.74881	2.28|2.28	0.09310|0.09310	P|P	0.9999999999999184|0.9999999999999184	B|.	0.12630|.	0.006|.	B|.	0.09377|.	0.004|.	T|T	0.04840|0.04840	-1.0923|-1.0923	8|4	0.59425|.	D|.	0.04|.	-2.4253|-2.4253	11.8682|11.8682	0.52505|0.52505	0.1747:0.8253:0.0:0.0|0.1747:0.8253:0.0:0.0	rs560219;rs1064840;rs3170834;rs560219|rs560219;rs1064840;rs3170834;rs560219	54|.	Q5TH74|.	CA201_HUMAN|.	I|F	54|31	.|.	ENSP00000337461:S54I|.	S|V	-|-	2|1	0|0	C1orf201|C1orf201	24590666|24590666	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.922000|0.922000	0.55478|0.55478	2.445000|2.445000	0.44899|0.44899	1.404000|1.404000	0.46819|0.46819	-0.169000|-0.169000	0.13324|0.13324	AGT|GTC	C|0.758;A|0.242	0.242	strong		0.403	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
PRDM7	11105	hgsc.bcm.edu	37	16	90124871	90124871	+	Missense_Mutation	SNP	G	G	T	rs7206111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90124871G>T	ENST00000449207.2	-	10	1324	c.1305C>A	c.(1303-1305)aaC>aaA	p.N435K	PRDM7_ENST00000407825.1_Missense_Mutation_p.T135K|PRDM7_ENST00000325921.6_Missense_Mutation_p.T135K	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	435			N -> K (in dbSNP:rs7206111).		regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)	p.T135K(1)		lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CGTTCCACATGTTGACTGAGA	0.483													.|||	436	0.0870607	0.1225	0.0259	5008	,	,		19923	0.1776		0.0517	False		,,,				2504	0.0256				p.N435K		Atlas-SNP	.											PRDM7,NS,carcinoma,0,1	PRDM7	53	1	1	Substitution - Missense(1)	stomach(1)	c.C1305A						PASS	.	G	LYS/ASN,LYS/THR	491,3905	229.1+/-243.8	22,447,1729	151.0	143.0	146.0		1305,404	2.7	0.1	16	dbSNP_116	146	512,8088	145.4+/-201.1	13,486,3801	no	missense,missense	PRDM7	NM_001098173.1,NM_052996.2	94,78	35,933,5530	TT,TG,GG		5.9535,11.1692,7.7178	possibly-damaging,possibly-damaging	435/493,135/172	90124871	1003,11993	2198	4300	6498	SO:0001583	missense	11105	exon10			CCACATGTTGACT	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"""Zinc fingers, C2H2-type"", ""-"""	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.1305C>A	16.37:g.90124871G>T	ENSP00000396732:p.Asn435Lys	Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	328	171	0.521341	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	180|180	0.08241758241758242|0.08241758241758242	57|57	0.11585365853658537|0.11585365853658537	11|11	0.03038674033149171|0.03038674033149171	68|68	0.11888111888111888|0.11888111888111888	44|44	0.05804749340369393|0.05804749340369393	G|G	12.21|12.21	1.869148|1.869148	0.32977|0.32977	0.111692|0.111692	0.059535|0.059535	ENSG00000126856|ENSG00000126856	ENST00000449207|ENST00000325921;ENST00000407825	T|T;T	0.12879|0.50277	2.64|0.75;0.75	2.69|2.69	2.69|2.69	0.31865|0.31865	.|.	.|.	.|.	.|.	.|.	T|T	0.01454|0.01454	0.0047|0.0047	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B|D	0.23316|0.76494	0.083|0.999	B|D	0.19391|0.69142	0.025|0.962	T|T	0.32214|0.32214	-0.9915|-0.9915	6|6	.|.	.|.	.|.	0.1464|0.1464	7.4136|7.4136	0.27032|0.27032	0.0:0.0:0.7407:0.2593|0.0:0.0:0.7407:0.2593	rs7206111;rs52835907;rs7206111|rs7206111;rs52835907;rs7206111	435|135	Q9NQW5|Q9NQW5-2	PRDM7_HUMAN|.	K|K	435|135	ENSP00000396732:N435K|ENSP00000315512:T135K;ENSP00000385121:T135K	.|.	N|T	-|-	3|2	2|0	PRDM7|PRDM7	88652372|88652372	0.981000|0.981000	0.34729|0.34729	0.100000|0.100000	0.21137|0.21137	0.502000|0.502000	0.33828|0.33828	3.065000|3.065000	0.49994|0.49994	1.471000|1.471000	0.48121|0.48121	0.467000|0.467000	0.42956|0.42956	AAC|ACA	G|0.923;T|0.077	0.077	strong		0.483	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
VWA8	23078	hgsc.bcm.edu	37	13	42264380	42264380	+	Missense_Mutation	SNP	C	C	T	rs2274810	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42264380C>T	ENST00000379310.3	-	33	3966	c.3898G>A	c.(3898-3900)Gaa>Aaa	p.E1300K	VWA8_ENST00000478987.1_5'UTR	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1300			E -> K (in dbSNP:rs2274810).			extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										CCCTCAGATTCGATGTGTGCA	0.398													C|||	182	0.0363419	0.034	0.0159	5008	,	,		18438	0.0635		0.0318	False		,,,				2504	0.0307				p.E1300K		Atlas-SNP	.											.	.	.	.	0			c.G3898A						PASS	.	C	LYS/GLU	159,3603		1,157,1723	111.0	104.0	106.0		3898	4.5	0.8	13	dbSNP_100	106	249,7979		7,235,3872	yes	missense	KIAA0564	NM_015058.1	56	8,392,5595	TT,TC,CC		3.0263,4.2265,3.4028	benign	1300/1906	42264380	408,11582	1881	4114	5995	SO:0001583	missense	23078	exon33			CAGATTCGATGTG	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.3898G>A	13.37:g.42264380C>T	ENSP00000368612:p.Glu1300Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	78	0.03571428571428571	21	0.042682926829268296	7	0.019337016574585635	28	0.04895104895104895	22	0.029023746701846966	C	15.76	2.929279	0.52759	0.042265	0.030263	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000478987	T	0.10005	2.92	5.43	4.54	0.55810	.	0.346115	0.28504	N	0.015106	T	0.01489	0.0048	L	0.38531	1.155	0.80722	D	1	B	0.16802	0.019	B	0.11329	0.006	T	0.20840	-1.0263	10	0.32370	T	0.25	.	15.6368	0.76961	0.0:0.8625:0.1375:0.0	rs2274810;rs17594720;rs52806629;rs2274810	1300	A3KMH1	K0564_HUMAN	K	1204;1300;71	ENSP00000368612:E1300K	ENSP00000251030:E1204K	E	-	1	0	KIAA0564	41162380	0.386000	0.25180	0.800000	0.32199	0.744000	0.42396	2.748000	0.47483	2.555000	0.86185	0.650000	0.86243	GAA	C|0.959;T|0.041	0.041	strong		0.398	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
TTN	7273	hgsc.bcm.edu	37	2	179396162	179396162	+	Missense_Mutation	SNP	C	C	G	rs56308529	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179396162C>G	ENST00000591111.1	-	308	100481	c.100257G>C	c.(100255-100257)gaG>gaC	p.E33419D	TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E35060D|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E26120D|TTN_ENST00000460472.2_Missense_Mutation_p.E25995D|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E26187D|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E32492D|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000450692.2_RNA			Q8WZ42	TITIN_HUMAN	titin	33419			E -> D. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCATACGCCTCTGTTCTTG	0.473													C|||	115	0.0229633	0.0	0.0793	5008	,	,		22749	0.0		0.0467	False		,,,				2504	0.0133				p.E35060D		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,-2,4	TTN	18412	4	0			c.G105180C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	43,3779		0,43,1868	120.0	119.0	119.0		78561,78360,97476,77985	3.7	1.0	2	dbSNP_129	119	360,7904		10,340,3782	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	45,45,45,45	10,383,5650	GG,GC,CC		4.3562,1.1251,3.3344	benign,benign,benign,benign	26187/27119,26120/27052,32492/33424,25995/26927	179396162	403,11683	1911	4132	6043	SO:0001583	missense	7273	exon358			ATACGCCTCTGTT	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.100257G>C	2.37:g.179396162C>G	ENSP00000465570:p.Glu33419Asp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	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		54	0.024725274725274724	0	0.0	18	0.049723756906077346	0	0.0	36	0.047493403693931395	C	12.52	1.961667	0.34659	0.011251	0.043562	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62498	0.02;0.26;0.24;0.22	5.45	3.67	0.42095	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.12646	0.0307	L	0.29908	0.895	0.34096	D	0.661338	B;B;B;B	0.18166	0.026;0.026;0.026;0.026	B;B;B;B	0.17433	0.018;0.018;0.018;0.018	T	0.42498	-0.9448	9	0.87932	D	0	.	8.1359	0.31054	0.0:0.6973:0.0:0.3027	rs56308529	25995;26120;26187;33419	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	32492;25995;26187;26120;25992	ENSP00000343764:E32492D;ENSP00000434586:E25995D;ENSP00000340554:E26187D;ENSP00000352154:E26120D	ENSP00000340554:E26187D	E	-	3	2	TTN	179104408	0.633000	0.27181	0.999000	0.59377	0.896000	0.52359	0.091000	0.15046	0.683000	0.31428	0.650000	0.86243	GAG	C|0.970;G|0.030	0.030	strong		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PNPLA7	375775	hgsc.bcm.edu	37	9	140361847	140361847	+	Silent	SNP	G	G	A	rs61738892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140361847G>A	ENST00000277531.4	-	25	3072	c.2886C>T	c.(2884-2886)atC>atT	p.I962I	PNPLA7_ENST00000406427.1_Silent_p.I987I|PNPLA7_ENST00000492278.1_5'UTR|PNPLA7_ENST00000371457.1_Silent_p.I568I	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	962	Patatin.				lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		CGAAGGCCCCGATGGACGTGC	0.647													G|||	154	0.0307508	0.0053	0.0432	5008	,	,		17944	0.002		0.0586	False		,,,				2504	0.0573				p.I987I		Atlas-SNP	.											.	PNPLA7	124	.	0			c.C2961T						PASS	.	G	,	52,4354	50.9+/-86.3	1,50,2152	105.0	84.0	91.0		2961,2886	-10.8	0.1	9	dbSNP_129	91	554,8046	152.8+/-207.3	15,524,3761	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	16,574,5913	AA,AG,GG		6.4419,1.1802,4.6594	,	987/1343,962/1318	140361847	606,12400	2203	4300	6503	SO:0001819	synonymous_variant	375775	exon26			GGCCCCGATGGAC	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.2886C>T	9.37:g.140361847G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																			G|0.956;A|0.044	0.044	strong		0.647	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
DNAH5	1767	hgsc.bcm.edu	37	5	13902220	13902220	+	Missense_Mutation	SNP	T	T	C	rs1530498	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	50	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	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	
C14orf39	317761	hgsc.bcm.edu	37	14	60903757	60903757	+	Missense_Mutation	SNP	G	G	A	rs1254319	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:60903757G>A	ENST00000321731.3	-	18	1729	c.1570C>T	c.(1570-1572)Ctt>Ttt	p.L524F		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	524				L -> F (in Ref. 1; BAC05253). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		GGCTTCTCAAGTAAGTTTCCT	0.299													A|||	2338	0.466853	0.5182	0.2406	5008	,	,		16553	0.6944		0.3012	False		,,,				2504	0.4939				p.L524F		Atlas-SNP	.											.	C14orf39	79	.	0			c.C1570T						PASS	.	A	PHE/LEU	2181,2225	580.0+/-385.0	541,1099,563	102.0	114.0	110.0		1570	4.0	1.0	14	dbSNP_87	110	2535,6063	688.6+/-404.3	362,1811,2126	yes	missense	C14orf39	NM_174978.2	22	903,2910,2689	AA,AG,GG		29.4836,49.5007,36.2658	benign	524/588	60903757	4716,8288	2203	4299	6502	SO:0001583	missense	317761	exon18			TCTCAAGTAAGTT	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1570C>T	14.37:g.60903757G>A	ENSP00000324920:p.Leu524Phe	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	148	76	0.513514	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	954	0.4368131868131868	243	0.49390243902439024	107	0.2955801104972376	385	0.6730769230769231	219	0.28891820580474936	A	0.031	-1.331798	0.01298	0.495007	0.294836	ENSG00000179008	ENST00000321731	T	0.15372	2.43	5.17	4.03	0.46877	.	0.103898	0.43260	N	0.000594	T	0.00012	0.0000	N	0.00104	-2.125	0.39087	P	0.03897099999999998	B	0.02656	0.0	B	0.01281	0.0	T	0.43278	-0.9401	9	0.02654	T	1	-4.4151	8.9267	0.35646	0.8474:0.0:0.1526:0.0	rs1254319;rs57641575;rs1254319	524	Q8N1H7	S6OS1_HUMAN	F	524	ENSP00000324920:L524F	ENSP00000324920:L524F	L	-	1	0	C14orf39	59973510	1.000000	0.71417	0.998000	0.56505	0.458000	0.32498	4.268000	0.58883	0.307000	0.22880	-1.266000	0.01441	CTT	G|0.588;A|0.412	0.412	strong		0.299	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	
XPO5	57510	hgsc.bcm.edu	37	6	43492578	43492578	+	Silent	SNP	G	G	A	rs2257082	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43492578G>A	ENST00000265351.7	-	30	3513	c.3303C>T	c.(3301-3303)taC>taT	p.Y1101Y	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	1101					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)			CCAGTGCCTCGTATATCTGGA	0.557													G|||	1627	0.32488	0.1611	0.2983	5008	,	,		21459	0.62		0.2853	False		,,,				2504	0.3016				p.Y1101Y		Atlas-SNP	.											.	XPO5	79	.	0			c.C3303T						PASS	.	G		720,3440		72,576,1432	57.0	61.0	60.0		3303	-6.1	0.9	6	dbSNP_100	60	2173,6235		274,1625,2305	no	coding-synonymous	XPO5	NM_020750.2		346,2201,3737	AA,AG,GG		25.8444,17.3077,23.0188		1101/1205	43492578	2893,9675	2080	4204	6284	SO:0001819	synonymous_variant	57510	exon30			TGCCTCGTATATC	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.3303C>T	6.37:g.43492578G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1	766	0.3507326007326007	90	0.18292682926829268	105	0.2900552486187845	351	0.6136363636363636	220	0.29023746701846964	G	3.527	-0.096513	0.07010	0.173077	0.258444	ENSG00000124571	ENST00000455285	.	.	.	6.08	-6.07	0.02158	.	.	.	.	.	T	0.47544	0.1451	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.57353	-0.7826	3	.	.	.	-16.2365	19.3651	0.94459	0.255:0.0:0.745:0.0	rs2257082;rs3198268;rs11544381;rs13212498;rs17287943;rs17846608;rs17859692;rs61216486;rs2257082	.	.	.	M	216	.	.	T	-	2	0	XPO5	43600556	0.233000	0.23772	0.921000	0.36526	0.496000	0.33645	-0.282000	0.08445	-0.948000	0.03668	-0.948000	0.02665	ACG	G|0.652;N|0.002	.	strong		0.557	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
VEZF1	7716	hgsc.bcm.edu	37	17	56056607	56056607	+	Silent	SNP	C	C	T	rs73995411|rs57786397|rs369163670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56056607C>T	ENST00000581208.1	-	5	1084	c.1044G>A	c.(1042-1044)caG>caA	p.Q348Q	VEZF1_ENST00000584396.1_Silent_p.Q339Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	348	Poly-Gln.				angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|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)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						gttgttgttgctgctgctgct	0.463																																					p.Q348Q		Atlas-SNP	.											VEZF1,caecum,carcinoma,0,3	VEZF1	50	3	0			c.G1044A						scavenged	.	C		287,4119	132.9+/-169.3	3,281,1919	144.0	136.0	139.0		1044	-2.6	0.3	17	dbSNP_130	139	56,8544	29.6+/-80.5	0,56,4244	no	coding-synonymous	VEZF1	NM_007146.2		3,337,6163	TT,TC,CC		0.6512,6.5138,2.6372		348/522	56056607	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			TTGTTGCTGCTGC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1044G>A	17.37:g.56056607C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	193	9	0.0466321	NM_007146		Silent	SNP	ENST00000581208.1	37	CCDS32687.1																																																																																			C|0.969;T|0.031	0.031	strong		0.463	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
MUC2	4583	hgsc.bcm.edu	37	11	1093769	1093769	+	Missense_Mutation	SNP	G	G	A	rs41361144	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093769G>A	ENST00000441003.2	+	30	5615	c.5588G>A	c.(5587-5589)cGg>cAg	p.R1863Q	MUC2_ENST00000333592.6_Missense_Mutation_p.R151Q|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4225					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.R1863L(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CAGACCTCTCGGTCCACCTCT	0.617													G|||	325	0.0648962	0.0681	0.0418	5008	,	,		18686	0.0585		0.0825	False		,,,				2504	0.0654				p.R1859Q		Atlas-SNP	.											.	MUC2	614	.	1	Substitution - Missense(1)	lung(1)	c.G5576A						PASS	.	G	GLN/ARG	241,4075		7,227,1924	246.0	294.0	278.0		5573	-3.4	0.0	11	dbSNP_127	278	662,7836		18,626,3605	yes	missense	MUC2	NM_002457.2	43	25,853,5529	AA,AG,GG		7.7901,5.5839,7.047	benign	1858/2813	1093769	903,11911	2158	4249	6407	SO:0001583	missense	4583	exon31			CCTCTCGGTCCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5588G>A	11.37:g.1093769G>A	ENSP00000415183:p.Arg1863Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		128	0.05860805860805861	23	0.046747967479674794	16	0.04419889502762431	29	0.050699300699300696	60	0.079155672823219	G	0.371	-0.934206	0.02340	0.055839	0.077901	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.12255	2.7;3.1	1.7	-3.39	0.04868	.	.	.	.	.	T	0.00328	0.0010	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43376	-0.9395	8	0.13108	T	0.6	.	4.124	0.10118	0.4559:0.3763:0.1678:0.0	rs41361144	1863	E7EUV1	.	Q	1863;151	ENSP00000415183:R1863Q;ENSP00000331373:R151Q	ENSP00000331373:R151Q	R	+	2	0	MUC2	1083769	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	-4.255000	0.00265	-1.321000	0.02281	-0.727000	0.03589	CGG	G|0.937;A|0.063	0.063	strong		0.617	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR2B11	127623	hgsc.bcm.edu	37	1	247614553	247614553	+	Silent	SNP	C	C	T	rs12086048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:247614553C>T	ENST00000318749.6	-	1	755	c.732G>A	c.(730-732)acG>acA	p.T244T		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T244T(11)		endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GGGAGGAACACGTCCCAAAGG	0.547													C|||	551	0.110024	0.1891	0.1758	5008	,	,		19727	0.001		0.1342	False		,,,				2504	0.044				p.T244T		Atlas-SNP	.											OR2B11,NS,carcinoma,0,11	OR2B11	102	11	11	Substitution - coding silent(11)	kidney(11)	c.G732A						PASS	.	C		864,3542	340.7+/-306.4	83,698,1422	138.0	134.0	135.0		732	-4.0	0.6	1	dbSNP_120	135	1245,7355	249.2+/-276.5	88,1069,3143	no	coding-synonymous	OR2B11	NM_001004492.1		171,1767,4565	TT,TC,CC		14.4767,19.6096,16.2156		244/318	247614553	2109,10897	2203	4300	6503	SO:0001819	synonymous_variant	127623	exon1			GGAACACGTCCCA		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"""GPCR / Class A : Olfactory receptors"""	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.732G>A	1.37:g.247614553C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_001004492	B2RP03	Silent	SNP	ENST00000318749.6	37	CCDS31090.1																																																																																			C|0.855;T|0.145	0.145	strong		0.547	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
FCGBP	8857	hgsc.bcm.edu	37	19	40373950	40373950	+	Missense_Mutation	SNP	G	G	T	rs200958848	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	888	1	0.00112613		WXS	Illumina HiSeq	Phase_I	43	40	0.930233	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	
RSF1	51773	hgsc.bcm.edu	37	11	77378388	77378388	+	Silent	SNP	T	T	C	rs4945197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:77378388T>C	ENST00000308488.6	-	16	4202	c.3900A>G	c.(3898-3900)ctA>ctG	p.L1300L	RSF1_ENST00000480887.1_Silent_p.L1048L|RSF1_ENST00000360355.2_Silent_p.L1269L			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1300					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)	p.L1300L(1)		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)			CAATCCGGTGTAGCCGTTTGC	0.562													T|||	983	0.196286	0.329	0.2147	5008	,	,		20309	0.1736		0.0984	False		,,,				2504	0.1278				p.L1300L		Atlas-SNP	.											RSF1,NS,carcinoma,0,1	RSF1	105	1	1	Substitution - coding silent(1)	stomach(1)	c.A3900G						PASS	.	T		1335,3065	446.7+/-348.1	204,927,1069	113.0	100.0	105.0		3900	0.0	1.0	11	dbSNP_111	105	831,7753	191.8+/-238.0	36,759,3497	yes	coding-synonymous	RSF1	NM_016578.3		240,1686,4566	CC,CT,TT		9.6808,30.3409,16.6821		1300/1442	77378388	2166,10818	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon16			CCGGTGTAGCCGT	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.3900A>G	11.37:g.77378388T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1																																																																																			T|0.813;C|0.187	0.187	strong		0.562	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
RPTN	126638	hgsc.bcm.edu	37	1	152127455	152127455	+	Missense_Mutation	SNP	T	T	C	rs75957773	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152127455T>C	ENST00000316073.3	-	3	2184	c.2120A>G	c.(2119-2121)gAa>gGa	p.E707G		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	707	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GCCCTGCTCTTCCTCTGCCCA	0.562													T|||	281	0.0561102	0.0053	0.0965	5008	,	,		21543	0.001		0.1362	False		,,,				2504	0.0706				p.E707G		Atlas-SNP	.											RPTN,NS,carcinoma,0,1	RPTN	123	1	0			c.A2120G						PASS	.	T	GLY/GLU	79,3057		0,79,1489	306.0	251.0	268.0		2120	2.8	0.0	1	dbSNP_131	268	981,6183		62,857,2663	yes	missense	RPTN	NM_001122965.1	98	62,936,4152	CC,CT,TT		13.6935,2.5191,10.2913	probably-damaging	707/785	152127455	1060,9240	1568	3582	5150	SO:0001583	missense	126638	exon3			TGCTCTTCCTCTG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.2120A>G	1.37:g.152127455T>C	ENSP00000317895:p.Glu707Gly	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	314	146	0.464968	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	149	0.06822344322344322	3	0.006097560975609756	40	0.11049723756906077	0	0.0	106	0.13984168865435356	T	11.43	1.636369	0.29068	0.025191	0.136935	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.23147	1.92	5.15	2.82	0.32997	.	.	.	.	.	T	0.10035	0.0246	M	0.61703	1.905	0.80722	P	0.0	B	0.32101	0.356	B	0.30855	0.121	T	0.13335	-1.0513	8	0.25751	T	0.34	0.1107	7.9769	0.30159	0.0:0.1718:0.0:0.8282	.	707	Q6XPR3	RPTN_HUMAN	G	707;362	ENSP00000317895:E707G	ENSP00000317895:E707G	E	-	2	0	RPTN	150394079	.	.	0.007000	0.13788	0.104000	0.19210	.	.	0.300000	0.22699	0.523000	0.50628	GAA	T|0.884;C|0.116	0.116	strong		0.562	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
TRPM8	79054	hgsc.bcm.edu	37	2	234905078	234905078	+	Silent	SNP	C	C	T	rs11563208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:234905078C>T	ENST00000324695.4	+	22	3088	c.3048C>T	c.(3046-3048)atC>atT	p.I1016I	TRPM8_ENST00000433712.2_Silent_p.I594I	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	1016					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)	TCCCCTTCATCGTCTTCGCTT	0.507													C|||	795	0.158746	0.0802	0.3184	5008	,	,		21633	0.0823		0.2525	False		,,,				2504	0.1339				p.I1016I		Atlas-SNP	.											.	TRPM8	146	.	0			c.C3048T						PASS	.	C		480,3926	227.2+/-242.5	31,418,1754	159.0	149.0	153.0		3048	-11.2	0.1	2	dbSNP_120	153	2394,6206	398.8+/-346.2	337,1720,2243	no	coding-synonymous	TRPM8	NM_024080.4		368,2138,3997	TT,TC,CC		27.8372,10.8942,22.0975		1016/1105	234905078	2874,10132	2203	4300	6503	SO:0001819	synonymous_variant	79054	exon22			CTTCATCGTCTTC	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.3048C>T	2.37:g.234905078C>T		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	261	261	1	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Silent	SNP	ENST00000324695.4	37	CCDS33407.1																																																																																			C|0.795;N|0.000	.	strong		0.507	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
HSD3B1	3283	hgsc.bcm.edu	37	1	120057158	120057158	+	Silent	SNP	C	C	T	rs6203	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:120057158C>T	ENST00000369413.3	+	4	1157	c.1012C>T	c.(1012-1014)Ctg>Ttg	p.L338L	HSD3B1_ENST00000235547.6_Silent_p.L340L|HSD3B1_ENST00000528909.1_Silent_p.L338L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	338					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)	TCAGCGAGATCTGGCGTATAA	0.512													C|||	1837	0.366813	0.0333	0.4813	5008	,	,		21293	0.6528		0.4254	False		,,,				2504	0.3814				p.L338L		Atlas-SNP	.											.	HSD3B1	53	.	0			c.C1012T	GRCh37	CM021275	HSD3B1	M	rs6203	PASS	.	C		457,3949	217.4+/-235.8	28,401,1774	88.0	77.0	81.0		1012	1.3	0.9	1	dbSNP_52	81	3730,4870	530.5+/-381.8	818,2094,1388	no	coding-synonymous	HSD3B1	NM_000862.2		846,2495,3162	TT,TC,CC		43.3721,10.3722,32.1928		338/374	120057158	4187,8819	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			CGAGATCTGGCGT	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.1012C>T	1.37:g.120057158C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	215	93	0.432558	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			C|0.647;T|0.353	0.353	strong		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
POTEG	404785	hgsc.bcm.edu	37	14	19553494	19553494	+	Silent	SNP	G	G	A	rs200256710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:19553494G>A	ENST00000409832.3	+	1	130	c.78G>A	c.(76-78)aaG>aaA	p.K26K		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													G|||	192	0.0383387	0.0174	0.0173	5008	,	,		41958	0.0575		0.0268	False		,,,				2504	0.0736				p.K26K		Atlas-SNP	.											POTEG,NS,carcinoma,0,1	POTEG	118	1	0			c.G78A						scavenged	.						4.0	7.0	6.0					14																	19553494		1219	2779	3998	SO:0001819	synonymous_variant	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>A	14.37:g.19553494G>A		Somatic	908	1	0.00110132		WXS	Illumina HiSeq	Phase_I	918	386	0.420479	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Silent	SNP	ENST00000409832.3	37	CCDS32018.1																																																																																			G|0.996;A|0.004	0.004	strong		0.582	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607758	84607758	+	Silent	SNP	T	T	A	rs10867826	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	396	0	0		WXS	Illumina HiSeq	Phase_I	405	216	0.533333	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	
PER2	8864	hgsc.bcm.edu	37	2	239155053	239155053	+	Missense_Mutation	SNP	C	C	T	rs934945	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:239155053C>T	ENST00000254657.3	-	23	4010	c.3731G>A	c.(3730-3732)gGa>gAa	p.G1244E	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	1244	CRY binding domain. {ECO:0000250|UniProtKB:Q9Z301}.		G -> E (in dbSNP:rs934945).		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)		CAAGGGGGATCCATTTTCGTC	0.498													C|||	875	0.17472	0.0083	0.317	5008	,	,		14600	0.2639		0.1789	False		,,,				2504	0.2025				p.G1244E		Atlas-SNP	.											.	PER2	85	.	0			c.G3731A						PASS	.	C	GLU/GLY	195,4211	120.8+/-158.4	8,179,2016	121.0	99.0	107.0		3731	2.9	0.0	2	dbSNP_86	107	1633,6967	298.1+/-303.7	134,1365,2801	yes	missense	PER2	NM_022817.2	98	142,1544,4817	TT,TC,CC		18.9884,4.4258,14.0551	benign	1244/1256	239155053	1828,11178	2203	4300	6503	SO:0001583	missense	8864	exon23			GGGGATCCATTTT	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.3731G>A	2.37:g.239155053C>T	ENSP00000254657:p.Gly1244Glu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	413	0.1891025641025641	6	0.012195121951219513	108	0.2983425414364641	157	0.2744755244755245	142	0.18733509234828497	C	9.836	1.189691	0.21954	0.044258	0.189884	ENSG00000132326	ENST00000254657	T	0.10192	2.9	5.03	2.88	0.33553	.	0.949170	0.08837	N	0.886421	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	1.0000000000287557E-6	B	0.17038	0.02	B	0.12837	0.008	T	0.45071	-0.9286	9	0.02654	T	1	-6.3897	5.5081	0.16866	0.2372:0.6604:0.0:0.1024	rs934945;rs52831204;rs56739665;rs934945	1244	O15055	PER2_HUMAN	E	1244	ENSP00000254657:G1244E	ENSP00000254657:G1244E	G	-	2	0	PER2	238819792	0.003000	0.15002	0.001000	0.08648	0.009000	0.06853	1.428000	0.34892	1.224000	0.43551	0.655000	0.94253	GGA	C|0.848;T|0.152	0.152	strong		0.498	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31803054	31803054	+	Missense_Mutation	SNP	G	G	A	rs999597	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:31803054G>A	ENST00000334068.2	+	1	483	c.461G>A	c.(460-462)cGc>cAc	p.R154H		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	154			R -> H (in dbSNP:rs999597).			intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						TGTGGATCTCGCTTCTATCAA	0.433													-|||	62	0.0123802	0.0053	0.0274	5008	,	,		17173	0.002		0.0298	False		,,,				2504	0.0041				p.R154H	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.G461A						PASS	.		HIS/ARG	30,4376		1,28,2174	92.0	95.0	94.0		461	0.4	0.0	21	dbSNP_86	94	280,8320		4,272,4024	yes	missense	KRTAP13-4	NM_181600.1	29	5,300,6198	AA,AG,GG		3.2558,0.6809,2.3835	possibly-damaging	154/161	31803054	310,12696	2203	4300	6503	SO:0001583	missense	284827	exon1			GATCTCGCTTCTA	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.461G>A	21.37:g.31803054G>A	ENSP00000334834:p.Arg154His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	37	0.01694139194139194	3	0.006097560975609756	8	0.022099447513812154	2	0.0034965034965034965	24	0.0316622691292876	-	14.66	2.600639	0.46423	0.006809	0.032558	ENSG00000186971	ENST00000334068	T	0.03152	4.03	4.67	0.445	0.16597	.	0.318065	0.22031	N	0.065594	T	0.01092	0.0036	L	0.40543	1.245	0.09310	N	1	P	0.45011	0.848	B	0.41946	0.371	T	0.41752	-0.9491	10	0.66056	D	0.02	.	5.1511	0.15009	0.2002:0.3157:0.4841:0.0	rs999597;rs52799706;rs999597	154	Q3LI77	KR134_HUMAN	H	154	ENSP00000334834:R154H	ENSP00000334834:R154H	R	+	2	0	KRTAP13-4	30724925	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.844000	0.04345	-0.040000	0.13580	-0.364000	0.07487	CGC	G|0.979;A|0.021	0.021	strong		0.433	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
FAM162B	221303	hgsc.bcm.edu	37	6	117086378	117086378	+	Missense_Mutation	SNP	C	C	A	rs654128	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	34	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	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	
EFCC1	79825	hgsc.bcm.edu	37	3	128755953	128755953	+	Missense_Mutation	SNP	G	G	A	rs3732430	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:128755953G>A	ENST00000480450.1	+	6	1583	c.1583G>A	c.(1582-1584)cGg>cAg	p.R528Q	EFCC1_ENST00000436022.2_Missense_Mutation_p.R91Q			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	528			R -> Q (in dbSNP:rs3732430).				calcium ion binding (GO:0005509)										CAGAGGCTCCGGGACCTGGTA	0.642													G|||	1618	0.323083	0.351	0.281	5008	,	,		16082	0.2063		0.4404	False		,,,				2504	0.3149				p.R528Q		Atlas-SNP	.											.	.	.	.	0			c.G1583A						PASS	.	G	GLN/ARG	1637,2767		317,1003,882	25.0	27.0	26.0		1583	3.5	1.0	3	dbSNP_107	26	3587,5013		743,2101,1456	yes	missense	CCDC48	NM_024768.2	43	1060,3104,2338	AA,AG,GG		41.7093,37.1708,40.1723	possibly-damaging	528/599	128755953	5224,7780	2202	4300	6502	SO:0001583	missense	79825	exon6			GGCTCCGGGACCT	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"""EF-hand domain containing"""	25692	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 73"", ""coiled-coil domain containing 48"""	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1583G>A	3.37:g.128755953G>A	ENSP00000420075:p.Arg528Gln	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_024768	A8MYE2	Missense_Mutation	SNP	ENST00000480450.1	37	CCDS3054.2	719	0.3292124542124542	168	0.34146341463414637	116	0.32044198895027626	101	0.17657342657342656	334	0.44063324538258575	G	24.9	4.580993	0.86748	0.371708	0.417093	ENSG00000114654	ENST00000480450;ENST00000436022	T;T	0.58652	0.48;0.32	4.36	3.48	0.39840	.	0.075929	0.46758	D	0.000280	T	0.00012	0.0000	L	0.54323	1.7	0.24098	P	0.99588451	D	0.56287	0.975	B	0.43680	0.427	T	0.44236	-0.9341	9	0.54805	T	0.06	.	10.1031	0.42517	0.0993:0.0:0.9007:0.0	rs3732430;rs60209959;rs3732430	528	Q9HA90	CCD48_HUMAN	Q	528;91	ENSP00000420075:R528Q;ENSP00000414597:R91Q	ENSP00000414597:R91Q	R	+	2	0	CCDC48	130238643	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	3.647000	0.54403	1.017000	0.39495	0.591000	0.81541	CGG	G|0.653;A|0.347	0.347	strong		0.642	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768	
FNDC7	163479	hgsc.bcm.edu	37	1	109260508	109260508	+	Silent	SNP	C	C	T	rs79836484	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109260508C>T	ENST00000370017.3	+	3	469	c.192C>T	c.(190-192)gaC>gaT	p.D64D	FNDC7_ENST00000271311.2_Silent_p.D65D	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	64	Fibronectin type-III 1. {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)		CGGCTGAAGACGGGGACACAG	0.517													C|||	54	0.0107827	0.0008	0.0144	5008	,	,		19731	0.0387		0.0	False		,,,				2504	0.0041				p.D64D		Atlas-SNP	.											.	FNDC7	113	.	0			c.C192T						PASS	.	C		0,1384		0,0,692	105.0	84.0	90.0		192	-6.4	0.4	1	dbSNP_131	90	5,3177		0,5,1586	no	coding-synonymous	FNDC7	NM_001144937.1		0,5,2278	TT,TC,CC		0.1571,0.0,0.1095		64/734	109260508	5,4561	692	1591	2283	SO:0001819	synonymous_variant	163479	exon3			TGAAGACGGGGAC		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.192C>T	1.37:g.109260508C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	143	64	0.447552	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1																																																																																			C|0.988;T|0.012	0.012	strong		0.517	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
PARVG	64098	hgsc.bcm.edu	37	22	44586522	44586522	+	Silent	SNP	C	C	T	rs2272942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:44586522C>T	ENST00000444313.3	+	7	964	c.480C>T	c.(478-480)gtC>gtT	p.V160V	PARVG_ENST00000415224.1_Silent_p.V160V|PARVG_ENST00000422871.1_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	58	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	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	
DGKB	1607	hgsc.bcm.edu	37	7	14217673	14217673	+	Silent	SNP	G	G	A	rs6966154	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:14217673G>A	ENST00000403951.2	-	24	2648	c.2229C>T	c.(2227-2229)tgC>tgT	p.C743C	DGKB_ENST00000258767.5_Silent_p.C743C|DGKB_ENST00000406247.3_Silent_p.C743C|DGKB_ENST00000444700.2_Silent_p.C724C|DGKB_ENST00000399322.3_Silent_p.C743C|DGKB_ENST00000402815.1_Silent_p.C742C|DGKB_ENST00000407950.1_Silent_p.C735C			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	743					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						CCACGCAGGAGCACTGAGCCA	0.507													G|||	1454	0.290335	0.5378	0.2003	5008	,	,		14132	0.2659		0.2078	False		,,,				2504	0.1299				p.C743C		Atlas-SNP	.											.	DGKB	166	.	0			c.C2229T						PASS	.	G	,	1910,2292		444,1022,635	53.0	62.0	59.0		2229,2229	3.1	1.0	7	dbSNP_116	59	1488,7060		122,1244,2908	no	coding-synonymous,coding-synonymous	DGKB	NM_004080.2,NM_145695.2	,	566,2266,3543	AA,AG,GG		17.4076,45.4545,26.651	,	743/805,743/774	14217673	3398,9352	2101	4274	6375	SO:0001819	synonymous_variant	1607	exon23			GCAGGAGCACTGA	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.2229C>T	7.37:g.14217673G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Silent	SNP	ENST00000403951.2	37	CCDS47547.1																																																																																			G|0.720;A|0.280	0.280	strong		0.507	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080	
DGKH	160851	hgsc.bcm.edu	37	13	42729441	42729441	+	Silent	SNP	C	C	T	rs3208827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42729441C>T	ENST00000337343.4	+	4	420	c.399C>T	c.(397-399)ttC>ttT	p.F133F	DGKH_ENST00000538674.1_5'UTR|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000379274.2_5'UTR|DGKH_ENST00000261491.5_Silent_p.F133F|DGKH_ENST00000540693.1_Silent_p.F133F|DGKH_ENST00000536612.1_5'UTR	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	133	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		TCACTCCATTCAGAAGGCTAA	0.403													C|||	258	0.0515176	0.0159	0.0476	5008	,	,		19636	0.0179		0.0994	False		,,,				2504	0.0879				p.F133F		Atlas-SNP	.											.	DGKH	106	.	0			c.C399T						PASS	.	C	,,,,	111,4295	87.3+/-125.9	1,109,2093	148.0	144.0	145.0		399,,,399,399	3.0	1.0	13	dbSNP_126	145	932,7668	206.5+/-248.5	51,830,3419	no	coding-synonymous,utr-5,utr-5,coding-synonymous,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	52,939,5512	TT,TC,CC		10.8372,2.5193,8.0194	,,,,	133/1165,,,133/1165,133/1221	42729441	1043,11963	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon5			TCCATTCAGAAGG	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.399C>T	13.37:g.42729441C>T		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	169	92	0.544379	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			C|0.928;T|0.072	0.072	strong		0.403	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
OR11A1	26531	hgsc.bcm.edu	37	6	29395180	29395180	+	Missense_Mutation	SNP	A	A	G	rs61978565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29395180A>G	ENST00000377149.1	-	5	711	c.239T>C	c.(238-240)aTg>aCg	p.M80T	OR11A1_ENST00000377147.2_Missense_Mutation_p.M80T|OR11A1_ENST00000377148.1_Missense_Mutation_p.M80T|OR5V1_ENST00000377154.1_Intron			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	63	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	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		
IFT74	80173	hgsc.bcm.edu	37	9	27062721	27062721	+	Missense_Mutation	SNP	C	C	T	rs3429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:27062721C>T	ENST00000443698.1	+	20	1961	c.1790C>T	c.(1789-1791)aCc>aTc	p.T597I	IFT74_ENST00000380062.5_Missense_Mutation_p.T597I|IFT74_ENST00000433700.1_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	143	0	0		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	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	
TPSD1	23430	hgsc.bcm.edu	37	16	1306927	1306927	+	Silent	SNP	C	C	T	rs79472859		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1306927C>T	ENST00000211076.3	+	3	532	c.384C>T	c.(382-384)gaC>gaT	p.D128D	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.D121D	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	128	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D128D(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CCGGGGCGGACATCGCCCTGC	0.647																																					p.D128D		Atlas-SNP	.											TPSD1,NS,carcinoma,0,1	TPSD1	47	1	1	Substitution - coding silent(1)	stomach(1)	c.C384T						PASS	.						75.0	72.0	73.0					16																	1306927		2199	4300	6499	SO:0001819	synonymous_variant	23430	exon3			GGCGGACATCGCC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.384C>T	16.37:g.1306927C>T		Somatic	384	1	0.00260417		WXS	Illumina HiSeq	Phase_I	613	219	0.357259	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			C|0.643;T|0.357	0.357	strong		0.647	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
APLP1	333	hgsc.bcm.edu	37	19	36363470	36363470	+	Silent	SNP	G	G	A	rs230261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36363470G>A	ENST00000221891.4	+	7	1128	c.936G>A	c.(934-936)agG>agA	p.R312R	APLP1_ENST00000537454.2_Silent_p.R273R|APLP1_ENST00000586861.1_Silent_p.R306R	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	312	Heparin-binding. {ECO:0000250}.				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)			GGTTCCTGAGGGCCAAGATGG	0.567													G|||	267	0.0533147	0.1324	0.0288	5008	,	,		17390	0.0109		0.0249	False		,,,				2504	0.0368				p.R312R		Atlas-SNP	.											.	APLP1	77	.	0			c.G936A						PASS	.	G	,	489,3917	229.4+/-244.0	30,429,1744	134.0	131.0	132.0		936,936	1.6	1.0	19	dbSNP_79	132	294,8306	108.0+/-168.7	2,290,4008	no	coding-synonymous,coding-synonymous	APLP1	NM_001024807.1,NM_005166.3	,	32,719,5752	AA,AG,GG		3.4186,11.0985,6.0203	,	312/652,312/651	36363470	783,12223	2203	4300	6503	SO:0001819	synonymous_variant	333	exon7			CCTGAGGGCCAAG	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.936G>A	19.37:g.36363470G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_005166	O00113|Q96A92	Silent	SNP	ENST00000221891.4	37	CCDS32997.1																																																																																			G|0.943;A|0.057	0.057	strong		0.567	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807	
PDE6A	5145	hgsc.bcm.edu	37	5	149323772	149323772	+	Silent	SNP	G	G	A	rs2277926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	68	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	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		
TNFSF8	944	hgsc.bcm.edu	37	9	117668142	117668142	+	Silent	SNP	C	C	T	rs3181195	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	164	84	0.512195	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		
SYT9	143425	hgsc.bcm.edu	37	11	7324584	7324584	+	Missense_Mutation	SNP	G	G	A	rs78477754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7324584G>A	ENST00000318881.6	+	2	697	c.460G>A	c.(460-462)Gtg>Atg	p.V154M	SYT9_ENST00000396716.2_Missense_Mutation_p.V122M	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	154			V -> M (in dbSNP:rs78477754). {ECO:0000269|PubMed:21220648}.		positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TGGCGTCCGCGTGCAGCGCCA	0.612													G|||	70	0.0139776	0.0151	0.0288	5008	,	,		17439	0.0		0.0288	False		,,,				2504	0.001				p.V154M		Atlas-SNP	.											.	SYT9	91	.	0			c.G460A						PASS	.	G	MET/VAL	75,4327	66.4+/-103.9	2,71,2128	50.0	43.0	45.0		460	1.3	0.0	11	dbSNP_131	45	276,8316	105.2+/-166.2	6,264,4026	yes	missense	SYT9	NM_175733.3	21	8,335,6154	AA,AG,GG		3.2123,1.7038,2.7012	benign	154/492	7324584	351,12643	2201	4296	6497	SO:0001583	missense	143425	exon2			GTCCGCGTGCAGC	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"""Synaptotagmins"""	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.460G>A	11.37:g.7324584G>A	ENSP00000324419:p.Val154Met	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	37	26	0.702703	NM_175733		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	37	0.01694139194139194	5	0.01016260162601626	13	0.03591160220994475	0	0.0	19	0.025065963060686015	G	4.269	0.049097	0.08243	0.017038	0.032123	ENSG00000170743	ENST00000396716;ENST00000318881	T;T	0.55760	0.5;0.53	5.73	1.29	0.21616	.	0.265273	0.32655	N	0.005811	T	0.06234	0.0161	N	0.03154	-0.405	0.09310	N	0.999996	B	0.12630	0.006	B	0.12156	0.007	T	0.09684	-1.0663	10	0.33940	T	0.23	.	8.3136	0.32086	0.4328:0.0:0.5672:0.0	.	154	Q86SS6	SYT9_HUMAN	M	122;154	ENSP00000379944:V122M;ENSP00000324419:V154M	ENSP00000324419:V154M	V	+	1	0	SYT9	7281160	0.957000	0.32711	0.009000	0.14445	0.461000	0.32589	2.068000	0.41471	0.368000	0.24481	-0.136000	0.14681	GTG	G|0.974;A|0.026	0.026	strong		0.612	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733	
PLB1	151056	hgsc.bcm.edu	37	2	28854958	28854958	+	Missense_Mutation	SNP	C	C	T	rs2199619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:28854958C>T	ENST00000327757.5	+	55	3997	c.3953C>T	c.(3952-3954)gCg>gTg	p.A1318V	AC074011.2_ENST00000431376.1_RNA|PLB1_ENST00000422425.2_Missense_Mutation_p.A1307V|PLB1_ENST00000541605.1_Missense_Mutation_p.A283V	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	1318	4 X 308-326 AA approximate repeats.		A -> V (in dbSNP:rs2199619).		glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					GAGGACTTTGCGGTTGTGGTG	0.547													C|||	1269	0.253395	0.1921	0.1844	5008	,	,		18352	0.3204		0.2823	False		,,,				2504	0.2863				p.A1318V		Atlas-SNP	.											.	PLB1	255	.	0			c.C3953T						PASS	.	C	VAL/ALA,VAL/ALA	966,3440	366.4+/-317.8	101,764,1338	151.0	120.0	130.0		3920,3953	4.5	0.0	2	dbSNP_96	130	2291,6309	385.9+/-341.7	312,1667,2321	yes	missense,missense	PLB1	NM_001170585.1,NM_153021.4	64,64	413,2431,3659	TT,TC,CC		26.6395,21.9246,25.0423	probably-damaging,probably-damaging	1307/1448,1318/1459	28854958	3257,9749	2203	4300	6503	SO:0001583	missense	151056	exon55			ACTTTGCGGTTGT		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.3953C>T	2.37:g.28854958C>T	ENSP00000330442:p.Ala1318Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	120	67	0.558333	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	568|568	0.2600732600732601|0.2600732600732601	110|110	0.22357723577235772|0.22357723577235772	69|69	0.19060773480662985|0.19060773480662985	165|165	0.28846153846153844|0.28846153846153844	224|224	0.2955145118733509|0.2955145118733509	C|C	17.28|17.28	3.349364|3.349364	0.61183|0.61183	0.219246|0.219246	0.266395|0.266395	ENSG00000163803|ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000541605|ENST00000404858	T;T;T|.	0.33654|.	1.4;1.4;1.4|.	5.37|5.37	4.49|4.49	0.54785|0.54785	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);|.	0.507528|.	0.19024|.	N|.	0.124729|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.67569|0.67569	2.06|2.06	0.80722|0.80722	P|P	0.0|0.0	D;D|.	0.63880|.	0.993;0.985|.	P;P|.	0.55011|.	0.655;0.766|.	T|T	0.14035|0.14035	-1.0487|-1.0487	9|4	0.46703|.	T|.	0.11|.	-3.2628|-3.2628	9.8924|9.8924	0.41298|0.41298	0.0:0.906:0.0:0.094|0.0:0.906:0.0:0.094	rs2199619;rs57133235;rs2199619|rs2199619;rs57133235;rs2199619	1307;1318|.	Q6P1J6-3;Q6P1J6|.	.;PLB1_HUMAN|.	V|W	1318;1307;283|1306	ENSP00000330442:A1318V;ENSP00000416440:A1307V;ENSP00000437426:A283V|.	ENSP00000330442:A1318V|.	A|R	+|+	2|1	0|2	PLB1|PLB1	28708462|28708462	0.011000|0.011000	0.17503|0.17503	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	2.540000|2.540000	0.45727|0.45727	1.290000|1.290000	0.44636|0.44636	0.655000|0.655000	0.94253|0.94253	GCG|CGG	C|0.742;A|0.002	.	strong		0.547	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
SMPDL3B	27293	hgsc.bcm.edu	37	1	28282292	28282292	+	Missense_Mutation	SNP	T	T	C	rs3813803	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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|SMPDL3B_ENST00000549094.1_Missense_Mutation_p.V215A|RP11-460I13.2_ENST00000448015.1_RNA	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	126	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	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	
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124781	26124781	+	Silent	SNP	C	C	T	rs143405410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26124781C>T	ENST00000602637.1	+	1	351	c.321C>T	c.(319-321)ggC>ggT	p.G107G	HIST1H2AC_ENST00000377791.2_Silent_p.G107G|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2BC_ENST00000396984.1_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	107						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						CTCAGGGCGGCGTCCTTCCTA	0.577													C|||	3	0.000599042	0.0	0.0	5008	,	,		19312	0.0		0.003	False		,,,				2504	0.0				p.G107G		Atlas-SNP	.											HIST1H2AC,colon,carcinoma,0,1	HIST1H2AC	29	1	0			c.C321T						scavenged	.	C		2,4404		0,2,2201	93.0	92.0	92.0		321	0.6	1.0	6	dbSNP_134	92	26,8574		0,26,4274	no	coding-synonymous	HIST1H2AC	NM_003512.3		0,28,6475	TT,TC,CC		0.3023,0.0454,0.2153		107/131	26124781	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			GGGCGGCGTCCTT	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.321C>T	6.37:g.26124781C>T		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			C|0.998;T|0.002	0.002	strong		0.577	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258035	25258035	+	Silent	SNP	A	A	G	rs11649280	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:25258035A>G	ENST00000328086.7	-	5	2285	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	494					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)		TACCACTGAGATTCTGAAACA	0.463													G|||	1682	0.335863	0.4758	0.3026	5008	,	,		23355	0.3294		0.2107	False		,,,				2504	0.3057				p.N494N		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.T1482C						PASS	.	G		1988,2406	614.6+/-392.4	454,1080,663	110.0	108.0	109.0		1482	2.5	1.0	16	dbSNP_120	109	1787,6813	733.2+/-406.9	181,1425,2694	no	coding-synonymous	ZKSCAN2	NM_001012981.4		635,2505,3357	GG,GA,AA		20.7791,45.2435,29.0519		494/968	25258035	3775,9219	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon5			ACTGAGATTCTGA	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.1482T>C	16.37:g.25258035A>G		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	260	129	0.496154	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			A|0.696;G|0.304	0.304	strong		0.463	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518214	161518214	+	Missense_Mutation	SNP	T	T	C	rs148181339	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161518214T>C	ENST00000436743.1	-	4	470	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	FCGR3A_ENST00000443193.1_Missense_Mutation_p.I141V|FCGR3A_ENST00000540048.1_Missense_Mutation_p.I106V|FCGR3A_ENST00000476031.1_5'UTR|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000367969.3_Missense_Mutation_p.I142V	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	106				I -> V (in Ref. 3; BAD96988/BAD97015). {ECO:0000305}.	Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AACTCACCGATATGGACTTCT	0.483																																					p.I142V		Atlas-SNP	.											FCGR3A,NS,carcinoma,+2,2	FCGR3A	38	2	0			c.A424G						PASS	.						83.0	81.0	82.0					1																	161518214		2203	4296	6499	SO:0001583	missense	2214	exon3			CACCGATATGGAC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.316A>G	1.37:g.161518214T>C	ENSP00000416607:p.Ile106Val	Somatic	418	0	0		WXS	Illumina HiSeq	Phase_I	507	150	0.295858	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	522|522	0.23901098901098902|0.23901098901098902	75|75	0.1524390243902439|0.1524390243902439	115|115	0.31767955801104975|0.31767955801104975	185|185	0.32342657342657344|0.32342657342657344	147|147	0.19393139841688653|0.19393139841688653	T|T	6.273|6.273	0.418469|0.418469	0.11870|0.11870	.|.	.|.	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336	.|T;T;T;T;T;T	.|0.03889	.|4.95;4.94;4.98;4.98;4.98;3.77	4.43|4.43	-8.86|-8.86	0.00795|0.00795	.|.	4.323350|4.323350	0.00674|0.00674	N|N	0.000659|0.000659	T|T	0.00468|0.00468	0.0015|0.0015	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.35699|0.35699	-0.9778|-0.9778	6|10	.|0.06236	.|T	.|0.91	.|.	8.7015|8.7015	0.34329|0.34329	0.0:0.1887:0.1973:0.614|0.0:0.1887:0.1973:0.614	.|.	.|106;141;106	.|P08637;E9PG94;Q9UPY7	.|FCG3A_HUMAN;.;.	M|V	122|142;141;106;106;106;105	.|ENSP00000356946:I142V;ENSP00000392047:I141V;ENSP00000416607:I106V;ENSP00000356944:I106V;ENSP00000444971:I106V;ENSP00000396567:I105V	.|ENSP00000356944:I106V	I|I	-|-	3|1	3|0	FCGR3A|FCGR3A	159784838|159784838	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-5.685000|-5.685000	0.00105|0.00105	-3.274000|-3.274000	0.00199|0.00199	-0.326000|-0.326000	0.08463|0.08463	ATA|ATC	.	.	weak		0.483	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
OLFM2	93145	hgsc.bcm.edu	37	19	9968139	9968139	+	Missense_Mutation	SNP	G	G	A	rs11556087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9968139G>A	ENST00000264833.4	-	4	565	c.380C>T	c.(379-381)aCg>aTg	p.T127M	OLFM2_ENST00000590841.1_Missense_Mutation_p.T49M	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	127			T -> M (in dbSNP:rs11556087). {ECO:0000269|Ref.1}.		protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						CAACAGTTCCGTCATCCTGTC	0.572													G|||	331	0.0660942	0.0121	0.1225	5008	,	,		20937	0.001		0.2028	False		,,,				2504	0.0256				p.T127M		Atlas-SNP	.											.	OLFM2	42	.	0			c.C380T						PASS	.	G	MET/THR	212,4194	130.2+/-166.9	7,198,1998	87.0	76.0	80.0		380	4.0	0.2	19	dbSNP_120	80	2079,6521	359.1+/-331.4	248,1583,2469	yes	missense	OLFM2	NM_058164.2	81	255,1781,4467	AA,AG,GG		24.1744,4.8116,17.6149	possibly-damaging	127/455	9968139	2291,10715	2203	4300	6503	SO:0001583	missense	93145	exon4			AGTTCCGTCATCC	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.380C>T	19.37:g.9968139G>A	ENSP00000264833:p.Thr127Met	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_058164	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	37	CCDS12221.1	208	0.09523809523809523	12	0.024390243902439025	48	0.13259668508287292	0	0.0	148	0.19525065963060687	G	12.36	1.914438	0.33815	0.048116	0.241744	ENSG00000105088	ENST00000264833	D	0.88354	-2.37	3.95	3.95	0.45737	.	0.485095	0.21123	N	0.079784	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	D	0.61697	0.99	P	0.46339	0.513	T	0.02251	-1.1188	8	.	.	.	.	8.8819	0.35380	0.0:0.0:0.7772:0.2228	rs11556087;rs11556087	127	O95897	NOE2_HUMAN	M	127	ENSP00000264833:T127M	.	T	-	2	0	OLFM2	9829139	0.000000	0.05858	0.199000	0.23439	0.614000	0.37383	0.681000	0.25320	2.047000	0.60756	0.462000	0.41574	ACG	G|0.859;A|0.141	0.141	strong		0.572	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1		
UBXN4	23190	hgsc.bcm.edu	37	2	136511817	136511817	+	Silent	SNP	A	A	G	rs1050115	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	131	128	0.977099	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	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2396611	2396611	+	Missense_Mutation	SNP	C	C	T	rs17685098	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2396611C>T	ENST00000332578.3	+	2	217	c.217C>T	c.(217-219)Cgg>Tgg	p.R73W	TMPRSS9_ENST00000592650.1_3'UTR	NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	73			R -> W (in dbSNP:rs17685098).		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)		CAGCAGTTTGCGGCGGGAGAC	0.677													C|||	1950	0.389377	0.4206	0.4524	5008	,	,		15343	0.504		0.2286	False		,,,				2504	0.3497				p.R73W		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C217T						PASS	.	C	TRP/ARG	1711,2693	486.2+/-360.5	314,1083,805	30.0	25.0	27.0		217	2.9	0.3	19	dbSNP_123	27	2118,6482	340.1+/-323.5	271,1576,2453	yes	missense	TMPRSS9	NM_182973.1	101	585,2659,3258	TT,TC,CC		24.6279,38.851,29.4448	possibly-damaging	73/1060	2396611	3829,9175	2202	4300	6502	SO:0001583	missense	360200	exon2			AGTTTGCGGCGGG	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.217C>T	19.37:g.2396611C>T	ENSP00000330264:p.Arg73Trp	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	834	0.38186813186813184	204	0.4146341463414634	146	0.40331491712707185	304	0.5314685314685315	180	0.23746701846965698	C	14.50	2.553839	0.45487	0.38851	0.246279	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.88277	-2.36	3.98	2.94	0.34122	.	0.554254	0.16316	N	0.219795	T	0.00012	0.0000	N	0.22421	0.69	0.40885	P	0.015978000000000048	P;D	0.69078	0.926;0.997	B;P	0.57283	0.153;0.817	T	0.33650	-0.9860	9	0.72032	D	0.01	.	10.2282	0.43238	0.0:0.8987:0.0:0.1013	rs17685098;rs52790524;rs61077488;rs17685098	73;73	Q7Z410;E7EMP4	TMPS9_HUMAN;.	W	73	ENSP00000330264:R73W	ENSP00000330264:R73W	R	+	1	2	TMPRSS9	2347611	0.578000	0.26717	0.274000	0.24659	0.016000	0.09150	1.370000	0.34238	0.795000	0.33922	0.555000	0.69702	CGG	C|0.673;T|0.327	0.327	strong		0.677	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
MUC16	94025	hgsc.bcm.edu	37	19	9059232	9059232	+	Missense_Mutation	SNP	T	T	C	rs12710265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9059232T>C	ENST00000397910.4	-	3	28417	c.28214A>G	c.(28213-28215)cAg>cGg	p.Q9405R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9407	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						CACCACTGACTGTGGAAATCT	0.537													T|||	907	0.18111	0.149	0.2075	5008	,	,		20338	0.0099		0.3121	False		,,,				2504	0.2474				p.Q9405R		Atlas-SNP	.											.	MUC16	4315	.	0			c.A28214G						PASS	.	T	ARG/GLN	633,3363		46,541,1411	121.0	118.0	119.0		28214	-0.0	0.0	19	dbSNP_121	119	2825,5559		498,1829,1865	yes	missense	MUC16	NM_024690.2	43	544,2370,3276	CC,CT,TT		33.6951,15.8408,27.9321	benign	9405/14508	9059232	3458,8922	1998	4192	6190	SO:0001583	missense	94025	exon3			ACTGACTGTGGAA	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.28214A>G	19.37:g.9059232T>C	ENSP00000381008:p.Gln9405Arg	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	170	93	0.547059	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	390	0.17857142857142858	68	0.13821138211382114	78	0.2154696132596685	5	0.008741258741258742	239	0.3153034300791557	t	4.217	0.039079	0.08148	0.158408	0.336951	ENSG00000181143	ENST00000397910	T	0.21932	1.98	2.14	-0.0415	0.13867	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	B	0.16603	0.018	B	0.17722	0.019	T	0.44636	-0.9315	8	0.87932	D	0	.	4.3999	0.11381	0.0:0.3505:0.0:0.6495	rs12710265;rs12710265	9405	B5ME49	.	R	9405	ENSP00000381008:Q9405R	ENSP00000381008:Q9405R	Q	-	2	0	MUC16	8920232	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-0.483000	0.06536	-0.076000	0.12775	0.255000	0.18592	CAG	T|0.786;C|0.214	0.214	strong		0.537	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LILRA4	23547	hgsc.bcm.edu	37	19	54849463	54849463	+	Silent	SNP	C	C	T	rs12976217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54849463C>T	ENST00000291759.4	-	4	455	c.399G>A	c.(397-399)gtG>gtA	p.V133V	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	133	Ig-like C2-type 2.				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)		CTCCTGAGGTCACCACAGGGC	0.577													C|||	1729	0.345248	0.3306	0.3963	5008	,	,		19054	0.2361		0.3509	False		,,,				2504	0.4356				p.V133V		Atlas-SNP	.											.	LILRA4	91	.	0			c.G399A						PASS	.	C		1510,2896		246,1018,939	56.0	58.0	57.0		399	1.6	0.8	19	dbSNP_121	57	3168,5432		581,2006,1713	no	coding-synonymous	LILRA4	NM_012276.3		827,3024,2652	TT,TC,CC		36.8372,34.2714,35.968		133/500	54849463	4678,8328	2203	4300	6503	SO:0001819	synonymous_variant	23547	exon4			TGAGGTCACCACA	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.399G>A	19.37:g.54849463C>T		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			C|0.657;T|0.343	0.343	strong		0.577	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
HS3ST6	64711	hgsc.bcm.edu	37	16	1962132	1962132	+	Missense_Mutation	SNP	G	G	A	rs8055325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1962132G>A	ENST00000293937.3	-	2	487	c.488C>T	c.(487-489)gCc>gTc	p.A163V	HS3ST6_ENST00000454677.2_Missense_Mutation_p.A180V|HS3ST6_ENST00000443547.1_Missense_Mutation_p.A132V			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	163					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						GCGGCGGGGGGCCTCTCGCGT	0.672													g|||	2379	0.47504	0.4418	0.3501	5008	,	,		12698	0.498		0.3867	False		,,,				2504	0.6759				p.A132V		Atlas-SNP	.											.	HS3ST6	26	.	0			c.C395T						PASS	.	G	VAL/ALA	1700,2684		315,1070,807	15.0	18.0	17.0		395	3.9	0.8	16	dbSNP_116	17	2972,5620		490,1992,1814	yes	missense	HS3ST6	NM_001009606.2	64	805,3062,2621	AA,AG,GG		34.5903,38.7774,36.0049	probably-damaging	132/312	1962132	4672,8304	2192	4296	6488	SO:0001583	missense	64711	exon2			CGGGGGGCCTCTC			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.488C>T	16.37:g.1962132G>A	ENSP00000293937:p.Ala163Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	72	19	0.263889	NM_001009606	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	37		958	0.43864468864468864	230	0.46747967479674796	125	0.3453038674033149	304	0.5314685314685315	299	0.3944591029023747	g	14.32	2.499876	0.44455	0.387774	0.345903	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	T;T	0.57273	0.41;0.41	4.83	3.87	0.44632	Sulfotransferase domain (1);	0.051606	0.85682	D	0.000000	T	0.00012	0.0000	N	0.21194	0.64	0.09310	P	0.99999828591	P	0.40302	0.712	B	0.44315	0.446	T	0.40156	-0.9578	9	0.13108	T	0.6	.	11.9296	0.52839	0.0851:0.0:0.9149:0.0	rs8055325;rs8055325	163	Q96QI5	HS3S6_HUMAN	V	163;132;202	ENSP00000293937:A163V;ENSP00000390354:A132V	ENSP00000293937:A163V	A	-	2	0	HS3ST6	1902133	1.000000	0.71417	0.837000	0.33122	0.870000	0.49936	4.707000	0.61852	1.035000	0.39972	0.500000	0.49745	GCC	G|0.549;A|0.451	0.451	strong		0.672	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
FAT2	2196	hgsc.bcm.edu	37	5	150914184	150914184	+	Silent	SNP	A	A	T	rs1432643	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150914184A>T	ENST00000261800.5	-	12	9225	c.9213T>A	c.(9211-9213)acT>acA	p.T3071T		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3071	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTCTAGGGCAGTGAGTGTGG	0.527													T|||	3169	0.632788	0.4932	0.6585	5008	,	,		18177	0.8085		0.5298	False		,,,				2504	0.728				p.T3071T		Atlas-SNP	.											.	FAT2	465	.	0			c.T9213A						PASS	.	T		2143,2263	597.7+/-388.9	535,1073,595	97.0	82.0	87.0		9213	-0.3	0.1	5	dbSNP_88	87	4642,3958	551.4+/-385.9	1260,2122,918	no	coding-synonymous	FAT2	NM_001447.2		1795,3195,1513	TT,TA,AA		46.0233,48.6382,47.8318		3071/4350	150914184	6785,6221	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon12			TAGGGCAGTGAGT	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.9213T>A	5.37:g.150914184A>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			T|0.561;N|0.000	0.561	strong		0.527	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15580694	15580694	+	Missense_Mutation	SNP	G	G	A	rs61734899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	33	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	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	
TACC2	10579	hgsc.bcm.edu	37	10	123845897	123845897	+	Silent	SNP	G	G	C	rs1106992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123845897G>C	ENST00000369005.1	+	4	4222	c.3882G>C	c.(3880-3882)ctG>ctC	p.L1294L	TACC2_ENST00000334433.3_Silent_p.L1294L|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Silent_p.L1294L|TACC2_ENST00000453444.2_Silent_p.L1294L|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Silent_p.L1294L	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1294					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)				TCGCCCCCCTGTTGCAACCAG	0.607													C|||	1024	0.204473	0.2973	0.1916	5008	,	,		18740	0.1022		0.2167	False		,,,				2504	0.181				p.L1294L		Atlas-SNP	.											.	TACC2	271	.	0			c.G3882C						PASS	.	C	,	1462,2944	674.0+/-402.9	243,976,984	33.0	34.0	34.0		,3882	2.0	0.0	10	dbSNP_86	34	1971,6629	719.9+/-406.3	224,1523,2553	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	467,2499,3537	CC,CG,GG		22.9186,33.182,26.3955	,	,1294/2949	123845897	3433,9573	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			CCCCCTGTTGCAA	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.3882G>C	10.37:g.123845897G>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			G|0.758;C|0.242	0.242	strong		0.607	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
TP53TG5	27296	hgsc.bcm.edu	37	20	44005936	44005936	+	Missense_Mutation	SNP	C	C	T	rs2231616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:44005936C>T	ENST00000372726.3	-	3	326	c.170G>A	c.(169-171)cGc>cAc	p.R57H	SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1-DBNDD2_ENST00000475242.1_Intron|TP53TG5_ENST00000494455.1_5'UTR|TP53TG5_ENST00000537995.1_Missense_Mutation_p.R41H	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	57			R -> H (in dbSNP:rs2231616).		intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						TTGGATCCGGCGGTTTGAGCT	0.502													C|||	1008	0.201278	0.0696	0.2579	5008	,	,		18364	0.2897		0.1123	False		,,,				2504	0.3395				p.R57H		Atlas-SNP	.											.	TP53TG5	36	.	0			c.G170A						PASS	.	C	HIS/ARG	429,3977	208.8+/-229.8	25,379,1799	175.0	168.0	170.0		170	-2.1	0.0	20	dbSNP_98	170	1122,7478	233.2+/-266.6	69,984,3247	yes	missense	TP53TG5	NM_014477.2	29	94,1363,5046	TT,TC,CC		13.0465,9.7367,11.9253	possibly-damaging	57/291	44005936	1551,11455	2203	4300	6503	SO:0001583	missense	27296	exon3			ATCCGGCGGTTTG	AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 10"""	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.170G>A	20.37:g.44005936C>T	ENSP00000361811:p.Arg57His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_014477		Missense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	338	0.15476190476190477	32	0.06504065040650407	73	0.20165745856353592	144	0.2517482517482518	89	0.11741424802110818	C	10.75	1.438782	0.25900	0.097367	0.130465	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.14022	2.54;2.54	5.52	-2.06	0.07298	.	0.660669	0.14744	N	0.301018	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.22276	0.067	B	0.12837	0.008	T	0.42565	-0.9444	9	0.36615	T	0.2	-0.0354	9.6207	0.39719	0.0:0.4882:0.317:0.1948	rs2231616;rs3746590;rs57771799;rs2231616	57	Q9Y2B4	T53G5_HUMAN	H	57;41	ENSP00000361811:R57H;ENSP00000438374:R41H	ENSP00000361811:R57H	R	-	2	0	TP53TG5	43439350	0.015000	0.18098	0.007000	0.13788	0.771000	0.43674	-1.108000	0.03313	-0.161000	0.10983	-0.176000	0.13171	CGC	C|0.863;T|0.137	0.137	strong		0.502	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477	
MLIP	90523	hgsc.bcm.edu	37	6	54095524	54095524	+	Missense_Mutation	SNP	C	C	T	rs2275769	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:54095524C>T	ENST00000274897.5	+	11	1239	c.1126C>T	c.(1126-1128)Cct>Tct	p.P376S	MLIP_ENST00000502396.1_Missense_Mutation_p.P911S|MLIP_ENST00000358276.5_Intron|MLIP_ENST00000370877.2_Intron|MLIP_ENST00000370876.2_Intron|MLIP_ENST00000509997.1_Intron	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	376			P -> S (in dbSNP:rs2275769).			nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						TGTAACAGTCCCTCCCAAGCC	0.468													C|||	800	0.159744	0.2345	0.1484	5008	,	,		18412	0.1845		0.0805	False		,,,				2504	0.1227				p.P376S		Atlas-SNP	.											.	MLIP	84	.	0			c.C1126T						PASS	.	C	SER/PRO	938,3468	359.1+/-314.7	96,746,1361	293.0	281.0	285.0		1126	1.8	1.0	6	dbSNP_100	285	540,8060	148.6+/-203.8	14,512,3774	yes	missense	MLIP	NM_138569.2	74	110,1258,5135	TT,TC,CC		6.2791,21.2892,11.364	possibly-damaging	376/459	54095524	1478,11528	2203	4300	6503	SO:0001583	missense	90523	exon11			ACAGTCCCTCCCA	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"""muscle-enriched A-type lamin interacting protein"""	614106	"""chromosome 6 open reading frame 142"""	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.1126C>T	6.37:g.54095524C>T	ENSP00000274897:p.Pro376Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_138569	B7Z2N0|D6RE05|Q96H08|Q96NF7	Missense_Mutation	SNP	ENST00000274897.5	37	CCDS4954.1	321	0.14697802197802198	115	0.23373983739837398	45	0.12430939226519337	106	0.1853146853146853	55	0.07255936675461741	C	11.53	1.667623	0.29604	0.212892	0.062791	ENSG00000146147	ENST00000274897;ENST00000502396;ENST00000514433	T;T;T	0.20881	2.38;2.04;2.06	4.58	1.75	0.24633	.	0.741193	0.11827	N	0.525585	T	0.05044	0.0135	L	0.36672	1.1	0.19300	P	0.9999789074	B;B	0.14012	0.001;0.009	B;B	0.10450	0.003;0.005	T	0.33929	-0.9849	9	0.37606	T	0.19	.	4.0359	0.09729	0.1847:0.617:0.0:0.1983	rs2275769;rs59972182;rs2275769	911;376	Q5VWP3-3;Q5VWP3	.;MLIP_HUMAN	S	376;911;305	ENSP00000274897:P376S;ENSP00000426290:P911S;ENSP00000421444:P305S	ENSP00000274897:P376S	P	+	1	0	MLIP	54203483	0.157000	0.22836	0.988000	0.46212	0.933000	0.57130	0.208000	0.17415	0.237000	0.21200	0.650000	0.86243	CCT	C|0.870;T|0.130	0.130	strong		0.468	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569	
TRIM45	80263	hgsc.bcm.edu	37	1	117656088	117656088	+	Missense_Mutation	SNP	A	A	G	rs1289658	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	125	0	0		WXS	Illumina HiSeq	Phase_I	103	38	0.368932	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	
CENPF	1063	hgsc.bcm.edu	37	1	214813782	214813782	+	Missense_Mutation	SNP	A	A	G	rs3795524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:214813782A>G	ENST00000366955.3	+	12	2269	c.2101A>G	c.(2101-2103)Atg>Gtg	p.M701V		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0			M -> V (in dbSNP:rs3795524).		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)		ACTAGCTTATATGGAGCTACA	0.423																																					p.M701V	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A2101G						PASS	.	G	VAL/MET	398,4008	775.0+/-414.1	18,362,1823	64.0	64.0	64.0		2101	0.3	0.0	1	dbSNP_107	64	466,8134	796.4+/-407.5	11,444,3845	yes	missense	CENPF	NM_016343.3	21	29,806,5668	GG,GA,AA		5.4186,9.0331,6.6431	benign	701/3115	214813782	864,12142	2203	4300	6503	SO:0001583	missense	1063	exon12			GCTTATATGGAGC	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.2101A>G	1.37:g.214813782A>G	ENSP00000355922:p.Met701Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	176	100	0.568182	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	231	0.10576923076923077	65	0.13211382113821138	40	0.11049723756906077	84	0.14685314685314685	42	0.055408970976253295	G	0.165	-1.077610	0.01903	0.090331	0.054186	ENSG00000117724	ENST00000366955	T	0.03035	4.07	5.81	0.273	0.15650	.	1.359190	0.05393	N	0.539243	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.16802	0.019	B	0.04013	0.001	T	0.49093	-0.8975	8	0.29301	T	0.29	.	5.9704	0.19349	0.3454:0.0:0.537:0.1176	rs3795524;rs11564985;rs17023316;rs52837943;rs3795524	701	P49454	CENPF_HUMAN	V	701	ENSP00000355922:M701V	ENSP00000355922:M701V	M	+	1	0	CENPF	212880405	0.016000	0.18221	0.000000	0.03702	0.093000	0.18481	1.864000	0.39469	-0.464000	0.06963	-0.912000	0.02778	ATG	A|0.914;G|0.086	0.086	strong		0.423	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
GJA3	2700	hgsc.bcm.edu	37	13	20716885	20716885	+	Silent	SNP	G	G	A	rs74607195	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:20716885G>A	ENST00000241125.3	-	2	719	c.543C>T	c.(541-543)tgC>tgT	p.C181C		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	181					cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		GCCAGCGGTCGCAGCGGTAGA	0.602													G|||	61	0.0121805	0.0015	0.0086	5008	,	,		14229	0.0		0.0487	False		,,,				2504	0.0041				p.C181C		Atlas-SNP	.											.	GJA3	32	.	0			c.C543T						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	54.0	52.0	52.0		543	-4.6	0.9	13	dbSNP_132	52	314,8286	111.0+/-171.3	7,300,3993	no	coding-synonymous	GJA3	NM_021954.3		7,320,6176	AA,AG,GG		3.6512,0.4539,2.568		181/436	20716885	334,12672	2203	4300	6503	SO:0001819	synonymous_variant	2700	exon2			GCGGTCGCAGCGG	AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"""Ion channels / Gap junction proteins (connexins)"""	4277	protein-coding gene	gene with protein product	"""connexin 46"""	121015	"""gap junction protein, alpha 3, 46kD (connexin 46)"", ""gap junction protein, alpha 3, 46kDa (connexin 46)"""	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.543C>T	13.37:g.20716885G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_021954	Q0VAB7|Q9H537	Silent	SNP	ENST00000241125.3	37	CCDS9289.1																																																																																			G|0.978;A|0.022	0.022	strong		0.602	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954	
SCNN1A	6337	hgsc.bcm.edu	37	12	6457062	6457062	+	Missense_Mutation	SNP	T	T	C	rs2228576	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6457062T>C	ENST00000228916.2	-	13	2085	c.1987A>G	c.(1987-1989)Acc>Gcc	p.T663A	SCNN1A_ENST00000358945.3_Missense_Mutation_p.T685A|SCNN1A_ENST00000360168.3_Missense_Mutation_p.T722A|SCNN1A_ENST00000396966.2_3'UTR|SCNN1A_ENST00000543768.1_Missense_Mutation_p.T686A|SCNN1A_ENST00000540037.1_Missense_Mutation_p.T363A	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	663			T -> A (in dbSNP:rs2228576). {ECO:0000269|PubMed:10404817, ECO:0000269|PubMed:10523338, ECO:0000269|PubMed:12107247, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15734793, ECO:0000269|PubMed:17766193, ECO:0000269|PubMed:19462466}.		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)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	AGAGGACAGGTGGAGGAACTG	0.667													C|||	3709	0.740615	0.9486	0.7392	5008	,	,		16307	0.496		0.6938	False		,,,				2504	0.7607				p.T722A		Atlas-SNP	.											.	SCNN1A	54	.	0			c.A2164G	GRCh37	CM994637	SCNN1A	M	rs2228576	PASS	.	C	ALA/THR,ALA/THR,ALA/THR	3760,418		1696,368,25	7.0	8.0	8.0		1987,2056,2164	1.9	0.0	12	dbSNP_98	8	5675,2515		2009,1657,429	yes	missense,missense,missense	SCNN1A	NM_001038.5,NM_001159575.1,NM_001159576.1	58,58,58	3705,2025,454	CC,CT,TT		30.7082,10.0048,23.7144	benign,benign,benign	663/670,686/693,722/729	6457062	9435,2933	2089	4095	6184	SO:0001583	missense	6337	exon12			GACAGGTGGAGGA	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.1987A>G	12.37:g.6457062T>C	ENSP00000228916:p.Thr663Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	1572	0.7197802197802198	465	0.9451219512195121	270	0.7458563535911602	318	0.5559440559440559	519	0.6846965699208444	C	0.055	-1.240246	0.01493	0.899952	0.692918	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000540037;ENST00000228916;ENST00000543768	T;T;T;T;T	0.67865	-0.29;-0.27;-0.08;-0.22;-0.25	3.95	1.89	0.25635	.	1.351300	0.05287	N	0.520473	T	0.00012	0.0000	N	0.00116	-2.08	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	0.43426	-0.9392	9	0.02654	T	1	-5.0385	3.4713	0.07569	0.0:0.4643:0.197:0.3387	rs2228576;rs3741912;rs17789406;rs60329095;rs2228576	686;663;722	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	A	722;685;363;663;686	ENSP00000353292:T722A;ENSP00000351825:T685A;ENSP00000440876:T363A;ENSP00000228916:T663A;ENSP00000438739:T686A	ENSP00000228916:T663A	T	-	1	0	SCNN1A	6327323	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.586000	0.05787	0.425000	0.26087	-0.227000	0.12334	ACC	T|0.279;C|0.719	0.719	strong		0.667	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
AFAP1	60312	hgsc.bcm.edu	37	4	7802227	7802227	+	Missense_Mutation	SNP	G	G	C	rs28406288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:7802227G>C	ENST00000360265.4	-	9	1442	c.1208C>G	c.(1207-1209)tCt>tGt	p.S403C	AFAP1_ENST00000382543.3_Missense_Mutation_p.S403C|AFAP1_ENST00000358461.2_Missense_Mutation_p.S403C|AFAP1_ENST00000420658.1_Missense_Mutation_p.S403C|AFAP1_ENST00000513842.1_5'Flank			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	403	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.		S -> C (in dbSNP:rs28406288). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			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						AGGATGTTTAGAATCCAAACC	0.532													g|||	617	0.123203	0.1558	0.2248	5008	,	,		19307	0.0089		0.1471	False		,,,				2504	0.1002				p.S403C		Atlas-SNP	.											.	AFAP1	93	.	0			c.C1208G						PASS	.	C	CYS/SER,CYS/SER	719,3687	298.4+/-285.3	71,577,1555	117.0	103.0	108.0		1208,1208	4.2	0.8	4	dbSNP_125	108	1345,7255	263.5+/-285.0	120,1105,3075	yes	missense,missense	AFAP1	NM_001134647.1,NM_198595.2	112,112	191,1682,4630	CC,CG,GG		15.6395,16.3187,15.8696	probably-damaging,probably-damaging	403/815,403/731	7802227	2064,10942	2203	4300	6503	SO:0001583	missense	60312	exon10			TGTTTAGAATCCA	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.1208C>G	4.37:g.7802227G>C	ENSP00000353402:p.Ser403Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	37	CCDS3397.1	264	0.12087912087912088	66	0.13414634146341464	77	0.212707182320442	6	0.01048951048951049	115	0.1517150395778364	g	12.70	2.018075	0.35606	0.163187	0.156395	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.0	4.16	0.48862	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.389678	0.29205	N	0.012830	T	0.00210	0.0006	N	0.22421	0.69	0.25845	P	0.984004	D;D	0.76494	0.999;0.998	D;D	0.69142	0.935;0.962	T	0.30179	-0.9987	9	0.66056	D	0.02	-8.4668	15.5676	0.76306	0.0:0.1384:0.8615:0.0	rs28406288	403;403	E9PDT7;Q8N556	.;AFAP1_HUMAN	C	403	ENSP00000353402:S403C;ENSP00000410689:S403C;ENSP00000351245:S403C;ENSP00000371983:S403C	ENSP00000351245:S403C	S	-	2	0	AFAP1	7853127	1.000000	0.71417	0.821000	0.32701	0.022000	0.10575	3.944000	0.56629	1.122000	0.41944	-0.352000	0.07741	TCT	G|0.843;C|0.157	0.157	strong		0.532	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
C2orf54	79919	hgsc.bcm.edu	37	2	241834944	241834944	+	Silent	SNP	T	T	C	rs4468809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	134	0	0		WXS	Illumina HiSeq	Phase_I	157	64	0.407643	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	
TTC28	23331	hgsc.bcm.edu	37	22	28559120	28559120	+	Silent	SNP	G	G	C	rs17486417	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:28559120G>C	ENST00000397906.2	-	6	1542	c.1401C>G	c.(1399-1401)ctC>ctG	p.L467L		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	467					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CCCGGTCCTTGAGATCCTCAG	0.552													G|||	678	0.135383	0.0794	0.0821	5008	,	,		18257	0.1736		0.1342	False		,,,				2504	0.2106				p.L467L		Atlas-SNP	.											.	TTC28	84	.	0			c.C1401G						PASS	.	G		116,1268		5,106,581	47.0	38.0	41.0		1401	2.6	1.0	22	dbSNP_123	41	450,2732		25,400,1166	no	coding-synonymous	TTC28	NM_001145418.1		30,506,1747	CC,CG,GG		14.142,8.3815,12.396		467/2482	28559120	566,4000	692	1591	2283	SO:0001819	synonymous_variant	23331	exon6			GTCCTTGAGATCC	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.1401C>G	22.37:g.28559120G>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.870;C|0.128	0.128	strong		0.552	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
TECTB	6975	hgsc.bcm.edu	37	10	114053546	114053546	+	Silent	SNP	C	C	G	rs726009	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:114053546C>G	ENST00000369422.3	+	5	534	c.534C>G	c.(532-534)tcC>tcG	p.S178S		NM_058222.1	NP_478129.1	Q96PL2	TECTB_HUMAN	tectorin beta	178	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.198)		Epithelial(162;0.0143)|all cancers(201;0.0242)		TGGAGGCATCCGAAATCGGTT	0.413																																					p.S178S		Atlas-SNP	.											.	TECTB	35	.	0			c.C534G						PASS	.	C		2451,1955	620.9+/-393.6	692,1067,444	150.0	147.0	148.0		534	-11.9	0.4	10	dbSNP_86	148	3956,4644	549.5+/-385.6	891,2174,1235	no	coding-synonymous	TECTB	NM_058222.1		1583,3241,1679	GG,GC,CC		46.0,44.3713,49.2619		178/330	114053546	6407,6599	2203	4300	6503	SO:0001819	synonymous_variant	6975	exon5			GGCATCCGAAATC	AF312827	CCDS7571.1	10q25-q26	2005-06-09			ENSG00000119913	ENSG00000119913			11721	protein-coding gene	gene with protein product		602653				9079715	Standard	NM_058222		Approved		uc001kzr.1	Q96PL2	OTTHUMG00000019056	ENST00000369422.3:c.534C>G	10.37:g.114053546C>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_058222	Q5VW53	Silent	SNP	ENST00000369422.3	37	CCDS7571.1																																																																																			C|0.418;G|0.582	0.582	strong		0.413	TECTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050381.1	NM_058222	
KIF22	3835	hgsc.bcm.edu	37	16	29816237	29816237	+	Missense_Mutation	SNP	G	G	A	rs146561986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:29816237G>A	ENST00000160827.4	+	12	1820	c.1780G>A	c.(1780-1782)Gat>Aat	p.D594N	MAZ_ENST00000562337.1_5'Flank|KIF22_ENST00000400751.5_Missense_Mutation_p.D526N|KIF22_ENST00000569382.2_Missense_Mutation_p.D540N|MAZ_ENST00000566906.2_5'Flank|MAZ_ENST00000219782.6_5'Flank|KIF22_ENST00000561482.1_Missense_Mutation_p.D526N|MAZ_ENST00000563402.1_5'Flank|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000545521.1_5'Flank|MAZ_ENST00000322945.6_5'Flank	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	594					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						AAAAATACTGGATCTGCTGAA	0.617													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19086	0.0		0.002	False		,,,				2504	0.001				p.D594N		Atlas-SNP	.											.	KIF22	29	.	0			c.G1780A						PASS	.	G	ASN/ASP	3,4391	6.2+/-15.9	0,3,2194	44.0	43.0	43.0		1780	1.4	0.4	16	dbSNP_134	43	23,8569	17.3+/-56.4	0,23,4273	yes	missense	KIF22	NM_007317.1	23	0,26,6467	AA,AG,GG		0.2677,0.0683,0.2002	benign	594/666	29816237	26,12960	2197	4296	6493	SO:0001583	missense	3835	exon12			ATACTGGATCTGC	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"""Kinesins"""	6391	protein-coding gene	gene with protein product		603213	"""kinesin-like 4"""	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.1780G>A	16.37:g.29816237G>A	ENSP00000160827:p.Asp594Asn	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Missense_Mutation	SNP	ENST00000160827.4	37	CCDS10653.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	15.07	2.723503	0.48728	6.83E-4	0.002677	ENSG00000079616	ENST00000160827;ENST00000400751	T;T	0.74106	-0.73;-0.81	5.64	1.38	0.22167	.	.	.	.	.	T	0.39911	0.1096	N	0.08118	0	0.80722	D	1	B;B	0.18166	0.002;0.026	B;B	0.18263	0.003;0.021	T	0.15521	-1.0434	9	0.39692	T	0.17	.	2.6855	0.05106	0.1508:0.2728:0.4355:0.1409	.	526;594	B7Z265;Q14807	.;KIF22_HUMAN	N	594;526	ENSP00000160827:D594N;ENSP00000383562:D526N	ENSP00000160827:D594N	D	+	1	0	KIF22	29723738	0.998000	0.40836	0.355000	0.25773	0.967000	0.64934	1.528000	0.35985	0.037000	0.15575	0.561000	0.74099	GAT	G|0.998;A|0.002	0.002	strong		0.617	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2		
ANAPC4	29945	hgsc.bcm.edu	37	4	25408838	25408838	+	Missense_Mutation	SNP	G	G	A	rs34811474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:25408838G>A	ENST00000315368.3	+	20	1536	c.1394G>A	c.(1393-1395)cGa>cAa	p.R465Q	ANAPC4_ENST00000510092.1_Missense_Mutation_p.R466Q	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	465			R -> Q (in dbSNP:rs34811474).		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				CTTTATAATCGAAAAGGAAAA	0.323													G|||	371	0.0740815	0.0189	0.1239	5008	,	,		16203	0.0		0.2167	False		,,,				2504	0.0429				p.R465Q		Atlas-SNP	.											ANAPC4,NS,carcinoma,+1,1	ANAPC4	61	1	0			c.G1394A						PASS	.	G	GLN/ARG	180,4226	101.6+/-140.2	7,166,2030	53.0	56.0	55.0		1394	5.1	1.0	4	dbSNP_126	55	1886,6710	323.5+/-316.1	207,1472,2619	yes	missense	ANAPC4	NM_013367.2	43	214,1638,4649	AA,AG,GG		21.9404,4.0853,15.8899	benign	465/809	25408838	2066,10936	2203	4298	6501	SO:0001583	missense	29945	exon20			ATAATCGAAAAGG	AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"""Anaphase promoting complex subunits"""	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.1394G>A	4.37:g.25408838G>A	ENSP00000318775:p.Arg465Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	86	52	0.604651	NM_013367	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	37	CCDS3434.1	223	0.1021062271062271	10	0.02032520325203252	54	0.14917127071823205	0	0.0	159	0.20976253298153033	G	13.01	2.110474	0.37242	0.040853	0.219404	ENSG00000053900	ENST00000315368;ENST00000510092	T;T	0.32023	1.47;1.47	5.13	5.13	0.70059	.	0.059354	0.64402	D	0.000001	T	0.00012	0.0000	L	0.27053	0.805	0.21445	P	0.999685615	B	0.25312	0.123	B	0.13407	0.009	T	0.21143	-1.0254	9	0.10377	T	0.69	-6.5303	12.3291	0.55028	0.078:0.0:0.922:0.0	rs34811474;rs61748742	465	Q9UJX5	APC4_HUMAN	Q	465;466	ENSP00000318775:R465Q;ENSP00000426654:R466Q	ENSP00000318775:R465Q	R	+	2	0	ANAPC4	25017936	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	6.177000	0.71961	2.569000	0.86673	0.591000	0.81541	CGA	G|0.858;A|0.142	0.142	strong		0.323	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367	
SLFN12	55106	hgsc.bcm.edu	37	17	33749546	33749546	+	Missense_Mutation	SNP	A	A	G	rs2586514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:33749546A>G	ENST00000394562.1	-	4	1025	c.502T>C	c.(502-504)Tgt>Cgt	p.C168R	SLFN12_ENST00000452764.3_Missense_Mutation_p.C168R|SLFN12_ENST00000304905.5_Missense_Mutation_p.C168R|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	168			C -> R (in dbSNP:rs2586514). {ECO:0000269|PubMed:15489334}.				ATP binding (GO:0005524)			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)		ATATCAACACAGGGCCTCTTT	0.398													G|||	2954	0.589856	0.6278	0.6354	5008	,	,		17852	0.4504		0.5905	False		,,,				2504	0.6493				p.C168R		Atlas-SNP	.											.	SLFN12	56	.	0			c.T502C						PASS	.	G	ARG/CYS	2769,1625		875,1019,303	75.0	78.0	77.0		502	-6.5	0.0	17	dbSNP_100	77	5123,3463		1532,2059,702	yes	missense	SLFN12	NM_018042.3	180	2407,3078,1005	GG,GA,AA		40.3331,36.9822,39.1988	possibly-damaging	168/579	33749546	7892,5088	2197	4293	6490	SO:0001583	missense	55106	exon2			CAACACAGGGCCT	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.502T>C	17.37:g.33749546A>G	ENSP00000378063:p.Cys168Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	1267	0.5801282051282052	327	0.6646341463414634	223	0.6160220994475138	249	0.4353146853146853	468	0.6174142480211082	g	3.337	-0.135420	0.06711	0.630178	0.596669	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.03468	3.92;3.92;3.92	3.23	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36114	-0.9761	8	0.23891	T	0.37	.	1.5985	0.02669	0.3055:0.3582:0.2094:0.1269	rs2586514;rs3744368;rs16970955;rs17846142;rs17859150;rs52828558;rs58226663;rs2586514	168	Q8IYM2	SLN12_HUMAN	R	168	ENSP00000378063:C168R;ENSP00000302077:C168R;ENSP00000394903:C168R	ENSP00000302077:C168R	C	-	1	0	SLFN12	30773659	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.790000	0.04604	-2.103000	0.00844	-1.786000	0.00637	TGT	A|0.416;G|0.584	0.584	strong		0.398	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
TSPAN8	7103	hgsc.bcm.edu	37	12	71523134	71523134	+	Missense_Mutation	SNP	A	A	C	rs1051334	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:71523134A>C	ENST00000393330.2	-	11	1189	c.637T>G	c.(637-639)Tca>Gca	p.S213A	TSPAN8_ENST00000552128.1_Missense_Mutation_p.S130A|TSPAN8_ENST00000546561.1_Missense_Mutation_p.S213A|TSPAN8_ENST00000247829.3_Missense_Mutation_p.S213A			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	128	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	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	
KIAA0408	9729	hgsc.bcm.edu	37	6	127771452	127771452	+	Missense_Mutation	SNP	T	T	G	rs3734447	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:127771452T>G	ENST00000483725.3	-	3	517	c.181A>C	c.(181-183)Agt>Cgt	p.S61R	SOGA3_ENST00000481848.2_3'UTR|SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000368268.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	61			S -> R (in dbSNP:rs3734447). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.							endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		ATCTTAGCACTTTCATTGATA	0.343													G|||	2110	0.421326	0.5802	0.4236	5008	,	,		17599	0.0714		0.5606	False		,,,				2504	0.4223				p.S61R		Atlas-SNP	.											.	KIAA0408	61	.	0			c.A181C						PASS	.	G	,ARG/SER	2560,1844	503.9+/-365.7	736,1088,378	68.0	70.0	69.0		,181	0.0	0.3	6	dbSNP_107	69	5158,3442	495.6+/-374.1	1537,2084,679	yes	utr-3,missense	KIAA0408,C6orf174	NM_001012279.2,NM_014702.4	,110	2273,3172,1057	GG,GT,TT		40.0233,41.871,40.649	,benign	,61/695	127771452	7718,5286	2202	4300	6502	SO:0001583	missense	9729	exon3			TAGCACTTTCATT	AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.181A>C	6.37:g.127771452T>G	ENSP00000435150:p.Ser61Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Missense_Mutation	SNP	ENST00000483725.3	37	CCDS34531.1	903	0.41346153846153844	263	0.5345528455284553	161	0.4447513812154696	44	0.07692307692307693	435	0.5738786279683378	G	2.174	-0.389154	0.04932	0.58129	0.599767	ENSG00000189367	ENST00000483725;ENST00000487331	T;T	0.40476	1.03;1.03	5.7	0.0112	0.14086	.	.	.	.	.	T	0.01835	0.0058	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33240	-0.9876	8	0.07644	T	0.81	0.3958	1.0242	0.01524	0.2802:0.1179:0.3625:0.2395	rs3734447;rs3734447	61	Q6ZU52	K0408_HUMAN	R	61;73	ENSP00000435150:S61R;ENSP00000434384:S73R	ENSP00000435150:S61R	S	-	1	0	KIAA0408	127813145	0.038000	0.19896	0.270000	0.24601	0.099000	0.18886	0.931000	0.28871	-0.150000	0.11195	-0.744000	0.03518	AGT	T|0.483;G|0.517	0.517	strong		0.343	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702	
COMP	1311	hgsc.bcm.edu	37	19	18896823	18896823	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18896823G>A	ENST00000222271.2	-	13	1485	c.1441C>T	c.(1441-1443)Cgg>Tgg	p.R481W	COMP_ENST00000542601.2_Missense_Mutation_p.R448W|COMP_ENST00000425807.1_Missense_Mutation_p.R428W	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	481					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CAGTTGTCCCGACTGTCAGGG	0.701																																					p.R481W		Atlas-SNP	.											.	COMP	62	.	0			c.C1441T						PASS	.						46.0	37.0	40.0					19																	18896823		2203	4300	6503	SO:0001583	missense	1311	exon13			TGTCCCGACTGTC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1441C>T	19.37:g.18896823G>A	ENSP00000222271:p.Arg481Trp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	37	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660379	0.67586	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.98362	-4.89;-4.89;-4.89	4.05	2.98	0.34508	.	0.243213	0.29133	U	0.013053	D	0.97901	0.9310	M	0.82716	2.605	0.37365	D	0.911397	P;P	0.47409	0.895;0.799	P;P	0.48114	0.469;0.567	D	0.98175	1.0454	10	0.72032	D	0.01	-29.5678	11.6098	0.51053	0.0:0.0:0.8201:0.1798	.	428;481	B4DKJ3;P49747	.;COMP_HUMAN	W	448;481;428;468	ENSP00000439156:R448W;ENSP00000222271:R481W;ENSP00000403792:R428W	ENSP00000222271:R481W	R	-	1	2	COMP	18757823	0.001000	0.12720	0.993000	0.49108	0.590000	0.36582	1.014000	0.29950	0.670000	0.31165	0.491000	0.48974	CGG	.	.	none		0.701	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095	
SCAI	286205	hgsc.bcm.edu	37	9	127764305	127764305	+	Silent	SNP	G	G	A	rs764304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:127764305G>A	ENST00000336505.6	-	12	1141	c.1083C>T	c.(1081-1083)agC>agT	p.S361S	SCAI_ENST00000487795.1_5'UTR|SCAI_ENST00000373549.4_Silent_p.S384S	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	361					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.S384S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TCAGAAGCACGCTATTGGCAG	0.418													G|||	765	0.152756	0.0877	0.1138	5008	,	,		19547	0.1121		0.2555	False		,,,				2504	0.2045				p.S384S		Atlas-SNP	.											SCAI,NS,carcinoma,0,1	SCAI	84	1	1	Substitution - coding silent(1)	stomach(1)	c.C1152T						PASS	.	G	,	366,3438		15,336,1551	107.0	103.0	105.0		1083,1152	-4.7	0.9	9	dbSNP_86	105	1893,6347		203,1487,2430	no	coding-synonymous,coding-synonymous	SCAI	NM_001144877.2,NM_173690.4	,	218,1823,3981	AA,AG,GG		22.9733,9.6215,18.7562	,	361/607,384/630	127764305	2259,9785	1902	4120	6022	SO:0001819	synonymous_variant	286205	exon13			AAGCACGCTATTG	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1083C>T	9.37:g.127764305G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Silent	SNP	ENST00000336505.6	37	CCDS48017.1																																																																																			G|0.838;A|0.162	0.162	strong		0.418	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
DDX55	57696	hgsc.bcm.edu	37	12	124104551	124104551	+	Missense_Mutation	SNP	A	A	G	rs10773019	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124104551A>G	ENST00000238146.4	+	14	1717	c.1667A>G	c.(1666-1668)aAt>aGt	p.N556S	DDX55_ENST00000421670.3_Missense_Mutation_p.N163S|DDX55_ENST00000538744.1_Missense_Mutation_p.N525S	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	556	Lys-rich.		N -> S (in dbSNP:rs10773019).			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)		GAACTTCTTAATGACACAAGA	0.348													A|||	505	0.100839	0.1498	0.0432	5008	,	,		19820	0.0883		0.0437	False		,,,				2504	0.1472				p.N556S		Atlas-SNP	.											.	DDX55	51	.	0			c.A1667G						PASS	.	A	SER/ASN	610,3796	264.7+/-266.2	43,524,1636	93.0	99.0	97.0		1667	4.5	1.0	12	dbSNP_120	97	397,8203	126.7+/-185.1	9,379,3912	yes	missense	DDX55	NM_020936.1	46	52,903,5548	GG,GA,AA		4.6163,13.8448,7.7426	benign	556/601	124104551	1007,11999	2203	4300	6503	SO:0001583	missense	57696	exon14			TTCTTAATGACAC	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.1667A>G	12.37:g.124104551A>G	ENSP00000238146:p.Asn556Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	80	27	0.3375	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	159	0.07280219780219781	68	0.13821138211382114	18	0.049723756906077346	41	0.07167832167832168	32	0.04221635883905013	A	9.409	1.080071	0.20309	0.138448	0.046163	ENSG00000111364	ENST00000238146;ENST00000538744;ENST00000421670	T;T;T	0.51817	0.69;0.69;0.69	5.62	4.47	0.54385	.	0.514144	0.24224	N	0.040417	T	0.00241	0.0007	L	0.28694	0.88	0.09310	P	0.999999093845	B	0.02656	0.0	B	0.06405	0.002	T	0.08554	-1.0716	9	0.10111	T	0.7	-30.3039	11.6517	0.51292	0.9303:0.0:0.0697:0.0	rs10773019;rs58894494;rs10773019	556	Q8NHQ9	DDX55_HUMAN	S	556;525;163	ENSP00000238146:N556S;ENSP00000443114:N525S;ENSP00000442332:N163S	ENSP00000238146:N556S	N	+	2	0	DDX55	122670504	1.000000	0.71417	0.987000	0.45799	0.844000	0.47949	5.492000	0.66893	0.950000	0.37743	-0.411000	0.06167	AAT	A|0.922;G|0.078	0.078	strong		0.348	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
UMODL1	89766	hgsc.bcm.edu	37	21	43547873	43547873	+	Missense_Mutation	SNP	G	G	A	rs220159	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43547873G>A	ENST00000408910.2	+	20	3622	c.3622G>A	c.(3622-3624)Gac>Aac	p.D1208N	UMODL1_ENST00000400427.1_Missense_Mutation_p.D1264N|UMODL1_ENST00000400424.2_Missense_Mutation_p.D1136N|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000408989.2_Missense_Mutation_p.D1336N	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1208	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		D -> N (in dbSNP:rs220159). {ECO:0000269|PubMed:16026467}.		adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CTTTATCAACGACTCCATCGT	0.488													A|||	1792	0.357827	0.3253	0.4236	5008	,	,		20774	0.369		0.3499	False		,,,				2504	0.3517				p.D1336N	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											UMODL1_ENST00000408989,colon,carcinoma,0,2	UMODL1	186	2	0			c.G4006A						PASS	.	A	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1242,2800		217,808,996	127.0	126.0	127.0		3622,3790,3406,4006	2.4	0.9	21	dbSNP_79	127	2939,5417		524,1891,1763	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	23,23,23,23	741,2699,2759	AA,AG,GG		35.1723,30.7274,33.7232	benign,benign,benign,benign	1208/1319,1264/1375,1136/1247,1336/1447	43547873	4181,8217	2021	4178	6199	SO:0001583	missense	89766	exon19			ATCAACGACTCCA		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.3622G>A	21.37:g.43547873G>A	ENSP00000386147:p.Asp1208Asn	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	162	64	0.395062	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	800	0.3663003663003663	161	0.32723577235772355	156	0.430939226519337	219	0.38286713286713286	264	0.3482849604221636	A	0.009	-1.855586	0.00558	0.307274	0.351723	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000434156	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	3.56	2.42	0.29668	Zona pellucida sperm-binding protein (3);	0.000000	0.48286	N	0.000200	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.36016	-0.9765	8	.	.	.	-26.8106	6.7343	0.23401	0.7075:0.0:0.2925:0.0	rs220159;rs512994;rs17177620;rs52807694;rs59318415;rs220159	1336;1208	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	N	1264;1136;1336;1208;93	ENSP00000383279:D1264N;ENSP00000383276:D1136N;ENSP00000386126:D1336N;ENSP00000386147:D1208N	.	D	+	1	0	UMODL1	42420942	0.993000	0.37304	0.924000	0.36721	0.050000	0.14768	0.913000	0.28611	0.263000	0.21812	-0.361000	0.07541	GAC	G|0.638;N|0.000	.	strong		0.488	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
RTN4	57142	hgsc.bcm.edu	37	2	55254165	55254165	+	Missense_Mutation	SNP	T	T	A	rs11677099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:55254165T>A	ENST00000337526.6	-	3	1313	c.1070A>T	c.(1069-1071)gAt>gTt	p.D357V	RTN4_ENST00000402434.2_Intron|RTN4_ENST00000354474.6_Missense_Mutation_p.D125V|RTN4_ENST00000404909.1_Missense_Mutation_p.D151V|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.D151V|RTN4_ENST00000394611.2_Missense_Mutation_p.D151V|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.D151V	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	357			D -> V (in dbSNP:rs11677099).		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.D151V(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						CACAACTTCATCCTCTTTAAC	0.343													T|||	124	0.0247604	0.0015	0.0101	5008	,	,		21251	0.0615		0.0298	False		,,,				2504	0.0235				p.D357V		Atlas-SNP	.											RTN4,NS,carcinoma,0,1	RTN4	189	1	1	Substitution - Missense(1)	stomach(1)	c.A1070T						scavenged	.	T	VAL/ASP,,,VAL/ASP	20,4386	27.2+/-55.0	0,20,2183	118.0	118.0	118.0		1070,,,452	3.9	0.6	2	dbSNP_120	118	212,8384	89.9+/-152.1	2,208,4088	yes	missense,intron,intron,missense	RTN4	NM_020532.4,NM_153828.2,NM_207520.1,NM_207521.1	152,,,152	2,228,6271	AA,AT,TT		2.4663,0.4539,1.7843	probably-damaging,,,probably-damaging	357/1193,,,151/987	55254165	232,12770	2203	4298	6501	SO:0001583	missense	57142	exon3			ACTTCATCCTCTT	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1070A>T	2.37:g.55254165T>A	ENSP00000337838:p.Asp357Val	Somatic	105	2	0.0190476		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	58	0.026556776556776556	0	0.0	4	0.011049723756906077	31	0.05419580419580419	23	0.030343007915567283	T	8.701	0.909659	0.17833	0.004539	0.024663	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.25414	1.8;1.8;2.32;1.8;1.8;1.83	5.06	3.9	0.45041	.	0.889178	0.09889	N	0.742595	T	0.09598	0.0236	M	0.64997	1.995	0.48236	D	0.999612	D	0.63880	0.993	P	0.58721	0.844	T	0.00643	-1.1630	10	0.87932	D	0	-8.3706	7.8349	0.29363	0.0:0.1643:0.0:0.8357	rs11677099;rs11677099	357	Q9NQC3	RTN4_HUMAN	V	151;151;357;151;151;125	ENSP00000384471:D151V;ENSP00000349944:D151V;ENSP00000337838:D357V;ENSP00000378109:D151V;ENSP00000385650:D151V;ENSP00000346465:D125V	ENSP00000337838:D357V	D	-	2	0	RTN4	55107669	0.365000	0.25006	0.557000	0.28306	0.042000	0.13812	1.426000	0.34870	0.770000	0.33336	-0.388000	0.06559	GAT	T|0.976;A|0.024	0.024	strong		0.343	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1		
KCTD20	222658	hgsc.bcm.edu	37	6	36446975	36446975	+	Missense_Mutation	SNP	G	G	C	rs2239808	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:36446975G>C	ENST00000373731.2	+	4	903	c.512G>C	c.(511-513)aGt>aCt	p.S171T	KCTD20_ENST00000449081.2_Intron|KCTD20_ENST00000474988.1_Intron|KCTD20_ENST00000544295.1_5'UTR|KCTD20_ENST00000536244.1_Missense_Mutation_p.S26T	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	171	BTB.		S -> T (in dbSNP:rs2239808). {ECO:0000269|PubMed:14702039}.		protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						GAAGGCATCAGTGCAACTGTA	0.453													G|||	1554	0.310304	0.4576	0.219	5008	,	,		21392	0.378		0.2227	False		,,,				2504	0.1963				p.S171T		Atlas-SNP	.											.	KCTD20	37	.	0			c.G512C						PASS	.	G	THR/SER	1812,2594	531.1+/-373.1	365,1082,756	204.0	151.0	169.0		512	5.3	1.0	6	dbSNP_98	169	1655,6945	305.6+/-307.5	149,1357,2794	yes	missense	KCTD20	NM_173562.3	58	514,2439,3550	CC,CG,GG		19.2442,41.1257,26.6569	possibly-damaging	171/420	36446975	3467,9539	2203	4300	6503	SO:0001583	missense	222658	exon4			GCATCAGTGCAAC	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"""chromosome 6 open reading frame 69"", ""potassium channel tetramerisation domain containing 20"""	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.512G>C	6.37:g.36446975G>C	ENSP00000362836:p.Ser171Thr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	193	106	0.549223	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	37	CCDS4821.1	694	0.31776556776556775	241	0.4898373983739837	67	0.1850828729281768	222	0.3881118881118881	164	0.21635883905013192	G	32	5.117970	0.94385	0.411257	0.192442	ENSG00000112078	ENST00000373731;ENST00000536244	T;D	0.94723	0.83;-3.5	5.29	5.29	0.74685	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.199717	0.47093	D	0.000257	D	0.97071	0.9043	M	0.83852	2.665	0.09310	P	1.0	D	0.71674	0.998	D	0.67103	0.949	D	0.96551	0.9408	9	0.52906	T	0.07	-21.5181	19.1338	0.93418	0.0:0.0:1.0:0.0	rs2239808;rs52792836;rs57808269;rs2239808	171	Q7Z5Y7	KCD20_HUMAN	T	171;26	ENSP00000362836:S171T;ENSP00000439118:S26T	ENSP00000362836:S171T	S	+	2	0	KCTD20	36554953	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.657000	0.98554	2.752000	0.94435	0.655000	0.94253	AGT	G|0.705;C|0.295	0.295	strong		0.453	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562	
C4orf26	152816	hgsc.bcm.edu	37	4	76489345	76489345	+	Missense_Mutation	SNP	C	C	T	rs2306175	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:76489345C>T	ENST00000311623.4	+	2	124	c.89C>T	c.(88-90)cCt>cTt	p.P30L	C4orf26_ENST00000435974.2_Missense_Mutation_p.L45F	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	30			P -> L (in dbSNP:rs2306175). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)		p.P30L(1)		kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GTATTTACGCCTCCTGGAGAT	0.542													C|||	1220	0.24361	0.3238	0.1715	5008	,	,		18003	0.244		0.2276	False		,,,				2504	0.2025				p.L45F		Atlas-SNP	.											C4orf26,NS,carcinoma,0,1	C4orf26	24	1	1	Substitution - Missense(1)	stomach(1)	c.C133T						PASS	.	C	PHE/LEU,LEU/PRO	1354,3052	450.0+/-349.2	201,952,1050	69.0	73.0	72.0		133,89	2.8	0.3	4	dbSNP_100	72	2014,6586	351.0+/-328.1	261,1492,2547	yes	missense,missense	C4orf26	NM_001206981.1,NM_178497.3	22,98	462,2444,3597	TT,TC,CC		23.4186,30.7308,25.8957	possibly-damaging,possibly-damaging	45/177,30/131	76489345	3368,9638	2203	4300	6503	SO:0001583	missense	152816	exon3			TTACGCCTCCTGG	AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.89C>T	4.37:g.76489345C>T	ENSP00000311307:p.Pro30Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	NM_001206981	B4DTI3|E7ETQ0|Q8TEC3	Missense_Mutation	SNP	ENST00000311623.4	37	CCDS3569.1	567|567	0.25961538461538464|0.25961538461538464	184|184	0.37398373983739835|0.37398373983739835	65|65	0.17955801104972377|0.17955801104972377	145|145	0.2534965034965035|0.2534965034965035	173|173	0.22823218997361477|0.22823218997361477	C|C	14.06|14.06	2.423024|2.423024	0.43020|0.43020	0.307308|0.307308	0.234186|0.234186	ENSG00000174792|ENSG00000174792	ENST00000435974|ENST00000311623	T|T	0.60424|0.64618	0.19|-0.11	4.6|4.6	2.84|2.84	0.33178|0.33178	.|.	.|0.145749	.|0.32120	.|N	.|0.006545	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.29908|0.29908	0.895|0.895	0.48185|0.48185	P|P	3.950000000000342E-4|3.950000000000342E-4	P|P	0.50943|0.35107	0.94|0.484	P|B	0.47015|0.35655	0.534|0.207	T|T	0.37103|0.37103	-0.9720|-0.9720	8|9	0.87932|0.33940	D|T	0|0.23	.|.	6.3991|6.3991	0.21628|0.21628	0.0:0.7141:0.1857:0.1002|0.0:0.7141:0.1857:0.1002	rs2306175;rs52816760;rs61113264;rs2306175|rs2306175;rs52816760;rs61113264;rs2306175	45|30	E7ETQ0|Q17RF5	.|CD026_HUMAN	F|L	45|30	ENSP00000406925:L45F|ENSP00000311307:P30L	ENSP00000406925:L45F|ENSP00000311307:P30L	L|P	+|+	1|2	0|0	C4orf26|C4orf26	76708369|76708369	0.182000|0.182000	0.23173|0.23173	0.304000|0.304000	0.25085|0.25085	0.213000|0.213000	0.24496|0.24496	1.953000|1.953000	0.40352|0.40352	0.663000|0.663000	0.31027|0.31027	0.551000|0.551000	0.68910|0.68910	CTC|CCT	C|0.741;T|0.259	0.259	strong		0.542	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497	
FLG	2312	hgsc.bcm.edu	37	1	152276377	152276377	+	Missense_Mutation	SNP	C	C	G	rs139284720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152276377C>G	ENST00000368799.1	-	3	11020	c.10985G>C	c.(10984-10986)aGt>aCt	p.S3662T	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3662	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S3662T(2)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTGGCCTGACTACCACTGGA	0.587									Ichthyosis																												p.S3662T		Atlas-SNP	.											FLG,extremity,malignant_melanoma,0,2	FLG	900	2	2	Substitution - Missense(2)	skin(2)	c.G10985C						scavenged	.						34.0	36.0	35.0					1																	152276377		2199	4266	6465	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCCTGACTACCAC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10985G>C	1.37:g.152276377C>G	ENSP00000357789:p.Ser3662Thr	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	211	26	0.123223	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.330609	0.24167	.	.	ENSG00000143631	ENST00000368799	T	0.20598	2.06	4.62	-2.36	0.06663	.	.	.	.	.	T	0.14874	0.0359	M	0.69823	2.125	0.09310	N	1	P	0.40211	0.707	P	0.54889	0.763	T	0.26883	-1.0090	9	0.25751	T	0.34	.	3.5688	0.07909	0.4266:0.3171:0.0:0.2564	.	3662	P20930	FILA_HUMAN	T	3662	ENSP00000357789:S3662T	ENSP00000357789:S3662T	S	-	2	0	FLG	150543001	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.742000	0.04850	-0.547000	0.06207	-0.240000	0.12126	AGT	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
RYR2	6262	hgsc.bcm.edu	37	1	237841390	237841390	+	Missense_Mutation	SNP	A	A	G	rs34967813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237841390A>G	ENST00000366574.2	+	61	9190	c.8873A>G	c.(8872-8874)cAa>cGa	p.Q2958R	RYR2_ENST00000542537.1_Missense_Mutation_p.Q2942R|RYR2_ENST00000609119.1_Intron|RYR2_ENST00000360064.6_Missense_Mutation_p.Q2956R	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2958			Q -> R (in dbSNP:rs34967813). {ECO:0000269|PubMed:11157710}.		BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CCTTATGAACAAGAAATCAAG	0.358													A|||	497	0.0992412	0.0113	0.1988	5008	,	,		19250	0.0		0.2942	False		,,,				2504	0.0491				p.Q2958R		Atlas-SNP	.											.	RYR2	1273	.	0			c.A8873G						PASS	.	A	ARG/GLN	199,3583		7,185,1699	109.0	106.0	107.0		8873	5.7	1.0	1	dbSNP_126	107	2499,5717		379,1741,1988	yes	missense	RYR2	NM_001035.2	43	386,1926,3687	GG,GA,AA		30.4163,5.2618,22.4871	possibly-damaging	2958/4968	237841390	2698,9300	1891	4108	5999	SO:0001583	missense	6262	exon61			ATGAACAAGAAAT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8873A>G	1.37:g.237841390A>G	ENSP00000355533:p.Gln2958Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	135	76	0.562963	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	313	0.1433150183150183	10	0.02032520325203252	77	0.212707182320442	0	0.0	226	0.29815303430079154	A	17.35	3.367905	0.61513	0.052618	0.304163	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;D;D	0.96745	-0.29;-4.08;-4.11	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000013	T	0.00039	0.0001	L	0.38649	1.16	0.09310	P	1.0	B	0.30605	0.287	B	0.20955	0.032	T	0.04708	-1.0932	9	0.21014	T	0.42	.	10.2872	0.43575	0.9266:0.0:0.0734:0.0	rs34967813	2958	Q92736	RYR2_HUMAN	R	2958;2956;2942	ENSP00000355533:Q2958R;ENSP00000353174:Q2956R;ENSP00000443798:Q2942R	ENSP00000353174:Q2956R	Q	+	2	0	RYR2	235908013	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.168000	0.77570	2.164000	0.68074	0.482000	0.46254	CAA	A|0.827;G|0.173	0.173	strong		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
FBF1	85302	hgsc.bcm.edu	37	17	73919521	73919521	+	Silent	SNP	C	C	T	rs7219918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73919521C>T	ENST00000586717.1	-	13	1401	c.1128G>A	c.(1126-1128)gtG>gtA	p.V376V	FBF1_ENST00000319129.5_Silent_p.V375V|FBF1_ENST00000389570.4_Silent_p.V376V			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	376					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						CAGGAGGAGGCACTGAGGGCG	0.652													C|||	343	0.0684904	0.1157	0.0519	5008	,	,		18965	0.0248		0.0378	False		,,,				2504	0.093				p.V375V		Atlas-SNP	.											.	FBF1	48	.	0			c.G1125A						PASS	.	C		371,3791		14,343,1724	26.0	31.0	29.0		1125	-5.4	0.0	17	dbSNP_116	29	358,8068		6,346,3861	no	coding-synonymous	FBF1	NM_001080542.1		20,689,5585	TT,TC,CC		4.2488,8.914,5.7912		375/1134	73919521	729,11859	2081	4213	6294	SO:0001819	synonymous_variant	85302	exon13			AGGAGGCACTGAG	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.1128G>A	17.37:g.73919521C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				C|0.955;T|0.045	0.045	strong		0.652	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
ANKLE2	23141	hgsc.bcm.edu	37	12	133306589	133306589	+	Missense_Mutation	SNP	C	C	T	rs10781634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:133306589C>T	ENST00000357997.5	-	11	2248	c.2159G>A	c.(2158-2160)cGt>cAt	p.R720H	ANKLE2_ENST00000542282.1_Missense_Mutation_p.R75H|ANKLE2_ENST00000539605.1_Missense_Mutation_p.R658H|ANKLE2_ENST00000542657.1_Missense_Mutation_p.R75H|ANKLE2_ENST00000542374.1_Intron	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	720			R -> H (in dbSNP:rs10781634). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		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)		TTCCTCCCCACGGGGGGCCTT	0.552													c|||	1238	0.247204	0.0802	0.2378	5008	,	,		15304	0.1944		0.4165	False		,,,				2504	0.3599				p.R720H		Atlas-SNP	.											.	ANKLE2	76	.	0			c.G2159A						PASS	.		HIS/ARG	495,3391		32,431,1480	78.0	83.0	81.0		2159	0.2	0.0	12	dbSNP_120	81	3297,4975		633,2031,1472	yes	missense	ANKLE2	NM_015114.1	29	665,2462,2952	TT,TC,CC		39.8574,12.738,31.1893	benign	720/939	133306589	3792,8366	1943	4136	6079	SO:0001583	missense	23141	exon11			TCCCCACGGGGGG	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.2159G>A	12.37:g.133306589C>T	ENSP00000350686:p.Arg720His	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	574	0.26282051282051283	48	0.0975609756097561	90	0.24861878453038674	110	0.19230769230769232	326	0.43007915567282323	C	14.07	2.425109	0.43020	0.12738	0.398574	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000542282;ENST00000542657;ENST00000538766	T;T;T;T;T	0.44083	1.94;1.93;0.93;0.93;0.93	5.76	0.237	0.15475	.	1.247070	0.04915	N	0.454003	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.46457	0.878	B	0.37198	0.243	T	0.36792	-0.9733	9	0.42905	T	0.14	0.0564	5.4233	0.16411	0.0:0.2898:0.3084:0.4018	rs10781634;rs17846348;rs17859383;rs10781634	720	Q86XL3	ANKL2_HUMAN	H	658;720;75;75;75	ENSP00000446268:R658H;ENSP00000350686:R720H;ENSP00000437807:R75H;ENSP00000438551:R75H;ENSP00000445760:R75H	ENSP00000350686:R720H	R	-	2	0	ANKLE2	131816662	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.164000	0.16542	-0.144000	0.11314	0.651000	0.88453	CGT	C|0.713;T|0.287	0.287	strong		0.552	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
ABCA13	154664	hgsc.bcm.edu	37	7	48428715	48428715	+	Missense_Mutation	SNP	A	A	T	rs17132289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:48428715A>T	ENST00000435803.1	+	37	11576	c.11552A>T	c.(11551-11553)tAt>tTt	p.Y3851F		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3851	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		Y -> F (in dbSNP:rs17132289). {ECO:0000269|Ref.5}.		transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.Y3851F(1)|p.Y3796F(1)		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						ACCAAGGAATATGAGGGCCAC	0.542													A|||	429	0.0856629	0.1339	0.0692	5008	,	,		16052	0.1121		0.0676	False		,,,				2504	0.0235				p.Y3851F		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,0,2	ABCA13	1192	2	2	Substitution - Missense(2)	stomach(2)	c.A11552T						PASS	.	A	PHE/TYR	387,3449		19,349,1550	72.0	74.0	73.0		11552	2.0	0.0	7	dbSNP_123	73	580,7710		26,528,3591	yes	missense	ABCA13	NM_152701.3	22	45,877,5141	TT,TA,AA		6.9964,10.0886,7.9746	possibly-damaging	3851/5059	48428715	967,11159	1918	4145	6063	SO:0001583	missense	154664	exon37			AGGAATATGAGGG	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.11552A>T	7.37:g.48428715A>T	ENSP00000411096:p.Tyr3851Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	201	0.09203296703296704	57	0.11585365853658537	30	0.08287292817679558	71	0.12412587412587413	43	0.05672823218997362	A	7.230	0.599165	0.13939	0.100886	0.069964	ENSG00000179869	ENST00000435803	D	0.94457	-3.43	4.59	2.01	0.26516	ABC transporter-like (1);	0.406771	0.17968	N	0.155957	T	0.12774	0.0310	N	0.21142	0.635	0.52501	P	4.4000000000044004E-5	P;D	0.56521	0.886;0.976	P;P	0.48368	0.514;0.575	T	0.63980	-0.6514	9	0.29301	T	0.29	.	5.7565	0.18176	0.6554:0.176:0.0:0.1686	rs17132289;rs52817806;rs17132289	1553;3851	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	F	3851	ENSP00000411096:Y3851F	ENSP00000411096:Y3851F	Y	+	2	0	ABCA13	48399261	0.988000	0.35896	0.004000	0.12327	0.055000	0.15305	4.165000	0.58196	0.173000	0.19788	-0.316000	0.08728	TAT	A|0.908;T|0.092	0.092	strong		0.542	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
KIAA1217	56243	hgsc.bcm.edu	37	10	24669877	24669877	+	Missense_Mutation	SNP	C	C	G	rs17506606	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:24669877C>G	ENST00000376454.3	+	3	464	c.434C>G	c.(433-435)gCt>gGt	p.A145G	KIAA1217_ENST00000430453.2_Missense_Mutation_p.A66G|KIAA1217_ENST00000376462.1_Missense_Mutation_p.A65G|KIAA1217_ENST00000458595.1_Missense_Mutation_p.A145G|KIAA1217_ENST00000376452.3_Missense_Mutation_p.A145G	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	145			A -> G (in dbSNP:rs17506606).		embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GAGACGTCCGCTGATTCTTTG	0.547													C|||	519	0.103634	0.0113	0.1196	5008	,	,		14086	0.002		0.2614	False		,,,				2504	0.1595				p.A145G		Atlas-SNP	.											KIAA1217,caecum,carcinoma,+1,1	KIAA1217	235	1	0			c.C434G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA	231,4175	136.9+/-172.8	5,221,1977	67.0	70.0	69.0		194,434,434	-0.2	0.0	10	dbSNP_123	69	2237,6363	380.1+/-339.5	297,1643,2360	yes	missense,missense,missense	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	60,60,60	302,1864,4337	GG,GC,CC		26.0116,5.2429,18.9759	benign,benign,benign	65/1265,145/1310,145/1944	24669877	2468,10538	2203	4300	6503	SO:0001583	missense	56243	exon3			CGTCCGCTGATTC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.434C>G	10.37:g.24669877C>G	ENSP00000365637:p.Ala145Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	271	0.12408424908424909	10	0.02032520325203252	55	0.15193370165745856	1	0.0017482517482517483	205	0.2704485488126649	C	10.81	1.455385	0.26161	0.052429	0.260116	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452;ENST00000430453	T;D;T;T;T;T	0.94793	-0.21;-3.52;-0.21;-0.21;-0.21;-0.21	5.54	-0.211	0.13172	.	0.377421	0.29932	N	0.010838	T	0.00073	0.0002	N	0.21282	0.65	0.38500	P	0.05179999999999996	B;B;B;B	0.10296	0.003;0.002;0.001;0.0	B;B;B;B	0.11329	0.002;0.006;0.002;0.0	T	0.16482	-1.0401	9	0.20046	T	0.44	.	15.5179	0.75840	0.0:0.735:0.1778:0.0872	rs17506606;rs56583113;rs17506606	145;145;145;145	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	G	65;145;145;145;145;66	ENSP00000365645:A65G;ENSP00000365639:A145G;ENSP00000392625:A145G;ENSP00000365637:A145G;ENSP00000365635:A145G;ENSP00000389680:A66G	ENSP00000365635:A145G	A	+	2	0	KIAA1217	24709883	0.640000	0.27243	0.008000	0.14137	0.498000	0.33706	1.095000	0.30964	-0.005000	0.14395	-0.282000	0.10007	GCT	C|0.845;G|0.155	0.155	strong		0.547	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
CCDC154	645811	hgsc.bcm.edu	37	16	1488697	1488697	+	Silent	SNP	G	G	A	rs187437805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1488697G>A	ENST00000389176.3	-	9	1141	c.975C>T	c.(973-975)gcC>gcT	p.A325A	CCDC154_ENST00000409671.1_Silent_p.A171A	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	325						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						GCTGGGCCACGGCAGCATCCA	0.697													G|||	12	0.00239617	0.0	0.0014	5008	,	,		12010	0.0079		0.003	False		,,,				2504	0.0				p.A316A		Atlas-SNP	.											.	CCDC154	27	.	0			c.C948T						PASS	.	G		1,1383		0,1,691	39.0	44.0	42.0		948	-4.9	0.1	16		42	10,3172		0,10,1581	no	coding-synonymous	CCDC154	NM_001143980.1		0,11,2272	AA,AG,GG		0.3143,0.0723,0.2409		316/668	1488697	11,4555	692	1591	2283	SO:0001819	synonymous_variant	645811	exon9			GGCCACGGCAGCA			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.975C>T	16.37:g.1488697G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_001143980	G9JV18	Silent	SNP	ENST00000389176.3	37																																																																																				G|0.998;A|0.002	0.002	strong		0.697	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
SLC7A9	11136	hgsc.bcm.edu	37	19	33353041	33353041	+	Silent	SNP	G	G	A	rs1007161	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33353041G>A	ENST00000023064.4	-	6	878	c.687C>T	c.(685-687)ctC>ctT	p.L229L	SLC7A9_ENST00000587772.1_Silent_p.L229L|SLC7A9_ENST00000590341.1_Silent_p.L229L|RN7SKP22_ENST00000365097.1_RNA	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	229					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)	CATAGGCCCAGAGTCCATTGT	0.507													G|||	1393	0.278155	0.3033	0.1772	5008	,	,		16825	0.3046		0.3668	False		,,,				2504	0.1973				p.L229L	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.C687T						PASS	.	G	,	1380,3026	454.9+/-350.8	214,952,1037	110.0	105.0	107.0		687,687	2.8	1.0	19	dbSNP_86	107	2909,5691	455.1+/-363.7	477,1955,1868	no	coding-synonymous,coding-synonymous	SLC7A9	NM_001126335.1,NM_014270.4	,	691,2907,2905	AA,AG,GG		33.8256,31.3209,32.9771	,	229/488,229/488	33353041	4289,8717	2203	4300	6503	SO:0001819	synonymous_variant	11136	exon6			GGCCCAGAGTCCA	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.687C>T	19.37:g.33353041G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																			G|0.698;A|0.302	0.302	strong		0.507	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
UBR2	23304	hgsc.bcm.edu	37	6	42627430	42627430	+	Silent	SNP	C	C	T	rs6916713	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42627430C>T	ENST00000372899.1	+	30	3537	c.3279C>T	c.(3277-3279)ggC>ggT	p.G1093G	UBR2_ENST00000372901.1_Silent_p.G1093G|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1093					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)			CAGCACTGGGCCCCGCACAAA	0.398													C|||	1265	0.252596	0.2042	0.1988	5008	,	,		16291	0.3026		0.2972	False		,,,				2504	0.2587				p.G1093G		Atlas-SNP	.											.	UBR2	134	.	0			c.C3279T						PASS	.	C		949,3457	359.9+/-315.0	105,739,1359	86.0	79.0	81.0		3279	0.6	1.0	6	dbSNP_116	81	2484,6116	405.5+/-348.5	360,1764,2176	no	coding-synonymous	UBR2	NM_015255.2		465,2503,3535	TT,TC,CC		28.8837,21.5388,26.3955		1093/1756	42627430	3433,9573	2203	4300	6503	SO:0001819	synonymous_variant	23304	exon30			ACTGGGCCCCGCA	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.3279C>T	6.37:g.42627430C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			C|0.739;T|0.261	0.261	strong		0.398	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
VN1R4	317703	hgsc.bcm.edu	37	19	53770569	53770569	+	Missense_Mutation	SNP	G	G	C	rs200548838|rs74359534		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53770569G>C	ENST00000311170.4	-	1	403	c.350C>G	c.(349-351)gCa>gGa	p.A117G	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	117					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)		TTTAAGTTTTGCCCACCTGGA	0.498										HNSCC(26;0.072)																											p.A117G		Atlas-SNP	.											.	VN1R4	65	.	0			c.C350G						PASS	.	G	GLY/ALA	589,3817		0,589,1614	65.0	49.0	54.0		350	-0.2	0.0	19	dbSNP_132	54	380,8220		0,380,3920	no	missense	VN1R4	NM_173857.2	60	0,969,5534	CC,CG,GG		4.4186,13.3681,7.4504	probably-damaging	117/302	53770569	969,12037	2203	4300	6503	SO:0001583	missense	317703	exon1			AGTTTTGCCCACC	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.350C>G	19.37:g.53770569G>C	ENSP00000310856:p.Ala117Gly	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	295	95	0.322034	NM_173857	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	156	0.07142857142857142	54	0.10975609756097561	16	0.04419889502762431	60	0.1048951048951049	26	0.03430079155672823	G	1.836	-0.468527	0.04445	0.133681	0.044186	ENSG00000228567	ENST00000311170	T	0.37058	1.22	2.28	-0.254	0.12992	GPCR, rhodopsin-like superfamily (1);	1.356640	0.05421	N	0.544248	T	0.00496	0.0016	M	0.70595	2.14	0.09310	N	1	B	0.30146	0.27	B	0.39562	0.303	T	0.31971	-0.9924	10	0.62326	D	0.03	.	5.3871	0.16224	0.0:0.4302:0.3517:0.2182	.	117	Q7Z5H5	VN1R4_HUMAN	G	117	ENSP00000310856:A117G	ENSP00000310856:A117G	A	-	2	0	VN1R4	58462381	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	0.522000	0.22909	0.038000	0.15604	-0.334000	0.08254	GCA	G|0.500;C|0.500	0.500	weak		0.498	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857	
GIMAP2	26157	hgsc.bcm.edu	37	7	150389593	150389593	+	Silent	SNP	T	T	C	rs1860871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150389593T>C	ENST00000223293.5	+	3	313	c.219T>C	c.(217-219)atT>atC	p.I73I		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	73	AIG1-type G.					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)		ATAGAGAGATTGTCATTATTG	0.483													T|||	496	0.0990415	0.0348	0.0821	5008	,	,		21860	0.2163		0.0865	False		,,,				2504	0.09				p.I73I		Atlas-SNP	.											.	GIMAP2	39	.	0			c.T219C						PASS	.	T		190,4216	120.0+/-157.7	8,174,2021	92.0	86.0	88.0		219	1.8	0.0	7	dbSNP_92	88	766,7834	182.6+/-231.0	42,682,3576	no	coding-synonymous	GIMAP2	NM_015660.2		50,856,5597	CC,CT,TT		8.907,4.3123,7.3505		73/338	150389593	956,12050	2203	4300	6503	SO:0001819	synonymous_variant	26157	exon3			AGAGATTGTCATT	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.219T>C	7.37:g.150389593T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	149	83	0.557047	NM_015660	Q96L25	Silent	SNP	ENST00000223293.5	37	CCDS5905.1																																																																																			T|0.910;C|0.090	0.090	strong		0.483	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
ARHGAP44	9912	hgsc.bcm.edu	37	17	12852459	12852459	+	Silent	SNP	A	A	G	rs2072254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:12852459A>G	ENST00000379672.5	+	11	1164	c.864A>G	c.(862-864)ggA>ggG	p.G288G	ARHGAP44_ENST00000262444.9_Silent_p.G288G|ARHGAP44_ENST00000340825.3_Silent_p.G288G	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	288	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						GTTGGTAGGGACTCTTCCGAG	0.577													A|||	527	0.105232	0.0325	0.1138	5008	,	,		18166	0.1845		0.0765	False		,,,				2504	0.1452				p.G288G		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.A864G						PASS	.	A		192,4000		5,182,1909	29.0	31.0	30.0		864	-1.0	1.0	17	dbSNP_96	30	686,7716		23,640,3538	no	coding-synonymous	ARHGAP44	NM_014859.4		28,822,5447	GG,GA,AA		8.1647,4.5802,6.9716		288/819	12852459	878,11716	2096	4201	6297	SO:0001819	synonymous_variant	9912	exon11			GTAGGGACTCTTC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.864A>G	17.37:g.12852459A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Silent	SNP	ENST00000379672.5	37	CCDS45616.1																																																																																			A|0.902;G|0.098	0.098	strong		0.577	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859	
AHNAK2	113146	hgsc.bcm.edu	37	14	105413204	105413204	+	Missense_Mutation	SNP	G	G	T	rs2582514	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105413204G>T	ENST00000333244.5	-	7	8703	c.8584C>A	c.(8584-8586)Cgc>Agc	p.R2862S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2862			R -> S (in dbSNP:rs2582514).			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)			GGCTGAATGCGGATGTCAGTG	0.627													.|||	2840	0.567093	0.7065	0.5173	5008	,	,		17045	0.3899		0.5328	False		,,,				2504	0.6319				p.R2862S		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,2	AHNAK2	719	2	0			c.C8584A						PASS	.	T	SER/ARG	2762,1142		1009,744,199	116.0	134.0	129.0		8584	0.5	0.0	14	dbSNP_100	129	4491,3805		1225,2041,882	no	missense	AHNAK2	NM_138420.2	110	2234,2785,1081	TT,TG,GG		45.8655,29.252,40.5492	benign	2862/5796	105413204	7253,4947	1952	4148	6100	SO:0001583	missense	113146	exon7			GAATGCGGATGTC	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.8584C>A	14.37:g.105413204G>T	ENSP00000353114:p.Arg2862Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	205	204	0.995122	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1067	0.48855311355311354	338	0.6869918699186992	184	0.5082872928176796	187	0.3269230769230769	358	0.47229551451187335	t	0.492	-0.875121	0.02550	0.70748	0.541345	ENSG00000185567	ENST00000333244	T	0.00705	5.81	3.07	0.525	0.17072	.	.	.	.	.	T	0.00012	0.0000	N	0.00081	-2.22	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03587	-1.1022	8	0.09084	T	0.74	.	5.562	0.17150	0.0:0.1895:0.4489:0.3616	.	2862	Q8IVF2	AHNK2_HUMAN	S	2862	ENSP00000353114:R2862S	ENSP00000353114:R2862S	R	-	1	0	AHNAK2	104484249	0.019000	0.18553	0.000000	0.03702	0.023000	0.10783	0.000000	0.12993	-0.439000	0.07222	-0.855000	0.03028	CGC	G|0.495;T|0.505	0.505	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
FAM118A	55007	hgsc.bcm.edu	37	22	45723842	45723842	+	Silent	SNP	G	G	A	rs17851057	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45723842G>A	ENST00000216214.3	+	5	1254	c.420G>A	c.(418-420)agG>agA	p.R140R	FAM118A_ENST00000405548.3_5'Flank|FAM118A_ENST00000405673.1_Silent_p.R140R|FAM118A_ENST00000441876.2_Silent_p.R140R	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	117	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	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	
ZHX2	22882	hgsc.bcm.edu	37	8	123964011	123964011	+	Silent	SNP	G	G	A	rs61752912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:123964011G>A	ENST00000314393.4	+	3	1096	c.261G>A	c.(259-261)acG>acA	p.T87T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	87					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCTACTCCACGCAAAACCTGA	0.468													G|||	115	0.0229633	0.0424	0.0331	5008	,	,		20913	0.0		0.0298	False		,,,				2504	0.0061				p.T87T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G261A						PASS	.	G		174,4232	114.6+/-152.6	5,164,2034	89.0	81.0	84.0		261	-6.5	0.7	8	dbSNP_129	84	278,8322	105.6+/-166.5	6,266,4028	no	coding-synonymous	ZHX2	NM_014943.3		11,430,6062	AA,AG,GG		3.2326,3.9492,3.4753		87/838	123964011	452,12554	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CTCCACGCAAAAC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.261G>A	8.37:g.123964011G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	52	18	0.346154	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.965;A|0.035	0.035	strong		0.468	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
PLIN4	729359	hgsc.bcm.edu	37	19	4511908	4511908	+	Silent	SNP	C	C	T	rs10423606	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4511908C>T	ENST00000301286.3	-	3	2021	c.2022G>A	c.(2020-2022)acG>acA	p.T674T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	674	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.T602T(1)|p.T674T(1)		NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CGGTCTTGGCCGTGTCTACAC	0.577																																					p.T674T		Atlas-SNP	.											.	PLIN4	191	.	2	Substitution - coding silent(2)	lung(2)	c.G2022A						PASS	.						149.0	159.0	156.0					19																	4511908		2123	4223	6346	SO:0001819	synonymous_variant	729359	exon3			CTTGGCCGTGTCT	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2022G>A	19.37:g.4511908C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	270	205	0.759259	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			C|0.500;T|0.500	0.500	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
OR6S1	341799	hgsc.bcm.edu	37	14	21109726	21109726	+	Missense_Mutation	SNP	G	G	A	rs11622794	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21109726G>A	ENST00000320704.3	-	1	124	c.125C>T	c.(124-126)aCa>aTa	p.T42I		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	42			T -> I (in dbSNP:rs11622794).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		CACATTGCCTGTCAGATTCAG	0.478													G|||	2305	0.460264	0.4902	0.5461	5008	,	,		21279	0.2897		0.5338	False		,,,				2504	0.4591				p.T42I		Atlas-SNP	.											.	OR6S1	49	.	0			c.C125T						PASS	.	G	ILE/THR	2257,2149	595.7+/-388.5	560,1137,506	97.0	94.0	95.0		125	1.5	0.5	14	dbSNP_120	95	4782,3818	611.6+/-395.8	1333,2116,851	yes	missense	OR6S1	NM_001001968.1	89	1893,3253,1357	AA,AG,GG		44.3953,48.7744,45.8788	benign	42/332	21109726	7039,5967	2203	4300	6503	SO:0001583	missense	341799	exon1			TTGCCTGTCAGAT	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.125C>T	14.37:g.21109726G>A	ENSP00000313110:p.Thr42Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	1030	0.4716117216117216	229	0.4654471544715447	213	0.5883977900552486	183	0.31993006993006995	405	0.5343007915567283	G	3.081	-0.189020	0.06299	0.512256	0.556047	ENSG00000181803	ENST00000320704	T	0.00420	7.47	5.84	1.53	0.23141	.	0.311322	0.23836	N	0.044083	T	0.00012	0.0000	N	0.13235	0.315	0.80722	P	0.0	B	0.17268	0.021	B	0.16722	0.016	T	0.02358	-1.1171	9	0.40728	T	0.16	-3.8757	8.4026	0.32594	0.4216:0.0:0.5784:0.0	rs11622794;rs17277529;rs56602434;rs57777215;rs11622794	42	Q8NH40	OR6S1_HUMAN	I	42	ENSP00000313110:T42I	ENSP00000313110:T42I	T	-	2	0	OR6S1	20179566	0.000000	0.05858	0.498000	0.27564	0.691000	0.40173	1.178000	0.31981	0.403000	0.25479	-0.126000	0.14955	ACA	G|0.491;A|0.508	0.508	strong		0.478	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
SEMA4B	10509	hgsc.bcm.edu	37	15	90768271	90768271	+	Silent	SNP	C	C	T	rs11547966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90768271C>T	ENST00000411539.2	+	10	1526	c.1266C>T	c.(1264-1266)ttC>ttT	p.F422F	SEMA4B_ENST00000379122.3_Silent_p.F417F|SEMA4B_ENST00000332496.6_Silent_p.F422F	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	417	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)			TGCTGAACTTCCTCAAGGACC	0.622													C|||	706	0.140974	0.0787	0.1571	5008	,	,		20691	0.0556		0.2575	False		,,,				2504	0.182				p.F422F		Atlas-SNP	.											.	SEMA4B	51	.	0			c.C1266T						PASS	.	C	,	403,3897		12,379,1759	84.0	95.0	91.0		1266,1266	5.2	1.0	15	dbSNP_120	91	2005,6499		224,1557,2471	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	236,1936,4230	TT,TC,CC		23.5771,9.3721,18.8066	,	422/838,422/838	90768271	2408,10396	2150	4252	6402	SO:0001819	synonymous_variant	10509	exon11			GAACTTCCTCAAG	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.1266C>T	15.37:g.90768271C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	37	CCDS45347.1																																																																																			C|0.835;T|0.165	0.165	strong		0.622	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
FAM157A	728262	hgsc.bcm.edu	37	3	197894668	197894668	+	lincRNA	SNP	G	G	A	rs200450190		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:197894668G>A	ENST00000437428.2	+	0	829							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A									p.R337K(1)		NS(1)|skin(1)	2						TTCCCGCTGAGGTGCCAGAAG	0.607											OREG0016022	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R337K		Atlas-SNP	.											FAM157A,NS,malignant_melanoma,0,1	FAM157A	4	1	1	Substitution - Missense(1)	NS(1)	c.G1010A						scavenged	.						33.0	31.0	31.0					3																	197894668		689	1588	2277			728262	exon5			CGCTGAGGTGCCA			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			3.37:g.197894668G>A		Somatic	671	9	0.0134128	2094	WXS	Illumina HiSeq	Phase_I	520	26	0.05	NM_001145248		Missense_Mutation	SNP	ENST00000437428.2	37		.	.	.	.	.	.	.	.	.	.	.	4.173	0.030697	0.08101	.	.	ENSG00000236438	ENST00000431569	.	.	.	0.467	0.467	0.16721	.	.	.	.	.	T	0.17365	0.0417	N	0.08118	0	0.09310	N	1	B	0.28667	0.219	B	0.32090	0.14	T	0.31888	-0.9927	6	.	.	.	.	.	.	.	.	337	C9JC47	F157A_HUMAN	K	337	.	.	R	+	2	0	FAM157A	199379065	0.074000	0.21230	0.015000	0.15790	0.049000	0.14656	0.293000	0.19029	0.539000	0.28788	0.388000	0.25769	AGG	.	.	weak		0.607	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79610710	79610710	+	Silent	SNP	A	A	G	rs1054283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:79610710A>G	ENST00000263849.4	+	7	768	c.666A>G	c.(664-666)ttA>ttG	p.L222L		NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	222							metal ion binding (GO:0046872)										TTCAGACCTTATCTCCCTCTC	0.343													A|||	3592	0.717252	0.4985	0.7968	5008	,	,		16940	0.8978		0.7157	False		,,,				2504	0.772				p.L222L		Atlas-SNP	.											FAM164A,rectum,carcinoma,0,1	.	.	1	0			c.A666G						PASS	.	A		2401,2005	615.4+/-392.6	668,1065,470	117.0	113.0	114.0		666	2.0	1.0	8	dbSNP_86	114	6317,2283	706.5+/-405.5	2325,1667,308	no	coding-synonymous	FAM164A	NM_016010.2		2993,2732,778	GG,GA,AA		26.5465,45.5061,32.9694		222/326	79610710	8718,4288	2203	4300	6503	SO:0001819	synonymous_variant	51101	exon7			GACCTTATCTCCC		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"""Zinc fingers, C2HC-type containing"""	24277	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 70"", ""family with sequence similarity 164, member A"""	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.666A>G	8.37:g.79610710A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	37	CCDS6223.1	1586	0.7261904761904762	244	0.4959349593495935	291	0.8038674033149171	508	0.8881118881118881	543	0.716358839050132	A	6.349	0.432414	0.12045	0.544939	0.734535	ENSG00000104427	ENST00000519307	.	.	.	5.85	2.0	0.26442	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999973996	.	.	.	.	.	.	T	0.15122	-1.0448	3	.	.	.	-4.1446	5.4563	0.16592	0.641:0.1342:0.2248:0.0	rs1054283;rs3194797;rs13258774;rs17418488;rs17845203;rs17858015;rs1054283	.	.	.	V	55	.	.	I	+	1	0	FAM164A	79773265	0.992000	0.36948	0.996000	0.52242	0.666000	0.39218	0.371000	0.20450	0.096000	0.17463	-0.379000	0.06801	ATC	A|0.323;G|0.677	0.677	strong		0.343	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010	
CLEC1B	51266	hgsc.bcm.edu	37	12	10150974	10150974	+	Missense_Mutation	SNP	A	A	G	rs2273986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:10150974A>G	ENST00000298527.6	-	2	249	c.70T>C	c.(70-72)Tct>Cct	p.S24P	CLEC1B_ENST00000428126.2_Intron|CLEC1B_ENST00000348658.4_Intron	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	24			S -> P (in dbSNP:rs2273986). {ECO:0000269|PubMed:12975309}.		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)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						GAGGATGCAGAGCCAACTGTA	0.567													G|||	2014	0.402157	0.469	0.4265	5008	,	,		17791	0.3363		0.492	False		,,,				2504	0.2699				p.S24P		Atlas-SNP	.											.	CLEC1B	39	.	0			c.T70C						PASS	.	G	,PRO/SER	1768,2436		373,1022,707	86.0	93.0	91.0		,70	1.3	0.0	12	dbSNP_100	91	3717,4713		846,2025,1344	yes	intron,missense	CLEC1B	NM_001099431.1,NM_016509.3	,74	1219,3047,2051	GG,GA,AA		44.0925,42.0552,43.4146	,benign	,24/230	10150974	5485,7149	2102	4215	6317	SO:0001583	missense	51266	exon2			ATGCAGAGCCAAC	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.70T>C	12.37:g.10150974A>G	ENSP00000298527:p.Ser24Pro	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	37	CCDS41752.1	901	0.4125457875457875	215	0.4369918699186992	150	0.4143646408839779	174	0.3041958041958042	362	0.47757255936675463	G	0.017	-1.503403	0.00992	0.420552	0.440925	ENSG00000165682	ENST00000298527	T	0.01414	4.92	4.37	1.28	0.21552	.	0.126684	0.36101	N	0.002786	T	0.00012	0.0000	N	0.00389	-1.56	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	9	0.02654	T	1	.	4.0145	0.09637	0.3312:0.1746:0.4942:0.0	rs2273986;rs60448232	24	Q9P126	CLC1B_HUMAN	P	24	ENSP00000298527:S24P	ENSP00000298527:S24P	S	-	1	0	CLEC1B	10042241	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.653000	0.05360	-0.334000	0.08463	-0.684000	0.03749	TCT	A|0.594;G|0.406	0.406	strong		0.567	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509	
KIF13A	63971	hgsc.bcm.edu	37	6	17799575	17799575	+	Silent	SNP	A	A	G	rs3734235	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:17799575A>G	ENST00000259711.6	-	22	2817	c.2712T>C	c.(2710-2712)gcT>gcC	p.A904A	KIF13A_ENST00000378826.2_Silent_p.A904A|KIF13A_ENST00000378816.5_Silent_p.A904A|KIF13A_ENST00000378843.2_Silent_p.A904A|KIF13A_ENST00000378814.5_Silent_p.A904A	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	904					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)			CCACCGGGGCAGCCACCGTAG	0.498													A|||	1040	0.207668	0.0998	0.1556	5008	,	,		16038	0.1964		0.2396	False		,,,				2504	0.3691				p.A904A		Atlas-SNP	.											.	KIF13A	276	.	0			c.T2712C						PASS	.	A	,,,	479,3361		28,423,1469	53.0	54.0	54.0		2712,2712,2712,2712	-4.8	1.0	6	dbSNP_107	54	1942,6288		229,1484,2402	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	257,1907,3871	GG,GA,AA		23.5966,12.474,20.058	,,,	904/1771,904/1758,904/1750,904/1806	17799575	2421,9649	1920	4115	6035	SO:0001819	synonymous_variant	63971	exon22			CGGGGCAGCCACC	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.2712T>C	6.37:g.17799575A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1	392	0.1794871794871795	47	0.09552845528455285	63	0.17403314917127072	91	0.1590909090909091	191	0.2519788918205805	A	10.39	1.336824	0.24253	0.12474	0.235966	ENSG00000137177	ENST00000358380	.	.	.	5.65	-4.84	0.03151	.	.	.	.	.	T	0.06781	0.0173	.	.	.	0.09310	P	0.9999999999999928	.	.	.	.	.	.	T	0.33777	-0.9855	3	.	.	.	.	2.8819	0.05649	0.4036:0.0852:0.3554:0.1558	rs3734235;rs17689294;rs59631674;rs3734235	.	.	.	P	298	.	.	L	-	2	0	KIF13A	17907554	0.150000	0.22732	0.985000	0.45067	0.791000	0.44710	-0.345000	0.07770	-0.408000	0.07565	0.460000	0.39030	CTG	A|0.813;G|0.187	0.187	strong		0.498	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
IL1B	3553	hgsc.bcm.edu	37	2	113590390	113590390	+	Silent	SNP	G	G	A	rs1143634	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:113590390G>A	ENST00000263341.2	-	5	525	c.315C>T	c.(313-315)ttC>ttT	p.F105F	IL1B_ENST00000491056.1_5'UTR	NM_000576.2	NP_000567.1	P01584	IL1B_HUMAN	interleukin 1, beta	105					activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular response to drug (GO:0035690)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to organic substance (GO:0071310)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|embryo implantation (GO:0007566)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|hyaluronan biosynthetic process (GO:0030213)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-1 beta production (GO:0032611)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|monocyte aggregation (GO:0070487)|negative regulation of adiponectin secretion (GO:0070164)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of MAP kinase activity (GO:0043407)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion molecule production (GO:0060355)|positive regulation of cell division (GO:0051781)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|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 lipid catabolic process (GO:0050996)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myosin light chain kinase activity (GO:0035505)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell mediated immunity (GO:0002711)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein kinase B signaling (GO:0043491)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of insulin secretion (GO:0050796)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|sequestering of triglyceride (GO:0030730)|signal transduction (GO:0007165)|smooth muscle adaptation (GO:0014805)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	cytokine activity (GO:0005125)|interleukin-1 receptor binding (GO:0005149)|protein domain specific binding (GO:0019904)			breast(2)|central_nervous_system(1)|large_intestine(1)|lung(8)	12					Canakinumab(DB06168)|Gallium nitrate(DB05260)|Minocycline(DB01017)|Rilonacept(DB06372)	CCCATGTGTCGAAGAAGATAG	0.488													G|||	665	0.132788	0.1225	0.1254	5008	,	,		23482	0.0228		0.2475	False		,,,				2504	0.1472				p.F105F		Atlas-SNP	.											.	IL1B	35	.	0			c.C315T	GRCh37	CM040228	IL1B	M	rs1143634	PASS	.	G		614,3792	265.9+/-266.9	34,546,1623	155.0	129.0	138.0		315	-4.7	0.0	2	dbSNP_86	138	2042,6558	356.9+/-330.5	229,1584,2487	no	coding-synonymous	IL1B	NM_000576.2		263,2130,4110	AA,AG,GG		23.7442,13.9355,20.4213		105/270	113590390	2656,10350	2203	4300	6503	SO:0001819	synonymous_variant	3553	exon5			TGTGTCGAAGAAG	M15330	CCDS2102.1	2q14	2014-01-30			ENSG00000125538	ENSG00000125538		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5992	protein-coding gene	gene with protein product		147720				2954882, 2989698	Standard	NM_000576		Approved	IL1F2, IL-1B, IL1-BETA	uc002tii.1	P01584	OTTHUMG00000131344	ENST00000263341.2:c.315C>T	2.37:g.113590390G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	197	101	0.51269	NM_000576	Q53X59|Q53XX2|Q7M4S7|Q7RU01|Q96HE5|Q9UCT6	Silent	SNP	ENST00000263341.2	37	CCDS2102.1																																																																																			G|0.828;A|0.172	0.172	strong		0.488	IL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254125.2	NM_000576	
SAG	6295	hgsc.bcm.edu	37	2	234235820	234235820	+	Silent	SNP	C	C	T	rs2304773	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	117	117	1	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	
NUP153	9972	hgsc.bcm.edu	37	6	17633033	17633033	+	Missense_Mutation	SNP	G	G	C	rs61744976	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:17633033G>C	ENST00000262077.2	-	17	2506	c.2507C>G	c.(2506-2508)tCt>tGt	p.S836C	NUP153_ENST00000537253.1_Missense_Mutation_p.S867C	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	836				S -> C (in Ref. 2; BAG58514). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|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)			AGAAGGCAGAGAGACAGGTAC	0.438													G|||	451	0.0900559	0.0295	0.1138	5008	,	,		11947	0.004		0.161	False		,,,				2504	0.1708				p.S836C		Atlas-SNP	.											.	NUP153	116	.	0			c.C2507G						PASS	.	G	CYS/SER	181,4225	117.1+/-155.0	4,173,2026	89.0	84.0	86.0		2507	4.4	0.2	6	dbSNP_129	86	1242,7358	248.6+/-276.2	95,1052,3153	yes	missense	NUP153	NM_005124.2	112	99,1225,5179	CC,CG,GG		14.4419,4.108,10.9411	probably-damaging	836/1476	17633033	1423,11583	2203	4300	6503	SO:0001583	missense	9972	exon17			GGCAGAGAGACAG	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.2507C>G	6.37:g.17633033G>C	ENSP00000262077:p.Ser836Cys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	37	CCDS4541.1	185	0.08470695970695971	24	0.04878048780487805	46	0.1270718232044199	0	0.0	115	0.1517150395778364	G	13.53	2.263342	0.39995	0.04108	0.144419	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.10288	2.9;2.89	5.28	4.4	0.53042	.	0.000000	0.51477	D	0.000091	T	0.23766	0.0575	M	0.87180	2.865	0.24556	P	0.99399956	D;D;D	0.61697	0.99;0.983;0.97	P;P;P	0.58013	0.831;0.682;0.571	T	0.30504	-0.9976	9	0.66056	D	0.02	-5.2724	16.1574	0.81676	0.0:0.1338:0.8662:0.0	rs61744976	867;816;836	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	C	836;816;867	ENSP00000262077:S836C;ENSP00000444029:S867C	ENSP00000262077:S836C	S	-	2	0	NUP153	17741012	1.000000	0.71417	0.188000	0.23233	0.021000	0.10359	6.062000	0.71155	1.350000	0.45770	0.591000	0.81541	TCT	G|0.894;C|0.106	0.106	strong		0.438	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
VPS13C	54832	hgsc.bcm.edu	37	15	62316035	62316035	+	Missense_Mutation	SNP	C	C	T	rs12595158	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:62316035C>T	ENST00000261517.5	-	7	531	c.458G>A	c.(457-459)cGt>cAt	p.R153H	VPS13C_ENST00000249837.3_Intron|VPS13C_ENST00000395898.3_Intron|VPS13C_ENST00000395896.4_Missense_Mutation_p.R153H	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						GTGCTTTTTACGTTTACGTCC	0.328													C|||	535	0.106829	0.0446	0.2003	5008	,	,		17797	0.2024		0.0268	False		,,,				2504	0.1084				p.R153H		Atlas-SNP	.											.	VPS13C	506	.	0			c.G458A						PASS	.	C	HIS/ARG,,,HIS/ARG	236,4168	137.7+/-173.5	8,220,1974	116.0	115.0	116.0		458,,,458	5.0	1.0	15	dbSNP_120	116	188,8410	83.1+/-145.7	2,184,4113	yes	missense,intron,intron,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	29,,,29	10,404,6087	TT,TC,CC		2.1866,5.3588,3.261	probably-damaging,,,probably-damaging	153/3629,,,153/3754	62316035	424,12578	2202	4299	6501	SO:0001583	missense	54832	exon7			TTTTTACGTTTAC	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.458G>A	15.37:g.62316035C>T	ENSP00000261517:p.Arg153His	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	205	0.09386446886446886	18	0.036585365853658534	46	0.1270718232044199	115	0.20104895104895104	26	0.03430079155672823	C	14.40	2.524377	0.44969	0.053588	0.021866	ENSG00000129003	ENST00000261517;ENST00000395896;ENST00000395898	T;T	0.47869	0.83;1.0	4.98	4.98	0.66077	.	0.093464	0.42294	D	0.000734	T	0.00073	0.0002	N	0.22421	0.69	0.09310	P	0.9999999999994341	D;B	0.64830	0.994;0.297	P;B	0.51415	0.669;0.015	T	0.04840	-1.0923	9	0.72032	D	0.01	.	13.4529	0.61182	0.0:0.8414:0.1586:0.0	rs12595158;rs17304031;rs52803423;rs12595158	153;153	Q709C8-2;Q709C8	.;VP13C_HUMAN	H	153	ENSP00000261517:R153H;ENSP00000379233:R153H	ENSP00000261517:R153H	R	-	2	0	VPS13C	60103327	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.380000	0.34351	2.302000	0.77476	0.591000	0.81541	CGT	C|0.939;T|0.061	0.061	strong		0.328	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ZMYM2	7750	hgsc.bcm.edu	37	13	20577061	20577061	+	Missense_Mutation	SNP	G	G	T	rs61749503		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:20577061G>T	ENST00000382874.2	+	5	1109	c.919G>T	c.(919-921)Gtg>Ttg	p.V307L	ZMYM2_ENST00000382883.3_5'Flank|ZMYM2_ENST00000382881.3_Missense_Mutation_p.V220L|ZMYM2_ENST00000382871.2_Missense_Mutation_p.V307L|ZMYM2_ENST00000382869.3_Missense_Mutation_p.V307L	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TTTATCACCAGTGGCCTCACT	0.418																																					p.V307L		Atlas-SNP	.											.	ZMYM2	191	.	0			c.G919T						PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	0,4404		0,0,2202	113.0	122.0	119.0		919,919,919,919	4.8	1.0	13	dbSNP_129	119	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	ZMYM2	NM_001190964.1,NM_001190965.1,NM_003453.3,NM_197968.2	32,32,32,32	0,1,6501	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	307/1378,307/1378,307/1378,307/1378	20577061	1,13003	2202	4300	6502	SO:0001583	missense	7750	exon5			TCACCAGTGGCCT	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"""Zinc fingers, MYM type"""	12989	protein-coding gene	gene with protein product		602221	"""zinc finger protein 198"""	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.919G>T	13.37:g.20577061G>T	ENSP00000372327:p.Val307Leu	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	187	95	0.508021	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	37	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.737626	0.49045	0.0	1.16E-4	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382881;ENST00000382874;ENST00000382871	T;T;T;T	0.20069	2.21;2.1;2.21;2.21	4.78	4.78	0.61160	.	0.336575	0.32015	N	0.006715	T	0.35508	0.0934	L	0.46157	1.445	0.80722	D	1	P;P;D	0.76494	0.937;0.937;0.999	P;P;D	0.64237	0.633;0.633;0.923	T	0.05354	-1.0890	10	0.12766	T	0.61	-13.4189	17.8191	0.88644	0.0:0.0:1.0:0.0	rs61749503	307;307;220	A8K126;Q9UBW7;Q9UBW7-2	.;ZMYM2_HUMAN;.	L	307;307;220;307;307	ENSP00000372322:V307L;ENSP00000372334:V220L;ENSP00000372327:V307L;ENSP00000372324:V307L	ENSP00000372322:V307L	V	+	1	0	ZMYM2	19475061	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.218000	0.95166	2.211000	0.71520	0.557000	0.71058	GTG	G|0.985;T|0.015	0.015	weak		0.418	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453	
PRRG4	79056	hgsc.bcm.edu	37	11	32874926	32874926	+	Silent	SNP	G	G	A	rs11032025	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:32874926G>A	ENST00000257836.3	+	6	787	c.534G>A	c.(532-534)ccG>ccA	p.P178P		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	178						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)					CTCCATTGCCGCCTTCTGTGG	0.522													G|||	2030	0.405351	0.3464	0.4841	5008	,	,		16145	0.4127		0.3986	False		,,,				2504	0.4284				p.P178P		Atlas-SNP	.											PRRG4,colon,carcinoma,0,1	PRRG4	15	1	0			c.G534A						PASS	.	G		1643,2761	505.1+/-366.0	309,1025,868	109.0	101.0	104.0		534	0.2	0.0	11	dbSNP_120	104	3277,5321	490.4+/-372.8	621,2035,1643	yes	coding-synonymous	PRRG4	NM_024081.5		930,3060,2511	AA,AG,GG		38.1135,37.307,37.8403		178/227	32874926	4920,8082	2202	4299	6501	SO:0001819	synonymous_variant	79056	exon6			ATTGCCGCCTTCT	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.534G>A	11.37:g.32874926G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_024081		Silent	SNP	ENST00000257836.3	37	CCDS7881.1																																																																																			G|0.604;A|0.396	0.396	strong		0.522	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416295	105416295	+	Silent	SNP	C	C	T	rs200753593	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105416295C>T	ENST00000333244.5	-	7	5612	c.5493G>A	c.(5491-5493)ccG>ccA	p.P1831P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1831						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)			CCCCGAACGACGGCATCTTGA	0.617													.|||	95	0.0189696	0.0582	0.0101	5008	,	,		18954	0.005		0.003	False		,,,				2504	0.0031				p.P1831P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	0			c.G5493A						scavenged	.	C		131,3699		9,113,1793	204.0	243.0	231.0		5493	-9.0	0.0	14	dbSNP_134	231	34,8130		4,26,4052	no	coding-synonymous	AHNAK2	NM_138420.2		13,139,5845	TT,TC,CC		0.4165,3.4204,1.3757		1831/5796	105416295	165,11829	1915	4082	5997	SO:0001819	synonymous_variant	113146	exon7			GAACGACGGCATC	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.5493G>A	14.37:g.105416295C>T		Somatic	270	4	0.0148148		WXS	Illumina HiSeq	Phase_I	304	123	0.404605	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.979;T|0.021	0.021	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SEPHS1	22929	hgsc.bcm.edu	37	10	13378273	13378273	+	Silent	SNP	G	G	C	rs62641683	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:13378273G>C	ENST00000327347.5	-	4	750	c.375C>G	c.(373-375)ctC>ctG	p.L125L	SEPHS1_ENST00000545675.1_Silent_p.L125L|SEPHS1_ENST00000378614.4_Silent_p.L125L|SEPHS1_ENST00000537130.1_Silent_p.L58L|SEPHS1_ENST00000494329.1_5'Flank	NM_001195602.1|NM_012247.4	NP_001182531.1|NP_036379.2	P49903	SPS1_HUMAN	selenophosphate synthetase 1	125					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|selenide, water dikinase activity (GO:0004756)			cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|stomach(1)	16						TGACTCCAAGGAGCATCAGCA	0.537													G|||	27	0.00539137	0.0008	0.0101	5008	,	,		18833	0.0		0.0119	False		,,,				2504	0.0072				p.L125L		Atlas-SNP	.											.	SEPHS1	99	.	0			c.C375G						PASS	.	G	,,	18,4388	25.3+/-52.1	0,18,2185	94.0	80.0	85.0		174,375,375	1.1	1.0	10	dbSNP_129	85	146,8454	71.6+/-134.2	1,144,4155	no	coding-synonymous,coding-synonymous,coding-synonymous	SEPHS1	NM_001195602.1,NM_001195604.1,NM_012247.4	,,	1,162,6340	CC,CG,GG		1.6977,0.4085,1.261	,,	58/326,125/322,125/393	13378273	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	22929	exon4			TCCAAGGAGCATC	BC000941	CCDS7098.1, CCDS55702.1, CCDS55703.1	10p14	2006-10-06			ENSG00000086475	ENSG00000086475			19685	protein-coding gene	gene with protein product		600902				7665581	Standard	NM_012247		Approved	SPS, SPS1	uc001imk.3	P49903	OTTHUMG00000017696	ENST00000327347.5:c.375C>G	10.37:g.13378273G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	52	0.658228	NM_012247	B4DWK0|D3DRS9|D6PSQ9|Q5T5U8|Q5T5U9|Q9BVT4	Silent	SNP	ENST00000327347.5	37	CCDS7098.1																																																																																			G|0.979;C|0.021	0.021	strong		0.537	SEPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046856.1	NM_012247	
OR10P1	121130	hgsc.bcm.edu	37	12	56030938	56030938	+	Missense_Mutation	SNP	C	C	T	rs10876838	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56030938C>T	ENST00000309675.2	+	1	295	c.263C>T	c.(262-264)cCg>cTg	p.P88L	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	88			P -> L (in dbSNP:rs10876838).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						CTGGGCTCCCCGCATCCCCAG	0.602													C|||	1355	0.270567	0.0794	0.3919	5008	,	,		21233	0.2331		0.4901	False		,,,				2504	0.2556				p.P88L		Atlas-SNP	.											OR10P1,NS,carcinoma,-1,1	OR10P1	48	1	0			c.C263T						scavenged	.	C	LEU/PRO	651,3755	280.5+/-275.4	50,551,1602	81.0	72.0	75.0		263	-2.4	0.0	12	dbSNP_120	75	3947,4653	548.4+/-385.4	917,2113,1270	yes	missense	OR10P1	NM_206899.1	98	967,2664,2872	TT,TC,CC		45.8953,14.7753,35.3529	benign	88/314	56030938	4598,8408	2203	4300	6503	SO:0001583	missense	121130	exon1			GCTCCCCGCATCC	BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"""GPCR / Class A : Olfactory receptors"""	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.263C>T	12.37:g.56030938C>T	ENSP00000308082:p.Pro88Leu	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_206899	B9EGY4	Missense_Mutation	SNP	ENST00000309675.2	37	CCDS31828.1	698	0.31959706959706957	46	0.09349593495934959	153	0.42265193370165743	135	0.23601398601398602	364	0.48021108179419525	C	1.011	-0.687846	0.03328	0.147753	0.458953	ENSG00000175398	ENST00000309675	T	0.01804	4.63	4.28	-2.44	0.06502	GPCR, rhodopsin-like superfamily (1);	1.960390	0.02595	N	0.100381	T	0.00012	0.0000	L	0.31664	0.95	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.39981	-0.9587	9	0.23891	T	0.37	.	1.4625	0.02398	0.1395:0.3924:0.1368:0.3312	rs10876838;rs57481452;rs10876838	88	Q8NGE3	O10P1_HUMAN	L	88	ENSP00000308082:P88L	ENSP00000308082:P88L	P	+	2	0	OR10P1	54317205	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.189000	0.09629	-0.552000	0.06167	0.561000	0.74099	CCG	C|0.675;T|0.325	0.325	strong		0.602	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1		
FAM46C	54855	hgsc.bcm.edu	37	1	118165577	118165577	+	Silent	SNP	C	C	G	rs865443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:118165577C>G	ENST00000369448.3	+	2	334	c.87C>G	c.(85-87)ctC>ctG	p.L29L		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	29										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)		ATGAGGTCCTCACTGAAGTTG	0.557			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			G|||	635	0.126797	0.2617	0.085	5008	,	,		21909	0.122		0.0626	False		,,,				2504	0.045				p.L29L		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C87G						PASS	.	G		948,3458	735.6+/-410.7	109,730,1364	102.0	87.0	92.0		87	4.1	1.0	1	dbSNP_86	92	501,8099	796.8+/-407.5	12,477,3811	no	coding-synonymous	FAM46C	NM_017709.3		121,1207,5175	GG,GC,CC		5.8256,21.5161,11.141		29/392	118165577	1449,11557	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			GGTCCTCACTGAA	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.87C>G	1.37:g.118165577C>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.882;G|0.118	0.118	strong		0.557	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
GLB1L2	89944	hgsc.bcm.edu	37	11	134239760	134239760	+	Silent	SNP	C	C	T	rs34063963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134239760C>T	ENST00000535456.2	+	11	1277	c.1089C>T	c.(1087-1089)gaC>gaT	p.D363D	GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.D363D|GLB1L2_ENST00000389881.3_Silent_p.D363D	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	363					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)		AGCTTCGAGACTTCTTCGGCT	0.537													C|||	155	0.0309505	0.1112	0.0072	5008	,	,		20784	0.0		0.003	False		,,,				2504	0.0				p.D363D		Atlas-SNP	.											.	GLB1L2	79	.	0			c.C1089T						PASS	.	C		315,4087	171.6+/-201.8	8,299,1894	155.0	137.0	143.0		1089	-11.3	0.0	11	dbSNP_126	143	7,8587	5.7+/-21.5	0,7,4290	no	coding-synonymous	GLB1L2	NM_138342.3		8,306,6184	TT,TC,CC		0.0815,7.1558,2.4777		363/637	134239760	322,12674	2201	4297	6498	SO:0001819	synonymous_variant	89944	exon11			TCGAGACTTCTTC		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.1089C>T	11.37:g.134239760C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	37	CCDS31724.1	63	0.028846153846153848	61	0.12398373983739837	2	0.0055248618784530384	0	0.0	0	0.0	C	4.109	0.018381	0.07959	0.071558	8.15E-4	ENSG00000149328	ENST00000525089;ENST00000533324	.	.	.	5.66	-11.3	0.00108	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.22918	N	0.998562	.	.	.	.	.	.	T	0.03576	-1.1023	4	.	.	.	-4.4127	1.5619	0.02596	0.3994:0.1015:0.2886:0.2106	rs34063963	.	.	.	F	302;191	.	.	L	+	1	0	GLB1L2	133744970	0.000000	0.05858	0.000000	0.03702	0.655000	0.38815	-4.333000	0.00251	-4.016000	0.00081	-0.181000	0.13052	CTT	C|0.976;T|0.024	0.024	strong		0.537	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
PCDHB16	57717	hgsc.bcm.edu	37	5	140563712	140563712	+	Missense_Mutation	SNP	G	G	T	rs17844653	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140563712G>T	ENST00000361016.2	+	1	2733	c.1578G>T	c.(1576-1578)gaG>gaT	p.E526D		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	526	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.			E -> A (in Ref. 1; AAF81914/AAG10030 and 7; AAH36062). {ECO:0000305}.	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)			CCCTGCGGGAGTTCGAGTTCC	0.692													g|||	1371	0.273762	0.3132	0.3329	5008	,	,		10033	0.1399		0.3688	False		,,,				2504	0.2188				p.E526D		Atlas-SNP	.											PCDHB16,NS,neuroblastoma,+1,1	PCDHB16	159	1	0			c.G1578T						scavenged	.						44.0	45.0	45.0					5																	140563712		1722	3311	5033	SO:0001583	missense	57717	exon1			GCGGGAGTTCGAG	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.1578G>T	5.37:g.140563712G>T	ENSP00000354293:p.Glu526Asp	Somatic	122	2	0.0163934		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	945	0.4326923076923077	218	0.44308943089430897	191	0.5276243093922652	182	0.3181818181818182	354	0.46701846965699206	g	0.492	-0.875102	0.02550	.	.	ENSG00000196963	ENST00000361016	T	0.01745	4.66	4.26	-8.52	0.00920	Cadherin (5);Cadherin-like (1);	0.934753	0.08675	N	0.910239	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B	0.17465	0.022	B	0.30495	0.116	T	0.41858	-0.9485	9	0.09084	T	0.74	.	9.8478	0.41037	0.0784:0.1247:0.612:0.1849	rs61743498	526	Q9NRJ7	PCDBG_HUMAN	D	526	ENSP00000354293:E526D	ENSP00000354293:E526D	E	+	3	2	PCDHB16	140543896	0.000000	0.05858	0.002000	0.10522	0.084000	0.17831	-1.151000	0.03175	-1.844000	0.01178	-3.684000	0.00024	GAG	G|0.570;T|0.430	0.430	strong		0.692	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
BAIAP3	8938	hgsc.bcm.edu	37	16	1384715	1384715	+	Missense_Mutation	SNP	T	T	C	rs200858324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1384715T>C	ENST00000324385.5	+	1	211	c.53T>C	c.(52-54)cTg>cCg	p.L18P	BAIAP3_ENST00000397489.1_5'UTR|BAIAP3_ENST00000426824.3_Intron|BAIAP3_ENST00000568887.1_Intron|BAIAP3_ENST00000421665.2_5'Flank|BAIAP3_ENST00000397488.2_Intron|BAIAP3_ENST00000562208.1_Intron	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	18					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)				GACCTGCACCTGGGCACCGCC	0.667													T|||	4	0.000798722	0.0	0.0	5008	,	,		13202	0.0		0.004	False		,,,				2504	0.0				p.L18P		Atlas-SNP	.											.	BAIAP3	88	.	0			c.T53C						PASS	.	T	PRO/LEU,,,	0,4224		0,0,2112	8.0	9.0	9.0		53,,,	-3.0	0.0	16		9	6,8358		0,6,4176	yes	missense,intron,intron,intron	BAIAP3	NM_003933.4,NM_001199097.1,NM_001199098.1,NM_001199099.1	98,,,	0,6,6288	CC,CT,TT		0.0717,0.0,0.0477	possibly-damaging,,,	18/1188,,,	1384715	6,12582	2112	4182	6294	SO:0001583	missense	8938	exon1			TGCACCTGGGCAC	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.53T>C	16.37:g.1384715T>C	ENSP00000324510:p.Leu18Pro	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	192	79	0.411458	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	T	9.024	0.985626	0.18889	0.0	7.17E-4	ENSG00000007516	ENST00000324385	T	0.73258	-0.73	1.48	-2.96	0.05547	.	5.452210	0.01821	U	0.034057	T	0.44767	0.1309	N	0.08118	0	0.09310	N	0.999994	P;P	0.44734	0.842;0.617	B;B	0.32342	0.144;0.065	T	0.49021	-0.8982	10	0.56958	D	0.05	.	6.6146	0.22771	0.0:0.0:0.4668:0.5332	.	18;18	B4DGA2;O94812	.;BAIP3_HUMAN	P	18	ENSP00000324510:L18P	ENSP00000324510:L18P	L	+	2	0	BAIAP3	1324716	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-2.273000	0.01164	-1.100000	0.03030	0.172000	0.16884	CTG	.	.	weak		0.667	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
FBXO16	157574	hgsc.bcm.edu	37	8	28304769	28304769	+	Missense_Mutation	SNP	C	C	T	rs386723954|rs1390963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:28304769C>T	ENST00000380254.2	-	7	910	c.762G>A	c.(760-762)atG>atA	p.M254I	FBXO16_ENST00000518734.1_Missense_Mutation_p.M242I|RP11-181B11.2_ENST00000523935.1_RNA|FBXO16_ENST00000346498.2_Missense_Mutation_p.M242I|RP11-181B11.2_ENST00000518819.1_RNA	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	254			M -> I (in dbSNP:rs1390963).	MT -> IN (in Ref. 3; AAI02028). {ECO:0000305}.						large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		AGTCTGGGGTCATTTGGTTTC	0.343													C|||	2377	0.474641	0.5976	0.4207	5008	,	,		19237	0.5506		0.3618	False		,,,				2504	0.3845				p.M254I		Atlas-SNP	.											.	FBXO16	29	.	0			c.G762A						PASS	.	C	ILE/MET	2373,2033	609.2+/-391.3	639,1095,469	163.0	162.0	162.0		762	5.0	1.0	8	dbSNP_88	162	3158,5442	476.1+/-369.3	569,2020,1711	yes	missense	FBXO16	NM_172366.2	10	1208,3115,2180	TT,TC,CC		36.7209,46.1416,42.5265	benign	254/293	28304769	5531,7475	2203	4300	6503	SO:0001583	missense	157574	exon7			TGGGGTCATTTGG	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.762G>A	8.37:g.28304769C>T	ENSP00000369604:p.Met254Ile	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	130	55	0.423077	NM_172366	Q3T1B2|Q3T1B3|Q3T1B4	Missense_Mutation	SNP	ENST00000380254.2	37	CCDS6068.1	997	0.4565018315018315	267	0.5426829268292683	146	0.40331491712707185	313	0.5472027972027972	271	0.3575197889182058	C	12.40	1.927336	0.34002	0.538584	0.367209	ENSG00000214050	ENST00000380254;ENST00000346498;ENST00000518734	T;T;T	0.13901	2.55;2.55;2.55	5.01	5.01	0.66863	.	0.854938	0.09795	U	0.754871	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	1.0	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.43782	-0.9370	9	0.23302	T	0.38	-10.9334	14.1747	0.65534	0.0:1.0:0.0:0.0	rs1390963;rs58113025;rs1390963	242;254	Q3T1B2;Q8IX29	.;FBX16_HUMAN	I	254;242;242	ENSP00000369604:M254I;ENSP00000341416:M242I;ENSP00000429687:M242I	ENSP00000341416:M242I	M	-	3	0	FBXO16	28360688	0.973000	0.33851	1.000000	0.80357	0.535000	0.34838	0.294000	0.19047	2.489000	0.83994	0.591000	0.81541	ATG	C|0.566;T|0.434	0.434	strong		0.343	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366	
MTTP	4547	hgsc.bcm.edu	37	4	100512849	100512849	+	Silent	SNP	T	T	C	rs113557405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100512849T>C	ENST00000265517.5	+	6	863	c.660T>C	c.(658-660)taT>taC	p.Y220Y	MTTP_ENST00000457717.1_Silent_p.Y220Y|MTTP_ENST00000511045.1_Silent_p.Y247Y			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	220	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				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)	TCACCACCTATAAGATAGAAG	0.333													T|||	49	0.00978435	0.0	0.036	5008	,	,		17422	0.001		0.0209	False		,,,				2504	0.002				p.Y220Y		Atlas-SNP	.											.	MTTP	127	.	0			c.T660C						PASS	.	T		26,4380	31.7+/-61.6	0,26,2177	71.0	72.0	71.0		660	3.0	1.0	4	dbSNP_132	71	306,8294	110.0+/-170.5	11,284,4005	no	coding-synonymous	MTTP	NM_000253.2		11,310,6182	CC,CT,TT		3.5581,0.5901,2.5527		220/895	100512849	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	4547	exon7			CACCTATAAGATA		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.660T>C	4.37:g.100512849T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_000253	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	37	CCDS3651.1																																																																																			T|0.971;C|0.029	0.029	strong		0.333	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
SPEN	23013	hgsc.bcm.edu	37	1	16255799	16255799	+	Missense_Mutation	SNP	G	G	A	rs115566585	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16255799G>A	ENST00000375759.3	+	11	3268	c.3064G>A	c.(3064-3066)Gtg>Atg	p.V1022M		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1022					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GCAGCCTGACGTGTCCTCTAG	0.423													G|||	12	0.00239617	0.0	0.0115	5008	,	,		20147	0.0		0.004	False		,,,				2504	0.0				p.V1022M		Atlas-SNP	.											.	SPEN	374	.	0			c.G3064A						PASS	.	G	MET/VAL	2,4404	2.1+/-5.4	0,2,2201	46.0	53.0	51.0		3064	-5.8	0.0	1	dbSNP_132	51	31,8569	18.5+/-59.3	0,31,4269	yes	missense	SPEN	NM_015001.2	21	0,33,6470	AA,AG,GG		0.3605,0.0454,0.2537	benign	1022/3665	16255799	33,12973	2203	4300	6503	SO:0001583	missense	23013	exon11			CCTGACGTGTCCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3064G>A	1.37:g.16255799G>A	ENSP00000364912:p.Val1022Met	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	0.012	-1.676123	0.00751	4.54E-4	0.003605	ENSG00000065526	ENST00000375759	T	0.09445	2.98	5.13	-5.85	0.02311	.	.	.	.	.	T	0.02304	0.0071	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41233	-0.9520	9	0.42905	T	0.14	6.4781	3.6799	0.08306	0.2371:0.3302:0.3421:0.0907	.	1022	Q96T58	MINT_HUMAN	M	1022	ENSP00000364912:V1022M	ENSP00000364912:V1022M	V	+	1	0	SPEN	16128386	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.308000	0.02730	-0.807000	0.04393	-0.150000	0.13652	GTG	G|0.998;A|0.002	0.002	strong		0.423	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
RYR2	6262	hgsc.bcm.edu	37	1	237755076	237755076	+	Missense_Mutation	SNP	A	A	G	rs56229512	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237755076A>G	ENST00000366574.2	+	32	4515	c.4198A>G	c.(4198-4200)Agc>Ggc	p.S1400G	RYR2_ENST00000542537.1_Missense_Mutation_p.S1384G|RYR2_ENST00000360064.6_Missense_Mutation_p.S1398G	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1400	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)			TTACAGCACAAGCCATTCTGC	0.393													a|||	36	0.0071885	0.0015	0.0086	5008	,	,		19481	0.0		0.0199	False		,,,				2504	0.0082				p.S1400G		Atlas-SNP	.											.	RYR2	1273	.	0			c.A4198G						PASS	.	A	GLY/SER	14,3780		0,14,1883	121.0	119.0	120.0		4198	3.2	0.7	1	dbSNP_129	120	180,8072		2,176,3948	yes	missense	RYR2	NM_001035.2	56	2,190,5831	GG,GA,AA		2.1813,0.369,1.6105	benign	1400/4968	237755076	194,11852	1897	4126	6023	SO:0001583	missense	6262	exon32			AGCACAAGCCATT	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.4198A>G	1.37:g.237755076A>G	ENSP00000355533:p.Ser1400Gly	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	21	0.009615384615384616	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	15	0.01978891820580475	a	11.57	1.676638	0.29783	0.00369	0.021813	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96685	-4.09;-4.06;-4.08	5.52	3.16	0.36331	B30.2/SPRY domain (1);	0.398927	0.23654	N	0.045898	D	0.83792	0.5331	N	0.14661	0.345	0.80722	D	1	B	0.11235	0.004	B	0.11329	0.006	T	0.79683	-0.1701	10	0.30854	T	0.27	.	9.9893	0.41860	0.8621:0.0:0.1379:0.0	rs56229512	1400	Q92736	RYR2_HUMAN	G	1400;1398;1384	ENSP00000355533:S1400G;ENSP00000353174:S1398G;ENSP00000443798:S1384G	ENSP00000353174:S1398G	S	+	1	0	RYR2	235821699	0.996000	0.38824	0.692000	0.30179	0.763000	0.43281	3.543000	0.53633	0.497000	0.27926	0.528000	0.53228	AGC	A|0.988;G|0.012	0.012	strong		0.393	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
TOR1A	1861	hgsc.bcm.edu	37	9	132580901	132580901	+	Missense_Mutation	SNP	C	C	G	rs1801968	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:132580901C>G	ENST00000351698.4	-	4	694	c.646G>C	c.(646-648)Gat>Cat	p.D216H	TOR1A_ENST00000473084.1_5'Flank	NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	216	Interaction with SNAPIN.		D -> H (in dbSNP:rs1801968).		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)			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)				AAAGCCACATCTGTGATCCTT	0.498													C|||	419	0.0836661	0.0023	0.1095	5008	,	,		22022	0.0556		0.1382	False		,,,				2504	0.1483				p.D216H		Atlas-SNP	.											.	TOR1A	36	.	0			c.G646C	GRCh37	CM061224	TOR1A	M	rs1801968	PASS	.	C	HIS/ASP	121,4285	89.7+/-128.4	1,119,2083	135.0	127.0	130.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	646	5.2	0.5	9	dbSNP_89	130	1203,7397	244.7+/-273.8	88,1027,3185	yes	missense	TOR1A	NM_000113.2	81	89,1146,5268	GG,GC,CC		13.9884,2.7463,10.1799	possibly-damaging	216/333	132580901	1324,11682	2203	4300	6503	SO:0001583	missense	1861	exon4			CCACATCTGTGAT	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.646G>C	9.37:g.132580901C>G	ENSP00000345719:p.Asp216His	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_000113	B2RB58|Q53Y64|Q96CA0	Missense_Mutation	SNP	ENST00000351698.4	37	CCDS6930.1	169	0.07738095238095238	3	0.006097560975609756	25	0.06906077348066299	30	0.05244755244755245	111	0.14643799472295516	C	18.49	3.634709	0.67130	0.027463	0.139884	ENSG00000136827	ENST00000427355;ENST00000351698	T	0.41400	1.0	6.08	5.17	0.71159	.	0.242038	0.48767	D	0.000178	T	0.00328	0.0010	M	0.62723	1.935	0.27162	P	0.9611358	P	0.48016	0.904	P	0.49561	0.615	T	0.18147	-1.0346	9	0.66056	D	0.02	-12.0048	9.8793	0.41222	0.0:0.845:0.0:0.155	rs1801968;rs3174211;rs56481474;rs1801968	216	O14656	TOR1A_HUMAN	H	185;216	ENSP00000345719:D216H	ENSP00000345719:D216H	D	-	1	0	TOR1A	131620722	0.708000	0.27876	0.492000	0.27490	0.966000	0.64601	1.255000	0.32909	1.557000	0.49525	0.655000	0.94253	GAT	C|0.907;G|0.093	0.093	strong		0.498	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464437	39464437	+	Missense_Mutation	SNP	G	G	C	rs72828116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	105	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	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	
GPAA1	8733	hgsc.bcm.edu	37	8	145139727	145139727	+	Silent	SNP	C	C	T	rs4977165	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145139727C>T	ENST00000355091.4	+	8	1234	c.1113C>T	c.(1111-1113)atC>atT	p.I371I	GPAA1_ENST00000361036.6_Silent_p.I311I	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	371					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein complex assembly (GO:0006461)|protein retention in ER lumen (GO:0006621)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	tubulin binding (GO:0015631)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCGTCTCCATCGGCCTCTACA	0.602													C|||	616	0.123003	0.3404	0.0648	5008	,	,		18028	0.001		0.0885	False		,,,				2504	0.0317				p.I371I		Atlas-SNP	.											.	GPAA1	40	.	0			c.C1113T						PASS	.	C		1208,2792		186,836,978	105.0	115.0	112.0		1113	-2.8	1.0	8	dbSNP_111	112	663,7701		25,613,3544	no	coding-synonymous	GPAA1	NM_003801.3		211,1449,4522	TT,TC,CC		7.9268,30.2,15.1326		371/622	145139727	1871,10493	2000	4182	6182	SO:0001819	synonymous_variant	8733	exon8			CTCCATCGGCCTC	AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858			4446	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	603048	"""anchor attachment protein 1 (Gaa1p, yeast) homolog"", ""GPAA1P anchor attachment protein 1 homolog (yeast)"", ""glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"""			9828142	Standard	NM_003801		Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.1113C>T	8.37:g.145139727C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_003801	Q9NSS0|Q9UQ31	Silent	SNP	ENST00000355091.4	37	CCDS43776.1																																																																																			C|0.892;T|0.108	0.108	strong		0.602	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801	
PRPF40A	55660	hgsc.bcm.edu	37	2	153533260	153533260	+	Silent	SNP	G	G	A	rs11544718	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:153533260G>A	ENST00000410080.1	-	10	1231	c.690C>T	c.(688-690)gcC>gcT	p.A230A		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	257					cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						TAGGGACTGGGGCTGTTGATG	0.468													G|||	773	0.154353	0.0295	0.098	5008	,	,		18533	0.2659		0.1789	False		,,,				2504	0.2229				p.A230A		Atlas-SNP	.											PRPF40A_ENST00000410080,caecum,carcinoma,0,3	PRPF40A	149	3	0			c.C690T						PASS	.	G		134,2936		1,132,1402	122.0	117.0	119.0		690	4.1	1.0	2	dbSNP_120	119	975,5029		74,827,2101	no	coding-synonymous	PRPF40A	NM_017892.3		75,959,3503	AA,AG,GG		16.2392,4.3648,12.2217		230/931	153533260	1109,7965	1535	3002	4537	SO:0001819	synonymous_variant	55660	exon10			GACTGGGGCTGTT	AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"""formin-binding protein 3"", ""formin binding protein 3"", ""PRP40 pre-mRNA processing factor 40 homolog A (yeast)"""	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.690C>T	2.37:g.153533260G>A		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	296	134	0.452703	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Silent	SNP	ENST00000410080.1	37	CCDS46430.1																																																																																			T|0.000;G|0.835;C|0.000;A|0.164	0.164	strong		0.468	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575	
HIF3A	64344	hgsc.bcm.edu	37	19	46823751	46823751	+	Silent	SNP	C	C	T	rs3764610	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:46823751C>T	ENST00000377670.4	+	9	1108	c.1077C>T	c.(1075-1077)caC>caT	p.H359H	HIF3A_ENST00000420102.2_Silent_p.H308H|HIF3A_ENST00000600383.1_Silent_p.H290H|HIF3A_ENST00000339613.2_Silent_p.H303H|HIF3A_ENST00000472815.1_Silent_p.H290H|HIF3A_ENST00000244303.6_Silent_p.H290H|HIF3A_ENST00000300862.3_Silent_p.H357H|AC007193.10_ENST00000596807.1_RNA	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	359					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CGGAGCAACACTCTCGCAGAC	0.652													C|||	1004	0.200479	0.0393	0.268	5008	,	,		16562	0.3224		0.1511	False		,,,				2504	0.2955				p.H359H		Atlas-SNP	.											HIF3A_ENST00000377670,NS,carcinoma,+1,2	HIF3A	154	2	0			c.C1077T						scavenged	.	C	,,,	305,4101	166.2+/-197.5	10,285,1908	93.0	85.0	88.0		870,1071,1077,870	-4.1	1.0	19	dbSNP_107	88	1452,7148	278.2+/-293.3	134,1184,2982	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HIF3A	NM_022462.4,NM_152794.3,NM_152795.3,NM_152796.2	,,,	144,1469,4890	TT,TC,CC		16.8837,6.9224,13.5091	,,,	290/601,357/668,359/670,290/451	46823751	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	64344	exon9			GCAACACTCTCGC	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1077C>T	19.37:g.46823751C>T		Somatic	56	2	0.0357143		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Silent	SNP	ENST00000377670.4	37	CCDS12681.2	429	0.19642857142857142	19	0.03861788617886179	81	0.22375690607734808	207	0.3618881118881119	122	0.16094986807387862	C	5.700	0.313625	0.10789	0.069224	0.168837	ENSG00000124440	ENST00000472815	.	.	.	4.47	-4.12	0.03916	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.35830	P	0.174763	.	.	.	.	.	.	T	0.43343	-0.9397	3	.	.	.	.	5.1733	0.15122	0.1579:0.2628:0.0:0.5793	rs3764610;rs60081426;rs3764610	.	.	.	F	332	.	.	L	+	1	0	HIF3A	51515591	0.464000	0.25807	0.961000	0.40146	0.668000	0.39293	-0.201000	0.09464	-0.393000	0.07739	-0.254000	0.11334	CTC	C|0.840;N|0.000	.	strong		0.652	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
EDNRA	1909	hgsc.bcm.edu	37	4	148461073	148461073	+	Silent	SNP	G	G	A	rs5334	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:148461073G>A	ENST00000324300.5	+	6	1520	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	EDNRA_ENST00000358556.4_Silent_p.E226E|EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000506066.1_Silent_p.E226E|EDNRA_ENST00000511804.1_Silent_p.E110E|EDNRA_ENST00000503721.1_3'UTR	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	335					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGTATAACGAGATGGACAAGA	0.348													G|||	1924	0.384185	0.6498	0.3372	5008	,	,		18834	0.2381		0.2237	False		,,,				2504	0.3742				p.E335E		Atlas-SNP	.											EDNRA,NS,carcinoma,+1,2	EDNRA	48	2	0			c.G1005A						PASS	.	G	,	2444,1962	621.4+/-393.7	684,1076,443	182.0	182.0	182.0		678,1005	3.6	1.0	4	dbSNP_52	182	2140,6460	367.3+/-334.7	275,1590,2435	no	coding-synonymous,coding-synonymous	EDNRA	NM_001166055.1,NM_001957.3	,	959,2666,2878	AA,AG,GG		24.8837,44.5302,35.2453	,	226/319,335/428	148461073	4584,8422	2203	4300	6503	SO:0001819	synonymous_variant	1909	exon6			TAACGAGATGGAC	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"""GPCR / Class A : Endothelin receptors"""	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.1005G>A	4.37:g.148461073G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	142	74	0.521127	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Silent	SNP	ENST00000324300.5	37	CCDS3769.1																																																																																			G|0.644;A|0.356	0.356	strong		0.348	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1		
PDE6C	5146	hgsc.bcm.edu	37	10	95389041	95389041	+	Silent	SNP	G	G	A	rs714550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:95389041G>A	ENST00000371447.3	+	8	1236	c.1098G>A	c.(1096-1098)gcG>gcA	p.A366A		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	366	GAF 2.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ATGCCCCTGCGGATGAATACT	0.507													G|||	1982	0.395767	0.4493	0.389	5008	,	,		21297	0.4792		0.3459	False		,,,				2504	0.2935				p.A366A		Atlas-SNP	.											.	PDE6C	97	.	0			c.G1098A						PASS	.	G		1894,2512	544.9+/-376.7	426,1042,735	175.0	153.0	160.0		1098	-8.3	0.7	10	dbSNP_86	160	2870,5730	451.3+/-362.6	474,1922,1904	no	coding-synonymous	PDE6C	NM_006204.3		900,2964,2639	AA,AG,GG		33.3721,42.9868,36.6292		366/859	95389041	4764,8242	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon8			CCCTGCGGATGAA	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1098G>A	10.37:g.95389041G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	174	47	0.270115	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			G|0.622;A|0.378	0.378	strong		0.507	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
LY75	4065	hgsc.bcm.edu	37	2	160738677	160738677	+	Silent	SNP	G	G	A	rs16822581	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160738677G>A	ENST00000263636.4	-	7	1231	c.1204C>T	c.(1204-1206)Cta>Tta	p.L402L	LY75_ENST00000553424.1_Silent_p.L402L|LY75-CD302_ENST00000504764.1_Silent_p.L402L|LY75-CD302_ENST00000505052.1_Silent_p.L402L|LY75_ENST00000554112.1_Silent_p.L402L	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	402	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)		ACATCTGCTAGAGAATGAATG	0.388													G|||	1070	0.213658	0.1112	0.3703	5008	,	,		22695	0.3185		0.16	False		,,,				2504	0.1881				p.L402L		Atlas-SNP	.											.	LY75	151	.	0			c.C1204T						PASS	.	G	,,	574,3832	256.7+/-261.4	42,490,1671	134.0	130.0	131.0		1204,1204,1204	1.7	0.9	2	dbSNP_123	131	1511,7089	286.3+/-297.7	121,1269,2910	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	163,1759,4581	AA,AG,GG		17.5698,13.0277,16.0311	,,	402/1874,402/1818,402/1723	160738677	2085,10921	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon7			CTGCTAGAGAATG	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.1204C>T	2.37:g.160738677G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	112	41	0.366071	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			G|0.816;A|0.184	0.184	strong		0.388	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
ATP11B	23200	hgsc.bcm.edu	37	3	182583338	182583338	+	Missense_Mutation	SNP	T	T	A	rs111933747	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:182583338T>A	ENST00000323116.5	+	13	1555	c.1295T>A	c.(1294-1296)aTt>aAt	p.I432N		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	432					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)			TACCAAGAAATTAATGGTAGA	0.368													T|||	43	0.00858626	0.0008	0.0187	5008	,	,		16795	0.0		0.0288	False		,,,				2504	0.0				p.I432N		Atlas-SNP	.											.	ATP11B	115	.	0			c.T1295A						PASS	.	T	ASN/ILE	18,4388	25.3+/-52.1	0,18,2185	126.0	126.0	126.0		1295	5.8	1.0	3	dbSNP_132	126	238,8362	96.1+/-157.9	2,234,4064	yes	missense	ATP11B	NM_014616.1	149	2,252,6249	AA,AT,TT		2.7674,0.4085,1.9683	benign	432/1178	182583338	256,12750	2203	4300	6503	SO:0001583	missense	23200	exon13			AAGAAATTAATGG	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.1295T>A	3.37:g.182583338T>A	ENSP00000321195:p.Ile432Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_014616	Q96FN1|Q9UKK7	Missense_Mutation	SNP	ENST00000323116.5	37	CCDS33896.1	29|29	0.013278388278388278|0.013278388278388278	0|0	0.0|0.0	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	21|21	0.027704485488126648|0.027704485488126648	T|T	14.45|14.45	2.540469|2.540469	0.45176|0.45176	0.004085|0.004085	0.027674|0.027674	ENSG00000058063|ENSG00000058063	ENST00000323116|ENST00000498086	T|.	0.70631|.	-0.5|.	5.82|5.82	5.82|5.82	0.92795|0.92795	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);|.	0.481828|.	0.22641|.	N|.	0.057451|.	T|T	0.34890|0.34890	0.0913|0.0913	L|L	0.38953|0.38953	1.18|1.18	0.80722|0.80722	D|D	1|1	D;B|.	0.56521|.	0.976;0.003|.	P;B|.	0.51016|.	0.656;0.014|.	T|T	0.44081|0.44081	-0.9351|-0.9351	10|5	0.24483|.	T|.	0.36|.	.|.	16.1744|16.1744	0.81842|0.81842	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	6;432|.	B3KSJ2;Q9Y2G3|.	.;AT11B_HUMAN|.	N|I	432|233	ENSP00000321195:I432N|.	ENSP00000321195:I432N|.	I|L	+|+	2|1	0|2	ATP11B|ATP11B	184066032|184066032	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.770000|5.770000	0.68873|0.68873	2.209000|2.209000	0.71365|0.71365	0.528000|0.528000	0.53228|0.53228	ATT|TTA	T|0.979;A|0.021	0.021	strong		0.368	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616	
GSTT2	2953	hgsc.bcm.edu	37	22	24323227	24323227	+	Splice_Site	SNP	G	G	A	rs76498342	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:24323227G>A	ENST00000215780.5	+	2	250		c.e2+1		DDT_ENST00000350608.3_5'Flank|DDT_ENST00000404092.1_5'Flank|GSTT2_ENST00000402588.3_Splice_Site	NM_000854.3	NP_000845.1	P0CG29	GST2_HUMAN	glutathione S-transferase theta 2							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			lung(1)	1						TGACCGAAAGGTGCCCTCCTT	0.617																																					.		Atlas-SNP	.											.	GSTT2	3	.	0			c.200+1G>A						PASS	.	G		349,4057		1,347,1855	439.0	350.0	380.0			3.1	1.0	22	dbSNP_131	380	1220,7376		7,1206,3085	no	splice-5	GSTT2	NM_000854.3		8,1553,4940	AA,AG,GG		14.1926,7.921,12.0674			24323227	1569,11433	2203	4298	6501	SO:0001630	splice_region_variant	2953	exon2			CGAAAGGTGCCCT	L38503		22q11.23	2012-06-21			ENSG00000099984	ENSG00000099984	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4642	protein-coding gene	gene with protein product		600437				7789971, 9729470	Standard	NM_000854		Approved		uc002zyw.4	P0CG29	OTTHUMG00000150786	ENST00000215780.5:c.200+1G>A	22.37:g.24323227G>A		Somatic	620	1	0.0016129		WXS	Illumina HiSeq	Phase_I	665	233	0.350376	NM_000854	O60665|P30712|Q6IPV7|Q9HD76	Splice_Site	SNP	ENST00000215780.5	37	CCDS13821.1	367	0.16804029304029305	37	0.07520325203252033	50	0.13812154696132597	170	0.2972027972027972	110	0.14511873350923482	.	13.58	2.279780	0.40294	0.07921	0.141926	ENSG00000099984	ENST00000215780;ENST00000402588	.	.	.	3.11	3.11	0.35812	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9816	0.41817	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GSTT2	22653227	1.000000	0.71417	0.966000	0.40874	0.223000	0.24884	3.348000	0.52209	1.807000	0.52817	0.591000	0.81541	.	G|0.873;A|0.127	0.127	strong		0.617	GSTT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320080.1	NM_000854	Intron
HMOX1	3162	hgsc.bcm.edu	37	22	35777185	35777185	+	Missense_Mutation	SNP	G	G	C	rs2071747	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	8	0	0		WXS	Illumina HiSeq	Phase_I	12	6	0.5	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		
NEDD9	4739	hgsc.bcm.edu	37	6	11193860	11193860	+	Silent	SNP	G	G	A	rs16871074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:11193860G>A	ENST00000379446.5	-	3	691	c.525C>T	c.(523-525)gaC>gaT	p.D175D	NEDD9_ENST00000504387.1_Silent_p.D175D|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	175	Interacts strongly with spindle- regulatory protein D1M1.				actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.D175D(1)		endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			TATCATAGACGTCCTTTTGGT	0.512													g|||	987	0.197085	0.1498	0.2104	5008	,	,		17740	0.256		0.1879	False		,,,				2504	0.2004				p.D175D		Atlas-SNP	.											NEDD9_ENST00000379446,NS,carcinoma,0,1	NEDD9	191	1	1	Substitution - coding silent(1)	stomach(1)	c.C525T						PASS	.		,	617,3789	270.7+/-269.8	37,543,1623	186.0	151.0	163.0		525,525	2.6	1.0	6	dbSNP_123	163	1675,6925	308.4+/-308.9	165,1345,2790	no	coding-synonymous,coding-synonymous	NEDD9	NM_001142393.1,NM_006403.3	,	202,1888,4413	AA,AG,GG		19.4767,14.0036,17.6226	,	175/835,175/835	11193860	2292,10714	2203	4300	6503	SO:0001819	synonymous_variant	4739	exon4			ATAGACGTCCTTT	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.525C>T	6.37:g.11193860G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	130	63	0.484615	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Silent	SNP	ENST00000379446.5	37	CCDS4520.1																																																																																			G|0.813;A|0.187	0.187	strong		0.512	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
FRMPD2	143162	hgsc.bcm.edu	37	10	49420008	49420008	+	Missense_Mutation	SNP	T	T	C	rs1864345	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:49420008T>C	ENST00000374201.3	-	13	1902	c.1600A>G	c.(1600-1602)Aag>Gag	p.K534E	FRMPD2_ENST00000407470.4_Missense_Mutation_p.K502E|FRMPD2_ENST00000305531.3_Missense_Mutation_p.K509E	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	75	0	0		WXS	Illumina HiSeq	Phase_I	77	28	0.363636	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	
MST1L	11223	hgsc.bcm.edu	37	1	17087593	17087593	+	RNA	SNP	C	C	T	rs12145944	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17087593C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										ATGGCGAGCGCTGCCCTGCAG	0.577																																					p.Q24Q		Atlas-SNP	.											Q13209_HUMAN,right_upper_lobe,carcinoma,0,2	.	.	2	0			c.G72A						PASS	.																																					11223	exon2			CGAGCGCTGCCCT	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17087593C>T		Somatic	728	1	0.00137363		WXS	Illumina HiSeq	Phase_I	777	130	0.16731	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				C|0.942;T|0.058	0.058	strong		0.577	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
RPS15	6209	hgsc.bcm.edu	37	19	1440374	1440374	+	Silent	SNP	C	C	T	rs139332437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1440374C>T	ENST00000586686.2	+	4	390	c.351C>T	c.(349-351)ggC>ggT	p.G117G	RPS15_ENST00000593052.1_Silent_p.G124G|RPS15_ENST00000233609.4_Silent_p.G90G|AC027307.3_ENST00000594262.1_5'Flank|RPS15_ENST00000591804.2_Silent_p.G84G|RPS15_ENST00000589656.2_Silent_p.G113G|RPS15_ENST00000591032.1_Silent_p.G84G|RPS15_ENST00000585665.1_Silent_p.G84G|RPS15_ENST00000586096.2_3'UTR			P62841	RS15_HUMAN	ribosomal protein S15	117					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)|osteoblast differentiation (GO:0001649)|ribosomal small subunit biogenesis (GO:0042274)|ribosomal small subunit export from nucleus (GO:0000056)|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)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		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)		ACTACCTGGGCGAGTTCTCCA	0.632													C|||	5	0.000998403	0.0008	0.0	5008	,	,		15262	0.0		0.004	False		,,,				2504	0.0				p.G117G	Ovarian(170;79 2680 5719 44260)	Atlas-SNP	.											.	RPS15	11	.	0			c.C351T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	39.0	40.0	40.0		351	2.3	1.0	19	dbSNP_134	40	27,8571	18.5+/-59.3	0,27,4272	no	coding-synonymous	RPS15	NM_001018.3		0,31,6471	TT,TC,CC		0.314,0.0908,0.2384		117/146	1440374	31,12973	2203	4299	6502	SO:0001819	synonymous_variant	6209	exon4			CCTGGGCGAGTTC		CCDS12067.1	19p13.3	2012-12-20			ENSG00000115268	ENSG00000115268		"""S ribosomal proteins"""	10388	protein-coding gene	gene with protein product	"""40S ribosomal protein S15"", ""homolog of rat insulinoma"", ""insulinoma protein"""	180535				2159154	Standard	NM_001018		Approved	RIG, MGC111130, S15	uc002lsp.1	P62841	OTTHUMG00000140099	ENST00000586686.2:c.351C>T	19.37:g.1440374C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_001018	A5D8V9|P11174|Q3KRA1|Q9UDC2	Silent	SNP	ENST00000586686.2	37	CCDS12067.1																																																																																			C|0.998;T|0.002	0.002	strong		0.632	RPS15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449609.4	NM_001018	
BAZ2B	29994	hgsc.bcm.edu	37	2	160294842	160294842	+	Missense_Mutation	SNP	A	A	G	rs3213790	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160294842A>G	ENST00000392783.2	-	8	1760	c.1265T>C	c.(1264-1266)tTa>tCa	p.L422S	BAZ2B_ENST00000355831.2_Missense_Mutation_p.L422S|BAZ2B_ENST00000343439.5_Missense_Mutation_p.L420S|BAZ2B_ENST00000392782.1_Missense_Mutation_p.L420S	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	422			L -> S (in dbSNP:rs3213790). {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)|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						ACTGGTCAATAAACTAGATTC	0.313													G|||	725	0.144768	0.1717	0.0735	5008	,	,		17996	0.1121		0.1103	False		,,,				2504	0.228				p.L422S		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T1265C						PASS	.	G	SER/LEU	572,3022		39,494,1264	53.0	49.0	50.0		1265	2.6	0.8	2	dbSNP_106	50	1014,7118		58,898,3110	yes	missense	BAZ2B	NM_013450.2	145	97,1392,4374	GG,GA,AA		12.4693,15.9154,13.5255	benign	422/2169	160294842	1586,10140	1797	4066	5863	SO:0001583	missense	29994	exon8			GTCAATAAACTAG	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.1265T>C	2.37:g.160294842A>G	ENSP00000376534:p.Leu422Ser	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	192	91	0.473958	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	266	0.12179487179487179	89	0.18089430894308944	34	0.09392265193370165	52	0.09090909090909091	91	0.12005277044854881	G	5.109	0.205678	0.09704	0.159154	0.124693	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14	5.35	2.62	0.31277	.	0.485309	0.15182	N	0.276044	T	0.00271	0.0008	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.15141	0.012;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.03394	-1.1041	9	0.14656	T	0.56	7.6494	8.6754	0.34176	0.2945:0.0:0.7054:0.0	rs3213790;rs17845345;rs17858190;rs52827970;rs57244036;rs3213790	422;420;420;422	Q9UIF8-3;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;BAZ2B_HUMAN	S	420;422;422;420;359	ENSP00000376533:L420S;ENSP00000376534:L422S;ENSP00000348087:L422S;ENSP00000339670:L420S	ENSP00000339670:L420S	L	-	2	0	BAZ2B	160003088	0.999000	0.42202	0.847000	0.33407	0.451000	0.32288	1.943000	0.40253	0.021000	0.15133	-0.733000	0.03571	TTA	A|0.860;G|0.140	0.140	strong		0.313	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
DOCK10	55619	hgsc.bcm.edu	37	2	225670901	225670901	+	Missense_Mutation	SNP	G	G	C	rs4674941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:225670901G>C	ENST00000258390.7	-	34	3823	c.3756C>G	c.(3754-3756)atC>atG	p.I1252M	DOCK10_ENST00000409592.3_Missense_Mutation_p.I1246M	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1252					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TTGCATGTTTGATAGCTGTCT	0.353													C|||	1248	0.249201	0.6634	0.1196	5008	,	,		19929	0.0228		0.1501	False		,,,				2504	0.1166				p.I1252M		Atlas-SNP	.											.	DOCK10	308	.	0			c.C3756G						PASS	.	C	MET/ILE	2089,1635		577,935,350	141.0	142.0	142.0		3756	6.0	1.0	2	dbSNP_111	142	1093,7089		80,933,3078	yes	missense	DOCK10	NM_014689.2	10	657,1868,3428	CC,CG,GG		13.3586,43.9044,26.726	benign	1252/2187	225670901	3182,8724	1862	4091	5953	SO:0001583	missense	55619	exon34			ATGTTTGATAGCT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3756C>G	2.37:g.225670901G>C	ENSP00000258390:p.Ile1252Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	478|478	0.21886446886446886|0.21886446886446886	301|301	0.6117886178861789|0.6117886178861789	48|48	0.13259668508287292|0.13259668508287292	16|16	0.027972027972027972|0.027972027972027972	113|113	0.14907651715039577|0.14907651715039577	C|C	1.091|1.091	-0.664100|-0.664100	0.03428|0.03428	0.560956|0.560956	0.133586|0.133586	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390|ENST00000422684	T;T|.	0.21734|.	1.99;1.99|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.088261|.	0.85682|.	N|.	0.000000|.	T|.	0.00012|.	0.0000|.	N|N	0.00347|0.00347	-1.61|-1.61	0.49915|0.49915	P|P	1.64000000000053E-4|1.64000000000053E-4	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|.	0.29243|.	-1.0018|.	9|.	0.08179|.	T|.	0.78|.	.|.	17.4358|17.4358	0.87552|0.87552	0.0:0.8755:0.1245:0.0|0.0:0.8755:0.1245:0.0	rs4674941;rs52829997;rs60007997;rs4674941|rs4674941;rs52829997;rs60007997;rs4674941	1252;115;1246|.	Q96BY6;B4DF07;B3FL70|.	DOC10_HUMAN;.;.|.	M|X	1246;1252|143	ENSP00000386694:I1246M;ENSP00000258390:I1252M|.	ENSP00000258390:I1252M|.	I|S	-|-	3|2	3|0	DOCK10|DOCK10	225379145|225379145	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	2.565000|2.565000	0.45939|0.45939	1.544000|1.544000	0.49359|0.49359	-0.120000|-0.120000	0.15030|0.15030	ATC|TCA	G|0.790;C|0.209	0.209	strong		0.353	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
OR9Q1	219956	hgsc.bcm.edu	37	11	57947264	57947264	+	Silent	SNP	C	C	G	rs11229273	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57947264C>G	ENST00000335397.3	+	3	664	c.348C>G	c.(346-348)gcC>gcG	p.A116A		NM_001005212.3	NP_001005212.1	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q, member 1	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Breast(21;0.222)				ACCTCTTGGCCCTCATGGCCT	0.557													C|||	1679	0.335264	0.093	0.2406	5008	,	,		22617	0.5754		0.2684	False		,,,				2504	0.5511				p.A116A		Atlas-SNP	.											.	OR9Q1	60	.	0			c.C348G						PASS	.	C		472,3930	223.3+/-239.8	28,416,1757	120.0	96.0	104.0		348	-2.9	0.9	11	dbSNP_120	104	2372,6220	395.6+/-345.1	319,1734,2243	no	coding-synonymous	OR9Q1	NM_001005212.3		347,2150,4000	GG,GC,CC		27.6071,10.7224,21.887		116/311	57947264	2844,10150	2201	4296	6497	SO:0001819	synonymous_variant	219956	exon3			CTTGGCCCTCATG	AB065734	CCDS31543.1	11q12.1	2012-08-09				ENSG00000186509		"""GPCR / Class A : Olfactory receptors"""	14724	protein-coding gene	gene with protein product							Standard	NM_001005212		Approved		uc001nmj.3	Q8NGQ5		ENST00000335397.3:c.348C>G	11.37:g.57947264C>G		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	387	209	0.540052	NM_001005212	Q2TAN3|Q96RA7	Silent	SNP	ENST00000335397.3	37	CCDS31543.1																																																																																			C|0.747;G|0.253	0.253	strong		0.557	OR9Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394538.2	NM_001005212	
COX6C	1345	hgsc.bcm.edu	37	8	100899793	100899793	+	Silent	SNP	G	G	A	rs1130569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:100899793G>A	ENST00000520468.2	-	3	622	c.168C>T	c.(166-168)taC>taT	p.Y56Y	COX6C_ENST00000297564.2_Silent_p.Y56Y|COX6C_ENST00000524245.1_Silent_p.Y56Y|COX6C_ENST00000517682.2_Silent_p.Y56Y|COX6C_ENST00000522940.1_Silent_p.Y56Y|COX6C_ENST00000518171.1_Silent_p.Y56Y|COX6C_ENST00000523016.1_Silent_p.Y56Y|COX6C_ENST00000520271.1_Silent_p.Y56Y	NM_004374.3	NP_004365.1	P09669	COX6C_HUMAN	cytochrome c oxidase subunit VIc	56					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)	p.Y56Y(1)	HMGA2/COX6C(2)	liver(1)|lung(2)	3			all cancers(13;8.32e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TCATGACATCGTAGTTTCTGT	0.343			T	HMGA2	uterine leiomyoma								A|||	1249	0.249401	0.5265	0.1758	5008	,	,		17900	0.13		0.1819	False		,,,				2504	0.1196				p.Y56Y	NSCLC(46;1123 1136 1705 23767 45086)	Atlas-SNP	.		Dom	yes		8	8q22-q23	1345	cytochrome c oxidase subunit VIc		M	COX6C_ENST00000520468,NS,carcinoma,0,1	COX6C	25	1	1	Substitution - coding silent(1)	stomach(1)	c.C168T						scavenged	.	A		2157,2249	592.6+/-387.8	520,1117,566	59.0	60.0	60.0		168	4.4	1.0	8	dbSNP_86	60	1546,7050	744.5+/-407.2	123,1300,2875	no	coding-synonymous	COX6C	NM_004374.3		643,2417,3441	AA,AG,GG		17.9851,48.956,28.4802		56/76	100899793	3703,9299	2203	4298	6501	SO:0001819	synonymous_variant	1345	exon3			GACATCGTAGTTT	X13238	CCDS6284.1	8q22.2	2011-07-04			ENSG00000164919	ENSG00000164919	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2285	protein-coding gene	gene with protein product		124090				10072584	Standard	NM_004374		Approved		uc003yiy.2	P09669	OTTHUMG00000164703	ENST00000520468.2:c.168C>T	8.37:g.100899793G>A		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	NM_004374	B2R4D7	Silent	SNP	ENST00000520468.2	37	CCDS6284.1																																																																																			G|0.733;A|0.267	0.267	strong		0.343	COX6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379834.3	NM_004374	
C6orf132	647024	hgsc.bcm.edu	37	6	42074925	42074925	+	Missense_Mutation	SNP	G	G	A	rs568578371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42074925G>A	ENST00000341865.4	-	4	724	c.725C>T	c.(724-726)cCt>cTt	p.P242L		NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	242										breast(1)	1						CACTGTGTGAGGAGATGCTGG	0.642													G|||	2	0.000399361	0.0	0.0014	5008	,	,		7599	0.0		0.001	False		,,,				2504	0.0				p.P242L		Atlas-SNP	.											.	C6orf132	48	.	0			c.C725T						PASS	.						6.0	7.0	6.0					6																	42074925		689	1585	2274	SO:0001583	missense	647024	exon4			GTGTGAGGAGATG		CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112			21288	protein-coding gene	gene with protein product							Standard	NM_001164446		Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.725C>T	6.37:g.42074925G>A	ENSP00000341368:p.Pro242Leu	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_001164446	A6NI05	Missense_Mutation	SNP	ENST00000341865.4	37	CCDS47428.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.525828	0.00147	.	.	ENSG00000188112	ENST00000341865	T	0.39997	1.05	3.67	0.7	0.18099	.	.	.	.	.	T	0.04815	0.0130	N	0.11560	0.145	0.19775	N	0.999957	.	.	.	.	.	.	T	0.39522	-0.9610	7	0.09843	T	0.71	.	3.0829	0.06269	0.2512:0.0:0.5395:0.2094	.	.	.	.	L	242	ENSP00000341368:P242L	ENSP00000341368:P242L	P	-	2	0	C6orf132	42182903	0.994000	0.37717	0.002000	0.10522	0.001000	0.01503	0.677000	0.25262	-0.119000	0.11830	-0.175000	0.13238	CCT	.	.	none		0.642	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040548.2	NM_001164446	
FLG2	388698	hgsc.bcm.edu	37	1	152327502	152327502	+	Silent	SNP	A	A	G	rs138997916	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152327502A>G	ENST00000388718.5	-	3	2832	c.2760T>C	c.(2758-2760)tcT>tcC	p.S920S	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	920	Ser-rich.				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)			GGCCATAGCTAGACTGATGTG	0.483													A|||	975	0.194688	0.0129	0.2939	5008	,	,		24864	0.4018		0.1044	False		,,,				2504	0.2495				p.S920S		Atlas-SNP	.											FLG2,NS,carcinoma,0,2	FLG2	431	2	0			c.T2760C						scavenged	.						324.0	278.0	293.0					1																	152327502		2202	4289	6491	SO:0001819	synonymous_variant	388698	exon3			ATAGCTAGACTGA	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.2760T>C	1.37:g.152327502A>G		Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	84	19	0.22619	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			A|0.902;G|0.098	0.098	strong		0.483	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
TMEM9	252839	hgsc.bcm.edu	37	1	201115964	201115964	+	Silent	SNP	G	G	A	rs139286836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201115964G>A	ENST00000367330.1	-	3	687	c.171C>T	c.(169-171)caC>caT	p.H57H	TMEM9_ENST00000367334.5_Silent_p.H57H|TMEM9_ENST00000485839.2_Silent_p.H57H|TMEM9_ENST00000367333.2_Silent_p.H57H|TMEM9_ENST00000472411.1_5'Flank|TMEM9_ENST00000367332.1_Silent_p.H60H			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	57					transport (GO:0006810)	integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)				liver(1)|lung(1)|stomach(1)	3		Breast(1374;0.000301)				GCTCCACCACGTGCAGGCAGT	0.612													G|||	20	0.00399361	0.0	0.0144	5008	,	,		19530	0.0		0.005	False		,,,				2504	0.0051				p.H57H		Atlas-SNP	.											.	TMEM9	12	.	0			c.C171T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	95.0	74.0	81.0		171	-1.5	1.0	1	dbSNP_134	81	83,8517	47.6+/-106.9	0,83,4217	no	coding-synonymous	TMEM9	NM_016456.3		0,86,6417	AA,AG,GG		0.9651,0.0681,0.6612		57/184	201115964	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	252839	exon4			CACCACGTGCAGG		CCDS1408.1, CCDS73001.1	1q41	2008-02-05			ENSG00000116857	ENSG00000116857			18823	protein-coding gene	gene with protein product							Standard	NM_001288565		Approved	TMEM9A	uc001gvy.3	Q9P0T7	OTTHUMG00000035831	ENST00000367330.1:c.171C>T	1.37:g.201115964G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_016456	B1ALM6|Q96NQ9|Q9BQF5	Silent	SNP	ENST00000367330.1	37	CCDS1408.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456	
NOM1	64434	hgsc.bcm.edu	37	7	156742965	156742965	+	Silent	SNP	G	G	C	rs61734937	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:156742965G>C	ENST00000275820.3	+	1	549	c.534G>C	c.(532-534)gcG>gcC	p.A178A		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	178	Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.					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)		TTTTAGCGGCGAACGAGGAGG	0.662													C|||	1099	0.219449	0.264	0.2421	5008	,	,		15301	0.2808		0.1511	False		,,,				2504	0.1503				p.A178A		Atlas-SNP	.											.	NOM1	73	.	0			c.G534C						PASS	.	C		1166,3232		148,870,1181	46.0	56.0	52.0		534	4.2	1.0	7	dbSNP_129	52	1237,7355		81,1075,3140	no	coding-synonymous	NOM1	NM_138400.1		229,1945,4321	CC,CG,GG		14.3971,26.5121,18.4988		178/861	156742965	2403,10587	2199	4296	6495	SO:0001819	synonymous_variant	64434	exon1			AGCGGCGAACGAG	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.534G>C	7.37:g.156742965G>C		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																			G|0.806;C|0.194	0.194	strong		0.662	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
FMN2	56776	hgsc.bcm.edu	37	1	240341268	240341268	+	Silent	SNP	A	A	G	rs3765588	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240341268A>G	ENST00000319653.9	+	3	2060	c.1830A>G	c.(1828-1830)tcA>tcG	p.S610S	RP11-567G24.3_ENST00000412311.1_RNA|RP11-567G24.3_ENST00000444308.1_RNA	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	610					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCACACACTCATTGGACTATT	0.418													G|||	1194	0.238419	0.3283	0.1138	5008	,	,		14859	0.2232		0.1789	False		,,,				2504	0.2822				p.S610S		Atlas-SNP	.											.	FMN2	451	.	0			c.A1830G						PASS	.	G		1286,3120	700.0+/-406.6	196,894,1113	98.0	95.0	96.0		1830	-11.0	0.4	1	dbSNP_107	96	1657,6943	740.4+/-407.1	160,1337,2803	no	coding-synonymous	FMN2	NM_020066.4		356,2231,3916	GG,GA,AA		19.2674,29.1875,22.628		610/1723	240341268	2943,10063	2203	4300	6503	SO:0001819	synonymous_variant	56776	exon3			ACACTCATTGGAC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1830A>G	1.37:g.240341268A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.768;G|0.232	0.232	strong		0.418	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350432	65350432	+	Missense_Mutation	SNP	C	C	T	rs369672448		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:65350432C>T	ENST00000284037.5	+	21	3675	c.3286C>T	c.(3286-3288)Cgg>Tgg	p.R1096W	ERBB2IP_ENST00000511297.1_Missense_Mutation_p.R1092W|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.R1096W|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.R1096W|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.R1096W|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.R1096W|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.R1096W|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.R1096W|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.R1096W	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1096					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		CTCTACAAGGCGGGCTCAGAT	0.493																																					p.R1096W		Atlas-SNP	.											ERBB2IP,NS,carcinoma,-1,1	ERBB2IP	120	1	0			c.C3286T						scavenged	.	C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	88.0	88.0	88.0		3286,3286	-0.9	0.8	5		88	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ERBB2IP	NM_001006600.1,NM_018695.2	101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1096/1303,1096/1372	65350432	1,13005	2203	4300	6503	SO:0001583	missense	55914	exon21			ACAAGGCGGGCTC		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.3286C>T	5.37:g.65350432C>T	ENSP00000284037:p.Arg1096Trp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	119	2	0.0168067	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745957	0.49151	0.0	1.16E-4	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T	0.57595	0.73;0.67;0.69;0.9;0.39;0.79;0.67;0.72;0.39	5.43	-0.866	0.10659	.	0.055231	0.64402	D	0.000001	T	0.63965	0.2556	L	0.46157	1.445	0.53688	D	0.999976	D;D;D;D;D;D;D	0.89917	0.999;0.999;0.997;0.997;0.997;1.0;0.998	P;P;P;P;P;D;P	0.74348	0.896;0.863;0.893;0.667;0.745;0.983;0.821	T	0.68577	-0.5372	10	0.87932	D	0	.	17.4613	0.87620	0.6542:0.3458:0.0:0.0	.	1096;1096;1096;1092;1096;1096;1096	Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;LAP2_HUMAN;.;.	W	1096;1096;1096;1096;1096;1096;1092;1096;1096	ENSP00000284037:R1096W;ENSP00000370330:R1096W;ENSP00000370326:R1096W;ENSP00000370323:R1096W;ENSP00000370322:R1096W;ENSP00000370325:R1096W;ENSP00000422766:R1092W;ENSP00000426632:R1096W;ENSP00000422015:R1096W	ENSP00000284037:R1096W	R	+	1	2	ERBB2IP	65386188	0.984000	0.35163	0.794000	0.32065	0.725000	0.41563	0.428000	0.21395	-0.051000	0.13334	0.650000	0.86243	CGG	.	.	weak		0.493	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
NCKAP5	344148	hgsc.bcm.edu	37	2	133541444	133541444	+	Silent	SNP	T	T	C	rs12691829	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133541444T>C	ENST00000409261.1	-	14	3313	c.2940A>G	c.(2938-2940)ccA>ccG	p.P980P	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Silent_p.P980P|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	980										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						AAGAAATAACTGGAGCAGAAA	0.507													C|||	3593	0.717452	0.851	0.6729	5008	,	,		17916	0.871		0.5219	False		,,,				2504	0.6115				p.P980P		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A2940G						PASS	.	C	,	3075,691		1280,515,88	29.0	31.0	30.0		2940,	-4.5	0.0	2	dbSNP_121	30	4458,3756		1234,1990,883	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	2514,2505,971	CC,CT,TT		45.7268,18.3484,37.1202	,	980/1910,	133541444	7533,4447	1883	4107	5990	SO:0001819	synonymous_variant	344148	exon14			AATAACTGGAGCA	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.2940A>G	2.37:g.133541444T>C		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	182	180	0.989011	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			T|0.320;C|0.680	0.680	strong		0.507	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
PARPBP	55010	hgsc.bcm.edu	37	12	102558369	102558369	+	Missense_Mutation	SNP	C	C	A	rs75438625	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102558369C>A	ENST00000358383.5	+	5	694	c.649C>A	c.(649-651)Caa>Aaa	p.Q217K	PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000541394.1_Missense_Mutation_p.Q294K|PARPBP_ENST00000378128.3_Missense_Mutation_p.Q217K|PARPBP_ENST00000543784.1_Missense_Mutation_p.Q103K|PARPBP_ENST00000392911.2_Missense_Mutation_p.Q136K|PARPBP_ENST00000327680.2_Missense_Mutation_p.Q136K			Q9NWS1	PARI_HUMAN	PARP1 binding protein	217					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						TCGAGAGAAACAAATGTCTAT	0.383													C|||	163	0.0325479	0.1082	0.0058	5008	,	,		17316	0.0		0.005	False		,,,				2504	0.0112				p.Q217K		Atlas-SNP	.											.	PARPBP	40	.	0			c.C649A						PASS	.	C	LYS/GLN	318,4088	170.1+/-200.6	16,286,1901	143.0	152.0	149.0		649	4.9	1.0	12	dbSNP_131	149	21,8579	15.3+/-51.7	0,21,4279	yes	missense	C12orf48	NM_017915.3	53	16,307,6180	AA,AC,CC		0.2442,7.2174,2.6065	benign	217/580	102558369	339,12667	2203	4300	6503	SO:0001583	missense	55010	exon5			GAGAAACAAATGT	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.649C>A	12.37:g.102558369C>A	ENSP00000351153:p.Gln217Lys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	30	0.333333	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	57	0.0260989010989011	52	0.10569105691056911	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	4.014	-0.000060	0.07819	0.072174	0.002442	ENSG00000185480	ENST00000378128;ENST00000327680;ENST00000541394;ENST00000543784;ENST00000358383;ENST00000392911;ENST00000417507;ENST00000412715	T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01	5.81	4.91	0.64330	.	0.653601	0.17239	N	0.181630	T	0.00440	0.0014	N	0.13043	0.29	0.26065	N	0.981294	B;B;B;B;B;B	0.16802	0.019;0.01;0.001;0.002;0.005;0.004	B;B;B;B;B;B	0.13407	0.009;0.006;0.003;0.003;0.004;0.006	T	0.05146	-1.0903	10	0.05721	T	0.95	0.0463	13.9017	0.63809	0.3925:0.6075:0.0:0.0	.	103;294;217;217;217;136	B4DT40;B4DZ31;Q9NWS1-6;Q9NWS1-7;Q9NWS1;Q9NWS1-2	.;.;.;.;PR1BP_HUMAN;.	K	217;136;294;103;217;136;184;184	ENSP00000367368:Q217K;ENSP00000332915:Q136K;ENSP00000440850:Q294K;ENSP00000444576:Q103K;ENSP00000351153:Q217K;ENSP00000376643:Q136K;ENSP00000411313:Q184K;ENSP00000393867:Q184K	ENSP00000332915:Q136K	Q	+	1	0	C12orf48	101082499	0.994000	0.37717	0.996000	0.52242	0.976000	0.68499	1.035000	0.30216	1.433000	0.47394	0.460000	0.39030	CAA	C|0.974;A|0.026	0.026	strong		0.383	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915	
ACAA1	30	hgsc.bcm.edu	37	3	38170810	38170810	+	Missense_Mutation	SNP	C	C	G	rs156265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:38170810C>G	ENST00000333167.8	-	6	688	c.516G>C	c.(514-516)gaG>gaC	p.E172D	ACAA1_ENST00000544624.1_Missense_Mutation_p.E20D|ACAA1_ENST00000444607.2_3'UTR|ACAA1_ENST00000301810.7_Intron|ACAA1_ENST00000480865.1_5'UTR|ACAA1_ENST00000450296.1_Missense_Mutation_p.E131D	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	172			E -> D (in dbSNP:rs156265).		alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		CTCTGGCCTTCTCCTTCTCCA	0.552													C|||	685	0.136781	0.025	0.1326	5008	,	,		21211	0.3244		0.1431	False		,,,				2504	0.091				p.E172D		Atlas-SNP	.											.	ACAA1	32	.	0			c.G516C						PASS	.	C	,ASP/GLU	206,4200	129.4+/-166.1	3,200,2000	173.0	138.0	150.0		,516	1.7	0.9	3	dbSNP_79	150	1251,7349	251.0+/-277.6	95,1061,3144	yes	intron,missense	ACAA1	NM_001130410.1,NM_001607.3	,45	98,1261,5144	GG,GC,CC		14.5465,4.6754,11.2025	,benign	,172/425	38170810	1457,11549	2203	4300	6503	SO:0001583	missense	30	exon6			GGCCTTCTCCTTC	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087	ENST00000333167.8:c.516G>C	3.37:g.38170810C>G	ENSP00000333664:p.Glu172Asp	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	209	90	0.430622	NM_001607	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	37	CCDS2673.1	361|361	0.1652930402930403|0.1652930402930403	15|15	0.03048780487804878|0.03048780487804878	49|49	0.13535911602209943|0.13535911602209943	188|188	0.32867132867132864|0.32867132867132864	109|109	0.1437994722955145|0.1437994722955145	C|C	11.98|11.98	1.800208|1.800208	0.31869|0.31869	0.046754|0.046754	0.145465|0.145465	ENSG00000060971|ENSG00000060971	ENST00000333167;ENST00000450296;ENST00000358122;ENST00000544624|ENST00000452171	D;D;D|.	0.90444|.	-2.67;-2.67;-2.67|.	5.96|5.96	1.68|1.68	0.24146|0.24146	Thiolase, N-terminal (1);Thiolase-like (1);|.	0.830821|.	0.11392|.	N|.	0.568720|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04705|0.04705	-0.18|-0.18	0.24790|0.24790	P|P	0.9927613|0.9927613	B;B;B|.	0.06786|.	0.0;0.001;0.0|.	B;B;B|.	0.08055|.	0.0;0.003;0.0|.	T|T	0.45396|0.45396	-0.9264|-0.9264	9|4	0.22706|.	T|.	0.39|.	-15.202|-15.202	3.3169|3.3169	0.07036|0.07036	0.3401:0.2881:0.2935:0.0783|0.3401:0.2881:0.2935:0.0783	rs156265;rs52826071;rs156265|rs156265;rs52826071;rs156265	104;131;172|.	F5GXL8;C9JDE9;P09110|.	.;.;THIK_HUMAN|.	D|T	172;131;104;20|45	ENSP00000333664:E172D;ENSP00000395183:E131D;ENSP00000445710:E20D|.	ENSP00000333664:E172D|.	E|R	-|-	3|2	2|0	ACAA1|ACAA1	38145814|38145814	0.024000|0.024000	0.19004|0.19004	0.907000|0.907000	0.35723|0.35723	0.765000|0.765000	0.43378|0.43378	0.247000|0.247000	0.18179|0.18179	0.791000|0.791000	0.33826|0.33826	-0.175000|-0.175000	0.13238|0.13238	GAG|AGA	C|0.865;G|0.135	0.135	strong		0.552	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607	
AQP3	360	hgsc.bcm.edu	37	9	33442952	33442952	+	Silent	SNP	G	G	A	rs2228332	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33442952G>A	ENST00000297991.4	-	4	470	c.390C>T	c.(388-390)ttC>ttT	p.F130F	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	130					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		GGTTGTCGGCGAAGTGCCAGA	0.567													A|||	3299	0.658746	0.7572	0.6859	5008	,	,		15964	0.6875		0.5934	False		,,,				2504	0.544				p.F130F		Atlas-SNP	.											.	AQP3	18	.	0			c.C390T						PASS	.	A		3282,1124	401.3+/-331.9	1220,842,141	89.0	94.0	92.0		390	-6.5	0.0	9	dbSNP_98	92	5042,3558	517.8+/-379.1	1484,2074,742	no	coding-synonymous	AQP3	NM_004925.4		2704,2916,883	AA,AG,GG		41.3721,25.5107,35.9988		130/293	33442952	8324,4682	2203	4300	6503	SO:0001819	synonymous_variant	360	exon4			GTCGGCGAAGTGC		CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"""Ion channels / Aquaporins"", ""Blood group antigens"""	636	protein-coding gene	gene with protein product	"""Gill blood group"""	600170	"""aquaporin 3"", ""aquaporin 3 (GIL blood group)"""			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.390C>T	9.37:g.33442952G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	150	61	0.406667	NM_004925	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Silent	SNP	ENST00000297991.4	37	CCDS6542.1																																																																																			G|0.344;N|0.000	.	strong		0.567	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925	
IGSF9B	22997	hgsc.bcm.edu	37	11	133814191	133814191	+	Silent	SNP	A	A	G	rs595986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:133814191A>G	ENST00000321016.8	-	3	563	c.333T>C	c.(331-333)taT>taC	p.Y111Y	IGSF9B_ENST00000533871.2_Silent_p.Y111Y			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	111	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)		CTTTGCACTCATACCAGCCCT	0.577													G|||	2444	0.488019	0.2602	0.5389	5008	,	,		19566	0.4028		0.7117	False		,,,				2504	0.6176				p.Y111Y		Atlas-SNP	.											.	IGSF9B	290	.	0			c.T333C						PASS	.	G		1510,2676		295,920,878	103.0	109.0	107.0		333	1.0	1.0	11	dbSNP_83	107	6041,2405		2147,1747,329	no	coding-synonymous	IGSF9B	NM_014987.1		2442,2667,1207	GG,GA,AA		28.475,36.0726,40.2232		111/1350	133814191	7551,5081	2093	4223	6316	SO:0001819	synonymous_variant	22997	exon3			GCACTCATACCAG	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.333T>C	11.37:g.133814191A>G		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				A|0.489;G|0.511	0.511	strong		0.577	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
OSBPL9	114883	hgsc.bcm.edu	37	1	52250216	52250216	+	Silent	SNP	C	C	T	rs144748323		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:52250216C>T	ENST00000428468.1	+	20	1793	c.1791C>T	c.(1789-1791)ttC>ttT	p.F597F	OSBPL9_ENST00000447887.1_Silent_p.F607F|OSBPL9_ENST00000462759.1_Silent_p.F419F|OSBPL9_ENST00000435686.2_Silent_p.F432F|OSBPL9_ENST00000371714.1_Silent_p.F584F|OSBPL9_ENST00000530544.1_Silent_p.F516F|OSBPL9_ENST00000361556.5_Silent_p.F487F|OSBPL9_ENST00000486942.1_Silent_p.F419F|OSBPL9_ENST00000337809.4_Silent_p.F602F|OSBPL9_ENST00000371710.3_Silent_p.F615F|OSBPL9_ENST00000453295.1_Silent_p.F580F|OSBPL9_ENST00000531828.1_Silent_p.F432F			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	597					lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						CTAAACCCTTCTATGGGGGCA	0.403																																					p.F607F		Atlas-SNP	.											.	OSBPL9	192	.	0			c.C1821T						PASS	.	T	,,,,,,	0,4406		0,0,2203	87.0	90.0	89.0		1791,1257,1257,1740,1461,1752,1821	2.7	1.0	1	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL9	NM_024586.5,NM_148904.3,NM_148905.3,NM_148906.2,NM_148907.2,NM_148908.3,NM_148909.3	,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,	597/737,419/559,419/559,580/720,487/627,584/724,607/747	52250216	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114883	exon20			ACCCTTCTATGGG	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.1791C>T	1.37:g.52250216C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_148909	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Silent	SNP	ENST00000428468.1	37	CCDS41332.3																																																																																			C|1.000;T|0.000	0.000	weak		0.403	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4		
CEP89	84902	hgsc.bcm.edu	37	19	33439187	33439187	+	Missense_Mutation	SNP	G	G	A	rs3764633	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	63	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	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	
CAMK2B	816	hgsc.bcm.edu	37	7	44282877	44282877	+	Silent	SNP	A	A	G	rs11542227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:44282877A>G	ENST00000395749.2	-	8	649	c.573T>C	c.(571-573)taT>taC	p.Y191Y	CAMK2B_ENST00000358707.3_Silent_p.Y191Y|CAMK2B_ENST00000457475.1_Silent_p.Y191Y|CAMK2B_ENST00000350811.3_Silent_p.Y191Y|CAMK2B_ENST00000353625.4_Silent_p.Y191Y|CAMK2B_ENST00000346990.4_Silent_p.Y191Y|CAMK2B_ENST00000347193.4_Silent_p.Y191Y|CAMK2B_ENST00000395747.2_Silent_p.Y191Y|CAMK2B_ENST00000440254.2_Silent_p.Y191Y|CAMK2B_ENST00000258682.6_Silent_p.Y191Y|CAMK2B_ENST00000502837.2_Silent_p.Y62Y	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	191	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						CAGGCTTGCCATACGCCTCTT	0.612													.|||	1051	0.209864	0.0976	0.2233	5008	,	,		19957	0.1131		0.3588	False		,,,				2504	0.2986				p.Y191Y		Atlas-SNP	.											.	CAMK2B	56	.	0			c.T573C						PASS	.	A	,,,,,,,	578,3828	255.2+/-260.5	34,510,1659	87.0	76.0	80.0		573,573,573,573,573,573,573,573	-1.5	0.9	7	dbSNP_120	80	3083,5517	471.3+/-368.1	543,1997,1760	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2B	NM_001220.4,NM_172078.2,NM_172079.2,NM_172080.2,NM_172081.2,NM_172082.2,NM_172083.2,NM_172084.2	,,,,,,,	577,2507,3419	GG,GA,AA		35.8488,13.1185,28.1485	,,,,,,,	191/667,191/543,191/519,191/518,191/504,191/493,191/480,191/450	44282877	3661,9345	2203	4300	6503	SO:0001819	synonymous_variant	816	exon8			CTTGCCATACGCC	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"""CaM-kinase II beta chain"", ""calcium/calmodulin-dependent protein kinase type II beta chain"", ""CaM kinase II beta subunit"", ""proline rich calmodulin-dependent protein kinase"""	607707	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"""	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.573T>C	7.37:g.44282877A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	133	48	0.360902	NM_172081	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Silent	SNP	ENST00000395749.2	37	CCDS5483.1																																																																																			A|0.735;G|0.265	0.265	strong		0.612	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253960	39253960	+	Missense_Mutation	SNP	C	C	T	rs144672535	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39253960C>T	ENST00000333822.4	-	1	433	c.377G>A	c.(376-378)cGc>cAc	p.R126H		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	126	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].			R -> H (in Ref. 2; CAC27579). {ECO:0000305}.	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						gcagctggggcggcagcagtt	0.672													T|||	1899	0.379193	0.4198	0.3948	5008	,	,		14996	0.2292		0.4543	False		,,,				2504	0.3906				p.R126H		Atlas-SNP	.											KRTAP4-8,right_lower_lobe,carcinoma,0,2	KRTAP4-8	57	2	0			c.G377A						PASS	.						3.0	5.0	4.0					17																	39253960		568	1364	1932	SO:0001583	missense	728224	exon1			CTGGGGCGGCAGC	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.377G>A	17.37:g.39253960C>T	ENSP00000328444:p.Arg126His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	19	0.311475	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	686	0.3141025641025641	142	0.2886178861788618	131	0.36187845303867405	103	0.18006993006993008	310	0.40897097625329815	.	14.80	2.642678	0.47153	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01548	4.78	3.36	-2.03	0.07365	.	1.816570	0.03571	U	0.228564	T	0.00012	0.0000	L	0.46614	1.455	0.80722	P	0.0	D	0.54207	0.965	P	0.46389	0.515	T	0.42258	-0.9462	9	0.32370	T	0.25	.	4.6421	0.12555	0.1571:0.5787:0.0:0.2642	.	126	Q9BYQ9	KRA48_HUMAN	H	126;111	ENSP00000328444:R126H	ENSP00000414561:R111H	R	-	2	0	KRTAP4-8	36507486	0.000000	0.05858	0.052000	0.19188	0.698000	0.40448	-0.965000	0.03829	-0.703000	0.05049	-0.384000	0.06662	CGC	C|0.500;T|0.500	0.500	strong		0.672	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
ASTN1	460	hgsc.bcm.edu	37	1	177001896	177001896	+	Silent	SNP	C	C	G	rs2076069	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:177001896C>G	ENST00000367654.3	-	3	772	c.561G>C	c.(559-561)ccG>ccC	p.P187P	ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000367657.3_Silent_p.P187P|ASTN1_ENST00000361833.2_Silent_p.P187P|ASTN1_ENST00000424564.2_Silent_p.P187P	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	187					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TCTGGGGCTGCGGGACCCGGC	0.612													G|||	751	0.14996	0.0272	0.2118	5008	,	,		17437	0.2599		0.1471	False		,,,				2504	0.1616				p.P187P		Atlas-SNP	.											.	ASTN1	314	.	0			c.G561C						PASS	.	G	,	228,4178	789.4+/-415.0	3,222,1978	38.0	39.0	38.0		561,561	-1.3	0.9	1	dbSNP_96	38	1418,7182	736.8+/-407.0	119,1180,3001	no	coding-synonymous,coding-synonymous	ASTN1	NM_004319.1,NM_207108.1	,	122,1402,4979	GG,GC,CC		16.4884,5.1748,12.6557	,	187/1295,187/1217	177001896	1646,11360	2203	4300	6503	SO:0001819	synonymous_variant	460	exon3			GGGCTGCGGGACC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.561G>C	1.37:g.177001896C>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	44	12	0.272727	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																				C|0.864;G|0.136	0.136	strong		0.612	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
PKHD1	5314	hgsc.bcm.edu	37	6	51947257	51947257	+	Silent	SNP	G	G	A	rs6901799	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:51947257G>A	ENST00000371117.3	-	4	489	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L	PKHD1_ENST00000340994.4_Silent_p.L72L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	72	IPT/TIG 1; atypical.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ACACTCCGCAGTGCGGGCACC	0.507													G|||	353	0.0704872	0.0651	0.0764	5008	,	,		19004	0.0367		0.1163	False		,,,				2504	0.0613				p.L72L		Atlas-SNP	.											.	PKHD1	927	.	0			c.C214T						PASS	.	G	,	356,4050	184.0+/-211.4	16,324,1863	163.0	168.0	166.0		214,214	-2.6	0.0	6	dbSNP_116	166	997,7603	214.8+/-254.3	65,867,3368	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	81,1191,5231	AA,AG,GG		11.593,8.0799,10.4029	,	72/4075,72/3397	51947257	1353,11653	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon4			TCCGCAGTGCGGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.214C>T	6.37:g.51947257G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			G|0.920;A|0.080	0.080	strong		0.507	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
OAS3	4940	hgsc.bcm.edu	37	12	113398919	113398919	+	Silent	SNP	G	G	A	rs2072136	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:113398919G>A	ENST00000228928.7	+	8	1880	c.1701G>A	c.(1699-1701)tcG>tcA	p.S567S	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	567	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						AGGTCTACTCGAGGCTCCTCA	0.537													G|||	1580	0.315495	0.0862	0.2752	5008	,	,		18330	0.6577		0.2346	False		,,,				2504	0.3845				p.S567S		Atlas-SNP	.											.	OAS3	63	.	0			c.G1701A						PASS	.	G		430,3478		30,370,1554	45.0	46.0	46.0		1701	-8.9	0.0	12	dbSNP_96	46	1909,6421		221,1467,2477	no	coding-synonymous	OAS3	NM_006187.2		251,1837,4031	AA,AG,GG		22.9172,11.0031,19.1126		567/1088	113398919	2339,9899	1954	4165	6119	SO:0001819	synonymous_variant	4940	exon8			CTACTCGAGGCTC	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.1701G>A	12.37:g.113398919G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			G|0.696;N|0.000	.	strong		0.537	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
ODF3L2	284451	hgsc.bcm.edu	37	19	464310	464310	+	Missense_Mutation	SNP	A	A	G	rs34551779	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:464310A>G	ENST00000315489.4	-	4	639	c.404T>C	c.(403-405)gTg>gCg	p.V135A	ODF3L2_ENST00000382696.3_Missense_Mutation_p.V99A	NM_182577.2	NP_872383.1	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	135	Pro-rich.		V -> A (in dbSNP:rs34551779). {ECO:0000269|PubMed:15489334}.			cytoplasmic microtubule (GO:0005881)				large_intestine(1)|lung(2)	3						CCGATGGCGCACAGGGGGCAC	0.677													a|||	2188	0.436901	0.2345	0.549	5008	,	,		11673	0.6637		0.4563	False		,,,				2504	0.3773				p.V135A		Atlas-SNP	.											.	ODF3L2	18	.	0			c.T404C						PASS	.	A	ALA/VAL	936,2648		147,642,1003	7.0	8.0	8.0		404	0.6	0.0	19	dbSNP_126	8	2842,4130		646,1550,1290	no	missense	ODF3L2	NM_182577.2	64	793,2192,2293	GG,GA,AA		40.7631,26.1161,35.7901	benign	135/290	464310	3778,6778	1792	3486	5278	SO:0001583	missense	284451	exon4			TGGCGCACAGGGG	AK097378	CCDS12027.1	19p13.3	2010-04-23	2008-07-04	2008-07-04		ENSG00000181781			26841	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 19"""	C19orf19		14702039	Standard	NM_182577		Approved	FLJ40059	uc002lor.3	Q3SX64		ENST00000315489.4:c.404T>C	19.37:g.464310A>G	ENSP00000318029:p.Val135Ala	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	NM_182577	Q3SX65|Q8N1L2	Missense_Mutation	SNP	ENST00000315489.4	37	CCDS12027.1	1033	0.47298534798534797	113	0.22967479674796748	184	0.5082872928176796	394	0.6888111888111889	342	0.45118733509234826	A	0.019	-1.449968	0.01080	0.261161	0.407631	ENSG00000181781	ENST00000315489;ENST00000382696	T;T	0.41400	1.54;1.0	4.06	0.605	0.17553	.	1.201840	0.05840	N	0.619156	T	0.00012	0.0000	N	0.15975	0.35	0.80722	P	0.0	B;B	0.14012	0.009;0.005	B;B	0.15052	0.012;0.012	T	0.42481	-0.9449	9	0.14656	T	0.56	-0.5868	3.6483	0.08194	0.4816:0.1994:0.3191:0.0	rs34551779	99;135	Q3SX64-2;Q3SX64	.;OD3L2_HUMAN	A	135;99	ENSP00000318029:V135A;ENSP00000372143:V99A	ENSP00000318029:V135A	V	-	2	0	ODF3L2	415310	0.577000	0.26708	0.037000	0.18230	0.001000	0.01503	1.422000	0.34826	0.016000	0.14998	-0.518000	0.04402	GTG	A|0.527;G|0.473	0.473	strong		0.677	ODF3L2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451849.2	NM_182577	
TCHH	7062	hgsc.bcm.edu	37	1	152081921	152081921	+	Missense_Mutation	SNP	G	G	C	rs2496253	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152081921G>C	ENST00000368804.1	-	2	3771	c.3772C>G	c.(3772-3774)Ctg>Gtg	p.L1258V		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1258			L -> V (in dbSNP:rs2496253). {ECO:0000269|PubMed:7685034}.		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)			CTGTCGCGCAGCTGGGAATCT	0.532													C|||	2847	0.56849	0.4781	0.647	5008	,	,		20914	0.5992		0.4016	False		,,,				2504	0.7751				p.L1258V		Atlas-SNP	.											.	TCHH	275	.	0			c.C3772G						PASS	.	C	VAL/LEU	1788,2272		383,1022,625	78.0	78.0	78.0		3772	3.1	0.0	1	dbSNP_100	78	3671,4677		810,2051,1313	yes	missense	TCHH	NM_007113.2	32	1193,3073,1938	CC,CG,GG		43.9746,44.0394,43.9958	benign	1258/1944	152081921	5459,6949	2030	4174	6204	SO:0001583	missense	7062	exon3			CGCGCAGCTGGGA	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.3772C>G	1.37:g.152081921G>C	ENSP00000357794:p.Leu1258Val	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	188	83	0.441489	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	1093	0.5004578754578755	234	0.47560975609756095	209	0.5773480662983426	332	0.5804195804195804	318	0.41952506596306066	C	7.800	0.713488	0.15306	0.440394	0.439746	ENSG00000159450	ENST00000368804	T	0.04083	3.71	4.07	3.14	0.36123	.	.	.	.	.	T	0.00724	0.0024	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49244	-0.8960	8	0.28530	T	0.3	.	12.1039	0.53801	0.0:0.4831:0.5169:0.0	rs2496253;rs17647316;rs52794498;rs57947083;rs2496253	1258	Q07283	TRHY_HUMAN	V	1258	ENSP00000357794:L1258V	ENSP00000357794:L1258V	L	-	1	2	TCHH	150348545	0.000000	0.05858	0.002000	0.10522	0.433000	0.31745	-0.233000	0.09041	0.218000	0.20820	-0.215000	0.12644	CTG	G|0.499;C|0.501	0.501	strong		0.532	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
OR8S1	341568	hgsc.bcm.edu	37	12	48919793	48919793	+	Missense_Mutation	SNP	T	T	C	rs2705143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	149	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	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		
CCDC93	54520	hgsc.bcm.edu	37	2	118743630	118743630	+	Missense_Mutation	SNP	G	G	A	rs33975708	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:118743630G>A	ENST00000376300.2	-	7	672	c.535C>T	c.(535-537)Cgt>Tgt	p.R179C	CCDC93_ENST00000460781.1_5'UTR|CCDC93_ENST00000319432.5_Missense_Mutation_p.R179C	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	179			R -> C (in dbSNP:rs33975708). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						TATTTCCGACGGGGCTTGTAC	0.507													G|||	204	0.0407348	0.0424	0.0706	5008	,	,		14933	0.0		0.0855	False		,,,				2504	0.0133				p.R179C		Atlas-SNP	.											.	CCDC93	70	.	0			c.C535T						PASS	.	G	CYS/ARG	208,4198	128.6+/-165.4	6,196,2001	156.0	148.0	151.0		535	4.8	1.0	2	dbSNP_126	151	636,7964	163.9+/-216.4	24,588,3688	yes	missense	CCDC93	NM_019044.4	180	30,784,5689	AA,AG,GG		7.3953,4.7208,6.4893	possibly-damaging	179/632	118743630	844,12162	2203	4300	6503	SO:0001583	missense	54520	exon7			TCCGACGGGGCTT	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.535C>T	2.37:g.118743630G>A	ENSP00000365477:p.Arg179Cys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	156	86	0.551282	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Missense_Mutation	SNP	ENST00000376300.2	37	CCDS2121.2	121	0.0554029304029304	21	0.042682926829268296	30	0.08287292817679558	0	0.0	70	0.09234828496042216	G	21.7	4.190677	0.78789	0.047208	0.073953	ENSG00000125633	ENST00000376300;ENST00000319432	T;T	0.47869	0.83;0.83	4.81	4.81	0.61882	.	0.261805	0.38005	N	0.001860	T	0.04724	0.0128	M	0.66939	2.045	0.20926	P	0.999825197	D	0.64830	0.994	P	0.56042	0.79	T	0.49476	-0.8936	9	0.72032	D	0.01	1.0E-4	13.2505	0.60050	0.0:0.0:1.0:0.0	rs33975708	179	Q567U6	CCD93_HUMAN	C	179	ENSP00000365477:R179C;ENSP00000324135:R179C	ENSP00000324135:R179C	R	-	1	0	CCDC93	118460100	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.980000	0.56895	2.497000	0.84241	0.555000	0.69702	CGT	G|0.938;A|0.062	0.062	strong		0.507	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044	
ZNF845	91664	hgsc.bcm.edu	37	19	53856409	53856409	+	Silent	SNP	A	A	G	rs145598405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53856409A>G	ENST00000595091.1	+	5	2700	c.2481A>G	c.(2479-2481)ggA>ggG	p.G827G	ZNF845_ENST00000458035.1_Silent_p.G827G			Q96IR2	ZN845_HUMAN	zinc finger protein 845	827					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TTCATAGTGGAGAGAAACCTT	0.398													.|||	63	0.0125799	0.0008	0.0173	5008	,	,		22352	0.0159		0.0249	False		,,,				2504	0.0092				p.G827G		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2481G						PASS	.	A		4,1380		0,4,688	46.0	43.0	44.0		2481	-3.1	0.0	19	dbSNP_134	44	48,3134		0,48,1543	no	coding-synonymous	ZNF845	NM_138374.1		0,52,2231	GG,GA,AA		1.5085,0.289,1.1389		827/971	53856409	52,4514	692	1591	2283	SO:0001819	synonymous_variant	91664	exon4			TAGTGGAGAGAAA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2481A>G	19.37:g.53856409A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			A|0.983;G|0.017	0.017	strong		0.398	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
TBX6	6911	hgsc.bcm.edu	37	16	30100401	30100401	+	Missense_Mutation	SNP	C	C	T	rs56098093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:30100401C>T	ENST00000395224.2	-	4	543	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	TBX6_ENST00000279386.2_Missense_Mutation_p.G162S|TBX6_ENST00000553607.1_Missense_Mutation_p.G162S	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	162			G -> S (in dbSNP:rs56098093).		anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						TCTGCCTTGCCGCTGGGCTCC	0.647													C|||	4	0.000798722	0.0	0.0	5008	,	,		13926	0.0		0.004	False		,,,				2504	0.0				p.G162S		Atlas-SNP	.											.	TBX6	29	.	0			c.G484A						PASS	.	C	SER/GLY	5,4389	9.9+/-24.2	0,5,2192	47.0	52.0	50.0		484	5.8	1.0	16	dbSNP_129	50	52,8546	32.3+/-84.9	0,52,4247	yes	missense	TBX6	NM_004608.3	56	0,57,6439	TT,TC,CC		0.6048,0.1138,0.4387	probably-damaging	162/437	30100401	57,12935	2197	4299	6496	SO:0001583	missense	6911	exon4			CCTTGCCGCTGGG	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"""T-boxes"""	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.484G>A	16.37:g.30100401C>T	ENSP00000378650:p.Gly162Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	37	CCDS10670.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	36	5.633723	0.96682	0.001138	0.006048	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.91237	-2.81;-2.81;-2.81	5.8	5.8	0.92144	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95019	0.8159	10	0.87932	D	0	.	18.8306	0.92137	0.0:1.0:0.0:0.0	rs56098093	162;162	O95947;Q9HA44	TBX6_HUMAN;.	S	162	ENSP00000378650:G162S;ENSP00000279386:G162S;ENSP00000461223:G162S	ENSP00000279386:G162S	G	-	1	0	TBX6	30007902	0.998000	0.40836	0.997000	0.53966	0.971000	0.66376	4.819000	0.62664	2.747000	0.94245	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.647	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758	
NUP98	4928	hgsc.bcm.edu	37	11	3752727	3752727	+	Silent	SNP	T	T	G	rs61751339	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:3752727T>G	ENST00000324932.7	-	14	2044	c.1624A>C	c.(1624-1626)Aga>Cga	p.R542R	NUP98_ENST00000359171.4_Silent_p.R542R|NUP98_ENST00000397007.4_Silent_p.R559R|NUP98_ENST00000397004.4_Silent_p.R542R|NUP98_ENST00000355260.3_Silent_p.R542R	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	559					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)		GGCCGGACTCTAGTGGCAGGG	0.473			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML								T|||	126	0.0251597	0.0023	0.0476	5008	,	,		13597	0.001		0.0746	False		,,,				2504	0.0143				p.R559R		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.A1675C						PASS	.	T	,,,	72,4330	63.5+/-100.7	0,72,2129	173.0	182.0	179.0		1675,1624,1624,1624	4.3	1.0	11	dbSNP_129	179	630,7966	162.0+/-214.8	33,564,3701	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NUP98	NM_005387.5,NM_016320.4,NM_139131.3,NM_139132.3	,,,	33,636,5830	GG,GT,TT		7.329,1.6356,5.4008	,,,	559/938,542/1801,542/921,542/1727	3752727	702,12296	2201	4298	6499	SO:0001819	synonymous_variant	4928	exon14			GGACTCTAGTGGC	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.1624A>C	11.37:g.3752727T>G		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	343	165	0.48105	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	37	CCDS7746.1	81	0.03708791208791209	0	0.0	23	0.06353591160220995	1	0.0017482517482517483	57	0.07519788918205805	T	10.64	1.407284	0.25378	0.016356	0.07329	ENSG00000110713	ENST00000527104	.	.	.	5.47	4.31	0.51392	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7722	0.46330	0.0:0.0:0.3045:0.6955	rs61751339	.	.	.	S	161	.	.	X	-	2	0	NUP98	3709303	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.951000	0.29135	0.867000	0.35654	0.383000	0.25322	TAG	T|0.946;G|0.054	0.054	strong		0.473	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
TATDN3	128387	hgsc.bcm.edu	37	1	212965284	212965284	+	Silent	SNP	C	C	G	rs61736926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:212965284C>G	ENST00000366974.4	+	1	115	c.21C>G	c.(19-21)ggC>ggG	p.G7G	NSL1_ENST00000473995.1_5'Flank|TATDN3_ENST00000366973.4_Silent_p.G7G|TATDN3_ENST00000526997.1_Silent_p.G7G|NSL1_ENST00000366976.1_5'Flank|NSL1_ENST00000366975.6_5'Flank|NSL1_ENST00000422588.2_5'Flank|TATDN3_ENST00000532324.1_Silent_p.G7G|TATDN3_ENST00000531963.1_Silent_p.G7G|NSL1_ENST00000366977.3_5'Flank|NSL1_ENST00000366978.1_5'Flank|TATDN3_ENST00000526641.1_Silent_p.G7G|TATDN3_ENST00000530441.1_Silent_p.G7G	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	159	3	0.0188679		WXS	Illumina HiSeq	Phase_I	193	112	0.580311	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	
PTPRH	5794	hgsc.bcm.edu	37	19	55699514	55699514	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55699514C>A	ENST00000376350.3	-	13	2429	c.2407G>T	c.(2407-2409)Gaa>Taa	p.E803*	PTPRH_ENST00000263434.5_Nonsense_Mutation_p.E625*	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	803					apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E803K(1)		breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GCGAAGTCTTCAGCTGGGATG	0.552																																					p.E803X		Atlas-SNP	.											PTPRH,NS,carcinoma,0,1	PTPRH	139	1	1	Substitution - Missense(1)	lung(1)	c.G2407T						scavenged	.						148.0	120.0	130.0					19																	55699514		2203	4300	6503	SO:0001587	stop_gained	5794	exon13			AGTCTTCAGCTGG		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2407G>T	19.37:g.55699514C>A	ENSP00000365528:p.Glu803*	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	125	2	0.016	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Nonsense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	C	16.02	3.004160	0.54254	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	.	.	.	4.15	-5.98	0.02220	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	5.8282	0.18566	0.0:0.3109:0.3836:0.3055	.	.	.	.	X	803;625	.	ENSP00000263434:E625X	E	-	1	0	PTPRH	60391326	0.003000	0.15002	0.013000	0.15412	0.036000	0.12997	0.039000	0.13884	-0.705000	0.05035	-0.367000	0.07326	GAA	.	.	none		0.552	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
B4GALT5	9334	hgsc.bcm.edu	37	20	48252914	48252914	+	Missense_Mutation	SNP	C	C	T	rs235035	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:48252914C>T	ENST00000371711.4	-	9	1289	c.1102G>A	c.(1102-1104)Gac>Aac	p.D368N		NM_004776.3	NP_004767.1	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5	368			D -> N (in dbSNP:rs235035).		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)|protein N-linked glycosylation via asparagine (GO:0018279)|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)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			TACAAGGCGTCGTATGTGATG	0.488													C|||	159	0.0317492	0.0068	0.0648	5008	,	,		22893	0.0		0.0805	False		,,,				2504	0.0245				p.D368N		Atlas-SNP	.											.	B4GALT5	40	.	0			c.G1102A						PASS	.	C	ASN/ASP	72,4334	66.4+/-103.9	1,70,2132	266.0	226.0	240.0		1102	4.6	0.9	20	dbSNP_79	240	751,7849	179.8+/-228.8	26,699,3575	yes	missense	B4GALT5	NM_004776.3	23	27,769,5707	TT,TC,CC		8.7326,1.6341,6.3278	benign	368/389	48252914	823,12183	2203	4300	6503	SO:0001583	missense	9334	exon9			AGGCGTCGTATGT	AB004550	CCDS13420.1	20q13.1-q13.2	2013-02-19			ENSG00000158470	ENSG00000158470		"""Beta 4-glycosyltransferases"""	928	protein-coding gene	gene with protein product	"""beta4-GalT IV"""	604016				9597550, 9435216	Standard	NM_004776		Approved	beta4GalT-V	uc002xuu.4	O43286	OTTHUMG00000033086	ENST00000371711.4:c.1102G>A	20.37:g.48252914C>T	ENSP00000360776:p.Asp368Asn	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	226	110	0.486726	NM_004776	E1P625|Q2M394|Q9UJQ8	Missense_Mutation	SNP	ENST00000371711.4	37	CCDS13420.1	94	0.04304029304029304	8	0.016260162601626018	27	0.07458563535911603	0	0.0	59	0.07783641160949868	C	12.91	2.079453	0.36662	0.016341	0.087326	ENSG00000158470	ENST00000371711	T	0.33438	1.41	5.52	4.57	0.56435	.	0.086620	0.85682	D	0.000000	T	0.00496	0.0016	N	0.05177	-0.1	0.41696	D	0.989376	B	0.12630	0.006	B	0.08055	0.003	T	0.18366	-1.0339	10	0.15066	T	0.55	-29.6971	9.7951	0.40731	0.0:0.786:0.1413:0.0728	rs235035;rs52821666;rs235035	368	O43286	B4GT5_HUMAN	N	368	ENSP00000360776:D368N	ENSP00000360776:D368N	D	-	1	0	B4GALT5	47686321	1.000000	0.71417	0.936000	0.37596	0.991000	0.79684	4.591000	0.61019	1.302000	0.44855	0.563000	0.77884	GAC	C|0.892;G|0.000;T|0.108	0.108	strong		0.488	B4GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080543.3	NM_004776	
AIRE	326	hgsc.bcm.edu	37	21	45712977	45712977	+	Silent	SNP	T	T	C	rs1800521	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45712977T>C	ENST00000291582.5	+	10	1324	c.1197T>C	c.(1195-1197)gcT>gcC	p.A399A	AIRE_ENST00000329347.4_Intron|AIRE_ENST00000355347.4_Silent_p.A192A	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	399					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)		ACCTGCCGGCTCCGCCTTCTG	0.682									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				C|||	1784	0.35623	0.4955	0.3184	5008	,	,		10777	0.247		0.3579	False		,,,				2504	0.3057				p.A399A		Atlas-SNP	.											AIRE_ENST00000397994,NS,carcinoma,0,2	AIRE	61	2	0			c.T1197C						PASS	.	C	,	2114,2268		543,1028,620	23.0	27.0	25.0		1197,606	2.0	0.0	21	dbSNP_89	25	2992,5602		519,1954,1824	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	1062,2982,2444	CC,CT,TT		34.815,48.2428,39.3496	,	399/546,202/349	45712977	5106,7870	2191	4297	6488	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	GCCGGCTCCGCCT	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.1197T>C	21.37:g.45712977T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.622;C|0.378	0.378	strong		0.682	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
VWDE	221806	hgsc.bcm.edu	37	7	12409522	12409522	+	Missense_Mutation	SNP	A	A	G	rs3823844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:12409522A>G	ENST00000275358.3	-	12	2598	c.2410T>C	c.(2410-2412)Tat>Cat	p.Y804H		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	804						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AAGGTGCTATACTCGGTGAGG	0.483													A|||	879	0.175519	0.2292	0.0893	5008	,	,		19521	0.2034		0.1044	False		,,,				2504	0.2086				p.Y804H		Atlas-SNP	.											.	VWDE	123	.	0			c.T2410C						PASS	.	A	HIS/TYR	320,1064		40,240,412	65.0	50.0	54.0		2410	-9.6	0.0	7	dbSNP_107	54	366,2816		20,326,1245	yes	missense	VWDE	NM_001135924.1	83	60,566,1657	GG,GA,AA		11.5022,23.1214,15.0241	benign	804/1591	12409522	686,3880	692	1591	2283	SO:0001583	missense	221806	exon12			TGCTATACTCGGT		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.2410T>C	7.37:g.12409522A>G	ENSP00000275358:p.Tyr804His	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	373	0.1707875457875458	112	0.22764227642276422	34	0.09392265193370165	140	0.24475524475524477	87	0.11477572559366754	A	0.009	-1.829336	0.00584	0.231214	0.115022	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.81499	-1.5	4.83	-9.65	0.00537	.	2.770660	0.00883	N	0.002145	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.10660	-1.0620	9	0.17369	T	0.5	.	5.0438	0.14473	0.2741:0.3194:0.3323:0.0742	rs3823844;rs52818573;rs60239349;rs3823844	804	Q8N2E2	VWDE_HUMAN	H	804;258	ENSP00000275358:Y804H	ENSP00000275358:Y804H	Y	-	1	0	VWDE	12376047	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.479000	0.02327	-3.386000	0.00174	-0.290000	0.09829	TAT	A|0.827;G|0.173	0.173	strong		0.483	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
HRNR	388697	hgsc.bcm.edu	37	1	152187276	152187276	+	Missense_Mutation	SNP	C	C	T	rs199952550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152187276C>T	ENST00000368801.2	-	3	6904	c.6829G>A	c.(6829-6831)Ggt>Agt	p.G2277S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2277					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCATGCTGACCGTGGCTGGAA	0.572																																					p.G2277S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.G6829A						scavenged	.						5.0	7.0	7.0					1																	152187276		1607	3791	5398	SO:0001583	missense	388697	exon3			GCTGACCGTGGCT	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6829G>A	1.37:g.152187276C>T	ENSP00000357791:p.Gly2277Ser	Somatic	836	1	0.00119617		WXS	Illumina HiSeq	Phase_I	712	50	0.0702247	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	8.412	0.844499	0.16963	.	.	ENSG00000197915	ENST00000368801	T	0.16196	2.36	3.98	-0.207	0.13189	.	.	.	.	.	T	0.01765	0.0056	N	0.19112	0.55	0.09310	N	1	D	0.52996	0.957	B	0.34242	0.178	T	0.38672	-0.9650	9	0.09590	T	0.72	.	6.592	0.22651	0.0:0.5599:0.0:0.4401	.	2277	Q86YZ3	HORN_HUMAN	S	2277	ENSP00000357791:G2277S	ENSP00000357791:G2277S	G	-	1	0	HRNR	150453900	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.276000	0.08514	-0.129000	0.11620	0.650000	0.86243	GGT	C|0.993;T|0.007	0.007	strong		0.572	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
OR5P2	120065	hgsc.bcm.edu	37	11	7818056	7818056	+	Missense_Mutation	SNP	T	T	C	rs73406604	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7818056T>C	ENST00000329434.2	-	1	464	c.434A>G	c.(433-435)tAc>tGc	p.Y145C	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ACCAGCTATGTAAACTACTAA	0.408													T|||	1184	0.236422	0.3472	0.2911	5008	,	,		19685	0.128		0.2763	False		,,,				2504	0.1186				p.Y145C		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	0			c.A434G						PASS	.	T	CYS/TYR	1369,2829		401,567,1131	63.0	75.0	71.0		434	3.2	0.2	11	dbSNP_130	71	2425,6159		393,1639,2260	yes	missense	OR5P2	NM_153444.1	194	794,2206,3391	CC,CT,TT		28.2502,32.6108,29.6824	benign	145/323	7818056	3794,8988	2099	4292	6391	SO:0001583	missense	120065	exon1			GCTATGTAAACTA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.434A>G	11.37:g.7818056T>C	ENSP00000331823:p.Tyr145Cys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	T	5.438	0.265978	0.10294	0.326108	0.282502	ENSG00000183303	ENST00000329434	T	0.38240	1.15	5.5	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	M	0.68952	2.095	0.80722	P	0.0	B	0.17667	0.023	B	0.33750	0.169	T	0.32402	-0.9908	9	0.66056	D	0.02	-38.8562	4.4769	0.11748	0.3014:0.0807:0.0:0.6179	.	145	Q8WZ92	OR5P2_HUMAN	C	145	ENSP00000331823:Y145C	ENSP00000331823:Y145C	Y	-	2	0	OR5P2	7774632	0.000000	0.05858	0.166000	0.22797	0.001000	0.01503	0.078000	0.14761	0.511000	0.28236	-0.456000	0.05471	TAC	T|0.738;C|0.262	0.262	strong		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
FAT4	79633	hgsc.bcm.edu	37	4	126238924	126238924	+	Missense_Mutation	SNP	A	A	T	rs6847454	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:126238924A>T	ENST00000394329.3	+	1	1371	c.1358A>T	c.(1357-1359)cAg>cTg	p.Q453L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	453	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> L (in dbSNP:rs6847454).		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						GCAGCAGTCCAGGCGCGCTCT	0.557											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2135	0.426318	0.615	0.4092	5008	,	,		18623	0.2371		0.4205	False		,,,				2504	0.3845				p.Q453L		Atlas-SNP	.											.	FAT4	1752	.	0			c.A1358T						PASS	.	A	LEU/GLN	2215,1847		622,971,438	43.0	46.0	45.0		1358	-2.6	0.1	4	dbSNP_116	45	3559,4781		753,2053,1364	yes	missense	FAT4	NM_024582.4	113	1375,3024,1802	TT,TA,AA		42.6739,45.4702,46.557	benign	453/4982	126238924	5774,6628	2031	4170	6201	SO:0001583	missense	79633	exon1			CAGTCCAGGCGCG	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.1358A>T	4.37:g.126238924A>T	ENSP00000377862:p.Gln453Leu	Somatic	118	1	0.00847458	1548	WXS	Illumina HiSeq	Phase_I	143	143	1	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	914	0.4184981684981685	309	0.6280487804878049	150	0.4143646408839779	134	0.23426573426573427	321	0.4234828496042216	A	1.356	-0.590036	0.03799	0.545298	0.426739	ENSG00000196159	ENST00000394329	T	0.53640	0.61	3.81	-2.64	0.06114	Cadherin (4);Cadherin-like (1);	1.015660	0.07944	U	0.979875	T	0.00012	0.0000	N	0.08118	0	0.38401	P	0.05432099999999995	B	0.09022	0.002	B	0.13407	0.009	T	0.45101	-0.9284	9	0.28530	T	0.3	.	7.174	0.25734	0.3191:0.1978:0.4831:0.0	rs6847454;rs52793335;rs58376448;rs6847454	453	Q6V0I7	FAT4_HUMAN	L	453	ENSP00000377862:Q453L	ENSP00000377862:Q453L	Q	+	2	0	FAT4	126458374	0.049000	0.20398	0.080000	0.20451	0.545000	0.35147	0.150000	0.16263	-0.504000	0.06577	0.459000	0.35465	CAG	A|0.518;T|0.482	0.482	strong		0.557	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993727	45993727	+	Missense_Mutation	SNP	A	A	C	rs148418343	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45993727A>C	ENST00000400374.3	+	1	122	c.92A>C	c.(91-93)gAc>gCc	p.D31A	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	31						keratin filament (GO:0045095)		p.D31A(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAGGTGGACGACTGCCCAGAG	0.687													.|||	308	0.0615016	0.0484	0.0288	5008	,	,		14764	0.1329		0.0249	False		,,,				2504	0.0665				p.D31A		Atlas-SNP	.											KRTAP10-4,NS,carcinoma,0,1	KRTAP10-4	44	1	1	Substitution - Missense(1)	pancreas(1)	c.A92C						scavenged	.	A	,ALA/ASP	231,3929		1,229,1850	60.0	65.0	64.0		,92	3.5	1.0	21	dbSNP_134	64	165,8221		1,163,4029	no	intron,missense	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,126	2,392,5879	CC,CA,AA		1.9676,5.5529,3.1564	,probably-damaging	,31/402	45993727	396,12150	2080	4193	6273	SO:0001583	missense	386672	exon1			TGGACGACTGCCC	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.92A>C	21.37:g.45993727A>C	ENSP00000383225:p.Asp31Ala	Somatic	87	5	0.0574713		WXS	Illumina HiSeq	Phase_I	114	33	0.289474	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	106	0.048534798534798536	13	0.026422764227642278	12	0.03314917127071823	70	0.12237762237762238	11	0.014511873350923483	N	13.44	2.238867	0.39598	0.055529	0.019676	ENSG00000215454	ENST00000400374;ENST00000334871	T	0.14893	2.47	4.69	3.52	0.40303	.	.	.	.	.	T	0.00440	0.0014	M	0.63843	1.955	0.40243	P	0.022011000000000003	D	0.67145	0.996	P	0.62740	0.906	T	0.04281	-1.0963	8	0.33141	T	0.24	.	7.9837	0.30198	0.8999:0.0:0.1001:0.0	.	31	P60372	KR104_HUMAN	A	31;20	ENSP00000383225:D31A	ENSP00000333987:D20A	D	+	2	0	KRTAP10-4	44818155	0.911000	0.30947	0.997000	0.53966	0.226000	0.24999	1.128000	0.31369	1.863000	0.54032	0.397000	0.26171	GAC	.	.	weak		0.687	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
SAMD9	54809	hgsc.bcm.edu	37	7	92732769	92732769	+	Missense_Mutation	SNP	T	T	C	rs140921998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:92732769T>C	ENST00000379958.2	-	3	2911	c.2642A>G	c.(2641-2643)gAt>gGt	p.D881G		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	881						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GGAATAAAAATCCTCAAAGTT	0.338													T|||	39	0.00778754	0.0053	0.0216	5008	,	,		18238	0.0		0.0169	False		,,,				2504	0.0				p.D881G		Atlas-SNP	.											.	SAMD9	239	.	0			c.A2642G						PASS	.	T	GLY/ASP,GLY/ASP	43,4363	44.6+/-78.6	0,43,2160	43.0	44.0	44.0		2642,2642	4.5	1.0	7	dbSNP_134	44	215,8379	87.9+/-150.2	2,211,4084	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	94,94	2,254,6244	CC,CT,TT		2.5017,0.9759,1.9846	probably-damaging,probably-damaging	881/1590,881/1590	92732769	258,12742	2203	4297	6500	SO:0001583	missense	54809	exon2			TAAAAATCCTCAA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.2642A>G	7.37:g.92732769T>C	ENSP00000369292:p.Asp881Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	22	0.010073260073260074	4	0.008130081300813009	10	0.027624309392265192	0	0.0	8	0.010554089709762533	T	12.02	1.811126	0.32053	0.009759	0.025017	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.23552	1.9;2.71	4.47	4.47	0.54385	.	0.367862	0.23928	U	0.043168	T	0.06462	0.0166	L	0.44542	1.39	0.25351	N	0.988869	P	0.43750	0.816	B	0.34590	0.186	T	0.09015	-1.0694	10	0.22706	T	0.39	-11.5585	12.6893	0.56966	0.0:0.0:0.0:1.0	.	881	Q5K651	SAMD9_HUMAN	G	881	ENSP00000369292:D881G;ENSP00000414529:D881G	ENSP00000369292:D881G	D	-	2	0	SAMD9	92570705	0.999000	0.42202	1.000000	0.80357	0.963000	0.63663	2.872000	0.48467	1.882000	0.54519	0.496000	0.49642	GAT	T|0.981;C|0.019	0.019	strong		0.338	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
RAB3GAP2	25782	hgsc.bcm.edu	37	1	220330672	220330672	+	Silent	SNP	C	C	T	rs11547779	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:220330672C>T	ENST00000358951.2	-	31	3611	c.3495G>A	c.(3493-3495)ttG>ttA	p.L1165L		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	1165					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		TGACTGCATACAAGATGGAGC	0.483													C|||	303	0.0605032	0.0076	0.0519	5008	,	,		19662	0.0496		0.0885	False		,,,				2504	0.1207				p.L1165L		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.G3495A						PASS	.	C		95,4311	76.8+/-115.0	2,91,2110	101.0	89.0	93.0		3495	-4.0	0.0	1	dbSNP_120	93	805,7795	187.2+/-234.5	40,725,3535	no	coding-synonymous	RAB3GAP2	NM_012414.3		42,816,5645	TT,TC,CC		9.3605,2.1562,6.9199		1165/1394	220330672	900,12106	2203	4300	6503	SO:0001819	synonymous_variant	25782	exon31			TGCATACAAGATG	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.3495G>A	1.37:g.220330672C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	180	73	0.405556	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Silent	SNP	ENST00000358951.2	37	CCDS31028.1																																																																																			T|0.069;C|0.931;A|0.000	0.069	strong		0.483	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414	
OR6S1	341799	hgsc.bcm.edu	37	14	21109671	21109671	+	Silent	SNP	A	A	G	rs11627574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21109671A>G	ENST00000320704.3	-	1	179	c.180T>C	c.(178-180)ccT>ccC	p.P60P		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		AGAAGTACATAGGGGTCTGTA	0.443													G|||	2309	0.461062	0.4902	0.5461	5008	,	,		21262	0.2897		0.5378	False		,,,				2504	0.4591				p.P60P		Atlas-SNP	.											.	OR6S1	49	.	0			c.T180C						PASS	.	G		2257,2149	581.7+/-385.4	560,1137,506	102.0	96.0	98.0		180	1.4	1.0	14	dbSNP_120	98	4805,3795	537.6+/-383.2	1344,2117,839	no	coding-synonymous	OR6S1	NM_001001968.1		1904,3254,1345	GG,GA,AA		44.1279,48.7744,45.702		60/332	21109671	7062,5944	2203	4300	6503	SO:0001819	synonymous_variant	341799	exon1			GTACATAGGGGTC	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.180T>C	14.37:g.21109671A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001001968	Q6IFJ9	Silent	SNP	ENST00000320704.3	37	CCDS32038.1																																																																																			A|0.484;G|0.516	0.516	strong		0.443	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
PRKCQ	5588	hgsc.bcm.edu	37	10	6527143	6527143	+	Missense_Mutation	SNP	G	G	A	rs2236379	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:6527143G>A	ENST00000263125.5	-	10	1088	c.989C>T	c.(988-990)cCg>cTg	p.P330L	PRKCQ_ENST00000397176.2_Missense_Mutation_p.P330L|PRKCQ_ENST00000539722.1_Missense_Mutation_p.P205L	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	330			P -> L (in dbSNP:rs2236379). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7686153, ECO:0000269|Ref.4}.		apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)	p.P330L(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TAAACATGGCGGCCTTGCTTC	0.458													.|||	1830	0.365415	0.3744	0.3674	5008	,	,		19593	0.38		0.2316	False		,,,				2504	0.4744				p.P330L	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											PRKCQ,NS,carcinoma,0,1	PRKCQ	113	1	1	Substitution - Missense(1)	stomach(1)	c.C989T						PASS	.	G	LEU/PRO,LEU/PRO	1535,2871		277,981,945	180.0	173.0	175.0		989,989	-2.7	0.0	10	dbSNP_98	175	2147,6453		281,1585,2434	yes	missense,missense	PRKCQ	NM_001242413.1,NM_006257.3	98,98	558,2566,3379	AA,AG,GG		24.9651,34.8389,28.31	benign,benign	330/644,330/707	6527143	3682,9324	2203	4300	6503	SO:0001583	missense	5588	exon10			CATGGCGGCCTTG	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.989C>T	10.37:g.6527143G>A	ENSP00000263125:p.Pro330Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	37	CCDS7079.1	704|704	0.32234432234432236|0.32234432234432236	175|175	0.3556910569105691|0.3556910569105691	141|141	0.38950276243093923|0.38950276243093923	220|220	0.38461538461538464|0.38461538461538464	168|168	0.22163588390501318|0.22163588390501318	.|.	8.301|8.301	0.819958|0.819958	0.16678|0.16678	0.348389|0.348389	0.249651|0.249651	ENSG00000065675|ENSG00000065675	ENST00000263125;ENST00000397176;ENST00000539722|ENST00000397178	T;T;T|.	0.68025|.	-0.3;-0.25;-0.28|.	5.22|5.22	-2.67|-2.67	0.06059|0.06059	.|.	0.528439|.	0.20037|.	N|.	0.100581|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02916|0.02916	-0.46|-0.46	0.51767|0.51767	P|P	6.700000000003925E-5|6.700000000003925E-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|T	0.46582|0.46582	-0.9181|-0.9181	9|4	0.23302|.	T|.	0.38|.	.|.	5.4646|5.4646	0.16635|0.16635	0.4512:0.0:0.4134:0.1355|0.4512:0.0:0.4134:0.1355	rs2236379;rs61306241;rs2236379|rs2236379;rs61306241;rs2236379	205;102;330;330|.	B4DF52;Q5JUN8;Q04759-2;Q04759|.	.;.;.;KPCT_HUMAN|.	L|C	330;330;205|103	ENSP00000263125:P330L;ENSP00000380361:P330L;ENSP00000441752:P205L|.	ENSP00000263125:P330L|.	P|R	-|-	2|1	0|0	PRKCQ|PRKCQ	6567149|6567149	0.011000|0.011000	0.17503|0.17503	0.003000|0.003000	0.11579|0.11579	0.004000|0.004000	0.04260|0.04260	0.733000|0.733000	0.26087|0.26087	-0.676000|-0.676000	0.05238|0.05238	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.675;T|0.002	.	strong		0.458	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
ITPR1	3708	hgsc.bcm.edu	37	3	4714929	4714929	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:4714929G>A	ENST00000443694.2	+	18	2269	c.2269G>A	c.(2269-2271)Gag>Aag	p.E757K	ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000456211.2_Missense_Mutation_p.E757K|ITPR1_ENST00000354582.6_Missense_Mutation_p.E772K|ITPR1_ENST00000357086.4_Missense_Mutation_p.E772K|ITPR1_ENST00000302640.8_Missense_Mutation_p.E757K|ITPR1_ENST00000423119.2_Missense_Mutation_p.E772K			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	772					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)	CATGTCTGACGAGAACCTGCC	0.557																																					p.E772K		Atlas-SNP	.											ITPR1_ENST00000357086,NS,carcinoma,0,3	ITPR1	659	3	0			c.G2314A						scavenged	.						67.0	70.0	69.0					3																	4714929		2082	4212	6294	SO:0001583	missense	3708	exon21			TCTGACGAGAACC	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.2269G>A	3.37:g.4714929G>A	ENSP00000401671:p.Glu757Lys	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.495999	0.44352	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.88;-2.88;-2.89;-2.89	4.74	3.85	0.44370	.	0.000000	0.85682	D	0.000000	D	0.92763	0.7699	L	0.45051	1.395	0.80722	D	1	P;B;D	0.76494	0.603;0.443;0.999	B;B;D	0.63597	0.142;0.06;0.916	D	0.90586	0.4533	10	0.22706	T	0.39	.	14.273	0.66162	0.0:0.0:0.8496:0.1504	.	757;772;772	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	K	772;757;772;772;772;757;757	ENSP00000306253:E757K;ENSP00000346595:E772K;ENSP00000405934:E772K;ENSP00000349597:E772K;ENSP00000397885:E757K;ENSP00000401671:E757K	ENSP00000306253:E757K	E	+	1	0	ITPR1	4689929	1.000000	0.71417	0.797000	0.32132	0.308000	0.27856	9.511000	0.98006	1.327000	0.45338	-0.282000	0.10007	GAG	.	.	none		0.557	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
ATXN7	6314	hgsc.bcm.edu	37	3	63967900	63967900	+	Missense_Mutation	SNP	A	A	G	rs1053338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:63967900A>G	ENST00000295900.6	+	7	1341	c.791A>G	c.(790-792)aAa>aGa	p.K264R	ATXN7_ENST00000487717.1_Missense_Mutation_p.K264R|ATXN7_ENST00000488239.1_3'UTR|ATXN7_ENST00000484332.1_Missense_Mutation_p.K119R|ATXN7_ENST00000398590.3_Missense_Mutation_p.K264R|ATXN7_ENST00000538065.1_Missense_Mutation_p.K264R	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	264			K -> R (in dbSNP:rs1053338). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9425224}.		cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		ATTCATCCGAAAATGGATGGC	0.522													A|||	574	0.114617	0.0121	0.1916	5008	,	,		16999	0.1478		0.1471	False		,,,				2504	0.1309				p.K264R		Atlas-SNP	.											.	ATXN7	126	.	0			c.A791G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	140,3846		3,134,1856	105.0	102.0	103.0		791,356,791	4.6	1.0	3	dbSNP_86	103	1091,7241		67,957,3142	yes	missense,missense,missense	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	26,26,26	70,1091,4998	GG,GA,AA		13.0941,3.5123,9.9935	probably-damaging,probably-damaging,probably-damaging	264/893,119/748,264/946	63967900	1231,11087	1993	4166	6159	SO:0001583	missense	6314	exon7			ATCCGAAAATGGA	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.791A>G	3.37:g.63967900A>G	ENSP00000295900:p.Lys264Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	178	76	0.426966	NM_000333	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	37	CCDS43102.1	279	0.12774725274725274	5	0.01016260162601626	63	0.17403314917127072	101	0.17657342657342656	110	0.14511873350923482	A	16.90	3.251328	0.59212	0.035123	0.130941	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332	T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35	5.72	4.57	0.56435	.	0.230389	0.44902	D	0.000408	T	0.00109	0.0003	L	0.39020	1.185	0.21416	P	0.999694523	D;P;P	0.69078	0.997;0.724;0.603	D;B;B	0.75020	0.985;0.183;0.089	T	0.03773	-1.1005	9	0.46703	T	0.11	-8.7245	11.6024	0.51010	0.9304:0.0:0.0696:0.0	rs1053338;rs3193849;rs3765033;rs17421116;rs52791474;rs61726608;rs1053338	119;264;264	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	R	264;264;264;264;119	ENSP00000381590:K264R;ENSP00000295900:K264R;ENSP00000420234:K264R;ENSP00000439585:K264R;ENSP00000428277:K119R	ENSP00000295900:K264R	K	+	2	0	ATXN7	63942940	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	4.062000	0.57492	1.005000	0.39183	0.459000	0.35465	AAA	A|0.876;G|0.124	0.124	strong		0.522	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333	
TMC4	147798	hgsc.bcm.edu	37	19	54676763	54676763	+	Missense_Mutation	SNP	C	C	T	rs641738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54676763C>T	ENST00000376591.4	-	1	181	c.50G>A	c.(49-51)gGg>gAg	p.G17E	TMC4_ENST00000301187.4_Missense_Mutation_p.G17E|TMC4_ENST00000476013.2_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	17			G -> E (in dbSNP:rs641738). {ECO:0000269|PubMed:12812529}.		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)					GGCCAGCCACCCCCTAGAGGA	0.632													C|||	1872	0.373802	0.32	0.3429	5008	,	,		15567	0.2173		0.4404	False		,,,				2504	0.5613				p.G17E		Atlas-SNP	.											.	TMC4	89	.	0			c.G50A						PASS	.	C	GLU/GLY,GLU/GLY	1567,2839	480.3+/-358.8	280,1007,916	91.0	105.0	100.0		50,50	0.2	0.0	19	dbSNP_83	100	3725,4875	524.7+/-380.6	785,2155,1360	yes	missense,missense	TMC4	NM_001145303.1,NM_144686.2	98,98	1065,3162,2276	TT,TC,CC		43.314,35.5651,40.6889	benign,benign	17/713,17/707	54676763	5292,7714	2203	4300	6503	SO:0001583	missense	147798	exon1			AGCCACCCCCTAG	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.50G>A	19.37:g.54676763C>T	ENSP00000365776:p.Gly17Glu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	737	0.3374542124542125	159	0.3231707317073171	128	0.35359116022099446	112	0.1958041958041958	338	0.44591029023746703	C	11.35	1.613979	0.28712	0.355651	0.43314	ENSG00000167608	ENST00000301187;ENST00000376591	T;T	0.72615	-0.62;-0.67	3.92	0.213	0.15244	.	6.366860	0.00725	N	0.000915	T	0.00012	0.0000	L	0.45581	1.43	0.58432	P	9.000000000036756E-6	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.29088	-1.0023	9	0.05351	T	0.99	-3.0961	4.0735	0.09892	0.0:0.5573:0.1929:0.2497	rs641738;rs61242378;rs641738	17;17	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	E	17	ENSP00000301187:G17E;ENSP00000365776:G17E	ENSP00000301187:G17E	G	-	2	0	TMC4	59368575	0.000000	0.05858	0.000000	0.03702	0.284000	0.27059	-1.506000	0.02271	0.015000	0.14971	0.462000	0.41574	GGG	C|0.615;T|0.385	0.385	strong		0.632	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
B4GALNT3	283358	hgsc.bcm.edu	37	12	662695	662695	+	Missense_Mutation	SNP	C	C	T	rs151321644	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:662695C>T	ENST00000266383.5	+	14	1619	c.1606C>T	c.(1606-1608)Cac>Tac	p.H536Y		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	536					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GCCTCCTGGGCACCCTGTGAA	0.607													C|||	26	0.00519169	0.0015	0.0029	5008	,	,		18966	0.0		0.005	False		,,,				2504	0.0174				p.H536Y		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.C1606T						PASS	.	C	TYR/HIS	10,4396	16.8+/-37.8	0,10,2193	39.0	43.0	42.0		1606	3.6	0.0	12	dbSNP_134	42	66,8530	37.8+/-93.5	0,66,4232	yes	missense	B4GALNT3	NM_173593.3	83	0,76,6425	TT,TC,CC		0.7678,0.227,0.5845	benign	536/999	662695	76,12926	2203	4298	6501	SO:0001583	missense	283358	exon14			CCTGGGCACCCTG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1606C>T	12.37:g.662695C>T	ENSP00000266383:p.His536Tyr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	7.508	0.654167	0.14580	0.00227	0.007678	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.32988	3.47;1.43	5.47	3.57	0.40892	.	1.800440	0.02229	N	0.064754	T	0.10423	0.0255	N	0.14661	0.345	0.09310	N	1	P;B	0.41450	0.75;0.002	B;B	0.31390	0.129;0.001	T	0.28235	-1.0050	10	0.02654	T	1	-2.3623	6.6712	0.23070	0.2924:0.6219:0.0:0.0858	.	439;536	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	Y	536;439	ENSP00000266383:H536Y;ENSP00000322953:H439Y	ENSP00000266383:H536Y	H	+	1	0	B4GALNT3	532956	0.343000	0.24818	0.002000	0.10522	0.002000	0.02628	2.541000	0.45735	0.611000	0.30052	0.609000	0.83330	CAC	C|0.996;T|0.004	0.004	strong		0.607	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
ANKS1B	56899	hgsc.bcm.edu	37	12	99139552	99139552	+	Intron	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:99139552C>T	ENST00000547776.2	-	25	3672				ANKS1B_ENST00000547446.1_Missense_Mutation_p.G384S|ANKS1B_ENST00000341752.7_Intron|ANKS1B_ENST00000549493.2_Missense_Mutation_p.G500S|ANKS1B_ENST00000549558.2_Intron|ANKS1B_ENST00000333732.7_Missense_Mutation_p.G279S|ANKS1B_ENST00000549025.2_Missense_Mutation_p.G347S|ANKS1B_ENST00000546568.1_Missense_Mutation_p.G416S|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000550693.2_Missense_Mutation_p.G440S|ANKS1B_ENST00000332712.7_Missense_Mutation_p.G440S	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B							cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GTATTAATGCCCCTCTTGGCT	0.537																																					p.G500S		Atlas-SNP	.											.	ANKS1B	180	.	0			c.G1498A						PASS	.						107.0	113.0	111.0					12																	99139552		1930	4139	6069	SO:0001627	intron_variant	56899	exon13			TAATGCCCCTCTT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3672+5580G>A	12.37:g.99139552C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_181670	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	C	8.874	0.949903	0.18431	.	.	ENSG00000185046	ENST00000550693;ENST00000549025;ENST00000549493;ENST00000547446;ENST00000333732;ENST00000546568;ENST00000332712;ENST00000407362	T;T;T;T;T;T;T	0.68903	0.01;0.57;0.0;-0.36;-0.04;0.07;0.33	4.66	3.76	0.43208	.	.	.	.	.	T	0.57548	0.2061	N	0.04508	-0.205	0.34764	D	0.733028	B;D;D;D;D;B;B;D;B	0.89917	0.019;1.0;1.0;1.0;1.0;0.14;0.027;1.0;0.077	B;D;D;D;D;B;B;D;B	0.85130	0.016;0.997;0.994;0.997;0.994;0.076;0.042;0.997;0.09	T	0.57837	-0.7742	9	0.02654	T	1	.	12.6737	0.56882	0.0:0.9195:0.0:0.0805	.	384;279;280;440;389;464;416;500;347	F8VPM3;F8VR14;B7Z9I9;Q7Z6G8-5;B1VKB5;F8VQW6;Q7Z6G8-2;Q7Z6G8-3;F8VZR9	.;.;.;.;.;.;.;.;.	S	440;347;500;384;279;416;440;340	ENSP00000447999:G440S;ENSP00000447312:G347S;ENSP00000448203:G500S;ENSP00000450015:G384S;ENSP00000331256:G279S;ENSP00000448205:G416S;ENSP00000332683:G440S	ENSP00000332683:G440S	G	-	1	0	ANKS1B	97663683	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.436000	0.59948	1.060000	0.40578	0.549000	0.68633	GGC	.	.	none		0.537	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
SH3BP2	6452	hgsc.bcm.edu	37	4	2826912	2826912	+	Silent	SNP	C	C	G	rs16843413	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:2826912C>G	ENST00000356331.5	+	5	678	c.417C>G	c.(415-417)ccC>ccG	p.P139P	SH3BP2_ENST00000511747.1_Silent_p.P139P|SH3BP2_ENST00000435136.2_Silent_p.P139P|SH3BP2_ENST00000503393.2_Silent_p.P196P|SH3BP2_ENST00000442312.2_Silent_p.P167P|SH3BP2_ENST00000452765.2_Silent_p.P139P|SH3BP2_ENST00000515183.1_3'UTR	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	161	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	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	
C9orf24	84688	hgsc.bcm.edu	37	9	34379692	34379692	+	Silent	SNP	C	C	T	rs3737242	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:34379692C>T	ENST00000297623.2	-	6	939	c.741G>A	c.(739-741)gtG>gtA	p.V247V	C9orf24_ENST00000379127.1_Missense_Mutation_p.C114Y|C9orf24_ENST00000379124.1_Missense_Mutation_p.C114Y|C9orf24_ENST00000481295.1_5'UTR|C9orf24_ENST00000379133.3_Silent_p.V112V|C9orf24_ENST00000379126.3_Missense_Mutation_p.C61Y|KIAA1161_ENST00000297625.7_5'Flank	NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	247					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		TGTAACAGCACACTGCATTCC	0.567											OREG0019150	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	709	0.141573	0.0408	0.1657	5008	,	,		17564	0.0942		0.2087	False		,,,				2504	0.2403				p.C114Y		Atlas-SNP	.											.	C9orf24	15	.	0			c.G341A						PASS	.	C	,,TYR/CYS	316,4090	166.5+/-197.7	12,292,1899	126.0	113.0	118.0		741,336,182	3.8	1.0	9	dbSNP_107	118	1739,6861	316.6+/-312.8	187,1365,2748	yes	coding-synonymous,coding-synonymous,missense	C9orf24	NM_032596.3,NM_147168.1,NM_147169.1	,,194	199,1657,4647	TT,TC,CC		20.2209,7.172,15.8004	,,	247/263,112/128,61/112	34379692	2055,10951	2203	4300	6503	SO:0001819	synonymous_variant	84688	exon4			ACAGCACACTGCA	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"""ciliated bronchial epithelium 1"", ""spermatid-specific manchette-related protein 1"""					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.741G>A	9.37:g.34379692C>T		Somatic	148	0	0	847	WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_001252195	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Missense_Mutation	SNP	ENST00000297623.2	37	CCDS6554.1	302	0.1382783882783883	16	0.032520325203252036	63	0.17403314917127072	61	0.10664335664335664	162	0.21372031662269128	C	20.2	3.942210	0.73672	0.07172	0.202209	ENSG00000164972	ENST00000379126;ENST00000379127;ENST00000379112;ENST00000379124	T;T	0.52295	0.67;0.67	4.73	3.82	0.43975	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.28668	P	0.9057922	B	0.13594	0.008	B	0.17433	0.018	T	0.05818	-1.0862	7	0.22706	T	0.39	-5.1863	10.4135	0.44307	0.0:0.904:0.0:0.096	rs3737242;rs52833185;rs60665408;rs3737242	61	Q8NCR6-3	.	Y	61;114;44;114	ENSP00000368422:C114Y;ENSP00000368419:C114Y	ENSP00000368407:C44Y	C	-	2	0	C9orf24	34369692	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.351000	0.44071	2.627000	0.88993	0.561000	0.74099	TGT	C|0.860;T|0.140	0.140	strong		0.567	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	
NF1	4763	hgsc.bcm.edu	37	17	29553485	29553485	+	Silent	SNP	G	G	A	rs2285892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	39	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	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	
CSF3	1440	hgsc.bcm.edu	37	17	38173143	38173143	+	Silent	SNP	G	G	A	rs25645	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38173143G>A	ENST00000225474.2	+	5	586	c.555G>A	c.(553-555)ctG>ctA	p.L185L	CSF3_ENST00000394149.3_Silent_p.L182L|RP11-387H17.6_ENST00000583462.1_lincRNA|CSF3_ENST00000394148.3_Silent_p.L149L|CSF3_ENST00000331769.2_Silent_p.L178L|CSF3_ENST00000577675.1_Silent_p.L142L			P09919	CSF3_HUMAN	colony stimulating factor 3 (granulocyte)	185					cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|granulocyte differentiation (GO:0030851)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of neuron death (GO:1901215)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|granulocyte colony-stimulating factor receptor binding (GO:0005130)			endometrium(1)|ovary(1)|prostate(1)	3	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)				GAGGGGTCCTGGTTGCCTCCC	0.637													G|||	1571	0.313698	0.0514	0.4135	5008	,	,		16552	0.4276		0.3668	False		,,,				2504	0.4254				p.L185L		Atlas-SNP	.											.	CSF3	9	.	0			c.G555A						PASS	.	G	,,,	432,3974	209.8+/-230.5	18,396,1789	45.0	40.0	42.0		555,438,546,447	4.2	1.0	17	dbSNP_72	42	3203,5397	481.4+/-370.6	583,2037,1680	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSF3	NM_000759.3,NM_001178147.1,NM_172219.2,NM_172220.2	,,,	601,2433,3469	AA,AG,GG		37.2442,9.8048,27.9486	,,,	185/208,146/169,182/205,149/172	38173143	3635,9371	2203	4300	6503	SO:0001819	synonymous_variant	1440	exon5			GGTCCTGGTTGCC		CCDS11357.1, CCDS11358.1, CCDS42314.1, CCDS11358.2	17q11.2-q12	2014-01-30			ENSG00000108342	ENSG00000108342		"""Endogenous ligands"""	2438	protein-coding gene	gene with protein product	"""granulocyte colony stimulating factor"", ""pluripoietin"", ""filgrastim"", ""lenograstim"""	138970	"""chromosome 17 open reading frame 33"""	GCSF, G-CSF, C17orf33		3499671, 3501046	Standard	NM_000759		Approved	MGC45931	uc002htp.3	P09919	OTTHUMG00000133247	ENST00000225474.2:c.555G>A	17.37:g.38173143G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_000759	A8MXR7	Silent	SNP	ENST00000225474.2	37	CCDS11357.1																																																																																			G|0.705;A|0.295	0.295	strong		0.637	CSF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256988.2	NM_172220	
DAB2	1601	hgsc.bcm.edu	37	5	39381651	39381651	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:39381651G>A	ENST00000320816.6	-	11	1876	c.1409C>T	c.(1408-1410)gCg>gTg	p.A470V	DAB2_ENST00000339788.6_Missense_Mutation_p.A252V|DAB2_ENST00000509337.1_Missense_Mutation_p.A449V|DAB2_ENST00000545653.1_Missense_Mutation_p.A449V	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	470					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)			TGTGGGTGACGCCTGGCCTGA	0.582																																					p.A470V		Atlas-SNP	.											.	DAB2	124	.	0			c.C1409T						PASS	.						129.0	126.0	127.0					5																	39381651		2203	4300	6503	SO:0001583	missense	1601	exon11			GGTGACGCCTGGC	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.1409C>T	5.37:g.39381651G>A	ENSP00000313391:p.Ala470Val	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	137	52	0.379562	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	G	8.024	0.760343	0.15914	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.38240	1.24;1.15;1.21;1.21	5.96	-0.00481	0.14020	.	1.030630	0.07591	N	0.921918	T	0.12008	0.0292	N	0.02539	-0.55	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.001;0.002	T	0.27938	-1.0059	10	0.02654	T	1	11.0513	6.3792	0.21525	0.5083:0.0:0.3716:0.12	.	470;449	P98082;P98082-3	DAB2_HUMAN;.	V	470;252;449;449	ENSP00000313391:A470V;ENSP00000345508:A252V;ENSP00000439919:A449V;ENSP00000426245:A449V	ENSP00000313391:A470V	A	-	2	0	DAB2	39417408	0.296000	0.24398	0.041000	0.18516	0.818000	0.46254	0.497000	0.22514	-0.303000	0.08856	-0.345000	0.07892	GCG	.	.	none		0.582	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
ROS1	6098	hgsc.bcm.edu	37	6	117622233	117622233	+	Missense_Mutation	SNP	C	C	T	rs529038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:117622233C>T	ENST00000368508.3	-	42	6835	c.6637G>A	c.(6637-6639)Gac>Aac	p.D2213N	RN7SKP51_ENST00000410781.1_RNA|RN7SKP18_ENST00000516005.1_RNA|ROS1_ENST00000368507.3_Missense_Mutation_p.D2207N	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2213	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> E (in dbSNP:rs75510639). {ECO:0000269|PubMed:17344846}.|D -> N (in dbSNP:rs529038). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2352949}.		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)	p.D2213N(1)	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)		TGAAGTTGGTCCTGAATTCTA	0.358			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								C|||	683	0.136382	0.0287	0.1628	5008	,	,		16126	0.1587		0.2197	False		,,,				2504	0.1544				p.D2213N		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	ROS1_ENST00000368508,NS,carcinoma,0,1	ROS1	728	1	1	Substitution - Missense(1)	stomach(1)	c.G6637A	GRCh37	CM053396	ROS1	M	rs529038	PASS	.	C	ASN/ASP	303,4103	164.7+/-196.3	11,281,1911	99.0	103.0	102.0		6637	3.2	1.0	6	dbSNP_83	102	2231,6369	376.4+/-338.1	266,1699,2335	yes	missense	ROS1	NM_002944.2	23	277,1980,4246	TT,TC,CC		25.9419,6.877,19.4833	benign	2213/2348	117622233	2534,10472	2203	4300	6503	SO:0001583	missense	6098	exon42			GTTGGTCCTGAAT	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.6637G>A	6.37:g.117622233C>T	ENSP00000357494:p.Asp2213Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	343	0.15705128205128205	18	0.036585365853658534	60	0.16574585635359115	87	0.1520979020979021	178	0.23482849604221637	C	13.60	2.286366	0.40494	0.06877	0.259419	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.88818	-2.43;-2.43	5.01	3.19	0.36642	.	0.362593	0.26542	N	0.023789	T	0.64438	0.2598	N	0.26130	0.795	0.40526	P	0.019113000000000047	B	0.14012	0.009	B	0.16289	0.015	T	0.47071	-0.9145	9	0.16896	T	0.51	.	7.3721	0.26808	0.0:0.703:0.1377:0.1594	rs529038;rs60571044;rs529038	2213	P08922	ROS1_HUMAN	N	2213;2207	ENSP00000357494:D2213N;ENSP00000357493:D2207N	ENSP00000357493:D2207N	D	-	1	0	ROS1	117728926	0.995000	0.38212	1.000000	0.80357	0.984000	0.73092	0.902000	0.28459	0.754000	0.32968	0.650000	0.86243	GAC	T|0.172;C|0.828	0.172	strong		0.358	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
ST3GAL1	6482	hgsc.bcm.edu	37	8	134474148	134474148	+	Silent	SNP	C	C	T	rs1048479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:134474148C>T	ENST00000319914.5	-	8	1846	c.819G>A	c.(817-819)tcG>tcA	p.S273S	ST3GAL1_ENST00000399640.2_Silent_p.S273S|ST3GAL1_ENST00000521180.1_Silent_p.S273S|ST3GAL1_ENST00000522652.1_Silent_p.S273S			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	273					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)			AGAAGATGACCGAGAGGATGC	0.582													C|||	2402	0.479633	0.3676	0.6758	5008	,	,		20205	0.4375		0.5179	False		,,,				2504	0.4959				p.S273S		Atlas-SNP	.											.	ST3GAL1	39	.	0			c.G819A						PASS	.	C	,	1709,2697	514.4+/-368.6	327,1055,821	173.0	143.0	153.0		819,819	-10.0	0.5	8	dbSNP_86	153	4148,4452	565.1+/-388.4	987,2174,1139	no	coding-synonymous,coding-synonymous	ST3GAL1	NM_003033.3,NM_173344.2	,	1314,3229,1960	TT,TC,CC		48.2326,38.788,45.0331	,	273/341,273/341	134474148	5857,7149	2203	4300	6503	SO:0001819	synonymous_variant	6482	exon9			GATGACCGAGAGG	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.819G>A	8.37:g.134474148C>T		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_173344	O60677|Q9UN51	Silent	SNP	ENST00000319914.5	37	CCDS6373.1																																																																																			C|0.549;T|0.451	0.451	strong		0.582	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033	
RBM12	10137	hgsc.bcm.edu	37	20	34243017	34243017	+	Silent	SNP	C	C	T	rs6121015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34243017C>T	ENST00000374114.3	-	3	491	c.228G>A	c.(226-228)aaG>aaA	p.K76K	RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000317619.3_Intron|RBM12_ENST00000374104.3_Silent_p.K76K|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000352393.4_Intron|RBM12_ENST00000359646.1_Silent_p.K76K	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	76						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GCATTTCCGTCTTACTACTCA	0.423											OREG0004046	type=REGULATORY REGION|Gene=RBM12|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	1358	0.271166	0.4228	0.1844	5008	,	,		21996	0.1339		0.1899	False		,,,				2504	0.3528				p.K76K		Atlas-SNP	.											.	RBM12	93	.	0			c.G228A						PASS	.	T	,,,,,,,,	1733,2673	648.4+/-398.7	331,1071,801	180.0	160.0	167.0		228,228,,228,228,,,,	5.4	1.0	20	dbSNP_114	167	1640,6960	741.6+/-407.2	172,1296,2832	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,intron,intron,intron,intron	CPNE1,RBM12	NM_001198838.1,NM_001198840.1,NM_001198863.1,NM_006047.5,NM_152838.3,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	,,,,,,,,	503,2367,3633	TT,TC,CC		19.0698,39.3327,25.9342	,,,,,,,,	76/933,76/933,,76/933,76/933,,,,	34243017	3373,9633	2203	4300	6503	SO:0001819	synonymous_variant	10137	exon2			TTCCGTCTTACTA	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.228G>A	20.37:g.34243017C>T		Somatic	262	1	0.00381679	846	WXS	Illumina HiSeq	Phase_I	268	127	0.473881	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Silent	SNP	ENST00000374114.3	37	CCDS13261.1																																																																																			C|0.753;T|0.247	0.247	strong		0.423	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
DHDH	27294	hgsc.bcm.edu	37	19	49442933	49442933	+	Silent	SNP	T	T	C	rs2270939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	38	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	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	
PLCD4	84812	hgsc.bcm.edu	37	2	219492924	219492924	+	Silent	SNP	T	T	C	rs612874	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:219492924T>C	ENST00000450993.2	+	7	1284	c.945T>C	c.(943-945)tgT>tgC	p.C315C	PLCD4_ENST00000432688.1_Silent_p.C315C|PLCD4_ENST00000417849.1_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	151	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	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		
PGLYRP3	114771	hgsc.bcm.edu	37	1	153279696	153279696	+	Missense_Mutation	SNP	C	C	T	rs55991125	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153279696C>T	ENST00000290722.1	-	2	155	c.103G>A	c.(103-105)Gcc>Acc	p.A35T		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	35			A -> T (in dbSNP:rs55991125).		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCCCTGCAGGCGAGCGGTCTT	0.627													C|||	93	0.0185703	0.0045	0.0303	5008	,	,		18833	0.0		0.0398	False		,,,				2504	0.0266				p.A35T		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.G103A						PASS	.	C	THR/ALA	47,4359	46.0+/-80.4	1,45,2157	45.0	42.0	43.0		103	1.9	0.3	1	dbSNP_129	43	503,8097	136.4+/-193.5	7,489,3804	yes	missense	PGLYRP3	NM_052891.1	58	8,534,5961	TT,TC,CC		5.8488,1.0667,4.2288	benign	35/342	153279696	550,12456	2203	4300	6503	SO:0001583	missense	114771	exon2			TGCAGGCGAGCGG	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I alpha precursor"""	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.103G>A	1.37:g.153279696C>T	ENSP00000290722:p.Ala35Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_052891	A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	38	0.0173992673992674	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	25	0.032981530343007916	C	4.156	0.027487	0.08054	0.010667	0.058488	ENSG00000159527	ENST00000290722	T	0.29142	1.58	4.21	1.87	0.25490	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (3);	0.308555	0.23642	N	0.046009	T	0.02929	0.0087	N	0.05078	-0.115	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43343	-0.9397	10	0.11794	T	0.64	2.1343	3.2751	0.06896	0.2022:0.1146:0.0:0.6832	rs55991125	35	Q96LB9	PGRP3_HUMAN	T	35	ENSP00000290722:A35T	ENSP00000290722:A35T	A	-	1	0	PGLYRP3	151546320	0.000000	0.05858	0.339000	0.25562	0.000000	0.00434	-0.174000	0.09839	0.269000	0.21961	-1.106000	0.02097	GCC	C|0.967;T|0.033	0.033	strong		0.627	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891	
NCOR2	9612	hgsc.bcm.edu	37	12	124841221	124841221	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124841221G>A	ENST00000405201.1	-	23	3208	c.3208C>T	c.(3208-3210)Ccg>Tcg	p.P1070S	NCOR2_ENST00000404621.1_Missense_Mutation_p.P1060S|NCOR2_ENST00000429285.2_Missense_Mutation_p.P1060S|NCOR2_ENST00000356219.3_Missense_Mutation_p.P1077S|NCOR2_ENST00000404121.2_Missense_Mutation_p.P631S|NCOR2_ENST00000397355.1_Missense_Mutation_p.P1061S			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1078					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)		GAGGGGTCCGGGGCATGCGGG	0.657																																					p.P1070S		Atlas-SNP	.											NCOR2_ENST00000405201,NS,carcinoma,+2,2	NCOR2	475	2	0			c.C3208T						scavenged	.						23.0	28.0	27.0					12																	124841221		1918	4124	6042	SO:0001583	missense	9612	exon25			GGTCCGGGGCATG	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.3208C>T	12.37:g.124841221G>A	ENSP00000384018:p.Pro1070Ser	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	240	3	0.0125	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	G	13.43	2.235225	0.39498	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.29655	2.32;2.58;2.32;2.58;2.32;2.58;1.56	4.35	3.4	0.38934	.	0.193328	0.34223	N	0.004160	T	0.18002	0.0432	N	0.08118	0	0.18873	N	0.999988	P;P;P	0.48407	0.91;0.851;0.908	B;B;P	0.45753	0.388;0.297;0.492	T	0.06643	-1.0815	10	0.31617	T	0.26	-11.1214	9.8731	0.41187	0.0:0.3:0.7:0.0	.	1060;1061;1070	C9J0Q5;C9J239;C9JFD3	.;.;.	S	1070;1060;1077;1061;1069;631;1060;1078	ENSP00000384018:P1070S;ENSP00000384202:P1060S;ENSP00000348551:P1077S;ENSP00000380513:P1061S;ENSP00000385618:P631S;ENSP00000400281:P1060S;ENSP00000402808:P1078S	ENSP00000348551:P1077S	P	-	1	0	NCOR2	123407174	0.978000	0.34361	0.928000	0.36995	0.990000	0.78478	1.444000	0.35068	0.900000	0.36469	0.561000	0.74099	CCG	.	.	none		0.657	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815522	23815522	+	Silent	SNP	C	C	T	rs3755863	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:23815522C>T	ENST00000264867.2	-	8	1703	c.1584G>A	c.(1582-1584)acG>acA	p.T528T	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	528	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)				AATAGGATTGCGTGCCATCCC	0.408													C|||	1764	0.352236	0.239	0.3343	5008	,	,		19235	0.4454		0.4284	False		,,,				2504	0.3436				p.T528T	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											PPARGC1A,colon,carcinoma,0,1	PPARGC1A	129	1	0			c.G1584A	GRCh37	CM035706	PPARGC1A	M	rs3755863	PASS	.	C		1052,3354	384.2+/-325.2	120,812,1271	145.0	138.0	140.0		1584	3.2	1.0	4	dbSNP_107	140	3512,5088	512.9+/-378.0	695,2122,1483	no	coding-synonymous	PPARGC1A	NM_013261.3		815,2934,2754	TT,TC,CC		40.8372,23.8765,35.0915		528/799	23815522	4564,8442	2203	4300	6503	SO:0001819	synonymous_variant	10891	exon8			GGATTGCGTGCCA	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.1584G>A	4.37:g.23815522C>T		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	37	CCDS3429.1																																																																																			C|0.640;T|0.360	0.360	strong		0.408	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
MOV10	4343	hgsc.bcm.edu	37	1	113243048	113243048	+	Silent	SNP	C	C	T	rs6679	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:113243048C>T	ENST00000413052.2	+	21	3321	c.2931C>T	c.(2929-2931)agC>agT	p.S977S	RP11-426L16.10_ENST00000471038.2_5'Flank|MOV10_ENST00000369645.1_Silent_p.S977S|MOV10_ENST00000357443.2_Silent_p.S977S|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.S921S	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	977					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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		GGCCCCACAGCCATGACTACC	0.607													T|||	1422	0.283946	0.1702	0.2911	5008	,	,		18569	0.5407		0.2346	False		,,,				2504	0.2188				p.S977S		Atlas-SNP	.											.	MOV10	74	.	0			c.C2931T						PASS	.	T	,	822,3584	749.2+/-412.0	90,642,1471	85.0	88.0	87.0		2931,2931	-0.8	0.0	1	dbSNP_52	87	1769,6831	734.4+/-406.9	182,1405,2713	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	272,2047,4184	TT,TC,CC		20.5698,18.6564,19.9216	,	977/1004,977/1004	113243048	2591,10415	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon21			CCACAGCCATGAC	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2931C>T	1.37:g.113243048C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			C|0.753;T|0.247	0.247	strong		0.607	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
PRG4	10216	hgsc.bcm.edu	37	1	186273994	186273994	+	Missense_Mutation	SNP	C	C	T	rs2273779	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:186273994C>T	ENST00000445192.2	+	6	583	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W	PRG4_ENST00000367483.4_Missense_Mutation_p.R139W|PRG4_ENST00000367484.3_Missense_Mutation_p.R139W|PRG4_ENST00000367485.4_Intron|PRG4_ENST00000367486.3_Intron	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	180	Ser-rich.		R -> W (in dbSNP:rs2273779). {ECO:0000269|Ref.1}.		cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ttcAACAATTCGGAAAATCAA	0.358													C|||	1160	0.231629	0.149	0.4063	5008	,	,		16449	0.129		0.33	False		,,,				2504	0.2239				p.R180W		Atlas-SNP	.											.	PRG4	259	.	0			c.C538T						PASS	.	C	TRP/ARG,TRP/ARG,,	822,3576	293.6+/-282.7	79,664,1456	41.0	44.0	43.0		415,538,,	4.3	1.0	1	dbSNP_100	43	3031,5567	451.4+/-362.6	537,1957,1805	yes	missense,missense,intron,intron	PRG4	NM_001127708.1,NM_005807.3,NM_001127709.1,NM_001127710.1	101,101,,	616,2621,3261	TT,TC,CC		35.2524,18.6903,29.6476	possibly-damaging,possibly-damaging,,	139/1364,180/1405,,	186273994	3853,9143	2199	4299	6498	SO:0001583	missense	10216	exon6			ACAATTCGGAAAA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.538C>T	1.37:g.186273994C>T	ENSP00000399679:p.Arg180Trp	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	167	68	0.407186	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	550	0.2518315018315018	65	0.13211382113821138	145	0.4005524861878453	77	0.1346153846153846	263	0.3469656992084433	C	18.69	3.677565	0.68042	0.186903	0.352524	ENSG00000116690	ENST00000367484;ENST00000533951;ENST00000367483;ENST00000445192	T;T;T;T	0.50548	2.96;0.74;2.87;2.92	5.17	4.26	0.50523	.	0.199396	0.25081	U	0.033299	T	0.00012	0.0000	N	0.19112	0.55	0.41286	P	0.013051999999999953	P;D	0.55172	0.949;0.97	B;P	0.46850	0.329;0.529	T	0.42085	-0.9472	9	0.62326	D	0.03	-4.2039	9.7397	0.40411	0.0:0.9046:0.0:0.0954	rs2273779;rs52813784;rs58219930;rs2273779	180;139	Q92954;Q92954-2	PRG4_HUMAN;.	W	139;89;139;180	ENSP00000356454:R139W;ENSP00000431330:R89W;ENSP00000356453:R139W;ENSP00000399679:R180W	ENSP00000356453:R139W	R	+	1	2	PRG4	184540617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.402000	0.34600	1.188000	0.43014	0.650000	0.86243	CGG	C|0.726;T|0.274	0.274	strong		0.358	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
CLSTN3	9746	hgsc.bcm.edu	37	12	7280880	7280880	+	5'Flank	SNP	C	C	G	rs7969705	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:7280880C>G	ENST00000266546.6	+	0	0				RP11-273B20.1_ENST00000538062.1_RNA|RBP5_ENST00000266560.3_Missense_Mutation_p.E70Q|RBP5_ENST00000542370.1_Missense_Mutation_p.E70Q|RP11-273B20.1_ENST00000544657.1_RNA	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3						homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						TCCTCAAACTCCACTCCCACA	0.577													C|||	529	0.105631	0.0219	0.0562	5008	,	,		-128	0.1399		0.0696	False		,,,				2504	0.2556				p.E70Q		Atlas-SNP	.											.	RBP5	20	.	0			c.G208C						PASS	.	C	GLN/GLU	113,4293	87.8+/-126.4	0,113,2090	162.0	128.0	140.0		208	3.5	0.9	12	dbSNP_116	140	756,7844	181.0+/-229.8	33,690,3577	yes	missense	RBP5	NM_031491.2	29	33,803,5667	GG,GC,CC		8.7907,2.5647,6.6815	probably-damaging	70/136	7280880	869,12137	2203	4300	6503	SO:0001631	upstream_gene_variant	83758	exon2			CAAACTCCACTCC	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167		12.37:g.7280880C>G	Exception_encountered	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	228	103	0.451754	NM_031491	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	161	0.07371794871794872	12	0.024390243902439025	20	0.055248618784530384	81	0.14160839160839161	48	0.0633245382585752	C	17.37	3.371329	0.61624	0.025647	0.087907	ENSG00000139194	ENST00000266560;ENST00000542370	T;T	0.34072	1.38;1.38	3.55	3.55	0.40652	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.055465	0.64402	D	0.000001	T	0.00552	0.0018	M	0.78285	2.405	0.09310	P	0.99999344584	P	0.50943	0.94	P	0.55667	0.781	T	0.19257	-1.0311	9	0.66056	D	0.02	.	13.4452	0.61136	0.0:0.8283:0.1717:0.0	rs7969705;rs52798160;rs59889358;rs7969705	70	P82980	RET5_HUMAN	Q	70	ENSP00000266560:E70Q;ENSP00000438083:E70Q	ENSP00000266560:E70Q	E	-	1	0	RBP5	7172147	1.000000	0.71417	0.918000	0.36340	0.276000	0.26787	5.633000	0.67825	2.270000	0.75569	0.491000	0.48974	GAG	C|0.933;G|0.067	0.067	strong		0.577	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
PAPPA	5069	hgsc.bcm.edu	37	9	118949998	118949998	+	Silent	SNP	C	C	T	rs12375498	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:118949998C>T	ENST00000328252.3	+	2	1350	c.981C>T	c.(979-981)tgC>tgT	p.C327C	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	327	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						CTCCTCTGTGCGGACAGACAT	0.572													C|||	591	0.118011	0.0189	0.1499	5008	,	,		20359	0.0942		0.2555	False		,,,				2504	0.1125				p.C327C		Atlas-SNP	.											.	PAPPA	243	.	0			c.C981T						PASS	.	C		244,4162	141.9+/-177.2	7,230,1966	73.0	68.0	70.0		981	-11.8	0.5	9	dbSNP_120	70	2087,6513	361.4+/-332.3	246,1595,2459	no	coding-synonymous	PAPPA	NM_002581.3		253,1825,4425	TT,TC,CC		24.2674,5.5379,17.9225		327/1628	118949998	2331,10675	2203	4300	6503	SO:0001819	synonymous_variant	5069	exon2			TCTGTGCGGACAG		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.981C>T	9.37:g.118949998C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			C|0.836;T|0.164	0.164	strong		0.572	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254126	39254126	+	Missense_Mutation	SNP	C	C	T	rs202107241		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254126C>T	ENST00000333822.4	-	1	267	c.211G>A	c.(211-213)Gtg>Atg	p.V71M		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	71	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						CAGCTGGACACACAGCAGCTG	0.667																																					p.V71M		Atlas-SNP	.											KRTAP4-8,colon,carcinoma,+2,2	KRTAP4-8	57	2	0			c.G211A						scavenged	.						5.0	8.0	7.0					17																	39254126		619	1441	2060	SO:0001583	missense	728224	exon1			TGGACACACAGCA	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.211G>A	17.37:g.39254126C>T	ENSP00000328444:p.Val71Met	Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	60	12	0.2	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	8.585	0.883304	0.17467	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01430	4.9	3.55	-7.1	0.01547	.	3.062900	0.01485	U	0.016837	T	0.03477	0.0100	M	0.81497	2.545	0.09310	N	1	P	0.40266	0.71	B	0.43623	0.425	T	0.15896	-1.0421	10	0.45353	T	0.12	.	7.8878	0.29661	0.0:0.5469:0.2514:0.2017	.	71	Q9BYQ9	KRA48_HUMAN	M	71	ENSP00000328444:V71M	ENSP00000414561:V71M	V	-	1	0	KRTAP4-8	36507652	0.000000	0.05858	0.019000	0.16419	0.121000	0.20230	-2.017000	0.01445	-1.974000	0.00998	-1.450000	0.01041	GTG	.	.	weak		0.667	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
MMP9	4318	hgsc.bcm.edu	37	20	44640225	44640225	+	Missense_Mutation	SNP	A	A	G	rs17576	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:44640225A>G	ENST00000372330.3	+	6	855	c.836A>G	c.(835-837)cAg>cGg	p.Q279R	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	279			Q -> R (common polymorphism; may be associated with susceptibility to IDD; dbSNP:rs17576). {ECO:0000269|PubMed:10598806, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2551898, ECO:0000269|Ref.4}.		collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CTCTACACCCAGGACGGCAAT	0.582											OREG0025989	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2281	0.455471	0.3442	0.2277	5008	,	,		18346	0.7391		0.3807	False		,,,				2504	0.5521				p.Q279R		Atlas-SNP	.											.	MMP9	84	.	0			c.A836G	GRCh37	CM062877	MMP9	M	rs17576	PASS	.	A	ARG/GLN	1533,2873	483.2+/-359.6	267,999,937	100.0	92.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	836	2.7	1.0	20	dbSNP_63	95	2991,5609	463.4+/-366.0	518,1955,1827	yes	missense	MMP9	NM_004994.2	43	785,2954,2764	GG,GA,AA		34.7791,34.7935,34.7839	benign	279/708	44640225	4524,8482	2203	4300	6503	SO:0001583	missense	4318	exon6			ACACCCAGGACGG		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.836A>G	20.37:g.44640225A>G	ENSP00000361405:p.Gln279Arg	Somatic	66	0	0	925	WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	983	0.4500915750915751	172	0.34959349593495936	103	0.2845303867403315	413	0.722027972027972	295	0.3891820580474934	A	11.82	1.753923	0.31046	0.347935	0.347791	ENSG00000100985	ENST00000372330	T	0.08984	3.03	3.92	2.71	0.32032	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (1);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.648390	0.14719	N	0.302456	T	0.00012	0.0000	N	0.11560	0.145	0.41443	P	0.012062000000000017	B	0.11235	0.004	B	0.14023	0.01	T	0.13124	-1.0521	9	0.30078	T	0.28	.	9.3516	0.38142	0.8401:0.0:0.0:0.1599	rs17576;rs2664538;rs17845069;rs17857851;rs52800421;rs61231474;rs17576	279	P14780	MMP9_HUMAN	R	279	ENSP00000361405:Q279R	ENSP00000361405:Q279R	Q	+	2	0	MMP9	44073632	0.132000	0.22450	1.000000	0.80357	0.949000	0.60115	2.309000	0.43699	1.778000	0.52293	0.459000	0.35465	CAG	A|0.578;G|0.422	0.422	strong		0.582	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		
NOTCH4	4855	hgsc.bcm.edu	37	6	32163541	32163541	+	Silent	SNP	A	A	C	rs1044507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32163541A>C	ENST00000375023.3	-	30	5823	c.5685T>G	c.(5683-5685)tcT>tcG	p.S1895S	GPSM3_ENST00000375040.3_5'Flank|GPSM3_ENST00000487761.1_5'Flank|GPSM3_ENST00000375043.3_5'Flank|NOTCH4_ENST00000443903.2_3'UTR	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1895					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						TCCGGCAATGAGAATAGGCCC	0.701													A|||	179	0.0357428	0.0144	0.0187	5008	,	,		13590	0.0278		0.0258	False		,,,				2504	0.0951				p.S1895S		Atlas-SNP	.											.	NOTCH4	201	.	0			c.T5685G						PASS	.	A		53,2953		0,53,1450	15.0	20.0	18.0		5685	-5.5	0.0	6	dbSNP_86	18	135,5251		3,129,2561	no	coding-synonymous	NOTCH4	NM_004557.3		3,182,4011	CC,CA,AA		2.5065,1.7631,2.2402		1895/2004	32163541	188,8204	1503	2693	4196	SO:0001819	synonymous_variant	4855	exon30			GCAATGAGAATAG		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.5685T>G	6.37:g.32163541A>C		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	31	30	0.967742	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			A|0.974;C|0.026	0.026	strong		0.701	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
RBM19	9904	hgsc.bcm.edu	37	12	114383651	114383651	+	Silent	SNP	C	C	T	rs12321179	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:114383651C>T	ENST00000545145.2	-	13	1686	c.1608G>A	c.(1606-1608)aaG>aaA	p.K536K	RBM19_ENST00000261741.5_Silent_p.K536K|RBM19_ENST00000392561.3_Silent_p.K536K	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	536					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K536K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					ACACTTGACTCTTGGTGGCGT	0.552													C|||	994	0.198482	0.3472	0.0764	5008	,	,		22010	0.1885		0.1133	False		,,,				2504	0.182				p.K536K		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.G1608A						PASS	.	C	,,	1440,2966	466.0+/-354.4	254,932,1017	161.0	119.0	133.0		1608,1608,1608	3.8	1.0	12	dbSNP_120	133	887,7713	199.4+/-243.5	39,809,3452	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	293,1741,4469	TT,TC,CC		10.314,32.6827,17.8917	,,	536/961,536/961,536/961	114383651	2327,10679	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon13			TTGACTCTTGGTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1608G>A	12.37:g.114383651C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	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	
IDI2	91734	hgsc.bcm.edu	37	10	1066710	1066710	+	Silent	SNP	C	C	T	rs34407608	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:1066710C>T	ENST00000277517.1	-	4	427	c.363G>A	c.(361-363)gaG>gaA	p.E121E	IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000420381.1_RNA|IDI2-AS1_ENST00000437374.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000434470.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	121	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		TGTGTACCTGCTCCCCAGGAA	0.572													C|||	425	0.0848642	0.0484	0.0764	5008	,	,		15943	0.0972		0.0905	False		,,,				2504	0.1217				p.E121E		Atlas-SNP	.											.	IDI2	20	.	0			c.G363A						PASS	.	C		304,4102	166.5+/-197.7	13,278,1912	91.0	75.0	80.0		363	-8.2	0.0	10	dbSNP_126	80	897,7703	200.6+/-244.3	49,799,3452	yes	coding-synonymous	IDI2	NM_033261.2		62,1077,5364	TT,TC,CC		10.4302,6.8997,9.2342		121/228	1066710	1201,11805	2203	4300	6503	SO:0001819	synonymous_variant	91734	exon4			TACCTGCTCCCCA	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.363G>A	10.37:g.1066710C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_033261		Silent	SNP	ENST00000277517.1	37	CCDS7055.1																																																																																			C|0.912;T|0.088	0.088	strong		0.572	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261	
ART1	417	hgsc.bcm.edu	37	11	3681051	3681051	+	Missense_Mutation	SNP	C	C	G	rs61998205	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:3681051C>G	ENST00000250693.1	+	3	403	c.302C>G	c.(301-303)aCc>aGc	p.T101S		NM_004314.2	NP_004305.2	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1	101					innate immune response (GO:0045087)|protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|skin(1)	8		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)		CTCAGCCCCACCCGTCCATCC	0.647													C|||	187	0.0373403	0.0038	0.0692	5008	,	,		15310	0.001		0.1103	False		,,,				2504	0.0225				p.T101S		Atlas-SNP	.											.	ART1	21	.	0			c.C302G						PASS	.	C	SER/THR	104,4298	77.3+/-115.6	3,98,2100	32.0	30.0	31.0		302	2.5	0.0	11	dbSNP_129	31	953,7643	196.5+/-241.4	62,829,3407	yes	missense	ART1	NM_004314.2	58	65,927,5507	GG,GC,CC		11.0866,2.3626,8.132	benign	101/328	3681051	1057,11941	2201	4298	6499	SO:0001583	missense	417	exon3			GCCCCACCCGTCC	S74683	CCDS7744.1	11p15	2006-02-23			ENSG00000129744	ENSG00000129744		"""CD molecules"""	723	protein-coding gene	gene with protein product		601625				8812442	Standard	NM_004314		Approved	ART2, CD296	uc001lye.1	P52961	OTTHUMG00000011845	ENST00000250693.1:c.302C>G	11.37:g.3681051C>G	ENSP00000250693:p.Thr101Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_004314	Q6NTD2|Q96KT9	Missense_Mutation	SNP	ENST00000250693.1	37	CCDS7744.1	120	0.054945054945054944	1	0.0020325203252032522	33	0.09116022099447514	1	0.0017482517482517483	85	0.11213720316622691	C	2.077	-0.411732	0.04799	0.023626	0.110866	ENSG00000129744	ENST00000250693	T	0.08102	3.13	4.49	2.5	0.30297	.	0.887780	0.09815	N	0.752274	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B	0.13145	0.007	B	0.15052	0.012	T	0.38023	-0.9680	8	.	.	.	.	6.3849	0.21556	0.0:0.7144:0.1826:0.1029	rs61998205	101	P52961	NAR1_HUMAN	S	101	ENSP00000250693:T101S	.	T	+	2	0	ART1	3637627	0.148000	0.22702	0.002000	0.10522	0.016000	0.09150	0.000000	0.12993	1.103000	0.41568	0.467000	0.42956	ACC	C|0.931;G|0.068;T|0.000	0.068	strong		0.647	ART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032765.1	NM_004314	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305785	39305785	+	Missense_Mutation	SNP	A	A	T	rs411367		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	84	0	0		WXS	Illumina HiSeq	Phase_I	80	12	0.15	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		
NCKAP5	344148	hgsc.bcm.edu	37	2	133554288	133554288	+	Silent	SNP	A	A	G	rs1868076	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:133554288A>G	ENST00000409261.1	-	12	1195	c.822T>C	c.(820-822)cgT>cgC	p.R274R	NCKAP5_ENST00000405974.3_Silent_p.R274R|NCKAP5_ENST00000317721.6_Silent_p.R274R|NCKAP5_ENST00000409213.1_Silent_p.R274R	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	274										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						GATCCAAGAGACGTGAGTGAA	0.408													G|||	3459	0.690695	0.7126	0.6729	5008	,	,		18207	0.8899		0.5398	False		,,,				2504	0.6237				p.R274R		Atlas-SNP	.											.	NCKAP5	322	.	0			c.T822C						PASS	.	G	,	2616,1088		925,766,161	63.0	60.0	61.0		822,822	0.1	0.0	2	dbSNP_92	61	4500,3706		1232,2036,835	no	coding-synonymous,coding-synonymous	NCKAP5	NM_207363.2,NM_207481.3	,	2157,2802,996	GG,GA,AA		45.1621,29.3737,40.2519	,	274/1910,274/591	133554288	7116,4794	1852	4103	5955	SO:0001819	synonymous_variant	344148	exon12			CAAGAGACGTGAG	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.822T>C	2.37:g.133554288A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			A|0.307;G|0.693	0.693	strong		0.408	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
KRT81	3887	hgsc.bcm.edu	37	12	52681056	52681056	+	Silent	SNP	C	C	T	rs4761856	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52681056C>T	ENST00000327741.5	-	7	1145	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	KRT86_ENST00000544024.1_Intron|KRT86_ENST00000423955.2_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	359	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACTGAGGGCCGCCTCACCCT	0.617													.|||	1921	0.383586	0.2995	0.3602	5008	,	,		18024	0.5377		0.334	False		,,,				2504	0.4059				p.A359A		Atlas-SNP	.											.	KRT81	46	.	0			c.G1077A						PASS	.	C		1321,3085		225,871,1107	28.0	30.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1077	-4.9	0.9	12	dbSNP_111	29	2681,5909		411,1859,2025	no	coding-synonymous	KRT81	NM_002281.3		636,2730,3132	TT,TC,CC		31.2107,29.9818,30.7941		359/506	52681056	4002,8994	2203	4295	6498	SO:0001819	synonymous_variant	3887	exon7			GAGGGCCGCCTCA	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.1077G>A	12.37:g.52681056C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	37	CCDS31805.1																																																																																			C|0.673;T|0.327	0.327	strong		0.617	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
GPRC5B	51704	hgsc.bcm.edu	37	16	19883364	19883364	+	Silent	SNP	G	G	A	rs61742688	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:19883364G>A	ENST00000300571.2	-	2	995	c.804C>T	c.(802-804)aaC>aaT	p.N268N	GPRC5B_ENST00000537135.1_Silent_p.N294N|GPRC5B_ENST00000569479.1_Silent_p.N268N|GPRC5B_ENST00000569847.1_Silent_p.N268N|GPRC5B_ENST00000535671.1_Silent_p.N268N	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	62	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	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		
PDE9A	5152	hgsc.bcm.edu	37	21	44180443	44180443	+	Silent	SNP	C	C	T	rs13047953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44180443C>T	ENST00000291539.6	+	12	963	c.903C>T	c.(901-903)tgC>tgT	p.C301C	PDE9A_ENST00000398229.3_Silent_p.C167C|PDE9A_ENST00000335440.6_Silent_p.C199C|PDE9A_ENST00000398234.3_Silent_p.C200C|PDE9A_ENST00000349112.3_Silent_p.C173C|PDE9A_ENST00000539837.1_Silent_p.C173C|PDE9A_ENST00000398227.3_Silent_p.C141C|PDE9A_ENST00000335512.4_Silent_p.C241C|PDE9A_ENST00000398225.3_Silent_p.C260C|PDE9A_ENST00000380328.2_Silent_p.C248C|PDE9A_ENST00000398236.3_Silent_p.C215C|PDE9A_ENST00000398232.3_Silent_p.C234C|PDE9A_ENST00000398224.3_Silent_p.C174C|PDE9A_ENST00000328862.6_Silent_p.C275C|PDE9A_ENST00000470987.1_3'UTR	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	301	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)	p.C301C(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)	CGCAGTTCTGCGTCCACGACA	0.607													C|||	1146	0.228834	0.0219	0.219	5008	,	,		16615	0.4127		0.4374	False		,,,				2504	0.1115				p.C301C		Atlas-SNP	.											PDE9A,NS,carcinoma,0,1	PDE9A	69	1	1	Substitution - coding silent(1)	stomach(1)	c.C903T						PASS	.	C	,,,,,,,,,,,,,,,,,,,	369,4037	186.7+/-213.5	17,335,1851	69.0	56.0	60.0		723,522,519,744,600,282,282,645,423,252,501,597,282,252,702,780,825,282,282,903	-1.1	1.0	21	dbSNP_121	60	3740,4860	531.7+/-382.0	823,2094,1383	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	,,,,,,,,,,,,,,,,,,,	840,2429,3234	TT,TC,CC		43.4884,8.3749,31.5931	,,,,,,,,,,,,,,,,,,,	241/534,174/467,173/466,248/541,200/493,94/387,94/387,215/508,141/434,84/377,167/460,199/492,94/387,84/377,234/527,260/553,275/568,94/387,94/387,301/594	44180443	4109,8897	2203	4300	6503	SO:0001819	synonymous_variant	5152	exon12			GTTCTGCGTCCAC	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.903C>T	21.37:g.44180443C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	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																																																																																			C|0.675;T|0.325	0.325	strong		0.607	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
HRNR	388697	hgsc.bcm.edu	37	1	152190945	152190945	+	Missense_Mutation	SNP	C	C	T	rs77376932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152190945C>T	ENST00000368801.2	-	3	3235	c.3160G>A	c.(3160-3162)Gag>Aag	p.E1054K	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1054					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGCGAGACTCTCGGTGACCT	0.552													C|||	1483	0.296126	0.0242	0.3905	5008	,	,		28894	0.619		0.1402	False		,,,				2504	0.4243				p.E1054K		Atlas-SNP	.											.	HRNR	403	.	0			c.G3160A						PASS	.	C	LYS/GLU	209,4197	126.1+/-163.2	8,193,2002	88.0	100.0	96.0		3160	1.4	0.0	1	dbSNP_131	96	1239,7355	245.3+/-274.2	99,1041,3157	no	missense	HRNR	NM_001009931.1	56	107,1234,5159	TT,TC,CC		14.417,4.7435,11.1385	possibly-damaging	1054/2851	152190945	1448,11552	2203	4297	6500	SO:0001583	missense	388697	exon3			GAGACTCTCGGTG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.3160G>A	1.37:g.152190945C>T	ENSP00000357791:p.Glu1054Lys	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	342	133	0.388889	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	569	0.26053113553113555	13	0.026422764227642278	115	0.31767955801104975	330	0.5769230769230769	111	0.14643799472295516	C	8.047	0.765129	0.15914	0.047435	0.14417	ENSG00000197915	ENST00000368801	T	0.02631	4.22	2.38	1.39	0.22231	.	.	.	.	.	T	0.00496	0.0016	N	0.22421	0.69	0.80722	P	0.0	P	0.37233	0.588	B	0.30943	0.122	T	0.36237	-0.9756	8	0.06365	T	0.9	.	7.4102	0.27014	0.0:0.8495:0.0:0.1505	.	1054	Q86YZ3	HORN_HUMAN	K	1054	ENSP00000357791:E1054K	ENSP00000357791:E1054K	E	-	1	0	HRNR	150457569	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.190000	0.09615	0.300000	0.22699	0.306000	0.20318	GAG	C|0.852;T|0.148	0.148	strong		0.552	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
ACTL7B	10880	hgsc.bcm.edu	37	9	111618163	111618163	+	Silent	SNP	G	G	A	rs3750468	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111618163G>A	ENST00000374667.3	-	1	1076	c.48C>T	c.(46-48)gaC>gaT	p.D16D		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	16						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CCTCTCCAGGGTCACCCTGAG	0.652													G|||	1134	0.226438	0.2247	0.2349	5008	,	,		17053	0.2113		0.2028	False		,,,				2504	0.2628				p.D16D		Atlas-SNP	.											.	ACTL7B	57	.	0			c.C48T						PASS	.	G		969,3437	365.6+/-317.5	108,753,1342	56.0	58.0	58.0		48	0.9	1.0	9	dbSNP_107	58	1767,6833	320.7+/-314.7	174,1419,2707	no	coding-synonymous	ACTL7B	NM_006686.3		282,2172,4049	AA,AG,GG		20.5465,21.9927,21.0364		16/416	111618163	2736,10270	2203	4300	6503	SO:0001819	synonymous_variant	10880	exon1			TCCAGGGTCACCC	BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.48C>T	9.37:g.111618163G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	25	0.367647	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	37	CCDS6771.1																																																																																			G|0.783;A|0.217	0.217	strong		0.652	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	
FUNDC1	139341	hgsc.bcm.edu	37	X	44401295	44401295	+	Silent	SNP	T	T	G	rs41298452	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:44401295T>G	ENST00000378045.4	-	2	249	c.81A>C	c.(79-81)gcA>gcC	p.A27A	FUNDC1_ENST00000483115.1_5'UTR	NM_173794.3	NP_776155.1	Q8IVP5	FUND1_HUMAN	FUN14 domain containing 1	27					mitochondrion degradation (GO:0000422)|response to hypoxia (GO:0001666)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane (GO:0005741)				breast(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						GGTGTCTTCTTGCATACTCAG	0.393													T|||	343	0.0908609	0.1233	0.0346	3775	,	,		14088	0.0665		0.0268	False		,,,				2504	0.0634				p.A27A		Atlas-SNP	.											.	FUNDC1	15	.	0			c.A81C						PASS	.	T		560,3275		34,406,86,1192,485	74.0	58.0	64.0		81	-1.0	1.0	X	dbSNP_127	64	270,6458		5,182,78,2241,1794	no	coding-synonymous	FUNDC1	NM_173794.3		39,588,164,3433,2279	GG,GT,G,TT,T		4.0131,14.6023,7.8576		27/156	44401295	830,9733	2203	4300	6503	SO:0001819	synonymous_variant	139341	exon2			TCTTCTTGCATAC	BC042813	CCDS14263.1	Xp11.4	2005-09-22			ENSG00000069509	ENSG00000069509			28746	protein-coding gene	gene with protein product		300871				12477932	Standard	NM_173794		Approved	MGC51029	uc004dgc.3	Q8IVP5	OTTHUMG00000021399	ENST00000378045.4:c.81A>C	X.37:g.44401295T>G		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	222	221	0.995495	NM_173794		Silent	SNP	ENST00000378045.4	37	CCDS14263.1																																																																																			T|0.917;G|0.083	0.083	strong		0.393	FUNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056320.1	NM_173794	
IFRD1	3475	hgsc.bcm.edu	37	7	112112892	112112892	+	Silent	SNP	G	G	A	rs11542468	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:112112892G>A	ENST00000403825.3	+	11	1503	c.1242G>A	c.(1240-1242)acG>acA	p.T414T	IFRD1_ENST00000005558.4_Silent_p.T414T|IFRD1_ENST00000535603.1_Silent_p.T364T	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	414					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						CGCTTAAAACGATGAAGATTT	0.378													G|||	227	0.0453275	0.0287	0.0375	5008	,	,		18284	0.0		0.0785	False		,,,				2504	0.0859				p.T414T		Atlas-SNP	.											.	IFRD1	46	.	0			c.G1242A						PASS	.	G	,,,	151,4255	104.3+/-142.8	3,145,2055	129.0	131.0	130.0		1242,1092,1092,1242	-11.6	0.6	7	dbSNP_120	130	700,7900	172.7+/-223.4	23,654,3623	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFRD1	NM_001007245.2,NM_001197079.1,NM_001197080.1,NM_001550.3	,,,	26,799,5678	AA,AG,GG		8.1395,3.4271,6.5431	,,,	414/452,364/402,364/402,414/452	112112892	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	3475	exon12			TAAAACGATGAAG	Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.1242G>A	7.37:g.112112892G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Silent	SNP	ENST00000403825.3	37	CCDS34736.1																																																																																			G|0.940;A|0.060	0.060	strong		0.378	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	
CAPN9	10753	hgsc.bcm.edu	37	1	230898494	230898494	+	Silent	SNP	C	C	T	rs2282319	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:230898494C>T	ENST00000271971.2	+	4	611	c.498C>T	c.(496-498)aaC>aaT	p.N166N	RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000366666.2_Silent_p.N103N|CAPN9_ENST00000354537.1_Silent_p.N166N	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	166	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)	p.N166N(1)		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)				CCGACCACAACGAGTTCTGGA	0.577													T|||	1667	0.332867	0.2716	0.4452	5008	,	,		18360	0.4385		0.3797	False		,,,				2504	0.1789				p.N166N		Atlas-SNP	.											CAPN9,NS,carcinoma,0,1	CAPN9	116	1	1	Substitution - coding silent(1)	stomach(1)	c.C498T						PASS	.	T	,	1176,3230	711.9+/-408.0	159,858,1186	94.0	81.0	85.0		498,498	-10.7	0.0	1	dbSNP_100	85	3211,5389	652.4+/-400.9	610,1991,1699	no	coding-synonymous,coding-synonymous	CAPN9	NM_006615.2,NM_016452.1	,	769,2849,2885	TT,TC,CC		37.3372,26.6909,33.7306	,	166/691,166/665	230898494	4387,8619	2203	4300	6503	SO:0001819	synonymous_variant	10753	exon4			CCACAACGAGTTC	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.498C>T	1.37:g.230898494C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	37	CCDS1586.1																																																																																			C|0.643;N|0.000	.	strong		0.577	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
RYR2	6262	hgsc.bcm.edu	37	1	237947171	237947171	+	Silent	SNP	G	G	A	rs41267517		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237947171G>A	ENST00000366574.2	+	90	12476	c.12159G>A	c.(12157-12159)gaG>gaA	p.E4053E	RYR2_ENST00000542537.1_Silent_p.E4037E|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Silent_p.E4059E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4053					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)	p.E4051D(1)		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)			AAGCGATGGAGAGCCATAAGC	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		19393	0.0		0.001	False		,,,				2504	0.0				p.E4053E		Atlas-SNP	.											RYR2,NS,carcinoma,0,1	RYR2	1273	1	1	Substitution - Missense(1)	lung(1)	c.G12159A						PASS	.	G		1,3925		0,1,1962	45.0	44.0	44.0		12159	4.2	1.0	1	dbSNP_127	44	15,8295		0,15,4140	no	coding-synonymous	RYR2	NM_001035.2		0,16,6102	AA,AG,GG		0.1805,0.0255,0.1308		4053/4968	237947171	16,12220	1963	4155	6118	SO:0001819	synonymous_variant	6262	exon90			GATGGAGAGCCAT	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.12159G>A	1.37:g.237947171G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			G|0.999;A|0.001	0.001	weak		0.448	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
CTBP2	1488	hgsc.bcm.edu	37	10	126715154	126715154	+	Intron	SNP	A	A	G	rs386748578|rs3781412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:126715154A>G	ENST00000337195.5	-	3	458				CTBP2_ENST00000309035.6_Missense_Mutation_p.L392P|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000411419.2_Intron|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)		TGCTGTCTGCAGAGGAGCCGC	0.701													A|||	1620	0.323482	0.2088	0.5548	5008	,	,		13818	0.2897		0.4155	False		,,,				2504	0.2546				p.L392P		Atlas-SNP	.											.	CTBP2	100	.	0			c.T1175C						PASS	.	A	,,PRO/LEU	757,3491		78,601,1445	9.0	7.0	8.0		,,1175	-0.2	0.7	10	dbSNP_107	8	2738,5566		495,1748,1909	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,98	573,2349,3354	GG,GA,AA		32.9721,17.8202,27.8442	,,probably-damaging	,,392/986	126715154	3495,9057	2124	4152	6276	SO:0001627	intron_variant	1488	exon1			GTCTGCAGAGGAG	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+12411T>C	10.37:g.126715154A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	770	0.3525641025641026	86	0.17479674796747968	194	0.5359116022099447	182	0.3181818181818182	308	0.40633245382585753	A	11.86	1.764684	0.31228	0.178202	0.329721	ENSG00000175029	ENST00000309035	D	0.84516	-1.86	2.92	-0.201	0.13212	.	1.333230	0.05872	N	0.624837	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999337	D	0.59767	0.986	P	0.59487	0.858	T	0.25916	-1.0118	8	0.87932	D	0	.	8.2922	0.31965	0.6765:0.0:0.0:0.3235	rs3781412;rs17710555;rs3781412	392	P56545-2	.	P	392	ENSP00000311825:L392P	ENSP00000311825:L392P	L	-	2	0	CTBP2	126705144	0.998000	0.40836	0.702000	0.30337	0.146000	0.21551	4.355000	0.59424	0.253000	0.21552	0.260000	0.18958	CTG	A|0.644;G|0.356	0.356	strong		0.701	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
TJP3	27134	hgsc.bcm.edu	37	19	3740658	3740658	+	Silent	SNP	T	T	G	rs10416362	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3740658T>G	ENST00000541714.2	+	14	2202	c.1740T>G	c.(1738-1740)ctT>ctG	p.L580L	TJP3_ENST00000262968.9_Silent_p.L613L|TJP3_ENST00000589378.1_Silent_p.L589L|TJP3_ENST00000587686.1_Silent_p.L599L|TJP3_ENST00000382008.3_Silent_p.L594L|TJP3_ENST00000539908.2_Silent_p.L544L	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	580	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCGGGGTCTTCGTCGAGGAG	0.692													T|||	2761	0.551318	0.5121	0.5865	5008	,	,		11836	0.5228		0.5099	False		,,,				2504	0.6513				p.L589L		Atlas-SNP	.											TJP3,NS,carcinoma,0,1	TJP3	79	1	0			c.T1767G						PASS	.	T		2313,2089		631,1051,519	15.0	18.0	17.0		1839	-9.7	0.0	19	dbSNP_119	17	4479,4113		1202,2075,1019	no	coding-synonymous	TJP3	NM_014428.1		1833,3126,1538	GG,GT,TT		47.8701,47.4557,47.7297		613/953	3740658	6792,6202	2201	4296	6497	SO:0001819	synonymous_variant	27134	exon14			GGGTCTTCGTCGA	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.1740T>G	19.37:g.3740658T>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			T|0.478;G|0.522	0.522	strong		0.692	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
RNF213	57674	hgsc.bcm.edu	37	17	78262161	78262161	+	Splice_Site	SNP	T	T	C	rs17857135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78262161T>C	ENST00000582970.1	+	4	952	c.809T>C	c.(808-810)aTg>aCg	p.M270T	RNF213_ENST00000456466.1_Splice_Site_p.M270T|RNF213_ENST00000319921.4_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	92	0	0		WXS	Illumina HiSeq	Phase_I	83	48	0.578313	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
C2CD2	25966	hgsc.bcm.edu	37	21	43327117	43327117	+	Silent	SNP	C	C	T	rs2277795	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	75	0	0		WXS	Illumina HiSeq	Phase_I	102	58	0.568627	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	
PRDM2	7799	hgsc.bcm.edu	37	1	14143003	14143003	+	Silent	SNP	A	A	G	rs1046331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:14143003A>G	ENST00000235372.7	+	9	5974	c.5118A>G	c.(5116-5118)ccA>ccG	p.P1706P	PRDM2_ENST00000503842.1_Missense_Mutation_p.Q34R|PRDM2_ENST00000376048.5_Missense_Mutation_p.Q198R|PRDM2_ENST00000505823.1_Missense_Mutation_p.Q34R	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1706					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TCAAAGCTCCAGCTGCAGCCC	0.577													G|||	4113	0.821286	0.9319	0.8573	5008	,	,		18792	0.7073		0.8569	False		,,,				2504	0.727				p.Q198R		Atlas-SNP	.											.	PRDM2	147	.	0			c.A593G						PASS	.	G	ARG/GLN,	4118,288	160.0+/-192.4	1926,266,11	66.0	65.0	65.0		593,5118	-4.3	0.0	1	dbSNP_86	65	7255,1345	263.1+/-284.8	3062,1131,107	yes	missense,coding-synonymous	PRDM2	NM_001135610.1,NM_012231.4	43,	4988,1397,118	GG,GA,AA		15.6395,6.5365,12.5557	,	198/227,1706/1719	14143003	11373,1633	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon7			AGCTCCAGCTGCA	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.5118A>G	1.37:g.14143003A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001135610	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	1821	0.8337912087912088	452	0.9186991869918699	321	0.8867403314917127	402	0.7027972027972028	646	0.8522427440633246	G	4.681	0.126580	0.08931	0.934635	0.843605	ENSG00000116731	ENST00000376048;ENST00000503842;ENST00000505823	T	0.54675	0.56	5.07	-4.33	0.03677	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.17167	-1.0378	7	0.17832	T	0.49	.	7.1999	0.25874	0.5513:0.2342:0.2145:0.0	rs1046331;rs60453526;rs1046331	198	B1AJZ4	.	R	198;34;34	ENSP00000365216:Q198R	ENSP00000365216:Q198R	Q	+	2	0	PRDM2	14015590	0.000000	0.05858	0.000000	0.03702	0.431000	0.31685	-1.880000	0.01627	-1.681000	0.01448	-0.812000	0.03155	CAG	A|0.147;G|0.853	0.853	strong		0.577	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
UIMC1	51720	hgsc.bcm.edu	37	5	176382995	176382995	+	Missense_Mutation	SNP	G	G	A	rs3733876	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:176382995G>A	ENST00000377227.4	-	8	1436	c.1304C>T	c.(1303-1305)cCa>cTa	p.P435L	UIMC1_ENST00000511320.1_Missense_Mutation_p.P435L|UIMC1_ENST00000377219.2_Missense_Mutation_p.P435L|UIMC1_ENST00000503273.1_5'UTR|UIMC1_ENST00000506128.1_Missense_Mutation_p.P269L			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	435	Necessary for interaction with NR6A1 C- terminus.		P -> L (common polymorphism not associated with susceptibility to breast cancer; dbSNP:rs3733876). {ECO:0000269|PubMed:18695986}.		double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGAACTCTCTGGCATAAGGAC	0.378													G|||	514	0.102636	0.0189	0.0879	5008	,	,		20269	0.1944		0.1571	False		,,,				2504	0.0757				p.P435L		Atlas-SNP	.											.	UIMC1	55	.	0			c.C1304T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	192,4214	121.7+/-159.2	4,184,2015	111.0	105.0	107.0		1304,1304,1304	5.5	1.0	5	dbSNP_107	107	1496,7104	284.7+/-296.8	142,1212,2946	yes	missense,missense,missense	UIMC1	NM_001199297.1,NM_001199298.1,NM_016290.4	98,98,98	146,1396,4961	AA,AG,GG		17.3953,4.3577,12.9786	probably-damaging,probably-damaging,probably-damaging	435/720,435/720,435/720	176382995	1688,11318	2203	4300	6503	SO:0001583	missense	51720	exon8			CTCTCTGGCATAA	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.1304C>T	5.37:g.176382995G>A	ENSP00000366434:p.Pro435Leu	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	220	92	0.418182	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	279	0.12774725274725274	14	0.028455284552845527	38	0.10497237569060773	99	0.17307692307692307	128	0.16886543535620052	G	12.80	2.047947	0.36085	0.043577	0.173953	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000323774	T;T;T;T	0.13901	2.58;2.58;2.58;2.55	5.53	5.53	0.82687	.	0.106427	0.40818	N	0.001018	T	0.00073	0.0002	L	0.43152	1.355	0.22034	P	0.999408074	D;D;D;D;P	0.89917	0.96;1.0;0.986;0.977;0.928	P;D;P;P;P	0.91635	0.55;0.999;0.775;0.73;0.494	T	0.00657	-1.1623	9	0.59425	D	0.04	.	15.1875	0.73016	0.0:0.1397:0.8603:0.0	rs3733876;rs52809311;rs56465845;rs58246171;rs3733876	435;154;269;65;357	Q96RL1;D6RCF3;C9JR12;Q96RL1-4;Q96RL1-3	UIMC1_HUMAN;.;.;.;.	L	435;435;435;269;357;65	ENSP00000366434:P435L;ENSP00000366425:P435L;ENSP00000421926:P435L;ENSP00000427480:P269L	ENSP00000314909:P65L	P	-	2	0	UIMC1	176315601	1.000000	0.71417	0.990000	0.47175	0.754000	0.42855	2.389000	0.44407	2.775000	0.95449	0.650000	0.86243	CCA	G|0.879;A|0.121	0.121	strong		0.378	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924219	43924219	+	Silent	SNP	T	T	C	rs12373124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43924219T>C	ENST00000329196.5	+	1	1964	c.1947T>C	c.(1945-1947)caT>caC	p.H649H	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	649						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										AGCTGGGCCATGTCCATGCCC	0.637													t|||	431	0.0860623	0.0151	0.1571	5008	,	,		18869	0.001		0.2396	False		,,,				2504	0.0613				p.H649H		Atlas-SNP	.											.	.	.	.	0			c.T1947C						PASS	.	C		204,4202	124.9+/-162.1	5,194,2004	38.0	38.0	38.0		1947	-8.8	0.0	17	dbSNP_120	38	1927,6673	331.1+/-319.5	222,1483,2595	yes	coding-synonymous	IMP5	NM_175882.2		227,1677,4599	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	22.407,4.63,16.3847		649/685	43924219	2131,10875	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			GGGCCATGTCCAT		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1947T>C	17.37:g.43924219T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	57	0.966102	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			A|0.854;G|0.146	.	strong		0.637	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
TRIM6	117854	hgsc.bcm.edu	37	11	5629607	5629607	+	Silent	SNP	G	G	A	rs10769121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5629607G>A	ENST00000278302.5	+	5	896	c.756G>A	c.(754-756)gtG>gtA	p.V252V	TRIM6-TRIM34_ENST00000354852.5_Silent_p.V280V|TRIM6_ENST00000507320.1_Silent_p.V77V|HBG2_ENST00000380259.2_Intron|TRIM6_ENST00000481603.1_3'UTR|AC015691.13_ENST00000394793.2_RNA|TRIM6_ENST00000380097.3_Silent_p.V280V|TRIM6_ENST00000380107.1_Silent_p.V226V|TRIM6_ENST00000445329.1_Silent_p.V77V|TRIM6_ENST00000506134.1_Silent_p.V77V|TRIM6_ENST00000515022.1_Silent_p.V77V	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	157	0	0		WXS	Illumina HiSeq	Phase_I	145	65	0.448276	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	
GGT1	2678	hgsc.bcm.edu	37	22	25023419	25023419	+	Silent	SNP	C	C	T	rs202087650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:25023419C>T	ENST00000400382.1	+	12	1796	c.1041C>T	c.(1039-1041)tcC>tcT	p.S347S	GGT1_ENST00000404532.1_Silent_p.S3S|GGT1_ENST00000400383.1_Silent_p.S347S|GGT1_ENST00000403838.1_Silent_p.S3S|GGT1_ENST00000248923.4_Silent_p.S347S|GGT1_ENST00000404223.1_Silent_p.S3S|GGT1_ENST00000404920.1_Silent_p.S3S|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000406383.2_Silent_p.S347S|GGT1_ENST00000401885.1_Silent_p.S3S|GGT1_ENST00000400380.1_Silent_p.S347S			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	347					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ACATGACCTCCGAGTTCTTCG	0.647																																					p.S347S		Atlas-SNP	.											GGT1,NS,carcinoma,0,2	GGT1	68	2	0			c.C1041T						scavenged	.						53.0	54.0	54.0					22																	25023419		2201	4297	6498	SO:0001819	synonymous_variant	2678	exon12			GACCTCCGAGTTC	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1041C>T	22.37:g.25023419C>T		Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	348	12	0.0344828	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			C|0.989;T|0.011	0.011	strong		0.647	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
OR2AK2	391191	hgsc.bcm.edu	37	1	248129240	248129240	+	Missense_Mutation	SNP	G	G	A	rs4478844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:248129240G>A	ENST00000366480.3	+	1	706	c.607G>A	c.(607-609)Gtg>Atg	p.V203M	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	203			V -> M (in dbSNP:rs4478844). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			ACTATCATTGGTGTGTCAGGA	0.433													.|||	2160	0.43131	0.0915	0.5706	5008	,	,		21676	0.4623		0.6531	False		,,,				2504	0.5317				p.V203M	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.G607A						PASS	.	G	MET/VAL,	856,3550		84,688,1431	92.0	79.0	83.0		607,	0.6	0.0	1	dbSNP_111	83	5510,3090		1752,2006,542	yes	missense,intron	OR2L13,OR2AK2	NM_001004491.1,NM_175911.2	21,	1836,2694,1973	AA,AG,GG		35.9302,19.4281,48.9466	probably-damaging,	203/336,	248129240	6366,6640	2203	4300	6503	SO:0001583	missense	391191	exon1			TCATTGGTGTGTC	BK004457	CCDS31102.1	1q44	2012-08-09			ENSG00000187080	ENSG00000187080		"""GPCR / Class A : Olfactory receptors"""	19569	protein-coding gene	gene with protein product				OR2AK1P			Standard	NM_001004491		Approved		uc010pzd.2	Q8NG84	OTTHUMG00000040201	ENST00000366480.3:c.607G>A	1.37:g.248129240G>A	ENSP00000355436:p.Val203Met	Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	221	221	1	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	1009	0.461996336996337	55	0.11178861788617886	202	0.5580110497237569	261	0.4562937062937063	491	0.6477572559366754	.	15.34	2.805213	0.50315	0.194281	0.640698	ENSG00000187080	ENST00000366480	T	0.00164	8.64	2.89	0.632	0.17705	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	D	0.89917	1.0	D	0.80764	0.994	T	0.13150	-1.0520	8	0.87932	D	0	.	3.3382	0.07108	0.1493:0.0:0.5046:0.346	rs4478844;rs52798156;rs56612913;rs58570819;rs4478844	203	Q8NG84	O2AK2_HUMAN	M	203	ENSP00000355436:V203M	ENSP00000355436:V203M	V	+	1	0	OR2AK2	246195863	0.000000	0.05858	0.013000	0.15412	0.568000	0.35870	-1.749000	0.01824	0.522000	0.28464	0.455000	0.32223	GTG	G|0.537;A|0.463	0.463	strong		0.433	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491	
OR4C16	219428	hgsc.bcm.edu	37	11	55339702	55339702	+	Silent	SNP	C	C	T	rs34100491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:55339702C>T	ENST00000314634.3	+	1	99	c.99C>T	c.(97-99)taC>taT	p.Y33Y		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	33						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				TGCGTCTCTACTTGGGAACAC	0.368													c|||	874	0.174521	0.1188	0.2392	5008	,	,		19090	0.1528		0.2117	False		,,,				2504	0.1881				p.Y33Y		Atlas-SNP	.											.	OR4C16	104	.	0			c.C99T						PASS	.	C		591,3811	261.0+/-264.0	39,513,1649	199.0	187.0	191.0		99	-6.9	0.0	11	dbSNP_126	191	1891,6701	337.4+/-322.3	227,1437,2632	no	coding-synonymous	OR4C16	NM_001004701.2		266,1950,4281	TT,TC,CC		22.0088,13.4257,19.1011		33/311	55339702	2482,10512	2201	4296	6497	SO:0001819	synonymous_variant	219428	exon1			TCTCTACTTGGGA	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.99C>T	11.37:g.55339702C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	138	77	0.557971	NM_001004701	Q6IEV8	Silent	SNP	ENST00000314634.3	37	CCDS31502.1																																																																																			C|0.816;T|0.184	0.184	strong		0.368	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
ASPG	374569	hgsc.bcm.edu	37	14	104563932	104563932	+	Silent	SNP	G	G	T	rs1465163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104563932G>T	ENST00000551177.1	+	5	563	c.471G>T	c.(469-471)ctG>ctT	p.L157L	ASPG_ENST00000546892.2_Silent_p.L157L|ASPG_ENST00000455920.2_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	109	0	0		WXS	Illumina HiSeq	Phase_I	140	76	0.542857	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	
ETNK2	55224	hgsc.bcm.edu	37	1	204120952	204120952	+	Missense_Mutation	SNP	G	G	T	rs3737655	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:204120952G>T	ENST00000367202.4	-	1	179	c.29C>A	c.(28-30)cCg>cAg	p.P10Q	ETNK2_ENST00000367199.2_5'UTR|ETNK2_ENST00000367201.3_Missense_Mutation_p.P10Q	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	10				P -> Q (in Ref. 1; BAA91793). {ECO:0000305}.	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)	p.P10R(1)		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)			GGACGCGCGCGGCTGAGGGGC	0.756													g|||	677	0.135184	0.177	0.1859	5008	,	,		8895	0.0724		0.1581	False		,,,				2504	0.0838				p.P10Q		Atlas-SNP	.											ETNK2_ENST00000367202,caecum,carcinoma,0,19	ETNK2	48	19	1	Substitution - Missense(1)	central_nervous_system(1)	c.C29A						PASS	.		GLN/PRO	323,2753		11,301,1226	2.0	2.0	2.0		29	2.1	0.3	1	dbSNP_107	2	618,5484		21,576,2454	yes	missense	ETNK2	NM_018208.2	76	32,877,3680	TT,TG,GG		10.1278,10.5007,10.2528	probably-damaging	10/387	204120952	941,8237	1538	3051	4589	SO:0001583	missense	55224	exon1			GCGCGCGGCTGAG	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.29C>A	1.37:g.204120952G>T	ENSP00000356170:p.Pro10Gln	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	11	9	0.818182	NM_018208	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	37	CCDS1442.2	331	0.15155677655677655	96	0.1951219512195122	64	0.17679558011049723	46	0.08041958041958042	125	0.16490765171503957	g	13.99	2.400423	0.42613	0.105007	0.101278	ENSG00000143845	ENST00000367201;ENST00000367202	T;T	0.57907	0.49;0.37	3.04	2.07	0.26955	.	.	.	.	.	T	0.00039	0.0001	L	0.36672	1.1	0.09310	P	0.999999999613206	B;B;B	0.18741	0.021;0.016;0.03	B;B;B	0.22152	0.013;0.007;0.038	T	0.07366	-1.0776	8	0.72032	D	0.01	.	9.01	0.36135	0.0:0.0:0.7782:0.2218	rs3737655	10;10;10	Q9NVF9-3;Q9NVF9;Q9NVF9-2	.;EKI2_HUMAN;.	Q	10	ENSP00000356169:P10Q;ENSP00000356170:P10Q	ENSP00000356169:P10Q	P	-	2	0	ETNK2	202387575	0.982000	0.34865	0.308000	0.25141	0.910000	0.53928	4.274000	0.58921	0.439000	0.26476	0.298000	0.19748	CCG	G|0.858;T|0.142	0.142	strong		0.756	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208	
TTLL2	83887	hgsc.bcm.edu	37	6	167754702	167754702	+	Silent	SNP	C	C	T	rs909546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	94	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	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	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45258457	45258457	+	Silent	SNP	A	A	G	rs8881	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45258457A>G	ENST00000389774.2	+	13	1518	c.1377A>G	c.(1375-1377)gcA>gcG	p.A459A	PRR5-ARHGAP8_ENST00000352766.7_Silent_p.A638A|ARHGAP8_ENST00000356099.6_Silent_p.A428A|ARHGAP8_ENST00000389773.5_Silent_p.A550A|ARHGAP8_ENST00000336963.4_3'UTR|ARHGAP8_ENST00000517296.3_Silent_p.A638A|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.A559A	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	459					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CCCTGATGGCAGCCAGAAGAC	0.557													A|||	242	0.0483227	0.0204	0.0893	5008	,	,		17995	0.001		0.1153	False		,,,				2504	0.0368				p.A550A		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.A1650G						PASS	.	A	,,,	177,4229	115.0+/-153.0	6,165,2032	71.0	60.0	63.0		1377,,1650,1284	-5.6	0.0	22	dbSNP_52	63	1145,7455	235.0+/-267.7	85,975,3240	no	coding-synonymous,utr-3,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	91,1140,5272	GG,GA,AA		13.314,4.0172,10.1645	,,,	459/465,,550/556,428/434	45258457	1322,11684	2203	4300	6503	SO:0001819	synonymous_variant	553158	exon15			GATGGCAGCCAGA	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1377A>G	22.37:g.45258457A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	135	0.061813186813186816	11	0.022357723577235773	34	0.09392265193370165	1	0.0017482517482517483	89	0.11741424802110818	A	3.285	-0.146116	0.06627	0.040172	0.13314	ENSG00000248405	ENST00000515632	.	.	.	2.78	-5.57	0.02521	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.10474	-1.0628	3	.	.	.	.	1.4089	0.02287	0.3695:0.2427:0.2669:0.121	rs8881;rs3171769;rs56598445;rs60182129;rs8881	.	.	.	R	499	.	.	Q	+	2	0	PRR5-ARHGAP8	43637121	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.357000	0.02607	-2.807000	0.00349	-2.545000	0.00179	CAG	A|0.917;G|0.083	0.083	strong		0.557	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
FLRT2	23768	hgsc.bcm.edu	37	14	86089315	86089315	+	Missense_Mutation	SNP	G	G	A	rs17646457	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:86089315G>A	ENST00000330753.4	+	2	2224	c.1457G>A	c.(1456-1458)cGa>cAa	p.R486Q	FLRT2_ENST00000554746.1_Missense_Mutation_p.R486Q	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	486	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q (in dbSNP:rs17646457). {ECO:0000269|PubMed:15489334}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.R486Q(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TTAGAGCCCCGATCCACCTAT	0.522													G|||	594	0.11861	0.0189	0.2118	5008	,	,		17172	0.0605		0.1481	False		,,,				2504	0.2168				p.R486Q		Atlas-SNP	.											FLRT2,NS,carcinoma,0,1	FLRT2	168	1	1	Substitution - Missense(1)	stomach(1)	c.G1457A						scavenged	.	G	GLN/ARG	151,4255	103.0+/-141.5	1,149,2053	149.0	130.0	136.0		1457	2.9	1.0	14	dbSNP_123	136	1287,7313	255.8+/-280.5	107,1073,3120	yes	missense	FLRT2	NM_013231.4	43	108,1222,5173	AA,AG,GG		14.9651,3.4271,11.0564	benign	486/661	86089315	1438,11568	2203	4300	6503	SO:0001583	missense	23768	exon2			AGCCCCGATCCAC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1457G>A	14.37:g.86089315G>A	ENSP00000332879:p.Arg486Gln	Somatic	291	2	0.00687285		WXS	Illumina HiSeq	Phase_I	264	122	0.462121	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	224	0.10256410256410256	13	0.026422764227642278	65	0.17955801104972377	36	0.06293706293706294	110	0.14511873350923482	G	9.487	1.099582	0.20552	0.034271	0.149651	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.56776	0.44;0.44	5.87	2.87	0.33458	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.339988	0.32120	N	0.006545	T	0.00073	0.0002	N	0.19112	0.55	0.28600	P	0.9092117	B	0.11235	0.004	B	0.09377	0.004	T	0.09079	-1.0691	9	0.21540	T	0.41	-5.0916	5.9999	0.19515	0.4962:0.0:0.5038:0.0	rs17646457;rs52800076;rs17646457	486	O43155	FLRT2_HUMAN	Q	486;486;139	ENSP00000332879:R486Q;ENSP00000451050:R486Q	ENSP00000332879:R486Q	R	+	2	0	FLRT2	85159068	1.000000	0.71417	0.989000	0.46669	0.367000	0.29736	3.060000	0.49955	0.865000	0.35603	0.655000	0.94253	CGA	G|0.899;A|0.101	0.101	strong		0.522	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
ZNF236	7776	hgsc.bcm.edu	37	18	74680208	74680208	+	Silent	SNP	C	C	T	rs73968242	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:74680208C>T	ENST00000253159.8	+	31	5649	c.5451C>T	c.(5449-5451)gaC>gaT	p.D1817D	ZNF236_ENST00000320610.9_Silent_p.D1819D	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1817					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)		CGGAGCAGGACGGGGAGGAGC	0.602													C|||	1583	0.316094	0.1808	0.3444	5008	,	,		15252	0.2956		0.4781	False		,,,				2504	0.3333				p.D1817D		Atlas-SNP	.											.	ZNF236	325	.	0			c.C5451T						PASS	.	C		932,3060		115,702,1179	69.0	78.0	75.0		5451	-9.9	0.0	18	dbSNP_130	75	4102,4268		1002,2098,1085	no	coding-synonymous	ZNF236	NM_007345.3		1117,2800,2264	TT,TC,CC		49.0084,23.3467,40.7216		1817/1846	74680208	5034,7328	1996	4185	6181	SO:0001819	synonymous_variant	7776	exon31			GCAGGACGGGGAG	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.5451C>T	18.37:g.74680208C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			C|0.596;T|0.404	0.404	strong		0.602	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
LEFTY1	10637	hgsc.bcm.edu	37	1	226074563	226074563	+	Missense_Mutation	SNP	T	T	G	rs360057	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226074563T>G	ENST00000272134.5	-	4	1044	c.965A>C	c.(964-966)gAc>gCc	p.D322A	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	322			D -> A (in dbSNP:rs360057).		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)					GGGCAGCGAGTCAGTCTCCGA	0.652													t|||	1276	0.254792	0.1407	0.3415	5008	,	,		16775	0.2073		0.3946	False		,,,				2504	0.2526				p.D322A		Atlas-SNP	.											LEFTY1,colon,carcinoma,0,1	LEFTY1	30	1	0			c.A965C						PASS	.	T	ALA/ASP	817,3589	308.8+/-290.8	69,679,1455	40.0	36.0	37.0		965	2.1	0.0	1	dbSNP_79	37	3097,5503	450.7+/-362.5	545,2007,1748	yes	missense	LEFTY1	NM_020997.3	126	614,2686,3203	GG,GT,TT		36.0116,18.5429,30.0938	benign	322/367	226074563	3914,9092	2203	4300	6503	SO:0001583	missense	10637	exon4			AGCGAGTCAGTCT	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.965A>C	1.37:g.226074563T>G	ENSP00000272134:p.Asp322Ala	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	252	121	0.480159	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	638	0.29212454212454214	76	0.15447154471544716	131	0.36187845303867405	122	0.21328671328671328	309	0.4076517150395778	t	0.011	-1.720453	0.00700	0.185429	0.360116	ENSG00000243709	ENST00000272134	T	0.70282	-0.47	4.14	2.09	0.27110	Transforming growth factor-beta, C-terminal (2);	0.418705	0.28146	N	0.016436	T	0.00012	0.0000	N	0.00554	-1.385	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.38714	-0.9648	9	0.21540	T	0.41	.	9.6529	0.39908	0.0:0.1533:0.6867:0.1599	rs360057	322	O75610	LFTY1_HUMAN	A	322	ENSP00000272134:D322A	ENSP00000272134:D322A	D	-	2	0	LEFTY1	224141186	1.000000	0.71417	0.011000	0.14972	0.063000	0.16089	5.788000	0.69020	0.753000	0.32945	-0.672000	0.03802	GAC	T|0.711;G|0.289	0.289	strong		0.652	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
MUC17	140453	hgsc.bcm.edu	37	7	100675976	100675976	+	Missense_Mutation	SNP	G	G	A	rs56103274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100675976G>A	ENST00000306151.4	+	3	1343	c.1279G>A	c.(1279-1281)Gct>Act	p.A427T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	427	59 X approximate tandem repeats.|Ser-rich.		A -> T (in dbSNP:rs56103274).		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)					TGTGACCACTGCTAGTGAAGC	0.463													T|||	1932	0.385783	0.1392	0.3372	5008	,	,		26428	0.5575		0.4871	False		,,,				2504	0.4724				p.A427T		Atlas-SNP	.											.	MUC17	804	.	0			c.G1279A						PASS	.	T	THR/ALA	859,3547		91,677,1435	197.0	204.0	202.0		1279	-2.4	0.0	7	dbSNP_129	202	4212,4388		1028,2156,1116	yes	missense	MUC17	NM_001040105.1	58	1119,2833,2551	AA,AG,GG		48.9767,19.4961,38.9897	benign	427/4494	100675976	5071,7935	2203	4300	6503	SO:0001583	missense	140453	exon3			ACCACTGCTAGTG	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.1279G>A	7.37:g.100675976G>A	ENSP00000302716:p.Ala427Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	891	0.40796703296703296	73	0.1483739837398374	133	0.3674033149171271	307	0.5367132867132867	378	0.49868073878627966	T	9.466	1.094472	0.20471	0.194961	0.489767	ENSG00000169876	ENST00000306151	T	0.02656	4.21	1.22	-2.44	0.06502	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.43956	-0.9359	8	0.08837	T	0.75	.	0.3248	0.00309	0.2857:0.2052:0.2858:0.2233	rs56103274	427	Q685J3	MUC17_HUMAN	T	427	ENSP00000302716:A427T	ENSP00000302716:A427T	A	+	1	0	MUC17	100462696	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.080000	0.00153	-3.488000	0.00154	-2.500000	0.00191	GCT	G|0.600;A|0.400	0.400	strong		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
OXR1	55074	hgsc.bcm.edu	37	8	107754473	107754473	+	Silent	SNP	G	G	A	rs1681904	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:107754473G>A	ENST00000442977.2	+	14	2442	c.2343G>A	c.(2341-2343)gaG>gaA	p.E781E	OXR1_ENST00000521592.1_Silent_p.E26E|OXR1_ENST00000531443.1_Silent_p.E753E|OXR1_ENST00000517566.2_Silent_p.E780E|OXR1_ENST00000297447.6_Silent_p.E150E|OXR1_ENST00000452423.2_Silent_p.E201E|OXR1_ENST00000449762.2_Silent_p.E123E|OXR1_ENST00000312046.6_Silent_p.E746E|OXR1_ENST00000445937.1_Silent_p.E753E	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	781	TLD.				adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TAGCATCTGAGCCACTGAAAG	0.343													G|||	1911	0.381589	0.2057	0.5216	5008	,	,		16724	0.3492		0.4433	False		,,,				2504	0.4898				p.E781E		Atlas-SNP	.											.	OXR1	190	.	0			c.G2343A						PASS	.	G	,,,,,	1065,3341	388.4+/-326.9	123,819,1261	194.0	180.0	185.0		2343,2340,450,369,2259,2238	4.3	1.0	8	dbSNP_89	185	3733,4867	530.5+/-381.8	804,2125,1371	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OXR1	NM_001198532.1,NM_001198533.1,NM_001198534.1,NM_001198535.1,NM_018002.3,NM_181354.4	,,,,,	927,2944,2632	AA,AG,GG		43.407,24.1716,36.8907	,,,,,	781/875,780/874,150/244,123/217,753/847,746/840	107754473	4798,8208	2203	4300	6503	SO:0001819	synonymous_variant	55074	exon14			ATCTGAGCCACTG	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.2343G>A	8.37:g.107754473G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	37	CCDS56548.1	838	0.3836996336996337	100	0.2032520325203252	181	0.5	213	0.3723776223776224	344	0.45382585751978893	G	8.497	0.863313	0.17250	0.241716	0.43407	ENSG00000164830	ENST00000519415	.	.	.	5.46	4.35	0.52113	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.51834	-0.8655	3	.	.	.	-12.3073	6.9569	0.24576	0.2445:0.0:0.7555:0.0	rs1681904;rs11538335;rs17351853;rs1681904	.	.	.	N	425	.	.	S	+	2	0	OXR1	107823649	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.822000	0.39052	2.715000	0.92844	0.563000	0.77884	AGC	G|0.627;A|0.373	0.373	strong		0.343	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
ACSM3	6296	hgsc.bcm.edu	37	16	20802172	20802172	+	Intron	SNP	C	C	T	rs2301770	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:20802172C>T	ENST00000289416.5	+	10	1801				ACSM3_ENST00000567387.1_Intron|ERI2_ENST00000300005.3_Splice_Site_p.G272D|ACSM3_ENST00000450120.2_Intron	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	197	0	0		WXS	Illumina HiSeq	Phase_I	172	90	0.523256	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	
MOV10L1	54456	hgsc.bcm.edu	37	22	50528916	50528916	+	Intron	SNP	C	C	T	rs9617018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50528916C>T	ENST00000262794.5	+	1	180				MOV10L1_ENST00000395843.1_Intron|MOV10L1_ENST00000545383.1_Intron|MOV10L1_ENST00000395858.3_Intron|MOV10L1_ENST00000540615.1_Silent_p.L4L|MOV10L1_ENST00000475190.1_Intron	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1						ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGTCGTTCCTCCCTGTCCGCA	0.617													c|||	825	0.164736	0.0946	0.3127	5008	,	,		15244	0.1944		0.1352	False		,,,				2504	0.1544				p.L4L		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C12T						PASS	.		,,	333,2803		20,293,1255	47.0	49.0	48.0		,12,	0.5	0.0	22	dbSNP_119	48	1056,6108		84,888,2610	no	intron,coding-synonymous,intron	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	104,1181,3865	TT,TC,CC		14.7404,10.6186,13.4854	,,	,4/1166,	50528916	1389,8911	1568	3582	5150	SO:0001627	intron_variant	54456	exon1			GTTCCTCCCTGTC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.97+302C>T	22.37:g.50528916C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_001164105	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.844;T|0.156	0.156	strong		0.617	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
MEP1B	4225	hgsc.bcm.edu	37	18	29795076	29795076	+	Silent	SNP	T	T	C	rs173032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:29795076T>C	ENST00000269202.6	+	12	1658	c.1611T>C	c.(1609-1611)tcT>tcC	p.S537S	MEP1B_ENST00000581447.1_Silent_p.S537S	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	537	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				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						ACAGGCCTTCTAAAGTGGGAA	0.408													C|||	3473	0.69349	0.5522	0.7522	5008	,	,		17000	0.873		0.6859	False		,,,				2504	0.6656				p.S537S		Atlas-SNP	.											.	MEP1B	54	.	0			c.T1611C						PASS	.	C		2009,1661		559,891,385	104.0	102.0	103.0		1611	0.8	1.0	18	dbSNP_79	103	5307,2865		1740,1827,519	no	coding-synonymous	MEP1B	NM_005925.2		2299,2718,904	CC,CT,TT		35.0587,45.2589,38.2199		537/702	29795076	7316,4526	1835	4086	5921	SO:0001819	synonymous_variant	4225	exon12			GCCTTCTAAAGTG	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.1611T>C	18.37:g.29795076T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	NM_005925	B7ZM35|B9EGL6|Q670J1	Silent	SNP	ENST00000269202.6	37	CCDS45846.1																																																																																			T|0.299;C|0.701	0.701	strong		0.408	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
GDF15	9518	hgsc.bcm.edu	37	19	18497141	18497141	+	Missense_Mutation	SNP	T	T	A	rs1059369	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18497141T>A	ENST00000252809.3	+	1	174	c.142T>A	c.(142-144)Tcc>Acc	p.S48T	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	48			S -> T (in dbSNP:rs1059369). {ECO:0000269|PubMed:9326641, ECO:0000269|PubMed:9348093, ECO:0000269|Ref.5}.		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						AGAGTTGCACTCCGAAGACTC	0.637													T|||	1345	0.26857	0.1762	0.3674	5008	,	,		13847	0.4236		0.2475	False		,,,				2504	0.1851				p.S48T		Atlas-SNP	.											.	GDF15	31	.	0			c.T142A						PASS	.	T	THR/SER	803,3603	318.5+/-295.7	80,643,1480	41.0	41.0	41.0		142	-4.9	0.0	19	dbSNP_86	41	2049,6551	355.1+/-329.8	258,1533,2509	yes	missense	GDF15	NM_004864.2	58	338,2176,3989	AA,AT,TT		23.8256,18.2251,21.9283	possibly-damaging	48/309	18497141	2852,10154	2203	4300	6503	SO:0001583	missense	9518	exon1			TTGCACTCCGAAG	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.142T>A	19.37:g.18497141T>A	ENSP00000252809:p.Ser48Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Missense_Mutation	SNP	ENST00000252809.3	37	CCDS12376.1	624	0.2857142857142857	82	0.16666666666666666	122	0.3370165745856354	233	0.40734265734265734	187	0.24670184696569922	T	19.67	3.870402	0.72065	0.182251	0.238256	ENSG00000130513	ENST00000252809	D	0.82167	-1.58	4.67	-4.94	0.03057	.	1.337000	0.05118	N	0.490127	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	P	0.39480	0.675	B	0.37144	0.242	T	0.21280	-1.0250	9	0.10636	T	0.68	.	1.2232	0.01928	0.1384:0.3008:0.2781:0.2827	rs1059369;rs3170465;rs3746177;rs17526140;rs17655466;rs1059369	48	Q99988	GDF15_HUMAN	T	48	ENSP00000252809:S48T	ENSP00000252809:S48T	S	+	1	0	GDF15	18358141	0.000000	0.05858	0.000000	0.03702	0.298000	0.27526	0.038000	0.13862	-1.219000	0.02597	0.260000	0.18958	TCC	T|0.760;N|0.000	.	strong		0.637	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864	
MED13	9969	hgsc.bcm.edu	37	17	60040329	60040329	+	Silent	SNP	C	C	T	rs2278812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	41	0	0		WXS	Illumina HiSeq	Phase_I	48	33	0.6875	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	
NRBP2	340371	hgsc.bcm.edu	37	8	144917880	144917880	+	Silent	SNP	G	G	A	rs72693365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144917880G>A	ENST00000442628.2	-	18	1597	c.1458C>T	c.(1456-1458)gcC>gcT	p.A486A	NRBP2_ENST00000327830.5_Silent_p.A243A|RP11-299M14.2_ENST00000534006.1_RNA	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2											central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCAGGAAGGCGGCCAGCTTCA	0.751													G|||	213	0.0425319	0.0106	0.0504	5008	,	,		11476	0.0109		0.0944	False		,,,				2504	0.0593				p.A486A		Atlas-SNP	.											.	NRBP2	20	.	0			c.C1458T						PASS	.	G		103,4299	79.9+/-118.3	3,97,2101	35.0	34.0	34.0		1458	-5.0	0.2	8	dbSNP_130	34	791,7807	180.8+/-229.6	44,703,3552	no	coding-synonymous	NRBP2	NM_178564.3		47,800,5653	AA,AG,GG		9.1998,2.3398,6.8769		486/502	144917880	894,12106	2201	4299	6500	SO:0001819	synonymous_variant	340371	exon18			GAAGGCGGCCAGC	BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24							19339	protein-coding gene	gene with protein product		615563				14702039	Standard	NM_178564		Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.1458C>T	8.37:g.144917880G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	30	0.681818	NM_178564		Silent	SNP	ENST00000442628.2	37	CCDS34959.2	105	0.04807692307692308	4	0.008130081300813009	25	0.06906077348066299	6	0.01048951048951049	70	0.09234828496042216	G	11.59	1.684044	0.29872	0.023398	0.091998	ENSG00000185189	ENST00000530123	.	.	.	3.8	-5.0	0.03001	.	.	.	.	.	T	0.00608	0.0020	.	.	.	0.23243	P	0.99805051	.	.	.	.	.	.	T	0.19679	-1.0298	3	.	.	.	-27.4645	2.2889	0.04134	0.4716:0.1213:0.2783:0.1288	.	.	.	.	L	78	.	.	P	-	2	0	NRBP2	144989868	0.000000	0.05858	0.212000	0.23672	0.794000	0.44872	-2.313000	0.01126	-1.097000	0.03042	-0.291000	0.09656	CCG	G|0.942;A|0.058	0.058	strong		0.751	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382247.1	NM_178564	
OBSCN	84033	hgsc.bcm.edu	37	1	228564884	228564884	+	Missense_Mutation	SNP	G	G	A	rs56174824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228564884G>A	ENST00000422127.1	+	101	23215	c.23171G>A	c.(23170-23172)cGc>cAc	p.R7724H	OBSCN_ENST00000570156.2_Missense_Mutation_p.R8681H|OBSCN_ENST00000366707.4_Missense_Mutation_p.R5358H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7724	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)				AAGGGCCTGCGCCACCCGCAC	0.692													G|||	705	0.140775	0.0983	0.0432	5008	,	,		16390	0.3085		0.0974	False		,,,				2504	0.1391				p.R8681H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G26042A						PASS	.	G	HIS/ARG	400,3686		14,372,1657	11.0	15.0	14.0		23171	-2.4	1.0	1	dbSNP_129	14	712,7690		31,650,3520	yes	missense	OBSCN	NM_001098623.1	29	45,1022,5177	AA,AG,GG		8.4742,9.7895,8.9045	benign	7724/7969	228564884	1112,11376	2043	4201	6244	SO:0001583	missense	84033	exon112			GCCTGCGCCACCC	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.23171G>A	1.37:g.228564884G>A	ENSP00000409493:p.Arg7724His	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	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	350	0.16025641025641027	64	0.13008130081300814	21	0.058011049723756904	190	0.3321678321678322	75	0.09894459102902374	G	16.84	3.232784	0.58777	0.097895	0.084742	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.40476	1.03;1.03	4.82	-2.4	0.06583	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	91.976500	0.00166	N	0.000001	T	0.00012	0.0000	N	0.13098	0.295	0.09310	P	0.9999999999999908	B	0.02656	0.0	B	0.04013	0.001	T	0.28586	-1.0039	9	0.20519	T	0.43	.	11.4116	0.49929	0.7104:0.0:0.2896:0.0	rs56174824	7724	Q5VST9	OBSCN_HUMAN	H	7724;5358	ENSP00000409493:R7724H;ENSP00000355668:R5358H	ENSP00000355668:R5358H	R	+	2	0	OBSCN	226631507	0.595000	0.26857	0.990000	0.47175	0.541000	0.35023	1.120000	0.31271	-0.332000	0.08489	-0.671000	0.03813	CGC	G|0.852;A|0.148	0.148	strong		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
DOT1L	84444	hgsc.bcm.edu	37	19	2226676	2226676	+	Missense_Mutation	SNP	G	G	A	rs3815308	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2226676G>A	ENST00000398665.3	+	27	4192	c.4156G>A	c.(4156-4158)Ggc>Agc	p.G1386S		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1386			G -> S (in dbSNP:rs3815308).		histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		GGGCAGCCGCGGCAAGGAGGC	0.726													G|||	1130	0.225639	0.0356	0.3069	5008	,	,		10935	0.1825		0.4692	False		,,,				2504	0.2188				p.G1386S		Atlas-SNP	.											.	DOT1L	205	.	0			c.G4156A						PASS	.	G	SER/GLY	373,3611		37,299,1656	6.0	9.0	8.0		4156	0.4	0.0	19	dbSNP_107	8	3524,4624		845,1834,1395	no	missense	DOT1L	NM_032482.2	56	882,2133,3051	AA,AG,GG		43.2499,9.3624,32.1217	benign	1386/1538	2226676	3897,8235	1992	4074	6066	SO:0001583	missense	84444	exon27			AGCCGCGGCAAGG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.4156G>A	19.37:g.2226676G>A	ENSP00000381657:p.Gly1386Ser	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	602	0.27564102564102566	19	0.03861788617886179	123	0.3397790055248619	113	0.19755244755244755	347	0.4577836411609499	G	0.015	-1.555274	0.00918	0.093624	0.432499	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000457590	T;T	0.28454	2.06;1.61	4.28	0.43	0.16515	.	0.858235	0.09817	N	0.751980	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.24533	0.105;0.012	B;B	0.12837	0.003;0.008	T	0.46303	-0.9201	9	0.87932	D	0	-4.2319	10.6441	0.45610	0.3992:0.0:0.6008:0.0	rs3815308;rs56900395	1386;1386	Q8TEK3;Q8TEK3-2	DOT1L_HUMAN;.	S	1386;1386;266	ENSP00000381657:G1386S;ENSP00000407411:G266S	ENSP00000221482:G1386S	G	+	1	0	DOT1L	2177676	0.363000	0.24989	0.007000	0.13788	0.002000	0.02628	1.858000	0.39408	-0.020000	0.14032	-1.134000	0.01955	GGC	G|0.722;A|0.278	0.278	strong		0.726	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
RBFA	79863	hgsc.bcm.edu	37	18	77805856	77805856	+	Missense_Mutation	SNP	A	A	C	rs3744872	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:77805856A>C	ENST00000306735.5	+	7	871	c.733A>C	c.(733-735)Aac>Cac	p.N245H	RP11-795F19.5_ENST00000564012.1_Intron|RBFA_ENST00000262197.7_Silent_p.S216S|RP11-795F19.5_ENST00000569722.1_Intron	NM_024805.2	NP_079081.2	Q8N0V3	RBFA_HUMAN	ribosome binding factor A (putative)	245			N -> H (in dbSNP:rs3744872). {ECO:0000269|PubMed:15489334}.		rRNA processing (GO:0006364)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						TGAGGCGCTCAACAAGCAGAT	0.577													A|||	1952	0.389776	0.2458	0.4697	5008	,	,		19105	0.4821		0.3161	False		,,,				2504	0.5082				p.N245H		Atlas-SNP	.											.	RBFA	27	.	0			c.A733C						PASS	.	A	,HIS/ASN	1012,3394	370.3+/-319.5	124,764,1315	66.0	74.0	71.0		648,733	2.1	1.0	18	dbSNP_107	71	2528,6072	410.2+/-350.1	368,1792,2140	yes	coding-synonymous,missense	RBFA	NM_001171967.1,NM_024805.2	,68	492,2556,3455	CC,CA,AA		29.3953,22.9687,27.2182	,possibly-damaging	216/243,245/344	77805856	3540,9466	2203	4300	6503	SO:0001583	missense	79863	exon7			GCGCTCAACAAGC	BC014195	CCDS12021.1, CCDS54194.1	18q23	2010-10-21	2010-10-21	2010-10-21	ENSG00000101546	ENSG00000101546			26120	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 22"""	C18orf22		12477932	Standard	NM_024805		Approved	FLJ21172, HsT169	uc002lns.3	Q8N0V3	OTTHUMG00000132923	ENST00000306735.5:c.733A>C	18.37:g.77805856A>C	ENSP00000305696:p.Asn245His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_024805	Q6PF07|Q8WZ65|Q9H776	Missense_Mutation	SNP	ENST00000306735.5	37	CCDS12021.1	801	0.36675824175824173	140	0.2845528455284553	158	0.43646408839779005	272	0.4755244755244755	231	0.30474934036939316	A	9.760	1.169886	0.21621	0.229687	0.293953	ENSG00000101546	ENST00000306735	T	0.27104	1.69	4.78	2.11	0.27256	.	0.540708	0.18128	N	0.150828	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999114157	P	0.42735	0.788	B	0.37731	0.257	T	0.49263	-0.8958	8	0.40728	T	0.16	-21.9528	10.1421	0.42740	0.6149:0.3851:0.0:0.0	rs3744872;rs17846552;rs17859627;rs59885162;rs3744872	245	Q8N0V3	RBFA_HUMAN	H	245	ENSP00000305696:N245H	ENSP00000305696:N245H	N	+	1	0	RBFA	75906844	1.000000	0.71417	0.983000	0.44433	0.175000	0.22909	1.650000	0.37292	0.741000	0.32674	0.533000	0.62120	AAC	A|0.688;C|0.312	0.312	strong		0.577	RBFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256436.2	NM_024805	
OR52W1	120787	hgsc.bcm.edu	37	11	6220596	6220596	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6220596G>C	ENST00000311352.2	+	1	221	c.143G>C	c.(142-144)gGa>gCa	p.G48A	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGGCAATGGAGCACTGCCG	0.562																																					p.G48A		Atlas-SNP	.											.	OR52W1	33	.	0			c.G143C						PASS	.						58.0	51.0	53.0					11																	6220596		2201	4296	6497	SO:0001583	missense	120787	exon1			GCAATGGAGCACT	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"""GPCR / Class A : Olfactory receptors"""	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.143G>C	11.37:g.6220596G>C	ENSP00000309673:p.Gly48Ala	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	G	8.442	0.851009	0.17034	.	.	ENSG00000175485	ENST00000311352	T	0.02050	4.48	5.92	2.93	0.34026	GPCR, rhodopsin-like superfamily (1);	0.580151	0.13011	N	0.420892	T	0.02380	0.0073	L	0.41492	1.28	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.44757	-0.9307	10	0.25106	T	0.35	.	7.8661	0.29539	0.0:0.307:0.328:0.365	.	48	Q6IF63	O52W1_HUMAN	A	48	ENSP00000309673:G48A	ENSP00000309673:G48A	G	+	2	0	OR52W1	6177172	0.000000	0.05858	0.759000	0.31340	0.903000	0.53119	-0.313000	0.08103	0.819000	0.34492	0.655000	0.94253	GGA	.	.	none		0.562	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178	
ETAA1	54465	hgsc.bcm.edu	37	2	67630980	67630980	+	Missense_Mutation	SNP	G	G	A	rs3770657	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:67630980G>A	ENST00000272342.5	+	5	1296	c.1166G>A	c.(1165-1167)aGt>aAt	p.S389N	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	389			S -> N (in dbSNP:rs3770657). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)		p.S389N(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TTACTAGGTAGTGAACCTTTT	0.353													A|||	3670	0.732827	0.8699	0.719	5008	,	,		19009	0.5685		0.7296	False		,,,				2504	0.7301				p.S389N		Atlas-SNP	.											ETAA1,NS,carcinoma,+1,2	ETAA1	88	2	1	Substitution - Missense(1)	stomach(1)	c.G1166A						PASS	.	A	ASN/SER	3752,654	274.9+/-272.2	1602,548,53	93.0	98.0	96.0		1166	3.4	0.6	2	dbSNP_107	96	6148,2446	403.5+/-347.8	2213,1722,362	yes	missense	ETAA1	NM_019002.3	46	3815,2270,415	AA,AG,GG		28.4617,14.8434,23.8462	benign	389/927	67630980	9900,3100	2203	4297	6500	SO:0001583	missense	54465	exon5			TAGGTAGTGAACC	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1166G>A	2.37:g.67630980G>A	ENSP00000272342:p.Ser389Asn	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	165	78	0.472727	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	1572	0.7197802197802198	430	0.8739837398373984	265	0.7320441988950276	325	0.5681818181818182	552	0.7282321899736148	A	0.005	-2.185214	0.00305	0.851566	0.715383	ENSG00000143971	ENST00000272342	T	0.14516	2.5	5.77	3.4	0.38934	.	0.289310	0.38111	N	0.001815	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35151	-0.9800	9	0.02654	T	1	-33.7308	8.8244	0.35045	0.7808:0.0:0.2192:0.0	rs3770657;rs56442704;rs59377126;rs3770657	389	Q9NY74	ETAA1_HUMAN	N	389	ENSP00000272342:S389N	ENSP00000272342:S389N	S	+	2	0	ETAA1	67484484	1.000000	0.71417	0.567000	0.28434	0.043000	0.13939	2.213000	0.42844	0.125000	0.18397	-0.254000	0.11334	AGT	G|0.257;N|0.000	.	strong		0.353	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
FAM35A	54537	hgsc.bcm.edu	37	10	88911841	88911841	+	Missense_Mutation	SNP	A	A	G	rs77879311	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:88911841A>G	ENST00000298784.1	+	3	844	c.730A>G	c.(730-732)Agt>Ggt	p.S244G	RN7SL733P_ENST00000582253.1_RNA|FAM35A_ENST00000298786.4_Missense_Mutation_p.S244G	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	244										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						AGAATTTCTCAGTATAATTAC	0.383													A|||	747	0.149161	0.2466	0.1009	5008	,	,		19063	0.0218		0.169	False		,,,				2504	0.1626				p.S244G	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											.	FAM35A	48	.	0			c.A730G						PASS	.	A	GLY/SER	910,3496		95,720,1388	30.0	30.0	30.0		730	4.1	0.9	10	dbSNP_131	30	1339,7255		95,1149,3053	no	missense	FAM35A	NM_019054.2	56	190,1869,4441	GG,GA,AA		15.5806,20.6537,17.3	probably-damaging	244/836	88911841	2249,10751	2203	4297	6500	SO:0001583	missense	54537	exon3			TTTCTCAGTATAA	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.730A>G	10.37:g.88911841A>G	ENSP00000298784:p.Ser244Gly	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	137	76	0.554745	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	283	0.1295787545787546	99	0.20121951219512196	39	0.10773480662983426	10	0.017482517482517484	135	0.17810026385224276	a	16.76	3.211731	0.58452	0.206537	0.155806	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.30714	1.53;1.52;1.52	4.09	4.09	0.47781	.	0.268115	0.31963	N	0.006794	T	0.00039	0.0001	M	0.71581	2.175	0.29511	P	0.8541799999999999	D	0.60160	0.987	P	0.61533	0.89	T	0.06661	-1.0814	9	0.72032	D	0.01	-3.893	8.8322	0.35091	0.8326:0.0:0.0:0.1674	.	244	Q86V20	FA35A_HUMAN	G	244	ENSP00000298786:S244G;ENSP00000298784:S244G;ENSP00000351064:S244G	ENSP00000298784:S244G	S	+	1	0	FAM35A	88901821	1.000000	0.71417	0.854000	0.33618	0.963000	0.63663	4.382000	0.59594	1.733000	0.51620	0.438000	0.28831	AGT	A|0.850;G|0.150	0.150	strong		0.383	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
KAL1	3730	hgsc.bcm.edu	37	X	8503641	8503641	+	Silent	SNP	G	G	A	rs809446	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:8503641G>A	ENST00000262648.3	-	12	1982	c.1833C>T	c.(1831-1833)atC>atT	p.I611I	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	611	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						CGGAAGGCAGGATCTGGGACT	0.488													G|||	1819	0.481854	0.2307	0.3458	3775	,	,		14845	0.506		0.505	False		,,,				2504	0.2618				p.I611I		Atlas-SNP	.											.	KAL1	78	.	0			c.C1833T						PASS	.	G		1347,2488		196,756,199,680,372	158.0	116.0	130.0		1833	-0.4	1.0	X	dbSNP_86	130	4483,2245		1086,1063,1248,279,624	no	coding-synonymous	KAL1	NM_000216.2		1282,1819,1447,959,996	AA,AG,A,GG,G		33.368,35.1239,44.8073		611/681	8503641	5830,4733	2203	4300	6503	SO:0001819	synonymous_variant	3730	exon12			AGGCAGGATCTGG		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1833C>T	X.37:g.8503641G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	197	194	0.984772	NM_000216	B2RPF8	Silent	SNP	ENST00000262648.3	37	CCDS14130.1																																																																																			G|0.471;0|0.003	.	strong		0.488	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
SON	6651	hgsc.bcm.edu	37	21	34924243	34924243	+	Silent	SNP	T	T	C	rs16990760	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:34924243T>C	ENST00000356577.4	+	3	3181	c.2706T>C	c.(2704-2706)gaT>gaC	p.D902D	SON_ENST00000381679.4_Silent_p.D902D|SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Silent_p.D902D|SON_ENST00000290239.6_Silent_p.D902D	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	902					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						GTACCCAAGATTCTGCTATGT	0.478													T|||	903	0.180312	0.0318	0.2435	5008	,	,		23576	0.1657		0.3101	False		,,,				2504	0.2178				p.D902D		Atlas-SNP	.											SON_ENST00000300278,NS,adenoma,0,2	SON	343	2	0			c.T2706C						PASS	.	T	,	333,4073	175.5+/-204.9	14,305,1884	67.0	66.0	67.0		2706,2706	1.9	1.0	21	dbSNP_123	67	2423,6177	400.5+/-346.8	335,1753,2212	no	coding-synonymous,coding-synonymous	SON	NM_032195.1,NM_138927.1	,	349,2058,4096	CC,CT,TT		28.1744,7.5579,21.1902	,	902/2304,902/2427	34924243	2756,10250	2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			CCAAGATTCTGCT	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.2706T>C	21.37:g.34924243T>C		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	243	106	0.436214	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	37	CCDS13629.1																																																																																			T|0.786;C|0.214	0.214	strong		0.478	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
MUC5B	727897	hgsc.bcm.edu	37	11	1264183	1264183	+	Missense_Mutation	SNP	G	G	A	rs34739266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1264183G>A	ENST00000529681.1	+	31	6131	c.6073G>A	c.(6073-6075)Gcc>Acc	p.A2025T	MUC5B_ENST00000447027.1_Missense_Mutation_p.A2028T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2025	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.		A -> T (in dbSNP:rs34739266). {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)		AGTGCTTACCGCCACGGCCAC	0.642													g|||	427	0.0852636	0.0325	0.0908	5008	,	,		17764	0.0208		0.1421	False		,,,				2504	0.1605				p.A2025T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G6073A						PASS	.	A	THR/ALA	188,4028		9,170,1929	136.0	163.0	154.0		6073	-1.7	0.0	11	dbSNP_134	154	1261,7159		92,1077,3041	no	missense	MUC5B	NM_002458.2	58	101,1247,4970	AA,AG,GG		14.9762,4.4592,11.4672	benign	2025/5763	1264183	1449,11187	2108	4210	6318	SO:0001583	missense	727897	exon31			CTTACCGCCACGG	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.6073G>A	11.37:g.1264183G>A	ENSP00000436812:p.Ala2025Thr	Somatic	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	341	167	0.489736	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	152	0.0695970695970696	12	0.024390243902439025	34	0.09392265193370165	9	0.015734265734265736	97	0.1279683377308707	g	4.339	0.062304	0.08388	0.044592	0.149762	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.16457	2.34;2.5	1.72	-1.71	0.08133	.	.	.	.	.	T	0.00039	0.0001	N	0.00368	-1.59	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44421	-0.9329	9	0.87932	D	0	.	6.783	0.23657	0.6669:0.0:0.3331:0.0	rs34739266;rs61867559	2718;2028	A7Y9J9;E9PBJ0	.;.	T	2025;2028;2026;2095	ENSP00000436812:A2025T;ENSP00000415793:A2028T	ENSP00000343037:A2026T	A	+	1	0	MUC5B	1220759	0.021000	0.18746	0.000000	0.03702	0.001000	0.01503	0.082000	0.14847	-1.757000	0.01316	-2.358000	0.00240	GCC	G|0.500;A|0.500	0.500	weak		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
GTF3C6	112495	hgsc.bcm.edu	37	6	111288941	111288941	+	Missense_Mutation	SNP	T	T	C	rs41289884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:111288941T>C	ENST00000329970.7	+	6	800	c.590T>C	c.(589-591)aTa>aCa	p.I197T	GTF3C6_ENST00000480191.1_3'UTR|AL357515.1_ENST00000583422.1_RNA	NM_138408.3	NP_612417.1	Q969F1	TF3C6_HUMAN	general transcription factor IIIC, polypeptide 6, alpha 35kDa	197					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			NS(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(87;0.00328)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|Colorectal(196;0.0466)|all_epithelial(87;0.0575)		OV - Ovarian serous cystadenocarcinoma(136;0.105)|all cancers(137;0.179)|Epithelial(106;0.186)		CTTATTGATATACCTTCTGAG	0.368													T|||	168	0.0335463	0.0008	0.0202	5008	,	,		17242	0.0119		0.0298	False		,,,				2504	0.1135				p.I197T		Atlas-SNP	.											.	GTF3C6	14	.	0			c.T590C						PASS	.	T	THR/ILE	40,4366	42.3+/-75.8	1,38,2164	93.0	96.0	95.0		590	0.0	0.0	6	dbSNP_127	95	326,8274	114.8+/-174.7	2,322,3976	yes	missense	GTF3C6	NM_138408.3	89	3,360,6140	CC,CT,TT		3.7907,0.9079,2.8141	benign	197/214	111288941	366,12640	2203	4300	6503	SO:0001583	missense	112495	exon6			TTGATATACCTTC	AK057977	CCDS5087.1	6q21	2010-03-23	2007-07-26	2007-07-26	ENSG00000155115	ENSG00000155115		"""General transcription factors"""	20872	protein-coding gene	gene with protein product		611784	"""chromosome 6 open reading frame 51"""	C6orf51		17409385	Standard	NM_138408		Approved	bA397G5.3, TFIIIC35	uc003pum.3	Q969F1	OTTHUMG00000015370	ENST00000329970.7:c.590T>C	6.37:g.111288941T>C	ENSP00000357863:p.Ile197Thr	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	213	103	0.483568	NM_138408	Q5VXN2	Missense_Mutation	SNP	ENST00000329970.7	37	CCDS5087.1	38	0.0173992673992674	2	0.0040650406504065045	6	0.016574585635359115	9	0.015734265734265736	21	0.027704485488126648	t	1.594	-0.528260	0.04112	0.009079	0.037907	ENSG00000155115	ENST00000329970	.	.	.	5.01	0.00227	0.14049	.	1.036740	0.07541	N	0.913832	T	0.05135	0.0137	N	0.17674	0.51	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35400	-0.9790	9	0.02654	T	1	-21.1238	5.3285	0.15920	0.0:0.2684:0.2183:0.5134	rs41289884;rs61733790	197	Q969F1	TF3C6_HUMAN	T	197	.	ENSP00000357863:I197T	I	+	2	0	GTF3C6	111395634	0.001000	0.12720	0.014000	0.15608	0.762000	0.43233	0.357000	0.20199	0.188000	0.20168	0.402000	0.26972	ATA	T|0.976;C|0.024	0.024	strong		0.368	GTF3C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041820.1	NM_138408	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417222	105417222	+	Silent	SNP	C	C	T	rs2013274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105417222C>T	ENST00000333244.5	-	7	4685	c.4566G>A	c.(4564-4566)aaG>aaA	p.K1522K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1522						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	0.617													.|||	1136	0.226837	0.0711	0.2709	5008	,	,		16148	0.0575		0.4751	False		,,,				2504	0.3252				p.K1522K		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4566A						PASS	.	C		164,3668		39,86,1791	141.0	99.0	113.0		4566	-0.7	0.0	14	dbSNP_92	113	1828,6008		704,420,2794	no	coding-synonymous	AHNAK2	NM_138420.2		743,506,4585	TT,TC,CC		23.3282,4.2797,17.0723		1522/5796	105417222	1992,9676	1916	3918	5834	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.4566G>A	14.37:g.105417222C>T		Somatic	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.851;T|0.149	0.149	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
FAM90A1	55138	hgsc.bcm.edu	37	12	8377346	8377346	+	Missense_Mutation	SNP	A	A	C	rs201155866		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8377346A>C	ENST00000538603.1	-	4	641	c.83T>G	c.(82-84)gTt>gGt	p.V28G	FAM90A1_ENST00000307435.6_Missense_Mutation_p.V28G	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	28							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.V28G(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		CCTTGGCCCAACTGGGGCCCT	0.647																																					p.V28G		Atlas-SNP	.											FAM90A1,NS,neuroblastoma,0,2	FAM90A1	68	2	1	Substitution - Missense(1)	skin(1)	c.T83G						scavenged	.						12.0	16.0	14.0					12																	8377346		2190	4271	6461	SO:0001583	missense	55138	exon4			GGCCCAACTGGGG	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.83T>G	12.37:g.8377346A>C	ENSP00000445418:p.Val28Gly	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	40	12	0.3	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	6.185	0.402301	0.11696	.	.	ENSG00000171847	ENST00000307435;ENST00000538603	T;T	0.14144	2.53;2.53	0.706	-1.41	0.08941	.	.	.	.	.	T	0.05960	0.0155	N	0.03608	-0.345	0.09310	N	1	P	0.45531	0.86	P	0.44561	0.453	T	0.20638	-1.0269	8	0.87932	D	0	-0.878	.	.	.	.	28	Q86YD7	F90A1_HUMAN	G	28	ENSP00000307798:V28G;ENSP00000445418:V28G	ENSP00000307798:V28G	V	-	2	0	FAM90A1	8268613	0.040000	0.19996	0.002000	0.10522	0.081000	0.17604	-1.127000	0.03251	-1.039000	0.03275	-1.131000	0.01979	GTT	.	.	weak		0.647	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
ANG	283	hgsc.bcm.edu	37	14	21161931	21161931	+	Missense_Mutation	SNP	A	A	G	rs121909541		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21161931A>G	ENST00000336811.6	+	2	808	c.208A>G	c.(208-210)Att>Gtt	p.I70V	ANG_ENST00000554073.1_Intron|AL163636.6_ENST00000553909.1_Intron|RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000555597.1_Intron|ANG_ENST00000397990.4_Missense_Mutation_p.I70V|RNASE4_ENST00000555835.1_Intron|RNASE4_ENST00000397995.2_Intron|RNASE4_ENST00000304704.4_Intron	NM_001145.4	NP_001136.1	P03950	ANGI_HUMAN	angiogenin, ribonuclease, RNase A family, 5	70			I -> V (in some ALS9 patients; pathogenicity uncertain; reduced ribonucleolytic activity; moderate reduction of thermal stability). {ECO:0000269|PubMed:16501576, ECO:0000269|PubMed:18087731}.		actin filament polymerization (GO:0030041)|activation of phospholipase A2 activity (GO:0032431)|activation of phospholipase C activity (GO:0007202)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|cell communication (GO:0007154)|cell death (GO:0008219)|cell migration (GO:0016477)|diacylglycerol biosynthetic process (GO:0006651)|homeostatic process (GO:0042592)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oocyte maturation (GO:0001556)|ovarian follicle development (GO:0001541)|placenta development (GO:0001890)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein secretion (GO:0050714)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|RNA phosphodiester bond hydrolysis (GO:0090501)|rRNA transcription (GO:0009303)	angiogenin-PRI complex (GO:0032311)|basal lamina (GO:0005605)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	actin binding (GO:0003779)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|heparin binding (GO:0008201)|peptide binding (GO:0042277)|receptor binding (GO:0005102)|ribonuclease activity (GO:0004540)|rRNA binding (GO:0019843)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)	5	all_cancers(95;0.00387)	all_cancers(140;0.196)|all_epithelial(140;0.156)	Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	OV - Ovarian serous cystadenocarcinoma(311;3.25e-17)|GBM - Glioblastoma multiforme(265;5.56e-07)		CAACACATTTATTCATGGCAA	0.478													A|||	1	0.000199681	0.0	0.0	5008	,	,		21764	0.0		0.001	False		,,,				2504	0.0				p.I70V		Atlas-SNP	.											.	ANG	8	.	0			c.A208G	GRCh37	CM060832	ANG	M	rs121909541	PASS	.	A	VAL/ILE,VAL/ILE,,	2,4404	4.2+/-10.8	0,2,2201	118.0	100.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	208,208,,	-3.4	0.8	14	dbSNP_133	106	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,intron,intron	ANG,RNASE4	NM_001097577.2,NM_001145.4,NM_002937.3,NM_194431.1	29,29,,	0,7,6496	GG,GA,AA		0.0581,0.0454,0.0538	benign,benign,,	70/148,70/148,,	21161931	7,12999	2203	4300	6503	SO:0001583	missense	283	exon2			ACATTTATTCATG		CCDS9554.1	14q11.1-q11.2	2014-09-17			ENSG00000214274	ENSG00000214274	3.1.27.-	"""Ribonucleases, RNase A"""	483	protein-coding gene	gene with protein product		105850				1978563	Standard	NM_001145		Approved	RNASE5	uc001vxw.4	P03950	OTTHUMG00000029576	ENST00000336811.6:c.208A>G	14.37:g.21161931A>G	ENSP00000336762:p.Ile70Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_001097577	Q05CV1|Q53X86|Q6P5T2|Q8WXE7	Missense_Mutation	SNP	ENST00000336811.6	37	CCDS9554.1	.	.	.	.	.	.	.	.	.	.	A	1.031	-0.681810	0.03353	4.54E-4	5.81E-4	ENSG00000214274	ENST00000336811;ENST00000397990	D;D	0.95788	-3.81;-3.81	4.73	-3.36	0.04913	Ribonuclease A, domain (4);	0.109560	0.31392	N	0.007721	D	0.88347	0.6412	N	0.25332	0.735	0.58432	A	0.999999	B	0.29508	0.246	B	0.30646	0.118	T	0.78914	-0.2016	9	0.15066	T	0.55	.	11.1811	0.48629	0.3918:0.0:0.6082:0.0	.	70	P03950	ANGI_HUMAN	V	70	ENSP00000336762:I70V;ENSP00000381077:I70V	ENSP00000336762:I70V	I	+	1	0	ANG	20231771	0.994000	0.37717	0.846000	0.33378	0.093000	0.18481	0.112000	0.15479	-0.882000	0.03987	-1.231000	0.01572	ATT	A|0.999;G|0.001	0.001	strong		0.478	ANG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073731.3	NM_001097577	
KIR3DL2	3812	hgsc.bcm.edu	37	19	55378008	55378008	+	Missense_Mutation	SNP	C	C	T	rs3745902	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55378008C>T	ENST00000326321.3	+	9	1223	c.1190C>T	c.(1189-1191)aCg>aTg	p.T397M	KIR3DL2_ENST00000270442.5_Missense_Mutation_p.T380M|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.T397M|RNU6-222P_ENST00000362438.1_RNA	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	397			T -> M (in dbSNP:rs3745902).		cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		CAGGAGGTGACGTACGCACAG	0.498													.|||	1312	0.261981	0.1051	0.3012	5008	,	,		18934	0.2778		0.3002	False		,,,				2504	0.3906				p.T397M		Atlas-SNP	.											.	KIR3DL2	55	.	0			c.C1190T						PASS	.	C	MET/THR	602,3804	263.4+/-265.5	36,530,1637	273.0	261.0	265.0		1190	0.5	0.0	19	dbSNP_107	265	2541,6059	415.3+/-351.7	355,1831,2114	yes	missense	KIR3DL2	NM_006737.3	81	391,2361,3751	TT,TC,CC		29.5465,13.6632,24.1658	benign	397/456	55378008	3143,9863	2203	4300	6503	SO:0001583	missense	3812	exon9			AGGTGACGTACGC	L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.1190C>T	19.37:g.55378008C>T	ENSP00000325525:p.Thr397Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_006737	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	552	0.25274725274725274	55	0.11178861788617886	123	0.3397790055248619	158	0.2762237762237762	216	0.2849604221635884	C	9.767	1.171560	0.21704	0.136632	0.295465	ENSG00000167633;ENSG00000240403;ENSG00000240403	ENST00000402254;ENST00000326321;ENST00000270442	T;T;T	0.00563	6.9;6.83;6.58	1.59	0.458	0.16670	.	.	.	.	.	T	0.00012	0.0000	M	0.87758	2.905	0.80722	P	0.0	D;D;B	0.65815	0.995;0.991;0.21	P;P;B	0.60886	0.88;0.8;0.03	T	0.49133	-0.8971	8	0.62326	D	0.03	.	5.8218	0.18532	0.0:0.6619:0.3381:0.0	rs3745902;rs52812816;rs56575421;rs60362316;rs3745902	380;397;397	Q95366;P43630;F6QF33	.;KI3L2_HUMAN;.	M	397;397;380	ENSP00000384528:T397M;ENSP00000325525:T397M;ENSP00000270442:T380M	ENSP00000384528:T397M	T	+	2	0	KIR3DL1;KIR3DL2	60069820	0.034000	0.19679	0.007000	0.13788	0.019000	0.09904	-0.389000	0.07342	0.049000	0.15920	-0.554000	0.04202	ACG	C|0.756;T|0.244	0.244	strong		0.498	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1		
PAX7	5081	hgsc.bcm.edu	37	1	19027239	19027239	+	Silent	SNP	A	A	G	rs2743201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19027239A>G	ENST00000375375.3	+	6	1477	c.879A>G	c.(877-879)ccA>ccG	p.P293P	PAX7_ENST00000400661.3_Silent_p.P291P|PAX7_ENST00000420770.2_Silent_p.P293P	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	293					anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		GAGGCTTCCCACCCACCGGCA	0.667			T	FOXO1A	alveolar rhabdomyosarcoma								G|||	2447	0.488618	0.643	0.3876	5008	,	,		14149	0.6042		0.2575	False		,,,				2504	0.4703				p.P293P		Atlas-SNP	.		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	PAX7_ENST00000420770,NS,carcinoma,0,3	PAX7	127	3	0			c.A879G						PASS	.	G	,,	2593,1813	519.1+/-369.9	761,1071,371	43.0	38.0	40.0		879,879,873	-9.6	0.1	1	dbSNP_100	40	2246,6354	700.1+/-405.1	308,1630,2362	no	coding-synonymous,coding-synonymous,coding-synonymous	PAX7	NM_001135254.1,NM_002584.2,NM_013945.2	,,	1069,2701,2733	GG,GA,AA		26.1163,41.1484,37.2059	,,	293/506,293/521,291/519	19027239	4839,8167	2203	4300	6503	SO:0001819	synonymous_variant	5081	exon6			CTTCCCACCCACC	X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709		"""Paired boxes"", ""Homeoboxes / PRD class"""	8621	protein-coding gene	gene with protein product		167410	"""paired box gene 7"""			7981748, 8431641	Standard	NM_001135254		Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000375375.3:c.879A>G	1.37:g.19027239A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	183	83	0.453552	NM_002584	E9PFV9|Q0VA99|Q2PJS5	Silent	SNP	ENST00000375375.3	37	CCDS186.1																																																																																			A|0.579;G|0.421	0.421	strong		0.667	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584	
RPTN	126638	hgsc.bcm.edu	37	1	152129115	152129115	+	Missense_Mutation	SNP	T	T	C	rs113327860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152129115T>C	ENST00000316073.3	-	3	524	c.460A>G	c.(460-462)Aga>Gga	p.R154G		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	154	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TGGGAATCTCTGTCTTGTCTC	0.517																																					p.R154G		Atlas-SNP	.											RPTN,NS,carcinoma,0,2	RPTN	123	2	0			c.A460G						scavenged	.	T	GLY/ARG	3,3133		0,3,1565	564.0	480.0	505.0		460	-9.3	0.0	1	dbSNP_132	505	20,7144		0,20,3562	no	missense	RPTN	NM_001122965.1	125	0,23,5127	CC,CT,TT		0.2792,0.0957,0.2233	probably-damaging	154/785	152129115	23,10277	1568	3582	5150	SO:0001583	missense	126638	exon3			AATCTCTGTCTTG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.460A>G	1.37:g.152129115T>C	ENSP00000317895:p.Arg154Gly	Somatic	311	1	0.00321543		WXS	Illumina HiSeq	Phase_I	280	34	0.121429	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.299774	0.40694	9.57E-4	0.002792	ENSG00000215853	ENST00000316073	T	0.14391	2.51	5.18	-9.31	0.00646	.	1.021040	0.07904	U	0.973153	T	0.04861	0.0131	M	0.77820	2.39	0.09310	N	1	P	0.41313	0.745	B	0.38562	0.276	T	0.07712	-1.0758	10	0.41790	T	0.15	0.1512	5.4246	0.16419	0.1067:0.1464:0.5432:0.2037	.	154	Q6XPR3	RPTN_HUMAN	G	154	ENSP00000317895:R154G	ENSP00000317895:R154G	R	-	1	2	RPTN	150395739	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.068000	0.14531	-1.180000	0.02734	-0.517000	0.04412	AGA	T|0.940;C|0.060	0.060	strong		0.517	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
MRC1	4360	hgsc.bcm.edu	37	10	17891705	17891705	+	Missense_Mutation	SNP	A	A	G	rs1926736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	0	0	.		WXS	Illumina HiSeq	Phase_I	236	234	0.991525	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		
SRP72	6731	hgsc.bcm.edu	37	4	57361553	57361553	+	Silent	SNP	A	A	G	rs34419325	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	223	110	0.493274	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		
RBAK	57786	hgsc.bcm.edu	37	7	5104359	5104359	+	Silent	SNP	G	G	A	rs12668616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:5104359G>A	ENST00000353796.3	+	6	1596	c.1272G>A	c.(1270-1272)acG>acA	p.T424T	RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Silent_p.T424T	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	424	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		GAACACACACGGGAGAGAAGC	0.413													A|||	889	0.177516	0.0446	0.1484	5008	,	,		20928	0.372		0.1272	False		,,,				2504	0.229				p.T424T		Atlas-SNP	.											RBAK_ENST00000396912,caecum,carcinoma,+1,1	RBAK	82	1	0			c.G1272A						PASS	.	A	,,	287,4119	796.4+/-415.4	6,275,1922	56.0	54.0	54.0		1272,,1272	-0.1	1.0	7	dbSNP_120	54	980,7620	769.7+/-407.6	53,874,3373	no	coding-synonymous,intron,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	59,1149,5295	AA,AG,GG		11.3953,6.5138,9.7417	,,	424/715,,424/715	5104359	1267,11739	2203	4300	6503	SO:0001819	synonymous_variant	57786	exon6			ACACACGGGAGAG	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.1272G>A	7.37:g.5104359G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			G|0.868;A|0.132	0.132	strong		0.413	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
FAM181B	220382	hgsc.bcm.edu	37	11	82444668	82444668	+	Missense_Mutation	SNP	C	C	G	rs144429777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:82444668C>G	ENST00000329203.3	-	1	238	c.104G>C	c.(103-105)gGc>gCc	p.G35A		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	35										large_intestine(1)|lung(2)|prostate(1)	4						GAAACAGCAGCCCTTGTCCAG	0.721													C|||	17	0.00339457	0.0	0.0014	5008	,	,		7441	0.0		0.008	False		,,,				2504	0.0082				p.G35A		Atlas-SNP	.											.	FAM181B	14	.	0			c.G104C						PASS	.	C	ALA/GLY	3,4381		0,3,2189	11.0	13.0	12.0		104	4.0	1.0	11	dbSNP_134	12	28,8548		0,28,4260	yes	missense	FAM181B	NM_175885.3	60	0,31,6449	GG,GC,CC		0.3265,0.0684,0.2392	possibly-damaging	35/427	82444668	31,12929	2192	4288	6480	SO:0001583	missense	220382	exon1			CAGCAGCCCTTGT	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.104G>C	11.37:g.82444668C>G	ENSP00000365295:p.Gly35Ala	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	21	0.777778	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.668634	0.29604	6.84E-4	0.003265	ENSG00000182103	ENST00000329203	T	0.36340	1.26	4.04	4.04	0.47022	.	0.636557	0.14564	U	0.311877	T	0.47358	0.1441	L	0.44542	1.39	0.25758	N	0.984974	D	0.89917	1.0	D	0.66602	0.945	T	0.22173	-1.0224	9	.	.	.	.	10.1105	0.42559	0.0:0.9066:0.0:0.0934	.	35	A6NEQ2	F181B_HUMAN	A	35	ENSP00000365295:G35A	.	G	-	2	0	FAM181B	82122316	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	2.111000	0.41883	2.073000	0.62155	0.455000	0.32223	GGC	C|0.997;G|0.003	0.003	strong		0.721	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885	
FMN1	342184	hgsc.bcm.edu	37	15	33359093	33359093	+	Intron	SNP	T	T	C	rs74655292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33359093T>C	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Silent_p.K331K|FMN1_ENST00000558197.1_Silent_p.K331K|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GATCAGTTGCTTTCTTCTCAC	0.522													T|||	29	0.00579073	0.0008	0.0202	5008	,	,		19662	0.0		0.0089	False		,,,				2504	0.0051				p.K331K		Atlas-SNP	.											.	FMN1	174	.	0			c.A993G						PASS	.	T		8,4060		0,8,2026	62.0	65.0	64.0		993	3.9	0.0	15	dbSNP_132	64	89,8257		0,89,4084	no	coding-synonymous	FMN1	NM_001103184.2		0,97,6110	CC,CT,TT		1.0664,0.1967,0.7814		331/1197	33359093	97,12317	2034	4173	6207	SO:0001627	intron_variant	342184	exon1			AGTTGCTTTCTTC	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-1818A>G	15.37:g.33359093T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	228	106	0.464912	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Silent	SNP	ENST00000559047.1	37																																																																																				T|0.992;C|0.008	0.008	strong		0.522	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
C15orf41	84529	hgsc.bcm.edu	37	15	36946303	36946303	+	Missense_Mutation	SNP	C	C	G	rs3784678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:36946303C>G	ENST00000566621.1	+	4	467	c.217C>G	c.(217-219)Ctg>Gtg	p.L73V	C15orf41_ENST00000569302.1_Missense_Mutation_p.L73V|C15orf41_ENST00000562877.1_5'UTR|C15orf41_ENST00000567389.1_5'UTR|RP11-16L14.2_ENST00000565366.1_RNA|C15orf41_ENST00000437989.2_Missense_Mutation_p.L73V|C15orf41_ENST00000338183.4_5'UTR	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	73			L -> V (in dbSNP:rs3784678).							kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GTCTAGGTACCTGAATGGAGT	0.448													C|||	2489	0.497005	0.3782	0.3818	5008	,	,		18193	0.6815		0.4423	False		,,,				2504	0.6053				p.L73V		Atlas-SNP	.											.	C15orf41	24	.	0			c.C217G						PASS	.	C	VAL/LEU,	1239,1893		241,757,568	96.0	85.0	89.0		217,	5.5	1.0	15	dbSNP_107	89	3286,3870		758,1770,1050	yes	missense,utr-5	C15orf41	NM_001130010.1,NM_032499.4	32,	999,2527,1618	GG,GC,CC		45.9195,39.5594,43.9833	possibly-damaging,	73/282,	36946303	4525,5763	1566	3578	5144	SO:0001583	missense	84529	exon4			AGGTACCTGAATG	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.217C>G	15.37:g.36946303C>G	ENSP00000455397:p.Leu73Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	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	
CDH17	1015	hgsc.bcm.edu	37	8	95158259	95158259	+	Silent	SNP	G	G	A	rs2251734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:95158259G>A	ENST00000027335.3	-	15	2188	c.2064C>T	c.(2062-2064)ttC>ttT	p.F688F	CDH17_ENST00000441892.2_Silent_p.F474F|CDH17_ENST00000450165.2_Silent_p.F688F	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	688	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			CAGTAGCCTCGAAAATGAGAC	0.483													G|||	1563	0.312101	0.4523	0.3804	5008	,	,		18213	0.1597		0.2604	False		,,,				2504	0.2843				p.F688F		Atlas-SNP	.											.	CDH17	119	.	0			c.C2064T						PASS	.	G	,	1847,2559	537.1+/-374.7	390,1067,746	102.0	90.0	94.0		2064,2064	-11.7	0.0	8	dbSNP_100	94	2410,6190	398.7+/-346.2	358,1694,2248	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	748,2761,2994	AA,AG,GG		28.0233,41.9201,32.731	,	688/833,688/833	95158259	4257,8749	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon15			AGCCTCGAAAATG	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.2064C>T	8.37:g.95158259G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	192	95	0.494792	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.692;A|0.308	0.308	strong		0.483	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
ZNF519	162655	hgsc.bcm.edu	37	18	14124427	14124427	+	Missense_Mutation	SNP	A	A	G	rs16941623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:14124427A>G	ENST00000590202.1	-	2	204	c.52T>C	c.(52-54)Tgg>Cgg	p.W18R	ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Missense_Mutation_p.W18R	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	18	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		W -> R (in dbSNP:rs16941623).		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						AGGCATTTCCACTCTTCTGGA	0.403													A|||	37	0.00738818	0.0272	0.0014	5008	,	,		15557	0.0		0.0	False		,,,				2504	0.0				p.W18R		Atlas-SNP	.											.	ZNF519	53	.	0			c.T52C						PASS	.	A	ARG/TRP	134,4272	97.6+/-136.3	2,130,2071	82.0	88.0	86.0		52		0.3	18	dbSNP_123	86	1,8599		0,1,4299	no	missense	ZNF519	NM_145287.3	101	2,131,6370	GG,GA,AA		0.0116,3.0413,1.038	probably-damaging	18/541	14124427	135,12871	2203	4300	6503	SO:0001583	missense	162655	exon2			ATTTCCACTCTTC	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.52T>C	18.37:g.14124427A>G	ENSP00000464872:p.Trp18Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	A	9.431	1.085594	0.20390	0.030413	1.16E-4	ENSG00000175322	ENST00000309305	.	.	.	.	.	.	Krueppel-associated box (4);	.	.	.	.	T	0.40196	0.1107	H	0.98155	4.16	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.59705	-0.7404	6	0.87932	D	0	.	.	.	.	rs16941623;rs52802058;rs60926256;rs16941623	18	Q8TB69	ZN519_HUMAN	R	18	.	ENSP00000307908:W18R	W	-	1	0	ZNF519	14114427	0.444000	0.25649	0.272000	0.24630	0.274000	0.26718	1.863000	0.39459	0.077000	0.16863	0.076000	0.15429	TGG	A|0.988;G|0.012	0.012	strong		0.403	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
SLC27A2	11001	hgsc.bcm.edu	37	15	50474900	50474900	+	Silent	SNP	C	C	T	rs34490804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:50474900C>T	ENST00000267842.5	+	1	508	c.276C>T	c.(274-276)gcC>gcT	p.A92A	SLC27A2_ENST00000380902.4_Silent_p.A92A	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	92					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)		ATCAAGTGGCCCGGGCGCTGC	0.662													C|||	345	0.0688898	0.056	0.0994	5008	,	,		15607	0.0347		0.1223	False		,,,				2504	0.045				p.A92A		Atlas-SNP	.											.	SLC27A2	50	.	0			c.C276T						PASS	.	C	,	315,4077	165.1+/-196.6	9,297,1890	48.0	53.0	51.0		276,276	-6.5	1.0	15	dbSNP_126	51	1031,7559	212.1+/-252.5	73,885,3337	no	coding-synonymous,coding-synonymous	SLC27A2	NM_001159629.1,NM_003645.3	,	82,1182,5227	TT,TC,CC		12.0023,7.1721,10.3682	,	92/568,92/621	50474900	1346,11636	2196	4295	6491	SO:0001819	synonymous_variant	11001	exon1			AGTGGCCCGGGCG	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.276C>T	15.37:g.50474900C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_003645	A8K2J7|Q53FY6|Q6PF09	Silent	SNP	ENST00000267842.5	37	CCDS10133.1																																																																																			C|0.905;T|0.095	0.095	strong		0.662	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412066	105412066	+	Missense_Mutation	SNP	C	C	T	rs77154428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.						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	189	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	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	
USP17L22	100287513	hgsc.bcm.edu	37	4	9270328	9270328	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	537	8	0.0148976		WXS	Illumina HiSeq	Phase_I	753	15	0.0199203	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	
RNFT1	51136	hgsc.bcm.edu	37	17	58031412	58031412	+	Silent	SNP	A	A	G	rs11368	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:58031412A>G	ENST00000305783.8	-	8	1222	c.1167T>C	c.(1165-1167)atT>atC	p.I389I	RNFT1_ENST00000442346.2_3'UTR|RP11-178C3.1_ENST00000591035.1_Intron	NM_016125.3	NP_057209.3	Q5M7Z0	RNFT1_HUMAN	ring finger protein, transmembrane 1	389						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)			TTACCTGACAAATGAGAAGAA	0.328													G|||	2901	0.579273	0.8797	0.5	5008	,	,		19138	0.5764		0.4195	False		,,,				2504	0.3967				p.I389I		Atlas-SNP	.											.	RNFT1	30	.	0			c.T1167C						PASS	.	G		2953,719		1192,569,75	51.0	50.0	50.0		1167	0.9	1.0	17	dbSNP_52	50	3587,4589		816,1955,1317	no	coding-synonymous	RNFT1	NM_016125.3		2008,2524,1392	GG,GA,AA		43.8723,19.5806,44.8008		389/436	58031412	6540,5308	1836	4088	5924	SO:0001819	synonymous_variant	51136	exon8			CTGACAAATGAGA	BC006971	CCDS11622.2	17q23.2	2013-01-09			ENSG00000189050	ENSG00000189050		"""RING-type (C3HC4) zinc fingers"""	30206	protein-coding gene	gene with protein product		615172				12477932	Standard	NM_016125		Approved	PTD016	uc002iya.3	Q5M7Z0	OTTHUMG00000148658	ENST00000305783.8:c.1167T>C	17.37:g.58031412A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	208	93	0.447115	NM_016125	Q8N7D0|Q96IZ9|Q9Y686	Silent	SNP	ENST00000305783.8	37	CCDS11622.2																																																																																			A|0.499;G|0.501	0.501	strong		0.328	RNFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308958.1	NM_016125	
CRTC2	200186	hgsc.bcm.edu	37	1	153926078	153926078	+	Missense_Mutation	SNP	T	T	C	rs11264680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153926078T>C	ENST00000368633.1	-	5	566	c.439A>G	c.(439-441)Atg>Gtg	p.M147V	CRTC2_ENST00000368630.3_Intron|CRTC2_ENST00000476883.1_5'UTR	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	147			M -> V (in dbSNP:rs11264680).		gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCCCAGGCCATCGTCCTGGGG	0.512													T|||	1317	0.262979	0.0991	0.4078	5008	,	,		18949	0.2847		0.2913	False		,,,				2504	0.3303				p.M147V		Atlas-SNP	.											.	CRTC2	58	.	0			c.A439G						PASS	.	T	VAL/MET	610,3796	268.9+/-268.7	31,548,1624	55.0	45.0	48.0		439	4.6	1.0	1	dbSNP_120	48	2538,6062	411.9+/-350.6	377,1784,2139	yes	missense	CRTC2	NM_181715.2	21	408,2332,3763	CC,CT,TT		29.5116,13.8448,24.2042	benign	147/694	153926078	3148,9858	2203	4300	6503	SO:0001583	missense	200186	exon5			AGGCCATCGTCCT	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.439A>G	1.37:g.153926078T>C	ENSP00000357622:p.Met147Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	37	CCDS30875.1	605	0.27701465201465203	60	0.12195121951219512	140	0.3867403314917127	174	0.3041958041958042	231	0.30474934036939316	T	11.10	1.540195	0.27563	0.138448	0.295116	ENSG00000160741	ENST00000368633	T	0.10763	2.84	4.56	4.56	0.56223	.	0.059133	0.64402	D	0.000004	T	0.02533	0.0077	N	0.22421	0.69	0.34011	P	0.348599	P	0.44734	0.842	B	0.40066	0.318	T	0.44112	-0.9349	9	0.27082	T	0.32	-12.9717	6.9169	0.24365	0.0:0.1023:0.0:0.8977	rs11264680;rs61553691;rs11264680	147	Q53ET0	CRTC2_HUMAN	V	147	ENSP00000357622:M147V	ENSP00000357622:M147V	M	-	1	0	CRTC2	152192702	0.934000	0.31675	0.997000	0.53966	0.601000	0.36947	0.927000	0.28818	2.048000	0.60808	0.374000	0.22700	ATG	T|0.748;C|0.252	0.252	strong		0.512	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715	
ZNF230	7773	hgsc.bcm.edu	37	19	44515352	44515352	+	Silent	SNP	T	T	G	rs1060880	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44515352T>G	ENST00000429154.2	+	5	1389	c.1161T>G	c.(1159-1161)acT>acG	p.T387T		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T387T(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				GGGTCCATACTGGAGAGAGAC	0.443													T|||	1106	0.220847	0.2746	0.2939	5008	,	,		4892	0.256		0.1789	False		,,,				2504	0.1033				p.T387T	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											ZNF230,NS,carcinoma,0,1	ZNF230	44	1	1	Substitution - coding silent(1)	stomach(1)	c.T1161G						PASS	.	T		1095,3311	395.1+/-329.5	126,843,1234	98.0	97.0	97.0		1161	-5.1	0.2	19	dbSNP_86	97	1371,7229	265.3+/-286.1	95,1181,3024	no	coding-synonymous	ZNF230	NM_006300.3		221,2024,4258	GG,GT,TT		15.9419,24.8525,18.9605		387/475	44515352	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	7773	exon5			CCATACTGGAGAG	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.1161T>G	19.37:g.44515352T>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Silent	SNP	ENST00000429154.2	37	CCDS33044.1																																																																																			T|0.801;G|0.199	0.199	strong		0.443	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		
EPS8L2	64787	hgsc.bcm.edu	37	11	722709	722709	+	Silent	SNP	C	C	T	rs10902205	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:722709C>T	ENST00000533256.1	+	15	1620	c.1245C>T	c.(1243-1245)taC>taT	p.Y415Y	EPS8L2_ENST00000318562.8_Silent_p.Y415Y|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000530636.1_Silent_p.Y415Y|EPS8L2_ENST00000526198.1_Silent_p.Y431Y			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	415					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		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;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGCCCCTCTACGTGCCCAAGT	0.682													c|||	538	0.107428	0.2474	0.0692	5008	,	,		9206	0.0357		0.0805	False		,,,				2504	0.047				p.Y415Y		Atlas-SNP	.											.	EPS8L2	42	.	0			c.C1245T						PASS	.			951,3443		95,761,1341	18.0	23.0	21.0		1245	-2.8	0.3	11	dbSNP_120	21	785,7807		44,697,3555	no	coding-synonymous	EPS8L2	NM_022772.3		139,1458,4896	TT,TC,CC		9.1364,21.6431,13.3682		415/716	722709	1736,11250	2197	4296	6493	SO:0001819	synonymous_variant	64787	exon14			CCTCTACGTGCCC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.1245C>T	11.37:g.722709C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	97	37	0.381443	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			A|0.000;C|0.882;G|0.000;T|0.118	0.118	strong		0.682	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
PIH1D2	120379	hgsc.bcm.edu	37	11	111941959	111941959	+	Missense_Mutation	SNP	G	G	A	rs1425917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:111941959G>A	ENST00000280350.4	-	4	572	c.350C>T	c.(349-351)gCa>gTa	p.A117V	PIH1D2_ENST00000528775.1_Missense_Mutation_p.A117V|PIH1D2_ENST00000431456.1_Missense_Mutation_p.A117V|C11orf57_ENST00000420986.2_5'Flank|PIH1D2_ENST00000530641.1_Missense_Mutation_p.A117V|PIH1D2_ENST00000521853.2_5'UTR|PIH1D2_ENST00000532211.1_Missense_Mutation_p.A117V	NM_138789.3	NP_620144.1	Q8WWB5	PIHD2_HUMAN	PIH1 domain containing 2	117			A -> V (in dbSNP:rs1425917).							endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(61;1.09e-14)|all_epithelial(67;7.64e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.19e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;6.18e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0508)		CTTTTCTGCTGCATGAAGAAC	0.373													G|||	162	0.0323482	0.003	0.0476	5008	,	,		17955	0.001		0.1014	False		,,,				2504	0.0225				p.A117V		Atlas-SNP	.											.	PIH1D2	24	.	0			c.C350T						PASS	.	G	VAL/ALA,VAL/ALA	96,4306	77.8+/-116.1	0,96,2105	159.0	151.0	154.0		350,350	1.7	1.0	11	dbSNP_88	154	885,7709	200.2+/-244.0	50,785,3462	yes	missense,missense	PIH1D2	NM_001082619.1,NM_138789.3	64,64	50,881,5567	AA,AG,GG		10.2979,2.1808,7.5485	benign,benign	117/289,117/316	111941959	981,12015	2201	4297	6498	SO:0001583	missense	120379	exon4			TCTGCTGCATGAA	BC019238	CCDS8355.1, CCDS44730.1	11q23.1	2007-01-31			ENSG00000150773	ENSG00000150773			25210	protein-coding gene	gene with protein product						12477932	Standard	NM_138789		Approved		uc001pmp.4	Q8WWB5	OTTHUMG00000166925	ENST00000280350.4:c.350C>T	11.37:g.111941959G>A	ENSP00000280350:p.Ala117Val	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	193	81	0.419689	NM_001082619	B4DU48|E9PD82	Missense_Mutation	SNP	ENST00000280350.4	37	CCDS8355.1	92	0.04212454212454213	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	69	0.09102902374670185	G	11.34	1.610901	0.28712	0.021808	0.102979	ENSG00000150773	ENST00000528775;ENST00000431456;ENST00000532211;ENST00000280350;ENST00000530641;ENST00000525744	T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25	5.9	1.73	0.24493	.	0.739486	0.13560	N	0.378898	T	0.00328	0.0010	L	0.50333	1.59	0.27100	N	0.962644	B;B;B	0.13145	0.004;0.007;0.005	B;B;B	0.17433	0.012;0.018;0.017	T	0.29852	-0.9998	10	0.29301	T	0.29	-1.2573	2.1303	0.03749	0.135:0.1864:0.3696:0.3089	rs1425917;rs52810609;rs58418432;rs1425917	117;117;117	B4DU48;E9PD82;Q8WWB5	.;.;PIHD2_HUMAN	V	117;117;117;117;117;82	ENSP00000434275:A117V;ENSP00000388209:A117V;ENSP00000431841:A117V;ENSP00000280350:A117V;ENSP00000431147:A117V;ENSP00000433297:A82V	ENSP00000280350:A117V	A	-	2	0	PIH1D2	111447169	0.991000	0.36638	0.998000	0.56505	0.791000	0.44710	0.577000	0.23758	0.373000	0.24621	0.591000	0.81541	GCA	G|0.939;A|0.061	0.061	strong		0.373	PIH1D2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391916.1	NM_138789	
TMEM51	55092	hgsc.bcm.edu	37	1	15541607	15541607	+	Silent	SNP	T	T	C	rs3820065	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15541607T>C	ENST00000428417.1	+	2	470	c.24T>C	c.(22-24)aaT>aaC	p.N8N	TMEM51_ENST00000376014.3_Silent_p.N8N|TMEM51_ENST00000400796.3_Silent_p.N8N|TMEM51_ENST00000376008.2_Silent_p.N8N|TMEM51_ENST00000434578.2_Silent_p.N8N	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	8						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CCAAGGCCAATGGCTCGCACT	0.577													C|||	797	0.159145	0.0764	0.1556	5008	,	,		19408	0.3294		0.162	False		,,,				2504	0.0951				p.N8N		Atlas-SNP	.											.	TMEM51	28	.	0			c.T24C						PASS	.	C	,,,	361,4045	775.5+/-414.1	18,325,1860	65.0	69.0	68.0		24,24,24,24	-0.3	1.0	1	dbSNP_107	68	1451,7149	733.4+/-406.9	125,1201,2974	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM51	NM_001136216.1,NM_001136217.1,NM_001136218.1,NM_018022.2	,,,	143,1526,4834	CC,CT,TT		16.8721,8.1934,13.932	,,,	8/254,8/254,8/254,8/254	15541607	1812,11194	2203	4300	6503	SO:0001819	synonymous_variant	55092	exon2			GGCCAATGGCTCG	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 72"""	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.24T>C	1.37:g.15541607T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_018022	A8K819	Silent	SNP	ENST00000428417.1	37	CCDS154.1																																																																																			T|0.843;C|0.157	0.157	strong		0.577	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022	
DPP10	57628	hgsc.bcm.edu	37	2	115822349	115822349	+	Intron	SNP	G	G	T	rs114821649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:115822349G>T	ENST00000410059.1	+	2	540				DPP10_ENST00000409163.1_Intron	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)							integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TCATCACAGAGGTGGCTGAGG	0.428													G|||	16	0.00319489	0.0023	0.0014	5008	,	,		17880	0.0		0.0099	False		,,,				2504	0.002				p.E5D		Atlas-SNP	.											.	DPP10	415	.	0			c.G15T						PASS	.																																			SO:0001627	intron_variant	57628	exon1			CACAGAGGTGGCT	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.61-244466G>T	2.37:g.115822349G>T		Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	268	131	0.488806	NM_001178037	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	0.476	-0.882031	0.02530	.	.	ENSG00000175497	ENST00000393146	.	.	.	2.54	-1.69	0.08186	.	.	.	.	.	T	0.09905	0.0243	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18053	-1.0349	8	0.27785	T	0.31	.	1.6277	0.02726	0.2314:0.1609:0.448:0.1596	.	5	Q0GLB9	.	D	5	.	ENSP00000376854:E5D	E	+	3	2	DPP10	115538819	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.978000	0.03778	-0.884000	0.03976	-2.947000	0.00085	GAG	G|0.996;T|0.004	0.004	strong		0.428	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
MARCH8	220972	hgsc.bcm.edu	37	10	45953767	45953767	+	Missense_Mutation	SNP	A	A	G	rs7908745	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:45953767A>G	ENST00000319836.3	-	7	1545	c.796T>C	c.(796-798)Tat>Cat	p.Y266H	MARCH8_ENST00000476962.1_5'UTR|MARCH8_ENST00000395769.2_Missense_Mutation_p.Y266H|MARCH8_ENST00000453424.2_Missense_Mutation_p.Y548H|MARCH8_ENST00000395771.3_Missense_Mutation_p.Y266H	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	266			Y -> H (in dbSNP:rs7908745). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						CAGATTCCATATCCATGTTTA	0.378													G|||	1517	0.302915	0.3328	0.3703	5008	,	,		18414	0.1706		0.3529	False		,,,				2504	0.2996				p.Y266H	NSCLC(102;658 1594 2173 16344 34808)	Atlas-SNP	.											.	MARCH8	29	.	0			c.T796C						PASS	.	G	HIS/TYR,HIS/TYR,HIS/TYR	1554,2852	669.9+/-402.2	280,994,929	118.0	119.0	118.0		796,796,796	0.5	0.0	10	dbSNP_116	118	2615,5985	688.1+/-404.3	406,1803,2091	yes	missense,missense,missense	MARCH8	NM_145021.4,NM_001002266.1,NM_001002265.1	83,83,83	686,2797,3020	GG,GA,AA		30.407,35.2701,32.0544	benign,benign,benign	266/292,266/292,266/292	45953767	4169,8837	2203	4300	6503	SO:0001583	missense	220972	exon7			TTCCATATCCATG	AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	23356	protein-coding gene	gene with protein product		613335	"""c-mir, cellular modulator of immune recognition"", ""membrane-associated ring finger (C3HC4) 8"""	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.796T>C	10.37:g.45953767A>G	ENSP00000317087:p.Tyr266His	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Missense_Mutation	SNP	ENST00000319836.3	37	CCDS7213.1	674|674	0.3086080586080586|0.3086080586080586	172|172	0.34959349593495936|0.34959349593495936	128|128	0.35359116022099446|0.35359116022099446	105|105	0.18356643356643357|0.18356643356643357	269|269	0.3548812664907652|0.3548812664907652	G|G	6.703|6.703	0.498336|0.498336	0.12762|0.12762	0.352701|0.352701	0.30407|0.30407	ENSG00000165406|ENSG00000165406	ENST00000453424|ENST00000395771;ENST00000319836;ENST00000395769	.|T;T;T	.|0.11063	.|2.81;2.81;2.81	5.67|5.67	0.455|0.455	0.16649|0.16649	.|.	.|2.502220	.|0.01143	.|N	.|0.006245	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.46775|0.46775	-0.9167|-0.9167	4|9	.|0.14252	.|T	.|0.57	-13.9368|-13.9368	5.5414|5.5414	0.17039|0.17039	0.2911:0.2462:0.4628:0.0|0.2911:0.2462:0.4628:0.0	rs7908745;rs17856729;rs52802616;rs56558105;rs58961986;rs7908745|rs7908745;rs17856729;rs52802616;rs56558105;rs58961986;rs7908745	.|266;430	.|Q5T0T0;Q5JQ16	.|MARH8_HUMAN;.	T|H	430|266	.|ENSP00000379118:Y266H;ENSP00000317087:Y266H;ENSP00000379116:Y266H	.|ENSP00000317087:Y266H	I|Y	-|-	2|1	0|0	MARCH8|MARCH8	45273773|45273773	0.987000|0.987000	0.35691|0.35691	0.004000|0.004000	0.12327|0.12327	0.945000|0.945000	0.59286|0.59286	2.648000|2.648000	0.46647|0.46647	-0.157000|-0.157000	0.11059|0.11059	-0.119000|-0.119000	0.15052|0.15052	ATA|TAT	A|0.697;G|0.303	0.303	strong		0.378	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021	
KRT38	8687	hgsc.bcm.edu	37	17	39594766	39594766	+	Missense_Mutation	SNP	C	C	T	rs138667284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39594766C>T	ENST00000246646.3	-	5	996	c.997G>A	c.(997-999)Gag>Aag	p.E333K		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	333	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)				GCTTGGCGCTCCACCTCCAGG	0.577													C|||	12	0.00239617	0.0	0.0043	5008	,	,		20557	0.0		0.0089	False		,,,				2504	0.0				p.E333K		Atlas-SNP	.											.	KRT38	63	.	0			c.G997A						PASS	.	C	LYS/GLU	5,4401		0,5,2198	156.0	119.0	131.0		997	4.2	1.0	17	dbSNP_134	131	82,8518		1,80,4219	no	missense	KRT38	NM_006771.3	56	1,85,6417	TT,TC,CC		0.9535,0.1135,0.6689	probably-damaging	333/457	39594766	87,12919	2203	4300	6503	SO:0001583	missense	8687	exon5			GGCGCTCCACCTC	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.997G>A	17.37:g.39594766C>T	ENSP00000246646:p.Glu333Lys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	176	86	0.488636	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	.	22.8	4.341180	0.81911	0.001135	0.009535	ENSG00000171360	ENST00000246646	D	0.92048	-2.96	4.2	4.2	0.49525	Filament (1);	0.000000	0.49916	D	0.000139	D	0.96005	0.8699	H	0.94423	3.535	0.30429	N	0.777356	D	0.89917	1.0	D	0.91635	0.999	D	0.93110	0.6516	10	0.87932	D	0	.	15.7694	0.78152	0.0:1.0:0.0:0.0	.	333	O76015	KRT38_HUMAN	K	333	ENSP00000246646:E333K	ENSP00000246646:E333K	E	-	1	0	KRT38	36848292	0.998000	0.40836	0.990000	0.47175	0.997000	0.91878	3.898000	0.56281	2.211000	0.71520	0.650000	0.86243	GAG	C|0.994;T|0.006	0.006	strong		0.577	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
SPTA1	6708	hgsc.bcm.edu	37	1	158592781	158592781	+	Silent	SNP	G	G	A	rs75931146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592781G>A	ENST00000368147.4	-	43	6292	c.6112C>T	c.(6112-6114)Cta>Tta	p.L2038L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2038					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)					ACCTTCTGTAGAGGCAGCTGT	0.443													G|||	270	0.0539137	0.1407	0.0303	5008	,	,		18220	0.0		0.0229	False		,,,				2504	0.0409				p.L2038L		Atlas-SNP	.											.	SPTA1	720	.	0			c.C6112T						PASS	.	G		527,3225		26,475,1375	139.0	139.0	139.0		6112	2.9	0.3	1	dbSNP_132	139	125,8097		2,121,3988	no	coding-synonymous	SPTA1	NM_003126.2		28,596,5363	AA,AG,GG		1.5203,14.0458,5.4451		2038/2420	158592781	652,11322	1876	4111	5987	SO:0001819	synonymous_variant	6708	exon43			TCTGTAGAGGCAG	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.6112C>T	1.37:g.158592781G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	167	70	0.419162	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.961;A|0.039	0.039	strong		0.443	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
KIAA0355	9710	hgsc.bcm.edu	37	19	34842488	34842488	+	Silent	SNP	T	T	C	rs392340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:34842488T>C	ENST00000299505.6	+	13	3768	c.2895T>C	c.(2893-2895)gaT>gaC	p.D965D	AC010504.2_ENST00000591311.1_RNA	NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	965										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					CGGTGGAGGATGTGAACCAGG	0.547													C|||	3018	0.602636	0.739	0.4049	5008	,	,		16866	0.8155		0.3897	False		,,,				2504	0.5583				p.D965D		Atlas-SNP	.											.	KIAA0355	105	.	0			c.T2895C						PASS	.	C		2819,1587	493.2+/-362.6	904,1011,288	84.0	68.0	73.0		2895	-1.7	0.2	19	dbSNP_80	73	3080,5520	658.6+/-401.6	544,1992,1764	no	coding-synonymous	KIAA0355	NM_014686.3		1448,3003,2052	CC,CT,TT		35.814,36.0191,45.356		965/1071	34842488	5899,7107	2203	4300	6503	SO:0001819	synonymous_variant	9710	exon13			GGAGGATGTGAAC		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.2895T>C	19.37:g.34842488T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	37	CCDS12436.1																																																																																			T|0.473;C|0.527	0.527	strong		0.547	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686	
POU2F3	25833	hgsc.bcm.edu	37	11	120187971	120187971	+	Missense_Mutation	SNP	G	G	A	rs2282537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:120187971G>A	ENST00000543440.2	+	12	1319	c.1169G>A	c.(1168-1170)aGg>aAg	p.R390K	POU2F3_ENST00000260264.4_Missense_Mutation_p.R392K	NM_014352.3	NP_055167.2	Q9UKI9	PO2F3_HUMAN	POU class 2 homeobox 3	390	Ser-rich.		R -> K (in dbSNP:rs2282537). {ECO:0000269|PubMed:14702039}.		epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|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)|sequence-specific DNA binding (GO:0043565)	p.R390K(1)		large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)	17		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)		AACAACAGCAGGCCTTCATCT	0.522													G|||	599	0.119609	0.0386	0.0922	5008	,	,		21511	0.1379		0.1183	False		,,,				2504	0.2311				p.R392K		Atlas-SNP	.											POU2F3,NS,carcinoma,0,2	POU2F3	44	2	1	Substitution - Missense(1)	prostate(1)	c.G1175A						PASS	.	G	LYS/ARG	246,4160	143.1+/-178.2	11,224,1968	145.0	136.0	139.0		1169	4.5	1.0	11	dbSNP_100	139	1226,7372	246.4+/-274.8	86,1054,3159	yes	missense	POU2F3	NM_014352.3	26	97,1278,5127	AA,AG,GG		14.2591,5.5833,11.3196	benign	390/437	120187971	1472,11532	2203	4299	6502	SO:0001583	missense	25833	exon12			ACAGCAGGCCTTC	AF133895	CCDS8431.1, CCDS58190.1	11q23.3	2011-06-20	2007-07-13		ENSG00000137709	ENSG00000137709		"""Homeoboxes / POU class"""	19864	protein-coding gene	gene with protein product		607394	"""POU domain class 2, transcription factor 3"""			10473598	Standard	NM_014352		Approved	OCT11, PLA-1, Skn-1a, Epoc-1	uc021qrk.1	Q9UKI9	OTTHUMG00000166140	ENST00000543440.2:c.1169G>A	11.37:g.120187971G>A	ENSP00000441687:p.Arg390Lys	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	210	107	0.509524	NM_001244682	A8K7H8|B4DY07|F5GWW6|Q3MIY3|Q9UKR7|Q9Y504	Missense_Mutation	SNP	ENST00000543440.2	37	CCDS8431.1	223	0.1021062271062271	16	0.032520325203252036	33	0.09116022099447514	88	0.15384615384615385	86	0.11345646437994723	G	16.87	3.242612	0.58995	0.055833	0.142591	ENSG00000137709	ENST00000543440;ENST00000260264;ENST00000533620;ENST00000532638	D;D;D;T	0.83075	-1.63;-1.62;-1.68;-1.39	5.38	4.47	0.54385	.	0.378221	0.27866	N	0.017534	T	0.00998	0.0033	L	0.29908	0.895	0.22531	P	0.999012329	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34775	-0.9815	9	0.27785	T	0.31	.	14.1572	0.65424	0.0721:0.0:0.9279:0.0	rs2282537;rs52821351;rs56430090;rs58401712;rs2282537	344;390	E9PIN6;Q9UKI9	.;PO2F3_HUMAN	K	392;390;344;175	ENSP00000441687:R392K;ENSP00000260264:R390K;ENSP00000435738:R344K;ENSP00000436236:R175K	ENSP00000260264:R390K	R	+	2	0	POU2F3	119693181	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.039000	0.57325	1.265000	0.44215	0.655000	0.94253	AGG	G|0.893;A|0.107	0.107	strong		0.522	POU2F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388039.2		
AKAP11	11215	hgsc.bcm.edu	37	13	42875683	42875683	+	Missense_Mutation	SNP	A	A	G	rs41288309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42875683A>G	ENST00000025301.2	+	8	2976	c.2801A>G	c.(2800-2802)aAt>aGt	p.N934S		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	934					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)		GCTAGTAGCAATAAGGACATG	0.358													A|||	50	0.00998403	0.0	0.0014	5008	,	,		19449	0.001		0.0099	False		,,,				2504	0.0389				p.N934S		Atlas-SNP	.											.	AKAP11	146	.	0			c.A2801G						PASS	.	A	SER/ASN	5,4401	8.1+/-20.4	0,5,2198	65.0	67.0	67.0		2801	-2.7	0.0	13	dbSNP_127	67	84,8516	48.1+/-107.5	0,84,4216	yes	missense	AKAP11	NM_016248.3	46	0,89,6414	GG,GA,AA		0.9767,0.1135,0.6843	benign	934/1902	42875683	89,12917	2203	4300	6503	SO:0001583	missense	11215	exon8			GTAGCAATAAGGA	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.2801A>G	13.37:g.42875683A>G	ENSP00000025301:p.Asn934Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	2.918	-0.223797	0.06061	0.001135	0.009767	ENSG00000023516	ENST00000025301	T	0.12774	2.65	6.03	-2.7	0.06004	.	1.233830	0.05477	N	0.554106	T	0.04272	0.0118	N	0.04880	-0.145	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42292	-0.9460	10	0.13108	T	0.6	.	10.713	0.45995	0.4485:0.1412:0.4102:0.0	rs41288309;rs61756565	934	Q9UKA4	AKA11_HUMAN	S	934	ENSP00000025301:N934S	ENSP00000025301:N934S	N	+	2	0	AKAP11	41773683	0.000000	0.05858	0.039000	0.18376	0.069000	0.16628	-0.237000	0.08990	-0.478000	0.06823	-0.250000	0.11733	AAT	A|0.993;G|0.007	0.007	strong		0.358	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
CNTRL	11064	hgsc.bcm.edu	37	9	123917020	123917020	+	Silent	SNP	T	T	A	rs3736855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123917020T>A	ENST00000373855.1	+	27	4454	c.4194T>A	c.(4192-4194)gtT>gtA	p.V1398V	CNTRL_ENST00000373847.1_Silent_p.V846V|CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Silent_p.V1398V|CNTRL_ENST00000373850.1_Silent_p.V846V			Q7Z7A1	CNTRL_HUMAN	centriolin	1398					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						ATGGAAATGTTGAGAGTCTTA	0.303													T|||	2164	0.432109	0.1233	0.5	5008	,	,		19598	0.5694		0.4513	False		,,,				2504	0.6401				p.V1398V		Atlas-SNP	.											.	CNTRL	161	.	0			c.T4194A						PASS	.	T		779,3627	311.1+/-291.9	79,621,1503	44.0	43.0	43.0		4194	1.6	1.0	9	dbSNP_107	43	3786,4814	533.9+/-382.5	875,2036,1389	no	coding-synonymous	CNTRL	NM_007018.4		954,2657,2892	AA,AT,TT		44.0233,17.6804,35.0992		1398/2326	123917020	4565,8441	2203	4300	6503	SO:0001819	synonymous_variant	11064	exon25			AAATGTTGAGAGT	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.4194T>A	9.37:g.123917020T>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Silent	SNP	ENST00000373855.1	37	CCDS35118.1																																																																																			A|0.373;N|0.000	0.373	strong		0.303	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
LAX1	54900	hgsc.bcm.edu	37	1	203743798	203743798	+	Missense_Mutation	SNP	C	C	T	rs41264261	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:203743798C>T	ENST00000442561.2	+	5	1576	c.1186C>T	c.(1186-1188)Cct>Tct	p.P396S	LAX1_ENST00000367215.1_3'UTR|LAX1_ENST00000367217.5_Missense_Mutation_p.P380S	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	396					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TCAGCTCCTTCCTGATGAATG	0.502													C|||	41	0.0081869	0.0015	0.0086	5008	,	,		19392	0.001		0.0288	False		,,,				2504	0.0031				p.P396S		Atlas-SNP	.											.	LAX1	48	.	0			c.C1186T						PASS	.	C	SER/PRO,SER/PRO	24,4382	29.9+/-59.1	0,24,2179	37.0	38.0	38.0		1138,1186	3.4	0.2	1	dbSNP_127	38	284,8316	100.1+/-161.6	4,276,4020	yes	missense,missense	LAX1	NM_001136190.1,NM_017773.3	74,74	4,300,6199	TT,TC,CC		3.3023,0.5447,2.3681	probably-damaging,probably-damaging	380/383,396/399	203743798	308,12698	2203	4300	6503	SO:0001583	missense	54900	exon5			CTCCTTCCTGATG	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"""LAT-like membrane associated protein"", ""linker for activation of x cells"""					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.1186C>T	1.37:g.203743798C>T	ENSP00000406970:p.Pro396Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Missense_Mutation	SNP	ENST00000442561.2	37	CCDS1441.2	27	0.012362637362637362	2	0.0040650406504065045	5	0.013812154696132596	1	0.0017482517482517483	19	0.025065963060686015	C	13.62	2.291450	0.40494	0.005447	0.033023	ENSG00000122188	ENST00000442561;ENST00000367217	.	.	.	5.4	3.4	0.38934	.	0.357044	0.20714	N	0.087035	T	0.06371	0.0164	N	0.14661	0.345	0.09310	N	0.999999	P;P	0.50943	0.94;0.94	P;P	0.47015	0.534;0.534	T	0.04153	-1.0973	9	0.19147	T	0.46	-2.1379	6.6324	0.22863	0.1774:0.7243:0.0:0.0983	rs41264261	380;396	B7Z744;Q8IWV1	.;LAX1_HUMAN	S	396;380	.	ENSP00000356186:P380S	P	+	1	0	LAX1	202010421	0.994000	0.37717	0.186000	0.23195	0.660000	0.38997	1.048000	0.30379	1.397000	0.46682	0.655000	0.94253	CCT	C|0.979;T|0.021	0.021	strong		0.502	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773	
MYOM2	9172	hgsc.bcm.edu	37	8	2021421	2021421	+	Missense_Mutation	SNP	G	G	T	rs2272720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:2021421G>T	ENST00000262113.4	+	10	1102	c.961G>T	c.(961-963)Gtg>Ttg	p.V321L	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	321	Ig-like C2-type 2.		V -> L (in dbSNP:rs2272720). {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)		TCTTTCAGACGTGCTGTTGAA	0.562													G|||	1402	0.279952	0.0257	0.379	5008	,	,		19795	0.3601		0.4046	False		,,,				2504	0.3425				p.V321L		Atlas-SNP	.											.	MYOM2	251	.	0			c.G961T						PASS	.	G	LEU/VAL	419,3987	205.2+/-227.1	16,387,1800	94.0	84.0	87.0		961	4.6	0.7	8	dbSNP_100	87	3691,4909	528.5+/-381.4	816,2059,1425	yes	missense	MYOM2	NM_003970.2	32	832,2446,3225	TT,TG,GG		42.9186,9.5098,31.6008	benign	321/1466	2021421	4110,8896	2203	4300	6503	SO:0001583	missense	9172	exon10			TCAGACGTGCTGT		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.961G>T	8.37:g.2021421G>T	ENSP00000262113:p.Val321Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	676	0.30952380952380953	13	0.026422764227642278	148	0.4088397790055249	207	0.3618881118881119	308	0.40633245382585753	G	8.677	0.904279	0.17760	0.095098	0.429186	ENSG00000036448	ENST00000262113	T	0.66815	-0.23	4.63	4.63	0.57726	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.323580	0.29342	N	0.012422	T	0.00012	0.0000	L	0.42686	1.345	0.09310	P	1.0	B	0.12013	0.005	B	0.17098	0.017	T	0.33828	-0.9853	9	0.20519	T	0.43	.	17.4931	0.87710	0.0:0.0:1.0:0.0	rs2272720;rs59193087;rs2272720	321	P54296	MYOM2_HUMAN	L	321	ENSP00000262113:V321L	ENSP00000262113:V321L	V	+	1	0	MYOM2	2008828	1.000000	0.71417	0.666000	0.29783	0.015000	0.08874	5.607000	0.67648	2.093000	0.63338	0.655000	0.94253	GTG	G|0.687;T|0.313	0.313	strong		0.562	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462936	37462936	+	Missense_Mutation	SNP	A	A	G	rs855791	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37462936A>G	ENST00000346753.3	-	17	2323	c.2207T>C	c.(2206-2208)gTc>gCc	p.V736A	TMPRSS6_ENST00000381792.2_Missense_Mutation_p.V749A|TMPRSS6_ENST00000406856.1_Missense_Mutation_p.V749A|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.V727A	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	736	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		V -> A (in dbSNP:rs855791). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:19818657}.		angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.V736A(1)		breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GTAGCGATAGACCTCGCTGCA	0.607													G|||	3028	0.604633	0.8994	0.487	5008	,	,		19711	0.4345		0.6123	False		,,,				2504	0.4571				p.V736A		Atlas-SNP	.											TMPRSS6,NS,carcinoma,0,1	TMPRSS6	99	1	1	Substitution - Missense(1)	stomach(1)	c.T2207C						PASS	.	G	ALA/VAL	3708,698	292.1+/-281.9	1560,588,55	135.0	99.0	111.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2207	4.7	1.0	22	dbSNP_86	111	4858,3742	531.3+/-382.0	1399,2060,841	yes	missense	TMPRSS6	NM_153609.2	64	2959,2648,896	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	43.5116,15.842,34.1381	benign	736/812	37462936	8566,4440	2203	4300	6503	SO:0001583	missense	164656	exon17			CGATAGACCTCGC	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.2207T>C	22.37:g.37462936A>G	ENSP00000334962:p.Val736Ala	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	175	102	0.582857	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	CCDS13941.1	1314	0.6016483516483516	430	0.8739837398373984	179	0.494475138121547	250	0.4370629370629371	455	0.600263852242744	G	13.30	2.197511	0.38806	0.84158	0.564884	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	4.72	4.72	0.59763	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.150864	0.44902	N	0.000412	T	0.00012	0.0000	N	0.03177	-0.4	0.48395	P	3.5200000000001896E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42515	-0.9447	9	0.22706	T	0.39	.	9.4664	0.38816	0.1631:0.0:0.8369:0.0	rs855791;rs17749938;rs59898578;rs855791	749;736	Q8IU80-5;Q8IU80	.;TMPS6_HUMAN	A	749;736;727;749	ENSP00000371211:V749A;ENSP00000334962:V736A;ENSP00000385453:V727A;ENSP00000384964:V749A	ENSP00000334962:V736A	V	-	2	0	TMPRSS6	35792882	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.736000	0.62059	0.980000	0.38523	-0.186000	0.12905	GTC	G|0.638;N|0.000	0.638	strong		0.607	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
C5	727	hgsc.bcm.edu	37	9	123716103	123716103	+	Silent	SNP	T	T	C	rs41258306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123716103T>C	ENST00000223642.1	-	40	4835	c.4806A>G	c.(4804-4806)aaA>aaG	p.K1602K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1602	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				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)	AGGTTACCTTTTTAATGAAGG	0.373													T|||	262	0.0523163	0.0711	0.0389	5008	,	,		22368	0.002		0.0606	False		,,,				2504	0.0798				p.K1602K		Atlas-SNP	.											.	C5	124	.	0			c.A4806G						PASS	.	T		293,4113	160.7+/-193.0	8,277,1918	113.0	105.0	108.0		4806	0.6	1.0	9	dbSNP_127	108	602,7998	159.7+/-212.9	32,538,3730	no	coding-synonymous	C5	NM_001735.2		40,815,5648	CC,CT,TT		7.0,6.65,6.8814		1602/1677	123716103	895,12111	2203	4300	6503	SO:0001819	synonymous_variant	727	exon40			TACCTTTTTAATG	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.4806A>G	9.37:g.123716103T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	168	60	0.357143	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			T|0.939;C|0.061	0.061	strong		0.373	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149212614	149212614	+	Silent	SNP	G	G	T	rs115557257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149212614G>T	ENST00000309241.5	+	5	1010	c.978G>T	c.(976-978)cgG>cgT	p.R326R	PPARGC1B_ENST00000403750.1_Silent_p.R262R|PPARGC1B_ENST00000394320.3_Silent_p.R326R|PPARGC1B_ENST00000360453.4_Silent_p.R287R	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	326					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)			TCAGATCCCGGCCCTGGTCCC	0.622													G|||	44	0.00878594	0.0061	0.0202	5008	,	,		16385	0.0		0.0149	False		,,,				2504	0.0072				p.R326R		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G978T						PASS	.	G	,,	43,4363	45.3+/-79.5	0,43,2160	51.0	57.0	55.0		861,786,978	2.7	0.0	5	dbSNP_132	55	200,8400	87.4+/-149.7	2,196,4102	no	coding-synonymous,coding-synonymous,coding-synonymous	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	,,	2,239,6262	TT,TG,GG		2.3256,0.9759,1.8684	,,	287/985,262/960,326/1024	149212614	243,12763	2203	4300	6503	SO:0001819	synonymous_variant	133522	exon5			ATCCCGGCCCTGG	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.978G>T	5.37:g.149212614G>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	166	89	0.536145	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	37	CCDS4298.1	21	0.009615384615384616	3	0.006097560975609756	8	0.022099447513812154	0	0.0	10	0.013192612137203167	G	0.025	-1.378899	0.01204	0.009759	0.023256	ENSG00000155846	ENST00000434684	.	.	.	5.61	2.74	0.32292	.	.	.	.	.	T	0.14399	0.0348	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.16660	-1.0395	4	.	.	.	-0.718	5.3707	0.16138	0.07:0.1258:0.5442:0.26	.	.	.	.	S	13	.	.	A	+	1	0	PPARGC1B	149192807	0.001000	0.12720	0.001000	0.08648	0.105000	0.19272	0.072000	0.14617	0.264000	0.21851	0.655000	0.94253	GCC	G|0.985;T|0.015	0.015	strong		0.622	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
CLCN4	1183	hgsc.bcm.edu	37	X	10180554	10180554	+	Silent	SNP	G	G	A	rs34148950	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:10180554G>A	ENST00000380833.4	+	10	1828	c.1437G>A	c.(1435-1437)gcG>gcA	p.A479A	CLCN4_ENST00000380829.1_Silent_p.A448A|CLCN4_ENST00000421085.2_Silent_p.A385A	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	479					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GCGCGATAGCGGGCAGGATGG	0.582													A|||	416	0.110199	0.2685	0.0533	3775	,	,		12946	0.0		0.0209	False		,,,				2504	0.0031				p.A479A	Melanoma(74;1050 1296 1576 30544 38374)	Atlas-SNP	.											.	CLCN4	84	.	0			c.G1437A						PASS	.	A		1194,2641		149,708,188,775,383	90.0	76.0	81.0		1437	-6.2	0.6	X	dbSNP_126	81	227,6501		2,155,68,2271,1804	no	coding-synonymous	CLCN4	NM_001830.3		151,863,256,3046,2187	AA,AG,A,GG,G		3.374,31.1343,13.4526		479/761	10180554	1421,9142	2203	4300	6503	SO:0001819	synonymous_variant	1183	exon10			GATAGCGGGCAGG	X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1437G>A	X.37:g.10180554G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	189	188	0.994709	NM_001830	A1L3U1|B7Z5Z4|Q9UBU1	Silent	SNP	ENST00000380833.4	37	CCDS14137.1																																																																																			G|0.869;A|0.131	0.131	strong		0.582	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1		
GPN2	54707	hgsc.bcm.edu	37	1	27210722	27210722	+	Silent	SNP	G	G	A	rs78109142	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:27210722G>A	ENST00000374135.4	-	4	989	c.789C>T	c.(787-789)ttC>ttT	p.F263F	GPN2_ENST00000374133.3_Silent_p.F84F|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						CTTGGGCTCTGAAACAGTATC	0.527													G|||	77	0.0153754	0.0008	0.0058	5008	,	,		19060	0.0327		0.0119	False		,,,				2504	0.0276				p.F263F		Atlas-SNP	.											GPN2,NS,carcinoma,-1,1	GPN2	18	1	0			c.C789T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	86.0	76.0	80.0		789	-9.6	0.5	1	dbSNP_132	80	123,8477	62.8+/-124.8	1,121,4178	no	coding-synonymous	GPN2	NM_018066.3		1,135,6367	AA,AG,GG		1.4302,0.3177,1.0534		263/311	27210722	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	54707	exon4			GGCTCTGAAACAG	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.789C>T	1.37:g.27210722G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	54	0.490909	NM_018066		Silent	SNP	ENST00000374135.4	37	CCDS289.1																																																																																			G|0.986;A|0.014	0.014	strong		0.527	GPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012175.2	NM_018066	
KIF20B	9585	hgsc.bcm.edu	37	10	91498127	91498127	+	Missense_Mutation	SNP	T	T	C	rs1886996	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:91498127T>C	ENST00000371728.3	+	20	3594	c.3529T>C	c.(3529-3531)Tgt>Cgt	p.C1177R	KIF20B_ENST00000394289.2_Missense_Mutation_p.C1177R|KIF20B_ENST00000260753.4_Missense_Mutation_p.C1137R|KIF20B_ENST00000416354.1_Missense_Mutation_p.C1207R|KIF20B_ENST00000478929.1_3'UTR	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1177			C -> R (in dbSNP:rs1886996). {ECO:0000269|PubMed:10695267, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:11470801, ECO:0000269|PubMed:12740395, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.9}.		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						GAAAGTTGAATGTAGTCATTC	0.338													C|||	4294	0.857428	0.848	0.8026	5008	,	,		18008	0.9355		0.7346	False		,,,				2504	0.955				p.C1137R		Atlas-SNP	.											.	KIF20B	191	.	0			c.T3409C						PASS	.	C	ARG/CYS	3709,691	269.5+/-269.1	1578,553,69	57.0	61.0	60.0		3409	0.5	0.0	10	dbSNP_92	60	6131,2465	382.7+/-340.5	2167,1797,334	yes	missense	KIF20B	NM_016195.2	180	3745,2350,403	CC,CT,TT		28.6761,15.7045,24.2844	benign	1137/1781	91498127	9840,3156	2200	4298	6498	SO:0001583	missense	9585	exon20			GTTGAATGTAGTC	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.3529T>C	10.37:g.91498127T>C	ENSP00000360793:p.Cys1177Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	127	65	0.511811	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		1765	0.8081501831501832	388	0.7886178861788617	282	0.7790055248618785	536	0.9370629370629371	559	0.737467018469657	C	0.010	-1.743058	0.00675	0.842955	0.713239	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.68765	-0.27;-0.28;-0.35;-0.28	5.82	0.459	0.16678	.	0.934169	0.09010	N	0.861730	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.41698	-0.9494	9	0.14252	T	0.57	0.4671	3.8752	0.09053	0.0873:0.1521:0.1599:0.6008	rs1886996;rs17406694;rs52808943;rs58446913;rs1886996	1177;1137	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	R	1137;1207;1177;1177	ENSP00000260753:C1137R;ENSP00000411545:C1207R;ENSP00000377830:C1177R;ENSP00000360793:C1177R	ENSP00000260753:C1137R	C	+	1	0	KIF20B	91488107	0.196000	0.23350	0.000000	0.03702	0.016000	0.09150	0.563000	0.23547	-0.115000	0.11915	-1.690000	0.00728	TGT	T|0.224;C|0.776	0.776	strong		0.338	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
TEX15	56154	hgsc.bcm.edu	37	8	30702739	30702739	+	Missense_Mutation	SNP	G	G	C	rs117362953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:30702739G>C	ENST00000256246.2	-	1	3869	c.3795C>G	c.(3793-3795)gaC>gaG	p.D1265E		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1265					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)			p.D1265D(1)		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)		ATATAAGTACGTCAGTTTTCG	0.333													G|||	9	0.00179712	0.0	0.0	5008	,	,		19980	0.0		0.008	False		,,,				2504	0.001				p.D1265E		Atlas-SNP	.											TEX15,NS,carcinoma,0,1	TEX15	350	1	1	Substitution - coding silent(1)	prostate(1)	c.C3795G						PASS	.	G	GLU/ASP	3,4403	6.2+/-15.9	0,3,2200	96.0	92.0	94.0		3795	-2.4	0.0	8	dbSNP_132	94	39,8559	25.7+/-73.6	0,39,4260	yes	missense	TEX15	NM_031271.3	45	0,42,6460	CC,CG,GG		0.4536,0.0681,0.323	possibly-damaging	1265/2790	30702739	42,12962	2203	4299	6502	SO:0001583	missense	56154	exon1			AAGTACGTCAGTT	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.3795C>G	8.37:g.30702739G>C	ENSP00000256246:p.Asp1265Glu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	134	58	0.432836	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	10.11	1.259447	0.23051	6.81E-4	0.004536	ENSG00000133863	ENST00000256246	T	0.21932	1.98	5.92	-2.44	0.06502	.	0.178401	0.39759	N	0.001263	T	0.27313	0.0670	L	0.55481	1.735	0.09310	N	0.999999	D	0.89917	1.0	D	0.74674	0.984	T	0.19289	-1.0310	10	0.87932	D	0	.	12.5257	0.56085	0.5481:0.0:0.4519:0.0	.	1265	Q9BXT5	TEX15_HUMAN	E	1265	ENSP00000256246:D1265E	ENSP00000256246:D1265E	D	-	3	2	TEX15	30822281	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.182000	0.03082	-0.565000	0.06061	-0.797000	0.03246	GAC	G|0.997;C|0.003	0.003	strong		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
IL19	29949	hgsc.bcm.edu	37	1	207015957	207015957	+	Missense_Mutation	SNP	T	T	C	rs2243191	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:207015957T>C	ENST00000270218.6	+	7	1463	c.524T>C	c.(523-525)tTc>tCc	p.F175S	IL19_ENST00000340758.2_Missense_Mutation_p.F213S	NM_013371.3	NP_037503.2	Q9UHD0	IL19_HUMAN	interleukin 19	175			F -> S (in dbSNP:rs2243191). {ECO:0000269|PubMed:11196675, ECO:0000269|PubMed:12370360, ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		apoptotic process (GO:0006915)|immune response (GO:0006955)|interleukin-6 biosynthetic process (GO:0042226)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|reactive oxygen species metabolic process (GO:0072593)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			central_nervous_system(2)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7			BRCA - Breast invasive adenocarcinoma(75;0.211)			GAAGTAATGTTCTCAGCTTGA	0.498													C|||	3370	0.672923	0.8185	0.6729	5008	,	,		18183	0.3363		0.7724	False		,,,				2504	0.7209				p.F213S		Atlas-SNP	.											.	IL19	31	.	0			c.T638C						PASS	.	C	SER/PHE,SER/PHE	3663,741		1527,609,66	59.0	58.0	58.0		524,638	4.7	0.0	1	dbSNP_98	58	6682,1906		2610,1462,222	yes	missense,missense	IL19	NM_013371.3,NM_153758.2	155,155	4137,2071,288	CC,CT,TT		22.1938,16.8256,20.3741	benign,benign	175/178,213/216	207015957	10345,2647	2202	4294	6496	SO:0001583	missense	29949	exon6			TAATGTTCTCAGC	AF192498	CCDS1468.1, CCDS1469.1	1q32.2	2008-07-18			ENSG00000142224	ENSG00000142224		"""Interleukins and interleukin receptors"""	5990	protein-coding gene	gene with protein product	"""melanoma differentiation associated protein-like protein"""	605687				11196675	Standard	NM_153758		Approved	IL-19, MDA1, ZMDA1, IL-10C, NG.1	uc001heo.3	Q9UHD0	OTTHUMG00000036387	ENST00000270218.6:c.524T>C	1.37:g.207015957T>C	ENSP00000270218:p.Phe175Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_153758	B6VEV9|Q5VUT3|Q96QR4|Q9NUA0	Missense_Mutation	SNP	ENST00000270218.6	37	CCDS1469.1	1414	0.6474358974358975	400	0.8130081300813008	260	0.7182320441988951	166	0.2902097902097902	588	0.7757255936675461	C	1.417	-0.574023	0.03882	0.831744	0.778062	ENSG00000142224	ENST00000340758;ENST00000270218	T;T	0.37411	1.2;1.44	5.62	4.71	0.59529	Four-helical cytokine-like, core (1);	0.636913	0.14961	N	0.288344	T	0.00012	0.0000	N	0.00677	-1.265	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37957	-0.9683	9	0.02654	T	1	.	9.2473	0.37534	0.0:0.8326:0.0:0.1674	rs2243191;rs11564973;rs17016959;rs52821537;rs2243191	175;213	Q9UHD0;Q5VUT3	IL19_HUMAN;.	S	213;175	ENSP00000343000:F213S;ENSP00000270218:F175S	ENSP00000270218:F175S	F	+	2	0	IL19	205082580	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.253000	0.18296	0.870000	0.35726	-0.119000	0.15052	TTC	C|0.638;N|0.000	0.638	strong		0.498	IL19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088567.2	NM_153758	
MICALL2	79778	hgsc.bcm.edu	37	7	1478525	1478525	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1478525C>T	ENST00000297508.7	-	10	2248	c.2073G>A	c.(2071-2073)gtG>gtA	p.V691V	MICALL2_ENST00000405088.4_Silent_p.V479V|MICALL2_ENST00000471899.1_5'UTR	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	691	Mediates targeting to the cell plasma membrane. {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)		TCCAGCTCTGCACTCGGGCTT	0.652																																					p.V691V		Atlas-SNP	.											.	MICALL2	63	.	0			c.G2073A						PASS	.						61.0	61.0	61.0					7																	1478525		2203	4300	6503	SO:0001819	synonymous_variant	79778	exon10			GCTCTGCACTCGG	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.2073G>A	7.37:g.1478525C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Silent	SNP	ENST00000297508.7	37	CCDS5324.1																																																																																			.	.	none		0.652	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144874815	144874815	+	Missense_Mutation	SNP	T	T	C	rs1778155	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:144874815T>C	ENST00000369354.3	-	30	4982	c.4793A>G	c.(4792-4794)cAt>cGt	p.H1598R	RP4-791M13.5_ENST00000531288.1_RNA|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.H1598R|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.H1554R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.H1734R|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.H1734R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1598	NBPF. {ECO:0000255|PROSITE- ProRule:PRU00647}.			H -> R (in Ref. 4; CAH18128). {ECO:0000305}.	cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGACAAGGCATGGCTGCTGGA	0.582			T	PDGFRB	MPD																																p.H1598R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A4793G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS	894,3512		0,894,1309	199.0	182.0	188.0		4793,4793,4661	-6.7	0.0	1	dbSNP_89	188	2610,5982		0,2610,1686	yes	missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1	29,29,29	0,3504,2995	CC,CT,TT		30.3771,20.2905,26.958	benign,benign,benign	1598/2347,1598/2363,1554/2241	144874815	3504,9494	2203	4296	6499	SO:0001583	missense	9659	exon30			AAGGCATGGCTGC	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.4793A>G	1.37:g.144874815T>C	ENSP00000358360:p.His1598Arg	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	230	51	0.221739	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	.	.	.	.	.	.	.	.	.	.	T	11.52	1.664153	0.29604	0.202905	0.303771	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.02656	4.21;4.32;4.31;4.33;4.33	5.91	-6.68	0.01778	DUF1220 (2);	.	.	.	.	T	0.00845	0.0028	N	0.16266	0.395	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.001;0.006	T	0.45920	-0.9228	9	0.41790	T	0.15	.	16.709	0.85380	0.0:0.1767:0.0:0.8233	rs1778155;rs61807893	1554;1598	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	R	1554;1598;1598;1734;1734	ENSP00000327209:H1554R;ENSP00000358360:H1598R;ENSP00000358363:H1598R;ENSP00000435654:H1734R;ENSP00000358366:H1734R	ENSP00000327209:H1554R	H	-	2	0	PDE4DIP	143586172	0.002000	0.14202	0.003000	0.11579	0.836000	0.47400	-0.066000	0.11598	-1.172000	0.02762	-0.137000	0.14449	CAT	T|0.500;C|0.500	0.500	strong		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SLC22A16	85413	hgsc.bcm.edu	37	6	110777962	110777962	+	Silent	SNP	A	A	G	rs6907567	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:110777962A>G	ENST00000368919.3	-	2	378	c.312T>C	c.(310-312)aaT>aaC	p.N104N	SLC22A16_ENST00000439654.1_Silent_p.N104N|SLC22A16_ENST00000330550.4_Silent_p.N70N|SLC22A16_ENST00000461487.1_5'UTR|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	246	0	0		WXS	Illumina HiSeq	Phase_I	253	115	0.454545	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	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376881	168376881	+	lincRNA	SNP	T	T	G	rs200170849|rs71305248		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168376881T>G	ENST00000538528.1	-	0	738																											CCTGCAGTGTTGGGGGAGGAG	0.607																																					p.Q151P		Atlas-SNP	.											.	.	.	.	0			c.A452C						PASS	.																																					0	exon1			CAGTGTTGGGGGA																													6.37:g.168376881T>G		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	194	52	0.268041	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				GTGTGGGGAGGAGG|0.500;TGGGGGAGGAGA|0.500	.	alt		0.607	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
MSH4	4438	hgsc.bcm.edu	37	1	76378502	76378502	+	Missense_Mutation	SNP	G	G	A	rs5745549	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:76378502G>A	ENST00000263187.3	+	20	2845	c.2741G>A	c.(2740-2742)aGt>aAt	p.S914N		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	914			S -> N (in dbSNP:rs5745549). {ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						ATATATTTAAGTAACCTCAAG	0.358								Mismatch excision repair (MMR)					G|||	319	0.0636981	0.1369	0.0519	5008	,	,		11111	0.006		0.0547	False		,,,				2504	0.0419				p.S914N		Atlas-SNP	.											.	MSH4	147	.	0			c.G2741A	GRCh37	CM067702	MSH4	M	rs5745549	PASS	.	G	ASN/SER	553,3853	245.9+/-254.7	37,479,1687	53.0	56.0	55.0		2741	-0.3	1.0	1	dbSNP_114	55	344,8256	116.3+/-176.0	6,332,3962	yes	missense	MSH4	NM_002440.3	46	43,811,5649	AA,AG,GG		4.0,12.5511,6.8968	benign	914/937	76378502	897,12109	2203	4300	6503	SO:0001583	missense	4438	exon20			ATTTAAGTAACCT	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.2741G>A	1.37:g.76378502G>A	ENSP00000263187:p.Ser914Asn	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	49	0.563218	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	123	0.05631868131868132	62	0.12601626016260162	17	0.04696132596685083	6	0.01048951048951049	38	0.05013192612137203	G	10.83	1.461891	0.26248	0.125511	0.04	ENSG00000057468	ENST00000263187	D	0.87650	-2.28	5.22	-0.339	0.12647	.	0.393563	0.29389	N	0.012283	T	0.56124	0.1964	L	0.36672	1.1	0.46631	P	8.669999999999511E-4	B	0.33413	0.411	B	0.32465	0.146	T	0.41787	-0.9489	9	0.22109	T	0.4	-23.8937	0.4337	0.00475	0.2774:0.1328:0.2897:0.3001	rs5745549;rs52800973;rs60751948;rs5745549	914	O15457	MSH4_HUMAN	N	914	ENSP00000263187:S914N	ENSP00000263187:S914N	S	+	2	0	MSH4	76151090	1.000000	0.71417	0.980000	0.43619	0.828000	0.46876	0.830000	0.27462	-0.014000	0.14175	0.467000	0.42956	AGT	G|0.936;A|0.064	0.064	strong		0.358	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	
LRRC2	79442	hgsc.bcm.edu	37	3	46580591	46580591	+	Missense_Mutation	SNP	G	G	T	rs17078944	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:46580591G>T	ENST00000395905.3	-	4	826	c.434C>A	c.(433-435)gCg>gAg	p.A145E	LRRC2_ENST00000296144.3_Missense_Mutation_p.A145E	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	145			A -> E (in dbSNP:rs17078944). {ECO:0000269|PubMed:11896456}.							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		AATTCTCATCGCTTGAAATAA	0.423													G|||	1435	0.286542	0.1195	0.2622	5008	,	,		22068	0.2768		0.3718	False		,,,				2504	0.4519				p.A145E		Atlas-SNP	.											.	LRRC2	37	.	0			c.C434A						PASS	.	G	GLU/ALA	656,3750	281.1+/-275.7	42,572,1589	147.0	134.0	139.0		434	1.8	0.2	3	dbSNP_123	139	2894,5706	453.3+/-363.2	481,1932,1887	yes	missense	LRRC2	NM_024512.4	107	523,2504,3476	TT,TG,GG		33.6512,14.8888,27.2951	benign	145/372	46580591	3550,9456	2203	4300	6503	SO:0001583	missense	79442	exon4			CTCATCGCTTGAA	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"""leucine-rich repeat-containing 2"""			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.434C>A	3.37:g.46580591G>T	ENSP00000379241:p.Ala145Glu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	183	90	0.491803	NM_024512	B2RDQ7|Q96LT5	Missense_Mutation	SNP	ENST00000395905.3	37	CCDS2741.1	601	0.2751831501831502	74	0.15040650406504066	87	0.24033149171270718	158	0.2762237762237762	282	0.3720316622691293	G	2.344	-0.350518	0.05173	0.148888	0.336512	ENSG00000163827	ENST00000395905;ENST00000296144	T;T	0.42900	0.96;0.96	5.09	1.79	0.24919	.	0.636520	0.15631	N	0.252392	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.45862	-0.9232	9	0.17832	T	0.49	.	6.0349	0.19702	0.0946:0.0:0.4145:0.4909	rs17078944;rs52823125;rs17078944	145	Q9BYS8	LRRC2_HUMAN	E	145	ENSP00000379241:A145E;ENSP00000296144:A145E	ENSP00000296144:A145E	A	-	2	0	LRRC2	46555595	0.969000	0.33509	0.221000	0.23827	0.806000	0.45545	2.517000	0.45529	0.654000	0.30846	0.650000	0.86243	GCG	G|0.726;T|0.274	0.274	strong		0.423	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2		
DMRTA1	63951	hgsc.bcm.edu	37	9	22447655	22447655	+	Silent	SNP	T	T	A	rs558612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:22447655T>A	ENST00000325870.2	+	1	816	c.591T>A	c.(589-591)ggT>ggA	p.G197G		NM_022160.2	NP_071443.2	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	197					male mating behavior (GO:0060179)|ovarian follicle development (GO:0001541)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)		TGGGACTGGGTGCCTTGAGAC	0.632													T|||	1561	0.311701	0.3669	0.3963	5008	,	,		11356	0.2331		0.3022	False		,,,				2504	0.2679				p.G197G		Atlas-SNP	.											.	DMRTA1	29	.	0			c.T591A						PASS	.	T		1435,2893		253,929,982	14.0	17.0	16.0		591	-8.7	0.0	9	dbSNP_83	16	2418,6140		347,1724,2208	no	coding-synonymous	DMRTA1	NM_022160.2		600,2653,3190	AA,AT,TT		28.2543,33.1562,29.9007		197/505	22447655	3853,9033	2164	4279	6443	SO:0001819	synonymous_variant	63951	exon1			ACTGGGTGCCTTG	AJ290954	CCDS6514.1	9p21.3	2008-05-15			ENSG00000176399	ENSG00000176399			13826	protein-coding gene	gene with protein product		614803					Standard	NM_022160		Approved		uc003zpp.1	Q5VZB9	OTTHUMG00000019693	ENST00000325870.2:c.591T>A	9.37:g.22447655T>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	62	17	0.274194	NM_022160	A1L481|Q8N8Y9|Q9H4B9	Silent	SNP	ENST00000325870.2	37	CCDS6514.1																																																																																			T|0.705;A|0.295	0.295	strong		0.632	DMRTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051935.2		
STK32B	55351	hgsc.bcm.edu	37	4	5333091	5333091	+	Silent	SNP	G	G	A	rs16837029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:5333091G>A	ENST00000282908.5	+	4	827	c.405G>A	c.(403-405)gaG>gaA	p.E135E	STK32B_ENST00000512636.1_Silent_p.E88E|STK32B_ENST00000510398.1_Silent_p.E88E	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						TGGCCCTGGAGTATCTTCAGA	0.577													G|||	422	0.0842652	0.2171	0.0245	5008	,	,		19648	0.0397		0.0328	False		,,,				2504	0.046				p.E135E		Atlas-SNP	.											.	STK32B	87	.	0			c.G405A						PASS	.	G		741,3665	304.9+/-288.7	63,615,1525	79.0	72.0	75.0		405	-1.6	0.9	4	dbSNP_123	75	222,8378	92.6+/-154.6	6,210,4084	no	coding-synonymous	STK32B	NM_018401.1		69,825,5609	AA,AG,GG		2.5814,16.818,7.4043		135/415	5333091	963,12043	2203	4300	6503	SO:0001819	synonymous_variant	55351	exon4			CCTGGAGTATCTT	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.405G>A	4.37:g.5333091G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_018401		Silent	SNP	ENST00000282908.5	37	CCDS3380.1																																																																																			G|0.926;A|0.074	0.074	strong		0.577	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
ZNF438	220929	hgsc.bcm.edu	37	10	31138817	31138817	+	Missense_Mutation	SNP	G	G	A	rs10160116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:31138817G>A	ENST00000361310.3	-	6	846	c.517C>T	c.(517-519)Ccc>Tcc	p.P173S	ZNF438_ENST00000538351.2_Missense_Mutation_p.P124S|ZNF438_ENST00000436087.2_Missense_Mutation_p.P173S|ZNF438_ENST00000444692.2_Missense_Mutation_p.P163S|ZNF438_ENST00000452305.1_Missense_Mutation_p.P163S|ZNF438_ENST00000375311.1_Intron|ZNF438_ENST00000331737.6_Missense_Mutation_p.P163S|ZNF438_ENST00000413025.1_Missense_Mutation_p.P173S|ZNF438_ENST00000442986.1_Missense_Mutation_p.P173S			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	173			P -> S (in dbSNP:rs10160116). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				AATGGACTGGGTTTGTACAGG	0.537													G|||	1880	0.375399	0.326	0.4308	5008	,	,		19303	0.3978		0.3479	False		,,,				2504	0.408				p.P173S		Atlas-SNP	.											.	ZNF438	90	.	0			c.C517T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	1464,2942	472.4+/-356.4	257,950,996	184.0	180.0	181.0		517,517,517,370,487,487,517	1.2	0.0	10	dbSNP_119	181	3242,5358	487.8+/-372.2	607,2028,1665	yes	missense,missense,missense,missense,missense,missense,missense	ZNF438	NM_001143766.1,NM_001143767.1,NM_001143768.1,NM_001143769.1,NM_001143770.1,NM_001143771.1,NM_182755.2	74,74,74,74,74,74,74	864,2978,2661	AA,AG,GG		37.6977,33.2274,36.1833	benign,benign,benign,benign,benign,benign,benign	173/829,173/829,173/829,124/780,163/819,163/819,173/829	31138817	4706,8300	2203	4300	6503	SO:0001583	missense	220929	exon7			GACTGGGTTTGTA	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"""Zinc fingers, C2H2-type"""	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.517C>T	10.37:g.31138817G>A	ENSP00000354663:p.Pro173Ser	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	144	70	0.486111	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	37	CCDS7168.1	831	0.3804945054945055	159	0.3231707317073171	164	0.4530386740331492	232	0.40559440559440557	276	0.3641160949868074	G	4.324	0.059571	0.08339	0.332274	0.376977	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351	T;T;T;T;T;T;T;T	0.09073	3.02;3.03;3.03;3.03;3.03;3.02;3.02;3.03	5.63	1.18	0.20946	.	0.795778	0.12376	N	0.474327	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B;B	0.21225	0.031;0.053	B;B	0.17722	0.009;0.019	T	0.45848	-0.9233	9	0.06757	T	0.87	-9.3051	2.5867	0.04832	0.0921:0.3113:0.2257:0.3709	rs10160116;rs59589778;rs10160116	173;163	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	S	163;173;173;173;173;163;163;124	ENSP00000333571:P163S;ENSP00000354663:P173S;ENSP00000406934:P173S;ENSP00000412363:P173S;ENSP00000387546:P173S;ENSP00000413060:P163S;ENSP00000410898:P163S;ENSP00000445461:P124S	ENSP00000333571:P163S	P	-	1	0	ZNF438	31178823	0.000000	0.05858	0.001000	0.08648	0.285000	0.27093	0.165000	0.16564	0.010000	0.14839	0.655000	0.94253	CCC	G|0.641;A|0.359	0.359	strong		0.537	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755	
OR51F1	256892	hgsc.bcm.edu	37	11	4790410	4790410	+	Silent	SNP	A	A	G	rs1030724	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4790410A>G	ENST00000380383.1	-	1	758	c.759T>C	c.(757-759)caT>caC	p.H253H	OR51F1_ENST00000343430.3_Silent_p.H246H|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, 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)			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)		CTGCTCCCACATGGGAGACAC	0.493													G|||	1079	0.215455	0.4561	0.2017	5008	,	,		21390	0.0		0.2704	False		,,,				2504	0.0654				p.H246H		Atlas-SNP	.											OR51F1,right_upper_lobe,carcinoma,-2,1	OR51F1	60	1	0			c.T738C						scavenged	.	G		1965,2437	619.1+/-393.3	445,1075,681	101.0	91.0	95.0		738	2.3	1.0	11	dbSNP_86	95	2178,6418	712.3+/-405.9	291,1596,2411	no	coding-synonymous	OR51F1	NM_001004752.1		736,2671,3092	GG,GA,AA		25.3374,44.6388,31.8741		246/313	4790410	4143,8855	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			TCCCACATGGGAG	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.759T>C	11.37:g.4790410A>G		Somatic	130	2	0.0153846		WXS	Illumina HiSeq	Phase_I	153	87	0.568627	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.707;G|0.293	0.293	strong		0.493	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
HERC2	8924	hgsc.bcm.edu	37	15	28422609	28422609	+	Silent	SNP	C	C	T	rs61756153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:28422609C>T	ENST00000261609.7	-	60	9318	c.9210G>A	c.(9208-9210)tcG>tcA	p.S3070S		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTTCGCCCCACGAAAACACTT	0.473													C|||	773	0.154353	0.0083	0.0836	5008	,	,		18473	0.3929		0.0855	False		,,,				2504	0.227				p.S3070S		Atlas-SNP	.											HERC2,NS,adenoma,-1,1	HERC2	501	1	0			c.G9210A						PASS	.	C		83,4323	67.6+/-105.2	1,81,2121	100.0	88.0	92.0		9210	-8.8	0.6	15	dbSNP_129	92	463,8137	138.4+/-195.2	13,437,3850	no	coding-synonymous	HERC2	NM_004667.4		14,518,5971	TT,TC,CC		5.3837,1.8838,4.1981		3070/4835	28422609	546,12460	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon60			GCCCCACGAAAAC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9210G>A	15.37:g.28422609C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|0.932;T|0.068	0.068	strong		0.473	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
GPATCH1	55094	hgsc.bcm.edu	37	19	33600764	33600764	+	Missense_Mutation	SNP	T	T	C	rs2287679	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	84	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	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	
NLRP13	126204	hgsc.bcm.edu	37	19	56410222	56410222	+	Silent	SNP	C	C	T	rs302827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56410222C>T	ENST00000342929.3	-	10	2870	c.2871G>A	c.(2869-2871)ttG>ttA	p.L957L	NLRP13_ENST00000588751.1_Silent_p.L957L	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	957							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		CTCCCAAATCCAAGATTTTCA	0.438													C|||	1395	0.278554	0.1626	0.2493	5008	,	,		20206	0.4246		0.2803	False		,,,				2504	0.3037				p.L957L		Atlas-SNP	.											.	NLRP13	220	.	0			c.G2871A						PASS	.	C		720,3686	299.8+/-286.0	61,598,1544	178.0	150.0	159.0		2871	0.7	0.0	19	dbSNP_79	159	2504,6096	409.9+/-350.0	366,1772,2162	no	coding-synonymous	NLRP13	NM_176810.2		427,2370,3706	TT,TC,CC		29.1163,16.3414,24.7886		957/1044	56410222	3224,9782	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon10			CAAATCCAAGATT	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.2871G>A	19.37:g.56410222C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			C|0.739;T|0.261	0.261	strong		0.438	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
RTEL1	51750	hgsc.bcm.edu	37	20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	rs190887884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62322290G>A	ENST00000360203.5	+	27	2871	c.2546G>A	c.(2545-2547)gGc>gAc	p.G849D	RTEL1_ENST00000318100.4_Missense_Mutation_p.G849D|RTEL1_ENST00000508582.2_Missense_Mutation_p.G873D|RTEL1_ENST00000370003.1_Missense_Mutation_p.G94D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.G849D|RTEL1_ENST00000370018.3_Missense_Mutation_p.G849D					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			GGGAGCCCTGGCGAGGAGCAG	0.687													G|||	23	0.00459265	0.0023	0.0058	5008	,	,		15022	0.0		0.0099	False		,,,				2504	0.0061				p.G873D		Atlas-SNP	.											.	RTEL1	114	.	0			c.G2618A						PASS	.	G	ASP/GLY,ASP/GLY	9,4167		0,9,2079	14.0	15.0	14.0		2546,2618	-0.1	0.0	20		14	113,8185		0,113,4036	yes	missense,missense	RTEL1	NM_016434.3,NM_032957.4	94,94	0,122,6115	AA,AG,GG		1.3618,0.2155,0.978	benign,benign	849/1220,873/1244	62322290	122,12352	2088	4149	6237	SO:0001583	missense	51750	exon27			GCCCTGGCGAGGA	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.2546G>A	20.37:g.62322290G>A	ENSP00000353332:p.Gly849Asp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	11.51	1.659474	0.29515	0.002155	0.013618	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	4.77	-0.131	0.13494	.	0.888187	0.09800	N	0.754121	T	0.04679	0.0127	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.34290	0.052;0.447;0.003;0.008	B;B;B;B	0.35413	0.075;0.202;0.017;0.046	T	0.38972	-0.9636	10	0.23302	T	0.38	-13.4816	2.5812	0.04818	0.4374:0.0:0.343:0.2196	.	873;94;849;849	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	D	849;849;873;849;94	ENSP00000359035:G849D;ENSP00000322287:G849D;ENSP00000424307:G873D;ENSP00000353332:G849D;ENSP00000359020:G94D	ENSP00000353332:G849D	G	+	2	0	AL353715.1	61792734	0.001000	0.12720	0.005000	0.12908	0.006000	0.05464	0.096000	0.15147	0.093000	0.17368	-0.217000	0.12591	GGC	G|0.994;A|0.006	0.006	strong		0.687	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
TRPV6	55503	hgsc.bcm.edu	37	7	142574544	142574544	+	Silent	SNP	G	G	A	rs138110961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142574544G>A	ENST00000359396.3	-	5	779	c.534C>T	c.(532-534)atC>atT	p.I178I	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	178					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)					GCAGCCGCACGATCTCCTCAC	0.597													G|||	3	0.000599042	0.0	0.0029	5008	,	,		20351	0.0		0.001	False		,,,				2504	0.0				p.I178I		Atlas-SNP	.											.	TRPV6	108	.	0			c.C534T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	101.0	86.0	91.0		534	-9.3	0.0	7	dbSNP_134	91	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	TRPV6	NM_018646.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		178/726	142574544	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon5			CCGCACGATCTCC	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.534C>T	7.37:g.142574544G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	167	86	0.51497	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			G|0.999;A|0.001	0.001	strong		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
ERBB3	2065	hgsc.bcm.edu	37	12	56494991	56494991	+	Silent	SNP	G	G	A	rs2271189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56494991G>A	ENST00000267101.3	+	27	3788	c.3348G>A	c.(3346-3348)agG>agA	p.R1116R	ERBB3_ENST00000450146.2_Silent_p.R473R|ERBB3_ENST00000549832.1_Silent_p.R236R|ERBB3_ENST00000553131.1_Silent_p.R357R|ERBB3_ENST00000415288.2_Silent_p.R1057R|RP11-603J24.9_ENST00000548861.1_5'Flank	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1116					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)			CAATGTGTAGGAGCCGGAGCA	0.617													G|||	1263	0.252196	0.0734	0.3718	5008	,	,		13537	0.2887		0.4036	False		,,,				2504	0.2157				p.R1116R		Atlas-SNP	.											.	ERBB3	350	.	0			c.G3348A						PASS	.	G		620,3786	269.8+/-269.2	44,532,1627	54.0	52.0	52.0		3348	-0.8	1.0	12	dbSNP_100	52	3413,5187	503.3+/-375.9	692,2029,1579	no	coding-synonymous	ERBB3	NM_001982.3		736,2561,3206	AA,AG,GG		39.686,14.0717,31.0088		1116/1343	56494991	4033,8973	2203	4300	6503	SO:0001819	synonymous_variant	2065	exon27			GTGTAGGAGCCGG	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.3348G>A	12.37:g.56494991G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	36	0.378947	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	37	CCDS31833.1																																																																																			G|0.703;A|0.297	0.297	strong		0.617	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
P2RX7	5027	hgsc.bcm.edu	37	12	121622304	121622304	+	Missense_Mutation	SNP	A	A	C	rs3751143	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:121622304A>C	ENST00000546057.1	+	13	1630	c.1487A>C	c.(1486-1488)gAg>gCg	p.E496A	P2RX7_ENST00000328963.5_Missense_Mutation_p.E326A|P2RX7_ENST00000535250.1_Missense_Mutation_p.E406A|P2RX7_ENST00000541446.1_Missense_Mutation_p.E207A|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	496			E -> A (polymorphism that results in a loss of function; dbSNP:rs3751143). {ECO:0000269|PubMed:11150303, ECO:0000269|PubMed:15489334}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGCCTGGAGGAGCTGTGCTGC	0.607													A|||	1039	0.207468	0.0847	0.1916	5008	,	,		16659	0.2669		0.2087	False		,,,				2504	0.3221				p.E496A		Atlas-SNP	.											.	P2RX7	53	.	0			c.A1487C	GRCh37	CM021316	P2RX7	M	rs3751143	PASS	.	A	ALA/GLU	396,4010	194.7+/-219.5	19,358,1826	41.0	40.0	40.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1487	5.2	1.0	12	dbSNP_107	40	1590,7010	294.4+/-301.9	151,1288,2861	yes	missense	P2RX7	NM_002562.5	107	170,1646,4687	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	18.4884,8.9877,15.2699	probably-damaging	496/596	121622304	1986,11020	2203	4300	6503	SO:0001583	missense	5027	exon13			TGGAGGAGCTGTG	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1487A>C	12.37:g.121622304A>C	ENSP00000442349:p.Glu496Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	421	0.19276556776556777	43	0.08739837398373984	77	0.212707182320442	146	0.25524475524475526	155	0.20448548812664907	A	25.1	4.606826	0.87157	0.089877	0.184884	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05580	4.32;3.93;4.1;3.42	5.21	5.21	0.72293	.	0.000000	0.45867	D	0.000340	T	0.00012	0.0000	M	0.80982	2.52	0.27905	P	0.9388482	D;D;D;D	0.71674	0.986;0.998;0.986;0.991	P;D;P;P	0.81914	0.84;0.995;0.84;0.831	T	0.13710	-1.0499	9	0.87932	D	0	-30.5986	12.4464	0.55653	1.0:0.0:0.0:0.0	rs3751143;rs17850236;rs58839176;rs3751143	326;207;406;496	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	A	496;326;406;207	ENSP00000442349:E496A;ENSP00000330696:E326A;ENSP00000442572:E406A;ENSP00000437471:E207A	ENSP00000330696:E326A	E	+	2	0	P2RX7	120106687	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.490000	0.73645	1.967000	0.57214	0.482000	0.46254	GAG	A|0.826;C|0.174	0.174	strong		0.607	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
TEX10	54881	hgsc.bcm.edu	37	9	103064530	103064530	+	Silent	SNP	G	G	A	rs7472	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	104	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	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	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993264	140993264	+	Missense_Mutation	SNP	G	G	A	rs176036	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:140993264G>A	ENST00000285879.4	+	4	360	c.74G>A	c.(73-75)tGt>tAt	p.C25Y	MAGEC1_ENST00000406005.2_5'UTR	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	25			C -> Y (in dbSNP:rs176036). {ECO:0000269|PubMed:9485030}.							breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CCTCAGAGTTGTCCTGAGGGG	0.562										HNSCC(15;0.026)			G|||	490	0.129801	0.1225	0.1182	3775	,	,		13207	0.0466		0.164	False		,,,				2504	0.0348				p.C25Y		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G74A						PASS	.	G	TYR/CYS	612,3223		43,438,88,1151,483	71.0	70.0	71.0		74	-0.3	0.0	X	dbSNP_79	71	1399,5329		100,803,396,1525,1476	yes	missense	MAGEC1	NM_005462.4	194	143,1241,484,2676,1959	AA,AG,A,GG,G		20.7937,15.9583,19.0382	possibly-damaging	25/1143	140993264	2011,8552	2203	4300	6503	SO:0001583	missense	9947	exon4			AGAGTTGTCCTGA	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.74G>A	X.37:g.140993264G>A	ENSP00000285879:p.Cys25Tyr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	255	0.15370705244122965	39	0.08441558441558442	30	0.09090909090909091	16	0.029411764705882353	85	0.12536873156342182	g	4.683	0.126992	0.08931	0.159583	0.207937	ENSG00000155495	ENST00000285879;ENST00000370511;ENST00000370510	T;T	0.12569	4.02;2.67	0.149	-0.298	0.12814	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.2000000000032E-5	P	0.42993	0.797	B	0.42343	0.384	T	0.37150	-0.9718	7	0.41790	T	0.15	.	.	.	.	rs176036;rs389145	25	O60732	MAGC1_HUMAN	Y	25;25;24	ENSP00000285879:C25Y;ENSP00000359542:C25Y	ENSP00000285879:C25Y	C	+	2	0	MAGEC1	140820930	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-2.582000	0.00905	-1.172000	0.02762	-1.175000	0.01729	TGT	G|0.829;A|0.171	0.171	strong		0.562	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
ZFHX3	463	hgsc.bcm.edu	37	16	72992221	72992221	+	Silent	SNP	G	G	A	rs61735550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:72992221G>A	ENST00000268489.5	-	2	2496	c.1824C>T	c.(1822-1824)agC>agT	p.S608S	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	608					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CACCCTCTGTGCTTTCATTTG	0.617													G|||	416	0.0830671	0.0174	0.098	5008	,	,		18070	0.0		0.2306	False		,,,				2504	0.0951				p.S608S		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C1824T						PASS	.	G	,	239,4157	140.4+/-175.9	9,221,1968	102.0	95.0	97.0		,1824	4.3	1.0	16	dbSNP_129	97	2109,6491	364.6+/-333.6	259,1591,2450	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	268,1812,4418	AA,AG,GG		24.5233,5.4368,18.0671	,	,608/3704	72992221	2348,10648	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCTGTGCTTTCA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1824C>T	16.37:g.72992221G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	210	95	0.452381	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			G|0.830;A|0.170	0.170	strong		0.617	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
TBCD	6904	hgsc.bcm.edu	37	17	80710097	80710097	+	Missense_Mutation	SNP	G	G	T	rs11550062	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80710097G>T	ENST00000355528.4	+	1	158	c.28G>T	c.(28-30)Ggc>Tgc	p.G10C	TBCD_ENST00000397466.2_5'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.G10C	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	10					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			ACCGGCCGCGGGCGGCCCCGA	0.741													G|||	564	0.11262	0.0045	0.0692	5008	,	,		8990	0.0685		0.1342	False		,,,				2504	0.3129				p.G10C		Atlas-SNP	.											TBCD_ENST00000355528,rectum,carcinoma,-2,1	TBCD	94	1	0			c.G28T						PASS	.	G	CYS/GLY	61,2941		0,61,1440	3.0	4.0	4.0		28	1.0	0.0	17	dbSNP_120	4	657,5909		15,627,2641	no	missense	TBCD	NM_005993.4	159	15,688,4081	TT,TG,GG		10.0061,2.032,7.5042	probably-damaging	10/1193	80710097	718,8850	1501	3283	4784	SO:0001583	missense	6904	exon1			GCCGCGGGCGGCC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.28G>T	17.37:g.80710097G>T	ENSP00000347719:p.Gly10Cys	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	16	11	0.6875	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	179	0.08195970695970696	10	0.02032520325203252	29	0.08011049723756906	39	0.06818181818181818	101	0.13324538258575197	G	16.63	3.175996	0.57692	0.02032	0.100061	ENSG00000141556	ENST00000355528;ENST00000269368;ENST00000536182	T	0.18960	2.18	2.39	0.978	0.19740	.	.	.	.	.	T	0.00178	0.0005	N	0.22421	0.69	0.27423	P	0.9542346	D;D;D	0.65815	0.986;0.995;0.982	P;P;P	0.52909	0.52;0.713;0.54	T	0.17623	-1.0363	7	.	.	.	.	6.572	0.22543	0.2283:0.0:0.7717:0.0	rs11550062	10;10;10	Q9BTW9;Q9BTW9-4;F5H8C7	TBCD_HUMAN;.;.	C	10	ENSP00000347719:G10C	.	G	+	1	0	TBCD	78303386	0.004000	0.15560	0.001000	0.08648	0.006000	0.05464	0.507000	0.22675	0.309000	0.22966	0.456000	0.33151	GGC	G|0.918;T|0.082	0.082	strong		0.741	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
PCNT	5116	hgsc.bcm.edu	37	21	47850484	47850484	+	Missense_Mutation	SNP	G	G	C	rs2070426	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47850484G>C	ENST00000359568.5	+	37	8084	c.7977G>C	c.(7975-7977)caG>caC	p.Q2659H	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2659			Q -> H (in dbSNP:rs2070426).		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)					AGAGTGAGCAGGGGAAGGGGC	0.627													G|||	2445	0.488219	0.3321	0.451	5008	,	,		20208	0.6141		0.5586	False		,,,				2504	0.5235				p.Q2659H		Atlas-SNP	.											.	PCNT	283	.	0			c.G7977C						PASS	.	G	HIS/GLN	1499,2885		286,927,979	32.0	28.0	29.0		7977	-9.5	0.0	21	dbSNP_96	29	4764,3790		1354,2056,867	yes	missense	PCNT	NM_006031.5	24	1640,2983,1846	CC,CG,GG		44.3068,34.1925,48.4078	benign	2659/3337	47850484	6263,6675	2192	4277	6469	SO:0001583	missense	5116	exon37			TGAGCAGGGGAAG	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.7977G>C	21.37:g.47850484G>C	ENSP00000352572:p.Gln2659His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	1126	0.5155677655677655	161	0.32723577235772355	166	0.4585635359116022	372	0.6503496503496503	427	0.5633245382585752	G	12.67	2.006586	0.35415	0.341925	0.556932	ENSG00000160299	ENST00000359568	T	0.02158	4.42	4.76	-9.46	0.00597	.	0.556644	0.13677	N	0.370482	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	B;B	0.18863	0.001;0.031	B;B	0.08055	0.003;0.003	T	0.46400	-0.9194	9	0.66056	D	0.02	.	4.3016	0.10927	0.0772:0.2126:0.3976:0.3127	rs2070426;rs58578374;rs2070426	2541;2659	O95613-2;O95613	.;PCNT_HUMAN	H	2659	ENSP00000352572:Q2659H	ENSP00000352572:Q2659H	Q	+	3	2	PCNT	46674912	0.000000	0.05858	0.000000	0.03702	0.187000	0.23431	-3.277000	0.00529	-1.418000	0.02014	-0.302000	0.09304	CAG	G|0.520;C|0.480	0.480	strong		0.627	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MUC5B	727897	hgsc.bcm.edu	37	11	1268955	1268955	+	Silent	SNP	C	C	T	rs2943523	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1268955C>T	ENST00000529681.1	+	31	10903	c.10845C>T	c.(10843-10845)ctC>ctT	p.L3615L	MUC5B_ENST00000447027.1_Silent_p.L3618L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3615	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)		CCCTGGGCCTCGAGTGCCGTG	0.677													-|||	648	0.129393	0.0862	0.2378	5008	,	,		12284	0.0645		0.1491	False		,,,				2504	0.1575				p.L3615L		Atlas-SNP	.											MUC5AC,colon,carcinoma,+1,1	MUC5B	473	1	0			c.C10845T						scavenged	.	T		348,3338		63,222,1558	30.0	32.0	31.0		10845	-8.0	0.0	11	dbSNP_134	31	1209,6841		266,677,3082	no	coding-synonymous	MUC5B	NM_002458.2		329,899,4640	TT,TC,CC		15.0186,9.4411,13.2669		3615/5763	1268955	1557,10179	1843	4025	5868	SO:0001819	synonymous_variant	727897	exon31			GGGCCTCGAGTGC	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.10845C>T	11.37:g.1268955C>T		Somatic	441	2	0.00453515		WXS	Illumina HiSeq	Phase_I	732	354	0.483607	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	weak		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SECTM1	6398	hgsc.bcm.edu	37	17	80280865	80280865	+	Silent	SNP	G	G	A	rs11077986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:80280865G>A	ENST00000269389.3	-	4	776	c.426C>T	c.(424-426)ccC>ccT	p.P142P	SECTM1_ENST00000580437.1_Intron	NM_003004.2	NP_002995.1	Q8WVN6	SCTM1_HUMAN	secreted and transmembrane 1	142					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)			ACCCAGTGTCGGGGGCGGACT	0.642													g|||	1639	0.327276	0.034	0.2795	5008	,	,		14758	0.5635		0.5328	False		,,,				2504	0.3027				p.P142P		Atlas-SNP	.											.	SECTM1	14	.	0			c.C426T						PASS	.			508,3898	222.0+/-238.9	38,432,1733	47.0	42.0	44.0		426	-3.1	0.0	17	dbSNP_120	44	4473,4125	572.5+/-389.7	1171,2131,997	yes	coding-synonymous	SECTM1	NM_003004.2		1209,2563,2730	AA,AG,GG		47.9763,11.5297,38.3036		142/249	80280865	4981,8023	2203	4299	6502	SO:0001819	synonymous_variant	6398	exon4			AGTGTCGGGGGCG	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.426C>T	17.37:g.80280865G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	139	69	0.496403	NM_003004	B2R7H0|O00466	Silent	SNP	ENST00000269389.3	37	CCDS11808.1																																																																																			G|0.614;A|0.386	0.386	strong		0.642	SECTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442856.1	NM_003004	
IGSF9B	22997	hgsc.bcm.edu	37	11	133805585	133805585	+	Silent	SNP	C	C	T	rs329637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:133805585C>T	ENST00000321016.8	-	7	1124	c.894G>A	c.(892-894)tcG>tcA	p.S298S	IGSF9B_ENST00000533871.2_Silent_p.S298S			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	298	Ig-like 3.				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)		TGTACTTCCCCGAGTCCTCCG	0.652													C|||	1498	0.299121	0.143	0.33	5008	,	,		19216	0.3284		0.4334	False		,,,				2504	0.32				p.S298S		Atlas-SNP	.											IGSF9B_ENST00000321016,NS,carcinoma,0,1	IGSF9B	290	1	0			c.G894A						PASS	.	C		807,3275		93,621,1327	25.0	30.0	28.0		894	-10.7	0.0	11	dbSNP_79	28	3452,4904		714,2024,1440	no	coding-synonymous	IGSF9B	NM_014987.1		807,2645,2767	TT,TC,CC		41.3116,19.7697,34.2418		298/1350	133805585	4259,8179	2041	4178	6219	SO:0001819	synonymous_variant	22997	exon7			CTTCCCCGAGTCC	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.894G>A	11.37:g.133805585C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				C|0.682;T|0.318	0.318	strong		0.652	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
B3GNT3	10331	hgsc.bcm.edu	37	19	17919024	17919024	+	Silent	SNP	A	A	T	rs2240813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17919024A>T	ENST00000318683.6	+	2	555	c.408A>T	c.(406-408)gtA>gtT	p.V136V	B3GNT3_ENST00000595387.1_Silent_p.V136V	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	136					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 plasma membrane (GO:0005887)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)|galactosyltransferase activity (GO:0008378)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						AGCGCAAGGTACGGGGTTTGC	0.682													G|||	646	0.128994	0.1309	0.1931	5008	,	,		13801	0.1577		0.0696	False		,,,				2504	0.1125				p.V136V		Atlas-SNP	.											.	B3GNT3	40	.	0			c.A408T						PASS	.	G		493,3913		23,447,1733	26.0	28.0	28.0		408	-5.4	0.0	19	dbSNP_98	28	615,7983		27,561,3711	no	coding-synonymous	B3GNT3	NM_014256.3		50,1008,5444	TT,TA,AA		7.1528,11.1893,8.5205		136/373	17919024	1108,11896	2203	4299	6502	SO:0001819	synonymous_variant	10331	exon2			CAAGGTACGGGGT	AB015630	CCDS12364.1	19p13.1	2013-02-19				ENSG00000179913		"""Beta 3-glycosyltransferases"""	13528	protein-coding gene	gene with protein product	"""putative type II membrane protein"", ""beta-1,3-N-acetylglucosaminyltransferase bGnT-3"", ""transmembrane protein 3"""	605863		TMEM3		10072769, 11042166	Standard	NM_014256		Approved	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3	uc002nhl.1	Q9Y2A9		ENST00000318683.6:c.408A>T	19.37:g.17919024A>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_014256	B2RAS4|Q6NWU9|Q6NXU9|Q8WWR6|Q9C0J2	Silent	SNP	ENST00000318683.6	37	CCDS12364.1																																																																																			A|0.903;T|0.097	0.097	strong		0.682	B3GNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466877.1	NM_014256	
B4GALT7	11285	hgsc.bcm.edu	37	5	177031348	177031348	+	Silent	SNP	T	T	C	rs11537644	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:177031348T>C	ENST00000029410.5	+	2	330	c.219T>C	c.(217-219)cgT>cgC	p.R73R		NM_007255.2	NP_009186.1	Q9UBV7	B4GT7_HUMAN	xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7	73					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|chondroitin sulfate metabolic process (GO:0030204)|extracellular fibril organization (GO:0043206)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of fibroblast proliferation (GO:0048147)|protein N-linked glycosylation (GO:0006487)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	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)|manganese ion binding (GO:0030145)|xylosylprotein 4-beta-galactosyltransferase activity (GO:0046525)			endometrium(2)|large_intestine(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	7	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)			GCCCTCCCCGTGCCTGCCCCC	0.706													t|||	3312	0.661342	0.6316	0.6859	5008	,	,		12131	0.7837		0.6332	False		,,,				2504	0.5869				p.R73R		Atlas-SNP	.											.	B4GALT7	21	.	0			c.T219C						PASS	.	G		2877,1523		951,975,274	15.0	14.0	15.0		219	0.9	0.0	5	dbSNP_120	15	5331,3243		1686,1959,642	no	coding-synonymous	B4GALT7	NM_007255.2		2637,2934,916	CC,CT,TT		37.8237,34.6136,36.735		73/328	177031348	8208,4766	2200	4287	6487	SO:0001819	synonymous_variant	11285	exon2			TCCCCGTGCCTGC	AB028600	CCDS4429.1	5q35.1-q35.3	2013-02-19	2012-07-18		ENSG00000027847	ENSG00000027847		"""Beta 4-glycosyltransferases"""	930	protein-coding gene	gene with protein product	"""galactosyltransferase I"""	604327				10438455, 10473568	Standard	NM_007255		Approved	XGALT-1, beta4Gal-T7	uc003mhy.3	Q9UBV7	OTTHUMG00000130851	ENST00000029410.5:c.219T>C	5.37:g.177031348T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_007255	B3KN39|Q9UHN2	Silent	SNP	ENST00000029410.5	37	CCDS4429.1																																																																																			T|0.352;C|0.648	0.648	strong		0.706	B4GALT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253421.1	NM_007255	
FAM71F2	346653	hgsc.bcm.edu	37	7	128315882	128315882	+	Missense_Mutation	SNP	C	C	A	rs17169357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:128315882C>A	ENST00000480462.1	+	2	440	c.334C>A	c.(334-336)Cct>Act	p.P112T	FAM71F2_ENST00000378704.3_Missense_Mutation_p.P103T|FAM71F2_ENST00000477515.1_Missense_Mutation_p.P112T|FAM71F2_ENST00000460349.1_3'UTR			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	112			P -> T (in dbSNP:rs17169357). {ECO:0000269|PubMed:15489334}.							NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						CTGGAGCACACCTGGTGACGC	0.587													.|||	1655	0.330471	0.177	0.3098	5008	,	,		15407	0.5615		0.2903	False		,,,				2504	0.3558				p.P112T		Atlas-SNP	.											.	FAM71F2	19	.	0			c.C334A						PASS	.	C	THR/PRO,THR/PRO	735,3091		76,583,1254	46.0	43.0	44.0		334,307	1.8	0.0	7	dbSNP_123	44	2459,5803		379,1701,2051	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	38,38	455,2284,3305	AA,AC,CC		29.7628,19.2107,26.4229	benign,benign	112/310,103/301	128315882	3194,8894	1913	4131	6044	SO:0001583	missense	346653	exon2			AGCACACCTGGTG	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.334C>A	7.37:g.128315882C>A	ENSP00000420140:p.Pro112Thr	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	708	0.3241758241758242	98	0.1991869918699187	101	0.27900552486187846	296	0.5174825174825175	213	0.28100263852242746	C	7.819	0.717347	0.15372	0.192107	0.297628	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001;ENST00000477515	T;T;T;T;T	0.35236	3.18;3.17;3.18;3.18;1.32	4.67	1.77	0.24775	.	0.291939	0.24851	N	0.035089	T	0.00012	0.0000	M	0.68593	2.085	0.80722	P	0.0	B;B	0.20671	0.047;0.028	B;B	0.21151	0.033;0.015	T	0.45891	-0.9230	9	0.20046	T	0.44	-12.2044	2.8366	0.05516	0.1903:0.5257:0.1841:0.0999	rs17169357;rs52807763;rs17169357	103;112	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	T	103;112;103;103;112	ENSP00000418907:P103T;ENSP00000420140:P112T;ENSP00000367976:P103T;ENSP00000401654:P103T;ENSP00000419649:P112T	ENSP00000367976:P103T	P	+	1	0	FAM71F2	128103118	0.014000	0.17966	0.005000	0.12908	0.419000	0.31324	1.082000	0.30803	0.653000	0.30826	0.557000	0.71058	CCT	C|0.664;A|0.335	0.335	strong		0.587	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
SACS	26278	hgsc.bcm.edu	37	13	23911820	23911820	+	Silent	SNP	A	A	G	rs4143768	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:23911820A>G	ENST00000382292.3	-	9	6468	c.6195T>C	c.(6193-6195)atT>atC	p.I2065I	SACS_ENST00000402364.1_Silent_p.I1315I|SACS_ENST00000382298.3_Silent_p.I2065I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2065					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)		CAATTTCTTGAATATTTGGAA	0.333													A|||	1302	0.259984	0.056	0.3617	5008	,	,		19205	0.3155		0.2783	False		,,,				2504	0.3875				p.I2065I		Atlas-SNP	.											.	SACS	871	.	0			c.T6195C						PASS	.	A		421,3981		22,377,1802	30.0	32.0	31.0		6195	-2.4	1.0	13	dbSNP_110	31	2223,6367		295,1633,2367	yes	coding-synonymous	SACS	NM_014363.4		317,2010,4169	GG,GA,AA		25.8789,9.5638,20.351		2065/4580	23911820	2644,10348	2201	4295	6496	SO:0001819	synonymous_variant	26278	exon10			TTCTTGAATATTT	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.6195T>C	13.37:g.23911820A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			A|0.760;G|0.240	0.240	strong		0.333	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
RELL2	285613	hgsc.bcm.edu	37	5	141019569	141019569	+	Missense_Mutation	SNP	G	G	C	rs17855844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:141019569G>C	ENST00000297164.3	+	5	1786	c.586G>C	c.(586-588)Ggt>Cgt	p.G196R	FCHSD1_ENST00000435817.2_3'UTR|RELL2_ENST00000444782.1_Missense_Mutation_p.G196R|RELL2_ENST00000521367.1_Missense_Mutation_p.G130R|RELL2_ENST00000518856.1_Missense_Mutation_p.G130R|RELL2_ENST00000518025.1_3'UTR|FCHSD1_ENST00000523856.1_5'UTR	NM_173828.4	NP_776189.3	Q8NC24	RELL2_HUMAN	RELT-like 2	196			G -> R (in dbSNP:rs17855844). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGGGCTCTGGTGGGGGACA	0.667													G|||	921	0.183906	0.1225	0.2205	5008	,	,		14783	0.1468		0.161	False		,,,				2504	0.3027				p.G196R		Atlas-SNP	.											.	RELL2	24	.	0			c.G586C						PASS	.	G	ARG/GLY,,ARG/GLY	605,3801		42,521,1640	38.0	44.0	42.0		586,,586	3.1	1.0	5	dbSNP_123	42	1673,6925		171,1331,2797	yes	missense,utr-3,missense	FCHSD1,RELL2	NM_001130029.1,NM_033449.2,NM_173828.4	125,,125	213,1852,4437	CC,CG,GG		19.458,13.7313,17.5177	possibly-damaging,,possibly-damaging	196/304,,196/304	141019569	2278,10726	2203	4299	6502	SO:0001583	missense	285613	exon5			GGCTCTGGTGGGG	AK054889	CCDS4265.1	5q31.3	2011-10-11	2007-06-15	2007-06-15	ENSG00000164620	ENSG00000164620			26902	protein-coding gene	gene with protein product		611213	"""chromosome 5 open reading frame 16"""	C5orf16		12975309, 16389068	Standard	NM_173828		Approved	FLJ90583	uc003lli.3	Q8NC24	OTTHUMG00000129612	ENST00000297164.3:c.586G>C	5.37:g.141019569G>C	ENSP00000297164:p.Gly196Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_173828	D3DQE2|Q6P4E7|Q6UXY2	Missense_Mutation	SNP	ENST00000297164.3	37	CCDS4265.1	351	0.16071428571428573	68	0.13821138211382114	78	0.2154696132596685	76	0.13286713286713286	129	0.17018469656992086	G	15.74	2.923004	0.52653	0.137313	0.19458	ENSG00000164620	ENST00000444782;ENST00000521367;ENST00000297164;ENST00000518856	T;T;T;T	0.16073	2.43;2.37;2.43;2.38	5.26	3.11	0.35812	.	0.520130	0.19414	N	0.114877	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.999999999857169	P;P	0.39250	0.665;0.535	P;B	0.46917	0.531;0.331	T	0.36089	-0.9762	9	0.38643	T	0.18	-2.0985	5.0989	0.14749	0.3678:0.0:0.6322:0.0	rs17855844	130;196	E5RHA7;Q8NC24	.;RELL2_HUMAN	R	196;130;196;130	ENSP00000409443:G196R;ENSP00000430948:G130R;ENSP00000297164:G196R;ENSP00000427992:G130R	ENSP00000297164:G196R	G	+	1	0	RELL2	140999753	0.033000	0.19621	1.000000	0.80357	0.907000	0.53573	-0.127000	0.10547	1.026000	0.39733	0.561000	0.74099	GGT	G|0.822;C|0.178	0.178	strong		0.667	RELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251807.2	NM_173828	
ITGA6	3655	hgsc.bcm.edu	37	2	173352103	173352103	+	Silent	SNP	C	C	T	rs2293649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:173352103C>T	ENST00000264106.6	+	16	2402	c.2199C>T	c.(2197-2199)gaC>gaT	p.D733D	ITGA6_ENST00000264107.7_Silent_p.D694D|ITGA6_ENST00000409532.1_Silent_p.D575D|ITGA6_ENST00000409080.1_Silent_p.D694D|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000343713.4_Silent_p.D689D|ITGA6_ENST00000375221.2_Silent_p.D733D			P23229	ITA6_HUMAN	integrin, alpha 6	733					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)			ATGGCGATGACGCCCATGAGG	0.423													C|||	1736	0.346645	0.202	0.3617	5008	,	,		20446	0.5417		0.2217	False		,,,				2504	0.4591				p.D694D		Atlas-SNP	.											.	ITGA6	171	.	0			c.C2082T						PASS	.	C	,	962,3444	360.1+/-315.1	107,748,1348	79.0	81.0	80.0		2082,2082	-7.9	0.4	2	dbSNP_100	80	1806,6794	324.7+/-316.6	191,1424,2685	no	coding-synonymous,coding-synonymous	ITGA6	NM_000210.2,NM_001079818.1	,	298,2172,4033	TT,TC,CC		21.0,21.8339,21.2825	,	694/1074,694/1092	173352103	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	3655	exon15			CGATGACGCCCAT		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.2199C>T	2.37:g.173352103C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	155	92	0.593548	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	37																																																																																				C|0.729;T|0.271	0.271	strong		0.423	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
SLC22A5	6584	hgsc.bcm.edu	37	5	131721174	131721174	+	Silent	SNP	A	A	G	rs274558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	140	0	0	1589	WXS	Illumina HiSeq	Phase_I	151	67	0.443709	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	
ACVR2A	92	hgsc.bcm.edu	37	2	148657117	148657117	+	Silent	SNP	G	G	A	rs1128919	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:148657117G>A	ENST00000241416.7	+	3	990	c.354G>A	c.(352-354)ccG>ccA	p.P118P	AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000535787.1_Silent_p.P10P|ACVR2A_ENST00000404590.1_Silent_p.P118P	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	118					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CTTATTTTCCGGAGATGGAAG	0.343													G|||	1766	0.352636	0.2852	0.4611	5008	,	,		15465	0.4673		0.327	False		,,,				2504	0.2751				p.P118P		Atlas-SNP	.											.	ACVR2A	125	.	0			c.G354A						PASS	.	G		1368,3036	424.0+/-340.3	223,922,1057	151.0	159.0	156.0		354	0.4	1.0	2	dbSNP_86	156	2710,5888	427.5+/-355.6	419,1872,2008	no	coding-synonymous	ACVR2A	NM_001616.3		642,2794,3065	AA,AG,GG		31.519,31.0627,31.3644		118/514	148657117	4078,8924	2202	4299	6501	SO:0001819	synonymous_variant	92	exon3			TTTTCCGGAGATG		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.354G>A	2.37:g.148657117G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	46	30	0.652174	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Silent	SNP	ENST00000241416.7	37	CCDS33301.1																																																																																			G|0.657;A|0.343	0.343	strong		0.343	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
FUOM	282969	hgsc.bcm.edu	37	10	135168903	135168903	+	Missense_Mutation	SNP	C	C	G	rs201940330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:135168903C>G	ENST00000368552.3	-	6	453	c.436G>C	c.(436-438)Ggg>Cgg	p.G146R	FUOM_ENST00000368551.1_Missense_Mutation_p.G101R|FUOM_ENST00000278025.4_3'UTR|FUOM_ENST00000447176.1_Missense_Mutation_p.G102R|FUOM_ENST00000465384.1_5'UTR	NM_001098483.1	NP_001091953.1	A2VDF0	FUCM_HUMAN	fucose mutarotase	146					female mating behavior (GO:0060180)|fucose metabolic process (GO:0006004)|fucosylation (GO:0036065)|negative regulation of neuron differentiation (GO:0045665)		fucose binding (GO:0042806)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)										GCAAGCACCCCCTTCCTGAGG	0.647													C|||	4	0.000798722	0.0008	0.0	5008	,	,		16903	0.002		0.001	False		,,,				2504	0.0				p.G146R		Atlas-SNP	.											.	.	.	.	0			c.G436C						PASS	.						24.0	26.0	25.0					10																	135168903		2196	4295	6491	SO:0001583	missense	282969	exon6			GCACCCCCTTCCT	AK129527	CCDS7680.1	10q26.3	2012-07-10	2012-07-10	2012-07-10	ENSG00000148803	ENSG00000148803	5.1.3.n2		24733	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 125"""	C10orf125		17602138	Standard	NM_001098483		Approved	FLJ26016, FucU, FucM	uc001lmt.2	A2VDF0	OTTHUMG00000019315	ENST00000368552.3:c.436G>C	10.37:g.135168903C>G	ENSP00000357540:p.Gly146Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_001098483	A1L300|Q5VWY2|Q5VWY3|Q6ZPD2	Missense_Mutation	SNP	ENST00000368552.3	37	CCDS44499.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.270065	0.59540	.	.	ENSG00000148803	ENST00000447176;ENST00000368551;ENST00000368552	.	.	.	3.47	3.47	0.39725	D-ribose pyranase RbsD-like (2);	.	.	.	.	T	0.82093	0.4962	M	0.93150	3.385	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85476	0.1176	8	0.87932	D	0	-7.9665	10.7723	0.46330	0.0:1.0:0.0:0.0	.	146	A2VDF0	FUCM_HUMAN	R	102;101;146	.	ENSP00000357539:G101R	G	-	1	0	C10orf125	135018893	0.922000	0.31269	0.994000	0.49952	0.775000	0.43874	1.930000	0.40124	2.249000	0.74217	0.467000	0.42956	GGG	C|1.000;T|0.000	.	strong		0.647	FUOM-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198472	
NDNF	79625	hgsc.bcm.edu	37	4	121957559	121957559	+	Silent	SNP	G	G	A	rs34766411	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:121957559G>A	ENST00000379692.4	-	4	2093	c.1567C>T	c.(1567-1569)Ctg>Ttg	p.L523L	NDNF_ENST00000506900.1_5'Flank	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	523	Fibronectin type-III 2.				cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						GCTTTCTGCAGGTTTTGACTG	0.418													G|||	1234	0.246406	0.1755	0.3429	5008	,	,		19471	0.2351		0.2058	False		,,,				2504	0.3272				p.L523L		Atlas-SNP	.											.	NDNF	72	.	0			c.C1567T						PASS	.	G		828,3578	328.3+/-300.5	83,662,1458	149.0	141.0	144.0		1567	4.0	1.0	4	dbSNP_126	144	1807,6793	325.2+/-316.8	190,1427,2683	no	coding-synonymous	NDNF	NM_024574.3		273,2089,4141	AA,AG,GG		21.0116,18.7926,20.2599		523/569	121957559	2635,10371	2203	4300	6503	SO:0001819	synonymous_variant	79625	exon4			TCTGCAGGTTTTG	BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.1567C>T	4.37:g.121957559G>A		Somatic	366	1	0.00273224		WXS	Illumina HiSeq	Phase_I	358	168	0.469274	NM_024574	A8K0Q0|Q6UWE5|Q9H5P7	Silent	SNP	ENST00000379692.4	37	CCDS3717.2																																																																																			G|0.789;A|0.211	0.211	strong		0.418	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2	NM_024574	
CEP350	9857	hgsc.bcm.edu	37	1	180000542	180000542	+	Missense_Mutation	SNP	G	G	T	rs12125245	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:180000542G>T	ENST00000367607.3	+	15	4056	c.3638G>T	c.(3637-3639)gGg>gTg	p.G1213V		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1213	Ser-rich.		G -> V (in dbSNP:rs12125245).		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						AAGAAATCTGGGACCAGCAGC	0.393													G|||	258	0.0515176	0.0045	0.062	5008	,	,		11324	0.0139		0.1123	False		,,,				2504	0.0838				p.G1213V		Atlas-SNP	.											.	CEP350	418	.	0			c.G3638T						PASS	.	G	VAL/GLY	114,4292	83.9+/-122.4	1,112,2090	49.0	50.0	50.0		3638	5.1	1.0	1	dbSNP_120	50	1038,7562	217.6+/-256.2	81,876,3343	yes	missense	CEP350	NM_014810.4	109	82,988,5433	TT,TG,GG		12.0698,2.5874,8.8575	benign	1213/3118	180000542	1152,11854	2203	4300	6503	SO:0001583	missense	9857	exon15			AATCTGGGACCAG	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.3638G>T	1.37:g.180000542G>T	ENSP00000356579:p.Gly1213Val	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	262	129	0.492366	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	120	0.054945054945054944	4	0.008130081300813009	23	0.06353591160220995	2	0.0034965034965034965	91	0.12005277044854881	G	8.716	0.913218	0.17907	0.025874	0.120698	ENSG00000135837	ENST00000367607	T	0.55930	0.49	6.02	5.05	0.67936	.	0.153716	0.29638	N	0.011596	T	0.00468	0.0015	N	0.11560	0.145	0.22541	P	0.999003279	B;B	0.13145	0.007;0.001	B;B	0.10450	0.005;0.002	T	0.04229	-1.0967	8	.	.	.	.	13.8485	0.63481	0.0:0.0:0.7807:0.2193	rs12125245;rs52816080;rs58708432;rs12125245	1213;1213	E7EU22;Q5VT06	.;CE350_HUMAN	V	1213	ENSP00000356579:G1213V	.	G	+	2	0	CEP350	178267165	0.993000	0.37304	1.000000	0.80357	0.841000	0.47740	2.281000	0.43452	2.850000	0.98022	0.650000	0.86243	GGG	G|0.929;T|0.071	0.071	strong		0.393	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
OR2H1	26716	hgsc.bcm.edu	37	6	29429733	29429733	+	Missense_Mutation	SNP	G	G	A	rs61732185	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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_ENST00000473369.1_Intron|OR2H1_ENST00000377133.1_Missense_Mutation_p.D63N|OR2H1_ENST00000396792.2_Missense_Mutation_p.D63N			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	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	253	120	0.474308	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		
PGM2L1	283209	hgsc.bcm.edu	37	11	74049569	74049569	+	Silent	SNP	A	A	G	rs3867270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:74049569A>G	ENST00000298198.4	-	13	2021	c.1710T>C	c.(1708-1710)agT>agC	p.S570S		NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	570					glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					GTTCTGTTCCACTTGTCCGAA	0.378													G|||	2778	0.554712	0.2133	0.6268	5008	,	,		18844	0.7887		0.6243	False		,,,				2504	0.6524				p.S570S		Atlas-SNP	.											.	PGM2L1	59	.	0			c.T1710C						PASS	.	G		1263,3137	702.1+/-406.8	191,881,1128	124.0	109.0	114.0		1710	-2.0	0.9	11	dbSNP_108	114	5406,3180	481.7+/-370.7	1702,2002,589	no	coding-synonymous	PGM2L1	NM_173582.3		1893,2883,1717	GG,GA,AA		37.037,28.7045,48.6447		570/623	74049569	6669,6317	2200	4293	6493	SO:0001819	synonymous_variant	283209	exon13			TGTTCCACTTGTC	AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"""glucose-1,6-bisphosphate synthase"""	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.1710T>C	11.37:g.74049569A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_173582	Q96MQ7|Q9UIK3	Silent	SNP	ENST00000298198.4	37	CCDS8231.1																																																																																			A|0.474;G|0.526	0.526	strong		0.378	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582	
FHL5	9457	hgsc.bcm.edu	37	6	97063555	97063555	+	Silent	SNP	A	A	G	rs9398148	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:97063555A>G	ENST00000326771.2	+	7	1142	c.762A>G	c.(760-762)aaA>aaG	p.K254K	FHL5_ENST00000541107.1_Silent_p.K254K	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	254	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.			K -> R (in Ref. 1; AAF85978). {ECO:0000305}.	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)		ACTGCGGGAAATGCTCTGTCT	0.463													G|||	1926	0.384585	0.5038	0.2997	5008	,	,		19407	0.3522		0.3489	False		,,,				2504	0.3538				p.K254K		Atlas-SNP	.											FHL5,caecum,carcinoma,+2,1	FHL5	73	1	0			c.A762G						PASS	.	G	,	2161,2245	594.3+/-388.2	533,1095,575	115.0	112.0	113.0		762,762	3.6	1.0	6	dbSNP_119	113	2871,5729	673.0+/-403.0	477,1917,1906	no	coding-synonymous,coding-synonymous	FHL5	NM_001170807.1,NM_020482.4	,	1010,3012,2481	GG,GA,AA		33.3837,49.0468,38.6898	,	254/285,254/285	97063555	5032,7974	2203	4300	6503	SO:0001819	synonymous_variant	9457	exon7			CGGGAAATGCTCT	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.762A>G	6.37:g.97063555A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	37	CCDS5035.1																																																																																			A|0.613;G|0.387	0.387	strong		0.463	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
UGT2B4	7363	hgsc.bcm.edu	37	4	70346564	70346564	+	Silent	SNP	G	G	T	rs67904882|rs13142440	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:70346564G>T	ENST00000305107.6	-	6	1421	c.1375C>A	c.(1375-1377)Cga>Aga	p.R459R	UGT2B4_ENST00000506580.1_5'UTR|AC108078.1_ENST00000583573.1_RNA|UGT2B4_ENST00000381096.3_Silent_p.R323R|UGT2B4_ENST00000512583.1_3'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	459					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.R459*(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	AAGACTGCTCGATCAAGGGGC	0.428													g|||	654	0.130591	0.1362	0.2205	5008	,	,		17789	0.0		0.2266	False		,,,				2504	0.0951				p.R459R		Atlas-SNP	.											UGT2B4,NS,carcinoma,0,1	UGT2B4	105	1	1	Substitution - Nonsense(1)	endometrium(1)	c.C1375A						PASS	.	G		631,3775		44,543,1616	113.0	113.0	113.0		1375	-1.0	0.0	4	dbSNP_121	113	2052,6548		260,1532,2508	no	coding-synonymous	UGT2B4	NM_021139.2		304,2075,4124	TT,TG,GG		23.8605,14.3214,20.6289		459/529	70346564	2683,10323	2203	4300	6503	SO:0001819	synonymous_variant	7363	exon6			CTGCTCGATCAAG	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.1375C>A	4.37:g.70346564G>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	148	70	0.472973	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			TT|1.000;|0.000	.	alt		0.428	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
FAM135A	57579	hgsc.bcm.edu	37	6	71238105	71238105	+	Missense_Mutation	SNP	A	A	G	rs2747701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:71238105A>G	ENST00000418814.2	+	16	4339	c.3725A>G	c.(3724-3726)gAt>gGt	p.D1242G	FAM135A_ENST00000370479.3_Missense_Mutation_p.D1029G|FAM135A_ENST00000505868.1_Missense_Mutation_p.D1242G|FAM135A_ENST00000505769.1_Missense_Mutation_p.D822G|FAM135A_ENST00000361499.3_Missense_Mutation_p.D1046G|FAM135A_ENST00000457062.2_Missense_Mutation_p.D1029G	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1242			D -> G (in dbSNP:rs2747701). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16192744}.							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						GAAGAAGAGGATGGTTCTGAA	0.403													A|||	1699	0.339257	0.0189	0.2507	5008	,	,		16392	0.5427		0.4761	False		,,,				2504	0.4847				p.D1242G		Atlas-SNP	.											.	FAM135A	181	.	0			c.A3725G						PASS	.	A	GLY/ASP,GLY/ASP,GLY/ASP	381,4025	192.3+/-217.7	13,355,1835	215.0	183.0	194.0		3137,3725,3086	3.8	0.7	6	dbSNP_100	194	4138,4462	564.9+/-388.4	1003,2132,1165	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	94,94,94	1016,2487,3000	GG,GA,AA		48.1163,8.6473,34.7455	benign,benign,benign	1046/1320,1242/1516,1029/1303	71238105	4519,8487	2203	4300	6503	SO:0001583	missense	57579	exon14			AAGAGGATGGTTC	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.3725A>G	6.37:g.71238105A>G	ENSP00000410768:p.Asp1242Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	779	0.3566849816849817	12	0.024390243902439025	98	0.27071823204419887	305	0.5332167832167832	364	0.48021108179419525	A	12.22	1.872457	0.33069	0.086473	0.481163	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.24538	2.16;2.16;1.85;2.16;2.16;2.15	4.92	3.77	0.43336	.	0.230845	0.51477	N	0.000093	T	0.14874	0.0359	M	0.67953	2.075	0.09310	P	0.99999351703	B;B;B;B;B	0.31040	0.305;0.11;0.067;0.076;0.11	B;B;B;B;B	0.33042	0.109;0.157;0.075;0.047;0.157	T	0.04053	-1.0981	9	0.59425	D	0.04	.	10.304	0.43670	0.9221:0.0:0.0779:0.0	rs2747701;rs3736753;rs60825985;rs2747701	822;1242;1242;1046;1029	D6RCC7;Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;.;F135A_HUMAN;.;.	G	1242;1029;822;1029;1046;1242	ENSP00000410768:D1242G;ENSP00000359510:D1029G;ENSP00000423785:D822G;ENSP00000409201:D1029G;ENSP00000354913:D1046G;ENSP00000423307:D1242G	ENSP00000354913:D1046G	D	+	2	0	FAM135A	71294826	1.000000	0.71417	0.723000	0.30687	0.305000	0.27757	6.153000	0.71819	0.843000	0.35070	0.482000	0.46254	GAT	A|0.647;G|0.353	0.353	strong		0.403	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
COL5A3	50509	hgsc.bcm.edu	37	19	10084292	10084292	+	Missense_Mutation	SNP	C	C	G	rs2287813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10084292C>G	ENST00000264828.3	-	50	3705	c.3620G>C	c.(3619-3621)cGa>cCa	p.R1207P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1207	Triple-helical region.		R -> P (in dbSNP:rs2287813).		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)			AGCGTCCCCTCGCTCACCCTG	0.627													G|||	2422	0.483626	0.7292	0.3199	5008	,	,		17798	0.3472		0.4304	False		,,,				2504	0.4632				p.R1207P		Atlas-SNP	.											COL5A3,NS,carcinoma,-1,1	COL5A3	243	1	0			c.G3620C						PASS	.	G	PRO/ARG	3012,1394	453.4+/-350.3	1019,974,210	51.0	55.0	54.0		3620	4.9	1.0	19	dbSNP_100	54	3727,4873	612.9+/-396.0	796,2135,1369	yes	missense	COL5A3	NM_015719.3	103	1815,3109,1579	GG,GC,CC		43.3372,31.6387,48.1855	benign	1207/1746	10084292	6739,6267	2203	4300	6503	SO:0001583	missense	50509	exon50			TCCCCTCGCTCAC	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.3620G>C	19.37:g.10084292C>G	ENSP00000264828:p.Arg1207Pro	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	1022	0.46794871794871795	357	0.725609756097561	125	0.3453038674033149	216	0.3776223776223776	324	0.42744063324538256	G	2.777	-0.254454	0.05829	0.683613	0.433372	ENSG00000080573	ENST00000264828	D	0.89810	-2.57	4.95	4.95	0.65309	.	0.164651	0.40908	N	0.000998	T	0.00012	0.0000	N	0.01128	-1	0.31748	P	0.634949	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	9	0.02654	T	1	.	13.5691	0.61836	0.0:0.1576:0.8424:0.0	rs2287813;rs57324291;rs2287813	1207	P25940	CO5A3_HUMAN	P	1207	ENSP00000264828:R1207P	ENSP00000264828:R1207P	R	-	2	0	COL5A3	9945292	1.000000	0.71417	0.994000	0.49952	0.753000	0.42808	3.938000	0.56583	1.226000	0.43582	-0.322000	0.08575	CGA	C|0.507;G|0.493	0.493	strong		0.627	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
IKBKAP	8518	hgsc.bcm.edu	37	9	111663754	111663754	+	Silent	SNP	G	G	A	rs2230791	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111663754G>A	ENST00000374647.5	-	18	2272	c.1965C>T	c.(1963-1965)acC>acT	p.T655T	IKBKAP_ENST00000537196.1_Silent_p.T306T	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	655					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						TATGGGAATGGGTTGTCAACA	0.403													G|||	393	0.0784744	0.1755	0.0346	5008	,	,		18415	0.0		0.0885	False		,,,				2504	0.0491				p.T655T		Atlas-SNP	.											.	IKBKAP	122	.	0			c.C1965T						PASS	.	G		664,3742	281.4+/-275.9	50,564,1589	94.0	82.0	86.0		1965	3.1	1.0	9	dbSNP_98	86	685,7915	170.9+/-221.9	28,629,3643	no	coding-synonymous	IKBKAP	NM_003640.3		78,1193,5232	AA,AG,GG		7.9651,15.0704,10.3721		655/1333	111663754	1349,11657	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon18			GGAATGGGTTGTC	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.1965C>T	9.37:g.111663754G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	40	0.40404	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			G|0.775;T|0.018	.	strong		0.403	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
TKT	7086	hgsc.bcm.edu	37	3	53259850	53259850	+	Silent	SNP	C	C	T	rs3163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:53259850C>T	ENST00000462138.1	-	14	1882	c.1794G>A	c.(1792-1794)ccG>ccA	p.P598P	TKT_ENST00000296289.6_Silent_p.P551P|TKT_ENST00000423525.2_Silent_p.P598P|TKT_ENST00000423516.1_Silent_p.P606P|TKT_ENST00000461139.1_5'UTR			P29401	TKT_HUMAN	transketolase	598					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		GCAGCTCAGCCGGCTTCCCAC	0.587													C|||	606	0.121006	0.0522	0.1354	5008	,	,		17021	0.1091		0.167	False		,,,				2504	0.1687				p.P606P	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.G1818A						PASS	.	C	,	393,4013	196.4+/-220.7	21,351,1831	90.0	75.0	80.0		1794,1794	-5.8	0.0	3	dbSNP_36	80	1650,6950	304.0+/-306.7	158,1334,2808	no	coding-synonymous,coding-synonymous	TKT	NM_001064.3,NM_001135055.2	,	179,1685,4639	TT,TC,CC		19.186,8.9197,15.7081	,	598/624,598/624	53259850	2043,10963	2203	4300	6503	SO:0001819	synonymous_variant	7086	exon15			CTCAGCCGGCTTC		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"""Wernicke-Korsakoff syndrome"""	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.1794G>A	3.37:g.53259850C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	146	68	0.465753	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Silent	SNP	ENST00000462138.1	37	CCDS2871.1																																																																																			C|0.860;T|0.140	0.140	strong		0.587	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
ACTL9	284382	hgsc.bcm.edu	37	19	8808373	8808373	+	Missense_Mutation	SNP	G	G	T	rs4804079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8808373G>T	ENST00000324436.3	-	1	799	c.679C>A	c.(679-681)Cac>Aac	p.H227N		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	227			H -> N (in dbSNP:rs4804079). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						GCGGTCAGGTGGTTGCCCGCC	0.642													G|||	3005	0.60004	0.5726	0.5159	5008	,	,		17063	0.6825		0.5427	False		,,,				2504	0.6708				p.H227N		Atlas-SNP	.											.	ACTL9	74	.	0			c.C679A						PASS	.	G	ASN/HIS	2430,1976	600.5+/-389.5	690,1050,463	40.0	40.0	40.0		679	4.6	1.0	19	dbSNP_111	40	4437,4163	573.1+/-389.8	1141,2155,1004	yes	missense	ACTL9	NM_178525.3	68	1831,3205,1467	TT,TG,GG		48.407,44.8479,47.2013	possibly-damaging	227/417	8808373	6867,6139	2203	4300	6503	SO:0001583	missense	284382	exon1			TCAGGTGGTTGCC		CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.679C>A	19.37:g.8808373G>T	ENSP00000316674:p.His227Asn	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	21	8	0.380952	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	1276	0.5842490842490843	297	0.6036585365853658	195	0.5386740331491713	386	0.6748251748251748	398	0.525065963060686	G	11.88	1.769430	0.31320	0.551521	0.51593	ENSG00000181786	ENST00000324436	T	0.07908	3.15	4.55	4.55	0.56014	.	0.440276	0.19257	N	0.118775	T	0.00012	0.0000	L	0.31845	0.965	0.31989	P	0.604815	D	0.57571	0.98	P	0.60236	0.871	T	0.04870	-1.0921	9	0.87932	D	0	.	6.6553	0.22984	0.0957:0.1832:0.721:0.0	rs4804079;rs17845741;rs17858692;rs17859418;rs4804079	227	Q8TC94	ACTL9_HUMAN	N	227	ENSP00000316674:H227N	ENSP00000316674:H227N	H	-	1	0	ACTL9	8669373	0.904000	0.30761	0.982000	0.44146	0.481000	0.33189	1.603000	0.36794	2.531000	0.85337	0.462000	0.41574	CAC	G|0.442;T|0.558	0.558	strong		0.642	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525	
TTN	7273	hgsc.bcm.edu	37	2	179579093	179579093	+	Missense_Mutation	SNP	T	T	C	rs12693164	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179579093T>C	ENST00000591111.1	-	89	25681	c.25457A>G	c.(25456-25458)aAt>aGt	p.N8486S	TTN_ENST00000589042.1_Missense_Mutation_p.N8803S|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N7559S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12654	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTCCAGCATTGGCTGGTTC	0.393													T|||	1237	0.247005	0.1936	0.1859	5008	,	,		21117	0.4365		0.1561	False		,,,				2504	0.2607				p.N8803S		Atlas-SNP	.											TTN_ENST00000342992,colon,carcinoma,0,1	TTN	18412	1	0			c.A26408G						scavenged	.	T	,,,SER/ASN	595,3173		45,505,1334	116.0	113.0	114.0		,,,22676	2.2	1.0	2	dbSNP_121	114	1240,6996		96,1048,2974	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,46	141,1553,4308	CC,CT,TT		15.0559,15.7909,15.2866	,,,benign	,,,7559/33424	179579093	1835,10169	1884	4118	6002	SO:0001583	missense	7273	exon91			CCAGCATTGGCTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25457A>G	2.37:g.179579093T>C	ENSP00000465570:p.Asn8486Ser	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	194	101	0.520619	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		512	0.23443223443223443	98	0.1991869918699187	55	0.15193370165745856	243	0.42482517482517484	116	0.15303430079155672	T	7.990	0.752982	0.15778	0.157909	0.150559	ENSG00000155657	ENST00000342992	T	0.68025	-0.3	5.96	2.25	0.28309	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.999999999999746	B	0.16603	0.018	B	0.09377	0.004	T	0.32025	-0.9922	8	0.87932	D	0	.	12.1749	0.54180	0.0:0.1656:0.0:0.8344	rs12693164;rs52822704;rs58566262;rs12693164	8486	Q8WZ42	TITIN_HUMAN	S	7559	ENSP00000343764:N7559S	ENSP00000343764:N7559S	N	-	2	0	TTN	179287338	1.000000	0.71417	0.983000	0.44433	0.345000	0.29048	0.818000	0.27295	-0.075000	0.12798	-2.240000	0.00288	AAT	T|0.765;C|0.235	0.235	strong		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FUT2	2524	hgsc.bcm.edu	37	19	49206417	49206417	+	Silent	SNP	A	A	G	rs492602	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49206417A>G	ENST00000425340.2	+	2	321	c.204A>G	c.(202-204)gcA>gcG	p.A68A	FUT2_ENST00000391876.4_Silent_p.A68A	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	68					carbohydrate metabolic process (GO:0005975)|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)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		CGATCAATGCAATAGGCCGCC	0.607													G|||	1611	0.321685	0.4909	0.3415	5008	,	,		18310	0.004		0.4414	False		,,,				2504	0.2832				p.A68A		Atlas-SNP	.											.	FUT2	30	.	0			c.A204G						PASS	.	G	,	2195,2211	590.3+/-387.3	554,1087,562	67.0	63.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	204,204	-8.6	0.0	19	dbSNP_83	64	4240,4360	581.0+/-391.1	1055,2130,1115	yes	coding-synonymous,coding-synonymous	FUT2	NM_000511.5,NM_001097638.2	,	1609,3217,1677	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	49.3023,49.8184,49.4772	,	68/344,68/344	49206417	6435,6571	2203	4300	6503	SO:0001819	synonymous_variant	2524	exon2			CAATGCAATAGGC		CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"""Fucosyltransferases"""	4013	protein-coding gene	gene with protein product	"""alpha (1,2) fucosyltransferase"", ""galactoside 2-alpha-L-fucosyltransferase 2"", ""GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2"", ""alpha(1,2)FT2"", ""secretor factor"", ""secretor blood group alpha-2-fucosyltransferase"""	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.204A>G	19.37:g.49206417A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_001097638	Q0VAG5|Q14338|Q5D0G2	Silent	SNP	ENST00000425340.2	37	CCDS33069.1																																																																																			A|0.570;G|0.430	0.430	strong		0.607	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511	
KCNH1	3756	hgsc.bcm.edu	37	1	210857457	210857457	+	Silent	SNP	A	A	G	rs1135317	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:210857457A>G	ENST00000271751.4	-	11	2163	c.2136T>C	c.(2134-2136)gaT>gaC	p.D712D	KCNH1_ENST00000367007.4_Silent_p.D685D			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	712	Calmodulin-binding.				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)		CACGTTTCACATCGCTGATCT	0.567													G|||	3703	0.739417	0.8071	0.6888	5008	,	,		20379	0.6528		0.7117	False		,,,				2504	0.8016				p.D712D		Atlas-SNP	.											KCNH1,NS,carcinoma,-1,1	KCNH1	199	1	0			c.T2136C						PASS	.	G	,	3505,901	337.3+/-304.8	1410,685,108	63.0	58.0	60.0		2055,2136	-5.6	0.5	1	dbSNP_86	60	6136,2462	390.1+/-343.2	2176,1784,339	no	coding-synonymous,coding-synonymous	KCNH1	NM_002238.3,NM_172362.2	,	3586,2469,447	GG,GA,AA		28.6346,20.4494,25.8613	,	685/963,712/990	210857457	9641,3363	2203	4299	6502	SO:0001819	synonymous_variant	3756	exon11			TTTCACATCGCTG	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.2136T>C	1.37:g.210857457A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_172362	B1AQ26|O76035|Q14CL3	Silent	SNP	ENST00000271751.4	37	CCDS1496.1																																																																																			A|0.277;G|0.723	0.723	strong		0.567	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
LRRK1	79705	hgsc.bcm.edu	37	15	101606889	101606889	+	Missense_Mutation	SNP	G	G	A	rs375358524|rs386787404|rs2924835	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:101606889G>A	ENST00000388948.3	+	33	6172	c.5813G>A	c.(5812-5814)gGc>gAc	p.G1938D	LRRK1_ENST00000284395.5_Missense_Mutation_p.G1935D|LRRK1_ENST00000532145.1_3'UTR|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AAGGATTCTGGCGCCCAGCGG	0.587													G|||	1363	0.272165	0.0794	0.3559	5008	,	,		18822	0.3403		0.3201	False		,,,				2504	0.3538				p.G1938D		Atlas-SNP	.											.	LRRK1	310	.	0			c.G5813A						PASS	.	G	ASP/GLY	418,3730		14,390,1670	160.0	175.0	170.0		5813	5.5	0.0	15	dbSNP_101	170	2545,5895		368,1809,2043	yes	missense	LRRK1	NM_024652.3	94	382,2199,3713	AA,AG,GG		30.154,10.0771,23.5383	benign	1938/2016	101606889	2963,9625	2074	4220	6294	SO:0001583	missense	79705	exon33			ATTCTGGCGCCCA	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.5813G>A	15.37:g.101606889G>A	ENSP00000373600:p.Gly1938Asp	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	495|495	0.22664835164835165|0.22664835164835165	38|38	0.07723577235772358|0.07723577235772358	94|94	0.2596685082872928|0.2596685082872928	177|177	0.3094405594405594|0.3094405594405594	186|186	0.24538258575197888|0.24538258575197888	G|G	8.438|8.438	0.850072|0.850072	0.17034|0.17034	0.100771|0.100771	0.30154|0.30154	ENSG00000154237|ENSG00000154237	ENST00000542170|ENST00000388948;ENST00000284395;ENST00000529762	.|T;T	.|0.72725	.|-0.65;-0.68	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.111323	.|0.64402	.|D	.|0.000007	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	P|P	6.999999999979245E-6|6.999999999979245E-6	.|B	.|0.16166	.|0.016	.|B	.|0.12156	.|0.007	T|T	0.03840|0.03840	-1.0999|-1.0999	4|9	.|0.59425	.|D	.|0.04	.|.	15.7379|15.7379	0.77859|0.77859	0.0:0.1366:0.8634:0.0|0.0:0.1366:0.8634:0.0	rs2959197;rs33925554;rs2959197|rs2959197;rs33925554;rs2959197	.|1938	.|Q38SD2	.|LRRK1_HUMAN	T|D	492|1938;1935;629	.|ENSP00000373600:G1938D;ENSP00000284395:G1935D	.|ENSP00000284395:G1935D	A|G	+|+	1|2	0|0	LRRK1|LRRK1	99424412|99424412	0.994000|0.994000	0.37717|0.37717	0.014000|0.014000	0.15608|0.15608	0.043000|0.043000	0.13939|0.13939	3.321000|3.321000	0.51999|0.51999	2.582000|2.582000	0.87167|0.87167	0.655000|0.655000	0.94253|0.94253	GCG|GGC	.	.	alt		0.587	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
PRELID2	153768	hgsc.bcm.edu	37	5	145199531	145199531	+	Missense_Mutation	SNP	C	C	T	rs142301961		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:145199531C>T	ENST00000334744.4	-	3	236	c.184G>A	c.(184-186)Gtg>Atg	p.V62M	PRELID2_ENST00000358004.2_Missense_Mutation_p.V62M|PRELID2_ENST00000505416.1_Missense_Mutation_p.V62M|PRELID2_ENST00000394450.2_Missense_Mutation_p.V33M|PRELID2_ENST00000511435.1_Missense_Mutation_p.V62M	NM_182960.2	NP_892005.1	Q8N945	PRLD2_HUMAN	PRELI domain containing 2	62	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTGGAACCACGTTCTGACAG	0.289													C|||	1	0.000199681	0.0	0.0	5008	,	,		16776	0.0		0.001	False		,,,				2504	0.0				p.V62M		Atlas-SNP	.											.	PRELID2	16	.	0			c.G184A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	88.0	95.0	93.0		97,184,184	5.3	1.0	5	dbSNP_134	93	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense,missense	PRELID2	NM_138492.4,NM_182960.2,NM_205846.1	21,21,21	0,11,6492	TT,TC,CC		0.1163,0.0227,0.0846	probably-damaging,probably-damaging,probably-damaging	33/149,62/190,62/178	145199531	11,12995	2203	4300	6503	SO:0001583	missense	153768	exon3			GAACCACGTTCTG	AK095695	CCDS34261.1, CCDS34262.1, CCDS43377.1	5q32	2012-04-23			ENSG00000186314	ENSG00000186314			28306	protein-coding gene	gene with protein product						12477932	Standard	NM_182960		Approved	MGC21644, FLJ38376	uc003lnq.1	Q8N945	OTTHUMG00000163384	ENST00000334744.4:c.184G>A	5.37:g.145199531C>T	ENSP00000335675:p.Val62Met	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_182960	G5EA01|Q96EQ3	Missense_Mutation	SNP	ENST00000334744.4	37	CCDS34262.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	21.1	4.095855	0.76870	2.27E-4	0.001163	ENSG00000186314	ENST00000358004;ENST00000334744;ENST00000394450;ENST00000505416;ENST00000511435	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	5.3	5.3	0.74995	PRELI/MSF1 (2);	0.000000	0.64402	D	0.000014	T	0.40956	0.1138	M	0.67953	2.075	0.43480	D	0.995704	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.992;0.998	T	0.07578	-1.0765	10	0.46703	T	0.11	-0.5438	16.2362	0.82377	0.0:1.0:0.0:0.0	.	62;62;62	D6RAB6;G5EA01;Q8N945	.;.;PRLD2_HUMAN	M	62;62;33;62;62	ENSP00000350694:V62M;ENSP00000335675:V62M;ENSP00000377965:V33M;ENSP00000424730:V62M;ENSP00000422789:V62M	ENSP00000335675:V62M	V	-	1	0	PRELID2	145179724	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.798000	0.47884	2.627000	0.88993	0.650000	0.86243	GTG	C|0.999;T|0.001	0.001	strong		0.289	PRELID2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000372970.1	NM_182960	
CISD3	284106	hgsc.bcm.edu	37	17	36889559	36889559	+	Missense_Mutation	SNP	C	C	T	rs2879097	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:36889559C>T	ENST00000439660.2	+	4	359	c.235C>T	c.(235-237)Cgc>Tgc	p.R79C	RNA5SP440_ENST00000363245.1_RNA|CISD3_ENST00000578573.1_3'UTR	NM_001136498.1	NP_001129970.1	P0C7P0	CISD3_HUMAN	CDGSH iron sulfur domain 3	79						mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			endometrium(2)	2						CTTCTTCCAACGCACTGGCCT	0.622													C|||	755	0.150759	0.0439	0.2925	5008	,	,		17132	0.1468		0.2167	False		,,,				2504	0.1309				p.R79C		Atlas-SNP	.											.	CISD3	12	.	0			c.C235T						PASS	.						65.0	53.0	57.0					17																	36889559		692	1591	2283	SO:0001583	missense	284106	exon4			TTCCAACGCACTG	AK097047	CCDS45662.1	17q12	2007-08-10				ENSG00000277972		"""CDGSH iron sulfur domain containing"""	27578	protein-coding gene	gene with protein product	"""mitoNEET related 2"""	611933				17376863, 17584744	Standard	NM_001136498		Approved	Miner2	uc010wds.1	P0C7P0		ENST00000439660.2:c.235C>T	17.37:g.36889559C>T	ENSP00000391402:p.Arg79Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_001136498		Missense_Mutation	SNP	ENST00000439660.2	37	CCDS45662.1	356	0.163003663003663	25	0.0508130081300813	95	0.26243093922651933	75	0.13111888111888112	161	0.21240105540897097	C	19.18	3.777203	0.70107	.	.	ENSG00000230055	ENST00000439660	.	.	.	5.41	3.31	0.37934	.	.	.	.	.	T	0.00012	0.0000	L	0.43923	1.385	0.26437	P	0.9758395	D	0.69078	0.997	P	0.50490	0.642	T	0.08597	-1.0714	7	0.59425	D	0.04	-11.4689	9.4137	0.38507	0.1578:0.6886:0.1536:0.0	rs2879097;rs35161534;rs58181077;rs2879097	79	P0C7P0	CISD3_HUMAN	C	79	.	ENSP00000391402:R79C	R	+	1	0	CISD3	34143085	0.386000	0.25180	1.000000	0.80357	0.975000	0.68041	1.441000	0.35035	2.527000	0.85204	0.455000	0.32223	CGC	C|0.849;T|0.151	0.151	strong		0.622	CISD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441921.1		
DRC7	84229	hgsc.bcm.edu	37	16	57758727	57758727	+	Missense_Mutation	SNP	T	T	C	rs115241876	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57758727T>C	ENST00000360716.3	+	13	1959	c.1738T>C	c.(1738-1740)Tca>Cca	p.S580P	CCDC135_ENST00000394337.4_Missense_Mutation_p.S580P|CCDC135_ENST00000336825.8_Missense_Mutation_p.S515P			Q8IY82	CC135_HUMAN		580					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						CAGTGCAGAGTCAAACCCCCG	0.597													.|||	10	0.00199681	0.0	0.0058	5008	,	,		18147	0.0		0.005	False		,,,				2504	0.001				p.S580P		Atlas-SNP	.											.	CCDC135	97	.	0			c.T1738C						PASS	.	T	PRO/SER	2,4392		0,2,2195	49.0	43.0	45.0		1738	4.1	0.2	16	dbSNP_132	45	39,8559		1,37,4261	yes	missense	CCDC135	NM_032269.5	74	1,39,6456	CC,CT,TT		0.4536,0.0455,0.3156	possibly-damaging	580/875	57758727	41,12951	2197	4299	6496	SO:0001583	missense	84229	exon12			GCAGAGTCAAACC																												ENST00000360716.3:c.1738T>C	16.37:g.57758727T>C	ENSP00000353942:p.Ser580Pro	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	.	18.06	3.538954	0.65085	4.55E-4	0.004536	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.10382	3.03;2.88;3.03	5.29	4.09	0.47781	.	0.814347	0.11090	N	0.600808	T	0.15609	0.0376	M	0.68317	2.08	0.09310	N	1	D;D	0.58970	0.984;0.966	P;P	0.56088	0.791;0.735	T	0.10132	-1.0643	10	0.37606	T	0.19	-14.6732	6.4912	0.22117	0.1385:0.0:0.2281:0.6334	.	515;580	Q8IY82-2;Q8IY82	.;CC135_HUMAN	P	580;515;580	ENSP00000377869:S580P;ENSP00000338938:S515P;ENSP00000353942:S580P	ENSP00000338938:S515P	S	+	1	0	CCDC135	56316228	0.001000	0.12720	0.236000	0.24074	0.737000	0.42083	0.422000	0.21296	2.004000	0.58718	0.533000	0.62120	TCA	T|0.997;C|0.003	0.003	strong		0.597	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
GLP2R	9340	hgsc.bcm.edu	37	17	9792768	9792768	+	Missense_Mutation	SNP	G	G	A	rs17681684	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:9792768G>A	ENST00000262441.5	+	13	1921	c.1408G>A	c.(1408-1410)Gac>Aac	p.D470N	GLP2R_ENST00000574745.1_Missense_Mutation_p.D290N	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	470			D -> N (in dbSNP:rs17681684). {ECO:0000269|PubMed:15489334}.		adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	CCTGGGGAAGGACTTCCGGTT	0.592													A|||	504	0.100639	0.0212	0.1571	5008	,	,		19847	0.002		0.2773	False		,,,				2504	0.0879				p.D470N		Atlas-SNP	.											.	GLP2R	90	.	0			c.G1408A						PASS	.	A	ASN/ASP	323,4083	784.0+/-414.7	11,301,1891	50.0	52.0	51.0		1408	1.8	1.0	17	dbSNP_123	51	2708,5892	669.9+/-402.7	428,1852,2020	yes	missense	GLP2R	NM_004246.1	23	439,2153,3911	AA,AG,GG		31.4884,7.3309,23.3046	benign	470/554	9792768	3031,9975	2203	4300	6503	SO:0001583	missense	9340	exon13			GGGAAGGACTTCC	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"""GPCR / Class B : Glucagon receptors"""	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1408G>A	17.37:g.9792768G>A	ENSP00000262441:p.Asp470Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	37	CCDS11150.1	306	0.1401098901098901	15	0.03048780487804878	69	0.19060773480662985	1	0.0017482517482517483	221	0.29155672823219	A	8.451	0.853055	0.17106	0.073309	0.314884	ENSG00000065325	ENST00000396206;ENST00000262441	T	0.53640	0.61	5.43	1.83	0.25207	.	0.340133	0.21431	N	0.074649	T	0.00012	0.0000	N	0.03029	-0.43	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40098	-0.9581	9	0.11485	T	0.65	.	5.4283	0.16438	0.5741:0.2756:0.1503:0.0	rs17681684;rs17681684	470	O95838	GLP2R_HUMAN	N	470	ENSP00000262441:D470N	ENSP00000262441:D470N	D	+	1	0	GLP2R	9733493	1.000000	0.71417	0.969000	0.41365	0.051000	0.14879	0.930000	0.28858	-0.146000	0.11274	-0.269000	0.10298	GAC	G|0.822;A|0.178	0.178	strong		0.592	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4		
OR13D1	286365	hgsc.bcm.edu	37	9	107456892	107456892	+	Missense_Mutation	SNP	C	C	G	rs13294411	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:107456892C>G	ENST00000318763.5	+	1	233	c.190C>G	c.(190-192)Ctc>Gtc	p.L64V		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	64			L -> V (in dbSNP:rs13294411). {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						CCTGCTCTGCCTCATCATGTA	0.438													C|||	267	0.0533147	0.0068	0.0533	5008	,	,		19195	0.002		0.0686	False		,,,				2504	0.1534				p.L64V		Atlas-SNP	.											.	OR13D1	42	.	0			c.C190G						PASS	.	C	VAL/LEU	67,4339	62.3+/-99.4	1,65,2137	123.0	123.0	123.0		190	1.7	1.0	9	dbSNP_121	123	742,7858	177.8+/-227.3	33,676,3591	no	missense	OR13D1	NM_001004484.1	32	34,741,5728	GG,GC,CC		8.6279,1.5207,6.2202	probably-damaging	64/347	107456892	809,12197	2203	4300	6503	SO:0001583	missense	286365	exon1			CTCTGCCTCATCA		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.190C>G	9.37:g.107456892C>G	ENSP00000317357:p.Leu64Val	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	37	CCDS35094.1	81	0.03708791208791209	7	0.014227642276422764	23	0.06353591160220995	1	0.0017482517482517483	50	0.06596306068601583	C	13.49	2.253189	0.39797	0.015207	0.086279	ENSG00000179055	ENST00000318763	T	0.01902	4.57	3.75	1.74	0.24563	.	0.000000	0.45606	D	0.000351	T	0.00271	0.0008	M	0.92923	3.36	0.25963	N	0.982599	P	0.51537	0.946	P	0.45577	0.486	T	0.17745	-1.0359	10	0.66056	D	0.02	.	6.7689	0.23583	0.0:0.7099:0.1807:0.1093	rs13294411	64	Q8NGV5	O13D1_HUMAN	V	64	ENSP00000317357:L64V	ENSP00000317357:L64V	L	+	1	0	OR13D1	106496713	0.000000	0.05858	0.998000	0.56505	0.672000	0.39443	-0.206000	0.09398	0.730000	0.32425	0.609000	0.83330	CTC	C|0.957;G|0.043	0.043	strong		0.438	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
FERMT1	55612	hgsc.bcm.edu	37	20	6064731	6064731	+	Silent	SNP	C	C	T	rs2232079	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:6064731C>T	ENST00000217289.4	-	13	2462	c.1674G>A	c.(1672-1674)gcG>gcA	p.A558A	FERMT1_ENST00000478194.1_5'UTR|FERMT1_ENST00000536936.1_Silent_p.A301A	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	558	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)		p.A558A(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						GTGACTGCCACGCCTGGATGA	0.527													C|||	583	0.116414	0.2284	0.072	5008	,	,		17985	0.0704		0.1123	False		,,,				2504	0.0481				p.A558A		Atlas-SNP	.											FERMT1,NS,carcinoma,0,2	FERMT1	106	2	1	Substitution - coding silent(1)	prostate(1)	c.G1674A						PASS	.	C		1085,3321	392.6+/-328.5	148,789,1266	72.0	55.0	61.0		1674	-9.6	0.3	20	dbSNP_98	61	907,7693	203.1+/-246.2	43,821,3436	no	coding-synonymous	FERMT1	NM_017671.4		191,1610,4702	TT,TC,CC		10.5465,24.6255,15.316		558/678	6064731	1992,11014	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon13			CTGCCACGCCTGG	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1674G>A	20.37:g.6064731C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			C|0.861;T|0.139	0.139	strong		0.527	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
SRMS	6725	hgsc.bcm.edu	37	20	62172244	62172244	+	Missense_Mutation	SNP	C	C	G	rs33933649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62172244C>G	ENST00000217188.1	-	8	1434	c.1394G>C	c.(1393-1395)aGc>aCc	p.S465T		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	465	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> T (in dbSNP:rs33933649). {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)			CTCGGGGCTGCTCCTCCAGCA	0.682													C|||	42	0.00838658	0.0038	0.013	5008	,	,		16998	0.0		0.0229	False		,,,				2504	0.0051				p.S465T		Atlas-SNP	.											.	SRMS	48	.	0			c.G1394C						PASS	.	C	THR/SER	32,4372	36.8+/-68.6	1,30,2171	91.0	86.0	88.0		1394	-3.8	0.0	20	dbSNP_126	88	253,8347	99.3+/-160.8	1,251,4048	yes	missense	SRMS	NM_080823.2	58	2,281,6219	GG,GC,CC		2.9419,0.7266,2.1916	benign	465/489	62172244	285,12719	2202	4300	6502	SO:0001583	missense	6725	exon8			GGGCTGCTCCTCC		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.1394G>C	20.37:g.62172244C>G	ENSP00000217188:p.Ser465Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	24	0.01098901098901099	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	5.972	0.363358	0.11296	0.007266	0.029419	ENSG00000125508	ENST00000217188	D	0.82803	-1.65	5.17	-3.81	0.04294	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.880119	0.09801	N	0.754091	T	0.42921	0.1224	N	0.13299	0.325	0.09310	N	1	B	0.17465	0.022	B	0.26416	0.069	T	0.49031	-0.8981	10	0.44086	T	0.13	.	7.2562	0.26177	0.0:0.2938:0.4425:0.2637	rs33933649	465	Q9H3Y6	SRMS_HUMAN	T	465	ENSP00000217188:S465T	ENSP00000217188:S465T	S	-	2	0	SRMS	61642688	0.000000	0.05858	0.008000	0.14137	0.033000	0.12548	-0.195000	0.09546	-0.615000	0.05679	-0.955000	0.02649	AGC	C|0.979;G|0.021	0.021	strong		0.682	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
RINL	126432	hgsc.bcm.edu	37	19	39360597	39360597	+	Missense_Mutation	SNP	C	C	T	rs113728915	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39360597C>T	ENST00000591812.1	-	9	1414	c.1328G>A	c.(1327-1329)cGa>cAa	p.R443Q	RINL_ENST00000340740.3_Missense_Mutation_p.R329Q|CTC-360G5.6_ENST00000593830.1_RNA|RINL_ENST00000598904.1_Missense_Mutation_p.R329Q|RINL_ENST00000602238.1_5'Flank			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	443	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						GTTCTCGCCTCGAGCCAGGCC	0.652											OREG0025454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	180	0.0359425	0.003	0.0735	5008	,	,		14470	0.0		0.1153	False		,,,				2504	0.0092				p.R443Q		Atlas-SNP	.											RINL,NS,carcinoma,0,1	RINL	32	1	0			c.G1328A						PASS	.	C	GLN/ARG,GLN/ARG	91,4123		3,85,2019	16.0	18.0	17.0		1328,986	-6.5	0.0	19	dbSNP_132	17	896,7562		56,784,3389	yes	missense,missense	RINL	NM_001195833.1,NM_198445.3	43,43	59,869,5408	TT,TC,CC		10.5935,2.1595,7.7888	benign,benign	443/567,329/453	39360597	987,11685	2107	4229	6336	SO:0001583	missense	126432	exon9			TCGCCTCGAGCCA	AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.1328G>A	19.37:g.39360597C>T	ENSP00000467107:p.Arg443Gln	Somatic	73	0	0	885	WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_001195833	B4DPG5	Missense_Mutation	SNP	ENST00000591812.1	37	CCDS59386.1	137	0.06272893772893773	16	0.032520325203252036	32	0.08839779005524862	5	0.008741258741258742	84	0.11081794195250659	C	7.812	0.715927	0.15306	0.021595	0.105935	ENSG00000187994	ENST00000340740;ENST00000536520	T	0.31510	1.49	4.17	-6.5	0.01884	Vacuolar sorting protein 9 (2);	2.320620	0.01291	N	0.010015	T	0.00178	0.0005	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.18741	0.03;0.016	B;B	0.10450	0.005;0.004	T	0.13575	-1.0504	9	0.09843	T	0.71	0.8182	4.5149	0.11930	0.1188:0.2033:0.5128:0.165	.	443;329	B4DPG5;Q6ZS11	.;RINL_HUMAN	Q	329	ENSP00000340369:R329Q	ENSP00000340369:R329Q	R	-	2	0	RINL	44052437	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-2.089000	0.01357	-0.961000	0.03609	-0.448000	0.05591	CGA	C|0.924;T|0.076	0.076	strong		0.652	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445	
TAPBPL	55080	hgsc.bcm.edu	37	12	6567907	6567907	+	Missense_Mutation	SNP	C	C	T	rs1045546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6567907C>T	ENST00000266556.7	+	5	1166	c.1001C>T	c.(1000-1002)aCg>aTg	p.T334M	TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	334	Ig-like C1-type.		T -> M (in dbSNP:rs1045546). {ECO:0000269|PubMed:11920573}.		negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GTGGTGGTGACGTGGACCCGA	0.597													C|||	486	0.0970447	0.0076	0.1196	5008	,	,		18973	0.0089		0.1819	False		,,,				2504	0.2055				p.T334M		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C1001T						PASS	.	C	MET/THR	174,4232	114.6+/-152.6	4,166,2033	126.0	111.0	116.0		1001	3.4	1.0	12	dbSNP_86	116	1708,6892	312.7+/-311.0	179,1350,2771	yes	missense	TAPBPL	NM_018009.4	81	183,1516,4804	TT,TC,CC		19.8605,3.9492,14.4702	benign	334/469	6567907	1882,11124	2203	4300	6503	SO:0001583	missense	55080	exon5			TGGTGACGTGGAC	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.1001C>T	12.37:g.6567907C>T	ENSP00000266556:p.Thr334Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	129	71	0.550388	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	213	0.09752747252747253	7	0.014227642276422764	59	0.16298342541436464	5	0.008741258741258742	142	0.18733509234828497	C	9.846	1.192328	0.21954	0.039492	0.198605	ENSG00000139192	ENST00000266556	T	0.03358	3.96	5.22	3.38	0.38709	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.513681	0.22672	N	0.057058	T	0.00012	0.0000	M	0.67517	2.055	0.34632	P	0.280239	B	0.29270	0.24	B	0.28139	0.086	T	0.34229	-0.9837	9	0.49607	T	0.09	-3.9285	7.175	0.25738	0.1669:0.7452:0.0:0.0879	rs1045546;rs17725699;rs52836810;rs1045546	334	Q9BX59	TPSNR_HUMAN	M	334	ENSP00000266556:T334M	ENSP00000266556:T334M	T	+	2	0	TAPBPL	6438168	0.006000	0.16342	0.992000	0.48379	0.131000	0.20780	-0.172000	0.09868	0.691000	0.31592	0.650000	0.86243	ACG	C|0.876;T|0.124	0.124	strong		0.597	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
C9orf24	84688	hgsc.bcm.edu	37	9	34397545	34397545	+	Silent	SNP	A	A	G	rs11790577	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:34397545A>G	ENST00000297623.2	-	1	285	c.87T>C	c.(85-87)taT>taC	p.Y29Y		NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	29					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		GTGGGTCCTTATAGACCTCCT	0.567													A|||	2025	0.404353	0.2844	0.3934	5008	,	,		18772	0.3968		0.5239	False		,,,				2504	0.4591				p.Y29Y		Atlas-SNP	.											.	C9orf24	15	.	0			c.T87C						PASS	.	A		1396,3010	459.0+/-352.1	227,942,1034	185.0	169.0	175.0		87	-2.7	1.0	9	dbSNP_120	175	4473,4127	590.6+/-392.7	1159,2155,986	yes	coding-synonymous	C9orf24	NM_032596.3		1386,3097,2020	GG,GA,AA		47.9884,31.6841,45.1253		29/263	34397545	5869,7137	2203	4300	6503	SO:0001819	synonymous_variant	84688	exon1			GTCCTTATAGACC	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"""ciliated bronchial epithelium 1"", ""spermatid-specific manchette-related protein 1"""					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.87T>C	9.37:g.34397545A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	109	59	0.541284	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	37	CCDS6554.1																																																																																			A|0.552;G|0.448	0.448	strong		0.567	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136324239	136324239	+	Silent	SNP	C	C	A	rs1055432	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:136324239C>A	ENST00000371929.3	+	29	4665	c.4221C>A	c.(4219-4221)acC>acA	p.T1407T	ADAMTS13_ENST00000356589.2_Silent_p.T1320T|CACFD1_ENST00000291722.7_5'Flank|ADAMTS13_ENST00000371910.1_Silent_p.T203T|ADAMTS13_ENST00000371916.1_3'UTR|CACFD1_ENST00000540581.1_5'Flank|ADAMTS13_ENST00000485925.1_3'UTR|CACFD1_ENST00000316948.4_5'Flank|CACFD1_ENST00000542192.1_5'Flank|ADAMTS13_ENST00000355699.2_Silent_p.T1351T	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	1407	CUB 2.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AGTACTGGACCCTCCAATCAT	0.592													C|||	1155	0.230631	0.025	0.3271	5008	,	,		17137	0.1925		0.334	False		,,,				2504	0.3732				p.T1407T		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C4221A						PASS	.	C	,,	333,4065	171.9+/-202.1	22,289,1888	40.0	37.0	38.0		4221,3960,4053	3.0	0.7	9	dbSNP_86	38	2881,5717	444.4+/-360.7	466,1949,1884	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	488,2238,3772	AA,AC,CC		33.5078,7.5716,24.7307	,,	1407/1428,1320/1341,1351/1372	136324239	3214,9782	2199	4299	6498	SO:0001819	synonymous_variant	11093	exon29			CTGGACCCTCCAA	AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.4221C>A	9.37:g.136324239C>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	48	0.440367	NM_139025	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			C|0.769;A|0.231	0.231	strong		0.592	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
SLC4A5	57835	hgsc.bcm.edu	37	2	74466594	74466594	+	Silent	SNP	G	G	A	rs4853018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:74466594G>A	ENST00000377634.4	-	21	2586	c.2187C>T	c.(2185-2187)ggC>ggT	p.G729G	SLC4A5_ENST00000377632.1_Silent_p.G729G|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000394019.2_Silent_p.G729G|SLC4A5_ENST00000346834.4_Silent_p.G729G|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000357822.5_Silent_p.G729G|SLC4A5_ENST00000423644.1_Silent_p.G729G|SLC4A5_ENST00000359484.4_Silent_p.G665G|SLC4A5_ENST00000358683.4_Silent_p.G665G					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						GCAGGCGCCCGCCGTAGCTCA	0.537													G|||	1135	0.226637	0.1384	0.2291	5008	,	,		19259	0.1954		0.4304	False		,,,				2504	0.1667				p.G729G		Atlas-SNP	.											SLC4A5_ENST00000377634,colon,carcinoma,0,2	SLC4A5	215	2	0			c.C2187T						PASS	.	G	,	876,3530	340.7+/-306.4	71,734,1398	75.0	74.0	74.0		2187,2187	-9.0	0.7	2	dbSNP_111	74	3620,4980	522.4+/-380.1	757,2106,1437	yes	coding-synonymous,coding-synonymous	SLC4A5	NM_021196.3,NM_133478.2	,	828,2840,2835	AA,AG,GG		42.093,19.882,34.5687	,	729/1138,729/1122	74466594	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	57835	exon16			GCGCCCGCCGTAG	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.2187C>T	2.37:g.74466594G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_021196		Silent	SNP	ENST00000377634.4	37	CCDS1936.1																																																																																			G|0.694;A|0.306	0.306	strong		0.537	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
PCNT	5116	hgsc.bcm.edu	37	21	47754471	47754471	+	Missense_Mutation	SNP	G	G	A	rs58106867	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.						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	189	0	0		WXS	Illumina HiSeq	Phase_I	238	42	0.176471	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	
EPRS	2058	hgsc.bcm.edu	37	1	220156729	220156729	+	Silent	SNP	C	C	T	rs5030754	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:220156729C>T	ENST00000366923.3	-	22	3371	c.3102G>A	c.(3100-3102)aaG>aaA	p.K1034K		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1034	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TCATTTCTGACTTTGTGATGA	0.348													C|||	567	0.113219	0.2428	0.0591	5008	,	,		18032	0.0526		0.0984	False		,,,				2504	0.0542				p.K1034K		Atlas-SNP	.											.	EPRS	140	.	0			c.G3102A						PASS	.	C		947,3459	351.3+/-311.2	110,727,1366	46.0	48.0	47.0		3102	2.6	1.0	1	dbSNP_113	47	701,7899	170.1+/-221.3	33,635,3632	no	coding-synonymous	EPRS	NM_004446.2		143,1362,4998	TT,TC,CC		8.1512,21.4934,12.6711		1034/1513	220156729	1648,11358	2203	4300	6503	SO:0001819	synonymous_variant	2058	exon22			TTCTGACTTTGTG	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3102G>A	1.37:g.220156729C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	37	CCDS31027.1																																																																																			C|0.883;T|0.117	0.117	strong		0.348	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	
FBF1	85302	hgsc.bcm.edu	37	17	73916423	73916423	+	Missense_Mutation	SNP	A	A	T	rs7213548	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73916423A>T	ENST00000586717.1	-	17	1993	c.1720T>A	c.(1720-1722)Tgc>Agc	p.C574S	FBF1_ENST00000319129.5_Missense_Mutation_p.C573S|FBF1_ENST00000389570.4_Missense_Mutation_p.C574S			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	574			C -> S (in dbSNP:rs7213548).		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						GCGGGGCTGCACTGAAGTTGC	0.687													T|||	633	0.126398	0.2769	0.085	5008	,	,		18826	0.0258		0.0577	False		,,,				2504	0.1268				p.C573S		Atlas-SNP	.											.	FBF1	48	.	0			c.T1717A						PASS	.	T	SER/CYS	935,3089		107,721,1184	17.0	21.0	20.0		1717	-1.4	0.6	17	dbSNP_116	20	582,7720		18,546,3587	yes	missense	FBF1	NM_001080542.1	112	125,1267,4771	TT,TA,AA		7.0104,23.2356,12.3073	benign	573/1134	73916423	1517,10809	2012	4151	6163	SO:0001583	missense	85302	exon17			GGCTGCACTGAAG	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.1720T>A	17.37:g.73916423A>T	ENSP00000465132:p.Cys574Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		214	0.09798534798534798	126	0.25609756097560976	30	0.08287292817679558	17	0.02972027972027972	41	0.05408970976253298	T	0.008	-1.868864	0.00547	0.232356	0.070104	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.15139	2.45;2.45	5.11	-1.4	0.08968	.	.	.	.	.	T	0.00012	0.0000	N	0.01109	-1.01	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	0.44003	-0.9356	8	0.06625	T	0.88	0.399	6.0614	0.19841	0.3042:0.5052:0.0:0.1906	rs7213548;rs7213548	588;574;573	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	S	574;574;573;587	ENSP00000374221:C574S;ENSP00000324292:C573S	ENSP00000324292:C573S	C	-	1	0	FBF1	71428018	0.000000	0.05858	0.550000	0.28217	0.005000	0.04900	-1.451000	0.02387	-0.252000	0.09528	-1.068000	0.02270	TGC	A|0.875;T|0.125	0.125	strong		0.687	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
CYB5RL	606495	hgsc.bcm.edu	37	1	54644859	54644859	+	Missense_Mutation	SNP	C	C	T	rs61738851	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:54644859C>T	ENST00000534324.1	-	5	706	c.707G>A	c.(706-708)cGt>cAt	p.R236H	CYB5RL_ENST00000537208.1_Intron|CYB5RL_ENST00000401046.3_Missense_Mutation_p.R88H|CYB5RL_ENST00000542737.1_Missense_Mutation_p.R236H|RP11-446E24.4_ENST00000311841.7_Intron|CYB5RL_ENST00000419823.2_Missense_Mutation_p.R236H|CYB5RL_ENST00000287899.8_Intron			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	236							cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						ATTCCAGAAACGGGCCTGCTC	0.488													C|||	258	0.0515176	0.003	0.0648	5008	,	,		23044	0.001		0.1004	False		,,,				2504	0.1094				p.R236H		Atlas-SNP	.											.	CYB5RL	17	.	0			c.G707A						PASS	.	C	HIS/ARG	61,3935		2,57,1939	66.0	70.0	69.0		707	3.3	0.5	1	dbSNP_129	69	880,7476		49,782,3347	yes	missense	CYB5RL	NM_001031672.2	29	51,839,5286	TT,TC,CC		10.5314,1.5265,7.6182	probably-damaging	236/316	54644859	941,11411	1998	4178	6176	SO:0001583	missense	606495	exon7			CAGAAACGGGCCT		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.707G>A	1.37:g.54644859C>T	ENSP00000434343:p.Arg236His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001031672	B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	37	CCDS44151.1	118	0.05402930402930403	3	0.006097560975609756	31	0.0856353591160221	0	0.0	84	0.11081794195250659	C	11.78	1.741169	0.30865	0.015265	0.105314	ENSG00000215883	ENST00000419823;ENST00000401046;ENST00000534324;ENST00000542737;ENST00000493530	D;D;D;D;D	0.95656	-2.17;-2.17;-2.17;-2.17;-3.77	5.19	3.33	0.38152	Oxidoreductase FAD/NAD(P)-binding (1);	0.225621	0.18555	U	0.137795	T	0.25005	0.0607	L	0.58101	1.795	0.19945	N	0.999947	P;P	0.37423	0.529;0.594	B;B	0.29785	0.107;0.031	T	0.58487	-0.7628	10	0.46703	T	0.11	-10.291	8.5464	0.33424	0.0:0.7619:0.0:0.2381	.	236;88	Q6IPT4;Q6IPT4-3	NB5R5_HUMAN;.	H	236;88;236;236;150	ENSP00000409075:R236H;ENSP00000383825:R88H;ENSP00000434343:R236H;ENSP00000438151:R236H;ENSP00000434606:R150H	ENSP00000383825:R88H	R	-	2	0	CYB5RL	54417447	0.735000	0.28153	0.467000	0.27180	0.732000	0.41865	1.081000	0.30791	0.700000	0.31782	0.655000	0.94253	CGT	C|0.933;T|0.067	0.067	strong		0.488	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672	
ZNF92	168374	hgsc.bcm.edu	37	7	64863392	64863392	+	Missense_Mutation	SNP	C	C	T	rs10265083	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:64863392C>T	ENST00000328747.7	+	4	564	c.365C>T	c.(364-366)gCa>gTa	p.A122V	ZNF92_ENST00000431504.1_Missense_Mutation_p.A46V|ZNF92_ENST00000450302.2_Missense_Mutation_p.A53V|ZNF92_ENST00000357512.2_Missense_Mutation_p.A90V	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	122			A -> V (in dbSNP:rs10265083).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				AGTGTGGATGCATGTAAGGTG	0.338													c|||	1662	0.331869	0.5234	0.4164	5008	,	,		18135	0.3145		0.161	False		,,,				2504	0.2065				p.A122V		Atlas-SNP	.											.	ZNF92	68	.	0			c.C365T						PASS	.	C	VAL/ALA,VAL/ALA	1981,2425	554.5+/-379.0	457,1067,679	95.0	98.0	97.0		158,365	-0.9	0.0	7	dbSNP_119	97	1418,7182	270.9+/-289.3	134,1150,3016	yes	missense,missense	ZNF92	NM_007139.2,NM_152626.2	64,64	591,2217,3695	TT,TC,CC		16.4884,44.9614,26.1341	benign,benign	53/518,122/587	64863392	3399,9607	2203	4300	6503	SO:0001583	missense	168374	exon4			TGGATGCATGTAA	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"""Zinc fingers, C2H2-type"", ""-"""	13168	protein-coding gene	gene with protein product		603974	"""zinc finger protein 92 (HTF12)"""			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.365C>T	7.37:g.64863392C>T	ENSP00000332595:p.Ala122Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_152626	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	37	CCDS34646.1	676	0.30952380952380953	261	0.5304878048780488	127	0.35082872928176795	178	0.3111888111888112	110	0.14511873350923482	C	5.570	0.289954	0.10567	0.449614	0.164884	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.05580	3.57;3.42;3.51;3.44	0.427	-0.854	0.10705	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.33022	0.1;0.394	B;B	0.30716	0.089;0.119	T	0.28964	-1.0027	8	0.36615	T	0.2	.	5.0094	0.14304	0.3417:0.6583:0.0:0.0	rs10265083;rs59262414;rs10265083	90;122	Q03936-3;Q03936	.;ZNF92_HUMAN	V	122;46;90;53	ENSP00000332595:A122V;ENSP00000400495:A46V;ENSP00000350113:A90V;ENSP00000396126:A53V	ENSP00000332595:A122V	A	+	2	0	ZNF92	64500827	0.005000	0.15991	0.009000	0.14445	0.009000	0.06853	0.049000	0.14099	-0.514000	0.06488	-0.518000	0.04402	GCA	C|0.725;T|0.275	0.275	strong		0.338	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38652963	38652963	+	Silent	SNP	G	G	A	rs62121443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:38652963G>A	ENST00000222345.6	+	14	4241	c.3732G>A	c.(3730-3732)ccG>ccA	p.P1244P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1244					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)			ACAAGCACCCGTCCAGGCAGG	0.627													G|||	12	0.00239617	0.0008	0.0029	5008	,	,		18738	0.0		0.008	False		,,,				2504	0.001				p.P1244P		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.G3732A						PASS	.	G		11,4395	17.9+/-39.9	0,11,2192	97.0	80.0	86.0		3732	2.5	0.8	19	dbSNP_129	86	55,8545	34.8+/-89.0	0,55,4245	no	coding-synonymous	SIPA1L3	NM_015073.1		0,66,6437	AA,AG,GG		0.6395,0.2497,0.5075		1244/1782	38652963	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	23094	exon14			GCACCCGTCCAGG	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.3732G>A	19.37:g.38652963G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	233	109	0.467811	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	37	CCDS33007.1																																																																																			G|0.996;A|0.004	0.004	strong		0.627	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
PRX	57716	hgsc.bcm.edu	37	19	40901604	40901604	+	Silent	SNP	A	A	G	rs268672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40901604A>G	ENST00000324001.7	-	7	2925	c.2655T>C	c.(2653-2655)ccT>ccC	p.P885P	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	885					axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTGCCACCTCAGGGCCCTCCA	0.637													G|||	2664	0.531949	0.8427	0.4784	5008	,	,		17346	0.2401		0.506	False		,,,				2504	0.4775				p.P885P		Atlas-SNP	.											.	PRX	151	.	0			c.T2655C						PASS	.	G	,	3471,935	339.1+/-305.6	1385,701,117	40.0	49.0	46.0		,2655	-7.2	0.0	19	dbSNP_79	46	4451,4149	555.1+/-386.6	1155,2141,1004	no	utr-3,coding-synonymous	PRX	NM_020956.2,NM_181882.2	,	2540,2842,1121	GG,GA,AA		48.2442,21.2211,39.0897	,	,885/1462	40901604	7922,5084	2203	4300	6503	SO:0001819	synonymous_variant	57716	exon7			CACCTCAGGGCCC	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.2655T>C	19.37:g.40901604A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																			A|0.457;G|0.543	0.543	strong		0.637	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
CIB2	10518	hgsc.bcm.edu	37	15	78398146	78398146	+	Silent	SNP	G	G	A	rs10456	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:78398146G>A	ENST00000258930.3	-	5	805	c.477C>T	c.(475-477)gaC>gaT	p.D159D	CIB2_ENST00000539011.1_Silent_p.D116D|CIB2_ENST00000557846.1_Silent_p.D110D|CIB2_ENST00000560618.1_Silent_p.D116D	NM_006383.2	NP_006374.1	O75838	CIB2_HUMAN	calcium and integrin binding family member 2	159	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion homeostasis (GO:0055074)|photoreceptor cell maintenance (GO:0045494)	blood microparticle (GO:0072562)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|photoreceptor inner segment (GO:0001917)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	11						TGCCGTCACCGTCCAAGTCAG	0.617													G|||	639	0.127596	0.0696	0.1556	5008	,	,		20455	0.0228		0.2495	False		,,,				2504	0.1687				p.D159D		Atlas-SNP	.											.	CIB2	24	.	0			c.C477T						PASS	.	G		343,4049	179.4+/-207.9	11,321,1864	197.0	159.0	172.0		477	-10.9	0.0	15	dbSNP_52	172	2095,6491	362.3+/-332.7	246,1603,2444	no	coding-synonymous	CIB2	NM_006383.2		257,1924,4308	AA,AG,GG		24.4002,7.8097,18.7856		159/188	78398146	2438,10540	2196	4293	6489	SO:0001819	synonymous_variant	10518	exon5			GTCACCGTCCAAG	BC047381	CCDS10296.1, CCDS61722.1, CCDS61723.1	15q24	2013-01-10			ENSG00000136425	ENSG00000136425		"""EF-hand domain containing"""	24579	protein-coding gene	gene with protein product		605564	"""deafness, autosomal recessive 48"", ""Usher syndrome 1J (autosomal recessive)"""	DFNB48, USH1J		9931475, 23023331	Standard	NM_006383		Approved	KIP2	uc002bdb.2	O75838	OTTHUMG00000143731	ENST00000258930.3:c.477C>T	15.37:g.78398146G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_006383	B4DDF0|H0YM71|Q05BT6	Silent	SNP	ENST00000258930.3	37	CCDS10296.1																																																																																			G|0.836;A|0.164	0.164	strong		0.617	CIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289798.1	NM_006383	
TTLL5	23093	hgsc.bcm.edu	37	14	76368544	76368544	+	Missense_Mutation	SNP	T	T	C	rs1133834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:76368544T>C	ENST00000298832.9	+	31	4005	c.3800T>C	c.(3799-3801)tTt>tCt	p.F1267S		NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1267			F -> S (in dbSNP:rs1133834). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:17116691}.		fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		CCTGCAGCCTTTGTGCCCATC	0.562													T|||	2131	0.425519	0.5832	0.366	5008	,	,		19061	0.494		0.1928	False		,,,				2504	0.4233				p.F1267S		Atlas-SNP	.											.	TTLL5	102	.	0			c.T3800C						PASS	.	T	SER/PHE	2238,2168	594.9+/-388.3	570,1098,535	85.0	77.0	80.0		3800	1.5	0.3	14	dbSNP_86	80	1537,7063	286.6+/-297.8	137,1263,2900	yes	missense	TTLL5	NM_015072.4	155	707,2361,3435	CC,CT,TT		17.8721,49.2056,29.0251	benign	1267/1282	76368544	3775,9231	2203	4300	6503	SO:0001583	missense	23093	exon31			CAGCCTTTGTGCC	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.3800T>C	14.37:g.76368544T>C	ENSP00000298832:p.Phe1267Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	835	0.3823260073260073	292	0.5934959349593496	125	0.3453038674033149	277	0.48426573426573427	141	0.18601583113456466	T	13.21	2.170428	0.38315	0.507944	0.178721	ENSG00000119685	ENST00000286653;ENST00000298832	T	0.02763	4.17	5.43	1.48	0.22813	.	2.780490	0.00890	N	0.002234	T	0.00012	0.0000	N	0.08118	0	0.58432	P	6.999999999979245E-6	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.38972	-0.9636	9	0.09590	T	0.72	.	1.2609	0.02001	0.1796:0.1055:0.1866:0.5283	rs1133834;rs2272583;rs3195915;rs52790173;rs61039434;rs1133834	341;1267	F8W7N3;Q6EMB2	.;TTLL5_HUMAN	S	341;1267	ENSP00000298832:F1267S	ENSP00000286653:F341S	F	+	2	0	TTLL5	75438297	0.014000	0.17966	0.310000	0.25168	0.975000	0.68041	0.410000	0.21098	0.346000	0.23899	-0.316000	0.08728	TTT	C|0.345;N|0.000	0.345	strong		0.562	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
NUAK1	9891	hgsc.bcm.edu	37	12	106460938	106460938	+	Missense_Mutation	SNP	G	G	C	rs3741883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:106460938G>C	ENST00000261402.2	-	7	3007	c.1628C>G	c.(1627-1629)cCt>cGt	p.P543R		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	543			P -> R (in dbSNP:rs3741883). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)	p.P543R(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GGGCATTTCAGGGCTGACCAG	0.622													G|||	1109	0.221446	0.0408	0.2133	5008	,	,		15631	0.4177		0.2207	False		,,,				2504	0.2699				p.P543R		Atlas-SNP	.											NUAK1_ENST00000261402,NS,carcinoma,0,2	NUAK1	196	2	2	Substitution - Missense(2)	stomach(2)	c.C1628G						PASS	.	G	ARG/PRO	306,4100	162.2+/-194.2	11,284,1908	60.0	67.0	65.0		1628	5.5	1.0	12	dbSNP_107	65	1961,6639	342.1+/-324.3	237,1487,2576	yes	missense	NUAK1	NM_014840.2	103	248,1771,4484	CC,CG,GG		22.8023,6.9451,17.4304	possibly-damaging	543/662	106460938	2267,10739	2203	4300	6503	SO:0001583	missense	9891	exon7			ATTTCAGGGCTGA	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.1628C>G	12.37:g.106460938G>C	ENSP00000261402:p.Pro543Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	37	CCDS31892.1	504	0.23076923076923078	21	0.042682926829268296	76	0.20994475138121546	243	0.42482517482517484	164	0.21635883905013192	G	9.640	1.138832	0.21123	0.069451	0.228023	ENSG00000074590	ENST00000261402	T	0.73575	-0.76	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000012	T	0.00012	0.0000	N	0.08118	0	0.26688	P	0.9714141	P	0.49961	0.93	B	0.42319	0.383	T	0.30937	-0.9961	9	0.27082	T	0.32	.	12.7544	0.57325	0.0749:0.0:0.9251:0.0	rs3741883;rs3741883	543	O60285	NUAK1_HUMAN	R	543	ENSP00000261402:P543R	ENSP00000261402:P543R	P	-	2	0	NUAK1	104985068	1.000000	0.71417	0.994000	0.49952	0.204000	0.24138	3.525000	0.53502	2.596000	0.87737	0.462000	0.41574	CCT	G|0.796;C|0.204	0.204	strong		0.622	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350481	65350481	+	Missense_Mutation	SNP	C	C	T	rs3805466	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:65350481C>T	ENST00000284037.5	+	21	3724	c.3335C>T	c.(3334-3336)tCa>tTa	p.S1112L	ERBB2IP_ENST00000511297.1_Missense_Mutation_p.S1108L|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.S1112L	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1112			S -> L (in dbSNP:rs3805466).		basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GAGTTCCACTCAGCGGGAAGA	0.488													C|||	418	0.0834665	0.0121	0.2219	5008	,	,		18342	0.1339		0.0417	False		,,,				2504	0.0726				p.S1112L		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.C3335T						PASS	.	C	LEU/SER,LEU/SER	101,4305	79.9+/-118.3	0,101,2102	60.0	58.0	59.0		3335,3335	5.8	1.0	5	dbSNP_107	59	410,8190	128.3+/-186.6	9,392,3899	yes	missense,missense	ERBB2IP	NM_001006600.1,NM_018695.2	145,145	9,493,6001	TT,TC,CC		4.7674,2.2923,3.929	benign,benign	1112/1303,1112/1372	65350481	511,12495	2203	4300	6503	SO:0001583	missense	55914	exon21			TCCACTCAGCGGG		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.3335C>T	5.37:g.65350481C>T	ENSP00000284037:p.Ser1112Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	208	0.09523809523809523	9	0.018292682926829267	67	0.1850828729281768	96	0.16783216783216784	36	0.047493403693931395	C	18.19	3.569735	0.65765	0.022923	0.047674	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T	0.39592	1.3;1.3;1.3;1.49;1.07;1.37;1.3;1.33;1.07	5.76	5.76	0.90799	.	0.259894	0.39985	N	0.001207	T	0.00109	0.0003	L	0.47190	1.495	0.20307	P	0.9999122916	P;P;B;P;P;P;P	0.48764	0.835;0.594;0.444;0.773;0.651;0.835;0.915	B;B;B;P;B;B;P	0.53185	0.311;0.164;0.206;0.529;0.084;0.407;0.72	T	0.00017	-1.2377	9	0.72032	D	0.01	.	19.943	0.97172	0.0:1.0:0.0:0.0	rs3805466;rs61274806;rs3805466	1112;1112;1112;1108;1112;1112;1112	Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;LAP2_HUMAN;.;.	L	1112;1112;1112;1112;1112;1112;1108;1112;1112	ENSP00000284037:S1112L;ENSP00000370330:S1112L;ENSP00000370326:S1112L;ENSP00000370323:S1112L;ENSP00000370322:S1112L;ENSP00000370325:S1112L;ENSP00000422766:S1108L;ENSP00000426632:S1112L;ENSP00000422015:S1112L	ENSP00000284037:S1112L	S	+	2	0	ERBB2IP	65386237	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.210000	0.77924	2.722000	0.93159	0.650000	0.86243	TCA	C|0.936;T|0.064	0.064	strong		0.488	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
CEP131	22994	hgsc.bcm.edu	37	17	79164488	79164488	+	Missense_Mutation	SNP	C	C	T	rs117616373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79164488C>T	ENST00000269392.4	-	24	3314	c.3067G>A	c.(3067-3069)Gcc>Acc	p.A1023T	AZI1_ENST00000575907.1_Missense_Mutation_p.A987T|AZI1_ENST00000374782.3_Missense_Mutation_p.A984T|AZI1_ENST00000450824.2_Missense_Mutation_p.A1020T	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		1023					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)			TGCAGCGTGGCCAGCTCGGCC	0.731													C|||	76	0.0151757	0.0023	0.0317	5008	,	,		11555	0.0		0.0427	False		,,,				2504	0.0082				p.A1020T		Atlas-SNP	.											.	AZI1	145	.	0			c.G3058A						PASS	.	C	THR/ALA,THR/ALA	38,4312		0,38,2137	9.0	11.0	11.0		2950,3058	1.1	0.9	17	dbSNP_132	11	408,8104		13,382,3861	no	missense,missense	AZI1	NM_001009811.2,NM_014984.2	58,58	13,420,5998	TT,TC,CC		4.7932,0.8736,3.4676	probably-damaging,probably-damaging	984/1045,1020/1081	79164488	446,12416	2175	4256	6431	SO:0001583	missense	22994	exon24			GCGTGGCCAGCTC																												ENST00000269392.4:c.3067G>A	17.37:g.79164488C>T	ENSP00000269392:p.Ala1023Thr	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37		46	0.021062271062271064	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	34	0.044854881266490766	C	14.54	2.564835	0.45694	0.008736	0.047932	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.15256	2.46;2.44;2.46	4.4	1.11	0.20524	.	0.361388	0.26248	N	0.025463	T	0.03564	0.0102	L	0.47716	1.5	0.40310	D	0.978706	D;P;P;P	0.63880	0.993;0.716;0.577;0.577	P;B;B;B	0.58172	0.834;0.407;0.187;0.187	T	0.01337	-1.1381	10	0.52906	T	0.07	-0.7262	4.9522	0.14021	0.2875:0.5524:0.0:0.1602	.	1020;1023;984;1020	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	T	1020;984;1023	ENSP00000393583:A1020T;ENSP00000363914:A984T;ENSP00000269392:A1023T	ENSP00000269392:A1023T	A	-	1	0	AZI1	76779083	0.958000	0.32768	0.933000	0.37362	0.010000	0.07245	0.274000	0.18680	0.506000	0.28125	-0.218000	0.12543	GCC	C|0.979;T|0.021	0.021	strong		0.731	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
C8A	731	hgsc.bcm.edu	37	1	57383358	57383358	+	Missense_Mutation	SNP	C	C	T	rs17300936	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:57383358C>T	ENST00000361249.3	+	11	1820	c.1724C>T	c.(1723-1725)cCa>cTa	p.P575L		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	575	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		P -> L (in dbSNP:rs17300936).	P -> S (in Ref. 3; AAA82124). {ECO:0000305}.	complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GCCTCGTGTCCAGGGCGGAAA	0.567													C|||	307	0.0613019	0.0174	0.0432	5008	,	,		17737	0.0585		0.1233	False		,,,				2504	0.0726				p.P575L		Atlas-SNP	.											.	C8A	103	.	0			c.C1724T						PASS	.	C	LEU/PRO	151,4255	104.7+/-143.2	2,147,2054	57.0	57.0	57.0		1724	1.6	0.5	1	dbSNP_123	57	1084,7516	227.5+/-262.8	75,934,3291	yes	missense	C8A	NM_000562.2	98	77,1081,5345	TT,TC,CC		12.6047,3.4271,9.4956	benign	575/585	57383358	1235,11771	2203	4300	6503	SO:0001583	missense	731	exon11			CGTGTCCAGGGCG	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1724C>T	1.37:g.57383358C>T	ENSP00000354458:p.Pro575Leu	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	286	135	0.472028	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	159	0.07280219780219781	12	0.024390243902439025	19	0.052486187845303865	33	0.057692307692307696	95	0.12532981530343007	C	0.124	-1.122112	0.01785	0.034271	0.126047	ENSG00000157131	ENST00000361249	T	0.54071	0.59	4.82	1.63	0.23807	.	0.346426	0.30879	N	0.008683	T	0.00271	0.0008	N	0.12471	0.22	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.06643	-1.0815	9	0.21540	T	0.41	-1.0877	6.014	0.19592	0.1444:0.5988:0.0:0.2568	rs17300936;rs58858987;rs17300936	575	P07357	CO8A_HUMAN	L	575	ENSP00000354458:P575L	ENSP00000354458:P575L	P	+	2	0	C8A	57155946	0.150000	0.22732	0.470000	0.27216	0.009000	0.06853	0.722000	0.25925	0.611000	0.30052	-0.251000	0.11542	CCA	C|0.917;N|0.000	.	strong		0.567	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
ZFC3H1	196441	hgsc.bcm.edu	37	12	72008421	72008421	+	Missense_Mutation	SNP	T	T	C	rs11541286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	58	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	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	
RNF8	9025	hgsc.bcm.edu	37	6	37349066	37349066	+	Silent	SNP	G	G	A	rs34150698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:37349066G>A	ENST00000373479.4	+	7	1570	c.1377G>A	c.(1375-1377)aaG>aaA	p.K459K	RNF8_ENST00000469731.1_Intron	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase	459					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|histone exchange (GO:0043486)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A ubiquitination (GO:0033522)|histone H2B ubiquitination (GO:0033523)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|mitotic nuclear division (GO:0007067)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|response to ionizing radiation (GO:0010212)|spermatid development (GO:0007286)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome, telomeric region (GO:0000781)|nucleolus (GO:0005730)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	13						GCATTAATAAGATGGTAAATA	0.408													G|||	146	0.0291534	0.0061	0.0519	5008	,	,		22775	0.001		0.0805	False		,,,				2504	0.0204				p.K459K		Atlas-SNP	.											RNF8,colon,carcinoma,+1,1	RNF8	78	1	0			c.G1377A						scavenged	.	G	,	59,4347	57.4+/-93.9	0,59,2144	115.0	104.0	108.0		1377,	2.0	1.0	6	dbSNP_126	108	623,7977	162.2+/-214.9	21,581,3698	no	coding-synonymous,intron	RNF8	NM_003958.3,NM_183078.2	,	21,640,5842	AA,AG,GG		7.2442,1.3391,5.2437	,	459/486,	37349066	682,12324	2203	4300	6503	SO:0001819	synonymous_variant	9025	exon7			TAATAAGATGGTA	AB012770	CCDS4833.1, CCDS4834.1	6p21.3	2013-01-09	2012-02-23		ENSG00000112130	ENSG00000112130		"""RING-type (C3HC4) zinc fingers"""	10071	protein-coding gene	gene with protein product		611685	"""ring finger protein (C3HC4 type) 8"", ""ring finger protein 8"""			9734811, 9852682	Standard	NM_003958		Approved	KIAA0646	uc003onq.4	O76064	OTTHUMG00000014620	ENST00000373479.4:c.1377G>A	6.37:g.37349066G>A		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_003958	A6NN24|A8MYC0|B4DPG0|Q53H16|Q5NKW5	Silent	SNP	ENST00000373479.4	37	CCDS4834.1																																																																																			G|0.947;A|0.053	0.053	strong		0.408	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2		
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253835	39253835	+	Missense_Mutation	SNP	C	C	T	rs72625995	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39253835C>T	ENST00000333822.4	-	1	558	c.502G>A	c.(502-504)Gcc>Acc	p.A168T		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	168				A -> T (in Ref. 2; CAC27579). {ECO:0000305}.	aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.A168T(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ATGACACAGGCTGGGCGATAG	0.662													T|||	3187	0.636382	0.9168	0.6326	5008	,	,		15964	0.4147		0.6183	False		,,,				2504	0.5072				p.A168T		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	1	Substitution - Missense(1)	prostate(1)	c.G502A						PASS	.						49.0	57.0	54.0					17																	39253835		692	1591	2283	SO:0001583	missense	728224	exon1			CACAGGCTGGGCG	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.502G>A	17.37:g.39253835C>T	ENSP00000328444:p.Ala168Thr	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	162	65	0.401235	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	3.713	-0.059042	0.07317	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.00570	6.51	3.73	2.63	0.31362	.	0.219558	0.22220	N	0.062972	T	0.00144	0.0004	N	0.00178	-1.915	0.58432	P	8.000000000008E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.10474	-1.0628	9	0.07990	T	0.79	.	5.1348	0.14928	0.0:0.2562:0.0:0.7438	.	168	Q9BYQ9	KRA48_HUMAN	T	168;138	ENSP00000328444:A168T	ENSP00000414561:A138T	A	-	1	0	KRTAP4-8	36507361	0.706000	0.27856	0.999000	0.59377	0.662000	0.39071	0.104000	0.15313	0.434000	0.26340	-0.572000	0.04151	GCC	C|0.980;T|0.020	0.020	strong		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
CHD6	84181	hgsc.bcm.edu	37	20	40079655	40079655	+	Missense_Mutation	SNP	G	G	C	rs41278126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:40079655G>C	ENST00000373233.3	-	23	3791	c.3614C>G	c.(3613-3615)gCc>gGc	p.A1205G	CHD6_ENST00000309279.7_Missense_Mutation_p.A688G	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1205					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTTGCAGGTGGCTAGCCAATC	0.532													G|||	59	0.0117812	0.0008	0.0086	5008	,	,		19751	0.0		0.0457	False		,,,				2504	0.0061				p.A1205G		Atlas-SNP	.											.	CHD6	312	.	0			c.C3614G						PASS	.	G	GLY/ALA	46,4360	48.9+/-83.8	1,44,2158	174.0	139.0	151.0		3614	5.8	1.0	20	dbSNP_127	151	360,8240	121.0+/-180.1	12,336,3952	yes	missense	CHD6	NM_032221.3	60	13,380,6110	CC,CG,GG		4.186,1.044,3.1216	possibly-damaging	1205/2716	40079655	406,12600	2203	4300	6503	SO:0001583	missense	84181	exon23			CAGGTGGCTAGCC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3614C>G	20.37:g.40079655G>C	ENSP00000362330:p.Ala1205Gly	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	215	105	0.488372	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	45|45	0.020604395604395604|0.020604395604395604	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	42|42	0.055408970976253295|0.055408970976253295	G|G	16.59|16.59	3.164784|3.164784	0.57476|0.57476	0.01044|0.01044	0.04186|0.04186	ENSG00000124177|ENSG00000124177	ENST00000373233;ENST00000309279|ENST00000440697	D;D|.	0.84800|.	-1.9;-1.9|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.199876|.	0.35739|.	N|.	0.003018|.	T|T	0.12518|0.12518	0.0304|0.0304	L|L	0.47716|0.47716	1.5|1.5	0.27988|0.27988	N|N	0.935797|0.935797	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.08973|0.08973	-1.0696|-1.0696	10|5	0.45353|.	T|.	0.12|.	-9.1677|-9.1677	20.0204|20.0204	0.97499|0.97499	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs41278126;rs61753662|rs41278126;rs61753662	1205|.	Q8TD26|.	CHD6_HUMAN|.	G|A	1205;688|391	ENSP00000362330:A1205G;ENSP00000308684:A688G|.	ENSP00000308684:A688G|.	A|P	-|-	2|1	0|0	CHD6|CHD6	39513069|39513069	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	6.429000|6.429000	0.73387|0.73387	2.729000|2.729000	0.93468|0.93468	0.650000|0.650000	0.86243|0.86243	GCC|CCA	G|0.971;C|0.029	0.029	strong		0.532	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537324	88537324	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537324C>T	ENST00000282478.7	+	4	3543	c.3510C>T	c.(3508-3510)gaC>gaT	p.D1170D	DSPP_ENST00000399271.1_Silent_p.D1170D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1170	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)		acagcagcgacagcagcgata	0.567																																					p.D1170D		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	0			c.C3510T						PASS	.						44.0	63.0	56.0					4																	88537324		1605	2847	4452	SO:0001819	synonymous_variant	1834	exon5			CAGCGACAGCAGC	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.3510C>T	4.37:g.88537324C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	183	11	0.0601093	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
FAM161A	84140	hgsc.bcm.edu	37	2	62053677	62053677	+	Silent	SNP	A	A	G	rs138464813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:62053677A>G	ENST00000405894.3	-	6	1997	c.1896T>C	c.(1894-1896)atT>atC	p.I632I	FAM161A_ENST00000404929.1_Silent_p.I688I	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	632	Glu-rich.				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						TGTTGGTATCAATAAAATAAT	0.328													A|||	6	0.00119808	0.0	0.0029	5008	,	,		19015	0.0		0.003	False		,,,				2504	0.001				p.I688I		Atlas-SNP	.											.	FAM161A	200	.	0			c.T2064C						PASS	.	A	,	3,3635		0,3,1816	107.0	98.0	101.0		2064,1896	3.0	1.0	2	dbSNP_134	101	33,8127		0,33,4047	yes	coding-synonymous,coding-synonymous	FAM161A	NM_001201543.1,NM_032180.2	,	0,36,5863	GG,GA,AA		0.4044,0.0825,0.3051	,	688/717,632/661	62053677	36,11762	1819	4080	5899	SO:0001819	synonymous_variant	84140	exon7			GGTATCAATAAAA		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.1896T>C	2.37:g.62053677A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	215	95	0.44186	NM_001201543	B4DJV7|Q9H8R2	Silent	SNP	ENST00000405894.3	37	CCDS42687.2																																																																																			A|0.998;G|0.002	0.002	strong		0.328	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
PEX26	55670	hgsc.bcm.edu	37	22	18561342	18561342	+	Missense_Mutation	SNP	A	A	G	rs201884779|rs267608189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:18561342A>G	ENST00000329627.7	+	2	406	c.200A>G	c.(199-201)aAc>aGc	p.N67S	PEX26_ENST00000399744.3_Missense_Mutation_p.N67S|PEX26_ENST00000428061.2_Missense_Mutation_p.N67S|XXbac-B476C20.9_ENST00000607927.1_RNA|XXbac-B476C20.9_ENST00000426483.1_RNA	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	67					protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGTCTGGCCAACCACGCCGTG	0.677													A|||	3	0.000599042	0.0	0.0	5008	,	,		13652	0.0		0.003	False		,,,				2504	0.0				p.N67S		Atlas-SNP	.											.	PEX26	27	.	0			c.A200G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4084		0,0,2042	6.0	7.0	7.0		200,200,200	-3.6	0.0	22		7	13,8139		0,13,4063	no	missense,missense,missense	PEX26	NM_001127649.2,NM_001199319.1,NM_017929.5	46,46,46	0,13,6105	GG,GA,AA		0.1595,0.0,0.1062	benign,benign,benign	67/306,67/257,67/306	18561342	13,12223	2042	4076	6118	SO:0001583	missense	55670	exon1			TGGCCAACCACGC	AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193			22965	protein-coding gene	gene with protein product		608666	"""peroxisome biogenesis factor 26"""			12717447, 12851857	Standard	NM_017929		Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.200A>G	22.37:g.18561342A>G	ENSP00000331106:p.Asn67Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_001127649	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Missense_Mutation	SNP	ENST00000329627.7	37	CCDS13750.1	.	.	.	.	.	.	.	.	.	.	A	5.785	0.329161	0.10956	0.0	0.001595	ENSG00000215193	ENST00000329627;ENST00000399744;ENST00000428061;ENST00000399746	D;D;D	0.92647	-3.08;-3.08;-3.08	5.21	-3.6	0.04570	.	1.979650	0.02715	U	0.113263	T	0.79975	0.4539	N	0.05199	-0.095	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.73088	-0.4093	10	0.09843	T	0.71	2.4468	7.7401	0.28837	0.265:0.4559:0.2791:0.0	.	67;67	F6UBB5;Q7Z412	.;PEX26_HUMAN	S	67	ENSP00000331106:N67S;ENSP00000382648:N67S;ENSP00000412441:N67S	ENSP00000331106:N67S	N	+	2	0	PEX26	16941342	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.459000	0.02370	-1.053000	0.03218	-0.435000	0.05868	AAC	A|0.994;G|0.006	0.006	weak		0.677	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3	NM_017929	
FLG	2312	hgsc.bcm.edu	37	1	152281690	152281690	+	Missense_Mutation	SNP	C	C	T	rs12407748	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281690C>T	ENST00000368799.1	-	3	5707	c.5672G>A	c.(5671-5673)cGg>cAg	p.R1891Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1891	Ser-rich.		R -> Q (in dbSNP:rs12407748).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGTCGGCCCGAGAGGAAGC	0.567									Ichthyosis				C|||	1440	0.28754	0.0113	0.3905	5008	,	,		19138	0.5843		0.1421	False		,,,				2504	0.4315				p.R1891Q		Atlas-SNP	.											.	FLG	900	.	0			c.G5672A						PASS	.	C	GLN/ARG	162,4244	108.6+/-147.0	2,158,2043	272.0	275.0	274.0		5672	-3.6	0.0	1	dbSNP_120	274	1242,7358	249.3+/-276.6	97,1048,3155	no	missense	FLG	NM_002016.1	43	99,1206,5198	TT,TC,CC		14.4419,3.6768,10.795	possibly-damaging	1891/4062	152281690	1404,11602	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCGGCCCGAGAGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5672G>A	1.37:g.152281690C>T	ENSP00000357789:p.Arg1891Gln	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	370	168	0.454054	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	549	0.25137362637362637	9	0.018292682926829267	114	0.3149171270718232	316	0.5524475524475524	110	0.14511873350923482	C	4.339	0.062313	0.08388	0.036768	0.144419	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.03358	3.96	1.78	-3.57	0.04612	.	.	.	.	.	T	0.00524	0.0017	N	0.13235	0.315	0.80722	P	0.0	P	0.39250	0.665	B	0.33890	0.172	T	0.39272	-0.9622	8	0.08599	T	0.76	.	7.8311	0.29342	0.0:0.7145:0.0:0.2855	rs12407748;rs35359555;rs12407748	1891	P20930	FILA_HUMAN	Q	1891;126	ENSP00000357789:R1891Q	ENSP00000271820:R126Q	R	-	2	0	FLG	150548314	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.006000	0.00315	-1.013000	0.03383	-1.309000	0.01313	CGG	C|0.851;T|0.149	0.149	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ADCY10	55811	hgsc.bcm.edu	37	1	167792356	167792356	+	Missense_Mutation	SNP	G	G	A	rs72697797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:167792356G>A	ENST00000367851.4	-	29	4242	c.4058C>T	c.(4057-4059)cCg>cTg	p.P1353L	RP1-313L4.3_ENST00000451545.1_RNA|ADCY10_ENST00000545172.1_Missense_Mutation_p.P1200L|ADCY10_ENST00000367848.1_Missense_Mutation_p.P1261L	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	1353					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						GATCAATTGCGGGTATCTATG	0.483													G|||	56	0.0111821	0.0008	0.0144	5008	,	,		18058	0.0		0.0378	False		,,,				2504	0.0072				p.P1353L		Atlas-SNP	.											.	ADCY10	175	.	0			c.C4058T						PASS	.	G	LEU/PRO,LEU/PRO	33,4373	36.8+/-68.6	1,31,2171	52.0	54.0	53.0		3599,4058	-1.8	0.0	1	dbSNP_130	53	348,8252	117.4+/-177.0	13,322,3965	yes	missense,missense	ADCY10	NM_001167749.1,NM_018417.4	98,98	14,353,6136	AA,AG,GG		4.0465,0.749,2.9294	benign,benign	1200/1458,1353/1611	167792356	381,12625	2203	4300	6503	SO:0001583	missense	55811	exon29			AATTGCGGGTATC	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.4058C>T	1.37:g.167792356G>A	ENSP00000356825:p.Pro1353Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	37	CCDS1265.1	39	0.017857142857142856	0	0.0	7	0.019337016574585635	0	0.0	32	0.04221635883905013	G	7.641	0.680910	0.14907	0.00749	0.040465	ENSG00000143199	ENST00000545172;ENST00000271426;ENST00000367851;ENST00000367848	T;T;T	0.75589	-0.95;-0.95;-0.95	5.09	-1.76	0.08006	.	0.721098	0.12502	N	0.463307	T	0.23171	0.0560	N	0.08118	0	0.24488	N	0.994312	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.04840	-1.0923	9	0.30078	T	0.28	-13.2241	1.4954	0.02465	0.2585:0.0819:0.2745:0.3851	.	1261;1353	Q96PN6-2;Q96PN6	.;ADCYA_HUMAN	L	1200;254;1353;1261	ENSP00000441992:P1200L;ENSP00000356825:P1353L;ENSP00000356822:P1261L	ENSP00000271426:P254L	P	-	2	0	ADCY10	166058980	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.066000	0.11598	-0.153000	0.11137	-2.213000	0.00299	CCG	G|0.973;A|0.027	0.027	strong		0.483	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
RGL1	23179	hgsc.bcm.edu	37	1	183876182	183876182	+	Silent	SNP	C	C	T	rs11591089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:183876182C>T	ENST00000360851.3	+	14	1687	c.1509C>T	c.(1507-1509)gaC>gaT	p.D503D	RGL1_ENST00000536277.1_Silent_p.D501D|RGL1_ENST00000304685.4_Silent_p.D538D|RGL1_ENST00000539189.1_Silent_p.D474D			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	503					cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.D538D(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						CAGCTGCTGACGCCAGCACCA	0.532													C|||	1087	0.217053	0.2201	0.2853	5008	,	,		18342	0.0754		0.3012	False		,,,				2504	0.2239				p.D538D		Atlas-SNP	.											RGL1,NS,carcinoma,0,1	RGL1	91	1	1	Substitution - coding silent(1)	stomach(1)	c.C1614T						PASS	.	C		1083,3323	386.5+/-326.1	138,807,1258	51.0	47.0	49.0		1614	-10.1	0.0	1	dbSNP_120	49	2562,6038	406.4+/-348.8	407,1748,2145	no	coding-synonymous	RGL1	NM_015149.3		545,2555,3403	TT,TC,CC		29.7907,24.5801,28.0255		538/804	183876182	3645,9361	2203	4300	6503	SO:0001819	synonymous_variant	23179	exon15			TGCTGACGCCAGC	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1509C>T	1.37:g.183876182C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Silent	SNP	ENST00000360851.3	37																																																																																				C|0.745;T|0.255	0.255	strong		0.532	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149	
CDC25A	993	hgsc.bcm.edu	37	3	48228212	48228212	+	Silent	SNP	G	G	A	rs3731494	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:48228212G>A	ENST00000302506.3	-	2	636	c.228C>T	c.(226-228)tcC>tcT	p.S76S	CDC25A_ENST00000351231.3_Silent_p.S76S	NM_001789.2	NP_001780.2	P30304	MPIP1_HUMAN	cell division cycle 25A	76					cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|DNA replication (GO:0006260)|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)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to radiation (GO:0009314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		TTGACTCGGAGGAGCCCATTC	0.413													g|||	27	0.00539137	0.0008	0.0043	5008	,	,		18325	0.0		0.0129	False		,,,				2504	0.0102				p.S76S		Atlas-SNP	.											.	CDC25A	40	.	0			c.C228T						PASS	.	C	,	21,4385	27.2+/-55.0	0,21,2182	92.0	79.0	83.0		228,228	2.3	1.0	3	dbSNP_107	83	153,8443	69.0+/-131.5	1,151,4146	no	coding-synonymous,coding-synonymous	CDC25A	NM_001789.2,NM_201567.1	,	1,172,6328	AA,AG,GG		1.7799,0.4766,1.3383	,	76/525,76/485	48228212	174,12828	2203	4298	6501	SO:0001819	synonymous_variant	993	exon2			CTCGGAGGAGCCC	M81933	CCDS2760.1, CCDS2761.1	3p21	2013-01-17	2013-01-17		ENSG00000164045	ENSG00000164045		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"""	1725	protein-coding gene	gene with protein product		116947	"""cell division cycle 25A"", ""cell division cycle 25 homolog A (S. cerevisiae)"", ""cell division cycle 25 homolog A (S. pombe)"""			1836978	Standard	NM_001789		Approved		uc003csh.1	P30304	OTTHUMG00000133535	ENST00000302506.3:c.228C>T	3.37:g.48228212G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_001789	Q8IZH5|Q96IL3|Q9H2F2	Silent	SNP	ENST00000302506.3	37	CCDS2760.1																																																																																			G|0.989;A|0.011	0.011	strong		0.413	CDC25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257512.2	NM_001789	
FAM21A	387680	hgsc.bcm.edu	37	10	51853633	51853633	+	Missense_Mutation	SNP	C	C	T	rs199520696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:51853633C>T	ENST00000282633.5	+	13	1181	c.1136C>T	c.(1135-1137)aCg>aTg	p.T379M	FAM21A_ENST00000314664.7_Missense_Mutation_p.T379M|FAM21A_ENST00000351071.6_Missense_Mutation_p.T379M|FAM21A_ENST00000399339.2_Missense_Mutation_p.T291M	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	379					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						GACCTCTTCACGGAAGCCCCC	0.488																																					p.T379M		Atlas-SNP	.											FAM21A,NS,carcinoma,0,4	FAM21A	32	4	0			c.C1136T						scavenged	.						1.0	1.0	1.0					10																	51853633		353	936	1289	SO:0001583	missense	387680	exon13			TCTTCACGGAAGC	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.1136C>T	10.37:g.51853633C>T	ENSP00000282633:p.Thr379Met	Somatic	750	1	0.00133333		WXS	Illumina HiSeq	Phase_I	979	212	0.216548	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Missense_Mutation	SNP	ENST00000282633.5	37	CCDS41527.1	.	.	.	.	.	.	.	.	.	.	C	6.414	0.444490	0.12164	.	.	ENSG00000099290	ENST00000351071;ENST00000314664;ENST00000434114;ENST00000282633;ENST00000399339	.	.	.	3.88	-5.37	0.02681	.	0.781535	0.12699	N	0.446536	T	0.14527	0.0351	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B	0.29253	0.05;0.02;0.005;0.02;0.239	B;B;B;B;B	0.16722	0.013;0.013;0.003;0.013;0.016	T	0.05767	-1.0865	9	0.42905	T	0.14	2.3495	2.2948	0.04147	0.3714:0.2592:0.2739:0.0955	.	379;379;291;379;273	E7ESD2;Q641Q2-2;F8W7U3;Q641Q2;Q5T1D7	.;.;.;FA21A_HUMAN;.	M	379;379;273;379;291	.	ENSP00000282633:T379M	T	+	2	0	FAM21A	51523639	0.024000	0.19004	0.096000	0.21009	0.033000	0.12548	-0.884000	0.04166	-1.796000	0.01253	-1.109000	0.02080	ACG	C|0.796;T|0.205	0.205	strong		0.488	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751	
TUBG2	27175	hgsc.bcm.edu	37	17	40811919	40811919	+	Silent	SNP	A	A	G	rs525911	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40811919A>G	ENST00000251412.7	+	2	316	c.117A>G	c.(115-117)gaA>gaG	p.E39E		NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	39					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		TCGTGGAGGAATTCGCCACCG	0.662																																					p.E39E		Atlas-SNP	.											.	TUBG2	43	.	0			c.A117G						PASS	.						44.0	58.0	53.0					17																	40811919		2200	4290	6490	SO:0001819	synonymous_variant	27175	exon2			GGAGGAATTCGCC	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.117A>G	17.37:g.40811919A>G		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	238	77	0.323529	NM_016437	A6NDI4|Q32NB2	Silent	SNP	ENST00000251412.7	37	CCDS32658.1																																																																																			A|0.485;G|0.515	0.515	strong		0.662	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
KANSL1	284058	hgsc.bcm.edu	37	17	44117119	44117119	+	Missense_Mutation	SNP	A	A	G	rs34043286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44117119A>G	ENST00000262419.6	-	8	2622	c.2152T>C	c.(2152-2154)Tca>Cca	p.S718P	KANSL1_ENST00000393476.3_Missense_Mutation_p.S75P|KANSL1_ENST00000574590.1_Missense_Mutation_p.S718P|KANSL1_ENST00000572904.1_Missense_Mutation_p.S718P|KANSL1_ENST00000575318.1_Missense_Mutation_p.S718P|KANSL1_ENST00000432791.1_Missense_Mutation_p.S718P	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	718			S -> P (in dbSNP:rs34043286).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TTACGAGCTGAATCTGGCAGA	0.498													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19661	0.001		0.2406	False		,,,				2504	0.0613				p.S718P		Atlas-SNP	.											.	.	.	.	0			c.T2152C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	202,4204	807.9+/-415.9	5,192,2006	114.0	106.0	109.0		2152,2152,2152	6.1	1.0	17	dbSNP_126	109	1927,6673	726.3+/-406.6	220,1487,2593	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	74,74,74	225,1679,4599	GG,GA,AA		22.407,4.5847,16.3694	benign,benign,benign	718/1105,718/1106,718/1106	44117119	2129,10877	2203	4300	6503	SO:0001583	missense	284058	exon8			GAGCTGAATCTGG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2152T>C	17.37:g.44117119A>G	ENSP00000262419:p.Ser718Pro	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	8.847	0.943571	0.18281	0.045847	0.22407	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.22336	2.74;2.74;1.96	6.05	6.05	0.98169	.	0.072151	0.64402	N	0.000014	T	0.00012	0.0000	N	0.00308	-1.67	0.46678	P	8.470000000000422E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38045	-0.9679	9	0.17369	T	0.5	-5.2424	12.6915	0.56976	0.0762:0.0:0.9238:0.0	rs34043286	49;718	Q7Z3B3-2;Q7Z3B3	.;K1267_HUMAN	P	718;718;75	ENSP00000262419:S718P;ENSP00000387393:S718P;ENSP00000377117:S75P	ENSP00000262419:S718P	S	-	1	0	KIAA1267	41472966	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	4.936000	0.63506	1.587000	0.49959	-0.128000	0.14901	TCA	A|0.853;G|0.147	0.147	strong		0.498	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414252	105414252	+	Silent	SNP	C	C	T	rs60106058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	214	0	0		WXS	Illumina HiSeq	Phase_I	225	224	0.995556	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	
FMN2	56776	hgsc.bcm.edu	37	1	240371075	240371075	+	Missense_Mutation	SNP	C	C	T	rs71646825		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371075C>T	ENST00000319653.9	+	5	3193	c.2963C>T	c.(2962-2964)cCt>cTt	p.P988L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	988	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGCATACCCCCTCCTCCCCCA	0.711																																					p.P988L		Atlas-SNP	.											.	FMN2	451	.	0			c.C2963T						PASS	.						13.0	15.0	15.0					1																	240371075		2181	4262	6443	SO:0001583	missense	56776	exon5			TACCCCCTCCTCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2963C>T	1.37:g.240371075C>T	ENSP00000318884:p.Pro988Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	136	18	0.132353	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	391	0.17902930402930403	114	0.23170731707317074	55	0.15193370165745856	93	0.16258741258741258	129	0.17018469656992086	C	8.181	0.793768	0.16327	.	.	ENSG00000155816	ENST00000319653	T	0.65549	-0.16	2.73	0.76	0.18442	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.00039	0.0001	M	0.90542	3.125	0.24734	P	0.99307642	B	0.12630	0.006	B	0.12156	0.007	T	0.08700	-1.0709	7	.	.	.	.	5.5141	0.16896	0.0:0.5739:0.1599:0.2661	.	988	Q9NZ56	FMN2_HUMAN	L	988	ENSP00000318884:P988L	.	P	+	2	0	FMN2	238437698	0.082000	0.21442	0.001000	0.08648	0.076000	0.17211	1.602000	0.36783	0.229000	0.21039	0.472000	0.43445	CCT	C|0.820;T|0.180	0.180	strong		0.711	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
SFRP2	6423	hgsc.bcm.edu	37	4	154709922	154709922	+	Silent	SNP	C	C	T	rs4075422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:154709922C>T	ENST00000274063.4	-	1	350	c.66G>A	c.(64-66)gcG>gcA	p.A22A		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	22					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)				AGAGCCCGCGCGCCGAGCCCA	0.682													C|||	238	0.047524	0.1445	0.036	5008	,	,		13869	0.0		0.0179	False		,,,				2504	0.0041				p.A22A		Atlas-SNP	.											.	SFRP2	45	.	0			c.G66A						PASS	.	C		575,3787		40,495,1646	15.0	19.0	17.0		66	0.2	1.0	4	dbSNP_108	17	80,8448		1,78,4185	no	coding-synonymous	SFRP2	NM_003013.2		41,573,5831	TT,TC,CC		0.9381,13.182,5.0815		22/296	154709922	655,12235	2181	4264	6445	SO:0001819	synonymous_variant	6423	exon1			CCCGCGCGCCGAG	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.66G>A	4.37:g.154709922C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_003013	B3KQR2|O14778|Q9HAP5	Silent	SNP	ENST00000274063.4	37	CCDS34082.1																																																																																			C|0.953;T|0.047	0.047	strong		0.682	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1		
CDHR3	222256	hgsc.bcm.edu	37	7	105658451	105658451	+	Missense_Mutation	SNP	G	G	A	rs6967330	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:105658451G>A	ENST00000317716.9	+	12	1666	c.1586G>A	c.(1585-1587)tGt>tAt	p.C529Y	CDHR3_ENST00000478080.1_Missense_Mutation_p.C441Y|CDHR3_ENST00000542731.1_Missense_Mutation_p.C529Y|CDHR3_ENST00000343407.5_Intron|CDHR3_ENST00000470188.1_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	529	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		C -> Y (in dbSNP:rs6967330).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AAAGTGGACTGTGAAACAACC	0.488													A|||	925	0.184704	0.2648	0.1427	5008	,	,		18561	0.0704		0.2078	False		,,,				2504	0.2004				p.C529Y		Atlas-SNP	.											.	CDHR3	153	.	0			c.G1586A						PASS	.	A	TYR/CYS	967,2915		121,725,1095	68.0	67.0	67.0		1586	4.4	0.9	7	dbSNP_116	67	1405,6889		136,1133,2878	yes	missense	CDHR3	NM_152750.4	194	257,1858,3973	AA,AG,GG		16.94,24.9098,19.4809	benign	529/886	105658451	2372,9804	1941	4147	6088	SO:0001583	missense	222256	exon12			TGGACTGTGAAAC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1586G>A	7.37:g.105658451G>A	ENSP00000325954:p.Cys529Tyr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	380	0.17399267399267399	127	0.258130081300813	61	0.1685082872928177	39	0.06818181818181818	153	0.20184696569920843	A	0.008	-1.879772	0.00537	0.249098	0.1694	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080	T;T;T	0.47177	0.85;0.85;0.85	5.66	4.39	0.52855	Cadherin (5);Cadherin-like (1);	0.441716	0.23328	N	0.049375	T	0.00012	0.0000	N	0.00033	-2.575	0.09310	P	0.9999999756686	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29427	-1.0012	9	0.02654	T	1	-2.7833	7.8022	0.29180	0.795:0.0:0.073:0.132	rs6967330;rs58478557;rs6967330	516;529	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	Y	529;529;441	ENSP00000439766:C529Y;ENSP00000325954:C529Y;ENSP00000417771:C441Y	ENSP00000325954:C529Y	C	+	2	0	CDHR3	105445687	1.000000	0.71417	0.931000	0.37212	0.057000	0.15508	3.349000	0.52217	0.986000	0.38683	-0.254000	0.11334	TGT	G|0.826;A|0.174	0.174	strong		0.488	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
NUDT19	390916	hgsc.bcm.edu	37	19	33200275	33200275	+	Missense_Mutation	SNP	A	A	T	rs371226805		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33200275A>T	ENST00000397061.3	+	2	899	c.899A>T	c.(898-900)gAt>gTt	p.D300V		NM_001105570.1	NP_001099040.1	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 19	300						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Esophageal squamous(110;0.137)					TTAACTGCTGATGGGATGGTC	0.473																																					p.D300V		Atlas-SNP	.											.	NUDT19	15	.	0			c.A899T						PASS	.	A	VAL/ASP	0,3924		0,0,1962	145.0	132.0	136.0		899	4.9	1.0	19		136	3,8289		0,3,4143	no	missense	NUDT19	NM_001105570.1	152	0,3,6105	TT,TA,AA		0.0362,0.0,0.0246	probably-damaging	300/376	33200275	3,12213	1962	4146	6108	SO:0001583	missense	390916	exon2			CTGCTGATGGGAT		CCDS42543.1	19q13.11	2011-11-16			ENSG00000213965	ENSG00000213965		"""Nudix motif containing"""	32036	protein-coding gene	gene with protein product							Standard	NM_001105570		Approved	RP2	uc010edf.3	A8MXV4		ENST00000397061.3:c.899A>T	19.37:g.33200275A>T	ENSP00000380251:p.Asp300Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_001105570		Missense_Mutation	SNP	ENST00000397061.3	37	CCDS42543.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.743338	0.69418	0.0	3.62E-4	ENSG00000213965	ENST00000397061	T	0.53206	0.63	4.88	4.88	0.63580	.	0.252366	0.32719	U	0.005722	T	0.67655	0.2916	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.72384	-0.4310	10	0.87932	D	0	-10.9605	11.1678	0.48554	1.0:0.0:0.0:0.0	.	300	A8MXV4	NUD19_HUMAN	V	300	ENSP00000380251:D300V	ENSP00000380251:D300V	D	+	2	0	NUDT19	37892115	1.000000	0.71417	0.981000	0.43875	0.072000	0.16883	4.851000	0.62896	1.948000	0.56530	0.482000	0.46254	GAT	.	.	weak		0.473	NUDT19-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000450338.3	XM_372723	
FAT1	2195	hgsc.bcm.edu	37	4	187540635	187540635	+	Missense_Mutation	SNP	T	T	G	rs77834784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187540635T>G	ENST00000441802.2	-	10	7314	c.7105A>C	c.(7105-7107)Acg>Ccg	p.T2369P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2369	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CTGCTCAGCGTGGGCATACCA	0.502										HNSCC(5;0.00058)			G|||	336	0.0670927	0.003	0.1499	5008	,	,		20820	0.1736		0.0338	False		,,,				2504	0.0194				p.T2369P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,colon,carcinoma,0,2	FAT1	500	2	0			c.A7105C						PASS	.	G	PRO/THR	38,4224		0,38,2093	92.0	94.0	94.0		7105	1.2	0.0	4	dbSNP_131	94	250,8226		4,242,3992	yes	missense	FAT1	NM_005245.3	38	4,280,6085	GG,GT,TT		2.9495,0.8916,2.261	benign	2369/4589	187540635	288,12450	2131	4238	6369	SO:0001583	missense	2195	exon10			TCAGCGTGGGCAT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7105A>C	4.37:g.187540635T>G	ENSP00000406229:p.Thr2369Pro	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	152	58	0.381579	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	187	0.08562271062271062	3	0.006097560975609756	40	0.11049723756906077	113	0.19755244755244755	31	0.040897097625329816	G	0	-2.850445	0.00066	0.008916	0.029495	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.42900	0.96	5.14	1.24	0.21308	Cadherin (4);Cadherin-like (1);	0.420019	0.27668	N	0.018357	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33497	-0.9866	9	0.02654	T	1	.	7.34	0.26632	0.0631:0.3383:0.482:0.1166	.	2369	Q14517	FAT1_HUMAN	P	2369;2371	ENSP00000406229:T2369P	ENSP00000260147:T2371P	T	-	1	0	FAT1	187777629	0.936000	0.31750	0.004000	0.12327	0.030000	0.12068	1.372000	0.34261	-0.109000	0.12044	-0.127000	0.14921	ACG	T|0.926;G|0.074	0.074	strong		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
UBQLNL	143630	hgsc.bcm.edu	37	11	5536852	5536852	+	Missense_Mutation	SNP	A	A	G	rs2017434	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5536852A>G	ENST00000380184.1	-	1	1083	c.820T>C	c.(820-822)Tat>Cat	p.Y274H	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	274			Y -> H (in dbSNP:rs2017434). {ECO:0000269|PubMed:15489334}.					p.Y274D(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		ATATCAGCATAGTTCTGACCC	0.468													A|||	1607	0.320887	0.3472	0.3487	5008	,	,		22946	0.375		0.2644	False		,,,				2504	0.2679				p.Y274H		Atlas-SNP	.											UBQLNL,colon,carcinoma,0,1	UBQLNL	74	1	1	Substitution - Missense(1)	large_intestine(1)	c.T820C						PASS	.	A	HIS/TYR	1480,2922	475.9+/-357.4	256,968,977	94.0	87.0	90.0		820	3.9	0.0	11	dbSNP_92	90	2366,6228	394.9+/-344.9	339,1688,2270	yes	missense	UBQLNL	NM_145053.4	83	595,2656,3247	GG,GA,AA		27.5308,33.6211,29.5937	probably-damaging	274/476	5536852	3846,9150	2201	4297	6498	SO:0001583	missense	143630	exon1			CAGCATAGTTCTG	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.820T>C	11.37:g.5536852A>G	ENSP00000369531:p.Tyr274His	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	170	68	0.4	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	37	CCDS31385.1	742	0.33974358974358976	181	0.3678861788617886	112	0.30939226519337015	237	0.4143356643356643	212	0.2796833773087071	A	7.494	0.651206	0.14516	0.336211	0.275308	ENSG00000175518	ENST00000380184	T	0.59906	0.23	5.09	3.94	0.45596	.	0.465067	0.18305	N	0.145300	T	0.00012	0.0000	M	0.85373	2.75	0.80722	P	0.0	P	0.43094	0.799	B	0.43623	0.425	T	0.27123	-1.0083	9	0.72032	D	0.01	-17.5765	8.8448	0.35164	0.8102:0.1898:0.0:0.0	rs2017434;rs3802975;rs17853351;rs57070605;rs2017434	274	Q8IYU4	UBQLN_HUMAN	H	274	ENSP00000369531:Y274H	ENSP00000369531:Y274H	Y	-	1	0	UBQLNL	5493428	0.002000	0.14202	0.003000	0.11579	0.002000	0.02628	1.024000	0.30077	0.925000	0.37094	-0.313000	0.08912	TAT	A|0.689;G|0.311	0.311	strong		0.468	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
Unknown	0	hgsc.bcm.edu	37	7	75130916	75130916	+	IGR	SNP	C	C	A	rs200010058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:75130916C>A								POM121C (15368 upstream) : PMS2P3 (6158 downstream)																							AAGAACCGCTCTCGCATACCC	0.582													.|||	286	0.0571086	0.025	0.0533	5008	,	,		18453	0.0109		0.1014	False		,,,				2504	0.1053				p.S264Y		Atlas-SNP	.											.	.	.	.	0			c.C791A						PASS	.	T	TYR/SER	115,2843		3,109,1367	138.0	166.0	156.0		791		0.0	7		156	492,4828		23,446,2191	no	missense	SPDYE5	NM_001099435.2	144	26,555,3558	AA,AC,CC		9.2481,3.8878,7.3327	benign	264/338	75130916	607,7671	1479	2660	4139	SO:0001628	intergenic_variant	442590	exon6			ACCGCTCTCGCAT																													7.37:g.75130916C>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	245	117	0.477551	NM_001099435		Missense_Mutation	SNP		37																																																																																				C|0.895;A|0.105	0.105	strong	0	0.582								
KLHL38	340359	hgsc.bcm.edu	37	8	124658210	124658210	+	Silent	SNP	C	C	T	rs16898671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:124658210C>T	ENST00000325995.7	-	3	1538	c.1515G>A	c.(1513-1515)gcG>gcA	p.A505A	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	505										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CTTTCATGTCCGCACATTTGA	0.512													c|||	805	0.160743	0.2133	0.0821	5008	,	,		20655	0.1637		0.1014	False		,,,				2504	0.2035				p.A505A		Atlas-SNP	.											KLHL38,NS,carcinoma,-1,2	KLHL38	81	2	0			c.G1515A						PASS	.	T		802,3380		70,662,1359	82.0	89.0	87.0		1515	-5.2	1.0	8	dbSNP_123	87	1000,7460		51,898,3281	no	coding-synonymous	KLHL38	NM_001081675.2		121,1560,4640	TT,TC,CC		11.8203,19.1774,14.2541		505/582	124658210	1802,10840	2091	4230	6321	SO:0001819	synonymous_variant	340359	exon3			CATGTCCGCACAT		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1515G>A	8.37:g.124658210C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	160	84	0.525	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	37	CCDS43766.1																																																																																			C|0.859;T|0.141	0.141	strong		0.512	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
ZBBX	79740	hgsc.bcm.edu	37	3	167023493	167023493	+	Missense_Mutation	SNP	C	C	T	rs35864545	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:167023493C>T	ENST00000392766.2	-	17	2003	c.1663G>A	c.(1663-1665)Gaa>Aaa	p.E555K	ZBBX_ENST00000307529.5_Missense_Mutation_p.E555K|ZBBX_ENST00000455345.2_Missense_Mutation_p.E555K|ZBBX_ENST00000392764.1_Missense_Mutation_p.E526K|ZBBX_ENST00000392767.2_Missense_Mutation_p.E555K	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	555			E -> K (in dbSNP:rs35864545).			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						TTGCTCAATTCCAAGGATTCT	0.323													C|||	237	0.0473243	0.0091	0.0677	5008	,	,		14234	0.0		0.1113	False		,,,				2504	0.0675				p.E555K		Atlas-SNP	.											.	ZBBX	299	.	0			c.G1663A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	100,3516		3,94,1711	73.0	65.0	67.0		1663,1576,1663	1.2	0.7	3	dbSNP_126	67	1001,7129		59,883,3123	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	56,56,56	62,977,4834	TT,TC,CC		12.3124,2.7655,9.3734	probably-damaging,probably-damaging,probably-damaging	555/840,526/772,555/801	167023493	1101,10645	1808	4065	5873	SO:0001583	missense	79740	exon17			TCAATTCCAAGGA	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.1663G>A	3.37:g.167023493C>T	ENSP00000376519:p.Glu555Lys	Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	245	105	0.428571	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	118	0.05402930402930403	6	0.012195121951219513	30	0.08287292817679558	0	0.0	82	0.10817941952506596	C	8.492	0.862156	0.17178	0.027655	0.123124	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.11277	2.96;2.96;2.9;2.9;2.79	5.3	1.23	0.21249	.	0.908278	0.09494	N	0.794526	T	0.00109	0.0003	N	0.24115	0.695	0.52501	P	4.8000000000048004E-5	B;B	0.16396	0.017;0.01	B;B	0.14578	0.011;0.005	T	0.40459	-0.9562	9	0.30854	T	0.27	-0.3875	4.1909	0.10421	0.0:0.5443:0.1711:0.2846	rs35864545	555;555	A8MT70-2;A8MT70	.;ZBBX_HUMAN	K	555;555;555;555;526	ENSP00000376519:E555K;ENSP00000376520:E555K;ENSP00000390232:E555K;ENSP00000305065:E555K;ENSP00000376517:E526K	ENSP00000305065:E555K	E	-	1	0	ZBBX	168506187	0.686000	0.27661	0.655000	0.29622	0.067000	0.16453	0.012000	0.13287	0.710000	0.31997	0.650000	0.86243	GAA	C|0.915;T|0.085	0.085	strong		0.323	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
RNASET2	8635	hgsc.bcm.edu	37	6	167344583	167344583	+	Silent	SNP	A	A	G	rs13213697	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:167344583A>G	ENST00000508775.1	-	8	1035	c.516T>C	c.(514-516)ctT>ctC	p.L172L	RNASET2_ENST00000366855.6_Silent_p.L134L|RP11-514O12.4_ENST00000507747.1_Intron|RNASET2_ENST00000476238.2_Silent_p.L172L|RNASET2_ENST00000496851.2_5'Flank	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	172					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)			large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		ATACTCTGGCAAGGGCATCTT	0.388													A|||	924	0.184505	0.3608	0.1513	5008	,	,		25713	0.0069		0.1948	False		,,,				2504	0.1421				p.L172L		Atlas-SNP	.											.	RNASET2	18	.	0			c.T516C						PASS	.	A		1524,2882	481.7+/-359.2	274,976,953	162.0	158.0	160.0		516	-5.7	0.6	6	dbSNP_121	160	1597,7003	297.0+/-303.2	139,1319,2842	no	coding-synonymous	RNASET2	NM_003730.4		413,2295,3795	GG,GA,AA		18.5698,34.5892,23.9966		172/257	167344583	3121,9885	2203	4300	6503	SO:0001819	synonymous_variant	8635	exon8			TCTGGCAAGGGCA	AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.516T>C	6.37:g.167344583A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Silent	SNP	ENST00000508775.1	37	CCDS5295.1																																																																																			A|0.780;G|0.220	0.220	strong		0.388	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730	
ZHX2	22882	hgsc.bcm.edu	37	8	123966159	123966159	+	Silent	SNP	G	G	C	rs3802265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:123966159G>C	ENST00000314393.4	+	3	3244	c.2409G>C	c.(2407-2409)gcG>gcC	p.A803A		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	803					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			AGGAGGATGCGATCTCAGATA	0.622													C|||	2338	0.466853	0.4773	0.4035	5008	,	,		19783	0.7421		0.3449	False		,,,				2504	0.3395				p.A803A	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G2409C						PASS	.	C		2144,2262	596.3+/-388.6	521,1102,580	108.0	83.0	91.0		2409	3.3	0.1	8	dbSNP_107	91	3025,5575	662.3+/-402.0	543,1939,1818	no	coding-synonymous	ZHX2	NM_014943.3		1064,3041,2398	CC,CG,GG		35.1744,48.6609,39.7432		803/838	123966159	5169,7837	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			GGATGCGATCTCA	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.2409G>C	8.37:g.123966159G>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	128	50	0.390625	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.561;C|0.439	0.439	strong		0.622	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
SLC52A3	113278	hgsc.bcm.edu	37	20	744450	744450	+	Silent	SNP	G	G	A	rs3746805	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:744450G>A	ENST00000217254.7	-	3	1006	c.765C>T	c.(763-765)ctC>ctT	p.L255L	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Silent_p.L255L	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	255					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)										GGTCATTGAGGAGGTCTTCCA	0.612													G|||	1546	0.308706	0.1278	0.4755	5008	,	,		18708	0.124		0.4881	False		,,,				2504	0.4407				p.L255L		Atlas-SNP	.											.	.	.	.	0			c.C765T						PASS	.	G		791,3615	317.7+/-295.3	78,635,1490	70.0	67.0	68.0		765	4.0	1.0	20	dbSNP_107	68	4089,4511	560.7+/-387.6	982,2125,1193	no	coding-synonymous	C20orf54	NM_033409.3		1060,2760,2683	AA,AG,GG		47.5465,17.9528,37.5211		255/470	744450	4880,8126	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon3			ATTGAGGAGGTCT	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.765C>T	20.37:g.744450G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.667;A|0.333	0.333	strong		0.612	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
NUP210L	91181	hgsc.bcm.edu	37	1	154115962	154115962	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154115962A>G	ENST00000368559.3	-	3	503	c.432T>C	c.(430-432)gaT>gaC	p.D144D	NUP210L_ENST00000271854.3_Silent_p.D144D	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	144					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CCAGTGGCGAATCATCTACAT	0.393																																					p.D144D		Atlas-SNP	.											.	NUP210L	181	.	0			c.T432C						PASS	.						125.0	126.0	126.0					1																	154115962		2069	4212	6281	SO:0001819	synonymous_variant	91181	exon3			TGGCGAATCATCT	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.432T>C	1.37:g.154115962A>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	199	105	0.527638	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Silent	SNP	ENST00000368559.3	37	CCDS41399.1																																																																																			.	.	none		0.393	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
EXD3	54932	hgsc.bcm.edu	37	9	140250749	140250749	+	Missense_Mutation	SNP	C	C	T	rs180687197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140250749C>T	ENST00000340951.4	-	8	923	c.728G>A	c.(727-729)cGt>cAt	p.R243H	EXD3_ENST00000342129.4_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CTCCTGCAGACGCAAGACCTG	0.652													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		16664	0.0		0.001	False		,,,				2504	0.0				p.R243H		Atlas-SNP	.											.	EXD3	86	.	0			c.G728A						PASS	.	C	HIS/ARG	1,4219		0,1,2109	28.0	33.0	31.0		728	1.4	0.0	9		31	7,8453		0,7,4223	yes	missense	EXD3	NM_017820.3	29	0,8,6332	TT,TC,CC		0.0827,0.0237,0.0631	benign	243/877	140250749	8,12672	2110	4230	6340	SO:0001583	missense	54932	exon8			TGCAGACGCAAGA		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.728G>A	9.37:g.140250749C>T	ENSP00000340474:p.Arg243His	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	13.54	2.267912	0.40095	2.37E-4	8.27E-4	ENSG00000187609	ENST00000340951	T	0.63580	-0.05	2.34	1.41	0.22369	.	0.270733	0.24044	N	0.042075	T	0.43567	0.1253	L	0.35854	1.095	0.80722	D	1	B	0.30179	0.271	B	0.19148	0.024	T	0.31166	-0.9953	10	0.72032	D	0.01	.	5.0914	0.14710	0.0:0.6764:0.0:0.3236	.	243	Q8N9H8	MUT7_HUMAN	H	243	ENSP00000340474:R243H	ENSP00000340474:R243H	R	-	2	0	EXD3	139370570	0.005000	0.15991	0.019000	0.16419	0.567000	0.35839	1.383000	0.34385	0.294000	0.22547	0.306000	0.20318	CGT	C|0.999;T|0.001	0.001	strong		0.652	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
ADCK2	90956	hgsc.bcm.edu	37	7	140394587	140394587	+	Missense_Mutation	SNP	C	C	T	rs1046515	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:140394587C>T	ENST00000072869.4	+	8	2043	c.1865C>T	c.(1864-1866)cCa>cTa	p.P622L	NDUFB2_ENST00000476470.1_5'Flank|NDUFB2_ENST00000476279.1_5'Flank|NDUFB2_ENST00000247866.4_5'Flank|NDUFB2-AS1_ENST00000465466.1_RNA|NDUFB2_ENST00000465506.1_5'Flank|NDUFB2_ENST00000472695.1_5'Flank|NDUFB2_ENST00000460088.1_5'Flank|NDUFB2_ENST00000461457.1_5'Flank|NDUFB2_ENST00000482954.1_Intron|NDUFB2_ENST00000471136.1_5'Flank|NDUFB2_ENST00000204307.5_5'Flank|ADCK2_ENST00000476491.1_Intron	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	622			P -> L (in dbSNP:rs1046515). {ECO:0000269|PubMed:17344846}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					CTCACGGGCCCAGTGTGCCCC	0.617													C|||	750	0.14976	0.1929	0.1628	5008	,	,		17638	0.1002		0.0775	False		,,,				2504	0.2076				p.P622L		Atlas-SNP	.											.	ADCK2	37	.	0			c.C1865T						PASS	.	C	LEU/PRO	766,3640	310.2+/-291.5	61,644,1498	73.0	68.0	69.0		1865	2.8	0.2	7	dbSNP_86	69	637,7963	164.1+/-216.5	25,587,3688	yes	missense	ADCK2	NM_052853.3	98	86,1231,5186	TT,TC,CC		7.407,17.3854,10.7873	benign	622/627	140394587	1403,11603	2203	4300	6503	SO:0001583	missense	90956	exon8			CGGGCCCAGTGTG	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.1865C>T	7.37:g.140394587C>T	ENSP00000072869:p.Pro622Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	37	CCDS5861.1	253	0.11584249084249085	95	0.19308943089430894	44	0.12154696132596685	50	0.08741258741258741	64	0.08443271767810026	C	11.63	1.696930	0.30142	0.173854	0.07407	ENSG00000133597	ENST00000072869;ENST00000473512	T;T	0.16597	3.16;2.33	4.66	2.8	0.32819	.	0.413038	0.25786	N	0.028318	T	0.00012	0.0000	N	0.16478	0.41	0.47621	P	5.260000000000264E-4	B	0.12630	0.006	B	0.06405	0.002	T	0.34104	-0.9842	9	0.38643	T	0.18	-1.9639	10.237	0.43288	0.0:0.8391:0.0:0.1609	rs1046515;rs3173555;rs58335969;rs1046515	622	Q7Z695	ADCK2_HUMAN	L	622;219	ENSP00000072869:P622L;ENSP00000420288:P219L	ENSP00000072869:P622L	P	+	2	0	ADCK2	140041056	0.002000	0.14202	0.205000	0.23548	0.091000	0.18340	0.604000	0.24164	0.371000	0.24564	0.561000	0.74099	CCA	C|0.890;T|0.110	0.110	strong		0.617	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
MTTP	4547	hgsc.bcm.edu	37	4	100496105	100496105	+	Silent	SNP	C	C	G	rs7667001	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100496105C>G	ENST00000265517.5	+	1	242	c.39C>G	c.(37-39)tcC>tcG	p.S13S	MTTP_ENST00000422897.2_Silent_p.S13S|MTTP_ENST00000457717.1_Silent_p.S13S|MTTP_ENST00000511045.1_Intron			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	13					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)	GCTTCATTTCCTCATATTCAG	0.428													C|||	361	0.0720847	0.1959	0.036	5008	,	,		20808	0.0		0.0398	False		,,,				2504	0.0378				p.S13S		Atlas-SNP	.											.	MTTP	127	.	0			c.C39G						PASS	.	C		704,3702	294.4+/-283.1	66,572,1565	340.0	294.0	310.0		39	4.1	1.0	4	dbSNP_116	310	342,8258	117.4+/-177.0	5,332,3963	no	coding-synonymous	MTTP	NM_000253.2		71,904,5528	GG,GC,CC		3.9767,15.9782,8.0424		13/895	100496105	1046,11960	2203	4300	6503	SO:0001819	synonymous_variant	4547	exon2			CATTTCCTCATAT		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.39C>G	4.37:g.100496105C>G		Somatic	472	1	0.00211864		WXS	Illumina HiSeq	Phase_I	430	218	0.506977	NM_000253	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	37	CCDS3651.1																																																																																			C|0.931;G|0.069	0.069	strong		0.428	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
NUF2	83540	hgsc.bcm.edu	37	1	163313539	163313539	+	Missense_Mutation	SNP	C	C	T	rs11802875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:163313539C>T	ENST00000271452.3	+	10	965	c.686C>T	c.(685-687)tCg>tTg	p.S229L	NUF2_ENST00000524800.1_Missense_Mutation_p.S229L|NUF2_ENST00000367900.3_Missense_Mutation_p.S229L	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	229	Interaction with the N-terminus of NDC80.		S -> L (in dbSNP:rs11802875). {ECO:0000269|PubMed:11266451, ECO:0000269|PubMed:11685532}.		chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					CTAAAATTGTCGGTGGTTTCT	0.274													C|||	621	0.124002	0.1664	0.1671	5008	,	,		14112	0.0228		0.1928	False		,,,				2504	0.0695				p.S229L		Atlas-SNP	.											NUF2_ENST00000271452,NS,carcinoma,0,2	NUF2	138	2	0			c.C686T						PASS	.	C	LEU/SER,LEU/SER	582,3586		39,504,1541	20.0	22.0	21.0		686,686	3.0	0.5	1	dbSNP_120	21	1469,7027		127,1215,2906	yes	missense,missense	NUF2	NM_031423.3,NM_145697.2	145,145	166,1719,4447	TT,TC,CC		17.2905,13.9635,16.1955	possibly-damaging,possibly-damaging	229/465,229/465	163313539	2051,10613	2084	4248	6332	SO:0001583	missense	83540	exon10			AATTGTCGGTGGT	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.686C>T	1.37:g.163313539C>T	ENSP00000271452:p.Ser229Leu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	310	0.14194139194139194	76	0.15447154471544716	63	0.17403314917127072	14	0.024475524475524476	157	0.20712401055408972	C	10.29	1.308613	0.23821	0.139635	0.172905	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.31247	1.54;1.5;1.5	4.83	2.96	0.34315	.	0.474249	0.23149	N	0.051374	T	0.06872	0.0175	L	0.47716	1.5	0.30934	P	0.726526	P;P	0.45569	0.861;0.861	B;B	0.25614	0.062;0.062	T	0.21177	-1.0253	9	0.28530	T	0.3	-1.4962	6.7062	0.23252	0.0:0.7141:0.0:0.2859	rs11802875;rs56525990;rs59877163;rs11802875	229;229	E9PQC4;Q9BZD4	.;NUF2_HUMAN	L	229	ENSP00000436888:S229L;ENSP00000356875:S229L;ENSP00000271452:S229L	ENSP00000271452:S229L	S	+	2	0	NUF2	161580163	0.477000	0.25909	0.455000	0.27031	0.560000	0.35617	1.227000	0.32576	0.763000	0.33175	0.585000	0.79938	TCG	C|0.865;N|0.000	.	strong		0.274	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	
C10orf35	219738	hgsc.bcm.edu	37	10	71391538	71391538	+	Silent	SNP	T	T	C	rs1381932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:71391538T>C	ENST00000373279.4	+	3	198	c.39T>C	c.(37-39)gaT>gaC	p.D13D	C10orf35_ENST00000491890.1_3'UTR	NM_145306.2	NP_660349.1	Q96D05	CJ035_HUMAN	chromosome 10 open reading frame 35	13						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5						TCGTGCAGGATGACGACCCCC	0.602													T|||	973	0.194289	0.2821	0.1513	5008	,	,		17823	0.0407		0.2087	False		,,,				2504	0.2495				p.D13D		Atlas-SNP	.											.	C10orf35	22	.	0			c.T39C						PASS	.	T		1296,3110	428.7+/-342.0	200,896,1107	165.0	122.0	137.0		39	-5.1	1.0	10	dbSNP_88	137	1916,6684	335.1+/-321.3	216,1484,2600	no	coding-synonymous	C10orf35	NM_145306.2		416,2380,3707	CC,CT,TT		22.2791,29.4144,24.6963		13/122	71391538	3212,9794	2203	4300	6503	SO:0001819	synonymous_variant	219738	exon3			GCAGGATGACGAC	BC013587	CCDS7295.1	10q22.2	2003-11-21			ENSG00000171224	ENSG00000171224			23519	protein-coding gene	gene with protein product						12477932	Standard	NM_145306		Approved		uc001jpq.4	Q96D05	OTTHUMG00000018383	ENST00000373279.4:c.39T>C	10.37:g.71391538T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_145306		Silent	SNP	ENST00000373279.4	37	CCDS7295.1																																																																																			T|0.773;C|0.227	0.227	strong		0.602	C10orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048454.1	NM_145306	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993737	140993737	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:140993737C>T	ENST00000285879.4	+	4	833	c.547C>T	c.(547-549)Cct>Tct	p.P183S	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	183										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGAGTTCCCCTGAGAGTAC	0.493										HNSCC(15;0.026)																											p.P183S		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C547T						PASS	.						80.0	91.0	87.0					X																	140993737		2203	4298	6501	SO:0001583	missense	9947	exon4			AGTTCCCCTGAGA	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.547C>T	X.37:g.140993737C>T	ENSP00000285879:p.Pro183Ser	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	230	13	0.0565217	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	c	6.525	0.465191	0.12402	.	.	ENSG00000155495	ENST00000285879	T	0.03301	3.98	.	.	.	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	0.999996	B	0.17038	0.02	B	0.09377	0.004	T	0.45086	-0.9285	8	0.87932	D	0	.	3.8388	0.08905	0.0:0.6604:0.0:0.3396	.	183	O60732	MAGC1_HUMAN	S	183	ENSP00000285879:P183S	ENSP00000285879:P183S	P	+	1	0	MAGEC1	140821403	0.149000	0.22717	0.039000	0.18376	0.039000	0.13416	1.804000	0.38873	0.054000	0.16065	0.054000	0.15206	CCT	.	.	none		0.493	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
EMR1	2015	hgsc.bcm.edu	37	19	6896483	6896483	+	Missense_Mutation	SNP	G	G	A	rs330877	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6896483G>A	ENST00000312053.4	+	3	206	c.169G>A	c.(169-171)Gct>Act	p.A57T	EMR1_ENST00000381404.4_Missense_Mutation_p.A57T|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000250572.8_Missense_Mutation_p.A57T|EMR1_ENST00000381407.5_Missense_Mutation_p.A57T|EMR1_ENST00000450315.3_Missense_Mutation_p.A57T|AC020895.1_ENST00000580648.1_RNA	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						PASS	.	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	188	0	0		WXS	Illumina HiSeq	Phase_I	175	92	0.525714	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		
HLA-B	3106	hgsc.bcm.edu	37	6	31324911	31324911	+	Missense_Mutation	SNP	C	C	G	rs1050462	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31324911C>G	ENST00000412585.2	-	1	53	c.25G>C	c.(25-27)Gtc>Ctc	p.V9L		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	9			V -> L (in dbSNP:rs1050462).		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						AGCAGGAGGACGGTTCGGGGC	0.692									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	1155	0.230631	0.1233	0.245	5008	,	,		8959	0.25		0.3062	False		,,,				2504	0.2679				p.V9L		Atlas-SNP	.											HLA-B,cerebellum,glioma,0,1	HLA-B	54	1	0			c.G25C						scavenged	.	C	LEU/VAL	238,3960		11,216,1872	13.0	12.0	12.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	25	2.5	0.1	6	dbSNP_86	12	981,7141		59,863,3139	yes	missense	HLA-B	NM_005514.6	32	70,1079,5011	GG,GC,CC		12.0783,5.6694,9.8945		9/363	31324911	1219,11101	2099	4061	6160	SO:0001583	missense	3106	exon1	Familial Cancer Database	;Lichen Sclerosis, Familial	GGAGGACGGTTCG	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.25G>C	6.37:g.31324911C>G	ENSP00000399168:p.Val9Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	494	0.2261904761904762	61	0.12398373983739837	84	0.23204419889502761	135	0.23601398601398602	214	0.28232189973614774	N	8.101	0.776701	0.16120	0.056694	0.120783	ENSG00000234745	ENST00000412585	T	0.00597	6.31	3.34	2.47	0.30058	.	0.330918	0.16642	N	0.205609	T	0.00109	0.0003	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.12400	-1.0549	8	0.02654	T	1	.	8.6444	0.33996	0.0:0.237:0.763:0.0	rs1050462;rs2308334;rs3177903;rs3190781;rs9266204;rs17416898;rs17840061	9	P01889	1B07_HUMAN	L	9	ENSP00000399168:V9L	ENSP00000399168:V9L	V	-	1	0	HLA-B	31432890	0.007000	0.16637	0.054000	0.19295	0.040000	0.13550	0.447000	0.21710	0.756000	0.33013	-0.435000	0.05868	GTC	C|0.792;G|0.208	0.208	strong		0.692	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781040	88781040	+	IGR	SNP	A	A	G	rs8059048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88781040A>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Missense_Mutation_p.Q329R|CTU2_ENST00000453996.2_Missense_Mutation_p.Q416R|CTU2_ENST00000567949.1_Missense_Mutation_p.Q487R|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.Q416R	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	126	0	0		WXS	Illumina HiSeq	Phase_I	149	85	0.57047	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	
COL28A1	340267	hgsc.bcm.edu	37	7	7545691	7545691	+	Missense_Mutation	SNP	G	G	C	rs10486176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	137	0	0		WXS	Illumina HiSeq	Phase_I	148	74	0.5	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	
NDST4	64579	hgsc.bcm.edu	37	4	115749005	115749005	+	Silent	SNP	C	C	T	rs6843860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:115749005C>T	ENST00000264363.2	-	14	3264	c.2586G>A	c.(2584-2586)tcG>tcA	p.S862S		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	862	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GTCTCAGCCACGATGGCAGAG	0.403													T|||	1543	0.308107	0.553	0.2493	5008	,	,		17302	0.1567		0.169	False		,,,				2504	0.318				p.S862S		Atlas-SNP	.											.	NDST4	193	.	0			c.G2586A						PASS	.	T		2205,2201	587.5+/-386.7	557,1091,555	110.0	107.0	108.0		2586	-7.0	0.2	4	dbSNP_116	108	1270,7328	759.3+/-407.5	101,1068,3130	no	coding-synonymous	NDST4	NM_022569.1		658,2159,3685	TT,TC,CC		14.7709,49.9546,26.7225		862/873	115749005	3475,9529	2203	4299	6502	SO:0001819	synonymous_variant	64579	exon14			CAGCCACGATGGC	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"""Sulfotransferases, membrane-bound"""	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2586G>A	4.37:g.115749005C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	80	28	0.35	NM_022569	Q2KHM8	Silent	SNP	ENST00000264363.2	37	CCDS3706.1																																																																																			C|0.735;T|0.265	0.265	strong		0.403	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569	
ELF1	1997	hgsc.bcm.edu	37	13	41533052	41533052	+	Missense_Mutation	SNP	T	T	C	rs7799	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:41533052T>C	ENST00000239882.3	-	3	487	c.173A>G	c.(172-174)aAt>aGt	p.N58S	ELF1_ENST00000442101.1_Missense_Mutation_p.N58S|ELF1_ENST00000498824.1_5'UTR	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	58			N -> S (in dbSNP:rs7799). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		AATCATGTCATTGGGCTCTTC	0.453													T|||	2156	0.430511	0.1891	0.67	5008	,	,		19736	0.1746		0.7147	False		,,,				2504	0.5583				p.N58S		Atlas-SNP	.											ELF1,colon,carcinoma,0,1	ELF1	65	1	0			c.A173G						PASS	.	T	SER/ASN,SER/ASN	1133,3273	403.1+/-332.6	139,855,1209	225.0	165.0	186.0		173,173	0.3	1.0	13	dbSNP_52	186	5931,2669	685.2+/-404.0	2034,1863,403	yes	missense,missense	ELF1	NM_001145353.1,NM_172373.3	46,46	2173,2718,1612	CC,CT,TT		31.0349,25.7149,45.6866	probably-damaging,probably-damaging	58/596,58/620	41533052	7064,5942	2203	4300	6503	SO:0001583	missense	1997	exon2			ATGTCATTGGGCT	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.173A>G	13.37:g.41533052T>C	ENSP00000239882:p.Asn58Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	163	70	0.429448	NM_001145353	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	1003	0.4592490842490842	110	0.22357723577235772	231	0.638121546961326	107	0.18706293706293706	555	0.7321899736147758	T	13.65	2.299755	0.40694	0.257149	0.689651	ENSG00000120690	ENST00000442101;ENST00000239882	T;T	0.46451	0.87;0.87	5.87	0.352	0.16051	.	0.274053	0.35970	N	0.002875	T	0.00012	0.0000	N	0.25485	0.75	0.35425	P	0.20647899999999997	B;B	0.15930	0.012;0.015	B;B	0.19666	0.019;0.026	T	0.30909	-0.9962	9	0.33940	T	0.23	.	9.5909	0.39545	0.0:0.3792:0.0:0.6208	rs7799;rs3208990;rs60754865;rs7799	58;58	E9PDQ9;P32519	.;ELF1_HUMAN	S	58	ENSP00000405580:N58S;ENSP00000239882:N58S	ENSP00000239882:N58S	N	-	2	0	ELF1	40431052	0.992000	0.36948	0.999000	0.59377	0.998000	0.95712	0.041000	0.13927	0.148000	0.19059	0.533000	0.62120	AAT	T|0.508;C|0.492	0.492	strong		0.453	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
NAP1L1	4673	hgsc.bcm.edu	37	12	76453966	76453966	+	Silent	SNP	G	G	A	rs4663	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:76453966G>A	ENST00000261182.8	-	5	786	c.300C>T	c.(298-300)caC>caT	p.H100H	NAP1L1_ENST00000544816.1_De_novo_Start_OutOfFrame|NAP1L1_ENST00000552342.1_Silent_p.H100H|NAP1L1_ENST00000542344.1_Silent_p.H59H|NAP1L1_ENST00000548044.1_Silent_p.H59H|NAP1L1_ENST00000549596.1_Silent_p.H100H|NAP1L1_ENST00000547773.1_Silent_p.H37H|NAP1L1_ENST00000393263.3_Silent_p.H100H|NAP1L1_ENST00000431879.3_Silent_p.H59H|NAP1L1_ENST00000535020.2_Silent_p.H100H|NAP1L1_ENST00000547993.1_5'Flank	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	100					DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				TTTCAAGATCGTGAACTTCCT	0.373													g|||	2937	0.586462	0.2489	0.6182	5008	,	,		18281	0.9554		0.5905	False		,,,				2504	0.636				p.H100H		Atlas-SNP	.											.	NAP1L1	33	.	0			c.C300T						PASS	.	A	,	1395,3011	458.4+/-352.0	212,971,1020	106.0	89.0	95.0		300,300	3.0	1.0	12	dbSNP_52	95	5180,3418	637.2+/-399.2	1567,2046,686	no	coding-synonymous,coding-synonymous	NAP1L1	NM_004537.4,NM_139207.2	,	1779,3017,1706	AA,AG,GG		39.7534,31.6614,49.4386	,	100/392,100/392	76453966	6575,6429	2203	4299	6502	SO:0001819	synonymous_variant	4673	exon5			AAGATCGTGAACT		CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.300C>T	12.37:g.76453966G>A		Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	336	150	0.446429	NM_004537	B3KNT8	Silent	SNP	ENST00000261182.8	37	CCDS9013.1																																																																																			.	.	weak		0.373	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207	
PAPOLB	56903	hgsc.bcm.edu	37	7	4900341	4900341	+	Silent	SNP	G	G	A	rs17135247	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:4900341G>A	ENST00000404991.1	-	1	1284	c.1098C>T	c.(1096-1098)agC>agT	p.S366S	RADIL_ENST00000399583.3_Intron|RADIL_ENST00000536091.1_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	366					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		TTTGAAAGAAGCTTGGAGCTT	0.418													G|||	1179	0.235423	0.0325	0.2622	5008	,	,		20833	0.3105		0.2515	False		,,,				2504	0.3967				p.S367S		Atlas-SNP	.											PAPOLB_ENST00000404991,NS,carcinoma,-1,2	PAPOLB	93	2	0			c.C1101T						PASS	.	G	,	281,4119	146.5+/-181.1	9,263,1928	128.0	130.0	129.0		,1101	4.5	1.0	7	dbSNP_123	129	2363,6237	387.8+/-342.3	330,1703,2267	no	intron,coding-synonymous	RADIL,PAPOLB	NM_018059.4,NM_020144.4	,	339,1966,4195	AA,AG,GG		27.4767,6.3864,20.3385	,	,367/638	4900341	2644,10356	2200	4300	6500	SO:0001819	synonymous_variant	56903	exon1			AAAGAAGCTTGGA	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1098C>T	7.37:g.4900341G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	232	232	1	NM_020144	Q75LH1|Q8NE14	Silent	SNP	ENST00000404991.1	37																																																																																				G|0.777;A|0.223	0.223	strong		0.418	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144	
MAVS	57506	hgsc.bcm.edu	37	20	3846397	3846397	+	Missense_Mutation	SNP	C	C	T	rs7269320	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	104	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	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	
DMRT2	10655	hgsc.bcm.edu	37	9	1056569	1056569	+	Missense_Mutation	SNP	G	G	A	rs140004479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:1056569G>A	ENST00000358146.2	+	3	982	c.982G>A	c.(982-984)Gtg>Atg	p.V328M	DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000302441.6_Missense_Mutation_p.V328M|DMRT2_ENST00000382251.3_Missense_Mutation_p.V328M			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	328					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)		TAATGTCAGCGTGGCCACAAC	0.458													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		21074	0.0		0.005	False		,,,				2504	0.0				p.V328M		Atlas-SNP	.											.	DMRT2	70	.	0			c.G982A						PASS	.	G	,,MET/VAL	5,4401	9.9+/-24.2	0,5,2198	96.0	101.0	99.0		,,982	5.6	1.0	9	dbSNP_134	99	35,8565	23.4+/-69.3	0,35,4265	yes	utr-3,utr-3,missense	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,21	0,40,6463	AA,AG,GG		0.407,0.1135,0.3076	,,probably-damaging	,,328/562	1056569	40,12966	2203	4300	6503	SO:0001583	missense	10655	exon4			GTCAGCGTGGCCA	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.982G>A	9.37:g.1056569G>A	ENSP00000350865:p.Val328Met	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	75	0.581395	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	20.8	4.048378	0.75846	0.001135	0.00407	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.38240	1.15;1.15;1.15	5.62	5.62	0.85841	.	0.121836	0.56097	D	0.000039	T	0.60483	0.2272	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.61579	-0.7034	10	0.87932	D	0	-22.0227	19.2806	0.94051	0.0:0.0:1.0:0.0	.	328;172	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	M	328	ENSP00000371686:V328M;ENSP00000305785:V328M;ENSP00000350865:V328M	ENSP00000305785:V328M	V	+	1	0	DMRT2	1046569	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.230000	0.95299	2.665000	0.90641	0.650000	0.86243	GTG	G|0.997;A|0.003	0.003	strong		0.458	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
FLG	2312	hgsc.bcm.edu	37	1	152277396	152277396	+	Silent	SNP	T	T	C	rs6681433	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152277396T>C	ENST00000368799.1	-	3	10001	c.9966A>G	c.(9964-9966)caA>caG	p.Q3322Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3322	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGATGAAGCTTGTCCACGCG	0.547									Ichthyosis				T|||	1708	0.341054	0.115	0.4193	5008	,	,		20684	0.6062		0.171	False		,,,				2504	0.4928				p.Q3322Q		Atlas-SNP	.											.	FLG	900	.	0			c.A9966G						PASS	.	T		582,3824	260.1+/-263.5	40,502,1661	416.0	405.0	409.0		9966	-6.5	0.0	1	dbSNP_116	409	1447,7153	276.8+/-292.5	129,1189,2982	no	coding-synonymous	FLG	NM_002016.1		169,1691,4643	CC,CT,TT		16.8256,13.2093,15.6005		3322/4062	152277396	2029,10977	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGAAGCTTGTCCA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9966A>G	1.37:g.152277396T>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	246	128	0.520325	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.794;C|0.206	0.206	strong		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SNRNP35	11066	hgsc.bcm.edu	37	12	123950408	123950408	+	Silent	SNP	A	A	G	rs28728202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:123950408A>G	ENST00000526639.2	+	2	900	c.321A>G	c.(319-321)aaA>aaG	p.K107K	SNRNP35_ENST00000350887.5_Silent_p.K107K|SNRNP35_ENST00000412157.2_Silent_p.K112K|SNRNP35_ENST00000527158.2_Intron	NM_022717.3	NP_073208.1	Q16560	U1SBP_HUMAN	small nuclear ribonucleoprotein 35kDa (U11/U12)	107	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CCGTGATCAAAGCTTACCGAG	0.532													A|||	8	0.00159744	0.0	0.0043	5008	,	,		18826	0.0		0.005	False		,,,				2504	0.0				p.K112K		Atlas-SNP	.											.	SNRNP35	28	.	0			c.A336G						PASS	.	A	,	6,4400	11.4+/-27.6	0,6,2197	107.0	105.0	106.0		321,336	-1.8	0.2	12	dbSNP_125	106	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous,coding-synonymous	SNRNP35	NM_022717.2,NM_180699.2	,	0,71,6432	GG,GA,AA		0.7558,0.1362,0.5459	,	107/247,112/252	123950408	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	11066	exon2			GATCAAAGCTTAC	BC054034	CCDS9249.1, CCDS45005.1	12q24.31	2013-02-12				ENSG00000184209		"""RNA binding motif (RRM) containing"""	30852	protein-coding gene	gene with protein product	"""U1 snRNP binding protein homolog"""					10520751, 8889548	Standard	XM_005253545		Approved	U1SNRNPBP	uc001ufb.1	Q16560		ENST00000526639.2:c.321A>G	12.37:g.123950408A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_180699	A8K262|Q5XKN9	Silent	SNP	ENST00000526639.2	37	CCDS9249.1																																																																																			A|0.995;G|0.005	0.005	strong		0.532	SNRNP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395197.2	NM_007020	
MNDA	4332	hgsc.bcm.edu	37	1	158813819	158813819	+	Silent	SNP	A	A	G	rs857870	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158813819A>G	ENST00000368141.4	+	4	738	c.477A>G	c.(475-477)ccA>ccG	p.P159P		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	159					B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					GTAAGCCCCCAGGTCCCTCAG	0.463													a|||	2645	0.528155	0.3071	0.5447	5008	,	,		17925	0.6954		0.5825	False		,,,				2504	0.5869				p.P159P		Atlas-SNP	.											.	MNDA	147	.	0			c.A477G						PASS	.	A		1628,2778	501.3+/-365.0	294,1040,869	215.0	181.0	192.0		477	-2.4	0.0	1	dbSNP_86	192	4936,3664	623.4+/-397.5	1404,2128,768	no	coding-synonymous	MNDA	NM_002432.1		1698,3168,1637	GG,GA,AA		42.6047,36.9496,49.531		159/408	158813819	6564,6442	2203	4300	6503	SO:0001819	synonymous_variant	4332	exon4			GCCCCCAGGTCCC	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.477A>G	1.37:g.158813819A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	154	62	0.402597	NM_002432		Silent	SNP	ENST00000368141.4	37	CCDS1177.1																																																																																			A|0.493;G|0.507	0.507	strong		0.463	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432	
VOPP1	81552	hgsc.bcm.edu	37	7	55540707	55540707	+	Silent	SNP	G	G	A	rs815957	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:55540707G>A	ENST00000285279.5	-	5	560	c.360C>T	c.(358-360)acC>acT	p.T120T	VOPP1_ENST00000428648.1_Silent_p.T53T|VOPP1_ENST00000453256.1_Silent_p.T53T|VOPP1_ENST00000545390.1_Silent_p.T117T|VOPP1_ENST00000428097.1_Silent_p.T53T|VOPP1_ENST00000433959.1_Silent_p.T111T|VOPP1_ENST00000418904.1_Silent_p.T103T|VOPP1_ENST00000454227.1_Silent_p.T57T|VOPP1_ENST00000427700.1_Silent_p.T118T	NM_001284282.1|NM_030796.3	NP_001271211.1|NP_110423.3	Q96AW1	VOPP1_HUMAN	vesicular, overexpressed in cancer, prosurvival protein 1	120	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|integral component of organelle membrane (GO:0031301)	signal transducer activity (GO:0004871)			endometrium(1)|lung(4)	5						CTCCTGGGTCGGTGTAATAGG	0.617													G|||	1708	0.341054	0.1422	0.5317	5008	,	,		16359	0.5109		0.2982	False		,,,				2504	0.3436				p.T120T		Atlas-SNP	.											.	VOPP1	14	.	0			c.C360T						PASS	.	G		742,3018		81,580,1219	32.0	37.0	36.0		360	-11.4	0.0	7	dbSNP_86	36	2441,5755		372,1697,2029	no	coding-synonymous	VOPP1	NM_030796.3		453,2277,3248	AA,AG,GG		29.7828,19.734,26.6226		120/173	55540707	3183,8773	1880	4098	5978	SO:0001819	synonymous_variant	81552	exon5			TGGGTCGGTGTAA		CCDS47588.1, CCDS64654.1, CCDS64656.1	7p11.2	2010-06-22			ENSG00000154978	ENSG00000154978			34518	protein-coding gene	gene with protein product	"""Glioblastoma-amplified secreted protein"", ""EGFR-coamplified and overexpressed protein"""	611915				15735698	Standard	NM_030796		Approved	ECop, GASP, FLJ20532, DKFZp564K0822	uc003tqs.3	Q96AW1	OTTHUMG00000156124	ENST00000285279.5:c.360C>T	7.37:g.55540707G>A		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	304	139	0.457237	NM_030796	B0AZU1|B2RAT4|B3KS72|C9JWR3|Q6FIE3|Q8NBN8|Q96RE5|Q9H0W4	Silent	SNP	ENST00000285279.5	37	CCDS47588.1																																																																																			G|0.651;A|0.348	0.348	strong		0.617	VOPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343074.1	NM_030796	
VILL	50853	hgsc.bcm.edu	37	3	38047680	38047680	+	Silent	SNP	G	G	A	rs11707277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:38047680G>A	ENST00000283713.6	+	18	2408	c.2142G>A	c.(2140-2142)ccG>ccA	p.P714P	VILL_ENST00000383759.2_Silent_p.P714P|VILL_ENST00000465644.1_Silent_p.P432P			O15195	VILL_HUMAN	villin-like	714					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.P714P(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)		AGAGCCACCCGTCCCACAAGG	0.617													G|||	546	0.109026	0.0545	0.098	5008	,	,		18268	0.0843		0.1252	False		,,,				2504	0.1994				p.P714P		Atlas-SNP	.											VILL,NS,carcinoma,+1,2	VILL	61	2	1	Substitution - coding silent(1)	stomach(1)	c.G2142A						PASS	.	G		430,3976	208.5+/-229.5	29,372,1802	78.0	83.0	82.0		2142	2.6	0.1	3	dbSNP_120	82	1299,7301	257.3+/-281.4	99,1101,3100	no	coding-synonymous	VILL	NM_015873.3		128,1473,4902	AA,AG,GG		15.1047,9.7594,13.2939		714/857	38047680	1729,11277	2203	4300	6503	SO:0001819	synonymous_variant	50853	exon17			CCACCCGTCCCAC		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.2142G>A	3.37:g.38047680G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	37	CCDS2670.2																																																																																			G|0.881;A|0.119	0.119	strong		0.617	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
OLFML1	283298	hgsc.bcm.edu	37	11	7507174	7507174	+	Missense_Mutation	SNP	C	C	T	rs80215761	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7507174C>T	ENST00000329293.3	+	1	462	c.68C>T	c.(67-69)cCg>cTg	p.P23L	CTD-2516F10.2_ENST00000530201.1_RNA|OLFML1_ENST00000530135.1_Missense_Mutation_p.P23L|OLFML1_ENST00000528758.1_Missense_Mutation_p.P23L	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	23						extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		CTGCCCCCGCCGCAGTGTACC	0.537													C|||	30	0.00599042	0.0015	0.0058	5008	,	,		18647	0.0		0.0219	False		,,,				2504	0.002				p.P23L		Atlas-SNP	.											.	OLFML1	54	.	0			c.C68T						PASS	.	C	LEU/PRO	30,4372	35.2+/-66.4	0,30,2171	126.0	113.0	117.0		68	4.7	0.0	11	dbSNP_132	117	283,8309	105.4+/-166.3	4,275,4017	yes	missense	OLFML1	NM_198474.3	98	4,305,6188	TT,TC,CC		3.2938,0.6815,2.4088	benign	23/403	7507174	313,12681	2201	4296	6497	SO:0001583	missense	283298	exon1			CCCCGCCGCAGTG	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.68C>T	11.37:g.7507174C>T	ENSP00000332511:p.Pro23Leu	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	221	146	0.660634	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	37	CCDS7779.1	22	0.010073260073260074	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	17	0.022427440633245383	C	12.53	1.966877	0.34659	0.006815	0.032938	ENSG00000183801	ENST00000530135;ENST00000329293;ENST00000534244;ENST00000528758	D;D	0.86956	-2.19;-2.19	5.59	4.67	0.58626	.	0.427258	0.22758	N	0.055984	T	0.55386	0.1917	L	0.33485	1.01	0.09310	N	0.999999	B;B	0.24317	0.008;0.101	B;B	0.17722	0.005;0.019	T	0.52480	-0.8570	10	0.02654	T	1	.	10.8203	0.46601	0.0:0.9115:0.0:0.0885	.	23;23	Q6UWY5;Q5HYE3	OLFL1_HUMAN;.	L	23	ENSP00000433455:P23L;ENSP00000332511:P23L	ENSP00000332511:P23L	P	+	2	0	OLFML1	7463750	0.022000	0.18835	0.041000	0.18516	0.645000	0.38454	1.839000	0.39220	1.332000	0.45431	0.591000	0.81541	CCG	C|0.983;T|0.017	0.017	strong		0.537	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474	
CCL3	6348	hgsc.bcm.edu	37	17	34416537	34416537	+	Silent	SNP	G	G	A	rs1130371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:34416537G>A	ENST00000225245.5	-	2	262	c.180C>T	c.(178-180)ccC>ccT	p.P60P	AC069363.1_ENST00000590992.1_RNA|AC069363.1_ENST00000592728.1_RNA|AC069363.1_ENST00000441575.1_RNA	NM_002983.2	NP_002974.1	P10147	CCL3_HUMAN	chemokine (C-C motif) ligand 3	60					astrocyte cell migration (GO:0043615)|behavior (GO:0007610)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|eosinophil degranulation (GO:0043308)|exocytosis (GO:0006887)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|monocyte chemotaxis (GO:0002548)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoclast differentiation (GO:0045671)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell migration (GO:0030335)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of tumor necrosis factor production (GO:0032760)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|response to toxic substance (GO:0009636)|signaling (GO:0023052)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)	calcium-dependent protein kinase C activity (GO:0004698)|CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			breast(2)|lung(3)|urinary_tract(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACATGACACCGGGCTTGGAGC	0.582													G|||	1107	0.221046	0.1331	0.1182	5008	,	,		18931	0.3532		0.2505	False		,,,				2504	0.2464				p.P60P		Atlas-SNP	.											.	CCL3	8	.	0			c.C180T						PASS	.	G		611,3795		40,531,1632	155.0	150.0	152.0		180	-10.8	1.0	17	dbSNP_86	152	2001,6599		243,1515,2542	no	coding-synonymous	CCL3	NM_002983.2		283,2046,4174	AA,AG,GG		23.2674,13.8675,20.083		60/93	34416537	2612,10394	2203	4300	6503	SO:0001819	synonymous_variant	6348	exon2			GACACCGGGCTTG	M23178	CCDS11307.1	17q12	2014-05-06	2002-08-22	2002-08-23	ENSG00000006075	ENSG00000277632		"""Chemokine ligands"", ""Endogenous ligands"""	10627	protein-coding gene	gene with protein product		182283	"""small inducible cytokine A3 (homologous to mouse Mip-1a)"""	SCYA3			Standard	NM_002983		Approved	G0S19-1, LD78ALPHA, MIP-1-alpha	uc002hkv.3	P10147	OTTHUMG00000188413	ENST00000225245.5:c.180C>T	17.37:g.34416537G>A		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	364	203	0.557692	NM_002983		Silent	SNP	ENST00000225245.5	37	CCDS11307.1																																																																																			G|0.795;A|0.205	0.205	strong		0.582	CCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256581.1	NM_002983	
PMS2	5395	hgsc.bcm.edu	37	7	6026942	6026942	+	Missense_Mutation	SNP	G	G	T	rs1805323	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:6026942G>T	ENST00000265849.7	-	11	1559	c.1454C>A	c.(1453-1455)aCg>aAg	p.T485K	PMS2_ENST00000382321.4_Intron|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.T485K|PMS2_ENST00000441476.2_Missense_Mutation_p.T379K	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	485			T -> K (in dbSNP:rs1805323). {ECO:0000269|PubMed:10480359}.		ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.T485K(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		CGCTCTGTCCGTAGGGTCACT	0.592			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				G|||	561	0.112021	0.0098	0.0173	5008	,	,		16417	0.3373		0.0457	False		,,,				2504	0.1534				p.T485K		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	PMS2,NS,carcinoma,+1,2	PMS2	88	2	1	Substitution - Missense(1)	stomach(1)	c.C1454A						PASS	.	G	LYS/THR	86,4320	72.0+/-110.0	1,84,2118	88.0	88.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1454	-10.2	0.0	7	dbSNP_98	88	350,8250	118.8+/-178.2	7,336,3957	no	missense	PMS2	NM_000535.5	78	8,420,6075	TT,TG,GG		4.0698,1.9519,3.3523	benign	485/863	6026942	436,12570	2203	4300	6503	SO:0001583	missense	5395	exon11	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTGTCCGTAGGGT		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1454C>A	7.37:g.6026942G>T	ENSP00000265849:p.Thr485Lys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	247	0.1130952380952381	4	0.008130081300813009	4	0.011049723756906077	203	0.3548951048951049	36	0.047493403693931395	g	2.010	-0.427336	0.04701	0.019519	0.040698	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.85339	1.13;1.13;-1.97	5.1	-10.2	0.00374	.	5.407520	0.00166	N	0.000000	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.21177	-1.0253	9	0.05833	T	0.94	0.8267	4.7783	0.13190	0.4093:0.4036:0.1016:0.0855	rs1805323;rs2266664	485;485;379	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	K	485;438;379;485	ENSP00000265849:T485K;ENSP00000392843:T379K;ENSP00000384308:T485K	ENSP00000265849:T485K	T	-	2	0	PMS2	5993468	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.027000	0.13621	-1.911000	0.01082	-0.355000	0.07637	ACG	G|0.944;T|0.056	0.056	strong		0.592	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
COL6A3	1293	hgsc.bcm.edu	37	2	238245107	238245107	+	Missense_Mutation	SNP	G	G	A	rs150907698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238245107G>A	ENST00000295550.4	-	40	9088	c.8636C>T	c.(8635-8637)aCg>aTg	p.T2879M	COL6A3_ENST00000347401.3_Missense_Mutation_p.T2678M|COL6A3_ENST00000353578.4_Missense_Mutation_p.T2673M|COL6A3_ENST00000346358.4_Missense_Mutation_p.T2679M|COL6A3_ENST00000472056.1_Missense_Mutation_p.T2272M|COL6A3_ENST00000409809.1_Missense_Mutation_p.T2673M	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2879	Nonhelical region.|Thr-rich.				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)		CGGCTTCGTCGTAGTCACCGG	0.458													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		18430	0.0		0.0	False		,,,				2504	0.001				p.T2879M		Atlas-SNP	.											COL6A3,rectum,carcinoma,0,1	COL6A3	608	1	0			c.C8636T						PASS	.	G	MET/THR,MET/THR,MET/THR	6,4400	11.4+/-27.6	0,6,2197	165.0	155.0	158.0		8636,6815,8018	3.7	0.2	2	dbSNP_134	158	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	81,81,81	0,22,6481	AA,AG,GG		0.186,0.1362,0.1692	probably-damaging,probably-damaging,probably-damaging	2879/3178,2272/2571,2673/2972	238245107	22,12984	2203	4300	6503	SO:0001583	missense	1293	exon40			TTCGTCGTAGTCA	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.8636C>T	2.37:g.238245107G>A	ENSP00000295550:p.Thr2879Met	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	198	103	0.520202	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	1.784	-0.481114	0.04383	0.001362	0.00186	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.89343	-2.5;-2.48;-2.47;-2.46;-2.47;-2.46	3.68	3.68	0.42216	.	.	.	.	.	D	0.92828	0.7719	M	0.78049	2.395	0.09310	N	0.999992	D;D;D	0.89917	0.999;1.0;0.999	P;P;P	0.60886	0.761;0.88;0.761	D	0.85291	0.1067	9	0.87932	D	0	.	11.2673	0.49118	0.0:0.0:1.0:0.0	.	2272;2673;2879	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	M	2879;2678;2673;2272;2673;2679	ENSP00000295550:T2879M;ENSP00000315609:T2678M;ENSP00000315873:T2673M;ENSP00000418285:T2272M;ENSP00000386844:T2673M;ENSP00000295546:T2679M	ENSP00000295550:T2879M	T	-	2	0	COL6A3	237909846	0.962000	0.33011	0.178000	0.23040	0.016000	0.09150	3.023000	0.49666	1.749000	0.51849	0.563000	0.77884	ACG	G|0.999;A|0.001	0.001	strong		0.458	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
CDK11A	728642	hgsc.bcm.edu	37	1	1635004	1635004	+	Silent	SNP	T	T	C	rs874516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:1635004T>C	ENST00000378633.1	-	18	2059	c.1980A>G	c.(1978-1980)aaA>aaG	p.K660K	CDK11A_ENST00000358779.5_Silent_p.K647K|CDK11A_ENST00000378638.2_Silent_p.K623K|CDK11A_ENST00000404249.3_Silent_p.K657K|CDK11A_ENST00000356200.3_Silent_p.K623K|CDK11A_ENST00000357760.2_Silent_p.K656K|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000495016.1_5'Flank			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	660					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						AGGTCATCTTTTTGACTACTG	0.577													-|||	2966	0.592252	0.916	0.5014	5008	,	,		11280	0.3849		0.5626	False		,,,				2504	0.4632				p.K657K	Pancreas(186;965 2119 30274 40311 50569)	Atlas-SNP	.											.	CDK11A	38	.	0			c.A1971G						PASS	.	C	,	2321,611		1089,143,234	21.0	49.0	41.0		1971,1941	1.6	0.8	1	dbSNP_86	41	4591,3553		1481,1629,962	no	coding-synonymous,coding-synonymous	CDK11A	NM_024011.2,NM_033529.2	,	2570,1772,1196	CC,CT,TT		43.6272,20.839,37.5948	,	657/781,647/771	1635004	6912,4164	1466	4072	5538	SO:0001819	synonymous_variant	728642	exon18			CATCTTTTTGACT	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.1980A>G	1.37:g.1635004T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	191	82	0.429319	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																																																																																				T|0.444;C|0.556	0.556	strong		0.577	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011	
NUP155	9631	hgsc.bcm.edu	37	5	37294473	37294473	+	Silent	SNP	T	T	C	rs1045908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:37294473T>C	ENST00000231498.3	-	33	4091	c.3888A>G	c.(3886-3888)ttA>ttG	p.L1296L	NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000513532.1_Silent_p.L1232L|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	186	0	0		WXS	Illumina HiSeq	Phase_I	212	109	0.514151	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408811	105408811	+	Missense_Mutation	SNP	A	A	G	rs2819421	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	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	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71365676	71365676	+	Silent	SNP	G	G	A	rs357756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71365676G>A	ENST00000244230.2	+	5	1507	c.1155G>A	c.(1153-1155)caG>caA	p.Q385Q	MPHOSPH10_ENST00000498451.2_Silent_p.Q385Q	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	385					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						AGCCGTGGCAGCTTCAGGGGG	0.413													G|||	1532	0.305911	0.261	0.3934	5008	,	,		14422	0.2639		0.2942	False		,,,				2504	0.3599				p.Q385Q		Atlas-SNP	.											MPHOSPH10,rectum,carcinoma,0,1	MPHOSPH10	81	1	0			c.G1155A						scavenged	.	G		1101,3305	393.3+/-328.8	137,827,1239	35.0	38.0	37.0		1155	-0.1	1.0	2	dbSNP_79	37	2544,6056	411.3+/-350.5	395,1754,2151	no	coding-synonymous	MPHOSPH10	NM_005791.2		532,2581,3390	AA,AG,GG		29.5814,24.9887,28.0255		385/682	71365676	3645,9361	2203	4300	6503	SO:0001819	synonymous_variant	10199	exon5			GTGGCAGCTTCAG	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.1155G>A	2.37:g.71365676G>A		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_005791	A0AVJ8	Silent	SNP	ENST00000244230.2	37	CCDS1916.1																																																																																			G|0.712;A|0.288	0.288	strong		0.413	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
SLC16A7	9194	hgsc.bcm.edu	37	12	60169010	60169010	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:60169010C>T	ENST00000261187.4	+	4	1098	c.934C>T	c.(934-936)Cga>Tga	p.R312*	SLC16A7_ENST00000547379.1_Nonsense_Mutation_p.R312*|SLC16A7_ENST00000543448.1_Nonsense_Mutation_p.R213*|SLC16A7_ENST00000552024.1_Nonsense_Mutation_p.R312*|SLC16A7_ENST00000552432.1_Nonsense_Mutation_p.R312*	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	312					lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	TATTCGACCTCGAATTCAGTA	0.423																																					p.R312X		Atlas-SNP	.											SLC16A7,NS,carcinoma,0,4	SLC16A7	82	4	0			c.C934T						scavenged	.						141.0	141.0	141.0					12																	60169010		2203	4300	6503	SO:0001587	stop_gained	9194	exon5			CGACCTCGAATTC	AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"""Solute carriers"""	10928	protein-coding gene	gene with protein product		603654	"""solute carrier family 16 (monocarboxylic acid transporters), member 7"""			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.934C>T	12.37:g.60169010C>T	ENSP00000261187:p.Arg312*	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	217	3	0.0138249	NM_001270622	Q8NEM3|Q9UPB3	Nonsense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	C	42	9.319100	0.99135	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448	.	.	.	5.76	5.76	0.90799	.	0.261657	0.32533	N	0.005972	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3006	0.60324	0.2577:0.7423:0.0:0.0	.	.	.	.	X	312;312;312;312;312;213	.	.	R	+	1	2	SLC16A7	58455277	0.989000	0.36119	0.998000	0.56505	0.797000	0.45037	2.839000	0.48207	2.880000	0.98712	0.650000	0.86243	CGA	.	.	none		0.423	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731	
LGI2	55203	hgsc.bcm.edu	37	4	25005193	25005193	+	Silent	SNP	G	G	A	rs2232028	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	153	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	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		
ASXL3	80816	hgsc.bcm.edu	37	18	31324934	31324934	+	Missense_Mutation	SNP	A	A	G	rs7232237	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:31324934A>G	ENST00000269197.5	+	12	5122	c.5122A>G	c.(5122-5124)Atg>Gtg	p.M1708V		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1708			M -> V (in dbSNP:rs7232237). {ECO:0000269|PubMed:11214970, 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)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AACACAGAACATGAAAGCTTC	0.552													G|||	3401	0.679113	0.7352	0.6816	5008	,	,		18940	0.8988		0.5189	False		,,,				2504	0.5399				p.M1708V		Atlas-SNP	.											.	ASXL3	405	.	0			c.A5122G						PASS	.	G	VAL/MET	3003,1067		1109,785,141	86.0	88.0	87.0		5122	-7.4	0.0	18	dbSNP_116	87	4324,4098		1104,2116,991	yes	missense	ASXL3	NM_030632.1	21	2213,2901,1132	GG,GA,AA		48.6583,26.2162,41.3465	benign	1708/2249	31324934	7327,5165	2035	4211	6246	SO:0001583	missense	80816	exon12			CAGAACATGAAAG	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.5122A>G	18.37:g.31324934A>G	ENSP00000269197:p.Met1708Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	1486	0.6804029304029304	353	0.717479674796748	233	0.643646408839779	517	0.9038461538461539	383	0.5052770448548812	G	0.001	-2.950943	0.00051	0.737838	0.513417	ENSG00000141431	ENST00000269197	T	0.12465	2.68	5.86	-7.36	0.01417	.	.	.	.	.	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	0.17319	-1.0373	8	0.12430	T	0.62	.	3.2945	0.06961	0.4653:0.0659:0.231:0.2378	rs7232237;rs17668829;rs57813627;rs7232237	1708	Q9C0F0	ASXL3_HUMAN	V	1708	ENSP00000269197:M1708V	ENSP00000269197:M1708V	M	+	1	0	ASXL3	29578932	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	-1.434000	0.02425	-1.640000	0.01525	-0.733000	0.03571	ATG	A|0.319;G|0.681	0.681	strong		0.552	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
TNC	3371	hgsc.bcm.edu	37	9	117853022	117853022	+	Silent	SNP	C	C	T	rs944510	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:117853022C>T	ENST00000350763.4	-	2	687	c.276G>A	c.(274-276)gtG>gtA	p.V92V	TNC_ENST00000535648.1_Silent_p.V92V|TNC_ENST00000537320.1_Silent_p.V92V|TNC_ENST00000542877.1_Silent_p.V92V|TNC_ENST00000341037.4_Silent_p.V92V|TNC_ENST00000340094.3_Silent_p.V92V|TNC_ENST00000423613.2_Silent_p.V92V|TNC_ENST00000345230.3_Silent_p.V92V|TNC_ENST00000346706.3_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						scavenged	.	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	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	145	83	0.572414	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	
TNIP1	10318	hgsc.bcm.edu	37	5	150425467	150425467	+	Silent	SNP	G	G	A	rs2233299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150425467G>A	ENST00000389378.2	-	9	1479	c.891C>T	c.(889-891)ggC>ggT	p.G297G	TNIP1_ENST00000521591.1_Silent_p.G297G|TNIP1_ENST00000523200.1_Silent_p.G297G|TNIP1_ENST00000521423.1_Intron|TNIP1_ENST00000523338.1_Silent_p.G297G|TNIP1_ENST00000315050.7_Silent_p.G297G|TNIP1_ENST00000520931.1_Silent_p.G244G|TNIP1_ENST00000518977.1_Silent_p.G297G|TNIP1_ENST00000522226.1_Silent_p.G297G|TNIP1_ENST00000524280.1_Silent_p.G297G	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	297	Interacts with Nef.				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCGGCTGCGCCCAAGGCCA	0.592													G|||	657	0.13119	0.0673	0.1758	5008	,	,		21120	0.0625		0.2803	False		,,,				2504	0.1033				p.G297G		Atlas-SNP	.											.	TNIP1	51	.	0			c.C891T						PASS	.	G		485,3921	226.5+/-242.0	32,421,1750	106.0	92.0	97.0		891	-5.7	0.6	5	dbSNP_98	97	2374,6226	396.2+/-345.3	351,1672,2277	no	coding-synonymous	TNIP1	NM_006058.3		383,2093,4027	AA,AG,GG		27.6047,11.0077,21.9822		297/637	150425467	2859,10147	2203	4300	6503	SO:0001819	synonymous_variant	10318	exon9			GGCTGCGCCCAAG	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.891C>T	5.37:g.150425467G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Silent	SNP	ENST00000389378.2	37	CCDS34280.1																																																																																			G|0.803;A|0.197	0.197	strong		0.592	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
CD300A	11314	hgsc.bcm.edu	37	17	72469966	72469966	+	Missense_Mutation	SNP	G	G	A	rs2272111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72469966G>A	ENST00000360141.3	+	2	620	c.332G>A	c.(331-333)cGa>cAa	p.R111Q	CD300A_ENST00000361933.3_Intron|CD300A_ENST00000577511.1_5'UTR|CD300A_ENST00000310828.5_Intron|CD300A_ENST00000392625.3_Intron	NM_001256841.1|NM_007261.3	NP_001243770.1|NP_009192.2	Q9UGN4	CLM8_HUMAN	CD300a molecule	111	Ig-like V-type.		R -> Q (in dbSNP:rs2272111). {ECO:0000269|PubMed:12483297, ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|immune system process (GO:0002376)|negative regulation of activation of JAK2 kinase activity (GO:1902569)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of eosinophil activation (GO:1902567)|negative regulation of eosinophil migration (GO:2000417)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell activation involved in immune response (GO:0033007)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of neutrophil activation (GO:1902564)|negative regulation of NK T cell activation (GO:0051134)|negative regulation of phagocytosis, engulfment (GO:0060101)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|regulation of T cell receptor signaling pathway (GO:0050856)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)|signaling receptor activity (GO:0038023)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(4)|urinary_tract(1)	16						CCATGGCTCCGAGACTTTCAT	0.567													G|||	1731	0.345647	0.705	0.2161	5008	,	,		17525	0.1964		0.1978	False		,,,				2504	0.2577				p.R111Q		Atlas-SNP	.											.	CD300A	40	.	0			c.G332A						PASS	.	G	GLN/ARG	2763,1643	659.8+/-400.6	875,1013,315	125.0	131.0	129.0		332	-2.2	0.0	17	dbSNP_100	129	1761,6839	319.5+/-314.2	187,1387,2726	no	missense	CD300A	NM_007261.2	43	1062,2400,3041	AA,AG,GG		20.4767,37.2901,34.7839	benign	111/300	72469966	4524,8482	2203	4300	6503	SO:0001583	missense	11314	exon2			GGCTCCGAGACTT	BC032352	CCDS32720.1, CCDS58590.1	17q25.2	2013-01-11	2006-03-28		ENSG00000167851	ENSG00000167851		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19319	protein-coding gene	gene with protein product		606790	"""CD300a antigen"""			9701027, 10746781	Standard	NM_007261		Approved	Irp60, CMRF35H, CMRF-35-H9, IRC1, IRC2, IGSF12	uc002jkv.4	Q9UGN4	OTTHUMG00000067612	ENST00000360141.3:c.332G>A	17.37:g.72469966G>A	ENSP00000353259:p.Arg111Gln	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	250	122	0.488	NM_007261	A8MW96|O95100|Q9HD97|Q9P0F3|Q9UBK4|Q9UMS9|Q9UMT0	Missense_Mutation	SNP	ENST00000360141.3	37	CCDS32720.1	652	0.29853479853479853	334	0.6788617886178862	71	0.19613259668508287	107	0.18706293706293706	140	0.18469656992084432	G	0.945	-0.708406	0.03230	0.627099	0.204767	ENSG00000167851	ENST00000360141	T	0.02863	4.13	1.13	-2.22	0.06952	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.16368	0.405	0.58432	P	1.999999999946489E-6	B	0.15473	0.013	B	0.16289	0.015	T	0.11717	-1.0576	8	0.12103	T	0.63	.	4.3704	0.11244	0.4976:0.0:0.5024:0.0	rs2272111;rs11869780;rs59752364;rs2272111	111	Q9UGN4	CLM8_HUMAN	Q	111	ENSP00000353259:R111Q	ENSP00000353259:R111Q	R	+	2	0	CD300A	69981561	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.049000	0.00629	-0.558000	0.06118	-1.277000	0.01392	CGA	.	.	weak		0.567	CD300A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145091.1	NM_007261	
IL1RL2	8808	hgsc.bcm.edu	37	2	102851708	102851708	+	Missense_Mutation	SNP	T	T	C	rs2302612	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	106	0	0	1369	WXS	Illumina HiSeq	Phase_I	107	63	0.588785	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	
DPCD	25911	hgsc.bcm.edu	37	10	103361088	103361088	+	Silent	SNP	C	C	T	rs7874	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103361088C>T	ENST00000370151.4	+	4	448	c.399C>T	c.(397-399)aaC>aaT	p.N133N	DPCD_ENST00000370148.2_Silent_p.N133N|MIR3158-1_ENST00000583596.1_RNA|DPCD_ENST00000370147.1_Silent_p.N133N	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	133					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						GAACAACCAACAAGAAGTGAG	0.517													c|||	500	0.0998403	0.0408	0.1369	5008	,	,		13063	0.0347		0.2217	False		,,,				2504	0.0951				p.N133N		Atlas-SNP	.											.	DPCD	15	.	0			c.C399T						PASS	.			329,4077	174.4+/-204.0	14,301,1888	152.0	130.0	137.0		399	5.9	1.0	10	dbSNP_52	137	1968,6632	346.9+/-326.4	236,1496,2568	no	coding-synonymous	DPCD	NM_015448.1		250,1797,4456	TT,TC,CC		22.8837,7.4671,17.6611		133/204	103361088	2297,10709	2203	4300	6503	SO:0001819	synonymous_variant	25911	exon4			AACCAACAAGAAG		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.399C>T	10.37:g.103361088C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Silent	SNP	ENST00000370151.4	37	CCDS7514.1																																																																																			C|0.854;T|0.146	0.146	strong		0.517	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2		
RLN1	6013	hgsc.bcm.edu	37	9	5339738	5339738	+	Silent	SNP	G	G	A	rs56235721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:5339738G>A	ENST00000223862.1	-	1	135	c.9C>T	c.(7-9)cgC>cgT	p.R3R	RLN1_ENST00000487557.2_5'Flank|RLN1_ENST00000223858.4_Silent_p.R3R	NM_006911.2	NP_008842.1	P04808	REL1_HUMAN	relaxin 1	3					female pregnancy (GO:0007565)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			large_intestine(1)|lung(4)	5	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.02)|Lung(218;0.0984)		ACAAGAACAGGCGAGGCATCC	0.547													G|||	235	0.0469249	0.087	0.0259	5008	,	,		16835	0.0119		0.0368	False		,,,				2504	0.0542				p.R3R		Atlas-SNP	.											.	RLN1	16	.	0			c.C9T						PASS	.	G		314,4090	157.0+/-190.0	20,274,1908	50.0	58.0	56.0		9	1.9	0.0	9	dbSNP_129	56	328,8270	113.9+/-173.9	5,318,3976	no	coding-synonymous	RLN1	NM_006911.2		25,592,5884	AA,AG,GG		3.8148,7.1299,4.9377		3/186	5339738	642,12360	2202	4299	6501	SO:0001819	synonymous_variant	6013	exon1			GAACAGGCGAGGC		CCDS6462.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107018	ENSG00000107018		"""Endogenous ligands"""	10026	protein-coding gene	gene with protein product	"""prorelaxin H1"""	179730	"""relaxin 1 (H1)"""				Standard	NM_006911		Approved	H1	uc003zjb.2	P04808	OTTHUMG00000019495	ENST00000223862.1:c.9C>T	9.37:g.5339738G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	208	91	0.4375	NM_006911	Q99936|Q9UQJ1	Silent	SNP	ENST00000223862.1	37	CCDS6462.1																																																																																			G|0.950;A|0.050	0.050	strong		0.547	RLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051617.1		
SUN2	25777	hgsc.bcm.edu	37	22	39134715	39134715	+	Silent	SNP	T	T	C	rs1062687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39134715T>C	ENST00000405510.1	-	17	2182	c.1824A>G	c.(1822-1824)caA>caG	p.Q608Q	SUN2_ENST00000216064.4_Silent_p.Q608Q|SUN2_ENST00000405018.1_Silent_p.Q629Q|SUN2_ENST00000406622.1_Silent_p.Q608Q|SUN2_ENST00000411587.2_Silent_p.Q597Q|RP3-508I15.14_ENST00000416406.1_RNA|RP3-508I15.20_ENST00000609428.1_RNA|RP3-508I15.18_ENST00000420118.1_RNA|RP3-508I15.19_ENST00000418803.1_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	69	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	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	
IZUMO2	126123	hgsc.bcm.edu	37	19	50666389	50666389	+	Silent	SNP	G	G	A	rs61742305	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50666389G>A	ENST00000293405.3	-	1	63	c.63C>T	c.(61-63)tgC>tgT	p.C21C		NM_152358.2	NP_689571.2	Q6UXV1	IZUM2_HUMAN	IZUMO family member 2	21						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						CGCACTGCAGGCAGCCCCAGC	0.706													G|||	587	0.117212	0.0159	0.1643	5008	,	,		12810	0.0625		0.2485	False		,,,				2504	0.1421				p.C21C		Atlas-SNP	.											IZUMO2,NS,carcinoma,0,1	IZUMO2	26	1	0			c.C63T						PASS	.	G		174,3710		4,166,1772	10.0	14.0	13.0		63	2.4	1.0	19	dbSNP_129	13	1851,6415		214,1423,2496	no	coding-synonymous	IZUMO2	NM_152358.2		218,1589,4268	AA,AG,GG		22.3929,4.4799,16.6667		21/222	50666389	2025,10125	1942	4133	6075	SO:0001819	synonymous_variant	126123	exon1			CTGCAGGCAGCCC	AY358196	CCDS12792.2	19q13.33	2014-02-17	2010-07-29	2010-07-29	ENSG00000161652	ENSG00000161652		"""-"""	28518	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 41"""	C19orf41		19658160, 22957301	Standard	XM_006723007		Approved	MGC33947, SCRL	uc002prp.1	Q6UXV1	OTTHUMG00000074063	ENST00000293405.3:c.63C>T	19.37:g.50666389G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_152358	Q5GRG3|Q5GRG4|Q6ZNM5|Q8NHR8	Silent	SNP	ENST00000293405.3	37	CCDS12792.2																																																																																			G|0.859;A|0.141	0.141	strong		0.706	IZUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157232.1	NM_152358	
KLHL30	377007	hgsc.bcm.edu	37	2	239049537	239049537	+	Missense_Mutation	SNP	C	C	T	rs573206585		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:239049537C>T	ENST00000409223.1	+	2	249	c.142C>T	c.(142-144)Cgc>Tgc	p.R48C	KLHL30_ENST00000305959.4_Missense_Mutation_p.R30C			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	48	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									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)		GCCATGCCACCGCGGCCTCCT	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		17775	0.0		0.0	False		,,,				2504	0.001				p.R48C		Atlas-SNP	.											.	KLHL30	79	.	0			c.C142T						PASS	.						36.0	43.0	41.0					2																	239049537		2132	4219	6351	SO:0001583	missense	377007	exon2			TGCCACCGCGGCC		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.142C>T	2.37:g.239049537C>T	ENSP00000386389:p.Arg48Cys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	68	44	0.647059	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563511	0.86335	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.75477	-0.94;-0.94	5.75	5.75	0.90469	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92575	0.6069	10	0.87932	D	0	.	18.7132	0.91666	0.0:1.0:0.0:0.0	.	48	Q0D2K2	KLH30_HUMAN	C	48;30	ENSP00000386389:R48C;ENSP00000302386:R30C	ENSP00000302386:R30C	R	+	1	0	KLHL30	238714276	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.627000	0.61276	2.720000	0.93068	0.655000	0.94253	CGC	.	.	none		0.692	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
FRMPD2	143162	hgsc.bcm.edu	37	10	49383976	49383976	+	Missense_Mutation	SNP	T	T	C	rs200957845		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:49383976T>C	ENST00000374201.3	-	23	3204	c.2902A>G	c.(2902-2904)Att>Gtt	p.I968V	FRMPD2_ENST00000407470.4_Missense_Mutation_p.I936V|FRMPD2_ENST00000305531.3_Missense_Mutation_p.I943V|FRMPD2_ENST00000474573.1_5'UTR|FRMPD2_ENST00000463706.1_5'UTR	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	968	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CTGGTGTTAATGCCACCCTGA	0.532																																					p.I968V		Atlas-SNP	.											FRMPD2,NS,carcinoma,0,1	FRMPD2	157	1	0			c.A2902G						scavenged	.						3.0	1.0	1.0					10																	49383976		81	163	244	SO:0001583	missense	143162	exon23			TGTTAATGCCACC	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2902A>G	10.37:g.49383976T>C	ENSP00000363317:p.Ile968Val	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	442	184	0.41629	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.452426	0.01080	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.26810	1.71;1.71;1.71	4.81	-0.335	0.12662	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.10723	0.0262	N	0.03891	-0.335	0.09310	N	1	B;B;B	0.18863	0.006;0.031;0.016	B;B;B	0.23419	0.016;0.046;0.024	T	0.39165	-0.9627	9	0.21540	T	0.41	.	9.0019	0.36088	0.0:0.3679:0.0:0.6321	.	943;968;936	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	V	968;943;936	ENSP00000363317:I968V;ENSP00000307079:I943V;ENSP00000384339:I936V	ENSP00000307079:I943V	I	-	1	0	FRMPD2	49053982	0.623000	0.27094	0.520000	0.27837	0.722000	0.41435	0.524000	0.22940	-0.339000	0.08401	0.528000	0.53228	ATT	T|0.500;C|0.500	0.500	weak		0.532	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412541	105412541	+	Missense_Mutation	SNP	C	C	T	rs386781092|rs12433837	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	200	0	0		WXS	Illumina HiSeq	Phase_I	80	78	0.975	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	
COL9A1	1297	hgsc.bcm.edu	37	6	70984436	70984436	+	Missense_Mutation	SNP	A	A	G	rs592121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:70984436A>G	ENST00000357250.6	-	11	1173	c.1015T>C	c.(1015-1017)Tca>Cca	p.S339P	COL9A1_ENST00000370499.4_Missense_Mutation_p.S96P|COL9A1_ENST00000320755.7_Missense_Mutation_p.S96P|COL9A1_ENST00000489611.1_5'UTR	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	339	Collagen-like 2.|Triple-helical region (COL3).		S -> P (in dbSNP:rs592121). {ECO:0000269|PubMed:11565064}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	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)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						TGTCCCTTTGACCCAATGGAG	0.383													G|||	2416	0.482428	0.7231	0.4294	5008	,	,		19229	0.3145		0.3628	False		,,,				2504	0.4908				p.S339P		Atlas-SNP	.											COL9A1_ENST00000320755,NS,adenoma,0,2	COL9A1	228	2	0			c.T1015C						scavenged	.	G	PRO/SER,PRO/SER	2993,1413	460.5+/-352.6	1017,959,227	109.0	104.0	105.0		1015,286	5.0	1.0	6	dbSNP_83	105	3247,5353	649.4+/-400.6	610,2027,1663	yes	missense,missense	COL9A1	NM_001851.4,NM_078485.3	74,74	1627,2986,1890	GG,GA,AA		37.7558,32.0699,47.9779	benign,benign	339/922,96/679	70984436	6240,6766	2203	4300	6503	SO:0001583	missense	1297	exon11			CCTTTGACCCAAT		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.1015T>C	6.37:g.70984436A>G	ENSP00000349790:p.Ser339Pro	Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	952	0.4358974358974359	349	0.709349593495935	146	0.40331491712707185	182	0.3181818181818182	275	0.3627968337730871	G	11.66	1.705769	0.30232	0.679301	0.377558	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.93811	-3.29;-2.63;-3.29	5.85	4.98	0.66077	.	0.049158	0.85682	N	0.000000	T	0.49525	0.1562	N	0.00069	-2.28	0.43782	P	0.0036840000000000206	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.48559	-0.9025	9	0.06099	T	0.92	.	12.1197	0.53885	0.1427:0.0:0.8573:0.0	rs592121;rs1753199;rs17582574;rs61160542;rs592121	339;96	P20849;P20849-2	CO9A1_HUMAN;.	P	339;96;96	ENSP00000349790:S339P;ENSP00000315252:S96P;ENSP00000359530:S96P	ENSP00000315252:S96P	S	-	1	0	COL9A1	71041157	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	2.383000	0.44354	1.496000	0.48567	-0.119000	0.15052	TCA	A|0.531;G|0.469	0.469	strong		0.383	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
TIMELESS	8914	hgsc.bcm.edu	37	12	56814656	56814656	+	Missense_Mutation	SNP	A	A	G	rs61376834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56814656A>G	ENST00000553532.1	-	25	3200	c.3050T>C	c.(3049-3051)aTc>aCc	p.I1017T	TIMELESS_ENST00000554616.1_Missense_Mutation_p.I514T|TIMELESS_ENST00000229201.4_Missense_Mutation_p.I1016T					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						TAGGAGCGGGATAGAAAAGCC	0.527													A|||	105	0.0209665	0.0038	0.0418	5008	,	,		19709	0.002		0.0537	False		,,,				2504	0.0153				p.I1017T		Atlas-SNP	.											.	TIMELESS	107	.	0			c.T3050C						PASS	.	A	THR/ILE	60,4346	57.4+/-93.9	1,58,2144	89.0	89.0	89.0		3050	2.4	1.0	12	dbSNP_129	89	450,8150	136.0+/-193.2	11,428,3861	yes	missense	TIMELESS	NM_003920.3	89	12,486,6005	GG,GA,AA		5.2326,1.3618,3.9213	benign	1017/1209	56814656	510,12496	2203	4300	6503	SO:0001583	missense	8914	exon25			AGCGGGATAGAAA	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.3050T>C	12.37:g.56814656A>G	ENSP00000450607:p.Ile1017Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	55	0.025183150183150184	1	0.0020325203252032522	15	0.04143646408839779	1	0.0017482517482517483	38	0.05013192612137203	A	2.073	-0.412480	0.04799	0.013618	0.052326	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.11821	2.74;2.74;2.74	5.4	2.41	0.29592	Timeless C-terminal (1);	0.366329	0.26971	N	0.021572	T	0.00666	0.0022	N	0.02011	-0.69	0.24692	N	0.993309	B	0.02656	0.0	B	0.01281	0.0	T	0.40001	-0.9586	10	0.28530	T	0.3	-0.1743	6.4923	0.22123	0.1722:0.2786:0.5492:0.0	rs61376834;rs61752529	1017	Q9UNS1	TIM_HUMAN	T	1016;1017;514	ENSP00000229201:I1016T;ENSP00000450607:I1017T;ENSP00000450848:I514T	ENSP00000229201:I1017T	I	-	2	0	TIMELESS	55100923	0.998000	0.40836	0.966000	0.40874	0.038000	0.13279	3.947000	0.56652	0.782000	0.33613	-0.252000	0.11476	ATC	A|0.964;G|0.036	0.036	strong		0.527	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45244930	45244930	+	Silent	SNP	C	C	T	rs2269543	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45244930C>T	ENST00000389774.2	+	11	1101	c.960C>T	c.(958-960)ctC>ctT	p.L320L	PRR5-ARHGAP8_ENST00000352766.7_Silent_p.L499L|ARHGAP8_ENST00000356099.6_Silent_p.L289L|ARHGAP8_ENST00000389773.5_Silent_p.L411L|ARHGAP8_ENST00000336963.4_Silent_p.L289L|ARHGAP8_ENST00000517296.3_Silent_p.L499L|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.L420L	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	83	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	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	
NUGGC	389643	hgsc.bcm.edu	37	8	27886903	27886903	+	Silent	SNP	C	C	T	rs9314357	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:27886903C>T	ENST00000413272.2	-	17	2176	c.2034G>A	c.(2032-2034)acG>acA	p.T678T	NUGGC_ENST00000341513.6_Silent_p.T678T	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	678					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										CTTTTTTGCCCGTGATCTGAG	0.547													C|||	1628	0.32508	0.4251	0.2939	5008	,	,		20199	0.1181		0.4274	False		,,,				2504	0.32				p.T678T		Atlas-SNP	.											.	.	.	.	0			c.G2034A						PASS	.	C		1663,2325		346,971,677	53.0	53.0	53.0		2034	-7.5	0.9	8	dbSNP_119	53	3648,4688		822,2004,1342	no	coding-synonymous	C8orf80	NM_001010906.1		1168,2975,2019	TT,TC,CC		43.762,41.7001,43.0948		678/797	27886903	5311,7013	1994	4168	6162	SO:0001819	synonymous_variant	389643	exon17			TTTGCCCGTGATC	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.2034G>A	8.37:g.27886903C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																			C|0.663;T|0.337	0.337	strong		0.547	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
STK33	65975	hgsc.bcm.edu	37	11	8435078	8435078	+	Missense_Mutation	SNP	A	A	C	rs3751096|rs386750506	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8435078A>C	ENST00000447869.1	-	11	2226	c.1308T>G	c.(1306-1308)gaT>gaG	p.D436E	STK33_ENST00000473980.1_5'UTR|STK33_ENST00000534493.1_Missense_Mutation_p.D395E|STK33_ENST00000396672.1_Missense_Mutation_p.D436E|STK33_ENST00000358872.3_Missense_Mutation_p.D249E|STK33_ENST00000315204.1_Missense_Mutation_p.D436E|STK33_ENST00000396673.1_Intron			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	436			D -> E (in dbSNP:rs3751096). {ECO:0000269|PubMed:17344846}.	DA -> ET (in Ref. 3; AAH31231). {ECO:0000305}.	protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		TGTAATTGGCATCAGGGACAT	0.418													A|||	1250	0.249601	0.1142	0.2565	5008	,	,		19582	0.2877		0.2545	False		,,,				2504	0.3834				p.D436E		Atlas-SNP	.											.	STK33	147	.	0			c.T1308G						PASS	.	A	GLU/ASP	68,4334		27,14,2160	283.0	259.0	267.0		1308	1.1	0.0	11	dbSNP_107	267	304,8288		108,88,4100	yes	missense	STK33	NM_030906.2	45	135,102,6260	CC,CA,AA		3.5382,1.5448,2.8629	benign	436/515	8435078	372,12622	2201	4296	6497	SO:0001583	missense	65975	exon13			ATTGGCATCAGGG	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.1308T>G	11.37:g.8435078A>C	ENSP00000416750:p.Asp436Glu	Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	402	190	0.472637	NM_030906	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	37	CCDS7789.1	407	0.18635531135531136	41	0.08333333333333333	101	0.27900552486187846	128	0.22377622377622378	137	0.18073878627968337	A	8.659	0.900084	0.17686	0.015448	0.035382	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000358872;ENST00000534493	T;T;T;T;T	0.70399	-0.42;-0.42;-0.42;-0.48;-0.41	4.67	1.14	0.20703	Protein kinase-like domain (1);	1.246700	0.05471	N	0.553072	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.23058	0.079	B	0.13407	0.009	T	0.03863	-1.0997	9	0.24483	T	0.36	.	6.1573	0.20344	0.6914:0.0:0.3086:0.0	rs3751096;rs52817219;rs61487076;rs3751096	436	Q9BYT3	STK33_HUMAN	E	436;436;436;249;395	ENSP00000416750:D436E;ENSP00000320754:D436E;ENSP00000379905:D436E;ENSP00000351743:D249E;ENSP00000436418:D395E	ENSP00000320754:D436E	D	-	3	2	STK33	8391654	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.097000	0.15168	0.379000	0.24794	-0.376000	0.06991	GAT	A|0.792;C|0.208	0.208	strong		0.418	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906	
ARHGAP33	115703	hgsc.bcm.edu	37	19	36273308	36273308	+	Silent	SNP	G	G	A	rs35297478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36273308G>A	ENST00000007510.4	+	13	1263	c.1119G>A	c.(1117-1119)ctG>ctA	p.L373L	ARHGAP33_ENST00000378944.5_Silent_p.L237L|ARHGAP33_ENST00000314737.5_Silent_p.L373L			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	373	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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						TCCCGGAGCTGTCTGGCCCTG	0.597													G|||	599	0.119609	0.0598	0.1916	5008	,	,		18912	0.1488		0.1123	False		,,,				2504	0.1268				p.L373L		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.G1119A						PASS	.		,	310,4096	167.3+/-198.3	7,296,1900	120.0	104.0	110.0		711,1119	4.3	1.0	19	dbSNP_126	110	845,7755	194.2+/-239.7	36,773,3491	no	coding-synonymous,coding-synonymous	ARHGAP33	NM_001172630.1,NM_052948.3	,	43,1069,5391	AA,AG,GG		9.8256,7.0359,8.8805	,	237/1124,373/1127	36273308	1155,11851	2203	4300	6503	SO:0001819	synonymous_variant	115703	exon13			GGAGCTGTCTGGC	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.1119G>A	19.37:g.36273308G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				G|0.905;A|0.095	0.095	strong		0.597	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
LRP6	4040	hgsc.bcm.edu	37	12	12284915	12284915	+	Silent	SNP	G	G	A	rs1012672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:12284915G>A	ENST00000261349.4	-	18	3886	c.3810C>T	c.(3808-3810)tgC>tgT	p.C1270C	LRP6_ENST00000540415.1_5'UTR|LRP6_ENST00000543091.1_Intron|BCL2L14_ENST00000396369.1_Intron	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1270	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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)				TAAACCCATCGCACCGCCAAG	0.488													g|||	197	0.0393371	0.0333	0.0533	5008	,	,		15964	0.0159		0.0825	False		,,,				2504	0.0174				p.C1270C		Atlas-SNP	.											.	LRP6	170	.	0			c.C3810T	GRCh37	CM073186	LRP6	M	rs1012672	PASS	.	A		166,4240	111.2+/-149.4	3,160,2040	99.0	88.0	92.0		3810	-7.4	0.2	12	dbSNP_86	92	654,7946	166.4+/-218.3	28,598,3674	no	coding-synonymous	LRP6	NM_002336.2		31,758,5714	AA,AG,GG		7.6047,3.7676,6.3048		1270/1614	12284915	820,12186	2203	4300	6503	SO:0001819	synonymous_variant	4040	exon18			CCCATCGCACCGC	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.3810C>T	12.37:g.12284915G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	234	112	0.478632	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																			G|0.943;A|0.057	0.057	strong		0.488	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
OGFR	11054	hgsc.bcm.edu	37	20	61443870	61443870	+	Silent	SNP	C	C	G	rs11086139	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:61443870C>G	ENST00000290291.6	+	7	928	c.903C>G	c.(901-903)ccC>ccG	p.P301P	OGFR_ENST00000370461.1_Silent_p.P249P	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	301					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)					GCTCTCTGCCCCATCCGCTCG	0.682													C|||	842	0.168131	0.2814	0.1542	5008	,	,		13683	0.0357		0.2475	False		,,,				2504	0.0798				p.P301P		Atlas-SNP	.											.	OGFR	63	.	0			c.C903G						PASS	.	C		1119,3203		166,787,1208	8.0	8.0	8.0		903	-1.7	0.0	20	dbSNP_120	8	1941,6545		244,1453,2546	yes	coding-synonymous	OGFR	NM_007346.2		410,2240,3754	GG,GC,CC		22.873,25.8908,23.8913		301/678	61443870	3060,9748	2161	4243	6404	SO:0001819	synonymous_variant	11054	exon7			TCTGCCCCATCCG	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.903C>G	20.37:g.61443870C>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	ENST00000290291.6	37	CCDS13504.1																																																																																			C|0.800;G|0.200	0.200	strong		0.682	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
COQ6	51004	hgsc.bcm.edu	37	14	74424938	74424938	+	Silent	SNP	T	T	C	rs3180946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74424938T>C	ENST00000334571.2	+	5	610	c.570T>C	c.(568-570)caT>caC	p.H190H	COQ6_ENST00000554920.1_Intron|COQ6_ENST00000394026.4_Silent_p.H165H|COQ6_ENST00000238709.4_Silent_p.H115H|ENTPD5_ENST00000557325.1_3'UTR	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	190					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		CTTGGGTTCATATTACCCTAG	0.473													T|||	926	0.184904	0.0325	0.3199	5008	,	,		19445	0.0496		0.4026	False		,,,				2504	0.2106				p.H190H		Atlas-SNP	.											.	COQ6	27	.	0			c.T570C						PASS	.	T	,	386,4020	194.3+/-219.2	17,352,1834	109.0	97.0	101.0		570,345	-4.1	0.9	14	dbSNP_105	101	3555,5045	517.7+/-379.1	726,2103,1471	no	coding-synonymous,coding-synonymous	COQ6	NM_182476.2,NM_182480.2	,	743,2455,3305	CC,CT,TT		41.3372,8.7608,30.3014	,	190/469,115/394	74424938	3941,9065	2203	4300	6503	SO:0001819	synonymous_variant	51004	exon5			GGTTCATATTACC	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"""coenzyme Q6 homolog (yeast)"", ""coenzyme Q6 homolog, monooxygenase (yeast)"", ""coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"""			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.570T>C	14.37:g.74424938T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	242	118	0.487603	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Silent	SNP	ENST00000334571.2	37	CCDS9823.1																																																																																			T|0.737;C|0.263	0.263	strong		0.473	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1		
GBF1	8729	hgsc.bcm.edu	37	10	104140355	104140355	+	Silent	SNP	C	C	T	rs112809254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:104140355C>T	ENST00000369983.3	+	38	5342	c.5082C>T	c.(5080-5082)ccC>ccT	p.P1694P		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1694					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GAGGCGGCCCCTCGGCCCTCT	0.572													C|||	170	0.0339457	0.087	0.0202	5008	,	,		19993	0.0		0.0169	False		,,,				2504	0.0245				p.P1694P		Atlas-SNP	.											.	GBF1	142	.	0			c.C5082T						PASS	.	C	,,	315,4091	166.2+/-197.5	9,297,1897	244.0	267.0	259.0		5073,5070,5082	5.0	1.0	10	dbSNP_132	259	199,8401	86.3+/-148.7	4,191,4105	no	coding-synonymous,coding-synonymous,coding-synonymous	GBF1	NM_001199378.1,NM_001199379.1,NM_004193.2	,,	13,488,6002	TT,TC,CC		2.314,7.1493,3.952	,,	1691/1857,1690/1856,1694/1860	104140355	514,12492	2203	4300	6503	SO:0001819	synonymous_variant	8729	exon38			CGGCCCCTCGGCC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.5082C>T	10.37:g.104140355C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_004193	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Silent	SNP	ENST00000369983.3	37	CCDS7533.1																																																																																			A|0.000;C|0.966;G|0.000;T|0.034	0.034	strong		0.572	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
COL6A3	1293	hgsc.bcm.edu	37	2	238277573	238277573	+	Silent	SNP	C	C	A	rs2645774	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238277573C>A	ENST00000295550.4	-	10	4985	c.4533G>T	c.(4531-4533)ggG>ggT	p.G1511G	COL6A3_ENST00000347401.3_Silent_p.G1310G|COL6A3_ENST00000353578.4_Silent_p.G1305G|COL6A3_ENST00000346358.4_Silent_p.G1311G|COL6A3_ENST00000472056.1_Silent_p.G904G|COL6A3_ENST00000409809.1_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	92	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	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	
TJP3	27134	hgsc.bcm.edu	37	19	3733831	3733831	+	Silent	SNP	G	G	A	rs34564453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3733831G>A	ENST00000541714.2	+	7	1260	c.798G>A	c.(796-798)ctG>ctA	p.L266L	TJP3_ENST00000262968.9_Silent_p.L285L|TJP3_ENST00000589378.1_Silent_p.L275L|TJP3_ENST00000587686.1_Silent_p.L285L|TJP3_ENST00000382008.3_Silent_p.L266L|TJP3_ENST00000539908.2_Silent_p.L230L	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	266	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		AGCTAAGCCTGCTGGTGCTGA	0.557													G|||	93	0.0185703	0.0083	0.0346	5008	,	,		20696	0.0		0.0417	False		,,,				2504	0.0164				p.L275L		Atlas-SNP	.											.	TJP3	79	.	0			c.G825A						PASS	.	G		38,4368	42.3+/-75.8	0,38,2165	154.0	126.0	136.0		855	2.4	1.0	19	dbSNP_126	136	323,8277	113.1+/-173.2	3,317,3980	no	coding-synonymous	TJP3	NM_014428.1		3,355,6145	AA,AG,GG		3.7558,0.8625,2.7756		285/953	3733831	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	27134	exon7			AAGCCTGCTGGTG	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.798G>A	19.37:g.3733831G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			G|0.974;A|0.026	0.026	strong		0.557	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
LRRC38	126755	hgsc.bcm.edu	37	1	13802325	13802325	+	Missense_Mutation	SNP	T	T	C	rs3013105	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	71	0	0		WXS	Illumina HiSeq	Phase_I	58	58	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		
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807536	18807536	+	Missense_Mutation	SNP	G	G	T	rs7512414	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:18807536G>T	ENST00000400664.1	+	1	113	c.61G>T	c.(61-63)Gtg>Ttg	p.V21L		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	21			V -> L (in dbSNP:rs7512414).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GACCGGCAAGGTGGTGCTGTC	0.627													G|||	473	0.0944489	0.1233	0.1239	5008	,	,		18132	0.0377		0.1233	False		,,,				2504	0.0634				p.V21L		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G61T						PASS	.	G	LEU/VAL	401,3739		18,365,1687	47.0	54.0	52.0		61	3.9	1.0	1	dbSNP_116	52	1033,7421		60,913,3254	yes	missense	KLHDC7A	NM_152375.2	32	78,1278,4941	TT,TG,GG		12.2191,9.686,11.3864	benign	21/778	18807536	1434,11160	2070	4227	6297	SO:0001583	missense	127707	exon1			GGCAAGGTGGTGC	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.61G>T	1.37:g.18807536G>T	ENSP00000383505:p.Val21Leu	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	262	122	0.465649	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	213	0.09752747252747253	45	0.09146341463414634	48	0.13259668508287292	29	0.050699300699300696	91	0.12005277044854881	G	9.454	1.091325	0.20471	0.09686	0.122191	ENSG00000179023	ENST00000400664	T	0.74209	-0.82	5.82	3.89	0.44902	.	.	.	.	.	T	0.00724	0.0024	N	0.12182	0.205	0.34395	P	0.30533699999999997	B	0.14012	0.009	B	0.10450	0.005	T	0.10268	-1.0637	8	0.02654	T	1	.	13.8326	0.63391	0.0:0.5191:0.4809:0.0	rs7512414;rs7512414	21	Q5VTJ3	KLD7A_HUMAN	L	21	ENSP00000383505:V21L	ENSP00000383505:V21L	V	+	1	0	KLHDC7A	18680123	1.000000	0.71417	0.999000	0.59377	0.075000	0.17131	1.846000	0.39289	1.452000	0.47756	0.591000	0.81541	GTG	G|0.888;T|0.112	0.112	strong		0.627	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
SCIN	85477	hgsc.bcm.edu	37	7	12610594	12610594	+	Missense_Mutation	SNP	A	A	G	rs2240572	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:12610594A>G	ENST00000297029.5	+	1	283	c.182A>G	c.(181-183)cAc>cGc	p.H61R	AC005281.2_ENST00000433040.1_RNA	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	61	Actin-severing. {ECO:0000255}.		H -> R (in dbSNP:rs2240572). {ECO:0000269|PubMed:15489334}.		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)		TTCACCTACCACCTGCACTTC	0.692													G|||	2018	0.402955	0.5681	0.3934	5008	,	,		13778	0.244		0.4066	False		,,,				2504	0.3466				p.H61R		Atlas-SNP	.											SCIN_ENST00000297029,NS,carcinoma,0,6	SCIN	105	6	0			c.A182G						PASS	.	G	ARG/HIS	731,653		198,335,159	16.0	26.0	23.0		182	4.9	1.0	7	dbSNP_98	23	1322,1858		289,744,557	yes	missense	SCIN	NM_001112706.2	29	487,1079,716	GG,GA,AA		41.5723,47.1821,44.9825	benign	61/716	12610594	2053,2511	692	1590	2282	SO:0001583	missense	85477	exon1			CCTACCACCTGCA	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.182A>G	7.37:g.12610594A>G	ENSP00000297029:p.His61Arg	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	851	0.38965201465201466	281	0.5711382113821138	149	0.4116022099447514	121	0.21153846153846154	300	0.39577836411609496	G	12.93	2.086308	0.36855	0.528179	0.415723	ENSG00000006747	ENST00000297029;ENST00000417018	T;T	0.54866	0.55;0.55	4.9	4.9	0.64082	Gelsolin domain (1);	0.223988	0.38005	N	0.001843	T	0.00012	0.0000	N	0.12920	0.275	0.09310	P	0.9999999999999861	B	0.02656	0.0	B	0.04013	0.001	T	0.43988	-0.9357	9	0.40728	T	0.16	-5.212	8.2742	0.31862	0.2373:0.0:0.7627:0.0	rs2240572;rs17856629;rs59501934;rs2240572	61	Q9Y6U3	ADSV_HUMAN	R	61	ENSP00000297029:H61R;ENSP00000404380:H61R	ENSP00000297029:H61R	H	+	2	0	SCIN	12577119	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	4.277000	0.58939	1.307000	0.44944	-0.215000	0.12644	CAC	A|0.609;G|0.391	0.391	strong		0.692	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
WWOX	51741	hgsc.bcm.edu	37	16	78420775	78420775	+	Missense_Mutation	SNP	G	G	A	rs11545029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:78420775G>A	ENST00000566780.1	+	6	901	c.535G>A	c.(535-537)Gca>Aca	p.A179T	WWOX_ENST00000408984.3_Missense_Mutation_p.A179T|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000406884.2_Intron|WWOX_ENST00000539474.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	179	Interaction with MAPT. {ECO:0000250}.		A -> T (in dbSNP:rs12918952). {ECO:0000269|PubMed:11572989, ECO:0000269|Ref.5}.		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)		CAAGGTAGAAGCAATGACCCT	0.418													G|||	1319	0.263379	0.1067	0.4035	5008	,	,		17481	0.0635		0.6064	False		,,,				2504	0.229				p.A179T		Atlas-SNP	.											.	WWOX	98	.	0			c.G535A						PASS	.	G	THR/ALA	757,3125		69,619,1253	116.0	109.0	111.0		535	5.5	1.0	16	dbSNP_121	111	4823,3443		1405,2013,715	yes	missense	WWOX	NM_016373.2	58	1474,2632,1968	AA,AG,GG		41.6526,19.5003,45.9335	benign	179/415	78420775	5580,6568	1941	4133	6074	SO:0001583	missense	51741	exon6			GTAGAAGCAATGA	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.535G>A	16.37:g.78420775G>A	ENSP00000457230:p.Ala179Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_016373	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	714	0.3269230769230769	64	0.13008130081300814	151	0.4171270718232044	43	0.07517482517482517	456	0.6015831134564644	G	16.46	3.128484	0.56721	0.195003	0.583474	ENSG00000186153	ENST00000408984;ENST00000299644	D	0.87650	-2.28	5.52	5.52	0.82312	NAD(P)-binding domain (1);	0.058121	0.64402	D	0.000002	T	0.00012	0.0000	N	0.25031	0.7	0.22468	P	0.999079915	B	0.24132	0.098	B	0.27076	0.076	T	0.45160	-0.9280	9	0.42905	T	0.14	.	19.4505	0.94865	0.0:0.0:1.0:0.0	rs12918952;rs52836483;rs12918952	179	Q9NZC7	WWOX_HUMAN	T	179;22	ENSP00000386161:A179T	ENSP00000299644:A22T	A	+	1	0	WWOX	76978276	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.072000	0.89496	2.597000	0.87782	0.655000	0.94253	GCA	G|0.653;A|0.347	0.347	strong		0.418	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1		
INO80D	54891	hgsc.bcm.edu	37	2	206911228	206911228	+	Splice_Site	SNP	G	G	A	rs2909111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:206911228G>A	ENST00000403263.1	-	5	1477	c.1073C>T	c.(1072-1074)gCg>gTg	p.A358V		NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	358			A -> V (in dbSNP:rs2909111). {ECO:0000269|PubMed:14702039}.		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						GAAGACTTACGCATGTCTTTG	0.512													G|||	1955	0.390375	0.236	0.3242	5008	,	,		15885	0.4792		0.3439	False		,,,				2504	0.6022				p.A358V		Atlas-SNP	.											.	INO80D	134	.	0			c.C1073T						PASS	.	G	VAL/ALA	864,2874		98,668,1103	72.0	69.0	70.0		1073	-1.7	1.0	2	dbSNP_101	70	2939,5251		540,1859,1696	yes	missense-near-splice	INO80D	NM_017759.4	64	638,2527,2799	AA,AG,GG		35.8852,23.114,31.883	benign	358/1028	206911228	3803,8125	1869	4095	5964	SO:0001630	splice_region_variant	54891	exon5			ACTTACGCATGTC		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.1073+1C>T	2.37:g.206911228G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	37	CCDS46500.1	807	0.3695054945054945	136	0.2764227642276423	123	0.3397790055248619	289	0.5052447552447552	259	0.341688654353562	G	13.70	2.316205	0.40996	0.23114	0.358852	ENSG00000114933	ENST00000403263;ENST00000233270;ENST00000424117	T;T	0.42513	0.97;0.97	5.54	-1.7	0.08159	.	0.628168	0.17112	N	0.186596	T	0.00012	0.0000	N	0.08118	0	0.44825	P	0.0021640000000000548	B	0.06786	0.001	B	0.01281	0.0	T	0.46925	-0.9156	8	.	.	.	.	4.9832	0.14176	0.5002:0.0:0.265:0.2348	rs2909111;rs52835029;rs60630711;rs2909111	358	Q53TQ3-2	.	V	358;358;253	ENSP00000384198:A358V;ENSP00000402369:A253V	.	A	-	2	0	INO80D	206619473	0.181000	0.23161	0.984000	0.44739	0.769000	0.43574	-0.045000	0.12003	-0.190000	0.10465	0.655000	0.94253	GCG	G|0.629;A|0.371	0.371	strong		0.512	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	Missense_Mutation
GABRR2	2570	hgsc.bcm.edu	37	6	89981413	89981413	+	Silent	SNP	T	T	C	rs282117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:89981413T>C	ENST00000402938.3	-	3	382	c.249A>G	c.(247-249)gtA>gtG	p.V83V	GABRR2_ENST00000602399.1_Silent_p.V108V|GABRR2_ENST00000602808.1_5'UTR	NM_002043.3	NP_002034.3	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 2	83					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)	TCTCCACCTGTACGTCCACGC	0.617													C|||	3467	0.692292	0.8207	0.5533	5008	,	,		18518	0.7292		0.5815	False		,,,				2504	0.6933				p.V83V		Atlas-SNP	.											GABRR2,NS,carcinoma,0,1	GABRR2	41	1	0			c.A249G						PASS	.	C		3447,959	355.6+/-313.1	1353,741,109	66.0	51.0	56.0		324	4.9	1.0	6	dbSNP_79	56	5161,3439	496.1+/-374.2	1540,2081,679	no	coding-synonymous	GABRR2	NM_002043.2		2893,2822,788	CC,CT,TT		39.9884,21.7658,33.8152		108/491	89981413	8608,4398	2203	4300	6503	SO:0001819	synonymous_variant	2570	exon3			CACCTGTACGTCC		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.249A>G	6.37:g.89981413T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_002043	A2BDE4|Q9H153	Silent	SNP	ENST00000402938.3	37	CCDS5020.3																																																																																			T|0.334;C|0.666	0.666	strong		0.617	GABRR2-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041482.3		
EIF2AK1	27102	hgsc.bcm.edu	37	7	6066461	6066461	+	Silent	SNP	T	T	C	rs2639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:6066461T>C	ENST00000199389.6	-	14	1808	c.1662A>G	c.(1660-1662)ccA>ccG	p.P554P	EIF2AK1_ENST00000536084.1_Silent_p.P430P	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	554	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)	p.P554P(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		TGGCTTGCACTGGACACCTTT	0.468													T|||	1690	0.33746	0.4448	0.219	5008	,	,		19204	0.4425		0.2048	False		,,,				2504	0.3047				p.P554P		Atlas-SNP	.											EIF2AK1,NS,carcinoma,0,1	EIF2AK1	76	1	1	Substitution - coding silent(1)	stomach(1)	c.A1662G						PASS	.	T	,	1932,2474	551.2+/-378.2	416,1100,687	140.0	128.0	132.0		1659,1662	-5.5	0.0	7	dbSNP_36	132	1688,6912	310.0+/-309.6	176,1336,2788	no	coding-synonymous,coding-synonymous	EIF2AK1	NM_001134335.1,NM_014413.3	,	592,2436,3475	CC,CT,TT		19.6279,43.8493,27.8333	,	553/630,554/631	6066461	3620,9386	2203	4300	6503	SO:0001819	synonymous_variant	27102	exon14			TTGCACTGGACAC	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1662A>G	7.37:g.6066461T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	149	67	0.449664	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Silent	SNP	ENST00000199389.6	37	CCDS5345.1																																																																																			T|0.699;C|0.301	0.301	strong		0.468	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
NLRC5	84166	hgsc.bcm.edu	37	16	57059427	57059427	+	Missense_Mutation	SNP	C	C	T	rs74439742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57059427C>T	ENST00000262510.6	+	6	797	c.572C>T	c.(571-573)cCg>cTg	p.P191L	NLRC5_ENST00000436936.1_Missense_Mutation_p.P191L|NLRC5_ENST00000539144.1_Missense_Mutation_p.P191L|NLRC5_ENST00000308149.7_Missense_Mutation_p.P191L	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	191					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)				TTAGACACTCCGGAGGGGGCC	0.617													C|||	616	0.123003	0.0303	0.1282	5008	,	,		18348	0.1845		0.168	False		,,,				2504	0.135				p.P191L		Atlas-SNP	.											.	NLRC5	186	.	0			c.C572T						PASS	.	C	LEU/PRO	239,4157	141.1+/-176.5	11,217,1970	96.0	102.0	100.0		572	0.2	0.3	16	dbSNP_131	100	1514,7086	285.0+/-296.9	133,1248,2919	yes	missense	NLRC5	NM_032206.3	98	144,1465,4889	TT,TC,CC		17.6047,5.4368,13.4888	benign	191/1867	57059427	1753,11243	2198	4300	6498	SO:0001583	missense	84166	exon5			ACACTCCGGAGGG	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.572C>T	16.37:g.57059427C>T	ENSP00000262510:p.Pro191Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	308	0.14102564102564102	16	0.032520325203252036	63	0.17403314917127072	107	0.18706293706293706	122	0.16094986807387862	C	9.665	1.145047	0.21288	0.054368	0.176047	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.75154	-0.7;-0.72;-0.91;-0.72	5.28	0.21	0.15231	.	0.546175	0.13851	N	0.358363	T	0.00073	0.0002	N	0.08118	0	0.49389	P	2.1700000000002273E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.03202	-1.1061	9	0.28530	T	0.3	.	1.3511	0.02173	0.3909:0.3106:0.1661:0.1324	.	191	Q86WI3	NLRC5_HUMAN	L	191	ENSP00000262510:P191L;ENSP00000308886:P191L;ENSP00000389739:P191L;ENSP00000441727:P191L	ENSP00000262510:P191L	P	+	2	0	NLRC5	55616928	0.000000	0.05858	0.309000	0.25155	0.002000	0.02628	-0.144000	0.10280	0.034000	0.15491	-1.331000	0.01271	CCG	C|0.861;T|0.139	0.139	strong		0.617	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
ERMARD	55780	hgsc.bcm.edu	37	6	170162537	170162537	+	Silent	SNP	C	C	T	rs11966349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170162537C>T	ENST00000366773.3	+	9	903	c.870C>T	c.(868-870)tgC>tgT	p.C290C	ERMARD_ENST00000418781.3_Silent_p.C290C|ERMARD_ENST00000366772.2_Silent_p.C290C|ERMARD_ENST00000392095.4_Silent_p.C164C|ERMARD_ENST00000588451.1_Silent_p.C164C	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	290					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TTGCTGACTGCGCCATATTGT	0.428													C|||	1007	0.201078	0.2436	0.17	5008	,	,		18512	0.2738		0.1014	False		,,,				2504	0.1933				p.C290C		Atlas-SNP	.											.	C6orf70	63	.	0			c.C870T						PASS	.	C		1060,3346	385.6+/-325.8	129,802,1272	134.0	128.0	130.0		870	-0.5	0.7	6	dbSNP_120	130	816,7784	188.3+/-235.3	46,724,3530	no	coding-synonymous	C6orf70	NM_018341.1		175,1526,4802	TT,TC,CC		9.4884,24.0581,14.4241		290/679	170162537	1876,11130	2203	4300	6503	SO:0001819	synonymous_variant	55780	exon9			TGACTGCGCCATA	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.870C>T	6.37:g.170162537C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	119	49	0.411765	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Silent	SNP	ENST00000366773.3	37	CCDS34576.1																																																																																			C|0.838;T|0.162	0.162	strong		0.428	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
CD4	920	hgsc.bcm.edu	37	12	6924109	6924109	+	Silent	SNP	C	C	T	rs11575099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6924109C>T	ENST00000011653.4	+	5	816	c.558C>T	c.(556-558)gtC>gtT	p.V186V	CD4_ENST00000541982.1_Silent_p.V131V|CD4_ENST00000538827.1_3'UTR	NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	186	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	CATGCACTGTCTTGCAGAACC	0.557													C|||	65	0.0129792	0.0189	0.0101	5008	,	,		-128	0.0		0.0288	False		,,,				2504	0.0041				p.V186V		Atlas-SNP	.											.	CD4	47	.	0			c.C558T						PASS	.	C	,,,,	73,4333	65.3+/-102.7	0,73,2130	86.0	70.0	75.0		558,,,,	0.7	0.0	12	dbSNP_120	75	236,8364	96.6+/-158.3	3,230,4067	no	coding-synonymous,utr-5,utr-5,utr-5,utr-5	CD4	NM_000616.4,NM_001195014.2,NM_001195015.2,NM_001195016.2,NM_001195017.2	,,,,	3,303,6197	TT,TC,CC		2.7442,1.6568,2.3758	,,,,	186/459,,,,	6924109	309,12697	2203	4300	6503	SO:0001819	synonymous_variant	920	exon5			CACTGTCTTGCAG	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1678	protein-coding gene	gene with protein product		186940	"""CD4 antigen (p55)"", ""T-cell surface glycoprotein CD4"""				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.558C>T	12.37:g.6924109C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	164	71	0.432927	NM_000616	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Silent	SNP	ENST00000011653.4	37	CCDS8562.1																																																																																			C|0.979;T|0.021	0.021	strong		0.557	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616	
CPNE1	8904	hgsc.bcm.edu	37	20	34219496	34219496	+	Missense_Mutation	SNP	T	T	C	rs6579255	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:34219496T>C	ENST00000317619.3	-	10	1026	c.632A>G	c.(631-633)cAa>cGa	p.Q211R	CPNE1_ENST00000397442.1_Missense_Mutation_p.Q211R|CPNE1_ENST00000397443.1_Missense_Mutation_p.Q211R|CPNE1_ENST00000397446.1_Missense_Mutation_p.Q211R|CPNE1_ENST00000317677.5_Missense_Mutation_p.Q216R|CPNE1_ENST00000397445.1_Missense_Mutation_p.Q211R|CPNE1_ENST00000352393.4_Missense_Mutation_p.Q211R			Q99829	CPNE1_HUMAN	copine I	211	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.		Q -> R (in dbSNP:rs6579255).		lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			ATCGGAGCATTGCACCTGAGG	0.562													C|||	1362	0.271965	0.4244	0.1844	5008	,	,		20547	0.1359		0.1899	False		,,,				2504	0.3528				p.Q216R		Atlas-SNP	.											.	CPNE1	44	.	0			c.A647G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	1738,2668	647.5+/-398.6	333,1072,798	68.0	50.0	56.0		632,647,632,632,632,632	4.5	1.0	20	dbSNP_116	56	1639,6961	741.0+/-407.1	172,1295,2833	yes	missense,missense,missense,missense,missense,missense	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	43,43,43,43,43,43	505,2367,3631	CC,CT,TT		19.0581,39.4462,25.9649	benign,benign,benign,benign,benign,benign	211/537,216/543,211/538,211/538,211/538,211/538	34219496	3377,9629	2203	4300	6503	SO:0001583	missense	8904	exon8			GAGCATTGCACCT	U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.632A>G	20.37:g.34219496T>C	ENSP00000326126:p.Gln211Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_003915	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Missense_Mutation	SNP	ENST00000317619.3	37	CCDS13260.1	482	0.2206959706959707	195	0.39634146341463417	78	0.2154696132596685	63	0.11013986013986014	146	0.19261213720316622	C	11.35	1.612918	0.28712	0.394462	0.190581	ENSG00000214078	ENST00000352393;ENST00000317677;ENST00000317619;ENST00000397446;ENST00000397445;ENST00000397443;ENST00000397442;ENST00000437340;ENST00000430570;ENST00000412056;ENST00000414664;ENST00000416778;ENST00000439806	T;T;T;T;T;T;T;T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.43	4.46	0.54185	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.839098	0.10589	N	0.657022	T	0.00012	0.0000	N	0.16307	0.4	0.50632	P	1.1200000000000099E-4	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.001;0.001;0.001	T	0.37820	-0.9689	9	0.15952	T	0.53	-17.6282	6.5162	0.22248	0.0:0.6028:0.0:0.3972	rs6579255;rs11543241;rs52798653;rs57435970;rs6579255	216;211;211;211;191	B0QZ18;E7ENH5;A6PVH9;Q99829;Q59EI4	.;.;.;CPNE1_HUMAN;.	R	211;216;211;211;211;211;211;211;187;187;211;187;211	ENSP00000336945:Q211R;ENSP00000317257:Q216R;ENSP00000326126:Q211R;ENSP00000380588:Q211R;ENSP00000380587:Q211R;ENSP00000380585:Q211R;ENSP00000380584:Q211R;ENSP00000415597:Q211R;ENSP00000390626:Q187R;ENSP00000416962:Q187R;ENSP00000404355:Q211R;ENSP00000389662:Q187R;ENSP00000387434:Q211R	ENSP00000326126:Q211R	Q	-	2	0	CPNE1	33682910	0.761000	0.28439	1.000000	0.80357	0.952000	0.60782	1.628000	0.37060	0.812000	0.34326	-0.119000	0.15052	CAA	T|0.753;C|0.247	0.247	strong		0.562	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
OR11H6	122748	hgsc.bcm.edu	37	14	20691962	20691962	+	Missense_Mutation	SNP	C	C	G	rs9323693	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20691962C>G	ENST00000315519.2	+	1	172	c.94C>G	c.(94-96)Ctc>Gtc	p.L32V		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	32			L -> V (in dbSNP:rs9323693).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		TGAGTTTGTCCTCCTGGGTTT	0.428													c|||	498	0.0994409	0.121	0.049	5008	,	,		20383	0.0903		0.0815	False		,,,				2504	0.1339				p.L32V		Atlas-SNP	.											.	OR11H6	60	.	0			c.C94G						PASS	.	C	VAL/LEU	429,3977	209.8+/-230.5	18,393,1792	133.0	130.0	131.0		94	4.6	1.0	14	dbSNP_119	131	633,7967	164.2+/-216.6	34,565,3701	yes	missense	OR11H6	NM_001004480.1	32	52,958,5493	GG,GC,CC		7.3605,9.7367,8.1655	benign	32/331	20691962	1062,11944	2203	4300	6503	SO:0001583	missense	122748	exon1			TTTGTCCTCCTGG		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.94C>G	14.37:g.20691962C>G	ENSP00000319071:p.Leu32Val	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	259	123	0.474903	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	204	0.09340659340659341	72	0.14634146341463414	17	0.04696132596685083	53	0.09265734265734266	62	0.08179419525065963	C	13.14	2.149408	0.37923	0.097367	0.073605	ENSG00000176219	ENST00000315519	T	0.00563	6.58	4.57	4.57	0.56435	.	0.000000	0.44483	D	0.000445	T	0.00012	0.0000	H	0.95611	3.695	0.35325	P	0.21487999999999996	P	0.45672	0.864	B	0.42214	0.38	T	0.18555	-1.0333	9	0.87932	D	0	.	15.2129	0.73241	0.0:1.0:0.0:0.0	rs9323693;rs17211271;rs52805624;rs9323693	32	Q8NGC7	O11H6_HUMAN	V	32	ENSP00000319071:L32V	ENSP00000319071:L32V	L	+	1	0	OR11H6	19761802	0.297000	0.24408	1.000000	0.80357	0.759000	0.43091	0.917000	0.28665	2.521000	0.84997	0.442000	0.29010	CTC	C|0.918;G|0.082	0.082	strong		0.428	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
NPHS1	4868	hgsc.bcm.edu	37	19	36339063	36339063	+	Silent	SNP	G	G	A	rs392702	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:36339063G>A	ENST00000378910.5	-	11	1319	c.1320C>T	c.(1318-1320)ccC>ccT	p.P440P	NPHS1_ENST00000353632.6_Silent_p.P440P	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	440	Ig-like C2-type 5.				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)			GTTTCTGGGCGGGATCTGGCG	0.622													G|||	426	0.0850639	0.233	0.0432	5008	,	,		15542	0.0109		0.0268	False		,,,				2504	0.0511				p.P440P		Atlas-SNP	.											.	NPHS1	165	.	0			c.C1320T						PASS	.	G		951,3455	341.8+/-306.9	98,755,1350	49.0	60.0	56.0		1320	-6.2	0.9	19	dbSNP_80	56	284,8316	103.8+/-164.8	2,280,4018	no	coding-synonymous	NPHS1	NM_004646.3		100,1035,5368	AA,AG,GG		3.3023,21.5842,9.4956		440/1242	36339063	1235,11771	2203	4300	6503	SO:0001819	synonymous_variant	4868	exon11			CTGGGCGGGATCT		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.1320C>T	19.37:g.36339063G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_004646	A6NDH2|C3RX61	Silent	SNP	ENST00000378910.5	37	CCDS32996.1																																																																																			G|0.919;A|0.081	0.081	strong		0.622	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
ZBTB49	166793	hgsc.bcm.edu	37	4	4304337	4304337	+	Silent	SNP	C	C	T	rs2916382	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:4304337C>T	ENST00000337872.4	+	3	895	c.774C>T	c.(772-774)gcC>gcT	p.A258A	ZBTB49_ENST00000538529.1_5'UTR|ZBTB49_ENST00000355834.3_Silent_p.A258A	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	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)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						AGCCTTGTGCCGTCAGTCATT	0.547													T|||	4004	0.799521	0.7602	0.8761	5008	,	,		19356	0.7629		0.8489	False		,,,				2504	0.7853				p.A258A		Atlas-SNP	.											.	ZBTB49	63	.	0			c.C774T						PASS	.	T		3475,931	357.6+/-314.0	1380,715,108	116.0	111.0	112.0		774	-10.4	0.0	4	dbSNP_101	112	7173,1427	274.6+/-291.3	2997,1179,124	no	coding-synonymous	ZBTB49	NM_145291.3		4377,1894,232	TT,TC,CC		16.593,21.1303,18.1301		258/766	4304337	10648,2358	2203	4300	6503	SO:0001819	synonymous_variant	166793	exon3			TTGTGCCGTCAGT	AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19883	protein-coding gene	gene with protein product			"""zinc finger protein 509"""	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.774C>T	4.37:g.4304337C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Silent	SNP	ENST00000337872.4	37	CCDS3375.1																																																																																			C|0.177;T|0.823	0.823	strong		0.547	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415748	105415748	+	Missense_Mutation	SNP	G	G	A	rs118171013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105415748G>A	ENST00000333244.5	-	7	6159	c.6040C>T	c.(6040-6042)Cct>Tct	p.P2014S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2014						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)			TTGGGTGCAGGCACATCCACC	0.597													.|||	1504	0.300319	0.1377	0.3631	5008	,	,		15992	0.0903		0.5447	False		,,,				2504	0.4407				p.P2014S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C6040T						PASS	.	A	SER/PRO	806,3058		129,548,1255	138.0	119.0	125.0		6040	-7.4	0.0	14	dbSNP_132	125	4479,3641		1443,1593,1024	no	missense	AHNAK2	NM_138420.2	74	1572,2141,2279	AA,AG,GG		44.8399,20.8592,44.1005	benign	2014/5796	105415748	5285,6699	1932	4060	5992	SO:0001583	missense	113146	exon7			GTGCAGGCACATC	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.6040C>T	14.37:g.105415748G>A	ENSP00000353114:p.Pro2014Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	657	0.3008241758241758	79	0.16056910569105692	137	0.3784530386740331	35	0.06118881118881119	406	0.5356200527704486	-	0.114	-1.134216	0.01742	0.208592	0.551601	ENSG00000185567	ENST00000333244	T	0.04015	3.73	3.72	-7.44	0.01379	.	.	.	.	.	T	0.00012	0.0000	N	0.00019	-2.785	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.49818	-0.8899	8	0.06891	T	0.86	-0.9503	1.4552	0.02383	0.2249:0.2846:0.3034:0.1871	.	2014	Q8IVF2	AHNK2_HUMAN	S	2014	ENSP00000353114:P2014S	ENSP00000353114:P2014S	P	-	1	0	AHNAK2	104486793	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-3.592000	0.00421	-1.485000	0.01854	-2.164000	0.00325	CCT	G|0.636;A|0.364	0.364	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
EXOC3L2	90332	hgsc.bcm.edu	37	19	45716364	45716364	+	Missense_Mutation	SNP	C	C	T	rs189063316	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45716364C>T	ENST00000252482.3	-	9	1220	c.1193G>A	c.(1192-1194)cGg>cAg	p.R398Q	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.R398Q|AC006126.3_ENST00000591569.1_Intron			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	398					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)		AGACGGAGGCCGGGGCCGAGG	0.687													C|||	43	0.00858626	0.0	0.0043	5008	,	,		13018	0.0		0.0199	False		,,,				2504	0.0204				p.R398Q		Atlas-SNP	.											EXOC3L2,NS,lymphoid_neoplasm,0,1	EXOC3L2	30	1	0			c.G1193A						scavenged	.	C	GLN/ARG	13,4303		0,13,2145	8.0	10.0	9.0		1193	1.3	0.1	19		9	108,8370		1,106,4132	no	missense	EXOC3L2	NM_138568.3	43	1,119,6277	TT,TC,CC		1.2739,0.3012,0.9458	possibly-damaging	398/410	45716364	121,12673	2158	4239	6397	SO:0001583	missense	90332	exon10			GGAGGCCGGGGCC	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.1193G>A	19.37:g.45716364C>T	ENSP00000252482:p.Arg398Gln	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	29	18	0.62069	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	37	CCDS12657.1	17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	15.67	2.903346	0.52333	0.003012	0.012739	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.15718	2.4;2.4	3.52	1.26	0.21427	.	0.302293	0.21905	U	0.067396	T	0.03651	0.0104	L	0.27053	0.805	0.09310	N	1	P	0.34629	0.46	B	0.23419	0.046	T	0.24154	-1.0168	10	0.54805	T	0.06	.	4.0747	0.09899	0.0:0.6097:0.249:0.1413	.	398	Q2M3D2	EX3L2_HUMAN	Q	398	ENSP00000252482:R398Q;ENSP00000400713:R398Q	ENSP00000252482:R398Q	R	-	2	0	EXOC3L2	50408204	0.077000	0.21312	0.112000	0.21494	0.386000	0.30323	0.957000	0.29215	0.444000	0.26612	0.305000	0.20034	CGG	C|0.992;T|0.008	0.008	strong		0.687	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
RRP12	23223	hgsc.bcm.edu	37	10	99141205	99141205	+	Silent	SNP	A	A	G	rs2275089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:99141205A>G	ENST00000370992.4	-	12	1467	c.1356T>C	c.(1354-1356)gcT>gcC	p.A452A	RRP12_ENST00000315563.6_Silent_p.A352A|RRP12_ENST00000536831.1_Silent_p.A170A|RRP12_ENST00000414986.1_Silent_p.A391A	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	452						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		AGCCAATGTCAGCCATGTGGG	0.607													G|||	2027	0.404752	0.553	0.3415	5008	,	,		18385	0.3125		0.337	False		,,,				2504	0.4141				p.A452A		Atlas-SNP	.											.	RRP12	97	.	0			c.T1356C						PASS	.	G	,	2176,2230	586.8+/-386.5	547,1082,574	70.0	56.0	60.0		1173,1356	-10.2	0.0	10	dbSNP_100	60	2738,5862	677.6+/-403.4	436,1866,1998	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	983,2948,2572	GG,GA,AA		31.8372,49.3872,37.7826	,	391/1237,452/1298	99141205	4914,8092	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon12			AATGTCAGCCATG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.1356T>C	10.37:g.99141205A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	176	97	0.551136	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			A|0.622;G|0.378	0.378	strong		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
LMO7	4008	hgsc.bcm.edu	37	13	76397731	76397731	+	Missense_Mutation	SNP	G	G	A	rs4884021	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:76397731G>A	ENST00000321797.8	+	13	2693	c.1972G>A	c.(1972-1974)Gtt>Att	p.V658I	LMO7_ENST00000377534.3_Missense_Mutation_p.V943I|LMO7_ENST00000357063.3_Missense_Mutation_p.V943I|LMO7_ENST00000526202.1_Missense_Mutation_p.V508I|LMO7_ENST00000465261.2_Missense_Mutation_p.V658I|LMO7_ENST00000341547.4_Missense_Mutation_p.V609I			Q8WWI1	LMO7_HUMAN	LIM domain 7	943					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)		TAATGGAGATGTTGAAGACAT	0.378													G|||	1300	0.259585	0.4289	0.2233	5008	,	,		18862	0.2391		0.16	False		,,,				2504	0.18				p.V658I		Atlas-SNP	.											.	LMO7	334	.	0			c.G1972A						PASS	.	G	ILE/VAL,ILE/VAL	1837,2569	536.2+/-374.4	378,1081,744	79.0	78.0	78.0		1825,1972	-1.5	0.0	13	dbSNP_111	78	1411,7189	271.6+/-289.6	93,1225,2982	yes	missense,missense	LMO7	NM_005358.5,NM_015842.2	29,29	471,2306,3726	AA,AG,GG		16.407,41.6931,24.9731	benign,benign	609/1350,658/1386	76397731	3248,9758	2203	4300	6503	SO:0001583	missense	4008	exon12			GGAGATGTTGAAG	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.1972G>A	13.37:g.76397731G>A	ENSP00000317802:p.Val658Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		569|569	0.26053113553113555|0.26053113553113555	222|222	0.45121951219512196|0.45121951219512196	84|84	0.23204419889502761|0.23204419889502761	138|138	0.24125874125874125|0.24125874125874125	125|125	0.16490765171503957|0.16490765171503957	G|G	13.31|13.31	2.199307|2.199307	0.38806|0.38806	0.416931|0.416931	0.16407|0.16407	ENSG00000136153|ENSG00000136153	ENST00000447038|ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261	.|T;T;T;T;T;T;T	.|0.51325	.|0.71;0.71;0.71;0.71;0.71;0.71;0.71	5.94|5.94	-1.53|-1.53	0.08611|0.08611	.|.	.|1.174380	.|0.06004	.|N	.|0.648394	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.33753|0.33753	1.03|1.03	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.13145	.|0.001;0.002;0.002;0.001;0.007	.|B;B;B;B;B	.|0.09377	.|0.002;0.004;0.001;0.002;0.004	T|T	0.45279|0.45279	-0.9272|-0.9272	4|9	.|0.29301	.|T	.|0.29	-0.5|-0.5	4.7068|4.7068	0.12853|0.12853	0.3858:0.0:0.3918:0.2224|0.3858:0.0:0.3918:0.2224	rs4884021;rs59730105;rs4884021|rs4884021;rs59730105;rs4884021	.|508;609;943;658;891	.|E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5	.|.;.;LMO7_HUMAN;.;.	Y|I	566|609;943;943;557;658;508;658	.|ENSP00000342112:V609I;ENSP00000349571:V943I;ENSP00000366757:V943I;ENSP00000366719:V557I;ENSP00000317802:V658I;ENSP00000431129:V508I;ENSP00000433352:V658I	.|ENSP00000317802:V658I	C|V	+|+	2|1	0|0	LMO7|LMO7	75295732|75295732	0.007000|0.007000	0.16637|0.16637	0.007000|0.007000	0.13788|0.13788	0.503000|0.503000	0.33858|0.33858	0.016000|0.016000	0.13377|0.13377	-0.073000|-0.073000	0.12842|0.12842	0.650000|0.650000	0.86243|0.86243	TGT|GTT	G|0.735;A|0.265	0.265	strong		0.378	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
CCDC109B	55013	hgsc.bcm.edu	37	4	110605744	110605744	+	Missense_Mutation	SNP	A	A	T	rs13846	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:110605744A>T	ENST00000394650.4	+	6	891	c.758A>T	c.(757-759)tAc>tTc	p.Y253F		NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	253			Y -> F (in dbSNP:rs13846).		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)		CCAGTTACATACTTCATCACA	0.463													A|||	1183	0.236222	0.059	0.2997	5008	,	,		17111	0.2252		0.2853	False		,,,				2504	0.3916				p.Y253F		Atlas-SNP	.											.	CCDC109B	47	.	0			c.A758T						PASS	.	A	PHE/TYR	399,4007	197.4+/-221.5	23,353,1827	223.0	203.0	210.0		758	3.1	1.0	4	dbSNP_52	210	2567,6033	417.4+/-352.4	385,1797,2118	yes	missense	CCDC109B	NM_017918.4	22	408,2150,3945	TT,TA,AA		29.8488,9.0558,22.8049	possibly-damaging	253/337	110605744	2966,10040	2203	4300	6503	SO:0001583	missense	55013	exon6			TTACATACTTCAT	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.758A>T	4.37:g.110605744A>T	ENSP00000378145:p.Tyr253Phe	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	214	104	0.485981	NM_017918	A8K4Y3|Q6IAC1	Missense_Mutation	SNP	ENST00000394650.4	37	CCDS3683.2	496	0.2271062271062271	29	0.05894308943089431	106	0.292817679558011	140	0.24475524475524477	221	0.29155672823219	A	15.96	2.987493	0.53934	0.090558	0.298488	ENSG00000005059	ENST00000394650	T	0.47177	0.85	5.57	3.09	0.35607	Coiled-coil domain containing protein 109, C-terminal (1);	0.124960	0.56097	N	0.000032	T	0.00012	0.0000	L	0.32530	0.975	0.20196	P	0.9999274501	B	0.31581	0.329	B	0.39840	0.311	T	0.34775	-0.9815	9	0.32370	T	0.25	-4.5468	7.1492	0.25601	0.7938:0.0:0.0714:0.1348	rs13846;rs3172725;rs17512121;rs52804573;rs13846	253	Q9NWR8	C109B_HUMAN	F	253	ENSP00000378145:Y253F	ENSP00000378145:Y253F	Y	+	2	0	CCDC109B	110825193	1.000000	0.71417	0.970000	0.41538	0.994000	0.84299	6.250000	0.72435	0.368000	0.24481	0.482000	0.46254	TAC	A|0.778;T|0.222	0.222	strong		0.463	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2883588	2883588	+	Missense_Mutation	SNP	C	C	A	rs17762452	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2883588C>A	ENST00000254695.8	+	9	694	c.604C>A	c.(604-606)Ctg>Atg	p.L202M	RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.L183M|RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.L187M|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.L202M	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	202			L -> M (in dbSNP:rs17762452).		negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CAGGTCCAAACTGAAGACGGT	0.547													C|||	1488	0.297125	0.1104	0.3112	5008	,	,		1167	0.3313		0.2972	False		,,,				2504	0.5041				p.L202M		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C604A						PASS	.	C	MET/LEU,MET/LEU	530,3480		43,444,1518	87.0	84.0	85.0		559,604	4.0	1.0	17	dbSNP_123	85	2656,5676		444,1768,1954	yes	missense,missense	RAP1GAP2	NM_001100398.1,NM_015085.4	15,15	487,2212,3472	AA,AC,CC		31.8771,13.217,25.8143	benign,benign	187/716,202/731	2883588	3186,9156	2005	4166	6171	SO:0001583	missense	23108	exon9			TCCAAACTGAAGA	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.604C>A	17.37:g.2883588C>A	ENSP00000254695:p.Leu202Met	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	37	CCDS45573.1	594	0.27197802197802196	58	0.11788617886178862	105	0.2900552486187845	204	0.35664335664335667	227	0.2994722955145119	C	11.10	1.540719	0.27563	0.13217	0.318771	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36	4.99	4.02	0.46733	.	0.484343	0.21364	N	0.075741	T	0.00012	0.0000	N	0.08118	0	0.46149	P	0.0011100000000000554	B;B	0.27264	0.173;0.108	B;B	0.34038	0.174;0.084	T	0.03433	-1.1037	9	0.31617	T	0.26	-8.9204	9.9318	0.41528	0.0:0.3971:0.6029:0.0	rs17762452;rs52833255;rs17762452	187;202	Q684P5-2;Q684P5	.;RPGP2_HUMAN	M	202;187;183;202	ENSP00000254695:L202M;ENSP00000389824:L187M;ENSP00000439688:L183M;ENSP00000444890:L202M	ENSP00000254695:L202M	L	+	1	2	RAP1GAP2	2830338	0.999000	0.42202	1.000000	0.80357	0.953000	0.61014	0.540000	0.23191	1.113000	0.41760	0.555000	0.69702	CTG	C|0.737;A|0.263	0.263	strong		0.547	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
TRIML2	205860	hgsc.bcm.edu	37	4	189012728	189012728	+	Silent	SNP	G	G	C	rs2279550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:189012728G>C	ENST00000512729.1	-	7	1337	c.963C>G	c.(961-963)ggC>ggG	p.G321G	TRIML2_ENST00000326754.3_Silent_p.G346G	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	321	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		CAAGGAAAACGCCAACTGTGT	0.517													C|||	3568	0.71246	0.8177	0.5663	5008	,	,		19434	0.9117		0.4642	False		,,,				2504	0.7239				p.G321G		Atlas-SNP	.											.	TRIML2	80	.	0			c.C963G						PASS	.	C		3361,1045	383.5+/-324.9	1279,803,121	141.0	157.0	152.0		963	-4.3	0.9	4	dbSNP_100	152	3933,4667	602.9+/-394.6	918,2097,1285	no	coding-synonymous	TRIML2	NM_173553.1		2197,2900,1406	CC,CG,GG		45.7326,23.7177,43.9182		321/388	189012728	7294,5712	2203	4300	6503	SO:0001819	synonymous_variant	205860	exon7			GAAAACGCCAACT	AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"""SPRY domain containing 6"""						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.963C>G	4.37:g.189012728G>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_173553	B7Z6J6	Silent	SNP	ENST00000512729.1	37	CCDS3850.1																																																																																			G|0.393;C|0.607	0.607	strong		0.517	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553	
NLRP4	147945	hgsc.bcm.edu	37	19	56369593	56369593	+	Silent	SNP	T	T	C	rs421810	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56369593T>C	ENST00000301295.6	+	3	1256	c.834T>C	c.(832-834)gcT>gcC	p.A278A	NLRP4_ENST00000346986.5_Silent_p.A278A|NLRP4_ENST00000587891.1_Silent_p.A203A	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	278	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TGCTCATCGCTATCAAACCCG	0.552													C|||	2661	0.53135	0.4523	0.4841	5008	,	,		16520	0.6657		0.4274	False		,,,				2504	0.6401				p.A278A		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,+2,1	NLRP4	331	1	0			c.T834C						PASS	.	C		1956,2450	618.8+/-393.2	434,1088,681	68.0	75.0	72.0		834	-8.2	0.0	19	dbSNP_80	72	3589,5011	627.5+/-398.0	754,2081,1465	no	coding-synonymous	NLRP4	NM_134444.4		1188,3169,2146	CC,CT,TT		41.7326,44.394,42.6342		278/995	56369593	5545,7461	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			CATCGCTATCAAA	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.834T>C	19.37:g.56369593T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	61	0.635417	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			T|0.545;C|0.454	0.454	strong		0.552	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408315	105408315	+	Silent	SNP	T	T	C	rs28600075	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	204	202	0.990196	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	
LRRC70	100130733	hgsc.bcm.edu	37	5	61876773	61876773	+	Missense_Mutation	SNP	C	C	T	rs115682516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:61876773C>T	ENST00000334994.5	+	2	1747	c.1508C>T	c.(1507-1509)cCg>cTg	p.P503L	IPO11_ENST00000325324.6_Intron|LRRC70_ENST00000448151.2_3'UTR|IPO11_ENST00000409296.3_Intron|IPO11_ENST00000409534.1_Intron	NM_181506.4	NP_852607.3	Q7Z2Q7	LRR70_HUMAN	leucine rich repeat containing 70	503						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)	2						AGTGCTCTACCGAATGATGCT	0.373													C|||	37	0.00738818	0.0008	0.0144	5008	,	,		20850	0.0		0.0239	False		,,,				2504	0.002				p.P503L		Atlas-SNP	.											.	LRRC70	19	.	0			c.C1508T						PASS	.	C	,,LEU/PRO	6,1378		0,6,686	181.0	139.0	152.0		,,1508	4.9	0.9	5	dbSNP_132	152	107,3075		5,97,1489	yes	intron,intron,missense	IPO11,LRRC70	NM_001134779.1,NM_016338.4,NM_181506.4	,,98	5,103,2175	TT,TC,CC		3.3627,0.4335,2.4748	,,possibly-damaging	,,503/623	61876773	113,4453	692	1591	2283	SO:0001583	missense	100130733	exon2			CTCTACCGAATGA		CCDS47218.1	5q12.1	2008-12-18			ENSG00000186105	ENSG00000186105			35155	protein-coding gene	gene with protein product	"""synleurin"""						Standard	NM_181506		Approved	SLRN, LOC100130733	uc011cqs.1	Q7Z2Q7	OTTHUMG00000154401	ENST00000334994.5:c.1508C>T	5.37:g.61876773C>T	ENSP00000399441:p.Pro503Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_181506	Q6ZWI5	Missense_Mutation	SNP	ENST00000334994.5	37	CCDS47218.1	25	0.011446886446886446	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	16	0.021108179419525065	C	14.34	2.507075	0.44558	0.004335	0.033627	ENSG00000186105	ENST00000334994	T	0.51574	0.7	4.87	4.87	0.63330	.	.	.	.	.	T	0.14700	0.0355	N	0.08118	0	0.80722	D	1	D	0.57257	0.979	P	0.47102	0.537	T	0.06991	-1.0796	8	.	.	.	.	18.5515	0.91066	0.0:1.0:0.0:0.0	.	503	Q7Z2Q7	LRR70_HUMAN	L	503	ENSP00000399441:P503L	.	P	+	2	0	LRRC70	61912529	0.054000	0.20591	0.942000	0.38095	0.928000	0.56348	1.551000	0.36233	2.695000	0.91970	0.655000	0.94253	CCG	C|0.988;T|0.012	0.012	strong		0.373	LRRC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335067.3	XR_042302	
LYZL2	119180	hgsc.bcm.edu	37	10	30915078	30915078	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:30915078C>T	ENST00000375318.2	-	3	448	c.392G>A	c.(391-393)cGc>cAc	p.R131H		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	85					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				CAGCTTTCCGCGTCTGCACCA	0.567																																					p.R131H		Atlas-SNP	.											.	LYZL2	33	.	0			c.G392A						PASS	.						173.0	144.0	154.0					10																	30915078		2203	4300	6503	SO:0001583	missense	119180	exon3			TTTCCGCGTCTGC	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.392G>A	10.37:g.30915078C>T	ENSP00000364467:p.Arg131His	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	210	93	0.442857	NM_183058	Q6NZ69	Missense_Mutation	SNP	ENST00000375318.2	37	CCDS7167.2	.	.	.	.	.	.	.	.	.	.	c	6.169	0.399451	0.11696	.	.	ENSG00000151033	ENST00000375318	T	0.69435	-0.4	2.27	-4.53	0.03462	.	1.768140	0.03329	N	0.193126	T	0.43211	0.1237	N	0.04148	-0.265	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39840	-0.9594	10	0.59425	D	0.04	-18.6248	8.4711	0.32986	0.0:0.4079:0.0:0.5921	.	131	Q7Z4W2-2	.	H	131	ENSP00000364467:R131H	ENSP00000364467:R131H	R	-	2	0	LYZL2	30955084	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.771000	0.00779	-1.432000	0.01979	-2.148000	0.00335	CGC	.	.	none		0.567	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058	
TBXA2R	6915	hgsc.bcm.edu	37	19	3595923	3595923	+	Silent	SNP	G	G	A	rs1131882	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3595923G>A	ENST00000375190.4	-	3	1188	c.795C>T	c.(793-795)atC>atT	p.I265I	TBXA2R_ENST00000411851.3_Silent_p.I265I|TBXA2R_ENST00000587717.1_5'Flank|TBXA2R_ENST00000589966.1_Missense_Mutation_p.R136C	NM_001060.5|NM_201636.2	NP_001051.1|NP_963998.2	P21731	TA2R_HUMAN	thromboxane A2 receptor	265					blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|second-messenger-mediated signaling (GO:0019932)|thromboxane A2 signaling pathway (GO:0038193)	acrosomal vesicle (GO:0001669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|thromboxane A2 receptor activity (GO:0004961)	p.I265I(1)		kidney(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)	CTGTCTGGGCGATGAAGACCT	0.697													G|||	1175	0.234625	0.0401	0.2795	5008	,	,		8200	0.5883		0.1471	False		,,,				2504	0.1912				p.I265I		Atlas-SNP	.											TBXA2R,NS,carcinoma,0,1	TBXA2R	31	1	1	Substitution - coding silent(1)	prostate(1)	c.C795T	GRCh37	CM022851	TBXA2R	M	rs1131882	PASS	.	G	,	226,3866		3,220,1823	11.0	12.0	12.0		795,795	-0.8	0.8	19	dbSNP_86	12	1276,7068		105,1066,3001	no	coding-synonymous,coding-synonymous	TBXA2R	NM_001060.5,NM_201636.2	,	108,1286,4824	AA,AG,GG		15.2924,5.523,12.0778	,	265/344,265/408	3595923	1502,10934	2046	4172	6218	SO:0001819	synonymous_variant	6915	exon3			CTGGGCGATGAAG		CCDS42467.1, CCDS54198.1	19p13.3	2014-09-17						"""GPCR / Class A : Prostanoid receptors"""	11608	protein-coding gene	gene with protein product		188070				1825698	Standard	NM_001060		Approved		uc021umv.1	P21731		ENST00000375190.4:c.795C>T	19.37:g.3595923G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_201636	O75228|Q6DK52|Q9UCY1|Q9UCY2	Silent	SNP	ENST00000375190.4	37	CCDS42467.1																																																																																			G|0.733;A|0.267	0.267	strong		0.697	TBXA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453081.2		
MLLT4	4301	hgsc.bcm.edu	37	6	168343838	168343838	+	Silent	SNP	T	T	C	rs1132306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168343838T>C	ENST00000447894.2	+	23	3108	c.3108T>C	c.(3106-3108)taT>taC	p.Y1036Y	MLLT4_ENST00000366806.2_Silent_p.Y1036Y|MLLT4_ENST00000392112.1_Silent_p.Y1020Y|MLLT4_ENST00000351017.4_Silent_p.Y1043Y|MLLT4_ENST00000400822.3_Silent_p.Y1035Y|MLLT4_ENST00000344191.4_Silent_p.Y1036Y|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000392108.3_Silent_p.Y1036Y			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1036	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		TAGGAATCTATGTGAAGTCGG	0.378			T	MLL	AL								T|||	2786	0.55631	0.4138	0.5605	5008	,	,		22196	0.7927		0.4066	False		,,,				2504	0.6564				p.Y1036Y		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.T3108C						PASS	.	T	,	1842,2564	536.8+/-374.6	379,1084,740	179.0	162.0	168.0		3108,3060	-4.9	0.9	6	dbSNP_86	168	3657,4943	525.8+/-380.8	771,2115,1414	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	1150,3199,2154	CC,CT,TT		42.5233,41.8066,42.2805	,	1036/1652,1020/1744	168343838	5499,7507	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon23			AATCTATGTGAAG	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.3108T>C	6.37:g.168343838T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	172	75	0.436047	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				T|0.525;C|0.475	0.475	strong		0.378	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
WDFY4	57705	hgsc.bcm.edu	37	10	50028308	50028308	+	Silent	SNP	C	C	T	rs41283279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50028308C>T	ENST00000325239.5	+	32	5562	c.5535C>T	c.(5533-5535)acC>acT	p.T1845T	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1845						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						CCCGGAACACCAGCAGTCCTG	0.627													C|||	167	0.0333466	0.0197	0.0461	5008	,	,		18569	0.001		0.0855	False		,,,				2504	0.0225				p.T1845T		Atlas-SNP	.											.	WDFY4	205	.	0			c.C5535T						PASS	.	C		47,1337		0,47,645	34.0	40.0	38.0		5535	0.9	0.0	10	dbSNP_127	38	206,2976		4,198,1389	no	coding-synonymous	WDFY4	NM_020945.1		4,245,2034	TT,TC,CC		6.4739,3.396,5.541		1845/3185	50028308	253,4313	692	1591	2283	SO:0001819	synonymous_variant	57705	exon33			GAACACCAGCAGT	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.5535C>T	10.37:g.50028308C>T		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	299	146	0.488294	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	90	0.04120879120879121	5	0.01016260162601626	18	0.049723756906077346	0	0.0	67	0.08839050131926121	C	5.066	0.197894	0.09652	0.03396	0.064739	ENSG00000128815	ENST00000312002;ENST00000374161	.	.	.	5.19	0.93	0.19454	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4899	0.11808	0.0:0.461:0.1611:0.3779	rs41283279;rs61838868	.	.	.	X	936;392	.	.	Q	+	1	0	WDFY4	49698314	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.030000	0.13688	0.270000	0.21984	0.591000	0.81541	CAG	C|0.958;T|0.042	0.042	strong		0.627	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
POLRMT	5442	hgsc.bcm.edu	37	19	621712	621712	+	Silent	SNP	A	A	G	rs2238547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:621712A>G	ENST00000588649.2	-	10	2070	c.1986T>C	c.(1984-1986)gcT>gcC	p.A662A	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	662					gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAGCAGGAAAGCACCAGAGT	0.682													G|||	3105	0.620008	0.7398	0.3905	5008	,	,		11355	0.5813		0.504	False		,,,				2504	0.7802				p.A662A		Atlas-SNP	.											POLRMT,NS,carcinoma,0,1	POLRMT	91	1	0			c.T1986C						PASS	.						16.0	19.0	18.0					19																	621712		2191	4288	6479	SO:0001819	synonymous_variant	5442	exon10			CAGGAAAGCACCA		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.1986T>C	19.37:g.621712A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			A|0.472;G|0.528	0.528	strong		0.682	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
C1orf106	55765	hgsc.bcm.edu	37	1	200867492	200867492	+	Silent	SNP	C	C	G	rs2271018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:200867492C>G	ENST00000367342.4	+	2	419	c.219C>G	c.(217-219)ccC>ccG	p.P73P	C1orf106_ENST00000413687.2_5'UTR	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	73										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GGTGTCCCCCCTCCCTGCTCT	0.522													C|||	993	0.198283	0.115	0.3112	5008	,	,		20525	0.1577		0.2495	False		,,,				2504	0.2198				p.P87P		Atlas-SNP	.											.	C1orf106	59	.	0			c.C261G						PASS	.	C	,	683,3723	286.9+/-279.0	60,563,1580	134.0	127.0	129.0		,219	0.4	0.1	1	dbSNP_100	129	2025,6575	354.2+/-329.4	266,1493,2541	no	utr-5,coding-synonymous	C1orf106	NM_001142569.2,NM_018265.3	,	326,2056,4121	GG,GC,CC		23.5465,15.5016,20.8212	,	,73/664	200867492	2708,10298	2203	4300	6503	SO:0001819	synonymous_variant	55765	exon2			TCCCCCCTCCCTG	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.219C>G	1.37:g.200867492C>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	59	0.572816	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	37																																																																																				C|0.788;G|0.212	0.212	strong		0.522	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
AHNAK2	113146	hgsc.bcm.edu	37	14	105413790	105413790	+	Silent	SNP	G	G	A	rs11848564	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	244	0	0		WXS	Illumina HiSeq	Phase_I	268	268	1	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	
BAIAP3	8938	hgsc.bcm.edu	37	16	1397815	1397815	+	Silent	SNP	C	C	T	rs1132358	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1397815C>T	ENST00000324385.5	+	31	3281	c.3123C>T	c.(3121-3123)gaC>gaT	p.D1041D	BAIAP3_ENST00000397489.1_Silent_p.D1023D|BAIAP3_ENST00000426824.3_Silent_p.D1006D|BAIAP3_ENST00000568887.1_Silent_p.D978D|BAIAP3_ENST00000421665.2_Silent_p.D970D|BAIAP3_ENST00000397488.2_Silent_p.D1023D|BAIAP3_ENST00000562208.1_Silent_p.D983D	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1041	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				TCCCCCTGGACGCCAACGGTG	0.677													C|||	1691	0.33766	0.1868	0.5879	5008	,	,		12493	0.2222		0.4592	False		,,,				2504	0.3579				p.D1041D		Atlas-SNP	.											BAIAP3,NS,carcinoma,0,1	BAIAP3	88	1	0			c.C3123T						PASS	.	C	,,,,	957,3393		114,729,1332	16.0	20.0	19.0		2910,3018,2949,2934,3123	-6.9	0.9	16	dbSNP_86	19	3804,4722		880,2044,1339	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	,,,,	994,2773,2671	TT,TC,CC		44.6165,22.0,36.9758	,,,,	970/1117,1006/1153,983/1130,978/1125,1041/1188	1397815	4761,8115	2175	4263	6438	SO:0001819	synonymous_variant	8938	exon31			CCTGGACGCCAAC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.3123C>T	16.37:g.1397815C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	37	CCDS10434.1																																																																																			C|0.656;T|0.344	0.344	strong		0.677	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
NUP188	23511	hgsc.bcm.edu	37	9	131767668	131767668	+	Silent	SNP	A	A	C	rs2287363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	52	0	0		WXS	Illumina HiSeq	Phase_I	55	55	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		
OR1S1	219959	hgsc.bcm.edu	37	11	57983194	57983194	+	Splice_Site	SNP	A	A	G	rs7103033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57983194A>G	ENST00000309433.6	+	1	978	c.978A>G	c.(976-978)tgA>tgG	p.*326W		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	0						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				CTTCCCTTTGATGCCCTGGAC	0.413													A|||	2171	0.433506	0.2224	0.428	5008	,	,		20118	0.7619		0.3141	False		,,,				2504	0.5072				p.X326W		Atlas-SNP	.											.	OR1S1	139	.	0			c.A978G						PASS	.	A	TRP/stop	1064,3338	386.5+/-326.1	126,812,1263	132.0	132.0	132.0		978	2.6	0.0	11	dbSNP_116	132	2806,5784	442.8+/-360.2	476,1854,1965	no	stop-lost	OR1S1	NM_001004458.1		602,2666,3228	GG,GA,AA		32.6659,24.1708,29.7876		326/326	57983194	3870,9122	2201	4295	6496	SO:0001630	splice_region_variant	219959	exon1			CCTTTGATGCCCT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.975+1A>G	11.37:g.57983194A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	903	0.41346153846153844	104	0.21138211382113822	150	0.4143646408839779	412	0.7202797202797203	237	0.31266490765171506	A	9.164	1.019495	0.19355	0.241708	0.326659	ENSG00000172774	ENST00000309433	.	.	.	2.61	2.61	0.31194	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0192	0.24904	1.0:0.0:0.0:0.0	rs7103033;rs7103033	.	.	.	W	326	.	.	X	+	3	0	OR1S1	57739770	0.001000	0.12720	0.014000	0.15608	0.012000	0.07955	0.032000	0.13732	1.200000	0.43188	0.392000	0.25879	TGA	A|0.672;G|0.328	0.328	strong		0.413	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	Nonstop_Mutation
WDR11	55717	hgsc.bcm.edu	37	10	122624679	122624679	+	Silent	SNP	G	G	A	rs10886789	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:122624679G>A	ENST00000263461.6	+	6	1080	c.834G>A	c.(832-834)acG>acA	p.T278T		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.T278T(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						TGAATCAGACGGTGGGTGTGA	0.363													G|||	1617	0.322883	0.171	0.4063	5008	,	,		17443	0.4177		0.333	False		,,,				2504	0.3609				p.T278T		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.G834A						scavenged	.	G		792,3614	320.2+/-296.5	74,644,1485	135.0	130.0	132.0		834	-2.8	1.0	10	dbSNP_120	132	2886,5714	452.3+/-362.9	468,1950,1882	no	coding-synonymous	WDR11	NM_018117.11		542,2594,3367	AA,AG,GG		33.5581,17.9755,28.2793		278/1225	122624679	3678,9328	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon6			TCAGACGGTGGGT	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.834G>A	10.37:g.122624679G>A		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	148	75	0.506757	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			G|0.708;A|0.292	0.292	strong		0.363	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
AHNAK2	113146	hgsc.bcm.edu	37	14	105418391	105418391	+	Missense_Mutation	SNP	C	C	T	rs11625007	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105418391C>T	ENST00000333244.5	-	7	3516	c.3397G>A	c.(3397-3399)Gtc>Atc	p.V1133I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1133						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)			GGGGCCTCGACGTCCACCTCC	0.637																																					p.V1133I		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,3	AHNAK2	719	3	0			c.G3397A						PASS	.	T	ILE/VAL	1510,2378		302,906,736	132.0	156.0	148.0		3397	-7.7	0.0	14	dbSNP_120	148	4406,3882		1187,2032,925	no	missense	AHNAK2	NM_138420.2	29	1489,2938,1661	TT,TC,CC		46.8388,38.8374,48.5874	benign	1133/5796	105418391	5916,6260	1944	4144	6088	SO:0001583	missense	113146	exon7			CCTCGACGTCCAC	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.3397G>A	14.37:g.105418391C>T	ENSP00000353114:p.Val1133Ile	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	896	0.41025641025641024	181	0.3678861788617886	144	0.39779005524861877	182	0.3181818181818182	389	0.5131926121372031	t	4.059	0.008661	0.07912	0.388374	0.531612	ENSG00000185567	ENST00000333244	T	0.00808	5.67	3.87	-7.74	0.01241	.	.	.	.	.	T	0.00012	0.0000	N	0.04820	-0.15	0.80722	P	0.0	B	0.16396	0.017	B	0.11329	0.006	T	0.34378	-0.9831	8	0.10111	T	0.7	.	4.0848	0.09942	0.0878:0.1485:0.0884:0.6753	rs55658674;rs61996050	1133	Q8IVF2	AHNK2_HUMAN	I	1133	ENSP00000353114:V1133I	ENSP00000353114:V1133I	V	-	1	0	AHNAK2	104489436	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-6.041000	0.00084	-1.837000	0.01189	-2.017000	0.00434	GTC	C|0.570;T|0.430	0.430	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
FLT1	2321	hgsc.bcm.edu	37	13	28893642	28893642	+	Silent	SNP	A	A	G	rs2296189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28893642A>G	ENST00000282397.4	-	24	3455	c.3204T>C	c.(3202-3204)ccT>ccC	p.P1068P	FLT1_ENST00000543394.1_Silent_p.P91P|FLT1_ENST00000540678.1_Silent_p.P286P	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1068	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGATAGATTCAGGAGCCATCC	0.478													A|||	1217	0.243011	0.2806	0.1124	5008	,	,		19391	0.1825		0.169	False		,,,				2504	0.4233				p.P1068P		Atlas-SNP	.											.	FLT1	393	.	0			c.T3204C						PASS	.	A		1161,3245	408.6+/-334.7	155,851,1197	67.0	60.0	62.0		3204	-11.0	0.7	13	dbSNP_100	62	1624,6976	298.2+/-303.8	160,1304,2836	no	coding-synonymous	FLT1	NM_002019.4		315,2155,4033	GG,GA,AA		18.8837,26.3504,21.4132		1068/1339	28893642	2785,10221	2203	4300	6503	SO:0001819	synonymous_variant	2321	exon24			AGATTCAGGAGCC	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.3204T>C	13.37:g.28893642A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																			A|0.792;G|0.208	0.208	strong		0.478	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
OR1S2	219958	hgsc.bcm.edu	37	11	57970967	57970967	+	Silent	SNP	G	G	A	rs138762515		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57970967G>A	ENST00000302592.6	-	1	686	c.687C>T	c.(685-687)ttC>ttT	p.F229F		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F229F(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				AGACATAGGAGAAGAAGATGA	0.438																																					p.F229F		Atlas-SNP	.											OR1S2,NS,carcinoma,0,2	OR1S2	119	2	1	Substitution - coding silent(1)	kidney(1)	c.C687T						scavenged	.						154.0	129.0	138.0					11																	57970967		2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			ATAGGAGAAGAAG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.687C>T	11.37:g.57970967G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	137	9	0.0656934	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.999;A|0.001	0.001	weak		0.438	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
FLG	2312	hgsc.bcm.edu	37	1	152280471	152280471	+	Missense_Mutation	SNP	C	C	G	rs78179835		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152280471C>G	ENST00000368799.1	-	3	6926	c.6891G>C	c.(6889-6891)gaG>gaC	p.E2297D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2297	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCTGGAGCTCTCTGCAGAGT	0.547									Ichthyosis																												p.E2297D		Atlas-SNP	.											.	FLG	900	.	0			c.G6891C						PASS	.	C	ASP/GLU	403,4003		10,383,1810	272.0	285.0	281.0		6891	-4.0	0.0	1	dbSNP_131	281	921,7679		0,921,3379	no	missense	FLG	NM_002016.1	45	10,1304,5189	GG,GC,CC		10.7093,9.1466,10.1799	benign	2297/4062	152280471	1324,11682	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGAGCTCTCTGCA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6891G>C	1.37:g.152280471C>G	ENSP00000357789:p.Glu2297Asp	Somatic	506	1	0.00197628		WXS	Illumina HiSeq	Phase_I	797	219	0.27478	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	
ACTL7B	10880	hgsc.bcm.edu	37	9	111618209	111618209	+	Start_Codon_SNP	SNP	A	A	G	rs17728850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:111618209A>G	ENST00000374667.3	-	1	1030	c.2T>C	c.(1-3)aTg>aCg	p.M1T		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	1						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CCTTGTCGCCATCTGCCTCCC	0.657													A|||	350	0.0698882	0.0651	0.1354	5008	,	,		17466	0.0		0.1074	False		,,,				2504	0.0634				p.M1T		Atlas-SNP	.											.	ACTL7B	57	.	0			c.T2C						PASS	.	A	THR/MET	306,4100	165.4+/-196.9	13,280,1910	50.0	50.0	50.0		2	4.0	1.0	9	dbSNP_123	50	888,7712	200.2+/-244.0	47,794,3459	yes	missense	ACTL7B	NM_006686.3	81	60,1074,5369	GG,GA,AA		10.3256,6.9451,9.1804	benign	1/416	111618209	1194,11812	2203	4300	6503	SO:0001582	initiator_codon_variant	10880	exon1			GTCGCCATCTGCC	BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.2T>C	9.37:g.111618209A>G	ENSP00000363799:p.Met1Thr	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_006686	B2R9Q2|Q5JSV1	Missense_Mutation	SNP	ENST00000374667.3	37	CCDS6771.1	178	0.0815018315018315	48	0.0975609756097561	44	0.12154696132596685	0	0.0	86	0.11345646437994723	A	11.81	1.748987	0.30955	0.069451	0.103256	ENSG00000148156	ENST00000374667	D	0.94931	-3.56	3.99	3.99	0.46301	.	0.556195	0.13318	N	0.396957	T	0.33498	0.0865	.	.	.	0.37717	P	0.075206	P	0.50156	0.932	P	0.55391	0.775	T	0.68788	-0.5316	8	0.87932	D	0	.	9.2214	0.37379	1.0:0.0:0.0:0.0	rs17728850;rs17728850	1	Q9Y614	ACL7B_HUMAN	T	1	ENSP00000363799:M1T	ENSP00000363799:M1T	M	-	2	0	ACTL7B	110658030	0.119000	0.22226	1.000000	0.80357	0.155000	0.21991	1.905000	0.39878	1.685000	0.51034	0.459000	0.35465	ATG	A|0.915;G|0.085	0.085	strong		0.657	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	Missense_Mutation
SMARCA1	6594	hgsc.bcm.edu	37	X	128582381	128582381	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:128582381C>T	ENST00000371122.4	-	24	3199	c.3070G>A	c.(3070-3072)Gag>Aag	p.E1024K	SMARCA1_ENST00000371123.1_Missense_Mutation_p.E1012K|SMARCA1_ENST00000371121.3_Missense_Mutation_p.E1012K	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	1024					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						TTTTCTTTCTCAATCAATGAA	0.323																																					p.E1024K		Atlas-SNP	.											.	SMARCA1	126	.	0			c.G3070A						PASS	.						125.0	117.0	120.0					X																	128582381		2203	4298	6501	SO:0001583	missense	6594	exon24			CTTTCTCAATCAA	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.3070G>A	X.37:g.128582381C>T	ENSP00000360163:p.Glu1024Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	120	7	0.0583333	NM_003069	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.645013	0.67358	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91792	-2.91;-2.91;-2.9;-2.89	5.87	5.87	0.94306	SLIDE (1);Homeodomain-like (1);	0.000000	0.64402	D	0.000009	D	0.96436	0.8837	M	0.84773	2.715	0.80722	D	1	D;D;D;D	0.76494	0.992;0.999;0.99;0.992	D;D;D;D	0.79784	0.979;0.993;0.964;0.979	D	0.95323	0.8422	10	0.35671	T	0.21	-17.3926	19.3889	0.94570	0.0:1.0:0.0:0.0	.	1003;1024;1012;1024	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	K	1012;1012;1024;1003	ENSP00000360162:E1012K;ENSP00000360164:E1012K;ENSP00000360163:E1024K;ENSP00000404275:E1003K	ENSP00000360162:E1012K	E	-	1	0	SMARCA1	128410062	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.177000	0.71961	2.618000	0.88619	0.600000	0.82982	GAG	.	.	none		0.323	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069	
MIOS	54468	hgsc.bcm.edu	37	7	7613039	7613039	+	Silent	SNP	C	C	T	rs61744397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:7613039C>T	ENST00000340080.4	+	4	1354	c.933C>T	c.(931-933)ccC>ccT	p.P311P	MIOS_ENST00000405785.1_Silent_p.P311P	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	311						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AAACTGAACCCACAATAATTG	0.403													C|||	498	0.0994409	0.0968	0.0893	5008	,	,		22630	0.0506		0.1143	False		,,,				2504	0.1452				p.P311P		Atlas-SNP	.											.	MIOS	68	.	0			c.C933T						PASS	.	C		281,3595		13,255,1670	116.0	111.0	113.0		933	1.6	1.0	7	dbSNP_129	113	883,7391		49,785,3303	no	coding-synonymous	MIOS	NM_019005.3		62,1040,4973	TT,TC,CC		10.672,7.2497,9.5802		311/876	7613039	1164,10986	1938	4137	6075	SO:0001819	synonymous_variant	54468	exon4			TGAACCCACAATA		CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"""WD repeat-containing protein mio"""	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.933C>T	7.37:g.7613039C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_019005	B2RTV6|O75216|Q7L551|Q9H092	Silent	SNP	ENST00000340080.4	37	CCDS43554.1																																																																																			C|0.902;T|0.098	0.098	strong		0.403	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005	
ACTL9	284382	hgsc.bcm.edu	37	19	8808942	8808942	+	Missense_Mutation	SNP	A	A	G	rs2340550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8808942A>G	ENST00000324436.3	-	1	230	c.110T>C	c.(109-111)tTc>tCc	p.F37S		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	37			F -> S (in dbSNP:rs2340550). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						CATGCCGGGGAAGTCCCGCTG	0.652													G|||	3965	0.791733	0.7995	0.7233	5008	,	,		13976	0.874		0.7117	False		,,,				2504	0.8272				p.F37S		Atlas-SNP	.											.	ACTL9	74	.	0			c.T110C						PASS	.	G	SER/PHE	3460,942		1391,678,132	39.0	50.0	46.0		110	2.1	0.0	19	dbSNP_100	46	5829,2751		1997,1835,458	yes	missense	ACTL9	NM_178525.3	155	3388,2513,590	GG,GA,AA		32.0629,21.3994,28.4471	benign	37/417	8808942	9289,3693	2201	4290	6491	SO:0001583	missense	284382	exon1			CCGGGGAAGTCCC		CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.110T>C	19.37:g.8808942A>G	ENSP00000316674:p.Phe37Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	147	66	0.44898	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	1696	0.7765567765567766	397	0.806910569105691	266	0.7348066298342542	493	0.8618881118881119	540	0.712401055408971	G	0.649	-0.810376	0.02798	0.786006	0.679371	ENSG00000181786	ENST00000324436	D	0.94330	-3.4	3.12	2.06	0.26882	.	2.076500	0.02918	N	0.137614	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	0.51466	-0.8702	9	0.62326	D	0.03	.	6.0629	0.19848	0.113:0.192:0.695:0.0	rs2340550;rs17398967;rs17856708;rs17857309;rs60008435;rs2340550	37	Q8TC94	ACTL9_HUMAN	S	37	ENSP00000316674:F37S	ENSP00000316674:F37S	F	-	2	0	ACTL9	8669942	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.444000	0.21661	0.347000	0.23924	-0.355000	0.07637	TTC	A|0.267;G|0.733	0.733	strong		0.652	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525	
UBP1	7342	hgsc.bcm.edu	37	3	33434831	33434831	+	Silent	SNP	G	G	A	rs2293250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:33434831G>A	ENST00000283629.3	-	14	2035	c.1506C>T	c.(1504-1506)acC>acT	p.T502T	UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Silent_p.T466T|UBP1_ENST00000283628.5_Silent_p.T502T	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	502					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						TGTGAATACCGGTGGGACCCT	0.368													A|||	2705	0.540136	0.5552	0.6326	5008	,	,		16560	0.6141		0.4732	False		,,,				2504	0.4468				p.T502T		Atlas-SNP	.											.	UBP1	42	.	0			c.C1506T						PASS	.	A	,,	2543,1863	540.7+/-375.6	712,1119,372	79.0	79.0	79.0		1398,1506,1506	-2.0	1.0	3	dbSNP_100	79	3856,4744	609.5+/-395.5	848,2160,1292	no	coding-synonymous,coding-synonymous,coding-synonymous	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	,,	1560,3279,1664	AA,AG,GG		44.8372,42.2833,49.2004	,,	466/505,502/541,502/541	33434831	6399,6607	2203	4300	6503	SO:0001819	synonymous_variant	7342	exon14			AATACCGGTGGGA	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.1506C>T	3.37:g.33434831G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_014517	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Silent	SNP	ENST00000283629.3	37	CCDS2659.1																																																																																			G|0.490;N|0.001	.	strong		0.368	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517	
PTK2B	2185	hgsc.bcm.edu	37	8	27301725	27301725	+	Silent	SNP	C	C	G	rs1128435	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:27301725C>G	ENST00000397501.1	+	28	2959	c.2151C>G	c.(2149-2151)ccC>ccG	p.P717P	PTK2B_ENST00000346049.5_Silent_p.P717P|PTK2B_ENST00000517339.1_Silent_p.P717P|PTK2B_ENST00000397497.4_Silent_p.P463P|PTK2B_ENST00000544172.1_Silent_p.P717P|PTK2B_ENST00000338238.4_Silent_p.P717P|PTK2B_ENST00000420218.2_Silent_p.P717P	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	717	Pro-rich.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|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 cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	CTCTCCAGCCCAGCCGACCTA	0.532													C|||	520	0.103834	0.0325	0.0648	5008	,	,		20200	0.1419		0.1014	False		,,,				2504	0.1912				p.P717P		Atlas-SNP	.											PTK2B_ENST00000544172,bladder,carcinoma,+1,3	PTK2B	304	3	0			c.C2151G						PASS	.	C	,,,	162,4244	108.6+/-147.0	3,156,2044	128.0	113.0	118.0		2151,2151,2151,2151	4.3	1.0	8	dbSNP_86	118	926,7674	205.2+/-247.7	57,812,3431	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	60,968,5475	GG,GC,CC		10.7674,3.6768,8.3654	,,,	717/1010,717/1010,717/968,717/1010	27301725	1088,11918	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon28			CCAGCCCAGCCGA	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.2151C>G	8.37:g.27301725C>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	94	60	0.638298	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			C|0.913;G|0.087	0.087	strong		0.532	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
NIPAL1	152519	hgsc.bcm.edu	37	4	48037926	48037926	+	Missense_Mutation	SNP	A	A	G	rs13116684	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:48037926A>G	ENST00000295461.5	+	6	1036	c.970A>G	c.(970-972)Atc>Gtc	p.I324V		NM_207330.1	NP_997213.1	Q6NVV3	NIPA3_HUMAN	NIPA-like domain containing 1	324			I -> V (in dbSNP:rs13116684).			integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|large_intestine(1)|lung(3)|skin(2)	8						TTGCTCTGCCATCTTATTCCA	0.413													A|||	1022	0.204073	0.2262	0.1916	5008	,	,		9725	0.1637		0.2187	False		,,,				2504	0.2096				p.I324V		Atlas-SNP	.											.	NIPAL1	29	.	0			c.A970G						PASS	.	A	VAL/ILE	898,3508	346.9+/-309.2	84,730,1389	166.0	152.0	157.0		970	2.2	1.0	4	dbSNP_121	157	1867,6733	333.7+/-320.7	208,1451,2641	yes	missense	NIPAL1	NM_207330.1	29	292,2181,4030	GG,GA,AA		21.7093,20.3813,21.2594	probably-damaging	324/411	48037926	2765,10241	2203	4300	6503	SO:0001583	missense	152519	exon6			TCTGCCATCTTAT	BC067881	CCDS3479.1	4p12	2009-03-24		2009-03-24	ENSG00000163293	ENSG00000163293			27194	protein-coding gene	gene with protein product				NPAL1			Standard	NM_207330		Approved	DKFZp686A06115	uc003gxw.3	Q6NVV3	OTTHUMG00000128622	ENST00000295461.5:c.970A>G	4.37:g.48037926A>G	ENSP00000295461:p.Ile324Val	Somatic	299	1	0.00334448		WXS	Illumina HiSeq	Phase_I	250	149	0.596	NM_207330	B3KTB0|Q68DA9	Missense_Mutation	SNP	ENST00000295461.5	37	CCDS3479.1	461	0.21108058608058608	119	0.241869918699187	72	0.19889502762430938	110	0.19230769230769232	160	0.21108179419525067	A	13.45	2.240068	0.39598	0.203813	0.217093	ENSG00000163293	ENST00000295461	D	0.92805	-3.11	5.96	2.24	0.28232	.	0.063928	0.64402	N	0.000005	T	0.00412	0.0013	M	0.74258	2.255	0.25630	P	0.9863127	D	0.64830	0.994	D	0.71656	0.974	T	0.00303	-1.1833	8	.	.	.	.	12.2212	0.54435	0.8724:0.0:0.1276:0.0	rs13116684;rs13116684	324	Q6NVV3	NIPA3_HUMAN	V	324	ENSP00000295461:I324V	.	I	+	1	0	NIPAL1	47732683	1.000000	0.71417	0.985000	0.45067	0.095000	0.18619	6.085000	0.71343	0.168000	0.19655	-1.122000	0.02009	ATC	A|0.792;G|0.208	0.208	strong		0.413	NIPAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250491.4	NM_207330	
FUT2	2524	hgsc.bcm.edu	37	19	49207206	49207206	+	Silent	SNP	A	A	G	rs485186	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49207206A>G	ENST00000425340.2	+	2	1110	c.993A>G	c.(991-993)acA>acG	p.T331T	FUT2_ENST00000391876.4_Silent_p.T331T	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	331					carbohydrate metabolic process (GO:0005975)|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)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		CGGAGTGGACAGGGATTGCCG	0.567													G|||	1653	0.330072	0.497	0.3501	5008	,	,		19175	0.004		0.4692	False		,,,				2504	0.2832				p.T331T		Atlas-SNP	.											.	FUT2	30	.	0			c.A993G						PASS	.	G	,	2242,2164	582.4+/-385.6	576,1090,537	59.0	57.0	58.0		993,993	-1.1	0.0	19	dbSNP_83	58	4463,4137	561.2+/-387.7	1170,2123,1007	no	coding-synonymous,coding-synonymous	FUT2	NM_000511.5,NM_001097638.2	,	1746,3213,1544	GG,GA,AA		48.1047,49.1148,48.4469	,	331/344,331/344	49207206	6705,6301	2203	4300	6503	SO:0001819	synonymous_variant	2524	exon2			GTGGACAGGGATT		CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"""Fucosyltransferases"""	4013	protein-coding gene	gene with protein product	"""alpha (1,2) fucosyltransferase"", ""galactoside 2-alpha-L-fucosyltransferase 2"", ""GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2"", ""alpha(1,2)FT2"", ""secretor factor"", ""secretor blood group alpha-2-fucosyltransferase"""	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.993A>G	19.37:g.49207206A>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	170	79	0.464706	NM_001097638	Q0VAG5|Q14338|Q5D0G2	Silent	SNP	ENST00000425340.2	37	CCDS33069.1																																																																																			A|0.553;G|0.447	0.447	strong		0.567	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511	
APOL5	80831	hgsc.bcm.edu	37	22	36122811	36122811	+	Silent	SNP	G	G	A	rs4821441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36122811G>A	ENST00000249044.2	+	3	696	c.696G>A	c.(694-696)aaG>aaA	p.K232K		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	232					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						GTGTTAATAAGTGTGTAAAAG	0.473													G|||	260	0.0519169	0.0923	0.0331	5008	,	,		19611	0.0		0.0656	False		,,,				2504	0.0501				p.K232K		Atlas-SNP	.											.	APOL5	45	.	0			c.G696A						PASS	.	G		316,4090	169.4+/-200.1	11,294,1898	137.0	146.0	143.0		696	-5.9	0.0	22	dbSNP_111	143	487,8113	141.1+/-197.5	19,449,3832	no	coding-synonymous	APOL5	NM_030642.1		30,743,5730	AA,AG,GG		5.6628,7.172,6.1741		232/434	36122811	803,12203	2203	4300	6503	SO:0001819	synonymous_variant	80831	exon3			TAATAAGTGTGTA	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.696G>A	22.37:g.36122811G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	203	76	0.374384	NM_030642	Q5TFL9|Q9UGW5	Silent	SNP	ENST00000249044.2	37	CCDS13920.1																																																																																			G|0.940;A|0.060	0.060	strong		0.473	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
RASGRP2	10235	hgsc.bcm.edu	37	11	64496357	64496357	+	Silent	SNP	G	G	T	rs2230414	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:64496357G>T	ENST00000354024.3	-	15	2001	c.1749C>A	c.(1747-1749)ggC>ggA	p.G583G	RASGRP2_ENST00000394432.3_Silent_p.G583G|RASGRP2_ENST00000377497.3_Silent_p.G583G|RASGRP2_ENST00000377494.1_Silent_p.G583G	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	583					blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGCCTCGCCTGCCAGGGCGGG	0.642													G|||	931	0.185903	0.118	0.3098	5008	,	,		16741	0.3284		0.0835	False		,,,				2504	0.1483				p.G583G		Atlas-SNP	.											.	RASGRP2	48	.	0			c.C1749A						PASS	.	G	,,	510,3892	233.6+/-246.7	32,446,1723	45.0	42.0	43.0		1749,1749,1749	-0.5	1.0	11	dbSNP_98	43	835,7759	191.4+/-237.6	40,755,3502	yes	coding-synonymous,coding-synonymous,coding-synonymous	RASGRP2	NM_001098670.1,NM_001098671.1,NM_153819.1	,,	72,1201,5225	TT,TG,GG		9.7161,11.5856,10.3493	,,	583/610,583/610,583/610	64496357	1345,11651	2201	4297	6498	SO:0001819	synonymous_variant	10235	exon15			TCGCCTGCCAGGG	U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"""EF-hand domain containing"""	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.1749C>A	11.37:g.64496357G>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_001098671	A6NDC7|O00538|Q9UL65	Silent	SNP	ENST00000354024.3	37	CCDS31598.1																																																																																			G|0.850;T|0.150	0.150	strong		0.642	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142062.1	NM_153819	
FAM26F	441168	hgsc.bcm.edu	37	6	116784797	116784797	+	Missense_Mutation	SNP	G	G	A	rs11544160	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:116784797G>A	ENST00000368605.1	+	3	972	c.877G>A	c.(877-879)Gaa>Aaa	p.E293K	RP1-93H18.6_ENST00000476099.1_RNA|FAM26F_ENST00000368606.3_Missense_Mutation_p.E121K	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	293			E -> K (in dbSNP:rs11544160).		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)		CAGGTCTACTGAAGGAGATAC	0.378													G|||	188	0.0375399	0.0023	0.0476	5008	,	,		17648	0.0099		0.0716	False		,,,				2504	0.0716				p.S293T		Atlas-SNP	.											.	FAM26F	12	.	0			c.T877A						PASS	.	G	LYS/GLU	67,4339	61.1+/-98.1	0,67,2136	169.0	180.0	176.0		877	1.8	0.0	6	dbSNP_120	176	683,7917	170.9+/-221.9	27,629,3644	yes	missense	FAM26F	NM_001010919.1	56	27,696,5780	AA,AG,GG		7.9419,1.5207,5.7666	probably-damaging	293/316	116784797	750,12256	2203	4300	6503	SO:0001583	missense	441168	exon3			TCTACTGAAGGAG	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.877G>A	6.37:g.116784797G>A	ENSP00000357594:p.Glu293Lys	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	187	102	0.545455	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	84	0.038461538461538464	0	0.0	19	0.052486187845303865	6	0.01048951048951049	59	0.07783641160949868	G	12.21	1.868797	0.32977	0.015207	0.079419	ENSG00000188820	ENST00000368606;ENST00000368605;ENST00000368604	T;T;T	0.34667	1.37;2.42;1.35	4.89	1.77	0.24775	.	1.107720	0.07034	N	0.828925	T	0.21550	0.0519	M	0.77313	2.365	0.09310	N	1	B	0.32653	0.379	B	0.28553	0.091	T	0.38308	-0.9667	10	0.59425	D	0.04	-0.5113	9.7317	0.40366	0.2707:0.0:0.7293:0.0	rs11544160;rs60777515;rs11544160	293	Q5R3K3	FA26F_HUMAN	K	121;293;136	ENSP00000357595:E121K;ENSP00000357594:E293K;ENSP00000357593:E136K	ENSP00000357593:E136K	E	+	1	0	FAM26F	116891490	0.001000	0.12720	0.003000	0.11579	0.002000	0.02628	0.322000	0.19576	0.591000	0.29711	0.655000	0.94253	GAA	G|0.951;A|0.049	0.049	strong		0.378	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919	
SPPL2C	162540	hgsc.bcm.edu	37	17	43924130	43924130	+	Missense_Mutation	SNP	G	G	A	rs12373139	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43924130G>A	ENST00000329196.5	+	1	1875	c.1858G>A	c.(1858-1860)Ggg>Agg	p.G620R	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	620			G -> R (in dbSNP:rs12373139).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CATCCCCCCTGGGGCCTCGGA	0.612													G|||	431	0.0860623	0.0151	0.1571	5008	,	,		19919	0.001		0.2396	False		,,,				2504	0.0613				p.G620R		Atlas-SNP	.											.	.	.	.	0			c.G1858A						PASS	.	G	ARG/GLY	201,4205	126.1+/-163.2	5,191,2007	77.0	68.0	71.0		1858	-2.5	0.0	17	dbSNP_120	71	1928,6672	340.7+/-323.7	221,1486,2593	yes	missense	IMP5	NM_175882.2	125	226,1677,4600	AA,AG,GG		22.4186,4.562,16.3694	possibly-damaging	620/685	43924130	2129,10877	2203	4300	6503	SO:0001583	missense	162540	exon1			CCCCCTGGGGCCT		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1858G>A	17.37:g.43924130G>A	ENSP00000332488:p.Gly620Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	3.902	-0.021756	0.07634	0.04562	0.224186	ENSG00000185294	ENST00000329196	T	0.04234	3.67	4.79	-2.5	0.06384	.	1.115670	0.06913	N	0.808070	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.48514	-0.9029	9	0.56958	D	0.05	-35.782	5.2551	0.15542	0.5093:0.1541:0.3366:0.0	rs12373139;rs60853039;rs12373139	620	Q8IUH8	IMP5_HUMAN	R	620	ENSP00000332488:G620R	ENSP00000332488:G620R	G	+	1	0	AC217771.1	41279910	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.187000	0.09656	-0.516000	0.06470	-0.165000	0.13383	GGG	G|0.856;A|0.144	0.144	strong		0.612	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
ZNF160	90338	hgsc.bcm.edu	37	19	53572917	53572917	+	Silent	SNP	G	G	A	rs10407463	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53572917G>A	ENST00000429604.1	-	7	1285	c.870C>T	c.(868-870)tgC>tgT	p.C290C	ZNF160_ENST00000599056.1_Silent_p.C290C|ZNF160_ENST00000418871.1_Silent_p.C290C|ZNF160_ENST00000601421.1_Silent_p.C254C	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	290					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		AGGTTTTGCCGCACTCACTGC	0.408													g|||	694	0.138578	0.2511	0.1167	5008	,	,		21331	0.0526		0.1481	False		,,,				2504	0.0808				p.C290C		Atlas-SNP	.											.	ZNF160	75	.	0			c.C870T						PASS	.	A	,,	997,3409	371.2+/-319.9	114,769,1320	150.0	142.0	144.0		870,870,870	-2.9	0.0	19	dbSNP_119	144	1342,7258	262.4+/-284.4	104,1134,3062	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF160	NM_001102603.1,NM_033288.3,NM_198893.2	,,	218,1903,4382	AA,AG,GG		15.6047,22.6282,17.984	,,	290/819,290/819,290/819	53572917	2339,10667	2203	4300	6503	SO:0001819	synonymous_variant	90338	exon7			TTTGCCGCACTCA	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.870C>T	19.37:g.53572917G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Silent	SNP	ENST00000429604.1	37	CCDS12859.1																																																																																			G|0.843;A|0.157	0.157	strong		0.408	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288	
WDR55	54853	hgsc.bcm.edu	37	5	140048544	140048544	+	Missense_Mutation	SNP	C	C	T	rs2286394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140048544C>T	ENST00000358337.5	+	5	866	c.629C>T	c.(628-630)tCt>tTt	p.S210F	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	210			S -> F (in dbSNP:rs2286394).		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)			GAACCTCAGTCTGGGGACCTG	0.542													C|||	1004	0.200479	0.0545	0.2161	5008	,	,		19980	0.3016		0.2396	False		,,,				2504	0.2423				p.S210F		Atlas-SNP	.											.	WDR55	27	.	0			c.C629T						PASS	.	C	PHE/SER	336,4070	177.3+/-206.3	11,314,1878	81.0	76.0	77.0		629	3.5	1.0	5	dbSNP_100	77	2014,6586	353.0+/-328.9	241,1532,2527	yes	missense	WDR55	NM_017706.4	155	252,1846,4405	TT,TC,CC		23.4186,7.626,18.0686	possibly-damaging	210/384	140048544	2350,10656	2203	4300	6503	SO:0001583	missense	54853	exon5			CTCAGTCTGGGGA	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.629C>T	5.37:g.140048544C>T	ENSP00000351100:p.Ser210Phe	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_017706	Q9NXK4	Missense_Mutation	SNP	ENST00000358337.5	37	CCDS4235.1	470	0.21520146520146521	34	0.06910569105691057	87	0.24033149171270718	162	0.28321678321678323	187	0.24670184696569922	C	16.24	3.066190	0.55539	0.07626	0.234186	ENSG00000120314	ENST00000358337	T	0.31510	1.49	5.44	3.55	0.40652	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.415951	0.22830	N	0.055103	T	0.00012	0.0000	L	0.44542	1.39	0.31277	P	0.691004	D;D	0.60575	0.967;0.988	P;P	0.54664	0.689;0.758	T	0.22695	-1.0209	9	0.72032	D	0.01	-9.5498	5.3458	0.16008	0.1201:0.5804:0.2139:0.0856	rs2286394;rs60780836;rs2286394	49;210	G3V1J0;Q9H6Y2	.;WDR55_HUMAN	F	210	ENSP00000351100:S210F	ENSP00000351100:S210F	S	+	2	0	WDR55	140028728	0.955000	0.32602	0.999000	0.59377	0.865000	0.49528	0.943000	0.29030	1.290000	0.44636	0.467000	0.42956	TCT	C|0.806;T|0.194	0.194	strong		0.542	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706	
KIAA1109	84162	hgsc.bcm.edu	37	4	123113428	123113428	+	Missense_Mutation	SNP	A	A	G	rs74643640	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123113428A>G	ENST00000264501.4	+	11	1319	c.946A>G	c.(946-948)Agc>Ggc	p.S316G	KIAA1109_ENST00000455637.1_Missense_Mutation_p.S316G|KIAA1109_ENST00000388738.3_Missense_Mutation_p.S316G			Q2LD37	K1109_HUMAN	KIAA1109	316					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGGAGAAATGAGCAGTGAGGA	0.368													A|||	314	0.0626997	0.0424	0.0346	5008	,	,		13237	0.1498		0.0308	False		,,,				2504	0.0532				p.S316G		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A946G						PASS	.	A	GLY/SER	185,3525		3,179,1673	125.0	121.0	122.0		946	5.9	1.0	4	dbSNP_131	122	282,7894		6,270,3812	yes	missense	KIAA1109	NM_015312.3	56	9,449,5485	GG,GA,AA		3.4491,4.9865,3.929	benign	316/5006	123113428	467,11419	1855	4088	5943	SO:0001583	missense	84162	exon9			GAAATGAGCAGTG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.946A>G	4.37:g.123113428A>G	ENSP00000264501:p.Ser316Gly	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	178	94	0.52809	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	127|127	0.05815018315018315|0.05815018315018315	22|22	0.044715447154471545|0.044715447154471545	12|12	0.03314917127071823|0.03314917127071823	71|71	0.12412587412587413|0.12412587412587413	22|22	0.029023746701846966|0.029023746701846966	A|A	14.69|14.69	2.611820|2.611820	0.46631|0.46631	0.049865|0.049865	0.034491|0.034491	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.25414	.|2.39;2.39;1.8	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	.|6.146860	.|0.00166	.|N	.|0.000001	T|T	0.00300|0.00300	0.0009|0.0009	N|N	0.08118|0.08118	0|0	0.26366|0.26366	N|N	0.976978|0.976978	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.28396|0.28396	-1.0045|-1.0045	5|10	.|0.29301	.|T	.|0.29	.|.	16.3756|16.3756	0.83387|0.83387	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|316	.|Q2LD37	.|K1109_HUMAN	G|G	148|316	.|ENSP00000264501:S316G;ENSP00000373390:S316G;ENSP00000389925:S316G	.|ENSP00000264501:S316G	E|S	+|+	2|1	0|0	KIAA1109|KIAA1109	123332878|123332878	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	2.646000|2.646000	0.46630|0.46630	2.270000|2.270000	0.75569|0.75569	0.460000|0.460000	0.39030|0.39030	GAG|AGC	A|0.952;G|0.048	0.048	strong		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
KLHL13	90293	hgsc.bcm.edu	37	X	117053499	117053499	+	Silent	SNP	C	C	T	rs6645994	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:117053499C>T	ENST00000262820.3	-	4	1464	c.555G>A	c.(553-555)gtG>gtA	p.V185V	KLHL13_ENST00000469946.1_Silent_p.V134V|KLHL13_ENST00000371882.1_Silent_p.V134V|KLHL13_ENST00000541812.1_Silent_p.V169V|KLHL13_ENST00000539496.1_Silent_p.V188V|KLHL13_ENST00000371876.1_Silent_p.V134V|KLHL13_ENST00000545703.1_Silent_p.V143V|KLHL13_ENST00000371878.1_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	165	0	0		WXS	Illumina HiSeq	Phase_I	136	136	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	
TANC1	85461	hgsc.bcm.edu	37	2	159954175	159954175	+	Missense_Mutation	SNP	C	C	T	rs34588551	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:159954175C>T	ENST00000263635.6	+	4	325	c.88C>T	c.(88-90)Cca>Tca	p.P30S	TANC1_ENST00000454300.1_Missense_Mutation_p.P30S	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	30			P -> S (in dbSNP:rs34588551).		dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						AGAGACTTCTCCAGTCCTGCA	0.458													C|||	683	0.136382	0.0295	0.2493	5008	,	,		18486	0.003		0.3469	False		,,,				2504	0.1217				p.P30S		Atlas-SNP	.											.	TANC1	157	.	0			c.C88T						PASS	.	C	SER/PRO,SER/PRO	309,3621		8,293,1664	119.0	113.0	115.0		88,88	0.7	0.0	2	dbSNP_126	115	2993,5307		533,1927,1690	yes	missense,missense	TANC1	NM_001145909.1,NM_033394.2	74,74	541,2220,3354	TT,TC,CC		36.0602,7.8626,26.9992	benign,benign	30/1391,30/1862	159954175	3302,8928	1965	4150	6115	SO:0001583	missense	85461	exon4			ACTTCTCCAGTCC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.88C>T	2.37:g.159954175C>T	ENSP00000263635:p.Pro30Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	386	0.17673992673992675	20	0.04065040650406504	112	0.30939226519337015	1	0.0017482517482517483	253	0.3337730870712401	C	7.078	0.569622	0.13560	0.078626	0.360602	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.68624	-0.34;-0.32	5.76	0.726	0.18248	.	0.550760	0.16234	N	0.223445	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.0	B;B	0.16289	0.015;0.0	T	0.33007	-0.9885	9	0.27082	T	0.32	.	2.2854	0.04124	0.124:0.4056:0.2705:0.2	rs34588551	30;30	Q9C0D5-2;Q9C0D5	.;TANC1_HUMAN	S	30	ENSP00000396339:P30S;ENSP00000263635:P30S	ENSP00000263635:P30S	P	+	1	0	TANC1	159662421	0.001000	0.12720	0.003000	0.11579	0.987000	0.75469	0.420000	0.21263	0.127000	0.18452	0.655000	0.94253	CCA	C|0.753;T|0.247	0.247	strong		0.458	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
TTN	7273	hgsc.bcm.edu	37	2	179578730	179578730	+	Silent	SNP	G	G	A	rs2562839	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179578730G>A	ENST00000591111.1	-	90	25928	c.25704C>T	c.(25702-25704)tcC>tcT	p.S8568S	TTN_ENST00000589042.1_Silent_p.S8885S|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.S7641S|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12732	Ig-like 68.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTAAGGCCGGATACTTTGT	0.448													A|||	2227	0.444688	0.4644	0.379	5008	,	,		20000	0.6567		0.2237	False		,,,				2504	0.4734				p.S8885S		Atlas-SNP	.											.	TTN	18412	.	0			c.C26655T						PASS	.	A	,,,	1514,2252		311,892,680	177.0	165.0	168.0		,22923,,	1.8	1.0	2	dbSNP_100	168	1660,6590		158,1344,2623	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	469,2236,3303	AA,AG,GG		20.1212,40.2018,26.4148	,,,	,7641/33424,,	179578730	3174,8842	1883	4125	6008	SO:0001819	synonymous_variant	7273	exon92			AAGGCCGGATACT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25704C>T	2.37:g.179578730G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	167	77	0.461078	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.613;A|0.387	0.387	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037419	33037419	+	Splice_Site	SNP	G	G	A	rs17850584|rs1126543	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33037419G>A	ENST00000419277.1	-	3	474	c.345C>T	c.(343-345)aaC>aaT	p.N115N	HLA-DPA1_ENST00000428995.1_Splice_Site_p.N115N|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	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	158	0	0		WXS	Illumina HiSeq	Phase_I	162	62	0.382716	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
EPPK1	83481	hgsc.bcm.edu	37	8	144940779	144940779	+	Missense_Mutation	SNP	G	G	A	rs11781942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144940779G>A	ENST00000525985.1	-	2	6714	c.6643C>T	c.(6643-6645)Cgc>Tgc	p.R2215C				P58107	EPIPL_HUMAN	epiplakin 1	2215						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)			CGCTTGACGCGGTCGTCCTCC	0.632													G|||	398	0.0794728	0.0166	0.0994	5008	,	,		18034	0.0377		0.169	False		,,,				2504	0.1012				p.R2215C		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6643T						PASS	.	G	CYS/ARG	147,3941		5,137,1902	126.0	130.0	129.0		6643	-9.3	0.0	8	dbSNP_120	129	1327,7033		103,1121,2956	yes	missense	EPPK1	NM_031308.1	180	108,1258,4858	AA,AG,GG		15.8732,3.5959,11.8413	possibly-damaging	2215/2420	144940779	1474,10974	2044	4180	6224	SO:0001583	missense	83481	exon1			TGACGCGGTCGTC	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.6643C>T	8.37:g.144940779G>A	ENSP00000436337:p.Arg2215Cys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		199	0.09111721611721611	11	0.022357723577235773	46	0.1270718232044199	16	0.027972027972027972	126	0.1662269129287599	G	18.06	3.539464	0.65085	0.035959	0.158732	ENSG00000227184	ENST00000525985	T	0.68479	-0.33	4.66	-9.32	0.00643	.	.	.	.	.	T	0.00109	0.0003	L	0.29908	0.895	0.80722	P	0.0	P	0.35401	0.499	B	0.22386	0.039	T	0.04191	-1.0970	8	0.56958	D	0.05	.	3.8336	0.08885	0.2465:0.4797:0.0807:0.1931	rs11781942	2215	E9PPU0	.	C	2215	ENSP00000436337:R2215C	ENSP00000436337:R2215C	R	-	1	0	EPPK1	145012767	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.190000	0.09615	-1.164000	0.02790	0.585000	0.79938	CGC	G|0.904;A|0.096	0.096	strong		0.632	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
XRCC4	7518	hgsc.bcm.edu	37	5	82648943	82648943	+	Splice_Site	SNP	G	G	A	rs1805377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:82648943G>A	ENST00000511817.1	+	8	973		c.e8-1		XRCC4_ENST00000338635.6_Splice_Site|XRCC4_ENST00000396027.4_Intron|XRCC4_ENST00000282268.3_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	201	0	0		WXS	Illumina HiSeq	Phase_I	185	86	0.464865	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
BCOR	54880	hgsc.bcm.edu	37	X	39933339	39933339	+	Silent	SNP	A	A	G	rs5917933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:39933339A>G	ENST00000378444.4	-	4	1488	c.1260T>C	c.(1258-1260)gaT>gaC	p.D420D	BCOR_ENST00000342274.4_Silent_p.D420D|BCOR_ENST00000378455.4_Silent_p.D420D|BCOR_ENST00000397354.3_Silent_p.D420D	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	420					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						GTGAGCTGCCATCTTTTCTGT	0.552			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic						G|||	3409	0.903046	0.7133	0.7017	3775	,	,		13299	0.7272		0.67	False		,,,				2504	0.5849				p.D420D		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.T1260C						PASS	.	G	,,,	3545,288		1403,217,522,11,49	56.0	41.0	46.0		1260,1260,1260,1260	-2.8	0.1	X	dbSNP_114	46	5915,813		1871,523,1650,34,222	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	3274,740,2172,45,271	GG,GA,G,AA,A		12.0838,7.5137,10.4251	,,,	420/1722,420/1704,420/1756,420/1722	39933339	9460,1101	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			GCTGCCATCTTTT	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.1260T>C	X.37:g.39933339A>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			A|0.093;0|0.003	.	strong		0.552	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
BDNF	627	hgsc.bcm.edu	37	11	27679916	27679916	+	Missense_Mutation	SNP	C	C	T	rs6265	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:27679916C>T	ENST00000525528.1	-	1	1289	c.196G>A	c.(196-198)Gtg>Atg	p.V66M	BDNF_ENST00000418212.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000530686.1_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395986.2_Missense_Mutation_p.V81M|BDNF_ENST00000530861.1_Missense_Mutation_p.V66M|BDNF_ENST00000395978.3_Missense_Mutation_p.V66M|BDNF_ENST00000525950.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000584049.1_5'UTR|BDNF_ENST00000314915.6_Missense_Mutation_p.V74M|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000439476.2_Missense_Mutation_p.V66M|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000532997.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000356660.4_Missense_Mutation_p.V66M|BDNF_ENST00000420794.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000438929.1_Missense_Mutation_p.V148M|BDNF_ENST00000395983.3_Missense_Mutation_p.V66M|BDNF_ENST00000533131.1_Missense_Mutation_p.V66M|BDNF_ENST00000395981.3_Missense_Mutation_p.V66M|BDNF_ENST00000395980.2_Missense_Mutation_p.V66M|BDNF_ENST00000533246.1_Missense_Mutation_p.V66M	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	66			V -> M (polymorphism that impairs localization to secretory granules or synapses; associated with poorer episodic memory; may have a protective effect in obsessive-compulsive disorder; dbSNP:rs6265). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12553913, ECO:0000269|PubMed:12836135, ECO:0000269|PubMed:12888803, ECO:0000269|PubMed:14566559, ECO:0000269|Ref.8}.		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						TCTTCTATCACGTGTTCGAAA	0.527													C|||	1008	0.201278	0.0106	0.1527	5008	,	,		18573	0.4881		0.1968	False		,,,				2504	0.2025				p.V148M		Atlas-SNP	.											.	BDNF	63	.	0			c.G442A	GRCh37	CM020369	BDNF	M	rs6265	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	184,4220	118.0+/-155.7	3,178,2021	207.0	197.0	200.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	196,196,196,196,283,442,196,196,196,196,196,196,220,196,196,241,196	5.2	1.0	11	dbSNP_52	200	1640,6958	303.3+/-306.4	166,1308,2825	yes	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	169,1486,4846	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	19.0742,4.178,14.0286	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	66/248,66/248,66/248,66/248,95/277,148/330,66/248,66/248,66/248,66/248,66/248,66/248,74/256,66/248,66/248,81/263,66/248	27679916	1824,11178	2202	4299	6501	SO:0001583	missense	627	exon3			CTATCACGTGTTC	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.196G>A	11.37:g.27679916C>T	ENSP00000437138:p.Val66Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000525528.1	37	CCDS7866.1	499	0.22847985347985347	7	0.014227642276422764	64	0.17679558011049723	274	0.479020979020979	154	0.20316622691292877	C	13.00	2.107047	0.37145	0.04178	0.190742	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	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	6.16	5.25	0.73442	.	0.063003	0.64402	N	0.000006	T	0.00012	0.0000	M	0.64997	1.995	0.09310	P	0.999999020481	D;P;D;D;D	0.76494	0.999;0.889;0.999;0.998;0.999	D;B;D;D;D	0.91635	0.999;0.134;0.991;0.981;0.991	T	0.42982	-0.9419	9	0.87932	D	0	-10.0315	15.4433	0.75204	0.0:0.9339:0.0:0.0661	rs6265;rs3829232;rs16917222;rs17855547;rs60760775;rs6265	95;148;74;66;81	P23560-5;P23560-4;P23560-2;P23560;P23560-3	.;.;.;BDNF_HUMAN;.	M	66;66;81;66;66;66;66;66;66;148;66;66;66;66;66;74;66;66	ENSP00000389345:V66M;ENSP00000437138:V66M;ENSP00000379309:V81M;ENSP00000432727:V66M;ENSP00000349084:V66M;ENSP00000400502:V66M;ENSP00000432376:V66M;ENSP00000435564:V66M;ENSP00000379307:V66M;ENSP00000414303:V148M;ENSP00000379304:V66M;ENSP00000435805:V66M;ENSP00000379305:V66M;ENSP00000379302:V66M;ENSP00000432035:V66M;ENSP00000320002:V74M;ENSP00000389564:V66M	ENSP00000320002:V74M	V	-	1	0	BDNF	27636492	0.999000	0.42202	0.996000	0.52242	0.911000	0.54048	3.967000	0.56802	1.612000	0.50221	0.650000	0.86243	GTG	C|0.815;T|0.185	0.185	strong		0.527	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037560	33037560	+	Silent	SNP	G	G	A	rs1042176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33037560G>A	ENST00000419277.1	-	3	333	c.204C>T	c.(202-204)gaC>gaT	p.D68D	HLA-DPA1_ENST00000428995.1_Silent_p.D68D|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	68	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TCTCCTTCTTGTCCAGATCCA	0.463													.|||	1301	0.259784	0.3971	0.2507	5008	,	,		19428	0.12		0.163	False		,,,				2504	0.3241				p.D68D		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C204T						PASS	.	G	,,	908,2114		141,626,744	67.0	90.0	82.0		204,204,204	2.1	0.9	6	dbSNP_86	82	808,4610		50,708,1951	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	191,1334,2695	AA,AG,GG		14.9133,30.0463,20.3318	,,	68/261,68/261,68/261	33037560	1716,6724	1511	2709	4220	SO:0001819	synonymous_variant	3113	exon2			CTTCTTGTCCAGA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.204C>T	6.37:g.33037560G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	130	51	0.392308	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	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116091629	116091629	+	Missense_Mutation	SNP	T	T	C	rs117043677	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:116091629T>C	ENST00000304129.4	-	4	277	c.248A>G	c.(247-249)aAt>aGt	p.N83S	AFAP1L2_ENST00000369271.3_Missense_Mutation_p.N83S|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.N83S			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	83					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)		GGGCTCCCCATTGGGTAGCAG	0.612													T|||	21	0.00419329	0.003	0.0043	5008	,	,		16175	0.0		0.0139	False		,,,				2504	0.0				p.N83S		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.A248G						PASS	.	T	SER/ASN,SER/ASN	8,4206		0,8,2099	48.0	34.0	39.0		248,248	5.5	1.0	10	dbSNP_132	39	58,8090		0,58,4016	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	46,46	0,66,6115	CC,CT,TT		0.7118,0.1898,0.5339	probably-damaging,probably-damaging	83/819,83/815	116091629	66,12296	2107	4074	6181	SO:0001583	missense	84632	exon4			TCCCCATTGGGTA	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.248A>G	10.37:g.116091629T>C	ENSP00000303042:p.Asn83Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	14	0.00641025641025641	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	10	0.013192612137203167	T	14.14	2.448016	0.43429	0.001898	0.007118	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000541919;ENST00000545353;ENST00000419268	T;T;T;T	0.31769	2.48;2.49;2.32;1.48	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.41050	0.1142	L	0.56769	1.78	0.46061	D	0.998848	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.998;0.997	D;D;D;D;P	0.87578	0.998;0.996;0.948;0.957;0.907	T	0.31696	-0.9934	10	0.30854	T	0.27	-34.4191	12.0678	0.53598	0.0:0.0:0.0:1.0	.	83;83;83;83;83	F5GZE1;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;AF1L2_HUMAN	S	83;83;82;101;83;101	ENSP00000358276:N83S;ENSP00000303042:N83S;ENSP00000444511:N83S;ENSP00000396781:N101S	ENSP00000303042:N83S	N	-	2	0	AFAP1L2	116081619	1.000000	0.71417	0.974000	0.42286	0.228000	0.25075	5.373000	0.66162	2.103000	0.63969	0.533000	0.62120	AAT	T|0.995;C|0.005	0.005	strong		0.612	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
SNX31	169166	hgsc.bcm.edu	37	8	101586133	101586133	+	Missense_Mutation	SNP	T	T	C	rs2022923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	110	0	0		WXS	Illumina HiSeq	Phase_I	116	47	0.405172	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	
ZNF718	255403	hgsc.bcm.edu	37	4	155713	155713	+	lincRNA	SNP	A	A	G	rs7440274	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155713A>G	ENST00000510175.1	+	0	1148							Q3SXZ3	ZN718_HUMAN	zinc finger protein 718						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)		CTGCATAATCATAAGAAAATT	0.348													A|||	957	0.191094	0.1551	0.2406	5008	,	,		20246	0.1528		0.1759	False		,,,				2504	0.2597				p.H413R		Atlas-SNP	.											.	.	.	.	0			c.A1238G						PASS	.	A	ARG/HIS	587,3559		39,509,1525	33.0	38.0	36.0		1049	1.0	0.0	4	dbSNP_116	36	1348,7154		108,1132,3011	no	missense	ZNF718	NM_001039127.3	29	147,1641,4536	GG,GA,AA		15.8551,14.1582,15.2989	possibly-damaging	350/416	155713	1935,10713	2073	4251	6324			255403	exon4			ATAATCATAAGAA	AK096662	CCDS75078.1, CCDS75079.1	4p16.3	2011-05-24			ENSG00000250312	ENSG00000250312		"""Zinc fingers, C2H2-type"""	26889	protein-coding gene	gene with protein product							Standard	XM_005278364		Approved	FLJ90036	uc003fzt.4	Q3SXZ3	OTTHUMG00000159873		4.37:g.155713A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_001039127	Q3SXZ4|Q3SXZ5	Missense_Mutation	SNP	ENST00000510175.1	37																																																																																				A|0.831;G|0.169	0.169	strong		0.348	ZNF718-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000357865.3	NM_001039127	
SNX29	92017	hgsc.bcm.edu	37	16	12492322	12492322	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12492322A>T	ENST00000566228.1	+	17	1988	c.1919A>T	c.(1918-1920)cAa>cTa	p.Q640L	SNX29_ENST00000323433.4_Missense_Mutation_p.Q255L|SNX29_ENST00000306030.3_Missense_Mutation_p.Q255L	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	640						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GATTTGAGTCAAACGTCCGAA	0.463																																					p.Q640L		Atlas-SNP	.											.	SNX29	60	.	0			c.A1919T						PASS	.						136.0	132.0	133.0					16																	12492322		1866	4116	5982	SO:0001583	missense	92017	exon17			TGAGTCAAACGTC	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.1919A>T	16.37:g.12492322A>T	ENSP00000456480:p.Gln640Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	180	80	0.444444	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	A	20.3	3.973375	0.74246	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.49236	0.1545	L	0.40543	1.245	0.31498	N	0.665135	.	.	.	.	.	.	T	0.58470	-0.7631	7	0.44086	T	0.13	-15.7683	13.779	0.63071	1.0:0.0:0.0:0.0	.	.	.	.	L	255	.	ENSP00000306940:Q255L	Q	+	2	0	SNX29	12399823	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.483000	0.73617	2.129000	0.65627	0.533000	0.62120	CAA	.	.	none		0.463	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
SVIL	6840	hgsc.bcm.edu	37	10	29769647	29769647	+	Silent	SNP	G	G	A	rs10763720	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:29769647G>A	ENST00000355867.4	-	29	5948	c.5196C>T	c.(5194-5196)gtC>gtT	p.V1732V	PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000535393.1_Silent_p.V646V|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000375400.3_Silent_p.V1306V|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000538146.1_Silent_p.V524V|PTCHD3P1_ENST00000423223.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000375398.2_Silent_p.V1732V	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1732					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AGCCACGGCCGACGTTCACTC	0.567													G|||	253	0.0505192	0.0371	0.0533	5008	,	,		16755	0.001		0.1362	False		,,,				2504	0.0297				p.V1732V		Atlas-SNP	.											.	SVIL	226	.	0			c.C5196T						PASS	.	G	,	223,4183	133.3+/-169.7	0,223,1980	174.0	148.0	157.0		3918,5196	-8.8	0.2	10	dbSNP_120	157	1131,7469	233.7+/-266.9	81,969,3250	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	81,1192,5230	AA,AG,GG		13.1512,5.0613,10.4106	,	1306/1789,1732/2215	29769647	1354,11652	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon29			ACGGCCGACGTTC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5196C>T	10.37:g.29769647G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			G|0.917;A|0.083	0.083	strong		0.567	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
TATDN2	9797	hgsc.bcm.edu	37	3	10302045	10302045	+	Silent	SNP	C	C	T	rs2241313	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:10302045C>T	ENST00000287652.4	+	3	1690	c.639C>T	c.(637-639)agC>agT	p.S213S	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Silent_p.S213S	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	213					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						CAAAACCAAGCGCAGCAGAGC	0.577													C|||	1656	0.330671	0.2421	0.2291	5008	,	,		16318	0.62		0.1024	False		,,,				2504	0.4591				p.S213S		Atlas-SNP	.											.	TATDN2	59	.	0			c.C639T						PASS	.	C		934,3472	355.1+/-312.9	104,726,1373	48.0	49.0	49.0		639	0.8	0.0	3	dbSNP_98	49	882,7718	198.9+/-243.1	44,794,3462	no	coding-synonymous	TATDN2	NM_014760.3		148,1520,4835	TT,TC,CC		10.2558,21.1984,13.9628		213/762	10302045	1816,11190	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon3			ACCAAGCGCAGCA	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.639C>T	3.37:g.10302045C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			C|0.822;T|0.178	0.178	strong		0.577	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
TFEB	7942	hgsc.bcm.edu	37	6	41658566	41658566	+	Silent	SNP	C	C	T	rs2273068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:41658566C>T	ENST00000230323.4	-	4	604	c.303G>A	c.(301-303)ggG>ggA	p.G101G	TFEB_ENST00000373033.1_Silent_p.G101G|TFEB_ENST00000358871.2_Silent_p.G115G|TFEB_ENST00000403298.4_Silent_p.G101G|TFEB_ENST00000420312.1_Intron|TFEB_ENST00000394283.1_Silent_p.G101G	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	101					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			CAAACTTGTTCCCATAGGTCT	0.637			T	ALPHA	renal (childhood epithelioid)								C|||	552	0.110224	0.059	0.085	5008	,	,		18584	0.1488		0.1521	False		,,,				2504	0.1145				p.G115G		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	.	TFEB	37	.	0			c.G345A						PASS	.	C	,	384,4022	190.2+/-216.2	18,348,1837	73.0	69.0	70.0		303,303	3.2	1.0	6	dbSNP_100	70	1168,7432	238.6+/-270.0	82,1004,3214	no	coding-synonymous,coding-synonymous	TFEB	NM_001167827.1,NM_007162.2	,	100,1352,5051	TT,TC,CC		13.5814,8.7154,11.933	,	101/477,101/477	41658566	1552,11454	2203	4300	6503	SO:0001819	synonymous_variant	7942	exon3			CTTGTTCCCATAG	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.303G>A	6.37:g.41658566C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Silent	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																			C|0.882;T|0.118	0.118	strong		0.637	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		
ASPM	259266	hgsc.bcm.edu	37	1	197070697	197070697	+	Missense_Mutation	SNP	T	T	C	rs41310927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:197070697T>C	ENST00000367409.4	-	18	7940	c.7684A>G	c.(7684-7686)Agc>Ggc	p.S2562G	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2562			S -> G (in dbSNP:rs41310927). {ECO:0000269|PubMed:14574646}.		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						CTGTAGGTGCTTTGTATTACG	0.348													T|||	1073	0.214257	0.0431	0.2277	5008	,	,		18944	0.1637		0.4105	False		,,,				2504	0.2863				p.S2562G		Atlas-SNP	.											.	ASPM	444	.	0			c.A7684G						PASS	.	T	,GLY/SER	456,3948	201.8+/-224.7	27,402,1773	67.0	59.0	62.0		,7684	5.2	1.0	1	dbSNP_127	62	3718,4878	513.7+/-378.2	813,2092,1393	yes	intron,missense	ASPM	NM_001206846.1,NM_018136.4	,56	840,2494,3166	CC,CT,TT		43.2527,10.3542,32.1077	,possibly-damaging	,2562/3478	197070697	4174,8826	2202	4298	6500	SO:0001583	missense	259266	exon18			AGGTGCTTTGTAT	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.7684A>G	1.37:g.197070697T>C	ENSP00000356379:p.Ser2562Gly	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	65	41	0.630769	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	536	0.2454212454212454	20	0.04065040650406504	101	0.27900552486187846	98	0.17132867132867133	317	0.4182058047493404	T	17.45	3.393627	0.62066	0.103542	0.432527	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.73469	-0.75	5.15	5.15	0.70609	.	0.259353	0.39146	N	0.001452	T	0.00012	0.0000	M	0.91612	3.225	0.09310	P	0.9999999999998456	D;D	0.69078	0.978;0.997	D;D	0.65573	0.932;0.936	T	0.15150	-1.0447	9	0.52906	T	0.07	.	10.5038	0.44821	0.1448:0.0:0.0:0.8552	rs41310927;rs61819077	548;2562	E7EQ84;Q8IZT6	.;ASPM_HUMAN	G	2562;548	ENSP00000356379:S2562G	ENSP00000356376:S548G	S	-	1	0	ASPM	195337320	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.494000	0.35616	2.053000	0.61076	0.455000	0.32223	AGC	T|0.700;C|0.300	0.300	strong		0.348	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
HUS1B	135458	hgsc.bcm.edu	37	6	656810	656810	+	Silent	SNP	A	A	G	rs61748571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:656810A>G	ENST00000380907.2	-	1	153	c.135T>C	c.(133-135)ggT>ggC	p.G45G	EXOC2_ENST00000230449.4_Intron|EXOC2_ENST00000448181.3_Intron	NM_148959.3	NP_683762.2	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint homolog b (S. pombe)	45					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)	checkpoint clamp complex (GO:0030896)|nucleolus (GO:0005730)				endometrium(3)|large_intestine(1)|lung(7)	11	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)		GGCCGCCGGAACCCGCGGGGC	0.662													A|||	428	0.0854633	0.0166	0.0548	5008	,	,		15750	0.129		0.0477	False		,,,				2504	0.1943				p.G45G		Atlas-SNP	.											.	HUS1B	26	.	0			c.T135C						PASS	.	A	,	141,4241		2,137,2052	14.0	14.0	14.0		,135	-5.6	0.0	6	dbSNP_129	14	442,8128		15,412,3858	no	intron,coding-synonymous	EXOC2,HUS1B	NM_018303.4,NM_148959.3	,	17,549,5910	GG,GA,AA		5.1575,3.2177,4.5012	,	,45/279	656810	583,12369	2191	4285	6476	SO:0001819	synonymous_variant	135458	exon1			GCCGGAACCCGCG	AF508547	CCDS4470.1	6p25.3	2008-08-08	2001-11-28		ENSG00000188996	ENSG00000188996			16485	protein-coding gene	gene with protein product		609713	"""HUS1 (S. pombe) checkpoint homolog b"""			11944979	Standard	NM_148959		Approved		uc003mtg.3	Q8NHY5	OTTHUMG00000090059	ENST00000380907.2:c.135T>C	6.37:g.656810A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	11	0.478261	NM_148959	Q5T4Z2	Silent	SNP	ENST00000380907.2	37	CCDS4470.1																																																																																			A|0.942;G|0.058	0.058	strong		0.662	HUS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205617.2	NM_148959	
RABEP1	9135	hgsc.bcm.edu	37	17	5271763	5271763	+	Splice_Site	SNP	G	G	C	rs61735455	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5271763G>C	ENST00000546142.2	+	12	2071	c.1884G>C	c.(1882-1884)atG>atC	p.M628I	NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000408982.2_Splice_Site_p.M628I|RP11-420A6.2_ENST00000572792.1_RNA|RABEP1_ENST00000262477.6_Splice_Site_p.M628I|RABEP1_ENST00000537505.1_Splice_Site_p.M585I|RABEP1_ENST00000341923.6_Splice_Site_p.M628I			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	628				M -> I (in Ref. 3; BAG36864). {ECO:0000305}.	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						AGGAACAGATGGTAAGTTTAC	0.398													G|||	93	0.0185703	0.0008	0.0303	5008	,	,		18803	0.0		0.0527	False		,,,				2504	0.0184				p.M628I		Atlas-SNP	.											.	RABEP1	59	.	0			c.G1884C						PASS	.	G	ILE/MET,ILE/MET	41,3683		1,39,1822	123.0	121.0	121.0		1884,1884	4.8	1.0	17	dbSNP_129	121	409,7793		13,383,3705	yes	missense-near-splice,missense-near-splice	RABEP1	NM_001083585.1,NM_004703.4	10,10	14,422,5527	CC,CG,GG		4.9866,1.101,3.7733	benign,benign	628/830,628/863	5271763	450,11476	1862	4101	5963	SO:0001630	splice_region_variant	9135	exon12			ACAGATGGTAAGT	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.1884+1G>C	17.37:g.5271763G>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_004703	B2RAG7|O95369|Q8IVX3	Missense_Mutation	SNP	ENST00000546142.2	37	CCDS45592.1	53	0.024267399267399268	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	42	0.055408970976253295	G	16.84	3.234026	0.58886	0.01101	0.049866	ENSG00000029725	ENST00000262477;ENST00000408982;ENST00000539669;ENST00000546142;ENST00000341923;ENST00000537505	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	4.78	4.78	0.61160	Rabaptin, GTPase-Rab5 binding (1);	0.082194	0.85682	D	0.000000	T	0.06645	0.0170	L	0.51422	1.61	0.80722	D	1	B;B;B;B;B	0.31153	0.112;0.31;0.077;0.136;0.008	B;B;B;B;B	0.28638	0.032;0.055;0.092;0.055;0.015	T	0.03231	-1.1058	10	0.20519	T	0.43	-11.5105	16.9269	0.86179	0.0:0.0:1.0:0.0	rs61735455	585;585;621;628;628	F5H355;B4DMM4;Q05BX6;Q15276;Q15276-2	.;.;.;RABE1_HUMAN;.	I	628;628;621;628;628;585	ENSP00000262477:M628I;ENSP00000386150:M628I;ENSP00000437701:M628I;ENSP00000339569:M628I;ENSP00000445408:M585I	ENSP00000262477:M628I	M	+	3	0	RABEP1	5212487	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.571000	0.90752	2.644000	0.89710	0.591000	0.81541	ATG	G|0.969;C|0.031	0.031	strong		0.398	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	Missense_Mutation
FANCA	2175	hgsc.bcm.edu	37	16	89839766	89839766	+	Missense_Mutation	SNP	G	G	C	rs17232910	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89839766G>C	ENST00000389301.3	-	22	1957	c.1927C>G	c.(1927-1929)Ccc>Gcc	p.P643A	FANCA_ENST00000567284.2_5'UTR|FANCA_ENST00000568369.1_Missense_Mutation_p.P643A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	643			P -> A (in dbSNP:rs17232910).		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GCAGAGTTGGGTTCTGCCCTC	0.542			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	371	0.0740815	0.0038	0.0202	5008	,	,		17511	0.2698		0.0626	False		,,,				2504	0.0174				p.P643A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C1927G						PASS	.	G	ALA/PRO	51,4029		0,51,1989	31.0	26.0	28.0		1927	-2.4	0.0	16	dbSNP_123	28	519,7361		11,497,3432	yes	missense	FANCA	NM_000135.2	27	11,548,5421	CC,CG,GG		6.5863,1.25,4.7659	benign	643/1456	89839766	570,11390	2040	3940	5980	SO:0001583	missense	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGTTGGGTTCTGC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1927C>G	16.37:g.89839766G>C	ENSP00000373952:p.Pro643Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	190	0.08699633699633699	3	0.006097560975609756	10	0.027624309392265192	127	0.22202797202797203	50	0.06596306068601583	G	6.741	0.505585	0.12822	0.0125	0.065863	ENSG00000187741	ENST00000389301	D	0.83591	-1.74	3.82	-2.44	0.06502	.	0.752143	0.11984	N	0.510486	T	0.00039	0.0001	N	0.08118	0	0.53688	P	2.6999999999999247E-5	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.03706	-1.1011	9	0.07030	T	0.85	-10.2216	2.1006	0.03679	0.1027:0.3278:0.2668:0.3028	rs17232910	643;643	B4DRI7;O15360	.;FANCA_HUMAN	A	643	ENSP00000373952:P643A	ENSP00000373952:P643A	P	-	1	0	FANCA	88367267	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-0.040000	0.12104	-0.163000	0.10946	-0.131000	0.14894	CCC	G|0.936;C|0.064	0.064	strong		0.542	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ATP1A2	477	hgsc.bcm.edu	37	1	160105367	160105367	+	Silent	SNP	C	C	T	rs17846715	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160105367C>T	ENST00000361216.3	+	16	2348	c.2259C>T	c.(2257-2259)gcC>gcT	p.A753A	ATP1A2_ENST00000392233.3_Silent_p.A753A	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	753					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)			ACAACTTTGCCTCCATCGTCA	0.572													C|||	316	0.063099	0.0045	0.1182	5008	,	,		22004	0.0615		0.0934	False		,,,				2504	0.0736				p.A753A		Atlas-SNP	.											.	ATP1A2	167	.	0			c.C2259T						PASS	.	C		98,4308	79.3+/-117.8	0,98,2105	116.0	90.0	98.0		2259	1.3	1.0	1	dbSNP_123	98	1007,7593	216.2+/-255.3	64,879,3357	no	coding-synonymous	ATP1A2	NM_000702.3		64,977,5462	TT,TC,CC		11.7093,2.2242,8.4961		753/1021	160105367	1105,11901	2203	4300	6503	SO:0001819	synonymous_variant	477	exon16			CTTTGCCTCCATC	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.2259C>T	1.37:g.160105367C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	180	83	0.461111	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1	152	0.0695970695970696	4	0.008130081300813009	40	0.11049723756906077	30	0.05244755244755245	78	0.10290237467018469	C	9.827	1.187327	0.21870	0.022242	0.117093	ENSG00000018625	ENST00000447527	.	.	.	4.31	1.26	0.21427	.	.	.	.	.	T	0.15739	0.0379	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14008	-1.0488	3	.	.	.	.	4.8725	0.13640	0.0:0.5574:0.1661:0.2765	rs17846715	.	.	.	L	464	.	.	P	+	2	0	ATP1A2	158371991	0.994000	0.37717	1.000000	0.80357	0.876000	0.50452	0.425000	0.21346	0.494000	0.27859	0.561000	0.74099	CCT	C|0.919;T|0.081	0.081	strong		0.572	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
TMX4	56255	hgsc.bcm.edu	37	20	7964476	7964476	+	Missense_Mutation	SNP	T	T	C	rs1135711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:7964476T>C	ENST00000246024.2	-	7	859	c.644A>G	c.(643-645)tAt>tGt	p.Y215C		NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	215			Y -> C (in dbSNP:rs1135711).		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						AAGTGGCACATAGAAACATTC	0.388													T|||	54	0.0107827	0.0008	0.0101	5008	,	,		16795	0.0		0.0408	False		,,,				2504	0.0051				p.Y215C		Atlas-SNP	.											.	TMX4	39	.	0			c.A644G						PASS	.	T	CYS/TYR	45,4361	48.2+/-83.0	0,45,2158	127.0	118.0	121.0		644	-0.5	0.1	20	dbSNP_86	121	491,8109	141.9+/-198.1	17,457,3826	yes	missense	TMX4	NM_021156.2	194	17,502,5984	CC,CT,TT		5.7093,1.0213,4.1212	benign	215/350	7964476	536,12470	2203	4300	6503	SO:0001583	missense	56255	exon7			GGCACATAGAAAC		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.644A>G	20.37:g.7964476T>C	ENSP00000246024:p.Tyr215Cys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Missense_Mutation	SNP	ENST00000246024.2	37	CCDS13101.1	40	0.018315018315018316	0	0.0	5	0.013812154696132596	0	0.0	35	0.04617414248021108	T	8.090	0.774247	0.16051	0.010213	0.057093	ENSG00000125827	ENST00000246024;ENST00000527925	T;T	0.17854	2.93;2.25	4.69	-0.494	0.12034	.	0.326315	0.33327	N	0.005024	T	0.00724	0.0024	N	0.19112	0.55	0.22719	N	0.998815	B	0.06786	0.001	B	0.06405	0.002	T	0.35919	-0.9769	10	0.12766	T	0.61	-1.6844	4.6526	0.12603	0.0:0.1729:0.3113:0.5158	rs1135711;rs3178985;rs17399910;rs52813832;rs1135711	215	Q9H1E5	TMX4_HUMAN	C	215;187	ENSP00000246024:Y215C;ENSP00000435735:Y187C	ENSP00000246024:Y215C	Y	-	2	0	TMX4	7912476	0.260000	0.24053	0.139000	0.22197	0.985000	0.73830	0.239000	0.18023	-0.101000	0.12219	0.477000	0.44152	TAT	T|0.968;C|0.032	0.032	strong		0.388	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
LSP1	4046	hgsc.bcm.edu	37	11	1887806	1887806	+	Intron	SNP	T	T	A	rs7938342	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1887806T>A	ENST00000311604.3	+	1	228				LSP1_ENST00000405957.2_5'Flank|AC051649.12_ENST00000509204.1_RNA|LSP1_ENST00000381775.1_Missense_Mutation_p.H34Q	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1						cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GCACACCTCATCCCAGCCTCC	0.657													T|||	3127	0.624401	0.531	0.7622	5008	,	,		13459	0.7688		0.6322	False		,,,				2504	0.4959				p.H34Q		Atlas-SNP	.											.	LSP1	59	.	0			c.T102A						PASS	.																																			SO:0001627	intron_variant	4046	exon2			ACCTCATCCCAGC	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.53+13379T>A	11.37:g.1887806T>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	37	CCDS31334.1	1429	0.6543040293040293	268	0.5447154471544715	249	0.6878453038674033	460	0.8041958041958042	452	0.5963060686015831	t	12.20	1.867727	0.32977	.	.	ENSG00000130592	ENST00000381775	T	0.26518	1.73	1.8	-0.645	0.11475	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.35982	0.531	B	0.29598	0.104	T	0.42515	-0.9447	7	0.02654	T	1	.	4.2569	0.10721	0.0:0.3731:0.0:0.6269	rs7938342;rs57757026	34	E9PFP3	.	Q	34	ENSP00000371194:H34Q	ENSP00000371194:H34Q	H	+	3	2	LSP1	1844382	0.000000	0.05858	0.000000	0.03702	0.672000	0.39443	-1.399000	0.02506	-0.182000	0.10602	0.172000	0.16884	CAT	T|0.346;A|0.654	0.654	strong		0.657	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
DST	667	hgsc.bcm.edu	37	6	56373536	56373536	+	Missense_Mutation	SNP	C	C	T	rs41271862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:56373536C>T	ENST00000361203.3	-	70	18077	c.18070G>A	c.(18070-18072)Gac>Aac	p.D6024N	DST_ENST00000370754.5_Missense_Mutation_p.D6313N|DST_ENST00000370788.2_Missense_Mutation_p.D3938N|DST_ENST00000244364.6_Missense_Mutation_p.D3721N|DST_ENST00000370769.4_Missense_Mutation_p.D6135N|DST_ENST00000340834.4_5'UTR|DST_ENST00000446842.2_Missense_Mutation_p.D5809N|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.D4047N			Q03001	DYST_HUMAN	dystonin	6020					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)			ACCATTTGGTCAAGCTTATCC	0.438													C|||	80	0.0159744	0.0	0.013	5008	,	,		21172	0.0		0.0557	False		,,,				2504	0.0153				p.D3721N		Atlas-SNP	.											.	DST	1427	.	0			c.G11161A						PASS	.	C	ASN/ASP	39,3815		0,39,1888	118.0	116.0	117.0		11161	5.5	1.0	6	dbSNP_127	117	407,7869		12,383,3743	yes	missense	DST	NM_015548.4	23	12,422,5631	TT,TC,CC		4.9178,1.0119,3.6768	probably-damaging	3721/5172	56373536	446,11684	1927	4138	6065	SO:0001583	missense	667	exon56			TTTGGTCAAGCTT	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.18070G>A	6.37:g.56373536C>T	ENSP00000354508:p.Asp6024Asn	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	175	81	0.462857	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		51	0.023351648351648352	0	0.0	4	0.011049723756906077	0	0.0	47	0.06200527704485488	C	20.9	4.070212	0.76301	0.010119	0.049178	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203;ENST00000537444	T;T;T;T;T;T;T	0.51071	1.26;1.26;1.26;1.26;1.26;1.26;0.72	5.54	5.54	0.83059	.	0.000000	0.56097	D	0.000022	T	0.57272	0.2042	L	0.53249	1.67	0.32212	N	0.576451	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.963	D;D;D;D;P	0.97110	0.999;1.0;0.999;0.966;0.792	T	0.42430	-0.9452	9	0.23302	T	0.38	.	19.8426	0.96695	0.0:1.0:0.0:0.0	rs41271862	4047;6135;6313;6133;3721	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	N	3721;6313;6135;4047;5809;3938;6024;137	ENSP00000244364:D3721N;ENSP00000359790:D6313N;ENSP00000359805:D6135N;ENSP00000400883:D4047N;ENSP00000393645:D5809N;ENSP00000359824:D3938N;ENSP00000354508:D6024N	ENSP00000244364:D3721N	D	-	1	0	DST	56481495	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	6.039000	0.70972	2.765000	0.95021	0.557000	0.71058	GAC	C|0.967;T|0.033	0.033	strong		0.438	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
MAPT	4137	hgsc.bcm.edu	37	17	44068924	44068924	+	Silent	SNP	G	G	A	rs1052551	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44068924G>A	ENST00000571987.1	+	8	1479	c.1479G>A	c.(1477-1479)ccG>ccA	p.P493P	MAPT_ENST00000347967.5_Silent_p.P82P|MAPT_ENST00000576518.1_Silent_p.P107P|MAPT_ENST00000351559.5_Silent_p.P176P|MAPT_ENST00000334239.8_Silent_p.P118P|MAPT_ENST00000431008.3_Silent_p.P176P|MAPT_ENST00000344290.5_Silent_p.P493P|MAPT_ENST00000420682.2_Silent_p.P147P|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000340799.5_Silent_p.P147P|MAPT_ENST00000415613.2_Silent_p.P493P|MAPT_ENST00000574436.1_Silent_p.P176P|MAPT_ENST00000446361.3_Silent_p.P118P|MAPT_ENST00000262410.5_Silent_p.P493P|MAPT_ENST00000535772.1_Silent_p.P176P			P10636	TAU_HUMAN	microtubule-associated protein tau	493					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)	CAAAAACCCCGCCCGCTCCAA	0.572													G|||	429	0.0856629	0.0129	0.1571	5008	,	,		15989	0.001		0.2406	False		,,,				2504	0.0613				p.P493P		Atlas-SNP	.											.	MAPT	135	.	0			c.G1479A						PASS	.	G	,,,,,,,	187,4219	120.0+/-157.7	4,179,2020	80.0	78.0	79.0		1479,441,441,528,528,354,1479,354	-8.5	0.1	17	dbSNP_86	79	1927,6673	337.6+/-322.4	220,1487,2593	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,	224,1666,4613	AA,AG,GG		22.407,4.2442,16.254	,,,,,,,	493/777,147/413,147/382,176/411,176/442,118/384,493/759,118/353	44068924	2114,10892	2203	4300	6503	SO:0001819	synonymous_variant	4137	exon9			AACCCCGCCCGCT	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.1479G>A	17.37:g.44068924G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			A|0.147;G|0.853;T|0.000	0.147	strong		0.572	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376107	113376107	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:113376107C>T	ENST00000478658.1	-	5	4439	c.4422G>A	c.(4420-4422)caG>caA	p.Q1474Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1474Q			Q68DE3	K2018_HUMAN	KIAA2018	1474	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgttgttgctgttgctgct	0.493																																					p.Q1474Q		Atlas-SNP	.											KIAA2018,colon,carcinoma,0,1	KIAA2018	180	1	0			c.G4422A						PASS	.						88.0	96.0	93.0					3																	113376107		2193	4279	6472	SO:0001819	synonymous_variant	205717	exon7			TTGTTGCTGTTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4422G>A	3.37:g.113376107C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	148	13	0.0878378	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	none		0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
FUT10	84750	hgsc.bcm.edu	37	8	33246538	33246538	+	Silent	SNP	A	A	G	rs16880849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:33246538A>G	ENST00000327671.5	-	4	1786	c.1155T>C	c.(1153-1155)gaT>gaC	p.D385D	FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Silent_p.D323D|FUT10_ENST00000524021.1_Silent_p.D357D|FUT10_ENST00000518672.1_Silent_p.D357D	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	385					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.D385D(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		ACTCAAATGCATCGATGTAAT	0.498													A|||	1496	0.298722	0.1808	0.17	5008	,	,		22022	0.4692		0.1938	False		,,,				2504	0.4816				p.D385D		Atlas-SNP	.											FUT10,NS,carcinoma,0,1	FUT10	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T1155C						PASS	.	A		916,3490	349.5+/-310.4	76,764,1363	246.0	207.0	220.0		1155	-0.1	0.9	8	dbSNP_123	220	1748,6852	317.0+/-313.0	177,1394,2729	no	coding-synonymous	FUT10	NM_032664.3		253,2158,4092	GG,GA,AA		20.3256,20.7898,20.4829		385/480	33246538	2664,10342	2203	4300	6503	SO:0001819	synonymous_variant	84750	exon4			AAATGCATCGATG	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1155T>C	8.37:g.33246538A>G		Somatic	422	0	0		WXS	Illumina HiSeq	Phase_I	419	190	0.453461	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Silent	SNP	ENST00000327671.5	37	CCDS6088.1																																																																																			A|0.769;G|0.231	0.231	strong		0.498	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
CRYGN	155051	hgsc.bcm.edu	37	7	151133271	151133271	+	Silent	SNP	G	G	A	rs2075001	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:151133271G>A	ENST00000337323.2	-	3	537	c.411C>T	c.(409-411)gaC>gaT	p.D137D	CRYGN_ENST00000476631.1_5'UTR|CRYGN_ENST00000491928.1_Intron|RP4-555L14.4_ENST00000465549.1_RNA|MIR3907_ENST00000579424.1_RNA	NM_144727.1	NP_653328.1	Q8WXF5	CRGN_HUMAN	crystallin, gamma N	137										central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(1)|lung(4)	8			OV - Ovarian serous cystadenocarcinoma(82;0.00358)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTCACGCTCCGTCCCCGTACA	0.672													G|||	1003	0.20028	0.0582	0.0403	5008	,	,		16387	0.4335		0.1024	False		,,,				2504	0.3661				p.D137D		Atlas-SNP	.											CRYGN,NS,adenoma,0,1	CRYGN	15	1	0			c.C411T						PASS	.	G		263,4143	149.2+/-183.4	6,251,1946	62.0	48.0	52.0		411	-5.5	0.9	7	dbSNP_96	52	867,7733	197.5+/-242.1	42,783,3475	no	coding-synonymous	CRYGN	NM_144727.1		48,1034,5421	AA,AG,GG		10.0814,5.9691,8.6883		137/183	151133271	1130,11876	2203	4300	6503	SO:0001819	synonymous_variant	155051	exon3			CGCTCCGTCCCCG	AF445455	CCDS5926.1	7q36.1	2003-02-25			ENSG00000127377	ENSG00000127377			20458	protein-coding gene	gene with protein product		609603					Standard	NM_144727		Approved		uc003wke.3	Q8WXF5	OTTHUMG00000157353	ENST00000337323.2:c.411C>T	7.37:g.151133271G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_144727	Q496G6	Silent	SNP	ENST00000337323.2	37	CCDS5926.1																																																																																			G|0.885;A|0.115	0.115	strong		0.672	CRYGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348553.1		
SYNE2	23224	hgsc.bcm.edu	37	14	64612858	64612858	+	Missense_Mutation	SNP	C	C	A	rs10151658	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64612858C>A	ENST00000344113.4	+	84	15768	c.15556C>A	c.(15556-15558)Ctg>Atg	p.L5186M	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.L1820M|SYNE2_ENST00000358025.3_Missense_Mutation_p.L5186M|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1571M|SYNE2_ENST00000554584.1_Missense_Mutation_p.L5103M|SYNE2_ENST00000357395.3_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	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	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	
TACC3	10460	hgsc.bcm.edu	37	4	1737502	1737502	+	Silent	SNP	C	C	T	rs11248073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	57	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	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		
LRIT1	26103	hgsc.bcm.edu	37	10	85992478	85992478	+	Silent	SNP	T	T	C	rs3814210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85992478T>C	ENST00000372105.3	-	4	1098	c.1077A>G	c.(1075-1077)ggA>ggG	p.G359G		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	359						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						CCCATAGTGCTCCTGGGCTCC	0.567													C|||	2470	0.493211	0.8669	0.4798	5008	,	,		21612	0.2589		0.3976	False		,,,				2504	0.3374				p.G359G		Atlas-SNP	.											LRIT1,NS,carcinoma,-1,1	LRIT1	73	1	0			c.A1077G						PASS	.	C		3424,982	364.4+/-316.9	1340,744,119	61.0	48.0	52.0		1077	-0.2	0.0	10	dbSNP_107	52	3352,5248	640.2+/-399.6	679,1994,1627	no	coding-synonymous	LRIT1	NM_015613.2		2019,2738,1746	CC,CT,TT		38.9767,22.2878,47.901		359/624	85992478	6776,6230	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon4			TAGTGCTCCTGGG	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.1077A>G	10.37:g.85992478T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			T|0.493;C|0.507	0.507	strong		0.567	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
CAV3	859	hgsc.bcm.edu	37	3	8775661	8775661	+	Silent	SNP	C	C	T	rs1008642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:8775661C>T	ENST00000343849.2	+	1	176	c.99C>T	c.(97-99)aaC>aaT	p.N33N	CAV3_ENST00000397368.2_Silent_p.N33N|CAV3_ENST00000472766.1_3'UTR|SSUH2_ENST00000478513.1_Intron	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	33			N -> K (in LGMD1C and MPDT; dbSNP:rs1008642). {ECO:0000269|PubMed:15564037, ECO:0000269|PubMed:15580566}.		actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)			breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						AGAACATTAACGAGGACATAG	0.577													C|||	1858	0.371006	0.621	0.3055	5008	,	,		15192	0.372		0.2684	False		,,,				2504	0.184				p.N33N		Atlas-SNP	.											.	CAV3	20	.	0			c.C99T	GRCh37	CM043264	CAV3	M	rs1008642	PASS	.	C	,	2409,1997	614.9+/-392.5	652,1105,446	114.0	102.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	99,99	1.6	1.0	3	dbSNP_86	106	2054,6546	356.3+/-330.2	251,1552,2497	no	coding-synonymous,coding-synonymous	CAV3	NM_001234.3,NM_033337.2	,	903,2657,2943	TT,TC,CC		23.8837,45.3246,34.3149	,	33/152,33/152	8775661	4463,8543	2203	4300	6503	SO:0001819	synonymous_variant	859	exon1			CATTAACGAGGAC	AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"""M-caveolin"""	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.99C>T	3.37:g.8775661C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_033337	A8K777|Q3T1A4	Silent	SNP	ENST00000343849.2	37	CCDS2569.1																																																																																			C|0.636;T|0.364	0.364	strong		0.577	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337	
CD101	9398	hgsc.bcm.edu	37	1	117554421	117554421	+	Missense_Mutation	SNP	A	A	G	rs3754112	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:117554421A>G	ENST00000256652.4	+	3	732	c.674A>G	c.(673-675)aAc>aGc	p.N225S	CD101_ENST00000369470.1_Missense_Mutation_p.N225S	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	225	Ig-like C2-type 2.		N -> S (in dbSNP:rs3754112).		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						GTACAGCTCAACAAACTGGGA	0.502													A|||	753	0.150359	0.0348	0.2017	5008	,	,		19749	0.0635		0.337	False		,,,				2504	0.1677				p.N225S		Atlas-SNP	.											CD101,NS,adenoma,0,1	CD101	95	1	0			c.A674G						PASS	.	A	SER/ASN	392,4014	197.4+/-221.5	19,354,1830	83.0	73.0	76.0		674	-2.3	0.1	1	dbSNP_107	76	2794,5806	442.4+/-360.1	457,1880,1963	yes	missense	CD101	NM_004258.3	46	476,2234,3793	GG,GA,AA		32.4884,8.897,24.4964	benign	225/1022	117554421	3186,9820	2203	4300	6503	SO:0001583	missense	9398	exon3			AGCTCAACAAACT	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.674A>G	1.37:g.117554421A>G	ENSP00000256652:p.Asn225Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	147	63	0.428571	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	371	0.16987179487179488	13	0.026422764227642278	92	0.2541436464088398	34	0.05944055944055944	232	0.30606860158311344	A	8.266	0.812367	0.16537	0.08897	0.324884	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.63913	-0.07;-0.07	5.57	-2.28	0.06826	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.652897	0.14980	N	0.287292	T	0.15869	0.0382	N	0.08118	0	0.42336	P	0.007686999999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.06516	-1.0822	9	0.42905	T	0.14	-6.1484	6.0936	0.20008	0.5508:0.1307:0.3185:0.0	rs3754112;rs17229361;rs17581002;rs52790018;rs57787687;rs3754112	225	Q93033	IGSF2_HUMAN	S	225	ENSP00000256652:N225S;ENSP00000358482:N225S	ENSP00000256652:N225S	N	+	2	0	CD101	117355944	0.989000	0.36119	0.077000	0.20336	0.004000	0.04260	0.914000	0.28624	-0.239000	0.09710	-0.285000	0.09966	AAC	G|0.210;N|0.000	0.210	strong		0.502	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
PRSS1	5644	hgsc.bcm.edu	37	7	142459626	142459626	+	Splice_Site	SNP	C	C	T	rs145867820		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142459626C>T	ENST00000311737.7	+	3	208	c.202C>T	c.(202-204)Cgc>Tgc	p.R68C	PRSS1_ENST00000486171.1_Splice_Site_p.R82C	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	68	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)	GCCCATCAGCCGCATCCAGGT	0.582																																					p.R68C		Atlas-SNP	.											PRSS1,colon,NS,-1,1	PRSS1	68	1	0			c.C202T						scavenged	.						128.0	125.0	126.0					7																	142459626		2203	4300	6503	SO:0001630	splice_region_variant	5644	exon3			ATCAGCCGCATCC	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.201-1C>T	7.37:g.142459626C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	96	6	0.0625	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	37	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.114437	0.37339	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243;ENST00000492062	D;D;D	0.89196	-2.48;-2.48;-2.48	3.28	3.28	0.37604	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.143154	0.64402	D	0.000003	D	0.85669	0.5750	M	0.62209	1.925	0.58432	D	0.999994	B;B	0.24092	0.097;0.04	B;B	0.22880	0.042;0.026	D	0.84953	0.0872	10	0.72032	D	0.01	.	9.6113	0.39665	0.2098:0.7902:0.0:0.0	.	82;68	E7EQ64;P07477	.;TRY1_HUMAN	C	82;68;68;18	ENSP00000417854:R82C;ENSP00000308720:R68C;ENSP00000419912:R18C	ENSP00000308720:R68C	R	+	1	0	PRSS1	142139200	0.449000	0.25689	0.996000	0.52242	0.613000	0.37349	1.114000	0.31196	1.789000	0.52484	0.398000	0.26397	CGC	.	.	weak		0.582	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		Missense_Mutation
PKD1	5310	hgsc.bcm.edu	37	16	2161153	2161153	+	Missense_Mutation	SNP	C	C	T	rs147141131	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2161153C>T	ENST00000262304.4	-	15	4223	c.4015G>A	c.(4015-4017)Gtg>Atg	p.V1339M	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.V1339M	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1339	PKD 8. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CACCCCCGCACGGTCGTGTTG	0.682																																					p.V1339M		Atlas-SNP	.											.	PKD1	184	.	0			c.G4015A						PASS	.	C	MET/VAL,MET/VAL	0,4374		0,0,2187	28.0	31.0	30.0		4015,4015	-0.2	0.0	16	dbSNP_134	30	4,8580	3.7+/-12.6	0,4,4288	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	21,21	0,4,6475	TT,TC,CC		0.0466,0.0,0.0309	benign,benign	1339/4303,1339/4304	2161153	4,12954	2187	4292	6479	SO:0001583	missense	5310	exon15			CCCGCACGGTCGT	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.4015G>A	16.37:g.2161153C>T	ENSP00000262304:p.Val1339Met	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	c	10.06	1.246377	0.22796	0.0	4.66E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.62788	0.0;0.0	5.58	-0.241	0.13043	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (4);	0.716298	0.14231	N	0.332727	T	0.69178	0.3082	M	0.63428	1.95	0.09310	N	1	D;D	0.62365	0.991;0.984	P;P	0.61132	0.884;0.88	T	0.60571	-0.7237	10	0.41790	T	0.15	.	9.8488	0.41043	0.0:0.5988:0.0:0.4012	.	1339;1339	P98161-3;P98161	.;PKD1_HUMAN	M	1339;1339;1020	ENSP00000262304:V1339M;ENSP00000399501:V1339M	ENSP00000262304:V1339M	V	-	1	0	PKD1	2101154	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.106000	0.03319	-0.296000	0.08947	-0.401000	0.06369	GTG	C|0.999;T|0.001	0.001	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
TAP2	6891	hgsc.bcm.edu	37	6	32797297	32797297	+	Silent	SNP	T	T	C	rs241441	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32797297T>C	ENST00000452392.2	-	11	1985	c.1812A>G	c.(1810-1812)ggA>ggG	p.G604G	TAP2_ENST00000374899.4_Silent_p.G604G|TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374897.2_Silent_p.G604G			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	CCAGCTGGCTTCCCTTCTCCC	0.552													C|||	1498	0.299121	0.1551	0.304	5008	,	,		20092	0.3621		0.2783	False		,,,				2504	0.4468				p.G604G		Atlas-SNP	.											.	TAP2	98	.	0			c.A1812G						PASS	.	C	,	815,3591	317.7+/-295.3	77,661,1465	70.0	72.0	71.0		1812,1812	-2.5	0.1	6	dbSNP_79	71	2259,6341	376.1+/-338.0	292,1675,2333	no	coding-synonymous,coding-synonymous	TAP2	NM_000544.3,NM_018833.2	,	369,2336,3798	CC,CT,TT		26.2674,18.4975,23.6352	,	604/704,604/654	32797297	3074,9932	2203	4300	6503	SO:0001819	synonymous_variant	6891	exon11			CTGGCTTCCCTTC	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1812A>G	6.37:g.32797297T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000452392.2	37																																																																																				T|0.748;C|0.252	0.252	strong		0.552	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
TEX29	121793	hgsc.bcm.edu	37	13	111980537	111980537	+	Silent	SNP	C	C	T	rs1359428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:111980537C>T	ENST00000283547.1	+	3	195	c.66C>T	c.(64-66)gaC>gaT	p.D22D		NM_152324.1	NP_689537.1	Q8N6K0	TEX29_HUMAN	testis expressed 29	22						integral component of membrane (GO:0016021)											CAGTGTGTGACGTTCCTCTGT	0.542													C|||	2713	0.541733	0.2466	0.6585	5008	,	,		17212	0.7927		0.492	False		,,,				2504	0.6503				p.D22D		Atlas-SNP	.											.	.	.	.	0			c.C66T						PASS	.	C		1282,3124	436.1+/-344.5	193,896,1114	154.0	126.0	136.0		66	0.9	1.0	13	dbSNP_88	136	4195,4405	570.1+/-389.3	1014,2167,1119	no	coding-synonymous	C13orf16	NM_152324.1		1207,3063,2233	TT,TC,CC		48.7791,29.0967,42.1113		22/152	111980537	5477,7529	2203	4300	6503	SO:0001819	synonymous_variant	121793	exon3			GTGTGACGTTCCT	BC029889	CCDS9522.1	13q34	2012-03-23	2012-02-07	2012-02-07	ENSG00000153495	ENSG00000153495			20370	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 16"""	C13orf16			Standard	NM_152324		Approved	bA474D23.1, MGC35169	uc001vsa.3	Q8N6K0	OTTHUMG00000017358	ENST00000283547.1:c.66C>T	13.37:g.111980537C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	183	82	0.448087	NM_152324		Silent	SNP	ENST00000283547.1	37	CCDS9522.1																																																																																			C|0.529;T|0.471	0.471	strong		0.542	TEX29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045812.2	NM_152324	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808069	18808069	+	Silent	SNP	A	A	G	rs7528572	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:18808069A>G	ENST00000400664.1	+	1	646	c.594A>G	c.(592-594)ggA>ggG	p.G198G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	198						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGCATCCAGGACTGGGGCAAC	0.602													G|||	473	0.0944489	0.1233	0.1239	5008	,	,		17039	0.0377		0.1233	False		,,,				2504	0.0634				p.G198G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.A594G						PASS	.	G		451,3955	781.1+/-414.5	22,407,1774	47.0	48.0	48.0		594	1.5	0.0	1	dbSNP_116	48	1063,7537	767.3+/-407.6	62,939,3299	no	coding-synonymous	KLHDC7A	NM_152375.2		84,1346,5073	GG,GA,AA		12.3605,10.236,11.6408		198/778	18808069	1514,11492	2203	4300	6503	SO:0001819	synonymous_variant	127707	exon1			TCCAGGACTGGGG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.594A>G	1.37:g.18808069A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			A|0.893;G|0.107	0.107	strong		0.602	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
RIPK1	8737	hgsc.bcm.edu	37	6	3083369	3083369	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3083369T>C	ENST00000259808.4	+	5	808	c.510T>C	c.(508-510)aaT>aaC	p.N170N	RIPK1_ENST00000380409.2_Silent_p.N170N|RIPK1_ENST00000541791.1_Silent_p.N124N|RIPK1_ENST00000479389.1_3'UTR			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|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 interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|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 production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|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)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				AACTGAATAATGAAGAGCACA	0.527																																					p.N170N		Atlas-SNP	.											.	RIPK1	56	.	0			c.T510C						PASS	.						133.0	117.0	123.0					6																	3083369		2203	4300	6503	SO:0001819	synonymous_variant	8737	exon4			GAATAATGAAGAG	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.510T>C	6.37:g.3083369T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	108	69	0.638889	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Silent	SNP	ENST00000259808.4	37	CCDS4482.1																																																																																			.	.	none		0.527	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804	
CARD14	79092	hgsc.bcm.edu	37	17	78166326	78166326	+	Missense_Mutation	SNP	G	G	A	rs61751629	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78166326G>A	ENST00000573882.1	+	11	1800	c.1264G>A	c.(1264-1266)Gag>Aag	p.E422K	CARD14_ENST00000573754.1_3'UTR|CARD14_ENST00000392434.2_Missense_Mutation_p.E185K|CARD14_ENST00000344227.2_Missense_Mutation_p.E422K|CARD14_ENST00000570421.1_Missense_Mutation_p.E422K			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	422					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)			CAGGACCAGGGAGCCCTGTCC	0.617													G|||	41	0.0081869	0.0008	0.0115	5008	,	,		16926	0.0		0.0288	False		,,,				2504	0.0031				p.E422K		Atlas-SNP	.											.	CARD14	98	.	0			c.G1264A						PASS	.	G	LYS/GLU,LYS/GLU	36,4370	36.0+/-67.5	0,36,2167	58.0	57.0	58.0		1264,553	3.6	0.1	17	dbSNP_129	58	251,8347	95.2+/-157.0	2,247,4050	yes	missense,missense	CARD14	NM_024110.3,NM_052819.2	56,56	2,283,6217	AA,AG,GG		2.9193,0.8171,2.207	possibly-damaging,possibly-damaging	422/1005,185/435	78166326	287,12717	2203	4299	6502	SO:0001583	missense	79092	exon9			ACCAGGGAGCCCT	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.1264G>A	17.37:g.78166326G>A	ENSP00000458715:p.Glu422Lys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	210	117	0.557143	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	26	0.011904761904761904	0	0.0	4	0.011049723756906077	0	0.0	22	0.029023746701846966	G	11.16	1.557964	0.27827	0.008171	0.029193	ENSG00000141527	ENST00000344227;ENST00000392434;ENST00000309710	T;T	0.33654	1.4;1.4	3.64	3.64	0.41730	.	0.676481	0.14270	N	0.330223	T	0.15652	0.0377	L	0.60455	1.87	0.09310	N	1	P;P;P	0.46784	0.608;0.884;0.884	B;P;B	0.46076	0.111;0.503;0.19	T	0.07046	-1.0793	10	0.41790	T	0.15	-13.2761	6.8704	0.24117	0.128:0.0:0.872:0.0	rs61751629	422;185;422	B8QQJ3;E7ETJ2;Q9BXL6	.;.;CAR14_HUMAN	K	422;185;185	ENSP00000344549:E422K;ENSP00000376229:E185K	ENSP00000308507:E185K	E	+	1	0	CARD14	75780921	0.375000	0.25089	0.061000	0.19648	0.098000	0.18820	2.150000	0.42254	1.854000	0.53819	0.561000	0.74099	GAG	G|0.979;A|0.021	0.021	strong		0.617	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
PRSS53	339105	hgsc.bcm.edu	37	16	31096495	31096495	+	Missense_Mutation	SNP	G	G	C	rs72785539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31096495G>C	ENST00000280606.6	-	7	1123	c.970C>G	c.(970-972)Ctg>Gtg	p.L324V		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	324	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						CCACAGGCCAGCTGTCCCTGG	0.637													G|||	4	0.000798722	0.0	0.0	5008	,	,		19514	0.0		0.004	False		,,,				2504	0.0				p.L324V		Atlas-SNP	.											.	PRSS53	29	.	0			c.C970G						PASS	.	G	VAL/LEU	2,4122		0,2,2060	21.0	26.0	25.0		970	4.6	0.9	16	dbSNP_130	25	24,8378		0,24,4177	yes	missense	PRSS53	NM_001039503.2	32	0,26,6237	CC,CG,GG		0.2856,0.0485,0.2076	possibly-damaging	324/554	31096495	26,12500	2062	4201	6263	SO:0001583	missense	339105	exon7			AGGCCAGCTGTCC		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.970C>G	16.37:g.31096495G>C	ENSP00000280606:p.Leu324Val	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	240	126	0.525	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.86	2.364215	0.41902	4.85E-4	0.002856	ENSG00000151006	ENST00000280606	T	0.30448	1.53	5.75	4.61	0.57282	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.302705	0.17712	U	0.164555	T	0.28466	0.0704	L	0.49699	1.58	0.09310	N	1	P	0.43231	0.801	B	0.41374	0.355	T	0.17501	-1.0367	10	0.42905	T	0.14	.	9.359	0.38184	0.0858:0.0:0.7657:0.1485	.	324	Q2L4Q9	PRS53_HUMAN	V	324	ENSP00000280606:L324V	ENSP00000280606:L324V	L	-	1	2	PRSS53	31003996	0.998000	0.40836	0.950000	0.38849	0.578000	0.36192	3.172000	0.50832	2.720000	0.93068	0.655000	0.94253	CTG	G|0.999;C|0.001	0.001	strong		0.637	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
CX3CR1	1524	hgsc.bcm.edu	37	3	39307162	39307162	+	Missense_Mutation	SNP	G	G	A	rs3732378	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:39307162G>A	ENST00000541347.1	-	2	1078	c.839C>T	c.(838-840)aCg>aTg	p.T280M	CX3CR1_ENST00000542107.1_Missense_Mutation_p.T280M|CX3CR1_ENST00000358309.3_Missense_Mutation_p.T312M|CX3CR1_ENST00000399220.2_Missense_Mutation_p.T280M	NM_001171171.1	NP_001164642.1	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	280			T -> M (common polymorphism in Caucasian population; associated with higher risk of developing ARMD12; chemotaxis of monocytes of individuals with homozygous Met-280 and Ile-249 genotypes is impaired in the presence of bound CX3CR1 protein; dbSNP:rs3732378). {ECO:0000269|PubMed:10731151, 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)		AAATGCAACCGTCTCAGTCAC	0.468													G|||	428	0.0854633	0.0083	0.1556	5008	,	,		22185	0.0288		0.172	False		,,,				2504	0.1094				p.T312M		Atlas-SNP	.											CX3CR1_ENST00000358309,NS,adenocarcinoma,+1,4	CX3CR1	91	4	0			c.C935T	GRCh37	CM000505	CX3CR1	M	rs3732378	PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	126,3788		2,122,1833	138.0	136.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	839,839,935,839	4.0	0.7	3	dbSNP_107	137	1432,6886		124,1184,2851	yes	missense,missense,missense,missense	CX3CR1	NM_001171171.1,NM_001171172.1,NM_001171174.1,NM_001337.3	81,81,81,81	126,1306,4684	AA,AG,GG		17.2157,3.2192,12.7371	probably-damaging,probably-damaging,probably-damaging,probably-damaging	280/356,280/356,312/388,280/356	39307162	1558,10674	1957	4159	6116	SO:0001583	missense	1524	exon2			GCAACCGTCTCAG	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.839C>T	3.37:g.39307162G>A	ENSP00000439140:p.Thr280Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_001171174	A0N0N6|B2R5Z4|J3KP17	Missense_Mutation	SNP	ENST00000541347.1	37	CCDS43069.1	211	0.09661172161172162	6	0.012195121951219513	57	0.1574585635359116	19	0.033216783216783216	129	0.17018469656992086	G	11.03	1.519699	0.27211	0.032192	0.172157	ENSG00000168329	ENST00000399220;ENST00000538756;ENST00000358309;ENST00000541347;ENST00000542107	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.77	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.227311	0.45361	N	0.000375	T	0.00300	0.0009	M	0.80028	2.48	0.42331	P	0.007707000000000019	P	0.42248	0.774	B	0.28139	0.086	T	0.29027	-1.0025	9	0.59425	D	0.04	.	6.1781	0.20455	0.155:0.0:0.6947:0.1503	rs3732378;rs17792900;rs52789411;rs60081475;rs3732378	280	P49238	CX3C1_HUMAN	M	280;288;312;280;280	ENSP00000382166:T280M;ENSP00000351059:T312M;ENSP00000439140:T280M;ENSP00000444928:T280M	ENSP00000351059:T312M	T	-	2	0	CX3CR1	39282166	0.922000	0.31269	0.681000	0.30009	0.221000	0.24807	1.916000	0.39986	0.790000	0.33803	0.655000	0.94253	ACG	A|0.101;C|0.011	0.101	strong		0.468	CX3CR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343613.1	NM_001337	
KNDC1	85442	hgsc.bcm.edu	37	10	135010568	135010568	+	Missense_Mutation	SNP	G	G	A	rs35152544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:135010568G>A	ENST00000304613.3	+	11	1762	c.1741G>A	c.(1741-1743)Ggc>Agc	p.G581S	KNDC1_ENST00000368571.2_Missense_Mutation_p.G516S|KNDC1_ENST00000368572.2_Missense_Mutation_p.G581S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	581	KIND 2. {ECO:0000255|PROSITE- ProRule:PRU00709}.		G -> S (in dbSNP:rs35152544).		cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCAGGTGTGCGGCAGCTACCT	0.642													G|||	240	0.0479233	0.0938	0.0418	5008	,	,		15259	0.001		0.0586	False		,,,				2504	0.0276				p.G581S		Atlas-SNP	.											.	KNDC1	155	.	0			c.G1741A						PASS	.	G	SER/GLY	367,4039	187.8+/-214.3	14,339,1850	72.0	55.0	61.0		1741	-5.0	0.0	10	dbSNP_126	61	577,8023	154.9+/-209.1	23,531,3746	yes	missense	KNDC1	NM_152643.6	56	37,870,5596	AA,AG,GG		6.7093,8.3296,7.2582	benign	581/1750	135010568	944,12062	2203	4300	6503	SO:0001583	missense	85442	exon11			GTGTGCGGCAGCT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.1741G>A	10.37:g.135010568G>A	ENSP00000304437:p.Gly581Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	110	0.05036630036630037	48	0.0975609756097561	15	0.04143646408839779	1	0.0017482517482517483	46	0.06068601583113457	G	3.258	-0.151765	0.06585	0.083296	0.067093	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.09073	3.02;3.02;3.02	3.76	-4.98	0.03019	KIND (2);	0.822927	0.10555	N	0.660916	T	0.00039	0.0001	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.20671	0.038;0.047	B;B	0.14023	0.01;0.007	T	0.30327	-0.9982	9	0.02654	T	1	-9.1876	4.8634	0.13596	0.4145:0.2857:0.2998:0.0	rs35152544	516;581	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	S	581;581;516	ENSP00000304437:G581S;ENSP00000357561:G581S;ENSP00000357560:G516S	ENSP00000304437:G581S	G	+	1	0	KNDC1	134860558	0.000000	0.05858	0.000000	0.03702	0.312000	0.27988	-0.475000	0.06599	-1.124000	0.02936	0.467000	0.42956	GGC	G|0.933;A|0.067	0.067	strong		0.642	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
NLRP4	147945	hgsc.bcm.edu	37	19	56370166	56370166	+	Silent	SNP	C	C	T	rs379327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56370166C>T	ENST00000301295.6	+	3	1829	c.1407C>T	c.(1405-1407)caC>caT	p.H469H	NLRP4_ENST00000346986.5_Silent_p.H469H|NLRP4_ENST00000587891.1_Silent_p.H394H	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	469	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TCAAGAGCCACCTTGATCATC	0.473													C|||	522	0.104233	0.0061	0.196	5008	,	,		19960	0.1647		0.1093	False		,,,				2504	0.1043				p.H469H		Atlas-SNP	.											NLRP4_ENST00000301295,right_upper_lobe,carcinoma,+1,1	NLRP4	331	1	0			c.C1407T						PASS	.	C		98,4308	77.3+/-115.6	1,96,2106	142.0	140.0	141.0		1407	0.6	0.0	19	dbSNP_80	141	1037,7563	220.6+/-258.3	74,889,3337	no	coding-synonymous	NLRP4	NM_134444.4		75,985,5443	TT,TC,CC		12.0581,2.2242,8.7267		469/995	56370166	1135,11871	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			GAGCCACCTTGAT	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1407C>T	19.37:g.56370166C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	223	107	0.479821	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.899;T|0.101	0.101	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
TSC1	7248	hgsc.bcm.edu	37	9	135772716	135772716	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:135772716C>T	ENST00000298552.3	-	22	3051	c.2830G>A	c.(2830-2832)Gca>Aca	p.A944T	TSC1_ENST00000440111.2_Missense_Mutation_p.A944T|TSC1_ENST00000545250.1_Missense_Mutation_p.A893T	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	944					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.A944T(1)|p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CTGCTCTCTGCGGCCTGCAGC	0.433			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.A944T		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	TSC1,colon,carcinoma,0,2	TSC1	167	2	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|bone(1)	c.G2830A						scavenged	.						95.0	100.0	99.0					9																	135772716		2203	4300	6503	SO:0001583	missense	7248	exon22	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCTCTGCGGCCTG	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.2830G>A	9.37:g.135772716C>T	ENSP00000298552:p.Ala944Thr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	210	4	0.0190476	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	37	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	C	14.88	2.666786	0.47677	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;T	0.81659	-1.52;-1.52;-1.32	5.61	5.61	0.85477	.	0.188397	0.47455	D	0.000221	T	0.73567	0.3603	L	0.56769	1.78	0.80722	D	1	P;P	0.42620	0.785;0.785	B;B	0.31101	0.124;0.124	T	0.73225	-0.4050	10	0.13470	T	0.59	-12.668	18.624	0.91331	0.0:1.0:0.0:0.0	.	893;944	B7Z897;Q92574	.;TSC1_HUMAN	T	944;944;893	ENSP00000298552:A944T;ENSP00000394524:A944T;ENSP00000444017:A893T	ENSP00000298552:A944T	A	-	1	0	TSC1	134762537	0.998000	0.40836	0.955000	0.39395	0.972000	0.66771	4.138000	0.58017	2.645000	0.89757	0.650000	0.86243	GCA	.	.	none		0.433	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
CEACAM20	125931	hgsc.bcm.edu	37	19	45016116	45016116	+	RNA	SNP	A	A	G	rs8100718	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45016116A>G	ENST00000454753.1	-	0	1813							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)		p.C511R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				GATATATTGCAATACTCAGGA	0.507													A|||	1925	0.384385	0.1679	0.4078	5008	,	,		18720	0.3919		0.4612	False		,,,				2504	0.5736				p.C512R		Atlas-SNP	.											CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	1	Substitution - Missense(1)	prostate(1)	c.T1534C						PASS	.	A	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	917,3079		106,705,1187	46.0	46.0	46.0		1535,1256,1256,1535	0.9	0.0	19	dbSNP_116	46	4182,4158		1069,2044,1057	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	180,180,180,180	1175,2749,2244	GG,GA,AA		49.8561,22.9479,41.3343	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	512/597,419/492,419/504,512/585	45016116	5099,7237	1998	4170	6168			125931	exon10			TATTGCAATACTC	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45016116A>G		Somatic	207	2	0.00966184		WXS	Illumina HiSeq	Phase_I	160	160	1	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				A|0.633;G|0.366	0.366	strong		0.507	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
COL4A1	1282	hgsc.bcm.edu	37	13	110818598	110818598	+	Missense_Mutation	SNP	T	T	G	rs3742207	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:110818598T>G	ENST00000375820.4	-	45	4123	c.4002A>C	c.(4000-4002)caA>caC	p.Q1334H	COL4A1_ENST00000467182.1_5'Flank	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1334	Triple-helical region.		Q -> H (in dbSNP:rs3742207). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21527998}.		axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CCGGGACGCCTTGATCGCCTT	0.473													T|||	1444	0.288339	0.2882	0.2334	5008	,	,		18983	0.2629		0.325	False		,,,				2504	0.316				p.Q1334H		Atlas-SNP	.											.	COL4A1	372	.	0			c.A4002C	GRCh37	CM083606	COL4A1	M	rs3742207	PASS	.	T	HIS/GLN	1243,3163	428.5+/-341.9	179,885,1139	183.0	167.0	173.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4002	-1.2	0.9	13	dbSNP_107	173	2935,5665	457.2+/-364.3	501,1933,1866	yes	missense	COL4A1	NM_001845.4	24	680,2818,3005	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	34.1279,28.2115,32.1236	benign	1334/1670	110818598	4178,8828	2203	4300	6503	SO:0001583	missense	1282	exon45			GACGCCTTGATCG	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.4002A>C	13.37:g.110818598T>G	ENSP00000364979:p.Gln1334His	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	219	217	0.990868	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	639	0.2925824175824176	142	0.2886178861788618	89	0.24585635359116023	142	0.24825174825174826	266	0.35092348284960423	T	6.850	0.526111	0.13066	0.282115	0.341279	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	D	0.93307	-3.2	4.68	-1.19	0.09585	.	0.072729	0.56097	D	0.000024	T	0.00012	0.0000	L	0.33093	0.98	0.09310	P	0.9999999999992717	B	0.29988	0.264	B	0.37550	0.253	T	0.04065	-1.0980	9	0.39692	T	0.17	.	10.2129	0.43152	0.0:0.3302:0.0:0.6698	rs3742207;rs17517176;rs61457243;rs3742207	1334	P02462	CO4A1_HUMAN	H	977;1334;983	ENSP00000364979:Q1334H	ENSP00000364973:Q977H	Q	-	3	2	COL4A1	109616599	1.000000	0.71417	0.874000	0.34290	0.050000	0.14768	0.460000	0.21924	-0.086000	0.12550	-1.070000	0.02257	CAA	T|0.688;G|0.312	0.312	strong		0.473	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
NRCAM	4897	hgsc.bcm.edu	37	7	107872816	107872816	+	Silent	SNP	G	G	A	rs2072546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:107872816G>A	ENST00000425651.2	-	4	380	c.381C>T	c.(379-381)aaC>aaT	p.N127N	NRCAM_ENST00000379024.4_Silent_p.N127N|NRCAM_ENST00000351718.4_Silent_p.N121N|NRCAM_ENST00000413765.2_Silent_p.N127N|NRCAM_ENST00000379028.3_Silent_p.N127N|NRCAM_ENST00000379022.4_Silent_p.N127N	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	127	Ig-like 1.				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						CTCCGCGTTCGTTCCTTGCTG	0.458													G|||	1067	0.213059	0.0061	0.2723	5008	,	,		18947	0.5466		0.1243	False		,,,				2504	0.1984				p.N127N		Atlas-SNP	.											NRCAM_ENST00000379028,colon,carcinoma,0,2	NRCAM	267	2	0			c.C381T						PASS	.	G	,,,,	144,4262	101.6+/-140.2	1,142,2060	193.0	174.0	181.0		381,381,381,381,363	-9.8	0.4	7	dbSNP_96	181	1168,7432	239.4+/-270.5	87,994,3219	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	88,1136,5279	AA,AG,GG		13.5814,3.2683,10.0877	,,,,	127/1305,127/1212,127/1193,127/1181,121/1184	107872816	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	4897	exon4			GCGTTCGTTCCTT		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.381C>T	7.37:g.107872816G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	178	75	0.421348	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1																																																																																			G|0.834;A|0.166	0.166	strong		0.458	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
PSMG4	389362	hgsc.bcm.edu	37	6	3264502	3264502	+	Intron	SNP	G	G	C	rs4959787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3264502G>C	ENST00000438998.2	+	2	379				PSMG4_ENST00000380306.4_Intron|PSMG4_ENST00000419065.2_Missense_Mutation_p.G104R|PSMG4_ENST00000380305.4_Intron|PSMG4_ENST00000451246.2_Intron|PSMG4_ENST00000473000.2_3'UTR	NM_001128591.1	NP_001122063.1	Q5JS54	PSMG4_HUMAN	proteasome (prosome, macropain) assembly chaperone 4											endometrium(1)	1						ATTAAGCAAAGGTCATGAGGC	0.592													G|||	3066	0.61222	0.2852	0.7651	5008	,	,		24648	0.6647		0.8419	False		,,,				2504	0.6554				p.G104R		Atlas-SNP	.											.	PSMG4	23	.	0			c.G310C						PASS	.	G	,ARG/GLY	498,886		86,326,280	261.0	203.0	220.0		,310	-1.6	0.0	6	dbSNP_111	220	2556,626		1019,518,54	yes	intron,missense	PSMG4	NM_001128591.1,NM_001128592.1	,125	1105,844,334	CC,CG,GG		19.6732,35.9827,33.1143	,benign	,104/163	3264502	3054,1512	692	1591	2283	SO:0001627	intron_variant	389362	exon3			AGCAAAGGTCATG		CCDS47360.1, CCDS47361.1, CCDS47362.1	6p25.2	2010-06-23	2008-02-25	2008-02-25	ENSG00000180822	ENSG00000180822			21108	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 86"""	C6orf86		17707236	Standard	NM_001128591		Approved	PAC4	uc010jnl.1	Q5JS54	OTTHUMG00000014142	ENST00000438998.2:c.250+509G>C	6.37:g.3264502G>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_001128592	C9J2F8|F8WBZ2|Q5JS53|Q5JS56	Missense_Mutation	SNP	ENST00000438998.2	37	CCDS47361.1	1446	0.6620879120879121	160	0.3252032520325203	277	0.7651933701657458	368	0.6433566433566433	641	0.8456464379947229	G	12.40	1.926440	0.34002	0.359827	0.803268	ENSG00000180822	ENST00000419065	.	.	.	3.73	-1.64	0.08318	.	.	.	.	.	T	0.04679	0.0127	N	0.08118	0	0.80722	P	0.0	B	0.22983	0.078	B	0.22601	0.04	T	0.35425	-0.9789	7	0.37606	T	0.19	.	1.2288	0.01939	0.2051:0.3243:0.3049:0.1657	rs4959787;rs56466809;rs4959787	104	C9J2F8	.	R	104	.	ENSP00000392353:G104R	G	+	1	0	PSMG4	3209501	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.020000	0.12525	-0.355000	0.08199	0.563000	0.77884	GGT	G|0.381;C|0.619	0.619	strong		0.592	PSMG4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039678.2		
UBP1	7342	hgsc.bcm.edu	37	3	33458266	33458266	+	Missense_Mutation	SNP	T	T	C	rs3736563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:33458266T>C	ENST00000283629.3	-	3	855	c.326A>G	c.(325-327)aAt>aGt	p.N109S	RNU7-110P_ENST00000516891.1_RNA|UBP1_ENST00000447368.2_Missense_Mutation_p.N109S|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	402	2	0.00497512		WXS	Illumina HiSeq	Phase_I	408	206	0.504902	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	
TRANK1	9881	hgsc.bcm.edu	37	3	36898036	36898036	+	Silent	SNP	G	G	A	rs62245253	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:36898036G>A	ENST00000429976.2	-	12	3292	c.3045C>T	c.(3043-3045)taC>taT	p.Y1015Y	TRANK1_ENST00000428977.2_Silent_p.Y465Y|TRANK1_ENST00000301807.6_Silent_p.Y465Y	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1015							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						CGATCACCGCGTACTCAAGCT	0.537													G|||	117	0.0233626	0.0038	0.0346	5008	,	,		19018	0.0		0.0666	False		,,,				2504	0.0215				p.Y1015Y		Atlas-SNP	.											.	TRANK1	398	.	0			c.C3045T						PASS	.	G		53,4091		0,53,2019	154.0	156.0	156.0		3045	-7.2	0.0	3	dbSNP_129	156	573,7805		18,537,3634	no	coding-synonymous	TRANK1	NM_014831.2		18,590,5653	AA,AG,GG		6.8393,1.279,4.9992		1015/2926	36898036	626,11896	2072	4189	6261	SO:0001819	synonymous_variant	9881	exon12			CACCGCGTACTCA	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.3045C>T	3.37:g.36898036G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	150	77	0.513333	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			G|0.965;A|0.035	0.035	strong		0.537	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
CCDC168	643677	hgsc.bcm.edu	37	13	103389885	103389885	+	5'Flank	SNP	T	T	G	rs77353067	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103389885T>G	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		ccgtcctctttcccttgctcc	0.498													T|||	19	0.00379393	0.0023	0.0029	5008	,	,		20066	0.0		0.0139	False		,,,				2504	0.0				p.K4388Q		Atlas-SNP	.											.	.	.	.	0			c.A13162C						PASS	.	T	GLN/LYS	2,1382		0,2,690	255.0	212.0	225.0		13162	0.7	0.0	13	dbSNP_132	225	36,3146		2,32,1557	yes	missense	CCDC168	NM_001146197.1	53	2,34,2247	GG,GT,TT		1.1314,0.1445,0.8322		4388/7082	103389885	38,4528	692	1591	2283	SO:0001631	upstream_gene_variant	643677	exon4			CCTCTTTCCCTTG		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		13.37:g.103389885T>G	Exception_encountered	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	213	108	0.507042	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37																																																																																				T|0.992;G|0.008	0.008	strong		0.498	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
NFRKB	4798	hgsc.bcm.edu	37	11	129754644	129754644	+	Silent	SNP	A	A	G	rs1131972	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:129754644A>G	ENST00000446488.3	-	6	841	c.738T>C	c.(736-738)acT>acC	p.T246T	NFRKB_ENST00000304521.5_Silent_p.T246T|NFRKB_ENST00000524746.1_Silent_p.T246T|NFRKB_ENST00000524794.1_Silent_p.T271T	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	246					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)		TCTCACCTGCAGTTTTCATAT	0.567													G|||	3828	0.764377	0.9788	0.6902	5008	,	,		15972	0.6647		0.7097	False		,,,				2504	0.6861				p.T271T		Atlas-SNP	.											.	NFRKB	101	.	0			c.T813C						PASS	.	G	,	4113,289	159.2+/-191.8	1928,257,16	66.0	74.0	71.0		738,813	-10.2	0.1	11	dbSNP_86	71	6141,2453	403.2+/-347.7	2187,1767,343	no	coding-synonymous,coding-synonymous	NFRKB	NM_001143835.1,NM_006165.3	,	4115,2024,359	GG,GA,AA		28.5432,6.5652,21.0988	,	246/1300,271/1325	129754644	10254,2742	2201	4297	6498	SO:0001819	synonymous_variant	4798	exon5			ACCTGCAGTTTTC		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.738T>C	11.37:g.129754644A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	73	70	0.958904	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																			A|0.224;G|0.776	0.776	strong		0.567	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
DPP9	91039	hgsc.bcm.edu	37	19	4702090	4702090	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4702090A>G	ENST00000598800.1	-	10	1379	c.874T>C	c.(874-876)Tct>Cct	p.S292P	DPP9_ENST00000262960.9_Missense_Mutation_p.S321P|DPP9_ENST00000597849.1_Missense_Mutation_p.S321P|DPP9_ENST00000594671.1_Missense_Mutation_p.S292P			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	292						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)	p.S400P(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		AGCGCAGGAGAGGGGACGTGA	0.597																																					p.S321P		Atlas-SNP	.											DPP9,NS,carcinoma,0,1	DPP9	59	1	1	Substitution - Missense(1)	kidney(1)	c.T961C						scavenged	.						96.0	104.0	101.0					19																	4702090		2022	4188	6210	SO:0001583	missense	91039	exon9			CAGGAGAGGGGAC	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"""dipeptidylpeptidase 9"""				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.874T>C	19.37:g.4702090A>G	ENSP00000469603:p.Ser292Pro	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	196	6	0.0306122	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	37		.	.	.	.	.	.	.	.	.	.	A	15.87	2.959971	0.53400	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.32753	1.44	4.67	4.67	0.58626	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.058305	0.64402	D	0.000001	T	0.56031	0.1958	M	0.83953	2.67	0.80722	D	1	P;P	0.52577	0.845;0.954	P;D	0.65987	0.781;0.94	T	0.60005	-0.7347	10	0.46703	T	0.11	-20.171	13.4274	0.61032	1.0:0.0:0.0:0.0	.	292;321	Q86TI2;Q1ZZB8	DPP9_HUMAN;.	P	400;262;321	ENSP00000262960:S321P	ENSP00000262960:S321P	S	-	1	0	DPP9	4653090	1.000000	0.71417	0.040000	0.18447	0.002000	0.02628	9.083000	0.94067	1.962000	0.57031	0.533000	0.62120	TCT	.	.	none		0.597	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2		
SFR1	119392	hgsc.bcm.edu	37	10	105882765	105882765	+	Missense_Mutation	SNP	A	A	G	rs10786783	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105882765A>G	ENST00000369727.3	+	2	75	c.56A>G	c.(55-57)gAc>gGc	p.D19G	SFR1_ENST00000463224.1_3'UTR|SFR1_ENST00000336358.5_Missense_Mutation_p.D81G|SFR1_ENST00000369729.3_Missense_Mutation_p.D6G	NM_001002759.1	NP_001002759.1	Q86XK3	SFR1_HUMAN	SWI5-dependent recombination repair 1	19			D -> G (in dbSNP:rs10786783). {ECO:0000269|PubMed:15489334}.		double-strand break repair via homologous recombination (GO:0000724)	nucleus (GO:0005634)|Swi5-Sfr1 complex (GO:0032798)											AGTCCGTCAGACTCAGCTGTG	0.368													A|||	1178	0.235224	0.3926	0.1427	5008	,	,		16366	0.2292		0.161	False		,,,				2504	0.1708				p.D19G		Atlas-SNP	.											.	.	.	.	0			c.A56G						PASS	.	A	GLY/ASP,GLY/ASP	1503,2903	479.5+/-358.5	256,991,956	82.0	82.0	82.0		56,17	0.9	0.0	10	dbSNP_120	82	1365,7235	266.3+/-286.6	110,1145,3045	yes	missense,missense	SFR1	NM_001002759.1,NM_145247.4	94,94	366,2136,4001	GG,GA,AA		15.8721,34.1126,22.0514	probably-damaging,probably-damaging	19/246,6/233	105882765	2868,10138	2203	4300	6503	SO:0001583	missense	119392	exon2			CGTCAGACTCAGC	BC020892	CCDS31279.1, CCDS31280.1	10q25.1	2013-10-11	2011-08-01	2011-08-01	ENSG00000156384	ENSG00000156384			29574	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 78"", ""MEI5 recombination repair protein homolog (S. cerevisiae)"""	C10orf78, MEIR5		21252223, 21779174, 20976249	Standard	NM_145247		Approved	MEI5, bA373N18.1, FLJ41960	uc001kxu.3	Q86XK3	OTTHUMG00000019000	ENST00000369727.3:c.56A>G	10.37:g.105882765A>G	ENSP00000358742:p.Asp19Gly	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_001002759	A8K569|B2RTV8|Q5JT39|Q5JT40|Q8WW47	Missense_Mutation	SNP	ENST00000369727.3	37	CCDS31279.1	476	0.21794871794871795	178	0.3617886178861789	57	0.1574585635359116	129	0.22552447552447552	112	0.14775725593667546	A	14.14	2.447906	0.43429	0.341126	0.158721	ENSG00000156384	ENST00000369729;ENST00000369727;ENST00000336358	T;T;T	0.62941	0.32;0.14;-0.01	4.87	0.86	0.19042	.	0.712209	0.14118	N	0.340210	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;B	0.40180	0.705;0.19	B;B	0.44044	0.439;0.081	T	0.24584	-1.0156	9	0.45353	T	0.12	-1.6448	5.9171	0.19061	0.5146:0.3276:0.0:0.1578	rs10786783;rs17845623;rs17858554;rs58753019;rs10786783	81;19	Q86XK3-2;Q86XK3	.;SFR1_HUMAN	G	6;19;81	ENSP00000358744:D6G;ENSP00000358742:D19G;ENSP00000338089:D81G	ENSP00000338089:D81G	D	+	2	0	SFR1	105872755	0.011000	0.17503	0.017000	0.16124	0.459000	0.32528	0.609000	0.24238	0.032000	0.15435	0.454000	0.30748	GAC	A|0.784;G|0.216	0.216	strong		0.368	SFR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050191.1	NM_145247	
COL18A1	80781	hgsc.bcm.edu	37	21	46929467	46929467	+	Silent	SNP	G	G	A	rs1050351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:46929467G>A	ENST00000359759.4	+	38	4713	c.4692G>A	c.(4690-4692)gcG>gcA	p.A1564A	COL18A1_ENST00000400337.2_Silent_p.A1149A|SLC19A1_ENST00000468508.1_5'Flank|COL18A1_ENST00000355480.5_Silent_p.A1329A|SLC19A1_ENST00000567670.1_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1564	Nonhelical region 11 (NC11).				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)		TGCGGCCGGCGCGACCCACAA	0.731													G|||	2522	0.503594	0.4985	0.5331	5008	,	,		9473	0.5744		0.4235	False		,,,				2504	0.499				p.A1326A		Atlas-SNP	.											.	COL18A1	129	.	0			c.G3978A						PASS	.	G	,	1341,2045		325,691,677	3.0	5.0	4.0		3987,3447	-8.6	0.0	21	dbSNP_86	4	2702,4614		621,1460,1577	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	946,2151,2254	AA,AG,GG		36.9328,39.6043,37.778	,	1329/1520,1149/1340	46929467	4043,6659	1693	3658	5351	SO:0001819	synonymous_variant	80781	exon39			GCCGGCGCGACCC		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.4692G>A	21.37:g.46929467G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37		1064	0.48717948717948717	243	0.49390243902439024	168	0.46408839779005523	338	0.5909090909090909	315	0.4155672823218997	G	0.442	-0.897882	0.02472	0.396043	0.369328	ENSG00000182871	ENST00000423214	.	.	.	4.3	-8.61	0.00885	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.25745	-1.0123	3	.	.	.	.	1.8031	0.03075	0.4365:0.2004:0.2121:0.151	rs1050351;rs3190648;rs17416842;rs58486368;rs1050351	.	.	.	H	134	.	.	R	+	2	0	COL18A1	45753895	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.970000	0.00668	-3.489000	0.00153	-1.036000	0.02392	CGC	G|0.516;A|0.484	0.484	strong		0.731	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
KANSL1	284058	hgsc.bcm.edu	37	17	44110541	44110541	+	Silent	SNP	G	G	A	rs35833914	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44110541G>A	ENST00000262419.6	-	13	3212	c.2742C>T	c.(2740-2742)gaC>gaT	p.D914D	KANSL1_ENST00000393476.3_Silent_p.D208D|KANSL1_ENST00000574590.1_Silent_p.D914D|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000572904.1_Silent_p.D914D|KANSL1_ENST00000575318.1_Silent_p.D850D|KANSL1_ENST00000432791.1_Silent_p.D914D	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	914	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CGAAGGCTGCGTCGGATAGGT	0.592													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19747	0.001		0.2406	False		,,,				2504	0.0613				p.D914D		Atlas-SNP	.											.	.	.	.	0			c.C2742T						PASS	.	G	,,	202,4204		5,192,2006	63.0	62.0	62.0		2739,2742,2742	-3.2	0.8	17	dbSNP_126	62	1914,6686		214,1486,2600	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	219,1678,4606	AA,AG,GG		22.2558,4.5847,16.2694	,,	913/1105,914/1106,914/1106	44110541	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon13			GGCTGCGTCGGAT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2742C>T	17.37:g.44110541G>A		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	176	176	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.144;C|0.000;G|0.856;T|0.000	0.144	strong		0.592	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768890	31768890	+	Silent	SNP	G	G	A	rs138330927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:31768890G>A	ENST00000240587.4	-	2	2136	c.1809C>T	c.(1807-1809)ccC>ccT	p.P603P		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	603					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)					AGTTTGTCTTGGGCATGGGGG	0.547													G|||	3	0.000599042	0.0	0.0	5008	,	,		17796	0.0		0.003	False		,,,				2504	0.0				p.P603P		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C1809T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	91.0	99.0	96.0		1809	3.1	1.0	19	dbSNP_134	96	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TSHZ3	NM_020856.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		603/1082	31768890	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			TGTCTTGGGCATG	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.1809C>T	19.37:g.31768890G>A		Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	244	108	0.442623	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.999;A|0.001	0.001	strong		0.547	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
MAVS	57506	hgsc.bcm.edu	37	20	3844929	3844929	+	Missense_Mutation	SNP	C	C	T	rs45437096	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3844929C>T	ENST00000428216.2	+	6	780	c.652C>T	c.(652-654)Cgt>Tgt	p.R218C	MAVS_ENST00000416600.2_Missense_Mutation_p.R77C|MAVS_ENST00000358134.6_3'UTR	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	218					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CACACCATCCCGTGGGCCTGT	0.602													C|||	263	0.052516	0.0106	0.0893	5008	,	,		18036	0.0		0.159	False		,,,				2504	0.0276				p.R218C		Atlas-SNP	.											.	MAVS	34	.	0			c.C652T						PASS	.	C	CYS/ARG,CYS/ARG	169,4237	111.6+/-149.8	6,157,2040	91.0	91.0	91.0		229,652	0.3	0.0	20	dbSNP_127	91	1418,7182	272.7+/-290.2	110,1198,2992	yes	missense,missense	MAVS	NM_001206491.1,NM_020746.4	180,180	116,1355,5032	TT,TC,CC		16.4884,3.8357,12.2021	benign,benign	77/400,218/541	3844929	1587,11419	2203	4300	6503	SO:0001583	missense	57506	exon6			CCATCCCGTGGGC	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"""virus-induced signaling adaptor"", ""IFN-B promoter stimulator 1"", ""CARD adaptor inducing IFN-beta"""	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.652C>T	20.37:g.3844929C>T	ENSP00000401980:p.Arg218Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	133	50	0.37594	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	163	0.07463369963369963	5	0.01016260162601626	38	0.10497237569060773	0	0.0	120	0.158311345646438	C	15.29	2.789708	0.50102	0.038357	0.164884	ENSG00000088888	ENST00000416600;ENST00000428216	T;T	0.34072	1.38;2.34	4.72	0.349	0.16032	.	1.472750	0.03891	N	0.278641	T	0.00109	0.0003	L	0.42245	1.32	0.80722	P	0.0	B	0.15930	0.015	B	0.12837	0.008	T	0.10965	-1.0607	9	0.34782	T	0.22	2.0676	4.4764	0.11746	0.0:0.5479:0.163:0.2891	rs45437096;rs62210536	218	Q7Z434	MAVS_HUMAN	C	77;218	ENSP00000413749:R77C;ENSP00000401980:R218C	ENSP00000413749:R77C	R	+	1	0	MAVS	3792929	0.000000	0.05858	0.012000	0.15200	0.954000	0.61252	-0.940000	0.03929	0.018000	0.15052	0.650000	0.86243	CGT	C|0.888;T|0.112	0.112	strong		0.602	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
NSF	4905	hgsc.bcm.edu	37	17	44828931	44828931	+	Silent	SNP	G	G	A	rs199533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44828931G>A	ENST00000398238.4	+	19	2213	c.2106G>A	c.(2104-2106)aaG>aaA	p.K702K	NSF_ENST00000575068.1_Silent_p.K697K|NSF_ENST00000225282.8_Silent_p.K608K	NM_006178.3	NP_006169.2	P46459	NSF_HUMAN	N-ethylmaleimide-sensitive factor	702					exocytosis (GO:0006887)|plasma membrane fusion (GO:0045026)|positive regulation of receptor recycling (GO:0001921)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|syntaxin-1 binding (GO:0017075)			kidney(2)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		AAGGGAAGAAGGTCTGGATAG	0.408													G|||	396	0.0790735	0.0106	0.1513	5008	,	,		17691	0.001		0.2227	False		,,,				2504	0.0532				p.K702K	Ovarian(25;472 742 1472 36813 50223)	Atlas-SNP	.											.	NSF	27	.	0			c.G2106A						PASS	.	G		146,3720		4,138,1791	115.0	107.0	110.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2106	0.6	1.0	17	dbSNP_79	110	1742,6542		181,1380,2581	yes	coding-synonymous	NSF	NM_006178.3		185,1518,4372	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	21.0285,3.7765,15.5391		702/745	44828931	1888,10262	1933	4142	6075	SO:0001819	synonymous_variant	4905	exon19			GAAGAAGGTCTGG		CCDS42354.1	17q21	2010-04-21			ENSG00000073969	ENSG00000073969		"""ATPases / AAA-type"""	8016	protein-coding gene	gene with protein product	"""N-ethylmaleimide-sensitive factor-like protein"""	601633				1315316, 8875895	Standard	NM_006178		Approved	SKD2	uc002iku.3	P46459	OTTHUMG00000134315	ENST00000398238.4:c.2106G>A	17.37:g.44828931G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_006178	A8K2D9|B4DFA2|Q8N6D7|Q9UKZ2	Silent	SNP	ENST00000398238.4	37	CCDS42354.1																																																																																			G|0.874;A|0.126	0.126	strong		0.408	NSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259348.2	NM_006178	
FLG	2312	hgsc.bcm.edu	37	1	152282917	152282917	+	Missense_Mutation	SNP	G	G	T	rs11204978	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152282917G>T	ENST00000368799.1	-	3	4480	c.4445C>A	c.(4444-4446)tCc>tAc	p.S1482Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1482	Ser-rich.		S -> Y (in dbSNP:rs11204978).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACCGTCTTGGGATGCTGAGTG	0.572									Ichthyosis				G|||	1438	0.287141	0.0113	0.3905	5008	,	,		21395	0.5823		0.1421	False		,,,				2504	0.4315				p.S1482Y		Atlas-SNP	.											.	FLG	900	.	0			c.C4445A						PASS	.	G	TYR/SER	161,4245	108.2+/-146.6	2,157,2044	367.0	352.0	357.0		4445	0.7	0.0	1	dbSNP_120	357	1240,7360	249.0+/-276.5	97,1046,3157	no	missense	FLG	NM_002016.1	144	99,1203,5201	TT,TG,GG		14.4186,3.6541,10.772	possibly-damaging	1482/4062	152282917	1401,11605	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTTGGGATGCTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4445C>A	1.37:g.152282917G>T	ENSP00000357789:p.Ser1482Tyr	Somatic	344	0	0		WXS	Illumina HiSeq	Phase_I	346	166	0.479769	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	572	0.2619047619047619	9	0.018292682926829267	118	0.3259668508287293	333	0.5821678321678322	112	0.14775725593667546	G	8.364	0.833852	0.16820	0.036541	0.144186	ENSG00000143631	ENST00000368799	T	0.03801	3.8	2.75	0.67	0.17923	.	.	.	.	.	T	0.01800	0.0057	M	0.81682	2.555	0.80722	P	0.0	P	0.41978	0.767	B	0.40825	0.341	T	0.36890	-0.9729	8	0.02654	T	1	.	4.9552	0.14035	0.0:0.24:0.5137:0.2463	rs11204978;rs52811516;rs11204978	1482	P20930	FILA_HUMAN	Y	1482	ENSP00000357789:S1482Y	ENSP00000357789:S1482Y	S	-	2	0	FLG	150549541	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.247000	0.18179	0.192000	0.20272	0.556000	0.70494	TCC	G|0.836;T|0.164	0.164	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CRB2	286204	hgsc.bcm.edu	37	9	126129904	126129904	+	Silent	SNP	C	C	T	rs10818812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:126129904C>T	ENST00000373631.3	+	6	994	c.993C>T	c.(991-993)aaC>aaT	p.N331N	CRB2_ENST00000373629.2_5'Flank|CRB2_ENST00000359999.3_Silent_p.N331N	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	331	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CATGCCTCAACGGAGGCCACT	0.652													C|||	1422	0.283946	0.087	0.3228	5008	,	,		8749	0.38		0.3767	False		,,,				2504	0.3282				p.N331N		Atlas-SNP	.											.	CRB2	86	.	0			c.C993T						PASS	.	C		497,3885		30,437,1724	45.0	36.0	39.0		993	-4.8	0.0	9	dbSNP_120	39	3194,5378		614,1966,1706	no	coding-synonymous	CRB2	NM_173689.5		644,2403,3430	TT,TC,CC		37.2608,11.3419,28.4931		331/1286	126129904	3691,9263	2191	4286	6477	SO:0001819	synonymous_variant	286204	exon6			CCTCAACGGAGGC	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.993C>T	9.37:g.126129904C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.729;T|0.271	0.271	strong		0.652	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
LAMA1	284217	hgsc.bcm.edu	37	18	7017322	7017322	+	Silent	SNP	A	A	G	rs539713	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	88	0	0		WXS	Illumina HiSeq	Phase_I	87	87	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	
FAM173B	134145	hgsc.bcm.edu	37	5	10239261	10239261	+	Missense_Mutation	SNP	G	G	A	rs2438652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:10239261G>A	ENST00000511437.1	-	2	236	c.224C>T	c.(223-225)aCg>aTg	p.T75M	FAM173B_ENST00000510047.1_Missense_Mutation_p.T75M|FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000280330.8_De_novo_Start_OutOfFrame	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	75			T -> M (in dbSNP:rs2438652). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						AATCTGCTTCGTAGTTGCAGG	0.522													G|||	1638	0.327077	0.1225	0.3401	5008	,	,		21138	0.7877		0.1551	False		,,,				2504	0.2965				p.T75M		Atlas-SNP	.											.	FAM173B	24	.	0			c.C224T						PASS	.	G	MET/THR	519,3553		36,447,1553	119.0	116.0	117.0		224	5.2	0.0	5	dbSNP_100	117	1149,7207		87,975,3116	yes	missense	FAM173B	NM_199133.2	81	123,1422,4669	AA,AG,GG		13.7506,12.7456,13.4213	benign	75/234	10239261	1668,10760	2036	4178	6214	SO:0001583	missense	134145	exon2			TGCTTCGTAGTTG		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.224C>T	5.37:g.10239261G>A	ENSP00000422338:p.Thr75Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	162	95	0.58642	NM_199133	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	37	CCDS43301.1	766	0.3507326007326007	69	0.1402439024390244	113	0.31215469613259667	467	0.8164335664335665	117	0.15435356200527706	G	11.71	1.720042	0.30503	0.127456	0.137506	ENSG00000150756	ENST00000511437;ENST00000510047	T;T	0.22336	1.96;1.96	5.19	5.19	0.71726	.	0.596788	0.18179	N	0.149210	T	0.00012	0.0000	M	0.65975	2.015	0.58432	P	4.000000000004E-6	D;B	0.67145	0.996;0.076	P;B	0.59056	0.851;0.009	T	0.02991	-1.1085	9	0.46703	T	0.11	-0.0589	17.7316	0.88379	0.0:0.0:1.0:0.0	rs2438652;rs17855827;rs61687093;rs2438652	75;75	E9PBZ4;Q6P4H8	.;F173B_HUMAN	M	75	ENSP00000422338:T75M;ENSP00000420876:T75M	ENSP00000424210:T75M	T	-	2	0	FAM173B	10292261	0.986000	0.35501	0.024000	0.17045	0.458000	0.32498	6.865000	0.75500	2.430000	0.82344	0.655000	0.94253	ACG	G|0.677;N|0.000	.	strong		0.522	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133	
CDCA4	55038	hgsc.bcm.edu	37	14	105478102	105478102	+	Silent	SNP	G	G	A	rs3803294	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105478102G>A	ENST00000336219.3	-	2	320	c.165C>T	c.(163-165)aaC>aaT	p.N55N	CDCA4_ENST00000392590.3_Silent_p.N55N	NM_017955.3	NP_060425.2	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	55	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.					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)		AGCGGCACAGGTTGGGCTCCA	0.607													G|||	2098	0.41893	0.2073	0.5317	5008	,	,		20191	0.3056		0.6471	False		,,,				2504	0.5072				p.N55N		Atlas-SNP	.											.	CDCA4	18	.	0			c.C165T						PASS	.	G	,	1268,3138	412.6+/-336.2	190,888,1125	66.0	51.0	56.0		165,165	1.5	1.0	14	dbSNP_107	56	5721,2879	638.0+/-399.3	1914,1893,493	no	coding-synonymous,coding-synonymous	CDCA4	NM_017955.3,NM_145701.2	,	2104,2781,1618	AA,AG,GG		33.4767,28.7789,46.2633	,	55/242,55/242	105478102	6989,6017	2203	4300	6503	SO:0001819	synonymous_variant	55038	exon2			GCACAGGTTGGGC	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.165C>T	14.37:g.105478102G>A		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	128	126	0.984375	NM_017955	Q8TB18|Q9NWK7	Silent	SNP	ENST00000336219.3	37	CCDS9996.1																																																																																			G|0.498;A|0.502	0.502	strong		0.607	CDCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410311.1	NM_145701	
ITPKB	3707	hgsc.bcm.edu	37	1	226923264	226923264	+	Silent	SNP	G	G	A	rs708775	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:226923264G>A	ENST00000272117.3	-	1	1895	c.1896C>T	c.(1894-1896)gcC>gcT	p.A632A	ITPKB_ENST00000366784.1_Silent_p.A632A|ITPKB_ENST00000429204.1_Silent_p.A632A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	632					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.A632A(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				TATGCAGGAAGGCTGAGTTGG	0.547													G|||	1410	0.28155	0.2428	0.317	5008	,	,		20089	0.2639		0.3141	False		,,,				2504	0.2935				p.A632A	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	1	Substitution - coding silent(1)	stomach(1)	c.C1896T						PASS	.	G		1123,3283	401.5+/-332.0	133,857,1213	130.0	123.0	125.0		1896	2.8	1.0	1	dbSNP_86	125	2530,6070	413.4+/-351.1	390,1750,2160	yes	coding-synonymous	ITPKB	NM_002221.3		523,2607,3373	AA,AG,GG		29.4186,25.488,28.087		632/947	226923264	3653,9353	2203	4300	6503	SO:0001819	synonymous_variant	3707	exon2			CAGGAAGGCTGAG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1896C>T	1.37:g.226923264G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	197	196	0.994924	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			G|0.716;A|0.284	0.284	strong		0.547	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
RTKN2	219790	hgsc.bcm.edu	37	10	63958112	63958112	+	Missense_Mutation	SNP	T	T	C	rs3125734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:63958112T>C	ENST00000373789.3	-	12	1481	c.1385A>G	c.(1384-1386)cAt>cGt	p.H462R	RTKN2_ENST00000315289.2_Missense_Mutation_p.H264R|RTKN2_ENST00000395265.1_Missense_Mutation_p.H483R	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	462			H -> R (in dbSNP:rs3125734). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)					GGATTCTTCATGCTGACCAAT	0.373													T|||	2949	0.588858	0.3132	0.7017	5008	,	,		17108	0.8998		0.6362	False		,,,				2504	0.5123				p.H462R		Atlas-SNP	.											.	RTKN2	68	.	0			c.A1385G						PASS	.	T	ARG/HIS	1687,2719	510.9+/-367.7	336,1015,852	106.0	106.0	106.0		1385	2.3	0.9	10	dbSNP_103	106	5514,3086	660.1+/-401.7	1751,2012,537	yes	missense	RTKN2	NM_145307.2	29	2087,3027,1389	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	35.8837,38.2887,44.6332	benign	462/610	63958112	7201,5805	2203	4300	6503	SO:0001583	missense	219790	exon12			TCTTCATGCTGAC	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.1385A>G	10.37:g.63958112T>C	ENSP00000362894:p.His462Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Missense_Mutation	SNP	ENST00000373789.3	37	CCDS7263.1	1416	0.6483516483516484	169	0.3434959349593496	243	0.6712707182320442	521	0.9108391608391608	483	0.637203166226913	T	1.595	-0.528166	0.04112	0.382887	0.641163	ENSG00000182010	ENST00000315289;ENST00000395265;ENST00000373789	T;T;T	0.40756	1.02;1.61;1.63	4.7	2.33	0.28932	.	0.503008	0.22698	N	0.056732	T	0.00012	0.0000	L	0.28274	0.84	0.43355	P	0.0045720000000000205	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.12243	-1.0555	9	0.40728	T	0.16	-13.7601	9.1159	0.36758	0.0:0.1528:0.0:0.8472	rs3125734;rs17573659;rs52835455;rs59388121;rs3125734	264;462	Q5SVY4;Q8IZC4	.;RTKN2_HUMAN	R	264;483;462	ENSP00000325379:H264R;ENSP00000378682:H483R;ENSP00000362894:H462R	ENSP00000325379:H264R	H	-	2	0	RTKN2	63628118	0.909000	0.30893	0.949000	0.38748	0.915000	0.54546	1.674000	0.37544	0.379000	0.24794	0.533000	0.62120	CAT	T|0.412;C|0.588	0.588	strong		0.373	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307	
MTUS1	57509	hgsc.bcm.edu	37	8	17612043	17612043	+	Missense_Mutation	SNP	G	G	A	rs61733694	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:17612043G>A	ENST00000262102.6	-	2	1498	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	MTUS1_ENST00000519263.1_Missense_Mutation_p.T425M|MTUS1_ENST00000381862.3_Missense_Mutation_p.T425M|MTUS1_ENST00000381869.3_Missense_Mutation_p.T425M	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	425			T -> M (in dbSNP:rs61733694). {ECO:0000269|PubMed:16650523}.		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)		CATGCACATCGTTTTGTCTGT	0.443													G|||	59	0.0117812	0.0023	0.0187	5008	,	,		20097	0.0		0.0378	False		,,,				2504	0.0051				p.T425M		Atlas-SNP	.											MTUS1,NS,carcinoma,+1,1	MTUS1	144	1	0			c.C1274T						scavenged	.	G	MET/THR,MET/THR	19,3811		0,19,1896	108.0	104.0	105.0		1274,1274	-7.3	0.0	8	dbSNP_129	105	325,7919		5,315,3802	yes	missense,missense	MTUS1	NM_001001924.2,NM_001001925.2	81,81	5,334,5698	AA,AG,GG		3.9423,0.4961,2.8491	benign,benign	425/1271,425/1217	17612043	344,11730	1915	4122	6037	SO:0001583	missense	57509	exon2			CACATCGTTTTGT	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.1274C>T	8.37:g.17612043G>A	ENSP00000262102:p.Thr425Met	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	40	0.018315018315018316	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	32	0.04221635883905013	G	0.230	-1.021691	0.02061	0.004961	0.039423	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.20881	3.0;3.05;3.0;2.04	4.46	-7.34	0.01427	.	1.573020	0.03550	N	0.225363	T	0.01695	0.0054	N	0.12182	0.205	0.09310	N	1	B;B;B	0.15473	0.013;0.013;0.013	B;B;B	0.08055	0.003;0.003;0.003	T	0.17623	-1.0363	10	0.24483	T	0.36	3.4404	1.3995	0.02267	0.4561:0.1804:0.1403:0.2233	rs61733694	425;425;425	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	M	425	ENSP00000371293:T425M;ENSP00000262102:T425M;ENSP00000430167:T425M;ENSP00000371286:T425M	ENSP00000262102:T425M	T	-	2	0	MTUS1	17656323	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.420000	0.07062	-1.777000	0.01283	-1.875000	0.00549	ACG	G|0.980;A|0.020	0.020	strong		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
RPSA	3921	hgsc.bcm.edu	37	3	39453160	39453160	+	Silent	SNP	G	G	A	rs2269350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:39453160G>A	ENST00000301821.6	+	5	628	c.519G>A	c.(517-519)ttG>ttA	p.L173L	RPSA_ENST00000443003.1_Silent_p.L178L|SNORA62_ENST00000365493.1_RNA|RPSA_ENST00000478027.1_3'UTR	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2			ribosomal protein SA											endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)		CAGTGGGTTTGATGTGGTGGA	0.512													G|||	1256	0.250799	0.152	0.3084	5008	,	,		20924	0.2778		0.3082	False		,,,				2504	0.2566				p.L173L		Atlas-SNP	.											.	RPSA	15	.	0			c.G519A						PASS	.	G	,	733,3673	303.8+/-288.1	51,631,1521	150.0	150.0	150.0		519,519	2.8	1.0	3	dbSNP_100	150	2788,5812	439.2+/-359.1	457,1874,1969	no	coding-synonymous,coding-synonymous	RPSA	NM_001012321.1,NM_002295.4	,	508,2505,3490	AA,AG,GG		32.4186,16.6364,27.0721	,	173/296,173/296	39453160	3521,9485	2203	4300	6503	SO:0001819	synonymous_variant	3921	exon4			GGGTTTGATGTGG	S37431	CCDS2686.1	3p21.3	2014-09-17	2002-08-29	2005-02-11	ENSG00000168028	ENSG00000168028			6502	protein-coding gene	gene with protein product		150370	"""laminin receptor 1 (67kD, ribosomal protein SA)"""	LAMR1		1534510, 8760291	Standard	NM_001012321		Approved	LRP, 37LRP, p40, SA	uc003cjp.3	P08865	OTTHUMG00000131296	ENST00000301821.6:c.519G>A	3.37:g.39453160G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_001012321		Silent	SNP	ENST00000301821.6	37	CCDS2686.1																																																																																			G|0.745;A|0.255	0.255	strong		0.512	RPSA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254064.3	NM_002295	
OR52E2	119678	hgsc.bcm.edu	37	11	5080068	5080068	+	Missense_Mutation	SNP	G	G	A	rs2500052	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5080068G>A	ENST00000321522.2	-	1	789	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	264			R -> C (in dbSNP:rs2500052). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|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)		CGGCCAAAGCGATGAGTCATA	0.468													G|||	2557	0.510583	0.6717	0.5086	5008	,	,		18255	0.2619		0.5089	False		,,,				2504	0.5521				p.R264C		Atlas-SNP	.											OR52E2,colon,carcinoma,0,1	OR52E2	63	1	0			c.C790T						PASS	.	G	CYS/ARG	2734,1668	656.7+/-400.1	869,996,336	92.0	92.0	92.0		790	3.8	0.9	11	dbSNP_100	92	4308,4288	577.8+/-390.6	1068,2172,1058	no	missense	OR52E2	NM_001005164.2	180	1937,3168,1394	AA,AG,GG		49.8837,37.8919,45.8224	probably-damaging	264/326	5080068	7042,5956	2201	4298	6499	SO:0001583	missense	119678	exon1			CAAAGCGATGAGT	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.790C>T	11.37:g.5080068G>A	ENSP00000322088:p.Arg264Cys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	1036	0.47435897435897434	330	0.6707317073170732	172	0.47513812154696133	149	0.26048951048951047	385	0.5079155672823219	G	14.78	2.636499	0.47049	0.621081	0.501163	ENSG00000176787	ENST00000321522	T	0.37411	1.2	3.76	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.123911	0.34200	N	0.004162	T	0.00012	0.0000	M	0.89353	3.025	0.29331	P	0.866687	D	0.54397	0.966	P	0.51385	0.668	T	0.47935	-0.9078	9	0.87932	D	0	.	10.7329	0.46107	0.0:0.0:0.8091:0.1909	rs2500052;rs12794355;rs17260181;rs2500052	264	Q8NGJ4	O52E2_HUMAN	C	264	ENSP00000322088:R264C	ENSP00000322088:R264C	R	-	1	0	OR52E2	5036644	0.000000	0.05858	0.937000	0.37676	0.695000	0.40330	0.184000	0.16939	2.425000	0.82216	0.644000	0.83932	CGC	G|0.476;A|0.524	0.524	strong		0.468	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
RP1L1	94137	hgsc.bcm.edu	37	8	10465097	10465097	+	Missense_Mutation	SNP	C	C	T	rs4354268	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10465097C>T	ENST00000382483.3	-	4	6734	c.6511G>A	c.(6511-6513)Gag>Aag	p.E2171K		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2251	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].		E -> K (in dbSNP:rs4354268).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGGGCCTCCTCTTCAGCCTCC	0.612													C|||	1563	0.312101	0.4228	0.3184	5008	,	,		17645	0.0208		0.4891	False		,,,				2504	0.2761				p.E2171K		Atlas-SNP	.											.	RP1L1	453	.	0			c.G6511A						PASS	.	C	LYS/GLU	1526,2284		304,918,683	166.0	180.0	176.0		6511	1.2	0.0	8	dbSNP_111	176	3835,4373		908,2019,1177	yes	missense	RP1L1	NM_178857.5	56	1212,2937,1860	TT,TC,CC		46.7227,40.0525,44.6081	benign	2171/2401	10465097	5361,6657	1905	4104	6009	SO:0001583	missense	94137	exon4			CCTCCTCTTCAGC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.6511G>A	8.37:g.10465097C>T	ENSP00000371923:p.Glu2171Lys	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	149	79	0.530201	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	721	0.3301282051282051	217	0.4410569105691057	124	0.3425414364640884	13	0.022727272727272728	367	0.4841688654353562	C	9.516	1.107149	0.20714	0.400525	0.467227	ENSG00000183638	ENST00000382483	T	0.07688	3.17	2.18	1.25	0.21368	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13145	0.007	B	0.08055	0.003	T	0.45086	-0.9285	8	0.05436	T	0.98	.	4.3001	0.10920	0.0:0.5052:0.2282:0.2665	rs4354268;rs17188537	2171	A6NKC6	.	K	2171	ENSP00000371923:E2171K	ENSP00000371923:E2171K	E	-	1	0	RP1L1	10502507	0.000000	0.05858	0.011000	0.14972	0.030000	0.12068	0.037000	0.13840	0.184000	0.20083	0.430000	0.28490	GAG	C|0.615;T|0.385	0.385	strong		0.612	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
ANO8	57719	hgsc.bcm.edu	37	19	17444607	17444607	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17444607T>G	ENST00000159087.4	-	2	267	c.109A>C	c.(109-111)Aag>Cag	p.K37Q	GTPBP3_ENST00000361619.5_5'Flank	NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	37					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						CCGAAAAGCTTATCTAGGGGG	0.652																																					p.K37Q		Atlas-SNP	.											.	ANO8	67	.	0			c.A109C						PASS	.						36.0	32.0	34.0					19																	17444607		2203	4299	6502	SO:0001583	missense	57719	exon2			AAAGCTTATCTAG	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.109A>C	19.37:g.17444607T>G	ENSP00000159087:p.Lys37Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_020959	A6NIJ0	Missense_Mutation	SNP	ENST00000159087.4	37	CCDS32949.1	.	.	.	.	.	.	.	.	.	.	t	24.8	4.569595	0.86439	.	.	ENSG00000074855	ENST00000159087	T	0.69040	-0.37	4.72	4.72	0.59763	.	0.106561	0.64402	D	0.000008	T	0.67562	0.2906	M	0.72479	2.2	0.33603	D	0.602613	P	0.44690	0.841	B	0.43386	0.418	T	0.79685	-0.1700	10	0.54805	T	0.06	.	12.1707	0.54157	0.0:0.0:0.0:1.0	.	37	Q9HCE9	ANO8_HUMAN	Q	37	ENSP00000159087:K37Q	ENSP00000159087:K37Q	K	-	1	0	ANO8	17305607	1.000000	0.71417	0.997000	0.53966	0.933000	0.57130	7.285000	0.78660	1.765000	0.52091	0.398000	0.26397	AAG	.	.	none		0.652	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
RADIL	55698	hgsc.bcm.edu	37	7	4876057	4876057	+	Missense_Mutation	SNP	C	C	T	rs3763384	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:4876057C>T	ENST00000399583.3	-	3	902	c.715G>A	c.(715-717)Gac>Aac	p.D239N	RADIL_ENST00000538469.1_5'UTR|RADIL_ENST00000536091.1_Missense_Mutation_p.D239N	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	239			D -> N (in dbSNP:rs3763384). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19690332}.		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CGCATGGCGTCGGGGCCGGGC	0.706													C|||	1257	0.250998	0.0401	0.2853	5008	,	,		13192	0.3264		0.2873	False		,,,				2504	0.3967				p.D239N		Atlas-SNP	.											.	RADIL	110	.	0			c.G715A						PASS	.	C	ASN/ASP	305,3815		19,267,1774	13.0	20.0	18.0		715	4.8	0.1	7	dbSNP_107	18	2586,5772		412,1762,2005	yes	missense	RADIL	NM_018059.4	23	431,2029,3779	TT,TC,CC		30.9404,7.4029,23.1688	benign	239/1076	4876057	2891,9587	2060	4179	6239	SO:0001583	missense	55698	exon3			TGGCGTCGGGGCC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.715G>A	7.37:g.4876057C>T	ENSP00000382492:p.Asp239Asn	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	524	0.23992673992673993	22	0.044715447154471545	94	0.2596685082872928	195	0.3409090909090909	213	0.28100263852242746	C	10.16	1.274597	0.23307	0.074029	0.309404	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091	T;T	0.24538	3.27;1.85	4.85	4.85	0.62838	.	0.607882	0.16897	N	0.195056	T	0.00012	0.0000	L	0.35414	1.06	0.80722	P	0.0	P	0.39782	0.688	B	0.25291	0.059	T	0.45411	-0.9263	9	0.14252	T	0.57	-25.6462	10.7848	0.46398	0.0:0.9079:0.0:0.0921	rs3763384;rs58768759;rs3763384	239	Q96JH8	RADIL_HUMAN	N	239;213;239	ENSP00000382492:D239N;ENSP00000442533:D239N	ENSP00000320946:D213N	D	-	1	0	RADIL	4842583	0.018000	0.18449	0.055000	0.19348	0.004000	0.04260	0.996000	0.29719	2.243000	0.73865	0.462000	0.41574	GAC	C|0.745;T|0.255	0.255	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
ANGPT4	51378	hgsc.bcm.edu	37	20	860426	860426	+	Silent	SNP	G	G	A	rs61737018	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	29	13	0.448276	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	
MOV10L1	54456	hgsc.bcm.edu	37	22	50582630	50582630	+	Silent	SNP	G	G	A	rs11704548	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:50582630G>A	ENST00000262794.5	+	18	2546	c.2463G>A	c.(2461-2463)ccG>ccA	p.P821P	MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.P821P|MOV10L1_ENST00000395858.3_Silent_p.P821P|MOV10L1_ENST00000540615.1_Silent_p.P801P|MOV10L1_ENST00000395852.1_5'Flank	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	821					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGCTACAGCCGGCCACCATGG	0.612													A|||	136	0.0271565	0.0038	0.0447	5008	,	,		19960	0.0		0.0726	False		,,,				2504	0.0276				p.P821P		Atlas-SNP	.											.	MOV10L1	238	.	0			c.G2463A						PASS	.	A	,,	55,4351	821.3+/-416.4	2,51,2150	103.0	90.0	94.0		2463,2403,2463	-11.0	0.0	22	dbSNP_120	94	624,7976	790.9+/-407.6	17,590,3693	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	19,641,5843	AA,AG,GG		7.2558,1.2483,5.2207	,,	821/1166,801/1166,821/1212	50582630	679,12327	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon18			ACAGCCGGCCACC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2463G>A	22.37:g.50582630G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			G|0.952;A|0.048	0.048	strong		0.612	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
RIN2	54453	hgsc.bcm.edu	37	20	19915769	19915769	+	Silent	SNP	C	C	T	rs181853315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:19915769C>T	ENST00000255006.6	+	3	380	c.231C>T	c.(229-231)atC>atT	p.I77I	RIN2_ENST00000440354.2_Silent_p.I28I|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	28					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						CCTCGGAGATCGGAGAACTGA	0.527													C|||	9	0.00179712	0.0	0.0072	5008	,	,		17587	0.0		0.003	False		,,,				2504	0.001				p.I77I		Atlas-SNP	.											.	RIN2	126	.	0			c.C231T						PASS	.	C	,	7,3941		0,7,1967	70.0	67.0	68.0		231,84	4.8	1.0	20		68	83,8219		0,83,4068	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	0,90,6035	TT,TC,CC		0.9998,0.1773,0.7347	,	77/945,28/896	19915769	90,12160	1974	4151	6125	SO:0001819	synonymous_variant	54453	exon3			GGAGATCGGAGAA	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.231C>T	20.37:g.19915769C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			C|0.995;T|0.005	0.005	strong		0.527	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
MMP2	4313	hgsc.bcm.edu	37	16	55527113	55527113	+	Silent	SNP	G	G	A	rs2287074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:55527113G>A	ENST00000219070.4	+	9	1889	c.1380G>A	c.(1378-1380)acG>acA	p.T460T	MMP2_ENST00000437642.2_Silent_p.T410T|MMP2_ENST00000570308.1_Silent_p.T384T|MMP2_ENST00000543485.1_Silent_p.T384T	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	460	Collagenase-like 2.|Required for inhibitor TIMP2 binding.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	CCACCCCCACGCTGGGCCCTG	0.577													G|||	1627	0.32488	0.1793	0.4395	5008	,	,		17229	0.2867		0.4344	False		,,,				2504	0.3671				p.T460T		Atlas-SNP	.											.	MMP2	119	.	0			c.G1380A						PASS	.	G	,	974,3422	366.6+/-317.9	115,744,1339	106.0	98.0	100.0		1230,1380	-10.8	0.5	16	dbSNP_100	100	3694,4906	528.9+/-381.5	810,2074,1416	no	coding-synonymous,coding-synonymous	MMP2	NM_001127891.1,NM_004530.4	,	925,2818,2755	AA,AG,GG		42.9535,22.1565,35.9187	,	410/611,460/661	55527113	4668,8328	2198	4300	6498	SO:0001819	synonymous_variant	4313	exon9			CCCCACGCTGGGC		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.1380G>A	16.37:g.55527113G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	123	54	0.439024	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	37	CCDS10752.1																																																																																			A|0.353;C|0.000;G|0.647	0.353	strong		0.577	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929674	2929674	+	Silent	SNP	T	T	C	rs12941934	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2929674T>C	ENST00000254695.8	+	21	1986	c.1896T>C	c.(1894-1896)cgT>cgC	p.R632R	RAP1GAP2_ENST00000540393.2_Silent_p.R613R|RAP1GAP2_ENST00000366401.4_Silent_p.R617R|RAP1GAP2_ENST00000542807.1_Silent_p.R632R	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	632	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.R632R(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						AAAACGGCCGTGCCATCTCCC	0.672													C|||	2914	0.581869	0.4312	0.6744	5008	,	,		16616	0.6429		0.5606	False		,,,				2504	0.6789				p.R632R		Atlas-SNP	.											RAP1GAP2_ENST00000254695,NS,lymphoid_neoplasm,0,2	RAP1GAP2	90	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1896C						scavenged	.	C	,	1939,2059		530,879,590	15.0	18.0	17.0		1851,1896	-9.8	0.3	17	dbSNP_121	17	4907,3181		1615,1677,752	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	2145,2556,1342	CC,CT,TT		39.3299,48.4992,43.3559	,	617/716,632/731	2929674	6846,5240	1999	4044	6043	SO:0001819	synonymous_variant	23108	exon21			CGGCCGTGCCATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1896T>C	17.37:g.2929674T>C		Somatic	205	2	0.0097561		WXS	Illumina HiSeq	Phase_I	204	83	0.406863	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			T|0.421;C|0.579	0.579	strong		0.672	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
GGT6	124975	hgsc.bcm.edu	37	17	4463796	4463796	+	Silent	SNP	G	G	A	rs7216474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4463796G>A	ENST00000574154.1	-	1	317	c.21C>T	c.(19-21)ccC>ccT	p.P7P	GGT6_ENST00000301395.3_Silent_p.P7P|GGT6_ENST00000573591.1_5'Flank|GGT6_ENST00000381550.3_Silent_p.P7P			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	7					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)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			endometrium(2)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						GATAGACCACGGGCTCTTCTG	0.657													G|||	740	0.147764	0.0658	0.111	5008	,	,		16135	0.0942		0.2286	False		,,,				2504	0.2566				p.P7P		Atlas-SNP	.											.	GGT6	22	.	0			c.C21T						PASS	.	G	,	371,4035	187.8+/-214.3	15,341,1847	69.0	61.0	64.0		21,21	-7.4	0.0	17	dbSNP_116	64	1957,6643	344.0+/-325.1	214,1529,2557	no	coding-synonymous,coding-synonymous	GGT6	NM_001122890.1,NM_153338.2	,	229,1870,4404	AA,AG,GG		22.7558,8.4203,17.8994	,	7/494,7/462	4463796	2328,10678	2203	4300	6503	SO:0001819	synonymous_variant	124975	exon1			GACCACGGGCTCT	AK074646	CCDS11047.1, CCDS45582.1, CCDS73942.1	17p13.2	2014-08-12	2008-03-10		ENSG00000167741	ENSG00000167741		"""Gamma-glutamyltransferases"""	26891	protein-coding gene	gene with protein product		612341	"""gamma-glutamyltransferase 6 homolog (rat)"""			18357469	Standard	NM_001122890		Approved	FLJ90165	uc002fyd.4	Q6P531	OTTHUMG00000177827	ENST00000574154.1:c.21C>T	17.37:g.4463796G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_001122890	B4DUH4|Q8NCM0	Silent	SNP	ENST00000574154.1	37	CCDS45582.1																																																																																			G|0.838;A|0.162	0.162	strong		0.657	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439122.1	NM_153338	
OR52N5	390075	hgsc.bcm.edu	37	11	5799468	5799468	+	Missense_Mutation	SNP	C	C	T	rs12360738	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5799468C>T	ENST00000317093.2	-	1	429	c.397G>A	c.(397-399)Gta>Ata	p.V133I	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	133			V -> I (in dbSNP:rs12360738). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		CAAATGGCTACATAGCGGTCT	0.493													C|||	822	0.164137	0.0363	0.1455	5008	,	,		17035	0.2937		0.1481	False		,,,				2504	0.2331				p.V133I		Atlas-SNP	.											.	OR52N5	58	.	0			c.G397A						PASS	.	C	ILE/VAL	254,3992		58,138,1927	127.0	103.0	111.0		397	-0.6	0.7	11	dbSNP_120	111	1219,6953		280,659,3147	yes	missense	OR52N5	NM_001001922.2	29	338,797,5074	TT,TC,CC		14.9168,5.9821,11.8618	benign	133/325	5799468	1473,10945	2123	4086	6209	SO:0001583	missense	390075	exon1			TGGCTACATAGCG	AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"""GPCR / Class A : Olfactory receptors"""	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.397G>A	11.37:g.5799468C>T	ENSP00000322866:p.Val133Ile	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_001001922	B9EH12|Q6IFG2	Missense_Mutation	SNP	ENST00000317093.2	37	CCDS31397.1	382	0.1749084249084249	23	0.046747967479674794	65	0.17955801104972377	177	0.3094405594405594	117	0.15435356200527706	C	6.344	0.431618	0.12045	0.059821	0.149168	ENSG00000181009	ENST00000317093	T	0.19250	2.16	3.7	-0.614	0.11590	GPCR, rhodopsin-like superfamily (1);	0.522424	0.11533	N	0.554463	T	0.00012	0.0000	L	0.54863	1.705	0.45962	P	0.0012180000000000524	B	0.12630	0.006	B	0.14578	0.011	T	0.38564	-0.9655	9	0.52906	T	0.07	.	3.2057	0.06665	0.1217:0.5112:0.1197:0.2474	rs12360738	133	Q8NH56	O52N5_HUMAN	I	133	ENSP00000322866:V133I	ENSP00000322866:V133I	V	-	1	0	OR52N5	5756044	0.000000	0.05858	0.659000	0.29680	0.218000	0.24690	-0.802000	0.04545	-0.499000	0.06623	-1.409000	0.01127	GTA	C|0.824;T|0.176	0.176	strong		0.493	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922	
EXD3	54932	hgsc.bcm.edu	37	9	140277826	140277826	+	Missense_Mutation	SNP	C	C	T	rs13291830	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140277826C>T	ENST00000340951.4	-	3	254	c.59G>A	c.(58-60)cGg>cAg	p.R20Q	EXD3_ENST00000475006.1_5'UTR|EXD3_ENST00000342129.4_5'UTR|EXD3_ENST00000479452.1_Missense_Mutation_p.R20Q	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0	Pro-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						GAGGGGGTCCCGGCCTGTGGA	0.672													N|||	2731	0.545327	0.7776	0.4539	5008	,	,		17067	0.3849		0.6203	False		,,,				2504	0.3845				p.R20Q		Atlas-SNP	.											.	EXD3	86	.	0			c.G59A						PASS	.		GLN/ARG	2895,851		1148,599,126	14.0	18.0	17.0		59	-2.2	0.9	9	dbSNP_121	17	4727,3179		1499,1729,725	yes	missense	EXD3	NM_017820.3	43	2647,2328,851	TT,TC,CC		40.21,22.7176,34.5863	benign	20/877	140277826	7622,4030	1873	3953	5826	SO:0001583	missense	54932	exon3			GGGTCCCGGCCTG		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.59G>A	9.37:g.140277826C>T	ENSP00000340474:p.Arg20Gln	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	236	102	0.432203	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	1200	0.5494505494505495	375	0.7621951219512195	166	0.4585635359116022	207	0.3618881118881119	452	0.5963060686015831	N	12.63	1.995825	0.35226	0.772824	0.5979	ENSG00000187609	ENST00000340951;ENST00000479452	T;T	0.49432	0.78;1.58	2.32	-2.21	0.06973	.	0.200505	0.34386	N	0.004019	T	0.00012	0.0000	N	0.00210	-1.845	0.09310	P	0.9999999999974808	B;B	0.10296	0.001;0.003	B;B	0.04013	0.001;0.0	T	0.28427	-1.0044	9	0.14252	T	0.57	.	7.97	0.30122	0.0:0.5901:0.0:0.4099	rs13291830	20;20	Q8N9H8-4;Q8N9H8	.;MUT7_HUMAN	Q	20	ENSP00000340474:R20Q;ENSP00000431859:R20Q	ENSP00000340474:R20Q	R	-	2	0	EXD3	139397647	0.011000	0.17503	0.910000	0.35882	0.407000	0.30961	-1.620000	0.02046	-1.248000	0.02503	-0.871000	0.02989	CGG	C|0.449;T|0.551	0.551	strong		0.672	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
MMP27	64066	hgsc.bcm.edu	37	11	102562700	102562700	+	Missense_Mutation	SNP	C	C	T	rs2509010	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102562700C>T	ENST00000260229.4	-	10	1430	c.1339G>A	c.(1339-1341)Gac>Aac	p.D447N		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	447			D -> N (in dbSNP:rs2509010). {ECO:0000269|PubMed:12975309}.		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GTCTTAATGTCGTATTCAAAT	0.333													C|||	820	0.163738	0.0696	0.2435	5008	,	,		17366	0.1081		0.2744	False		,,,				2504	0.1779				p.D447N		Atlas-SNP	.											.	MMP27	84	.	0			c.G1339A						PASS	.	C	ASN/ASP	475,3931	223.6+/-240.1	26,423,1754	89.0	80.0	83.0		1339	3.9	1.0	11	dbSNP_100	83	2437,6155	402.7+/-347.6	353,1731,2212	yes	missense	MMP27	NM_022122.2	23	379,2154,3966	TT,TC,CC		28.3636,10.7808,22.4034	benign	447/514	102562700	2912,10086	2203	4296	6499	SO:0001583	missense	64066	exon10			TAATGTCGTATTC	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1339G>A	11.37:g.102562700C>T	ENSP00000260229:p.Asp447Asn	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	393	0.17994505494505494	32	0.06504065040650407	78	0.2154696132596685	60	0.1048951048951049	223	0.2941952506596306	C	14.06	2.422247	0.43020	0.107808	0.283636	ENSG00000137675	ENST00000260229	T	0.14144	2.53	5.96	3.86	0.44501	Hemopexin/matrixin (2);	0.085303	0.50627	D	0.000108	T	0.00012	0.0000	L	0.41079	1.255	0.30645	P	0.75601	P	0.36974	0.576	B	0.20767	0.031	T	0.48514	-0.9029	9	0.18710	T	0.47	.	10.2161	0.43168	0.0:0.7788:0.1407:0.0804	rs2509010;rs52836586;rs2509010	447	Q9H306	MMP27_HUMAN	N	447	ENSP00000260229:D447N	ENSP00000260229:D447N	D	-	1	0	MMP27	102067910	0.990000	0.36364	0.980000	0.43619	0.808000	0.45660	1.080000	0.30779	2.819000	0.97034	0.585000	0.79938	GAC	C|0.800;T|0.200	0.200	strong		0.333	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415281	105415281	+	Silent	SNP	G	G	C	rs386781098|rs146449084	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105415281G>C	ENST00000333244.5	-	7	6626	c.6507C>G	c.(6505-6507)ggC>ggG	p.G2169G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2169						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)			CGATGGACTTGCCTGGGGCAG	0.587													.|||	634	0.126597	0.0446	0.1412	5008	,	,		16871	0.0456		0.2744	False		,,,				2504	0.1585				p.G2169G		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	0			c.C6507G						scavenged	.						197.0	129.0	151.0					14																	105415281		1941	3991	5932	SO:0001819	synonymous_variant	113146	exon7			GGACTTGCCTGGG	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.6507C>G	14.37:g.105415281G>C		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.842;C|0.158	0.158	strong		0.587	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR2B11	127623	hgsc.bcm.edu	37	1	247614407	247614407	+	Missense_Mutation	SNP	G	G	A	rs12065526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:247614407G>A	ENST00000318749.6	-	1	901	c.878C>T	c.(877-879)aCc>aTc	p.T293I		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	293			T -> I (in dbSNP:rs12065526).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CAGGGTGTAGGTGAAGGGATT	0.478													A|||	560	0.111821	0.1967	0.1758	5008	,	,		18555	0.001		0.1342	False		,,,				2504	0.0429				p.T293I		Atlas-SNP	.											.	OR2B11	102	.	0			c.C878T						PASS	.	A	ILE/THR	880,3526	741.3+/-411.3	86,708,1409	181.0	195.0	191.0		878	5.1	1.0	1	dbSNP_120	191	1249,7351	761.4+/-407.6	89,1071,3140	yes	missense	OR2B11	NM_001004492.1	89	175,1779,4549	AA,AG,GG		14.5233,19.9728,16.3694	benign	293/318	247614407	2129,10877	2203	4300	6503	SO:0001583	missense	127623	exon1			GTGTAGGTGAAGG		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"""GPCR / Class A : Olfactory receptors"""	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.878C>T	1.37:g.247614407G>A	ENSP00000325682:p.Thr293Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001004492	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	37	CCDS31090.1	268	0.1227106227106227	106	0.21544715447154472	66	0.18232044198895028	1	0.0017482517482517483	95	0.12532981530343007	A	0.142	-1.100774	0.01843	0.199728	0.145233	ENSG00000177535	ENST00000318749	T	0.20738	2.05	5.09	5.09	0.68999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	N	0.000056	T	0.00012	0.0000	N	0.00000	-4.12	0.43527	P	0.004190999999999945	B	0.02656	0.0	B	0.01281	0.0	T	0.34030	-0.9845	9	0.02654	T	1	.	9.4144	0.38512	0.9157:0.0:0.0843:0.0	rs12065526;rs52805485;rs60174442;rs12065526	293	Q5JQS5	OR2BB_HUMAN	I	293	ENSP00000325682:T293I	ENSP00000325682:T293I	T	-	2	0	OR2B11	245681030	1.000000	0.71417	1.000000	0.80357	0.231000	0.25187	5.090000	0.64498	1.076000	0.40961	-0.268000	0.10319	ACC	G|0.854;A|0.146	0.146	strong		0.478	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
POLD3	10714	hgsc.bcm.edu	37	11	74347275	74347275	+	Missense_Mutation	SNP	C	C	T	rs572105600		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:74347275C>T	ENST00000263681.2	+	11	1282	c.1153C>T	c.(1153-1155)Cgc>Tgc	p.R385C	POLD3_ENST00000527458.1_Missense_Mutation_p.R346C|POLD3_ENST00000532497.1_Missense_Mutation_p.R279C	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	385					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.R385G(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					AAAACGAAAACGCGTACTAAA	0.358																																					p.R385C		Atlas-SNP	.											POLD3_ENST00000263681,NS,carcinoma,0,2	POLD3	87	2	2	Substitution - Missense(2)	endometrium(2)	c.C1153T						PASS	.						83.0	80.0	81.0					11																	74347275		2200	4293	6493	SO:0001583	missense	10714	exon11			CGAAAACGCGTAC	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.1153C>T	11.37:g.74347275C>T	ENSP00000263681:p.Arg385Cys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	163	60	0.368098	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Missense_Mutation	SNP	ENST00000263681.2	37	CCDS8233.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629880	0.67015	.	.	ENSG00000077514	ENST00000263681;ENST00000527458;ENST00000532497	.	.	.	5.7	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.78272	0.4257	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80627	-0.1298	9	0.87932	D	0	-18.0768	14.9973	0.71443	0.1522:0.8478:0.0:0.0	.	385	Q15054	DPOD3_HUMAN	C	385;346;279	.	ENSP00000263681:R385C	R	+	1	0	POLD3	74024923	0.997000	0.39634	0.943000	0.38184	0.845000	0.48019	1.348000	0.33987	2.696000	0.92011	0.561000	0.74099	CGC	.	.	none		0.358	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591	
FOXR2	139628	hgsc.bcm.edu	37	X	55651001	55651001	+	Missense_Mutation	SNP	T	T	C	rs2375465	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:55651001T>C	ENST00000339140.3	+	1	1169	c.857T>C	c.(856-858)gTc>gCc	p.V286A		NM_198451.3	NP_940853.1	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	286			V -> A (in dbSNP:rs2375465).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	19						GAGACTCGTGTCTTAGCCTTT	0.502													C|||	3064	0.811656	0.2973	0.7017	3775	,	,		15500	0.7579		0.7406	False		,,,				2504	0.6902				p.V286A		Atlas-SNP	.											.	FOXR2	42	.	0			c.T857C						PASS	.	C	ALA/VAL	1919,1916		419,793,288,420,283	123.0	97.0	106.0		857	1.2	0.0	X	dbSNP_100	106	6546,182		2299,128,1820,1,52	yes	missense	FOXR2	NM_198451.3	64	2718,921,2108,421,335	CC,CT,C,TT,T		2.7051,49.9609,19.8618	benign	286/312	55651001	8465,2098	2203	4300	6503	SO:0001583	missense	139628	exon1			CTCGTGTCTTAGC	BC012934	CCDS35308.1	Xp11	2006-12-15			ENSG00000189299	ENSG00000189299		"""Forkhead boxes"""	30469	protein-coding gene	gene with protein product						15202009, 15202027	Standard	NM_198451		Approved	MGC21658, FOXN6	uc004duo.3	Q6PJQ5	OTTHUMG00000021661	ENST00000339140.3:c.857T>C	X.37:g.55651001T>C	ENSP00000427329:p.Val286Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_198451		Missense_Mutation	SNP	ENST00000339140.3	37	CCDS35308.1	1423	0.8577456298975287	124	0.31794871794871793	174	0.8613861386138614	284	1.0	393	0.9538834951456311	C	0.140	-1.103155	0.01828	0.500391	0.972949	ENSG00000189299	ENST00000339140	D	0.93076	-3.16	3.54	1.2	0.21068	Transcription factor, fork head (1);	0.339109	0.10834	N	0.628961	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.37888	-0.9686	9	0.02654	T	1	.	4.4161	0.11457	0.0:0.5373:0.1748:0.2879	rs2375465;rs52825841;rs2375465	286	Q6PJQ5	FOXR2_HUMAN	A	286	ENSP00000427329:V286A	ENSP00000427329:V286A	V	+	2	0	FOXR2	55667726	0.998000	0.40836	0.001000	0.08648	0.012000	0.07955	0.685000	0.25378	-0.090000	0.12462	-0.170000	0.13304	GTC	T|0.212;C|0.788	0.788	strong		0.502	FOXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056877.2	NM_198451	
NKTR	4820	hgsc.bcm.edu	37	3	42679777	42679777	+	Missense_Mutation	SNP	T	T	G	rs33969824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:42679777T>G	ENST00000232978.8	+	13	2769	c.2581T>G	c.(2581-2583)Ttg>Gtg	p.L861V	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	861			L -> V (in dbSNP:rs33969824).		protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		AAAAAGAACTTTGAAAGAGAA	0.378													T|||	962	0.192093	0.3185	0.0735	5008	,	,		20550	0.1022		0.1402	False		,,,				2504	0.2515				p.L861V		Atlas-SNP	.											.	NKTR	116	.	0			c.T2581G						PASS	.	T	VAL/LEU	1247,3145		179,889,1128	44.0	49.0	47.0		2581	-1.5	0.0	3	dbSNP_126	47	1060,7536		59,942,3297	yes	missense	NKTR	NM_005385.3	32	238,1831,4425	GG,GT,TT		12.3313,28.3925,17.7626	benign	861/1463	42679777	2307,10681	2196	4298	6494	SO:0001583	missense	4820	exon13			AGAACTTTGAAAG		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.2581T>G	3.37:g.42679777T>G	ENSP00000232978:p.Leu861Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	37	CCDS2702.1	355	0.16254578754578755	147	0.29878048780487804	31	0.0856353591160221	70	0.12237762237762238	107	0.14116094986807387	T	2.472	-0.321741	0.05386	0.283925	0.123313	ENSG00000114857	ENST00000232978	T	0.11930	2.73	5.67	-1.53	0.08611	.	1.554750	0.03379	N	0.200163	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B;B	0.10296	0.003;0.002	B;B	0.09377	0.004;0.001	T	0.46303	-0.9201	9	0.31617	T	0.26	2.9233	7.5111	0.27575	0.0:0.2064:0.456:0.3376	rs33969824	561;861	Q6M1B8;P30414	.;NKTR_HUMAN	V	861	ENSP00000232978:L861V	ENSP00000232978:L861V	L	+	1	2	NKTR	42654781	0.000000	0.05858	0.001000	0.08648	0.620000	0.37586	0.105000	0.15333	-0.148000	0.11234	0.533000	0.62120	TTG	T|0.832;G|0.168	0.168	strong		0.378	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
FLNB	2317	hgsc.bcm.edu	37	3	58118555	58118555	+	Missense_Mutation	SNP	G	G	A	rs12632456	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58118555G>A	ENST00000295956.4	+	26	4576	c.4411G>A	c.(4411-4413)Gtg>Atg	p.V1471M	FLNB_ENST00000493452.1_Missense_Mutation_p.V1302M|FLNB_ENST00000357272.4_Missense_Mutation_p.V1471M|FLNB_ENST00000429972.2_Missense_Mutation_p.V1471M|FLNB_ENST00000348383.5_Missense_Mutation_p.V1471M|FLNB_ENST00000358537.3_Missense_Mutation_p.V1471M|FLNB_ENST00000490882.1_Missense_Mutation_p.V1502M|FLNB_ENST00000419752.2_Missense_Mutation_p.V1302M	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1471	Interaction with FBLP1.		V -> M (in dbSNP:rs12632456). {ECO:0000269|PubMed:11153914, ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:9651345}.		actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GCCAGTGAACGTGGTGGACAA	0.512													G|||	3046	0.608227	0.6422	0.4813	5008	,	,		23390	0.9692		0.2833	False		,,,				2504	0.6145				p.V1502M		Atlas-SNP	.											.	FLNB	430	.	0			c.G4504A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	2573,1833	636.4+/-396.6	741,1091,371	148.0	127.0	134.0		4504,4411,4411,4411	2.8	0.7	3	dbSNP_120	134	2109,6491	363.6+/-333.2	265,1579,2456	yes	missense,missense,missense,missense	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	21,21,21,21	1006,2670,2827	AA,AG,GG		24.5233,41.6024,35.9988	benign,benign,benign,benign	1502/2634,1471/2592,1471/2579,1471/2603	58118555	4682,8324	2203	4300	6503	SO:0001583	missense	2317	exon27			GTGAACGTGGTGG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4411G>A	3.37:g.58118555G>A	ENSP00000295956:p.Val1471Met	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	1232	0.5641025641025641	315	0.6402439024390244	153	0.42265193370165743	554	0.9685314685314685	210	0.2770448548812665	G	18.29	3.592206	0.66219	0.583976	0.245233	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	5.81	2.75	0.32379	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.199780	0.43110	D	0.000613	T	0.00012	0.0000	M	0.83774	2.66	0.25432	P	0.9881714	P;P;B;B;P;P	0.46395	0.877;0.588;0.382;0.057;0.807;0.807	B;B;B;B;B;B	0.43536	0.37;0.194;0.278;0.055;0.423;0.423	T	0.33828	-0.9853	9	0.49607	T	0.09	.	5.5883	0.17287	0.3207:0.1285:0.5508:0.0	rs12632456;rs52793889;rs61428936;rs12632456	1471;1502;1302;1302;1471;1471	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	M	1471;1502;1471;1471;1471;1471;1302;1302	ENSP00000295956:V1471M;ENSP00000420213:V1502M;ENSP00000351339:V1471M;ENSP00000415599:V1471M;ENSP00000232447:V1471M;ENSP00000349819:V1471M;ENSP00000418510:V1302M;ENSP00000414532:V1302M	ENSP00000295956:V1471M	V	+	1	0	FLNB	58093595	1.000000	0.71417	0.669000	0.29828	0.915000	0.54546	2.951000	0.49089	0.228000	0.21019	0.557000	0.71058	GTG	G|0.538;A|0.462	0.462	strong		0.512	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
KRT84	3890	hgsc.bcm.edu	37	12	52777502	52777502	+	Silent	SNP	A	A	G	rs1945297	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52777502A>G	ENST00000257951.3	-	2	693	c.627T>C	c.(625-627)aaT>aaC	p.N209N	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	209	Linker 1.|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)		GTGGCTCCAGATTGCTCCTGA	0.552													G|||	2485	0.496206	0.6475	0.4798	5008	,	,		20714	0.6776		0.2584	False		,,,				2504	0.3609				p.N209N		Atlas-SNP	.											.	KRT84	61	.	0			c.T627C						PASS	.	G		2600,1806	530.4+/-372.9	791,1018,394	77.0	75.0	76.0		627	1.3	0.8	12	dbSNP_92	76	2317,6283	704.6+/-405.4	310,1697,2293	no	coding-synonymous	KRT84	NM_033045.3		1101,2715,2687	GG,GA,AA		26.9419,40.9896,37.8056		209/601	52777502	4917,8089	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			CTCCAGATTGCTC	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.627T>C	12.37:g.52777502A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	150	66	0.44	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.586;G|0.414	0.414	strong		0.552	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
CFAP53	220136	hgsc.bcm.edu	37	18	47788544	47788544	+	Silent	SNP	T	T	G	rs112087763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:47788544T>G	ENST00000398545.4	-	2	232	c.115A>C	c.(115-117)Aga>Cga	p.R39R		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)		CGTCGGATTCTTTCTAGATGG	0.438													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19087	0.0		0.004	False		,,,				2504	0.001				p.R39R		Atlas-SNP	.											.	CCDC11	59	.	0			c.A115C						PASS	.	T		1,3831		0,1,1915	113.0	108.0	109.0		115	4.0	0.2	18	dbSNP_132	109	24,8220		0,24,4098	no	coding-synonymous	CCDC11	NM_145020.3		0,25,6013	GG,GT,TT		0.2911,0.0261,0.207		39/515	47788544	25,12051	1916	4122	6038	SO:0001819	synonymous_variant	220136	exon2			GGATTCTTTCTAG																												ENST00000398545.4:c.115A>C	18.37:g.47788544T>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_145020		Silent	SNP	ENST00000398545.4	37	CCDS11940.2																																																																																			T|0.997;G|0.003	0.003	strong		0.438	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
ETV3L	440695	hgsc.bcm.edu	37	1	157062696	157062696	+	Silent	SNP	G	G	T	rs1176537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:157062696G>T	ENST00000454449.2	-	5	1115	c.831C>A	c.(829-831)ctC>ctA	p.L277L		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	277	Pro-rich.				cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				AGGCCCCTGGGAGGCTCCTAG	0.652													G|||	1121	0.223842	0.0908	0.2637	5008	,	,		16092	0.2381		0.3728	False		,,,				2504	0.2076				p.L277L		Atlas-SNP	.											ETV3L_ENST00000454449,NS,adenoma,0,2	ETV3L	73	2	0			c.C831A						PASS	.	G		613,3793	255.5+/-260.7	31,551,1621	25.0	29.0	27.0		831	2.8	0.5	1	dbSNP_87	27	3231,5369	457.8+/-364.4	621,1989,1690	no	coding-synonymous	ETV3L	NM_001004341.2		652,2540,3311	TT,TG,GG		37.5698,13.9128,29.5556		277/362	157062696	3844,9162	2203	4300	6503	SO:0001819	synonymous_variant	440695	exon5			CCCTGGGAGGCTC	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.831C>A	1.37:g.157062696G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_001004341		Silent	SNP	ENST00000454449.2	37	CCDS30893.1																																																																																			G|0.720;T|0.280	0.280	strong		0.652	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341	
TMEM87A	25963	hgsc.bcm.edu	37	15	42565588	42565588	+	Silent	SNP	C	C	A	rs2277533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:42565588C>A	ENST00000389834.4	-	1	273	c.9G>T	c.(7-9)gcG>gcT	p.A3A	GANC_ENST00000566442.1_5'Flank|TMEM87A_ENST00000307216.6_Silent_p.A3A|GANC_ENST00000440615.2_5'Flank|GANC_ENST00000318010.8_5'Flank|TMEM87A_ENST00000448392.1_5'UTR|TMEM87A_ENST00000568432.1_5'Flank	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	3						integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-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;1.03e-06)		GCCACGCAGCCGCCGCCATCT	0.597													C|||	800	0.159744	0.0091	0.1902	5008	,	,		17168	0.3353		0.1163	False		,,,				2504	0.2055				p.A3A		Atlas-SNP	.											TMEM87A_ENST00000307216,NS,carcinoma,0,2	TMEM87A	56	2	0			c.G9T						scavenged	.	C	,	161,4245	107.3+/-145.7	4,153,2046	53.0	51.0	52.0		9,9	1.5	1.0	15	dbSNP_100	52	1141,7457	228.7+/-263.7	68,1005,3226	no	coding-synonymous,coding-synonymous	TMEM87A	NM_001110503.1,NM_015497.3	,	72,1158,5272	AA,AC,CC		13.2705,3.6541,10.0123	,	3/182,3/556	42565588	1302,11702	2203	4299	6502	SO:0001819	synonymous_variant	25963	exon1			CGCAGCCGCCGCC	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.9G>T	15.37:g.42565588C>A		Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_001110503	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Silent	SNP	ENST00000389834.4	37	CCDS32205.1																																																																																			C|0.876;A|0.124	0.124	strong		0.597	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497	
FRRS1	391059	hgsc.bcm.edu	37	1	100206374	100206374	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:100206374G>T	ENST00000414213.1	-	6	1152	c.551C>A	c.(550-552)cCt>cAt	p.P184H	FRRS1_ENST00000287474.5_Missense_Mutation_p.P184H			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	184						integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		GGAAACGGGAGGTAACGTTGG	0.428																																					p.P184H		Atlas-SNP	.											FRRS1,right_upper_lobe,carcinoma,0,1	FRRS1	50	1	0			c.C551A						scavenged	.						224.0	220.0	221.0					1																	100206374		2203	4300	6503	SO:0001583	missense	391059	exon6			ACGGGAGGTAACG	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.551C>A	1.37:g.100206374G>T	ENSP00000393884:p.Pro184His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	103	3	0.0291262	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		.	.	.	.	.	.	.	.	.	.	G	5.089	0.202076	0.09652	.	.	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.54	3.61	0.41365	.	0.837278	0.10568	N	0.659435	T	0.07143	0.0181	N	0.08118	0	0.09310	N	1	B	0.25904	0.137	B	0.25291	0.059	T	0.25502	-1.0130	9	0.44086	T	0.13	-5.1375	5.5947	0.17321	0.0792:0.284:0.5144:0.1224	.	184	Q6ZNA5-2	.	H	184	.	ENSP00000287474:P184H	P	-	2	0	FRRS1	99978962	0.016000	0.18221	0.003000	0.11579	0.003000	0.03518	1.076000	0.30729	1.336000	0.45506	-0.150000	0.13652	CCT	.	.	none		0.428	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
MAVS	57506	hgsc.bcm.edu	37	20	3838441	3838441	+	Missense_Mutation	SNP	C	C	G	rs17857295	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:3838441C>G	ENST00000428216.2	+	3	405	c.277C>G	c.(277-279)Cag>Gag	p.Q93E	MAVS_ENST00000416600.2_Intron|MAVS_ENST00000358134.6_Missense_Mutation_p.Q93E	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	93			Q -> E (in dbSNP:rs17857295). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16127453, ECO:0000269|PubMed:16153868}.		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						CTCTGTCTACCAGAGCTACCA	0.632													C|||	1457	0.290935	0.0779	0.2882	5008	,	,		15267	0.5605		0.2833	False		,,,				2504	0.3108				p.Q93E		Atlas-SNP	.											.	MAVS	34	.	0			c.C277G						PASS	.	C	,GLU/GLN	452,3954	217.8+/-236.0	27,398,1778	113.0	87.0	96.0		,277	2.5	0.4	20	dbSNP_123	96	2136,6464	368.6+/-335.1	250,1636,2414	yes	intron,missense	MAVS	NM_001206491.1,NM_020746.4	,29	277,2034,4192	GG,GC,CC		24.8372,10.2587,19.8985	,possibly-damaging	,93/541	3838441	2588,10418	2203	4300	6503	SO:0001583	missense	57506	exon3			GTCTACCAGAGCT	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.277C>G	20.37:g.3838441C>G	ENSP00000401980:p.Gln93Glu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	663	0.30357142857142855	38	0.07723577235772358	96	0.26519337016574585	323	0.5646853146853147	206	0.2717678100263852	C	10.82	1.458798	0.26248	0.102587	0.248372	ENSG00000088888	ENST00000428216;ENST00000358134	T;T	0.12039	2.88;2.72	4.67	2.53	0.30540	.	0.520418	0.17532	N	0.170837	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	P;P;P	0.46784	0.571;0.884;0.759	B;B;B	0.42851	0.37;0.4;0.4	T	0.39583	-0.9607	9	0.31617	T	0.26	-4.6837	6.7646	0.23560	0.2075:0.5973:0.1952:0.0	rs17857295;rs59161240	93;93;93	B2BD34;Q7Z434;Q7Z434-2	.;MAVS_HUMAN;.	E	93	ENSP00000401980:Q93E;ENSP00000350852:Q93E	ENSP00000350852:Q93E	Q	+	1	0	MAVS	3786441	0.000000	0.05858	0.401000	0.26359	0.936000	0.57629	-0.228000	0.09114	1.093000	0.41377	0.609000	0.83330	CAG	C|0.764;G|0.236	0.236	strong		0.632	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
OR51D1	390038	hgsc.bcm.edu	37	11	4661568	4661568	+	Missense_Mutation	SNP	A	A	G	rs61746547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4661568A>G	ENST00000357605.2	+	1	624	c.548A>G	c.(547-549)cAa>cGa	p.Q183R		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCTACTGCCAAACACATACT	0.483													G|||	193	0.0385383	0.0113	0.0677	5008	,	,		23825	0.001		0.0835	False		,,,				2504	0.047				p.Q183R		Atlas-SNP	.											OR51D1,colon,carcinoma,-1,1	OR51D1	49	1	0			c.A548G						PASS	.	G	ARG/GLN	95,4307	817.6+/-416.3	3,89,2109	281.0	237.0	252.0		548	-3.5	0.0	11	dbSNP_129	252	786,7810	783.2+/-407.6	32,722,3544	yes	missense	OR51D1	NM_001004751.2	43	35,811,5653	GG,GA,AA		9.1438,2.1581,6.778	benign	183/325	4661568	881,12117	2201	4298	6499	SO:0001583	missense	390038	exon1			ACTGCCAAACACA	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"""GPCR / Class A : Olfactory receptors"""	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.548A>G	11.37:g.4661568A>G	ENSP00000350222:p.Gln183Arg	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	37	CCDS31357.1	105	0.04807692307692308	6	0.012195121951219513	35	0.09668508287292818	1	0.0017482517482517483	63	0.08311345646437995	G	0	-2.700617	0.00097	0.021581	0.091438	ENSG00000197428	ENST00000357605	T	0.00076	8.76	4.43	-3.5	0.04710	GPCR, rhodopsin-like superfamily (1);	1.400730	0.05041	N	0.476301	T	0.00012	0.0000	N	0.01686	-0.76	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24476	-1.0159	9	0.02654	T	1	.	13.0848	0.59133	0.6231:0.0:0.3769:0.0	rs61746547	183	Q8NGF3	O51D1_HUMAN	R	183	ENSP00000350222:Q183R	ENSP00000350222:Q183R	Q	+	2	0	OR51D1	4618144	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.469000	0.22067	-0.905000	0.03871	-0.964000	0.02622	CAA	A|0.938;G|0.062	0.062	strong		0.483	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751	
ICAM5	7087	hgsc.bcm.edu	37	19	10404519	10404519	+	Silent	SNP	G	G	A	rs17852402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10404519G>A	ENST00000221980.4	+	7	1674	c.1611G>A	c.(1609-1611)gaG>gaA	p.E537E		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	537	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)			CCGTCATCGAGGGGCTGTTGC	0.662													G|||	475	0.0948482	0.0227	0.1398	5008	,	,		17077	0.0476		0.1292	False		,,,				2504	0.1738				p.E537E		Atlas-SNP	.											.	ICAM5	53	.	0			c.G1611A						PASS	.	G		179,4227	115.0+/-153.0	5,169,2029	72.0	79.0	76.0		1611	3.2	0.7	19	dbSNP_123	76	1262,7338	252.6+/-278.6	91,1080,3129	no	coding-synonymous	ICAM5	NM_003259.3		96,1249,5158	AA,AG,GG		14.6744,4.0626,11.0795		537/925	10404519	1441,11565	2203	4300	6503	SO:0001819	synonymous_variant	7087	exon7			CATCGAGGGGCTG	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.1611G>A	19.37:g.10404519G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	37	CCDS12233.1																																																																																			G|0.891;A|0.109	0.109	strong		0.662	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
ERCC6L2	375748	hgsc.bcm.edu	37	9	98638306	98638306	+	Missense_Mutation	SNP	C	C	T	rs56108623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:98638306C>T	ENST00000288985.7	+	1	324	c.19C>T	c.(19-21)Cct>Tct	p.P7S	LINC00476_ENST00000429781.1_RNA	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	7					DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										GGGCTCGGCCCCTCCCCCTGG	0.716													C|||	472	0.0942492	0.0182	0.1441	5008	,	,		15622	0.1617		0.1044	False		,,,				2504	0.0818				p.P7S		Atlas-SNP	.											C9orf102,NS,carcinoma,0,2	.	.	2	0			c.C19T						PASS	.	C	SER/PRO	115,4199		4,107,2046	9.0	10.0	10.0		19	3.2	0.0	9	dbSNP_129	10	721,7749		33,655,3547	yes	missense	C9orf102	NM_001010895.2	74	37,762,5593	TT,TC,CC		8.5124,2.6657,6.5394	possibly-damaging	7/713	98638306	836,11948	2157	4235	6392	SO:0001583	missense	375748	exon1			TCGGCCCCTCCCC	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"""chromosome 9 open reading frame 102"", ""excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"""	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.19C>T	9.37:g.98638306C>T	ENSP00000288985:p.Pro7Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	37	CCDS35072.1	238	0.10897435897435898	17	0.034552845528455285	45	0.12430939226519337	99	0.17307692307692307	77	0.10158311345646438	C	18.11	3.550969	0.65311	0.026657	0.085124	ENSG00000182150	ENST00000288985	D	0.89552	-2.53	3.19	3.19	0.36642	.	.	.	.	.	T	0.00754	0.0025	N	0.22421	0.69	0.28150	P	0.9294088	B	0.27498	0.18	B	0.21546	0.035	T	0.48422	-0.9037	8	0.52906	T	0.07	-0.3472	10.1498	0.42786	0.0:1.0:0.0:0.0	rs56108623	7	Q5T890	RAD26_HUMAN	S	7	ENSP00000288985:P7S	ENSP00000288985:P7S	P	+	1	0	C9orf102	97678127	0.119000	0.22226	0.022000	0.16811	0.078000	0.17371	1.190000	0.32126	2.084000	0.62774	0.591000	0.81541	CCT	C|0.888;T|0.112	0.112	strong		0.716	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	
CREB3L3	84699	hgsc.bcm.edu	37	19	4159722	4159722	+	Silent	SNP	C	C	T	rs144868958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4159722C>T	ENST00000078445.2	+	4	666	c.519C>T	c.(517-519)tcC>tcT	p.S173S	CREB3L3_ENST00000602147.1_Silent_p.S173S|CREB3L3_ENST00000252587.3_Intron|CREB3L3_ENST00000595923.1_Silent_p.S172S|CREB3L3_ENST00000602257.1_Silent_p.S173S	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	173					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)		TGGACCTGTCCCCACGATGCA	0.632													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17296	0.0		0.002	False		,,,				2504	0.0				p.S173S		Atlas-SNP	.											.	CREB3L3	53	.	0			c.C519T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	92.0	84.0	87.0		519	-6.4	0.0	19	dbSNP_134	87	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	CREB3L3	NM_032607.1		0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		173/462	4159722	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	84699	exon4			CCTGTCCCCACGA		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.519C>T	19.37:g.4159722C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_001271997	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			C|0.998;T|0.002	0.002	strong		0.632	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
TUBG2	27175	hgsc.bcm.edu	37	17	40818699	40818699	+	Missense_Mutation	SNP	A	A	G	rs1046097	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:40818699A>G	ENST00000251412.7	+	11	1436	c.1237A>G	c.(1237-1239)Atg>Gtg	p.M413V	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	413			M -> V (in dbSNP:rs1046097).		cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		TAAGGAGGACATGTTCAAGGA	0.502													A|||	2393	0.477835	0.3147	0.4697	5008	,	,		20591	0.4643		0.5258	False		,,,				2504	0.6687				p.M413V		Atlas-SNP	.											.	TUBG2	43	.	0			c.A1237G						PASS	.	A	VAL/MET	1500,2906	479.5+/-358.5	261,978,964	121.0	108.0	112.0		1237	5.1	1.0	17	dbSNP_86	112	4683,3917	605.5+/-395.0	1298,2087,915	yes	missense	TUBG2	NM_016437.2	21	1559,3065,1879	GG,GA,AA		45.5465,34.0445,47.5396	benign	413/452	40818699	6183,6823	2203	4300	6503	SO:0001583	missense	27175	exon11			GAGGACATGTTCA	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.1237A>G	17.37:g.40818699A>G	ENSP00000251412:p.Met413Val	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	220	100	0.454545	NM_016437	A6NDI4|Q32NB2	Missense_Mutation	SNP	ENST00000251412.7	37	CCDS32658.1	996	0.45604395604395603	178	0.3617886178861789	156	0.430939226519337	262	0.458041958041958	400	0.5277044854881267	A	10.96	1.498948	0.26861	0.340445	0.544535	ENSG00000037042	ENST00000251412	D	0.85013	-1.93	5.07	5.07	0.68467	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.219619	0.45361	D	0.000374	T	0.00012	0.0000	L	0.41236	1.265	0.29642	P	0.8446549999999999	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	9	0.11182	T	0.66	-17.4115	14.9891	0.71371	1.0:0.0:0.0:0.0	rs1046097;rs3186067;rs17355568;rs1046097	413	Q9NRH3	TBG2_HUMAN	V	413	ENSP00000251412:M413V	ENSP00000251412:M413V	M	+	1	0	TUBG2	38072225	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.164000	0.77533	2.132000	0.65825	0.459000	0.35465	ATG	A|0.531;G|0.469	0.469	strong		0.502	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
MS4A6A	64231	hgsc.bcm.edu	37	11	59945745	59945745	+	Silent	SNP	T	T	C	rs12453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:59945745T>C	ENST00000530839.1	-	5	819	c.327A>G	c.(325-327)ttA>ttG	p.L109L	MS4A6A_ENST00000528851.1_Silent_p.L109L|MS4A6A_ENST00000426738.2_Silent_p.L64L|MS4A6A_ENST00000420732.2_Silent_p.L109L|MS4A6A_ENST00000412309.2_Silent_p.L137L|MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000323961.3_Silent_p.L109L|MS4A6A_ENST00000529054.1_Silent_p.L137L|MS4A6A_ENST00000533023.1_Intron	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	109						integral component of membrane (GO:0016021)		p.L109L(1)		endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AAAGCTTGGTTAACCTTTTCT	0.383													T|||	1539	0.307308	0.1581	0.2723	5008	,	,		18602	0.2252		0.4046	False		,,,				2504	0.5184				p.L137L		Atlas-SNP	.											MS4A6A_ENST00000529054,NS,carcinoma,0,3	MS4A6A	85	3	1	Substitution - coding silent(1)	stomach(1)	c.A411G						PASS	.	T	,,	882,3520	343.8+/-307.8	79,724,1398	154.0	143.0	147.0		327,327,327	-5.8	0.0	11	dbSNP_52	147	3431,5159	506.1+/-376.5	702,2027,1566	no	coding-synonymous,coding-synonymous,coding-synonymous	MS4A6A	NM_022349.2,NM_152851.1,NM_152852.1	,,	781,2751,2964	CC,CT,TT		39.9418,20.0363,33.1974	,,	109/226,109/179,109/249	59945745	4313,8679	2201	4295	6496	SO:0001819	synonymous_variant	64231	exon5			CTTGGTTAACCTT	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.327A>G	11.37:g.59945745T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	37	CCDS7981.1																																																																																			T|0.688;C|0.312	0.312	strong		0.383	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
SCPEP1	59342	hgsc.bcm.edu	37	17	55079471	55079471	+	Silent	SNP	T	T	C	rs12940187	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:55079471T>C	ENST00000262288.3	+	12	1280	c.1225T>C	c.(1225-1227)Ttg>Ctg	p.L409L	AC007114.1_ENST00000580911.1_RNA	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	409					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					CCCTAAATCTTTGGAAACATC	0.463													T|||	379	0.0756789	0.0098	0.1671	5008	,	,		19712	0.002		0.17	False		,,,				2504	0.0787				p.L409L		Atlas-SNP	.											.	SCPEP1	35	.	0			c.T1225C						PASS	.	T		188,4218	119.2+/-156.9	5,178,2020	131.0	117.0	122.0		1225	0.9	0.0	17	dbSNP_121	122	1568,7032	292.8+/-301.0	158,1252,2890	no	coding-synonymous	SCPEP1	NM_021626.2		163,1430,4910	CC,CT,TT		18.2326,4.2669,13.5015		409/453	55079471	1756,11250	2203	4300	6503	SO:0001819	synonymous_variant	59342	exon12			AAATCTTTGGAAA	AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"""retinoid inducible serine carboxypeptidase"""					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.1225T>C	17.37:g.55079471T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_021626	Q96A94|Q9H3F0	Silent	SNP	ENST00000262288.3	37	CCDS11593.1																																																																																			T|0.884;C|0.116	0.116	strong		0.463	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626	
MGAT1	4245	hgsc.bcm.edu	37	5	180218668	180218668	+	Missense_Mutation	SNP	A	A	G	rs634501	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:180218668A>G	ENST00000446023.2	-	3	2054	c.1304T>C	c.(1303-1305)cTg>cCg	p.L435P	MGAT1_ENST00000333055.3_Missense_Mutation_p.L435P|MGAT1_ENST00000307826.4_Missense_Mutation_p.L435P|MGAT1_ENST00000393340.3_Missense_Mutation_p.L435P|MGAT1_ENST00000427865.2_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	140	139	0.992857	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	
DDX60L	91351	hgsc.bcm.edu	37	4	169348435	169348435	+	Silent	SNP	T	T	C	rs2712120	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:169348435T>C	ENST00000511577.1	-	14	1963	c.1716A>G	c.(1714-1716)aaA>aaG	p.K572K	DDX60L_ENST00000260184.7_Silent_p.K572K|DDX60L_ENST00000505890.1_Silent_p.K572K			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	572							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.K572K(1)		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)		GAAATGACTTTTTCTTACTCT	0.328													T|||	1035	0.206669	0.5401	0.1441	5008	,	,		19157	0.006		0.1272	False		,,,				2504	0.089				p.K572K		Atlas-SNP	.											DDX60L,NS,carcinoma,0,1	DDX60L	116	1	1	Substitution - coding silent(1)	stomach(1)	c.A1716G						PASS	.	T		1644,1996		393,858,569	121.0	103.0	109.0		1716	-6.5	0.0	4	dbSNP_100	109	1050,7118		81,888,3115	no	coding-synonymous	DDX60L	NM_001012967.1		474,1746,3684	CC,CT,TT		12.855,45.1648,22.815		572/1707	169348435	2694,9114	1820	4084	5904	SO:0001819	synonymous_variant	91351	exon14			TGACTTTTTCTTA	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.1716A>G	4.37:g.169348435T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	179	95	0.530726	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				T|0.783;C|0.217	0.217	strong		0.328	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
SLMAP	7871	hgsc.bcm.edu	37	3	57882601	57882601	+	Splice_Site	SNP	C	C	T	rs17058639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:57882601C>T	ENST00000428312.1	+	15	1486	c.1392C>T	c.(1390-1392)gaC>gaT	p.D464D	SLMAP_ENST00000495364.1_5'UTR|SLMAP_ENST00000442599.2_5'UTR|SLMAP_ENST00000449503.2_Splice_Site_p.D426D|SLMAP_ENST00000295951.3_Splice_Site_p.D447D|SLMAP_ENST00000494088.1_5'UTR|SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000295952.3_Splice_Site_p.D447D|SLMAP_ENST00000472546.1_3'UTR|SLMAP_ENST00000383718.3_Splice_Site_p.D460D			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	464					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)		TCTCTGTAGACGCCCAAATGG	0.348													C|||	1500	0.299521	0.1218	0.3429	5008	,	,		18552	0.4752		0.2654	False		,,,				2504	0.363				p.D447D		Atlas-SNP	.											.	SLMAP	46	.	0			c.C1341T						PASS	.	C		661,3745	283.4+/-277.1	51,559,1593	134.0	136.0	135.0		1341	2.5	1.0	3	dbSNP_123	135	2081,6519	359.9+/-331.7	256,1569,2475	yes	coding-synonymous-near-splice	SLMAP	NM_007159.2		307,2128,4068	TT,TC,CC		24.1977,15.0023,21.0826		447/812	57882601	2742,10264	2203	4300	6503	SO:0001630	splice_region_variant	7871	exon14			TGTAGACGCCCAA	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.1391-1C>T	3.37:g.57882601C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	37		682|682	0.31227106227106227|0.31227106227106227	65|65	0.13211382113821138|0.13211382113821138	123|123	0.3397790055248619|0.3397790055248619	278|278	0.486013986013986|0.486013986013986	216|216	0.2849604221635884|0.2849604221635884	C|C	12.22|12.22	1.873458|1.873458	0.33069|0.33069	0.150023|0.150023	0.241977|0.241977	ENSG00000163681|ENSG00000163681	ENST00000416658;ENST00000438794|ENST00000417128	.|.	.|.	.|.	6.17|6.17	2.48|2.48	0.30137|0.30137	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999999999|0.999999999999999	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.48758|0.48758	-0.9007|-0.9007	3|3	.|.	.|.	.|.	.|.	9.5685|9.5685	0.39414|0.39414	0.0:0.6048:0.0:0.3951|0.0:0.6048:0.0:0.3951	rs17058639;rs59762822;rs17058639|rs17058639;rs59762822;rs17058639	.|.	.|.	.|.	C|M	72;43|48	.|.	.|.	R|T	+|+	1|2	0|0	SLMAP|SLMAP	57857641|57857641	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.835000|0.835000	0.47333|0.47333	0.831000|0.831000	0.27476|0.27476	0.191000|0.191000	0.20236|0.20236	-0.140000|-0.140000	0.14226|0.14226	CGC|ACG	C|0.740;T|0.260	0.260	strong		0.348	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159	Silent
TLR10	81793	hgsc.bcm.edu	37	4	38776180	38776180	+	Silent	SNP	C	C	A	rs11096956	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:38776180C>A	ENST00000308973.4	-	4	1637	c.1032G>T	c.(1030-1032)ccG>ccT	p.P344P	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Silent_p.P344P|TLR10_ENST00000506111.1_Silent_p.P344P|TLR10_ENST00000361424.2_Silent_p.P344P	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	344					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						TAGGATAATTCGGGAAAAGCA	0.323													A|||	1495	0.298522	0.2118	0.3184	5008	,	,		21199	0.4325		0.2495	False		,,,				2504	0.3139				p.P344P		Atlas-SNP	.											TLR10,NS,malignant_melanoma,-2,2	TLR10	87	2	0			c.G1032T						PASS	.	A	,,,,	979,3425	724.9+/-409.6	100,779,1323	94.0	96.0	95.0		1032,1032,1032,990,1032	1.0	0.5	4	dbSNP_120	95	1748,6852	729.1+/-406.7	189,1370,2741	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	,,,,	289,2149,4064	AA,AC,CC		20.3256,22.2298,20.9705	,,,,	344/812,344/812,344/812,330/798,344/812	38776180	2727,10277	2202	4300	6502	SO:0001819	synonymous_variant	81793	exon2			ATAATTCGGGAAA	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.1032G>T	4.37:g.38776180C>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			C|0.732;A|0.268	0.268	strong		0.323	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
HCN2	610	hgsc.bcm.edu	37	19	603634	603634	+	Silent	SNP	T	T	C	rs56131056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:603634T>C	ENST00000251287.2	+	2	776	c.723T>C	c.(721-723)acT>acC	p.T241T		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	241					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)		ATGAGACCACTGCCCCGTGGA	0.552													c|||	1197	0.239018	0.2405	0.0908	5008	,	,		16192	0.2877		0.0984	False		,,,				2504	0.4366				p.T241T	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.T723C						PASS	.	C		1063,3337		135,793,1272	96.0	86.0	89.0		723	-6.4	0.7	19	dbSNP_129	89	864,7730		47,770,3480	no	coding-synonymous	HCN2	NM_001194.3		182,1563,4752	CC,CT,TT		10.0535,24.1591,14.8299		241/890	603634	1927,11067	2200	4297	6497	SO:0001819	synonymous_variant	610	exon2			GACCACTGCCCCG	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.723T>C	19.37:g.603634T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			T|0.856;C|0.144	0.144	strong		0.552	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
SIMC1	375484	hgsc.bcm.edu	37	5	175772208	175772208	+	Silent	SNP	C	C	T	rs17622467	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:175772208C>T	ENST00000443967.1	+	12	2786	c.2379C>T	c.(2377-2379)atC>atT	p.I793I	RP11-843P14.2_ENST00000508187.1_RNA|SIMC1_ENST00000341199.6_Silent_p.I378I|SIMC1_ENST00000430704.2_Silent_p.I378I|KIAA1191_ENST00000393728.2_5'Flank|SIMC1_ENST00000332772.4_Silent_p.I254I			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	793							SUMO polymer binding (GO:0032184)										GTTCCGTGATCGACCGAAAGG	0.423													C|||	559	0.111621	0.0514	0.1556	5008	,	,		19676	0.1111		0.1312	False		,,,				2504	0.1421				p.I378I		Atlas-SNP	.											.	.	.	.	0			c.C1134T						PASS	.	C		303,4103	164.7+/-196.3	10,283,1910	106.0	105.0	105.0		1134	-8.2	0.2	5	dbSNP_123	105	1159,7441	237.8+/-269.5	80,999,3221	no	coding-synonymous	C5orf25	NM_198567.4		90,1282,5131	TT,TC,CC		13.4767,6.877,11.241		378/458	175772208	1462,11544	2203	4300	6503	SO:0001819	synonymous_variant	375484	exon9			CGTGATCGACCGA	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.2379C>T	5.37:g.175772208C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	129	68	0.527132	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Silent	SNP	ENST00000443967.1	37																																																																																				C|0.896;N|0.000	.	strong		0.423	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567	
ECM2	1842	hgsc.bcm.edu	37	9	95284873	95284873	+	Silent	SNP	A	A	G	rs9299405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:95284873A>G	ENST00000344604.5	-	2	425	c.276T>C	c.(274-276)agT>agC	p.S92S	ECM2_ENST00000375540.1_Silent_p.S92S|CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.S92S	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	92					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.S92S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						ACACATTATAACTTGATTCTA	0.408													A|||	1680	0.335463	0.7564	0.2435	5008	,	,		15137	0.0903		0.2932	False		,,,				2504	0.1278				p.S92S		Atlas-SNP	.											ECM2,NS,carcinoma,0,1	ECM2	147	1	1	Substitution - coding silent(1)	stomach(1)	c.T276C						PASS	.	A	,,,	2912,1492	653.6+/-399.6	966,980,256	56.0	59.0	58.0		,276,276,276	0.7	1.0	9	dbSNP_119	58	2498,6102	406.7+/-348.9	372,1754,2174	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	1338,2734,2430	GG,GA,AA		29.0465,33.8783,41.6026	,,,	,92/678,92/644,92/700	95284873	5410,7594	2202	4300	6502	SO:0001819	synonymous_variant	1842	exon2			ATTATAACTTGAT	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.276T>C	9.37:g.95284873A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			A|0.691;G|0.309	0.309	strong		0.408	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
TEKT3	64518	hgsc.bcm.edu	37	17	15215660	15215660	+	Silent	SNP	T	T	C	rs2286516	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:15215660T>C	ENST00000395930.1	-	7	1203	c.1017A>G	c.(1015-1017)caA>caG	p.Q339Q	RNU6-799P_ENST00000363567.1_RNA|TEKT3_ENST00000338696.2_Silent_p.Q339Q	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	339					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)		CTTTGTTGAATTGATTCCACA	0.448													T|||	1174	0.234425	0.1445	0.2896	5008	,	,		21481	0.252		0.2793	False		,,,				2504	0.2526				p.Q339Q		Atlas-SNP	.											.	TEKT3	64	.	0			c.A1017G						PASS	.	T		744,3662	306.0+/-289.3	64,616,1523	130.0	113.0	118.0		1017	2.2	1.0	17	dbSNP_100	118	2224,6376	377.6+/-338.6	274,1676,2350	no	coding-synonymous	TEKT3	NM_031898.2		338,2292,3873	CC,CT,TT		25.8605,16.8861,22.8202		339/491	15215660	2968,10038	2203	4300	6503	SO:0001819	synonymous_variant	64518	exon7			GTTGAATTGATTC	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.1017A>G	17.37:g.15215660T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	191	189	0.989529	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Silent	SNP	ENST00000395930.1	37	CCDS11169.1																																																																																			T|0.770;C|0.230	0.230	strong		0.448	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
TLR10	81793	hgsc.bcm.edu	37	4	38774785	38774785	+	Silent	SNP	A	A	G	rs10776482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:38774785A>G	ENST00000308973.4	-	4	3032	c.2427T>C	c.(2425-2427)gaT>gaC	p.D809D	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Silent_p.D809D|TLR10_ENST00000506111.1_Silent_p.D809D|TLR10_ENST00000361424.2_Silent_p.D809D	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	809					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						TTTATAGACAATCTGTTCTCA	0.378													G|||	1496	0.298722	0.2126	0.3184	5008	,	,		18229	0.4325		0.2495	False		,,,				2504	0.3139				p.D809D		Atlas-SNP	.											TLR10,colon,carcinoma,0,1	TLR10	87	1	0			c.T2427C						PASS	.	G	,,,,	980,3426	732.4+/-410.4	100,780,1323	69.0	67.0	68.0		2427,2427,2427,2385,2427	0.1	0.1	4	dbSNP_120	68	1747,6853	734.7+/-406.9	188,1371,2741	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	,,,,	288,2151,4064	GG,GA,AA		20.314,22.2424,20.9672	,,,,	809/812,809/812,809/812,795/798,809/812	38774785	2727,10279	2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			TAGACAATCTGTT	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.2427T>C	4.37:g.38774785A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	112	63	0.5625	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			A|0.739;G|0.261	0.261	strong		0.378	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
SCP2D1	140856	hgsc.bcm.edu	37	20	18794754	18794754	+	Missense_Mutation	SNP	C	C	T	rs1053839	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:18794754C>T	ENST00000377428.2	+	1	385	c.295C>T	c.(295-297)Cct>Tct	p.P99S	C20orf78_ENST00000463425.1_5'Flank|C20orf78_ENST00000278779.4_Intron	NM_178483.2	NP_848578.1	Q9UJQ7	SCP2D_HUMAN	SCP2 sterol-binding domain containing 1	99	SCP2.		P -> S (in dbSNP:rs1053839).														GTATCCGGGACCTGCCAGGCT	0.512													C|||	1139	0.227436	0.4266	0.196	5008	,	,		17984	0.0417		0.1839	False		,,,				2504	0.2168				p.P99S		Atlas-SNP	.											.	.	.	.	0			c.C295T						PASS	.	C	,SER/PRO	1664,2742	507.9+/-366.8	335,994,874	72.0	75.0	74.0		,295	-3.5	0.0	20	dbSNP_86	74	1500,7100	284.4+/-296.6	136,1228,2936	yes	intron,missense	C20orf79,LOC100128496	NM_001242671.1,NM_178483.2	,74	471,2222,3810	TT,TC,CC		17.4419,37.7667,24.3272	,benign	,99/157	18794754	3164,9842	2203	4300	6503	SO:0001583	missense	140856	exon1			CCGGGACCTGCCA	AL035563	CCDS13139.1	20p11.23	2012-10-29	2012-10-29	2012-10-29	ENSG00000132631	ENSG00000132631			16211	protein-coding gene	gene with protein product	"""sterol carrier protein 2-like protein"""		"""chromosome 20 open reading frame 79"""	C20orf79		16501878	Standard	NM_178483		Approved	dJ1068E13.2, HSD22	uc002wrk.3	Q9UJQ7	OTTHUMG00000031983	ENST00000377428.2:c.295C>T	20.37:g.18794754C>T	ENSP00000366645:p.Pro99Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	119	67	0.563025	NM_178483	Q548A4	Missense_Mutation	SNP	ENST00000377428.2	37	CCDS13139.1	439	0.20100732600732601	194	0.3943089430894309	67	0.1850828729281768	38	0.06643356643356643	140	0.18469656992084432	C	3.991	-0.004557	0.07773	0.377667	0.174419	ENSG00000132631	ENST00000377428	T	0.20738	2.05	6.08	-3.53	0.04667	SCP2 sterol-binding domain (2);	0.551776	0.17911	N	0.157842	T	0.00012	0.0000	N	0.11845	0.185	0.80722	P	0.0	B	0.14805	0.011	B	0.21360	0.034	T	0.47394	-0.9121	9	0.20519	T	0.43	0.1716	6.5669	0.22517	0.2368:0.4803:0.0:0.2829	rs1053839;rs3171304;rs1053839	99	Q9UJQ7	CT079_HUMAN	S	99	ENSP00000366645:P99S	ENSP00000366645:P99S	P	+	1	0	C20orf79	18742754	0.378000	0.25114	0.009000	0.14445	0.373000	0.29922	0.042000	0.13949	-0.999000	0.03442	-0.229000	0.12294	CCT	C|0.772;T|0.228	0.228	strong		0.512	SCP2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078193.1	NM_178483	
RSC1A1	6248	hgsc.bcm.edu	37	1	15987602	15987602	+	Silent	SNP	A	A	G	rs35549389	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15987602A>G	ENST00000345034.1	+	1	1239	c.1239A>G	c.(1237-1239)caA>caG	p.Q413Q	DDI2_ENST00000480945.1_3'UTR	NM_006511.1	NP_006502.1	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1, member 1	413					intestinal absorption (GO:0050892)|negative regulation of transport (GO:0051051)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	brush border (GO:0005903)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel inhibitor activity (GO:0008200)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)	11		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|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)		AGTGTCCACAAGTCTCCTTTC	0.408													A|||	63	0.0125799	0.0166	0.0144	5008	,	,		21918	0.0		0.0219	False		,,,				2504	0.0092				p.Q413Q		Atlas-SNP	.											.	RSC1A1	29	.	0			c.A1239G						PASS	.	A		79,4327	67.0+/-104.6	1,77,2125	63.0	62.0	62.0		1239	-3.9	0.3	1	dbSNP_126	62	227,8373	90.9+/-153.0	3,221,4076	no	coding-synonymous	RSC1A1	NM_006511.1		4,298,6201	GG,GA,AA		2.6395,1.793,2.3528		413/618	15987602	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	6248	exon1			TCCACAAGTCTCC	BN000122, X82877	CCDS161.1	1p36.1	1998-08-25			ENSG00000215695	ENSG00000215695			10458	protein-coding gene	gene with protein product		601966					Standard	NM_006511		Approved	RS1	uc010obn.2	Q92681	OTTHUMG00000067830	ENST00000345034.1:c.1239A>G	1.37:g.15987602A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_006511	B2RBP5	Silent	SNP	ENST00000345034.1	37	CCDS161.1																																																																																			A|0.979;G|0.021	0.021	strong		0.408	RSC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145500.1	NM_006511	
CCDC94	55702	hgsc.bcm.edu	37	19	4254375	4254375	+	Silent	SNP	C	C	T	rs11085068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	120	0	0		WXS	Illumina HiSeq	Phase_I	104	41	0.394231	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	
POLR1A	25885	hgsc.bcm.edu	37	2	86259443	86259443	+	Silent	SNP	C	C	T	rs2276626	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	185	0	0		WXS	Illumina HiSeq	Phase_I	190	90	0.473684	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	
MYOCD	93649	hgsc.bcm.edu	37	17	12656111	12656111	+	Silent	SNP	T	T	C	rs12453883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:12656111T>C	ENST00000343344.4	+	10	1506	c.1506T>C	c.(1504-1506)aaT>aaC	p.N502N	AC005358.1_ENST00000609971.1_Silent_p.N406N|MYOCD_ENST00000395988.1_3'UTR|MYOCD_ENST00000425538.1_Silent_p.N502N			Q8IZQ8	MYCD_HUMAN	myocardin	502	Ser-rich.				cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|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 from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|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 (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		GCAGCCTGAATGGGGGCTCTG	0.587													C|||	309	0.0617013	0.0182	0.0634	5008	,	,		18801	0.1905		0.0109	False		,,,				2504	0.0389				p.N502N		Atlas-SNP	.											.	MYOCD	291	.	0			c.T1506C						PASS	.	C	,,	110,4296	816.0+/-416.2	1,108,2094	49.0	47.0	48.0		1506,1218,1506	-10.8	0.0	17	dbSNP_120	48	62,8538	816.5+/-406.9	1,60,4239	yes	coding-synonymous,coding-synonymous,coding-synonymous	MYOCD	NM_001146312.1,NM_001146313.1,NM_153604.2	,,	2,168,6333	CC,CT,TT		0.7209,2.4966,1.3225	,,	502/987,406/685,502/939	12656111	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	93649	exon10			CCTGAATGGGGGC	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.1506T>C	17.37:g.12656111T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	35	0.364583	NM_001146312	Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	37	CCDS11163.1																																																																																			T|0.962;C|0.038	0.038	strong		0.587	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604	
OR2S2	56656	hgsc.bcm.edu	37	9	35957669	35957669	+	Missense_Mutation	SNP	T	T	C	rs2233564	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35957669T>C	ENST00000341959.2	-	1	482	c.427A>G	c.(427-429)Atg>Gtg	p.M143V		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	143			M -> V (in dbSNP:rs2233564).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			GCCATGGGCATGTAGGCAGCC	0.537													C|||	1588	0.317093	0.4017	0.2896	5008	,	,		23981	0.2976		0.2793	False		,,,				2504	0.2812				p.M143V	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.A427G						PASS	.	C	VAL/MET	1741,2665	647.6+/-398.6	328,1085,790	91.0	80.0	84.0		427	2.1	0.3	9	dbSNP_98	84	2837,5763	674.6+/-403.1	509,1819,1972	yes	missense	OR2S2	NM_019897.2	21	837,2904,2762	CC,CT,TT		32.9884,39.5143,35.1991	benign	143/320	35957669	4578,8428	2203	4300	6503	SO:0001583	missense	56656	exon1			TGGGCATGTAGGC	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"""GPCR / Class A : Olfactory receptors"""	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.427A>G	9.37:g.35957669T>C	ENSP00000344040:p.Met143Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	37	CCDS6596.2	700	0.32051282051282054	206	0.4186991869918699	121	0.3342541436464088	163	0.28496503496503495	210	0.2770448548812665	C	0.001	-3.007357	0.00043	0.395143	0.329884	ENSG00000122718	ENST00000341959	T	0.34667	1.35	3.98	2.09	0.27110	GPCR, rhodopsin-like superfamily (1);	0.149772	0.30547	N	0.009391	T	0.00012	0.0000	N	0.00459	-1.475	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44345	-0.9334	9	0.02654	T	1	.	3.956	0.09390	0.0:0.5234:0.1778:0.2988	rs2233564;rs3739616;rs52803098;rs2233564	143	Q9NQN1	OR2S1_HUMAN	V	143	ENSP00000344040:M143V	ENSP00000344040:M143V	M	-	1	0	OR2S2	35947669	0.000000	0.05858	0.335000	0.25508	0.040000	0.13550	-1.843000	0.01680	0.236000	0.21180	-0.119000	0.15052	ATG	T|0.657;C|0.343	0.343	strong		0.537	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
SENP3	26168	hgsc.bcm.edu	37	17	7468277	7468277	+	Splice_Site	SNP	C	C	T	rs35596387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7468277C>T	ENST00000429205.2	+	4	1006	c.957C>T	c.(955-957)agC>agT	p.S319S	SENP3_ENST00000321337.7_Splice_Site_p.S319S|SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	319						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TTCCACCAGGCATCTTGGACG	0.532													C|||	125	0.0249601	0.0	0.0086	5008	,	,		19654	0.0		0.0388	False		,,,				2504	0.0818				p.S319S		Atlas-SNP	.											.	SENP3	18	.	0			c.C957T						PASS	.	C		21,3889		0,21,1934	53.0	56.0	55.0		957	4.5	1.0	17	dbSNP_126	55	266,8028		7,252,3888	yes	coding-synonymous-near-splice	SENP3	NM_015670.5		7,273,5822	TT,TC,CC		3.2071,0.5371,2.3517		319/575	7468277	287,11917	1955	4147	6102	SO:0001630	splice_region_variant	26168	exon4			ACCAGGCATCTTG	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.956-1C>T	17.37:g.7468277C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																				C|0.976;T|0.024	0.024	strong		0.532	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	Silent
RFPL4A	342931	hgsc.bcm.edu	37	19	56274453	56274453	+	Missense_Mutation	SNP	G	G	A	rs75239380	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56274453G>A	ENST00000434937.2	+	3	947	c.776G>A	c.(775-777)gGa>gAa	p.G259E		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	259	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.G259E(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						CATAAACGTGGAAGTCAAGAT	0.438																																					p.G259E		Atlas-SNP	.											ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	1	Substitution - Missense(1)	stomach(1)	c.G776A						scavenged	.						18.0	22.0	21.0					19																	56274453		691	1590	2281	SO:0001583	missense	342931	exon3			AACGTGGAAGTCA		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.776G>A	19.37:g.56274453G>A	ENSP00000392936:p.Gly259Glu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	229	32	0.139738	NM_001145014		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.580299	0.00879	.	.	ENSG00000223638	ENST00000434937	T	0.62498	0.02	2.78	-5.56	0.02529	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.24928	0.0605	N	0.01751	-0.74	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.10776	-1.0615	8	0.25751	T	0.34	-12.9296	1.2915	0.02061	0.279:0.1414:0.3715:0.2082	.	259	A6NLU0	RFPLA_HUMAN	E	259	ENSP00000392936:G259E	ENSP00000392936:G259E	G	+	2	0	RFPL4A	60966265	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.179000	0.03090	-1.696000	0.01421	-1.408000	0.01128	GGA	G|0.760;A|0.240	0.240	strong		0.438	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465094	39465094	+	Missense_Mutation	SNP	C	C	T	rs12453338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	207	2	0.00966184		WXS	Illumina HiSeq	Phase_I	238	135	0.567227	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	
MLLT3	4300	hgsc.bcm.edu	37	9	20414376	20414376	+	Silent	SNP	A	A	G	rs1761445|rs373338988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:20414376A>G	ENST00000380338.4	-	5	754	c.468T>C	c.(466-468)agT>agC	p.S156S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S153S|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	156	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.527			T	MLL	ALL								A|||	608	0.121406	0.1354	0.1037	5008	,	,		12979	0.0774		0.1282	False		,,,				2504	0.1534				p.S156S		Atlas-SNP	.		Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	MLLT3,colon,carcinoma,0,3	MLLT3	125	3	0			c.T468C						scavenged	.						9.0	14.0	13.0					9																	20414376		1854	3811	5665	SO:0001819	synonymous_variant	4300	exon5			GCTGCTACTGCTG	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.468T>C	9.37:g.20414376A>G		Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																			A|0.906;G|0.094	0.094	strong		0.527	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
SPATA17	128153	hgsc.bcm.edu	37	1	217804767	217804767	+	Missense_Mutation	SNP	A	A	G	rs34652544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:217804767A>G	ENST00000366933.4	+	1	102	c.47A>G	c.(46-48)aAt>aGt	p.N16S	GPATCH2_ENST00000366935.3_5'Flank|GPATCH2_ENST00000366934.3_5'Flank	NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	16			N -> S (in dbSNP:rs34652544).			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)		ACTGTAGGAAATCAGTACTAC	0.502													A|||	76	0.0151757	0.0008	0.0043	5008	,	,		17950	0.0		0.0527	False		,,,				2504	0.0194				p.N16S		Atlas-SNP	.											.	SPATA17	59	.	0			c.A47G						PASS	.	A	SER/ASN	45,4361	48.2+/-83.0	0,45,2158	93.0	83.0	86.0		47	-0.4	0.0	1	dbSNP_126	86	401,8199	127.2+/-185.5	8,385,3907	yes	missense	SPATA17	NM_138796.2	46	8,430,6065	GG,GA,AA		4.6628,1.0213,3.4292	benign	16/362	217804767	446,12560	2203	4300	6503	SO:0001583	missense	128153	exon1			TAGGAAATCAGTA	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.47A>G	1.37:g.217804767A>G	ENSP00000355900:p.Asn16Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_138796	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	37	CCDS1519.1	52	0.023809523809523808	0	0.0	5	0.013812154696132596	0	0.0	47	0.06200527704485488	A	2.593	-0.294729	0.05568	0.010213	0.046628	ENSG00000162814	ENST00000366933	T	0.70749	-0.51	4.47	-0.386	0.12466	.	1.304130	0.04702	N	0.416073	T	0.07458	0.0188	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06588	-1.0818	10	0.12766	T	0.61	-1.3493	8.0133	0.30365	0.6052:0.0:0.3948:0.0	rs34652544	16	Q96L03	SPT17_HUMAN	S	16	ENSP00000355900:N16S	ENSP00000355900:N16S	N	+	2	0	SPATA17	215871390	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.088000	0.14979	0.032000	0.15435	-0.250000	0.11733	AAT	A|0.968;G|0.032	0.032	strong		0.502	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
SATL1	340562	hgsc.bcm.edu	37	X	84363140	84363140	+	Missense_Mutation	SNP	A	A	G	rs10126146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:84363140A>G	ENST00000395409.3	-	1	834	c.274T>C	c.(274-276)Tgg>Cgg	p.W92R	SATL1_ENST00000509231.1_Missense_Mutation_p.W279R|SATL1_ENST00000332921.5_Missense_Mutation_p.W92R			Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	92	Gln-rich.		W -> R (in dbSNP:rs10126146). {ECO:0000269|PubMed:15489334}.				N-acetyltransferase activity (GO:0008080)			NS(1)|breast(5)|endometrium(2)|large_intestine(3)|lung(13)|skin(3)|stomach(1)|urinary_tract(1)	29						CTTGCACTCCATTGGTTCATG	0.433													G|||	2858	0.757086	0.6006	0.572	3775	,	,		17880	0.4841		0.5477	False		,,,				2504	0.6421				p.W279R		Atlas-SNP	.											.	SATL1	70	.	0			c.T835C						PASS	.	G	ARG/TRP	2972,863		993,560,426,79,145	265.0	214.0	231.0		835	-5.4	0.0	X	dbSNP_119	231	4591,2137		1119,1059,1294,250,578	yes	missense	SATL1	NM_001012980.2	101	2112,1619,1720,329,723	GG,GA,G,AA,A		31.7628,22.5033,28.401	benign	279/633	84363140	7563,3000	2203	4300	6503	SO:0001583	missense	340562	exon1			CACTCCATTGGTT	BC043215	CCDS35343.1, CCDS35343.2	Xq21	2008-02-05			ENSG00000184788	ENSG00000184788			27992	protein-coding gene	gene with protein product						12477932	Standard	NM_001012980		Approved		uc004een.3	Q86VE3	OTTHUMG00000021931	ENST00000395409.3:c.274T>C	X.37:g.84363140A>G	ENSP00000378804:p.Trp92Arg	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	305	304	0.996721	NM_001012980	A0AVK7|E9PB72|Q5H8V9	Missense_Mutation	SNP	ENST00000395409.3	37		1213	0.731163351416516	213	0.696078431372549	143	0.5860655737704918	190	0.5	293	0.5813492063492064	G	0.011	-1.726338	0.00694	0.774967	0.682372	ENSG00000184788	ENST00000395409;ENST00000332921;ENST00000509231	T;T;T	0.37235	1.21;1.21;1.21	2.7	-5.39	0.02664	.	3.270730	0.01318	N	0.010859	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.16396	0.0;0.017	B;B	0.09377	0.0;0.004	T	0.23190	-1.0195	9	0.15066	T	0.55	-0.0923	4.4697	0.11706	0.5825:0.1033:0.2097:0.1045	rs10126146;rs41380046;rs10126146	92;279	Q86VE3;E9PB72	SATL1_HUMAN;.	R	92;92;279	ENSP00000378804:W92R;ENSP00000329115:W92R;ENSP00000425421:W279R	ENSP00000329115:W92R	W	-	1	0	SATL1	84249796	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.336000	0.07863	-3.898000	0.00093	-3.007000	0.00075	TGG	A|0.262;0|0.014	.	strong		0.433	SATL1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_291339	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376869	168376869	+	lincRNA	SNP	C	C	T	rs71305249|rs201374833	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:168376869C>T	ENST00000538528.1	-	0	750																											GGGGTCATTCCCCCTGCAGTG	0.602													C|||	1272	0.253994	0.1241	0.2536	5008	,	,		19408	0.4167		0.2445	False		,,,				2504	0.272				p.G155E		Atlas-SNP	.											.	.	.	.	0			c.G464A						PASS	.						30.0	27.0	28.0					6																	168376869		692	1591	2283			0	exon1			TCATTCCCCCTGC																													6.37:g.168376869C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	203	31	0.152709	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				.	.	weak		0.602	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
ERMARD	55780	hgsc.bcm.edu	37	6	170176647	170176647	+	Silent	SNP	C	C	T	rs386708934|rs4716399	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170176647C>T	ENST00000366773.3	+	16	1650	c.1617C>T	c.(1615-1617)atC>atT	p.I539I	ERMARD_ENST00000418781.3_Intron|ERMARD_ENST00000366772.2_Intron|ERMARD_ENST00000392095.4_Silent_p.I413I|ERMARD_ENST00000588451.1_Silent_p.I403I	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	539					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TCCGAAGCATCAGCGAACAGT	0.632													C|||	1721	0.34365	0.497	0.304	5008	,	,		21048	0.3304		0.2366	False		,,,				2504	0.2883				p.I539I		Atlas-SNP	.											.	C6orf70	63	.	0			c.C1617T						PASS	.	C		2113,2293	572.6+/-383.4	503,1107,593	95.0	72.0	80.0		1617	1.3	0.0	6	dbSNP_111	80	1913,6687	335.9+/-321.6	235,1443,2622	no	coding-synonymous	C6orf70	NM_018341.1		738,2550,3215	TT,TC,CC		22.2442,47.9573,30.9549		539/679	170176647	4026,8980	2203	4300	6503	SO:0001819	synonymous_variant	55780	exon16			AAGCATCAGCGAA	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.1617C>T	6.37:g.170176647C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Silent	SNP	ENST00000366773.3	37	CCDS34576.1																																																																																			C|0.694;T|0.306	0.306	strong		0.632	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
OR5AU1	390445	hgsc.bcm.edu	37	14	21623648	21623648	+	Silent	SNP	G	G	A	rs7161544	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21623648G>A	ENST00000304418.3	-	1	574	c.537C>T	c.(535-537)aaC>aaT	p.N179N		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		AGAGCAGGGGGTTACAAATAG	0.517													G|||	1742	0.347843	0.3162	0.3501	5008	,	,		22270	0.1389		0.5755	False		,,,				2504	0.3701				p.N179N		Atlas-SNP	.											.	OR5AU1	46	.	0			c.C537T						PASS	.	G		1590,2816	493.9+/-362.8	281,1028,894	63.0	61.0	62.0		537	-2.3	0.0	14	dbSNP_116	62	5015,3585	627.4+/-398.0	1453,2109,738	no	coding-synonymous	OR5AU1	NM_001004731.1		1734,3137,1632	AA,AG,GG		41.686,36.0872,49.2157		179/363	21623648	6605,6401	2203	4300	6503	SO:0001819	synonymous_variant	390445	exon1			CAGGGGGTTACAA	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"""GPCR / Class A : Olfactory receptors"""	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.537C>T	14.37:g.21623648G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001004731	B2RP78|Q6IEU2|Q96R10	Silent	SNP	ENST00000304418.3	37	CCDS32042.1																																																																																			G|0.567;A|0.433	0.433	strong		0.517	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1		
GPR35	2859	hgsc.bcm.edu	37	2	241569492	241569492	+	Silent	SNP	G	G	C	rs61734451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241569492G>C	ENST00000319838.5	+	6	1065	c.123G>C	c.(121-123)gcG>gcC	p.A41A	GPR35_ENST00000403859.1_Silent_p.A41A|GPR35_ENST00000430267.1_Silent_p.A41A|GPR35_ENST00000407714.1_Silent_p.A41A|GPR35_ENST00000438013.2_Silent_p.A72A	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	41					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)		ACAGCCTGGCGCTCTGGGTGT	0.652													g|||	22	0.00439297	0.0008	0.0043	5008	,	,		17820	0.0		0.0139	False		,,,				2504	0.0041				p.A72A		Atlas-SNP	.											.	GPR35	43	.	0			c.G216C						PASS	.	G	,,	25,4381	31.7+/-61.6	0,25,2178	75.0	69.0	71.0		216,216,123	-3.3	1.0	2	dbSNP_129	71	145,8455	71.3+/-133.9	2,141,4157	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR35	NM_001195381.1,NM_001195382.1,NM_005301.3	,,	2,166,6335	CC,CG,GG		1.686,0.5674,1.3071	,,	72/341,72/341,41/310	241569492	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	2859	exon6			CCTGGCGCTCTGG		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.123G>C	2.37:g.241569492G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Silent	SNP	ENST00000319838.5	37	CCDS2541.1																																																																																			G|0.990;C|0.010	0.010	strong		0.652	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382	
MC1R	4157	hgsc.bcm.edu	37	16	89986608	89986608	+	Silent	SNP	A	A	G	rs2228478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89986608A>G	ENST00000555147.1	+	1	2322	c.942A>G	c.(940-942)acA>acG	p.T314T	RP11-566K11.7_ENST00000570217.1_RNA|RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Silent_p.T314T|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	184	0	0		WXS	Illumina HiSeq	Phase_I	202	98	0.485149	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	
MFSD9	84804	hgsc.bcm.edu	37	2	103334969	103334969	+	Silent	SNP	G	G	A	rs1052431	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	110	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	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	
PCNT	5116	hgsc.bcm.edu	37	21	47852085	47852085	+	Missense_Mutation	SNP	G	G	A	rs35147998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47852085G>A	ENST00000359568.5	+	38	8814	c.8707G>A	c.(8707-8709)Gct>Act	p.A2903T	PCNT_ENST00000480896.1_Intron	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2903			A -> T (in dbSNP:rs35147998).		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)					GAGCCCAGCGGCTGCGGAGCA	0.597													G|||	193	0.0385383	0.0091	0.0576	5008	,	,		17638	0.0129		0.0815	False		,,,				2504	0.047				p.A2903T		Atlas-SNP	.											.	PCNT	283	.	0			c.G8707A						PASS	.	G	THR/ALA	75,4331	64.1+/-101.4	0,75,2128	27.0	30.0	29.0		8707	2.0	0.0	21	dbSNP_126	29	712,7888	167.8+/-219.5	26,660,3614	yes	missense	PCNT	NM_006031.5	58	26,735,5742	AA,AG,GG		8.2791,1.7022,6.0511	benign	2903/3337	47852085	787,12219	2203	4300	6503	SO:0001583	missense	5116	exon38			CCAGCGGCTGCGG	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.8707G>A	21.37:g.47852085G>A	ENSP00000352572:p.Ala2903Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	115	45	0.391304	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	104	0.047619047619047616	4	0.008130081300813009	28	0.07734806629834254	8	0.013986013986013986	64	0.08443271767810026	G	8.066	0.769098	0.15983	0.017022	0.082791	ENSG00000160299	ENST00000359568	T	0.01446	4.88	3.84	2.0	0.26442	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.09310	N	1	B	0.23650	0.089	B	0.17722	0.019	T	0.50591	-0.8810	9	0.16896	T	0.51	.	8.4887	0.33086	0.0878:0.1561:0.7561:0.0	rs35147998	2903	O95613	PCNT_HUMAN	T	2903	ENSP00000352572:A2903T	ENSP00000352572:A2903T	A	+	1	0	PCNT	46676513	0.989000	0.36119	0.000000	0.03702	0.001000	0.01503	3.812000	0.55628	0.585000	0.29608	-0.300000	0.09419	GCT	G|0.943;C|0.000;A|0.056	0.056	strong		0.597	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MUC5B	727897	hgsc.bcm.edu	37	11	1272754	1272754	+	Missense_Mutation	SNP	A	A	G	rs3021156	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1272754A>G	ENST00000529681.1	+	31	14702	c.14644A>G	c.(14644-14646)Acc>Gcc	p.T4882A	MUC5B_ENST00000447027.1_Missense_Mutation_p.T4885A|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4882	Thr-rich.		T -> A (in dbSNP:rs3021156). {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)		AGTGGTGACCACCATGGCCAC	0.662													a|||	330	0.0658946	0.0234	0.111	5008	,	,		19066	0.0496		0.0825	False		,,,				2504	0.091				p.T4882A		Atlas-SNP	.											.	MUC5B	473	.	0			c.A14644G						PASS	.	A	ALA/THR	79,4233		0,79,2077	53.0	71.0	65.0		14644	-1.7	0.0	11	dbSNP_101	65	611,7867		23,565,3651	yes	missense	MUC5B	NM_002458.2	58	23,644,5728	GG,GA,AA		7.2069,1.8321,5.3948	benign	4882/5763	1272754	690,12100	2156	4239	6395	SO:0001583	missense	727897	exon31			GTGACCACCATGG	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.14644A>G	11.37:g.1272754A>G	ENSP00000436812:p.Thr4882Ala	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	166	73	0.439759	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	156	0.07142857142857142	12	0.024390243902439025	38	0.10497237569060773	43	0.07517482517482517	63	0.08311345646437995	A	6.943	0.543758	0.13312	0.018321	0.072069	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.19250	2.16;2.27	2.44	-1.72	0.08107	.	.	.	.	.	T	0.00300	0.0009	L	0.29908	0.895	0.58432	P	8.000000000008E-6	B;B	0.32396	0.068;0.369	B;B	0.26969	0.048;0.075	T	0.21930	-1.0231	8	0.87932	D	0	.	3.9262	0.09265	0.5653:0.1871:0.2477:0.0	rs3021156;rs3021156	5204;4885	A7Y9J9;E9PBJ0	.;.	A	4882;4885;4826;4581	ENSP00000436812:T4882A;ENSP00000415793:T4885A	ENSP00000343037:T4826A	T	+	1	0	MUC5B	1229330	0.000000	0.05858	0.009000	0.14445	0.026000	0.11368	-2.134000	0.01307	-0.234000	0.09782	0.254000	0.18369	ACC	A|0.924;G|0.076	0.076	strong		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
NOTCH2	4853	hgsc.bcm.edu	37	1	120539668	120539668	+	Missense_Mutation	SNP	T	T	A	rs200464440		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:120539668T>A	ENST00000256646.2	-	4	922	c.703A>T	c.(703-705)Acc>Tcc	p.T235S	NOTCH2_ENST00000602566.1_Missense_Mutation_p.T196S	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	235	EGF-like 6. {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)		TGCCGACAGGTGCCTCCATTG	0.572			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.T235S		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	NOTCH2_ENST00000369342,NS,carcinoma,0,2	NOTCH2	348	2	0			c.A703T						scavenged	.						50.0	40.0	43.0					1																	120539668		2203	4299	6502	SO:0001583	missense	4853	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GACAGGTGCCTCC	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.703A>T	1.37:g.120539668T>A	ENSP00000256646:p.Thr235Ser	Somatic	321	2	0.00623053		WXS	Illumina HiSeq	Phase_I	356	7	0.0196629	NM_001200001	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.508758	0.85282	.	.	ENSG00000134250	ENST00000256646;ENST00000539617;ENST00000401649;ENST00000369342	T	0.33438	1.41	5.83	5.83	0.93111	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38897	U	0.001527	T	0.42471	0.1204	L	0.58510	1.815	0.80722	D	1	P;D;D	0.71674	0.924;0.998;0.965	P;D;P	0.77004	0.585;0.989;0.834	T	0.25082	-1.0142	10	0.41790	T	0.15	.	15.3661	0.74523	0.0:0.0:0.0:1.0	.	196;235;235	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	S	235;196;208;196	ENSP00000256646:T235S	ENSP00000256646:T235S	T	-	1	0	NOTCH2	120341191	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.185000	0.72013	2.216000	0.71823	0.477000	0.44152	ACC	.	.	weak		0.572	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
TFR2	7036	hgsc.bcm.edu	37	7	100226937	100226937	+	Silent	SNP	G	G	A	rs368298121		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100226937G>A	ENST00000462107.1	-	11	1616	c.1329C>T	c.(1327-1329)tcC>tcT	p.S443S	TFR2_ENST00000544242.1_5'UTR|TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000223051.3_Silent_p.S443S			Q9UP52	TFR2_HUMAN	transferrin receptor 2	443					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	TCCCCACAGCGGATTTAGCTG	0.627																																					p.S443S		Atlas-SNP	.											TFR2,NS,carcinoma,-1,1	TFR2	53	1	0			c.C1329T						PASS	.	G	,	0,4406		0,0,2203	104.0	91.0	95.0		816,1329	-8.8	0.5	7		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TFR2	NM_001206855.1,NM_003227.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	272/631,443/802	100226937	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7036	exon10			CACAGCGGATTTA	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1329C>T	7.37:g.100226937G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	37	CCDS34707.1																																																																																			.	.	weak		0.627	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227	
ADAM12	8038	hgsc.bcm.edu	37	10	127737930	127737930	+	Silent	SNP	G	G	A	rs2292692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	117	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	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		
RYR2	6262	hgsc.bcm.edu	37	1	237778084	237778084	+	Missense_Mutation	SNP	G	G	A	rs3766871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237778084G>A	ENST00000366574.2	+	37	5973	c.5656G>A	c.(5656-5658)Ggc>Agc	p.G1886S	RYR2_ENST00000542537.1_Missense_Mutation_p.G1870S|RYR2_ENST00000360064.6_Missense_Mutation_p.G1884S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1886	4 X approximate repeats.		G -> S (in dbSNP:rs3766871).		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)			AGCCAAGGGGGGCAAGCGGCC	0.522													G|||	382	0.076278	0.1551	0.0303	5008	,	,		19105	0.0635		0.0268	False		,,,				2504	0.0665				p.G1886S		Atlas-SNP	.											RYR2,colon,carcinoma,-2,1	RYR2	1273	1	0			c.G5656A						PASS	.	G	SER/GLY	515,3479		34,447,1516	45.0	48.0	47.0		5656	4.8	0.0	1	dbSNP_107	47	259,8063		3,253,3905	yes	missense	RYR2	NM_001035.2	56	37,700,5421	AA,AG,GG		3.1122,12.8943,6.2845	benign	1886/4968	237778084	774,11542	1997	4161	6158	SO:0001583	missense	6262	exon37			AAGGGGGGCAAGC	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.5656G>A	1.37:g.237778084G>A	ENSP00000355533:p.Gly1886Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	155	0.07097069597069597	80	0.16260162601626016	13	0.03591160220994475	38	0.06643356643356643	24	0.0316622691292876	G	11.53	1.665014	0.29604	0.128943	0.031122	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.72282	-0.64;-0.64;-0.64	4.8	4.8	0.61643	.	0.501385	0.16722	N	0.202239	T	0.00300	0.0009	N	0.11064	0.09	0.09310	P	1.0	B	0.09022	0.002	B	0.12156	0.007	T	0.04347	-1.0958	9	0.22109	T	0.4	.	18.0637	0.89384	0.0:0.0:1.0:0.0	rs3766871;rs52805786;rs3766871	1886	Q92736	RYR2_HUMAN	S	1886;1884;1870	ENSP00000355533:G1886S;ENSP00000353174:G1884S;ENSP00000443798:G1870S	ENSP00000353174:G1884S	G	+	1	0	RYR2	235844707	0.265000	0.24102	0.019000	0.16419	0.367000	0.29736	2.380000	0.44327	2.486000	0.83907	0.650000	0.86243	GGC	G|0.916;A|0.084	0.084	strong		0.522	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
KANSL1	284058	hgsc.bcm.edu	37	17	44249199	44249199	+	Missense_Mutation	SNP	T	T	G	rs543087095	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44249199T>G	ENST00000262419.6	-	2	781	c.311A>C	c.(310-312)aAg>aCg	p.K104T	KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Missense_Mutation_p.K104T|KANSL1_ENST00000572904.1_Missense_Mutation_p.K104T|KANSL1_ENST00000575318.1_Missense_Mutation_p.K104T|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000432791.1_Missense_Mutation_p.K104T	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	104			K -> T (in dbSNP:rs17585974).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GACTGTCTGCTTGCTGAAGAC	0.463													T|||	364	0.0726837	0.0113	0.1398	5008	,	,		24790	0.001		0.1998	False		,,,				2504	0.0511				p.K104T		Atlas-SNP	.											.	.	.	.	0			c.A311C						PASS	.	T	THR/LYS,THR/LYS,THR/LYS	169,4237		0,169,2034	115.0	148.0	137.0		311,311,311	5.9	1.0	17	dbSNP_123	137	1576,7024		0,1576,2724	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	78,78,78	0,1745,4758	GG,GT,TT		18.3256,3.8357,13.4169	probably-damaging,probably-damaging,probably-damaging	104/1105,104/1106,104/1106	44249199	1745,11261	2203	4300	6503	SO:0001583	missense	284058	exon2			GTCTGCTTGCTGA	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.311A>C	17.37:g.44249199T>G	ENSP00000262419:p.Lys104Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	183	62	0.338798	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	215	0.09844322344322344	10	0.02032520325203252	58	0.16022099447513813	1	0.0017482517482517483	146	0.19261213720316622	T	17.53	3.413865	0.62511	0.038357	0.183256	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.26518	1.73;1.73	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.994	T	0.00657	-1.1623	10	0.87932	D	0	-15.2649	13.6649	0.62389	0.0:0.0:0.0:1.0	rs17585974;rs52790918;rs17585974	104;104	C9JHY2;Q7Z3B3	.;K1267_HUMAN	T	104	ENSP00000262419:K104T;ENSP00000387393:K104T	ENSP00000262419:K104T	K	-	2	0	KIAA1267	41604976	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.677000	0.74503	2.244000	0.73946	0.533000	0.62120	AAG	T|0.893;G|0.107	0.107	strong		0.463	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
A2ML1	144568	hgsc.bcm.edu	37	12	8995756	8995756	+	Silent	SNP	A	A	G	rs7308106	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8995756A>G	ENST00000299698.7	+	12	1455	c.1275A>G	c.(1273-1275)gtA>gtG	p.V425V	A2ML1_ENST00000539547.1_5'Flank	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AAGACTTAGTATATAATCCGG	0.468													A|||	187	0.0373403	0.0045	0.0706	5008	,	,		-128	0.001		0.1103	False		,,,				2504	0.0204				p.V425V		Atlas-SNP	.											.	A2ML1	199	.	0			c.A1275G						PASS	.	A		66,3806		3,60,1873	84.0	85.0	84.0		1275	0.5	0.0	12	dbSNP_116	84	866,7408		38,790,3309	no	coding-synonymous	A2ML1	NM_144670.3		41,850,5182	GG,GA,AA		10.4665,1.7045,7.6733		425/1455	8995756	932,11214	1936	4137	6073	SO:0001819	synonymous_variant	144568	exon12			CTTAGTATATAAT	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.1275A>G	12.37:g.8995756A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_144670		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																			A|0.939;G|0.061	0.061	strong		0.468	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
SGSM2	9905	hgsc.bcm.edu	37	17	2266799	2266799	+	Missense_Mutation	SNP	G	G	A	rs745400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:2266799G>A	ENST00000426855.2	+	7	888	c.713G>A	c.(712-714)aGg>aAg	p.R238K	SGSM2_ENST00000574563.1_Missense_Mutation_p.R238K|SGSM2_ENST00000268989.3_Missense_Mutation_p.R238K	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	238			R -> K (in dbSNP:rs745400). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17509819}.		late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		TCGGAGGACAGGCTGGCTGCC	0.647													G|||	2765	0.552117	0.4962	0.3386	5008	,	,		17006	0.7639		0.4284	False		,,,				2504	0.6881				p.R238K		Atlas-SNP	.											.	SGSM2	60	.	0			c.G713A						PASS	.	G	LYS/ARG,LYS/ARG	2166,2240		549,1068,586	24.0	27.0	26.0		713,713	3.7	1.0	17	dbSNP_86	26	3936,4656		912,2112,1272	yes	missense,missense	SGSM2	NM_001098509.1,NM_014853.2	26,26	1461,3180,1858	AA,AG,GG		45.8101,49.1602,46.9457	benign,benign	238/1007,238/1052	2266799	6102,6896	2203	4296	6499	SO:0001583	missense	9905	exon7			AGGACAGGCTGGC	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.713G>A	17.37:g.2266799G>A	ENSP00000415107:p.Arg238Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001098509	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Missense_Mutation	SNP	ENST00000426855.2	37	CCDS45570.1	1135	0.5196886446886447	236	0.4796747967479675	138	0.3812154696132597	426	0.7447552447552448	335	0.4419525065963061	G	16.77	3.215159	0.58452	0.491602	0.458101	ENSG00000141258	ENST00000268989;ENST00000426855	T;T	0.12879	2.64;2.67	5.73	3.73	0.42828	.	0.152619	0.56097	D	0.000035	T	0.00012	0.0000	L	0.31926	0.97	0.26048	P	0.9815136	B;B;B	0.12630	0.004;0.006;0.006	B;B;B	0.14023	0.01;0.005;0.009	T	0.12682	-1.0538	9	0.25106	T	0.35	-20.9523	9.2868	0.37762	0.221:0.0:0.779:0.0	rs745400;rs3815470;rs17857177;rs57385222;rs745400	238;238;238	O43147-5;O43147;O43147-2	.;SGSM2_HUMAN;.	K	238	ENSP00000268989:R238K;ENSP00000415107:R238K	ENSP00000268989:R238K	R	+	2	0	SGSM2	2213549	0.979000	0.34478	0.994000	0.49952	0.823000	0.46562	2.476000	0.45171	1.440000	0.47531	0.655000	0.94253	AGG	G|0.501;A|0.499	0.499	strong		0.647	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
PRSS1	5644	hgsc.bcm.edu	37	7	142460313	142460313	+	Silent	SNP	T	T	C	rs6666	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142460313T>C	ENST00000311737.7	+	4	492	c.486T>C	c.(484-486)gaT>gaC	p.D162D	PRSS1_ENST00000486171.1_Silent_p.D176D	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	162	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)	AGTGCCTGGATGCTCCTGTGC	0.517													C|||	1986	0.396565	0.407	0.5288	5008	,	,		19819	0.2192		0.5835	False		,,,				2504	0.2791				p.D162D		Atlas-SNP	.											.	PRSS1	68	.	0			c.T486C	GRCh37	CM086253	PRSS1	M	rs6666	PASS	.						315.0	306.0	309.0					7																	142460313		2203	4300	6503	SO:0001819	synonymous_variant	5644	exon4			CCTGGATGCTCCT	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.486T>C	7.37:g.142460313T>C		Somatic	545	0	0		WXS	Illumina HiSeq	Phase_I	342	98	0.28655	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Silent	SNP	ENST00000311737.7	37	CCDS5872.1																																																																																			T|0.437;C|0.563	0.563	strong		0.517	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
MPEG1	219972	hgsc.bcm.edu	37	11	58978684	58978684	+	Missense_Mutation	SNP	G	G	A	rs7926933	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58978684G>A	ENST00000361050.3	-	1	1740	c.1655C>T	c.(1654-1656)cCg>cTg	p.P552L		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	552			P -> L (in dbSNP:rs7926933). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				TTTCAGAGACGGTGCCCCTAA	0.567													G|||	575	0.114816	0.0144	0.0403	5008	,	,		15770	0.3046		0.1153	False		,,,				2504	0.1074				p.P552L		Atlas-SNP	.											.	MPEG1	72	.	0			c.C1655T						PASS	.	G	LEU/PRO	88,3646		1,86,1780	41.0	46.0	44.0		1655	4.7	0.0	11	dbSNP_116	44	949,7241		59,831,3205	yes	missense	MPEG1	NM_001039396.1	98	60,917,4985	AA,AG,GG		11.5873,2.3567,8.6967	probably-damaging	552/717	58978684	1037,10887	1867	4095	5962	SO:0001583	missense	219972	exon1			AGAGACGGTGCCC	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1655C>T	11.37:g.58978684G>A	ENSP00000354335:p.Pro552Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	256	0.11721611721611722	12	0.024390243902439025	19	0.052486187845303865	138	0.24125874125874125	87	0.11477572559366754	G	11.39	1.623521	0.28889	0.023567	0.115873	ENSG00000197629	ENST00000361050	T	0.22743	1.94	5.57	4.66	0.58398	.	0.122446	0.37178	N	0.002202	T	0.00012	0.0000	L	0.50333	1.59	0.46298	P	0.0010250000000000536	B	0.27951	0.195	B	0.20577	0.03	T	0.22871	-1.0204	9	0.49607	T	0.09	-3.2086	11.5241	0.50569	0.0836:0.0:0.9164:0.0	rs7926933;rs17153443;rs52824778;rs7926933	552	Q2M385	MPEG1_HUMAN	L	552	ENSP00000354335:P552L	ENSP00000354335:P552L	P	-	2	0	MPEG1	58735260	1.000000	0.71417	0.014000	0.15608	0.002000	0.02628	3.854000	0.55949	1.364000	0.46038	0.655000	0.94253	CCG	G|0.884;A|0.116	0.116	strong		0.567	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
TNN	63923	hgsc.bcm.edu	37	1	175049379	175049379	+	Missense_Mutation	SNP	G	G	A	rs16847812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:175049379G>A	ENST00000239462.4	+	4	978	c.865G>A	c.(865-867)Gat>Aat	p.D289N		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	289	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		D -> N (in dbSNP:rs16847812).		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)		CAGCCAGGTGGATCACTACCT	0.582													G|||	639	0.127596	0.0053	0.0735	5008	,	,		17710	0.251		0.1272	False		,,,				2504	0.2045				p.D289N		Atlas-SNP	.											.	TNN	297	.	0			c.G865A						PASS	.	G	ASN/ASP	120,4286	91.1+/-129.8	2,116,2085	68.0	68.0	68.0		865	5.7	1.0	1	dbSNP_123	68	1287,7313	255.4+/-280.3	85,1117,3098	yes	missense	TNN	NM_022093.1	23	87,1233,5183	AA,AG,GG		14.9651,2.7236,10.8181	benign	289/1300	175049379	1407,11599	2203	4300	6503	SO:0001583	missense	63923	exon4			CAGGTGGATCACT	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.865G>A	1.37:g.175049379G>A	ENSP00000239462:p.Asp289Asn	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	309	0.14148351648351648	6	0.012195121951219513	29	0.08011049723756906	160	0.27972027972027974	114	0.1503957783641161	G	19.23	3.786596	0.70337	0.027236	0.149651	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.58940	0.3	5.69	5.69	0.88448	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.046701	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87971	2.92	0.20975	P	0.999815479	B;B	0.24675	0.109;0.016	B;B	0.37451	0.25;0.098	T	0.04495	-1.0947	9	0.48119	T	0.1	.	19.4166	0.94703	0.0:0.0:1.0:0.0	rs16847812;rs52834449;rs16847812	289;289	B3KXB6;Q9UQP3	.;TENN_HUMAN	N	289	ENSP00000239462:D289N	ENSP00000239462:D289N	D	+	1	0	TNN	173316002	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	8.072000	0.89496	2.679000	0.91253	0.650000	0.86243	GAT	G|0.872;A|0.128	0.128	strong		0.582	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
UBQLNL	143630	hgsc.bcm.edu	37	11	5536415	5536415	+	Silent	SNP	C	C	T	rs10769023	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5536415C>T	ENST00000380184.1	-	1	1520	c.1257G>A	c.(1255-1257)gaG>gaA	p.E419E	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	419										endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		AGCTGCTCTGCTCATCTGACA	0.483													C|||	1445	0.288538	0.2458	0.3184	5008	,	,		22239	0.371		0.2614	False		,,,				2504	0.2679				p.E419E		Atlas-SNP	.											.	UBQLNL	74	.	0			c.G1257A						PASS	.	C		1114,3288	400.8+/-331.7	147,820,1234	129.0	116.0	121.0		1257	-5.5	0.0	11	dbSNP_120	121	2345,6249	392.8+/-344.1	331,1683,2283	no	coding-synonymous	UBQLNL	NM_145053.4		478,2503,3517	TT,TC,CC		27.2865,25.3067,26.6159		419/476	5536415	3459,9537	2201	4297	6498	SO:0001819	synonymous_variant	143630	exon1			GCTCTGCTCATCT	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.1257G>A	11.37:g.5536415C>T		Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	206	102	0.495146	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	37	CCDS31385.1																																																																																			C|0.719;T|0.281	0.281	strong		0.483	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
TMEM63C	57156	hgsc.bcm.edu	37	14	77708804	77708804	+	Silent	SNP	C	C	T	rs61731611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:77708804C>T	ENST00000298351.4	+	14	1323	c.1179C>T	c.(1177-1179)gaC>gaT	p.D393D		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	393					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		ACCCCAAAGACATTATTTGGT	0.542													C|||	733	0.146366	0.0106	0.1902	5008	,	,		19087	0.1042		0.2555	False		,,,				2504	0.2301				p.D393D		Atlas-SNP	.											.	TMEM63C	77	.	0			c.C1179T						PASS	.	C		190,3786		4,182,1802	178.0	173.0	175.0		1179	4.1	1.0	14	dbSNP_129	175	2000,6328		234,1532,2398	no	coding-synonymous	TMEM63C	NM_020431.2		238,1714,4200	TT,TC,CC		24.0154,4.7787,17.7991		393/807	77708804	2190,10114	1988	4164	6152	SO:0001819	synonymous_variant	57156	exon14			CAAAGACATTATT		CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"""calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"""		"""chromosome 14 open reading frame 171"""	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.1179C>T	14.37:g.77708804C>T		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_020431	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Silent	SNP	ENST00000298351.4	37	CCDS45141.1																																																																																			C|0.813;T|0.187	0.187	strong		0.542	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1		
CAPN12	147968	hgsc.bcm.edu	37	19	39229075	39229075	+	Silent	SNP	C	C	T	rs201486563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39229075C>T	ENST00000328867.4	-	7	1181	c.873G>A	c.(871-873)acG>acA	p.T291T	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.T142T	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	291	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			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)			TCCAGGCCCCCGTCCACTCCA	0.697													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		14837	0.0		0.0	False		,,,				2504	0.0				p.T291T		Atlas-SNP	.											.	CAPN12	43	.	0			c.G873A						PASS	.	C		1,4399	2.1+/-5.4	0,1,2199	29.0	32.0	31.0		873	-7.4	0.5	19		31	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	CAPN12	NM_144691.3		0,2,6497	TT,TC,CC		0.0116,0.0227,0.0154		291/720	39229075	2,12996	2200	4299	6499	SO:0001819	synonymous_variant	147968	exon7			GGCCCCCGTCCAC	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.873G>A	19.37:g.39229075C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			C|1.000;T|0.000	0.000	strong		0.697	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
DNAH14	127602	hgsc.bcm.edu	37	1	225533684	225533684	+	Missense_Mutation	SNP	A	A	G	rs6667999	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225533684A>G	ENST00000445597.2	+	48	8011	c.8011A>G	c.(8011-8013)Aaa>Gaa	p.K2671E	DNAH14_ENST00000439375.2_Missense_Mutation_p.K3474E|DNAH14_ENST00000430092.1_Missense_Mutation_p.K3474E			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2671			K -> E (in dbSNP:rs6667999).		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AGATGATGACAAAATTGTAGA	0.328													G|||	2649	0.528954	0.6399	0.4697	5008	,	,		18280	0.5089		0.4046	False		,,,				2504	0.5695				p.K3474E		Atlas-SNP	.											.	DNAH14	300	.	0			c.A10420G						PASS	.	G	GLU/LYS	842,542		268,306,118	62.0	46.0	51.0		10420	3.4	0.0	1	dbSNP_116	51	1406,1776		323,760,508	yes	missense	DNAH14	NM_001373.1	56	591,1066,626	GG,GA,AA		44.186,39.1618,49.2335	benign	3474/4516	225533684	2248,2318	692	1591	2283	SO:0001583	missense	127602	exon68			GATGACAAAATTG	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.8011A>G	1.37:g.225533684A>G	ENSP00000409472:p.Lys2671Glu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	G	0.005	-2.137791	0.00335	0.608382	0.44186	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.54071	0.59;0.59;0.59	5.34	3.37	0.38596	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	7	0.02654	T	1	.	7.3982	0.26948	0.1499:0.0:0.7149:0.1352	rs6667999;rs52791604;rs60868380;rs6667999	3474	Q0VDD8-4	.	E	2671;3474;3474	ENSP00000409472:K2671E;ENSP00000414402:K3474E;ENSP00000392061:K3474E	ENSP00000414402:K3474E	K	+	1	0	DNAH14	223600307	0.836000	0.29430	0.026000	0.17262	0.022000	0.10575	1.958000	0.40402	0.621000	0.30232	-0.294000	0.09567	AAA	A|0.507;G|0.493	0.493	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
HRASLS5	117245	hgsc.bcm.edu	37	11	63233710	63233710	+	Silent	SNP	A	A	G	rs2275999	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:63233710A>G	ENST00000301790.4	-	5	778	c.619T>C	c.(619-621)Ttg>Ctg	p.L207L	HRASLS5_ENST00000539221.1_Silent_p.L207L|HRASLS5_ENST00000540857.1_Silent_p.L197L			Q96KN8	HRSL5_HUMAN	HRAS-like suppressor family, member 5	207							transferase activity, transferring acyl groups (GO:0016746)			endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	14						TCCACCGGCAAGGGCAGGTAC	0.507													G|||	1194	0.238419	0.3971	0.2752	5008	,	,		20315	0.1756		0.0765	False		,,,				2504	0.229				p.L207L		Atlas-SNP	.											.	HRASLS5	28	.	0			c.T619C						PASS	.	G	,,	1503,2899	669.0+/-402.1	259,985,957	222.0	168.0	187.0		619,589,619	4.2	1.0	11	dbSNP_100	187	540,8056	793.0+/-407.5	14,512,3772	no	coding-synonymous,coding-synonymous,coding-synonymous	HRASLS5	NM_001146728.1,NM_001146729.1,NM_054108.3	,,	273,1497,4729	GG,GA,AA		6.282,34.1436,15.7178	,,	207/254,197/270,207/280	63233710	2043,10955	2201	4298	6499	SO:0001819	synonymous_variant	117245	exon5			CCGGCAAGGGCAG	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.619T>C	11.37:g.63233710A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	238	129	0.542017	NM_001146728	B7X6T1|F5GZ87|F5H4Y9	Silent	SNP	ENST00000301790.4	37	CCDS8044.1																																																																																			A|0.825;G|0.175	0.175	strong		0.507	HRASLS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396375.1	NM_054108	
TMEM232	642987	hgsc.bcm.edu	37	5	109960989	109960989	+	Silent	SNP	A	A	G	rs61730920	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:109960989A>G	ENST00000455884.2	-	7	797	c.747T>C	c.(745-747)taT>taC	p.Y249Y	TMEM232_ENST00000429839.2_Silent_p.Y249Y|TMEM232_ENST00000515518.2_5'UTR			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	281	0	0		WXS	Illumina HiSeq	Phase_I	269	125	0.464684	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	
KRT34	3885	hgsc.bcm.edu	37	17	39535388	39535388	+	Missense_Mutation	SNP	T	T	C	rs2071599	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	148	0	0		WXS	Illumina HiSeq	Phase_I	146	72	0.493151	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	
GLRA3	8001	hgsc.bcm.edu	37	4	175688138	175688138	+	Silent	SNP	A	A	G	rs7696263	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:175688138A>G	ENST00000274093.3	-	3	745	c.243T>C	c.(241-243)ttT>ttC	p.F81F	GLRA3_ENST00000340217.5_Silent_p.F81F	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	81					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)	CGATAGAGCCAAAGCTGTTGA	0.353													G|||	3960	0.790735	0.6694	0.7305	5008	,	,		15969	0.998		0.7445	False		,,,				2504	0.8313				p.F81F		Atlas-SNP	.											.	GLRA3	76	.	0			c.T243C						PASS	.	G	,	2950,1456		1088,774,341	166.0	159.0	161.0		243,243	0.4	1.0	4	dbSNP_116	161	5856,2744		2506,844,950	no	coding-synonymous,coding-synonymous	GLRA3	NM_001042543.1,NM_006529.2	,	3594,1618,1291	GG,GA,AA		31.907,33.0458,32.2928	,	81/450,81/465	175688138	8806,4200	2203	4300	6503	SO:0001819	synonymous_variant	8001	exon3			AGAGCCAAAGCTG	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.243T>C	4.37:g.175688138A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	37	CCDS3822.1																																																																																			A|0.226;G|0.774	0.774	strong		0.353	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1		
CDH12	1010	hgsc.bcm.edu	37	5	22078584	22078584	+	Missense_Mutation	SNP	C	C	T	rs4371716	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:22078584C>T	ENST00000382254.1	-	5	1288	c.202G>A	c.(202-204)Gtg>Atg	p.V68M	CDH12_ENST00000522262.1_Missense_Mutation_p.V68M|CDH12_ENST00000504376.2_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	scavenged	.	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	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	182	98	0.538462	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	
GBP6	163351	hgsc.bcm.edu	37	1	89847372	89847372	+	Missense_Mutation	SNP	G	G	T	rs4658359	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89847372G>T	ENST00000370456.4	+	7	1084	c.991G>T	c.(991-993)Gct>Tct	p.A331S	GBP6_ENST00000535065.1_Missense_Mutation_p.A201S	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	331			A -> S (in dbSNP:rs4658359). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		GCAGAGGGCAGCTGACTACTA	0.587													G|||	4036	0.805911	0.9092	0.8415	5008	,	,		18227	0.7262		0.7465	False		,,,				2504	0.7843				p.A331S		Atlas-SNP	.											.	GBP6	87	.	0			c.G991T						PASS	.	G	SER/ALA	3878,528	777.4+/-414.2	1713,452,38	78.0	73.0	75.0		991	-0.0	0.2	1	dbSNP_111	75	6411,2189	711.7+/-405.9	2382,1647,271	yes	missense	GBP6	NM_198460.2	99	4095,2099,309	TT,TG,GG		25.4535,11.9837,20.8904	benign	331/634	89847372	10289,2717	2203	4300	6503	SO:0001583	missense	163351	exon7			AGGGCAGCTGACT	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.991G>T	1.37:g.89847372G>T	ENSP00000359485:p.Ala331Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	1730	0.7921245421245421	447	0.9085365853658537	300	0.8287292817679558	424	0.7412587412587412	559	0.737467018469657	G	12.14	1.848592	0.32699	0.880163	0.745465	ENSG00000183347	ENST00000544311;ENST00000370456;ENST00000535065	T;T	0.02216	4.39;4.39	4.97	-0.0232	0.13944	Guanylate-binding protein, C-terminal (3);	0.671285	0.14966	N	0.288077	T	0.01421	0.0046	L	0.55103	1.725	0.80722	P	0.0	P	0.44429	0.835	P	0.49477	0.612	T	0.49123	-0.8972	9	0.46703	T	0.11	-4.7565	3.3515	0.07154	0.2378:0.0:0.2438:0.5184	rs4658359;rs17437177;rs60529881;rs4658359	331	Q6ZN66	GBP6_HUMAN	S	302;331;201	ENSP00000359485:A331S;ENSP00000442530:A201S	ENSP00000359485:A331S	A	+	1	0	GBP6	89619960	0.002000	0.14202	0.198000	0.23420	0.269000	0.26545	0.050000	0.14120	0.093000	0.17368	0.585000	0.79938	GCT	G|0.211;T|0.789	0.789	strong		0.587	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
ZFYVE1	53349	hgsc.bcm.edu	37	14	73459917	73459917	+	Silent	SNP	C	C	T	rs2333016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:73459917C>T	ENST00000556143.1	-	4	1857	c.1137G>A	c.(1135-1137)gaG>gaA	p.E379E	ZFYVE1_ENST00000553891.1_Silent_p.E379E|ZFYVE1_ENST00000318876.5_Silent_p.E379E	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	379					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		CTAGTAGCTGCTCCAAAGCAC	0.552													C|||	1387	0.276957	0.1921	0.2176	5008	,	,		16874	0.3542		0.3608	False		,,,				2504	0.2679				p.E379E		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.G1137A						PASS	.	C		978,3428	365.4+/-317.4	115,748,1340	69.0	74.0	72.0		1137	3.5	1.0	14	dbSNP_100	72	3104,5496	475.0+/-369.0	555,1994,1751	no	coding-synonymous	ZFYVE1	NM_021260.2		670,2742,3091	TT,TC,CC		36.093,22.197,31.3855		379/778	73459917	4082,8924	2203	4300	6503	SO:0001819	synonymous_variant	53349	exon4			TAGCTGCTCCAAA	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.1137G>A	14.37:g.73459917C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																			C|0.689;T|0.311	0.311	strong		0.552	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
KIF26A	26153	hgsc.bcm.edu	37	14	104639519	104639519	+	Silent	SNP	C	C	G	rs61743517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104639519C>G	ENST00000423312.2	+	8	1626	c.1626C>G	c.(1624-1626)ctC>ctG	p.L542L	KIF26A_ENST00000315264.7_Silent_p.L403L	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	542	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CTGGCAGCCTCCAGGACACCC	0.731													C|||	111	0.0221645	0.0038	0.036	5008	,	,		13918	0.0		0.0577	False		,,,				2504	0.0235				p.L542L		Atlas-SNP	.											.	KIF26A	84	.	0			c.C1626G						PASS	.	C		48,3966		0,48,1959	13.0	19.0	17.0		1626	-5.6	0.1	14	dbSNP_129	17	521,7751		21,479,3636	no	coding-synonymous	KIF26A	NM_015656.1		21,527,5595	GG,GC,CC		6.2984,1.1958,4.6313		542/1883	104639519	569,11717	2007	4136	6143	SO:0001819	synonymous_variant	26153	exon8			CAGCCTCCAGGAC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.1626C>G	14.37:g.104639519C>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	37	36	0.972973	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			C|0.973;G|0.027	0.027	strong		0.731	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
SPPL2C	162540	hgsc.bcm.edu	37	17	43923654	43923654	+	Missense_Mutation	SNP	G	G	C	rs12185233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43923654G>C	ENST00000329196.5	+	1	1399	c.1382G>C	c.(1381-1383)cGc>cCc	p.R461P	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	461			R -> P (in dbSNP:rs12185233).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TACTGTTGCCGCTTTGATGTG	0.587													G|||	431	0.0860623	0.0151	0.1571	5008	,	,		22035	0.001		0.2396	False		,,,				2504	0.0613				p.R461P		Atlas-SNP	.											IMP5,NS,carcinoma,0,1	.	.	1	0			c.G1382C						PASS	.	G	PRO/ARG	203,4203	127.0+/-164.0	5,193,2005	153.0	117.0	129.0		1382	5.2	1.0	17	dbSNP_120	129	1928,6672	340.3+/-323.5	221,1486,2593	yes	missense	IMP5	NM_175882.2	103	226,1679,4598	CC,CG,GG		22.4186,4.6074,16.3847	possibly-damaging	461/685	43923654	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			GTTGCCGCTTTGA		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1382G>C	17.37:g.43923654G>C	ENSP00000332488:p.Arg461Pro	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	15.02	2.709293	0.48517	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.27104	1.69	5.2	5.2	0.72013	.	0.000000	0.41823	D	0.000810	T	0.00039	0.0001	M	0.91768	3.24	0.09310	P	0.9999999837478	P	0.36712	0.566	B	0.44133	0.442	T	0.02781	-1.1111	9	0.87932	D	0	-2.5538	16.2754	0.82642	0.0:0.0:1.0:0.0	rs12185233;rs17763711;rs12185233	461	Q8IUH8	IMP5_HUMAN	P	461	ENSP00000332488:R461P	ENSP00000332488:R461P	R	+	2	0	AC217771.1	41279434	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	6.410000	0.73294	2.698000	0.92095	0.563000	0.77884	CGC	G|0.509;C|0.491	0.491	strong		0.587	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
SLC30A5	64924	hgsc.bcm.edu	37	5	68419111	68419111	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:68419111C>T	ENST00000396591.3	+	14	2467	c.1857C>T	c.(1855-1857)ttC>ttT	p.F619F	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	619					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)		TTGGATGGTTCATCGCTGACC	0.388																																					p.F619F		Atlas-SNP	.											SLC30A5,upper_leg,malignant_melanoma,+2,1	SLC30A5	54	1	0			c.C1857T						scavenged	.						138.0	122.0	127.0					5																	68419111		2203	4300	6503	SO:0001819	synonymous_variant	64924	exon14			ATGGTTCATCGCT	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.1857C>T	5.37:g.68419111C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	78	3	0.0384615	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Silent	SNP	ENST00000396591.3	37	CCDS3996.1																																																																																			.	.	none		0.388	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2		
KDM6B	23135	hgsc.bcm.edu	37	17	7754993	7754993	+	Silent	SNP	G	G	A	rs12939056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:7754993G>A	ENST00000448097.2	+	17	4375	c.4044G>A	c.(4042-4044)ctG>ctA	p.L1348L	KDM6B_ENST00000254846.5_Silent_p.L1348L			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1348	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						AGGAGCTGCTGAAGCTGCCCG	0.647											OREG0024145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	937	0.187101	0.0129	0.2709	5008	,	,		16032	0.002		0.5785	False		,,,				2504	0.1513				p.L1348L		Atlas-SNP	.											.	KDM6B	95	.	0			c.G4044A						PASS	.	G		485,3899		44,397,1751	17.0	18.0	17.0		4044	2.0	1.0	17	dbSNP_121	17	4839,3737		1398,2043,847	no	coding-synonymous	KDM6B	NM_001080424.1		1442,2440,2598	AA,AG,GG		43.5751,11.063,41.0802		1348/1683	7754993	5324,7636	2192	4288	6480	SO:0001819	synonymous_variant	23135	exon17			GCTGCTGAAGCTG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.4044G>A	17.37:g.7754993G>A		Somatic	40	0	0	644	WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001080424	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																				A|0.324;C|0.000;G|0.675	0.324	strong		0.647	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
ZNF133	7692	hgsc.bcm.edu	37	20	18297193	18297193	+	Silent	SNP	T	T	C	rs1050476	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:18297193T>C	ENST00000316358.4	+	4	1795	c.1698T>C	c.(1696-1698)atT>atC	p.I566I	ZNF133_ENST00000535822.1_Silent_p.I471I|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000402618.2_Silent_p.I503I|ZNF133_ENST00000377671.3_Silent_p.I565I|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000396026.3_Silent_p.I569I|ZNF133_ENST00000538547.1_Silent_p.I471I|ZNF133_ENST00000401790.1_Silent_p.I566I	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	566					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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						CAGCTCTAATTACACACAAGC	0.532													C|||	378	0.0754792	0.112	0.0749	5008	,	,		21562	0.0149		0.0726	False		,,,				2504	0.092				p.I565I		Atlas-SNP	.											.	ZNF133	63	.	0			c.T1695C						PASS	.	C	,	464,3942	783.8+/-414.6	23,418,1762	96.0	81.0	86.0		1695,1695	1.0	0.0	20	dbSNP_86	86	712,7888	787.3+/-407.6	36,640,3624	no	coding-synonymous,coding-synonymous	ZNF133	NM_001083330.1,NM_003434.4	,	59,1058,5386	CC,CT,TT		8.2791,10.5311,9.042	,	565/654,565/654	18297193	1176,11830	2203	4300	6503	SO:0001819	synonymous_variant	7692	exon4			TCTAATTACACAC	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1698T>C	20.37:g.18297193T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Silent	SNP	ENST00000316358.4	37																																																																																				T|0.915;C|0.085	0.085	strong		0.532	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
FLG	2312	hgsc.bcm.edu	37	1	152281534	152281534	+	Missense_Mutation	SNP	A	A	T	rs113544881	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152281534A>T	ENST00000368799.1	-	3	5863	c.5828T>A	c.(5827-5829)cTt>cAt	p.L1943H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1943	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCAGATCCAAGATGGTTTCT	0.562									Ichthyosis				-|||	1570	0.313498	0.3336	0.3285	5008	,	,		24124	0.4335		0.1302	False		,,,				2504	0.3405				p.L1943H		Atlas-SNP	.											.	FLG	900	.	0			c.T5828A						PASS	.						240.0	230.0	233.0					1																	152281534		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATCCAAGATGGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5828T>A	1.37:g.152281534A>T	ENSP00000357789:p.Leu1943His	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	482	129	0.267635	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	c	2.070	-0.413379	0.04799	.	.	ENSG00000143631	ENST00000368799	T	0.00808	5.67	2.69	0.209	0.15226	.	.	.	.	.	T	0.00073	0.0002	N	0.00210	-1.845	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32824	-0.9892	9	0.36615	T	0.2	0.0549	0.4679	0.00527	0.2155:0.1344:0.2221:0.428	.	1943	P20930	FILA_HUMAN	H	1943	ENSP00000357789:L1943H	ENSP00000357789:L1943H	L	-	2	0	FLG	150548158	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.730000	0.00805	-0.267000	0.09325	-1.521000	0.00933	CTT	A|0.949;T|0.051	0.051	strong		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LHX5	64211	hgsc.bcm.edu	37	12	113906140	113906140	+	Missense_Mutation	SNP	G	G	A	rs139906449	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:113906140G>A	ENST00000261731.3	-	3	1040	c.467C>T	c.(466-468)aCg>aTg	p.T156M		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	156					cell proliferation in forebrain (GO:0021846)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|forebrain neuron differentiation (GO:0021879)|hippocampus development (GO:0021766)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						CGAGTTGTCCGTCTCTTTGGG	0.657													G|||	8	0.00159744	0.0	0.0014	5008	,	,		17361	0.0		0.007	False		,,,				2504	0.0				p.T156M		Atlas-SNP	.											.	LHX5	39	.	0			c.C467T						PASS	.	G	MET/THR	16,4390	23.3+/-48.9	1,14,2188	115.0	93.0	101.0		467	4.7	1.0	12	dbSNP_134	101	166,8434	77.5+/-140.1	1,164,4135	yes	missense	LHX5	NM_022363.2	81	2,178,6323	AA,AG,GG		1.9302,0.3631,1.3994	possibly-damaging	156/403	113906140	182,12824	2203	4300	6503	SO:0001583	missense	64211	exon3			TTGTCCGTCTCTT	AF291181	CCDS9171.1	12q24.13	2014-01-15			ENSG00000089116	ENSG00000089116		"""Homeoboxes / LIM class"""	14216	protein-coding gene	gene with protein product		605992					Standard	NM_022363		Approved		uc001tvj.1	Q9H2C1	OTTHUMG00000169552	ENST00000261731.3:c.467C>T	12.37:g.113906140G>A	ENSP00000261731:p.Thr156Met	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	177	90	0.508475	NM_022363	Q32MA4	Missense_Mutation	SNP	ENST00000261731.3	37	CCDS9171.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	G	31	5.073646	0.94000	0.003631	0.019302	ENSG00000089116	ENST00000261731	D	0.91351	-2.83	4.7	4.7	0.59300	Homeodomain-related (1);	0.000000	0.53938	D	0.000044	T	0.82089	0.4961	L	0.44542	1.39	0.80722	D	1	P	0.51240	0.943	P	0.46320	0.512	D	0.84932	0.0860	10	0.34782	T	0.22	.	17.647	0.88151	0.0:0.0:1.0:0.0	.	156	Q9H2C1	LHX5_HUMAN	M	156	ENSP00000261731:T156M	ENSP00000261731:T156M	T	-	2	0	LHX5	112390523	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	9.833000	0.99426	2.131000	0.65755	0.491000	0.48974	ACG	G|0.989;A|0.011	0.011	strong		0.657	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363	
SEMG1	6406	hgsc.bcm.edu	37	20	43837278	43837278	+	Missense_Mutation	SNP	G	G	A	rs79500955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:43837278G>A	ENST00000372781.3	+	2	1397	c.1340G>A	c.(1339-1341)cGt>cAt	p.R447H	SEMG1_ENST00000244069.6_Missense_Mutation_p.R387H	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	447					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)				GACAGTGATCGTCATTTGGCA	0.398													g|||	14	0.00279553	0.0	0.0029	5008	,	,		21943	0.0		0.0099	False		,,,				2504	0.002				p.R447H		Atlas-SNP	.											SEMG1,colon,carcinoma,+1,1	SEMG1	71	1	0			c.G1340A						scavenged	.	A	HIS/ARG	16,4390	23.3+/-48.9	0,16,2187	128.0	119.0	122.0		1340	1.5	0.0	20	dbSNP_131	122	59,8541	36.4+/-91.3	1,57,4242	yes	missense	SEMG1	NM_003007.3	29	1,73,6429	AA,AG,GG		0.686,0.3631,0.5767		447/463	43837278	75,12931	2203	4300	6503	SO:0001583	missense	6406	exon2			GTGATCGTCATTT		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.1340G>A	20.37:g.43837278G>A	ENSP00000361867:p.Arg447His	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	222	98	0.441441	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	g	0.027	-1.359398	0.01245	0.003631	0.00686	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.06449	3.3;3.3	1.47	1.47	0.22746	.	.	.	.	.	T	0.01627	0.0052	N	0.02539	-0.55	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	0.45026	-0.9289	9	0.39692	T	0.17	.	3.4522	0.07502	0.7668:0.0:0.2332:0.0	.	387;447;387	P04279-2;P04279;E7EPD3	.;SEMG1_HUMAN;.	H	387;447	ENSP00000244069:R387H;ENSP00000361867:R447H	ENSP00000244069:R387H	R	+	2	0	SEMG1	43270692	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.261000	0.08694	0.052000	0.16007	-0.381000	0.06696	CGT	G|0.996;A|0.004	0.004	strong		0.398	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
NEIL3	55247	hgsc.bcm.edu	37	4	178256913	178256913	+	Missense_Mutation	SNP	C	C	G	rs7689099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:178256913C>G	ENST00000264596.3	+	3	468	c.350C>G	c.(349-351)cCt>cGt	p.P117R		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	117			P -> R (in dbSNP:rs7689099). {ECO:0000269|PubMed:15489334, 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)		GGAGCTTCTCCTGTTTTGGAA	0.323								Base excision repair (BER), DNA glycosylases					C|||	360	0.071885	0.0408	0.1182	5008	,	,		15048	0.0258		0.1183	False		,,,				2504	0.0808				p.P117R		Atlas-SNP	.											.	NEIL3	89	.	0			c.C350G						PASS	.	C	ARG/PRO	268,4134	142.7+/-177.9	6,256,1939	59.0	66.0	64.0		350	5.1	1.0	4	dbSNP_116	64	1013,7587	214.8+/-254.3	49,915,3336	yes	missense	NEIL3	NM_018248.2	103	55,1171,5275	GG,GC,CC		11.7791,6.0881,9.8523	probably-damaging	117/606	178256913	1281,11721	2201	4300	6501	SO:0001583	missense	55247	exon3			CTTCTCCTGTTTT	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.350C>G	4.37:g.178256913C>G	ENSP00000264596:p.Pro117Arg	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	236	115	0.487288	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	153	0.07005494505494506	20	0.04065040650406504	37	0.10220994475138122	19	0.033216783216783216	77	0.10158311345646438	C	13.06	2.125028	0.37533	0.060881	0.117791	ENSG00000109674	ENST00000264596	T	0.28454	1.61	5.14	5.14	0.70334	DNA glycosylase/AP lyase, catalytic domain (2);	0.173062	0.52532	N	0.000075	T	0.00524	0.0017	M	0.75264	2.295	0.09310	P	0.999999880221	P	0.44344	0.833	B	0.35655	0.207	T	0.14337	-1.0476	9	0.62326	D	0.03	-2.4229	17.7745	0.88503	0.0:1.0:0.0:0.0	rs7689099;rs17727101;rs17845788;rs17858749;rs52806877;rs7689099	117	Q8TAT5	NEIL3_HUMAN	R	117	ENSP00000264596:P117R	ENSP00000264596:P117R	P	+	2	0	NEIL3	178493907	0.995000	0.38212	1.000000	0.80357	0.602000	0.36980	5.205000	0.65186	2.666000	0.90696	0.561000	0.74099	CCT	C|0.910;G|0.090	0.090	strong		0.323	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471888	39471888	+	Silent	SNP	C	C	T	rs34354631	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	39	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	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		
GALNT9	50614	hgsc.bcm.edu	37	12	132862976	132862976	+	Silent	SNP	G	G	A	rs28503969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:132862976G>A	ENST00000328957.8	-	2	278	c.279C>T	c.(277-279)ggC>ggT	p.G93G		NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	93					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		CCTGGCCCAGGCCTCCTGGCC	0.677													G|||	1715	0.342452	0.3411	0.2277	5008	,	,		10324	0.4415		0.3072	False		,,,				2504	0.3599				p.G93G	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C279T						PASS	.						30.0	31.0	31.0					12																	132862976		692	1591	2283	SO:0001819	synonymous_variant	50614	exon2			GCCCAGGCCTCCT	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.279C>T	12.37:g.132862976G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37																																																																																				G|0.670;A|0.330	0.330	strong		0.677	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
GZMA	3001	hgsc.bcm.edu	37	5	54404057	54404057	+	Silent	SNP	C	C	G	rs1051846	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54404057C>G	ENST00000274306.6	+	4	497	c.462C>G	c.(460-462)ggC>ggG	p.G154G		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	154	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				CAGGGTGGGGCAGGACTCACA	0.403													G|||	968	0.193291	0.2572	0.1023	5008	,	,		18366	0.2688		0.1342	False		,,,				2504	0.1544				p.G154G		Atlas-SNP	.											.	GZMA	60	.	0			c.C462G						PASS	.	G		993,3413	730.1+/-410.1	123,747,1333	78.0	74.0	76.0		462	-10.1	0.0	5	dbSNP_86	76	1199,7401	762.2+/-407.6	82,1035,3183	no	coding-synonymous	GZMA	NM_006144.3		205,1782,4516	GG,GC,CC		13.9419,22.5374,16.8538		154/263	54404057	2192,10814	2203	4300	6503	SO:0001819	synonymous_variant	3001	exon4			GTGGGGCAGGACT		CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"""CTL tryptase"", ""Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"""	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.462C>G	5.37:g.54404057C>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	162	160	0.987654	NM_006144	A4PHN1|Q6IB36	Silent	SNP	ENST00000274306.6	37	CCDS3965.1																																																																																			C|0.828;G|0.172	0.172	strong		0.403	GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144	
TTN	7273	hgsc.bcm.edu	37	2	179583496	179583496	+	Missense_Mutation	SNP	T	T	G	rs16866465	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179583496T>G	ENST00000591111.1	-	82	23704	c.23480A>C	c.(23479-23481)gAa>gCa	p.E7827A	TTN_ENST00000589042.1_Missense_Mutation_p.E8144A|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.E6900A|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13366	Ig-like 60.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCTCCACTTTCTAATGGCTG	0.453													T|||	1196	0.238818	0.1732	0.183	5008	,	,		20020	0.4375		0.1571	False		,,,				2504	0.2464				p.E8144A		Atlas-SNP	.											.	TTN	18412	.	0			c.A24431C						PASS	.	T	,,,ALA/GLU	590,3382		38,514,1434	75.0	76.0	76.0		,,,20699	6.0	0.5	2	dbSNP_123	76	1266,7082		97,1072,3005	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,107	135,1586,4439	GG,GT,TT		15.1653,14.854,15.0649	,,,benign	,,,6900/33424	179583496	1856,10464	1986	4174	6160	SO:0001583	missense	7273	exon84			CCACTTTCTAATG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23480A>C	2.37:g.179583496T>G	ENSP00000465570:p.Glu7827Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		500	0.22893772893772893	86	0.17479674796747968	54	0.14917127071823205	244	0.42657342657342656	116	0.15303430079155672	T	7.627	0.678028	0.14841	0.14854	0.151653	ENSG00000155657	ENST00000342992	T	0.67865	-0.29	6.01	6.01	0.97437	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B	0.10296	0.003	B	0.15870	0.014	T	0.29366	-1.0014	8	0.87932	D	0	.	16.5285	0.84344	0.0:0.0:0.0:1.0	rs16866465;rs52832346;rs16866465	7827	Q8WZ42	TITIN_HUMAN	A	6900	ENSP00000343764:E6900A	ENSP00000343764:E6900A	E	-	2	0	TTN	179291741	1.000000	0.71417	0.490000	0.27465	0.387000	0.30353	5.942000	0.70203	2.307000	0.77673	0.528000	0.53228	GAA	T|0.778;G|0.222	0.222	strong		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KRT32	3882	hgsc.bcm.edu	37	17	39619186	39619186	+	Missense_Mutation	SNP	G	G	C	rs2604956	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	105	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	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	
FTSJ3	117246	hgsc.bcm.edu	37	17	61901197	61901197	+	Missense_Mutation	SNP	T	T	A	rs2727288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:61901197T>A	ENST00000427159.2	-	13	1915	c.1270A>T	c.(1270-1272)Agc>Tgc	p.S424C		NM_017647.3	NP_060117.3			FtsJ homolog 3 (E. coli)											breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CGGATGGTGCTCAAGGAGAAC	0.577													G|||	3638	0.726438	0.9569	0.6787	5008	,	,		16633	0.5556		0.5984	False		,,,				2504	0.7566				p.S424C		Atlas-SNP	.											.	FTSJ3	63	.	0			c.A1270T						PASS	.	G	CYS/SER	3940,466		1759,422,22	131.0	126.0	127.0		1270	4.7	0.9	17	dbSNP_100	127	5216,3384		1599,2018,683	yes	missense	FTSJ3	NM_017647.3	112	3358,2440,705	AA,AT,TT		39.3488,10.5765,29.6017	benign	424/848	61901197	9156,3850	2203	4300	6503	SO:0001583	missense	117246	exon13			TGGTGCTCAAGGA	AF327355	CCDS11644.1	17q23.3	2014-09-11			ENSG00000108592	ENSG00000108592			17136	protein-coding gene	gene with protein product	"""SPB1 RNA methyltransferase homolog (S. cerevisiae)"""						Standard	NM_017647		Approved	SPB1	uc002jca.3	Q8IY81	OTTHUMG00000179012	ENST00000427159.2:c.1270A>T	17.37:g.61901197T>A	ENSP00000396673:p.Ser424Cys	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	167	166	0.994012	NM_017647		Missense_Mutation	SNP	ENST00000427159.2	37	CCDS11644.1	1488	0.6813186813186813	470	0.9552845528455285	229	0.6325966850828729	333	0.5821678321678322	456	0.6015831134564644	G	6.589	0.477083	0.12521	0.894235	0.606512	ENSG00000108592	ENST00000427159	T	0.33216	1.42	5.65	4.68	0.58851	.	0.266108	0.37857	N	0.001907	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.39624	0.681	B	0.35971	0.215	T	0.18999	-1.0319	9	0.72032	D	0.01	-3.2134	8.945	0.35753	0.0769:0.0:0.7739:0.1492	rs2727288;rs3744292;rs11549663;rs17639101;rs17844828;rs17857126;rs17857539;rs52805130;rs56861461;rs2727288	424	Q8IY81	RRMJ3_HUMAN	C	424	ENSP00000396673:S424C	ENSP00000396673:S424C	S	-	1	0	FTSJ3	59254929	0.000000	0.05858	0.934000	0.37439	0.950000	0.60333	0.028000	0.13644	0.948000	0.37687	-0.121000	0.15023	AGC	T|0.319;A|0.681	0.681	strong		0.577	FTSJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444386.1		
TEX12	56158	hgsc.bcm.edu	37	11	112040027	112040027	+	Silent	SNP	A	A	G	rs360712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:112040027A>G	ENST00000280358.4	+	2	168	c.36A>G	c.(34-36)agA>agG	p.R12R	RP11-356J5.4_ENST00000527589.1_RNA|SDHD_ENST00000532699.1_Intron|TEX12_ENST00000530752.1_Silent_p.R12R|AP002884.3_ENST00000532612.1_5'Flank|SDHD_ENST00000525468.1_3'UTR	NM_031275.4	NP_112565.1	Q9BXU0	TEX12_HUMAN	testis expressed 12	12					meiotic DNA repair synthesis (GO:0000711)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				endometrium(1)|large_intestine(2)|lung(1)	4		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.2e-06)|BRCA - Breast invasive adenocarcinoma(274;1.4e-06)|all cancers(92;1.97e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		CTGATAATAGAAATTGCAAGA	0.383													A|||	815	0.16274	0.0507	0.2637	5008	,	,		19313	0.1171		0.2664	False		,,,				2504	0.183				p.R12R		Atlas-SNP	.											TEX12,NS,carcinoma,+1,1	TEX12	14	1	0			c.A36G						scavenged	.	A		411,3991	201.8+/-224.7	18,375,1808	211.0	225.0	220.0		36	5.2	1.0	11	dbSNP_79	220	2166,6428	370.2+/-335.8	288,1590,2419	no	coding-synonymous	TEX12	NM_031275.4		306,1965,4227	GG,GA,AA		25.2036,9.3367,19.8292		12/124	112040027	2577,10419	2201	4297	6498	SO:0001819	synonymous_variant	56158	exon2			TAATAGAAATTGC	AF285600	CCDS31679.1	11q23.1	2013-09-20	2007-03-13						11734	protein-coding gene	gene with protein product		605791	"""testis expressed sequence 12"""			11279525	Standard	NM_031275		Approved		uc001pnc.3	Q9BXU0		ENST00000280358.4:c.36A>G	11.37:g.112040027A>G		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	161	66	0.409938	NM_031275	A6NDL9|B0YIX3	Silent	SNP	ENST00000280358.4	37	CCDS31679.1																																																																																			A|0.832;G|0.168	0.168	strong		0.383	TEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392417.1		
ZNF57	126295	hgsc.bcm.edu	37	19	2917857	2917857	+	Missense_Mutation	SNP	C	C	T	rs148390269		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917857C>T	ENST00000306908.5	+	4	1386	c.1238C>T	c.(1237-1239)aCg>aTg	p.T413M	ZNF57_ENST00000523428.1_Missense_Mutation_p.T381M|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		CATTTGAGGACGCACACTGGA	0.438													C|||	1	0.000199681	0.0	0.0014	5008	,	,		22852	0.0		0.0	False		,,,				2504	0.0				p.T413M	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											ZNF57,NS,carcinoma,0,1	ZNF57	57	1	0			c.C1238T						scavenged	.						100.0	90.0	93.0					19																	2917857		2203	4300	6503	SO:0001583	missense	126295	exon4			TGAGGACGCACAC	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.1238C>T	19.37:g.2917857C>T	ENSP00000303696:p.Thr413Met	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	156	2	0.0128205	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	C	9.937	1.216517	0.22373	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.13089	2.62;2.62	2.08	-2.04	0.07343	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17577	0.0422	L	0.50847	1.595	0.09310	N	1	D	0.57899	0.981	P	0.52343	0.696	T	0.15665	-1.0429	9	0.52906	T	0.07	.	6.5785	0.22581	0.0:0.5038:0.0:0.4962	.	413	Q68EA5	ZNF57_HUMAN	M	413;415;381	ENSP00000303696:T413M;ENSP00000430223:T381M	ENSP00000303696:T413M	T	+	2	0	ZNF57	2868857	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-4.310000	0.00255	-0.255000	0.09486	-0.424000	0.05967	ACG	C|0.999;T|0.001	0.001	weak		0.438	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
INSL3	3640	hgsc.bcm.edu	37	19	17932190	17932190	+	Silent	SNP	T	T	C	rs1047233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17932190T>C	ENST00000317306.7	-	1	142	c.126A>G	c.(124-126)ctA>ctG	p.L42L	INSL3_ENST00000379695.5_Silent_p.L42L	NM_005543.3	NP_005534.2	P51460	INSL3_HUMAN	insulin-like 3 (Leydig cell)	42					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|perinuclear region of cytoplasm (GO:0048471)	insulin receptor binding (GO:0005158)|protease binding (GO:0002020)|receptor binding (GO:0005102)			breast(1)|lung(1)	2						ACACGCGCACTAGCGCGCGTA	0.721													C|||	1288	0.257188	0.3941	0.3127	5008	,	,		12303	0.005		0.4076	False		,,,				2504	0.138				p.L42L		Atlas-SNP	.											INSL3,NS,carcinoma,0,1	INSL3	8	1	0			c.A126G						PASS	.	C		1224,2548		247,730,909	4.0	7.0	6.0		126	-1.9	1.0	19	dbSNP_86	6	2298,4938		486,1326,1806	no	coding-synonymous	INSL3	NM_005543.2		733,2056,2715	CC,CT,TT		31.7579,32.4496,31.9949		42/132	17932190	3522,7486	1886	3618	5504	SO:0001819	synonymous_variant	3640	exon1			GCGCACTAGCGCG		CCDS12365.1, CCDS58655.1	19p13.2-p12	2013-02-26	2003-05-13			ENSG00000248099		"""Endogenous ligands"""	6086	protein-coding gene	gene with protein product	"""prepro-INSL3"""	146738	"""relaxin-like factor"""	RLNL		8020942	Standard	NM_001265587		Approved	RLF, MGC119818, MGC119819	uc010ebf.2	P51460		ENST00000317306.7:c.126A>G	19.37:g.17932190T>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	11	4	0.363636	NM_005543	B4DZ72|G3XAG0|Q3KPI5|Q3KPI6|Q6YNB5|Q9UEA2|Q9UPH6	Silent	SNP	ENST00000317306.7	37	CCDS12365.1																																																																																			T|0.715;G|0.000;C|0.284;A|0.000	0.284	strong		0.721	INSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466836.1	NM_005543	
ADCY10	55811	hgsc.bcm.edu	37	1	167849414	167849414	+	Silent	SNP	A	A	G	rs203849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:167849414A>G	ENST00000367851.4	-	11	1339	c.1155T>C	c.(1153-1155)ggT>ggC	p.G385G	ADCY10_ENST00000545172.1_Silent_p.G232G|ADCY10_ENST00000367848.1_Silent_p.G293G	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	385	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				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)	p.G385G(1)		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						CACTGGCAACACCGATGGATA	0.483													G|||	2470	0.493211	0.6687	0.4597	5008	,	,		19729	0.3224		0.504	False		,,,				2504	0.4448				p.G385G		Atlas-SNP	.											ADCY10,NS,carcinoma,0,1	ADCY10	175	1	1	Substitution - coding silent(1)	stomach(1)	c.T1155C						PASS	.	G	,	2826,1580	492.2+/-362.3	903,1020,280	66.0	59.0	61.0		696,1155	-1.5	0.1	1	dbSNP_79	61	4122,4476	585.4+/-391.9	1002,2118,1179	yes	coding-synonymous,coding-synonymous	ADCY10	NM_001167749.1,NM_018417.4	,	1905,3138,1459	GG,GA,AA		47.9414,35.8602,46.5703	,	232/1458,385/1611	167849414	6948,6056	2203	4299	6502	SO:0001819	synonymous_variant	55811	exon11			GGCAACACCGATG	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.1155T>C	1.37:g.167849414A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	173	74	0.427746	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Silent	SNP	ENST00000367851.4	37	CCDS1265.1																																																																																			G|0.516;N|0.000	0.516	strong		0.483	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
DOK7	285489	hgsc.bcm.edu	37	4	3494956	3494956	+	Missense_Mutation	SNP	C	C	T	rs16844464	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:3494956C>T	ENST00000340083.5	+	7	1308	c.1243C>T	c.(1243-1245)Cct>Tct	p.P415S	DOK7_ENST00000389653.2_Missense_Mutation_p.P415S|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000512714.1_3'UTR	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	415			P -> S (in dbSNP:rs16844464). {ECO:0000269|PubMed:22661499}.		neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TTGCCTGGCTCCTAGAGACCA	0.706													.|||	407	0.08127	0.1566	0.0807	5008	,	,		14763	0.0397		0.0348	False		,,,				2504	0.0706				p.P415S		Atlas-SNP	.											DOK7,NS,carcinoma,0,1	DOK7	44	1	0			c.C1243T						PASS	.	C	,SER/PRO	533,3845		36,461,1692	14.0	15.0	15.0		,1243	1.0	0.0	4	dbSNP_123	15	288,8290		7,274,4008	yes	utr-3,missense	DOK7	NM_001164673.1,NM_173660.4	,74	43,735,5700	TT,TC,CC		3.3574,12.1745,6.3368	,probably-damaging	,415/505	3494956	821,12135	2189	4289	6478	SO:0001583	missense	285489	exon7			CTGGCTCCTAGAG	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.1243C>T	4.37:g.3494956C>T	ENSP00000344432:p.Pro415Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Missense_Mutation	SNP	ENST00000340083.5	37	CCDS3370.2	130	0.05952380952380952	58	0.11788617886178862	27	0.07458563535911603	21	0.03671328671328671	24	0.0316622691292876	C	4.330	0.060659	0.08339	0.121745	0.033574	ENSG00000175920	ENST00000389653;ENST00000340083	T;T	0.63580	-0.05;0.03	3.77	1.02	0.19986	.	0.483231	0.18723	N	0.132972	T	0.02571	0.0078	M	0.70595	2.14	0.09310	N	1	P;D;B	0.89917	0.454;1.0;0.007	B;D;B	0.87578	0.032;0.998;0.007	T	0.04140	-1.0974	10	0.33940	T	0.23	-7.2048	4.6184	0.12438	0.142:0.4983:0.2764:0.0833	rs16844464;rs60265678;rs16844464	415;277;415	Q18PE1-3;Q18PE1-2;Q18PE1	.;.;DOK7_HUMAN	S	415	ENSP00000374304:P415S;ENSP00000344432:P415S	ENSP00000344432:P415S	P	+	1	0	DOK7	3464754	0.065000	0.20965	0.002000	0.10522	0.046000	0.14306	0.199000	0.17237	-0.006000	0.14370	0.555000	0.69702	CCT	C|0.935;T|0.065	0.065	strong		0.706	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
OR1S1	219959	hgsc.bcm.edu	37	11	57982620	57982620	+	Missense_Mutation	SNP	A	A	G	rs1966834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:57982620A>G	ENST00000309433.6	+	1	404	c.404A>G	c.(403-405)cAc>cGc	p.H135R		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	135			H -> R (in dbSNP:rs1966834).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GCCTATGACCACTTTGTGGCG	0.438													G|||	2598	0.51877	0.2844	0.5418	5008	,	,		22010	0.8036		0.4205	False		,,,				2504	0.6268				p.H135R		Atlas-SNP	.											.	OR1S1	139	.	0			c.A404G	GRCh37	CM035848	OR1S1	M	rs1966834	PASS	.	G	ARG/HIS	1324,3078	695.1+/-405.9	197,930,1074	182.0	173.0	176.0		404	3.5	1.0	11	dbSNP_92	176	3621,4971	625.0+/-397.7	779,2063,1454	yes	missense	OR1S1	NM_001004458.1	29	976,2993,2528	GG,GA,AA		42.1439,30.0772,38.056	benign	135/326	57982620	4945,8049	2201	4296	6497	SO:0001583	missense	219959	exon1			ATGACCACTTTGT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.404A>G	11.37:g.57982620A>G	ENSP00000311688:p.His135Arg	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	281	139	0.494662	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1083	0.4958791208791209	148	0.3008130081300813	187	0.5165745856353591	433	0.756993006993007	315	0.4155672823218997	G	0.809	-0.752849	0.03041	0.300772	0.421439	ENSG00000172774	ENST00000309433	T	0.04809	3.55	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	N	0.000173	T	0.00012	0.0000	N	0.00006	-3.19	0.46458	P	9.470000000000312E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.32107	-0.9919	9	0.02654	T	1	.	10.0632	0.42288	0.102:0.0:0.898:0.0	rs1966834;rs52803988;rs1966834	135	Q8NH92	OR1S1_HUMAN	R	135	ENSP00000311688:H135R	ENSP00000311688:H135R	H	+	2	0	OR1S1	57739196	1.000000	0.71417	1.000000	0.80357	0.381000	0.30169	6.004000	0.70709	0.671000	0.31185	-0.348000	0.07805	CAC	A|0.569;G|0.431	0.431	strong		0.438	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
OGDHL	55753	hgsc.bcm.edu	37	10	50944529	50944529	+	Silent	SNP	G	G	A	rs12357255	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:50944529G>A	ENST00000374103.4	-	21	2713	c.2628C>T	c.(2626-2628)gcC>gcT	p.A876A	OGDHL_ENST00000419399.1_Silent_p.A819A|OGDHL_ENST00000432695.1_Silent_p.A667A|OGDHL_ENST00000490844.1_5'UTR	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	876					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						CCCGTGCTGCGGCCCCATCTT	0.637													G|||	86	0.0171725	0.0045	0.0086	5008	,	,		19124	0.0		0.0467	False		,,,				2504	0.0276				p.A876A		Atlas-SNP	.											.	OGDHL	149	.	0			c.C2628T						PASS	.	G	,,	25,4381	32.6+/-62.9	1,23,2179	53.0	59.0	57.0		2457,2001,2628	-10.8	0.0	10	dbSNP_120	57	342,8258	116.6+/-176.3	8,326,3966	no	coding-synonymous,coding-synonymous,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	9,349,6145	AA,AG,GG		3.9767,0.5674,2.8218	,,	819/954,667/802,876/1011	50944529	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon21			TGCTGCGGCCCCA	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.2628C>T	10.37:g.50944529G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			G|0.972;A|0.028	0.028	strong		0.637	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
GLRX3	10539	hgsc.bcm.edu	37	10	131959150	131959150	+	Missense_Mutation	SNP	C	C	T	rs2274217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:131959150C>T	ENST00000368644.1	+	4	389	c.367C>T	c.(367-369)Ccc>Tcc	p.P123S	GLRX3_ENST00000331244.5_Missense_Mutation_p.P123S	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	123			P -> S (in dbSNP:rs2274217). {ECO:0000269|PubMed:10636891, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		CTCCTTCCTACCCAGCGCTAA	0.438													C|||	957	0.191094	0.1241	0.1282	5008	,	,		16273	0.1101		0.2853	False		,,,				2504	0.3129				p.P123S		Atlas-SNP	.											TXNL2,colon,carcinoma,0,2	GLRX3	39	2	0			c.C367T						PASS	.	C	SER/PRO,SER/PRO	596,3810	261.9+/-264.6	47,502,1654	114.0	101.0	106.0		367,367	4.4	0.2	10	dbSNP_100	106	2244,6356	381.3+/-340.0	315,1614,2371	yes	missense,missense	GLRX3	NM_001199868.1,NM_006541.4	74,74	362,2116,4025	TT,TC,CC		26.093,13.527,21.8361	benign,benign	123/336,123/336	131959150	2840,10166	2203	4300	6503	SO:0001583	missense	10539	exon4			TTCCTACCCAGCG	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"""glutaredoxin 4"""	612754	"""thioredoxin-like 2"""	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.367C>T	10.37:g.131959150C>T	ENSP00000357633:p.Pro123Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_006541	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	386	0.17673992673992675	64	0.13008130081300814	53	0.1464088397790055	56	0.0979020979020979	213	0.28100263852242746	C	2.176	-0.388811	0.04932	0.13527	0.26093	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.08546	3.08;3.08	4.39	4.39	0.52855	Thioredoxin-like fold (1);	0.372544	0.26227	N	0.025598	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45249	-0.9274	9	0.08381	T	0.77	-2.8796	10.9948	0.47569	0.0:0.6927:0.3073:0.0	rs2274217;rs17297963;rs2274217	123	O76003	GLRX3_HUMAN	S	123	ENSP00000330836:P123S;ENSP00000357633:P123S	ENSP00000330836:P123S	P	+	1	0	GLRX3	131849140	0.090000	0.21635	0.206000	0.23566	0.141000	0.21300	0.666000	0.25097	2.284000	0.76573	0.655000	0.94253	CCC	C|0.799;T|0.201	0.201	strong		0.438	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541	
SP140L	93349	hgsc.bcm.edu	37	2	231256814	231256814	+	Missense_Mutation	SNP	A	A	G	rs183267141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:231256814A>G	ENST00000415673.2	+	12	1063	c.977A>G	c.(976-978)aAg>aGg	p.K326R	SP140L_ENST00000396563.4_Missense_Mutation_p.K291R|SP140L_ENST00000243810.6_Missense_Mutation_p.K326R|SP140L_ENST00000444636.1_Missense_Mutation_p.K326R	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	326	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						ACCTTGGCAAAGTGTATACAG	0.502													A|||	8	0.00159744	0.0	0.0029	5008	,	,		19306	0.0		0.006	False		,,,				2504	0.0				p.K326R		Atlas-SNP	.											.	SP140L	68	.	0			c.A977G						PASS	.	A	ARG/LYS	1,3985		0,1,1992	106.0	112.0	110.0		977	-0.4	0.0	2		110	42,8344		0,42,4151	no	missense	SP140L	NM_138402.4	26	0,43,6143	GG,GA,AA		0.5008,0.0251,0.3476	benign	326/581	231256814	43,12329	1993	4193	6186	SO:0001583	missense	93349	exon12			TGGCAAAGTGTAT	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.977A>G	2.37:g.231256814A>G	ENSP00000397911:p.Lys326Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	11.98	1.800033	0.31869	2.51E-4	0.005008	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	3.44	-0.423	0.12325	.	.	.	.	.	T	0.55386	0.1917	L	0.31420	0.93	0.09310	N	1	P;P	0.48230	0.811;0.907	P;P	0.49665	0.618;0.615	T	0.50651	-0.8803	9	0.35671	T	0.21	.	2.4941	0.04617	0.5579:0.0:0.2383:0.2038	.	291;326	Q9H930-2;Q9H930-4	.;.	R	326;326;326;291	ENSP00000395195:K326R;ENSP00000397911:K326R;ENSP00000243810:K326R;ENSP00000379811:K291R	ENSP00000243810:K326R	K	+	2	0	SP140L	230965058	0.259000	0.24043	0.000000	0.03702	0.011000	0.07611	0.573000	0.23699	-0.079000	0.12707	-0.326000	0.08463	AAG	A|0.997;G|0.003	0.003	strong		0.502	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552537	43552537	+	Silent	SNP	G	G	A	rs71238846	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	149	0	0		WXS	Illumina HiSeq	Phase_I	176	170	0.965909	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	
ZNF8	7554	hgsc.bcm.edu	37	19	58806686	58806686	+	Silent	SNP	A	A	G	rs17853924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58806686A>G	ENST00000196548.5	+	4	1643	c.1512A>G	c.(1510-1512)caA>caG	p.Q504Q	AC010642.1_ENST00000591325.1_3'UTR|ZNF8_ENST00000608843.1_Silent_p.Q504Q			P17098	ZNF8_HUMAN	zinc finger protein 8	504					BMP signaling pathway (GO:0030509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	19		all_cancers(17;6.46e-05)|Lung NSC(17;0.0233)|all_neural(62;0.0381)|all_epithelial(17;0.0427)|all_lung(17;0.057)|Ovarian(87;0.17)|Colorectal(82;0.227)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.00619)		GGCGTGAACAATCCTCGAGCA	0.587													A|||	238	0.047524	0.1165	0.0187	5008	,	,		16872	0.001		0.0517	False		,,,				2504	0.0184				p.Q504Q		Atlas-SNP	.											.	ZNF8	60	.	0			c.A1512G						PASS	.	A		431,3975	209.2+/-230.0	21,389,1793	107.0	118.0	114.0		1512	-4.4	0.0	19	dbSNP_123	114	293,8307	107.6+/-168.3	6,281,4013	no	coding-synonymous	ZNF8	NM_021089.2		27,670,5806	GG,GA,AA		3.407,9.7821,5.5667		504/576	58806686	724,12282	2203	4300	6503	SO:0001819	synonymous_variant	7554	exon4			TGAACAATCCTCG	M29581	CCDS12974.1	19q13.43	2013-01-08	2006-05-09					"""Zinc fingers, C2H2-type"", ""-"""	13154	protein-coding gene	gene with protein product		194532	"""zinc finger protein 8 (clone HF.18)"""			2106481	Standard	NM_021089		Approved	HF.18, Zfp128	uc002qry.1	P17098		ENST00000196548.5:c.1512A>G	19.37:g.58806686A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_021089	Q6PI99	Silent	SNP	ENST00000196548.5	37	CCDS12974.1																																																																																			A|0.946;G|0.054	0.054	strong		0.587	ZNF8-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000459135.1	NM_021089	
SGOL1	151648	hgsc.bcm.edu	37	3	20216519	20216519	+	Silent	SNP	T	T	A	rs61729306	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:20216519T>A	ENST00000263753.4	-	6	643	c.504A>T	c.(502-504)acA>acT	p.T168T	SGOL1_ENST00000429446.3_Intron|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000412868.1_Silent_p.T168T|SGOL1_ENST00000412997.1_Silent_p.T168T|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000437051.1_Silent_p.T168T|SGOL1_ENST00000452020.1_Intron|SGOL1_ENST00000419233.2_Silent_p.T168T|SGOL1_ENST00000443724.1_Silent_p.T168T|SGOL1_ENST00000306698.2_Intron|SGOL1_ENST00000417364.1_Silent_p.T168T|SGOL1_ENST00000383774.1_Silent_p.T168T|SGOL1_ENST00000442720.1_Intron|SGOL1_ENST00000425061.1_Silent_p.T168T|SGOL1_ENST00000421451.1_Silent_p.T168T	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	168	Necessary for interaction with PPP2CA and PPP2R1A.				attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)			kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						CAACTCCCAGTGTGTCTTGAG	0.313													T|||	1331	0.265775	0.1687	0.2882	5008	,	,		19471	0.4167		0.165	False		,,,				2504	0.3292				p.T168T		Atlas-SNP	.											.	SGOL1	55	.	0			c.A504T						PASS	.	T	,,,,,,,,,,,,	748,3658	284.9+/-277.9	64,620,1519	46.0	47.0	47.0		504,504,504,504,,504,504,504,504,,,504,	-0.6	0.0	3	dbSNP_129	47	1385,7213	263.2+/-284.9	125,1135,3039	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	SGOL1	NM_001012409.2,NM_001012410.3,NM_001012411.2,NM_001012412.3,NM_001012413.2,NM_001199251.1,NM_001199252.1,NM_001199253.1,NM_001199254.1,NM_001199255.1,NM_001199256.1,NM_001199257.1,NM_138484.3	,,,,,,,,,,,,	189,1755,4558	AA,AT,TT		16.1084,16.9768,16.4026	,,,,,,,,,,,,	168/528,168/562,168/276,168/310,,168/528,168/562,168/276,168/310,,,168/216,	20216519	2133,10871	2203	4299	6502	SO:0001819	synonymous_variant	151648	exon6			TCCCAGTGTGTCT	BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.504A>T	3.37:g.20216519T>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	216	106	0.490741	NM_001199253	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Silent	SNP	ENST00000263753.4	37	CCDS33716.1																																																																																			T|0.811;A|0.189	0.189	strong		0.313	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484	
SPRY2	10253	hgsc.bcm.edu	37	13	80911525	80911525	+	Missense_Mutation	SNP	G	G	A	rs504122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:80911525G>A	ENST00000377102.1	-	2	1293	c.316C>T	c.(316-318)Cct>Tct	p.P106S	SPRY2_ENST00000540649.1_Missense_Mutation_p.P106S|SPRY2_ENST00000377104.3_Missense_Mutation_p.P106S			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	106			P -> S (in dbSNP:rs504122).		bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		CTGGACAGAGGGGCTCGTGCA	0.597													G|||	1436	0.286741	0.0182	0.4539	5008	,	,		20149	0.4345		0.3529	False		,,,				2504	0.3108				p.P106S		Atlas-SNP	.											.	SPRY2	28	.	0			c.C316T						PASS	.	G	SER/PRO	354,4052	180.8+/-209.0	13,328,1862	92.0	87.0	89.0		316	0.6	0.1	13	dbSNP_83	89	3087,5513	469.1+/-367.5	550,1987,1763	yes	missense	SPRY2	NM_005842.2	74	563,2315,3625	AA,AG,GG		35.8953,8.0345,26.457	benign	106/316	80911525	3441,9565	2203	4300	6503	SO:0001583	missense	10253	exon2			ACAGAGGGGCTCG	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.316C>T	13.37:g.80911525G>A	ENSP00000366306:p.Pro106Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_005842	B2R9J9|Q5T6Z7	Missense_Mutation	SNP	ENST00000377102.1	37	CCDS9463.1	674	0.3086080586080586	14	0.028455284552845527	148	0.4088397790055249	245	0.42832167832167833	267	0.35224274406332456	G	9.125	1.009882	0.19277	0.080345	0.358953	ENSG00000136158	ENST00000377104;ENST00000377102;ENST00000541655;ENST00000540649	T;T;T	0.57107	0.42;0.42;0.42	5.48	0.638	0.17742	.	0.226724	0.45867	N	0.000333	T	0.00012	0.0000	M	0.66939	2.045	0.44175	P	0.0030120000000000147	B	0.02656	0.0	B	0.04013	0.001	T	0.36720	-0.9736	9	0.36615	T	0.2	.	4.6416	0.12552	0.1252:0.2223:0.5371:0.1154	rs504122;rs3825414;rs17845004;rs17857765;rs57585481;rs504122	106	O43597	SPY2_HUMAN	S	106	ENSP00000366308:P106S;ENSP00000366306:P106S;ENSP00000439027:P106S	ENSP00000366306:P106S	P	-	1	0	SPRY2	79809526	0.534000	0.26362	0.051000	0.19133	0.952000	0.60782	0.958000	0.29227	-0.211000	0.10124	0.655000	0.94253	CCT	G|0.726;N|0.000	.	strong		0.597	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1		
SLK	9748	hgsc.bcm.edu	37	10	105758670	105758670	+	Silent	SNP	A	A	G	rs10883960	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105758670A>G	ENST00000369755.3	+	5	1073	c.528A>G	c.(526-528)gtA>gtG	p.V176V	SLK_ENST00000335753.4_Silent_p.V176V	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		ATTTTGGAGTATCAGCTAAAA	0.308													A|||	837	0.167133	0.0802	0.2147	5008	,	,		18987	0.1389		0.2256	False		,,,				2504	0.2198				p.V176V	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A528G						PASS	.	A		510,3894	232.3+/-245.9	36,438,1728	92.0	94.0	93.0		528	-2.2	1.0	10	dbSNP_120	93	2067,6531	357.0+/-330.6	232,1603,2464	no	coding-synonymous	SLK	NM_014720.2		268,2041,4192	GG,GA,AA		24.0405,11.5804,19.82		176/1236	105758670	2577,10425	2202	4299	6501	SO:0001819	synonymous_variant	9748	exon5			TGGAGTATCAGCT		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.528A>G	10.37:g.105758670A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Silent	SNP	ENST00000369755.3	37	CCDS7553.1																																																																																			A|0.817;G|0.183	0.183	strong		0.308	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
CUL9	23113	hgsc.bcm.edu	37	6	43152366	43152366	+	Silent	SNP	C	C	A	rs41274928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	154	0	0		WXS	Illumina HiSeq	Phase_I	185	84	0.454054	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	
OR1M1	125963	hgsc.bcm.edu	37	19	9203994	9203994	+	Missense_Mutation	SNP	C	C	T	rs61738474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9203994C>T	ENST00000429566.3	+	1	140	c.74C>T	c.(73-75)aCg>aTg	p.T25M		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T25K(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GAGCAGGAGACGCTTCTCTTT	0.522													c|||	58	0.0115815	0.0424	0.0029	5008	,	,		16171	0.0		0.0	False		,,,				2504	0.0				p.T25M		Atlas-SNP	.											OR1M1,NS,carcinoma,0,1	OR1M1	52	1	1	Substitution - Missense(1)	lung(1)	c.C74T						PASS	.	C	MET/THR	169,4237	111.6+/-149.8	6,157,2040	116.0	98.0	104.0		74	2.4	0.0	19	dbSNP_129	104	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR1M1	NM_001004456.1	81	6,159,6338	TT,TC,CC		0.0233,3.8357,1.3148	probably-damaging	25/314	9203994	171,12835	2203	4300	6503	SO:0001583	missense	125963	exon1			AGGAGACGCTTCT		CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"""GPCR / Class A : Olfactory receptors"""	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.74C>T	19.37:g.9203994C>T	ENSP00000401966:p.Thr25Met	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	185	75	0.405405	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	37	CCDS32896.1	32	0.014652014652014652	32	0.06504065040650407	0	0.0	0	0.0	0	0.0	c	11.15	1.552933	0.27739	0.038357	2.33E-4	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.00428	7.44	3.49	2.44	0.29823	.	2.059810	0.02106	N	0.054364	T	0.00039	0.0001	N	0.11789	0.175	0.09310	N	1	D	0.54047	0.964	P	0.44477	0.451	T	0.48525	-0.9028	10	0.62326	D	0.03	.	5.4607	0.16615	0.0:0.6579:0.0:0.3421	rs61738474	25	Q8NGA1	OR1M1_HUMAN	M	28;25	ENSP00000401966:T25M	ENSP00000303195:T28M	T	+	2	0	OR1M1	9064994	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-4.203000	0.00275	0.801000	0.34066	0.400000	0.26472	ACG	C|0.987;T|0.013	0.013	strong		0.522	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1		
PNPO	55163	hgsc.bcm.edu	37	17	46022065	46022065	+	Missense_Mutation	SNP	G	G	A	rs17679445	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:46022065G>A	ENST00000225573.4	+	3	452	c.347G>A	c.(346-348)cGa>cAa	p.R116Q	PNPO_ENST00000434554.2_Missense_Mutation_p.R116Q|RP11-6N17.6_ENST00000582142.1_RNA|RP11-6N17.6_ENST00000580372.1_RNA|RP11-6N17.9_ENST00000582262.1_RNA|PNPO_ENST00000544840.1_Missense_Mutation_p.R116Q|PNPO_ENST00000534893.1_Missense_Mutation_p.R21Q	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	116			R -> Q (in dbSNP:rs17679445).		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						TTCGAGAGTCGAAAAGGAAAA	0.517													G|||	149	0.0297524	0.0008	0.0519	5008	,	,		19988	0.0		0.0666	False		,,,				2504	0.046				p.R116Q		Atlas-SNP	.											.	PNPO	18	.	0			c.G347A						PASS	.	G	GLN/ARG	70,4336	64.7+/-102.0	1,68,2134	131.0	128.0	129.0		347	5.2	1.0	17	dbSNP_123	129	605,7995	159.1+/-212.4	21,563,3716	yes	missense	PNPO	NM_018129.3	43	22,631,5850	AA,AG,GG		7.0349,1.5887,5.1899	probably-damaging	116/262	46022065	675,12331	2203	4300	6503	SO:0001583	missense	55163	exon3			AGAGTCGAAAAGG	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.347G>A	17.37:g.46022065G>A	ENSP00000225573:p.Arg116Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Missense_Mutation	SNP	ENST00000225573.4	37	CCDS11522.1	75	0.034340659340659344	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	48	0.0633245382585752	G	35	5.496731	0.96355	0.015887	0.070349	ENSG00000108439	ENST00000225573;ENST00000434554;ENST00000544840;ENST00000534893	T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69	5.22	5.22	0.72569	Pyridoxamine 5&apos (1);FMN-binding split barrel-related (1);-phosphate oxidase-like, FMN-binding domain (1);FMN-binding split barrel (1);	0.000000	0.85682	D	0.000000	T	0.19167	0.0460	M	0.62088	1.915	0.80722	D	1	D;D;D	0.56035	0.964;0.957;0.974	P;B;B	0.45343	0.477;0.364;0.303	T	0.57705	-0.7765	10	0.52906	T	0.07	-18.454	17.5368	0.87834	0.0:0.0:1.0:0.0	rs17679445;rs17679445	116;116;116	B4E152;B4E1D7;Q9NVS9	.;.;PNPO_HUMAN	Q	116;116;116;21	ENSP00000225573:R116Q;ENSP00000399960:R116Q;ENSP00000446182:R116Q;ENSP00000437480:R21Q	ENSP00000225573:R116Q	R	+	2	0	PNPO	43377064	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.533000	0.81994	2.443000	0.82685	0.655000	0.94253	CGA	G|0.956;A|0.044	0.044	strong		0.517	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
CSRNP3	80034	hgsc.bcm.edu	37	2	166535883	166535883	+	Missense_Mutation	SNP	G	G	C	rs61738743	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:166535883G>C	ENST00000342316.4	+	5	1650	c.1378G>C	c.(1378-1380)Gtc>Ctc	p.V460L	CSRNP3_ENST00000409420.1_Missense_Mutation_p.V492L|CSRNP3_ENST00000314499.7_Missense_Mutation_p.V460L	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	460					apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						AAGAGACACTGTCAAAAATGG	0.453													G|||	187	0.0373403	0.0787	0.0432	5008	,	,		18894	0.0		0.0398	False		,,,				2504	0.0133				p.V460L		Atlas-SNP	.											.	CSRNP3	73	.	0			c.G1378C						PASS	.	G	LEU/VAL,LEU/VAL	282,4124	157.0+/-190.0	9,264,1930	78.0	80.0	79.0		1378,1378	4.1	1.0	2	dbSNP_129	79	267,8333	102.9+/-164.1	2,263,4035	yes	missense,missense	CSRNP3	NM_001172173.1,NM_024969.3	32,32	11,527,5965	CC,CG,GG		3.1047,6.4004,4.2211	possibly-damaging,possibly-damaging	460/586,460/586	166535883	549,12457	2203	4300	6503	SO:0001583	missense	80034	exon7			GACACTGTCAAAA	AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30729	protein-coding gene	gene with protein product	"""TGF beta induced apotosis protein 2"", ""protein phosphatase 1, regulatory subunit 73"""		"""family with sequence similarity 130, member A2"""	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.1378G>C	2.37:g.166535883G>C	ENSP00000344042:p.Val460Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001172173	B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	37	CCDS2225.1	101	0.04624542124542125	49	0.09959349593495935	19	0.052486187845303865	0	0.0	33	0.04353562005277045	G	14.97	2.695078	0.48202	0.064004	0.031047	ENSG00000178662	ENST00000314499;ENST00000342316;ENST00000409420	T;T;T	0.49720	0.77;0.77;0.77	5.88	4.09	0.47781	.	0.457005	0.25175	N	0.032572	T	0.00906	0.0030	L	0.27053	0.805	0.27990	P	0.9357131	B	0.17465	0.022	B	0.16289	0.015	T	0.08806	-1.0704	8	.	.	.	-10.4185	12.1281	0.53928	0.1371:0.0:0.8629:0.0	rs61738743	460	Q8WYN3	CSRN3_HUMAN	L	460;460;492	ENSP00000318258:V460L;ENSP00000344042:V460L;ENSP00000387195:V492L	.	V	+	1	0	CSRNP3	166244129	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	4.282000	0.58971	0.829000	0.34733	0.655000	0.94253	GTC	G|0.957;C|0.043	0.043	strong		0.453	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969	
PSPH	5723	hgsc.bcm.edu	37	7	56088789	56088789	+	Silent	SNP	G	G	A	rs199851385	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	150	0	0		WXS	Illumina HiSeq	Phase_I	158	25	0.158228	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	
ATL2	64225	hgsc.bcm.edu	37	2	38536626	38536626	+	Silent	SNP	T	T	G	rs2305243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:38536626T>G	ENST00000378954.4	-	9	967	c.966A>C	c.(964-966)cgA>cgC	p.R322R	ATL2_ENST00000419554.2_Silent_p.R322R|ATL2_ENST00000332337.4_Silent_p.R304R|ATL2_ENST00000452935.2_Silent_p.R304R|ATL2_ENST00000406122.1_Silent_p.R151R|ATL2_ENST00000539122.1_Silent_p.R151R|ATL2_ENST00000546051.1_Silent_p.R151R|ATL2_ENST00000402054.1_Silent_p.R151R	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	322	GB1/RHD3-type G.				endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.R322R(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						TTCGAAGCTCTCGTTTAAAGT	0.338													T|||	1640	0.327476	0.2708	0.3285	5008	,	,		16258	0.1925		0.3718	False		,,,				2504	0.4969				p.R322R		Atlas-SNP	.											ATL2,NS,carcinoma,0,1	ATL2	49	1	1	Substitution - coding silent(1)	stomach(1)	c.A966C						PASS	.	T	,	1198,3208	412.6+/-336.2	191,816,1196	79.0	79.0	79.0		966,966	5.0	1.0	2	dbSNP_100	79	3094,5506	471.0+/-368.0	521,2052,1727	yes	coding-synonymous,coding-synonymous	ATL2	NM_001135673.1,NM_022374.2	,	712,2868,2923	GG,GT,TT		35.9767,27.1902,33.0002	,	322/584,322/580	38536626	4292,8714	2203	4300	6503	SO:0001819	synonymous_variant	64225	exon9			AAGCTCTCGTTTA		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"""ADP-ribosylation factor-like 6 interacting protein 2"""	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.966A>C	2.37:g.38536626T>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Silent	SNP	ENST00000378954.4	37	CCDS46260.1	635	0.2907509157509158	125	0.2540650406504065	120	0.3314917127071823	110	0.19230769230769232	280	0.36939313984168864	T	10.52	1.372303	0.24857	0.271902	0.359767	ENSG00000119787	ENST00000443098	.	.	.	6.17	5.03	0.67393	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.46076	-0.9217	3	.	.	.	-3.7788	4.7877	0.13232	0.1389:0.1491:0.0:0.712	rs2305243;rs17846505;rs17859575;rs59178725	.	.	.	A	241	.	.	E	-	2	0	ATL2	38390130	0.396000	0.25262	1.000000	0.80357	0.998000	0.95712	-0.313000	0.08103	1.168000	0.42723	0.533000	0.62120	GAG	T|0.679;G|0.321	0.321	strong		0.338	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374	
ZNF423	23090	hgsc.bcm.edu	37	16	49671177	49671177	+	Missense_Mutation	SNP	T	T	C	rs34214571	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:49671177T>C	ENST00000561648.1	-	4	1939	c.1886A>G	c.(1885-1887)aAt>aGt	p.N629S	ZNF423_ENST00000567169.1_Missense_Mutation_p.N512S|ZNF423_ENST00000262383.2_Missense_Mutation_p.N629S|ZNF423_ENST00000563137.2_Missense_Mutation_p.N569S|ZNF423_ENST00000562871.1_Missense_Mutation_p.N569S|ZNF423_ENST00000562520.1_Missense_Mutation_p.N569S|ZNF423_ENST00000535559.1_Missense_Mutation_p.N512S	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	629			N -> S (in dbSNP:rs34214571).		cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|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)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				ATACTCCCCATTGGAGATGGA	0.577													T|||	111	0.0221645	0.0129	0.0144	5008	,	,		21834	0.0149		0.0398	False		,,,				2504	0.0297				p.N629S		Atlas-SNP	.											.	ZNF423	463	.	0			c.A1886G						PASS	.	T	SER/ASN	82,4314	70.3+/-108.2	0,82,2116	76.0	71.0	73.0		1886	4.8	1.0	16	dbSNP_126	73	275,8325	104.8+/-165.8	4,267,4029	yes	missense	ZNF423	NM_015069.2	46	4,349,6145	CC,CT,TT		3.1977,1.8653,2.747	benign	629/1285	49671177	357,12639	2198	4300	6498	SO:0001583	missense	23090	exon4			TCCCCATTGGAGA	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1886A>G	16.37:g.49671177T>C	ENSP00000455426:p.Asn629Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	48	0.02197802197802198	7	0.014227642276422764	5	0.013812154696132596	5	0.008741258741258742	31	0.040897097625329816	T	5.315	0.243536	0.10077	0.018653	0.031977	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08720	3.06;3.11	4.78	4.78	0.61160	.	0.044527	0.85682	D	0.000000	T	0.01287	0.0042	N	0.19112	0.55	0.45403	D	0.998388	B	0.09022	0.002	B	0.09377	0.004	T	0.43458	-0.9390	9	.	.	.	.	14.3363	0.66592	0.0:0.0:0.0:1.0	rs34214571	629	Q2M1K9	ZN423_HUMAN	S	629;512	ENSP00000262383:N629S;ENSP00000442321:N512S	.	N	-	2	0	ZNF423	48228678	1.000000	0.71417	0.987000	0.45799	0.959000	0.62525	5.940000	0.70187	1.793000	0.52555	0.459000	0.35465	AAT	T|0.972;C|0.028	0.028	strong		0.577	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
MYPN	84665	hgsc.bcm.edu	37	10	69909802	69909802	+	Silent	SNP	G	G	A	rs10997948	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:69909802G>A	ENST00000358913.5	+	6	1739	c.1251G>A	c.(1249-1251)caG>caA	p.Q417Q	MYPN_ENST00000540630.1_Silent_p.Q417Q|MYPN_ENST00000373675.3_Silent_p.Q417Q|MYPN_ENST00000354393.2_Silent_p.Q142Q	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	417	Interaction with CARP.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						ACCAGTGTCAGAGCCCCACCA	0.353													G|||	422	0.0842652	0.1717	0.0706	5008	,	,		19456	0.002		0.0686	False		,,,				2504	0.0767				p.Q417Q		Atlas-SNP	.											.	MYPN	189	.	0			c.G1251A						PASS	.	G		702,3704	292.4+/-282.0	57,588,1558	116.0	115.0	115.0		1251	5.5	1.0	10	dbSNP_120	115	710,7890	173.7+/-224.2	24,662,3614	no	coding-synonymous	MYPN	NM_032578.2		81,1250,5172	AA,AG,GG		8.2558,15.9328,10.8565		417/1321	69909802	1412,11594	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon6			GTGTCAGAGCCCC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1251G>A	10.37:g.69909802G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			G|0.903;A|0.097	0.097	strong		0.353	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
TBC1D14	57533	hgsc.bcm.edu	37	4	6925237	6925237	+	Missense_Mutation	SNP	C	C	G	rs34860182	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:6925237C>G	ENST00000409757.4	+	2	245	c.121C>G	c.(121-123)Ctc>Gtc	p.L41V	TBC1D14_ENST00000448507.1_Missense_Mutation_p.L41V	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	41			L -> V (in dbSNP:rs34860182). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:19077034}.		negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						GCCCCGACTCCTCTCCGCGCC	0.587													C|||	359	0.0716853	0.0121	0.1052	5008	,	,		16556	0.0268		0.1044	False		,,,				2504	0.1411				p.L41V		Atlas-SNP	.											.	TBC1D14	110	.	0			c.C121G						PASS	.	C	VAL/LEU,VAL/LEU	101,4305	80.9+/-119.3	1,99,2103	78.0	79.0	78.0		121,121	3.7	0.1	4	dbSNP_126	78	998,7602	215.7+/-255.0	55,888,3357	yes	missense,missense	TBC1D14	NM_001113361.1,NM_020773.2	32,32	56,987,5460	GG,GC,CC		11.6047,2.2923,8.4499	benign,benign	41/694,41/694	6925237	1099,11907	2203	4300	6503	SO:0001583	missense	57533	exon2			CGACTCCTCTCCG	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.121C>G	4.37:g.6925237C>G	ENSP00000386921:p.Leu41Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	37	CCDS3394.2	143	0.06547619047619048	10	0.02032520325203252	37	0.10220994475138122	14	0.024475524475524476	82	0.10817941952506596	C	3.283	-0.146646	0.06627	0.022923	0.116047	ENSG00000132405	ENST00000444368;ENST00000448507;ENST00000409757;ENST00000427736	T;T;T;T	0.55413	0.82;3.59;3.59;0.52	4.51	3.67	0.42095	.	0.092622	0.44097	D	0.000487	T	0.00496	0.0016	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.06405	0.002	T	0.06463	-1.0825	9	0.21540	T	0.41	-7.493	5.1169	0.14838	0.1669:0.6586:0.0:0.1745	rs34860182;rs61746322	41	Q9P2M4	TBC14_HUMAN	V	41	ENSP00000414951:L41V;ENSP00000404041:L41V;ENSP00000386921:L41V;ENSP00000411760:L41V	ENSP00000386921:L41V	L	+	1	0	TBC1D14	6976138	0.007000	0.16637	0.092000	0.20876	0.036000	0.12997	0.134000	0.15932	1.133000	0.42147	-0.136000	0.14681	CTC	C|0.919;G|0.081	0.081	strong		0.587	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773	
ANKRD33	341405	hgsc.bcm.edu	37	12	52284668	52284668	+	Missense_Mutation	SNP	C	C	A	rs12368048	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52284668C>A	ENST00000340970.4	+	5	934	c.563C>A	c.(562-564)aCc>aAc	p.T188N	ANKRD33_ENST00000301190.6_Missense_Mutation_p.T313N|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Missense_Mutation_p.T119N			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	188			T -> N (in dbSNP:rs12368048).		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)		ACTGCCACAACCAGCCTGGCC	0.627													C|||	827	0.165136	0.0885	0.1196	5008	,	,		13040	0.1677		0.2326	False		,,,				2504	0.229				p.T313N		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C938A						PASS	.	C	ASN/THR,ASN/THR	426,3980		22,382,1799	58.0	38.0	45.0		563,938	4.7	1.0	12	dbSNP_120	45	1961,6639		222,1517,2561	yes	missense,missense	ANKRD33	NM_001130015.1,NM_182608.3	65,65	244,1899,4360	AA,AC,CC		22.8023,9.6686,18.3531	probably-damaging,probably-damaging	188/273,313/453	52284668	2387,10619	2203	4300	6503	SO:0001583	missense	341405	exon5			CCACAACCAGCCT		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.563C>A	12.37:g.52284668C>A	ENSP00000344690:p.Thr188Asn	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	376	0.17216117216117216	43	0.08739837398373984	49	0.13535911602209943	96	0.16783216783216784	188	0.24802110817941952	C	23.5	4.429357	0.83776	0.096686	0.228023	ENSG00000167612	ENST00000301190;ENST00000538991;ENST00000340970	T;T;T	0.52983	0.64;0.89;1.7	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.76727	2.345	0.21020	P	0.999806233	D;D;D	0.71674	0.976;0.993;0.998	P;D;D	0.67548	0.631;0.91;0.952	T	0.01053	-1.1467	9	0.72032	D	0.01	-12.3288	15.02	0.71624	0.0:1.0:0.0:0.0	rs12368048;rs17700840;rs61190404;rs12368048	188;119;313	Q7Z3H0;Q0VAA8;Q7Z3H0-2	ANR33_HUMAN;.;.	N	313;119;188	ENSP00000301190:T313N;ENSP00000443722:T119N;ENSP00000344690:T188N	ENSP00000301190:T313N	T	+	2	0	ANKRD33	50570935	1.000000	0.71417	0.975000	0.42487	0.929000	0.56500	5.042000	0.64202	2.601000	0.87937	0.561000	0.74099	ACC	A|0.176;C|0.824;G|0.000	0.176	strong		0.627	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
ROBO4	54538	hgsc.bcm.edu	37	11	124764176	124764176	+	Silent	SNP	T	T	C	rs11820142	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	100	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	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	
C20orf85	128602	hgsc.bcm.edu	37	20	56728608	56728608	+	Missense_Mutation	SNP	G	G	A	rs16984945	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:56728608G>A	ENST00000371168.3	+	2	138	c.77G>A	c.(76-78)cGt>cAt	p.R26H		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	26			R -> H (in dbSNP:rs16984945).					p.R26L(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)			AGGAAATACCGTCTGAAGGCT	0.483													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		18716	0.0		0.0	False		,,,				2504	0.0				p.R26H		Atlas-SNP	.											C20orf85,NS,carcinoma,+1,3	C20orf85	35	3	1	Substitution - Missense(1)	lung(1)	c.G77A						scavenged	.	G	HIS/ARG	84,4322	71.4+/-109.4	0,84,2119	99.0	103.0	102.0		77	4.9	1.0	20	dbSNP_123	102	5,8595	5.0+/-18.6	0,5,4295	yes	missense	C20orf85	NM_178456.2	29	0,89,6414	AA,AG,GG		0.0581,1.9065,0.6843	benign	26/138	56728608	89,12917	2203	4300	6503	SO:0001583	missense	128602	exon2			AATACCGTCTGAA	AL354776	CCDS13465.1	20q13.32	2012-10-29			ENSG00000124237	ENSG00000124237			16216	protein-coding gene	gene with protein product	"""Low in Lung Cancer 1"""						Standard	NM_178456		Approved	bA196N14.1, LLC1	uc002xyv.3	Q9H1P6	OTTHUMG00000032836	ENST00000371168.3:c.77G>A	20.37:g.56728608G>A	ENSP00000360210:p.Arg26His	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	127	2	0.015748	NM_178456		Missense_Mutation	SNP	ENST00000371168.3	37	CCDS13465.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	10.76	1.440189	0.25900	0.019065	5.81E-4	ENSG00000124237	ENST00000371168	T	0.18174	2.23	5.82	4.87	0.63330	.	0.106722	0.46758	D	0.000272	T	0.04048	0.0113	N	0.20986	0.625	0.34849	D	0.741426	B	0.29531	0.247	B	0.24541	0.054	T	0.22765	-1.0207	10	0.14252	T	0.57	-10.1333	6.9718	0.24652	0.1825:0.0:0.8175:0.0	rs16984945;rs52810072;rs16984945	26	Q9H1P6	CT085_HUMAN	H	26	ENSP00000360210:R26H	ENSP00000360210:R26H	R	+	2	0	C20orf85	56162014	0.060000	0.20803	0.998000	0.56505	0.808000	0.45660	1.285000	0.33261	2.760000	0.94817	0.655000	0.94253	CGT	G|0.992;A|0.008	0.008	strong		0.483	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456	
STON1	11037	hgsc.bcm.edu	37	2	48807976	48807976	+	Silent	SNP	T	T	C	rs3828340	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48807976T>C	ENST00000406226.1	+	3	399	c.204T>C	c.(202-204)gaT>gaC	p.D68D	STON1-GTF2A1L_ENST00000405008.1_Silent_p.D68D|STON1-GTF2A1L_ENST00000394754.1_Silent_p.D68D|STON1-GTF2A1L_ENST00000402114.2_Silent_p.D68D|STON1-GTF2A1L_ENST00000394751.3_Silent_p.D68D|STON1_ENST00000309835.3_Silent_p.D68D|STON1-GTF2A1L_ENST00000309827.2_Silent_p.D68D|STON1_ENST00000404752.1_Silent_p.D68D	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	68					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CCATTGTAGATTTTTATTTCA	0.507													C|||	1700	0.339457	0.2791	0.3184	5008	,	,		8441	0.3919		0.326	False		,,,				2504	0.3957				p.D68D		Atlas-SNP	.											.	STON1	100	.	0			c.T204C						PASS	.	C	,,,,	1316,3090	697.2+/-406.2	195,926,1082	123.0	125.0	124.0		204,204,204,204,204	1.0	0.7	2	dbSNP_107	124	2829,5771	675.3+/-403.2	488,1853,1959	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	683,2779,3041	CC,CT,TT		32.8953,29.8684,31.8699	,,,,	68/1159,68/1136,68/736,68/736,68/1183	48807976	4145,8861	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			TGTAGATTTTTAT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.204T>C	2.37:g.48807976T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	164	86	0.52439	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			T|0.674;C|0.326	0.326	strong		0.507	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60987737	60987737	+	Missense_Mutation	SNP	C	C	T	rs6089366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:60987737C>T	ENST00000252998.1	-	13	1975	c.1819G>A	c.(1819-1821)Gag>Aag	p.E607K		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	607			E -> K (in dbSNP:rs6089366).			extracellular space (GO:0005615)											TGCCCGTGCTCCTGGGTGCAG	0.697													C|||	293	0.0585064	0.0356	0.1196	5008	,	,		17782	0.0		0.1421	False		,,,				2504	0.0204				p.E607K		Atlas-SNP	.											.	.	.	.	0			c.G1819A						PASS	.	C	LYS/GLU	274,4128	150.7+/-184.7	8,258,1935	62.0	63.0	63.0		1819	2.3	0.0	20	dbSNP_114	63	1328,7272	259.5+/-282.7	101,1126,3073	no	missense	C20orf151	NM_080833.2	56	109,1384,5008	TT,TC,CC		15.4419,6.2244,12.3212	possibly-damaging	607/665	60987737	1602,11400	2201	4300	6501	SO:0001583	missense	140893	exon13			CGTGCTCCTGGGT	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.1819G>A	20.37:g.60987737C>T	ENSP00000252998:p.Glu607Lys	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	29	0.630435	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	174	0.07967032967032966	20	0.04065040650406504	51	0.1408839779005525	0	0.0	103	0.1358839050131926	C	11.90	1.778096	0.31502	0.062244	0.154419	ENSG00000130701	ENST00000252998	T	0.21361	2.01	3.31	2.3	0.28687	.	0.749692	0.11067	N	0.603324	T	0.00109	0.0003	L	0.46157	1.445	0.80722	P	0.0	B	0.21452	0.056	B	0.15484	0.013	T	0.16988	-1.0384	9	0.26408	T	0.33	-11.2853	8.7343	0.34519	0.0:0.7644:0.2356:0.0	rs6089366;rs6089366	607	Q8NC74	CT151_HUMAN	K	607	ENSP00000252998:E607K	ENSP00000252998:E607K	E	-	1	0	C20orf151	60421132	0.001000	0.12720	0.004000	0.12327	0.006000	0.05464	0.226000	0.17776	0.645000	0.30675	0.491000	0.48974	GAG	C|0.890;T|0.110	0.110	strong		0.697	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
VDR	7421	hgsc.bcm.edu	37	12	48238757	48238757	+	Silent	SNP	A	A	G	rs731236	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:48238757A>G	ENST00000395324.2	-	10	1324	c.1056T>C	c.(1054-1056)atT>atC	p.I352I	VDR_ENST00000549336.1_Silent_p.I352I|VDR_ENST00000550325.1_Silent_p.I402I|VDR_ENST00000535672.1_Silent_p.I320I|VDR_ENST00000229022.3_Silent_p.I352I			P11473	VDR_HUMAN	vitamin D (1,25- dihydroxyvitamin D3) receptor	352	Ligand-binding.				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)	GGATGGCCTCAATCAGCGCGG	0.642													A|||	1385	0.276558	0.2852	0.255	5008	,	,		16737	0.0675		0.3996	False		,,,				2504	0.3691				p.I402I		Atlas-SNP	.											VDR,NS,carcinoma,0,1	VDR	47	1	0			c.T1206C						scavenged	.	A	,,	1230,3176	427.2+/-341.4	190,850,1163	106.0	111.0	109.0		1056,1056,1206	-7.9	0.0	12	dbSNP_86	109	3392,5208	501.9+/-375.6	679,2034,1587	no	coding-synonymous,coding-synonymous,coding-synonymous	VDR	NM_000376.2,NM_001017535.1,NM_001017536.1	,,	869,2884,2750	GG,GA,AA		39.4419,27.9165,35.5374	,,	352/428,352/428,402/478	48238757	4622,8384	2203	4300	6503	SO:0001819	synonymous_variant	7421	exon10			GGCCTCAATCAGC	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.1056T>C	12.37:g.48238757A>G		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_001017536	B2R5Q1|G3V1V9|Q5PSV3	Silent	SNP	ENST00000395324.2	37	CCDS8757.1																																																																																			A|0.692;G|0.308	0.308	strong		0.642	VDR-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406433.1		
CEACAM18	729767	hgsc.bcm.edu	37	19	51984656	51984656	+	Missense_Mutation	SNP	G	G	A	rs62115071	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:51984656G>A	ENST00000396477.4	+	3	431	c.410G>A	c.(409-411)aGc>aAc	p.S137N	CEACAM18_ENST00000451626.1_Missense_Mutation_p.S198N	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	137										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAGTTGGGAAGCAATCTGGGC	0.527													g|||	674	0.134585	0.0787	0.111	5008	,	,		20642	0.1091		0.1839	False		,,,				2504	0.2025				p.S198N		Atlas-SNP	.											.	CEACAM18	96	.	0			c.G593A						PASS	.	G	ASN/SER	372,3574		19,334,1620	52.0	49.0	50.0		593	-5.3	0.0	19	dbSNP_129	50	1563,6741		148,1267,2737	yes	missense	CEACAM18	NM_001080405.1	46	167,1601,4357	AA,AG,GG		18.8223,9.4273,15.7959	possibly-damaging	198/399	51984656	1935,10315	1973	4152	6125	SO:0001583	missense	729767	exon4			TGGGAAGCAATCT			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.410G>A	19.37:g.51984656G>A	ENSP00000379738:p.Ser137Asn	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	93	32	0.344086	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		274	0.12545787545787546	41	0.08333333333333333	44	0.12154696132596685	56	0.0979020979020979	133	0.17546174142480211	.	5.067	0.197947	0.09652	0.094273	0.188223	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.06142	3.34	2.63	-5.27	0.02763	.	.	.	.	.	T	0.00012	0.0000	M	0.73430	2.235	0.80722	P	0.0	B	0.12013	0.005	B	0.19148	0.024	T	0.41448	-0.9508	8	0.44086	T	0.13	.	1.1296	0.01743	0.3907:0.2791:0.1895:0.1408	rs62115071	198	A8MTB9	CEA18_HUMAN	N	198;137;137	ENSP00000402203:S198N	ENSP00000379738:S137N	S	+	2	0	CEACAM18	56676468	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.583000	0.02115	-1.933000	0.01052	0.558000	0.71614	AGC	G|0.862;A|0.138	0.138	strong		0.527	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
TRAF1	7185	hgsc.bcm.edu	37	9	123688217	123688217	+	Missense_Mutation	SNP	G	G	A	rs34119250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123688217G>A	ENST00000373887.3	-	2	2582	c.137C>T	c.(136-138)cCg>cTg	p.P46L	TRAF1_ENST00000540010.1_Missense_Mutation_p.P46L	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	46					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						ACCTCACCTCGGGTTCTCAGA	0.632													G|||	171	0.0341454	0.0068	0.036	5008	,	,		18352	0.003		0.0567	False		,,,				2504	0.0787				p.P46L		Atlas-SNP	.											.	TRAF1	42	.	0			c.C137T						PASS	.	G	LEU/PRO,LEU/PRO	92,4314	75.7+/-113.9	0,92,2111	51.0	51.0	51.0		137,137	0.2	0.3	9	dbSNP_126	51	566,8034	154.5+/-208.7	27,512,3761	yes	missense,missense	TRAF1	NM_001190945.1,NM_005658.4	98,98	27,604,5872	AA,AG,GG		6.5814,2.0881,5.0592	benign,benign	46/417,46/417	123688217	658,12348	2203	4300	6503	SO:0001583	missense	7185	exon2			CACCTCGGGTTCT	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.137C>T	9.37:g.123688217G>A	ENSP00000362994:p.Pro46Leu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	213	108	0.507042	NM_005658	B4DJ77|Q658U1|Q8NF13	Missense_Mutation	SNP	ENST00000373887.3	37	CCDS6825.1	63	0.028846153846153848	6	0.012195121951219513	13	0.03591160220994475	1	0.0017482517482517483	43	0.05672823218997362	G	4.284	0.051910	0.08291	0.020881	0.065814	ENSG00000056558	ENST00000373887;ENST00000540010	T;T	0.27104	1.69;1.69	5.31	0.251	0.15540	.	0.541665	0.12625	U	0.452676	T	0.00552	0.0018	N	0.01352	-0.895	0.25312	N	0.989199	B	0.02656	0.0	B	0.01281	0.0	T	0.37337	-0.9710	10	0.19147	T	0.46	.	7.7727	0.29019	0.6455:0.0:0.3545:0.0	rs34119250	46	Q13077	TRAF1_HUMAN	L	46	ENSP00000362994:P46L;ENSP00000443183:P46L	ENSP00000362994:P46L	P	-	2	0	TRAF1	122728038	0.050000	0.20438	0.252000	0.24328	0.779000	0.44077	0.266000	0.18534	-0.115000	0.11915	-0.339000	0.08088	CCG	G|0.955;A|0.045	0.045	strong		0.632	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658	
DCHS1	8642	hgsc.bcm.edu	37	11	6652618	6652618	+	Silent	SNP	C	C	T	rs2659871	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6652618C>T	ENST00000299441.3	-	8	4107	c.3696G>A	c.(3694-3696)ccG>ccA	p.P1232P	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1232	Cadherin 12. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAGTGTTCCCGGAGGCACGC	0.542													T|||	2261	0.451478	0.5946	0.415	5008	,	,		22321	0.4325		0.3797	False		,,,				2504	0.3773				p.P1232P		Atlas-SNP	.											DCHS1,colon,carcinoma,0,1	DCHS1	277	1	0			c.G3696A						PASS	.	T		2464,1938	550.9+/-378.2	700,1064,437	159.0	135.0	143.0		3696	4.2	1.0	11	dbSNP_100	143	3321,5271	644.6+/-400.1	637,2047,1612	no	coding-synonymous	DCHS1	NM_003737.2		1337,3111,2049	TT,TC,CC		38.6522,44.0254,44.5205		1232/3299	6652618	5785,7209	2201	4296	6497	SO:0001819	synonymous_variant	8642	exon8			TGTTCCCGGAGGC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.3696G>A	11.37:g.6652618C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	143	57	0.398601	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			C|0.532;T|0.468	0.468	strong		0.542	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
THSD4	79875	hgsc.bcm.edu	37	15	72040774	72040774	+	Silent	SNP	C	C	T	rs1872056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:72040774C>T	ENST00000355327.3	+	14	2390	c.2256C>T	c.(2254-2256)tgC>tgT	p.C752C	THSD4_ENST00000261862.6_Silent_p.C752C|THSD4_ENST00000357769.4_Silent_p.C392C|THSD4_ENST00000567838.1_3'UTR			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	157	0	0		WXS	Illumina HiSeq	Phase_I	147	71	0.482993	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	
LRRC37A2	474170	hgsc.bcm.edu	37	17	44626347	44626347	+	Missense_Mutation	SNP	T	T	C	rs62073349		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44626347T>C	ENST00000576629.1	+	10	4337	c.3842T>C	c.(3841-3843)aTt>aCt	p.I1281T	ARL17A_ENST00000573185.1_Intron|ARL17A_ENST00000445552.2_Intron|ARL17A_ENST00000337845.7_Intron|ARL17A_ENST00000329240.4_Intron|LRRC37A2_ENST00000333412.3_Missense_Mutation_p.I1281T			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	1281			I -> T (in dbSNP:rs62073349). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		GCTATTTCCATTTTAGAAAGT	0.473																																					p.I1281T		Atlas-SNP	.											.	LRRC37A2	37	.	0			c.T3842C						PASS	.	T	THR/ILE,	188,4164		0,188,1988	42.0	72.0	62.0		3842,	0.6	0.1	17	dbSNP_129	62	1695,6885		5,1685,2600	no	missense,intron	ARL17A,LRRC37A2	NM_001006607.2,NM_016632.2	89,	5,1873,4588	CC,CT,TT		19.7552,4.3199,14.5608	benign,	1281/1701,	44626347	1883,11049	2176	4290	6466	SO:0001583	missense	474170	exon9			TTTCCATTTTAGA	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"""c114 SLIT-like testicular protein"""						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.3842T>C	17.37:g.44626347T>C	ENSP00000459551:p.Ile1281Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	259	170	0.656371	NM_001006607	B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	37	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	t	7.146	0.582772	0.13749	0.043199	0.197552	ENSG00000238083	ENST00000333412	T	0.58652	0.32	2.91	0.618	0.17624	.	.	.	.	.	T	0.00073	0.0002	L	0.44542	1.39	0.09310	N	1	B;B;B	0.31680	0.064;0.335;0.025	B;B;B	0.31751	0.012;0.135;0.008	T	0.02115	-1.1211	9	0.37606	T	0.19	.	4.4111	0.11434	0.0:0.3258:0.0:0.6742	.	1281;242;1281	C9JSP5;B3KRJ4;A6NM11	.;.;L37A2_HUMAN	T	1281	ENSP00000333071:I1281T	ENSP00000333071:I1281T	I	+	2	0	LRRC37A2	41981663	0.746000	0.28272	0.099000	0.21106	0.015000	0.08874	0.854000	0.27791	0.341000	0.23771	0.147000	0.16070	ATT	.	.	weak		0.473	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
TECPR1	25851	hgsc.bcm.edu	37	7	97863145	97863145	+	Silent	SNP	G	G	A	rs2291750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97863145G>A	ENST00000447648.2	-	11	1559	c.1260C>T	c.(1258-1260)gtC>gtT	p.V420V	TECPR1_ENST00000379795.3_Silent_p.V420V|TECPR1_ENST00000542604.1_Silent_p.V350V			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	420					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						CTGGTCTCTCGACTTCCGAGG	0.627													G|||	1496	0.298722	0.1982	0.1945	5008	,	,		16414	0.4266		0.2266	False		,,,				2504	0.4509				p.V420V		Atlas-SNP	.											.	TECPR1	77	.	0			c.C1260T						PASS	.	G		829,3477		94,641,1418	12.0	14.0	13.0		1260	-8.9	0.0	7	dbSNP_100	13	1917,6585		238,1441,2572	no	coding-synonymous	TECPR1	NM_015395.1		332,2082,3990	AA,AG,GG		22.5476,19.2522,21.4397		420/1166	97863145	2746,10062	2153	4251	6404	SO:0001819	synonymous_variant	25851	exon11			TCTCTCGACTTCC		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.1260C>T	7.37:g.97863145G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	148	84	0.567568	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			G|0.724;A|0.276	0.276	strong		0.627	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
CMTR2	55783	hgsc.bcm.edu	37	16	71317545	71317545	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71317545T>C	ENST00000338099.5	-	3	2615	c.2279A>G	c.(2278-2280)gAa>gGa	p.E760G	CMTR2_ENST00000434935.2_Missense_Mutation_p.E760G			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	760					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)										GATAATTTCTTCTCTCTCTCT	0.373																																					p.E760G		Atlas-SNP	.											.	FTSJD1	70	.	0			c.A2279G						PASS	.						37.0	41.0	40.0					16																	71317545		2198	4298	6496	SO:0001583	missense	55783	exon3			ATTTCTTCTCTCT	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.2279A>G	16.37:g.71317545T>C	ENSP00000337512:p.Glu760Gly	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866136	0.51588	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.15603	2.41;2.41	5.08	5.08	0.68730	.	0.364292	0.26234	N	0.025558	T	0.11537	0.0281	N	0.14661	0.345	0.27675	N	0.946633	B	0.27498	0.18	B	0.25405	0.06	T	0.15867	-1.0422	10	0.66056	D	0.02	-4.0194	13.2858	0.60243	0.0:0.0:0.0:1.0	.	760	Q8IYT2	FTSJ1_HUMAN	G	760	ENSP00000337512:E760G;ENSP00000411148:E760G	ENSP00000337512:E760G	E	-	2	0	FTSJD1	69875046	1.000000	0.71417	0.981000	0.43875	0.796000	0.44982	3.431000	0.52814	2.213000	0.71641	0.477000	0.44152	GAA	.	.	none		0.373	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
CFLAR	8837	hgsc.bcm.edu	37	2	202025621	202025621	+	Silent	SNP	A	A	G	rs1594	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202025621A>G	ENST00000309955.3	+	9	1775	c.1260A>G	c.(1258-1260)ccA>ccG	p.P420P	CFLAR_ENST00000341582.6_Silent_p.P385P|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000457277.1_Silent_p.P420P|CFLAR_ENST00000443227.1_Silent_p.P324P|CFLAR_ENST00000340870.5_Silent_p.P420P|CFLAR_ENST00000479953.2_Silent_p.P324P|CFLAR_ENST00000423241.2_Silent_p.P420P	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	420	Interaction with TRAF1 and TRAF2.|Interaction with caspase-3.|Interaction with caspase-8 subunits p18 and p10.|Interaction with caspase-8.|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						ACAGCTCACCATCCCTGTACC	0.572													G|||	1997	0.398762	0.4614	0.4035	5008	,	,		18859	0.2569		0.5109	False		,,,				2504	0.3415				p.P420P	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.A1260G						PASS	.	G	,,,,,,	2072,2334	601.9+/-389.8	485,1102,616	45.0	43.0	44.0		1260,525,1155,972,972,972,1260	-11.2	0.0	2	dbSNP_36	44	4425,4175	561.3+/-387.7	1119,2187,994	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	,,,,,,	1604,3289,1610	GG,GA,AA		48.5465,47.0268,49.9539	,,,,,,	420/481,175/236,385/446,324/385,324/367,324/367,420/481	202025621	6497,6509	2203	4300	6503	SO:0001819	synonymous_variant	8837	exon9			CTCACCATCCCTG	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.1260A>G	2.37:g.202025621A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	98	35	0.357143	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																																																																																			A|0.549;G|0.451	0.451	strong		0.572	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229948	87229948	+	Silent	SNP	T	T	A	rs4621787	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	66	0	0		WXS	Illumina HiSeq	Phase_I	72	25	0.347222	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	
FRAS1	80144	hgsc.bcm.edu	37	4	79300993	79300993	+	Missense_Mutation	SNP	G	G	A	rs12512164	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79300993G>A	ENST00000325942.6	+	27	3846	c.3406G>A	c.(3406-3408)Gaa>Aaa	p.E1136K	FRAS1_ENST00000264895.6_Missense_Mutation_p.E1136K	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1136			E -> K (in dbSNP:rs12512164).		cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.E1136K(4)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GGGTAGGGTCGAAGATCTCCT	0.483													G|||	1068	0.213259	0.1195	0.3487	5008	,	,		19674	0.2173		0.2704	False		,,,				2504	0.181				p.E1136K		Atlas-SNP	.											FRAS1_ENST00000325942,NS,carcinoma,0,3	FRAS1	779	3	4	Substitution - Missense(4)	prostate(4)	c.G3406A						PASS	.	G	LYS/GLU,LYS/GLU	560,3214		46,468,1373	84.0	81.0	82.0		3406,3406	3.5	0.8	4	dbSNP_120	82	2256,5954		308,1640,2157	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	56,56	354,2108,3530	AA,AG,GG		27.4787,14.8384,23.498	benign,benign	1136/1977,1136/4013	79300993	2816,9168	1887	4105	5992	SO:0001583	missense	80144	exon27			AGGGTCGAAGATC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.3406G>A	4.37:g.79300993G>A	ENSP00000326330:p.Glu1136Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	510	0.23351648351648352	63	0.12804878048780488	115	0.31767955801104975	125	0.21853146853146854	207	0.27308707124010556	G	3.779	-0.046038	0.07452	0.148384	0.274787	ENSG00000138759	ENST00000325942;ENST00000264895	T;T	0.76186	-1.0;-1.0	5.63	3.55	0.40652	.	0.341617	0.29348	N	0.012411	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	1.0000000000287557E-6	P;P	0.45986	0.867;0.87	B;B	0.30716	0.085;0.119	T	0.21042	-1.0257	9	0.23302	T	0.38	.	7.925	0.29870	0.1533:0.1598:0.6869:0.0	rs12512164;rs17460067;rs52813123;rs60971831;rs12512164	1136;1136	E9PHH6;A2RRR8	.;.	K	1136	ENSP00000326330:E1136K;ENSP00000264895:E1136K	ENSP00000264895:E1136K	E	+	1	0	FRAS1	79520017	1.000000	0.71417	0.837000	0.33122	0.031000	0.12232	3.882000	0.56160	1.351000	0.45789	0.591000	0.81541	GAA	G|0.776;A|0.224	0.224	strong		0.483	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
ZDHHC11	79844	hgsc.bcm.edu	37	5	843815	843815	+	Silent	SNP	C	C	T	rs71591190	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:843815C>T	ENST00000283441.8	-	4	911	c.528G>A	c.(526-528)tcG>tcA	p.S176S	ZDHHC11_ENST00000511539.1_5'UTR|ZDHHC11_ENST00000503758.2_5'Flank|ZDHHC11_ENST00000424784.2_Silent_p.S176S	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	176						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)			CAGCTGTGGCCGAGGCCACAG	0.667																																					p.S176S		Atlas-SNP	.											ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	0			c.G528A						PASS	.						27.0	22.0	23.0					5																	843815		2199	4276	6475	SO:0001819	synonymous_variant	79844	exon4			TGTGGCCGAGGCC	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.528G>A	5.37:g.843815C>T		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	399	98	0.245614	NM_024786	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																			C|0.856;T|0.144	0.144	strong		0.667	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
MUC5B	727897	hgsc.bcm.edu	37	11	1264767	1264767	+	Silent	SNP	G	G	A	rs2943501	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1264767G>A	ENST00000529681.1	+	31	6715	c.6657G>A	c.(6655-6657)tcG>tcA	p.S2219S	MUC5B_ENST00000447027.1_Silent_p.S2222S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2219	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGGCCACCTCGGGCATCTTGG	0.652																																					p.S2219S		Atlas-SNP	.											MUC5B,NS,neuroblastoma,0,2	MUC5B	473	2	0			c.G6657A						scavenged	.						86.0	102.0	97.0					11																	1264767		2068	4181	6249	SO:0001819	synonymous_variant	727897	exon31			CACCTCGGGCATC	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.6657G>A	11.37:g.1264767G>A		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	404	26	0.0643564	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	weak		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
BANP	54971	hgsc.bcm.edu	37	16	88052146	88052146	+	Silent	SNP	C	C	T	rs17850504	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:88052146C>T	ENST00000393207.1	+	7	965	c.744C>T	c.(742-744)gcC>gcT	p.A248A	BANP_ENST00000393208.2_Silent_p.A217A|BANP_ENST00000355163.5_Silent_p.A223A|BANP_ENST00000479780.2_Silent_p.A217A|BANP_ENST00000538234.1_Silent_p.A256A|BANP_ENST00000286122.7_Silent_p.A248A|BANP_ENST00000355022.4_Silent_p.A217A	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	248	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.|Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		GCCGCACGGCCGAGAAGATGG	0.647													c|||	260	0.0519169	0.0061	0.1037	5008	,	,		19807	0.003		0.1153	False		,,,				2504	0.0624				p.A256A		Atlas-SNP	.											.	BANP	67	.	0			c.C768T						PASS	.	C	,,,,,,	113,4281	84.4+/-122.9	1,111,2085	55.0	44.0	48.0		768,669,651,768,744,651,651	-2.1	1.0	16	dbSNP_123	48	1129,7471	231.2+/-265.3	74,981,3245	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	,,,,,,	75,1092,5330	TT,TC,CC		13.1279,2.5717,9.5583	,,,,,,	256/506,223/498,217/467,256/509,248/520,217/470,217/492	88052146	1242,11752	2197	4300	6497	SO:0001819	synonymous_variant	54971	exon7			CACGGCCGAGAAG	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.744C>T	16.37:g.88052146C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			C|0.922;T|0.078	0.078	strong		0.647	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
PPP1R1C	151242	hgsc.bcm.edu	37	2	182981968	182981968	+	Silent	SNP	A	A	G	rs1882212	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:182981968A>G	ENST00000409137.3	+	5	519	c.276A>G	c.(274-276)gcA>gcG	p.A92A	PPP1R1C_ENST00000475249.1_Intron|PPP1R1C_ENST00000409702.1_Silent_p.A92A|PPP1R1C_ENST00000452904.1_Silent_p.A92A|PPP1R1C_ENST00000280295.3_Silent_p.A99A	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	303	0	0		WXS	Illumina HiSeq	Phase_I	289	289	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	
UPK3BL	100134938	hgsc.bcm.edu	37	7	102279601	102279601	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:102279601G>T	ENST00000340457.8	-	4	580	c.531C>A	c.(529-531)acC>acA	p.T177T	POLR2J2_ENST00000476151.1_3'UTR|RP11-514P8.6_ENST00000519541.1_Silent_p.T177T|POLR2J2_ENST00000591000.1_3'UTR	NM_001114403.2	NP_001107875.1	B0FP48	UPK3L_HUMAN	uroplakin 3B-like	177						integral component of membrane (GO:0016021)		p.T177T(2)		kidney(2)|stomach(1)	3						TGGACCACTTGGTTTCAGCCA	0.622																																					p.T177T		Atlas-SNP	.											UPK3BL,NS,carcinoma,0,2	UPK3BL	6	2	2	Substitution - coding silent(2)	kidney(2)	c.C531A						scavenged	.						126.0	79.0	93.0					7																	102279601		691	1582	2273	SO:0001819	synonymous_variant	100134938	exon4			CCACTTGGTTTCA	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.531C>A	7.37:g.102279601G>T		Somatic	760	0	0		WXS	Illumina HiSeq	Phase_I	460	26	0.0565217	NM_001114403		Silent	SNP	ENST00000340457.8	37	CCDS47675.1																																																																																			G|0.500;T|0.500	0.500	weak		0.622	UPK3BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381510.1	NM_001114403	
LILRA6	79168	hgsc.bcm.edu	37	19	54744387	54744387	+	Missense_Mutation	SNP	C	C	T	rs71263238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:54744387C>T	ENST00000396365.2	-	6	1060	c.1021G>A	c.(1021-1023)Gtg>Atg	p.V341M	LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.V341M|LILRA6_ENST00000419410.2_Missense_Mutation_p.V341M|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	341	Ig-like C2-type 2.				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)		AGCAGGGTCACGTTCTCTCCT	0.582																																					p.V341M		Atlas-SNP	.											.	LILRA6	75	.	0			c.G1021A						PASS	.	C	MET/VAL	1667,2543		384,899,822	40.0	57.0	51.0		1021	1.1	0.4	19	dbSNP_130	51	3076,5426		408,2260,1583	yes	missense	LILRA6	NM_024318.2	21	792,3159,2405	TT,TC,CC		36.1797,39.5962,37.3112		341/482	54744387	4743,7969	2105	4251	6356	SO:0001583	missense	79168	exon6			GGGTCACGTTCTC	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.1021G>A	19.37:g.54744387C>T	ENSP00000379651:p.Val341Met	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	168	126	0.75	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	744	0.34065934065934067	195	0.39634146341463417	123	0.3397790055248619	162	0.28321678321678323	264	0.3482849604221636	C	13.36	2.213853	0.39102	0.395962	0.361797	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.01215	5.16;5.16;5.16	2.16	1.1	0.20463	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	1.027150	0.07816	N	0.958912	T	0.00012	0.0000	M	0.86651	2.83	0.31233	P	0.696064	D;D;D	0.89917	1.0;0.974;1.0	P;P;D	0.83275	0.906;0.703;0.996	T	0.44877	-0.9299	9	0.48119	T	0.1	.	4.6406	0.12546	0.0:0.8064:0.0:0.1936	.	341;341;341	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	M	341	ENSP00000411227:V341M;ENSP00000379651:V341M;ENSP00000245621:V341M	ENSP00000245621:V341M	V	-	1	0	LILRA6	59436199	0.006000	0.16342	0.448000	0.26945	0.180000	0.23129	0.793000	0.26944	0.470000	0.27294	0.195000	0.17529	GTG	C|0.659;T|0.341	0.341	strong		0.582	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
PNPLA5	150379	hgsc.bcm.edu	37	22	44287062	44287062	+	Silent	SNP	A	A	G	rs2071884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:44287062A>G	ENST00000597664.1	-	2	435	c.306T>C	c.(304-306)gaT>gaC	p.D102D	PNPLA5_ENST00000216177.4_Silent_p.D102D|PNPLA5_ENST00000593866.1_Intron|PNPLA5_ENST00000381198.2_Intron			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	102	Patatin.				lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GGGGCAGAGCATCCTGCAGCT	0.667													G|||	1773	0.354034	0.2027	0.3242	5008	,	,		14974	0.4335		0.3877	False		,,,				2504	0.4632				p.D102D		Atlas-SNP	.											PNPLA5,NS,carcinoma,0,3	PNPLA5	46	3	0			c.T306C						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	148	0	0		WXS	Illumina HiSeq	Phase_I	197	99	0.502538	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	
SCFD2	152579	hgsc.bcm.edu	37	4	54011526	54011526	+	Missense_Mutation	SNP	A	A	G	rs7675987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:54011526A>G	ENST00000401642.3	-	5	1668	c.1535T>C	c.(1534-1536)tTg>tCg	p.L512S	SCFD2_ENST00000388940.4_Missense_Mutation_p.L512S	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	512			L -> S (in dbSNP:rs7675987).		protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CAAAGGTGACAATCCAGATTC	0.403													A|||	1266	0.252796	0.1906	0.2781	5008	,	,		20849	0.2143		0.3907	False		,,,				2504	0.2168				p.L512S		Atlas-SNP	.											.	SCFD2	78	.	0			c.T1535C						PASS	.	A	SER/LEU	942,3464	358.9+/-314.6	111,720,1372	146.0	130.0	135.0		1535	4.8	0.9	4	dbSNP_116	135	3162,5438	479.6+/-370.2	598,1966,1736	yes	missense	SCFD2	NM_152540.3	145	709,2686,3108	GG,GA,AA		36.7674,21.3799,31.5547	probably-damaging	512/685	54011526	4104,8902	2203	4300	6503	SO:0001583	missense	152579	exon5			GGTGACAATCCAG	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1535T>C	4.37:g.54011526A>G	ENSP00000384182:p.Leu512Ser	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	189	76	0.402116	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	599	0.2742673992673993	92	0.18699186991869918	102	0.281767955801105	102	0.17832167832167833	303	0.3997361477572559	A	12.45	1.942212	0.34283	0.213799	0.367674	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.80393	-1.37;-1.32	4.81	4.81	0.61882	.	0.000000	0.56097	D	0.000029	T	0.00012	0.0000	M	0.61703	1.905	0.27248	P	0.9589737	D;D	0.89917	0.999;1.0	D;D	0.72982	0.976;0.979	T	0.26052	-1.0114	9	0.22109	T	0.4	.	10.8679	0.46866	0.9232:0.0:0.0768:0.0	rs7675987;rs17703439;rs52828053;rs60150787;rs7675987	512;512	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	S	512	ENSP00000384182:L512S;ENSP00000373592:L512S	ENSP00000373592:L512S	L	-	2	0	SCFD2	53706283	0.558000	0.26554	0.914000	0.36105	0.160000	0.22226	2.669000	0.46825	2.142000	0.66516	0.460000	0.39030	TTG	A|0.710;G|0.290	0.290	strong		0.403	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
MUC16	94025	hgsc.bcm.edu	37	19	9049149	9049149	+	Missense_Mutation	SNP	G	G	A	rs12461007	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9049149G>A	ENST00000397910.4	-	5	32685	c.32482C>T	c.(32482-32484)Cct>Tct	p.P10828S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10830	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTGTGCAGGATGCGTGACC	0.483													G|||	997	0.199081	0.1982	0.2695	5008	,	,		23097	0.0258		0.2813	False		,,,				2504	0.2444				p.P10828S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C32482T						PASS	.		SER/PRO	750,3182		72,606,1288	172.0	156.0	161.0		32482	-6.0	0.0	19	dbSNP_120	161	2519,5795		401,1717,2039	yes	missense	MUC16	NM_024690.2	74	473,2323,3327	AA,AG,GG		30.2983,19.0743,26.6944	benign	10828/14508	9049149	3269,8977	1966	4157	6123	SO:0001583	missense	94025	exon5			GTGCAGGATGCGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32482C>T	19.37:g.9049149G>A	ENSP00000381008:p.Pro10828Ser	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	169	92	0.544379	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	426	0.19505494505494506	103	0.20934959349593496	95	0.26243093922651933	11	0.019230769230769232	217	0.2862796833773087	g	5.293	0.239478	0.10023	0.190743	0.302983	ENSG00000181143	ENST00000397910	T	0.03124	4.04	3.0	-5.99	0.02213	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.20052	0.041	B	0.15870	0.014	T	0.50466	-0.8825	8	0.87932	D	0	.	6.055	0.19807	0.3575:0.1554:0.487:0.0	rs12461007;rs52811941;rs61073913;rs12461007	10828	B5ME49	.	S	10828	ENSP00000381008:P10828S	ENSP00000381008:P10828S	P	-	1	0	MUC16	8910149	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	-0.091000	0.11146	-1.512000	0.01791	-0.633000	0.03987	CCT	G|0.783;A|0.217	0.217	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FLG2	388698	hgsc.bcm.edu	37	1	152327667	152327667	+	Silent	SNP	C	C	T	rs12738471	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152327667C>T	ENST00000388718.5	-	3	2667	c.2595G>A	c.(2593-2595)tcG>tcA	p.S865S	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	865	Ser-rich.				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)			ATGTCTGTCCCGAACTTGACC	0.502													c|||	787	0.157149	0.0091	0.2565	5008	,	,		24019	0.3373		0.0696	False		,,,				2504	0.1912				p.S865S		Atlas-SNP	.											FLG2,rectum,carcinoma,0,2	FLG2	431	2	0			c.G2595A						scavenged	.						377.0	328.0	344.0					1																	152327667		2203	4294	6497	SO:0001819	synonymous_variant	388698	exon3			CTGTCCCGAACTT	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.2595G>A	1.37:g.152327667C>T		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	106	11	0.103774	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			C|0.500;T|0.500	0.500	strong		0.502	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
TLL2	7093	hgsc.bcm.edu	37	10	98133483	98133483	+	Silent	SNP	G	G	A	rs61741039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:98133483G>A	ENST00000357947.3	-	19	2757	c.2532C>T	c.(2530-2532)gcC>gcT	p.A844A		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	844	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)		CCAGAATGGGGGCCAGGCTGT	0.552													G|||	766	0.152955	0.1611	0.1282	5008	,	,		18795	0.0933		0.1451	False		,,,				2504	0.229				p.A844A		Atlas-SNP	.											.	TLL2	122	.	0			c.C2532T						PASS	.	G		673,3733	282.5+/-276.6	42,589,1572	57.0	61.0	60.0		2532	1.9	1.0	10	dbSNP_129	60	1204,7396	242.8+/-272.6	81,1042,3177	no	coding-synonymous	TLL2	NM_012465.3		123,1631,4749	AA,AG,GG		14.0,15.2746,14.4318		844/1016	98133483	1877,11129	2203	4300	6503	SO:0001819	synonymous_variant	7093	exon19			AATGGGGGCCAGG	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.2532C>T	10.37:g.98133483G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Silent	SNP	ENST00000357947.3	37	CCDS7449.1																																																																																			G|0.865;A|0.135	0.135	strong		0.552	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1		
YWHAG	7532	hgsc.bcm.edu	37	7	75959188	75959188	+	Silent	SNP	G	G	A	rs2072435	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:75959188G>A	ENST00000307630.3	-	2	672	c.450C>T	c.(448-450)tcC>tcT	p.S150S		NM_012479.3	NP_036611.2	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma	150					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of neuron differentiation (GO:0045664)|regulation of signal transduction (GO:0009966)|regulation of synaptic plasticity (GO:0048167)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	insulin-like growth factor receptor binding (GO:0005159)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)|protein kinase C inhibitor activity (GO:0008426)			endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8						AGGCCTTCTCGGAGGACTCCA	0.562													G|||	1565	0.3125	0.329	0.2896	5008	,	,		17236	0.4454		0.2982	False		,,,				2504	0.184				p.S150S		Atlas-SNP	.											.	YWHAG	24	.	0			c.C450T						PASS	.	G		1334,3072	448.1+/-348.6	198,938,1067	148.0	151.0	150.0		450	-10.8	0.1	7	dbSNP_96	150	2450,6150	405.0+/-348.4	351,1748,2201	no	coding-synonymous	YWHAG	NM_012479.3		549,2686,3268	AA,AG,GG		28.4884,30.2769,29.0943		150/248	75959188	3784,9222	2203	4300	6503	SO:0001819	synonymous_variant	7532	exon2			CTTCTCGGAGGAC	AF142498	CCDS5584.1	7q11.23	2014-06-13	2013-12-03		ENSG00000170027	ENSG00000170027			12852	protein-coding gene	gene with protein product	"""14-3-3 gamma"", ""protein phosphatase 1, regulatory subunit 170"""	605356	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"""			10486217, 10433554	Standard	NM_012479		Approved	PPP1R170	uc011kgj.1	P61981	OTTHUMG00000022862	ENST00000307630.3:c.450C>T	7.37:g.75959188G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_012479	O70457|P35214|Q6FH52|Q9UDP2|Q9UN99	Silent	SNP	ENST00000307630.3	37	CCDS5584.1																																																																																			G|0.697;A|0.303	0.303	strong		0.562	YWHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253002.1	NM_012479	
FMO3	2328	hgsc.bcm.edu	37	1	171083242	171083242	+	Missense_Mutation	SNP	A	A	G	rs2266780	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:171083242A>G	ENST00000367755.4	+	7	1034	c.923A>G	c.(922-924)gAg>gGg	p.E308G	FMO3_ENST00000392085.2_Missense_Mutation_p.E308G|FMO3_ENST00000538429.1_Missense_Mutation_p.E245G|FMO3_ENST00000542847.1_Missense_Mutation_p.E288G	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	308			E -> G (16% reduction in catalytic efficiency toward trimethylamine and 40% increase toward benzydamine and methyl p- tolyl sulfide; dbSNP:rs2266780). {ECO:0000269|PubMed:10479479, ECO:0000269|PubMed:17050781, ECO:0000269|PubMed:9536088, ECO:0000269|Ref.4}.		drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	GAATTCACAGAGACCTCGGCC	0.463													A|||	458	0.0914537	0.0189	0.0821	5008	,	,		19038	0.1687		0.172	False		,,,				2504	0.0337				p.E308G		Atlas-SNP	.											.	FMO3	73	.	0			c.A923G	GRCh37	CM992885	FMO3	M	rs2266780	PASS	.	A	GLY/GLU,GLY/GLU	189,4217	118.8+/-156.5	6,177,2020	149.0	131.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	923,923	3.6	1.0	1	dbSNP_100	137	1619,6981	300.5+/-305.0	157,1305,2838	yes	missense,missense	FMO3	NM_001002294.2,NM_006894.5	98,98	163,1482,4858	GG,GA,AA		18.8256,4.2896,13.9013	benign,benign	308/533,308/533	171083242	1808,11198	2203	4300	6503	SO:0001583	missense	2328	exon7			TCACAGAGACCTC	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.923A>G	1.37:g.171083242A>G	ENSP00000356729:p.Glu308Gly	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	215	104	0.483721	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	283	0.1295787545787546	9	0.018292682926829267	29	0.08011049723756906	106	0.1853146853146853	139	0.18337730870712401	A	15.62	2.887923	0.52014	0.042896	0.188256	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.62498	0.02;0.02;0.02;0.02	4.73	3.58	0.41010	.	0.153914	0.64402	D	0.000020	T	0.57213	0.2038	L	0.45470	1.425	0.20403	P	0.9999083861	D;P;P	0.89917	1.0;0.713;0.939	D;P;P	0.80764	0.994;0.673;0.859	T	0.55976	-0.8055	9	0.18710	T	0.47	-22.3006	11.4047	0.49892	0.8481:0.1519:0.0:0.0	rs2266780;rs17564742;rs57076237;rs2266780	245;288;308	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	G	308;308;288;245	ENSP00000356729:E308G;ENSP00000375935:E308G;ENSP00000444073:E288G;ENSP00000439500:E245G	ENSP00000356729:E308G	E	+	2	0	FMO3	169349866	1.000000	0.71417	0.959000	0.39883	0.591000	0.36615	5.276000	0.65580	0.728000	0.32382	0.528000	0.53228	GAG	A|0.877;G|0.123	0.123	strong		0.463	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
PZP	5858	hgsc.bcm.edu	37	12	9312951	9312951	+	Missense_Mutation	SNP	G	G	A	rs57006764	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:9312951G>A	ENST00000261336.2	-	24	3036	c.3008C>T	c.(3007-3009)aCg>aTg	p.T1003M	PZP_ENST00000381997.2_Missense_Mutation_p.T789M|PZP_ENST00000539983.1_5'Flank	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	124	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	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	
OR9G1	390174	hgsc.bcm.edu	37	11	56468440	56468440	+	Missense_Mutation	SNP	G	G	T	rs397849038|rs12421330		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56468440G>T	ENST00000312153.1	+	1	577	c.577G>T	c.(577-579)Ggc>Tgc	p.G193C		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CGAGAAGGGCGGCTATAAAAT	0.478																																					p.G193C		Atlas-SNP	.											.	.	.	.	0			c.G577T						PASS	.						117.0	118.0	118.0					11																	56468440		2201	4296	6497	SO:0001583	missense	504191	exon1			AAGGGCGGCTATA	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.577G>T	11.37:g.56468440G>T	ENSP00000309012:p.Gly193Cys	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	202	29	0.143564	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	G	5.488	0.275107	0.10403	.	.	ENSG00000174914	ENST00000312153	T	0.00091	8.74	4.52	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.649761	0.14366	N	0.324095	T	0.00241	0.0007	L	0.28400	0.85	0.09310	N	1	P	0.46859	0.885	P	0.62184	0.899	T	0.56208	-0.8017	10	0.72032	D	0.01	-12.3577	8.9994	0.36072	0.2548:0.0:0.7452:0.0	rs12421330	193	Q8NH87	OR9G1_HUMAN	C	193	ENSP00000309012:G193C	ENSP00000309012:G193C	G	+	1	0	OR9G1	56225016	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-1.080000	0.03407	0.630000	0.30394	-1.202000	0.01658	GGC	G|0.625;T|0.375	0.375	strong		0.478	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
BDP1	55814	hgsc.bcm.edu	37	5	70858342	70858342	+	Missense_Mutation	SNP	A	A	G	rs34246164|rs115185087	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:70858342A>G	ENST00000358731.4	+	38	8001	c.7738A>G	c.(7738-7740)Act>Gct	p.T2580A	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	2580				T -> A (in Ref. 6; CAE46010). {ECO:0000305}.	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)		CAGCTCAGCAACTCAGGTATG	0.343													.|||	184	0.0367412	0.0015	0.1354	5008	,	,		18275	0.001		0.0507	False		,,,				2504	0.0368				p.T2580A		Atlas-SNP	.											.	BDP1	204	.	0			c.A7738G						PASS	.	A	ALA/THR	48,3638		1,46,1796	88.0	81.0	83.0		7738	-11.3	0.0	5	dbSNP_132	83	406,7776		9,388,3694	yes	missense	BDP1	NM_018429.2	58	10,434,5490	GG,GA,AA		4.9621,1.3022,3.8254	benign	2580/2625	70858342	454,11414	1843	4091	5934	SO:0001583	missense	55814	exon38			TCAGCAACTCAGG	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.7738A>G	5.37:g.70858342A>G	ENSP00000351575:p.Thr2580Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	84	0.038461538461538464	2	0.0040650406504065045	48	0.13259668508287292	0	0.0	34	0.044854881266490766	A	0.715	-0.785678	0.02907	0.013022	0.049621	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.03468	3.92	5.75	-11.3	0.00108	.	1.038050	0.07595	N	0.922731	T	0.00039	0.0001	N	0.10837	0.055	0.36621	D	0.875773	B	0.06786	0.001	B	0.06405	0.002	T	0.46233	-0.9206	10	0.02654	T	1	.	11.1616	0.48518	0.1176:0.1005:0.6896:0.0923	.	2580	A6H8Y1	BDP1_HUMAN	A	2580;2128	ENSP00000351575:T2580A	ENSP00000351575:T2580A	T	+	1	0	BDP1	70894098	0.001000	0.12720	0.002000	0.10522	0.126000	0.20510	-1.312000	0.02720	-1.884000	0.01119	-0.256000	0.11100	ACT	A|0.956;G|0.044	0.044	strong		0.343	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
C19orf45	374877	hgsc.bcm.edu	37	19	7573301	7573301	+	Silent	SNP	C	C	T	rs1133380|rs113917984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:7573301C>T	ENST00000361664.2	+	9	1644	c.1503C>T	c.(1501-1503)tgC>tgT	p.C501C	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	501										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						TGTACCTGTGCCCCAGCCAGC	0.607													C|||	1199	0.239417	0.1725	0.3285	5008	,	,		17982	0.1756		0.337	False		,,,				2504	0.2321				p.C501C		Atlas-SNP	.											.	C19orf45	36	.	0			c.C1503T						PASS	.	C		814,3590		90,634,1478	25.0	24.0	24.0		1503	1.5	1.0	19	dbSNP_86	24	2762,5838		459,1844,1997	no	coding-synonymous	C19orf45	NM_198534.2		549,2478,3475	TT,TC,CC		32.1163,18.4832,27.4992		501/506	7573301	3576,9428	2202	4300	6502	SO:0001819	synonymous_variant	374877	exon9			CCTGTGCCCCAGC	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.1503C>T	19.37:g.7573301C>T		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_198534	Q8N115	Silent	SNP	ENST00000361664.2	37	CCDS12179.2																																																																																			.	.	weak		0.607	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
ZNF544	27300	hgsc.bcm.edu	37	19	58772579	58772579	+	Missense_Mutation	SNP	C	C	G	rs6510130	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58772579C>G	ENST00000596652.1	+	6	841	c.607C>G	c.(607-609)Cat>Gat	p.H203D	CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000269829.4_Missense_Mutation_p.H203D|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000600044.1_Missense_Mutation_p.H175D|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000599953.1_Missense_Mutation_p.H61D|ZNF544_ENST00000600220.1_Missense_Mutation_p.H175D|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000415203.2_Missense_Mutation_p.H175D			Q6NX49	ZN544_HUMAN	zinc finger protein 544	203			H -> D (in dbSNP:rs6510130).		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(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|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;0.17)|GBM - Glioblastoma multiforme(193;0.018)		TTTCATTAATCATGAGAAAAA	0.383													C|||	408	0.0814696	0.1944	0.1182	5008	,	,		21501	0.0258		0.0219	False		,,,				2504	0.0215				p.H203D		Atlas-SNP	.											.	ZNF544	57	.	0			c.C607G						PASS	.	C	ASP/HIS	659,3747	274.9+/-272.2	52,555,1596	58.0	57.0	57.0		607	0.7	0.2	19	dbSNP_116	57	171,8427	77.2+/-139.8	1,169,4129	yes	missense	ZNF544	NM_014480.2	81	53,724,5725	GG,GC,CC		1.9888,14.9569,6.3827	possibly-damaging	203/716	58772579	830,12174	2203	4299	6502	SO:0001583	missense	27300	exon7			ATTAATCATGAGA	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"""Zinc fingers, C2H2-type"", ""-"""	16759	protein-coding gene	gene with protein product	"""zinc finger protein AF020591"""						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.607C>G	19.37:g.58772579C>G	ENSP00000469635:p.His203Asp	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	154	71	0.461039	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	173	0.07921245421245421	110	0.22357723577235772	31	0.0856353591160221	15	0.026223776223776224	17	0.022427440633245383	C	11.45	1.642517	0.29246	0.149569	0.019888	ENSG00000198131	ENST00000269829;ENST00000415203	T;T	0.08546	3.19;3.08	3.25	0.716	0.18191	.	.	.	.	.	T	0.00012	0.0000	M	0.79475	2.455	0.40515	P	0.019228000000000023	D;B	0.58970	0.984;0.348	P;B	0.53809	0.735;0.248	T	0.21930	-1.0231	8	0.62326	D	0.03	.	5.6233	0.17469	0.2007:0.4363:0.363:0.0	rs6510130;rs52833823;rs6510130	175;203	B4DL50;Q6NX49	.;ZN544_HUMAN	D	203;175	ENSP00000269829:H203D;ENSP00000394341:H175D	ENSP00000269829:H203D	H	+	1	0	ZNF544	63464391	0.002000	0.14202	0.233000	0.24025	0.101000	0.19017	0.312000	0.19397	0.654000	0.30846	0.655000	0.94253	CAT	C|0.935;G|0.065	0.065	strong		0.383	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480	
MUC2	4583	hgsc.bcm.edu	37	11	1081141	1081141	+	Splice_Site	SNP	C	C	T	rs41375149	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1081141C>T	ENST00000441003.2	+	11	1464	c.1437C>T	c.(1435-1437)acC>acT	p.T479T	MUC2_ENST00000359061.5_Splice_Site_p.T479T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	479	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCCACGTGACCGGTGAGTTGT	0.657													C|||	283	0.0565096	0.0408	0.0461	5008	,	,		16341	0.0506		0.0934	False		,,,				2504	0.0532				p.T479T		Atlas-SNP	.											.	MUC2	614	.	0			c.C1437T						PASS	.	C		167,3805		4,159,1823	31.0	37.0	35.0		1437	-7.3	0.6	11	dbSNP_127	35	744,7582		33,678,3452	yes	coding-synonymous-near-splice	MUC2	NM_002457.2		37,837,5275	TT,TC,CC		8.9359,4.2044,7.4077		479/2813	1081141	911,11387	1986	4163	6149	SO:0001630	splice_region_variant	4583	exon11			CGTGACCGGTGAG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.1438+1C>T	11.37:g.1081141C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.939;T|0.061	0.061	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Silent
FAM83H	286077	hgsc.bcm.edu	37	8	144810322	144810322	+	Missense_Mutation	SNP	G	G	A	rs28573699	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144810322G>A	ENST00000388913.3	-	5	1434	c.1309C>T	c.(1309-1311)Cac>Tac	p.H437Y		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	437					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TCGTCGCCGTGGCTGAGGAAC	0.701													G|||	270	0.0539137	0.003	0.0605	5008	,	,		6022	0.0734		0.0924	False		,,,				2504	0.0583				p.H437Y		Atlas-SNP	.											.	FAM83H	68	.	0			c.C1309T						PASS	.	G	TYR/HIS	49,4203		1,47,2078	21.0	33.0	29.0		1309	3.2	0.1	8	dbSNP_125	29	528,7894		22,484,3705	yes	missense	FAM83H	NM_198488.3	83	23,531,5783	AA,AG,GG		6.2693,1.1524,4.5526	possibly-damaging	437/1180	144810322	577,12097	2126	4211	6337	SO:0001583	missense	286077	exon5			CGCCGTGGCTGAG	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1309C>T	8.37:g.144810322G>A	ENSP00000373565:p.His437Tyr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	131	0.059981684981684984	2	0.0040650406504065045	26	0.0718232044198895	34	0.05944055944055944	69	0.09102902374670185	g	10.52	1.372294	0.24857	0.011524	0.062693	ENSG00000180921	ENST00000388913	T	0.15834	2.39	4.96	3.16	0.36331	.	0.881947	0.09529	N	0.789796	T	0.00524	0.0017	L	0.27053	0.805	0.22112	N	0.999359	D	0.59357	0.985	P	0.49799	0.622	T	0.17868	-1.0355	10	0.20519	T	0.43	.	5.0497	0.14501	0.171:0.0:0.5748:0.2542	rs28573699	437	Q6ZRV2	FA83H_HUMAN	Y	437	ENSP00000373565:H437Y	ENSP00000373565:H437Y	H	-	1	0	FAM83H	144882310	1.000000	0.71417	0.055000	0.19348	0.021000	0.10359	3.004000	0.49513	0.491000	0.27793	-0.300000	0.09419	CAC	G|0.940;A|0.060	0.060	strong		0.701	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
GSTT2	2953	hgsc.bcm.edu	37	22	24325062	24325062	+	Splice_Site	SNP	G	G	A	rs2301423	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:24325062G>A	ENST00000215780.5	+	4	402	c.352G>A	c.(352-354)Gtg>Atg	p.V118M	DDT_ENST00000404092.1_5'Flank|GSTT2_ENST00000402588.3_Splice_Site_p.V118M	NM_000854.3	NP_000845.1	P0CG29	GST2_HUMAN	glutathione S-transferase theta 2	118	GST C-terminal.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			lung(1)	1						CCCCCATCAGGTGTTGGGGCC	0.607																																					p.V118M		Atlas-SNP	.											.	GSTT2	3	.	0			c.G352A						PASS	.	G	MET/VAL	149,4255		2,145,2055	51.0	48.0	49.0		352	0.6	0.0	22	dbSNP_131	49	1352,7244		45,1262,2991	no	missense-near-splice	GSTT2	NM_000854.3	21	47,1407,5046	AA,AG,GG		15.7282,3.3833,11.5462	possibly-damaging	118/245	24325062	1501,11499	2202	4298	6500	SO:0001630	splice_region_variant	2953	exon4			CATCAGGTGTTGG	L38503		22q11.23	2012-06-21			ENSG00000099984	ENSG00000099984	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4642	protein-coding gene	gene with protein product		600437				7789971, 9729470	Standard	NM_000854		Approved		uc002zyw.4	P0CG29	OTTHUMG00000150786	ENST00000215780.5:c.352-1G>A	22.37:g.24325062G>A		Somatic	522	0	0		WXS	Illumina HiSeq	Phase_I	728	333	0.457418	NM_000854	O60665|P30712|Q6IPV7|Q9HD76	Missense_Mutation	SNP	ENST00000215780.5	37	CCDS13821.1	350	0.16025641025641027	4	0.008130081300813009	52	0.143646408839779	167	0.291958041958042	127	0.16754617414248021	g	7.443	0.641125	0.14386	0.033833	0.157282	ENSG00000099984	ENST00000215780;ENST00000402588	T;T	0.18810	2.19;2.19	1.71	0.639	0.17747	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.686514	0.13739	N	0.366086	T	0.00012	0.0000	L	0.52905	1.665	0.49130	P	2.4500000000005073E-4	D;P	0.76494	0.999;0.907	P;B	0.57846	0.828;0.408	T	0.28870	-1.0030	8	.	.	.	-14.4526	4.1421	0.10198	0.2239:0.0:0.7761:0.0	.	118;118	B5MCL2;P0CG29	.;GST2_HUMAN	M	118	ENSP00000215780:V118M;ENSP00000385765:V118M	.	V	+	1	0	GSTT2	22655062	0.240000	0.23847	0.016000	0.15963	0.391000	0.30476	-0.244000	0.08903	0.321000	0.23259	0.385000	0.25706	GTG	G|0.850;A|0.151	0.151	strong		0.607	GSTT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320080.1	NM_000854	Missense_Mutation
MUC21	394263	hgsc.bcm.edu	37	6	30955010	30955010	+	Missense_Mutation	SNP	C	C	T	rs41288689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30955010C>T	ENST00000376296.3	+	2	1299	c.1058C>T	c.(1057-1059)aCc>aTc	p.T353I	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	353	28 X 15 AA approximate tandem repeats.|Ser-rich.			T -> V (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGCACAACCTCCAGTGGG	0.632													c|||	565	0.112819	0.202	0.0605	5008	,	,		22778	0.0784		0.1133	False		,,,				2504	0.0644				p.T353I		Atlas-SNP	.											.	MUC21	98	.	0			c.C1058T						PASS	.	C	ILE/THR	645,3761	264.7+/-266.2	53,539,1611	138.0	138.0	138.0		1058	3.5	0.0	6	dbSNP_127	138	794,7802	179.6+/-228.7	43,708,3547	no	missense	MUC21	NM_001010909.2	89	96,1247,5158	TT,TC,CC		9.2369,14.6391,11.0675	possibly-damaging	353/567	30955010	1439,11563	2203	4298	6501	SO:0001583	missense	394263	exon2			GCACAACCTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1058C>T	6.37:g.30955010C>T	ENSP00000365473:p.Thr353Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	132	111	0.840909	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	230	0.10531135531135531	77	0.1565040650406504	20	0.055248618784530384	46	0.08041958041958042	87	0.11477572559366754	c	10.46	1.355681	0.24598	0.146391	0.092369	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.11385	2.78	4.38	3.48	0.39840	.	.	.	.	.	T	0.02807	0.0084	L	0.27053	0.805	0.80722	P	0.0	P	0.45474	0.859	B	0.40009	0.316	T	0.47749	-0.9093	8	0.16896	T	0.51	-0.7087	12.1722	0.54165	0.0:0.8257:0.1742:0.0	rs41288689	353	Q5SSG8	MUC21_HUMAN	I	203;353	ENSP00000365473:T353I	ENSP00000365473:T353I	T	+	2	0	MUC21	31062989	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.123000	0.10611	1.155000	0.42497	0.461000	0.40582	ACC	C|0.898;T|0.102	0.102	strong		0.632	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
WDR49	151790	hgsc.bcm.edu	37	3	167217971	167217971	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:167217971G>T	ENST00000308378.3	-	14	2250	c.1945C>A	c.(1945-1947)Caa>Aaa	p.Q649K	WDR49_ENST00000453925.2_Missense_Mutation_p.Q614K|WDR49_ENST00000476376.1_Missense_Mutation_p.Q474K|WDR49_ENST00000479765.1_Intron	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	649										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						TCCAGAATTTGGGGACGCTCT	0.423																																					p.Q649K		Atlas-SNP	.											.	WDR49	188	.	0			c.C1945A						PASS	.						131.0	149.0	143.0					3																	167217971		2203	4300	6503	SO:0001583	missense	151790	exon14			GAATTTGGGGACG	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.1945C>A	3.37:g.167217971G>T	ENSP00000311343:p.Gln649Lys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.588097	0.00128	.	.	ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925	T;T;T	0.47177	0.85;2.16;1.33	5.13	0.462	0.16695	.	0.427611	0.20451	N	0.092100	T	0.28632	0.0709	L	0.39898	1.24	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30794	-0.9966	10	0.02654	T	1	.	7.4361	0.27156	0.0:0.2474:0.2598:0.4928	.	614;649	E7EQK3;Q8IV35	.;WDR49_HUMAN	K	649;474;614	ENSP00000311343:Q649K;ENSP00000420508:Q474K;ENSP00000410863:Q614K	ENSP00000311343:Q649K	Q	-	1	0	WDR49	168700665	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.770000	0.26618	0.135000	0.18707	0.467000	0.42956	CAA	.	.	none		0.423	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
CCDC129	223075	hgsc.bcm.edu	37	7	31682853	31682853	+	Silent	SNP	T	T	C	rs38397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:31682853T>C	ENST00000407970.3	+	11	1907	c.1869T>C	c.(1867-1869)agT>agC	p.S623S	CCDC129_ENST00000319386.3_Silent_p.S475S|CCDC129_ENST00000451887.2_Silent_p.S649S|CCDC129_ENST00000409210.1_Silent_p.S531S	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	623										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AGGAAAGCAGTGGATTCTGTC	0.473													T|||	680	0.135783	0.0182	0.1556	5008	,	,		23363	0.1786		0.2177	False		,,,				2504	0.1524				p.S649S		Atlas-SNP	.											LOC223075,caecum,carcinoma,+1,2	CCDC129	127	2	0			c.T1947C						PASS	.	T		222,4184	132.9+/-169.3	9,204,1990	128.0	115.0	120.0		1869	-4.1	0.0	7	dbSNP_76	120	1729,6871	315.0+/-312.1	183,1363,2754	no	coding-synonymous	CCDC129	NM_194300.2		192,1567,4744	CC,CT,TT		20.1047,5.0386,15.0008		623/1045	31682853	1951,11055	2203	4300	6503	SO:0001819	synonymous_variant	223075	exon11			AAGCAGTGGATTC	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.1869T>C	7.37:g.31682853T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			T|0.862;C|0.138	0.138	strong		0.473	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
POLR2H	5437	hgsc.bcm.edu	37	3	184082931	184082931	+	Silent	SNP	T	T	C	rs11556518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184082931T>C	ENST00000456318.1	+	4	1217	c.168T>C	c.(166-168)ttT>ttC	p.F56F	POLR2H_ENST00000296223.3_Silent_p.F56F|POLR2H_ENST00000438240.1_Silent_p.F20F|POLR2H_ENST00000430783.1_Silent_p.F56F|POLR2H_ENST00000429568.1_Silent_p.F56F|EIF2B5_ENST00000444495.1_Intron|POLR2H_ENST00000443489.1_Silent_p.F20F|POLR2H_ENST00000452961.1_Silent_p.F20F	NM_001278699.1	NP_001265628.1	P52434	RPAB3_HUMAN	polymerase (RNA) II (DNA directed) polypeptide H	56					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GTGACAAGTTTCGGTTGGTCA	0.418													C|||	430	0.0858626	0.1256	0.0288	5008	,	,		20699	0.128		0.0686	False		,,,				2504	0.047				p.F56F		Atlas-SNP	.											.	POLR2H	17	.	0			c.T168C						PASS	.	T		485,3921	226.5+/-242.0	31,423,1749	203.0	186.0	192.0		168	1.8	1.0	3	dbSNP_120	192	550,8050	150.7+/-205.6	17,516,3767	no	coding-synonymous	POLR2H	NM_006232.2		48,939,5516	CC,CT,TT		6.3953,11.0077,7.9579		56/151	184082931	1035,11971	2203	4300	6503	SO:0001819	synonymous_variant	5437	exon3			CAAGTTTCGGTTG		CCDS3264.1, CCDS63861.1, CCDS63862.1, CCDS63859.1, CCDS63860.1	3q28	2013-01-21			ENSG00000163882	ENSG00000163882		"""RNA polymerase subunits"""	9195	protein-coding gene	gene with protein product		606023					Standard	NM_001278698		Approved	RPB8	uc003fok.2	P52434	OTTHUMG00000156746	ENST00000456318.1:c.168T>C	3.37:g.184082931T>C		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	193	90	0.466321	NM_006232	C9J413|C9JBJ6|C9JCU7|C9JUA8|P53802|Q969R0	Silent	SNP	ENST00000456318.1	37	CCDS3264.1																																																																																			T|0.918;C|0.082	0.082	strong		0.418	POLR2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345558.1	NM_006232	
GRIN3B	116444	hgsc.bcm.edu	37	19	1004823	1004823	+	Silent	SNP	G	G	A	rs4806908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1004823G>A	ENST00000234389.3	+	3	1342	c.1323G>A	c.(1321-1323)gcG>gcA	p.A441A	AC004528.4_ENST00000588380.1_RNA|GRIN3B_ENST00000588335.1_3'UTR	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	441					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)	AGTGCCCAGCGGGGCAGCTGT	0.667													a|||	1297	0.258986	0.3154	0.2205	5008	,	,		15523	0.0893		0.3489	False		,,,				2504	0.2924				p.A441A		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G1323A						PASS	.	A		1422,2984	666.9+/-401.8	220,982,1001	48.0	49.0	49.0		1323	-9.2	0.0	19	dbSNP_111	49	3031,5563	645.9+/-400.2	530,1971,1796	no	coding-synonymous	GRIN3B	NM_138690.1		750,2953,2797	AA,AG,GG		35.2688,32.2742,34.2538		441/1044	1004823	4453,8547	2203	4297	6500	SO:0001819	synonymous_variant	116444	exon3			CCCAGCGGGGCAG		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.1323G>A	19.37:g.1004823G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			G|0.697;A|0.303	0.303	strong		0.667	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
RASSF1	11186	hgsc.bcm.edu	37	3	50369546	50369546	+	Missense_Mutation	SNP	C	C	A	rs2073498	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:50369546C>A	ENST00000357043.2	-	3	444	c.409G>T	c.(409-411)Gct>Tct	p.A137S	RASSF1_ENST00000395126.3_5'UTR|RASSF1_ENST00000359365.4_Missense_Mutation_p.A133S|RASSF1_ENST00000327761.3_Missense_Mutation_p.A63S					Ras association (RalGDS/AF-6) domain family member 1											lung(2)|ovary(1)|skin(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TCAATCTCAGCTTGAGAAAGG	0.547													C|||	356	0.0710863	0.0076	0.0807	5008	,	,		20741	0.0556		0.1183	False		,,,				2504	0.1176				p.A137S		Atlas-SNP	.											.	RASSF1	46	.	0			c.G409T	GRCh37	CM063088	RASSF1	M	rs2073498	PASS	.	C	,SER/ALA,,SER/ALA,SER/ALA	98,4308	79.3+/-117.8	0,98,2105	133.0	108.0	116.0		,397,,187,409	4.5	1.0	3	dbSNP_96	116	864,7736	196.3+/-241.3	38,788,3474	yes	utr-5,missense,utr-5,missense,missense	RASSF1	NM_001206957.1,NM_007182.4,NM_170712.2,NM_170713.2,NM_170714.1	,99,,99,99	38,886,5579	AA,AC,CC		10.0465,2.2242,7.3966	,benign,,benign,benign	,133/341,,63/271,137/345	50369546	962,12044	2203	4300	6503	SO:0001583	missense	11186	exon3			TCTCAGCTTGAGA	AF132675	CCDS2820.1, CCDS2821.1, CCDS2822.1, CCDS43096.1	3p21.3	2008-02-22	2008-02-22		ENSG00000068028	ENSG00000068028			9882	protein-coding gene	gene with protein product		605082					Standard	NM_170713		Approved	NORE2A, REH3P21, RDA32, 123F2	uc003dad.1	Q9NS23	OTTHUMG00000149958	ENST00000357043.2:c.409G>T	3.37:g.50369546C>A	ENSP00000349547:p.Ala137Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	35	0.360825	NM_170714		Missense_Mutation	SNP	ENST00000357043.2	37	CCDS2820.1	166	0.076007326007326	6	0.012195121951219513	28	0.07734806629834254	38	0.06643356643356643	94	0.12401055408970976	C	11.17	1.560853	0.27827	0.022242	0.100465	ENSG00000068028	ENST00000327761;ENST00000357043;ENST00000359365	T;T;T	0.75938	2.77;-0.98;-0.98	5.5	4.52	0.55395	.	0.278640	0.39834	N	0.001252	T	0.01189	0.0039	N	0.15975	0.35	0.25265	P	0.9895621	B;B;B	0.14012	0.004;0.009;0.003	B;B;B	0.15484	0.013;0.007;0.004	T	0.14924	-1.0455	9	0.23891	T	0.37	-11.3149	11.1963	0.48715	0.0:0.8767:0.0:0.1233	rs2073498;rs52807901;rs2073498	133;137;63	Q9NS23-2;Q9NS23;Q5TZT2	.;RASF1_HUMAN;.	S	63;137;133	ENSP00000333327:A63S;ENSP00000349547:A137S;ENSP00000352323:A133S	ENSP00000333327:A63S	A	-	1	0	RASSF1	50344550	0.917000	0.31117	1.000000	0.80357	0.978000	0.69477	2.556000	0.45862	2.590000	0.87494	0.462000	0.41574	GCT	C|0.925;A|0.075	0.075	strong		0.547	RASSF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314304.1		
SLC5A9	200010	hgsc.bcm.edu	37	1	48708250	48708250	+	Missense_Mutation	SNP	C	C	T	rs78427303	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:48708250C>T	ENST00000438567.2	+	13	1851	c.1799C>T	c.(1798-1800)gCg>gTg	p.A600V	SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000236495.5_Missense_Mutation_p.A625V|SLC5A9_ENST00000533824.1_Missense_Mutation_p.A621V	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	600					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						GGAGGTGGAGCGGCAGAGAAC	0.647													c|||	164	0.0327476	0.0045	0.0533	5008	,	,		15556	0.001		0.0915	False		,,,				2504	0.0286				p.A625V		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C1874T						PASS	.	C	VAL/ALA,VAL/ALA	81,4325	70.3+/-108.2	1,79,2123	30.0	34.0	33.0		1799,1874	-9.3	0.0	1	dbSNP_132	33	797,7803	182.5+/-230.9	42,713,3545	yes	missense,missense	SLC5A9	NM_001011547.2,NM_001135181.1	64,64	43,792,5668	TT,TC,CC		9.2674,1.8384,6.7507	benign,benign	600/682,625/707	48708250	878,12128	2203	4300	6503	SO:0001583	missense	200010	exon14			GTGGAGCGGCAGA	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.1799C>T	1.37:g.48708250C>T	ENSP00000401730:p.Ala600Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	72	0.585366	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	103	0.04716117216117216	3	0.006097560975609756	27	0.07458563535911603	1	0.0017482517482517483	72	0.09498680738786279	c	5.018	0.189038	0.09547	0.018384	0.092674	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	T;T;T	0.64085	-0.08;-0.08;-0.08	4.65	-9.29	0.00653	.	0.957662	0.08646	N	0.914845	T	0.01061	0.0035	N	0.11698	0.16	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.04915	-1.0918	9	0.19147	T	0.46	.	0.2848	0.00250	0.2517:0.283:0.1836:0.2817	.	621;600;625	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	V	621;600;625	ENSP00000431900:A621V;ENSP00000401730:A600V;ENSP00000236495:A625V	ENSP00000236495:A625V	A	+	2	0	SLC5A9	48480837	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.855000	0.00729	-3.616000	0.00131	-3.307000	0.00045	GCG	C|0.939;T|0.061	0.061	strong		0.647	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
ZCCHC16	340595	hgsc.bcm.edu	37	X	111698613	111698613	+	Silent	SNP	T	T	C	rs7053563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:111698613T>C	ENST00000340433.2	+	1	887	c.657T>C	c.(655-657)caT>caC	p.H219H		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	219							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						ACAAGAAACATAGTGACAGGC	0.507													T|||	1275	0.337748	0.3797	0.2205	3775	,	,		15140	0.2619		0.159	False		,,,				2504	0.2004				p.H219H		Atlas-SNP	.											.	ZCCHC16	66	.	0			c.T657C						PASS	.	T		1659,2176		293,821,252,518,319	161.0	140.0	147.0		657	-4.2	0.0	X	dbSNP_116	147	1354,5374		103,776,372,1549,1500	no	coding-synonymous	ZCCHC16	NM_001004308.2		396,1597,624,2067,1819	CC,CT,C,TT,T		20.1249,43.2595,28.5241		219/311	111698613	3013,7550	2203	4300	6503	SO:0001819	synonymous_variant	340595	exon3			GAAACATAGTGAC	AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"""Zinc fingers, CCHC domain containing"""	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.657T>C	X.37:g.111698613T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_001004308	B2RPG1	Silent	SNP	ENST00000340433.2	37	CCDS35369.1																																																																																			T|0.694;C|0.306	0.306	strong		0.507	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254142	39254142	+	Silent	SNP	A	A	G	rs375280428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39254142A>G	ENST00000333822.4	-	1	251	c.195T>C	c.(193-195)tgT>tgC	p.C65C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	65	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						AGCTGGGGCGACAGCAGGTGG	0.657													G|||	2063	0.411941	0.469	0.4352	5008	,	,		13020	0.3234		0.4453	False		,,,				2504	0.3753				p.C65C		Atlas-SNP	.											KRTAP4-8,rectum,carcinoma,0,2	KRTAP4-8	57	2	0			c.T195C						scavenged	.						6.0	9.0	8.0					17																	39254142		633	1475	2108	SO:0001819	synonymous_variant	728224	exon1			GGGGCGACAGCAG	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.195T>C	17.37:g.39254142A>G		Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	58	20	0.344828	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			.	.	weak		0.657	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
ZC3H14	79882	hgsc.bcm.edu	37	14	89042232	89042232	+	Silent	SNP	G	G	A	rs147484262		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:89042232G>A	ENST00000251038.5	+	8	1296	c.1071G>A	c.(1069-1071)aaG>aaA	p.K357K	ZC3H14_ENST00000359301.3_Silent_p.K323K|ZC3H14_ENST00000556945.1_Silent_p.K357K|ZC3H14_ENST00000393514.5_Silent_p.K357K|ZC3H14_ENST00000557605.1_3'UTR|ZC3H14_ENST00000557607.1_Silent_p.K202K|ZC3H14_ENST00000555755.1_Silent_p.K357K|ZC3H14_ENST00000302216.8_Silent_p.K357K|ZC3H14_ENST00000336693.4_Silent_p.K323K	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	357						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						TGATTTTGAAGGCTATATCTG	0.299													G|||	1	0.000199681	0.0	0.0	5008	,	,		18726	0.0		0.001	False		,,,				2504	0.0				p.K357K		Atlas-SNP	.											.	ZC3H14	71	.	0			c.G1071A						PASS	.	G	,,,,	0,4406		0,0,2203	99.0	102.0	101.0		1071,1071,1071,1071,969	3.7	1.0	14	dbSNP_134	101	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZC3H14	NM_001160103.1,NM_001160104.1,NM_024824.4,NM_207660.3,NM_207661.2	,,,,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,,,,	357/736,357/731,357/737,357/580,323/572	89042232	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	79882	exon8			TTTGAAGGCTATA	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"""Zinc fingers, CCCH-type domain containing"""	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.1071G>A	14.37:g.89042232G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Silent	SNP	ENST00000251038.5	37	CCDS32133.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	8.970	0.972602	0.18736	0.0	4.65E-4	ENSG00000100722	ENST00000556000	.	.	.	5.77	3.71	0.42584	.	.	.	.	.	T	0.47948	0.1473	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42766	-0.9432	4	.	.	.	-19.8172	4.4076	0.11416	0.4411:0.0:0.5589:0.0	.	.	.	.	K	273	.	.	R	+	2	0	ZC3H14	88111985	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.779000	0.47734	1.436000	0.47453	0.655000	0.94253	AGG	G|1.000;A|0.000	0.000	strong		0.299	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824	
ANO2	57101	hgsc.bcm.edu	37	12	5674754	5674754	+	Silent	SNP	G	G	A	rs2277398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:5674754G>A	ENST00000356134.5	-	26	2771	c.2700C>T	c.(2698-2700)tcC>tcT	p.S900S	ANO2_ENST00000546188.1_Silent_p.S900S|ANO2_ENST00000327087.8_Silent_p.S899S	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	904					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CCAGACGGGCGGACAGAATAA	0.502													g|||	1714	0.342252	0.211	0.3646	5008	,	,		18034	0.3284		0.4553	False		,,,				2504	0.4018				p.S899S		Atlas-SNP	.											.	ANO2	309	.	0			c.C2697T						PASS	.	A		894,2850		123,648,1101	43.0	42.0	42.0		2697	-0.5	1.0	12	dbSNP_100	42	3835,4387		877,2081,1153	no	coding-synonymous	ANO2	NM_020373.2		1000,2729,2254	AA,AG,GG		46.6432,23.8782,39.5203		899/999	5674754	4729,7237	1872	4111	5983	SO:0001819	synonymous_variant	57101	exon25			ACGGGCGGACAGA	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.2700C>T	12.37:g.5674754G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	37																																																																																				G|0.645;A|0.355	0.355	strong		0.502	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
FAM124B	79843	hgsc.bcm.edu	37	2	225244888	225244888	+	Missense_Mutation	SNP	A	A	G	rs3738954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:225244888A>G	ENST00000409685.3	-	2	1035	c.770T>C	c.(769-771)aTc>aCc	p.I257T	FAM124B_ENST00000389874.3_3'UTR	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	257			I -> T (in dbSNP:rs3738954).							endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		AGCTCCCAAGATGCCATTCTT	0.502													G|||	899	0.179513	0.0968	0.1585	5008	,	,		19430	0.2431		0.169	False		,,,				2504	0.2515				p.I257T		Atlas-SNP	.											.	FAM124B	71	.	0			c.T770C						PASS	.	G	THR/ILE,	145,1239		9,127,556	44.0	45.0	45.0		770,	-2.8	0.0	2	dbSNP_107	45	431,2751		31,369,1191	yes	missense,utr-3	FAM124B	NM_001122779.1,NM_024785.2	89,	40,496,1747	GG,GA,AA		13.5449,10.4769,12.615	benign,	257/456,	225244888	576,3990	692	1591	2283	SO:0001583	missense	79843	exon2			CCCAAGATGCCAT	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.770T>C	2.37:g.225244888A>G	ENSP00000386895:p.Ile257Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001122779	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	CCDS46527.1	380	0.17399267399267399	64	0.13008130081300814	62	0.1712707182320442	132	0.23076923076923078	122	0.16094986807387862	G	5.104	0.204764	0.09704	0.104769	0.135449	ENSG00000124019	ENST00000409685	T	0.30981	1.51	5.71	-2.82	0.05787	.	.	.	.	.	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	0.38286	-0.9668	8	0.11794	T	0.64	1.0163	0.2122	0.00158	0.3423:0.2316:0.1835:0.2426	rs3738954;rs61599074;rs3738954	257	Q9H5Z6	F124B_HUMAN	T	257	ENSP00000386895:I257T	ENSP00000386895:I257T	I	-	2	0	FAM124B	224953132	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.563000	0.05943	-0.481000	0.06792	-0.726000	0.03593	ATC	A|0.830;G|0.170	0.170	strong		0.502	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785	
COL17A1	1308	hgsc.bcm.edu	37	10	105793750	105793750	+	Missense_Mutation	SNP	T	T	C	rs17116350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105793750T>C	ENST00000353479.5	-	52	4399	c.4109A>G	c.(4108-4110)gAt>gGt	p.D1370G	COL17A1_ENST00000369733.3_Missense_Mutation_p.D1288G	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1370	Triple-helical region.		D -> G (in dbSNP:rs17116350). {ECO:0000269|PubMed:9012408}.		cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GTAATCCAGATCTCCAGCAAA	0.582													C|||	1295	0.258586	0.3865	0.245	5008	,	,		16412	0.1359		0.2366	False		,,,				2504	0.2444				p.D1370G		Atlas-SNP	.											COL17A1,colon,carcinoma,0,1	COL17A1	149	1	0			c.A4109G						PASS	.	C	GLY/ASP	1649,2757	659.9+/-400.6	321,1007,875	119.0	116.0	117.0		4109	-0.4	1.0	10	dbSNP_123	117	2126,6474	715.4+/-406.1	256,1614,2430	yes	missense	COL17A1	NM_000494.3	94	577,2621,3305	CC,CT,TT		24.7209,37.4262,29.0251	benign	1370/1498	105793750	3775,9231	2203	4300	6503	SO:0001583	missense	1308	exon52			TCCAGATCTCCAG	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.4109A>G	10.37:g.105793750T>C	ENSP00000340937:p.Asp1370Gly	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	216	116	0.537037	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	510	0.23351648351648352	177	0.3597560975609756	77	0.212707182320442	81	0.14160839160839161	175	0.23087071240105542	C	0.946	-0.708078	0.03230	0.374262	0.247209	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.90955	-2.76;-2.76	4.87	-0.367	0.12541	.	0.941840	0.08723	N	0.903109	T	0.00012	0.0000	N	0.16266	0.395	0.20196	P	0.9999218909	B	0.02656	0.0	B	0.01281	0.0	T	0.03278	-1.1053	9	0.27082	T	0.32	-0.1527	6.4563	0.21932	0.0:0.1656:0.2387:0.5957	rs17116350;rs17879742;rs17116350	1370	Q9UMD9	COHA1_HUMAN	G	1370;1288	ENSP00000340937:D1370G;ENSP00000358748:D1288G	ENSP00000340937:D1370G	D	-	2	0	COL17A1	105783740	0.003000	0.15002	0.989000	0.46669	0.578000	0.36192	0.142000	0.16096	0.017000	0.15025	-0.974000	0.02594	GAT	C|0.269;N|0.000	0.269	strong		0.582	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
PLEC	5339	hgsc.bcm.edu	37	8	144994028	144994028	+	Missense_Mutation	SNP	C	C	T	rs34132016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144994028C>T	ENST00000322810.4	-	32	10541	c.10372G>A	c.(10372-10374)Ggg>Agg	p.G3458R	PLEC_ENST00000354589.3_Missense_Mutation_p.G3321R|PLEC_ENST00000345136.3_Missense_Mutation_p.G3321R|PLEC_ENST00000356346.3_Missense_Mutation_p.G3307R|PLEC_ENST00000357649.2_Missense_Mutation_p.G3325R|PLEC_ENST00000436759.2_Missense_Mutation_p.G3348R|PLEC_ENST00000398774.2_Missense_Mutation_p.G3289R|PLEC_ENST00000527096.1_Missense_Mutation_p.G3344R|PLEC_ENST00000354958.2_Missense_Mutation_p.G3299R	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3458	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						CTGAGGACCCCGGAAGCCAGG	0.657													C|||	17	0.00339457	0.0	0.0086	5008	,	,		15858	0.0		0.0109	False		,,,				2504	0.0				p.G3458R		Atlas-SNP	.											.	PLEC	1144	.	0			c.G10372A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	7,3991		0,7,1992	31.0	35.0	34.0		10042,9919,9895,10372,9865,9961,9973,9961	-8.5	0.0	8	dbSNP_126	34	62,8276		0,62,4107	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	125,125,125,125,125,125,125,125	0,69,6099	TT,TC,CC		0.7436,0.1751,0.5593	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	3348/4575,3307/4534,3299/4526,3458/4685,3289/4516,3321/4548,3325/4552,3321/4548	144994028	69,12267	1999	4169	6168	SO:0001583	missense	5339	exon32			GGACCCCGGAAGC	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.10372G>A	8.37:g.144994028C>T	ENSP00000323856:p.Gly3458Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	11	0.005036630036630037	0	0.0	7	0.019337016574585635	0	0.0	4	0.005277044854881266	C	6.871	0.530015	0.13127	0.001751	0.007436	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	4.81	-8.46	0.00942	.	0.635159	0.14191	N	0.335373	T	0.27313	0.0670	N	0.17631	0.505	0.09310	N	1	B;B;B;B;B;B;B;B	0.16396	0.017;0.017;0.017;0.01;0.017;0.017;0.017;0.017	B;B;B;B;B;B;B;B	0.09377	0.003;0.004;0.004;0.001;0.004;0.003;0.003;0.003	T	0.07443	-1.0772	10	0.31617	T	0.26	.	6.4723	0.22015	0.0813:0.2192:0.0813:0.6181	rs34132016	3348;3307;3299;3458;3289;3321;3325;3321	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	R	3321;3325;3321;3289;3458;3299;3307;3348;3344	ENSP00000344848:G3321R;ENSP00000350277:G3325R;ENSP00000346602:G3321R;ENSP00000381756:G3289R;ENSP00000323856:G3458R;ENSP00000347044:G3299R;ENSP00000348702:G3307R;ENSP00000388180:G3348R;ENSP00000434583:G3344R	ENSP00000323856:G3458R	G	-	1	0	PLEC	145066016	0.000000	0.05858	0.000000	0.03702	0.879000	0.50718	-0.166000	0.09954	-2.128000	0.00818	-1.671000	0.00744	GGG	C|0.994;T|0.006	0.006	strong		0.657	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
STAG1	10274	hgsc.bcm.edu	37	3	136062724	136062724	+	Missense_Mutation	SNP	C	C	G	rs34149860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	155	0	0		WXS	Illumina HiSeq	Phase_I	164	73	0.445122	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	
CYP2C8	1558	hgsc.bcm.edu	37	10	96818119	96818119	+	Missense_Mutation	SNP	G	G	C	rs1058930	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:96818119G>C	ENST00000371270.3	-	5	886	c.792C>G	c.(790-792)atC>atG	p.I264M	CYP2C8_ENST00000535898.1_Missense_Mutation_p.I162M|CYP2C8_ENST00000539050.1_Missense_Mutation_p.I178M	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	264			I -> M (in allele CYP2C8*4; dbSNP:rs1058930). {ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:2009263, ECO:0000269|PubMed:3500169, 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)	GGAAGCAATCGATAAAGTCCC	0.358													G|||	83	0.0165735	0.0038	0.0187	5008	,	,		17620	0.0		0.0577	False		,,,				2504	0.0072				p.I264M		Atlas-SNP	.											.	CYP2C8	73	.	0			c.C792G	GRCh37	CM076141	CYP2C8	M	rs1058930	PASS	.	G	MET/ILE,MET/ILE,MET/ILE,MET/ILE	57,4349	55.5+/-91.7	0,57,2146	179.0	157.0	165.0		792,582,486,582	-2.8	0.6	10	dbSNP_86	165	471,8129	139.5+/-196.2	10,451,3839	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	10,10,10,10	10,508,5985	CC,CG,GG		5.4767,1.2937,4.0597	probably-damaging,probably-damaging,probably-damaging,probably-damaging	264/491,194/421,162/389,194/421	96818119	528,12478	2203	4300	6503	SO:0001583	missense	1558	exon5			GCAATCGATAAAG	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.792C>G	10.37:g.96818119G>C	ENSP00000360317:p.Ile264Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	56	0.02564102564102564	0	0.0	10	0.027624309392265192	0	0.0	46	0.06068601583113457	G	8.979	0.974787	0.18736	0.012937	0.054767	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.71934	-0.61;-0.61;-0.61	4.17	-2.77	0.05877	.	0.000000	0.64402	U	0.000001	T	0.32436	0.0829	M	0.77103	2.36	0.33139	D	0.544156	D;D;D;D	0.71674	0.997;0.994;0.998;0.994	D;D;D;D	0.73708	0.976;0.976;0.981;0.976	T	0.67726	-0.5596	10	0.72032	D	0.01	.	5.6627	0.17678	0.6246:0.0:0.2522:0.1232	rs56489507	178;162;232;264	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	M	264;231;162;178	ENSP00000360317:I264M;ENSP00000445062:I162M;ENSP00000442343:I178M	ENSP00000360317:I264M	I	-	3	3	CYP2C8	96808109	0.909000	0.30893	0.619000	0.29118	0.104000	0.19210	0.045000	0.14013	-0.793000	0.04475	-2.332000	0.00249	ATC	.	.	weak		0.358	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195348	18195348	+	Missense_Mutation	SNP	C	C	T	rs11024532	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:18195348C>T	ENST00000314254.3	+	1	965	c.545C>T	c.(544-546)gCg>gTg	p.A182V	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	182			A -> V (in dbSNP:rs11024532). {ECO:0000269|PubMed:11850634, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						ATCCCAGTCGCGTGGCTGATT	0.512													C|||	636	0.126997	0.0461	0.1441	5008	,	,		20406	0.0347		0.2644	False		,,,				2504	0.1779				p.A182V		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.C545T						PASS	.	C	VAL/ALA	389,4009	193.6+/-218.7	12,365,1822	210.0	199.0	203.0		545	-0.4	0.0	11	dbSNP_120	203	2493,6093	409.6+/-349.9	390,1713,2190	yes	missense	MRGPRX4	NM_054032.3	64	402,2078,4012	TT,TC,CC		29.0356,8.8449,22.1965	benign	182/323	18195348	2882,10102	2199	4293	6492	SO:0001583	missense	117196	exon1			CAGTCGCGTGGCT	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.545C>T	11.37:g.18195348C>T	ENSP00000314042:p.Ala182Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	307	0.14056776556776557	28	0.056910569105691054	61	0.1685082872928177	17	0.02972027972027972	201	0.26517150395778366	C	10.12	1.263710	0.23136	0.088449	0.290356	ENSG00000179817	ENST00000314254	T	0.33865	1.39	2.85	-0.447	0.12234	GPCR, rhodopsin-like superfamily (1);	1.195330	0.05937	N	0.636357	T	0.00012	0.0000	L	0.28740	0.885	0.80722	P	0.0	B	0.24963	0.115	B	0.28385	0.089	T	0.37888	-0.9686	9	0.30854	T	0.27	.	3.211	0.06682	0.0:0.4219:0.2751:0.303	rs11024532;rs52828189;rs58386901;rs11024532	182	Q96LA9	MRGX4_HUMAN	V	182	ENSP00000314042:A182V	ENSP00000314042:A182V	A	+	2	0	MRGPRX4	18151924	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.465000	0.06680	0.074000	0.16767	-0.573000	0.04149	GCG	C|0.817;T|0.183	0.183	strong		0.512	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
TTN	7273	hgsc.bcm.edu	37	2	179427186	179427186	+	Silent	SNP	A	A	G	rs2366751	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179427186A>G	ENST00000591111.1	-	276	78974	c.78750T>C	c.(78748-78750)ggT>ggC	p.G26250G	TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.G27891G|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.G18951G|TTN_ENST00000460472.2_Silent_p.G18826G|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.G19018G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Silent_p.G25323G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26250	Fibronectin type-III 91. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTGCTGCCACCATCACTTT	0.433													G|||	2548	0.508786	0.5673	0.4078	5008	,	,		21523	0.7153		0.2535	False		,,,				2504	0.5511				p.G27891G		Atlas-SNP	.											.	TTN	18412	.	0			c.T83673C						PASS	.	G	,,,	2019,1847		546,927,460	65.0	67.0	67.0		56478,75969,56853,57054	-1.6	1.0	2	dbSNP_100	67	1847,6443		193,1461,2491	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	739,2388,2951	GG,GA,AA		22.2799,47.7755,31.8032	,,,	18826/26927,25323/33424,18951/27052,19018/27119	179427186	3866,8290	1933	4145	6078	SO:0001819	synonymous_variant	7273	exon326			GCTGCCACCATCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.78750T>C	2.37:g.179427186A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.562;G|0.438	0.438	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LRRK1	79705	hgsc.bcm.edu	37	15	101593597	101593597	+	Silent	SNP	C	C	T	rs41418955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:101593597C>T	ENST00000388948.3	+	26	4385	c.4026C>T	c.(4024-4026)ctC>ctT	p.L1342L	LRRK1_ENST00000284395.5_Silent_p.L1339L|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCAGCAGCCTCAACACCGTGC	0.731													C|||	15	0.00299521	0.0	0.0043	5008	,	,		15960	0.0		0.0109	False		,,,				2504	0.001				p.L1342L		Atlas-SNP	.											.	LRRK1	310	.	0			c.C4026T						PASS	.	C		8,4328		0,8,2160	14.0	17.0	16.0		4026	3.0	1.0	15	dbSNP_127	16	75,8439		0,75,4182	no	coding-synonymous	LRRK1	NM_024652.3		0,83,6342	TT,TC,CC		0.8809,0.1845,0.6459		1342/2016	101593597	83,12767	2168	4257	6425	SO:0001819	synonymous_variant	79705	exon26			CAGCCTCAACACC	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.4026C>T	15.37:g.101593597C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			C|0.993;T|0.007	0.007	strong		0.731	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
TNRC6A	27327	hgsc.bcm.edu	37	16	24788645	24788645	+	Missense_Mutation	SNP	T	T	A	rs11639856	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:24788645T>A	ENST00000395799.3	+	5	684	c.555T>A	c.(553-555)aaT>aaA	p.N185K	TNRC6A_ENST00000315183.7_Missense_Mutation_p.N185K	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	185	Interaction with argonaute family proteins.		N -> K (in dbSNP:rs11639856).		cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		AGCCACAAAATAACGGAGAGG	0.413													T|||	844	0.16853	0.2284	0.1484	5008	,	,		19450	0.128		0.162	False		,,,				2504	0.1503				p.N185K		Atlas-SNP	.											.	TNRC6A	171	.	0			c.T555A						PASS	.	T	LYS/ASN	770,3306		77,616,1345	131.0	133.0	132.0		555	2.4	1.0	16	dbSNP_120	132	1574,6846		147,1280,2783	yes	missense	TNRC6A	NM_014494.2	94	224,1896,4128	AA,AT,TT		18.6936,18.8911,18.758	benign	185/1963	24788645	2344,10152	2038	4210	6248	SO:0001583	missense	27327	exon5			ACAAAATAACGGA	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.555T>A	16.37:g.24788645T>A	ENSP00000379144:p.Asn185Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	319	0.14606227106227107	92	0.18699186991869918	56	0.15469613259668508	61	0.10664335664335664	110	0.14511873350923482	T	5.027	0.190761	0.09547	0.188911	0.186936	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.10860	2.83;2.83	5.84	2.44	0.29823	.	0.313190	0.33144	N	0.005233	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.99999840025	B	0.02656	0.0	B	0.01281	0.0	T	0.43556	-0.9384	9	0.06236	T	0.91	-1.0666	4.4847	0.11783	0.1455:0.2438:0.0:0.6107	rs11639856;rs52830311;rs60905112;rs11639856	185	Q8NDV7	TNR6A_HUMAN	K	185	ENSP00000326900:N185K;ENSP00000379144:N185K	ENSP00000326900:N185K	N	+	3	2	TNRC6A	24696146	0.915000	0.31059	1.000000	0.80357	0.998000	0.95712	0.825000	0.27393	1.040000	0.40099	0.482000	0.46254	AAT	T|0.853;A|0.147	0.147	strong		0.413	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
NBEAL1	65065	hgsc.bcm.edu	37	2	203922075	203922075	+	Silent	SNP	A	A	G	rs146121994	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:203922075A>G	ENST00000449802.1	+	6	747	c.414A>G	c.(412-414)gaA>gaG	p.E138E	NBEAL1_ENST00000478884.1_3'UTR	NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	138										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AAGAGAAGGAAATGGCAGATC	0.313													A|||	7	0.00139776	0.0	0.0	5008	,	,		17801	0.0		0.006	False		,,,				2504	0.001				p.E138E		Atlas-SNP	.											.	NBEAL1	266	.	0			c.A414G						PASS	.	A		2,1382		0,2,690	169.0	146.0	153.0		414	2.5	1.0	2	dbSNP_134	153	29,3151		0,29,1561	no	coding-synonymous	NBEAL1	NM_001114132.1		0,31,2251	GG,GA,AA		0.9119,0.1445,0.6792		138/2695	203922075	31,4533	692	1590	2282	SO:0001819	synonymous_variant	65065	exon6			GAAGGAAATGGCA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.414A>G	2.37:g.203922075A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Silent	SNP	ENST00000449802.1	37	CCDS46495.1																																																																																			A|0.997;G|0.003	0.003	strong		0.313	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
LINC00283	100874057	hgsc.bcm.edu	37	13	103397387	103397387	+	RNA	SNP	T	T	G	rs7339187	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:103397387T>G	ENST00000430111.1	+	0	1760									long intergenic non-protein coding RNA 283																		TGTGCCATTTTGGGTCTGGAG	0.393													T|||	329	0.0656949	0.1271	0.0144	5008	,	,		21811	0.1042		0.0268	False		,,,				2504	0.0194				p.Q1887P		Atlas-SNP	.											.	.	.	.	0			c.A5660C						PASS	.	T	PRO/GLN	145,1239		9,127,556	199.0	149.0	164.0		5660	1.1	0.0	13	dbSNP_116	164	68,3112		2,64,1524	yes	missense	CCDC168	NM_001146197.1	76	11,191,2080	GG,GT,TT		2.1384,10.4769,4.667		1887/7082	103397387	213,4351	692	1590	2282			643677	exon4			CCATTTTGGGTCT			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.103397387T>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				T|0.916;G|0.084	0.084	strong		0.393	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
C5	727	hgsc.bcm.edu	37	9	123782299	123782299	+	Silent	SNP	G	G	A	rs2230214	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123782299G>A	ENST00000223642.1	-	12	1490	c.1461C>T	c.(1459-1461)acC>acT	p.T487T		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	487					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)	GGCTTTTGGGGGTAACAATAA	0.353													G|||	445	0.0888578	0.1278	0.0533	5008	,	,		18437	0.0367		0.0984	False		,,,				2504	0.1053				p.T487T		Atlas-SNP	.											.	C5	124	.	0			c.C1461T						PASS	.	G		631,3775	269.8+/-269.2	40,551,1612	107.0	109.0	108.0		1461	-3.9	1.0	9	dbSNP_98	108	910,7690	202.7+/-245.9	52,806,3442	no	coding-synonymous	C5	NM_001735.2		92,1357,5054	AA,AG,GG		10.5814,14.3214,11.8484		487/1677	123782299	1541,11465	2203	4300	6503	SO:0001819	synonymous_variant	727	exon12			TTTGGGGGTAACA	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.1461C>T	9.37:g.123782299G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	143	55	0.384615	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			G|0.895;A|0.105	0.105	strong		0.353	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
ERMARD	55780	hgsc.bcm.edu	37	6	170176648	170176648	+	Missense_Mutation	SNP	A	A	G	rs386708934|rs4716346	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:170176648A>G	ENST00000366773.3	+	16	1651	c.1618A>G	c.(1618-1620)Agc>Ggc	p.S540G	ERMARD_ENST00000418781.3_Intron|ERMARD_ENST00000366772.2_Intron|ERMARD_ENST00000392095.4_Missense_Mutation_p.S414G|ERMARD_ENST00000588451.1_Missense_Mutation_p.S404G	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	540			S -> G (in dbSNP:rs4716346). {ECO:0000269|PubMed:14702039}.		multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											CCGAAGCATCAGCGAACAGTG	0.627													G|||	1721	0.34365	0.497	0.304	5008	,	,		21067	0.3304		0.2366	False		,,,				2504	0.2883				p.S540G		Atlas-SNP	.											.	C6orf70	63	.	0			c.A1618G						PASS	.	G	GLY/SER	2113,2293	600.2+/-389.4	503,1107,593	94.0	71.0	79.0		1618	-6.8	0.0	6	dbSNP_111	79	1913,6687	726.4+/-406.6	235,1443,2622	yes	missense	C6orf70	NM_018341.1	56	738,2550,3215	GG,GA,AA		22.2442,47.9573,30.9549	benign	540/679	170176648	4026,8980	2203	4300	6503	SO:0001583	missense	55780	exon16			AGCATCAGCGAAC	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.1618A>G	6.37:g.170176648A>G	ENSP00000355735:p.Ser540Gly	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	573	0.2623626373626374	178	0.3617886178861789	92	0.2541436464088398	159	0.27797202797202797	144	0.18997361477572558	G	12.19	1.863197	0.32884	0.479573	0.222442	ENSG00000130023	ENST00000366773;ENST00000392095;ENST00000366771	T;T	0.47528	0.84;0.84	5.37	-6.82	0.01698	.	0.716909	0.14165	N	0.337097	T	0.12008	0.0292	L	0.46885	1.475	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10917	-1.0609	9	0.22109	T	0.4	.	5.928	0.19122	0.5017:0.0:0.3028:0.1955	rs4716346;rs17860646;rs59930119;rs4716346	540	Q5T6L9	CF070_HUMAN	G	540;414;188	ENSP00000355735:S540G;ENSP00000375945:S414G	ENSP00000355733:S188G	S	+	1	0	C6orf70	169918573	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.628000	0.05515	-1.767000	0.01300	-1.485000	0.00982	AGC	A|0.706;G|0.294	0.294	strong		0.627	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
CNTRL	11064	hgsc.bcm.edu	37	9	123860689	123860689	+	Missense_Mutation	SNP	C	C	T	rs10818504	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:123860689C>T	ENST00000373855.1	+	7	907	c.647C>T	c.(646-648)cCg>cTg	p.P216L	CNTRL_ENST00000238341.5_Missense_Mutation_p.P216L|CNTRL_ENST00000373865.2_Missense_Mutation_p.P216L			Q7Z7A1	CNTRL_HUMAN	centriolin	216			P -> L (in dbSNP:rs10818504).		cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						AAGTTGAAACCGCTTCAAGAT	0.328													c|||	2158	0.430911	0.1233	0.4957	5008	,	,		17973	0.5704		0.4503	False		,,,				2504	0.637				p.P216L		Atlas-SNP	.											.	CNTRL	161	.	0			c.C647T						PASS	.	T	LEU/PRO	795,3611	318.2+/-295.5	83,629,1491	110.0	103.0	105.0		647	4.7	1.0	9	dbSNP_120	105	3746,4854	532.8+/-382.3	852,2042,1406	yes	missense	CNTRL	NM_007018.4	98	935,2671,2897	TT,TC,CC		43.5581,18.0436,34.9147	probably-damaging	216/2326	123860689	4541,8465	2203	4300	6503	SO:0001583	missense	11064	exon5			TGAAACCGCTTCA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.647C>T	9.37:g.123860689C>T	ENSP00000362962:p.Pro216Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	920	0.42124542124542125	63	0.12804878048780488	178	0.49171270718232046	335	0.5856643356643356	344	0.45382585751978893	c	20.6	4.018530	0.75275	0.180436	0.435581	ENSG00000119397	ENST00000373865;ENST00000373855;ENST00000238341;ENST00000454238	T;T	0.54675	0.56;0.56	5.62	4.73	0.59995	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.25997	P	0.9821766	D	0.71674	0.998	P	0.54372	0.75	T	0.48811	-0.9002	8	0.62326	D	0.03	.	13.8885	0.63724	0.0:0.9269:0.0:0.0731	rs10818504;rs52806091;rs56916629;rs10818504	216	Q7Z7A1	CNTRL_HUMAN	L	216	ENSP00000362962:P216L;ENSP00000238341:P216L	ENSP00000238341:P216L	P	+	2	0	CNTRL	122900510	0.989000	0.36119	0.998000	0.56505	0.975000	0.68041	1.322000	0.33689	1.382000	0.46385	-0.119000	0.15052	CCG	C|0.626;T|0.374	0.374	strong		0.328	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
C1RL	51279	hgsc.bcm.edu	37	12	7254669	7254669	+	Silent	SNP	A	A	C	rs3742088	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:7254669A>C	ENST00000266542.4	-	3	407	c.315T>G	c.(313-315)ggT>ggG	p.G105G	C1RL_ENST00000545280.1_Missense_Mutation_p.V29G|C1RL_ENST00000545337.1_Silent_p.G105G|C1RL_ENST00000544702.1_Silent_p.G105G	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	105	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTGGATCCGAACCGACGAATG	0.602													C|||	613	0.122404	0.121	0.062	5008	,	,		-128	0.1409		0.0596	False		,,,				2504	0.2127				p.G105G		Atlas-SNP	.											.	C1RL	39	.	0			c.T315G						PASS	.	C		521,3885	777.3+/-414.2	28,465,1710	91.0	93.0	92.0		315	1.9	0.0	12	dbSNP_107	92	711,7889	786.0+/-407.6	31,649,3620	no	coding-synonymous	C1RL	NM_016546.2		59,1114,5330	CC,CA,AA		8.2674,11.8248,9.4726		105/488	7254669	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	51279	exon3			ATCCGAACCGACG	AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.315T>G	12.37:g.7254669A>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_016546	Q53GX9	Silent	SNP	ENST00000266542.4	37	CCDS8573.1	191|191	0.08745421245421245|0.08745421245421245	48|48	0.0975609756097561|0.0975609756097561	19|19	0.052486187845303865|0.052486187845303865	82|82	0.14335664335664336|0.14335664335664336	42|42	0.055408970976253295|0.055408970976253295	C|C	7.434|7.434	0.639341|0.639341	0.14386|0.14386	0.118248|0.118248	0.082674|0.082674	ENSG00000139178|ENSG00000139178	ENST00000534950|ENST00000545280	.|.	.|.	.|.	3.76|3.76	1.88|1.88	0.25563|0.25563	.|.	.|.	.|.	.|.	.|.	T|T	0.00241|0.00241	0.0007|0.0007	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.12656|0.12656	-1.0539|-1.0539	3|3	.|.	.|.	.|.	.|.	3.1438|3.1438	0.06464|0.06464	0.2088:0.5581:0.0:0.233|0.2088:0.5581:0.0:0.233	rs3742088;rs17198416;rs60912221;rs3742088|rs3742088;rs17198416;rs60912221;rs3742088	.|.	.|.	.|.	V|G	5|29	.|.	.|.	F|V	-|-	1|2	0|0	C1RL|C1RL	7145945|7145945	0.001000|0.001000	0.12720|0.12720	0.003000|0.003000	0.11579|0.11579	0.001000|0.001000	0.01503|0.01503	0.341000|0.341000	0.19909|0.19909	0.184000|0.184000	0.20083|0.20083	-0.358000|-0.358000	0.07595|0.07595	TTC|GTT	A|0.904;C|0.096	0.096	strong		0.602	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546	
CAPN11	11131	hgsc.bcm.edu	37	6	44141088	44141088	+	Missense_Mutation	SNP	G	G	A	rs6938938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:44141088G>A	ENST00000398776.1	+	7	834	c.796G>A	c.(796-798)Gtg>Atg	p.V266M	CAPN11_ENST00000542245.1_Missense_Mutation_p.V266M	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	266	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		V -> M (in dbSNP:rs6938938).		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)			TAGGAAGGCCGTGGAGCGATC	0.587													G|||	710	0.141773	0.239	0.072	5008	,	,		18803	0.1062		0.1083	False		,,,				2504	0.1309				p.V266M		Atlas-SNP	.											.	CAPN11	66	.	0			c.G796A						PASS	.	G	MET/VAL	731,3199		71,589,1305	26.0	29.0	28.0		796	-8.5	0.0	6	dbSNP_116	28	719,7565		30,659,3453	yes	missense	CAPN11	NM_007058.3	21	101,1248,4758	AA,AG,GG		8.6794,18.6005,11.8716	possibly-damaging	266/740	44141088	1450,10764	1965	4142	6107	SO:0001583	missense	11131	exon7			AAGGCCGTGGAGC	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.796G>A	6.37:g.44141088G>A	ENSP00000381758:p.Val266Met	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	37	CCDS47436.1	278	0.12728937728937728	112	0.22764227642276422	19	0.052486187845303865	62	0.10839160839160839	85	0.11213720316622691	G	12.50	1.956180	0.34565	0.186005	0.086794	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.89050	-2.46;-2.46	4.25	-8.51	0.00923	Peptidase C2, calpain, catalytic domain (3);	1.255730	0.05836	N	0.618473	T	0.60521	0.2275	L	0.48935	1.535	0.80722	P	0.0	P	0.34934	0.476	B	0.22386	0.039	T	0.53486	-0.8432	9	0.87932	D	0	.	4.2948	0.10895	0.1137:0.2636:0.4759:0.1468	rs6938938;rs57707167;rs6938938	266	Q9UMQ6	CAN11_HUMAN	M	266	ENSP00000381758:V266M;ENSP00000441078:V266M	ENSP00000381758:V266M	V	+	1	0	CAPN11	44249066	0.000000	0.05858	0.000000	0.03702	0.319000	0.28217	-1.323000	0.02692	-4.254000	0.00061	-0.355000	0.07637	GTG	G|0.864;A|0.136	0.136	strong		0.587	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
SEMA5B	54437	hgsc.bcm.edu	37	3	122646734	122646734	+	Silent	SNP	C	C	T	rs2276775	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:122646734C>T	ENST00000357599.3	-	8	1139	c.753G>A	c.(751-753)acG>acA	p.T251T	SEMA5B_ENST00000195173.4_Silent_p.T251T|AC078794.1_ENST00000408284.1_RNA|SEMA5B_ENST00000451055.2_Silent_p.T305T	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	251	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		AGTCGATGACCGTGGCTGCAT	0.587													C|||	421	0.0840655	0.0726	0.1167	5008	,	,		18724	0.0575		0.0954	False		,,,				2504	0.092				p.T305T		Atlas-SNP	.											.	SEMA5B	303	.	0			c.G915A						PASS	.	C		324,4082	174.1+/-203.8	9,306,1888	87.0	82.0	84.0		753	-11.1	0.0	3	dbSNP_100	84	948,7652	209.0+/-250.3	54,840,3406	no	coding-synonymous	SEMA5B	NM_001031702.2		63,1146,5294	TT,TC,CC		11.0233,7.3536,9.7801		251/1152	122646734	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	54437	exon8			GATGACCGTGGCT	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.753G>A	3.37:g.122646734C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																			C|0.906;T|0.094	0.094	strong		0.587	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
C6orf201	404220	hgsc.bcm.edu	37	6	4122249	4122249	+	Missense_Mutation	SNP	C	C	A	rs643232	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:4122249C>A	ENST00000380175.4	+	4	1116	c.351C>A	c.(349-351)aaC>aaA	p.N117K	ECI2_ENST00000465828.1_Intron|C6orf201_ENST00000333388.5_Missense_Mutation_p.N120K|ECI2_ENST00000361538.2_Intron|ECI2_ENST00000380125.2_Intron|ECI2_ENST00000380118.3_Intron|C6orf201_ENST00000430835.2_Missense_Mutation_p.N117K|ECI2_ENST00000413766.2_Intron	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	117			N -> K (in dbSNP:rs643232). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.							central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				AACTGAGAAACCTGCCAACAA	0.378													A|||	1610	0.321486	0.3404	0.3602	5008	,	,		15599	0.3591		0.332	False		,,,				2504	0.2188				p.N117K		Atlas-SNP	.											.	C6orf201	17	.	0			c.C351A						PASS	.	A	LYS/ASN,,,	1209,2503		203,803,850	78.0	73.0	75.0		351,,,	-1.7	0.0	6	dbSNP_83	75	2488,5730		382,1724,2003	yes	missense,intron,intron,intron	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	94,,,	585,2527,2853	AA,AC,CC		30.275,32.57,30.9891	benign,,,	117/141,,,	4122249	3697,8233	1856	4109	5965	SO:0001583	missense	404220	exon4			GAGAAACCTGCCA	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.351C>A	6.37:g.4122249C>A	ENSP00000420610:p.Asn117Lys	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	207	92	0.444444	NM_001085401	A6NLI6|Q6NXN5	Missense_Mutation	SNP	ENST00000380175.4	37	CCDS43419.1	753|753	0.3447802197802198|0.3447802197802198	153|153	0.31097560975609756|0.31097560975609756	130|130	0.35911602209944754|0.35911602209944754	210|210	0.36713286713286714|0.36713286713286714	260|260	0.34300791556728233|0.34300791556728233	A|A	0.005|0.005	-2.123401|-2.123401	0.00346|0.00346	0.3257|0.3257	0.30275|0.30275	ENSG00000185689|ENSG00000185689	ENST00000333388;ENST00000380175;ENST00000427996;ENST00000451679;ENST00000430835|ENST00000541127	T;T;T;T;T|.	0.50813|.	2.01;2.01;0.73;2.01;1.81|.	2.54|2.54	-1.7|-1.7	0.08159|0.08159	.|.	.|3.055170	.|0.01408	.|N	.|0.013894	T|T	0.02929|0.02929	0.0087|0.0087	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.10428|0.10428	-1.0630|-1.0630	8|6	0.05525|0.02654	T|T	0.97|1	.|.	4.3166|4.3166	0.10997|0.10997	0.3732:0.2021:0.4247:0.0|0.3732:0.2021:0.4247:0.0	rs643232;rs643232|rs643232;rs643232	117;117|.	B4DXB2;Q7Z4U5|.	.;CF201_HUMAN|.	K|T	120;117;120;117;117|192	ENSP00000330777:N120K;ENSP00000420610:N117K;ENSP00000419568:N120K;ENSP00000420763:N117K;ENSP00000396912:N117K|.	ENSP00000330777:N120K|ENSP00000439073:P192T	N|P	+|+	3|1	2|0	C6orf201|C6orf201	4067248|4067248	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	0.085000|0.085000	0.14912|0.14912	-0.784000|-0.784000	0.04528|0.04528	-0.363000|-0.363000	0.07495|0.07495	AAC|CCT	C|0.679;A|0.321	0.321	strong		0.378	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	
OR9Q2	219957	hgsc.bcm.edu	37	11	57958497	57958497	+	Missense_Mutation	SNP	T	T	C	rs34337292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						PASS	.	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	341	0	0		WXS	Illumina HiSeq	Phase_I	366	190	0.519126	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	
FANCL	55120	hgsc.bcm.edu	37	2	58388696	58388696	+	Silent	SNP	A	A	G	rs848291	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:58388696A>G	ENST00000233741.4	-	12	1017	c.981T>C	c.(979-981)tcT>tcC	p.S327S	FANCL_ENST00000403295.3_Silent_p.S299S|FANCL_ENST00000402135.3_Silent_p.S332S|FANCL_ENST00000403676.1_Silent_p.S210S	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	327					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|gamete generation (GO:0007276)|protein monoubiquitination (GO:0006513)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)	8						GTCCACACTGAGAATTATCAC	0.313								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	3538	0.70647	0.947	0.6412	5008	,	,		19414	0.5883		0.6173	False		,,,				2504	0.6411				p.S332S		Atlas-SNP	.											.	FANCL	35	.	0			c.T996C						PASS	.	G	,	3966,438	207.5+/-228.8	1797,372,33	99.0	102.0	101.0		996,981	-0.5	0.0	2	dbSNP_86	101	5190,3410	501.6+/-375.5	1567,2056,677	no	coding-synonymous,coding-synonymous	FANCL	NM_001114636.1,NM_018062.3	,	3364,2428,710	GG,GA,AA		39.6512,9.9455,29.5909	,	332/381,327/376	58388696	9156,3848	2202	4300	6502	SO:0001819	synonymous_variant	55120	exon12	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ACACTGAGAATTA	AK001197	CCDS1860.1, CCDS46294.1	2p16.1	2014-09-17	2003-10-14	2003-10-15	ENSG00000115392	ENSG00000115392		"""Zinc fingers, PHD-type"", ""Fanconi anemia, complementation groups"""	20748	protein-coding gene	gene with protein product		608111	"""PHD finger protein 9"""	PHF9			Standard	NM_018062		Approved	FLJ10335, FAAP43, Pog	uc002rzx.4	Q9NW38	OTTHUMG00000129349	ENST00000233741.4:c.981T>C	2.37:g.58388696A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	186	89	0.478495	NM_001114636	Q6GU60	Silent	SNP	ENST00000233741.4	37	CCDS1860.1																																																																																			A|0.313;G|0.687	0.687	strong		0.313	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062	
TANC1	85461	hgsc.bcm.edu	37	2	160035195	160035195	+	Silent	SNP	C	C	T	rs12988603	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:160035195C>T	ENST00000263635.6	+	14	2268	c.2031C>T	c.(2029-2031)aaC>aaT	p.N677N	TANC1_ENST00000454300.1_Silent_p.N571N	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	677					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						TCCTCAGCAACATCTCCCTGA	0.567													C|||	800	0.159744	0.0703	0.2478	5008	,	,		18770	0.0635		0.3688	False		,,,				2504	0.1022				p.N677N		Atlas-SNP	.											.	TANC1	157	.	0			c.C2031T						PASS	.	C	,	549,3793		35,479,1657	55.0	58.0	57.0		2007,2031	5.0	1.0	2	dbSNP_121	57	3069,5431		549,1971,1730	no	coding-synonymous,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	584,2450,3387	TT,TC,CC		36.1059,12.6439,28.1732	,	669/1391,677/1862	160035195	3618,9224	2171	4250	6421	SO:0001819	synonymous_variant	85461	exon14			CAGCAACATCTCC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.2031C>T	2.37:g.160035195C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	190	100	0.526316	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			C|0.763;T|0.237	0.237	strong		0.567	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
SLC25A41	284427	hgsc.bcm.edu	37	19	6430106	6430106	+	Missense_Mutation	SNP	C	C	T	rs34488963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6430106C>T	ENST00000321510.6	-	3	498	c.430G>A	c.(430-432)Ggc>Agc	p.G144S		NM_173637.3	NP_775908.2			solute carrier family 25, member 41									p.G144S(1)		large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	6						GAGCGGAAGCCGCCCTCCTGG	0.617													c|||	509	0.101637	0.09	0.0476	5008	,	,		15595	0.1538		0.0845	False		,,,				2504	0.1196				p.G144S		Atlas-SNP	.											SLC25A41,NS,carcinoma,0,1	SLC25A41	26	1	1	Substitution - Missense(1)	stomach(1)	c.G430A						PASS	.	C	SER/GLY	306,3762		6,294,1734	30.0	37.0	34.0		430	3.2	0.1	19	dbSNP_126	34	478,7940		18,442,3749	yes	missense	SLC25A41	NM_173637.3	56	24,736,5483	TT,TC,CC		5.6783,7.5221,6.279	probably-damaging	144/371	6430106	784,11702	2034	4209	6243	SO:0001583	missense	284427	exon3			GGAAGCCGCCCTC	AK097761	CCDS45937.1	19p13.3	2013-05-22			ENSG00000181240	ENSG00000181240		"""Solute carriers"""	28533	protein-coding gene	gene with protein product		610822				16949250	Standard	NM_173637		Approved	FLJ40442, MGC34725, APC4	uc010dus.3	Q8N5S1		ENST00000321510.6:c.430G>A	19.37:g.6430106C>T	ENSP00000322649:p.Gly144Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	51	0.662338	NM_173637		Missense_Mutation	SNP	ENST00000321510.6	37	CCDS45937.1	194	0.08882783882783883	45	0.09146341463414634	20	0.055248618784530384	74	0.12937062937062938	55	0.07255936675461741	c	19.83	3.900127	0.72754	0.075221	0.056783	ENSG00000181240	ENST00000321510	D	0.95137	-3.62	4.31	3.25	0.37280	Mitochondrial carrier domain (2);	.	.	.	.	T	0.37517	0.1006	M	0.86502	2.82	0.09310	P	1.0	D	0.89917	1.0	D	0.79784	0.993	T	0.62932	-0.6749	8	0.72032	D	0.01	-14.8076	12.9865	0.58594	0.0:0.8353:0.1647:0.0	rs34488963;rs34488963	144	Q8N5S1	S2541_HUMAN	S	144	ENSP00000322649:G144S	ENSP00000322649:G144S	G	-	1	0	SLC25A41	6381106	1.000000	0.71417	0.093000	0.20910	0.448000	0.32197	7.146000	0.77373	0.998000	0.38996	-0.529000	0.04317	GGC	C|0.911;T|0.089	0.089	strong		0.617	SLC25A41-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462222.1	NM_173637	
KIAA1804	84451	hgsc.bcm.edu	37	1	233515413	233515413	+	Silent	SNP	G	G	A	rs1402815	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:233515413G>A	ENST00000366624.3	+	9	2922	c.2661G>A	c.(2659-2661)ccG>ccA	p.P887P	MLK4_ENST00000366622.1_Silent_p.P333P	NM_032435.2	NP_115811.2																					AACATAGACCGTCACATCACA	0.423													G|||	1095	0.21865	0.0144	0.1599	5008	,	,		21358	0.3294		0.3469	False		,,,				2504	0.2904				p.P887P		Atlas-SNP	.											.	KIAA1804	129	.	0			c.G2661A						PASS	.	G		295,4111	162.2+/-194.2	8,279,1916	80.0	71.0	74.0		2661	-4.4	0.0	1	dbSNP_88	74	2908,5692	454.1+/-363.4	472,1964,1864	no	coding-synonymous	KIAA1804	NM_032435.2		480,2243,3780	AA,AG,GG		33.814,6.6954,24.6271		887/1037	233515413	3203,9803	2203	4300	6503	SO:0001819	synonymous_variant	0	exon9			TAGACCGTCACAT																												ENST00000366624.3:c.2661G>A	1.37:g.233515413G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_032435		Silent	SNP	ENST00000366624.3	37	CCDS1598.1																																																																																			G|0.748;A|0.252	0.252	strong		0.423	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
CUBN	8029	hgsc.bcm.edu	37	10	16919052	16919052	+	Missense_Mutation	SNP	T	T	C	rs1801239	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:16919052T>C	ENST00000377833.4	-	57	9015	c.8950A>G	c.(8950-8952)Att>Gtt	p.I2984V		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2984	CUB 22. {ECO:0000255|PROSITE- ProRule:PRU00059}.		I -> V (in dbSNP:rs1801239). {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)	CCTCTGATAATGTGCACGCCA	0.517													T|||	315	0.0628994	0.025	0.085	5008	,	,		18185	0.002		0.0915	False		,,,				2504	0.1319				p.I2984V		Atlas-SNP	.											.	CUBN	515	.	0			c.A8950G						PASS	.	T	VAL/ILE	148,4258	101.6+/-140.2	1,146,2056	99.0	76.0	84.0	http://www.ncbi.nlm.nih.gov/pubmed?term	8950	3.6	1.0	10	dbSNP_89	84	889,7711	199.0+/-243.2	49,791,3460	yes	missense	CUBN	NM_001081.3	29	50,937,5516	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	10.3372,3.3591,7.9732	benign	2984/3624	16919052	1037,11969	2203	4300	6503	SO:0001583	missense	8029	exon57			TGATAATGTGCAC	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.8950A>G	10.37:g.16919052T>C	ENSP00000367064:p.Ile2984Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	91	51	0.56044	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	115	0.052655677655677656	14	0.028455284552845527	33	0.09116022099447514	0	0.0	68	0.08970976253298153	T	5.376	0.254611	0.10185	0.033591	0.103372	ENSG00000107611	ENST00000377833	T	0.58797	0.31	5.91	3.63	0.41609	CUB (5);	0.000000	0.47455	D	0.000224	T	0.01061	0.0035	N	0.17764	0.52	0.09310	P	0.9999999999999635	B	0.16166	0.016	B	0.17098	0.017	T	0.07520	-1.0768	9	0.11794	T	0.64	.	10.0703	0.42328	0.0:0.1217:0.0:0.8783	rs1801239;rs17427010;rs52799504;rs57524627;rs1801239	2984	O60494	CUBN_HUMAN	V	2984	ENSP00000367064:I2984V	ENSP00000367064:I2984V	I	-	1	0	CUBN	16959058	1.000000	0.71417	0.963000	0.40424	0.023000	0.10783	2.000000	0.40816	2.254000	0.74563	0.533000	0.62120	ATT	T|0.930;C|0.070	0.070	strong		0.517	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
HGFAC	3083	hgsc.bcm.edu	37	4	3446132	3446132	+	Missense_Mutation	SNP	C	C	G	rs111368413|rs1987546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:3446132C>G	ENST00000382774.3	+	6	808	c.693C>G	c.(691-693)ttC>ttG	p.F231L	HGFAC_ENST00000511533.1_Missense_Mutation_p.F231L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	231	Fibronectin type-I. {ECO:0000255|PROSITE- ProRule:PRU00478}.		F -> L (in dbSNP:rs1987546). {ECO:0000269|PubMed:15489334}.		proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GCGAGTGCTTCGGGGGCCGGA	0.677													G|||	3676	0.734026	0.6619	0.7262	5008	,	,		15879	0.9236		0.7197	False		,,,				2504	0.6564				p.F231L		Atlas-SNP	.											.	HGFAC	69	.	0			c.C693G						PASS	.	G	LEU/PHE	2876,1482		989,898,292	11.0	13.0	12.0		693	-2.2	0.0	4	dbSNP_92	12	5811,2755		2018,1775,490	no	missense	HGFAC	NM_001528.2	22	3007,2673,782	GG,GC,CC		32.162,34.0064,32.784	benign	231/656	3446132	8687,4237	2179	4283	6462	SO:0001583	missense	3083	exon6			GTGCTTCGGGGGC	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.693C>G	4.37:g.3446132C>G	ENSP00000372224:p.Phe231Leu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	1683	0.7706043956043956	326	0.6626016260162602	263	0.7265193370165746	536	0.9370629370629371	558	0.7361477572559367	G	0.365	-0.937015	0.02340	0.659936	0.67838	ENSG00000109758	ENST00000382774;ENST00000511533	T;T	0.37584	1.19;1.19	3.61	-2.24	0.06909	Fibronectin, type I (4);	2.027680	0.02261	N	0.067530	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	0.36089	-0.9762	9	0.26408	T	0.33	.	8.6734	0.34165	0.0:0.4709:0.1813:0.3478	rs1987546;rs60554660	231;231	D6RAR4;Q04756	.;HGFA_HUMAN	L	231	ENSP00000372224:F231L;ENSP00000421801:F231L	ENSP00000372224:F231L	F	+	3	2	HGFAC	3415930	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.770000	0.00371	-0.409000	0.07553	-0.647000	0.03941	TTC	C|0.293;G|0.707	0.707	strong		0.677	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
RDH8	50700	hgsc.bcm.edu	37	19	10132290	10132290	+	Silent	SNP	C	C	T	rs747574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10132290C>T	ENST00000171214.1	+	6	1050	c.801C>T	c.(799-801)ctC>ctT	p.L267L	RDH8_ENST00000591589.1_Silent_p.L287L	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	267					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TGACCACGCTCAAAACCGTGG	0.602													C|||	1068	0.213259	0.0688	0.1974	5008	,	,		18015	0.3938		0.1451	False		,,,				2504	0.3037				p.L287L		Atlas-SNP	.											.	RDH8	51	.	0			c.C861T						PASS	.	C		403,4003	200.1+/-223.5	17,369,1817	109.0	103.0	105.0		801	2.1	0.5	19	dbSNP_86	105	1278,7322	254.6+/-279.8	90,1098,3112	no	coding-synonymous	RDH8	NM_015725.2		107,1467,4929	TT,TC,CC		14.8605,9.1466,12.9248		267/312	10132290	1681,11325	2203	4300	6503	SO:0001819	synonymous_variant	50700	exon6			CACGCTCAAAACC	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	14423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 28C, member 2"""	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.801C>T	19.37:g.10132290C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	37																																																																																				C|0.835;T|0.165	0.165	strong		0.602	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
PRKD3	23683	hgsc.bcm.edu	37	2	37518105	37518105	+	Silent	SNP	A	A	G	rs138302731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:37518105A>G	ENST00000379066.1	-	4	1227	c.465T>C	c.(463-465)caT>caC	p.H155H	PRKD3_ENST00000234179.2_Silent_p.H155H			O94806	KPCD3_HUMAN	protein kinase D3	155					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)				CATAGAGAGTATGTGGACGAA	0.388													A|||	2	0.000399361	0.0	0.0	5008	,	,		19716	0.0		0.0	False		,,,				2504	0.002				p.H155H	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.T465C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	163.0	158.0	159.0		465	1.0	1.0	2	dbSNP_134	159	3,8597	2.2+/-6.3	0,3,4297	yes	coding-synonymous	PRKD3	NM_005813.3		0,4,6499	GG,GA,AA		0.0349,0.0227,0.0308		155/891	37518105	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon3			GAGAGTATGTGGA	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.465T>C	2.37:g.37518105A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			A|1.000;G|0.000	0.000	strong		0.388	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
ZNF611	81856	hgsc.bcm.edu	37	19	53209553	53209553	+	Missense_Mutation	SNP	G	G	A	rs4085566|rs34846371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:53209553G>A	ENST00000319783.1	-	7	1071	c.755C>T	c.(754-756)cCc>cTc	p.P252L	ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000543227.1_Missense_Mutation_p.P252L|ZNF611_ENST00000595798.1_Missense_Mutation_p.P183L|ZNF611_ENST00000540744.1_Missense_Mutation_p.P252L|ZNF611_ENST00000453741.2_Missense_Mutation_p.P183L|ZNF611_ENST00000602162.1_Missense_Mutation_p.P183L	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	151	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	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	
GFRAL	389400	hgsc.bcm.edu	37	6	55196587	55196587	+	Missense_Mutation	SNP	C	C	T	rs12199003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	83	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	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	
VN1R1	57191	hgsc.bcm.edu	37	19	57967133	57967133	+	Missense_Mutation	SNP	G	G	A	rs28649880	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57967133G>A	ENST00000321039.3	-	1	721	c.722C>T	c.(721-723)tCc>tTc	p.S241F	AC004076.9_ENST00000415705.3_Intron|AC004076.9_ENST00000596831.1_Intron	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	241			S -> F (in allele VN1R1*3; dbSNP:rs28649880). {ECO:0000269|PubMed:10973240, ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		GAAGACCATGGAGCCACTGGC	0.468													G|||	2073	0.413938	0.3124	0.451	5008	,	,		19142	0.5913		0.2793	False		,,,				2504	0.4806				p.S241F		Atlas-SNP	.											VN1R1,NS,adenoma,0,1	VN1R1	48	1	0			c.C722T						PASS	.	G	PHE/SER	1344,3062	450.6+/-349.4	189,966,1048	112.0	87.0	95.0		722	0.4	0.0	19	dbSNP_125	95	2453,6147	403.9+/-348.0	330,1793,2177	yes	missense	VN1R1	NM_020633.3	155	519,2759,3225	AA,AG,GG		28.5233,30.5039,29.1942	probably-damaging	241/354	57967133	3797,9209	2203	4300	6503	SO:0001583	missense	57191	exon1			ACCATGGAGCCAC	AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	13548	protein-coding gene	gene with protein product		605234	"""vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"""	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.722C>T	19.37:g.57967133G>A	ENSP00000322339:p.Ser241Phe	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	211	211	1	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	878	0.40201465201465203	149	0.30284552845528456	135	0.3729281767955801	368	0.6433566433566433	226	0.29815303430079154	G	11.87	1.766615	0.31228	0.305039	0.285233	ENSG00000178201	ENST00000321039	T	0.08370	3.1	4.11	0.384	0.16244	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	L	0.48877	1.53	0.80722	P	0.0	P	0.45283	0.855	P	0.47573	0.55	T	0.30179	-0.9987	8	0.08599	T	0.76	.	2.0499	0.03568	0.1073:0.1653:0.4256:0.3017	rs28649880	241	Q9GZP7	VN1R1_HUMAN	F	241	ENSP00000322339:S241F	ENSP00000322339:S241F	S	-	2	0	VN1R1	62658945	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	-0.546000	0.06062	0.461000	0.27071	0.603000	0.83216	TCC	G|0.674;A|0.326	0.326	strong		0.468	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633	
RNF112	7732	hgsc.bcm.edu	37	17	19316656	19316656	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19316656G>A	ENST00000461366.1	+	5	867	c.652G>A	c.(652-654)Gcc>Acc	p.A218T	CTB-187M2.2_ENST00000579897.1_RNA|RNF112_ENST00000580109.1_3'UTR	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	218	GB1/RHD3-type G.					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						CAGGTGGGGCGCCAATGGCCT	0.642																																					p.A218T		Atlas-SNP	.											.	RNF112	37	.	0			c.G652A						PASS	.						20.0	24.0	23.0					17																	19316656		1952	4129	6081	SO:0001583	missense	7732	exon5			TGGGGCGCCAATG	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.652G>A	17.37:g.19316656G>A	ENSP00000454919:p.Ala218Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_007148	O60633|Q7Z5V9	Missense_Mutation	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			.	.	none		0.642	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
AHNAK2	113146	hgsc.bcm.edu	37	14	105408955	105408955	+	Missense_Mutation	SNP	A	A	G	rs2819422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	184	0	0		WXS	Illumina HiSeq	Phase_I	208	206	0.990385	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	
COL6A3	1293	hgsc.bcm.edu	37	2	238243292	238243292	+	Missense_Mutation	SNP	G	G	A	rs1131296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:238243292G>A	ENST00000295550.4	-	41	9658	c.9206C>T	c.(9205-9207)aCc>aTc	p.T3069I	COL6A3_ENST00000347401.3_Missense_Mutation_p.T2868I|COL6A3_ENST00000353578.4_Missense_Mutation_p.T2863I|COL6A3_ENST00000346358.4_Missense_Mutation_p.T2869I|COL6A3_ENST00000472056.1_Missense_Mutation_p.T2462I|COL6A3_ENST00000409809.1_Missense_Mutation_p.T2863I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3069	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region.		T -> I (in dbSNP:rs1131296). {ECO:0000269|PubMed:17886299}.		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)		TCCGTGGTAGGTGGCTCTGAC	0.502													G|||	1734	0.346246	0.2504	0.3256	5008	,	,		18933	0.4802		0.4036	False		,,,				2504	0.2935				p.T3069I		Atlas-SNP	.											.	COL6A3	608	.	0			c.C9206T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	1256,3150	430.6+/-342.6	191,874,1138	71.0	60.0	63.0		8588,7385,9206	-1.1	0.2	2	dbSNP_86	63	3456,5144	507.7+/-376.9	696,2064,1540	yes	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	89,89,89	887,2938,2678	AA,AG,GG		40.186,28.5066,36.2294	benign,benign,benign	2863/2972,2462/2571,3069/3178	238243292	4712,8294	2203	4300	6503	SO:0001583	missense	1293	exon41			TGGTAGGTGGCTC	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.9206C>T	2.37:g.238243292G>A	ENSP00000295550:p.Thr3069Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	132	57	0.431818	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	826	0.3782051282051282	127	0.258130081300813	121	0.3342541436464088	284	0.4965034965034965	294	0.38786279683377306	G	11.26	1.586755	0.28268	0.285066	0.40186	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	5.43	-1.13	0.09775	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.851480	0.10078	N	0.718837	T	0.00012	0.0000	N	0.14661	0.345	0.42095	P	0.008685999999999972	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.11329	0.003;0.006;0.003	T	0.48703	-0.9012	9	0.25751	T	0.34	.	9.5989	0.39591	0.4842:0.0:0.5158:0.0	rs1131296;rs2270670;rs3088291;rs3191076;rs11547644;rs17352867;rs59730490;rs1131296	2462;2863;3069	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	I	3069;2868;2863;2462;2863;2869	ENSP00000295550:T3069I;ENSP00000315609:T2868I;ENSP00000315873:T2863I;ENSP00000418285:T2462I;ENSP00000386844:T2863I;ENSP00000295546:T2869I	ENSP00000295550:T3069I	T	-	2	0	COL6A3	237908031	0.913000	0.31002	0.164000	0.22755	0.986000	0.74619	0.603000	0.24149	-0.602000	0.05775	0.557000	0.71058	ACC	G|0.635;A|0.365	0.365	strong		0.502	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
GFM1	85476	hgsc.bcm.edu	37	3	158408032	158408032	+	Missense_Mutation	SNP	G	G	A	rs62288347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:158408032G>A	ENST00000486715.1	+	16	2347	c.1990G>A	c.(1990-1992)Gta>Ata	p.V664I	GFM1_ENST00000264263.5_Missense_Mutation_p.V683I|RP11-379F4.7_ENST00000607624.1_lincRNA	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)			TCAGGGACAAGTAATTGCAGG	0.393													G|||	35	0.00698882	0.0	0.0058	5008	,	,		17035	0.0		0.0258	False		,,,				2504	0.0051				p.V664I		Atlas-SNP	.											.	GFM1	83	.	0			c.G1990A						PASS	.	G	ILE/VAL	10,4396	19.1+/-41.9	0,10,2193	167.0	167.0	167.0		1990	5.8	0.4	3	dbSNP_129	167	175,8425	80.4+/-143.0	0,175,4125	yes	missense	GFM1	NM_024996.5	29	0,185,6318	AA,AG,GG		2.0349,0.227,1.4224	possibly-damaging	664/752	158408032	185,12821	2203	4300	6503	SO:0001583	missense	85476	exon16			GGACAAGTAATTG	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.1990G>A	3.37:g.158408032G>A	ENSP00000419038:p.Val664Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	37	CCDS33885.1	27	0.012362637362637362	0	0.0	3	0.008287292817679558	0	0.0	24	0.0316622691292876	G	19.54	3.846986	0.71603	0.00227	0.020349	ENSG00000168827	ENST00000486715;ENST00000264263	T;T	0.60299	0.2;0.2	5.8	5.8	0.92144	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.063724	0.64402	D	0.000007	T	0.31702	0.0805	N	0.26092	0.79	0.80722	D	1	P;P	0.41848	0.72;0.763	B;P	0.45946	0.365;0.498	T	0.48536	-0.9027	10	0.54805	T	0.06	-5.1032	20.0589	0.97667	0.0:0.0:1.0:0.0	rs62288347	683;664	Q96RP9-2;Q96RP9	.;EFGM_HUMAN	I	664;683	ENSP00000419038:V664I;ENSP00000264263:V683I	ENSP00000264263:V683I	V	+	1	0	GFM1	159890726	1.000000	0.71417	0.420000	0.26596	0.975000	0.68041	7.491000	0.81471	2.732000	0.93576	0.650000	0.86243	GTA	G|0.986;A|0.014	0.014	strong		0.393	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
CALCR	799	hgsc.bcm.edu	37	7	93108763	93108763	+	Silent	SNP	G	G	C	rs144326254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:93108763G>C	ENST00000394441.1	-	3	423	c.108C>G	c.(106-108)ccC>ccG	p.P36P	CALCR_ENST00000421592.1_Silent_p.P36P|CALCR_ENST00000360249.4_Silent_p.P36P|CALCR_ENST00000359558.2_Silent_p.P54P|CALCR_ENST00000426151.1_Silent_p.P36P	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	54					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	GAAATGGCTTGGGCTCTATTG	0.418													G|||	27	0.00539137	0.0121	0.0072	5008	,	,		16950	0.0		0.006	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											.	CALCR	200	.	0			c.C162G						PASS	.	G	,,	35,4371	40.0+/-72.8	0,35,2168	179.0	168.0	171.0		162,108,108	-7.4	0.0	7	dbSNP_134	171	30,8570	21.6+/-65.8	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	,,	0,65,6438	CC,CG,GG		0.3488,0.7944,0.4998	,,	54/509,36/475,36/475	93108763	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	799	exon5			TGGCTTGGGCTCT	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.108C>G	7.37:g.93108763G>C		Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	276	132	0.478261	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Silent	SNP	ENST00000394441.1	37	CCDS5631.1																																																																																			G|0.995;C|0.005	0.005	strong		0.418	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
SLC6A5	9152	hgsc.bcm.edu	37	11	20623023	20623023	+	Silent	SNP	C	C	T	rs2241941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:20623023C>T	ENST00000525748.1	+	2	625	c.352C>T	c.(352-354)Ctg>Ttg	p.L118L		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	118					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CGGCAACGCGCTGCACTGTAA	0.701													C|||	1637	0.326877	0.326	0.3199	5008	,	,		15702	0.3641		0.3489	False		,,,				2504	0.272				p.L118L		Atlas-SNP	.											.	SLC6A5	151	.	0			c.C352T						PASS	.	C		1389,3017		206,977,1020	44.0	44.0	44.0		352	1.7	0.9	11	dbSNP_98	44	2831,5767		472,1887,1940	no	coding-synonymous	SLC6A5	NM_004211.3		678,2864,2960	TT,TC,CC		32.9263,31.5252,32.4516		118/798	20623023	4220,8784	2203	4299	6502	SO:0001819	synonymous_variant	9152	exon2			AACGCGCTGCACT	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.352C>T	11.37:g.20623023C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	44	43	0.977273	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			C|0.662;A|0.004	.	strong		0.701	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
ABCC3	8714	hgsc.bcm.edu	37	17	48761105	48761105	+	Silent	SNP	C	C	T	rs2277624	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48761105C>T	ENST00000285238.8	+	27	4022	c.3942C>T	c.(3940-3942)caC>caT	p.H1314H		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1314	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TGCATGTGCACGGTGGCGAGA	0.622													c|||	1437	0.286941	0.4032	0.268	5008	,	,		19433	0.2411		0.2227	False		,,,				2504	0.2566				p.H1314H		Atlas-SNP	.											.	ABCC3	138	.	0			c.C3942T						PASS	.			1560,2846	490.4+/-361.8	279,1002,922	128.0	120.0	123.0		3942	-11.9	0.0	17	dbSNP_100	123	1882,6718	335.6+/-321.5	206,1470,2624	no	coding-synonymous	ABCC3	NM_003786.3		485,2472,3546	TT,TC,CC		21.8837,35.4063,26.4647		1314/1528	48761105	3442,9564	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon27			TGTGCACGGTGGC	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.3942C>T	17.37:g.48761105C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			C|0.739;T|0.261	0.261	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
CFAP43	80217	hgsc.bcm.edu	37	10	105900732	105900732	+	Silent	SNP	C	C	T	rs45618238	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:105900732C>T	ENST00000357060.3	-	34	4414	c.4299G>A	c.(4297-4299)caG>caA	p.Q1433Q	WDR96_ENST00000428666.1_Silent_p.Q1405Q|WDR96_ENST00000479392.1_5'UTR	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						TCAAATTCAACTGGAATCTCA	0.313													C|||	32	0.00638978	0.0023	0.0101	5008	,	,		16685	0.0		0.0169	False		,,,				2504	0.0051				p.Q1433Q		Atlas-SNP	.											.	WDR96	183	.	0			c.G4299A						PASS	.	C		22,4384	29.9+/-59.1	1,20,2182	75.0	73.0	74.0		4299	2.5	1.0	10	dbSNP_127	74	229,8365	93.3+/-155.3	6,217,4074	no	coding-synonymous	WDR96	NM_025145.5		7,237,6256	TT,TC,CC		2.6646,0.4993,1.9308		1433/1666	105900732	251,12749	2203	4297	6500	SO:0001819	synonymous_variant	80217	exon34			ATTCAACTGGAAT																												ENST00000357060.3:c.4299G>A	10.37:g.105900732C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_025145		Silent	SNP	ENST00000357060.3	37	CCDS31281.1	17	0.007783882783882784	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	11	0.014511873350923483	C	7.393	0.631080	0.14322	0.004993	0.026646	ENSG00000197748	ENST00000457071;ENST00000434629	.	.	.	5.51	2.53	0.30540	.	.	.	.	.	T	0.21841	0.0526	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.10965	-1.0607	4	.	.	.	.	2.6726	0.05071	0.3131:0.4295:0.1522:0.1052	rs45618238	.	.	.	N	282;765	.	.	S	-	2	0	WDR96	105890722	0.409000	0.25368	0.997000	0.53966	0.993000	0.82548	0.504000	0.22626	0.247000	0.21414	-0.181000	0.13052	AGT	C|0.985;T|0.015	0.015	strong		0.313	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
EPHA10	284656	hgsc.bcm.edu	37	1	38184343	38184343	+	Missense_Mutation	SNP	T	T	C	rs201769517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:38184343T>C	ENST00000373048.4	-	16	2901	c.2902A>G	c.(2902-2904)Atg>Gtg	p.M968V	EPHA10_ENST00000330210.7_Missense_Mutation_p.M463V|EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000427468.2_Missense_Mutation_p.M968V|EPHA10_ENST00000446149.2_5'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	968	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)				TGGGCAGTCATCTCGGCCACG	0.662													T|||	4	0.000798722	0.0	0.0029	5008	,	,		17173	0.001		0.001	False		,,,				2504	0.0				p.M968V		Atlas-SNP	.											.	EPHA10	120	.	0			c.A2902G						PASS	.	T	VAL/MET	0,3998		0,0,1999	24.0	28.0	26.0		2902	3.7	1.0	1		26	4,8338		0,4,4167	no	missense	EPHA10	NM_001099439.1	21	0,4,6166	CC,CT,TT		0.048,0.0,0.0324	possibly-damaging	968/1009	38184343	4,12336	1999	4171	6170	SO:0001583	missense	284656	exon16			CAGTCATCTCGGC	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.2902A>G	1.37:g.38184343T>C	ENSP00000362139:p.Met968Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	149	83	0.557047	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.348125	0.41599	0.0	4.8E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000373048	T;T;T	0.52295	0.67;0.67;0.67	4.88	3.67	0.42095	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.47455	D	0.000232	T	0.54919	0.1888	L	0.56199	1.76	0.80722	D	1	P	0.52170	0.951	P	0.57679	0.825	T	0.53187	-0.8474	10	0.38643	T	0.18	.	10.8344	0.46679	0.0:0.0:0.158:0.842	.	968	Q5JZY3	EPHAA_HUMAN	V	463;968;968	ENSP00000330379:M463V;ENSP00000397746:M968V;ENSP00000362139:M968V	ENSP00000330379:M463V	M	-	1	0	EPHA10	37956930	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	4.864000	0.62990	1.969000	0.57287	0.402000	0.26972	ATG	T|0.998;C|0.002	0.002	strong		0.662	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
CHST15	51363	hgsc.bcm.edu	37	10	125798111	125798111	+	Silent	SNP	T	T	C	rs28375663	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:125798111T>C	ENST00000346248.5	-	5	1752	c.1110A>G	c.(1108-1110)ccA>ccG	p.P370P	CHST15_ENST00000421115.1_Silent_p.P370P|CHST15_ENST00000435907.1_Silent_p.P370P	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	370					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)			endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						TCAGAAACGGTGGCTCGCCAT	0.532													T|||	594	0.11861	0.1891	0.1585	5008	,	,		16463	0.0089		0.164	False		,,,				2504	0.0613				p.P370P		Atlas-SNP	.											CHST15_ENST00000421115,NS,carcinoma,0,2	CHST15	134	2	0			c.A1110G						PASS	.	T	,	754,3652	310.0+/-291.3	62,630,1511	124.0	97.0	106.0		1110,1110	-10.2	0.3	10	dbSNP_125	106	1402,7198	270.8+/-289.2	120,1162,3018	no	coding-synonymous,coding-synonymous	CHST15	NM_014863.2,NM_015892.3	,	182,1792,4529	CC,CT,TT		16.3023,17.113,16.577	,	370/507,370/562	125798111	2156,10850	2203	4300	6503	SO:0001819	synonymous_variant	51363	exon5			AAACGGTGGCTCG	AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1110A>G	10.37:g.125798111T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_014863	O60338|O60474|Q86VM4	Silent	SNP	ENST00000346248.5	37	CCDS7638.1																																																																																			T|0.852;C|0.148	0.148	strong		0.532	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892	
OR4A5	81318	hgsc.bcm.edu	37	11	51411740	51411740	+	Missense_Mutation	SNP	A	A	T	rs35083184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:51411740A>T	ENST00000319760.6	-	1	708	c.656T>A	c.(655-657)cTa>cAa	p.L219Q		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	219			L -> Q (in dbSNP:rs35083184).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				AAGGGAGCTTAGGATGACTCC	0.438													.|||	406	0.0810703	0.056	0.0591	5008	,	,		19988	0.0863		0.1252	False		,,,				2504	0.0798				p.L219Q		Atlas-SNP	.											.	OR4A5	116	.	0			c.T656A						PASS	.	A	GLN/LEU	240,4162		7,226,1968	60.0	60.0	60.0		656	0.7	0.3	11	dbSNP_126	60	1040,7550		60,920,3315	yes	missense	OR4A5	NM_001005272.3	113	67,1146,5283	TT,TA,AA		12.1071,5.4521,9.8522	possibly-damaging	219/316	51411740	1280,11712	2201	4295	6496	SO:0001583	missense	81318	exon1			GAGCTTAGGATGA	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.656T>A	11.37:g.51411740A>T	ENSP00000367664:p.Leu219Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	185	0.08470695970695971	30	0.06097560975609756	28	0.07734806629834254	35	0.06118881118881119	92	0.12137203166226913	.	8.099	0.776258	0.16051	0.054521	0.121071	ENSG00000221840	ENST00000319760	T	0.00249	8.44	1.93	0.659	0.17861	GPCR, rhodopsin-like superfamily (1);	0.204155	0.24258	N	0.040117	T	0.00012	0.0000	H	0.96576	3.845	0.80722	P	0.0	P	0.38370	0.628	P	0.53689	0.732	T	0.08848	-1.0702	9	0.87932	D	0	.	6.1148	0.20120	0.7386:0.2614:0.0:0.0	rs35083184	219	Q8NH83	OR4A5_HUMAN	Q	219	ENSP00000367664:L219Q	ENSP00000367664:L219Q	L	-	2	0	OR4A5	51268316	0.004000	0.15560	0.262000	0.24481	0.026000	0.11368	1.313000	0.33585	0.166000	0.19597	0.136000	0.15936	CTA	A|0.903;T|0.097	0.097	strong		0.438	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
MTRNR2L5	100463289	hgsc.bcm.edu	37	10	57359697	57359697	+	Missense_Mutation	SNP	C	C	T	rs11004928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:57359697C>T	ENST00000512524.2	+	1	948	c.38C>T	c.(37-39)aCc>aTc	p.T13I	RP11-168O22.1_ENST00000457975.2_RNA|PCDH15_ENST00000373957.3_Intron	NM_001190478.1	NP_001177407.1			MT-RNR2-like 5																		ttactttcaaccagtgaaatt	0.413													C|||	1779	0.355232	0.2057	0.3674	5008	,	,		17367	0.4861		0.329	False		,,,				2504	0.4407				p.T13I		Atlas-SNP	.											.	.	.	.	0			c.C38T						PASS	.																																			SO:0001583	missense	100463289	exon1			TTTCAACCAGTGA		CCDS53537.1	10q21.1	2014-02-18			ENSG00000249860	ENSG00000249860			37162	protein-coding gene	gene with protein product	"""humanin-like 5"""					19477263	Standard	NM_001190478		Approved		uc021pra.1	P0CJ72	OTTHUMG00000184965	ENST00000512524.2:c.38C>T	10.37:g.57359697C>T	ENSP00000437910:p.Thr13Ile	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001190478		Missense_Mutation	SNP	ENST00000512524.2	37	CCDS53537.1	778	0.35622710622710624	102	0.2073170731707317	124	0.3425414364640884	297	0.5192307692307693	255	0.33641160949868076	.	4.758	0.140908	0.09083	.	.	ENSG00000249860	ENST00000512524	.	.	.	0.66	-1.32	0.09201	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999881	.	.	.	.	.	.	T	0.45352	-0.9267	4	0.87932	D	0	.	4.253	0.10703	0.0:0.2635:0.0:0.7365	rs11004928;rs59643989	.	.	.	I	13	.	ENSP00000437910:T13I	T	+	2	0	MTRNR2L5	57029703	1.000000	0.71417	0.701000	0.30321	0.141000	0.21300	2.757000	0.47557	-0.387000	0.07809	-0.708000	0.03648	ACC	C|0.642;T|0.358	0.358	strong		0.413	MTRNR2L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469382.1	NM_001190478	
ITGB4	3691	hgsc.bcm.edu	37	17	73747128	73747128	+	Silent	SNP	G	G	A	rs61735289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73747128G>A	ENST00000200181.3	+	30	3916	c.3729G>A	c.(3727-3729)ccG>ccA	p.P1243P	ITGB4_ENST00000579662.1_Silent_p.P1243P|ITGB4_ENST00000449880.2_Silent_p.P1243P|ITGB4_ENST00000450894.3_Silent_p.P1243P|ITGB4_ENST00000339591.3_Silent_p.P1243P	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1243	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGCTGAGCCGGCTGAGACCA	0.597													G|||	76	0.0151757	0.0015	0.0173	5008	,	,		22177	0.0		0.0348	False		,,,				2504	0.0276				p.P1243P		Atlas-SNP	.											ITGB4,rectum,carcinoma,0,1	ITGB4	165	1	0			c.G3729A						PASS	.	G	,,	30,4376	35.2+/-66.4	0,30,2173	92.0	85.0	88.0		3729,3729,3729	-10.7	0.0	17	dbSNP_129	88	323,8277	114.2+/-174.2	6,311,3983	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,,	6,341,6156	AA,AG,GG		3.7558,0.6809,2.7141	,,	1243/1823,1243/1806,1243/1753	73747128	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	3691	exon30			TGAGCCGGCTGAG		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3729G>A	17.37:g.73747128G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																			G|0.951;A|0.049	0.049	strong		0.597	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
NUDT6	11162	hgsc.bcm.edu	37	4	123838758	123838758	+	Missense_Mutation	SNP	A	A	G	rs12648093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:123838758A>G	ENST00000304430.5	-	2	373	c.340T>C	c.(340-342)Tgc>Cgc	p.C114R	NUDT6_ENST00000339154.2_5'UTR	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	114			C -> R (in dbSNP:rs12648093).			mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)	p.C114R(1)		endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						TGGTGAAAGCAGAAGCCCAGG	0.512													A|||	3033	0.605631	0.1959	0.6412	5008	,	,		18356	0.9415		0.7386	False		,,,				2504	0.6513				p.C114R		Atlas-SNP	.											NUDT6_ENST00000304430,NS,carcinoma,0,1	NUDT6	50	1	1	Substitution - Missense(1)	prostate(1)	c.T340C						scavenged	.	A	ARG/CYS,	1307,2715		221,865,925	136.0	135.0	135.0		340,	-7.9	0.5	4	dbSNP_120	135	6240,2138		2337,1566,286	yes	missense,utr-5	NUDT6	NM_007083.3,NM_198041.1	180,	2558,2431,1211	GG,GA,AA		25.5192,32.4963,39.1371	benign,	114/317,	123838758	7547,4853	2011	4189	6200	SO:0001583	missense	11162	exon2			GAAAGCAGAAGCC	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.340T>C	4.37:g.123838758A>G	ENSP00000306070:p.Cys114Arg	Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	202	108	0.534653	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	1429	0.6543040293040293	91	0.18495934959349594	242	0.6685082872928176	540	0.9440559440559441	556	0.7335092348284961	A	0.029	-1.345983	0.01266	0.324963	0.744808	ENSG00000170917	ENST00000304430	T	0.32753	1.44	4.63	-7.93	0.01156	NUDIX hydrolase domain-like (1);	1.421260	0.04236	N	0.336117	T	0.00012	0.0000	N	0.21373	0.66	0.41993	P	0.009149999999999991	B	0.02656	0.0	B	0.04013	0.001	T	0.21965	-1.0230	9	0.19147	T	0.46	-0.0013	2.8204	0.05469	0.1211:0.2256:0.3856:0.2677	rs12648093;rs17475160;rs52799868;rs58308287;rs12648093	114	P53370	NUDT6_HUMAN	R	114	ENSP00000306070:C114R	ENSP00000306070:C114R	C	-	1	0	NUDT6	124058208	0.000000	0.05858	0.535000	0.28026	0.005000	0.04900	-0.941000	0.03925	-1.553000	0.01702	-1.590000	0.00845	TGC	A|0.369;G|0.631	0.631	strong		0.512	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
ZNF492	57615	hgsc.bcm.edu	37	19	22847072	22847072	+	Missense_Mutation	SNP	G	G	C	rs146300593	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	396	0	0		WXS	Illumina HiSeq	Phase_I	410	171	0.417073	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	
TMEM81	388730	hgsc.bcm.edu	37	1	205052998	205052998	+	Missense_Mutation	SNP	G	G	T	rs369137007		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205052998G>T	ENST00000367167.3	-	1	647	c.451C>A	c.(451-453)Cag>Aag	p.Q151K		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	151	Ig-like.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9	all_cancers(21;0.144)|Breast(84;0.0437)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			TCATACTCCTGAGCATATTTA	0.478																																					p.Q151K		Atlas-SNP	.											TMEM81,NS,carcinoma,+2,1	TMEM81	23	1	0			c.C451A						scavenged	.	G	LYS/GLN	0,4406		0,0,2203	77.0	84.0	82.0		451	2.8	0.0	1		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	TMEM81	NM_203376.1	53	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign	151/256	205052998	1,13005	2203	4300	6503	SO:0001583	missense	388730	exon1			ACTCCTGAGCATA	BC061592	CCDS1450.1	1q32.1	2013-01-11			ENSG00000174529	ENSG00000174529		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	32349	protein-coding gene	gene with protein product							Standard	NM_203376		Approved	UNQ2788, MGC75217, HC3107, KVLA2788	uc001hbt.3	Q6P7N7	OTTHUMG00000037103	ENST00000367167.3:c.451C>A	1.37:g.205052998G>T	ENSP00000356135:p.Gln151Lys	Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_203376	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	37	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	G	3.064	-0.192683	0.06259	0.0	1.16E-4	ENSG00000174529	ENST00000367167	T	0.42900	0.96	5.93	2.81	0.32909	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.586479	0.17141	N	0.185438	T	0.23572	0.0570	L	0.43152	1.355	0.09310	N	1	B	0.21225	0.053	B	0.13407	0.009	T	0.28459	-1.0043	10	0.05436	T	0.98	-10.0286	1.3267	0.02127	0.183:0.1403:0.435:0.2417	.	151	Q6P7N7	TMM81_HUMAN	K	151	ENSP00000356135:Q151K	ENSP00000356135:Q151K	Q	-	1	0	TMEM81	203319621	0.004000	0.15560	0.012000	0.15200	0.685000	0.39939	1.419000	0.34793	0.793000	0.33875	0.655000	0.94253	CAG	.	.	none		0.478	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376	
GPAM	57678	hgsc.bcm.edu	37	10	113935379	113935379	+	Missense_Mutation	SNP	T	T	C	rs10787428	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	74	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	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	
CAPN1	823	hgsc.bcm.edu	37	11	64950970	64950970	+	Silent	SNP	C	C	T	rs17583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:64950970C>T	ENST00000527323.1	+	3	603	c.363C>T	c.(361-363)atC>atT	p.I121I	CAPN1_ENST00000524773.1_Silent_p.I121I|CAPN1_ENST00000527469.1_3'UTR|CAPN1_ENST00000279247.6_Silent_p.I121I|CAPN1_ENST00000533129.1_Silent_p.I121I|AP003068.23_ENST00000526623.1_5'Flank|CAPN1_ENST00000533820.1_Silent_p.I121I			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	121	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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)		TGGCGGCCATCGCCTCCCTCA	0.637													C|||	1225	0.244609	0.053	0.4035	5008	,	,		17061	0.2966		0.3012	False		,,,				2504	0.2791				p.I121I		Atlas-SNP	.											CAPN1,colon,carcinoma,0,1	CAPN1	44	1	0			c.C363T						PASS	.	C	,,	387,3821		14,359,1731	43.0	49.0	47.0		363,363,363	-3.1	0.9	11	dbSNP_63	47	2406,6032		320,1766,2133	no	coding-synonymous,coding-synonymous,coding-synonymous	CAPN1	NM_001198868.1,NM_001198869.1,NM_005186.3	,,	334,2125,3864	TT,TC,CC		28.5139,9.1968,22.086	,,	121/715,121/715,121/715	64950970	2793,9853	2104	4219	6323	SO:0001819	synonymous_variant	823	exon4			GGCCATCGCCTCC	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	ENST00000527323.1:c.363C>T	11.37:g.64950970C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_001198869	Q2TTR0|Q6DHV4	Silent	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			C|0.734;T|0.266	0.266	strong		0.637	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
CCL8	6355	hgsc.bcm.edu	37	17	32647891	32647891	+	Missense_Mutation	SNP	C	C	A	rs117180331	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:32647891C>A	ENST00000394620.1	+	3	731	c.265C>A	c.(265-267)Cat>Aat	p.H89N		NM_005623.2	NP_005614.2	P80075	CCL8_HUMAN	chemokine (C-C motif) ligand 8	89					calcium ion transport (GO:0006816)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|exocytosis (GO:0006887)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)|heparin binding (GO:0008201)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			NS(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Ovarian(249;0.0443)|Breast(31;0.151)				TTCCATGAAGCATCTGGACCA	0.488													C|||	12	0.00239617	0.0015	0.0014	5008	,	,		15783	0.0		0.006	False		,,,				2504	0.0031				p.H89N		Atlas-SNP	.											.	CCL8	12	.	0			c.C265A						PASS	.	C	ASN/HIS	5,4401	9.9+/-24.2	0,5,2198	68.0	61.0	64.0		265	3.3	0.0	17	dbSNP_132	64	45,8555	29.6+/-80.5	0,45,4255	yes	missense	CCL8	NM_005623.2	68	0,50,6453	AA,AC,CC		0.5233,0.1135,0.3844	benign	89/100	32647891	50,12956	2203	4300	6503	SO:0001583	missense	6355	exon3			ATGAAGCATCTGG	X99886	CCDS11280.1	17q11.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000108700	ENSG00000108700		"""Chemokine ligands"", ""Endogenous ligands"""	10635	protein-coding gene	gene with protein product		602283	"""small inducible cytokine subfamily A (Cys-Cys), member 8 (monocyte chemotactic protein 2)"""	SCYA8		9119400	Standard	NM_005623		Approved	MCP-2, HC14	uc002hib.3	P80075	OTTHUMG00000132883	ENST00000394620.1:c.265C>A	17.37:g.32647891C>A	ENSP00000378118:p.His89Asn	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	152	64	0.421053	NM_005623	A0AV77|P78388	Missense_Mutation	SNP	ENST00000394620.1	37	CCDS11280.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	13.07	2.126578	0.37533	0.001135	0.005233	ENSG00000108700	ENST00000394620;ENST00000225840	.	.	.	5.34	3.31	0.37934	Chemokine interleukin-8-like domain (3);	1.696870	0.03585	N	0.230781	T	0.24314	0.0589	.	.	.	0.09310	N	1	B	0.17465	0.022	B	0.18263	0.021	T	0.18085	-1.0348	8	0.32370	T	0.25	.	6.7614	0.23542	0.1745:0.7354:0.0:0.0901	.	89	P80075	CCL8_HUMAN	N	99;89	.	ENSP00000225840:H89N	H	+	1	0	CCL8	29672004	0.000000	0.05858	0.000000	0.03702	0.614000	0.37383	-0.385000	0.07379	0.612000	0.30071	0.563000	0.77884	CAT	C|0.995;A|0.005	0.005	strong		0.488	CCL8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256376.2	NM_005623	
DLK1	8788	hgsc.bcm.edu	37	14	101200645	101200645	+	Silent	SNP	T	T	C	rs1802710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:101200645T>C	ENST00000341267.4	+	5	806	c.564T>C	c.(562-564)atT>atC	p.I188I	DLK1_ENST00000331224.6_Silent_p.I188I	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	188	EGF-like 5. {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)		p.I188I(1)		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)				GCACTGACATTGGGGGCGACT	0.667													C|||	3722	0.743211	0.7731	0.6844	5008	,	,		14848	0.994		0.5447	False		,,,				2504	0.6902				p.I188I		Atlas-SNP	.											DLK1,NS,carcinoma,0,3	DLK1	57	3	1	Substitution - coding silent(1)	prostate(1)	c.T564C						PASS	.	C		3287,1119	384.4+/-325.3	1229,829,145	51.0	56.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	564	3.5	1.0	14	dbSNP_89	54	4287,4313	557.5+/-387.1	1092,2103,1105	no	coding-synonymous	DLK1	NM_003836.5		2321,2932,1250	CC,CT,TT		49.8488,25.3972,41.7653		188/384	101200645	7574,5432	2203	4300	6503	SO:0001819	synonymous_variant	8788	exon5			TGACATTGGGGGC	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.564T>C	14.37:g.101200645T>C		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	174	173	0.994253	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			T|0.353;C|0.647	0.647	strong		0.667	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
SOX7	83595	hgsc.bcm.edu	37	8	10583616	10583616	+	Missense_Mutation	SNP	C	C	T	rs180762782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10583616C>T	ENST00000304501.1	-	2	877	c.799G>A	c.(799-801)Ggc>Agc	p.G267S	SOX7_ENST00000553390.1_Missense_Mutation_p.G319S|SOX7_ENST00000554914.1_Missense_Mutation_p.G319S	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	267					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		ATGGAGACGCCGGGGGACTGG	0.672													C|||	6	0.00119808	0.0	0.0	5008	,	,		13618	0.0		0.006	False		,,,				2504	0.0				p.G267S		Atlas-SNP	.											.	SOX7	50	.	0			c.G799A						PASS	.	C	SER/GLY	5,4381		0,5,2188	23.0	30.0	27.0		799	2.9	0.4	8		27	73,8499		0,73,4213	yes	missense	SOX7	NM_031439.2	56	0,78,6401	TT,TC,CC		0.8516,0.114,0.6019	benign	267/389	10583616	78,12880	2193	4286	6479	SO:0001583	missense	83595	exon2			AGACGCCGGGGGA	AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"""SRY (sex determining region Y)-boxes"""	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.799G>A	8.37:g.10583616C>T	ENSP00000301921:p.Gly267Ser	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_031439	B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	CCDS5977.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	6.489	0.458490	0.12342	0.00114	0.008516	ENSG00000171056;ENSG00000171056;ENSG00000258724	ENST00000304501;ENST00000553390;ENST00000554914	T;T;T	0.75477	-0.94;-0.94;-0.94	4.84	2.92	0.33932	.	0.176595	0.48286	N	0.000186	T	0.47192	0.1432	L	0.38531	1.155	0.20074	N	0.999936	P;B	0.52170	0.951;0.205	B;B	0.40134	0.32;0.023	T	0.49606	-0.8922	10	0.07644	T	0.81	.	7.2334	0.26055	0.0:0.6938:0.1419:0.1643	.	319;267	B4DKV0;Q9BT81	.;SOX7_HUMAN	S	267;319;319	ENSP00000301921:G267S;ENSP00000452017:G319S;ENSP00000451145:G319S	ENSP00000346908:G319S	G	-	1	0	SOX7;CTD-2135J3.4	10621026	0.000000	0.05858	0.377000	0.26055	0.354000	0.29330	-0.036000	0.12185	1.021000	0.39600	-0.379000	0.06801	GGC	C|0.997;T|0.003	0.003	strong		0.672	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1		
P2RY11	5032	hgsc.bcm.edu	37	19	10226256	10226256	+	IGR	SNP	A	A	G	rs7710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:10226256A>G	ENST00000321826.4	+	0	1943				EIF3G_ENST00000253108.4_Silent_p.F282F	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11						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)			TGATGAAGGCAAAGCCCTGTG	0.667													G|||	2273	0.453874	0.407	0.5303	5008	,	,		14409	0.371		0.494	False		,,,				2504	0.5072				p.F282F		Atlas-SNP	.											.	EIF3G	16	.	0			c.T846C						PASS	.	G		1779,2627	638.1+/-396.9	350,1079,774	49.0	49.0	49.0		846	-1.9	1.0	19	dbSNP_52	49	3911,4687	602.8+/-394.6	895,2121,1283	no	coding-synonymous	EIF3G	NM_003755.3		1245,3200,2057	GG,GA,AA		45.4873,40.3768,43.7558		282/321	10226256	5690,7314	2203	4299	6502	SO:0001628	intergenic_variant	8666	exon10			GAAGGCAAAGCCC	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		19.37:g.10226256A>G		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_003755	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			A|0.564;G|0.436	0.436	strong		0.667	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
NDUFA8	4702	hgsc.bcm.edu	37	9	124914613	124914613	+	Silent	SNP	C	C	T	rs4679	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:124914613C>T	ENST00000373768.3	-	2	267	c.126G>A	c.(124-126)gaG>gaA	p.E42E	NDUFA8_ENST00000537618.1_Silent_p.E42E	NM_014222.2	NP_055037.1	P51970	NDUA8_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8, 19kDa	42	CHCH 1.				cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|protein complex binding (GO:0032403)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9						AGAGCATAAACTCCTTGTTGG	0.458													C|||	1692	0.337859	0.0908	0.3689	5008	,	,		16609	0.2014		0.6074	False		,,,				2504	0.5133				p.E42E		Atlas-SNP	.											NDUFA8,colon,carcinoma,0,1	NDUFA8	20	1	0			c.G126A						PASS	.	C		690,3716	289.2+/-280.3	55,580,1568	82.0	70.0	74.0		126	4.3	1.0	9	dbSNP_52	74	5277,3323	644.8+/-400.1	1615,2047,638	no	coding-synonymous	NDUFA8	NM_014222.2		1670,2627,2206	TT,TC,CC		38.6395,15.6605,45.8788		42/173	124914613	5967,7039	2203	4300	6503	SO:0001819	synonymous_variant	4702	exon2			CATAAACTCCTTG	AF044953	CCDS6835.1	9q33.2	2011-07-04	2002-08-29		ENSG00000119421	ENSG00000119421		"""Mitochondrial respiratory chain complex / Complex I"""	7692	protein-coding gene	gene with protein product	"""complex I PGIV subunit"""	603359	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8 (19kD, PGIV)"""			9763677	Standard	NM_014222		Approved	PGIV, MGC793	uc004blv.3	P51970	OTTHUMG00000020598	ENST00000373768.3:c.126G>A	9.37:g.124914613C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_014222	B1AM93|Q9Y6N0	Silent	SNP	ENST00000373768.3	37	CCDS6835.1																																																																																			C|0.603;T|0.397	0.397	strong		0.458	NDUFA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053909.1	NM_014222	
ASAH2	56624	hgsc.bcm.edu	37	10	52005057	52005057	+	Silent	SNP	T	T	C	rs201282742		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:52005057T>C	ENST00000395526.4	-	2	284	c.285A>G	c.(283-285)ctA>ctG	p.L95L	ASAH2_ENST00000329428.6_Silent_p.L76L|ASAH2_ENST00000447815.1_Silent_p.L95L	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	95					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						AGTTCTGAAATAGAGGAGACT	0.517																																					p.L95L		Atlas-SNP	.											.	ASAH2	69	.	0			c.A285G						PASS	.	T	,	0,4406		0,0,2203	176.0	181.0	179.0		285,285	-10.3	0.0	10		179	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ASAH2	NM_001143974.1,NM_019893.2	,	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	,	95/746,95/781	52005057	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	56624	exon2			CTGAAATAGAGGA	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.285A>G	10.37:g.52005057T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	173	85	0.491329	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Silent	SNP	ENST00000395526.4	37	CCDS7239.2																																																																																			T|0.999;C|0.001	0.001	weak		0.517	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893	
SLC46A1	113235	hgsc.bcm.edu	37	17	26731959	26731959	+	Silent	SNP	G	G	C	rs185900287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:26731959G>C	ENST00000440501.1	-	2	851	c.756C>G	c.(754-756)gtC>gtG	p.V252V	SLC46A1_ENST00000584729.1_5'UTR|SLC46A1_ENST00000321666.5_Silent_p.V252V|CTD-2350C19.2_ENST00000580714.1_RNA|CTD-2350C19.1_ENST00000583956.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	252					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	CATAGAGCTGGACAATGGATC	0.542													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18170	0.0		0.001	False		,,,				2504	0.002				p.V252V		Atlas-SNP	.											.	SLC46A1	17	.	0			c.C756G						PASS	.	G	,	0,3912		0,0,1956	120.0	126.0	124.0		756,756	4.4	0.4	17		124	17,8283		0,17,4133	no	coding-synonymous,coding-synonymous	SLC46A1	NM_001242366.1,NM_080669.4	,	0,17,6089	CC,CG,GG		0.2048,0.0,0.1392	,	252/432,252/460	26731959	17,12195	1956	4150	6106	SO:0001819	synonymous_variant	113235	exon2			GAGCTGGACAATG	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.756C>G	17.37:g.26731959G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	129	72	0.55814	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Silent	SNP	ENST00000440501.1	37																																																																																				G|0.999;C|0.001	0.001	strong		0.542	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669	
OR2S2	56656	hgsc.bcm.edu	37	9	35958047	35958047	+	Missense_Mutation	SNP	T	T	C	rs2233558	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35958047T>C	ENST00000341959.2	-	1	104	c.49A>G	c.(49-51)Agg>Ggg	p.R17G		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	17			R -> G (in dbSNP:rs2233558).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			GCAGAGAGCCTCAGGAGAACG	0.537													C|||	1729	0.345248	0.4939	0.2968	5008	,	,		21441	0.2996		0.2793	False		,,,				2504	0.2935				p.R17G	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.A49G						PASS	.	C	GLY/ARG	2032,2374	599.7+/-389.3	448,1136,619	49.0	48.0	48.0		49	4.1	1.0	9	dbSNP_98	48	2830,5770	665.2+/-402.2	508,1814,1978	yes	missense	OR2S2	NM_019897.2	125	956,2950,2597	CC,CT,TT		32.907,46.1189,37.3827	benign	17/320	35958047	4862,8144	2203	4300	6503	SO:0001583	missense	56656	exon1			AGAGCCTCAGGAG	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"""GPCR / Class A : Olfactory receptors"""	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.49A>G	9.37:g.35958047T>C	ENSP00000344040:p.Arg17Gly	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	37	CCDS6596.2	760	0.34798534798534797	262	0.532520325203252	124	0.3425414364640884	164	0.2867132867132867	210	0.2770448548812665	C	1.590	-0.529238	0.04112	0.461189	0.32907	ENSG00000122718	ENST00000341959	T	0.00198	8.57	4.07	4.07	0.47477	.	0.000000	0.49916	N	0.000121	T	0.00012	0.0000	N	0.00007	-3.175	0.41380	P	0.012454999999999994	B	0.02656	0.0	B	0.01281	0.0	T	0.17531	-1.0366	9	0.02654	T	1	.	10.395	0.44196	0.0:0.9022:0.0:0.0978	rs2233558;rs3739615;rs2233558	17	Q9NQN1	OR2S1_HUMAN	G	17	ENSP00000344040:R17G	ENSP00000344040:R17G	R	-	1	2	OR2S2	35948047	0.841000	0.29509	0.988000	0.46212	0.430000	0.31655	2.444000	0.44890	1.308000	0.44962	-0.119000	0.15052	AGG	T|0.637;C|0.363	0.363	strong		0.537	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
NME8	51314	hgsc.bcm.edu	37	7	37907304	37907304	+	Splice_Site	SNP	T	T	C	rs10250905	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:37907304T>C	ENST00000199447.4	+	11	994	c.622T>C	c.(622-624)Tgt>Cgt	p.C208R	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Splice_Site_p.C208R	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	208	NDK 1.		C -> R (in dbSNP:rs10250905). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										TATTTTGTAGTGTGACTTCGA	0.388													C|||	3723	0.743411	0.9039	0.7349	5008	,	,		19975	0.5466		0.7545	False		,,,				2504	0.7239				p.C208R		Atlas-SNP	.											TXNDC3,colon,carcinoma,-1,1	.	.	1	0			c.T622C						PASS	.	C	ARG/CYS	3805,601	264.1+/-265.8	1659,487,57	103.0	100.0	101.0		622	4.9	1.0	7	dbSNP_119	101	6432,2168	371.3+/-336.2	2392,1648,260	yes	missense-near-splice	TXNDC3	NM_016616.4	180	4051,2135,317	CC,CT,TT		25.2093,13.6405,21.2902	benign	208/589	37907304	10237,2769	2203	4300	6503	SO:0001630	splice_region_variant	51314	exon11			TTGTAGTGTGACT	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.622-1T>C	7.37:g.37907304T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	127	51	0.401575	NM_016616	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	1595	0.7303113553113553	448	0.9105691056910569	260	0.7182320441988951	312	0.5454545454545454	575	0.758575197889182	C	11.27	1.588573	0.28357	0.863595	0.747907	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.40225	1.04;1.04	4.94	4.94	0.65067	.	0.000000	0.45361	D	0.000370	T	0.00012	0.0000	N	0.08118	0	0.34765	P	0.266919	B	0.06786	0.001	B	0.01281	0.0	T	0.28170	-1.0052	8	.	.	.	-3.8386	10.1589	0.42840	0.0:0.9054:0.0:0.0946	rs10250905;rs56798174;rs10250905	208	Q8N427	TXND3_HUMAN	R	208	ENSP00000199447:C208R;ENSP00000397063:C208R	.	C	+	1	0	TXNDC3	37873829	1.000000	0.71417	1.000000	0.80357	0.498000	0.33706	0.995000	0.29706	1.420000	0.47138	-0.213000	0.12676	TGT	T|0.241;C|0.759	0.759	strong		0.388	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	Missense_Mutation
RNASE6	6039	hgsc.bcm.edu	37	14	21250124	21250124	+	Missense_Mutation	SNP	G	G	A	rs1045922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21250124G>A	ENST00000304677.2	+	2	559	c.266G>A	c.(265-267)cGg>cAg	p.R89Q	RP11-219E7.1_ENST00000556624.1_RNA	NM_005615.4	NP_005606.1	Q93091	RNAS6_HUMAN	ribonuclease, RNase A family, k6	89			R -> Q (in dbSNP:rs1045922).		defense response (GO:0006952)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			large_intestine(1)	1	all_cancers(95;0.00406)		Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)		AAAAATCGTCGGCACAACTGC	0.488													G|||	1527	0.304912	0.1089	0.2983	5008	,	,		19883	0.4286		0.2485	False		,,,				2504	0.5051				p.R89Q		Atlas-SNP	.											.	RNASE6	7	.	0			c.G266A						PASS	.	G	GLN/ARG	586,3820	260.4+/-263.7	36,514,1653	150.0	143.0	145.0		266	-9.9	0.0	14	dbSNP_86	145	2145,6455	367.9+/-334.9	266,1613,2421	yes	missense	RNASE6	NM_005615.4	43	302,2127,4074	AA,AG,GG		24.9419,13.3,20.998	benign	89/151	21250124	2731,10275	2203	4300	6503	SO:0001583	missense	6039	exon2			ATCGTCGGCACAA	U64998	CCDS9558.1	14q11	2008-07-09			ENSG00000169413	ENSG00000169413		"""Ribonucleases, RNase A"""	10048	protein-coding gene	gene with protein product	"""RNase k6"""	601981		RNS6		8836175, 9647635	Standard	NM_005615		Approved		uc001vye.4	Q93091	OTTHUMG00000029585	ENST00000304677.2:c.266G>A	14.37:g.21250124G>A	ENSP00000302046:p.Arg89Gln	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	235	235	1	NM_005615		Missense_Mutation	SNP	ENST00000304677.2	37	CCDS9558.1	560	0.2564102564102564	52	0.10569105691056911	99	0.27348066298342544	228	0.3986013986013986	181	0.23878627968337732	G	2.735	-0.263495	0.05754	0.133	0.249419	ENSG00000169413	ENST00000304677	T	0.72505	-0.66	4.97	-9.94	0.00449	Ribonuclease A, domain (4);	1.849040	0.02663	N	0.107763	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.15141	0.012	B	0.08055	0.003	T	0.19582	-1.0301	9	0.12103	T	0.63	1.7176	14.2487	0.66004	0.1507:0.0:0.6666:0.1826	rs1045922;rs3168885;rs57753708;rs1045922	89	Q93091	RNAS6_HUMAN	Q	89	ENSP00000302046:R89Q	ENSP00000302046:R89Q	R	+	2	0	RNASE6	20319964	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.580000	0.00907	-3.814000	0.00103	-2.909000	0.00091	CGG	G|0.764;A|0.236	0.236	strong		0.488	RNASE6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073750.2		
MYO16	23026	hgsc.bcm.edu	37	13	109777503	109777503	+	Missense_Mutation	SNP	A	A	G	rs157024	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:109777503A>G	ENST00000357550.2	+	29	3554	c.3513A>G	c.(3511-3513)atA>atG	p.I1171M	MYO16_ENST00000457511.2_Missense_Mutation_p.I683M|MYO16_ENST00000356711.2_Missense_Mutation_p.I1171M	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)			TTCAGAGAATAAGCATCAGAC	0.423													G|||	665	0.132788	0.093	0.1902	5008	,	,		19256	0.1141		0.1441	False		,,,				2504	0.1534				p.I1193M		Atlas-SNP	.											.	MYO16	285	.	0			c.A3579G						PASS	.	G	MET/ILE,MET/ILE	474,3932	782.5+/-414.6	17,440,1746	71.0	69.0	69.0		3579,3513	3.7	1.0	13	dbSNP_79	69	1189,7411	764.2+/-407.6	79,1031,3190	yes	missense,missense	MYO16	NM_001198950.1,NM_015011.1	10,10	96,1471,4936	GG,GA,AA		13.8256,10.7581,12.7864	benign,benign	1193/1881,1171/1859	109777503	1663,11343	2203	4300	6503	SO:0001583	missense	23026	exon30			GAGAATAAGCATC		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.3513A>G	13.37:g.109777503A>G	ENSP00000350160:p.Ile1171Met	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	288	130	0.451389	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	283	0.1295787545787546	43	0.08739837398373984	59	0.16298342541436464	75	0.13111888111888112	106	0.13984168865435356	G	3.681	-0.065551	0.07273	0.107581	0.138256	ENSG00000041515	ENST00000356711;ENST00000357550;ENST00000457511	D;D;D	0.95518	-3.73;-3.73;-3.73	5.51	3.68	0.42216	.	0.277746	0.24573	N	0.037361	T	0.01592	0.0051	N	0.02539	-0.55	0.54753	P	1.3000000000040757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49244	-0.8960	8	.	.	.	.	9.7733	0.40603	0.2358:0.0:0.7642:0.0	rs157024;rs17393560;rs52818809;rs56579413;rs57240489;rs157024	683;1171	F8W883;Q9Y6X6	.;MYO16_HUMAN	M	1171;1171;683	ENSP00000349145:I1171M;ENSP00000350160:I1171M;ENSP00000401633:I683M	.	I	+	3	3	MYO16	108575504	1.000000	0.71417	0.976000	0.42696	0.311000	0.27955	2.054000	0.41335	0.247000	0.21414	-0.699000	0.03677	ATA	A|0.869;G|0.131	0.131	strong		0.423	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
LYST	1130	hgsc.bcm.edu	37	1	235945294	235945294	+	Silent	SNP	T	T	C	rs6696123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	89	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	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		
NLE1	54475	hgsc.bcm.edu	37	17	33464864	33464864	+	Missense_Mutation	SNP	C	C	T	rs7215209	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:33464864C>T	ENST00000442241.4	-	5	545	c.506G>A	c.(505-507)aGg>aAg	p.R169K	NLE1_ENST00000586869.1_5'UTR|NLE1_ENST00000593176.1_5'UTR|NLE1_ENST00000360831.5_Intron	NM_001014445.1|NM_018096.3	NP_001014445.1|NP_060566.2	Q9NVX2	NLE1_HUMAN	notchless homolog 1 (Drosophila)	169			R -> K (in dbSNP:rs7215209). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		hematopoietic stem cell homeostasis (GO:0061484)|inner cell mass cell differentiation (GO:0001826)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of mitotic cell cycle (GO:0045930)|Notch signaling pathway (GO:0007219)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|ribosomal large subunit biogenesis (GO:0042273)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	22		Ovarian(249;0.17)				GGCCAGCTTCCTGCCATCTGG	0.512													T|||	4251	0.848842	0.8676	0.8602	5008	,	,		18343	0.9137		0.7048	False		,,,				2504	0.8967				p.R169K		Atlas-SNP	.											.	NLE1	42	.	0			c.G506A						PASS	.	T	,LYS/ARG	3831,575	256.1+/-261.0	1670,491,42	61.0	60.0	61.0		,506	4.0	1.0	17	dbSNP_116	61	6191,2409	399.2+/-346.4	2236,1719,345	yes	utr-5,missense	NLE1	NM_001014445.1,NM_018096.3	,26	3906,2210,387	TT,TC,CC		28.0116,13.0504,22.9433	,benign	,169/486	33464864	10022,2984	2203	4300	6503	SO:0001583	missense	54475	exon5			AGCTTCCTGCCAT		CCDS11291.1, CCDS45647.1	17q12	2013-01-10		2005-08-09	ENSG00000073536	ENSG00000073536		"""WD repeat domain containing"""	19889	protein-coding gene	gene with protein product	"""Notchless gene homolog, (Drosophila)"""						Standard	XM_005257989		Approved	FLJ10458	uc002hiy.1	Q9NVX2	OTTHUMG00000132928	ENST00000442241.4:c.506G>A	17.37:g.33464864C>T	ENSP00000413572:p.Arg169Lys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_018096	O60868|Q59GJ8|Q9BU54	Missense_Mutation	SNP	ENST00000442241.4	37	CCDS11291.1	1790	0.8195970695970696	427	0.8678861788617886	303	0.8370165745856354	529	0.9248251748251748	531	0.7005277044854882	T	6.477	0.456156	0.12283	0.869496	0.719884	ENSG00000073536	ENST00000442241;ENST00000537697	T	0.28454	1.61	5.02	3.95	0.45737	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.090843	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01809	-0.71	0.09310	P	0.9999999999999998	B	0.02656	0.0	B	0.04013	0.001	T	0.39603	-0.9606	9	0.02654	T	1	-13.8384	6.4974	0.22150	0.0:0.2744:0.0:0.7256	rs7215209;rs17856385;rs59830316;rs7215209	169	Q9NVX2	NLE1_HUMAN	K	169	ENSP00000413572:R169K	ENSP00000413572:R169K	R	-	2	0	NLE1	30488977	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.347000	0.44036	0.414000	0.25790	-0.332000	0.08345	AGG	C|0.201;T|0.799	0.799	strong		0.512	NLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256441.2	NM_018096	
DRC7	84229	hgsc.bcm.edu	37	16	57756643	57756643	+	Missense_Mutation	SNP	C	C	T	rs3809611	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57756643C>T	ENST00000360716.3	+	11	1519	c.1298C>T	c.(1297-1299)cCg>cTg	p.P433L	CCDC135_ENST00000394337.4_Missense_Mutation_p.P433L|CCDC135_ENST00000336825.8_Missense_Mutation_p.P368L			Q8IY82	CC135_HUMAN		433			P -> L (in dbSNP:rs3809611). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						ACCCGCTGCCCGAACGGGAAG	0.577													.|||	1055	0.210663	0.2322	0.1441	5008	,	,		18750	0.1548		0.2465	False		,,,				2504	0.2495				p.P433L		Atlas-SNP	.											CCDC135,NS,carcinoma,-1,1	CCDC135	97	1	0			c.C1298T						scavenged	.	C	LEU/PRO	970,3426		104,762,1332	80.0	78.0	79.0		1298	5.1	0.9	16	dbSNP_107	79	2022,6578		232,1558,2510	yes	missense	CCDC135	NM_032269.5	98	336,2320,3842	TT,TC,CC		23.5116,22.0655,23.0225	probably-damaging	433/875	57756643	2992,10004	2198	4300	6498	SO:0001583	missense	84229	exon10			GCTGCCCGAACGG																												ENST00000360716.3:c.1298C>T	16.37:g.57756643C>T	ENSP00000353942:p.Pro433Leu	Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	429	0.19642857142857142	100	0.2032520325203252	58	0.16022099447513813	85	0.1486013986013986	186	0.24538258575197888	.	16.58	3.162039	0.57368	0.220655	0.235116	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.07114	3.22;3.22;3.22	5.12	5.12	0.69794	.	0.054186	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87971	2.92	0.09310	P	0.99999999748828	B;P	0.44090	0.07;0.826	B;B	0.35353	0.024;0.201	T	0.36625	-0.9740	9	0.49607	T	0.09	-27.9479	17.1416	0.86755	0.0:1.0:0.0:0.0	rs3809611;rs17857125;rs58281850;rs3809611	368;433	Q8IY82-2;Q8IY82	.;CC135_HUMAN	L	433;368;433	ENSP00000377869:P433L;ENSP00000338938:P368L;ENSP00000353942:P433L	ENSP00000338938:P368L	P	+	2	0	CCDC135	56314144	0.997000	0.39634	0.940000	0.37924	0.685000	0.39939	3.831000	0.55776	2.384000	0.81235	0.650000	0.86243	CCG	C|0.781;T|0.218	0.218	strong		0.577	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
NUP210L	91181	hgsc.bcm.edu	37	1	153994647	153994647	+	Missense_Mutation	SNP	C	C	T	rs11264875	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:153994647C>T	ENST00000368559.3	-	32	4542	c.4471G>A	c.(4471-4473)Gtt>Att	p.V1491I	NUP210L_ENST00000271854.3_Missense_Mutation_p.V1491I|NUP210L_ENST00000368553.1_Missense_Mutation_p.V424I	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1491			V -> I (in dbSNP:rs11264875).		Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ATATCTCCAACAAAGGTAAGC	0.448													C|||	1353	0.270168	0.1407	0.4035	5008	,	,		18037	0.2817		0.2793	False		,,,				2504	0.3292				p.V1491I		Atlas-SNP	.											.	NUP210L	181	.	0			c.G4471A						PASS	.	C	ILE/VAL,ILE/VAL	655,3409		49,557,1426	131.0	132.0	132.0		4471,4471	6.1	1.0	1	dbSNP_120	132	2291,6073		303,1685,2194	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	29,29	352,2242,3620	TT,TC,CC		27.3912,16.1171,23.7045	possibly-damaging,possibly-damaging	1491/1737,1491/1889	153994647	2946,9482	2032	4182	6214	SO:0001583	missense	91181	exon32			CTCCAACAAAGGT	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.4471G>A	1.37:g.153994647C>T	ENSP00000357547:p.Val1491Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	619	0.2834249084249084	87	0.17682926829268292	138	0.3812154696132597	170	0.2972027972027972	224	0.2955145118733509	C	22.5	4.294589	0.81025	0.161171	0.273912	ENSG00000143552	ENST00000368559;ENST00000368553;ENST00000271854	T;T;T	0.30714	3.13;1.52;2.89	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000016	T	0.31765	0.0807	M	0.72353	2.195	0.24686	P	0.99333916	D;D	0.57899	0.981;0.981	P;P	0.49799	0.622;0.622	T	0.08994	-1.0695	9	0.33141	T	0.24	-13.2334	14.8816	0.70537	0.0:0.8571:0.1429:0.0	rs11264875;rs59633782;rs11264875	1491;1491	E7EP56;Q5VU65	.;P210L_HUMAN	I	1491;424;1491	ENSP00000357547:V1491I;ENSP00000357541:V424I;ENSP00000271854:V1491I	ENSP00000271854:V1491I	V	-	1	0	NUP210L	152261271	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.188000	0.58351	2.894000	0.99253	0.591000	0.81541	GTT	C|0.741;T|0.259	0.259	strong		0.448	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
PDLIM1	9124	hgsc.bcm.edu	37	10	97023630	97023630	+	Missense_Mutation	SNP	T	T	C	rs2296961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:97023630T>C	ENST00000329399.6	-	4	632	c.524A>G	c.(523-525)aAc>aGc	p.N175S	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	175			N -> S (in dbSNP:rs2296961). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		CGGTCTGCTGTTCGCCTCCAC	0.572													T|||	949	0.189497	0.1626	0.2666	5008	,	,		18027	0.0278		0.3072	False		,,,				2504	0.2168				p.N175S		Atlas-SNP	.											.	PDLIM1	33	.	0			c.A524G						PASS	.	T	SER/ASN	861,3545	337.0+/-304.7	85,691,1427	71.0	70.0	70.0		524	3.3	0.0	10	dbSNP_100	70	2530,6070	413.0+/-351.0	355,1820,2125	yes	missense	PDLIM1	NM_020992.2	46	440,2511,3552	CC,CT,TT		29.4186,19.5415,26.0726	benign	175/330	97023630	3391,9615	2203	4300	6503	SO:0001583	missense	9124	exon4			CTGCTGTTCGCCT	U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"""carboxyl terminal LIM domain protein 1"", ""elfin"""	605900	"""PDZ and LIM domain 1 (elfin)"""	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.524A>G	10.37:g.97023630T>C	ENSP00000360305:p.Asn175Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	139	84	0.604317	NM_020992	B2RBS6|Q5VZH5|Q9BPZ9	Missense_Mutation	SNP	ENST00000329399.6	37	CCDS7441.1	419	0.19184981684981686	81	0.16463414634146342	95	0.26243093922651933	13	0.022727272727272728	230	0.3034300791556728	T	1.955	-0.440236	0.04636	0.195415	0.294186	ENSG00000107438	ENST00000329399	T	0.21191	2.02	5.65	3.31	0.37934	.	0.341399	0.39020	N	0.001487	T	0.00012	0.0000	N	0.05078	-0.115	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.47995	-0.9073	9	0.18710	T	0.47	-11.7743	7.4555	0.27264	0.0:0.0769:0.4079:0.5152	rs2296961;rs2296961	175	O00151	PDLI1_HUMAN	S	175	ENSP00000360305:N175S	ENSP00000360305:N175S	N	-	2	0	PDLIM1	97013620	0.019000	0.18553	0.006000	0.13384	0.150000	0.21749	0.818000	0.27295	0.553000	0.29044	0.533000	0.62120	AAC	T|0.769;C|0.231	0.231	strong		0.572	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1		
SLC24A4	123041	hgsc.bcm.edu	37	14	92909073	92909073	+	Silent	SNP	T	T	C	rs941650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:92909073T>C	ENST00000532405.1	+	6	721	c.495T>C	c.(493-495)caT>caC	p.H165H	SLC24A4_ENST00000393265.2_Silent_p.H101H|SLC24A4_ENST00000298877.1_Silent_p.H148H|SLC24A4_ENST00000351924.5_Silent_p.H148H|SLC24A4_ENST00000531433.1_Silent_p.H165H			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	165					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)		TCATCACCCATGGGGACGTCG	0.587													C|||	4292	0.857029	0.8691	0.8184	5008	,	,		17433	0.9871		0.7425	False		,,,				2504	0.8517				p.H165H	NSCLC(10;315 435 10383 28450 38798)	Atlas-SNP	.											.	SLC24A4	112	.	0			c.T495C						PASS	.	C	,,	3779,627	269.2+/-268.9	1616,547,40	152.0	132.0	139.0		495,495,303	-4.4	0.7	14	dbSNP_86	139	6301,2299	386.3+/-341.8	2295,1711,294	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC24A4	NM_153646.3,NM_153647.3,NM_153648.3	,,	3911,2258,334	CC,CT,TT		26.7326,14.2306,22.4973	,,	165/623,165/604,101/559	92909073	10080,2926	2203	4300	6503	SO:0001819	synonymous_variant	123041	exon7			CACCCATGGGGAC	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.495T>C	14.37:g.92909073T>C		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	203	103	0.507389	NM_153647	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Silent	SNP	ENST00000532405.1	37	CCDS9903.2	1861	0.8521062271062271	435	0.8841463414634146	293	0.8093922651933702	567	0.9912587412587412	566	0.7467018469656992	C	5.961	0.361213	0.11296	0.857694	0.732674	ENSG00000140090	ENST00000525557	.	.	.	4.89	-4.38	0.03622	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999994	.	.	.	.	.	.	T	0.24835	-1.0149	3	.	.	.	.	16.0825	0.81014	0.0:0.324:0.0:0.676	rs941650;rs17783606;rs59390382;rs941650	.	.	.	R	50	.	.	W	+	1	0	SLC24A4	91978826	0.000000	0.05858	0.663000	0.29738	0.645000	0.38454	-1.951000	0.01529	-1.358000	0.02177	-0.726000	0.03593	TGG	T|0.185;C|0.815	0.815	strong		0.587	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646	
CNR2	1269	hgsc.bcm.edu	37	1	24201920	24201920	+	Missense_Mutation	SNP	T	T	C	rs35761398|rs2501432	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24201920T>C	ENST00000374472.4	-	2	349	c.188A>G	c.(187-189)cAa>cGa	p.Q63R	CNR2_ENST00000536471.1_Missense_Mutation_p.Q63R	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	63			Q -> R (high incidence in Japanese depressed subjects; dbSNP:rs2501432). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18286196}.		G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)	p.Q63R(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		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;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	CCGGCGGAGTTGGTGGGAGGA	0.557													C|||	3272	0.653355	0.7943	0.6383	5008	,	,		20063	0.502		0.5875	False		,,,				2504	0.6973				p.Q63R		Atlas-SNP	.											CNR2,NS,carcinoma,0,2	CNR2	78	2	1	Substitution - Missense(1)	stomach(1)	c.A188G						PASS	.	C	ARG/GLN	3208,1198		1258,692,253	61.0	71.0	68.0		188	5.1	0.9	1	dbSNP_100	68	4732,3868		1403,1926,971	yes	missense	CNR2	NM_001841.2	43	2661,2618,1224	CC,CT,TT		44.9767,27.1902,38.9513	benign	63/361	24201920	7940,5066	2203	4300	6503	SO:0001583	missense	1269	exon2			CGGAGTTGGTGGG	X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822		"""GPCR / Class A : Cannabinoid receptors"""	2160	protein-coding gene	gene with protein product		605051					Standard	NM_001841		Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000374472.4:c.188A>G	1.37:g.24201920T>C	ENSP00000363596:p.Gln63Arg	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Missense_Mutation	SNP	ENST00000374472.4	37	CCDS245.1	1127	0.5160256410256411	298	0.6056910569105691	203	0.5607734806629834	271	0.4737762237762238	355	0.4683377308707124	C	0.013	-1.626255	0.00813	0.728098	0.550233	ENSG00000188822	ENST00000374472;ENST00000536471	T;T	0.70749	-0.51;-0.51	6.04	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.527042	0.20481	N	0.091487	T	0.00012	0.0000	N	0.01134	-0.995	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40608	-0.9554	9	0.11182	T	0.66	.	8.6774	0.34187	0.0:0.7287:0.0:0.2713	rs2501432	63	P34972	CNR2_HUMAN	R	63	ENSP00000363596:Q63R;ENSP00000442830:Q63R	ENSP00000363596:Q63R	Q	-	2	0	CNR2	24074507	0.286000	0.24305	0.910000	0.35882	0.091000	0.18340	1.434000	0.34958	1.585000	0.49928	-0.215000	0.12644	CAA	T|0.468;C|0.532	0.532	strong		0.557	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
TMEM237	65062	hgsc.bcm.edu	37	2	202490812	202490812	+	Missense_Mutation	SNP	C	C	A	rs73989521	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:202490812C>A	ENST00000409883.2	-	12	1212	c.1096G>T	c.(1096-1098)Gct>Tct	p.A366S	TMEM237_ENST00000409444.2_Missense_Mutation_p.A358S|TMEM237_ENST00000466839.1_5'Flank	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	366					cilium assembly (GO:0042384)|regulation of Wnt signaling pathway (GO:0030111)	ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)	7						ACCAGAAGAGCCACCACGAGA	0.393													C|||	313	0.0625	0.174	0.0447	5008	,	,		15641	0.0		0.0447	False		,,,				2504	0.0072				p.A366S		Atlas-SNP	.											.	TMEM237	21	.	0			c.G1096T						PASS	.	C	SER/ALA,SER/ALA	546,3116		44,458,1329	62.0	60.0	61.0		1072,1096	2.0	0.9	2	dbSNP_130	61	439,7731		14,411,3660	yes	missense,missense	TMEM237	NM_152388.2,NM_001044385.1	99,99	58,869,4989	AA,AC,CC		5.3733,14.9099,8.3249	benign,benign	358/401,366/409	202490812	985,10847	1831	4085	5916	SO:0001583	missense	65062	exon11			GAAGAGCCACCAC	AB053301	CCDS46489.1, CCDS46490.1	2q33	2012-05-08	2011-05-20	2011-05-20	ENSG00000155755	ENSG00000155755			14432	protein-coding gene	gene with protein product		614423	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4"""	ALS2CR4		11586298, 20375344	Standard	NM_001044385		Approved	JBTS14	uc021vvg.2	Q96Q45	OTTHUMG00000154526	ENST00000409883.2:c.1096G>T	2.37:g.202490812C>A	ENSP00000386264:p.Ala366Ser	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	176	77	0.4375	NM_001044385	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Missense_Mutation	SNP	ENST00000409883.2	37	CCDS46489.1	125	0.05723443223443223	74	0.15040650406504066	15	0.04143646408839779	0	0.0	36	0.047493403693931395	C	13.20	2.167621	0.38315	0.149099	0.053733	ENSG00000155755	ENST00000409444;ENST00000409883;ENST00000435876;ENST00000426684;ENST00000409099	.	.	.	6.1	1.98	0.26296	.	0.151190	0.64402	D	0.000015	T	0.00178	0.0005	L	0.28740	0.885	0.23156	P	0.99820467	B;B	0.25441	0.126;0.054	B;B	0.20767	0.031;0.031	T	0.06250	-1.0837	8	0.39692	T	0.17	-1.3093	6.0385	0.19720	0.1239:0.5787:0.0:0.2974	.	366;390	E9PAR8;Q96Q45	.;TM237_HUMAN	S	358;366;366;388;271	.	ENSP00000386949:A271S	A	-	1	0	TMEM237	202199057	0.991000	0.36638	0.888000	0.34837	0.795000	0.44927	0.711000	0.25764	0.069000	0.16605	-0.142000	0.14014	GCT	C|0.943;A|0.057	0.057	strong		0.393	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388	
NANOG	79923	hgsc.bcm.edu	37	12	7945757	7945757	+	Silent	SNP	C	C	T	rs4438116	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	128	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	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	
RFX8	731220	hgsc.bcm.edu	37	2	102018908	102018908	+	Missense_Mutation	SNP	A	A	G	rs2175968|rs386648636	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102018908A>G	ENST00000376826.2	-	14	1573	c.1574T>C	c.(1573-1575)aTg>aCg	p.M525T	RFX8_ENST00000428343.1_Missense_Mutation_p.M412T			Q6ZV50	RFX8_HUMAN	RFX family member 8, lacking RFX DNA binding domain	525				M -> T (in Ref. 1; BAG60794). {ECO:0000305}.	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						CTTATTGCCCATGGCAGTGTC	0.562													g|||	2266	0.452476	0.4569	0.3372	5008	,	,		18997	0.4861		0.5457	False		,,,				2504	0.3978				p.M412T		Atlas-SNP	.											.	RFX8	16	.	0			c.T1235C						PASS	.	G	THR/MET	647,737		156,335,201	34.0	34.0	34.0		1235	3.8	0.9	2	dbSNP_96	34	1692,1490		458,776,357	yes	missense	RFX8	NM_001145664.1	81	614,1111,558	GG,GA,AA		46.8259,46.7486,48.7735	benign	412/474	102018908	2339,2227	692	1591	2283	SO:0001583	missense	731220	exon11			TTGCCCATGGCAG	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.1574T>C	2.37:g.102018908A>G	ENSP00000366022:p.Met525Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_001145664	B4DQ32	Missense_Mutation	SNP	ENST00000376826.2	37		1054	0.4826007326007326	225	0.4573170731707317	134	0.3701657458563536	265	0.4632867132867133	430	0.5672823218997362	G	0.320	-0.962543	0.02249	0.467486	0.531741	ENSG00000196460	ENST00000376826;ENST00000428343	T;T	0.72505	-0.66;1.29	4.7	3.81	0.43845	.	0.000000	0.56097	N	0.000021	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43196	-0.9406	9	0.02654	T	1	-9.8171	6.7948	0.23719	0.2067:0.0:0.7933:0.0	rs2175968;rs61081659;rs2175968	412;525	Q6ZV50-3;Q6ZV50	.;RFX8_HUMAN	T	525;412	ENSP00000366022:M525T;ENSP00000401536:M412T	ENSP00000366022:M525T	M	-	2	0	RFX8	101385340	0.815000	0.29118	0.854000	0.33618	0.936000	0.57629	0.966000	0.29331	1.354000	0.45846	-0.479000	0.04858	ATG	A|0.523;G|0.477	0.477	strong		0.562	RFX8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145664	
MGLL	11343	hgsc.bcm.edu	37	3	127540635	127540635	+	Silent	SNP	C	C	T	rs11538698	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:127540635C>T	ENST00000434178.2	-	2	923	c.27G>A	c.(25-27)cgG>cgA	p.R9R	MGLL_ENST00000265052.5_Silent_p.R19R|MGLL_ENST00000453507.2_Silent_p.R19R|MGLL_ENST00000398104.1_Silent_p.R9R			Q99685	MGLL_HUMAN	monoglyceride lipase	9					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						TCTGCGGGGTCCGCCTGGGGG	0.522													C|||	78	0.0155751	0.0	0.0216	5008	,	,		15700	0.0		0.0507	False		,,,				2504	0.0123				p.R19R		Atlas-SNP	.											.	MGLL	19	.	0			c.G57A						PASS	.	C	,	32,3730		0,32,1849	113.0	119.0	117.0		27,57	2.0	1.0	3	dbSNP_120	117	345,7867		8,329,3769	no	coding-synonymous,coding-synonymous	MGLL	NM_001003794.1,NM_007283.5	,	8,361,5618	TT,TC,CC		4.2012,0.8506,3.1485	,	9/304,19/314	127540635	377,11597	1881	4106	5987	SO:0001819	synonymous_variant	11343	exon2			CGGGGTCCGCCTG	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.27G>A	3.37:g.127540635C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	127	74	0.582677	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	37	CCDS43148.1																																																																																			T|0.033;G|0.000;C|0.967	0.033	strong		0.522	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
EBI3	10148	hgsc.bcm.edu	37	19	4237067	4237067	+	Silent	SNP	A	A	G	rs4905	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	32	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	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		
SHROOM3	57619	hgsc.bcm.edu	37	4	77662486	77662486	+	Missense_Mutation	SNP	G	G	T	rs71607374	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77662486G>T	ENST00000296043.6	+	5	4113	c.3160G>T	c.(3160-3162)Gtg>Ttg	p.V1054L		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1054					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GGAGAGCAGCGTGGCCGACCG	0.687													G|||	189	0.0377396	0.031	0.0375	5008	,	,		11140	0.005		0.0905	False		,,,				2504	0.0266				p.V1054L		Atlas-SNP	.											SHROOM3,NS,carcinoma,0,1	SHROOM3	134	1	0			c.G3160T						PASS	.	G	LEU/VAL	145,4259		3,139,2060	17.0	18.0	18.0		3160	3.1	0.1	4	dbSNP_130	18	779,7817		33,713,3552	yes	missense	SHROOM3	NM_020859.3	32	36,852,5612	TT,TG,GG		9.0624,3.2925,7.1077	probably-damaging	1054/1997	77662486	924,12076	2202	4298	6500	SO:0001583	missense	57619	exon5			AGCAGCGTGGCCG	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.3160G>T	4.37:g.77662486G>T	ENSP00000296043:p.Val1054Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	107	0.04899267399267399	25	0.0508130081300813	17	0.04696132596685083	2	0.0034965034965034965	63	0.08311345646437995	G	12.89	2.074449	0.36566	0.032925	0.090624	ENSG00000138771	ENST00000296043	T	0.47528	0.84	4.91	3.11	0.35812	Apx/shroom, ASD1 (1);	0.896159	0.09325	N	0.817696	T	0.02929	0.0087	M	0.64404	1.975	0.31938	P	0.611326	P;B;B	0.39831	0.69;0.446;0.446	B;B;B	0.41466	0.358;0.257;0.257	T	0.23190	-1.0195	9	0.66056	D	0.02	-8.2468	11.3605	0.49640	0.0:0.1375:0.7195:0.143	.	878;1054;832	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	L	1054	ENSP00000296043:V1054L	ENSP00000296043:V1054L	V	+	1	0	SHROOM3	77881510	1.000000	0.71417	0.135000	0.22099	0.004000	0.04260	4.682000	0.61671	0.432000	0.26286	0.563000	0.77884	GTG	G|0.935;T|0.065	0.065	strong		0.687	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
VWA3A	146177	hgsc.bcm.edu	37	16	22155629	22155629	+	Missense_Mutation	SNP	A	A	G	rs9937453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	246	2	0.00813008		WXS	Illumina HiSeq	Phase_I	257	134	0.521401	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		
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	1284	47	0.0366044		WXS	Illumina HiSeq	Phase_I	1056	50	0.0473485	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	
KRTAP7-1	337878	hgsc.bcm.edu	37	21	32201835	32201835	+	RNA	SNP	A	A	C	rs9982675	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	179	0	0		WXS	Illumina HiSeq	Phase_I	176	176	1	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	
KRT37	8688	hgsc.bcm.edu	37	17	39579112	39579112	+	Missense_Mutation	SNP	G	G	A	rs16966811	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39579112G>A	ENST00000225550.3	-	3	649	c.650C>T	c.(649-651)gCg>gTg	p.A217V	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	217	Coil 1B.|Rod.		A -> V (in dbSNP:rs16966811).			extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				GGCCAGGGTCGCGTCATCCAG	0.657													G|||	868	0.173323	0.0378	0.1268	5008	,	,		18610	0.3224		0.1759	False		,,,				2504	0.2331				p.A217V		Atlas-SNP	.											.	KRT37	61	.	0			c.C650T						PASS	.	G	VAL/ALA	255,4151		9,237,1957	78.0	68.0	71.0		650	1.4	0.7	17	dbSNP_123	71	1522,7078		120,1282,2898	yes	missense	KRT37	NM_003770.4	64	129,1519,4855	AA,AG,GG		17.6977,5.7876,13.6629	benign	217/450	39579112	1777,11229	2203	4300	6503	SO:0001583	missense	8688	exon3			AGGGTCGCGTCAT	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.650C>T	17.37:g.39579112G>A	ENSP00000225550:p.Ala217Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	384	0.17582417582417584	24	0.04878048780487805	48	0.13259668508287292	178	0.3111888111888112	134	0.17678100263852242	.	10.94	1.492672	0.26774	0.057876	0.176977	ENSG00000108417	ENST00000225550	D	0.90004	-2.6	4.86	1.39	0.22231	Filament (1);	1.577570	0.04549	N	0.389541	T	0.00012	0.0000	L	0.37507	1.11	0.58432	P	1.999999999946489E-6	B	0.10296	0.003	B	0.08055	0.003	T	0.12293	-1.0553	9	0.72032	D	0.01	.	8.1678	0.31237	0.7857:0.0:0.2143:0.0	rs16966811;rs16966811	217	O76014	KRT37_HUMAN	V	217	ENSP00000225550:A217V	ENSP00000225550:A217V	A	-	2	0	KRT37	36832638	0.041000	0.20044	0.743000	0.31040	0.247000	0.25773	2.537000	0.45702	0.233000	0.21120	-0.136000	0.14681	GCG	G|0.849;A|0.151	0.151	strong		0.657	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
SCAF11	9169	hgsc.bcm.edu	37	12	46322449	46322449	+	Silent	SNP	C	C	T	rs10880868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:46322449C>T	ENST00000369367.3	-	11	1268	c.1035G>A	c.(1033-1035)ggG>ggA	p.G345G	SCAF11_ENST00000465950.1_Silent_p.G30G|SCAF11_ENST00000549162.1_Silent_p.G153G|SCAF11_ENST00000419565.2_Silent_p.G345G	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	345					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)	p.G345G(1)		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						GGGCATCACACCCAGAATTGT	0.453													C|||	557	0.111222	0.0068	0.0994	5008	,	,		15358	0.1319		0.2038	False		,,,				2504	0.1442				p.G345G		Atlas-SNP	.											SCAF11,NS,carcinoma,0,1	SCAF11	145	1	1	Substitution - coding silent(1)	stomach(1)	c.G1035A						PASS	.	C		172,4234	114.2+/-152.2	3,166,2034	193.0	189.0	190.0		1035	0.7	1.0	12	dbSNP_120	190	1815,6785	326.8+/-317.6	179,1457,2664	no	coding-synonymous	SCAF11	NM_004719.2		182,1623,4698	TT,TC,CC		21.1047,3.9038,15.2776		345/1464	46322449	1987,11019	2203	4300	6503	SO:0001819	synonymous_variant	9169	exon11			ATCACACCCAGAA	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.1035G>A	12.37:g.46322449C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	201	200	0.995025	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			C|0.857;T|0.143	0.143	strong		0.453	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
RP1L1	94137	hgsc.bcm.edu	37	8	10467647	10467647	+	Missense_Mutation	SNP	G	G	C	rs200373757		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	173	26	0.150289	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		
GMNC	647309	hgsc.bcm.edu	37	3	190578566	190578566	+	Missense_Mutation	SNP	A	A	G	rs13075089	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	115	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	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	
FUT2	2524	hgsc.bcm.edu	37	19	49206462	49206462	+	Silent	SNP	C	C	T	rs681343	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49206462C>T	ENST00000425340.2	+	2	366	c.249C>T	c.(247-249)taC>taT	p.Y83Y	FUT2_ENST00000391876.4_Silent_p.Y83Y	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	83					carbohydrate metabolic process (GO:0005975)|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)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		CCACACTGTACGCCCTGGCCA	0.637													c|||	1611	0.321685	0.4909	0.3429	5008	,	,		17694	0.004		0.4404	False		,,,				2504	0.2832				p.Y83Y		Atlas-SNP	.											FUT2,caecum,carcinoma,0,1	FUT2	30	1	0			c.C249T						PASS	.	T	,	2195,2211	582.4+/-385.6	554,1087,562	45.0	43.0	43.0		249,249	-7.6	0.2	19	dbSNP_83	43	4240,4360	571.4+/-389.5	1055,2130,1115	no	coding-synonymous,coding-synonymous	FUT2	NM_000511.5,NM_001097638.2	,	1609,3217,1677	TT,TC,CC		49.3023,49.8184,49.4772	,	83/344,83/344	49206462	6435,6571	2203	4300	6503	SO:0001819	synonymous_variant	2524	exon2			ACTGTACGCCCTG		CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"""Fucosyltransferases"""	4013	protein-coding gene	gene with protein product	"""alpha (1,2) fucosyltransferase"", ""galactoside 2-alpha-L-fucosyltransferase 2"", ""GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2"", ""alpha(1,2)FT2"", ""secretor factor"", ""secretor blood group alpha-2-fucosyltransferase"""	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.249C>T	19.37:g.49206462C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_001097638	Q0VAG5|Q14338|Q5D0G2	Silent	SNP	ENST00000425340.2	37	CCDS33069.1																																																																																			C|0.571;T|0.429	0.429	strong		0.637	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511	
RPTN	126638	hgsc.bcm.edu	37	1	152129101	152129101	+	Silent	SNP	A	A	G	rs117596468	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:152129101A>G	ENST00000316073.3	-	3	538	c.474T>C	c.(472-474)caT>caC	p.H158H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						CAGACTGACCATGGTGGGAAT	0.502																																					p.H158H		Atlas-SNP	.											RPTN,NS,carcinoma,0,1	RPTN	123	1	1	Deletion - In frame(1)	stomach(1)	c.T474C						scavenged	.						472.0	411.0	430.0					1																	152129101		1563	3567	5130	SO:0001819	synonymous_variant	126638	exon3			CTGACCATGGTGG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474T>C	1.37:g.152129101A>G		Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	290	47	0.162069	NM_001122965	B7ZBZ3	Silent	SNP	ENST00000316073.3	37	CCDS41397.1																																																																																			A|0.953;G|0.047	0.047	strong		0.502	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
CAND2	23066	hgsc.bcm.edu	37	3	12861586	12861586	+	Splice_Site	SNP	T	T	C	rs4684883	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12861586T>C	ENST00000456430.2	+	11	2987	c.2946T>C	c.(2944-2946)ggT>ggC	p.G982G	CAND2_ENST00000295989.5_Splice_Site_p.G889G	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	982					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						GTCCTGCAGGTCGGCCACACA	0.597													T|||	743	0.148363	0.0454	0.304	5008	,	,		18115	0.1171		0.1799	False		,,,				2504	0.1769				p.G982G	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T2946C						PASS	.	T	,	251,4061		4,243,1909	107.0	116.0	113.0		2946,2667	-0.2	0.9	3	dbSNP_111	113	1537,6939		153,1231,2854	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CAND2	NM_001162499.1,NM_012298.2	,	157,1474,4763	CC,CT,TT		18.1336,5.821,13.9819	,	982/1237,889/1120	12861586	1788,11000	2156	4238	6394	SO:0001630	splice_region_variant	23066	exon11			TGCAGGTCGGCCA		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.2945-1T>C	3.37:g.12861586T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	46	0.613333	NM_001162499	B9EGM9|E9KL24	Silent	SNP	ENST00000456430.2	37	CCDS54554.1																																																																																			T|0.852;C|0.148	0.148	strong		0.597	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	Silent
C1orf127	148345	hgsc.bcm.edu	37	1	11014118	11014118	+	Missense_Mutation	SNP	C	C	T	rs45537241	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11014118C>T	ENST00000377008.4	-	9	1002	c.556G>A	c.(556-558)Gcc>Acc	p.A186T	C1orf127_ENST00000377004.4_Missense_Mutation_p.A353T			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	186										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)		AGGACCGGGGCAGCCATCTCG	0.567													C|||	1099	0.219449	0.0666	0.2752	5008	,	,		19057	0.2331		0.164	False		,,,				2504	0.4294				p.A353T		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1057A						PASS	.	C	THR/ALA	334,4072	176.2+/-205.4	10,314,1879	127.0	127.0	127.0		1057	-9.4	0.0	1	dbSNP_127	127	1301,7299	258.1+/-281.9	109,1083,3108	yes	missense	C1orf127	NM_001170754.1	58	119,1397,4987	TT,TC,CC		15.1279,7.5806,12.5711	possibly-damaging	353/824	11014118	1635,11371	2203	4300	6503	SO:0001583	missense	148345	exon10			CCGGGGCAGCCAT	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.556G>A	1.37:g.11014118C>T	ENSP00000366207:p.Ala186Thr	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	250	119	0.476	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		404	0.184981684981685	37	0.07520325203252033	95	0.26243093922651933	140	0.24475524475524477	132	0.1741424802110818	C	10.67	1.414656	0.25465	0.075806	0.151279	ENSG00000175262	ENST00000377004;ENST00000377008	T;T	0.23950	1.88;1.88	5.07	-9.42	0.00610	.	1.465320	0.04235	N	0.335928	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.14012	0.009;0.009;0.009	B;B;B	0.14023	0.007;0.007;0.01	T	0.26360	-1.0105	9	0.20519	T	0.43	-0.8287	0.8276	0.01124	0.2794:0.1313:0.1779:0.4113	rs45537241	204;204;186	B7ZLG7;Q8N9H9-2;Q8N9H9	.;.;CA127_HUMAN	T	353;186	ENSP00000366203:A353T;ENSP00000366207:A186T	ENSP00000366203:A353T	A	-	1	0	C1orf127	10936705	0.000000	0.05858	0.000000	0.03702	0.391000	0.30476	-1.475000	0.02335	-2.102000	0.00845	-0.345000	0.07892	GCC	C|0.852;T|0.148	0.148	strong		0.567	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
KRIT1	889	hgsc.bcm.edu	37	7	91864857	91864857	+	Missense_Mutation	SNP	T	T	C	rs140396626		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:91864857T>C	ENST00000340022.2	-	8	1607	c.589A>G	c.(589-591)Act>Gct	p.T197A	KRIT1_ENST00000394507.1_Missense_Mutation_p.T197A|KRIT1_ENST00000394505.2_Missense_Mutation_p.T197A|KRIT1_ENST00000412043.2_Missense_Mutation_p.T197A|KRIT1_ENST00000394503.2_Missense_Mutation_p.T197A	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	197					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)			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)			CCTGATTCAGTAGCATATGCA	0.378																																					p.T197A		Atlas-SNP	.											.	KRIT1	66	.	0			c.A589G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	0,4406		0,0,2203	185.0	179.0	181.0		589,589,589,589,589	1.4	1.0	7	dbSNP_134	181	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense	KRIT1	NM_001013406.1,NM_004912.3,NM_194454.1,NM_194455.1,NM_194456.1	58,58,58,58,58	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign,benign,benign,benign,benign	197/689,197/737,197/737,197/737,197/737	91864857	2,13004	2203	4300	6503	SO:0001583	missense	889	exon9			ATTCAGTAGCATA	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.589A>G	7.37:g.91864857T>C	ENSP00000344668:p.Thr197Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Missense_Mutation	SNP	ENST00000340022.2	37	CCDS5624.1	.	.	.	.	.	.	.	.	.	.	T	9.752	1.167806	0.21621	0.0	2.33E-4	ENSG00000001631	ENST00000394507;ENST00000340022;ENST00000412043;ENST00000394505;ENST00000394503;ENST00000415227;ENST00000458177	T;T;T;T;T;D	0.85258	1.03;1.03;1.03;1.03;-0.48;-1.96	5.21	1.36	0.22044	.	0.546663	0.21326	N	0.076374	T	0.64405	0.2595	N	0.12182	0.205	0.24873	N	0.992278	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46707	-0.9172	10	0.09843	T	0.71	3.0499	4.3536	0.11167	0.1369:0.247:0.0:0.6161	.	197;197	A6NNU0;O00522	.;KRIT1_HUMAN	A	197	ENSP00000378015:T197A;ENSP00000344668:T197A;ENSP00000410909:T197A;ENSP00000378013:T197A;ENSP00000378011:T197A;ENSP00000391675:T197A	ENSP00000344668:T197A	T	-	1	0	KRIT1	91702793	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	1.687000	0.37680	-0.014000	0.14175	0.377000	0.23210	ACT	T|1.000;C|0.000	0.000	weak		0.378	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1		
MUC17	140453	hgsc.bcm.edu	37	7	100681762	100681762	+	Silent	SNP	A	A	G	rs10953316	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100681762A>G	ENST00000306151.4	+	3	7129	c.7065A>G	c.(7063-7065)acA>acG	p.T2355T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2355	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)					GTTTTGAAACAAGCACACTTT	0.478													N|||	3616	0.722045	0.8079	0.4697	5008	,	,		26636	0.8393		0.6243	False		,,,				2504	0.7648				p.T2355T		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.A7065G						PASS	.	C		3453,953		1361,731,111	234.0	232.0	232.0		7065	-2.8	0.0	7	dbSNP_120	232	5312,3288		1658,1996,646	no	coding-synonymous	MUC17	NM_001040105.1		3019,2727,757	GG,GA,AA		38.2326,21.6296,32.608		2355/4494	100681762	8765,4241	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TGAAACAAGCACA	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.7065A>G	7.37:g.100681762A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.326;G|0.674	0.674	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
HELZ2	85441	hgsc.bcm.edu	37	20	62194128	62194128	+	Missense_Mutation	SNP	G	G	A	rs3810485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62194128G>A	ENST00000467148.1	-	8	6116	c.6047C>T	c.(6046-6048)cCg>cTg	p.P2016L	HELZ2_ENST00000427522.2_Missense_Mutation_p.P1447L	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2016			P -> L (in dbSNP:rs3810485). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:12189208, ECO:0000269|PubMed:16239304}.		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)										CGTGGGAGCCGGCAGCCCCTC	0.697													G|||	1375	0.274561	0.2163	0.3833	5008	,	,		12463	0.2659		0.2336	False		,,,				2504	0.3272				p.P2016L		Atlas-SNP	.											.	.	.	.	0			c.C6047T						PASS	.	G	LEU/PRO,LEU/PRO	896,3400		107,682,1359	10.0	12.0	12.0		6047,4340	-8.6	0.0	20	dbSNP_107	12	2189,6271		320,1549,2361	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	98,98	427,2231,3720	AA,AG,GG		25.8747,20.8566,24.1847	benign,benign	2016/2650,1447/2081	62194128	3085,9671	2148	4230	6378	SO:0001583	missense	85441	exon9			GGAGCCGGCAGCC	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.6047C>T	20.37:g.62194128G>A	ENSP00000417401:p.Pro2016Leu	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	572	0.2619047619047619	120	0.24390243902439024	129	0.356353591160221	140	0.24475524475524477	183	0.24142480211081793	G	7.368	0.626191	0.14257	0.208566	0.258747	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.79940	-1.32;-1.21	4.32	-8.56	0.00904	.	1.245660	0.06001	N	0.647856	T	0.00012	0.0000	L	0.31294	0.92	0.49389	P	2.1999999999999797E-4	B;B	0.22211	0.022;0.066	B;B	0.11329	0.003;0.006	T	0.08411	-1.0723	9	0.32370	T	0.25	-9.7697	0.534	0.00633	0.2582:0.2606:0.1268:0.3544	rs3810485;rs60386207	2016;1447	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	L	1447;2016	ENSP00000393257:P1447L;ENSP00000417401:P2016L	ENSP00000393257:P1447L	P	-	2	0	RP4-697K14.7	61664572	0.000000	0.05858	0.008000	0.14137	0.225000	0.24961	-0.362000	0.07602	-1.196000	0.02676	-0.802000	0.03209	CCG	G|0.740;A|0.260	0.260	strong		0.697	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516903	173516903	+	Silent	SNP	A	A	G	rs10494490	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:173516903A>G	ENST00000367714.3	-	13	1904	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Silent_p.N392N	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	494					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TCTTCATATCATTATGTGAAA	0.338													G|||	2430	0.485224	0.671	0.3732	5008	,	,		18236	0.6448		0.2147	False		,,,				2504	0.4274				p.N494N		Atlas-SNP	.											SLC9A11,NS,carcinoma,-2,1	.	.	1	0			c.T1482C						PASS	.	G		2607,1799	529.7+/-372.7	790,1027,386	148.0	131.0	137.0		1482	-3.2	0.0	1	dbSNP_119	137	1797,6803	733.2+/-406.9	188,1421,2691	no	coding-synonymous	SLC9A11	NM_178527.3		978,2448,3077	GG,GA,AA		20.8953,40.8307,33.8613		494/1125	173516903	4404,8602	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon13			CATATCATTATGT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1482T>C	1.37:g.173516903A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	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	
HLA-B	3106	hgsc.bcm.edu	37	6	31324143	31324143	+	Nonsense_Mutation	SNP	G	G	T	rs12697944	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31324143G>T	ENST00000412585.2	-	3	448	c.420C>A	c.(418-420)taC>taA	p.Y140*		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	140	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGTCGTAGGCGTACTGGTCAT	0.711									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				G|||	485	0.096845	0.0802	0.0764	5008	,	,		9016	0.121		0.0994	False		,,,				2504	0.1063				p.Y140X		Atlas-SNP	.											HLA-B,colon,carcinoma,-1,1	HLA-B	54	1	0			c.C420A						scavenged	.						26.0	21.0	23.0					6																	31324143		2088	4190	6278	SO:0001587	stop_gained	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	GTAGGCGTACTGG	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.420C>A	6.37:g.31324143G>T	ENSP00000399168:p.Tyr140*	Somatic	93	11	0.11828		WXS	Illumina HiSeq	Phase_I	85	56	0.658824	NM_005514	Q29764	Nonsense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	13.76	2.331843	0.41297	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	.	.	.	3.18	-2.31	0.06765	.	1.609830	0.05070	U	0.481455	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.2996	0.02076	0.292:0.1494:0.3998:0.1588	rs12697944	.	.	.	X	140;19;19;151	.	ENSP00000399168:Y140X	Y	-	3	2	HLA-B	31432122	0.000000	0.05858	0.045000	0.18777	0.003000	0.03518	-5.040000	0.00157	-0.425000	0.07371	-0.929000	0.02709	TAC	T|0.046;G|0.954	0.046	strong		0.711	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
DENND1A	57706	hgsc.bcm.edu	37	9	126146138	126146138	+	Silent	SNP	T	T	C	rs2808410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:126146138T>C	ENST00000373624.2	-	21	1833	c.1632A>G	c.(1630-1632)gcA>gcG	p.A544A	DENND1A_ENST00000542603.1_Silent_p.A329A|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Silent_p.A555A	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	544					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						CTGGACTCTCTGCCTCGTCGC	0.652													T|||	47	0.00938498	0.0136	0.0058	5008	,	,		18499	0.0		0.0229	False		,,,				2504	0.002				p.A544A		Atlas-SNP	.											.	DENND1A	112	.	0			c.A1632G						PASS	.	T		82,4324	70.3+/-108.2	1,80,2122	82.0	82.0	82.0		1632	-9.6	0.0	9	dbSNP_100	82	154,8446	73.8+/-136.5	2,150,4148	no	coding-synonymous	DENND1A	NM_020946.1		3,230,6270	CC,CT,TT		1.7907,1.8611,1.8145		544/1010	126146138	236,12770	2203	4300	6503	SO:0001819	synonymous_variant	57706	exon21			ACTCTCTGCCTCG	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1632A>G	9.37:g.126146138T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																			T|0.986;C|0.014	0.014	strong		0.652	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
ENTPD5	957	hgsc.bcm.edu	37	14	74441684	74441684	+	Silent	SNP	G	G	A	rs2074932	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74441684G>A	ENST00000334696.6	-	11	1046	c.727C>T	c.(727-729)Ctg>Ttg	p.L243L	ENTPD5_ENST00000557325.1_Silent_p.L243L	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	243					'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)		CCAAATCCCAGGTAACTGTAA	0.483													A|||	2442	0.48762	0.3707	0.6787	5008	,	,		19267	0.2649		0.6123	False		,,,				2504	0.6115				p.L243L		Atlas-SNP	.											ENTPD5,NS,carcinoma,+1,1	ENTPD5	26	1	0			c.C727T						PASS	.	A		1737,2669	647.9+/-398.6	361,1015,827	139.0	129.0	132.0		727	5.3	1.0	14	dbSNP_96	132	5360,3240	486.5+/-371.9	1674,2012,614	no	coding-synonymous	ENTPD5	NM_001249.2		2035,3027,1441	AA,AG,GG		37.6744,39.4235,45.4329		243/429	74441684	7097,5909	2203	4300	6503	SO:0001819	synonymous_variant	957	exon11			ATCCCAGGTAACT	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.727C>T	14.37:g.74441684G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001249	A1L4C5|Q96RX0	Silent	SNP	ENST00000334696.6	37	CCDS9825.1																																																																																			G|0.494;A|0.506	0.506	strong		0.483	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
OR5W2	390148	hgsc.bcm.edu	37	11	55681130	55681130	+	Missense_Mutation	SNP	A	A	T	rs34573569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	42	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	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	
MYSM1	114803	hgsc.bcm.edu	37	1	59126851	59126851	+	Silent	SNP	A	A	G	rs376987710		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:59126851A>G	ENST00000472487.1	-	19	2358	c.2319T>C	c.(2317-2319)tgT>tgC	p.C773C	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	773					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CTTTCTGCAAACAAGTCAGGT	0.373																																					p.C773C		Atlas-SNP	.											.	MYSM1	50	.	0			c.T2319C						PASS	.	A		0,3664		0,0,1832	94.0	88.0	90.0		2319	4.1	1.0	1		90	2,8168		0,2,4083	no	coding-synonymous	MYSM1	NM_001085487.2		0,2,5915	GG,GA,AA		0.0245,0.0,0.0169		773/829	59126851	2,11832	1832	4085	5917	SO:0001819	synonymous_variant	114803	exon19			CTGCAAACAAGTC	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.2319T>C	1.37:g.59126851A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																			.	.	none		0.373	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
NLRP5	126206	hgsc.bcm.edu	37	19	56552456	56552456	+	Silent	SNP	G	G	T	rs61732213	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56552456G>T	ENST00000390649.3	+	11	2955	c.2955G>T	c.(2953-2955)ctG>ctT	p.L985L		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	985					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TGCAGAGGCTGATGTGAGTCT	0.532													G|||	1125	0.224641	0.0272	0.2262	5008	,	,		22018	0.4792		0.1252	False		,,,				2504	0.3303				p.L985L		Atlas-SNP	.											.	NLRP5	217	.	0			c.G2955T						PASS	.	G		177,3947		1,175,1886	191.0	188.0	189.0		2955	2.0	0.4	19	dbSNP_129	189	1288,7142		105,1078,3032	no	coding-synonymous	NLRP5	NM_153447.4		106,1253,4918	TT,TG,GG		15.2788,4.2919,11.6696		985/1201	56552456	1465,11089	2062	4215	6277	SO:0001819	synonymous_variant	126206	exon11			GAGGCTGATGTGA	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2955G>T	19.37:g.56552456G>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			G|0.815;T|0.185	0.185	strong		0.532	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
DSCAML1	57453	hgsc.bcm.edu	37	11	117308795	117308795	+	Silent	SNP	G	G	A	rs2253440	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:117308795G>A	ENST00000321322.6	-	25	4429	c.4428C>T	c.(4426-4428)ttC>ttT	p.F1476F	DSCAML1_ENST00000527706.1_Silent_p.F1206F	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1416	Fibronectin type-III 5. {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)		ACTGTAGCACGAAGCCTGCGG	0.627													G|||	823	0.164337	0.1725	0.1254	5008	,	,		16762	0.0565		0.2187	False		,,,				2504	0.2362				p.F1476F		Atlas-SNP	.											DSCAML1,colon,carcinoma,0,1	DSCAML1	286	1	0			c.C4428T						PASS	.	G		882,3520	340.5+/-306.2	82,718,1401	61.0	48.0	52.0		4428	-3.0	1.0	11	dbSNP_100	52	2041,6551	351.5+/-328.3	242,1557,2497	no	coding-synonymous	DSCAML1	NM_020693.2		324,2275,3898	AA,AG,GG		23.7547,20.0363,22.495		1476/2114	117308795	2923,10071	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon25			TAGCACGAAGCCT		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.4428C>T	11.37:g.117308795G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			G|0.808;A|0.192	0.192	strong		0.627	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
SLC2A9	56606	hgsc.bcm.edu	37	4	9828099	9828099	+	Silent	SNP	G	G	A	rs144428359	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:9828099G>A	ENST00000264784.3	-	12	1598	c.1545C>T	c.(1543-1545)tcC>tcT	p.S515S	SLC2A9_ENST00000506583.1_Silent_p.S486S|SLC2A9_ENST00000309065.3_Silent_p.S486S	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	515					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)	TGTTCCTTTTGGAAAATGCCT	0.428													G|||	8	0.00159744	0.0	0.0014	5008	,	,		18329	0.0		0.007	False		,,,				2504	0.0				p.S515S		Atlas-SNP	.											.	SLC2A9	158	.	0			c.C1545T						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	170.0	158.0	162.0		1458,1545	5.9	1.0	4	dbSNP_134	162	49,8551	31.7+/-84.0	0,49,4251	no	coding-synonymous,coding-synonymous	SLC2A9	NM_001001290.1,NM_020041.2	,	0,52,6451	AA,AG,GG		0.5698,0.0681,0.3998	,	486/512,515/541	9828099	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	56606	exon12			CCTTTTGGAAAAT	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.1545C>T	4.37:g.9828099G>A		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	234	120	0.512821	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Silent	SNP	ENST00000264784.3	37	CCDS3407.1																																																																																			G|0.995;A|0.005	0.005	strong		0.428	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
CATSPER4	378807	hgsc.bcm.edu	37	1	26527863	26527863	+	Silent	SNP	C	C	T	rs17163674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26527863C>T	ENST00000456354.2	+	9	1285	c.1218C>T	c.(1216-1218)cgC>cgT	p.R406R		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	406					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		AGGAGGTGCGCGCAATCCGCT	0.627													C|||	450	0.0898562	0.0121	0.0764	5008	,	,		17973	0.0972		0.1193	False		,,,				2504	0.1667				p.R406R		Atlas-SNP	.											.	CATSPER4	59	.	0			c.C1218T						PASS	.	C		112,4294	86.3+/-125.0	2,108,2093	67.0	62.0	64.0		1218	1.6	1.0	1	dbSNP_123	64	1165,7435	238.3+/-269.8	86,993,3221	no	coding-synonymous	CATSPER4	NM_198137.1		88,1101,5314	TT,TC,CC		13.5465,2.542,9.8185		406/473	26527863	1277,11729	2203	4300	6503	SO:0001819	synonymous_variant	378807	exon9			GGTGCGCGCAATC	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1218C>T	1.37:g.26527863C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_198137	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																			C|0.906;T|0.094	0.094	strong		0.627	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
SNX5	27131	hgsc.bcm.edu	37	20	17932210	17932210	+	Silent	SNP	C	C	T	rs2273448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:17932210C>T	ENST00000377768.3	-	7	855	c.543G>A	c.(541-543)gaG>gaA	p.E181E	SNX5_ENST00000483485.1_5'UTR|SNX5_ENST00000377759.4_Silent_p.E181E	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	181					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						CACCAAACATCTCTTTAGTAT	0.343													C|||	1488	0.297125	0.115	0.232	5008	,	,		18237	0.4375		0.2634	False		,,,				2504	0.4796				p.E181E		Atlas-SNP	.											.	SNX5	38	.	0			c.G543A						PASS	.	C	,	710,3696	291.8+/-281.7	64,582,1557	111.0	106.0	108.0		543,543	4.3	1.0	20	dbSNP_100	108	2500,6100	407.9+/-349.3	353,1794,2153	no	coding-synonymous,coding-synonymous	SNX5	NM_014426.2,NM_152227.1	,	417,2376,3710	TT,TC,CC		29.0698,16.1144,24.6809	,	181/405,181/405	17932210	3210,9796	2203	4300	6503	SO:0001819	synonymous_variant	27131	exon6			AAACATCTCTTTA	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.543G>A	20.37:g.17932210C>T		Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	366	177	0.483607	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			C|0.749;T|0.251	0.251	strong		0.343	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
USP43	124739	hgsc.bcm.edu	37	17	9586165	9586165	+	Silent	SNP	C	C	T	rs12453943	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:9586165C>T	ENST00000285199.7	+	7	1227	c.1131C>T	c.(1129-1131)tcC>tcT	p.S377S	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Silent_p.S377S	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	377	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						TGTCGGCCTCCCCACGCCTGG	0.552													C|||	2254	0.45008	0.5234	0.3112	5008	,	,		15519	0.6488		0.2306	False		,,,				2504	0.4703				p.S377S		Atlas-SNP	.											.	USP43	65	.	0			c.C1131T						PASS	.	C		1815,2129		427,961,584	82.0	85.0	84.0		1131	1.6	0.9	17	dbSNP_120	84	1865,6449		225,1415,2517	no	coding-synonymous	USP43	NM_153210.3		652,2376,3101	TT,TC,CC		22.432,46.0193,30.0212		377/1124	9586165	3680,8578	1972	4157	6129	SO:0001819	synonymous_variant	124739	exon7			GGCCTCCCCACGC	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.1131C>T	17.37:g.9586165C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Silent	SNP	ENST00000285199.7	37	CCDS45610.1																																																																																			C|0.627;T|0.373	0.373	strong		0.552	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
ZBTB40	9923	hgsc.bcm.edu	37	1	22852880	22852880	+	Missense_Mutation	SNP	G	G	C	rs45502998	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:22852880G>C	ENST00000375647.4	+	18	3918	c.3711G>C	c.(3709-3711)gaG>gaC	p.E1237D	ZBTB40_ENST00000404138.1_Missense_Mutation_p.E1237D|ZBTB40_ENST00000374651.4_Missense_Mutation_p.E1125D	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	1237					bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		TCTGTGGTGAGGCCAAATGAG	0.597													G|||	132	0.0263578	0.0015	0.0187	5008	,	,		20073	0.0		0.0368	False		,,,				2504	0.0818				p.E1237D		Atlas-SNP	.											.	ZBTB40	87	.	0			c.G3711C						PASS	.	G	ASP/GLU,ASP/GLU	31,4375	36.8+/-68.6	0,31,2172	131.0	118.0	122.0		3711,3711	3.7	1.0	1	dbSNP_127	122	304,8296	110.2+/-170.6	6,292,4002	yes	missense,missense	ZBTB40	NM_001083621.1,NM_014870.3	45,45	6,323,6174	CC,CG,GG		3.5349,0.7036,2.5757	benign,benign	1237/1240,1237/1240	22852880	335,12671	2203	4300	6503	SO:0001583	missense	9923	exon19			TGGTGAGGCCAAA	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.3711G>C	1.37:g.22852880G>C	ENSP00000364798:p.Glu1237Asp	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	37	CCDS224.1	41	0.018772893772893772	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	28	0.036939313984168866	G	15.08	2.726291	0.48833	0.007036	0.035349	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	T;T;T	0.09538	2.97;2.97;2.99	5.7	3.74	0.42951	.	0.000000	0.56097	D	0.000030	T	0.02156	0.0067	L	0.32530	0.975	0.33714	D	0.616155	P;P	0.46784	0.884;0.816	P;B	0.46208	0.507;0.31	T	0.19257	-1.0311	10	0.45353	T	0.12	-26.467	7.6071	0.28107	0.2788:0.0:0.7212:0.0	rs45502998;rs61741571	1125;1237	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	D	1237;1237;1125	ENSP00000384527:E1237D;ENSP00000364798:E1237D;ENSP00000363782:E1125D	ENSP00000363782:E1125D	E	+	3	2	ZBTB40	22725467	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.652000	0.37313	0.678000	0.31325	0.655000	0.94253	GAG	G|0.974;C|0.026	0.026	strong		0.597	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84639314	84639314	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:84639314C>T	ENST00000286744.5	+	20	2793	c.2569C>T	c.(2569-2571)Ccc>Tcc	p.P857S	ADAMTSL3_ENST00000567716.1_3'UTR|ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.P857S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	857	TSP type-1 7. {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)			TCGGCGCATCCCCCTCAGTGA	0.522																																					p.P857S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C2569T						PASS	.						189.0	166.0	174.0					15																	84639314		2203	4300	6503	SO:0001583	missense	57188	exon20			CGCATCCCCCTCA	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.2569C>T	15.37:g.84639314C>T	ENSP00000286744:p.Pro857Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	58	0.568627	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640716	0.29157	.	.	ENSG00000156218	ENST00000286744	T	0.51574	0.7	4.39	-0.603	0.11630	.	1.472120	0.04463	N	0.374714	T	0.33702	0.0872	L	0.44542	1.39	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.11329	0.006;0.005	T	0.10613	-1.0622	10	0.08599	T	0.76	.	3.5686	0.07909	0.2274:0.39:0.296:0.0866	.	857;857	P82987-2;P82987	.;ATL3_HUMAN	S	857	ENSP00000286744:P857S	ENSP00000286744:P857S	P	+	1	0	ADAMTSL3	82430318	0.000000	0.05858	0.000000	0.03702	0.244000	0.25665	0.095000	0.15127	0.064000	0.16427	0.650000	0.86243	CCC	.	.	none		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
AP1M1	8907	hgsc.bcm.edu	37	19	16314299	16314299	+	Silent	SNP	C	C	T	rs117647142	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:16314299C>T	ENST00000291439.3	+	2	521	c.72C>T	c.(70-72)gaC>gaT	p.D24D	AP1M1_ENST00000444449.2_Silent_p.D24D|AP1M1_ENST00000590756.1_Intron|AP1M1_ENST00000429941.2_Silent_p.D24D|AP1M1_ENST00000541844.1_Intron	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	24					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						ACCGTGGCGACGTGGACATGT	0.597													C|||	37	0.00738818	0.0015	0.0043	5008	,	,		21002	0.0		0.0258	False		,,,				2504	0.0061				p.D24D		Atlas-SNP	.											AP1M1,NS,carcinoma,+2,1	AP1M1	48	1	0			c.C72T						scavenged	.	C	,	21,4385	27.2+/-55.0	0,21,2182	98.0	81.0	87.0		72,72	-6.0	0.9	19	dbSNP_132	87	298,8302	108.6+/-169.2	6,286,4008	no	coding-synonymous,coding-synonymous	AP1M1	NM_001130524.1,NM_032493.3	,	6,307,6190	TT,TC,CC		3.4651,0.4766,2.4527	,	24/436,24/424	16314299	319,12687	2203	4300	6503	SO:0001819	synonymous_variant	8907	exon2			TGGCGACGTGGAC		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.72C>T	19.37:g.16314299C>T		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_001130524	Q4TTY5	Silent	SNP	ENST00000291439.3	37	CCDS12342.1																																																																																			C|0.981;T|0.019	0.019	strong		0.597	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493	
GRIN2B	2904	hgsc.bcm.edu	37	12	13764774	13764774	+	Silent	SNP	G	G	A	rs1805482	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:13764774G>A	ENST00000609686.1	-	8	1874	c.1665C>T	c.(1663-1665)agC>agT	p.S555S		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	555					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)	ATACGTCAGCGCTGAATGGCT	0.453													g|||	952	0.190096	0.1536	0.3718	5008	,	,		21319	0.0089		0.33	False		,,,				2504	0.1534				p.S555S		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C1665T						PASS	.	A		769,3637	313.6+/-293.2	76,617,1510	120.0	105.0	110.0		1665	-8.0	0.5	12	dbSNP_92	110	2874,5726	451.1+/-362.6	484,1906,1910	no	coding-synonymous	GRIN2B	NM_000834.3		560,2523,3420	AA,AG,GG		33.4186,17.4535,28.0101		555/1485	13764774	3643,9363	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon8			GTCAGCGCTGAAT		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.1665C>T	12.37:g.13764774G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	53	0.602273	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.753;A|0.247	0.247	strong		0.453	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
FLT3	2322	hgsc.bcm.edu	37	13	28608459	28608459	+	Silent	SNP	T	T	C	rs34374211	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28608459T>C	ENST00000241453.7	-	13	1764	c.1683A>G	c.(1681-1683)ctA>ctG	p.L561L	FLT3_ENST00000380982.4_Silent_p.L561L|FLT3_ENST00000537084.1_Silent_p.L561L	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	561					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.L561L(5)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGTGACAAATTAGCAGGGTTA	0.378			"""Mis, O"""		"""AML, ALL"""								T|||	700	0.139776	0.236	0.0403	5008	,	,		20547	0.129		0.0308	False		,,,				2504	0.2035				p.L561L		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	FLT3,colon,carcinoma,-2,8	FLT3	15525	8	5	Substitution - coding silent(5)	haematopoietic_and_lymphoid_tissue(5)	c.A1683G						PASS	.	T		924,3482	354.9+/-312.8	106,712,1385	86.0	81.0	83.0		1683	-11.7	0.0	13	dbSNP_126	83	324,8276	113.7+/-173.7	10,304,3986	no	coding-synonymous	FLT3	NM_004119.2		116,1016,5371	CC,CT,TT		3.7674,20.9714,9.5956		561/994	28608459	1248,11758	2203	4300	6503	SO:0001819	synonymous_variant	2322	exon13			ACAAATTAGCAGG	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1683A>G	13.37:g.28608459T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	37	CCDS31953.1																																																																																			T|0.897;C|0.103	0.103	strong		0.378	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
MYO5A	4644	hgsc.bcm.edu	37	15	52643564	52643564	+	Missense_Mutation	SNP	G	G	A	rs1058219	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52643564G>A	ENST00000399231.3	-	28	3979	c.3736C>T	c.(3736-3738)Cgt>Tgt	p.R1246C	MYO5A_ENST00000399233.2_Missense_Mutation_p.R1246C|MYO5A_ENST00000356338.6_Missense_Mutation_p.R1246C|MYO5A_ENST00000358212.6_Missense_Mutation_p.R1246C|MYO5A_ENST00000553916.1_Missense_Mutation_p.R1246C	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1246			R -> C (in dbSNP:rs1058219). {ECO:0000269|PubMed:10733681, ECO:0000269|PubMed:9207796}.		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)		ATGAGGACACGGTAGGCAGGT	0.532													G|||	744	0.148562	0.0991	0.1499	5008	,	,		17379	0.1716		0.1819	False		,,,				2504	0.1564				p.R1246C		Atlas-SNP	.											.	MYO5A	145	.	0			c.C3736T	GRCh37	CM971009	MYO5A	M	rs1058219	PASS	.	G	CYS/ARG,CYS/ARG	414,3626		25,364,1631	122.0	131.0	128.0		3736,3736	2.3	1.0	15	dbSNP_86	128	1402,6966		122,1158,2904	yes	missense,missense	MYO5A	NM_000259.3,NM_001142495.1	180,180	147,1522,4535	AA,AG,GG		16.7543,10.2475,14.6357	possibly-damaging,possibly-damaging	1246/1856,1246/1829	52643564	1816,10592	2020	4184	6204	SO:0001583	missense	4644	exon28			GGACACGGTAGGC		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.3736C>T	15.37:g.52643564G>A	ENSP00000382177:p.Arg1246Cys	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	242	132	0.545455	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	369	0.16895604395604397	49	0.09959349593495935	68	0.1878453038674033	114	0.1993006993006993	138	0.1820580474934037	G	18.84	3.708960	0.68615	0.102475	0.167543	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916;ENST00000399228	T;T;T;T;T;T	0.19394	3.53;3.53;2.15;3.53;3.53;3.53	5.38	2.26	0.28386	.	0.310806	0.32548	N	0.005954	T	0.00012	0.0000	N	0.08118	0	0.21105	P	0.999788348	P;D	0.69078	0.592;0.997	B;P	0.50708	0.276;0.648	T	0.25572	-1.0128	9	0.72032	D	0.01	.	8.5865	0.33662	0.0793:0.0:0.5061:0.4146	rs1058219;rs3198826;rs52837957;rs1058219	1246;1246	Q9Y4I1;Q9Y4I1-2	MYO5A_HUMAN;.	C	1246;780;1246;1246;1246;876;1246;39	ENSP00000382177:R1246C;ENSP00000382179:R1246C;ENSP00000348693:R1246C;ENSP00000350945:R1246C;ENSP00000451109:R1246C;ENSP00000382174:R39C	ENSP00000348693:R1246C	R	-	1	0	MYO5A	50430856	1.000000	0.71417	0.975000	0.42487	0.972000	0.66771	2.503000	0.45407	0.734000	0.32515	-0.302000	0.09304	CGT	G|0.833;A|0.167	0.167	strong		0.532	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
DEDD	9191	hgsc.bcm.edu	37	1	161094190	161094190	+	Silent	SNP	A	A	G	rs1135783	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161094190A>G	ENST00000368006.3	-	3	277	c.63T>C	c.(61-63)caT>caC	p.H21H	NIT1_ENST00000368008.1_3'UTR|DEDD_ENST00000368005.1_Silent_p.H21H|DEDD_ENST00000392188.1_Silent_p.H21H|DEDD_ENST00000489249.1_Intron|DEDD_ENST00000545495.1_Silent_p.H21H|DEDD_ENST00000490843.2_Silent_p.H21H|DEDD_ENST00000458050.2_Silent_p.H21H	NM_032998.2	NP_127491.1	O75618	DEDD_HUMAN	death effector domain containing	21					decidualization (GO:0046697)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|regulation of apoptotic process (GO:0042981)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)			cervix(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|skin(1)	10	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TGTACAGCCCATGTTCCTGCT	0.557													A|||	465	0.0928514	0.1067	0.0663	5008	,	,		18162	0.0675		0.0746	False		,,,				2504	0.138				p.H21H		Atlas-SNP	.											.	DEDD	22	.	0			c.T63C						PASS	.	A	,,,	510,3896	236.8+/-248.8	35,440,1728	102.0	94.0	97.0		63,63,,63	-6.8	0.7	1	dbSNP_86	97	681,7919	170.7+/-221.8	32,617,3651	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous	NIT1,DEDD	NM_001039711.1,NM_001039712.1,NM_001185092.1,NM_032998.2	,,,	67,1057,5379	GG,GA,AA		7.9186,11.5751,9.1573	,,,	21/319,21/319,,21/319	161094190	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	9191	exon2			CAGCCCATGTTCC	AF043733	CCDS1219.1	1q23.1	2008-02-05	2002-01-14		ENSG00000158796	ENSG00000158796			2755	protein-coding gene	gene with protein product		606841	"""death effector domain-containing"""			9774341, 9832420	Standard	XM_005245597		Approved	DEFT, FLDED1, CASP8IP1, KE05, DEDD1	uc001fxz.3	O75618	OTTHUMG00000033104	ENST00000368006.3:c.63T>C	1.37:g.161094190A>G		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	244	133	0.545082	NM_001039711	D3DVF5|O60737	Silent	SNP	ENST00000368006.3	37	CCDS1219.1																																																																																			A|0.915;G|0.085	0.085	strong		0.557	DEDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080582.1	NM_004216	
RRP1B	23076	hgsc.bcm.edu	37	21	45106786	45106786	+	Missense_Mutation	SNP	T	T	G	rs138939671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45106786T>G	ENST00000340648.4	+	12	1228	c.1111T>G	c.(1111-1113)Tta>Gta	p.L371V		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	371					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		AAATAAACTTTTAGAGAAAAC	0.438													T|||	11	0.00219649	0.0008	0.0014	5008	,	,		18271	0.0		0.006	False		,,,				2504	0.0031				p.L371V		Atlas-SNP	.											.	RRP1B	51	.	0			c.T1111G						PASS	.	T	VAL/LEU	6,4400	11.4+/-27.6	0,6,2197	94.0	97.0	96.0		1111	-10.6	0.0	21	dbSNP_134	96	63,8537	38.8+/-94.9	0,63,4237	yes	missense	RRP1B	NM_015056.2	32	0,69,6434	GG,GT,TT		0.7326,0.1362,0.5305	possibly-damaging	371/759	45106786	69,12937	2203	4300	6503	SO:0001583	missense	23076	exon12			AAACTTTTAGAGA	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 136"""	610654	"""KIAA0179"", ""ribosomal RNA processing 1 homolog B (S. cerevisiae)"""	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.1111T>G	21.37:g.45106786T>G	ENSP00000339145:p.Leu371Val	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	37	CCDS33577.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	3.798	-0.042253	0.07452	0.001362	0.007326	ENSG00000160208	ENST00000340648	T	0.01005	5.45	5.3	-10.6	0.00265	.	2.342010	0.01390	N	0.013218	T	0.00815	0.0027	M	0.71581	2.175	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.49214	-0.8963	10	0.87932	D	0	-2.2485	1.3182	0.02111	0.1812:0.2897:0.2753:0.2539	.	371	Q14684	RRP1B_HUMAN	V	371	ENSP00000339145:L371V	ENSP00000339145:L371V	L	+	1	2	RRP1B	43931214	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.909000	0.00337	-1.445000	0.01948	-1.275000	0.01399	TTA	T|0.996;G|0.004	0.004	strong		0.438	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056	
HDLBP	3069	hgsc.bcm.edu	37	2	242179134	242179134	+	Silent	SNP	G	G	A	rs10153800	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242179134G>A	ENST00000391975.1	-	19	2720	c.2493C>T	c.(2491-2493)ggC>ggT	p.G831G	HDLBP_ENST00000427183.2_Silent_p.G798G|HDLBP_ENST00000310931.4_Silent_p.G831G|HDLBP_ENST00000391976.2_Silent_p.G831G	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	831	KH 10. {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)		CCATCACCCCGCCATACTCTT	0.587													G|||	681	0.135982	0.1725	0.1902	5008	,	,		19432	0.001		0.2684	False		,,,				2504	0.0511				p.G831G		Atlas-SNP	.											.	HDLBP	118	.	0			c.C2493T						PASS	.	G	,	774,3632	313.8+/-293.3	58,658,1487	84.0	79.0	80.0		2493,2493	-10.8	0.0	2	dbSNP_119	80	2092,6508	360.6+/-332.0	257,1578,2465	no	coding-synonymous,coding-synonymous	HDLBP	NM_005336.4,NM_203346.3	,	315,2236,3952	AA,AG,GG		24.3256,17.567,22.036	,	831/1269,831/1269	242179134	2866,10140	2203	4300	6503	SO:0001819	synonymous_variant	3069	exon19			CACCCCGCCATAC		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.2493C>T	2.37:g.242179134G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	37	CCDS2547.1	352|352	0.16117216117216118|0.16117216117216118	72|72	0.14634146341463414|0.14634146341463414	78|78	0.2154696132596685|0.2154696132596685	1|1	0.0017482517482517483|0.0017482517482517483	201|201	0.26517150395778366|0.26517150395778366	G|G	6.986|6.986	0.552057|0.552057	0.13374|0.13374	0.17567|0.17567	0.243256|0.243256	ENSG00000115677|ENSG00000115677	ENST00000427487|ENST00000373292	.|.	.|.	.|.	5.41|5.41	-10.8|-10.8	0.00216|0.00216	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999710125|0.999999999710125	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.14839|0.14839	-1.0458|-1.0458	3|3	.|.	.|.	.|.	-18.8764|-18.8764	3.2359|3.2359	0.06765|0.06765	0.2438:0.0884:0.4068:0.2609|0.2438:0.0884:0.4068:0.2609	rs10153800;rs10153800|rs10153800;rs10153800	.|.	.|.	.|.	V|W	233|640	.|.	.|.	A|R	-|-	2|1	0|2	HDLBP|HDLBP	241827807|241827807	0.000000|0.000000	0.05858|0.05858	0.026000|0.026000	0.17262|0.17262	0.604000|0.604000	0.37047|0.37047	-2.605000|-2.605000	0.00889|0.00889	-1.863000|-1.863000	0.01150|0.01150	-1.288000|-1.288000	0.01363|0.01363	GCG|CGG	G|0.800;A|0.200	0.200	strong		0.587	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
AHNAK2	113146	hgsc.bcm.edu	37	14	105406238	105406238	+	Missense_Mutation	SNP	A	A	C	rs2819419	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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						scavenged	.	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	21	1	0.047619		WXS	Illumina HiSeq	Phase_I	46	46	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	
OR5D14	219436	hgsc.bcm.edu	37	11	55563738	55563738	+	Missense_Mutation	SNP	G	G	A	rs67863827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	184	0	0		WXS	Illumina HiSeq	Phase_I	176	80	0.454545	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	
TRAF3IP3	80342	hgsc.bcm.edu	37	1	209936914	209936914	+	Silent	SNP	C	C	T	rs17015169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:209936914C>T	ENST00000367024.1	+	8	1200	c.684C>T	c.(682-684)gcC>gcT	p.A228A	TRAF3IP3_ENST00000010338.4_Silent_p.A208A|TRAF3IP3_ENST00000367026.3_Silent_p.A208A|TRAF3IP3_ENST00000367025.3_Silent_p.A228A|TRAF3IP3_ENST00000400959.3_Silent_p.A208A			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	228						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)		TGATTCAGGCCTCTGACAGCT	0.468													C|||	1906	0.380591	0.6906	0.2752	5008	,	,		19722	0.3075		0.2306	False		,,,				2504	0.2658				p.A228A		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.C684T						PASS	.	C		2815,1591	664.0+/-401.3	909,997,297	81.0	86.0	84.0		684	0.6	1.0	1	dbSNP_123	84	1900,6700	336.9+/-322.1	213,1474,2613	no	coding-synonymous	TRAF3IP3	NM_025228.2		1122,2471,2910	TT,TC,CC		22.093,36.1099,36.2525		228/552	209936914	4715,8291	2203	4300	6503	SO:0001819	synonymous_variant	80342	exon8			TCAGGCCTCTGAC		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.684C>T	1.37:g.209936914C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Silent	SNP	ENST00000367024.1	37	CCDS1490.2																																																																																			C|0.642;T|0.358	0.358	strong		0.468	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2		
ZNF804A	91752	hgsc.bcm.edu	37	2	185803364	185803364	+	Missense_Mutation	SNP	C	C	G	rs3731834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:185803364C>G	ENST00000302277.6	+	4	3835	c.3241C>G	c.(3241-3243)Ctg>Gtg	p.L1081V		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1081			L -> V (in dbSNP:rs3731834).				metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TAGCACACCTCTGCAGCCTTT	0.532													C|||	773	0.154353	0.034	0.1239	5008	,	,		20558	0.2044		0.1819	False		,,,				2504	0.2587				p.L1081V		Atlas-SNP	.											.	ZNF804A	322	.	0			c.C3241G						PASS	.	C	VAL/LEU	296,4110	161.4+/-193.6	7,282,1914	92.0	88.0	90.0		3241	3.2	1.0	2	dbSNP_107	90	1517,7083	286.5+/-297.7	128,1261,2911	yes	missense	ZNF804A	NM_194250.1	32	135,1543,4825	GG,GC,CC		17.6395,6.7181,13.9397	possibly-damaging	1081/1210	185803364	1813,11193	2203	4300	6503	SO:0001583	missense	91752	exon4			ACACCTCTGCAGC	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.3241C>G	2.37:g.185803364C>G	ENSP00000303252:p.Leu1081Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	153	79	0.51634	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	338	0.15476190476190477	13	0.026422764227642278	49	0.13535911602209943	133	0.23251748251748253	143	0.18865435356200527	C	1.870	-0.460565	0.04508	0.067181	0.176395	ENSG00000170396	ENST00000302277	T	0.07444	3.19	5.07	3.23	0.37069	.	0.206931	0.24072	N	0.041817	T	0.00012	0.0000	N	0.20530	0.585	0.40134	P	0.023241999999999985	B	0.27882	0.192	B	0.25987	0.065	T	0.48340	-0.9044	9	0.35671	T	0.21	-1.1323	4.7089	0.12863	0.0:0.5724:0.1716:0.256	rs3731834;rs52819327;rs56895785;rs3731834	1081	Q7Z570	Z804A_HUMAN	V	1081	ENSP00000303252:L1081V	ENSP00000303252:L1081V	L	+	1	2	ZNF804A	185511609	0.686000	0.27661	0.953000	0.39169	0.683000	0.39861	1.039000	0.30266	0.502000	0.28037	-0.657000	0.03884	CTG	C|0.853;G|0.147	0.147	strong		0.532	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
GABRB3	2562	hgsc.bcm.edu	37	15	27018797	27018797	+	5'Flank	SNP	G	G	A	rs20318	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:27018797G>A	ENST00000311550.5	-	0	0				GABRB3_ENST00000541819.2_Intron|GABRB3_ENST00000557641.1_Intron|GABRB3_ENST00000299267.4_Silent_p.P25P	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3						cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTCACCTGCGGGGCTCAGAGC	0.751													G|||	992	0.198083	0.0068	0.3372	5008	,	,		5180	0.3075		0.1849	False		,,,				2504	0.2587				p.P25P		Atlas-SNP	.											GABRB3_ENST00000299267,NS,carcinoma,0,1	GABRB3	338	1	0			c.C75T						PASS	.	G		152,4102		8,136,1983	12.0	14.0	13.0		75	0.5	1.0	15	dbSNP_63	13	1303,7081		101,1101,2990	no	coding-synonymous	GABRB3	NM_021912.4		109,1237,4973	AA,AG,GG		15.5415,3.5731,11.5129		25/474	27018797	1455,11183	2127	4192	6319	SO:0001631	upstream_gene_variant	2562	exon1			CCTGCGGGGCTCA		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231		15.37:g.27018797G>A	Exception_encountered	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	43	0.641791	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			G|0.791;A|0.209	0.209	strong		0.751	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
ABCC3	8714	hgsc.bcm.edu	37	17	48761385	48761385	+	Missense_Mutation	SNP	A	A	G	rs150601692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48761385A>G	ENST00000285238.8	+	28	4110	c.4030A>G	c.(4030-4032)Aag>Gag	p.K1344E		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1344	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	GGAGGCGGCAAAGGGTGAAAT	0.622													A|||	5	0.000998403	0.0	0.0	5008	,	,		20086	0.0		0.0	False		,,,				2504	0.0051				p.K1344E		Atlas-SNP	.											.	ABCC3	138	.	0			c.A4030G						PASS	.	A	GLU/LYS	1,4405	2.1+/-5.4	0,1,2202	54.0	48.0	50.0		4030	2.1	0.1	17	dbSNP_134	50	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ABCC3	NM_003786.3	56	0,7,6496	GG,GA,AA		0.0698,0.0227,0.0538	benign	1344/1528	48761385	7,12999	2203	4300	6503	SO:0001583	missense	8714	exon28			GCGGCAAAGGGTG	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.4030A>G	17.37:g.48761385A>G	ENSP00000285238:p.Lys1344Glu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	85	60	0.705882	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	A	2.739	-0.262675	0.05754	2.27E-4	6.98E-4	ENSG00000108846	ENST00000285238	D	0.92752	-3.1	5.24	2.06	0.26882	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.385040	0.29473	N	0.012046	T	0.76744	0.4030	N	0.05259	-0.085	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.62258	-0.6892	10	0.02654	T	1	-18.184	7.7134	0.28690	0.2169:0.1322:0.6509:0.0	.	1344	O15438	MRP3_HUMAN	E	1344	ENSP00000285238:K1344E	ENSP00000285238:K1344E	K	+	1	0	ABCC3	46116384	0.002000	0.14202	0.127000	0.21898	0.980000	0.70556	1.360000	0.34125	0.656000	0.30886	-0.242000	0.12053	AAG	A|0.999;G|0.001	0.001	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
C2orf54	79919	hgsc.bcm.edu	37	2	241830969	241830969	+	Silent	SNP	G	G	A	rs10171067	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	113	60	0.530973	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	
SETBP1	26040	hgsc.bcm.edu	37	18	42532693	42532693	+	Missense_Mutation	SNP	C	C	A	rs1064204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:42532693C>A	ENST00000282030.5	+	4	3684	c.3388C>A	c.(3388-3390)Cct>Act	p.P1130T		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1130			P -> T (in dbSNP:rs1064204).			nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TGACATGCAGCCTTCTCTGAA	0.527									Schinzel-Giedion syndrome				C|||	594	0.11861	0.0182	0.2435	5008	,	,		20858	0.1895		0.1103	False		,,,				2504	0.1012				p.P1130T		Atlas-SNP	.											.	SETBP1	577	.	0			c.C3388A						PASS	.	C	THR/PRO	212,4194	130.2+/-166.9	5,202,1996	109.0	87.0	94.0		3388	4.1	1.0	18	dbSNP_86	94	1030,7570	219.0+/-257.2	57,916,3327	yes	missense	SETBP1	NM_015559.2	38	62,1118,5323	AA,AC,CC		11.9767,4.8116,9.5494	benign	1130/1597	42532693	1242,11764	2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ATGCAGCCTTCTC	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3388C>A	18.37:g.42532693C>A	ENSP00000282030:p.Pro1130Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	289	0.13232600732600733	11	0.022357723577235773	74	0.20441988950276244	120	0.2097902097902098	84	0.11081794195250659	C	5.865	0.343735	0.11126	0.048116	0.119767	ENSG00000152217	ENST00000282030	T	0.69175	-0.38	5.88	4.09	0.47781	.	0.283324	0.36482	N	0.002561	T	0.00039	0.0001	N	0.24115	0.695	0.33516	P	0.40827899999999995	B	0.02656	0.0	B	0.08055	0.003	T	0.05716	-1.0868	9	0.39692	T	0.17	.	2.183	0.03879	0.1765:0.4964:0.1718:0.1553	rs1064204;rs3205204;rs3744826;rs52806906;rs61239753;rs1064204	1130	Q9Y6X0	SETBP_HUMAN	T	1130	ENSP00000282030:P1130T	ENSP00000282030:P1130T	P	+	1	0	SETBP1	40786691	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	1.873000	0.39558	0.823000	0.34589	0.561000	0.74099	CCT	C|0.892;A|0.108	0.108	strong		0.527	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
IL18	3606	hgsc.bcm.edu	37	11	112020916	112020916	+	Silent	SNP	T	T	G	rs549908	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:112020916T>G	ENST00000280357.7	-	4	324	c.105A>C	c.(103-105)tcA>tcC	p.S35S	IL18_ENST00000533858.1_5'UTR|SDHD_ENST00000532699.1_Intron|IL18_ENST00000528832.1_Silent_p.S35S|IL18_ENST00000524595.1_Silent_p.S31S	NM_001562.3	NP_001553.1	Q14116	IL18_HUMAN	interleukin 18	35					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)						all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		CAAAGTAATCTGATTCCAGGT	0.274													T|||	1101	0.219848	0.1846	0.3357	5008	,	,		17668	0.1181		0.3082	False		,,,				2504	0.1994				p.S35S		Atlas-SNP	.											.	IL18	10	.	0			c.A105C	GRCh37	CM056601	IL18	M	rs549908	PASS	.	T		727,2843		73,581,1131	70.0	65.0	66.0		105	2.5	1.0	11	dbSNP_83	66	2455,5663		377,1701,1981	no	coding-synonymous	IL18	NM_001562.3		450,2282,3112	GG,GT,TT		30.2414,20.3641,27.2245		35/194	112020916	3182,8506	1785	4059	5844	SO:0001819	synonymous_variant	3606	exon4			GTAATCTGATTCC	U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782		"""Interleukins and interleukin receptors"""	5986	protein-coding gene	gene with protein product	"""interferon-gamma-inducing factor"""	600953	"""interleukin 18 (interferon-gamma-inducing factor)"""			7477296, 9693051	Standard	NM_001562		Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000280357.7:c.105A>C	11.37:g.112020916T>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_001562	O75599|Q6FGY3|Q6WWJ7	Silent	SNP	ENST00000280357.7	37	CCDS44731.1																																																																																			T|0.780;G|0.220	0.220	strong		0.274	IL18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392409.1	NM_001562	
SCN8A	6334	hgsc.bcm.edu	37	12	52162823	52162823	+	Missense_Mutation	SNP	C	C	T	rs117217073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52162823C>T	ENST00000354534.6	+	17	3254	c.3076C>T	c.(3076-3078)Cgt>Tgt	p.R1026C	SCN8A_ENST00000545061.1_Missense_Mutation_p.R1026C	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1026					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CTTTAAGCAGCGTGAGGCTGA	0.512													C|||	24	0.00479233	0.0	0.0086	5008	,	,		22384	0.0		0.0169	False		,,,				2504	0.001				p.R1026C		Atlas-SNP	.											.	SCN8A	331	.	0			c.C3076T						PASS	.	C	CYS/ARG,CYS/ARG	8,4130		0,8,2061	73.0	75.0	74.0		3076,3076	4.6	1.0	12	dbSNP_132	74	131,8311		0,131,4090	yes	missense,missense	SCN8A	NM_001177984.1,NM_014191.2	180,180	0,139,6151	TT,TC,CC		1.5518,0.1933,1.1049	probably-damaging,probably-damaging	1026/1940,1026/1981	52162823	139,12441	2069	4221	6290	SO:0001583	missense	6334	exon17			AAGCAGCGTGAGG	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.3076C>T	12.37:g.52162823C>T	ENSP00000346534:p.Arg1026Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	C	16.02	3.004177	0.54254	0.001933	0.015518	ENSG00000196876	ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961	D;D;D	0.84298	-1.83;-1.83;-1.83	4.55	4.55	0.56014	Sodium ion transport-associated (1);	0.110372	0.64402	D	0.000020	T	0.80944	0.4721	L	0.49778	1.585	0.48040	D	0.999573	D;D	0.89917	1.0;0.997	D;P	0.65987	0.94;0.849	D	0.84692	0.0723	10	0.87932	D	0	.	10.947	0.47306	0.3118:0.6882:0.0:0.0	.	1026;1026	F8VWM7;Q9UQD0	.;SCN8A_HUMAN	C	1026;1026;1026;939	ENSP00000346534:R1026C;ENSP00000440360:R1026C;ENSP00000347255:R1026C	ENSP00000346534:R1026C	R	+	1	0	SCN8A	50449090	0.999000	0.42202	1.000000	0.80357	0.704000	0.40688	1.398000	0.34554	2.816000	0.96949	0.563000	0.77884	CGT	C|0.991;T|0.009	0.009	strong		0.512	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
PTPRG	5793	hgsc.bcm.edu	37	3	61989028	61989028	+	Missense_Mutation	SNP	A	A	G	rs140777402		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:61989028A>G	ENST00000474889.1	+	4	753	c.376A>G	c.(376-378)Atc>Gtc	p.I126V	PTPRG_ENST00000295874.10_Missense_Mutation_p.I126V	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	126	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		CACAGTCGCCATCCTTCTGAA	0.428													A|||	1	0.000199681	0.0	0.0	5008	,	,		20437	0.0		0.001	False		,,,				2504	0.0				p.I126V		Atlas-SNP	.											PTPRG,NS,malignant_melanoma,-2,1	PTPRG	153	1	0			c.A376G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	89.0	89.0	89.0		376	5.0	1.0	3	dbSNP_134	89	5,8595	3.7+/-12.6	0,5,4295	yes	missense	PTPRG	NM_002841.3	29	0,5,6498	GG,GA,AA		0.0581,0.0,0.0384	benign	126/1446	61989028	5,13001	2203	4300	6503	SO:0001583	missense	5793	exon4			GTCGCCATCCTTC	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.376A>G	3.37:g.61989028A>G	ENSP00000418112:p.Ile126Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	19.50	3.839240	0.71373	0.0	5.81E-4	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.61742	0.08;0.08	6.16	5.0	0.66597	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.052424	0.85682	D	0.000000	T	0.41213	0.1149	N	0.12637	0.245	0.53688	D	0.999973	B;B	0.25272	0.1;0.122	B;B	0.27380	0.047;0.079	T	0.43261	-0.9402	10	0.87932	D	0	.	12.6615	0.56815	0.9349:0.0:0.0651:0.0	.	126;126	P23470-2;P23470	.;PTPRG_HUMAN	V	126	ENSP00000418112:I126V;ENSP00000295874:I126V	ENSP00000295874:I126V	I	+	1	0	PTPRG	61964068	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.799000	0.62517	2.367000	0.80283	0.528000	0.53228	ATC	A|1.000;G|0.000	0.000	strong		0.428	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
